# hmmscan :: search sequence(s) against a profile database
# HMMER 3.2.1 (June 2018); http://hmmer.org/
# Copyright (C) 2018 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query sequence file:             /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Methanosaeta_thermophila_PT_uid58469/NC_008553.faa
# target HMM database:             /oak/stanford/groups/akundaje/marinovg/genomes/PFam/PFam32.0/Pfam-A.hmm
# output directed to file:         /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Methanosaeta_thermophila_PT_uid58469/NC_008553.PFam32-A
# per-seq hits tabular output:     /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Methanosaeta_thermophila_PT_uid58469/NC_008553.PFam32-A.tblout
# number of worker threads:        20
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       gi|116753326|ref|YP_842444.1|  [L=306]
Description: quinolinate synthetase complex, A subunit [Methanosaeta thermophila PT]
Scores for complete 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-120  401.0   0.5   3.2e-120  400.8   0.5    1.0  1  NadA      Quinolinate synthetase A protein


Domain annotation for each model (and alignments):
>> NadA  Quinolinate synthetase A protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  400.8   0.5  1.8e-124  3.2e-120       2     299 .]      14     305 ..      13     305 .. 0.98

  Alignments for each domain:
  == domain 1  score: 400.8 bits;  conditional E-value: 1.8e-124
                                    HHHHHHHHHTEEEEEETTS-HHHHHH-SEEE-HHHHHHHCCC-SSSEEEEES-HHHHHHHHHHSTTSEEE-SSTT---HH CS
                           NadA   2 eikelkkeknavilaHnYqedeiqeiadfvGDSleLarkaaeteaevivfcGVhFMaetakiLspekkvllpdleagCsl 81 
                                    ei +lk+e+na+ilaHnYq  ++q+iad++GDSleL+r+aa+ +++v+vfcGV+FMaeta+iLspek v+ pd++a C++
  gi|116753326|ref|YP_842444.1|  14 EILRLKSERNAIILAHNYQPGDVQDIADLTGDSLELSRAAATIDCKVLVFCGVDFMAETAAILSPEKIVIHPDTSACCPM 93 
                                    899***************************************************************************** PP

                                    HCT--HHHHHHHHHHSTTS-EEEESSS-HHHHTT-SEEE-TTTHHHHHHHSS-SEEEEES-HHHHHHHHHHH.SEEEEES CS
                           NadA  82 admitaeeveelkeelpdaavvtYvNssaevKalsdivcTSsnavkvvealkekkilflPDqnLgryvakklgekkiilw 161
                                    a+mi+ ++v++l+e++pdaavv+YvNssa+vKa+sdi+cTS+n v+vv+al+ ++ilf+PD+nL++yva+++ +k+ii w
  gi|116753326|ref|YP_842444.1|  94 AQMISPHDVRSLREKHPDAAVVCYVNSSADVKAESDICCTSANGVQVVNALDADEILFIPDRNLAAYVARHT-DKRIIPW 172
                                    ***********************************************************************9.668**** PP

                                    SSS-GCGGG--CHHHHHHHHCSTT-EEEE-TTS-HHHHHCSSEE--HHHHCCCCGTTSSSCEEEES-THHHHHHHHH-TT CS
                           NadA 162 kgaCsvHeefkaeeveelkeehpdakvlvHPEckeevveaadvvgSTsqiikavkeseakefiigTelglverlkkeape 241
                                    +g+C+vH++++a++v+e++++hpda++lvHPEc++ev+++ad v STs+++k++++s a+efiigTe+g+++rl +e+pe
  gi|116753326|ref|YP_842444.1| 173 DGYCYVHDRYTASDVSEARKKHPDAELLVHPECRPEVIDMADGVYSTSGMLKHARASGANEFIIGTEVGILHRLCAENPE 252
                                    ******************************************************************************** PP

                                    SEEE.....ECSSSSSTTGGG--HHHHHHHHHHT-S.B----HHHHHHHHHHHHHHHH CS
                           NadA 242 kefialsaeaaeeavCetMkkitleklleaLeeleeeeikvdeevaekAkkalermle 299
                                    k f+ ls+     avCe+Mkki+l+k+l+aLe+l++ +++v++++a +A++a+erml+
  gi|116753326|ref|YP_842444.1| 253 KMFYPLSS----GAVCEDMKKISLKKVLRALETLSP-RVEVPQTTAVRARRAIERMLA 305
                                    ****6644....589*********************.*******************95 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:                      347  (0.0193541); 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: 1955.43
//
Query:       gi|116753327|ref|YP_842445.1|  [L=202]
Description: hypothetical protein Mthe_0002 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1474.54
//
Query:       gi|116753328|ref|YP_842446.1|  [L=337]
Description: RNA 3'-terminal-phosphate cyclase [Methanosaeta thermophila PT]
Scores for complete 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-81  272.0   0.0    3.2e-81  271.8   0.0    1.0  1  RTC         RNA 3'-terminal phosphate cyclase
      5e-17   62.3   0.0      1e-16   61.3   0.0    1.5  1  RTC_insert  RNA 3'-terminal phosphate cyclase (RTC), insert d
  ------ inclusion threshold ------
       0.36   10.6   2.2       0.96    9.2   0.4    2.4  2  RPEL        RPEL repeat


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 !  271.8   0.0   5.3e-85   3.2e-81       1     222 []      13     323 ..      13     323 .. 0.98

  Alignments for each domain:
  == domain 1  score: 271.8 bits;  conditional E-value: 5.3e-85
                                    STTTSTHHHHHHHHHHHHH---EEEESTTTTSSS-S--HHHHHHHHHHHHHHT-EEE--STT-SEEEEE------SEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            RTC   1 lgegGgqiLRtalaLsaltgkpvrIenIRanRkkPGLraqhltavrllakitnaevegaeigsteleFkPgeikageyev 80 
                                    +gegGgqi+Rt++aLs+ltg pvrI+nIR nR++PGL+aqh+ a+++la+i++ae++g ++gs+e+eF Pg+i+ag+y+v
  gi|116753328|ref|YP_842446.1|  13 YGEGGGQIVRTSVALSTLTGIPVRIKNIRRNRPRPGLAAQHVRAIEALAQISRAETRGVHLGSEEIEFIPGRISAGSYDV 92 
                                    69****************************************************************************** PP

                                    EEESSEBHHHHHHHHHHHHTTSSS-EEEEEEEBSBBTTS--HHHHHHTHHHHHHHHT.-EEEEEEEE--BTTTB-EEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            RTC  81 digtAGsitlllqtllplllfakkpseltlkGgTnvsaapsvdylktvllpllkrfgvlelelelkkrGfypkGgGevel 160
                                    digtAGs+tll+q+llp+l  a++p+++t++GgT+v+++p+vdyl++v lp+++ fg ++++++ ++rG+yp+GgG v+l
  gi|116753328|ref|YP_842446.1|  93 DIGTAGSVTLLIQCLLPALTAAEGPVTVTVRGGTDVRWSPTVDYLEHVALPAMHLFG-VTATFRCERRGYYPRGGGVVVL 171
                                    *********************************************************.6********************* PP

                                    EEE-.-S---EB.................................................................... CS
                                    xxxxxxxxxxxx.................................................................... RF
                            RTC 161 evepskklkpie.................................................................... 172
                                    +++ps +l+p +                                                                    
  gi|116753328|ref|YP_842446.1| 172 STRPS-RLRPARlelieegicgishcgslpehvarrqadaalellkekgydaridiqtmsssspgsgitlwsgfrgssal 250
                                    **996.79998899999*************************************************************** PP

                                    .........................BSS-HHHHHHHHHHHHHHT.-EEEEESS--HHHHHHHHHHHHHSS-EEEE CS
                                    .........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            RTC 173 .........................acvDehlqdqlilfmaLakgksrirvaeltlhtetairvieqflgvkfkv 222
                                                             a vD hl+dqli+++aLa g  +++++e+++ht+t+i++++++l +++++
  gi|116753328|ref|YP_842446.1| 251 gergvraedvgreaakalidelkskASVDVHLADQLIPYIALAGG--EYTTREISSHTRTNIWTAQRILRCRIDI 323
                                    *******************************************98..7**********************99986 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 !   61.3   0.0   1.7e-20     1e-16       8     102 ..     189     272 ..     188     273 .. 0.93

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 1.7e-20
                                    EEEEEEEEESS-THHHHHHHHHHHHHHTTTSSEEEEEEE.EE-CGGC-SS-EEEEEEEEE-T.TS-EEEEEEEE-TT--H CS
                     RTC_insert   8 rirGvafaarvspsvanrmveaargvLnkllpdvyiytdvvkegkesgkspGfgisLvaetttegvllgaealgekgvpp 87 
                                     i G++++  ++ +va+r+++aa ++L++ ++d  i ++       s++spG+gi+L+  +       g++alge+gv++
  gi|116753328|ref|YP_842446.1| 189 GICGISHCGSLPEHVARRQADAALELLKEKGYDARIDIQ-----TMSSSSPGSGITLWSGFR------GSSALGERGVRA 257
                                    589********************************8888.....678899********8884......79********** PP

                                    HHHHHHHHHHHHHHH CS
                     RTC_insert  88 edvGeeaaeeLleei 102
                                    edvG+eaa++L++e+
  gi|116753328|ref|YP_842446.1| 258 EDVGREAAKALIDEL 272
                                    ************998 PP

>> RPEL  RPEL repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.2     0.097   5.8e+02       6      12 ..     171     177 ..     171     178 .. 0.91
   2 ?    9.2   0.4   0.00016      0.96       9      20 ..     179     190 ..     177     190 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.097
                           RPEL   6 LshRPtr 12 
                                    Ls RP+r
  gi|116753328|ref|YP_842446.1| 171 LSTRPSR 177
                                    8****99 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00016
                           RPEL   9 RPtreELvernI 20 
                                    RP r EL+e +I
  gi|116753328|ref|YP_842446.1| 179 RPARLELIEEGI 190
                                    ***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); 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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2337.34
//
Query:       gi|116753329|ref|YP_842447.1|  [L=91]
Description: RNA polymerase, dimerisation [Methanosaeta thermophila PT]
Scores for complete 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-19   67.2   0.0    9.9e-19   66.9   0.0    1.1  1  RNA_pol_L_2  RNA polymerase Rpb3/Rpb11 dimerisation domain
    1.9e-05   24.0   0.0    2.6e-05   23.5   0.0    1.2  1  RNA_pol_L    RNA polymerase Rpb3/Rpb11 dimerisation domain


Domain annotation for each model (and alignments):
>> RNA_pol_L_2  RNA polymerase Rpb3/Rpb11 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.9   0.0   1.1e-22   9.9e-19       1      74 [.      12      84 ..      12      85 .. 0.96

  Alignments for each domain:
  == domain 1  score: 66.9 bits;  conditional E-value: 1.1e-22
                                   EEEEEEES--HHHHHHHHHHHTTSTTEEEEEEECSSTTTSEEEEEEEESTSS-HHHHHHHHHHHHHHHHHHHHH CS
                    RNA_pol_L_2  1 eltfeingEDhTLgnlLrhlllknpsVefagYkipHPlepkmnlriqtkssnnpleaLkkalkdlldicdelee 74
                                   el++e++gE hTL+nlLr +ll++++V +a+Y+ ++P  ++  +r +t+ + +pl+++++a  ++ d+cde+ +
  gi|116753329|ref|YP_842447.1| 12 ELRIEFEGERHTLLNLLRSELLEDERVVIATYDAKFPIMDNPVFRLKTR-GVDPLDVIRDASARIADLCDEFLR 84
                                   589*********************************************7.6********************975 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 !   23.5   0.0   2.9e-09   2.6e-05       3      69 .]      16      79 ..      14      79 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2.9e-09
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      RNA_pol_L  3 llrgvdhtlgNaLRrillsevpgvaiea.....pvvkvntdkdklilevetdgslkPeealkeAlkiLkekl 69
                                   +++g+ htl N LR  ll e + v i++     p+       d+ +++ +t g+ +P ++++ A   + + +
  gi|116753329|ref|YP_842447.1| 16 EFEGERHTLLNLLRSELL-EDERVVIATydakfPI------MDNPVFRLKTRGV-DPLDVIRDASARIADLC 79
                                   689***************.***********99988......78899****7776.9********99988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 627.04
//
Query:       gi|116753330|ref|YP_842448.1|  [L=185]
Description: exosome complex RNA-binding protein Csl4 [Methanosaeta thermophila PT]
Scores for complete 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-14   52.1   0.3    7.4e-14   51.3   0.3    1.5  1  ECR1_N          Exosome complex exonuclease RRP4 N-terminal r
     0.0068   16.3   0.8      0.012   15.5   0.8    1.3  1  DUF5363         Family of unknown function (DUF5363)
     0.0097   16.0   1.9      0.016   15.3   1.9    1.3  1  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
  ------ inclusion threshold ------
      0.013   15.6   0.8       0.02   14.9   0.8    1.2  1  DZR             Double zinc ribbon
      0.013   15.5   1.4      0.041   13.9   1.4    1.8  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.016   15.8   0.4      0.055   14.1   0.4    1.7  1  EXOSC1          Exosome component EXOSC1/CSL4
       0.11   12.4   1.6       0.17   11.9   1.6    1.2  1  zinc-ribbons_6  zinc-ribbons
       0.24   11.2   3.1        8.4    6.3   0.4    2.3  2  zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
       0.37   10.7   2.8       0.59   10.1   2.8    1.3  1  zf-C3HC4        Zinc finger, C3HC4 type (RING finger)


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 !   51.3   0.3   3.7e-17   7.4e-14       1      37 [.       5      41 ..       5      42 .. 0.96

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 3.7e-17
                                   EE-TT-EEEETTTSEE-TTEEEETTEEEESSSEEEEE CS
                         ECR1_N  1 iVtPGevlttdeefmrGhGTYvrggtiyAsvaGtvev 37
                                   +V+PG++++++eef++Gh TYv gg+iyAs +G+v +
  gi|116753330|ref|YP_842448.1|  5 LVLPGDRIGSAEEFVPGHDTYVFGGNIYASTTGVVDI 41
                                   69*********************************87 PP

>> DUF5363  Family of unknown function (DUF5363)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.8   5.9e-06     0.012      21      47 ..     140     167 ..     139     174 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.9e-06
                        DUF5363  21 kelGvdkgaCRgC.vPvvkfDeegnlkk 47 
                                    +++Gv k+ C++C +P+vk D  ++ ++
  gi|116753330|ref|YP_842448.1| 140 DDMGVIKAYCSSCtTPLVKKDSRLECPE 167
                                    69*******************9887665 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 !   15.3   1.9   8.2e-06     0.016      16      39 ..     147     168 ..     145     169 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 8.2e-06
                  Auto_anti-p27  16 etCpvCgvPLmrdrkggkvyCvaC 39 
                                    ++C+ C++PL++  k+ ++ C+ C
  gi|116753330|ref|YP_842448.1| 147 AYCSSCTTPLVK--KDSRLECPEC 168
                                    69**********..689******* PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.8     1e-05      0.02      13      37 ..     147     171 ..     141     177 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1e-05
                            DZR  13 rfCseCgtklkavaaedrCpsCgek 37 
                                     +Cs C t+l +  +   Cp+C++ 
  gi|116753330|ref|YP_842448.1| 147 AYCSSCTTPLVKKDSRLECPECKRT 171
                                    69********99999*******975 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 ?   13.9   1.4   2.1e-05     0.041      57      98 ..     130     174 ..      46     179 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.1e-05
                                    TTT-EEEEEEE-...-EEEETTTS-EEECHHHHHS-TTTSSS-EE CS
                           HypA  57 legaeLeieevp...vkvrCreCgkefeleekalrCpkCgsadve 98 
                                    +++ +L+ e  +   +k++C++C +   +++++l+Cp+C++++++
  gi|116753330|ref|YP_842448.1| 130 ARQMRLSTEPDDmgvIKAYCSSCTTPLVKKDSRLECPECKRTEMR 174
                                    4444455443332226889*****9998776589******98876 PP

>> EXOSC1  Exosome component EXOSC1/CSL4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.4   2.7e-05     0.055       1      54 [.      57     118 ..      57     136 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.7e-05
                                    -S-T..T-EEEEEEEEEESSEEEEEEEEECTB.....SBCCCEEECCCTTSS--STS.TTSS CS
                         EXOSC1   1 lPke..gdvVLarvtrlrkkqalveilsvege.....nnvlsdsgvgangegavkei.eagg 54 
                                    lP++  gd+V + v++++++ +++ +  ++g       +  +  +++++++++vk++ +  g
  gi|116753330|ref|YP_842448.1|  57 LPRVenGDIVVGEVVDIKENLVILALAFKKGYesrplPELDATIHISNVKSSYVKDLkQMFG 118
                                    566656***********************998776654555789***********9944444 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.6   8.6e-05      0.17       2      25 ..     148     171 ..     147     178 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.6e-05
                                    --SSS-S--EE-SSEEE-TTT--E CS
                 zinc-ribbons_6   2 kCpeCqqelekrgeqyhCeaCqed 25 
                                    +C +C ++l+k++++++C +C++ 
  gi|116753330|ref|YP_842448.1| 148 YCSSCTTPLVKKDSRLECPECKRT 171
                                    8********************984 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1     0.007        14       3      17 ..     148     162 ..     146     164 .. 0.90
   2 ?    6.3   0.4    0.0042       8.4       3      19 ..     164     181 ..     162     182 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.007
                                    E-SSS--EEEEEE-S CS
                 zf-C4_Topoisom   3 kCPkCggdLvlkrgk 17 
                                     C +C  +Lv+k ++
  gi|116753330|ref|YP_842448.1| 148 YCSSCTTPLVKKDSR 162
                                    7***********998 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0042
                                    E-SSS-.-EEEEEE-SSS CS
                 zf-C4_Topoisom   3 kCPkCg.gdLvlkrgkkG 19 
                                    +CP+C+  ++ + ++ +G
  gi|116753330|ref|YP_842448.1| 164 ECPECKrTEMRKLSTYYG 181
                                    7*****999988777666 PP

>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   2.8    0.0003      0.59      21      41 .]     148     168 ..     147     168 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0003
                                    B-CHHHHHHHHCTSSB--TTT CS
                       zf-C3HC4  21 fCskCirkilksrkkvkCPlC 41 
                                    +Cs+C + ++k+++  +CP+C
  gi|116753330|ref|YP_842448.1| 148 YCSSCTTPLVKKDSRLECPEC 168
                                    8**********999999**** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); 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: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1346.05
//
Query:       gi|116753331|ref|YP_842449.1|  [L=209]
Description: methyltransferase small [Methanosaeta thermophila PT]
Scores for complete 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   54.3   0.0    1.4e-14   54.0   0.0    1.1  1  MTS              Methyltransferase small domain
    5.9e-14   52.2   0.1    8.1e-14   51.7   0.1    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    2.4e-11   43.6   0.1    3.7e-11   43.0   0.1    1.3  1  Methyltransf_31  Methyltransferase domain
    4.4e-11   43.3   0.1      8e-11   42.5   0.1    1.5  1  Methyltransf_25  Methyltransferase domain
    5.5e-09   36.0   0.6    7.9e-08   32.2   0.6    2.0  1  UPF0020          Putative RNA methylase family UPF0020
    2.1e-08   34.7   0.0    3.8e-08   33.9   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    3.4e-06   26.7   0.0    4.7e-06   26.3   0.0    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    3.6e-05   23.6   0.0    4.2e-05   23.4   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
     0.0004   20.1   0.0    0.00059   19.5   0.0    1.2  1  Cons_hypoth95    Conserved hypothetical protein 95
    0.00086   18.9   0.0      0.001   18.7   0.0    1.1  1  MetW             Methionine biosynthesis protein MetW
     0.0014   18.6   0.0     0.0018   18.3   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
     0.0069   16.3   0.0     0.0097   15.8   0.0    1.2  1  Methyltransf_18  Methyltransferase domain
  ------ inclusion threshold ------
      0.011   16.5   0.0      0.017   15.9   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
      0.032   13.9   0.2      0.072   12.7   0.0    1.6  3  NodS             Nodulation protein S (NodS)
      0.059   12.7   0.0      0.082   12.2   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
      0.093   12.3   0.0       0.14   11.6   0.0    1.2  1  FmrO             Ribosomal RNA methyltransferase (FmrO)
        0.1   12.9   0.0       0.17   12.2   0.0    1.3  1  AdoMet_MTase     Predicted AdoMet-dependent methyltransferase
       0.17   11.3   0.0       0.33   10.4   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 !   54.0   0.0   1.4e-17   1.4e-14      24     126 ..      39     135 ..      31     161 .. 0.84

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 1.4e-17
                                    HHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEEE CS
                            MTS  24 letlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdlivs 103
                                    + ++  els +v+DlGcG+G+l++ +a          vd+d +Al++a+en+e  +++v+++  d+   +  +++ ++++
  gi|116753331|ref|YP_842449.1|  39 IAYMRGELS-QVIDLGCGTGILAIGAALLGAM--AYGVDIDRQALRIARENAEMLGVHVDFILGDIERIAF-RRVKTVIM 114
                                    455666555.7*************99998877..79*****************************998888.******** PP

                                    ---STTTCHCHHHHHHHHHHHHH CS
                            MTS 104 NPPfhagkatelavaeeliaeAk 126
                                    NPPf a++a   +  ++++++A 
  gi|116753331|ref|YP_842449.1| 115 NPPFGAQRAS--RGDRAFLKKAV 135
                                    *****99994..44455666665 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.7   0.1   8.2e-17   8.1e-14     163     213 ..      47      96 ..      35     115 .. 0.82

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 8.2e-17
                           PrmA 163 eevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveakl 213
                                    ++v+D+G+G+GiLai+aa+Lga  +++vDiD +A+++a+eNae+ +v+  +
  gi|116753331|ref|YP_842449.1|  47 SQVIDLGCGTGILAIGAALLGAM-AYGVDIDRQALRIARENAEMLGVHVDF 96 
                                    59*******************96.8******************99888766 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   0.1   3.8e-14   3.7e-11       5      67 ..      47     105 ..      44     147 .. 0.87

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 3.8e-14
                Methyltransf_31   5 lrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieele 67 
                                     +v+DlGCGtG l++ +a +lg  a  +G+Di+ +a++ Arena+ lg+  v F  gdie + 
  gi|116753331|ref|YP_842449.1|  47 SQVIDLGCGTGILAIGAA-LLG--AMAYGVDIDRQALRIARENAEMLGVH-VDFILGDIERIA 105
                                    58****************.776..6788*********************6.*********976 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   0.1     8e-14     8e-11       1      70 [.      49     114 ..      49     138 .. 0.86

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 8e-14
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEE CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvs 70 
                                    v+dlGcGtG l++ +a   g a  +gvDi+ ++l++are+ae  g++v+f+ gd+e++ f    +  v++
  gi|116753331|ref|YP_842449.1|  49 VIDLGCGTGILAIGAALL-G-AMAYGVDIDRQALRIARENAEMLGVHVDFILGDIERIAFRR--VKTVIM 114
                                    89*************988.5.*************************************9975..666665 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.6   7.9e-11   7.9e-08      14     138 ..      30     125 ..      27     138 .. 0.84

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 7.9e-11
                                    HHHHHHHHHHTT--TT.S-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHHHHH CS
                        UPF0020  14 etLAaalvrlagwkpg.epllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsDldrrvvqga 92 
                                    ++LA+ l+++a ++ + ++ +D  CG+G ++I aallga ++                          g+D+dr++++ a
  gi|116753331|ref|YP_842449.1|  30 PSLASDLLYIAYMRGElSQVIDLGCGTGILAIGAALLGAMAY--------------------------GVDIDRQALRIA 83 
                                    578889999999888734688999**************9998..........................************ PP

                                    HHHHHHTT-GGGEEEEE--GGG--STTS---EEEE----------H CS
                        UPF0020  93 reNaekagvgdliefsqadaakLrlkegevdvivtnpPYGerlgsk 138
                                    reNae  gv   ++f   d+  +      v +++ npP+G    s 
  gi|116753331|ref|YP_842449.1|  84 RENAEMLGVH--VDFILGDIERIA--FRRVKTVIMNPPFGAQRASR 125
                                    *****98875..777778888777..33699*********866555 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0   3.8e-11   3.8e-08       2      58 ..      51     107 ..      50     114 .. 0.96

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 3.8e-11
                                    EET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS- CS
                Methyltransf_11   2 dvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfe 58 
                                    d+GcGtG+la   a  ga  +gvD++ ++l++a+e+a+  g++v+f+ +d+e++ f+
  gi|116753331|ref|YP_842449.1|  51 DLGCGTGILAIGAALLGAMAYGVDIDRQALRIARENAEMLGVHVDFILGDIERIAFR 107
                                    9****************************************************9997 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   4.8e-09   4.7e-06       3      84 ..      48     121 ..      46     157 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 4.8e-09
                Methyltransf_15   3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvflSpPwG 82 
                                     ++Dl +G+G  +i  al +   ++++i+++ l +a +Nae+ gv  +++++lgd++ +  +    ++    v++ pP G
  gi|116753331|ref|YP_842449.1|  48 QVIDLGCGTGILAIGAALLGAMAYGVDIDRQALRIARENAEMLGV--HVDFILGDIERIAFR----RV--KTVIMNPPFG 119
                                    58*****************************************88..69******9875422....22..3467888888 PP

                Methyltransf_15  83 Gp 84 
                                      
  gi|116753331|ref|YP_842449.1| 120 AQ 121
                                    65 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   4.2e-08   4.2e-05      21      62 ..      44     117 ..      22     188 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 4.2e-08
                Methyltransf_23  21 raggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae................................k 62 
                                     + + v+d+GcGtGil+  ++  g+  +gvD++++a  ia+                                 
  gi|116753331|ref|YP_842449.1|  44 GELSQVIDLGCGTGILAIGAALLGAMAYGVDIDRQALRIARenaemlgvhvdfilgdieriafrrvktvimnpP 117
                                    56679**********************************99888888888888888776666666554333330 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   5.9e-07   0.00059      40     128 ..      44     123 ..      36     148 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 5.9e-07
                                    HCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEEE CS
                  Cons_hypoth95  40 iegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdivfl 119
                                    +e ++v+Dl +G+G l++ A+  ga  a+ v+ d++a++i +en e+l+++  ++ +  d ++ + ++      +  v +
  gi|116753331|ref|YP_842449.1|  44 GELSQVIDLGCGTGILAIGAALLGA-MAYGVDIDRQALRIARENAEMLGVH--VDFILGDIERIAFRR------VKTVIM 114
                                    556789******************5.7899*******************66..455555555444444......567999 PP

                                    --SSSTTCH CS
                  Cons_hypoth95 120 DPPyakell 128
                                    +PP+ ++ +
  gi|116753331|ref|YP_842449.1| 115 NPPFGAQRA 123
                                    ****98875 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0     1e-06     0.001       3     113 ..      35     148 ..      33     173 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1e-06
                           MetW   3 dfeliaelikpgsrvldlGcGdGellellkeekqvdgrGleldeeg..vaecvakGlsviqgdldkdlenfedksfdyvv 80 
                                    d+ +ia +  + s+v+dlGcG G l  + +   +  ++G+++d+++  +a+  a  l v+ + +  d+e  + ++   v+
  gi|116753331|ref|YP_842449.1|  35 DLLYIAYMRGELSQVIDLGCGTGIL-AIGAALLGAMAYGVDIDRQAlrIARENAEMLGVHVDFILGDIERIAFRRVKTVI 113
                                    88999999999************65.66778899********99973356667788889989999999999999999999 PP

                           MetW  81 lsqtlqat...rnpkevldellrigrraivsfPnfG 113
                                    ++  + a    r  +  l++ + i++ +i +  n G
  gi|116753331|ref|YP_842449.1| 114 MNPPFGAQrasRGDRAFLKKAVEIAD-VIYTIHNAG 148
                                    99766544000455677888777775.566666665 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   1.8e-06    0.0018      26      93 ..      46     105 ..      32     157 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.8e-06
                Methyltransf_32  26 altvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsfaelsieeat 93 
                                      +v+D+G+G g L+   al    ++   +g+d+ ++  + a++ ae lg  +  ++ f+ ++ie++ 
  gi|116753331|ref|YP_842449.1|  46 LSQVIDLGCGTGILAIGAAL----LGAMAYGVDIDRQALRIARENAEMLG--V--HVDFILGDIERIA 105
                                    568****************9....69************************..4..6677777776664 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   9.7e-06    0.0097       7      86 ..      38     112 ..      32     115 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 9.7e-06
                Methyltransf_18   7 aiaslvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklkeeevdtv 86 
                                     ia +  + s+v+D G+  g+l+i ++  g +  ++ +Di +++l+ a+en+e  g+  +++++l+d +e +  + v+tv
  gi|116753331|ref|YP_842449.1|  38 YIAYMRGELSQVIDLGCGTGILAIGAALLGAM--AYGVDIDRQALRIARENAEMLGV--HVDFILGD-IERIAFRRVKTV 112
                                    56777778899****************98877..9******************9988..68888887.455554455555 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.9   0.0   1.7e-05     0.017       2      40 ..      51      87 ..      50     115 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.7e-05
                Methyltransf_12  2 eiGcGtGsllralleklpdieytgvDispsaiedakekl 40
                                   ++GcGtG l+   +    ++  +gvDi+++a+  a+e  
  gi|116753331|ref|YP_842449.1| 51 DLGCGTGILAIGAALL--GAMAYGVDIDRQALRIARENA 87
                                   9******998888888..**************6666654 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   7.2e-05     0.072      33     103 ..      35     106 ..      29     115 .. 0.87
   2 ?   -3.7   0.0       7.7   7.7e+03     112     125 ..     137     150 ..     133     165 .. 0.73
   3 ?   -2.8   0.0       4.1   4.1e+03      89     105 ..     181     197 ..     161     201 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.2e-05
                           NodS  33 qilrlslaqgsiadalevGcaaGalterlapyckrltvvdvveeaiararervkes.shiswivsdvqqfst 103
                                    ++l ++   g++++++++Gc +G l+   a +      vd+  +a+  are  +    h+ +i  d++++  
  gi|116753331|ref|YP_842449.1|  35 DLLYIAYMRGELSQVIDLGCGTGILAIGAALLGAMAYGVDIDRQALRIARENAEMLgVHVDFILGDIERIAF 106
                                    68889999*************************************988888776542799******999865 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 7.7
                           NodS 112 vaevlyyiedvael 125
                                    +a+v+y i++   l
  gi|116753331|ref|YP_842449.1| 137 IADVIYTIHNAGSL 150
                                    68888888876655 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 4.1
                           NodS  89 shiswivsdvqqfstde 105
                                     ++ wi+ ++ ++  ++
  gi|116753331|ref|YP_842449.1| 181 KDVEWIEVELYRIACKQ 197
                                    47778777777766555 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   8.3e-05     0.082      49     115 ..      47     109 ..      37     140 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.3e-05
                                    TEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T CS
                Ubie_methyltran  49 akvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfedd 115
                                    ++v+D+ +Gtg la+  +   g+     ++Di+ + L+++++ ++  g+ +++f+ ++ e++ f   
  gi|116753331|ref|YP_842449.1|  47 SQVIDLGCGTGILAIGAALL-GA--MAYGVDIDRQALRIARENAEMLGV-HVDFILGDIERIAFRRV 109
                                    589*********99985543.33..45789**************99997.79*****9999998764 PP

>> FmrO  Ribosomal RNA methyltransferase (FmrO)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00014      0.14     108     156 ..      47      93 ..      39     103 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00014
                           FmrO 108 asvlDvaCgLnpLavpwlllaadatylasDidsdlvefldrflalveve 156
                                    + v+D++Cg   La++  ll a  + ++ Did + + +     ++++v+
  gi|116753331|ref|YP_842449.1|  47 SQVIDLGCGTGILAIGAALLGA--MAYGVDIDRQALRIARENAEMLGVH 93 
                                    579**************99976..558*********9999999998876 PP

>> AdoMet_MTase  Predicted AdoMet-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00017      0.17      59      91 ..      46      78 ..      35      89 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00017
                   AdoMet_MTase 59 etsfvdvgcgngllvyvlaaegykgygidlrkr 91
                                       +d+gcg g+l    a  g   yg+d+ ++
  gi|116753331|ref|YP_842449.1| 46 LSQVIDLGCGTGILAIGAALLGAMAYGVDIDRQ 78
                                   55689***********9************9765 PP

>> AviRa  RRNA methyltransferase AviRa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00033      0.33      55     103 ..      47      91 ..      28      94 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00033
                          AviRa  55 ltlyDpCCGgayLltvlgllhgkkikkvlasDvdeevlelakkNLsLLt 103
                                     ++ D  CG++ L+   +ll +      ++ D+d+++l++a++N ++L 
  gi|116753331|ref|YP_842449.1|  47 SQVIDLGCGTGILAIGAALLGAM----AYGVDIDRQALRIARENAEMLG 91 
                                    4678999***9999999998764....59***************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); 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 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1474.09
//
Query:       gi|116753332|ref|YP_842450.1|  [L=584]
Description: putative ATPase RIL [Methanosaeta thermophila PT]
Scores for complete 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-39  134.5   0.0    9.7e-20   71.5   0.0    2.6  2  ABC_tran      ABC transporter
    3.7e-12   46.2   8.9    3.5e-06   26.6   1.5    4.1  3  SMC_N         RecF/RecN/SMC N terminal domain
    3.8e-12   45.8   2.7    8.6e-12   44.7   2.7    1.6  1  RLI           Possible Fer4-like domain in RNase L inhibitor,
    3.2e-09   37.0  13.6      0.019   14.8   0.0    4.2  4  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    6.9e-08   32.0   4.2    6.9e-08   32.0   4.2    2.4  2  Fer4          4Fe-4S binding domain
    1.5e-07   31.2  13.3    2.4e-06   27.4   2.8    2.4  2  Fer4_6        4Fe-4S binding domain
    5.7e-05   22.8   0.6      0.077   12.7   0.1    2.4  2  AAA_29        P-loop containing region of AAA domain
    0.00016   22.3   2.5       0.16   12.4   0.3    2.3  2  AAA_23        AAA domain
    0.00038   20.3   0.0       0.98    9.1   0.0    3.2  3  AAA_15        AAA ATPase domain
    0.00065   19.7   0.2        1.8    8.4   0.1    2.6  2  Rad17         Rad17 P-loop domain
    0.00078   20.0   1.1    0.00078   20.0   1.1    2.3  2  Fer4_7        4Fe-4S dicluster domain
    0.00094   19.1   0.1        1.8    8.4   0.0    2.5  2  RsgA_GTPase   RsgA GTPase
     0.0012   19.0   7.3     0.0019   18.3   7.3    1.4  1  Fer4_21       4Fe-4S dicluster domain
     0.0017   18.5   7.5     0.0035   17.5   7.5    1.5  1  Fer4_9        4Fe-4S dicluster domain
     0.0032   17.9   1.4       0.85   10.0   0.0    2.9  2  AAA_16        AAA ATPase domain
     0.0048   16.9   2.6     0.0048   16.9   2.6    2.4  2  Fer4_2        4Fe-4S binding domain
     0.0061   16.6   1.4     0.0061   16.6   1.4    2.2  2  Fer4_10       4Fe-4S dicluster domain
     0.0066   17.0   0.3        1.8    9.1   0.0    3.0  2  AAA_18        AAA domain
  ------ inclusion threshold ------
      0.013   15.3   0.9        3.5    7.3   0.1    2.4  2  AAA_24        AAA domain
      0.015   15.5   0.1         15    5.9   0.1    3.0  2  SbcCD_C       Putative exonuclease SbcCD, C subunit
      0.034   15.1   1.2      0.034   15.1   1.2    2.4  1  Fer4_16       4Fe-4S double cluster binding domain
      0.035   14.5   0.1         11    6.4   0.1    2.5  2  RNA_helicase  RNA helicase
      0.046   14.3  12.5      0.069   13.7   3.0    2.3  2  Fer4_4        4Fe-4S binding domain
      0.055   12.4   1.2        2.2    7.2   0.1    2.2  2  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
       0.18   11.4   0.1         15    5.1   0.0    2.3  2  AAA_27        AAA domain
       0.21   11.6   0.4         29    4.7   0.0    3.1  3  AAA_14        AAA domain
       0.96    9.3   3.0         61    3.5   0.1    3.5  3  NTPase_1      NTPase
        1.4    8.4   3.2         19    4.8   0.0    3.1  3  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 !   60.3   0.0   4.2e-19   2.7e-16      10     134 ..      94     231 ..      93     233 .. 0.75
   2 !   71.5   0.0   1.5e-22   9.7e-20       8     137 .]     355     475 ..     348     475 .. 0.80

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 4.2e-19
                                    TTSEEEEEESTTSSHHHHHHHHTTSS--SEEEE........EETTCEGGG..B-HHHCCHCEEEE-SS.--S-TTSBHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxx..xxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                       ABC_tran  10 egekvaivGenGaGKStLlkllagllkpteGei........lldgkdlke..qeleslrkeigvlpqe.pqlfpeltvre 78 
                                    eg++++i+G+nG GKSt +++l+gll+p+ G+         ++ g  + +  ++  +   + ++ pq  +++ + +    
  gi|116753332|ref|YP_842450.1|  94 EGKVTGILGPNGIGKSTAVAILSGLLRPNLGKDatwdevleRFAGSAIGDylKKVAEKGVRTAYKPQYiDRIPKSY---- 169
                                    699*************************999984444444433444444455444445555555566642222222.... PP

                                    H..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEES CS
                                    x..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  79 n..........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDE 134
                                    +          +++ e+++++++lgl++l d+ +     sLSgG+ qrva+a++ +++++++++DE
  gi|116753332|ref|YP_842450.1| 170 RgsvrellkrtNERGELDALVDRLGLSHLLDREI----DSLSGGELQRVAIAATAARDADFYFFDE 231
                                    0234455987777778******************....***************************9 PP

  == domain 2  score: 71.5 bits;  conditional E-value: 1.5e-22
                                    EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH........ CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........ RF
                       ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren........ 79 
                                    ++++e+v+i+G+nG GKSt +k+l g +kpt+G+i              ++ +i++ pq  +  +++tv+          
  gi|116753332|ref|YP_842450.1| 355 IRRSEVVGILGPNGIGKSTYIKILGGIEKPTNGRI-------------DAKLKISYKPQYLKAESDVTVEALlrsitpdf 421
                                    7899*******************************.............46667777777777777776666566664444 PP

                                    HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                    +s+   +++++ l l+ l d+ +    ++LSgG+ qrva+ ++l  +++l+llDEp+a
  gi|116753332|ref|YP_842450.1| 422 DSSYYQSEFVKPLALDRLLDQSM----TELSGGELQRVAIIACLSMDADLYLLDEPSA 475
                                    55555666666666666666666....*****************************75 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   1.5   5.5e-09   3.5e-06      20     201 ..      91     266 ..      82     279 .. 0.72
   2 ?    4.6   0.1      0.03        20      25      41 ..     359     375 ..     341     379 .. 0.84
   3 !   14.0   0.1   3.9e-05     0.025     134     195 ..     444     503 ..     385     524 .. 0.71

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 5.5e-09
                                    EETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTT.TCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  20 lpfsksftaivGpNGSGKsnlldAilFvLGersakkl.rseklsdlihkskekasvkkaeveitfdnedkklkiekeevs 98 
                                    +p++ ++t i+GpNG GKs  +  ++ +L      +l + ++ ++++ +     ++ +a  + + +  +k +++  +  +
  gi|116753332|ref|YP_842450.1|  91 IPVEGKVTGILGPNGIGKSTAVAILSGLLR----PNLgKDATWDEVLER-----FAGSAIGDYLKKVAEKGVRTAYKPQY 161
                                    6788899************98765544443....234034444444444.....44444333333334444566777788 PP

                                    EEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  99 isrrvkrkgeseykingkevtkkevsellesagiske......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLD 172
                                    i r  k+   s  ++ +++ ++ e+  l+ + g+s        +LSgGe + va+a      +++ a +y++Dei   LD
  gi|116753332|ref|YP_842450.1| 162 IDRIPKSYRGSVRELLKRTNERGELDALVDRLGLSHLldreidSLSGGELQRVAIA----ATAARDADFYFFDEISPYLD 237
                                    88888887778888888888888888888888876434444449*****9988876....45789999************ PP

                                    HHHHHHHHHHHHHHCTTSEEEEE-SSHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 173 eknvkkvaellkeksknaQfivislreem 201
                                     +++   a++l+   +n  ++v+ ++  +
  gi|116753332|ref|YP_842450.1| 238 INQRILAARMLQDLASNKAVMVVEHDLAL 266
                                    *********************99887665 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.03
                                    SEEEEEESTTSSHHHHH CS
                                    xxxxxxxxxxxxxxxxx RF
                          SMC_N  25 sftaivGpNGSGKsnll 41 
                                    ++  i+GpNG GKs  +
  gi|116753332|ref|YP_842450.1| 359 EVVGILGPNGIGKSTYI 375
                                    57789*********765 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 3.9e-05
                                    TTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxx RF
                          SMC_N 134 kelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivi 195
                                    +++LSgGe + v  a++ A  ++  a lyllDe  a+LD +++   a+++++  ++    ++v+
  gi|116753332|ref|YP_842450.1| 444 MTELSGGELQRV--AII-ACLSM-DADLYLLDEPSAHLDVEQRMMAARVMRRFAESteRSVVVV 503
                                    347****96655..555.55544.467*****************99999996555411344444 PP

>> RLI  Possible Fer4-like domain in RNase L inhibitor, RLI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   2.7   1.3e-14   8.6e-12       1      35 []       1      32 [.       1      32 [. 0.97

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 1.3e-14
                                   --EEEES---------TTHHHHHTTSEEEESS--S CS
                            RLI  1 mrlAivdadqCdPKKCtgkkcarfcpvrlvrtgkk 35
                                   mr+A+v++d+C+P+KC   +c+ fcp   vrtg++
  gi|116753332|ref|YP_842450.1|  1 MRIAVVNRDRCQPRKCAR-ECEYFCPP--VRTGDE 32
                                   9*****************.********..****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 !   14.4   0.5   3.8e-05     0.024       1      24 [.      97     120 ..      97     145 .. 0.82
   2 ?    5.5   0.1      0.02        13     189     291 ..     173     256 ..     139     268 .. 0.64
   3 !    9.0   1.0    0.0017       1.1       2      22 ..     361     381 ..     360     411 .. 0.84
   4 !   14.8   0.0     3e-05     0.019     232     302 ..     442     510 ..     411     511 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.8e-05
                         AAA_21   1 lnvliGpNgsGKSnLLdaldllar 24 
                                    ++++ GpNg GKS+   +l++l r
  gi|116753332|ref|YP_842450.1|  97 VTGILGPNGIGKSTAVAILSGLLR 120
                                    699*******************86 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.02
                         AAA_21 189 vrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEn 268
                                    vr+l+++ +e   l++                v  l  ++  ++ +++lS G ++  a+++  +r++   +++++DE+  
  gi|116753332|ref|YP_842450.1| 173 VRELLKRTNERGELDA---------------LVDRLGLSHLLDREIDSLSGGELQRVAIAATAARDA---DFYFFDEISP 234
                                    3333333333333333...............444444455556679********999********99...9*******98 PP

                         AAA_21 269 gLHPkllrrll.ellkelsrngaQ 291
                                     L+   +r l+ ++l +l++ +  
  gi|116753332|ref|YP_842450.1| 235 YLDI-NQRILAaRMLQDLAS-NKA 256
                                    8888.555555577755555.444 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0017
                         AAA_21   2 nvliGpNgsGKSnLLdaldll 22 
                                     ++ GpNg GKS+ +++l ++
  gi|116753332|ref|YP_842450.1| 361 VGILGPNGIGKSTYIKILGGI 381
                                    689**************9776 PP

  == domain 4  score: 14.8 bits;  conditional E-value: 3e-05
                         AAA_21 232 lparelSdGtkrllalltallralkkgsllliDEpEngLHPkll...rrllellkelsrngaQviltTHSplll 302
                                     +++elS G ++  a+++ l  ++   +l+l+DEp ++L+ +     +r+++ + e ++    v+++ H+ +l+
  gi|116753332|ref|YP_842450.1| 442 QSMTELSGGELQRVAIIACLSMDA---DLYLLDEPSAHLDVEQRmmaARVMRRFAESTE--RSVVVVDHDIYLI 510
                                    578999****99999999999999...9*************554457888888866666..6777777777776 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       5.6   3.6e+03       2       8 ..       5      11 ..       4      12 .. 0.87
   2 !   32.0   4.2   1.1e-10   6.9e-08       1      24 []      41      64 ..      41      64 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 5.6
                                   EEETTTS CS
                           Fer4  2 videekC 8 
                                   v++ ++C
  gi|116753332|ref|YP_842450.1|  5 VVNRDRC 11
                                   89***** PP

  == domain 2  score: 32.0 bits;  conditional E-value: 1.1e-10
                                   EEEETTTSSS-THHHHHSTTTEEE CS
                           Fer4  1 vvideekCigCGaCvevCPvgAIt 24
                                   +vi e++C+gCG+Cv  CP+gAIt
  gi|116753332|ref|YP_842450.1| 41 PVITENLCVGCGICVRKCPFGAIT 64
                                   6899*******************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 !    9.0   3.0    0.0023       1.5       1      20 [.       3      25 ..       3      30 .. 0.89
   2 !   27.4   2.8   3.8e-09   2.4e-06       1      24 []      40      63 ..      40      63 .. 0.96

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0023
                         Fer4_6  1 vveidpdkCi..gC.gdCvrvCP 20
                                   ++++++d+C    C ++C+  CP
  gi|116753332|ref|YP_842450.1|  3 IAVVNRDRCQprKCaRECEYFCP 25
                                   689******9888*888*****9 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 3.8e-09
                         Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                   +++i +++C+gCg Cvr CP+gai
  gi|116753332|ref|YP_842450.1| 40 KPVITENLCVGCGICVRKCPFGAI 63
                                   6899*******************8 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 !   12.7   0.1   0.00012     0.077      18      48 ..      90     121 ..      83     126 .. 0.78
   2 !    7.9   0.0    0.0039       2.5      21      39 ..     357     375 ..     347     377 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                         AAA_29  18 eidlkg.atlltGpsGsGKSTllDAiqalLvp 48 
                                    +i ++g +t + Gp+G GKST +  ++ lL p
  gi|116753332|ref|YP_842450.1|  90 PIPVEGkVTGILGPNGIGKSTAVAILSGLLRP 121
                                    5666788999***********99444555555 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0039
                         AAA_29  21 lkgatlltGpsGsGKSTll 39 
                                    +++++ + Gp+G GKST +
  gi|116753332|ref|YP_842450.1| 357 RSEVVGILGPNGIGKSTYI 375
                                    4557779**********76 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.3   0.00026      0.16      17      38 ..      93     114 ..      82     125 .. 0.83
   2 !    9.5   0.1     0.002       1.3      19      37 ..     358     376 ..     340     380 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00026
                         AAA_23  17 FskgltlItGpNGaGKTTildA 38 
                                     + ++t I GpNG GK+T +  
  gi|116753332|ref|YP_842450.1|  93 VEGKVTGILGPNGIGKSTAVAI 114
                                    56789*************8765 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.002
                         AAA_23  19 kgltlItGpNGaGKTTild 37 
                                    + ++ I GpNG GK+T + 
  gi|116753332|ref|YP_842450.1| 358 SEVVGILGPNGIGKSTYIK 376
                                    56889***********875 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0    0.0015      0.98      19      50 ..      91     122 ..      86     168 .. 0.83
   2 ?    4.6   0.0     0.035        22      25      43 ..     360     378 ..     354     412 .. 0.87
   3 ?    2.6   0.0      0.14        88     323     367 ..     464     508 ..     457     510 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0015
                         AAA_15  19 idlseeltvliGkNnsGKSsilealdlFlnnk 50 
                                    i+++ ++t + G+N++GKS+++ +l  +l  +
  gi|116753332|ref|YP_842450.1|  91 IPVEGKVTGILGPNGIGKSTAVAILSGLLRPN 122
                                    556666999****************9888765 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.035
                         AAA_15  25 ltvliGkNnsGKSsileal 43 
                                    +  + G+N++GKS+ +++l
  gi|116753332|ref|YP_842450.1| 360 VVGILGPNGIGKSTYIKIL 378
                                    55688***********998 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.14
                         AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSph 367
                                    + +++l++EP ahL  ++ ++ ++ +++ a++++  v++  H  +
  gi|116753332|ref|YP_842450.1| 464 DADLYLLDEPSAHLDVEQRMMAARVMRRFAESTERSVVVVDHDIY 508
                                    5689***************************99887777777655 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.1    0.0028       1.8      50      72 ..     100     122 ..      93     128 .. 0.84
   2 !    8.4   0.0    0.0028       1.8      45      67 ..     358     380 ..     348     407 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0028
                          Rad17  50 isGPsGCgkstvvkvLskelgik 72 
                                    i GP G gkst+v +Ls  l ++
  gi|116753332|ref|YP_842450.1| 100 ILGPNGIGKSTAVAILSGLLRPN 122
                                    88**************9877665 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0028
                          Rad17  45 kriLLisGPsGCgkstvvkvLsk 67 
                                     +++ i GP G gkst +k+L  
  gi|116753332|ref|YP_842450.1| 358 SEVVGILGPNGIGKSTYIKILGG 380
                                    4577899*************975 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   3.1       2.4   1.6e+03      32      49 ..       5      25 ..       1      27 [. 0.74
   2 !   20.0   1.1   1.2e-06   0.00078       2      25 ..      48      71 ..      47      83 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 2.4
                         Fer4_7 32 eidpekCl..gCga.CvavCP 49
                                   +++ ++C+   C + C+  CP
  gi|116753332|ref|YP_842450.1|  5 VVNRDRCQprKCAReCEYFCP 25
                                   567789975578877999999 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 1.2e-06
                         Fer4_7  2 CigCgaCvaaCpvkaieldeeene 25
                                   C+gCg Cv+ Cp +ai++++  +e
  gi|116753332|ref|YP_842450.1| 48 CVGCGICVRKCPFGAITITNLPEE 71
                                   *****************9876544 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0    0.0041       2.6      97     121 ..      93     117 ..      65     130 .. 0.82
   2 !    8.4   0.0    0.0028       1.8      99     130 ..     357     389 ..     338     395 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0041
                                    CTTSEEEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase  97 lkdktsvlvGqSGvGKStLinallp 121
                                    +++k++ ++G+ G+GKSt +  l +
  gi|116753332|ref|YP_842450.1|  93 VEGKVTGILGPNGIGKSTAVAILSG 117
                                    7899**************9887765 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0028
                                    T.SEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                    RsgA_GTPase  99 d.ktsvlvGqSGvGKStLinallpelelktgev 130
                                      +++ ++G+ G+GKSt i+ l + ++   g +
  gi|116753332|ref|YP_842450.1| 357 RsEVVGILGPNGIGKSTYIKILGGIEKPTNGRI 389
                                    4478889************99987666555555 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   7.3     3e-06    0.0019       1      58 [.       4      64 ..       4      65 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3e-06
                        Fer4_21  1 AridedkCi..gCgk.CliaCe..dtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58
                                   A++++d+C   +C + C   C+   t+ + i + +++   ++e+ CvGC +C+  CP  ++i+
  gi|116753332|ref|YP_842450.1|  4 AVVNRDRCQprKCAReCEYFCPpvRTGDETIVFVDDKP-VITENLCVGCGICVRKCPF-GAIT 64
                                   67888888422454336666653346677777665544.456899************7.9987 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   7.5   5.4e-06    0.0035       4      51 .]      15      63 ..      10      65 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 5.4e-06
                         Fer4_9  4 gCga.CveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                   +C + C++ Cp   + ++     +      e+ C+gCg Cv +Cp gai
  gi|116753332|ref|YP_842450.1| 15 KCAReCEYFCPPVRTGDETIVFVDDKPVITENLCVGCGICVRKCPFGAI 63
                                   465348888877777777766666666666689************9987 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.3     0.027        17      29      46 ..     100     117 ..      91     278 .. 0.72
   2 !   10.0   0.0    0.0013      0.85      23     142 ..     357     504 ..     348     517 .. 0.58

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.027
                         AAA_16  29 lsGesGvGKsslvrellr 46 
                                    + G+ G+GKs+ v  l  
  gi|116753332|ref|YP_842450.1| 100 ILGPNGIGKSTAVAILSG 117
                                    89*********9965553 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0013
                         AAA_16  23 rpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysa.laqalareellrqllde....aesaeleaw 97 
                                    r+e+v + G+ G+GKs+ ++ l   +ek     ++g+ d    +i+y + +++a   +  +++ll+         + +++
  gi|116753332|ref|YP_842450.1| 357 RSEVVGILGPNGIGKSTYIKILG-GIEKP----TNGRIDAK-LKISYKPqYLKAE-SDVTVEALLRSitpdF---DSSYY 426
                                    4588999************7777.78888....55555554.4444544444444.3344444444443220...22233 PP

                         AAA_16  98 rekleeala.....................................avpelagaeasrllellkrllallsrderplvlv 140
                                    + ++ + la                                     ++++l+ +++   +++++r+++ +   er  v+v
  gi|116753332|ref|YP_842450.1| 427 QSEFVKPLAldrlldqsmtelsggelqrvaiiaclsmdadlylldePSAHLDVEQRMMAARVMRRFAEST---ER-SVVV 502
                                    3333333333333333333555555555555555556688888877777777777766666666666333...44.5666 PP

                         AAA_16 141 lD 142
                                    +D
  gi|116753332|ref|YP_842450.1| 503 VD 504
                                    66 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   3.7      0.39   2.5e+02       3      21 ..       4      25 ..       2      26 .. 0.82
   2 !   16.9   2.6   7.6e-06    0.0048       2      21 ..      40      59 ..      39      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.39
                         Fer4_2  3 vvvdtdrC.ig.C.gaCvsaCP 21
                                   +vv++drC  + C + C   CP
  gi|116753332|ref|YP_842450.1|  4 AVVNRDRCqPRkCaRECEYFCP 25
                                   789*****65679779*****9 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 7.6e-06
                         Fer4_2  2 pvvvdtdrCigCgaCvsaCP 21
                                   ++v+ ++ C+gCg+Cv  CP
  gi|116753332|ref|YP_842450.1| 40 KPVITENLCVGCGICVRKCP 59
                                   5788899************* PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9  13.2    0.0025       1.6       2      56 .]       4      59 ..       3      59 .. 0.82
   2 !   16.6   1.4   9.6e-06    0.0061       2      23 ..      41      62 ..      40      83 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0025
                        Fer4_10  2 vvidddtC..irCg.kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                   +v+++d+C   +C+ +C  +CP    + g + +   +++  +    C gcg Cv++CP
  gi|116753332|ref|YP_842450.1|  4 AVVNRDRCqpRKCArECEYFCPP--VRTGDETIVFVDDKPVITENLCVGCGICVRKCP 59
                                   578999**77799989*******..666666666677777777788***********9 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 9.6e-06
                        Fer4_10  2 vvidddtCirCgkCvkaCPadl 23
                                   +vi ++ C++Cg Cv+ CP+ +
  gi|116753332|ref|YP_842450.1| 41 PVITENLCVGCGICVRKCPFGA 62
                                   68999**************955 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0    0.0028       1.8       3      94 ..     100     205 ..      99     257 .. 0.71
   2 ?    4.3   0.2     0.086        55       1      19 [.     361     383 ..     361     526 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0028
                         AAA_18   3 ltGtpGvGKttlakeLskrl.gf...................gvnlrdvakenglllevdpealdeskrldedkldklld 62 
                                    + G+ G GK+t    Ls +l  +                   g+ l++va + g ++ + p+     +r+ + ++ ++ +
  gi|116753332|ref|YP_842450.1| 100 ILGPNGIGKSTAVAILSGLLrPNlgkdatwdevlerfagsaiGDYLKKVAEK-GVRTAYKPQ---YIDRIPKSYRGSVRE 175
                                    89**************999876689999999999999*55555555555555.566666665...8999999999***** PP

                         AAA_18  63 aleenssaleegknlvidghlaeleseaakdi 94 
                                    +l++ ++ ++e +  ++d +   ++ ++ +d 
  gi|116753332|ref|YP_842450.1| 176 LLKRTNE-RGELDA-LVDRLGLSHLLDREIDS 205
                                    ****987.444444.88888777777776665 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.086
                         AAA_18   1 IlltGtpGvGKttlakeL....s 19 
                                    +++ G+ G GK+t  k L    +
  gi|116753332|ref|YP_842450.1| 361 VGILGPNGIGKSTYIKILggieK 383
                                    6799999******9999955541 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1     0.011       7.2       3      22 ..      96     115 ..      94     127 .. 0.83
   2 ?    7.3   0.1    0.0055       3.5       4      22 ..     360     378 ..     357     391 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.011
                         AAA_24   3 lkiliyGpsgiGKTtlakel 22 
                                    +   i Gp+giGK+t ++ l
  gi|116753332|ref|YP_842450.1|  96 KVTGILGPNGIGKSTAVAIL 115
                                    56789**********98765 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0055
                         AAA_24   4 kiliyGpsgiGKTtlakel 22 
                                     + i Gp+giGK+t +k l
  gi|116753332|ref|YP_842450.1| 360 VVGILGPNGIGKSTYIKIL 378
                                    5789**********99877 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.029        19      24      48 ..     197     221 ..     176     229 .. 0.81
   2 ?    5.9   0.1     0.024        15      26      49 ..     440     462 ..     424     491 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.029
                        SbcCD_C  24 kelsrssgtlSGGekqflaylalaa 48 
                                      l+r++ +lSGGe q +a  a aa
  gi|116753332|ref|YP_842450.1| 197 HLLDREIDSLSGGELQRVAIAATAA 221
                                    45899**********9988877775 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.024
                        SbcCD_C  26 lsrssgtlSGGekqflaylalaaa 49 
                                    l++s+++lSGGe q +a +a + +
  gi|116753332|ref|YP_842450.1| 440 LDQSMTELSGGELQRVAIIACL-S 462
                                    7889999*****9776665544.3 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   1.2   5.2e-05     0.034       2      19 ..      48      65 ..      47      76 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.2e-05
                        Fer4_16  2 CgtCgkCaevCPtnaike 19
                                   C++Cg C+  CP +ai+ 
  gi|116753332|ref|YP_842450.1| 48 CVGCGICVRKCPFGAITI 65
                                   ***************985 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.035        23       3      19 ..     100     116 ..      99     137 .. 0.81
   2 ?    6.4   0.1     0.018        11       3      18 ..     363     378 ..     361     397 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.035
                   RNA_helicase   3 lyGpsgeGKStlakeLa 19 
                                    + Gp+g+GKSt++  L+
  gi|116753332|ref|YP_842450.1| 100 ILGPNGIGKSTAVAILS 116
                                    67**********98865 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.018
                   RNA_helicase   3 lyGpsgeGKStlakeL 18 
                                    + Gp+g+GKSt++k L
  gi|116753332|ref|YP_842450.1| 363 ILGPNGIGKSTYIKIL 378
                                    78**********9985 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   2.1     0.042        27       2      15 ..       9      25 ..       8      36 .. 0.82
   2 ?   13.7   3.0   0.00011     0.069       2      17 .]      46      61 ..      45      61 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.042
                         Fer4_4  2 erCi..gCgs.CvaaCP 15
                                   +rC+   C + C+++CP
  gi|116753332|ref|YP_842450.1|  9 DRCQprKCAReCEYFCP 25
                                   78855599966*****9 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00011
                         Fer4_4  2 erCigCgsCvaaCPqg 17
                                   + C+gCg Cv+ CP+g
  gi|116753332|ref|YP_842450.1| 46 NLCVGCGICVRKCPFG 61
                                   57************86 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 ?    3.8   0.1     0.038        24      30      55 ..      96     121 ..      91     158 .. 0.82
   2 ?    7.2   0.1    0.0034       2.2      28      50 ..     357     379 ..     344     387 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.038
                                    EEEEEEE-TTSSHHHHHHHHHHHHHC CS
                           MeaB  30 qvvGltGvPGaGkstlvealglelrr 55 
                                    +v G+ G  G Gkst+v  l   lr 
  gi|116753332|ref|YP_842450.1|  96 KVTGILGPNGIGKSTAVAILSGLLRP 121
                                    6889*************999877765 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0034
                                    -SEEEEEEE-TTSSHHHHHHHHH CS
                           MeaB  28 raqvvGltGvPGaGkstlvealg 50 
                                    r++vvG+ G  G Gkst ++ lg
  gi|116753332|ref|YP_842450.1| 357 RSEVVGILGPNGIGKSTYIKILG 379
                                    899***************99875 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.023        15      27      50 ..      96     119 ..      76     120 .. 0.80
   2 ?    3.8   0.0     0.057        36       8      44 ..     333     376 ..     332     382 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.023
                         AAA_27  27 dlhliyGpNEAGKstalrAisdll 50 
                                    +++ i+GpN  GKsta++ +s ll
  gi|116753332|ref|YP_842450.1|  96 KVTGILGPNGIGKSTAVAILSGLL 119
                                    56669***********99888776 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.057
                         AAA_27   8 LeryGkftdr..sldfsa.....eeadlhliyGpNEAGKstalr 44 
                                    L  yG+f+ +   +++sa      ++++  i+GpN  GKst ++
  gi|116753332|ref|YP_842450.1| 333 LVEYGEFSKSynGFELSAmpgviRRSEVVGILGPNGIGKSTYIK 376
                                    567788877622344444444444788888***********875 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.15        97       2      20 ..      95     113 ..      94     129 .. 0.86
   2 ?   -0.6   0.0         2   1.3e+03      64      80 ..     223     239 ..     198     259 .. 0.74
   3 ?    4.7   0.0     0.046        29       3      22 ..     359     378 ..     357     424 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.15
                         AAA_14   2 rkilvitGaRrvGKTtllk 20 
                                    +k+  i G+  +GK+t + 
  gi|116753332|ref|YP_842450.1|  95 GKVTGILGPNGIGKSTAVA 113
                                    58999***********975 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2
                         AAA_14  64 kktylflDEiqevpewe 80 
                                    +  + f+DEi+ + ++ 
  gi|116753332|ref|YP_842450.1| 223 DADFYFFDEISPYLDIN 239
                                    56789*****9776655 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.046
                         AAA_14   3 kilvitGaRrvGKTtllkql 22 
                                    +++ i G+  +GK+t++k l
  gi|116753332|ref|YP_842450.1| 359 EVVGILGPNGIGKSTYIKIL 378
                                    7899***********99866 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.095        61       4      23 ..     100     119 ..      97     158 .. 0.90
   2 ?    1.0   0.0      0.53   3.4e+02      83     135 ..     213     264 ..     205     277 .. 0.75
   3 ?    2.5   0.3      0.19   1.2e+02       2      17 ..     361     376 ..     360     385 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.095
                                    EE--TTSSHHHHHHHHHHHH CS
                       NTPase_1   4 iTGppGvGKtTlvkkvlell 23 
                                    i Gp G+GK+T v  ++ ll
  gi|116753332|ref|YP_842450.1| 100 ILGPNGIGKSTAVAILSGLL 119
                                    669*********99887776 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.53
                                    HHHHHHHHHHHHHH-EEEE---ST.TGGG-HHHHHHHHHHHTTTSEEEEE--SS CS
                       NTPase_1  83 elalealrkalseadviviDEiGk.mElkskkfkeaveevLksekpvlavihrr 135
                                    ++a++a  +a ++ad +  DEi + +  + + ++  + + L+s+k v++v h  
  gi|116753332|ref|YP_842450.1| 213 RVAIAA--TAARDADFYFFDEISPyLDINQRILAARMLQDLASNKAVMVVEHDL 264
                                    444444..45699*********98678888899999999999999888877754 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.19
                                    EEEE--TTSSHHHHHH CS
                       NTPase_1   2 vfiTGppGvGKtTlvk 17 
                                    v i Gp G+GK+T +k
  gi|116753332|ref|YP_842450.1| 361 VGILGPNGIGKSTYIK 376
                                    5688*********986 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1       0.2   1.3e+02      32      51 ..      94     113 ..      90     119 .. 0.87
   2 ?    4.8   0.0      0.03        19      26      48 ..     351     373 ..     349     376 .. 0.93
   3 ?   -0.6   0.1       1.3   8.6e+02      82     149 ..     448     504 ..     444     515 .. 0.53

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.2
                         AAA_25  32 agelallaGapgtGKttlal 51 
                                    +g+++ + G+ g GK+t++ 
  gi|116753332|ref|YP_842450.1|  94 EGKVTGILGPNGIGKSTAVA 113
                                    7899999**********875 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.03
                         AAA_25  26 vkgllpagelallaGapgtGKtt 48 
                                    ++g++++ e++ + G+ g GK+t
  gi|116753332|ref|YP_842450.1| 351 MPGVIRRSEVVGILGPNGIGKST 373
                                    78********************9 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.3
                         AAA_25  82 sedelrrRlravgealrddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviD 149
                                    s  el+r +  ++  +  da+l++ld ++    +L    + +++  a+ + +++ +e+  +  +vv+D
  gi|116753332|ref|YP_842450.1| 448 SGGELQRVAIIACLSM--DADLYLLDEPSA---HL----DVEQRMMAA-RVMRRFAES-TERSVVVVD 504
                                    5566677777677776..688888886543...33....233332222.112222222.334555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (584 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.43
# Mc/sec: 4052.72
//
Query:       gi|116753333|ref|YP_842451.1|  [L=139]
Description: hypothetical protein Mthe_0008 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.036   13.4   0.0      0.041   13.3   0.0    1.0  1  Umbravirus_LDM   Umbravirus long distance movement (LDM) fami
      0.039   14.3   1.5      0.073   13.4   1.4    1.5  1  Phage_holin_5_2  Phage holin family Hol44, in holin superfami


Domain annotation for each model (and alignments):
>> Umbravirus_LDM  Umbravirus long distance movement (LDM) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.5e-06     0.041      94     147 ..       6      63 ..       1      75 [. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.5e-06
                 Umbravirus_LDM  94 arRraRRgGgldsRqstaqpkqrga...eteiraerR.AeidglLppLLdtidGqilg 147
                                     + ++R +G  ++ q+++++++  +   + +++ erR A+i+g+  +L+ +i G i g
  gi|116753333|ref|YP_842451.1|   6 KKAKSRETGRKEPPQKPPETQKEVKkvlKKKTPEERRkAQIEGIKKTLVPSILGIISG 63 
                                    56689**************99876612256888887669*********9999998765 PP

>> Phage_holin_5_2  Phage holin family Hol44, in holin superfamily V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.4   8.1e-06     0.073      15      39 ..      46      70 ..      44     100 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.1e-06
                Phage_holin_5_2 15 tekvkdkyIPlilgiiGiilgvviv 39
                                   +e +k+ ++P ilgii++il+  i+
  gi|116753333|ref|YP_842451.1| 46 IEGIKKTLVPSILGIISGILCYYIL 70
                                   67799****************4333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1266  (0.0706119); expected 358.6 (0.02)
Passed bias filter:                      719  (0.0401026); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1070.73
//
Query:       gi|116753334|ref|YP_842452.1|  [L=92]
Description: MoaD family protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-14   54.0   0.0    2.2e-14   53.9   0.0    1.0  1  ThiS      ThiS family
  ------ inclusion threshold ------
      0.099   13.0   0.0       0.11   12.9   0.0    1.1  1  Urm1      Urm1 (Ubiquitin related modifier)
       0.15   12.1   0.0        3.6    7.7   0.0    2.2  2  OmdA      Bacteriocin-protection, YdeI or OmpD-Associated


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 !   53.9   0.0   3.6e-18   2.2e-14       3      77 .]       7      92 .]       5      92 .] 0.97

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 3.6e-18
                                   ETTCCHHHHT.CEEEEESSTSBHHHHHHHHHHHTCHHG.........TTTTEEEEETTEEEGC.CTTTSB--TTCEEEEEES CS
                           ThiS  3 lfaelrelag.eeelelaegstvaelleaLgerypela.........lerrvavavNgeivpr.lwldtelkdgDevailpp 73
                                    fa+ re+ g e  +e+++gs+v++l+++L e  p l          l++ +++++N + ++  + l ++l+d+Devai+pp
  gi|116753334|ref|YP_842452.1|  7 AFASFREILGkEMMVEIESGSNVSDLINHLCEIKPDLRralysdtgeLRDYFIIMLNRRRLNMpEDLGAALSDNDEVAIFPP 88
                                   69****************************999999999********99********************************* PP

                                   TTC- CS
                           ThiS 74 VaGG 77
                                   VaGG
  gi|116753334|ref|YP_842452.1| 89 VAGG 92
                                   ***9 PP

>> Urm1  Urm1 (Ubiquitin related modifier)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.8e-05      0.11      22      96 .]      19      92 .]       8      92 .] 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.8e-05
                                   EEE-SSSSS-BHHHHHHHHCCCC-SSGHHHCBSTTSB-TTEEEEETTCEHHHCTCCCSB--TTEEEEEEETTT-- CS
                           Urm1 22 veleieseevnleeliayikknlikerkevFlekdkvrPGilvLindaDwellgekdyelkdkDkivFistlhGG 96
                                   + +ei ++  n+++li+++++   + r+ ++ + +++r   ++++n    ++ +++   l d+D++     + GG
  gi|116753334|ref|YP_842452.1| 19 MMVEI-ESGSNVSDLINHLCEIKPDLRRALYSDTGELRDYFIIMLNRRRLNMPEDLGAALSDNDEVAIFPPVAGG 92
                                   45553.35679*********988777****************************************987777666 PP

>> OmdA  Bacteriocin-protection, YdeI or OmpD-Associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.027   1.6e+02       3      22 ..      38      58 ..      37      61 .. 0.81
   2 ?    7.7   0.0    0.0006       3.6       2      19 ..      67      84 ..      66      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.027
                           OmdA  3 evPedlaaaLdadp.aakaaF 22
                                   e+ +dl++aL  d  +++++F
  gi|116753334|ref|YP_842452.1| 38 EIKPDLRRALYSDTgELRDYF 58
                                   7899******87774577777 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0006
                           OmdA  2 levPedlaaaLdadpaak 19
                                   l +Pedl aaL ++ +++
  gi|116753334|ref|YP_842452.1| 67 LNMPEDLGAALSDNDEVA 84
                                   579********9998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 650.67
//
Query:       gi|116753335|ref|YP_842453.1|  [L=131]
Description: molybdopterin biosynthesis MoaE [Methanosaeta thermophila PT]
Scores for complete 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-31  107.3   0.1    5.9e-31  107.1   0.1    1.0  1  MoaE      MoaE protein
  ------ inclusion threshold ------
      0.012   16.0   0.0      0.022   15.1   0.0    1.4  1  DUF2218   Uncharacterized protein conserved in bacteria (DUF2


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 !  107.1   0.1   6.6e-35   5.9e-31       1     113 []       2     111 ..       2     111 .. 0.95

  Alignments for each domain:
  == domain 1  score: 107.1 bits;  conditional E-value: 6.6e-35
                                    EESS---HHHHHHHH--TT--EEEEEEEE------TS-EEEEEECC-HHHHHHHHHHHHHHHHCCCTTSEEEEEEE-EEE CS
                           MoaE   1 lteepldvaeiealvaspkaGAvvlFvGtvRdsfdgkkvteLeyeayepmaektleeiaeearerwelervavvHrlGel 80 
                                    ++++++d++ei     +p++GAvv F+G+vR    +  v  +e eay++ a+++l++i eea +r++l+ v vvHr G+l
  gi|116753335|ref|YP_842453.1|   2 ISDSEIDLEEILGRSINPDYGAVVAFIGVVR---ADPGVLGMEVEAYDEAALEELKRIKEEAIARFGLSFVDVVHRKGRL 78 
                                    5788999***9998889**************...3456****************************************** PP

                                    ETTSEEEEEEEEESSHHHHHHHHHHHHHHHHHH CS
                           MoaE  81 evgeasvvvavssahRkeafeaceylidelKkr 113
                                     +ge +v v+++s+hRkeaf+acey+idelK+r
  gi|116753335|ref|YP_842453.1|  79 LLGEVIVAVVCASSHRKEAFQACEYVIDELKRR 111
                                    *******************************86 PP

>> DUF2218  Uncharacterized protein conserved in bacteria (DUF2218)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   2.5e-06     0.022      43      78 ..      30      65 ..      16      72 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.5e-06
                                   EEEEETTEEEEEEEESSHHHHHHHHHHHHHHHHHTS CS
                        DUF2218 43 rleaeddaLtlrveaedaeslarlkavvarhLerfa 78
                                    ++a+++ L ++vea d+++l++lk++ ++ ++rf+
  gi|116753335|ref|YP_842453.1| 30 VVRADPGVLGMEVEAYDEAALEELKRIKEEAIARFG 65
                                   679*******************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       721  (0.0402142); expected 358.6 (0.02)
Passed bias filter:                      652  (0.0363657); 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: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 954.40
//
Query:       gi|116753336|ref|YP_842454.1|  [L=105]
Description: CutA1 divalent ion tolerance protein [Methanosaeta thermophila PT]
Scores for complete 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-32  109.9   0.0    4.8e-32  109.8   0.0    1.0  1  CutA1            CutA1 divalent ion tolerance protein
  ------ inclusion threshold ------
       0.12   12.3   0.0        3.9    7.4   0.0    2.1  2  Arg_repressor_C  Arginine repressor, C-terminal domain


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 !  109.8   0.0   5.3e-36   4.8e-32       2      98 ..       7     102 ..       6     103 .. 0.95

  Alignments for each domain:
  == domain 1  score: 109.8 bits;  conditional E-value: 5.3e-36
                                    EEEEEESSHHHHHHHHHHHHHTTS-SEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEGGGHHHHHHHHHHHSSSSS-EEE CS
                          CutA1   2 lvlvtapseeeakklaralveeklaACvnilpkieSvYrWkgkieedkEvllliktreekveelekrvkelhpyevpeii 81 
                                    ++++t++   +a+++a +lvee+laACvn++p ++S++ W+gki ++kE +l++kt+ + +e++ +r+ elh+y++peii
  gi|116753336|ref|YP_842454.1|   7 MMVITTAPPGDADRIAYTLVEERLAACVNVIP-VRSHFIWEGKISREKEEMLFVKTTPDAAERVRRRILELHSYQLPEII 85 
                                    56666666999*********************.*********************************************** PP

                                    EEEESEEEHHHHHHHHH CS
                          CutA1  82 alpieagseaYlkWiee 98 
                                    al+i +g+e+Y++Wi+e
  gi|116753336|ref|YP_842454.1|  86 ALEIADGHEPYMRWIHE 102
                                    ***************98 PP

>> Arg_repressor_C  Arginine repressor, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.011        97      14      31 ..       7      25 ..       3      35 .. 0.74
   2 ?    7.4   0.0   0.00044       3.9      11      35 ..      53      77 ..      50      87 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.011
                                   EEEEE-.STTHHHHHHHHH CS
                Arg_repressor_C 14 lvvikT.lpGaAqavAaai 31
                                   ++vi T +pG A+ +A+ +
  gi|116753336|ref|YP_842454.1|  7 MMVITTaPPGDADRIAYTL 25
                                   45555527899**999987 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00044
                                   ETTEEEEE-STTHHHHHHHHHHH-. CS
                Arg_repressor_C 11 aenlvvikTlpGaAqavAaaiDsle 35
                                    e ++ +kT p aA  v + i +l+
  gi|116753336|ref|YP_842454.1| 53 KEEMLFVKTTPDAAERVRRRILELH 77
                                   589************9998888753 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.32u 0.25s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 840.39
//
Query:       gi|116753337|ref|YP_842455.1|  [L=155]
Description: hypothetical protein Mthe_0012 [Methanosaeta thermophila PT]
Scores for complete 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   43.6   2.9      5e-11   43.1   2.9    1.2  1  CxxCxxCC  Putative zinc- or iron-chelating domain


Domain annotation for each model (and alignments):
>> CxxCxxCC  Putative zinc- or iron-chelating domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   2.9   2.8e-15     5e-11       1      84 [.      37     135 ..      37     136 .. 0.87

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 2.8e-15
                       CxxCxxCC   1 eCkeCgaCCkelkvk.lteedlerlkaaevaeeeeeskkiak...........adgrCvfldeetklCkiYeeRpkicrl 68 
                                    eC +Cg CC+++++  + +e+ + ++++  + ++   +++              d+ Cv+l+++  +C iY  Rp  cr 
  gi|116753337|ref|YP_842455.1|  37 ECIRCGRCCRSQGIVwVSPEECSAIADFLGVSQDVLIRDYLLecehgfvlrdhLDMSCVMLQGD--RCIIYPARPHQCRS 114
                                    6*********8776527899**********99999999998799********************..9************* PP

                       CxxCxxCC  69 fpas.....ekeellaraetC 84 
                                    +p++     + +++l  a+ C
  gi|116753337|ref|YP_842455.1| 115 YPFWaeileSRDAWLSEASRC 135
                                    ***977766555566555556 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1137.82
//
Query:       gi|116753338|ref|YP_842456.1|  [L=427]
Description: phenylacetate--CoA ligase [Methanosaeta thermophila PT]
Scores for complete 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   69.6   0.0    6.4e-19   68.1   0.0    1.9  2  AMP-binding_C_2  AMP-binding enzyme C-terminal domain
    4.1e-18   65.2   0.6    5.4e-18   64.8   0.1    1.4  2  AMP-binding      AMP-binding enzyme
    5.6e-07   28.9   0.0    0.00011   21.4   0.0    2.1  2  LuxE             Acyl-protein synthetase, LuxE


Domain annotation for each model (and alignments):
>> AMP-binding_C_2  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0         2   1.2e+04      53      71 ..     212     230 ..     192     232 .. 0.59
   2 !   68.1   0.0   1.1e-22   6.4e-19       1      95 [.     337     422 ..     337     423 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2
                                    HHHHHHHHHHHHHHHHSS- CS
                AMP-binding_C_2  53 lealekkiakklksklgvs 71 
                                     e++++++++++ + lgv+
  gi|116753338|ref|YP_842456.1| 212 AETFSDAMKRRISTGLGVE 230
                                    3455566666666666665 PP

  == domain 2  score: 68.1 bits;  conditional E-value: 1.1e-22
                                    TEEE-HHHHHHHHHT-TTEEEEEEEEEEEETTEEEEEEEEEE-TT----HHHHHHHHHHHHHHHHHHHSS--EEEEE-TT CS
                AMP-binding_C_2   1 GvnvfPsqieevlkeieevepeYqivvtregelDelevkvEvkegfsdelkelealekkiakklksklgvsvkvelvepg 80 
                                    Gvn+fP+q+e++l++i++++++Yqi+v++ ++  e++++vE+++g++            ++k+lk++lg+s+k ++++ g
  gi|116753338|ref|YP_842456.1| 337 GVNFFPKQVEQALMQIPGIGANYQIIVEDIDGVKEIRINVEAEPGVTG---------YIVEKALKEALGFSPKGDVFPIG 407
                                    9********************************************965.........4799******************* PP

                                    -S---------EEE- CS
                AMP-binding_C_2  81 tlprsegKakrviDk 95 
                                    +lpr+egKa+rvi +
  gi|116753338|ref|YP_842456.1| 408 SLPRTEGKAQRVIHR 422
                                    ************986 PP

>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.8   0.1     9e-22   5.4e-18     153     370 ..      79     287 ..      10     290 .. 0.76
   2 ?   -3.2   0.1      0.38   2.3e+03     412     422 ..     325     335 ..     324     336 .. 0.89

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 9e-22
                                    CCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHH.HHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EE CS
                    AMP-binding 153 eeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslk.letrfklkeddvvlsilplahifglilelllallsGatv 231
                                     + +  d+++ +  +SG+TG+P    ++ + l++ +  ++ ++   ++ ++   ++i pl+  f   ++++    + +  
  gi|116753338|ref|YP_842456.1|  79 LSCVPRDSIVEMHMSSGSTGTPVIMPYTEGDLAQWAECMArCYMMSGA-RRGDAVQITPLFGLFNGGFGMYHGARAAGLF 157
                                    44567788999999********99999999997765554443322333.3445689999999999889999999988888 PP

                                    EE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTCE CS
                    AMP-binding 232 vllpkdaaldpklllelieklkvtviagvPrvlealle.sgalkaakkakdlsslrlvllggeplspellrffralfgee 310
                                    v++ +   +   + ++l ++lk ++i+gv +   +l+e  ++l+     ++l+ l++ ++g+e  s ++ r+++  +g e
  gi|116753338|ref|YP_842456.1| 158 VIPAGPGNTV--RQIKLAKDLKTRIITGVVSYGVRLIEvMNELN-----EELPDLEIGIFGAETFSDAMKRRISTGLGVE 230
                                    8888776633..3479********************99776666.....499**************************** PP

                                    EEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEE CS
                    AMP-binding 311 vlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvr 370
                                    v+++YG+TEt+gv t l  +++ +  g +     +  v+ivD++tgepv+dge+Gel+v 
  gi|116753338|ref|YP_842456.1| 231 VFDIYGMTETGGVGT-LG-MDCAAHDG-IHVWEDHYIVEIVDPKTGEPVEDGETGELVVT 287
                                    **************9.44.55533343.55555699**********************97 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.38
                                    EEEECCCEEEE CS
                    AMP-binding 412 ivgRkkdlikl 422
                                    i+gR++d++++
  gi|116753338|ref|YP_842456.1| 325 ITGRIDDMLIV 335
                                    89******997 PP

>> LuxE  Acyl-protein synthetase, LuxE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.4   0.0    0.0013       7.6      20     103 ..      14     100 ..       6     127 .. 0.79
   2 !   21.4   0.0   1.9e-08   0.00011     265     358 ..     230     329 ..     213     340 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0013
                           LuxE  20 seeekeklrkkflldelvnhykhneeyrkycqknkvddlvtegevddiPviPvsvfkaigtk....llsvsedeikaklq 95 
                                    s e+   +  k l   +++ y+ n  yr+    + v +  ++  +dd+  +P+     + +     l+ v  d i     
  gi|116753338|ref|YP_842456.1|  14 SREKLRDIQTKGLRRTVRHVYESNPVYRRLFDAHGVSPEEIK-TLDDLQRLPMTNKELLRENyplgLSCVPRDSIVEMHM 92 
                                    5666778889999999*********************98877.7999998887654444332222278888888888888 PP

                           LuxE  96 ssatsGlk 103
                                    ss+++G +
  gi|116753338|ref|YP_842456.1|  93 SSGSTGTP 100
                                    88888766 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 1.9e-08
                           LuxE 265 dvvdiygfteqvelntpdfk.delkrkrvysdviir...deetlkvvgdGkvGlleyvdalstsyPafvvltddlG.vie 339
                                    +v diyg+te  ++ t  ++ +    ++v  d +i    d++t ++v dG +G l   + + ++ P     t dl  +i+
  gi|116753338|ref|YP_842456.1| 230 EVFDIYGMTETGGVGTLGMDcAAHDGIHVWEDHYIVeivDPKTGEPVEDGETGELVVTSITREALPVIRFRTADLTrIIS 309
                                    699*******99988865542445678999988876677****************************99999998659** PP

                           LuxE 340 eslcegqkaGklvk.vlrrv 358
                                    +  c+++++  ++  + +r+
  gi|116753338|ref|YP_842456.1| 310 RERCDCGRTHIRIApITGRI 329
                                    ********999875355666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 3200.39
//
Query:       gi|116753339|ref|YP_842457.1|  [L=127]
Description: phosphoribosylaminoimidazole carboxylase [Methanosaeta thermophila PT]
Scores for complete 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-46  155.5   0.7    7.5e-46  155.4   0.7    1.0  1  AIRC      AIR carboxylase


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 !  155.4   0.7   4.2e-50   7.5e-46       1     127 [.       3     125 ..       3     127 .] 0.97

  Alignments for each domain:
  == domain 1  score: 155.4 bits;  conditional E-value: 4.2e-50
                                    EEEEEESSGGGHHHHHHHHHHHHHTT-EEEEEE--TTTSHHHHHHHHHHCHTTTEEEEEEEEESS--HHHHHHHHSSS-E CS
                           AIRC   1 kVgiimGSdsDlevmkkaaeilkelgveyevrvvSahrtpeelleyaeeaeerglkviIagAGgaahLpgvvaslttlPV 80 
                                    +V ii GS+sD +++ ++ ++l+e g +ye rv+Sahr+p+el +y+e+ ++   +v+Ia+AG++a+Lpg+va+ t+ PV
  gi|116753339|ref|YP_842457.1|   3 DVSIISGSRSDQHIVDRILRVLDEHGASYEHRVISAHRNPKELDQYIESSNA---RVFIAVAGMSAALPGAVAARTERPV 79 
                                    599********************************************98876...6************************ PP

                                    EEEEE--STTCCHHHHHHHHT--TTS--EE-SSTHHHHHHHHHHHHH CS
                           AIRC  81 igvPvkskalkgldsllSivqmPsgvpvatvaigkaknAallAaqil 127
                                    igvPv+  +l g+d+llSivqmP+gvpva+v+i+ ++nAallA+++l
  gi|116753339|ref|YP_842457.1|  80 IGVPVSG-KLLGIDALLSIVQMPPGVPVACVGIDAGENAALLALRML 125
                                    ******9.99***********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1003.84
//
Query:       gi|116753340|ref|YP_842458.1|  [L=143]
Description: UspA domain-containing protein [Methanosaeta thermophila PT]
Scores for 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-34  117.6   3.4    6.9e-34  117.4   3.4    1.0  1  Usp              Universal stress protein family
  ------ inclusion threshold ------
      0.037   14.0   0.0      0.051   13.6   0.0    1.2  1  DNA_photolyase   DNA photolyase
      0.084   12.3   0.2       0.13   11.7   0.2    1.3  1  AP_endonuc_2     Xylose isomerase-like TIM barrel
        0.1   12.7   0.4       0.13   12.4   0.4    1.2  1  Cytidylate_kin2  Cytidylate kinase-like family


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.4   3.4   1.5e-37   6.9e-34       1     141 []       1     143 []       1     143 [] 0.90

  Alignments for each domain:
  == domain 1  score: 117.4 bits;  conditional E-value: 1.5e-37
                                    S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH..HHHHHHCT CS
                            Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada..akaaaeag 78 
                                    mykrIl+a+Dgs+ s+ A+e +lelaka gae+ +l+v+ +   +++     + ++e +++ +++ e++    k++ e+ 
  gi|116753340|ref|YP_842458.1|   1 MYKRILIATDGSDKSRLAAEEGLELAKALGAEVLALYVVNEVVIASAVRQLGADKKEVEAKLQRQGEKALddIKEMGEKL 80 
                                    9**************************************99998887766666555555555555554445799****** PP

                                    TCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                            Usp  79 gvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                    gvkve+v++ g pa +i++va+ e++d iV+Gs+g+sg+s+ll+GSv ++vl  a+ pVlvVr
  gi|116753340|ref|YP_842458.1|  81 GVKVETVIRIGAPANVIIDVARTENIDCIVMGSHGESGVSKLLIGSVVQKVLYWATTPVLVVR 143
                                    **************************************************************8 PP

>> DNA_photolyase  DNA photolyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.1e-05     0.051      10      94 ..      16     111 ..      12     118 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.1e-05
                                    -STT-HHHHHHHCTTSEEEEEEEE-HH....HHTCG.....S-CHHHHHHHHHHHHHHHHHHHHTT..--EEEEESSHHH CS
                 DNA_photolyase  10 RlhDNpALaaAaasgepvipvfvldpe....kahkl.....rvgaarvdfllesLadLdeeLrelg..irLvvrrgdpad 78 
                                    Rl+  + L+ A a g++v++++v+++     + ++l     +v+a+ ++   + L d++e  ++lg  ++ v+r g pa+
  gi|116753340|ref|YP_842458.1|  16 RLAAEEGLELAKALGAEVLALYVVNEVviasAVRQLgadkkEVEAKLQRQGEKALDDIKEMGEKLGvkVETVIRIGAPAN 95 
                                    8888999*******************988764444477676566666666666677777777777755788999999*** PP

                                    HHHHHHHHCTECEEEE CS
                 DNA_photolyase  79 vlpelakelgasavva 94 
                                    v+ ++a++ +++ +v+
  gi|116753340|ref|YP_842458.1|  96 VIIDVARTENIDCIVM 111
                                    ********99999987 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 ?   11.7   0.2   2.8e-05      0.13      65     127 ..      12      84 ..       4      95 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.8e-05
                                    HHHHHHHHHHHHHHHHHHTBSEEEEEBCC..........GBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEE CS
                   AP_endonuc_2  65 reesvdalkraielaaaLGapllvlhpGt..........agagpkgseeeawerlaeslneladyaekegvkl 127
                                    +++s+ a+++ +ela+aLGa++l l + +           ga  k+ e+   ++  ++l+++ +++ek gvk+
  gi|116753340|ref|YP_842458.1|  12 SDKSRLAAEEGLELAKALGAEVLALYVVNevviasavrqLGADKKEVEAKLQRQGEKALDDIKEMGEKLGVKV 84 
                                    567799999*************999988889999988765555666666666666779999999999999985 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.4   2.9e-05      0.13      10     105 ..      20     115 ..      15     121 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.9e-05
                Cytidylate_kin2  10 sgGetigeaL.AekLglpfydreiieevakelglseeeveevdersrlssflskllaarvagdtldeklddelf.eaqer 87 
                                      G ++++aL Ae L l ++++ +i+ ++++lg +++eve+  +r+  +++l+ +     +g++l+ k ++ ++  a ++
  gi|116753340|ref|YP_842458.1|  20 EEGLELAKALgAEVLALYVVNEVVIASAVRQLGADKKEVEAKLQRQG-EKALDDIK---EMGEKLGVKVETVIRiGAPAN 95 
                                    5789999*998999*************************77777566.66676653...335555556555554145588 PP

                Cytidylate_kin2  88 virela..aeesvVivGRga 105
                                    vi ++a  ++ +++++G  +
  gi|116753340|ref|YP_842458.1|  96 VIIDVArtENIDCIVMGSHG 115
                                    99999865555788888655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       749  (0.0417759); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); 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: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1059.83
//
Query:       gi|116753341|ref|YP_842459.1|  [L=344]
Description: radical SAM domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.2e-07   31.4   0.1    7.1e-07   29.8   0.1    2.2  1  Radical_SAM  Radical SAM superfamily
    2.8e-05   24.2   0.0      5e-05   23.4   0.0    1.4  1  Fer4_14      4Fe-4S single cluster domain
     0.0014   18.9   0.0     0.0025   18.1   0.0    1.4  1  Fer4_12      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.1   1.2e-10   7.1e-07       3     109 ..      34     141 ..      32     299 .. 0.93

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 1.2e-10
                                    EESEESS--TTTSCCTT.....HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC.CC CS
                                    xxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                    Radical_SAM   3 vtrgCnlrCsfCarpet.....vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla.vp 76 
                                    vt  C+++C +C+ +               + s+ +ilee++++     + +  ++ggepl+  d+v ++ r+ k+   +
  gi|116753341|ref|YP_842459.1|  34 VTGVCTRGCFYCPLSVErrgreIIFANERIVSSPKDILEEARAID----ALGTGITGGEPLFKLDLVLDTIRMLKRNlGS 109
                                    6788***********999988777777777888888888888887....9999**********************99888 PP

                                    TEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  77 giritvetngtlpdeeklerllelgvdrvslgl 109
                                    + +i++ t  +   e +l +l+++g+d + ++ 
  gi|116753341|ref|YP_842459.1| 110 EHHIHLYTGIVP-GESVLSKLRKAGLDELRIHP 141
                                    888888885555.5***********99998865 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   8.4e-09     5e-05       1      90 [.      32     120 ..      32     135 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 8.4e-09
                        Fer4_14   1 lfvrlsgCnlsCkgCdnketwkselgkpqteelleqilk..dlkkseikiqglvltGGePLhyenkkellklvkrlkeey 78 
                                    lfv ++ C+  C  C  + + +   + ++++e +++  k    +++ i++ g  +tGGePL   + + +l+ +++lk++ 
  gi|116753341|ref|YP_842459.1|  32 LFV-TGVCTRGCFYCPLSVERR-GREIIFANERIVSSPKdiLEEARAIDALGTGITGGEPL--FKLDLVLDTIRMLKRNL 107
                                    578.999999999999766333.3344455555544444233666777888999*******..6899************9 PP

                        Fer4_14  79 .pekkiwletngt 90 
                                      e++i+l+t+ +
  gi|116753341|ref|YP_842459.1| 108 gSEHHIHLYTGIV 120
                                    999*******975 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   4.3e-07    0.0025       4      95 ..      26     120 ..      23     136 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 4.3e-07
                        Fer4_12   4 eGvrlslfvsg.CnlsCkgCfnketwsfksgkeft....kelleeiiedlkkesiegltllGGEPllpenaeallelvke 78 
                                    +G  l+lfv+g C++ C +C   ++ +  ++  f         + i+e++      g  ++GGEPl   + + +l+ ++ 
  gi|116753341|ref|YP_842459.1|  26 QGASLVLFVTGvCTRGCFYCP-LSVERRGREIIFAneriVSSPKDILEEARAIDALGTGITGGEPLF--KLDLVLDTIRM 102
                                    6788999*8777**9999987.6666666666665212223335566666555568889********..*********** PP

                        Fer4_12  79 vkeekp.ekdiwlytgyt 95 
                                    +k++   e  i lytg  
  gi|116753341|ref|YP_842459.1| 103 LKRNLGsEHHIHLYTGIV 120
                                    ***999899999***975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2604.15
//
Query:       gi|116753342|ref|YP_842460.1|  [L=100]
Description: hypothetical protein Mthe_0017 [Methanosaeta thermophila PT]
Scores for complete 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  105.3   0.2    1.6e-30  105.1   0.2    1.1  1  DUF2551        Protein of unknown function (DUF2551)
     0.0016   18.6   0.0     0.0021   18.2   0.0    1.1  1  FUR            Ferric uptake regulator family
  ------ inclusion threshold ------
      0.012   15.3   0.0      0.094   12.5   0.0    2.0  2  Arg_repressor  Arginine repressor, DNA binding domain


Domain annotation for each model (and alignments):
>> DUF2551  Protein of unknown function (DUF2551)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.1   0.2   2.8e-34   1.6e-30       1      83 []      12      93 ..      12      93 .. 0.98

  Alignments for each domain:
  == domain 1  score: 105.1 bits;  conditional E-value: 2.8e-34
                        DUF2551  1 LkkylerDksGiRrevLklfleakkltveeiyeklkek.fdvsykgvasmvGliasrlGIlkvkkeskgeknvYsLkeeyad 81
                                   L++yl+rD  GiR++vLklfl+ +++t+e+i+++l+++ f+vsy+gv++mvGl+++rlGIl++  +++g++nvYsLk++++ 
  gi|116753342|ref|YP_842460.1| 12 LRNYLKRDGIGIRKAVLKLFLSDSSFTTEDIFTHLEKEgFNVSYRGVSAMVGLMNTRLGILSI--DVSGDHNVYSLKNDHKM 91
                                   89*************************************************************..***************99 PP

                        DUF2551 82 lv 83
                                   +v
  gi|116753342|ref|YP_842460.1| 92 IV 93
                                   87 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   3.6e-07    0.0021      10      79 ..      24      90 ..      22      96 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.6e-07
                                   HHHHHHHHHHHSSSBEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEETTSEEEEEESSSSSEE CS
                            FUR 10 RekilevlekseehlsaeevykelkeedpeislaTVYrtLklleeaglvkelefedgesryelakkehhd 79
                                   R+++l+++ +    ++ e+++ +l++e+ ++s   V  ++ l++ +  + ++++++++++y l+++  h+
  gi|116753342|ref|YP_842460.1| 24 RKAVLKLFLSDSS-FTTEDIFTHLEKEGFNVSYRGVSAMVGLMNTRLGILSIDVSGDHNVYSLKND--HK 90
                                   8899999987655.688*****************************999**************964..33 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 ?    1.9   0.0     0.031   1.9e+02      20      39 ..       7      26 ..       1      29 [. 0.80
   2 ?   12.5   0.0   1.6e-05     0.094       8      69 ..      26      90 ..      22      91 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.031
                                   -SHHHHHHHHHTTT----HH CS
                  Arg_repressor 20 ssQkelvelLkeeGidvtQa 39
                                   + Q+ l + Lk +Gi +  a
  gi|116753342|ref|YP_842460.1|  7 RIQERLRNYLKRDGIGIRKA 26
                                   56999999******998766 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 1.6e-05
                                   HHHHHHHHHS---SHHHHHHHHHTTT----HHHHHHHH....HHHT-EEEETTSTSEEEE-B-SS- CS
                  Arg_repressor  8 klikkiikeekissQkelvelLkeeGidvtQatvSRdL....kelglvkvraengeyvYvlpaets 69
                                   +++k  ++  ++ + +++   L++eG++v    vS ++    + lg+  +   +++ vY+l ++ +
  gi|116753342|ref|YP_842460.1| 26 AVLKLFLSDSSF-TTEDIFTHLEKEGFNVSYRGVSAMVglmnTRLGILSIDVSGDHNVYSLKNDHK 90
                                   444444555555.4589************9999998875555789999999999999**9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); 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: 0.30u 0.29s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 793.34
//
Query:       gi|116753343|ref|YP_842461.1|  [L=497]
Description: radical SAM domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.5e-11   43.1   0.0    1.6e-10   41.6   0.0    1.8  1  Radical_SAM  Radical SAM superfamily
    0.00016   21.7   0.1     0.0038   17.2   0.0    2.8  3  B12-binding  B12 binding domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   0.0   1.8e-14   1.6e-10       1     166 [.     214     397 ..     214     398 .. 0.82

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 1.8e-14
                                    EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS........TTHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxx RF
                    Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly........pdfvellerlak 72 
                                    v+++rgC ++C fC+ +      +  r+++v +ile v+ +  + g + v+l++ +++ y        pd+v +l+r +k
  gi|116753343|ref|YP_842461.1| 214 VEIGRGCWRGCAFCSPT-----MRSLRHRPVSSILEDVRVN-MREGMRDVLLHSEDVFTYgsrgmrpePDKVLELFRSVK 287
                                    5799*************.....7******************.8************************************* PP

                                    TC....CCTEEEEEEECSSCHG.HHHHHHHHHTT....-SEEEEEEBSSSHHHHHHHHT.CTSHH.......HHHHHHHH CS
                                    xx....xxxxxxxxxxxxxxxx.xxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxx.xxxxx.......xxxxxxxx RF
                    Radical_SAM  73 la....vpgiritvetngtlpd.eeklerllelg....vdrvslgleaaddekvlklmn.rghtf.......eevleale 135
                                    +      +  ++++ t +   d  + + +++  g         +g+e+++ +  l++++ r+  +       + v e+  
  gi|116753343|ref|YP_842461.1| 288 ELsphtIDVSHLSLATVHQSMDlLREISEIVGVGtdqrYMSAWIGIETGSCR-MLEMHMpRKALPesperwpDIVRECYA 366
                                    9899998888888888888888999999999999544444455778888888.666666444444666444455555555 PP

                                    HHHHTTSETEEEEEEEBTTTSHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM 136 klreagikrvvdrivglpGendeeleellel 166
                                    +++e  + +v + ++glpGe+ ++++ + el
  gi|116753343|ref|YP_842461.1| 367 LFHEEHWVPVASLVLGLPGETADDVVRTTEL 397
                                    555555555****************999877 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   4.3e-07    0.0038      14     120 ..      60     178 ..      55     179 .. 0.70
   2 ?   -2.2   0.0      0.44     4e+03      42      76 ..     281     315 ..     270     320 .. 0.73
   3 ?    0.6   0.0     0.061   5.5e+02      58      87 ..     442     471 ..     435     488 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.3e-07
                    B12-binding  14 plGlavlaaalrdagfeVqllganvenedivaairaekpdvvglSal..................ltsqleavkelvel. 74 
                                    p G++ + aal +agf+ +  ++ v ++d +++++  + ++vg++                    + ++   + +l++  
  gi|116753343|ref|YP_842461.1|  60 PCGMRKVEAALLEAGFSRD--EVMVAHPDHLDKAIGSDTEIVGITHDdpmgkiavreiediinkgPPHNRHSFLRLINHp 137
                                    6677777777777777553..33566677777777777777777433555666666666666777889999999999999 PP

                    B12-binding  75 .lkrirprvkvvvGGahpsldpeetleaklgiddvvvgegedaleal 120
                                     +k+ +p   +vvGG ++  +++e      g+d++ +gege+ ++++
  gi|116753343|ref|YP_842461.1| 138 lIKKHDP--VIVVGGNGAWELADE---D-VGVDHIYLGEGESKFPEV 178
                                    8888866..788888763333333...3.*************99986 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.44
                    B12-binding  42 divaairaekpdvvglSalltsqleavkelvellk 76 
                                    ++ ++++++ p+ + +S l+ +++ +  +l++++ 
  gi|116753343|ref|YP_842461.1| 281 ELFRSVKELSPHTIDVSHLSLATVHQSMDLLREIS 315
                                    56678888899999998887777777777777654 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.061
                    B12-binding  58 Salltsqleavkelvel.lkrirprvkvvvG 87 
                                    ++ +  +l++ k+l +l ++r++p+  v vG
  gi|116753343|ref|YP_842461.1| 442 TC-MEYNLRHLKKLHNLyKERMTPNPMVHVG 471
                                    47.9999**********99999999999888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (497 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 3625.32
//
Query:       gi|116753344|ref|YP_842462.1|  [L=503]
Description: hypothetical protein Mthe_0019 [Methanosaeta thermophila PT]
Scores for complete 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-140  468.0   0.0   1.8e-140  467.7   0.0    1.1  1  HcyBio    Homocysteine biosynthesis enzyme, sulfur-incorporat
    8.7e-26   90.1  10.8      5e-13   49.3   0.4    3.3  4  CBS       CBS domain
  ------ inclusion threshold ------
      0.079   13.2   0.7         19    5.6   0.0    2.9  3  IF3_N     Translation initiation factor IF-3, N-terminal doma
       0.18   12.0   0.0       0.33   11.1   0.0    1.5  1  DUF2379   Protein of unknown function (DUF2379)


Domain annotation for each model (and alignments):
>> HcyBio  Homocysteine biosynthesis enzyme, sulfur-incorporation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  467.7   0.0    4e-144  1.8e-140       2     347 .]      20     356 ..      19     356 .. 0.98

  Alignments for each domain:
  == domain 1  score: 467.7 bits;  conditional E-value: 4e-144
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         HcyBio   2 vVltaeelkklvrekgekkaaeevDVVttgTfgvmsssgallnlgvaepkikiekvwLngvpayaglaavdlylgataes 81 
                                     V+taee+ ++v+e g + a++evDVVttgTfg+m+ssg++lnlg+++p+iki+++wLn+v+ay g+aavdl+lgat++s
  gi|116753344|ref|YP_842462.1|  20 RVVTAEEMPSIVEELGPDGAVREVDVVTTGTFGAMCSSGVFLNLGHSDPPIKISRAWLNQVEAYGGVAAVDLFLGATQPS 99 
                                    69****************************************************************************** PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         HcyBio  82 eddkeeeeyGGghviedLvagkeveleaeaketdcyprkeieteitlddlneailvnpRnayqnYnaavNsseetiytym 161
                                    ed  ++ eyGG+hviedLv+g+ v++  e+ +tdcypr eiet+++l+dln+a +vnpRnayq+Ynaa+Nss++t++tym
  gi|116753344|ref|YP_842462.1| 100 ED--RGIEYGGAHVIEDLVSGRAVDVMGEGVGTDCYPRMEIETTLHLEDLNQALMVNPRNAYQRYNAATNSSDRTLHTYM 177
                                    *4..345************************************************************************* PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         HcyBio 162 gelkpnlgnatysgaGelsPllnDpelktigiGtrilLgGaeGyvigeGTqsspekkrengvplgpagtLavigdlkeMs 241
                                    g+l p++gn++ysgaG l+P+ nDp +++ig+G ri+LgGa+Gy++g GTq+sp +          ++tL+v gdlk Ms
  gi|116753344|ref|YP_842462.1| 178 GTLLPHFGNVHYSGAGVLNPISNDPGFEYIGTGVRIFLGGAQGYIVGPGTQHSPGTG---------FATLMVSGDLKRMS 248
                                    *****************************************************7655.........9************* PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxx RF
                         HcyBio 242 peylrgafltsyGpelivgvgipiPvldeevleelavkdedielpvvDvserrrerktlgevsYael..Gkieiegkevk 319
                                    +e+lr+a++t+yGp+l+vgvg+piP+l+e+++ ++av+d+di++pvvD++++rr+r++l+++sYael  G +ei+gkev+
  gi|116753344|ref|YP_842462.1| 249 SEFLRAATFTKYGPTLYVGVGVPIPILNERLALSTAVRDSDITVPVVDYGVQRRDRPVLKSTSYAELrsGFVEINGKEVP 328
                                    ******************************************************************************** PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         HcyBio 320 tarlsslkrareiaeeLkewiekgeflL 347
                                    ta+lss+ +ar +a +Lk+wie+geflL
  gi|116753344|ref|YP_842462.1| 329 TASLSSFHMARMVAGTLKKWIERGEFLL 356
                                    **************************97 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.75   3.4e+03      17      36 ..       6      23 ..       4      31 .. 0.77
   2 ?   -3.8   0.1         4   1.8e+04      32      40 ..     291     298 ..     283     299 .. 0.70
   3 !   49.3   0.4   1.1e-16     5e-13       1      56 [.     381     436 ..     381     437 .. 0.95
   4 !   47.1   0.2   5.4e-16   2.4e-12       1      54 [.     443     496 ..     443     499 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.75
                                   BHHHHHHHHHHHTSSEEEEE CS
                            CBS 17 tleealelmrekgvsrlPVV 36
                                   +l+e+ e++r+  v r+ V+
  gi|116753344|ref|YP_842462.1|  6 SLSEINERIRDGSV-RV-VT 23
                                   799******76557.77.77 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 4
                                    EEEEEETTT CS
                            CBS  32 rlPVVdedg 40 
                                     +PVVd +g
  gi|116753344|ref|YP_842462.1| 291 TVPVVD-YG 298
                                    589994.65 PP

  == domain 3  score: 49.3 bits;  conditional E-value: 1.1e-16
                                    HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                            CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                    Vgd+m+rdvvtv ++ ++ ea++ ++ +++++lPVV +dgkl Gi+t  D+ +a++
  gi|116753344|ref|YP_842462.1| 381 VGDVMNRDVVTVGENISVPEAARVIVGSRFDHLPVVSDDGKLMGIITTWDISKAVA 436
                                    89***********************9999*******99*************98875 PP

  == domain 4  score: 47.1 bits;  conditional E-value: 5.4e-16
                                    HHHHSBSSCEEEETTSBHHHHHHHHHH.HTSSEEEEEETTTBEEEEEEHHHHHHH CS
                            CBS   1 Vgdimtrdvvtvppdttleealelmre.kgvsrlPVVdedgklvGivtlrDllra 54 
                                    V++imtr+v t++pd+++e a+++m + + +s+lPVVd+d++++G++t  Dl r+
  gi|116753344|ref|YP_842462.1| 443 VSEIMTRRVYTATPDEPIELAARTM-DiHSISALPVVDKDNRVIGMITSNDLSRL 496
                                    89***********************.62559********************9776 PP

>> IF3_N  Translation initiation factor IF-3, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1    0.0061        28       1      18 [.      10      26 ..      10      50 .. 0.83
   2 ?    5.6   0.0    0.0043        19       7      31 ..     410     434 ..     392     443 .. 0.85
   3 ?   -3.9   0.0       3.9   1.7e+04      12      27 ..     477     492 ..     474     496 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0061
                                   ETTS--SSEEEEE-SSS- CS
                          IF3_N  1 iNeqIrarevrlvdedGe 18
                                   iNe+Ir   vr+v+++ e
  gi|116753344|ref|YP_842462.1| 10 INERIRDGSVRVVTAE-E 26
                                   8************987.3 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0043
                                    SSEEEEE-SSS-EEEEEEHHHHHHH CS
                          IF3_N   7 arevrlvdedGeqlGvistreAlrl 31 
                                    +++  +v++dG+ +G+i+t+++ + 
  gi|116753344|ref|YP_842462.1| 410 FDHLPVVSDDGKLMGIITTWDISKA 434
                                    667789**************98775 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 3.9
                                    EE-SSS-EEEEEEHHH CS
                          IF3_N  12 lvdedGeqlGvistre 27 
                                    +vd+d+  +G+i+ ++
  gi|116753344|ref|YP_842462.1| 477 VVDKDNRVIGMITSND 492
                                    8999998899887766 PP

>> DUF2379  Protein of unknown function (DUF2379)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   7.5e-05      0.33      55      97 ..       2      43 ..       1      48 [. 0.76

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 7.5e-05
                        DUF2379 55 sAlaLlreiarRiregskrLvdallrmlrlrdagDldgArqel 97
                                   +A++ l+ei++Rir+gs r+v+a   m    ++   dgA +e+
  gi|116753344|ref|YP_842462.1|  2 EAKKSLSEINERIRDGSVRVVTAEE-MPSIVEELGPDGAVREV 43
                                   68999****************9975.55555555567776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (503 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); 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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 3825.97
//
Query:       gi|116753345|ref|YP_842463.1|  [L=128]
Description: 4Fe-4S ferredoxin iron-sulfur binding domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.9e-15   55.4  17.0    4.9e-09   35.6   2.6    2.7  3  Fer4        4Fe-4S binding domain
    6.8e-12   45.8  26.2    2.5e-09   37.6  13.8    2.1  2  Fer4_7      4Fe-4S dicluster domain
      1e-11   44.3  18.3    6.7e-08   32.3   2.9    2.7  3  Fer4_6      4Fe-4S binding domain
    4.2e-10   39.6  11.5    4.2e-10   39.6  11.5    1.6  2  Fer4_10     4Fe-4S dicluster domain
    4.3e-10   39.1  18.4    8.1e-07   28.8   3.9    2.5  2  Fer4_2      4Fe-4S binding domain
    1.8e-08   34.4  13.9    0.00025   21.2   2.4    2.3  2  Fer4_9      4Fe-4S dicluster domain
    1.9e-08   35.1  10.7    0.00082   20.3   3.0    2.4  2  Fer4_16     4Fe-4S double cluster binding domain
    6.7e-08   32.5  18.1    0.00013   22.2   3.3    2.5  2  Fer4_4      4Fe-4S binding domain
    2.8e-07   30.6  13.6    0.00024   21.2   0.6    2.7  2  Fer4_21     4Fe-4S dicluster domain
    3.1e-06   27.7  20.1     0.0081   17.0   6.8    2.4  2  Fer4_3      4Fe-4S binding domain
    4.9e-05   23.1   0.0    6.6e-05   22.7   0.0    1.2  1  NIL         NIL domain
    0.00027   21.1  13.0     0.0034   17.5  13.1    2.2  1  Fer4_18     4Fe-4S dicluster domain
    0.00083   19.8  16.2      0.085   13.3   4.7    2.3  2  Fer4_8      4Fe-4S dicluster domain
    0.00097   19.6  14.5      0.043   14.4   3.6    2.3  3  Fer4_17     4Fe-4S dicluster domain
     0.0029   18.1  18.4      0.079   13.5   3.6    2.6  3  Fer4_13     4Fe-4S single cluster domain of Ferredoxin I
  ------ inclusion threshold ------
      0.011   16.5  11.5       0.14   12.9   1.4    2.9  3  Fer4_15     4Fe-4S single cluster domain
       0.12   13.2  15.9       0.97   10.3   3.3    2.3  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 ?   -2.1   0.1       3.7   3.9e+03       4       8 ..      47      51 ..      45      53 .. 0.72
   2 !   28.9   2.7   6.4e-10   6.7e-07       3      22 ..      74      93 ..      72      95 .. 0.90
   3 !   35.6   2.6   4.7e-12   4.9e-09       1      23 [.     101     123 ..     101     124 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.7
                                   ETTTS CS
                           Fer4  4 deekC 8 
                                     +kC
  gi|116753345|ref|YP_842463.1| 47 SDDKC 51
                                   67999 PP

  == domain 2  score: 28.9 bits;  conditional E-value: 6.4e-10
                                   EETTTSSS-THHHHHSTTTE CS
                           Fer4  3 ideekCigCGaCvevCPvgA 22
                                    +ee C++CGaC+ +CP+g 
  gi|116753345|ref|YP_842463.1| 74 RNEEECVHCGACIAICPTGT 93
                                   59****************95 PP

  == domain 3  score: 35.6 bits;  conditional E-value: 4.7e-12
                                    EEEETTTSSS-THHHHHSTTTEE CS
                           Fer4   1 vvideekCigCGaCvevCPvgAI 23 
                                    vv d+ kCi CGaCv +CP+ A+
  gi|116753345|ref|YP_842463.1| 101 VVTDPGKCIQCGACVTACPHRAL 123
                                    578******************98 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   4.4   5.9e-07   0.00062      32      51 ..      73      92 ..      34      93 .. 0.75
   2 !   37.6  13.8   2.4e-12   2.5e-09       2      52 .]      79     122 ..      78     122 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 5.9e-07
                         Fer4_7 32 eidpekClgCgaCvavCPtg 51
                                     ++e+C++CgaC+a CPtg
  gi|116753345|ref|YP_842463.1| 73 MRNEEECVHCGACIAICPTG 92
                                   336899************98 PP

  == domain 2  score: 37.6 bits;  conditional E-value: 2.4e-12
                         Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                    C++CgaC a Cp++++++d+        kv+ dp kC++CgaCv++CP+ a
  gi|116753345|ref|YP_842463.1|  79 CVHCGACIAICPTGTFRFDDW-------KVVTDPGKCIQCGACVTACPHRA 122
                                    ******************997.......6999****************875 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.2       3.7   3.9e+03       5      10 ..      47      52 ..      45      53 .. 0.73
   2 !   21.6   2.8   1.5e-07   0.00016       6      22 ..      76      92 ..      74      94 .. 0.87
   3 !   32.3   2.9   6.3e-11   6.7e-08       1      24 []     100     123 ..     100     123 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.7
                         Fer4_6  5 dpdkCi 10
                                    +dkC 
  gi|116753345|ref|YP_842463.1| 47 SDDKCK 52
                                   679996 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 1.5e-07
                         Fer4_6  6 pdkCigCgdCvrvCPeg 22
                                   ++ C++Cg+C+++CP+g
  gi|116753345|ref|YP_842463.1| 76 EEECVHCGACIAICPTG 92
                                   666************98 PP

  == domain 3  score: 32.3 bits;  conditional E-value: 6.3e-11
                         Fer4_6   1 vveidpdkCigCgdCvrvCPegai 24 
                                    +v+ dp kCi+Cg+Cv++CP+ a+
  gi|116753345|ref|YP_842463.1| 100 KVVTDPGKCIQCGACVTACPHRAL 123
                                    6889*****************986 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       7.6     8e+03       7       9 ..      49      51 ..      36      55 .. 0.63
   2 !   39.6  11.5   3.9e-13   4.2e-10       3      56 .]      73     119 ..      71     119 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 7.6
                        Fer4_10  7 dtC 9 
                                   d+C
  gi|116753345|ref|YP_842463.1| 49 DKC 51
                                   334 PP

  == domain 2  score: 39.6 bits;  conditional E-value: 3.9e-13
                        Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                     ++++ C++Cg+C + CP+         ++ ++ +v ++++kC++cgaCv aCP
  gi|116753345|ref|YP_842463.1|  73 MRNEEECVHCGACIAICPT-------GTFRFDDWKVVTDPGKCIQCGACVTACP 119
                                    57899**************.......9**************************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 !   18.3   4.0   1.7e-06    0.0017       4      22 .]      73      91 ..      71      91 .. 0.88
   2 !   28.8   3.9   7.7e-10   8.1e-07       1      22 []      99     120 ..      99     120 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.7e-06
                         Fer4_2  4 vvdtdrCigCgaCvsaCPa 22
                                     +++ C++CgaC+  CP+
  gi|116753345|ref|YP_842463.1| 73 MRNEEECVHCGACIAICPT 91
                                   568999************7 PP

  == domain 2  score: 28.8 bits;  conditional E-value: 7.7e-10
                         Fer4_2   1 apvvvdtdrCigCgaCvsaCPa 22 
                                    ++vv d+ +Ci+CgaCv+aCP+
  gi|116753345|ref|YP_842463.1|  99 WKVVTDPGKCIQCGACVTACPH 120
                                    68999****************7 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   2.4   2.3e-07   0.00025      33      49 ..      71      92 ..      34      94 .. 0.75
   2 !   19.2   3.7   9.8e-07     0.001      34      50 ..     106     122 ..      93     123 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 2.3e-07
                         Fer4_9 33 e.....eaCigCgaCveaCpkg 49
                                         e+C++CgaC+++Cp+g
  gi|116753345|ref|YP_842463.1| 71 PvmrneEECVHCGACIAICPTG 92
                                   04444478************97 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 9.8e-07
                         Fer4_9  34 eaCigCgaCveaCpkga 50 
                                     +Ci+CgaCv aCp+ a
  gi|116753345|ref|YP_842463.1| 106 GKCIQCGACVTACPHRA 122
                                    57999999999999875 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.9   1.6e-06    0.0017       2      20 ..      79      97 ..      78     105 .. 0.85
   2 !   20.3   3.0   7.8e-07   0.00082       1      18 [.     107     124 ..     107     127 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.6e-06
                        Fer4_16  2 CgtCgkCaevCPtnaikek 20
                                   C+ Cg+C+ +CPt+ ++ +
  gi|116753345|ref|YP_842463.1| 79 CVHCGACIAICPTGTFRFD 97
                                   **************99887 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 7.8e-07
                        Fer4_16   1 rCgtCgkCaevCPtnaik 18 
                                    +C++Cg+C+ +CP++a++
  gi|116753345|ref|YP_842463.1| 107 KCIQCGACVTACPHRALQ 124
                                    6***************97 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   3.3   1.2e-07   0.00013       2      17 .]      77      92 ..      76      92 .. 0.92
   2 !   19.2   3.1   1.1e-06    0.0012       3      15 ..     107     119 ..     105     124 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.2e-07
                         Fer4_4  2 erCigCgsCvaaCPqg 17
                                   e C++Cg+C+a+CP+g
  gi|116753345|ref|YP_842463.1| 77 EECVHCGACIAICPTG 92
                                   78************86 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 1.1e-06
                         Fer4_4   3 rCigCgsCvaaCP 15 
                                    +Ci+Cg+Cv aCP
  gi|116753345|ref|YP_842463.1| 107 KCIQCGACVTACP 119
                                    8***********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 !   13.2   6.4     7e-05     0.074      37      53 ..      75      91 ..      27      95 .. 0.79
   2 !   21.2   0.6   2.3e-07   0.00024       4      26 ..     104     126 ..     101     128 .] 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7e-05
                        Fer4_21 37 vedeCvGCnlCssvCPv 53
                                    e+eCv C  C+++CP+
  gi|116753345|ref|YP_842463.1| 75 NEEECVHCGACIAICPT 91
                                   37888888888888885 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 2.3e-07
                        Fer4_21   4 dedkCigCgkCliaCedtshqai 26 
                                    d+ kCi+Cg C++aC+  + q +
  gi|116753345|ref|YP_842463.1| 104 DPGKCIQCGACVTACPHRALQLV 126
                                    7889************9988865 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   5.3   1.1e-05     0.012       1      14 [.      79      92 ..      79      93 .. 0.96
   2 !   17.0   6.8   7.7e-06    0.0081       1      15 []     108     122 ..     108     122 .. 0.96

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.1e-05
                         Fer4_3  1 CtgCgaCvevCPvg 14
                                   C++CgaC   CP+g
  gi|116753345|ref|YP_842463.1| 79 CVHCGACIAICPTG 92
                                   ************98 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 7.7e-06
                         Fer4_3   1 CtgCgaCvevCPvgA 15 
                                    C++CgaCv +CP +A
  gi|116753345|ref|YP_842463.1| 108 CIQCGACVTACPHRA 122
                                    ************987 PP

>> NIL  NIL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   6.3e-08   6.6e-05       6      71 ..       6      65 ..       2      66 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 6.3e-08
                                   EEES-S-SS-HHHHHHHHHT-EEEEEEEEEEEETTEEEEEEEEEEES-HHHHHHHHHHHHHTT-EE CS
                            NIL  6 tftgksavePllshlvrqlglevnIlqGsveriqgtpfGqlvielsgsqesiaaalqylrkrnvdv 71
                                   ++    +++Pl+++++ + g  +nI  +s++     + G +v+ +s  +++ +++++ +++r+vdv
  gi|116753345|ref|YP_842463.1|  6 RVAPGIVRKPLIASVILETGALINIERASID----AVSGEIVLDVS--DDKCKQVKDAFERRGVDV 65
                                   555666899*********************8....56999*****6..899**************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 !   17.5  13.1   3.3e-06    0.0034      55      95 ..      73     118 ..      33     120 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.3e-06
                        Fer4_18  55 ekgagdcidcescvkvcPtgidirkGlql.....eciscllcidac 95 
                                     +++ +c++c++c+++cPtg    +  ++     +ci+c+ c+ ac
  gi|116753345|ref|YP_842463.1|  73 MRNEEECVHCGACIAICPTGTFRFDDWKVvtdpgKCIQCGACVTAC 118
                                    56789**************9855555554334458*********** PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   3.0   0.00015      0.16       4      17 ..      78      91 ..      75     104 .. 0.79
   2 !   13.3   4.7     8e-05     0.085       4      16 ..     107     119 ..     104     127 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00015
                         Fer4_8  4 kCieCgaCqsaCpv 17
                                   +C++CgaC + Cp+
  gi|116753345|ref|YP_842463.1| 78 ECVHCGACIAICPT 91
                                   68888888888884 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 8e-05
                         Fer4_8   4 kCieCgaCqsaCp 16 
                                    kCi+CgaC +aCp
  gi|116753345|ref|YP_842463.1| 107 KCIQCGACVTACP 119
                                    6888888888887 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   0.00035      0.36      44      58 ..      77      91 ..      52      93 .. 0.79
   2 !   11.3   2.1   0.00038       0.4       1      15 [.      78      92 ..      78     105 .. 0.77
   3 !   14.4   3.6   4.1e-05     0.043      45      58 ..     107     120 ..      95     123 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00035
                        Fer4_17 44 slCieCgeCerkCPq 58
                                   ++C++Cg C + CP 
  gi|116753345|ref|YP_842463.1| 77 EECVHCGACIAICPT 91
                                   667777777777775 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00038
                        Fer4_17  1 rCiqCgyClpeCpsy 15
                                   +C +Cg+C++ Cp++
  gi|116753345|ref|YP_842463.1| 78 ECVHCGACIAICPTG 92
                                   588888888888864 PP

  == domain 3  score: 14.4 bits;  conditional E-value: 4.1e-05
                        Fer4_17  45 lCieCgeCerkCPq 58 
                                    +Ci+Cg C+++CP+
  gi|116753345|ref|YP_842463.1| 107 KCIQCGACVTACPH 120
                                    78888888888886 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       7.5   7.9e+03      38      48 ..      48      58 ..      44      60 .. 0.56
   2 !   13.5   3.6   7.5e-05     0.079       2      23 ..      75      97 ..      72     103 .. 0.83
   3 !   12.3   4.5   0.00018      0.18       2      18 ..     104     120 ..     101     121 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 7.5
                        Fer4_13 38 eeekadaeeAa 48
                                   +++ +++++A+
  gi|116753345|ref|YP_842463.1| 48 DDKCKQVKDAF 58
                                   44455566655 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 7.5e-05
                        Fer4_13  2 DrdtCiacgaCvelaPd.vFeed 23
                                   ++++C+ cgaC +++P  +F+ d
  gi|116753345|ref|YP_842463.1| 75 NEEECVHCGACIAICPTgTFRFD 97
                                   579*************6456665 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00018
                        Fer4_13   2 DrdtCiacgaCvelaPd 18 
                                    D  +Ci cgaCv ++P+
  gi|116753345|ref|YP_842463.1| 104 DPGKCIQCGACVTACPH 120
                                    6679************5 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0       1.4   1.5e+03      43      56 ..      45      58 ..      22      68 .. 0.68
   2 ?    8.7   1.3    0.0028       2.9       5      25 ..      76      97 ..      72     100 .. 0.78
   3 ?   12.9   1.4   0.00013      0.14       1      20 [.     101     120 ..     101     124 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 1.4
                        Fer4_15 43 evpddeeeaaqeAa 56
                                   +v dd+ +++++A 
  gi|116753345|ref|YP_842463.1| 45 DVSDDKCKQVKDAF 58
                                   67777777777664 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0028
                        Fer4_15  5 rdaCigcglCvaeape.vfeld 25
                                   +++C  cg+C+a +p+  f++d
  gi|116753345|ref|YP_842463.1| 76 EEECVHCGACIAICPTgTFRFD 97
                                   789***********74266666 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 0.00013
                        Fer4_15   1 VvvDrdaCigcglCvaeape 20 
                                    Vv D  +Ci cg+Cv+++p 
  gi|116753345|ref|YP_842463.1| 101 VVTDPGKCIQCGACVTACPH 120
                                    678999************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 ?    9.9   4.4    0.0012       1.3      81      94 ..      78      91 ..      46      93 .. 0.70
   2 ?   10.3   3.3   0.00092      0.97       1      15 [.      78      92 ..      78     103 .. 0.86
   3 ?    7.2   4.5    0.0088       9.2       1      13 [.     107     119 ..     107     122 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0012
                        Fer4_22 81 gCvGCgRCieacpv 94
                                    Cv Cg Ci+ cp+
  gi|116753345|ref|YP_842463.1| 78 ECVHCGACIAICPT 91
                                   55555555555554 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00092
                        Fer4_22  1 rClsCgaCtlvCptC 15
                                   +C++CgaC ++Cpt 
  gi|116753345|ref|YP_842463.1| 78 ECVHCGACIAICPTG 92
                                   5999********995 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0088
                        Fer4_22   1 rClsCgaCtlvCp 13 
                                    +C++CgaC ++Cp
  gi|116753345|ref|YP_842463.1| 107 KCIQCGACVTACP 119
                                    6999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       777  (0.0433376); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); 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):              17  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 902.99
//
Query:       gi|116753346|ref|YP_842464.1|  [L=328]
Description: protein of unknown function Met10 [Methanosaeta thermophila PT]
Scores for 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-56  188.8   0.0    1.3e-55  188.3   0.0    1.2  1  Met_10           Met-10+ like-protein
    8.7e-13   47.9   0.0    1.9e-12   46.9   0.0    1.5  1  Trm5_N           tRNA methyltransferase 5 N-terminal domain
    2.7e-08   34.4   0.0    5.6e-08   33.4   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
    4.3e-08   32.9   0.0    1.4e-07   31.2   0.0    1.7  2  MTS              Methyltransferase small domain
    1.5e-06   28.8   0.0      3e-06   27.8   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
    3.6e-06   26.7   0.0    6.1e-06   26.0   0.0    1.4  1  Cons_hypoth95    Conserved hypothetical protein 95
    1.2e-05   25.1   0.0    2.4e-05   24.2   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
    6.1e-05   22.5   0.0    8.8e-05   22.0   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    9.3e-05   22.1   0.0    0.00015   21.4   0.0    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    0.00018   21.2   0.1    0.00061   19.5   0.2    1.8  2  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
     0.0019   17.7   0.4     0.0038   16.7   0.1    1.6  2  SAM_MT           Putative SAM-dependent methyltransferase
     0.0023   17.9   0.0       0.12   12.3   0.0    2.3  2  ADH_zinc_N       Zinc-binding dehydrogenase
     0.0054   15.9   0.0     0.0076   15.5   0.0    1.2  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
  ------ inclusion threshold ------
      0.016   14.6   0.0      0.024   14.0   0.0    1.3  1  DNA_methylase    C-5 cytosine-specific DNA methylase
      0.027   14.3   0.0       0.04   13.8   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
      0.029   13.8   0.0      0.048   13.1   0.0    1.3  1  TehB             Tellurite resistance protein TehB
      0.053   13.2   0.0      0.089   12.5   0.0    1.3  1  N6_N4_Mtase      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 !  188.3   0.0   1.2e-58   1.3e-55       2     199 .]      72     263 ..      71     263 .. 0.96

  Alignments for each domain:
  == domain 1  score: 188.3 bits;  conditional E-value: 1.2e-58
                                    EEEEETTEEEEEB-TTSSHHHHHHHHHHHHHS.S-SCEEEE-S-SBTTTTB--EEEEEES-.SEEEEEETTEEEEEETTT CS
                         Met_10   2 kfeiiGdvvilnlreelkeykkvigevildkt.kvktvlrkvsevegefRtfelevlaGsdstetihkEngcrfklDvsk 80 
                                    +fe+iGd+++++ +e  +      +e+i+ ++  ++tvl+  s vegefR ++++++aG+ +t tih+E+g+r+k+D+ +
  gi|116753346|ref|YP_842464.1|  72 SFETIGDIAVVEDEEPERS-----AEAIMAVHrGIRTVLTPISDVEGEFRLRRYRHVAGEMKTLTIHREHGIRYKVDLER 146
                                    69*********98877666.....889999999*********************************************** PP

                                    S---GGGHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-G CS
                         Met_10  81 vyfsskleaErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDg 160
                                     yfs++l++Er r+a++v++g++Vvd+fAG+Gpf++ +ak  ++ rv+aid+nP + k+lken ++N+++  +   ++D+
  gi|116753346|ref|YP_842464.1| 147 AYFSPRLSTERLRVAEQVRPGDLVVDMFAGVGPFSLLMAK--RGARVIAIDKNPCAAKLLKENARMNRLDVEI--REGDA 222
                                    ****************************************..99*************************9888..68999 PP

                                    GG---..TT-EEEEEE--TTTGGGGHHHHHHHEEEEEEEEE CS
                         Met_10 161 revir..eqladrvvmnlpksaieFldkvlaalkdggvihy 199
                                      +++   ++ad+vvmnlp+sa  Fl ++++++k+ggv+hy
  gi|116753346|ref|YP_842464.1| 223 SSLTEdlADKADHVVMNLPHSASLFLTEAIRTAKNGGVVHY 263
                                    9999888999******************************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 !   46.9   0.0   1.8e-15   1.9e-12       8      44 ..       1      37 [.       1      40 [. 0.95

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 1.8e-15
                                   GHHHHHHHHHHTT-B-TTS--EEETTEEEEEB-S--H CS
                         Trm5_N  8 egEkvRkkLlekglLdrnyKIksdddylyIPvkeepe 44
                                   +gE++R++L+e+g+Ld++ +I+sdd ++yIPv ++++
  gi|116753346|ref|YP_842464.1|  1 MGERIRRALIEMGALDKGKRIRSDDSHVYIPVLDSIS 37
                                   69*******************************9987 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.0   5.3e-11   5.6e-08       1      97 []     170     259 ..     170     259 .. 0.90

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 5.3e-11
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSS.STTTEEEEEEESTGGGSSH CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpf.edgsfDlvvssgalhhlsd 79 
                                    v+d+ +G G ++l +akr+  a+v+++D ++ + +  +e+a+ ++l+ve+++gda++l +  +++ D vv++  l h   
  gi|116753346|ref|YP_842464.1| 170 VVDMFAGVGPFSLLMAKRG--ARVIAIDKNPCAAKLLKENARMNRLDVEIREGDASSLTEdLADKADHVVMN--LPH--- 242
                                    899***************5..************************************9852677*******5..556... PP

                                    HHHHHHHHHHHHHEEEEE CS
                Methyltransf_25  80 edlekalkeiarvLkpgG 97 
                                      +  +l e+ r  k+gG
  gi|116753346|ref|YP_842464.1| 243 -SASLFLTEAIRTAKNGG 259
                                    .34689999999999998 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   1.4e-10   1.4e-07      32     109 ..     167     244 ..     151     257 .. 0.85
   2 ?   -1.5   0.0       1.5   1.6e+03      66     102 ..     274     310 ..     268     311 .. 0.84

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 1.4e-10
                                    CSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTST..TS-EEEEEE---STT CS
                            MTS  32 sgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeve..ekkfdlivsNPPfha 109
                                     + v+D+ +G+G+ ++ +ak+  +  v ++d++  A ++ ken++ n+l+ve+++ d+ + +e   +k d++v+N P  a
  gi|116753346|ref|YP_842464.1| 167 GDLVVDMFAGVGPFSLLMAKRGAR--VIAIDKNPCAAKLLKENARMNRLDVEIREGDASSLTEdlADKADHVVMNLPHSA 244
                                    4569****************9888..99**************************9998776663349********99665 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.5
                                    HHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEE CS
                            MTS  66 rAlesakenleanklevevvasdvleeveekkfdliv 102
                                    r +++ +e +++ ++++ v+ ++v+   +++k+++++
  gi|116753346|ref|YP_842464.1| 274 RDVRIIEEKARELGCKAAVTYRSVVRSYAPRKYNVVI 310
                                    5677888889999999999999999999999999998 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   2.8e-09     3e-06       5      94 ..     175     261 ..     171     263 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 2.8e-09
                                    -TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCT..SS-TT-EEEEEEES-CCC-CCHHHHHH CS
                Methyltransf_11   5 cGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaekl..pfednsfDlvvssevlhhvedpekalk 82 
                                    +G G ++  +akrgarv+++D ++ + kl ke+a+ ++l ve++++da++l   ++d + D vv++    h    + +l 
  gi|116753346|ref|YP_842464.1| 175 AGVGPFSLLMAKRGARVIAIDKNPCAAKLLKENARMNRLDVEIREGDASSLteDLAD-KADHVVMNL--PH--SASLFLT 249
                                    69999*********************************************8544888.899998883..44..4689*** PP

                                    HHHHHEEEEEEE CS
                Methyltransf_11  83 eiaRvLkpgGll 94 
                                    e+ R  k+gG++
  gi|116753346|ref|YP_842464.1| 250 EAIRTAKNGGVV 261
                                    *********986 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   5.8e-09   6.1e-06      42     142 ..     167     261 ..     150     300 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 5.8e-09
                                    C-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEEE-- CS
                  Cons_hypoth95  42 garvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdivflDP 121
                                    g  v+D+faG G  +l  + Rg +++++++k++ a+k+lken ++ +l+  +++   da++  + la    + d v ++ 
  gi|116753346|ref|YP_842464.1| 167 GDLVVDMFAGVGPFSLLMAKRG-ARVIAIDKNPCAAKLLKENARMNRLD--VEIREGDASSLTEDLA---DKADHVVMNL 240
                                    56699*****************.689*******************9977..5666666666666664...45799***** PP

                                    SSSTTCH.HHHHHHHHHTT-E CS
                  Cons_hypoth95 122 Pyakellieevlelleekkll 142
                                    P  ++l++ e++++ ++ +++
  gi|116753346|ref|YP_842464.1| 241 PHSASLFLTEAIRTAKNGGVV 261
                                    *******99999999887776 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   2.3e-08   2.4e-05       7     110 ..     170     264 ..     165     294 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 2.3e-08
                Methyltransf_31   7 vlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevlna 86 
                                    v+D  +G G +++ +a++   +a+v+ iD ++ a +l +ena+ + ld ve ++gd+ +l ++l+ +k D ++ n     
  gi|116753346|ref|YP_842464.1| 170 VVDMFAGVGPFSLLMAKR---GARVIAIDKNPCAAKLLKENARMNRLD-VEIREGDASSLTEDLA-DKADHVVMNL---- 240
                                    89**************65...799***********************8.**********997777.7999999973.... PP

                Methyltransf_31  87 ladpdkileeiervlkpggillie 110
                                      +   +l e++r  k+gg++   
  gi|116753346|ref|YP_842464.1| 241 PHSASLFLTEAIRTAKNGGVVHYY 264
                                    334455667777777777776555 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   8.3e-08   8.8e-05     157     255 ..     162     260 ..     153     263 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 8.3e-08
                           PrmA 157 klvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklev....alseellkeekadviva 232
                                    ++v++g+ v+D+ +G G  ++  ak ga +v+a+D ++ A k  keNa++N+++ +++      l+e+l  + kad +v 
  gi|116753346|ref|YP_842464.1| 162 EQVRPGDLVVDMFAGVGPFSLLMAKRGA-RVIAIDKNPCAAKLLKENARMNRLDVEIREgdasSLTEDL--ADKADHVVM 238
                                    56899**********************8.699*******************999888652221233444..469****** PP

                           PrmA 233 NILaevlielaedikklvkeggl 255
                                    N   +    ++ ++ ++ k+gg+
  gi|116753346|ref|YP_842464.1| 239 NL-PHSASLFLTEAIRTAKNGGV 260
                                    *5.44445555555566666665 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 !   21.4   0.0   1.4e-07   0.00015       3      80 ..     169     241 ..     167     248 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.4e-07
                Methyltransf_15   3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvflSpP 80 
                                    +++D+f+G G  +  +a+ + +viai++n+   ++ ++Na++      + +  gd  +l++ l  ++   d v++  P
  gi|116753346|ref|YP_842464.1| 169 LVVDMFAGVGPFSLLMAKRGARVIAIDKNPCAAKLLKENARMN--RLDVEIREGDASSLTEDLADKA---DHVVMNLP 241
                                    689***************************************9..6667778899888887765443...45655555 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 !   19.5   0.2   5.8e-07   0.00061       8      95 ..     166     248 ..     160     264 .. 0.81
   2 ?   -0.5   0.0      0.77   8.1e+02     121     140 ..     248     267 ..     244     282 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 5.8e-07
                                    TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC..EEEEEEEE CS
                Methyltr_RsmB-F   8 eeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfDriLlDa 87 
                                    +++ ++D+ a+ G    +   + k  ++v+A+d+n   +k ++en  r++  ++ + e+Da+   ++l++ + D++ +  
  gi|116753346|ref|YP_842464.1| 166 PGDLVVDMFAGVGPFSLL---MAKRGARVIAIDKNPCAAKLLKENA-RMNRLDVEIREGDASSLTEDLAD-KADHVVMNL 240
                                    667778888877764433...446789***************9995.56666677**************6.99******* PP

                                    --CCGGGT CS
                Methyltr_RsmB-F  88 PCsgtgvi 95 
                                    P s+   +
  gi|116753346|ref|YP_842464.1| 241 PHSASLFL 248
                                    *9997655 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.77
                                    HHHHCCCEEEEEEEEEEES- CS
                Methyltr_RsmB-F 121 lsaaidllkkgGvlvYsTCs 140
                                    l+ ai + k+gGv+ Y T +
  gi|116753346|ref|YP_842464.1| 248 LTEAIRTAKNGGVVHYYTFA 267
                                    77889999********9965 PP

>> SAM_MT  Putative SAM-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   3.6e-06    0.0038      74     127 ..     169     222 ..     153     245 .. 0.84
   2 ?   -2.7   0.0         3   3.2e+03      32      51 ..     302     321 ..     290     325 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.6e-06
                         SAM_MT  74 tvlDaTaGlGrDafvlaslGckvtliErhpvvaaLLedglkRakqdaeigella 127
                                     v+D  aG+G  + ++a  G++v  i+++p  a LL++  +  + d ei+e  a
  gi|116753346|ref|YP_842464.1| 169 LVVDMFAGVGPFSLLMAKRGARVIAIDKNPCAAKLLKENARMNRLDVEIREGDA 222
                                    69************************************9999999998887544 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3
                         SAM_MT  32 ekklgavlvdfvsgaaahRr 51 
                                    ++++ +v++df+ ++ a+R 
  gi|116753346|ref|YP_842464.1| 302 APRKYNVVIDFMVKKDAQRG 321
                                    45677899999999988885 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   0.00012      0.12       1      90 [.     176     266 ..     176     279 .. 0.69
   2 ?    3.3   0.0     0.074        78      28      67 ..     281     314 ..     275     322 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00012
                                    HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEET....TTCHHHHHHHHHTTTSSEEEEEESSC.SHHHHHHH CS
                     ADH_zinc_N   1 gvGlaavqlAkalGaeviavdsseeklelakklGadeviny....keadlverikeltggegvdvvfecvG.sgatleaa 75 
                                    gvG + + +Ak  Ga+via+d ++  ++l+k++     ++        d ++  ++l  ++  +vv++ +  +   l++a
  gi|116753346|ref|YP_842464.1| 176 GVGPFSLLMAK-RGARVIAIDKNPCAAKLLKENARMNRLDVeireG--DASSLTEDLA-DKADHVVMNLPHsASLFLTEA 251
                                    67777777777.6*******************97666666654313..5566666666.32334444444312566799* PP

                                    HHCEEEEEEEEECSC CS
                     ADH_zinc_N  76 lkllkpgGrlvvvGg 90 
                                    ++ +k gG + ++ +
  gi|116753346|ref|YP_842464.1| 252 IRTAKNGGVVHYYTF 266
                                    ********9998876 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.074
                                    HHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSC CS
                     ADH_zinc_N  28 elakklGadevinykeadlverikeltggegvdvvfecvG 67 
                                    e+a++lG++++++y      + +++   +++++vv+++  
  gi|116753346|ref|YP_842464.1| 281 EKARELGCKAAVTY-----RSVVRSYA-PRKYNVVIDFMV 314
                                    689***********.....47888888.899999999875 PP

>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   7.2e-06    0.0076      74     149 ..     188     261 ..     153     265 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.2e-06
                                    EEEEEEE-S-HHHHHHHHHHHHHTT--GGEEEE-S-HHHHHC--SS-EEEEEE--SS--GGGHHHHHHHEEEEEEE CS
                            TRM  74 vkevlaNDisekAvelikeNvklneveeivvineddAnvllaekkkrfdviDlDPfGspapfldsavqsvkekglL 149
                                      +v+a D ++ A +l+keN+++n  +  v+i+e+dA+ l +    + d++ +    s++ fl  a++++k++g++
  gi|116753346|ref|YP_842464.1| 188 GARVIAIDKNPCAAKLLKENARMNRLD--VEIREGDASSLTEDLADKADHVVMNLPHSASLFLTEAIRTAKNGGVV 261
                                    4679999****************9986..59***********9998889888887789**************9986 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 ?   14.0   0.0   2.3e-05     0.024       3      59 ..     170     230 ..     169     241 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.3e-05
                                    EEEES-TT-HHHHHHHHTT-EEEEEEE--TTTHHHHHHH-..-SEEEES-TTTS-....GS- CS
                  DNA_methylase   3 fidLfaGiGGfrlgleaagfecvaaseidkkaaktYeanfk.kvsigDitkidkk....klp 59 
                                    ++d+faG+G f+l +++ g   v+a+++++ aak+++ n + +    +i++ d +    +l+
  gi|116753346|ref|YP_842464.1| 170 VVDMFAGVGPFSLLMAKRG-ARVIAIDKNPCAAKLLKENARmNRLDVEIREGDASslteDLA 230
                                    69***********888887.88999***************6644455555555554444444 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   3.8e-05      0.04       7      89 ..     151     239 ..     143     314 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.8e-05
                Methyltransf_23   7 eelsdklerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae......kakkaqkdqfdeqeaaepq 80 
                                     +ls +++r+++  r+g  v+d+ +G+G ++ +++++g+ v+++D +p a ++++        +  + +   ++  ++ +
  gi|116753346|ref|YP_842464.1| 151 PRLSTERLRVAEQVRPGDLVVDMFAGVGPFSLLMAKRGARVIAIDKNPCAAKLLKenarmnRLDVEIREGDASSLTEDLA 230
                                    578899999999999999******************************98888876444442222222222222333344 PP

                Methyltransf_23  81 gkfdlIvlr 89 
                                    +k d +v++
  gi|116753346|ref|YP_842464.1| 231 DKADHVVMN 239
                                    455555544 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.6e-05     0.048      18      88 ..     153     223 ..     140     251 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.6e-05
                                    --HHHHHHCCCS-S-E.EEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GG CS
                           TehB  18 thsevveavkivkpgk.vldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistalydin 88 
                                      +e +  ++ v+pg  v+d+  g g  sl ++  g  v a+dkn  + + l+e +  + l+ ++ +  d  
  gi|116753346|ref|YP_842464.1| 153 LSTERLRVAEQVRPGDlVVDMFAGVGPFSLLMAKRGARVIAIDKNPCAAKLLKENARMNRLD-VEIREGDAS 223
                                    5567778889999*97479**********************************999999998.666655554 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   8.4e-05     0.089     189     230 ..     164     205 ..     149     206 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.4e-05
                                    S-TT-EEEETT-TTTHHHHHHHHTT-EEEEEESSHHHHHHHH CS
                    N6_N4_Mtase 189 tkkgdivlDpFaGSGtTavaakelgrkfiGieieeeyvelae 230
                                     ++gd+v+D FaG G      ++ g + i i++++ +++l +
  gi|116753346|ref|YP_842464.1| 164 VRPGDLVVDMFAGVGPFSLLMAKRGARVIAIDKNPCAAKLLK 205
                                    679*******************************98887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2366.78
//
Query:       gi|116753347|ref|YP_842465.1|  [L=633]
Description: glutamyl-tRNA(Gln) amidotransferase subunit E [Methanosaeta thermophila PT]
Scores for 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-69  235.0   0.0      2e-69  234.0   0.0    1.5  1  GatB_N     GatB/GatE catalytic domain
    2.7e-19   69.5   0.0    6.7e-19   68.2   0.0    1.7  2  GatB_Yqey  GatB domain
    4.4e-15   55.7   0.0    9.1e-15   54.7   0.0    1.6  1  GAD        GAD domain
    5.8e-06   26.4   0.3    1.3e-05   25.3   0.3    1.6  1  YqeY       Yqey-like protein
  ------ inclusion threshold ------
       0.17   12.5   1.2          1   10.0   0.3    2.4  2  MDMPI_N    Mycothiol maleylpyruvate isomerase N-terminal doma


Domain annotation for each model (and alignments):
>> GatB_N  GatB/GatE catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  234.0   0.0   5.6e-73     2e-69       1     273 []      13     447 ..      13     447 .. 0.96

  Alignments for each domain:
  == domain 1  score: 234.0 bits;  conditional E-value: 5.6e-73
                                    EEEEEEEEEEB--SB-SSSSSBSSSSCE.............STTSS--TTTTTS.......................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxx.............xxxxxxxxxxxxx.......................... RF
                         GatB_N   1 lviGlEiHaqlktksKlFssasteeege.............epnsevsevdlal.......................... 41 
                                    lv+G+EiH+ql+t+ KlF+s++t + +e              ++se++e+d a+                          
  gi|116753347|ref|YP_842465.1|  13 LVCGIEIHQQLDTRCKLFCSCPTVH-REvedsnfeffrylrPARSELGEIDRAAleetlvsrrfvyksynttclveadee 91 
                                    58********************873.2223467888889845899999999999***********************999 PP

                                    TT..--.EEHHHHHHHHHHHHHTTEEE-SEE-EEEEE-TCTTCTTSEEEEESSS.SEEEEEEEE.TEEEEEEEEEEEE-- CS
                                    xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                         GatB_N  42 PGtlPv.lnkeavelaikaalalnceiaeeskfdRKnyfypdlpkgyQitqkeeplakeGslel.ekkvrierihlEeDa 119
                                    P   P+ ln+ea+e+a+ +a  l+++i +e++++RK+++++++++g+Q+t+    +a++Gs+++    v+i  ++lEe+a
  gi|116753347|ref|YP_842465.1|  92 P---PReLNREALEIALVIARLLKMRIVDEIHTMRKTVIDGSNTSGFQRTA---FIASSGSIDTsCGPVGIGILCLEEEA 165
                                    8...999********************************************...788******866789*********** PP

                                    -EEEEEETTEEEEETTSTT-EEEEEEE-STB-SHHHHHHHHHHHHHHHHHHTSB--SGGGTTEEEEEEEEECTSETTSSS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         GatB_N 120 aksvheekeeslvdlnRaGvpLiEivtepdlrspeearavveklrellralgvsdgnmeeGslRcDvNvSvreeekgeee 199
                                    a+ v+++ +e++++l+R+G+pL+Ei t+pd+ sp++ar+v+++++++lr++g +++++  G++R+DvNvS++        
  gi|116753347|ref|YP_842465.1| 166 ARIVEDRGDEVVYSLDRLGIPLVEIGTAPDIVSPQHAREVAQHIGMILRSTGRVKRGL--GTIRQDVNVSIAG------- 236
                                    **********************************************************..************4....... PP

                                    .--EEEEEE-SHHHHHHHHHHHHHHHHHHH.................................................. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................................. RF
                         GatB_N 200 gtrvEiKnlnslksiekaieyeierqiell.................................................. 229
                                    g+rvEiK++++l+ ie+++e e+ rq++ll                                                  
  gi|116753347|ref|YP_842465.1| 237 GARVEIKGVQELNLIERIVELEVIRQVRLLeirdelrrrnarvcgdvvdatglfsntrskvvakalksggavlatklagf 316
                                    59****************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                         GatB_N 230 ................................................................................ 229
                                                                                                                    
  gi|116753347|ref|YP_842465.1| 317 kgiigkevqpgrrlgtelsdrakragvggifhtdelpaygiteeevsslrsllsceesdavvmvaapperarkaieavie 396
                                    ******************************************************************************** PP

                                    ..........-EEEEEETTTTEEEEECC--.--...-EEE-TTS--EE--HHHHH CS
                                    ..........xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                         GatB_N 230 ..........qeTrkfdedkgetvslRske.eaedYryfpepdlppleiseelie 273
                                              +eTr++ +d g+++++R+ + +a   r++pe+d+pp+++++e++e
  gi|116753347|ref|YP_842465.1| 397 rareaiagvpEETRRALPD-GTSEYMRPLPgSA---RMYPETDVPPVVVNKEMVE 447
                                    *******************.**********555...****************986 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       2.3   8.3e+03      95     119 ..     388     412 ..     384     415 .. 0.72
   2 !   68.2   0.0   1.9e-22   6.7e-19       1     148 []     483     625 ..     483     625 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.3
                                    HHHHHHHHHTXHHHHHHHTTXXTTS CS
                      GatB_Yqey  95 eklveeviaenpkavedyksgkeka 119
                                    +k++e vi++  +a++ + + + +a
  gi|116753347|ref|YP_842465.1| 388 RKAIEAVIERAREAIAGVPEETRRA 412
                                    6788888888888887776666655 PP

  == domain 2  score: 68.2 bits;  conditional E-value: 1.9e-22
                                    HHHHHHHHHSS.HHHHHHHHHTCHHHHHHHHTXXTTCSSTTHHHHHHHHHHHHTTSSGHHHHHHHHHHHHHH.TXXHHHH CS
                      GatB_Yqey   1 dffeevvkegadaklaanwllnellgelnkegleieelkltpeqlaellkliaegkIskkiakevleellee.gkspeei 79 
                                    ++fee+v+ +  +++++   l+ +  el + g+++ +  l+++++   ++l+++++I+k+ +  +l++++e+ + +pe++
  gi|116753347|ref|YP_842465.1| 483 QLFEEIVRVYRVQPSLVVRSLESTPVELARDGVPVYR--LSERHFMGCFDLLSQKRIAKEGIPALLKAMAENpDADPESA 560
                                    68999999998888888888999999*********99..9**************************************** PP

                                    HHHCTXXXXXXSSXHHHHHHHHHHTXHHHHHHHTTXXTTSTHHHHHHHHHTTSSXSXHHHHHHHHHHHS CS
                      GatB_Yqey  80 ieekgLkqisdeeeleklveeviaenpkavedyksgkekalkflvGqvMkktkGkadpklvnellkekL 148
                                     e  gL  +   +e+e++++e+++++   v+ ++++ e+a++ l+G  M +++Gkad++ v+ l+k+++
  gi|116753347|ref|YP_842465.1| 561 AEAAGLMSLGA-SEVERIIHEIVSAK---VDLVRERGERAIGPLMGLAMEQLRGKADGAAVSALIKKEI 625
                                    *********98.**************...*************************************986 PP

>> GAD  GAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.7   0.0   2.5e-18   9.1e-15       3      94 ..     300     390 ..     298     391 .. 0.96

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 2.5e-18
                                    HHHHSTEEEEEEEETTG-TTTSHHHHHHHHHHHHHTTHSHCEEEEESSGGEETTTCCC.S-HHHHHHHHHHCT--TTEEE CS
                            GAD   3 ealksggsvkalrvpggaaklsrkeideleefakelgakglawikvegegltgpiakf.lteeevkklleavgaeegDil 81 
                                    +alksgg v a ++ g ++++++ke+++++++++el+++++   +v+g ++t++++++ +teeev+ l+  ++ ee D++
  gi|116753347|ref|YP_842465.1| 300 KALKSGGAVLATKLAG-FKGIIGKEVQPGRRLGTELSDRAKRA-GVGGIFHTDELPAYgITEEEVSSLRSLLSCEESDAV 377
                                    799*************.8**********************976.************************************ PP

                                    EEEEEEHHHHHHH CS
                            GAD  82 lfvAdkkktvnka 94 
                                    ++vA + + + ka
  gi|116753347|ref|YP_842465.1| 378 VMVAAPPERARKA 390
                                    ******9999987 PP

>> YqeY  Yqey-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.3   3.6e-09   1.3e-05      96     142 ..     578     624 ..     567     625 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 3.6e-09
                                    HHHHHHHHHHHTT--BGGGHHHHHHHHHHHHTTTS-HHHHHHHHHHH CS
                           YqeY  96 iealvkeaiaevgaesmkdmGkvmkalkpkvkGkaDgkkvsalvkek 142
                                    i+++v++ ++ v +++ +++G +m++++++++GkaDg++vsal+k++
  gi|116753347|ref|YP_842465.1| 578 IHEIVSAKVDLVRERGERAIGPLMGLAMEQLRGKADGAAVSALIKKE 624
                                    445555555667999******************************87 PP

>> MDMPI_N  Mycothiol maleylpyruvate isomerase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.3   0.00029         1      74     127 ..     375     429 ..     322     432 .. 0.81
   2 ?    0.3   0.0      0.29   1.1e+03      92     140 ..     540     588 ..     538     589 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00029
                        MDMPI_N  74 avdlaaslapeallaafraavtrlaaalaalppdaiadrl.gipggprslgeflr 127
                                    ++    +++pe+ ++a++a ++r+++a+a +p++ +++   g++   r+l+  +r
  gi|116753347|ref|YP_842465.1| 375 DAVVMVAAPPERARKAIEAVIERAREAIAGVPEETRRALPdGTSEYMRPLPGSAR 429
                                    55566789**************************999988777766666665555 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.29
                        MDMPI_N  92 aavtrlaaalaalppdaiadrlgipggprslge.flrtrlvEavvHglDl 140
                                    +++++l++a+a+ p+++++     ++g +slg+  + + ++E+v   +Dl
  gi|116753347|ref|YP_842465.1| 540 EGIPALLKAMAENPDADPESAA-EAAGLMSLGAsEVERIIHEIVSAKVDL 588
                                    6788999999999999988888.778888888878888888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (633 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); 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: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 4161.12
//
Query:       gi|116753348|ref|YP_842466.1|  [L=75]
Description: transcription factor [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.3e-16   58.2   0.7    8.1e-16   58.1   0.7    1.0  1  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a
    6.3e-10   39.5   0.2    7.6e-10   39.3   0.2    1.1  1  Histone        Core histone H2A/H2B/H3/H4
    4.9e-06   26.6   0.5    5.1e-06   26.6   0.5    1.1  1  TAF            TATA box binding protein associated factor (TA
    2.2e-05   24.5   0.0    2.4e-05   24.4   0.0    1.0  1  CENP-T_C       Centromere kinetochore component CENP-T histon
    0.00035   20.5   0.0    0.00039   20.4   0.0    1.1  1  Bromo_TP       Bromodomain associated
    0.00042   20.6   0.0    0.00042   20.6   0.0    1.2  1  CENP-S         CENP-S protein
     0.0011   19.0   0.0     0.0013   18.8   0.0    1.0  1  TFIID-31kDa    Transcription initiation factor IID, 31kD subu
  ------ inclusion threshold ------
       0.11   12.0   0.0       0.12   11.9   0.0    1.1  1  PP_kinase_C_1  Polyphosphate kinase C-terminal domain 1
       0.13   12.0   0.0       0.15   11.8   0.0    1.1  1  Peptidase_C39  Peptidase C39 family


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 !   58.1   0.7   4.1e-19   8.1e-16       3      64 ..       4      64 ..       2      65 .. 0.97

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 4.1e-19
                                   XXHHHHHHHHHCCTTXS-B-HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHHHHHH CS
                  CBFD_NFYB_HMF  3 LPiarvkkImksdpdarkiakdAkeliaecveefieelaseAaeickkekrKtikaehiklA 64
                                   LP+a+v+++++ + +a+++++dA + +a ++e +  e+a+eA + ++++krKt+ ae+ik A
  gi|116753348|ref|YP_842466.1|  4 LPVAPVARLIRMA-GAKRVSEDASIELASILENYGIEIAKEAIDWANHAKRKTVRAEDIKEA 64
                                   9************.*********************************************987 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 !   39.3   0.2   3.8e-13   7.6e-10      66     129 ..       5      66 ..       2      68 .. 0.86

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 3.8e-13
                                    HHHHHHHHHH.TTSSSXEEXHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTXSEEXHHHHHHHHH CS
                        Histone  66 pfaRvvreivksekedlrisaeavlalqealEallvelfeeAnllakhaKRvTitpkDiqlArr 129
                                    p+a v r i+      +r+s +a+  l+++lE++ +e+++eA   a+haKR+T+ ++Di+ A++
  gi|116753348|ref|YP_842466.1|   5 PVAPVARLIRM--AGAKRVSEDASIELASILENYGIEIAKEAIDWANHAKRKTVRAEDIKEAAK 66 
                                    44444445554..5679********************************************987 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 !   26.6   0.5   2.6e-09   5.1e-06      13      64 ..      13      64 ..       1      69 [. 0.88

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 2.6e-09
                                   HHHTT---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHH CS
                            TAF 13 AeslGitnLsdeaaalLaedveyrlkeivqeaakfmrhskRqkLtvaDvdsA 64
                                     + G + +s++a+ +La  +e    ei++ea+ + +h+kR++  ++D+ +A
  gi|116753348|ref|YP_842466.1| 13 IRMAGAKRVSEDASIELASILENYGIEIAKEAIDWANHAKRKTVRAEDIKEA 64
                                   5689999**************99999***********************998 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 !   24.4   0.0   1.2e-08   2.4e-05       8      79 ..       4      70 ..       1      74 [. 0.86

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.2e-08
                       CENP-T_C  8 lPaavvkklakrfakasgskaklekealkalekasdkffeqvgeDLeayakHagRKtidesDvilLmkrqrk 79
                                   lP+a v +l +++       ++++++a   l ++++++   ++++   +a+Ha+RKt+ ++D+    kr r 
  gi|116753348|ref|YP_842466.1|  4 LPVAPVARLIRMA-----GAKRVSEDASIELASILENYGIEIAKEAIDWANHAKRKTVRAEDIKEAAKRVRP 70
                                   6777777776665.....55699****************************************999999885 PP

>> Bromo_TP  Bromodomain associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0     2e-07   0.00039      12      67 ..       9      64 ..       3      69 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2e-07
                                   HHHHHHHHT-SEE-HHHHHHHHHHHHHHHHHHHHHHHHHHTTSS-SS--HHHHHHH CS
                       Bromo_TP 12 vsqileeaGfdsaeesaLEtLteiaqkYirelgeqaksfaehagRseptlkDvvlt 67
                                   v+ + + aG +++ e a   L  i+++Y  e++++a  +a+ha R ++  +D+  +
  gi|116753348|ref|YP_842466.1|  9 VARLIRMAGAKRVSEDASIELASILENYGIEIAKEAIDWANHAKRKTVRAEDIKEA 64
                                   66667777777666555555899*****************************9865 PP

>> CENP-S  CENP-S protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   2.1e-07   0.00042      44      73 ..      39      68 ..       8      71 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.1e-07
                         CENP-S 44 nlakDLeaFakHAkRstittdDvlLlaRrn 73
                                   ++ak    +a+HAkR+t++++D++  a+r 
  gi|116753348|ref|YP_842466.1| 39 EIAKEAIDWANHAKRKTVRAEDIKEAAKRV 68
                                   677888889***************999986 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 !   18.8   0.0   6.5e-07    0.0013      11      67 ..       9      65 ..       5      70 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 6.5e-07
                    TFIID-31kDa 11 ihliLaslgvteyeerVvlqLldfayrytssvLedAkvlaehakkkevslddvrlAi 67
                                   ++ +++  g + ++e+    L  +  +y +++ ++A   a+hak+k+v ++d++ A 
  gi|116753348|ref|YP_842466.1|  9 VARLIRMAGAKRVSEDASIELASILENYGIEIAKEAIDWANHAKRKTVRAEDIKEAA 65
                                   5667888899999999999***********************************885 PP

>> PP_kinase_C_1  Polyphosphate kinase C-terminal domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   6.1e-05      0.12      75     118 ..      20      63 ..       9      74 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.1e-05
                                    SS--HHHHHHHHHHHHHT-EEEE--TT--B--EEEEEEE---S- CS
                  PP_kinase_C_1  75 rfdeenNiewakkleeagvkvvygvvglkvhaklllvvrreeek 118
                                    r  e++ ie+a+ le+ g++++    ++  hak  +v  ++ ++
  gi|116753348|ref|YP_842466.1|  20 RVSEDASIELASILENYGIEIAKEAIDWANHAKRKTVRAEDIKE 63 
                                    889******************************99998776544 PP

>> Peptidase_C39  Peptidase C39 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   7.8e-05      0.15      18      57 ..      29      68 ..      18      70 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.8e-05
                  Peptidase_C39 18 lamilkyygsevsleeLrelagtdeeGlslsgLkkaakkl 57
                                   la il++yg+e++ e +    + +++ ++++++k+aak++
  gi|116753348|ref|YP_842466.1| 29 LASILENYGIEIAKEAIDWANHAKRKTVRAEDIKEAAKRV 68
                                   89***********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); 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: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 518.60
//
Query:       gi|116753349|ref|YP_842467.1|  [L=161]
Description: 3-isopropylmalate dehydratase small subunit [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.7e-20   72.2   0.2      1e-19   71.1   0.2    1.7  1  Aconitase_C    Aconitase C-terminal domain
     0.0066   16.1   0.1      0.058   13.0   0.0    1.9  2  Aconitase_2_N  Aconitate hydratase 2 N-terminus


Domain annotation for each model (and alignments):
>> Aconitase_C  Aconitase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.1   0.2   1.2e-23     1e-19      73     123 ..      48      97 ..       5     104 .. 0.90

  Alignments for each domain:
  == domain 1  score: 71.1 bits;  conditional E-value: 1.2e-23
                                    T--EEEE--SSBTBS---THHHHHHHHTTEEEEEES-B-HHHHHHHHHTT- CS
                    Aconitase_C  73 gaklvviagknfGeGSSRehAAkalrllGikaviaeSFerIfennlikngl 123
                                      +++v++  nfG+GSSRehA++a ++ G++avia SF+rIf +n+i+ gl
  gi|116753349|ref|YP_842467.1|  48 HGDIIVAG-TNFGCGSSREHAPLAIKAAGVEAVIARSFARIFFRNSINIGL 97 
                                    56677766.****************************************96 PP

>> Aconitase_2_N  Aconitate hydratase 2 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.033     3e+02      55      72 ..      50      67 ..      32      79 .. 0.84
   2 !   13.0   0.0   6.5e-06     0.058      96     167 ..      79     151 ..      70     156 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.033
                                   -EEEEEEEEEES---THH CS
                  Aconitase_2_N 55 playvgdvvGtGssRksa 72
                                    ++  g   G GssR  a
  gi|116753349|ref|YP_842467.1| 50 DIIVAGTNFGCGSSREHA 67
                                   467788899******876 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 6.5e-06
                                    EEEEEE-HHHH.HHHHHTT-EEEE---TT--TT-EEEEETTTTEEEETT--EEEE---S-TCHHHHHHHTSHH CS
                  Aconitase_2_N  96 vlGgkiaPiFf.ntvedsGalpieadvskletGdvieikpkegkikkeegevvsefklkpetlldevraggri 167
                                    v+  + a iFf n ++    l i ad +k++ Gd + ++  +g +++ +++     +  p  l++ vr+gg +
  gi|116753349|ref|YP_842467.1|  79 VIARSFARIFFrNSINIGLPLLICADAEKIDDGDSVVVDISRGIVQNISKKESYPTTPLPPFLQEIVRSGGLL 151
                                    677788999993455555579999***********************66666666666688999******965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 1110.25
//
Query:       gi|116753350|ref|YP_842468.1|  [L=374]
Description: 3-isopropylmalate dehydrogenase [Methanosaeta thermophila PT]
Scores for complete 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-99  333.3   0.0    1.8e-99  333.2   0.0    1.0  1  Iso_dh    Isocitrate/isopropylmalate dehydrogenase


Domain annotation for each model (and alignments):
>> Iso_dh  Isocitrate/isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  333.2   0.0    1e-103   1.8e-99       1     348 []       4     367 ..       4     367 .. 0.97

  Alignments for each domain:
  == domain 1  score: 333.2 bits;  conditional E-value: 1e-103
                                    EEEEEEESTTHHHHHHHHHHHHHHHHHHHT-EEEEEE---THHHHHHHSSSS-HHHHHHHHHSSEEEEEE---CS.SSSS CS
                         Iso_dh   1 kiallegdgiGpevveaalkvlkaakekaglelefeevdvGgaaidetgeplpeetleaikeadvvllgavgtpk.ekev 79 
                                    k+++++gdgiGpe++++  kvl++a++k+g ++e+ e+ +G+  + +tge ++eetl+ + +++++ lga+g p  + +v
  gi|116753350|ref|YP_842468.1|   4 KVPVIPGDGIGPEIIAEGRKVLETAADKHGFDIEWIEYPLGADHYLRTGELVSEETLKELGRYRAIYLGAIGDPRvKPGV 83 
                                    699************************************************************************66666 PP

                                    SHHHHHHHHHHHTTEEEEEEEEE-BCCTTCCSSBTHHHHCT-EEEEEEE-SSCGGCSSEEEEET................ CS
                         Iso_dh  80 rpengLlaLrkeldlfanlrpvkvfeklkvksplkrevveevdlvivReltggiYfgeekekkg................ 143
                                      +  Lla+r  +d + nlrpvk++  ++v +plk++ ++++d+v+vRe+t++ Y+g+   +++                
  gi|116753350|ref|YP_842468.1|  84 LEKGILLAMRFYFDQYINLRPVKLL--EGVWTPLKDKGPKDIDFVVVRENTEDFYIGQGGRARSgrshadlevkrslynv 161
                                    666689*******************..89*****************************9999999*************** PP

                                    .......TG.GGGEEEEEEEEEHHHHHHHHHHHHHHHHHTTTSEEEEEESTTTTHHHH.HHHHHHHHHHCCTTTTSEEEE CS
                         Iso_dh 144 .......sifteevavdtklyseeeieriaraafelAlkrgkkkvtlvdKanvlksse.lwrkiveevaeeeypdieleh 215
                                           s  ++e a+++ ++s+e+  r++++af+lA++r +k+v +vdKanvl+    +wr+i+e+v +  yp+++ + 
  gi|116753350|ref|YP_842468.1| 162 kfgldidS-DSDEIAYQIGMVSREGCTRVIKYAFDLAMER-RKHVSSVDKANVLSDIYgFWREIFEDVGK-SYPEVTTDF 238
                                    ****9853.6899***************************.*************98877***********.********* PP

                                    EEHHHHHHHHHHSGGGGSEEEE-HHHHHHHHHHHHHHTTSGCC-EEEEEETSS-EEEEESS---CCCTTSS-S-THHHHH CS
                         Iso_dh 216 qlvDsaamqlvkspkqfdVivtkNlfGDilSDeaaalvGslGllpSaslgekkvaifEavHGsapdiagkdkaNpiavil 295
                                     +vD+++m  vk+p+ fdV+v++N+fGDi+ D+ a++ G+lGl+p+a+l+++++ +fE++HGsap++ g +k+Npia+i 
  gi|116753350|ref|YP_842468.1| 239 NFVDAITMWFVKNPEWFDVVVAPNMFGDIITDLGAMIQGGLGLAPGANLNPEGTSMFEPIHGSAPKYKGMNKINPIATIW 318
                                    ******************************************************************************** PP

                                    HHHHHHHHTTT-HHHHHHHHHHHHHHHHH.TSCCHHHCTTSTCCCHHHHHHHHH CS
                         Iso_dh 296 SaalmLryslgleeaAdkiekAvekvlea.givTkDlageaakevstsefgdav 348
                                    + a++L++ lg++eaA+++ +A+e +l++ +++T+Dl+g++    +tse+gd++
  gi|116753350|ref|YP_842468.1| 319 AGAMLLEH-LGEKEAAQDVVRAIELSLREgRVRTYDLGGSS----TTSEVGDEI 367
                                    ********.********************889*********....******997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2648.87
//
Query:       gi|116753351|ref|YP_842469.1|  [L=78]
Description: DNA-directed RNA polymerase subunit H [Methanosaeta thermophila PT]
Scores for complete 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  101.8   0.3    1.5e-29  101.7   0.3    1.0  1  RNA_pol_Rpb5_C  RNA polymerase Rpb5, C-terminal domain
  ------ inclusion threshold ------
      0.012   15.8   0.0      0.014   15.4   0.0    1.2  1  Ribosomal_S17   Ribosomal protein S17


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 !  101.7   0.3   1.6e-33   1.5e-29       2      73 .]       5      76 ..       4      76 .. 0.98

  Alignments for each domain:
  == domain 1  score: 101.7 bits;  conditional E-value: 1.6e-33
                                   .-TSSSS--EEEEE-HHHHHHHHHHTT--TTCSS-EETTSHHHHCCT--TTSEEEEEEEETTTEEEEEEEEE CS
                 RNA_pol_Rpb5_C  2 nitkHelvPkhevlseeekkellkklkikeeqLPkisksDpvarylglkkGdvvkItrksetageavtYRlV 73
                                    +++HelvP+h +l++ee++++l +++++  +LPki+ +Dpva+++g+k Gd++kI rks+ta+e++ YRlV
  gi|116753351|ref|YP_842469.1|  5 AVQDHELVPEHILLTPEEAQQVLMQYGVEARHLPKIHVTDPVAKEIGAKVGDIIKIKRKSPTAKESIFYRLV 76
                                   689********************************************************************9 PP

>> Ribosomal_S17  Ribosomal protein S17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.0   1.6e-06     0.014      32      62 ..      37      70 ..      22      76 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.6e-06
                                   EEEEEEE-TTTS...--TT-EEEEEEECECSSSE CS
                  Ribosomal_S17 32 rkkylahdenns...vkvGDiVrieecrPlSktk 62
                                     k+++ d+  +   +kvGDi++i+  +P +k+ 
  gi|116753351|ref|YP_842469.1| 37 LPKIHVTDPVAKeigAKVGDIIKIKRKSPTAKES 70
                                   56999999988888****************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); 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 0.23s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 574.06
//
Query:       gi|116753352|ref|YP_842470.1|  [L=496]
Description: DNA-directed RNA polymerase subunit beta'' [Methanosaeta thermophila PT]
Scores for 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-53  179.4   0.5    7.2e-53  179.1   0.5    1.1  1  RNA_pol_Rpb2_1  RNA polymerase beta subunit
    1.9e-29  102.6   0.2    2.9e-29  102.1   0.2    1.2  1  RNA_pol_Rpb2_2  RNA polymerase Rpb2, domain 2
    1.9e-25   88.8   0.0    3.6e-25   87.9   0.0    1.5  1  RNA_pol_Rpb2_3  RNA polymerase Rpb2, domain 3


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb2_1  RNA polymerase beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.1   0.5   1.2e-56   7.2e-53       2     202 ..      17     384 ..      16     385 .. 0.98

  Alignments for each domain:
  == domain 1  score: 179.1 bits;  conditional E-value: 1.2e-56
                                    TTHHHHHHHHHHHHTHHHHHCTTSSECCHCSSSHCSSSCEEEEEEEEEEESCSSECTTSCEEES.HHHHHHCTSBXEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb2_1   2 LvsqqldSFnkfveqdlekiikeeaaieseeeiqssgeelelkfvsirlgkPvvdesdasereiyPkearlrnltYsapl 81 
                                    Lv+ +++SFn+f++  l+k+i+e   ie++ e+       ++k+++ir++kPvv e+d+s +++yP++arlrnltY +p+
  gi|116753352|ref|YP_842470.1|  17 LVHHHINSFNEFIDRGLQKVIDEVRIIETNIEN------TYVKLGKIRVEKPVVMEADGSVERLYPNDARLRNLTYASPI 90 
                                    99*********************9999998886......69*************************************** PP

                                    EEEEEEEECCCCTCCEEEEEEEEEEEEEXBTTSTTSSSTTS.HHHHHHTTS.TTS..SSEEETTCEEEEXEEEE...... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...... RF
                 RNA_pol_Rpb2_1  82 yvklklvvyekdnkeeikeeevyiGelPlMlrskacvlseaseeelvelkEcpldqGGyFiinGtekvivaqek...... 155
                                     +++  v      +ee+++ e  iG lP+M+ sk c+l+++seee+v  +E+pld+GGyFi+nG+e+vi+ +e+      
  gi|116753352|ref|YP_842470.1|  91 KLEMSIVD----RGEEKEPVEAMIGMLPIMVMSKVCNLYGMSEEEMVSYGEDPLDPGGYFIVNGSERVIMTLEDlapnki 166
                                    99998888....89****************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                 RNA_pol_Rpb2_1 156 ................................................................................ 155
                                                                                                                    
  gi|116753352|ref|YP_842470.1| 167 lveynqrydefievakvfsqrqgyrslvivergkrsilevsfpsvagrinfvtlvralgletdmdivkavsdnpeimkfm 246
                                    ******************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                 RNA_pol_Rpb2_1 156 ................................................................................ 155
                                                                                                                    
  gi|116753352|ref|YP_842470.1| 247 lenleeaevstteealekignrvaagqakeyqkkraayvldryllphigveekdryakalflsrmaeacfelalgkrged 326
                                    ******************************************************************************** PP

                                    ...........XHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSSSSSHHHHSCSHHHH CS
                                    ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb2_1 156 ...........laGeLlaslfrvllkklerdvkerlqksleklddlmlqllvnakpit 202
                                               l G+L+++lfrv++++l+rd+k +l++   ++++l++  +v+a+ +t
  gi|116753352|ref|YP_842470.1| 327 dkdhyankrlkLSGDLMEDLFRVAFNRLTRDIKYQLERASMRNRELNVITTVRADVLT 384
                                    *****************************************************99876 PP

>> RNA_pol_Rpb2_2  RNA polymerase Rpb2, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.1   0.2   4.8e-33   2.9e-29      12     190 .]     162     337 ..     152     337 .. 0.87

  Alignments for each domain:
  == domain 1  score: 102.1 bits;  conditional E-value: 4.8e-33
                                    SSSSE.............SSSCCEECCCEEEEECCCCSTSCEEEEECTTSSSEEEHHHHHHHTT--STTHHHHHHTSSST CS
                 RNA_pol_Rpb2_2  12 dknki.............satvtsslisqrgsvlklekdgktliwtriskkrkipivivlkAlglvsdreIlericydse 78 
                                    ++nki             +a+v s +  +r++v++++ ++++l ++ +s+  +i++v + +Algl +d +I+++++    
  gi|116753352|ref|YP_842470.1| 162 APNKIlveynqrydefieVAKVFSQRQGYRSLVIVERGKRSILEVSFPSVAGRINFVTLVRALGLETDMDIVKAVS---- 237
                                    444444444444455589999*******************************************************.... PP

                                    THHHHHHHHHHHHHHCTSSSCHHHHHHHHHCSSTTSSSCCCCCHHHHHHHCHHHHHHHTTTTSSTTTTTSSSTCHH...H CS
                 RNA_pol_Rpb2_2  79 dsqlleelleeleekeeiqtqeealdyigkvvalrrgeearlqsareilqkrydlgeigreklnkhlglseslenkr.lk 157
                                    d   + +++ e+ e++e+ t+eeal++ig++va+++ +e + ++a  +l         +r+ l+ h+g++e+   +r +k
  gi|116753352|ref|YP_842470.1| 238 DNPEIMKFMLENLEEAEVSTTEEALEKIGNRVAAGQAKEYQKKRAAYVL---------DRYLLP-HIGVEEK---DRyAK 304
                                    4555566666677777888999********9999999999999999998.........8*****.*******...5669* PP

                                    HHHHHHHHHHHHHHHTTSSSS--TTSGGGEEEE CS
                 RNA_pol_Rpb2_2 158 aqdilymidrLlslklgrrevDDiDhlgnkRvr 190
                                    a ++  m+++ ++l+lg+r +DD+Dh++nkR++
  gi|116753352|ref|YP_842470.1| 305 ALFLSRMAEACFELALGKRGEDDKDHYANKRLK 337
                                    *******************************96 PP

>> RNA_pol_Rpb2_3  RNA polymerase Rpb2, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.9   0.0   6.1e-29   3.6e-25       1      64 [.     405     465 ..     405     469 .. 0.97

  Alignments for each domain:
  == domain 1  score: 87.9 bits;  conditional E-value: 6.1e-29
                 RNA_pol_Rpb2_3   1 qvldrlnplselshlrrvsslrgglskerkttevRdlhpshwGriCpveTPEGencGlvksLal 64 
                                    q+ldr+ ++++lshlrrv s+   ls+++ ++e Rdlh+++wGriCp+eTPEG+ncGlvk++a+
  gi|116753352|ref|YP_842470.1| 405 QLLDRTDYMASLSHLRRVISP---LSRSQPHFETRDLHATQWGRICPSETPEGPNCGLVKNFAQ 465
                                    89*******************...**************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (496 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); 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: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 3375.17
//
Query:       gi|116753353|ref|YP_842471.1|  [L=604]
Description: DNA-directed RNA polymerase subunit B' [Methanosaeta thermophila PT]
Scores for complete 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-126  421.9   0.0   3.1e-126  421.6   0.0    1.1  1  RNA_pol_Rpb2_6   RNA polymerase Rpb2, domain 6
      3e-29  101.2   0.0    5.7e-29  100.4   0.0    1.5  1  RNA_pol_Rpb2_7   RNA polymerase Rpb2, domain 7
    9.3e-23   80.3   1.4    1.8e-22   79.4   1.4    1.5  1  RNA_pol_Rpb2_4   RNA polymerase Rpb2, domain 4
    3.2e-10   40.4   3.3    8.6e-10   39.0   3.3    1.7  1  RNA_pol_Rpb2_5   RNA polymerase Rpb2, domain 5
  ------ inclusion threshold ------
      0.018   15.3   0.2      0.052   13.8   0.2    1.7  1  RNA_pol_Rpb2_45  RNA polymerase beta subunit external 1 domai
      0.035   13.6   1.2          4    7.0   0.1    2.6  2  TF_Zn_Ribbon     TFIIB zinc-binding
      0.044   13.6   0.6       0.28   11.0   0.4    2.2  2  Cys_rich_CPCC    Cysteine-rich CPCC
       0.12   12.5   2.1       0.23   11.7   2.1    1.4  1  Auto_anti-p27    Sjogren's syndrome/scleroderma autoantigen 1


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb2_6  RNA polymerase Rpb2, domain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  421.6   0.0  1.4e-129  3.1e-126       2     390 .]     136     507 ..     135     507 .. 0.96

  Alignments for each domain:
  == domain 1  score: 421.6 bits;  conditional E-value: 1.4e-129
                                    HHT-SS-TTB-HHHHHHHHHHGGGB-S---TTTTT---SSEEEESS----SSB-S.TTTTTS........GGGS-SEEEE CS
                 RNA_pol_Rpb2_6   2 aklapvvehvqspriiiqaamekqalgiyslnkfkrsnqktyllcinqkPlvktgdkveagqvldgpatekgelalGqna 81 
                                    ++l+p++eh+ spr+++ a m kq lg+  +n   r +++ + l+++q+P+v+t+ +++a++        +++ ++Gqn+
  gi|116753353|ref|YP_842471.1| 136 TALVPYPEHNASPRNTMGAGMIKQCLGFPMANIRLRPDTRGHYLHYPQQPIVSTR-TAKAIG--------FDKRPAGQNF 206
                                    5689***************************************************.999999........********** PP

                                    EBBBS--TTTTTTT-EEEBCHHHHTTTT-EEEEEE..EEE--SSSS---.-S--..-.....-SS-GGGS-TTSB--SS- CS
                 RNA_pol_Rpb2_6  82 vVAvmsyeGYniEDaiilnerlvdrdvftsihikeyeveardtklgeeeitrdipnv.....seealkkLdedGivrvga 156
                                    vVAv++yeGYniEDa+++n+++v+r++++s++++  e e r++++g+e+ ++ ++ +     ++e + +Ld dG+v+++a
  gi|116753353|ref|YP_842471.1| 207 VVAVLAYEGYNIEDALVMNKSAVERGLARSHFFRVSEAEERKYPGGQEDKFEIPDLEvrgarGSETYGQLDADGLVNPNA 286
                                    ***********************************9***********88777666558999999**************** PP

                                    EEETT-EEE---..B-----...-----------..-B---EE--TT-EEEEEEEEE.......EE-TT--EEEEEEEEE CS
                 RNA_pol_Rpb2_6 157 evkegdilvgkvtkgeteltpeekllraifgekarevkdtslrvksgeegvVdkvkvfsrekgdelkagvnklvkvyvaq 236
                                     v ++d+l+gk+  ++ ++ +e     ++fg + ++ ++ts++++s+e+gvVd v++       ++++++n+l+kv++++
  gi|116753353|ref|YP_842471.1| 287 DVGPNDVLIGKT--SPPRFLEE----PTEFGISPQQRRETSVTMRSNEKGVVDLVIL-------TESQNGNRLAKVKTRD 353
                                    ***********8..88888744....356777777899*******************.......9999************ PP

                                    EE---TT-BEEETTS---BBEEEB-TTTSEEETTS---SEEE-GGGCHHH-BTTHHHHHHHHHCCCSSSS--B--TT-.. CS
                 RNA_pol_Rpb2_6 237 kRklqvGDKfasrhGqKGvvslilpqeDmPfledGivvDivlNPlgvPSRmtigqllEtllgkaaalegkkvdatvFdga 316
                                    +R +++GDKfasrhGqKGvv+l+lpqeDmPf e+G+v+D++lNP+++PSRmt+g++lE++ gk+++leg+++dat+F g+
  gi|116753353|ref|YP_842471.1| 354 QRIPELGDKFASRHGQKGVVGLLLPQEDMPFSESGMVPDLLLNPHAIPSRMTVGHVLEMIGGKVGSLEGRFIDATAFLGE 433
                                    ******************************************************************************** PP

                                    .-HHHHHHHHHTTS-TT-EE-EEETTTS-B-SS-EEB-EEEEEEBS--CCCS----SS--B-TTT--B-SCGGG CS
                 RNA_pol_Rpb2_6 317 keeeikelLeeagleasGkevlydGrtGekleaeifvGviYylkLkhlvedKihaRstGpyslltqQPlgGkaq 390
                                    ke +++++L++ g++++GkevlydG tGe+++a+ifvGvi y+kL+h+v+ K+haRs+Gp+++lt+QP++G+a+
  gi|116753353|ref|YP_842471.1| 434 KEWDLRSALTRLGFAHTGKEVLYDGATGERIQADIFVGVILYQKLYHMVTGKMHARSRGPVQVLTRQPTEGRAR 507
                                    ************************************************************************96 PP

>> RNA_pol_Rpb2_7  RNA polymerase Rpb2, domain 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.4   0.0   2.5e-32   5.7e-29       1      86 [.     509     600 ..     509     601 .. 0.98

  Alignments for each domain:
  == domain 1  score: 100.4 bits;  conditional E-value: 2.5e-32
                                    BBEEEEHHHHHHHHHHTBHHHHHHHHTTTTTEEEEEEESSSSSCCCEE......EBTTTTCSSSEEEEEEEHHHHHHHHH CS
                 RNA_pol_Rpb2_7   1 GGlrfGEMErdaliayGaaalLkerltikSDavevdvcgrckllaaan......eCkivkseekiekveipeafklLlqe 74 
                                    GGlrfGEMErd+lia+Gaa  Lkerl+++SD+v+  vc++c+++a+ +       C+++ ++++i +ve+++afklLl+e
  gi|116753353|ref|YP_842471.1| 509 GGLRFGEMERDVLIAHGAALALKERLVEESDKVTELVCSKCGVIAIHDrrrnmdLCPVCGTDTDIYPVEMSYAFKLLLDE 588
                                    9*********************************************99*****9************************** PP

                                    HHHTTBEEEEES CS
                 RNA_pol_Rpb2_7  75 Lqslgialklll 86 
                                    ++slg+a++l+l
  gi|116753353|ref|YP_842471.1| 589 IKSLGVAPRLML 600
                                    ********9986 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 !   79.4   1.4   8.2e-26   1.8e-22       1      62 []       6      67 ..       6      67 .. 0.99

  Alignments for each domain:
  == domain 1  score: 79.4 bits;  conditional E-value: 8.2e-26
                                   EECTT-BEEE-S-HCCHHHHHHHHCCTTSS-TT-EEEE-TTT--EEEE-SSEEB-EEEEE-S CS
                 RNA_pol_Rpb2_4  1 VfvNGrllGvtrdpkklvetlRelRRkgkiseevsivlnekqkevkiatDgGRvcRPliiVe 62
                                   Vf+NG+++G++ +p+klv ++R+lRR+g is++++++++++++e+ i+tD+GR++RPliiVe
  gi|116753353|ref|YP_842471.1|  6 VFINGEIVGHHPEPEKLVAEIRRLRRAGVISNQINVAYYDRTNEIVINTDSGRARRPLIIVE 67
                                   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 !   39.0   3.3   3.8e-13   8.6e-10       1      58 []      88     128 ..      88     128 .. 0.92

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 3.8e-13
                                    HHHHHHTTSEEEEEHHHHTT--EESSTTTCSST-SSTTTSS--TTSSSST-SEEES-G CS
                 RNA_pol_Rpb2_5   1 wddLlregvvEylDaeEEetamIamtpedleksreekealeekenskshtyTHcEIhP 58 
                                    +ddL+reg +EylDaeEEe+a+Ia+ ++dl+++                 +TH+E++P
  gi|116753353|ref|YP_842471.1|  88 FDDLVREGKIEYLDAEEEENAYIAIWENDLTEE-----------------HTHLEVDP 128
                                    9*****************************876.................68888887 PP

>> RNA_pol_Rpb2_45  RNA polymerase beta subunit external 1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   2.3e-05     0.052       9      36 ..      94     121 ..      79     127 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.3e-05
                                    EEEEEEEEHHHHTTSEEE-SSS-BETTS CS
                RNA_pol_Rpb2_45   9 tdevvYLtAdeEekyviAqAnapldeeg 36 
                                    + +++YL A+eEe+ +iA  +  l ee 
  gi|116753353|ref|YP_842471.1|  94 EGKIEYLDAEEEENAYIAIWENDLTEEH 121
                                    5689**************9888888776 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1    0.0018         4      18      27 ..     542     551 ..     531     553 .. 0.80
   2 ?    4.6   0.1      0.01        23       3      13 ..     564     574 ..     563     581 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0018
                                    TCEEESSSSB CS
                   TF_Zn_Ribbon  18 gelvCtdCGl 27 
                                    +elvC++CG+
  gi|116753353|ref|YP_842471.1| 542 TELVCSKCGV 551
                                    79*******7 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.01
                                    ETTTTCEECHE CS
                   TF_Zn_Ribbon   3 CPnCgstnlve 13 
                                    CP+Cg++++++
  gi|116753353|ref|YP_842471.1| 564 CPVCGTDTDIY 574
                                    *****988665 PP

>> Cys_rich_CPCC  Cysteine-rich CPCC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.42   9.4e+02      23      40 ..     110     126 ..      98     152 .. 0.70
   2 ?   11.0   0.4   0.00013      0.28       3      31 ..     546     574 ..     544     582 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.42
                  Cys_rich_CPCC  23 vCfWedDlvqlkapdleg 40 
                                    + +We+Dl++ +  +le+
  gi|116753353|ref|YP_842471.1| 110 IAIWENDLTEEH-THLEV 126
                                    779****99744.44555 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00013
                  Cys_rich_CPCC   3 CpcCgyltleeeegsydiCpvCfWedDlv 31 
                                    C  Cg + +++++ ++d+CpvC  + D +
  gi|116753353|ref|YP_842471.1| 546 CSKCGVIAIHDRRRNMDLCPVCGTDTDIY 574
                                    999******9999*********9887765 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 ?   11.7   2.1    0.0001      0.23      16      40 .]     544     568 ..     540     568 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0001
                  Auto_anti-p27  16 etCpvCgvPLmrdrkggkvyCvaCd 40 
                                     +C++Cgv+   dr ++  +C++C+
  gi|116753353|ref|YP_842471.1| 544 LVCSKCGVIAIHDRRRNMDLCPVCG 568
                                    68************65666*****6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (604 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); 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:                         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 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 3964.87
//
Query:       gi|116753354|ref|YP_842472.1|  [L=876]
Description: DNA-directed RNA polymerase subunit A' [Methanosaeta thermophila PT]
Scores for complete 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-104  349.9   0.0   3.3e-104  348.6   0.0    1.6  2  RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
    5.5e-72  241.4   0.2    8.5e-72  240.8   0.2    1.3  1  RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
    2.9e-33  115.0   0.0      5e-33  114.2   0.0    1.4  1  RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
    2.4e-32  111.1   0.0    4.8e-32  110.1   0.0    1.5  1  RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4
    2.5e-28   99.3   0.0    3.8e-28   98.7   0.0    1.3  1  RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
  ------ inclusion threshold ------
      0.029   14.3   0.0      0.056   13.3   0.0    1.4  1  TraB            TraB family
       0.14   11.8   0.0       0.26   10.9   0.0    1.3  1  DUF1287         Domain of unknown function (DUF1287)


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 !  348.6   0.0  1.3e-107  3.3e-104       2     312 .]       5     309 ..       4     309 .. 0.93
   2 ?   -2.0   0.0      0.69   1.8e+03     153     194 ..     465     531 ..     415     542 .. 0.74

  Alignments for each domain:
  == domain 1  score: 348.6 bits;  conditional E-value: 1.3e-107
                                    E---EEEEEE--HHHHHHH-SBB--STTSTCSTSSSSBBSSSSSSSSS-SSSSSTSTTTSSTTTT-----EEEEEECEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_1   2 kkikeiqfgiaspeeirkwSvvevtkaetieekslkPeegGllDerlgtidkdleCetCgkkkkeCeghfGhieLakPvf 81 
                                    k+i +i+fg++sp+e+rk+Svv+v +a+t++++  +P e+Gl+D+rlg+id  l+C+tCg    eC+ghfGhi+L +Pv+
  gi|116753354|ref|YP_842472.1|   5 KRIGKIRFGLISPQEFRKMSVVKVITADTYDDDG-FPIEMGLMDPRLGVIDPGLRCRTCGGRPGECPGHFGHIDLVAPVI 83 
                                    899*****************************95.********************************************* PP

                                    -HHHHHHHHHHCTTCETTTTEBSS-TTSH....HHHHHHCSSSCC....CCHHHHHHHHCCS-BE-SSSSB-EEEEEETT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_1  82 higffklilkilecvckecskllldeekkkllsklkkrekleelk....krlkaieelckkinlcekCgavqpkleeege 157
                                    h+gf kli+kil+ +c+ecskl+l+e +kk + ++  +++le+l     + ++++ +  +k+++c  Cg  +p+ e ++e
  gi|116753354|ref|YP_842472.1|  84 HVGFAKLIRKILRAICRECSKLMLSELEKKEFLRQ--IRTLEDLGqpteDVVNKVFAEARKHKTCPYCG--APQREIKFE 159
                                    **************************977555443..333444433334899999999***********..666666777 PP

                                    EEEEEESSSSTSCEEEE-HHHHHHHHHCSTHHHHHHTTSBTTTB-GGGCCECCEEE--GGGS-BEESSSSSEEBECCCCH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_1 158 klkaalkkskeeekeklsaekvkkllkriededvevlgfkssgsrPewliltvlPVpPpeiRPsvqldggrrsedDltek 237
                                    +  + +++ ++     l+++++++ ++ri+ded+ v+g++++ +rPew iltvlPVpP+++RPs++l++g+rsedDlt+k
  gi|116753354|ref|YP_842472.1| 160 RPLSYIEDGHK-----LTPSDIRDRFERISDEDIMVMGMNPETARPEWTILTVLPVPPVTMRPSITLESGQRSEDDLTHK 234
                                    77777777777.....**************************************************************** PP

                                    HHHHHHHHHHHHHHHHSSSSSTCHHHHHHHHHHHHHHCC-TTSSSSSEEBSTTSSS--THHHHHTSSSSCCCCCT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_1 238 lrdiikrNnrLkkaeeegapeliieeekelLQehvatlfdneisglkpatqkskrplkslsqrLkGKeGrfRgnL 312
                                    l+dii++N+r+++++e+gap+liie+ +elLQ+hv+t++dn +sg++pa+++s+rplk+lsqrLkGKeGrfRg+L
  gi|116753354|ref|YP_842472.1| 235 LVDIIRINQRFQENREAGAPQLIIEDLWELLQYHVTTFLDNTVSGVPPARHRSGRPLKTLSQRLKGKEGRFRGSL 309
                                    *************************************************************************98 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.69
                                    EEETTEEEEEESSSST.........................SCEEEE-HHHHHHHHHCSTHHHHHHT CS
                                    xxxxxxxxxxxxxxxx.........................xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_1 153 eeegeklkaalkkske.........................eekeklsaekvkkllkriededvevl 194
                                    ee   + +  ++ +++                         ++++ l++++++++lk++  +d+ v 
  gi|116753354|ref|YP_842472.1| 465 EEARAEAEILMRVQENilsprfggpiiggihdyvtgsflltHKERRLNKDRLMEVLKKLDISDIPVP 531
                                    4444455555555555666666666666666666677777677899999********9999998775 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 !  240.8   0.2   3.3e-75   8.5e-72       1     166 []     311     477 ..     311     477 .. 0.98

  Alignments for each domain:
  == domain 1  score: 240.8 bits;  conditional E-value: 3.3e-75
                                    SEEESSEEEEEEEEESSS-TTEEEEEHHHHTTSEEEEE-STTTHHHHHHHHHHTTTSSSSEEEEESTTSSEEETTTT-S. CS
                 RNA_pol_Rpb1_2   1 GkrvdysaRsvispdpnlkldevgvPisvakkltvpeivtelnikklrklvengpevyPgasyvkredgsekklkakkr. 79 
                                    Gkrv++saR+visp pnl+++evgvPi+vak ltvp +vt+ ni+ +rk+v++gp+++Pg +yv+r+dg++ k+++ +  
  gi|116753354|ref|YP_842472.1| 311 GKRVNFSARTVISPYPNLSINEVGVPIEVAKELTVPIMVTPKNIEVVRKYVMRGPDNHPGVNYVTRADGRRVKVTERNCq 390
                                    9*************************************************************************999886 PP

                                    CHHCCTTTTSEEEEE--TTSEEEEE-SSTTSGGGEEEEEEEEESSSSEEEEGGGHCCCT--SSS-EEEEE--SSHHHHHH CS
                 RNA_pol_Rpb1_2  80 klakelekgdiverhvkdgdvvllNRqPsLhklsimahrvkvlekktlrlnlsvttayNaDFDGDemnlhlpqseearaE 159
                                    ++a++le+g++v r++ dgd+vl+NRqPsLh++simahrvkv+++kt+rln +v+ +yNaDFDGDemnlh+pq+eearaE
  gi|116753354|ref|YP_842472.1| 391 EVAEQLEVGWKVDRQLADGDIVLFNRQPSLHRMSIMAHRVKVMPYKTFRLNPAVCPPYNADFDGDEMNLHVPQTEEARAE 470
                                    8******************************************************************************* PP

                                    HHHCSBT CS
                 RNA_pol_Rpb1_2 160 aeelllv 166
                                    ae l+ v
  gi|116753354|ref|YP_842472.1| 471 AEILMRV 477
                                    ***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 !  114.2   0.0     2e-36     5e-33       1     156 [.     480     645 ..     480     646 .. 0.93

  Alignments for each domain:
  == domain 1  score: 114.2 bits;  conditional E-value: 2e-36
                                    CSEETTTTEESSS--THHHHHHHHHSSTTEEEEHHHHHHHHHHSSSCCSSSSSSSSSBESS.SEBEEHHHHHHCCCHCCC CS
                 RNA_pol_Rpb1_3   1 nilspqsgkPvigivQDsllGvyllTkedvfidreeaqqllykgvgsdsktvtlrpailkp.kelwtgkqtfsrilpnei 79 
                                    nilsp+ g P+ig ++D ++G++llT+++  ++++  +++l+k + sd +   +++    + ++ wtgkq+fs+ilp+++
  gi|116753354|ref|YP_842472.1| 480 NILSPRFGGPIIGGIHDYVTGSFLLTHKERRLNKDRLMEVLKKLDISDIP---VPAGYDENgDPYWTGKQIFSLILPKDL 556
                                    9*******************************************887544...67777777899**************99 PP

                                    CEEEE.....SSSS........STSEEECSSEEEES--SHHHHSSSSTTSHHHHHHHHCHHHHHHHHHHHHHHHHHHHHH CS
                 RNA_pol_Rpb1_3  80 nyerk.....neek........dgkvlikngelikGvidkkvvgkksqgslihvlakeygiketvrfldslqrlgfkyll 146
                                    n+  k     n++         d +v+i+ng+l+kG+id ++vg + +g++i+ ++key +  +++fld+++ l+ + ++
  gi|116753354|ref|YP_842472.1| 557 NLTFKadfcsNCPVckgedcenDAYVVIRNGVLLKGTIDAEAVG-AFKGKVIDRIIKEYDPGVASQFLDRMTLLALRGIM 635
                                    9999887665444499999999**********************.999******************************** PP

                                    HHCEB-TGGG CS
                 RNA_pol_Rpb1_3 147 qsgftigigD 156
                                     +gf++gi+D
  gi|116753354|ref|YP_842472.1| 636 LAGFSFGISD 645
                                    ********99 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 !  110.1   0.0   1.9e-35   4.8e-32       2     108 .]     672     777 ..     671     777 .. 0.96

  Alignments for each domain:
  == domain 1  score: 110.1 bits;  conditional E-value: 1.9e-35
                                    HHHCTHTCCHHHTTHCHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTTSHHHHHHHCTSSS-HHHHHHHHTB-EEEEBTTB CS
                 RNA_pol_Rpb1_4   2 eeaerygkledlpgksleelfeakinkilnkardkagkiaskslaasNsiliMvksGaKGsiinisqiagclGqqnvegk 81 
                                    e+++  g+le+lpg++lee++e++i++ l kard+ag+ia ++l  +Ns ++M+ sGa+Gs++n++q+a+c+Gqq+v+g+
  gi|116753354|ref|YP_842472.1| 672 EAYRA-GELEPLPGRTLEETLEMRIMQTLGKARDAAGQIAGRYLGLDNSGVVMAVSGARGSMLNLTQMAACVGQQSVRGE 750
                                    55566.9**************************************66********************************* PP

                                    SS--SSTSCSSTTSSSSESSTTTSSEE CS
                 RNA_pol_Rpb1_4  82 ripkgfsgrtlphfkkidespesrGFv 108
                                    ri++g+++rtlphfk+ d ++e++GFv
  gi|116753354|ref|YP_842472.1| 751 RIKRGYTDRTLPHFKRGDLGAEAHGFV 777
                                    **************************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 !   98.7   0.0   1.5e-31   3.8e-28       1      66 [.     784     849 ..     784     875 .. 0.90

  Alignments for each domain:
  == domain 1  score: 98.7 bits;  conditional E-value: 1.5e-31
                                    B--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTEEEETTSEEEETTS-EEESSGGGTS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_5   1 GLkvkefffhtmggReGLiDtAvkTaesGYlqRrlvkaledvvvkyddtvrnsggeivqflygedg 66 
                                    GL+++efffh+ ggReGL+DtA++T++sGYlqRrlv+al+d+ v+yd+tvr++ g ivqf+ygedg
  gi|116753354|ref|YP_842472.1| 784 GLSPTEFFFHAIGGREGLVDTAIRTSQSGYLQRRLVNALQDLEVNYDGTVRETRGMIVQFKYGEDG 849
                                    9****************************************************************8 PP

>> TraB  TraB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.2e-05     0.056     157     238 ..     642     725 ..     625     732 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.2e-05
                           TraB 157 slpdeeqlealeetldele.eakdlleelveaykegdleal..eleaeaeeefpelkevlldeRnrrwaekie.all..k 230
                                    +++de++ ++ +e++++   +ak+++++l+eay++g+le l  +  + +e+    ++++l + R++  a +i+ ++l  +
  gi|116753354|ref|YP_842472.1| 642 GISDEDVPREAAEQIQDVTrSAKESVQRLIEAYRAGELEPLpgR--TLEETLEMRIMQTLGKARDA--AGQIAgRYLglD 717
                                    5999***********9999899*******************653..24444456679999999987..666664344434 PP

                           TraB 231 epgsvfva 238
                                    ++g v+++
  gi|116753354|ref|YP_842472.1| 718 NSGVVMAV 725
                                    44555555 PP

>> DUF1287  Domain of unknown function (DUF1287)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0    0.0001      0.26      79     130 ..     378     429 ..     360     437 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0001
                        DUF1287  79 DfRRvknlevffkrkgasltvskdaedeyqpGdivvfkleekleHigivsdk 130
                                    D RRvk  e   ++ +++l+v  +++++ + Gdiv+f+ + +l+ ++i++++
  gi|116753354|ref|YP_842472.1| 378 DGRRVKVTERNCQEVAEQLEVGWKVDRQLADGDIVLFNRQPSLHRMSIMAHR 429
                                    88*******************999999***********98888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (876 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); 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: 0.68u 0.27s 00:00:00.95 Elapsed: 00:00:00.44
# Mc/sec: 6028.03
//
Query:       gi|116753355|ref|YP_842473.1|  [L=384]
Description: DNA-directed RNA polymerase subunit A'' [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-56  191.1   1.3    3.1e-56  190.8   1.3    1.1  1  RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
  ------ inclusion threshold ------
      0.013   15.9   0.3        1.8    9.1   0.1    2.9  2  Ribosomal_L9_C  Ribosomal protein L9, C-terminal domain
      0.081   12.9   0.2       0.21   11.6   0.2    1.7  1  NAC             NAC domain
        0.1   13.1   0.0         11    6.6   0.0    2.6  2  HTH_26          Cro/C1-type HTH DNA-binding domain


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.8   1.3   6.9e-60   3.1e-56      63     265 ..      47     326 ..      21     328 .. 0.90

  Alignments for each domain:
  == domain 1  score: 190.8 bits;  conditional E-value: 6.9e-60
                                    GGTS...B--TT-BHHHHHHHHHHHHHHCCCSSTTSSTCSSTSSSSSSHHHHHHHHTT-SS-SS-EEEEEB-SSSSSCHH CS
                                    xxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_5  63 gedg...lvepGeavGiiaaQSiGePgTQltlnTFHfaGvasknvtlGvprlkeilnvskniksksltvllvdeeakele 139
                                     ed     vep eavG++aaQSiGePgTQ+t++TFH+aGva+ nvtlG+prl ei+++ k+ +++++t++l++e+a++++
  gi|116753355|ref|YP_842473.1|  47 VEDYehaRVEPCEAVGVVAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIVDARKIPSTPTMTIRLLPEYASDRD 126
                                    333344489*********************************************************************** PP

                                    HCHHHHHHHSE..................................................................... CS
                                    xxxxxxxxxxx..................................................................... RF
                 RNA_pol_Rpb1_5 140 kakkvkkaiek..................................................................... 150
                                     a++v+ aie                                                                      
  gi|116753355|ref|YP_842473.1| 127 MAREVAWAIEAtsilhlgsiatdlaemnvvielnedamaqrkitaedvaeklrdatgltvdqkgntiimapeepsyrell 206
                                    *****9999999999***************************************************************** PP

                                    ............CBTTEEEEEEEEEEEEEEETEEEEEEECS--HHHHTTSTTTBETTTEEESSHHHHHHHHCHHHHHHHH CS
                                    ............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_5 151 ............gikkikrilvkeaekgkeeekelvletegvnlsevlkveevvdageilsndiaeileilgieaarkal 218
                                                g+ +ikr++++     ke  +e+vl teg +l+evl+ e+ vd +++ +n+i+ei+e+lgieaar+a+
  gi|116753355|ref|YP_842473.1| 207 qlverikkvtlkGVDGIKRVVIR-----KEG-DEYVLYTEGSSLKEVLEFEG-VDPTRTKTNNINEICEVLGIEAARNAI 279
                                    *7777777777777777777776.....222.6789****************.*************************** PP

                                    HHHHHHHHHHTTS---HHHHHHHHHHHTTTSS---SSTTCHCCSSSH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_5 219 lkeiqevykvqgvsvndrHlelivdqmtkkgeivavnrsGinkaels 265
                                    ++e +e++++qg++v+ rH++l++d+mt+ g +++++r+G+  ++ s
  gi|116753355|ref|YP_842473.1| 280 INEATETLREQGLQVDVRHIMLVADIMTCDGDVKQIGRHGVSGEKAS 326
                                    ****************************************9887765 PP

>> Ribosomal_L9_C  Ribosomal protein L9, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1   0.00039       1.8      30      53 ..     167     190 ..     143     199 .. 0.74
   2 ?    3.7   0.0     0.019        86      38      68 ..     284     320 ..     280     338 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00039
                                    S---HHHHHHHHHHHT-----GGG CS
                 Ribosomal_L9_C  30 GsVtakdIaealkkklgieidkkk 53 
                                     ++ta+d+ae+l++++g+++d+k 
  gi|116753355|ref|YP_842473.1| 167 RKITAEDVAEKLRDATGLTVDQKG 190
                                    479******************985 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.019
                                    HHHHHHHT-----GGGEE-.......TTT-SBSSEEEE CS
                 Ribosomal_L9_C  38 aealkkklgieidkkkiel.......eepiktlGeyev 68 
                                     e l+++ g+++d ++i l       +  +k++G + v
  gi|116753355|ref|YP_842473.1| 284 TETLREQ-GLQVDVRHIMLvadimtcDGDVKQIGRHGV 320
                                    5789999.**********98888876667999999977 PP

>> NAC  NAC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   4.7e-05      0.21       7      31 ..     211     234 ..     207     237 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.7e-05
                            NAC   7 alkklglkeipgieeVtirksdgkv 31 
                                     +kk  lk ++gi++V+irk+++ +
  gi|116753355|ref|YP_842473.1| 211 RIKKVTLKGVDGIKRVVIRKEGD-E 234
                                    589*****************994.4 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 ?    6.6   0.0    0.0024        11       5      26 ..     163     188 ..     161     208 .. 0.77
   2 ?    3.6   0.0      0.02        88      35      52 ..     255     272 ..     250     275 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0024
                         HTH_26   5 lmadrgitkseLar....gtgisaat 26 
                                    +ma+r+it+ ++a+    +tg++ ++
  gi|116753355|ref|YP_842473.1| 163 AMAQRKITAEDVAEklrdATGLTVDQ 188
                                    8***********97555688887766 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.02
                         HTH_26  35 pervsldtLdkiCdaLgc 52 
                                    p+r +++ ++ iC++Lg+
  gi|116753355|ref|YP_842473.1| 255 PTRTKTNNINEICEVLGI 272
                                    789999**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); 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: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2786.24
//
Query:       gi|116753356|ref|YP_842474.1|  [L=103]
Description: ribosomal protein L7Ae/L30e/S12e/Gadd45 [Methanosaeta thermophila PT]
Scores for complete 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   53.9   0.0    1.3e-14   53.7   0.0    1.1  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 !   53.7   0.0   7.2e-19   1.3e-14       3      94 ..       4      91 ..       2      92 .. 0.95

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 7.2e-19
                                   HHHHHHHHHHHTEEEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHHHTTEEEEEESCHHHHHHHTTSSSECSEEE CS
                 Ribosomal_L7Ae  3 ieevlkkakkagklvlGlkevtkalergeaklvilAedvepeekkkllealckekevpyvkvkskkeLGelvgkkrpvsala 84
                                   i ++l+ + ++gk+vlG + ++ +  rg akl+i A+d+++   +k     + e +v+ ++ ++  +LG+++gk++pv+ala
  gi|116753356|ref|YP_842474.1|  4 IDRALRSSIRTGKVVLGSNSSLEHGLRGDAKLIIYASDCPEHVRQK---LRSLEVPVYAYQSSG-RDLGAACGKPFPVAALA 81
                                   677899999**********************************999...7788********999.***************** PP

                                   EEESTTTHHH CS
                 Ribosomal_L7Ae 85 ikdegdskdl 94
                                   ++++gds+++
  gi|116753356|ref|YP_842474.1| 82 VIEPGDSEIM 91
                                   *******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 787.13
//
Query:       gi|116753357|ref|YP_842475.1|  [L=143]
Description: NusA family protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-21   74.4   4.7      6e-15   54.8   1.2    2.1  2  KH_2      KH domain
    4.3e-17   61.9   1.0    4.3e-17   61.9   1.0    2.1  2  KH_5      NusA-like KH domain
    3.5e-10   39.6   1.0    2.6e-05   24.0   0.1    2.2  2  KH_4      KH domain
    9.1e-05   22.2   2.2      0.001   18.8   0.5    2.3  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 !   54.8   1.2   1.3e-18     6e-15       2      64 ..      12      74 ..      11      78 .. 0.95
   2 !   21.3   0.1   3.8e-08   0.00017       2      56 ..      77     133 ..      76     138 .. 0.80

  Alignments for each domain:
  == domain 1  score: 54.8 bits;  conditional E-value: 1.3e-18
                                   HHHHHHHHTECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTT CS
                           KH_2  2 ipeslaveikkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegk 64
                                   ++++l++++++  +++++++++++r+i+vi+++ +g +IG++Gsni++++k ++k+ie++e++
  gi|116753357|ref|YP_842475.1| 12 RYIALFESLTGGMARDCIVDEENDRIIFVIQKGDMGAAIGRKGSNINRVKKSIGKQIEIVEYS 74
                                   5789*******************************************************9987 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 3.8e-08
                                    HHHHHHHHTECETEEEEEEECCS.CEEEEEEEESC.HHHHHTGGGHHHHHHHHHHHH CS
                           KH_2   2 ipeslaveikkagvskveIerta.nrviiviresq.pgivIGkgGsnikkigkelrk 56 
                                    ++e+l++ ++ a+v+++ + +++ +r+ +v+ +++ +gi+IG+ G+ni k +  +++
  gi|116753357|ref|YP_842475.1|  77 VKEFLQNLFQPADVKNIMVVNKNnKRLAYVEVANKdKGIAIGRDGRNILKAKMLAQR 133
                                    5688888889999666666664449***99987654*************99999886 PP

>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.9   1.0   9.6e-21   4.3e-17       2      68 ..      34      94 ..      33      95 .. 0.97
   2 ?    1.1   0.2     0.097   4.4e+02      11      31 ..     110     125 ..      94     129 .. 0.77

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 9.6e-21
                           KH_5  2 GertkvaVkshnpnvdpvGaivgkkGsrikavsseLkgekidvvewseDlaefianalsPaevlsVk 68
                                   ++r+++++++++     +Ga++g+kGs+i+ v++ + g++i++ve+s+D++ef +n+++Pa+v+++ 
  gi|116753357|ref|YP_842475.1| 34 NDRIIFVIQKGD-----MGAAIGRKGSNINRVKKSI-GKQIEIVEYSDDVKEFLQNLFQPADVKNIM 94
                                   689*********.....*******************.***************************996 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.097
                           KH_5  11 shnpnvdpvGaivgkkGsrik 31 
                                    +++      G ++g+ G++i 
  gi|116753357|ref|YP_842475.1| 110 NKD-----KGIAIGRDGRNIL 125
                                    444.....79999***99985 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   5.7e-06     0.026      22      52 ..      28      58 ..      16      61 .. 0.88
   2 !   24.0   0.1   5.7e-09   2.6e-05       2      51 ..      75     124 ..      74     131 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.7e-06
                           KH_4 22 eeeeeeeveielnvegedlGrvIGkrGrtld 52
                                   +  +ee+++i   +++ d+G  IG++G +++
  gi|116753357|ref|YP_842475.1| 28 CIVDEENDRIIFVIQKGDMGAAIGRKGSNIN 58
                                   556778999******************9986 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 5.7e-09
                           KH_4   2 elvedilkalvddpeevevtee.eeeeeveielnvegedlGrvIGkrGrtl 51 
                                    + v+++l++l+ +p++v+  +  ++++++   ++v+ +d+G+ IG++Gr++
  gi|116753357|ref|YP_842475.1|  75 DDVKEFLQNLF-QPADVKNIMVvNKNNKRLAYVEVANKDKGIAIGRDGRNI 124
                                    5799*******.5776665554499999999******************87 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.5   2.3e-07     0.001       4      40 ..      39      76 ..      29      99 .. 0.85
   2 ?    2.8   0.0     0.023     1e+02       4      22 ..     106     124 ..     104     126 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.3e-07
                                   EEEGGGHHHHHHTGGGHHHHHHHHHH.T-EEEEES.STT CS
                           KH_1  4 ilvPsslvgriIGkgGsnIkeIreet.gakIkvpk.sed 40
                                   + + +  +g+ IG++GsnI++ ++ + g +I +++ s+d
  gi|116753357|ref|YP_842475.1| 39 FVIQKGDMGAAIGRKGSNINRVKK-SiGKQIEIVEySDD 76
                                   56777889****************.99*****9966655 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.023
                                    EEEGGGHHHHHHTGGGHHH CS
                           KH_1   4 ilvPsslvgriIGkgGsnI 22 
                                    ++v ++  g  IG+ G+nI
  gi|116753357|ref|YP_842475.1| 106 VEVANKDKGIAIGRDGRNI 124
                                    67888889999*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       699  (0.0389871); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); 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: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1049.33
//
Query:       gi|116753358|ref|YP_842476.1|  [L=140]
Description: 30S ribosomal protein S12P [Methanosaeta thermophila PT]
Scores for complete 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-47  159.2   0.6      3e-47  159.0   0.6    1.0  1  Ribosom_S12_S23  Ribosomal protein S12/S23


Domain annotation for each model (and alignments):
>> Ribosom_S12_S23  Ribosomal protein S12/S23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.0   0.6   1.7e-51     3e-47       1     113 [.      25     138 ..      25     139 .. 0.97

  Alignments for each domain:
  == domain 1  score: 159.0 bits;  conditional E-value: 1.7e-51
                                    --------S-TSSTTSSEEEEEEEEEEEE---TT--S-EEEEEEEET.TSEEEEEEE-SSS..----TT-EEEEEE--.. CS
                Ribosom_S12_S23   1 rkelrkktksdalegapqkrGvvlekvtveakkPnsAlRkvvrvrLikngkevtafipgegalnfldEhdevlvrGirrk 80 
                                    r++l++k k+d+l gap +rG+vlekv+veak+PnsA+Rk+vr++Likng++vtaf+pg+ga+ f+dEhdev+v+ i+++
  gi|116753358|ref|YP_842476.1|  25 RRALGLKVKADPLGGAPRARGIVLEKVGVEAKQPNSAIRKCVRIQLIKNGRQVTAFCPGDGAIGFIDEHDEVVVERIGGR 104
                                    688999*********************************************************************99988 PP

                                    ....BTTSTTEEEEBETS---TSSSTTTTT---- CS
                Ribosom_S12_S23  81 .gkavkDlpGvrykvvkvagvslkalskykkekp 113
                                     g++++D+pGvr+kvv v++vsl++++ ++kekp
  gi|116753358|ref|YP_842476.1| 105 mGRSMGDIPGVRFKVVAVNNVSLEEMVSGRKEKP 138
                                    8*******************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1043.09
//
Query:       gi|116753359|ref|YP_842477.1|  [L=185]
Description: 30S ribosomal protein S7P [Methanosaeta thermophila PT]
Scores for complete 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-40  137.6   3.5    2.9e-40  137.3   3.5    1.0  1  Ribosomal_S7  Ribosomal protein S7p/S5e


Domain annotation for each model (and alignments):
>> Ribosomal_S7  Ribosomal protein S7p/S5e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.3   3.5   1.6e-44   2.9e-40      16     149 .]      43     185 .]      32     185 .] 0.95

  Alignments for each domain:
  == domain 1  score: 137.3 bits;  conditional E-value: 1.6e-44
                                    SSTTSBHHHHHHHHHSB....TTBHHHHHHHHHHHHHHHHHHHSS-HHHHHHHHHHHCS-SEEEEEEBSSSSBEEEEEEE CS
                   Ribosomal_S7  16 pkynselveklinklmk....dGkkslAekivygaldiieektkkdplevleeAlenvkPrvevksrrvGGatyqvpvev 91 
                                    +k + ++ve+link+m+    +G+k++A++iv++a+dii+++tk++pl+vl++A++n+ Pr+ev ++++GG+t++ +v+ 
  gi|116753359|ref|YP_842477.1|  43 KKSELHVVERLINKMMRkeknTGQKQIAYRIVEEAFDIIHSRTKENPLSVLVRAISNAGPREEVVRLKYGGITVPKAVDT 122
                                    347789**************9*********************************************************** PP

                                    -HHHHHHHHHHHHHHHH...STSSSS-HHHHHHHHHHHHHTT-..SHHHHHHHHHHHHHHHTG CS
                   Ribosomal_S7  92 rpkRrqalAlrwiieaa...rkrkeksmaekLaeElidAaege..gaavkkreethrmAeanr 149
                                    +p+Rr+++Al+ i+++a   ++++ +s++++La+E+i+Aa+ +  + av++++ ++r+A+a+r
  gi|116753359|ref|YP_842477.1| 123 APQRRVDTALMLIAKGAwqaSFKSRRSIQNCLADEIIAAANYDvkSFAVSRKDSIERVAKAAR 185
                                    ****************9999999*******************999****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       782  (0.0436165); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1378.41
//
Query:       gi|116753360|ref|YP_842478.1|  [L=238]
Description: formate dehydrogenase family accessory protein FdhD [Methanosaeta thermophila PT]
Scores for complete 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-58  196.0   0.8    1.2e-55  188.8   0.8    2.0  1  FdhD-NarQ  FdhD/NarQ family


Domain annotation for each model (and alignments):
>> FdhD-NarQ  FdhD/NarQ family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.8   0.8   6.6e-60   1.2e-55       1     236 [.      18     228 ..      18     229 .. 0.91

  Alignments for each domain:
  == domain 1  score: 188.8 bits;  conditional E-value: 6.6e-60
                                    E--EEEEEEETTEEEEEEEE-SSSHHHHHHHHHHHCTS--SGGGEEEEEEETTTEEEE-S.........----------- CS
                      FdhD-NarQ   1 veEepltivvngrelatlmatpadleelalGfllsegliesaediesievdedeasvavatrakaedkeerrtakrvvts 80 
                                    +eE++l++++ng  l  ++ +p + +e+++G+llseg++ + edi++i+++ + a+v++++++ +     +rt k++v+s
  gi|116753360|ref|YP_842478.1|  18 AEERQLELRINGDLLRRVTLSPCHIREFVVGHLLSEGYMGALEDIAAIHIEGHLADVTLRPACDQ-----KRTEKHTVHS 92 
                                    58***************************************************999999976632.....3333223332 PP

                                    ----.---...--H-----------EEGGGHHHHHHHHHTS-SHHHHHS--EEEEEEE.TTEEEEEEEESSHHHHHHHHH CS
                      FdhD-NarQ  81 gCglcgkesleelletlelpesdlklsaeallrlmdalrekqelfketggvHaaalfdadgellavreDvGRHnAlDkvi 160
                                                       + + l +++++++r+m+ l + ++ ++ tgg+H a++f  ++    ++eD+GRHnA+Dk+i
  gi|116753360|ref|YP_842478.1|  93 EK-----------------T-EGLAVRTDTVFRAMRMLLD-SDAHRITGGFHRAGVFC-EDGTAWMAEDIGRHNAMDKAI 152
                                    22.................2.368999*********9997.6779************9.667999*************** PP

                                    HHHHT.TSS-SSSEEEESS-B-HHHHHHHHHHT-SEEEESS-B-HHHHHHHHHHT-EEEEEEETTEEEEEE-GGGE CS
                      FdhD-NarQ 161 GaallegldlsdkilvvsgRlssemvqKaaragipvlvsvsaptslavelAeeagltlvgfvrgkrfnvYtgaeRi 236
                                    G++lle++dls+ ++v+++R+ss +  K+ ragi++l+s+ aptsla+e+A+++g+tl+gfvr++r+n+Yt++eR+
  gi|116753360|ref|YP_842478.1| 153 GHCLLERIDLSRVFVVMTSRISSGLTLKCSRAGISILASRGAPTSLALEIADAVGITLMGFVREERMNIYTHPERL 228
                                    ***************************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1787.86
//
Query:       gi|116753361|ref|YP_842479.1|  [L=325]
Description: daunorubicin resistance ABC transporter ATPase subunit [Methanosaeta thermophila PT]
Scores for complete 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-34  118.4   0.0    4.8e-34  117.8   0.0    1.3  1  ABC_tran     ABC transporter
    6.6e-13   49.1   0.0    2.3e-07   31.0   0.0    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    7.5e-09   36.2   0.0    1.4e-08   35.3   0.0    1.5  1  DUF4162      Domain of unknown function (DUF4162)
    8.3e-05   22.4   0.0       0.11   12.2   0.0    2.1  2  AAA_15       AAA ATPase domain
    0.00018   21.2   0.1    0.00033   20.3   0.1    1.4  1  AAA_29       P-loop containing region of AAA domain
    0.00033   21.2   0.0    0.00053   20.6   0.0    1.3  1  AAA_23       AAA domain
    0.00039   19.9   0.0       0.64    9.4   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
     0.0026   18.2   0.1      0.038   14.4   0.1    2.6  1  AAA          ATPase family associated with various cellular a
  ------ inclusion threshold ------
      0.011   16.1   0.0      0.027   14.8   0.0    1.6  1  AAA_16       AAA ATPase domain
      0.044   12.8   0.1      0.071   12.1   0.1    1.3  1  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
      0.073   13.0   0.0       0.14   12.0   0.0    1.4  1  RsgA_GTPase  RsgA GTPase
       0.12   12.7   0.1        0.4   11.0   0.1    2.0  1  AAA_22       AAA domain
       0.14   12.0   0.0       0.26   11.2   0.0    1.3  1  Rad17        Rad17 P-loop domain
       0.15   11.8   0.1       0.28   10.9   0.1    1.4  1  AAA_30       AAA domain
       0.18   10.6   0.0       0.28   10.0   0.0    1.2  1  AAA_PrkA     PrkA AAA domain
       0.43   10.3   1.4        4.3    7.0   0.2    2.4  3  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 !  117.8   0.0   4.3e-37   4.8e-34       2     136 ..      21     163 ..      20     164 .. 0.98

  Alignments for each domain:
  == domain 1  score: 117.8 bits;  conditional E-value: 4.3e-37
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                    ++v+l++k+ge+ +++G+nGaGKSt++k+l+ +l+pt Ge  + g+++ + e+  +r+ igv++q+p+++ +lt+ren  
  gi|116753361|ref|YP_842479.1|  21 DDVNLSVKRGEIFGLLGPNGAGKSTIIKMLTTMLRPTGGEAYVWGHHIVR-ERDAVRSCIGVVFQDPSVDGKLTARENld 99 
                                    89****************************************9******9.9**************************** PP

                                    ...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                               e++++i+++l+ ++l++++d  +    +++SgG+++r+++ar l+ +p +l+lDEpt
  gi|116753361|ref|YP_842479.1| 100 fhgrmygmpgdERKRRIAEVLELVELSDKADVLL----EEFSGGMRRRLEIARGLMHRPHVLFLDEPT 163
                                    ****************************888888....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   6.2e-06    0.0069       2      30 ..      33      55 ..      32      76 .. 0.78
   2 !   31.0   0.0     2e-10   2.3e-07     219     298 ..     111     194 ..      79     198 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6.2e-06
                         AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdve 30
                                    +l GpNg+GKS++++ l  +      ++
  gi|116753361|ref|YP_842479.1| 33 FGLLGPNGAGKSTIIKMLTTM------LR 55
                                   689*************99554......33 PP

  == domain 2  score: 31.0 bits;  conditional E-value: 2e-10
                         AAA_21 219 r.......gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQ 291
                                    +        + ++e +d  ++ + e+S G++r l ++  l  ++    +l++DEp +gL+ +  r +++ +++l+++++ 
  gi|116753361|ref|YP_842479.1| 111 ErkrriaeVLELVELSDKADVLLEEFSGGMRRRLEIARGLMHRP---HVLFLDEPTLGLDTQTRRYIWDYIRDLNKEDVT 187
                                    03334444778889999999**************9999999999...89******************************* PP

                         AAA_21 292 viltTHS 298
                                    v++tTH 
  gi|116753361|ref|YP_842479.1| 188 VVITTHY 194
                                    ******5 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.0   1.3e-11   1.4e-08       5      81 .]     221     305 ..     218     305 .. 0.74

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 1.3e-11
                                    HHHTTS-SSEEEEE..-------.....--.-EEEE-TTS-EEEEE--.-----------.----EEEEEEEE---HHHH CS
                        DUF4162   5 eiKrsygknrieve..adaeellee...pg.veeveeeggelelkled.eeaanellkal.tsgveirsFeeeePsLndI 76 
                                     +K+ +g++++++e  ++ e l+++    + v++ +  +g+++l +++ ++  +e+  a+ ++gv+i+s++++eP+L+d+
  gi|116753361|ref|YP_842479.1| 221 SLKSMIGTDTLTLEvsDGLERLRDLlleFSwVQSFDASNGYVRLSVDSaQSRIPEVVLAAcRAGVQIKSVSVHEPTLEDV 300
                                    79999*******99953344444443223336666777799******765555555555549****************** PP

                                    HHHHH CS
                        DUF4162  77 Fiekv 81 
                                    F++++
  gi|116753361|ref|YP_842479.1| 301 FLKYT 305
                                    **986 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   9.7e-05      0.11      28      48 ..      35      55 ..      21      79 .. 0.87
   2 !    8.3   0.0    0.0015       1.7     322     364 ..     152     193 ..     109     194 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.7e-05
                         AAA_15 28 liGkNnsGKSsilealdlFln 48
                                   l G+N++GKS+i+++l  +l 
  gi|116753361|ref|YP_842479.1| 35 LLGPNGAGKSTIIKMLTTMLR 55
                                   78**************99987 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0015
                         AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                     ++++l+++EP + L +q  + +++++++l +++   v+itTH
  gi|116753361|ref|YP_842479.1| 152 HRPHVLFLDEPTLGLDTQTRRYIWDYIRDLNKEDV-TVVITTH 193
                                    4689**************************99996.9****** 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 !   20.3   0.1   2.9e-07   0.00033      14      50 ..      22      58 ..      18      62 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.9e-07
                         AAA_29 14 ghtieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                   +  +++++ +++ l Gp+G+GKST++  ++++L p+ 
  gi|116753361|ref|YP_842479.1| 22 DVNLSVKRGEIFGLLGPNGAGKSTIIKMLTTMLRPTG 58
                                   5667777666999*************99999999875 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   4.7e-07   0.00053      20      43 ..      31      54 ..      13     101 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 4.7e-07
                         AAA_23 20 gltlItGpNGaGKTTildAiklaL 43
                                    ++ + GpNGaGK+Ti+  ++ +L
  gi|116753361|ref|YP_842479.1| 31 EIFGLLGPNGAGKSTIIKMLTTML 54
                                   5999**************999887 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0     0.001       1.1      28      44 ..      34      50 ..      21      62 .. 0.84
   2 !    9.4   0.0   0.00057      0.64     124     208 ..     123     201 ..      69     212 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.001
                                   EEEESTTSSHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxx RF
                          SMC_N 28 aivGpNGSGKsnlldAi 44
                                    ++GpNG+GKs ++  +
  gi|116753361|ref|YP_842479.1| 34 GLLGPNGAGKSTIIKML 50
                                   589**********9866 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00057
                                    HHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 124 sellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemle 203
                                     el  +a++  e++SgG +  + +a      + +p+ l+ lDe    LD + ++ + ++++  +k+   +vi+   + +e
  gi|116753361|ref|YP_842479.1| 123 VELSDKADVLLEEFSGGMRRRLEIARG---LMHRPHVLF-LDEPTLGLDTQTRRYIWDYIRDLNKEDVTVVITT--HYME 196
                                    444555566666777777665555543...456676665.8********************9998855555543..3455 PP

                                    C-SCE CS
                                    xxxxx RF
                          SMC_N 204 kadkl 208
                                    +ad+l
  gi|116753361|ref|YP_842479.1| 197 EADNL 201
                                    55554 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 !   14.4   0.1   3.4e-05     0.038       3     120 ..      35     203 ..      33     212 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.4e-05
                                    EESSTTSSHHHHHHHHHHHHTHE......................................................... CS
                            AAA   3 lyGppGtGKTllakavakelgve......................................................... 25 
                                    l Gp G GK++++k + + l  +                                                         
  gi|116753361|ref|YP_842479.1|  35 LLGPNGAGKSTIIKMLTTMLRPTggeayvwghhivrerdavrscigvvfqdpsvdgkltarenldfhgrmygmpgderkr 114
                                    78*****************8433333445555555566666666666666666666666666666666666666666666 PP

                                    .....EEEEETTTCSSS..........STTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHH CS
                            AAA  26 .....fleisgsellsk..........yvgesekkirelfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqL 89 
                                         +          +          +++e +  +r  ++ a+    +p++lf+DE      ++          +   +
  gi|116753361|ref|YP_842479.1| 115 riaevL----------ElvelsdkadvLLEEFSGGMRRRLEIARGLMhRPHVLFLDEPTLGLDTQ----------TRRYI 174
                                    665542..........0444444444499999999999999998888899*******87777777..........77888 PP

                                    HHHHHHTTTSSSTEEEEEEESSGGGSTHHHH CS
                            AAA  90 lteldgvkkkeskvivigatnrpdkldpall 120
                                       + +++k  ++v+v+++t+++++ d+   
  gi|116753361|ref|YP_842479.1| 175 WDYIRDLNK--EDVTVVITTHYMEEADNLCN 203
                                    888888888..47999999999998887665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   2.4e-05     0.027      24      76 ..      30      83 ..      19     164 .. 0.51

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.4e-05
                         AAA_16 24 pelvllsGesGvGKsslvrellralekdggif.lrgkcdqlesaipysalaqal 76
                                   +e+  l G+ G GKs+++++l + l+ +gg + ++g+    e+++ +s +  ++
  gi|116753361|ref|YP_842479.1| 30 GEIFGLLGPNGAGKSTIIKMLTTMLRPTGGEAyVWGHHIVRERDAVRSCIGVVF 83
                                   478889****************99999975545888888886664443333333 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 ?   12.1   0.1   6.4e-05     0.071      28      58 ..      29      59 ..      19      64 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.4e-05
                                   -SEEEEEEE-TTSSHHHHHHHHHHHHHCTT- CS
                           MeaB 28 raqvvGltGvPGaGkstlvealglelrrrGk 58
                                   r +  Gl G  GaGkst+++ l++ lr  G 
  gi|116753361|ref|YP_842479.1| 29 RGEIFGLLGPNGAGKSTIIKMLTTMLRPTGG 59
                                   67889*********************98885 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00013      0.14      98     122 ..      29      53 ..      14      76 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                                    TTSEEEEECSTTSSHHHHHHHHCTT CS
                    RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpe 122
                                    ++++  l+G+ G+GKSt+i++l+  
  gi|116753361|ref|YP_842479.1|  29 RGEIFGLLGPNGAGKSTIIKMLTTM 53 
                                    3488899*************99865 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   0.00035       0.4      10      38 ..      35      77 ..      27     209 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00035
                         AAA_22 10 vtGesGtGKTtllrrlleqldeeakaee................e 38
                                   + G+ G+GK+t +++l+  l       e                 
  gi|116753361|ref|YP_842479.1| 35 LLGPNGAGKSTIIKMLTTMLRPTGG--EayvwghhivrerdavrS 77
                                   78***************99843222..144666666655555554 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00023      0.26      42      69 ..      27      54 ..      17      62 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00023
                          Rad17 42 srkkriLLisGPsGCgkstvvkvLskel 69
                                    ++ +i  + GP G gkst++k+L+  l
  gi|116753361|ref|YP_842479.1| 27 VKRGEIFGLLGPNGAGKSTIIKMLTTML 54
                                   4555688999**************9776 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00025      0.28      20      47 ..      32      59 ..      23      70 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00025
                         AAA_30 20 vavltGpAGtGKttalkalreaweaagg 47
                                   +  l Gp G+GK+t++k l+ +++  gg
  gi|116753361|ref|YP_842479.1| 32 IFGLLGPNGAGKSTIIKMLTTMLRPTGG 59
                                   67789***************99988864 PP

>> AAA_PrkA  PrkA AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00025      0.28      88     114 ..      30      56 ..      16      73 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00025
                       AAA_PrkA  88 kqilyllGPvggGksslverlkkllea 114
                                     +i+ llGP g+Gks+++++l ++l  
  gi|116753361|ref|YP_842479.1|  30 GEIFGLLGPNGAGKSTIIKMLTTMLRP 56 
                                    47889****************998875 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.2    0.0038       4.3       6      22 ..      34      50 ..      30      63 .. 0.86
   2 ?    1.2   0.1      0.23   2.5e+02     108     137 ..     171     200 ..     168     213 .. 0.81
   3 ?   -1.8   0.0       1.9   2.1e+03      24      73 ..     211     268 ..     192     283 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0038
                         AAA_24  6 liyGpsgiGKTtlakel 22
                                    + Gp+g+GK+t++k+l
  gi|116753361|ref|YP_842479.1| 34 GLLGPNGAGKSTIIKML 50
                                   589************98 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.23
                         AAA_24 108 aeefrrllkklqelrknvifiahektrkde 137
                                    ++ +++++++l++ + +v+++ h  ++ d 
  gi|116753361|ref|YP_842479.1| 171 RRYIWDYIRDLNKEDVTVVITTHYMEEADN 200
                                    5667888888888888*******9999876 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.9
                         AAA_24  24 pkplfidtekGlksldadkfpdie...swedfldevvel.....aaeladyktlviDt 73 
                                     +++ +dt ++lks+ +++  ++e   ++e ++d + e+      ++ ++y  l +D+
  gi|116753361|ref|YP_842479.1| 211 GRIVALDTPMSLKSMIGTDTLTLEvsdGLERLRDLLLEFswvqsFDASNGYVRLSVDS 268
                                    5667778888888888887777766665555555554444445544555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); 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: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 2380.19
//
Query:       gi|116753362|ref|YP_842480.1|  [L=255]
Description: ABC-2 type transporter [Methanosaeta thermophila PT]
Scores for complete 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-36  124.2  19.4    6.1e-36  123.8  19.4    1.2  1  ABC2_membrane    ABC-2 type transporter
    8.4e-15   54.7  19.4    8.4e-15   54.7  19.4    1.4  1  ABC2_membrane_3  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.8  19.4   6.8e-40   6.1e-36       2     208 ..       8     218 ..       7     220 .. 0.93

  Alignments for each domain:
  == domain 1  score: 123.8 bits;  conditional E-value: 6.8e-40
                  ABC2_membrane   2 qikallkreflqrwrdpslgllwrliqplllalvfgtvfgnlg....nsedglnr..pgllffsvlflafsaltsvapvf 75 
                                     i+ l+ re+++++r +s   + +++ p++++ ++gt f+++        d++n+  pg++++++lf +  +++++++++
  gi|116753362|ref|YP_842480.1|   8 AIYSLWLREMIRFFRLKSRV-VGSIAPPFFFLAFLGTGFSGMAsrvpAGVDYINYlaPGIIGMTLLFSS--TFAGMSVLW 84 
                                    6899*************888.*******************9665333455555559*************..9999999** PP

                  ABC2_membrane  76 erergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldls..rf.flflllllltalaasslgllis 152
                                    +re g+l + +v+p+ ++ ++vl+++++ ++ ++lq++i+l+  + + g++++   + +l l+l+++++ +++++gl+++
  gi|116753362|ref|YP_842480.1|  85 DREFGFLREIMVAPV-TRLSIVLGRTAGGVTQAVLQGIIILIPGIAM-GVKIKglTGlLLSLALMVIISATFIGVGLAFA 162
                                    ***************.*******************************.****977446********************** PP

                  ABC2_membrane 153 alapsfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrsn 208
                                    + ++++  ++++++++++p +llsG+++p++++p+ ++ ++y+ Plty+v+alr+ 
  gi|116753362|ref|YP_842480.1| 163 SRMKDMSGFGLIMNFMIFPVFLLSGALFPVQNLPGPVRILSYIDPLTYGVDALRGC 218
                                    *********************************999******************86 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.7  19.4   9.4e-19   8.4e-15     158     345 .]      57     247 ..      53     247 .. 0.88

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 9.4e-19
                ABC2_membrane_3 158 nvasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllill..lafglgipf 235
                                    ++ ++l++ i+ + ++++++f+ +s++ ++e + +  ++v++v++l+++l++  g ++ ++lq ++il+  +a g  + +
  gi|116753362|ref|YP_842480.1|  57 DYINYLAPGIIGMTLLFSSTFAGMSVLWDREFGFLREIMVAPVTRLSIVLGRTAGGVTQAVLQGIIILIpgIAMG--VKI 134
                                    688999996666677778888999************9*******************************9999999..666 PP

                ABC2_membrane_3 236 g...nlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsiiPffapglg 312
                                    +   +l+l l l+++ + ++i +g+++ s +k+++   +++ ++i++ ++++g+lfp+++lp++++++++i P+++  ++
  gi|116753362|ref|YP_842480.1| 135 KgltGLLLSLALMVIISATFIGVGLAFASRMKDMSGFGLIMNFMIFPVFLLSGALFPVQNLPGPVRILSYIDPLTYGVDA 214
                                    622566666677777777888888888888888888888899999999******************************** PP

                ABC2_membrane_3 313 llrlitgdplweillsliilalfavvylllall 345
                                    l   + g++ ++++l+ ++l + ++++++++++
  gi|116753362|ref|YP_842480.1| 215 LRGCLVGANSFPVILDALLLTGCCAATMAIGAY 247
                                    ********99***********999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); 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 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 2020.66
//
Query:       gi|116753363|ref|YP_842481.1|  [L=138]
Description: hypothetical protein Mthe_0038 [Methanosaeta thermophila PT]
Scores for complete 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   32.5   0.0    9.6e-08   32.1   0.0    1.2  1  Crystall  Beta/Gamma crystallin
  ------ inclusion threshold ------
       0.15   12.3   0.0       0.31   11.3   0.0    1.6  1  IL4_i_Ig  Interleukin-4 inducing immunoglobulin-binding domai


Domain annotation for each model (and alignments):
>> Crystall  Beta/Gamma crystallin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0   1.1e-11   9.6e-08       2      82 .]      57     137 ..      56     137 .. 0.88

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 1.1e-11
                                    EEEEEECCCEEEEEEES.STBSTHHHHTSTTC-SEEEEEESEEEEEEETTTEE.EEEEE-SEEESSCCCCTGSSSBS-EE CS
                       Crystall   2 ivlfekenfqGksvels.edcpslqergfeskvsSikVlsGaWvlYekpnfrG.rqylleegeypdlsdwgasndrisSl 79 
                                    +vlf + n +G + ++  +d +   +  f+   +S+ VlsG+W lY +pnf+  +   + +g yp++ d+g   + i+S+
  gi|116753363|ref|YP_842481.1|  57 AVLFADANQRGVHKHIFeSDADVGADIAFNATPRSMVVLSGVWRLYREPNFQSpYEAEFGPGIYPSIADYGI--NVIGSM 134
                                    689********8777664889999999************************974567788*********995..899999 PP

                                    EEE CS
                       Crystall  80 rpi 82 
                                    ++i
  gi|116753363|ref|YP_842481.1| 135 KRI 137
                                    997 PP

>> IL4_i_Ig  Interleukin-4 inducing immunoglobulin-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   3.5e-05      0.31       4      85 ..      59     135 ..      57     138 .] 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.5e-05
                                    EESSGGG-S-EEEE-S-BS--SS..-B--SEEE----------EEEEEESSSTT-SSEEE.EETT-EES-GGGSS-S-B- CS
                       IL4_i_Ig   4 lYseanerGswsdicdsnellspllvwttrsvCapenqdskreryWllyeqpeftGryil.lgpgeCiddvrkyglksis 82 
                                    l+ +an+rG +  i++s   +   +++++    +p       + +W+ly +p+f+ +y + +gpg     +  yg++ i+
  gi|116753363|ref|YP_842481.1|  59 LFADANQRGVHKHIFESDADVGADIAFNA----TPRS-MVVLSGVWRLYREPNFQSPYEAeFGPG-IYPSIADYGINVIG 132
                                    78889999999999999999888666654....2332.4455679************97614444.55688999999999 PP

                                    EEE CS
                       IL4_i_Ig  83 sil 85 
                                    s++
  gi|116753363|ref|YP_842481.1| 133 SMK 135
                                    886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); 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: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1038.44
//
Query:       gi|116753364|ref|YP_842482.1|  [L=135]
Description: hypothetical protein Mthe_0039 [Methanosaeta thermophila PT]
Scores for complete 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-60  200.8   0.9    5.8e-60  200.7   0.9    1.0  1  DUF1699    Protein of unknown function (DUF1699)
     0.0013   18.8   1.3      0.061   13.3   1.3    2.1  1  IMS        impB/mucB/samB family
  ------ inclusion threshold ------
       0.14   12.6   0.4       0.25   11.8   0.2    1.9  2  Rep_fac_C  Replication factor C C-terminal domain


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 !  200.7   0.9   9.7e-64   5.8e-60       1     130 []       1     130 [.       1     130 [. 0.99

  Alignments for each domain:
  == domain 1  score: 200.7 bits;  conditional E-value: 9.7e-64
                        DUF1699   1 mkirvvsskeeietlnenekivHlafrpsntdilslvkkcpklkaiqvpeSykktlsksakmfleiqgiellegdvwghr 80 
                                    m++rvvssk+ei++ln+ne++vHlafr+sn+d+++lv++cp+lka+q+p+Sy++t+sk+a++fle+qgie+++gdvwghr
  gi|116753364|ref|YP_842482.1|   1 MRLRVVSSKKEISDLNRNEQVVHLAFRASNMDVMNLVRTCPRLKAVQIPPSYYQTMSKAAQQFLELQGIEIIKGDVWGHR 80 
                                    9******************************************************************************* PP

                        DUF1699  81 kdineyyevseevierikelkseglseeeiaeklsketklspdlikfllk 130
                                    kdi+eyy+vse+vi+ri +l++eg+s +e ++k+++etkls+dli++llk
  gi|116753364|ref|YP_842482.1|  81 KDIDEYYSVSEKVIDRIASLMAEGYSIDETVKKVHRETKLSEDLIRYLLK 130
                                    ************************************************86 PP

>> IMS  impB/mucB/samB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   1.3     1e-05     0.061      49     112 ..      29     122 ..      27     133 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1e-05
                                    TTSBHHHHHTTHTT-EEE.................................EEE-HHHHHHHHHHHHHHHHH-S..EEEE CS
                            IMS  49 rgmrikeakklcpdlivv.................................kvdlekyrraskkileilkrfispkveka 95 
                                    ++m + +  + cp l  v                                 + d+++y ++s+k+++ +++  +   e +
  gi|116753364|ref|YP_842482.1|  29 SNMDVMNLVRTCPRLKAVqippsyyqtmskaaqqflelqgieiikgdvwghRKDIDEYYSVSEKVIDRIASL-M--AEGY 105
                                    57888899999999877778889999999999999999999999999999999************9999999.5..69** PP

                                    ETTEEEEE-HHHHHHHH CS
                            IMS  96 siDEayldltgleelae 112
                                    siDE +  + +  +l+e
  gi|116753364|ref|YP_842482.1| 106 SIDETVKKVHRETKLSE 122
                                    ****9988887666555 PP

>> 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 ?   -3.2   0.0         2   1.2e+04      46      62 ..       5      21 ..       4      26 .. 0.60
   2 ?   11.8   0.2   4.2e-05      0.25      19      51 ..      91     122 ..      28     135 .] 0.81

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2
                                   HGCCS..S-HHHHHHHH CS
                      Rep_fac_C 46 vvkeqeelpeaqkleil 62
                                   vv +++e+++  ++e +
  gi|116753364|ref|YP_842482.1|  5 VVSSKKEISDLNRNEQV 21
                                   55555667776666655 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 4.2e-05
                                    HHHHHHHHHHHHHC---HHHHHHHHHHHGCCS. CS
                      Rep_fac_C  19 eeaykklrellvekGysaediltqlhrvvkeqe 51 
                                    e++ + ++  l+++Gys ++ ++++hr  k +e
  gi|116753364|ref|YP_842482.1|  91 EKVIDRIA-SLMAEGYSIDETVKKVHRETKLSE 122
                                    34445587.89999**************98643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 951.86
//
Query:       gi|116753365|ref|YP_842483.1|  [L=157]
Description: hypothetical protein Mthe_0040 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1151.57
//
Query:       gi|116753366|ref|YP_842484.1|  [L=231]
Description: triosephosphate isomerase [Methanosaeta thermophila PT]
Scores for complete 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   47.6   0.0    1.6e-12   47.3   0.0    1.2  1  TIM       Triosephosphate isomerase
    0.00051   19.4   0.4    0.00051   19.4   0.4    1.7  2  ThiG      Thiazole biosynthesis protein ThiG
     0.0055   16.1   1.6     0.0055   16.1   1.6    1.8  2  NMO       Nitronate monooxygenase
  ------ inclusion threshold ------
      0.032   13.3   2.0      0.062   12.3   2.0    1.4  1  FMN_dh    FMN-dependent dehydrogenase
      0.071   12.3   0.0        0.1   11.7   0.0    1.5  1  IGPS      Indole-3-glycerol phosphate synthase


Domain annotation for each model (and alignments):
>> TIM  Triosephosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   0.0   4.5e-16   1.6e-12       2     132 ..      14     139 ..      13     178 .. 0.88

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 4.5e-16
                                    EEEEE-TBTS..-HHHHHHHHHHHHHHCHGCTSEEEEE--GGGHHHHHHHHTTSSECEEES--BSSSSBS-TT--BHHHH CS
                            TIM   2 liagNwKmnk..tleeakellkklkaklkeekvevviappflylekvkklleesklklgaqnvsaeksGafTGevsaeml 79 
                                    li+ N+K++   t ++a +l k +++  +e  v++++ap++  +++v+++++   + ++aq v+    G+fTG ++a+ +
  gi|116753366|ref|YP_842484.1|  14 LIVLNFKTYReaTGDSAVALSKICESIASEYGVDIAVAPQAADIRAVASAVS---IPVYAQHVDGVGFGSFTGHITAASV 90 
                                    6888***9983344455555555666666699**************999996...************************* PP

                                    HHTT-SEEEES-HHHHHHST--HHHHHHHHHHHHHTT-EEEEEE---HHHHHT CS
                            TIM  80 kdlgvkyviiGHsErrqlfkEtdelvakKvkaalksglkpilCvGEtleerea 132
                                    k +g++  +i HsErr  + +    +++ ++a+ ++gl+ i+C  +  ++r a
  gi|116753366|ref|YP_842484.1|  91 KAAGASGSLINHSERRLRLAD----IEASLRACRSEGLTSIICTNNVATTRAA 139
                                    ****************98865....6788999***********9998888766 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       0.5   1.8e+03     209     226 ..      53      70 ..      32     103 .. 0.67
   2 !   19.4   0.4   1.4e-07   0.00051     173     214 ..     180     221 ..     154     231 .] 0.86

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.5
                                    TSSSHHHHHHHHHHHHHH CS
                           ThiG 209 eakdpvamArafklavea 226
                                    +a+d+ a+A+a++  v a
  gi|116753366|ref|YP_842484.1|  53 QAADIRAVASAVSIPVYA 70 
                                    455555555555554444 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 1.4e-07
                                    H-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHH CS
                           ThiG 173 eakvPvivDAGigspsdaaqamelGadavllntavaeakdpv 214
                                    e +v v+  AGi +  d  +a+elGa +vll++ + +akd  
  gi|116753366|ref|YP_842484.1| 180 EKDVGVLCGAGITHGDDLRAAIELGAVGVLLASGIVKAKDQR 221
                                    45899**********************************975 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.2      0.18   6.6e+02     186     198 ..      58      70 ..      27     100 .. 0.77
   2 !   16.1   1.6   1.5e-06    0.0055     134     230 ..     121     219 ..     110     224 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.18
                            NMO 186 pqvldavdiPviA 198
                                      v++av+iPv A
  gi|116753366|ref|YP_842484.1|  58 RAVASAVSIPVYA 70 
                                    4678888888877 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.5e-06
                            NMO 134 eagvvliptissvkearkvearGaDalivqGpeaGGh.qGtpevgdkglfaLvpqvldavd..iPviAaGGiidrrgvaa 210
                                      g+  i+ +  v   r+++a+ +D + v+ pe  G  ++ ++++d + ++   +++ a++  + v+   Gi  + ++ a
  gi|116753366|ref|YP_842484.1| 121 SEGLTSIICTNNVATTRAAAALRPDYVAVEPPELIGSgIP-VSKADPEVVRGSVEAVRAIEkdVGVLCGAGITHGDDLRA 199
                                    5678889999999999**************9997664144.6666555554444444455478***************** PP

                            NMO 211 aLalGAsgvqigtrfLltke 230
                                    a+ lGA gv +++  + +k+
  gi|116753366|ref|YP_842484.1| 200 AIELGAVGVLLASGIVKAKD 219
                                    ************99988887 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   2.0   1.7e-05     0.062     263     303 ..     174     214 ..     164     224 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.7e-05
                                    HHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHH CS
                         FMN_dh 263 eiveavggrievlvDgGirrGsDvlkAlalGAdavllGRpf 303
                                    e v+a+++++ vl+  Gi++G D   A+ lGA +vll+  +
  gi|116753366|ref|YP_842484.1| 174 EAVRAIEKDVGVLCGAGITHGDDLRAAIELGAVGVLLASGI 214
                                    56778888999*************************98665 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.9e-05       0.1     203     254 .]     176     227 ..     106     227 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.9e-05
                                    CHCC-TTSEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC-TTHHHHHHHH CS
                           IGPS 203 aklvpkdvllvaeSGiktredveklkeegvnafLvGeslmrqedvekairel 254
                                    +  ++kdv + +  Gi++ +d+++  e g+ ++L  + +++++d++ka+++l
  gi|116753366|ref|YP_842484.1| 176 VRAIEKDVGVLCGAGITHGDDLRAAIELGAVGVLLASGIVKAKDQRKALEDL 227
                                    5668999****************************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); 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: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1568.14
//
Query:       gi|116753367|ref|YP_842485.1|  [L=90]
Description: acylphosphatase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-23   81.0   0.0    6.8e-23   80.9   0.0    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 !   80.9   0.0   3.8e-27   6.8e-23       1      85 []       5      88 ..       5      88 .. 0.98

  Alignments for each domain:
  == domain 1  score: 80.9 bits;  conditional E-value: 3.8e-27
                Acylphosphatase  1 vrllvtGrVQgvgFRkfvrrlAkelglkGyvrNlsdgsVeivaegeeekvekfleelksgppkarvdeveveeleeeeefkd 82
                                   vr++v+GrVQgvg+R+++  +Ak lg+kG++rNl+ g Ve+v+ege+++v ++l  +ksgp  a v+ +e+ e+e +++ +d
  gi|116753367|ref|YP_842485.1|  5 VRVRVSGRVQGVGYRYYTTTHAKALGVKGWIRNLPGGGVEAVLEGERKSVGELLGLMKSGPSGAMVSGMEIAEVECKGH-DD 85
                                   5899**************************************************************************9.9* PP

                Acylphosphatase 83 Fei 85
                                   F+i
  gi|116753367|ref|YP_842485.1| 86 FKI 88
                                   998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       213  (0.0118802); expected 358.6 (0.02)
Passed bias filter:                      188  (0.0104858); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 639.85
//
Query:       gi|116753368|ref|YP_842486.1|  [L=59]
Description: 4Fe-4S ferredoxin iron-sulfur binding domain-containing protein [Methanosaeta thermophila PT]
Scores for 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-11   42.2  18.1    4.5e-07   29.4   2.6    2.1  2  Fer4        4Fe-4S binding domain
    2.2e-10   40.9  23.6    8.4e-06   26.3  15.7    2.0  3  Fer4_7      4Fe-4S dicluster domain
    1.9e-09   38.3  10.4    2.8e-05   24.9   1.3    2.0  2  Fer4_16     4Fe-4S double cluster binding domain
    5.9e-08   32.7  13.4    8.4e-05   22.6   1.9    2.0  2  Fer4_10     4Fe-4S dicluster domain
      6e-08   32.3  12.0    0.00025   20.9   1.7    2.2  2  Fer4_2      4Fe-4S binding domain
    1.1e-05   25.4  14.2    8.6e-05   22.6  14.7    1.9  2  Fer4_9      4Fe-4S dicluster domain
    1.4e-05   24.9  16.3    0.00013   21.8   2.7    2.2  2  Fer4_6      4Fe-4S binding domain
     0.0002   21.7  11.0      0.013   16.0   2.0    2.1  3  Fer4_8      4Fe-4S dicluster domain
    0.00051   20.3  16.6     0.0017   18.7   3.3    2.4  2  Fer4_4      4Fe-4S binding domain
    0.00053   20.7   4.4    0.00053   20.7   4.4    2.3  2  Fer4_3      4Fe-4S binding domain
     0.0013   18.8  16.1     0.0044   17.1   1.9    2.0  2  Fer4_21     4Fe-4S dicluster domain
     0.0018   18.8  14.7     0.0084   16.6   2.0    2.1  2  Fer4_17     4Fe-4S dicluster domain
     0.0076   16.4   1.6     0.0076   16.4   1.6    2.0  2  Fer4_18     4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.014   15.9   1.7      0.014   15.9   1.7    2.1  2  Fer4_13     4Fe-4S single cluster domain of Ferredoxin I
      0.024   15.3   9.9       0.45   11.3   0.8    2.2  2  Fer4_15     4Fe-4S single cluster domain
      0.059   14.2  16.9       0.16   12.8   3.6    2.1  2  Fer4_22     4Fe-4S dicluster domain
      0.074   12.9   0.4       0.26   11.2   0.3    1.9  2  zf-C2H2_9   C2H2 type zinc-finger (1 copy)
        6.5    6.9  11.3    1.1e+02    3.0  11.3    2.8  1  Fer4_19     Divergent 4Fe-4S mono-cluster


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   7.8   9.3e-07   0.00092       1      20 [.       2      21 ..       2      25 .. 0.91
   2 !   29.4   2.6   4.5e-10   4.5e-07       6      23 ..      35      52 ..      33      53 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 9.3e-07
                                   EEEETTTSSS-THHHHHSTT CS
                           Fer4  1 vvideekCigCGaCvevCPv 20
                                   ++i+   C +CGaCv vCPv
  gi|116753368|ref|YP_842486.1|  2 ITINRYVCGYCGACVGVCPV 21
                                   5799999************8 PP

  == domain 2  score: 29.4 bits;  conditional E-value: 4.5e-10
                                   TTSSS-THHHHHSTTTEE CS
                           Fer4  6 ekCigCGaCvevCPvgAI 23
                                   + Ci CG+Cv+ CP+gA+
  gi|116753368|ref|YP_842486.1| 35 DGCIECGRCVKLCPTGAL 52
                                   67***************8 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   6.8   0.00069      0.69      34      50 ..       5      21 ..       2      23 .. 0.75
   2 !   26.3  15.7   8.4e-09   8.4e-06       2      52 .]       9      51 ..       8      51 .. 0.95
   3 !   24.7   1.0   2.6e-08   2.6e-05       2      22 ..      37      57 ..      36      59 .] 0.90

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00069
                         Fer4_7 34 dpekClgCgaCvavCPt 50
                                   +   C +CgaCv vCP+
  gi|116753368|ref|YP_842486.1|  5 NRYVCGYCGACVGVCPV 21
                                   55669999999999997 PP

  == domain 2  score: 26.3 bits;  conditional E-value: 8.4e-09
                         Fer4_7  2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                   C  CgaCv +Cpv a+el e         +  +++ C+ Cg+Cv+ CPtga
  gi|116753368|ref|YP_842486.1|  9 CGYCGACVGVCPVCALELVET--------WLEVSDGCIECGRCVKLCPTGA 51
                                   999***************775........9999****************98 PP

  == domain 3  score: 24.7 bits;  conditional E-value: 2.6e-08
                         Fer4_7  2 CigCgaCvaaCpvkaieldee 22
                                   Ci+Cg+Cv+ Cp++a++l+e+
  gi|116753368|ref|YP_842486.1| 37 CIECGRCVKLCPTGALSLEEA 57
                                   ****************99886 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 !   18.8   2.2   2.3e-06    0.0023       2      20 ..       9      27 ..       8      34 .. 0.87
   2 !   24.9   1.3   2.9e-08   2.8e-05       2      21 ..      37      56 ..      36      59 .] 0.90

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.3e-06
                        Fer4_16  2 CgtCgkCaevCPtnaikek 20
                                   Cg Cg+C+ vCP+ a++  
  gi|116753368|ref|YP_842486.1|  9 CGYCGACVGVCPVCALELV 27
                                   **************99876 PP

  == domain 2  score: 24.9 bits;  conditional E-value: 2.9e-08
                        Fer4_16  2 CgtCgkCaevCPtnaikekk 21
                                   C++Cg+C++ CPt+a++ ++
  gi|116753368|ref|YP_842486.1| 37 CIECGRCVKLCPTGALSLEE 56
                                   ****************9884 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   3.5   4.7e-06    0.0047       2      22 ..       2      22 ..       1      33 [. 0.86
   2 !   22.6   1.9   8.5e-08   8.4e-05       5      21 ..      33      49 ..      29      59 .] 0.79

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.7e-06
                        Fer4_10  2 vvidddtCirCgkCvkaCPad 22
                                   + i++  C  Cg+Cv +CP++
  gi|116753368|ref|YP_842486.1|  2 ITINRYVCGYCGACVGVCPVC 22
                                   6799999************94 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 8.5e-08
                        Fer4_10  5 dddtCirCgkCvkaCPa 21
                                    +d Ci+Cg+Cvk CP+
  gi|116753368|ref|YP_842486.1| 33 VSDGCIECGRCVKLCPT 49
                                   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 !   16.9   3.1   4.8e-06    0.0048       3      21 ..       2      20 ..       1      21 [. 0.90
   2 !   20.9   1.7   2.5e-07   0.00025       7      22 .]      34      49 ..      30      49 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.8e-06
                         Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                   + +++  C  CgaCv +CP
  gi|116753368|ref|YP_842486.1|  2 ITINRYVCGYCGACVGVCP 20
                                   5789999************ PP

  == domain 2  score: 20.9 bits;  conditional E-value: 2.5e-07
                         Fer4_2  7 tdrCigCgaCvsaCPa 22
                                   +d Ci+Cg Cv+ CP+
  gi|116753368|ref|YP_842486.1| 34 SDGCIECGRCVKLCPT 49
                                   688************7 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   5.5    0.0015       1.5      36      48 ..       9      21 ..       2      25 .. 0.76
   2 !   22.6  14.7   8.6e-08   8.6e-05       2      50 ..       9      51 ..       8      52 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0015
                         Fer4_9 36 CigCgaCveaCpk 48
                                   C  CgaCv +Cp 
  gi|116753368|ref|YP_842486.1|  9 CGYCGACVGVCPV 21
                                   8889999999986 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 8.6e-08
                         Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50
                                   C  CgaCv +Cp ++ +  +   +++        Ci+Cg+Cv+ Cp+ga
  gi|116753368|ref|YP_842486.1|  9 CGYCGACVGVCPVCALELVETWLEVSD------GCIECGRCVKLCPTGA 51
                                   889*********999988777777775......5*************97 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   5.9    0.0015       1.5       2      21 ..       2      21 ..       1      24 [. 0.83
   2 !   21.8   2.7   1.3e-07   0.00013       9      24 .]      37      52 ..      34      52 .. 0.95

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0015
                         Fer4_6  2 veidpdkCigCgdCvrvCPe 21
                                   ++i++  C  Cg+Cv vCP 
  gi|116753368|ref|YP_842486.1|  2 ITINRYVCGYCGACVGVCPV 21
                                   6777778888*********5 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 1.3e-07
                         Fer4_6  9 CigCgdCvrvCPegai 24
                                   Ci Cg+Cv+ CP+ga+
  gi|116753368|ref|YP_842486.1| 37 CIECGRCVKLCPTGAL 52
                                   **************97 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   5.8    0.0012       1.2       5      19 ..       9      23 ..       6      29 .. 0.80
   2 !   16.0   1.8   1.3e-05     0.013      49      63 ..      35      49 ..      23      51 .. 0.61
   3 !   16.0   2.0   1.3e-05     0.013       4      18 ..      36      50 ..      32      58 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0012
                         Fer4_8  5 CieCgaCqsaCpvlr 19
                                   C+ CgaC   Cpv+ 
  gi|116753368|ref|YP_842486.1|  9 CGYCGACVGVCPVCA 23
                                   889999999999875 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.3e-05
                         Fer4_8 49 wsCttcgaCtevCpv 63
                                   + C +cg+C++ Cp+
  gi|116753368|ref|YP_842486.1| 35 DGCIECGRCVKLCPT 49
                                   455555555555554 PP

  == domain 3  score: 16.0 bits;  conditional E-value: 1.3e-05
                         Fer4_8  4 kCieCgaCqsaCpvl 18
                                    CieCg+C + Cp+ 
  gi|116753368|ref|YP_842486.1| 36 GCIECGRCVKLCPTG 50
                                   588888888888864 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   5.5    0.0079       7.9       7      16 ..      12      21 ..       7      27 .. 0.93
   2 !   18.7   3.3   1.7e-06    0.0017       2      17 .]      35      50 ..      34      50 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0079
                         Fer4_4  7 CgsCvaaCPq 16
                                   Cg+Cv +CP+
  gi|116753368|ref|YP_842486.1| 12 CGACVGVCPV 21
                                   *********6 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 1.7e-06
                         Fer4_4  2 erCigCgsCvaaCPqg 17
                                   + Ci+Cg+Cv  CP+g
  gi|116753368|ref|YP_842486.1| 35 DGCIECGRCVKLCPTG 50
                                   78************86 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8  11.6     0.031        30       3      15 .]      11      23 ..       8      23 .. 0.82
   2 !   20.7   4.4   5.3e-07   0.00053       1      15 []      37      51 ..      37      51 .. 0.98

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.031
                         Fer4_3  3 gCgaCvevCPvgA 15
                                    CgaCv vCPv A
  gi|116753368|ref|YP_842486.1| 11 YCGACVGVCPVCA 23
                                   49********965 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 5.3e-07
                         Fer4_3  1 CtgCgaCvevCPvgA 15
                                   C+ Cg+Cv+ CP+gA
  gi|116753368|ref|YP_842486.1| 37 CIECGRCVKLCPTGA 51
                                   **************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 !    7.1   6.8    0.0059       5.9      37      53 ..       5      21 ..       1      27 [. 0.75
   2 !   17.1   1.9   4.4e-06    0.0044       6      22 ..      35      51 ..      31      57 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0059
                        Fer4_21 37 vedeCvGCnlCssvCPv 53
                                       C  C  C+ vCPv
  gi|116753368|ref|YP_842486.1|  5 NRYVCGYCGACVGVCPV 21
                                   55568889999999998 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 4.4e-06
                        Fer4_21  6 dkCigCgkCliaCedts 22
                                   d Ci+Cg+C++ C++++
  gi|116753368|ref|YP_842486.1| 35 DGCIECGRCVKLCPTGA 51
                                   56888888888888654 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   4.8    0.0032       3.2       2      17 ..       9      24 ..       8      30 .. 0.86
   2 !   16.6   2.0   8.4e-06    0.0084      43      59 ..      34      50 ..      26      52 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0032
                        Fer4_17  2 CiqCgyClpeCpsyea 17
                                   C  Cg+C+ +Cp ++ 
  gi|116753368|ref|YP_842486.1|  9 CGYCGACVGVCPVCAL 24
                                   999*********9875 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 8.4e-06
                        Fer4_17 43 aslCieCgeCerkCPqg 59
                                    + CieCg+C++ CP g
  gi|116753368|ref|YP_842486.1| 34 SDGCIECGRCVKLCPTG 50
                                   57899999999999975 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   5.0     0.033        33      61      73 ..       9      21 ..       4      26 .. 0.88
   2 !   16.4   1.6   7.7e-06    0.0076      58      74 ..      34      50 ..      23      57 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.033
                        Fer4_18 61 cidcescvkvcPt 73
                                   c  c++cv vcP+
  gi|116753368|ref|YP_842486.1|  9 CGYCGACVGVCPV 21
                                   889*********7 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 7.7e-06
                        Fer4_18 58 agdcidcescvkvcPtg 74
                                   +  ci+c+ cvk+cPtg
  gi|116753368|ref|YP_842486.1| 34 SDGCIECGRCVKLCPTG 50
                                   567*************8 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   4.0      0.03        30       1      17 [.       4      20 ..       4      22 .. 0.89
   2 ?   15.9   1.7   1.4e-05     0.014       4      17 ..      35      48 ..      33      50 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.03
                        Fer4_13  1 VDrdtCiacgaCvelaP 17
                                   ++r  C  cgaCv ++P
  gi|116753368|ref|YP_842486.1|  4 INRYVCGYCGACVGVCP 20
                                   67888***********9 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.4e-05
                        Fer4_13  4 dtCiacgaCvelaP 17
                                   d Ci+cg Cv+l+P
  gi|116753368|ref|YP_842486.1| 35 DGCIECGRCVKLCP 48
                                   89************ PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   2.6    0.0027       2.7       1      19 [.       2      20 ..       2      26 .. 0.90
   2 ?   11.3   0.8   0.00045      0.45       6      20 ..      35      49 ..      30      56 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0027
                        Fer4_15  1 VvvDrdaCigcglCvaeap 19
                                   ++++r  C  cg+Cv ++p
  gi|116753368|ref|YP_842486.1|  2 ITINRYVCGYCGACVGVCP 20
                                   7999*************98 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00045
                        Fer4_15  6 daCigcglCvaeape 20
                                   d Ci cg+Cv+++p+
  gi|116753368|ref|YP_842486.1| 35 DGCIECGRCVKLCPT 49
                                   88***********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 ?    8.6   4.9    0.0035       3.4       2      16 ..       9      23 ..       8      35 .. 0.85
   2 ?   12.8   3.6   0.00016      0.16      80      94 ..      35      49 ..      27      51 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0035
                        Fer4_22  2 ClsCgaCtlvCptCs 16
                                   C  CgaC  vCp C 
  gi|116753368|ref|YP_842486.1|  9 CGYCGACVGVCPVCA 23
                                   889***********7 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00016
                        Fer4_22 80 sgCvGCgRCieacpv 94
                                    gC+ CgRC++ cp+
  gi|116753368|ref|YP_842486.1| 35 DGCIECGRCVKLCPT 49
                                   578888888888886 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 ?   11.2   0.3   0.00026      0.26       3      19 ..      18      35 ..      16      41 .. 0.86
   2 ?   -1.2   0.0         2   1.9e+03       3      12 ..      46      55 ..      44      58 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00026
                                   B-TTT--B-S.SHHHHHH CS
                      zf-C2H2_9  3 lCPvCevkfn.swkdlse 19
                                   +CPvC +++  +w ++s+
  gi|116753368|ref|YP_842486.1| 18 VCPVCALELVeTWLEVSD 35
                                   7*******977*****98 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2
                                   B-TTT--B-S CS
                      zf-C2H2_9  3 lCPvCevkfn 12
                                   lCP   ++++
  gi|116753368|ref|YP_842486.1| 46 LCPTGALSLE 55
                                   8998777766 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 ?    3.0  11.3      0.11   1.1e+02       8      61 ..       2      54 ..       1      57 [. 0.78

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.11
                        Fer4_19  8 iednrelCihsgnCvkglpevFdpkrkpwikpdeasteeiievverCPSGALsy 61
                                   i+ nr +C   g Cv   p       + w +   + +e   + v+ CP GALs+
  gi|116753368|ref|YP_842486.1|  2 ITINRYVCGYCGACVGVCPVCALELVETWLEVSDGCIE-CGRCVKLCPTGALSL 54
                                   77888899999999987777666666678888777665.6789*********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); 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: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 430.58
//
Query:       gi|116753369|ref|YP_842487.1|  [L=391]
Description: geranylgeranyl reductase [Methanosaeta thermophila PT]
Scores for complete 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   66.6   5.1    2.6e-13   50.0   1.6    3.0  2  FAD_binding_3   FAD binding domain
    3.8e-11   42.7   3.2    1.3e-08   34.4   0.2    2.5  3  FAD_binding_2   FAD binding domain
    4.7e-10   39.4   6.2    2.3e-09   37.1   6.2    1.9  1  FAD_oxidored    FAD dependent oxidoreductase
    9.4e-09   34.8   1.0    0.00035   19.7   0.6    2.2  2  Lycopene_cycl   Lycopene cyclase protein
    8.9e-08   31.2   0.8    1.6e-07   30.4   0.8    1.4  1  HI0933_like     HI0933-like protein
    2.1e-07   30.9   2.0    0.00097   18.8   0.1    2.3  2  DAO             FAD dependent oxidoreductase
    7.4e-07   28.4   0.2      0.023   13.6   0.0    2.2  2  Trp_halogenase  Tryptophan halogenase
    2.2e-06   27.2   2.1    2.2e-06   27.2   2.1    2.1  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    4.1e-06   26.9   0.1      1e-05   25.6   0.1    1.7  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    9.3e-06   25.0   0.1    3.1e-05   23.3   0.1    1.9  1  Thi4            Thi4 family
      3e-05   23.3   1.4    5.6e-05   22.4   0.3    1.9  2  GIDA            Glucose inhibited division protein A
    9.6e-05   21.5   0.0    0.00013   21.0   0.0    1.1  1  CF222           C6orf222, uncharacterised family
     0.0022   17.3   0.1     0.0049   16.2   0.1    1.6  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
     0.0029   18.1   0.3     0.0029   18.1   0.3    2.3  1  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.011   15.6   0.3       0.03   14.2   0.1    1.9  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
      0.016   14.5   0.3      0.028   13.7   0.3    1.4  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
      0.063   13.8   0.0       0.19   12.2   0.0    1.9  2  XdhC_C          XdhC Rossmann domain
       0.19   10.8   0.1       0.29   10.2   0.1    1.2  1  SE              Squalene epoxidase


Domain annotation for each model (and alignments):
>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.0   1.6   2.6e-16   2.6e-13       1     176 [.       2     168 ..       2     183 .. 0.81
   2 !   14.6   0.1   1.5e-05     0.015     282     345 ..     268     333 ..     263     336 .. 0.85

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 2.6e-16
                                    EEEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS.--EEEHHHHHHHHHTT-HHHHHHHSE..ECCCCEEEEE CS
                  FAD_binding_3   1 etdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpr.adglnqrtmellrqlGledrilaega..pnelmgealy 77 
                                    ++dV++VGaGp G m+a+  +e+G +vvlvekr++  +  r a+g+++  + ++        i+ + +   +e+ g  ly
  gi|116753369|ref|YP_842487.1|   2 RCDVVVVGAGPGGSMAAKTAAEKGLKVVLVEKRQEIGDPVRcAEGVSKARLSSM--------IKPDPKwiASEVKGARLY 73 
                                    59*******************************998877764667666666665........443332113667888999 PP

                                    EECCCCCEEEEEHHCH.HCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEE CS
                  FAD_binding_3  78 nelsdtpkaradlele.sspervtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrak 156
                                    ++      +++ ++++ s+ e  +v+  + ++r+L+ +a+++g++v  kt+ + l++ + +v+     +  ge+ +++a+
  gi|116753369|ref|YP_842487.1|  74 AP----DGSNVVMSEDkSGDEVGYVLERKIFDRALAMDAARAGARVMVKTRALDLLRANGSVKGIRAMR-YGEIIDIEAD 148
                                    99....4455555555266666688999999******************************99976666.79999***** PP

                                    EEEE--GTT-HHHHHHTGGE CS
                  FAD_binding_3 157 YlvGaDGgrStvrktlgief 176
                                     ++GaDG+ S+v + +gi+ 
  gi|116753369|ref|YP_842487.1| 149 VVIGADGVESKVGRWAGIDT 168
                                    **************999985 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1.5e-05
                                    EETTEEE-GGGTEEE-STTSHHHHHHHHHHHHHHHHHH.HHHTTSS-GGGGHHHHHH.HHHHHHHH CS
                  FAD_binding_3 282 rkgrvflaGDAaHihpPtgGqGlNtaiqDavnLawkLa.avlkGeAkeelLdtYeee.rravaqav 345
                                      + v+l+GDAa    P +G G+  a+q  +  +   a av +G+ + e L +Ye++ r+ +++++
  gi|116753369|ref|YP_842487.1| 268 IADGVMLVGDAARQSDPITGGGILNAMQAGMIAGEVVAdAVSSGDTGVEGLMAYEKRwRESIGKQI 333
                                    5789*********************************956789***********987355566655 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.2   1.3e-11   1.3e-08       1      49 [.       4      52 ..       4      69 .. 0.90
   2 !    8.6   0.1   0.00084      0.84     148     200 ..     105     155 ..      92     170 .. 0.88
   3 ?   -2.9   0.0       2.6   2.6e+03     129     178 ..     275     319 ..     244     329 .. 0.74

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 1.3e-11
                                   SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-EE-TT CS
                  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgidavl 49
                                   Dv+V+G+G +G +AA +aae+Glkv++vek qe g    +++G   a l
  gi|116753369|ref|YP_842487.1|  4 DVVVVGAGPGGSMAAKTAAEKGLKVVLVEKRQEIGDPVRCAEGVSKARL 52
                                   9********************************9999999999877665 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00084
                                    HHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE--- CS
                  FAD_binding_2 148 vesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatg 200
                                    +  a +ag +++ +t+a++L++ +g v G+ ++  + g++  i+a+ v+ a g
  gi|116753369|ref|YP_842487.1| 105 AMDAARAGARVMVKTRALDLLRANGSVKGIRAM--RYGEIIDIEADVVIGADG 155
                                    445667789************************..**********99998876 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 2.6
                                    STT-.......HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEE CS
                  FAD_binding_2 129 aadarr.etlvtghallarlvesarkagvdfqerteadeLivedgrvtGav 178
                                    ++da r    +tg ++l ++ +++      +  +  ad++   d +v G +
  gi|116753369|ref|YP_842487.1| 275 VGDAARqSDPITGGGILNAMQAGM------IAGEVVADAVSSGDTGVEGLM 319
                                    556666677888888888888877......556666666666666666655 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   6.2   2.3e-12   2.3e-09       1     154 [.       4     166 ..       4     173 .. 0.68

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 2.3e-12
                   FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGll.tsglv.atdignkaeeqvvtgiarefl.erlrqrgga.... 73 
                                    DvvVvG+gp+G +AA +Aa++G kv+Lve+r+ +G  +  +++v  + +  ++ +   + ia e+  +rl + +g+    
  gi|116753369|ref|YP_842487.1|   4 DVVVVGAGPGGSMAAKTAAEKGLKVVLVEKRQEIGDPVrCAEGVsKARLSSMI-KPDPKWIASEVKgARLYAPDGSnvvm 82 
                                    9**********************************643122222022222222.22333344444313444433332332 PP

                   FAD_oxidored  74 rlkkrskwn....tfepevakavleemlaeagvtvllntrlvevekegkriesvtveskegrktirAkvfiDATg.dGdl 148
                                    + +++s+      + e +++ ++l    a+ag +v+ +tr+ +  + ++ ++++++ +  + + i+A+v+i A g + ++
  gi|116753369|ref|YP_842487.1|  83 S-EDKSG-DevgyVLERKIFDRALAMDAARAGARVMVKTRALDLLRANGSVKGIRAMRYGEIIDIEADVVIGADGvESKV 160
                                    1.11222.12345899999999988888999***************9889******66557**********986646666 PP

                   FAD_oxidored 149 aalaGv 154
                                    + +aG+
  gi|116753369|ref|YP_842487.1| 161 GRWAGI 166
                                    666666 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.6   3.5e-07   0.00035       1     142 [.       4     156 ..       4     180 .. 0.65
   2 !   13.5   0.0   2.7e-05     0.027     221     315 ..     236     336 ..     233     381 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3.5e-07
                  Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfpnnyvWsdefedlgaleecv..ehsW.....sgtivylddgk 73 
                                    Dvvv+GaGp g s+Aa+  +a++glkvvl+e  +++   ++ v + e+    +l +++  + +W     +g+++y++dg+
  gi|116753369|ref|YP_842487.1|   4 DVVVVGAGPGG-SMAAKT-AAEKGLKVVLVEKRQEI---GDPVRCAEGVSKARLSSMIkpDPKWiasevKGARLYAPDGS 78 
                                    9********88.666666.6***********99999...67777777777777777763334663333356667778877 PP

                  Lycopene_cycl  74 killg.......raYgrvsskrlkeellerlv.engvklleakvesveeeea.geslvvleggr..kirarlvvdargla 142
                                    ++ ++         Y  +++k + + l+ + +  +++ +++ ++     ++   +   ++  g+   i+a +v+ a g  
  gi|116753369|ref|YP_842487.1|  79 NVVMSedksgdeVGY-VLERKIFDRALAMDAArAGARVMVKTRALDLLRANGsVKGIRAMRYGEiiDIEADVVIGADG-V 156
                                    776665666654444.45777777777777773333445666666666555533334444455556777777777777.3 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 2.7e-05
                  Lycopene_cycl 221 laaylralglkvkevveeEqgviPvtlggslprleqk.vlaiGaaaglvhPaTGYsvarslaeapllasaiaaalres.. 297
                                    l ++  +  + ++++ve   g +Pv   g+++r+ +  v+ +G aa    P TG  + +++++  +  +++a+a  +   
  gi|116753369|ref|YP_842487.1| 236 LLRRFVERRMPEARIVEMVVGGVPV--SGPIERTIADgVMLVGDAARQSDPITGGGILNAMQAGMIAGEVVADAVSSGdt 313
                                    66777778889999***********..88888877777***********************9999888888888875467 PP

                  Lycopene_cycl 298 .....slsarawatlwprerkrq 315
                                          ++++ w+++ +++++r+
  gi|116753369|ref|YP_842487.1| 314 gveglMAYEKRWRESIGKQIARH 336
                                    66666566666666666655554 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.8   1.7e-10   1.6e-07       1      40 [.       3      42 ..       3      47 .. 0.92

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 1.7e-10
                                   -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHH CS
                    HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakklgrKil 40
                                   +dv+v+G+G+ G maA +aa++g +V+l+ek +++g  ++
  gi|116753369|ref|YP_842487.1|  3 CDVVVVGAGPGGSMAAKTAAEKGLKVVLVEKRQEIGDPVR 42
                                   59*********************************98766 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   9.8e-07   0.00097       1      33 [.       4      38 ..       4      72 .. 0.93
   2 !   11.6   0.3   0.00015      0.15     148     350 ..     100     305 ..      89     307 .. 0.55

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 9.8e-07
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                            DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                                   dvv++G+G  G+ +A  +a++g  V+l+ek+ ++g
  gi|116753369|ref|YP_842487.1|  4 DVVVVGAGPGGSMAAKTAAEKGlkVVLVEKRQEIG 38
                                   9******************************9887 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00015
                                    HHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEE.E.EEEEEEE--GGGHH..HHHTTCTTTSEEEE... CS
                            DAO 148 ltaalaraaealGveilegtevtgleeedgkvwgverttp.gen.d.aadavVnaaGawsd..llgllkeldlpisp... 219
                                    + +ala +a+++G+++  +t++ +l + +g v+g+ r+ + ge+ d +ad v+ a G+ s+   +     +d  ++p   
  gi|116753369|ref|YP_842487.1| 100 FDRALAMDAARAGARVMVKTRALDLLRANGSVKGI-RAMRyGEIiDiEADVVIGADGVESKvgRW---AGIDTALKPgdi 175
                                    6689********************9888999****.77777888544667799999999875544...333333333333 PP

                                    .EEEEEEEE.EECCTHSTGSGCSEEEEEEEETTTTEEEEEETTSEEE..EEESSEEETTCSSTSCSHHHHHHHHHHHHHH CS
                            DAO 220 .vrgqvlvl.kplseklvspaailpvpetdddgrgvyvtprkdgrvl..vGgtadeesgdddpevdeedidellealrkl 295
                                     v +q l + k +++    ++  + +     +g++v  +p  +g++l  vG      ++      + + +  l++ ++++
  gi|116753369|ref|YP_842487.1| 176 eVCAQFLLYdKGIDD----EYCEFFLGNELAPGGYVWSFP--KGEHLanVGLGV--IGSRS---EPGAPVKLLRRFVERR 244
                                    377777777222222....232222222344444444444..344442233332..22222...2223356677777777 PP

                                    SGGGCGEEEEEEEEEE.......E.TTSSEEEEEEETEEEEEEEEECTTTHHHHHHHHHHHHH CS
                            DAO 296 fPqlgdvlrkwaGlrp.......l.pdglpligetpgvkglylatGhsghGltlapatGklla 350
                                    +P+ +++++  +G  p       +  dg  l+g + + ++ +   G+  ++++ ++ +G+++a
  gi|116753369|ref|YP_842487.1| 245 MPE-ARIVEMVVGGVPvsgpierTiADGVMLVGDAARQSDPITGGGI-LNAMQAGMIAGEVVA 305
                                    777.5555555554443323222134666666664323233333333.555555555555555 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   4.1e-05      0.04       1      35 [.       4      35 ..       4      43 .. 0.89
   2 !   13.6   0.0   2.3e-05     0.023     142     342 ..      86     296 ..      65     330 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.1e-05
                                   EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SS CS
                 Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlvesee 35
                                   ++v+vG+G+ G++aA + a+ +   l+v lve+ +
  gi|116753369|ref|YP_842487.1|  4 DVVVVGAGPGGSMAAKTAAEKG---LKVVLVEKRQ 35
                                   69*************9999888...99*****864 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 2.3e-05
                                    -B-S--EEEE-HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETT.S-..EEE-SEEEE-SGGG-II..... CS
                 Trp_halogenase 142 lsalsyAyhldaalyakfLrrvaearGvtrvegkvvevqldedgrveslrled.gr..eveadlfiDcsGfrgll..... 213
                                     s+ + +y l+++ +++ L   a ++G +++  + +   l+++g+v+++r    g+   +ead +i + G ++++     
  gi|116753369|ref|YP_842487.1|  86 KSGDEVGYVLERKIFDRALAMDAARAGARVMVKTRALDLLRANGSVKGIRAMRyGEiiDIEADVVIGADGVESKVgrwag 165
                                    55667899**********************999999999999*****99876656522689**********998655555 PP

                                    IIIIT---.EEE-TTT----EEEEEEEE--H---SSEEEEE-SSEEEEEEEETTEEEE.EEEE-TTTS-HHHHHHHHHHH CS
                 Trp_halogenase 214 ieqaLktg.fedwsdvLltdrAlavqveseelvepytrataekaGWtWkiPLqhrlgn.GyvyssahadddeAlaellae 291
                                    i+ aLk g +e  +++Ll d+++      +e  e + +      G +W  P  + l n G+ +  ++  +  A  +ll++
  gi|116753369|ref|YP_842487.1| 166 IDTALKPGdIEVCAQFLLYDKGID-----DEYCEFFLGNELAPGGYVWSFPKGEHLANvGLGVIGSRS-EPGAPVKLLRR 239
                                    999999762666789999999886.....777888888888899999999999999888887776665.55666666666 PP

                                    CT--TTTS-EEEE---EE......ES-SEETTEEE-CCCTEE--CCCS-HHHHHHHH CS
                 Trp_halogenase 292 ldgkleaeprkirfttGr......rkqawvknvvalGlasgfvePlestsihliqaa 342
                                    +  +   e+r +++ +G        +++   +v+++G+a+   +P+ + +i  +++a
  gi|116753369|ref|YP_842487.1| 240 FVERRMPEARIVEMVVGGvpvsgpIERTIADGVMLVGDAARQSDPITGGGILNAMQA 296
                                    666777777999999988888888999999999999999999999999999877665 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 !   27.2   2.1   2.2e-09   2.2e-06       2      33 ..       4      35 ..       3     225 .. 0.80
   2 ?   -1.5   0.0       1.1   1.1e+03     265     279 ..     266     282 ..     247     298 .. 0.71

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 2.2e-09
                                   SEEEE--SHHHHHHHHHHHHHTS-EEEEETTH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlveleg 33
                                   dvvv+G+Gp+G  aa+t+a++g+kv+lve+++
  gi|116753369|ref|YP_842487.1|  4 DVVVVGAGPGGSMAAKTAAEKGLKVVLVEKRQ 35
                                   8***************************7433 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.1
                                    BESSTTEEE-GGGC..T CS
                                    xxxxxxxxxxxxxx..x RF
                    Pyr_redox_2 265 rtnvpgiyaiGDva..g 279
                                    rt  +g+ ++GD a  +
  gi|116753369|ref|YP_842487.1| 266 RTIADGVMLVGDAArqS 282
                                    67799*******99441 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.1     1e-08     1e-05       1      32 [.       7      38 ..       7      57 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1e-08
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSS CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlG 32
                                   +vGaG +G+ aA ++a++g++v+l+ekr+ +G
  gi|116753369|ref|YP_842487.1|  7 VVGAGPGGSMAAKTAAEKGLKVVLVEKRQEIG 38
                                   8******************************9 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.1   3.1e-08   3.1e-05      17      54 ..       2      38 ..       1      45 [. 0.92

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 3.1e-08
                                   EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS-- CS
                           Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailersvspG 54
                                     Dvv+vGaG+ G  aa++ a+k +lkv+++e++  +G
  gi|116753369|ref|YP_842487.1|  2 RCDVVVVGAGPGGSMAAKTAAEK-GLKVVLVEKRQEIG 38
                                   67*********************.********998777 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.3   5.6e-08   5.6e-05       1      36 [.       4      38 ..       4      56 .. 0.86
   2 ?   -1.1   0.0      0.77   7.7e+02      15      46 ..     105     133 ..     102     159 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 5.6e-08
                                   CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT CS
                           GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkldtia 36
                                   dv+V+G+G  G+ AA +aa++G+kv+L+ +k ++i+
  gi|116753369|ref|YP_842487.1|  4 DVVVVGAGPGGSMAAKTAAEKGLKVVLV-EKRQEIG 38
                                   79*************************9.5555554 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.77
                                    HHHHHHTT--EEEEES-GGGTT--SSSSEEE- CS
                           GIDA  15 AlaaarlGakvlLithkldtiaelsCnpsigg 46 
                                    A+ aar+Ga+v+  t  ld +   +   s++g
  gi|116753369|ref|YP_842487.1| 105 AMDAARAGARVMVKTRALDLLRANG---SVKG 133
                                    8899999999999888887765543...3333 PP

>> CF222  C6orf222, uncharacterised family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.3e-07   0.00013     525     583 ..     306     364 ..     299     375 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.3e-07
                          CF222 525 galeskEliiqkLvalLqevDgqLGkqirrhPSfkkffyelsdsslrkLvAtLrsqeah 583
                                    +a+ s ++ ++ L+a  + + + +Gkqi rh  +k+ff +lsd  l+kL+  ++s + +
  gi|116753369|ref|YP_842487.1| 306 DAVSSGDTGVEGLMAYEKRWRESIGKQIARHLDLKEFFIRLSDDDLNKLMHSIQSEDVS 364
                                    677778888889999999999*****************************999998765 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 !   16.2   0.1     5e-06    0.0049      29      69 ..       3      43 ..       1      73 [. 0.75

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5e-06
                                   -EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH CS
                    AlaDh_PNT_C 29 akvlviGgGvaGlqAiatakglgakVtvlDvrparleqles 69
                                   + v+v+G+G  G  A++ta++ g kV+++++r++    ++ 
  gi|116753369|ref|YP_842487.1|  3 CDVVVVGAGPGGSMAAKTAAEKGLKVVLVEKRQEIGDPVRC 43
                                   78******************************987666654 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.3   2.9e-06    0.0029       2      35 ..       5      38 ..       4      49 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.9e-06
                                   EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                      Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                   vvvvG+G  g ++A+++ae g kV +ve + ++ 
  gi|116753369|ref|YP_842487.1|  5 VVVVGAGPGGSMAAKTAAEKGLKVVLVEKRQEIG 38
                                   8*****************************9997 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1     3e-05      0.03       2      34 ..       5      37 ..       4      61 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3e-05
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHH CS
                        3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseea 34
                                   v v+GaG  G+  a+ +a++gl+Vvlv+ ++e+
  gi|116753369|ref|YP_842487.1|  5 VVVVGAGPGGSMAAKTAAEKGLKVVLVEKRQEI 37
                                   89**************************99886 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.3   2.8e-05     0.028       1      33 [.       6      38 ..       6      43 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.8e-05
                    Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg.nig 33
                                   +++GaGP G  aa ++ ++gl +++ +Ek  +ig
  gi|116753369|ref|YP_842487.1|  6 VVVGAGPGGSMAAKTAAEKGL-KVVLVEKRqEIG 38
                                   79*******************.699999985666 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00019      0.19       1      45 [.       5      77 ..       5     123 .. 0.73
   2 ?   -2.7   0.0       8.1     8e+03      72      82 ..     221     231 ..     216     252 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00019
                                   EEEE--STTHHHHHHHHHHHTEEEEEEES-GGGG-GGG-TT-SE............................- CS
                         XdhC_C  1 lvifGaghvaqalarlaaalgfrvtvvdpreefatkerfpeade............................t 45
                                   +v++Gag+ +   a+ aa+ g++v++v++r+e+ ++ r +e  +                             
  gi|116753369|ref|YP_842487.1|  5 VVVVGAGPGGSMAAKTAAEKGLKVVLVEKRQEIGDPVRCAEGVSkarlssmikpdpkwiasevkgarlyapdG 77
                                   689****************************998666655433344444444455555555555555555554 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 8.1
                                    EEESS-HHHHH CS
                         XdhC_C  72 igllGSrkkaa 82 
                                    +g++GSr+   
  gi|116753369|ref|YP_842487.1| 221 LGVIGSRSEPG 231
                                    69999998654 PP

>> SE  Squalene epoxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00029      0.29     129     164 ..     269     304 ..     230     317 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00029
                             SE 129 kkGlillGDalnmRHPltggGmtvalnDivllskll 164
                                      G++l+GDa     P+tggG+  a++  ++  +++
  gi|116753369|ref|YP_842487.1| 269 ADGVMLVGDAARQSDPITGGGILNAMQAGMIAGEVV 304
                                    58*******************999888776666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); 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 0.29s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 2554.28
//
Query:       gi|116753370|ref|YP_842488.1|  [L=154]
Description: peptidylprolyl isomerase [Methanosaeta thermophila PT]
Scores for complete 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-52  175.7   0.0    8.6e-52  175.6   0.0    1.0  1  Pro_isomerase  Cyclophilin type peptidyl-prolyl cis-trans iso


Domain annotation for each model (and alignments):
>> Pro_isomerase  Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.6   0.0   4.8e-56   8.6e-52       2     158 .]       7     152 ..       6     152 .. 0.94

  Alignments for each domain:
  == domain 1  score: 175.6 bits;  conditional E-value: 4.8e-56
                  Pro_isomerase   2 vdietsskGrivieLfadkaPktvenFlklvkegfYdgttFhRvikgfmvqgGdptgktsageqekkggesiraipdEit 81 
                                    v ++ts +G++vieL++d  P+t++nFlklv++gfYdg++FhRvi gfm+q+Gdptg++        gg   ++ipdE++
  gi|116753370|ref|YP_842488.1|   7 VLLKTS-LGDVVIELYDDM-PITAGNFLKLVESGFYDGVIFHRVIAGFMIQTGDPTGTGY-------GG-PGYTIPDEFS 76 
                                    568996.*********998.*************************************966.......23.2469*****9 PP

                  Pro_isomerase  82 sklkhkrGalamartgkepnsagsqFfItlkeaphldgkytvFGkVveGmdvvekiekvetde.erpkknvkivsaev 158
                                    ++ +++rG++ama++g  pn++gsqFfI+l ++++ld+ + vFG+VveGmdvv+ki +v+td+ +rp ++v+ivsa+v
  gi|116753370|ref|YP_842488.1|  77 RHNRNDRGTVAMANAG--PNTGGSQFFINLVNNNYLDRMHPVFGRVVEGMDVVDKIGDVRTDAeDRPIEDVVIVSARV 152
                                    99999*********98..8*******************************************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 1061.60
//
Query:       gi|116753371|ref|YP_842489.1|  [L=685]
Description: carbohydrate-binding and sugar hydrolysis [Methanosaeta thermophila PT]
Scores for 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-61  205.8  60.9    1.6e-26   93.0  14.8    4.3  4  NosD             Periplasmic copper-binding protein (NosD)
    1.9e-50  170.8  98.4    4.1e-18   65.7  24.5    5.1  5  Beta_helix       Right handed beta helix region
    1.9e-07   31.1  30.4      0.013   15.4   2.7    5.1  4  Pectate_lyase_3  Pectate lyase superfamily protein
  ------ inclusion threshold ------
      0.063   13.4   0.3       0.16   12.2   0.3    1.6  1  HupF_HypC        HupF/HypC family


Domain annotation for each model (and alignments):
>> NosD  Periplasmic copper-binding protein (NosD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   7.6   2.1e-06    0.0092      24     130 ..      89     189 ..      43     193 .. 0.62
   2 !   66.0  22.2   6.8e-22     3e-18      46     182 ..     172     305 ..     170     340 .. 0.93
   3 !   49.7   0.3   6.3e-17   2.8e-13      19     153 ..     357     491 ..     326     492 .. 0.86
   4 !   93.0  14.8   3.6e-30   1.6e-26      29     237 ..     479     674 ..     474     678 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.1e-06
                           NosD  24 segseisnneisnsrdgilldnssnntitgntienlryGihlensesntiedntlssnesGialmsssnntlenNtisnn 103
                                    s gs+isn +i  s    ++  +  +++tg+ i+n++ Gi    +++ ++++nt+s + +Gi l  s   ++enNtis+ 
  gi|116753371|ref|YP_842489.1|  89 SYGSSISNLTILGSGRDPAVVVEGYASVTGCNIKNSSIGIA---AYKGVVSNNTISATAYGIRLNGSA--IVENNTISGP 163
                                    35555555555555555556666666677777777655554...333466777777777777777777..7777777777 PP

                           NosD 104 enyGillsdssnntisnNtisnnnkGi 130
                                     ++Gi ++  s + i  N +++ +++i
  gi|116753371|ref|YP_842489.1| 164 LGAGIEVRCNS-SRILSNIVTSAGNAI 189
                                    77666655444.456666666666665 PP

  == domain 2  score: 66.0 bits;  conditional E-value: 6.8e-22
                           NosD  46 ssnntitgntienlryGihlensesntiedntlssnesGialmsssnntlenNtisnnenyGillsdssnntisnNtisn 125
                                    +++ +i  n +++  ++i ++++++ t+  n lss++ Gi l+sss+n++ nNt  +n+++G++l+ds+nn++s N++++
  gi|116753371|ref|YP_842489.1| 172 CNSSRILSNIVTSAGNAIDVVGNNN-TVLFNHLSSSNIGIRLKSSSDNIMMNNTCEKNRIAGVYLEDSRNNSVSSNRFLR 250
                                    5677888888888899999998876.****************************************************** PP

                           NosD 126 nnkGiflensssntitgNriesnqkiGilllsssegntiynNyFinnsenvkydgsn 182
                                    n++Gi l++ss+n+i gN +e n ++Gi  +++s gn++ +N +i n  +++++++n
  gi|116753371|ref|YP_842489.1| 251 NGNGILLKSSSGNKIIGNIVELN-EYGIS-MKGSGGNLLRENVLISNIYSLRIEAGN 305
                                    ***********************.*****.*******************99999876 PP

  == domain 3  score: 49.7 bits;  conditional E-value: 6.3e-17
                           NosD  19 iqlensegseisnneisnsrdgilldnssnntitgntienlryGihlensesntiedntlssnesGialmsssnntlenN 98 
                                    + l   e+ +++n++isns+++i+l  + + +i++++++ ++ G+ + +s+++++e+ t++s++ G+++ +s++ +++++
  gi|116753371|ref|YP_842489.1| 357 VGLIDCENITMRNQSISNSSAAIMLVGAIDSRISDCRLSRSEIGLSILDSKGCVVENTTAESCGIGFWFGRSQDIFVRKS 436
                                    34555689999999999999999999999999999999999999999999999999999999999999999999999999 PP

                           NosD  99 tisnnenyGillsdssnntisnNtisnnnkGiflensssntitgNriesnqkiGi 153
                                     + n+++ G+ l++ + + i++ ++ n+ +G +l ++ s++i ++ri+s+ + Gi
  gi|116753371|ref|YP_842489.1| 437 AALNCTESGFRLEGDRRSRITDSRAENCTAGMHLLDALSSEIVRSRISSSSEDGI 491
                                    9999999999999999999999999999999999999999999999999988887 PP

  == domain 4  score: 93.0 bits;  conditional E-value: 3.6e-30
                           NosD  29 isnneisnsrdgilldnssnntitgntienlryGihlensesntiedntlssnesGialmsssnntlenNtisnnenyGi 108
                                    +++   s+s+dgi l  s+  t+++n ++ +++Gi +++s+++++  n +s n+ Gi +++ s+    +N++ +n++ Gi
  gi|116753371|ref|YP_842489.1| 479 VRSRISSSSEDGIRLVRSHRSTVKENEVTGNDNGIAISGSNQCVLAMNNASANGIGIRIEQLSGGSAADNIAFRNRE-GI 557
                                    4666778999*****************************************************99************.** PP

                           NosD 109 llsdssnntisnNtis.nnnkGiflensssntitgNriesnqkiGilllsssegntiynNyFinnsenvkydgsn..nne 185
                                    ++++ ++ +  +N+is n+  G ++ +ss+  i++Nr+ +n+  G+  l+++++n+iy N+Fi+n   +  ++     n 
  gi|116753371|ref|YP_842489.1| 558 FVNGVKEFQFIGNNISmNERFGMRMGSSSGCNISDNRFVGNGMLGLS-LTDCSDNRIYHNSFIENGSMFGQNAVDngSNL 636
                                    ***********************************************.*****************9988877766689** PP

                           NosD 186 WnttktsgtniiggpylgGNyWsdydgeDadgDGigDtpYeindgviDylpl 237
                                    W+           gp++gGNyWsd + +   g   gDtp +++++ +D++p 
  gi|116753371|ref|YP_842489.1| 637 WD--M--------GPVIGGNYWSDHQVS---G-NPGDTPKNVPSKGVDRYPF 674
                                    *3..3........77*********8876...2.2478888888888888886 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 !   27.1  17.6     7e-10   3.2e-06      12     152 ..      61     199 ..      51     202 .. 0.82
   2 !   65.7  24.5   9.2e-22   4.1e-18       1     157 [.     145     291 ..     145     292 .. 0.95
   3 !   39.5   0.5   1.1e-13   4.9e-10       7     119 ..     361     469 ..     320     473 .. 0.64
   4 !   54.0   5.3   3.8e-18   1.7e-14       2     149 ..     400     542 ..     399     551 .. 0.93
   5 !   40.8  20.5   4.3e-14   1.9e-10      11     139 ..     499     627 ..     496     656 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 7e-10
                                    EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT.........-S-EEES-EEE---SEEE-TT--S--EE CS
                     Beta_helix  12 tiknntisnsggyGiylrgssnvvienneiannsgsGiyilgs.........snntisnntisdnngggialfgasnnli 82 
                                    +++ n++ +++gyG  ++g ++++++  + +++s s++ ilgs          ++ +++++i ++   gia++   + ++
  gi|116753371|ref|YP_842489.1|  61 SVDVNKLVSIKGYGAIIDGMGRTTFQM-RSYGSSISNLTILGSgrdpavvveGYASVTGCNIKNSS-IGIAAY---KGVV 135
                                    578899999999999999999988883.3333355555555555568888889**********999.999988...899* PP

                                    ES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS--E CS
                     Beta_helix  83 enneitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsssnvt 152
                                    +nn+i+ ++  Gi+ln+  + ++enN+i++  g+Gi+++ +s   ++  N++t+++ ++i+vvg+++ v 
  gi|116753371|ref|YP_842489.1| 136 SNNTISATAY-GIRLNG--SAIVENNTISGPLGAGIEVRCNS--SRILSNIVTSAG-NAIDVVGNNNTVL 199
                                    ********87.**9985..89*********************..667******997.*******999444 PP

  == domain 2  score: 65.7 bits;  conditional E-value: 9.2e-22
                                    -SEEE-SS-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S-- CS
                     Beta_helix   1 sgisingssnvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasnn 80 
                                    +gi +ngs    ++nntis++ g+Gi +r +s+ +i +n +++  g+ i++ g +nnt+  n+ s +n  gi l+ +s n
  gi|116753371|ref|YP_842489.1| 145 YGIRLNGSAI--VENNTISGPLGAGIEVRCNSS-RILSNIVTS-AGNAIDVVG-NNNTVLFNHLSSSN-IGIRLKSSSDN 218
                                    6899999999..*********************.666699999.*******98.**************.*********** PP

                                    EEES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS--EEES-E CS
                     Beta_helix  81 lienneitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsssnvtvrnNt 157
                                    ++ nn++++n+ +G+yl++s nn+++ N++  n+ +Gi + +ss ++++ +N++  n  +Gi   gs++ + +r+N+
  gi|116753371|ref|YP_842489.1| 219 IMMNNTCEKNRIAGVYLEDSRNNSVSSNRFLRNG-NGILLKSSS-GNKIIGNIVELNE-YGISMKGSGG-NLLRENV 291
                                    **********************************.*********.************8.***7777777.*999997 PP

  == domain 3  score: 39.5 bits;  conditional E-value: 1.1e-13
                                    SS-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES-E CS
                     Beta_helix   7 gssnvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasnnlienne 86 
                                    +++n+t +n  isn ++++i+l g+ + +i++++++  s+ G++il s++++++n t + ++  g+++  ++   ++++ 
  gi|116753371|ref|YP_842489.1| 361 DCENITMRNQSISN-SSAAIMLVGAIDSRISDCRLSR-SEIGLSILDSKGCVVENTTAESCG-IGFWFGRSQDIFVRKSA 437
                                    35555666666666.4666666666666666666666.666666666666666666666666.66666666666666666 PP

                                    EES-SS-SEE-TT-S--EEES-EEESTT--SEE CS
                     Beta_helix  87 itdnggsGiylnyssnntienNiidnnagsGiv 119
                                      ++ +sG++l++  + +i++++++n++ +G++
  gi|116753371|ref|YP_842489.1| 438 ALNCTESGFRLEGDRRSRITDSRAENCT-AGMH 469
                                    6666666666666666666666666666.5554 PP

  == domain 4  score: 54.0 bits;  conditional E-value: 3.8e-18
                                    SEEE-SS-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--E CS
                     Beta_helix   2 gisingssnvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasnnl 81 
                                    g+si +s+++ ++n t ++ +g G++++ s+++ ++++   n+++sG++++g+ ++ i++++ ++++  g++l +a  + 
  gi|116753371|ref|YP_842489.1| 400 GLSILDSKGCVVENTTAES-CGIGFWFGRSQDIFVRKSAALNCTESGFRLEGDRRSRITDSRAENCT-AGMHLLDALSSE 477
                                    7788999999999999999.6**********************************************.************ PP

                                    EES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS CS
                     Beta_helix  82 ienneitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsss 149
                                    i +++i+  +++Gi+l  s++ t+++N +++n  +Gi i+ s+ +++   N+++ n+  Gi +   s+
  gi|116753371|ref|YP_842489.1| 478 IVRSRISSSSEDGIRLVRSHRSTVKENEVTGND-NGIAISGSN-QCVLAMNNASANG-IGIRIEQLSG 542
                                    *********************************.*********.**********997.9998877766 PP

  == domain 5  score: 40.8 bits;  conditional E-value: 4.3e-14
                                    .EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES-EEES- CS
                     Beta_helix  11 vtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasnnlienneitdn 90 
                                     t+k n++++ +++Gi + gs+++v+  n+ +  +g Gi+i++ s+    +n   +n   gi ++g +   + +n+i++n
  gi|116753371|ref|YP_842489.1| 499 STVKENEVTG-NDNGIAISGSNQCVLAMNNASA-NGIGIRIEQLSGGSAADNIAFRNR-EGIFVNGVKEFQFIGNNISMN 575
                                    599*******.6***************888888.899999999977777666666666.7******************** PP

                                    SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-S....S CS
                     Beta_helix  91 ggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnk....g 139
                                    ++ G+++ +ss + i++N++ +n+  G++++d s ++++ +N++  n+    +
  gi|116753371|ref|YP_842489.1| 576 ERFGMRMGSSSGCNISDNRFVGNGMLGLSLTDCS-DNRIYHNSFIENGsmfgQ 627
                                    **********************************.9999*****999855442 PP

>> Pectate_lyase_3  Pectate lyase superfamily protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9  11.1   0.00027       1.2      48     214 ..      89     255 ..      31     256 .. 0.68
   2 !   13.1   0.1   1.4e-05     0.063     103     214 ..     362     468 ..     319     469 .. 0.64
   3 !    5.6   0.1    0.0029        13     133     178 ..     481     521 ..     455     524 .. 0.67
   4 !   15.4   2.7   2.9e-06     0.013     132     209 ..     520     597 ..     517     609 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00027
                                    S-EEE-SSEEEEES-TTTEEEEE-TT-SS--SEEES-TTT-..-EEEEEEEEEEEGGGG-SS---SSEEE.......ES- CS
                Pectate_lyase_3  48 spiilksgvqLvGdgngrpvlkaaaafvgaglidgdpyvsggsealiatnnfyrqirnlkiditavapga.......tgi 120
                                    s  ++ s+ ++ G g++++v+    a+v+   i++++++ ++ ++++++n+++ ++  ++++ +a+ +++       +gi
  gi|116753371|ref|YP_842489.1|  89 SYGSSISNLTILGSGRDPAVVVEGYASVTGCNIKNSSIGIAAYKGVVSNNTISATAYGIRLNGSAIVENNtisgplgAGI 168
                                    44456688888888888888877777766666666666633347788888888888888888888833333455665666 PP

                                    EEEEEEEEEEES-SSEEE-SSS---TT---SS--EEEEES-EEES-SS-SEEE.S.-EEEEEES-EEE-S--SEEE-TT- CS
                Pectate_lyase_3 121 hwqtaqatslenvefemseasgtkhqgifiengsggflndlvfsglgdigiav.g.nqqftvrnitfnnattgievlwgw 198
                                    ++  ++   l+n+++   +a      ++ + n ++   n+l  s+   igi++ + ++++ ++n   +n   g+++++++
  gi|116753371|ref|YP_842489.1| 169 EVRCNSSRILSNIVTSAGNAI-----DV-VGNNNTVLFNHLSSSN---IGIRLkSsSDNIMMNNTCEKNRIAGVYLEDSR 239
                                    666666666777633222222.....22.4444443338888877...77777543666777776667777788888788 PP

                                    EEEEEEEEEESSSEEE CS
                Pectate_lyase_3 199 gwtlknvkinncegGi 214
                                    + +++++++   ++Gi
  gi|116753371|ref|YP_842489.1| 240 NNSVSSNRFLRNGNGI 255
                                    8999999998888887 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 1.4e-05
                                    GGGG-SS---SSEEEES-EEEEEEEEEEES-SSEEE-SSS---TT---SS--EEEEES-EEES-SS-SEEE.S-EEEEEE CS
                Pectate_lyase_3 103 irnlkiditavapgatgihwqtaqatslenvefemseasgtkhqgifiengsggflndlvfsglgdigiav.gnqqftvr 181
                                      n+++  +++++++++i  + a +  ++++  ++s ++     g+ i +++g ++++ +++   +ig+ + ++q++ vr
  gi|116753371|ref|YP_842489.1| 362 CENITMRNQSISNSSAAIMLVGAIDSRISDC--RLSRSE----IGLSILDSKGCVVENTTAES-CGIGFWFgRSQDIFVR 434
                                    4555555555555556666666666666666..444444....46777777776668888887.7788888447777777 PP

                                    S-EEE-.S--SEEE-TT-EEEEEEEEEESSSEEE CS
                Pectate_lyase_3 182 nitfnn.attgievlwgwgwtlknvkinncegGi 214
                                    + +  n ++ g++++ +++  + + + +nc+ G+
  gi|116753371|ref|YP_842489.1| 435 KSAALNcTESGFRLEGDRRSRITDSRAENCTAGM 468
                                    7777772345666666777777788888888776 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.0029
                                    -SSEEE-SSS---TT---SS--EEEEES-EEES-SS-SEEE.S-EEE CS
                Pectate_lyase_3 133 vefemseasgtkhqgifiengsggflndlvfsglgdigiav.gnqqf 178
                                      +  s++   +++gi++ ++ ++++++ +++g  d gia+ g++q 
  gi|116753371|ref|YP_842489.1| 481 SRI--SSS---SEDGIRLVRSHRSTVKENEVTG-NDNGIAIsGSNQC 521
                                    322..222...3568888888888898888888.8888888667775 PP

  == domain 4  score: 15.4 bits;  conditional E-value: 2.9e-06
                                    S-SSEEE-SSS---TT---SS--EEEE.ES-EEES-SS-SEEE.S..-EEEEEES-EEE-S--SEEE-TT-EEEEEEEEE CS
                Pectate_lyase_3 132 nvefemseasgtkhqgifiengsggfl.ndlvfsglgdigiav.g..nqqftvrnitfnnattgievlwgwgwtlknvki 207
                                    ++++ m++as  ++ gi+ie+ sgg   +++ f++  + gi v g  + qf+ +ni +n+   g+++++++g  ++++++
  gi|116753371|ref|YP_842489.1| 520 QCVLAMNNAS-ANGIGIRIEQLSGGSAaDNIAFRN--REGIFVnGvkEFQFIGNNISMNE-RFGMRMGSSSGCNISDNRF 595
                                    578999****.79***********98879999999..6777764466999999****999.*******999999999987 PP

                                    ES CS
                Pectate_lyase_3 208 nn 209
                                     +
  gi|116753371|ref|YP_842489.1| 596 VG 597
                                    54 PP

>> HupF_HypC  HupF/HypC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.3   3.5e-05      0.16      15      55 ..      23      64 ..      11      70 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.5e-05
                                   TEEEEECT..TEEEEEEGTTCTTB-TT-EEEEETTEEEEEE-H CS
                      HupF_HypC 15 elAlvdvg..GvrrevslalveevkvGdyVLvhvGfAiekide 55
                                   ++ +vd +  G  r v+ al + ++ Gd +Lv +G+ +e +d 
  gi|116753371|ref|YP_842489.1| 23 RILVVDQEatGAIRSVNAALAN-AQNGDEILVMAGYYRESVDV 64
                                   4555555555**********96.***************99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (685 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); 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: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 4694.05
//
Query:       gi|116753372|ref|YP_842490.1|  [L=162]
Description: AsnC family transcriptional regulator [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.4e-31  106.6   0.9    1.4e-30  105.2   0.1    1.9  2  AsnC_trans_reg2  AsnC-like ligand binding domain
    4.6e-11   42.3   0.5      2e-10   40.3   0.2    2.2  2  HTH_AsnC-type    AsnC-type helix-turn-helix domain
    2.3e-06   27.1   1.3    2.9e-05   23.5   1.3    2.3  1  HTH_24           Winged helix-turn-helix DNA-binding
    0.00046   20.2   0.2    0.00088   19.3   0.0    1.6  2  HTH_20           Helix-turn-helix domain
     0.0039   16.9   0.0     0.0065   16.2   0.0    1.3  1  LexA_DNA_bind    LexA DNA binding domain
  ------ inclusion threshold ------
      0.028   14.3   0.1      0.046   13.6   0.1    1.4  1  MarR_2           MarR family
      0.032   14.2   0.1      0.072   13.1   0.0    1.5  1  HTH_Crp_2        Crp-like helix-turn-helix domain
      0.082   12.8   0.0       0.15   11.9   0.0    1.5  1  HTH_5            Bacterial regulatory protein, arsR family
      0.082   12.9   0.1       0.17   11.9   0.1    1.5  1  AsnC_trans_reg   Lrp/AsnC ligand binding domain
      0.084   12.8   0.0       0.16   11.9   0.0    1.5  1  MarR             MarR family
      0.086   12.8   0.0       0.41   10.6   0.0    2.0  2  HTH_36           Helix-turn-helix domain
        0.1   12.4   0.1       0.27   11.1   0.0    1.7  2  HTH_IclR         IclR helix-turn-helix domain
       0.11   11.9   0.0       0.52    9.8   0.0    2.1  2  HTH_Tnp_ISL3     Helix-turn-helix domain of transposase famil
       0.13   12.2   0.1        0.3   11.1   0.1    1.7  1  HTH_11           HTH domain


Domain annotation for each model (and alignments):
>> AsnC_trans_reg2  AsnC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       1.1   1.4e+03      57      78 ..       2      23 ..       1      25 [. 0.83
   2 !  105.2   0.1   1.1e-33   1.4e-30       2      82 .]      73     156 ..      72     156 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.1
                AsnC_trans_reg2 57 eevlaeiaaatgledyevLpst 78
                                   +e +++++++++++d+ +L ++
  gi|116753372|ref|YP_842490.1|  2 QEDASRMSQEMDQTDLTLLRAL 23
                                   6778999999*99999999876 PP

  == domain 2  score: 105.2 bits;  conditional E-value: 1.1e-33
                AsnC_trans_reg2   2 lGfkanalvawkvpeerveevaevvaelpevtHcYeR....ewpynlyfmvharseeeveevlaeiaaatgledyevLps 77 
                                    lG+ ana+++wkv e+++e+++ ++a+++evtHcY+R     wpynly++vh rs+ee+ee++++i++atg+++y++L+s
  gi|116753372|ref|YP_842490.1|  73 LGIIANAMIVWKV-EDDIERIGCIMASFEEVTHCYQRatcdGWPYNLYTVVHSRSREECEEIASRISEATGVKEYRILFS 151
                                    8************.789********************77755************************************** PP

                AsnC_trans_reg2  78 trefK 82 
                                    ++e+K
  gi|116753372|ref|YP_842490.1| 152 EKEYK 156
                                    ****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 !   40.3   0.2   1.6e-13     2e-10       1      42 []      12      56 ..      12      56 .. 0.98
   2 ?   -1.2   0.0       1.5   1.9e+03      22      27 ..     132     137 ..     125     146 .. 0.57

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 1.6e-13
                  HTH_AsnC-type  1 LDeiDrkILeaLqed...aRisyaeLAervGlSestvlrRvrrLe 42
                                   +D++D+ +L+aLq        +++e+++r+Gl+e+tv+ R+r+L+
  gi|116753372|ref|YP_842490.1| 12 MDQTDLTLLRALQDGipiVPHPFKEIGDRLGLDENTVISRLRALR 56
                                   9******************************************97 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.5
                  HTH_AsnC-type  22 eLAerv 27 
                                    e+A r+
  gi|116753372|ref|YP_842490.1| 132 EIASRI 137
                                    555443 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 !   23.5   1.3   2.3e-08   2.9e-05       1      48 []      12      62 ..      12      62 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2.3e-08
                         HTH_24  1 ldetdrkILelLqk...nprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                   +d+td+ +L++Lq+       + +e+ +rlgl  +tv  rl+ L e+G+++
  gi|116753372|ref|YP_842490.1| 12 MDQTDLTLLRALQDgipIVPHPFKEIGDRLGLDENTVISRLRALRESGVVR 62
                                   78888999999999877777899**************************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 !   19.3   0.0   6.9e-07   0.00088      13      55 ..      17      62 ..      12      63 .. 0.87
   2 ?   -3.5   0.0       9.2   1.2e+04      27      34 ..     130     137 ..     129     141 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 6.9e-07
                                   HHHHHHH...STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                         HTH_20 13 rrilraL...araegltaselaerldlskntlsyHLrvLeeagLve 55
                                   + +lraL    +  ++ ++e+ +rl+l+ nt+  +Lr+L+e g v+
  gi|116753372|ref|YP_842490.1| 17 LTLLRALqdgIPIVPHPFKEIGDRLGLDENTVISRLRALRESGVVR 62
                                   567777777777789****************************998 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 9.2
                                    HHHHHHHH CS
                         HTH_20  27 aselaerl 34 
                                    ++e+a r+
  gi|116753372|ref|YP_842490.1| 130 CEEIASRI 137
                                    88999885 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 !   16.2   0.0     5e-06    0.0065      28      58 ..      34      63 ..      16      67 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5e-06
                                   HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE- CS
                  LexA_DNA_bind 28 ireiaralglkSpsaveehLkaLerKGyier 58
                                    +ei+++lgl   ++v ++L+aL+  G+++r
  gi|116753372|ref|YP_842490.1| 34 FKEIGDRLGLD-ENTVISRLRALRESGVVRR 63
                                   68*********.9****************98 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   3.6e-05     0.046       4      53 ..      13      63 ..      10      72 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.6e-05
                                   -HHHHHHHHHHHCTTTSEE...EHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                         MarR_2  4 tpaqarvLaaLgrrpgrdl...tvgelarrlglsksavsrilkrLvaaGLver 53
                                   + +++ +L aL ++ +  +     +e+ +rlgl+  +v  +l+ L + G v+r
  gi|116753372|ref|YP_842490.1| 13 DQTDLTLLRALQDGIP--IvphPFKEIGDRLGLDENTVISRLRALRESGVVRR 63
                                   5677778888888886..455699***************************98 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.6e-05     0.072      20      53 ..      30      63 ..      16      73 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.6e-05
                                   EEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEE CS
                      HTH_Crp_2 20 lpltqeelAsmlGltretvsrilseLkreglisr 53
                                   +p   +e++++lGl   tv   l++L++ g+++r
  gi|116753372|ref|YP_842490.1| 30 VPHPFKEIGDRLGLDENTVISRLRALRESGVVRR 63
                                   566678*************************995 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00012      0.15       6      46 ..      18      62 ..      13      63 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                                   HHHHHHTT....SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_5  6 kILklLae....gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                    +L++L++     ++ + e+ + lgl + tv   L++Lre+G+V+
  gi|116753372|ref|YP_842490.1| 18 TLLRALQDgipiVPHPFKEIGDRLGLDENTVISRLRALRESGVVR 62
                                   566666666555677789999**********************96 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 ?   11.9   0.1   0.00013      0.17      11      71 ..      87     150 ..      81     154 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                                    THHHHHHHHHHTSTTEEEEEEES...S.SSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEE CS
                 AsnC_trans_reg  11 eqleefeealaelpeVvecyrvt...G.dydyllkvvvrdlealerflreklaslpgvartetsi 71 
                                    +++e++   +a ++eV++cy+ +   G +y++   v++r+ e+ e++ ++ +++  gv++++ ++
  gi|116753372|ref|YP_842490.1|  87 DDIERIGCIMASFEEVTHCYQRAtcdGwPYNLYTVVHSRSREECEEIASR-ISEATGVKEYRILF 150
                                    557777888999********75433389*******************999.*********99887 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00012      0.16      17      50 ..      31      64 ..      13      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                                   TEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                           MarR 17 plsvseLakklgvskstvtrvldrLekkGlieRs 50
                                   p+  +e++++lg++  tv   l++L + G ++R 
  gi|116753372|ref|YP_842490.1| 31 PHPFKEIGDRLGLDENTVISRLRALRESGVVRRF 64
                                   57788***************************96 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00032      0.41      28      53 ..      34      59 ..      18      61 .. 0.84
   2 ?   -0.4   0.0      0.87   1.1e+03      12      26 ..      94     107 ..      91     148 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00032
                         HTH_36 28 qetlakrlglsknTvsraikeLeqlG 53
                                   ++ +  rlgl++nTv++ ++ L++ G
  gi|116753372|ref|YP_842490.1| 34 FKEIGDRLGLDENTVISRLRALRESG 59
                                   677889****************9988 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.87
                         HTH_36  12 gslasfanknggcfp 26 
                                    +++asf  + ++c+ 
  gi|116753372|ref|YP_842490.1|  94 CIMASFE-EVTHCYQ 107
                                    6777777.6666664 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00021      0.27      19      50 ..      32      63 ..      17      63 .. 0.85
   2 ?   -3.4   0.0       6.9   8.8e+03      22      29 ..     135     142 ..     133     143 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00021
                                   -BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                       HTH_IclR 19 ltlselArrtglpkStvhRlLqtLvelGyveq 50
                                     ++e+ +r+gl   tv   L+ L e G v++
  gi|116753372|ref|YP_842490.1| 32 HPFKEIGDRLGLDENTVISRLRALRESGVVRR 63
                                   5799**************************96 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 6.9
                                    HHHHHHHT CS
                       HTH_IclR  22 selArrtg 29 
                                    s ++++tg
  gi|116753372|ref|YP_842490.1| 135 SRISEATG 142
                                    67999998 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 ?    9.8   0.0    0.0004      0.52      29      50 ..      33      54 ..      32      56 .. 0.92
   2 ?   -1.9   0.0       1.7   2.2e+03      14      25 ..      62      73 ..      62      74 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0004
                   HTH_Tnp_ISL3 29 svkavArqlgvSwtTVwrildr 50
                                   ++k++ ++lg++++TV+ +l++
  gi|116753372|ref|YP_842490.1| 33 PFKEIGDRLGLDENTVISRLRA 54
                                   89****************9986 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.7
                   HTH_Tnp_ISL3 14 lrleayilelll 25
                                   +r++a i +++l
  gi|116753372|ref|YP_842490.1| 62 RRFAATIGHRAL 73
                                   6999***99875 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00024       0.3      18      44 ..      34      60 ..      17      69 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00024
                         HTH_11 18 geeLAeeLnvSrrtvrrdIkaLeelgv 44
                                    +e+ ++L++ + tv  +++aL+e+gv
  gi|116753372|ref|YP_842490.1| 34 FKEIGDRLGLDENTVISRLRALRESGV 60
                                   589**********************94 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1195.62
//
Query:       gi|116753373|ref|YP_842491.1|  [L=411]
Description: glutamyl-tRNA reductase [Methanosaeta thermophila PT]
Scores for complete 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  138.5   0.1    3.6e-40  137.2   0.1    1.7  1  Shikimate_DH   Shikimate / quinate 5-dehydrogenase
      2e-36  125.0   0.9    3.6e-36  124.1   0.1    1.8  2  GlutR_N        Glutamyl-tRNAGlu reductase, N-terminal domain
    4.8e-20   71.8   6.1    1.3e-19   70.4   6.1    1.8  1  GlutR_dimer    Glutamyl-tRNAGlu reductase, dimerisation domai
    2.2e-05   25.0   0.4     0.0001   22.8   0.1    2.3  2  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
     0.0078   15.8   0.0      0.019   14.6   0.0    1.6  1  DEAD_2         DEAD_2
  ------ inclusion threshold ------
      0.021   14.1   0.2       0.16   11.2   0.3    2.3  2  THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase,
      0.047   12.8   0.0      0.067   12.3   0.0    1.1  1  Peptidase_M36  Fungalysin metallopeptidase (M36)
       0.18   11.9   4.6       0.48   10.5   4.6    1.8  1  Mst1_SARAH     C terminal SARAH domain of Mst1
       0.18   12.3   1.8       0.38   11.3   1.8    1.6  1  DUF2115        Uncharacterized protein conserved in archaea (


Domain annotation for each model (and alignments):
>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.2   0.1   1.8e-43   3.6e-40       1     138 []     156     290 ..     156     290 .. 0.99

  Alignments for each domain:
  == domain 1  score: 137.2 bits;  conditional E-value: 1.8e-43
                                    HHHHHHHS..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEE CS
                   Shikimate_DH   1 elakkkleslkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvi 80 
                                    +la+++l+ l++k vl+iGaGe++el+ k+L++k++ ++ v+NRt+  a +la +l+g+   a+++ee+k+ ++eadvvi
  gi|116753373|ref|YP_842491.1| 156 DLAEQILGGLEGKSVLVIGAGETGELISKALVSKNIGSLYVTNRTFGTALSLAASLGGT---AVPYEEMKRKIREADVVI 232
                                    59******************************************************999...****************** PP

                                    E-SSSSS-SB-HHHHHCCHHH.S..EEEEE--SS-SB-TTGGGSTTCCCEEHHHHHHH CS
                   Shikimate_DH  81 sataseepilekeeveealkkrkkplllvDiavPRdvepevaeledvrlytvDdLkev 138
                                    sat+++++il k+++e+a++ rk++ll++Dia+PRdv+++v+e+e+v+l+++D Lk++
  gi|116753373|ref|YP_842491.1| 233 SATSAPHYILLKDDIERAMEGRKNKLLIIDIANPRDVDEAVREIEGVELHNIDSLKQI 290
                                    *******************************************************987 PP

>> GlutR_N  Glutamyl-tRNAGlu reductase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.1   0.1   1.8e-39   3.6e-36       3     146 .]       3     141 ..       2     141 .. 0.84
   2 ?   -2.1   0.1       1.5   2.9e+03     111     112 ..     344     345 ..     303     379 .. 0.56

  Alignments for each domain:
  == domain 1  score: 124.1 bits;  conditional E-value: 1.8e-39
                        GlutR_N   3 inhktapvelreklafseee.lkellkeleekvkeaviLsTCNRtEiylsaeeeeeaseellellaevsleelkeklyvl 81 
                                    ++hk+a+++  e+++  + e l + +++   +v+e+++L+TCNR+Eiy+++ +    ++ l+e+ +++  +  ++ + ++
  gi|116753373|ref|YP_842491.1|   3 VTHKKASISEIENAWHGDVEaLLKWVSSH-DTVEECAVLKTCNRVEIYVVSPR---GEKVLFEIAKKA--RVSSRIIDIH 76 
                                    68**********99996444255555553.4899**************76655...445445544332..33447899** PP

                        GlutR_N  82 egeeavrHlfrVasGLdSlvlGEdqIlgQvkeayelakeagtlgkvLerlfqkaikvakrvrtet 146
                                    +++e++ Hl+r+asGL+S+++GEdqIlgQ+ke y++ak+ g++g vL++ f+kai+v+krvr+et
  gi|116753373|ref|YP_842491.1|  77 DHDESLLHLLRLASGLESMIIGEDQILGQMKELYRTAKSLGYTGWVLDTAFKKAIQVGKRVRKET 141
                                    ***************************************************************98 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.5
                        GlutR_N 111 vk 112
                                    v+
  gi|116753373|ref|YP_842491.1| 344 VR 345
                                    22 PP

>> GlutR_dimer  Glutamyl-tRNAGlu reductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.4   6.1   6.4e-23   1.3e-19       2      97 .]     305     405 ..     304     405 .. 0.93

  Alignments for each domain:
  == domain 1  score: 70.4 bits;  conditional E-value: 6.4e-23
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-S......--------TTHHHHHHHHHHHHHHHHH CS
                    GlutR_dimer   2 AeaiIeeeveefeawlkslevvptIkalrekaeeireeeleralkkla....ldgedreelekltrslvnkllheptarL 77 
                                    +eaiIeee+e + a++k++e+++++++++++ae+i+e+e++ra++kl+    l + ++++l ++++s+vnk++ ept++L
  gi|116753373|ref|YP_842491.1| 305 VEAIIEEELELLRAKYKRREAEELLARIYSEAEKIKEQEVRRAMNKLSayhtLGEIEQKVLMDMSHSIVNKIFAEPTKAL 384
                                    8**************************************************777777777******************** PP

                                    HSS-TTTT.HHHHHHHHH... CS
                    GlutR_dimer  78 keaedeee.ellealrrlFnl 97 
                                    k+a+++++ e+l+ + +lF l
  gi|116753373|ref|YP_842491.1| 385 KSAAERGNtEMLRYAMELFRL 405
                                    ***555556**********86 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         2   3.9e+03      26      49 ..      46      69 ..      34      77 .. 0.76
   2 !   22.8   0.1   5.1e-08    0.0001       3      97 .]     171     266 ..     169     266 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2
                                   GCEEEEEESSCCCHHHHHHHHC-E CS
                  F420_oxidored 26 heivvansrnpekaeelaeelgvk 49
                                    ei+v++ r ++ + e+a+++ v+
  gi|116753373|ref|YP_842491.1| 46 VEIYVVSPRGEKVLFEIAKKARVS 69
                                   578889888888889998887754 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 5.1e-08
                                    EEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHH...HHH-SEEEE-S-HHHHHHHHH CS
                  F420_oxidored   3 giiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneea...aeeadvvvlavkpedveevls 79 
                                     +iGaG+ ge + + l++++    +++ +++r+  +a +la++lg ++ +  +ee+   ++eadvv+ a    ++  + +
  gi|116753373|ref|YP_842491.1| 171 LVIGAGETGELISKALVSKN--IGSLY-VTNRTFGTALSLAASLGGTAVP--YEEMkrkIREADVVISATSAPHYILLKD 245
                                    58*****************9..88889.55**************966666..555511266*************999999 PP

                                    HC...GHHHHTTSEEEEESSS CS
                  F420_oxidored  80 el...akdalkgklvisvlag 97 
                                    ++   ++  +++ l+i+++++
  gi|116753373|ref|YP_842491.1| 246 DIeraMEGRKNKLLIIDIANP 266
                                    997767777888889999996 PP

>> DEAD_2  DEAD_2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   9.3e-06     0.019     110     172 ..     216     282 ..     208     285 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.3e-06
                                    -HHHHHHHHHCCTSEEE....EEHHHHTSCCCHHHHHT..GCGCEEEECTC..CCHHHHHHHCC-EEEE CS
                         DEAD_2 110 CPYylsrelledadiii....lpYqyLldekireslkgislknsivilDEA..hNiedvceeaasveis 172
                                     PY  +++ + +ad++i    +p+ +Ll+  i ++++g   kn+ +i+D A  + +++ ++e+  ve++
  gi|116753373|ref|YP_842491.1| 216 VPYEEMKRKIREADVVIsatsAPHYILLKDDIERAMEG--RKNKLLIIDIAnpRDVDEAVREIEGVELH 282
                                    6***************966556999***********95..9********88335899999999998886 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 ?   -3.4   0.0       2.5   5.1e+03      35      50 ..      90     105 ..      88     110 .. 0.84
   2 ?   11.2   0.3   8.2e-05      0.16      21      93 ..     152     241 ..     130     268 .. 0.69

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.5
                                    TT-EEEEE---TTTHH CS
                  THF_DHG_CYH_C  35 egkkvvvvGrsnivgk 50 
                                    +g + +++G+ +i+g+
  gi|116753373|ref|YP_842491.1|  90 SGLESMIIGEDQILGQ 105
                                    57888999*9999996 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 8.2e-05
                                    HHHHHHHHHCT---TT-EEEEE---TTTHHHHHHHHHCT..................T-EEEEE-TTS......CCHHHH CS
                  THF_DHG_CYH_C  21 kgvvellketgielegkkvvvvGrsnivgkplallLlek..................natVtvchskt......kdlaei 76 
                                     + v+l ++    legk+v+v+G++++ g+ ++  L +k                   a               ++++++
  gi|116753373|ref|YP_842491.1| 152 SAAVDLAEQILGGLEGKSVLVIGAGET-GELISKALVSKnigslyvtnrtfgtalslAASL------GgtavpyEEMKRK 224
                                    566788888888899999999999876.333333333332444444435553333222233......133455599**** PP

                                    HCCSSEEEE-SS-TT-B CS
                  THF_DHG_CYH_C  77 treadivvvavGkpeli 93 
                                    +read+v++a+  p+ i
  gi|116753373|ref|YP_842491.1| 225 IREADVVISATSAPHYI 241
                                    **************987 PP

>> Peptidase_M36  Fungalysin metallopeptidase (M36)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.4e-05     0.067     242     327 ..     318     404 ..     303     409 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.4e-05
                                    SHHHHT-TT-SSSS-B-S-TTT----GGGG.GG--SHHHHHHHHHHHHHHHHHHHHHHH-----EETT.EESSHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                  Peptidase_M36 242 gtyaanqpkgiRkypYstdltvnpltYkdlkeelsevhaiGevWaeiLwevtwalidkhGfsadlkke.vpkeGnnlalq 320
                                    ++y   +++ +  + Ys   ++++++ +++ ++ls+ h +Ge+  ++L ++ +++++k   +++   + ++++Gn+ +l+
  gi|116753373|ref|YP_842491.1| 318 AKYKRREAEELLARIYSEAEKIKEQEVRRAMNKLSAYHTLGEIEQKVLMDMSHSIVNKIFAEPTKALKsAAERGNTEMLR 397
                                    567777777788899*********99999989**************************998885444437888******9 PP

                                    HHHHHHH CS
                                    xxxxxxx RF
                  Peptidase_M36 321 lvldglk 327
                                    + ++ ++
  gi|116753373|ref|YP_842491.1| 398 YAMELFR 404
                                    9987655 PP

>> Mst1_SARAH  C terminal SARAH domain of Mst1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   4.6   0.00024      0.48       2      36 ..     285     322 ..     284     324 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00024
                     Mst1_SARAH   2 efLkflsvdeLqqrlasLD...peMEqEieelrkrYqa 36 
                                    + Lk++s ++++ r+ ++    + +E+E+e lr++Y++
  gi|116753373|ref|YP_842491.1| 285 DSLKQISDENMRLRMREIErveAIIEEELELLRAKYKR 322
                                    78*************988622267************86 PP

>> DUF2115  Uncharacterized protein conserved in archaea (DUF2115)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.8   0.00019      0.38       7      68 ..     288     347 ..     284     396 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00019
                        DUF2115   7 eilkkeaskisieDlmkisarlekeikklpekyrkelseslteylfeaykelknkrsgdkse 68 
                                    + + +e  ++ ++++++++a +e+e++ l +ky+++  e+l   ++++ +++k+  ++  + 
  gi|116753373|ref|YP_842491.1| 288 KQISDENMRLRMREIERVEAIIEEELELLRAKYKRREAEELLARIYSEAEKIKE--QEVRRA 347
                                    67899999*********************************************9..222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1335  (0.0744604); expected 358.6 (0.02)
Passed bias filter:                      675  (0.0376485); 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: 0.56u 0.24s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 2973.79
//
Query:       gi|116753374|ref|YP_842492.1|  [L=317]
Description: delta-aminolevulinic acid dehydratase [Methanosaeta thermophila PT]
Scores for complete 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-144  481.3   0.2   1.4e-144  481.2   0.2    1.0  1  ALAD      Delta-aminolevulinic acid dehydratase


Domain annotation for each model (and alignments):
>> ALAD  Delta-aminolevulinic acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  481.2   0.2  7.6e-149  1.4e-144       2     315 ..       2     313 ..       1     315 [. 0.99

  Alignments for each domain:
  == domain 1  score: 481.2 bits;  conditional E-value: 7.6e-149
                                    --GGGGGSSHHHHHHC-S----GGGEEEEEEEESS-SS-EE-TTSTT-EEEEGGGHHHHHHHHHHTT--EEEEEEE-SS- CS
                           ALAD   2 krlrrlrksealrelvretrlsasdlilplfvkegeeekeeiksmpgvyrlsvdelvkeveelvklgikavllFgvpeek 81 
                                    +r+rrlr+ + +re+v+etr+s++dli+p+fv+e+ +++ +i+smpg++r s++++++e+ ++ +lgi+av+lFg+p++k
  gi|116753374|ref|YP_842492.1|   2 RRMRRLRR-PGIREMVAETRISVRDLIMPVFVDERIDQPVPISSMPGQMRQSLNSVAEEAGRIEDLGIPAVILFGIPSRK 80 
                                    68999986.67********************************************************************* PP

                                    BSS-GGGGSTTSHHHHHHHHHHHH-TTSEEEEEE-STTTBSS-SSSEEESS.EEHHHHHHHHHHHHHHHHHCT-SEEEE- CS
                           ALAD  82 deegsealnedglvqrairaikeevpelvvitDvclceytshGhcgileekevdndetlellakvavsqaeaGadivapS 161
                                    d+ gs a+++dg++q+a+r+ike+ ++lvvitD+clceytshGhcg+++ +e+ ndetl ll ++avsqae+GadivapS
  gi|116753374|ref|YP_842492.1|  81 DDLGSGAYDHDGVIQKAVRRIKES-TDLVVITDLCLCEYTSHGHCGVIRGQEIVNDETLPLLGRTAVSQAESGADIVAPS 159
                                    **********************99.89***************************************************** PP

                                    S--TTHHHHHHHHHHHTT-TT-EEB---EEB--CGGHHHHHHHT---S.S--TTTSB-TT-HHHHHHHHHHHHHTT-SBE CS
                           ALAD 162 dmmDgrvaaireaLdeagfeevailsYsaKyaSafYgPFrdaaesapsfgdrktYqmdpansrealreveldleeGADiv 241
                                    +mmD +v+air+aLd++g+++vailsY+aKyaS fYgPFr+aaes  +fgdr++Yqmdpan++eal ev+ld+eeGAD+v
  gi|116753374|ref|YP_842492.1| 160 GMMDHMVRAIRSALDDNGYTDVAILSYAAKYASYFYGPFREAAESGFAFGDRRSYQMDPANANEALWEVQLDIEEGADMV 239
                                    ******************************************************************************** PP

                                    EEES-TTGHHHHHHHHTT-SS-EEEEE-HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHTT-SEEEETTHHHHH CS
                           ALAD 242 mvKPalaylDiirevkeefdlpvaayqvSGEYamikaaaengwldekkvvlEsllsikRAGadliltYfakeva 315
                                    mvKPal+ylDi+r vke+f++p+aayqvSGEY+mi+aaae++w+d + v+lE+l+sikRAGad+i+tY+ak++a
  gi|116753374|ref|YP_842492.1| 240 MVKPALPYLDILRMVKERFSMPTAAYQVSGEYSMIMAAAERNWIDGDGVMLETLTSIKRAGADMIITYYAKDFA 313
                                    ***********************************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); 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: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2362.56
//
Query:       gi|116753375|ref|YP_842493.1|  [L=149]
Description: hypothetical protein Mthe_0051 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1115.21
//
Query:       gi|116753376|ref|YP_842494.1|  [L=196]
Description: hypothetical protein Mthe_0052 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-05   24.1   0.3      5e-05   23.3   0.3    1.4  1  TraB          TraB family
  ------ inclusion threshold ------
      0.017   14.5   0.0      0.029   13.8   0.0    1.5  1  GSH-S_ATP     Prokaryotic glutathione synthetase, ATP-grasp d
       0.33   10.3   4.0        1.9    7.8   0.1    2.1  2  SF-assemblin  SF-assemblin/beta giardin


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 !   23.3   0.3   8.3e-09     5e-05     127     244 ..      78     178 ..      56     183 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 8.3e-09
                           TraB 127 vDrylaktakragkpvgglEtveeqlsllsslpdeeqlealeetldeleeakdlleelveaykegdlealeleaeaeeef 206
                                    ++r +++ta++  ++ + +E++ e  + ++     e+ e l    +e +  k+++++  e            +  a e++
  gi|116753376|ref|YP_842494.1|  78 GERIIRETASKGSRNYQIIEKLMERGARIE---ATESPELLL---REYQHIKAMVSTTGE-----------EQRRALEAY 140
                                    677777788888888888888777777773...444555553...455555667777777...........235788889 PP

                           TraB 207 pelkevlldeRnrrwaekieallkepgsvfvaVGagHl 244
                                     + k++lldeR+++ a++i++ l+++++ +  +Ga H 
  gi|116753376|ref|YP_842494.1| 141 NKEKDRLLDERDAYIARRIAETLQDDETGLLFIGAHHN 178
                                    999********************999*********996 PP

>> GSH-S_ATP  Prokaryotic glutathione synthetase, ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.9e-06     0.029     105     148 ..     129     174 ..      72     180 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.9e-06
                                    -SS-S---GGGTSCEEEEE--HHHHHHHHHHHHHHHHT..T--EEE CS
                      GSH-S_ATP 105 aegevRsnlaaggraeatelterdreiaeelapkLkek..GllfvG 148
                                    + +e R  l+a  +++ + l+erd  ia+++a++L+++  Gllf+G
  gi|116753376|ref|YP_842494.1| 129 TGEEQRRALEAYNKEKDRLLDERDAYIARRIAETLQDDetGLLFIG 174
                                    56789999***************************86444****99 PP

>> SF-assemblin  SF-assemblin/beta giardin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1   0.00032       1.9      12      43 ..      41      71 ..      34      73 .. 0.80
   2 ?    3.5   1.1    0.0065        39     137     192 ..      81     134 ..      75     165 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00032
                   SF-assemblin 12 ervegfekelenEieqkrvdektrvklikeai 43
                                    r+e+f++ele Ei+     + tr+++ ++ +
  gi|116753376|ref|YP_842494.1| 41 IRIERFWDELEREIDRL-ELDPTRLRIYQDGL 71
                                   59************855.55789999988865 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.0065
                   SF-assemblin 137 ideEkaerkkkedqlnkkveEdlkklsakidtEkniRdsevsaltaeveeiklekk 192
                                    i +E a +  ++ q+++k+ E  ++++a    E   R+  ++ ++a v  +  e++
  gi|116753376|ref|YP_842494.1|  81 IIRETASKGSRNYQIIEKLMERGARIEATESPELLLRE--YQHIKAMVSTTGEEQR 134
                                    56788888889999**************9999999986..6666666665555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       782  (0.0436165); expected 358.6 (0.02)
Passed bias filter:                      576  (0.0321267); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1404.82
//
Query:       gi|116753377|ref|YP_842495.1|  [L=204]
Description: hypothetical protein Mthe_0053 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.8e-07   29.6   0.1    1.2e-06   28.0   0.1    1.9  2  ArsA_HSP20  HSP20-like domain found in ArsA
    5.2e-05   23.3   0.1      0.048   13.8   0.1    2.4  2  HSP20       Hsp20/alpha crystallin family
     0.0011   19.0   0.2     0.0019   18.3   0.2    1.3  1  GvpH        GvpH
  ------ inclusion threshold ------
       0.19   11.6   0.1       0.31   10.9   0.1    1.4  1  HSBP1       Heat shock factor binding protein 1


Domain annotation for each model (and alignments):
>> ArsA_HSP20  HSP20-like domain found in ArsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.027   1.2e+02       8      31 ..     121     146 ..     120     147 .. 0.87
   2 !   28.0   0.1   2.6e-10   1.2e-06       3      61 ..     141     197 ..     139     199 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.027
                     ArsA_HSP20   8 ldLPfvdkee..idlsrsgdeLtIki 31 
                                    +++P+  +++  +d+  +g+ +t+ +
  gi|116753377|ref|YP_842495.1| 121 VRIPGTPRKDpiVDVMDEGKSITVVA 146
                                    799***9998789**********987 PP

  == domain 2  score: 28.0 bits;  conditional E-value: 2.6e-10
                     ArsA_HSP20   3 eyvlkldLPfvdkeeidlsrsgdeLtIkignfrRqitLPsvlarkevtsAkfedgvLeI 61 
                                     + ++++LP+v+++e++++ ++  L I++g f +++ LP   a++ + s +f++g L  
  gi|116753377|ref|YP_842495.1| 141 SITVVAELPGVEEDELSVTVREGVLEIRAGEFLKEVKLPPD-AGD-IISRSFKNGILQL 197
                                    6889************************************9.555.77999****9976 PP

>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   1.1e-05     0.048       1      37 [.     134     170 ..     134     171 .. 0.92
   2 !   10.2   0.0   0.00014      0.64      51      87 ..     166     201 ..     164     204 .] 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.1e-05
                                    E--SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE CS
                          HSP20   1 dikeeeeefevkldvpglkkeelkvkvednrvlvkge 37 
                                    d+++e ++++v +++pg++++el v+v+++++ ++++
  gi|116753377|ref|YP_842495.1| 134 DVMDEGKSITVVAELPGVEEDELSVTVREGVLEIRAG 170
                                    57889999************************99986 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00014
                                    SS---EEEEEE--STTB-TTT-EEEEETTEEEEEEEB CS
                          HSP20  51 erssrkFsrkftLPenvdadkvkaslkdGvLtvtvpk 87 
                                    e ++++F ++++LP ++  d ++ s+k+G+L++ +++
  gi|116753377|ref|YP_842495.1| 166 EIRAGEFLKEVKLPPDAG-DIISRSFKNGILQLRIDR 201
                                    67889*********9875.5677777*******9987 PP

>> GvpH  GvpH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.2   4.2e-07    0.0019      98     165 ..     137     201 ..     133     204 .] 0.85

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 4.2e-07
                           GvpH  98 ddsdelvvvadlpGvtdedvdvaletdeqaltlrvdddvverlvlddpdvaitdltlrnqvlelrlar 165
                                    d++  + vva+lpGv ++++ v++   e+ l +r ++ +   + l      i + + +n +l+lr+ r
  gi|116753377|ref|YP_842495.1| 137 DEGKSITVVAELPGVEEDELSVTVR--EGVLEIRAGEFLK-EVKLPPDAGDIISRSFKNGILQLRIDR 201
                                    778899***************9999..9******998665.567765556789999*********987 PP

>> HSBP1  Heat shock factor binding protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1     7e-05      0.31      27      48 ..       7      28 ..       1      31 [. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 7e-05
                          HSBP1 27 sriDdMssriDdLEksiadlmt 48
                                   +r++ +++r+D++Ek +++l++
  gi|116753377|ref|YP_842495.1|  7 DRLEKIERRLDEIEKVLKSLTS 28
                                   79***************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      665  (0.0370907); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1574.79
//
Query:       gi|116753378|ref|YP_842496.1|  [L=90]
Description: hypothetical protein Mthe_0054 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.26s 00:00:00.58 Elapsed: 00:00:00.40
# Mc/sec: 677.81
//
Query:       gi|116753379|ref|YP_842497.1|  [L=205]
Description: gas vesicle synthesis GvpLGvpF [Methanosaeta thermophila PT]
Scores for complete 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-35  122.3   0.4    3.7e-17   63.1   0.2    2.0  2  GvpL_GvpF     Gas vesicle synthesis protein GvpL/GvpF
  ------ inclusion threshold ------
       0.13   11.9   0.0       0.36   10.5   0.0    1.7  2  Transket_pyr  Transketolase, pyrimidine binding domain


Domain annotation for each model (and alignments):
>> GvpL_GvpF  Gas vesicle synthesis protein GvpL/GvpF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.1   0.2   4.1e-21   3.7e-17      19     123 ..       8     110 ..       2     115 .. 0.92
   2 !   58.1   0.0   1.4e-19   1.2e-15     169     244 .]     113     188 ..     109     188 .. 0.95

  Alignments for each domain:
  == domain 1  score: 63.1 bits;  conditional E-value: 4.1e-21
                      GvpL_GvpF  19 d...tGvdgepVrlvragglaavvsdvpeeeydaerleqverwllaHqrVvealmaegtvlPlrFgtvlkdeeavrelLe 95 
                                    d   +G ++++V+++++++l  vvs++   eyd ++++     +  H rVv+++m+e+ vlP+ +g+v+k+++ +  +++
  gi|116753379|ref|YP_842497.1|   8 DfgpIGFGNSEVHTIEYRDLYPVVSEAVLREYDVDERD-----VEIHRRVVRRVMEEHDVLPVAYGMVFKGRKNLAVAMS 82 
                                    23349*********************************.....************************************* PP

                      GvpL_GvpF  96 eeadelreaLerlagkvEygvkvlwdee 123
                                    + ++ +++a   ++gkvE+gvkv   ++
  gi|116753379|ref|YP_842497.1|  83 AGYAAMKKAWPVVEGKVELGVKVIRPKN 110
                                    ***********************98874 PP

  == domain 2  score: 58.1 bits;  conditional E-value: 1.4e-19
                      GvpL_GvpF 169 erreelaeeleeaLaplaeevrerepqdeemvlnaafLvdrdreeefgeaveelaarldglevrltGPwpPYsFvp 244
                                     + +el +e+ e L++ +++++  +  +++ +ln afLv+r+r +ef ++v+++ +++ +l+  ++GPwpPY+Fv+
  gi|116753379|ref|YP_842497.1| 113 GQYDELKREIVECLSASSVDFKNLDLFSDRLLLNTAFLVERSRIDEFSKRVSAVIEEHSDLRTSYSGPWPPYNFVD 188
                                    56789999******************************************************************95 PP

>> Transket_pyr  Transketolase, pyrimidine binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0     4e-05      0.36      46      85 ..      45      86 ..      23     106 .. 0.82
   2 ?   -1.6   0.0       0.2   1.8e+03     138     158 ..     102     122 ..      86     125 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 4e-05
                                   T...TEGEEE--S-HHHHHHHHHHHHHHCTTEEEEEEEEHHHH CS
                   Transket_pyr 46 g...egrvidsgisEqavlgfavGaalagpllviveaqFgdFa 85
                                   +   ++rv++  + E+ vl +a+G+ ++g+ + +++a+ + +a
  gi|116753379|ref|YP_842497.1| 45 DveiHRRVVRRVMEEHDVLPVAYGMVFKGR-KNLAVAMSAGYA 86
                                   144567***********************5.889999888776 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.2
                                    TEEEE--SSHHHHHHHHHHHH CS
                   Transket_pyr 138 glkvvrPsdpaetkhllrrai 158
                                    g+kv+rP++++  +  l+r i
  gi|116753379|ref|YP_842497.1| 102 GVKVIRPKNANGQYDELKREI 122
                                    58999**99998777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); 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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1547.77
//
Query:       gi|116753380|ref|YP_842498.1|  [L=90]
Description: gas vesicle synthesis family protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.1e-28   96.6   0.1    6.5e-28   96.5   0.1    1.0  1  GvpO      Gas vesicle synthesis protein GvpO
  ------ inclusion threshold ------
       0.14   12.0   0.0       0.16   11.8   0.0    1.3  1  DUF2835   Protein of unknown function (DUF2835)


Domain annotation for each model (and alignments):
>> GvpO  Gas vesicle synthesis protein GvpO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.5   0.1   7.3e-32   6.5e-28      12      91 ..       3      82 ..       1      85 [. 0.94

  Alignments for each domain:
  == domain 1  score: 96.5 bits;  conditional E-value: 7.3e-32
                           GvpO 12 rleaaeaarkareqlaeLlgrelegvssvertedgWrvevevlElervPdttdilasYeveldeegeltgYrrvrRYrRg 91
                                   + ++++  r ar++++eLlg+++e++ss++rtedgW v+vevlE++++Pdt+di+++Ye+++de+g++tgYrr++  +Rg
  gi|116753380|ref|YP_842498.1|  3 KPNLKDMLRIARTSAEELLGKRFESISSISRTEDGWIVNVEVLERRAIPDTQDIIGRYEMSFDENGDITGYRRMELRHRG 82
                                   56788999******************************************************************977777 PP

>> DUF2835  Protein of unknown function (DUF2835)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.8e-05      0.16      28      70 ..      33      75 ..       9      88 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.8e-05
                        DUF2835 28 raedGrrvqlpashlrpfvthdGvrGrFrleldeqnkfvsler 70
                                   r+edG  v+++    r   + + + Gr+++++de++ + + +r
  gi|116753380|ref|YP_842498.1| 33 RTEDGWIVNVEVLERRAIPDTQDIIGRYEMSFDENGDITGYRR 75
                                   7899999999999999999999**************9887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 653.15
//
Query:       gi|116753381|ref|YP_842499.1|  [L=120]
Description: hypothetical protein Mthe_0057 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); 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: 0.36u 0.28s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 858.30
//
Query:       gi|116753382|ref|YP_842500.1|  [L=351]
Description: gas vesicle protein GvpN [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-16   60.2   0.0    2.5e-15   56.7   0.0    2.2  1  AAA_5            AAA domain (dynein-related subfamily)
    5.9e-06   26.7   0.0    1.3e-05   25.6   0.0    1.8  1  AAA              ATPase family associated with various cellul
    5.7e-05   22.7   0.0    0.00011   21.8   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
    0.00038   20.1   0.0     0.0008   19.0   0.0    1.6  1  AAA_25           AAA domain
    0.00067   20.1   0.0     0.0018   18.7   0.0    1.6  1  AAA_16           AAA ATPase domain
      0.001   18.4   0.0      0.085   12.1   0.0    2.4  2  Zeta_toxin       Zeta toxin
      0.004   17.7   0.0      0.012   16.1   0.0    1.9  2  ABC_tran         ABC transporter
     0.0051   16.2   0.0       0.01   15.3   0.0    1.5  1  IPT              Isopentenyl transferase
     0.0074   16.1   0.0       0.16   11.8   0.0    2.3  1  AAA_3            ATPase family associated with various cellul
     0.0098   16.1   0.0      0.019   15.1   0.0    1.5  1  AAA_33           AAA domain
  ------ inclusion threshold ------
      0.013   15.7   0.2      0.052   13.8   0.0    2.1  2  AAA_28           AAA domain
      0.016   14.9   0.0      0.033   13.9   0.0    1.5  1  IstB_IS21        IstB-like ATP binding protein
      0.022   14.8   0.0       0.51   10.4   0.0    2.4  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.023   15.0   0.0      0.095   13.0   0.0    2.0  2  AAA_22           AAA domain
      0.032   14.6   0.0      0.076   13.4   0.0    1.7  1  RNA_helicase     RNA helicase
      0.033   13.9   0.0      0.068   12.9   0.0    1.5  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.033   14.1   0.0       0.14   12.0   0.0    2.0  2  NACHT            NACHT domain
      0.068   13.3   0.0       0.17   12.0   0.0    1.7  2  Sigma54_activ_2  Sigma-54 interaction domain
      0.081   12.1   0.0       0.18   11.0   0.0    1.5  1  TIP49            TIP49 P-loop domain
      0.097   13.2   0.0       0.25   11.9   0.0    1.7  1  AAA_18           AAA domain
       0.12   11.8   0.0       0.26   10.7   0.0    1.5  1  PhoH             PhoH-like protein
       0.14   11.1   0.0       0.37    9.7   0.0    1.7  2  AAA_6            Hydrolytic ATP binding site of dynein motor 


Domain annotation for each model (and alignments):
>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.7   0.0   3.1e-18   2.5e-15       2     138 .]      89     242 ..      88     242 .. 0.90

  Alignments for each domain:
  == domain 1  score: 56.7 bits;  conditional E-value: 3.1e-18
                                    EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--...........................------- CS
                          AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik..................ngttslvdsplvraa 63 
                                    v L+Gp+G+gK++la+++a+ ++r+v+ +++ +++t++dl+g+++                      + ++vd+pl  a+
  gi|116753382|ref|YP_842500.1|  89 VHLIGPTGCGKTSLAMHVARQFGRPVVWINGDESITTADLIGGYSQIenesvrdkyihnvfkskdVMKVEWVDNPLSLAC 168
                                    77******************************************976899999999999998776667889999999999 PP

                                    -G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--..-TT-TTHHHHTT- CS
                          AAA_5  64 regeilvlDEveraesevlnsLlslleerrllleeggelvkaknddllerfrviatanpld.rslnelspalrsRf 138
                                    + g +l+ +E+ r ++++ n++ls++ee  l l+  +++ +  +    ++fr i t+n+ +  + ++ + al++R+
  gi|116753382|ref|YP_842500.1| 169 KYGYTLIYNEFSRTKPAANNVFLSVFEEGVLELPTKFGEDRYIR--VHPEFRAILTSNSIEyAGIHRPQDALLDRM 242
                                    9**********************************999987666..5566**********9966666688999986 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   1.6e-08   1.3e-05       2      38 ..      90     132 ..      89     244 .. 0.79

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.6e-08
                                    EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS......S CS
                            AAA   2 llyGppGtGKTllakavakelgvefleisgsellsk......y 38 
                                     l+Gp G+GKT+la  va+++g++++ i+g e +        y
  gi|116753382|ref|YP_842500.1|  90 HLIGPTGCGKTSLAMHVARQFGRPVVWINGDESITTadliggY 132
                                    699***************************9988444555551 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 !   21.8   0.0   1.4e-07   0.00011      11      57 ..      64     110 ..      59     119 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.4e-07
                          AAA_7  11 eilVptvdtvrysyllelllknkkpvllvGptGtGKtviikdllkkl 57 
                                    e +V+t +   ++  ++l l++++pv l+GptG+GKt++++++ +++
  gi|116753382|ref|YP_842500.1|  64 EHFVETPEVRETEARMKLWLDAGYPVHLIGPTGCGKTSLAMHVARQF 110
                                    579************************************99988776 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   9.8e-07    0.0008      13      55 ..      65     108 ..      54     126 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 9.8e-07
                         AAA_25  13 adlaa.pppprrwlvkgllpagelallaGapgtGKttlaldlal 55 
                                    +++++ + ++ +  +k +l ag  + l+G++g+GKt la+++a 
  gi|116753382|ref|YP_842500.1|  65 HFVETpEVRETEARMKLWLDAGYPVHLIGPTGCGKTSLAMHVAR 108
                                    555555677888999************************99986 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   2.2e-06    0.0018      27      61 ..      89     122 ..      83     143 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.2e-06
                         AAA_16  27 vllsGesGvGKsslvrellralekdggiflrgkcd 61 
                                    v l+G+ G+GK+sl+ +++r++ +  +++++g+  
  gi|116753382|ref|YP_842500.1|  89 VHLIGPTGCGKTSLAMHVARQFGRP-VVWINGDES 122
                                    789*********************9.555665543 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0    0.0001     0.085      21      67 ..      91     138 ..      79     183 .. 0.67
   2 ?    3.8   0.0     0.037        30      49      87 ..     205     243 ..     200     279 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0001
                     Zeta_toxin  21 lgGqpGAGKselaellkdelerqgnvvrldpDd...lRelhPeyeeilka 67 
                                    l G +G+GK++la  +++++  ++ vv +++D+      l+  y++i+++
  gi|116753382|ref|YP_842500.1|  91 LIGPTGCGKTSLAMHVARQF--GRPVVWINGDEsitTADLIGGYSQIENE 138
                                    56899***************..9*********822234567777777775 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.037
                     Zeta_toxin  49 ldpDdlRelhPeyeeilkadpkkaseltqkdaselvekl 87 
                                    + +D++ + hPe+++il  ++ +++   +++   l +++
  gi|116753382|ref|YP_842500.1| 205 FGEDRYIRVHPEFRAILTSNSIEYAGIHRPQDALLDRMV 243
                                    56899*************999999888777766666665 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0         9   7.3e+03      38      62 ..      30      55 ..      19      74 .. 0.59
   2 !   16.1   0.0   1.5e-05     0.012       4      35 ..      79     110 ..      76     167 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 9
                                   SEEEEEET.TCEGGGB-HHHCCHCEE CS
                                   xxxxxxxx.xxxxxxxxxxxxxxxxx RF
                       ABC_tran 38 teGeilld.gkdlkeqeleslrkeig 62
                                   + +ei+++ + ++  ++ e lrkei+
  gi|116753382|ref|YP_842500.1| 30 EREEIQVKvQSQTAARDPETLRKEIE 55
                                   44445444223333345555555554 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.5e-05
                                    EEEEEETTSEEEEEESTTSSHHHHHHHHTTSS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   4 vslklkegekvaivGenGaGKStLlkllagll 35 
                                    ++l l +g  v ++G++G+GK++L++ +a++ 
  gi|116753382|ref|YP_842500.1|  79 MKLWLDAGYPVHLIGPTGCGKTSLAMHVARQF 110
                                    5677889999***************9998875 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.2e-05      0.01       6      32 ..      91     117 ..      87     146 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.2e-05
                            IPT   6 ifGatttGKtaeaiklaketgapvivl 32 
                                    + G+t+ GKt+ a+++a++ g pv+ +
  gi|116753382|ref|YP_842500.1|  91 LIGPTGCGKTSLAMHVARQFGRPVVWI 117
                                    45**********************964 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0    0.0002      0.16      65     129 ..     173     242 ..      89     244 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0002
                          AAA_3  65 llladeinrappktqsalleameerqvtv.....egethklpepflvlatqnPieqeGtyplpeaqldrf 129
                                     l+ +e  r++p ++  +l + ee  + +     e++  +++  f  + t n ie+ G +   +a ldr+
  gi|116753382|ref|YP_842500.1| 173 TLIYNEFSRTKPAANNVFLSVFEEGVLELptkfgEDRYIRVHPEFRAILTSNSIEYAGIHRPQDALLDRM 242
                                    5788999****************998765222223455689999*************************7 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.3e-05     0.019       2      35 ..      89     124 ..      89     170 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.3e-05
                         AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrr 35 
                                    v l+G+ G+GK+ la +++++ g  +v ++ d+ ++
  gi|116753382|ref|YP_842500.1|  89 VHLIGPTGCGKTSLAMHVARQFGrpVVWINGDESIT 124
                                    5689******************99888899998444 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       3.1   2.5e+03     103     103 ..      48      48 ..      11      84 .. 0.54
   2 ?   13.8   0.0   6.4e-05     0.052       2      28 ..      89     116 ..      88     139 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 3.1
                         AAA_28 103 a 103
                                    +
  gi|116753382|ref|YP_842500.1|  48 E 48 
                                    2 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 6.4e-05
                         AAA_28   2 ivitGgestGKTtlleaLaar.gypvvp 28 
                                    + ++G+ ++GKT+l+ + a++ g pvv+
  gi|116753382|ref|YP_842500.1|  89 VHLIGPTGCGKTSLAMHVARQfGRPVVW 116
                                    569****************999999986 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0     4e-05     0.033      40      70 ..      79     109 ..      60     139 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4e-05
                      IstB_IS21  40 tlsfiekkenivllGpsGvGKshlaialgve 70 
                                       ++++   + l+Gp+G GK+ la+ ++++
  gi|116753382|ref|YP_842500.1|  79 MKLWLDAGYPVHLIGPTGCGKTSLAMHVARQ 109
                                    45699999*****************988776 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00062      0.51      19      44 ..      86     111 ..      64     118 .. 0.76
   2 ?    1.6   0.0      0.31   2.6e+02      77     102 ..     137     162 ..     129     181 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00062
                                    TEEEEEEESTTSSHHHHHHHHHHHTT CS
                           TsaE  19 gdvilLeGdLGaGKTtlvrglakalg 44 
                                    g  ++L G+ G+GKT l+ ++a+++g
  gi|116753382|ref|YP_842500.1|  86 GYPVHLIGPTGCGKTSLAMHVARQFG 111
                                    44599*****************9987 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.31
                                    THHHHHCTTCCCCSTSCEEEEETGGG CS
                           TsaE  77 eeeleelgleeyleeeavvlvEWpek 102
                                    +e++ +  ++++++++ v+ vEW ++
  gi|116753382|ref|YP_842500.1| 137 NESVRDKYIHNVFKSKDVMKVEWVDN 162
                                    56678888999999778******987 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       4.5   3.7e+03      43      65 ..      34      59 ..      17      79 .. 0.63
   2 ?   13.0   0.0   0.00012     0.095      10      51 ..      91     123 ..      84     142 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 4.5
                         AAA_22 43 vfvtlpsst...sskdllrellralg 65
                                   + v+++s+t   ++++l++e+ +a+ 
  gi|116753382|ref|YP_842500.1| 34 IQVKVQSQTaarDPETLRKEIEEAFL 59
                                   44444444444666666666666654 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00012
                         AAA_22  10 vtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst 51 
                                    ++G++G+GKT l+  +++q+         +++vv ++  +s 
  gi|116753382|ref|YP_842500.1|  91 LIGPTGCGKTSLAMHVARQF---------GRPVVWINGDESI 123
                                    89*****************9.........7777766665555 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   9.3e-05     0.076       2      31 ..      90     119 ..      89     156 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.3e-05
                   RNA_helicase   2 wlyGpsgeGKStlakeLakallkklklkkk 31 
                                     l Gp+g+GK++la ++a+++ + +  ++ 
  gi|116753382|ref|YP_842500.1|  90 HLIGPTGCGKTSLAMHVARQFGRPVVWING 119
                                    689***************999877644444 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 ?   12.9   0.0   8.3e-05     0.068      36      87 ..      89     140 ..      66     157 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.3e-05
                         RuvB_N  36 vllyGpPGlGkttlakiiakelgvklkitsgPvlekagdlaalltnleekdv 87 
                                    v l+Gp G Gkt+la+ +a+++g  +    g     ++dl++  +++e++ v
  gi|116753382|ref|YP_842500.1|  89 VHLIGPTGCGKTSLAMHVARQFGRPVVWINGDESITTADLIGGYSQIENESV 140
                                    6799*******************99999999888888898888888887766 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00018      0.14       3      24 ..      89     110 ..      87     115 .. 0.87
   2 ?   -1.9   0.0       3.4   2.7e+03     107     148 ..     173     214 ..     168     216 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00018
                                    EEEEC-TTTCHHHHHHHHHHHH CS
                          NACHT   3 vilqGeaGsGKTtLlqklalaw 24 
                                    v l G+ G+GKT L+ ++a++ 
  gi|116753382|ref|YP_842500.1|  89 VHLIGPTGCGKTSLAMHVARQF 110
                                    7899**************9875 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.4
                                    ..HHHHHCTTTTT--EEEEEEECCCHHHHCTTSSCE..EEEE CS
                          NACHT 107 tlLselirkkllpeasllltvrpralrdleeqleeaivleve 148
                                    tl+ + ++++ +  + ++l+v  +++ +l+ ++ e +++ v 
  gi|116753382|ref|YP_842500.1| 173 TLIYNEFSRTKPAANNVFLSVFEEGVLELPTKFGEDRYIRVH 214
                                    788888999999999999999999999999999998888775 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 ?   -2.4   0.0       5.9   4.8e+03      42      81 ..      27      66 ..      24      70 .. 0.66
   2 ?   12.0   0.0   0.00021      0.17       6      44 ..      71     109 ..      66     127 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 5.9
                                   --TTS-EE--SSTTHHHH-HHHHHHHTTTSEEEEEE-TT- CS
                Sigma54_activ_2 42 hknsgpwleifvverlaklpldlleqakggtLylkdiadl 81
                                    +++ + ++++v  + a+   ++l +  +  +++++++++
  gi|116753382|ref|YP_842500.1| 27 LSKEREEIQVKVQSQTAARDPETLRKEIEEAFLMPEVEHF 66
                                   4444555777777777776677777777777778888765 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00021
                                    HHHHHHHHHHHHHT-SS-EEEEEETT--HHHHHHCC--T CS
                Sigma54_activ_2   6 aiqelkerLeqaaqsklpvfltGekGsgkelvArlLhkn 44 
                                     + e + r++    +  pv+l+G+ G+gk++ A   + +
  gi|116753382|ref|YP_842500.1|  71 EVRETEARMKLWLDAGYPVHLIGPTGCGKTSLAMHVARQ 109
                                    56667778888888999**************99877665 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00022      0.18      49      84 ..      85     118 ..      80     127 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00022
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49  49 aGravLlaGpsgtGktalaiaiskelgedvpfvals 84 
                                    aG  v l Gp+g Gkt+la+ +++++g+    v ++
  gi|116753382|ref|YP_842500.1|  85 AGYPVHLIGPTGCGKTSLAMHVARQFGRP--VVWIN 118
                                    56778899******************964..44455 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0    0.0003      0.25       3      44 ..      91     138 ..      89     162 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0003
                         AAA_18   3 ltGtpGvGKttlakeLskrlgf......gvnlrdvakenglllevdpe 44 
                                    l G+ G+GKt+la ++++  g       g++++ +a   g +   ++e
  gi|116753382|ref|YP_842500.1|  91 LIGPTGCGKTSLAMHVARQFGRpvvwinGDESITTADLIGGYSQIENE 138
                                    89****************976678866666666666655555555555 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00032      0.26      22      41 ..      89     108 ..      76     112 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00032
                                    EEEE--TTSSTTHHHHHHHH CS
                           PhoH  22 vfaiGpaGtGKtylavalav 41 
                                    v  iGp+G+GKt la+ +a 
  gi|116753382|ref|YP_842500.1|  89 VHLIGPTGCGKTSLAMHVAR 108
                                    6789************9985 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 ?    9.7   0.0   0.00046      0.37      36      73 ..      90     127 ..      64     135 .. 0.88
   2 ?   -1.8   0.0       1.5   1.2e+03     125     148 ..     207     231 ..     145     289 .. 0.53

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00046
                          AAA_6  36 apaGpagtGKtEtvkdLakalakqvvvfncsdqldyks 73 
                                     + Gp+g GKt     +a+++++ vv +n ++++++  
  gi|116753382|ref|YP_842500.1|  90 HLIGPTGCGKTSLAMHVARQFGRPVVWINGDESITTAD 127
                                    568*****************************998765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.5
                          AAA_6 125 egkeiklnksvgifitmnp.gyagr 148
                                    e++ i++++++++++t n+ +yag 
  gi|116753382|ref|YP_842500.1| 207 EDRYIRVHPEFRAILTSNSiEYAGI 231
                                    4555666666666666655455554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); 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: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 2328.91
//
Query:       gi|116753383|ref|YP_842501.1|  [L=299]
Description: hypothetical protein Mthe_0059 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.9e-05   23.3  21.2      0.013   15.4   4.9    2.7  2  Apolipoprotein  Apolipoprotein A1/A4/E domain
  ------ inclusion threshold ------
      0.012   14.8   4.2        0.5    9.5   1.4    2.4  2  DLP_helical     Dynamin-like helical domain
      0.047   14.0   0.3        1.6    9.0   0.1    2.7  2  DUF3135         Protein of unknown function (DUF3135)
      0.076   11.6   0.7       0.13   10.8   0.7    1.4  1  Zw10            Centromere/kinetochore Zw10
      0.084   12.4   4.9        1.2    8.6   0.3    2.5  2  Tsc35           Testis-specific protein 35
       0.13   12.6   3.7        1.1    9.5   0.2    3.6  3  WXG100          Proteins of 100 residues with WXG
       0.13   12.3   6.6       0.13   12.3   0.4    3.2  3  ApoLp-III       Apolipophorin-III precursor (apoLp-III)
       0.18   11.8   2.7        6.1    6.8   0.1    3.6  4  ApoO            Apolipoprotein O
       0.36   11.0   1.9        1.4    9.0   0.3    2.4  2  Fib_alpha       Fibrinogen alpha/beta chain family
       0.47    8.4   1.8        2.6    5.9   0.4    2.0  2  Prominin        Prominin
       0.49   10.5   6.4        2.2    8.4   0.1    3.3  3  Flagellin_N     Bacterial flagellin N-terminal helical region
       0.52    9.0   8.4       0.55    8.9   1.5    2.6  2  Tektin          Tektin family
       0.55    9.7   5.7        5.9    6.4   0.1    2.4  2  DUF334          Domain of unknown function (DUF334)
        1.2    9.7   5.7        2.5    8.6   1.8    3.2  2  DUF16           Protein of unknown function DUF16
        2.6    8.1   8.6          6    6.9   0.4    3.7  4  DUF1664         Protein of unknown function (DUF1664)
        4.7    6.6   7.4         54    3.1   4.0    3.1  2  DUF4618         Domain of unknown function (DUF4618)
        5.3    7.1  10.6        7.5    6.6   0.2    3.8  4  COG2            COG (conserved oligomeric Golgi) complex comp
        8.1    6.9  10.2        1.8    9.0   1.3    3.6  4  kleA_kleC       Uncharacterized KorC regulated protein A


Domain annotation for each model (and alignments):
>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7  10.0   0.00018      0.18      43     177 ..      14     172 ..       1     175 [. 0.77
   2 !   15.4   4.9   1.3e-05     0.013      77     182 ..     175     282 ..     170     287 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00018
                                    HHHHHHHHHHCC.CCHHHHHHCCCHHHHHHHHHCCHHHHHHHH...........HHHHCHHCCHHCHCCHCHH....... CS
                 Apolipoprotein  43 raeleevrarle.pyrdevqeqlgqnleelrqrlapyteelre...........rlaadaeelqeqlavyaee....... 103
                                    r+elee   +l  + +   ++ql++++ e r+r +p + e               + ++a            e       
  gi|116753383|ref|YP_842501.1|  14 RRELEEMAVKLGiQSLGGTKAQLAESIVEARRRAQPQIAESGTaevqvkpeeqkGVPEKAA-----------Evkpqvsp 82 
                                    6677777777643677777888888888888888888777754333333333333333333...........26777777 PP

                                    .............HHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH-----..---...--SSSHHHHHHHTS-TTS CS
                 Apolipoprotein 104 .............lrerlerhvealkarlapyveelrqklaerleelkeslaphaeeve...erlssrveelrekleeqa 167
                                                  +e ++r+ ++l++   +++ee+++++a+++ +lk+s++ ++ e +   ++++  v++++ + +++ 
  gi|116753383|ref|YP_842501.1|  83 evppvvpgkgvraRQEAMRRKSSELRSAGVAIREEGVSRMAKSVNALKKSIEGQVTENKkgiAKIRTGVRQMKLSINKTS 162
                                    7888******99888889999************************************9999******************* PP

                                    HHHHHS--XX CS
                 Apolipoprotein 168 eelrerlean 177
                                    +elr + e++
  gi|116753383|ref|YP_842501.1| 163 DELRKSGERI 172
                                    ****998876 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.3e-05
                                    HHHHHHHHHHHHCHHCCHHCHCCHCHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH-----..-----SSSHH CS
                 Apolipoprotein  77 pyteelrerlaadaeelqeqlavyaeelrerlerhvealkarlapyveelrqklaerleelkeslaphaeeveerlssrv 156
                                    + ++el+e l++   +l  q+++  +++ +r+ +++ ++++ ++  + ++r++ ++  ee  ++l++ ++++++ l+s+v
  gi|116753383|ref|YP_842501.1| 175 EGARELNEGLRRFRADLDSQIRK-NRDAVSRMGSGAAEIRSAMDKMSVDFRKSGDHIREEGARELNEGLRRFRADLDSQV 253
                                    5689999999999999****998.7788899************************************************* PP

                                    HHHHHTS-T...TSHHHHHS--XXXXXXX CS
                 Apolipoprotein 157 eelreklee...qaeelrerleanleelk 182
                                    +e r++ ++   +a+el+ r+ a  +e++
  gi|116753383|ref|YP_842501.1| 254 RENRDAISRmniAAKELHSRALALRDEMQ 282
                                    *********99999999999988655554 PP

>> DLP_helical  Dynamin-like helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   1.4    0.0005       0.5      66     134 ..     127     196 ..     104     200 .. 0.83
   2 ?    7.4   0.2    0.0022       2.2      74     135 ..     193     255 ..     191     291 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0005
                    DLP_helical  66 svirdvlerqlpeaeerleelekevekleesakriekelaelkkeiee.arielreelkayfsdLilqvk 134
                                      ++  +e q+ e ++ + ++ + v++ + s +++++el++  ++i e  ++el+e l++++ dL  q++
  gi|116753383|ref|YP_842501.1| 127 NALKKSIEGQVTENKKGIAKIRTGVRQMKLSINKTSDELRKSGERIREeGARELNEGLRRFRADLDSQIR 196
                                    456677777888889999999999**********************7516789************99987 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0022
                    DLP_helical  74 rqlpeaeerleelekevekleesakriekelaelkkeiee.arielreelkayfsdLilqvkg 135
                                     q+ + +++++++ + +++ ++++ +++ ++++   +i e  ++el+e l++++ dL  qv+ 
  gi|116753383|ref|YP_842501.1| 193 SQIRKNRDAVSRMGSGAAEIRSAMDKMSVDFRKSGDHIREeGARELNEGLRRFRADLDSQVRE 255
                                    6778888999999999**********************7516799************999975 PP

>> DUF3135  Protein of unknown function (DUF3135)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.27   2.7e+02      38      76 ..     180     218 ..     169     221 .. 0.80
   2 ?    9.0   0.1    0.0017       1.6      39      81 .]     239     281 ..     230     281 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.27
                        DUF3135  38 mqrrLrglqfqiDmqlsraknPvaacvalsrmmqeklve 76 
                                      + Lr+ + ++D q+++ ++ v ++   +++ +  +++
  gi|116753383|ref|YP_842501.1| 180 LNEGLRRFRADLDSQIRKNRDAVSRMGSGAAEIRSAMDK 218
                                    566799999*************99997777776666665 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0017
                        DUF3135  39 qrrLrglqfqiDmqlsraknPvaacvalsrmmqeklvelrraL 81 
                                     + Lr+ + ++D q++  ++ + +++ ++++++ +  +lr+ +
  gi|116753383|ref|YP_842501.1| 239 NEGLRRFRADLDSQVRENRDAISRMNIAAKELHSRALALRDEM 281
                                    5679999*****************************9999865 PP

>> Zw10  Centromere/kinetochore Zw10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.7   0.00013      0.13      15     170 ..     118     282 ..     114     293 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00013
                           Zw10  15 kisklekkveeikeevskmivkkYseflelsssaeellerveslskeidalkkkveneieqdlkaaveel.aelkqqlke 93 
                                     +s++ k v+ +k+++  ++ ++ ++  ++ +   ++   +++ s+e   + +++ +e  ++l++    + a+l  q+++
  gi|116753383|ref|YP_842501.1| 118 GVSRMAKSVNALKKSIEGQVTENKKGIAKIRTGVRQMKLSINKTSDELRKSGERIREEGARELNEGLRRFrADLDSQIRK 197
                                    5899***********************************************************999988779******99 PP

                           Zw10  94 kevvle.llealkkieealeelkealknk.......aflvaadlleelkslldlekvekafqlkilkalrkelsvlsenl 165
                                    ++  ++ +     +i +a+ ++    ++          ++  + l++ ++ ld++  e  + +  ++  +kel+  +  l
  gi|116753383|ref|YP_842501.1| 198 NRDAVSrMGSGAAEIRSAMDKMSVDFRKSgdhireeGARELNEGLRRFRADLDSQVRENRDAISRMNIAAKELHSRALAL 277
                                    98765413344556666665555443333222222144445555555555555554444444555666666666666666 PP

                           Zw10 166 qykLg 170
                                    +++++
  gi|116753383|ref|YP_842501.1| 278 RDEMQ 282
                                    66655 PP

>> Tsc35  Testis-specific protein 35
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.6     0.011        11      35      67 ..     163     195 ..     122     207 .. 0.82
   2 ?    8.6   0.3    0.0012       1.2      37     101 ..     223     288 ..     208     294 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.011
                          Tsc35  35 kgvkqeGlltkkGvtkelknelrevreelkekm 67 
                                     ++++ G  +++ +++el + lr  r +l  ++
  gi|116753383|ref|YP_842501.1| 163 DELRKSGERIREEGARELNEGLRRFRADLDSQI 195
                                    47999***********************98776 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0012
                          Tsc35  37 vkqeGlltkkGvtkelknelrevreelkekmeeikqikdimdkdfdklkef.veimkemqkdmdek 101
                                    +++ G  +++ +++el + lr  r +l  ++ e +   + m+     l+   + +  emq+ +d+ 
  gi|116753383|ref|YP_842501.1| 223 FRKSGDHIREEGARELNEGLRRFRADLDSQVRENRDAISRMNIAAKELHSRaLALRDEMQRYVDQD 288
                                    6789****************************9999888898888888865156667888888865 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 ?    9.5   0.2    0.0011       1.1       4      83 ..      95     174 ..      92     177 .. 0.86
   2 ?    0.2   0.0      0.89   8.8e+02       8      28 ..     215     235 ..     213     256 .. 0.79
   3 ?    0.0   0.1         1     1e+03      10      35 ..     257     282 ..     248     288 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0011
                                    SHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHCGCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100   4 vdpeelrqaaarfqkqaeelede.lqrlkaevdalqsgWsGaaadafqaefeewkqaaqklvdaLeeisealkqaanafe 82 
                                    +  e++r ++++++++   +++e ++r++++v+al+ + +G+  +  ++ +++++ ++++++   +++s++l++++++ +
  gi|116753383|ref|YP_842501.1|  95 ARQEAMRRKSSELRSAGVAIREEgVSRMAKSVNALKKSIEGQVTE-NKKGIAKIRTGVRQMKLSINKTSDELRKSGERIR 173
                                    56688999999999999998765378***************9755.58899***********************999876 PP

                                    H CS
                         WXG100  83 d 83 
                                    +
  gi|116753383|ref|YP_842501.1| 174 E 174
                                    5 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.89
                                    HHHHHHHHHHHHHHHHHHHHH CS
                         WXG100   8 elrqaaarfqkqaeeledelq 28 
                                    ++++++ +f+k+ +++++e +
  gi|116753383|ref|YP_842501.1| 215 AMDKMSVDFRKSGDHIREEGA 235
                                    688888888888888887755 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 1
                                    HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100  10 rqaaarfqkqaeeledelqrlkaevd 35 
                                    r+a++r++ +a+el+++  +l+ e++
  gi|116753383|ref|YP_842501.1| 257 RDAISRMNIAAKELHSRALALRDEMQ 282
                                    78888888888888888877777776 PP

>> ApoLp-III  Apolipophorin-III precursor (apoLp-III)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.8      0.44   4.4e+02      95     123 ..      25      53 ..       2      77 .. 0.81
   2 ?   12.3   0.4   0.00013      0.13      29      79 ..     117     170 ..     112     226 .. 0.73
   3 ?   -0.2   0.0      0.94   9.4e+02      60      75 ..     246     261 ..     207     291 .. 0.51

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.44
                      ApoLp-III  95 gvqslvkesqklaeslkensqeakeklak 123
                                    g+qsl    ++laes+ e+ + a++++a+
  gi|116753383|ref|YP_842501.1|  25 GIQSLGGTKAQLAESIVEARRRAQPQIAE 53 
                                    67888888888899999999999988875 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00013
                      ApoLp-III  29 ensenlvdqlkqvikslqeelkkksd...eleealkevkkkieetadklseenP 79 
                                    e+++ ++++++++ ks++ +++++     ++   ++++k  i++t d+l+++  
  gi|116753383|ref|YP_842501.1| 117 EGVSRMAKSVNALKKSIEGQVTENKKgiaKIRTGVRQMKLSINKTSDELRKSGE 170
                                    6789999************998854411144566999999**********9533 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.94
                      ApoLp-III  60 lkevkkkieetadkls 75 
                                      ++ +++ e +d +s
  gi|116753383|ref|YP_842501.1| 246 RADLDSQVRENRDAIS 261
                                    2223333333333333 PP

>> ApoO  Apolipoprotein O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.46   4.6e+02      14      46 ..      34      66 ..      25      95 .. 0.74
   2 ?    6.8   0.1    0.0061       6.1       9      64 ..     109     170 ..      91     173 .. 0.85
   3 ?    1.0   0.0      0.39   3.9e+02      10      47 ..     174     211 ..     166     220 .. 0.78
   4 ?    0.2   0.0      0.67   6.6e+02      10      42 ..     232     264 ..     217     286 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.46
                           ApoO 14 drLeegvrslRkslepytsavqdelnkvkskve 46
                                    +L+e++ ++R+ ++p++++   +  +vk+  +
  gi|116753383|ref|YP_842501.1| 34 AQLAESIVEARRRAQPQIAESGTAEVQVKPEEQ 66
                                   68999**********999887777666666555 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0061
                           ApoO   9 s......eeptdrLeegvrslRkslepytsavqdelnkvkskvetaeqsvtdtiasLkeppe 64 
                                    s      ee ++r++++v+ l ks+e ++++ ++ + k++++v + + s+++t ++L ++ e
  gi|116753383|ref|YP_842501.1| 109 SagvairEEGVSRMAKSVNALKKSIEGQVTENKKGIAKIRTGVRQMKLSINKTSDELRKSGE 170
                                    055666678899*******************************************9998755 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.39
                           ApoO  10 eeptdrLeegvrslRkslepytsavqdelnkvkskvet 47 
                                    ee +++L eg r+ R  l +++ +  d+++++ s++ +
  gi|116753383|ref|YP_842501.1| 174 EEGARELNEGLRRFRADLDSQIRKNRDAVSRMGSGAAE 211
                                    56688999999999999999999999999887776655 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 0.67
                           ApoO  10 eeptdrLeegvrslRkslepytsavqdelnkvk 42 
                                    ee +++L eg r+ R  l +++ +  d++++++
  gi|116753383|ref|YP_842501.1| 232 EEGARELNEGLRRFRADLDSQVRENRDAISRMN 264
                                    667888999999999999999988888876554 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   0.3    0.0015       1.4      22     124 ..     122     222 ..     118     237 .. 0.74
   2 ?    4.7   0.1     0.033        33      24     122 ..     182     278 ..     179     294 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0015
                                    HHHCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCH CS
                      Fib_alpha  22 lqdlllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqe 101
                                    +++ ++  +k+++ ++++ ++ +++i+   ++++  +++++d lr+  +  +  ++  +++++ l++  ++l+ +i ++ 
  gi|116753383|ref|YP_842501.1| 122 MAKSVNALKKSIEGQVTENKKGIAKIRTGVRQMKLSINKTSDELRKSGERIR--EEGARELNEGLRRFRADLDSQIRKNR 199
                                    6666677777788888888888888888888888888888888888877777..57777777777777777777777777 PP

                                    HHHHHHHHHHHHHHHHHHHHHHH CS
                      Fib_alpha 102 snirvLqnvlesneqkiqkLeqd 124
                                      +  + +   + ++ + k+ +d
  gi|116753383|ref|YP_842501.1| 200 DAVSRMGSGAAEIRSAMDKMSVD 222
                                    77777777777777777777665 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.033
                                    HCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHH CS
                      Fib_alpha  24 dlllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesn 103
                                    + l + + d++ +++k ++ ++++ +   e+++ + +++   r+   + +  ++  +++++ l++  ++l+ ++ ++   
  gi|116753383|ref|YP_842501.1| 182 EGLRRFRADLDSQIRKNRDAVSRMGSGAAEIRSAMDKMSVDFRKSGDHIR--EEGARELNEGLRRFRADLDSQVRENRDA 259
                                    55667777888888888888888888888888888888888877777766..4555666666666666666666666655 PP

                                    HHHHHHHHHHHHHHHHHHH CS
                      Fib_alpha 104 irvLqnvlesneqkiqkLe 122
                                    i  +    ++++++   L+
  gi|116753383|ref|YP_842501.1| 260 ISRMNIAAKELHSRALALR 278
                                    5555444444444443333 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.4    0.0026       2.6     657     733 ..     121     197 ..      79     206 .. 0.58
   2 ?    2.4   0.1      0.03        30     229     289 ..     190     255 ..     181     291 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0026
                       Prominin 657 dlraiqqelvlplessvkklkksvkkldeensdlqesikkllaaveraenflkkngseiinneskklldrileqfee 733
                                     + +  + l + +e +v + kk + k+ +  ++++ si+k  ++++++ + ++++g++ +n+  +++ +   +q+++
  gi|116753383|ref|YP_842501.1| 121 RMAKSVNALKKSIEGQVTENKKGIAKIRTGVRQMKLSINKTSDELRKSGERIREEGARELNEGLRRFRADLDSQIRK 197
                                    22222233333344444444444444444455577777777777777777777777777777777776666666655 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.03
                       Prominin 229 tlesnvlpaLaelerllenlkeakeqLeqv....nklekeLrksg.sqLrdglrgvkrdlnqalsn 289
                                     l+s++ +  +++ r++    e++ ++ ++    +k+   +r++g ++L++glr  + dl++ + +
  gi|116753383|ref|YP_842501.1| 190 DLDSQIRKNRDAVSRMGSGAAEIRSAMDKMsvdfRKSGDHIREEGaRELNEGLRRFRADLDSQVRE 255
                                    455555555666666666666666666655222256777788765257888888888888887766 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 ?   -0.4   0.1       1.2   1.2e+03      47      82 ..      97     133 ..      92     153 .. 0.63
   2 ?    3.1   0.7     0.093        93      11      74 ..     148     208 ..     139     222 .. 0.65
   3 ?    8.4   0.1    0.0022       2.2      50      90 ..     242     283 ..     234     292 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.2
                                    HHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHH CS
                    Flagellin_N  47 svslrsqiaglsql.vrnnslgisrlqtaqgalsels 82 
                                     + +r+++++l ++ v  ++ g sr++ + +al++ +
  gi|116753383|ref|YP_842501.1|  97 QEAMRRKSSELRSAgVAIREEGVSRMAKSVNALKKSI 133
                                    5666777766655424556667777777777776654 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.093
                                    HHHHHHHHHHHHHHHHHH.TTSBTTSSTTS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Flagellin_N  11 rsnlnknqaelqkaqeel.stGlridsalddaaglaisvslrsqiaglsqlvrnnslgisrlqta 74 
                                    r+ +++++ +++k++ el  +G+ri    + +a+    + lr+  a+l++ +r+n ++ sr+ + 
  gi|116753383|ref|YP_842501.1| 148 RTGVRQMKLSINKTSDELrKSGERIR---EEGAREL-NEGLRRFRADLDSQIRKNRDAVSRMGSG 208
                                    66777777777777777744777775...4455443.5667777777777777777777777654 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0022
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHH CS
                    Flagellin_N  50 lrsqiaglsqlvrnnslgisrlqtaqgalselsdilqr.lke 90 
                                    lr+  a+l++ vr+n ++isr+ +a + l + + +l + ++ 
  gi|116753383|ref|YP_842501.1| 242 LRRFRADLDSQVRENRDAISRMNIAAKELHSRALALRDeMQR 283
                                    7788899********************999887777666665 PP

>> Tektin  Tektin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   1.5   0.00055      0.55     211     290 ..      95     174 ..      91     177 .. 0.92
   2 ?    3.1   0.3     0.032        32     219     282 ..     219     282 ..     211     291 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00055
                         Tektin 211 eraekerqasakLreaidsilkqtandlraqaeavnealrkrieetedaknkleeqlkkvleeiaeleknieeLekaird 290
                                     r e+ r++s +Lr+a   i+++  +++ +  +a  ++++ +++e ++   k+++  ++++  i+++ +++++  + ir+
  gi|116753383|ref|YP_842501.1|  95 ARQEAMRRKSSELRSAGVAIREEGVSRMAKSVNALKKSIEGQVTENKKGIAKIRTGVRQMKLSINKTSDELRKSGERIRE 174
                                    577999************************************************************99999987777765 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.032
                         Tektin 219 asakLreaidsilkqtandlraqaeavnealrkrieetedaknkleeqlkkvleeiaeleknie 282
                                     s+++r++ d+i+++ a++l +  ++  + l+ +++e +da + ++   k++  +  +l ++++
  gi|116753383|ref|YP_842501.1| 219 MSVDFRKSGDHIREEGARELNEGLRRFRADLDSQVRENRDAISRMNIAAKELHSRALALRDEMQ 282
                                    5888999999999999999999999999999999999999999999888888777766666665 PP

>> DUF334  Domain of unknown function (DUF334)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   1.5     0.019        19      67     121 ..     146     198 ..      93     206 .. 0.66
   2 ?    6.4   0.1    0.0059       5.9      74     120 ..     210     255 ..     207     275 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.019
                         DUF334  67 dlrekelkeikselkkatkdfrdkskkvrndfvdllqkklkrvdaeelkiilrkd 121
                                    ++r    +++k ++ k+++++r+ + ++r++  + l++ l+r  a +l+ ++rk+
  gi|116753383|ref|YP_842501.1| 146 KIRT-GVRQMKLSINKTSDELRKSGERIREEGARELNEGLRRFRA-DLDSQIRKN 198
                                    3332.4567888899999999999999999999999999998876.566666664 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0059
                         DUF334  74 keikselkkatkdfrdkskkvrndfvdllqkklkrvdaeelkiilrk 120
                                     ei+s + k + dfr+ + ++r++  + l++ l+r  a +l+ ++r 
  gi|116753383|ref|YP_842501.1| 210 AEIRSAMDKMSVDFRKSGDHIREEGARELNEGLRRFRA-DLDSQVRE 255
                                    589*******************************9987.56665554 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       4.8   4.7e+03      36      36 ..      36      36 ..       4      77 .. 0.52
   2 ?    8.6   1.8    0.0026       2.5      28      67 ..     129     175 ..     121     293 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 4.8
                                   H CS
                          DUF16 36 L 36
                                   L
  gi|116753383|ref|YP_842501.1| 36 L 36
                                   2 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0026
                                    B-.........BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHH CS
                          DUF16  28 fkds.......nkqrLkkieakvdklgeqinkleqkvekqgekikel 67 
                                     k+s       nk+ + ki + v++ + +ink  ++ +k ge+i+e 
  gi|116753383|ref|YP_842501.1| 129 LKKSiegqvteNKKGIAKIRTGVRQMKLSINKTSDELRKSGERIREE 175
                                    55555555555999999999999999999999999999999999864 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1       0.7   6.9e+02      55      81 ..      27      53 ..       6      81 .. 0.54
   2 ?    6.9   0.4     0.006         6      71     115 ..     119     163 ..      98     171 .. 0.81
   3 ?    1.9   0.0      0.22   2.2e+02      55      98 ..     182     225 ..     163     232 .. 0.59
   4 ?    1.9   0.1      0.22   2.2e+02      65     113 ..     239     277 ..     199     292 .. 0.47

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.7
                        DUF1664 55 eslaatkrhLssridrvdkkldeqkei 81
                                   +sl  tk +L++ i +  ++ + q++ 
  gi|116753383|ref|YP_842501.1| 27 QSLGGTKAQLAESIVEARRRAQPQIAE 53
                                   445555555555554444444444333 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.006
                        DUF1664  71 vdkkldeqkeiskeikeevtevredlseigedvesvkeavegles 115
                                    v +  +++++++k+i+ +vte ++++++i++ v+++k  +++   
  gi|116753383|ref|YP_842501.1| 119 VSRMAKSVNALKKSIEGQVTENKKGIAKIRTGVRQMKLSINKTSD 163
                                    566667788899999999999999999999999999988876555 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.22
                        DUF1664  55 eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlse 98 
                                    e l++ + +L s+i +  + +  +   ++ei++ +++++ d ++
  gi|116753383|ref|YP_842501.1| 182 EGLRRFRADLDSQIRKNRDAVSRMGSGAAEIRSAMDKMSVDFRK 225
                                    44555555555555555555555555555555555555555544 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.22
                        DUF1664  65 ssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegl 113
                                    ++ + r            ++++++v e r+ +s+++   +++++    l
  gi|116753383|ref|YP_842501.1| 239 NEGLRR----------FRADLDSQVRENRDAISRMNIAAKELHSRALAL 277
                                    333332..........222333333333333333333333333333333 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       4.8   4.8e+03      69      77 ..      14      22 ..       3      47 .. 0.54
   2 ?    3.1   4.0     0.055        54      68     105 ..     129     166 ..     113     285 .. 0.54

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 4.8
                        DUF4618 69 kaeLqewee 77
                                   ++eL+e++ 
  gi|116753383|ref|YP_842501.1| 14 RRELEEMAV 22
                                   333333332 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.055
                        DUF4618  68 akaeLqeweekeekklekLeqqleqlnakvqklqeeln 105
                                    +k+ ++   ++ +k ++k++  ++q++  ++k+++el 
  gi|116753383|ref|YP_842501.1| 129 LKKSIEGQVTENKKGIAKIRTGVRQMKLSINKTSDELR 166
                                    34444444444444444444444444444444444432 PP

>> COG2  COG (conserved oligomeric Golgi) complex component, COG2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       2.2   2.2e+03      95     118 ..       1      24 [.       1      43 [. 0.77
   2 ?    4.4   0.5     0.037        37      69     107 ..     117     155 ..      98     170 .. 0.67
   3 ?    1.5   0.2      0.29   2.9e+02      29      86 ..     159     217 ..     147     259 .. 0.62
   4 ?    6.6   0.2    0.0075       7.5      27      58 ..     262     293 ..     241     294 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.2
                           COG2  95 reeeveskleeakeleekrellkl 118
                                    +ee+ve+ + + ++ e +++ +kl
  gi|116753383|ref|YP_842501.1|   1 MEETVEELVTKHTRRELEEMAVKL 24 
                                    567888888888888877777665 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.037
                           COG2  69 eeleevesplaaarkkvesvreklsereeeveskleeak 107
                                    e ++++ ++++a++k +e  + + ++ +++++  +++ k
  gi|116753383|ref|YP_842501.1| 117 EGVSRMAKSVNALKKSIEGQVTENKKGIAKIRTGVRQMK 155
                                    456666666777777777666666666666666666654 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.29
                           COG2  29 eslrrdLeaylkllekellelvnedyadF.vslSghLvglqeeleevesplaaarkkve 86 
                                    ++ +++L++  + +++e ++  ne ++ F  +l ++ +  +++++++ s  a++r+ ++
  gi|116753383|ref|YP_842501.1| 159 NKTSDELRKSGERIREEGARELNEGLRRFrADLDSQIRKNRDAVSRMGSGAAEIRSAMD 217
                                    45555555555555555555555555554345555555555555555555555554444 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.0075
                           COG2  27 pLeslrrdLeaylkllekellelvnedyadFv 58 
                                     ++   ++L++ +  l++e+ + v++d++ ++
  gi|116753383|ref|YP_842501.1| 262 RMNIAAKELHSRALALRDEMQRYVDQDVNKYI 293
                                    5666789*********************9886 PP

>> kleA_kleC  Uncharacterized KorC regulated protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       3.2   3.2e+03      38      45 ..     102     109 ..      93     151 .. 0.52
   2 ?   -0.2   0.1       1.3   1.3e+03      32      48 ..     161     177 ..     152     198 .. 0.74
   3 ?    1.1   0.1      0.51   5.1e+02      16      43 ..     192     219 ..     187     236 .. 0.79
   4 ?    9.0   1.3    0.0018       1.8      16      48 ..     250     282 ..     246     286 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 3.2
                      kleA_kleC  38 rqaeeLRa 45 
                                    r+  eLR 
  gi|116753383|ref|YP_842501.1| 102 RKSSELRS 109
                                    33333332 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.3
                      kleA_kleC  32 eAeeLvrqaeeLRakvy 48 
                                      +eL +  e++R +  
  gi|116753383|ref|YP_842501.1| 161 TSDELRKSGERIREEGA 177
                                    56788888888887644 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.51
                      kleA_kleC  16 atdlvarRdkiAaklaeAeeLvrqaeeL 43 
                                    + +++ +Rd++  +   A+e+    +++
  gi|116753383|ref|YP_842501.1| 192 DSQIRKNRDAVSRMGSGAAEIRSAMDKM 219
                                    5789999****99999999987766655 PP

  == domain 4  score: 9.0 bits;  conditional E-value: 0.0018
                      kleA_kleC  16 atdlvarRdkiAaklaeAeeLvrqaeeLRakvy 48 
                                    + +++ +Rd+i  +   A+eL  +a +LR +  
  gi|116753383|ref|YP_842501.1| 250 DSQVRENRDAISRMNIAAKELHSRALALRDEMQ 282
                                    567899***********************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1065  (0.059401); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); 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):              18  [number of targets reported over threshold]
# CPU time: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.44
# Mc/sec: 2035.28
//
Query:       gi|116753384|ref|YP_842502.1|  [L=76]
Description: gas vesicle synthesis protein GvpA [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.3e-15   55.3   6.7    6.9e-15   54.9   6.7    1.2  1  Gas_vesicle  Gas vesicle protein


Domain annotation for each model (and alignments):
>> Gas_vesicle  Gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.9   6.7   3.8e-19   6.9e-15       1      39 []      10      48 ..      10      48 .. 0.99

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 3.8e-19
                    Gas_vesicle  1 sLaDlLDrvLdkGvVIdgditisvagieLltikLrlviA 39
                                   sLa++LDr+LdkG+V+d + ++s++gie+lt+++r+v+A
  gi|116753384|ref|YP_842502.1| 10 SLAEVLDRILDKGIVVDVWARVSLVGIEILTVEARVVVA 48
                                   8*************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); 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: 0.32u 0.24s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 617.56
//
Query:       gi|116753385|ref|YP_842503.1|  [L=74]
Description: gas vesicle synthesis protein GvpA [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      5e-15   55.4   6.7    6.4e-15   55.0   6.7    1.2  1  Gas_vesicle  Gas vesicle protein


Domain annotation for each model (and alignments):
>> Gas_vesicle  Gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.0   6.7   3.6e-19   6.4e-15       1      39 []      10      48 ..      10      48 .. 0.99

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 3.6e-19
                    Gas_vesicle  1 sLaDlLDrvLdkGvVIdgditisvagieLltikLrlviA 39
                                   sLa++LDr+LdkG+V+d + ++s++gie+lt+++r+v+A
  gi|116753385|ref|YP_842503.1| 10 SLAEVLDRILDKGIVVDVWARVSLVGIEILTVEARVVVA 48
                                   8*************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); 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 0.26s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 551.36
//
Query:       gi|116753386|ref|YP_842504.1|  [L=74]
Description: gas vesicle synthesis protein GvpA [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      5e-15   55.4   6.7    6.4e-15   55.0   6.7    1.2  1  Gas_vesicle  Gas vesicle protein


Domain annotation for each model (and alignments):
>> Gas_vesicle  Gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.0   6.7   3.6e-19   6.4e-15       1      39 []      10      48 ..      10      48 .. 0.99

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 3.6e-19
                    Gas_vesicle  1 sLaDlLDrvLdkGvVIdgditisvagieLltikLrlviA 39
                                   sLa++LDr+LdkG+V+d + ++s++gie+lt+++r+v+A
  gi|116753386|ref|YP_842504.1| 10 SLAEVLDRILDKGIVVDVWARVSLVGIEILTVEARVVVA 48
                                   8*************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 518.45
//
Query:       gi|116753387|ref|YP_842505.1|  [L=74]
Description: gas vesicle synthesis protein GvpA [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      5e-15   55.4   6.7    6.4e-15   55.0   6.7    1.2  1  Gas_vesicle  Gas vesicle protein


Domain annotation for each model (and alignments):
>> Gas_vesicle  Gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.0   6.7   3.6e-19   6.4e-15       1      39 []      10      48 ..      10      48 .. 0.99

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 3.6e-19
                    Gas_vesicle  1 sLaDlLDrvLdkGvVIdgditisvagieLltikLrlviA 39
                                   sLa++LDr+LdkG+V+d + ++s++gie+lt+++r+v+A
  gi|116753387|ref|YP_842505.1| 10 SLAEVLDRILDKGIVVDVWARVSLVGIEILTVEARVVVA 48
                                   8*************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); 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 0.26s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 559.48
//
Query:       gi|116753388|ref|YP_842506.1|  [L=119]
Description: response regulator receiver protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.1e-30  104.6   0.1    3.4e-30  104.5   0.1    1.0  1  Response_reg  Response regulator receiver domain
  ------ inclusion threshold ------
      0.012   15.3   0.0      0.078   12.7   0.0    1.8  2  LUD_dom       LUD domain
      0.075   13.1   0.0      0.091   12.8   0.0    1.2  1  B12-binding   B12 binding domain


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.5   0.1   5.7e-34   3.4e-30       1     111 [.       3     112 ..       3     113 .. 0.98

  Alignments for each domain:
  == domain 1  score: 104.5 bits;  conditional E-value: 5.7e-34
                                    EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEESS CS
                   Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireedpelpviiltah 80 
                                    vl+vdD p ++++lr+ le +g+ e++ea++g+eal  ++  ++d++l+Di mpgm+G+ +++ei + dp+ ++i++ta 
  gi|116753388|ref|YP_842506.1|   3 VLVVDDAPFILRALRDSLEARGF-EIHEAQSGEEALSAYRDIRPDVVLMDILMPGMNGISVTREIMNIDPSANIIVITAI 81 
                                    8**********************.******************************************************** PP

                                    TSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
                   Response_reg  81 seeedavealkagaddflsKpfdpeeLlkal 111
                                    ++    +e+++aga++f+ Kpf++++Ll+ +
  gi|116753388|ref|YP_842506.1|  82 GKPGLEKECMDAGAKGFILKPFRMRDLLDLI 112
                                    ***************************9876 PP

>> LUD_dom  LUD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.3e-05     0.078       4      47 ..      16      65 ..      13      75 .. 0.77
   2 ?    4.3   0.0     0.005        30      75     115 ..      40      79 ..      38      85 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.3e-05
                        LUD_dom  4 fienleangaevyyaktaeealelilellkeksv......vseggstdlg 47
                                   + ++lea+g+e+++a+++eeal + +++ ++         ++ g+s++ +
  gi|116753388|ref|YP_842506.1| 16 LRDSLEARGFEIHEAQSGEEALSAYRDIRPDVVLmdilmpGMNGISVTRE 65
                                   6799******************9999987776446667777777776655 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.005
                        LUD_dom  75 reelrekfltadvgitganfaiAetGtlvlvdnegnrralt 115
                                     +++r     +d+ + g+n +i+ t +++++d + n   +t
  gi|116753388|ref|YP_842506.1|  40 YRDIRPDVVLMDILMPGMN-GISVTREIMNIDPSANIIVIT 79 
                                    5789999999*********.**************9985444 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.5e-05     0.091      15      78 ..      11      73 ..       3      97 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.5e-05
                    B12-binding 15 lGlavlaaalrdagfeVqllganvenedivaairaekpdvvglSalltsqleav...kelvellkri 78
                                   + l++l + l+++gfe+   +a+   e+ ++a r+ +pdvv++ + l   ++++   +e+++   ++
  gi|116753388|ref|YP_842506.1| 11 FILRALRDSLEARGFEI--HEAQS-GEEALSAYRDIRPDVVLMDI-LMPGMNGIsvtREIMNIDPSA 73
                                   55788999999999999..44444.499999**************.666665551114444444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 919.88
//
Query:       gi|116753389|ref|YP_842507.1|  [L=377]
Description: PAS/PAC sensor signal transduction histidine kinase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.4e-28   98.4   0.1    7.3e-28   97.3   0.0    1.6  2  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    9.3e-18   64.0   0.1    9.3e-18   64.0   0.1    2.0  3  HisKA        His Kinase A (phospho-acceptor) domain
    4.2e-11   43.1   0.0    6.4e-11   42.5   0.0    1.3  1  PAS_4        PAS fold
    3.3e-05   24.1   0.0    9.1e-05   22.7   0.0    1.8  1  PAS_9        PAS domain
    5.3e-05   23.1   0.1     0.0022   17.9   0.0    2.5  2  HATPase_c_5  GHKL domain
    7.8e-05   22.6   0.0     0.0002   21.3   0.0    1.7  1  PAS          PAS fold
    0.00094   19.7   0.0     0.0021   18.6   0.0    1.6  1  PAS_10       PAS domain
  ------ inclusion threshold ------
      0.023   14.5   0.1      0.046   13.5   0.1    1.5  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
      0.056   13.4   1.2       0.21   11.5   0.1    2.4  2  BORCS8       BLOC-1-related complex sub-unit 8
       0.12   12.3   0.1       0.85    9.6   0.0    2.4  2  Thiamine_BP  Thiamine-binding protein
       0.29   11.0   3.8        4.5    7.1   0.2    3.0  3  DASH_Duo1    DASH complex subunit Duo1
       0.38   10.9   2.3        3.5    7.8   0.0    2.5  2  Nod1         Gef2-related medial cortical node protein Nod1


Domain annotation for each model (and alignments):
>> 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 ?   -3.4   0.0       9.4   1.4e+04      45      63 ..      48      64 ..      41      77 .. 0.60
   2 !   97.3   0.0   4.9e-31   7.3e-28       2     109 ..     262     369 ..     261     372 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 9.4
                                   SSSSSTTHHHTGTCS.TTCH CS
                      HATPase_c 45 nGiGipkedlkklfe.kfsq 63
                                   n iG+      k+f   f+q
  gi|116753389|ref|YP_842507.1| 48 NAIGMHL---SKIFSpVFMQ 64
                                   5555543...4677777777 PP

  == domain 2  score: 97.3 bits;  conditional E-value: 4.9e-31
                                    HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHHH CS
                      HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsiv 81 
                                    d+k+++q++snl++Na+k++++ g+iev +  + +++ +s++DnGiGi +ed +++fekf   +++k+   g GlGlsi 
  gi|116753389|ref|YP_842507.1| 262 DPKKIMQVLSNLLTNAIKYTPDRGQIEVVLGGDAENVLVSIRDNGIGIREEDKDRIFEKFFVMSNEKSADIGMGLGLSIT 341
                                    7899***************88**********7669***********************9999456666668********* PP

                                    HHHHHHTTTEEEEEEETTTEEEEEEEEE CS
                      HATPase_c  82 kklvelmgGeiwvesepgrGttftftlp 109
                                    k +ve +gG+iw+es+ g+G+tf+ftlp
  gi|116753389|ref|YP_842507.1| 342 KDIVEAHGGRIWFESRFGEGSTFYFTLP 369
                                    ***************************9 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1       7.4   1.1e+04      59      66 ..     118     125 ..     114     145 .. 0.61
   2 !   64.0   0.1   6.2e-21   9.3e-18       2      66 ..     148     214 ..     147     215 .. 0.97
   3 ?   -2.9   0.1       4.8   7.1e+03      38      51 ..     227     240 ..     218     245 .. 0.50

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 7.4
                                    HHHCCHHH CS
                          HisKA  59 Ldlsriea 66 
                                     +++r+e+
  gi|116753389|ref|YP_842507.1| 118 TEMTRLEE 125
                                    44444443 PP

  == domain 2  score: 64.0 bits;  conditional E-value: 6.2e-21
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHH CS
                          HisKA   2 lgrflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdlsriea 66 
                                    +++f+++v+HELrtPL++i  ++e+ ++   g+lt+ +ke l+ i+s+++ + +lv+d+Ld+ ri++
  gi|116753389|ref|YP_842507.1| 148 KSEFVSMVSHELRTPLTVINSYIEMFEDGmlGDLTDVQKEKLQLIRSQTDTMIQLVNDMLDILRIGS 214
                                    79************************************************************99986 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 4.8
                                    HHHHHHHHHHHHHH CS
                          HisKA  38 keyletiesearrl 51 
                                    +e++++++ +  rl
  gi|116753389|ref|YP_842507.1| 227 EELIRSVIASLSRL 240
                                    34444444444444 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   0.0   4.3e-14   6.4e-11       2     108 ..      16     120 ..      15     122 .. 0.95

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 4.3e-14
                          PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgeerhy 81 
                                    + +p  ++++d+ + vlyaN+++     ++ + ++G++l  ++++   +rl + +++v + +ep + ++++ +  ++r+y
  gi|116753389|ref|YP_842507.1|  16 ETIPSTIIIVDRRLEVLYANRNFYLKSFRTEKNAIGMHLSKIFSPVFMQRLNSRIEKVFSAGEPFDGEQIRYP--GGRFY 93 
                                    568999****************9999*******************************************8888..99*** PP

                          PAS_4  82 elrllPlrdesGevigvlvisrDiTer 108
                                      r++Pl+++ G v  +++++ DiTe 
  gi|116753389|ref|YP_842507.1|  94 FYRIHPLKEAGGYVSKAVIFIEDITEM 120
                                    *******998888************95 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   6.1e-08   9.1e-05       3     104 .]      21     119 ..      19     119 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 6.1e-08
                          PAS_9   3 gilidnpdgrilyaNeaalrllGyspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetfwvll 80 
                                     i+i++   ++lyaN+ +      +++  +g +++ +f  v+ ++ n+r+++++ +g+  ++++e + +   g+ +    
  gi|116753389|ref|YP_842507.1|  21 TIIIVDRRLEVLYANRNFYLKSFRTEKNAIGMHLSKIFspVFMQRLNSRIEKVFSAGE--PFDGEQIRYPG-GRFY--FY 95 
                                    5778889************997799999**********99999999999999999999..88877555544.4444..57 PP

                          PAS_9  81 taspvkdddgelvgiivilrDite 104
                                    ++ p+k+++g +  ++++++Dite
  gi|116753389|ref|YP_842507.1|  96 RIHPLKEAGGYVSKAVIFIEDITE 119
                                    99****99888888*********8 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.083   1.2e+02      13      52 ..     133     171 ..     128     206 .. 0.72
   2 !   17.9   0.0   1.5e-06    0.0022       3      89 ..     263     356 ..     261     367 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.083
                    HATPase_c_5  13 lLdNAieacskiee.ekrfIrltvrekkksliisieNsyeg 52 
                                     L+NA+   +++++ +++f+++  +e    + +++ Nsy +
  gi|116753389|ref|YP_842507.1| 133 KLENAYAELKELDSiKSEFVSMVSHELR--TPLTVINSYIE 171
                                    599********99988888887666544..45566676655 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 1.5e-06
                    HATPase_c_5   3 dldlcvilgnlLdNAieacskieeekrfIrltvrekkksliisieNsyeg....ek....kkle...sskskkeehGiGl 71 
                                    ++ ++ +l+nlL NAi    +    +  I++ +  + +++++si  +  g    +k    +k++   ++ks +  +G+Gl
  gi|116753389|ref|YP_842507.1| 263 PKKIMQVLSNLLTNAIKYTPD----RGQIEVVLGGDAENVLVSIRDNGIGireeDKdrifEKFFvmsNEKSADIGMGLGL 338
                                    677999*********976544....668******999999988876633334332234443333543668888899**** PP

                    HATPase_c_5  72 ksireivkkykgnlsiea 89 
                                    +  + iv+ ++g +++e 
  gi|116753389|ref|YP_842507.1| 339 SITKDIVEAHGGRIWFES 356
                                    **************9986 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   1.3e-07    0.0002       6      87 ..      14      93 ..      11     117 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.3e-07
                                   HHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEECTTSSEE CS
                            PAS  6 ileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfklrdgrpi 87
                                   i+e++p+ i++vD++ ++ly+N+++      +++ ++g +l+  +++  ++ l++++e++ ++ge++ +++i+ +   gr++
  gi|116753389|ref|YP_842507.1| 14 IIETIPSTIIIVDRRLEVLYANRNFYLKSFRTEKNAIGMHLSKIFSPVFMQRLNSRIEKVFSAGEPFDGEQIRYPG--GRFY 93
                                   9*****************************************9999888889********************8877..5554 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.4e-06    0.0021       4     106 .]      14     118 ..      12     118 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.4e-06
                         PAS_10   4 lLnstpieltflDdnlqirrFtpa.akklfklipadvGrpladihpkkavknveeviealrtgekdevevvvp.kngkwv 81 
                                    +++++p  ++ +D+ l++++ +++ + k f+  ++ +G +l++i ++  ++++++ ie++ +  +  +  ++    g+++
  gi|116753389|ref|YP_842507.1|  14 IIETIPSTIIIVDRRLEVLYANRNfYLKSFRTEKNAIGMHLSKIFSPVFMQRLNSRIEKVFSAGEPFDGEQIRyPGGRFY 93 
                                    5789999****************95679***************************999999988888888886589**** PP

                         PAS_10  82 lvrylpyrdedgeiaGvvetfvDit 106
                                      r+ p+++  g +  +v+++ Dit
  gi|116753389|ref|YP_842507.1|  94 FYRIHPLKEAGGYVSKAVIFIEDIT 118
                                    *********************9997 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   3.1e-05     0.046       5      62 ..     268     327 ..     264     346 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.1e-05
                    HATPase_c_3   5 kAlaelvdNsld..AdaenvkievnknrgktgeivieDdGkGmseeelknal.rlatsske 62 
                                    ++l  l+ N++    d  ++++++  +  ++  ++i+D+G G+ ee+ ++ + ++   s+e
  gi|116753389|ref|YP_842507.1| 268 QVLSNLLTNAIKytPDRGQIEVVLGGDA-ENVLVSIRDNGIGIREEDKDRIFeKFFVMSNE 327
                                    5788999999765599999*****9986.68899************988877334333333 PP

>> BORCS8  BLOC-1-related complex sub-unit 8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00014      0.21      45      95 ..     114     165 ..     107     171 .. 0.88
   2 ?   -0.8   0.1      0.95   1.4e+03      79     101 ..     220     242 ..     185     249 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00014
                         BORCS8  45 vekkkevkeleeelqgacydveyaisavksikesessf.eniqelLknsifl 95 
                                    +e  +e+++leeel++++  +e+a + +k+++ ++s+f + +++ L++ + +
  gi|116753389|ref|YP_842507.1| 114 IEDITEMTRLEEELRDSYIKLENAYAELKELDSIKSEFvSMVSHELRTPLTV 165
                                    566789********************************88888889887765 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.95
                         BORCS8  79 essfeniqelLknsiflkqqlka 101
                                    ++++++++el+++ i+  ++l+a
  gi|116753389|ref|YP_842507.1| 220 KKELSSMEELIRSVIASLSRLAA 242
                                    56778888888888888777765 PP

>> Thiamine_BP  Thiamine-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.6   3.8e+03       6      36 ..      98     128 ..      96     143 .. 0.72
   2 ?    9.6   0.0   0.00057      0.85      19      57 ..     230     274 ..     217     289 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.6
                                    EECSSSSSGHHHHHHHHHHHHHTTSSEEEEE CS
                    Thiamine_BP   6 iPlgtegesvskyVakvvevlkesglkyelt 36 
                                     Pl+  g+ vsk+V  + ++ + + l+ el 
  gi|116753389|ref|YP_842507.1|  98 HPLKEAGGYVSKAVIFIEDITEMTRLEEELR 128
                                    6777778888888877777777777776665 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00057
                                    HHHHHHHH......HTTSSEEEEETTEEEEEEEHHHHHHHHHHHH CS
                    Thiamine_BP  19 Vakvvevl......kesglkyeltpmgTtiegeldevmevvkkah 57 
                                    +  v++ l      ke+ ++++ +  +T+ie + +++m+v+ ++ 
  gi|116753389|ref|YP_842507.1| 230 IRSVIASLsrlaalKEHTITFRCERANTLIECDPKKIMQVLSNLL 274
                                    44444444444455**************************98765 PP

>> DASH_Duo1  DASH complex subunit Duo1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       2.6   3.8e+03       4      19 ..     139     154 ..     138     161 .. 0.76
   2 ?    3.6   0.2     0.038        57       6      51 ..     163     210 ..     155     212 .. 0.74
   3 ?    7.1   0.2     0.003       4.5       4      44 ..     221     259 ..     218     261 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.6
                      DASH_Duo1   4 kEleqLrkinevienv 19 
                                    +El++L++i + + ++
  gi|116753389|ref|YP_842507.1| 139 AELKELDSIKSEFVSM 154
                                    6999999998766555 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.038
                      DASH_Duo1   6 leqLrkinevie.nviesLkkak.sniervketvestntLLdkWirIl 51 
                                    l+ +++ +e++e ++ ++L +++ ++++ + ++++++ +L++   +Il
  gi|116753389|ref|YP_842507.1| 163 LTVINSYIEMFEdGMLGDLTDVQkEKLQLIRSQTDTMIQLVNDMLDIL 210
                                    44444444444435778999999999********99999999888887 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.003
                      DASH_Duo1   4 kEleqLrkinevienviesLkkak.sniervketvestntLL 44 
                                    k   +L ++ e i +vi+sL +    + ++++ ++e +ntL+
  gi|116753389|ref|YP_842507.1| 221 K---ELSSMEELIRSVIASLSRLAaLKEHTITFRCERANTLI 259
                                    4...455666667777777766666677789999******98 PP

>> Nod1  Gef2-related medial cortical node protein Nod1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0    0.0024       3.5       6      55 ..      12      67 ..       7      82 .. 0.74
   2 ?    1.9   0.8      0.15   2.3e+02      66     118 ..     184     235 ..     165     245 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0024
                           Nod1  6 eeiakepkrealleslpskilfgsFlkYlkdkilek..aGylLsekl....iqrLe 55
                                   e+i ++ + ++ + + + ++l++   +Ylk++ +ek   G+ Ls+++    +qrL+
  gi|116753389|ref|YP_842507.1| 12 EDIIETIPSTIIIVDRRLEVLYANRNFYLKSFRTEKnaIGMHLSKIFspvfMQRLN 67
                                   789999999999*******************9888744476666655111155553 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.15
                           Nod1  66 lkekavqqvkslleeLpesklklLevvfsivselllkLplkdqcetvlasiaa 118
                                     +++ +q ++s +  + + ++ +L+++      l lk +l  + e+++ s+ a
  gi|116753389|ref|YP_842507.1| 184 VQKEKLQLIRSQTDTMIQLVNDMLDILRIGSRRLRLKKEL-SSMEELIRSVIA 235
                                    4455569999999999999999999764444445455443.344444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       797  (0.0444531); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 2837.39
//
Query:       gi|116753390|ref|YP_842508.1|  [L=199]
Description: hypothetical protein Mthe_0066 [Methanosaeta thermophila PT]
Scores for 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-27   93.4   0.0    1.3e-26   92.9   0.0    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 !   92.9   0.0   7.4e-31   1.3e-26      18     136 .]      74     191 ..      64     191 .. 0.93

  Alignments for each domain:
  == domain 1  score: 92.9 bits;  conditional E-value: 7.4e-31
                         DUF835  18 egvkvlaitRenpkkirekvkienvkviwltkveeentvsPtnlekltetivkflkeaekgvvliDgleyLvlengFesv 97 
                                    +  ++l++t ++p++ir+++ +++++++w+++  e  +   +nle++ ++  +fl++ ++ vvl+Dgle+Lv+ ngF + 
  gi|116753390|ref|YP_842508.1|  74 KRAQGLCFTTQHPEQIRNRYVLQTTPIFWISRRGES-QTTVSNLEIMADITARFLEKSHNPVVLLDGLELLVVTNGFVQA 152
                                    4589****************************9973.344579999********************************** PP

                         DUF835  98 lkflltlkDavllkngtlilvidkealeekelalLkref 136
                                    ++fl  +  +v ++ g+li+ ++++al+e+e+al++r +
  gi|116753390|ref|YP_842508.1| 153 IRFLRDIMEMVFISRGILIVPVNPSALSEREMALIERDM 191
                                    ************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       781  (0.0435607); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1528.74
//
Query:       gi|116753391|ref|YP_842509.1|  [L=129]
Description: PadR-like family transcriptional regulator [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.3e-16   57.9   0.1    9.8e-16   57.5   0.1    1.2  1  PadR      Transcriptional regulator PadR-like family
  ------ inclusion threshold ------
       0.02   14.7   0.0      0.036   13.9   0.0    1.5  1  DUF1495   Winged helix DNA-binding domain (DUF1495)
       0.14   12.7   0.0       0.26   11.8   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 !   57.5   0.1   1.6e-19   9.8e-16       1      74 [.      37     106 ..      37     107 .. 0.94

  Alignments for each domain:
  == domain 1  score: 57.5 bits;  conditional E-value: 1.6e-19
                                    HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHH CS
                           PadR   1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrela 74 
                                    iL++l+e+p+ Gy++ike+ ++++  + ls+G +Yp+L ++ ++g++ se ++   + ++k+Y+lT++G++ ++
  gi|116753391|ref|YP_842509.1|  37 ILSILGERPMCGYDLIKEIYRRYN--VLLSQGAVYPILYSMVDDGILRSEYSR--GNMRTKIYTLTPKGQEVMR 106
                                    8*********************85..69**********************886..799************9987 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 ?   13.9   0.0   5.9e-06     0.036      51      87 ..      67     105 ..      43     107 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.9e-06
                        DUF1495  51 krynsessLielGLveeeee..seglklYklteeGieiv 87 
                                      y    s++  G+ ++e +  +  +k+Y+lt++G+e++
  gi|116753391|ref|YP_842509.1|  67 AVYPILYSMVDDGILRSEYSrgNMRTKIYTLTPKGQEVM 105
                                    55677789*******988873355566*********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 ?   11.8   0.0   4.4e-05      0.26      21      68 .]      52     101 ..      30     101 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.4e-05
                         HTH_27  21 ladlcgrlnvedshis.y.slkkLtekGLvertgdeadrrekrvrlTdkG 68 
                                    ++++ +r+nv  s+++ y +l  ++  G + ++ ++ + r+k ++lT+kG
  gi|116753391|ref|YP_842509.1|  52 IKEIYRRYNVLLSQGAvYpILYSMVDDGILRSEYSRGNMRTKIYTLTPKG 101
                                    5899999999999988854999***************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.46
# Mc/sec: 844.75
//
Query:       gi|116753392|ref|YP_842510.1|  [L=226]
Description: signal transduction ATPase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-26   91.9   0.0    4.4e-26   91.7   0.0    1.0  1  ATPase    KaiC
    1.5e-05   24.7   0.0    2.1e-05   24.2   0.0    1.1  1  AAA_25    AAA domain
     0.0063   15.2   0.0     0.0071   15.0   0.0    1.2  1  GvpD      GvpD gas vesicle protein


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.7   0.0   7.4e-30   4.4e-26       5     227 ..       3     216 ..       1     219 [. 0.91

  Alignments for each domain:
  == domain 1  score: 91.7 bits;  conditional E-value: 7.4e-30
                         ATPase   5 IeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeegkla 84 
                                    I glD+il+   p g+v l+tG+ Gt K+ ++l  + + +e   e g++ ++e+++ +  +n+ s+G+ ++   e+  l 
  gi|116753392|ref|YP_842510.1|   3 IDGLDRILEADPPAGSVLLVTGGEGTLKSSLVLAMMSRYLEGSAEHGLYASLEQTKDSHLRNMDSIGIRWH---EN--LH 77 
                                    99***************************************99************************9875...44..88 PP

                         ATPase  85 iidasesaeesaeekdkedleelieelaeaikeika.krvviDsitglayeekeavaReilrqlvrvlkklgvTailvse 163
                                    i d   +++e  ++++ +  +  ++ l  +i++++  +   +Ds+++l   +++  +R+ +  ++++l+++ +T+il+ e
  gi|116753392|ref|YP_842510.1|  78 IFDYRDMRIE-WKDHRLDMFSMTKDVLDMYIDRYRDlTIFAMDSLNALYALSSKTNLRRNVYDFLTMLRDRCLTSILILE 156
                                    9999999887.44455666666778999******9989999*******88888889************************ PP

                         ATPase 164 kssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIteegikvl 227
                                         +  +g g e f++dg+i L + e  + ++R+l+i+kmRg +h +++h + ++++g +v+
  gi|116753392|ref|YP_842510.1| 157 ----TGDDSGKGGERFLSDGIIELGVIESYNGVKRYLQIRKMRGVRHLMEKHHLVVKPGGLEVV 216
                                    ....467789999***********************************************9996 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   3.5e-09   2.1e-05      31     172 ..      15     144 ..       3     152 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 3.5e-09
                         AAA_25  31 pagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgealrddarllvldlag 110
                                    pag++ l++G +gt K+ l+l ++  +++G+             ly s+E++ d   r +  +g  +   ++l++ d+ +
  gi|116753392|ref|YP_842510.1|  15 PAGSVLLVTGGEGTLKSSLVLAMMSRYLEGSAE---------HGLYASLEQTKDSHLRNMDSIGIRW--HENLHIFDYRD 83 
                                    89****************************954.........56*********999999**999877..79*****9977 PP

                         AAA_25 111 veslpLfakdrggtl..ltadvdaleaaieevegvrlvviDplsralggdensn..sdvgalveal 172
                                    + ++    kd++      t dv  l+  i+++ ++     D+l+++++ +++ n  + v  ++++l
  gi|116753392|ref|YP_842510.1|  84 M-RIEW--KDHRLDMfsMTKDV--LDMYIDRYRDLTIFAMDSLNALYALSSKTNlrRNVYDFLTML 144
                                    5.4443..33333333588888..9999***999***********999955544214456666555 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.2e-06    0.0071      96     195 ..     105     198 ..      10     218 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.2e-06
                           GvpD  96 efvdeiaaiatkliialdswelvyeylaerydsPediktvkndlvvlaresgvrlvlvletaansrl...eyivdGvvtl 172
                                     ++d      +  i a+ds + +y +l+ + +          d+ ++ r+  +  +l+let  +s      ++ dG++ l
  gi|116753392|ref|YP_842510.1| 105 MYID---RYRDLTIFAMDSLNALY-ALSSKTNLRR----NVYDFLTMLRDRCLTSILILETGDDSGKggeRFLSDGIIEL 176
                                    4455...44455677888855544.3444444433....334555588999**********998864232699******* PP

                           GvpD 173 nvkeddrgrlrrdlrleklrGvr 195
                                     v e   g ++r l++ k+rGvr
  gi|116753392|ref|YP_842510.1| 177 GVIESYNG-VKRYLQIRKMRGVR 198
                                    ***99555.799**********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); 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 0.24s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1574.03
//
Query:       gi|116753393|ref|YP_842511.1|  [L=82]
Description: hypothetical protein Mthe_0069 [Methanosaeta thermophila PT]
Scores for complete 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   0.7      3e-08   33.6   0.7    1.1  1  GvpG      Gas vesicle protein G


Domain annotation for each model (and alignments):
>> GvpG  Gas vesicle protein G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.7   1.7e-12     3e-08      12      70 ..      21      79 ..      13      82 .] 0.92

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 1.7e-12
                           GvpG 12 viWiaeqvqeraeeqlddqenlrkeLaaLqqeLdaGeIdeeeFdrrEeelLdrLealer 70
                                   +iW +eq+   a+++l+++e +r ++ +  +  + Ge++ e++ +r e+l++rL   e+
  gi|116753393|ref|YP_842511.1| 21 LIWTLEQIRGYAQRELYNPERIRNQIKETRLLYEFGEMSHEDYLERTEQLMQRLRIAEQ 79
                                   89****************************************************96665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); 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: 00:00:00.40
# Mc/sec: 618.26
//
Query:       gi|116753394|ref|YP_842512.1|  [L=126]
Description: gas vesicle protein GVPa [Methanosaeta thermophila PT]
Scores for complete 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-16   58.7   5.8      6e-16   58.3   5.8    1.2  1  Gas_vesicle     Gas vesicle protein
     0.0026   17.6   1.8     0.0026   17.6   1.8    1.5  2  Cys_rich_CPCC   Cysteine-rich CPCC
  ------ inclusion threshold ------
      0.038   14.0   1.6      0.059   13.4   1.6    1.3  1  DZR             Double zinc ribbon
      0.054   12.9   8.7       0.36   10.3   8.7    2.1  1  zf-ribbon_3     zinc-ribbon domain
       0.17   11.9   4.3       0.18   11.8   0.2    2.3  2  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
       0.27   11.1   5.7       0.88    9.4   0.6    2.3  2  zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
        3.2    7.6   8.3        1.3    8.9   0.3    2.3  2  zinc_ribbon_2   zinc-ribbon domain
        7.2    6.8   8.2        1.6    8.9   0.8    2.2  2  Zn-ribbon_8     Zinc ribbon domain


Domain annotation for each model (and alignments):
>> Gas_vesicle  Gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.3   5.8   2.7e-19     6e-16       2      39 .]      12      49 ..      11      49 .. 0.97

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 2.7e-19
                    Gas_vesicle  2 LaDlLDrvLdkGvVIdgditisvagieLltikLrlviA 39
                                   La  +Dr+LdkG+VI++dit+svag+eLl+ik+r+++A
  gi|116753394|ref|YP_842512.1| 12 LAGAIDRILDKGLVINADITVSVAGVELLGIKVRAALA 49
                                   8999********************************98 PP

>> Cys_rich_CPCC  Cysteine-rich CPCC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       4.7   1.1e+04      21      29 ..      67      75 ..      65      78 .. 0.72
   2 !   17.6   1.8   1.1e-06    0.0026       2      29 ..      81     107 ..      80     118 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 4.7
                  Cys_rich_CPCC 21 CpvCfWedD 29
                                   C+   W d 
  gi|116753394|ref|YP_842512.1| 67 CETGAWRDA 75
                                   777788875 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 1.1e-06
                  Cys_rich_CPCC   2 qCpcCgyltleeeegsydiCpvCfWedD 29 
                                    +Cp Cg ++l ee   ++ Cp C W   
  gi|116753394|ref|YP_842512.1|  81 ECPQCGKKVLREE-LMHECCPWCGWTSA 107
                                    6************.9**********865 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.6   2.6e-05     0.059      28      49 .]      79     103 ..      53     109 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.6e-05
                            DZR  28 edrCpsCgekvdpearf...CpeCG 49 
                                     + Cp+Cg+kv  e+ +   Cp CG
  gi|116753394|ref|YP_842512.1|  79 REECPQCGKKVLREELMhecCPWCG 103
                                    5666666666544433233366666 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   8.7   0.00016      0.36       4      23 ..      81     103 ..      78     105 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00016
                    zf-ribbon_3   4 rCPnCGa.plssd..dnvCpyCG 23 
                                    +CP+CG+ +l+++    +Cp+CG
  gi|116753394|ref|YP_842512.1|  81 ECPQCGKkVLREElmHECCPWCG 103
                                    8******99*99944568****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 ?   11.8   0.2   8.1e-05      0.18       1      13 [.      81      93 ..      81      96 .. 0.94
   2 ?    1.1   0.6      0.19   4.3e+02       2       6 ..      99     103 ..      98     111 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.1e-05
                 DNA_ligase_ZBD  1 hCPvCGsavvRee 13
                                   +CP CG +v Ree
  gi|116753394|ref|YP_842512.1| 81 ECPQCGKKVLREE 93
                                   5**********98 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.19
                 DNA_ligase_ZBD   2 CPvCG 6  
                                    CP CG
  gi|116753394|ref|YP_842512.1|  99 CPWCG 103
                                    ****9 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.6   0.00039      0.88       2      12 ..      80      90 ..      79      93 .. 0.83
   2 ?    4.1   0.5     0.017        39       3       8 ..      98     103 ..      96     111 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00039
                                   EE-SSS--EEE CS
                 zf-C4_Topoisom  2 ekCPkCggdLv 12
                                   e+CP+Cg++++
  gi|116753394|ref|YP_842512.1| 80 EECPQCGKKVL 90
                                   79*****8865 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.017
                                    E-SSS- CS
                 zf-C4_Topoisom   3 kCPkCg 8  
                                     CP+Cg
  gi|116753394|ref|YP_842512.1|  98 CCPWCG 103
                                    6****9 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.3   0.00057       1.3       2       9 ..      82      89 ..      81      93 .. 0.83
   2 ?    2.0   2.6     0.083   1.9e+02       1       6 [.      98     103 ..      98     105 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00057
                  zinc_ribbon_2  2 CpnCGael 9 
                                   Cp+CG+++
  gi|116753394|ref|YP_842512.1| 82 CPQCGKKV 89
                                   99999986 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.083
                  zinc_ribbon_2   1 fCpnCG 6  
                                    +Cp CG
  gi|116753394|ref|YP_842512.1|  98 CCPWCG 103
                                    699998 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.8   0.00071       1.6      26      38 ..      79      91 ..      66      92 .. 0.74
   2 ?    2.2   7.6     0.089     2e+02       7      33 ..      81     103 ..      81     110 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00071
                    Zn-ribbon_8 26 ltaCPeCgsevrr 38
                                    ++CP+Cg++v r
  gi|116753394|ref|YP_842512.1| 79 REECPQCGKKVLR 91
                                   446*****97755 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.089
                    Zn-ribbon_8   7 rCeeCghefevlqsisdapltaCPeCg 33 
                                    +C +Cg++  +   ++    ++CP Cg
  gi|116753394|ref|YP_842512.1|  81 ECPQCGKKVLREELMH----ECCPWCG 103
                                    5888887666555444....4689888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); 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: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 855.76
//
Query:       gi|116753395|ref|YP_842513.1|  [L=230]
Description: gas vesicle protein GVPa [Methanosaeta thermophila PT]
Scores for complete 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-16   58.2   8.0    6.3e-16   58.2   8.0    1.9  2  Gas_vesicle  Gas vesicle protein


Domain annotation for each model (and alignments):
>> Gas_vesicle  Gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.2   8.0   3.5e-20   6.3e-16       2      39 .]      11      48 ..      10      48 .. 0.98
   2 ?   -0.8   0.0     0.097   1.7e+03      26      35 ..     154     163 ..     153     164 .. 0.91

  Alignments for each domain:
  == domain 1  score: 58.2 bits;  conditional E-value: 3.5e-20
                    Gas_vesicle  2 LaDlLDrvLdkGvVIdgditisvagieLltikLrlviA 39
                                   L+DlLDrvL kGvV+++d++isvag++Ll+++Lr+v+A
  gi|116753395|ref|YP_842513.1| 11 LVDLLDRVLTKGVVLNADVIISVAGVPLLGLSLRAVLA 48
                                   9***********************************98 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.097
                    Gas_vesicle  26 gieLltikLr 35 
                                    ++++l+i Lr
  gi|116753395|ref|YP_842513.1| 154 DTDILHIHLR 163
                                    789*****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); 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 0.28s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1639.12
//
Query:       gi|116753396|ref|YP_842514.1|  [L=104]
Description: gas vesicle K [Methanosaeta thermophila PT]
Scores for complete 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   63.9   4.9    1.2e-17   63.7   4.9    1.1  1  GvpK      Gas vesicle protein K
     0.0062   16.9   0.6     0.0081   16.6   0.6    1.3  1  BAG       BAG domain
  ------ inclusion threshold ------
      0.057   13.4   0.8      0.071   13.1   0.8    1.1  1  Lig_C     Ligase Pab1020 C-terminal region


Domain annotation for each model (and alignments):
>> GvpK  Gas vesicle protein K
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.7   4.9   2.1e-21   1.2e-17       2      72 ..       3      73 ..       2      88 .. 0.91

  Alignments for each domain:
  == domain 1  score: 63.7 bits;  conditional E-value: 2.1e-21
                           GvpK  2 ldadpesverglakLvLtvveLlrqllErqaiRRmeagdlsdeeierlgetLmkleeeleelkesfgleee 72
                                   l+ d++++++g+  Lv+++ve++r++l  qa+RRme+g+l++ee++rlge+Lm+l+ +l+e+k++ g++e+
  gi|116753396|ref|YP_842514.1|  3 LNIDESNLKHGILGLVIALVEVIRDALRIQALRRMESGTLTEEEVNRLGEALMELDIALDEIKREQGITES 73
                                   78899***************************************************************986 PP

>> BAG  BAG domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.6   1.3e-06    0.0081      24      58 ..      42      78 ..      10      92 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.3e-06
                                   ..HHH..HHHHHHHHHHHHHHTCEESTH..HHHHHHH CS
                            BAG 24 kkekeylylsElLlklLlkLDsieiegd..eeaRekR 58
                                    +e+e ++l+E L++l ++LD+i  e    e +++ R
  gi|116753396|ref|YP_842514.1| 42 LTEEEVNRLGEALMELDIALDEIKREQGitESVKAVR 78
                                   23788889****************9655588888877 PP

>> Lig_C  Ligase Pab1020 C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.8   1.2e-05     0.071      18      70 ..      24      77 ..      20      92 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.2e-05
                                   HHHHHH..HHHHH--SHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---EEEEEEE CS
                          Lig_C 18 viReaf..qavefeeseeelrerakeLGesiLepmvetikkvkeeekvkeefrvr 70
                                   viR+a+  qa    es   ++e +++LGe+++e +  ++ ++k+e+ + e ++  
  gi|116753396|ref|YP_842514.1| 24 VIRDALriQALRRMESGTLTEEEVNRLGEALME-LDIALDEIKREQGITESVKAV 77
                                   89999733677788899999*************.9999************99754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       885  (0.0493614); expected 358.6 (0.02)
Passed bias filter:                      674  (0.0375927); 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: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 794.67
//
Query:       gi|116753397|ref|YP_842515.1|  [L=344]
Description: gas vesicle synthesis GvpLGvpF [Methanosaeta thermophila PT]
Scores for complete 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-64  216.3   0.1    1.5e-62  211.7   0.0    2.0  2  GvpL_GvpF  Gas vesicle synthesis protein GvpL/GvpF
  ------ inclusion threshold ------
      0.021   14.9   0.1      0.062   13.4   0.0    1.8  2  YpjP       YpjP-like protein
      0.047   13.7   0.1       0.26   11.3   0.1    2.0  2  DUF45      Protein of unknown function DUF45


Domain annotation for each model (and alignments):
>> GvpL_GvpF  Gas vesicle synthesis protein GvpL/GvpF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.018   1.1e+02     162     196 ..       5      39 ..       2      68 .. 0.84
   2 !  211.7   0.0   2.5e-66   1.5e-62       1     243 [.      96     344 .]      96     344 .] 0.95

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.018
                      GvpL_GvpF 162 rleealeerreelaeeleeaLaplaeevrerepqd 196
                                     l++a++e  ++ ++++ ++Lap+ +ev++ e ++
  gi|116753397|ref|YP_842515.1|   5 DLRDAIAEMVRAEVKAIGDELAPVISEVVRAELMP 39 
                                    6889999999*******************999988 PP

  == domain 2  score: 211.7 bits;  conditional E-value: 2.5e-66
                      GvpL_GvpF   1 glYvYgivdadsddseaadtGvdgepVrlvragglaavvsdvpeeeydaerleqverwllaHqrVvealm.aegtvlPlr 79 
                                    glY+Y+ivda+ ++s +   G+dg +V++++++g++avv+++p e+y+++++e+v+rw+ +Hq+Vve ++ ++gtv+P+ 
  gi|116753397|ref|YP_842515.1|  96 GLYLYCIVDASVSTSLGH-MGIDGCEVYTIPHEGVSAVVHSCPLEPYRSDDEETVKRWVKSHQEVVELAAeRFGTVMPFG 174
                                    79******9999999998.***************************************************99******** PP

                      GvpL_GvpF  80 Fgtvlk.....deeav.relLeeeadelreaLerlagkvEygvkvlwdeealleelleedpelrelreeieaasesgtay 153
                                    F+t++      + e+v ++++++e de+r+++er++gk+Eyg+++++d+  +++++++e++++r ++ee++++++ g ay
  gi|116753397|ref|YP_842515.1| 175 FDTIIMpkefcTAEEVlKKWISDELDEIRAKMERIQGKKEYGIQIFYDPLVFTKRVEDESDDVRIIKEEMASKPP-GIAY 253
                                    ****9999999889999**********************************************************.99** PP

                      GvpL_GvpF 154 llrkrlgqrleealeerreelaeeleeaLaplaeevrerepqd....eemvlnaafLvdrdreeefgeaveelaarldgl 229
                                    + r+rl+++++++++e   +++++++e++++ a+++++++ ++      m++n+++L++  +e+++g+a++ +aa+ +g+
  gi|116753397|ref|YP_842515.1| 254 MYRQRLEAAVRRRMDELIGAYFKDFYERIQSNADDIKVEKVRKsdgdMVMMMNLSVLAS--DEKALGQALDGIAAE-PGI 330
                                    ****************************************9999955556667777765..5679***********.9** PP

                      GvpL_GvpF 230 evrltGPwpPYsFv 243
                                    +v++tGPw PYsFv
  gi|116753397|ref|YP_842515.1| 331 SVQFTGPWQPYSFV 344
                                    *************8 PP

>> YpjP  YpjP-like protein
   #    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       7      81 ..       6      83 ..       1      90 [. 0.83
   2 ?   -2.9   0.0       1.1   6.4e+03      20      28 ..     276     284 ..     251     306 .. 0.48

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1e-05
                           YpjP  7 lellleeaeeqsllKlGkkiaekiedefeeeilpkieeviee.llekv..eeekleeleisekpasgkgEkifhiynk 81
                                   l+ ++ e++   ++ +G+++a++i++ ++ e++p ++++i e +l+++   + +++  e+s+     + Eki +++ +
  gi|116753397|ref|YP_842515.1|  6 LRDAIAEMVRAEVKAIGDELAPVISEVVRAELMPALRAAIREaILRELstYSGDADFREVSQGSVFSEPEKIKNVTAE 83
                                   56678888999999**************************995555553345677889999999999999*9999765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.1
                           YpjP  20 lKlGkkiae 28 
                                    + + ++i++
  gi|116753397|ref|YP_842515.1| 276 KDFYERIQS 284
                                    222222222 PP

>> DUF45  Protein of unknown function DUF45
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.19   1.1e+03      22      44 ..     145     167 ..     140     172 .. 0.79
   2 ?   11.3   0.1   4.4e-05      0.26      34     140 ..     192     295 ..     177     302 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.19
                          DUF45  22 seeeiedfvkkkakwiekklakl 44 
                                    +ee+++++vk++++ +e   +++
  gi|116753397|ref|YP_842515.1| 145 DEETVKRWVKSHQEVVELAAERF 167
                                    57889999999999888766665 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 4.4e-05
                          DUF45  34 akwiekklakleerakeaekelesgesfpllGkkyrlkvekgkeasvklkreelelavkkeeeeeklrkaleewlrkeak 113
                                    +kwi ++l++++++ +  + + e g ++ +    +  +ve+++    +    ++e+a+k+   +   r++le  +r+++ 
  gi|116753397|ref|YP_842515.1| 192 KKWISDELDEIRAKMERIQGKKEYGIQIFYDPLVFTKRVEDES---DDVRIIKEEMASKPPGIAYMYRQRLEAAVRRRMD 268
                                    5799999999999655555666667777665555555555555...777888899999********************** PP

                          DUF45 114 eeleerlaklaaklgvkprsvsikdmk 140
                                    e + ++ +++ ++++ ++ ++++++ +
  gi|116753397|ref|YP_842515.1| 269 ELIGAYFKDFYERIQSNADDIKVEKVR 295
                                    **********************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); 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: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2469.93
//
Query:       gi|116753398|ref|YP_842516.1|  [L=279]
Description: hypothetical protein Mthe_0074 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2040.76
//
Query:       gi|116753399|ref|YP_842517.1|  [L=139]
Description: hypothetical protein Mthe_0075 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       262  (0.0146132); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 1064.64
//
Query:       gi|116753400|ref|YP_842518.1|  [L=108]
Description: PRC-barrel domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-14   52.8   0.8    3.7e-14   52.6   0.8    1.1  1  PRC       PRC-barrel domain


Domain annotation for each model (and alignments):
>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   0.8     2e-18   3.7e-14       1      77 [.      19      99 ..      19     101 .. 0.96

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 2e-18
                                   XEECCS---TT-EEEETTSSEEEEEEEEEEETTTTEEEEEEEEETTT..........-EEEEEGG.CEECCCTEEEETTS-G CS
                            PRC  1 edefrasdliGkeVytedGeklGkVkDvvidekegrvralvvsvggflgi.....gekevliPfdlavkigkdriivdapke 77
                                   ++ ++asdl Gke++t dG  lG+++++ ++ ++g+++ lvv+  + l+      ++k+v iPf  av ++kd+i+vd+ k+
  gi|116753400|ref|YP_842518.1| 19 MKKVFASDLAGKEIVTVDGIVLGELENITFNADTGELVDLVVKPDRNLSRvryraDGKFVRIPFS-AVCAIKDYIVVDEGKS 99
                                   67899****************************************99988***************.************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       225  (0.0125495); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 893.34
//
Query:       gi|116753401|ref|YP_842519.1|  [L=739]
Description: AAA family ATPase, CDC48 subfamily protein [Methanosaeta thermophila PT]
Scores for complete 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-100  331.6   0.0    7.5e-49  165.5   0.0    2.5  2  AAA              ATPase family associated with various cellul
    5.4e-37  125.4   2.2    1.1e-17   63.5   0.6    3.0  2  AAA_lid_3        AAA+ lid domain
    1.9e-29  101.7   0.1    7.6e-29   99.7   0.1    2.1  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
    3.1e-16   58.9   0.1    2.9e-15   55.8   0.2    2.4  2  CDC48_2          Cell division protein 48 (CDC48), domain 2
    1.2e-15   57.7   0.0    1.2e-06   28.4   0.0    3.4  3  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    2.1e-14   54.3   0.0    1.9e-05   25.1   0.0    3.5  3  AAA_16           AAA ATPase domain
    1.7e-12   47.5   0.2    6.6e-05   22.9   0.0    3.6  2  AAA_5            AAA domain (dynein-related subfamily)
    9.4e-12   45.4   0.0    3.2e-05   24.1   0.0    2.6  2  AAA_2            AAA domain (Cdc48 subfamily)
    4.9e-11   42.4   0.0    0.00013   21.3   0.0    2.7  2  TIP49            TIP49 P-loop domain
    1.3e-09   38.4   0.4     0.0082   16.4   0.0    3.9  2  AAA_22           AAA domain
    6.6e-09   36.1   0.0     0.0013   18.9   0.0    2.5  2  AAA_33           AAA domain
    2.3e-08   34.7   0.0     0.0079   16.7   0.0    2.8  2  AAA_18           AAA domain
    3.1e-08   33.7   0.0     0.0067   16.5   0.0    2.3  2  AAA_14           AAA domain
    2.2e-07   30.8   0.1       0.02   14.6   0.0    2.8  2  IstB_IS21        IstB-like ATP binding protein
    8.8e-07   28.5   0.2      0.048   13.0   0.0    2.5  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    1.1e-06   28.3   0.0      0.047   13.2   0.0    2.6  2  AAA_7            P-loop containing dynein motor region
    3.4e-06   27.4   0.0       0.13   12.7   0.0    2.5  2  RNA_helicase     RNA helicase
    5.5e-06   26.1   4.6      0.088   12.4   0.3    4.0  2  AAA_25           AAA domain
    7.4e-06   25.9   0.1       0.12   12.4   0.0    2.8  2  Vps4_C           Vps4 C terminal oligomerisation domain
    7.5e-06   26.3   0.0      0.055   13.7   0.0    2.5  2  AAA_28           AAA domain
    7.9e-06   25.4   0.2       0.31   10.4   0.0    3.4  3  ATPase           KaiC
      8e-06   25.7   0.0       0.16   11.7   0.0    2.7  2  AAA_24           AAA domain
    1.2e-05   25.1   0.0       0.27   10.9   0.0    2.8  2  Sigma54_activat  Sigma-54 interaction domain
    1.3e-05   24.4   0.1       0.11   11.6   0.0    2.2  2  Parvo_NS1        Parvovirus non-structural protein NS1
    1.8e-05   24.8   0.0       0.22   11.4   0.0    3.4  3  ATPase_2         ATPase domain predominantly from Archaea
    4.3e-05   23.5   0.0        0.4   10.7   0.0    2.5  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    6.3e-05   22.4   0.0       0.27   10.4   0.0    2.2  2  DUF2075          Uncharacterized conserved protein (DUF2075)
    6.6e-05   22.3   0.1       0.12   11.6   0.0    2.5  2  Zeta_toxin       Zeta toxin
    0.00012   22.5   0.0       0.68   10.3   0.0    2.9  2  AAA_17           AAA domain
    0.00014   21.7   0.0        0.5   10.2   0.0    2.6  2  AAA_3            ATPase family associated with various cellul
    0.00017   20.8   0.0       0.67    9.1   0.0    2.7  2  DUF815           Protein of unknown function (DUF815)
    0.00027   20.5   0.5       0.77    9.2   0.0    2.5  2  PhoH             PhoH-like protein
    0.00038   19.7   0.0        1.1    8.3   0.0    2.7  2  NB-ARC           NB-ARC domain
    0.00043   20.8   0.0       0.69   10.4   0.0    2.5  2  ABC_tran         ABC transporter
    0.00051   19.9   0.0       0.77    9.5   0.0    2.3  2  AAA_11           AAA domain
    0.00072   19.3   0.0        1.4    8.6   0.0    2.6  2  AAA_30           AAA domain
    0.00085   19.4   0.0       0.89    9.7   0.0    2.5  2  Sigma54_activ_2  Sigma-54 interaction domain
    0.00086   18.8   0.7       0.68    9.3   0.0    2.7  2  IPT              Isopentenyl transferase
     0.0023   18.3   3.2        1.7    9.0   0.2    3.1  3  AAA_19           AAA domain
     0.0043   17.2   0.0       0.97    9.5   0.0    2.3  2  Cytidylate_kin2  Cytidylate kinase-like family
     0.0045   16.8   0.0        1.7    8.4   0.0    3.0  2  Bac_DnaA         Bacterial dnaA  protein
     0.0056   16.4   0.5        4.3    7.0   0.1    2.6  2  Cytidylate_kin   Cytidylate kinase
      0.006   16.5   0.0        3.1    7.7   0.0    2.4  2  Rad17            Rad17 P-loop domain
     0.0088   16.0   0.2          5    7.0   0.0    3.0  2  NACHT            NACHT domain
     0.0096   15.8   0.1        3.4    7.5   0.0    2.8  2  NTPase_1         NTPase
  ------ inclusion threshold ------
      0.011   15.8   0.0        1.7    8.6   0.0    2.4  2  ResIII           Type III restriction enzyme, res subunit
      0.013   15.0   0.0        7.4    5.9   0.0    3.0  3  TniB             Bacterial TniB protein
      0.013   15.6   0.0        6.8    6.8   0.0    2.6  2  SKI              Shikimate kinase
      0.015   14.6   0.0       0.64    9.2   0.0    2.7  3  KAP_NTPase       KAP family P-loop domain
      0.017   14.8   0.0        1.9    8.1   0.0    2.3  2  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
       0.05   13.3   0.2         58    3.3   0.0    3.8  4  Guanylate_kin    Guanylate kinase
      0.065   13.0   0.0         17    5.2   0.0    2.5  2  AAA_29           P-loop containing region of AAA domain
       0.07   13.4   0.1         19    5.4   0.0    2.5  2  Hydin_ADK        Hydin Adenylate kinase-like domain
      0.087   12.7   0.0         14    5.4   0.0    2.5  2  CPT              Chloramphenicol phosphotransferase-like prot
        0.1   13.0   0.0       0.47   10.9   0.0    2.1  1  YCII             YCII-related domain
       0.19   10.6   0.0         15    4.3   0.0    2.2  2  AFG1_ATPase      AFG1-like ATPase


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 !  165.5   0.0   2.3e-51   7.5e-49       1     131 [.     229     358 ..     229     359 .. 0.98
   2 !  163.7   0.0   8.5e-51   2.7e-48       1     131 [.     501     631 ..     501     632 .. 0.97

  Alignments for each domain:
  == domain 1  score: 165.5 bits;  conditional E-value: 2.3e-51
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCH CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgsese 80 
                                    vllyGppGtGKTl+akava+e+g++f++i g+e++sky gese+++re+f+ea ++  psi+fiDE+d++a++rs+ + e
  gi|116753401|ref|YP_842519.1| 229 VLLYGPPGTGKTLIAKAVANESGASFFSIAGPEIMSKYYGESEQRLREIFEEANSNT-PSIVFIDELDSIAPKRSEVTGE 307
                                    79***************************************************9997.********************** PP

                                    HHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                            AAA  81 eeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                    +e+rvv+qLl+++dg+k++ ++++vigatnr+d +dpal+r gRfdr+iei+
  gi|116753401|ref|YP_842519.1| 308 VERRVVAQLLAMMDGLKER-GQLVVIGATNRIDAIDPALRRpGRFDREIEIG 358
                                    ******************7.56***************************996 PP

  == domain 2  score: 163.7 bits;  conditional E-value: 8.5e-51
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.TTCCC CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr.sgses 79 
                                    +llyGppGtGKTl+a+ava+e++++f+++ g++llsk+vgese+ ire+f++ak+ + p+i+f+DE+da+a+ r  ++  
  gi|116753401|ref|YP_842519.1| 501 ILLYGPPGTGKTLIAQAVANETNANFISVRGPQLLSKWVGESERAIREIFRKAKQVS-PTIIFFDELDAIAPMRgMDEGA 579
                                    69******************************************************9.****************988899 PP

                                    HHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                            AAA  80 eeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                    +++ervvnqLl+e+dg+++ ++ vivigatnrpd++dpallr gRfdr i i+
  gi|116753401|ref|YP_842519.1| 580 RVTERVVNQLLAEMDGLEDLKN-VIVIGATNRPDMIDPALLRsGRFDRLIMIG 631
                                    *******************855.*************************99875 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.3   0.0   3.7e-19   1.2e-16       1      42 [.     381     422 ..     381     441 .. 0.80
   2 !   63.5   0.6   3.6e-20   1.1e-17       1      42 [.     654     697 ..     654     714 .. 0.95

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 3.7e-19
                      AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitmed 42 
                                    dv+l+eLA rT+G++GAD+aalc+eAa+ Alrr ++ +++ed
  gi|116753401|ref|YP_842519.1| 381 DVNLEELANRTHGFVGADIAALCKEAAMKALRRYLPDLGTED 422
                                    9********************************766433332 PP

  == domain 2  score: 63.5 bits;  conditional E-value: 3.6e-20
                      AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgik.e.itmed 42 
                                    dv+l+eLAe+T+Gy+GADl alcreA+llAlr+++  e ++m++
  gi|116753401|ref|YP_842519.1| 654 DVNLEELAELTDGYVGADLGALCREAVLLALRENENaEiVEMKH 697
                                    9*********************************9974799*99 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 !   99.7   0.1   2.4e-31   7.6e-29       1      84 [.       8      91 ..       8      92 .. 0.98

  Alignments for each domain:
  == domain 1  score: 99.7 bits;  conditional E-value: 2.4e-31
                                   CEEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEEEEE CS
                        CDC48_N  1 rLrVaeapqedvgrgivridpedmeelglepgdvveiegkrkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVtVrk 82
                                   +L+Va+a+++d+ rgi+r+dp+++  l+l+pgd++eiegk+ T+a+vw+a+++d+ +++Ir+dg++R+nagv+i d+V+Vrk
  gi|116753401|ref|YP_842519.1|  8 QLKVAKAYPNDSARGIARLDPSALLTLRLSPGDIIEIEGKKITAAKVWRADRQDWIQDYIRIDGFIRQNAGVGISDRVKVRK 89
                                   69******99***********************************************************************9 PP

                                   E- CS
                        CDC48_N 83 ae 84
                                   a+
  gi|116753401|ref|YP_842519.1| 90 AR 91
                                   85 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 ?   -0.1   0.0       2.6   8.4e+02      18      30 ..      35      47 ..       5      55 .. 0.74
   2 !   55.8   0.2   9.2e-18   2.9e-15       1      63 [.     109     179 ..     109     180 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 2.6
                                   EE-TTEEEEECCT CS
                        CDC48_2 18 pvtkGdlvvfefk 30
                                    +++Gd++ +e k
  gi|116753401|ref|YP_842519.1| 35 RLSPGDIIEIEGK 47
                                   4778888877765 PP

  == domain 2  score: 55.8 bits;  conditional E-value: 9.2e-18
                                    ..SCCCCHHHHCCCTTEEE-TTEEEEECCT........CCCEEEEEEEECCCCSCEEECTSCCEEESTTCC CS
                        CDC48_2   1 ridgdemaylkrqFlgrpvtkGdlvvfefk........gqeiklvVvstePkgpvgitetTeielgtkpve 63 
                                    ++  d ++++krq l+rpv++Gd+++++          + +i+lvV+ t+P g+v+it+ Tei l++kp++
  gi|116753401|ref|YP_842519.1| 109 QFGPDAVDMIKRQTLKRPVVAGDILPVMSTsgqaflgrMEAIPLVVTATDPGGIVVITDRTEILLMDKPAR 179
                                    57889888*****************9988667777888*******************************86 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 !   28.4   0.0   3.7e-09   1.2e-06      35     103 ..     228     304 ..     202     353 .. 0.79
   2 !   25.0   0.0   4.1e-08   1.3e-05      19      70 ..     476     535 ..     459     627 .. 0.70
   3 ?   -0.6   0.0       3.1     1e+03      22      42 ..     613     633 ..     584     647 .. 0.64

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 3.7e-09
                         RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsraveev 103
                                     vllyGpPG Gkt +ak +a+e g+++ + +gP +      e ++ l  ++ + +++   ++fide+  ++++  ev
  gi|116753401|ref|YP_842519.1| 228 GVLLYGPPGTGKTLIAKAVANESGASFFSIAGPEImskyygESEQRLREIFEEANSNtpSIVFIDELDSIAPKRSEV 304
                                    69*******************************994433333456788888766554237*******9999888776 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 4.1e-08
                         RuvB_N  19 lkifieaakkreealdh........vllyGpPGlGkttlakiiakelgvklkitsgPvle 70 
                                    l  +ie   kr e  +h        +llyGpPG Gkt +a+ +a+e ++++ +  gP l 
  gi|116753401|ref|YP_842519.1| 476 LIEAIEWPLKRPERFEHmgikppkgILLYGPPGTGKTLIAQAVANETNANFISVRGPQLL 535
                                    55555555555555555333333337*******************************873 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 3.1
                         RuvB_N  22 fieaakkreealdhvllyGpP 42 
                                    +i+ a  r+   d ++++GpP
  gi|116753401|ref|YP_842519.1| 613 MIDPALLRSGRFDRLIMIGPP 633
                                    344455555555555555555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   6.1e-08   1.9e-05      23     140 ..     225     332 ..     196     339 .. 0.71
   2 !   18.1   0.0   8.7e-06    0.0028      24      62 ..     498     533 ..     488     540 .. 0.81
   3 ?    6.6   0.0      0.03       9.5     122     170 .]     545     605 ..     542     605 .. 0.69

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 6.1e-08
                         AAA_16  23 rpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekle 102
                                     p  vll+G++G+GK+ ++++++++  ++   f++    +  ++  y    q l r e++++ +++   +    + ++l+
  gi|116753401|ref|YP_842519.1| 225 PPKGVLLYGPPGTGKTLIAKAVANESGAS---FFSIAGPEI-MSKYYGESEQRL-R-EIFEEANSN---TPSIVFIDELD 295
                                    3599*******************855555...777776776.222232244444.3.444444444...44455555566 PP

                         AAA_16 103 ealaavpelagaeasrllellkrllallsrderplvlv 140
                                    + +   +e++g+ ++r+ ++l ++++ l+++++ lv++
  gi|116753401|ref|YP_842519.1| 296 SIAPKRSEVTGEVERRVVAQLLAMMDGLKERGQ-LVVI 332
                                    66668999999999***********99999777.7765 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 8.7e-06
                         AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrgkcdq 62 
                                    p  +ll+G++G+GK+ ++++++++ +++   f++ +  q
  gi|116753401|ref|YP_842519.1| 498 PKGILLYGPPGTGKTLIAQAVANETNAN---FISVRGPQ 533
                                    4789******************977766...66655555 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.03
                         AAA_16 122 llkrllallsrderplvlvlDdlq............wade.aslqllaaLlrlleskpllvv 170
                                    +++++++++++  +p+++++D+l+            ++ e    qlla++  l + k+++v+
  gi|116753401|ref|YP_842519.1| 545 AIREIFRKAKQ-VSPTIIFFDELDaiapmrgmdegaRVTErVVNQLLAEMDGLEDLKNVIVI 605
                                    68889999999.889*********66666666665544443444556666666665688776 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 !   20.1   0.0   1.6e-06    0.0005       1     135 [.     228     346 ..     228     348 .. 0.64
   2 !   22.9   0.0   2.1e-07   6.6e-05       2     135 ..     501     619 ..     500     622 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.6e-06
                                    EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG-- CS
                          AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEverae 78 
                                    +vlL GppGtgK+ +a+ +a   +++++ +++++ +++     + +           ++ ++a+  +++i+++DE++ + 
  gi|116753401|ref|YP_842519.1| 228 GVLLYGPPGTGKTLIAKAVANESGASFFSIAGPEIMSKYYGESEQR---------LREIFEEANsnTPSIVFIDELDSIA 298
                                    59*******************************9887643333333.........3566666666788899999988776 PP

                                    ...HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHH CS
                          AAA_5  79 ...sevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalr 135
                                       sev++++ +    + l +++g ++ +         + vi+++n+ d     ++palr
  gi|116753401|ref|YP_842519.1| 299 pkrSEVTGEVERRVVAQLLAMMDGLKERGQ--------LVVIGATNRID----AIDPALR 346
                                    222334444433333333333333333322........66777777766....6666665 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 2.1e-07
                                    EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG--H CS
                          AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEveraes 79 
                                    +lL GppGtgK+ +a+ +a  +n+++  v +++      l+ ++    g+ ++   ++ r+a+  ++ i+++DE++ + +
  gi|116753401|ref|YP_842519.1| 501 ILLYGPPGTGKTLIAQAVANETNANFISVRGPQ------LLSKWV---GESERAIREIFRKAKqvSPTIIFFDELDAIAP 571
                                    89****************************998......666676...555566677888888899*********95553 PP

                                    HHHHHHHHHHHSSEEE..-SSSEEE---..........-EEEEEESS--.-TT-TTHHHH CS
                          AAA_5  80 evlnsLlslleerrllleeggelvkakndd.ller...frviatanpldrslnelspalr 135
                                          ++ ++e  + +e   ++  a+ d+    +   + vi+++n++d     ++pal+
  gi|116753401|ref|YP_842519.1| 572 ------MRGMDEGARVTERVVNQLLAEMDGlE--DlknVIVIGATNRPD----MIDPALL 619
                                    ......24455555555555555555554421..222389999999988....6677765 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   9.9e-08   3.2e-05       6     105 ..     229     322 ..     224     325 .. 0.87
   2 !   18.4   0.0   5.7e-06    0.0018       6     103 ..     501     593 ..     496     597 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 9.9e-08
                                    EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG---- CS
                          AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpk 83 
                                    +ll gp g+Gkt++aka+a+   +    ++  +   e++     + + ++++  ++   +a+ +   iv++DE+d i+pk
  gi|116753401|ref|YP_842519.1| 229 VLLYGPPGTGKTLIAKAVANESGA----SFFSIAGPEIMS----KYYGESEQRLREIFEEANSNTpsIVFIDELDSIAPK 300
                                    6899*****************996....9999999*****....88889999999999988888899************9 PP

                                    .---------HHHHHHHHHHHH- CS
                          AAA_2  84 .essgadvSregVqrdLLqileg 105
                                     ++ + +v r  V+  LL +++g
  gi|116753401|ref|YP_842519.1| 301 rSEVTGEVERR-VVAQLLAMMDG 322
                                    77788888776.66778888886 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 5.7e-06
                                    EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG---- CS
                          AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpk 83 
                                    ill gp g+Gkt++a+a+a+  ++    ++i +   +ll     + + +++   ++   +a++    i+++DE+d i+p 
  gi|116753401|ref|YP_842519.1| 501 ILLYGPPGTGKTLIAQAVANETNA----NFISVRGPQLLS----KWVGESERAIREIFRKAKQVSptIIFFDELDAIAPM 572
                                    8999******************96....9*********99....55555566666666666666688************8 PP

                                    ..---------HHHHHHHHHHH CS
                          AAA_2  84 ..essgadvSregVqrdLLqil 103
                                        +ga    e V++ LL  +
  gi|116753401|ref|YP_842519.1| 573 rgMDEGAR-VTERVVNQLLAEM 593
                                    64333444.4567777777655 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   4.8e-06    0.0015      51      97 ..     227     271 ..     221     282 .. 0.87
   2 !   21.3   0.0     4e-07   0.00013      51     108 ..     499     555 ..     493     558 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.8e-06
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte 97 
                                    ++vLl Gp+gtGkt +a a+++e g    f +++g e+ s     +e
  gi|116753401|ref|YP_842519.1| 227 KGVLLYGPPGTGKTLIAKAVANESG--ASFFSIAGPEIMSKYYGESE 271
                                    89*********************98..679********998766665 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 4e-07
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXX CS
                          TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte.vltqalrksig 108
                                    +++Ll Gp+gtGkt +a a+++e +    f+++ g ++ s  v  +e ++ + +rk+ +
  gi|116753401|ref|YP_842519.1| 499 KGILLYGPPGTGKTLIAQAVANETN--ANFISVRGPQLLSKWVGESErAIREIFRKAKQ 555
                                    89********************987..78**************99985788999*9965 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1     4e-05     0.013       8      63 ..     229     284 ..     224     332 .. 0.73
   2 !   16.4   0.0   2.6e-05    0.0082       8      48 ..     501     532 ..     495     613 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4e-05
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlpsstsskdllrellra 63 
                                    ++++G++GtGKT+ ++ ++++  + ++   ++pe++ +++  s+  ++++++e  ++
  gi|116753401|ref|YP_842519.1| 229 VLLYGPPGTGKTLIAKAVANESGA-SFFSIAGPEIMsKYYGESEQRLREIFEEANSN 284
                                    689*****************9742.22222566655566666666666666655554 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 2.6e-05
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlp 48 
                                    ++++G++GtGKT+ ++ ++++          ++ +++v  p
  gi|116753401|ref|YP_842519.1| 501 ILLYGPPGTGKTLIAQAVANET---------NANFISVRGP 532
                                    89******************98.........6666666555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   4.2e-06    0.0013       2      79 ..     229     336 ..     229     375 .. 0.74
   2 !   14.7   0.0   7.9e-05     0.025       2      46 ..     501     547 ..     501     617 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 4.2e-06
                         AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt............................dytrv 51 
                                    vll G+pG+GK+  a+ ++++ g  ++ ++ ++++++++g+ +q+++                               +v
  gi|116753401|ref|YP_842519.1| 229 VLLYGPPGTGKTLIAKAVANESGasFFSIAGPEIMSKYYGESEQRLReifeeansntpsivfideldsiapkrseVTGEV 308
                                    7899*******************99999************8888887666666666666666666666666444322234 PP

                         AAA_33  52 ldrlyqilnelarkalsagrnvildatn 79 
                                    + r+ ++l ++ +   ++g+ v++ atn
  gi|116753401|ref|YP_842519.1| 309 ERRVVAQLLAMMDGLKERGQLVVIGATN 336
                                    4445555556665555555556666665 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 7.9e-05
                         AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt 46 
                                    +ll G+pG+GK+  a+ +++++   ++ ++ ++l+++ +g+ ++ ++
  gi|116753401|ref|YP_842519.1| 501 ILLYGPPGTGKTLIAQAVANETNanFISVRGPQLLSKWVGESERAIR 547
                                    6789***************9999888889999988888876555544 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   8.7e-05     0.028       1      43 [.     229     269 ..     229     333 .. 0.68
   2 !   16.7   0.0   2.5e-05    0.0079       1      67 [.     501     596 ..     501     611 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8.7e-05
                         AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdp 43 
                                    +ll G+pG+GKt +ak+++++   g    ++a  + ++ ++ +
  gi|116753401|ref|YP_842519.1| 229 VLLYGPPGTGKTLIAKAVANES--GASFFSIAGPEIMSKYYGE 269
                                    799***************9987..4444444444444333333 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 2.5e-05
                         AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.................gvnlrdvakenglllevdpe...........aldeskr 51 
                                    Ill G+pG+GKt +a+++++++ ++                  + +r+++++   + +   +             de  r
  gi|116753401|ref|YP_842519.1| 501 ILLYGPPGTGKTLIAQAVANETnANfisvrgpqllskwvgesERAIREIFRKAKQVSPTIIFfdeldaiapmrGMDEGAR 580
                                    99****************99984337888888888888888866666666666666666655555666677666777777 PP

                         AAA_18  52 ldedkldklldaleen 67 
                                    + e ++++ll ++++ 
  gi|116753401|ref|YP_842519.1| 581 VTERVVNQLLAEMDGL 596
                                    7777777777766665 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   2.1e-05    0.0067       5      77 ..     229     310 ..     226     353 .. 0.73
   2 !   14.8   0.0   6.7e-05     0.022       5      77 ..     501     580 ..     498     627 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.1e-05
                         AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev........ 76 
                                    +++ G+  +GKT ++k +++e+     s++ i+  +   k + ++e+ l++i+e+++++  +++f+DE   +        
  gi|116753401|ref|YP_842519.1| 229 VLLYGPPGTGKTLIAKAVANESG---ASFFSIAGPEIMSKYYGESEQRLREIFEEANSNTPSIVFIDELDSIapkrsevt 305
                                    7899***************9999...999999999988888877775666666665556999******999855555555 PP

                         AAA_14  77 ....p 77 
                                        +
  gi|116753401|ref|YP_842519.1| 306 geveR 310
                                    54443 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 6.7e-05
                         AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev........ 76 
                                    +++ G+  +GKT +++ +++e      +++ +   +   k   ++e+ +++i++k+k+   t++f+DE   +        
  gi|116753401|ref|YP_842519.1| 501 ILLYGPPGTGKTLIAQAVANETN---ANFISVRGPQLLSKWVGESERAIREIFRKAKQVSPTIIFFDELDAIapmrgmde 577
                                    7899**********999997776...777777777766666666666666666665666899******988755555554 PP

                         AAA_14  77 ..p 77 
                                      +
  gi|116753401|ref|YP_842519.1| 578 gaR 580
                                    443 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 !   12.9   0.0   0.00021     0.068      47      71 ..     226     250 ..     219     262 .. 0.87
   2 !   14.6   0.0   6.4e-05      0.02      48      78 ..     499     529 ..     493     567 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00021
                      IstB_IS21  47 kenivllGpsGvGKshlaialgvea 71 
                                     ++++l Gp+G+GK+ +a a++ e 
  gi|116753401|ref|YP_842519.1| 226 PKGVLLYGPPGTGKTLIAKAVANES 250
                                    57899***************99875 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 6.4e-05
                      IstB_IS21  48 enivllGpsGvGKshlaialgveavraglsv 78 
                                    ++i+l Gp+G+GK+ +a a++ e+ ++ +sv
  gi|116753401|ref|YP_842519.1| 499 KGILLYGPPGTGKTLIAQAVANETNANFISV 529
                                    6899****************99887666665 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   0.00019     0.062      25      42 ..     229     246 ..     226     249 .. 0.90
   2 !   13.0   0.0   0.00015     0.048      25      43 ..     501     519 ..     495     526 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00019
                   Mg_chelatase  25 lllvGppGsGKtmlakrl 42 
                                    +ll+GppG+GKt++ak++
  gi|116753401|ref|YP_842519.1| 229 VLLYGPPGTGKTLIAKAV 246
                                    79*************987 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00015
                   Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                    +ll+GppG+GKt++a++++
  gi|116753401|ref|YP_842519.1| 501 ILLYGPPGTGKTLIAQAVA 519
                                    89*************9875 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      58 ..     226     251 ..     216     300 .. 0.85
   2 !   13.2   0.0   0.00015     0.047      31      62 ..     496     526 ..     486     532 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00032
                          AAA_7  33 kkpvllvGptGtGKtviikdllkkld 58 
                                     k vll+Gp GtGKt+i+k + ++  
  gi|116753401|ref|YP_842519.1| 226 PKGVLLYGPPGTGKTLIAKAVANESG 251
                                    678****************9888765 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00015
                          AAA_7  31 knkkpvllvGptGtGKtviikdllkkldkeky 62 
                                    k  k +ll+Gp GtGKt+i++ + ++ +  ++
  gi|116753401|ref|YP_842519.1| 496 KPPKGILLYGPPGTGKTLIAQAVANETN-ANF 526
                                    566889****************999988.444 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0    0.0005      0.16       1      26 [.     229     254 ..     229     303 .. 0.76
   2 !   12.7   0.0   0.00041      0.13       1      26 [.     501     526 ..     501     600 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0005
                   RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                                    ++lyGp+g+GK+++ak +a++   ++
  gi|116753401|ref|YP_842519.1| 229 VLLYGPPGTGKTLIAKAVANESGASF 254
                                    689**************888766555 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00041
                   RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                                    i+lyGp+g+GK+++a+ +a++   ++
  gi|116753401|ref|YP_842519.1| 501 ILLYGPPGTGKTLIAQAVANETNANF 526
                                    789**************998877555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.6    0.0022      0.69      36     153 ..     229     337 ..     223     342 .. 0.53
   2 !   12.4   0.3   0.00028     0.088      35     148 ..     500     604 ..     471     605 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0022
                         AAA_25  36 allaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgealrddarllvldlagv.esl 114
                                    +ll+G+pgtGKt +a    +a  +G +++ +     g+ ++    +     ++Rlr+++e++    +  ++ ++ + +s+
  gi|116753401|ref|YP_842519.1| 229 VLLYGPPGTGKTLIAKA--VANESGASFFSI----AGPEIMSKYYGES---EQRLREIFEEA-NSNTPSIVFID-ElDSI 297
                                    689*********98754..333377778773....4444444444333...45666666654.34444444442.21333 PP

                         AAA_25 115 pLfakdrggtl...ltadvdaleaaieeveg.vrlvviDplsr 153
                                       a++r + +     ++v++l a ++  ++  +lvvi   +r
  gi|116753401|ref|YP_842519.1| 298 ---APKRSEVTgevERRVVAQLLAMMDGLKErGQLVVIGATNR 337
                                    ...3333333322134455555555555544567777766665 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00028
                         AAA_25  35 lallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgealrddarllvldlagvesl 114
                                     +ll+G+pgtGKt +a  +a ++    ++   + p+    ++   E +  e+ r++++v  ++ + ++l+++        
  gi|116753401|ref|YP_842519.1| 500 GILLYGPPGTGKTLIAQAVANETN--ANFISVRGPQLLSKWVGESERAIREIFRKAKQVSPTIIFFDELDAI-------A 570
                                    579***********9987776655..3454433456777777777777767777777777666444444444.......3 PP

                         AAA_25 115 pLfakdrggtlltadvdaleaaieevegvrlvvi 148
                                    p++ +d g  +++++v++l a+++  e+++ v++
  gi|116753401|ref|YP_842519.1| 571 PMRGMDEGARVTERVVNQLLAEMDGLEDLKNVIV 604
                                    5556677777788888888888888888777765 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 !   10.3   0.1    0.0017      0.53      17      45 ..     422     450 ..     419     458 .. 0.85
   2 !   12.4   0.0   0.00038      0.12      28      55 ..     692     719 ..     686     724 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0017
                         Vps4_C  17 mdipsdkllePpvtlkDflkalkkarptV 45 
                                     dip++ +   +vt++Df+ alk+  p+ 
  gi|116753401|ref|YP_842519.1| 422 DDIPPEIVESMKVTRDDFEMALKEIEPSA 450
                                    68998878888**************9985 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00038
                         Vps4_C  28 pvtlkDflkalkkarptVskeDLekhee 55 
                                     v++k+ l+alk++rp+V ++ +  +e+
  gi|116753401|ref|YP_842519.1| 692 IVEMKHYLEALKRVRPSVEESMISYYER 719
                                    699******************9999986 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   0.00017     0.055       2      48 ..     229     276 ..     228     309 .. 0.75
   2 !   10.1   0.0    0.0022       0.7       2      23 ..     501     525 ..     500     575 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00017
                         AAA_28   2 ivitGgestGKTtlleaLaar.gypvvpEaareileeklakgedalpw 48 
                                    + + G+++tGKT +++a a++ g + +  a+ ei+++ + + e+ l++
  gi|116753401|ref|YP_842519.1| 229 VLLYGPPGTGKTLIAKAVANEsGASFFSIAGPEIMSKYYGESEQRLRE 276
                                    6799***************87776666555555555444444444443 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0022
                         AAA_28   2 ivitGgestGKTtlleaLaar...g 23 
                                    i + G+++tGKT +++a a++   +
  gi|116753401|ref|YP_842519.1| 501 ILLYGPPGTGKTLIAQAVANEtnaN 525
                                    7899***************654341 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0    0.0024      0.77      15      38 ..     222     245 ..     215     254 .. 0.82
   2 ?    1.5   0.0      0.48   1.5e+02     109     154 ..     272     323 ..     261     336 .. 0.68
   3 !   10.4   0.0   0.00096      0.31      13      38 ..     492     517 ..     484     529 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0024
                         ATPase  15 GipegrvvlitGepGtGKtifalq 38 
                                    Gi   + vl++G pGtGKt++a+ 
  gi|116753401|ref|YP_842519.1| 222 GIDPPKGVLLYGPPGTGKTLIAKA 245
                                    67777889************9975 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.48
                         ATPase 109 eelaeaikeika...krvviDsitgl...ayeekeavaReilrqlvrvlkkl 154
                                    ++l+e+ +e +    + v iD ++++     e + +v R+ + ql+ ++ +l
  gi|116753401|ref|YP_842519.1| 272 QRLREIFEEANSntpSIVFIDELDSIapkRSEVTGEVERRVVAQLLAMMDGL 323
                                    5566666665554446677776666632145566678999999999999665 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00096
                         ATPase  13 kgGipegrvvlitGepGtGKtifalq 38 
                                    + Gi   + +l++G pGtGKt++a+ 
  gi|116753401|ref|YP_842519.1| 492 HMGIKPPKGILLYGPPGTGKTLIAQA 517
                                    568888899**************985 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    0.0005      0.16       5      22 ..     229     246 ..     226     302 .. 0.78
   2 !   11.0   0.0   0.00079      0.25       5      22 ..     501     518 ..     498     531 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0005
                         AAA_24   5 iliyGpsgiGKTtlakel 22 
                                    +l+yGp+g+GKT +ak  
  gi|116753401|ref|YP_842519.1| 229 VLLYGPPGTGKTLIAKAV 246
                                    89************9987 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00079
                         AAA_24   5 iliyGpsgiGKTtlakel 22 
                                    il+yGp+g+GKT +a   
  gi|116753401|ref|YP_842519.1| 501 ILLYGPPGTGKTLIAQAV 518
                                    89**********999876 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00089      0.29      23      47 ..     227     251 ..     212     262 .. 0.86
   2 !   10.9   0.0   0.00083      0.27      23      51 ..     499     524 ..     485     537 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00089
                                    S-EEEECSTTSSHHHHHHHHHHHST CS
                Sigma54_activat  23 lsvlitGesGtGKellaraiheask 47 
                                      vl+ G  GtGK+l+a+a+ ++s 
  gi|116753401|ref|YP_842519.1| 227 KGVLLYGPPGTGKTLIAKAVANESG 251
                                    679****************988775 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00083
                                    S-EEEECSTTSSHHHHHHHHHHHSTTTTS CS
                Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrkek 51 
                                      +l+ G  GtGK+l+a+a+ ++++   +
  gi|116753401|ref|YP_842519.1| 499 KGILLYGPPGTGKTLIAQAVANETN---A 524
                                    679****************987655...4 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 !   10.5   0.0   0.00072      0.23     117     137 ..     229     249 ..     224     252 .. 0.90
   2 !   11.6   0.0   0.00035      0.11     117     137 ..     501     521 ..     495     528 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00072
                      Parvo_NS1 117 vwfyGpantGktnlaeaIaka 137
                                    v++yGp+ tGkt +a+a a+ 
  gi|116753401|ref|YP_842519.1| 229 VLLYGPPGTGKTLIAKAVANE 249
                                    89***************9985 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00035
                      Parvo_NS1 117 vwfyGpantGktnlaeaIaka 137
                                    +++yGp+ tGkt +a+a a+ 
  gi|116753401|ref|YP_842519.1| 501 ILLYGPPGTGKTLIAQAVANE 521
                                    89***************9985 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00068      0.22      21     118 ..     227     328 ..     216     336 .. 0.61
   2 ?    5.5   0.0     0.043        14      22      46 ..     500     523 ..     491     534 .. 0.74
   3 ?    3.6   0.0      0.17        53     107     151 ..     543     595 ..     525     668 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00068
                       ATPase_2  21 eiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekal............giavpk 88 
                                    + +++YGp g GKt + k +++++       ++ ia  e+ ++++ e+  e +  +++ + +            ++ +  
  gi|116753401|ref|YP_842519.1| 227 KGVLLYGPPGTGKTLIAKAVANES----GASFFSIAGPEIMSKYYGES--E-QRLREIFEEAnsntpsivfideLDSIAP 299
                                    56799*********8888888777....35789999999999999999..3.3333333333244444444444222222 PP

                       ATPase_2  89 aeleeilkeksklvfkaielllekikkkgk 118
                                    ++  e+  e  + v +++ ++++ +k++g+
  gi|116753401|ref|YP_842519.1| 300 KRS-EVTGEVERRVVAQLLAMMDGLKERGQ 328
                                    222.33345555555555566666666655 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.043
                       ATPase_2  22 iyfiYGpegsGKtaLlkeiienled 46 
                                     +++YGp g GKt  + +++ n  +
  gi|116753401|ref|YP_842519.1| 500 GILLYGPPGTGKTL-IAQAVANETN 523
                                    5789********95.5555555544 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.17
                       ATPase_2 107 elllekikkkgkk...iiiiiDelqklidl.gln....gaellvkeLlnlies 151
                                    e+++++i +k+k+    ii++Del  +  + g++      e +v++Ll  ++ 
  gi|116753401|ref|YP_842519.1| 543 ERAIREIFRKAKQvspTIIFFDELDAIAPMrGMDegarVTERVVNQLLAEMDG 595
                                    567778888888888789******99985533333333455566666666655 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0    0.0012       0.4      20      59 ..     227     266 ..     200     277 .. 0.76
   2 !   10.1   0.0    0.0019       0.6      20      51 ..     499     532 ..     468     536 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0012
                                    EEEEEEESTTSSHHHHHHHHHHHTT--..----TTTTSEEEE CS
                           TsaE  20 dvilLeGdLGaGKTtlvrglakalgve..evkSPTFtlveeY 59 
                                    + +lL+G+ G+GKT +++++a++ g +  ++  P   ++++Y
  gi|116753401|ref|YP_842519.1| 227 KGVLLYGPPGTGKTLIAKAVANESGASffSIAGP--EIMSKY 266
                                    449*******************999887777777..455555 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0019
                                    EEEEEEESTTSSHHHHHHHHHHHTT--..----T CS
                           TsaE  20 dvilLeGdLGaGKTtlvrglakalgve..evkSP 51 
                                    + ilL+G+ G+GKT +++++a++ + +  +v+ P
  gi|116753401|ref|YP_842519.1| 499 KGILLYGPPGTGKTLIAQAVANETNANfiSVRGP 532
                                    349******************9998876666655 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0    0.0012      0.39       4      34 ..     229     253 ..     226     309 .. 0.67
   2 !   10.4   0.0   0.00084      0.27       4      34 ..     501     524 ..     498     567 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0012
                        DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeerta 34 
                                    vl  G +GtGKt+++ ++++e         +
  gi|116753401|ref|YP_842519.1| 229 VLLYGPPGTGKTLIAKAVANES------GAS 253
                                    6789*************99998......233 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00084
                        DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeerta 34 
                                    +l  G +GtGKt+++ ++++e        +a
  gi|116753401|ref|YP_842519.1| 501 ILLYGPPGTGKTLIAQAVANET-------NA 524
                                    6789**************9998.......33 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.1    0.0053       1.7      15      40 ..     225     250 ..     218     261 .. 0.89
   2 !   11.6   0.0   0.00037      0.12      14      50 ..     496     530 ..     487     535 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0053
                     Zeta_toxin  15 rPklillgGqpGAGKselaellkdel 40 
                                     Pk +ll G pG GK+ +a+++++e 
  gi|116753401|ref|YP_842519.1| 225 PPKGVLLYGPPGTGKTLIAKAVANES 250
                                    5999******************9997 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00037
                     Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrld 50 
                                    + Pk ill G pG GK+ +a+++++e+  + n++ + 
  gi|116753401|ref|YP_842519.1| 496 KPPKGILLYGPPGTGKTLIAQAVANET--NANFISVR 530
                                    5699**********************9..88888775 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0    0.0052       1.7       1      26 [.     232     257 ..     232     301 .. 0.85
   2 !   10.3   0.0    0.0021      0.68       1      52 [.     504     556 ..     504     611 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0052
                                    EE-TTSSHHHHHHHHHHHHTEEEEEH CS
                         AAA_17   1 lGgPGsGKgtqceklvekygfthlsa 26 
                                    +G+PG GK+ +++ ++ + g +++s 
  gi|116753401|ref|YP_842519.1| 232 YGPPGTGKTLIAKAVANESGASFFSI 257
                                    7******************9999985 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0021
                                    EE-TTSSHHHHHHHHHHHHTEEEEEH.HHHHHHHHHTTTSHSSHHHHCTSHHH CS
                         AAA_17   1 lGgPGsGKgtqceklvekygfthlsa.Gdllreeakrgglakardemrklple 52 
                                    +G+PG GK+ +++ ++ + +  ++s  G  l +    ++    r+ +rk++++
  gi|116753401|ref|YP_842519.1| 504 YGPPGTGKTLIAQAVANETNANFISVrGPQLLSKWVGESERAIREIFRKAKQV 556
                                    7*****************98888886555555444444333466666666555 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 !    9.0   0.0    0.0039       1.2       2      30 ..     229     257 ..     228     314 .. 0.89
   2 !   10.2   0.0    0.0015       0.5       2      31 ..     501     530 ..     500     596 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0039
                          AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                    vll g PG++ktl++ka+a+  +++f  i
  gi|116753401|ref|YP_842519.1| 229 VLLYGPPGTGKTLIAKAVANESGASFFSI 257
                                    7999****************999988665 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0015
                          AAA_3   2 vllegvPGlaktllvkalakaldlefkriq 31 
                                    +ll g PG++ktl+++a+a+  +++f  ++
  gi|116753401|ref|YP_842519.1| 501 ILLYGPPGTGKTLIAQAVANETNANFISVR 530
                                    7999*******************9997764 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0    0.0021      0.67      54     116 ..     227     294 ..     219     337 .. 0.71
   2 !    8.6   0.0    0.0028       0.9      50      82 ..     495     527 ..     448     569 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0021
                         DUF815  54 nnvLLwGarGtGKSslvkallneyaeegLrli..evekedlkelpklvell.r..erperfilfvDDL 116
                                    + vLL+G  GtGK  + ka+ ne  ++   +   e+  +   e ++ ++++ +  ++++  i+f+D L
  gi|116753401|ref|YP_842519.1| 227 KGVLLYGPPGTGKTLIAKAVANESGASFFSIAgpEIMSKYYGESEQRLREIfEeaNSNTPSIVFIDEL 294
                                    679*******************9988875553336655444433332222212114455567777776 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0028
                         DUF815  50 glpannvLLwGarGtGKSslvkallneyaeegL 82 
                                     +p + +LL+G  GtGK  + +a+ ne++++ +
  gi|116753401|ref|YP_842519.1| 495 IKPPKGILLYGPPGTGKTLIAQAVANETNANFI 527
                                    467889*********************998764 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.1     0.003      0.95      22      40 ..     229     247 ..     222     253 .. 0.87
   2 !    9.2   0.0    0.0024      0.77      23      42 ..     502     521 ..     493     529 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.003
                                    EEEE--TTSSTTHHHHHHH CS
                           PhoH  22 vfaiGpaGtGKtylavala 40 
                                    v   Gp GtGKt++a a+a
  gi|116753401|ref|YP_842519.1| 229 VLLYGPPGTGKTLIAKAVA 247
                                    6789***********9998 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0024
                                    EEE--TTSSTTHHHHHHHHH CS
                           PhoH  23 faiGpaGtGKtylavalave 42 
                                       Gp GtGKt++a a+a e
  gi|116753401|ref|YP_842519.1| 502 LLYGPPGTGKTLIAQAVANE 521
                                    678***********999865 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0036       1.1      23      44 ..     229     250 ..     215     269 .. 0.87
   2 !    8.3   0.0    0.0037       1.2      23      44 ..     501     522 ..     495     558 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0036
                                    EEEEESTTSSHHHHHHHHCCSH CS
                         NB-ARC  23 valvGmgGvGKttlakqilnks 44 
                                    v l+G +G GKt +ak + n+s
  gi|116753401|ref|YP_842519.1| 229 VLLYGPPGTGKTLIAKAVANES 250
                                    789***************9984 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0037
                                    EEEEESTTSSHHHHHHHHCCSH CS
                         NB-ARC  23 valvGmgGvGKttlakqilnks 44 
                                    + l+G +G GKt +a+ + n+ 
  gi|116753401|ref|YP_842519.1| 501 ILLYGPPGTGKTLIAQAVANET 522
                                    679***************9983 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0     0.015       4.8       7      36 ..     222     251 ..     219     330 .. 0.81
   2 !   10.4   0.0    0.0021      0.69       7      92 ..     494     593 ..     492     609 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.015
                                    EEETTSEEEEEESTTSSHHHHHHHHTTSS- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   7 klkegekvaivGenGaGKStLlkllagllk 36 
                                     + + + v + G+ G+GK+ ++k++a+++ 
  gi|116753401|ref|YP_842519.1| 222 GIDPPKGVLLYGPPGTGKTLIAKAVANESG 251
                                    566777899***************998865 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0021
                                    EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHH...... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx...... RF
                       ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvren...... 79 
                                     +k+ + + + G+ G+GK+ +++++a++++  +  i ++g +l ++   ++++ i+ ++ + +q+ p++   ++      
  gi|116753401|ref|YP_842519.1| 494 GIKPPKGILLYGPPGTGKTLIAQAVANETN--ANFISVRGPQLLSKWVGESERAIREIFRKaKQVSPTIIFFDEldaiap 571
                                    677778899*******************97..578888999999988888899998888887888888876666677777 PP

                                    .........HHHTCHHHHHHHS CS
                                    .........xxxxxxxxxxxxx RF
                       ABC_tran  80 .........esdeeiekalskl 92 
                                               ++ ++++l+++
  gi|116753401|ref|YP_842519.1| 572 mrgmdegarVTERVVNQLLAEM 593
                                    7766655543333355555555 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0068       2.2      20      39 ..     229     248 ..     214     287 .. 0.80
   2 !    9.5   0.0    0.0024      0.77      19      42 ..     500     523 ..     473     560 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0068
                         AAA_11  20 tliqGPPGtgKTktivells 39 
                                    +l+ GPPGtgKT    ++ +
  gi|116753401|ref|YP_842519.1| 229 VLLYGPPGTGKTLIAKAVAN 248
                                    6999********76655555 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0024
                         AAA_11  19 itliqGPPGtgKTktivellsqll 42 
                                      l+ GPPGtgKT    ++ ++ +
  gi|116753401|ref|YP_842519.1| 500 GILLYGPPGTGKTLIAQAVANETN 523
                                    46999********88888887774 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0044       1.4      21      40 ..     229     248 ..     216     297 .. 0.89
   2 !    8.0   0.0    0.0069       2.2      22      44 ..     502     524 ..     490     533 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0044
                         AAA_30  21 avltGpAGtGKttalkalre 40 
                                    ++l Gp+GtGKt + ka+++
  gi|116753401|ref|YP_842519.1| 229 VLLYGPPGTGKTLIAKAVAN 248
                                    6899**********999975 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0069
                         AAA_30  22 vltGpAGtGKttalkalreawea 44 
                                    +l Gp+GtGKt + +a+++  +a
  gi|116753401|ref|YP_842519.1| 502 LLYGPPGTGKTLIAQAVANETNA 524
                                    688**********9999876655 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 !    9.7   0.0    0.0028      0.89      24      51 ..     229     254 ..     225     308 .. 0.68
   2 ?    7.0   0.0     0.018       5.8      24      47 ..     501     524 ..     494     573 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0028
                                    EEEEEETT--HHHHHHCC--TTS-EE-- CS
                Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpwlei 51 
                                    v+l G++G+gk+l+A++ +++sg   + 
  gi|116753401|ref|YP_842519.1| 229 VLLYGPPGTGKTLIAKAVANESGA--SF 254
                                    9******************99987..33 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.018
                                    EEEEEETT--HHHHHHCC--TTS- CS
                Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgp 47 
                                    ++l G++G+gk+l+A++ +++   
  gi|116753401|ref|YP_842519.1| 501 ILLYGPPGTGKTLIAQAVANETNA 524
                                    799**************9987654 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1     0.011       3.4       5      30 ..     230     255 ..     227     258 .. 0.90
   2 !    9.3   0.0    0.0021      0.68       5      53 ..     502     550 ..     499     606 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.011
                            IPT   5 lifGatttGKtaeaiklaketgapvi 30 
                                    l++G+ +tGKt  a ++a+e ga+  
  gi|116753401|ref|YP_842519.1| 230 LLYGPPGTGKTLIAKAVANESGASFF 255
                                    89********************9865 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0021
                            IPT   5 lifGatttGKtaeaiklaketgapvivlDRvqcyselavgsGrpleeel 53 
                                    l++G+ +tGKt  a ++a+et a  i++   q  s+    s r++ e +
  gi|116753401|ref|YP_842519.1| 502 LLYGPPGTGKTLIAQAVANETNANFISVRGPQLLSKWVGESERAIREIF 550
                                    89**********************9998777777766666666666655 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.2    0.0098       3.1      11      31 ..     227     247 ..     223     256 .. 0.84
   2 ?   -1.6   0.0       9.8   3.1e+03      97     126 ..     280     309 ..     261     324 .. 0.68
   3 !    9.0   0.2    0.0052       1.7      11      35 ..     499     523 ..     495     609 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0098
                         AAA_19  11 kvllvtaGpGtGKTrvlkhiv 31 
                                    k +l+ ++pGtGKT + k++ 
  gi|116753401|ref|YP_842519.1| 227 KGVLLYGPPGTGKTLIAKAVA 247
                                    56899*********9987765 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 9.8
                         AAA_19  97 ekklqeeellivDEfqdvdelqyrLlkall 126
                                    e + +   ++++DE   + +   ++  ++ 
  gi|116753401|ref|YP_842519.1| 280 EANSNTPSIVFIDELDSIAPKRSEVTGEVE 309
                                    33343455999***9999887777666665 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0052
                         AAA_19  11 kvllvtaGpGtGKTrvlkhivallv 35 
                                    k +l+ ++pGtGKT + +++ ++ +
  gi|116753401|ref|YP_842519.1| 499 KGILLYGPPGTGKTLIAQAVANETN 523
                                    56899*********99887776654 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0     0.003      0.97       8      54 ..     235     283 ..     231     333 .. 0.81
   2 ?    5.4   0.0     0.056        18       8      60 ..     507     560 ..     501     606 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.003
                Cytidylate_kin2   8 yGsgGetigeaLAekLglpfydreiieevakelglseeev.eevde.rs 54 
                                     G+g++ i++a+A++ g  f++ + +e ++k  g se+ + e ++e +s
  gi|116753401|ref|YP_842519.1| 235 PGTGKTLIAKAVANESGASFFSIAGPEIMSKYYGESEQRLrEIFEEaNS 283
                                    59**************************************666666422 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.056
                Cytidylate_kin2   8 yGsgGetigeaLAekLglpfydreiieevakelglseeev.eevdersrlssfl 60 
                                     G+g++ i++a+A++ + +f++ + ++ ++k  g se  + e + +++ +s ++
  gi|116753401|ref|YP_842519.1| 507 PGTGKTLIAQAVANETNANFISVRGPQLLSKWVGESERAIrEIFRKAKQVSPTI 560
                                    69******************************9999999955555544444444 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0      0.07        22      37      60 ..     229     252 ..     225     395 .. 0.71
   2 !    8.4   0.0    0.0053       1.7      37      70 ..     501     534 ..     495     664 .. 0.66

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.07
                                    EEEE-SSSSSHHHHHHHHHHHHHH CS
                       Bac_DnaA  37 lfiygevGlGktHLlkaignevle 60 
                                    +++yg+ G Gkt + ka++ne  +
  gi|116753401|ref|YP_842519.1| 229 VLLYGPPGTGKTLIAKAVANESGA 252
                                    799**********99999987544 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0053
                                    EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEE CS
                       Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYl 70 
                                    +++yg+ G Gkt + +a++ne+ +n+ + r   l
  gi|116753401|ref|YP_842519.1| 501 ILLYGPPGTGKTLIAQAVANETNANFISVRGPQL 534
                                    79********************999888775555 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1     0.014       4.3       4      28 ..     232     256 ..     229     259 .. 0.90
   2 ?    7.0   0.0     0.014       4.4       3      28 ..     503     528 ..     501     530 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.014
                                    E-STTSSHHHHHHHHHHHHT-EEEE CS
                 Cytidylate_kin   4 DGPagsGKssvaralaeklglkyld 28 
                                     GP g+GK  +a+a+a++ g+++++
  gi|116753401|ref|YP_842519.1| 232 YGPPGTGKTLIAKAVANESGASFFS 256
                                    6*******************99986 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.014
                                    EE-STTSSHHHHHHHHHHHHT-EEEE CS
                 Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyld 28 
                                    + GP g+GK  +a+a+a++ ++++++
  gi|116753401|ref|YP_842519.1| 503 LYGPPGTGKTLIAQAVANETNANFIS 528
                                    67********************9986 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.026       8.5      48      81 ..     229     262 ..     220     307 .. 0.74
   2 !    7.7   0.0    0.0098       3.1      48     112 ..     501     566 ..     478     604 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.026
                          Rad17  48 LLisGPsGCgkstvvkvLskelgiklrewlnpvs 81 
                                    +L+ GP+G gk+ + k ++ e g ++     p  
  gi|116753401|ref|YP_842519.1| 229 VLLYGPPGTGKTLIAKAVANESGASFFSIAGPEI 262
                                    6899******************999877666644 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0098
                          Rad17  48 LLisGPsGCgkstvvkvLskelgiklrewlnpvslkepdn.qksdfkgltekesrflsqiesfkel 112
                                    +L+ GP+G gk+ + + ++ e   +++    p +l +     +  ++ ++ k ++  + i  f el
  gi|116753401|ref|YP_842519.1| 501 ILLYGPPGTGKTLIAQAVANETNANFISVRGPQLLSKWVGeSERAIREIFRKAKQVSPTIIFFDEL 566
                                    6889*********************99999998876543337778888888888888888888887 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.041        13       3      22 ..     229     248 ..     227     253 .. 0.88
   2 ?    7.0   0.0     0.016         5       3      23 ..     501     521 ..     499     527 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.041
                                    EEEEC-TTTCHHHHHHHHHH CS
                          NACHT   3 vilqGeaGsGKTtLlqklal 22 
                                    v+l G++G GKT  ++ +a 
  gi|116753401|ref|YP_842519.1| 229 VLLYGPPGTGKTLIAKAVAN 248
                                    799************99986 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.016
                                    EEEEC-TTTCHHHHHHHHHHH CS
                          NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                    ++l G++G GKT  +q +a +
  gi|116753401|ref|YP_842519.1| 501 ILLYGPPGTGKTLIAQAVANE 521
                                    7899************99976 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.056        18       2      31 ..     229     258 ..     228     275 .. 0.80
   2 ?    7.5   0.0     0.011       3.4       2      32 ..     501     531 ..     500     550 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.056
                                    EEEE--TTSSHHHHHHHHHHHH...GGGEE CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvg 31 
                                    v++ GppG+GKt + k v+++   s ++++
  gi|116753401|ref|YP_842519.1| 229 VLLYGPPGTGKTLIAKAVANESGASFFSIA 258
                                    6788********999999987665555555 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.011
                                    EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                    +++ GppG+GKt + + v+++ + + ++v+G
  gi|116753401|ref|YP_842519.1| 501 ILLYGPPGTGKTLIAQAVANETNANFISVRG 531
                                    6788****************99888888887 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 ?    4.7   0.0     0.087        28      22      45 ..     224     247 ..     198     294 .. 0.84
   2 ?    8.6   0.0    0.0053       1.7       9      51 ..     474     525 ..     442     565 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.087
                                    .TTSEEEEEESTTSTHHHHHHHHH CS
                         ResIII  22 krdkrglikmaTGtGKTlvaakli 45 
                                    +  k +l+  + GtGKTl+a +++
  gi|116753401|ref|YP_842519.1| 224 DPPKGVLLYGPPGTGKTLIAKAVA 247
                                    56678889999********96665 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0053
                                    HHHHHHHT...............TTSEEEEEESTTSTHHHHHHHHHHHH-S. CS
                         ResIII   9 eeaienlleklks.........krdkrglikmaTGtGKTlvaaklierllkk 51 
                                    +e ie+++  lk          k  k +l+  + GtGKTl+a +++ +   +
  gi|116753401|ref|YP_842519.1| 474 QELIEAIEWPLKRperfehmgiKPPKGILLYGPPGTGKTLIAQAVANETNAN 525
                                    55666666555556666667778899999*************9888877664 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.038        12      35      58 ..     226     249 ..     201     258 .. 0.82
   2 ?   -2.5   0.0         9   2.9e+03     120     151 ..     286     321 ..     265     353 .. 0.56
   3 ?    5.9   0.0     0.023       7.4      34      60 ..     497     523 ..     472     531 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.038
                           TniB  35 mpnlllvGdsnnGKtmivekFarl 58 
                                    ++ +ll+G++ +GKt i++  a++
  gi|116753401|ref|YP_842519.1| 226 PKGVLLYGPPGTGKTLIAKAVANE 249
                                    6789*************9987765 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 9
                           TniB 120 vrvLiiDEihnll....agsarkqreflnalksLgn 151
                                    + ++ iDE++++     + + +  r+++++l  +++
  gi|116753401|ref|YP_842519.1| 286 PSIVFIDELDSIApkrsEVTGEVERRVVAQLLAMMD 321
                                    567888888887611112233334444444444444 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.023
                           TniB  34 rmpnlllvGdsnnGKtmivekFarlhp 60 
                                     ++ +ll+G++ +GKt i++  a++ +
  gi|116753401|ref|YP_842519.1| 497 PPKGILLYGPPGTGKTLIAQAVANETN 523
                                    45789*************998877665 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.033        10       1      22 [.     235     256 ..     235     283 .. 0.82
   2 ?    6.8   0.0     0.021       6.8       1      23 [.     507     529 ..     507     556 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.033
                                    TTSSHHHHHHHHHHHHTSEEEE CS
                            SKI   1 mGaGKstvGkllAkklglefiD 22 
                                    +G+GK+ ++k++A++ g +f+ 
  gi|116753401|ref|YP_842519.1| 235 PGTGKTLIAKAVANESGASFFS 256
                                    69****************9985 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.021
                                    TTSSHHHHHHHHHHHHTSEEEEH CS
                            SKI   1 mGaGKstvGkllAkklglefiDl 23 
                                    +G+GK+ +++++A++ + +fi +
  gi|116753401|ref|YP_842519.1| 507 PGTGKTLIAQAVANETNANFISV 529
                                    69******************975 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       4.1   1.3e+03      22      41 ..     228     247 ..     214     258 .. 0.83
   2 ?    9.2   0.0     0.002      0.64     170     199 ..     280     311 ..     262     315 .. 0.77
   3 ?    1.5   0.0      0.44   1.4e+02      18      48 ..     496     526 ..     488     620 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 4.1
                     KAP_NTPase  22 vvgLygkWGsGKssllnkle 41 
                                     v Lyg+ G+GK+ + + + 
  gi|116753401|ref|YP_842519.1| 228 GVLLYGPPGTGKTLIAKAVA 247
                                    589**********8777655 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.002
                     KAP_NTPase 170 a..lqkrlVvviDdLDrceteevlqlleavkl 199
                                    +  ++++ +v+iD+LD++ ++++  + e+ + 
  gi|116753401|ref|YP_842519.1| 280 EanSNTPSIVFIDELDSIAPKRSEVTGEVERR 311
                                    24579*****************9998887665 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.44
                     KAP_NTPase  18 atpivvgLygkWGsGKssllnkledelkefa 48 
                                    ++p  + Lyg+ G+GK+ + + + +e + + 
  gi|116753401|ref|YP_842519.1| 496 KPPKGILLYGPPGTGKTLIAQAVANETNANF 526
                                    566678999999****999999999888774 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.093        30      18      67 ..     230     285 ..     227     324 .. 0.74
   2 ?    8.1   0.0     0.006       1.9      18      65 ..     502     555 ..     498     613 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.093
                                    EEEESTTSSHHHHHHHHHHHSSTS.....S.EEEEEEESEEHHHHHHHHHHCHHSS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxx.....x.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab  18 lipgafgvGktvisqslskqsnsd.....d.aiiyvgiGergnevaevleefpegt 67 
                                    l+ g  g+Gkt i+++++++s ++        i     Ge ++ ++e++ee +++t
  gi|116753401|ref|YP_842519.1| 230 LLYGPPGTGKTLIAKAVANESGASffsiaGpEIMSKYYGESEQRLREIFEEANSNT 285
                                    678999**************977766665236666668888888888888877744 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.006
                                    EEEESTTSSHHHHHHHHHHHSSTS....SEEEEEE.......ESEEHHHHHHHHHHCHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxx.......xxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab  18 lipgafgvGktvisqslskqsnsd....daiiyvg.......iGergnevaevleefpe 65 
                                    l+ g  g+Gkt i+q++++++n++    +     g       +Ge ++ ++e++++ ++
  gi|116753401|ref|YP_842519.1| 502 LLYGPPGTGKTLIAQAVANETNANfisvR-----GpqllskwVGESERAIREIFRKAKQ 555
                                    678999**************988844441.....2455555589999998888887766 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.18        58       4      30 ..     228     254 ..     226     262 .. 0.85
   2 ?    1.5   0.0      0.65   2.1e+02      75      95 ..     263     283 ..     257     301 .. 0.82
   3 ?    2.9   0.0      0.23        75       4      30 ..     500     526 ..     498     533 .. 0.87
   4 ?   -1.0   0.0       3.9   1.2e+03      77      96 ..     537     556 ..     530     564 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.18
                                    EEEEESTTTSSHHHHHHHHHHHSTTTE CS
                  Guanylate_kin   4 pvvlvgpsgaGksslkkaLlselpekf 30 
                                     v l gp g+Gk  + ka+ +e   +f
  gi|116753401|ref|YP_842519.1| 228 GVLLYGPPGTGKTLIAKAVANESGASF 254
                                    6899***************99998887 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.65
                                    TTEEEEEEHHHHHHHHHTTSE CS
                  Guanylate_kin  75 sgnlygtsveaieevlekgki 95 
                                     +++yg+s +  +e++e++ +
  gi|116753401|ref|YP_842519.1| 263 MSKYYGESEQRLREIFEEANS 283
                                    679*************99876 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.23
                                    EEEEESTTTSSHHHHHHHHHHHSTTTE CS
                  Guanylate_kin   4 pvvlvgpsgaGksslkkaLlselpekf 30 
                                     + l gp g+Gk  + +a+ +e + +f
  gi|116753401|ref|YP_842519.1| 500 GILLYGPPGTGKTLIAQAVANETNANF 526
                                    6899***************99998887 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 3.9
                                    EEEEEEHHHHHHHHHTTSEE CS
                  Guanylate_kin  77 nlygtsveaieevlekgkiv 96 
                                    +  g+s  ai+e++ k+k+v
  gi|116753401|ref|YP_842519.1| 537 KWVGESERAIREIFRKAKQV 556
                                    567999**********9986 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.071        23      21      38 ..     226     242 ..     217     248 .. 0.75
   2 ?    5.2   0.0     0.053        17      21      41 ..     498     517 ..     480     520 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.071
                         AAA_29  21 lkgatlltGpsGsGKSTl 38 
                                    +kg +ll Gp G+GK+ +
  gi|116753401|ref|YP_842519.1| 226 PKG-VLLYGPPGTGKTLI 242
                                    355.9**********866 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.053
                         AAA_29  21 lkgatlltGpsGsGKSTllDA 41 
                                    +kg +ll Gp G+GK+ +  A
  gi|116753401|ref|YP_842519.1| 498 PKG-ILLYGPPGTGKTLIAQA 517
                                    356.9**********866555 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 ?    5.4   0.0     0.061        19       2      31 ..     229     258 ..     228     288 .. 0.87
   2 ?    5.3   0.0     0.068        22       2      30 ..     501     529 ..     500     531 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.061
                      Hydin_ADK   2 iivhGaPlsGKtatavtLakkYeaAlltiD 31 
                                    +++ G+P +GKt +a ++a + +a++++i 
  gi|116753401|ref|YP_842519.1| 229 VLLYGPPGTGKTLIAKAVANESGASFFSIA 258
                                    5789*********************99985 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.068
                      Hydin_ADK   2 iivhGaPlsGKtatavtLakkYeaAllti 30 
                                    i++ G+P +GKt +a ++a + +a ++++
  gi|116753401|ref|YP_842519.1| 501 ILLYGPPGTGKTLIAQAVANETNANFISV 529
                                    7889******************9999987 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.087        28       4      34 ..     229     259 ..     227     319 .. 0.88
   2 ?    5.4   0.0     0.045        14       4      34 ..     501     531 ..     499     570 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.087
                                    EEEEE-TTSSHHHHHHHHHHHSSS-EEEEEH CS
                            CPT   4 ilLnGgsssGKsslaralqevldepwlhlgv 34 
                                    +lL G + +GK+ +a+a+ + + ++++ ++ 
  gi|116753401|ref|YP_842519.1| 229 VLLYGPPGTGKTLIAKAVANESGASFFSIAG 259
                                    89******************99999998875 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.045
                                    EEEEE-TTSSHHHHHHHHHHHSSS-EEEEEH CS
                            CPT   4 ilLnGgsssGKsslaralqevldepwlhlgv 34 
                                    ilL G + +GK+ +a+a+ + +++ ++ +  
  gi|116753401|ref|YP_842519.1| 501 ILLYGPPGTGKTLIAQAVANETNANFISVRG 531
                                    89******************99999998765 PP

>> YCII  YCII-related domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0    0.0015      0.47      14      47 ..     305     339 ..     296     344 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0015
                                    H.HHHHHHHHHHHHHHHHHHHTTGEEEEEEEECSC CS
                           YCII  14 l.eeraallaahlayleelkkeGvllaaGpklvid 47 
                                      e +++++a++la+++ lk+ G+l+++G+++ id
  gi|116753401|ref|YP_842519.1| 305 TgEVERRVVAQLLAMMDGLKERGQLVVIGATNRID 339
                                    2588999*************************999 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.048        15      58      78 ..     222     242 ..     196     249 .. 0.82
   2 ?    3.7   0.0     0.072        23      59      78 ..     495     514 ..     472     524 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.048
                    AFG1_ATPase  58 svepvrglYlwGgvGrGKtyl 78 
                                       p++g+ l+G+ G GKt +
  gi|116753401|ref|YP_842519.1| 222 GIDPPKGVLLYGPPGTGKTLI 242
                                    567****************76 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.072
                    AFG1_ATPase  59 vepvrglYlwGgvGrGKtyl 78 
                                     +p++g+ l+G+ G GKt +
  gi|116753401|ref|YP_842519.1| 495 IKPPKGILLYGPPGTGKTLI 514
                                    479***************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (739 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        56  (0.00312343); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              56  [number of targets reported over threshold]
# CPU time: 0.78u 0.31s 00:00:01.09 Elapsed: 00:00:00.46
# Mc/sec: 4806.86
//
Query:       gi|116753402|ref|YP_842520.1|  [L=624]
Description: peptidyl-arginine deiminase [Methanosaeta thermophila PT]
Scores for complete 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-121  405.0   0.0   6.5e-121  403.5   0.0    1.8  3  PAD_porph     Porphyromonas-type peptidyl-arginine deiminase
      1e-58  198.7   0.0    1.4e-58  198.3   0.0    1.1  1  CN_hydrolase  Carbon-nitrogen hydrolase


Domain annotation for each model (and alignments):
>> PAD_porph  Porphyromonas-type peptidyl-arginine deiminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.33     3e+03      16     272 ..      48      85 ..      18      91 .. 0.48
   2 ?   -3.4   0.1      0.49   4.4e+03     113     147 ..     201     237 ..     187     243 .. 0.62
   3 !  403.5   0.0  7.2e-125  6.5e-121       1     319 []     292     622 ..     292     622 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.33
                                    --S.TTSGCGGGHHHHHHHHHHHHHHHHTTSEEEEEESSHHHHHHHHHCEEEEE---SSS-HHHHS-EEEE.ETEEEEEE CS
                      PAD_porph  16 wPhkeesdweekleeaqeefaelakaiaefepvtllvedeeaeearellvelveiptndlWlRDtgpifvvkkelaavdf 95 
                                    +P +++ ++++++e +  e ++  + +a++                                                  
  gi|116753402|ref|YP_842520.1|  48 FPREKNAKVQQYAETIPGESTAAFSRLAARM------------------------------------------------- 78 
                                    3333333344444444444444444444444................................................. PP

                                    E--HHHHTSSHHTTHHHHHHHHHHTT-CEEEEEEE--GGGEEEESSSEEEEEHHHHTCTTTSTTS-HHHHHHHHHHHHT- CS
                      PAD_porph  96 rFnaWGgkyeeaekdnavarklaeaglerveadlvlEGGsievdGeGtllttescllnpnRNpglskeeieaeLkellgv 175
                                                                                                                    
  gi|116753402|ref|YP_842520.1|   - --------------------------------------------------------------------------------   -
                                    ................................................................................ PP

                                    SEEEEESS-STTTTSSS-GGGTEEEEETTEEEEEE-S-TTSTTHHHHHHHHHHHHTTB-TTSSB-EEEEEEB-S--EEEE CS
                      PAD_porph 176 ekviwlkeGlagddtdgHiDtlarfvapgtvllareddeedenyealkealeiLkaatdakgrklevvelplpeevrerl 255
                                                                                                                    
  gi|116753402|ref|YP_842520.1|   - --------------------------------------------------------------------------------   -
                                    ................................................................................ PP

                                    --BTT--EEETTEEEEE CS
                      PAD_porph 256 pasYaNflivngavlvp 272
                                              n +v+vp
  gi|116753402|ref|YP_842520.1|  79 ----------NVVVIVP 85 
                                    ..........4444444 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.49
                                    HHHHHHHTT-CEEE..EEEE--GGGEEEESSSEEEEE CS
                      PAD_porph 113 varklaeaglerve..adlvlEGGsievdGeGtlltt 147
                                    +a+ +  a ++rv    ++   GGs+ +d  G ll+ 
  gi|116753402|ref|YP_842520.1| 201 IANGVHVAAVNRVGveGEIAFWGGSFVCDSFGNLLAH 237
                                    4444422333333321447888999999999999875 PP

  == domain 3  score: 403.5 bits;  conditional E-value: 7.2e-125
                                    EE--TTS-EEEEEEE--S.TTSGCGGGHHHHHHHHHHHHHHHHTTSEEEEEESSHH.HHHHHHHC........EEEEE-- CS
                      PAD_porph   1 rmpaEwepqeavwlawPhkeesdweekleeaqeefaelakaiaefepvtllvedee.aeearell........velveip 71 
                                    +mpaEwe++++vwlawPh++  d+ ++++++++++++++ka++  e+v+llv+dee  e++++ll        +++++i+
  gi|116753402|ref|YP_842520.1| 292 HMPAEWERHDGVWLAWPHDT--DTFNDIDSVERAYVSMIKALHVGETVNLLVRDEEmRERVEHLLqrdvrmssLRIHTID 369
                                    59****************66..5689**************************9888688888888*************** PP

                                    -SSS-HHHHS-EEEE....ETEEEEEEE--HHHHTSSHHTTHHHHHHHHHH.TT-CEEEEEEE--GGGEEEESSSEEEEE CS
                      PAD_porph  72 tndlWlRDtgpifvv...kkelaavdfrFnaWGgkyeeaekdnavarklae.aglerveadlvlEGGsievdGeGtlltt 147
                                    + d+W+RD+gp+fvv   +k+l +v ++FnaWGgky e+  d +++  +a+ +g+++++  +vlEGGsi+v+G Gtl+tt
  gi|116753402|ref|YP_842520.1| 370 YADVWFRDYGPTFVVnkkEKRLGMVAWNFNAWGGKYCELMGDVKIPCYIARdLGVRCFRPGIVLEGGSIDVNGSGTLMTT 449
                                    ***************86333677********************************************************* PP

                                    HHHHTCTTTSTTS-HHHHHHHHHHHHT-SEEEEESS-STTTTSSS-GGGTEEEEETTEEEEEE-S-TTSTTHHHHHHHHH CS
                      PAD_porph 148 escllnpnRNpglskeeieaeLkellgvekviwlkeGlagddtdgHiDtlarfvapgtvllareddeedenyealkeale 227
                                    e+cllnpnRNp +s+ ++e +L+e+lgv+k+iwl++G+agddtdgH+D++arfv+p +v+la e+d++den+e l+e++e
  gi|116753402|ref|YP_842520.1| 450 EQCLLNPNRNPLMSRWDMEFYLREYLGVRKIIWLRRGIAGDDTDGHVDDVARFVSPRRVVLAFEEDKDDENHEPLRENYE 529
                                    ******************************************************************************** PP

                                    HHHTTB-TTSSB-EEEEEEB-S--E..EEE--BTT--EEETTEEEEEE-SSTTCHHHHHHHHHHHSTTSEEEEEETTTGG CS
                      PAD_porph 228 iLkaatdakgrklevvelplpeevr..erlpasYaNflivngavlvptfgdeekDekAleilqelfpdrevvgvdaralv 305
                                    iLk++td++g++lev++lp+p  v   erlpasYaNf+i n+avlvp+fg+ ++D++Al+i+ +lfpdrevvg+da a+v
  gi|116753402|ref|YP_842520.1| 530 ILKHETDQDGNPLEVIRLPMPGYVGdeERLPASYANFYIGNRAVLVPVFGH-RNDARALSIIGALFPDREVVGIDALAMV 608
                                    *********************8766767***********************.89************************** PP

                                    GGS--TGGGEEEEE CS
                      PAD_porph 306 lggGsiHCitqqvP 319
                                     g G+iHC+tqq+P
  gi|116753402|ref|YP_842520.1| 609 YGLGTIHCVTQQQP 622
                                    *************9 PP

>> CN_hydrolase  Carbon-nitrogen hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.3   0.0   1.6e-62   1.4e-58       1     254 [.       3     252 ..       3     254 .. 0.97

  Alignments for each domain:
  == domain 1  score: 198.3 bits;  conditional E-value: 1.6e-62
                                    EEEEEEBB-STTHHHHHHHHHHHHHHHHHHTTESEEEEETTTTTBS...SSHHHHHHHHBHSSSHHHHHHHHHHHHHTEE CS
                   CN_hydrolase   1 rvAvvQlpqkaadleanlqklleliaeAarkgadLivlPElfitgy...keeahfleaAeaglgetlallaalarkngia 77 
                                    rv +vQ +  ++dl  nl+++l+l++ Aa +ga++++lPEl  t y   + +a++ ++Ae+++ge++a++++la++++++
  gi|116753402|ref|YP_842520.1|   3 RVGLVQTRV-TEDLNFNLARALDLVEDAANRGAEIVCLPELYRTSYfprEKNAKVQQYAETIPGESTAAFSRLAARMNVV 81 
                                    688999999.79******************************************************************** PP

                                    EEEEEEEEECCTTEEEEEEEEEEEETTSEEEEEEE-SS--EECTTSCECCGHHTSCS-SSS-EEEETTEEEEEEEGGGGG CS
                   CN_hydrolase  78 vvigliereltngklqayntavlldldgklvgkyrKlhLfpgeprpptaverelfepgdgipvfdtpvgkiGaaiCyeig 157
                                    v+++l+er  ++ ++  yn+a ++d+dg+++g yrK+h    +p  p ++e+ +f +gdg+ vf t+++++ ++iCy+++
  gi|116753402|ref|YP_842520.1|  82 VIVPLFER--YGSVY--YNSAAVIDADGSIAGVYRKSH----IPCDPMFYEKMYFFQGDGFRVFRTRHACLAVLICYDQW 153
                                    ********..*****..*********************....5899********************************** PP

                                    SHHHHHHHHHTT-SEEEE......BH.GCCCTCHHHHHHHHHHHHHHHHHHTSEEEEEEBEEEHCETTEEEE--EEEE-T CS
                   CN_hydrolase 158 fpellralalkgaeilvn......lserapvpksmgppqwellgraralengcfviaanqvggyeqlilwpvghSaiidp 231
                                    fpe++r + l+ga+i+++      +  ++++ +  ++  we+++r +a++ng+ v+a+n+vg+  ++ + ++g+S++ d 
  gi|116753402|ref|YP_842520.1| 154 FPEAARSVVLDGADIIFYptaigrV-RGVEQAEGDWQTAWETVQRGHAIANGVHVAAVNRVGV--EGEIAFWGGSFVCDS 230
                                    *******************988653.5899*********************************..*************** PP

                                    TS-EEEECCSSSTEEEEEEEEHH CS
                   CN_hydrolase 232 dGrilaglgeeeegvliaeidla 254
                                     G++la +g +ee vl a++dl+
  gi|116753402|ref|YP_842520.1| 231 FGNLLAHAGSDEE-VLLADLDLS 252
                                    ************7.*******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (624 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 4282.16
//
Query:       gi|116753403|ref|YP_842521.1|  [L=211]
Description: 30S ribosomal protein S3Ae [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-68  229.8   0.2    2.5e-68  229.6   0.2    1.0  1  Ribosomal_S3Ae  Ribosomal S3Ae family
  ------ inclusion threshold ------
      0.038   14.0   0.0      0.057   13.5   0.0    1.3  1  DUF4460         Domain of unknown function (DUF4460)


Domain annotation for each model (and alignments):
>> Ribosomal_S3Ae  Ribosomal S3Ae family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  229.6   0.2   2.8e-72   2.5e-68       3     202 .]       5     193 ..       3     193 .. 0.97

  Alignments for each domain:
  == domain 1  score: 229.6 bits;  conditional E-value: 2.8e-72
                                    ----S-TCCSEEEEEEEB-TTSSSSEEEEEEEE--BSSSESHHSHTT-EEEEESHHHHTCS.HTSSSEEEEEEEEEEESS CS
                 Ribosomal_S3Ae   3 kkkvvDkfkkKeWydvkaPslfgkreiGktlvnrtqgtkiaseklkgrvvevslaDLtnde.keqafrklklkieevqgk 81 
                                    ++++ ++ k K+Wy+v aP++fg++++G+tl+       ++++kl grv+e++l+DLtn++ k+  ++kl++ki+ v+g+
  gi|116753403|ref|YP_842521.1|   5 AQRKAERAKVKQWYKVLAPEMFGRTPVGETLA-------NDPNKLLGRVIETTLGDLTNNFsKQ--NTKLRFKIDAVAGD 75 
                                    57889999************************.......**********************555..************** PP

                                    EEEEEEEEEEE-HHHHHHH--SSB-EEEEEEEEEESSSEEEEEEEEEEE-STTB---HHHHHHHHHHHHHHHHHHHHHS- CS
                 Ribosomal_S3Ae  82 naltnFkgmeltrDklrslvrkwsslIeaivdvktkDgyllrvfvvafTkkrnsYakssqkkaIrkkmveilteeaseld 161
                                    +a+t+F g+e+t+D++rslv++++s+I+a+vdv+t+Dgyl+rv++ +fT kr   a+++q+kaIr++ ++++ ++a + d
  gi|116753403|ref|YP_842521.1|  76 TAYTKFIGHEMTTDYIRSLVKRRTSRIDAVVDVTTSDGYLVRVKPSCFTVKR---ARANQVKAIREISRQVIISRAGNID 152
                                    ****************************************************...************************* PP

                                    HHHHHHHHTTTHHHHHHHHHHTTTS-EEEEEEEEEEEEE-S CS
                 Ribosomal_S3Ae 162 lkelvkklipeslgkeiekeakkIyplrnveirKvkvlkkP 202
                                    l+ l+++++  +l+ +i+k ak +yplr+veirK+++l  P
  gi|116753403|ref|YP_842521.1| 153 LNGLIQEVVLGKLSLDIYKDAKAVYPLRRVEIRKTEILAGP 193
                                    **********77*************************9765 PP

>> DUF4460  Domain of unknown function (DUF4460)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   6.4e-06     0.057       3      71 ..       3      71 ..       1     107 [. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.4e-06
                        DUF4460  3 ralskkelrnaLrpFYlavhPDlfgqyPkekkvNeeSLklLnsyleelkkeekksikpekkkLtFyvre 71
                                   r++++k  r+  +++Y+   P++fg+ P   +  ++  klL  ++e+     +++++++++kL F++  
  gi|116753403|ref|YP_842521.1|  3 RRAQRKAERAKVKQWYKVLAPEMFGRTPVGETLANDPNKLLGRVIETTLGDLTNNFSKQNTKLRFKIDA 71
                                   566777778889*****************997777777**********999999************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); 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: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1580.58
//
Query:       gi|116753404|ref|YP_842522.1|  [L=290]
Description: ATP phosphoribosyltransferase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.5e-45  152.8   0.0      1e-44  152.3   0.0    1.2  1  HisG      ATP phosphoribosyltransferase
    6.7e-26   90.2   0.6    3.6e-25   87.9   0.1    2.2  2  HisG_C    HisG, C-terminal domain


Domain annotation for each model (and alignments):
>> HisG  ATP phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.3   0.0   1.2e-48     1e-44       1     153 [.      49     204 ..      49     212 .. 0.91

  Alignments for each domain:
  == domain 1  score: 152.3 bits;  conditional E-value: 1.2e-48
                                    -GGGHHHHHHTTSSSEEEEEHHHHHHCT...TEEEEEEESESE.....EEEEEEEETTSS--SGCGG.TT-.EEEEES-H CS
                           HisG   1 raadiptyVeegavdlGitGkDvveEskeeeeveelldLgfgk.....cklvvavpeesevkslkdlvedkgkriaTsyp 75 
                                    r+++iptyV +g +dlGi G D++ Es++  +v+++ +L++gk     +k+vvavpe+++++s ++ +   g r+aT+yp
  gi|116753404|ref|YP_842522.1|  49 RPQEIPTYVSRGYFDLGISGTDWIVESGA--DVVTVANLNYGKqgpgvVKIVVAVPESMQITSSREIP--PGSRVATEYP 124
                                    89************************864..6*************************99999888764..467******* PP

                                    HHHHHHHHHTT-EEEEEE-SS-CTHHHHTTS-SEEEEEESSSHHHHHTTEEEEEEEEEEEEEEEEEHHHHHS...HHHHH CS
                           HisG  76 nlakkyfeekglkveiiklsGsvEaapalglaDaIvDlvetGeTLrangLkaietilessavLiankkslkk...kekie 152
                                    n++++yfe++g+ ve+  ++G++Ea+++  l D++vDl+etG+TL +ngLk+i+ iles++ Lian++s+++   +e+ie
  gi|116753404|ref|YP_842522.1| 125 NITRSYFERLGIPVEVQFSYGATEAKVPE-LTDVVVDLTETGSTLIKNGLKIIDVILESTSELIANQQSWSDpskREEIE 203
                                    ***************************99.9***************************************9734333555 PP

                                    H CS
                           HisG 153 e 153
                                     
  gi|116753404|ref|YP_842522.1| 204 A 204
                                    4 PP

>> HisG_C  HisG, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.12     1e+03      30      49 ..      81     104 ..      74     109 .. 0.65
   2 !   87.9   0.1     4e-29   3.6e-25       1      73 []     215     287 ..     215     287 .. 0.98

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.12
                                    EEEE-.....SS-EEEEEEEEECC CS
                         HisG_C  30 Tvspla....degwvaVsavveek 49 
                                    Tv++l+     +g+v + + v+e+
  gi|116753404|ref|YP_842522.1|  81 TVANLNygkqGPGVVKIVVAVPES 104
                                    777775565566677777766665 PP

  == domain 2  score: 87.9 bits;  conditional E-value: 4e-29
                                    TTTEEEEEEEEEGGGHHHHHHH---SSS-EEEE-.SS-EEEEEEEEECCCHHHHHHHHHCTT-EEEEEEE-S- CS
                         HisG_C   1 ArkyvllmynvpkesleevlkilPGlrsPTvspladegwvaVsavveekevaevideLkaaGAsdIlvlpiek 73 
                                    Ar++ ll++nv ++++e+v++ilP++++PT+s+l+++g++a+++vv++k+++ +i++Lk+aGAsdIl+++i+k
  gi|116753404|ref|YP_842522.1| 215 ARGKALLKMNVSESNIEQVISILPSMKHPTISKLYNSGYYAIESVVDKKDINLLIPKLKKAGASDILEIDISK 287
                                    899*******************************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 2132.43
//
Query:       gi|116753405|ref|YP_842523.1|  [L=270]
Description: hypothetical protein Mthe_0081 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1948.41
//
Query:       gi|116753406|ref|YP_842524.1|  [L=635]
Description: beta-lactamase domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-29  102.1   2.3    2.1e-26   91.7   0.2    2.9  2  KH_7           KH domain
    9.5e-25   87.0   0.0    2.2e-24   85.9   0.0    1.7  1  Beta-Casp      Beta-Casp domain
    1.3e-15   57.1   0.0    3.2e-15   55.8   0.0    1.7  1  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
    1.2e-13   51.6   0.3    1.4e-12   48.0   0.3    2.3  1  Lactamase_B    Metallo-beta-lactamase superfamily
      1e-12   47.9   0.0    2.5e-12   46.6   0.0    1.6  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
    9.1e-10   38.4   0.0    3.4e-09   36.5   0.0    1.9  2  Lactamase_B_2  Beta-lactamase superfamily domain
    0.00033   20.4   1.7      0.002   17.9   0.5    2.8  2  KH_2           KH domain
    0.00069   19.5   0.0     0.0022   17.9   0.0    1.8  2  Lactamase_B_3  Beta-lactamase superfamily domain
      0.006   16.4   0.2      0.014   15.2   0.2    1.7  1  KH_4           KH domain
  ------ inclusion threshold ------
      0.054   13.3   0.1        0.2   11.5   0.1    2.0  1  KH_1           KH domain
      0.088   13.2   0.2        6.7    7.1   0.0    3.1  2  DinI           DinI-like family


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 !   91.7   0.2   1.3e-29   2.1e-26       1      68 []       4      71 ..       4      71 .. 0.98
   2 !    9.4   0.1   0.00064         1       5      41 ..      75     113 ..      73     128 .. 0.75

  Alignments for each domain:
  == domain 1  score: 91.7 bits;  conditional E-value: 1.3e-29
                           KH_7  1 eevleelkekieeklPkevkitdveFEGPelViYtknpklfaengdlirklAkelrkRiviRpDpsvl 68
                                   eevl+el+++i++ lP+++++t +eFEGPelViYt++p+ +a++g++ir+lAk+lrkR+v+RpD +vl
  gi|116753406|ref|YP_842524.1|  4 EEVLSELRRRIQSRLPPDINVTGLEFEGPELVIYTDDPRRLADDGEIIRSLAKDLRKRVVVRPDLKVL 71
                                   6899************************************************************9987 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00064
                           KH_7   5 eelkekieeklPkevkitdveFEG..PelViYtknpklf 41 
                                    ee  +ki+e +Pke+ +t+++F G   e++i ++ p l+
  gi|116753406|ref|YP_842524.1|  75 EEAIKKIQEVVPKEAVLTNYHFDGetGEVIIEAEKPGLV 113
                                    57789*****************99334677766666555 PP

>> Beta-Casp  Beta-Casp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.9   0.0   1.3e-27   2.2e-24       2     110 .]     422     545 ..     421     545 .. 0.89

  Alignments for each domain:
  == domain 1  score: 85.9 bits;  conditional E-value: 1.3e-27
                                    HHHHHHH..HCTT..TTS-S-EEEEE-HHHHHHHHHGGGGGG.......................E-SHH....HHHH.. CS
                      Beta-Casp   2 qellylLeelwkekkledlklpiyldsplaskatevYkeyae.......................veakslewmeskke. 57 
                                    qe++++Lee+++++   + ++p+yld+ ++++at+++++y+e                       v+  +    +sk++ 
  gi|116753406|ref|YP_842524.1| 422 QEVMVVLEEAIRKGL--IGEFPVYLDG-MIYEATAIHTSYPEylnnelrdmifhkginpflaecfVQ-VE----NSKQRd 493
                                    9**********9954..5569******.*******************************98888633.33....556444 PP

                                    .HHHS-SSEEEEES-TTSSSSHHHHHHHHHTTSTTSEEEESS---TTSHHHHH CS
                      Beta-Casp  58 elnsskgpkvilassgmlegGrsrellkklledprntvilvgyqaegTlgrkl 110
                                    e+ +  +p+vila+sgml+gG++ e+lk l +d++nt+++vgyqaegTlgr++
  gi|116753406|ref|YP_842524.1| 494 EIIN-GEPAVILATSGMLNGGPIMEYLKGLGPDEKNTLVIVGYQAEGTLGRRI 545
                                    5555.59********************************************97 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 !   55.8   0.0   1.9e-18   3.2e-15       1      61 [.     562     625 ..     562     626 .. 0.94

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 1.9e-18
                          RMMBL   1 tipvkarieeid.fSgHadknellelirklkprn..vilvHGeeeatsalarllkeeegidvfi 61 
                                    t+++++++ ++d fSgH+d+n+l+e++r++ p++  +i +HG+e  +++la+ + +++ i + +
  gi|116753406|ref|YP_842524.1| 562 TVKMNMEVVTVDgFSGHSDRNQLMEYVRRVYPKPsrIITNHGDESNCLDLASSIYKKYRIPTSA 625
                                    689***************************************************9999887665 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.0   0.3   8.6e-16   1.4e-12       4     163 ..     192     379 ..     190     414 .. 0.80

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 8.6e-16
                                    CSSEEEEEEETTCEEEES--SCHHHHHHHH..HHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHC CS
                    Lactamase_B   4 dpvnsyliegdggviLiDtGtsteaaraal..elaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapa 81 
                                    ++ +++l+ ++++ i++D+G+    ++ a   ++  + +++ ++dav+lTH+HlDH G ++ l +     ++++   ++ 
  gi|116753406|ref|YP_842524.1| 192 VGRSCMLLSTPESKIIVDCGINVGSDDSATpyLYVPEVYPLSQIDAVVLTHAHLDHSGLVPMLYKYGYEGPIYCTPPTRD 271
                                    5679********************99999999******************************************999999 PP

                                    CHCHHHHHHHHHCCHH..............TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEE CS
                    Lactamase_B  82 lfmeeaddaasrkgll..............lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlf 147
                                    l      d+ +  g +              l+     + + ++++ +++ + ++  +  ++ g+   h+++++g  +v+f
  gi|116753406|ref|YP_842524.1| 272 LYVLLQLDYIEVAGREgkrlpydssmireaLKHTITLNYGDVTDIAPDTKLTMHNAG--HILGSAIAHFHIGDGLYNVAF 349
                                    9999998888888888999****9876666555555555555555555555555543..566777889************ PP

                                    ECTTTSSHHCCCCCC............... CS
                    Lactamase_B 148 tGDallagetgridl..............t 163
                                    tGD+ ++  ++ ++               t
  gi|116753406|ref|YP_842524.1| 350 TGDFKYEKTRLFDPAvnsfprletlvieaT 379
                                    ******777666666666666665555554 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 !   46.6   0.0   1.5e-15   2.5e-12       1     169 [.     198     360 ..     198     375 .. 0.81

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 1.5e-15
                  Lactamase_B_6   1 lLeldnvkiLlDvGwdeskvslesalkelekv..iptvdliLLshatlehlGayallyakfksklllnipvyatlpvvkL 78 
                                    lL+  + ki++D+G +  ++++ +   ++ +v  ++++d+++L+ha l+h G  ++ly+     ++ + p+y+t p+  L
  gi|116753406|ref|YP_842524.1| 198 LLSTPESKIIVDCGINVGSDDSATPYLYVPEVypLSQIDAVVLTHAHLDHSGLVPMLYK-----YGYEGPIYCTPPTRDL 272
                                    5677789*********77777767777777764568****************6666664.....67899*********** PP

                  Lactamase_B_6  79 GrvslldlyaskgllgpedseeleledideafdkiktlkYsQklelkskldgltitaynaGhtlGGti..Wkiskeseki 156
                                      ++ ld+++ +g +g+      + + i+ea ++ +tl Y   +++     +  +t +naGh lG +i  ++i +++ ++
  gi|116753406|ref|YP_842524.1| 273 YVLLQLDYIEVAGREGKRL--PYDSSMIREALKHTITLNYGDVTDIAP---DTKLTMHNAGHILGSAIahFHIGDGLYNV 347
                                    ********99998887553..3466779***************99995...4557789********98667788888888 PP

                  Lactamase_B_6 157 vYavdwnhakesh 169
                                     +  d+  +k ++
  gi|116753406|ref|YP_842524.1| 348 AFTGDFKYEKTRL 360
                                    8777777666665 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 ?   -2.3   0.0       1.6   2.7e+03     178     199 ..      71      92 ..      62      94 .. 0.87
   2 !   36.5   0.0   2.1e-12   3.4e-09       3     165 ..     206     379 ..     204     396 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.6
                                    ---STSHHHHCTTSSSSEEEEE CS
                  Lactamase_B_2 178 Hltpeeaveaaadlgakrlvli 199
                                     ++peea++ ++++ +k +vl+
  gi|116753406|ref|YP_842524.1|  71 LMDPEEAIKKIQEVVPKEAVLT 92 
                                    6999**********99999987 PP

  == domain 2  score: 36.5 bits;  conditional E-value: 2.1e-12
                                    EEES--TTHHHH..HTCGG.S--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHH........... CS
                  Lactamase_B_2   3 iLiDagpdlrqq..alral.qPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvla........... 68 
                                    i++D+g ++     a+++l  P   +  l++idaV+lthaH DH   +++l + ++ + p+y+++ +++           
  gi|116753406|ref|YP_842524.1| 206 IIVDCGINVGSDdsATPYLyVPE--VYPLSQIDAVVLTHAHLDHSGLVPMLYK-YGYEGPIYCTPPTRDlyvllqldyie 282
                                    99******877788999996665..566668**************55666666.45558*****9999987776666554 PP

                                    ...HCCTTCGHHHCHTT.............TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEEC CS
                  Lactamase_B_2  69 ...vleanfvylaleee.............pavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlrieg 132
                                                    e             +  ++ +l+ g+ ++++ ++ ++t++ a h  g         ++ + i++
  gi|116753406|ref|YP_842524.1| 283 vagR------------EgkrlpydssmireALKHTITLNYGDVTDIA-PDTKLTMHNAGHILGS-------AIAHFHIGD 342
                                    4431............1333444444555556677888899999998.5789999999999999.......89999999* PP

                                    TTEEEEEESS-S---....HHHHHHHCT-SEEEEE-S CS
                  Lactamase_B_2 133 ggkrvyyigDtgyip....eeigerlggadlllldit 165
                                    g  +v+++gD +y +    + + + +  ++ l++++t
  gi|116753406|ref|YP_842524.1| 343 GLYNVAFTGDFKYEKtrlfDPAVNSFPRLETLVIEAT 379
                                    **********998663333223356666666666665 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.56   9.2e+02      44      59 ..      48      63 ..      46      89 .. 0.73
   2 !   17.9   0.5   1.2e-06     0.002      28      62 ..     102     136 ..      76     150 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.56
                                   GHHHHHHHHHHHHHHH CS
                           KH_2 44 Gsnikkigkelrkdie 59
                                   G+ i+++ k+lrk++ 
  gi|116753406|ref|YP_842524.1| 48 GEIIRSLAKDLRKRVV 63
                                   8889999999999994 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 1.2e-06
                                    EEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHH CS
                           KH_2  28 iiviresqpgivIGkgGsnikkigkelrkdiekle 62 
                                    +++i +++pg+vIG+ G+++++i+k ++   ++++
  gi|116753406|ref|YP_842524.1| 102 EVIIEAEKPGLVIGRHGATLREITKLIGWTPKVVR 136
                                    6899*********************9986555555 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 ?   -3.7   0.0       5.9   9.6e+03     141     157 ..      71      87 ..      64      97 .. 0.66
   2 !   17.9   0.0   1.3e-06    0.0022       6      50 ..     193     248 ..     191     292 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 5.9
                  Lactamase_B_3 141 tlgqeealelakrLkpk 157
                                    ++++eea++ ++++ pk
  gi|116753406|ref|YP_842524.1|  71 LMDPEEAIKKIQEVVPK 87 
                                    46666666666666665 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 1.3e-06
                  Lactamase_B_3   6 ghnsflletagarilvDPfkanlgyeppa............eeaDlvlisqaledHa 50 
                                    g +++ll+t++ +i+vD +  n+g + +a             ++D+v++++a+ dH 
  gi|116753406|ref|YP_842524.1| 193 GRSCMLLSTPESKIIVDCGI-NVGSDDSAtpylyvpevyplSQIDAVVLTHAHLDHS 248
                                    89***************883.44444444445666677777***************7 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.2   8.8e-06     0.014      27      52 ..      97     122 ..      75     129 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8.8e-06
                           KH_4  27 eeveielnvegedlGrvIGkrGrtld 52 
                                    ++++ e+ +e e+ G+vIG++G tl+
  gi|116753406|ref|YP_842524.1|  97 DGETGEVIIEAEKPGLVIGRHGATLR 122
                                    45666888999*************97 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00012       0.2       3      27 ..     102     126 ..     100     131 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                                    EEEEGGGHHHHHHTGGGHHHHHHHH CS
                           KH_1   3 rilvPsslvgriIGkgGsnIkeIre 27 
                                    ++++ +++ g++IG+ G++++eI +
  gi|116753406|ref|YP_842524.1| 102 EVIIEAEKPGLVIGRHGATLREITK 126
                                    577888888**************86 PP

>> DinI  DinI-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.14   2.2e+02       5      21 ..       3      19 ..       2      25 .. 0.78
   2 ?    7.1   0.0    0.0041       6.7      12      55 ..     541     591 ..     535     594 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.14
                                   HHHHHHHHHHHHHHH-S CS
                           DinI  5 iealeaELskRiqevfP 21
                                   +e   +EL +Riq++ P
  gi|116753406|ref|YP_842524.1|  3 VEEVLSELRRRIQSRLP 19
                                   577789*******9876 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0041
                                    HHHHHHHH-SS-EEEE......EEESS-EEEEES.--HHHHHHHHHHHHHH CS
                           DinI  12 LskRiqevfPdaevrv......rkasanglsveG.askedkeriseiLQet 55 
                                    L +Riq+ + ++ ++v      +k++++ ++v+G    +d+++++e +  +
  gi|116753406|ref|YP_842524.1| 541 LGRRIQKGWKEIPLTVegktqtVKMNMEVVTVDGfSGHSDRNQLMEYVRRV 591
                                    89999999999666552222226888899****************988665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (635 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); 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: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.44
# Mc/sec: 4369.37
//
Query:       gi|116753407|ref|YP_842525.1|  [L=207]
Description: proteasome endopeptidase complex [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.2e-52  177.3   0.1    2.5e-52  177.1   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 !  177.1   0.1   1.4e-56   2.5e-52       3     188 ..       6     185 ..       4     187 .. 0.96

  Alignments for each domain:
  == domain 1  score: 177.1 bits;  conditional E-value: 1.4e-56
                                    HS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTCHH CS
                     Proteasome   3 kGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrpipve 82 
                                    kGtt+vGi +++gvvla+++rat+gs + +++t++Ki++idd +g+++aG ++Da++lvr+++aea+lyr++ g+p++++
  gi|116753407|ref|YP_842525.1|   6 KGTTTVGIVCDGGVVLASESRATMGSFI-ASRTAKKIYQIDDLVGLTTAGVVGDAQALVRMIQAEARLYRMQRGEPLTIK 84 
                                    8***************************.66669********************************************** PP

                                    HHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHSTTBSHHH CS
                     Proteasome  83 rlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekeykedltlee 162
                                        +++++l++ +  ++  pf+v+l+++gvd+ g p+++++d  G  iee d+v++Gsgs  a+++le++yk+ l+ ++
  gi|116753407|ref|YP_842525.1|  85 ----AITSLLSNILSARRYFPFLVQLVVGGVDKMG-PKIFSLDALGGQIEEHDIVSTGSGSPIAYGVLESLYKPGLSIQD 159
                                    ....888888888888899*************888.***************9**************************** PP

                                    HHHHHHHHHHHHHHHBTTSCSSEEEE CS
                     Proteasome 163 avelavkalkealerdklsgknieva 188
                                    +  l v+a++ a++rd++sg++i ++
  gi|116753407|ref|YP_842525.1| 160 GSVLCVRAVHTAMKRDSASGNGIALV 185
                                    **********************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1552.95
//
Query:       gi|116753408|ref|YP_842526.1|  [L=402]
Description: ammonium transporter [Methanosaeta thermophila PT]
Scores for complete 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-128  426.6  42.7   8.7e-128  426.4  42.7    1.0  1  Ammonium_transp  Ammonium Transporter Family


Domain annotation for each model (and alignments):
>> Ammonium_transp  Ammonium Transporter Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  426.4  42.7  4.8e-132  8.7e-128       1     399 []       9     401 ..       9     401 .. 0.95

  Alignments for each domain:
  == domain 1  score: 426.4 bits;  conditional E-value: 4.8e-132
                                    HHHHHHHHHHHHHHHHHHHHHHHHSSGGGHHHHHHHHHHHHHHHHHHHHHTHHHHHHSSCBSSSSSCE-...TTTTSCCG CS
                Ammonium_transp   1 aflllsaalvifmqagfalleaglvrsknvlnilvknlldlavvvllyvlfGyslafgkskgvsgfign...lglsaagv 77 
                                    a++++saalv++m++g++l+++glvrsk+v++++  ++l++ + ++++vl+Gys++fg++  + g+ig    ++++++g+
  gi|116753408|ref|YP_842526.1|   9 AWIMISAALVMLMTPGVGLFYGGLVRSKSVISMISLSILAISLASIQWVLIGYSISFGHD--MMGLIGGldfIFMRNVGM 86 
                                    7**********************************************************9..888888778855555555 PP

                                    CCTTCCHHH....HHHHHHHHHHHHHHHHHHHCTTTB-HHHHHHHHHHHHHHTHHHHHHHHHS.SSHHHHTT--.-SSST CS
                Ammonium_transp  78 qdetlldgl....fflfqlafaataitivsgavaerikfsayllfsallgtlvyppvahwvwgeggwlaklgvliDfAgs 153
                                    ++++l + +    +++fql+faa++++i ++avaerik+s+++++s+l++tlvy p+ahwvw+ ggwla+lg+l DfAg+
  gi|116753408|ref|YP_842526.1|  87 NEAPLAESVphlaYMMFQLVFAAVTLAILTSAVAERIKLSSFIVLSILWTTLVYDPLAHWVWA-GGWLASLGAL-DFAGG 164
                                    5554444434444**************************************************.**********.***** PP

                                    TTTHHHHHHHHHHHHHHHS-STTTTGTTTSS--GSBHHHHHHHHHHHHHHHHHHHHGGGSSSSHHHHH.HHHHHHHHHHH CS
                Ammonium_transp 154 tvVHlvggvagLaaalvlgkregrfegkeeaikghnlpfavlGtllLwfgWfgFNaGsaltankrararaavtTllAaaa 233
                                    tvVH+ +g+++La+alv+gkr g     ++ +++hn+p+a++G++lLwfgWfgFNaGsalta + a++ a+v+T+++aaa
  gi|116753408|ref|YP_842526.1| 165 TVVHISSGFSALAIALVIGKRVGFD---SYVLEPHNIPMAMIGAALLWFGWFGFNAGSALTAGGLAAS-AFVVTNTSAAA 240
                                    **********************965...9***************************************.*********** PP

                                    HHHHHHHHHHHHCSS-BHHHHHHHHHHHHHHHTTTTTTS-HHHHHHHHHHHHHHHHHHHHHHHHHHTC-CTTHHHHHHHH CS
                Ammonium_transp 234 galtallisrlkegkinvlglanGilAGlVAiTaacavvepwgAliiGlvAgvlsvlgvkklkeklkidDsldvvavHgv 313
                                    gal++ll s+l+ gk++ lg+++G++AGlVAiT+a+++v+ ++Al+iG+ Ag++++ ++ +++  +++d+sld++avHgv
  gi|116753408|ref|YP_842526.1| 241 GALAWLLGSWLR-GKPSALGMVSGAIAGLVAITPAAGYVDAMSALLIGAFAGLICYSAL-LFRVSIGLDESLDAWAVHGV 318
                                    ************.**********************************************.6******************* PP

                                    HHHHHHHHHHHHTSHHHCSSHSSTTGGGT-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSB--HHHHHHSHHHHH CS
                Ammonium_transp 314 gGiwGllavgifaaekvvaskisggllsgegkqlvvqligilvilayafvvtlilllllklllgLrvseeeeevglDvae 393
                                    gG+wG+la+gifa++ v+   +++gl++g++ q+++q++++l+ +ayafv++++l+ l+++++gLrv+e+ee+vglD+a 
  gi|116753408|ref|YP_842526.1| 319 GGLWGALATGIFANPAVN---TYTGLIYGNTGQFTAQVVAVLASVAYAFVISYVLARLVDATIGLRVTEDEEYVGLDIAV 395
                                    ***************865...*********************************************************** PP

                                    HSSSSB CS
                Ammonium_transp 394 hgetay 399
                                    hge+ay
  gi|116753408|ref|YP_842526.1| 396 HGEKAY 401
                                    ****99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       878  (0.0489709); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2952.63
//
Query:       gi|116753409|ref|YP_842527.1|  [L=112]
Description: nitrogen regulatory protein P-II [Methanosaeta thermophila PT]
Scores for complete 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   1.0    1.4e-32  112.3   1.0    1.0  1  P-II      Nitrogen regulatory protein P-II


Domain annotation for each model (and alignments):
>> P-II  Nitrogen regulatory protein P-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.3   1.0   7.7e-37   1.4e-32       1     102 []       4     105 ..       4     105 .. 0.99

  Alignments for each domain:
  == domain 1  score: 112.3 bits;  conditional E-value: 7.7e-37
                                    EEEEEEGGGHHHHHHHHHHTTGGCEEEEEEEEEESTCCEEEECTTEEEEEEEEEEEEEEEEEEGGGHHHHHHHHHHHH-S CS
                           P-II   1 ieaiirpekleevkeaLekagvkgltvtevkGrGkqkghtelyrgaeyevellpkvkleivvsdedvekvveaiikaakt 80 
                                    ieaiir e+l +vk aLe+ g+ ++tvt+v+GrG+qkg    yrg + ev++lpk+k+e+ v+dedve+v+++++++a+t
  gi|116753409|ref|YP_842527.1|   4 IEAIIREERLGHVKRALEEKGFVAMTVTRVLGRGEQKGIRLQYRGGSIEVDMLPKLKIEMFVRDEDVETVMRTVCDSART 83 
                                    89****************************************************************************** PP

                                    SSTTSEEEEEEEESEEEETTTT CS
                           P-II  81 geiGDGkiFvlpveevirirtg 102
                                    g++GDG+iFv+pv+   ++rtg
  gi|116753409|ref|YP_842527.1|  84 GRFGDGRIFVMPVTISGKVRTG 105
                                    *********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 835.08
//
Query:       gi|116753410|ref|YP_842528.1|  [L=636]
Description: acetyl-CoA hydrolase/transferase [Methanosaeta thermophila PT]
Scores for 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-61  204.4   0.0    1.3e-60  203.8   0.0    1.3  1  AcetylCoA_hyd_C  Acetyl-CoA hydrolase/transferase C-terminal 
    5.5e-41  140.7   0.0      3e-40  138.3   0.0    2.0  2  AcetylCoA_hydro  Acetyl-CoA hydrolase/transferase N-terminal 
    2.1e-11   44.1   0.0    4.3e-11   43.1   0.0    1.5  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    3.2e-09   37.6   0.0      6e-09   36.7   0.0    1.5  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
    1.1e-07   32.2   0.0    2.7e-07   30.9   0.0    1.7  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    3.9e-07   30.0   0.1    9.2e-07   28.8   0.1    1.5  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    4.7e-06   26.8   0.0    9.7e-06   25.8   0.0    1.5  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    2.4e-05   24.2   0.0    5.6e-05   23.0   0.0    1.5  1  FR47             FR47-like protein
      8e-05   22.1   0.0       0.16   11.4   0.0    2.6  2  CoA_trans        Coenzyme A transferase
    0.00039   20.4   0.1     0.0089   16.0   0.0    3.1  4  DeoRC            DeoR C terminal sensor domain
  ------ inclusion threshold ------
      0.029   14.5   0.0       0.24   11.6   0.0    2.4  2  Acetyltransf_CG  GCN5-related N-acetyl-transferase
      0.039   13.7   0.0      0.071   12.8   0.0    1.4  1  Acetyltransf_8   Acetyltransferase (GNAT) domain
       0.04   12.3   0.2       0.23    9.7   0.0    1.9  2  Mal_decarbox_Al  Malonate decarboxylase, alpha subunit, trans


Domain annotation for each model (and alignments):
>> AcetylCoA_hyd_C  Acetyl-CoA hydrolase/transferase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.8   0.0   9.4e-64   1.3e-60       2     154 .]     292     444 ..     291     444 .. 0.99

  Alignments for each domain:
  == domain 1  score: 203.8 bits;  conditional E-value: 9.4e-64
                                    -HHHHHHHTT-TTEEE-BHHHHT-HHHHTTSTTEEEEEE-SEEETTS-EESSECTTCCTCGGTTHHHHHHHHHHSTT-EE CS
                AcetylCoA_hyd_C   2 skklydfldenpkielrpveyvndpeviaqnkkvvsinsalevdltGqvnseslggrvvsGvGgqldFvrgaalskggks 81 
                                    s++ y++ld np++e+++++y+n+p +ia+++++v+insale+dltGq+++eslgg+ +sG+Ggq dF+rgaa+++ggk+
  gi|116753410|ref|YP_842528.1| 292 SRETYRYLDGNPDVEFKQIDYTNNPLIIAKQRNMVAINSALEIDLTGQATAESLGGTLYSGIGGQADFMRGAAMAPGGKT 371
                                    5789**************************************************************************** PP

                                    EEE--SEETTTTEESEESS-STTSSECE-TTT-SEEEETTEEEE-TT--HHHHHHHHHTTS-HHHHHHHHHHH CS
                AcetylCoA_hyd_C  82 iialpStakkgeiSrIvpslkegahvtttrhdvdyvvTEyGiadLrgkslreraealikiAhpdfreeLleea 154
                                    ++alpSta++g++SrIvp l++ a+vt tr dv+yvvTEyGia+L+g++lrera+ali++Ahp+fr +L+eea
  gi|116753410|ref|YP_842528.1| 372 VLALPSTARDGSVSRIVPCLRSCAGVTLTRGDVRYVVTEYGIAYLHGRNLRERAMALIAVAHPKFRAWLIEEA 444
                                    **********************************************************************997 PP

>> AcetylCoA_hydro  Acetyl-CoA hydrolase/transferase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.3   0.0   2.2e-43     3e-40       6     193 ..      16     202 ..      13     207 .. 0.97
   2 ?   -0.6   0.0      0.83   1.1e+03     110     155 ..     512     563 ..     498     571 .. 0.79

  Alignments for each domain:
  == domain 1  score: 138.3 bits;  conditional E-value: 2.2e-43
                AcetylCoA_hydro   6 ekklke.peeaaelvkngshielsgftavgtakaipkylakrkvekenvkkkllidlavgavlsagPeeevleekdavly 84 
                                    e +++  pe++a+   ++  i+ ++++++gt +a+p+ l++  v+++   +  ++d++v  v ++g  +++++ek+ +++
  gi|116753410|ref|YP_842528.1|  16 EEMRSRwPEKFAPERTIFRNIHPGDRIFIGTGCAEPQHLVRSLVDYVSRYPTAFFDAEVIHVSTLG-VAPYTDEKFKLNF 94 
                                    5677778***********************************************************.************* PP

                AcetylCoA_hydro  85 rpapkqvgellrkainqglvsfvdkhlsevpqklekgfvpiDvalieataldedGylnlGvgvrakKviiEvaelvvivv 164
                                    r  ++++ge +r  in   +++++++ls +p+++  g + iD+ali+at+++e G + lG++v++ K++iE a  vv++v
  gi|116753410|ref|YP_842528.1|  95 RLDSFFIGESTRDPINRADADYTPIFLSALPELFRNGSINIDLALIQATPPNESGDMSLGISVDIIKAVIENASRVVVQV 174
                                    ******************************************************************************** PP

                AcetylCoA_hydro 165 kknpPrvngydelialdkvdyivvdpekv 193
                                    + ++P+v g d li +d vdy+v ++e  
  gi|116753410|ref|YP_842528.1| 175 NPQMPYVYG-DTLINIDSVDYVVYHEEPL 202
                                    *********.***************9865 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.83
                AcetylCoA_hydro 110 hlsevpqklekgfvpiDva...lieataldedGylnlGvg...vrakKviiE 155
                                    + +e+p +l ++ + iD++   +i at + ++  +++G+g   v+ +K  ++
  gi|116753410|ref|YP_842528.1| 512 MRREIPRDLLQKLTMIDYTnrmVILATLPGKERDVVIGIGqyeVNKDKYTAD 563
                                    5689999999999999998777899999999999999999877777776555 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   0.0   3.1e-14   4.3e-11      37     117 .]     536     617 ..     493     617 .. 0.81

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 3.1e-14
                                    E....EEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHHHHHHH CS
                 Acetyltransf_1  37 v....aeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveedndaairlY 112
                                    +    ++e + +iG  ++  + d   ++++ + laV+ +y+++G+Gs+Ll +l + ar++g+    ++v + n++  rl+
  gi|116753410|ref|YP_842528.1| 536 LatlpGKERDVVIGIGQYEVNKD---KYTADIALAVRDDYQNQGVGSELLSYLTQLARKNGLLGFTAEVLAENNRVFRLF 612
                                    23445666788999999999999...899999******************************66688************* PP

                                    HHTTE CS
                 Acetyltransf_1 113 eklGF 117
                                    ek+GF
  gi|116753410|ref|YP_842528.1| 613 EKMGF 617
                                    ****9 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.0   4.3e-12     6e-09       2     138 .]     480     618 ..     479     618 .. 0.72

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 4.3e-12
                 Acetyltransf_3   2 LlLrplteeD...lealfelrsdpe.vmrylpe....pltleeaeewlerawaeeseeegygwaivl..kdtgv.iGsvg 70 
                                    +l+rp++  D   l+++f  +sd+   +r+++     p++l +  ++++  +++    + + +a  l  k+ +v iG+  
  gi|116753410|ref|YP_842528.1| 480 ILMRPVRINDeplLKDFFYSLSDESrYQRFISMrreiPRDLLQKLTMID--YTN----RMVILAT-LpgKERDVvIGIGQ 552
                                    6889999999444444433367777788884433244555555555555..543....3433333.35666666699887 PP

                 Acetyltransf_3  71 lrdleeedeeaelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGfe 138
                                    +    ++  +a++ + ++++++++G+++e ++ l+++a ++ gl  + a++ +eN + +r++ek+Gfe
  gi|116753410|ref|YP_842528.1| 553 YEVN-KDKYTADIALAVRDDYQNQGVGSELLSYLTQLA-RKNGLLGFTAEVLAENNRVFRLFEKMGFE 618
                                    7744.44455****************************.6677999*********************7 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0     2e-10   2.7e-07      13      75 ..     546     618 ..     531     619 .. 0.66

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 2e-10
                                    EEEEEEEEEEES...TCTEE..EEE-GGGTTSSHHHHHHHH.....TTSEEEEE.EEEE..THHHHHHHHHHTTEE CS
                 Acetyltransf_7  13 kivGfialslld...aeitr..laVdpeyrgkGiGraLlea.....aekgiile.qlel..naekaikfYeklGFe 75 
                                     ++G   +++++   +      laV+ +y+++G+G++Ll +     +++g+    ++e+  ++++  +++ek+GFe
  gi|116753410|ref|YP_842528.1| 546 VVIGIGQYEVNKdkyTA--DiaLAVRDDYQNQGVGSELLSYltqlaRKNGLL-GfTAEVlaENNRVFRLFEKMGFE 618
                                    44665555555553444..255******************866554225532.333333333336777*******8 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.1   6.7e-10   9.2e-07      56     111 ..     565     622 ..     531     634 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 6.7e-10
                Acetyltransf_10  56 llfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavpfYeklGFkavge 111
                                     l+V+++y+ qG+g++Ll ++ + a+k+g+   + +v a +    +++ek+GF+a + 
  gi|116753410|ref|YP_842528.1| 565 ALAVRDDYQNQGVGSELLSYLTQLARKNGLLGfTAEVLAENnRVFRLFEKMGFEAEKV 622
                                    479**********************9999999*999999998999*********9754 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0     7e-09   9.7e-06      56     140 ..     543     623 ..     505     631 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 7e-09
                 Acetyltransf_4  56 esdrivGyaylgqfkkrakdwkaelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFe 135
                                    e d ++G+ +++ ++k   +  a +   + + d +++g+g+el+ +l q +++++++ ++ae+ ++n     +++++GFe
  gi|116753410|ref|YP_842528.1| 543 ERDVVIGIGQYE-VNK--DKYTADIALAV-RDDYQNQGVGSELLSYLTQLARKNGLLGFTAEVLAENNRVFRLFEKMGFE 618
                                    578889999998.455..35556666667.579**********************************************9 PP

                 Acetyltransf_4 136 lvgif 140
                                     ++  
  gi|116753410|ref|YP_842528.1| 619 AEKVN 623
                                    87765 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0     4e-08   5.6e-05      25      80 ..     564     620 ..     554     624 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 4e-08
                                    EEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S.-EEEEEETT-HHHHHHHHHHT-EEE CS
                           FR47  25 galqvlpehrrrGlgsrlvkalakeiaergk.tvllvvvasNtpsirlyeklGfeki 80 
                                     al v+++ +++G gs l + l++  +++g    ++ v a+N++  rl+ek+Gfe+ 
  gi|116753410|ref|YP_842528.1| 564 IALAVRDDYQNQGVGSELLSYLTQLARKNGLlGFTAEVLAENNRVFRLFEKMGFEAE 620
                                    689*************************9972578999****************986 PP

>> CoA_trans  Coenzyme A transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0013       1.7       7      41 ..      31      63 ..      27      89 .. 0.80
   2 !   11.4   0.0   0.00011      0.16       3      69 ..     216     276 ..     214     310 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0013
                                   HHCTT--TTEEEEE-SBTTBTHHHHHHHHHHHHTT CS
                      CoA_trans  7 avakeikdGmtvavGGFgligiPealiaalarsgv 41
                                   ++ ++i+ G+ +++G  +++ +P++l+++l++   
  gi|116753410|ref|YP_842528.1| 31 TIFRNIHPGDRIFIG--TGCAEPQHLVRSLVDYVS 63
                                   66789**********..9999*********98654 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00011
                                    HHHHHHCTT--TTEEEEE-SBTTBT.HHHHHHHHHHHHTTTSEEEEESTTTEECCHHHHHTTTEEEEE CS
                      CoA_trans   3 taaeavakeikdGmtvavGGFglig.iPealiaalarsgvkdltviiseagvlglgplllngsvkkvi 69 
                                    ++ + va+ ++dG+t+ vG     g iP+a   +l ++   ++  ++ e  + g+  l+++g v++ +
  gi|116753410|ref|YP_842528.1| 216 QIGKYVARIVEDGATIQVG----YGsIPNAVLSNLHDK---KHLGVHTELLTDGIVELMKSGAVDNSM 276
                                    5778899************....888**7777777775...899999999999999999999998876 PP

>> DeoRC  DeoR C terminal sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.5   2.1e+03      15      29 ..      34      48 ..      30      60 .. 0.77
   2 ?   -1.9   0.0         2   2.7e+03     117     134 ..     157     174 ..     132     177 .. 0.80
   3 !   16.0   0.0   6.5e-06    0.0089       7      49 ..     215     257 ..     211     269 .. 0.93
   4 ?   -1.3   0.0       1.3   1.8e+03      40      79 ..     522     560 ..     512     573 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.5
                          DeoRC 15 eliedgdtifldaGt 29
                                   + i++gd if+++G 
  gi|116753410|ref|YP_842528.1| 34 RNIHPGDRIFIGTGC 48
                                   5699*******9996 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2
                          DeoRC 117 aevkralieaarrvilla 134
                                    + + +a+ie+a+rv++ +
  gi|116753410|ref|YP_842528.1| 157 VDIIKAVIENASRVVVQV 174
                                    6778999******99965 PP

  == domain 3  score: 16.0 bits;  conditional E-value: 6.5e-06
                          DeoRC   7 rrIAkaAaeliedgdtifldaGtTtlelaraLaekknltvvTn 49 
                                    ++I+k++a+++edg+ti ++ G+   ++ ++L++kk+l v T 
  gi|116753410|ref|YP_842528.1| 215 QQIGKYVARIVEDGATIQVGYGSIPNAVLSNLHDKKHLGVHTE 257
                                    79*************************************9997 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 1.3
                          DeoRC  40 ekknltvvTnslnvaeeLsekedikvillGGevrkksesl 79 
                                    +k ++  +Tn + + ++L  ke+  vi +G +++ +++ +
  gi|116753410|ref|YP_842528.1| 522 QKLTMIDYTNRMVILATLPGKERDVVIGIG-QYEVNKDKY 560
                                    444555579*********999777776666.455555555 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 ?   -1.0   0.0       1.4   1.9e+03      40      67 ..     154     181 ..     153     185 .. 0.89
   2 ?   11.6   0.0   0.00017      0.24      11      58 ..     547     594 ..     538     595 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.4
                Acetyltransf_CG  40 GiAkkLvkaalddareeglkvvptCsyv 67 
                                    Gi   ++ka+++ a +   +v p+ +yv
  gi|116753410|ref|YP_842528.1| 154 GISVDIIKAVIENASRVVVQVNPQMPYV 181
                                    7777889*****************9998 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00017
                Acetyltransf_CG  11 evafleYevrkegvldfthTeVpeelrGkGiAkkLvkaalddareegl 58 
                                     +++ +Yev+k++  +     V + ++ +G++++L  +  + ar++gl
  gi|116753410|ref|YP_842528.1| 547 VIGIGQYEVNKDKYTADIALAVRDDYQNQGVGSELLSYLTQLARKNGL 594
                                    577889996666666666889*************************97 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   5.1e-05     0.071      71     141 ..     551     621 ..     518     625 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.1e-05
                                    GCS---TT-EEEEEEES.SHHHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-EEEE CS
                 Acetyltransf_8  71 eyydaepgdrGiHllig.eaeargkglttallralvhylfadprtrrvvvEPdvrNerairllekaGfekek 141
                                    + y++++     +++++   ++ ++g++++ll+ l++++ ++ +     +E  ++N r+ rl+ek+Gfe ek
  gi|116753410|ref|YP_842528.1| 551 GQYEVNKDKYTADIALAvRDDYQNQGVGSELLSYLTQLARKN-GLLGFTAEVLAENNRVFRLFEKMGFEAEK 621
                                    568999999999999995566799999999999988776655.999***********************987 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 ?   -0.1   0.1      0.16   2.2e+02     140     208 ..     137     202 ..     126     221 .. 0.73
   2 ?    9.7   0.0   0.00017      0.23     446     483 ..     397     433 ..     391     479 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.16
                Mal_decarbox_Al 140 valvaaekadreGnlytGantedtPaiveatafkdgiviaqvneivdkl.prvdiPadwvdfvveadkpf 208
                                    +al+ a+  +++G++  G + +   a++e +    + v++qvn  +  +     i  d vd+vv  ++p 
  gi|116753410|ref|YP_842528.1| 137 LALIQATPPNESGDMSLGISVDIIKAVIENA----SRVVVQVNPQMPYVyGDTLINIDSVDYVVYHEEPL 202
                                    6788888888888888888888777777765....46888888776654134557778888888888775 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00017
                Mal_decarbox_Al 446 vmiygddvthvvteeGiayllkaesleereqairavaG 483
                                    v +   dv +vvte Giayl+  ++l er  a+ ava 
  gi|116753410|ref|YP_842528.1| 397 VTLTRGDVRYVVTEYGIAYLH-GRNLRERAMALIAVAH 433
                                    5666789************97.6788899999888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (636 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); 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: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 4380.63
//
Query:       gi|116753411|ref|YP_842529.1|  [L=366]
Description: TPR repeat-containing protein [Methanosaeta thermophila PT]
Scores for 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-85  275.2   1.8    5.7e-10   38.6   0.0   10.3 10  TPR_1            Tetratricopeptide repeat
    3.4e-72  232.8   6.6    1.4e-08   34.2   0.0   10.4 10  TPR_2            Tetratricopeptide repeat
    2.1e-58  193.8   4.9    1.9e-08   33.8   0.0    9.5 10  TPR_11           TPR repeat
    1.8e-54  177.4   5.3    5.4e-06   26.2   0.1   10.9 11  TPR_8            Tetratricopeptide repeat
    7.7e-51  170.5  13.2    2.4e-09   37.7   0.2    7.4  8  TPR_16           Tetratricopeptide repeat
    1.3e-45  150.1  16.0    2.5e-05   24.7   0.2    9.4  9  TPR_14           Tetratricopeptide repeat
    1.3e-44  147.4   0.1    0.00015   21.9   0.0   10.3 10  TPR_17           Tetratricopeptide repeat
    1.3e-41  140.8  14.6    2.8e-09   37.1   0.2    8.4  7  TPR_12           Tetratricopeptide repeat
      2e-38  130.7   1.0    2.1e-07   31.3   0.0    6.1  5  TPR_19           Tetratricopeptide repeat
    1.1e-34  115.9   9.0    0.00026   20.8   0.0   10.3 10  TPR_7            Tetratricopeptide repeat
    3.3e-32  110.5  16.7    1.3e-07   31.6   2.0    6.9  8  TPR_9            Tetratricopeptide repeat
    8.1e-28   95.2   2.2      0.019   15.6   0.0   10.3 10  TPR_6            Tetratricopeptide repeat
    1.5e-24   86.0   2.5    9.2e-06   25.8   0.0    5.4  6  ANAPC3           Anaphase-promoting complex, cyclosome, subun
      1e-18   66.5  15.2      0.053   13.4   0.1    9.5  9  TPR_10           Tetratricopeptide repeat
    3.5e-18   65.4   0.7      0.051   13.7   0.0    8.0  8  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
    5.3e-15   55.4   0.8     0.0019   17.5   0.0    5.9  7  TPR_15           Tetratricopeptide repeat
    7.4e-15   55.6  10.8      0.015   15.8   0.0    5.8  6  BTAD             Bacterial transcriptional activator domain
    9.5e-11   41.6  16.7       0.38   10.8   0.0    8.1  8  MIT              MIT (microtubule interacting and transport) 
    1.4e-10   41.0   0.9       0.95    9.5   0.0    6.8  6  TPR_3            Tetratricopeptide repeat
      4e-10   39.9   5.1      0.073   13.1   0.1    6.5  6  DUF3856          Domain of Unknown Function (DUF3856)
    3.3e-09   36.2   0.0     0.0025   16.8   0.0    4.4  4  NARP1            NMDA receptor-regulated protein 1
    3.4e-08   33.7   0.0       0.83   10.0   0.0    5.7  6  TPR_20           Tetratricopeptide repeat
    1.2e-07   31.6   6.1        1.7    9.5   0.1    7.9  6  TPR_4            Tetratricopeptide repeat
    7.3e-07   28.9   0.1       0.47    9.8   0.0    4.9  5  Coatomer_E       Coatomer epsilon subunit
      1e-06   28.7   0.1         22    4.8   0.0    7.2  8  DUF5113          Domain of unknown function (DUF5113)
    7.4e-06   26.2   1.0        0.3   11.3   0.0    4.6  4  TPR_5            Tetratrico peptide repeat
    8.2e-06   25.7   7.2         14    6.2   0.0    7.5  7  PPR              PPR repeat
    2.4e-05   24.3   0.0       0.14   12.2   0.0    4.0  4  SRP_TPR_like     Putative TPR-like repeat
      7e-05   22.7   0.4         23    4.6   0.0    6.1  5  TOM20_plant      Plant specific mitochondrial import receptor
    7.9e-05   22.6   0.1        2.4    8.2   0.0    4.2  4  DUF627           Protein of unknown function (DUF627)
     0.0002   21.9   0.0         14    6.2   0.0    4.7  4  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
    0.00037   20.3   0.1        4.1    7.1   0.0    3.8  4  TPR_21           Tetratricopeptide repeat-like domain
     0.0011   17.8   0.0       0.77    8.4   0.0    3.1  3  PknG_TPR         Protein kinase G tetratricopeptide repeat
     0.0012   18.6   3.4         13    5.5   0.0    5.9  7  RPN7             26S proteasome subunit RPN7
     0.0021   18.3  10.3         13    6.1   0.0    7.0  7  NRBF2_MIT        MIT domain of nuclear receptor-binding facto
     0.0022   17.1   0.0       0.25   10.3   0.0    3.3  4  ChAPs            ChAPs (Chs5p-Arf1p-binding proteins)
     0.0038   16.5   0.0        1.2    8.3   0.0    3.3  2  FAT              FAT domain
     0.0064   16.6   0.1        8.7    6.5   0.0    3.3  3  MAS20            MAS20 protein import receptor
  ------ inclusion threshold ------
      0.014   14.9   1.7         27    4.3   0.0    4.6  5  SHNi-TPR         SHNi-TPR
      0.015   15.0   0.0         24    4.9   0.0    5.2  5  PPTA             Protein prenyltransferase alpha subunit repe
      0.019   14.4   0.2        6.3    6.1   0.0    4.1  4  TPR_MalT         MalT-like TPR region
      0.024   14.7   0.1         11    6.1   0.0    2.9  3  Type_III_YscG    Bacterial type II secretion system chaperone
      0.051   13.5   0.6         52    3.7   0.0    4.2  6  Wzy_C_2          Virulence factor membrane-bound polymerase, 
       0.12   12.4   1.3         37    4.4   0.0    3.9  4  DUF1896          Domain of unknown function (DUF1896)
       0.17   11.9   2.2        9.6    6.3   0.0    3.6  2  Ubiq-assoc       Ubiquitin-associated
        2.4    7.8   4.8         98    2.7   0.0    5.1  6  HTH_Bact         Helix-turn-helix bacterial domain


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.4   1.8e-07     7e-05       3      34 .]       6      37 ..       4      37 .. 0.88
   2 !   31.9   0.0   1.8e-10   7.1e-08       3      34 .]      40      71 ..      38      71 .. 0.96
   3 !   17.3   0.0   7.7e-06     0.003       3      33 ..      74     104 ..      72     105 .. 0.93
   4 !   38.6   0.0   1.5e-12   5.7e-10       1      33 [.     121     153 ..     121     154 .. 0.97
   5 !   29.1   0.0   1.5e-09   5.7e-07       3      34 .]     157     188 ..     155     188 .. 0.93
   6 !   30.4   0.0   5.8e-10   2.3e-07       3      33 ..     191     221 ..     189     222 .. 0.91
   7 !   23.8   0.0   6.8e-08   2.7e-05       2      34 .]     224     256 ..     223     256 .. 0.96
   8 !   34.2   0.0   3.6e-11   1.4e-08       1      34 []     257     290 ..     257     290 .. 0.96
   9 !   19.7   0.1   1.4e-06   0.00055       1      32 [.     291     322 ..     291     323 .. 0.96
  10 !   15.3   0.0   3.2e-05     0.013       2      30 ..     326     354 ..     325     355 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.8e-07
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                          TPR_1  3 alynlGnayfklgkydeAleyyekALelnPnn 34
                                   al +++   +  g ydeA+eyy+++L ++P n
  gi|116753411|ref|YP_842529.1|  6 ALLQKAEEKYLDGSYDEAIEYYDRVLDIDPMN 37
                                   7778888889999*****************65 PP

  == domain 2  score: 31.9 bits;  conditional E-value: 1.8e-10
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                          TPR_1  3 alynlGnayfklgkydeAleyyekALelnPnn 34
                                   a++++G+a+f   +y++Ale+y++A+e +P++
  gi|116753411|ref|YP_842529.1| 40 AWCGRGMACFCFSRYEDALECYSRAIEADPEC 71
                                   9*****************************85 PP

  == domain 3  score: 17.3 bits;  conditional E-value: 7.7e-06
                                    HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                          TPR_1   3 alynlGnayfklgkydeAleyyekALelnPn 33 
                                    a+  ++ ++f lg+ deA+  y++A+  +P 
  gi|116753411|ref|YP_842529.1|  74 AWECRAEVLFILGRCDEAISSYQEAIDRDPA 104
                                    8889*************************95 PP

  == domain 4  score: 38.6 bits;  conditional E-value: 1.5e-12
                                    HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                          TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPn 33 
                                    a+++ ++G+a++++g+y+eA+e+y+ AL ++P+
  gi|116753411|ref|YP_842529.1| 121 AESWRQKGLALLSMGRYEEAIEAYRMALDIDPS 153
                                    799*****************************7 PP

  == domain 5  score: 29.1 bits;  conditional E-value: 1.5e-09
                                    HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                          TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                     ++ lG  ++  g++ eAle++e+ALel P++
  gi|116753411|ref|YP_842529.1| 157 DWCILGESLQTIGRHSEALECFERALELSPSD 188
                                    5999**************************86 PP

  == domain 6  score: 30.4 bits;  conditional E-value: 5.8e-10
                                    HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                          TPR_1   3 alynlGnayfklgkydeAleyyekALelnPn 33 
                                    ++ ++G   ++ g+ydeAle+ye+AL+l+P 
  gi|116753411|ref|YP_842529.1| 191 CWIRMGESMHSTGRYDEALECYEEALRLDPG 221
                                    78999999999*******************5 PP

  == domain 7  score: 23.8 bits;  conditional E-value: 6.8e-08
                                    HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                          TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                    +a+ ++G +y+ +g + +A+++ + AL+l+P++
  gi|116753411|ref|YP_842529.1| 224 QAWHGKGITYRAMGIPSKAIDAIDSALTLDPEH 256
                                    79*****************************86 PP

  == domain 8  score: 34.2 bits;  conditional E-value: 3.6e-11
                                    HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                          TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                    a+++y +G +++ +g y++Ale+++++L+++P n
  gi|116753411|ref|YP_842529.1| 257 AQSWYAKGITFRAMGLYEDALECFDRVLRIDPGN 290
                                    789*****************************87 PP

  == domain 9  score: 19.7 bits;  conditional E-value: 1.4e-06
                                    HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                          TPR_1   1 akalynlGnayfklgkydeAleyyekALelnP 32 
                                    a al+ ++  +++lg+y eAl ++e A+++nP
  gi|116753411|ref|YP_842529.1| 291 ASALKSRAWSLYNLGRYAEALSACEGAISVNP 322
                                    679**************************999 PP

  == domain 10  score: 15.3 bits;  conditional E-value: 3.2e-05
                                    HHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                          TPR_1   2 kalynlGnayfklgkydeAleyyekALel 30 
                                    +a+yn+G ++  lg+y e   ++ kA e+
  gi|116753411|ref|YP_842529.1| 326 DAWYNMGIVLKALGRYTESDMAFIKAREI 354
                                    79**************9987777777665 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.2   8.4e-06    0.0033       4      32 ..       7      35 ..       4      37 .. 0.83
   2 !   23.8   0.0   7.9e-08   3.1e-05       2      33 ..      39      70 ..      38      71 .. 0.95
   3 !   18.1   0.0   5.2e-06     0.002       3      33 ..      74     104 ..      72     105 .. 0.94
   4 !   30.0   0.1   7.8e-10   3.1e-07       1      33 [.     121     153 ..     121     154 .. 0.96
   5 !   25.8   0.0   1.8e-08   7.1e-06       2      34 .]     156     188 ..     155     188 .. 0.93
   6 !   34.2   0.0   3.7e-11   1.4e-08       3      33 ..     191     221 ..     189     222 .. 0.95
   7 !   17.1   0.0   1.1e-05    0.0042       2      34 .]     224     256 ..     223     256 .. 0.96
   8 !   26.6   0.0   9.7e-09   3.8e-06       1      34 []     257     290 ..     257     290 .. 0.96
   9 !   21.6   0.1     4e-07   0.00015       2      32 ..     292     322 ..     291     324 .. 0.92
  10 !   10.6   0.0    0.0013      0.49       2      20 ..     326     344 ..     325     354 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 8.4e-06
                          TPR_2  4 lynlGlayyklgdyeeAleafekAleldP 32
                                   l + ++  y  g y+eA+e+++++l +dP
  gi|116753411|ref|YP_842529.1|  7 LLQKAEEKYLDGSYDEAIEYYDRVLDIDP 35
                                   5566666788899***************9 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 7.9e-08
                          TPR_2  2 ealynlGlayyklgdyeeAleafekAleldPn 33
                                    a++ +G+a++   +ye+Ale++ +A+e dP+
  gi|116753411|ref|YP_842529.1| 39 AAWCGRGMACFCFSRYEDALECYSRAIEADPE 70
                                   59*****************************8 PP

  == domain 3  score: 18.1 bits;  conditional E-value: 5.2e-06
                          TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                    a+ +++++++ lg+ +eA+  +++A+  dP 
  gi|116753411|ref|YP_842529.1|  74 AWECRAEVLFILGRCDEAISSYQEAIDRDPA 104
                                    89***************************96 PP

  == domain 4  score: 30.0 bits;  conditional E-value: 7.8e-10
                          TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                    ae + + Gla++ +g+yeeA+ea++ Al +dP 
  gi|116753411|ref|YP_842529.1| 121 AESWRQKGLALLSMGRYEEAIEAYRMALDIDPS 153
                                    799****************************95 PP

  == domain 5  score: 25.8 bits;  conditional E-value: 1.8e-08
                          TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                    + ++ lG+++   g++ eAle+fe+Alel P +
  gi|116753411|ref|YP_842529.1| 156 RDWCILGESLQTIGRHSEALECFERALELSPSD 188
                                    66999**************************75 PP

  == domain 6  score: 34.2 bits;  conditional E-value: 3.7e-11
                          TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                    ++ ++G++    g+y+eAle++e+Al+ldP+
  gi|116753411|ref|YP_842529.1| 191 CWIRMGESMHSTGRYDEALECYEEALRLDPG 221
                                    79****************************7 PP

  == domain 7  score: 17.1 bits;  conditional E-value: 1.1e-05
                          TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                    +a++  G  y+++g + +A++a + Al ldP++
  gi|116753411|ref|YP_842529.1| 224 QAWHGKGITYRAMGIPSKAIDAIDSALTLDPEH 256
                                    69*****************************86 PP

  == domain 8  score: 26.6 bits;  conditional E-value: 9.7e-09
                          TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                    a+ +y+ G   +++g ye+Ale+f+++l++dP+n
  gi|116753411|ref|YP_842529.1| 257 AQSWYAKGITFRAMGLYEDALECFDRVLRIDPGN 290
                                    678*****************************97 PP

  == domain 9  score: 21.6 bits;  conditional E-value: 4e-07
                          TPR_2   2 ealynlGlayyklgdyeeAleafekAleldP 32 
                                     al  +++++y+lg+y+eAl a+e A++ +P
  gi|116753411|ref|YP_842529.1| 292 SALKSRAWSLYNLGRYAEALSACEGAISVNP 322
                                    68889************************99 PP

  == domain 10  score: 10.6 bits;  conditional E-value: 0.0013
                          TPR_2   2 ealynlGlayyklgdyeeA 20 
                                    +a+yn+G ++ +lg+y e 
  gi|116753411|ref|YP_842529.1| 326 DAWYNMGIVLKALGRYTES 344
                                    69**************985 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   4.2e-08   1.6e-05       5      37 ..      15      47 ..      11      49 .. 0.90
   2 !   18.6   0.0   2.9e-06    0.0011       9      39 ..      53      83 ..      52      86 .. 0.89
   3 !   21.8   0.1   2.9e-07   0.00011       3      31 ..      81     109 ..      79     112 .. 0.92
   4 ?    3.6   0.0      0.13        52      24      42 .]     117     135 ..     114     135 .. 0.91
   5 !   32.8   0.0     1e-10   3.9e-08       1      40 [.     128     167 ..     128     169 .. 0.91
   6 !   15.8   0.0   2.2e-05    0.0085       8      42 .]     169     203 ..     165     203 .. 0.87
   7 !   33.8   0.0     5e-11   1.9e-08       4      42 .]     199     237 ..     196     237 .. 0.92
   8 !    7.9   0.0    0.0064       2.5      13      42 .]     242     271 ..     240     271 .. 0.85
   9 !   18.9   0.0   2.3e-06   0.00088       4      42 .]     267     305 ..     264     305 .. 0.88
  10 !   20.3   0.1   8.1e-07   0.00032       4      42 .]     301     339 ..     298     339 .. 0.96

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 4.2e-08
                         TPR_11  5 yeqGkyeeAieaYkkAlkldPdnaeayynLGla 37
                                   y  G y+eAie Y + l++dP n  a++++G a
  gi|116753411|ref|YP_842529.1| 15 YLDGSYDEAIEYYDRVLDIDPMNTAAWCGRGMA 47
                                   6679**************************965 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 2.9e-06
                         TPR_11  9 kyeeAieaYkkAlkldPdnaeayynLGlayy 39
                                   +ye+A+e+Y++A++ dP+ + a+ +++++++
  gi|116753411|ref|YP_842529.1| 53 RYEDALECYSRAIEADPECVPAWECRAEVLF 83
                                   7*****************9999999998887 PP

  == domain 3  score: 21.8 bits;  conditional E-value: 2.9e-07
                         TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeay 31 
                                    +++ +G+ +eAi +Y++A++ dP +a a+
  gi|116753411|ref|YP_842529.1|  81 VLFILGRCDEAISSYQEAIDRDPAYALAW 109
                                    7899**********************997 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.13
                         TPR_11  24 dPdnaeayynLGlayykqG 42 
                                    +Pd+ae +   Gla++ +G
  gi|116753411|ref|YP_842529.1| 117 RPDDAESWRQKGLALLSMG 135
                                    7**************9988 PP

  == domain 5  score: 32.8 bits;  conditional E-value: 1e-10
                         TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayyk 40 
                                    G a+ + G+yeeAieaY+ Al++dP++a+ ++ LG+ ++ 
  gi|116753411|ref|YP_842529.1| 128 GLALLSMGRYEEAIEAYRMALDIDPSQARDWCILGESLQT 167
                                    8899*************************99999988776 PP

  == domain 6  score: 15.8 bits;  conditional E-value: 2.2e-05
                         TPR_11   8 GkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                    G+  eA+e++++Al+l+P++   +  +G+ ++  G
  gi|116753411|ref|YP_842529.1| 169 GRHSEALECFERALELSPSDSACWIRMGESMHSTG 203
                                    899****************9888888887777665 PP

  == domain 7  score: 33.8 bits;  conditional E-value: 5e-11
                         TPR_11   4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                     ++ G+y+eA+e+Y++Al+ldP ++ a+++ G +y ++G
  gi|116753411|ref|YP_842529.1| 199 MHSTGRYDEALECYEEALRLDPGSVQAWHGKGITYRAMG 237
                                    5789******************************98877 PP

  == domain 8  score: 7.9 bits;  conditional E-value: 0.0064
                         TPR_11  13 AieaYkkAlkldPdnaeayynLGlayykqG 42 
                                    Ai a   Al ldP+ a  +y+ G ++ ++G
  gi|116753411|ref|YP_842529.1| 242 AIDAIDSALTLDPEHAQSWYAKGITFRAMG 271
                                    6777778****************9987766 PP

  == domain 9  score: 18.9 bits;  conditional E-value: 2.3e-06
                         TPR_11   4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                    +++ G ye+A+e++ + l++dP na+a+  ++  +y++G
  gi|116753411|ref|YP_842529.1| 267 FRAMGLYEDALECFDRVLRIDPGNASALKSRAWSLYNLG 305
                                    8999***********************988887777776 PP

  == domain 10  score: 20.3 bits;  conditional E-value: 8.1e-07
                         TPR_11   4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                    +y +G+y eA+ a + A+  +P + +a+yn+G ++ ++G
  gi|116753411|ref|YP_842529.1| 301 LYNLGRYAEALSACEGAISVNPLDEDAWYNMGIVLKALG 339
                                    7899*******************************9998 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.3   4.7e-05     0.018       5      32 ..       8      35 ..       4      37 .. 0.82
   2 !   12.3   0.0   0.00041      0.16       3      34 .]      40      71 ..      38      71 .. 0.88
   3 !   13.9   0.0   0.00013     0.049       7      33 ..      78     104 ..      72     105 .. 0.88
   4 ?    0.1   0.0       3.3   1.3e+03      20      34 .]     106     120 ..     106     120 .. 0.87
   5 !   26.2   0.1   1.4e-08   5.4e-06       1      33 [.     121     153 ..     121     154 .. 0.94
   6 !   21.6   0.0   4.2e-07   0.00016       4      34 .]     158     188 ..     155     188 .. 0.95
   7 !   22.3   0.0   2.5e-07   9.6e-05       4      32 ..     192     220 ..     189     222 .. 0.90
   8 !   11.0   0.0     0.001       0.4       2      34 .]     224     256 ..     223     256 .. 0.96
   9 !   20.2   0.0   1.2e-06   0.00047       1      33 [.     257     289 ..     257     290 .. 0.96
  10 !   11.3   0.0   0.00081      0.32       8      32 ..     298     322 ..     292     322 .. 0.92
  11 !   12.8   0.0   0.00027       0.1       2      27 ..     326     351 ..     325     355 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.7e-05
                                   HHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                          TPR_8  5 ynlgsiylklgdyeeAkeyyekaleldp 32
                                   ++++      g y+eA+eyy ++l++dp
  gi|116753411|ref|YP_842529.1|  8 LQKAEEKYLDGSYDEAIEYYDRVLDIDP 35
                                   556666666799***************9 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00041
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                          TPR_8  3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34
                                   a++  g++++   +ye A e+y +a+e+dp++
  gi|116753411|ref|YP_842529.1| 40 AWCGRGMACFCFSRYEDALECYSRAIEADPEC 71
                                   68888888888889****************86 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 0.00013
                                    HHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                          TPR_8   7 lgsiylklgdyeeAkeyyekaleldpd 33 
                                     + +++ lg+ +eA+++y++a++ dp+
  gi|116753411|ref|YP_842529.1|  78 RAEVLFILGRCDEAISSYQEAIDRDPA 104
                                    5788999*******************7 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 3.3
                                    HHHHHHHHHHHHHH. CS
                          TPR_8  20 Akeyyekaleldpdn 34 
                                    A +++e++++ +pd+
  gi|116753411|ref|YP_842529.1| 106 ALAWIERCIDSRPDD 120
                                    67899*******986 PP

  == domain 5  score: 26.2 bits;  conditional E-value: 1.4e-08
                                    CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                          TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                    ae++ ++g+++l++g+yeeA+e+y+ al++dp+
  gi|116753411|ref|YP_842529.1| 121 AESWRQKGLALLSMGRYEEAIEAYRMALDIDPS 153
                                    678889*************************96 PP

  == domain 6  score: 21.6 bits;  conditional E-value: 4.2e-07
                                    HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                          TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                    ++ lg  +++ g++ eA e++e+alel+p++
  gi|116753411|ref|YP_842529.1| 158 WCILGESLQTIGRHSEALECFERALELSPSD 188
                                    899**************************75 PP

  == domain 7  score: 22.3 bits;  conditional E-value: 2.5e-07
                                    HHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                          TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldp 32 
                                    + ++g   +++g+y+eA e+ye+al+ldp
  gi|116753411|ref|YP_842529.1| 192 WIRMGESMHSTGRYDEALECYEEALRLDP 220
                                    7888888899******************9 PP

  == domain 8  score: 11.0 bits;  conditional E-value: 0.001
                                    CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                          TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                    +a++ +g +y+ +g   +A+ ++  al+ldp++
  gi|116753411|ref|YP_842529.1| 224 QAWHGKGITYRAMGIPSKAIDAIDSALTLDPEH 256
                                    89*****************************86 PP

  == domain 9  score: 20.2 bits;  conditional E-value: 1.2e-06
                                    CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                          TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                    a+++y +g + + +g ye A e++ ++l++dp 
  gi|116753411|ref|YP_842529.1| 257 AQSWYAKGITFRAMGLYEDALECFDRVLRIDPG 289
                                    799****************************96 PP

  == domain 10  score: 11.3 bits;  conditional E-value: 0.00081
                                    HHHHHHTT-HHHHHHHHHHHHHHHH CS
                          TPR_8   8 gsiylklgdyeeAkeyyekaleldp 32 
                                    ++ + +lg+y eA +++e a++ +p
  gi|116753411|ref|YP_842529.1| 298 AWSLYNLGRYAEALSACEGAISVNP 322
                                    77889*****************998 PP

  == domain 11  score: 12.8 bits;  conditional E-value: 0.00027
                                    CHHHHHHHHHHHTT-HHHHHHHHHHH CS
                          TPR_8   2 eayynlgsiylklgdyeeAkeyyeka 27 
                                    +a+yn+g +++ lg+y e+  ++ ka
  gi|116753411|ref|YP_842529.1| 326 DAWYNMGIVLKALGRYTESDMAFIKA 351
                                    69********************9998 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   5.9e-05     0.023      10      46 ..      17      50 ..       8      54 .. 0.85
   2 !   35.5   0.1     3e-11   1.2e-08      12      67 ..      53     105 ..      51     106 .. 0.96
   3 !   26.3   0.3   2.2e-08   8.4e-06      21      67 ..     111     154 ..     104     155 .. 0.91
   4 !   29.0   0.0   3.2e-09   1.2e-06       4      67 ..     162     222 ..     161     222 .. 0.94
   5 !   29.0   0.0   3.1e-09   1.2e-06      11      67 ..     203     256 ..     201     257 .. 0.96
   6 !   26.3   0.0   2.2e-08   8.8e-06       7      68 .]     233     291 ..     229     291 .. 0.92
   7 !   37.7   0.2     6e-12   2.4e-09       1      62 [.     261     319 ..     261     325 .. 0.92
   8 !   23.4   0.1   1.8e-07   7.2e-05       3      52 ..     297     343 ..     296     351 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.9e-05
                         TPR_16 10 agdyddAaaaleaalkrdpssPdaaeAllllgdaalr 46
                                    g yd+A+++++++l+ d   P + +A+ ++g a++ 
  gi|116753411|ref|YP_842529.1| 17 DGSYDEAIEYYDRVLDID---PMNTAAWCGRGMACFC 50
                                   589***************...************9985 PP

  == domain 2  score: 35.5 bits;  conditional E-value: 3e-11
                         TPR_16  12 dyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                    +y+dA++ + +a+++d   P+++ A+  ++++++ +gr +eA+  y++a++ +p +
  gi|116753411|ref|YP_842529.1|  53 RYEDALECYSRAIEAD---PECVPAWECRAEVLFILGRCDEAISSYQEAIDRDPAY 105
                                    9***************...**********************************986 PP

  == domain 3  score: 26.3 bits;  conditional E-value: 2.2e-08
                         TPR_16  21 eaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                    e+ ++++   Pd+ae++  +g+a+l  gr++eA+++yr al+ +p+ 
  gi|116753411|ref|YP_842529.1| 111 ERCIDSR---PDDAESWRQKGLALLSMGRYEEAIEAYRMALDIDPSQ 154
                                    6668899...**********************************986 PP

  == domain 4  score: 29.0 bits;  conditional E-value: 3.2e-09
                         TPR_16   4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                    + ++   g+  +A++ +e+al++    P + + +   g++    gr++eA++ y++alr +p++
  gi|116753411|ref|YP_842529.1| 162 GESLQTIGRHSEALECFERALELS---PSDSACWIRMGESMHSTGRYDEALECYEEALRLDPGS 222
                                    67788889****************...99999******************************85 PP

  == domain 5  score: 29.0 bits;  conditional E-value: 3.1e-09
                         TPR_16  11 gdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                    g+yd+A++ +e+al++d   P  ++A+ ++g  + + g   +A++++++al+ +p +
  gi|116753411|ref|YP_842529.1| 203 GRYDEALECYEEALRLD---PGSVQAWHGKGITYRAMGIPSKAIDAIDSALTLDPEH 256
                                    9****************...*******************************999975 PP

  == domain 6  score: 26.3 bits;  conditional E-value: 2.2e-08
                         TPR_16   7 alragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapdap 68 
                                    +++ g + +A+ a + al +d   P++a++++++g  + + g +++A++ +++ lr +p+++
  gi|116753411|ref|YP_842529.1| 233 YRAMGIPSKAIDAIDSALTLD---PEHAQSWYAKGITFRAMGLYEDALECFDRVLRIDPGNA 291
                                    666777889************...***********************************985 PP

  == domain 7  score: 37.7 bits;  conditional E-value: 6e-12
                         TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalr 62 
                                    +a++  +++ g y+dA++ ++++l+ d   P +a Al  ++++++ +gr+aeA+ +++ a+ 
  gi|116753411|ref|YP_842529.1| 261 YAKGITFRAMGLYEDALECFDRVLRID---PGNASALKSRAWSLYNLGRYAEALSACEGAIS 319
                                    78899999*******************...************************99998875 PP

  == domain 8  score: 23.4 bits;  conditional E-value: 1.8e-07
                         TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlae 52 
                                    +a +++++g+y++A+ a e a+  +   P++ +A+++ g ++ ++gr++e
  gi|116753411|ref|YP_842529.1| 297 RAWSLYNLGRYAEALSACEGAISVN---PLDEDAWYNMGIVLKALGRYTE 343
                                    6999*********************...99999***************98 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   0.00021     0.083       2      38 ..       5      41 ..       4      47 .. 0.86
   2 !   14.3   0.1   0.00014     0.054       3      43 ..      40      80 ..      38      81 .. 0.86
   3 !   24.5   0.1   7.7e-08     3e-05       3      40 ..      74     111 ..      72     114 .. 0.95
   4 !   24.7   0.2   6.5e-08   2.5e-05       2      42 ..     122     162 ..     121     165 .. 0.92
   5 !   21.8   0.0   5.7e-07   0.00022       7      43 ..     161     197 ..     156     198 .. 0.91
   6 !   23.4   0.0   1.8e-07   6.9e-05       4      40 ..     192     228 ..     190     232 .. 0.91
   7 !    9.0   0.0    0.0072       2.8       4      40 ..     226     262 ..     225     264 .. 0.87
   8 !   18.9   0.0   4.8e-06    0.0019       3      38 ..     259     294 ..     257     298 .. 0.92
   9 !   20.4   0.1   1.5e-06   0.00059       3      42 ..     293     332 ..     291     335 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00021
                         TPR_14  2 eallalaeallalGdpdeAiallrralalaPddaeaw 38
                                   +all+ ae  +  G +deAi++++r+l+ +P + +aw
  gi|116753411|ref|YP_842529.1|  5 AALLQKAEEKYLDGSYDEAIEYYDRVLDIDPMNTAAW 41
                                   5788888888999******************777777 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 0.00014
                         TPR_14  3 allalaeallalGdpdeAiallrralalaPddaeawlllaq 43
                                   a+  ++ a++   ++++A++++ ra++++P+   aw   a+
  gi|116753411|ref|YP_842529.1| 40 AWCGRGMACFCFSRYEDALECYSRAIEADPECVPAWECRAE 80
                                   56667778888889**********************99886 PP

  == domain 3  score: 24.5 bits;  conditional E-value: 7.7e-08
                         TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawll 40 
                                    a+ ++ae+l+ lG+ deAi  +++a++++P+ a aw++
  gi|116753411|ref|YP_842529.1|  74 AWECRAEVLFILGRCDEAISSYQEAIDRDPAYALAWIE 111
                                    899*********************************87 PP

  == domain 4  score: 24.7 bits;  conditional E-value: 6.5e-08
                         TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                    e +++ + all  G+++eAi+++r al+ +P++a+ w  l+
  gi|116753411|ref|YP_842529.1| 122 ESWRQKGLALLSMGRYEEAIEAYRMALDIDPSQARDWCILG 162
                                    7899******************************9998776 PP

  == domain 5  score: 21.8 bits;  conditional E-value: 5.7e-07
                         TPR_14   7 laeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                    l+e l + G++ eA+++++ral+l P+d + w+++++
  gi|116753411|ref|YP_842529.1| 161 LGESLQTIGRHSEALECFERALELSPSDSACWIRMGE 197
                                    78889999**************************996 PP

  == domain 6  score: 23.4 bits;  conditional E-value: 1.8e-07
                         TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawll 40 
                                    + +++e +   G++deA++++++al+l+P++ +aw  
  gi|116753411|ref|YP_842529.1| 192 WIRMGESMHSTGRYDEALECYEEALRLDPGSVQAWHG 228
                                    88999999***************************75 PP

  == domain 7  score: 9.0 bits;  conditional E-value: 0.0072
                         TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawll 40 
                                    +   +  ++a G p +Ai++ + al l+P++a+ w++
  gi|116753411|ref|YP_842529.1| 226 WHGKGITYRAMGIPSKAIDAIDSALTLDPEHAQSWYA 262
                                    66668899999********************998876 PP

  == domain 8  score: 18.9 bits;  conditional E-value: 4.8e-06
                         TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeaw 38 
                                     ++a +  ++a G +++A+++++r+l+ +P++a a+
  gi|116753411|ref|YP_842529.1| 259 SWYAKGITFRAMGLYEDALECFDRVLRIDPGNASAL 294
                                    79******************************9987 PP

  == domain 9  score: 20.4 bits;  conditional E-value: 1.5e-06
                         TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                    al+ +a+ l++lG+++eA+ +++ a++ +P d++aw+ ++
  gi|116753411|ref|YP_842529.1| 293 ALKSRAWSLYNLGRYAEALSACEGAISVNPLDEDAWYNMG 332
                                    78889*******************************9987 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0      0.14        53       1      24 [.      26      49 ..      26      59 .. 0.80
   2 !   10.2   0.0    0.0021      0.81       1      28 [.      60      87 ..      60      93 .. 0.89
   3 ?    7.4   0.0     0.016       6.3       2      18 ..      95     111 ..      94     112 .. 0.92
   4 !   21.9   0.0     4e-07   0.00015       3      34 .]     111     142 ..     110     142 .. 0.96
   5 !    8.4   0.0    0.0077         3       2      34 .]     144     176 ..     143     176 .. 0.93
   6 !   17.2   0.0   1.3e-05    0.0049       1      34 []     177     210 ..     177     210 .. 0.97
   7 !   17.4   0.0     1e-05     0.004       1      30 [.     211     240 ..     211     244 .. 0.88
   8 !   12.5   0.0   0.00038      0.15       5      34 .]     249     278 ..     245     278 .. 0.93
   9 !   19.4   0.0   2.4e-06   0.00093       1      33 [.     279     311 ..     279     312 .. 0.96
  10 !   15.7   0.0   3.7e-05     0.015       2      30 ..     314     342 ..     313     347 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.14
                         TPR_17  1 lylkaleldPnnadaynnLAelll 24
                                   +y ++l++dP n  a++ ++ +  
  gi|116753411|ref|YP_842529.1| 26 YYDRVLDIDPMNTAAWCGRGMACF 49
                                   69***************9998755 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0021
                         TPR_17  1 lylkaleldPnnadaynnLAelllknGd 28
                                   +y +a+e dP  ++a+  +Ae+l  +G+
  gi|116753411|ref|YP_842529.1| 60 CYSRAIEADPECVPAWECRAEVLFILGR 87
                                   899********************99987 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.016
                         TPR_17   2 ylkaleldPnnadaynn 18 
                                    y++a+++dP +a a+ +
  gi|116753411|ref|YP_842529.1|  95 YQEAIDRDPAYALAWIE 111
                                    9*************976 PP

  == domain 4  score: 21.9 bits;  conditional E-value: 4e-07
                         TPR_17   3 lkaleldPnnadaynnLAelllknGdlmtArq 34 
                                    +++++  P++a+++ +++ +ll+ G++++A++
  gi|116753411|ref|YP_842529.1| 111 ERCIDSRPDDAESWRQKGLALLSMGRYEEAIE 142
                                    89****************************86 PP

  == domain 5  score: 8.4 bits;  conditional E-value: 0.0077
                         TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                    y+ al++dP+ a  ++ L+e l  +G++ +A++
  gi|116753411|ref|YP_842529.1| 144 YRMALDIDPSQARDWCILGESLQTIGRHSEALE 176
                                    889************************999975 PP

  == domain 6  score: 17.2 bits;  conditional E-value: 1.3e-05
                         TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                    ++++alel P+++  +  ++e +++ G++++A++
  gi|116753411|ref|YP_842529.1| 177 CFERALELSPSDSACWIRMGESMHSTGRYDEALE 210
                                    89******************************85 PP

  == domain 7  score: 17.4 bits;  conditional E-value: 1e-05
                         TPR_17   1 lylkaleldPnnadaynnLAelllknGdlm 30 
                                    +y++al+ldP ++ a++ ++ +++  G + 
  gi|116753411|ref|YP_842529.1| 211 CYEEALRLDPGSVQAWHGKGITYRAMGIPS 240
                                    8**********************9988555 PP

  == domain 8  score: 12.5 bits;  conditional E-value: 0.00038
                         TPR_17   5 aleldPnnadaynnLAelllknGdlmtArq 34 
                                    al ldP +a +++ ++ +++  G +++A++
  gi|116753411|ref|YP_842529.1| 249 ALTLDPEHAQSWYAKGITFRAMGLYEDALE 278
                                    8999*******************9999975 PP

  == domain 9  score: 19.4 bits;  conditional E-value: 2.4e-06
                         TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                    ++ ++l++dP na a+  +A+ l+++G++++A+
  gi|116753411|ref|YP_842529.1| 279 CFDRVLRIDPGNASALKSRAWSLYNLGRYAEAL 311
                                    799****************************96 PP

  == domain 10  score: 15.7 bits;  conditional E-value: 3.7e-05
                         TPR_17   2 ylkaleldPnnadaynnLAelllknGdlm 30 
                                    ++ a+  +P + da++n++ +l+ +G++ 
  gi|116753411|ref|YP_842529.1| 314 CEGAISVNPLDEDAWYNMGIVLKALGRYT 342
                                    6779**********************985 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.6     6e-07   0.00023       8      76 ..       9      69 ..       3      70 .. 0.85
   2 !   33.7   0.3   8.2e-11   3.2e-08       6      76 ..      75     152 ..      72     153 .. 0.83
   3 !   37.1   0.2   7.3e-12   2.8e-09       9      75 ..     161     219 ..     158     221 .. 0.93
   4 !   25.5   0.0   3.1e-08   1.2e-05       4      75 ..     191     253 ..     188     255 .. 0.88
   5 !   19.7   0.0     2e-06   0.00076       5      75 ..     225     287 ..     221     289 .. 0.91
   6 !   23.7   0.4   1.1e-07   4.2e-05       3      66 ..     257     312 ..     255     320 .. 0.77
   7 !   16.2   0.0   2.5e-05    0.0098       5      34 ..     327     356 ..     324     364 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 6e-07
                         TPR_12  8 nlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76
                                   + a+  +  g ydeA+e+++++l+i    +   +    ++ ++ g++++ + rye+Ale + +a+++++
  gi|116753411|ref|YP_842529.1|  9 QKAEEKYLDGSYDEAIEYYDRVLDID---PM--N---TAAWCGRGMACFCFSRYEDALECYSRAIEADP 69
                                   667777889*****************...44..4...3589************************9875 PP

  == domain 2  score: 33.7 bits;  conditional E-value: 8.2e-11
                         TPR_12   6 lnnlaavlrrlgrydeAlellekale.......iarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                    +  +a+vl+ lgr+deA++ +++a++       ++ +   + +p+ a++ r  g +++ +gryeeA+e+++ al+i++
  gi|116753411|ref|YP_842529.1|  75 WECRAEVLFILGRCDEAISSYQEAIDrdpayalAWIERCIDSRPDDAESWRQKGLALLSMGRYEEAIEAYRMALDIDP 152
                                    6679*******************86522222223445555789********************************976 PP

  == domain 3  score: 37.1 bits;  conditional E-value: 7.3e-12
                         TPR_12   9 laavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                    l++ l+  gr+ eAle++e+ale+      p     +++ + +g+  + +gry+eAle +eeal+++
  gi|116753411|ref|YP_842529.1| 161 LGESLQTIGRHSEALECFERALELS-----PS---DSACWIRMGESMHSTGRYDEALECYEEALRLD 219
                                    89***********************.....64...589**************************986 PP

  == domain 4  score: 25.5 bits;  conditional E-value: 3.1e-08
                         TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                    +   ++++  +  grydeAle++e+al++      p     +++ ++ g++yra+g + +A+++   al ++
  gi|116753411|ref|YP_842529.1| 191 CWI-RMGESMHSTGRYDEALECYEEALRLD-----PG---SVQAWHGKGITYRAMGIPSKAIDAIDSALTLD 253
                                    555.89999*****************9999.....54...599********************999999876 PP

  == domain 5  score: 19.7 bits;  conditional E-value: 2e-06
                         TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                    a++  + ++r++g   +A++  + al +      p+h   a++ ++ g+++ra+g ye+Ale + ++l+i+
  gi|116753411|ref|YP_842529.1| 225 AWHGKGITYRAMGIPSKAIDAIDSALTLD-----PEH---AQSWYAKGITFRAMGLYEDALECFDRVLRID 287
                                    78889999999999999999999999999.....998...99**************************996 PP

  == domain 6  score: 23.7 bits;  conditional E-value: 1.1e-07
                         TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAle 66 
                                    a++++  + + r++g y++Ale+++++l+i      p +   a++l   ++ ++ lgry+eAl+
  gi|116753411|ref|YP_842529.1| 257 AQSWYAKGITFRAMGLYEDALECFDRVLRID-----PGN---ASALKSRAWSLYNLGRYAEALS 312
                                    6788899************************.....433...6677777777777777777765 PP

  == domain 7  score: 16.2 bits;  conditional E-value: 2.5e-05
                         TPR_12   5 alnnlaavlrrlgrydeAlellekaleiar 34 
                                    a++n++ vl +lgry+e+   + ka+ei+ 
  gi|116753411|ref|YP_842529.1| 327 AWYNMGIVLKALGRYTESDMAFIKAREIRV 356
                                    789************************984 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   7.1e-08   2.8e-05       4      59 ..      17      73 ..      14      76 .. 0.94
   2 !   19.2   0.5   3.3e-06    0.0013       5      59 ..     101     155 ..      82     157 .. 0.89
   3 !   31.3   0.0   5.4e-10   2.1e-07       5      62 ..     169     227 ..     169     229 .. 0.94
   4 !   21.6   0.0   5.8e-07   0.00023       3      64 ..     235     294 ..     233     298 .. 0.89
   5 !   23.9   0.0   1.2e-07   4.6e-05       5      43 ..     305     343 ..     301     345 .. 0.96

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 7.1e-08
                         TPR_19  4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd.a 59
                                   +g y+eA++++ ++l+ dp n +a+ +   a++   ++++A ++ +++ e+dp + +
  gi|116753411|ref|YP_842529.1| 17 DGSYDEAIEYYDRVLDIDPMNTAAWCGRGMACFCFSRYEDALECYSRAIEADPECvP 73
                                   79**************************************************98655 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 3.3e-06
                         TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdda 59 
                                     d+a Ala  e+ ++  p++ae + +   all++g+++eA+++   +++ dp +a
  gi|116753411|ref|YP_842529.1| 101 RDPAYALAWIERCIDSRPDDAESWRQKGLALLSMGRYEEAIEAYRMALDIDPSQA 155
                                    5778889999999999********************************9999854 PP

  == domain 3  score: 31.3 bits;  conditional E-value: 5.4e-10
                         TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd.arya 62 
                                    g++ eAl+ +e+al+ +p +++ ++++ e + ++g++deA ++ +++++ dp + ++++
  gi|116753411|ref|YP_842529.1| 169 GRHSEALECFERALELSPSDSACWIRMGESMHSTGRYDEALECYEEALRLDPGSvQAWH 227
                                    7999************************************************9756655 PP

  == domain 4  score: 21.6 bits;  conditional E-value: 5.8e-07
                         TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasL 64 
                                    a+g +  A+++  +al+ dp++a  +++  +   a+g +++A ++ d++++ dp   ++++L
  gi|116753411|ref|YP_842529.1| 235 AMGIPSKAIDAIDSALTLDPEHAQSWYAKGITFRAMGLYEDALECFDRVLRIDPG--NASAL 294
                                    5666789***********************************************9..44444 PP

  == domain 5  score: 23.9 bits;  conditional E-value: 1.2e-07
                         TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqlde 43 
                                    g+yaeAl++ e a++ +p +++a++++ ++l alg+++e
  gi|116753411|ref|YP_842529.1| 305 GRYAEALSACEGAISVNPLDEDAWYNMGIVLKALGRYTE 343
                                    9************************************98 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.1    0.0028       1.1      13      28 ..      18      33 ..       6      35 .. 0.84
   2 !   10.7   0.0    0.0011      0.44       3      33 ..      42      70 ..      40      72 .. 0.83
   3 !    8.4   0.0    0.0059       2.3      12      32 ..      85     103 ..      79     104 .. 0.92
   4 !   16.0   0.1   2.2e-05    0.0087       6      33 ..     128     153 ..     123     156 .. 0.79
   5 !   16.2   0.0     2e-05    0.0076       3      34 ..     159     188 ..     158     190 .. 0.82
   6 !   20.8   0.0   6.7e-07   0.00026       3      34 ..     193     222 ..     191     224 .. 0.83
   7 ?    3.3   0.0      0.26     1e+02       2      35 ..     226     257 ..     225     258 .. 0.87
   8 !   15.8   0.0   2.7e-05     0.011       1      35 [.     259     291 ..     259     292 .. 0.87
   9 ?    7.2   0.0     0.015       5.8       6      34 ..     298     324 ..     293     326 .. 0.79
  10 ?    2.0   0.0      0.67   2.6e+02       1      17 [.     327     343 ..     327     345 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0028
                          TPR_7 13 GdyeeAielyeqsLal 28
                                   G y+eAie+y ++L +
  gi|116753411|ref|YP_842529.1| 18 GSYDEAIEYYDRVLDI 33
                                   669*********6654 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0011
                          TPR_7  3 lnLarlysrlGdyeeAielyeqsLaltkdpe 33
                                   +  + +++   +ye+A+e+y +  a++ dpe
  gi|116753411|ref|YP_842529.1| 42 CGRGMACFCFSRYEDALECYSR--AIEADPE 70
                                   55677888999***********..9999886 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0059
                          TPR_7  12 lGdyeeAielyeqsLaltkdp 32 
                                    lG+ +eAi+ y++  a+++dp
  gi|116753411|ref|YP_842529.1|  85 LGRCDEAISSYQE--AIDRDP 103
                                    7999*********..****98 PP

  == domain 4  score: 16.0 bits;  conditional E-value: 2.2e-05
                          TPR_7   6 arlysrlGdyeeAielyeqsLaltkdpe 33 
                                    + +  ++G+yeeAie y+   al+ dp+
  gi|116753411|ref|YP_842529.1| 128 GLALLSMGRYEEAIEAYRM--ALDIDPS 153
                                    678899*************..6666655 PP

  == domain 5  score: 16.2 bits;  conditional E-value: 2e-05
                          TPR_7   3 lnLarlysrlGdyeeAielyeqsLaltkdped 34 
                                    + L++  +  G+++eA+e++e+  al+ +p+d
  gi|116753411|ref|YP_842529.1| 159 CILGESLQTIGRHSEALECFER--ALELSPSD 188
                                    668999999*************..66666665 PP

  == domain 6  score: 20.8 bits;  conditional E-value: 6.7e-07
                          TPR_7   3 lnLarlysrlGdyeeAielyeqsLaltkdped 34 
                                     ++++  ++ G+y+eA+e+ye+  al+ dp+ 
  gi|116753411|ref|YP_842529.1| 193 IRMGESMHSTGRYDEALECYEE--ALRLDPGS 222
                                    5677777899************..99999875 PP

  == domain 7  score: 3.3 bits;  conditional E-value: 0.26
                          TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdpeda 35 
                                    ++  + +y+++G  ++Ai+      alt dpe+a
  gi|116753411|ref|YP_842529.1| 226 WHGKGITYRAMGIPSKAIDAIDS--ALTLDPEHA 257
                                    5666899****************..999999986 PP

  == domain 8  score: 15.8 bits;  conditional E-value: 2.7e-05
                          TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdpeda 35 
                                    ++++ + +++++G ye+A+e++ +  +l+ dp++a
  gi|116753411|ref|YP_842529.1| 259 SWYAKGITFRAMGLYEDALECFDR--VLRIDPGNA 291
                                    5788899*****************..888888765 PP

  == domain 9  score: 7.2 bits;  conditional E-value: 0.015
                          TPR_7   6 arlysrlGdyeeAielyeqsLaltkdped 34 
                                    a    +lG+y+eA++ +e   a+   p+d
  gi|116753411|ref|YP_842529.1| 298 AWSLYNLGRYAEALSACEG--AISVNPLD 324
                                    555567*************..99888876 PP

  == domain 10  score: 2.0 bits;  conditional E-value: 0.67
                          TPR_7   1 aLlnLarlysrlGdyee 17 
                                    a++n++ +  +lG+y e
  gi|116753411|ref|YP_842529.1| 327 AWYNMGIVLKALGRYTE 343
                                    799************87 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.024       9.3      11      38 ..      20      47 ..      17      49 .. 0.91
   2 !   16.5   0.9   1.7e-05    0.0068      10      61 ..      53     104 ..      51     108 .. 0.95
   3 !   31.6   2.0   3.3e-10   1.3e-07       9      62 ..     101     154 ..     100     157 .. 0.93
   4 !   22.1   0.2   3.3e-07   0.00013      12      63 ..     138     189 ..     138     191 .. 0.95
   5 !   25.4   0.1   2.9e-08   1.1e-05       8      64 ..     202     258 ..     197     263 .. 0.93
   6 !   26.5   0.1   1.3e-08   5.2e-06      12      65 ..     240     293 ..     239     298 .. 0.92
   7 !   24.5   0.3   5.8e-08   2.2e-05      11      65 ..     273     327 ..     268     331 .. 0.95
   8 !    8.5   0.0    0.0056       2.2       9      47 ..     305     343 ..     300     348 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.024
                          TPR_9 11 weralavverllllaPddpeerrdRGll 38
                                   +++a+++++r+l ++P     +  RG++
  gi|116753411|ref|YP_842529.1| 20 YDEAIEYYDRVLDIDPMNTAAWCGRGMA 47
                                   799*******************999976 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.7e-05
                          TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                    ++e al+++ r +  +P+ +  +  R+ +l+ lG+  +A+   + +++ +p+
  gi|116753411|ref|YP_842529.1|  53 RYEDALECYSRAIEADPECVPAWECRAEVLFILGRCDEAISSYQEAIDRDPA 104
                                    7899*********************************************996 PP

  == domain 3  score: 31.6 bits;  conditional E-value: 3.3e-10
                          TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapda 62 
                                    +d + ala +er +   Pdd+e +r  Gl+l  +G++++A+++   +l+++p+ 
  gi|116753411|ref|YP_842529.1| 101 RDPAYALAWIERCIDSRPDDAESWRQKGLALLSMGRYEEAIEAYRMALDIDPSQ 154
                                    57788***********************************************54 PP

  == domain 4  score: 22.1 bits;  conditional E-value: 3.3e-07
                          TPR_9  12 eralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdap 63 
                                    e+a++++ + l ++P +++++   G  l+  G+ s+Al+++e++l+l+p++ 
  gi|116753411|ref|YP_842529.1| 138 EEAIEAYRMALDIDPSQARDWCILGESLQTIGRHSEALECFERALELSPSDS 189
                                    5799*********************************************986 PP

  == domain 5  score: 25.4 bits;  conditional E-value: 2.9e-08
                          TPR_9   8 eedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapd 64 
                                      ++++al+++e  l l+P +++ +   G+ +  +G +s+A+++ + +l l+p+ ++
  gi|116753411|ref|YP_842529.1| 202 TGRYDEALECYEEALRLDPGSVQAWHGKGITYRAMGIPSKAIDAIDSALTLDPEHAQ 258
                                    6789*************************************************7665 PP

  == domain 6  score: 26.5 bits;  conditional E-value: 1.3e-08
                          TPR_9  12 eralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                    ++a+ ++++ l l+P++++ ++  G+    +G ++ Al+++++ l+++p ++ a
  gi|116753411|ref|YP_842529.1| 240 SKAIDAIDSALTLDPEHAQSWYAKGITFRAMGLYEDALECFDRVLRIDPGNASA 293
                                    589**********************************************77666 PP

  == domain 7  score: 24.5 bits;  conditional E-value: 5.8e-08
                          TPR_9  11 weralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                    +e al++ +r+l ++P  ++ +  R+  l+ lG++++Al + e +++++p ++da
  gi|116753411|ref|YP_842529.1| 273 YEDALECFDRVLRIDPGNASALKSRAWSLYNLGRYAEALSACEGAISVNPLDEDA 327
                                    789*********************************************9988876 PP

  == domain 8  score: 8.5 bits;  conditional E-value: 0.0056
                          TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsa 47 
                                     ++++al ++e  + ++P d + ++  G++l  lG++ +
  gi|116753411|ref|YP_842529.1| 305 GRYAEALSACEGAISVNPLDEDAWYNMGIVLKALGRYTE 343
                                    58999******************************9965 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.2    0.0025      0.97       2      31 ..       6      35 ..       5      35 .. 0.81
   2 ?    3.1   0.0      0.47   1.9e+02      15      31 ..      53      69 ..      44      70 .. 0.88
   3 ?    5.8   0.0     0.062        24      13      31 ..      85     103 ..      76     105 .. 0.81
   4 !   12.6   0.0   0.00044      0.17       7      31 ..     128     152 ..     124     153 .. 0.90
   5 ?    8.2   0.0     0.011       4.3       6      31 ..     161     186 ..     160     188 .. 0.89
   6 !   15.6   0.0   4.8e-05     0.019       5      33 .]     194     222 ..     191     222 .. 0.94
   7 ?    3.8   0.0      0.28   1.1e+02       2      32 ..     225     255 ..     224     256 .. 0.83
   8 !   10.5   0.0    0.0021      0.81       3      32 ..     260     289 ..     258     290 .. 0.87
   9 ?    6.7   0.0     0.032        13       6      27 ..     297     318 ..     296     323 .. 0.84
  10 ?    6.0   0.0     0.053        21       1      23 [.     326     348 ..     326     354 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0025
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHH-T CS
                          TPR_6  2 AlyklalsyrklgdtdkAlealerlikeYP 31
                                   Al++ a+  +  g +d+A+e+++r+++  P
  gi|116753411|ref|YP_842529.1|  6 ALLQKAEEKYLDGSYDEAIEYYDRVLDIDP 35
                                   6777777777757************99766 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.47
                                   HHHHHHHHHHHHHHH-T CS
                          TPR_6 15 dtdkAlealerlikeYP 31
                                   ++++Ale + r i+  P
  gi|116753411|ref|YP_842529.1| 53 RYEDALECYSRAIEADP 69
                                   799**********9888 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.062
                                    HHHHHHHHHHHHHHHHH-T CS
                          TPR_6  13 lgdtdkAlealerlikeYP 31 
                                    lg+ d+A+  +++ i++ P
  gi|116753411|ref|YP_842529.1|  85 LGRCDEAISSYQEAIDRDP 103
                                    36889***********998 PP

  == domain 4  score: 12.6 bits;  conditional E-value: 0.00044
                                    HHHHHHHHHHHHHHHHHHHHHHH-T CS
                          TPR_6   7 alsyrklgdtdkAlealerlikeYP 31 
                                    +l+++++g++++A+ea++  ++  P
  gi|116753411|ref|YP_842529.1| 128 GLALLSMGRYEEAIEAYRMALDIDP 152
                                    89999*9************999877 PP

  == domain 5  score: 8.2 bits;  conditional E-value: 0.011
                                    HHHHHHHHHHHHHHHHHHHHHHHH-T CS
                          TPR_6   6 lalsyrklgdtdkAlealerlikeYP 31 
                                    l++s++  g++++Ale +er ++  P
  gi|116753411|ref|YP_842529.1| 161 LGESLQTIGRHSEALECFERALELSP 186
                                    799999978************99877 PP

  == domain 6  score: 15.6 bits;  conditional E-value: 4.8e-05
                                    HHHHHHHHHHHHHHHHHHHHHHHHH-TT- CS
                          TPR_6   5 klalsyrklgdtdkAlealerlikeYPdS 33 
                                    ++++s+ ++g++d+Ale +e+ ++  P+S
  gi|116753411|ref|YP_842529.1| 194 RMGESMHSTGRYDEALECYEEALRLDPGS 222
                                    89******99**************99987 PP

  == domain 7  score: 3.8 bits;  conditional E-value: 0.28
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                          TPR_6   2 AlyklalsyrklgdtdkAlealerlikeYPd 32 
                                    A    +  yr++g ++kA++a ++ ++  P+
  gi|116753411|ref|YP_842529.1| 225 AWHGKGITYRAMGIPSKAIDAIDSALTLDPE 255
                                    55667899*************9999888776 PP

  == domain 8  score: 10.5 bits;  conditional E-value: 0.0021
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                          TPR_6   3 lyklalsyrklgdtdkAlealerlikeYPd 32 
                                     y  +  +r++g +++Ale ++r+++  P+
  gi|116753411|ref|YP_842529.1| 260 WYAKGITFRAMGLYEDALECFDRVLRIDPG 289
                                    56678899999**************99986 PP

  == domain 9  score: 6.7 bits;  conditional E-value: 0.032
                                    HHHHHHHHHHHHHHHHHHHHHH CS
                          TPR_6   6 lalsyrklgdtdkAlealerli 27 
                                    +a+s+++lg++++Al a e  i
  gi|116753411|ref|YP_842529.1| 297 RAWSLYNLGRYAEALSACEGAI 318
                                    59*****99******9977655 PP

  == domain 10  score: 6.0 bits;  conditional E-value: 0.053
                                    HHHHHHHHHHHHHHHHHHHHHHH CS
                          TPR_6   1 dAlyklalsyrklgdtdkAleal 23 
                                    dA y+++  +++lg+++++  a+
  gi|116753411|ref|YP_842529.1| 326 DAWYNMGIVLKALGRYTESDMAF 348
                                    89**********99***999888 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 !   14.1   0.2    0.0001     0.041      26      81 ..       7      63 ..       3      64 .. 0.90
   2 !   16.2   0.4   2.3e-05    0.0089       5      81 ..      20      97 ..      19     101 .. 0.89
   3 !   25.8   0.0   2.4e-08   9.2e-06       8      81 ..     106     180 ..     104     181 .. 0.96
   4 !   16.3   0.0   2.2e-05    0.0086      31      81 ..     163     214 ..     161     215 .. 0.91
   5 !   18.9   0.0   3.4e-06    0.0013       2      81 ..     202     282 ..     201     283 .. 0.96
   6 !   24.3   0.0   6.9e-08   2.7e-05       3      77 ..     271     346 ..     269     351 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 0.0001
                                   HHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                         ANAPC3 26 ayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81
                                   ++ +A+  yl+g y++A+e++++  ++++ + +++   + +++  ++ye+A+ ++++
  gi|116753411|ref|YP_842529.1|  7 LLQKAEEKYLDGSYDEAIEYYDRVlDIDPMNTAAWCGRGMACFCFSRYEDALECYSR 63
                                   45568888********************************************99865 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 2.3e-05
                                   HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                         ANAPC3  5 yknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81
                                   y++Ai +++r+l  ++ +  +    + + +  ++y+ A+e +++a + +++   ++ + A++l+ L++ +eAi+ +++
  gi|116753411|ref|YP_842529.1| 20 YDEAIEYYDRVLDIDPMNTAAWCGRGMACFCFSRYEDALECYSRAiEADPECVPAWECRAEVLFILGRCDEAISSYQE 97
                                   99**********666666666666799**********************************************98876 PP

  == domain 3  score: 25.8 bits;  conditional E-value: 2.4e-08
                                    HHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                         ANAPC3   8 AiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                    A+ ++er   + ++++e+   ++l+l+++g+y++A+e +r a +++++  + + +++++l  ++++ eA+ ++e+
  gi|116753411|ref|YP_842529.1| 106 ALAWIERCIDSRPDDAESWRQKGLALLSMGRYEEAIEAYRMAlDIDPSQARDWCILGESLQTIGRHSEALECFER 180
                                    88999****999999999999***************************************************997 PP

  == domain 4  score: 16.3 bits;  conditional E-value: 2.2e-05
                                    HHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                         ANAPC3  31 lclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                    ++l   g++ +A+e +++a +l +++ +c++ ++++    ++y+eA+ ++e+
  gi|116753411|ref|YP_842529.1| 163 ESLQTIGRHSEALECFERAlELSPSDSACWIRMGESMHSTGRYDEALECYEE 214
                                    5666678999**************************************9987 PP

  == domain 5  score: 18.9 bits;  conditional E-value: 3.4e-06
                                    TT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                         ANAPC3   2 qnnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                    +++y++A+ ++e +l  ++ s ++ + ++ ++  +g   +A++ +++a  l++++ +++y ++ +  +++ ye+A+ +++
  gi|116753411|ref|YP_842529.1| 202 TGRYDEALECYEEALRLDPGSVQAWHGKGITYRAMGIPSKAIDAIDSAlTLDPEHAQSWYAKGITFRAMGLYEDALECFD 281
                                    579**************************************************************************998 PP

                                    S CS
                         ANAPC3  81 k 81 
                                    +
  gi|116753411|ref|YP_842529.1| 282 R 282
                                    6 PP

  == domain 6  score: 24.3 bits;  conditional E-value: 6.9e-08
                                    T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHH CS
                         ANAPC3   3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAia 77 
                                    + y++A+ +++r+l  ++ +++++   A +ly++g+y +A+  ++ a   n+ ++ ++y ++ +l +L++y e  +
  gi|116753411|ref|YP_842529.1| 271 GLYEDALECFDRVLRIDPGNASALKSRAWSLYNLGRYAEALSACEGAiSVNPLDEDAWYNMGIVLKALGRYTESDM 346
                                    68************9999999999999********************************************99655 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0      0.11        41      16      31 ..      18      33 ..      14      33 .. 0.88
   2 ?    2.4   0.0      0.39   1.5e+02      25      39 ..      54      68 ..      46      70 .. 0.79
   3 ?    4.2   0.0      0.11        42       9      30 ..      79     100 ..      78     101 .. 0.88
   4 !    9.0   0.2    0.0033       1.3       9      31 ..     128     150 ..     127     150 .. 0.91
   5 !   10.8   0.0   0.00087      0.34       8      31 ..     161     184 ..     161     185 .. 0.92
   6 !   13.4   0.1   0.00014     0.053      13      30 ..     200     217 ..     195     218 .. 0.88
   7 ?    4.7   0.0     0.072        28       9      31 ..     264     286 ..     263     286 .. 0.84
   8 !    9.8   0.1    0.0019      0.74       8      30 ..     297     319 ..     291     321 .. 0.84
   9 !    8.2   0.0    0.0061       2.4       7      32 ..     330     355 ..     329     361 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.11
                         TPR_10 16 grydeAealleealai 31
                                   g ydeA ++++++l+i
  gi|116753411|ref|YP_842529.1| 18 GSYDEAIEYYDRVLDI 33
                                   789**********986 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.39
                         TPR_10 25 leealairrrllGpd 39
                                   +e+al+++ r+ ++d
  gi|116753411|ref|YP_842529.1| 54 YEDALECYSRAIEAD 68
                                   688888888877666 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.11
                         TPR_10   9 analrqrgrydeAealleeala 30 
                                    a +l+ +gr deA   ++ea++
  gi|116753411|ref|YP_842529.1|  79 AEVLFILGRCDEAISSYQEAID 100
                                    6688999*************97 PP

  == domain 4  score: 9.0 bits;  conditional E-value: 0.0033
                         TPR_10   9 analrqrgrydeAealleealai 31 
                                    + al ++gry+eA + ++ al+i
  gi|116753411|ref|YP_842529.1| 128 GLALLSMGRYEEAIEAYRMALDI 150
                                    68999*************99976 PP

  == domain 5  score: 10.8 bits;  conditional E-value: 0.00087
                         TPR_10   8 LanalrqrgrydeAealleealai 31 
                                    L+  l+  gr+ eA++ +e+al++
  gi|116753411|ref|YP_842529.1| 161 LGESLQTIGRHSEALECFERALEL 184
                                    78899999**************96 PP

  == domain 6  score: 13.4 bits;  conditional E-value: 0.00014
                         TPR_10  13 rqrgrydeAealleeala 30 
                                    +++grydeA++ +eeal+
  gi|116753411|ref|YP_842529.1| 200 HSTGRYDEALECYEEALR 217
                                    679*************97 PP

  == domain 7  score: 4.7 bits;  conditional E-value: 0.072
                         TPR_10   9 analrqrgrydeAealleealai 31 
                                    +++ r++g y++A++ ++++l+i
  gi|116753411|ref|YP_842529.1| 264 GITFRAMGLYEDALECFDRVLRI 286
                                    67778999999999999999876 PP

  == domain 8  score: 9.8 bits;  conditional E-value: 0.0019
                         TPR_10   8 LanalrqrgrydeAealleeala 30 
                                     a  l+++gry+eA+  +e a++
  gi|116753411|ref|YP_842529.1| 297 RAWSLYNLGRYAEALSACEGAIS 319
                                    5889***************9997 PP

  == domain 9  score: 8.2 bits;  conditional E-value: 0.0061
                         TPR_10   7 NLanalrqrgrydeAealleealair 32 
                                    N++++l ++gry+e+   +++a +ir
  gi|116753411|ref|YP_842529.1| 330 NMGIVLKALGRYTESDMAFIKAREIR 355
                                    9**************99999998887 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0029       1.1      15      35 ..      18      38 ..      14      40 .. 0.91
   2 ?    3.5   0.0      0.19        74      11      34 ..      48      71 ..      45      75 .. 0.86
   3 ?    6.8   0.0     0.019       7.3       9      33 ..     129     153 ..     127     156 .. 0.89
   4 ?    4.1   0.0      0.12        48      14      33 ..     168     187 ..     167     190 .. 0.91
   5 !    8.2   0.0    0.0067       2.6      15      37 ..     203     225 ..     201     227 .. 0.93
   6 ?   -0.9   0.0       4.6   1.8e+03      18      36 ..     240     258 ..     240     259 .. 0.87
   7 !   13.7   0.0   0.00013     0.051      14      38 ..     270     294 ..     269     296 .. 0.92
   8 !    8.2   0.0    0.0066       2.6      11      36 ..     301     326 ..     297     328 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0029
                                   T-HHHHHHHHHHHHHHTTS-H CS
                     Fis1_TPR_C 15 geYseArryvdalLeiEPenr 35
                                   g Y+eA +y d++L i+P n 
  gi|116753411|ref|YP_842529.1| 18 GSYDEAIEYYDRVLDIDPMNT 38
                                   78****************996 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.19
                                   HHHHT-HHHHHHHHHHHHHHTTS- CS
                     Fis1_TPR_C 11 hyklgeYseArryvdalLeiEPen 34
                                   ++   +Y++A+++  + +e +Pe+
  gi|116753411|ref|YP_842529.1| 48 CFCFSRYEDALECYSRAIEADPEC 71
                                   556679****************96 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.019
                                    HHHHHHT-HHHHHHHHHHHHHHTTS CS
                     Fis1_TPR_C   9 lGhyklgeYseArryvdalLeiEPe 33 
                                    l+ + +g+Y+eA +  ++ L i+P+
  gi|116753411|ref|YP_842529.1| 129 LALLSMGRYEEAIEAYRMALDIDPS 153
                                    567789*****************96 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.12
                                    HT-HHHHHHHHHHHHHHTTS CS
                     Fis1_TPR_C  14 lgeYseArryvdalLeiEPe 33 
                                    +g++seA+++ ++ Le+ P+
  gi|116753411|ref|YP_842529.1| 168 IGRHSEALECFERALELSPS 187
                                    689**************997 PP

  == domain 5  score: 8.2 bits;  conditional E-value: 0.0067
                                    T-HHHHHHHHHHHHHHTTS-HHH CS
                     Fis1_TPR_C  15 geYseArryvdalLeiEPenrQa 37 
                                    g+Y+eA+++ +  L+++P+  Qa
  gi|116753411|ref|YP_842529.1| 203 GRYDEALECYEEALRLDPGSVQA 225
                                    89****************99998 PP

  == domain 6  score: -0.9 bits;  conditional E-value: 4.6
                                    HHHHHHHHHHHHHTTS-HH CS
                     Fis1_TPR_C  18 seArryvdalLeiEPenrQ 36 
                                    s+A   +d  L ++Pe  Q
  gi|116753411|ref|YP_842529.1| 240 SKAIDAIDSALTLDPEHAQ 258
                                    5788999********9888 PP

  == domain 7  score: 13.7 bits;  conditional E-value: 0.00013
                                    HT-HHHHHHHHHHHHHHTTS-HHHH CS
                     Fis1_TPR_C  14 lgeYseArryvdalLeiEPenrQaq 38 
                                    +g Y++A+++ d++L+i+P+n  a+
  gi|116753411|ref|YP_842529.1| 270 MGLYEDALECFDRVLRIDPGNASAL 294
                                    678******************9986 PP

  == domain 8  score: 8.2 bits;  conditional E-value: 0.0066
                                    HHHHT-HHHHHHHHHHHHHHTTS-HH CS
                     Fis1_TPR_C  11 hyklgeYseArryvdalLeiEPenrQ 36 
                                     y lg+Y eA+  ++  +++ P  + 
  gi|116753411|ref|YP_842529.1| 301 LYNLGRYAEALSACEGAISVNPLDED 326
                                    699****************9997765 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       3.8   1.5e+03     159     180 ..      17      38 ..       5      41 .. 0.72
   2 ?    5.0   0.0      0.03        12     148     178 ..      74     104 ..      51     110 .. 0.83
   3 ?    3.3   0.1       0.1        40     144     178 ..     119     153 ..     107     157 .. 0.80
   4 !   10.8   0.0   0.00052       0.2     145     180 ..     154     189 ..     151     191 .. 0.92
   5 !   17.5   0.0   4.7e-06    0.0019     145     182 ..     188     225 ..     187     229 .. 0.93
   6 ?   -1.6   0.0       3.1   1.2e+03     156     179 ..     233     256 ..     231     259 .. 0.87
   7 !   13.8   0.1   6.6e-05     0.026     145     229 ..     256     340 ..     240     344 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.8
                         TPR_15 159 egqtdaAlrdyreAlalapdss 180
                                     g  d+A++ y ++l+ +p ++
  gi|116753411|ref|YP_842529.1|  17 DGSYDEAIEYYDRVLDIDPMNT 38 
                                    5777888899999988888776 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.03
                         TPR_15 148 fllaraelyrqegqtdaAlrdyreAlalapd 178
                                     +  rae+    g+ d+A+  y+eA++++p+
  gi|116753411|ref|YP_842529.1|  74 AWECRAEVLFILGRCDEAISSYQEAIDRDPA 104
                                    5889999999999999999999999999997 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.1
                         TPR_15 144 qsaafllaraelyrqegqtdaAlrdyreAlalapd 178
                                    ++a  +   + + +  g+ ++A+++yr Al+ +p 
  gi|116753411|ref|YP_842529.1| 119 DDAESWRQKGLALLSMGRYEEAIEAYRMALDIDPS 153
                                    56677777777888889999999999999999886 PP

  == domain 4  score: 10.8 bits;  conditional E-value: 0.00052
                         TPR_15 145 saafllaraelyrqegqtdaAlrdyreAlalapdss 180
                                    +a+ + +++e+ +  g++ +Al+++++Al+l+p +s
  gi|116753411|ref|YP_842529.1| 154 QARDWCILGESLQTIGRHSEALECFERALELSPSDS 189
                                    67789****************************997 PP

  == domain 5  score: 17.5 bits;  conditional E-value: 4.7e-06
                         TPR_15 145 saafllaraelyrqegqtdaAlrdyreAlalapdssel 182
                                    ++a +++++e+   +g+ d+Al++y+eAl+l+p+s ++
  gi|116753411|ref|YP_842529.1| 188 DSACWIRMGESMHSTGRYDEALECYEEALRLDPGSVQA 225
                                    7899******************************9876 PP

  == domain 6  score: -1.6 bits;  conditional E-value: 3.1
                         TPR_15 156 yrqegqtdaAlrdyreAlalapds 179
                                    yr+ g + +A+ ++  Al+l+p+ 
  gi|116753411|ref|YP_842529.1| 233 YRAMGIPSKAIDAIDSALTLDPEH 256
                                    78889999*************986 PP

  == domain 7  score: 13.8 bits;  conditional E-value: 6.6e-05
                         TPR_15 145 saafllaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkara...esdasLwgpla 221
                                     a+ ++a +   r+ g  ++Al+++ ++l+ +p+++++ +   W l +lgr+ae   +l+a +++      d++ w  ++
  gi|116753411|ref|YP_842529.1| 256 HAQSWYAKGITFRAMGLYEDALECFDRVLRIDPGNASALKSRAWSLYNLGRYAE---ALSACEGAIsvnPLDEDAWYNMG 332
                                    688999999999*****************************************8...77777776655555566666666 PP

                         TPR_15 222 aAlllLgr 229
                                      l +Lgr
  gi|116753411|ref|YP_842529.1| 333 IVLKALGR 340
                                    55555555 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.1   0.00037      0.14      62     122 ..       4      64 ..       2      68 .. 0.92
   2 ?    3.1   0.0      0.29   1.1e+02      64      93 ..      74     103 ..      67     109 .. 0.83
   3 !   10.4   0.1    0.0017      0.66      85     122 ..     110     147 ..     104     155 .. 0.86
   4 !   14.7   0.2   7.9e-05     0.031      72     124 ..     165     217 ..     160     219 .. 0.92
   5 ?    1.4   0.0         1     4e+02      79     123 ..     240     284 ..     232     291 .. 0.81
   6 !   15.8   0.0   3.8e-05     0.015      56     115 ..     285     344 ..     273     360 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00037
                                    HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                           BTAD  62 lealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                    ++al + ae++   G ++ea++++++ ++ +P++ ++++    A ++  r ++ALe Y r+
  gi|116753411|ref|YP_842529.1|   4 IAALLQKAEEKYLDGSYDEAIEYYDRVLDIDPMNTAAWCGRGMACFCFSRYEDALECYSRA 64 
                                    677788889899999*******************************************997 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.29
                                    HHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                           BTAD  64 alealaeaelrlGraeealaelealvaehP 93 
                                    a e +ae ++ lGr +ea++ ++++++ +P
  gi|116753411|ref|YP_842529.1|  74 AWECRAEVLFILGRCDEAISSYQEAIDRDP 103
                                    677888999999999999999999998888 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.0017
                                    HHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                           BTAD  85 lealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                     e+ ++  P + +++rq  +Al  +Gr +eA+e+Y+ +
  gi|116753411|ref|YP_842529.1| 110 IERCIDSRPDDAESWRQKGLALLSMGRYEEAIEAYRMA 147
                                    678888999999***********************976 PP

  == domain 4  score: 14.7 bits;  conditional E-value: 7.9e-05
                                    HHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           BTAD  72 elrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                    + ++Gr++eal+  e+++++ P + + +  + +  + +Gr  eALe Ye++ r
  gi|116753411|ref|YP_842529.1| 165 LQTIGRHSEALECFERALELSPSDSACWIRMGESMHSTGRYDEALECYEEALR 217
                                    5679*********************************************9865 PP

  == domain 5  score: 1.4 bits;  conditional E-value: 1
                                    HHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                           BTAD  79 eealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlr 123
                                    ++a++  +++++++P + +++ +     +++G  ++ALe ++r+ 
  gi|116753411|ref|YP_842529.1| 240 SKAIDAIDSALTLDPEHAQSWYAKGITFRAMGLYEDALECFDRVL 284
                                    678888888899999999999988888999999999999988875 PP

  == domain 6  score: 15.8 bits;  conditional E-value: 3.8e-05
                                    HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHH CS
                           BTAD  56 rleelrlealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeA 115
                                    r++    +al+++a  +  lGr++eal+  e++++ +Pl+E+++  +   l ++Gr  e 
  gi|116753411|ref|YP_842529.1| 285 RIDPGNASALKSRAWSLYNLGRYAEALSACEGAISVNPLDEDAWYNMGIVLKALGRYTES 344
                                    55555678999999999****************************999999999997776 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   1.1      0.01       3.9       6      29 ..       6      29 ..       5      33 .. 0.88
   2 ?    6.2   0.2     0.028        11      19      32 ..      53      66 ..      52      67 .. 0.91
   3 ?    4.8   0.0     0.074        29      19      32 ..      87     100 ..      85     101 .. 0.87
   4 !    8.6   0.0    0.0048       1.9      16      32 ..     133     149 ..     121     150 .. 0.84
   5 ?    1.3   0.0      0.94   3.7e+02      19      33 ..     170     184 ..     166     185 .. 0.82
   6 !   10.8   0.0   0.00098      0.38      16      32 ..     201     217 ..     193     218 .. 0.84
   7 ?    5.1   0.0     0.062        24      23      40 ..     269     287 ..     240     299 .. 0.83
   8 ?   -0.5   0.0       3.5   1.4e+03       4      25 ..     291     312 ..     289     319 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.01
                            MIT  6 elvkkAveeDnagnyeeAlelYke 29
                                   +l++kA e+   g y+eA+e+Y  
  gi|116753411|ref|YP_842529.1|  6 ALLQKAEEKYLDGSYDEAIEYYDR 29
                                   6899******************86 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.028
                            MIT 19 nyeeAlelYkeale 32
                                    ye+Ale+Y+ a+e
  gi|116753411|ref|YP_842529.1| 53 RYEDALECYSRAIE 66
                                   69**********98 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.074
                            MIT  19 nyeeAlelYkeale 32 
                                      +eA++ Y+ea++
  gi|116753411|ref|YP_842529.1|  87 RCDEAISSYQEAID 100
                                    568*********98 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.0048
                            MIT  16 nagnyeeAlelYkeale 32 
                                    + g yeeA+e+Y+ al+
  gi|116753411|ref|YP_842529.1| 133 SMGRYEEAIEAYRMALD 149
                                    6699***********98 PP

  == domain 5  score: 1.3 bits;  conditional E-value: 0.94
                            MIT  19 nyeeAlelYkealel 33 
                                      +eAle+++ alel
  gi|116753411|ref|YP_842529.1| 170 RHSEALECFERALEL 184
                                    678999999999986 PP

  == domain 6  score: 10.8 bits;  conditional E-value: 0.00098
                            MIT  16 nagnyeeAlelYkeale 32 
                                    + g y+eAle+Y+eal+
  gi|116753411|ref|YP_842529.1| 201 STGRYDEALECYEEALR 217
                                    6799***********97 PP

  == domain 7  score: 5.1 bits;  conditional E-value: 0.062
                            MIT  23 AlelYkealelLlqalk.e 40 
                                    A+ lY++ale +  +l+  
  gi|116753411|ref|YP_842529.1| 269 AMGLYEDALECFDRVLRiD 287
                                    899**********999843 PP

  == domain 8  score: -0.5 bits;  conditional E-value: 3.5
                            MIT   4 AlelvkkAveeDnagnyeeAle 25 
                                    A +l ++A  + n g y+eAl+
  gi|116753411|ref|YP_842529.1| 291 ASALKSRAWSLYNLGRYAEALS 312
                                    6677778888889999999997 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.2    0.0073       2.8      12      25 ..      15      28 ..      11      32 .. 0.86
   2 ?   -0.1   0.0       2.4   9.5e+02      16      25 ..      53      62 ..      52      70 .. 0.83
   3 !    9.5   0.0    0.0024      0.95      13      33 ..     133     151 ..     128     153 .. 0.83
   4 ?    6.8   0.0     0.017       6.8      12      27 ..     200     213 ..     197     220 .. 0.83
   5 ?    1.3   0.0      0.95   3.7e+02       4      28 ..     260     283 ..     259     286 .. 0.78
   6 ?    5.3   0.0     0.053        20       8      21 ..     298     311 ..     293     313 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0073
                                   HHTT-HHHHHHH.. CS
                          TPR_3 12 ynkkkyqeArelfs 25
                                   y+ + y+eA+e+++
  gi|116753411|ref|YP_842529.1| 15 YLDGSYDEAIEYYD 28
                                   88899*******98 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 2.4
                                   -HHHHHHH.. CS
                          TPR_3 16 kyqeArelfs 25
                                   +y++A+e +s
  gi|116753411|ref|YP_842529.1| 53 RYEDALECYS 62
                                   799***9988 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0024
                                    HTT-HHHHHHH..HHHHHHH- CS
                          TPR_3  13 nkkkyqeArelfsYallaild 33 
                                    ++++y+eA+e+  Y+ +  +d
  gi|116753411|ref|YP_842529.1| 133 SMGRYEEAIEA--YRMALDID 151
                                    69*********..99987666 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.017
                                    HHTT-HHHHHHH..HH CS
                          TPR_3  12 ynkkkyqeArelfsYa 27 
                                    ++ ++y+eA+e   Y+
  gi|116753411|ref|YP_842529.1| 200 HSTGRYDEALEC--YE 213
                                    999********9..75 PP

  == domain 5  score: 1.3 bits;  conditional E-value: 0.95
                                    HHHHHHHHHHTT-HHHHHHH..HHH CS
                          TPR_3   4 lysyAaefynkkkyqeArelfsYal 28 
                                    +y+ + +f  ++ y++A+e f+ ++
  gi|116753411|ref|YP_842529.1| 260 WYAKGITFRAMGLYEDALECFD-RV 283
                                    6666777778999******998.55 PP

  == domain 6  score: 5.3 bits;  conditional E-value: 0.053
                                    HHHHHHTT-HHHHH CS
                          TPR_3   8 AaefynkkkyqeAr 21 
                                    A ++yn ++y eA+
  gi|116753411|ref|YP_842529.1| 298 AWSLYNLGRYAEAL 311
                                    789**********7 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1     0.068        26      13      64 ..       8      57 ..       2      67 .. 0.60
   2 !   13.1   0.1   0.00019     0.073      68     128 ..      92     149 ..      54     155 .. 0.78
   3 ?    4.5   0.0     0.087        34     107     129 ..     162     184 ..     155     187 .. 0.83
   4 ?    7.3   0.0     0.012       4.8      54      83 ..     188     217 ..     185     220 .. 0.85
   5 ?    4.0   0.0      0.12        47     101     124 ..     292     315 ..     261     326 .. 0.73
   6 ?    3.2   0.0      0.22        85     103     124 ..     294     315 ..     291     358 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.068
                                   HHHHHHHHHHT-HHHHHHHHHHHHHHHTTS-TTS---HHHHHHHHHHHHHHH CS
                        DUF3856 13 lseaekqleegayeeaaasyrkalevsrtipaeeafdheGfdalchaglsea 64
                                   l +ae++  +g+y+ea + y + l++     +  a+   G+  +c++   +a
  gi|116753411|ref|YP_842529.1|  8 LQKAEEKYLDGSYDEAIEYYDRVLDIDPM--NTAAWCGRGMACFCFSRYEDA 57
                                   56777777777888888777777776532..223444555555555544444 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00019
                                    TT-HHHHHHH.HHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                        DUF3856  68 lgrydeales.adkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmage 128
                                    + +y+ea+    + al + +r  + + d+ + W     +++ al ++Gr++ea++a+rma +
  gi|116753411|ref|YP_842529.1|  92 ISSYQEAIDRdPAYALAWIERCIDSRPDDAESWR----QKGLALLSMGRYEEAIEAYRMALD 149
                                    3445555432134578899999999999999995....79*******************976 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.087
                                    HHHHHHTT-HHHHHHHHHHHHHH CS
                        DUF3856 107 avaleelGrkdealkafrmagem 129
                                    + +l+ +Gr++eal+ f+ a e+
  gi|116753411|ref|YP_842529.1| 162 GESLQTIGRHSEALECFERALEL 184
                                    56789999999999999998875 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.012
                                    HHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                        DUF3856  54 dalchaglsealaklgrydealesadkalr 83 
                                    d+ c+  + e++   grydeale+ ++alr
  gi|116753411|ref|YP_842529.1| 188 DSACWIRMGESMHSTGRYDEALECYEEALR 217
                                    677888889999999999999999999987 PP

  == domain 5  score: 4.0 bits;  conditional E-value: 0.12
                                    HHHHHHHHHHHHTT-HHHHHHHHH CS
                        DUF3856 101 aavfsravaleelGrkdealkafr 124
                                    +a+ sra +l +lGr++eal a +
  gi|116753411|ref|YP_842529.1| 292 SALKSRAWSLYNLGRYAEALSACE 315
                                    567777777778888777776654 PP

  == domain 6  score: 3.2 bits;  conditional E-value: 0.22
                                    HHHHHHHHHHTT-HHHHHHHHH CS
                        DUF3856 103 vfsravaleelGrkdealkafr 124
                                    + sra +l +lGr++eal a +
  gi|116753411|ref|YP_842529.1| 294 LKSRAWSLYNLGRYAEALSACE 315
                                    5566666666666666665543 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0059       2.3     207     256 ..      53     102 ..      26     105 .. 0.81
   2 ?    5.9   0.0     0.013       5.1     207     256 ..     100     151 ..      94     160 .. 0.81
   3 !   16.8   0.0   6.3e-06    0.0025     188     256 ..     187     253 ..     159     256 .. 0.82
   4 ?    1.7   0.0      0.24        94      14      77 ..     267     331 ..     255     352 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0059
                                    -SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
                          NARP1 207 srekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                                    ++e Ale+ ++aie +p++v  +  +a++l   G  ++A++  +ea   D
  gi|116753411|ref|YP_842529.1|  53 RYEDALECYSRAIEADPECVPAWECRAEVLFILGRCDEAISSYQEAIDRD 102
                                    57788888888888888888888888888888888888888777775555 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.013
                                    -SH..HHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
                          NARP1 207 sre..kAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                                    +r+   Al  i+++i++ p   e + +K+  l  +G  ++A+e+   a  +D
  gi|116753411|ref|YP_842529.1| 100 DRDpaYALAWIERCIDSRPDDAESWRQKGLALLSMGRYEEAIEAYRMALDID 151
                                    4444478999999999999999999999999999999999999887776666 PP

  == domain 3  score: 16.8 bits;  conditional E-value: 6.3e-06
                                    SSHHHHHHHHHHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
                          NARP1 188 esallwvlyflAqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                                      + +w+ +  ++h   +g++++Ale+ ++a++ +p +v+ +  K+  ++ +G ++kA++++++a  lD
  gi|116753411|ref|YP_842529.1| 187 SDSACWIRMGESMH--STGRYDEALECYEEALRLDPGSVQAWHGKGITYRAMGIPSKAIDAIDSALTLD 253
                                    55556666555555..5799**********************************************999 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.24
                                    HHHHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-T.T-CHHHHH CS
                          NARP1  14 ieeagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernp.enskYyeg 77 
                                    ++  g +e+Ale ++++ +    + + ++ +a  l +Lgr++eA ++ e  ++ np ++ ++y+ 
  gi|116753411|ref|YP_842529.1| 267 FRAMGLYEDALECFDRVLRIDPGNASALKSRAWSLYNLGRYAEALSACEGAISVNPlDEDAWYNM 331
                                    56677788888888888777777788888888899999999999999888888887455555543 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       5.8   2.3e+03      24      43 ..       6      25 ..       4      37 .. 0.84
   2 ?    1.6   0.0      0.89   3.5e+02      11      55 ..      61     105 ..      52     107 .. 0.85
   3 !   10.0   0.0    0.0021      0.83       8      52 ..     107     151 ..     100     158 .. 0.83
   4 ?    7.6   0.0     0.012       4.6       4      44 ..     171     211 ..     169     222 .. 0.88
   5 ?    4.5   0.0      0.11        43       6      53 ..     241     288 ..     239     298 .. 0.90
   6 ?    1.4   0.0       1.1   4.1e+02       6      40 ..     309     343 ..     306     350 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 5.8
                         TPR_20 24 arldlAlallaagryeeAle 43
                                   a l+ A+  +  g y+eA+e
  gi|116753411|ref|YP_842529.1|  6 ALLQKAEEKYLDGSYDEAIE 25
                                   67889999999*******98 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.89
                         TPR_20  11 leaalaanpddldarldlAlallaagryeeAleqLleilkrdrkw 55 
                                      +a++a+p+ + a    A++l+  gr +eA++   e + rd ++
  gi|116753411|ref|YP_842529.1|  61 YSRAIEADPECVPAWECRAEVLFILGRCDEAISSYQEAIDRDPAY 105
                                    567899999999999999999**********99999999998776 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.0021
                         TPR_20   8 laeleaalaanpddldarldlAlallaagryeeAleqLleilkrd 52 
                                    la +e+ + ++pdd +   +  lall+ gryeeA+e+  + l  d
  gi|116753411|ref|YP_842529.1| 107 LAWIERCIDSRPDDAESWRQKGLALLSMGRYEEAIEAYRMALDID 151
                                    566788899**************************9876666655 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.012
                         TPR_20   4 dapelaeleaalaanpddldarldlAlallaagryeeAleq 44 
                                    +++ l+ +e+al+ +p+d +  + + +  ++ gry+eAle 
  gi|116753411|ref|YP_842529.1| 171 HSEALECFERALELSPSDSACWIRMGESMHSTGRYDEALEC 211
                                    567788899******************************85 PP

  == domain 5  score: 4.5 bits;  conditional E-value: 0.11
                         TPR_20   6 pelaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdr 53 
                                    + ++++++al+ +p+  +  ++      a g ye+Ale + ++l+ d 
  gi|116753411|ref|YP_842529.1| 241 KAIDAIDSALTLDPEHAQSWYAKGITFRAMGLYEDALECFDRVLRIDP 288
                                    578999********************************9988888876 PP

  == domain 6  score: 1.4 bits;  conditional E-value: 1.1
                         TPR_20   6 pelaeleaalaanpddldarldlAlallaagryee 40 
                                    + l++ e a+  np d da +++  +l a gry e
  gi|116753411|ref|YP_842529.1| 309 EALSACEGAISVNPLDEDAWYNMGIVLKALGRYTE 343
                                    568899999****************9999999987 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0       2.2   8.5e+02       7      20 ..      78      91 ..      73      93 .. 0.88
   2 ?    2.5   0.1      0.77     3e+02       8      24 ..     128     144 ..     121     146 .. 0.81
   3 ?    2.2   0.0         1   3.9e+02       7      26 .]     161     180 ..     151     180 .. 0.88
   4 ?    8.2   0.0     0.011       4.4       5      26 .]     193     214 ..     189     214 .. 0.85
   5 !    9.5   0.1    0.0044       1.7       7      23 ..     297     313 ..     291     315 .. 0.87
   6 ?    1.7   0.0       1.4   5.4e+02       3      18 ..     327     342 ..     326     344 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 2.2
                          TPR_4  7 LArallalGdldeA 20
                                   +A++l+ lG+ deA
  gi|116753411|ref|YP_842529.1| 78 RAEVLFILGRCDEA 91
                                   8*********9998 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.77
                          TPR_4   8 ArallalGdldeArall 24 
                                    + all  G+++eA ++ 
  gi|116753411|ref|YP_842529.1| 128 GLALLSMGRYEEAIEAY 144
                                    7899999******7665 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 1
                          TPR_4   7 LArallalGdldeAraller 26 
                                    L++ l+  G++ eA++ +er
  gi|116753411|ref|YP_842529.1| 161 LGESLQTIGRHSEALECFER 180
                                    78888888*******99987 PP

  == domain 4  score: 8.2 bits;  conditional E-value: 0.011
                          TPR_4   5 laLArallalGdldeAraller 26 
                                    + +++ ++ +G++deA++  e+
  gi|116753411|ref|YP_842529.1| 193 IRMGESMHSTGRYDEALECYEE 214
                                    667999999********99886 PP

  == domain 5  score: 9.5 bits;  conditional E-value: 0.0044
                          TPR_4   7 LArallalGdldeAral 23 
                                    +A+ l+ lG+++eA+ +
  gi|116753411|ref|YP_842529.1| 297 RAWSLYNLGRYAEALSA 313
                                    8*************976 PP

  == domain 6  score: 1.7 bits;  conditional E-value: 1.4
                          TPR_4   3 allaLArallalGdld 18 
                                    a ++++ +l alG++ 
  gi|116753411|ref|YP_842529.1| 327 AWYNMGIVLKALGRYT 342
                                    6799**********86 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.049        19     183     232 ..      20      69 ..      17      74 .. 0.86
   2 ?    2.5   0.0       0.2        79     208     235 ..      79     106 ..      73     123 .. 0.85
   3 ?    2.7   0.0      0.18        72     209     234 ..     129     154 ..     124     183 .. 0.84
   4 ?    2.4   0.0      0.21        83     213     233 ..     201     221 ..     167     257 .. 0.75
   5 !    9.8   0.0    0.0012      0.47     180     259 ..     270     349 ..     240     359 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.049
                                    HHHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-T CS
                     Coatomer_E 183 iqdAyyifqelsekykstplllngkAvvslllgryeeAeslLkeaLdkda 232
                                    + +A   ++ + +  +++++   g+ +++ +  rye+A +    a++ d+
  gi|116753411|ref|YP_842529.1|  20 YDEAIEYYDRVLDIDPMNTAAWCGRGMACFCFSRYEDALECYSRAIEADP 69 
                                    66777777777788889999999*********************999886 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.2
                                    HHHHHHTT-HHHHHHHHHHHHHH-TT-H CS
                     Coatomer_E 208 AvvslllgryeeAeslLkeaLdkdakde 235
                                    A v   lgr +eA s+ +ea+d+d+ ++
  gi|116753411|ref|YP_842529.1|  79 AEVLFILGRCDEAISSYQEAIDRDPAYA 106
                                    66778899****************9886 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.18
                                    HHHHHTT-HHHHHHHHHHHHHH-TT- CS
                     Coatomer_E 209 vvslllgryeeAeslLkeaLdkdakd 234
                                     + l +gryeeA +  + aLd d+ +
  gi|116753411|ref|YP_842529.1| 129 LALLSMGRYEEAIEAYRMALDIDPSQ 154
                                    567899***************98865 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.21
                                    HTT-HHHHHHHHHHHHHH-TT CS
                     Coatomer_E 213 llgryeeAeslLkeaLdkdak 233
                                     +gry+eA +  +eaL  d+ 
  gi|116753411|ref|YP_842529.1| 201 STGRYDEALECYEEALRLDPG 221
                                    478999999999999988776 PP

  == domain 5  score: 9.8 bits;  conditional E-value: 0.0012
                                    TTHHHHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHHHHHH CS
                     Coatomer_E 180 gekiqdAyyifqelsekykstplllngkAvvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevsernl 259
                                     + ++dA+  f+ +    + +   l+ +A     lgry+eA s  + a+  ++ de++  N+ ++ + lg+ +e+   ++
  gi|116753411|ref|YP_842529.1| 270 MGLYEDALECFDRVLRIDPGNASALKSRAWSLYNLGRYAEALSACEGAISVNPLDEDAWYNMGIVLKALGRYTESDMAFI 349
                                    456777777777777776778889999999999*************************************9999877666 PP

>> DUF5113  Domain of unknown function (DUF5113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.31   1.2e+02      14      37 ..      10      33 ..       3      39 .. 0.84
   2 ?    0.9   0.0      0.89   3.5e+02      13      36 ..      43      66 ..      27      68 .. 0.83
   3 ?    1.4   0.0      0.65   2.5e+02       8      36 ..     121     149 ..     114     150 .. 0.87
   4 ?    2.5   0.0      0.28   1.1e+02       8      36 ..     155     183 ..     153     185 .. 0.87
   5 ?    4.8   0.0     0.056        22      12      36 ..     193     217 ..     187     219 .. 0.87
   6 ?    3.7   0.0      0.12        47      15      49 ..     230     264 ..     222     277 .. 0.82
   7 ?    2.1   0.0      0.38   1.5e+02      10      36 ..     259     285 ..     255     286 .. 0.79
   8 ?   -0.2   0.0         2   7.8e+02      10      36 ..     293     319 ..     289     347 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.31
                        DUF5113 14 layylnvegeyeeALeyldsaley 37
                                    a + + +g+y+eA+ey d +l++
  gi|116753411|ref|YP_842529.1| 10 KAEEKYLDGSYDEAIEYYDRVLDI 33
                                   56778899************9975 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.89
                        DUF5113 13 nlayylnvegeyeeALeyldsale 36
                                     +++++   +ye+ALe+ + a+e
  gi|116753411|ref|YP_842529.1| 43 GRGMACFCFSRYEDALECYSRAIE 66
                                   5678899999*********99986 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.65
                        DUF5113   8 andYanlayylnvegeyeeALeyldsale 36 
                                    a+ +++ + +l   g+yeeA+e  + al+
  gi|116753411|ref|YP_842529.1| 121 AESWRQKGLALLSMGRYEEAIEAYRMALD 149
                                    78889999999999*********999997 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.28
                        DUF5113   8 andYanlayylnvegeyeeALeyldsale 36 
                                    a d+  l+  l + g+++eALe+++ ale
  gi|116753411|ref|YP_842529.1| 155 ARDWCILGESLQTIGRHSEALECFERALE 183
                                    66777888999999*************97 PP

  == domain 5  score: 4.8 bits;  conditional E-value: 0.056
                        DUF5113  12 anlayylnvegeyeeALeyldsale 36 
                                      ++  +  +g+y+eALe+ ++al+
  gi|116753411|ref|YP_842529.1| 193 IRMGESMHSTGRYDEALECYEEALR 217
                                    567889999**************97 PP

  == domain 6  score: 3.7 bits;  conditional E-value: 0.12
                        DUF5113  15 ayylnvegeyeeALeyldsaleylNahyekYakkk 49 
                                    + ++ + g +++A++ +dsal++  +h ++++ k 
  gi|116753411|ref|YP_842529.1| 230 GITYRAMGIPSKAIDAIDSALTLDPEHAQSWYAKG 264
                                    5567788999******************9999875 PP

  == domain 7  score: 2.1 bits;  conditional E-value: 0.38
                        DUF5113  10 dYanlayylnvegeyeeALeyldsale 36 
                                     +   + +  + g ye+ALe++d +l+
  gi|116753411|ref|YP_842529.1| 259 SWYAKGITFRAMGLYEDALECFDRVLR 285
                                    5555667778899**********9997 PP

  == domain 8  score: -0.2 bits;  conditional E-value: 2
                        DUF5113  10 dYanlayylnvegeyeeALeyldsale 36 
                                    + ++ a  l+  g+y eAL+  + a++
  gi|116753411|ref|YP_842529.1| 293 ALKSRAWSLYNLGRYAEALSACEGAIS 319
                                    555666677778999999999998886 PP

>> TPR_5  Tetratrico peptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0       1.6   6.4e+02      13      29 ..      84     100 ..      74     104 .. 0.75
   2 !   11.3   0.0   0.00077       0.3      13      66 ..     133     183 ..     124     191 .. 0.82
   3 ?    4.6   0.0     0.094        37      10      29 ..     198     217 ..     188     229 .. 0.86
   4 ?    3.8   0.0      0.17        65      17      65 ..     266     318 ..     248     351 .. 0.54

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 1.6
                          TPR_5  13 stGhedkavplYrraLa 29 
                                      G+ d+a+  Y++a++
  gi|116753411|ref|YP_842529.1|  84 ILGRCDEAISSYQEAID 100
                                    56888899999999886 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00077
                          TPR_5  13 stGhedkavplYrraLaeGLagarrrratiqLassLRnlGeaeealaLLraele 66 
                                    s+G+ ++a++ Yr aL+  ++ +++r   i L  sL  +G+  eal+  +  le
  gi|116753411|ref|YP_842529.1| 133 SMGRYEEAIEAYRMALD--IDPSQARDWCI-LGESLQTIGRHSEALECFERALE 183
                                    89**************9..57777777766.9*************998876655 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.094
                          TPR_5  10 arDstGhedkavplYrraLa 29 
                                    ++ stG+ d+a + Y++aL 
  gi|116753411|ref|YP_842529.1| 198 SMHSTGRYDEALECYEEALR 217
                                    5789**************95 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.17
                          TPR_5  17 edkavplYrraLa...eGLa.garrrratiqLassLRnlGeaeealaLLrael 65 
                                      +a+ lY+ aL+   + L+ +  +  a    a sL nlG+ +eal   ++ +
  gi|116753411|ref|YP_842529.1| 266 TFRAMGLYEDALEcfdRVLRiDPGNASALKSRAWSLYNLGRYAEALSACEGAI 318
                                    45555555555541112222122233333344556666666666655444433 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.74   2.9e+02      14      26 ..      18      30 ..      16      33 .. 0.86
   2 ?    1.0   0.1       1.6   6.4e+02       9      26 ..      47      64 ..      46      68 .. 0.80
   3 ?    0.2   0.0       2.9   1.1e+03      13      26 ..      85      98 ..      81     102 .. 0.79
   4 ?    2.8   0.1      0.43   1.7e+02      10      24 ..     131     145 ..     130     149 .. 0.83
   5 ?    3.1   0.0      0.35   1.4e+02      14      26 ..     169     181 ..     167     185 .. 0.86
   6 ?    6.2   0.0     0.035        14      13      27 ..     202     216 ..     197     219 .. 0.86
   7 ?    4.8   0.0     0.097        38      13      27 ..     270     284 ..     267     287 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.74
                            PPR 14 GkleeAlelfkeM 26
                                   G ++eA+e++++ 
  gi|116753411|ref|YP_842529.1| 18 GSYDEAIEYYDRV 30
                                   899*******985 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 1.6
                            PPR  9 gycknGkleeAlelfkeM 26
                                   ++    ++e+Ale++ + 
  gi|116753411|ref|YP_842529.1| 47 ACFCFSRYEDALECYSRA 64
                                   6777889*******9875 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 2.9
                            PPR 13 nGkleeAlelfkeM 26
                                    G+++eA++ ++e 
  gi|116753411|ref|YP_842529.1| 85 LGRCDEAISSYQEA 98
                                   69*****9988875 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.43
                            PPR  10 ycknGkleeAlelfk 24 
                                    + + G++eeA+e ++
  gi|116753411|ref|YP_842529.1| 131 LLSMGRYEEAIEAYR 145
                                    6689*******9886 PP

  == domain 5  score: 3.1 bits;  conditional E-value: 0.35
                            PPR  14 GkleeAlelfkeM 26 
                                    G+++eAle+f++ 
  gi|116753411|ref|YP_842529.1| 169 GRHSEALECFERA 181
                                    899*******985 PP

  == domain 6  score: 6.2 bits;  conditional E-value: 0.035
                            PPR  13 nGkleeAlelfkeMk 27 
                                     G+++eAle+++e +
  gi|116753411|ref|YP_842529.1| 202 TGRYDEALECYEEAL 216
                                    69**********966 PP

  == domain 7  score: 4.8 bits;  conditional E-value: 0.097
                            PPR  13 nGkleeAlelfkeMk 27 
                                     G++e+Ale+f++ +
  gi|116753411|ref|YP_842529.1| 270 MGLYEDALECFDRVL 284
                                    69**********976 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 ?    1.6   0.0      0.67   2.6e+02       4      40 ..      26      64 ..      19     107 .. 0.74
   2 ?    4.9   0.0     0.067        26      17      37 ..     124     144 ..     115     159 .. 0.83
   3 ?   -2.0   0.0       8.8   3.4e+03      28      39 ..     203     214 ..     198     222 .. 0.65
   4 !   12.2   0.0   0.00035      0.14       3      70 ..     278     350 ..     276     361 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.67
                   SRP_TPR_like  4 eyekilrlegkelkkf..kvvaliklekyeeaLkllkkg 40
                                    y+++l ++  +   +  + +a     +ye+aL+  + +
  gi|116753411|ref|YP_842529.1| 26 YYDRVLDIDPMNTAAWcgRGMACFCFSRYEDALECYSRA 64
                                   566666666666666677888889999999999877655 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.067
                   SRP_TPR_like  17 kkfkvvaliklekyeeaLkll 37 
                                     + k +al+++++yeea+++ 
  gi|116753411|ref|YP_842529.1| 124 WRQKGLALLSMGRYEEAIEAY 144
                                    567899***********9875 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 8.8
                   SRP_TPR_like  28 ekyeeaLkllkk 39 
                                    ++y+eaL+  ++
  gi|116753411|ref|YP_842529.1| 203 GRYDEALECYEE 214
                                    566666665554 PP

  == domain 4  score: 12.2 bits;  conditional E-value: 0.00035
                   SRP_TPR_like   3 eeyekilrle..gkelkkfkvvaliklekyeeaLkllkkgs...alsedvrfEkaYvlYklkkykkalkilkk 70 
                                    e+++++lr++  ++   k+++ +l +l++y+eaL++++ +     l+ed  +    vl  l +y+++   + k
  gi|116753411|ref|YP_842529.1| 278 ECFDRVLRIDpgNASALKSRAWSLYNLGRYAEALSACEGAIsvnPLDEDAWYNMGIVLKALGRYTESDMAFIK 350
                                    567788888733455568899***************9976544478999****99999999999998766655 PP

>> TOM20_plant  Plant specific mitochondrial import receptor subunit TOM20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.45   1.7e+02      53      97 ..      22      55 ..      11      72 .. 0.58
   2 ?    4.6   0.0      0.06        23      19      53 ..     115     149 ..     108     227 .. 0.73
   3 ?    0.4   0.0       1.2   4.8e+02      52      76 ..     206     230 ..     196     248 .. 0.76
   4 ?    2.8   0.0      0.22        87      53      97 ..     241     274 ..     232     303 .. 0.63
   5 ?    4.4   0.0     0.073        28      52      88 ..     308     344 ..     304     354 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.45
                                   HHHHHHHHHHHH-TT-HHHHHH.HHHHHHHHHHH---HHHHHHHHH CS
                    TOM20_plant 53 daiskleeallidPkkhdalWc.ignaytsfafltpdeeeakenfe 97
                                   +ai  ++  l idP+   a Wc  g a  +f++           +e
  gi|116753411|ref|YP_842529.1| 22 EAIEYYDRVLDIDPMNT-AAWCgRGMACFCFSR-----------YE 55
                                   67777777777777754.556612333333333...........33 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.06
                                    HH-TT-HHHHHHHHHHHHHHHHHS-HHHHHHHHHH CS
                    TOM20_plant  19 kknPldadnllrWggallelsqfqsvaeakqmiqd 53 
                                     + P da+   + g all + ++++ +ea +m  d
  gi|116753411|ref|YP_842529.1| 115 DSRPDDAESWRQKGLALLSMGRYEEAIEAYRMALD 149
                                    56789999999999999999999999999888765 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 1.2
                                    HHHHHHHHHHHHH-TT-HHHHHHHH CS
                    TOM20_plant  52 qdaiskleeallidPkkhdalWcig 76 
                                    ++a+  +eeal +dP   +a    g
  gi|116753411|ref|YP_842529.1| 206 DEALECYEEALRLDPGSVQAWHGKG 230
                                    5788888999999998888765555 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.22
                                    HHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHH---HHHHHHHHH CS
                    TOM20_plant  53 daiskleeallidPkkhdalWcignaytsfafltpdeeeakenfe 97 
                                    +ai  ++ al++dP+  ++ +  g ++ + + +           e
  gi|116753411|ref|YP_842529.1| 241 KAIDAIDSALTLDPEHAQSWYAKGITFRAMGLY-----------E 274
                                    577777777777777777666555555554443...........3 PP

  == domain 5  score: 4.4 bits;  conditional E-value: 0.073
                                    HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHH--- CS
                    TOM20_plant  52 qdaiskleeallidPkkhdalWcignaytsfafltpd 88 
                                     +a+s  e a+ ++P  +da + +g    + +++t+ 
  gi|116753411|ref|YP_842529.1| 308 AEALSACEGAISVNPLDEDAWYNMGIVLKALGRYTES 344
                                    589999******************9999999998864 PP

>> DUF627  Protein of unknown function (DUF627)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.099        39      62      97 ..      57      99 ..      51     105 .. 0.90
   2 ?    0.6   0.0       1.5   5.7e+02      62     104 ..     140     182 ..     137     184 .. 0.69
   3 !    8.2   0.0    0.0063       2.4      61     105 ..     173     217 ..     169     219 .. 0.92
   4 ?    4.4   0.0     0.095        37      62     106 ..     276     320 ..     272     322 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.099
                         DUF627 62 svecfseavels.......rfyArsLfelasqlgsklyYkkav 97
                                   ++ec+s+a e         +  A+ Lf l++  +  + Y++a+
  gi|116753411|ref|YP_842529.1| 57 ALECYSRAIEADpecvpawECRAEVLFILGRCDEAISSYQEAI 99
                                   89*********99*****************9888888999987 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.5
                         DUF627  62 svecfseavelsrfyArsLfelasqlgsklyYkkavkkakraL 104
                                    ++e++++a  +    Ar  + l++ l++     +a++  +raL
  gi|116753411|ref|YP_842529.1| 140 AIEAYRMALDIDPSQARDWCILGESLQTIGRHSEALECFERAL 182
                                    7888888888887777777777777776666666666555555 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0063
                         DUF627  61 asvecfseavelsrfyArsLfelasqlgsklyYkkavkkakraLs 105
                                     ++ecf++a els       + +++ + s+  Y +a++  ++aL 
  gi|116753411|ref|YP_842529.1| 173 EALECFERALELSPSDSACWIRMGESMHSTGRYDEALECYEEALR 217
                                    699*********************************998888885 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.095
                         DUF627  62 svecfseavelsrfyArsLfelasqlgsklyYkkavkkakraLsv 106
                                    ++ecf +  ++  + A+ L   a  l +   Y +a++ ++ a+sv
  gi|116753411|ref|YP_842529.1| 276 ALECFDRVLRIDPGNASALKSRAWSLYNLGRYAEALSACEGAISV 320
                                    89**********777777777777777777799999999988887 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.035        14      70     105 ..       5      40 ..       1      98 [. 0.86
   2 ?    0.6   0.0       1.9   7.2e+02      76     122 ..     128     174 ..     119     179 .. 0.85
   3 ?    0.3   0.0       2.3   8.8e+02      73     118 ..     193     238 ..     179     251 .. 0.85
   4 ?    6.1   0.0     0.036        14      81     123 ..     269     311 ..     255     321 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.035
                                    HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHH CS
                Alkyl_sulf_dimr  70 ekvlekakealkegdyrwaaellnhlvfadpenaea 105
                                    +++l+ka+e++ +g y  a+e  + ++  dp n++a
  gi|116753411|ref|YP_842529.1|   5 AALLQKAEEKYLDGSYDEAIEYYDRVLDIDPMNTAA 40 
                                    78999**********************999999766 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.9
                                    HHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SS CS
                Alkyl_sulf_dimr  76 akealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaes 122
                                      + l+ g y+ a+e   +++  dp++a+   ++ ++l+ +g+++e+
  gi|116753411|ref|YP_842529.1| 128 GLALLSMGRYEEAIEAYRMALDIDPSQARDWCILGESLQTIGRHSEA 174
                                    55677889999***************999999999999999999886 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 2.3
                                    HHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHH CS
                Alkyl_sulf_dimr  73 lekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgy 118
                                    +++ ++  + g y  a+e  + ++  dp   +a + k  +++++g 
  gi|116753411|ref|YP_842529.1| 193 IRMGESMHSTGRYDEALECYEEALRLDPGSVQAWHGKGITYRAMGI 238
                                    667778889999*****************99999999999998885 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.036
                                    HTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSH CS
                Alkyl_sulf_dimr  81 kegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesa 123
                                    + g y+ a+e  + ++  dp na+a + +a +l +lg+ ae+ 
  gi|116753411|ref|YP_842529.1| 269 AMGLYEDALECFDRVLRIDPGNASALKSRAWSLYNLGRYAEAL 311
                                    5677999*******************************99976 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       5.8   2.2e+03      78     104 ..       6      32 ..       4      39 .. 0.79
   2 ?    6.9   0.0     0.012       4.6     150     180 ..      76     106 ..      53     122 .. 0.86
   3 ?    7.1   0.0      0.01       4.1     151     180 ..     126     155 ..     120     168 .. 0.85
   4 ?    0.9   0.0      0.84   3.3e+02     153     175 ..     196     218 ..     188     229 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 5.8
                         TPR_21  78 aaLllAkaaveagdlaaAkaqLewvle 104
                                    a L++A++++  g +++A + +++vl+
  gi|116753411|ref|YP_842529.1|   6 ALLQKAEEKYLDGSYDEAIEYYDRVLD 32 
                                    557889999999999999888887765 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.012
                         TPR_21 150 elrGDilvaqgkldeAraaYqaAlaaleeka 180
                                    e r ++l+  g+ deA + Yq+A+++  + a
  gi|116753411|ref|YP_842529.1|  76 ECRAEVLFILGRCDEAISSYQEAIDRDPAYA 106
                                    778899******************9987765 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.01
                         TPR_21 151 lrGDilvaqgkldeAraaYqaAlaaleeka 180
                                     +G +l+++g+ +eA +aY+ Al+   ++a
  gi|116753411|ref|YP_842529.1| 126 QKGLALLSMGRYEEAIEAYRMALDIDPSQA 155
                                    58999******************9888776 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.84
                         TPR_21 153 GDilvaqgkldeAraaYqaAlaa 175
                                    G+ + ++g+ deA + Y++Al+ 
  gi|116753411|ref|YP_842529.1| 196 GESMHSTGRYDEALECYEEALRL 218
                                    67778899999999999999975 PP

>> PknG_TPR  Protein kinase G tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.85   3.3e+02     140     228 ..      16     105 ..      10     121 .. 0.73
   2 !    8.4   0.0     0.002      0.77     104     220 ..     131     248 ..     111     258 .. 0.81
   3 ?    5.1   0.0     0.021       8.1     131     162 ..     259     291 ..     250     296 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.85
                                    HHT-HHHHHHHHHHHHHHSTT-SHHHHHHHHHHHHHT-.--TT-HHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHH CS
                       PknG_TPR 140 legdyeeAaaeFdevlaalpGEiaPklaLAataElage.tdeekyYrtVwrtdrgvvsAaFGlaRqlaaagdraaAvaaL 218
                                    l+g y+eA++ +d+vl++ p  +a   +  +++    + +d+ + Y+     d   v A    a  l   g+ ++A++  
  gi|116753411|ref|YP_842529.1|  16 LDGSYDEAIEYYDRVLDIDPMNTAAWCGRGMACFCFSRyEDALECYSRAIEADPECVPAWECRAEVLFILGRCDEAISSY 95 
                                    67889999999999999988888888877777776644144567788888888888888777788888888888887777 PP

                                    HTS-TTSTTH CS
                       PknG_TPR 219 deVpatSrhy 228
                                    +e  +    y
  gi|116753411|ref|YP_842529.1|  96 QEAIDRDPAY 105
                                    6665555555 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.002
                                    HHHCT-HHHHHHHHH...HHHHHH---HHHHHHHHHHHHHHT-HHHHHHHHHHHHHHSTT-SHHHHHHHHHHHHHT---T CS
                       PknG_TPR 104 hldlGdveearelLd...eleeeveedWrldWyrglaeLlegdyeeAaaeFdevlaalpGEiaPklaLAataElagetde 180
                                     l +G  eea e  +   ++++++++dW +    g +  + g+ +eA ++F++ l++ p ++a  + +      +g+ de
  gi|116753411|ref|YP_842529.1| 131 LLSMGRYEEAIEAYRmalDIDPSQARDWCI---LGESLQTIGRHSEALECFERALELSPSDSACWIRMGESMHSTGRYDE 207
                                    566666666555443111455555556655...466666678999******************************99997 PP

                                    T.-HHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHT CS
                       PknG_TPR 181 e.kyYrtVwrtdrgvvsAaFGlaRqlaaagdraaAvaaLde 220
                                    + + Y+   r d g v A +G   +  a g  ++A++a+d+
  gi|116753411|ref|YP_842529.1| 208 AlECYEEALRLDPGSVQAWHGKGITYRAMGIPSKAIDAIDS 248
                                    559********************************999997 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.021
                                    HHH.HHHHHHHHT-HHHHHHHHHHHHHHSTT-S CS
                       PknG_TPR 131 dWy.rglaeLlegdyeeAaaeFdevlaalpGEi 162
                                    +Wy +g++  ++g ye A ++Fd+vl++ pG +
  gi|116753411|ref|YP_842529.1| 259 SWYaKGITFRAMGLYEDALECFDRVLRIDPGNA 291
                                    699459999999******************986 PP

>> RPN7  26S proteasome subunit RPN7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.9   7.4e+02      44      64 ..      13      32 ..       2      41 .. 0.73
   2 ?   -1.8   0.0       5.5   2.1e+03      52      64 ..      54      66 ..      48      73 .. 0.86
   3 ?    1.1   0.0      0.75   2.9e+02      40      64 ..      76     100 ..      66     104 .. 0.83
   4 ?    1.9   0.0       0.4   1.5e+02     119     134 ..     127     142 ..     122     158 .. 0.62
   5 ?    5.5   0.0     0.033        13      30      66 ..     149     185 ..     137     196 .. 0.81
   6 ?    2.1   0.0      0.34   1.3e+02      42      63 ..     195     216 ..     189     222 .. 0.82
   7 ?    1.6   0.0      0.49   1.9e+02      34      63 ..     255     284 ..     242     293 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.9
                                   HHHHHCT-HHHHHHHHHTCCC CS
                           RPN7 44 ehYlkigdleeAlkaysrire 64
                                   e Yl+ g ++eA+++y r+++
  gi|116753411|ref|YP_842529.1| 13 EKYLD-GSYDEAIEYYDRVLD 32
                                   44444.899*******99876 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 5.5
                                   HHHHHHHHHTCCC CS
                           RPN7 52 leeAlkaysrire 64
                                   +e Al++ysr++e
  gi|116753411|ref|YP_842529.1| 54 YEDALECYSRAIE 66
                                   689******9876 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.75
                                    HHHHHHHHHCT-HHHHHHHHHTCCC CS
                           RPN7  40 ldlaehYlkigdleeAlkaysrire 64 
                                    + +ae  +  g ++eA+  y+++++
  gi|116753411|ref|YP_842529.1|  76 ECRAEVLFILGRCDEAISSYQEAID 100
                                    5567777889************987 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.4
                                    HHHHHHHTT-HHHHHH CS
                           RPN7 119 eGlallairkfkeAae 134
                                    +Glall++++++eA e
  gi|116753411|ref|YP_842529.1| 127 KGLALLSMGRYEEAIE 142
                                    4555555555555533 PP

  == domain 5  score: 5.5 bits;  conditional E-value: 0.033
                                    T-HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTCCCC- CS
                           RPN7  30 lgkeeirrakldlaehYlkigdleeAlkaysrireyc 66 
                                     ++ + +r +  l+e   +ig ++eAl++++r++e +
  gi|116753411|ref|YP_842529.1| 149 DIDPSQARDWCILGESLQTIGRHSEALECFERALELS 185
                                    567778888889999999**************99865 PP

  == domain 6  score: 2.1 bits;  conditional E-value: 0.34
                                    HHHHHHHCT-HHHHHHHHHTCC CS
                           RPN7  42 laehYlkigdleeAlkaysrir 63 
                                     +e  +++g ++eAl++y++++
  gi|116753411|ref|YP_842529.1| 195 MGESMHSTGRYDEALECYEEAL 216
                                    56667789***********986 PP

  == domain 7  score: 1.6 bits;  conditional E-value: 0.49
                                    HHHHHHHHHHHHHHHCT-HHHHHHHHHTCC CS
                           RPN7  34 eirrakldlaehYlkigdleeAlkaysrir 63 
                                    e ++ +++++  +  +g +e Al+++ r++
  gi|116753411|ref|YP_842529.1| 255 EHAQSWYAKGITFRAMGLYEDALECFDRVL 284
                                    6788899999999999********999954 PP

>> NRBF2_MIT  MIT domain of nuclear receptor-binding factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1       1.3     5e+02      22      36 ..      52      66 ..      35      73 .. 0.83
   2 ?    2.5   0.0      0.43   1.7e+02      13      34 ..      77      98 ..      65     104 .. 0.89
   3 ?    6.1   0.0     0.033        13      16      34 ..     129     147 ..     120     156 .. 0.83
   4 ?    1.1   0.0       1.2   4.8e+02      18      36 ..     165     183 ..     153     192 .. 0.70
   5 ?    4.1   0.0      0.14        54      14      34 ..     195     215 ..     189     219 .. 0.84
   6 ?    1.5   0.0      0.88   3.4e+02       9      33 ..     256     282 ..     247     287 .. 0.73
   7 ?   -0.3   0.0       3.4   1.3e+03      13      31 ..     296     314 ..     287     320 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 1.3
                      NRBF2_MIT 22 Gkyeeaischkkaaa 36
                                    +ye+a+ c+ +a +
  gi|116753411|ref|YP_842529.1| 52 SRYEDALECYSRAIE 66
                                   68********99976 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.43
                      NRBF2_MIT 13 rkadrllaaGkyeeaischkka 34
                                    +a+ l+  G+ +eais ++ a
  gi|116753411|ref|YP_842529.1| 77 CRAEVLFILGRCDEAISSYQEA 98
                                   58999************99987 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.033
                      NRBF2_MIT  16 drllaaGkyeeaischkka 34 
                                      ll+ G+yeeai  ++ a
  gi|116753411|ref|YP_842529.1| 129 LALLSMGRYEEAIEAYRMA 147
                                    5699*********999877 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 1.2
                      NRBF2_MIT  18 llaaGkyeeaischkkaaa 36 
                                    l + G++ ea+ c ++a +
  gi|116753411|ref|YP_842529.1| 165 LQTIGRHSEALECFERALE 183
                                    5566777777777776644 PP

  == domain 5  score: 4.1 bits;  conditional E-value: 0.14
                      NRBF2_MIT  14 kadrllaaGkyeeaischkka 34 
                                      + + ++G+y+ea+ c++ a
  gi|116753411|ref|YP_842529.1| 195 MGESMHSTGRYDEALECYEEA 215
                                    56777899*********9887 PP

  == domain 6  score: 1.5 bits;  conditional E-value: 0.88
                      NRBF2_MIT   9 hqqsrkad..rllaaGkyeeaischkk 33 
                                    h qs  a+   + a G ye+a+ c  +
  gi|116753411|ref|YP_842529.1| 256 HAQSWYAKgiTFRAMGLYEDALECFDR 282
                                    667766651134699*********865 PP

  == domain 7  score: -0.3 bits;  conditional E-value: 3.4
                      NRBF2_MIT  13 rkadrllaaGkyeeaisch 31 
                                     +a  l   G+y ea+s  
  gi|116753411|ref|YP_842529.1| 296 SRAWSLYNLGRYAEALSAC 314
                                    467788999******9865 PP

>> ChAPs  ChAPs (Chs5p-Arf1p-binding proteins)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.25        97     245     288 ..      51      92 ..      22      97 .. 0.84
   2 ?    2.5   0.0      0.15        57     226     288 ..     113     175 ..     104     175 .. 0.78
   3 !   10.3   0.0   0.00065      0.25     240     288 ..     161     209 ..     131     214 .. 0.80
   4 ?   -1.7   0.0       2.9   1.1e+03     223     274 ..     280     331 ..     251     342 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.25
                                    HHSS--HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHH CS
                          ChAPs 245 lskkkeelAlevakravksaPsefktWalLvkvYikledienAL 288
                                       +++e Ale+ +ra+++ P     W + ++v   l+ +++A+
  gi|116753411|ref|YP_842529.1|  51 F--SRYEDALECYSRAIEADPECVPAWECRAEVLFILGRCDEAI 92 
                                    4..456779**********************9999999888886 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.15
                                    HH-SSS-HHHHHHHHHHHHHHSS--HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHH CS
                          ChAPs 226 eleeeekdaelLllqaefllskkkeelAlevakravksaPsefktWalLvkvYikledienAL 288
                                     ++++++dae    +   lls  ++e A+e+ + a ++ Ps+ + W +L ++  +++  ++AL
  gi|116753411|ref|YP_842529.1| 113 CIDSRPDDAESWRQKGLALLSMGRYEEAIEAYRMALDIDPSQARDWCILGESLQTIGRHSEAL 175
                                    55566666666666666799999**************************99877777666665 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00065
                                    HHHHHHHSS--HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHH CS
                          ChAPs 240 qaefllskkkeelAlevakravksaPsefktWalLvkvYikledienAL 288
                                      e l+   +++ Ale+ +ra +++Ps+++ W+++ ++  + + +++AL
  gi|116753411|ref|YP_842529.1| 161 LGESLQTIGRHSEALECFERALELSPSDSACWIRMGESMHSTGRYDEAL 209
                                    5566667778889***********************9999999999998 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 2.9
                                    HHHHH-SSS-HHHHHHHHHHHHHHSS--HHHHHHHHHHHHH-TT-HHHHHHH CS
                          ChAPs 223 lneeleeeekdaelLllqaefllskkkeelAlevakravksaPsefktWalL 274
                                      + l+ ++ +a+ L+ +a  l +  ++  Al++ + a+++ P +   W+ +
  gi|116753411|ref|YP_842529.1| 280 FDRVLRIDPGNASALKSRAWSLYNLGRYAEALSACEGAISVNPLDEDAWYNM 331
                                    4455555566677777777778888888889999999999999999999876 PP

>> FAT  FAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.076        30     269     290 ..      55      76 ..      17     176 .. 0.79
   2 !    8.3   0.0    0.0031       1.2     245     290 ..     189     227 ..     162     228 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.076
                                    SSCCHHHHCCHHCTCCCHSTTC CS
                            FAT 269 eeilqsysaateidpswykawh 290
                                    e++l++ys+a e dp++  aw 
  gi|116753411|ref|YP_842529.1|  55 EDALECYSRAIEADPECVPAWE 76 
                                    6788888888888888888885 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0031
                                    HHCCCTCCCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTC CS
                            FAT 245 arcylkkGewqealqkldwseekieeilqsysaateidpswykawh 290
                                    + c  + Ge ++++++        +e+l++y +a ++dp++ +awh
  gi|116753411|ref|YP_842529.1| 189 SACWIRMGESMHSTGR-------YDEALECYEEALRLDPGSVQAWH 227
                                    5566667777777777.......99********************9 PP

>> MAS20  MAS20 protein import receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       7.9   3.1e+03      80     104 ..     126     150 ..     126     155 .. 0.82
   2 ?    6.1   0.0     0.029        11      81     107 ..     161     187 ..     159     192 .. 0.91
   3 ?    6.5   0.0     0.022       8.7      79     105 ..     193     219 ..     190     224 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 7.9
                          MAS20  80 qlGEellaqgeeeeaaehlynAlkv 104
                                    q+G  ll+ g++eea+e+   Al +
  gi|116753411|ref|YP_842529.1| 126 QKGLALLSMGRYEEAIEAYRMALDI 150
                                    567789999*******999998876 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.029
                          MAS20  81 lGEellaqgeeeeaaehlynAlkvcpq 107
                                    lGE+l + g++ ea+e++ +Al + p+
  gi|116753411|ref|YP_842529.1| 161 LGESLQTIGRHSEALECFERALELSPS 187
                                    79999999**************99886 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.022
                          MAS20  79 vqlGEellaqgeeeeaaehlynAlkvc 105
                                    +++GE++ + g+++ea+e+   Al++ 
  gi|116753411|ref|YP_842529.1| 193 IRMGESMHSTGRYDEALECYEEALRLD 219
                                    78********************99875 PP

>> SHNi-TPR  SHNi-TPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       2.5   9.6e+02      15      29 ..      52      66 ..      51      66 .. 0.83
   2 ?   -2.5   0.1       9.2   3.6e+03      18      28 ..      89      99 ..      87     100 .. 0.85
   3 ?    4.3   0.0     0.071        27      15      30 ..     135     150 ..     132     150 .. 0.89
   4 ?    1.2   0.0      0.68   2.6e+02       7      30 ..     161     184 ..     160     184 .. 0.83
   5 ?    3.8   0.0       0.1        39      13      30 ..     201     218 ..     189     218 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 2.5
                       SHNi-TPR 15 enFpqAveDlrkaLe 29
                                   +++++A+e + +a+e
  gi|116753411|ref|YP_842529.1| 52 SRYEDALECYSRAIE 66
                                   69*****98888865 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 9.2
                       SHNi-TPR 18 pqAveDlrkaL 28
                                   ++A++ +++a+
  gi|116753411|ref|YP_842529.1| 89 DEAISSYQEAI 99
                                   68999999997 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.071
                       SHNi-TPR  15 enFpqAveDlrkaLeL 30 
                                    +++++A+e +r aL++
  gi|116753411|ref|YP_842529.1| 135 GRYEEAIEAYRMALDI 150
                                    79************87 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.68
                       SHNi-TPR   7 LGEislEnenFpqAveDlrkaLeL 30 
                                    LGE  ++ ++ ++A+e +++aLeL
  gi|116753411|ref|YP_842529.1| 161 LGESLQTIGRHSEALECFERALEL 184
                                    666667778899**********98 PP

  == domain 5  score: 3.8 bits;  conditional E-value: 0.1
                       SHNi-TPR  13 EnenFpqAveDlrkaLeL 30 
                                     ++++++A+e +++aL L
  gi|116753411|ref|YP_842529.1| 201 STGRYDEALECYEEALRL 218
                                    679************976 PP

>> PPTA  Protein prenyltransferase alpha subunit repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       6.8   2.7e+03       8      19 ..      30      41 ..      28      42 .. 0.84
   2 ?   -0.7   0.0       3.3   1.3e+03       7      23 ..      63      79 ..      62      83 .. 0.78
   3 ?    4.9   0.0      0.06        24       6      20 ..     213     227 ..     213     227 .. 0.94
   4 ?    1.9   0.0      0.51     2e+02       6      20 ..     247     261 ..     243     261 .. 0.88
   5 ?   -1.9   0.0       8.3   3.2e+03       8      18 ..     283     293 ..     281     293 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 6.8
                                   HHHH-TT-CHHH CS
                           PPTA  8 liekdpkNYsaW 19
                                   +++ dp N  aW
  gi|116753411|ref|YP_842529.1| 30 VLDIDPMNTAAW 41
                                   6899**9*9999 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 3.3
                                   HHHHH-TT-CHHHHHHH CS
                           PPTA  7 kliekdpkNYsaWnyRr 23
                                    +ie dp +  aW  R 
  gi|116753411|ref|YP_842529.1| 63 RAIEADPECVPAWECRA 79
                                   6899***9999997775 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.06
                                    HHHHHH-TT-CHHHH CS
                           PPTA   6 ekliekdpkNYsaWn 20 
                                    e+++++dp + +aW+
  gi|116753411|ref|YP_842529.1| 213 EEALRLDPGSVQAWH 227
                                    689***********9 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.51
                                    HHHHHH-TT-CHHHH CS
                           PPTA   6 ekliekdpkNYsaWn 20 
                                    ++++ +dp + + W+
  gi|116753411|ref|YP_842529.1| 247 DSALTLDPEHAQSWY 261
                                    67999*********6 PP

  == domain 5  score: -1.9 bits;  conditional E-value: 8.3
                                    HHHH-TT-CHH CS
                           PPTA   8 liekdpkNYsa 18 
                                    +++ dp N sa
  gi|116753411|ref|YP_842529.1| 283 VLRIDPGNASA 293
                                    6899****886 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       2.8   1.1e+03      80     109 ..       4      33 ..       2      81 .. 0.82
   2 ?    0.1   0.0       1.1   4.2e+02      79     107 ..      71      99 ..      52     102 .. 0.76
   3 ?    6.1   0.0     0.016       6.3      65     113 ..     142     188 ..     127     218 .. 0.60
   4 ?   -0.9   0.0       2.2   8.5e+02       7      48 ..     297     340 ..     290     353 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.8
                       TPR_MalT  80 llallqqaeilvaqGrLheAletyeqalql 109
                                    + allq ae    +G+ +eA+e y + l  
  gi|116753411|ref|YP_842529.1|   4 IAALLQKAEEKYLDGSYDEAIEYYDRVLDI 33 
                                    678888899888889999999999888764 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.1
                       TPR_MalT  79 allallqqaeilvaqGrLheAletyeqal 107
                                     ++a  + ae+l+  Gr +eA+  y++a+
  gi|116753411|ref|YP_842529.1|  71 CVPAWECRAEVLFILGRCDEAISSYQEAI 99 
                                    45666677999999999999999999987 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.016
                       TPR_MalT  65 eaeklarqadslhvallallqqaeilvaqGrLheAletyeqalqlateq 113
                                    ea+++a+++d +++  +  + ++e l++ Gr  eAle +e+al+l +  
  gi|116753411|ref|YP_842529.1| 142 EAYRMALDIDPSQARDW--CILGESLQTIGRHSEALECFERALELSPSD 188
                                    44555666666664333..444777777777777777777777776554 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 2.2
                       TPR_MalT   7 rAllaiasgdaeralelArqALal..lpeddllariaatavlGe 48 
                                    rA+   + g+  +al  ++ A++   l+ed+++  ++++ +lG+
  gi|116753411|ref|YP_842529.1| 297 RAWSLYNLGRYAEALSACEGAISVnpLDEDAWYNMGIVLKALGR 340
                                    78888889999999999999988733667778777888777774 PP

>> Type_III_YscG  Bacterial type II secretion system chaperone protein (type_III_yscG)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       9.1   3.5e+03      49      62 ..     130     143 ..     110     150 .. 0.78
   2 ?    5.1   0.0     0.057        22      21      64 ..     170     213 ..     161     226 .. 0.77
   3 ?    6.1   0.0     0.028        11      45      65 ..     296     316 ..     270     349 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 9.1
                                    HHHHTT-HHHHHHH CS
                  Type_III_YscG  49 sLmnkGkyeealal 62 
                                    +L   G+yeea + 
  gi|116753411|ref|YP_842529.1| 130 ALLSMGRYEEAIEA 143
                                    57778999999764 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.057
                                    -HHHHHHHHHHHHHTT-H.HHHHHHHH.HHHHHTT-HHHHHHHHT CS
                  Type_III_YscG  21 rheeaniiadwLeekeeeeeavrlirl.ssLmnkGkyeealalae 64 
                                    rh ea+   +   e + + + +  ir+  s+   G+y+eal+  e
  gi|116753411|ref|YP_842529.1| 170 RHSEALECFERALELSPS-DSACWIRMgESMHSTGRYDEALECYE 213
                                    688887655555555555.57788888469999*******99766 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.028
                                    HHHHHHHHTT-HHHHHHHHTT CS
                  Type_III_YscG  45 irlssLmnkGkyeealalaek 65 
                                     r+ sL n G+y+eal+  e+
  gi|116753411|ref|YP_842529.1| 296 SRAWSLYNLGRYAEALSACEG 316
                                    5999************98765 PP

>> Wzy_C_2  Virulence factor membrane-bound polymerase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       9.8   3.8e+03     155     180 ..      16      41 ..       9      42 .. 0.85
   2 ?   -1.4   0.0       4.9   1.9e+03     132     180 ..      60     109 ..      53     113 .. 0.67
   3 ?   -0.1   0.1         2   7.7e+02     129     180 ..     106     158 ..      89     162 .. 0.67
   4 ?    3.7   0.0      0.13        52     150     182 ..     162     194 ..     129     200 .. 0.85
   5 ?    2.4   0.0      0.33   1.3e+02     134     180 ..     179     226 ..     173     234 .. 0.79
   6 ?    3.0   0.0      0.21        82     128     180 ..     275     328 ..     255     332 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 9.8
                        Wzy_C_2 155 llGdedeAeqilararalfpeedakw 180
                                    l G  deA  +++r+  + p + a+w
  gi|116753411|ref|YP_842529.1|  16 LDGSYDEAIEYYDRVLDIDPMNTAAW 41 
                                    78999********9998888888877 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.9
                        Wzy_C_2 132 larklihlsPe.pavierlilslallGdedeAeqilararalfpeedakw 180
                                     ++++i+  Pe     e  ++ l +lG+ deA   +++a+   p+++ +w
  gi|116753411|ref|YP_842529.1|  60 CYSRAIEADPEcVPAWECRAEVLFILGRCDEAISSYQEAIDRDPAYALAW 109
                                    55555555555224455567788899999999999999887666666655 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 2
                        Wzy_C_2 129 klalarklihlsPepavierl.ilslallGdedeAeqilararalfpeedakw 180
                                     la+ ++ i + P  a   r+  l+l   G+ +eA   ++ a  + p ++ +w
  gi|116753411|ref|YP_842529.1| 106 ALAWIERCIDSRPDDAESWRQkGLALLSMGRYEEAIEAYRMALDIDPSQARDW 158
                                    56677777777776665444414566667888888888877777766666666 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.13
                        Wzy_C_2 150 ilslallGdedeAeqilararalfpeedakwvq 182
                                     +sl+  G+++eA+   +ra  l p + a w++
  gi|116753411|ref|YP_842529.1| 162 GESLQTIGRHSEALECFERALELSPSDSACWIR 194
                                    57999****************999999999965 PP

  == domain 5  score: 2.4 bits;  conditional E-value: 0.33
                        Wzy_C_2 134 rklihlsPe.pavierlilslallGdedeAeqilararalfpeedakw 180
                                    +++++lsP   a   r+ +s   +G+ deA+  +++a  l p + ++w
  gi|116753411|ref|YP_842529.1| 179 ERALELSPSdSACWIRMGESMHSTGRYDEALECYEEALRLDPGSVQAW 226
                                    66777777523556788899999**************99999988888 PP

  == domain 6  score: 3.0 bits;  conditional E-value: 0.21
                        Wzy_C_2 128 aklalarklihlsPepav.ierlilslallGdedeAeqilararalfpeedakw 180
                                    + l+   ++++  P+ a  ++  ++sl  lG+ +eA+   + a+ + p ++ +w
  gi|116753411|ref|YP_842529.1| 275 DALECFDRVLRIDPGNASaLKSRAWSLYNLGRYAEALSACEGAISVNPLDEDAW 328
                                    566666677777777665156679***************999999999888888 PP

>> DUF1896  Domain of unknown function (DUF1896)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.094        37      29      64 ..      48      83 ..      21      86 .. 0.83
   2 ?    4.3   0.0       0.1        39      27      50 ..      80     103 ..      74     109 .. 0.83
   3 ?   -2.1   0.0       9.3   3.6e+03      34      47 ..     136     149 ..     131     156 .. 0.81
   4 ?    1.4   0.0      0.79   3.1e+02      32      49 ..     202     219 ..     172     227 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.094
                                   HHHHHHHHHHHHHHHHHHHHT--HHHHHHHHHHHHH CS
                        DUF1896 29 efikeRadeAaeayeeaveeGlsvaeaeelanevLy 64
                                    f  +R + A+e y++a+e++ ++  a e   evL+
  gi|116753411|ref|YP_842529.1| 48 CFCFSRYEDALECYSRAIEADPECVPAWECRAEVLF 83
                                   577789***************999999999988887 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.1
                                    -HHHHHHHHHHHHHHHHHHHHHT- CS
                        DUF1896  27 dkefikeRadeAaeayeeaveeGl 50 
                                    +  fi  R deA+ +y+ea++++ 
  gi|116753411|ref|YP_842529.1|  80 EVLFILGRCDEAISSYQEAIDRDP 103
                                    5679***************99875 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 9.3
                                    HHHHHHHHHHHHHH CS
                        DUF1896  34 RadeAaeayeeave 47 
                                    R +eA+eay  a++
  gi|116753411|ref|YP_842529.1| 136 RYEEAIEAYRMALD 149
                                    8899*****99976 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.79
                                    HHHHHHHHHHHHHHHHHT CS
                        DUF1896  32 keRadeAaeayeeaveeG 49 
                                    + R deA+e yeea++ +
  gi|116753411|ref|YP_842529.1| 202 TGRYDEALECYEEALRLD 219
                                    5699**********9865 PP

>> Ubiq-assoc  Ubiquitin-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.2      0.28   1.1e+02      19      29 ..      19      29 ..      16      34 .. 0.89
   2 ?    6.3   0.0     0.025       9.6      16      33 ..     250     267 ..     249     278 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.28
                                   -SHHHHHHHHH CS
                     Ubiq-assoc 19 sidkAneyYek 29
                                   s+d+A eyY++
  gi|116753411|ref|YP_842529.1| 19 SYDEAIEYYDR 29
                                   89*******97 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.025
                                    H---SHHHHHHHHHH-SS CS
                     Ubiq-assoc  16 LGLsidkAneyYekGilY 33 
                                    L L+ ++A+++Y kGi++
  gi|116753411|ref|YP_842529.1| 250 LTLDPEHAQSWYAKGITF 267
                                    668999**********98 PP

>> HTH_Bact  Helix-turn-helix bacterial domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       5.3   2.1e+03       2      12 ..      20      30 ..      19      33 .. 0.80
   2 ?    2.7   0.0      0.25        98       1      14 [.      53      66 ..      53      69 .. 0.93
   3 ?   -1.3   0.1       4.3   1.7e+03       1      14 [.     136     149 ..     136     151 .. 0.82
   4 ?   -0.0   0.0       1.7   6.7e+02       3      16 ..     172     185 ..     170     189 .. 0.87
   5 ?    0.6   0.0       1.1   4.3e+02       1      14 [.     204     217 ..     204     219 .. 0.85
   6 ?   -0.7   0.0       2.7   1.1e+03       1      14 [.     306     319 ..     306     321 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 5.3
                                   HHHHHHHHHHH CS
                       HTH_Bact  2 YeeaLeqvnkA 12
                                   Y+ea+e+ ++ 
  gi|116753411|ref|YP_842529.1| 20 YDEAIEYYDRV 30
                                   9****998875 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.25
                                   -HHHHHHHHHHHHH CS
                       HTH_Bact  1 rYeeaLeqvnkAie 14
                                   rYe aLe   +Aie
  gi|116753411|ref|YP_842529.1| 53 RYEDALECYSRAIE 66
                                   7************8 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 4.3
                                    -HHHHHHHHHHHHH CS
                       HTH_Bact   1 rYeeaLeqvnkAie 14 
                                    rYeea+e  + A+ 
  gi|116753411|ref|YP_842529.1| 136 RYEEAIEAYRMALD 149
                                    79***999888876 PP

  == domain 4  score: -0.0 bits;  conditional E-value: 1.7
                                    HHHHHHHHHHHHHH CS
                       HTH_Bact   3 eeaLeqvnkAieiS 16 
                                     eaLe  ++A+e+S
  gi|116753411|ref|YP_842529.1| 172 SEALECFERALELS 185
                                    689********998 PP

  == domain 5  score: 0.6 bits;  conditional E-value: 1.1
                                    -HHHHHHHHHHHHH CS
                       HTH_Bact   1 rYeeaLeqvnkAie 14 
                                    rY+eaLe  + A+ 
  gi|116753411|ref|YP_842529.1| 204 RYDEALECYEEALR 217
                                    7******9998875 PP

  == domain 6  score: -0.7 bits;  conditional E-value: 2.7
                                    -HHHHHHHHHHHHH CS
                       HTH_Bact   1 rYeeaLeqvnkAie 14 
                                    rY+eaL   + Ai 
  gi|116753411|ref|YP_842529.1| 306 RYAEALSACEGAIS 319
                                    7*******999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        48  (0.00267723); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              46  [number of targets reported over threshold]
# CPU time: 0.85u 0.30s 00:00:01.14 Elapsed: 00:00:00.58
# Mc/sec: 1898.75
//
Query:       gi|116753412|ref|YP_842530.1|  [L=210]
Description: hypothetical protein Mthe_0088 [Methanosaeta thermophila PT]
Scores for complete sequence (score 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       0.41   11.0   0.0    1.7  2  DUF5342   Family of unknown function (DUF5342)


Domain annotation for each model (and alignments):
>> DUF5342  Family of unknown function (DUF5342)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.35   6.3e+03      27      42 ..      18      33 ..       5      41 .. 0.72
   2 ?   11.0   0.0   2.3e-05      0.41      30      62 ..     150     182 ..     146     188 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.35
                        DUF5342 27 kkrvegiYhkdGsiew 42
                                   +   +++Y  +G+++ 
  gi|116753412|ref|YP_842530.1| 18 GAAWAADYVFNGALNL 33
                                   5566788888888765 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 2.3e-05
                        DUF5342  30 vegiYhkdGsiewtsaapeeeeeeelekqiHeL 62 
                                    +e+++  +G+i wt+++ ++++  el++++ eL
  gi|116753412|ref|YP_842530.1| 150 MEATFIGNGRIAWTTRQRNDKRTLELSRSVEEL 182
                                    789999***********************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); 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: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1508.38
//
Query:       gi|116753413|ref|YP_842531.1|  [L=205]
Description: orotate phosphoribosyltransferase-like protein [Methanosaeta thermophila PT]
Scores for complete 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   73.1   0.6    2.7e-20   72.5   0.6    1.2  1  Pribosyltran    Phosphoribosyl transferase domain
    0.00054   19.5   0.1     0.0008   18.9   0.1    1.3  1  UPRTase         Uracil phosphoribosyltransferase
     0.0011   19.1   0.2     0.0018   18.3   0.2    1.4  1  Pribosyl_synth  Phosphoribosyl synthetase-associated domain
     0.0026   17.3   0.2      0.083   12.4   0.2    2.1  2  PRTase_2        Phosphoribosyl transferase
  ------ inclusion threshold ------
      0.017   14.9   0.0       0.04   13.7   0.0    1.6  1  HTH_23          Homeodomain-like domain
      0.018   15.0   0.2      0.047   13.6   0.2    1.7  1  HTH_11          HTH domain
      0.037   13.6   0.0      0.083   12.5   0.0    1.6  1  GerE            Bacterial regulatory proteins, luxR family
       0.05   13.7   0.1        0.1   12.7   0.1    1.4  1  HTH_7           Helix-turn-helix domain of resolvase
      0.078   12.6   0.3       0.34   10.6   0.1    2.2  3  GntR            Bacterial regulatory proteins, gntR family
       0.17   11.4   0.1       0.56    9.8   0.1    1.8  1  Sigma70_r4      Sigma-70, region 4


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.5   0.6   1.5e-23   2.7e-20      11     127 ..      72     185 ..      65     188 .. 0.89

  Alignments for each domain:
  == domain 1  score: 72.5 bits;  conditional E-value: 1.5e-23
                                    EEEEEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----TTSEE CS
                   Pribosyltran  11 ildavarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledpagkkV 90 
                                    i++a  +++ +il+e++  +d+vvg+a  Gvp+a+ +ad+++v la+   +k  +++  + + ++s    + +d+ g+ +
  gi|116753413|ref|YP_842531.1|  72 IAQALTEMIFDILDEKELDIDIVVGVALSGVPLASMVADHMGVGLAVYMPTKQMASQDVKPHGNLST---NFSDVSGREC 148
                                    67899*****************************************666666666666666666665...9********* PP

                                    EEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-H CS
                   Pribosyltran  91 liVDDildtGgTllaalelLkekgpeevriavlvdkp 127
                                    +iVDD++++G+Tl++a+  L ++g++   iavl+dk+
  gi|116753413|ref|YP_842531.1| 149 VIVDDVITSGRTLEEAVAYLDDRGAKTNVIAVLIDKK 185
                                    **************************99999*99986 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   4.5e-07    0.0008     114     170 ..     135     191 ..      93     195 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 4.5e-07
                        UPRTase 114 kLPkki...aertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegvkrla 170
                                    +L +++   + r+ +++D vi +G+++ +a+  L +rg++     v++vl  ++g++++a
  gi|116753413|ref|YP_842531.1| 135 NLSTNFsdvSGRECVIVDDVITSGRTLEEAVAYLDDRGAK---TNVIAVLIDKKGIDSIA 191
                                    4444443337788***********************9986...55778888888887765 PP

>> Pribosyl_synth  Phosphoribosyl synthetase-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.2     1e-06    0.0018      76     113 ..     138     175 ..     104     191 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1e-06
                                    -EES--TTSEEEEEEEEE-S-HHHHHHHHHHHHTT--E CS
                 Pribosyl_synth  76 tvvGdvgGriaiivddliddvesfvaaaevlkerGayk 113
                                    t   dv+Gr  +ivdd+i   +++ +a   l +rGa  
  gi|116753413|ref|YP_842531.1| 138 TNFSDVSGRECVIVDDVITSGRTLEEAVAYLDDRGAKT 175
                                    3468*******************************953 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.034        61      34      96 ..      71     134 ..      53     144 .. 0.70
   2 !   12.4   0.2   4.6e-05     0.083     121     160 ..     145     183 ..     135     191 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.034
                       PRTase_2  34 eagaaLaellaeakkeelpepvlvigfAEtAtaLghgvadal.eeealylhtTRekvagveell 96 
                                    ++++aL+e++ +  +e+  +  +v+g+A   + L+  vad++  + a y+ t   + ++v++  
  gi|116753413|ref|YP_842531.1|  71 HIAQALTEMIFDILDEKELDIDIVVGVALSGVPLASMVADHMgVGLAVYMPTKQMASQDVKPHG 134
                                    444555555554444455556688*****************96667888877777666666655 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 4.6e-05
                       PRTase_2 121 akelvLvDDEistGktalnliralqeklprkryvvvslvd 160
                                     +e v+vDD i++G+t+ + +  l ++  ++++ ++ l+d
  gi|116753413|ref|YP_842531.1| 145 GRECVIVDDVITSGRTLEEAVAYLDDRGAKTNV-IAVLID 183
                                    4789*****************999988776654.555665 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   0.0   2.2e-05      0.04      15      35 ..      18      38 ..       9      47 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.2e-05
                         HTH_23 15 aeGlsvreIAreLgvsrrTvy 35
                                    eGls  +I++eL+vsr T+ 
  gi|116753413|ref|YP_842531.1| 18 SEGLSEGQISEELNVSRETIT 38
                                   359****************94 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   2.6e-05     0.047      11      32 ..      15      37 ..       6      38 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.6e-05
                         HTH_11 11 eargp.isgeeLAeeLnvSrrtv 32
                                   e ++  +s  +++eeLnvSr t+
  gi|116753413|ref|YP_842531.1| 15 ELKSEgLSEGQISEELNVSRETI 37
                                   445555999*************9 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.6e-05     0.083      15      37 ..      18      40 ..      15      46 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.6e-05
                                   CTTS-HHHHHHHHTS-HHHHHHH CS
                           GerE 15 aeGksnkeIAeelniSekTVkvh 37
                                    eG+s  +I+eeln+S +T++  
  gi|116753413|ref|YP_842531.1| 18 SEGLSEGQISEELNVSRETITWL 40
                                   68*****************9865 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 ?   12.7   0.1   5.6e-05       0.1      11      38 ..      10      37 ..       4      37 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.6e-05
                                   HGGGGSSTTTT--STTTSSSS---SSSS CS
                          HTH_7 11 inrvvkLleeGisiskIAkevnisRsTv 38
                                   i  + +L +eG s  +I +e+n+sR+T+
  gi|116753413|ref|YP_842531.1| 10 IKKATELKSEGLSEGQISEELNVSRETI 37
                                   556789999******************7 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00019      0.34       6      42 ..       3      38 ..       1      47 [. 0.85
   2 ?   -2.5   0.0       2.3   4.1e+03       4      13 ..      71      80 ..      70      82 .. 0.82
   3 ?   -2.7   0.0       2.7   4.8e+03       8      37 ..      88     115 ..      86     117 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00019
                                   HHHHHHHHHTTSS-TTSB---HHHHHHHHTS-HHHHH CS
                           GntR  6 yerLredIlsgelrpGdkLPsereLaaefgVsrttvR 42
                                      ++++I++ +    + L se ++++e++Vsr t+ 
  gi|116753413|ref|YP_842531.1|  3 MKSIEDLIKKATELKSEGL-SEGQISEELNVSRETIT 38
                                   567888888888888899*.***************96 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.3
                                   HHHHHHHHHH CS
                           GntR  4 qvyerLredI 13
                                   +++++L+e+I
  gi|116753413|ref|YP_842531.1| 71 HIAQALTEMI 80
                                   7999999998 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 2.7
                                    HHHHHHHTTSS-TTSB---HHHHHHHHTS- CS
                           GntR   8 rLredIlsgelrpGdkLPsereLaaefgVs 37 
                                    +L+ dI+ g+   G +L   + +a+ +gV+
  gi|116753413|ref|YP_842531.1|  88 ELDIDIVVGVALSGVPL--ASMVADHMGVG 115
                                    67777777777777777..55666666665 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00031      0.56      19      37 ..      19      37 ..      16      45 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00031
                                   TT--HHHHHHHHTS-HHHH CS
                     Sigma70_r4 19 eglTleEIgerlgiSrerV 37
                                   egl+  +I+e+l++Sre++
  gi|116753413|ref|YP_842531.1| 19 EGLSEGQISEELNVSRETI 37
                                   5677789***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      630  (0.0351386); 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: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1472.05
//
Query:       gi|116753414|ref|YP_842532.1|  [L=149]
Description: hypothetical protein Mthe_0090 [Methanosaeta thermophila PT]
Scores for 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   57.0   0.2      3e-15   56.5   0.2    1.3  1  PIN_6           PIN domain of ribonuclease
    9.6e-05   22.9   0.4    0.00013   22.5   0.4    1.2  1  PIN             PIN domain
    0.00043   19.8   0.5     0.0012   18.3   0.2    1.8  1  PIN_5           PINc domain ribonuclease
     0.0015   18.4   2.1     0.0027   17.6   2.1    1.3  1  Prok-RING_1     Prokaryotic RING finger family 1
     0.0045   16.5   0.1      0.016   14.8   0.1    2.0  1  RecR            RecR protein
  ------ inclusion threshold ------
      0.087   12.9   1.7       0.23   11.5   1.6    1.7  2  DZR             Double zinc ribbon
       0.12   12.1   0.1       0.19   11.5   0.1    1.3  1  DUF5615         Domain of unknown function (DUF5615)
        0.3   11.2   3.7        9.1    6.5   0.4    2.3  2  DUF2256         Uncharacterized protein conserved in bacteria
       0.63    9.5   6.0        2.6    7.6   0.3    2.3  2  zf-ribbon_3     zinc-ribbon domain
       0.76    9.7   6.8        1.8    8.5   6.8    1.6  1  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
       0.83    9.8   5.9        9.2    6.5   0.4    2.6  3  Zn-ribbon_8     Zinc ribbon domain
          1    9.4   6.9       0.18   11.8   1.1    2.1  2  zf-C2HC_2       zinc-finger of a C2HC-type
          1    9.4   5.9        2.5    8.2   1.3    2.5  2  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
        1.4    8.8   6.6        3.5    7.5   0.4    2.6  2  Rad50_zn_hook   Rad50 zinc hook motif
        2.7    7.8   5.0         85    2.9   5.0    2.0  1  FdhE            Protein involved in formate dehydrogenase for
        6.1    6.6   8.0         11    5.7   0.4    2.4  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain


Domain annotation for each model (and alignments):
>> PIN_6  PIN domain of ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.5   0.2   2.7e-18     3e-15       1      88 [.       3      83 ..       3      84 .. 0.93

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 2.7e-18
                          PIN_6  1 lVlDagaliknslsslqnlaeklyttpeVvaEirdkkarerlellplelevrePspesvkkvtefakktGDlsvLSktDiev 82
                                   +V+Da+ +i    +    l+ +++t+p+V +E++d ++r +l++   +++++ P++e +k++te+a+ tGDl  LS+tD+ev
  gi|116753414|ref|YP_842532.1|  3 IVADASVFILG--K---PLKGEVITVPAVEQELKDIRSRIKLQI--SDVRIEPPTKETLKRATEAARDTGDLCRLSQTDLEV 77
                                   799******88..5...55789***************9999999..6999******************************** PP

                          PIN_6 83 lALtye 88
                                   lA ++e
  gi|116753414|ref|YP_842532.1| 78 LAKAIE 83
                                   **8875 PP

>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.4   1.1e-07   0.00013      40     120 ..      19      99 ..       3     101 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.1e-07
                                    HHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHHHHHHHHHHHHHHH....SBHHHHHHHHHHHHHT-EEE.ESSTH CS
                            PIN  40 Ellyvlarrkskrekaaelvelllllsalkilpidaeiaeeaaeialkyg....llpnDaliaAtAkehgikliatfDed 115
                                    E++ v a    ++e+++ + + +l+ s+++i p ++e +++a e a+  g    l+  D+ ++A A+e+++ +iat D  
  gi|116753414|ref|YP_842532.1|  19 EVITVPAV---EQELKDIRSRIKLQISDVRIEPPTKETLKRATEAARDTGdlcrLSQTDLEVLAKAIEYDA-AIATDDYA 94 
                                    66677777...56666667777777**********************************************.666***99 PP

                                    HHHHH CS
                            PIN 116 frrva 120
                                    + +va
  gi|116753414|ref|YP_842532.1|  95 LQNVA 99 
                                    99987 PP

>> PIN_5  PINc domain ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.2   1.1e-06    0.0012     156     191 ..      71     106 ..      59     121 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.1e-06
                          PIN_5 156 saeDldvllLAkELdaavvssDeGikkwaeklGlrl 191
                                    s+ Dl+vl  A E daa+ ++D  ++++a +lGlr+
  gi|116753414|ref|YP_842532.1|  71 SQTDLEVLAKAIEYDAAIATDDYALQNVAVHLGLRV 106
                                    899*******************************96 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 !   17.6   2.1   2.4e-06    0.0027       4      31 ..     121     144 ..     119     146 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.4e-06
                    Prok-RING_1   4 gkkCpvCgkelkeedDiVvCpeCgtpyH 31 
                                     ++Cp Cg++++ +     Cp+Cgtp  
  gi|116753414|ref|YP_842532.1| 121 TQRCPGCGRAFEGD----LCPVCGTPPK 144
                                    689**********9....9******965 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   1.4e-05     0.016       9      37 ..     114     142 ..     111     145 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.4e-05
                                    HHHHHHH-EE-TTT--EESSSS-CCCCST CS
                           RecR   9 LqeakekvrhCsrCgnlteedlCaICsdp 37 
                                    +++  ++ ++C+ Cg   e dlC++C  p
  gi|116753414|ref|YP_842532.1| 114 IRRFIKRTQRCPGCGRAFEGDLCPVCGTP 142
                                    66777899******************765 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   1.7   0.00095       1.1      28      49 .]     121     140 ..      66     140 .. 0.75
   2 ?   11.5   1.6    0.0002      0.23      12      39 ..     121     144 ..     115     149 .] 0.76

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00095
                            DZR  28 edrCpsCgekvdpearfCpeCG 49 
                                     +rCp Cg++ + +   Cp CG
  gi|116753414|ref|YP_842532.1| 121 TQRCPGCGRAFEGD--LCPVCG 140
                                    56777777766544..677776 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.0002
                            DZR  12 arfCseCgtklkavaaedrCpsCgekvd 39 
                                     + C+ Cg + +     d Cp Cg++ +
  gi|116753414|ref|YP_842532.1| 121 TQRCPGCGRAFE----GDLCPVCGTPPK 144
                                    567999999998....799999988755 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00017      0.19       6      56 ..      43      93 ..      40     109 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00017
                        DUF5615  6 DenlsprlvellreaghdvlhvrelglegasDeeileyAkeedriivTkDk 56
                                   D  + p   e l++a   +  + +l   + +D e+l+ A+e d++i T D 
  gi|116753414|ref|YP_842532.1| 43 DVRIEPPTKETLKRATEAARDTGDLCRLSQTDLEVLAKAIEYDAAIATDDY 93
                                   77788888999999999899999999889*******************995 PP

>> DUF2256  Uncharacterized protein conserved in bacteria (DUF2256)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.2     0.015        17       6      18 ..     120     132 ..     117     133 .. 0.87
   2 ?    6.5   0.4    0.0081       9.1       9      22 ..     135     148 ..     134     149 .] 0.93

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.015
                        DUF2256   6 psKiCavCgrpft 18 
                                    ++  C+ Cgr f+
  gi|116753414|ref|YP_842532.1| 120 RTQRCPGCGRAFE 132
                                    5778******996 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0081
                        DUF2256   9 iCavCgrpftwRkk 22 
                                     C+vCg p + Rkk
  gi|116753414|ref|YP_842532.1| 135 LCPVCGTPPKRRKK 148
                                    5************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 ?    3.4   6.1     0.047        52       2      25 ..     121     142 ..     120     142 .. 0.77
   2 ?    7.6   0.3    0.0023       2.6       5      14 ..     136     145 ..     132     149 .] 0.80

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.047
                    zf-ribbon_3   2 tvrCPnCGa.plssddnvCpyCGtk 25 
                                    t+rCP CG     ++d  Cp CGt+
  gi|116753414|ref|YP_842532.1| 121 TQRCPGCGRaF--EGD-LCPVCGTP 142
                                    78999999977..333.89999986 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0023
                    zf-ribbon_3   5 CPnCGaplss 14 
                                    CP CG+p++ 
  gi|116753414|ref|YP_842532.1| 136 CPVCGTPPKR 145
                                    999*996576 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 ?    8.5   6.8    0.0016       1.8      11      33 ..     121     141 ..     120     143 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0016
                        DUF35_N  11 gqrCpdCGtvqfPPravCphCgs 33 
                                     qrCp CG+ +      Cp Cg 
  gi|116753414|ref|YP_842532.1| 121 TQRCPGCGRAF--EGDLCPVCGT 141
                                    59********5..77******95 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       4.4   4.9e+03       8      22 ..      68      82 ..      67      87 .. 0.76
   2 ?    6.5   0.4    0.0082       9.2      27      35 ..     121     130 ..     110     134 .. 0.72
   3 ?    4.3   6.6      0.04        45       7      37 ..     123     145 ..     123     147 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.4
                    Zn-ribbon_8  8 CeeCghefevlqsis 22
                                   C+  +++ evl+++ 
  gi|116753414|ref|YP_842532.1| 68 CRLSQTDLEVLAKAI 82
                                   777888899998865 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0082
                    Zn-ribbon_8  27 ta.CPeCgse 35 
                                    t+ CP Cg +
  gi|116753414|ref|YP_842532.1| 121 TQrCPGCGRA 130
                                    5668888864 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.04
                    Zn-ribbon_8   7 rCeeCghefevlqsisdapltaCPeCgs.evr 37 
                                    rC  Cg+ fe            CP Cg  + r
  gi|116753414|ref|YP_842532.1| 123 RCPGCGRAFE---------GDLCPVCGTpPKR 145
                                    7999**9999.........456*****94444 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 ?   11.8   1.1   0.00016      0.18       2      12 ..     121     131 ..     120     133 .. 0.90
   2 ?    0.6   0.5      0.52   5.8e+02       5       9 ..     136     140 ..     135     140 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00016
                      zf-C2HC_2   2 lvpCpkCgRsF 12 
                                    ++ Cp+CgR F
  gi|116753414|ref|YP_842532.1| 121 TQRCPGCGRAF 131
                                    789******99 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.52
                      zf-C2HC_2   5 CpkCg 9  
                                    Cp Cg
  gi|116753414|ref|YP_842532.1| 136 CPVCG 140
                                    ****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 ?    2.9   0.2     0.099   1.1e+02       1       8 [.     123     130 ..     123     132 .. 0.81
   2 ?    8.2   1.3    0.0022       2.5       2       8 ..     136     142 ..     136     147 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.099
                 DNA_ligase_ZBD   1 hCPvCGsa 8  
                                    +CP CG a
  gi|116753414|ref|YP_842532.1| 123 RCPGCGRA 130
                                    5****965 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0022
                 DNA_ligase_ZBD   2 CPvCGsa 8  
                                    CPvCG++
  gi|116753414|ref|YP_842532.1| 136 CPVCGTP 142
                                    *****98 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 ?    7.5   0.4    0.0031       3.5      19      31 ..     121     133 ..     118     135 .. 0.82
   2 ?    4.1   1.2     0.036        40      21      28 ..     135     142 ..     132     142 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0031
                                    SEE-TTT--EE-H CS
                  Rad50_zn_hook  19 kgcCPlCgRelde 31 
                                    +++CP CgR ++ 
  gi|116753414|ref|YP_842532.1| 121 TQRCPGCGRAFEG 133
                                    569*******986 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.036
                                    E-TTT--E CS
                  Rad50_zn_hook  21 cCPlCgRe 28 
                                     CP+Cg +
  gi|116753414|ref|YP_842532.1| 135 LCPVCGTP 142
                                    5****976 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 ?    2.9   5.0     0.076        85     167     178 ..     132     143 ..      22     145 .. 0.65

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.076
                                    T-SS-TTT---E CS
                           FdhE 167 ekglCPvCgsaP 178
                                    e  lCPvCg++P
  gi|116753414|ref|YP_842532.1| 132 EGDLCPVCGTPP 143
                                    345788888877 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   1.9     0.035        39       2      11 ..     120     129 ..     119     131 .. 0.66
   2 ?    5.7   0.4      0.01        11       6      12 ..     136     142 ..     135     147 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.035
                  zf-NADH-PPase   2 thrFCgrCGa 11 
                                    +++ C+ CG 
  gi|116753414|ref|YP_842532.1| 120 RTQRCPGCGR 129
                                    5677777774 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.01
                  zf-NADH-PPase   6 CgrCGap 12 
                                    C+ CG+p
  gi|116753414|ref|YP_842532.1| 136 CPVCGTP 142
                                    9****99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      617  (0.0344135); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1170.02
//
Query:       gi|116753415|ref|YP_842533.1|  [L=310]
Description: cobalt ABC transporter, inner membrane subunit CbiQ [Methanosaeta thermophila PT]
Scores for complete 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-33  115.7  13.8    4.1e-33  114.9  13.8    1.3  1  CbiQ      Cobalt transport protein
  ------ inclusion threshold ------
        6.2    6.0   7.4         11    5.2   7.4    1.3  1  Bunya_G2  Bunyavirus glycoprotein G2


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 !  114.9  13.8   4.5e-37   4.1e-33       5     211 ..      54     274 ..      51     280 .. 0.81

  Alignments for each domain:
  == domain 1  score: 114.9 bits;  conditional E-value: 4.5e-37
                                    CCS-HHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHTTS---.......HHHHHHHCCCHCHHHHHHHHHHE.... CS
                           CbiQ   5 lhrldprvkliwlfllllalvlapnlvtlliiiallllllllvilp.......rvlaqalilpllflllgllillf.... 73 
                                    l  ldpr kli +++l++a+++  nl+ +  ++ l++l+++   +        rv+++++i+ +   ++      +    
  gi|116753415|ref|YP_842533.1|  54 LQSLDPRIKLISMLSLIFAISMTKNLEIIA-LFYLMTLIFAYLSSIsivffvkRVWLFIPIFTGVIAIP------Mtlni 126
                                    6789**********************9994.44444444443333322444455555555555554444......45555 PP

                                    ...................EECTTEEE....E-TTHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHCCCSS--HHHH CS
                           CbiQ  74 ............qlittegefvfaggg.qisitseGllrglllalRiltllslllllalTTppeeltsslerlgvPlela 140
                                                +  ++  ++   ++   i its+G+  ++l+++R+++++s+++ll+lTTp   l++sl+++gvP++ +
  gi|116753415|ref|YP_842533.1| 127 flpgdvliplvdL--GQRAHIGPFAMPeSIYITSQGTRAAVLFTIRVAACVSAVVLLFLTTPQRALFKSLRSIGVPKVYV 204
                                    559****987541..3344444333335899************************************************* PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHTTTTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS-SS CS
                           CbiQ 141 lillLayRfiflLleevqrikqAqklRlgdsklgirrslrslgkliaalflralkraervalAmeaRGYtg 211
                                    l+l  a R+ifl++e v++++ A ++R+++s+ ++++  r +g  i+ ++++al+++e+v  Am +RG++g
  gi|116753415|ref|YP_842533.1| 205 LTLEMANRYIFLFMEMVRDLYIAKRSRTIKSRGTLAE-QRWVGGRIGYMLIKALDMSEKVHMAMISRGFSG 274
                                    *******************************888888.9*******************************9 PP

>> Bunya_G2  Bunyavirus glycoprotein G2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   7.4    0.0012        11     173     222 ..      65     117 ..      58     127 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0012
                       Bunya_G2 173 silpgsiaisicqnieliilvilallifilliilsktyi...cyllipvfipi 222
                                    s+l   +ais+ +n+e+i l  l  lif  l+ +s  +    ++l+ip+f  +
  gi|116753415|ref|YP_842533.1|  65 SMLSLIFAISMTKNLEIIALFYLMTLIFAYLSSISIVFFvkrVWLFIPIFTGV 117
                                    56667789********************9998888776522257888888754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       830  (0.0462937); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 2085.71
//
Query:       gi|116753416|ref|YP_842534.1|  [L=282]
Description: ABC transporter related [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.1e-32  111.6   0.0    6.1e-32  111.0   0.0    1.3  1  ABC_tran     ABC transporter
    1.4e-17   64.5   0.6    4.3e-10   39.9   0.0    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    3.2e-08   33.3   0.0    7.1e-08   32.1   0.0    1.6  1  SMC_N        RecF/RecN/SMC N terminal domain
    3.5e-08   33.5   0.0     0.0022   17.8   0.1    2.1  2  AAA_15       AAA ATPase domain
    8.2e-06   25.5   0.0    1.7e-05   24.5   0.0    1.5  1  AAA_29       P-loop containing region of AAA domain
     0.0046   17.5   0.0     0.0064   17.0   0.0    1.3  1  AAA_23       AAA domain
  ------ inclusion threshold ------
      0.026   14.9   0.0      0.036   14.4   0.0    1.5  1  AAA_16       AAA ATPase domain
      0.045   14.0   0.0       0.22   11.8   0.0    2.1  2  AAA_28       AAA domain
       0.05   13.8   0.0       0.62   10.3   0.0    2.3  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
      0.058   13.3   0.1       0.24   11.3   0.0    1.9  2  NACHT        NACHT domain
       0.11   12.4   0.0       0.29   11.1   0.0    1.7  1  AAA_5        AAA domain (dynein-related subfamily)
       0.14   12.1   0.0       0.29   11.0   0.0    1.5  1  RsgA_GTPase  RsgA GTPase
        0.2   12.6   0.5       0.44   11.5   0.5    1.5  1  Pup          Pup-like protein


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.0   0.0   4.4e-35   6.1e-32       1     137 []      26     181 ..      26     181 .. 0.93

  Alignments for each domain:
  == domain 1  score: 111.0 bits;  conditional E-value: 4.4e-35
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.........B-HHHCCHCEEEE-SS..-- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxx..xx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.........qeleslrkeigvlpqe..pq 69 
                                    l++++l +++ge va++G nG+GKStLl+++  l  pt+G+    g++++e         + ++++r+++g+++q+   q
  gi|116753416|ref|YP_842534.1|  26 LEDINLRISQGEQVALLGANGSGKSTLLAIIDALIYPTSGQYYAFGTHVNEeifgtlkdnEFKRFFRSKVGFVFQNpdVQ 105
                                    689***************************************77788888889999988777889***********7777 PP

                                    S-TTSBHHHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    xxxxxxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  70 lfpeltvren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                    lf+ + v ++             e  +++e++++ lg+++l+++      ++LSgG+k++v++a +l+++p++lllDEpt
  gi|116753416|ref|YP_842534.1| 106 LFSST-VFDEiafgphqldmpmeEVGRRVEELMEMLGISKLRNRAP----HTLSGGEKKKVCIASVLATNPDVLLLDEPT 180
                                    77777.77778*********99999999************999998....*****************************9 PP

                                    T CS
                                    x RF
                       ABC_tran 137 a 137
                                    a
  gi|116753416|ref|YP_842534.1| 181 A 181
                                    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 !   22.8   0.2   5.1e-08   7.1e-05       3      53 ..      40      93 ..      39      99 .. 0.84
   2 !   39.9   0.0   3.1e-13   4.3e-10     194     303 .]     110     216 ..     106     216 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 5.1e-08
                         AAA_21  3 vliGpNgsGKSnLLdaldllarl...drdvegltdelsggggirkipslldlyd 53
                                   +l G+NgsGKS+LL ++d l      + +++g++ ++  +g++++ +++ ++++
  gi|116753416|ref|YP_842534.1| 40 ALLGANGSGKSTLLAIIDALIYPtsgQYYAFGTHVNEEIFGTLKDNEFKRFFRS 93
                                   799***************997769999999999999988888888887777665 PP

  == domain 2  score: 39.9 bits;  conditional E-value: 3.1e-13
                         AAA_21 194 lveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPk 273
                                    +v++e+ +  ++ ++++++  r  e+ +  l  ++ +++ ++ lS G k+  ++++ l+  +   ++ll+DEp +gL+P+
  gi|116753416|ref|YP_842534.1| 110 TVFDEIAFGPHQLDMPMEEVGRRVEELMEMLGISKLRNRAPHTLSGGEKKKVCIASVLATNP---DVLLLDEPTAGLDPR 186
                                    5667777777788888888888888888888899999999***********88888888777...9************** PP

                         AAA_21 274 llrrllellkelsrngaQviltTHSpllld 303
                                     +  l+ell+el++ g  +i +TH+  ++d
  gi|116753416|ref|YP_842534.1| 187 SQLWLIELLNELASCGKTIITATHDLDIID 216
                                    ************9999999******99987 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 !   32.1   0.0   5.2e-11   7.1e-08      25     198 ..      37     210 ..      15     231 .. 0.73

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 5.2e-11
                                    SEEEEEESTTSSHHH...HHHHHHHHCTT.TTTTTTCHCCCCCC--..BTTCSSTTEEEEEEEEEETTEESSSSSSCEEE CS
                                    xxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  25 sftaivGpNGSGKsn...lldAilFvLGersakklrseklsdlihk..skekasvkkaeveitfdnedkklkiekeevsi 99 
                                    +  a++G+NGSGKs    ++dA+ +  + + + ++  +  +++      +e ++  + +v  +f+n+d +l    ++++ 
  gi|116753416|ref|YP_842534.1|  37 EQVALLGANGSGKSTllaIIDALIYPTSGQYY-AFGTHVNEEIFGTlkDNEFKRFFRSKVGFVFQNPDVQLF---SSTVF 112
                                    46789*********7333689**999997666.8988888887766656778888999**********9933...33344 PP

                                    EEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT...CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 100 srrvkrkgeseykingkevtkkevsellesagiske...lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknv 176
                                       ++   + ++ +++   + +e++e+l  +++      +LSgGek+ v +a ++A++   p  + llDe  a LD +  
  gi|116753416|ref|YP_842534.1| 113 DEIAFGPHQLDMPMEEVGRRVEELMEMLGISKLRNRaphTLSGGEKKKVCIASVLATN---PD-VLLLDEPTAGLDPRSQ 188
                                    4444444555666666666666666666666664324449************999875...55.5699************ PP

                                    HHHHHHHHHHCTTSEEEEE-SS CS
                                    xxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 177 kkvaellkeksknaQfivislr 198
                                      + ell+e  +    i+++ +
  gi|116753416|ref|YP_842534.1| 189 LWLIELLNELASCGKTIITATH 210
                                    **********999888777543 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   1.6e-06    0.0022      12      50 ..      24      63 ..      23     110 .. 0.70
   2 !   13.4   0.0   3.3e-05     0.046     322     369 .]     169     215 ..     157     215 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.6e-06
                         AAA_15 12 Rslkdveidlsee.ltvliGkNnsGKSsilealdlFlnnk 50
                                   ++l+d+ + +s      l G+N+sGKS++l ++d ++  +
  gi|116753416|ref|YP_842534.1| 24 KALEDINLRISQGeQVALLGANGSGKSTLLAIIDALIYPT 63
                                   67888777777767889******************99866 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 3.3e-05
                         AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSphii 369
                                    +++++ll++EP a L p  q  li+ll ela+ +k  +i  TH   ii
  gi|116753416|ref|YP_842534.1| 169 TNPDVLLLDEPTAGLDPRSQLWLIELLNELASCGK-TIITATHDLDII 215
                                    5789******************************8.78888**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 !   24.5   0.0   1.2e-08   1.7e-05      17      50 ..      31      64 ..      15      70 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.2e-08
                         AAA_29 17 ieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                   ++i++ + + l G++GsGKSTll  i al++p++
  gi|116753416|ref|YP_842534.1| 31 LRISQGEQVALLGANGSGKSTLLAIIDALIYPTS 64
                                   566645599**************77888999887 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   4.7e-06    0.0064      22      48 ..      39      65 ..      20     137 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.7e-06
                         AAA_23 22 tlItGpNGaGKTTildAiklaLygetp 48
                                   +++ G NG+GK+T+l  i    y  ++
  gi|116753416|ref|YP_842534.1| 39 VALLGANGSGKSTLLAIIDALIYPTSG 65
                                   4789**********9888777775433 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   2.6e-05     0.036      19      51 ..      31      63 ..      21     206 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.6e-05
                         AAA_16 19 vrsgrpelvllsGesGvGKsslvrellralekd 51
                                   +r +++e v l G+ G+GKs+l+  +   +  +
  gi|116753416|ref|YP_842534.1| 31 LRISQGEQVALLGANGSGKSTLLAIIDALIYPT 63
                                   34455588***************8777544433 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00016      0.22       2      25 ..      39      62 ..      38     135 .. 0.78
   2 ?   -0.3   0.0      0.83   1.1e+03       9      40 ..     200     238 ..     199     263 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00016
                         AAA_28  2 ivitGgestGKTtlleaLaargyp 25
                                   ++++G+ ++GK+tll+ + a  yp
  gi|116753416|ref|YP_842534.1| 39 VALLGANGSGKSTLLAIIDALIYP 62
                                   89*************998866333 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.83
                         AAA_28   9 stGKTtll..eaLa.....argypvvpEaareileekla 40 
                                    s+GKT ++    L      +r   v+ E +r +++ + +
  gi|116753416|ref|YP_842534.1| 200 SCGKTIITatHDLDiidkiSRRAIVIGENHRVVVDRGVD 238
                                    899996552255555544333455667777777766654 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   0.0   0.00045      0.62      28      89 ..     148     196 ..     132     197 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00045
                        SbcCD_C  28 rssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                    r   tlSGGek     +++a    +++        ++++++LDE  ++lD++s+  l+ell+
  gi|116753416|ref|YP_842534.1| 148 RAPHTLSGGEK---KKVCIA----SVLAT------NPDVLLLDEPTAGLDPRSQLWLIELLN 196
                                    55578888888...566666....33333......5899*************9999998886 PP

>> NACHT  NACHT domain
   #    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       2      20 ..      38      56 ..      37      68 .. 0.87
   2 ?   -0.8   0.0       0.9   1.2e+03      91     130 ..     177     210 ..     149     225 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00017
                                   CEEEEC-TTTCHHHHHHHH CS
                          NACHT  2 lvilqGeaGsGKTtLlqkl 20
                                   +v+l G++GsGK+tLl+ +
  gi|116753416|ref|YP_842534.1| 38 QVALLGANGSGKSTLLAII 56
                                   689*************855 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.9
                                    TT-SS-TCH.........HHHHHCTTTTT--EEEEEEECC CS
                          NACHT  91 DelvtdlgqkekqpvrtlLselirkkllpeasllltvrpr 130
                                    De  + l++    +++ +L el+++  l ++   +++ + 
  gi|116753416|ref|YP_842534.1| 177 DEPTAGLDP----RSQLWLIELLNE--LASCGKTIITATH 210
                                    666666666....778889999999..5555555444444 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 ?   11.1   0.0   0.00021      0.29       2      38 ..      39      76 ..      38      98 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00021
                                   EEEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT--H CS
                          AAA_5  2 vlLvGppGtgKselaerlaaal.nreveyvqltrdtte 38
                                   v L+G+ G+gKs+l   + a++  ++ +y+++    +e
  gi|116753416|ref|YP_842534.1| 39 VALLGANGSGKSTLLAIIDALIyPTSGQYYAFGTHVNE 76
                                   779*******************9999999998877665 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      87     119 ..      23      56 ..      10      65 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00021
                                    HTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHH CS
                    RsgA_GTPase  87 kegleelkellkd.ktsvlvGqSGvGKStLinal 119
                                     ++le+++ ++++ + ++l+G  G GKStL+  +
  gi|116753416|ref|YP_842534.1|  23 LKALEDINLRISQgEQVALLGANGSGKSTLLAII 56 
                                    5678888888887799**************9766 PP

>> Pup  Pup-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.5   0.00032      0.44      36      54 ..     233     251 ..     220     254 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00032
                            Pup  36 lsedvDdlLDeIDevLEeN 54 
                                    ++  vDd+L++ID +LE+N
  gi|116753416|ref|YP_842534.1| 233 VDRGVDDVLNDIDLLLETN 251
                                    5678**************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); 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: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2006.88
//
Query:       gi|116753417|ref|YP_842535.1|  [L=346]
Description: TGS domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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-29   99.9   0.0    1.4e-28   99.0   0.0    1.5  1  MMR_HSR1_Xtn   C-terminal region of MMR_HSR1 domain
    8.1e-20   70.6   0.0    1.9e-19   69.5   0.0    1.7  1  TGS            TGS domain
    2.7e-06   27.4   0.0    6.3e-06   26.2   0.0    1.7  1  MMR_HSR1       50S ribosome-binding GTPase
     0.0002   21.3   0.1     0.0064   16.4   0.0    2.4  2  RsgA_GTPase    RsgA GTPase
    0.00028   20.4   0.0      0.014   15.0   0.0    2.3  2  FeoB_N         Ferrous iron transport protein B
    0.00061   18.9   0.1        0.9    8.5   0.2    2.4  2  MeaB           Methylmalonyl Co-A mutase-associated GTPase Me
     0.0019   18.7   0.9     0.0047   17.5   0.0    2.1  2  ABC_tran       ABC transporter
     0.0061   16.1   0.2        1.1    8.8   0.0    3.0  2  GTP_EFTU       Elongation factor Tu GTP binding domain
  ------ inclusion threshold ------
      0.018   14.0   0.0      0.027   13.4   0.0    1.2  1  AAA_PrkA       PrkA AAA domain
       0.02   14.5   0.1      0.064   12.8   0.0    1.9  2  cobW           CobW/HypB/UreG, nucleotide-binding domain
      0.024   14.4   0.4      0.085   12.6   0.6    1.9  2  AAA_30         AAA domain
      0.032   14.4   0.6        1.1    9.5   0.0    2.8  1  YchF-GTPase_C  Protein of unknown function (DUF933)
      0.033   14.5   0.0      0.072   13.4   0.0    1.7  1  AAA_22         AAA domain
      0.037   14.1   1.8       0.81    9.7   0.0    2.4  2  Dynamin_N      Dynamin family
       0.04   14.3   0.6      0.097   13.0   0.5    2.0  1  AAA_16         AAA ATPase domain
       0.04   13.3   0.0      0.071   12.5   0.0    1.3  1  Mg_chelatase   Magnesium chelatase, subunit ChlI
       0.05   13.8   0.1       0.38   11.0   0.0    2.1  2  Roc            Ras of Complex, Roc, domain of DAPkinase
      0.057   13.2   0.0       0.61    9.8   0.0    2.1  2  ATP_bind_1     Conserved hypothetical ATP binding protein
      0.058   12.8   1.6      0.073   12.5   0.0    1.8  2  SRPRB          Signal recognition particle receptor beta subu
      0.063   13.0   0.6       0.13   12.0   0.6    1.4  1  AAA_29         P-loop containing region of AAA domain
      0.064   13.3   0.0       0.11   12.5   0.0    1.3  1  TsaE           Threonylcarbamoyl adenosine biosynthesis prote
      0.068   13.3   0.6       0.17   12.1   0.0    1.9  2  AAA_33         AAA domain
        0.1   12.7   0.0       0.16   12.1   0.0    1.3  1  MnmE_helical   MnmE helical domain
       0.14   11.1   0.4       0.26   10.2   0.4    1.3  1  Spore_IV_A     Stage IV sporulation protein A (spore_IV_A)
       0.25   10.2   1.2        0.4    9.5   0.2    1.7  2  AFG1_ATPase    AFG1-like ATPase
       0.72   10.1   0.0       0.72   10.1   0.0    2.5  3  AAA_28         AAA domain
        8.1    6.6  14.2        3.3    7.8   3.2    2.6  2  DUF1192        Protein of unknown function (DUF1192)


Domain annotation for each model (and alignments):
>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.0   0.0   2.1e-31   1.4e-28       1     106 []     169     270 ..     169     270 .. 0.96

  Alignments for each domain:
  == domain 1  score: 99.0 bits;  conditional E-value: 2.1e-31
                   MMR_HSR1_Xtn   1 kgGikitstvkltkldeetvkkilkeykihnaevliredvtvDdlidviegnrvYipclyvlNKiDlisleeldelarep 80 
                                    +gGi++tstv+   +d+  +++il+eykih+a+vlire++t++++id++e nr Yi+++ v+NK+D ++ +el+    + 
  gi|116753417|ref|YP_842535.1| 169 RGGISVTSTVD-PGIDKGSIEAILREYKIHSADVLIRERLTQERFIDALEANRRYIKAIHVMNKVDILDPDELEF---DG 244
                                    69*********.55********************************************************99975...55 PP

                   MMR_HSR1_Xtn  81 nsvviSaekelnldeLkekiweeLnL 106
                                    +++++Sa ++++l++Lk++i+e+L+L
  gi|116753417|ref|YP_842535.1| 245 DVIPTSAVDGTGLERLKDEIFERLDL 270
                                    89**********************97 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.5   0.0   2.8e-22   1.9e-19       1      59 [.     271     343 ..     271     344 .. 0.99

  Alignments for each domain:
  == domain 1  score: 69.5 bits;  conditional E-value: 2.8e-22
                                    EEEEE.TTSSEEE......EETTB-HHHHHHHHSTTHHHHEEEEEECS.......EEEETTSBB-SSEEEEEE CS
                            TGS   1 irvyt.PdGkvpd......lprgatveDfAykIhrslakkfiyAlVnG.......qrvgldhvLedgdvveIv 59 
                                    ir+++ P+Gk pd      ++rga + D++ +Ih+++ ++f+yA V+G       qr gldh L dgd+v+Iv
  gi|116753417|ref|YP_842535.1| 271 IRIFMkPQGKPPDldepmiMRRGANIGDLCDRIHKDFRQRFRYATVWGssakhngQRAGLDHILSDGDIVTIV 343
                                    89**********************************************************************8 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   9.5e-09   6.3e-06       2      84 ..      63     135 ..      62     166 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 9.5e-09
                                    EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHCTSEEEE CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflaleeadlill 81 
                                    v +vG   +GKStL+++ltg+  ++s+ p    +i+ g ++++g +i+++D+p  i         g+a+ a++++dl+ll
  gi|116753417|ref|YP_842535.1|  63 VTLVGPVGAGKSTLVSRLTGA--RTSEDP-YSMEITPGILQHRGAKIQILDVPD-IT------VSGDALSAVRDSDLVLL 132
                                    889*****************5..555555.457888888888899*********.65......58999999999*****9 PP

                                    EEE CS
                       MMR_HSR1  82 vvd 84 
                                    v +
  gi|116753417|ref|YP_842535.1| 133 VTE 135
                                    987 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   9.6e-06    0.0064      97     123 ..      58      84 ..       9     108 .. 0.77
   2 ?    2.7   0.0      0.16   1.1e+02      36      65 ..     210     240 ..     177     271 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 9.6e-06
                                    CTTSEEEEECSTTSSHHHHHHHHCTT- CS
                    RsgA_GTPase  97 lkdktsvlvGqSGvGKStLinallpel 123
                                      d t++lvG+ G+GKStL+ +l++  
  gi|116753417|ref|YP_842535.1|  58 SGDATVTLVGPVGAGKSTLVSRLTGAR 84 
                                    3468999****************9864 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.16
                                    HHHHHHHH..HTT-EEEEEEE-GGG--HHHHH CS
                    RsgA_GTPase  36 drfLvlae..ekgiepvivlnKiDlleeeeel 65 
                                    +rf+ ++e  ++ i+ + v+nK+D+l+ +e l
  gi|116753417|ref|YP_842535.1| 210 ERFIDALEanRRYIKAIHVMNKVDILDPDE-L 240
                                    566654440055689999*******99988.3 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 !   15.0   0.0   2.1e-05     0.014       2      56 ..      62     113 ..      61     122 .. 0.93
   2 ?    3.2   0.0     0.083        55     133     156 .]     241     264 ..     213     264 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.1e-05
                                    EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE--- CS
                         FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPG 56 
                                    tv+lvG   +Gk+tl+ +ltga+++   ++   +e + g l+++g +++i+D+P 
  gi|116753417|ref|YP_842535.1|  62 TVTLVGPVGAGKSTLVSRLTGARTSEDPYS---MEITPGILQHRGAKIQILDVPD 113
                                    799********************9999886...899*****************96 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.083
                                    HHTS-EEEEBTTTTBTHHHHHHHH CS
                         FeoB_N 133 kLgvpvvktsakkkegieellkai 156
                                    +++ +v++tsa +++g+e+l+++i
  gi|116753417|ref|YP_842535.1| 241 EFDGDVIPTSAVDGTGLERLKDEI 264
                                    46678***************9986 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.2    0.0014       0.9      24      50 ..      56      81 ..      33      88 .. 0.81
   2 !    7.8   0.0    0.0021       1.4     188     231 ..     227     270 ..     198     280 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0014
                                   GG-S-SEEEEEEE-TTSSHHHHHHHHH CS
                           MeaB 24 akaGraqvvGltGvPGaGkstlvealg 50
                                    k+G a+ v l G  GaGkstlv++l+
  gi|116753417|ref|YP_842535.1| 56 RKSGDAT-VTLVGPVGAGKSTLVSRLT 81
                                   6777776.679999***********97 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0021
                                    HHHHHHHHCSTTBTTB--EEEEEBCCCTBSHHHHHHHHHHHHHH CS
                           MeaB 188 elraaleleeekekeWrpkvlktsavegeGidelvdaieehrev 231
                                    ++++ +++++++e e+   v+ tsav g G+++l d+i e  + 
  gi|116753417|ref|YP_842535.1| 227 HVMNKVDILDPDELEFDGDVIPTSAVDGTGLERLKDEIFERLDL 270
                                    23334445555899***********************9887665 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0     7e-06    0.0047      12      36 ..      61      85 ..      54     126 .. 0.84
   2 ?   -2.2   0.0       8.3   5.5e+03      31      52 ..     190     214 ..     166     263 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 7e-06
                                   SEEEEEESTTSSHHHHHHHHTTSS- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran 12 ekvaivGenGaGKStLlkllagllk 36
                                    +v +vG+ GaGKStL++ l+g  +
  gi|116753417|ref|YP_842535.1| 61 ATVTLVGPVGAGKSTLVSRLTGART 85
                                   6899****************99765 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 8.3
                                    HTTSS--SEEEEEETTCEGGG...B CS
                                    xxxxxxxxxxxxxxxxxxxxx...x RF
                       ABC_tran  31 lagllkpteGeilldgkdlke...q 52 
                                    +++++k  + ++l++++ ++e   +
  gi|116753417|ref|YP_842535.1| 190 ILREYKIHSADVLIRERLTQErfiD 214
                                    4444444444444444444442221 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 !    8.8   0.0    0.0016       1.1       6      26 ..      63      83 ..      60     134 .. 0.90
   2 ?    3.4   0.0     0.072        48     118     136 ..     218     239 ..     207     268 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0016
                                   EEEEESTTSSHHHHHHHHHHH CS
                       GTP_EFTU  6 igiighvDhGKtTLtdrLlyk 26
                                   ++++g v +GK+TL+ rL+ +
  gi|116753417|ref|YP_842535.1| 63 VTLVGPVGAGKSTLVSRLTGA 83
                                   7899**************855 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.072
                                    HHHTTTEEEEEEESCGST...H CS
                       GTP_EFTU 118 alkegvpiivfiNKmDrl...k 136
                                    a+++ ++ i ++NK+D l   +
  gi|116753417|ref|YP_842535.1| 218 ANRRYIKAIHVMNKVDILdpdE 239
                                    5556677888888888774332 PP

>> AAA_PrkA  PrkA AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     4e-05     0.027      91     124 ..      63      96 ..      46     101 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4e-05
                       AAA_PrkA  91 lyllGPvggGksslverlkklleaapiyalegsP 124
                                    + l+GPvg+Gks+lv rl  +  ++  y +e +P
  gi|116753417|ref|YP_842535.1|  63 VTLVGPVGAGKSTLVSRLTGARTSEDPYSMEITP 96 
                                    679***************9888777778877776 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   9.7e-05     0.064       3      24 ..      63      84 ..      61      94 .. 0.80
   2 ?   -1.8   0.0         3     2e+03     145     156 ..     227     238 ..     195     245 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.7e-05
                                   EEEEESTTCCHHHHHHHHHCT- CS
                           cobW  3 tvltGflGsGKTtLlnhllenr 24
                                   + l+G++G+GK+tL+++l+  r
  gi|116753417|ref|YP_842535.1| 63 VTLVGPVGAGKSTLVSRLTGAR 84
                                   679**************99333 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3
                                    EEEE-HHHHCHC CS
                           cobW 145 lvlnKtDlldee 156
                                     v+nK+D ld +
  gi|116753417|ref|YP_842535.1| 227 HVMNKVDILDPD 238
                                    488999988766 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.6   0.00013     0.085      12      45 ..      54      87 ..      36      97 .. 0.86
   2 ?   -2.4   0.0       4.8   3.2e+03       4      23 ..     324     343 ..     323     344 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00013
                         AAA_30 12 alltsgdrvavltGpAGtGKttalkalreaweaa 45
                                    + +sgd +++l+Gp G+GK+t+++ l+ a +++
  gi|116753417|ref|YP_842535.1| 54 GVRKSGDATVTLVGPVGAGKSTLVSRLTGARTSE 87
                                   5678999******************999887776 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.8
                         AAA_30   4 aeQaaavealltsgdrvavl 23 
                                    ++Q+a ++++l++gd v+++
  gi|116753417|ref|YP_842535.1| 324 NGQRAGLDHILSDGDIVTIV 343
                                    58************988775 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 ?    9.5   0.0    0.0016       1.1      17      45 ..     290     318 ..     288     344 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0016
                  YchF-GTPase_C  17 ikkgttapqaAgviHsDfekgFiraevik 45 
                                    +++g+++ + +  iH+Df++ F  a v  
  gi|116753417|ref|YP_842535.1| 290 MRRGANIGDLCDRIHKDFRQRFRYATVWG 318
                                    57889999999***********9999865 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   0.00011     0.072       6      29 ..      61      84 ..      56     164 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00011
                         AAA_22  6 gilvvtGesGtGKTtllrrlleql 29
                                     ++++G++G+GK+tl+ rl+   
  gi|116753417|ref|YP_842535.1| 61 ATVTLVGPVGAGKSTLVSRLTGAR 84
                                   56789**************98765 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.7      0.14        93      47      87 ..      16      56 ..       5      59 .. 0.76
   2 ?    9.7   0.0    0.0012      0.81       1      22 [.      63      84 ..      63     135 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.14
                                   CCS...SSEEEET-EB--CHHHHHHHHHHHHHHHTSSSS-- CS
                      Dynamin_N 47 seravkeelkekekkledfsevreeieketekiagankgis 87
                                   +++++k++ +   +   ++ ++ree+ek+t+  a+++kg+ 
  gi|116753417|ref|YP_842535.1| 16 RTQKNKATEHHIGRLKAKIARLREEQEKRTASRAKKGKGVR 56
                                   3445555555559999******************9999986 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0012
                                   EEEEEBTTTTHHHHHHHHHTS- CS
                      Dynamin_N  1 iavvGsqSsGKSSvlnaLlged 22
                                   +++vG + +GKS+++  L+g++
  gi|116753417|ref|YP_842535.1| 63 VTLVGPVGAGKSTLVSRLTGAR 84
                                   689*****************98 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.5   0.00015     0.097      21      51 ..      57      87 ..      37     273 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00015
                         AAA_16 21 sgrpelvllsGesGvGKsslvrellralekd 51
                                   +++   v l+G+ G GKs+lv +l  a + +
  gi|116753417|ref|YP_842535.1| 57 KSGDATVTLVGPVGAGKSTLVSRLTGARTSE 87
                                   33337999*************9998544444 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00011     0.071       9      44 ..      47      82 ..      41      95 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                   Mg_chelatase  9 eeakraleiaaaGgHnlllvGppGsGKtmlakrlps 44
                                   ++ak+   +  +G   + lvGp G+GK+ l +rl++
  gi|116753417|ref|YP_842535.1| 47 SRAKKGKGVRKSGDATVTLVGPVGAGKSTLVSRLTG 82
                                   567888889999*********************986 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00058      0.38       2      27 ..      63      88 ..      62     111 .. 0.83
   2 ?    0.2   0.0       1.2   8.1e+02      94     119 ..     208     233 ..     192     234 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00058
                                   EEEESSTTSSHHHHHHCHCT-CCC-E CS
                            Roc  2 vvlvGdsgvGKtsllkrfvedkfsek 27
                                   v lvG  g+GK++l++r++  + se+
  gi|116753417|ref|YP_842535.1| 63 VTLVGPVGAGKSTLVSRLTGARTSED 88
                                   789***************99887765 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.2
                                    CHHHHHHHHHHHCSSS-EEEEEE-TT CS
                            Roc  94 nlkeWlkelkkvagkspvilvgnkiD 119
                                    + ++ ++ l+++++ +++i v+nk+D
  gi|116753417|ref|YP_842535.1| 208 TQERFIDALEANRRYIKAIHVMNKVD 233
                                    4567899999999999********99 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00091      0.61       2      21 ..      66      85 ..      65      96 .. 0.84
   2 ?    0.8   0.0      0.52   3.4e+02     155     178 ..     221     245 ..     203     275 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00091
                     ATP_bind_1  2 vGpaGsGKttfvgalseile 21
                                   vGp+G+GK+t+v++l+  ++
  gi|116753417|ref|YP_842535.1| 66 VGPVGAGKSTLVSRLTGART 85
                                   8************9987665 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.52
                     ATP_bind_1 155 lelPhvvvlnkfDllkek.lekele 178
                                      +  + v+nk+D+l+ + le++ +
  gi|116753417|ref|YP_842535.1| 221 RYIKAIHVMNKVDILDPDeLEFDGD 245
                                    5567899*******99665555544 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 ?   -2.0   0.6       3.2   2.1e+03     136     169 ..       9      52 ..       4      56 .. 0.57
   2 ?   12.5   0.0   0.00011     0.073       4      57 ..      61     112 ..      58     116 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 3.2
                                    HHHHHHHHHHHCHHHHHH--..........----T....T---- CS
                          SRPRB 136 aLEkElnkiierrskalkel..........deeedksavlakkg 169
                                    aLE+E+ + +++++ + +            +e+e+++a  akkg
  gi|116753417|ref|YP_842535.1|   9 ALEEEILRTQKNKATEHHIGrlkakiarlrEEQEKRTASRAKKG 52 
                                    78888877666666544333455555555555555555555555 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00011
                                    -EEEEE-STTSSHHHHHHHHHHSS---B---SS-EEETTG...GGTT-SEEEET CS
                          SRPRB   4 pavllvGlsdsGKTslftrLttdsvkktvtSqessaalkvksekgskltliDfP 57 
                                     +v lvG+  +GK +l  rLt   + +   S+e  ++  + +++g k++++D+P
  gi|116753417|ref|YP_842535.1|  61 ATVTLVGPVGAGKSTLVSRLTGARTSEDPYSME--ITPGILQHRGAKIQILDVP 112
                                    5899*******************9999999997..455566689********99 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.6    0.0002      0.13      23      39 ..      59      77 ..      51      83 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0002
                         AAA_29 23 g..atlltGpsGsGKSTll 39
                                   g  ++ l+Gp G+GKSTl+
  gi|116753417|ref|YP_842535.1| 59 GdaTVTLVGPVGAGKSTLV 77
                                   3356789***********8 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00017      0.11      18      40 ..      55      81 ..      29      91 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00017
                                   H....TEEEEEEESTTSSHHHHHHHHH CS
                           TsaE 18 l....gdvilLeGdLGaGKTtlvrgla 40
                                   +     ++++L G++GaGK+tlv  l 
  gi|116753417|ref|YP_842535.1| 55 VrksgDATVTLVGPVGAGKSTLVSRLT 81
                                   13333456**************99876 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.2         8   5.3e+03     110     114 ..      36      40 ..      11      56 .. 0.51
   2 ?   12.1   0.0   0.00025      0.17       2      23 ..      63      84 ..      63     102 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 8
                         AAA_33 110 tlkeR 114
                                     l+e 
  gi|116753417|ref|YP_842535.1|  36 RLREE 40 
                                    33333 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00025
                         AAA_33  2 vllvGlpGsGKstlaerllkkl 23
                                   v lvG+ G+GKstl+ rl  ++
  gi|116753417|ref|YP_842535.1| 63 VTLVGPVGAGKSTLVSRLTGAR 84
                                   568**************97655 PP

>> MnmE_helical  MnmE helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00024      0.16      59     132 ..      15     269 ..       2     296 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00024
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxx...................................... RF
                   MnmE_helical  59 leelseeelaekleelkeelekllatakrgellr....eGik...................................... 96 
                                    l   ++++ ++ + +lk+++ +l ++ ++    r    +G++                                      
  gi|116753417|ref|YP_842535.1|  15 LRTQKNKATEHHIGRLKAKIARLREEQEKRTASRakkgKGVRksgdatvtlvgpvgagkstlvsrltgartsedpysmei 94 
                                    33344446777778888888888877776666665545566688889999999999999999999999999999999999 PP

                                    ................................................................................ RF
                   MnmE_helical  97 ................................................................................ 96 
                                                                                                                    
  gi|116753417|ref|YP_842535.1|  95 tpgilqhrgakiqildvpditvsgdalsavrdsdlvllvtepyggqldpylnrlyqsgvrlnqnppsvlirktsrggisv 174
                                    999999999999999999999999999999999999999999999999999999999999******************** PP

                                    ..........................................................xxxxxxxxxxxxxxxxxxxxxx RF
                   MnmE_helical  97 ..........................................................DllkekeekeeeevlkiSaktg 118
                                                                                              D+l+ +e + + +v+ +Sa +g
  gi|116753417|ref|YP_842535.1| 175 tstvdpgidkgsieailreykihsadvlirerltqerfidaleanrryikaihvmnkvDILDPDELEFDGDVIPTSAVDG 254
                                    ***************************************9999999999999999999888888889999999******* PP

                                    xxxxxxxxxxxx.xx RF
                   MnmE_helical 119 egieeLeeaike.le 132
                                    +g+e+L+++i e l 
  gi|116753417|ref|YP_842535.1| 255 TGLERLKDEIFErLD 269
                                    **********77554 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 ?   10.2   0.4   0.00039      0.26      13      37 ..      56      80 ..      51      84 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00039
                     Spore_IV_A 13 rtngdiyigvvGpvRtGKStfikrf 37
                                   r +gd  + +vGpv +GKSt++ r+
  gi|116753417|ref|YP_842535.1| 56 RKSGDATVTLVGPVGAGKSTLVSRL 80
                                   889*******************997 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.2    0.0006       0.4      16      80 ..      17      78 ..       6      83 .. 0.70
   2 ?   -1.5   0.1       1.3   8.9e+02     172     203 ..     202     233 ..     198     235 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0006
                    AFG1_ATPase 16 ivadaaqaeavealdrlteelaaqdlarkssalgklfgrkrksvepvrglYlwGgvGrGKtylmd 80
                                   +++++a ++ + +l+   ++l+ +++ r++s+ +k  g +   +     + l G+vG GK+ l+ 
  gi|116753417|ref|YP_842535.1| 17 TQKNKATEHHIGRLKAKIARLREEQEKRTASRAKKGKGVR---KSGDATVTLVGPVGAGKSTLVS 78
                                   4556666777777777777777777777766665554433...3345677899********9985 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.3
                    AFG1_ATPase 172 LykdglqrqrFLpaIdlleshlevlevdggvD 203
                                    L +++l ++rF+ a+++ ++ ++ ++v  +vD
  gi|116753417|ref|YP_842535.1| 202 LIRERLTQERFIDALEANRRYIKAIHVMNKVD 233
                                    8899999****999999999888888887777 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.6       1.9   1.2e+03      38      73 ..      18      52 ..       3      55 .. 0.57
   2 ?   10.1   0.0    0.0011      0.72       2      29 ..      63      93 ..      62     114 .. 0.73
   3 ?   -2.3   0.0       6.8   4.5e+03      98     124 ..     211     238 ..     199     242 .. 0.61

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.9
                         AAA_28 38 klakgedalpwv.edllafaervleeqleeeaaaaan 73
                                   +  k ++  ++  + + ++a++++e++++++ +a+++
  gi|116753417|ref|YP_842535.1| 18 QKNKATE--HHIgRLKAKIARLREEQEKRTASRAKKG 52
                                   3222222..2233556778888888888777777554 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0011
                         AAA_28  2 ivitGgestGKTtlleaLa.ar..gypvvpE 29
                                   + ++G+ ++GK+tl+++L+ ar  + p+  E
  gi|116753417|ref|YP_842535.1| 63 VTLVGPVGAGKSTLVSRLTgARtsEDPYSME 93
                                   7799**************9533344445455 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 6.8
                         AAA_28  98 aeleaaarekrydlvfllppapei.ddd 124
                                    + ++a ++ +ry + +++ +  +i d+d
  gi|116753417|ref|YP_842535.1| 211 RFIDALEANRRYIKAIHVMNKVDIlDPD 238
                                    3344445555677777777766665666 PP

>> DUF1192  Protein of unknown function (DUF1192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   3.5      0.09        60      25      43 ..       3      21 ..       2      26 .. 0.85
   2 ?    7.8   3.2     0.005       3.3      28      51 ..      26      49 ..      23      50 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.09
                        DUF1192 25 LeerIalLeaEIaRleaai 43
                                   +ee I +Le+EI R+++  
  gi|116753417|ref|YP_842535.1|  3 IEEEIRALEEEILRTQKNK 21
                                   6899**********98765 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.005
                        DUF1192 28 rIalLeaEIaRleaaiakkkasra 51
                                    I  L+a IaRl+++ +k++asra
  gi|116753417|ref|YP_842535.1| 26 HIGRLKAKIARLREEQEKRTASRA 49
                                   6999******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       847  (0.0472419); expected 358.6 (0.02)
Passed bias filter:                      681  (0.0379832); expected 358.6 (0.02)
Passed Vit filter:                       123  (0.00686039); 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: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 2352.35
//
Query:       gi|116753418|ref|YP_842536.1|  [L=125]
Description: carboxymuconolactone decarboxylase [Methanosaeta thermophila PT]
Scores for 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-16   57.8   0.0    1.2e-15   57.4   0.0    1.2  1  CMD       Carboxymuconolactone decarboxylase family


Domain annotation for each model (and alignments):
>> CMD  Carboxymuconolactone decarboxylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.4   0.0   6.4e-20   1.2e-15       1      76 [.      35     109 ..      35     114 .. 0.97

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 6.4e-20
                                    HHHHHHHHHHHHHHCCGSSTS-HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHSHHHH CS
                            CMD   1 pellraltalreallareggLdpkereLialavsaangceyCvdaHtraAleaGvteeeiaevlaqaaayagwpaa 76 
                                    pel++++++l+  ll+ +g+Ld+k++ Liala  +++ ce+Cv   ++ A++ G+t++ei e+l +  +++g+p +
  gi|116753418|ref|YP_842536.1|  35 PELMELIERLDRVLLE-DGALDKKTKRLIALACVITRMCEDCVYPQAKVAVNYGATKDEILETLEICMITGGVPTF 109
                                    99*************9.********************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 888.54
//
Query:       gi|116753419|ref|YP_842537.1|  [L=267]
Description: hypothetical protein Mthe_0095 [Methanosaeta thermophila PT]
Scores for 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-57  191.8   0.0    1.2e-56  191.5   0.0    1.1  1  tRNA_deacylase  D-aminoacyl-tRNA deacylase


Domain annotation for each model (and alignments):
>> tRNA_deacylase  D-aminoacyl-tRNA deacylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.5   0.0   6.5e-61   1.2e-56       4     204 ..      65     258 ..      62     259 .. 0.97

  Alignments for each domain:
  == domain 1  score: 191.5 bits;  conditional E-value: 6.5e-61
                                    --SEEEEEEEEE-TT---EEEEE--B-SS--TTSS-TT-B--B-HHHHHHHHHHHHGGGGGSTT-EEEE--S-SS----- CS
                 tRNA_deacylase   4 dvdliiflSrHssesgkplLTvHvtGnlgeaelGGkpeelapaaPrllkallralkkiaekleefevtlEatHHGPtelk 83 
                                    ++ liif+SrH s++++p L  H+tG ++e        el+++aP +lk+ll al+++a  +++f+ + EatHHGP++l+
  gi|116753419|ref|YP_842537.1|  65 SPRLIIFASRHISKEAVPWLGGHFTGVVRE-----GSFELSRPAPYALKKLLMALQRHA--PSTFRLSAEATHHGPVDLR 137
                                    6789**************************.....3569********************..******************* PP

                                    S-EEEEEEEESHHHHT-HHHHHHHHHHHHHHHH--.----EEEEEE-S-TT-HHHHHHHHHBSEEEEEEE-GGGGGG--H CS
                 tRNA_deacylase  84 vPslFvEiGSteeeWkdedaaeavaeavlellese.eekekvlvgiGGgHYaprftklvletevavGhilskyaleelke 162
                                    +PslF+EiGS e++W d++a++ava+a+lel + e +++e+vl+giGGgHY++r+t+l+l++ va+Gh++sky++++l+ 
  gi|116753419|ref|YP_842537.1| 138 TPSLFAEIGSCEQHWIDPAAGAAVARAILELESYEaHADETVLLGIGGGHYVQRQTELILSRPVAFGHMFSKYQASMLNV 217
                                    *******************************88888999***************************************** PP

                                    HHHHHHHHHH.T-SEEEE-TTT--HHHHHHHHHHHHHHT-EE CS
                 tRNA_deacylase 163 evikqaleksegadvalidkkslkseqkeaieelleelgiev 204
                                    e+ik+a + s ga+ +++d ks++s++++++ee++++l+++v
  gi|116753419|ref|YP_842537.1| 218 EAIKKAADLS-GASGVYLDGKSFRSDERRRLEEIAASLDLNV 258
                                    **********.***************************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 1893.69
//
Query:       gi|116753420|ref|YP_842538.1|  [L=348]
Description: AsnC family transcriptional regulator [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0012   18.7   0.0       0.29   11.1   0.0    2.4  2  MarR            MarR family
     0.0034   16.9   0.0      0.021   14.4   0.0    2.2  2  HTH_24          Winged helix-turn-helix DNA-binding
     0.0057   16.7   0.0       0.84    9.7   0.0    2.8  2  HTH_3           Helix-turn-helix
  ------ inclusion threshold ------
      0.017   15.0   0.0        3.3    7.7   0.0    2.5  2  TrmB            Sugar-specific transcriptional regulator TrmB
      0.019   14.8   0.0          1    9.3   0.0    2.4  2  MarR_2          MarR family
      0.021   14.8   0.0         12    6.0   0.0    2.9  2  HTH_Crp_2       Crp-like helix-turn-helix domain
       0.12   12.6   0.0       0.27   11.4   0.0    1.7  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
       0.23   11.5   0.0         24    5.0   0.0    2.2  2  DUF1013         Protein of unknown function (DUF1013)


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 !   11.1   0.0   0.00013      0.29       1      36 [.      10      45 ..      10      57 .. 0.87
   2 !    5.2   0.0    0.0089        20      18      53 ..     203     238 ..     188     243 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00013
                                   --HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHH CS
                           MarR  1 ltltqfviLrilyeqgplsvseLakklgvskstvtr 36
                                   lt  + ++L+ l++ ++ls ++La+ + v++st+ +
  gi|116753420|ref|YP_842538.1| 10 LTSKEKLVLYGLARYPGLSDIDLASLIDVDRSTIFK 45
                                   67888899*************************987 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0089
                                    EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEET CS
                           MarR  18 lsvseLakklgvskstvtrvldrLekkGlieRsksp 53 
                                    ls  eL k+ g+s++t++    r  +++ + R+ + 
  gi|116753420|ref|YP_842538.1| 203 LSDLELSKRTGISRPTISGKRSRFFDANILLREAHV 238
                                    44449*************999999999999998876 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 ?   -0.9   0.0      0.53   1.2e+03      13      34 ..      22      43 ..      15      45 .. 0.87
   2 !   14.4   0.0   9.2e-06     0.021       1      35 [.     186     220 ..     186     221 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.53
                         HTH_24 13 qknprisqreLAerlglSpstv 34
                                    + p++s  +LA  +++ +st+
  gi|116753420|ref|YP_842538.1| 22 ARYPGLSDIDLASLIDVDRSTI 43
                                   566999999****999999986 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 9.2e-06
                         HTH_24   1 ldetdrkILelLqknprisqreLAerlglSpstvn 35 
                                    l+e+dr  L +  k p++s  eL++r+g+S++t++
  gi|116753420|ref|YP_842538.1| 186 LSEKDRLTLYAFVKYPNLSDLELSKRTGISRPTIS 220
                                    57889999999999*******************86 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.023        53       9      26 ..      26      43 ..      25      45 .. 0.91
   2 !    9.7   0.0   0.00037      0.84       9      27 ..     202     220 ..     201     221 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.023
                                   THHHHHHHHHHTSSHHHH CS
                          HTH_3  9 glsqeeLAeklGvsrsti 26
                                   gls  +LA +++v rsti
  gi|116753420|ref|YP_842538.1| 26 GLSDIDLASLIDVDRSTI 43
                                   89999************9 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00037
                                    THHHHHHHHHHTSSHHHHH CS
                          HTH_3   9 glsqeeLAeklGvsrstis 27 
                                    +ls  eL++++G+sr tis
  gi|116753420|ref|YP_842538.1| 202 NLSDLELSKRTGISRPTIS 220
                                    67888*************9 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.013        28       5      45 ..       9      49 ..       5      58 .. 0.86
   2 ?    7.7   0.0    0.0015       3.3       3      39 ..     183     219 ..     181     222 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.013
                                   HHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHH CS
                           TrmB  5 GLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrs 45
                                    L++ E  v   L ++  ++  ++a+ ++v+rs++ ++ r+
  gi|116753420|ref|YP_842538.1|  9 KLTSKEKLVLYGLARYPGLSDIDLASLIDVDRSTIFKSKRK 49
                                   589999999999***********************987665 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0015
                                    HCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCH CS
                           TrmB   3 klGLseyEakvYlaLlklgpatadeiaeelgvprskv 39 
                                    +l Lse +  +  a +k+ +++  e+++++g++r+++
  gi|116753420|ref|YP_842538.1| 183 ALKLSEKDRLTLYAFVKYPNLSDLELSKRTGISRPTI 219
                                    5779999999999**********************99 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00046         1       3      53 ..      10      58 ..       9      65 .. 0.90
   2 ?    2.9   0.0     0.045     1e+02      26      39 ..     207     220 ..     190     242 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00046
                                   --HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                         MarR_2  3 ltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                   lt  +  vL+ L+r pg  l+  +la   ++++s++ +  +++ +  L++ 
  gi|116753420|ref|YP_842538.1| 10 LTSKEKLVLYGLARYPG--LSDIDLASLIDVDRSTIFKSKRKFRDWQLIRL 58
                                   5667788**********..*******************9999999999985 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.045
                                    HHHHHHTSSHHHHH CS
                         MarR_2  26 elarrlglsksavs 39 
                                    el +r+g+s++++s
  gi|116753420|ref|YP_842538.1| 207 ELSKRTGISRPTIS 220
                                    899*********99 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 ?    6.0   0.0    0.0053        12      22      52 ..      27      57 ..      13      64 .. 0.89
   2 ?    5.5   0.0    0.0073        16      21      51 ..     202     232 ..     183     240 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0053
                                   HHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE CS
                      HTH_Crp_2 22 ltqeelAsmlGltretvsrilseLkreglis 52
                                   l+  +lAs++ + r+t+ +  +++++ +li+
  gi|116753420|ref|YP_842538.1| 27 LSDIDLASLIDVDRSTIFKSKRKFRDWQLIR 57
                                   56679*********************99998 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0073
                                    EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSE CS
                      HTH_Crp_2  21 pltqeelAsmlGltretvsrilseLkregli 51 
                                    +l+  el+ + G++r t+s   s++ +++++
  gi|116753420|ref|YP_842538.1| 202 NLSDLELSKRTGISRPTISGKRSRFFDANIL 232
                                    69999*************9877777776665 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 ?   11.4   0.0   0.00012      0.27      12      53 ..      20      61 ..      12     116 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                 B-block_TFIIIC 12 assRysGitqsdLakeskqdprslfyrlksLekkgLIvkqsi 53
                                   + +Ry G+   dLa++++ d + +f+  ++  + +LI  +++
  gi|116753420|ref|YP_842538.1| 20 GLARYPGLSDIDLASLIDVDRSTIFKSKRKFRDWQLIRLLNV 61
                                   678*********************************987777 PP

>> DUF1013  Protein of unknown function (DUF1013)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.019        43      70     105 ..      13      48 ..       8      60 .. 0.81
   2 ?    5.0   0.0     0.011        24      74     106 ..     193     225 ..     182     235 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.019
                        DUF1013  70 kpdaiawllknhpelkdaqiakLvgtTketieaird 105
                                    k + +++ l ++p l+d  +a L+   ++ti + + 
  gi|116753420|ref|YP_842538.1|  13 KEKLVLYGLARYPGLSDIDLASLIDVDRSTIFKSKR 48 
                                    6667889999********************977544 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.011
                        DUF1013  74 iawllknhpelkdaqiakLvgtTketieairdr 106
                                     ++   ++p+l+d  ++k  g  ++ti+  r r
  gi|116753420|ref|YP_842538.1| 193 TLYAFVKYPNLSDLELSKRTGISRPTISGKRSR 225
                                    5677789********************988877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); 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: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2459.84
//
Query:       gi|116753421|ref|YP_842539.1|  [L=158]
Description: hypothetical protein Mthe_0097 [Methanosaeta thermophila PT]
Scores for complete 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   43.5   0.2    2.7e-05   24.2   0.0    2.1  2  PurS           Phosphoribosylformylglycinamidine (FGAM) synth
  ------ inclusion threshold ------
      0.099   11.8   0.0       0.13   11.4   0.0    1.2  1  Prophage_tail  Prophage endopeptidase tail


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 !   17.6   0.1   3.6e-07    0.0032       9      75 ..      10      73 ..       2      75 .. 0.79
   2 !   24.2   0.0   3.1e-09   2.7e-05      12      75 ..      93     154 ..      85     155 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.6e-07
                                   -TTS--HHHHHHHHHH.HHTTHTT.EEEEEEEEEEEEEEE-SSHHHHHHHHHHHHHHTTS-TTTEEEEE CS
                           PurS  9 KkgvlDpqGkavkkal.kslgyee.vedvrvgkyieleleaedeeeaeeeveemceklLaNpviedyei 75
                                   K  + D+++ +vk++l +++gy++ v+dv   +++++e+++ +  + e+ ++++ ++ L+N + e++ +
  gi|116753421|ref|YP_842539.1| 10 K--IPDAEAATVKNTLlRRMGYQGiVRDVMRERLLSIEVDEVS--DPETLIKQLTRE-LVNENKESFAV 73
                                   4..89********9962667****999*************875..446788888877.77877777766 PP

  == domain 2  score: 24.2 bits;  conditional E-value: 3.1e-09
                                    S--HHHHHHHHHH.HHTTHTTEEEEEEEEEEEEEEE-SSHHHHHHHHHHHHHHTTS-TTTEEEEE CS
                           PurS  12 vlDpqGkavkkal.kslgyeevedvrvgkyieleleaedeeeaeeeveemceklLaNpviedyei 75 
                                    + D ++  +++ l k+lg++ v++v+ +++ +l ++++d e   + +++++e+lL+Np+   yei
  gi|116753421|ref|YP_842539.1|  93 IEDGEAISIRDRLvKRLGLKMVRSVQRANIWKLYIDGDDPE---SVARRIAEELLVNPNKDRYEI 154
                                    66777777776652788*******************99877...58999**********999997 PP

>> Prophage_tail  Prophage endopeptidase tail
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   1.5e-05      0.13     222     276 ..      42     105 ..      31     117 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.5e-05
                                    --EE-TT-SS-TTHHHHH------S..-EEEEEE------..........------EEEEEETT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxx RF
                  Prophage_tail 222 spitddeitdqdaLkeeaknqlkknnePevsltvtaaklek.........dielGDvvriidke 276
                                      i++de+ d+++L +++ ++l + n+ +  ++v+  +l++          ie G+ + i+d+ 
  gi|116753421|ref|YP_842539.1|  42 LSIEVDEVSDPETLIKQLTRELVNENKESFAVSVNSLELSNgcvpvkvslWIEDGEAISIRDRL 105
                                    5699***********************************9999999998888888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); 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: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1144.62
//
Query:       gi|116753422|ref|YP_842540.1|  [L=262]
Description: phosphoribosylformylglycinamidine synthase I [Methanosaeta thermophila PT]
Scores for complete 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-52  176.1   0.0    8.2e-52  175.9   0.0    1.0  1  GATase_5       CobB/CobQ-like glutamine amidotransferase doma
      2e-09   37.5   0.1      3e-09   36.9   0.1    1.6  1  GATase         Glutamine amidotransferase class-I
    1.4e-07   31.3   0.0    3.5e-07   30.0   0.0    1.7  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
    2.6e-06   27.3   0.0    4.3e-06   26.6   0.0    1.3  1  DJ-1_PfpI      DJ-1/PfpI family
    1.3e-05   25.2   0.0    2.4e-05   24.3   0.0    1.4  1  SNO            SNO glutamine amidotransferase family
     0.0055   16.5   0.0     0.0085   15.9   0.0    1.3  1  Peptidase_C26  Peptidase C26


Domain annotation for each model (and alignments):
>> GATase_5  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.9   0.0   2.7e-55   8.2e-52       3     260 .]       2     257 ..       1     257 [. 0.88

  Alignments for each domain:
  == domain 1  score: 175.9 bits;  conditional E-value: 2.7e-55
                       GATase_5   3 kvailreeGvngeyemaaafekaGfeavdvhmsdllegrvslddfqilalpGGfsygDelgsgkgwakslllneklreal 82 
                                    ++a++ ++G+n+e e+  a+++ G++ + +      + +++l +f + ++pGGfsy D   +g +++k     e + + l
  gi|116753422|ref|YP_842540.1|   2 RIAVIQFPGTNCEHETLVAVRECGMDGEIFRW---NRPEQELCEFDGYVIPGGFSYQDRVRAGVIASK-----EPVMATL 73 
                                    89*************************88755...455889**********************98885.....5556666 PP

                       GATase_5  83 ekflnredtlaLGiCnGfqlLvklglvpggeiee.a.eksptltrNksgr..fesrlvsv.vvsek...spsvflkgmeg 154
                                    ++  ++ ++ ++GiCnGfq+Lv+ g++p g+  + a ++++ +   ++ r  + + ++++ +  e+   s s +l+ +e+
  gi|116753422|ref|YP_842540.1|  74 REEAAN-GKPIIGICNGFQILVESGILPFGDGVRlAlAQNVMIRGGEIVRrgYYCAWTMLrHDAEEkrcSGSYILRRGEI 152
                                    666677.9*********************99888644777777777776666********543333344678899***** PP

                       GATase_5 155 lslpvahGeGrfvfkseevlkeleangqvalrYvdeegkpteeyplNPNgSpegiagitspdGRvlalmpHpervveavq 234
                                    ls+p+ah+eG++v+++++v+++l++  q+++rY+ ++g++ +e+p+N NgS+e+iagi +p+G vl++mpHper++ a+q
  gi|116753422|ref|YP_842540.1| 153 LSIPIAHAEGNLVASDRKVIERLIEDDQIVFRYCSPQGEIINEFPVNVNGSTENIAGISNPEGNVLGMMPHPERAFFAWQ 232
                                    ******************************************************************************** PP

                       GATase_5 235 ksiipeeeeeevspwlrlFenavkyv 260
                                     +  ++ +  +++p+ ++F ++ +y+
  gi|116753422|ref|YP_842540.1| 233 LPRKHP-RIPGYGPGRKIFDSMKRYI 257
                                    **6655.44568**********9995 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.1     1e-12     3e-09      15      87 ..      19      96 ..      10     232 .. 0.81

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 1e-12
                                   HHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.........TTTHHHHHHHHCTSTS-EEEETHHHHHHHHH CS
                         GATase 15 halvelgvkvevvpidasaeeilellknpdgilvsgGpgspg.........vegkieaikearenkiPiLGICLGmQllaie 87
                                    a++e+g++ e+++++ + +e     +++dg +++gG+ +            e  +++++e + n++Pi+GIC G+Q+l+++
  gi|116753422|ref|YP_842540.1| 19 VAVRECGMDGEIFRWNRPEQEL----CEFDGYVIPGGFSYQDrvragviasKEPVMATLREEAANGKPIIGICNGFQILVES 96
                                   5899************988887....79************9999999965544444555555558**************986 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 !   30.0   0.0   1.2e-10   3.5e-07      26      91 ..      30      96 ..       2     109 .. 0.79

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 1.2e-10
                       GATase_3 26 rvrfvplkdeslgedadlvilpGgkdtiq...dlallresgldeaikeaaeaggpvlgiCGGlqmLGee 91
                                    +r+ + ++++l e  d +++pGg+++ +   +  ++ ++ +   ++e a++g+p++giC G+q+L e+
  gi|116753422|ref|YP_842540.1| 30 IFRWNR-PEQELCE-FDGYVIPGGFSYQDrvrAGVIASKEPVMATLREEAANGKPIIGICNGFQILVES 96
                                   456666.8999966.*********8766511055678889999***********************887 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 !   26.6   0.0   1.5e-09   4.3e-06      61     114 ..      42     100 ..      25     104 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 1.5e-09
                                    G-SEEEE--BHHHHHHHHT.....SHHHHHHHHHHHHTT-EEEEETTTHHHHHHTTTTT CS
                      DJ-1_PfpI  61 eyDalvlpGGragperlre.....nekvvelvkefaekgklvaaICagpqlLaaagvlk 114
                                    e+D  v+pGG +  +r+r+     +e v+++++e a +gk++  IC g q+L++ g+l+
  gi|116753422|ref|YP_842540.1|  42 EFDGYVIPGGFSYQDRVRAgviasKEPVMATLREEAANGKPIIGICNGFQILVESGILP 100
                                    79**********999987533333789*****************************985 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   8.1e-09   2.4e-05       6      82 ..      10      94 ..       5     105 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 8.1e-09
                                   SSHHHHHH..HHHHTTSEE..EEE-SGG.GGCC-SEEEE-SS-HHH....HHHHHHHTT-HHHHHHHHHTT.--EEEETHHH CS
                            SNO  6 Gaveehve..aikkclaen..ktvkrke.dlaevdaliiPGGesta....mskliertglyedllefvknsekvvlGtCaGl 78
                                   G   eh+   a+++c++++      r+e +l e d+ +iPGG s       + ++ +  ++ +l+e ++n+ k+++G C G+
  gi|116753422|ref|YP_842540.1| 10 GTNCEHETlvAVRECGMDGeiFRWNRPEqELCEFDGYVIPGGFSYQdrvrAGVIASKEPVMATLREEAANG-KPIIGICNGF 90
                                   66677765337899***9955333455516************986422226789*****************.*********9 PP

                                   HHHC CS
                            SNO 79 ills 82
                                    +l 
  gi|116753422|ref|YP_842540.1| 91 QILV 94
                                   7764 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.9e-06    0.0085      95     120 ..      70      94 ..      42      99 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.9e-06
                  Peptidase_C26  95 laLiraalergvPilgiCrGlqllnv 120
                                    +a +r++ ++g+Pi+giC G+q+l v
  gi|116753422|ref|YP_842540.1|  70 MATLREEAANGKPIIGICNGFQIL-V 94 
                                    56789999***************9.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.30s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1751.41
//
Query:       gi|116753423|ref|YP_842541.1|  [L=768]
Description: phosphoribosylformylglycinamidine synthase II [Methanosaeta thermophila PT]
Scores for complete 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-37  127.3   0.0    1.4e-17   64.3   0.0    2.4  2  AIRS_C          AIR synthase related protein, C-terminal doma
    7.6e-37  125.9   0.3      2e-17   63.6   0.3    2.4  2  AIRS            AIR synthase related protein, N-terminal doma
    1.2e-13   51.4   0.0    4.9e-13   49.4   0.0    2.0  2  FGAR-AT_linker  Formylglycinamide ribonucleotide amidotransfe


Domain annotation for each model (and alignments):
>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.3   0.0   2.3e-21   1.4e-17       4     153 ..     217     378 ..     214     381 .. 0.85
   2 !   60.7   0.0   2.9e-20   1.7e-16       1     148 [.     599     736 ..     599     756 .. 0.92

  Alignments for each domain:
  == domain 1  score: 64.3 bits;  conditional E-value: 2.3e-21
                                    EEEEEEET...SSCTCCHHHHHHHCHHHCTSHTT.TSEHHHHHHHHHHHHHHHHHHHH...HTTECEEEE--TTHHHHHH CS
                         AIRS_C   4 dvliltgs...lGlggagtslkrkileeegldds.avqlgdvlleptliyvkralaal...kglvkaahDvTgGGLlgal 76 
                                    dv++  ++   +Glgg+  ++++++ eee++  + avq+ d++l++ l ++++ l +l   kg   +++D++gGGL++a 
  gi|116753423|ref|YP_842541.1| 217 DVILIGKPtdsSGLGGVI-FASDTLREEEEEANRgAVQIPDPFLKNVLFKANEDLFRLvreKGVEIGFKDLGGGGLTCAS 295
                                    66777777898*******.7777777777776668*************************6666679************* PP

                                    HHHHHTTTEEEEEECGTHHHHHHHHHHHHHHHCSTTTEEEEEEEHGGHHHHHHHHH........HTTCCCEEEEEEEEES CS
                         AIRS_C  77 aemapasgvgaeidldkvpifdelesplemllsensGrllvavppeeadavlaile........eeglpeaavIGevtak 148
                                    +em +a+g g+eidld++ +  e   p+ + ++e+++r l+++p+e ++++l+i +         eg   a+vIG+vt  
  gi|116753423|ref|YP_842541.1| 296 SEMGAAGGYGMEIDLDRLHVAGEF-PPEVLCIAETQERFLIIAPRELRERILKIYNedwdlpnvYEGA-RASVIGRVTTH 373
                                    ****************88888886.67777777**********************9655555544555.7********98 PP

                                    SSEEE CS
                         AIRS_C 149 eelsv 153
                                    ++  v
  gi|116753423|ref|YP_842541.1| 374 DRYIV 378
                                    87665 PP

  == domain 2  score: 60.7 bits;  conditional E-value: 2.9e-20
                                    STTEEEEEEET..SSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHHHH CS
                         AIRS_C   1 kpGdvliltgs..lGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaalkglvkaahDvTgGGLlgalae 78 
                                    ++Gd l+l+g+  + lgg+ ++   ++++ + ++     ++   le+ +iy +  +  + +  +aahD+++GG + ++ae
  gi|116753423|ref|YP_842541.1| 599 EAGDGLYLLGPrfDELGGSEYYRLIWGVTGANVP-----VVRFPLERSMIYTVIDAVDR-EILRAAHDISNGGMAITAAE 672
                                    58***********************9**999998.....******************98.******************** PP

                                    HHHTTTEEEEEECGTHHHHHHHHHHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEES CS
                         AIRS_C  79 mapasgvgaeidldkvpifdelesplemllsensGrllvavppeeadavlaileeeglpeaavIGevtak 148
                                    m+  s+ g+ id++   + d      ++l+se+sG  +v v+  +++++++i+++++l +  ++G v  +
  gi|116753423|ref|YP_842541.1| 673 MCMLSDHGISIDIS--DLGDMR--SDKLLFSESSG-FVVEVADGAEQEFVSIARSYDL-NPVRLGSVSTG 736
                                    **************..777765..68999999999.66778888888**********9.78999999876 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 !   63.6   0.3   3.4e-21     2e-17       2      94 .]      81     197 ..      80     197 .. 0.92
   2 !   59.9   0.0   4.7e-20   2.8e-16       2      94 .]     471     586 ..     459     586 .. 0.89

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 3.4e-21
                                    SSE.........EEEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC............HHHHHHH CS
                           AIRS   2 Daa.........vvvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp............wleevvr 60 
                                    Da+         vv++ +shn+p+ + p ++ +a++++++++D+ +mGAr +a  + l ++             +e+vv+
  gi|116753423|ref|YP_842541.1|  81 DAGivsiddewcVVISHESHNHPSQILPNEG-AATGIGGIVRDVNCMGARVVATADPLRFGdpygressrvrwVAEGVVD 159
                                    6775444444446******************.****************************************88899*** PP

                                    HHHHHHHHTT-EEEEEEEEEESS....EEEEEEEEEEE CS
                           AIRS  61 glaeaaeelgvplvgGdtsfsne....ptisvtavGlv 94 
                                    g+ +++++lgvp++ Gd+ fs +    ++++v+a+G+v
  gi|116753423|ref|YP_842541.1| 160 GIWQYGNALGVPVIAGDVVFSRCfdynCLVNVVAIGVV 197
                                    ********************9999999*********97 PP

  == domain 2  score: 59.9 bits;  conditional E-value: 4.7e-20
                                    SSEEEEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.........HHHHHHHHHHHHHHHTT-. CS
                           AIRS   2 DaavvvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp.........wleevvrglaeaaeelgv. 71 
                                    D ++++++ds++ +  ++p+ + Ga+ava++++++aa GA+P  l+++l+++         +++e vrgla+aa+ l   
  gi|116753423|ref|YP_842541.1| 471 DFGIALSVDSNPFYGRISPYWG-GATAVAEAMRNVAAIGATPSTLTDCLNFGnpekpeafwEFRESVRGLADAARNLWLk 549
                                    33469*****************.**************************************************9999655 PP

                                    .......EEEEEEEEEESS.......EEEEEEEEEEE CS
                           AIRS  72 .......plvgGdtsfsne.......ptisvtavGlv 94 
                                           p+v+G++sf+ne       p++++++vG++
  gi|116753423|ref|YP_842541.1| 550 ghpnqpvPIVSGNVSFYNEspegavdPSPVIACVGIM 586
                                    5566666**********999***************96 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 !   49.4   0.0   8.1e-17   4.9e-13       1      50 []      11      57 ..      11      57 .. 0.95
   2 ?   -1.7   0.0      0.77   4.6e+03       8      23 ..     664     679 ..     660     687 .. 0.81

  Alignments for each domain:
  == domain 1  score: 49.4 bits;  conditional E-value: 8.1e-17
                 FGAR-AT_linker  1 LeeankelglaLsdeEidylqeafeklgrnPtdvElemfaqvwSEHCrHK 50
                                   Le+  ++ g ++s +E + ++++   lgr+Pt +El+++ ++wSEHC++K
  gi|116753423|ref|YP_842541.1| 11 LESSLRKAGIGMSASEARSIASI---LGRDPTLAELFCYDAMWSEHCSYK 57
                                   56677899***************...9**********************9 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.77
                 FGAR-AT_linker   8 lglaLsdeEidylqea 23 
                                     g+a++ +E+ +l ++
  gi|116753423|ref|YP_842541.1| 664 GGMAITAAEMCMLSDH 679
                                    6899999999888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (768 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 5294.51
//
Query:       gi|116753424|ref|YP_842542.1|  [L=137]
Description: hypothetical protein Mthe_0100 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       289  (0.0161191); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.29s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 944.30
//
Query:       gi|116753425|ref|YP_842543.1|  [L=341]
Description: glycerophosphoryl diester phosphodiesterase [Methanosaeta thermophila PT]
Scores for complete 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  133.0   0.0    1.2e-26   94.0   0.0    2.1  2  GDPD      Glycerophosphoryl diester phosphodiesterase family
    1.6e-25   88.8   6.7    2.9e-25   88.0   6.7    1.3  1  zf-like   Cysteine-rich small domain
     0.0012   19.2   0.4      0.003   18.0   0.4    1.7  1  GDPD_2    Glycerophosphoryl diester phosphodiesterase family


Domain annotation for each model (and alignments):
>> GDPD  Glycerophosphoryl diester phosphodiesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.0   0.0     2e-30   1.2e-26       1      96 [.      18     114 ..      18     130 .. 0.86
   2 !   36.7   0.0   6.4e-13   3.8e-09     214     257 ..     188     229 ..     171     231 .. 0.89

  Alignments for each domain:
  == domain 1  score: 94.0 bits;  conditional E-value: 2e-30
                                    TTTTTTTSSTTSHHHHHHHHHTT-SEEEEEEEE-TTS-EEE-SSSBSTTTCSCCCH.BGGGS-HHHHHTSTECCTTCCCC CS
                           GDPD   1 HRGasgnlpEnTlesfakAaelGadyiEfDvqlTkDgvpVvlHDfnldrttdvagrldvkdltleelkrldkiakenkaq 80 
                                    HRGa++  pEnTl+ ++kA + Gad++E+Dv+l++Dgv+V++HD+++drtt+++g  +v+dl++ el+ ld  a ++  +
  gi|116753425|ref|YP_842543.1|  18 HRGAPALAPENTLQGIRKAHSCGADMVEMDVRLSSDGVLVLMHDETVDRTTNGSG--RVEDLSIGELRGLD--AGGEPVP 93 
                                    *******************************************************..**************..6777566 PP

                                    SCCCSSGCC.....B...BHH CS
                           GDPD  81 lsenrvrle.....fpfptle 96 
                                    + ++++rl+     +p++ ++
  gi|116753425|ref|YP_842543.1|  94 TLKEALRLAevlgiQPIVEMK 114
                                    666666555455554444444 PP

  == domain 2  score: 36.7 bits;  conditional E-value: 6.4e-13
                                    B.CHHHHHHHTT-EEEEBSB-THSHHHHHHHHCCC-SEEEES-H CS
                           GDPD 214 dpdlVkraksrglvvhvytvnnedeeemkrlleagvdgvitDfp 257
                                     p   k a+++gl+v+++tvn++  e+ ++ll++g dg++tD+p
  gi|116753425|ref|YP_842543.1| 188 SPNIFKIAHKSGLKVYPWTVNTP--ERAAWLLRLGADGIVTDDP 229
                                    4678999****************..*****************98 PP

>> zf-like  Cysteine-rich small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.0   6.7   4.9e-29   2.9e-25       7      80 ..     245     319 ..     241     320 .. 0.96

  Alignments for each domain:
  == domain 1  score: 88.0 bits;  conditional E-value: 4.9e-29
                        zf-like   7 nkeCeyyPCHktedenClfCyCPlYaledeelGefveteng.kvkdCskCllvHkkevadellkklkeileelkk 80 
                                    +++CeyyPCH+ e+++C++C+CPlY+++d elG+fv t+ g + ++C +C+lvH +eva +l +++++ +eelk+
  gi|116753425|ref|YP_842543.1| 245 QENCEYYPCHHFEGQDCTHCFCPLYPCKDPELGRFVRTKRGkRFWSCIDCVLVHIPEVARYLEANPDAGTEELKN 319
                                    79***************************************9*************************99999886 PP

>> GDPD_2  Glycerophosphoryl diester phosphodiesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.4   4.9e-07     0.003       1      29 [.     201     229 ..     201     229 .. 0.96

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.9e-07
                         GDPD_2   1 kvrfWttddeavwrelvgaGVdgInTDdl 29 
                                    kv+ Wt++++   + l+++G+dgI TDd+
  gi|116753425|ref|YP_842543.1| 201 KVYPWTVNTPERAAWLLRLGADGIVTDDP 229
                                    6899************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 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:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2504.36
//
Query:       gi|116753426|ref|YP_842544.1|  [L=395]
Description: Sep-tRNA:Cys-tRNA synthetase [Methanosaeta thermophila PT]
Scores for 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-48  163.7   0.0    7.8e-48  163.1   0.0    1.3  1  SepSecS          O-phosphoseryl-tRNA(Sec) selenium transferas
    1.6e-12   47.1   0.0    2.2e-12   46.7   0.0    1.1  1  Aminotran_5      Aminotransferase class-V
    8.3e-10   38.4   0.0    1.2e-09   37.9   0.0    1.2  1  Aminotran_1_2    Aminotransferase class I and II
     0.0014   17.4   0.0     0.0021   16.9   0.0    1.2  1  OKR_DC_1         Orn/Lys/Arg decarboxylase, major domain
     0.0028   16.3   0.0     0.0041   15.7   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
     0.0077   15.6   0.0      0.014   14.7   0.0    1.4  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
  ------ inclusion threshold ------
      0.032   13.5   0.0      0.043   13.1   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase


Domain annotation for each model (and alignments):
>> SepSecS  O-phosphoseryl-tRNA(Sec) selenium transferase, SepSecS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.1   0.0   3.1e-51   7.8e-48      98     389 .]     105     387 ..      99     387 .. 0.93

  Alignments for each domain:
  == domain 1  score: 163.1 bits;  conditional E-value: 3.1e-51
                                    HCC--CCEEEEEETC...HHHHHHHCTT-EEEEE-EEECTTEEEEHHHHHHHHH..HCCTCCCEEEEEECSSTTTTB--- CS
                        SepSecS  98 rskakkviwvridek...SslkavelaGleialvekvlegDelitdvedveeii..ekkreevilavlstlsffaprspD 172
                                    +s  +   ++++d +    ++ a+e+aGlei  ve+  e+++ i ++   e+i     ++  v +avl++++++++++ D
  gi|116753426|ref|YP_842544.1| 105 HSLCDAGDYIVADGNahyTTVLAAERAGLEISYVENSGEPEYTINPEGYREAIRdaADQGYRVSMAVLTYPDGNYGNLVD 184
                                    555555667777777444778899**********************998888875456688999**************** PP

                                    -HHHHHHHHHCCT--EEEEGCCCCT-HHHHHHHHHHHHHTTC-EECCCHCHCCCEECCHCCCCESSCHCCCCCHCCCHCH CS
                        SepSecS 173 dvkeiakiCaeydvPhlvNgAYaiqsekyieklkkalkvGRvdvvvksldknllvpvGgaiiaasdesfikeiskeypgr 252
                                      +++a+iC+e +vP+l+NgAY+i               GR++v+ ++ld++++v++G++++a+s+++++ + ++ey+++
  gi|116753426|ref|YP_842544.1| 185 -ARRVAEICHEEGVPLLLNGAYSI---------------GRMPVSARELDADIVVGSGHKSMASSGPIGVLGAKQEYADI 248
                                    .9**********************...............***************************************** PP

                                    CTSCHCCCCCCCHHHCCHHHCCHHHHHHHHHHHHHHHHHHHHHHCCC..............EEESSSTT-SSEEEEE-CC CS
                        SepSecS 253 asaapskdvlisllllGskaykkllkeqkesfkllreklkklaeeve..............ekllevpeNpissaltlet 318
                                    + ++++ +++++++llG++ +++ l + ++sf+++ e++ +++eev+              e+ +e+p+N+++++++ e 
  gi|116753426|ref|YP_842544.1| 249 IFRRSKSKKNKEVELLGCTVRGAGLLTMMASFPHVLERVGRWQEEVDkarwfsseleelgiEQQGEKPHNHDLMFFKSER 328
                                    ******************************************************************************** PP

                                    CHCCCC...THHHHHHHHHHHTTECSSE.EE-SSTCECTTSSS-SSSEEEEEE-TT--HHHHHHHHHHHHHHHH CS
                        SepSecS 319 ldeikk...karldlaseLfsrkvtGargvrasdsklTshlkeyhsrYlkiasaiGlkdedvdkvlerldeile 389
                                    l+ei+k   k+r +l+ eL+ r + G++      ++lT        r +k+ s++ +  ed++ v+ +++ei+e
  gi|116753426|ref|YP_842544.1| 329 LYEISKsarKGRYFLYHELKDRGICGIK------PGLT--------RQFKL-STYLIPREDLERVVSAFHEIIE 387
                                    *****99999******************......9999........88999.9999999999999999999885 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.0   8.4e-16   2.2e-12      64     218 ..      90     246 ..      75     268 .. 0.86

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 8.4e-16
                                    EEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBE..GGGHHHH-..... CS
                    Aminotran_5  64 iiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeld..ldelekll..... 136
                                    +  t+G+ e++ ++++sl    ++gd iv   + h  ++     +a+r g+++ +++   e e++  ++ +++++     
  gi|116753426|ref|YP_842544.1|  90 VRITHGAREGMYAAMHSL---CDAGDYIVADGNAHYTTV----LAAERAGLEISYVENSGEPEYTinPEGYREAIrdaad 162
                                    6679**************...9********999999998....5566778*****9887666666448889999955554 PP

                                    .-TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTTTTSSTT.-EEEEEE CS
                    Aminotran_5 137 .nektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghKllgPtG.iGvlyvr 214
                                       ++++  +t      G++ +  +++++++++g+ +l+ +a ++g +p+  ++l++D+++ sghK ++ +G iGvl ++
  gi|116753426|ref|YP_842544.1| 163 qGYRVSMAVLTYPDGNYGNLVDARRVAEICHEEGVPLLLNGAYSIGRMPVSARELDADIVVGSGHKSMASSGpIGVLGAK 242
                                    3356778889999999**************************************************9999999****999 PP

                                    HHHH CS
                    Aminotran_5 215 kell 218
                                    +e+ 
  gi|116753426|ref|YP_842544.1| 243 QEYA 246
                                    9875 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 !   37.9   0.0   4.5e-13   1.2e-09      68     242 ..      88     248 ..      72     279 .. 0.92

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 4.5e-13
                                    GEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTE CS
                  Aminotran_1_2  68 eaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnk 147
                                    +  v  + Ga ++  a++  l +++gd i+++   +     +++ +g+e+ +++ + e++++++ e++ ea+++a+ +  
  gi|116753426|ref|YP_842544.1|  88 D-DVRITHGAREGMYAAMHSL-CDAGDYIVADGNAHYTTVLAAERAGLEISYVENSGEPEYTINPEGYREAIRDAADQGY 165
                                    3.788999*************.8*******************************9999********************** PP

                                    TEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGG CS
                  Aminotran_1_2 148 ktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaG 227
                                    ++ + +++ p  + G + +   + ++   +++ ++ l++  aY+++ +         + + e +++++vgs  K++++ G
  gi|116753426|ref|YP_842544.1| 166 RVSMAVLTYPDGNYGNLVDARRVAEI---CHEEGVPLLLNGAYSIGRMP--------VSARELDADIVVGSGHKSMASSG 234
                                    *******************9999999...*****************998........556666668************** PP

                                    G-EEEEEEEHHHHHH CS
                  Aminotran_1_2 228 eRvGyilgnaavvsq 242
                                      +G + +++++++ 
  gi|116753426|ref|YP_842544.1| 235 -PIGVLGAKQEYADI 248
                                    .99998888877665 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   8.2e-07    0.0021      88     244 ..      93     232 ..      89     259 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 8.2e-07
                                    SSHHHHHHHHHHHHH--TTEEEEEESS--HHHHHHHHHS-EEEEEE--E.B-TTS-BE---GGGGSHHHHHHHHHHSTTT CS
                       OKR_DC_1  88 vnGTsssnkvvlnavltpgdlvlvdRNcHKSiehalvlsgatPvylepe.rnalgiiggidlkefeeetlkekikevpda 166
                                    ++G   +  + +++++ +gd ++ d N+H     a   +g +  y+e + + ++ i         ++e  +e+i++ +d+
  gi|116753426|ref|YP_842544.1|  93 THGAREGMYAAMHSLCDAGDYIVADGNAHYTTVLAAERAGLEISYVENSgEPEYTI---------NPEGYREAIRDAADQ 163
                                    5677778889999*********************************9985555543.........457889999999999 PP

                                    GS.ESEEEEESS.-TTSEEE-HHHHHHHHTTSESEEEEE-TT-TTGGGSGGGTTSSSSSSS-BTTBEEEEEEEHCCCCS- CS
                       OKR_DC_1 167 ka.prlavitns.TYdGvlynakeivdkleklsdrilfDeAwvgyeqfiplyadaskllaenendpgilvtqSvHKllaa 244
                                        ++av+t +   +G l +a+ + +  ++ ++++l+  A+     +  ++++a +l a+       +v+ S HK  a+
  gi|116753426|ref|YP_842544.1| 164 GYrVSMAVLTYPdGNYGNLVDARRVAEICHEEGVPLLLNGAYS----IGRMPVSARELDAD-------IVVGSGHKSMAS 232
                                    8768899999983479***********************9985....67899999999999.......888899998776 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 !   15.7   0.0   1.6e-06    0.0041      80     199 ..     100     229 ..      65     247 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.6e-06
                                    HHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEEST.......TSHHHHHHHCCT......TEEEEEEESS CS
                Cys_Met_Meta_PP  80 iaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdt.......sdleelekaike......ntklvylEtp 146
                                    + aa+ +l+ aGd iv++ +++  t       +++ g+e+++v+         ++e  ++ai++      ++++  l  p
  gi|116753426|ref|YP_842544.1| 100 MYAAMHSLCDAGDYIVADGNAHYTTVLA----AERAGLEISYVENsgepeytINPEGYREAIRDaadqgyRVSMAVLTYP 175
                                    4455778888888888887776666543....445555555555433333333445555555552222455555555556 PP

                                    -TTTT----HHHHHHHHHHTT-EEEEEGTTTHT.TTS-GGGGT-SEEEEETTTT CS
                Cys_Met_Meta_PP 147 tnpllkvvDiekiaklakkagvlvvvDntfasp.llqrplklgaDivvhSaTKy 199
                                         ++vD +++a++++++gv++++  +++ + + + + +l+aDivv S+ K 
  gi|116753426|ref|YP_842544.1| 176 DGNYGNLVDARRVAEICHEEGVPLLLNGAYSIGrMPVSARELDADIVVGSGHKS 229
                                    6667799************************99899**************9885 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 !   14.7   0.0   5.5e-06     0.014      45     150 ..      94     208 ..      63     214 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.5e-06
                                    SSHHHHHHHHHHH.TTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-.TTTSSB-GGGCGGG--TTE.......EEE CS
                DegT_DnrJ_EryC1  45 ssGtaAlhlaLra.lgvgpgdeVIvpsltFvatanavlelgakpvfvDvd.pdtynidpaaieaaitert.......kaI 115
                                      + +++  a++  ++  +gd+++   +   +t+ a+ ++g++  +v+   +  y+i+p+  ++ai            a+
  gi|116753426|ref|YP_842544.1|  94 HGAREGMYAAMHSlCD--AGDYIVADGNAHYTTVLAAERAGLEISYVENSgEPEYTINPEGYREAIRDAAdqgyrvsMAV 171
                                    5555677777777444..46***************************9762679*************9999999666555 PP

                                    E..EB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT CS
                DegT_DnrJ_EryC1 116 l..pVhlyGqvadmdalkaiaakhglkvieDaAhAlG 150
                                    l  p   yG+ +d  ++ +i+++ g++++   A ++G
  gi|116753426|ref|YP_842544.1| 172 LtyPDGNYGNLVDARRVAEICHEEGVPLLLNGAYSIG 208
                                    52234579********************999988887 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.7e-05     0.043      62     274 ..     102     308 ..      68     326 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.7e-05
                                    HHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTT CS
                Beta_elim_lyase  62 illkillqrgeevivtepahihfdetgaiaelagvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntag 141
                                     ++  l+  g+ ++++ +ah+ +  +   a l+ + + +   +e  ++++e  ++ai++  +   ++++ +l  T     
  gi|116753426|ref|YP_842544.1| 102 AAMHSLCDAGDYIVADGNAHYTTVLAAERAGLEISYVENSGEPE-YTINPEGYREAIRDAADQGYRVSMAVL--TYPD-- 176
                                    57788999999999888888655544444444444344444444.9999*********97763344444444..4444.. PP

                                    TB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHHTTSSEEEEESSSTT--SS-..EEEEE-HH....HH CS
                Beta_elim_lyase 142 GqvvsleelrevaaiakkygiplhlDgARfanaakslgeivkemfsyvDsvtmslkKdllanvG..gvlafrddeledyl 219
                                    G+   l   r+va+i++++g+pl+l gA  +     + ++++e+   +D+v+ s+ K +    G  gvl  +++ + d +
  gi|116753426|ref|YP_842544.1| 177 GNYGNLVDARRVAEICHEEGVPLLLNGAYSIG---RMPVSAREL--DADIVVGSGHKSMA-SSGpiGVLGAKQE-YADII 249
                                    6777778889**************99985443...335555554..68888888888854.4554445544444.87777 PP

                                    HHHHHH.....HHHHT---SSTHHHHH..HHHHHHHHSSTTHHHHHHHHHHHHHHHHHCT CS
                Beta_elim_lyase 220 aerveq.....rkylggglrqagvlaaleagiraleeglaslerdhktaeqlaeklelvr 274
                                     +r +      ++ lg   r ag+l   +a    + e + + +++ ++a+   ++le++ 
  gi|116753426|ref|YP_842544.1| 250 FRRSKSkknkeVELLGCTVRGAGLLTM-MASFPHVLERVGRWQEEVDKARWFSSELEELG 308
                                    777666444446667777777777776.55555555555666666666666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); 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: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 3043.37
//
Query:       gi|116753427|ref|YP_842545.1|  [L=88]
Description: hypothetical protein Mthe_0103 [Methanosaeta thermophila PT]
Scores for complete sequence (score 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   13.0   0.1       0.09   12.6   0.1    1.1  1  DRTGG        DRTGG domain
      0.084   13.3   0.0       0.14   12.5   0.0    1.4  1  Herpes_UL33  Herpesvirus UL33-like protein


Domain annotation for each model (and alignments):
>> DRTGG  DRTGG domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1     1e-05      0.09      50     101 ..      11      62 ..       8      65 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1e-05
                                    -HHHHHHHTT-TEEEEEEETT----HHHHHHHHHHT.--EEE-SS-HHHHHHH CS
                          DRTGG  50 RediqlaaleagiaalilTgglepseevlklaeeag.lpvlsveldtfttakr 101
                                    R+ ++l a+e + ++l +T++ e+ +e+++++ + + +  ++++l+t+ +++r
  gi|116753427|ref|YP_842545.1|  11 RALMHLKAIECA-HGLTITNKSEIVSEIASRVSDERsVLTICTSLNTWVAMNR 62 
                                    666788999999.****************999888879999*******98876 PP

>> Herpes_UL33  Herpesvirus UL33-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.6e-05      0.14      41      71 ..      18      48 ..       3      49 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.6e-05
                    Herpes_UL33 41 kaaCvhgevLeekrerlaqviskildldqiL 71
                                     +C+hg  +++k+e++ ++ s++ d  ++L
  gi|116753427|ref|YP_842545.1| 18 AIECAHGLTITNKSEIVSEIASRVSDERSVL 48
                                   245********************98877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); 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: 0.33u 0.28s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 657.02
//
Query:       gi|116753428|ref|YP_842546.1|  [L=129]
Description: sirohydrochlorin cobaltochelatase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-25   90.1   0.0    1.2e-25   89.9   0.0    1.0  1  CbiX      CbiX
    3.2e-05   23.4   0.0    3.8e-05   23.1   0.0    1.0  1  CbiK      Cobalt chelatase (CbiK)


Domain annotation for each model (and alignments):
>> CbiX  CbiX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.9   0.0   1.3e-29   1.2e-25       1     105 [.      11     121 ..      11     123 .. 0.98

  Alignments for each domain:
  == domain 1  score: 89.9 bits;  conditional E-value: 1.3e-29
                                    -STSSCCHHHHHHHHHHHHHHHCCSCCCEECESCCCECCSCCSSHHHHC-SBSEEEEEEESSSSSHHHHTHHHHHCT--S CS
                           CbiX   1 HGSrdpesneeveklaeelrekgpfkpvelgfleleepsleealrelaeqgvkrivvvPlflfaGvhvkeDIpeeleeae 80 
                                    HGS +p+ ++ ve+la ++++k+p  pv++++l+++ p+++e+l ++a  +v++iv++Plfl+aGvh+ eDIp+el+  +
  gi|116753428|ref|YP_842546.1|  11 HGSTLPYNKALVEELAGMIKRKHP-GPVRTAYLNANDPKIPEGLMSFAGTNVRKIVAIPLFLAAGVHTLEDIPRELGIPK 89 
                                    ************************.******************************************************* PP

                                    SSS-.......TTEEEEE---CCCSCCHHHHH CS
                           CbiX  81 eahp.......kdveieytepLGthplvaevl 105
                                     +h        +dve++++epLG ++ +a++ 
  gi|116753428|ref|YP_842546.1|  90 GKHVgvikidgRDVEVTCAEPLGVDECIADLA 121
                                    ****************************9986 PP

>> CbiK  Cobalt chelatase (CbiK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   4.2e-09   3.8e-05     144     252 ..       6     120 ..       2     128 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 4.2e-09
                                    EEEEE---SCHHHHHH.HHHHHHHHHCT-S.EEEEETTS.SS-HHHHHHHHHHHT--EEEEEE-SSS--HHHHCCCCSS. CS
                           CbiK 144 lvfvgHGtehesnavy.aeldkvlkekdfkqvvvgtveg.yPeveevieelkkkgikevkliPlmlvAGdHaknDmasd. 220
                                    l+ +gHG++ + n++  +el  ++k k+   v  + +++ +P++ e + +  +++++++  iPl+l AG H  +D+  + 
  gi|116753428|ref|YP_842546.1|   6 LLVLGHGSTLPYNKALvEELAGMIKRKHPGPVRTAYLNAnDPKIPEGLMSFAGTNVRKIVAIPLFLAAGVHTLEDIPREl 85 
                                    5679******998765278999**9999999****998747***********************************8763 PP

                                    ..STTSHHHHHHHTT--EEE.----GGGSHHHHHH CS
                           CbiK 221 ..eedswkealeaaGikvei.ilkgLGeieeirsi 252
                                       +++++  ++ +G  ve+   + LG +e i+++
  gi|116753428|ref|YP_842546.1|  86 giPKGKHVGVIKIDGRDVEVtCAEPLGVDECIADL 120
                                    33478888899999999987345778887777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 1017.91
//
Query:       gi|116753429|ref|YP_842547.1|  [L=402]
Description: Mur ligase middle domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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-07   29.4   0.0    1.1e-06   28.8   0.0    1.3  1  Mur_ligase_M  Mur ligase middle domain


Domain annotation for each model (and alignments):
>> Mur_ligase_M  Mur ligase middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   6.3e-11   1.1e-06       1     120 [.      86     213 ..      86     225 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 6.3e-11
                                    EESSS-HHHHHHHHHHHHHCT..EEEEETTC..................SS-THHHHHHHHHHHHHTT-SEEEEE--HCH CS
                   Mur_ligase_M   1 vTGtnGKTTtteliaaileka..gkvigtvg..................ttnneiglpktlaemekkeaeyavlEvsshg 60 
                                    +TGt GKTTt+ l+a +l++   +  ++t g                  t  n i  ++      +++a++++ Evs   
  gi|116753429|ref|YP_842547.1|  86 ITGTRGKTTTALLLALMLSHDmrVVSHTTSGielwnrgrrslirsglsiTPGNLIAAHQIA---SEERADFLISEVSLG- 161
                                    8*****************999444444555599**********999986655555555544...44568*******999. PP

                                    HHCTTTCCHCBESEEEE---TSTTHHHHSSHHHHHHHHHHHHHTSETTCEEEEETTSC.. CS
                   Mur_ligase_M  61 lgekrlegllkpdvavitnispdHldfhgtlenyaeaKaelferlkeegiavinaddpya 120
                                           g+  +dv++it++  d l   g++ +  +aK ++++   +++  v n d + +
  gi|116753429|ref|YP_842547.1| 162 -------GTGAFDVGIITSLAGDYLIAGGSMWA-STAKLQMLSLSDPDARIVANTDAKLS 213
                                    .......33579***************999988.689******99999999999998854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 2773.88
//
Query:       gi|116753430|ref|YP_842548.1|  [L=369]
Description: hypothetical protein Mthe_0106 [Methanosaeta thermophila PT]
Scores for complete 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-20   71.4   0.1      1e-19   70.6   0.0    1.4  2  Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
  ------ inclusion threshold ------
      0.011   15.5   0.8      0.025   14.3   0.8    1.7  1  SHOCT           Short C-terminal domain


Domain annotation for each model (and alignments):
>> Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.6   0.0   1.1e-23     1e-19      17     134 ..      29     140 ..      15     182 .. 0.88
   2 ?   -3.4   0.0      0.34     3e+03     211     235 ..     211     235 ..     183     260 .. 0.61

  Alignments for each domain:
  == domain 1  score: 70.6 bits;  conditional E-value: 1.1e-23
                                    EEEEES-HHHHHCCCCHHHCHHSS-HS-EEEE--HHHHSSSSHHHHHHHHHHHHHHC-TSEEEEEE-HHHHHTTTTHHHH CS
                 Oxidored_nitro  17 lplvhGpqGCatyaralltrhfrepiplastdltekdavfGgeekLkeaikeivkrykpkaIgVittClteliGdDieav 96 
                                    ++++hGp GC++ + +ll       + +++t l+ek  vfGg+e+L++ ++ +v+ ++pk+I+V+ tC++ +iG+D++  
  gi|116753430|ref|YP_842548.1|  29 VIILHGPSGCCFKHARLLEEDG---VRVLTTGLDEKGFVFGGQEQLVRLLRRAVELFHPKIIAVAGTCSSMIIGEDLHKA 105
                                    789********99999995554...48****************************************************9 PP

                                    HHHHHHHHTSSEEEEEE--TTSSSHHHHHHHHHHHHHH CS
                 Oxidored_nitro  97 areaeeelgeipvipvstpgfggsqseGydaalealvr 134
                                    + ea+     +pvi +++     + ++G  ++lea  +
  gi|116753430|ref|YP_842548.1| 106 VVEANIG---VPVIEAEVHAGYRDNTKGVIITLEAARD 140
                                    9999753...49****9999999999999999988765 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.34
                                    HHHHHH---EEEEE-SSSHHHHHHH CS
                 Oxidored_nitro 211 lleekfgvpyiklvspiGleatdaf 235
                                    ++ ++ +   i++    G e+  ++
  gi|116753430|ref|YP_842548.1| 211 YMFADINLSLIEVARALGCEEKIRT 235
                                    3333344444444444444444444 PP

>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.8   2.7e-06     0.025       5      27 ..     134     156 ..     132     157 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.7e-06
                          SHOCT   5 kLkeLyarGeIteEEFeakKakL 27 
                                    +L + +++G+I++ E +++K+ L
  gi|116753430|ref|YP_842548.1| 134 TLEAARDAGIIDDQELNRQKKLL 156
                                    68999****************88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); 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 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2647.58
//
Query:       gi|116753431|ref|YP_842549.1|  [L=99]
Description: hypothetical protein Mthe_0107 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-23   81.6   0.0      5e-23   81.2   0.0    1.2  1  DUF1805   Domain of unknown function (DUF1805)
     0.0031   17.5   0.0     0.0031   17.5   0.0    1.1  1  IMS       impB/mucB/samB family


Domain annotation for each model (and alignments):
>> DUF1805  Domain of unknown function (DUF1805)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.2   0.0   5.6e-27     5e-23       1      63 []      36      99 .]      36      99 .] 0.98

  Alignments for each domain:
  == domain 1  score: 81.2 bits;  conditional E-value: 5.6e-27
                                   E-TT--HHHHHHTT--EEE-.....-S--SHHHHHHSB-SEE-HHHHHTT--TT-BHHHHGGGG CS
                        DUF1805  1 mCGaLdvealeklgdlaarvivag.sGVrtledllaapvesvteaAeelGikeGmtgkeaLekl 63
                                   +CGa dv+al+++g++aarv+ ++   ++t++dll+++v ++++aA++lGikeGm+g+eaLe+l
  gi|116753431|ref|YP_842549.1| 36 GCGAYDVSALDRHGYPAARVRSSTgGLIATVDDLLRGEVFEANSAARKLGIKEGMSGREALEHL 99
                                   7********************999999***********************************87 PP

>> IMS  impB/mucB/samB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   3.4e-07    0.0031      31      58 ..      59      97 ..       9      99 .] 0.79

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.4e-07
                                   .............TEEEEE-HHHHTTT--TTSBHHHHHT CS
                            IMS 31 k...........rgiviavsyeArayGvkrgmrikeakk 58
                                   +           rg v  ++ +Ar+ G+k+gm+ +ea++
  gi|116753431|ref|YP_842549.1| 59 TggliatvddllRGEVFEANSAARKLGIKEGMSGREALE 97
                                   055555555667999*********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); 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: 0.35u 0.28s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 710.68
//
Query:       gi|116753432|ref|YP_842550.1|  [L=295]
Description: radical SAM domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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   49.3   0.0    1.1e-12   48.6   0.0    1.3  1  Radical_SAM     Radical SAM superfamily
  ------ inclusion threshold ------
      0.038   14.2   0.0        0.1   12.9   0.0    1.7  2  Fer4_12         4Fe-4S single cluster domain
      0.047   13.7   0.1      0.099   12.7   0.1    1.5  1  Sulfolobus_pRN  Sulfolobus plasmid regulatory protein


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 !   48.6   0.0   1.9e-16   1.1e-12       3     159 ..      23     179 ..      21     186 .. 0.86

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 1.9e-16
                                    EESEESS--TTTSCCTT.HHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEE CS
                                    xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   3 vtrgCnlrCsfCarpet.vrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlaklavpgiri 80 
                                    +++ C+++C +C ++ t   + +r r+++ e +++e+ +++ + +     + g+gep+l++ + e++++++k    ++ i
  gi|116753432|ref|YP_842550.1|  23 PLKTCSMDCCYCEIGATtCLTMRRDRYVPEEAVIREISRVS-SVDfDYLTFAGSGEPTLHSGLGEIIRAARKQ--IDRPI 99 
                                    5789*************9999*******************7.555366666679*******************..7**** PP

                                    EEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT..CTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  81 tvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn..rghtfeevlealeklreagikrvvdrivglpGende 158
                                    +v+tn  l+  +++++ +    d v  +l+aa+ e++ ++++   g  +e+++e+l+++r+  + + +  +++++  n++
  gi|116753432|ref|YP_842550.1| 100 AVITNSSLLIYKHVRKEVAQ-ADLVLPSLDAATQETFERINRpaAGLKIEDIIEGLRAFRSEFGGEMWLEVMLVREINES 178
                                    ********966666666665.5*************77777765577888***********99666699999999999998 PP

                                    H CS
                                    x RF
                    Radical_SAM 159 e 159
                                    +
  gi|116753432|ref|YP_842550.1| 179 D 179
                                    7 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.7e-05       0.1      12     102 ..      24     116 ..      14     141 .. 0.75
   2 ?   -2.3   0.0      0.81   4.9e+03      62      92 ..     206     235 ..     176     249 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.7e-05
                        Fer4_12  12 vsgCnlsCkgCfnketwsfk..sgkeftkelleeiiedlkkesiegltllG.GEPllpenaeallelvkevkeekpekdi 88 
                                    ++ C++ C +C   +t + +  + + +++e+  + i +++    + lt+ G GEP l    + l e+++  +++   +  
  gi|116753432|ref|YP_842550.1|  24 LKTCSMDCCYCEIGATTCLTmrRDRYVPEEAVIREISRVSSVDFDYLTFAGsGEPTL---HSGLGEIIRAARKQIDRPIA 100
                                    678********988888766215555688888888899989999*************...88999999999999876555 PP

                        Fer4_12  89 wlytgy..tleelskk 102
                                    ++++ +  ++++++k+
  gi|116753432|ref|YP_842550.1| 101 VITNSSllIYKHVRKE 116
                                    5555441155555544 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.81
                        Fer4_12  62 EPllpenaeallelvkevkeekpekdiwlyt 92 
                                    EP+lp  ++++l++++ +k + +    w ++
  gi|116753432|ref|YP_842550.1| 206 EPVLPLRRDEMLRMLRLFKGAEL-IPDWDWS 235
                                    88888888888888888887766.3345555 PP

>> Sulfolobus_pRN  Sulfolobus plasmid regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   1.7e-05     0.099      13      53 ..     246     286 ..     238     290 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.7e-05
                 Sulfolobus_pRN  13 ilsrrcatleeleektGiekeellvyltrlykrGlisrkWr 53 
                                     l r  +tleel+ k+G+  e+ + yl  l + G isr  r
  gi|116753432|ref|YP_842550.1| 246 DLLREPMTLEELRSKSGLIYEDTVKYLKILEDAGRISRSIR 286
                                    577899*******************************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 2102.18
//
Query:       gi|116753433|ref|YP_842551.1|  [L=460]
Description: (R)-citramalate synthase [Methanosaeta thermophila PT]
Scores for 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-64  216.4   0.7    9.5e-64  215.5   0.7    1.5  1  HMGL-like   HMGL-like
    3.8e-33  114.2   0.6    7.8e-33  113.2   0.6    1.6  1  LeuA_dimer  LeuA allosteric (dimerisation) domain
     0.0084   16.0   0.1      0.057   13.3   0.1    2.2  2  DUF5486     Family of unknown function (DUF5486)


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 !  215.5   0.7   1.6e-67   9.5e-64      33     264 .]       2     227 ..       1     227 [. 0.99

  Alignments for each domain:
  == domain 1  score: 215.5 bits;  conditional E-value: 1.6e-67
                                    HHHT-SEE--TSGGGT.THHHHHHHS---TT-B..--EE-SSHHHHHHHHH....TT-SEEEEEEES-HHHHHHHHSSTH CS
                      HMGL-like  33 deagvdeiEvgfpaaseddfevvraiakavkkarilalvrarekdikaavealkgagakrvhvfiatselhlkaklkkdr 112
                                    de+gvd+iE+g +  s +++e++raia+a+ +a+i++ +ra+ kdi+aa +    + ++++h+++++s+lh++ kl+ dr
  gi|116753433|ref|YP_842551.1|   2 DELGVDVIEAGSAITSDGERESIRAIASAGLNAEICSFARAHRKDIDAALD----CDVDSLHLVVPVSDLHIERKLRSDR 77 
                                    89*************************************************....************************* PP

                                    HHHHHHHHHHHHHHHHTT-ETTT-BTTTBS--HHHHHHHHHHHHHHT-SEEEEEETTS---HHHHHHHHHHHHHHS-.GG CS
                      HMGL-like 113 eevakkaeeavkaarslgkdvelsledasrtdleflaevveaaeeaGatriniaDtvGvltPneaaelisalkervkdkv 192
                                    e v++ka+ea+++a+ +g  vels edasr+dl++l  ++ a +eaGa+r+ + DtvGvl P+  ae++++l++  k   
  gi|116753433|ref|YP_842551.1|  78 ESVLRKAVEATEYAKAHGLIVELSGEDASRADLDYLESIYRATIEAGADRLCFCDTVGVLLPERTAEIFQRLRSLGK--- 154
                                    *************************************************************************9999... PP

                                    GEEEEEB-TTS-HHHHHHHHHHTT--EEEEBTTS--SSBBB-BHHHHHHHHHHTT.-B----HHHHHHHHHHH CS
                      HMGL-like 193 ilsvHcHndlGlAvantlaAveaGadrvdgtvnGlGeraGnaaleelvaalealg.vdtgldlqklrsiaalv 264
                                    ++s+HcH+d+G+A+ant+aA+++Ga +  +t+nGlGeraGn++lee+v+ le+l  + tg++ + l++i+++v
  gi|116753433|ref|YP_842551.1| 155 PVSIHCHDDFGMATANTVAALRNGAMQAHVTINGLGERAGNTSLEEVVMCLENLYgIRTGIKCNLLYQISRVV 227
                                    *****************************************************977**************997 PP

>> LeuA_dimer  LeuA allosteric (dimerisation) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.2   0.6   1.3e-36   7.8e-33       2     132 ..     323     454 ..     322     455 .. 0.96

  Alignments for each domain:
  == domain 1  score: 113.2 bits;  conditional E-value: 1.3e-36
                                    XXXXXXXXXXXXXXXXXX.--EEEEEEEEEEETTCEEEEEEEEEE.TTEEEEEEEE-SSHHHHHHHHHHHHHHH..T-EE CS
                     LeuA_dimer   2 vtdedlealvkdelleae.erlkleklqvssgedelstatvklevkdgeekeasaeGnGpvdAllnAlrkalgv..dikL 78 
                                    v+d+dl+++++++l ++   r+ le+l+v+sg++ ++ta+vkl + dg+e+ +++ G+GpvdA++nA+r+a++   di+L
  gi|116753433|ref|YP_842551.1| 323 VSDADLQSIADTVLSRELkPRVLLEELTVVSGNRVTPTASVKLIL-DGRETLEAGAGVGPVDAAVNAVRRAISGvtDIRL 401
                                    89**************9989*************************.*************************99889**** PP

                                    EEEEEE--TT-TT--EEEEEEEE--GGGEEEEEEEESSHHHHHHHHHHHHHHHH CS
                     LeuA_dimer  79 ldYsvhaitegtdaqaevrVelevddgkkvsgvGvdsdiveASlkAlisalnrl 132
                                    ++Y+v+ait+gt+a++ev V++   ++++++++G+ +di++AS++A+++++nrl
  gi|116753433|ref|YP_842551.1| 402 EEYHVDAITGGTNALVEVWVTMA-IGDRSITARGAGADIIMASVEAVLEGINRL 454
                                    ***********************.55555***********************98 PP

>> DUF5486  Family of unknown function (DUF5486)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.1   9.6e-06     0.057       8      33 ..      72      97 ..      67      99 .. 0.94
   2 ?   -0.9   0.0      0.26   1.6e+03      14      28 ..     307     321 ..     304     324 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.6e-06
                        DUF5486  8 kirssreemmrrfkeahdkakaeGti 33
                                   k+rs re ++r+  ea + aka G i
  gi|116753433|ref|YP_842551.1| 72 KLRSDRESVLRKAVEATEYAKAHGLI 97
                                   99**********************88 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.26
                        DUF5486  14 eemmrrfkeahdkak 28 
                                    +e++ r ke  dk k
  gi|116753433|ref|YP_842551.1| 307 NEIVSRVKELGDKGK 321
                                    58999********88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); 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 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3405.50
//
Query:       gi|116753434|ref|YP_842552.1|  [L=557]
Description: acetolactate synthase 3 catalytic subunit [Methanosaeta thermophila PT]
Scores for complete 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-58  197.4   0.0    2.8e-58  196.4   0.0    1.5  1  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
    9.6e-55  184.1   0.2    1.6e-54  183.3   0.2    1.4  1  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
    3.9e-52  176.1   0.0    1.5e-51  174.2   0.1    2.0  2  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
  ------ inclusion threshold ------
      0.028   14.2   0.5      0.061   13.1   0.5    1.5  1  POR_N         Pyruvate flavodoxin/ferredoxin oxidoreductase, 


Domain annotation for each model (and alignments):
>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.4   0.0   6.1e-62   2.8e-58       1     167 [.       5     169 ..       5     173 .. 0.98

  Alignments for each domain:
  == domain 1  score: 196.4 bits;  conditional E-value: 6.1e-62
                                    EEHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCH CS
                   TPP_enzyme_N   1 mtvaealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnal 80 
                                    mt+aea++++L+++gve++fg+pG+ +lpl+dal  ++ +r++l+rhEq+aa+aAdgyaratg++gv+l+tsgpGatn++
  gi|116753434|ref|YP_842552.1|   5 MTGAEAIIECLRREGVEVIFGLPGGVLLPLYDALYSSD-MRHILVRHEQAAAHAADGYARATGRVGVCLATSGPGATNLV 83 
                                    89***********************************6.***************************************** PP

                                    HHHHHHHHHT--EEEEEEE--CCCHHS..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EEEEEEE CS
                   TPP_enzyme_N  81 talaeAkvdriPllvlsgdrptslrgqgvlqqeldqlalfrpvtkyaervtspeelpealrrAirtalsgrpgPvylelp 160
                                    t++a+A+ d++P+++++g+++t l+g++++q e d++++  p+tk+++ ++s++++p+++r+A+ +a +grpgPv+++lp
  gi|116753434|ref|YP_842552.1|  84 TGIATAYMDSVPIVAMTGQVNTGLIGKDAFQ-EADITGITMPITKHNYLIKSSRDIPRVFREAFYIARTGRPGPVLIDLP 162
                                    *******************************.************************************************ PP

                                    HHHCC-E CS
                   TPP_enzyme_N 161 kdvllee 167
                                    +d+  +e
  gi|116753434|ref|YP_842552.1| 163 RDITVDE 169
                                    **98776 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 !  183.3   0.2   3.6e-58   1.6e-54       1     137 []     193     328 ..     193     328 .. 0.99

  Alignments for each domain:
  == domain 1  score: 183.3 bits;  conditional E-value: 3.6e-58
                                    HHHHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEEESGGGSCHHHHHHHHH-SE CS
                   TPP_enzyme_M   1 iekaaellkaakrpvilvGggvarsgaseelrelaeklgiPvvttlmgkgvipedhplylgmlglhgskaanealeeaDl 80 
                                    i++aae+l aa+rpvi++Gggv++++a+eel +la +l++Pv+ttlmg g++p dhpl+lgmlg+hg+k+an a++eaD+
  gi|116753434|ref|YP_842552.1| 193 IRRAAEALMAAERPVIYAGGGVRYANAHEELFQLATRLNAPVTTTLMGMGCFPTDHPLSLGMLGMHGTKYANLAVQEADV 272
                                    789***************************************************************************** PP

                                    EEEES-SSSTCCCTTTTTTTTTT-EEEEEESSCCCCTTCC--SEEEECTHHHHHHHH CS
                   TPP_enzyme_M  81 vlalGarfddirttgsepefapeakiihididpaeigknyqvdlaivgdvketleaL 137
                                    +la+Garfdd r+tg+   fap+a+iihid+d+aeigkn++vd+++vgd+k +l++L
  gi|116753434|ref|YP_842552.1| 273 LLAVGARFDD-RVTGKIASFAPKARIIHIDVDAAEIGKNVRVDIPVVGDAKIALTEL 328
                                    **********.*****************************************99987 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 ?   -2.6   0.0      0.93   4.2e+03     129     152 ..     134     160 ..     113     161 .. 0.79
   2 !  174.2   0.1   3.3e-55   1.5e-51       2     152 ..     384     530 ..     383     531 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.93
                                    SH.HHHHHHHHHHHH.....CSSSEEEEE CS
                   TPP_enzyme_C 129 kadveeleealkeal.....ekkgpalie 152
                                    ++   ++ ++++ea+      + gp+li+
  gi|116753434|ref|YP_842552.1| 134 SS--RDIPRVFREAFyiartGRPGPVLID 160
                                    55..6777888888777778899999998 PP

  == domain 2  score: 174.2 bits;  conditional E-value: 3.3e-55
                                    SSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-SEEEEEEE CS
                   TPP_enzyme_C   2 iGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnlpitvvvln 81 
                                    +G++++waa+++k k pr+++tsgglgtmGyg+paAiGak+ +p+ ev+ i+GDG+f+m++qelatav +++p+++ +ln
  gi|116753434|ref|YP_842552.1| 384 VGQNQMWAAQFFKHKDPRKFITSGGLGTMGYGFPAAIGAKVGRPECEVIDIAGDGSFQMNIQELATAVVNDIPVKIAILN 463
                                    9******************************************************************************* PP

                                    -SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHHCSSSEEEEE CS
                   TPP_enzyme_C  82 NegygmtggqqepfggkrksgpagkdlkpvdfaklaealGakgarvekadveeleealkealekkgpalie 152
                                    N+++gm++++q+ f+gkr+s+++   ++ +df+k+aea+Ga g+r +k+  +e+e++l+e l++++p++ +
  gi|116753434|ref|YP_842552.1| 464 NGVLGMVRQWQTLFFGKRYSHTT--LGDVPDFVKVAEAYGAVGLRATKP--SEVEDVLREGLASDRPTVMD 530
                                    *********************99..58889***************7788..******************98 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 ?   13.1   0.5   1.4e-05     0.061      37      93 ..      42     100 ..      32     103 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.4e-05
                                    E.EEEE-SSHHHHHHHHHH.HHCTT-EE.EEEEECCHHHHCCCCHHHHHHTT--EEEEE CS
                          POR_N  37 dvevvqmesEigaisaviG.AaaaGara.aTaTSgqGllLmienlglaageelPvvivv 93 
                                    d++ + +  E +a+ a+ G A a+G  +   aTSg+G    +  +  a ++ +P+v + 
  gi|116753434|ref|YP_842552.1|  42 DMRHILVRHEQAAAHAADGyARATGRVGvCLATSGPGATNLVTGIATAYMDSVPIVAMT 100
                                    677888999**********6667787651469************************886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (557 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); 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:                         4  (0.000223102); expected 0.2 (1e-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 0.24s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 4127.33
//
Query:       gi|116753435|ref|YP_842553.1|  [L=165]
Description: acetolactate synthase, small subunit [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.5e-30  103.4   1.9    5.5e-30  103.4   1.9    1.9  2  ALS_ss_C         Small subunit of acetolactate synthase
      7e-19   67.4   1.0    1.4e-17   63.3   0.0    2.6  2  ACT_5            ACT domain
    1.4e-14   53.5   0.5    3.3e-14   52.3   0.1    1.8  2  ACT              ACT domain
    8.6e-09   35.9   2.3    1.2e-08   35.5   0.3    2.0  2  ACT_4            ACT domain
    7.6e-05   22.6   0.8       0.63   10.1   0.2    3.3  2  ACT_6            ACT domain
    0.00031   20.5   0.3        1.2    9.0   0.0    2.6  3  NIL              NIL domain
  ------ inclusion threshold ------
      0.012   15.9   0.2        6.7    7.2   0.0    2.3  2  Acylphosphatase  Acylphosphatase
      0.026   14.9   0.3       0.12   12.8   0.1    2.1  3  Saccharop_dh_N   LOR/SDH bifunctional enzyme conserved region
      0.057   13.5   1.5       0.12   12.4   0.5    1.7  2  DUF2096          Uncharacterized protein conserved in archaea
        0.1   12.5   0.0       0.14   12.1   0.0    1.3  1  SCO1-SenC        SCO1/SenC


Domain annotation for each model (and alignments):
>> ALS_ss_C  Small subunit of acetolactate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       0.6   1.1e+03      37      65 ..      46      75 ..      42      75 .. 0.70
   2 !  103.4   1.9   3.1e-33   5.5e-30       1      74 []      84     157 ..      84     157 .. 0.99

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.6
                                   EEEEEEE-HHHHHHHHHHS-.GGGEEEEEE CS
                       ALS_ss_C 37 liieltgteekidaliellk.pfgilevvR 65
                                   ++i + g+   ++++++ l+  ++++ v+R
  gi|116753435|ref|YP_842553.1| 46 MTISVEGDDVVLEQVVKQLSkLINVIRVSR 75
                                   788888888888888888862444666665 PP

  == domain 2  score: 103.4 bits;  conditional E-value: 3.1e-33
                                    EEEEEEEEE.-SCHHHHHHHHHHHTT-EEEEEETTEEEEEEEE-HHHHHHHHHHS-GGGEEEEEEEEEEEEEST CS
                       ALS_ss_C   1 RElaLiKVkaekeerseileiaeifrakivdvspdsliieltgteekidaliellkpfgilevvRtGrvAleRG 74 
                                    REla+iKV+a+k++rsei++i+++fra+i+dvsp sliie+tg+e+k+dal ++l++fgi+e++RtG+v + RG
  gi|116753435|ref|YP_842553.1|  84 RELAIIKVSANKDTRSEIMQIVSVFRARIIDVSPRSLIIEVTGDEKKVDALQQMLRQFGIKEMARTGKVSMVRG 157
                                    9**********************************************************************998 PP

>> ACT_5  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.3   0.0   7.6e-21   1.4e-17       2      62 .]      12      73 ..      11      73 .. 0.98
   2 ?    2.2   0.2      0.09   1.6e+02      35      54 ..     119     139 ..     100     142 .. 0.83

  Alignments for each domain:
  == domain 1  score: 63.3 bits;  conditional E-value: 7.6e-21
                          ACT_5  2 apgvLeRvlrvvrrrgFevkslnmsttedggtvrieltVes.ersvelLsnQleKLidVlkV 62
                                   +pgvL R+ ++++rrgF+++sl++ +t++  ++r++++Ve+ +  +e++++Ql+KLi+V++V
  gi|116753435|ref|YP_842553.1| 12 KPGVLTRISGLFSRRGFNIESLSVGATDNPAYSRMTISVEGdDVVLEQVVKQLSKLINVIRV 73
                                   7**********************************************************998 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.09
                          ACT_5  35 rieltVes.ersvelLsnQle 54 
                                    ++ ++V++ e+ v+ L+  l+
  gi|116753435|ref|YP_842553.1| 119 SLIIEVTGdEKKVDALQQMLR 139
                                    688999999999999987665 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.3   0.1   1.9e-17   3.3e-14       1      66 [.       3      68 ..       3      69 .. 0.97
   2 ?   -1.7   0.0       1.5   2.6e+03      44      55 ..     119     130 ..     105     140 .. 0.48

  Alignments for each domain:
  == domain 1  score: 52.3 bits;  conditional E-value: 1.9e-17
                                   EEEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHTTC CS
                            ACT  1 tvlrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkkle 66
                                   +++ v v+++PG+L r++g++++rg+Ni+s++++ ++    +++++ +++d+ +le+v+++l kl+
  gi|116753435|ref|YP_842553.1|  3 HTIAVIVENKPGVLTRISGLFSRRGFNIESLSVGATDNPAYSRMTISVEGDDVVLEQVVKQLSKLI 68
                                   68899**********************************************************997 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.5
                                    EEEEEEEEHHHH CS
                            ACT  44 vfvvivvdeedl 55 
                                    + +++v+++e  
  gi|116753435|ref|YP_842553.1| 119 SLIIEVTGDEKK 130
                                    334444443333 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.3   6.4e-12   1.2e-08       8      80 .]       4      75 ..       1      75 [. 0.92
   2 ?   -0.4   0.1      0.99   1.8e+03      19      38 ..      97     116 ..      86     120 .. 0.66

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 6.4e-12
                          ACT_4  8 rleveaedrkglLaditqviseekanivsvnaktrkkdglaeikitveVk.dvehLsrviakLraipgVisVeR 80
                                   ++ v++e+++g+L++i+ ++s  + ni+s+++ +  +d+ a  ++t++V+ d   L++v+++L ++ +Vi+V+R
  gi|116753435|ref|YP_842553.1|  4 TIAVIVENKPGVLTRISGLFSRRGFNIESLSVGA--TDNPAYSRMTISVEgDDVVLEQVVKQLSKLINVIRVSR 75
                                   799*******************************..5789999999999834557*****************99 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.99
                          ACT_4  19 lLaditqviseekanivsvn 38 
                                      ++i+q++s  +a+i +v+
  gi|116753435|ref|YP_842553.1|  97 TRSEIMQIVSVFRARIIDVS 116
                                    34678888888888877765 PP

>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0    0.0016       2.9       7      64 ..       7      66 ..       5      74 .. 0.78
   2 !   10.1   0.2   0.00035      0.63      17      65 ..      99     141 ..      92     148 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0016
                          ACT_6  7 vtGpdrpGltasLtsvlaefgvnilDieqavihgrlsLgllvsgped..alarlekaLlf 64
                                   v+ +++pG++ +++++ ++ g ni  + +    +     + +s++ d   l+++ k+L++
  gi|116753435|ref|YP_842553.1|  7 VIVENKPGVLTRISGLFSRRGFNIESLSVGATDNPAYSRMTISVEGDdvVLEQVVKQLSK 66
                                   55679*******************998888888877766666666442477888888776 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00035
                          ACT_6  17 asLtsvlaefgvnilDieqavihgrlsLgllvsgpedalarlekaLlfl 65 
                                    +++++++++f+++i+D+         sL++ v+g+e+++ +l+++L++ 
  gi|116753435|ref|YP_842553.1|  99 SEIMQIVSVFRARIIDVSP------RSLIIEVTGDEKKVDALQQMLRQF 141
                                    789*************964......578899999999999999988875 PP

>> NIL  NIL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0   0.00067       1.2      28      67 ..      28      67 ..      12      73 .. 0.86
   2 ?   -2.1   0.0       1.9   3.5e+03      53      71 ..      97     115 ..      88     117 .. 0.64
   3 !    8.9   0.0   0.00075       1.3      45      69 ..     119     143 ..     118     145 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00067
                                   EEEEEEEEEEETTEEEEEEEEEEES-HHHHHHHHHHHHHT CS
                            NIL 28 vnIlqGsveriqgtpfGqlvielsgsqesiaaalqylrkr 67
                                   +nI + sv+  ++ ++ +++i+++g++  ++++++ l+k 
  gi|116753435|ref|YP_842553.1| 28 FNIESLSVGATDNPAYSRMTISVEGDDVVLEQVVKQLSKL 67
                                   66666689999999********************999986 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.9
                                    -HHHHHHHHHHHHHTT-EE CS
                            NIL  53 sqesiaaalqylrkrnvdv 71 
                                    ++ +i +++  +r r +dv
  gi|116753435|ref|YP_842553.1|  97 TRSEIMQIVSVFRARIIDV 115
                                    3347888888888887776 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.00075
                                    EEEEEEES-HHHHHHHHHHHHHTT- CS
                            NIL  45 qlvielsgsqesiaaalqylrkrnv 69 
                                    +l+ie++g++++++a+ q lr+ ++
  gi|116753435|ref|YP_842553.1| 119 SLIIEVTGDEKKVDALQQMLRQFGI 143
                                    59*******************9877 PP

>> Acylphosphatase  Acylphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0038       6.7      29      74 ..      36      81 ..      33      88 .. 0.86
   2 ?    6.7   0.0    0.0054       9.8      40      66 ..     121     149 ..     114     160 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0038
                Acylphosphatase 29 GyvrNlsdgsVeivaegeeekvekfleelksgppkarvdeveveel 74
                                   G + N +  +  i +eg++  +e+++++l++    +rv++++ +e+
  gi|116753435|ref|YP_842553.1| 36 GATDNPAYSRMTISVEGDDVVLEQVVKQLSKLINVIRVSRLDPQES 81
                                   677788888999******************9999999999987765 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0054
                Acylphosphatase  40 eivaegeeekvekfleelks.gppk.arv 66 
                                     i+++g+e+kv++++++l++ g ++ ar 
  gi|116753435|ref|YP_842553.1| 121 IIEVTGDEKKVDALQQMLRQfGIKEmART 149
                                    699***************99755555555 PP

>> Saccharop_dh_N  LOR/SDH bifunctional enzyme conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   6.7e-05      0.12      30      71 ..      28      69 ..      14     100 .. 0.72
   2 ?   -0.7   0.0       1.1     2e+03      47      74 ..      87     113 ..      78     133 .. 0.66
   3 ?   -0.8   0.0       1.1     2e+03      50      74 ..     123     146 ..     113     163 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.7e-05
                                   EEEEEEEXXSSTT.SXEEEEEEEEESSHHHHHHHHHHHHHHHH CS
                 Saccharop_dh_N 30 fevlefevGkkkk.dtSyaelevsaedeevLeeileeltelga 71
                                   f++++++vG++ + + S  +++v+++d  vLe+++++l++l +
  gi|116753435|ref|YP_842553.1| 28 FNIESLSVGATDNpAYSRMTISVEGDD-VVLEQVVKQLSKLIN 69
                                   99*******875414455555555555.79********99833 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.1
                                    EEEEEEESSHHHHHHHHHHHHHHHHHSC CS
                 Saccharop_dh_N  47 aelevsaedeevLeeileeltelgaelv 74 
                                    a ++vsa++ ++ +ei++ ++ + a+++
  gi|116753435|ref|YP_842553.1|  87 AIIKVSANK-DTRSEIMQIVSVFRARII 113
                                    556777765.444666666666555555 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.1
                                    EEEESSHHHHHHHHHHHHHHHHHSC CS
                 Saccharop_dh_N  50 evsaedeevLeeileeltelgaelv 74 
                                    ev++++ ++++++ + l ++g + +
  gi|116753435|ref|YP_842553.1| 123 EVTGDE-KKVDALQQMLRQFGIKEM 146
                                    555544.455555555555555544 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 ?   -1.4   0.0       1.2   2.1e+03     147     167 ..      47      67 ..      43      69 .. 0.72
   2 ?   12.4   0.5   6.9e-05      0.12     109     164 ..      82     137 ..      77     142 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.2
                        DUF2096 147 vvvvyGdkedikkaLkelsel 167
                                    ++ v+Gd+  +++ +k+ls+l
  gi|116753435|ref|YP_842553.1|  47 TISVEGDDVVLEQVVKQLSKL 67 
                                    577888887777777777765 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 6.9e-05
                        DUF2096 109 vprgfetirvklkkpleeerlqeiaEyegvIiefeeddv.vvvyGdkedikkaLkel 164
                                    v r+ ++i+v  +k+ ++e++q ++ +   Ii+++  +  ++v Gd++++  aL+++
  gi|116753435|ref|YP_842553.1|  82 VERELAIIKVSANKDTRSEIMQIVSVFRARIIDVSPRSLiIEVTGDEKKVD-ALQQM 137
                                    678999******************************99989******9995.66666 PP

>> SCO1-SenC  SCO1/SenC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   7.7e-05      0.14      56     108 ..      82     143 ..      45     161 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.7e-05
                      SCO1-SenC  56 ekvqplfiTvDPerDtpevlkeyleafdpriig.........ltGskeeiakaakefrvyve 108
                                     + ++ +i v  ++Dt +++ + ++ f +rii          +tG++++++++ +  r +  
  gi|116753435|ref|YP_842553.1|  82 VERELAIIKVSANKDTRSEIMQIVSVFRARIIDvsprsliieVTGDEKKVDALQQMLRQFGI 143
                                    5667778889999********************9***********99999877665554433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       938  (0.0523175); expected 358.6 (0.02)
Passed bias filter:                      644  (0.0359195); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1211.19
//
Query:       gi|116753436|ref|YP_842554.1|  [L=332]
Description: ketol-acid reductoisomerase [Methanosaeta thermophila PT]
Scores for complete 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-74  248.0   0.0    4.6e-74  247.5   0.0    1.3  1  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
    5.5e-62  208.3   1.1      8e-62  207.8   1.1    1.2  1  IlvC           Acetohydroxy acid isomeroreductase, catalytic 
    4.2e-08   32.8   0.0    6.6e-08   32.1   0.0    1.3  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    1.6e-05   25.1   0.0    3.8e-05   23.9   0.0    1.6  2  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd
    0.00054   20.1   0.0    0.00097   19.2   0.0    1.3  1  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi
    0.00085   19.9   0.0     0.0019   18.8   0.0    1.6  1  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
       0.11   12.1   0.0       0.21   11.3   0.0    1.4  1  ApbA           Ketopantoate reductase PanE/ApbA


Domain annotation for each model (and alignments):
>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  247.5   0.0   1.8e-77   4.6e-74       1     165 []      14     178 ..      14     178 .. 0.99

  Alignments for each domain:
  == domain 1  score: 247.5 bits;  conditional E-value: 1.8e-77
                                    HHHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHHHHHHHH CS
                           IlvN   1 llkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelqkevyeee 80 
                                    +lk+k+ia+iGyG+qGhaq+ nl+dsgldv+ +  ++s  +k+A+++g++v+tv ea+k+ad++ il+PDelq ++y+e+
  gi|116753436|ref|YP_842554.1|  14 VLKDKTIAIIGYGNQGHAQGANLKDSGLDVIAADLKDSPAWKRAEKDGLRVMTVPEASKEADFIQILLPDELQPRIYREQ 93 
                                    59****************************************************************************** PP

                                    TGGG--TT-EEEESSSHHHHTTSS---TTSEEEEEEESS-SHHHHHHHHTT----EEEEEEE-SSS-HHHHHHHHHHHTT CS
                           IlvN  81 iepnlkegkalafahGfnihfglikppkdvdvvlvAPkgpGhlvreeyeegkGvpaliaveqdasgkakelalayakgiG 160
                                    i+p+l+eg++l f+hGfnihf++i pp+ vdvv+vAPkgpG+lvr+++ egkGvp+l+av+qd+s++ak +alayakgiG
  gi|116753436|ref|YP_842554.1|  94 IAPYLEEGNILGFSHGFNIHFNQIIPPEYVDVVMVAPKGPGDLVRRQFLEGKGVPCLVAVKQDYSKSAKRIALAYAKGIG 173
                                    ******************************************************************************** PP

                                    HHHH- CS
                           IlvN 161 atraG 165
                                    +traG
  gi|116753436|ref|YP_842554.1| 174 GTRAG 178
                                    ****9 PP

>> IlvC  Acetohydroxy acid isomeroreductase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.8   1.1   3.1e-65     8e-62       1     144 []     184     327 ..     184     327 .. 1.00

  Alignments for each domain:
  == domain 1  score: 207.8 bits;  conditional E-value: 3.1e-65
                                    HHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHTT--HHHHHHHHTHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHHHHH CS
                           IlvC   1 FkeEtetDlfgEqavLcGgvselveagFetlveaGyspelAyfeclhelklivdliyegGiakmresiSdtaeygdltag 80 
                                    F eEtetDlfgEq+ LcGgv+++++a+Fet+v+aGy+pe+Ayfe +helkli+dli+egG+ km++s+S+taeyg+lt+g
  gi|116753436|ref|YP_842554.1| 184 FAEETETDLFGEQVDLCGGVTAMIKAAFETMVQAGYQPEIAYFEACHELKLITDLIHEGGLMKMWNSVSNTAEYGGLTRG 263
                                    89****************************************************************************** PP

                                    HHHS-HHHHHHHHHHHHHHHTTHHHHHHHHHHHTTSHHHHHHHHHHHTSHHHHHHHHHHHCHTT CS
                           IlvC  81 prviteevkeemkeileeiqsGefakevieenkagrpelkklrkeeaeheiekvgkklralmpw 144
                                    +r+i+e+++e+m eileeiqsG+fa+e+i+e +ag p  k+l+++e+eh iekvg++lra+mpw
  gi|116753436|ref|YP_842554.1| 264 DRIINEQSREAMWEILEEIQSGKFAREWILESQAGLPVKKALEQQESEHLIEKVGAELRAMMPW 327
                                    **************************************************************98 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0   2.6e-11   6.6e-08      27     100 ..       8      82 ..       2     105 .. 0.90

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 2.6e-11
                                    CCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH.CHHHHTCEECSHHHHHHH-SEEEE-S- CS
                   2-Hacid_dh_C  27 kallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkee.eeeelgvelvsleellaesDivslhlp 100
                                    k+   + l++kt++iiG+G+ G+a    lk  g++via d + ++   ++e+ g++++++ e+ +e+D++ + lp
  gi|116753436|ref|YP_842554.1|   8 KDADLRVLKDKTIAIIGYGNQGHAQGANLKDSGLDVIAADLKDSPAWkRAEKDGLRVMTVPEASKEADFIQILLP 82 
                                    56667789**********************************9987778889999*****************999 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   1.5e-08   3.8e-05       1      86 [.      19     104 ..      19     113 .. 0.92
   2 ?   -3.3   0.0       3.6   9.2e+03      33      59 ..     209     235 ..     203     247 .. 0.57

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.5e-08
                                    EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCCC- CS
                  NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieglleal 80 
                                    +i++iG G+ G+    nl+++g +v++ +++ + + + +++    + ++ e+ +++d++ ++++++ + +   e+++++l
  gi|116753436|ref|YP_842554.1|  19 TIAIIGYGNQGHAQGANLKDSGLDVIAADLKDSPAWKRAEKDGLRVMTVPEASKEADFIQILLPDELQPRIYREQIAPYL 98 
                                    59***************************9998888888777667777788******************999999***** PP

                                    -TT-EE CS
                  NAD_binding_2  81 kkgdil 86 
                                    ++g+il
  gi|116753436|ref|YP_842554.1|  99 EEGNIL 104
                                    ***986 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.6
                                    HHHHHHHHTTEEE-SSHHHHHHHCSEE CS
                  NAD_binding_2  33 ekveelvaegakaaesieelvasldvv 59 
                                    +++e++v++g ++     e++++l+++
  gi|116753436|ref|YP_842554.1| 209 AAFETMVQAGYQPEIAYFEACHELKLI 235
                                    455555555555555555555555555 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 !   19.2   0.0   3.8e-07   0.00097      20      82 ..      14      77 ..       3      82 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 3.8e-07
                                   --TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHH.HHHCTT-EE--HHHCTTT-SEE CS
                  AdoHcyase_NAD 20 llaGkvavvaGyGdvGkGcaaslkglGarvivtevdPical.qaameGfevvtleevvkkadiv 82
                                   +l  k++ ++GyG+ G    a lk  G  vi +++    a  +a  +G++v+t+ e+ k+ad++
  gi|116753436|ref|YP_842554.1| 14 VLKDKTIAIIGYGNQGHAQGANLKDSGLDVIAADLKDSPAWkRAEKDGLRVMTVPEASKEADFI 77
                                   57789*****************************987777626889***************976 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   7.3e-07    0.0019       1      70 [.      19      82 ..      19     102 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 7.3e-07
                                   EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S- CS
                  F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavk 70
                                   +i+iiG+Gn+g+a   +l  +g    +++ a++ + + a + ae+ g +v++    ea +ead++ + ++
  gi|116753436|ref|YP_842554.1| 19 TIAIIGYGNQGHAQGANLKDSG---LDVI-AADLKDSPAWKRAEKDGLRVMT--VPEASKEADFIQILLP 82
                                   69********************...****.6588888888888888877766..99********977665 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0     8e-05      0.21       1      46 [.      20      67 ..      20      84 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8e-05
                                   EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH..HHHHHHHHCEEEEET CS
                           ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr..rlealkknGlrltse 46
                                   iai+G G +G   +a+L+  g dv+  + ++    ++ +k+Glr+ ++
  gi|116753436|ref|YP_842554.1| 20 IAIIGYGNQGHAQGANLKDSGLDVIAADLKDspAWKRAEKDGLRVMTV 67
                                   89***************99****9998766654455588888887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); 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: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2559.77
//
Query:       gi|116753437|ref|YP_842555.1|  [L=149]
Description: hypothetical protein Mthe_0115 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     0.0002   21.2   0.1    0.00042   20.1   0.1    1.5  1  TrmB        Sugar-specific transcriptional regulator TrmB
     0.0055   16.8   0.1      0.011   15.8   0.1    1.5  1  DUF2250     Uncharacterized protein conserved in archaea (DUF
  ------ inclusion threshold ------
      0.014   15.9   1.6      0.021   15.3   0.0    2.1  3  HTH_27      Winged helix DNA-binding domain
      0.016   15.1   0.1      0.023   14.6   0.1    1.2  1  Ferritin    Ferritin-like domain
      0.052   13.5   0.0      0.081   12.9   0.0    1.3  1  HTH_45      Winged helix-turn-helix
      0.065   13.0   0.0       0.16   11.8   0.0    1.6  1  FtsK_gamma  Ftsk gamma domain
      0.098   12.4   0.0       0.13   12.0   0.0    1.2  1  DUF4364     Domain of unknown function (DUF4364)


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 !   20.1   0.1   1.6e-07   0.00042       6      63 ..       9      66 ..       7      69 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.6e-07
                                   HHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEE CS
                           TrmB  6 LseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYr 63
                                   L+e  +++ la+l+l+ a a+ i+++++   +   ++L++Le++GlV+++ + + +Y+
  gi|116753437|ref|YP_842555.1|  9 LKEKPCQALLAILELDHAYASLISKKIDSTFAHTLRILSQLEQAGLVYTRTEGRVKYV 66
                                   6777899*******************************************99999885 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 !   15.8   0.1   4.4e-06     0.011      19      64 ..      22      67 ..       5      70 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.4e-06
                        DUF2250 19 kanvdYaksiakeleipleevrellkkLeelGLlervegktikrte 64
                                   +++  Ya +i+k+++  + +  ++l +Le++GL+   ++  +k+ e
  gi|116753437|ref|YP_842555.1| 22 ELDHAYASLISKKIDSTFAHTLRILSQLEQAGLVYTRTEGRVKYVE 67
                                   566779*****************************99999999865 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 ?   15.3   0.0   8.3e-06     0.021      16      65 ..      23      69 ..       9      72 .. 0.81
   2 ?   -1.9   0.0         2   5.1e+03      37      37 ..      94      94 ..      73     109 .. 0.54
   3 ?   -1.7   0.1       1.7   4.3e+03       5      25 ..     123     144 ..     121     147 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 8.3e-06
                         HTH_27 16 rrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlT 65
                                   ++ + ++ ++++ + + +h+  +l++L+ +GLv +    +++r k v+lT
  gi|116753437|ref|YP_842555.1| 23 LDHAYASLISKKIDSTFAHTLRILSQLEQAGLVYTR---TEGRVKYVELT 69
                                   6666678899999********************333...779******99 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2
                         HTH_27 37 y 37
                                   +
  gi|116753437|ref|YP_842555.1| 94 K 94
                                   2 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.7
                         HTH_27   5 qalvLhlirhrrrrkkl.adlc 25 
                                    + ++L++i   r+  +l ++++
  gi|116753437|ref|YP_842555.1| 123 DLALLRSITDSREIEHLeSRIR 144
                                    6778888887777777766665 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   9.2e-06     0.023      36     110 ..      30     107 ..      24     112 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.2e-06
                                    HHHHHHHHHHHHHHHHHHHHHHTTS....SHH..HHHHC-SSSS.CSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                       Ferritin  36 ffdeqaeeerehadklaerilalGgtpvltra..eleeieapke.fgsveevleaalehekkvteslrelielaeeeg 110
                                    ++ ++++    h  +++  + + G + + t+   ++ e+ +p +  ++++ +l++a+e+  +v +++++++el+++++
  gi|116753437|ref|YP_842555.1|  30 LISKKIDSTFAHTLRILSQLEQAGLVYTRTEGrvKYVELTGPGRrAAEALRMLRDAIEDAAEVKKRIKRIHELVDAAE 107
                                    55666666667777777777777766666544226666888888556**************************99875 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.2e-05     0.081      11      74 ..      17      84 ..      13      87 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.2e-05
                         HTH_45 11 ILeaisegeakkTkimykanLsykllnkYLdmLvekgli...kkskekYv.lTekGlelleklkelee 74
                                   +L +++ ++a  + i +k + ++  + + L++L + gl+   ++   kYv lT  G++  e l+ l++
  gi|116753437|ref|YP_842555.1| 17 LLAILELDHAYASLISKKIDSTFAHTLRILSQLEQAGLVytrTEGRVKYVeLTGPGRRAAEALRMLRD 84
                                   567777899999***************************9887778888559******9999998877 PP

>> FtsK_gamma  Ftsk gamma domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   6.1e-05      0.16       9      52 ..      15      58 ..      13      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.1e-05
                     FtsK_gamma  9 eavelvveegkaStSllQRrlriGYnRAarlidqLeeeGiVgpa 52
                                   +a+  ++e ++a +Sl+ ++    ++   r++ qLe++G+V   
  gi|116753437|ref|YP_842555.1| 15 QALLAILELDHAYASLISKKIDSTFAHTLRILSQLEQAGLVYTR 58
                                   5667788999999***************************9765 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   5.1e-05      0.13      32      74 ..      38      80 ..      25     110 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.1e-05
                        DUF4364 32 nYfdlqqalseLvesglieeeekenktlykiTekGketlelfe 74
                                   ++ +   +ls+L+++gl+ ++++   ++ ++T  G++++e + 
  gi|116753437|ref|YP_842555.1| 38 TFAHTLRILSQLEQAGLVYTRTEGRVKYVELTGPGRRAAEALR 80
                                   66777889***************************98776543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       838  (0.0467399); expected 358.6 (0.02)
Passed bias filter:                      598  (0.0333538); 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: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1097.88
//
Query:       gi|116753438|ref|YP_842556.1|  [L=307]
Description: hypothetical protein Mthe_0116 [Methanosaeta thermophila PT]
Scores for complete sequence (score 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   13.5   0.0       0.15   11.4   0.0    1.9  1  DUF2092   Predicted periplasmic protein (DUF2092)


Domain annotation for each model (and alignments):
>> DUF2092  Predicted periplasmic protein (DUF2092)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   8.5e-06      0.15     126     166 ..     163     240 ..     150     251 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.5e-06
                        DUF2092 126 sakyvgtskvngqecehl.....................................afrnkdvdwqlWIsqgdkpLprk 166
                                    + +++g+++v+g++c +l                                     + rn+ +dw  WIs++dk+L+++
  gi|116753438|ref|YP_842556.1| 163 TLDVIGSETVDGTDCWKLkvspenttihaavialevsdvlglpaqillamfntteLERNSSIDWTAWISKEDKRLVKR 240
                                    6678888888888888888888888888888888888888888888899888888889*****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2182.09
//
Query:       gi|116753439|ref|YP_842557.1|  [L=52]
Description: rubredoxin-type Fe(Cys)4 protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-26   90.7   6.2    4.6e-26   90.6   6.2    1.0  1  Rubredoxin       Rubredoxin
     0.0017   18.4   3.0      0.029   14.5   3.0    2.1  1  Zn-ribbon_8      Zinc ribbon domain
     0.0035   17.4   0.2     0.0045   17.1   0.2    1.2  1  PHD_4            PHD-finger
     0.0044   16.5   1.9        1.1    8.8   0.0    2.3  2  TF_Zn_Ribbon     TFIIB zinc-binding
  ------ inclusion threshold ------
      0.011   15.5   1.1       0.82    9.5   0.0    2.2  2  A2L_zn_ribbon    A2L zinc ribbon domain
      0.013   14.8   1.7       0.12   11.7   0.2    2.1  2  zf-RanBP         Zn-finger in Ran binding protein and others
      0.018   15.0   1.0       0.43   10.6   0.1    2.1  2  Prok-RING_1      Prokaryotic RING finger family 1
      0.025   14.5   1.9        2.4    8.1   0.1    2.1  2  Zn_ribbon_SprT   SprT-like zinc ribbon domain
      0.031   14.0   0.7       0.65    9.8   0.0    2.1  2  zinc_ribbon_10   Predicted integral membrane zinc-ribbon meta
      0.053   13.4   1.0       0.68    9.9   1.0    2.0  1  HalOD2           Halobacterial output domain 2
      0.054   13.1   0.6      0.054   13.1   0.6    1.8  2  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
      0.057   13.3   0.6       0.65   10.0   0.6    2.0  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.059   13.0   1.8        0.8    9.3   0.1    2.1  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
      0.078   12.9   2.7        3.8    7.5   0.1    2.3  2  Nudix_N_2        Nudix N-terminal
       0.11   12.5   0.1       0.13   12.3   0.1    1.1  1  HypA             Hydrogenase/urease nickel incorporation, met
       0.12   12.4   4.3        3.9    7.6   0.7    2.3  2  UPF0547          Uncharacterised protein family UPF0547
       0.15   11.5   5.0       0.42   10.1   0.3    2.3  2  zf-ribbon_3      zinc-ribbon domain
       0.16   12.0   3.6        2.9    7.9   3.7    2.1  1  ADK_lid          Adenylate kinase, active site lid
       0.17   12.4   2.5        3.5    8.3   0.5    2.2  2  zf-C2H2          Zinc finger, C2H2 type
       0.19   12.2   1.8         15    6.2   0.1    2.2  2  zf-H2C2_2        Zinc-finger double domain
       0.21   11.4   4.7        2.4    8.0   0.7    2.5  2  zinc_ribbon_2    zinc-ribbon domain
       0.24   12.3   1.7        7.5    7.7   0.3    2.2  2  zf-C2H2_4        C2H2-type zinc finger
       0.32   11.1   2.1        7.5    6.7   0.6    2.1  2  zf-C2H2_6        C2H2-type zinc finger
       0.69    9.7   7.0          2    8.2   1.1    2.1  2  Rubredoxin_2     Rubredoxin metal binding domain
        2.9    7.8   5.3        1.3    8.9   1.1    2.2  2  VATC             Vms1-associating treble clef domain


Domain annotation for each model (and alignments):
>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.6   6.2   6.5e-29   4.6e-26       1      47 []       3      49 ..       3      49 .. 0.99

  Alignments for each domain:
  == domain 1  score: 90.6 bits;  conditional E-value: 6.5e-29
                                   EEEETTT-BEEETTTBBGGGTB-TT--GGGS-TT-BBTTTB-BGGGE CS
                     Rubredoxin  1 kyeCkvCgyvYdpakGdpdegiapgTkFedlPddWvCPdCgvekeqF 47
                                   +y+C++Cgy+Ydp+kGdpd+g++pgT+Fe+lPddWvCP+Cg+ k++F
  gi|116753439|ref|YP_842557.1|  3 RYKCTICGYIYDPEKGDPDNGVEPGTPFEKLPDDWVCPECGAAKDAF 49
                                   7********************************************99 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   3.0     4e-05     0.029       6      34 ..       4      44 ..       3      51 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4e-05
                    Zn-ribbon_8  6 YrCeeCghefe..............vlqsisdaplta.CPeCgs 34
                                   Y+C+ Cg  ++              ++ +     +   CPeCg+
  gi|116753439|ref|YP_842557.1|  4 YKCTICGYIYDpekgdpdngvepgtPFEKLP---DDWvCPECGA 44
                                   9**********77777777776444444433...5555*****8 PP

>> PHD_4  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.2   6.2e-06    0.0045      32      67 ..       5      42 ..       1      43 [. 0.86

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.2e-06
                          PHD_4 32 eCsvCyeivHpeClkek..egegvvnedlpnsWeCpkC 67
                                    C++C  i  pe  +     ++g+  e lp +W Cp+C
  gi|116753439|ref|YP_842557.1|  5 KCTICGYIYDPEKGDPDngVEPGTPFEKLPDDWVCPEC 42
                                   7**********98877644557899************* PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.4    0.0042         3       1      19 [.       4      19 ..       4      25 .. 0.86
   2 !    8.8   0.0    0.0015       1.1       2       9 ..      38      45 ..      36      51 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0042
                                   EEETTTTCEECHEETSTTC CS
                   TF_Zn_Ribbon  1 ykCPnCgstnlveDperge 19
                                   ykC +Cg   +++Dpe g+
  gi|116753439|ref|YP_842557.1|  4 YKCTICG---YIYDPEKGD 19
                                   7999999...489999886 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0015
                                   EETTTTCE CS
                   TF_Zn_Ribbon  2 kCPnCgst 9 
                                   +CP+Cg  
  gi|116753439|ref|YP_842557.1| 38 VCPECGAA 45
                                   68888864 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 ?    4.8   0.4     0.032        23       1      10 [.       1      10 [.       1      13 [. 0.78
   2 ?    9.5   0.0    0.0011      0.82      20      29 ..      35      44 ..      34      46 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.032
                  A2L_zn_ribbon  1 snlkvCsvCg 10
                                   ++ ++C+ Cg
  gi|116753439|ref|YP_842557.1|  1 MDRYKCTICG 10
                                   6778898887 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0011
                  A2L_zn_ribbon 20 gylvCieCga 29
                                   ++ vC+eCga
  gi|116753439|ref|YP_842557.1| 35 DDWVCPECGA 44
                                   5779*****8 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 ?    2.8   0.1       0.1        75       6      12 ..       5      11 ..       3      12 .. 0.72
   2 ?   11.7   0.2   0.00017      0.12       3      11 ..      35      43 ..      33      45 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.1
                                   E-SSS-- CS
                       zf-RanBP  6 dCskClv 12
                                   +C+ C++
  gi|116753439|ref|YP_842557.1|  5 KCTICGY 11
                                   5777775 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00017
                                   SSEE-SSS- CS
                       zf-RanBP  3 gdWdCskCl 11
                                   +dW C+ C+
  gi|116753439|ref|YP_842557.1| 35 DDWVCPECG 43
                                   89******8 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 ?    3.8   0.1     0.076        54       5      12 ..       4      11 ..       1      21 [. 0.76
   2 ?   10.6   0.1   0.00059      0.43      13      29 ..      29      45 ..      24      48 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.076
                    Prok-RING_1  5 kkCpvCgk 12
                                    kC++Cg 
  gi|116753439|ref|YP_842557.1|  4 YKCTICGY 11
                                   68999986 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00059
                    Prok-RING_1 13 elkeedDiVvCpeCgtp 29
                                   ++++  D  vCpeCg+ 
  gi|116753439|ref|YP_842557.1| 29 PFEKLPDDWVCPECGAA 45
                                   5666666679*****96 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.2     0.013       9.2       4      14 ..       3      11 ..       2      21 .. 0.80
   2 ?    8.1   0.1    0.0034       2.4       4      11 ..      36      43 ..      34      46 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.013
                 Zn_ribbon_SprT  4 vYrCtgCgrey 14
                                    Y+Ct Cg  y
  gi|116753439|ref|YP_842557.1|  3 RYKCTICG--Y 11
                                   59999999..3 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0034
                 Zn_ribbon_SprT  4 vYrCtgCg 11
                                    ++C+ Cg
  gi|116753439|ref|YP_842557.1| 36 DWVCPECG 43
                                   5******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 ?    3.0   0.5      0.12        86      44      52 ..       3      11 ..       1      13 [. 0.86
   2 ?    9.8   0.0   0.00091      0.65      32      52 ..      22      44 ..      19      46 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.12
                 zinc_ribbon_10 44 kyrCpkCga 52
                                   +y+C  Cg 
  gi|116753439|ref|YP_842557.1|  3 RYKCTICGY 11
                                   7******97 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00091
                 zinc_ribbon_10 32 nGlapkeeleev..kyrCpkCga 52
                                   nG+ p   +e++   ++Cp+Cga
  gi|116753439|ref|YP_842557.1| 22 NGVEPGTPFEKLpdDWVCPECGA 44
                                   666664444555448******98 PP

>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.0   0.00095      0.68       4      42 ..       5      47 ..       3      50 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00095
                         HalOD2  4 kCseCsldWttrhGdgl.....GeGyrqLGayvWkCtrCGevqa 42
                                   kC+ C++ +   +Gd +     G  +++L  + W C +CG+ + 
  gi|116753439|ref|YP_842557.1|  5 KCTICGYIYDPEKGDPDngvepGTPFEKLP-DDWVCPECGAAKD 47
                                   788888888888877654333366688885.66*******9765 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.6   7.5e-05     0.054       5      15 ..       2      12 ..       1      14 [. 0.86
   2 ?   -1.3   0.1       2.4   1.7e+03       9      13 ..      39      43 ..      36      45 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.5e-05
                                   -EEE-TTT--E CS
                Desulfoferrod_N  5 evYkCevCGni 15
                                   + YkC++CG i
  gi|116753439|ref|YP_842557.1|  2 DRYKCTICGYI 12
                                   78*******87 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.4
                                   -TTT- CS
                Desulfoferrod_N  9 CevCG 13
                                   C  CG
  gi|116753439|ref|YP_842557.1| 39 CPECG 43
                                   66677 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.6    0.0009      0.65      30      58 ..       5      48 ..       4      48 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0009
                 OrfB_Zn_ribbon 30 tCseCgsknke...............alsgrtfkCpnCgfeadr 58
                                   +C  Cg++ ++               ++ ++ ++Cp+Cg+  d+
  gi|116753439|ref|YP_842557.1|  5 KCTICGYIYDPekgdpdngvepgtpfEKLPDDWVCPECGAAKDA 48
                                   57778877777777777777777777778899*******98776 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.2     0.069        49       1       9 [.       2      10 ..       2      17 .. 0.86
   2 ?    9.3   0.1    0.0011       0.8       1      10 [.      35      44 ..      35      51 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.069
                         zf_UBZ  1 dtylCerCg 9 
                                   d y C  Cg
  gi|116753439|ref|YP_842557.1|  2 DRYKCTICG 10
                                   679*****9 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0011
                         zf_UBZ  1 dtylCerCgk 10
                                   d ++C++Cg+
  gi|116753439|ref|YP_842557.1| 35 DDWVCPECGA 44
                                   689*****97 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   0.1    0.0053       3.8      22      31 ..       3      12 ..       1      13 [. 0.91
   2 ?    5.6   0.3     0.021        15      24      29 ..      38      43 ..      37      46 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0053
                                   EEEETTTTEE CS
                      Nudix_N_2 22 RlvCpaCgti 31
                                   R+ C+ Cg+i
  gi|116753439|ref|YP_842557.1|  3 RYKCTICGYI 12
                                   999******9 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.021
                                   EETTTT CS
                      Nudix_N_2 24 vCpaCg 29
                                   vCp Cg
  gi|116753439|ref|YP_842557.1| 38 VCPECG 43
                                   666666 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 ?   12.3   0.1   0.00018      0.13      71      96 ..       4      46 ..       2      51 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00018
                                   EEETTTS-EEECHH.H.HH...............S-TTTSSS- CS
                           HypA 71 vrCreCgkefelee.k.al...............rCpkCgsad 96
                                   ++C+ Cg+ ++ e+ + +                 Cp+Cg+a+
  gi|116753439|ref|YP_842557.1|  4 YKCTICGYIYDPEKgDpDNgvepgtpfeklpddwVCPECGAAK 46
                                   79*********886444337899*****************986 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.2     0.015        11      16      25 ..       5      14 ..       3      15 .. 0.85
   2 ?    7.6   0.7    0.0054       3.9       2       7 ..      38      43 ..      38      45 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.015
                        UPF0547 16 fCphCGyvFq 25
                                   +C  CGy+++
  gi|116753439|ref|YP_842557.1|  5 KCTICGYIYD 14
                                   7999***986 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0054
                        UPF0547  2 vCPeCe 7 
                                   vCPeC 
  gi|116753439|ref|YP_842557.1| 38 VCPECG 43
                                   578876 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.5     0.083        59      18      24 ..       5      11 ..       3      11 .. 0.85
   2 ?   10.1   0.3   0.00059      0.42      15      24 ..      35      44 ..      34      47 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.083
                    zf-ribbon_3 18 vCpyCGt 24
                                   +C+ CG+
  gi|116753439|ref|YP_842557.1|  5 KCTICGY 11
                                   6999996 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00059
                    zf-ribbon_3 15 ddnvCpyCGt 24
                                   dd vCp CG+
  gi|116753439|ref|YP_842557.1| 35 DDWVCPECGA 44
                                   6666777774 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 ?    7.9   3.7    0.0041       2.9       1      28 [.       3      43 ..       3      44 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0041
                                   EEE-TTT--EEETT.............T.B--SSTTB-TTT- CS
                        ADK_lid  1 RrvCpkCGrsYhvv.............f.npPkveglCDkCG 28
                                   R  C  CG +Y  +             f + P  + +C +CG
  gi|116753439|ref|YP_842557.1|  3 RYKCTICGYIYDPEkgdpdngvepgtpFeKLP-DDWVCPECG 43
                                   67788899999644444444445555543444.888999988 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.5    0.0048       3.5       1      10 [.       4      13 ..       4      16 .. 0.88
   2 ?    4.2   0.1     0.093        67       2       7 ..      38      43 ..      37      48 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0048
                                   EEETTTTEEE CS
                        zf-C2H2  1 ykCpdCgksF 10
                                   ykC++Cg+ +
  gi|116753439|ref|YP_842557.1|  4 YKCTICGYIY 13
                                   9******876 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.093
                                   EETTTT CS
                        zf-C2H2  2 kCpdCg 7 
                                   +Cp+Cg
  gi|116753439|ref|YP_842557.1| 38 VCPECG 43
                                   7****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 ?    6.2   0.1     0.021        15      14      22 ..       3      11 ..       1      14 [. 0.85
   2 ?    6.0   0.1     0.024        17      15      21 ..      37      43 ..      26      51 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.021
                      zf-H2C2_2 14 pyeCplCdk 22
                                   +y+C  C++
  gi|116753439|ref|YP_842557.1|  3 RYKCTICGY 11
                                   6******99 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.024
                      zf-H2C2_2 15 yeCplCd 21
                                   + Cp+C+
  gi|116753439|ref|YP_842557.1| 37 WVCPECG 43
                                   69****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 ?    4.6   0.2      0.04        29       1       7 [.       5      11 ..       4      16 .. 0.73
   2 ?    8.0   0.7    0.0034       2.4       2       7 ..      39      44 ..      38      47 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.04
                  zinc_ribbon_2  1 fCpnCGa 7 
                                   +C+ CG+
  gi|116753439|ref|YP_842557.1|  5 KCTICGY 11
                                   6888886 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0034
                  zinc_ribbon_2  2 CpnCGa 7 
                                   Cp+CGa
  gi|116753439|ref|YP_842557.1| 39 CPECGA 44
                                   666665 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.3      0.01       7.5       1      10 [.       4      13 ..       4      17 .. 0.81
   2 ?    4.2   0.1      0.14     1e+02       2       8 ..      38      44 ..      37      48 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.01
                      zf-C2H2_4  1 fkCpiCgksF 10
                                   +kC+iCg  +
  gi|116753439|ref|YP_842557.1|  4 YKCTICGYIY 13
                                   8*****8766 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.14
                      zf-C2H2_4  2 kCpiCgk 8 
                                    Cp Cg+
  gi|116753439|ref|YP_842557.1| 38 VCPECGA 44
                                   7****85 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 ?    6.7   0.6      0.01       7.5       1       8 [.       3      10 ..       3      11 .. 0.90
   2 ?    4.1   0.0     0.068        49       3       9 ..      38      44 ..      37      45 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.01
                      zf-C2H2_6  1 vheCsvCs 8 
                                   +++C++C+
  gi|116753439|ref|YP_842557.1|  3 RYKCTICG 10
                                   59*****7 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.068
                      zf-C2H2_6  3 eCsvCsk 9 
                                   +C++C++
  gi|116753439|ref|YP_842557.1| 38 VCPECGA 44
                                   6****97 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.5     0.029        21       1       9 [.       4      12 ..       4      14 .. 0.88
   2 ?    8.2   1.1    0.0028         2      15      22 ..      37      44 ..      37      44 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.029
                   Rubredoxin_2  1 YvCsqCGfe 9 
                                   Y C  CG+ 
  gi|116753439|ref|YP_842557.1|  4 YKCTICGYI 12
                                   99*****96 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0028
                   Rubredoxin_2 15 GrCpsCgs 22
                                   + Cp+Cg+
  gi|116753439|ref|YP_842557.1| 37 WVCPECGA 44
                                   99999996 PP

>> VATC  Vms1-associating treble clef domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   1.1    0.0019       1.3       4      22 ..       4      33 ..       1      36 [. 0.87
   2 ?    0.5   0.2      0.77   5.5e+02       4      12 ..      37      45 ..      34      51 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0019
                           VATC  4 lrCsiCgesleg...........kvyFekf 22
                                    +C iCg  + +            ++Fek+
  gi|116753439|ref|YP_842557.1|  4 YKCTICGYIYDPekgdpdngvepGTPFEKL 33
                                   68********998999999988888***98 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.77
                           VATC  4 lrCsiCges 12
                                   + C  Cg++
  gi|116753439|ref|YP_842557.1| 37 WVCPECGAA 45
                                   789999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); 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: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.90
# Mc/sec: 173.83
//
Query:       gi|116753440|ref|YP_842558.1|  [L=172]
Description: Ferritin, Dps family protein [Methanosaeta thermophila PT]
Scores for complete 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-44  150.6   0.3    2.9e-44  150.4   0.3    1.0  1  Ferritin         Ferritin-like domain
  ------ inclusion threshold ------
      0.074   12.6   0.1       0.13   11.9   0.1    1.3  1  Acid_phosphat_B  HAD superfamily, subfamily IIIB (Acid phosph
      0.084   13.3   0.1       0.12   12.8   0.1    1.4  1  Rubrerythrin     Rubrerythrin


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 !  150.4   0.3   4.9e-48   2.9e-44       2     141 ..       8     143 ..       7     144 .. 0.98

  Alignments for each domain:
  == domain 1  score: 150.4 bits;  conditional E-value: 4.9e-48
                                    HHHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHHC-SSSS.CSS CS
                       Ferritin   2 kaLneqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalGgtpvltraeleeieapke.fgs 80 
                                    +aLn+q++ el+++y yl+m+ y++++gl+g+a +++ qa+ee+ ha+k++++i+ +Gg     r++l +ie+p+  ++s
  gi|116753440|ref|YP_842558.1|   8 DALNKQVNWELYSSYFYLSMSGYFESTGLKGFASWMRAQAQEELFHAMKFYDYIISRGG-----RVKLMRIEEPPGeWES 82 
                                    89*********************************************************.....******9988888*** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Ferritin  81 veevleaalehekkvteslrelielaeeegDpatadfledfleeqeeheweleallekler 141
                                    +++v+e++  he+kvt  ++ l +la e++D+ t+++l++f++eq+e+e++ e++++kl++
  gi|116753440|ref|YP_842558.1|  83 PLNVFEDVHVHEQKVTGLIHALLDLAIEVKDYPTQSMLQWFVNEQVEEEANAEEIVQKLRL 143
                                    **********************************************************997 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 ?   11.9   0.1   2.1e-05      0.13     100     135 ..      33      68 ..      14      71 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.1e-05
                                    HH-TTHHHHHHHTTGGCCECCHHHHHHHHHHTTEEE CS
                Acid_phosphat_B 100 kfdpekfdewvnkgeakaipgalelikkvverGvki 135
                                    ++  + f  w++++ ++ + +a+++++++ +rG+ +
  gi|116753440|ref|YP_842558.1|  33 STGLKGFASWMRAQAQEELFHAMKFYDYIISRGGRV 68 
                                    333478***************************987 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1     2e-05      0.12       2      67 ..       9      75 ..       8     142 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2e-05
                                   HHHHHHHHHHHHHHHHHHHHHCHH.TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSB CS
                   Rubrerythrin  2 iLekAiagEssarrlYkelaekak.egypqiaelFeelAeeEreHakilnklleklepelelevkek 67
                                    L+k +  E     +Y +++  ++  g++  a  +++ A+eE  Ha ++++ + ++ +  +l + e+
  gi|116753440|ref|YP_842558.1|  9 ALNKQVNWELYSSYFYLSMSGYFEsTGLKGFASWMRAQAQEELFHAMKFYDYIISRGGRVKLMRIEE 75
                                   57777778889999*************************************9999888888444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); 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: 00:00:00.42
# Mc/sec: 1219.03
//
Query:       gi|116753441|ref|YP_842559.1|  [L=248]
Description: hypothetical protein Mthe_0119 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.085   13.1   0.0       0.17   12.1   0.0    1.5  1  RNase_Zc3h12a_2  Zc3h12a-like Ribonuclease NYN domain


Domain annotation for each model (and alignments):
>> RNase_Zc3h12a_2  Zc3h12a-like Ribonuclease NYN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   9.3e-06      0.17      48      89 ..      98     141 ..      79     160 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.3e-06
                RNase_Zc3h12a_2  48 dlvafqklidldfi..kfiteaenfkwfnvvadladrigavfvs 89 
                                    d + f    dl+++   + t +++ kw+++++ +  rigav   
  gi|116753441|ref|YP_842559.1|  98 DYINFTSEQDLEYMpvSYQTGTYDQKWIDKLCVQNYRIGAVVTE 141
                                    778899999****955668999******************9754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); 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: 00:00:00.41
# Mc/sec: 1798.38
//
Query:       gi|116753442|ref|YP_842560.1|  [L=170]
Description: 30S ribosomal protein S15P [Methanosaeta thermophila PT]
Scores for complete 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   85.6   0.3    3.7e-24   84.5   0.3    1.6  1  Ribosomal_S13_N  Ribosomal S13/S15 N-terminal domain
    1.7e-09   37.7   0.5    5.5e-09   36.1   0.5    1.8  1  Ribosomal_S15    Ribosomal protein S15
  ------ inclusion threshold ------
       0.14   13.1   0.0       0.22   12.4   0.0    1.4  1  WRNPLPNID        Putative WW-binding domain and destruction b


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 !   84.5   0.3   6.1e-28   3.7e-24       1      60 []       1      60 [.       1      60 [. 1.00

  Alignments for each domain:
  == domain 1  score: 84.5 bits;  conditional E-value: 6.1e-28
                                   X--SSSSSS--------S-SS--TTS---HHHHHHHHHHHHHTT--HHHHHHHHHHCCT- CS
                Ribosomal_S13_N  1 MarmhsrgkGkSgSarPyrreapsWlklskeeveelivklakkGltpSqIGviLRDqyGv 60
                                   Marmhsr+kG+SgS  P+  + p+W+++skee+e++i+ l+++G++ ++IG++LRDqyGv
  gi|116753442|ref|YP_842560.1|  1 MARMHSRKKGSSGSRPPVVDKLPEWCDVSKEELEKTIMTLHERGMSNAMIGLTLRDQYGV 60
                                   ***********************************************************8 PP

>> Ribosomal_S15  Ribosomal protein S15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.5   9.2e-13   5.5e-09      17      80 ..      83     164 ..      69     165 .. 0.91

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 9.2e-13
                                    SHHHHHHHHHHHHHHHHHHHHC................TTT-HHHHHHHHHHHHHHHHHHHHHHHH-H..HHHHHHHHHC CS
                  Ribosomal_S15  17 spevqiallterInnltehlke................nkkDkhsrrgLlklvskRrkllkYLkrkdv..erYkkliekl 78 
                                    ++++++ +l++++ +l++hl +                + kD h++r+L++++sk+r+l++Y+k+  +  +++++  e++
  gi|116753442|ref|YP_842560.1|  83 EIPEDLSNLMRKALRLRRHLLRaqprgtvsdtsisrlpRTKDIHNKRALQLVESKIRRLVRYYKQVGRlpATWEYRPETA 162
                                    789999**************9999**********999999**************************9999*****99998 PP

                                    TS CS
                  Ribosomal_S15  79 gl 80 
                                    ++
  gi|116753442|ref|YP_842560.1| 163 EI 164
                                    87 PP

>> WRNPLPNID  Putative WW-binding domain and destruction box
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.8e-05      0.22       4      25 ..      72      93 ..      69     115 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.8e-05
                      WRNPLPNID  4 nSFlFWRnPLPeidleLeeLll 25
                                   +SFl  Rn LPei ++L  L+ 
  gi|116753442|ref|YP_842560.1| 72 SSFLRDRNALPEIPEDLSNLMR 93
                                   8*****************9994 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 1164.91
//
Query:       gi|116753443|ref|YP_842561.1|  [L=427]
Description: phosphoesterase domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-15   56.4   0.1    7.9e-15   55.5   0.1    1.5  1  DHHA1     DHHA1 domain
     0.0046   17.2   0.0     0.0082   16.4   0.0    1.4  1  DHH       DHH family


Domain annotation for each model (and alignments):
>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   0.1   8.8e-19   7.9e-15      45     138 .]     329     421 ..     295     421 .. 0.78

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 8.8e-19
                                    EECHCCHHH.HHHHHH.HHHHHTHGBTTCEEEEEEEECTEEEEEEEESSH....SS-HHHHHHHHHHHTTCCEEEETCEE CS
                          DHHA1  45 aevgeewda.galgia.adklksklkkpvivfvakeegdkvkvsarskkd....gvdagelakeaaaklgggGGGHdlAa 118
                                    ae     +  g+++++ + +l +  +kp iv+  k +g +v+vsar ++     g+d++ ++++aa+ +gg+GGGH  A+
  gi|116753443|ref|YP_842561.1| 329 AEN---LHGgGVIAGLgIRYLYT--DKPLIVLNNK-DG-TVRVSARGNRPlirrGLDLSIALRAAAESVGGKGGGHSIAS 401
                                    443...56557788884445555..4455555555.56.9********99****************************** PP

                                    EEEEEHCHHHHHHHHHHHHH CS
                          DHHA1 119 Gagipaekleealealeeai 138
                                    Ga+ip++  +++l +l+e+i
  gi|116753443|ref|YP_842561.1| 402 GASIPPGTEKQFLLKLNEII 421
                                    *****************987 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   9.1e-07    0.0082       2     100 ..      21     145 ..      20     147 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 9.1e-07
                                    EEEE-ECSSSHHHHHHHHHHHH.............................CECS--TCGGCGCCHHCCCSEEEEEEE-S CS
                                    xxxxxxxxxxxxxxxxxxxxxx.............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DHH   2 ilivghknpDtDsigSaialan.............................llvDhneksqavegeakeeaedviiiDHH 52 
                                    +++  + + D+D+i Sa ++ n                             + +D+++ + +v+      + +v ++DHH
  gi|116753443|ref|YP_842561.1|  21 VVV--VSHDDADGISSAGLICNalaragipfqarltqrltadtieglkppiVFCDMGSGQPDVIS---GIKGEVFVLDHH 95 
                                    455..8889*******999999888888888888888888888888888888********99998...788899****** PP

                                    ---S.......S---SS--EE..EE-SSS-HHHHHHHHHHHTT----HHHHHHHHHH CS
                                    xxxx.......xxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DHH  53 rlge.......efetlapilf..lnepvgstaeivaelleekkeeiskeiaellllg 100
                                    ++         +     p  f        s++++v+ ++++ +++  +++a+l l+g
  gi|116753443|ref|YP_842561.1|  96 KPVGslncislN-----PHNFgiDGAFEISASGVVYSVVRKMGDN--RDLAGLALVG 145
                                    *98788655441.....3333002223358999999999887776..7777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2833.49
//
Query:       gi|116753444|ref|YP_842562.1|  [L=72]
Description: hypothetical protein Mthe_0122 [Methanosaeta thermophila PT]
Scores for complete sequence (score 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   13.6   0.0      0.065   13.4   0.0    1.1  1  Pcc1      Transcription factor Pcc1


Domain annotation for each model (and alignments):
>> Pcc1  Transcription factor Pcc1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.6e-06     0.065      17      72 ..      16      66 ..       9      68 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.6e-06
                                   HHHHHHHHCHC-TTECEEEEEEETTEEEEEEEESSHHHHHHHHHHHHHHHHHHHHH CS
                           Pcc1 17 alrtLqvDkelsplavkrslslegnvLqveykAttnrmLRvavngfleslglvlet 72
                                   + ++L++D+ +s +     +s+++  L +e +A+       +v+ +l +++++ e 
  gi|116753444|ref|YP_842562.1| 16 ISKALEPDNLPSMN-----VSVQDDELIIELRAERIGTVLSTVDDLLMNIKVAEEA 66
                                   56788888766554.....678899***************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); 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: 0.32u 0.25s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 563.02
//
Query:       gi|116753445|ref|YP_842563.1|  [L=500]
Description: seryl-tRNA synthetase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-55  187.0   0.0    2.7e-55  186.6   0.0    1.2  1  tRNA_bind_4   tRNA-binding domain
    1.6e-09   38.0   0.0    2.6e-09   37.3   0.0    1.3  1  tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, 
  ------ inclusion threshold ------
      0.017   14.6   0.0      0.032   13.7   0.0    1.4  1  tRNA-synt_2d  tRNA synthetases class II core domain (F)


Domain annotation for each model (and alignments):
>> tRNA_bind_4  tRNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.6   0.0   4.5e-59   2.7e-55       1     160 [.       1     161 [.       1     162 [. 0.99

  Alignments for each domain:
  == domain 1  score: 186.6 bits;  conditional E-value: 4.5e-59
                                    EEEEEEEEEEESS-SCCCHHHHHHHHHHHCCTGGGTTSSTTT.S.SSEEEEEEE-SSEEEEEEEEESSS-HHHHHHHHHH CS
                    tRNA_bind_4   1 lkfelkgklklskdieeaeeeieefieeanktiLkkGvpegkeeegakitewkiegnelkleieSgryvRahdallrlkk 80 
                                    +kf+l+++lkls+d+++ae +++ef+e+++ ++LkkG+peg+   gak+  w+i+g++l+++ieS+ryvRahdallrl+k
  gi|116753445|ref|YP_842563.1|   1 MKFHLEVSLKLSGDAANAEGDLAEFFEKQAVDLLKKGAPEGM---GAKVAGWRITGDQLEIKIESDRYVRAHDALLRLRK 77 
                                    9****************************************9...*********************************** PP

                                    HHHHHCCCCCS--EEEEEEEEEEEEEE-SS--HH---TTECEEEEETTEEEEEEES--H......HHHHTTHHHHHHHHH CS
                    tRNA_bind_4  81 plaeklGkkyriGvRgikveeyeieiesekelkaekipeveeveveegkitlelkdvde......selkkrvvdRiiklv 154
                                    pla++lG+k+r+G+Rgi+v+++ei+ies++++ +++ip+v+e ++e+g +tl+l  v++      ++l++r++dRi++l+
  gi|116753445|ref|YP_842563.1|  78 PLANLLGRKHRLGIRGINVSRFEIQIESNRQI-THRIPYVRESRYEDGLLTLIL-GVEDpkrgwtWMLENRIPDRIVNLL 155
                                    *******************************9.9********************.****9999999************** PP

                                    HHHHCC CS
                    tRNA_bind_4 155 eekiek 160
                                    eek+++
  gi|116753445|ref|YP_842563.1| 156 EEKLQS 161
                                    ***986 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 !   37.3   0.0   4.3e-13   2.6e-09      19     176 ..     308     472 ..     299     475 .. 0.81

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 4.3e-13
                                    HHHHHHHHHHEEEBGGSSEEEEE.EEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGHHHHHHHHHHHHHHHHHHTT.S CS
                                    xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2b  19 etfvelirdevlrskrLPlklyq.iqtkyRdEksdsrGLlRvreFhqkdgyvfhaeaslddslrdlikaisriferlgle 97 
                                    +tf    +  +l + +LP+k+++  +t +R+E   ++G+ Rv eFh  + +  ++++++ ++ + l + +++ife+++ e
  gi|116753445|ref|YP_842563.1| 308 PTFWVFLQGATLPNDELPIKVFDrSGTSHRYESGGIHGIERVDEFHRIEIVWLGTKQQVMEEAERLKERYKHIFEEIL-E 386
                                    5555555555554445****997368*******99*****************************************96.3 PP

                                    C...........EEEEEEGTTSCBTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTSSEEEEEEEEEEE CS
                                    x...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2b  98 f...........raiielmsaksadykdkkefeavsesltkgieigtiqklgtrlserlgatvldennreksvimicaai 166
                                                 a ++ ++  +++++ + + ea+ + ++  ie    +  g+++++ +++++    ++ +s   +c ++
  gi|116753445|ref|YP_842563.1| 387 LrwrmawvtpwfMAQEGRTGLAEMEGAGTIDYEALLPYSGNWIEFQNLSVNGEKYPKGFSVKA----QSGESLWSGCSGV 462
                                    323444333333333333555569************************************999....77788889***** PP

                                    EHHHHHHHHH CS
                                    xxxxxxxxxx RF
                   tRNA-synt_2b 167 gveRllsail 176
                                    g+eR  s+ l
  gi|116753445|ref|YP_842563.1| 463 GLERWTSVFL 472
                                    ****988876 PP

>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.4e-06     0.032      93     166 ..     317     394 ..     312     475 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.4e-06
                                    HHHTTS-SSEEEEE.EEEEEBSST...-SSSB-SEEEEEEEEEEETT--HHHHHHHHHHHHHHHCTSTEEEEEEECEE CS
                   tRNA-synt_2d  93 rtlekkkppikiis.igrvfRrda...vDathlaeFhqveglvvdenvsladlkgvleellkklfgaevkvrfrpsyf 166
                                     tl + ++pik++   g  +R ++       +  eFh +e ++++++ ++ +    l+e +k++f++ +++r+r ++ 
  gi|116753445|ref|YP_842563.1| 317 ATLPNDELPIKVFDrSGTSHRYESggiHGIERVDEFHRIEIVWLGTKQQVMEEAERLKERYKHIFEEILELRWRMAWV 394
                                    5788899999999626889999996656778999***************************************98753 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (500 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 3552.77
//
Query:       gi|116753446|ref|YP_842564.1|  [L=208]
Description: hypothetical protein Mthe_0124 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-49  168.0   0.0    1.5e-49  167.8   0.0    1.0  1  AMMECR1   AMMECR1


Domain annotation for each model (and alignments):
>> AMMECR1  AMMECR1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.8   0.0   8.3e-54   1.5e-49       1     166 []      17     188 ..      17     188 .. 0.95

  Alignments for each domain:
  == domain 1  score: 167.8 bits;  conditional E-value: 8.3e-54
                                    HHHHHHHHHHHTTSS-S-H.H---HHHHSEEEEEEEEEEE..CCECCCECEEEEEEHHHHHHHHHHHHHHT-TTS----H CS
                        AMMECR1   1 lklareaieealkeekkle.eeakeelkekaglFVtlkekkgeLRGCiGtleperpLaeevaenAlaaAfeDpRFspvta 79 
                                    ++lar+a+++++++++ ++ ++ +  ++e++g+FVtl+ k+geLRGCiG+ ++  pL++++++ A++a+++DpRF++v++
  gi|116753446|ref|YP_842564.1|  17 VRLARDALTAYVHRKEIINpHDLPGVFNERRGVFVTLE-KDGELRGCIGYPRAVLPLGKAIVDSAINAGTRDPRFPRVRP 95 
                                    689*****99********9777777************9.77*************************************** PP

                                    HHHTTEEEEEEEE---EE-...-...GGG--TTT-EEEEEETTEEEEE-THHHHHTT--HHHHHHHHHHHHTS-TTCCCS CS
                        AMMECR1  80 eElpeleveVsvLtepepi...v...ledlevgkhGliiekgsrsatlLPqvaveqgwdkeeflasllrKaglrpdewkd 153
                                    eEl+e+++eV+vLtep+ +   +   +e++++g+hGli+++g  s++lLPqva+e+g d  +fl +++ Kagl+ d+w d
  gi|116753446|ref|YP_842564.1|  96 EELDEITIEVTVLTEPQVMdgdKktlPERVQIGRHGLIVTRGMCSGLLLPQVAPEYGFDSVDFLCQTCLKAGLPVDAWLD 175
                                    *******************6551567899*************************************************9* PP

                                    TTSEEEEE-EEEE CS
                        AMMECR1 154 seikltryevekf 166
                                    +++ ++ +e+++f
  gi|116753446|ref|YP_842564.1| 176 DDTVIECFEAQIF 188
                                    **********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1480.18
//
Query:       gi|116753447|ref|YP_842565.1|  [L=252]
Description: hypothetical protein Mthe_0125 [Methanosaeta thermophila PT]
Scores for complete 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  155.4  13.2    2.1e-45  154.8  13.2    1.3  1  DUF1614   Protein of unknown function (DUF1614)
  ------ inclusion threshold ------
       0.53   10.8   2.9       0.42   11.1   0.3    2.1  2  DUF4231   Protein of unknown function (DUF4231)


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 !  154.8  13.2   2.3e-49   2.1e-45       1     170 []      53     231 ..      53     231 .. 0.89

  Alignments for each domain:
  == domain 1  score: 154.8 bits;  conditional E-value: 2.3e-49
                        DUF1614   1 llgslinipvaelkske.elvevkvlgisykvpvleeeekktvvavNvGGaviPlllslylllrlavsllaallavliva 79 
                                    ++gs+i+ip+++   ++ ++  v ++g +++vp ++   + + + vNvGG+++P+l+s+ ll r+++ + +all+ ++va
  gi|116753447|ref|YP_842565.1|  53 IIGSMIDIPLHSGVITTyPAFMVDLMG-TMDVP-VSF--HPVRLLVNVGGCIVPVLVSIDLLRRHRAPVSTALLGAVVVA 128
                                    69***********99774555577666.46777.333..4599***********************99************ PP

                        DUF1614  80 avvyllarpvpgvGivvpllipplvaalaalllaeeea..aavaYisgvlGtLiGadllnl...kkieklgap....... 147
                                    +++y++a+pvp+vGi++p++ipp+ aal+a++l + ++  +a+aYisg++GtL+Gad++nl   + + +l+ p       
  gi|116753447|ref|YP_842565.1| 129 ILTYTMAEPVPNVGITLPVYIPPVSAALVAVVLCRGYRtaPAIAYISGSIGTLLGADVMNLltpGVLPALAPPsayprpl 208
                                    ******************************8887777778*********************9887777777668889999 PP

                        DUF1614 148 vvsIGGaGtFdGifltgilavll 170
                                     +sIGGaG+FdGifltg++avll
  gi|116753447|ref|YP_842565.1| 209 ALSIGGAGIFDGIFLTGVMAVLL 231
                                    *********************98 PP

>> DUF4231  Protein of unknown function (DUF4231)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.3   4.7e-05      0.42      17      59 ..      87     128 ..      85     137 .. 0.84
   2 ?   -3.1   0.1       1.2   1.1e+04      54      63 ..     225     234 ..     218     240 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.7e-05
                        DUF4231  17 frllrlitivlgallpilvssklgagvsvlkiltallsalvai 59 
                                    f+ +rl+  v+g ++p+lvs ++    + ++++tall+a+v+ 
  gi|116753447|ref|YP_842565.1|  87 FHPVRLLVNVGGCIVPVLVS-IDLLRRHRAPVSTALLGAVVVA 128
                                    566899999***********.899999**********998764 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.2
                        DUF4231  54 salvailaal 63 
                                    ++++++la+l
  gi|116753447|ref|YP_842565.1| 225 GVMAVLLASL 234
                                    3333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       848  (0.0472977); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); 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):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1852.39
//
Query:       gi|116753448|ref|YP_842566.1|  [L=177]
Description: hypothetical protein Mthe_0126 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-47  160.3   0.0    2.8e-47  160.1   0.0    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 !  160.1   0.0   1.5e-51   2.8e-47       2     154 ..      11     163 ..      10     164 .. 0.98

  Alignments for each domain:
  == domain 1  score: 160.1 bits;  conditional E-value: 1.5e-51
                         DUF116   2 llkllgrllgldkdklkrvfievnnklvrkkfkkvppekrllllPhClraadCpaklteeglnCkrCgkCkigelkklae 81 
                                    ++k+++ l + d++ +++v i+++n ++r kf  +p+ +r++++P+Clr+ +Cpaklt+eg++C  Cg+C ige+kk+ae
  gi|116753448|ref|YP_842566.1|  11 FVKAIFWLARADDKIVDDVGISLMNYINRGKFYATPVGDRFVFMPQCLRSVECPAKLTPEGIKCVGCGRCGIGEAKKIAE 90 
                                    578999999*********************************************************************** PP

                         DUF116  82 klgykvyivtggtlarkiikekkpkaiigvaCerdltegiqdlkklpvigqlvllekggCinTkvdveeleel 154
                                    + gy++++v+g++++++ii++++pk+i+gv Ce++++eg+  ++++++++++v+l++ gC++T++++e+l+++
  gi|116753448|ref|YP_842566.1|  91 SRGYRFFVVPGSSFIKRIIQRYHPKGIVGVGCEMEIKEGLILCHSHGIPAIGVPLSTAGCVSTTLEWERLYDV 163
                                    **********************************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); 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: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 1274.55
//
Query:       gi|116753449|ref|YP_842567.1|  [L=374]
Description: hypothetical protein Mthe_0127 [Methanosaeta thermophila PT]
Scores for complete 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-126  420.9   0.6   5.1e-126  420.6   0.6    1.0  1  DUF373           Domain of unknown function (DUF373)
  ------ inclusion threshold ------
        0.1   11.1   0.1        0.2   10.1   0.0    1.5  2  Aldedh           Aldehyde dehydrogenase family
       0.19   12.0   0.1       0.35   11.1   0.1    1.3  1  MutS_II          MutS domain II


Domain annotation for each model (and alignments):
>> DUF373  Domain of unknown function (DUF373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  420.6   0.6  8.6e-130  5.1e-126       2     334 ..       3     345 ..       2     346 .. 0.97

  Alignments for each domain:
  == domain 1  score: 420.6 bits;  conditional E-value: 8.6e-130
                         DUF373   2 tLvlcvDrDdDlgrkagvktPvvGreavleaavklaladPeDSDvNalfgaikvydeLkaegedvevavvtGdekvgvea 81 
                                    +Lvlc+DrDdDlgrkag+k+PvvGre++l+aa +l+ladPe+SD+N++fg++k+ydeL+a +++ve+a++tGdekvg++a
  gi|116753449|ref|YP_842567.1|   3 VLVLCIDRDDDLGRKAGIKSPVVGREENLNAALTLGLADPEESDTNTIFGGLKIYDELAA-ERSVEIATITGDEKVGLSA 81 
                                    7**********************************************************5.789**************** PP

                         DUF373  82 drkiaeqldevlskleadsaivVsDGaeDesvlpiiqsrvkvdsvkrVvVkqsrniEstyyllkkalkdpelrktiLvpl 161
                                    drk+aeql++++++l+++s+ivVsDGaeDe++lpiiqsr+kvd+v+r++Vkq+++iEstyyllk++++dp++++ti++p+
  gi|116753449|ref|YP_842567.1|  82 DRKLAEQLEQLIERLDPKSVIVVSDGAEDEAILPIIQSRIKVDGVRRILVKQNPSIESTYYLLKQVFTDPKISHTIFIPP 161
                                    ******************************************************************************** PP

                         DUF373 162 GlllliyalllllglpelalaiillllGlylllrGfgldelleelleklkesleegritfvtyvvallllligiisgyis 241
                                    Gl+ll++++++ll++p+ a+++i++ +Glyll+rG+gld+ l+e+ ++l+ sl++g+i+fvty++a +l++i++i+g+++
  gi|116753449|ref|YP_842567.1| 162 GLALLMFSIFYLLNYPNGAIIAITGSVGLYLLFRGLGLDDFLDETKKTLRGSLYAGKISFVTYILAGMLIIIATIQGIAN 241
                                    ******************************************************************************** PP

                         DUF373 242 lesvssasvssglltlilafiygavewlalailtaslgkiideylkreekdiarllllpflvlaiglvlygasaylls.. 319
                                    ++ ++++++++g+ltl++ fi+++v+w+++a+++a +gk+id+ l++   +  r++++pf+++a+gl+++gas  +l+  
  gi|116753449|ref|YP_842567.1| 242 VWYSYKGPIWYGYLTLLMLFINASVWWYVAAGICANVGKLIDMHLEG--IKDPRTYSYPFFLFATGLIFWGASIVILAnf 319
                                    *********************************************43..45558999*******************9999 PP

                         DUF373 320 ...........lsilalslvvgivva 334
                                               ++++a+  ++++++a
  gi|116753449|ref|YP_842567.1| 320 tqdfsmsplssIQYFAVCAMGAMATA 345
                                    99999999888888888888887765 PP

>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   3.3e-05       0.2     187     262 ..      48     121 ..      40     134 .. 0.88
   2 ?   -4.1   0.0      0.67     4e+03     307     338 ..     338     369 ..     337     372 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 3.3e-05
                                    EE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTTSEEEEEE---EEEEE-TTSHHHHHHHHHHHHHH CS
                         Aldedh 187 nvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknlkrvtlElGGknplivledaDldkaveaivkgaf 262
                                    n + g g ++ ++l+++++v+  ++tG  +vg    ++ a++l +++  l  k+ ++v + a+ d+a+  i+++ +
  gi|116753449|ref|YP_842567.1|  48 NTIFG-GLKIYDELAAERSVEIATITGDEKVGLSADRKLAEQLEQLIERLDPKSVIVVSDGAE-DEAILPIIQSRI 121
                                    66677.889999**************************999*********************9.777776766665 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 0.67
                                    SB---SSHHHHHHHHHHHHHHHHTTSEEEE-T CS
                         Aldedh 307 dvGPliseaqlekvekyveeakeegaklllGg 338
                                     +G+++++    k+++y+++   +g +ll +g
  gi|116753449|ref|YP_842567.1| 338 AMGAMATALLGIKLKSYIAKRNGAGRELLKEG 369
                                    58999999999999999999999999998877 PP

>> MutS_II  MutS domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   5.9e-05      0.35      23      77 ..      71     126 ..      67     149 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.9e-05
                                    TTTEEEEEEEEE...-HHHHHHHHHH-ESEEEEESS-SCCCHHHHHHCHCTTT-EEEE CS
                        MutS_II  23 stgefvvsefed...feeleaeLsrlsPkElllpedlsestaeeessklrelrsrvgv 77 
                                     tg+  v  ++d    e le ++ rl Pk +++ +d  e++a   ++ +++++++ gv
  gi|116753449|ref|YP_842567.1|  71 ITGDEKVGLSADrklAEQLEQLIERLDPKSVIVVSDGAEDEA--ILPIIQSRIKVDGV 126
                                    5777778888899999*********************99955..66666666665444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       757  (0.0422221); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); 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):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 2650.78
//
Query:       gi|116753450|ref|YP_842568.1|  [L=269]
Description: hypothetical protein Mthe_0128 [Methanosaeta thermophila PT]
Scores for complete 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-36  125.3  13.3      4e-36  124.6  13.3    1.3  1  Vut_1     Putative vitamin uptake transporter


Domain annotation for each model (and alignments):
>> Vut_1  Putative vitamin uptake transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.6  13.3   2.2e-40     4e-36       4     150 .]      77     253 ..      76     253 .. 0.90

  Alignments for each domain:
  == domain 1  score: 124.6 bits;  conditional E-value: 2.2e-40
                          Vut_1   4 vllfpltflitdiisevyGkkaarkvvllgflanllalillllalllpa..........ea...............lesv 58 
                                     +++++tf+++d+i++  G +aa ++++l++l+nlla++++++++l+pa          +a               ++s+
  gi|116753450|ref|YP_842568.1|  77 GFIYSMTFTWRDLIHKQLGMRAAITTIWLSALINLLAALYFQIVVLMPAepdwaanggqAAwqflfgifetsggpwWQSI 156
                                    79**********************************************9888877777611555555566667777**** PP

                          Vut_1  59 fgltprivlasliaylvsqlldvyvfhrlkkltkgkk.lwlrnigStlvsqlvdtlifvtiaflg....eqlleiilsqy 133
                                    f+l++rivl+s+i++++++l+d+ ++h + +  ++++ +w+r+++S+++s  vd+++f +iaf+g    + +++++ +++
  gi|116753450|ref|YP_842568.1| 157 FSLQLRIVLGSVITMVIAELTDTEIYHLWVTGWGRNRpQWARVAISNAISIPVDSILFPLIAFTGiigfDAMIQMFQTNI 236
                                    *****************************655555566*************************99*************** PP

                          Vut_1 134 likllialldtplvylv 150
                                    ++k++++ll ++++ylv
  gi|116753450|ref|YP_842568.1| 237 AVKTIVTLLSFWTIYLV 253
                                    ***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); 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 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1926.59
//
Query:       gi|116753451|ref|YP_842569.1|  [L=404]
Description: queuine tRNA-ribosyltransferase [Methanosaeta thermophila PT]
Scores for complete 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-112  376.3   0.0   1.7e-111  372.8   0.0    1.9  1  TGT       Queuine tRNA-ribosyltransferase


Domain annotation for each model (and alignments):
>> TGT  Queuine tRNA-ribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  372.8   0.0  9.4e-116  1.7e-111       3     346 ..      18     398 ..      14     402 .. 0.95

  Alignments for each domain:
  == domain 1  score: 372.8 bits;  conditional E-value: 9.4e-116
                                    EEEEEEEETTEEEEESEEEEBETTSSBTTB-HHHHH.HTTES-EEEEHHHHHHTTTHHHHHHTTHHHHHHT--S-EEEE- CS
                            TGT   3 aRlGklelphgtietPafmpvgtqgtvkgltpdelkeelgaqiilsntyhlelrpgeelvakagglhkflgwdkpiltds 82 
                                    aRlG +++++g ietP f+pv+t ++v++l +d+l+ +lg+q+i++ntyhl+lr ge+l++++gglh+f+++d+pi tds
  gi|116753451|ref|YP_842569.1|  18 ARLGVIRTRRGIIETPQFIPVATVASVRALGSDDLR-ALGVQAIFANTYHLHLRTGEDLIRRMGGLHRFMSFDGPIFTDS 96 
                                    9**********************************5.99***************************************** PP

                                    SHHHHHHH......................E......EEESSEEEEE-TTTS-EEEE-HHHHHHHHHHHT-SEEE----- CS
                            TGT  83 ggfqvfsl......................k......kiteegvsfqsridGskvlltpeesieiqeklgsDiimalddv 134
                                    ggfq fsl                      +      +it+egv f+s +dG  ++++p++ ++iq++lgsDi+ma+d++
  gi|116753451|ref|YP_842569.1|  97 GGFQAFSLglgrehniskigsifphgrrsaErrenltRITDEGVAFKSLVDGGWHFIDPRSAMRIQSRLGSDIVMAFDEC 176
                                    *******999***99999998888877665156668789***************************************** PP

                                    --SS--HHHHHHHHHHHHHHHHHHHHHH...SEEEEEE--TT-HHHHHHHHHHHHHH--SEEEE-SSSSSSHHHHHHHHH CS
                            TGT 135 vpspaskkrveksverTlrwldrcleah...qalfgivqGglyedlreesaeelakrdfdgyaigGlsvgeekeellevv 211
                                    +++ +++++ ++++erT+rw+ ++l++h   qa+ gi+qGg +edlr+esa+ ++++ fdg+aigG s+g+ k+++ +v+
  gi|116753451|ref|YP_842569.1| 177 TSPLSDYDYTREAMERTHRWAVQSLRYHdrrQAIYGIIQGGWFEDLRRESADFIKSLPFDGIAIGG-SLGNCKADMHQVL 255
                                    ******************************999*********************************.9************ PP

                                    HHHGGGS-TTS-EEETTB-SHHHHHHHHHTT--EEEESHHHHHHHTTEEEE...TTE.......EEETTSGGGTT--SBS CS
                            TGT 212 eavtellpedkprylmGvgtPedlleavalGvDmfdcvyptrtarngralt...seg.......elnlknakyaedfspl 281
                                    e v+++l + +pr+l G+g   d+ e+v++G+D fdcv ptr+ar+g++++   s g       ++++k++ +++d +p+
  gi|116753451|ref|YP_842569.1| 256 EWVVPRL-DARPRHLLGIGEIPDIFECVERGIDTFDCVHPTRIARRGNLYIspaS-GgclenkfRISIKSSVFKDDKRPV 333
                                    *******.669****************************************5541.357777779*************** PP

                                    SSS--SHHHHH-BHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHH CS
                            TGT 282 degCsCytCknytraylhhllktkemlgaiLltiHNlhyylelfkriReaIkegtfeefveefar 346
                                    d+ C C+tC+ y+rayl+hl+ ++e+   + +t+HN++++l+l+++iR++I++g+f ++++++++
  gi|116753451|ref|YP_842569.1| 334 DPRCGCPTCRMYSRAYLRHLYISNELSYFRAATVHNVYFMLRLMESIRKSIRSGKFSALKRRWMK 398
                                    ***************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2821.77
//
Query:       gi|116753452|ref|YP_842570.1|  [L=224]
Description: NADPH-dependent FMN reductase [Methanosaeta thermophila PT]
Scores for complete 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-26   91.3   0.0    6.5e-26   90.9   0.0    1.1  1  FMN_red       NADPH-dependent FMN reductase
    5.6e-14   52.3   0.0    8.4e-14   51.7   0.0    1.3  1  Flavodoxin_2  Flavodoxin-like fold


Domain annotation for each model (and alignments):
>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.9   0.0   7.3e-30   6.5e-26       1     120 [.       1     128 [.       1     142 [. 0.85

  Alignments for each domain:
  == domain 1  score: 90.9 bits;  conditional E-value: 7.3e-30
                                    -EEEEEES--S.TT-HHHHHHHHHHCCT-T.T-CEEEEETTTS..--.....---HCHGHT..CGGSHHHHHHHHHHHH- CS
                        FMN_red   1 mkilvisGSlr.kgsntrklaewaaealkeagaevelidladl.ilpc...alcdkdlese..gqtsddvaellekiaaa 73 
                                    mk+l+i+GS++ +++nt ++++ +++ ++eaga+vel++ ++l i pc   + c  ++ ++  ++++dd++ l+ k ++a
  gi|116753452|ref|YP_842570.1|   1 MKVLAINGSPKmDDGNTARILNPFLDGMREAGADVELFHTRKLkIGPCngdMSC--WFRNSgkCGQNDDMQMLYPKFEDA 78 
                                    9**********888***********************************86434..4444455***************** PP

                                    SCEEEEEEECTTCE-HHHHHHHHCHT-....SSCHCCTT-EEEEEEE-SS CS
                        FMN_red  74 daliivtPeYngsysgllKnalDrlsr...trgkkelrgKpvalvavggg 120
                                    d+++++tP+Y+ +++g+lKn++Dr  +   +      ++K+v++ + g++
  gi|116753452|ref|YP_842570.1|  79 DVIVWATPVYFSGVTGPLKNLMDRQLPlhvPGTTPKKKQKVVLVSSCGAW 128
                                    ************************86677544444445777777766655 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.7   0.0   9.4e-18   8.4e-14       1     137 [.       1     128 [.       1     152 [. 0.82

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 9.4e-18
                                    -EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCCT-----CCCCHCC.HHHHTT.C.HHHHHHHHHHHHC CS
                   Flavodoxin_2   1 mkiLiinahprpeksfssalaqafvealekagphevtvrdLyadflpvlttrdlaak.layeek.p.adveseqieklla 77 
                                    mk+L in++p+ ++ ++ ++++ f++++++ag ++v+ ++  ++ +  ++  d+++  +++ +  +  d ++    k+++
  gi|116753452|ref|YP_842570.1|   1 MKVLAINGSPKMDDGNTARILNPFLDGMREAG-ADVELFHTRKLKIGPCNG-DMSCWfRNSGKCgQnDDMQMLY-PKFED 77 
                                    9*******************************.89***9999996666665.6666433443324547778888.***** PP

                                    SSEEEEEEE-BTTB--HHHHHHHHHHS-TTTSCEETTCSSCCCCTTTTSEEEEEEEESS- CS
                   Flavodoxin_2  78 adaivlqfPlwwfgvPailKgwiDrvltagfafyteeggegrgggLkgkkalvivttGgp 137
                                    ad+iv+++P+++ gv   lK+ +Dr l  +          ++++  k  k+++++++G+ 
  gi|116753452|ref|YP_842570.1|  78 ADVIVWATPVYFSGVTGPLKNLMDRQLPLHV---------PGTTPKKKQKVVLVSSCGAW 128
                                    *************************887777.........32344456788888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); 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: 00:00:00.40
# Mc/sec: 1671.95
//
Query:       gi|116753453|ref|YP_842571.1|  [L=187]
Description: hypothetical protein Mthe_0131 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); 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: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1404.12
//
Query:       gi|116753454|ref|YP_842572.1|  [L=156]
Description: hypothetical protein Mthe_0132 [Methanosaeta thermophila PT]
Scores for 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  149.0   0.1      8e-44  148.8   0.1    1.0  1  DUF2240   Uncharacterized protein conserved in archaea (DUF22
  ------ inclusion threshold ------
      0.097   12.9   0.1         15    5.9   0.1    2.3  2  DUF4777   Domain of unknown function (DUF4777)


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 !  148.8   0.1     9e-48     8e-44       1     143 [.       7     142 ..       7     143 .. 0.96

  Alignments for each domain:
  == domain 1  score: 148.8 bits;  conditional E-value: 9e-48
                        DUF2240   1 elkiavaapfkkkrkdklsesdfvfalsldrkwlspdqakklldraeeegLlekkdgdlvpnfdvaeveiPlgFkpdeel 80 
                                    e ++ va pfkk++k++l+ sdf+falsld+kw +p+++++ll++ae+egL++ + gd+v  +++a++eiP gFkp+   
  gi|116753454|ref|YP_842572.1|   7 EKRYLVALPFKKRGKSSLKISDFIFALSLDMKWGPPEKVRALLMEAENEGLVRID-GDVV--YSNADIEIPVGFKPA--- 80 
                                    57899*************************************************5.5555..699************... PP

                        DUF2240  81 lkekstferildaiaastgiekkevvaeinelqeelkglvdveaaalvvakkegvdvddliee 143
                                       + +fer++++i+++tg+++ke++a+ine+q++l++lv+++++al+va++ ++dv+d+++e
  gi|116753454|ref|YP_842572.1|  81 -PVEGIFERAVRMISSKTGMSRKEIIAMINERQDSLQRLVELDVVALLVARELEIDVSDMARE 142
                                    .99*********************************************************997 PP

>> DUF4777  Domain of unknown function (DUF4777)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0    0.0037        33      42      61 ..      43      62 ..      36      67 .. 0.88
   2 ?    5.9   0.1    0.0017        15      13      48 ..      92     127 ..      85     131 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0037
                        DUF4777 42 kvVkntLeaAvrhGFlkken 61
                                   ++V+ +L +A+++G+++ ++
  gi|116753454|ref|YP_842572.1| 43 EKVRALLMEAENEGLVRIDG 62
                                   68**************9776 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0017
                        DUF4777  13 lkvlnrPaTldEivervaerydlseeelkkvVkntL 48 
                                    + + +++++ +Ei+  + er d  ++ ++ +V  +L
  gi|116753454|ref|YP_842572.1|  92 MISSKTGMSRKEIIAMINERQDSLQRLVELDVVALL 127
                                    56679******************9999999997777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); 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: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1151.14
//
Query:       gi|116753455|ref|YP_842573.1|  [L=368]
Description: geranylgeranyl reductase [Methanosaeta thermophila PT]
Scores for 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-10   38.4   0.0    1.3e-09   38.0   0.0    1.2  1  FAD_oxidored    FAD dependent oxidoreductase
      5e-09   36.2   2.0     0.0014   18.3   0.9    2.3  2  DAO             FAD dependent oxidoreductase
    8.8e-08   31.6   0.0     0.0005   19.2   0.0    2.3  2  Lycopene_cycl   Lycopene cyclase protein
    1.3e-07   31.2   0.0    1.9e-07   30.6   0.0    1.3  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
      9e-07   28.1   0.1      0.017   14.0   0.0    3.1  3  Trp_halogenase  Tryptophan halogenase
      2e-06   27.3   0.2      7e-05   22.2   0.0    2.5  2  FAD_binding_3   FAD binding domain
    2.9e-06   26.6   2.3    2.1e-05   23.8   1.9    2.2  2  FAD_binding_2   FAD binding domain
    7.8e-06   24.8   0.1    0.00012   20.9   0.1    2.0  2  HI0933_like     HI0933-like protein
    7.2e-05   22.0   0.0    0.00011   21.5   0.0    1.2  1  GIDA            Glucose inhibited division protein A
     0.0046   16.3   0.7     0.0072   15.6   0.7    1.3  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
     0.0092   16.2   0.1      0.028   14.6   0.1    1.9  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
  ------ inclusion threshold ------
       0.01   16.4   0.0       0.17   12.4   0.0    2.4  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
       0.15   11.3   0.1        0.3   10.3   0.1    1.5  1  Thi4            Thi4 family


Domain annotation for each model (and alignments):
>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.0   9.2e-13   1.3e-09       1     131 [.       3     137 ..       3     144 .. 0.70

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 9.2e-13
                   FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLve.....ergvlGGlltsglvatdignkaee....qvvtgiareflerlrqrg 71 
                                    D++V+GGgpaG  AA+  a  G +vlL+e     +++ +GG l+ ++++ +   ++++    + v++i   f++r+++  
  gi|116753455|ref|YP_842573.1|   3 DLIVIGGGPAGASAALEGAGLGLSVLLIEkekfpRYKPCGGALSEKARSYLRF-RIPDevidAEVSRIRIFFRDRCAEIS 81 
                                    99***************************4444445559*******9776655.55664555555555555666664422 PP

                   FAD_oxidored  72 garlkkrskwntfepevakavleeml....aeagvtvllntrlvevekegkriesvtveskegr 131
                                         +r         v ++v++++l    a+ag +vl++++++++  e++ ++ +  es +gr
  gi|116753455|ref|YP_842573.1|  82 RP---ER-----LSTLVTRSVFDDILvrraADAGAEVLFGKKATGISEEDGCVRIMAGESYKGR 137
                                    22...33.....44556666666666666599***************99865665555555455 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.9   9.9e-07    0.0014       1      32 [.       3      36 ..       3      54 .. 0.91
   2 !   16.2   0.0   4.3e-06     0.006     152     233 ..      99     172 ..      83     212 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 9.9e-07
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEESSSST CS
                            DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdia 32
                                   d+++iGGG +G+s+A+e a  g  V+l+ek++++
  gi|116753455|ref|YP_842573.1|  3 DLIVIGGGPAGASAALEGAGLGlsVLLIEKEKFP 36
                                   789***************9999********9765 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 4.3e-06
                                    HHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEEEEEEEEEE--GGGHH.HHHTTCTTTSEEEEEEEEEEEEEEC CS
                            DAO 152 laraaealGveilegtevtgleeedgkvwgverttpgendaadavVnaaGawsd.llgllkeldlpispvrgqvlvlkpl 230
                                    l r+a+++G+e+l+g ++tg++eedg v        ge  + + +V+a G+  + l+   +++ +p  ++rg  lv +  
  gi|116753455|ref|YP_842573.1|  99 LVRRAADAGAEVLFGKKATGISEEDGCVRIM-A---GESYKGRLLVLADGHT-GmLS---RKI-CPGDGMRGVCLVSEVA 169
                                    7899*****************9999997777.3...65545589******55.5455...666.8889999999998554 PP

                                    CTH CS
                            DAO 231 sek 233
                                     e+
  gi|116753455|ref|YP_842573.1| 170 AEE 172
                                    443 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   3.6e-07    0.0005       1     140 [.       3     144 ..       3     163 .. 0.66
   2 !   10.3   0.0   0.00019      0.26     243     299 ..     232     286 ..     228     340 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 3.6e-07
                  Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfpnnyvWsdefedlga.....leecvehsWsgtivylddgkki 75 
                                    D++viG+GpAg s A +   a  gl+v+lie  + + + +       +++ +       +e++++  s+ ++ + d    
  gi|116753455|ref|YP_842573.1|   3 DLIVIGGGPAGASAALEG--AGLGLSVLLIEKEKFPRYKPC-GGALSEKARSYlrfriPDEVIDAEVSRIRIFFRDRCAE 79 
                                    9*****************..**********76554433222.22222222222334545677788888888877776555 PP

                  Lycopene_cycl  76 llg..raYgrvsskrlkeellerlvengvklleak.vesveeeeageslvvleggrkirarlvvdarg 140
                                     +   r    v+++ +   l +r +++g++ l +k ++ + ee+     v + +g+  ++rl v a g
  gi|116753455|ref|YP_842573.1|  80 ISRpeRLSTLVTRSVFDDILVRRAADAGAEVLFGKkATGISEEDG---CVRIMAGESYKGRLLVLADG 144
                                    444446667778888888888888877777665541555555555...56666677777777766666 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00019
                  Lycopene_cycl 243 iPvtlggslprle.qkvlaiGaaaglvhPaTGYsvarslaeapllasaiaaalressl 299
                                    iP+   g+ + l   +++  G  ag+v P TG  +a +++  ++ a++ ++ l   + 
  gi|116753455|ref|YP_842573.1| 232 IPL--SGPSRYLGgRRTMLCGDSAGMVDPFTGEGIAYAVRSGQIAAQVASEHLSD-GC 286
                                    677..444444440559999*********************99777776666663.33 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0   1.4e-10   1.9e-07       1     128 [.       2     166 ..       2     206 .. 0.77

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 1.4e-10
                                    CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHH...HCHHHHHHHHHHHHH.................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxx.................... RF
                    Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcll...skallgvaedaeias.................... 57 
                                    +d++viGgGpAG +aal+ a  g+ v+l+e ++ ++  ++     s++++++ +++   +                    
  gi|116753455|ref|YP_842573.1|   2 YDLIVIGGGPAGASAALEGAGLGLSVLLIE-KEKFPRYKPCGgalSEKARSYLRFRIPDEvidaevsririffrdrcaei 80 
                                    689**************************5.444555554432336666666666644446778888888889******* PP

                                    .....................HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BC.. CS
                                    .....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                    Pyr_redox_2  58 .....................evvkklnqgielllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdl.. 114
                                                         +      +g e+l g+++++i ++ ++v +       +e+++   lvlA G +  +   
  gi|116753455|ref|YP_842573.1|  81 srperlstlvtrsvfddilvrR---AADAGAEVLFGKKATGISEEDGCVRI-----MAGESYKGRLLVLADGHTGMLSrk 152
                                    ********99999999985541...45568999999999999999999999.....67889*********9975555444 PP

                                    TCTTC.TTBEECCS CS
                                    xxxxxxxxxxxxxx RF
                    Pyr_redox_2 115 gipGvaenvgklvr 128
                                     +pG++  ++ lv+
  gi|116753455|ref|YP_842573.1| 153 ICPGDGMRGVCLVS 166
                                    45555334444444 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   1.2e-05     0.017       2      48 ..       4      47 ..       3      69 .. 0.74
   2 !    6.7   0.0     0.002       2.8     153     216 ..      92     152 ..      86     160 .. 0.90
   3 ?    3.7   0.0     0.017        23     319     372 ..     247     300 ..     238     310 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.2e-05
                                   EEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS---SS-EE--TH CS
                 Trp_halogenase  2 ivivGGGtaGwlaAaalakalkgklevtlveseeigtvgvGeatips 48
                                   ++++GGG+aG  aA   a  +   l+v+l+e+e++++++   +++ +
  gi|116753455|ref|YP_842573.1|  4 LIVIGGGPAGASAALEGAGLG---LSVLLIEKEKFPRYKPCGGALSE 47
                                   789*******77775555544...*************9876555554 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.002
                                    HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGGG-IIIII CS
                 Trp_halogenase 153 aalyakfLrrvaearGvtrvegkvvevqldedgrveslrledgreveadlfiDcsGfrgllieq 216
                                    ++ ++++L r a ++G +++ gk ++   +edg v       g++++++l + + G+ g+l  +
  gi|116753455|ref|YP_842573.1|  92 RSVFDDILVRRAADAGAEVLFGKKATGISEEDGCVRI---MAGESYKGRLLVLADGHTGMLSRK 152
                                    6789*****************************9865...568999*************99876 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.017
                                    EE-CCCTEE--CCCS-HHHHHHHHHHHHHHT--BTT--HHHHHHHHHHHHHHHH CS
                 Trp_halogenase 319 valGlasgfvePlestsihliqaalrrLlallpdksdepaaiaefnrevarele 372
                                    ++ G+++g v+P  + +i+ + ++ +  +++  ++  +  ++ e+ ++ +re++
  gi|116753455|ref|YP_842573.1| 247 MLCGDSAGMVDPFTGEGIAYAVRSGQIAAQVASEHLSDGCDLVEYQHRCKREIG 300
                                    678*****************9998776666666666678899999999999876 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   5.1e-08     7e-05       3     136 ..       3     124 ..       1     153 [. 0.77
   2 ?    2.4   0.0     0.053        73     281     309 ..     240     269 ..     237     284 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 5.1e-08
                                    EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEEEECCC CS
                  FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradglnqrtmellrqlGledrilaegapnelmgealynelsd 82 
                                    d +++G+GpaG+++al+ +  G +v+l+ek +   ++p ++ l+++    lr   + d++++     + ++++++ +   
  gi|116753455|ref|YP_842573.1|   3 DLIVIGGGPAGASAALEGAGLGLSVLLIEKEKFPRYKPCGGALSEKARSYLRF-RIPDEVIDAE--VSRIRIFFRDR--- 76 
                                    678***********************************999999998777775.5777776666..23445565555... PP

                                    CCEEEEEHHCHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCC CS
                  FAD_binding_3  83 tpkaradlelesspervtvypqteleriLvehaeerglqvrfktevesleqdee 136
                                         a+++     +  t++  + ++ iLv +a+ +g++v f+++ +++ +++ 
  gi|116753455|ref|YP_842573.1|  77 ----CAEIS--RPERLSTLVTRSVFDDILVRRAADAGAEVLFGKKATGISEEDG 124
                                    ....34444..4455557777777888888888888888888888887777665 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.053
                                    SEET.TEEE-GGGTEEE-STTSHHHHHHHH CS
                  FAD_binding_3 281 yrkg.rvflaGDAaHihpPtgGqGlNtaiq 309
                                    y  g r +l GD+a ++ P +G G+  a++
  gi|116753455|ref|YP_842573.1| 240 YLGGrRTMLCGDSAGMVDPFTGEGIAYAVR 269
                                    55676999****************988875 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   1.9   1.5e-08   2.1e-05       1      32 [.       3      34 ..       3      39 .. 0.95
   2 ?    0.6   0.0      0.17   2.3e+02     126     175 ..      77     127 ..      39     146 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.5e-08
                                   SEEEE--SHHHHHHHHHHHHTTT-EEEEESSS CS
                  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeq 32
                                   D+iViG+G AG +AAle a  Gl+v+++eke+
  gi|116753455|ref|YP_842573.1|  3 DLIVIGGGPAGASAALEGAGLGLSVLLIEKEK 34
                                   89****************************97 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.17
                                    E-.STT-.......HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEE CS
                  FAD_binding_2 126 lhdaadarr.etlvtghallarlvesarkagvdfqerteadeLivedgrvt 175
                                    +++ ++++r  tlvt       lv++a +ag ++++  +a+ +  edg v+
  gi|116753455|ref|YP_842573.1|  77 CAEISRPERlSTLVTRSVFDDILVRRAADAGAEVLFGKKATGISEEDGCVR 127
                                    5568999999999999999999*********************88888665 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.1   8.9e-08   0.00012       2      33 ..       3      34 ..       2      39 .. 0.92
   2 ?    1.7   0.0     0.059        81     113     164 ..      97     145 ..      91     150 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 8.9e-08
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
                    HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekak 33
                                   d+iviGgG+AG  aA++ a  g +Vll+ek+k
  gi|116753455|ref|YP_842573.1|  3 DLIVIGGGPAGASAALEGAGLGLSVLLIEKEK 34
                                   89****************************97 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.059
                                    HHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE---- CS
                    HI0933_like 113 dallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGG 164
                                    d+l++++ +ag ++   ++ +++++ edg +r+ +  +e+++ + lvlA G 
  gi|116753455|ref|YP_842573.1|  97 DILVRRAADAGAEVLFGKKATGISE-EDGCVRIMA--GESYKGRLLVLADGH 145
                                    6899*******************55.666577776..9***********885 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   7.7e-08   0.00011       1      30 [.       3      32 ..       3      55 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 7.7e-08
                                   CEEEE-SSHHHHHHHHHHHHTT--EEEEES CS
                           GIDA  1 dviViGgGhAGceAAlaaarlGakvlLith 30
                                   d+iViGgG AG  AAl+ a lG++vlLi +
  gi|116753455|ref|YP_842573.1|  3 DLIVIGGGPAGASAALEGAGLGLSVLLIEK 32
                                   689************************933 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 !   15.6   0.7   5.2e-06    0.0072       1      31 [.       5      34 ..       5      38 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.2e-06
                    Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgn 31
                                   i+iG+GPaG +aa+e   +gl ++l +Ek++
  gi|116753455|ref|YP_842573.1|  5 IVIGGGPAGASAALEGAGLGL-SVLLIEKEK 34
                                   89*******************.7******86 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 !   14.6   0.1   2.1e-05     0.028       1      28 [.       6      33 ..       6      65 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.1e-05
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SS CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekr 28
                                   ++G+G +G++aA + a  g++vll+ek 
  gi|116753455|ref|YP_842573.1|  6 VIGGGPAGASAALEGAGLGLSVLLIEKE 33
                                   8*************************96 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00013      0.17       2      50 ..       4      53 ..       3      57 .. 0.86
   2 ?    1.1   0.0      0.44   6.1e+02      44      71 ..      97     124 ..      84     131 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                                   EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS.TTSSHHHHHHHHHHH CS
                      Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll.rllDeeaskilqekl 50
                                   ++v+GgG  g  +A + a lg +V ++e ++ ++ + ++ ++s+  + +l
  gi|116753455|ref|YP_842573.1|  4 LIVIGGGPAGASAALEGAGLGLSVLLIEKEKFPRyKPCGGALSEKARSYL 53
                                   68***************************999987777777776666665 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.44
                                    HHHHHHHHHTTEEEECSEEEEEEEEETT CS
                      Pyr_redox  44 kilqeklekngievllntkveeiegsed 71 
                                    +il ++  + g evl+++k++ i +++ 
  gi|116753455|ref|YP_842573.1|  97 DILVRRAADAGAEVLFGKKATGISEEDG 124
                                    6788999999************996664 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00022       0.3      19      50 ..       3      33 ..       1      46 [. 0.88

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00022
                                   EEEEE--SHHHHHHHHHHHHCTTS-EEEEESS CS
                           Thi4 19 DvvivGaGssGLtaayylakkpdlkvailers 50
                                   D++++G+G++G +aa   a   +l v+++e++
  gi|116753455|ref|YP_842573.1|  3 DLIVIGGGPAGASAALEGAGL-GLSVLLIEKE 33
                                   99*************999998.*******985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2603.84
//
Query:       gi|116753456|ref|YP_842574.1|  [L=100]
Description: hypothetical protein Mthe_0134 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00025   21.7   6.8     0.0003   21.4   6.8    1.2  1  CxxCxxCC  Putative zinc- or iron-chelating domain


Domain annotation for each model (and alignments):
>> CxxCxxCC  Putative zinc- or iron-chelating domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   6.8   1.7e-08    0.0003       1      72 [.       2      77 ..       2      98 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.7e-08
                       CxxCxxCC  1 eCkeCgaCCkelkvklteedlerlkaaevaeeeeeskkiakadgrCvfldeetk..lCkiYe...eRpkicrlfpas 72
                                   +C +Cg CC +l+v +++ d  r   +   ++++    +++a+++C++l+  ++   C+i+e    R + c+lf+++
  gi|116753456|ref|YP_842574.1|  2 KCLRCGCCCIHLDVAIPNPDAIRPDGTLD-KTHRMPVMFKRAGEPCPHLTFADGiaVCRIHEmecYRGSPCELFEQV 77
                                   6*********8888888877777666666.444444455569********888888******877899****99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); 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: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 719.72
//
Query:       gi|116753457|ref|YP_842575.1|  [L=392]
Description: lysine 2,3-aminomutase YodO family protein [Methanosaeta thermophila PT]
Scores for complete 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   38.6   0.0    3.9e-09   37.1   0.0    1.8  1  Radical_SAM  Radical SAM superfamily
    6.2e-06   26.3   0.0    5.6e-05   23.3   0.0    2.3  3  Fer4_14      4Fe-4S single cluster domain
    9.3e-05   22.7   0.0    0.00027   21.2   0.0    1.7  2  Fer4_12      4Fe-4S single cluster domain
  ------ inclusion threshold ------
       0.11   12.8   0.0       0.24   11.6   0.0    1.4  1  Hydrolase    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 !   37.1   0.0   8.7e-13   3.9e-09       3     164 ..      92     249 ..      90     252 .. 0.78

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 8.7e-13
                                    EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritv 82 
                                    v+++C   C+fC r++      ++++ +  ++ + ++++++++ + +v+l+gg+pl+ +  ++l e  ++l+ +  ++ +
  gi|116753457|ref|YP_842575.1|  92 VSNACGSLCRFCFRKR---IFIDSHHETAIDLPRALDYIREHREITNVLLSGGDPLMLS-TERLEEIVRRLR-DIDHVQI 166
                                    789************8...6*******************95555*************86.334444444443.5666666 PP

                                    EECSSCHG..........HHHHHHHHHTT..-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEE CS
                                    xxxxxxxx..........xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  83 etngtlpd..........eeklerllelg..vdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdriv 150
                                    +  gt++           +  le  +++     r+++ ++  +++     +      +e+l+a+  l eag   +v+ ++
  gi|116753457|ref|YP_842575.1| 167 IRIGTKLPvynpfritedPSLLEIVKRYSheNRRIYFVIQFNHPK----EI-----SSETLKAVSQLQEAGAI-TVSQTP 236
                                    666666655556666688666666666666679999999999998....34.....4899**********999.****** PP

                                    EBTTTSHHHHHHHH CS
                                    xxxxxxxxxxxxxx RF
                    Radical_SAM 151 glpGendeeleell 164
                                    +l+G+nd   e l+
  gi|116753457|ref|YP_842575.1| 237 LLRGVNDNP-ETLA 249
                                    *******85.5555 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   1.2e-08   5.6e-05       6      85 ..      94     169 ..      89     176 .. 0.81
   2 ?   -0.2   0.0      0.23     1e+03      58      82 ..     178     202 ..     176     233 .. 0.72
   3 ?   -3.1   0.0       1.8   8.3e+03      81      96 ..     277     292 ..     272     312 .. 0.65

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1.2e-08
                        Fer4_14   6 sgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekkiwl 85 
                                    + C   C++C++k  + ++ +  +t  +l + l+   +++  i ++ l+GG+PL+  +++ l ++v+rl++  +   i++
  gi|116753457|ref|YP_842575.1|  94 NACGSLCRFCFRKRIFIDSHH--ETAIDLPRALDYIREHRE-ITNVLLSGGDPLML-STERLEEIVRRLRDIDHVQIIRI 169
                                    7899**********8877655..578899999987777777.566*********55.9***********98776666665 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.23
                        Fer4_14  58 PLhyenkkellklvkrlkeeypekk 82 
                                    P+  +++++ll++vkr+ +e + + 
  gi|116753457|ref|YP_842575.1| 178 PFRITEDPSLLEIVKRYSHENRRIY 202
                                    888999999******9999885543 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 1.8
                        Fer4_14  81 kkiwletngtleiele 96 
                                    +++ +et++ +  + +
  gi|116753457|ref|YP_842575.1| 277 FQVPVETSYAIVEKAK 292
                                    6788889998876655 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 !   21.2   0.0   6.1e-08   0.00027       8      81 ..      89     160 ..      81     172 .. 0.75
   2 ?   -2.4   0.0       1.2   5.2e+03      63      84 ..     178     199 ..     177     226 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 6.1e-08
                        Fer4_12   8 lslfvsgCnlsCkgCfnketwsfksgkeftkelleeiiedlk.kesiegltllGGEPllpenaeallelvkevke 81 
                                    l+l  + C   C++Cf  +    +s++e+  +l  ++++ +  +++i+ + l+GG+Pl+   +e l e+v++++ 
  gi|116753457|ref|YP_842575.1|  89 LMLVSNACGSLCRFCFR-KRIFIDSHHETAIDLP-RALDYIReHREITNVLLSGGDPLM-LSTERLEEIVRRLRD 160
                                    45667789********5.5555666666554443.334444415899************.999********9986 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.2
                        Fer4_12  63 Pllpenaeallelvkevkeekp 84 
                                    P+  ++++ lle+vk+   e+ 
  gi|116753457|ref|YP_842575.1| 178 PFRITEDPSLLEIVKRYSHENR 199
                                    7777788999999999888876 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.4e-05      0.24     103     156 ..     168     256 ..     111     280 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.4e-05
                                    H.............................TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEE......SSEHHH CS
                                    x.............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxx RF
                      Hydrolase 103 l.............................qaralavftiadplkvkpeaaeavasLkaagievvllt......gdnpet 147
                                                                  + r++ v+ + +p+++  e+ +av +L++ag  +v  t      +dnpet
  gi|116753457|ref|YP_842575.1| 168 RigtklpvynpfritedpslleivkrysheNRRIYFVIQFNHPKEISSETLKAVSQLQEAGAITVSQTpllrgvNDNPET 247
                                    155555556666666666666666677777889***************************99999999999999999999 PP

                                    HHHHHHHTT CS
                                    xxxxxxxxx RF
                      Hydrolase 148 aeraanqlG 156
                                       + ++l 
  gi|116753457|ref|YP_842575.1| 248 LAQLFKKLS 256
                                    998888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); 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 0.26s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2725.52
//
Query:       gi|116753458|ref|YP_842576.1|  [L=310]
Description: NAD-dependent epimerase/dehydratase [Methanosaeta thermophila PT]
Scores for complete 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-62  210.8   0.0    2.4e-62  210.5   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    1.5e-56  192.2   0.0    8.1e-56  189.8   0.0    1.8  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    3.6e-27   95.1   0.0    4.9e-27   94.6   0.0    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    1.2e-14   54.1   0.0    1.1e-13   51.0   0.0    2.1  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    7.6e-10   38.4   0.0    6.2e-07   28.9   0.0    2.6  1  NAD_binding_4    Male sterility protein
    3.2e-09   36.3   0.0    4.3e-09   35.9   0.0    1.1  1  RmlD_sub_bind    RmlD substrate binding domain
    5.1e-08   33.0   0.0    7.7e-08   32.4   0.0    1.2  1  NAD_binding_10   NAD(P)H-binding
    0.00028   21.2   0.0    0.00044   20.5   0.0    1.4  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0019   17.8   0.0      0.003   17.2   0.0    1.3  1  NmrA             NmrA-like family
     0.0023   17.4   0.1     0.0033   16.9   0.1    1.3  1  adh_short        short chain dehydrogenase
  ------ inclusion threshold ------
      0.032   14.2   0.1      0.064   13.2   0.1    1.6  1  KR               KR domain
      0.096   13.0   0.0       0.18   12.1   0.0    1.5  1  TrkA_N           TrkA-N domain
       0.12   12.5   0.0       0.18   11.9   0.0    1.3  1  DapB_N           Dihydrodipicolinate reductase, N-terminus


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 !  210.5   0.0   1.8e-65   2.4e-62       1     241 []       6     241 ..       6     241 .. 0.94

  Alignments for each domain:
  == domain 1  score: 210.5 bits;  conditional E-value: 1.8e-65
                                    EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC....EEEE--TT-HHHHHHHHHHHT-SEEEE--S--- CS
                      Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl....elveldltdrsalerlfkeeqpdavihlAavgg 76 
                                    i VtG++GfiGs++v+al +++ +v+++d+ s+++++++ + l    ++ve+d+ d + l+r f+   +d+v+h Aa  +
  gi|116753458|ref|YP_842576.1|   6 IAVTGGAGFIGSNIVRALCDEN-DVTVIDNMSTGRRENL-RGLegriRFVECDINDIKMLKREFE--SVDYVLHQAALPS 81 
                                    78******************97.9999999966666554.4445999******************..8************ PP

                                    HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHH CS
                      Epimerase  77 vaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklveay 156
                                    v++s+ dp ++ ++n+ gtl +l aa ++gvkr++f+sSs+vYG+++e pk e++     +p spYa++Kl ge++++ +
  gi|116753458|ref|YP_842576.1|  82 VQRSIMDPMATNRSNIDGTLSVLVAAMDCGVKRVVFASSSAVYGDSPELPKRESL---IPRPMSPYAVTKLVGEHYCRVF 158
                                    **************************************************99999...569******************* PP

                                    HHHHT-EEEEEEESEEESTT.S-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT-STT CS
                      Epimerase 157 aaqyglnaiilrlfnlyGpr.ngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvdagdkg 235
                                     + yg+++++lr+fn++Gp+ ++ +e + vip++i  +l+g  + +++gdg++ Rdf+yv+Dv++a++l+      g++g
  gi|116753458|ref|YP_842576.1| 159 YEIYGIECVSLRYFNVFGPGqDPASEYAAVIPKFIDAVLSGS-QPVVYGDGEQTRDFVYVDDVVRANILACLS--PGAPG 235
                                    ********************999999****************.999***********************9999..44566 PP

                                    EEEEES CS
                      Epimerase 236 eiyniG 241
                                     ++niG
  gi|116753458|ref|YP_842576.1| 236 LAINIG 241
                                    799998 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 !  189.8   0.0   5.8e-59   8.1e-56       2     332 .]       8     304 ..       7     304 .. 0.86

  Alignments for each domain:
  == domain 1  score: 189.8 bits;  conditional E-value: 5.8e-59
                                    EETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE CS
                  GDP_Man_Dehyd   2 iTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevyn 81 
                                    +TG+aGfiGs++++ L+++  +v++i++    ++tgr e+l+      le++++++++D++D + l+r +++v  d v++
  gi|116753458|ref|YP_842576.1|   8 VTGGAGFIGSNIVRALCDE-NDVTVIDN----MSTGRRENLRG-----LEGRIRFVECDINDIKMLKREFESV--DYVLH 75 
                                    9*****************8.67888765....45778888874.....5689*******************99..9**** PP

                                    --S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHHHHHHHHH CS
                  GDP_Man_Dehyd  82 LAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYaaaKlyad 161
                                     AA   V++s+ +P +t + n+ Gtl +L a+ ++g++   r+++aS+s vYG+  e p +E+   +P sPYa++Kl+ +
  gi|116753458|ref|YP_842576.1|  76 QAALPSVQRSIMDPMATNRSNIDGTLSVLVAAMDCGVK---RVVFASSSAVYGDSPELPKRESLIPRPMSPYAVTKLVGE 152
                                    ************************************96...99************************************* PP

                                    HHHHHHHHHH---EEEEEE-EEESTTS-TT.SCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHHCS CS
                  GDP_Man_Dehyd 162 wivvnyreayglfavngilfnhesprrget.fvtrkitravarialgkqevlylGnldakRdwghvkDyveamwlmlqqd 240
                                    + ++ ++e yg+ +v+ ++fn  +p + +       i++++  ++ g q+v+ +G+++++Rd+ +v+D+v+a  l++ + 
  gi|116753458|ref|YP_842576.1| 153 HYCRVFYEIYGIECVSLRYFNVFGPGQDPAsEYAAVIPKFIDAVLSGSQPVV-YGDGEQTRDFVYVDDVVRANILACLSP 231
                                    ***************************975257789************9876.8******************77765543 PP

                                    S---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB--B-THHHHHHH--- CS
                  GDP_Man_Dehyd 241 kpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlllgdaskakeeLgWk 320
                                           a g   ++++    ++ +l   i                 k +++  +   rpg+v+  ++d++ a+e Lg+ 
  gi|116753458|ref|YP_842576.1| 232 G------APGLAINIGTGYATSLNRLLDAIGR-------------VLKRYIHPIYTEPRPGDVRDSVADITLAREVLGYA 292
                                    3......3444455555555444444433221.............12334444467789********************* PP

                                    -SS-HHHHHHHH CS
                  GDP_Man_Dehyd 321 pkvsfeelvrem 332
                                    p++++e++++em
  gi|116753458|ref|YP_842576.1| 293 PEYGLEDGLNEM 304
                                    *********998 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 !   94.6   0.0   3.6e-30   4.9e-27       1     229 [.       7     228 ..       7     232 .. 0.84

  Alignments for each domain:
  == domain 1  score: 94.6 bits;  conditional E-value: 3.6e-30
                      3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskv.nvkkviegDvtdkdkleealegvdvvihlaslvdv 79 
                                    +vtGgaGF+G+++v++L +++   +v v+D     +  e+l+ + +++ ++e+D++d + l++  e+vd v+h a+l  v
  gi|116753458|ref|YP_842576.1|   7 AVTGGAGFIGSNIVRALCDEN---DVTVIDNMSTGRR-ENLRGLeGRIRFVECDINDIKMLKREFESVDYVLHQAALPSV 82 
                                    69****************999...69****8766666.56665515566******************************9 PP

                      3Beta_HSD  80 ag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKalaEklvl 158
                                    +   +      + n+ GT +vl a++++gv+++v+ Ss  v g+   + e+     ++ + + ++++y+ +K + E++  
  gi|116753458|ref|YP_842576.1|  83 QRsIMDPMATNRSNIDGTLSVLVAAMDCGVKRVVFASSSAVYGD---SPELP---KRESLIPRPMSPYAVTKLVGEHYCR 156
                                    984555667889********************************...66666...3445567799************986 PP

                      3Beta_HSD 159 kaNgrtlknggrlyTcaLRpagiyGegdk......llvpllkqlaklglalfkigdeevlsdrvYvgNvawahilAa 229
                                          + ++  +  ++LR   ++G+g++       + p +  ++ +g + + +gd e++ d+vYv+ v+ a ilA 
  gi|116753458|ref|YP_842576.1| 157 V-----FYEIYGIECVSLRYFNVFGPGQDpaseyaAVIPKFIDAVLSGSQPVVYGDGEQTRDFVYVDDVVRANILAC 228
                                    5.....555667899************9722222234556677788999999***********************95 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   0.0   8.1e-17   1.1e-13       1     211 [.       6     222 ..       6     235 .. 0.79

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 8.1e-17
                                    EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SE CS
                Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdv 80 
                                    + vtG++G iGs++vr +++++   + ++++  +   e  +          l+ +i  v +d++d + l++ +e  +vd+
  gi|116753458|ref|YP_842576.1|   6 IAVTGGAGFIGSNIVRALCDEN--DVTVIDNMSTGRRENLRG---------LEGRIRFVECDINDIKMLKREFE--SVDY 72 
                                    67**************998775..566777654443332222.........3333345589*************..**** PP

                                    EEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGGGS..............S--SHHHHHHHHHH CS
                Polysacc_synt_2  81 vfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStDKAv..............nPtnvmGatKrlae 146
                                    v+h AAl  V    + p+ + + N+ gt +v+ aa+++gvk+vv+ S+                  +P++ + +tK++ e
  gi|116753458|ref|YP_842576.1|  73 VLHQAALPSVQRSIMDPMATNRSNIDGTLSVLVAAMDCGVKRVVFASSSAVYgdspelpkreslipRPMSPYAVTKLVGE 152
                                    *********************************************99853323333333333334479999********* PP

                                    HHHHHGGG--SSS--EEEEEEE-EETT......G.TTSSHHHHHHHHHTT.SSEEES-TT-EEEEE-HHHHHH CS
                Polysacc_synt_2 147 kllqalakeseekktkfvvvRfGNVlg......S.rGSviplFkkqikeg.gpvtvTdpemtRyfmtieeavq 211
                                     ++  + +       + v  R+ NV+g      S    vip+F + + +g +pv   d e tR f+ +++ v+
  gi|116753458|ref|YP_842576.1| 153 HYCRVFYEIY---GIECVSLRYFNVFGpgqdpaSeYAAVIPKFIDAVLSGsQPVVYGDGEQTRDFVYVDDVVR 222
                                    ***9999998...899999******9844333322368******99999989999999999999999988775 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   4.5e-10   6.2e-07       1     256 [.       8     223 ..       8     224 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 4.5e-10
                                    EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHHHHHHHHHHT-SS-HHHHHHHHHTTTEEEEE--TTSGGGG--HHH CS
                  NAD_binding_4   1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksgesaeeRleeelekkelfsallkelaerikvveGDlseprlGLseed 80 
                                    +TG+ GF+G+ +++ L ++++   +++    ++g   +e             +l + l+ ri++ve D+++ +       
  gi|116753458|ref|YP_842576.1|   8 VTGGAGFIGSNIVRALCDEND---VTVIDNMSTG--RRE-------------NL-RGLEGRIRFVECDINDIK------M 62 
                                    577777777777777777764...3332222222..111.............12.235788888888888766......5 PP

                                    HHHHHHH--EEEE--SS-S.STTSSEEHHH...HHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H.... CS
                  NAD_binding_4  81 lqelaeevdviihsaAtvnfdepykellrv...NveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegek 157
                                    l++  e+vd ++h aA  ++++++ + +++   N++Gt  vl  a  +  +  +++ S+++v+g++ +            
  gi|116753458|ref|YP_842576.1|  63 LKREFESVDYVLHQAALPSVQRSIMDPMATnrsNIDGTLSVLVAAMDCGVK-RVVFASSSAVYGDSPEL----------- 130
                                    67778999**************9999765522279*************999.99999999999999943........... PP

                                    ..HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE--SSST---TTSHHHHHHHHHHHH-EEES- CS
                  NAD_binding_4 158 eekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitgesktGwingsdlgirgllgliakgvlpei 237
                                          + ++        Y  +K ++E+ +r   +  g+ +v +R  ++ g  +  +++    +i  ++ ++  g  p +
  gi|116753458|ref|YP_842576.1| 131 -----PKRESLIPRPMSPYAVTKLVGEHYCRVFYEIYGIECVSLRYFNVFGPGQDPASEYAA-VIPKFIDAVLSGSQPVV 204
                                    .....3445666667779****************99***************66666667777.88888889999999999 PP

                                    SB---TT--EEEHHHHHHH CS
                  NAD_binding_4 238 lgdkeavldlvpvDyvana 256
                                    +gd e++ d+v vD v++a
  gi|116753458|ref|YP_842576.1| 205 YGDGEQTRDFVYVDDVVRA 223
                                    9999999*******99987 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 !   35.9   0.0   3.1e-12   4.3e-09       2     138 ..       5     157 ..       4     182 .. 0.88

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 3.1e-12
                                    EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT..................T--TTSHHHHHHHHHHH--SEEEE------ CS
                  RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre..................eldltdaeavaellkeakpdvvvnaAAyta 63 
                                    ki vtG+ G +Gs+++++l  e+ +v+ +++                   e+d++d + +++ +++   d v + AA   
  gi|116753458|ref|YP_842576.1|   5 KIAVTGGAGFIGSNIVRALCDEN-DVTVIDNMstgrrenlrglegrirfvECDINDIKMLKREFES--VDYVLHQAALPS 81 
                                    799*************9998766.6666654456888***************************99..789********* PP

                                    HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-E.EEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHH CS
                  RmlD_sub_bind  64 vDkaEseeeaayavnaeavealAeaaaavgal.LihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavla 138
                                    v +   ++ a ++ n +++  +  aa  +g++ +++ S+  V+  + + p +e+  + P++ Y+ tKl GE+  + 
  gi|116753458|ref|YP_842576.1|  82 VQRSIMDPMATNRSNIDGTLSVLVAAMDCGVKrVVFASSSAVYGDSPELPKRESLIPRPMSPYAVTKLVGEHYCRV 157
                                    ******************************95499********999999**********************98765 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 !   32.4   0.0   5.6e-11   7.7e-08       1     131 [.      10     155 ..      10     160 .. 0.74

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 5.6e-11
                                    TTTSHHHHHHHHHHHHC-T-EEEEEETT..HHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES-.......... CS
                 NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRn..peklaeleaeeglevvegdvtdvedlaealkgadaVvsal.......... 68 
                                    G+ G +G+ +v+ l ++++++v   + +   e l  le   +++ ve d++d + l++ ++ +d V+  +          
  gi|116753458|ref|YP_842576.1|  10 GGAGFIGSNIVRALCDENDVTVIDNMSTgrRENLRGLE--GRIRFVECDINDIKMLKREFESVDYVLHQAalpsvqrsim 87 
                                    99***************855543222222245555554..8*************************99886676555555 PP

                                    ...--TCCHHHHHHHHHHHHHHCT--EEEEEEETTTTSGCGCH..HHHHHHHCCHHHHHHHHHHHHHH CS
                 NAD_binding_10  69 ...ggggkdeegaknivdaakeagvkRfvlvsaigvgdevpge..fgewnkellkaylaakraaeell 131
                                       ++++++ +g+ +++ aa   gvkR+v+ s+  v+ ++p+    +++  + +++y+  k   e++ 
  gi|116753458|ref|YP_842576.1|  88 dpmATNRSNIDGTLSVLVAAMDCGVKRVVFASSSAVYGDSPELpkRESLIPRPMSPYAVTKLVGEHYC 155
                                    5443333344559999999999**************98766531144566677888888888777775 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   3.2e-07   0.00044       5      83 ..      11      84 ..       6     111 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 3.2e-07
                                   --SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE.-SSGGGHH CS
                Sacchrp_dh_NADP  5 GaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvn.lsppissl 83
                                   GaG++G+ +++ l +++dv    tv+d   ++ ++ +   l+ r+ ++++d+++++  L++  ++ d v++ ++ p   +
  gi|116753458|ref|YP_842576.1| 11 GAGFIGSNIVRALCDENDV----TVIDNMSTGRRENLR-GLEGRIRFVECDINDIKM-LKREFESVDYVLHqAALPSVQR 84
                                   77**************986....9****9999777765.59****************.********99997344455555 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.2e-06     0.003       1     102 [.       6     120 ..       6     134 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.2e-06
                                    EEESSTTSHHHHHHHHHHHH.HT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE---GG.... CS
                           NmrA   1 IlviGaTGrqGksvvrallk.aghkvralvRdtkselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtgfy.... 75 
                                    I+v+G++G +G+ +vral + ++ +v   +   ++e+++ l+ +   +v+ d++d ++l++ ++ vd v    ++     
  gi|116753458|ref|YP_842576.1|   6 IAVTGGAGFIGSNIVRALCDeNDVTVIDNMSTGRRENLRGLEGR-IRFVECDINDIKMLKREFESVDYVLHQAALPsvqr 84 
                                    89*****************9444555445555588888888766.899*********************98877657789 PP

                                    .........S-HHHHHHHHHHHHHHHS-SEEEEEE- CS
                           NmrA  76 .........skeiedgkklvdAakeaGvkhfiySsl 102
                                             + +i+    +  Aa   Gvk+++++s 
  gi|116753458|ref|YP_842576.1|  85 simdpmatnRSNIDGTLSVLVAAMDCGVKRVVFASS 120
                                    999999998888988899999************985 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   2.4e-06    0.0033       1      71 [.       4      70 ..       4     123 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.4e-06
                                   SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHH CS
                      adh_short  1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealveka 71
                                   k + vtG+++ IG +i+++l  e  +v+v+d+ +   +e +     ++ ++ ++++D++d + +++ +e +
  gi|116753458|ref|YP_842576.1|  4 KKIAVTGGAGFIGSNIVRALCDE-NDVTVIDNMSTGRRENLRG---LEGRIRFVECDINDIKMLKREFESV 70
                                   6799*****************99.6788888888877555555...5568*********998888766554 PP

>> KR  KR 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     0.064       5      76 ..       8      71 ..       5     128 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.6e-05
                                   EETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHH CS
                             KR  5 itGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeik 76
                                   +tGG+G +G  ++r l+++   +++    +         + ++l+ l+ ++++v++D+ d + +++ +e+++
  gi|116753458|ref|YP_842576.1|  8 VTGGAGFIGSNIVRALCDENDVTVIDNMST--------GRRENLRGLEGRIRFVECDINDIKMLKREFESVD 71
                                   9*****************998887743322........223566677779**********999998887765 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00013      0.18       5      57 ..      11      65 ..       6      98 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                                   S-SHHHHHHHHHHHHTTEEEEEEESSH.HHHHHHHHTT..SEEEES-TTSHHHHHH CS
                         TrkA_N  5 GlGrvGrslaeeLseggkdvvvidkde.erveelreeg..levvvgdatdeevLee 57
                                   G+G +G+++++ L +++ dv+vid+    r e+lr  +  +++v  d  d ++L++
  gi|116753458|ref|YP_842576.1| 11 GAGFIGSNIVRALCDEN-DVTVIDNMStGRRENLRGLEgrIRFVECDINDIKMLKR 65
                                   89*************99.6******8844566666544478899999999999886 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00013      0.18       2      36 ..       5      39 ..       4      97 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                                   EEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTC CS
                         DapB_N  2 kvavvGasGrmGkevvkaveeaedlelvaavdrke 36
                                   k+av+G +G +G+++v+a+ +++d+++   +++ +
  gi|116753458|ref|YP_842576.1|  5 KIAVTGGAGFIGSNIVRALCDENDVTVIDNMSTGR 39
                                   8*************************999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); 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: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2246.35
//
Query:       gi|116753459|ref|YP_842577.1|  [L=122]
Description: hypothetical protein Mthe_0137 [Methanosaeta thermophila PT]
Scores for complete 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   30.6   0.0    3.9e-07   29.9   0.0    1.3  1  MarR_2          MarR family
    6.1e-07   29.5   0.0    9.6e-07   28.9   0.0    1.3  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
    8.9e-06   25.2   0.0    1.4e-05   24.5   0.0    1.3  1  HTH_24          Winged helix-turn-helix DNA-binding
      2e-05   24.4   0.0    2.6e-05   24.0   0.0    1.2  1  MarR            MarR family
      0.008   16.7   0.1      0.012   16.1   0.1    1.3  1  HTH_27          Winged helix DNA-binding domain
     0.0088   15.9   0.0      0.013   15.4   0.0    1.2  1  TrmB            Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.047   12.5   0.0       0.05   12.4   0.0    1.0  1  HTH_micro       HTH-like
       0.13   12.5   0.0       0.19   11.9   0.0    1.3  1  Rio2_N          Rio2, N-terminal
       0.18   11.9   0.0        0.3   11.2   0.0    1.3  1  CtsR_C          CtsR C-terminal dimerization 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 !   29.9   0.0   1.9e-10   3.9e-07      10      60 ..       5      54 ..       3      54 .. 0.95

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 1.9e-10
                                   HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSS CS
                         MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDk 60
                                   +L +++ +p++ + +++l ++lg++    sri+++L + GL++r++ ++D+
  gi|116753459|ref|YP_842577.1|  5 ALEYIRSNPDG-VLQSDLWKALGIDSRKCSRIVAKLLKDGLITREEELADG 54
                                   6999*****98.9********************************999996 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 !   28.9   0.0   4.8e-10   9.6e-07      11      52 ..       9      49 ..       4      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 4.8e-10
                 B-block_TFIIIC 11 IassRysGitqsdLakeskqdprslfyrlksLekkgLIvkqs 52
                                   I +s  +G++qsdL+k++++d+r+   ++ +L k gLI++ +
  gi|116753459|ref|YP_842577.1|  9 I-RSNPDGVLQSDLWKALGIDSRKCSRIVAKLLKDGLITREE 49
                                   5.67789********************************975 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 !   24.5   0.0   7.1e-09   1.4e-05       9      48 .]       6      46 ..       3      46 .. 0.96

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 7.1e-09
                         HTH_24  9 LelLqknpr.isqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                   Le+++ np+   q++L ++lg+ +  ++r + +L ++GlI+
  gi|116753459|ref|YP_842577.1|  6 LEYIRSNPDgVLQSDLWKALGIDSRKCSRIVAKLLKDGLIT 46
                                   99**************************************6 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   1.3e-08   2.6e-05      18      53 ..      16      51 ..       4      54 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.3e-08
                                   EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEET CS
                           MarR 18 lsvseLakklgvskstvtrvldrLekkGlieRsksp 53
                                     +s+L+k+lg+++   +r++ +L k+Gli+R+   
  gi|116753459|ref|YP_842577.1| 16 VLQSDLWKALGIDSRKCSRIVAKLLKDGLITREEEL 51
                                   6689****************************9765 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   5.8e-06     0.012      17      57 ..      14      54 ..       4      64 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.8e-06
                         HTH_27 17 rrkkladlcgrlnvedshisyslkkLtekGLvertgdeadr 57
                                   +++ ++dl ++l +++   s ++ kL + GL++r++  ad+
  gi|116753459|ref|YP_842577.1| 14 DGVLQSDLWKALGIDSRKCSRIVAKLLKDGLITREEELADG 54
                                   445559**************************888877666 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   6.4e-06     0.013      26      62 ..      19      60 ..      15      65 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6.4e-06
                                   CHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.....TTEE CS
                           TrmB 26 deiaeelgvprskvYevLrsLedkGlVerekgr.....pklY 62
                                   +++ ++lg++  k+ +++ +L++ Gl++re++      +++ 
  gi|116753459|ref|YP_842577.1| 19 SDLWKALGIDSRKCSRIVAKLLKDGLITREEELadgvrTYRL 60
                                   57889*************************986666544444 PP

>> HTH_micro  HTH-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.5e-05      0.05      99     255 ..       8      61 ..       1      77 [. 0.55

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.5e-05
                      HTH_micro  99 flvkakdyvkaaelraklnidpKklfYvikkLakkglieqktkeeakivikinkDesgsvvkkldkeklleinkedtitl 178
                                    ++  ++d v +++l + l id++k + ++ kL k gl                                           
  gi|116753459|ref|YP_842577.1|   8 YIRSNPDGVLQSDLWKALGIDSRKCSRIVAKLLKDGL------------------------------------------- 44 
                                    4444445555555555555555555555555555555........................................... PP

                      HTH_micro 179 pekiipmeylieiplidqikkkienteeGitskdlkdkfGislkqglklLnklieeeedsiktkeefegkikrlkfy 255
                                                                                                i+++ee+  ++++++  
  gi|116753459|ref|YP_842577.1|  45 ------------------------------------------------------------ITREEELADGVRTYRLR 61 
                                    ............................................................55555555555555544 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   9.7e-05      0.19      14      65 ..       5      56 ..       2      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.7e-05
                         Rio2_N 14 avEmgmrnhevVptelieeisrlkeeevkkrlsrllkaklisrktakydGYk 65
                                   a+E+   n + V ++ + +  ++++ ++++ + +llk +li r++   dG +
  gi|116753459|ref|YP_842577.1|  5 ALEYIRSNPDGVLQSDLWKALGIDSRKCSRIVAKLLKDGLITREEELADGVR 56
                                   788889999999999999999**********************999888855 PP

>> CtsR_C  CtsR C-terminal dimerization domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00015       0.3      17      39 ..      27      49 ..      24      51 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00015
                         CtsR_C 17 iseqdaeaiiqrLleegliterE 39
                                   i+++++ +i+++Ll++glit+ E
  gi|116753459|ref|YP_842577.1| 27 IDSRKCSRIVAKLLKDGLITREE 49
                                   899******************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); 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: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 967.21
//
Query:       gi|116753460|ref|YP_842578.1|  [L=74]
Description: like-Sm ribonucleoprotein, core [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.3e-18   64.0   1.4    8.1e-18   63.9   1.4    1.0  1  LSM       LSM domain


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.9   1.4   4.5e-22   8.1e-18       2      67 .]       6      72 ..       5      72 .. 0.94

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 4.5e-22
                                   HHHHTTTSEEEEEETTS..EEEEEEEEEEETTSEEEEEEEEEEETTETEEEEEEEEEEEGGGEEEEEE CS
                            LSM  2 flkklinkkvtvelkng..relrGtLkgfDqfmNlvLedveetlkdkkekrklglvliRGnnivlisl 67
                                   ++++li+ k++ve+k+   ++l+G+L ++D+++Nl+L +++e+++++ ++r+lg v++RGnni+lis+
  gi|116753460|ref|YP_842578.1|  6 KVQSLIGTKIQVEMKGSqrHVLEGILNSVDEYLNLHLLETVEIVNGE-RTRSLGSVILRGNNIILISP 72
                                   6789************65589*************************9.******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 564.50
//
Query:       gi|116753461|ref|YP_842579.1|  [L=75]
Description: NifU domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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   85.9   0.3    1.7e-24   85.8   0.3    1.0  1  NifU             NifU-like domain
      3e-05   24.1   0.0     0.0001   22.4   0.0    1.8  1  FeS_assembly_P   Iron-sulfur cluster assembly protein
  ------ inclusion threshold ------
      0.054   13.1   0.8       0.19   11.4   0.1    1.9  2  Nbl1_Borealin_N  Nbl1 / Borealin N terminal


Domain annotation for each model (and alignments):
>> NifU  NifU-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.8   0.3   2.8e-28   1.7e-24       1      67 []       8      73 ..       8      73 .. 0.98

  Alignments for each domain:
  == domain 1  score: 85.8 bits;  conditional E-value: 2.8e-28
                                   HHHHHHH.HGGG--GG--EEEEEEEETTEEEEEEESGGGG-....THHHHHHHHHHHHH-TT--EEE CS
                           NifU  1 ieevleeeirPaLasdGGdielvdvdegvVkvrlqGaCsgCpsstvtlkegiekaLkeevpevkeVe 67
                                   +e++le+ ir  L+  GGd+elvd+++gvV+v+l+G+C+gCp s++tl++ +e+ Lk++v+ vk+Ve
  gi|116753461|ref|YP_842579.1|  8 VESTLES-IRNVLRIEGGDVELVDINDGVVYVKLTGSCAGCPFSQMTLRNFVERELKKNVSGVKAVE 73
                                   7999***.*********************************************************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 !   22.4   0.0   1.7e-08    0.0001      24      73 ..      24      73 ..       5      74 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.7e-08
                                   T---EEEE-T-EEEEEE--SSTT-T.THHHHHHHHHHHHC..STT--EEEEE CS
                 FeS_assembly_P 24 glvreidieggkVsvditltypacs.laeairadaeaalr.alpgvevveVe 73
                                   g v+ +di++g+V+v++t   ++c+ +   +r+ +e+ l+  + g  v  Ve
  gi|116753461|ref|YP_842579.1| 24 GDVELVDINDGVVYVKLTGSCAGCPfSQMTLRNFVERELKkNVSG--VKAVE 73
                                   567779*******************99999***************..55554 PP

>> Nbl1_Borealin_N  Nbl1 / Borealin N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   3.2e-05      0.19      17      38 ..       1      22 [.       1      23 [. 0.92
   2 ?    0.2   0.1       0.1   6.1e+02      48      56 ..      51      59 ..      49      64 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.2e-05
                Nbl1_Borealin_N 17 irrlraelelllktlrnrfele 38
                                   ++ +++e+e++l+++rn +++e
  gi|116753461|ref|YP_842579.1|  1 MQSMKEEVESTLESIRNVLRIE 22
                                   578***************9986 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.1
                Nbl1_Borealin_N 48 kmtmkelle 56
                                   +mt++ ++e
  gi|116753461|ref|YP_842579.1| 51 QMTLRNFVE 59
                                   566666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); 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: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 554.71
//
Query:       gi|116753462|ref|YP_842580.1|  [L=141]
Description: hypothetical protein Mthe_0140 [Methanosaeta thermophila PT]
Scores for complete 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  153.3   0.1    2.4e-45  153.0   0.1    1.1  1  Nit_Regul_Hom  Uncharacterized protein, homolog of nitrogen r
  ------ inclusion threshold ------
       0.16   12.0   1.0        1.8    8.7   0.1    2.3  2  DUF3674        RNA dependent RNA polymerase


Domain annotation for each model (and alignments):
>> Nit_Regul_Hom  Uncharacterized protein, homolog of nitrogen regulatory protein PII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.0   0.1   2.6e-49   2.4e-45       1     106 [.      34     139 ..      34     140 .. 0.99

  Alignments for each domain:
  == domain 1  score: 153.0 bits;  conditional E-value: 2.6e-49
                  Nit_Regul_Hom   1 mkvllklfvesenlgkvinalseagitGfylieYkGlsPqewkgflleedpesaikiikdlseeavlintvvdeekveki 80 
                                    mk ++k+f+++e+l kv+n+l+e+gitGfy++eYkG+sP  wk+f+l+edpe+++++i+++se++v++ntvv+++++e++
  gi|116753462|ref|YP_842580.1|  34 MKSMVKVFIDHEHLLKVMNILTEVGITGFYIYEYKGMSPGVWKDFRLREDPEMTLDAIRNFSEPGVMVNTVVSSNRCERL 113
                                    89****************************************************************************** PP

                  Nit_Regul_Hom  81 keeleeklkderytiieipvekikvn 106
                                    +++le+ lk++r+t+i +pv++ikv+
  gi|116753462|ref|YP_842580.1| 114 VQSLEQGLKGKRFTVIIQPVTSIKVR 139
                                    ************************97 PP

>> DUF3674  RNA dependent RNA polymerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1     0.027   2.4e+02      22      29 ..      18      25 ..       4      27 .. 0.82
   2 ?    8.7   0.1    0.0002       1.8      28      38 ..      62      72 ..      48      73 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.027
                        DUF3674 22 tHksqPYY 29
                                    Hk qP Y
  gi|116753462|ref|YP_842580.1| 18 QHKRQPIY 25
                                   4*****98 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0002
                        DUF3674 28 YYiPDYkGmEP 38
                                   +Yi +YkGm P
  gi|116753462|ref|YP_842580.1| 62 FYIYEYKGMSP 72
                                   8********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1091.10
//
Query:       gi|116753463|ref|YP_842581.1|  [L=180]
Description: cobalt-precorrin-6Y C(5)-methyltransferase [Methanosaeta thermophila PT]
Scores for 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-20   71.4   0.3    3.9e-18   66.2   0.3    2.5  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.2   0.3   2.2e-22   3.9e-18      15     210 ..       2     163 ..       1     166 [. 0.85

  Alignments for each domain:
  == domain 1  score: 66.2 bits;  conditional E-value: 2.2e-22
                   TP_methylase  15 lTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealragkdVvllvsGDPlvyg 94 
                                    +T++A++a+++a++++g++ ra +++ d++++        g +          + + ++ +     d+v+l++GDP+++g
  gi|116753463|ref|YP_842581.1|   2 ITLEAIEAIRAAKLIYGSE-RAVALAADHIPP--------GCD--------VRVIRDYRSLRSLPDDAVVLSTGDPMLSG 64 
                                    8******************.******999865........222........2366777788888888************* PP

                   TP_methylase  95 tgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvllpglakeeereleallangdtlvllkapr.kl 173
                                     g                +viPG+ss+q a+arlg++l     ++++  ++    +++ ++  l++g+ ++ll + + +l
  gi|116753463|ref|YP_842581.1|  65 LGYL-----GG-------DVIPGISSMQVACARLGLSLLRVVPITFHG-RK---MDPEAVAFELEHGRCVFLLADDStDL 128
                                    9544.....34.......7********************999999999.44...3456666677889999999888877* PP

                   TP_methylase 174 aelaelLkealyddttpvavveragtedervvrgtle 210
                                    +el++ L  +  + +++v+v +++g+++er+ +gt +
  gi|116753463|ref|YP_842581.1| 129 DELCRYLENR--GIQRDVVVLRDLGYPEERINVGTTR 163
                                    *******999..8899***************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1452.01
//
Query:       gi|116753464|ref|YP_842582.1|  [L=344]
Description: cobalt-precorrin-6A synthase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-47  161.4   0.3    3.2e-47  161.0   0.3    1.1  1  CbiD      CbiD
  ------ inclusion threshold ------
      0.077   12.8   0.0       0.24   11.2   0.0    1.9  2  TrkA_C    TrkA-C domain
       0.23   11.7   1.1       0.59   10.3   0.3    2.1  2  NifU      NifU-like domain


Domain annotation for each model (and alignments):
>> CbiD  CbiD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.0   0.3   5.4e-51   3.2e-47       1     219 [.      53     262 ..      53     286 .. 0.90

  Alignments for each domain:
  == domain 1  score: 161.0 bits;  conditional E-value: 5.4e-51
                           CbiD   1 lrsGyTtGscAaAAakaAllallkgekleeveielpkgekleipiekvalleeeaavikdaGdd.pDvTngaeivaeve. 78 
                                    lr+G+TtG++A AA+k+A+l l     +eev++ +p+g+++++++e       ++a +kdaGd+  D+T+g+ iva+ + 
  gi|116753464|ref|YP_842582.1|  53 LRRGLTTGTTASAACKGAVLSL--AGDVEEVDVWTPSGITVRVKVEASCG---RCAARKDAGDHgSDITHGMMIVASASp 127
                                    699*******************..44679***************765544...6*********845************** PP

                           CbiD  79 .eeieiegGeGvGrvtkpgLevevgeaAInpvprkmieenveevleea.kegvevtisvpeGeelAkkTlNprlGivgGi 156
                                     e+ e+ +G+G+Gr+ ++gL++++g++AI++ +r++i +++ee ++e+   g++v +svp+G+++A kTlNp +G+ gGi
  gi|116753464|ref|YP_842582.1| 128 sERSELIAGDGIGRIGRSGLSTDIGKPAISRSARAQIMRAIEEGVRETgLGGARVHLSVPDGRRIALKTLNPSVGVDGGI 207
                                    *789*****************************************9998569**************************** PP

                           CbiD 157 SiLGTtGivepmSeeallesireelkvaaaeglkelvlvtGnkgeklakkklglpeealvkvs 219
                                    SiLG tG vep+  e l + i+e+l+v      +++v +tG++g ++ +    +pe++ v ++
  gi|116753464|ref|YP_842582.1| 208 SILGSTGFVEPWN-EHLEDCISESLNVL-----DRVVATTGRTGLRYSRM--LFPEHTAVLIG 262
                                    ***********85.56788888888875.....899**********9987..47777777666 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       1.8   1.1e+04      12      24 ..     260     272 ..     256     277 .. 0.69
   2 ?   11.2   0.0   4.1e-05      0.24       8      39 ..     309     340 ..     303     344 .] 0.88

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.8
                                    GTTSBHHHHTHHH CS
                         TrkA_C  12 lvGktlkelnlra 24 
                                    l+G +l+ l++r+
  gi|116753464|ref|YP_842582.1| 260 LIGSKLDLLRMRT 272
                                    7788888777766 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 4.1e-05
                                    --GGGTTSBHHHHTHHHH..S-EEEEEE-T-EEE CS
                         TrkA_C   8 agsplvGktlkelnlrar..gvlvvairRggeli 39 
                                    +++p +++ l +  l+++  g ++v i+R+g ++
  gi|116753464|ref|YP_842582.1| 309 PDHPAIDRALEH--LEKMfpGTRIVLIKRDGSIY 340
                                    799*********..****************8776 PP

>> NifU  NifU-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.3   9.9e-05      0.59      17      43 ..      75     104 ..      67     108 .. 0.87
   2 ?   -2.4   0.0      0.91   5.4e+03       5      18 ..     194     206 ..     192     207 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 9.9e-05
                                    --EEEEEEEETT...EEEEEEESGGGG-.. CS
                           NifU  17 GGdielvdvdeg...vVkvrlqGaCsgCps 43 
                                     Gd+e vdv +    +V+v+++ +C+ C++
  gi|116753464|ref|YP_842582.1|  75 AGDVEEVDVWTPsgiTVRVKVEASCGRCAA 104
                                    69*******887799*************87 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.91
                                    HHH.HGGG--GG-- CS
                           NifU   5 leeeirPaLasdGG 18 
                                    l++ ++P +  dGG
  gi|116753464|ref|YP_842582.1| 194 LKT-LNPSVGVDGG 206
                                    777.99*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); 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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2819.73
//
Query:       gi|116753465|ref|YP_842583.1|  [L=209]
Description: precorrin-8X methylmutase CbiC/CobH [Methanosaeta thermophila PT]
Scores for complete 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-57  193.1   2.8    4.3e-57  192.9   2.8    1.0  1  CbiC      Precorrin-8X methylmutase


Domain annotation for each model (and alignments):
>> CbiC  Precorrin-8X methylmutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.9   2.8   2.4e-61   4.3e-57       1     196 []      16     203 ..      16     203 .. 0.97

  Alignments for each domain:
  == domain 1  score: 192.9 bits;  conditional E-value: 2.4e-61
                                    HHHHHHHHHHHCHC-TT.S-CHHHHHHHHHHHHHT-CCHHHHEEE-TTHHHHHHHHHHCT-EEEESSHHHHCCS-HHHHH CS
                           CbiC   1 eIeaeSfaiideelgeeelseeeeevvrRvihatadfelaellrfspdaveaglealkagapivtDvemvkaGitkkrle 80 
                                    eI + S ++i + +g+e   + e+++ +R++ at+d+++ae lrf  d v+ag +al + a+i++D++mv+aGi kk ++
  gi|116753465|ref|YP_842583.1|  16 EISRASRELIARIVGDE---TLEDKIKQRCVMATGDPSIAESLRFVMDPVRAGFRALDDAADIFVDIRMVEAGIVKKGHR 92 
                                    6999***********88...99****************************************************999998 PP

                                    TTC-EEEECTC-HHHHHHHHHHTS-HHHHHHHHHHHCTTTCEEEESS-HHHHHHHHHHHHHS..HTSEEEE----SCCHH CS
                           CbiC  81 klgnevlclladpevaelakekgitrsaaamekaaeelegaivviGnAPtALlellelieegkvkpalvigvPvGFvgaa 160
                                    +   ++++l++    +e+a++ g+tr++a++ +a++el+ga+vviGnAPtALl+l++++e+ ++ p+lvig+PvGFv aa
  gi|116753465|ref|YP_842583.1|  93 S---RIRTLIDMG--EEIASRLGVTRASAGVIAAKDELDGAVVVIGNAPTALLALCDIMERREAMPSLVIGIPVGFVRAA 167
                                    8...688999888..7899************************************************************* PP

                                    HHHHHHHCSSS-EEEESSS---HHHHHHHHHHHHHH CS
                           CbiC 161 esKealaesevpyitveGrkGGsavAaaivnaLlel 196
                                    esKe+l++ evp+i + G++GG+++A+a++n+++++
  gi|116753465|ref|YP_842583.1| 168 ESKERLRRIEVPSISNVGTRGGTPIAVAAMNEIINM 203
                                    ********************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.36
# Mc/sec: 1730.91
//
Query:       gi|116753466|ref|YP_842584.1|  [L=464]
Description: uroporphyrin-III C/tetrapyrrole methyltransferase [Methanosaeta thermophila PT]
Scores for complete 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-66  223.0   0.5    2.8e-40  138.5   0.1    2.0  2  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.5   0.1   1.6e-44   2.8e-40       1     211 [.       6     211 ..       6     213 .. 0.88
   2 !   83.1   0.1   1.4e-27   2.6e-23       2     212 ..     239     426 ..     238     427 .. 0.80

  Alignments for each domain:
  == domain 1  score: 138.5 bits;  conditional E-value: 1.6e-44
                   TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealragk 80 
                                    +l +VG+GpG+p  +T+rA+r++k+ad v+g++ r+l+++++ll++        ++    + ++  e a+  +e+l++g 
  gi|116753466|ref|YP_842584.1|   6 RLSIVGIGPGNPGSMTLRARRMIKDADFVVGYR-RYLDLIQPLLKD--------KRVYPGRMGGEVERARLAVELLDDG- 75 
                                    588******************************.*********976........3444455566778888889999999. PP

                   TP_methylase  81 dVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl..lpglakeeereleall 158
                                     V+l++sGDP+vyg++s  +e++       ++ev+PGv++++aaa+r+g+   ++  v+s++  l++++++ +r + a++
  gi|116753466|ref|YP_842584.1|  76 SVALISSGDPNVYGMASLALEIALTSVDPSRIEVVPGVTAFSAAACRAGVVFRDSLAVVSLSdlLTPWEDIWRRVRLAAS 155
                                    5*******************96666666789**************************************99999998876 PP

                   TP_methylase 159 angdtlvllkapr..k....laelaelLkealyddttpvavveragtedervvrgtlee 211
                                       +  ++l++pr  +    l+e++e+Lk a +   + v+v++++++++e ++r+t+ e
  gi|116753466|ref|YP_842584.1| 156 M--GMPLALYNPRssRrdwqLSEALEILKNA-GRGGRTVVVARNVSRKGESIRRSTVDE 211
                                    6..77777779995538999***********.555678******************987 PP

  == domain 2  score: 83.1 bits;  conditional E-value: 1.4e-27
                   TP_methylase   2 lylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealragkd 81 
                                    + ++GvGpG+ e lT ++++ +++a +vlg++  +le++++++a e       ++ + ++e ++ +  e+ + +l++g  
  gi|116753466|ref|YP_842584.1| 239 ISIAGVGPGSIENLTHEVVEKVRSATLVLGAE-MHLECIKEIIAGE------VFTGAGSREDRQVQRLERAVCELENGGL 311
                                    679*****************************.*********9873......4444455555666666666666777777 PP

                   TP_methylase  82 VvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvllpglakeeereleallang 161
                                     v+ v+GDP++++++++ +   r         ++PGvs+++aaaar+g+p+++++  ls +       ++++l+al+++g
  gi|116753466|ref|YP_842584.1| 312 PVITVGGDPSIFSAAGRYIGMGRS------LGMLPGVSAFSAAAARAGAPISNDFALLSGS------VPPEKLSALADAG 379
                                    99999*******999988844444......88********************999999999......3556888888766 PP

                   TP_methylase 162 dtlvllkaprklaelaelLkealyddttpvavveragtedervvrgtleel 212
                                     +++l+ + +  a++++ +++ l++  +p+av+++++++de + +++ +el
  gi|116753466|ref|YP_842584.1| 380 FSMFLY-NAS--AYTIKSISDWLPG-SRPCAVARDVTRRDEILEVCRASEL 426
                                    666666.655..5555555554455.67*************9998888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 3684.93
//
Query:       gi|116753467|ref|YP_842585.1|  [L=254]
Description: cobalamin biosynthesis protein CbiG [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-28   98.5   0.4    4.7e-28   97.0   0.0    2.0  3  CbiG_N    Cobalamin synthesis G N-terminal
    5.6e-21   75.3   0.3    8.2e-21   74.7   0.3    1.3  1  CbiG_C    Cobalamin synthesis G C-terminus


Domain annotation for each model (and alignments):
>> CbiG_N  Cobalamin synthesis G N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.0   0.0   5.2e-32   4.7e-28       4      82 .]       2      79 ..       1      79 [. 0.99
   2 ?   -2.8   0.0      0.71   6.4e+03      37      47 ..     123     133 ..     118     152 .. 0.67
   3 ?   -3.5   0.0       1.2   1.1e+04      36      44 ..     228     236 ..     226     238 .. 0.78

  Alignments for each domain:
  == domain 1  score: 97.0 bits;  conditional E-value: 5.2e-32
                                   HHHCCC-SEEEEES-HHHHHHHHHHH---TTT--EEEEE-TT--EEEEEE-TT.TTHHHHHHHHHHHTT-EE-XXXXX. CS
                         CbiG_N  4 relfkeydalvfilaaGivvRliapllkdKktDpaVvvvdeagrfvisllsGhlggAnelAeeiaallgaepviTtatd 82
                                   +elf+eyd +++++a+GivvR ++pll+dK+tD +Vv+vd+a + ++++++Gh +gAn+lA  + + lg  p+iTtatd
  gi|116753467|ref|YP_842585.1|  2 EELFREYDMILALMAVGIVVRQVCPLLRDKWTDKPVVAVDSALKTAVPVIGGH-HGANDLALYLFKHLGIYPAITTATD 79
                                   799**************************************************.************************8 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.71
                                    -EEEEE-TT-- CS
                         CbiG_N  37 paVvvvdeagr 47 
                                    p +v+vd++  
  gi|116753467|ref|YP_842585.1| 123 PRIVIVDKDVA 133
                                    55666666543 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 1.2
                                    --EEEEE-T CS
                         CbiG_N  36 DpaVvvvde 44 
                                    +paV+++++
  gi|116753467|ref|YP_842585.1| 228 EPAVLALAQ 236
                                    799999876 PP

>> CbiG_C  Cobalamin synthesis G C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.7   0.3   9.1e-25   8.2e-21       1     115 [.     140     252 ..     140     253 .. 0.97

  Alignments for each domain:
  == domain 1  score: 74.7 bits;  conditional E-value: 9.1e-25
                                    EEEEEEE-SS--HHHHHHHHHHHHHHCT--GGGEEEEEESSCCSHHHHHHHHHHHCTSTEEEE-HHHHHCHHCSCT-CHH CS
                         CbiG_C   1 lvvGiGcrrgtsaeeieeaieealeeaglseeavaalatidlKadepgllelaeklglplktfsaeeLaavevpnpsefv 80 
                                    l++G+G+r+g++a+ei +a+++a +eag + ++v+ +at ++K+  p +  +a+klg+++++++ ++L+a +  +ps + 
  gi|116753467|ref|YP_842585.1| 140 LIAGLGARKGATADEILSAVRSATAEAGRDVSEVRVIATSEIKSCDPEISRAAAKLGVSVVYLPDDALNAQKPLTPSRAS 219
                                    689********************************************************************977999987 PP

                                    HCCCSSS-HHHHHHHHHC.EECSCEEEETTEEEEE CS
                         CbiG_C  81 kkevGvpsVaEaaAllaaarllvpKqakggvTvAi 115
                                       +G+ +VaE+a l+ a+r+++pK+ +g+vTvA+
  gi|116753467|ref|YP_842585.1| 220 --MLGLSGVAEPAVLALAQRMILPKKVYGRVTVAL 252
                                    ..6*******************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 2112.22
//
Query:       gi|116753468|ref|YP_842586.1|  [L=245]
Description: precorrin-4 C11-methyltransferase [Methanosaeta thermophila PT]
Scores for complete 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-50  171.8   0.2    2.2e-50  171.5   0.2    1.1  1  TP_methylase     Tetrapyrrole (Corrin/Porphyrin) Methylases
  ------ inclusion threshold ------
      0.072   13.5   0.0       0.16   12.4   0.0    1.8  1  Radical_SAM      Radical SAM superfamily
       0.11   12.6   0.0        0.2   11.8   0.0    1.4  1  FPRL1_inhibitor  Formyl peptide receptor-like 1 inhibitory pr
       0.24   10.2   0.0       0.34    9.7   0.0    1.1  1  VipB             Type VI secretion protein, EvpB/VC_A0108, ta


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 !  171.5   0.2     5e-54   2.2e-50       1     212 [.      11     210 ..      11     211 .. 0.95

  Alignments for each domain:
  == domain 1  score: 171.5 bits;  conditional E-value: 5e-54
                   TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealragk 80 
                                    k+y+VG+GpGdp+l+T++++r+lk+ad+v++ +s++ + ll+ l+          + +++++   eei +++   +ra k
  gi|116753468|ref|YP_842586.1|  11 KVYFVGAGPGDPDLITLKGYRLLKEADLVIYTGSLVNRDLLRGLRS---------ELVDSSNLSLEEITDRILSSVRASK 81 
                                    79*******************************9999999888875.........678889999**************** PP

                   TP_methylase  81 dVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl..lpglakeeereleall 158
                                    +Vv+l+sGDP++yg+  e ++ l++  +g+evev+PGvssl aaaa+l++ lt +g++ s++  +p+ a+ e++e+++l+
  gi|116753468|ref|YP_842586.1|  82 KVVRLHSGDPSLYGAILEQMRPLEE--NGVEVEVVPGVSSLFAAAAALKTQLTLKGVSESLIitRPSGATLERDEIRELS 159
                                    *************************..*************************************9*************** PP

                   TP_methylase 159 angdtlvllkaprklaelaelLkealyddttpvavveragtedervvrgtleel 212
                                    ++g t++++ + +++ e++    +  ++ +tpvavv +a+++d++v +gtl+++
  gi|116753468|ref|YP_842586.1| 160 QHGSTMAVFLGAERIREIVSSV-KL-PA-DTPVAVVYHASWPDQQVLTGTLGDI 210
                                    *******************999.44.46.55*********************98 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.5e-05      0.16      24      82 ..      59     113 ..      40     228 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.5e-05
                                    HHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  24 grgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritv 82 
                                    +++ +ls+eei + + +  ++  +k+v l++g+p+ly  + e ++ l ++   g+++ v
  gi|116753468|ref|YP_842586.1|  59 VDSSNLSLEEITDRILSS-VRASKKVVRLHSGDPSLYGAILEQMRPLEEN---GVEVEV 113
                                    567899*********999.8988**************7777776666666...333333 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 ?   11.8   0.0   4.5e-05       0.2      55      94 ..      74     114 ..      54     119 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.5e-05
                FPRL1_inhibitor  55 lsqgdvkkavvrikdggprdyyt.fdltrpleenrknikvv 94 
                                    ls     k vvr++ g p  y + ++  rpleen  +++vv
  gi|116753468|ref|YP_842586.1|  74 LSSVRASKKVVRLHSGDPSLYGAiLEQMRPLEENGVEVEVV 114
                                    677778899**********99752799********999998 PP

>> VipB  Type VI secretion protein, EvpB/VC_A0108, tail sheath
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   7.6e-05      0.34     375     416 ..     100     141 ..      92     144 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 7.6e-05
                           VipB 375 aryPLreakveVeevpgkpGayraklslrPhfqleeltvslr 416
                                      +PL+e  veVe vpg    ++a++ l+ ++ l++++ sl 
  gi|116753468|ref|YP_842586.1| 100 QMRPLEENGVEVEVVPGVSSLFAAAAALKTQLTLKGVSESLI 141
                                    569*********************************999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); 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:                         4  (0.000223102); expected 0.2 (1e-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 0.22s 00:00:00.63 Elapsed: 00:00:00.36
# Mc/sec: 2052.85
//
Query:       gi|116753469|ref|YP_842587.1|  [L=202]
Description: cobalt-precorrin-2 C(20)-methyltransferase [Methanosaeta thermophila PT]
Scores for 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-31  107.8   0.0    3.6e-30  105.5   0.0    1.8  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.5   0.0     2e-34   3.6e-30       1     209 [.       1     186 [.       1     188 [. 0.91

  Alignments for each domain:
  == domain 1  score: 105.5 bits;  conditional E-value: 2e-34
                   TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealragk 80 
                                    +l++V +GpGdp llT+rA+++l++++ v++++++a e++++++++e  l +pm+ + e+lee +e +a+++a ++++  
  gi|116753469|ref|YP_842587.1|   1 MLVGVSLGPGDPGLLTLRAIEVLRASEKVFAPGELAAELARPYCEPE-ILDFPMTDDLERLEEIWERNADTVASYAEKCL 79 
                                    699******************************88********9887.9*****************************97 PP

                   TP_methylase  81 dVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvllpglakeeereleallan 160
                                       +++ GD + ++t+s+l + l++r++gie++++PGv ++ aaaar+gi  + ++ v++ +                 +
  gi|116753469|ref|YP_842587.1|  80 -TSFACLGDVNTFSTFSHLRRVLMRRHPGIEIDTVPGVGIIPAAAARFGIGFERSFLVSDGS-----------------E 141
                                    .9*************************************************99776666666.................2 PP

                   TP_methylase 161 gdtlvllkaprklaelaelLkealyddttpvavveragtedervvrgtl 209
                                    +d ++ lka+r +a++a++L e+  +  t+ ++++r+ t+de + rg++
  gi|116753469|ref|YP_842587.1| 142 PDAVLRLKATR-PASIAAELHEE--G-YTEFILGSRLYTPDEIILRGKM 186
                                    36677787787.99999999999..5.4599999999999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.36
# Mc/sec: 1660.64
//
Query:       gi|116753470|ref|YP_842588.1|  [L=171]
Description: precorrin-8W decarboxylase [Methanosaeta thermophila PT]
Scores for complete 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-06   25.8   0.0    7.9e-06   25.4   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
    6.2e-06   26.8   0.0    8.7e-06   26.4   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    1.1e-05   25.2   0.0    1.7e-05   24.7   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    1.3e-05   25.8   0.0    2.2e-05   25.0   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    0.00021   20.8   0.1    0.00029   20.3   0.1    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0018   18.1   0.0     0.0026   17.6   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
     0.0019   18.0   0.0     0.0027   17.5   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
     0.0033   17.0   0.0     0.0047   16.5   0.0    1.2  1  MTS              Methyltransferase small domain
     0.0095   15.6   0.0      0.013   15.1   0.0    1.2  1  Cons_hypoth95    Conserved hypothetical protein 95
  ------ inclusion threshold ------
      0.028   14.6   0.0      0.046   13.9   0.0    1.3  1  CRS1_YhbY        CRS1 / YhbY (CRM) domain
      0.038   14.7   0.0      0.081   13.7   0.0    1.7  1  Methyltransf_12  Methyltransferase domain
      0.084   12.4   0.0       0.13   11.8   0.0    1.2  1  DOT1             Histone methylation protein DOT1
       0.13   11.8   0.0        0.2   11.2   0.0    1.2  1  NodS             Nodulation protein S (NodS)
       0.14   12.1   0.0        0.2   11.6   0.0    1.2  1  Methyltransf_32  Methyltransferase domain


Domain annotation for each model (and alignments):
>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   6.2e-09   7.9e-06      46     100 ..       8      61 ..       5      74 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 6.2e-09
                                    HHHHHHHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHH CS
                           CMAS  46 AqlaKldlileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqakl 100
                                     q + ++++++kl++ +Gm  LdiGcG G++   a++ry  ++ g+   +e  + 
  gi|116753470|ref|YP_842588.1|   8 TQPENIQIAMGKLDIGKGMLFLDIGCGSGAVS-LAASRYTDRIYGIDRRHEAVEA 61 
                                    688999***********************976.5789999999999766666555 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   6.8e-09   8.7e-06       2      59 ..      29      80 ..      28     111 .. 0.80

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 6.8e-09
                                   EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBS CS
                Methyltransf_25  2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlp 59
                                   Ld+GcG+G ++la+++     +++g+D  +e++ea r+ +    +  +f++g+a d+ 
  gi|116753470|ref|YP_842588.1| 29 LDIGCGSGAVSLAASRYT--DRIYGIDRRHEAVEASRSLV----PGGNFICGEAVDVI 80
                                   9**************996..9****************999....77888888886643 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   1.3e-08   1.7e-05       2      46 ..      23      64 ..      22      71 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.3e-08
                Methyltransf_31  2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielAre 46
                                    kg+ +lD+GCG+G+ ++++ +      +++GiD+  ea+e +r+
  gi|116753470|ref|YP_842588.1| 23 GKGMLFLDIGCGSGAVSLAASRY---TDRIYGIDRRHEAVEASRS 64
                                   688999*************9954...457************9986 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   1.7e-08   2.2e-05       1      58 [.      29      84 ..      29      94 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.7e-08
                                   EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCT.S.S- CS
                Methyltransf_11  1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaekl.p.fe 58
                                   Ld+GcG+G+++ a  ++  r++g+D  +e+++++++ +++ +    f++++a ++ p ++
  gi|116753470|ref|YP_842588.1| 29 LDIGCGSGAVSLAASRYTDRIYGIDRRHEAVEASRSLVPGGN----FICGEAVDViPgLP 84
                                   8**************999**************9999999876....58888877434355 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   2.3e-07   0.00029     163     201 ..      26      63 ..      15      67 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.3e-07
                           PrmA 163 eevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvak 201
                                      +lD+G+GSG  ++aa++  +++++++D  + Av++++
  gi|116753470|ref|YP_842588.1|  26 MLFLDIGCGSGAVSLAASRY-TDRIYGIDRRHEAVEASR 63 
                                    5679**************97.689************997 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0     2e-06    0.0026      26      61 ..      28      63 ..      12     118 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2e-06
                Methyltransf_23 26 vLdiGcGtGillevlrengfsvtgvDlspeaveiae 61
                                    LdiGcG+G ++  ++++   ++g+D + eave  +
  gi|116753470|ref|YP_842588.1| 28 FLDIGCGSGAVSLAASRYTDRIYGIDRRHEAVEASR 63
                                   69***********9999999********99999765 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   2.1e-06    0.0027      55     116 ..       6      64 ..       1      70 [. 0.85

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.1e-06
                                    EE--HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHH CS
                           PCMT  55 tiSaphmvalalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakr 116
                                    t  +p  + +a+  l++ kg+  L++G+GsG  +   +r+  +   + +i+r +e ve+++ 
  gi|116753470|ref|YP_842588.1|   6 TATQPENIQIAMGKLDIGKGMLFLDIGCGSGAVSLAASRYTDR---IYGIDRRHEAVEASRS 64 
                                    6778999999999******************888888887765...559**99999999876 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   3.7e-06    0.0047      35      73 ..      28      64 ..      14      73 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.7e-06
                                   EEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHH CS
                            MTS 35 vlDlGcGaGvlgaalakespeaevtlvdvdarAlesake 73
                                    lD+GcG G++++a+ + +++  +  +d  ++A+e+++ 
  gi|116753470|ref|YP_842588.1| 28 FLDIGCGSGAVSLAASRYTDR--IYGIDRRHEAVEASRS 64
                                   69***********99998877..9***********9985 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.1e-05     0.013      40      79 ..      23      61 ..      12      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.1e-05
                                   HCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHH CS
                  Cons_hypoth95 40 iegarvLDlfaGsGalglEAlSRgakkavlvekdkeavki 79
                                   ++g  +LD+ +GsGa++l A+SR+ ++++ +++ +eav++
  gi|116753470|ref|YP_842588.1| 23 GKGMLFLDIGCGSGAVSL-AASRYTDRIYGIDRRHEAVEA 61
                                   567789************.88****************986 PP

>> CRS1_YhbY  CRS1 / YhbY (CRM) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   3.6e-05     0.046      17      50 ..     113     147 ..      99     157 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.6e-05
                      CRS1_YhbY  17 kpkvkiGkaGvtkevvdeiheklkteelvkvkc.e 50 
                                    + +v + + G+t ++v+++++++  ee++ +++ +
  gi|116753470|ref|YP_842588.1| 113 RLVVDVARIGMTSKIVRLVEDHFTLEEVIQINIfR 147
                                    5578999************************9964 PP

>> Methyltransf_12  Methyltransferase 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     0.081       1      36 [.      29      62 ..      29     114 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.3e-05
                Methyltransf_12  1 LeiGcGtGsllralleklpdieytgvDispsaieda 36
                                   L+iGcG+G+++ a  ++  + +++g+D   +a+e+ 
  gi|116753470|ref|YP_842588.1| 29 LDIGCGSGAVSLAASRY--TDRIYGIDRRHEAVEAS 62
                                   8*************999..********999999444 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0    0.0001      0.13      26      73 ..       8      53 ..       6      65 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0001
                                   B-HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHH--SEEEEEE CS
                           DOT1 26 llpeflsevldkvnlkkedvFvDLGSGvGnvvlqaalevgcklsvGvE 73
                                   ++pe ++  + k++++k  +F+D+G G G v l a+ ++     +G++
  gi|116753470|ref|YP_842588.1|  8 TQPENIQIAMGKLDIGKGMLFLDIGCGSGAVSLAASRYTD--RIYGID 53
                                   56788899999******************99988877654..346665 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00016       0.2      47      88 ..      28      69 ..      10      81 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00016
                           NodS 47 alevGcaaGalterlapyckrltvvdvveeaiararervkes 88
                                    l++Gc +Ga++   + y++r+  +d  +ea++ +r  v   
  gi|116753470|ref|YP_842588.1| 28 FLDIGCGSGAVSLAASRYTDRIYGIDRRHEAVEASRSLVPGG 69
                                   599******************************999877665 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00016       0.2      29      69 ..      28      64 ..      13      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00016
                Methyltransf_32 29 vvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaek 69
                                    +D+G+G g  s + +     y  +++gid ++e ve+++ 
  gi|116753470|ref|YP_842588.1| 28 FLDIGCGSGAVSLAASR----YTDRIYGIDRRHEAVEASRS 64
                                   68*******88887777....999************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       220  (0.0122706); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1236.94
//
Query:       gi|116753471|ref|YP_842589.1|  [L=1113]
Description: S-layer-like domain-containing protein [Methanosaeta thermophila PT]
Scores for 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-193  639.3  13.4    3.7e-98  327.7   2.4    2.2  2  S-layer          S-layer protein
    1.2e-08   34.9   7.0    3.9e-05   23.6   0.1    4.1  4  CarbopepD_reg_2  CarboxypepD_reg-like domain
    5.1e-08   32.7   6.9     0.0037   17.1   0.0    4.7  5  PEGA             PEGA domain
     0.0019   18.1   0.6        1.3    8.9   0.1    3.6  3  tRNA-synt_1c_C   tRNA synthetases class I (E and Q), anti-cod
     0.0037   17.1   1.5        2.3    8.2   0.0    3.9  3  DUF1533          Protein of unknown function (DUF1533)
     0.0045   17.2  17.9      0.005   17.1   2.0    4.6  5  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
  ------ inclusion threshold ------
      0.026   14.5   0.1       0.23   11.4   0.0    2.6  2  Y_Y_Y            Y_Y_Y domain
       0.12   12.6   0.0        9.1    6.5   0.0    3.2  2  PrcB_C           PrcB C-terminal
        1.4    9.2   6.1        3.3    8.0   0.0    3.7  4  DUF4198          Domain of unknown function (DUF4198)


Domain annotation for each model (and alignments):
>> S-layer  S-layer protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  317.1   3.5   3.1e-98   6.3e-95       6     258 .]     274     528 ..     270     528 .. 0.97
   2 !  327.7   2.4  1.8e-101   3.7e-98       4     258 .]     553     806 ..     550     806 .. 0.97

  Alignments for each domain:
  == domain 1  score: 317.1 bits;  conditional E-value: 3.1e-98
                        S-layer   6 eseeltwtasnFsgfyydiddglssEsltlele...sksdrtieegelvYsttpvekefefeewgsYevigflaekYfag 82 
                                    ++e++twt+++Fsgf+yd+dd++++E+lt++l+      +r i++g+++Y++ +++ +fef++wg+Y+v+gf+aekYfag
  gi|116753471|ref|YP_842589.1| 274 MPETYTWTPQTFSGFFYDLDDMVGTEKLTVSLSrsgGGYNRAIDTGNIRYTSDVQDISFEFDDWGKYQVLGFMAEKYFAG 353
                                    6799***************************99655339***************************************** PP

                        S-layer  83 ydnsaetsddvsllsdekLskvlidedeektlksgssleLeegYeleikqiDvdgdkvwleLtkdgeevdskvissska. 161
                                    y+ ++ + ddvsl+++++L++vlid+d+ekt++sgs+l LeegYel+ik+iD++g+kv l L+kdg+e+dskvis+++  
  gi|116753471|ref|YP_842589.1| 354 YSGTE-VVDDVSLINENQLRRVLIDSDDEKTITSGSVLPLEEGYELRIKEIDINGNKVHLALAKDGDEIDSKVISPDDLk 432
                                    *8888.899*******************************************************************8879 PP

                        S-layer 162 dstyvyekdlgdeddvviiavhvdevfrgtedslvviegifqisddvleieegdefgkmevksvseneiemenddsitLs 241
                                    + ty+ye+++g+ +dv++i+ hv++vf g+e+slv+i+g+fqisd++ ++eegd+++kmev svs++ ie+en+ds+tL+
  gi|116753471|ref|YP_842589.1| 433 SATYMYEEEIGG-KDVPLIMAHVSNVFAGAESSLVTIDGLFQISDTYASVEEGDKYDKMEVVSVSDSGIELENEDSVTLR 511
                                    9***********.77***************************************************************** PP

                        S-layer 242 rdktieimddlkfkvaD 258
                                    +++ti++m+ + ++vaD
  gi|116753471|ref|YP_842589.1| 512 KGRTIQLMGGVGLQVAD 528
                                    ****************8 PP

  == domain 2  score: 327.7 bits;  conditional E-value: 1.8e-101
                        S-layer   4 eeeseeltwtasnFsgfyydiddglssEsltlelesksdrtieegelvYsttpvekefefeewgsYevigflaekYfagy 83 
                                     ++ +++twt+ nF+gfyydid+++++E+l+++    s+++i++g+l+Y+t+p+++efef+ wg+Y+vigf+a+kYfagy
  gi|116753471|ref|YP_842589.1| 553 PNKVDSFTWTPYNFEGFYYDIDEDIGTEKLVARF---SGSKIDDGDLKYETSPQPVEFEFNGWGKYDVIGFMADKYFAGY 629
                                    5677899*************************95...689**************************************** PP

                        S-layer  84 dnsaetsddvsllsdekLskvlidedeektlksgssleLeegYeleikqiDvdgdkvwleLtkdgeevdskvissska.. 161
                                    +n++  +d+ s+++d++L+kvlid+dee+t++sgs+l Le+gYel+ik++D+dg+kvwl+Ltkdg+evdskv+++ +   
  gi|116753471|ref|YP_842589.1| 630 NNETLFTDEFSIINDGELRKVLIDSDEESTISSGSVLPLEDGYELQIKEVDLDGNKVWLSLTKDGDEVDSKVVTPVSGdl 709
                                    ****9*********************************************************************987789 PP

                        S-layer 162 .dstyvyekdlgdeddvviiavhvdevfrgtedslvviegifqisddvleieegdefgkmevksvseneiemenddsitL 240
                                      sty+y+  +g+ +dv+iia h+++vfrg+e +l++++gifq+sd++ ++eegd++gkmev+s+s++ i+m+nd si+L
  gi|116753471|ref|YP_842589.1| 710 eASTYTYKVRIGS-EDVPIIAAHISNVFRGREADLATVDGIFQVSDTPESVEEGDKHGKMEVESLSDDGITMKNDGSISL 788
                                    9***********9.78**************************************************************** PP

                        S-layer 241 srdktieimddlkfkvaD 258
                                     r+k++eim++l+++vaD
  gi|116753471|ref|YP_842589.1| 789 GRGKDVEIMGNLRLRVAD 806
                                    *****************8 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.86   1.7e+03      45      71 ..      55      81 ..      46      94 .. 0.72
   2 ?   -4.0   0.2       7.7   1.5e+04      17      32 ..     220     235 ..     214     245 .. 0.72
   3 !   12.4   0.0   5.8e-05      0.12       8      71 ..     843     905 ..     839     923 .. 0.79
   4 !   23.6   0.1   1.9e-08   3.9e-05      10      64 ..     931     984 ..     926     999 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.86
                CarbopepD_reg_2 45 kytLvvsyvGyktqekkvtvskektld 71
                                     t++++ +G +t++  v++ + +t+ 
  gi|116753471|ref|YP_842589.1| 55 GITVTFKRLGNNTAKTPVSLGSRNTTV 81
                                   479999999****99999998776543 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 7.7
                CarbopepD_reg_2  17 atVyvkgtkkgtvTde 32 
                                    a+++ ++ ++  vT+e
  gi|116753471|ref|YP_842589.1| 220 ANISAENLTAENVTEE 235
                                    7777777777777765 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 5.8e-05
                CarbopepD_reg_2   8 ketkeplpgatVyvkgtkkgtvTdenGnFelknlpagkytLvvsyvGyktqekkvtvskektld 71 
                                    +++++++ ga+V+v g + gt Td+ G  + +   ag ++++++  Gy+ ++ ++ v +e +l 
  gi|116753471|ref|YP_842589.1| 843 TSGGQAVSGAKVLVDGREIGT-TDAGGMIRYTPERAGSVQVQAKLSGYEDASGTLLVRTEAELR 905
                                    45689**************97.9*****99999999***************9999998765543 PP

  == domain 4  score: 23.6 bits;  conditional E-value: 1.9e-08
                CarbopepD_reg_2  10 tkeplpgatVyvkgtkkgtvTdenGnFelknlpagkytLvvsyvGyktqekkvtv 64 
                                      ++++ga+V++ +  +g vTd++G+ +++  + g++t+ v++ Gy+ ++k+v+v
  gi|116753471|ref|YP_842589.1| 931 ATQAIAGANVSIDNMPAG-VTDSKGSVSVSINDTGDHTISVEAAGYDRATKSVKV 984
                                    5689********776665.8*********************************98 PP

>> PEGA  PEGA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.2      0.89   1.8e+03       8      29 ..      51      74 ..      48      81 .. 0.72
   2 ?   -2.2   0.0       2.1   4.1e+03      43      65 ..     670     691 ..     669     693 .. 0.83
   3 !   15.1   0.1   7.9e-06     0.016      11      61 ..     850     905 ..     842     910 .. 0.84
   4 !   17.1   0.0   1.8e-06    0.0037      11      54 ..     936     984 ..     934     990 .. 0.92
   5 ?   -2.0   0.0       1.7   3.5e+03      46      65 ..    1031    1050 ..    1013    1054 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.89
                           PEGA  8 SnpeGatVyid..GkylGkTPvtl 29
                                   ++ +G tV++   G+++ kTPv+l
  gi|116753471|ref|YP_842589.1| 51 TSSSGITVTFKrlGNNTAKTPVSL 74
                                   566677777643378888***987 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.1
                           PEGA  43 eGYedlektvtvtagetvklnlt 65 
                                    +GYe   k+v+++ g +v+l+lt
  gi|116753471|ref|YP_842589.1| 670 DGYELQIKEVDLD-GNKVWLSLT 691
                                    6999999999999.888888876 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 7.9e-06
                           PEGA  11 eGatVyidGkylGkTP....vtls.leaGnyslrvekeGYedlektvtvtagetvk 61 
                                    +Ga+V +dG+++G T     ++++   aG+ +++ ++ GYed++ t  v+ + +++
  gi|116753471|ref|YP_842589.1| 850 SGAKVLVDGREIGTTDaggmIRYTpERAGSVQVQAKLSGYEDASGTLLVRTEAELR 905
                                    7************998333356666789*******************999777665 PP

  == domain 4  score: 17.1 bits;  conditional E-value: 1.8e-06
                           PEGA  11 eGatVyidGkylG....kTPvtls.leaGnyslrvekeGYedlektvtv 54 
                                    +Ga+V+id +  G    k  v++s  ++G++++ ve+ GY  ++k v+v
  gi|116753471|ref|YP_842589.1| 936 AGANVSIDNMPAGvtdsKGSVSVSiNDTGDHTISVEAAGYDRATKSVKV 984
                                    69***********77777789***999*******************998 PP

  == domain 5  score: -2.0 bits;  conditional E-value: 1.7
                           PEGA   46 edlektvtvtagetvklnlt 65  
                                      + +k +tv +get k++ +
  gi|116753471|ref|YP_842589.1| 1031 VTGNKSITVAPGETEKVTFE 1050
                                     56688999999999888765 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 !    8.9   0.1   0.00063       1.3      46      99 ..     372     423 ..     366     435 .. 0.89
   2 ?    1.3   0.0      0.14   2.8e+02      40      75 ..     491     527 ..     465     561 .. 0.80
   3 ?    3.3   0.0     0.033        65      46      99 ..     648     699 ..     639     716 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00063
                 tRNA-synt_1c_C  46 keiyiereDakrlkpgeevrLkelynikveevekdesgevtelkleydgeslee 99 
                                    ++++i+ +D k+++ g+ + L e+y ++++e+  d +g+ ++l l  dg+++++
  gi|116753471|ref|YP_842589.1| 372 RRVLIDSDDEKTITSGSVLPLEEGYELRIKEI--DINGNKVHLALAKDGDEIDS 423
                                    689*****************************..78999999999999888754 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.14
                 tRNA-synt_1c_C  40 rkvpfsk.eiyiereDakrlkpgeevrLkelynikve 75 
                                      v +s+  i +e+eD  +l +g++++L++++ ++v 
  gi|116753471|ref|YP_842589.1| 491 EVVSVSDsGIELENEDSVTLRKGRTIQLMGGVGLQVA 527
                                    455566337999*****************98877775 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.033
                 tRNA-synt_1c_C  46 keiyiereDakrlkpgeevrLkelynikveevekdesgevtelkleydgeslee 99 
                                    ++++i+ +   +++ g+ + L ++y ++++ev  d +g+ + l+l+ dg+++++
  gi|116753471|ref|YP_842589.1| 648 RKVLIDSDEESTISSGSVLPLEDGYELQIKEV--DLDGNKVWLSLTKDGDEVDS 699
                                    689*****************************..56899999899999988844 PP

>> DUF1533  Protein of unknown function (DUF1533)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1     0.028        55       4      27 ..     396     423 ..     393     436 .. 0.75
   2 ?    1.3   0.0      0.17   3.3e+02       4      24 ..     672     696 ..     670     709 .. 0.79
   3 !    8.2   0.0    0.0011       2.3      37      57 ..     959     979 ..     956     982 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.028
                        DUF1533   4 wrnaIsevtvNGkkl....ennkyslss 27 
                                    +  +I+e+ +NG k     +++ ++++s
  gi|116753471|ref|YP_842589.1| 396 YELRIKEIDINGNKVhlalAKDGDEIDS 423
                                    7889*********987777555555554 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.17
                        DUF1533   4 wrnaIsevtvNGkkl....ennkys 24 
                                    +  +I+ev ++G k     +++ ++
  gi|116753471|ref|YP_842589.1| 672 YELQIKEVDLDGNKVwlslTKDGDE 696
                                    6789********9987766555555 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0011
                        DUF1533  37 vfnkaGentIvIkakGYeDvt 57 
                                    ++n  G++tI + a+GY  +t
  gi|116753471|ref|YP_842589.1| 959 SINDTGDHTISVEAAGYDRAT 979
                                    58999************8666 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.2       4.5   8.9e+03      52      72 ..      58      77 ..      49      97 .. 0.55
   2 ?   -3.4   0.0       6.3   1.3e+04      52      74 ..     493     515 ..     492     518 .. 0.81
   3 !    9.5   0.4    0.0006       1.2       7      70 ..     843     899 ..     838     911 .. 0.79
   4 !   17.1   2.0   2.5e-06     0.005      10      69 ..     931     984 ..     920     997 .. 0.82
   5 ?   -2.3   0.0       2.7   5.5e+03      63      80 ..    1034    1050 ..    1006    1052 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.5
                CarboxypepD_reg 52 vtvsapGyatatreevtltag 72
                                   vt+ + G  ta    v+l   
  gi|116753471|ref|YP_842589.1| 58 VTFKRLGNNTAKT-PVSLGSR 77
                                   4444444444443.2444433 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 6.3
                CarboxypepD_reg  52 vtvsapGyatatreevtltagqt 74 
                                    v vs +G +  +  +vtl++g+t
  gi|116753471|ref|YP_842589.1| 493 VSVSDSGIELENEDSVTLRKGRT 515
                                    77888899999999999999987 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0006
                CarboxypepD_reg   7 tdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtlt 70 
                                    t + g++++ga+V v       +   ttda G  r +   +g+ +v++  +Gy+ a+ + + ++
  gi|116753471|ref|YP_842589.1| 843 T-SGGQAVSGAKVLVD-----GREIGTTDAGGMIRYTPERAGSVQVQAKLSGYEDASGT-LLVR 899
                                    3.689***********.....5666789****999987888*************99975.4444 PP

  == domain 4  score: 17.1 bits;  conditional E-value: 2.5e-06
                CarboxypepD_reg  10 sgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtl 69 
                                      ++iaga+V++ n         +td++G+ +++   +g++++ v+a+Gy+ at++ v +
  gi|116753471|ref|YP_842589.1| 931 ATQAIAGANVSIDN-----MPAGVTDSKGSVSVSINDTGDHTISVEAAGYDRATKS-VKV 984
                                    4689*********4.....66679**********9999****************75.554 PP

  == domain 5  score: -2.3 bits;  conditional E-value: 2.7
                CarboxypepD_reg   63 treevtltagqtttldit 80  
                                     + +++t+++g+t+ ++++
  gi|116753471|ref|YP_842589.1| 1034 N-KSITVAPGETEKVTFE 1050
                                     3.5699999999998875 PP

>> Y_Y_Y  Y_Y_Y domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.9   3.7e+03      26      48 ..     952     973 ..     949     981 .. 0.83
   2 ?   11.4   0.0   0.00012      0.23      27      48 ..    1044    1066 ..    1031    1071 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.9
                                    STS.EEEEES--SEEEEEEEEEE CS
                          Y_Y_Y  26 dysqeasytnlppGdYtlkVkak 48 
                                    + + ++s + +  Gd t+ V+a 
  gi|116753471|ref|YP_842589.1| 952 SKG-SVSVSINDTGDHTISVEAA 973
                                    445.899999********99985 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00012
                                     TS..EEEEES--SEEEEEEEEEE CS
                          Y_Y_Y   27 ysq.easytnlppGdYtlkVkak 48  
                                       + +++y++++pG Yt++V ++
  gi|116753471|ref|YP_842589.1| 1044 TEKvTFEYRPKEPGVYTFEVDGI 1066
                                     33379**************9765 PP

>> PrcB_C  PrcB C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.12   2.3e+02      13      34 ..     394     415 ..     393     428 .. 0.80
   2 ?    6.5   0.0    0.0046       9.1      13      52 ..     670     705 ..     668     706 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.12
                         PrcB_C  13 gGYsievdkvyetenaiyvktt 34 
                                    +GY ++++++  ++n++++ + 
  gi|116753471|ref|YP_842589.1| 394 EGYELRIKEIDINGNKVHLALA 415
                                    7**********99999998765 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0046
                         PrcB_C  13 gGYsievdkvyetenaiyvkttllgPepgeevtqaltyPy 52 
                                    +GY +++++v +++n++ + +t    ++g+ev  ++ +P+
  gi|116753471|ref|YP_842589.1| 670 DGYELQIKEVDLDGNKVWLSLT----KDGDEVDSKVVTPV 705
                                    7********************9....78888888777775 PP

>> DUF4198  Domain of unknown function (DUF4198)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.2      0.91   1.8e+03      18     148 ..      33     186 ..      23     221 .. 0.50
   2 ?    8.0   0.0    0.0017       3.3     145     210 ..     830     885 ..     824     888 .. 0.79
   3 ?    0.4   0.0      0.35   6.9e+02     163     210 ..     934     971 ..     895     975 .. 0.54
   4 ?    0.2   0.1       0.4   7.9e+02     129     177 ..     998    1050 ..     979    1071 .. 0.64

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.91
                        DUF4198  18 gewvtvdlafghdpfead..heplkle.klkvlapdg.e.ktdlgkylstfdvallkpekegtyklaa..akkpgdwkey 90 
                                    +++vt  +a  +d f  d     +  +  +k l+ +  +  ++lg++ +t+  +  ++ek  t  ++a  + +p+  +e+
  gi|116753471|ref|YP_842589.1|  33 EQSVTSAAALQDDFFSTDtsSSGI--TvTFKRLGNNTaKtPVSLGSRNTTVSTVDRDAEKNATSGANAttEGRPAGASEN 110
                                    456666666666555555222222..223433333333225555555555555555555544444444223335555554 PP

                        DUF4198  91 gdpk..............lakevp...aeaaelkvvkysqyaktfvtvgkpse.twdkpv...glglEivPlthpydlk 148
                                    +  +              +        a a+++++v ++  ++  +t++++se +++ ++   g  + + ++  p +l 
  gi|116753471|ref|YP_842589.1| 111 VSSAveqnrtaqsaapsmAI---AsgaAPASNVSAVATEGLTEGNLTSNATSEsGASNATaapGISTNLTAVVTPEGLA 186
                                    43333333443333332211...12213333355666666666666666554432222222224445555555555554 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0017
                        DUF4198 145 ydlkageelevqvlldGkPlagaeveveyggtryrdapdeikvktdadGvvtftlpkaGlwlleae 210
                                    ++  +g ++ +qv+  G+ ++ga+v v  +      + +    +tda G + +t+++aG   ++a 
  gi|116753471|ref|YP_842589.1| 830 TEAIVGKPIMIQVTSGGQAVSGAKVLVDGR------EIG----TTDAGGMIRYTPERAGSVQVQAK 885
                                    55668999******************9532......223....79999999999999997766665 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.35
                        DUF4198 163 PlagaeveveyggtryrdapdeikvktdadGvvtftlpkaGlwlleae 210
                                      aga v+         + p      td++G v++ +   G   +++e
  gi|116753471|ref|YP_842589.1| 934 AIAGANVS-------IDNMPAG---VTDSKGSVSVSINDTGDHTISVE 971
                                    33333333.......3444444...67777777777776665555554 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 0.4
                        DUF4198  129 dkpvglglEivPlthpydlkageelevqvlldGkPlagaeveveyggt.....r 177 
                                     d+ +g++l iv+  + ++ ka ++ ++q+l++     + +++v +g+t     +
  gi|116753471|ref|YP_842589.1|  998 DAIAGKPLKIVAEVQ-NTGKAPDSRQLQLLVNKNVTGNKSITVAPGETekvtfE 1050
                                     455677777777333.34467777777777776666677777777766333222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        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):               9  [number of targets reported over threshold]
# CPU time: 0.75u 0.27s 00:00:01.02 Elapsed: 00:00:00.44
# Mc/sec: 7676.38
//
Query:       gi|116753472|ref|YP_842590.1|  [L=295]
Description: leucine-rich repeat-containing protein [Methanosaeta thermophila PT]
Scores for complete 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  136.3  28.8    1.6e-07   31.3   0.3   10.2 10  LRV       Leucine rich repeat variant
    3.1e-06   27.0  23.3        1.3    9.5   0.0    9.0 10  HEAT      HEAT repeat
    0.00054   19.5   7.0       0.26   10.7   0.1    3.8  4  DUF2336   Uncharacterised protein conserved in bacteria (DUF2
     0.0022   18.3  13.9        1.5    9.2   0.9    6.6  3  HEAT_2    HEAT repeats
  ------ inclusion threshold ------
      0.021   14.5   0.0      0.076   12.7   0.0    1.9  2  DUF4042   Domain of unknown function (DUF4042)
       0.12   12.1   0.0         44    3.9   0.0    3.9  5  DUF4116   Domain of unknown function (DUF4116)


Domain annotation for each model (and alignments):
>> LRV  Leucine rich repeat variant
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.073   2.2e+02      12      23 ..      20      31 ..      16      32 .. 0.85
   2 !   14.7   0.3   9.8e-06     0.029       1      24 [.      35      58 ..      35      60 .. 0.96
   3 !   31.3   0.3   5.2e-11   1.6e-07       3      26 .]      63      86 ..      62      86 .. 0.97
   4 !   12.0   0.1   7.6e-05      0.23       3      25 ..      89     111 ..      89     112 .. 0.96
   5 ?    4.6   0.0     0.016        49       5      22 ..     128     145 ..     126     150 .. 0.81
   6 !   10.1   0.2   0.00029      0.85       2      15 ..     151     164 ..     150     175 .. 0.79
   7 !   23.6   1.3   1.4e-08   4.3e-05       1      24 [.     176     199 ..     176     200 .. 0.96
   8 !   11.0   0.0   0.00015      0.44       1      24 [.     202     225 ..     202     227 .. 0.88
   9 !   28.6   0.1   3.8e-10   1.1e-06       2      23 ..     229     250 ..     228     251 .. 0.94
  10 !   10.2   0.0   0.00028      0.83       3      26 .]     256     279 ..     254     279 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.073
                            LRV 12 dlPpeaLerLah 23
                                   d+ pe+Le+L++
  gi|116753472|ref|YP_842590.1| 20 DTEPEVLEELSR 31
                                   899*******86 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 9.8e-06
                            LRV  1 reVRaaVArrPdlPpeaLerLahD 24
                                   ++VR+aV  +P++P+++L  L++D
  gi|116753472|ref|YP_842590.1| 35 WRVRRAVGWNPSTPVAVLKVLSRD 58
                                   9*********************99 PP

  == domain 3  score: 31.3 bits;  conditional E-value: 5.2e-11
                            LRV  3 VRaaVArrPdlPpeaLerLahDPd 26
                                   VR+aVA +P +P+++Le+La+DPd
  gi|116753472|ref|YP_842590.1| 63 VREAVAGNPKTPLDVLEALARDPD 86
                                   9**********************9 PP

  == domain 4  score: 12.0 bits;  conditional E-value: 7.6e-05
                            LRV   3 VRaaVArrPdlPpeaLerLahDP 25 
                                    VR aVA++ ++P   L +L+ D+
  gi|116753472|ref|YP_842590.1|  89 VRSAVALNTATPDSLLSELSEDE 111
                                    9********************97 PP

  == domain 5  score: 4.6 bits;  conditional E-value: 0.016
                            LRV   5 aaVArrPdlPpeaLerLa 22 
                                    +aVA +P++P   + rL+
  gi|116753472|ref|YP_842590.1| 128 EAVAKNPRTPEHDIIRLS 145
                                    69********98776665 PP

  == domain 6  score: 10.1 bits;  conditional E-value: 0.00029
                            LRV   2 eVRaaVArrPdlPp 15 
                                    +VRaaVA++P  P+
  gi|116753472|ref|YP_842590.1| 151 DVRAAVASNPKVPV 164
                                    7*********9886 PP

  == domain 7  score: 23.6 bits;  conditional E-value: 1.4e-08
                            LRV   1 reVRaaVArrPdlPpeaLerLahD 24 
                                    + VR  VAr+P +Ppe+L+rLa+D
  gi|116753472|ref|YP_842590.1| 176 WLVRFRVARNPVTPPEVLGRLADD 199
                                    89*********************9 PP

  == domain 8  score: 11.0 bits;  conditional E-value: 0.00015
                            LRV   1 reVRaaVArrPdlPpeaLerLahD 24 
                                    ++VR+aVA++   Pp+ L +L+ D
  gi|116753472|ref|YP_842590.1| 202 TDVRVAVAANVKSPPDSLISLSKD 225
                                    58**************99888766 PP

  == domain 9  score: 28.6 bits;  conditional E-value: 3.8e-10
                            LRV   2 eVRaaVArrPdlPpeaLerLah 23 
                                    eVR+aVA++P++P+eaLe+La 
  gi|116753472|ref|YP_842590.1| 229 EVRCAVAENPSTPVEALEALAG 250
                                    8*******************96 PP

  == domain 10  score: 10.2 bits;  conditional E-value: 0.00028
                            LRV   3 VRaaVArrPdlPpeaLerLahDPd 26 
                                    VR+aVA + ++P      L+ DPd
  gi|116753472|ref|YP_842590.1| 256 VREAVAKNRSTPISIMKMLSSDPD 279
                                    *********************998 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       3.2   9.6e+03      10      16 ..      19      25 ..      16      34 .. 0.78
   2 ?    0.9   0.3      0.25   7.4e+02      13      22 ..      34      43 ..      23      44 .. 0.80
   3 ?    2.5   0.1     0.076   2.3e+02       5      21 ..      51      68 ..      48      70 .. 0.80
   4 !    7.5   0.0    0.0019       5.8       4      22 ..      77      95 ..      74      98 .. 0.80
   5 ?    2.9   0.2     0.055   1.6e+02       6      22 ..     142     158 ..     140     159 .. 0.83
   6 !    5.4   0.0    0.0087        26       7      22 ..     169     184 ..     163     185 .. 0.84
   7 ?    1.7   0.1      0.14   4.1e+02       5      24 ..     192     212 ..     190     214 .. 0.74
   8 ?    4.9   0.1     0.013        38       5      23 ..     219     237 ..     217     237 .. 0.87
   9 ?   -0.7   0.0      0.81   2.4e+03      16      23 ..     256     263 ..     253     263 .. 0.84
  10 !    9.5   0.0   0.00043       1.3       5      20 ..     270     286 ..     267     291 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.2
                                   T-SSHHH CS
                           HEAT 10 sDpspeV 16
                                   +D++peV
  gi|116753472|ref|YP_842590.1| 19 HDTEPEV 25
                                   7999999 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.25
                                   SHHHHHHHHH CS
                           HEAT 13 speVReaAak 22
                                   s++VR+a+ +
  gi|116753472|ref|YP_842590.1| 34 SWRVRRAVGW 43
                                   8*****9865 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.076
                                   HHHHH.T-SSHHHHHHHH CS
                           HEAT  5 llkll.sDpspeVReaAa 21
                                   +lk l +D    VRea+a
  gi|116753472|ref|YP_842590.1| 51 VLKVLsRDRVQWVREAVA 68
                                   4566669*********98 PP

  == domain 4  score: 7.5 bits;  conditional E-value: 0.0019
                                   HHHHHHT-SSHHHHHHHHH CS
                           HEAT  4 lllkllsDpspeVReaAak 22
                                   +l  l +Dp+  VR+a+a+
  gi|116753472|ref|YP_842590.1| 77 VLEALARDPDGYVRSAVAL 95
                                   555666***********97 PP

  == domain 5  score: 2.9 bits;  conditional E-value: 0.055
                                    HHHHT-SSHHHHHHHHH CS
                           HEAT   6 lkllsDpspeVReaAak 22 
                                    ++l  ++s +VR+a+a 
  gi|116753472|ref|YP_842590.1| 142 IRLSASQSDDVRAAVAS 158
                                    67778899******997 PP

  == domain 6  score: 5.4 bits;  conditional E-value: 0.0087
                                    HHHT-SSHHHHHHHHH CS
                           HEAT   7 kllsDpspeVReaAak 22 
                                    kl +D+s+ VR  +a+
  gi|116753472|ref|YP_842590.1| 169 KLSRDQSWLVRFRVAR 184
                                    6679*******99886 PP

  == domain 7  score: 1.7 bits;  conditional E-value: 0.14
                                    HHHHH.T-SSHHHHHHHHHHH CS
                           HEAT   5 llkll.sDpspeVReaAakaL 24 
                                    +l  l  D   +VR a+a ++
  gi|116753472|ref|YP_842590.1| 192 VLGRLaDDRITDVRVAVAANV 212
                                    556664778888****99876 PP

  == domain 8  score: 4.9 bits;  conditional E-value: 0.013
                                    HHHHHT-SSHHHHHHHHHH CS
                           HEAT   5 llkllsDpspeVReaAaka 23 
                                    l++l +D   eVR+a+a++
  gi|116753472|ref|YP_842590.1| 219 LISLSKDRMIEVRCAVAEN 237
                                    788899**********985 PP

  == domain 9  score: -0.7 bits;  conditional E-value: 0.81
                                    HHHHHHHH CS
                           HEAT  16 VReaAaka 23 
                                    VRea+ak+
  gi|116753472|ref|YP_842590.1| 256 VREAVAKN 263
                                    9****985 PP

  == domain 10  score: 9.5 bits;  conditional E-value: 0.00043
                                    HHHHH.T-SSHHHHHHH CS
                           HEAT   5 llkll.sDpspeVReaA 20 
                                    ++k+l sDp+p+V +aA
  gi|116753472|ref|YP_842590.1| 270 IMKMLsSDPDPSVQKAA 286
                                    899*99*********99 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 ?    3.7   0.1     0.013        37      26      62 ..      61      97 ..      52     128 .. 0.76
   2 !   10.7   0.1   8.7e-05      0.26      10      62 ..     134     186 ..     130     188 .. 0.88
   3 ?    0.2   0.1      0.14   4.1e+02      28      61 ..     178     211 ..     171     213 .. 0.88
   4 !    6.6   0.0    0.0016       4.8      16      67 ..     218     269 ..     215     275 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.013
                        DUF2336 26 qahllaIAsRpdlsaaVadalaergdeevvrallaNp 62
                                   q  + a+A+ p+ +  V +ala+  d  v  a++ N 
  gi|116753472|ref|YP_842590.1| 61 QWVREAVAGNPKTPLDVLEALARDPDGYVRSAVALNT 97
                                   5579999999999999****99999999999998874 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 8.7e-05
                        DUF2336  10 pvLtdedLvdiartgsqahllaIAsRpdlsaaVadalaergdeevvrallaNp 62 
                                    p+ +++d + + +++s++ ++a+As p++++ +++ l +     v  ++++Np
  gi|116753472|ref|YP_842590.1| 134 PRTPEHDIIRLSASQSDDVRAAVASNPKVPVYITEKLSRDQSWLVRFRVARNP 186
                                    566899*******************************9888777777777776 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.14
                        DUF2336  28 hllaIAsRpdlsaaVadalaergdeevvrallaN 61 
                                     +  +A+ p  +++V   la+ + ++v  a++aN
  gi|116753472|ref|YP_842590.1| 178 VRFRVARNPVTPPEVLGRLADDRITDVRVAVAAN 211
                                    67889999**********************9999 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.0016
                        DUF2336  16 dLvdiartgsqahllaIAsRpdlsaaVadalaergdeevvrallaNpgAels 67 
                                     L+++ +++  + ++a+A+ p+ +++  +ala +    v +a+++N++  +s
  gi|116753472|ref|YP_842590.1| 218 SLISLSKDRMIEVRCAVAENPSTPVEALEALAGHWSFLVREAVAKNRSTPIS 269
                                    68889999999***********************************998887 PP

>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.9   0.00052       1.5      29      52 ..      70      94 ..      10      97 .. 0.67
   2 ?    1.2   0.1      0.16   4.9e+02      33      52 ..     138     157 ..     100     159 .. 0.64
   3 !    5.2   1.8    0.0095        28      12      51 ..     236     286 ..     163     291 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00052
                         HEAT_2 29 np.ealpaLvellededpavRraaa 52
                                   np + l+ L  l++d+d +vR a+a
  gi|116753472|ref|YP_842590.1| 70 NPkTPLDVLEALARDPDGYVRSAVA 94
                                   3313366777777777777777765 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.16
                         HEAT_2  33 lpaLvellededpavRraaa 52 
                                       +++l  +++ +vR+a+a
  gi|116753472|ref|YP_842590.1| 138 EHDIIRLSASQSDDVRAAVA 157
                                    45556666666666666665 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.0095
                         HEAT_2  12 pdpevrraairaLg...........rignpealpaLvellededpavRraa 51 
                                    ++p +  +a++aL+            ++  + + ++  l +d+dp v++aa
  gi|116753472|ref|YP_842590.1| 236 ENPSTPVEALEALAghwsflvreavAKNRSTPISIMKMLSSDPDPSVQKAA 286
                                    556666666666666665555443323333446666666677777777776 PP

>> DUF4042  Domain of unknown function (DUF4042)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.65   1.9e+03      34      63 ..      67      97 ..      61     108 .. 0.76
   2 ?   12.7   0.0   2.5e-05     0.076      21      60 ..     247     286 ..     230     291 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.65
                        DUF4042 34 vlqerkseatLltillkDpspkvRaa.alqv 63
                                   v+ + k+   +l  l++Dp   vR a al++
  gi|116753472|ref|YP_842590.1| 67 VAGNPKTPLDVLEALARDPDGYVRSAvALNT 97
                                   5667788888999999999999996515544 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 2.5e-05
                        DUF4042  21 slygyWhvllpdevlqerkseatLltillkDpspkvRaaa 60 
                                     l g W+ l+ + v+++r++  +++++l +Dp p v  aa
  gi|116753472|ref|YP_842590.1| 247 ALAGHWSFLVREAVAKNRSTPISIMKMLSSDPDPSVQKAA 286
                                    5889******************************998887 PP

>> DUF4116  Domain of unknown function (DUF4116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.8   5.5e+03      30      39 ..      77      86 ..      77     109 .. 0.59
   2 ?    2.5   0.0     0.042   1.2e+02       4      13 ..     125     134 ..     123     145 .. 0.71
   3 ?    3.9   0.0     0.015        44       5      26 ..     152     173 ..     149     177 .. 0.90
   4 ?   -1.1   0.0      0.56   1.7e+03      22      39 ..     221     239 ..     212     245 .. 0.78
   5 ?   -2.2   0.0       1.2   3.5e+03      30      39 ..     256     265 ..     255     277 .. 0.61

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.8
                        DUF4116 30 vlkAvkqngt 39
                                   vl+A+ ++++
  gi|116753472|ref|YP_842590.1| 77 VLEALARDPD 86
                                   3444444443 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.042
                        DUF4116   4 ivleavkkng 13 
                                    iv+eav kn+
  gi|116753472|ref|YP_842590.1| 125 IVMEAVAKNP 134
                                    5666666665 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.015
                        DUF4116   5 vleavkkngsalkylseeLknD 26 
                                    v  av +n+++  y+ e+L++D
  gi|116753472|ref|YP_842590.1| 152 VRAAVASNPKVPVYITEKLSRD 173
                                    567999*************999 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 0.56
                        DUF4116  22 eLknDkei.vlkAvkqngt 39 
                                    +L++D+ i v  Av  n++
  gi|116753472|ref|YP_842590.1| 221 SLSKDRMIeVRCAVAENPS 239
                                    5788998877778887775 PP

  == domain 5  score: -2.2 bits;  conditional E-value: 1.2
                        DUF4116  30 vlkAvkqngt 39 
                                    v +Av +n +
  gi|116753472|ref|YP_842590.1| 256 VREAVAKNRS 265
                                    6778877774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); 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:                         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: 00:00:00.44
# Mc/sec: 2012.23
//
Query:       gi|116753473|ref|YP_842591.1|  [L=305]
Description: hypothetical protein Mthe_0151 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-15   56.7   0.4    8.9e-15   55.1   0.0    1.9  2  acVLRF1          Actinobacteria/chloroflexi VLRF1 release fac
    1.3e-06   28.7   0.0      3e-06   27.6   0.0    1.6  1  baeRF_family10   Bacterial archaeo-eukaryotic release factor 
    0.00028   21.2   0.3     0.0005   20.4   0.0    1.5  1  eRF1_2           eRF1 domain 2
     0.0015   19.0   0.2     0.0022   18.5   0.2    1.2  1  T3SSipB          Type III cell invasion protein SipB
     0.0015   18.6   1.7     0.0016   18.5   0.0    1.8  2  baeRF_family2    Bacterial archaeo-eukaryotic release factor 
     0.0088   16.0   6.9      0.067   13.1   4.9    2.2  2  DASH_Spc19       Spc19
  ------ inclusion threshold ------
       0.01   15.8   6.9      0.024   14.7   6.9    1.6  1  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
       0.02   15.1   5.0       0.02   15.1   5.0    1.8  1  DUF4164          Domain of unknown function (DUF4164)
      0.024   13.5   3.1      0.037   12.9   3.1    1.2  1  DUF812           Protein of unknown function (DUF812)
      0.027   14.5   0.4      0.041   13.9   0.4    1.2  1  DUF1043          Protein of unknown function (DUF1043)
      0.027   14.6   0.3        7.5    6.7   0.3    2.3  2  AcylCoA_dehyd_C  Acyl-CoA dehydrogenase C terminal
        0.1   12.2   0.8       0.14   11.8   0.8    1.2  1  Phage_GPO        Phage capsid scaffolding protein (GPO) serin
        0.1   11.9   0.8       0.15   11.3   0.8    1.1  1  HemX             HemX, putative uroporphyrinogen-III C-methyl
       0.17   10.6   5.9       0.29    9.9   5.9    1.3  1  Tektin           Tektin family
        0.2   12.0   3.8       0.11   12.8   1.5    1.7  1  KxDL             Uncharacterized conserved protein
       0.29   10.3   1.0       0.41    9.9   1.0    1.1  1  TMPIT            TMPIT-like protein
       0.33   11.4   1.3       0.95    9.9   1.3    1.7  1  FlaC_arch        Flagella accessory protein C (FlaC)
       0.51    9.2   6.1       0.77    8.6   6.1    1.2  1  Spc7             Spc7 kinetochore protein
       0.73   10.1   2.9        1.3    9.3   2.9    1.4  1  Spc24            Spc24 subunit of Ndc80
       0.98    8.9   3.1        1.6    8.3   3.1    1.3  1  4HB_MCP_1        Four helix bundle sensory module for signal 
        1.5    7.8   4.2        2.2    7.3   4.2    1.2  1  Atg14            Vacuolar sorting 38 and autophagy-related su
        1.6    8.8  16.4       0.17   11.9  10.7    2.0  2  DHR10            Designed helical repeat protein 10 domain
        5.9    7.2   6.0        3.4    8.0   3.3    1.9  2  XhlA             Haemolysin XhlA


Domain annotation for each model (and alignments):
>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1         3   2.4e+03     105     123 ..      29      47 ..       9      65 .. 0.46
   2 !   55.1   0.0   1.1e-17   8.9e-15      19     117 ..     195     294 ..     177     300 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 3
                        acVLRF1 105 elldvpdprravLedavrr 123
                                    el  + + r++ L++    
  gi|116753473|ref|YP_842591.1|  29 ELKHTLEKREERLKKITSA 47 
                                    2333333333333332222 PP

  == domain 2  score: 55.1 bits;  conditional E-value: 1.1e-17
                        acVLRF1  19 e.ggelvaskvgtrdvqgrtaaGGwSqqRfaRrrenqadalleavaeaaarllaeesae...vvlgGdrslvaevledar 94 
                                      ++++++++  ++ v++++++GGwSq+Rf+R re+ ++++ e+ +e+++  ++++++    v++ G++ l++ v ++  
  gi|116753473|ref|YP_842591.1| 195 LgADQIESFEIVRTPVKEKHSKGGWSQRRFERLREEDIRRHGEHLRERVECAVERYAPLvkyVAVSGEPDLIRYVNQCFS 274
                                    3467888899999*************************************999777777899*************99976 PP

                        acVLRF1  95 laplatlareelldvpdprravL 117
                                    l  ++++  +  +d  +p ++ L
  gi|116753473|ref|YP_842591.1| 275 LPVIRARLGK--HDERNP-EKTL 294
                                    5555544444..555555.5555 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 !   27.6   0.0   3.8e-09     3e-06      34     111 ..     198     276 ..     177     295 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 3.8e-09
                 baeRF_family10  34 geleeveevegevpgrtktggwksqdrfqrreeeqaerhlkevAellaklleerg..verlvlgGdeeetaalldrlpka 111
                                    +++e  e v+ +v++++ +ggw sq+rf+r +ee ++rh +++ e ++ ++e+    v+ + ++G ++ +  + ++++ +
  gi|116753473|ref|YP_842591.1| 198 DQIESFEIVRTPVKEKHSKGGW-SQRRFERLREEDIRRHGEHLRERVECAVERYAplVKYVAVSGEPDLIRYVNQCFSLP 276
                                    56777888999***********.*******************************999*********99988888887655 PP

>> eRF1_2  eRF1 domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   6.4e-07    0.0005      20      67 ..     198     245 ..     187     264 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 6.4e-07
                                    SCEEEEEEEE------BSTTBSCCCCHHHHHHHHHHHHHHHHHHHHHH CS
                         eRF1_2  20 srtevlkkievsvPkKhkrGgqsarrfeRlreekleeflkkvaeaank 67 
                                     ++e  + + + v  Kh +Gg s+rrfeRlree +++  +++ e ++ 
  gi|116753473|ref|YP_842591.1| 198 DQIESFEIVRTPVKEKHSKGGWSQRRFERLREEDIRRHGEHLRERVEC 245
                                    566667777778889******************999887777776654 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 !   18.5   0.2   2.9e-06    0.0022      36      96 ..       8      67 ..       5      85 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.9e-06
                                   HTTTTT----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---- CS
                        T3SSipB 36 aqqeaasklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeLaPd 96
                                    +qe  s+l   lq+++ e ++++  le+  e+++++ sa+++  ++++ea  rl +  P+
  gi|116753473|ref|YP_842591.1|  8 RHQERISELEGMLQDLTREKEELKHTLEKREERLKKITSAYQETRRALKEAELRLRGT-PE 67
                                   57889999999******************************************99887.43 PP

>> baeRF_family2  Bacterial archaeo-eukaryotic release factor family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.4       3.5   2.8e+03     103     126 ..      13      36 ..       6      62 .. 0.49
   2 !   18.5   0.0     2e-06    0.0016      22      86 ..     197     264 ..     179     287 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.5
                  baeRF_family2 103 vvevegggraagadrealaeevae 126
                                    ++e+eg  ++   ++e+l++ +++
  gi|116753473|ref|YP_842591.1|  13 ISELEGMLQDLTREKEELKHTLEK 36 
                                    555554444444444444444443 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 2e-06
                  baeRF_family2  22 eeeeetveGghdpv.hkvraggwshrryqrraeeswerNaeavAeevdrlvresga..elVvlaGDvr 86 
                                    +++ e+ e  + pv +k ++ggws+rr++r  ee ++r  e   e+v+ +v++ ++  + V ++G++ 
  gi|116753473|ref|YP_842591.1| 197 ADQIESFEIVRTPVkEKHSKGGWSQRRFERLREEDIRRHGEHLRERVECAVERYAPlvKYVAVSGEPD 264
                                    6677778888888945559999*******************************998445688999876 PP

>> DASH_Spc19  Spc19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   4.9   8.5e-05     0.067      67     115 ..      11      59 ..       9      98 .. 0.69
   2 ?    2.5   0.0      0.15   1.2e+02      38      66 ..     220     248 ..     219     254 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.5e-05
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHT-XXXX CS
                     DASH_Spc19  67 ellekaekeleklerreetLkaklelqegrlsnaesskkeeeeseeske 115
                                    e ++++e  l+ l+r++e+Lk +le++e rl++ +s  +e+  + +++e
  gi|116753473|ref|YP_842591.1|  11 ERISELEGMLQDLTREKEELKHTLEKREERLKKITSAYQETRRALKEAE 59 
                                    678999***************************6544444444433333 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.15
                                    HH-------TTTHHHHHHHHHHHTTTHHH CS
                     DASH_Spc19  38 ttrvFeLipesdleaakaslaeeiePqie 66 
                                    ++r Fe + e d++++ ++l+e +e ++e
  gi|116753473|ref|YP_842591.1| 220 SQRRFERLREEDIRRHGEHLRERVECAVE 248
                                    6899******************9997776 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 ?   14.7   6.9   3.1e-05     0.024      65     118 ..      10      63 ..       5      75 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.1e-05
                 CENP-F_leu_zip  65 aeelreleldLvalrsekeeLekelqkkqervseLeslnsslenlleekEqekv 118
                                    +e+ +ele  L++l++ekeeL+  l+k  er +   s+  ++++ l+e+E   +
  gi|116753473|ref|YP_842591.1|  10 QERISELEGMLQDLTREKEELKHTLEKREERLKKITSAYQETRRALKEAELRLR 63 
                                    578899*******************************************97655 PP

>> DUF4164  Domain of unknown function (DUF4164)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   5.0   2.6e-05      0.02      30      81 ..       9      60 ..       4      65 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.6e-05
                        DUF4164 30 aerkrdeleaeiealgedrsRLaeeLdqaearaarleevnrEvsrrLkaaie 81
                                    ++  +ele  ++ l+++++ L + L ++e r++++ ++ +E+ r+Lk a  
  gi|116753473|ref|YP_842591.1|  9 HQERISELEGMLQDLTREKEELKHTLEKREERLKKITSAYQETRRALKEAEL 60
                                   566679******************************************9865 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   3.1   4.7e-05     0.037     325     380 ..       6      61 ..       5     104 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.7e-05
                         DUF812 325 kkkreeeleelqeqieeleskieeleeeikklessikqveeeleeekeeneeleke 380
                                    kk+ +e ++el+ ++++l ++ eel+++++k e+++k+++++++e+++  +e e  
  gi|116753473|ref|YP_842591.1|   6 KKRHQERISELEGMLQDLTREKEELKHTLEKREERLKKITSAYQETRRALKEAELR 61 
                                    5788999****************************************999988755 PP

>> DUF1043  Protein of unknown function (DUF1043)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.4   5.2e-05     0.041      25      89 ..       8      74 ..       3     100 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.2e-05
                        DUF1043 25 kqkklekelekakaeleeqkqeledHfaqsaelLetlaedyqkLyqhlaksseeL..lpeleeqelf 89
                                   ++++   ele   + l++ k+el++ +++  e L+++++ yq+  + l++ + +L  +pe + +e++
  gi|116753473|ref|YP_842591.1|  8 RHQERISELEGMLQDLTREKEELKHTLEKREERLKKITSAYQETRRALKEAELRLrgTPERSSDETP 74
                                   4445557899999************************************999999775555555544 PP

>> AcylCoA_dehyd_C  Acyl-CoA dehydrogenase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.3    0.0096       7.5      13      46 ..      26      59 ..      18      61 .. 0.89
   2 ?    5.4   0.0     0.024        19      10      51 ..     225     266 ..     218     271 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0096
                                   GGS---GGGHHHHHHHHHHHHHHHHHHHHHHTT- CS
                AcylCoA_dehyd_C 13 eaeevseeleelkarlkemtekyeeavakVkeak 46
                                   e+ee++++le+ ++rlk++t+ y+e+  + kea+
  gi|116753473|ref|YP_842591.1| 26 EKEELKHTLEKREERLKKITSAYQETRRALKEAE 59
                                   78999********************999999875 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.024
                                    HTGGGS---GGGHHHHHHHHHHHHHHHHHHHHHHTT--HHHH CS
                AcylCoA_dehyd_C  10 keyeaeevseeleelkarlkemtekyeeavakVkeakdqell 51 
                                    +++ +e+++ + e+l++r++  +e+y+ +v++V+ +++ +l+
  gi|116753473|ref|YP_842591.1| 225 ERLREEDIRRHGEHLRERVECAVERYAPLVKYVAVSGEPDLI 266
                                    67788999999**********************877776655 PP

>> Phage_GPO  Phage capsid scaffolding protein (GPO) serine peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.8   0.00018      0.14     187     265 ..       6      80 ..       1      84 [. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                      Phage_GPO 187 kkkksddarfadveeavelvAeevkelsekveallaleaelaalkkeveklkaeleaLkekLsktda.kekqrpeatGee 265
                                    k  k++++r++++e  ++++ +e +el++++e   + e++l++++++ ++++++l++ + +L  t++ ++++ pea+G +
  gi|116753473|ref|YP_842591.1|   6 K--KRHQERISELEGMLQDLTREKEELKHTLE---KREERLKKITSAYQETRRALKEAELRLRGTPErSSDETPEAPGVQ 80 
                                    4..456789********************999...88999***************************8899999999944 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 ?   11.3   0.8   0.00019      0.15      62     115 ..       7      61 ..       4      68 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00019
                           HemX  62 qeleerlqqlaeklealekeleqlqkqleelqqqlskvsga.erkdWlLaeAdfL 115
                                    ++ +er+ +l++ l++l++e+e+l++ le+ +++l+k+ +a +++ + L eA+  
  gi|116753473|ref|YP_842591.1|   7 KRHQERISELEGMLQDLTREKEELKHTLEKREERLKKITSAyQETRRALKEAELR 61 
                                    556789999999**************************99988899999999965 PP

>> Tektin  Tektin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   5.9   0.00037      0.29     250     309 ..      10      69 ..       7      77 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00037
                         Tektin 250 rkrieetedaknkleeqlkkvleeiaeleknieeLekairdkeaplklaqtRlenRtqRp 309
                                    ++ri+e+e + + l  +++++++ +++ e+ ++++ +a +++ ++lk a+ Rl    +R 
  gi|116753473|ref|YP_842591.1|  10 QERISELEGMLQDLTREKEELKHTLEKREERLKKITSAYQETRRALKEAELRLRGTPERS 69 
                                    68**************************************************98766665 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.5   0.00014      0.11      21      65 ..      19      63 ..       9      70 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00014
                           KxDL 21 tsgrlnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLe 65
                                   +++ l  +++eL++  ++ +erl+k+++ +++  ++lke    L+
  gi|116753473|ref|YP_842591.1| 19 MLQDLTREKEELKHTLEKREERLKKITSAYQETRRALKEAELRLR 63
                                   899999********************************9877776 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.0   0.00052      0.41       2      77 ..      11      88 ..      10     103 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00052
                          TMPIT  2 eeweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeee..eveelkeelke 77
                                   e+++ele  +++l  +++e+k++le+ ++  +k++++ ++ ++ lke + +l+ + +++++e+ e   v++l+ ++++
  gi|116753473|ref|YP_842591.1| 11 ERISELEGMLQDLTREKEELKHTLEKREERLKKITSAYQETRRALKEAELRLRGTPERSSDETPEapGVQKLAPRIMK 88
                                   67899999********************************************99998876554441246666655554 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.3    0.0012      0.95       7      44 ..      11      48 ..       8      50 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0012
                      FlaC_arch  7 nklsklsteletvkkeneelsksveelkenVkdllsLY 44
                                   +++s+l+ +l+ + +e eel+ ++e+ +e+ k++ s Y
  gi|116753473|ref|YP_842591.1| 11 ERISELEGMLQDLTREKEELKHTLEKREERLKKITSAY 48
                                   68999***************************998777 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   6.1   0.00098      0.77     205     254 ..      10      59 ..       6      73 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00098
                           Spc7 205 reelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeae 254
                                    +e+++el+  ++ + +e +el+  le+ ee+++++++ ++e++ +++eae
  gi|116753473|ref|YP_842591.1|  10 QERISELEGMLQDLTREKEELKHTLEKREERLKKITSAYQETRRALKEAE 59 
                                    45666666666666666666666666666666666666666666666666 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   2.9    0.0017       1.3       9      56 ..       9      61 ..       5      64 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0017
                          Spc24  9 iakelsdleselesleselaelkeeleeleeesee.....keserve.detllk 56
                                    ++ +s+le  l++l+ e++elk++le+ ee  ++     +e++r + +e+ l+
  gi|116753473|ref|YP_842591.1|  9 HQERISELEGMLQDLTREKEELKHTLEKREERLKKitsayQETRR-AlKEAELR 61
                                   567899***********************9999997665433333.33555555 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 ?    8.3   3.1     0.002       1.6      59     110 ..       9      60 ..       5      62 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.002
                      4HB_MCP_1  59 relradlleliltkdkaekdellkdieeleaeidkllekyektilteeEkel 110
                                    +++r++ le +l + ++ek+el+ ++e++e+++ k++++y +t    +E+el
  gi|116753473|ref|YP_842591.1|   9 HQERISELEGMLQDLTREKEELKHTLEKREERLKKITSAYQETRRALKEAEL 60 
                                    689999*************************************999999875 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   4.2    0.0028       2.2      78     128 ..       8      58 ..       5      96 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0028
                          Atg14  78 dlrerlqelkdklsqlkkeieekkkklaklsdklkkRrsdleslqneleer 128
                                    + +er++el+  l+ l++e ee k++l+k+ + lkk +s  + ++  l+e+
  gi|116753473|ref|YP_842591.1|   8 RHQERISELEGMLQDLTREKEELKHTLEKREERLKKITSAYQETRRALKEA 58 
                                    568999999999999999999999999999999996666666666666554 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 ?   11.9  10.7   0.00022      0.17      60     111 ..       7      58 ..       5      64 .. 0.93
   2 ?   -0.5   0.3       1.6   1.2e+03      73      95 ..     229     251 ..     220     255 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00022
                          DHR10  60 kelrdaleekeielrelerkeerlqrqlenaeeklerlreqaeekreaakar 111
                                    k+++++++e+e  l++l+r++e l+  le+ ee+l + +   +e r+a k++
  gi|116753473|ref|YP_842591.1|   7 KRHQERISELEGMLQDLTREKEELKHTLEKREERLKKITSAYQETRRALKEA 58 
                                    89**********************************************9987 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.6
                          DHR10  73 lrelerkeerlqrqlenaeekle 95 
                                     +++ r+ e+l+ ++e a e+++
  gi|116753473|ref|YP_842591.1| 229 EEDIRRHGEHLRERVECAVERYA 251
                                    45667777777777777777765 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   3.3    0.0043       3.4       7      46 ..       7      46 ..       7      49 .. 0.94
   2 ?   -2.7   0.0       9.3   7.2e+03      10      18 ..      91      99 ..      87     104 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0043
                           XhlA  7 erietkldnleervdkleekaaeaeekiknleedlkkles 46
                                   +r+++++ +le  +++l + ++e +  ++  ee+lkk++s
  gi|116753473|ref|YP_842591.1|  7 KRHQERISELEGMLQDLTREKEELKHTLEKREERLKKITS 46
                                   5999********9*************************98 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 9.3
                           XhlA 10 etkldnlee 18
                                    ++ldn+e+
  gi|116753473|ref|YP_842591.1| 91 LRRLDNIES 99
                                   567777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1522  (0.0848904); expected 358.6 (0.02)
Passed bias filter:                     1111  (0.0619666); expected 358.6 (0.02)
Passed Vit filter:                       253  (0.0141112); 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: 0.65u 0.26s 00:00:00.91 Elapsed: 00:00:00.43
# Mc/sec: 2127.79
//
Query:       gi|116753474|ref|YP_842592.1|  [L=183]
Description: transcription factor [Methanosaeta thermophila PT]
Scores for complete 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-59  197.1   0.3    6.3e-29   99.8   0.0    2.0  2  TBP       Transcription factor TFIID (or TATA-binding protein
    1.3e-09   38.1   0.0    0.00075   19.6   0.0    2.2  2  DUF3378   Domain of unknown function (DUF3378)


Domain annotation for each model (and alignments):
>> TBP  Transcription factor TFIID (or TATA-binding protein, TBP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.8   0.2   1.2e-31   1.1e-27       2      84 ..       5      85 ..       4      86 .. 0.97
   2 !   99.8   0.0     7e-33   6.3e-29       2      84 ..      97     179 ..      96     180 .. 0.96

  Alignments for each domain:
  == domain 1  score: 95.8 bits;  conditional E-value: 1.2e-31
                                   EEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHHHHH CS
                            TBP  2 fkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkiapilk 83
                                   ++i+Nvvas++l  e+dL k+++++  ++aeY++e+fpglvyr+++pk+++liF+sGkvv+tGak++e++r+++ ++a+ lk
  gi|116753474|ref|YP_842592.1|  5 INIENVVASTKLADEFDLVKIESEL--EGAEYNKEKFPGLVYRVKSPKAAFLIFTSGKVVCTGAKNVEDVRTVITNMARTLK 84
                                   79*******************9887..*****************************************************98 PP

                                   H CS
                            TBP 84 k 84
                                    
  gi|116753474|ref|YP_842592.1| 85 S 85
                                   6 PP

  == domain 2  score: 99.8 bits;  conditional E-value: 7e-33
                                    EEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHHH CS
                            TBP   2 fkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkiapi 81 
                                    +++qN+vasa+l+ +l+L+++al +  +n+eYepe+fpglvyr+++pkv++liFssGk+v+tG ks+ee++e ++ + + 
  gi|116753474|ref|YP_842592.1|  97 IHVQNIVASADLKTDLNLNAIALGLGLENIEYEPEQFPGLVYRIKQPKVVVLIFSSGKLVVTGGKSPEECEEGVRIVRQQ 176
                                    78********************9988*************************************************99988 PP

                                    HHH CS
                            TBP  82 lkk 84 
                                    l++
  gi|116753474|ref|YP_842592.1| 177 LEN 179
                                    875 PP

>> DUF3378  Domain of unknown function (DUF3378)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   7.8e-07     0.007      16      55 ..      27      67 ..      14      84 .. 0.81
   2 !   19.6   0.0   8.3e-08   0.00075      24      59 ..     130     165 ..     125     168 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 7.8e-07
                        DUF3378 16 eyyksk.lrskkppyavfaakkndttItaYtSgKVlFQGkn 55
                                   ++++    +++k p+ v++ k++++   ++tSgKV+  G++
  gi|116753474|ref|YP_842592.1| 27 SELEGAeYNKEKFPGLVYRVKSPKAAFLIFTSGKVVCTGAK 67
                                   5555442456679***********************99876 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 8.3e-08
                        DUF3378  24 skkppyavfaakkndttItaYtSgKVlFQGknaeae 59 
                                     ++ p+ v+++k++++++ ++ SgK+++ G +  +e
  gi|116753474|ref|YP_842592.1| 130 PEQFPGLVYRIKQPKVVVLIFSSGKLVVTGGKSPEE 165
                                    5789************************99876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1390.59
//
Query:       gi|116753475|ref|YP_842593.1|  [L=805]
Description: peptidase U32 [Methanosaeta thermophila PT]
Scores for complete 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-104  346.0   0.0    1.9e-83  279.2   0.0    3.0  2  Peptidase_U32  Peptidase family U32
    5.3e-17   62.4   0.0      1e-16   61.5   0.0    1.5  1  DUF3656        Collagenase


Domain annotation for each model (and alignments):
>> Peptidase_U32  Peptidase family U32
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  279.2   0.0   2.2e-87   1.9e-83       1     230 [.      77     310 ..      77     312 .. 0.96
   2 !   62.5   0.1   3.5e-21   3.1e-17      11     229 ..     607     798 ..     600     801 .. 0.90

  Alignments for each domain:
  == domain 1  score: 279.2 bits;  conditional E-value: 2.2e-87
                  Peptidase_U32   1 leklrkyleklaelgvdavivqDpgvlelareeapelelhlStqanitnseavrflkelGasrvvlaRElsleeikaike 80 
                                    +++l++yl ++ e+g+da+ vqD gv++lar+++pelelh+Stq++i+++++vr+ +++G +rvvl+REls+++ik+ik+
  gi|116753475|ref|YP_842593.1|  77 IDELEDYLVEICEIGADAILVQDTGVVRLARDIVPELELHASTQMTIHSADGVRWAARNGLKRVVLSRELSVDDIKNIKN 156
                                    5899**************************************************************************** PP

                  Peptidase_U32  81 kvp..dvelEvfvhGalcvaysGrcllssylsgrsanrgecaqpcrldyrlieekekgeeepieedekgt..yllspkdl 156
                                      +  +v lEvfvhGalc++ysG+cllss ++grs+nrg+caqpcr++y+l++ + +++ + ++ +++g   ylls++dl
  gi|116753475|ref|YP_842593.1| 157 VSDdlGVGLEVFVHGALCYSYSGQCLLSSSMGGRSGNRGMCAQPCRKPYTLLRGTSDEYGRLKDLRRRGGecYLLSTRDL 236
                                    999778********************************************9999988777777766666689******** PP

                  Peptidase_U32 157 clieelpelleaGvdslKIeGRmkspeyvatvvrvYreaidallagreevkeelkeeleklanrgltsgfllgr 230
                                    c++  l++++ aGvd+lKIeGRmks+eyva v+rvYr+a+da+++g ++++    ++l+ ++nrg+t+g++lg 
  gi|116753475|ref|YP_842593.1| 237 CTYPSLDKIVSAGVDALKIEGRMKSAEYVAIVTRVYRDALDAIARGDWAQDDGEIQRLALAFNRGFTEGYILGA 310
                                    **********************************************************************9875 PP

  == domain 2  score: 62.5 bits;  conditional E-value: 3.5e-21
                  Peptidase_U32  11 laelgvdavivqDpgvlelareeapelelhlStqanitnseavrflkelGasrvvlaRElsleeikaikekvpdvelEvf 90 
                                    l++   ++++v  +g+le a+++  e e+      ni+ns +v +l+  Ga+ + l+ Els+ +i  i+   +  +lEv 
  gi|116753475|ref|YP_842593.1| 607 LRDFRLNKIMVENLGALEAAERY--ECEIFGGQGLNIWNSLSVCMLS--GARALTLSPELSASQISSIASLRDRPDLEVI 682
                                    66778899***************..***************9999986..99*********************99****** PP

                  Peptidase_U32  91 vhGalcvaysGrcllssylsgrsanrgecaqpcrldyrlieekekgeeepieedekgtyllspkdlclieelpelleaGv 170
                                     +G++ +a+    l+s+         + ca   r+    +++++ g             +l++ ++cl+++lp++  +Gv
  gi|116753475|ref|YP_842593.1| 683 AQGNIVIAVTEDRLISEG--------DVCAIRDRRHIFPVRRDAAGVT----------NILNSVETCLLDYLPQISLMGV 744
                                    *****************9........8899888888775555554433..........6********************* PP

                  Peptidase_U32 171 dslKIeGRmkspeyvatvvrvYreaidallagreevkeelkeeleklanrgltsgfllg 229
                                    ds+ I+ R ++++y+ +++ +Y +a+ +l +     +++lk  ++++a +g+t g++l+
  gi|116753475|ref|YP_842593.1| 745 DSVAIDARWRTKKYAREMAGIYSRAVGELSE-----LPKLKSMVRRMAMGGITAGHFLR 798
                                    **************************99765.....55999999999999999999875 PP

>> DUF3656  Collagenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.5   0.0   1.2e-20     1e-16       1     106 [.     391     510 ..     391     511 .. 0.84

  Alignments for each domain:
  == domain 1  score: 61.5 bits;  conditional E-value: 1.2e-20
                        DUF3656   1 vyrtsdkklteelekslekseerkipvdlelaakeg............eplkltvtde..leeAkkrplteenirkqLsk 66 
                                    +y t+++++ + +e+ +++  + +ip+dl+++ ++g             +++l+v+ +  +e+A++ pl+  +i++q+++
  gi|116753475|ref|YP_842593.1| 391 LYITRSARMRDDAERIIRR-GRDRIPIDLRISFDNGvpvadvylagpsGRIELSVKGDfvMEAARTLPLSPSQIESQMRR 469
                                    6999999888888888887.7788****999999995554444443333668888766********************** PP

                        DUF3656  67 lGgtpFeleeieidldgl.fiPvseLnelRRealekLeear 106
                                    +Ggt+F+++e+ id+ g+ +  +++Ln+lRR++l + e+a+
  gi|116753475|ref|YP_842593.1| 470 TGGTQFVFREVVIDYPGGlYTTPAKLNQLRRDILRAAENAL 510
                                    ***************8555999**************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (805 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.25s 00:00:00.90 Elapsed: 00:00:00.43
# Mc/sec: 5564.95
//
Query:       gi|116753476|ref|YP_842594.1|  [L=182]
Description: XRE family transcriptional regulator [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-14   53.3   0.0    2.9e-14   52.5   0.0    1.4  1  Cupin_2          Cupin domain
    1.4e-06   28.3   0.0    2.1e-06   27.7   0.0    1.3  1  HTH_19           Helix-turn-helix domain
    3.2e-06   27.1   0.0    4.5e-06   26.6   0.0    1.2  1  HTH_3            Helix-turn-helix
    8.3e-06   26.1   0.0    1.3e-05   25.4   0.0    1.3  1  HTH_31           Helix-turn-helix domain
     0.0072   16.0   0.0      0.013   15.2   0.0    1.4  1  Cupin_3          Protein of unknown function (DUF861)
  ------ inclusion threshold ------
      0.042   13.8   0.0      0.052   13.4   0.0    1.2  1  MannoseP_isomer  Mannose-6-phosphate isomerase
       0.09   12.5   0.0       0.15   11.9   0.0    1.3  1  EutQ             Ethanolamine utilisation protein EutQ


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 !   52.5   0.0   1.1e-17   2.9e-14       2      71 .]     112     181 ..     111     181 .. 0.93

  Alignments for each domain:
  == domain 1  score: 52.5 bits;  conditional E-value: 1.1e-17
                                    EEEEETTEEEEEEC.SSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEEEE CS
                        Cupin_2   2 lvelppGesapshr.HpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparllvvy 71 
                                    +v+++p  + p+ + Hpg+ ef y+leG++++++ ++e++l++Gds++f++   H+++   + par+lv++
  gi|116753476|ref|YP_842594.1| 112 IVTVEPRSEKPAVYsHPGQ-EFDYILEGTIKIYIHNNEIVLNEGDSIFFDSSYDHAMEALNNRPARMLVIV 181
                                    799***996665555****.************************************************995 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0   8.1e-10   2.1e-06       1      62 [.       9      69 ..       9      72 .. 0.96

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 8.1e-10
                         HTH_19  1 GerLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgidleyllqg 62
                                   G r++e+Re  +++ ee+a+ l++    +  +E+g   +++a+ll kia+ l++d   ll+g
  gi|116753476|ref|YP_842594.1|  9 GSRIRELRELSKISPEEMAGYLKVPLETYCGYESGHL-DIPASLLFKIAQRLDVDMSLLLTG 69
                                   89*********************************88.999******************998 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   1.8e-09   4.5e-06       1      55 []      12      66 ..      12      66 .. 0.97

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 1.8e-09
                                   HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEHHHH CS
                          HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvsldel 55
                                   ++elR+  ++s ee+A +l v+  t+  +E+G+  +  + l+k+a+ L+v+++ l
  gi|116753476|ref|YP_842594.1| 12 IRELRELSKISPEEMAGYLKVPLETYCGYESGHLDIPASLLFKIAQRLDVDMSLL 66
                                   8**************************************************9865 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   5.1e-09   1.3e-05       1      60 [.       7      65 ..       7      68 .. 0.94

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 5.1e-09
                         HTH_31  1 aLGalLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgldpae 60
                                   ++G + r+lRe + +s ee+A+ l v   t+  +E+G  +  + + l ++a+ l++d ++
  gi|116753476|ref|YP_842594.1|  7 EIGSRIRELRELSKISPEEMAGYLKVPLETYCGYESGHLD-IPASLLFKIAQRLDVDMSL 65
                                   589************************************8.77*************9776 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   5.1e-06     0.013      26      57 ..     130     160 ..     113     169 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.1e-06
                                    EEEEEEEECEEEEEETTTEEEEEETTEEEEE- CS
                        Cupin_3  26 dEfcyileGevkvtpeggetvelraGDlvvlp 57 
                                    +Ef yileG +k++  + +++ l +GD++++ 
  gi|116753476|ref|YP_842594.1| 130 QEFDYILEGTIKIYI-HNNEIVLNEGDSIFFD 160
                                    89*************.*************996 PP

>> MannoseP_isomer  Mannose-6-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     2e-05     0.052      68     130 ..     113     175 ..      83     182 .] 0.79

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2e-05
                MannoseP_isomer  68 itvkPgeklslqkhhhraehWvvvkGtakvtvddevlllkenestyiplgaihrlenpGkipl 130
                                    +tv+P ++      h   e   +++Gt k+ +++++++l+e +s++   +  h++e   + p 
  gi|116753476|ref|YP_842594.1| 113 VTVEPRSEKPAVYSHPGQEFDYILEGTIKIYIHNNEIVLNEGDSIFFDSSYDHAMEALNNRPA 175
                                    678887666655566667888899**************************9999987666554 PP

>> EutQ  Ethanolamine utilisation protein EutQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   5.7e-05      0.15      96     125 ..     130     159 ..     125     172 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.7e-05
                           EutQ  96 deidyvieGrldvlidGrkvvaeaGdvili 125
                                     e dy++eG +++ i  +++v + Gd i+ 
  gi|116753476|ref|YP_842594.1| 130 QEFDYILEGTIKIYIHNNEIVLNEGDSIFF 159
                                    599***********************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1339.62
//
Query:       gi|116753477|ref|YP_842595.1|  [L=627]
Description: AMP-dependent synthetase and ligase [Methanosaeta thermophila PT]
Scores for complete 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-73  247.8   0.0    1.9e-73  247.5   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    3.7e-25   88.7   0.6    8.5e-25   87.5   0.6    1.7  1  AMP-binding_C  AMP-binding enzyme C-terminal domain
      8e-09   36.0   8.2    1.7e-08   34.9   8.2    1.5  1  Fer4_7         4Fe-4S dicluster domain
      4e-08   33.3   4.4     0.0031   17.6   1.0    2.4  2  Fer4_21        4Fe-4S dicluster domain
    3.9e-07   30.1   6.7    8.5e-07   29.0   6.7    1.6  1  Fer4_10        4Fe-4S dicluster domain
    5.1e-07   29.2  17.7    0.00012   21.8   3.4    2.4  2  Fer4           4Fe-4S binding domain
    9.8e-07   28.8   6.5      2e-06   27.9   6.5    1.5  1  Fer4_9         4Fe-4S dicluster domain
    8.2e-05   22.8  12.3      0.009   16.4   3.1    2.5  2  Fer4_4         4Fe-4S binding domain
    9.4e-05   22.3  13.5      0.019   15.0   2.9    2.7  2  Fer4_2         4Fe-4S binding domain
    9.7e-05   23.1   3.5       0.13   13.2   0.1    2.5  2  Fer4_22        4Fe-4S dicluster domain
     0.0001   22.2  16.2      0.028   14.5   4.6    2.5  2  Fer4_6         4Fe-4S binding domain
    0.00027   21.8  10.7       0.38   11.7  10.8    2.5  2  Fer4_16        4Fe-4S double cluster binding domain
     0.0062   17.4  17.1        0.4   11.7   4.5    2.5  2  Fer4_3         4Fe-4S binding domain
     0.0066   16.9  11.2       0.47   10.9   2.7    2.4  3  Fer4_8         4Fe-4S dicluster domain
     0.0098   16.4   9.8       0.82   10.3  11.0    2.4  2  Fer4_17        4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.061   13.9  11.0       0.15   12.6   2.3    2.8  2  Fer4_13        4Fe-4S single cluster domain of Ferredoxin I
       0.29   11.9   6.7        3.4    8.5   0.8    2.9  2  Fer4_15        4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  247.5   0.0   1.8e-76   1.9e-73       4     422 ..      42     458 ..      39     459 .. 0.84

  Alignments for each domain:
  == domain 1  score: 247.5 bits;  conditional E-value: 1.8e-76
                                    HHHHSTTSEEEEE...CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETT CS
                    AMP-binding   4 qaaktpdkvalvd...sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnpt 80 
                                     a+++pdk+alv+   +ge + +T++++++ ++r+A+ + s G++kgd+V++ l+ ++++ + ++++ k+Gav++p    
  gi|116753477|ref|YP_842595.1|  42 YAQEQPDKIALVWcndHGEERIFTFKDMKHWSDRAANLFSSYGIRKGDTVMLTLKSRYDFWICMIGLNKIGAVAIPSTHM 121
                                    5899***********9999************************************************************* PP

                                    S-HHHHHHHHHHHTESEEE........ETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS...- CS
                    AMP-binding  81 ltaeelayiledseakvli........atvdselleklleaaakleavklvivldadellkeeelkeeeeseekae...k 149
                                    l+a+++ y +++++ k+++        ++     ++ ++++ +++    ++  + +++ ++e + +++   +e+++   +
  gi|116753477|ref|YP_842595.1| 122 LKAKDIVYRIKKANLKMVVciiedgvpEE-----VDLAHKELGDVN--LIKAFVGREDQEREGWINFRRALAEASPdftR 194
                                    *******************7654322111.....222223333222..22333333333444444444433333324666 PP

                                    TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSC.CTTT-EE.EESS-TTSCHHHHHHHHHHHHT CS
                    AMP-binding 150 peeeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletrfk.lkeddvv.lsilplahifglilelllalls 227
                                    p+ ee+++++d+++  +TSGTTG PK V + + + +  + ++k   +++ + +dd + +++++  ++      +++  ++
  gi|116753477|ref|YP_842595.1| 195 PVGEEATRNEDVLIAYFTSGTTGYPKMVKHDQTYPLGHILTAK---YWQnV-ADDGLhYTVADTGWAKCAWGKIYGQWIA 270
                                    777888999***********************99999989974...54425.5555548889999986655********* PP

                                    T-EEEE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHH CS
                    AMP-binding 228 GatvvllpkdaaldpklllelieklkvtviagvPrvlealle.sgalkaakkakdlsslrlvllggeplspellrffral 306
                                    G++v +++ d ++d+++++e ++k+kvt+++++P++++ +++ +        ++d+s l++++++gepl+p++ ++f ++
  gi|116753477|ref|YP_842595.1| 271 GSAVFVYDYD-RFDAGRMMEKLSKYKVTTFCAPPTIYRFMIKgD-MS-----KYDFSTLKYAVTAGEPLNPSVYERFLEV 343
                                    ***9999966.569999***********************9944.33.....35************************** PP

                                    HTCEEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEET.....TS-SEBTT- CS
                    AMP-binding 307 fgeevlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgp.....gvmkgYlkk 381
                                    +g +++egYG+TEt + ++++p +e+  k+gs Gkp pg ++ ++ ++  + ++ geeGe+++r       g++  Y+ +
  gi|116753477|ref|YP_842595.1| 344 TGLKLMEGYGQTETVVTIANFPWMEP--KPGSMGKPAPGFDIVLLKDS--RQCEVGEEGEIVIRTDkgkpvGLFIDYHLD 419
                                    *99*************9986665666..8****************997..77889*********98777888******** PP

                                    HHHHHHHEEETCCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                    AMP-binding 382 peataeafdsegrwlrTGDlgrldedGyleivgRkkdlikl 422
                                    p++ + ++   +++++TGD +++dedGy+++vgR++d+ik+
  gi|116753477|ref|YP_842595.1| 420 PDRVRNTWH--DGYYHTGDTAWVDEDGYIWFVGRTDDMIKT 458
                                    *******97..57***************************8 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 !   87.5   0.6   8.1e-28   8.5e-25       1      76 []     467     545 ..     467     545 .. 0.94

  Alignments for each domain:
  == domain 1  score: 87.5 bits;  conditional E-value: 8.1e-28
                                    HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE---..-.--HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                  AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg..s.ealeeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                    evEsal++hpaV e+a+ Gvpd+++G++++a Vvl +g  + e+l++eL++hv++  +py+ p+ v+fv+elpkt sGK
  gi|116753477|ref|YP_842595.1| 467 EVESALMTHPAVLECAITGVPDPIRGQVIKATVVLTKGytPsEELKRELQEHVKRVTAPYKYPRIVEFVEELPKTISGK 545
                                    8**********************************779642344**********************************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 !   34.9   8.2   1.6e-11   1.7e-08       2      49 ..     566     613 ..     565     615 .. 0.96

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 1.6e-11
                         Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCP 49 
                                    C gC++C  aCpv+++++ ee n +g ++ ++  + C+gCgaC  +CP
  gi|116753477|ref|YP_842595.1| 566 CKGCERCILACPVNVLRMSEELNSRGYRYSVYAGDGCIGCGACYYTCP 613
                                    **************************9999999*************** PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   1.0   2.9e-06    0.0031      34      59 .]     558     583 ..     546     583 .. 0.74
   2 !   16.3   0.1   7.6e-06     0.008       6      27 ..     600     621 ..     586     626 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.9e-06
                        Fer4_21  34 lkvv.edeCvGCnlCssvCPvedciem 59 
                                    ++++ + eC GC+ C+  CPv ++++m
  gi|116753477|ref|YP_842595.1| 558 YPIInAMECKGCERCILACPV-NVLRM 583
                                    34442779************9.77766 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 7.6e-06
                        Fer4_21   6 dkCigCgkCliaCedtshqaie 27 
                                    d CigCg C+ +C++    a++
  gi|116753477|ref|YP_842595.1| 600 DGCIGCGACYYTCPEPNALAVH 621
                                    5688888888888876666655 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   6.7   8.1e-10   8.5e-07       3      56 .]     560     613 ..     558     614 .. 0.85

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 8.1e-10
                        Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                    +i++  C +C++C  aCP+++ +++ +    +      + + C+gcgaC+  CP
  gi|116753477|ref|YP_842595.1| 560 IINAMECKGCERCILACPVNVLRMSEELNSRGYRYSVYAGDGCIGCGACYYTCP 613
                                    789999*************88777776666666667778889***********9 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   3.4   1.1e-07   0.00012       1      23 [.     559     581 ..     559     582 .. 0.92
   2 !   12.8   6.4   7.5e-05     0.079       7      19 ..     601     613 ..     599     614 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.1e-07
                                    EEEETTTSSS-THHHHHSTTTEE CS
                           Fer4   1 vvideekCigCGaCvevCPvgAI 23 
                                    ++i+   C gC +C+ +CPv+++
  gi|116753477|ref|YP_842595.1| 559 PIINAMECKGCERCILACPVNVL 581
                                    58999****************97 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 7.5e-05
                                    TSSS-THHHHHST CS
                           Fer4   7 kCigCGaCvevCP 19 
                                     CigCGaC+  CP
  gi|116753477|ref|YP_842595.1| 601 GCIGCGACYYTCP 613
                                    5************ PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   6.5   1.9e-09     2e-06       1      48 [.     565     614 ..     565     618 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1.9e-09
                         Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase..eaCigCgaCveaCpk 48 
                                    +C gC +C+ aCp +v ++++  + + +r   +  + CigCgaC+  Cp+
  gi|116753477|ref|YP_842595.1| 565 ECKGCERCILACPVNVLRMSEELNSRGYRYSVYagDGCIGCGACYYTCPE 614
                                    5***************977766555555443336689************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 !   10.8   1.8   0.00055      0.58       4      17 .]     566     579 ..     562     581 .. 0.91
   2 !   16.4   3.1   8.6e-06     0.009       3      15 ..     601     613 ..     599     617 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00055
                         Fer4_4   4 CigCgsCvaaCPqg 17 
                                    C gC +C+ aCP++
  gi|116753477|ref|YP_842595.1| 566 CKGCERCILACPVN 579
                                    ************75 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 8.6e-06
                         Fer4_4   3 rCigCgsCvaaCP 15 
                                     CigCg+C+++CP
  gi|116753477|ref|YP_842595.1| 601 GCIGCGACYYTCP 613
                                    6***********9 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   3.0   0.00016      0.17       2      21 ..     558     577 ..     557     578 .. 0.85
   2 !   15.0   2.9   1.8e-05     0.019       9      22 .]     601     614 ..     596     614 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00016
                         Fer4_2   2 pvvvdtdrCigCgaCvsaCP 21 
                                    ++ +++  C gC+ C+ aCP
  gi|116753477|ref|YP_842595.1| 558 YPIINAMECKGCERCILACP 577
                                    57788778************ PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.8e-05
                         Fer4_2   9 rCigCgaCvsaCPa 22 
                                     CigCgaC+  CP+
  gi|116753477|ref|YP_842595.1| 601 GCIGCGACYYTCPE 614
                                    5************5 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.1   0.00012      0.13      71      95 ..     555     579 ..     517     580 .. 0.78
   2 !   10.1   0.7    0.0011       1.1      78      94 ..     598     614 ..     582     616 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00012
                        Fer4_22  71 sefkekfgesgCvGCgRCieacpvk 95 
                                     +    ++++ C GC RCi acpv+
  gi|116753477|ref|YP_842595.1| 555 DKPYPIINAMECKGCERCILACPVN 579
                                    44445568999************97 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0011
                        Fer4_22  78 gesgCvGCgRCieacpv 94 
                                       gC+GCg C  +cp+
  gi|116753477|ref|YP_842595.1| 598 AGDGCIGCGACYYTCPE 614
                                    56789999999999986 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   3.8     8e-05     0.084       9      24 .]     566     581 ..     565     581 .. 0.94
   2 !   14.5   4.6   2.6e-05     0.028       9      23 ..     602     617 ..     600     618 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8e-05
                         Fer4_6   9 CigCgdCvrvCPegai 24 
                                    C gC++C+ +CP +++
  gi|116753477|ref|YP_842595.1| 566 CKGCERCILACPVNVL 581
                                    ************9986 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 2.6e-05
                         Fer4_6   9 CigCgdCvrvCPe.ga 23 
                                    CigCg+C+  CPe +a
  gi|116753477|ref|YP_842595.1| 602 CIGCGACYYTCPEpNA 617
                                    ************9666 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7  10.8   0.00036      0.38       2      65 ..     566     613 ..     565     614 .. 0.75
   2 ?    6.7   3.5     0.014        14       2      14 ..     602     614 ..     601     621 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00036
                        Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCP 65 
                                    C++C++C+ +CP+n++++   +e+++r                + + + +  ++gC++C  +CP
  gi|116753477|ref|YP_842595.1| 566 CKGCERCILACPVNVLRMS--EELNSRGY--------------RYSVYAGDGCIGCGACYYTCP 613
                                    *******************..56654443..............223344557889999999998 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.014
                        Fer4_16   2 CgtCgkCaevCPt 14 
                                    C++Cg+C  +CP+
  gi|116753477|ref|YP_842595.1| 602 CIGCGACYYTCPE 614
                                    9999999999997 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   4.7   0.00056       0.6       1      14 [.     566     579 ..     566     580 .. 0.95
   2 !   11.7   4.5   0.00038       0.4       1      15 []     602     617 ..     602     617 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00056
                         Fer4_3   1 CtgCgaCvevCPvg 14 
                                    C gC++C  +CPv+
  gi|116753477|ref|YP_842595.1| 566 CKGCERCILACPVN 579
                                    9***********98 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00038
                         Fer4_3   1 CtgCgaCvevCPv.gA 15 
                                    C+gCgaC   CP+ +A
  gi|116753477|ref|YP_842595.1| 602 CIGCGACYYTCPEpNA 617
                                    ************5376 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   1.9    0.0014       1.4      45      65 .]     560     580 ..     533     580 .. 0.74
   2 !   10.7  12.7   0.00054      0.57       2      63 ..     563     614 ..     562     617 .. 0.84
   3 !   10.9   2.7   0.00045      0.47       4      17 ..     601     614 ..     598     626 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0014
                         Fer4_8  45 eealwsCttcgaCtevCpvgi 65 
                                      ++ +C +c++C  +Cpv++
  gi|116753477|ref|YP_842595.1| 560 IINAMECKGCERCILACPVNV 580
                                    566788999999999999986 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00054
                         Fer4_8   2 lekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63 
                                    +++C +C++C  aCpv   +  + l++rg +   v            + C +cgaC   Cp+
  gi|116753477|ref|YP_842595.1| 563 AMECKGCERCILACPVNVLRMSEELNSRGYRYS-VYAG---------DGCIGCGACYYTCPE 614
                                    578************766666899999999888.6555.........56************7 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00045
                         Fer4_8   4 kCieCgaCqsaCpv 17 
                                     Ci+CgaC  +Cp 
  gi|116753477|ref|YP_842595.1| 601 GCIGCGACYYTCPE 614
                                    6***********95 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   1.2   0.00098         1      39      60 ..     556     580 ..     529     581 .. 0.66
   2 !   10.3  11.0   0.00077      0.82       1      58 [.     565     614 ..     565     615 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00098
                        Fer4_17  39 ke...ekaslCieCgeCerkCPqgl 60 
                                    k     +a +C +C++C  +CP ++
  gi|116753477|ref|YP_842595.1| 556 KPypiINAMECKGCERCILACPVNV 580
                                    2234359999***********9775 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00077
                        Fer4_17   1 rCiqCgyClpeCpsyeaydn...epkkllraaklglleeaekeekaslCieCgeCerkCPq 58 
                                    +C +C+ C+ +Cp +  + +   + + +++ +++g           + Ci+Cg C + CP+
  gi|116753477|ref|YP_842595.1| 565 ECKGCERCILACPVNVLRMSeelNSRGYRYSVYAG-----------DGCIGCGACYYTCPE 614
                                    6************9988444111344555555554...........78************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 ?    6.3   0.4     0.014        14       2      17 ..     562     577 ..     561     591 .. 0.79
   2 ?   12.6   2.3   0.00014      0.15       4      18 ..     600     614 ..     599     615 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.014
                        Fer4_13   2 DrdtCiacgaCvelaP 17 
                                    +  +C +c+ C  ++P
  gi|116753477|ref|YP_842595.1| 562 NAMECKGCERCILACP 577
                                    6679***********9 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00014
                        Fer4_13   4 dtCiacgaCvelaPd 18 
                                    d Ci+cgaC+ ++P+
  gi|116753477|ref|YP_842595.1| 600 DGCIGCGACYYTCPE 614
                                    79************7 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.3     0.021        22       5      19 ..     563     577 ..     560     592 .. 0.81
   2 ?    8.5   0.8    0.0032       3.4       6      20 ..     600     614 ..     596     619 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.021
                        Fer4_15   5 rdaCigcglCvaeap 19 
                                      +C gc++C+ ++p
  gi|116753477|ref|YP_842595.1| 563 AMECKGCERCILACP 577
                                    568***********8 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0032
                        Fer4_15   6 daCigcglCvaeape 20 
                                    d Cigcg+C+  +pe
  gi|116753477|ref|YP_842595.1| 600 DGCIGCGACYYTCPE 614
                                    78***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (627 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.60u 0.25s 00:00:00.85 Elapsed: 00:00:00.42
# Mc/sec: 4433.88
//
Query:       gi|116753478|ref|YP_842596.1|  [L=347]
Description: 2-ketoisovalerate ferredoxin reductase [Methanosaeta thermophila PT]
Scores for complete 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-52  176.6   0.0    8.2e-52  176.2   0.0    1.1  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    5.4e-23   81.2   0.0    9.8e-23   80.4   0.0    1.4  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
    3.8e-06   26.8   0.0    8.2e-06   25.7   0.0    1.5  1  Transketolase_C  Transketolase, C-terminal domain


Domain annotation for each model (and alignments):
>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.2   0.0   1.4e-55   8.2e-52       2     188 ..      15     201 ..      14     242 .. 0.88

  Alignments for each domain:
  == domain 1  score: 176.2 bits;  conditional E-value: 1.4e-55
                                    HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCCHHH CS
                          POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmienlgl 81 
                                    +a++ag+d +++YPITP+sei++e++++ ++++    ++vq+esE +ai++v GAaaaG r++ a+Sg+G++L++e + +
  gi|116753478|ref|YP_842596.1|  15 GAMYAGCDCFFGYPITPASEILQEASRYFPMVGR---KFVQAESEEAAINMVYGAAAAGHRVLAASSGPGMSLKQEGISY 91 
                                    799******************************7...9****************************************** PP

                                    HHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHH......S---EEEE-SSHHHHHHHHHHHHHHHHHCTSEEEEEEEH CS
                          POR_N  82 aageelPvvivvvaRalpstglsirtdqsDlmaar......dtglivlasenvqeafdlalvAfnlAekvrvPvivlfDg 155
                                     ag+elP+viv+++Ra+p    +i ++qsD ++         +  ivla+++vqe+ d +++Af lA+k+r P++vl Dg
  gi|116753478|ref|YP_842596.1|  92 LAGAELPCVIVDINRAGPGL-GNIGPEQSDYNQTVkggghgCYRNIVLAPNSVQEMCDHTIKAFELAFKYRNPAVVLADG 170
                                    ********************.9*************9**7777778*********************************** PP

                                    HHH.HEEEEEEC-SGG.GS-----SBXXXXXXX CS
                          POR_N 156 fllshevekvelpdeedelklikekleeyerke 188
                                    +l+ h+ve++++p+   +  +i++ +    +k 
  gi|116753478|ref|YP_842596.1| 171 VLG-HMVEPLRFPESA-ITPVIDTSWAVCGTKG 201
                                    ***.*********988.7777777766555555 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 !   80.4   0.0   1.6e-26   9.8e-23       1     102 []     246     338 ..     246     338 .. 0.97

  Alignments for each domain:
  == domain 1  score: 80.4 bits;  conditional E-value: 1.6e-26
                                    -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHHTGG CS
                        PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaalkk 80 
                                    Aevv+v +G++++ a+savd++R++gi++Gl+r++tl+PFP ++lke++++  ++++++++      Gq+ e++  a+ +
  gi|116753478|ref|YP_842596.1| 246 AEVVLVSYGISSRIARSAVDAARRDGINAGLFRPITLFPFPDKALKEIAERGCRLISVEMSD-----GQMREDIILATGA 320
                                    9*************************************************************.....**********875 PP

                                    GTSEEEEEE--GGG----HHHH CS
                        PFOR_II  81 skvkvvnfvaglgGrditvedi 102
                                         v++v++ gG++it e+i
  gi|116753478|ref|YP_842596.1| 321 D----VELVSRYGGNLITREEI 338
                                    5....*************9987 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   1.4e-09   8.2e-06       8      68 ..     244     304 ..     238     309 .. 0.95

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.4e-09
                                    TTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEE CS
                Transketolase_C   8 egkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvve 68 
                                    +  +v+lv+yG   + a  A+++++++gi+a +  ++t+ p+  + ++e++++  rl+ ve
  gi|116753478|ref|YP_842596.1| 244 DDAEVVLVSYGISSRIARSAVDAARRDGINAGLFRPITLFPFPDKALKEIAERGCRLISVE 304
                                    6789*****************************************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); 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 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2629.72
//
Query:       gi|116753479|ref|YP_842597.1|  [L=470]
Description: thiamine pyrophosphate binding domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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  110.2   0.0      5e-31  108.1   0.0    1.9  1  POR           Pyruvate ferredoxin/flavodoxin oxidoreductase
    8.7e-23   80.8   0.1    1.4e-22   80.1   0.1    1.4  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b


Domain annotation for each model (and alignments):
>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.1   0.0   5.6e-35     5e-31       1     176 [.     304     462 ..     304     463 .. 0.91

  Alignments for each domain:
  == domain 1  score: 108.1 bits;  conditional E-value: 5.6e-35
                                    CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEEEEE CS
                            POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglkpgg 80 
                                    GGqGv+++g  la+aa  +   v+++++yg+e+rGg s+++v is e +++s+ v+e d+lva++  +l+++ + ++   
  gi|116753479|ref|YP_842597.1| 304 GGQGVLSMGLALAQAAYLSRRFVSWYPDYGPEQRGGTSNCTVVISGE-PISSPVVDEIDILVAFNRPSLEKFSSSVR--E 380
                                    9**********************************************.7899999**********************..8 PP

                                    EEEEECTCGTT-CCHHHCTS-HHHHHHHT-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHT..S-HHHHHHHHHCCS CS
                            POR  81 iiiynseelkpdelkkakeeerelkerlgvrvygvdatkiakeiggneraaNtvmlGalaallg..lplealeeaikkrf 158
                                    +i+y+       e++ ++            r ++v at+ia+++g  + aaNt+mlGal+a +   lp+++   aik++f
  gi|116753479|ref|YP_842597.1| 381 LILYDML---AGEFQGSV------------RSIPVAATEIATQKGA-QQAANTAMLGALMATGRlgLPEDSYVGAIKDAF 444
                                    *****92...23332222............3479*********988.************8887755778*********** PP

                                    -CH.HHHHHHHHHHHHHH CS
                            POR 159 pkkkeviekNlkafragy 176
                                     kk +++ +Nl+ frag 
  gi|116753479|ref|YP_842597.1| 445 SKKPKLVPLNLEIFRAGA 462
                                    ****************97 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 !   80.1   0.1   1.6e-26   1.4e-22       3     152 ..      61     218 ..      59     219 .. 0.89

  Alignments for each domain:
  == domain 1  score: 80.1 bits;  conditional E-value: 1.6e-26
                                    SHHHHHHHHHHTTSSSSEEECET.TTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEEEEEE CS
                   TPP_enzyme_C   3 Gcltlwaarllkvkrprsyltsg.glgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpitvvvl 80 
                                    Gc  +           + yl++g + +++G++ ++++G+++a+ d+ v+++ GDG+++ i l+e+++a++r+ ++ v+ +
  gi|116753479|ref|YP_842597.1|  61 GCAVF----------AYYYLDCGhVQAAHGRAPAIGTGISRAEDDAIVISYQGDGDLASIgLNETIQAANRGEKMAVFFI 130
                                    55555..........556778554999***************99************************************ PP

                                    E-SBCCCHHHH...HHHHTCCTTTTSBB.....BS----HHHHHHHTTSEEE..EESSH.HHHH...HHHHHHHH....C CS
                   TPP_enzyme_C  81 nNegygmtggq...qepfggkrksgpagk....dlkpvdfaklaealGakga..rvekadveel...eealkeal....e 144
                                    nN +ygmtggq   ++  g+ ++++p+g+     ++p++++++   l a+++  rv+ +d+e++   ++a+++al    +
  gi|116753479|ref|YP_842597.1| 131 NNTVYGMTGGQmapTTLVGEVTSTTPTGRdpreAGYPLHVCEILDTLKAPVYieRVSLSDIEHIrkaRRAVRKALeiqrD 210
                                    **************9*************9**977****************888*99999999984446677777799999 PP

                                    SSSEEEEE CS
                   TPP_enzyme_C 145 kkgpalie 152
                                    kkg a++e
  gi|116753479|ref|YP_842597.1| 211 KKGYAFVE 218
                                    99999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (470 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); 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 0.24s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 3675.25
//
Query:       gi|116753480|ref|YP_842598.1|  [L=244]
Description: F420-dependent oxidoreductase, putative [Methanosaeta thermophila PT]
Scores for 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-57  192.2   0.0    1.1e-56  191.9   0.0    1.0  1  F420_ligase  F420-0:Gamma-glutamyl ligase


Domain annotation for each model (and alignments):
>> F420_ligase  F420-0:Gamma-glutamyl ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.9   0.0   6.2e-61   1.1e-56       4     244 .]      13     218 ..      12     218 .. 0.98

  Alignments for each domain:
  == domain 1  score: 191.9 bits;  conditional E-value: 6.2e-61
                                    -----TT--HHHHHHCCS-.....--TT-EEEEEHHHHHHHTT-EEEGGGS---HHHHHHHHHH.TS-H........... CS
                    F420_ligase   4 tplikegddlaeivvesvkkagleledgDivvvtekvvakaegnyvsledikpsekAeeiaeklkvidpilSrnrfsliL 83 
                                    +p+i++gd la+++ ++++     l dgD ++++++vv+k+eg++ +l++ +p e+A  ia++l ++dp           
  gi|116753480|ref|YP_842598.1|  13 LPVINKGDSLADLIQSRFE-----LLDGDLICIASTVVSKSEGRVRELSSYTPCERALAIAKNL-GKDP----------- 75 
                                    79*************9999.....9***************************************.****........... PP

                                    .......HHHHHHHHTEEEEEE-..S-EEEE.......TTS-EEEGGG-B-TTS-TTEEE---S-HHHHHHHHHHHHHHH CS
                    F420_ligase  84 kalakatrkvevvlsepsdevgn..qlidekytdevlvklGllgsnagidesnveegllkllPedpdksaeeikkklker 161
                                           r+v++vl+e+s+++ +  +l++++       ++G++++nagid+snv+ g ++llPe+p+ sae i+++l+  
  gi|116753480|ref|YP_842598.1|  76 -------RFVQAVLEESSEILLDrpFLLVVT-------RFGHVCVNAGIDQSNVPPGKILLLPENPSLSAEMIRRELN-- 139
                                    .......***************999999999.......*************************************995.. PP

                                    HS---EEEE..EEEEEETTEECEEEEEEEEESB-SEEE-TT-B-TTS-B-S--EEEHHHHHHHHHHHHC-SSSS---EEE CS
                    F420_ligase 162 tgkdveVliygkDpegriweladpvvaigtsglealrdlrgkkdldgkelgttpravtdelgsladLvsGsadegtPvvl 241
                                      +d+ V+i  +D++gr+++ + ++vaig+sgl+++rd+r  +d +g++l++t +av+de++ +a+L++G+a ++tP+v+
  gi|116753480|ref|YP_842598.1| 140 --RDCPVII--TDTCGRPFRFGVTGVAIGWSGLSPIRDWREATDIHGRKLEITLEAVADEIAGMANLLMGEAGDSTPAVV 215
                                    ..699****..********************************************************************* PP

                                    EES CS
                    F420_ligase 242 vrg 244
                                    vrg
  gi|116753480|ref|YP_842598.1| 216 VRG 218
                                    **8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1783.87
//
Query:       gi|116753481|ref|YP_842599.1|  [L=221]
Description: hypothetical protein Mthe_0159 [Methanosaeta thermophila PT]
Scores for complete 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-37  127.7   0.0    4.2e-37  127.4   0.0    1.0  1  CofC          Guanylyl transferase CofC like
    1.5e-05   25.4   0.0    3.9e-05   24.1   0.0    1.6  2  NTP_transf_3  MobA-like NTP transferase domain


Domain annotation for each model (and alignments):
>> CofC  Guanylyl transferase CofC like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.4   0.0   4.6e-41   4.2e-37       3     202 ..       7     205 ..       5     217 .. 0.87

  Alignments for each domain:
  == domain 1  score: 127.4 bits;  conditional E-value: 4.6e-41
                           CofC   3 viiPvsainsaktrlseilseeerkellkamlldvidalkrld.vlvvse...deevleyaldelgvevvkekekdlnta 78 
                                     ++P+++    ktrls+ ls+e+r +l+ aml dv  +l ++  v v+++    e+++     +l+   ++     ln+ 
  gi|116753481|ref|YP_842599.1|   7 CVVPFKSSG-CKTRLSSALSGEQRWQLAVAMLRDVLRTLRSIGmVTVLARpgmREDIIADLDATLRFSELELG-DALNGF 84 
                                    689**9998.9******************************99555665422256666555546666666555.78**** PP

                           CofC  79 vekafeeieekeviiipsdiPlikkedvkdllelekradvviaPargGGtnllllrksalevkyedfsflkhleearkrg 158
                                    +++   +   ++++i+++d+Pli++edv +++ + +   vv+aP+rgGGtn++l+r s ++ +y++ sf kh +ea + g
  gi|116753481|ref|YP_842599.1|  85 IDENTAAGWPADILIVMADLPLIREEDVLEMIRTPG--GVVLAPGRGGGTNMILIRDSRFRTRYKGLSFAKHKREAEELG 162
                                    *999899999*************************9..9***************************************** PP

                           CofC 159 lkvkiydsfylsvdinteedlgeillhGegtkakeylrklgfsv 202
                                    +++    s+    di+++ dl eillh +g+ ++  l ++g+ +
  gi|116753481|ref|YP_842599.1| 163 IEAGYCYSYRAGCDIDEPGDLIEILLHTNGE-SRALLERFGLRI 205
                                    ***9999*********************995.778888887766 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 !   24.1   0.0   4.3e-09   3.9e-05      25     145 ..      35     150 ..      16     166 .. 0.82
   2 ?   -1.6   0.0      0.35   3.2e+03      41      66 ..     185     209 ..     170     214 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 4.3e-09
                                    CHHHHHHHHHCTT.-CEEEEECSHCHHHHHHTTCTS-EEE-TTSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHH CS
                   NTP_transf_3  25 pllervldalraagvdevvvvggdeevlaalarlgvrvvededpgkgplaslaaalraaadadavlvlacDmPlltpelv 104
                                     +l+ vl++lr+   + v+v +++   ++ +a+l++++   e +    l ++     aa++   +l++++D+Pl+++e v
  gi|116753481|ref|YP_842599.1|  35 AMLRDVLRTLRSI--GMVTVLARPGMREDIIADLDATLRFSELELGDALNGFIDENTAAGWPADILIVMADLPLIREEDV 112
                                    699********87..68*******999**************99888899998888888999999**************** PP

                                    HHHHHCHHHHTSSEEEEESSSEEEECCEEEGGGHHHHHHHC CS
                   NTP_transf_3 105 erllaaaaasgadvvvptyegerghpllfrarllsalaall 145
                                     ++++     g+ v++p + g+    l+  +r + + + l+
  gi|116753481|ref|YP_842599.1| 113 LEMIRT---PGGVVLAPGRGGGTNMILIRDSRFRTRYKGLS 150
                                    999997...46666667666666444455666666665554 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.35
                                    EEEEECSHCHHHHHHTTCTS-EEE-T CS
                   NTP_transf_3  41 evvvvggdeevlaalarlgvrvvede 66 
                                    e+++ ++ e+ +a l+r+g+r++e +
  gi|116753481|ref|YP_842599.1| 185 EILLHTNGES-RALLERFGLRILESD 209
                                    6677777765.568999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       236  (0.013163); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1633.68
//
Query:       gi|116753482|ref|YP_842600.1|  [L=586]
Description: molybdenum cofactor synthesis domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-43  147.7   1.6    3.5e-43  147.1   1.6    1.3  1  MoeA_N         MoeA N-terminal region (domain I and II)
    2.5e-21   75.9   0.0    7.7e-21   74.3   0.0    1.9  2  MoCF_biosynth  Probable molybdopterin binding domain
    1.5e-14   53.9   0.0    9.6e-14   51.3   0.0    2.4  2  MoeA_C         MoeA C-terminal region (domain IV)
    3.2e-08   32.9   0.0    7.5e-07   28.5   0.0    2.4  1  PBP_like       PBP superfamily 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 !  147.1   1.6   7.8e-47   3.5e-43       1     157 []       9     173 ..       9     173 .. 0.89

  Alignments for each domain:
  == domain 1  score: 147.1 bits;  conditional E-value: 7.8e-47
                                    B-HHHHHHHHHHH-HH-EEE.EEGGCG-TT-BBSS-EE-SS-BSSS-EESSSEEEEEEBTTB--................ CS
                         MoeA_N   1 lsveealaiilaaleleeee.vplaaealgrvlaedvvApedvPpfdnSamDGYAvraeagsgaseeep........saa 71 
                                    +s+++a+++ l  ++ ++ + v+l ++algrvlae+v+A++dvP+fd++amDGYAvr+e+   ase++p        + a
  gi|116753482|ref|YP_842600.1|   9 ISLDKAIELALGDAPRPRVRiVNL-ESALGRVLAENVIAEIDVPHFDRAAMDGYAVRSEDCIIASESSPvrlrivgsVSA 87 
                                    588999998888885456666999.99**************************************************888 PP

                                    ...-S---TT-.EEEE-TTSB--TT--EEEEGGGE..E....EETTES--STTTTEE-TTSSB-TTSEEE-TTBB--CCC CS
                         MoeA_N  72 geeperllpgg.avrimTGaplPegadaVvpvEdte.eeeaketvevkavkpgenvrraGedikaGevllragtrltpae 149
                                    g+ p+++  +g av++ TG+++PegadaVv+vE+++ ++     + +++v+p env+r+G d++ Ge +l+agt+l+p+e
  gi|116753482|ref|YP_842600.1|  88 GSIPDASAGPGeAVEVSTGSAMPEGADAVVMVEYADaAD--GYVMIRRPVHPYENVQRRGADLSLGERVLSAGTHLGPRE 165
                                    888888888888**********************95322..2223338******************************** PP

                                    HHHHHHCT CS
                         MoeA_N 150 igllasvG 157
                                    ig+la++G
  gi|116753482|ref|YP_842600.1| 166 IGMLAALG 173
                                    ******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 !   74.3   0.0   1.7e-24   7.7e-21       2     143 ..     186     321 ..     185     322 .. 0.92
   2 ?   -2.7   0.0      0.91   4.1e+03     107     130 ..     487     513 ..     410     516 .. 0.50

  Alignments for each domain:
  == domain 1  score: 74.3 bits;  conditional E-value: 1.7e-24
                                    EEEE-HHHH.......TTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSSTT--H CS
                  MoCF_biosynth   2 vitvGdell.......sgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGptpdDvt 74 
                                    v ++G+e+        + ki+D n+++++++l+++g+e   y+v pD +++++e++++al + d+ i++G t++++ D+ 
  gi|116753482|ref|YP_842600.1| 186 VASTGNEIQspdehlmPCKIYDVNTYTISSALSQIGAEPVVYGVFPDSYDALSESIATALIDCDMMILSGSTSAGRGDML 265
                                    5677888877777778999*************************************9999999***************** PP

                                    HHHHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EETTEEEEE-SSHHHHHHHHHHHHHGGHH CS
                  MoCF_biosynth  75 pealaklfekelegfeeafrrvslkpgkpvgvapgailsravgktiigLPGspkavkealeeillpale 143
                                    ++++++l+e        +f++++lkpgkp++++++   ++   k++igLPG+p ++ +++  +++p ++
  gi|116753482|ref|YP_842600.1| 266 YRVVSDLGE-------LVFHGINLKPGKPTLFGRV---GG---KHVIGLPGYPTSALTVFWQLVSPLVH 321
                                    *********.......8*****************9...44...58**************9999988775 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.91
                                    GGGGGGE.EE..TTEEE..EE-SSHHHH CS
                  MoCF_biosynth 107 apgailsrav..gktii..gLPGspkav 130
                                    a++a ++r    g  i+  +LPG+ ++v
  gi|116753482|ref|YP_842600.1| 487 AAFAAWGRDSgvG-CIMdsMLPGVRRSV 513
                                    3334444443211.13334677776665 PP

>> MoeA_C  MoeA C-terminal region (domain IV)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.66     3e+03      47      56 ..     124     133 ..     118     139 .. 0.82
   2 !   51.3   0.0   2.2e-17   9.6e-14       1      72 []     334     399 ..     334     399 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.66
                                    T--EEEEE-T CS
                         MoeA_C  47 eAnglivipe 56 
                                     A+g+++i +
  gi|116753482|ref|YP_842600.1| 124 AADGYVMIRR 133
                                    59*****986 PP

  == domain 2  score: 51.3 bits;  conditional E-value: 2.2e-17
                                    EEEESS-EE--SSS-EEEEEEEES-S-EEEEEE-S---TT-GGGCTT--EEEEE-TT--EE-TT-EEEEEE- CS
                         MoeA_C   1 karlaedlksdpgrreflRvilteedgeyvaeptgkqgSglLsslaeAnglivipegtegleaGeeVevill 72 
                                    ka+la++++s++ rr++l+vi++    + +a+p+  +gSg++++l  ++g+i +p+++e+l+aGe+++v++l
  gi|116753482|ref|YP_842600.1| 334 KATLARPFRSES-RRQMLPVIIH----RGKAYPF-DRGSGAVTTLGASDGIIDVPADREYLHAGEVFDVHPL 399
                                    799*********.**********....789****.**********************************987 PP

>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   1.7e-10   7.5e-07      10     178 ..     424     562 ..     417     576 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.7e-10
                                    TCEEEEEES-HHHHHHHHHTTS-SEEEESS---CCCHHCCCCCEEEEEEEEEEEE-CC-HCHCCCCHCCHHHS--BGGGC CS
                       PBP_like  10 gvrvavanvGsggGlkalrageadiagshlldketeeynapalrkaldgievvlvnlarreqglvvakgnpkkitnwkdl 89 
                                    ++r+++ + Gs+ +l+ l++g adia +   ++             l++ ++ +v  +rre gl+ +           dl
  gi|116753482|ref|YP_842600.1| 424 NLRFRYLVRGSMRALTDLQDGLADIACITATQE-------------LPE-DLRVVASYRRELGLISRNP---------DL 480
                                    68999999*****************98765553.............445.689************9988.........55 PP

                                    ..-S-B-EEEEE-TTSHHHHHHHHHHC-CEECTE-SSTTSEEESSHHHHHCCHCCETTCCECCCGG-HCCCCCCECTTCE CS
                       PBP_like  90 ..adaplrlvnRetGSGtrdlfdellkkegiskssikgyaqearshlavaaaVaagradvgvgieavaeelkgldfvpla 167
                                      ++ ++ ++  +++SG    +d++l +      ++   + e+r+h  +a aV +g+ad ++g + +a  + gl f  la
  gi|116753482|ref|YP_842600.1| 481 llNSDGAAFAAWGRDSGVGCIMDSMLPG-----VRR---SVEVRTHTGAALAVLQGKADLALGAREAAGMW-GLHFRYLA 551
                                    5699**********************43.....222...459**************************866.****9999 PP

                                    -EEEEEEEECT CS
                       PBP_like 168 eerydlvvrke 178
                                    +    +v r +
  gi|116753482|ref|YP_842600.1| 552 DDGISIVARMD 562
                                    87666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (586 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); 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 0.24s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 4299.85
//
Query:       gi|116753483|ref|YP_842601.1|  [L=373]
Description: chorismate synthase [Methanosaeta thermophila PT]
Scores for 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-147  488.6   0.1   6.8e-147  488.4   0.1    1.0  1  Chorismate_synt  Chorismate synthase


Domain annotation for each model (and alignments):
>> Chorismate_synt  Chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  488.4   0.1  3.8e-151  6.8e-147       1     327 []      11     365 ..      11     365 .. 0.96

  Alignments for each domain:
  == domain 1  score: 488.4 bits;  conditional E-value: 3.8e-151
                                    SEEEEE-SCCSSEEEEEEE---BT-B--HHHHHHHHHHHTCTSSSSSSHHHCS-EEEEESSEETTEE-SS-EEEEEE-TT CS
                Chorismate_synt   1 lrvttfGeShgkalgavidgvpagleldeediqkeLdrRrpgqsklttqrkEkDeveilsGvfegktlGtpiallieNkd 80 
                                    +rvtt+GeShg+a+g+v+dg+pag+el+e d+q+eLdrRrpgqs++tt+r+E+D+veilsG+feg t+Gtpi++l++N+d
  gi|116753483|ref|YP_842601.1|  11 FRVTTWGESHGRAIGVVVDGCPAGIELSEMDVQRELDRRRPGQSTATTERHEADSVEILSGIFEGITTGTPISMLVWNRD 90 
                                    89****************************************************************************** PP

                                    S-..SSSSSTSBE-TTSTCHHHHHHC-S.STHCCCCCTHHCHHHHHHHHHHHHHHHHTTTEEEEEEEEEETTE....... CS
                Chorismate_synt  81 qrskdyeeikevpRpgHADltyalkYgirdlrgggrsSaReTaarvaaGavakklLkelgieivayvssigei....... 153
                                    +rs++y++i+++pRpgHAD+ty++kYgird+rgggr+SaReT++rvaaGava+klL+e+g+ei++yvs++g+i       
  gi|116753483|ref|YP_842601.1|  91 ARSSHYDSIRHTPRPGHADYTYHVKYGIRDHRGGGRASARETVGRVAAGAVARKLLSEFGVEIAGYVSELGGIsaslprw 170
                                    ***********************************************************************888888888 PP

                                    ...............CHHHHHTT-BS-CCCHHHHHHHHHHHHHTT--B-EEEEEEEES--TT-SBTTTB-HHHHHHHHHH CS
                Chorismate_synt 154 ...............ekeaenpvrcpdeeaaeemeeaieeakkegdslGgvvevvvkgvpaGlGepvfdkldakLakalm 218
                                                   e+++++p+rcpd++a+++m +++++++++gds+Ggvvev++ gvp+GlGepvfdklda+Lakalm
  gi|116753483|ref|YP_842601.1| 171 tsrgsiereelldirERAESSPIRCPDAAASSRMLSLLDSVRSDGDSIGGVVEVIAIGVPPGLGEPVFDKLDADLAKALM 250
                                    888888888888875434667*********************************************************** PP

                                    TSTTEEEEEETTGGGGGGSBHHHHS--EEEE......SS-TTTTEETTEEBSS-EEEEEEE--SS--SSEEEEEBTTS-E CS
                Chorismate_synt 219 sipAvkgveiGsGfeaaelkGseanDeivlr......ktnnaGGieGGisnGepivvrvavKpipsiakeqktvdletke 292
                                    si+Avk+veiG+Gfe+a+l+Gse+nD+++++      ++nnaGGi+GGis+G+pi++r+avKp+psia++q+tvd+ + e
  gi|116753483|ref|YP_842601.1| 251 SIGAVKAVEIGAGFESARLRGSEMNDPLFYEngrisfERNNAGGILGGISTGAPILCRMAVKPTPSIARSQRTVDMVSGE 330
                                    ****************************944556678******************************************* PP

                                    -EEEE--S-S-S-THHHHHHHHHHHHHHHHHHHHH CS
                Chorismate_synt 293 evelevkgrhDpcvvpravvvveamvalvladall 327
                                    +v+++v+grhDp++ pr+v+v+eamvalvlad++l
  gi|116753483|ref|YP_842601.1| 331 SVDISVRGRHDPSIPPRIVPVAEAMVALVLADHIL 365
                                    ********************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       262  (0.0146132); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2666.63
//
Query:       gi|116753484|ref|YP_842602.1|  [L=142]
Description: ribonuclease H [Methanosaeta thermophila PT]
Scores for 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-16   57.8   0.0    9.9e-16   57.7   0.0    1.1  1  RVT_3     Reverse transcriptase-like
    7.3e-08   32.7   0.0    1.2e-07   32.1   0.0    1.3  1  RNase_H   RNase H
  ------ inclusion threshold ------
       0.11   12.2   0.0       0.22   11.2   0.0    1.5  1  Cupin_3   Protein of unknown function (DUF861)


Domain annotation for each model (and alignments):
>> RVT_3  Reverse transcriptase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.7   0.0   1.7e-19   9.9e-16      19     124 .]      24     131 ..       5     131 .. 0.80

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 1.7e-19
                          RVT_3  19 irdsnGevllagaek..lqgkasveeAElqALlrGLqlalklg.irrlvvegDsktvvqllngrekvksselanlldeir 95 
                                    ++  nGe+l+ g      ++++++ +AE++ALl +++ ++k+   +r+v++gDs  v+++++g+++v+s   ++++  i+
  gi|116753484|ref|YP_842602.1|  24 LVYRNGELLHRGWGVvgEGSGMTNNVAEYEALLAAIRWIQKNApGERVVFKGDSNLVIKQMSGEWRVRSHTSKRYVPIIK 103
                                    5555666665544442236799*****************99872588*******************99999999999999 PP

                          RVT_3  96 kllksfesvsvehipReqNrvAdalAkra 124
                                    ++l+   + ++ ++pRe+N  Adal+k+a
  gi|116753484|ref|YP_842602.1| 104 SMLEGI-EHEFVWVPREENAEADALSKHA 131
                                    999998.89*****************987 PP

>> RNase_H  RNase H
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0   1.9e-11   1.2e-07       4     141 ..       2     131 ..       1     133 [. 0.69

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 1.9e-11
                                    EEEEEEEEEECTTTCE..EEEEEECTT.....EEEEEEEC.CCCHHHHHHHHHHHHHHH.TT.SC...SEEEEEES-HHH CS
                        RNase_H   4 vvvYtDGsclgnpgeg..gagavlykeg...arnisaple.eaqtnnraELsAvieaLk.alksd...ekvniytDSkYv 73 
                                    ++v+ DG c+ ++  g   +g+++y++g   +r +    e    tnn aE +A+ +a++   +++   e+v+ + DS+ v
  gi|116753484|ref|YP_842602.1|   2 ITVFFDGLCSPKNPGGvaAYGYLVYRNGellHRGWGVVGEgSGMTNNVAEYEALLAAIRwI-QKNapgERVVFKGDSNLV 80 
                                    68*******9886666336666779998886556665555679****************54.4444789*********** PP

                                    HHHHHCCCHHHHHTTSSSETTSSBHTTHHHHHHHHHCHCSSEEEEEE-SCCSSSTHHHHHHHHHHHHH CS
                        RNase_H  74 vkgitqwvhrwkknawkttseqkpvknkdlaellkelakkkkvqlkwvkgHaGvpkgNemaDrlAkea 141
                                    +k   q+  +w+ ++  t++         +  ++k++ +  + ++ wv+      ++N +aD l k+a
  gi|116753484|ref|YP_842602.1|  81 IK---QMSGEWRVRSH-TSKR--------YVPIIKSMLEGIEHEFVWVP----R-EENAEADALSKHA 131
                                    99...55567755444.3333........33333344566667777777....3.5677777777665 PP

>> Cupin_3  Protein of unknown function (DUF861)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.7e-05      0.22      49      74 .]      73      98 ..      64      98 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.7e-05
                                   ETTEEEEE-TTEEECCCEEEEEEEEE CS
                        Cupin_3 49 raGDlvvlpkglsgtwdvsetvrKaY 74
                                    +GD+  + k +sg+w+v+ ++ K+Y
  gi|116753484|ref|YP_842602.1| 73 FKGDSNLVIKQMSGEWRVRSHTSKRY 98
                                   4799999999**************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); 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:                         3  (0.000167327); expected 0.2 (1e-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 0.27s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 971.10
//
Query:       gi|116753485|ref|YP_842603.1|  [L=195]
Description: NADPH-dependent FMN reductase [Methanosaeta thermophila PT]
Scores for 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-33  113.1   0.0    1.3e-32  112.7   0.0    1.1  1  FMN_red       NADPH-dependent FMN reductase
    3.5e-09   36.6   0.0    4.5e-09   36.3   0.0    1.2  1  Flavodoxin_2  Flavodoxin-like fold


Domain annotation for each model (and alignments):
>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.7   0.0   1.4e-36   1.3e-32       3     145 ..       4     150 ..       2     157 .. 0.91

  Alignments for each domain:
  == domain 1  score: 112.7 bits;  conditional E-value: 1.4e-36
                                    EEEEES--STT-HHHHHHHHHHCCT-T.T-CEEEEETTTS..--..---HCHGHT....CGGSHHHHHHHHHHHH-SCEE CS
                        FMN_red   3 ilvisGSlrkgsntrklaewaaealkeagaevelidladl.ilpcalcdkdlese....gqtsddvaellekiaaadali 77 
                                    +l+isGS+++g+nt+ l+++a++ + e+g  +e +  + l    c   ++  e++    ++ +dd+ +++e +++ad+++
  gi|116753485|ref|YP_842603.1|   4 VLGISGSPKSGRNTEYLLQRALRVASERGYRTESVLCSRLrVGFC---TDCGECSkgkpCPIDDDMVKIYELLQNADGIV 80 
                                    89*********************************9999966664...333333346669******************** PP

                                    EEEEECTTCE-HHHHHHHHCHT-..SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHH.HTT-EEEEC CS
                        FMN_red  78 ivtPeYngsysgllKnalDrlsr.trgkkelrgKpvalvavgggrrgglraeeqlrqvla.elgaivvpr 145
                                    +++P+Y+gs++++lK+++Dr+ + +r++  lr+K++ ++avgg+r+gg++ + ++ ++++ ++g+ivv++
  gi|116753485|ref|YP_842603.1|  81 VASPVYFGSVTAQLKAIFDRTLPlRRQGFRLRDKAGCAIAVGGSRNGGQEKTIEAIHAWMhIHGMIVVGD 150
                                    ********************9779************************************88******98 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.0     5e-13   4.5e-09       3     167 ..       4     145 ..       2     172 .. 0.77

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 5e-13
                                    EEEEE--TTGGCCHHHCHHHHHHHHHCCCTT..TEEEEEEHHCCT-----CCCCHCCHHHHTT..CHHHHHHH.HHHHHC CS
                   Flavodoxin_2   3 iLiinahprpeksfssalaqafvealekagp..hevtvrdLyadflpvlttrdlaaklayeek..padveseq.ieklla 77 
                                    +L i ++p+  + ++  l+q++++ + + g   + v +  L  +f+  + +        ++ k  p+d ++ +  e l++
  gi|116753485|ref|YP_842603.1|   4 VLGISGSPKS-GRNTEYLLQRALRVASERGYrtESVLCSRLRVGFCTDCGE-------CSKGKpcPIDDDMVKiYELLQN 75 
                                    6779999999.5888999999999999998767778888888876666665.......6666664599999999****** PP

                                    SSEEEEEEE-BTTB--HHHHHHHHHHS-TTTSCEETTCSSCCCCTTT.TSEEEEEEEESS-GGGSSTTSSS-S-HHHHHH CS
                   Flavodoxin_2  78 adaivlqfPlwwfgvPailKgwiDrvltagfafyteeggegrgggLk.gkkalvivttGgpeesyqerglegaamdellp 156
                                    ad iv+++P+++ +v a+lK+ +Dr l   +            +g++   ka +++++Gg+       g++    + ++ 
  gi|116753485|ref|YP_842603.1|  76 ADGIVVASPVYFGSVTAQLKAIFDRTLPLRR------------QGFRlRDKAGCAIAVGGSRN-----GGQ----EKTIE 134
                                    *************************977666............45555778999999999932.....222....34444 PP

                                    HHHHHHHHTT- CS
                   Flavodoxin_2 157 plrgilgfiGi 167
                                      +++++  G+
  gi|116753485|ref|YP_842603.1| 135 AIHAWMHIHGM 145
                                    45566666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 1355.39
//
Query:       gi|116753486|ref|YP_842604.1|  [L=200]
Description: hypothetical protein Mthe_0165 [Methanosaeta thermophila PT]
Scores for complete 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   49.7   0.0    1.5e-12   48.0   0.0    1.8  2  CxxCxxCC  Putative zinc- or iron-chelating domain
  ------ inclusion threshold ------
      0.043   14.2   0.0      0.077   13.4   0.0    1.3  1  AAA_17    AAA domain


Domain annotation for each model (and alignments):
>> CxxCxxCC  Putative zinc- or iron-chelating domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.0   0.0   1.7e-16   1.5e-12       2      72 ..      26     116 ..      25     131 .. 0.87
   2 ?   -1.1   0.0      0.37   3.3e+03      26      50 ..     151     184 ..     127     188 .. 0.55

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 1.7e-16
                       CxxCxxCC   2 CkeCgaCCk..elkvklteedlerlkaaevaeeeeeskkiak..................adgrCvfldeetklCkiYee 61 
                                    C++Cg+CC+  +++v + + +++r+  +   +  e  +  ++                  +++ C ++d +++ C+iY  
  gi|116753486|ref|YP_842604.1|  26 CRRCGDCCRgpDAEVLVFPSEVRRIISYTNLTWLEVVEPPKTgvwdvdgdfhtlewmlrrSENGCAYYDATSGSCRIYPV 105
                                    *********998999999******99888877777777766699************************************ PP

                       CxxCxxCC  62 Rpkicrlfpas 72 
                                    Rp+icr++p+ 
  gi|116753486|ref|YP_842604.1| 106 RPDICRTYPFY 116
                                    *********96 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.37
                       CxxCxxCC  26 aaevaeeeeeskkiak.........adgrCvfld 50 
                                      e++ee e ++++ k          +g Cv+ d
  gi|116753486|ref|YP_842604.1| 151 ISEIMEEREARSRFSKfvvadrpekPTGVCVVHD 184
                                    3334333333333333444445555566666665 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   8.6e-06     0.077      21      80 ..     113     173 ..     110     183 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.6e-06
                                    EEEEEHHHHHH.HHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE-S CS
                         AAA_17  21 fthlsaGdllr.eeakrgglakardemrklpleekkelqkeaaekiaeeakkkgvlvdghp 80 
                                    ++++  Gd+lr +e++  gl+++ de  +  ++ k++l  e++e+ + +++ ++++v   p
  gi|116753486|ref|YP_842604.1| 113 YPFYLDGDVLRvSECRGLGLEMDYDEALRIAEDLKRRLISEIMEEREARSRFSKFVVADRP 173
                                    667777*****9****99**99999998888888999999998888888888999998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1433.09
//
Query:       gi|116753487|ref|YP_842605.1|  [L=181]
Description: GMP synthase subunit A [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-32  111.9   0.0    3.5e-32  111.7   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
      2e-13   50.6   3.3    1.1e-12   48.2   1.2    2.5  2  Peptidase_C26  Peptidase C26
  ------ inclusion threshold ------
        0.2   11.2   0.6       0.75    9.4   0.6    1.8  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.7   0.0   5.8e-36   3.5e-32       2     187 ..       5     176 ..       4     179 .. 0.92

  Alignments for each domain:
  == domain 1  score: 111.7 bits;  conditional E-value: 5.8e-36
                                    EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTTTTTHHHHHHHHCTSTS-EEEETHHH CS
                         GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspgvegkieaikearenkiPiLGICLGm 81 
                                    +++ny ++++ + +++   +v+  ++ ++++ e i      +dg+++ gGp     +    + +++r+ +iP+LGICLG+
  gi|116753487|ref|YP_842605.1|   5 VVNNYGQFNHLIYRSIK-DRVEARMISNETPVEDIV-----ADGLILGGGPSMDRSGR---CSEYLRTLDIPVLGICLGL 75 
                                    899******99999877.567**********99995.....9********98776665...566777899********** PP

                                    HHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEEET CS
                         GATase  82 QllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelmeiiekk 161
                                    Q++a  fg+kv++ k  ++   ++++ + e ++l+g + ++ ++ +H + v+     p +++v+a+s + + +++i +++
  gi|116753487|ref|YP_842605.1|  76 QIMAVTFGGKVEPGKVGGYASVEIEVLE-EDGILRGVPHRFMAWASHADQVTI---CPPEFRVIARS-SICDIEAICHES 150
                                    **************************99.67*********************7...***********.6689******** PP

                                    TTEEEESSBTTSTTSTTHHHHHHHHH CS
                         GATase 162 npfvgvQFHPEststpegpellfnfl 187
                                    +p++gvQ+HPE+ +t+ g+e++ nfl
  gi|116753487|ref|YP_842605.1| 151 RPLYGVQWHPEVAHTEYGEEVFDNFL 176
                                    *********************99986 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.37   2.2e+03      59      70 ..      40      51 ..      29      55 .. 0.80
   2 !   48.2   1.2   1.8e-16   1.1e-12     104     216 .]      64     161 ..      57     161 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.37
                  Peptidase_C26 59 ldgllltGgqdv 70
                                    dgl+l Gg+ +
  gi|116753487|ref|YP_842605.1| 40 ADGLILGGGPSM 51
                                   59******9865 PP

  == domain 2  score: 48.2 bits;  conditional E-value: 1.8e-16
                  Peptidase_C26 104 rgvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavk.vekgsllaellgseeievnslHhqaikela 182
                                     ++P+lgiC+Glq+++v++GG++                  +a s +++ +e++++l  +    +++    H   ++   
  gi|116753487|ref|YP_842605.1|  64 LDIPVLGICLGLQIMAVTFGGKVEPGKVG------G-----YA-SVEIEvLEEDGILRGVPH--RFMAWASHADQVTICP 129
                                    579******************98664331......2.....22.334441579999999988..8999999********* PP

                  Peptidase_C26 183 eelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                    +e+rv+A+++   iEai +e++  +++gvQwHPE
  gi|116753487|ref|YP_842605.1| 130 PEFRVIARSSICDIEAICHESR--PLYGVQWHPE 161
                                    *******************994..6********9 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.6   0.00013      0.75      10      92 ..       6      82 ..       1     103 [. 0.64

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00013
                       GATase_3 10 isnytdldpLeaep...evrvrfvplkdeslg.edadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqm 87
                                   ++ny+ ++ L +++   +v+ r+++ +++ ++   ad +il+Gg +        r+ +  e +++    ++pvlgiC Glq+
  gi|116753487|ref|YP_842605.1|  6 VNNYGQFNHLIYRSikdRVEARMIS-NETPVEdIVADGLILGGGPSMD------RSGRCSEYLRT---LDIPVLGICLGLQI 77
                                   6777777777665411133334444.3333334237889999987654......44444555666...479*********** PP

                       GATase_3 88 LGeei 92
                                   +  ++
  gi|116753487|ref|YP_842605.1| 78 MAVTF 82
                                   98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       247  (0.0137766); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1371.24
//
Query:       gi|116753488|ref|YP_842606.1|  [L=505]
Description: phosphoglyceromutase [Methanosaeta thermophila PT]
Scores for complete 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-84  283.2   0.0    1.5e-84  282.8   0.0    1.2  1  iPGM_N         BPG-independent PGAM N-terminus (iPGM_N)
    2.4e-82  276.0   0.0    2.8e-82  275.8   0.0    1.0  1  Metalloenzyme  Metalloenzyme superfamily
     0.0013   18.2   0.0      0.002   17.6   0.0    1.4  1  Sulfatase      Sulfatase
  ------ inclusion threshold ------
       0.06   12.9   0.0      0.094   12.3   0.0    1.3  1  Phosphodiest   Type I phosphodiesterase / nucleotide pyrophos
       0.17   12.1   0.0       0.33   11.1   0.0    1.4  1  NdhO           Cyanobacterial and plant NDH-1 subunit O


Domain annotation for each model (and alignments):
>> iPGM_N  BPG-independent PGAM N-terminus (iPGM_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  282.8   0.0   4.2e-88   1.5e-84       1     215 []      80     290 ..      80     290 .. 0.96

  Alignments for each domain:
  == domain 1  score: 282.8 bits;  conditional E-value: 4.2e-88
                                    HHHHHHCTGGGG-HHHHHHHHHHHHCTSEEEEEEE-SS--SS--CHHHHHHHHHHHHTT-SEEEEEEEE-SSSSTTT-HH CS
                         iPGM_N   1 inkaiedgslfenealkeaiekakkngkalHllGLlSdGgVHShidhllallelakeegvkkvvvhaflDGRDtapksal 80 
                                    i+ aie+++l++ ++l++a+ ka+++g++lHl+GLlSdGgVHShi+hl+all++ake g+kkv+vh +lDGRD++p+sal
  gi|116753488|ref|YP_842606.1|  80 ISLAIEQDRLKDAKQLVDAMVKARDSGRNLHLMGLLSDGGVHSHITHLFALLDMAKELGAKKVYVHPILDGRDVPPRSAL 159
                                    6789**************************************************************************** PP

                                    HHHHHHHHHHHHCT--EEEEEEEHHHHT--SS-HHHHHHHHHHHCCSSSEEECTTHHHHHHHHHHTT--GGG---EEE.. CS
                         iPGM_N  81 eyleeleeklkelgvgkiasvsGRyyaMDRdkrwervekaydalvkgegeskaesaveaieesyakgetDefveptviae 160
                                    +y+++leekl+++g+g+ia++sGRyyaMDRdkrw+r+e ay+a+++g g + a++avea++  y++getDef++ptvi  
  gi|116753488|ref|YP_842606.1| 160 TYVTQLEEKLTRIGIGRIATISGRYYAMDRDKRWDRTEAAYRAMTEGLGIH-AATAVEAVRLGYDRGETDEFLTPTVI-- 236
                                    **********************************************98766.789***********************.. PP

                                    .TCCGGS--TT-EEEE----CCCCHHHHHHHHSTTHHCC..--TT-EEEESS-S-T CS
                         iPGM_N 161 egkkegtikdgDaviffNFRaDRareltraltdkefkefe.kakklklvtmteYde 215
                                      +++g +++gD++iffNFR+DRar++tra+++++f+efe +  +  +v+mt+Yde
  gi|116753488|ref|YP_842606.1| 237 --DPNGLVREGDSIIFFNFRPDRARQITRAFVQPDFNEFErRYLRPFFVCMTQYDE 290
                                    ..89***********************************94333335*******96 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  275.8   0.0   7.8e-86   2.8e-82       2     248 .]       3     492 ..       2     492 .. 0.99

  Alignments for each domain:
  == domain 1  score: 275.8 bits;  conditional E-value: 7.8e-86
                                    EEEEEEETTBB----GGGTTHHHS--HHHHHHHHH.......SEEEEEESSSTT----HHHHHHHH.............. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............. RF
                  Metalloenzyme   2 kvvlvvlDGlGeapadelnaihvAktPtldkLkkeaPerwlikahgtavglpeddmgnsevgHlel.............. 67 
                                    +vvl+++DG+G ++++e na+  A +P+ld+Lk ++P++  ++a+g++vglp ++mgnsevgHl+l              
  gi|116753488|ref|YP_842606.1|   3 PVVLIIMDGYGLSEETEGNAVAGAHKPNLDRLKSQYPHT-SLGASGLDVGLPRGQMGNSEVGHLNLgagrivyqdytris 81 
                                    79*************************************.9*************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                  Metalloenzyme  68 ................................................................................ 67 
                                                                                                                    
  gi|116753488|ref|YP_842606.1|  82 laieqdrlkdakqlvdamvkardsgrnlhlmgllsdggvhshithlfalldmakelgakkvyvhpildgrdvpprsalty 161
                                    ******************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                  Metalloenzyme  68 ................................................................................ 67 
                                                                                                                    
  gi|116753488|ref|YP_842606.1| 162 vtqleekltrigigriatisgryyamdrdkrwdrteaayramteglgihaataveavrlgydrgetdefltptvidpngl 241
                                    ******************************************************************************** PP

                                    .............................................................................HHH CS
                                    .............................................................................xxx RF
                  Metalloenzyme  68 .............................................................................lri 70 
                                                                                                                 lri
  gi|116753488|ref|YP_842606.1| 242 vregdsiiffnfrpdrarqitrafvqpdfneferrylrpffvcmtqydesidapvafppeylketlgeilskagltqLRI 321
                                    ******************************************************************************** PP

                                    HTT-----EEEEEEEE-S---SSHHHHHT--EEEE--SHHSTT--HHHHHHHHHHHH.CC.-SEEEEEE-HHHHHHHTT- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Metalloenzyme  71 setvkfahvtffwnggrsgyfnpleereeipsdtvitfdlqpemkavevaekaldailsgkfdlvvvniknaDmvGHtgd 150
                                    +et+k+ahvt+f+nggr+++f++ e+r+ ips+++ t+dl+pem+a ev+  +++ i+sgk+d+v++n++n+DmvGHtg 
  gi|116753488|ref|YP_842606.1| 322 AETEKYAHVTYFFNGGREEPFPG-EDRILIPSPKIPTYDLKPEMSAPEVTSTVVERIKSGKYDVVIMNYANPDMVGHTGI 400
                                    ***********************.******************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHTTS-TTTEEEEEE-SSB--TTTSS.........-----EEEEEESTT----S--SSHHHHT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Metalloenzyme 151 leatiaaieaaDeavkeildaieqvdgilvvtADHgnaedmvkrdk.qplTsHtlepVPilivgkglapdkvkegakfre 229
                                    +ea+++a+ea+D+ v++++d++ +  gi ++tADHgnae+mv+r++ +p+T+Ht++ VP+++vg +  +     g+ +r 
  gi|116753488|ref|YP_842606.1| 401 YEAAVRAVEAVDRGVGMVVDEVLSRRGIALITADHGNAEKMVDRSTgEPHTAHTTNRVPFILVGCD--R-----GIVLRD 473
                                    *******************************************9989*****************96..4.....889999 PP

                                    T-TTEEEEGGGHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxx RF
                  Metalloenzyme 230 kggLanvaatllnllglea 248
                                    +g La+va+t+l llg+e+
  gi|116753488|ref|YP_842606.1| 474 DGILADVAPTILALLGIEK 492
                                    ****************985 PP

>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   5.5e-07     0.002     209     309 .]     399     490 ..     250     490 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 5.5e-07
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEEEESSSSCCCGHHTTSSSCTTCSSSHHHHBEEEEEEETTTSHCE CS
                      Sulfatase 209 qlleaylnsveyvDdligrvlaaLeenglldntlvvftSDhgasleesngplrggkganayeggtrvPllvwwpgekapr 288
                                      +ea  ++ve vD ++g v++++    l++  + ++t+Dhg +    + + r + +  + +   rvP+++ + ++    
  gi|116753488|ref|YP_842606.1| 399 GIYEAAVRAVEAVDRGVGMVVDEV----LSRRGIALITADHGNAE---KMVDRSTGEPHTAHTTNRVPFILVGCDRGIVL 471
                                    6789999*****************....***************54...56777777778999999******998887775 PP

                                    EECSEEEGGGHHHHHHHHTTE CS
                      Sulfatase 289 vseelvshiDlfptildlagi 309
                                    +++++    D++ptil+l+gi
  gi|116753488|ref|YP_842606.1| 472 RDDGILA--DVAPTILALLGI 490
                                    7777765..*********997 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.6e-05     0.094     170     235 ..     377     438 ..     299     457 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.6e-05
                                    T..SSESEEEEEECCCHHHHHHH-TTSHHHHHHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES---E CS
                   Phosphodiest 170 l..ekpdlllvyleetDtvgHkfGpdspevedalrrvDkaigdLlealderglsaetniilvSDHGma 235
                                       +k+d++++++ ++D vgH  G+++ +   a++ vD+ +g  ++++  r        ++++DHG a
  gi|116753488|ref|YP_842606.1| 377 IksGKYDVVIMNYANPDMVGH-TGIYEAA-VRAVEAVDRGVGMVVDEVLSR---RGI-ALITADHGNA 438
                                    1359*****************.7788766.568************999988...333.5789***965 PP

>> NdhO  Cyanobacterial and plant NDH-1 subunit O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   9.3e-05      0.33      12      50 ..     286     332 ..     282     335 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.3e-05
                           NdhO  12 ekyenSlealAsdgrlpdYifedkGEvldl..........kgdYalvkf 50 
                                     +y++S++a   +  +p+Y+ e+ GE+l+           ++ Ya v +
  gi|116753488|ref|YP_842606.1| 286 TQYDESIDAP--VAFPPEYLKETLGEILSKagltqlriaeTEKYAHVTY 332
                                    6899***998..99**************987777777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (505 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); 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 0.29s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 3454.94
//
Query:       gi|116753489|ref|YP_842607.1|  [L=213]
Description: hypothetical protein Mthe_0168 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.043   14.4   0.1        6.8    7.3   0.0    2.5  2  Chitin_bind_4  Insect cuticle protein


Domain annotation for each model (and alignments):
>> Chitin_bind_4  Insect cuticle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0   0.00038       6.8      18      43 ..      89     120 ..      77     121 .. 0.73
   2 ?    4.5   0.0    0.0029        53      23      44 ..     180     201 ..     162     202 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00038
                  Chitin_bind_4  18 r......tgtedeglvvqGsYsyvdpdGktrt 43 
                                    +      + +++++++ +Gs+s +  dG++++
  gi|116753489|ref|YP_842607.1|  89 TtaesidAVEQRAQINLSGSWSMNLSDGRHVE 120
                                    2333345567779***************9976 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0029
                  Chitin_bind_4  23 deglvvqGsYsyvdpdGktrtV 44 
                                    +e+  ++GsYs  + +G    V
  gi|116753489|ref|YP_842607.1| 180 QENNTISGSYSRFGTNGDAAIV 201
                                    78999******99999976555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); 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 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1533.59
//
Query:       gi|116753490|ref|YP_842608.1|  [L=90]
Description: translation initiation factor eIF-1A [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-24   84.9   1.2      3e-24   84.6   1.2    1.1  1  eIF-1a    Translation initiation factor 1A / IF-1
  ------ inclusion threshold ------
      0.046   13.9   0.0      0.062   13.5   0.0    1.2  1  DUF2007   Putative prokaryotic signal transducing protein


Domain annotation for each model (and alignments):
>> eIF-1a  Translation initiation factor 1A / IF-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.6   1.2   3.3e-28     3e-24       2      64 .]      10      71 ..       9      71 .. 0.98

  Alignments for each domain:
  == domain 1  score: 84.6 bits;  conditional E-value: 3.3e-28
                                   EEEEEEEEEETTTEEEEEE.SSSSBEEEEE-HHHHCT----TT-EEEEEE-TT-TTEEEEES- CS
                         eIF-1a  2 evigkViealgnnlfrVelpdngkevlaeipgkfRnkiwikrGdyVlVelspydltkGrIvyr 64
                                   ev g V+ +lg+n+++V+++d g++++a+ipgk++++iwi++Gd+V+V +++++++k+++++r
  gi|116753490|ref|YP_842608.1| 10 EVFGYVESLLGSNRIKVRCMD-GQTRIARIPGKMKKRIWIREGDVVIVVPWEFQDDKADVIWR 71
                                   899*****************6.***************************************98 PP

>> DUF2007  Putative prokaryotic signal transducing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   6.9e-06     0.062      14      56 ..      13      53 ..       6      54 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.9e-06
                        DUF2007 14 elikslLeeagIeavvkdeftssileGal.gelpvrilVaeedl 56
                                   ++++slL ++ I+++++d   ++i+   + g  + ri+++e d+
  gi|116753490|ref|YP_842608.1| 13 GYVESLLGSNRIKVRCMDGQ-TRIAR--IpGKMKKRIWIREGDV 53
                                   589****************9.55544..447778*****99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 689.99
//
Query:       gi|116753491|ref|YP_842609.1|  [L=265]
Description: protein of unknown function RIO1 [Methanosaeta thermophila PT]
Scores for complete 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-61  205.8   0.0    5.6e-61  205.4   0.0    1.1  1  RIO1      RIO1 family
    1.8e-05   24.8   2.2     0.0003   20.8   0.2    2.4  2  APH       Phosphotransferase enzyme family
    5.3e-05   22.7   0.0    9.8e-05   21.8   0.0    1.6  1  Pkinase   Protein kinase domain
    0.00087   18.7   0.1      0.014   14.8   0.1    2.3  2  Kdo       Lipopolysaccharide kinase (Kdo/WaaP) family


Domain annotation for each model (and alignments):
>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.4   0.0   1.3e-64   5.6e-61       1     179 [.      64     240 ..      64     247 .. 0.96

  Alignments for each domain:
  == domain 1  score: 205.4 bits;  conditional E-value: 1.3e-64
                                    EEEEEEETTTEEEEEEEE-S---SS-HHHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEEEET CS
                           RIO1   1 nVyhavsedgkevaiKiyktstteFkkrkkyvsgekrfkdrksktnprklvklwaekEfrnLkrleeagvpvPkpielkr 80 
                                    nV+ha  + gk++a+Kiy+++t++Fk ++ y+ g++rf++   k n+r+lv++w++kE+rnL r+ee gv+vP+p+++++
  gi|116753491|ref|YP_842609.1|  64 NVFHALGRGGKHLALKIYRVATSDFKAMQDYILGDPRFRSV--KGNKRSLVNAWTRKEYRNLLRAEEVGVRVPHPYAVRE 141
                                    7*************************************976..9************************************ PP

                                    TEEEEE--EETTEEGGBHHHCG.-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETTEEEE--GTTEEETTSTT CS
                           RIO1  81 hvlvmefigedgvaapklkdve.eeeeaeelyeevleemrklykeaglvHaDLSeyNvlvdedkvviIDvsQaveldhpn 159
                                    ++lvm+f+g+dg aap l++v  e eeae++y+ + +++  l ++aglvHaDLSe+N+l+ ++++v+ID++Qav+ldhpn
  gi|116753491|ref|YP_842609.1| 142 NILVMDFVGTDGAAAPLLREVAlEGEEAERAYRRIADYIVLLHNRAGLVHADLSEFNILY-DGEPVLIDMGQAVTLDHPN 220
                                    **********************8899*******************************776.577**************** PP

                                    HHHHHHHHHHHHHHHHHTTC CS
                           RIO1 160 alefLerDveniikfFrrkg 179
                                    a efL+rD++n+++fFr ++
  gi|116753491|ref|YP_842609.1| 221 AMEFLKRDISNLVRFFRERY 240
                                    ****************9876 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   1.0    0.0002      0.88       7     107 ..      59     185 ..      56     186 .. 0.65
   2 !   20.8   0.2   6.8e-08    0.0003     139     197 ..     164     214 ..     151     219 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0002
                                    -.SSCEEEEEEETT.--EEEEE..........................E-TTS-HHHHHHHHHHHHHHHHTT-B--B-CT CS
                            APH   7 ggasnrtylvttpa.gryvlrr..........................npparaaeeirrevallrlLakagvpvPevla 59 
                                     g +  +++  + + ++++l++                          n  +   + +r+e++ l   ++ gv+vP ++a
  gi|116753491|ref|YP_842609.1|  59 RGKEANVFHALGRGgKHLALKIyrvatsdfkamqdyilgdprfrsvkgNKRSLVNAWTRKEYRNLLRAEEVGVRVPHPYA 138
                                    5666666676666644777777555555555555555555555555543333345556788888888888888******* PP

                                    TBS-EEETTEEEEEEE----EE-SS..HHHHHHHHHHHHHHHHHHCCHHC CS
                            APH  60 gdtddeeigllfalieyvpgrsllr..klsaaqlpellealgeflaalhq 107
                                        ++ + + f+   +  +  l r  +l  ++++++++++++++  lh+
  gi|116753491|ref|YP_842609.1| 139 V--RENILVMDFVGTDGAAAPLL-RevALEGEEAERAYRRIADYIVLLHN 185
                                    3..34444445666666444444.46*******************99995 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 6.8e-08
                                    CCTCCHHHHHHHHHHHHHHHH--S.SS-EEEE-SS-SGGGEEEC..TTEEEEE---TT-E CS
                            APH 139 selldlleeleeqvlaalaallpg.elptvllHgDlhpgNllvdpddgrvtGviDfedag 197
                                    +e     ee+e+ +++++a+     + +++l+H Dl+  N+l d  + +v  +iD + a+
  gi|116753491|ref|YP_842609.1| 164 LE----GEEAER-AYRRIADYIVLlHNRAGLVHADLSEFNILYD--GEPV--LIDMGQAV 214
                                    23....345666.66666666666679*****************..9999..***99886 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   2.2e-08   9.8e-05      72     153 ..     141     221 ..      53     250 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 2.2e-08
                                    EEEEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHH.HTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESSS CS
                        Pkinase  72 elylvleyveggeladllerkgslseeeakkiakqilegleylH.skgiiHrDlKpeNiLidekgelKitDFGlakeles 150
                                    e +lv+++v ++  a  l r+++l+ eea++  ++i+  +  lH ++g++H Dl   NiL+d  ge  ++D G a  l++
  gi|116753491|ref|YP_842609.1| 141 ENILVMDFVGTDGAAAPLLREVALEGEEAERAYRRIADYIVLLHnRAGLVHADLSEFNILYD--GEPVLIDMGQAVTLDH 218
                                    5579*****999888878789***********************6678**************..9999*******99988 PP

                                    SCS CS
                        Pkinase 151 ssk 153
                                     + 
  gi|116753491|ref|YP_842609.1| 219 PNA 221
                                    764 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0      0.87   3.9e+03      91     107 ..      12      28 ..       4      68 .. 0.53
   2 !   14.8   0.1     3e-06     0.014      58     191 ..     116     237 ..     102     261 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.87
                            Kdo  91 rAlllterlegaqdLed 107
                                    r +l  +r+++a+dL++
  gi|116753491|ref|YP_842609.1|  12 RIDLFRRRIKDANDLKV 28 
                                    55666667777777754 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 3e-06
                            Kdo  58 avrEfrllkrLeeagvavpkpvaagavkvgleyrAlllterlegaqdLedllakwaelaeelkrallkavgrliaklh.r 136
                                     ++E+r+l r ee+gv+vp p a +++         +l+ +  g+   ++ l +   l++e  ++ +++++  i  lh r
  gi|116753491|ref|YP_842609.1| 116 TRKEYRNLLRAEEVGVRVPHPYAVREN---------ILVMDFVGTDGAAAPLLREVALEGEEAERAYRRIADYIVLLHnR 186
                                    678888888888888888888776543.........444455555555555555444889999**************967 PP

                            Kdo 137 agvnHadlyaknillqqeeeeeaeiwliDldkarlrlr..adrwrekdLarLkrsfl 191
                                    ag+ Hadl   nil + e       +liD+ +a +     a    ++d+ +L r f 
  gi|116753491|ref|YP_842609.1| 187 AGLVHADLSEFNILYDGEP------VLIDMGQAVTLDHpnAMEFLKRDISNLVRFFR 237
                                    9**************9987......99999988877663334455777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1844.58
//
Query:       gi|116753492|ref|YP_842610.1|  [L=174]
Description: putative RNA-processing protein [Methanosaeta thermophila PT]
Scores for 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-16   57.4   1.7    4.2e-08   32.9   0.0    2.2  2  KH_1       KH domain
      0.002   17.9   1.7        2.5    8.0   0.7    2.8  3  KH_2       KH domain
     0.0061   16.4   3.9        1.7    8.6   0.7    3.4  3  KH_4       KH domain
  ------ inclusion threshold ------
      0.073   13.4   1.0       0.24   11.8   1.0    1.8  1  GNAT_like  GCN5-related N-acetyltransferase like 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 !   32.9   0.0   9.4e-12   4.2e-08       4      62 ..       3      57 ..       1      61 [. 0.77
   2 !   23.6   0.6   7.5e-09   3.4e-05      11      63 ..     101     145 ..      97     149 .. 0.86

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 9.4e-12
                                   EEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEEESHHHHHHHHH CS
                           KH_1  4 ilvPsslvgriIGkgGsnIkeIreetgakIkvpksedegsderevtisGspeavekAke 62
                                   i++Ps+ +g++IG++G++ + ++e++ ++ +++ se+   +  +vt +G++ +  +A++
  gi|116753492|ref|YP_842610.1|  3 IKIPSDRIGAVIGPNGETKRYLEERCSVSLDID-SES---GAVTVTSQGDALDAMRAID 57
                                   89**********************999999987.654...4556665675555555555 PP

  == domain 2  score: 23.6 bits;  conditional E-value: 7.5e-09
                                    HHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEEESHHHHHHHHHH CS
                           KH_1  11 vgriIGkgGsnIkeIreetgakIkvpksedegsderevtisGspeavekAkel 63 
                                     griIGk G++   +++ tga+I v  +       ++v i+G pe+++  + +
  gi|116753492|ref|YP_842610.1| 101 KGRIIGKDGKTRELMESLTGARISVY-G-------KTVSIIGYPEQIKVVRSA 145
                                    59*********99999999*****87.5.......58*****99999877665 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0   0.00074       3.3      29      53 ..       3      27 ..       1      43 [. 0.85
   2 !    8.0   0.7   0.00056       2.5      36      68 ..     101     132 ..     100     135 .. 0.90
   3 ?   -0.8   0.0      0.31   1.4e+03      46      71 ..     138     163 ..     136     168 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00074
                                   EEEEESCHHHHHTGGGHHHHHHHHH CS
                           KH_2 29 iviresqpgivIGkgGsnikkigke 53
                                   i i + + g vIG +G++ + +++ 
  gi|116753492|ref|YP_842610.1|  3 IKIPSDRIGAVIGPNGETKRYLEER 27
                                   6777889***********9988876 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00056
                                    HHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEE CS
                           KH_2  36 pgivIGkgGsnikkigkelrkdieklegkkVkl 68 
                                    +g++IGk G++ + +++  + +i  + gk V++
  gi|116753492|ref|YP_842610.1| 101 KGRIIGKDGKTRELMESLTGARIS-VYGKTVSI 132
                                    89********************95.88888875 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.31
                                    HHHHHHHHHHHHHHHHHTTCEEEEEE CS
                           KH_2  46 nikkigkelrkdieklegkkVklniv 71 
                                     ik ++++l+  i+   +++V+ +++
  gi|116753492|ref|YP_842610.1| 138 QIKVVRSALEMLIDGAPHGNVYSFLE 163
                                    68999999999998888888886665 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.6   0.0    0.0031        14      32      50 ..       2      20 ..       1      22 [. 0.92
   2 ?    1.3   0.0     0.069   3.1e+02      28      57 ..      27      56 ..      21      64 .. 0.75
   3 !    8.6   0.7   0.00038       1.7      40      60 ..     101     121 ..      90     133 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0031
                           KH_4 32 elnvegedlGrvIGkrGrt 50
                                   ++++ ++ +G vIG +G+t
  gi|116753492|ref|YP_842610.1|  2 NIKIPSDRIGAVIGPNGET 20
                                   79999************98 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.069
                           KH_4 28 eveielnvegedlGrvIGkrGrtldAlqyl 57
                                   + ++ l++++e  ++ +  +G  ldA++ +
  gi|116753492|ref|YP_842610.1| 27 RCSVSLDIDSESGAVTVTSQGDALDAMRAI 56
                                   566677777777777777789999999975 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.00038
                           KH_4  40 lGrvIGkrGrtldAlqylvsa 60 
                                    +Gr+IGk+G+t   +  l+ a
  gi|116753492|ref|YP_842610.1| 101 KGRIIGKDGKTRELMESLTGA 121
                                    6*********96655555555 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 ?   11.8   1.0   5.3e-05      0.24       6      30 ..      34      62 ..      32      65 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.3e-05
                      GNAT_like  6 vevdggaltvsgtga....gdpldglRAl 30
                                   ++ + ga+tv+++g+      ++d+lRA+
  gi|116753492|ref|YP_842610.1| 34 IDSESGAVTVTSQGDaldaMRAIDVLRAI 62
                                   678899*******5334445555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); 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: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 1257.26
//
Query:       gi|116753493|ref|YP_842611.1|  [L=518]
Description: peptidase M50 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-23   82.8   0.0    1.6e-22   80.0   0.0    2.1  1  Peptidase_M50  Peptidase family M50
    6.1e-06   26.5   0.9    1.5e-05   25.2   0.0    1.9  2  PDZ_2          PDZ domain
  ------ inclusion threshold ------
       0.12   12.2   0.0       0.35   10.8   0.0    1.8  1  PDZ_6          PDZ domain
        5.6    7.3  12.2       0.64   10.3   0.4    3.2  3  DUF3267        Putative zincin peptidase


Domain annotation for each model (and alignments):
>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.0   0.0   3.6e-26   1.6e-22       4     245 ..     122     493 ..     119     498 .. 0.79

  Alignments for each domain:
  == domain 1  score: 80.0 bits;  conditional E-value: 3.6e-26
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M50   4 lllgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallpLGGyVkmageepeeelseeeakaflkks 83 
                                    ++l + +vvHEl H+++ + +g++v+++++ f                 l+p+G++V+ ++ e   +     +k+  k++
  gi|116753493|ref|YP_842611.1| 122 IALCVTIVVHELSHGILCRVEGIRVKSMGLIF----------------LLFPIGAFVEPDDSELFGD-----EKNPPKAT 180
                                    89*************************99999................89*********99885444.....33346899 PP

                                    XXXXXXXXXXXXXXXXXXXXXXXXX....................................................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx....................................................... RF
                  Peptidase_M50  84 pwqrllivlAGplanfilailvfvv....................................................... 108
                                    + +r++i+ AG +anf++a l++ +                                                       
  gi|116753493|ref|YP_842611.1| 181 CQARIRILSAGVIANFLVAALALSLffgpvisalspvdrvvvvdvdpesrfagdvragmvvsgassleelyriasegrsl 260
                                    *******************99999999***************************************************** PP

                                    ............................................................................-EEE CS
                                    ............................................................................xxxx RF
                  Peptidase_M50 109 ............................................................................pkks 112
                                                                                                                    
  gi|116753493|ref|YP_842611.1| 261 elfddtsraiisgepvlgvqvvdtfdgspakdagmperfvitdindtrvdslesfrdymnstypgqilkinttkgsY--- 337
                                    **********************************************************9999999999887655431... PP

                                    CE....CTTTSCEE-SEEEC-...................XXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXX....XXX. CS
                                    xx....xxxxxxxxxxxxxxx...................xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx....xxx. RF
                  Peptidase_M50 113 ke....seeekrgviGvspkp...................vkkegllealk.egvektlkvvvltvkalgkl....itg. 163
                                     +     + +++g+iGv  +                         l++++  +g++ + +++ l ++ ++++    ++g 
  gi|116753493|ref|YP_842611.1| 338 -SvklaPKGDGTGMIGVAISGtalyldgvtfqelqperflA----LMRSIPsSGLKGFNTLMGLPFTGVVGFtsdgFQGf 412
                                    .1445678999999999999889999999877655533331....22222101222222222222222222200002222 PP

                                    XXXXXXXXXXXXXXXXXXXXXXXXXX.......XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M50 164 klslktlggpisiaqlaseaaeagls.......sflqllalisvnLgilNLlPipvLDGghllfalleairrkplserke 236
                                    + s+  l  p + a+                  ++l ++ +i++  g++N lP  +LDGgh+++ ++ ++  k +ser  
  gi|116753493|ref|YP_842611.1| 413 SGSMLYLFEPAGWAEPL--------GgkifwiaNLLLWIGWINMYAGLFNCLPTIPLDGGHIARDMIRMLLDKVMSERSA 484
                                    22222233333333322........13344557*******************************************9998 PP

                                    XXXXXXXXX CS
                                    xxxxxxxxx RF
                  Peptidase_M50 237 evanlvgla 245
                                    e  ++  +a
  gi|116753493|ref|YP_842611.1| 485 ERFTRGIVA 493
                                    877766555 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.57   2.5e+03      14      29 ..     218     233 ..     208     242 .. 0.75
   2 !   25.2   0.0   3.4e-09   1.5e-05      14      71 ..     277     334 ..     264     342 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.57
                                    .-EEEEEE-TTSGGGG CS
                          PDZ_2  14 ggvlvvsVkeggPaak 29 
                                     +v+vv+V++++ +a+
  gi|116753493|ref|YP_842611.1| 218 DRVVVVDVDPESRFAG 233
                                    4799999999987665 PP

  == domain 2  score: 25.2 bits;  conditional E-value: 3.4e-09
                                    .-EEEEEE-TTSGGGGT.--TT-EEEEETTB--SSHHHHHHHHHTS-TT-EEEEEEEE CS
                          PDZ_2  14 ggvlvvsVkeggPaakaglkagDvilkvdgkkvksledlislllkkkpGdtVkltvlR 71 
                                     gv vv+  +g+Pa++ag+    vi+ +++++v+sle+++ +++++ pG+ +k++ + 
  gi|116753493|ref|YP_842611.1| 277 LGVQVVDTFDGSPAKDAGMPERFVITDINDTRVDSLESFRDYMNSTYPGQILKINTTK 334
                                    5899**********************************************99998765 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   7.7e-05      0.35       8      44 ..     287     321 ..     278     331 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 7.7e-05
                          PDZ_6   8 gsPAdrAGlrvGDiilsvNGqpveglsladvaallrg 44 
                                    gsPA  AG+    +i+ +N++ v   sl+ +++++ +
  gi|116753493|ref|YP_842611.1| 287 GSPAKDAGMPERFVITDINDTRV--DSLESFRDYMNS 321
                                    7**********************..*******99973 PP

>> DUF3267  Putative zincin peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   1.3     0.017        76      46      75 ..      58      87 ..      39      93 .. 0.85
   2 ?   10.3   0.4   0.00014      0.64       2      23 ..     125     146 ..     124     161 .. 0.78
   3 ?   -3.7   0.2       3.3   1.5e+04      77      88 ..     438     449 ..     431     454 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.017
                        DUF3267 46 skkqfiiillaPfvllgilllllalllpss 75
                                   s ++  +  ++P+v  g++ +ll+lll  +
  gi|116753493|ref|YP_842611.1| 58 SLWRLTTTIFMPIVMAGMIYFLLLLLLMVY 87
                                   679999999*************99997654 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00014
                        DUF3267   2 lvlvilHEllHglffklfgkkp 23 
                                    +v++++HEl Hg+++++ g ++
  gi|116753493|ref|YP_842611.1| 125 CVTIVVHELSHGILCRVEGIRV 146
                                    789*************865443 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 3.3
                        DUF3267  77 lllllllalnaa 88 
                                    +lll+++++n+ 
  gi|116753493|ref|YP_842611.1| 438 NLLLWIGWINMY 449
                                    377888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (518 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       766  (0.0427241); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.41
# Mc/sec: 3753.14
//
Query:       gi|116753494|ref|YP_842612.1|  [L=335]
Description: hydantoinase/oxoprolinase [Methanosaeta thermophila PT]
Scores for complete 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-17   61.8   0.1      2e-16   60.1   0.0    1.9  2  Hydantoinase_A  Hydantoinase/oxoprolinase
  ------ inclusion threshold ------
      0.063   11.9   0.0        2.6    6.5   0.0    2.1  2  MutL            MutL protein


Domain annotation for each model (and alignments):
>> Hydantoinase_A  Hydantoinase/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.1      0.62   5.5e+03      82      95 ..       3      16 ..       2      22 .. 0.79
   2 !   60.1   0.0   2.3e-20     2e-16       3     272 ..      51     299 ..      49     321 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 0.62
                 Hydantoinase_A 82 ItfDmGGTstDvsl 95
                                   +++D+GG  t+++ 
  gi|116753494|ref|YP_842612.1|  3 LGVDIGGANTKAAS 16
                                   689****9999886 PP

  == domain 2  score: 60.1 bits;  conditional E-value: 2.3e-20
                 Hydantoinase_A   3 etavvnAylspilreylesvekslekrgak..arlmvmqsdGglvsadearkkpvetilSGPaaGvvgaaatsklagekk 80 
                                    + +v++++l+++++ + ++v  +  +++ +  +++ +   +G   s++  r+  ++++++++ a+++ + +     ++ +
  gi|116753494|ref|YP_842612.1|  51 VGVVMTGELADCFECRRDGVLFIASEVERAfeCPVHFWGLSGFHRSVS--REMALDLAAANWSASAALLLK-----DVGS 123
                                    6799***************9888877655444**********999999..56667***********99999.....5555 PP

                 Hydantoinase_A  81 vItfDmGGTstDvslikdgevevsleteiagvkvrlpaldirtvgagGgsil.vvdeggklrvgpesagadpgpacyrkG 159
                                    +I+ DmG+T+tD++++   ++            ++l++l   ++ + G +++ +      +++ + s+  +++       
  gi|116753494|ref|YP_842612.1| 124 CILADMGSTTTDIIPVM-DRP--------LSGCTDLERLLRGELLYTGLLRTnLAALLPGVELFGGSVPLSSEL------ 188
                                    *****************.666........47889******************9999999999999*******99...... PP

                 Hydantoinase_A 160 gteltvTDanlvLGrlqpedfls.gpdgdqkldvelarraf.eelakelnlk...veevAegilsvavenmanavrklsv 234
                                      + +++D +l LG ++p+++++ +pdg  k+ + ++rr + + +++  +l+   +  +A+++ s + + +   + ++  
  gi|116753494|ref|YP_842612.1| 189 --FSITADVYLALGDIEPDAYTCeTPDGGPKSLKGALRRLArTVCSDLDELGedgALSIAAQAKSRQISIVSTGISRI-- 264
                                    ..99*********************************99995666554433344566777777777777777777777.. PP

                 Hydantoinase_A 235 ergldpkeltlvvfGGaGaqhaaalaeelgvkkvivpp 272
                                       +++++   vv +G G+++++ ++e+ g++++   +
  gi|116753494|ref|YP_842612.1| 265 ---AERHKIRRVVAAGVGEFIVEDACERAGLECIRLSE 299
                                    ...9999*******************999998875433 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0    0.0029        26     249     264 ..       2      17 ..       1      29 [. 0.84
   2 ?    6.5   0.0   0.00029       2.6     238     265 ..     117     140 ..      76     151 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.0029
                           MutL 249 llvvDvGGaTTdvhsv 264
                                    +l+vD+GGa T   s 
  gi|116753494|ref|YP_842612.1|   2 ILGVDIGGANTKAASS 17 
                                    589*********9997 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.00029
                           MutL 238 laeeeekglgdllvvDvGGaTTdvhsva 265
                                    l +    ++g +++ D+G++TTd++ v+
  gi|116753494|ref|YP_842612.1| 117 LLK----DVGSCILADMGSTTTDIIPVM 140
                                    333....6999*************9885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); 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: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2406.07
//
Query:       gi|116753495|ref|YP_842613.1|  [L=362]
Description: coenzyme F420 hydrogenase/dehydrogenase beta subunit [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-42  145.3   0.0    1.8e-42  144.8   0.0    1.2  1  FrhB_FdhB_C  Coenzyme F420 hydrogenase/dehydrogenase, beta su
    2.2e-24   85.4   0.6    4.3e-24   84.4   0.6    1.5  1  FrhB_FdhB_N  Coenzyme F420 hydrogenase/dehydrogenase, beta su
  ------ inclusion threshold ------
      0.042   14.4   6.7        2.6    8.7   3.8    2.7  2  Fer4_17      4Fe-4S dicluster domain
      0.053   14.5   4.0         19    6.3   0.0    3.1  3  Fer4_16      4Fe-4S double cluster binding domain
       0.11   13.1  10.3       0.79   10.4   0.2    2.8  2  Fer4_4       4Fe-4S binding domain
        0.5   10.9   5.2         16    6.2   2.0    2.6  2  Fer4_13      4Fe-4S single cluster domain of Ferredoxin I
       0.54   10.9  10.5        2.1    9.0   0.0    2.8  2  Fer4_7       4Fe-4S dicluster domain
        1.3    9.3  12.3        4.9    7.4  10.8    2.6  3  Fer4_9       4Fe-4S dicluster domain
        2.2    8.2  19.6        0.7    9.8   0.4    2.9  3  Fer4         4Fe-4S binding domain
        3.7    7.7  14.0         12    6.1  12.0    2.5  3  Fer4_10      4Fe-4S dicluster domain
        8.9    6.6  17.2        2.5    8.3   0.4    3.4  3  Fer4_6       4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> FrhB_FdhB_C  Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.8   0.0   1.1e-45   1.8e-42       2     154 ..     179     331 ..     178     332 .. 0.96

  Alignments for each domain:
  == domain 1  score: 144.8 bits;  conditional E-value: 1.1e-45
                    FrhB_FdhB_C   2 kkvavvGtPCqiaalrklqk.....kklkekilltiglfCggnfspealrk..lleelgvdpedvkklefrgkgkfrvel 74 
                                    +k++++GtPCqi+alrk+q      +  +e+i+l+iglfC++nf+++ l++  ++e+++++p dv+++e+ + g frv  
  gi|116753495|ref|YP_842613.1| 179 TKIGFTGTPCQIQALRKAQLldepyQFGQERIALMIGLFCMENFDYQRLMTglVKEKMNLQPTDVERFEI-QRGMFRVIS 257
                                    689****************98999878899**********************99****************.89*****99 PP

                    FrhB_FdhB_C  75 kd.ekeislkeleefirpsCkvCkdktaelADisvGdvwgpekkgdddegvstvlvrtekgeellekaveageleleeld 153
                                    k+ +ke++l+e++ef+ p+C  C+d+taelAD+svG+v      g +++g+stvlvrt+ ge+++++a++ag +e+++l+
  gi|116753495|ref|YP_842613.1| 258 KEgTKEVPLQETDEFTWPGCGPCFDFTAELADVSVGSV------G-SPGGWSTVLVRTDPGESIYRSALSAGVIEEKALT 330
                                    99*99*********************************......8.*******************************988 PP

                    FrhB_FdhB_C 154 e 154
                                    +
  gi|116753495|ref|YP_842613.1| 331 D 331
                                    6 PP

>> FrhB_FdhB_N  Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.4   0.6   2.7e-27   4.3e-24       2      75 ..      98     168 ..      97     171 .. 0.95

  Alignments for each domain:
  == domain 1  score: 84.4 bits;  conditional E-value: 2.7e-27
                    FrhB_FdhB_N   2 vaArstdkeirkkaqsGGivtallkylLeegiidgvivvapskdpwrpkpviattkeellaaaGskYtlspnlk 75 
                                    +aAr+t    r k q+GG+vtall ++Le+g id+++v++++ ++w++ p +att+ee++aaaG+kYt++p ++
  gi|116753495|ref|YP_842613.1|  98 MAARATPV--RGKVQDGGVVTALLVHALETGVIDCAVVTDRN-SRWQTTPKVATTPEEIIAAAGTKYTIAPSIA 168
                                    68999975..********************************.79*************************9875 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   3.8    0.0016       2.6       2      23 ..      30      51 ..      29      56 .. 0.83
   2 ?    5.9   0.0     0.012        20      49      59 ..      59      69 ..      57     101 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0016
                        Fer4_17  2 CiqCgyClpeCpsyeaydnepk 23
                                   C+ Cg C++ Cp+  + + +p 
  gi|116753495|ref|YP_842613.1| 30 CCLCGTCIALCPRIGQQNRKPT 51
                                   ************9988877765 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.012
                        Fer4_17 49 CgeCerkCPqg 59
                                   Cg+C ++CP +
  gi|116753495|ref|YP_842613.1| 59 CGLCYAYCPRS 69
                                   66666666654 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 ?    6.1   2.0     0.013        21       2      13 ..      30      41 ..      17      52 .. 0.81
   2 ?    6.3   0.0     0.012        19       5      20 ..      59      74 ..      57     101 .. 0.83
   3 ?   -0.9   0.0         2   3.3e+03      35      61 ..     255     281 ..     235     283 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.013
                        Fer4_16  2 CgtCgkCaevCP 13
                                   C  Cg C+  CP
  gi|116753495|ref|YP_842613.1| 30 CCLCGTCIALCP 41
                                   667777777777 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.012
                        Fer4_16  5 CgkCaevCPtnaikek 20
                                   Cg C   CP + ++++
  gi|116753495|ref|YP_842613.1| 59 CGLCYAYCPRSFFDMP 74
                                   99*******9988877 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 2
                        Fer4_16  35 taekkdlaedeekckkqeaitgCdiCq 61 
                                    ++ k++ +e   +++ +    gC+ C 
  gi|116753495|ref|YP_842613.1| 255 VISKEGTKEVPLQETDEFTWPGCGPCF 281
                                    455555555555555555667999885 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   4.9     0.031        50       4      15 ..      30      41 ..      26      49 .. 0.88
   2 ?   10.4   0.2   0.00049      0.79       7      15 ..      59      67 ..      58      80 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.031
                         Fer4_4  4 CigCgsCvaaCP 15
                                   C  Cg C+a CP
  gi|116753495|ref|YP_842613.1| 30 CCLCGTCIALCP 41
                                   899********* PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00049
                         Fer4_4  7 CgsCvaaCP 15
                                   Cg C+a+CP
  gi|116753495|ref|YP_842613.1| 59 CGLCYAYCP 67
                                   ********* 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 ?    6.2   2.0    0.0095        16       5      19 ..      29      43 ..      25      49 .. 0.85
   2 ?    5.1   0.1      0.02        32       9      20 ..      59      70 ..      58     100 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0095
                        Fer4_13  5 tCiacgaCvelaPdv 19
                                    C  cg+C +l+P +
  gi|116753495|ref|YP_842613.1| 29 ICCLCGTCIALCPRI 43
                                   6999*********86 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.02
                        Fer4_13  9 cgaCvelaPdvF 20
                                   cg+C++ +P  F
  gi|116753495|ref|YP_842613.1| 59 CGLCYAYCPRSF 70
                                   9********988 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   3.1     0.012        19      36      49 ..      28      41 ..       6      44 .. 0.80
   2 ?    9.0   0.0    0.0013       2.1       5      24 ..      59      78 ..      58     106 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.012
                         Fer4_7 36 ekClgCgaCvavCP 49
                                     C  Cg C+a CP
  gi|116753495|ref|YP_842613.1| 28 GICCLCGTCIALCP 41
                                   45888999999998 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0013
                         Fer4_7  5 CgaCvaaCpvkaieldeeen 24
                                   Cg C a+Cp + ++++ +e+
  gi|116753495|ref|YP_842613.1| 59 CGLCYAYCPRSFFDMPFFEK 78
                                   **********9999987643 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   5.4    0.0062        10      36      48 ..      30      42 ..      16      46 .. 0.77
   2 ?    7.4  10.8     0.003       4.9       2      49 ..      30      69 ..      29      71 .. 0.78
   3 ?   -2.1   0.0       2.8   4.6e+03      38      43 ..     276     281 ..     255     283 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0062
                         Fer4_9 36 CigCgaCveaCpk 48
                                   C  Cg+C++ Cp+
  gi|116753495|ref|YP_842613.1| 30 CCLCGTCIALCPR 42
                                   8889999999987 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.003
                         Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49
                                   C+ Cg+C++ Cp    ++++ +  ++++         Cg C++ Cp+ 
  gi|116753495|ref|YP_842613.1| 30 CCLCGTCIALCPRIGQQNRKPT-LMEYDP-------LCGLCYAYCPRS 69
                                   ************9776666555.455544.......5*********96 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 2.8
                         Fer4_9  38 gCgaCv 43 
                                    gCg C+
  gi|116753495|ref|YP_842613.1| 276 GCGPCF 281
                                    566665 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   6.7    0.0023       3.7       5      19 ..      27      41 ..      23      42 .. 0.85
   2 ?    9.8   0.4   0.00043       0.7      11      20 ..      59      68 ..      58      71 .. 0.90
   3 ?   -2.3   0.5       2.9   4.7e+03      10      15 ..     276     281 ..     276     282 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0023
                                   TTTSSS-THHHHHST CS
                           Fer4  5 eekCigCGaCvevCP 19
                                      C  CG+C+  CP
  gi|116753495|ref|YP_842613.1| 27 RGICCLCGTCIALCP 41
                                   567************ PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00043
                                   -THHHHHSTT CS
                           Fer4 11 CGaCvevCPv 20
                                   CG+C+  CP 
  gi|116753495|ref|YP_842613.1| 59 CGLCYAYCPR 68
                                   *********6 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.9
                                    S-THHH CS
                           Fer4  10 gCGaCv 15 
                                    gCG C 
  gi|116753495|ref|YP_842613.1| 276 GCGPCF 281
                                    8**996 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1  12.0    0.0074        12       4      56 .]      25      67 ..      22      67 .. 0.80
   2 ?    4.9   0.3     0.018        29      12      21 ..      59      68 ..      57     111 .. 0.75
   3 ?   -3.0   0.1       5.2   8.5e+03      11      16 ..     276     281 ..     275     283 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0074
                        Fer4_10  4 idddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                   +++  C  Cg+C + CP           + +++++ + +e  + cg C++ CP
  gi|116753495|ref|YP_842613.1| 25 VQRGICCLCGTCIALCPR----------IGQQNRKPTLMEYDPLCGLCYAYCP 67
                                   66789***********99..........5566666666666689******999 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.018
                        Fer4_10 12 CgkCvkaCPa 21
                                   Cg C + CP 
  gi|116753495|ref|YP_842613.1| 59 CGLCYAYCPR 68
                                   8888888887 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 5.2
                        Fer4_10  11 rCgkCv 16 
                                    +Cg C 
  gi|116753495|ref|YP_842613.1| 276 GCGPCF 281
                                    577776 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   4.5     0.038        62       3      20 ..      24      41 ..      24      45 .. 0.89
   2 ?    8.3   0.4    0.0015       2.5      11      20 ..      58      67 ..      56      73 .. 0.89
   3 ?    1.7   0.4      0.18     3e+02      11      16 ..     276     281 ..     275     282 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.038
                         Fer4_6  3 eidpdkCigCgdCvrvCP 20
                                   ++++  C  Cg C++ CP
  gi|116753495|ref|YP_842613.1| 24 VVQRGICCLCGTCIALCP 41
                                   57888999*********9 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0015
                         Fer4_6 11 gCgdCvrvCP 20
                                    Cg C++ CP
  gi|116753495|ref|YP_842613.1| 58 LCGLCYAYCP 67
                                   6********* PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.18
                         Fer4_6  11 gCgdCv 16 
                                    gCg+C+
  gi|116753495|ref|YP_842613.1| 276 GCGPCF 281
                                    9****7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); 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):              11  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2752.32
//
Query:       gi|116753496|ref|YP_842614.1|  [L=390]
Description: translation-associated GTPase [Methanosaeta thermophila PT]
Scores for complete 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-34  117.4   0.0    8.4e-34  116.5   0.0    1.4  1  MMR_HSR1_C     GTPase of unknown function C-terminal
    2.1e-20   72.9   0.0    3.7e-19   68.9   0.0    2.6  3  MMR_HSR1       50S ribosome-binding GTPase
    3.4e-14   52.6   0.0    7.2e-14   51.6   0.0    1.6  1  TGS            TGS domain
    2.1e-08   33.8   0.0    5.9e-07   29.1   0.0    2.4  2  FeoB_N         Ferrous iron transport protein B
  ------ inclusion threshold ------
      0.043   14.0   0.1         10    6.4   0.0    2.5  2  YchF-GTPase_C  Protein of unknown function (DUF933)
      0.059   13.4   0.0       0.14   12.2   0.0    1.6  2  MMR_HSR1_Xtn   C-terminal region of MMR_HSR1 domain
       0.13   11.8   0.1          2    7.9   0.0    2.5  3  GTP_EFTU       Elongation factor Tu GTP binding domain


Domain annotation for each model (and alignments):
>> MMR_HSR1_C  GTPase of unknown function C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.5   0.0   3.3e-37   8.4e-34       1     112 []     219     321 ..     219     321 .. 0.98

  Alignments for each domain:
  == domain 1  score: 116.5 bits;  conditional E-value: 3.3e-37
                     MMR_HSR1_C   1 alNKaDlpaadenieklkekypkdkkvvpvsAaaElaLrkaakqglikYepgdedfeikedklkeldekqkkaLekirdl 80 
                                    a+NK+Dl a++eni++l+e ++    vvpvs+aaE+aLr a+k+g+i+Y pgd dfei ++    l+++qk+ L+kir  
  gi|116753496|ref|YP_842614.1| 219 AANKIDL-APRENIRRLMELDE---IVVPVSGAAEIALRMADKAGVIRYLPGDPDFEIVGE----LNRAQKAGLDKIRV- 289
                                    89*****.************88...8***********************************....*************9. PP

                     MMR_HSR1_C  81 vlkrygsTGVqealnaavfelldlivVYPVed 112
                                    +lk+ygsTGVqe++n+avf+lld+i+VYPVed
  gi|116753496|ref|YP_842614.1| 290 LLKEYGSTGVQECINRAVFDLLDYITVYPVED 321
                                    99****************************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 !   68.9   0.0   1.5e-22   3.7e-19       2      93 ..       4     129 ..       3     170 .. 0.78
   2 ?    0.7   0.0      0.21   5.5e+02      93     114 .]     201     222 ..     169     222 .. 0.73
   3 ?   -2.4   0.0       1.9   4.8e+03      68      87 ..     348     373 ..     312     387 .. 0.56

  Alignments for each domain:
  == domain 1  score: 68.9 bits;  conditional E-value: 1.5e-22
                                    EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEE.......................EEEEECGGCSS CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgke.......................ielvDtpGlie 58 
                                    ++++G+pN+GKSt+++a t + ++++++p+tT+d n+g   ++  +                       +el+D++Gl+ 
  gi|116753496|ref|YP_842614.1|   4 IGLAGKPNAGKSTFFKAATLADVEIANYPFTTIDANHGVSYVRV-KcpcvelgieggcgrcingsrfvpVELIDVAGLVP 82 
                                    89************************************766431.234444555555555566666666********999 PP

                                    HHHHHHHHHHHHHHHHC.TSEEEEEEETT...........TTCSHHH CS
                       MMR_HSR1  59 gaseekglgkaflalee.adlillvvdas...........eeklkpl 93 
                                    +a+ ++glg++fl+  + a+++++v+das            ++++pl
  gi|116753496|ref|YP_842614.1|  83 DAHLGRGLGNEFLDSLRlAEVVIHVLDASgstdaegnpvgIGNYDPL 129
                                    9*************99989********99776655554442234444 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.21
                                    HHHHHHHHHHHTTSEEEEEEES CS
                       MMR_HSR1  93 ldeeleelleeakkplilvlnk 114
                                    + ++++ell+++ kp+i+++nk
  gi|116753496|ref|YP_842614.1| 201 DLRRFAELLRQSSKPMIIAANK 222
                                    336778888899********98 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.9
                                    HHHHHHHCT.SEEEEEEETT.....T CS
                       MMR_HSR1  68 kaflaleea.dlillvvdas.....e 87 
                                     a++ + e  + +l+ +da+      
  gi|116753496|ref|YP_842614.1| 348 LAYRVHTELgESFLFAIDARrklrvG 373
                                    34444555437788888877444332 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.6   0.0   2.8e-17   7.2e-14       3      59 ..     331     387 ..     325     388 .. 0.92

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 2.8e-17
                                    EEETTSSEEEEETTB-HHHHHHHHSTTHHHHEEEEEECS..EEEETTSBB-SSEEEEEE CS
                            TGS   3 vytPdGkvpdlprgatveDfAykIhrslakkfiyAlVnG..qrvgldhvLedgdvveIv 59 
                                    v++Pd+ +  ++rg+t++D+Ay++h++l+++f+ A+      rvg +++L+dgdv++Iv
  gi|116753496|ref|YP_842614.1| 331 VVLPDAFL--MKRGSTARDLAYRVHTELGESFLFAIDARrkLRVGEKYELKDGDVIKIV 387
                                    67777777..*****************************877****************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 !   29.1   0.0   2.3e-10   5.9e-07       2      42 ..       3      43 ..       2      53 .. 0.91
   2 ?    2.0   0.0      0.05   1.3e+02     102     124 ..     210     232 ..     196     253 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 2.3e-10
                                   EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEE CS
                         FeoB_N  2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegkl 42
                                   ++ l+G+pn+Gk+t+f a t a+ +++N+p +t++ ++g  
  gi|116753496|ref|YP_842614.1|  3 SIGLAGKPNAGKSTFFKAATLADVEIANYPFTTIDANHGVS 43
                                   5889*******************************999875 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.05
                                    HHTTSSEEEEEETHHHHHHTTEE CS
                         FeoB_N 102 lelgvpvvlalnmideaekkgie 124
                                     + ++p+++a n+id a +++i+
  gi|116753496|ref|YP_842614.1| 210 RQSSKPMIIAANKIDLAPRENIR 232
                                    45679***********9998875 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 ?    6.4   0.0     0.004        10      15      41 ..     337     363 ..     334     369 .. 0.90
   2 ?    5.0   0.1     0.011        28      66      81 ..     371     386 ..     363     388 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.004
                  YchF-GTPase_C  15 WtikkgttapqaAgviHsDfekgFira 41 
                                    + +k+g+ta + A  +H+++ + F+ a
  gi|116753496|ref|YP_842614.1| 337 FLMKRGSTARDLAYRVHTELGESFLFA 363
                                    6789******************99866 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.011
                  YchF-GTPase_C  66 legkdyvvqdgDiilf 81 
                                    + g +y ++dgD+i +
  gi|116753496|ref|YP_842614.1| 371 RVGEKYELKDGDVIKI 386
                                    5699*********976 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 ?   12.2   0.0   5.5e-05      0.14      56      93 ..     214     252 ..     196     257 .. 0.81
   2 ?   -4.0   0.0         6   1.5e+04      16      28 ..     283     295 ..     277     303 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.5e-05
                   MMR_HSR1_Xtn  56 ipclyvlNKiDlisleeldelare.pnsvviSaekelnl 93 
                                    +p++++ NKiDl+  e++++l +  + +v++S + e+ l
  gi|116753496|ref|YP_842614.1| 214 KPMIIAANKIDLAPRENIRRLMELdEIVVPVSGAAEIAL 252
                                    799********************7256778998887765 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 6
                   MMR_HSR1_Xtn  16 deetvkkilkeyk 28 
                                      ++++ +lkey+
  gi|116753496|ref|YP_842614.1| 283 GLDKIRVLLKEYG 295
                                    4577888899987 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.11   2.7e+02       4      21 ..       2      19 ..       1      35 [. 0.83
   2 ?   -2.7   0.0       1.4   3.5e+03      86     104 ..      93     111 ..      91     116 .. 0.79
   3 ?    7.9   0.0   0.00078         2     112     142 ..     203     234 ..     198     318 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.11
                                   EEEEEEESTTSSHHHHHH CS
                       GTP_EFTU  4 rnigiighvDhGKtTLtd 21
                                   + ig++g  ++GK+T+  
  gi|116753496|ref|YP_842614.1|  2 LSIGLAGKPNAGKSTFFK 19
                                   579999*********976 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.4
                                    HHHHHHHT-SEEEEEEETT CS
                       GTP_EFTU  86 evirglrvlDgavlvvdav 104
                                    e   +lr +++++ v+da+
  gi|116753496|ref|YP_842614.1|  93 EFLDSLRLAEVVIHVLDAS 111
                                    5667899999999999986 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.00078
                                    HHHHHHHHHTTTEEEEEEESCGST....HHHHHHH CS
                       GTP_EFTU 112 eevlrlalkegvpiivfiNKmDrl....kaelkei 142
                                    ++ ++l+++   p+i++ NK+D +    +   +++
  gi|116753496|ref|YP_842614.1| 203 RRFAELLRQSSKPMIIAANKIDLAprenI---RRL 234
                                    56778999999************985442...332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); 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: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 3000.32
//
Query:       gi|116753497|ref|YP_842615.1|  [L=472]
Description: aspartyl/glutamyl-tRNA amidotransferase subunit B [Methanosaeta thermophila PT]
Scores for complete 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-102  342.4   0.0   2.6e-102  341.9   0.0    1.1  1  GatB_N     GatB/GatE catalytic domain
    5.6e-40  136.6   0.0    9.2e-40  135.9   0.0    1.3  1  GatB_Yqey  GatB 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 !  341.9   0.0  2.9e-106  2.6e-102       1     269 [.       4     282 ..       4     284 .. 0.97

  Alignments for each domain:
  == domain 1  score: 341.9 bits;  conditional E-value: 2.9e-106
                                    EEEEEEEEEEB--.SB-SSSSSBSSSSCESTTSS--TTTTTSTT..--EEHHHHHHHHHHHHHTTEEE-SEE-EEEEE-T CS
                                    xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         GatB_N   1 lviGlEiHaqlkt.ksKlFssasteeegeepnsevsevdlalPGtlPvlnkeavelaikaalalnceiaeeskfdRKnyf 79 
                                    ++iGlEiH+ql++ +sK+F+++st  +++ pn+++++v+l+lPG+lPv+n++ave  ik+alalnc+iaee++f+RKny+
  gi|116753497|ref|YP_842615.1|   4 VIIGLEIHVQLNKlRSKMFCGCSTGYHDAPPNTHTCPVCLGLPGSLPVINRRAVEFGIKVALALNCSIAEETMFYRKNYY 83 
                                    58*********998*********7767778************************************************** PP

                                    CTTCTTSEEEEESSS.SEEEEEEEE......TEEEEEEEEEEEE---EEEE....EETTEEEEETTSTT-EEEEEEE-ST CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxx RF
                         GatB_N  80 ypdlpkgyQitqkeeplakeGslel......ekkvrierihlEeDaaksvh....eekeeslvdlnRaGvpLiEivtepd 149
                                    ypdlpkg+Qi+q++ pla++G++ +      e+++ri+r+h+EeD ++ vh    ++++++lvd+nR+G+pL+E+vtepd
  gi|116753497|ref|YP_842615.1|  84 YPDLPKGFQISQYDYPLATGGYVLIkgddgqERRIRITRVHMEEDPGRLVHagtiDRARYTLVDYNRCGMPLLEVVTEPD 163
                                    ***********************9999*999999*****************99987888********************* PP

                                    B-SHHHHHHHHHHHHHHHHHHTSB--SGGGTTEEEEEEEEECTSETTSSS.--EEEEEE-SHHHHHHHHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         GatB_N 150 lrspeearavveklrellralgvsdgnmeeGslRcDvNvSvreeekgeeegtrvEiKnlnslksiekaieyeierqiell 229
                                    lrsp+ear++++klr++l++l+v dgn+ eGslR+D N+S++        g rvE+Kn++s k +eka++yei+rq +l 
  gi|116753497|ref|YP_842615.1| 164 LRSPKEARQFLDKLRTILEYLDVFDGNL-EGSLRVDSNISLAG-------GDRVEVKNISSHKGVEKALSYEITRQRNLK 235
                                    ****************************.7************4.......49***************************9 PP

                                    .......-EEEEEETTTTEEEEECC----...-EEE-TTS--EE--H CS
                                    .......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         GatB_N 230 .......qeTrkfdedkgetvslRskeeaedYryfpepdlppleise 269
                                           qeTr++de +g tvs+R+keea+dYryfpe dl+pl+i +
  gi|116753497|ref|YP_842615.1| 236 rrgievvQETRHYDELRGVTVSIRTKEEAHDYRYFPEMDLVPLRIAD 282
                                    *******************************************9975 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.9   0.0     1e-43   9.2e-40       2     148 .]     325     467 ..     324     467 .. 0.96

  Alignments for each domain:
  == domain 1  score: 135.9 bits;  conditional E-value: 1e-43
                                    HHHHHHHHSS.HHHHHHHHHTCHHHHHHHHTXXTTCSSTTHHHHHHHHHHHHTTSSGHHHHHHHHHHHHHHTXXHHHHHH CS
                      GatB_Yqey   2 ffeevvkegadaklaanwllnellgelnkegleieelkltpeqlaellkliaegkIskkiakevleelleegkspeeiie 81 
                                    f+ e v++++d++laa w+++ l geln+++l+i++  ++ e++ e+++++++ +I+++ a +v++++l+ g+sp+e++e
  gi|116753497|ref|YP_842615.1| 325 FY-EWVAARSDPRLAAVWIADVLKGELNYRNLTIDS--FKRESMLEIVRMLSDREITDEVAVTVIRTILDRGGSPRELVE 401
                                    44.5556667**************************..9***************************************** PP

                                    HCTXXXXXXSSXHHHHHHHHHHTXHHHHHHHTTXXTTSTHHHHHHHHHTTSSXSXHHHHHHHHHHHS CS
                      GatB_Yqey  82 ekgLkqisdeeeleklveeviaenpkavedyksgkekalkflvGqvMkktkGkadpklvnellkekL 148
                                     +gLk + d + + ++v e+ia  ++av+dy sg+++a++++vGqvMk+tkG+adp ++ +l++e++
  gi|116753497|ref|YP_842615.1| 402 SMGLKRADD-DYVVQAVREAIADSQEAVRDYLSGNTRAINYIVGQVMKRTKGRADPSVAHRLVREEI 467
                                    *******99.******************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); 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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 3599.87
//
Query:       gi|116753498|ref|YP_842616.1|  [L=471]
Description: glutamyl-tRNA(Gln) amidotransferase, A subunit [Methanosaeta thermophila PT]
Scores for complete 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-159  531.9   0.0   1.6e-159  531.7   0.0    1.0  1  Amidase   Amidase


Domain annotation for each model (and alignments):
>> Amidase  Amidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  531.7   0.0  8.9e-164  1.6e-159       2     451 .]      17     451 ..      16     451 .. 0.98

  Alignments for each domain:
  == domain 1  score: 531.7 bits;  conditional E-value: 8.9e-164
                                    HHHHHHHHHHHHHHHH--EEEEEHCCCCHHHHT---TTT......TTTT-EEEEETTB--TTSB--TTSGGGTT-B-SS- CS
                        Amidase   2 lveaflkrieavneklnalvtvfieealaqAakldkkrargkekgpLhGvPisvKDnidvkgvpttaGskalenypaekD 81 
                                     ++ +++rie+  ++lna+ t+++e+al++A++ d++     + g L+G+P+++KDni+++g++tt++s++l+++++++D
  gi|116753498|ref|YP_842616.1|  17 YLHRLFERIER--SRLNAFTTLAKESALEAAREFDARP----WGGALAGIPVAIKDNICTRGIETTCSSRILKGFIPPYD 90 
                                    57888999999..99********************998....6************************************* PP

                                    -HHHHHHHHTT-EEEEEE--SGGG-SSSSTT-TT---BBTTCTCCB--SSSHHHHHHHHTTSSSCEEEEESSSTTHHHHH CS
                        Amidase  82 atvverLkkaGavilgkTnmdefamgsstensvfgptrNPwdksrtpGGSSGGsAAavAaglvplaiGtDtGGSiRiPAs 161
                                    a+v+erL+++Ga+i+gkTnmdefamg+ste+s+fgptrNPwd++r+pGGSSGGsAAavAag +p a+G+DtGGS+R+PAs
  gi|116753498|ref|YP_842616.1|  91 AHVIERLRAEGAIIIGKTNMDEFAMGTSTETSCFGPTRNPWDLERVPGGSSGGSAAAVAAGEAPCALGSDTGGSVRCPAS 170
                                    ******************************************************************************** PP

                                    HCTSEEEE--TTSC--TTB--SSTTT-EEEEEESSHHHHHHHHHHHBS--TT-TTS----HHHHHHHHCTT---TT-EEE CS
                        Amidase 162 fcglvGlKPtygrvSragvvalessldvvGplarsvedlalllrvilgedpkdstssvipeesedlaeelkkslkglriG 241
                                    fcg+vG+KPtyg+vSr+g++a+++sl+++Gp++++ved+alll+vi+g+dp+dsts  +   ++++ ++ + + +g+ iG
  gi|116753498|ref|YP_842616.1| 171 FCGTVGMKPTYGLVSRYGLIAYANSLEQIGPITKTVEDAALLLDVIAGHDPRDSTSIAS---EGNYLSSIGRDIRGICIG 247
                                    *********************************************************94...59**************** PP

                                    EEGGGCSS---CCHHHHHHHHHHHHHCTT-EEEEEE-CCGGGHHHHHHHHHHHHHHHHTTT-SSSSS.---SS-SCCCCC CS
                        Amidase 242 vvkedgvasldpevqravekalkaLeeaGhevvevelpsleealslyylilvaeassnlarylgvry.erlsetkvlsel 320
                                    v++e++ + +dp v+rav +a+  Le +G+   +++lp+ ++al++yy+i+++eassnlar++g ry  r  e+k+++++
  gi|116753498|ref|YP_842616.1| 248 VPEEYFGEGVDPGVERAVWDAVSVLEGLGASWRKISLPHTKYALPAYYIIAMSEASSNLARFDGLRYgLRVGEDKDWHTT 327
                                    ******************************************************************************** PP

                                    CCHHHHCCS-HHHHHHHHHHHHHCSCCCCCCCHHHHHHHHHHHHHHHHHHCCCBSEEEEESSSSS--BCCCCCHHHCSHH CS
                        Amidase 321 lpksraellgeevkrrielgnyalsaeasskyylkaqkvrrllrrefakafeelDvllsPtaptpaprlgekdktidsyt 400
                                    ++++ra ++g+e+krri lg+yalsa++++ yylka kvr+l++r+f  a++++D+++sPt+p pa+++ge+    ++++
  gi|116753498|ref|YP_842616.1| 328 FSEIRAMGFGKETKRRILLGTYALSAGYYGRYYLKALKVRTLIKRDFEHALNKVDIIASPTMPFPAFKIGERI---TDPL 404
                                    **********************************************************************996...79** PP

                                    HHHGCCTTT...HHHHHTT--EEEEECCCCT.TECEEEEEEESTT-HHHHH CS
                        Amidase 401 vlynlldftavvvpvnlaglpalsvpagksedglPvGvqvigkafqeetlL 451
                                    +ly +++ft   vp nlag pa+svp+g+s+ glPvG+q+++++f+e+ lL
  gi|116753498|ref|YP_842616.1| 405 SLYMSDVFT---VPINLAGIPAISVPCGFSD-GLPVGLQLMARPFDEALLL 451
                                    *********...*****************96.****************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); 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 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 3351.47
//
Query:       gi|116753499|ref|YP_842617.1|  [L=93]
Description: glutamyl-tRNA(Gln) amidotransferase, C subunit [Methanosaeta thermophila PT]
Scores for complete 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-24   83.9   1.3      9e-24   83.5   1.3    1.1  1  Glu-tRNAGln  Glu-tRNAGln amidotransferase C subunit


Domain annotation for each model (and alignments):
>> Glu-tRNAGln  Glu-tRNAGln amidotransferase C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.5   1.3     5e-28     9e-24       2      61 ..      19      88 ..      18      88 .. 0.96

  Alignments for each domain:
  == domain 1  score: 83.5 bits;  conditional E-value: 5e-28
                                   -HHHHHHHHHHHHHHHHHHTTCGCS--TT----S.......-EB-S--.....HHHHHTT-SSEETTEEE CS
                    Glu-tRNAGln  2 seeEleklakelnsildyveqLqevdttgveplthp.....vlReDev.....reelLknApetedgyfv 61
                                   seeE e+l  ++n ildy++qL+evdt+gvep++++     v+ReD++     ++e+L+nAp +e+gyf+
  gi|116753499|ref|YP_842617.1| 19 SEEEREELVAQFNTILDYFQQLDEVDTEGVEPTYRVvdlanVFREDVPrdsltQDEALRNAPRREEGYFR 88
                                   9*********************************************8789999999*************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      587  (0.0327403); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 696.14
//
Query:       gi|116753500|ref|YP_842618.1|  [L=77]
Description: hypothetical protein Mthe_0179 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       317  (0.0176809); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 570.45
//
Query:       gi|116753501|ref|YP_842619.1|  [L=208]
Description: translation initiation factor IF-2 subunit beta [Methanosaeta thermophila PT]
Scores for complete 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   0.0    3.3e-39  133.4   0.0    1.2  1  eIF-5_eIF-2B  Domain found in IF2B/IF5
    1.3e-12   47.5   0.4    3.5e-12   46.1   0.6    1.6  2  TRAM          TRAM domain
  ------ inclusion threshold ------
      0.056   13.8   1.3        1.6    9.1   0.1    2.6  2  S1            S1 RNA binding domain
      0.089   13.1   0.3       0.18   12.2   0.3    1.6  1  ZF-HD_dimer   ZF-HD protein dimerisation region
       0.66    9.3   0.1       0.66    9.3   0.1    1.9  2  zf-RanBP      Zn-finger in Ran binding protein and others


Domain annotation for each model (and alignments):
>> eIF-5_eIF-2B  Domain found in IF2B/IF5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.4   0.0   9.2e-43   3.3e-39       6     117 .]      20     129 ..      16     129 .. 0.97

  Alignments for each domain:
  == domain 1  score: 133.4 bits;  conditional E-value: 9.2e-43
                                    SSSS--SSTT--EEEETT.EEEETTHHHHHHHHTTSHHHHHHHHHHHHTSEEEESETTEEEESSSSSCCHHHHHHHHHHH CS
                   eIF-5_eIF-2B   6 dkkerykmpklqvkvegkkktvivNfeeiakaLnrdpehvlkyllkelgtqgsidengrlilngkfeakkleklldkyie 85 
                                     +ker+++p +++ +egk +tv+ Nf+ ia+aLnrdp+h++k+ll+elgt+g+i e++r +++gkf+++ +++ + +y++
  gi|116753501|ref|YP_842619.1|  20 GTKERFQIPVPRIFYEGK-TTVLDNFAAIADALNRDPDHLMKFLLQELGTAGKI-EGHRGVFQGKFTEQAIQNQIAAYVD 97 
                                    5789**************.***********************************.999********************** PP

                                    HHTSTSSSTSTCEEECCSSSCEEEEESSSTCE CS
                   eIF-5_eIF-2B  86 eyVlCkeCkspetelekeerllvlkCkaCgak 117
                                    eyV+C+eCk p+t+l+k++r+l+lkC+aCga+
  gi|116753501|ref|YP_842619.1|  98 EYVICSECKLPDTHLIKSDRVLMLKCDACGAH 129
                                    ******************************85 PP

>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.6   9.3e+03      14      31 ..      85     101 ..      82     107 .. 0.70
   2 !   46.1   0.6   9.9e-16   3.5e-12       3      62 .]     147     202 ..     146     202 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.6
                                    EE-.TTSEEEEEET.TEE CS
                           TRAM  14 glsksegegiGrtdngkv 31 
                                    +++  + ++ +++d++ +
  gi|116753501|ref|YP_842619.1|  85 EQA-IQNQIAAYVDEYVI 101
                                    555.67788888885544 PP

  == domain 2  score: 46.1 bits;  conditional E-value: 9.9e-16
                                    XXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEEEE CS
                           TRAM   3 yvGstqeVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGell 62 
                                    ++G+t+e  +e ++ s+g+gi+++d ++ +fvp++++  G++V++k++k     +++e++
  gi|116753501|ref|YP_842619.1| 147 EEGETYELRIESVG-SKGDGIAKVD-KYLIFVPNTSK--GEIVKAKVKKISGTLAFAEIV 202
                                    58************.**********.***********..******************987 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1     0.034   1.2e+02      44      66 ..     140     162 ..     111     172 .. 0.84
   2 ?    9.1   0.1   0.00045       1.6       4      27 ..     181     203 ..     179     207 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.034
                                    SCHHHCEETTEEEEEEEEEEETT CS
                             S1  44 edpdevlkvGdevkvkvlkvdkd 66 
                                     +  +v+ +G++++++++ v  +
  gi|116753501|ref|YP_842619.1| 140 VVARDVIEEGETYELRIESVGSK 162
                                    56779************998655 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00045
                                    TTCEEEEEEEEEETTEEEEEETTT CS
                             S1   4 kgevveGeVtsvtkgGafVelgng 27 
                                    kge+v+++V++++   af e++ +
  gi|116753501|ref|YP_842619.1| 181 KGEIVKAKVKKISGTLAFAEIV-E 203
                                    9*****************9998.4 PP

>> ZF-HD_dimer  ZF-HD protein dimerisation region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.3   4.9e-05      0.18      36      53 ..     119     136 ..      96     138 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.9e-05
                    ZF-HD_dimer  36 eaLkCaaCgChrnFHrre 53 
                                     +LkC aCg hr   +r+
  gi|116753501|ref|YP_842619.1| 119 LMLKCDACGAHRPVKKRK 136
                                    579*********887776 PP

>> zf-RanBP  Zn-finger in Ran binding protein and others
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.5      0.35   1.3e+03       6      11 ..     101     106 ..     101     107 .. 0.79
   2 ?    9.3   0.1   0.00018      0.66      19      29 ..     121     131 ..     120     132 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.35
                                    E-SSS- CS
                       zf-RanBP   6 dCskCl 11 
                                    +Cs C+
  gi|116753501|ref|YP_842619.1| 101 ICSECK 106
                                    599997 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00018
                                    SB-TTT--BTS CS
                       zf-RanBP  19 tkCvaCqapkp 29 
                                    +kC aC+a++p
  gi|116753501|ref|YP_842619.1| 121 LKCDACGAHRP 131
                                    59********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); 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: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1491.61
//
Query:       gi|116753502|ref|YP_842620.1|  [L=170]
Description: 50S ribosomal protein L10e [Methanosaeta thermophila PT]
Scores for 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-37  126.1   0.0      1e-36  125.8   0.0    1.0  1  Ribosomal_L16  Ribosomal protein L16p/L10e


Domain annotation for each model (and alignments):
>> Ribosomal_L16  Ribosomal protein L16p/L10e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.8   0.0   5.8e-41     1e-36       4     132 .]      19     167 ..      17     167 .. 0.95

  Alignments for each domain:
  == domain 1  score: 125.8 bits;  conditional E-value: 5.8e-41
                                    SXXBSSSXXSSTSXX.XSXXXXXESX........EEEEESSXEEEEHHHHHHHHHHHCTCCCCTSXC...EEXXSXXXXE CS
                  Ribosomal_L16   4 kkyrKsrkryirgvs.tkgtklefgd........ygLvalekgqltaealeaariainrylkkkrgk...klwirvfphh 71 
                                    ++y++++  yi gv+ +k  ++++g+        ++Lv+ e++q++++aleaar+a+nryl k+ g+   +l++rv+phh
  gi|116753502|ref|YP_842620.1|  19 RPYTRRE--YIGGVPgSKVVHYDMGNlteefpvkLSLVVREPCQIRHTALEAARVAANRYLLKTLGRndfHLKLRVYPHH 96 
                                    689**99..***********************9999****************************99999*********** PP

                                    EEEE-.....SS-TTTSSSS....XEEEEEEEEEXSSCEEEEE...TTXXXSHHHHHHHHHHHHTSSSXEEEE CS
                  Ribosomal_L16  72 pvtkk.....agedRmgkGk....Gkpegwvarvkigqiifei...kagvneeiakealrraasKlpiktkiv 132
                                    +++++     ag+dR+++G+    Gkp g++a+v++gq if++       + e ak alrra +Klp +++i+
  gi|116753502|ref|YP_842620.1|  97 VIRENkqatgAGADRVSSGMrrafGKPVGTAAQVYTGQRIFTLgvhP--EHIEEAKTALRRAGHKLPSPVQII 167
                                    *******************************************5332..377789**************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       240  (0.0133861); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1299.58
//
Query:       gi|116753503|ref|YP_842621.1|  [L=1440]
Description: hypothetical protein Mthe_0182 [Methanosaeta thermophila PT]
Scores for complete 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-40  140.0   0.0      2e-40  139.2   0.0    1.3  1  Peptidase_C25  Peptidase family C25
     0.0024   18.1   0.0       0.01   16.1   0.0    2.1  2  DUF11          Domain of unknown function DUF11
     0.0026   17.2   0.0     0.0043   16.5   0.0    1.3  1  CHAT           CHAT domain
     0.0082   15.3   0.0      0.015   14.4   0.0    1.3  1  GHL10          Glycosyl hydrolase-like 10
  ------ inclusion threshold ------
      0.019   14.1   0.1      0.091   11.8   0.0    2.0  2  ANF_receptor   Receptor family ligand binding region
       0.16   12.1   0.0       0.48   10.6   0.0    1.7  1  GHL6           Hypothetical glycosyl hydrolase 6


Domain annotation for each model (and alignments):
>> Peptidase_C25  Peptidase family C25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.2   0.0   6.7e-44     2e-40      61     377 ..     844    1153 ..     806    1154 .. 0.85

  Alignments for each domain:
  == domain 1  score: 139.2 bits;  conditional E-value: 6.7e-44
                                     HTT.--SEEEEES-T..............TTS--EE-.....TTT-SEESHHHHS-T.....TSSS-SSEEEEE--SS CS
                  Peptidase_C25   61 sas.klkYllLvGdtsivvkv.kspitksdliptyqiakslgnestiptDdyyasldgnedsddltpdlavGRipvts 136 
                                     +++ +++Yll vGd        + p+t++++ +           s+ ++ dy + +d     dd+++++a+GR+   s
  gi|116753503|ref|YP_842621.1|  844 EKKlRPEYLLVVGDPG----SlPFPTTGVKQELEG------DPISYDVYRDYRIEMD-----DDNYTEVATGRFIGLS 906 
                                     334689*********3....234444444332222......3556789999******.....9*************** PP

                                     HHHHHHHHHHHHHHHCT--S-G....GGGEEEEEE--.........HHTHHHHHHHHHHHTSSGGGT-SEEEEE-SS- CS
                  Peptidase_C25  137 aaeaaavvnKiiaYerntengsaagqwrnkvlliagdvvgeweaadgneiagttaettpseynvnklyadlaayeaet 214 
                                     + +++++v+++++Yer+      +g+w+n+ l++a                    +  p  + +++++ad  a  +  
  gi|116753503|ref|YP_842621.1|  907 VYDVSQMVARTLSYERL------HGDWKNTSLVVATP---------------VEWPWSPVPIRIKEYLAD--AGLNSR 961 
                                     ****************9......689*********99...............5689**************..999999 PP

                                     -.............TTTTHHHHH--SEEEEES-EETTEE.......TTTTEEHHHHHT---TT--EEEEEESSSTT-T CS
                  Peptidase_C25  215 etevpaanqpllttqnllkalnqGvlfvnytGHGsetaw.......adeslstndisaltntnklpiaitaaCltgaf 285 
                                     + ++++a     t q++ + +n+Gv++v++ +HGse +w       +d  l+ ++++++  ++  +++++++Cl++++
  gi|116753503|ref|YP_842621.1|  962 DLRWEEA-----TFQRVSAFMNNGVGIVHFDHHGSEKGWalsswsmTDSFLDETQVKQFVLAP--QLTTSNSCLSSRL 1032
                                     9555444.....566*************************99999888888**********99..9************ PP

                                     TSSS-................-HHHHHHHSTTSSEEEEEEESS---SS--SHHHHHHHHHHHHHHH...T-S-SS-HH CS
                  Peptidase_C25  286 deetkr...............sfgeklvlnangGavayigatrlgysgvndrlsraffealfadaartlGealllakn 348 
                                      ++ +                s++ ++v   ++Gav+y+g++ l++++v++++++ f++al+ ++a t Geal +a+n
  gi|116753503|ref|YP_842621.1| 1033 -KGFSInvsgtemyipmrlddSIALAFV---RAGAVGYVGSSALVWIYVSEDYNKRFYQALVFENA-TAGEALSQAEN 1105
                                     .443336988888888887777777777...***********************************.5********** PP

                                     HHHHH..................................EEEEE-TT-- CS
                  Peptidase_C25  349 elletgl.................aqsiskgm.nkrt..fnllGDPalr 377 
                                      ++ +++                  +s +k+m n++   f+l+GDP++r
  gi|116753503|ref|YP_842621.1| 1106 LYIMKMKgaekisferieemlppwEYS-MKEMmNQTAssFMLFGDPEFR 1153
                                     ***9999*************9775444.56665666677*******988 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   3.5e-06      0.01      12      77 ..     577     663 ..     571     671 .. 0.71
   2 ?   -3.9   0.0       5.8   1.7e+04      34      49 ..     783     799 ..     778     816 .. 0.60

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.5e-06
                          DUF11  12 pGdtvtytltvtNtgpasangvvvtDtl............................Paglayvsvsasqgtasaltsvgs 63 
                                    +G+ v+ ++t++Ntg+ +++gv + D+                             Pag  +  +  +       +  ++
  gi|116753503|ref|YP_842621.1| 577 AGEVVRMNITLRNTGTEPLEGVSLVDMFangryvrmpiyykgklaitdpiskepsdPAGAFFNGSILT-------WDLEK 649
                                    79************************996666666666666666666655555444444433333333.......55577 PP

                          DUF11  64 Leagesatlsftvr 77 
                                    L + es  l+++v 
  gi|116753503|ref|YP_842621.1| 650 LDPDESVSLNLEVV 663
                                    77777777777665 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 5.8
                          DUF11  34 vvtDtlPagl.ayvsvs 49 
                                     v+ tlP++  ++ s++
  gi|116753503|ref|YP_842621.1| 783 EVRSTLPPNNvTAFSHT 799
                                    56677776540444443 PP

>> CHAT  CHAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.5e-06    0.0043     100     265 ..     942    1106 ..     841    1149 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.5e-06
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CHAT  100 fpelpgteaEaeaiakllaegelkvllgeaatesalksalsrryrvvHfatHgvfnanpplqsglvlsaenseedglL 177 
                                     +++ p   +E  a a l +    + l  e+at++++++ ++  + +vHf  Hg+ +       g +ls  ++  d++L
  gi|116753503|ref|YP_842621.1|  942 WSPVPIRIKEYLADAGLNS----RDLRWEEATFQRVSAFMNNGVGIVHFDHHGSEK-------GWALSSWSM-TDSFL 1007
                                     4555555444444444332....4577899*********99*************99.......999998777.9**** PP

                                     xxxxxxxxxxxxxxxxxxxxxxxx.....xxxxx...xxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CHAT  178 taeeilelnldgaelVvLsACqtg.....lgevi...dgegvlg......LaralllaGarsviaslwpVddeatalL 241 
                                     +  ++ ++ l  ++l + ++C ++     +   i   ++e ++        a a+++aGa   ++s   V    +++ 
  gi|116753503|ref|YP_842621.1| 1008 DETQVKQFVLA-PQLTTSNSCLSSrlkgfS---InvsGTEMYIPmrlddsIALAFVRAGAVGYVGSSALVWIYVSEDY 1081
                                     ********999.***********9876652...233255556657777789*************************** PP

                                     xxxxxxxxxx.xxxxxxxxxxxxxx RF
                           CHAT  242 mkrfyqnlla.glskaeALreaqlk 265 
                                      krfyq+l   ++++ eAL++a + 
  gi|116753503|ref|YP_842621.1| 1082 NKRFYQALVFeNATAGEALSQAENL 1106
                                     ********98899999*****9865 PP

>> GHL10  Glycosyl hydrolase-like 10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   5.2e-06     0.015     130     221 ..     194     289 ..     178     319 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.2e-06
                          GHL10 130 wlnPliPevqdfitklvvevvkrYdvDgvqlDDy.fylpesfGydlidvalYrqetkk...ealsnkeddlwidWRrdki 205
                                     l P+ P+v++ + + ++e++  Y vDg+ l  + f   +    d+ + + Yr  + +      s  + + w+ WR +k+
  gi|116753503|ref|YP_842621.1| 194 LLCPVNPNVREDLYARIEEIIDEYKVDGIVLYRFgFDGEDYCFCDVCKEEFYRDTGLDltrIRSSGYNYQKWLSWREQKV 273
                                    578***************************99873444445557888899999888421002234445556********9 PP

                          GHL10 206 sqlvkklnatikavkP 221
                                     ++ ++  ++ +   P
  gi|116753503|ref|YP_842621.1| 274 LEIAREARNITRNLGP 289
                                    8887776666666555 PP

>> ANF_receptor  Receptor family ligand binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0     3e-05     0.091     166     224 ..      89     152 ..      76     180 .. 0.84
   2 ?   -1.4   0.0      0.32   9.5e+02      52      83 ..     444     476 ..     419     486 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3e-05
                                    HHHHHHHHTT.T--EEEEEE-HHHHHHHHHHHHHTTS-STTEEEE......ETCHCCCECTTS-CC CS
                   ANF_receptor 166 vrkllkeiks.karvivlfcssedarellkaarrlgltgeeyvwi......asdawtsslvldkpe 224
                                    ++++l+ + s +  + +++ s+ed++ l+k+a+++g+ +  y+ +       ++ wts   ++ ++
  gi|116753503|ref|YP_842621.1|  89 MDAILQTMTSgNVSALIIHGSGEDVKTLVKTAQKQGMKT--YMTVslepesDEERWTSTTLVNAND 152
                                    7899999***999*************************9..7766778888777777777777665 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.32
                                    EEEEE-SSHHHHHHHHHHHCCTT-EEEESS-..- CS
                   ANF_receptor  52 vaviGpssssvsdavaslanlfkiPvisygs..t 83 
                                    v+++G  +  + +++a++a++++ Pv+ ++s  +
  gi|116753503|ref|YP_842621.1| 444 VVLVGDNY-TAGIQAATIASYLNWPVLFFSSniS 476
                                    44444444.48899*************8877432 PP

>> GHL6  Hypothetical glycosyl hydrolase 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00016      0.48     104     135 ..     193     224 ..     170     225 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00016
                           GHL6 104 wptlCinsgyqeklaeeleealkrldlDGifl 135
                                       +++n + +e l + +ee+++++++DGi l
  gi|116753503|ref|YP_842621.1| 193 SLLCPVNPNVREDLYARIEEIIDEYKVDGIVL 224
                                    334889***********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.81u 0.30s 00:00:01.11 Elapsed: 00:00:00.42
# Mc/sec: 10270.43
//
Query:       gi|116753504|ref|YP_842622.1|  [L=519]
Description: hypothetical protein Mthe_0183 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00012   22.7   0.0    0.00093   19.9   0.0    2.4  3  N_BRCA1_IG    Ig-like domain from next to BRCA1 gene
     0.0003   21.0   0.0       0.17   12.2   0.0    3.7  4  NPCBM_assoc   NPCBM-associated, NEW3 domain of alpha-galactos
  ------ inclusion threshold ------
      0.011   16.4   0.3        8.9    7.1   0.1    2.5  2  CW_binding_2  Putative cell wall binding repeat 2
      0.024   15.0   0.4         18    5.7   0.0    3.6  3  DUF11         Domain of unknown function DUF11
       0.07   13.2   0.0        1.5    8.9   0.0    2.7  2  DUF1573       Protein of unknown function (DUF1573)


Domain annotation for each model (and alignments):
>> 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 !   19.9   0.0   2.6e-07   0.00093       7      85 ..      31     107 ..      27     120 .. 0.86
   2 ?   -1.5   0.0       1.1   4.1e+03      73      96 ..     316     339 ..     302     342 .. 0.78
   3 ?   -3.7   0.0         5   1.8e+04      26      38 ..     437     449 ..     430     463 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.6e-07
                     N_BRCA1_IG   7 vvppgteftktWrlrNtGseaWpagtklvfvgGdkmgsasaeessvsvpavapgeevevsvelkaP..skpgryisywrl 84 
                                    +++pg+ + k+ +l+NtG+e+  + ++   vgGd+         ++  +a+ pg++++v + ++aP  +kpg y+  + +
  gi|116753504|ref|YP_842622.1|  31 EIHPGEVIHKVLTLTNTGEEPV-SRIRTTAVGGDAKD---MIMIDIPKKAIDPGDDMDVDIFFMAPpeTKPGLYTGFFYI 106
                                    689*****************97.89999999999993...3346889999****************87789999887766 PP

                     N_BRCA1_IG  85 a 85 
                                     
  gi|116753504|ref|YP_842622.1| 107 F 107
                                    5 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.1
                     N_BRCA1_IG  73 skpgryisywrlatedgseFGdrl 96 
                                    ++p+ y   +r+++ +g+ F  ++
  gi|116753504|ref|YP_842622.1| 316 TEPSGYAIVFRMVDTNGVPFPPEV 339
                                    678888999*****9999997655 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 5
                     N_BRCA1_IG  26 eaWpagtklvfvg 38 
                                    + W+++t++v+ g
  gi|116753504|ref|YP_842622.1| 437 KMWSNQTAVVVSG 449
                                    5788888888766 PP

>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.035   1.2e+02       3      26 ..      34      57 ..      32      62 .. 0.83
   2 ?    0.3   0.0      0.24   8.7e+02      46      71 ..      76     101 ..      68     101 .. 0.90
   3 !   12.2   0.0   4.6e-05      0.17       1      74 [.     147     226 ..     147     229 .. 0.81
   4 ?   -2.5   0.0       1.8   6.6e+03      14      47 ..     330     366 ..     322     376 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.035
                    NPCBM_assoc  3 pGetvtltltvtndgtaaatnvsl 26
                                   pGe     lt+tn+g++++++++ 
  gi|116753504|ref|YP_842622.1| 34 PGEVIHKVLTLTNTGEEPVSRIRT 57
                                   677777789***********9986 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.24
                    NPCBM_assoc  46 slapGetveatvkVtppagaaaGdye 71 
                                    +++pG+ + +++   +p+++++G y+
  gi|116753504|ref|YP_842622.1|  76 AIDPGDDMDVDIFFMAPPETKPGLYT 101
                                    689999*****************996 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 4.6e-05
                    NPCBM_assoc   1 vepGetvtltltvtndg.taaatnvslslslPeGWtvvevspas.aa.....slapGetveatvkVtppagaaaGdyevt 73 
                                    v+p+e+v+++l+v n+g  + + +v++  ++P+GW+ +  ++++ ++     +l+ G +   t+kV ++++a  G  +++
  gi|116753504|ref|YP_842622.1| 147 VTPDEPVEFDLEVRNTGrFRDLIEVYI-PEVPAGWQPRLYDGDEeIDlpyslALPSGSSHHLTLKVEVNENARSGSMRIV 225
                                    689**************6677778877.79******66555554222337779999*****************9997776 PP

                    NPCBM_assoc  74 a 74 
                                    +
  gi|116753504|ref|YP_842622.1| 226 G 226
                                    5 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 1.8
                    NPCBM_assoc  14 tndgtaaatnvslslslPeGWt.vvevspasaa..sl 47 
                                    tn+   + + v+l++  P+G   +++++p+ +a  sl
  gi|116753504|ref|YP_842622.1| 330 TNGVPFPPEVVYLEAVEPSGLAvITSADPRYMAvaSL 366
                                    5666667788999999999988667777776654455 PP

>> CW_binding_2  Putative cell wall binding repeat 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1    0.0025       8.9      28      71 .]     364     411 ..     347     411 .. 0.68
   2 ?    7.0   0.0    0.0026       9.3       1      45 [.     421     476 ..     421     510 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0025
                                    HHHHHHHHT.--EEEE-.TSSS.-.HHHHHHH.....EEEES-TTTS-HHHH CS
                   CW_binding_2  28 aaalaakkn.aPiLLtd.kldtal.kalksat.....vyilGGegvvsdsve 71 
                                    a+ l +++   P++ ++ + ++++ +     +     v+ilG e+ vs+++e
  gi|116753504|ref|YP_842622.1| 364 ASLLSGNNTtVPVIQVEdRVSKDImDM----LlpysdVIILGSESEVSSKIE 411
                                    445555544469999974222223333....24555899*********9986 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0026
                                    EE--SSHHHHHHHHHHH........EEET..THHHHHHHHHHHHHT--EEEE-.TS CS
                   CW_binding_2   1 RiaGaDRyeTaaaiaka........latg..faDALsaaalaakknaPiLLtd.kl 45 
                                    RiaG+D  eT+  +a++        +++g    D      +a++ + P++    +l
  gi|116753504|ref|YP_842622.1| 421 RIAGSDLAETSWILADKmwsnqtavVVSGpsEIDVFRSYQIAKRSGLPLVVCGdEL 476
                                    9***************5599999976999988999999999999889999986322 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.005        18       9      33 ..      31      55 ..      20      61 .. 0.84
   2 ?    4.6   0.0     0.011        39      59      85 ..     195     220 ..     138     225 .. 0.62
   3 ?   -1.6   0.2      0.94   3.4e+03      16      51 ..     323     358 ..     310     383 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.005
                          DUF11  9 evrpGdtvtytltvtNtgpasangv 33
                                   e+ pG+ +  +lt+tNtg  + +++
  gi|116753504|ref|YP_842622.1| 31 EIHPGEVIHKVLTLTNTGEEPVSRI 55
                                   6889**************9998765 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.011
                          DUF11  59 tsvgsLeagesatlsftvrvtrtaasg 85 
                                    +s   L+ g+s  l+++v+v+  a+sg
  gi|116753504|ref|YP_842622.1| 195 YS-LALPSGSSHHLTLKVEVNENARSG 220
                                    33.58999************9999987 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.94
                          DUF11  16 vtytltvtNtgpasangvvvtDtlPaglayvsvsas 51 
                                    +++  + tN  p + + v ++ + P+gla +++   
  gi|116753504|ref|YP_842622.1| 323 IVFRMVDTNGVPFPPEVVYLEAVEPSGLAVITSADP 358
                                    555556677777777777777777888887777666 PP

>> DUF1573  Protein of unknown function (DUF1573)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00041       1.5      13      68 ..      32      91 ..      21     122 .. 0.77
   2 ?    1.0   0.0      0.12   4.3e+02      11      30 ..     145     164 ..     135     173 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00041
                        DUF1573 13 ieegekvtatFeftNtgkaplvitnvktsCg....CttpeypkepiapGesgkikvtfna 68
                                   i+ ge ++ + ++tNtg++p+   + ++  g     +  ++pk++i pG+ +++ + f a
  gi|116753504|ref|YP_842622.1| 32 IHPGEVIHKVLTLTNTGEEPVSRIRTTAVGGdakdMIMIDIPKKAIDPGDDMDVDIFFMA 91
                                   55678888999*********976666655551222456678*************998865 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.12
                        DUF1573  11 gkieegekvtatFeftNtgk 30 
                                    g+++ +e+v+ + e++Ntg 
  gi|116753504|ref|YP_842622.1| 145 GEVTPDEPVEFDLEVRNTGR 164
                                    8889999***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (519 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); 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:                         5  (0.000278878); expected 0.2 (1e-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 0.28s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 3586.52
//
Query:       gi|116753505|ref|YP_842623.1|  [L=356]
Description: 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.9e-55  185.7   0.1      8e-55  185.3   0.1    1.1  1  DUF1297      Domain of unknown function (DUF1297)
    1.5e-42  144.4   0.0    2.5e-42  143.7   0.0    1.3  1  DUF1246      Protein of unknown function (DUF1246)
    4.2e-06   26.9   0.0    1.6e-05   25.0   0.0    1.9  1  ATP-grasp_3  ATP-grasp domain
    0.00022   20.8   0.0    0.00043   19.8   0.0    1.4  1  CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP bindin
  ------ inclusion threshold ------
      0.024   14.2   0.3       0.52    9.9   0.0    2.2  2  ATP-grasp    ATP-grasp domain
      0.082   13.3   0.0       0.16   12.4   0.0    1.4  1  sCache_3_3   Single cache domain 3
      0.096   12.3   0.0       0.17   11.5   0.0    1.3  1  RimK         RimK-like ATP-grasp domain


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 !  185.3   0.1   3.1e-58     8e-55      19     187 ..     180     355 ..     168     356 .] 0.94

  Alignments for each domain:
  == domain 1  score: 185.3 bits;  conditional E-value: 3.1e-58
                                    HHCCEEEEE---SEEEEEEEEEETTT........TEEEEEEEEEEEEEECCCHCCS-HHHHHCCT-.---EEEEEEEEEE CS
                        DUF1297  19 dlkkasieeyvvGanfnlnyfysplk........eevellgidrRyesnldglvrlpakeqlelev.epeyvvvGnipvv 89 
                                    + +k +i+e+++G+++++++fysp++        +++++lgidrR+esn d++ r+ + ++le+    p++vv+Gn p+v
  gi|116753505|ref|YP_842623.1| 180 QGQKYTIQEFILGTRYYIHFFYSPIRekgyrlrkGTLDMLGIDRRVESNADEIFRIGSVNELEAAGiYPSFVVTGNLPLV 259
                                    557899********************99****999*********************999998876559************ PP

                                    E-GGGHHHHHHHHHHHHHHHHHHSTT---EEEEEEEEE-TTS-EEEEEEESSB-GGGGGGTT--CCHHHTTSS---HHHH CS
                        DUF1297  90 lREsllekvfelgekfveaakklvppGiiGpFcLqsvvtkdlelvvfdvsaRivggtnvymegspyskllfgeplsmGrr 169
                                    lREsll+kvf+lge++ve++ +l+  G++GpF+L+++vt+dl++ vf++saRiv+gtn++++gspys l  ++ ls+Grr
  gi|116753505|ref|YP_842623.1| 260 LRESLLPKVFDLGERVVETSIELFG-GMVGPFSLETIVTDDLDFKVFEISARIVAGTNLFISGSPYSDL-IEKGLSTGRR 337
                                    *********************9997.*****************************************87.589******* PP

                                    HHHHHHHHHHCT-GGGCE CS
                        DUF1297 170 ialEikeaiekdrleeiv 187
                                    ia Ei  a + + l e++
  gi|116753505|ref|YP_842623.1| 338 IAQEIALARSMGALGEVI 355
                                    ****************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 !  143.7   0.0   9.6e-46   2.5e-42       1     122 []      21     142 ..      21     142 .. 0.98

  Alignments for each domain:
  == domain 1  score: 143.7 bits;  conditional E-value: 9.6e-46
                                    EEEESSTTHHHHHHHHHHTT--EEEEC-CCCHHHHHTTTT-..SEEEE.S.S..TTSS--HHHHHHTTCEE--BTTHHHH CS
                        DUF1246   1 iatlaSHsalqilkgAkkegfrtlavcekgreklYekfkvi..devivldkfkdilkeevqeklreenailvPhgsfveY 78 
                                    iat++SHs+lqi++gAk+egfrtl +c     ++Y++f+++  d +i ld++k +l+e+  ++l++enai++Phgs+veY
  gi|116753505|ref|YP_842623.1|  21 IATVCSHSSLQIFHGAKQEGFRTLGICIGPPPRFYDAFPLAkpDAFISLDSYKAMLDES--DRLIDENAIIIPHGSMVEY 98 
                                    89************************************99989*************998..******************* PP

                                    C-HHHHHC-SS-EES-TTHHHHHCSHHHHHHHHHHTT-BB--BE CS
                        DUF1246  79 vgiekieelkvpifGnrkllrwEerrekkrkyLekAgiriPkki 122
                                    +gi+++e l vp+fGnr++l wE++re++r++L +Ag+++P+++
  gi|116753505|ref|YP_842623.1|  99 LGIQNFEALPVPTFGNRRCLAWESDREMEREWLLRAGVNVPMRF 142
                                    *****************************************976 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   6.1e-09   1.6e-05       8      86 ..     128     206 ..     122     314 .. 0.69

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 6.1e-09
                                    HHHHTTT.S---....-EESS--SSSEEEEESS-------B--SS--TTE.........EEEE---SEEEEEEEEE.SSS CS
                    ATP-grasp_3   8 ykkLkeagvkvPtkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve..lvqefieGkplSvsllsdgek 85 
                                     ++L +agv+vP  ++ e++e  + +++vK   + gg++ +++++kee +++i++ +   +qefi G+ + + +  +  +
  gi|116753505|ref|YP_842623.1| 128 REWLLRAGVNVP--MRFENAELIDRPVIVKYHGAKGGKGFFIAKNKEEFQSKIQQGQkyTIQEFILGTRYYIHFFYSPIR 205
                                    579999******..99***********************************99988888*********999988776555 PP

                                    E CS
                    ATP-grasp_3  86 v 86 
                                     
  gi|116753505|ref|YP_842623.1| 206 E 206
                                    5 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 !   19.8   0.0   1.7e-07   0.00043      32      78 ..     143     189 ..     134     206 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.7e-07
                                    HHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHH CS
                    CPSase_L_D2  32 aiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaaf 78 
                                    + a+ i  Pvi+k   + GGkG  +a+n+ee++  ++++++ +   f
  gi|116753505|ref|YP_842623.1| 143 ENAELIDRPVIVKYHGAKGGKGFFIAKNKEEFQSKIQQGQKYTIQEF 189
                                    66888999******************************999886555 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0    0.0002      0.52      24      70 ..     145     188 ..     137     193 .. 0.82
   2 ?    2.1   0.0     0.049   1.3e+02     134     159 ..     285     310 ..     253     313 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0002
                                    HHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHCGTTCEEEEE CS
                      ATP-grasp  24 aeelglpvvvKarrlgydGkGqsvvrseedleqalealkeekvivEe 70 
                                    ae ++ pv+vK   ++  GkG ++ +++e+ ++ +++   +k  + e
  gi|116753505|ref|YP_842623.1| 145 AELIDRPVIVK-YHGAKGGKGFFIAKNKEEFQSKIQQG--QKYTIQE 188
                                    57899******.999****************9988765..4455555 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.049
                                    TSSEEEEEEEEEETTCTEEEEEEESS CS
                      ATP-grasp 134 ggvGvfavElFvledgellvnElapR 159
                                    g+vG f++E  v++d +  v E++ R
  gi|116753505|ref|YP_842623.1| 285 GMVGPFSLETIVTDDLDFKVFEISAR 310
                                    579**********9999******999 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 ?   12.4   0.0   6.4e-05      0.16      49      82 ..     171     206 ..     162     219 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.4e-05
                     sCache_3_3  49 eevaeavlkkGetysgraeilgkkylta..YePlkd 82 
                                    +e +++ +++G++y+ +++ilg++y+    Y P+++
  gi|116753505|ref|YP_842623.1| 171 KEEFQSKIQQGQKYTIQEFILGTRYYIHffYSPIRE 206
                                    558999********************8544999987 PP

>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   6.5e-05      0.17      39      82 ..     148     190 ..     131     195 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.5e-05
                                    .-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHHGGG--EEEEE- CS
                           RimK  39 lrfPvvvKsvegsqGikvvlakkeqklkqvlealkeailvqeyi 82 
                                    +  Pv+vK   ++ G + ++ak++++ ++ ++   ++  +qe+i
  gi|116753505|ref|YP_842623.1| 148 IDRPVIVKYHGAKGGKGFFIAKNKEEFQSKIQQG-QKYTIQEFI 190
                                    578*************************998764.445678888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); 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:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2653.05
//
Query:       gi|116753506|ref|YP_842624.1|  [L=397]
Description: sugar phosphate isomerase [Methanosaeta thermophila PT]
Scores for 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-08   32.1   0.0     0.0021   17.9   0.0    2.9  2  SIS             SIS domain
  ------ inclusion threshold ------
       0.18   11.7   0.1        2.5    8.1   0.0    2.2  2  Trm5_N          tRNA methyltransferase 5 N-terminal domain
       0.19   10.2   0.0       0.29    9.6   0.0    1.2  1  Lys-AminoMut_A  D-Lysine 5,6-aminomutase TIM-barrel domain of


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 !   10.3   0.0   7.6e-05      0.46      58      97 ..      98     137 ..      91     146 .. 0.92
   2 !   17.9   0.0   3.6e-07    0.0021       6      95 ..     236     319 ..     231     325 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 7.6e-05
                                    EEEESSSHHHHHHHHHHHHHHTTSEEEEEESSTTSHHHHH CS
                            SIS  58 ilisfsgetkdlvaaaelakergakiiaITdskgsplare 97 
                                    i++s sget+++++ +e +  +g++i +IT + + +++r 
  gi|116753506|ref|YP_842624.1|  98 IAVSGSGETPSVNKYIEDVMGQGGEIKLITANRNGTAYRL 137
                                    99******************************99998875 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 3.6e-07
                                    SEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHTTSEEEE CS
                            SIS   6 kriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelakergakiia 85 
                                     r ++ G G+s+ +a+ + + + ++++i +   d  +      +  + +d+ i i+  g+t + ++ a+ a ++ga +  
  gi|116753506|ref|YP_842624.1| 236 GRYVIGGVGRSGLVARAFEMRFTHLNKISYWERDFNT------PSFQIGDVYIPITGGGNTYEALEGARNAFRNGADVMP 309
                                    5788999***************999999887666555......778899******************************* PP

                                    EESSTTSHHH CS
                            SIS  86 ITdskgspla 95 
                                    IT ++gs l 
  gi|116753506|ref|YP_842624.1| 310 ITANSGSNLM 319
                                    *******985 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 ?    1.1   0.0     0.063   3.8e+02      34      41 ..     279     286 ..     278     292 .. 0.78
   2 ?    8.1   0.0   0.00042       2.5      31      45 ..     328     342 ..     323     345 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.063
                                    EEEEEB-S CS
                         Trm5_N  34 ylyIPvke 41 
                                     +yIP++ 
  gi|116753506|ref|YP_842624.1| 279 DVYIPITG 286
                                    79****96 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00042
                                    ETTEEEEEB-S--HH CS
                         Trm5_N  31 dddylyIPvkeepeg 45 
                                     dd ++IPvk++ eg
  gi|116753506|ref|YP_842624.1| 328 LDDVVFIPVKKDYEG 342
                                    69**********998 PP

>> Lys-AminoMut_A  D-Lysine 5,6-aminomutase TIM-barrel domain of alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   4.8e-05      0.29     152     190 ..     284     322 ..     270     327 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 4.8e-05
                                    EE--S-HHHHHHHHHHHHHTT-SEEEE---TTGGG-SS- CS
                 Lys-AminoMut_A 152 ivatGniyedvvqakaaarqGadviavirstgqslldyv 190
                                    i   Gn ye ++ a++a r+Gadv+ +    g  l+  v
  gi|116753506|ref|YP_842624.1| 284 ITGGGNTYEALEGARNAFRNGADVMPITANSGSNLMALV 322
                                    66789********************99999999888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2871.23
//
Query:       gi|116753507|ref|YP_842625.1|  [L=179]
Description: phosphodiesterase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-26   93.4   0.0      2e-26   93.1   0.0    1.0  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    0.00011   22.7   1.6     0.0087   16.6   0.1    2.2  2  Metallophos    Calcineurin-like phosphoesterase


Domain annotation for each model (and alignments):
>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.1   0.0   2.2e-30     2e-26       1     157 [.       1     139 [.       1     146 [. 0.91

  Alignments for each domain:
  == domain 1  score: 93.1 bits;  conditional E-value: 2.2e-30
                  Metallophos_2   1 MklaiiSDlHsnldaleavlealkevgvdaiihaGDleeeepevleellelapvlaVrGNnDeevveedvlreaaelgtd 80 
                                    Mk+++iSD+H   ++ e++l+ l++   d+i+haGDl  ++ ev  +l+ l + +aV GN D             +++++
  gi|116753507|ref|YP_842625.1|   1 MKILLISDTH-LDRISEELLKTLSGY--DMILHAGDL--VSMEVYTDLKTLGETHAVAGNSD-----------HPDVRRS 64 
                                    **********.56788999****999..********9..***********************...........999**** PP

                  Metallophos_2  81 lpeeaelelagekvlliHgdpl.gvkdalaellkeaeegsdvvvcGHtHvpevekeggvlvvnPGsvgeprdgdpety 157
                                    lpe+ +l+++g +v++iH   +  ++ +++ +++e  +++d++v+GH H+p  e++g++++v PGs++ pr + p ++
  gi|116753507|ref|YP_842625.1|  65 LPERLKLDIEGLRVGIIHRPSHsPDSPGISLMARE--MDVDLLVFGHFHKPVFERDGSRMMVCPGSPTCPRLSPP-SV 139
                                    *******************9666667777777777..9999****************************998877.44 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   9.7e-07    0.0087       1      47 [.       1      38 [.       1      78 [. 0.65
   2 !    5.5   0.1    0.0024        21     169     204 .]      83     113 ..      74     113 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 9.7e-07
                                   EEEEEEESBTBTTCCTHHHHHH.HHHHHHHHHTTESEEEEESTSSSSS CS
                    Metallophos  1 lrilvigDlHlalgggqlddll.kllddllreekpdlvllaGDlvdrg 47
                                   ++il+i+D+H       ld++  +ll+ l   ++ d++l+aGDlv   
  gi|116753507|ref|YP_842625.1|  1 MKILLISDTH-------LDRISeELLKTL---SGYDMILHAGDLVSME 38
                                   89********.......333331333333...578********98755 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0024
                                    SESSCSSSCSCCHHHHHHHHHHTTESEEEEESSSSE CS
                    Metallophos 169 splyrgsgylfgdealedllkkygvdlvisGHtHvy 204
                                    +p +     + +++ +    ++ +vdl ++GH H++
  gi|116753507|ref|YP_842625.1|  83 RPSH-----SPDSPGISLMAREMDVDLLVFGHFHKP 113
                                    4444.....444455554478889**********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       206  (0.0114898); expected 358.6 (0.02)
Passed bias filter:                      200  (0.0111551); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1386.90
//
Query:       gi|116753508|ref|YP_842626.1|  [L=88]
Description: hypothetical protein Mthe_0187 [Methanosaeta thermophila PT]
Scores for complete 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-26   91.4   0.6      3e-26   91.2   0.6    1.0  1  HTH_45    Winged helix-turn-helix
      0.005   16.6   0.1      0.005   16.6   0.1    1.1  1  DUF4364   Domain of unknown function (DUF4364)
      0.008   16.0   0.0      0.013   15.4   0.0    1.4  1  TrmB      Sugar-specific transcriptional regulator TrmB
     0.0082   16.6   0.1      0.027   15.0   0.0    1.9  3  HTH_27    Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.024   14.7   0.0       0.03   14.4   0.0    1.3  1  DUF2250   Uncharacterized protein conserved in archaea (DUF22
      0.062   13.1   0.1      0.091   12.6   0.1    1.3  1  DUF1495   Winged helix DNA-binding domain (DUF1495)
      0.074   13.0   0.0      0.091   12.7   0.0    1.2  1  DUF5043   Domain of unknown function (DUF5043)
       0.11   11.8   0.1        0.2   11.0   0.1    1.5  1  SAMP      SAMP Motif


Domain annotation for each model (and alignments):
>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.2   0.6   1.4e-29     3e-26       1      76 [.       4      81 ..       4      82 .. 0.95

  Alignments for each domain:
  == domain 1  score: 91.2 bits;  conditional E-value: 1.4e-29
                         HTH_45  1 rRskleIiadILeaisegeakkTkimykanLsykllnkYLdmLvekgli...kkskekYvlTekGlelleklkeleela 76
                                   +R+kl+Ii++IL+++  g+a+kT+i+y++nL++k++n YLd L+ +gli   + s+ +Y++TekG +lle+lk+++++ 
  gi|116753508|ref|YP_842626.1|  4 KRDKLSIISEILQKC-IGGATKTAIVYQVNLNFKTVNPYLDLLIARGLIeisQGSTVTYTTTEKGIKLLEDLKRVHDVL 81
                                   8**************.********************************988555999******************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 !   16.6   0.1   2.2e-06     0.005      27      74 ..      29      75 ..      10      87 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.2e-06
                        DUF4364 27 eneytnYfdlqqalseLvesglieeeekenktlykiTekGketlelfe 74
                                    +  +n+ +++ +l+ L+  glie  ++ ++ +y+ TekG + le ++
  gi|116753508|ref|YP_842626.1| 29 YQVNLNFKTVNPYLDLLIARGLIEI-SQGSTVTYTTTEKGIKLLEDLK 75
                                   5567899*****************8.569*************999775 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   5.7e-06     0.013      21      64 ..      20      63 ..      11      66 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.7e-06
                                   CCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE CS
                           TrmB 21 gpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYra 64
                                   g at + i  ++++   +v+ +L  L+ +Gl+e+++g++  Y +
  gi|116753508|ref|YP_842626.1| 20 GGATKTAIVYQVNLNFKTVNPYLDLLIARGLIEISQGSTVTYTT 63
                                   7899999*******************************999986 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 ?   -1.0   0.0       1.2   2.6e+03      28      43 ..       3      19 ..       2      21 .. 0.72
   2 !   15.0   0.0   1.2e-05     0.027      17      68 .]      20      67 ..       9      67 .. 0.87
   3 ?   -2.5   0.0       3.4   7.5e+03      24      30 ..      74      80 ..      69      87 .. 0.48

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.2
                         HTH_27 28 lnvedshis.yslkkLt 43
                                   l++++ +i+ ++l k++
  gi|116753508|ref|YP_842626.1|  3 LKRDKLSIIsEILQKCI 19
                                   56777777778888876 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.2e-05
                         HTH_27 17 rrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                   +++++++++  +n++  ++   l+ L+++GL+e ++      +++++ T+kG
  gi|116753508|ref|YP_842626.1| 20 GGATKTAIVYQVNLNFKTVNPYLDLLIARGLIEISQG----STVTYTTTEKG 67
                                   67899***************************43333....36********9 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 3.4
                         HTH_27 24 lcgrlnv 30
                                   l ++++v
  gi|116753508|ref|YP_842626.1| 74 LKRVHDV 80
                                   3333333 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.4e-05      0.03      27      66 ..      26      65 ..       2      86 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.4e-05
                        DUF2250 27 siakeleipleevrellkkLeelGLlervegktikrteak 66
                                    i+ +++++++ v+ +l+ L   GL+e  +g+t+ +t  +
  gi|116753508|ref|YP_842626.1| 26 AIVYQVNLNFKTVNPYLDLLIARGLIEISQGSTVTYTTTE 65
                                   467789999*************************987543 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 ?   12.6   0.1     4e-05     0.091      59      89 ..      45      73 ..      36      74 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4e-05
                        DUF1495 59 LielGLveeeeeseglklYklteeGieivev 89
                                   Li++GL+e   ++  + +Y+ te+Gi++ e 
  gi|116753508|ref|YP_842626.1| 45 LIARGLIE--ISQGSTVTYTTTEKGIKLLED 73
                                   9******6..56777789*********9875 PP

>> DUF5043  Domain of unknown function (DUF5043)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.1e-05     0.091      99     148 ..      22      70 ..       3      73 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.1e-05
                        DUF5043  99 nsdtGkvdevefeftafspyatvPvsvyrkievklkeeivfklteeGkkl 148
                                     ++t +v +v+ +f++++py  + +     ie+     + ++ te+G kl
  gi|116753508|ref|YP_842626.1|  22 ATKTAIVYQVNLNFKTVNPYLDLLIA-RGLIEISQGSTVTYTTTEKGIKL 70 
                                    47899***************998765.4579****************886 PP

>> SAMP  SAMP Motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   8.8e-05       0.2       7      14 ..      13      20 ..      12      22 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.8e-05
                           SAMP  7 dlLqeCIg 14
                                   ++Lq+CIg
  gi|116753508|ref|YP_842626.1| 13 EILQKCIG 20
                                   9******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); 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: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 655.46
//
Query:       gi|116753509|ref|YP_842627.1|  [L=226]
Description: ribosome biogenesis protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-46  158.5   0.0    1.8e-46  158.3   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 !  158.3   0.0   9.8e-51   1.8e-46       2     194 .]       5     216 ..       4     216 .. 0.91

  Alignments for each domain:
  == domain 1  score: 158.3 bits;  conditional E-value: 9.8e-51
                                    EEEEES--B--GG................SCGGSB--HHHHCGG.TTSTTGGGSS-CHHHHHHHHHHHCSCHHCTT.EEE CS
                           EMG1   2 vLeeasLelvkvk................kkseqLLnsddhkkilkklkreakeaRpDIvHqcLlalldspLnkagllqv 65 
                                    +L++++Lelv+++                ++ +++L+++ h+++++ l    +++RpDIvH +Ll +l+s+Ln+ g+l+v
  gi|116753509|ref|YP_842627.1|   5 LLADSELELVPREivgypavrlnarkrnkSPAKSILDASLHHSAMRALPMGDRRGRPDIVHVFLLVALESVLNRVGQLRV 84 
                                    799************************99999************************************************ PP

                                    EEEETTSEEEEE-TT----SSHHHHHHHHHHHHCCSEEEETTEE.SCEEE.ECS-HHHHCCC...SEEEEE-TTSEE-.. CS
                           EMG1  66 yihttknvlIevnpqtRiPrtfkrFagLmvqLLkklsirategeekLlkv.iknpitdhlpp..gskiillsesaekklv 142
                                    yiht++n++I+++p+tRiP+++ rF+gLm++L++k+s+++ e   +L+ +  +++i  ++ +  ++k+ills +++   v
  gi|116753509|ref|YP_842627.1|  85 YIHTRNNEMITIDPTTRIPKNYPRFVGLMESLFEKGSVPERE---PLIVMqRDRDIGACIGEipHEKVILLSPKGR--RV 159
                                    ***************************************976...4555515689*****99889***********..77 PP

                                    .............EEEE-SSSS....---HH...EEESSSS---HHHHHHHHHHHCH CS
                           EMG1 143 dleefv..vkpvvfvigamskgsvkidykee...eisisnypLsaavvcskiltafE 194
                                    +l+++v   ++  f++g+++kg+   d+ +e   +isi++++Ls ++v+s+il ++E
  gi|116753509|ref|YP_842627.1| 160 RLSDYVkeCDNALFILGGFPKGEFISDVLSEaddTISIYEESLSVWTVASEILVNYE 216
                                    8*****6656999*********555555553556******************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       258  (0.0143901); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1738.55
//
Query:       gi|116753510|ref|YP_842628.1|  [L=245]
Description: beta-lactamase domain-containing protein [Methanosaeta thermophila PT]
Scores for 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  103.7   1.0      1e-29  103.5   1.0    1.1  1  Lactamase_B_2  Beta-lactamase superfamily domain
    8.8e-18   65.0   0.2    1.3e-17   64.5   0.2    1.3  1  Lactamase_B    Metallo-beta-lactamase superfamily
    1.1e-06   28.6   0.1    1.8e-06   27.9   0.1    1.3  1  Lactamase_B_3  Beta-lactamase superfamily domain
     0.0044   16.5   0.0     0.0068   15.9   0.0    1.2  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 !  103.5   1.0   2.3e-33     1e-29       2     200 ..      48     219 ..      47     220 .. 0.89

  Alignments for each domain:
  == domain 1  score: 103.5 bits;  conditional E-value: 2.3e-33
                                    EEEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHT CS
                  Lactamase_B_2   2 riLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylalee 81 
                                    r+LiD++pdlr q l ++        ++++daV++thaHyDH+ag+ ++ + ++ ++p+ya++++l+++ + + +  l +
  gi|116753510|ref|YP_842628.1|  48 RVLIDTSPDLRWQ-LIKM-------GISKVDAVIWTHAHYDHYAGFGDFHRVQN-HVPVYATRSTLDYVISYLYF--LRP 116
                                    8**********99.5555.......578***********************876.5***************9654..444 PP

                                    TTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---.HHHHHHHCT-SEE CS
                  Lactamase_B_2  82 epavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyip.eeigerlggadll 160
                                    +    +h++++ e+fe++  g+e+t+++++h   +        t+G+++  ggkrv+ + Dt+    ee  + +++adl 
  gi|116753510|ref|YP_842628.1| 117 Q----RHDVEPLEPFEIA--GMEFTLFEVNHPPVE--------TMGVLVSAGGKRVVITSDTNDALsEESLDIMRDADLF 182
                                    4....7799999*****9..899*****9998888........********************655599999******** PP

                                    EEE-S-SSTTHHHHHHT---STSHHHHCTTSSSSEEEEES CS
                  Lactamase_B_2 161 llditayeddemirhmgHltpeeaveaaadlgakrlvliH 200
                                    + d+ +    +    + H++ +ea+ +a +l+a+++vl+H
  gi|116753510|ref|YP_842628.1| 183 IADAIMPPGYK---LNKHMNADEAISLAHRLNARQTVLTH 219
                                    *9977555544...689*********************** PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.5   0.2   2.9e-21   1.3e-17       5     162 ..      36     175 ..      32     208 .. 0.89

  Alignments for each domain:
  == domain 1  score: 64.5 bits;  conditional E-value: 2.9e-21
                                    SSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHC CS
                    Lactamase_B   5 pvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfm 84 
                                      +s+l+e+d+g +LiDt  + +++++       + ++ +vdavi TH+H+DH++g g++ +  + ++++    +  +  
  gi|116753510|ref|YP_842628.1|  36 LRFSILLENDEGRVLIDTSPDLRWQLI-------KMGISKVDAVIWTHAHYDHYAGFGDFHRVQNHVPVYATRSTLDYVI 108
                                    5689**********************5.......89*****************************999999999999999 PP

                                    HHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC CS
                    Lactamase_B  85 eeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetgridl 162
                                     ++++            +++ +dv ++e  ++ag+  +l  + +p+   +++ v++gg++v++t D+  a +++++d 
  gi|116753510|ref|YP_842628.1| 109 SYLYF-----------LRPQRHDVEPLEPFEIAGMEFTLFEVNHPPVETMGVLVSAGGKRVVITSDTNDALSEESLDI 175
                                    99944...........66678899999999999999999999999999******************977777666666 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 !   27.9   0.1   4.1e-10   1.8e-06       9     163 .]      39     219 ..      38     219 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 4.1e-10
                  Lactamase_B_3   9 sflletagarilvDPfkanlgyeppa...eeaDlvlisqaledHahletl.kqlaenvkvlee................. 67 
                                    s+lle ++ r+l+D  ++ l ++  +    ++D+v+ ++a+ dH++   +  ++++ v+v ++                 
  gi|116753510|ref|YP_842628.1|  39 SILLENDEGRVLIDT-SPDLRWQLIKmgiSKVDAVIWTHAHYDHYAGFGDfHRVQNHVPVYATrstldyvisylyflrpq 117
                                    7899**********5.45777777778889***************97654156645555555555555555555555533 PP

                  Lactamase_B_3  68 ......geslevggleiravatshdavggsergenngflleqdgltiyhlGhlahelsseelkelgrvDvvltPvgg... 138
                                           e +e++g+e++ ++ +h      ++ e +g l++ +g +++   ++   ls+e+l+ + ++D++++  +    
  gi|116753510|ref|YP_842628.1| 118 rhdvepLEPFEIAGMEFTLFEVNH------PPVETMGVLVSAGGKRVVITSDTNDALSEESLDIMRDADLFIADAIMppg 191
                                    211111444555555555555555......67778999***********************************9999999 PP

                  Lactamase_B_3 139 ...pltlgqeealelakrLkpklvlPmh 163
                                       ++ ++++ea+ la+rL+++  + +h
  gi|116753510|ref|YP_842628.1| 192 yklNKHMNADEAISLAHRLNARQTVLTH 219
                                    99999****************9888776 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 !   15.9   0.0   1.5e-06    0.0068       1      74 [.      41     102 ..      41     108 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.5e-06
                  Lactamase_B_6   1 lLeldnvkiLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayallyakfksklllnipvyatlp 74 
                                    lLe d+ ++L+D + d          + ++  i++vd+++ +ha  +h +++      f+ ++  ++pvyat  
  gi|116753510|ref|YP_842628.1|  41 LLENDEGRVLIDTSPDLR-------WQLIKMGISKVDAVIWTHAHYDHYAGF----GDFH-RVQNHVPVYATRS 102
                                    789999999999999864.......4567888*******************8....4553.67889*****976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1925.05
//
Query:       gi|116753511|ref|YP_842629.1|  [L=425]
Description: ATPase central domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-35  122.3   0.1      7e-35  120.3   0.0    2.0  2  AAA           ATPase family associated with various cellular 
    1.9e-12   46.8   0.3    4.4e-12   45.6   0.3    1.6  1  AAA_lid_3     AAA+ lid domain
    0.00022   21.5   1.5      0.031   14.5   0.1    3.3  3  AAA_22        AAA domain
    0.00043   20.8   0.1     0.0047   17.5   0.0    2.4  2  AAA_18        AAA domain
     0.0009   19.5   0.1      0.003   17.8   0.0    2.1  2  AAA_28        AAA domain
     0.0015   18.5   0.0      0.006   16.6   0.0    2.1  1  AAA_5         AAA domain (dynein-related subfamily)
     0.0019   18.4   0.0     0.0067   16.6   0.0    2.1  1  AAA_33        AAA domain
     0.0034   17.8   0.9       0.44   10.9   0.0    3.0  3  AAA_16        AAA ATPase domain
  ------ inclusion threshold ------
      0.013   16.0   1.2      0.048   14.1   0.1    2.6  2  AAA_17        AAA domain
      0.018   14.6   0.2       0.11   12.1   0.1    2.4  2  AAA_25        AAA domain
      0.026   13.7   0.0      0.041   13.0   0.0    1.4  1  DUF815        Protein of unknown function (DUF815)
      0.026   14.3   0.0      0.058   13.1   0.0    1.6  1  RuvB_N        Holliday junction DNA helicase RuvB P-loop doma
      0.033   14.3   0.1        7.4    6.7   0.0    2.6  2  ADK           Adenylate kinase
      0.045   13.0   0.2        1.5    8.1   0.0    2.3  2  Zeta_toxin    Zeta toxin
      0.052   13.9   0.4       0.18   12.1   0.4    2.1  1  AAA_19        AAA domain
      0.062   13.6   0.1       0.16   12.2   0.1    1.7  1  FeoA          FeoA domain
      0.078   12.7   0.3       0.16   11.7   0.3    1.6  1  AAA_30        AAA domain
        0.1   12.7   0.1        0.3   11.2   0.0    1.8  2  SKI           Shikimate kinase
        0.1   12.7   0.0       0.47   10.6   0.0    2.2  1  AAA_2         AAA domain (Cdc48 subfamily)
       0.15   11.4   0.1       0.57    9.5   0.1    2.0  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
       0.16   11.7   0.1       0.31   10.8   0.0    1.5  1  AAA_11        AAA domain
       0.18   11.9   0.0       0.44   10.7   0.0    1.7  1  MMR_HSR1      50S ribosome-binding GTPase
       0.21   11.1   0.1       0.51    9.8   0.1    1.7  1  AAA_7         P-loop containing dynein motor region
       0.34   11.4   2.2         21    5.6   0.1    2.5  2  AAA_23        AAA domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.3   0.0   9.4e-38     7e-35       2     131 ..     215     342 ..     214     343 .. 0.98
   2 ?   -1.6   0.1       4.4   3.3e+03      64      94 ..     366     394 ..     350     410 .. 0.63

  Alignments for each domain:
  == domain 1  score: 120.3 bits;  conditional E-value: 9.4e-38
                                    EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHH CS
                            AAA   2 llyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgsesee 81 
                                    l++G pGtGKT++a+a+a+ lg +++e+ +s ++s+y+ge++k+i ++f+ ak+ + p++lf+DE+d +ak+r+++e++ 
  gi|116753511|ref|YP_842629.1| 215 LFVGSPGTGKTTTARAIAEWLGLPLIEVRLSMITSQYLGETSKNIDKVFDLAKRLS-PCVLFVDEFDFVAKTRTSDEHGA 293
                                    89*****************************************************9.*********************** PP

                                    HHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEEEETT CS
                            AAA  82 eervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrkieie 131
                                     +r+vn+Ll+++d+ +  e+ v++i+atn+p+ ld a   +Rfd+++ ++
  gi|116753511|ref|YP_842629.1| 294 IKRAVNTLLKAIDEISLVEDGVLFIAATNHPQLLDYAAW-RRFDKVLDFP 342
                                    ***************************************.7*****9987 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.4
                                    EETGGGHHHHHTTCCCHHHHHHHHHHHHHHH CS
                            AAA  64 iDEidalaksrsgseseeeervvnqLlteld 94 
                                    iDEi +l+     s s+ +  v +++l++l 
  gi|116753511|ref|YP_842629.1| 366 IDEIASLTDGY--SGSDLRLVVREAMLNALL 394
                                    78888886655..334444444444444433 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.3   5.9e-15   4.4e-12       2      42 ..     364     404 ..     363     411 .. 0.91

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 5.9e-15
                      AAA_lid_3   2 vdlkeLAerTeGySGADlaalcreAallAlrrgikeitmed 42 
                                    vd++e+A++T+GySG Dl  ++reA l+Al +++k+++  d
  gi|116753511|ref|YP_842629.1| 364 VDIDEIASLTDGYSGSDLRLVVREAMLNALLEDRKTLKHID 404
                                    9********************************99876555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   4.2e-05     0.031      10      40 ..     216     237 ..     212     252 .. 0.83
   2 ?    3.5   0.0      0.11        80      82     112 ..     262     301 ..     239     327 .. 0.71
   3 ?    0.4   0.1      0.98   7.3e+02      76     112 ..     346     393 ..     312     416 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.2e-05
                         AAA_22  10 vtGesGtGKTtllrrlleqldeeakaeeerp 40 
                                     +G +GtGKTt++r ++e+l         + 
  gi|116753511|ref|YP_842629.1| 216 FVGSPGTGKTTTARAIAEWL---------GL 237
                                    68*****************9.........44 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.11
                         AAA_22  82 leqalraravielliiDEaqhlr....s......eealeeL 112
                                    + + +++ +   +l +DE++++     s      ++a+++L
  gi|116753511|ref|YP_842629.1| 262 VFDLAKRLSP-CVLFVDEFDFVAktrtSdehgaiKRAVNTL 301
                                    4455666666.9*********97765425666676666666 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.98
                         AAA_22  76 eellealeqalraravielliiDEaqhlr...s.........eealeeL 112
                                    e +++++ + + ++ + + + iDE+  l+   s         e++l+ L
  gi|116753511|ref|YP_842629.1| 346 ELMRRRILEKILSKID-AEVDIDEIASLTdgySgsdlrlvvrEAMLNAL 393
                                    4444666666666666.66667777777655523345555556666666 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1       1.3   9.5e+02     108     125 ..     136     153 ..     104     164 .. 0.70
   2 !   17.5   0.0   6.2e-06    0.0047       3     109 ..     216     350 ..     215     370 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.3
                         AAA_18 108 eRlekRgyeeakikenee 125
                                     R+++R++ ea+ike  e
  gi|116753511|ref|YP_842629.1| 136 PRFADREWIEARIKELQE 153
                                    4999********996544 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 6.2e-06
                         AAA_18   3 ltGtpGvGKttlakeLskrlgf.....................gvnlrdvakenglllevdpe.......aldeskrlde 54 
                                      G pG+GKtt a+++++ lg+                      +++ d+ak   ++  + +e        +++++ + +
  gi|116753511|ref|YP_842629.1| 216 FVGSPGTGKTTTARAIAEWLGLplievrlsmitsqylgetsknIDKVFDLAKRLSPCVLFVDEfdfvaktRTSDEHGAIK 295
                                    5799**************99999999999999999999999999999999999999999999988888664444444444 PP

                         AAA_18  55 dkldklldaleenssaleegknlvidghla.eleseaakdikkvvLtasp.eelleR 109
                                      ++ ll+a++e+s  l e ++l i      +l+++aa+++   vL+ +  +el++R
  gi|116753511|ref|YP_842629.1| 296 RAVNTLLKAIDEIS--LVEDGVLFIAATNHpQLLDYAAWRRFDKVLDFPLpDELMRR 350
                                    44477777777776..46666665555544044466666666567776655555555 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       7.4   5.5e+03      73     143 ..     134     150 ..     117     157 .. 0.59
   2 !   17.8   0.0   3.9e-06     0.003       3      50 ..     215     263 ..     213     303 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 7.4
                         AAA_28  73 nkvlfcDrglldtlaYarayggeaeaeleaaarekrydlvfllppapeidddgeRredleereaiderlre 143
                                    nk                                                       ++++re+i++r++e
  gi|116753511|ref|YP_842629.1| 134 NKP------------------------------------------------------RFADREWIEARIKE 150
                                    333......................................................34555555555555 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 3.9e-06
                         AAA_28   3 vitGgestGKTtlleaLaar.gypvvpEaareileeklakgedalpwve 50 
                                     ++G ++tGKTt+++a+a+  g p ++    +i+++ l ++ +++++v+
  gi|116753511|ref|YP_842629.1| 215 LFVGSPGTGKTTTARAIAEWlGLPLIEVRLSMITSQYLGETSKNIDKVF 263
                                    589****************889999987777777777766666666665 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     8e-06     0.006       3     137 ..     215     334 ..     213     335 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 8e-06
                                    EEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------.G-SEEEEESGGG--HHH CS
                          AAA_5   3 lLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar.egeilvlDEveraesev 81 
                                    l vG pGtgK++ a+ +a+ l+ ++ +v l+  t+  + +g+++      +  d+++  a r ++++l++DE++ + +  
  gi|116753511|ref|YP_842629.1| 215 LFVGSPGTGKTTTARAIAEWLGLPLIEVRLSMITS--QYLGETS------KNIDKVFDLAKRlSPCVLFVDEFDFVAKTR 286
                                    789*********************99999986332..2233333......344555554444677777777777666666 PP

                                    HHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHTT CS
                          AAA_5  82 lnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrsR 137
                                    ++  +  + +    l +   +++  +d+    + +ia++n ++     l+ a ++R
  gi|116753511|ref|YP_842629.1| 287 TSDEHGAIKRAVNTLLKAIDEISLVEDG----VLFIAATNHPQ----LLDYAAWRR 334
                                    6666666666666666666666555555....66666666666....555555555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0     9e-06    0.0067       3      32 ..     215     246 ..     214     377 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 9e-06
                         AAA_33   3 llvGlpGsGKstlaerllkklg..avllssdt 32 
                                    l+vG pG+GK+t a+ +++ lg   + ++   
  gi|116753511|ref|YP_842629.1| 215 LFVGSPGTGKTTTARAIAEWLGlpLIEVRLSM 246
                                    79****************99997633333333 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0    0.0006      0.44      14      46 ..     201     233 ..     187     244 .. 0.83
   2 ?    3.7   0.0     0.098        73     125     146 ..     261     287 ..     255     318 .. 0.70
   3 ?    0.2   0.0       1.2   8.8e+02      46     128 ..     307     391 ..     296     418 .. 0.44

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0006
                         AAA_16  14 salervrsgrpelvllsGesGvGKsslvrellr 46 
                                    ++l+rv   + +  l++G +G+GK++ +r++++
  gi|116753511|ref|YP_842629.1| 201 EYLRRVGLREIGKSLFVGSPGTGKTTTARAIAE 233
                                    5666776666677799*************9985 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.098
                         AAA_16 125 rllallsrderplvlvlDdlq......w 146
                                    + ++l++r  +p vl++D+++       
  gi|116753511|ref|YP_842629.1| 261 KVFDLAKR-LSPCVLFVDEFDfvaktrT 287
                                    55678888.778*********7444431 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 1.2
                         AAA_16  46 r.alekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekleeala.........avpelagae 115
                                    + +l +dg++f++++++          l++++a+ + + ++ld +   +    r+ le+ l+         +        
  gi|116753511|ref|YP_842629.1| 307 EiSLVEDGVLFIAATNHPQ--------LLDYAAW-RRFDKVLDFPLP-DELMRRRILEKILSkidaevdidE-------- 368
                                    4456666777766666666........5555544.444444433222.111111112222222223332331........ PP

                         AAA_16 116 a.........srllellkrll.a 128
                                              s+l+ ++++++ +
  gi|116753511|ref|YP_842629.1| 369 IasltdgysgSDLRLVVREAMlN 391
                                    11122233345555555555443 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       4.3   3.2e+03      62      62 ..     178     178 ..     137     211 .. 0.56
   2 ?   14.1   0.1   6.5e-05     0.048       1      48 [.     217     261 ..     217     372 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 4.3
                                    H CS
                         AAA_17  62 a 62 
                                     
  gi|116753511|ref|YP_842629.1| 178 G 178
                                    1 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 6.5e-05
                                    EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHH.HHHHTTTSHSSHHHHCT CS
                         AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllr.eeakrgglakardemrk 48 
                                    +G PG GK+t ++ ++e +g++ ++    +r ++++++ l+++ ++++k
  gi|116753511|ref|YP_842629.1| 217 VGSPGTGKTTTARAIAEWLGLPLIE----VRlSMITSQYLGETSKNIDK 261
                                    799********************99....44466667777666666665 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       2.7     2e+03     118     139 ..     135     157 ..      85     167 .. 0.57
   2 ?   12.1   0.1   0.00014      0.11      10      51 ..     188     229 ..     182     311 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.7
                         AAA_25 118 akdrggtl.ltadvdaleaaiee 139
                                    ++++ +   ++a +++l++ +++
  gi|116753511|ref|YP_842629.1| 135 KPRFADREwIEARIKELQESVQD 157
                                    22222222345555555555555 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00014
                         AAA_25  10 vsvadlaapppprrwlvk.gllpagelallaGapgtGKttlal 51 
                                    ++++++++++++r++l + gl ++ + +l++G pgtGKtt a 
  gi|116753511|ref|YP_842629.1| 188 AEISKIEKAIEHREYLRRvGL-REIGKSLFVGSPGTGKTTTAR 229
                                    467889999*********555.79****************875 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   5.5e-05     0.041      55     154 ..     213     326 ..     149     337 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.5e-05
                         DUF815  55 nvLLwGarGtGKSslvkallneyaeeg..Lrlievekedlkelpklvellrerper...filfvDDLsFeeeeeey.... 125
                                    + L++G+ GtGK ++ +a+ + +      +rl  ++ + l e +k ++++ + ++r   ++lfvD   F ++ ++     
  gi|116753511|ref|YP_842629.1| 213 KSLFVGSPGTGKTTTARAIAEWLGLPLieVRLSMITSQYLGETSKNIDKVFDLAKRlspCVLFVDEFDFVAKTRTSdehg 292
                                    4599***************99987766567888888888888888777776555543338******99976544332222 PP

                         DUF815 126 ...ksLksvLeG..sleakpenvliyaTsNrRhL 154
                                       +++ ++L     ++   + vl+ a +N+ +L
  gi|116753511|ref|YP_842629.1| 293 aikRAVNTLLKAidEISLVEDGVLFIAATNHPQL 326
                                    3333444444321134445556666666666555 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   7.8e-05     0.058      35      93 ..     213     279 ..     186     290 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.8e-05
                         RuvB_N  35 hvllyGpPGlGkttlakiiakelgvkl.....k.itsgPvlekagdlaal..ltnleekdvlfidei 93 
                                      l++G+PG Gktt a+ ia+ lg  l       its    e ++++  +  l++  +  vlf+de 
  gi|116753511|ref|YP_842629.1| 213 KSLFVGSPGTGKTTTARAIAEWLGLPLievrlSmITSQYLGETSKNIDKVfdLAKRLSPCVLFVDEF 279
                                    679*****************99875431111131334333344444433311222223347777776 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0099       7.4       2      23 ..     217     238 ..     216     266 .. 0.88
   2 ?    5.0   0.0     0.032        24     101     123 ..     333     367 ..     319     416 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0099
                                    EESTTSSHHHHHHHHHHHHTSE CS
                                    xxxxxxxxxxxxxxxxxxxxxx RF
                            ADK   2 lGaPgaGKGtqaeklvkkygla 23 
                                    +G+Pg+GK t a+ +++ +gl+
  gi|116753511|ref|YP_842629.1| 217 VGSPGTGKTTTARAIAEWLGLP 238
                                    8**************9987765 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.032
                                    SEESEEEEEE--HHHHHHHHHT............G CS
                                    xxxxxxxxxxxxxxxxxxxxxx............x RF
                            ADK 101 vkldlvleldvpeevlveRltg............D 123
                                     + d vl++ +p+e++ +R+++            D
  gi|116753511|ref|YP_842629.1| 333 RRFDKVLDFPLPDELMRRRILEkilskidaevdiD 367
                                    5789****************997777776666552 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1      0.11        83     140     188 ..     128     171 ..     118     185 .. 0.79
   2 ?    8.1   0.0    0.0019       1.5      20      39 ..     215     234 ..     213     244 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.11
                     Zeta_toxin 140 vldRyeeevaegRlvpkeehdeafeglresvealeeekqldrvkikdrd 188
                                    +++R  ++   +R+++ e +++  ++l+esv+    e  l+ v+ik  +
  gi|116753511|ref|YP_842629.1| 128 AEARRANK---PRFADREWIEARIKELQESVQDS--EDMLKLVQIKSPE 171
                                    45566666...9********************94..4456666676555 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0019
                     Zeta_toxin  20 llgGqpGAGKselaellkde 39 
                                    l +G+pG GK+++a+++++ 
  gi|116753511|ref|YP_842629.1| 215 LFVGSPGTGKTTTARAIAEW 234
                                    568************99875 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.4   0.00025      0.18      14      35 ..     215     236 ..     208     370 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00025
                         AAA_19  14 lvtaGpGtGKTrvlkhivallv 35 
                                    l ++ pGtGKT++ ++i ++l 
  gi|116753511|ref|YP_842629.1| 215 LFVGSPGTGKTTTARAIAEWLG 236
                                    6789***********9999875 PP

>> FeoA  FeoA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00022      0.16       6      35 ..     182     210 ..     180     223 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00022
                                    --TT-EEEEEEE-TT.SSHHHHHHHHT--T CS
                           FeoA   6 lkeGergeiarisdedpellrrLremGlvp 35 
                                    l++ +r+ei++i ++  e++ +Lr++Gl++
  gi|116753511|ref|YP_842629.1| 182 LTDEQRAEISKIEKA-IEHREYLRRVGLRE 210
                                    67899*******988.************86 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   0.00021      0.16      21      41 ..     214     234 ..     203     313 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00021
                         AAA_30  21 avltGpAGtGKttalkalrea 41 
                                    ++ +G +GtGKtt+ +a++e 
  gi|116753511|ref|YP_842629.1| 214 SLFVGSPGTGKTTTARAIAEW 234
                                    5789*************9985 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       8.4   6.3e+03      90     116 ..     143     170 ..     139     195 .. 0.65
   2 ?   11.2   0.0    0.0004       0.3       1      23 [.     220     242 ..     220     260 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 8.4
                                    EEE--HHHHHHHHHHTTS.SGGGCSCHH CS
                            SKI  90 yLdvsleellerlkadke.RPllqeksk 116
                                    ++++ ++el+e +++ ++   l+q ks+
  gi|116753511|ref|YP_842629.1| 143 WIEARIKELQESVQDSEDmLKLVQIKSP 170
                                    6677777777777666664334444444 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0004
                                    TTSSHHHHHHHHHHHHTSEEEEH CS
                            SKI   1 mGaGKstvGkllAkklglefiDl 23 
                                    +G+GK+t+++++A+ lgl++i++
  gi|116753511|ref|YP_842629.1| 220 PGTGKTTTARAIAEWLGLPLIEV 242
                                    69*****************9985 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00063      0.47       2     105 ..     210     307 ..     209     325 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00063
                                    ----EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTSEEEEETGGG-- CS
                          AAA_2   2 piisilllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegGivllDEidKih 81 
                                    +i++ l++g+ g+Gkt +a+a+ae l +    +li +  s ++   +     s+ i +     ++    ++++DE d ++
  gi|116753511|ref|YP_842629.1| 210 EIGKSLFVGSPGTGKTTTARAIAEWLGL----PLIEVRLSMITS--QYLGETSKNIDKVFDLAKRLSPCVLFVDEFDFVA 283
                                    78899*********************97....555555554444..2222333333333344444456699999999999 PP

                                    -----------HHHHHHHHHHHH- CS
                          AAA_2  82 pkessgadvSregVqrdLLqileg 105
                                    ++++s +    +  ++ LL+ +++
  gi|116753511|ref|YP_842629.1| 284 KTRTSDEHGAIKRAVNTLLKAIDE 307
                                    974444444444445666666665 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1   0.00076      0.57      26      46 ..     215     235 ..     211     323 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00076
                   Mg_chelatase  26 llvGppGsGKtmlakrlpsll 46 
                                    l+vG+pG+GKt  a+++++ l
  gi|116753511|ref|YP_842629.1| 215 LFVGSPGTGKTTTARAIAEWL 235
                                    89*************998765 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00041      0.31       7      39 ..     187     233 ..     181     274 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00041
                         AAA_11   7 reai...ksalsese...........itliqGPPGtgKTktivells 39 
                                    r  i   ++a++++e            +l+ G PGtgKT+t  ++ +
  gi|116753511|ref|YP_842629.1| 187 RAEIskiEKAIEHREylrrvglreigKSLFVGSPGTGKTTTARAIAE 233
                                    555544466666666666666777779************99877765 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00058      0.44       3      45 ..     215     267 ..     213     339 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00058
                                    EEEESTTSSHHHHHHHHHT.........S.TEEESSSTTSSSSEEEEEEEETT CS
                       MMR_HSR1   3 aivGrpNvGKStLinaltg.........e.kaivsdkpgtTrdinegrvklkg 45 
                                    ++vG p +GK+t  +a+ +         +   i+s++ g T + + + ++l +
  gi|116753511|ref|YP_842629.1| 215 LFVGSPGTGKTTTARAIAEwlglplievRlSMITSQYLGETSKNIDKVFDLAK 267
                                    69***************98777888755446799*******999888877443 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 ?    9.8   0.1   0.00068      0.51      34      58 ..     212     236 ..     198     290 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00068
                          AAA_7  34 kpvllvGptGtGKtviikdllkkld 58 
                                     + l+vG+ GtGKt++++ + + l 
  gi|116753511|ref|YP_842629.1| 212 GKSLFVGSPGTGKTTTARAIAEWLG 236
                                    5679************998776655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1     0.027        21     153     194 ..     137     199 ..      36     203 .. 0.78
   2 ?    5.1   0.3      0.04        30      23      40 ..     215     232 ..     211     237 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.027
                         AAA_23 153 e.........rleelekeleeledekkllekl............eqekekekeleeleeelee 194
                                              r++el+++ ++ ed+ kl++ +                e+++e++++e+++e 
  gi|116753511|ref|YP_842629.1| 137 RfadrewieaRIKELQESVQDSEDMLKLVQIKspedirerigdlVLTDEQRAEISKIEKAIEH 199
                                    133444444499999999999999999999999999988888874556778899999999875 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.04
                         AAA_23  23 lItGpNGaGKTTildAik 40 
                                    l++G  G+GKTT  +Ai 
  gi|116753511|ref|YP_842629.1| 215 LFVGSPGTGKTTTARAIA 232
                                    899*************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       991  (0.0552736); expected 358.6 (0.02)
Passed bias filter:                      818  (0.0456244); expected 358.6 (0.02)
Passed Vit filter:                       121  (0.00674884); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.44
# Mc/sec: 2888.11
//
Query:       gi|116753512|ref|YP_842630.1|  [L=201]
Description: GDSL family lipase [Methanosaeta thermophila PT]
Scores for complete 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   98.9   0.0    5.2e-28   98.7   0.0    1.1  1  Lipase_GDSL_2  GDSL-like Lipase/Acylhydrolase family
    8.8e-17   61.7   0.0    1.1e-16   61.4   0.0    1.1  1  Lipase_GDSL    GDSL-like Lipase/Acylhydrolase


Domain annotation for each model (and alignments):
>> Lipase_GDSL_2  GDSL-like Lipase/Acylhydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.7   0.0   5.8e-32   5.2e-28       1     179 []      22     192 ..      22     192 .. 0.91

  Alignments for each domain:
  == domain 1  score: 98.7 bits;  conditional E-value: 5.8e-32
                                    EEESHHHHTCTTBCCHCHHCCCCCCCHHHTT...-EEEEE.EEHCCH-H..HHHHHHHH.CTGGG-TSEEEEE--CCCCC CS
                  Lipase_GDSL_2   1 alGDSiTaGygadgggrsypaylarllaarl...gldvvnnlgvsGattallrllerlr.dllrlkpdlvtiliGtNDlg 76 
                                    a+GDSiTaGy   +  +++p ++ ++l++++   + + +n  gvsG+tt  ++ l rl+ ++l ++pdlvti++G+ND++
  gi|116753512|ref|YP_842630.1|  22 AFGDSITAGY---AVRHGFPYFWKQALQEKYpdaRIEMHN-EGVSGDTT--RDGLARLEhSVLYHRPDLVTINFGINDAA 95 
                                    7*********...88999*************654444444.********..999999999******************** PP

                                    TT--HHHHHHH..HHHHHHHHCCC...GEEECEEEEE-TTT-TTSTCCHHHHHHHHHHHHHHHHHHCT-EEE-H...HHH CS
                  Lipase_GDSL_2  77 rgvpaaaaaandnleelidalraaapgarilvlgplpptpeaaadarelnaviaaynealrevaaeegvpfvDl...hda 153
                                    +g   ++++an  l ++++ + +        ++  +   ++++  +++ ++ + +y  a+ evaa+ gv fvD+   + +
  gi|116753512|ref|YP_842630.1|  96 YGIGLDEFRAN--LSRMVEIILSE-------CCSEIILLSSQPLLTPYYDKLVLDYYSAIGEVAAAMGVGFVDVyaaWMV 166
                                    ***********..***********.......78888888888888888899***********************887777 PP

                                    HHHCCCCCGGBBTTS.SSB-HHHHHH CS
                  Lipase_GDSL_2 154 ladsgerladlladdglHPnaaGyrl 179
                                       sg +l+ l  ++  HPn++Gyr+
  gi|116753512|ref|YP_842630.1| 167 RVRSGMPLESLVLPGLDHPNEDGYRI 192
                                    79999********999********96 PP

>> Lipase_GDSL  GDSL-like Lipase/Acylhydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.4   0.0   1.2e-20   1.1e-16       1     200 []      20     197 ..      20     197 .. 0.84

  Alignments for each domain:
  == domain 1  score: 61.4 bits;  conditional E-value: 1.2e-20
                                    EEEEESHHHHTT....THHHHHHHCCCCEECCCTTC.GCEEEEEEECTTHHHHHHHCCHECTTTECHHHHHCTTSEEEEE CS
                                    xxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Lipase_GDSL   1 ivafGDSltdGd....gaatlntiqlktpknlnefdlaldrianignkgasdnelqqllnkyplkseqlkalhpdlviis 76 
                                    ivafGDS+t+G+    g++ +++  l+     + +      + n g  g+ ++    +l      ++     +pdlv+i+
  gi|116753512|ref|YP_842630.1|  20 IVAFGDSITAGYavrhGFPYFWKQALQEKY--PDA---RIEMHNEGVSGDTTRDGLARL------EHSVLYHRPDLVTIN 88 
                                    8***********999999999999888844..433...224455555555555555555......9999999******** PP

                                    --CTCC-EECSSCTTTCEEHHHHHHHHHHHHHHHHHHHHTTEEEEEEE-SSTCHCTCCCCHCCHHHHHHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Lipase_GDSL  77 lGtNDsnlgkkstdaakkeaeeyiknlreaikelkeegapkaivvlvsppglgpqeekdakklgekgnefvgeynqrlnd 156
                                    +G ND         a++   +e+++nl  +++ + +e     i++l+s+p l+p            + ++v  y + +++
  gi|116753512|ref|YP_842630.1|  89 FGINDA--------AYGIGLDEFRANLSRMVEIILSEC-CSEIILLSSQPLLTP-----------YYDKLVLDYYSAIGE 148
                                    ******........******************999777.899************...........9************** PP

                                    HHHHCTEEEECHHHHHHHTHCCGCHCH.......TSSSB-HHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxx RF
                    Lipase_GDSL 157 laekdgfavvDlydelqglsgieqlka.......DglHpsekgyeklaell 200
                                    +a+ +g+ +vD+y  +  +   + + +       D  Hp+e gy+++ae+l
  gi|116753512|ref|YP_842630.1| 149 VAAAMGVGFVDVYAAWMVRVRSGMPLEslvlpglD--HPNEDGYRIIAEEL 197
                                    *******************8777777455554444..***********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1534.00
//
Query:       gi|116753513|ref|YP_842631.1|  [L=267]
Description: tryptophan synthase, alpha subunit [Methanosaeta thermophila PT]
Scores for complete 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-80  269.2   0.0    2.9e-80  268.9   0.0    1.0  1  Trp_syntA     Tryptophan synthase alpha chain
    8.3e-05   22.2   0.0    0.00014   21.4   0.0    1.4  1  His_biosynth  Histidine biosynthesis protein
     0.0025   17.3   0.0     0.0066   15.9   0.0    1.6  2  PcrB          PcrB family
  ------ inclusion threshold ------
       0.13   12.6   0.0          9    6.6   0.0    2.3  2  Radical_SAM   Radical SAM superfamily
       0.64    9.7   3.0        1.4    8.5   0.3    2.5  3  Pterin_bind   Pterin binding enzyme


Domain annotation for each model (and alignments):
>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  268.9   0.0     8e-84   2.9e-80      12     251 ..      18     253 ..      13     262 .. 0.94

  Alignments for each domain:
  == domain 1  score: 268.9 bits;  conditional E-value: 8e-84
                                    EEEEEETTSS-HHHHHHHHHHHHHCT-SSEEEE---S--TTS-HHHHHHHHCCCCTT--HHHHHHHHHHHHHHCSSS-EE CS
                      Trp_syntA  12 fvpyvtagdpdleqsleilkalekagadviElGlpfsdPladGPvIqaanlraLakgvtlekvlelveevrkkevevPiv 91 
                                    ++ y+ agdp+ +++++i + + +agadv+ElGlp sdP+adGPvIqaa++ra+a+g++++  +++ ++++     vP v
  gi|116753513|ref|YP_842631.1|  18 LIVYICAGDPSPDETVDIADRIVRAGADVLELGLPHSDPIADGPVIQAASQRAIAAGMNTDLYFDVASKID----GVPKV 93 
                                    899********************************************************************....9**** PP

                                    EEE-CHHHCCC-HHHHCHHHHHCTEEEEEETTSBCCCHHHHHHHHHHTT-EEEEEE-TTS-HHHHHHHHHH--S-EEEES CS
                      Trp_syntA  92 lltylnlvlsygeerflaelkeagvdglivpDlPleeaeelveaakkkglelvflvapttsderlkevveqaegfvYvvs 171
                                    +++y+n+v+++g erf+ +++  g+ g+ivpDlP+ee+++l+e+ +++g++l+ ++ap+t+d+r++ +v++++gfvY+v+
  gi|116753513|ref|YP_842631.1|  94 FMGYYNMVYRRGLERFVSDCRASGICGMIVPDLPMEESRPLREVTSRHGVDLINMIAPNTPDKRIRDIVSTSSGFVYLVA 173
                                    ******************************************************************************** PP

                                    TTC-SSTTSSB-TTHHHHHHHHHHCTSS-EEEESSS-SHHHHHHHH.TT-SEEEE-HHHHHHHHC.TTTSHHHHHHHHHH CS
                      Trp_syntA 172 raGvTgaenavaaevdelverlkkltavPvavGFGistkeqvkqva.kvadGvivGSalvkkiee.eaeekeqaleklee 249
                                    r GvTga++ +++++++lver+  +   P avGFG+s++e++++++ ++adGvivGSa v+ i + e ++ e  ++ +++
  gi|116753513|ref|YP_842631.1| 174 RSGVTGARADLQESTKHLVERVPPVI--PRAVGFGVSRPEHAAELVrAGADGVIVGSACVDLIGKkELDQLEDLIRSMKK 251
                                    **********************9986..****************999****************97345555555555555 PP

                                    HH CS
                      Trp_syntA 250 la 251
                                     +
  gi|116753513|ref|YP_842631.1| 252 AI 253
                                    44 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   3.8e-08   0.00014      57     107 ..     184     232 ..     171     261 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 3.8e-08
                                    THHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH CS
                   His_biosynth  57 greanldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavk 107
                                     +e  ++lve++     ip  vG G+++ e+++el++agad vi+g+a v+
  gi|116753513|ref|YP_842631.1| 184 LQESTKHLVERVPPV--IPRAVGFGVSRPEHAAELVRAGADGVIVGSACVD 232
                                    466778899999999..******************************9885 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.59   2.1e+03      10      34 ..      23      47 ..      14      51 .. 0.70
   2 !   15.9   0.0   1.8e-06    0.0066     157     213 ..     169     232 ..     165     252 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.59
                                   EEE-TTSS-CHHHHHHHHCTT-SEE CS
                           PcrB 10 tklDPeeenpdEiveiviesgtDav 34
                                      DP  +++ +i++ +++ g+D +
  gi|116753513|ref|YP_842631.1| 23 CAGDPSPDETVDIADRIVRAGADVL 47
                                   5557777777777777788888865 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.8e-06
                                    EEEE-.TTSSS-H....HHHHHHHHHHSS.SEEEEESS--SHHHHHHHHCC.SSEEEE-CHHHH CS
                           PcrB 157 iYlEa.sGaledv....eevialkkklek.arlivGGGirsaEkAkevvea.ADvivvGnvvee 213
                                    +Yl a sG+++      e +++l+ ++   +   vG G+  +E+A+e v+a AD ++vG +  +
  gi|116753513|ref|YP_842631.1| 169 VYLVArSGVTGARadlqESTKHLVERVPPvIPRAVGFGVSRPEHAAELVRAgADGVIVGSACVD 232
                                    68888888776552014455555555443134579************************97654 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0025         9      87     115 ..      27      57 ..       5      88 .. 0.79
   2 ?    4.0   0.0     0.017        60      54     109 ..     175     228 ..     134     259 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0025
                                    SCHG..HHHHHHHHHTT-SEEEEEEBSSSHH CS
                                    xxxx..xxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  87 tlpd..eeklerllelgvdrvslgleaadde 115
                                    + pd   ++++r++++g d+++lgl + d+ 
  gi|116753513|ref|YP_842631.1|  27 PSPDetVDIADRIVRAGADVLELGLPHSDPI 57 
                                    33336699*******************9996 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.017
                                    SSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHG.HHHHHHHHHTT-SEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  54 ggepllypdfvellerlaklavpgiritvetngtlpd.eeklerllelgvdrvslgl 109
                                    +g   +++d++e +++l+++      +   + g+ ++ +e++++l+++g d v +g 
  gi|116753513|ref|YP_842631.1| 175 SGVTGARADLQESTKHLVER---VPPVIPRAVGFGVSrPEHAAELVRAGADGVIVGS 228
                                    56666778888888888887...4444444444444459**********99998775 PP

>> Pterin_bind  Pterin binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.3    0.0004       1.4      19      55 ..      28      64 ..      24      75 .. 0.84
   2 ?   -2.1   0.0      0.68   2.4e+03      97     106 ..     146     155 ..     125     188 .. 0.53
   3 ?    0.3   0.2      0.13   4.5e+02      25      74 ..     211     256 ..     209     262 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0004
                                   HHHHHHHHHHHHHHTT-SEEEEESS-TSTT--CCHHH CS
                    Pterin_bind 19 dldkalaqarkmveeGAdilDiggestrPgaervdee 55
                                   ++d+ ++ a + v++GAd+l +g   + P a+    +
  gi|116753513|ref|YP_842631.1| 28 SPDETVDIADRIVRAGADVLELGLPHSDPIADGPVIQ 64
                                   68999*********************99998765555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.68
                                    EEETTTTSSS CS
                    Pterin_bind  97 vNdvsgeerd 106
                                    +N +   + d
  gi|116753513|ref|YP_842631.1| 146 INMIAPNTPD 155
                                    3333333222 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.13
                                    HHHHHHHHTT-SEEEEESS-TSTT--CCHHHHHHHHHHHHHHHHHHHC.TS CS
                    Pterin_bind  25 aqarkmveeGAdilDiggestrPgaervdeeeelervvpvlealrdea.dv 74 
                                    ++a ++v++GAd + +g + +      + +++el+++  +++++++ + +v
  gi|116753513|ref|YP_842631.1| 211 EHAAELVRAGADGVIVGSACV-----DLIGKKELDQLEDLIRSMKKAIsEV 256
                                    689999999999998888888.....7778889999999999888864344 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1944.34
//
Query:       gi|116753514|ref|YP_842632.1|  [L=394]
Description: tryptophan synthase subunit beta [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-39  135.8   0.9    2.5e-39  135.5   0.9    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 !  135.5   0.9   1.4e-43   2.5e-39       4     274 ..      54     362 ..      52     379 .. 0.88

  Alignments for each domain:
  == domain 1  score: 135.5 bits;  conditional E-value: 1.4e-43
                                    CSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-EEEE CS
                           PALP   4 gigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGlkvti 83 
                                    + +pTPl r+++ls++lg  ++lK+E+l ++g++K++      + +k  ++++ ++e+++G+hg+a+A+++allG++ +i
  gi|116753514|ref|YP_842632.1|  54 AGRPTPLYRAENLSRALGRTVYLKREDLLHGGAHKINNTLGQGLLAKYMKKRRLIAETGAGQHGVATAIVGALLGFETEI 133
                                    579*************************************88888888889999999*********************** PP

                                    EEETTS-H...HHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTT.......SHH...HHHHHHTHHHHH CS
                           PALP  84 vvpadasp...ekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfd.......npt...viegygtiglEi 150
                                    ++ + + +    +v +++llGa+v+ v+++  + ++a++e+++++   y   ++        +p+   v e +  ig E 
  gi|116753514|ref|YP_842632.1| 134 YMGELDIErqrMNVFRMELLGARVIPVKSGSRTLKDAINEALRDWAASYESTHYLlgtvagpHPYpsmVREFQRVIGDET 213
                                    **9999954459***************999888888888888885555555555555556575557756666******** PP

                                    H....HHTTTTEEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEEC..TTCGGTTCCS..S.SS..B............ CS
                           PALP 151 l....eqlggkpdavvvpvGgGgliaGiaaglkerrpdvrvigvepe..gsdalarslragrrvtvpvs........... 213
                                         ++ ++ pd +v++vGgG++++Gi + + e    vr+i+ve+   gs   ars+++g  + + ++           
  gi|116753514|ref|YP_842632.1| 214 RsqilAEEKRLPDSIVACVGGGSNAMGIFTSFLE--DAVRLIAVEAGgrGSGRGARSAEHGASLALGEPgvlhgamtkil 291
                                    844445555************************9..569*******9999999999999999999999899********* PP

                                    ..........SSS.CCSTCSCGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHH CS
                           PALP 214 ..........dtiadglavgspselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaal 274
                                               +ia gl+ + ++++   l++    e    sde+a+ + + l r egi++   sa+a+  +
  gi|116753514|ref|YP_842632.1| 292 qdpygqilesYSIAAGLDYPGVGPELAHLAETGRVETAMASDETAIMGFKALSRLEGIIPALESAHAVGFA 362
                                    ******************************************************************99777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); 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 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2847.30
//
Query:       gi|116753515|ref|YP_842633.1|  [L=78]
Description: hypothetical protein Mthe_0194 [Methanosaeta thermophila PT]
Scores for complete 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   37.2   2.2    2.6e-09   37.0   2.2    1.0  1  MtN3_slv  Sugar efflux transporter for intercellular exchange
    1.1e-08   34.7   1.3    1.1e-08   34.7   1.3    2.0  2  PQ-loop   PQ loop repeat


Domain annotation for each model (and alignments):
>> 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 !   37.0   2.2   2.9e-13   2.6e-09      21      84 ..       7      70 ..       5      73 .. 0.95

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 2.9e-13
                       MtN3_slv 21 ilrkiikkksveelsfllflagllsallWllYGllkkdaliiivNlvgvlleliylllflvyak 84
                                   ++ k++++k v +ls+++ l  + + +lWllYG+ ++++++i+ N v ++  l+ ++l+l y  
  gi|116753515|ref|YP_842633.1|  7 QIIKMYRTKLVGDLSLPMLLQYTTGIFLWLLYGIYLENTILIVSNAVSLASFLCGIILYLKYNA 70
                                   57899*********************************************************75 PP

>> PQ-loop  PQ loop repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   1.3   1.3e-12   1.1e-08      15      55 ..       2      42 ..       1      48 [. 0.92
   2 !    3.2   0.9    0.0084        76       1      18 [.      49      66 ..      49      66 .. 0.89

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 1.3e-12
                        PQ-loop 15 vsyiPQiikNykrkSteGlSilflllwllGdilsllyliln 55
                                   + ++PQiik y++k ++ lS+ +ll  ++G +l+lly i  
  gi|116753515|ref|YP_842633.1|  2 FGFYPQIIKMYRTKLVGDLSLPMLLQYTTGIFLWLLYGIYL 42
                                   679**********************************9875 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.0084
                        PQ-loop  1 lseilgyislvlwlvsyi 18
                                   +s++++++s+++ +++y+
  gi|116753515|ref|YP_842633.1| 49 VSNAVSLASFLCGIILYL 66
                                   589999********9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); 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: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 604.58
//
Query:       gi|116753516|ref|YP_842634.1|  [L=116]
Description: hypothetical protein Mthe_0195 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); 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 0.28s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 850.69
//
Query:       gi|116753517|ref|YP_842635.1|  [L=289]
Description: transposase, IS4 family protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.2e-33  113.1   0.0    3.2e-31  107.9   0.0    2.2  2  DDE_Tnp_1_5  Transposase DDE domain
      9e-21   74.5   0.1    1.6e-20   73.7   0.1    1.4  1  DDE_Tnp_1    Transposase DDE domain


Domain annotation for each model (and alignments):
>> DDE_Tnp_1_5  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.9   0.0   3.6e-35   3.2e-31       2     111 ..      18     125 ..      17     126 .. 0.95
   2 ?    2.8   0.0     0.016   1.4e+02      40      67 ..     252     281 ..     246     287 .. 0.82

  Alignments for each domain:
  == domain 1  score: 107.9 bits;  conditional E-value: 3.6e-35
                    DDE_Tnp_1_5   2 kRGsltiwldeeaiaawkek...kkngkrgrpqvysdaaiqtcltvkvlfklplRqlqGfvqsllklaglellvpdystl 78 
                                    +RG  +++l+++++++w+e+    +++k+grp++y++++iq+c +++++++lp+Rql+Gf+q+l+ ++   ll++dystl
  gi|116753517|ref|YP_842635.1|  18 RRG--WFYLSTDFVNNWDEEllkMNKNKNGRPYRYPETFIQFCGLAYAFLHLPYRQLEGFIQALSGFVPG-LLAADYSTL 94 
                                    799..************9987745569******************************************9.99******* PP

                    DDE_Tnp_1_5  79 srraktlevkipvkrkskglhlvvdstGlkvlg 111
                                    ++r ++le++ip+ +++  l+++vdstG+kv++
  gi|116753517|ref|YP_842635.1|  95 WQRITNLELNIPIPDND--LVVAVDSTGMKVTN 125
                                    **************999..99**********97 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.016
                    DDE_Tnp_1_5  40 tcltvkvlfklplRql..qGfvqsllklag 67 
                                    ++  +k++f+ ++R++  +G+++ + ++ +
  gi|116753517|ref|YP_842635.1| 252 VFSAIKRIFGETVRATskEGMIREVRRMFT 281
                                    56789*********9855699999988876 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.7   0.1   1.8e-24   1.6e-20       5     200 ..     112     271 ..     108     285 .. 0.83

  Alignments for each domain:
  == domain 1  score: 73.7 bits;  conditional E-value: 1.8e-24
                      DDE_Tnp_1   5 evlivDattvrvpgtkedarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrprkgklvlaDa 84 
                                     v++vD+t ++v+  + ++r++++  + + ++k+hiavd +++ ++ ++it+  v d++ +k+ll+ +   k    l+D+
  gi|116753517|ref|YP_842635.1| 112 LVVAVDSTGMKVTNRGDWMRESHGVER-RGWIKVHIAVDVETRKPVTFEITDETVTDHEMVKPLLEDV---KLEDSLMDG 187
                                    699******************888666.79************************************99...89******* PP

                      DDE_Tnp_1  85 GYasaelldtleekgvd.yiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgdvyyvtntnsells 163
                                    +Y++++++d+++ekgvd + i+++kn+ ++        r +    +++  +  +++ +++                    
  gi|116753517|ref|YP_842635.1| 188 AYDKEGVFDFMKEKGVDmPGIKIRKNAIVKAG----SSRAEPVLEFMKYGYHSWKIVHGY-------------------- 243
                                    ****************9568899999988866....344445555555555555555555.................... PP

                      DDE_Tnp_1 164 aeevaelyrlRwqiErvFkwlkrkfgldrlryrglnr 200
                                             +Rw  E+vF+ +kr fg + +r+ ++++
  gi|116753517|ref|YP_842635.1| 244 --------GRRWAAESVFSAIKRIFG-ETVRATSKEG 271
                                    ........***************998.6666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2236.69
//
Query:       gi|116753518|ref|YP_842636.1|  [L=795]
Description: von Willebrand factor, type A [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      1e-26   94.2   0.0    3.7e-22   79.4   0.0    2.5  2  VWA        von Willebrand factor type A domain
    5.1e-22   78.5   0.1    1.5e-12   48.1   0.0    2.4  2  VWA_2      von Willebrand factor type A domain
    1.2e-06   28.5   0.0    8.1e-06   25.9   0.0    2.1  2  VWA_3      von Willebrand factor type A domain
    0.00053   19.4   0.6      0.073   12.4   0.2    2.3  2  VWA_CoxE   VWA domain containing CoxE-like protein
     0.0033   17.7   1.7       0.56   10.5   0.0    2.7  2  DUF11      Domain of unknown function DUF11
  ------ inclusion threshold ------
        0.1   12.6   0.0       0.29   11.2   0.0    1.8  1  PGF-CTERM  PGF-CTERM motif


Domain annotation for each model (and alignments):
>> VWA  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.4   0.0   1.3e-25   3.7e-22       1     174 [.      65     232 ..      65     233 .. 0.92
   2 !   12.2   0.0   5.2e-05      0.16       1      58 [.     400     485 ..     400     557 .. 0.60

  Alignments for each domain:
  == domain 1  score: 79.4 bits;  conditional E-value: 1.3e-25
                                    EEEEEEE-STTSCHHHHH.HHHHHHHHHHHHHTBTTTTEEEEEEEESSSEEEEEETTSHCHHHHHHHHHHTGSGGGGSSC CS
                            VWA   1 DivfvlDgSgsmgeenfe.kvkefikklveklevgpegtrvglvqfssevktefslndysskeellsalnnlkysgggtt 79 
                                    D+v+ +D+Sgsm+ ++    +k+++k++v  l+     +rvg+v+ +++  + ++l++ +  +++ sa+++ + ++g+t 
  gi|116753518|ref|YP_842636.1|  65 DVVLSIDSSGSMTTSDPGdLRKSAAKEFVTGLD--LSMDRVGVVSWNTS-AISWPLTNNT--KDIESAIDS-TGADGNTC 138
                                    9***********6666555**************..8889*******976.5899****55..9********.57777777 PP

                                    -HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CSS.......HTHHHHHHHHGCTEEEEEEEESSSHHHHHHHHHS CS
                            VWA  80 ntgkalkyaleklfkssagaRenakkviilltdGksndg.......dpkeaaneakeqgikvfavGvgnadekelLnkia 152
                                     ++++lk a++ l+++ +g     +kvi+lltdG s+dg        p  +++ea+++gi vf++G g + ++ +L++ia
  gi|116753518|ref|YP_842636.1| 139 -LDTGLKSAID-LLSECSG-----SKVIVLLTDGISTDGghytppgVPGSPVDEARSKGILVFTIGLGPDADARNLTEIA 211
                                    .**********.99999**.....**************66*****9999*********************99999***** PP

                                    SSSCHHCEEEESSHHHHHHHHH CS
                            VWA 153 sepgeghvftvtdfeeleelfe 174
                                     ++g g ++ ++d ++l  +++
  gi|116753518|ref|YP_842636.1| 212 HSTG-GEFYSAPDANALAGIYK 232
                                    ****.**********9998876 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 5.2e-05
                                    EEEEEEE-STTS......CHHHHHHHHHHHHHHHHHHTB..TTTTEEEEEEEES....................SSEEEE CS
                            VWA   1 DivfvlDgSgsm......geenfekvkefikklveklev..gpegtrvglvqfs....................sevkte 52 
                                    Di fv+D Sgsm      g +n e ++ ++ ++++  +     +++r+++v+                      ++++++
  gi|116753518|ref|YP_842636.1| 400 DILFVIDKSGSMrdldksGLKNYEIMQAALYEMLNMASNtpELRNARIAIVSWDdldgtdedrittldpqwlavGDPRIK 479
                                    9***********99977766677788888888888888545788899999987755555444443333333333333333 PP

                                    EETTSH CS
                            VWA  53 fslndy 58 
                                    + +++y
  gi|116753518|ref|YP_842636.1| 480 ATIQQY 485
                                    333333 PP

>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   0.0   5.1e-16   1.5e-12       1     106 [.      66     165 ..      66     166 .. 0.90
   2 !   28.2   0.0   7.8e-10   2.3e-06       1     104 [.     401     533 ..     401     536 .. 0.77

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 5.1e-16
                          VWA_2   1 lvfvlDtSgSmrngdygptrleaakdaveallkslpgdrvglvtfsdgpevlipltkdkakilnalrnleakgggtnlaa 80 
                                    +v+ +D+SgSm+++d g  r +aak++v+ l  s   drvg+v+ +++  +  plt + ++i++a++++ a+ g+t+l++
  gi|116753518|ref|YP_842636.1|  66 VVLSIDSSGSMTTSDPGDLRKSAAKEFVTGLDLS--MDRVGVVSWNTS-AISWPLTNNTKDIESAIDSTGAD-GNTCLDT 141
                                    6888***********8888888888888887555..79*******865.5899*****************96.******* PP

                          VWA_2  81 aLqlarkalkkrrkgekrvivlitDg 106
                                    +L+ a ++l++   + ++vivl+tDg
  gi|116753518|ref|YP_842636.1| 142 GLKSAIDLLSEC--SGSKVIVLLTDG 165
                                    **********66..6**********9 PP

  == domain 2  score: 28.2 bits;  conditional E-value: 7.8e-10
                          VWA_2   1 lvfvlDtSgSmrngdy.gptrleaakdaveallk......slpgdrvglvtfsd..gp..evliplt.....kdkakiln 64 
                                    ++fv+D SgSmr+ d  g +++e++++a+ ++l+      +l++ r+++v+ +d  g    ++++l+      +  +i++
  gi|116753518|ref|YP_842636.1| 401 ILFVIDKSGSMRDLDKsGLKNYEIMQAALYEMLNmasntpELRNARIAIVSWDDldGTdeDRITTLDpqwlaVGDPRIKA 480
                                    68**********99874699**************87544444999*********86333355555544355555677777 PP

                          VWA_2  65 alrnleak....gggtnlaaaLqlarkalkkrr.........kgekrvivlit 104
                                     +++ +++    ++ t ++++Lq+a++++++r            ++r i++it
  gi|116753518|ref|YP_842636.1| 481 TIQQYNEEtckeTDLTFYETGLQKAMQIMHSRIlsqandplsCDTRRFIIFIT 533
                                    777777777777999*************9877666666777767777777777 PP

>> VWA_3  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   2.7e-09   8.1e-06       2     152 ..      65     217 ..      64     220 .. 0.85
   2 ?   -0.2   0.0      0.27   8.2e+02       2      16 ..     400     414 ..     399     456 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 2.7e-09
                          VWA_3   2 evvivvDvsssmsaen..klvkdaLsvalrqLptnd.kiavllfgtkprplfpgsravsaaelqealqkikelelslgas 78 
                                    +vv+ +D+s sm  +   +l k+a + ++ +L  +  ++ v+++ t++   +p   + +     +++ +i+   + +g++
  gi|116753518|ref|YP_842636.1|  65 DVVLSIDSSGSMTTSDpgDLRKSAAKEFVTGLDLSMdRVGVVSWNTSAI-SWPLTNNTK-----DIESAIDSTGA-DGNT 137
                                    79*********9888889*************875544**********66.778877777.....78888888777.**** PP

                          VWA_3  79 nlegaLkealrqpakpgevrsvilltDgssaqgeervsdlisrar.....ek.irfhalglgsslsaamlqaLAeasgGt 152
                                     l   Lk a++  +     + ++lltDg s+ g +++   +  ++     +k i ++++glg++++a++l ++A  +gG 
  gi|116753518|ref|YP_842636.1| 138 CLDTGLKSAIDLLSECSGSKVIVLLTDGISTDGGHYTPPGVPGSPvdearSKgILVFTIGLGPDADARNLTEIAHSTGGE 217
                                    ***********99999999***********99888887665544444332447*************************96 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.27
                          VWA_3   2 evvivvDvsssmsae 16 
                                    ++ +v+D s sm++ 
  gi|116753518|ref|YP_842636.1| 400 DILFVIDKSGSMRDL 414
                                    899*********985 PP

>> VWA_CoxE  VWA domain containing CoxE-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.2   2.4e-05     0.073      56     164 ..      62     169 ..      58     174 .. 0.82
   2 !    5.0   0.0    0.0048        14      46      72 ..     387     413 ..     357     432 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.4e-05
                       VWA_CoxE  56 kprelvllvDvSgSmaays.......aiflallhAllqqlprtevfaFdtrlvd..lTralrerDpaeaLarvsaavedl 126
                                    +p ++vl +D SgSm + s            ++ +l  +++r+ v+  +t+ ++  lT++ +  D ++a++++       
  gi|116753518|ref|YP_842636.1|  62 SPVDVVLSIDSSGSMTT-SdpgdlrkSAAKEFVTGLDLSMDRVGVVSWNTSAISwpLTNNTK--DIESAIDSTG-----A 133
                                    57799**********98.52222222467789999999999**********99844566666..********98.....9 PP

                       VWA_CoxE 127 gGgTrigaalaeflelvtrpaLsrravvvlvsDglerg 164
                                    +G T + ++l+++++l +  +     v+vl++Dg  ++
  gi|116753518|ref|YP_842636.1| 134 DGNTCLDTGLKSAIDLLSECS--GSKVIVLLTDGISTD 169
                                    ******************766..6779999***98877 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0048
                       VWA_CoxE  46 elvrrkprerkprelvllvDvSgSmaa 72 
                                    ++ +  p ++ ++++++++D SgSm +
  gi|116753518|ref|YP_842636.1| 387 KITLDAPEKSCSADILFVIDKSGSMRD 413
                                    5666777788889************87 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.4   0.4    0.0078        23      30      78 ..     243     302 ..     239     307 .. 0.70
   2 !   10.5   0.0   0.00019      0.56      36      78 ..     643     681 ..     622     685 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0078
                          DUF11  30 angvvvtDtlPaglayvsvsas..........qgtas.altsvgsLeagesatlsftvrv 78 
                                    a++v+vt +lP++++   +  s          +g  +  ++++g+++a +s+ lsf v+ 
  gi|116753518|ref|YP_842636.1| 243 AKDVTVTYVLPSSMNVNLSPYSgsqpvatvrnEGDSTvLTWRMGTIQANQSRMLSFDVSS 302
                                    789********9888666655566777777653332203444499999999999998875 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00019
                          DUF11  36 tDtlPaglayvsvsasqgtasaltsvgsLeagesatlsftvrv 78 
                                     D+lP++++y +  ++    + ++++g+L+ ge++  ++  +v
  gi|116753518|ref|YP_842636.1| 643 ADPLPSAVTYNRDGST----TLRWNIGTLNSGERWSATIDTSV 681
                                    6888********9999....799999********999987665 PP

>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   9.7e-05      0.29       1      22 [.     773     793 ..     773     794 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 9.7e-05
                      PGF-CTERM   1 tPGFGavlAlaGLLaaalLaRR 22 
                                    +PGF+ vl++  L+  ++L  R
  gi|116753518|ref|YP_842636.1| 773 QPGFEGVLGVLSLIT-GYLCIR 793
                                    7************99.865444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (795 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); 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: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.42
# Mc/sec: 5706.82
//
Query:       gi|116753519|ref|YP_842637.1|  [L=862]
Description: pentapeptide repeat-containing protein [Methanosaeta thermophila PT]
Scores for complete 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-106  347.2  70.8    4.4e-11   42.2   0.7   14.8 18  Pentapeptide    Pentapeptide repeats (8 copies)
    5.4e-58  193.1   0.0    5.1e-08   33.0   0.0    8.1 11  Pentapeptide_4  Pentapeptide repeats (9 copies)
    5.5e-44  148.1   0.0    5.9e-06   26.3   0.4   12.3 11  Pentapeptide_3  Pentapeptide repeats (9 copies)
    8.9e-08   31.7   0.0    1.8e-07   30.7   0.0    1.4  1  ABC_sub_bind    ABC transporter substrate binding protein
    0.00016   21.7   0.2        2.1    8.3   0.0    4.2  6  CfAFP           Choristoneura fumiferana antifreeze protein (
  ------ inclusion threshold ------
       0.01   15.7   0.1         61    3.6   0.0    5.9  7  DNA_ligase_OB   NAD-dependent DNA ligase OB-fold domain


Domain annotation for each model (and alignments):
>> Pentapeptide  Pentapeptide repeats (8 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.1   3.4e-05       0.1      20      40 .]     330     350 ..     329     350 .. 0.94
   2 !   33.9   1.5   5.7e-12   1.7e-08       1      40 []     346     385 ..     346     385 .. 0.98
   3 !   37.9   0.0   3.3e-13   9.8e-10       1      40 []     386     425 ..     386     425 .. 0.97
   4 !   31.7   0.2   2.8e-11   8.3e-08       1      40 []     416     455 ..     416     455 .. 0.96
   5 !   27.4   0.3   6.3e-10   1.9e-06       1      32 [.     431     462 ..     431     467 .. 0.76
   6 !   37.0   1.1   6.1e-13   1.8e-09       3      40 .]     453     490 ..     452     490 .. 0.96
   7 !   41.9   1.7   1.9e-14   5.6e-11       1      40 []     471     510 ..     471     510 .. 0.97
   8 !   26.7   0.1     1e-09     3e-06       2      38 ..     492     528 ..     492     530 .. 0.97
   9 !   33.8   0.5   6.5e-12   1.9e-08       4      39 ..     514     549 ..     511     550 .. 0.96
  10 !   26.5   4.0   1.2e-09   3.7e-06       1      38 [.     531     568 ..     531     569 .. 0.95
  11 !   42.2   0.7   1.5e-14   4.4e-11       1      39 [.     576     614 ..     576     614 .. 0.98
  12 !   30.8   0.1   5.4e-11   1.6e-07       1      38 [.     611     648 ..     611     650 .. 0.96
  13 !   34.7   0.6   3.3e-12   9.7e-09       5      38 ..     655     688 ..     654     688 .. 0.93
  14 !   32.3   0.9   1.9e-11   5.6e-08      11      36 ..     696     721 ..     686     723 .. 0.46
  15 !   18.4   0.8     4e-07    0.0012       6      40 .]     731     765 ..     728     765 .. 0.90
  16 !   21.6   0.2     4e-08   0.00012       4      35 ..     754     785 ..     754     787 .. 0.79
  17 !   28.7   0.1   2.5e-10   7.4e-07       4      40 .]     789     825 ..     789     825 .. 0.96
  18 ?   -3.5   0.0         3   8.9e+03      10      19 ..     838     847 ..     836     848 .. 0.50

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.4e-05
                                    SEEECT-B-TT-EECCEEECT CS
                   Pentapeptide  20 gAnLtgAnlsgAdLsganLsg 40 
                                    +A+L++ nls+ dLsga L++
  gi|116753519|ref|YP_842637.1| 330 RADLSHMNLSWHDLSGASLNQ 350
                                    8*****************997 PP

  == domain 2  score: 33.9 bits;  conditional E-value: 5.7e-12
                                    -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
                   Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                                    A+L++++L g++Ls+anl+gA L+++ +++A+Ls a+Lsg
  gi|116753519|ref|YP_842637.1| 346 ASLNQTYLNGSDLSNANLTGAYLRYSMIYDANLSLADLSG 385
                                    89*************************************8 PP

  == domain 3  score: 37.9 bits;  conditional E-value: 3.3e-13
                                    -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
                   Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                                    A+ +gA+ ++++L++a l+gA+L+g++l+++dLs+a+L+g
  gi|116753519|ref|YP_842637.1| 386 ADIEGADIHNTDLREARLRGAKLIGVDLTRSDLSRADLTG 425
                                    6789***********************************8 PP

  == domain 4  score: 31.7 bits;  conditional E-value: 2.8e-11
                                    -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
                   Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                                    ++Ls+A+L+ga+++ a lsgA Ltg+ + gAdL+g+++ g
  gi|116753519|ref|YP_842637.1| 416 SDLSRADLTGAHMEIARLSGALLTGTMMDGADLNGTKMDG 455
                                    69**********************************9876 PP

  == domain 5  score: 27.4 bits;  conditional E-value: 6.3e-10
                                    -B-TT-B-CCSCCEECCCESEEECT-B-TT-E CS
                   Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAd 32 
                                    A+LsgA L+g+ ++ga+l+g++++g+nlsgA 
  gi|116753519|ref|YP_842637.1| 431 ARLSGALLTGTMMDGADLNGTKMDGCNLSGAY 462
                                    67888888888888888888888888888875 PP

  == domain 6  score: 37.0 bits;  conditional E-value: 6.1e-13
                                    -TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
                   Pentapeptide   3 LsgAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                                    + g+nLsga+ + a+ ++AnL++AnlsgA++sg++Lsg
  gi|116753519|ref|YP_842637.1| 453 MDGCNLSGAYVRSAFVYRANLRDANLSGANMSGSDLSG 490
                                    679*********************************98 PP

  == domain 7  score: 41.9 bits;  conditional E-value: 1.9e-14
                                    -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
                   Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                                    AnL++AnLsgan+sg++lsg +Lt+A l+ +dL++a +++
  gi|116753519|ref|YP_842637.1| 471 ANLRDANLSGANMSGSDLSGVDLTRAALIYSDLRNASMQD 510
                                    9***********************************9975 PP

  == domain 8  score: 26.7 bits;  conditional E-value: 1e-09
                                    B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEE CS
                   Pentapeptide   2 nLsgAnLsganLsganlsgAnLtgAnlsgAdLsganL 38 
                                    +L++A L  ++L++a++ +++ ++Anl+g++L+ga++
  gi|116753519|ref|YP_842637.1| 492 DLTRAALIYSDLRNASMQDSVIRDANLTGSQLTGAIM 528
                                    79*********************************97 PP

  == domain 9  score: 33.8 bits;  conditional E-value: 6.5e-12
                                    TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEEC CS
                   Pentapeptide   4 sgAnLsganLsganlsgAnLtgAnlsgAdLsganLs 39 
                                    ++AnL+g+ L+ga + ++n +gAnls++dLs+++++
  gi|116753519|ref|YP_842637.1| 514 RDANLTGSQLTGAIMMQSNISGANLSFTDLSNTDMR 549
                                    79********************************98 PP

  == domain 10  score: 26.5 bits;  conditional E-value: 1.2e-09
                                    -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEE CS
                   Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganL 38 
                                    +n sgAnLs ++Ls+++++++ +  ++l gA+L++a+L
  gi|116753519|ref|YP_842637.1| 531 SNISGANLSFTDLSNTDMRRCCMLFTDLVGARLNNARL 568
                                    6889********************************98 PP

  == domain 11  score: 42.2 bits;  conditional E-value: 1.5e-14
                                    -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEEC CS
                   Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLs 39 
                                    AnLs+A L  a+L+g++lsg++L++A+l+gAd+++a+L+
  gi|116753519|ref|YP_842637.1| 576 ANLSRASLVSASLQGVDLSGSDLSEADLRGADMTNAKLT 614
                                    9************************************97 PP

  == domain 12  score: 30.8 bits;  conditional E-value: 5.4e-11
                                    -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEE CS
                   Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganL 38 
                                    A L+++ L+ga++sga l gA+Lt A +++  L++an+
  gi|116753519|ref|YP_842637.1| 611 AKLTETVLEGADMSGARLLGADLTQARMHDLILTRANM 648
                                    789*********************************97 PP

  == domain 13  score: 34.7 bits;  conditional E-value: 3.3e-12
                                    T-B-CCSCCEECCCESEEECT-B-TT-EECCEEE CS
                   Pentapeptide   5 gAnLsganLsganlsgAnLtgAnlsgAdLsganL 38 
                                    +++Lsga Ls+a l++A L gA+lsg+dLsga+L
  gi|116753519|ref|YP_842637.1| 655 WVDLSGARLSRALLTRAELFGADLSGTDLSGADL 688
                                    689*****************************98 PP

  == domain 14  score: 32.3 bits;  conditional E-value: 1.9e-11
                                    SCCEECCCESEEECT-B-TT-EECCE CS
                   Pentapeptide  11 anLsganlsgAnLtgAnlsgAdLsga 36 
                                    anLsga+l++A+L++A++sgA L+ga
  gi|116753519|ref|YP_842637.1| 696 ANLSGADLTDAKLDDADFSGAILRGA 721
                                    44444444444444444444444444 PP

  == domain 15  score: 18.4 bits;  conditional E-value: 4e-07
                                    -B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
                   Pentapeptide   6 AnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                                    +n+ +a+Ls+a++sg+ +     s+A ++ an+++
  gi|116753519|ref|YP_842637.1| 731 VNFGQADLSDADMSGCRFEALYVSNAVMRSANMRN 765
                                    89999999999999999999999999999999986 PP

  == domain 16  score: 21.6 bits;  conditional E-value: 4e-08
                                    TT-B-CCSCCEECCCESEEECT-B-TT-EECC CS
                   Pentapeptide   4 sgAnLsganLsganlsgAnLtgAnlsgAdLsg 35 
                                    s+A  + an+++a ++g  + +++ls AdL++
  gi|116753519|ref|YP_842637.1| 754 SNAVMRSANMRNAIFRGVMFENCDLSMADLKR 785
                                    57888888888888888888888888888875 PP

  == domain 17  score: 28.7 bits;  conditional E-value: 2.5e-10
                                    TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
                   Pentapeptide   4 sgAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                                    +g++L++++Lsga+l+++ L+++ +++ dL+ga+L g
  gi|116753519|ref|YP_842637.1| 789 TGVYLTNTSLSGADLRDSELYSVGFTNVDLRGARLDG 825
                                    699*******************************976 PP

  == domain 18  score: -3.5 bits;  conditional E-value: 3
                                    CSCCEECCCE CS
                   Pentapeptide  10 ganLsganls 19 
                                    + nL+g+++s
  gi|116753519|ref|YP_842637.1| 838 QQNLDGVSMS 847
                                    4555555554 PP

>> Pentapeptide_4  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   3.7e-10   1.1e-06       4      75 ..     349     426 ..     329     428 .. 0.90
   2 !   19.4   0.0   2.9e-07   0.00087       1      73 [.     421     494 ..     406     498 .. 0.55
   3 !   23.8   0.0   1.2e-08   3.7e-05       4      70 ..     479     545 ..     442     551 .. 0.62
   4 !   20.4   0.4   1.4e-07   0.00043       4      76 ..     514     587 ..     501     588 .. 0.70
   5 !   20.0   0.1   1.8e-07   0.00055       9      75 ..     539     606 ..     530     607 .. 0.78
   6 !   22.2   0.0   3.9e-08   0.00012       5      66 ..     585     646 ..     581     651 .. 0.89
   7 !   20.9   0.0     1e-07    0.0003       1      76 [.     606     687 ..     606     695 .. 0.87
   8 !   25.0   0.0   5.2e-09   1.5e-05       3      76 ..     668     742 ..     666     743 .. 0.93
   9 !   22.8   0.0   2.6e-08   7.7e-05      10      68 ..     695     753 ..     690     762 .. 0.74
  10 !   25.1   0.1     5e-09   1.5e-05      16      69 ..     731     784 ..     728     788 .. 0.53
  11 !   33.0   0.0   1.7e-11   5.1e-08       2      74 ..     762     835 ..     761     837 .. 0.93

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 3.7e-10
                 Pentapeptide_4   4 trcsfnncklsnvnFsearlrdcnFtecrl.....snvnFdecnlsdvdfaevdlkrasFsgcnlknvnfsd.klkdi 75 
                                     +  +n+++lsn+n++ a+lr + + +++l     s +  + ++++++d++e++l+ a + g++l+ + +s+  l+++
  gi|116753519|ref|YP_842637.1| 349 NQTYLNGSDLSNANLTGAYLRYSMIYDANLsladlSGADIEGADIHNTDLREARLRGAKLIGVDLTRSDLSRaDLTGA 426
                                    5666899***********999999999999999999999*******************************76588875 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 2.9e-07
                 Pentapeptide_4   1 aeftrcsfnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnfsd.klk 73 
                                    a++t ++++ + ls++ ++ + + ++++++++++ +n++ + ++++ ++ ++l++a++sg n +++ +s+  l+
  gi|116753519|ref|YP_842637.1| 421 ADLTGAHMEIARLSGALLTGTMMDGADLNGTKMDGCNLSGAYVRSAFVYRANLRDANLSGANMSGSDLSGvDLT 494
                                    23444444444444444444445555555555566666666666666666666666777777666666665665 PP

  == domain 3  score: 23.8 bits;  conditional E-value: 1.2e-08
                 Pentapeptide_4   4 trcsfnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnfsd 70 
                                    + + + +++ls+v+++ a l+ ++++++ +++ + +++nl  ++++++ +  +++sg nl+ + +s+
  gi|116753519|ref|YP_842637.1| 479 SGANMSGSDLSGVDLTRAALIYSDLRNASMQDSVIRDANLTGSQLTGAIMMQSNISGANLSFTDLSN 545
                                    3344555666666666666666666666666666666666666666666666666666666666644 PP

  == domain 4  score: 20.4 bits;  conditional E-value: 1.4e-07
                 Pentapeptide_4   4 trcsfnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnfsd.klkdid 76 
                                    +++ + +++l+++ + ++++ ++n++ ++lsn+ +++c    +d+ +++l++a++  ++l  +n+s+ +l++++
  gi|116753519|ref|YP_842637.1| 514 RDANLTGSQLTGAIMMQSNISGANLSFTDLSNTDMRRCCMLFTDLVGARLNNARLDSSMLFRANLSRaSLVSAS 587
                                    44555566666666666666666666666688888888888888888888888888888888888655787765 PP

  == domain 5  score: 20.0 bits;  conditional E-value: 1.8e-07
                 Pentapeptide_4   9 nncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnfsd.klkdi 75 
                                      ++lsn++++ + +  ++++++rl+n+++d++ l  ++++ ++l +as++g++l+++ +s+  l+++
  gi|116753519|ref|YP_842637.1| 539 SFTDLSNTDMRRCCMLFTDLVGARLNNARLDSSMLFRANLSRASLVSASLQGVDLSGSDLSEaDLRGA 606
                                    45788888888888888888888889999999999999999999999999999999999965477766 PP

  == domain 6  score: 22.2 bits;  conditional E-value: 3.9e-08
                 Pentapeptide_4   5 rcsfnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknv 66 
                                    ++s+ +++ls+ ++sea+lr++++t+++l++++++ ++ s +++ ++dl+ a+ +   l+ +
  gi|116753519|ref|YP_842637.1| 585 SASLQGVDLSGSDLSEADLRGADMTNAKLTETVLEGADMSGARLLGADLTQARMHDLILTRA 646
                                    678999********************************************999887777665 PP

  == domain 7  score: 20.9 bits;  conditional E-value: 1e-07
                 Pentapeptide_4   1 aeftrcsfnncklsnvnFsearlrdcnFtecrl.....snvnFdecnlsdvdfaevdlkrasFsgcnlknvnfsd.klkd 74 
                                    a++t++++ ++ l+++++s arl ++++t++r+     + +n+  +  ++vd+++++l ra +++ +l ++ +s+  l +
  gi|116753519|ref|YP_842637.1| 606 ADMTNAKLTETVLEGADMSGARLLGADLTQARMhdlilTRANMLGARANWVDLSGARLSRALLTRAELFGADLSGtDLSG 685
                                    689******************************99999999999999999999999999998888888888887645766 PP

                 Pentapeptide_4  75 id 76 
                                    +d
  gi|116753519|ref|YP_842637.1| 686 AD 687
                                    55 PP

  == domain 8  score: 25.0 bits;  conditional E-value: 5.2e-09
                 Pentapeptide_4   3 ftrcsfnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnf.sdklkdid 76 
                                    +tr+ + +++ls++++s a+l  +    ++ls + +++++l+d+df+++ l+ a   +  +++vnf  + l d+d
  gi|116753519|ref|YP_842637.1| 668 LTRAELFGADLSGTDLSGADLVKAYALRANLSGADLTDAKLDDADFSGAILRGAKMPELVIRSVNFgQADLSDAD 742
                                    78888999**********************************************************667898876 PP

  == domain 9  score: 22.8 bits;  conditional E-value: 2.6e-08
                 Pentapeptide_4  10 ncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnf 68 
                                    +++ls+++++ a+l d++F+++ l  +++ e ++++v+f ++dl +a  sgc+++    
  gi|116753519|ref|YP_842637.1| 695 RANLSGADLTDAKLDDADFSGAILRGAKMPELVIRSVNFGQADLSDADMSGCRFEALYV 753
                                    57788888888888888888888888888888888888888888888888887776554 PP

  == domain 10  score: 25.1 bits;  conditional E-value: 5e-09
                 Pentapeptide_4  16 vnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnfs 69 
                                    vnF +a+l d+++++cr+ +   ++++ ++++ +++ ++ + F++c+l+ + ++
  gi|116753519|ref|YP_842637.1| 731 VNFGQADLSDADMSGCRFEALYVSNAVMRSANMRNAIFRGVMFENCDLSMADLK 784
                                    566666666666666666555555555555555555555555555555544443 PP

  == domain 11  score: 33.0 bits;  conditional E-value: 1.7e-11
                 Pentapeptide_4   2 eftrcsfnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnfsd.klkd 74 
                                     ++++ f+++ ++n+++s a+l++   t++ l+n++++ ++l+d++++ v ++++ + g +l +++ ++ +l++
  gi|116753519|ref|YP_842637.1| 762 NMRNAIFRGVMFENCDLSMADLKRIKATGVYLTNTSLSGADLRDSELYSVGFTNVDLRGARLDGIRYDRpTLES 835
                                    6899***********************************************************99998767775 PP

>> Pentapeptide_3  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.0    0.0034        10       9      39 ..     346     374 ..     334     379 .. 0.52
   2 !   14.5   0.0   9.5e-06     0.029       3      47 ..     375     416 ..     373     417 .. 0.93
   3 !   10.9   0.0   0.00013       0.4       2      45 ..     404     444 ..     403     447 .. 0.75
   4 !   17.5   0.0   1.1e-06    0.0034       2      47 ..     449     491 ..     443     507 .. 0.74
   5 !   15.2   0.4   5.8e-06     0.017       1      44 [.     478     523 ..     478     582 .. 0.86
   6 !   14.6   0.0   8.9e-06     0.027       2      47 ..     574     616 ..     573     617 .. 0.94
   7 !   12.3   0.0   4.9e-05      0.15       2      47 ..     614     661 ..     613     662 .. 0.88
   8 !    7.1   0.0    0.0021       6.2       1      36 [.     658     691 ..     658     700 .. 0.87
   9 !   15.3   0.0   5.7e-06     0.017       2      48 .]     674     717 ..     673     723 .. 0.86
  10 !   26.3   0.4     2e-09   5.9e-06       1      47 [.     733     776 ..     733     785 .. 0.95
  11 !   11.2   0.0   0.00011      0.32       2      39 ..     794     829 ..     793     833 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0034
                 Pentapeptide_3   9 aadFrgatFsgaasFsnadFgsadFsgarFt 39 
                                    a ++  +  +g+ + sna++++a ++ + ++
  gi|116753519|ref|YP_842637.1| 346 A-SLNQTYLNGS-DLSNANLTGAYLRYSMIY 374
                                    2.3333333333.555555555555555555 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 9.5e-06
                 Pentapeptide_3   3 ganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFsga 47 
                                    +an+s a d++ga  +ga +  n+d+++a+++ga    +vd++++
  gi|116753519|ref|YP_842637.1| 375 DANLSLA-DLSGADIEGA-DIHNTDLREARLRGAKLI-GVDLTRS 416
                                    6888889.**********.******************.***9987 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00013
                 Pentapeptide_3   2 sganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFs 45 
                                    +ga + g  d++++  s+a + ++a+++ a++sga  t ++ ++
  gi|116753519|ref|YP_842637.1| 404 RGAKLIGV-DLTRSDLSRA-DLTGAHMEIARLSGALLT-GTMMD 444
                                    56677777.8888888888.888888888888888888.66555 PP

  == domain 4  score: 17.5 bits;  conditional E-value: 1.1e-06
                 Pentapeptide_3   2 sganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFsga 47 
                                    +g+ ++g+ +++ga  ++a ++ +a++++a++sga+++ ++d+sg+
  gi|116753519|ref|YP_842637.1| 449 NGTKMDGC-NLSGAYVRSA-FVYRANLRDANLSGANMS-GSDLSGV 491
                                    45555555.5555555555.788888899999999988.8888875 PP

  == domain 5  score: 15.2 bits;  conditional E-value: 5.8e-06
                 Pentapeptide_3   1 FsganFsgaadFrgatFsgaa....sFsnadFgsadFsgarFtgdvdF 44 
                                    +sgan+sg+ d++g+  ++aa    + +na ++++  ++a+ t ++++
  gi|116753519|ref|YP_842637.1| 478 LSGANMSGS-DLSGVDLTRAAliysDLRNASMQDSVIRDANLT-GSQL 523
                                    589******.**********95555566666666666666665.5555 PP

  == domain 6  score: 14.6 bits;  conditional E-value: 8.9e-06
                 Pentapeptide_3   2 sganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFsga 47 
                                    ++an+s+a ++  a  +g  + s++d+++ad++ga +t ++ ++++
  gi|116753519|ref|YP_842637.1| 574 FRANLSRA-SLVSASLQGV-DLSGSDLSEADLRGADMT-NAKLTET 616
                                    689*****.**********.******************.9999887 PP

  == domain 7  score: 12.3 bits;  conditional E-value: 4.9e-05
                 Pentapeptide_3   2 sganFsgaadFrgatFsgaasFsnadF.....gsadFsgarFtgdvdFsga 47 
                                    ++++++ga d++ga+  ga + ++a++     ++a+  gar + +vd+sga
  gi|116753519|ref|YP_842637.1| 614 TETVLEGA-DMSGARLLGA-DLTQARMhdlilTRANMLGARAN-WVDLSGA 661
                                    6899999*.**********.*******8888888888888888.8888887 PP

  == domain 8  score: 7.1 bits;  conditional E-value: 0.0021
                 Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadFgsadFsga 36 
                                    +sga++s+a  +++a   ga + s++d+++ad+ +a
  gi|116753519|ref|YP_842637.1| 658 LSGARLSRA-LLTRAELFGA-DLSGTDLSGADLVKA 691
                                    589******.**********.***********9887 PP

  == domain 9  score: 15.3 bits;  conditional E-value: 5.7e-06
                 Pentapeptide_3   2 sganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFsgat 48 
                                    +ga +sg+ d++ga   +a +  +a++++ad+ +a  + d+dFsga+
  gi|116753519|ref|YP_842637.1| 674 FGADLSGT-DLSGADLVKA-YALRANLSGADLTDAKLD-DADFSGAI 717
                                    68899999.9999999999.899999999999999998.99998875 PP

  == domain 10  score: 26.3 bits;  conditional E-value: 2e-09
                 Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFsga 47 
                                    F +a +s+a d++g++F+   ++sna+++sa+ ++a+F  +v F+++
  gi|116753519|ref|YP_842637.1| 733 FGQADLSDA-DMSGCRFEAL-YVSNAVMRSANMRNAIFR-GVMFENC 776
                                    778899999.**********.9****************8.*****99 PP

  == domain 11  score: 11.2 bits;  conditional E-value: 0.00011
                 Pentapeptide_3   2 sganFsgaadFrgatFsgaasFsnadFgsadFsgarFt 39 
                                    +++++sga d+r++  ++   F+n d+++a+++g r +
  gi|116753519|ref|YP_842637.1| 794 TNTSLSGA-DLRDSELYSV-GFTNVDLRGARLDGIRYD 829
                                    799*****.**********.9************98865 PP

>> ABC_sub_bind  ABC transporter substrate binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.0   6.1e-11   1.8e-07      82     262 ..     116     294 ..     108     311 .. 0.84

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 6.1e-11
                                    S-EEEEEES-TTTTTS-S-SSS--SSEEEEE----HHHHHHHHHHHSTT--EEEEEE-TT-HHHHHHHHHHHHHHHHTT- CS
                   ABC_sub_bind  82 iPiVfaavtdpvgakLvksleapgenvTGvsdaekvektieLikkllPnvkkigilyspgeansvslveelkklakkagl 161
                                    +P+Vf +v d       +++     + TGv  ++ +e+ti+L+ +l P+  ki ++ + +    +++ ++l  + +k+++
  gi|116753519|ref|YP_842637.1| 116 VPVVFCGVKDF-----RPEMLSNVSGFTGVLLNVSIEDTIDLMLRLHPDTNKIVVV-NDNTTTGMANRRILEGVIPKFNI 189
                                    57777777443.....33333444578****9********************9776.66777799*************** PP

                                    EEEEEE-SSGGGHHHHHHHHHTT-SEEEE-S-HHHHHTHHHHHHHH....HHTT--EEESSHHHHHTT-SEEEE--HHHH CS
                   ABC_sub_bind 162 kvveaavknvndvesavsslaekvdaiyiltdnliasafeavvkaa....nqakiPviasddesvkegalaalgvnekel 237
                                    +   +    v ++   vs l   v ++    +   a    +  ++a    +++++Pv+   +    +g +  +      +
  gi|116753519|ref|YP_842637.1| 190 TFDVLDNVTVDELRENVSRLGPGVLVLLLTFNRDRAGEVFTYEESAeilrQVSRVPVYGVWEMCLGHGIVGGYLSSGDAQ 269
                                    ***99999**************99999888777666655554444422227899************************** PP

                                    HHHHHHHHHHHHTT--GGGS--EE- CS
                   ABC_sub_bind 238 GvqagkvvvkiLkGkkpkdipvsra 262
                                    G++a++++++iL G++p++ip++  
  gi|116753519|ref|YP_842637.1| 270 GMKAAEIAARILHGADPESIPIVSH 294
                                    *********************8765 PP

>> CfAFP  Choristoneura fumiferana antifreeze protein (CfAFP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.45   1.3e+03      55      91 ..     369     405 ..     342     436 .. 0.45
   2 !    8.3   0.0   0.00071       2.1      38      96 ..     437     495 ..     416     502 .. 0.91
   3 !    6.5   0.1    0.0026       7.7      31      98 ..     505     572 ..     499     588 .. 0.87
   4 ?    0.1   0.0      0.24   7.3e+02      44      98 ..     563     617 ..     551     639 .. 0.62
   5 ?   -1.6   0.0      0.79   2.4e+03      47      79 ..     739     768 ..     716     805 .. 0.48
   6 ?   -0.3   0.0      0.33     1e+03      44      91 ..     773     820 ..     753     829 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.45
                          CfAFP  55 trsqysdayvkksvttdcnidksqlygttctgsrydG 91 
                                      s   da++  +  + ++i+ ++++ t   ++r  G
  gi|116753519|ref|YP_842637.1| 369 RYSMIYDANLSLADLSGADIEGADIHNTDLREARLRG 405
                                    2233333444444444444444444444333333333 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00071
                          CfAFP  38 tltncyidnselessictrsqysdayvkksvttdcnidksqlygttctgsrydGvyits 96 
                                     lt   +d ++l+ +    ++ s+ayv+++ +  +n+++++l g+  +gs   Gv +t 
  gi|116753519|ref|YP_842637.1| 437 LLTGTMMDGADLNGTKMDGCNLSGAYVRSAFVYRANLRDANLSGANMSGSDLSGVDLTR 495
                                    578889999**********************************************9986 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0026
                          CfAFP  31 nskcvkstltncyidnselessictrsqysdayvkksvttdcnidksqlygttctgsrydGvyitsst 98 
                                    n+    s++   ++  s+l  +i  +s+ s+a++  +  ++++++++ +  t   g+r +   + ss 
  gi|116753519|ref|YP_842637.1| 505 NASMQDSVIRDANLTGSQLTGAIMMQSNISGANLSFTDLSNTDMRRCCMLFTDLVGARLNNARLDSSM 572
                                    6777889999999999***999*************9999*******9999999999999999999886 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.24
                          CfAFP  44 idnselessictrsqysdayvkksvttdcnidksqlygttctgsrydGvyitsst 98 
                                    ++n++l+ss+  r++ s a ++++    ++++ s+l  +   g+     ++t + 
  gi|116753519|ref|YP_842637.1| 563 LNNARLDSSMLFRANLSRASLVSASLQGVDLSGSDLSEADLRGADMTNAKLTETV 617
                                    6788888888888888888888777766666655555444444443333333333 PP

  == domain 5  score: -1.6 bits;  conditional E-value: 0.79
                          CfAFP  47 selessictrsqysdayvkksvttdcnidksql 79 
                                    s+ + s c   +++  yv ++v  ++n++++ +
  gi|116753519|ref|YP_842637.1| 739 SDADMSGC---RFEALYVSNAVMRSANMRNAIF 768
                                    33333333...3444444444444444444432 PP

  == domain 6  score: -0.3 bits;  conditional E-value: 0.33
                          CfAFP  44 idnselessictrsqysdayvkksvttdcnidksqlygttctgsrydG 91 
                                     +n +l  +   r + ++ y++++  + +++++s+ly+   t+    G
  gi|116753519|ref|YP_842637.1| 773 FENCDLSMADLKRIKATGVYLTNTSLSGADLRDSELYSVGFTNVDLRG 820
                                    456666666678888889999999999999999999998888765555 PP

>> DNA_ligase_OB  NAD-dependent DNA ligase OB-fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.6   4.8e+03      21      39 ..     346     364 ..     345     367 .. 0.87
   2 ?    1.8   0.0     0.073   2.2e+02      21      43 ..     376     398 ..     371     404 .. 0.87
   3 ?    0.3   0.0      0.22   6.6e+02      14      40 ..     424     450 ..     409     472 .. 0.81
   4 ?   -1.8   0.0      0.98   2.9e+03      21      38 ..     481     498 ..     464     516 .. 0.71
   5 ?    3.6   0.0      0.02        61      20      45 ..     585     610 ..     580     616 .. 0.88
   6 ?   -1.9   0.0       1.1   3.3e+03      25      41 ..     655     671 ..     646     691 .. 0.71
   7 ?   -1.9   0.0       1.1   3.1e+03      20      42 ..     780     802 ..     779     807 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.6
                                    XXXXXXXXXXXXXXXXXXX CS
                  DNA_ligase_OB  21 AeLepvelaGttVsratLh 39 
                                    A L+   l+G+  s+a+L 
  gi|116753519|ref|YP_842637.1| 346 ASLNQTYLNGSDLSNANLT 364
                                    7899999*********996 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.073
                                    XXXXXXXXXXXXXXXXXXXXXXX CS
                  DNA_ligase_OB  21 AeLepvelaGttVsratLhnede 43 
                                    A+L+  +l+G  ++ a +hn d 
  gi|116753519|ref|YP_842637.1| 376 ANLSLADLSGADIEGADIHNTDL 398
                                    8999999*************985 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.22
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                  DNA_ligase_OB  14 tGaltpvAeLepvelaGttVsratLhn 40 
                                    tGa   +A+L+   l Gt++  a L+ 
  gi|116753519|ref|YP_842637.1| 424 TGAHMEIARLSGALLTGTMMDGADLNG 450
                                    788888888888888888888887764 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 0.98
                                    XXXXXXXXXXXXXXXXXX CS
                  DNA_ligase_OB  21 AeLepvelaGttVsratL 38 
                                    A+++  +l+G+  +ra L
  gi|116753519|ref|YP_842637.1| 481 ANMSGSDLSGVDLTRAAL 498
                                    555666666666666665 PP

  == domain 5  score: 3.6 bits;  conditional E-value: 0.02
                                    XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                  DNA_ligase_OB  20 vAeLepvelaGttVsratLhnedeie 45 
                                     A L+ v+l+G+  s+a L  +d  +
  gi|116753519|ref|YP_842637.1| 585 SASLQGVDLSGSDLSEADLRGADMTN 610
                                    599****************9999765 PP

  == domain 6  score: -1.9 bits;  conditional E-value: 1.1
                                    XXXXXXXXXXXXXXXXX CS
                  DNA_ligase_OB  25 pvelaGttVsratLhne 41 
                                     v+l+G + sra L  +
  gi|116753519|ref|YP_842637.1| 655 WVDLSGARLSRALLTRA 671
                                    57788888888877654 PP

  == domain 7  score: -1.9 bits;  conditional E-value: 1.1
                                    XXXXXXXXXXXXXXXXXXXXXXX CS
                  DNA_ligase_OB  20 vAeLepvelaGttVsratLhned 42 
                                    +A+L+ ++  G+  ++ +L  +d
  gi|116753519|ref|YP_842637.1| 780 MADLKRIKATGVYLTNTSLSGAD 802
                                    69999**********99998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (862 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       241  (0.0134419); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.72u 0.29s 00:00:01.01 Elapsed: 00:00:00.45
# Mc/sec: 5732.77
//
Query:       gi|116753520|ref|YP_842638.1|  [L=398]
Description: hypothetical protein Mthe_0199 [Methanosaeta thermophila PT]
Scores for complete 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-90  303.9   0.0    1.8e-90  303.4   0.0    1.2  1  Nre_N     Archaeal Nre, N-terminal
    9.5e-37  125.3   0.2    1.5e-36  124.6   0.2    1.3  1  Nre_C     Archaeal Nre, C-terminal
  ------ inclusion threshold ------
      0.065   13.4   0.0       0.15   12.2   0.0    1.6  1  DUF1581   Protein of unknown function (DUF1581)


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 !  303.4   0.0   3.1e-94   1.8e-90       1     270 []      13     271 ..      13     271 .. 0.96

  Alignments for each domain:
  == domain 1  score: 303.4 bits;  conditional E-value: 3.1e-94
                          Nre_N   1 LcglkkcpileklravekakkkisskeleGsspPsvfVGrygYPkVsvgplvppvegdasvldspekwlglslediiklr 80 
                                    Lcg++ cp+l kl++++ +  +i +++l G+spP++fVGr+gYP V++gpl+p      s+ ++p     l++ +ii+ r
  gi|116753520|ref|YP_842638.1|  13 LCGRPVCPLLIKLEELAGL-PRI-GNRLAGESPPEIFVGRHGYPLVRAGPLLPIG----SSPEQP----ALDIVKIISHR 82 
                                    8****************96.555.7**************************9974....344444....689******** PP

                          Nre_N  81 lslvrgekkvkvkkak.edklleeiqelalsekpvdvevelekkpkaklkfdevlaPvGpsaeleklkvaenpkvprkve 159
                                    ++++r+e +++v++ak + +lle+ q++a+s++pv++ev++ k+p+ ++ fd+vl+P+Gp +++e++++++np vprkv+
  gi|116753520|ref|YP_842638.1|  83 TRMIRSELEIHVHDAKdPGRLLESAQQIAMSSRPVETEVSFVKPPEGRMLFDGVLSPMGPGGRIEDMDITGNPFVPRKVD 162
                                    ****************9999************************************************************ PP

                          Nre_N 160 klveDtdlkAeeavveLyrsgvdvykiqrlLSvGlLGekkkrrlVPTrWsITAvddivgkelkkeikdlpeidevevfsg 239
                                    ++v Dtd+kA++av+eLy+s + +++i+rlLS+GlLG+  +rrlVPTrW+ITA ddi+g++l++++ d+pe+  +e++sg
  gi|116753520|ref|YP_842638.1| 163 QIVGDTDVKAASAVYELYSSSICIDHISRLLSIGLLGR--DRRLVPTRWAITASDDIIGNALRSRVLDMPELGGYELYSG 240
                                    *************************************9..**************************************** PP

                          Nre_N 240 eylgNrflviLaPgkwsfelvEawapgslwn 270
                                     +lgN+f +iL+Pg++sfel+E+w+pgs w+
  gi|116753520|ref|YP_842638.1| 241 GILGNHFQIILMPGAYSFELIEIWHPGSAWS 271
                                    ******************************6 PP

>> Nre_C  Archaeal Nre, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.6   0.2   2.6e-40   1.5e-36       1     110 []     282     388 ..     282     388 .. 0.95

  Alignments for each domain:
  == domain 1  score: 124.6 bits;  conditional E-value: 2.6e-40
                          Nre_C   1 egyegrkeyseiaGaYyaarlavleaLekikrqakvivlreitpeYwaPvGvWqvReavrkalekkpkefesleealeev 80 
                                    eg+++r++ys++aG+Yyaarl+vle+L ++krqa+v+ lreit+eYwaP+GvW+vR+++r+al+++p +fe+leea++++
  gi|116753520|ref|YP_842638.1| 282 EGTTERRSYSPLAGGYYAARLPVLEHLLRMKRQAGVLALREITEEYWAPLGVWVVRDTARAALASRPLRFETLEEAIRSA 361
                                    67889*************************************************************************** PP

                          Nre_C  81 seklklplkkllkkskllkelkkqktLddF 110
                                    ++++++++++++++sk +++   q+tL++F
  gi|116753520|ref|YP_842638.1| 362 ESRMRTKSSAWKHHSKSFSR---QTTLSSF 388
                                    *************9987765...7888887 PP

>> DUF1581  Protein of unknown function (DUF1581)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.5e-05      0.15      41      62 ..     144     165 ..     135     177 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.5e-05
                        DUF1581  41 gvvrnlritGePeiPdkvdlve 62 
                                    g ++++ itG+P +P+kvd + 
  gi|116753520|ref|YP_842638.1| 144 GRIEDMDITGNPFVPRKVDQIV 165
                                    789***************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); 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 0.24s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 3022.43
//
Query:       gi|116753521|ref|YP_842639.1|  [L=484]
Description: radical SAM domain-containing protein [Methanosaeta thermophila PT]
Scores for 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    7.3e-15   55.7   0.0    2.7  3  Radical_SAM  Radical SAM superfamily
      5e-15   55.6   0.1    1.1e-14   54.5   0.1    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 ?    2.3   0.0     0.022     2e+02     108     146 ..      46      91 ..      15     131 .. 0.76
   2 !   55.7   0.0   8.2e-19   7.3e-15       1     163 [.     190     351 ..     190     355 .. 0.91
   3 ?   -2.7   0.0      0.73   6.5e+03      47      75 ..     360     394 ..     353     429 .. 0.58

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.022
                                    EEBSSSHHHHHHHHTCTSHH..........HHHHHHHHHHHHTTSETEE CS
                                    xxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM 108 gleaaddekvlklmnrghtf..........eevlealeklreagikrvv 146
                                    g++ +d++ v+++ nr +++           + le+ +++++ag + vv
  gi|116753521|ref|YP_842639.1|  46 GIKDPDEF-VRRHANR-YDLigltamsfqyARALELARIAKDAGAE-VV 91 
                                    66777777.7777754.55567777777777777777777777766.32 PP

  == domain 2  score: 55.7 bits;  conditional E-value: 8.2e-19
                                    EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC...CCT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxx RF
                    Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla...vpg 77 
                                    v+++rgC+++C+fC+++++   ++  r   + +++e ++ + +e+g++ +++  ++ +l+ +  e++  ++  a   +  
  gi|116753521|ref|YP_842639.1| 190 VETSRGCTQGCKFCSINSM--YGRSFRKFEIKRVIEDIQDA-EEHGAGSIFFPDDNITLDVKRLEAICDAIIDAgltHLR 266
                                    5789*************97..99999999999999999999.9999*************98888888888887799999* PP

                                    EEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  78 iritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGend 157
                                    +++  +++g+  +e+ ++++ e+g+d v lg+e+a+++  l+ +++g   ++  +a+++l++++i +++  i g p  + 
  gi|116753521|ref|YP_842639.1| 267 YKTQASASGIASSERLVKKMGEAGFDGVFLGVESASKR-NLQFFGKGRMSDHAERAVRYLHDNDIIVSTGLIGGNPDDTA 345
                                    ***********99*************************.*****999*******************88888888888999 PP

                                    HHHHHH CS
                                    xxxxxx RF
                    Radical_SAM 158 eeleel 163
                                    e++++ 
  gi|116753521|ref|YP_842639.1| 346 EDMWAN 351
                                    988765 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 0.73
                                    SEEEEEESSTGGGSTTHHHHHHHHHHTC......C CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxx......x RF
                    Radical_SAM  47 vkevilgggepllypdfvellerlakla......v 75 
                                    v++ i+   +p    ++ e+ler+  +        
  gi|116753521|ref|YP_842639.1| 360 VDFPIFYINTPYPKTPMREELERMGLITnndfrfY 394
                                    55556666666666666666666665554444442 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.5   0.1   1.2e-18   1.1e-14      12     120 ..      21     128 ..      19     129 .. 0.89

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 1.2e-18
                    B12-binding  12 lhplGlavlaaalrd.agfeVqllganvenedivaairaekpdvvglSalltsqleavkelvellkrirprvkvvvGGah 90 
                                    +++lGl +laaa+ d   ++V +l    +++++v++ +  ++d++gl+a ++ q++ + el++ +k +++   vv+GG h
  gi|116753521|ref|YP_842639.1|  21 IPDLGLVSLAAAIDDlCDVHVADLHGIKDPDEFVRRHAN-RYDLIGLTA-MSFQYARALELARIAKDAGA--EVVIGGYH 96 
                                    799************447777777777778999998765.5********.****************9955..79****** PP

                    B12-binding  91 psldpeetleak..lgiddvvvgegedaleal 120
                                    p+l ++e+ +    + id++v+gege ++++l
  gi|116753521|ref|YP_842639.1|  97 PTLFYREIGSSSdlMLIDYIVRGEGERTFREL 128
                                    *******998889****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (484 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); 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 0.22s 00:00:00.71 Elapsed: 00:00:00.37
# Mc/sec: 3910.95
//
Query:       gi|116753522|ref|YP_842640.1|  [L=454]
Description: radical SAM domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-12   47.8   3.8    6.1e-12   46.2   1.2    2.9  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 ?   -0.1   0.0     0.058     1e+03     128     143 ..      84      99 ..      53     110 .. 0.66
   2 !   46.2   1.2   3.4e-16   6.1e-12       3     165 ..     165     335 ..     163     337 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.058
                                    HHHHHHHHHHHHTTSE CS
                                    xxxxxxxxxxxxxxxx RF
                    Radical_SAM 128 eevlealeklreagik 143
                                     e+le +e++r++gi+
  gi|116753522|ref|YP_842640.1|  84 HEILEMVEAARARGIN 99 
                                    4566666666666665 PP

  == domain 2  score: 46.2 bits;  conditional E-value: 3.4e-16
                                    EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC........ CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........ RF
                    Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla........ 74 
                                    +trgC  +C+fC++p      +++  +++e+i++ v ++k ++++++vi+   +  ++++ ++ + ++  +         
  gi|116753522|ref|YP_842640.1| 165 TTRGCGVGCKFCQTPC---FAPKPTPIPLESIERVVNYYK-KNNINVVIIEDENFGANRRHADRVVEILDEYdmvwgcma 240
                                    69*************9...8*******************6.555*************************99877666666 PP

                                    .......CCTEEEEEEECSSCHG..HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETE CS
                                    .......xxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  75 .......vpgiritvetngtlpd..eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrv 145
                                           + +  +t+          +  ++r++  g+   ++g+e ++ e  l+ +++++++e+++e++++l ++g+  v
  gi|116753522|ref|YP_842640.1| 241 radylreKIDEWVTMRRRV---ArrDGSARRMVS-GFAGAAIGIENLHQE-RLDDIKKREGVEDIVETIKLLQSHGMGTV 315
                                    6666544333344444444...14599*******.99*************.89999999********************* PP

                                    EEEEEEBTTTSHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM 146 vdrivglpGendeeleelle 165
                                     + ++g++  + + ++e ++
  gi|116753522|ref|YP_842640.1| 316 GYYMIGFEDDTVRSIDEDVK 335
                                    *********99999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); 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: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.50
# Mc/sec: 2754.80
//
Query:       gi|116753523|ref|YP_842641.1|  [L=205]
Description: metal-binding protein-like [Methanosaeta thermophila PT]
Scores for complete 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-52  177.9   0.3    1.4e-52  177.7   0.3    1.0  1  DUF2284   Predicted metal-binding protein (DUF2284)


Domain annotation for each model (and alignments):
>> DUF2284  Predicted metal-binding protein (DUF2284)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.7   0.3     8e-57   1.4e-52       2     164 .]      27     204 ..      26     204 .. 0.97

  Alignments for each domain:
  == domain 1  score: 177.7 bits;  conditional E-value: 8e-57
                        DUF2284   2 lidaedivveervrlkCekgCknYgknlsCPPavptveefrkilkeYkkallvqtkaeledeedd...keemkevkeele 78 
                                    li++  +vv e+vr+kC++gC+ Ygk+l+CPP++p++ee++++l++Y+ a+l ++  ++++ ++    ++ +++  ++l+
  gi|116753523|ref|YP_842641.1|  27 LISTGIVVVGEWVRWKCRYGCRAYGKHLCCPPYAPSPEETKRMLEDYDFAVLARFLPTPTPGYEPrrlHHYLWNSLTSLH 106
                                    7999*********************************************************99999999*********** PP

                        DUF2284  79 killelekeafeagypkalalsagsCtlCetCayeegep............CrhpekarpsmealGidvfktaekaglel 146
                                    k+++ele++af +g++ka++++a +Ct+CetC++ee+ +            Crh+e++rps+ea+Gidvf+t+++ag++l
  gi|116753523|ref|YP_842641.1| 107 KTIFELERQAFLMGCYKAFGMGAMPCTFCETCVAEEKIAkgespapadavlCRHKEMMRPSLEACGIDVFATLRNAGYDL 186
                                    ************************************6558999************************************* PP

                        DUF2284 147 evgkeeketvslvglvLl 164
                                    +v+++++e++sl+g+vLl
  gi|116753523|ref|YP_842641.1| 187 KVLRSYQERFSLFGMVLL 204
                                    ****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1447.87
//
Query:       gi|116753524|ref|YP_842642.1|  [L=250]
Description: hypothetical protein Mthe_0204 [Methanosaeta thermophila PT]
Scores for complete 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  258.4   0.0    6.1e-77  258.2   0.0    1.0  1  SAM_adeno_trans  S-adenosyl-l-methionine hydroxide adenosyltr
  ------ inclusion threshold ------
      0.023   14.3   0.1       0.05   13.2   0.1    1.5  1  T4-Gluco-transf  Bacteriophage T4 beta-glucosyltransferase


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 !  258.2   0.0   6.8e-81   6.1e-77       1     234 [.       5     241 ..       5     242 .. 0.91

  Alignments for each domain:
  == domain 1  score: 258.2 bits;  conditional E-value: 6.8e-81
                                    EEEEESSTSSSSHHHHHHHHHHHH-TTSEEEEEES-S-TT-HHHHHHHHHHHHGGS-TTEEEEEE--TTTTSS--EEEEE CS
                SAM_adeno_trans   1 itLlTDFGlkdpyvgamkgvilsiapdarivDitHdippfdvreaaflLaaalpyfpkgtvhlavVDpgvgterralvve 80 
                                    it+lTDFG  + y ++mkgvil++ +d+  v+i+ dipp+dvr++af+L+ a +yfp+gt+h+avVDpgvgter a++ve
  gi|116753524|ref|YP_842642.1|   5 ITFLTDFG--SFYLSQMKGVILQRTKDVVFVEISTDIPPQDVRSGAFALMVASRYFPRGTIHIAVVDPGVGTERAAICVE 82 
                                    9*******..********************************************************************** PP

                                    ETTSEEEEESSSTTHHHH...SEEEEEEGSSCC.--TS-HHHHTHHHHHHHHHCT--GGGCSEEESGGGS.-SSS.E..C CS
                SAM_adeno_trans  81 akggyfvgPDNGlltlal...lleeaveieeee.ssatFhgrDvFapvaarlaagvsleelgeeldpeel.vrle.e..d 152
                                    ++g++f+gPDNG+l++a+   +   a+ ++ +e +s tFhgrDvFap+aa++a g+ +e++g +++p++l +  + +  +
  gi|116753524|ref|YP_842642.1|  83 SGGHVFIGPDNGILMPAAyalGSPVAWVLDVPEgASPTFHGRDVFAPAAAEIACGTHPEDMGIPFEPKDLdL-GSpRvvA 161
                                    *****************9866447899999999999*******************************88843.3344468 PP

                                    SCEEEEEEEE-TTS-EEEEEE...EHHHHHTTCEE..EEEEESSGGGSTTTSEEEEE-TTSEEEEEETTC-HHHHHT--T CS
                SAM_adeno_trans 153 erlegevlyvDrFGNvitniskelleelekerkva..klkkvetyaevaegellalvnssglleiavnkgsaaellglkv 230
                                    + +e +v+++D+FGNv++n+++   ++++        +lk+v+ty+e+  +e l++++s+g+ eiavn gsaa+l+gl++
  gi|116753524|ref|YP_842642.1| 162 NGVETTVIHIDNFGNVVLNMKSVPDSDMRL----MgrRLKRVRTYGEAGWNESLITLGSHGFAEIAVNGGSAAKLFGLST 237
                                    89******************9333333322....13477899************************************** PP

                                    T-EE CS
                SAM_adeno_trans 231 gdev 234
                                    gd++
  gi|116753524|ref|YP_842642.1| 238 GDKI 241
                                    **98 PP

>> T4-Gluco-transf  Bacteriophage T4 beta-glucosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   5.6e-06      0.05       3      22 ..     169     188 ..     168     191 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.6e-06
                                    EEEEESSS--SSSSSHHHHH CS
                T4-Gluco-transf   3 iAiinmGnnvinFKtvPssE 22 
                                    i i n Gn v+n K vP s+
  gi|116753524|ref|YP_842642.1| 169 IHIDNFGNVVLNMKSVPDSD 188
                                    6788*************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); 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: 00:00:00.39
# Mc/sec: 1916.24
//
Query:       gi|116753525|ref|YP_842643.1|  [L=318]
Description: methylenetetrahydromethanopterin reductase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-68  230.6   0.0    3.7e-68  230.3   0.0    1.0  1  Bac_luciferase  Luciferase-like monooxygenase


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  230.3   0.0   2.1e-72   3.7e-68      28     313 ..      18     294 ..      11     295 .. 0.94

  Alignments for each domain:
  == domain 1  score: 230.3 bits;  conditional E-value: 2.1e-72
                 Bac_luciferase  28 laraaEelGfdavwvaehhggpggaldaftllaalaaaTerirlgtavtplytrhPavlAqqaatLdhlsgGRfglglgt 107
                                    l ++aE++Gf++vw+++h+++    +d +++la+l++ T+rirlgt+vt++ytr+P+++A ++a++++lsgGR++lg+g 
  gi|116753525|ref|YP_842643.1|  18 LSKLAEDVGFETVWITDHYNN----RDVYSTLAVLSMLTNRIRLGTGVTNPYTRSPIITASSIASINELSGGRAILGIGP 93 
                                    6799****************9....******************************************************* PP

                 Bac_luciferase 108 ggpaveerrfGvdhderyarlrEfvevlrrlwrgeevdfeGeffsvkgalllprpgqgpiPvyvaaaspaglelaarhad 187
                                    g  a+  +++G+ +++++ r rE v v+r+l+r+e+v+  G     +++  +       iP+y++a +p++lela+++ad
  gi|116753525|ref|YP_842643.1|  94 GDKATF-DAMGIAWEKPLTRVRESVSVIRALLRKERVTQGGMN---AQLSFSAGN----IPIYMGAQGPKMLELAGEIAD 165
                                    *99888.999**********************99999988866...233333333....9******************** PP

                 Bac_luciferase 188 glllageppeeaaelierlragaaeagrdpadirvgisltvivadteeeAraea...raliagldfyaldsegagreaea 264
                                    g+l++ ++pe+ +++i+ +r g ++agrdp+d++v++ ++++v++++ +A +ea    a+ia +   a  +++    +e+
  gi|116753525|ref|YP_842643.1| 166 GVLINASHPEDFRAAIPLIRNGVQRAGRDPEDVKVCAYTSFSVDRDRSKAASEArkvVAFIAAGSPDAVLERHGIGVQER 245
                                    ******************************************************77777777777999999999999999 PP

                 Bac_luciferase 265 aeiqeeedanlwagaadavpdelvaatalvGtpeqvaerlaayaeagvd 313
                                    ++i+++ +++++a+a+++v+d++++ + + Gtp+++++r++++ ++gv+
  gi|116753525|ref|YP_842643.1| 246 DAISKAISKGDFASAMSSVTDKMLDVFSVTGTPDDCRARVDELLATGVN 294
                                    9*****************************************9999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 2414.37
//
Query:       gi|116753526|ref|YP_842644.1|  [L=170]
Description: nicotinamide-nucleotide adenylyltransferase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-14   53.9   0.0      3e-13   50.2   0.0    2.0  1  CTP_transf_like  Cytidylyltransferase-like
  ------ inclusion threshold ------
       0.19   10.9   0.0        7.1    5.7   0.1    2.0  2  HIGH_NTase1      HIGH Nucleotidyl Transferase


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2   0.0   3.4e-17     3e-13       1     142 [.       5     132 ..       5     133 .. 0.86

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 3.4e-17
                                    EEEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-SCSSTHHHHHHHHHHH.TTCTTEEEEEEESEHHHHHHH CS
                CTP_transf_like   1 lagGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkkkplasaeeRlemlela.kevdevisvdpweltrevlkk 79 
                                    ++ G+F+p H GH  +leq+ ++++e +ivg+ +++ ++   +++++a eR++m+  a +e  +++     ++ +  l +
  gi|116753526|ref|YP_842644.1|   5 FYIGRFQPYHMGHHLVLEQISREVDE-IIVGIGTAQISHTV-TDPFTAGERIAMIYGAlRELGRWF-----YIIP--LPD 75 
                                    589***********************.************99.****************66666655.....4444..222 PP

                                    TTTTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHHH CS
                CTP_transf_like  80 lkpdklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkire 142
                                    ++ +  ++v    +++       +e +++n++lvv+ + e   +v  ++++r++ +S+t ir+
  gi|116753526|ref|YP_842644.1|  76 INRN-AVWVSHVKSMTP-----PFEVVYSNNPLVVELFMEAGMEVRRPPMYRREVYSGTVIRR 132
                                    3222.378887777776.....79*************************************97 PP

>> HIGH_NTase1  HIGH Nucleotidyl Transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1   0.00079       7.1      10      29 ..      10      29 ..       6      36 .. 0.82
   2 ?    3.1   0.0    0.0049        44     201     237 ..     122     155 ..     111     169 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.00079
                    HIGH_NTase1 10 YNPfHnGHlyhlekakeltg 29
                                   + P+H GH   le++ ++++
  gi|116753526|ref|YP_842644.1| 10 FQPYHMGHHLVLEQISREVD 29
                                   78*************99864 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.0049
                    HIGH_NTase1 201 eeiaSAtaiRkalkeekkleelkklvPestleilkee 237
                                    +e+ S t iR+++ e     + ++lvP++++++++e 
  gi|116753526|ref|YP_842644.1| 122 REVYSGTVIRRLMIEG---GDWRQLVPDAVAKVIDEI 155
                                    4789*********555...579*********999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1233.74
//
Query:       gi|116753527|ref|YP_842645.1|  [L=386]
Description: hypothetical protein Mthe_0207 [Methanosaeta thermophila PT]
Scores for complete 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-155  517.6   0.0     2e-155  517.5   0.0    1.0  1  DUF521    Protein of unknown function (DUF521)


Domain annotation for each model (and alignments):
>> DUF521  Protein of unknown function (DUF521)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  517.5   0.0  1.1e-159    2e-155       1     401 []       1     380 [.       1     380 [. 0.97

  Alignments for each domain:
  == domain 1  score: 517.5 bits;  conditional E-value: 1.1e-159
                         DUF521   1 mkLtkeeeamlnGeeGealqkameilvalGeilgAerLvpvtsahvsgvsyktigdaglefleelaekgakvrvpttlnp 80 
                                    m+Ltk+ee +l+Ge+G++l+ ameilvalG+i+gAe+L++++sa+++gvsyktigdagle++++l    +kv+vp++lnp
  gi|116753527|ref|YP_842645.1|   1 MHLTKDEELLLQGERGDTLRRAMEILVALGDIYGAEQLIEIKSAQIAGVSYKTIGDAGLEWISDLD---GKVAVPSILNP 77 
                                    9*****************************************************************...*********** PP

                         DUF521  81 igvdlerweelgvdeefaekqeriieayeklGveltftCtpyll.gnapkkGehlawsESsavvyaNSvlGarTnreggp 159
                                    +g+dl rw+e+++de+fa+kq +ii+ay++lGv++++tCtpyll +++ ++G+hlawsESsav+yaNSv+Ga+Tnreggp
  gi|116753527|ref|YP_842645.1|  78 AGMDLLRWREMSIDEDFARKQLEIINAYRRLGVTIECTCTPYLLyESIASRGDHLAWSESSAVSYANSVIGAMTNREGGP 157
                                    *******************************************8799********************************* PP

                         DUF521 160 salaaAitGrtpeyGlhldenRkptvlveveaesedeadygalGylvGkkvgeriPvlkglekpsedelKalgAalaasg 239
                                    salaaA++G+tp yG+hl+enR+pt++++v+a+     +ygalG+lvGk+vg+++P++ + ++p++d+lKalgAa+aasg
  gi|116753527|ref|YP_842645.1| 158 SALAAALVGKTPLYGYHLEENRVPTHVIRVDAD---LKEYGALGFLVGKIVGDGVPLFVMRSRPDRDDLKALGAAMAASG 234
                                    *****************************8665...89**********************9999**************** PP

                         DUF521 240 avalfhiegvTPeaetleealgekekaekititkedleevleelskakeekvdlvalGcPhlsleElrelaellkgkkkk 319
                                    +val+++++vT e ++ +e     ++ e ++i++e++++v++++      +vd+valGcPh+s++El+++a+ll  +++k
  gi|116753527|ref|YP_842645.1| 235 SVALYYVKDVTQEPPEHDE-----DACEFVEIEEEEIRSVYDST-----IDVDIVALGCPHCSMQELERIADLL--EGRK 302
                                    *************555544.....459***************66.....89***********************..7777 PP

                         DUF521 320 vkvelwvttsrevkeeaerlglveklekaGvkvlsdtCmvvsplikkkevkkvatnSgKaahYlpgltgvkvalgsleec 399
                                    v+ elw++t+r ++e a +l  v+++e+ G++v++dtCmvvsp++++  +k++++nSgKa+ Y+pg++g ++ +gsleec
  gi|116753527|ref|YP_842645.1| 303 VSSELWICTARRIAESAPEL--VRRIESTGARVICDTCMVVSPASER--FKHMMVNSGKALAYIPGMCGISASFGSLEEC 378
                                    7******************9..***********************95..9****************************** PP

                         DUF521 400 ve 401
                                    ++
  gi|116753527|ref|YP_842645.1| 379 ID 380
                                    95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2920.47
//
Query:       gi|116753528|ref|YP_842646.1|  [L=137]
Description: hypothetical protein Mthe_0208 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-35  120.9   0.4    2.5e-35  120.1   0.4    1.4  1  DUF126    Aconitase X swivel domain


Domain annotation for each model (and alignments):
>> DUF126  Aconitase X swivel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.1   0.4   1.4e-39   2.5e-35       1      80 []      24     103 ..      24     103 .. 0.99

  Alignments for each domain:
  == domain 1  score: 120.1 bits;  conditional E-value: 1.4e-39
                                    --TTS-B-TTT-BB-S.-SSSTT-B-TTSEEEES--S--SS-TTHHHHHHHHT-S-SEEEESS--HHHHHHHHHHT--EE CS
                         DUF126   1 lSflggvdpetGkvidkghplegqsiagkiLvlpsgkGStvgsyvllelakngtaPaAlilreadpilalGaivadiPlv 80 
                                    +Sflg+vdpetG+v+d+ h+l+g+siag +L++p+gkGStvgsyv+++l+k+g+aPaA+i+ + +pi+a+Gai++diPlv
  gi|116753528|ref|YP_842646.1|  24 ISFLGNVDPETGVVVDPAHELYGRSIAGVVLIFPGGKGSTVGSYVIYQLRKRGMAPAAMINLKSEPIVAVGAIISDIPLV 103
                                    8*****************************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 1133.09
//
Query:       gi|116753529|ref|YP_842647.1|  [L=98]
Description: hypothetical protein Mthe_0209 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); 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: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 809.91
//
Query:       gi|116753530|ref|YP_842648.1|  [L=63]
Description: hypothetical protein Mthe_0210 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0055   16.6   0.8     0.0061   16.4   0.8    1.2  1  SprT-like     SprT-like family
  ------ inclusion threshold ------
      0.079   13.7   0.0      0.082   13.6   0.0    1.1  1  RNA_polI_A14  Yeast RNA polymerase I subunit RPA14
       0.19   11.3   0.0        0.2   11.2   0.0    1.0  1  Pec_lyase_C   Pectate lyase


Domain annotation for each model (and alignments):
>> SprT-like  SprT-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.8     1e-06    0.0061      70     104 ..       4      36 ..       3      58 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1e-06
                      SprT-like  70 HElcHlalfvisgvrnnpHGaeFkawaakvekala 104
                                    HE  Hl+ + i++  n+ H ++F+  a+++++ + 
  gi|116753530|ref|YP_842648.1|   4 HEAEHLLKHWIEH--NESHSRSFRDRAKQINDISP 36 
                                    ************9..***************99864 PP

>> RNA_polI_A14  Yeast RNA polymerase I subunit RPA14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.4e-05     0.082      14      58 ..       2      46 ..       1      58 [. 0.78

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.4e-05
                   RNA_polI_A14 14 skeevekfLteFIdekEssaselageesstkeaatglsvdtelss 58
                                   ++ e+e++L+++I+++Es + ++  ++++ ++++ ++++  e ++
  gi|116753530|ref|YP_842648.1|  2 ERHEAEHLLKHWIEHNESHSRSFRDRAKQINDISPEAAKAIEEAA 46
                                   5789**************999999999999888744444444444 PP

>> Pec_lyase_C  Pectate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.3e-05       0.2      89     125 ..      11      47 ..       4      57 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.3e-05
                    Pec_lyase_C  89 nvWvDHveisdksfeddkttdkdvqfdkaldikkasd 125
                                    + W++H+e   +sf d     +d+  ++a  i++a+ 
  gi|116753530|ref|YP_842648.1|  11 KHWIEHNESHSRSFRDRAKQINDISPEAAKAIEEAAS 47 
                                    68***************************99999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1290  (0.0719505); expected 358.6 (0.02)
Passed bias filter:                      844  (0.0470746); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 492.14
//
Query:       gi|116753531|ref|YP_842649.1|  [L=264]
Description: glutamate synthase alpha subunit [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-35  122.0   6.1    2.6e-35  121.7   6.1    1.1  1  GXGXG     GXGXG motif


Domain annotation for each model (and alignments):
>> GXGXG  GXGXG motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.7   6.1   1.4e-39   2.6e-35      12     172 ..      40     204 ..      26     220 .. 0.86

  Alignments for each domain:
  == domain 1  score: 121.7 bits;  conditional E-value: 1.4e-39
                                    H......HHHHHHHHHHTTT--...-.-EEEEEEEEEE-TTTTTT--TTEEEEEEEEE-STTTTT-ESSEEEEE--TT-S CS
                          GXGXG  12 t......ilsneiakrygeegl...pedtikiklkGsaGqslgaflakGltleleGdandyvGkglsgGkivikpskesk 82 
                                           +l n++++ry+ + l   ++  ++i+++G++G++lgafl  G ++ ++G+a+d vG+++++G+ivi++ +   
  gi|116753531|ref|YP_842649.1|  40 LcgyekvVLRNVCGQRYIGTRLyspQRRVMTIEIYGTPGNDLGAFL-FGHRILVHGNAQDGVGNTMESGEIVINGRA--- 115
                                    3555556899*********999433346789***************.9*****************************... PP

                                    S-GGGSB-S-SSTTTT--SEEEEESSB--SSTTTT-.....SS-EEEESEB.-SSTTTT-EEEEEEE-S-B....-SSBT CS
                          GXGXG  83 fkaeeniivGnvvlygatgGklfirgkageRfavrn.....sgatavvegv.gdhgceYmtGGvvvvLgkt....grnfa 152
                                             G+v+  +++gG++f++g++++R+a ++     +++++vv+g+  d+++eYm+GG+v++Lg      +r ++
  gi|116753531|ref|YP_842649.1| 116 ---------GDVTGMSMRGGRIFVKGDVSYRAALHMkehglKKPVIVVGGTsQDFLGEYMAGGIVILLGLYrahtARFIG 186
                                    .........***************************9999999********99****************87667699*** PP

                                    TT--EEEEEEE-SSSTHHHH CS
                          GXGXG 153 aGmsgGiayvldedekfekk 172
                                    +Gm+gG++y++ e ++  ++
  gi|116753531|ref|YP_842649.1| 187 SGMHGGAIYIRGEVGE--EQ 204
                                    **********955544..34 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); 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: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2091.90
//
Query:       gi|116753532|ref|YP_842650.1|  [L=497]
Description: glutamate synthase (NADPH) [Methanosaeta thermophila PT]
Scores for 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-141  470.8   0.1     3e-141  470.8   0.1    1.8  1  Glu_synthase     Conserved region in glutamate synthase
    2.6e-17   63.2   0.0    2.6e-09   37.0   0.1    2.2  2  Glu_syn_central  Glutamate synthase central domain
      2e-08   33.6   6.6      2e-08   33.6   6.6    1.5  2  IMPDH            IMP dehydrogenase / GMP reductase domain
    2.3e-07   30.8  11.5    2.3e-07   30.8  11.5    2.4  2  Fer4_9           4Fe-4S dicluster domain
    1.5e-06   27.5   8.3    1.5e-06   27.5   8.3    2.6  3  FMN_dh           FMN-dependent dehydrogenase
    3.9e-06   26.5   4.6    6.9e-06   25.7   4.6    1.3  1  NMO              Nitronate monooxygenase
    0.00029   21.4  19.6     0.0055   17.3  13.6    3.1  3  Fer4_7           4Fe-4S dicluster domain
    0.00034   21.5   0.6    0.00034   21.5   0.6    3.3  3  Fer4_16          4Fe-4S double cluster binding domain
    0.00093   18.7   1.4     0.0022   17.5   0.1    2.0  2  His_biosynth     Histidine biosynthesis protein
     0.0011   18.7   2.5     0.0011   18.7   2.5    3.6  3  Fer4             4Fe-4S binding domain
      0.009   16.1  19.8      0.023   14.8   1.5    3.3  3  Fer4_10          4Fe-4S dicluster domain
     0.0092   16.1   8.8     0.0092   16.1   8.8    2.4  2  Fer4_21          4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.046   13.1   1.0       0.24   10.8   0.1    2.1  2  G3P_antiterm     Glycerol-3-phosphate responsive antiterminat
      0.072   12.3   5.6       0.23   10.6   5.6    1.8  1  DHO_dh           Dihydroorotate dehydrogenase
       0.14   12.3  21.6       0.16   12.1   1.4    3.4  3  Fer4_6           4Fe-4S binding domain
       0.29   11.6  20.8        2.9    8.4  13.9    3.2  2  Fer4_8           4Fe-4S dicluster domain
       0.37   10.2   7.4        4.2    6.8   0.2    2.9  3  PcrB             PcrB family
       0.42   10.5   1.8       0.93    9.4   1.8    1.5  1  zf_PR_Knuckle    PR zinc knuckle motif
       0.83   10.2  21.3         44    4.7   0.6    3.4  2  Fer4_17          4Fe-4S dicluster domain
          8    7.2  28.4       0.25   11.9   2.6    3.6  3  Fer4_4           4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  470.8   0.1  3.4e-144    3e-141       4     368 .]     107     465 ..     104     465 .. 0.98

  Alignments for each domain:
  == domain 1  score: 470.8 bits;  conditional E-value: 3.4e-144
                                    -HHHHHHHHHHHHH---HHHHHHHHHHHTS.-S-SGGGGEEE--SS--.--GGGS--HHHHHTTEE---B-TTTS-HHHH CS
                   Glu_synthase   4 eievikllqkavqveskesidkyrekleerevlkakrdlleldaaeealikleevepalkikkriltsamSyGalseeah 83 
                                    +i+++++l +a+qv +++sid +re++e r++l++k++ l l++ e+        +p+l++++++l+samSyGa+s +a 
  gi|116753532|ref|YP_842650.1| 107 RIYWDHILLNASQV-TNPSIDPLREPMELRTFLGSKPESLSLSDMEAG------TDPVLTLETPMLFSAMSYGAISYNAF 179
                                    6899**********.***************************777776......589*********************** PP

                                    HHHHHHHHHHT-B-EETTS---GGGGS-----SEEEE-TT-TT--HHHHHH-SEEEEE---TTSTTS--EE-GGG--HHH CS
                   Glu_synthase  84 ealakamnrlgtksntGEGGedeerlktakdvaikQvasgrFGvteeyLnnakaleikiaQGakpgeGgqlpgeKvseei 163
                                    +ala+a++r gt++ntGEGG+++e +++ k+ +i+QvasgrFG+++eyLn+++a+eiki+QGakpg+Gg+lpgeKvs+++
  gi|116753532|ref|YP_842650.1| 180 QALAIAASRSGTFFNTGEGGMPAEMRSQFKEHTIVQVASGRFGIDAEYLNSGAAVEIKIGQGAKPGIGGHLPGEKVSQHV 259
                                    **********************99999999999*********************************************** PP

                                    HHHHTS-TT--EE--SS-TT-SSHHHHHHHHHHHHHH-.TTSEEEEEEE-STTHHHHHHHHHHTT-SEEEEE-TT---SS CS
                   Glu_synthase 164 akiRkikpgvdliSPaphhdiysiedlaqliedLkevn.keakvsvKlvaeagvetiaagvakanadiilidGleGGTGA 242
                                    a++R+i++g+d+iSPaphhdiysiedl++li+++kev+ +e++v vK++a +++ +ia+g+++a+adii+idG++GGTGA
  gi|116753532|ref|YP_842650.1| 260 AATRMIPEGTDAISPAPHHDIYSIEDLEMLISAIKEVTnYEKPVIVKVAAVHNISAIASGIVRAGADIIAIDGMRGGTGA 339
                                    *************************************99***************************************** PP

                                    EEHHHHHHB---HHHHHHHHHHHHHHTT-GGG-EEEEESS--SHHHHHHHHHHT-SEEE-SHHHHHHTT--S---GGGT- CS
                   Glu_synthase 243 spkssikhaGlPlelalaevdqtlkeeglrdrvsliadGglktgadvvkalalGAdavgigtaalialgCimarvChtnt 322
                                    +pk +++++G+P+ela++ vd++l++eg+r+r s+ia Gg++++advvka+alGAdav+igtaalia+gC+ +++C+t+ 
  gi|116753532|ref|YP_842650.1| 340 APKAIRDNVGIPIELAVSSVDRRLRDEGIRERCSIIAGGGIRCSADVVKAIALGADAVYIGTAALIAMGCTLCQRCYTGR 419
                                    ******************************************************************************** PP

                                    -TTSSS---HHHH..TT----HHHHHHHHHHHHHHHHHHHHHHT-S CS
                   Glu_synthase 323 CpvGvatqdpeLrkrlkveekaervvnyikalaeevrellaalgin 368
                                    C +G++tqdp L +rl+vee+a+r+vn++ a+++e++e+l+ +gin
  gi|116753532|ref|YP_842650.1| 420 CSWGICTQDPGLMRRLNVEEAAQRLVNLLSAWSHEIKEMLGGMGIN 465
                                    *******************************************986 PP

>> Glu_syn_central  Glutamate synthase central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   2.2e-08     2e-05      54     105 ..     116     168 ..      77     212 .. 0.81
   2 !   37.0   0.1   2.9e-12   2.6e-09     134     271 ..     307     474 ..     263     483 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 2.2e-08
                                    ----SSS----TTTTGGG-B--EEES----SSS...--GGGG-EEEESSSB--HH CS
                Glu_syn_central  54 lfAqVTNPpiDpiREelvmsletllGkegnlle...eeeeqakrlklesPiLtee 105
                                    + +qVTNP+iDp+RE   m l+t+lG++++ l+    e+ +   l+le+P+L ++
  gi|116753532|ref|YP_842650.1| 116 NASQVTNPSIDPLREP--MELRTFLGSKPESLSlsdMEAGTDPVLTLETPMLFSA 168
                                    568************6..89*********99984333334558999999999765 PP

  == domain 2  score: 37.0 bits;  conditional E-value: 2.9e-12
                                    HHHHHHHHHHHHHHHHTT-SEEEEESS........--STTEEE--HHHHHHHHHHHHHHTT-GGG-EEEEEESS--SHHH CS
                Glu_syn_central 134 eealerlceeaeeavregaeilvLsDr........kvseervpipslLavgavhhhLvrkglrtkvslvvesgearevhh 205
                                     +a++++ + a+  vr+ga+i+ ++          k+ +++v ip  Lav++v+++L ++g r ++s++   g +r   +
  gi|116753532|ref|YP_842650.1| 307 VAAVHNISAIASGIVRAGADIIAIDGMrggtgaapKAIRDNVGIPIELAVSSVDRRLRDEGIRERCSIIAG-GGIRCSAD 385
                                    578999******************9987777777667789***************************9875.669999** PP

                                    HHHHHHTT-SEEEEHHHHHHH.......HHHHTTT...............S-.....----HH..HHHHHHHHHHHHHHH CS
                Glu_syn_central 206 favllgyGadavnPylaleti.......eklveeg...............al.....aeeele..knyrkavekGllKim 256
                                    ++  +++Gadav+   a  ++       +                      +     +e++ +   n+ +a ++ +   +
  gi|116753532|ref|YP_842650.1| 386 VVKAIALGADAVYIGTAALIAmgctlcqR-----CytgrcswgictqdpgLMrrlnvEEAA-QrlVNLLSAWSHEIKEML 459
                                    ************86665555534334330.....244445554444444400444433332.2469************** PP

                                    HHTT--BHHHHHHS- CS
                Glu_syn_central 257 skmGistlqSYkgaq 271
                                      mGi  ++S +g +
  gi|116753532|ref|YP_842650.1| 460 GGMGINAIESLRGNR 474
                                    **********99964 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   6.6   2.3e-11     2e-08     131     237 ..     288     401 ..     257     409 .. 0.82
   2 ?   -4.1   0.0       6.8   6.1e+03     301     327 ..     446     472 ..     440     475 .. 0.79

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 2.3e-11
                                    HHHHHHHHHHHHTTTSEEEEEEE-SHHH.HHHHHHTT-SEEEE.-SS-STTBHHHHH.CSB---HHHHHHHHHHHHCTCT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx.xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 131 kvleavkeikkkveeveviaGnvataeg.akaLieagadavkv.GiGpGsiCttrvv.agvGvpqltAvaevaeaakkag 207
                                    + ++a+ke+ +  ++v v +  v + ++ a+ +++agad++ + G+  G     + +   vG+p   Av++v +  ++ g
  gi|116753532|ref|YP_842650.1| 288 MLISAIKEVTNYEKPVIVKVAAVHNISAiASGIVRAGADIIAIdGMRGGTGAAPKAIrDNVGIPIELAVSSVDRRLRDEG 367
                                    5567777777666555444555555554166799********999988877777766268*****************999 PP

                                    ....-EEEEES---SHHHHHHHHHTT-SEEEESC CS
                                    ....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 208 ....vpviaDGGikysgdivkAlaaGadavmlGs 237
                                          +ia GGi+ s d+vkA+a+Gadav +G 
  gi|116753532|ref|YP_842650.1| 368 irerCSIIAGGGIRCSADVVKAIALGADAVYIGT 401
                                    555568**************************97 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 6.8
                                    HHHHHHHHHHHHHHHHHT-SSHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 301 evveqlvgglrsgmgylGaktieelke 327
                                    ++++   +++++ +g +G + ie+l+ 
  gi|116753532|ref|YP_842650.1| 446 NLLSAWSHEIKEMLGGMGINAIESLRG 472
                                    566777788999999999999999986 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8  11.5   2.6e-10   2.3e-07       2      51 .]      17      63 ..      16      63 .. 0.95
   2 ?    4.9   1.6     0.032        29       2      17 ..     409     425 ..     381     442 .. 0.70

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 2.6e-10
                         Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                   C +C+aC+++C +gv+++da++ ++  +++   +C gC++C+  Cpkgai
  gi|116753532|ref|YP_842650.1| 17 CDRCRACEHQCSFGVHTYDASQDMMISDNY---RCAGCQRCAVFCPKGAI 63
                                   **************************9887...8**************97 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.032
                         Fer4_9   2 CtgCgaCvea.Cpagvv 17 
                                    Ct C++C +  C  g++
  gi|116753532|ref|YP_842650.1| 409 CTLCQRCYTGrCSWGIC 425
                                    66666664444655555 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       3.2   2.9e+03      57      91 ..     160     193 ..     159     198 .. 0.80
   2 !   27.5   8.3   1.7e-09   1.5e-06     268     308 ..     368     408 ..     285     411 .. 0.78
   3 ?    0.4   0.0      0.28   2.5e+02     313     342 ..     442     471 ..     437     476 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.2
                                    ESSSEEE--BSTGGGTSTTHHHHHHHHHHHHTS-E CS
                         FMN_dh  57 lslPvliaPvglaklahpdgelalaraaakagipf 91 
                                    l++P+l++++++  +   ++  ala aa++ g+ f
  gi|116753532|ref|YP_842650.1| 160 LETPMLFSAMSYGAISY-NAFQALAIAASRSGTFF 193
                                    67899999999988877.77778888999888876 PP

  == domain 2  score: 27.5 bits;  conditional E-value: 1.7e-09
                                    H..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHHHHHH CS
                         FMN_dh 268 vggrievlvDgGirrGsDvlkAlalGAdavllGRpflygla 308
                                    +++r+ +++ gGir  +Dv+kA+alGAdav +G ++l ++ 
  gi|116753532|ref|YP_842650.1| 368 IRERCSIIAGGGIRCSADVVKAIALGADAVYIGTAALIAMG 408
                                    3679*******************************999875 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.28
                                    HHHHHHHHHHHHHHHHHHHHHT-SBHHHHH CS
                         FMN_dh 313 eGvervleilraelertmallGvksvaeld 342
                                    +++ ++l+ +++e+++ +  +G++ +++l+
  gi|116753532|ref|YP_842650.1| 442 QRLVNLLSAWSHEIKEMLGGMGINAIESLR 471
                                    5666789999****************9986 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   4.6   7.7e-09   6.9e-06     139     232 ..     303     410 ..     287     414 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 7.7e-09
                            NMO 139 liptissvkearkve....arGaDalivqGpeaG.GhqGtpevgdkglfaLvpqvldavd...........iPviAaGGi 202
                                    +i+ +++v+++ +++    ++GaD++ ++G+ +G G  +  ++ d +    ++ +++ vd             +iA GGi
  gi|116753532|ref|YP_842650.1| 303 VIVKVAAVHNISAIAsgivRAGADIIAIDGMRGGtGAAP-KAIRD-NVGIPIELAVSSVDrrlrdegirerCSIIAGGGI 380
                                    5666777776655441111689*********98844444.44443.3334466666777778899**9************ PP

                            NMO 203 idrrgvaaaLalGAsgvqigtrfLltkesd 232
                                        +v  a+alGA +v+igt+ L++  ++
  gi|116753532|ref|YP_842650.1| 381 RCSADVVKAIALGADAVYIGTAALIAMGCT 410
                                    ************************998776 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3  13.6   6.1e-06    0.0055       1      52 []      16      62 ..      16      62 .. 0.88
   2 !   16.6   2.8     1e-05    0.0089       1      22 [.      47      68 ..      47      92 .. 0.82
   3 ?    5.0   0.7     0.041        37      30      51 ..     401     423 ..     380     424 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 6.1e-06
                         Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                   +C  C+aC+  C+ ++ ++d ++     + +  d  +C gC++C+  CP+ga
  gi|116753532|ref|YP_842650.1| 16 SCDRCRACEHQCSFGVHTYDASQ-----DMMISDNYRCAGCQRCAVFCPKGA 62
                                   5******************9983.....33556789**************98 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1e-05
                         Fer4_7  1 rCigCgaCvaaCpvkaieldee 22
                                   rC gC++C++ Cp +aie+++ 
  gi|116753532|ref|YP_842650.1| 47 RCAGCQRCAVFCPKGAIEIRPT 68
                                   7*****************9864 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.041
                         Fer4_7  30 kveidpekClgCgaCva.vCPtg 51 
                                    ++++ ++ C+ C++C + +C +g
  gi|116753532|ref|YP_842650.1| 401 TAALIAMGCTLCQRCYTgRCSWG 423
                                    55667889*******98778887 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.4     0.052        46       2      15 ..      17      30 ..       8      44 .. 0.78
   2 !   21.5   0.6   3.8e-07   0.00034       1      57 [.      47     100 ..      47     102 .. 0.60
   3 ?    0.3   1.0       1.6   1.4e+03       2       8 ..     409     415 ..     395     423 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.052
                        Fer4_16  2 CgtCgkCaevCPtn 15
                                   C +C++C   C  +
  gi|116753532|ref|YP_842650.1| 17 CDRCRACEHQCSFG 30
                                   88888888888655 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 3.8e-07
                        Fer4_16   1 rCgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgC 57 
                                    rC +C++Ca  CP +ai+ +  +++  r + s++ +  +d++ ++e+   +  +tgC
  gi|116753532|ref|YP_842650.1|  47 RCAGCQRCAVFCPKGAIEIRPTPSFY-RPNASWSRERIEDIKRQAETG--GVILTGC 100
                                    6*****************99777765.444455333333333333322..2333666 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 1.6
                        Fer4_16   2 CgtCgkC 8  
                                    C+ C++C
  gi|116753532|ref|YP_842650.1| 409 CTLCQRC 415
                                    4444444 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.87   7.8e+02     181     210 ..     302     331 ..     290     343 .. 0.79
   2 !   17.5   0.1   2.5e-06    0.0022      74     106 ..     372     404 ..     361     413 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.87
                                    HHHHHHHHHHSSEEEEESS--SHHHHHHHH CS
                   His_biosynth 181 eltkelaeavkipviasGGvgsledlkelk 210
                                    +++ ++a+  +i+ iasG v+  +d+ +++
  gi|116753532|ref|YP_842650.1| 302 PVIVKVAAVHNISAIASGIVRAGADIIAID 331
                                    456788888899999999999998888776 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 2.5e-06
                                    SEEEEESSSSSHHHHHHHHHCT-SEEEESHHHH CS
                   His_biosynth  74 ipvqvGGGIrsledveelleagadkviigtaav 106
                                    + +  GGGIr   dv +++ +gad v igtaa+
  gi|116753532|ref|YP_842650.1| 372 CSIIAGGGIRCSADVVKAIALGADAVYIGTAAL 404
                                    67899*************************997 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   1.3    0.0027       2.4       6      21 ..      15      30 ..      13      31 .. 0.86
   2 !   18.7   2.5   1.2e-06    0.0011       4      24 .]      44      64 ..      41      64 .. 0.91
   3 ?    0.7   1.3      0.57   5.1e+02       8      15 ..     409     416 ..     405     417 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0027
                                   TTSSS-THHHHHSTTT CS
                           Fer4  6 ekCigCGaCvevCPvg 21
                                   + C +C aC+  C +g
  gi|116753532|ref|YP_842650.1| 15 DSCDRCRACEHQCSFG 30
                                   89*********99665 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 1.2e-06
                                   ETTTSSS-THHHHHSTTTEEE CS
                           Fer4  4 deekCigCGaCvevCPvgAIt 24
                                   d  +C gC +C+  CP gAI+
  gi|116753532|ref|YP_842650.1| 44 DNYRCAGCQRCAVFCPKGAIE 64
                                   6779****************6 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.57
                                    SSS-THHH CS
                           Fer4   8 CigCGaCv 15 
                                    C+ C +C+
  gi|116753532|ref|YP_842650.1| 409 CTLCQRCY 416
                                    99**9997 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5  13.8    0.0012       1.1       4      56 .]      12      59 ..       9      59 .. 0.80
   2 !   14.8   1.5   2.5e-05     0.023       2      24 ..      41      79 ..      40     102 .. 0.68
   3 ?    4.9   0.5     0.033        29       8      19 ..     408     420 ..     402     456 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0012
                        Fer4_10  4 idddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                     +d+C rC++C   C +     + ++ as++ ++++  ++C gc  C+  CP
  gi|116753532|ref|YP_842650.1| 12 SRSDSCDRCRACEHQCSF----GVHTYDASQDMMISD-NYRCAGCQRCAVFCP 59
                                   5679************44....666666666666666.779***********9 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 2.5e-05
                        Fer4_10  2 vvidddtCirCgkCvkaCPadl................t 24
                                   ++ d  +C +C++C  +CP  +                +
  gi|116753532|ref|YP_842650.1| 41 MISDNYRCAGCQRCAVFCPKGAieirptpsfyrpnaswS 79
                                   7789999************96666666666666555553 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.033
                        Fer4_10   8 tCirCgkCvka.C 19 
                                     C+ C++C +  C
  gi|116753532|ref|YP_842650.1| 408 GCTLCQRCYTGrC 420
                                    5999999998658 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   8.8     1e-05    0.0092       6      58 ..      15      64 ..      11      65 .. 0.69
   2 ?    1.5   2.8      0.38   3.4e+02      17      47 ..     381     415 ..     370     420 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1e-05
                        Fer4_21  6 dkCigCgkCliaCedtshqaieidaktvlkv.vedeCvGCnlCssvCPvedcie 58
                                   d+C  C  C   C+ + +   ++da++ + +  + +C GC+ C+  CP +++ie
  gi|116753532|ref|YP_842650.1| 15 DSCDRCRACEHQCSFG-VH--TYDASQDMMIsDNYRCAGCQRCAVFCP-KGAIE 64
                                   6677777777777743.33..455555444415779************.79997 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.38
                        Fer4_21  17 aCedtshqaieidaktvl....kvvedeCvGCnlC 47 
                                     C+   ++ai + a++v+    ++++  C+ C+ C
  gi|116753532|ref|YP_842650.1| 381 RCSADVVKAIALGADAVYigtaALIAMGCTLCQRC 415
                                    68888888887766654422224455555555555 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 ?    0.5   0.1       0.4   3.5e+02     130     156 ..     303     329 ..     283     334 .. 0.80
   2 ?   10.8   0.1   0.00027      0.24     139     171 ..     371     403 ..     352     405 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.4
                                    HHCTSTTS...EEEEESS--SHHHHHH CS
                   G3P_antiterm 130 vikeikkelkipiiaGGLietkedvee 156
                                    vi ++    +i  ia+G+++   d+ +
  gi|116753532|ref|YP_842650.1| 303 VIVKVAAVHNISAIASGIVRAGADIIA 329
                                    667777788889999999988888765 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00027
                                    ..EEEEESS--SHHHHHHHCTT.SSEEEE--HH CS
                   G3P_antiterm 139 kipiiaGGLietkedveealkaGaiavstsnke 171
                                    ++ iiaGG i+ + dv +a++ Ga+av  ++ +
  gi|116753532|ref|YP_842650.1| 371 RCSIIAGGGIRCSADVVKAIALGADAVYIGTAA 403
                                    799************************877665 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   5.6   0.00026      0.23     240     284 ..     367     412 ..     278     418 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00026
                                    HTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHH.HHHHGTCHH CS
                         DHO_dh 240 rlkkeipiIgvGGiesgeDalekieaGAslvqvyta.lvfegpkia 284
                                     ++++  iI+ GGi  + D++  i  GA +v ++ta l+  g +++
  gi|116753532|ref|YP_842650.1| 367 GIRERCSIIAGGGIRCSADVVKAIALGADAVYIGTAaLIAMGCTLC 412
                                    4677899****************************72445555555 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.4   0.00018      0.16       7      23 ..      15      31 ..      11      32 .. 0.91
   2 ?   10.5   3.0   0.00055       0.5       8      24 .]      47      63 ..      43      63 .. 0.91
   3 ?    0.2   2.3         1   9.1e+02       9      19 ..     409     420 ..     409     424 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00018
                         Fer4_6  7 dkCigCgdCvrvCPega 23
                                   d+C+ C++C+  C +g+
  gi|116753532|ref|YP_842650.1| 15 DSCDRCRACEHQCSFGV 31
                                   99***********9986 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00055
                         Fer4_6  8 kCigCgdCvrvCPegai 24
                                   +C gC +C++ CP gai
  gi|116753532|ref|YP_842650.1| 47 RCAGCQRCAVFCPKGAI 63
                                   8**************98 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 1
                         Fer4_6   9 CigCgdCvrv.C 19 
                                    C+ C +C++  C
  gi|116753532|ref|YP_842650.1| 409 CTLCQRCYTGrC 420
                                    99*****98655 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4  13.9    0.0033       2.9       3      64 ..      15      61 ..      13      62 .. 0.83
   2 ?    4.3   0.6     0.064        57      49      58 ..     407     416 ..     381     456 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0033
                         Fer4_8  3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                                   ++C +C aC+++C     ++ h +da ++ +     +++       ++C +c++C++ Cp+g
  gi|116753532|ref|YP_842650.1| 15 DSCDRCRACEHQCS----FGVHTYDASQDMMI----SDN-------YRCAGCQRCAVFCPKG 61
                                   68***********4....55666777777666....667.......9*************97 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.064
                         Fer4_8  49 wsCttcgaCt 58 
                                      Ct c++C 
  gi|116753532|ref|YP_842650.1| 407 MGCTLCQRCY 416
                                    4566666663 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.2    0.0047       4.2      26      74 ..     264     316 ..     250     321 .. 0.76
   2 ?    0.6   0.1      0.37   3.3e+02      24      69 ..     318     360 ..     313     366 .. 0.83
   3 ?    5.6   0.8     0.011       9.5     181     210 ..     372     402 ..     367     406 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0047
                                    HHCTT-SEEEEECST....CHHHHHHHHHHHHHCTSSS-EEEEESSGGG--TT CS
                           PcrB  26 viesgtDavmigGsq....svtldntvrllkkvsriklPivlepsnvegvvry 74 
                                    +i +gtDa+  +  +    + +l+  + ++k+v++++ P+++ +++v++++  
  gi|116753532|ref|YP_842650.1| 264 MIPEGTDAISPAPHHdiysIEDLEMLISAIKEVTNYEKPVIVKVAAVHNISAI 316
                                    46778888877666554434567788899********************9975 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.37
                                    HHHHCTT-SEEEEECSTCHHHHHHHHHHHHHCTSSS-EEEEESSGG CS
                           PcrB  24 eiviesgtDavmigGsqsvtldntvrllkkvsriklPivlepsnve 69 
                                      +++ g+D + i G  + t   + ++++++  +++Pi l +s v+
  gi|116753532|ref|YP_842650.1| 318 SGIVRAGADIIAIDGMRGGT-GAAPKAIRDN--VGIPIELAVSSVD 360
                                    556799*********99776.5788999999..9****99999887 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.011
                                    SEEEEESS--SHHHHHHHHCC.SSEEEE-CH CS
                           PcrB 181 arlivGGGirsaEkAkevvea.ADvivvGnv 210
                                      +i GGGir + +  + +   AD++ +G++
  gi|116753532|ref|YP_842650.1| 372 CSIIAGGGIRCSADVVKAIALgADAVYIGTA 402
                                    679*******777766666666******986 PP

>> zf_PR_Knuckle  PR zinc knuckle motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   1.8     0.001      0.93       9      24 ..     405     420 ..     401     423 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.001
                  zf_PR_Knuckle   9 fsiWCtLCeksYpSdC 24 
                                     ++ CtLC++ Y+  C
  gi|116753532|ref|YP_842650.1| 405 IAMGCTLCQRCYTGRC 420
                                    5667*********999 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  14.5     0.088        79       2      59 ..      17      61 ..      16      63 .. 0.84
   2 ?    4.7   0.6     0.049        44      43      56 ..     406     420 ..     381     452 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.088
                        Fer4_17  2 CiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPqg 59
                                   C +C++C+ +C+++  + +  + ++                  +C++C++C+  CP+g
  gi|116753532|ref|YP_842650.1| 17 CDRCRACEHQCSFGVHTYDASQDMMIS-------------DNYRCAGCQRCAVFCPKG 61
                                   99***********99988877776666.............2369************86 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.049
                        Fer4_17  43 aslCieCgeCe.rkC 56 
                                    a  C+ C++C   +C
  gi|116753532|ref|YP_842650.1| 406 AMGCTLCQRCYtGRC 420
                                    566777777765555 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   4.8    0.0052       4.6       1      17 []      14      30 ..      14      30 .. 0.90
   2 ?   11.9   2.6   0.00028      0.25       3      16 ..      47      60 ..      45      68 .. 0.93
   3 ?   -1.6   5.4       6.1   5.5e+03       4      12 ..     409     417 ..     406     427 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0052
                         Fer4_4  1 qerCigCgsCvaaCPqg 17
                                   +++C +C++C+  C++g
  gi|116753532|ref|YP_842650.1| 14 SDSCDRCRACEHQCSFG 30
                                   599***********875 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00028
                         Fer4_4  3 rCigCgsCvaaCPq 16
                                   rC gC +C  +CP 
  gi|116753532|ref|YP_842650.1| 47 RCAGCQRCAVFCPK 60
                                   8************6 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 6.1
                         Fer4_4   4 CigCgsCva 12 
                                    C+ C +C+ 
  gi|116753532|ref|YP_842650.1| 409 CTLCQRCYT 417
                                    999****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (497 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); 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):              20  [number of targets reported over threshold]
# CPU time: 0.58u 0.24s 00:00:00.82 Elapsed: 00:00:00.39
# Mc/sec: 3775.31
//
Query:       gi|116753533|ref|YP_842651.1|  [L=378]
Description: glutamine amidotransferase, class-II [Methanosaeta thermophila PT]
Scores for complete 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   52.7   0.1      7e-12   44.8   0.0    2.5  2  GATase_2  Glutamine amidotransferases class-II
    1.7e-08   34.7   0.0    7.3e-07   29.5   0.0    2.2  1  GATase_6  Glutamine amidotransferase domain
    6.4e-07   29.3   0.0     0.0046   16.9   0.0    2.3  2  GATase_7  Glutamine amidotransferase domain


Domain annotation for each model (and alignments):
>> GATase_2  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1      0.19   1.1e+03      16      33 ..      29      46 ..      14      49 .. 0.73
   2 !   44.8   0.0   1.2e-15     7e-12      73     371 ..      66     341 ..      53     351 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.19
                                   HHHHHHHHHHHHGGGGS- CS
                       GATase_2 16 kivekalealenleHRGa 33
                                      e+ ++a++n++HRG 
  gi|116753533|ref|YP_842651.1| 29 FTGERVIRAMANMHHRGN 46
                                   555778999*******95 PP

  == domain 2  score: 44.8 bits;  conditional E-value: 1.2e-15
                                    EEEEEEE-SSHHHHHHHHHHHHHHHHHTT-EEEEEEE--B-GGGS-HHHHHH--EEEEEEEE-TT---HHHHHHHHHHHH CS
                       GATase_2  73 avgmlflpkdeekaeeakkileeiveeeglevlgwRevpvdksvlgeaakesePsieqvfvekkedlseeelerklyviR 152
                                    a   +f   d+++++eak++ ee +  ++++v+   e+p  ++v      +  P + + f++ +++ ++ +l  + yv+R
  gi|116753533|ref|YP_842651.1|  66 AFHLMFT-GDARAQREAKRAAEEFL-FRNFDVVHDEEIPHSDDVY----VRDPPLLWRYFLSPSKHGEDIHLPDDEYVVR 139
                                    4444444.55555566666665554.4567888888888877765....4567999999**9999999999********* PP

                                    HHHGGG.....-BTTBEEEEEESSEEEEEESS-GGGHHHHBHGGGSTT--BSEEEEEE---SSSS--GGGSSS-SSE... CS
                       GATase_2 153 kriekeiakkkaekefYicslssrtivYkglltseqlkefykdlkdeelesalalvHsRfstntfPsWelaqPlRll... 229
                                    k ++ + a     ++ Yi s  ++   +kg+  +e++++++  + d+ ++ +l   H Rf tn    W  a+P+ ll   
  gi|116753533|ref|YP_842651.1| 140 KVVHVNSA----IDNAYIFSSGKNMGCFKGVGYPEEIGRYF--MLDRLYRGYLWTAHGRFPTNSQAWWGGAHPFGLLdtt 213
                                    *9998865....6899*************************..5899***************************764332 PP

                                    .EEEE--TTHHHHHHHHHHHCTT--BT-HH.HHHTC--S--TTS-HHHHHHHHHHHHHHTT.--HHHHHHHHS----TT- CS
                       GATase_2 230 .aHnGEintlrGnknwmkareaelksellgdelekllPivneegsDsasldnvlellvlsg.rslaealmlliPeawenn 307
                                      HnGEi    G ++w          e+lg +         + + D++ +  +++ll++     ++  + +l P++we+ 
  gi|116753533|ref|YP_842651.1| 214 vVHNGEISSY-GTNRWYL--------EMLGYK--------CTLHTDTEVVAYAVDLLMRRQdLPMEVVAKILAPPTWETI 276
                                    28*****986.5555642........233311........22357999999*****9998724555566899******** PP

                                    GGGTHHHHHHHHHHTTT---..--SS.EEEEEE-SSEEEEEE-TT--S--EEEEETT--EEEESSTT CS
                       GATase_2 308 ksldkekkafyeyasalmep..WDGP.alivftdGkvvgavLDRnGLRPaRylvtkddlvvlasEvG 371
                                    +++d + +++      +  p   +GP a+i+ + G+++g + DR  LRP   + t+ ++++++sE  
  gi|116753533|ref|YP_842651.1| 277 DRMDVRERELLTTLRRIYGPllMNGPfAVIIAQSGRMIGLT-DRIRLRPLT-VATRGEMFYISSEEA 341
                                    *****9999999999999984459**445556779999965.*******86.678888888888764 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0   1.2e-10   7.3e-07       8      89 ..     180     264 ..     174     339 .. 0.80

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 1.2e-10
                       GATase_6   8 slvedevalaHvRlaivglaeeegaqPfpsedgrlllvhNGeiynykelreelpalkglafrsrsDtevllall...... 81 
                                    +l+++ ++ aH R  ++  a   ga+Pf       ++vhNGei+ y++ r  l+   g+++  ++Dtev++ ++      
  gi|116753533|ref|YP_842651.1| 180 RLYRGYLWTAHGRFPTNSQAWWGGAHPF--GLLDTTVVHNGEISSYGTNRWYLEM-LGYKCTLHTDTEVVAYAVdllmrr 256
                                    5667778899**********99999***..888899***********88888888.****************98777777 PP

                       GATase_6  82 eelGeevl 89 
                                    ++l+ ev+
  gi|116753533|ref|YP_842651.1| 257 QDLPMEVV 264
                                    66665555 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   7.7e-07    0.0046      24      63 ..     212     251 ..     201     267 .. 0.87
   2 !   10.0   0.0    0.0001       0.6      74     119 ..     299     341 ..     294     344 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 7.7e-07
                       GATase_7  24 lvivfnGeiyNykelreeLeakghrfrtksDtevllalle 63 
                                     ++v+nGei  y   r  Le  g++++ ++Dtev++ +++
  gi|116753533|ref|YP_842651.1| 212 TTVVHNGEISSYGTNRWYLEMLGYKCTLHTDTEVVAYAVD 251
                                    689*******************************977765 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0001
                       GATase_7  74 lnGmfAfaiwdeeekrlllaRDrlGikPLyygedkgdallfaSelk 119
                                    +nG fA++i ++ +  ++   Dr+  +PL ++++ g+ ++++Se  
  gi|116753533|ref|YP_842651.1| 299 MNGPFAVIIAQSGR--MIGLTDRIRLRPLTVATR-GEMFYISSEEA 341
                                    69999999988877..******************.89******965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2621.37
//
Query:       gi|116753534|ref|YP_842652.1|  [L=102]
Description: hypothetical protein Mthe_0214 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-27   95.6   0.1    3.1e-27   95.4   0.1    1.0  1  DUF5611   Domain of unknown function (DUF5611)


Domain annotation for each model (and alignments):
>> DUF5611  Domain of unknown function (DUF5611)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.4   0.1   1.7e-31   3.1e-27       3     103 .]       2      97 ..       1      97 [. 0.97

  Alignments for each domain:
  == domain 1  score: 95.4 bits;  conditional E-value: 1.7e-31
                                    EE---SSS--SH.HHHHHHHHHHT.-EEEEETTEEEEE-TTBS-EEEEE..-SS-EEEEE--.B...-TTS-HHHHHHHH CS
                        DUF5611   3 eYkiKrGfkkeeeerlkelleeyfggeveeegdllvvsfgaikklevkisskkkklvvdteerdaeeeddeaaldtvkkf 82 
                                    eY++KrG+ ++  +r++ +l+e+f   ++++gd ++ s+ga+k+ +++i  +kkkl v te+     + d++++dt+++f
  gi|116753534|ref|YP_842652.1|   2 EYTFKRGYAPDM-DRIEGILKEVFSSGFTRNGDRITLSYGALKSCQIWI--EKKKLNVITES--LLGAPDDVIMDTNRRF 76 
                                    9***********.************************************..***********..4569************ PP

                                    HHHHHHHH---GGGHHHHH-- CS
                        DUF5611  83 ndFLeeaTGydaKeRkkkakk 103
                                    ++FLe+aTGy+aK+R+++akk
  gi|116753534|ref|YP_842652.1|  77 RKFLEKATGYTAKQRVQMAKK 97 
                                    *******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 777.04
//
Query:       gi|116753535|ref|YP_842653.1|  [L=168]
Description: hypothetical protein Mthe_0215 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.3   11.3   1.2       0.49   10.6   1.2    1.3  1  DUF3270   Protein of unknown function (DUF3270)


Domain annotation for each model (and alignments):
>> DUF3270  Protein of unknown function (DUF3270)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.2   2.7e-05      0.49      48      65 ..      18      35 ..      16      53 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 2.7e-05
                        DUF3270 48 Fsvitvlvsfillalkla 65
                                   F++++vlv+f+l+a  l+
  gi|116753535|ref|YP_842653.1| 18 FCILIVLVAFVLVASLLT 35
                                   ************997544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       893  (0.0498076); expected 358.6 (0.02)
Passed bias filter:                      619  (0.0345251); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1221.61
//
Query:       gi|116753536|ref|YP_842654.1|  [L=558]
Description: arginyl-tRNA synthetase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-37  127.9   0.2    5.5e-37  127.5   0.2    1.1  1  tRNA-synt_1d     tRNA synthetases class I (R)
    1.2e-30  106.2   0.2    1.5e-29  102.5   0.1    2.5  2  DALR_1           DALR anticodon binding domain
    2.1e-08   34.6   0.0      5e-08   33.4   0.0    1.7  1  Arg_tRNA_synt_N  Arginyl tRNA synthetase N terminal domain
      1e-07   31.2   0.0     0.0018   17.3   0.0    2.2  2  tRNA-synt_1f     tRNA synthetases class I (K)
    9.9e-05   21.2   0.1      0.089   11.5   0.1    2.6  3  tRNA-synt_1g     tRNA synthetases class I (M)
     0.0045   16.4   0.1      0.013   14.8   0.0    1.9  2  tRNA-synt_1e     tRNA synthetases class I (C) catalytic domai
     0.0089   14.3   0.1      0.014   13.7   0.1    1.2  1  tRNA-synt_1      tRNA synthetases class I (I, L, M and V)
  ------ inclusion threshold ------
      0.041   13.6   0.0        2.1    8.0   0.0    2.4  2  MAGE             MAGE family
       0.11   11.9   0.0       0.18   11.1   0.0    1.2  1  MCR_alpha_N      Methyl-coenzyme M reductase alpha subunit, N


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 !  127.5   0.2   2.7e-40   5.5e-37      19     341 ..     109     422 ..      93     430 .. 0.89

  Alignments for each domain:
  == domain 1  score: 127.5 bits;  conditional E-value: 2.7e-40
                                    T-EEEEE----BTTS--BHHHHHHHHHHHHHHHHHHHCT-EEEEEE--B-SSTCHHHHHHHHHHHTTTTTTS-----SCC CS
                   tRNA-synt_1d  19 kkkvvvdfssPniakemhvGhLrstiiGdavsrlleflGydvirlnhvGDWGtqfGlLiaylekkqdekllqeqelqdLe 98 
                                       vvv+++s n   ++hvGh+r  +iGd+++r+l  +Gy+v    +v D G+q  +++ + ++   +    +++   + 
  gi|116753536|ref|YP_842654.1| 109 SGSVVVEHTSANPDGPLHVGHIRNSVIGDTIVRILRRAGYNVEAQYYVNDMGRQTAMVVWGCDHLDLDD---SKPDHAIA 185
                                    557*******************************************************99999988887...45777788 PP

                                    CHHHHHHHHCCCSHCCCHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHCT---EC.--CC..CCCCCHHHHHH CS
                   tRNA-synt_1d  99 afykeakkdydeeeifaerarnyvvkLqsgdedirklwkllvditrtelqklydrldvtlie.rGes..lykeslneivk 175
                                     +y  a+k ++e  +++ +  + + + +s+d++i k +++   ++    +++  r+++     + es  +++ s++ei++
  gi|116753536|ref|YP_842654.1| 186 RVYIAAHKIMNEKPELSAEVDELMRRYESRDPEIVKKFQRAARYAISGIERTLHRMNIHHDSyKWESefVWDGSVDEILE 265
                                    9********************************9999999999999999*********9866755665599********* PP

                                    HHHCTT-EEECTTCEEEEECCCTSSCCEECC-TTS-B-HHHHHHHHHHHHHHTT--SEEEEEEECCCHHHHHHHHHHHHC CS
                   tRNA-synt_1d 176 elkkkglvkesdGalvvfldefgkrlgvvvqksDGgylytttDiaaakerkeelkadkvlyvidsrqslhlqqiflilkk 255
                                     l++ g  + +dGal ++l+e g + ++v+++ DG++lytt+D+a  k   + ++ ++v+ v+ +  +l   q+  +l++
  gi|116753536|ref|YP_842654.1| 266 MLERTGRTVLKDGALQLDLSEEGFEKSLVLRRADGTTLYTTRDLAYHKW--KAENYERVVEVLGADHKLISAQLRTALRM 343
                                    ********************************************97765..566789*********************** PP

                                    TT.SSTTTSEEEEEEE--EE-TTSSBSBCSSSTC-BHHHHHHHHHHHHHHHHCCCCCCTS-CCCCHCHHHHHHHHHHHHC CS
                   tRNA-synt_1d 256 ig.yvpeskdlehanfGmvlgkdkkkfktrkGetvkLadlLdealeralqlikeknkdkvlqadelekvaeavgvgaiky 334
                                    +g  +pe++  e      v   d  +++tr+G+ +  ++lLde  ++a   ++ + ++  +  + +  va  v+vga++y
  gi|116753536|ref|YP_842654.1| 344 LGiGEPEVVIFE-----FVSLPD-GSMSTRRGKFISADELLDEVEKQAYLEVTKRRPE--MDEEFRRDVAGKVAVGAVRY 415
                                    **4466665444.....332244.58************************99999999..9999999************9 PP

                                    CCCTS-T CS
                   tRNA-synt_1d 335 aDlsknr 341
                                      ++   
  gi|116753536|ref|YP_842654.1| 416 DIVRVSA 422
                                    7665544 PP

>> DALR_1  DALR anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.28   5.6e+02     100     117 ..     333     350 ..     330     352 .. 0.82
   2 !  102.5   0.1   7.8e-33   1.5e-29       1     119 []     444     558 .]     444     558 .] 0.95

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.28
                                    HHHHHHHHHHHTT----S CS
                         DALR_1 100 vrqvLangLdlLGieape 117
                                    ++  L+++L++LGi  pe
  gi|116753536|ref|YP_842654.1| 333 ISAQLRTALRMLGIGEPE 350
                                    55689*********8887 PP

  == domain 2  score: 102.5 bits;  conditional E-value: 7.8e-33
                                    HHHHHHHHHHHHHHTTCTTCCCCHCCHCCS-SHHHHHHHHHHHTHHHHHHHHHHHT-THHHHHHHHHHHHHHHHHHHHCT CS
                         DALR_1   1 vqyahaRiksilrkaeeegekleeealalleeeeekeLlkalaqfpevleeaaeelephklaeylyeLaatfhkfYnker 80 
                                    +qy+haR++si +ka+e +e    +  + l ++ e++L+k++a+f  v+e+aa+el+ph+la+y+ eLa+ f+ fY+  +
  gi|116753536|ref|YP_842654.1| 444 IQYSHARACSIINKAGELDE---FDPGL-LRDDYEIALIKKIAEFDLVIERAARELKPHQLATYARELAERFNLFYRYDP 519
                                    7***************9884...33444.599************************************************ PP

                                    STTSCTHHH.HHHHHHHHHHHHHHHHHHHHTT----S-- CS
                         DALR_1  81 vlkeeeeelaaaRLaLvkavrqvLangLdlLGieapekm 119
                                    vl+++  el++aRL Lv+a r+ L+ +Ld LGi+ape m
  gi|116753536|ref|YP_842654.1| 520 VLDAKPVELRNARLGLVRASRNALSATLDTLGIDAPESM 558
                                    *************************************99 PP

>> Arg_tRNA_synt_N  Arginyl tRNA synthetase N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.0   2.5e-11     5e-08      32      84 ..      33      85 ..       7      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 2.5e-11
                                   GGG-SEEEEGGGG--TT-..-HHHHHHHHHHT---TTT.EEEEEEETT.EEEEE CS
                Arg_tRNA_synt_N 32 pkfGDyatnvamqlakklkknPreiAeeiaekleksei.iekvevagpGFiNff 84
                                   + ++D++t +a++l+  l+k P+++A+ei + + ++   ++++e +gp +iNf+
  gi|116753536|ref|YP_842654.1| 33 SPHADLSTTIAFRLSPVLRKDPKDVAAEIYNSMGSPSRwVDRAELVGP-YINFY 85
                                   569*********************************99**********.****7 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.1   4.5e-05      0.09      25      71 ..     112     159 ..      92     163 .. 0.86
   2 !   17.3   0.0   9.1e-07    0.0018     229     319 ..     313     400 ..     275     409 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.5e-05
                   tRNA-synt_1f  25 vvve.sGispSGliHiGnlrevltadlvaralrkrgeevrlilisDdm 71 
                                    vvve + + p G++H+G +r+ + +d ++r lr+ g +v+  ++++dm
  gi|116753536|ref|YP_842654.1| 112 VVVEhTSANPDGPLHVGHIRNSVIGDTIVRILRRAGYNVEAQYYVNDM 159
                                    444337889*******************************99999998 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 9.1e-07
                   tRNA-synt_1f 229 rWaalgV..dfEpaGkDhaaaGgSvdvsskia.eilggeaPekvvYelillkggekmssSkGnvltledwlevaepevlr 305
                                    +W+a++   ++E  G Dh     S+  + + a ++lg+ +Pe v++e+++l  g  ms  +G++++ +++l+ +e++   
  gi|116753536|ref|YP_842654.1| 313 KWKAENYerVVEVLGADHKL--ISA--QLRTAlRMLGIGEPEVVIFEFVSLPDG-SMSTRRGKFISADELLDEVEKQAYL 387
                                    67776652258********9..444..4455559******************99.9***************988887533 PP

                   tRNA-synt_1f 306 flilrrkPkkakkl 319
                                      + +r+P+   ++
  gi|116753536|ref|YP_842654.1| 388 E-VTKRRPEMDEEF 400
                                    2.344466666555 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 !   11.5   0.1   4.5e-05     0.089      10      39 ..     121     150 ..     112     168 .. 0.90
   2 ?   -1.8   0.0       0.5     1e+03      73     112 ..     233     272 ..     177     288 .. 0.82
   3 !    6.8   0.0    0.0012       2.5     276     349 ..     314     385 ..     301     407 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.5e-05
                                    -SS---HHHHHHHHHHHHHHHHHHHTT-EE CS
                   tRNA-synt_1g  10 angklHlGhllevisaDifaRykrlrgeev 39 
                                    ++g+lH+Gh+++ +++D ++R  r  g++v
  gi|116753536|ref|YP_842654.1| 121 PDGPLHVGHIRNSVIGDTIVRILRRAGYNV 150
                                    5799***********************997 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.5
                                    HHHHHHHHTT---SEEEETTSHHHHHHHHHHHHHHHHTT- CS
                   tRNA-synt_1g  73 eikelfkklnisfdkygrttseehkelvqeifkklkekgl 112
                                     i+++++++ni++d+y+  ++      v ei++ l++ g 
  gi|116753536|ref|YP_842654.1| 233 GIERTLHRMNIHHDSYKWESEFVWDGSVDEILEMLERTGR 272
                                    4678888999999999888888888888888888877775 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0012
                                    --S......EEEEEGGGHHHHHTHHHHHHHHTT----S-EEEE--EEE--------------HHHHHHHH-HHH CS
                   tRNA-synt_1g 276 WakdkevelvhfigkdiikFHtifwPaillgaelklpkkvvaheyltvegkKlSkSrgvvvkakealerldadl 349
                                    W++++  ++v+++g d     + + +a+ +  ++  p +vv  e++ + ++ +S+ rg ++ a+e+l+++++++
  gi|116753536|ref|YP_842654.1| 314 WKAENYERVVEVLGADHKLISAQLRTALRM-LGIGEP-EVVIFEFVSLPDGSMSTRRGKFISADELLDEVEKQA 385
                                    336666777777777744444443333322.455555.57789*************************988765 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 !   14.8   0.0   6.6e-06     0.013      23      55 ..     125     157 ..     119     292 .. 0.86
   2 ?   -2.5   0.0       1.2   2.5e+03      44      71 ..     471     497 ..     465     518 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6.6e-06
                                    -BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB CS
                   tRNA-synt_1e  23 shlGhaRslvafDilrrilqalgYdvqfvqnvt 55 
                                     h+Gh R+ v+ D + ril+ +gY+v+    v 
  gi|116753536|ref|YP_842654.1| 125 LHVGHIRNSVIGDTIVRILRRAGYNVEAQYYVN 157
                                    6*************************7544444 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.2
                                    TT-EEEEEEEBB--SHHHHHHHHHTTS- CS
                   tRNA-synt_1e  44 lgYdvqfvqnvtDidDkiikrareeeks 71 
                                     +Y++++++ + + d  +i+ra++e k 
  gi|116753536|ref|YP_842654.1| 471 DDYEIALIKKIAEFD-LVIERAARELKP 497
                                    5799999**999986.577777665443 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 !   13.7   0.1   7.1e-06     0.014      33      70 ..     120     157 ..     109     169 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.1e-06
                    tRNA-synt_1  33 yvtGslHiGhalaktlkdivirykrmkGkevlyvpGwD 70 
                                    +  G lH+Gh+ ++++ d+++r+ r  G++v+ +  + 
  gi|116753536|ref|YP_842654.1| 120 NPDGPLHVGHIRNSVIGDTIVRILRRAGYNVEAQYYVN 157
                                    56799**************************9876555 PP

>> MAGE  MAGE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.04        79     144     180 ..     234     271 ..     229     272 .. 0.80
   2 ?    8.0   0.0    0.0011       2.1     138     193 ..     331     397 ..     324     407 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.04
                           MAGE 144 LekyLkrlgldenst..skeitklklkldelLkklvkqg 180
                                    +e+ L+r++++++s   +  +   ++++de+L++l++ g
  gi|116753536|ref|YP_842654.1| 234 IERTLHRMNIHHDSYkwES-EFVWDGSVDEILEMLERTG 271
                                    5799*********874322.345789*********9975 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0011
                           MAGE 138 siseqeLekyLkrlgldenst............skeitklklkldelLkklvkqgYlvrekeskasde 193
                                    ++   +L++ L++lg+ e ++              +    ++++delL++ +kq Yl+ +k +  +++
  gi|116753536|ref|YP_842654.1| 331 KLISAQLRTALRMLGIGEPEVvifefvslpdgsMSTRRGKFISADELLDEVEKQAYLEVTKRR-PEMD 397
                                    556678999999999988866899999998887444677899****************99983.3333 PP

>> MCR_alpha_N  Methyl-coenzyme M reductase alpha subunit, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   8.9e-05      0.18     168     229 ..     371     431 ..     365     451 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.9e-05
                                    EES-HHHHTTS-GGGB--HHHHS-HHHHHHHHHHH-S-EEEEEE--HHHHHHS-HHHHHHHH CS
                    MCR_alpha_N 168 ftGddeladeidkqflidinkefpeeqaeqlkkaiGkklyqvvriPtivsrtcdGgttsrws 229
                                    f   del de++kq  +++ k+ pe   e  ++  Gk    +vr   iv  ++d +tt  w+
  gi|116753536|ref|YP_842654.1| 371 FISADELLDEVEKQAYLEVTKRRPEMDEEFRRDVAGKVAVGAVRY-DIVRVSADKATTFDWK 431
                                    55679**********************999999999999999997.5888899999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (558 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 3801.52
//
Query:       gi|116753537|ref|YP_842655.1|  [L=397]
Description: hypothetical protein Mthe_0217 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.1e-12   45.7   0.1    1.5e-11   44.4   0.1    1.6  1  DUF4139   Domain of unknown function (DUF4139)
    0.00038   20.6   0.7    0.00077   19.6   0.7    1.5  1  Top6b_C   Type 2 DNA topoisomerase 6 subunit B C-terminal dom
     0.0051   16.7   4.1      0.011   15.6   0.5    2.5  3  DUF4897   Domain of unknown function (DUF4897)


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 !   44.4   0.1   2.5e-15   1.5e-11       3     204 ..     112     389 ..     110     391 .. 0.82

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 2.5e-15
                                    xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxx...... RF
                        DUF4139   3 vsyvvseag.WsPlYdlrldtakeevqltykAkvyQktgeDWknvnLtLstakpnrg..gsppelspwylrvvn...... 73 
                                    +sy+v++ g W P Y ++l ++   + lt++A ++    eD knv++ L  a p+r+   +     p  ++ ++      
  gi|116753537|ref|YP_842655.1| 112 LSYLVRNGGyWAPNYYMHLLNDS--MLLTANALINVDLKEDLKNVQIRLV-AMPEREipIMMRAPAPTAAKAEElsvydi 188
                                    7888887654*********9988..9***********************9.6666652333333333344443378888* PP

                                    ..........................................................xxxxxxxxxxxxxxxxxxxxxx RF
                        DUF4139  74 ..........................................................evteggtsvtfeipkkvsipsd 95 
                                                                                              e+ +++t+     +++v++  d
  gi|116753537|ref|YP_842655.1| 189 aagaptgeletlfvfvlenrtdlvagksiglplfedlapawrvytwdayynpdgpaneEIRANNTADHPWPNGNVQVFRD 268
                                    *****999999999999999999999999999999999999999999999999999875555555555555888888887 PP

                                    xxxxxxx...............xxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        DUF4139  96 geetkvt...............Gvdpkikverkllkkkksetgli......gsqrrveyaytitvkNtksepvtlkvedq 154
                                    ge +++                G   ++k++ kl++ +   ++++       + ++++++y++++k +++++++l+v+d 
  gi|116753537|ref|YP_842655.1| 269 GEYVTTLsmpytakganaslslGPSADLKLSKKLMDYNIT-ENVVsfgngtAKVTTENWTYQLEIKSNTDKEIDLEVKDT 347
                                    777666689999999999999**************99888.67766888777888999********************** PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        DUF4139 155 vPvSrdeeikveledaepskaevdkdtgilewklklapgekkkiefsyev 204
                                    +P+ + + i v     +p+++e +    +l+w+l++ap+e+ ki+++y+v
  gi|116753537|ref|YP_842655.1| 348 IPM-EAKVIDV-----SPEPSEMT--ATLLKWNLSVAPREEMKIRYAYRV 389
                                    **9.4566777.....45544544..45********************98 PP

>> Top6b_C  Type 2 DNA topoisomerase 6 subunit B C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.7   1.3e-07   0.00077      29      94 ..     324     388 ..     306     396 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.3e-07
                                    S-EEEEEEE---------EEE--EES-----------EEE-SSSEEE-EEE---TT-EEEE----S CS
                        Top6b_C  29 dgvevslkvkNfsdkkeefelheilpaeieeaspeakvvemdneydlkWelsvsageskvleYsvd 94 
                                    ++ + +l++k ++dk+ ++e+++++p+e++ ++ +++  em     lkW+lsv++ e+  ++Y   
  gi|116753537|ref|YP_842655.1| 324 ENWTYQLEIKSNTDKEIDLEVKDTIPMEAKVIDVSPEPSEMTAT-LLKWNLSVAPREEMKIRYAYR 388
                                    4567899**************************99******876.69**************99754 PP

>> DUF4897  Domain of unknown function (DUF4897)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.035   2.1e+02      99     125 ..      49      74 ..       9      91 .. 0.72
   2 ?   -3.5   0.0       1.4   8.5e+03     118     139 ..     159     181 ..     144     183 .. 0.67
   3 !   15.6   0.5   1.8e-06     0.011      89     144 ..     316     372 ..     296     378 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.035
                        DUF4897  99 vetslgdiklnlagdselvvslPkdak 125
                                    +   +g+++l   g  ++v+ +P++a+
  gi|116753537|ref|YP_842655.1|  49 FIKRMGSMDLTE-GTHKFVIDIPENAD 74 
                                    345678777654.4445********97 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.4
                        DUF4897 118 vslPk.daklisvePtPtkiven 139
                                    v +P+ +  ++   P+Pt + ++
  gi|116753537|ref|YP_842655.1| 159 VAMPErEIPIMMRAPAPTAAKAE 181
                                    44554245677778999987765 PP

  == domain 3  score: 15.6 bits;  conditional E-value: 1.8e-06
                        DUF4897  89 kglvkvengvvetslgdiklnlagdselvv..slPkdaklisvePtPtkivenellWk 144
                                    +g +kv+ +    +l+ ik n+ ++  l v  ++P +ak+i+v P P+++++  l W+
  gi|116753537|ref|YP_842655.1| 316 NGTAKVTTENWTYQLE-IKSNTDKEIDLEVkdTIPMEAKVIDVSPEPSEMTATLLKWN 372
                                    4567777665555553.4455555555555226*******************999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 2912.60
//
Query:       gi|116753538|ref|YP_842656.1|  [L=251]
Description: ABC transporter related [Methanosaeta thermophila PT]
Scores for complete 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-32  111.8   0.0    4.9e-32  111.3   0.0    1.2  1  ABC_tran      ABC transporter
    2.1e-08   34.4   0.0    0.00049   20.0   0.1    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
      1e-05   26.0   0.3    0.00011   22.7   0.3    2.1  1  AAA           ATPase family associated with various cellular 
    0.00067   19.6   0.0     0.0012   18.8   0.0    1.3  1  RsgA_GTPase   RsgA GTPase
    0.00075   19.3   0.0      0.017   14.9   0.0    2.0  2  AAA_15        AAA ATPase domain
     0.0025   18.1   0.1       0.01   16.1   0.0    2.0  2  AAA_28        AAA domain
     0.0032   17.7   0.2      0.026   14.8   0.1    2.3  2  AAA_22        AAA domain
      0.009   15.8   0.0      0.044   13.5   0.0    2.1  2  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
     0.0098   16.1   0.0      0.027   14.6   0.0    1.8  1  AAA_33        AAA domain
  ------ inclusion threshold ------
       0.01   16.3   0.1       0.02   15.3   0.0    1.5  2  AAA_16        AAA ATPase domain
      0.016   15.7   0.0      0.026   15.0   0.0    1.3  1  AAA_23        AAA domain
      0.018   15.0   0.0       0.12   12.3   0.0    2.0  2  ATPase_2      ATPase domain predominantly from Archaea
       0.02   14.7   0.0      0.036   13.8   0.0    1.5  1  AAA_29        P-loop containing region of AAA domain
      0.028   14.3   0.0      0.051   13.5   0.0    1.4  1  Rad17         Rad17 P-loop domain
      0.032   14.2   0.1      0.072   13.0   0.1    1.6  1  NACHT         NACHT domain
      0.036   13.7   0.0      0.065   12.8   0.0    1.4  1  AAA_25        AAA domain
       0.04   14.5   0.0      0.087   13.4   0.0    1.6  1  AAA_18        AAA domain
      0.063   13.3   0.0       0.18   11.8   0.0    1.8  1  AAA_5         AAA domain (dynein-related subfamily)
      0.067   12.9   0.0       0.12   12.1   0.0    1.3  1  IstB_IS21     IstB-like ATP binding protein
      0.078   13.0   0.0       0.15   12.1   0.0    1.4  1  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
       0.15   11.3   0.1       0.25   10.5   0.1    1.3  1  NB-ARC        NB-ARC domain
       0.15   11.4   0.0       0.64    9.4   0.0    1.9  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
       0.17   11.3   0.0         17    4.8   0.0    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
        0.2   12.1   0.0        0.4   11.1   0.0    1.5  1  RNA_helicase  RNA helicase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.3   0.0   6.6e-35   4.9e-32       1     136 [.      23     162 ..      23     163 .. 0.90

  Alignments for each domain:
  == domain 1  score: 111.3 bits;  conditional E-value: 6.6e-35
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                    l+++s+++ ege + ++G++G+GK+tLl+++agl+ p +G++lldg+++k         e g+++qe +lfp  tv +n 
  gi|116753538|ref|YP_842656.1|  23 LREISMSVDEGEFICFIGPSGCGKTTLLRIIAGLEFPSSGSVLLDGTPIKG-----PGPERGMVFQEYSLFPWRTVLDNv 97 
                                    6789*********************************************99.....9999******************** PP

                                    .........HHHTC...HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    .........xxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 .........esdee...iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                              ++e+   + ++l+ +gl+ ++ +      ++LSgG+kqrva+aral+++pk ll+DEp+
  gi|116753538|ref|YP_842656.1|  98 afgpeiqgvPKEERyriAREYLKMVGLERFESRYP----HELSGGMKQRVAIARALVNNPKALLMDEPF 162
                                    ********944444234667777777777777766....*****************************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 !   20.0   0.1   6.5e-07   0.00049       1      24 [.      35      58 ..      35     118 .. 0.79
   2 !   12.8   0.0    0.0001     0.078     233     298 ..     131     194 ..      89     197 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 6.5e-07
                         AAA_21  1 lnvliGpNgsGKSnLLdaldllar 24
                                   + ++iGp g+GK++LL+++ +l +
  gi|116753538|ref|YP_842656.1| 35 FICFIGPSGCGKTTLLRIIAGLEF 58
                                   5789***************99943 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.0001
                         AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrll..ellkelsrngaQviltTHS 298
                                     ++elS G+k+  a++ al   +   + ll DEp   L+   +r ++  ell++ +r++  +i++THS
  gi|116753538|ref|YP_842656.1| 131 YPHELSGGMKQRVAIARALVNNP---KALLMDEPFGALDA-QTRNVMqsELLRIWERERKTIIFVTHS 194
                                    6899********99999999888...67************.7788888888877777778*******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 !   22.7   0.3   1.4e-07   0.00011       1     113 [.      36     196 ..      36     223 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.4e-07
                                    EEEESSTTSSHHHHHHHHHHH......HTHE................................................. CS
                            AAA   1 vllyGppGtGKTllakavake......lgve................................................. 25 
                                    ++++Gp G+GKT+l + +a        +                                                    
  gi|116753538|ref|YP_842656.1|  36 ICFIGPSGCGKTTLLRIIAGLefpssgS--Vlldgtpikgpgpergmvfqeyslfpwrtvldnvafgpeiqgvpkeeryr 113
                                    689****************985554440..04444445566666777777777777778888888888888888888888 PP

                                    ....EEEEETTTCS.SSSTTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS CS
                            AAA  26 ....fleisgsell.skyvgesekkirelfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk 99 
                                        +l++ g e + s y  e +  +++ ++ a++   +p+ l++DE      ++       ++ ++++Ll+ +++++k 
  gi|116753538|ref|YP_842656.1| 114 iareYLKMVGLERFeSRYPHELSGGMKQRVAIARALVnNPKALLMDEPFGALDAQ------TRNVMQSELLRIWERERK- 186
                                    8888777777666657799999999999999988887889*******76666666......78999**********999. PP

                                    SSTEEEEEEESSGG CS
                            AAA 100 eskvivigatnrpd 113
                                        ++i +t+++d
  gi|116753538|ref|YP_842656.1| 187 ----TIIFVTHSVD 196
                                    ....4555555544 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.6e-06    0.0012      78     121 ..      11      55 ..       5      64 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.6e-06
                                    EEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase  78 evllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                    +v+ v+ kt e l+e++  +++ ++++++G+SG GK+tL+  +++
  gi|116753538|ref|YP_842656.1|  11 KVFDVDGKTIEVLREISMSVDEgEFICFIGPSGCGKTTLLRIIAG 55 
                                    57778888889999999999988*****************98876 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.3e-05     0.017      15      43 ..      24      53 ..      22      57 .. 0.86
   2 ?    2.3   0.0      0.15   1.1e+02     323     365 ..     152     194 ..     130     196 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.3e-05
                         AAA_15 15 kdveidlsee.ltvliGkNnsGKSsileal 43
                                   ++++++++e  + ++iG+ ++GK+++l+++
  gi|116753538|ref|YP_842656.1| 24 REISMSVDEGeFICFIGPSGCGKTTLLRII 53
                                   66777777778****************998 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.15
                         AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                    +++ ll++EP   L  q  +v+   l+++ + +++ +i+ THS
  gi|116753538|ref|YP_842656.1| 152 NPKALLMDEPFGALDAQTRNVMQSELLRIWERERKTIIFVTHS 194
                                    4555899999999999**************************9 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   1.3e-05      0.01       2      21 ..      36      55 ..      35     104 .. 0.89
   2 ?   -0.3   0.0       1.5   1.1e+03      98     116 ..     175     193 ..     111     205 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.3e-05
                         AAA_28  2 ivitGgestGKTtlleaLaa 21
                                   i+++G++++GKTtll+ +a 
  gi|116753538|ref|YP_842656.1| 36 ICFIGPSGCGKTTLLRIIAG 55
                                   9**************99884 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.5
                         AAA_28  98 aeleaaarekrydlvfllp 116
                                     el ++++++r + +f++ 
  gi|116753538|ref|YP_842656.1| 175 SELLRIWERERKTIIFVTH 193
                                    2233333333333333332 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   3.4e-05     0.026       5      24 ..      33      52 ..      28      57 .. 0.87
   2 ?    0.5   0.0      0.92   6.8e+02     112     112 ..     177     177 ..     106     247 .. 0.56

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.4e-05
                         AAA_22  5 agilvvtGesGtGKTtllrr 24
                                     +++ +G+sG+GKTtllr 
  gi|116753538|ref|YP_842656.1| 33 GEFICFIGPSGCGKTTLLRI 52
                                   6799*************985 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.92
                         AAA_22 112 L 112
                                    L
  gi|116753538|ref|YP_842656.1| 177 L 177
                                    2 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   5.9e-05     0.044       4      25 ..      36      57 ..      34      75 .. 0.88
   2 ?   -2.1   0.0       3.8   2.8e+03     103     122 ..     107     126 ..     102     128 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.9e-05
                      PduV-EutP  4 illiGkvgsGKttLtqalkgee 25
                                   i +iG++g+GKttL + + g e
  gi|116753538|ref|YP_842656.1| 36 ICFIGPSGCGKTTLLRIIAGLE 57
                                   789************9999876 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.8
                      PduV-EutP 103 edeenieaveelLksaGaek 122
                                     +ee+ ++++e+Lk++G e+
  gi|116753538|ref|YP_842656.1| 107 PKEERYRIAREYLKMVGLER 126
                                    578889999******99875 PP

>> AAA_33  AAA 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     0.027       2      79 ..      36     177 ..      35     217 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.6e-05
                         AAA_33   2 vllvGlpGsGKstlaerllkklg....avllssdt............................................. 32 
                                    + ++G++G+GK+tl++ ++  +      vll+  t                                             
  gi|116753538|ref|YP_842656.1|  36 ICFIGPSGCGKTTLLRIIAGLEFpssgSVLLDG-Tpikgpgpergmvfqeyslfpwrtvldnvafgpeiqgvpkeeryri 114
                                    679***********9977633324553444433.2356666777777777777776666666666666666666666666 PP

                         AAA_33  33 ..lrrrlfgtdqqsktdytrvldrlyqilnelarkalsagrnvildat...............n 79 
                                      ++ +++g ++   +++ +++  ++q++ ++ar      ++++ d +               +
  gi|116753538|ref|YP_842656.1| 115 arEYLKMVGLERFESRYPHELSGGMKQRV-AIARALVNNPKALLMDEPfgaldaqtrnvmqseL 177
                                    55444566655555556666666666666.6666666666666666665544444443333333 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   2.7e-05      0.02      20      44 ..      31      53 ..      17      83 .. 0.81
   2 ?   -2.7   0.0       8.9   6.6e+03     111     111 ..     165     165 ..     108     191 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.7e-05
                         AAA_16 20 rsgrpelvllsGesGvGKsslvrel 44
                                    +  +e + ++G+sG+GK++l+r +
  gi|116753538|ref|YP_842656.1| 31 DE--GEFICFIGPSGCGKTTLLRII 53
                                   33..38899*************966 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 8.9
                         AAA_16 111 l 111
                                    l
  gi|116753538|ref|YP_842656.1| 165 L 165
                                    2 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   3.5e-05     0.026      20      39 ..      34      53 ..       7      59 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.5e-05
                         AAA_23 20 gltlItGpNGaGKTTildAi 39
                                    + +++Gp G+GKTT+l+ i
  gi|116753538|ref|YP_842656.1| 34 EFICFIGPSGCGKTTLLRII 53
                                   5789*************988 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   0.00016      0.12      16      40 ..      31      53 ..      18      61 .. 0.72
   2 ?    0.5   0.0      0.66   4.9e+02       9      25 ..     175     191 ..     130     222 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00016
                       ATPase_2 16 erepneiyfiYGpegsGKtaLlkei 40
                                   ++  + i fi Gp g+GKt+Ll+ i
  gi|116753538|ref|YP_842656.1| 31 DE-GEFICFI-GPSGCGKTTLLRII 53
                                   43.3455555.***********976 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.66
                       ATPase_2   9 keleeilerepneiyfi 25 
                                    +el++i ere+++i+f+
  gi|116753538|ref|YP_842656.1| 175 SELLRIWERERKTIIFV 191
                                    24444444444444444 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   0.0   4.9e-05     0.036      17      39 ..      28      50 ..      19      64 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.9e-05
                         AAA_29 17 ieidlkgatlltGpsGsGKSTll 39
                                   +++d+ +++ ++GpsG GK+Tll
  gi|116753538|ref|YP_842656.1| 28 MSVDEGEFICFIGPSGCGKTTLL 50
                                   5667555999************8 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   6.8e-05     0.051      47      66 ..      35      54 ..      16      72 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.8e-05
                          Rad17 47 iLLisGPsGCgkstvvkvLs 66
                                    +   GPsGCgk+t +++++
  gi|116753538|ref|YP_842656.1| 35 FICFIGPSGCGKTTLLRIIA 54
                                   55677************987 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   9.7e-05     0.072       3      21 ..      36      54 ..      34      56 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.7e-05
                                   EEEEC-TTTCHHHHHHHHH CS
                          NACHT  3 vilqGeaGsGKTtLlqkla 21
                                   ++  G++G+GKTtLl+ +a
  gi|116753538|ref|YP_842656.1| 36 ICFIGPSGCGKTTLLRIIA 54
                                   7899***********9886 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   8.8e-05     0.065      16      50 ..      17      50 ..       4      55 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.8e-05
                         AAA_25 16 aapppprrwlvkgllpagelallaGapgtGKttla 50
                                    ++++ +r + + +  +ge++ ++G++g+GKttl+
  gi|116753538|ref|YP_842656.1| 17 GKTIEVLREISMSV-DEGEFICFIGPSGCGKTTLL 50
                                   44777788777888.9*****************97 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   0.00012     0.087       1      21 [.      36      56 ..      36      88 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00012
                         AAA_18  1 IlltGtpGvGKttlakeLskr 21
                                   I+  G++G+GKttl + ++ +
  gi|116753538|ref|YP_842656.1| 36 ICFIGPSGCGKTTLLRIIAGL 56
                                   899*************99765 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   0.0   0.00024      0.18       2      20 ..      36      54 ..      35      62 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00024
                                   EEEE--SSSSHHHHHHHGG CS
                          AAA_5  2 vlLvGppGtgKselaerla 20
                                   ++ +Gp+G+gK++l + +a
  gi|116753538|ref|YP_842656.1| 36 ICFIGPSGCGKTTLLRIIA 54
                                   689***********99887 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00016      0.12      29      63 ..      14      49 ..       4      58 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00016
                      IstB_IS21 29 sldkrkvkeLatlsf.iekkenivllGpsGvGKshl 63
                                   ++d ++++ L++ s  +++ e i+++GpsG GK+ l
  gi|116753538|ref|YP_842656.1| 14 DVDGKTIEVLREISMsVDEGEFICFIGPSGCGKTTL 49
                                   56778888887777549999**************87 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0    0.0002      0.15       8      40 ..      20      54 ..      15      61 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0002
                                   HHHHHHHHHCH..TEEEEEEESTTSSHHHHHHHHH CS
                           TsaE  8 ealgkklakal..gdvilLeGdLGaGKTtlvrgla 40
                                    ++ +++  ++  g++i++ G+ G+GKTtl r +a
  gi|116753538|ref|YP_842656.1| 20 IEVLREISMSVdeGEFICFIGPSGCGKTTLLRIIA 54
                                   4555555555566889***************9876 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00033      0.25      16      40 ..      31      53 ..      17      56 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00033
                                   TTSCSEEEEEEESTTSSHHHHHHHH CS
                         NB-ARC 16 delqslvvalvGmgGvGKttlakqi 40
                                   de +  ++ + G  G+GKttl++ i
  gi|116753538|ref|YP_842656.1| 31 DEGE--FICFIGPSGCGKTTLLRII 53
                                   3444..99999**********9765 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00086      0.64      17      48 ..      28      59 ..      12      73 .. 0.75
   2 ?   -1.0   0.0       1.3   9.7e+02     178     197 ..     128     147 ..     120     155 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00086
                   Mg_chelatase 17 iaaaGgHnlllvGppGsGKtmlakrlpsllpp 48
                                   +++  g  + ++Gp+G+GKt l + +++l  p
  gi|116753538|ref|YP_842656.1| 28 MSVDEGEFICFIGPSGCGKTTLLRIIAGLEFP 59
                                   55555667899***********9999887555 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.3
                   Mg_chelatase 178 ierYlsklsgplldRidlqv 197
                                     +rY + lsg +  R+ +  
  gi|116753538|ref|YP_842656.1| 128 ESRYPHELSGGMKQRVAIAR 147
                                    579999*********99865 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   0.0     0.023        17      25      42 ..      34      51 ..      22      56 .. 0.82
   2 ?    4.6   0.0     0.026        19     135     197 ..     133     193 ..      91     215 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.023
                                   SEEEEEESTTSSHHHHHH CS
                                   xxxxxxxxxxxxxxxxxx RF
                          SMC_N 25 sftaivGpNGSGKsnlld 42
                                   +f + +Gp G+GK+ ll 
  gi|116753538|ref|YP_842656.1| 34 EFICFIGPSGCGKTTLLR 51
                                   68899*********9986 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.026
                                    TCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHH.HHH..HHCTTSEEEEE-S CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx..xxxxxxxxxxxxx RF
                          SMC_N 135 elLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvae.llk..eksknaQfivisl 197
                                    ++LSgG k+ va+a  +     +p++l l+De   aLD++ ++ + + ll+  e++ ++ +i +++
  gi|116753538|ref|YP_842656.1| 133 HELSGGMKQRVAIARAL---VNNPKAL-LMDEPFGALDAQTRNVMQSeLLRiwERERKT-IIFVTH 193
                                    489***99999888653...3456655.89********999987754144442333333.333333 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00054       0.4       1      18 [.      36      53 ..      36      65 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00054
                   RNA_helicase  1 iwlyGpsgeGKStlakeL 18
                                   i++ Gpsg+GK+tl + +
  gi|116753538|ref|YP_842656.1| 36 ICFIGPSGCGKTTLLRII 53
                                   799***********9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); 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: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 1902.61
//
Query:       gi|116753539|ref|YP_842657.1|  [L=354]
Description: NAD(P)-dependent glycerol-1-phosphate dehydrogenase [Methanosaeta thermophila PT]
Scores for complete 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    1.6e-68  231.1   0.6    1.1  1  Fe-ADH_2      Iron-containing alcohol dehydrogenase
    2.1e-25   89.3   4.8    4.9e-25   88.1   4.8    1.6  1  Fe-ADH        Iron-containing alcohol dehydrogenase
    3.5e-05   23.1   0.1    9.4e-05   21.7   0.1    1.7  1  DHQ_synthase  3-dehydroquinate synthase


Domain annotation for each model (and alignments):
>> Fe-ADH_2  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  231.1   0.6   2.8e-72   1.6e-68       2     250 .]      20     277 ..      19     277 .. 0.91

  Alignments for each domain:
  == domain 1  score: 231.1 bits;  conditional E-value: 2.8e-72
                       Fe-ADH_2   2 igegaleklgellkelelk.kvllvadentkkaagekveeslkeagikvevveeveeeadleeveklvealreketdlvv 80 
                                     g gal ++g+++ +l+l+ ++l++++ +t ++ag++++ sl++ g +++vv   + ++   ev ++ + +   ++d+++
  gi|116753539|ref|YP_842657.1|  20 AGAGALANIGDVCVDLRLSgRALVITGPQTRSVAGDNLAASLTDCGFEADVV--ITRDPRPAEVDRVKSFALDYKADFLI 97 
                                    5789*************987*****************************977..467777777877888777889***** PP

                       Fe-ADH_2  81 avGgGtiiDiakyvsaklnvpyvsvpTaaSvDGfaspgaslvvdgkkrtvakaaaPlaviaDldvlaeAPrrllasGvGD 160
                                    + GgG+ iDiak+++++l++py+svpTaaS+DG+as +asl +dg+++++ +++aPla+iaD+ ++++AP rl+ +G+GD
  gi|116753539|ref|YP_842657.1|  98 GAGGGRSIDIAKLAAYHLDIPYLSVPTAASHDGIASAMASLNMDGETKSI-PTRAPLAIIADTGIISKAPPRLMSAGCGD 176
                                    *************************************************9.***************************** PP

                       Fe-ADH_2 161 llgkytaladwklan........evseplaklsaamvqeaaeklve..dkketealeellea.lalsgigisrpaSGsEH 229
                                    ++++yta+ dw+la+        e+++ l+ ++a+mv++ a ++    ++  + ++++l+++ +a+s++g+srpaSGsEH
  gi|116753539|ref|YP_842657.1| 177 IISNYTAILDWRLAKrlkcedysEYAAALSSMTAKMVVDMAPSIKPghEPSAKVVVQALISSgVAMSIAGSSRPASGSEH 256
                                    ***************9999988888999*********999998865423444555555555427**************** PP

                       Fe-ADH_2 230 liSHaldmlalkqalHGeqVG 250
                                    +++Hal+++a+ + lHGe +G
  gi|116753539|ref|YP_842657.1| 257 MFAHALNRIAPGRGLHGELCG 277
                                    ******************987 PP

>> Fe-ADH  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.1   4.8   8.1e-29   4.9e-25       1     276 [.      15     278 ..      15     333 .. 0.83

  Alignments for each domain:
  == domain 1  score: 88.1 bits;  conditional E-value: 8.1e-29
                                    -SEEEEETTGGGGHHHHHTTT-...EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HHHHHHHHTTS-T CS
                         Fe-ADH   1 Ptrivfgkgaleelgellkklgak.ralivtdkgslkksglldkvlesleeagievtvfdgvepnptleeveeaaalare 79 
                                    P+r+v g+gal+++g+ + +l ++ ral++t++++  +s + d++ +sl+++g+e +v   ++ +p+ +ev+++ ++a +
  gi|116753539|ref|YP_842657.1|  15 PRRVVAGAGALANIGDVCVDLRLSgRALVITGPQT--RSVAGDNLAASLTDCGFEADV--VITRDPRPAEVDRVKSFALD 90 
                                    89*******************9767*********5..5889****************6..789***************** PP

                                    T.--EEEEEESHHHHHHHHHHHHHTT..................--EEEEESS-S-S-TT-SEEEEE.-TTSEEEEE-.. CS
                         Fe-ADH  80 egadvviavGGGsviDtAKaialllanpevedylgegkakkkkalpliaiPTtaGtGsevtplavitdeeegeklsifdp 159
                                     +ad++i+ GGG +iD+AK++a+ l                   +p   +PT a+ +  +++ a +  ++  e +si   
  gi|116753539|ref|YP_842657.1|  91 YKADFLIGAGGGRSIDIAKLAAYHLD------------------IPYLSVPTAASHDGIASAMASLN-MDG-ETKSIP-- 148
                                    **************************..................***********************.666.566666.. PP

                                    SS--SEEEEEHHHHHHS-HHHHHHHHHHHHHHHHHHHHHH........T---TTSSB--HHHHHHHHHHHHHHHHHHHHH CS
                         Fe-ADH 160 ellPdlaivDpeltltlPkrvtaatglDalahalEayvsk........kanplsdalaleairliaknleravadgedle 231
                                    +  P ++i D+ ++ ++P+r++ a+ +D+++ +   +  +          +++  al+   ++++++  + +   ++   
  gi|116753539|ref|YP_842657.1| 149 TRAPLAIIADTGIISKAPPRLMSAGCGDIISNYTAILDWRlakrlkceDYSEYAAALSSMTAKMVVDMAPSIK--PGHEP 226
                                    789***************************9987765556333454445555555555566666666666543..44556 PP

                                    HHHHHHHHHHHHHHHHHSS---.....HHHHHHHHHHC.CGGG....GGS-HHH CS
                         Fe-ADH 232 areqmllastlaglafsnaglg.....avHalahalgalfgip....hglanai 276
                                      + +++a + +g+a+s ag +       H++ahal  +   p    hg++++i
  gi|116753539|ref|YP_842657.1| 227 SAKVVVQALISSGVAMSIAGSSrpasgSEHMFAHALNRIA--PgrglHGELCGI 278
                                    66666666666999999999888888899*******9954..234578888887 PP

>> DHQ_synthase  3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1   1.6e-08   9.4e-05      30     240 ..      92     305 ..      81     328 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.6e-08
                                    TT-EEEEEESHHHHHHHHHHHHHBTT--EEEEEE-SHHHHHTTTSSSEEEEEETTEEEEEEEE---SEEEEEGGGGGGS- CS
                   DHQ_synthase  30 RksllialGGGvvgDlaGfvAatylRGvrfvqvPttllaqvDssvGgKtainlplgKNliGafaqPkavlidlevLktLp 109
                                    + + li  GGG   D+a ++A  y+  + ++ vPt+  a  D    +  ++n++     i +   P a+++d+ +++  p
  gi|116753539|ref|YP_842657.1|  92 KADFLIGAGGGRSIDIAKLAA--YHLDIPYLSVPTA--ASHDGIASAMASLNMDGETKSIPT-RAPLAIIADTGIISKAP 166
                                    56789************9987..8889********7..88999999999***********88.78*************** PP

                                    HHHHHHHHHHHH.HHHHHT-HHHHHHHHHHHHHHHC.......TTTHHHHHHHH.......HHHHHHHHHHHHHCCTTTT CS
                   DHQ_synthase 110 erelraGlaEvi.Kyalikdeelfelleenaeallk.......eeeeealeeli.......arsievkaevveeDekekg 174
                                    +r ++aG++++i  y++i d +l ++l+ ++ +  +       +       +++       +   e  a+vv +    +g
  gi|116753539|ref|YP_842657.1| 167 PRLMSAGCGDIIsNYTAILDWRLAKRLKCEDYSEYAaalssmtA-------KMVvdmapsiKPGHEPSAKVVVQALISSG 239
                                    **********995699***********99888877744444432.......44334433335555666777777777766 PP

                                    GGGG........GGTTHHHHHHHHHHHTTTTS-HHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHTT--- CS
                   DHQ_synthase 175 lral........LnlGHtigHaiEallgyekllHGeaVaiGmvlaaelseklgllkkeeverllkllkklglpv 240
                                    + +             H ++Ha+ +++   + lHGe   iG ++ ++l          + + +++ lk lg p 
  gi|116753539|ref|YP_842657.1| 240 VAMSiagssrpaSGSEHMFAHALNRIAPG-RGLHGELCGIGTIIMMYLHG-------GDWRMIREALKVLGAPA 305
                                    6555222222225677********99977.9**********999988762.......22334445555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 2678.91
//
Query:       gi|116753540|ref|YP_842658.1|  [L=149]
Description: hypothetical protein Mthe_0220 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-54  183.5   0.6      2e-54  183.3   0.6    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 !  183.3   0.6   1.1e-58     2e-54       1     140 []       7     147 ..       7     147 .. 0.99

  Alignments for each domain:
  == domain 1  score: 183.3 bits;  conditional E-value: 1.1e-58
                        UPF0179   1 kitLigkklAkeGteFiylgeaeeCekCklkkvClnLekgrkYrivevrekteheCavheegvvaveveeapiealiesk 80 
                                    +itLig+klA+ G+eFi+ g+++eCe+Ckl+++C+nLe+gr+Yri +++ + +heC++heegv+avev+e+p++a+++++
  gi|116753540|ref|YP_842658.1|   7 QITLIGTKLATIGMEFIFNGPTPECESCKLRNTCMNLEPGRRYRILGIKGELVHECPLHEEGVRAVEVTESPTIAAMDAR 86 
                                    59****************************************************************************** PP

                        UPF0179  81 kavegskitleseeCdevecesyelcepeglkegekvkivevlgeiee.ckkgrslkkvel 140
                                    k ++gski +e+ +Cd ++c++y++c+p+glk+g++++ivev+ge++e c++g++lk+vel
  gi|116753540|ref|YP_842658.1|  87 KSFAGSKIIYEPINCDVTDCRMYDICHPAGLKRGDRCTIVEVVGEAPEeCARGYKLKLVEL 147
                                    ***********************************************99**********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1104.76
//
Query:       gi|116753541|ref|YP_842659.1|  [L=326]
Description: FO synthase subunit 1 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.6e-16   60.0   0.0    3.9e-15   56.6   0.0    2.2  2  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.6   0.0   2.2e-19   3.9e-15       1     165 [.      25     186 ..      25     188 .. 0.93
   2 !    3.7   0.0    0.0041        73      27      90 ..     181     250 ..     179     324 .. 0.74

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 2.2e-19
                                    EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS.....TTHHHHHHHHHHTCC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxx RF
                    Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly.....pdfvellerlaklav 75 
                                    ++vt  C+++C +C++++   + +r+r++s  e  ++++++ ++ g+ e ++++g+          ++ e+l +l++la 
  gi|116753541|ref|YP_842659.1|  25 IPVTDLCRNACGYCSFRR---DPDRARVISRSEAQRLMERA-QSAGCSEALFSMGDRPWEvrgdrLELLEYLVELCELA- 99 
                                    679999***********8...8*******************.9***888888888776656666699999999999997. PP

                                    CTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  76 pgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGe 155
                                     ++ +   tn++ +++e le+l++++   + l le++   k++++  +g+ +e +++++  + +++i+  +++i+++ Ge
  gi|116753541|ref|YP_842659.1| 100 LEMGLLPHTNAGILTREELELLAPYN-ASMGLMLESTAHLKIHERS-PGKRPEVRIRTISDAGALRIP-FTTGILVGIGE 176
                                    **************************.*******************.*********************.*********** PP

                                    SHHHHHHHHH CS
                                    xxxxxxxxxx RF
                    Radical_SAM 156 ndeeleelle 165
                                    + e++   le
  gi|116753541|ref|YP_842659.1| 177 SSEDRIRSLE 186
                                    ***9887766 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0041
                                    HHHHHHHHHHHHHHHHHHTTSEEEEEE...........SSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHG CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  27 rslsveeileevkelkaekgvkevilg...........ggepllypdfvellerlaklavpgiritvetngtlpd 90 
                                    r++s+e i+e+ +++  +  + evi+            g++p +  d+v+l+  ++++    ++i++ +++ l d
  gi|116753541|ref|YP_842659.1| 181 RIRSLEVIAELHRRYG-H--IQEVIIQpldpkpgteseGMHPPAMTDMVKLVSIARRIL--PLEISIQVPPNLMD 250
                                    6788888888888885.4..8888888899999999999999999******99999994..66666655555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); 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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2495.46
//
Query:       gi|116753542|ref|YP_842660.1|  [L=161]
Description: hypothetical protein Mthe_0222 [Methanosaeta thermophila PT]
Scores for complete 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    1.7e-09   37.9   0.0    1.1  1  F420H2_quin_red  F420H(2)-dependent quinone reductase
  ------ inclusion threshold ------
      0.038   14.0   0.0      0.094   12.7   0.0    1.7  2  Pyridox_ox_2     Pyridoxamine 5'-phosphate oxidase


Domain annotation for each model (and alignments):
>> F420H2_quin_red  F420H(2)-dependent quinone reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.0   1.9e-13   1.7e-09      22      99 ..      35     109 ..      20     120 .. 0.82

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 1.9e-13
                                    S---EEEEEE-TTT-SEEEEEEEEEEETTEEEEE-SGGGGSSS-HHHHHHHH--EEEEEETTEEEEEEEEE--HHHHH CS
                F420H2_quin_red  22 gvpvllLtttGrktgkprktplgfvrdgdsylvvaskgGapkhpswylNlkanPrvevqvgakkldvtAreveddeka 99 
                                       v++L   Gr+tg+ r tp+g++  +++       g +  +  wylNl a+Pr e+   + +  + A+ v+d+e +
  gi|116753542|ref|YP_842660.1|  35 TGRVMVLILKGRRTGRTRYTPVGYATMNGRIYC--YRG-GRSRGAWYLNLLAEPRLEIMLPEGRIRGCAEVVTDEEEK 109
                                    34789999*********************9765..455.567889****************************87754 PP

>> Pyridox_ox_2  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.39   3.5e+03      27      40 ..      53      66 ..      35      77 .. 0.76
   2 ?   12.7   0.0     1e-05     0.094      84     107 ..      96     119 ..      95     155 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.39
                                   EEEEEEEEETTEEE CS
                   Pyridox_ox_2 27 ilPvnyvvdgdsly 40
                                    +Pv y++ ++++y
  gi|116753542|ref|YP_842660.1| 53 YTPVGYATMNGRIY 66
                                   57888888888877 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 1e-05
                                    EEEEEEEE--HHHHHHHCCCHHHH CS
                   Pyridox_ox_2  84 vrGraeevtdeeekaealellvek 107
                                    +rG+ae+vtdeeek +al++++++
  gi|116753542|ref|YP_842660.1|  96 IRGCAEVVTDEEEKFTALRKILKN 119
                                    79*****************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1268.99
//
Query:       gi|116753543|ref|YP_842661.1|  [L=602]
Description: ATPase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-10   41.0   0.0      2e-10   40.2   0.0    1.3  1  T2SSE         Type II/IV secretion system protein
    1.1e-08   35.5   0.2    3.6e-08   33.9   0.0    2.0  1  PIN           PIN domain
    1.6e-08   34.3   0.6    4.7e-08   32.7   0.6    1.8  1  KH_1          KH domain
    6.8e-06   25.8   0.4      4e-05   23.3   0.4    2.4  1  KH_2          KH domain
     0.0005   20.5   0.0     0.0013   19.1   0.0    1.6  1  AAA_16        AAA ATPase domain
     0.0017   18.9   0.0     0.0038   17.8   0.0    1.6  1  AAA_18        AAA domain
     0.0026   17.7   0.0     0.0053   16.8   0.0    1.6  1  AAA_5         AAA domain (dynein-related subfamily)
      0.003   17.8   0.0     0.0085   16.4   0.0    1.7  1  PIN_4         PIN domain
     0.0037   17.0   0.0      0.009   15.7   0.0    1.6  1  AAA_29        P-loop containing region of AAA domain
     0.0066   16.4   0.0       0.03   14.2   0.0    2.1  1  NTPase_1      NTPase
       0.01   16.3   0.0      0.023   15.1   0.0    1.6  1  AAA           ATPase family associated with various cellular 
  ------ inclusion threshold ------
      0.012   14.8   1.9      0.016   14.4   0.1    2.0  2  TIP49         TIP49 P-loop domain
      0.012   15.0   0.0      0.031   13.6   0.0    1.6  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.017   15.3   0.0      0.056   13.6   0.0    1.9  1  AAA_33        AAA domain
      0.025   13.8   0.0      0.059   12.5   0.0    1.6  2  NB-ARC        NB-ARC domain
      0.032   13.5   0.0      0.069   12.4   0.0    1.5  1  Zeta_toxin    Zeta toxin
      0.033   14.1   0.0      0.059   13.3   0.0    1.4  1  NACHT         NACHT domain
      0.034   14.2   0.0      0.077   13.0   0.0    1.5  1  AAA_14        AAA domain
      0.037   14.3   0.0       0.13   12.5   0.0    1.9  1  AAA_22        AAA domain
      0.043   13.5   0.0      0.074   12.8   0.0    1.3  1  IstB_IS21     IstB-like ATP binding protein
      0.044   14.3   0.0       0.13   12.8   0.0    1.8  1  ABC_tran      ABC transporter
      0.048   13.4   0.0       0.12   12.1   0.0    1.6  1  AAA_30        AAA domain
      0.052   13.9   0.0       0.14   12.6   0.0    1.8  1  RNA_helicase  RNA helicase
      0.054   13.6   1.3       0.23   11.5   0.1    2.6  2  KH_5          NusA-like KH domain
      0.099   12.1   0.0       0.18   11.3   0.0    1.3  1  KTI12         Chromatin associated protein KTI12
        0.1   12.3   0.0       0.21   11.3   0.0    1.5  1  ATP_bind_1    Conserved hypothetical ATP binding protein
       0.11   12.3   0.0       0.18   11.6   0.0    1.2  1  AAA_11        AAA domain
       0.12   12.0   0.0        0.3   10.6   0.0    1.6  1  AAA_25        AAA domain
       0.12   12.6   0.0        0.3   11.3   0.0    1.7  1  AAA_28        AAA domain
       0.15   12.5   0.7       0.56   10.6   0.1    2.3  2  AAA_17        AAA domain
       0.16   12.0   0.0       0.31   11.0   0.0    1.4  1  ResIII        Type III restriction enzyme, res subunit
        0.2   11.4   0.1       0.42   10.3   0.1    1.5  1  AAA_24        AAA domain


Domain annotation for each model (and alignments):
>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.0   3.5e-13     2e-10      76     247 ..     217     377 ..     172     397 .. 0.77

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 3.5e-13
                          T2SSE  76 kgvrlrvvllPvvag.ealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkein 154
                                    + +r+ +  +P + g e  ++R    ++++ld +  +     ++++ l++    +  il++G+ gsGK+tl+  + +++ 
  gi|116753543|ref|YP_842661.1| 217 GPMRIAITRPPFSDGlEITAVRPV--AKVDLDSYKHAD----ELKARLSEG---QRGILIAGPPGSGKSTLAAGIAEYLL 287
                                    568899999999999899999954..455677776655....455567777...8899********************** PP

                          T2SSE 155 ksderivtvEDpvEiqleganqvqlnakkakvtfadllraaLRlrPDrimvGEiRdketleilkAvnTGHlgslsTlHan 234
                                    k++  + t+E p+ +q+  ++++q  + ++++++++    +L  rPD  +  E+R ++ + +   +     g ++ +Han
  gi|116753543|ref|YP_842661.1| 288 KCNYVVKTMESPRDLQVP-PEVTQYGPLEGSMEASSE--ILLLVRPDYTIYDEVRKTQDFVVFADMRLAGVGMIGVVHAN 364
                                    **99************95.456666666556666665..578889************9999966666555666******* PP

                          T2SSE 235 saagalerLeqlg 247
                                    ++++al+rL   +
  gi|116753543|ref|YP_842661.1| 365 KPIDALQRLLGRV 377
                                    ********97544 PP

>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0   6.5e-11   3.6e-08       1     120 [.       5     119 ..       5     121 .. 0.96

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 6.5e-11
                                    EEE-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHS.SCHCHHHHHHHHHHHHHHHTSEEEEBCHHHHH CS
                            PIN   1 ivlDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlar.rkskrekaaelvelllllsalkilpidaeiae 79 
                                    +v DTsv+i   +g++ a+    +l++  ++v++++v+aEl + ++  r+ +++ ++el++l +l++a ki     +++ 
  gi|116753543|ref|YP_842661.1|   5 VVPDTSVVI---DGRVSARVKSGALAG-RRIVIPEAVVAELEAQANHgREIGIKGLEELRRLSELAKAGKIELEYVGVRP 80 
                                    578******...9999999999***99.**************************************************** PP

                                    HHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHHH CS
                            PIN  80 eaaeialkygllpnDaliaAtAkehgikliatfDedfrrva 120
                                       +i+l    + +Da+i  +A+e g++ + t D+  ++va
  gi|116753543|ref|YP_842661.1|  81 DLDQIKLAG-GGEIDAMIRDVALELGASFL-TSDTIQYKVA 119
                                    *******86.*****************999.****999987 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.6   8.4e-11   4.7e-08       3      47 ..     488     529 ..     486     543 .. 0.81

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 8.4e-11
                                    EEEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEES.STT...T.-E CS
                           KH_1   3 rilvPsslvgriIGkgGsnIkeIreetgakIkvpk.sedegsdere 47 
                                    +++vP s+++r+IGk G+nI +I++  g +I++ + +e+++    +
  gi|116753543|ref|YP_842661.1| 488 VVTVPESQIPRVIGKAGRNIEQIERALGMHIDIRGkREEPD----V 529
                                    789**********************67*****986555543....3 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.4   7.2e-08     4e-05       8      63 ..     467     522 ..     462     542 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 7.2e-08
                                    HHTECETEEEEEEEC.CSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHT CS
                           KH_2   8 veikkagvskveIer.tanrviiviresqpgivIGkgGsnikkigkelrkdiekleg 63 
                                    +e++   ++ +e+e  +    ++++ esq  +vIGk G+ni++i+ +l+  i+ ++g
  gi|116753543|ref|YP_842661.1| 467 KELAHHVKGPFEVEMiSDSSMVVTVPESQIPRVIGKAGRNIEQIERALGMHID-IRG 522
                                    5554444566666664458899***************************9996.544 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   2.3e-06    0.0013      18      51 ..     257     289 ..     249     322 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2.3e-06
                         AAA_16  18 rvrsgrpelvllsGesGvGKsslvrellralekd 51 
                                    r+++g+ + +l+ G++G+GKs+l+  ++++l k 
  gi|116753543|ref|YP_842661.1| 257 RLSEGQ-RGILIAGPPGSGKSTLAAGIAEYLLKC 289
                                    555665.9****************9999988765 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   6.8e-06    0.0038       1      26 [.     265     291 ..     265     322 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 6.8e-06
                         AAA_18   1 IlltGtpGvGKttlakeLskrl.gfgv 26 
                                    Il++G+pG+GK+tla  +++ l ++ +
  gi|116753543|ref|YP_842661.1| 265 ILIAGPPGSGKSTLAAGIAEYLlKCNY 291
                                    99*************999998766633 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 !   16.8   0.0   9.5e-06    0.0053       2      34 ..     265     298 ..     264     345 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 9.5e-06
                                    EEEE--SSSSHHHHHHHGGGGB.S--EEEEE--T CS
                          AAA_5   2 vlLvGppGtgKselaerlaaal.nreveyvqltr 34 
                                    +l+ GppG+gKs+la  +a+ l +++++++ + +
  gi|116753543|ref|YP_842661.1| 265 ILIAGPPGSGKSTLAAGIAEYLlKCNYVVKTMES 298
                                    7999****************99977777766654 PP

>> PIN_4  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.5e-05    0.0085       2     102 ..       6     108 ..       5     129 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.5e-05
                          PIN_4   2 VlDTnvlLhdpealksf....keehdvviPitVleELdklKkgsserelarlarqanrlldellekesgrlkvqtsaeel 77 
                                    V DT+v+++   +   +        ++viP  V+ EL+++ ++ +  e++ +  + +r l el +  + +l    ++ +l
  gi|116753543|ref|YP_842661.1|   6 VPDTSVVIDGRVSAR-VksgaLAGRRIVIPEAVVAELEAQANHGR--EIGIKGLEELRRLSELAKAGKIELEYVGVRPDL 82 
                                    889999998764433.335777999***************99998..999999999999999999999999888888888 PP

                          PIN_4  78 pee.eseseknDnrIlavalelkeek 102
                                    ++   + + + D +I +valel    
  gi|116753543|ref|YP_842661.1|  83 DQIkLAGGGEIDAMIRDVALELGASF 108
                                    87644448899********9997764 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.6e-05     0.009      20      39 ..     259     279 ..     244     291 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.6e-05
                         AAA_29  20 dlkg.atlltGpsGsGKSTll 39 
                                    ++ +  +l++Gp GsGKSTl 
  gi|116753543|ref|YP_842661.1| 259 SEGQrGILIAGPPGSGKSTLA 279
                                    4333569************96 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   5.3e-05      0.03       2      31 ..     265     294 ..     264     301 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.3e-05
                                    EEEE--TTSSHHHHHHHHHHHH...GGGEE CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvg 31 
                                    ++i GppG+GK+Tl   ++e l + ++ v+
  gi|116753543|ref|YP_842661.1| 265 ILIAGPPGSGKSTLAAGIAEYLLKCNYVVK 294
                                    789*******************99998886 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 !   15.1   0.0   4.2e-05     0.023       1      24 [.     265     289 ..     265     305 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.2e-05
                                    EEEESSTTSSHHHHHHHHHHHH.TH CS
                            AAA   1 vllyGppGtGKTllakavakel.gv 24 
                                    +l+ GppG GK++la  +a+ l + 
  gi|116753543|ref|YP_842661.1| 265 ILIAGPPGSGKSTLAAGIAEYLlKC 289
                                    699****************996443 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   2.8e-05     0.016      50      74 ..     262     286 ..     254     296 .. 0.87
   2 ?   -2.0   0.3       2.7   1.5e+03     276     312 ..     384     425 ..     377     428 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.8e-05
                                    XXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49  50 GravLlaGpsgtGktalaiaiskel 74 
                                     r++L+aGp+g+Gk+ la +i++ l
  gi|116753543|ref|YP_842661.1| 262 QRGILIAGPPGSGKSTLAAGIAEYL 286
                                    599******************9876 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.7
                                    XXXXXXXXXX..X.XXXXXXXXXXXXXX.XXXXXXX.XXXXX CS
                          TIP49 276 eivpGvlfiD..e.vhmlDiecfsylnr.alesela.Pivil 312
                                    ++v  v+fi+  e +++lD+e    +    +e +la P+v++
  gi|116753543|ref|YP_842661.1| 384 QVVDTVVFIErgEvTKLLDVEFVVKVPTgMVEADLArPVVVV 425
                                    789999999733325799999877665415688887567665 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   5.6e-05     0.031      21      46 ..     261     286 ..     246     300 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.6e-05
                   Mg_chelatase  21 GgHnlllvGppGsGKtmlakrlpsll 46 
                                    G+  +l++GppGsGK+ la+ +++ l
  gi|116753543|ref|YP_842661.1| 261 GQRGILIAGPPGSGKSTLAAGIAEYL 286
                                    8899***************9987766 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0    0.0001     0.056       2      21 ..     265     284 ..     265     310 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.0001
                         AAA_33   2 vllvGlpGsGKstlaerllk 21 
                                    +l+ G+pGsGKstla ++++
  gi|116753543|ref|YP_842661.1| 265 ILIAGPPGSGKSTLAAGIAE 284
                                    5789***********99885 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       5.9   3.3e+03     179     195 ..     182     197 ..     174     200 .. 0.75
   2 ?   12.5   0.0   0.00011     0.059       3      41 ..     249     283 ..     247     291 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 5.9
                                    HH..CHHHHHHHHHHCT CS
                         NB-ARC 179 ekesleevakeivekck 195
                                    ek +l+e+a+ei+e+ k
  gi|116753543|ref|YP_842661.1| 182 EK-DLREMAREIIERAK 197
                                    34.599*******9876 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00011
                                    HHHHHHHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHC CS
                         NB-ARC   3 ksvekviekLlekdelqslvvalvGmgGvGKttlakqil 41 
                                    k+ ++++ +L+ +++ +   + + G +G+GK+tla+ i 
  gi|116753543|ref|YP_842661.1| 249 KHADELKARLS-EGQRG---ILIAGPPGSGKSTLAAGIA 283
                                    678999999*9.88888...89*************9886 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00012     0.069      19      46 ..     265     291 ..     252     298 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                     Zeta_toxin  19 illgGqpGAGKselaellkdelerqgnv 46 
                                    il++G pG+GKs+la+ ++++l  + n+
  gi|116753543|ref|YP_842661.1| 265 ILIAGPPGSGKSTLAAGIAEYLL-KCNY 291
                                    89***************999984.4444 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   0.00011     0.059       3      23 ..     265     285 ..     263     294 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00011
                                    EEEEC-TTTCHHHHHHHHHHH CS
                          NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                    +++ G++GsGK+tL++++a+ 
  gi|116753543|ref|YP_842661.1| 265 ILIAGPPGSGKSTLAAGIAEY 285
                                    899***************975 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00014     0.077       5      80 ..     265     345 ..     262     352 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00014
                         AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe........kllelileklke....ekktylflDE 72 
                                    ++i G+  +GK+tl+  +++ ll  k +++  +++++rd +   pe          +e+      e     +  y + DE
  gi|116753543|ref|YP_842661.1| 265 ILIAGPPGSGKSTLAAGIAEYLL--KCNYVVKTMESPRDLQVP-PEvtqygpleGSMEASS----EilllVRPDYTIYDE 337
                                    789****************9999..889999999999996544.22222322222222222....244445779999999 PP

                         AAA_14  73 iqevpewe 80 
                                    + + +++ 
  gi|116753543|ref|YP_842661.1| 338 VRKTQDFV 345
                                    99998886 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00024      0.13       4      27 ..     261     284 ..     256     303 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00024
                         AAA_22   4 tagilvvtGesGtGKTtllrrlle 27 
                                    +++ +++ G++G+GK+tl++ ++e
  gi|116753543|ref|YP_842661.1| 261 GQRGILIAGPPGSGKSTLAAGIAE 284
                                    78889*************987665 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 ?   12.8   0.0   0.00013     0.074      47      79 ..     262     294 ..     242     347 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                      IstB_IS21  47 kenivllGpsGvGKshlaialgveavraglsvl 79 
                                    + +i++ Gp+G GKs la+ ++    + ++ v 
  gi|116753543|ref|YP_842661.1| 262 QRGILIAGPPGSGKSTLAAGIAEYLLKCNYVVK 294
                                    6789*****************999888887775 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00023      0.13       4      32 ..     254     283 ..     236     295 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00023
                                    EEEEEETTSE.EEEEESTTSSHHHHHHHHT CS
                                    xxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   4 vslklkegek.vaivGenGaGKStLlklla 32 
                                    ++  l+eg++ + i G+ G+GKStL++ +a
  gi|116753543|ref|YP_842661.1| 254 LKARLSEGQRgILIAGPPGSGKSTLAAGIA 283
                                    667788888746789**********99886 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   0.00021      0.12      11      42 ..     255     286 ..     250     296 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00021
                         AAA_30  11 ealltsgdrvavltGpAGtGKttalkalreaw 42 
                                    +a l++g+r  ++ Gp+G+GK+t+ ++++e +
  gi|116753543|ref|YP_842661.1| 255 KARLSEGQRGILIAGPPGSGKSTLAAGIAEYL 286
                                    56678889999****************99976 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00025      0.14       1      25 [.     265     289 ..     265     351 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00025
                   RNA_helicase   1 iwlyGpsgeGKStlakeLakallkk 25 
                                    i++ Gp+g GKStla  +a+ llk 
  gi|116753543|ref|YP_842661.1| 265 ILIAGPPGSGKSTLAAGIAEYLLKC 289
                                    6899**************9999954 PP

>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00042      0.23       2      49 ..     484     525 ..     483     532 .. 0.84
   2 ?   -1.2   0.1       3.9   2.2e+03      22      44 ..     566     597 ..     554     597 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00042
                           KH_5   2 GertkvaVkshnpnvdpvGaivgkkGsrikavsseLkgekidvvewse 49 
                                    ++ ++v V +++     +  ++gk G++i+++++ L g  id+  + e
  gi|116753543|ref|YP_842661.1| 484 DSSMVVTVPESQ-----IPRVIGKAGRNIEQIERAL-GMHIDIRGKRE 525
                                    567888888888.....999****************.****9966655 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.9
                           KH_5  22 ivgkkGsrikavsseLk.........gekidv 44 
                                     +g++G++  a sse++         ge+++v
  gi|116753543|ref|YP_842661.1| 566 TIGRRGDIRIAKSSEIArhvlnrlrrGERVEV 597
                                    56666666555555555555555558888876 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      0.18       4      34 ..     265     295 ..     264     307 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00032
                                    EEEE--TTSSHHHHHHHHHHHHHHTT--EEE CS
                          KTI12   4 vvltGlPssGKstrakeLakaleeekrsvvv 34 
                                    +++ G P sGKst+a+ +a++l + ++ v  
  gi|116753543|ref|YP_842661.1| 265 ILIAGPPGSGKSTLAAGIAEYLLKCNYVVKT 295
                                    799*******************998877765 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00037      0.21       1      28 [.     267     294 ..     267     297 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00037
                     ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgrsva 28 
                                    ++Gp+GsGK+t+   ++e+l ++++ v+
  gi|116753543|ref|YP_842661.1| 267 IAGPPGSGKSTLAAGIAEYLLKCNYVVK 294
                                    79*****************999876665 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00031      0.18      19      43 ..     264     294 ..     248     329 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00031
                         AAA_11  19 itliqGPPGtgKTktivellsqll......s 43 
                                      li GPPG+gK++  +++ ++ll      +
  gi|116753543|ref|YP_842661.1| 264 GILIAGPPGSGKSTLAAGIAEYLLkcnyvvK 294
                                    469*****************99974433330 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00054       0.3      36      54 ..     265     283 ..     250     300 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00054
                         AAA_25  36 allaGapgtGKttlaldla 54 
                                    +l+aG+pg+GK+tla  +a
  gi|116753543|ref|YP_842661.1| 265 ILIAGPPGSGKSTLAAGIA 283
                                    5789***********8776 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00053       0.3       2      24 ..     265     291 ..     264     302 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00053
                         AAA_28   2 ivitGgestGKTtlleaLaar....gy 24 
                                    i i G++++GK+tl++ +a+     +y
  gi|116753543|ref|YP_842661.1| 265 ILIAGPPGSGKSTLAAGIAEYllkcNY 291
                                    789**************9987664444 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       8.2   4.6e+03      50      67 ..     179     195 ..     126     208 .. 0.61
   2 ?   10.6   0.1   0.00099      0.56       2      18 ..     269     285 ..     268     296 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 8.2
                                    HHHHHHHHHHHHHHHHHH CS
                         AAA_17  50 pleekkelqkeaaekiae 67 
                                    p  ++k+l+++a e i++
  gi|116753543|ref|YP_842661.1| 179 P-IREKDLREMAREIIER 195
                                    2.2234455555444433 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00099
                                    E-TTSSHHHHHHHHHHH CS
                         AAA_17   2 GgPGsGKgtqceklvek 18 
                                    G+PGsGK+t+++ ++e 
  gi|116753543|ref|YP_842661.1| 269 GPPGSGKSTLAAGIAEY 285
                                    9***********99984 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   0.00055      0.31      14      52 ..     253     290 ..     235     296 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00055
                                    HHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.. CS
                         ResIII  14 nlleklkskrdkrglikmaTGtGKTlvaaklierllkkg 52 
                                    +l++ l+ ++++ +li+ + G+GK+ +aa ++e+llk +
  gi|116753543|ref|YP_842661.1| 253 ELKARLS-EGQRGILIAGPPGSGKSTLAAGIAEYLLKCN 290
                                    4556665.999***********************99865 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00076      0.42       5      22 ..     265     282 ..     262     296 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00076
                         AAA_24   5 iliyGpsgiGKTtlakel 22 
                                    ili Gp+g+GK+tla+ +
  gi|116753543|ref|YP_842661.1| 265 ILIAGPPGSGKSTLAAGI 282
                                    89************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (602 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); 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: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.42
# Mc/sec: 4321.38
//
Query:       gi|116753544|ref|YP_842662.1|  [L=178]
Description: hypothetical protein Mthe_0224 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1289.63
//
Query:       gi|116753545|ref|YP_842663.1|  [L=213]
Description: Zn-dependent hydrolase of the beta-lactamase fold [Methanosaeta thermophila PT]
Scores for complete 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-50  170.4   0.1      4e-50  169.9   0.1    1.2  1  Lactamase_B_3  Beta-lactamase superfamily domain
    6.6e-09   35.6   5.1    6.6e-06   25.8   0.1    2.1  2  Lactamase_B_2  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.9   0.1   4.4e-54     4e-50       2     163 .]       3     162 ..       2     162 .. 0.99

  Alignments for each domain:
  == domain 1  score: 169.9 bits;  conditional E-value: 4.4e-54
                  Lactamase_B_3   2 ltwlghnsflleta.garilvDPfkanlgyeppaeeaDlvlisqaledHahletlkqlaenvkvleegeslevggleira 80 
                                    ++w+gh++f ++++ g ++++DP ++++gy+ p+ +aD+vlis+++ dH++++++ +    + v+++++ ++++g+e+++
  gi|116753545|ref|YP_842663.1|   3 IKWFGHSCFQITDSiGRTVVTDPPDESVGYTLPPIRADIVLISHDHFDHNNADAVLG---SPIVIKHPGIYKAAGIEVKG 79 
                                    89***********88******************************************...******************** PP

                  Lactamase_B_3  81 vatshdavggsergenngflleqdgltiyhlGhlahelsseelkelgrvDvvltPvggpltlgqeealelakrLkpklvl 160
                                    v t+hd+ gg+ rg+n++f +++d+++++hlG+l+h l++++  ++g+vD++l+Pvgg++t++++ al ++ +Lkp+lv+
  gi|116753545|ref|YP_842663.1|  80 VGTYHDDAGGKLRGTNTVFCFTMDDIRVCHLGDLGHVLNDNDARAIGDVDILLIPVGGTFTIDARGALAVIDKLKPNLVI 159
                                    ******************************************************************************** PP

                  Lactamase_B_3 161 Pmh 163
                                    Pmh
  gi|116753545|ref|YP_842663.1| 160 PMH 162
                                    **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 !   11.2   1.7   2.1e-05      0.19      30      44 ..      38      52 ..      19      59 .. 0.75
   2 !   25.8   0.1   7.3e-10   6.6e-06     101     201 .]      73     163 ..      56     163 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.1e-05
                                   SEEEEE-SS--HHHH CS
                  Lactamase_B_2 30 pidaVllthaHyDHl 44
                                   + d Vl++h+H+DH 
  gi|116753545|ref|YP_842663.1| 38 RADIVLISHDHFDHN 52
                                   3488**********6 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 7.3e-10
                                    TTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---.HHHHHHHCT-SEEEEE-S-SSTTHHHHHHT-- CS
                  Lactamase_B_2 101 ggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyip.eeigerlggadllllditayeddemirhmgHl 179
                                    +g+e++ +   h+ +   ++ +g++  ++++ ++ rv+++gD+g++  +  ++ +g++d+ll++++         + +++
  gi|116753545|ref|YP_842663.1|  73 AGIEVKGVGTYHDDAG--GKLRGTNTVFCFTMDDIRVCHLGDLGHVLnDNDARAIGDVDILLIPVG---------GTFTI 141
                                    5788888888888888..8889999999*****************996555679999*********.........88999 PP

                                    -STSHHHHCTTSSSSEEEEESB CS
                  Lactamase_B_2 180 tpeeaveaaadlgakrlvliHi 201
                                    + ++a++++++l++  ++++H+
  gi|116753545|ref|YP_842663.1| 142 DARGALAVIDKLKPNLVIPMHY 163
                                    99*******************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       161  (0.00897987); expected 358.6 (0.02)
Passed bias filter:                      157  (0.00875676); 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: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 1462.64
//
Query:       gi|116753546|ref|YP_842664.1|  [L=302]
Description: GMP synthase subunit B [Methanosaeta thermophila PT]
Scores for complete 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-33  112.9   0.0    1.3e-32  111.7   0.0    1.7  1  GMP_synt_C       GMP synthase C terminal domain
    2.3e-10   40.0   0.0    2.6e-05   23.5   0.0    2.1  2  NAD_synthase     NAD synthase
    6.2e-05   22.6   0.0    0.00064   19.3   0.0    2.0  2  QueC             Queuosine biosynthesis protein QueC
    0.00021   20.2   0.1     0.0069   15.2   0.1    2.1  2  tRNA_Me_trans    tRNA methyl transferase
    0.00024   20.7   0.3     0.0053   16.4   0.1    2.8  2  ThiI             Thiamine biosynthesis protein (ThiI)
  ------ inclusion threshold ------
      0.019   14.3   0.0      0.083   12.2   0.0    1.8  2  Arginosuc_synth  Arginosuccinate synthase
      0.068   12.9   0.0        0.1   12.3   0.0    1.5  1  ATP_bind_3       PP-loop family
      0.092   12.4   0.0       0.15   11.7   0.0    1.3  1  Asn_synthase     Asparagine synthase


Domain annotation for each model (and alignments):
>> GMP_synt_C  GMP synthase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.7   0.0   5.8e-36   1.3e-32      11      92 .]     221     301 ..     210     301 .. 0.95

  Alignments for each domain:
  == domain 1  score: 111.7 bits;  conditional E-value: 5.8e-36
                                    GSSEEEEEEEEEEE----------EEEEEEEEE---------B----HHHHHHHHHHHHHHSTT---EEEE---TTTS-S CS
                     GMP_synt_C  11 kiwQafavllpvksvGvmgdkRtyeyvvalRaveseDamtadvaelpyevLekissrivnevkgvnrvvyditskPpati 90 
                                    k wQafa+++  k++Gv+gd+R y++vva+Rav+s+Damtadv elp+  L++issri+ e++gv+rvvydit kPp+ti
  gi|116753546|ref|YP_842664.1| 221 KPWQAFAAVIG-KATGVKGDNRVYGWVVAVRAVTSRDAMTADVLELPWGALRRISSRITGEIPGVSRVVYDITPKPPGTI 299
                                    67*******98.9******************************************************************* PP

                                    -- CS
                     GMP_synt_C  91 Ew 92 
                                    E+
  gi|116753546|ref|YP_842664.1| 300 EF 301
                                    *7 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   1.2e-08   2.6e-05      11      53 ..      12      53 ..       2      96 .. 0.75
   2 !   14.6   0.0   6.1e-06     0.014     146     177 ..     153     184 ..     134     191 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.2e-08
                                   HHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE-- CS
                   NAD_synthase 11 eyvkkagakgvvlGlSGGvDSslvaalavkalgkenvlalllP 53
                                   ++++++   ++++ lSGGvDSs+ a+la +alg en + +++ 
  gi|116753546|ref|YP_842664.1| 12 DEIRREVKGKAIIALSGGVDSSVCAVLAHRALG-ENLVPVYVD 53
                                   44555556789*********************6.566666655 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 6.1e-06
                                    -SBETTTTS-HHHHHHHHHHTT--HHHHCS-- CS
                   NAD_synthase 146 adlapiaellKtevkeLakelnvPervlkkpP 177
                                    + ++p+ +l+K ev+e a++l+ P ++ ++ P
  gi|116753546|ref|YP_842664.1| 153 GIIEPMRDLYKDEVREVARALGLPMEISERMP 184
                                    6689*************************998 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   2.9e-07   0.00064       1      55 [.      21      76 ..      21      99 .. 0.83
   2 ?    1.0   0.0      0.11   2.5e+02     154     179 ..     154     179 ..     103     182 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.9e-07
                                   EEEEE--SSHHHHHHHHHHHHH-.SEEEEEEEESS-TTSHHHHHHHHHHHHT--.- CS
                           QueC  1 kavvllSGGlDSttvlalakkeg.kevealtfdYgqrhkkeleaakkiakelgvee 55
                                   ka++ lSGG+DS+++++la+++  +++  + +d g  ++ e e   +++++l++ +
  gi|116753546|ref|YP_842664.1| 21 KAIIALSGGVDSSVCAVLAHRALgENLVPVYVDSGLMRRFESERIVELFSHLNLMK 76
                                   79*****************9875388999999999999999999999999999843 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.11
                                    EE-TTTT--HHHHHHHHHHTTHHHHH CS
                           QueC 154 ieaPlidlsKaeivklgkelgvplee 179
                                    i  P+ dl K e+ +++  lg+p+e 
  gi|116753546|ref|YP_842664.1| 154 IIEPMRDLYKDEVREVARALGLPMEI 179
                                    778******************99885 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   3.1e-06    0.0069       3      31 ..      22      51 ..      20      64 .. 0.81
   2 ?    2.9   0.0     0.017        39     164     187 ..     154     177 ..     148     182 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.1e-06
                  tRNA_Me_trans  3 vvvalSgGVDSsvaaallkeq.gyevigvf 31
                                    ++alSgGVDSsv a+l +++ g +++ v+
  gi|116753546|ref|YP_842664.1| 22 AIIALSGGVDSSVCAVLAHRAlGENLVPVY 51
                                   689*************99987345565555 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.017
                  tRNA_Me_trans 164 llfPlgeltKeevrkiAkeaglav 187
                                    ++ P+ +l K+evr++A++ gl++
  gi|116753546|ref|YP_842664.1| 154 IIEPMRDLYKDEVREVARALGLPM 177
                                    66799*************999975 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   2.4e-06    0.0053       2     116 ..      18     124 ..      17     189 .. 0.70
   2 ?    0.3   0.0       0.2   4.5e+02     145     169 ..     198     222 ..     191     238 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.4e-06
                           ThiI   2 tqgkvlaLlSgGiDSpVaaylllkR.Gcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdf.kevlkei 79 
                                    ++gk++  lSgG+DS V a l+ +  G + v v++++ ++   e     e+++el+++ +      l+ vd  ++ l+ +
  gi|116753546|ref|YP_842664.1|  18 VKGKAIIALSGGVDSSVCAVLAHRAlGENLVPVYVDSGLMRRFES----ERIVELFSHLN------LMKVDAsERFLNAL 87 
                                    689****************9998745999999**98777665554....34555554444......44444404555666 PP

                           ThiI  80 lekvkekltivllkrkmlriAekvaeeegakalvtGe 116
                                    +  ++++++  ++  +++r+ e+va e ga+ l++G 
  gi|116753546|ref|YP_842664.1|  88 RGVTDPEQKRKIIGETFIRVFEEVASEVGAEYLIQGT 124
                                    6666677777778889999999999999999999995 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.2
                           ThiI 145 igldKeeiiklAkeigtyeisieke 169
                                    i+ +K e++++A++i  +eis  k+
  gi|116753546|ref|YP_842664.1| 198 ITREKLEVVRTANAIVEEEISSFKP 222
                                    677899**************98765 PP

>> Arginosuc_synth  Arginosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   3.7e-05     0.083       1      64 [.      23      84 ..      23      90 .. 0.82
   2 ?   -0.9   0.0      0.34   7.6e+02     136     169 ..     154     185 ..     145     187 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.7e-05
                Arginosuc_synth  1 vLaysGGlDtsviikllkeklgeeviavavdvGqeeedldevkekalklgavksvvvDakeefv 64
                                   ++a sGG+D sv+  l +  lge+ + v vd G     +++ +   + ++ ++ + vDa+e f 
  gi|116753546|ref|YP_842664.1| 23 IIALSGGVDSSVCAVLAHRALGENLVPVYVDSGLM-RRFESERI-VELFSHLNLMKVDASERFL 84
                                   6899*****************************98.66665443.4446777888888888876 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.34
                Arginosuc_synth 136 viaPvReleltReeeieyakekgipvevtkkkpy 169
                                    +i P+R+  l+++e  e a++ g+p+e++++ py
  gi|116753546|ref|YP_842664.1| 154 IIEPMRD--LYKDEVREVARALGLPMEISERMPY 185
                                    7889997..689999999**********999998 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.6e-05       0.1       2      61 ..      22      77 ..      21     177 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.6e-05
                                   EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EE CS
                     ATP_bind_3  2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikl 61
                                   +++A+SgG+DS +  +l+++    lg +lv ++vd gl  + ++ +++v+ +++ + +k+
  gi|116753546|ref|YP_842664.1| 22 AIIALSGGVDSSVCAVLAHRA---LGENLVPVYVDSGLMRRFES-ERIVELFSHLNLMKV 77
                                   79**********999888887...45588889999888654433.344444444444444 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   6.5e-05      0.15      22      41 ..      24      43 ..      15      72 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.5e-05
                   Asn_synthase 22 alLSGGlDSSliaalaarqs 41
                                   + LSGG+DSS+ a la r +
  gi|116753546|ref|YP_842664.1| 24 IALSGGVDSSVCAVLAHRAL 43
                                   57***********9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); 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: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2264.81
//
Query:       gi|116753547|ref|YP_842665.1|  [L=268]
Description: MscS mechanosensitive ion channel [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-36  126.4   1.4    1.4e-36  126.0   1.4    1.2  1  MS_channel     Mechanosensitive ion channel
  ------ inclusion threshold ------
      0.069   13.4   0.0       0.13   12.6   0.0    1.5  1  PSP1           PSP1 C-terminal conserved region
       0.11   12.6   0.1       0.25   11.5   0.1    1.5  1  HAS-barrel     HAS barrel domain
        8.2    6.4   5.5       0.87    9.5   0.4    1.9  2  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 !  126.0   1.4   3.1e-40   1.4e-36       5     204 ..      70     267 ..      66     268 .] 0.90

  Alignments for each domain:
  == domain 1  score: 126.0 bits;  conditional E-value: 3.1e-40
                                    HHHHHHHHHHHHHHTTT--...SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEEEE-S CS
                     MS_channel   5 kiliivvgilivlsllgvn...vsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtVedigl 81 
                                       i+v gi +v  ++ +      alla++ ++gla+g+a+kd +snl++G+++ + +p+++GD+v++ +  G+Vedi+l
  gi|116753547|ref|YP_842665.1|  70 VASIYVAGIALVVLQIPQLyriAIALLAGASLAGLAIGFAAKDALSNLISGVFIAVFQPIRVGDYVTFRNDYGYVEDITL 149
                                    555666677777666666655456899***************************************************** PP

                                    SEEEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-TTS-EEEEEE CS
                     MS_channel  82 rttkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlkdkellvvld 161
                                    r t i+ +d+r +++Pns ++t+ i+N+s++++ +  +v++ ++ +s+   ++++ ++++e+++++p+vlk++e +v+l 
  gi|116753547|ref|YP_842665.1| 150 RHTVICIWDKRRIVVPNSVISTEVIVNWSMRDPVSVWTVDFLIQDASN---IDRAKSIILEIARSQPHVLKEMEIKVLLV 226
                                    ******************************999999************...***************************** PP

                                    EE-SSSEEEEEEEEEET...TTHHHHHHHHHHHHHHHHHHHT- CS
                     MS_channel 162 efgdsslnfevrvfvktvvpeeylsvqseinlrikkileeegi 204
                                    e + ++ ++++++   +   +  +++   i ++ kk++ +e i
  gi|116753547|ref|YP_842665.1| 227 ESTKDGNKLRLYFNSLN--RDLAFDTGCHILEEAKKAFMRERI 267
                                    ***99998888776666..788899999999999999998887 PP

>> PSP1  PSP1 C-terminal conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.9e-05      0.13      10      63 ..      45     244 ..      36     250 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.9e-05
                           PSP1  10 edvstnlenkqdeekalhiaqeklkeln.................................................... 37 
                                    + + + ++ ++++++++hi+ +++  +                                                     
  gi|116753547|ref|YP_842665.1|  45 NNILQAEHVEEERTRTFHIIIRRIVVASiyvagialvvlqipqlyriaiallagaslaglaigfaakdalsnlisgvfia 124
                                    56667777777777777777776666666777777777777777777777777777888888888888888888888888 PP

                           PSP1  38 ................................................................................ 37 
                                                                                                                    
  gi|116753547|ref|YP_842665.1| 125 vfqpirvgdyvtfrndygyveditlrhtviciwdkrrivvpnsvistevivnwsmrdpvsvwtvdfliqdasnidraksi 204
                                    88888888888888888888888888888888888888888888888888888888888888888888888888888888 PP

                           PSP1  38 ..............lnmklldaefqfdrkkltfyYvaeer 63 
                                                  +++k+l +e + d++kl +y+ + +r
  gi|116753547|ref|YP_842665.1| 205 ileiarsqphvlkeMEIKVLLVESTKDGNKLRLYFNSLNR 244
                                    888888888888889********************99777 PP

>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   5.5e-05      0.25      11      48 ..     119     149 ..     115     162 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.5e-05
                     HAS-barrel  11 sslifrvegskdvkvGeyVeielpdgeivlGmvtdirr 48 
                                    s++ ++v    +++vG+yV ++++     +G v+di  
  gi|116753547|ref|YP_842665.1| 119 SGVFIAVFQ--PIRVGDYVTFRND-----YGYVEDITL 149
                                    555666666..8************.....9****9987 PP

>> Bacillus_PapR  Bacillus PapR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.6      0.97   4.3e+03      10      22 ..      70      82 ..      68      85 .. 0.77
   2 ?    9.5   0.4   0.00019      0.87       6      32 ..      92     118 ..      90     128 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.97
                  Bacillus_PapR 10 vavamLaGvaFGv 22
                                   va   +aG+a  v
  gi|116753547|ref|YP_842665.1| 70 VASIYVAGIALVV 82
                                   7778899999877 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00019
                  Bacillus_PapR   6 aCsLvavamLaGvaFGvGqDqaLtnqq 32 
                                    a +L a a LaG a G     aL n  
  gi|116753547|ref|YP_842665.1|  92 AIALLAGASLAGLAIGFAAKDALSNLI 118
                                    7899*******************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       958  (0.053433); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); 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: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1923.00
//
Query:       gi|116753548|ref|YP_842666.1|  [L=749]
Description: Hef nuclease [Methanosaeta thermophila PT]
Scores for 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-25   87.7   0.0    4.5e-22   78.5   0.0    2.6  2  Helicase_C     Helicase conserved C-terminal domain
    5.7e-24   85.1   0.0    3.3e-23   82.6   0.0    2.1  2  ERCC4          ERCC4 domain
    5.5e-19   68.6   0.0    1.2e-18   67.5   0.0    1.6  1  DEAD           DEAD/DEAH box helicase
    1.3e-17   64.3   0.0    2.6e-17   63.3   0.0    1.5  1  ResIII         Type III restriction enzyme, res subunit
    2.1e-12   47.4   0.2    8.3e-11   42.3   0.0    3.2  3  HHH_5          Helix-hairpin-helix domain
    3.4e-11   43.1   0.0    1.1e-10   41.5   0.0    1.8  1  HHH_2          Helix-hairpin-helix motif
    2.2e-08   33.6   0.3     0.0012   18.6   0.0    3.4  3  HHH            Helix-hairpin-helix motif
     0.0022   18.3   0.0       0.37   11.2   0.0    3.4  2  HHH_8          Helix-hairpin-helix domain
     0.0033   18.0   0.1      0.088   13.4   0.0    3.2  2  5_3_exonuc     5'-3' exonuclease, C-terminal SAM fold
     0.0072   16.6   0.0       0.48   10.7   0.0    3.0  2  HHH_3          Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.016   14.5   0.0      0.023   14.0   0.0    1.3  1  SecA_DEAD      SecA DEAD-like domain
      0.038   13.2   0.0      0.067   12.4   0.0    1.3  1  ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
      0.071   13.4   1.0        3.3    8.0   0.1    4.0  5  AAA_22         AAA domain


Domain annotation for each model (and alignments):
>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.0    0.0071       9.9       8      96 ..      49     140 ..      42     155 .. 0.79
   2 !   78.5   0.0   3.3e-25   4.5e-22       3     110 ..     350     467 ..     345     468 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0071
                                    HHHHHTTTTSEEEEEESSHHHHHH.HHHHHHHT...TSTEEEESTTSTHHHHHHHHHHHH.TTSSSEEEESGGGTSSSTS CS
                     Helicase_C   8 ellkleeeggkilifvntidrlek.vklllekk...gikvavlhgelpqnereeileqfn.kgesdvLiatdvaerGidi 82 
                                     +l  + e+g++l  ++t+  +e+ + +l ++       va ++ge+  ++r ei ++ + + ++  ++  d ++  +d+
  gi|116753548|ref|YP_842666.1|  49 VML-ARLEKGRVLFLAPTRPLVEQhAAFL-RRVltsPDLVASVTGETDPESRAEIWRSCRiAVSTPQVVENDLLSGRMDL 126
                                    444.6788999999999999888853333.222444578899******************777777************** PP

                                    TTESEEEESSSSSS CS
                     Helicase_C  83 pkvnlVinfdlprn 96 
                                     +v+lVi+ ++ r 
  gi|116753548|ref|YP_842666.1| 127 RDVSLVIFDEAHRA 140
                                    *******8777655 PP

  == domain 2  score: 78.5 bits;  conditional E-value: 3.3e-25
                                    HHHHHHHHHHTTTTSEEEEEESSHHHHHH.HHHHHHHT..TSTEEEESTT........STHHHHHHHHHHHHTTSSSEEE CS
                     Helicase_C   3 leallellkleeeggkilifvntidrlek.vklllekk..gikvavlhge........lpqnereeileqfnkgesdvLi 71 
                                    le++ + l +++ +++i++f+n++d++   +++l+ +   ++k +++ g+        l+q+++ eile+f++ge++vLi
  gi|116753548|ref|YP_842666.1| 350 LEIIEDQL-ETSPESRIIVFTNYRDTATAlLRFLQANAsdAVKPVRFVGQasrendegLSQRKQSEILEKFRAGEYNVLI 428
                                    45666667.89999***********886556666433377444444555444555555********************** PP

                                    ESGGGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSST CS
                     Helicase_C  72 atdvaerGidipkvnlVinfdlprnvtsyiqriGRtgRa 110
                                    at+v+e+Gidip+ ++V ++++  +  + iqr+GRtgRa
  gi|116753548|ref|YP_842666.1| 429 ATSVGEEGIDIPSTDMVLFYEPVPSEIRSIQRKGRTGRA 467
                                    **************************************8 PP

>> ERCC4  ERCC4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       0.9   1.2e+03       9      57 ..     175     228 ..     169     336 .. 0.79
   2 !   82.6   0.0   2.4e-26   3.3e-23       1     154 [.     543     660 ..     543     662 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.9
                                    HHHH..HHTTTS.EEEEE--SSSSE.EE...CTT.......................E CS
                          ERCC4   9 gieeylleelgv.evvietlpigdyilwrrkvkaeynleldieepceek........v 57 
                                    +i e  +++lg+ +++ ++ + +d+  +   v+++++++   e+p++ +         
  gi|116753548|ref|YP_842666.1| 175 RIAEI-CANLGIeSIEMKSESDPDVAPF---VHHREIEWIKVEVPEQLQkirgvidgL 228
                                    46666.8999988888888888999889...999888888888887766666555553 PP

  == domain 2  score: 82.6 bits;  conditional E-value: 2.4e-26
                                    EEGGGCTSHHHH..HHTTTSEEEEE--SSSSE.EE...CTT...............EEEEEEEHHHHHHHHCC..SHHHH CS
                          ERCC4   1 iDsrelksgieeylleelgvevvietlpigdyilwrrkvkaeynleldieepceekvlverksaddlvasikd..grlee 78 
                                    +Dsre  +++ +  le+ g+++v ++l++gdy ++   + +                 +erk+addl++si+d  ++l++
  gi|116753548|ref|YP_842666.1| 543 VDSRE--RDMARL-LEKTGLRIVLRSLEVGDY-VL---SER---------------LGIERKTADDLIDSIIDpeRDLFR 600
                                    799**..778888.******************.99...999...............******************99**** PP

                                    HHHHHHH.H-SEEEEEEES-GGGTT................THHH.HHHHHHHHHHHHS-EEEEESSHHHHHHHHH CS
                          ERCC4  79 qvsrlkrngykkpillvegldqykrknknsrnkqykakvrqinrktiesaLvqlqldfgvsilttesanetaewla 154
                                    q+ +l+r  y++p+l++eg + y r+               ++++++ ++L+++++dfgv+i+ t s +eta ++a
  gi|116753548|ref|YP_842666.1| 601 QIGDLAR-TYDRPLLIIEGQNLYARQ---------------VHPNSVRGILATIAVDFGVPIVPTGSIEETAALIA 660
                                    *******.****************99...............********************************997 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.5   0.0   8.9e-22   1.2e-18      12     139 ..      28     147 ..      18     176 .. 0.78

  Alignments for each domain:
  == domain 1  score: 67.5 bits;  conditional E-value: 8.9e-22
                                    HTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  12 lgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardql 91 
                                    l  g+ lv ++TG GKT ++l+ +l+++      ++ ++l+++Ptr L+eq++  l++++   dl ++  ++g++  + +
  gi|116753548|ref|YP_842666.1|  28 L-RGSTLVVMPTGLGKTIVALMVMLARL------EKGRVLFLAPTRPLVEQHAAFLRRVLTSPDLVAS--VTGETDPESR 98 
                                    4.45899******************887......5679***********************9885444..6666666777 PP

                                    HHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHT.TTH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                           DEAD  92 skldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldq.gfs 139
                                    +++ ++++i v+tp+ + + l +g+++l++v+++++DEa+r   +  + 
  gi|116753548|ref|YP_842666.1|  99 AEIWRSCRIAVSTPQVVENDLLSGRMDLRDVSLVIFDEAHRAAGNyAYV 147
                                    777799************97767******************99883333 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 !   63.3   0.0   1.9e-20   2.6e-17      26     169 ..      31     169 ..      11     171 .. 0.85

  Alignments for each domain:
  == domain 1  score: 63.3 bits;  conditional E-value: 1.9e-20
                                    EEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--........- CS
                         ResIII  26 rglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseaykeigkkvsgdkkka.kekdstnk 104
                                      l++m+TG GKT+va+ ++ + l+kg   ++lfl+p++ l+eq    ++++l +++     +v+g+++ + +++   ++
  gi|116753548|ref|YP_842666.1|  31 STLVVMPTGLGKTIVALMVMLARLEKG---RVLFLAPTRPLVEQHAAFLRRVLTSPD--LVASVTGETDPEsRAEIWRSC 105
                                    679*************99999999974...7***************99999999997..78888888888855557799* PP

                                    SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHHHHT---....SEEEEEESS- CS
                         ResIII 105 kilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswreilekfke....avllglTATp 169
                                    +i v+t q + +d+      s +++     ++i+DEaHr++++ ++  i+e +++     ++lg+TA p
  gi|116753548|ref|YP_842666.1| 106 RIAVSTPQVVENDL-----LSGRMDLRDVSLVIFDEAHRAAGNYAYVYIAERYRReardPLVLGMTASP 169
                                    **************.....89999999999************88888886666444555********98 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       5.8     8e+03      22      44 ..     275     298 ..     271     299 .. 0.75
   2 ?    0.9   0.0      0.53   7.2e+02      41      54 ..     577     590 ..     554     593 .. 0.83
   3 !   42.3   0.0   6.1e-14   8.3e-11       3      53 ..     691     741 ..     689     743 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 5.8
                                    T--SHHHHHHS-HH.HHHTSTTS- CS
                          HHH_5  22 Giesvedlaaadve.eLakipGiG 44 
                                    Gi+ +++++++  + eLa+ +G++
  gi|116753548|ref|YP_842666.1| 275 GISLLAEIMKLKHAvELAETQGVS 298
                                    477788999886544899999987 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.53
                                    TTS-HHHHHHHHHH CS
                          HHH_5  41 pGiGkktAeriile 54 
                                     Gi  ktA+ +i++
  gi|116753548|ref|YP_842666.1| 577 LGIERKTADDLIDS 590
                                    59999999999976 PP

  == domain 3  score: 42.3 bits;  conditional E-value: 6.1e-14
                                    HHHT.STT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHH CS
                          HHH_5   3 eLls.vsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriil 53 
                                    +L+s ++G+Gp++A++ll++ ++sve ++ a++ eL ++  +G+ktA ri +
  gi|116753548|ref|YP_842666.1| 691 YLISaLPGVGPSVARNLLRH-FGSVERIMTASEGELMSVDKVGPKTAARIRE 741
                                    566559**************.*****************************76 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   0.0   7.7e-14   1.1e-10       8      54 ..     696     742 ..     692     746 .. 0.94

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 7.7e-14
                          HHH_2   8 IrhVGektAklLakrFksldaLkkasleeLlevddiGeeiAqsivef 54 
                                    ++ VG ++A++L ++F+s++++++as+ eL +vd +G+++A+ i+e 
  gi|116753548|ref|YP_842666.1| 696 LPGVGPSVARNLLRHFGSVERIMTASEGELMSVDKVGPKTAARIREI 742
                                    589*****************************************985 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.7   2.3e+03      10      19 ..     215     224 ..     215     224 .. 0.91
   2 !   11.0   0.0   0.00022       0.3      14      28 ..     694     708 ..     692     710 .. 0.85
   3 !   18.6   0.0   8.8e-07    0.0012       1      30 []     713     742 ..     713     742 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.7
                                    HHHHHTSTT- CS
                            HHH  10 reeLlalPGV 19 
                                    +e+L+++ GV
  gi|116753548|ref|YP_842666.1| 215 PEQLQKIRGV 224
                                    59******98 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00022
                                    HTSTT-SHHHHHHHH CS
                            HHH  14 lalPGVGpktAeaIl 28 
                                     alPGVGp++A+  l
  gi|116753548|ref|YP_842666.1| 694 SALPGVGPSVARNLL 708
                                    68*********9877 PP

  == domain 3  score: 18.6 bits;  conditional E-value: 8.8e-07
                                    SHHHHHTSSHHHHHTSTT-SHHHHHHHHHH CS
                            HHH   1 sleglipasreeLlalPGVGpktAeaIlsy 30 
                                    s+e++++as+ eL+++  VGpktA +I+++
  gi|116753548|ref|YP_842666.1| 713 SVERIMTASEGELMSVDKVGPKTAARIREI 742
                                    6899***********************986 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0       0.1   1.4e+02      43      61 ..     686     705 ..     672     711 .. 0.72
   2 !   11.2   0.0   0.00027      0.37      43      67 ..     718     743 ..     712     744 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.1
                                    HHHTT..HCTTSTT--HHHHH CS
                          HHH_8  43 tslee..eltklpgiGkkiaa 61 
                                    ++ ++   +++lpg+G+++a+
  gi|116753548|ref|YP_842666.1| 686 KE-QQeyLISALPGVGPSVAR 705
                                    34.22444488*******997 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00027
                                    HHH.TTHCTTSTT--HHHHHHHHHHH CS
                          HHH_8  43 tsl.eeeltklpgiGkkiaakieeil 67 
                                     ++ e+el +++ +G+k+aa+i+ei+
  gi|116753548|ref|YP_842666.1| 718 MTAsEGELMSVDKVGPKTAARIREIV 743
                                    4553559******************8 PP

>> 5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       3.4   4.7e+03      27      27 ..     316     316 ..     276     362 .. 0.52
   2 !   13.4   0.0   6.4e-05     0.088      20      50 ..     693     724 ..     688     741 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.4
                     5_3_exonuc  27 G 27 
                                    G
  gi|116753548|ref|YP_842666.1| 316 G 316
                                    3 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 6.4e-05
                     5_3_exonuc  20 ipGvpgiGektAakLlkeygsleeilenld.e 50 
                                    i   pg+G+  A +Ll+++gs+e i+ + + e
  gi|116753548|ref|YP_842666.1| 693 ISALPGVGPSVARNLLRHFGSVERIMTASEgE 724
                                    66789********************9966543 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       4.6   6.3e+03      43      52 ..     215     224 ..     202     227 .. 0.65
   2 !   10.7   0.0   0.00035      0.48      16      61 ..     693     740 ..     689     743 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4.6
                          HHH_3  43 reeLlkvkgl 52 
                                    +e+L+k++g+
  gi|116753548|ref|YP_842666.1| 215 PEQLQKIRGV 224
                                    6666666664 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00035
                          HHH_3  16 LqklpGlgpklAknIvayReknG..pfksreeLlkvkglgpktfeqla 61 
                                    ++ lpG+gp++A+n++++  +      +s  eL++v ++gpkt  +++
  gi|116753548|ref|YP_842666.1| 693 ISALPGVGPSVARNLLRHFGSVEriMTASEGELMSVDKVGPKTAARIR 740
                                    677888888888888888766651134455678888888888888876 PP

>> SecA_DEAD  SecA DEAD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.7e-05     0.023      85     195 ..      24     133 ..      12     340 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.7e-05
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      SecA_DEAD  85 GglvlhegkiaemkTGEGKtlvatlpaylnaltgkgvhvvtvndYLakrdaewmgpvyeflGlsvgvieseleseerrea 164
                                    ++ +l   +++ m TG GKt+va +  +l+ l++  v  ++    L ++ a+ +++v ++  l  +v   e+++e+r e+
  gi|116753548|ref|YP_842666.1|  24 AARALRGSTLVVMPTGLGKTIVALMV-MLARLEKGRVLFLAPTRPLVEQHAAFLRRVLTSPDLVASVT-GETDPESRAEI 101
                                    577888899999**********9875.6778998899999999********************77665.78899999999 PP

                                    xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      SecA_DEAD 165 Ye.aditYgtnnelgfdyLrDnlalskeelvq 195
                                    ++ + i   t + ++ d L  ++ l+  +lv 
  gi|116753548|ref|YP_842666.1| 102 WRsCRIAVSTPQVVENDLLSGRMDLRDVSLVI 133
                                    95499***************999998877743 PP

>> ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   4.8e-05     0.067      90     154 ..     408     470 ..     401     494 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.8e-05
                  ERCC3_RAD25_C  90 seaerlkilqkfkknpkvntiflskvgDtsiDlPeanvliqisshfgsrrqeaqrlGriLrakkk 154
                                    s++++++il+kf++  ++n+++   vg++ iD+P+  +++  +  + s  +  qr Gr  ra+++
  gi|116753548|ref|YP_842666.1| 408 SQRKQSEILEKFRAG-EYNVLIATSVGEEGIDIPSTDMVLFYE-PVPSEIRSIQRKGRTGRARTG 470
                                    688899*******87.789999999**********99988665.566777789999999999875 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1    0.0024       3.3       5     103 ..      29     140 ..      25     163 .. 0.73
   2 ?   -1.5   0.0         2   2.7e+03      22      69 ..     150     188 ..     146     208 .. 0.73
   3 ?   -1.8   0.0       2.5   3.5e+03      70      91 ..     289     313 ..     248     340 .. 0.67
   4 ?   -3.2   0.0       6.8   9.3e+03      51      77 ..     369     406 ..     345     422 .. 0.63
   5 ?    0.0   0.0       0.7   9.6e+02      75      98 ..     595     617 ..     577     651 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0024
                         AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst..sskdllrellralglelka....erlsseel 78 
                                    +g+++v+ ++G GKT ++ +++    e       + +v+f  ++ +     + +lr++l   +l ++      + s+ e+
  gi|116753548|ref|YP_842666.1|  29 RGSTLVVMPTGLGKTIVALMVMLARLE-------KGRVLFLAPTRPLveQHAAFLRRVLTSPDLVASVtgetDPESRAEI 101
                                    68999999************9999864.......5566655555554556666777777766665555666655666666 PP

                         AAA_22  79 lealeqalrarav..............ielliiDEaqhl 103
                                    ++ ++ a+++ +v              ++l+i DEa++ 
  gi|116753548|ref|YP_842666.1| 102 WRSCRIAVSTPQVvendllsgrmdlrdVSLVIFDEAHRA 140
                                    666666666666677777777778888999999999985 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2
                         AAA_22  22 lrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelk 69 
                                    ++r+++++         r+++v+   +s++s ++   e++ +lg e  
  gi|116753548|ref|YP_842666.1| 150 AERYRREA---------RDPLVLGMTASPGSEAERIAEICANLGIESI 188
                                    45555555.........7777766666677788888999999997765 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 2.5
                         AAA_22  70 a...erlsseellealeqalrarav 91 
                                        e++  ++l+++le+ +++++ 
  gi|116753548|ref|YP_842666.1| 289 VelaETQGVSALRQYLERLAQEARS 313
                                    1333556666666666666555543 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 6.8
                         AAA_22  51 tsskdllrellralglelka...........erlssee 77 
                                    t+ +d +++llr+l+ ++++           +r + e 
  gi|116753548|ref|YP_842666.1| 369 TNYRDTATALLRFLQANASDavkpvrfvgqaSRENDEG 406
                                    45566666677777666655555555555554444444 PP

  == domain 5  score: 0.0 bits;  conditional E-value: 0.7
                         AAA_22  75 seellealeqalraravielliiD 98 
                                    +++l++++ + +r++++ +llii+
  gi|116753548|ref|YP_842666.1| 595 ERDLFRQIGDLARTYDR-PLLIIE 617
                                    68999************.999994 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (749 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); 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 0.27s 00:00:00.91 Elapsed: 00:00:00.43
# Mc/sec: 5220.05
//
Query:       gi|116753549|ref|YP_842667.1|  [L=41]
Description: hypothetical protein Mthe_0229 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       115  (0.00641419); expected 358.6 (0.02)
Passed bias filter:                       98  (0.005466); 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: 0.31u 0.22s 00:00:00.53 Elapsed: 00:00:00.37
# Mc/sec: 329.71
//
Query:       gi|116753550|ref|YP_842668.1|  [L=463]
Description: amidophosphoribosyltransferase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-22   79.3   0.0    3.4e-22   78.7   0.0    1.3  1  GATase_7      Glutamine amidotransferase domain
    2.4e-22   79.6   0.0    4.8e-22   78.6   0.0    1.4  1  GATase_6      Glutamine amidotransferase domain
    4.3e-08   32.4   0.0    4.5e-06   25.8   0.0    2.3  2  GATase_4      Glutamine amidotransferases class-II
    4.8e-06   26.2   0.2      9e-06   25.3   0.2    1.4  1  Pribosyltran  Phosphoribosyl transferase domain


Domain annotation for each model (and alignments):
>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.7   0.0   7.5e-26   3.4e-22      11     122 ..      78     195 ..      68     196 .. 0.94

  Alignments for each domain:
  == domain 1  score: 78.7 bits;  conditional E-value: 7.5e-26
                       GATase_7  11 agaQPmvs.sedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea........ewgeealerlnGmfAfa 81 
                                    +++QP++   +d+++++++nG ++N  elr+eLe +g  f+t+sDtev+++ll +        + ++++++rl G++++a
  gi|116753550|ref|YP_842668.1|  78 ENSQPILVkYRDKTIAVAHNGNLVNSGELRSELEGAGDIFSTTSDTEVIAHLLVKeiqrydlaDAVRAVMRRLVGSYSLA 157
                                    6789*998789*****************************************9999******999*************** PP

                       GATase_7  82 iwdeeekrlllaRDrlGikPLyygedkgdallfaSelkall 122
                                    i+ +++  ++  RD+lGikPL +g  + d++++aSe  a+ 
  gi|116753550|ref|YP_842668.1| 158 IMCNDT--VIGLRDPLGIKPLCIGAID-DGIVVASESVAID 195
                                    ***999..******************6.7*******99986 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.6   0.0   1.1e-25   4.8e-22      11     134 .]      59     190 ..      42     190 .. 0.87

  Alignments for each domain:
  == domain 1  score: 78.6 bits;  conditional E-value: 1.1e-25
                       GATase_6  11 edevalaHvRlaivglaeeega.qPf..psedgrlllvhNGeiynykelreelpalkglafrsrsDtevllall....ee 83 
                                     + v+++HvR  ++g   + ++ qP+  + +d++++++hNG   n +elr el+  +g  f ++sDtev+++ll    ++
  gi|116753550|ref|YP_842668.1|  59 PGAVGIGHVRYPTSGAH-TLENsQPIlvKYRDKTIAVAHNGNLVNSGELRSELEG-AGDIFSTTSDTEVIAHLLvkeiQR 136
                                    3459************9.66666***9999*************************.9999************88888866 PP

                       GATase_6  84 lG.....eevlerlrGmfafaiwdkrentlilardrlgvkplyyavdesglafase 134
                                    ++      +v++rl+G ++ ai+   ++t+i +rd lg+kpl+++  ++g+++ase
  gi|116753550|ref|YP_842668.1| 137 YDladavRAVMRRLVGSYSLAIMC--NDTVIGLRDPLGIKPLCIGAIDDGIVVASE 190
                                    668788556669********9987..6889999**********************8 PP

>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0     1e-09   4.5e-06      73     145 ..      62     138 ..       5     158 .. 0.78
   2 !    4.3   0.0    0.0035        16     235     257 ..     200     222 ..     179     233 .. 0.67

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 1e-09
                       GATase_4  73 nvvaHiRkatqGevklenthpFvRelwgrewifAHnGdlke...ykpklegrfePvGsT.DsElafCelleelasrf 145
                                    + + H+R  t G+ +len++p   ++ ++++  AHnG+l +   ++ +leg      +T D+E++   l++e++++ 
  gi|116753550|ref|YP_842668.1|  62 VGIGHVRYPTSGAHTLENSQPILVKYRDKTIAVAHNGNLVNsgeLRSELEGAGDIFSTTsDTEVIAHLLVKEIQRYD 138
                                    5699***********************************66233445554444433333488888777778877665 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0035
                       GATase_4 235 etWkklepGellvfrdGalvata 257
                                       ++++pGe++v+rdG++    
  gi|116753550|ref|YP_842668.1| 200 RLIRDVAPGEMVVLRDGEMNCIR 222
                                    456789***********987654 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.2     2e-09     9e-06      26     120 ..     266     367 ..     247     369 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 2e-09
                                    --GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE...............EE----TTSEEEEE-SEES CS
                   Pribosyltran  26 yngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes.......rlledpagkkVliVDDild 98 
                                     +   d+v +i+  G+++a  ++++ ++++   + + ++ +++  ++ +s+ e        +  ++++g+++++VDD + 
  gi|116753550|ref|YP_842668.1| 266 HPADADIVSPIPDSGITMAVGYHQRSGIRYKECLMKNRYVGRTFIMPDQSMREAavrmkmnTIRPNIEGQRIVLVDDSIV 345
                                    455789999*****************999888888888888888888888888888888889****************** PP

                                    SSHHHHHHHHHHHCC-BSEEEE CS
                   Pribosyltran  99 tGgTllaalelLkekgpeevri 120
                                     G+T +++++ +k++g+++v++
  gi|116753550|ref|YP_842668.1| 346 RGTTSRRIVKMVKDAGAQKVHV 367
                                    ******************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 3564.19
//
Query:       gi|116753551|ref|YP_842669.1|  [L=56]
Description: 50S ribosomal protein L37e [Methanosaeta thermophila PT]
Scores for 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-22   78.5  13.0    3.3e-22   78.4  13.0    1.0  1  Ribosomal_L37e  Ribosomal protein L37e
  ------ inclusion threshold ------
      0.025   14.4   5.5        1.1    9.2   0.7    2.2  2  zf-HIT          HIT zinc finger
       0.23   11.1   1.3       0.36   10.4   1.3    1.3  1  MraY_sig1       Phospho-N-acetylmuramoyl-pentapeptide-transfe
       0.35   10.4   5.0        1.6    8.3   4.7    2.2  2  zn-ribbon_14    Zinc-ribbon
       0.77    9.5   5.7         11    5.8   0.3    2.9  3  Rubredoxin_2    Rubredoxin metal binding domain


Domain annotation for each model (and alignments):
>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.4  13.0   9.2e-26   3.3e-22       1      53 [.       2      54 ..       2      55 .. 0.97

  Alignments for each domain:
  == domain 1  score: 78.4 bits;  conditional E-value: 9.2e-26
                 Ribosomal_L37e  1 tkGtssfGkrqkkktHilCrrCgkrsyhvqkktCascGy.psaklrkynWsaKa 53
                                   +kGt+s+Gk+ +k+tH++CrrCg+ sy++++ktC +cG+ +s++lr+y+W +Ka
  gi|116753551|ref|YP_842669.1|  2 SKGTPSMGKC-HKRTHVRCRRCGRLSYNFNRKTCVACGFgRSKRLRSYKWMRKA 54
                                   69********.899**************************************97 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.7   0.00031       1.1       8      20 ..      11      23 ..       7      26 .. 0.90
   2 ?    7.9   0.4   0.00076       2.7       2      13 ..      31      43 ..      30      44 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00031
                                   T-SB-SEE-TTT- CS
                         zf-HIT  8 CgfpakYkCpkCn 20
                                   C++    +C++C+
  gi|116753551|ref|YP_842669.1| 11 CHKRTHVRCRRCG 23
                                   ************8 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00076
                                   --B-TTT-S.B-S CS
                         zf-HIT  2 rklCgvCgf.pak 13
                                   rk C+ Cgf  +k
  gi|116753551|ref|YP_842669.1| 31 RKTCVACGFgRSK 43
                                   89******97765 PP

>> MraY_sig1  Phospho-N-acetylmuramoyl-pentapeptide-transferase signature 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.3    0.0001      0.36       2       8 ..       3       9 ..       3       9 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0001
                      MraY_sig1 2 kGTPTMG 8
                                  kGTP+MG
  gi|116753551|ref|YP_842669.1| 3 KGTPSMG 9
                                  8*****9 PP

>> zn-ribbon_14  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   4.7   0.00045       1.6       2      18 ..      18      37 ..      17      39 .. 0.81
   2 ?    3.3   0.4     0.017        60       2       8 ..      33      39 ..      32      45 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00045
                   zn-ribbon_14  2 kCerCGylS...SqkiCkAC 18
                                   +C+rCG lS   + k C AC
  gi|116753551|ref|YP_842669.1| 18 RCRRCGRLSynfNRKTCVAC 37
                                   8********44455999999 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.017
                   zn-ribbon_14  2 kCerCGy 8 
                                   +C  CG+
  gi|116753551|ref|YP_842669.1| 33 TCVACGF 39
                                   7999997 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   0.0       0.4   1.4e+03      14      17 ..       8      11 ..       7      13 .. 0.77
   2 ?    5.8   0.3    0.0031        11       2      10 ..      18      26 ..      18      29 .. 0.78
   3 ?    5.5   0.2    0.0039        14       3      11 ..      34      42 ..      33      45 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.4
                   Rubredoxin_2 14 fGrC 17
                                   +G+C
  gi|116753551|ref|YP_842669.1|  8 MGKC 11
                                   7899 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0031
                   Rubredoxin_2  2 vCsqCGfes 10
                                   +C++CG  s
  gi|116753551|ref|YP_842669.1| 18 RCRRCGRLS 26
                                   799999766 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.0039
                   Rubredoxin_2  3 CsqCGfesa 11
                                   C +CGf  +
  gi|116753551|ref|YP_842669.1| 34 CVACGFGRS 42
                                   *****9766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); 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: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.43
# Mc/sec: 391.28
//
Query:       gi|116753552|ref|YP_842670.1|  [L=71]
Description: small nuclear ribonucleoprotein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-23   80.1   0.1    7.6e-23   80.0   0.1    1.0  1  LSM       LSM domain
     0.0039   17.3   0.0     0.0043   17.2   0.0    1.2  1  SM-ATX    Ataxin 2 SM domain


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.0   0.1   8.5e-27   7.6e-23       3      67 .]       9      71 .]       7      71 .] 0.96

  Alignments for each domain:
  == domain 1  score: 80.0 bits;  conditional E-value: 8.5e-27
                                   HHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTETEEEEEEEEEEEGGGEEEEEE CS
                            LSM  3 lkklinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkkekrklglvliRGnnivlisl 67
                                   l++++n+ v+v+lk+gr +rG L+g+D +mNlvLe++ee+ ++  + rk+g v++RG+n+v+is+
  gi|116753552|ref|YP_842670.1|  9 LNESLNSPVIVRLKDGRAFRGELQGYDIHMNLVLENTEEIAEG--TARKIGAVIVRGDNVVYISP 71
                                   899**************************************88..7*****************96 PP

>> SM-ATX  Ataxin 2 SM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   4.8e-07    0.0043      14      51 ..      15      50 ..       3      69 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.8e-07
                                   SEEEEEETTS-EEEEEEEEE-T..T--EEEEEEEETTS CS
                         SM-ATX 14 kevevtvknGevyeGifstvslekdfsvvLkmarkvkk 51
                                   ++v v++k+G  ++G +++++    +++vL+++ ++++
  gi|116753552|ref|YP_842670.1| 15 SPVIVRLKDGRAFRGELQGYDI--HMNLVLENTEEIAE 50
                                   689*******************..***********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.33u 0.26s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 533.19
//
Query:       gi|116753553|ref|YP_842671.1|  [L=161]
Description: putative RNA-binding protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-16   59.1   1.0    3.1e-16   59.1   1.0    1.6  2  PUA       PUA domain
    0.00074   19.7   0.0     0.0012   19.1   0.0    1.3  1  UPF0113   UPF0113 PUA domain
     0.0028   17.9   0.0     0.0047   17.2   0.0    1.4  1  DUF1947   Domain of unknown function (DUF1947)
  ------ inclusion threshold ------
      0.046   14.4   0.0       0.15   12.7   0.0    1.8  1  Pre-PUA   Pre-PUA-like domain


Domain annotation for each model (and alignments):
>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       1.8   7.9e+03      65      73 ..      11      19 ..       5      28 .. 0.55
   2 !   59.1   1.0     7e-20   3.1e-16       2      73 ..      81     152 ..      80     153 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.8
                                   SEEEEEEEE CS
                            PUA 65 gksveierv 73
                                   +k+ e++r+
  gi|116753553|ref|YP_842671.1| 11 LKGSEVKRI 19
                                   444444444 PP

  == domain 2  score: 59.1 bits;  conditional E-value: 7e-20
                                    EEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETT.SCEEEEEEESS-HHHHHHHCTSEEEEEEEE CS
                            PUA   2 rvvvddgAvkallsgasLlapGvvevegdfeegdvVaivded.gelvavGlanysseelakikggksveierv 73 
                                    +vvvd gAv+++++ga+++ pG+v+++ +++ gd V++v e  ++++avG+a+  + e+ k +g+ ++ i++v
  gi|116753553|ref|YP_842671.1|  81 TVVVDSGAVRFIANGADVMGPGIVQADPEIQTGDLVVVVEERhRKPLAVGRALRAGPEM-KGEGKAVESIHHV 152
                                    79***************************************88****************.6678888878776 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   2.7e-07    0.0012       3      71 ..      82     153 ..      80     155 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2.7e-07
                        UPF0113   3 vvkekaeklFL.YGrdvlkesilkitesvkenqvvvVlne.ngeplGiGkirkdt.kaspgkivvknlaDiG 71 
                                    vv  +++ +F+  G dv++ +i++ ++++++++ vvV+ e  ++pl++G++ + + + + +++ v+ +  +G
  gi|116753553|ref|YP_842671.1|  82 VVVDSGAVRFIaNGADVMGPGIVQADPEIQTGDLVVVVEErHRKPLAVGRALRAGpEMKGEGKAVESIHHVG 153
                                    44445666665269****************88777775551689*******998854788888888776666 PP

>> DUF1947  Domain of unknown function (DUF1947)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0     1e-06    0.0047       1      52 [.       7      60 ..       7      70 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1e-06
                                   --EE--HHHHHHHHHHHHTTT---TT--...-EEEE-S.S-EEEEETTEEEEEE CS
                        DUF1947  1 kRHfLSkKeakeileklkekyisislesdk.iEieeek.keklYlingvpilfe 52
                                   +RH L+  e k+il+ ++e+ ++ +   +   E++e++ ++ ++ +ng+p+l+ 
  gi|116753553|ref|YP_842671.1|  7 SRHHLKGSEVKRILSAIEERIEDPDGLRKAsMELAETDeGFEIIIVNGRPLLMI 60
                                   6********************9999887777******999**********9975 PP

>> Pre-PUA  Pre-PUA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.4e-05      0.15       6      71 ..       4      61 ..       2      77 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.4e-05
                        Pre-PUA  6 kvksntqlksSdrrkLraklleqfpslseeqleellpkkeevkvvklqgehvelyvvdgeplffqd 71
                                   ++ks+++lk+S+ +++ + + e+ +       + l   k++++++ +  e  e+++v+g pl++  
  gi|116753553|ref|YP_842671.1|  4 RIKSRHHLKGSEVKRILSAIEERIEDP-----DGL--RKASMELAETD-EGFEIIIVNGRPLLMII 61
                                   79******************9985333.....222..35556666666.66666666666655544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1259.90
//
Query:       gi|116753554|ref|YP_842672.1|  [L=99]
Description: hypothetical protein Mthe_0234 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); 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:                         0  (0); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 774.60
//
Query:       gi|116753555|ref|YP_842673.1|  [L=128]
Description: hypothetical protein Mthe_0235 [Methanosaeta thermophila PT]
Scores for complete sequence (score 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   15.5   0.9      0.022   14.7   0.9    1.3  1  PriA_CRR  PriA DNA helicase Cys-rich region (CRR) domain


Domain annotation for each model (and alignments):
>> 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 ?   14.7   0.9   1.2e-06     0.022      15      24 ..       3      12 ..       2      13 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.2e-06
                       PriA_CRR 15 nrLrCHyCgy 24
                                   ++L+CH+Cg+
  gi|116753555|ref|YP_842673.1|  3 KKLICHHCGS 12
                                   68*******6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); 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: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 945.10
//
Query:       gi|116753556|ref|YP_842674.1|  [L=311]
Description: DHH domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-30  103.6   0.6    8.9e-30  102.9   0.6    1.3  1  DHH       DHH family
    2.2e-24   86.3   0.9    3.4e-24   85.7   0.9    1.3  1  DHHA2     DHHA2 domain
  ------ inclusion threshold ------
      0.031   14.3   0.0      0.083   13.0   0.0    1.7  1  YmgD      YmgD protein


Domain annotation for each model (and alignments):
>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.9   0.6   1.5e-33   8.9e-30       1     101 []       4     146 ..       4     146 .. 0.89

  Alignments for each domain:
  == domain 1  score: 102.9 bits;  conditional E-value: 1.5e-33
                                    EEEEE-ECSSSHHHHHHHHHHHH.............................................CECS--TCGGCG CS
                                    xxxxxxxxxxxxxxxxxxxxxxx.............................................xxxxxxxxxxxx RF
                            DHH   1 kilivghknpDtDsigSaialan.............................................llvDhneksqav 35 
                                    +i++vghk+pDtDs++Sai +an                                             +lvDhne  qav
  gi|116753556|ref|YP_842674.1|   4 NIYVVGHKSPDTDSVTSAITYANlknqlgmkdvvpaaageinnetkyvleyfkiappvvlndatdkkvILVDHNEVGQAV 83 
                                    69*********************7777777777777777777777777777777777777777777777*********** PP

                                    CCHHCCCSEEEEEEE-S---SS---SS--EEEE-SSS-HHHHHHHHHHHTT----HHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DHH  36 egeakeeaedviiiDHHrlgeefetlapilflnepvgstaeivaelleekkeeiskeiaellllgi 101
                                    ++  + +a++++iiDHH++g +++t +pi+f+nepvg+t +i+a ++e +++ iske+a+l++++i
  gi|116753556|ref|YP_842674.1|  84 DN--IMKADILEIIDHHKIG-DIQTGKPIFFHNEPVGATGTIIASMYELNGVAISKEMAGLMMAAI 146
                                    **..****************.*******************************************98 PP

>> DHHA2  DHHA2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.7   0.9   5.7e-28   3.4e-24       1     143 []     182     308 ..     182     308 .. 0.81

  Alignments for each domain:
  == domain 1  score: 85.7 bits;  conditional E-value: 5.7e-28
                                    HHHHHHHT-STTS-HHHHTTTTEEEEE.ETTEEEEEEEEEES-HHHHHT.THHHHHHHHHHHH.HHT-SEEEEEEE.... CS
                          DHHA2   1 kelkkaksdlsglsledllrrDyKeftgeggvkvgiasvpvslsewleekrkgellaalekfaeerkldllvlmttfeee 80 
                                    +e+ kaksd+++++++d+l  D+K+f+  +gvk g+++++v++ + l  kr +e+la+++k  e++kld++vlm+t    
  gi|116753556|ref|YP_842674.1| 182 MEMLKAKSDIKSKTAKDILFGDFKKFD-FSGVKAGVGQIEVMDLADLAPKR-EEILAEMRKALESEKLDMIVLMLT---- 255
                                    59*************************.********************966.77*********9999*********.... PP

                                    .ETTT.EEEEEE....STT.HHHHHT---B.T.EEET...............T---HHHHTHHHHHHH CS
                          DHHA2  81 gdirr.elllaal.daaek.laealekase.e.leLeewkegaewrrvykqgnvkasRKqvaPllrea 143
                                    + i++ + ll++  +aa++ +++a++ + + + +  e               +v +++Kqv+P l++a
  gi|116753556|ref|YP_842674.1| 256 DVIKEaSDLLFVGtAAAKEgFEKAFGGKVTnNsIYKE---------------KVLSRKKQVIPPLESA 308
                                    5555595555553222222466666666443334434...............9***********9875 PP

>> YmgD  YmgD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.4e-05     0.083      29      69 ..     138     180 ..     119     188 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.4e-05
                                    HHHHHHHHHCCCSS..-----HHHHHHHHHHHHHHHHH-TT-B CS
                           YmgD  29 vavlGnasvesrdl..kikkspeldkdvveklnqvcakdPqml 69 
                                    +a l  a++ s  +  k    ++ dk+ vekl ++c +dPq +
  gi|116753556|ref|YP_842674.1| 138 MAGLMMAAILSDTVlfKSPTCTDKDKATVEKLSKICGEDPQKF 180
                                    5555555555554311444567999***************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); 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:                         3  (0.000167327); expected 0.2 (1e-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: 2130.00
//
Query:       gi|116753557|ref|YP_842675.1|  [L=114]
Description: deoxyribodipyrimidine photolyase-like [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-12   47.7   0.0    1.8e-12   47.6   0.0    1.1  1  DNA_photolyase  DNA photolyase


Domain annotation for each model (and alignments):
>> DNA_photolyase  DNA photolyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   0.0     1e-16   1.8e-12      22     101 ..       4      80 ..       1      92 [. 0.92

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 1e-16
                                    CTTSEEEEEEEE-HHHHTCGS-CHHHHHHHHHHHHHHHHHHHHTT--EEEEESSHHHHHHHHHHHCTECEEEEE---SHH CS
                 DNA_photolyase  22 asgepvipvfvldpekahklrvgaarvdfllesLadLdeeLrelgirLvvrrgdpadvlpelakelgasavvanreyepd 101
                                    + ++++++vf+l p+ +     g+++ +f+l +L++L+++L +lgi +++ +gdp +v+pe++ + ga  ++a++++ + 
  gi|116753557|ref|YP_842675.1|   4 RLNASLAVVFCLAPQ-FPGA--GDRSYRFMLDGLRELEQRLSSLGIAFIFTHGDPGNVIPEIIDDSGAGMLIADFSPLRI 80 
                                    66789**********.6667..***************************************************9998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       198  (0.0110436); expected 358.6 (0.02)
Passed bias filter:                      194  (0.0108205); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 875.48
//
Query:       gi|116753558|ref|YP_842676.1|  [L=367]
Description: tubulin/FtsZ, GTPase [Methanosaeta thermophila PT]
Scores for 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-35  120.8   0.0    1.4e-34  120.0   0.0    1.4  1  Tubulin    Tubulin/FtsZ family, GTPase domain
    2.5e-06   27.0   0.0    9.1e-06   25.1   0.0    2.0  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 !  120.0   0.0   1.6e-38   1.4e-34       2     195 ..       4     182 ..       3     184 .. 0.92

  Alignments for each domain:
  == domain 1  score: 120.0 bits;  conditional E-value: 1.6e-38
                                    EEEEEEHHHHHHHHHHHHH...HHHCH....HHHT.....TTEEEEE....EEESBHHHHHTS-GS......EEEE--CC CS
                        Tubulin   2 iivigvGqcGnqignelwellakehgiqsdgdslesfFsesgkveyiprsvaidtdpqvlneikagselfnpnklllgke 81 
                                    ++++gvGqcGn+i++++ +   +++g     ++l +++s+++  + +  ++ai+t  ++l+e+k       +++l++   
  gi|116753558|ref|YP_842676.1|   4 VLMLGVGQCGNRILDAVNR---QAFGG----SRLAKYYSKQRFPSRV-ETIAINTAINDLKELKFT---AAKDRLHV--- 69 
                                    899****************...56555....999******7766666.677****77777777777...77799999... PP

                                    CCTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE.SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTSEEEEEEEE--GG. CS
                        Tubulin  82 gagnngaggypevgkeaaeeileeirkevekcdslqgffitaslgGGTGSGlgpvilevlkeeypkalvvtvvvlPsefs 161
                                      + +g+g++++ gk+   e++e+i +e+ek   ++ +f+++s++GGTGS+++p++++ lk++y++a++v + vlP+++ 
  gi|116753558|ref|YP_842676.1|  70 -PNLHGVGANRSKGKQGFWENQEMILEEIEKRGDFDLIFVMTSVSGGTGSSFSPLMIHELKKRYKNATIVPIAVLPFRE- 147
                                    .7789************************************************************************99. PP

                                    G-HHHHHHHHHHHHHHHHT.-SEEEEEEHHHHHCC CS
                        Tubulin 162 evvvepynailalkeliee.sdavividNdaLlki 195
                                    e++++ +na+++l+e+ie  +d +i++dN+ L+++
  gi|116753558|ref|YP_842676.1| 148 EGTIYLQNAAFCLREMIEVeADGMILVDNQYLKRF 182
                                    ******************88************986 PP

>> Tubulin_2  Tubulin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0     0.064   5.8e+02       1      48 [.       5      58 ..       5      66 .. 0.74
   2 !   25.1   0.0     1e-09   9.1e-06     104     227 ..      63     173 ..      37     226 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.064
                      Tubulin_2  1 lviGLGGtGgkvlaelrrrlreel......gslelpdkvqFlyiDtdeneknrl 48
                                   l+ G+G  G ++l+++ r+ +          +++ p  v+ ++i t  n++++l
  gi|116753558|ref|YP_842676.1|  5 LMLGVGQCGNRILDAVNRQAFGGSrlakyySKQRFPSRVETIAINTAINDLKEL 58
                                   6789************99987665667766566677778888888887777655 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 1e-09
                      Tubulin_2 104 eleelrkapeseGAGqiRtvGRlalfanleeirealrdaikrlrgsageeeglnvfVvgSLaGGTGSGiflDvayllrki 183
                                     +++l+++++ +G G +R+ G+  + +n e i+e+++++ +             +fV++S++GGTGS+    +++ l+k 
  gi|116753558|ref|YP_842676.1|  63 AKDRLHVPNL-HGVGANRSKGKQGFWENQEMILEEIEKRGD-FD---------LIFVMTSVSGGTGSSFSPLMIHELKKR 131
                                    5566677766.999999999999999999999999987643.22.........49**************99999999999 PP

                      Tubulin_2 184 lkeekqkvkiiglvllPdvfplnkeggervkaNayaaLkELna.......l 227
                                    +k++     i+++++lP       e+g+ + +Na+  L E+         l
  gi|116753558|ref|YP_842676.1| 132 YKNAT----IVPIAVLPFR-----EEGTIYLQNAAFCLREMIEveadgmiL 173
                                    99988....9*******86.....568999999999999987755555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 2871.19
//
Query:       gi|116753559|ref|YP_842677.1|  [L=382]
Description: hypothetical protein Mthe_0240 [Methanosaeta thermophila PT]
Scores for complete 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   50.4   0.8    1.3e-10   41.4   0.0    2.6  2  DUF11          Domain of unknown function DUF11
    1.8e-11   43.7   0.3    2.2e-08   33.7   0.3    2.4  2  TRAP_beta      Translocon-associated protein beta (TRAPB)
    1.7e-10   41.0   0.2    6.6e-05   23.1   0.0    2.5  2  CARDB          CARDB
    4.3e-06   26.9   0.1      0.094   13.0   0.1    3.1  3  NPCBM_assoc    NPCBM-associated, NEW3 domain of alpha-galacto
    0.00014   20.8   6.7    0.00099   18.0   6.7    2.1  1  BatD           Oxygen tolerance
  ------ inclusion threshold ------
      0.039   14.4   0.5         13    6.2   0.0    2.5  2  Arrestin_C     Arrestin (or S-antigen), C-terminal domain
      0.067   13.5   1.0        8.7    6.7   0.4    2.7  2  DUF4352        Domain of unknown function (DUF4352)
       0.16   12.0   2.8         16    5.6   0.0    3.5  4  BsuPI          Intracellular proteinase inhibitor
       0.26   11.2   0.6        0.5   10.2   0.6    1.5  1  TTc_toxin_rep  Tripartite Tc toxins repeat
          1    9.6   4.8       0.23   11.7   0.7    2.0  2  Cohesin        Cohesin domain


Domain annotation for each model (and alignments):
>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   0.0   7.4e-14   1.3e-10       1      81 [.     136     210 ..     136     225 .. 0.88
   2 !    6.7   0.1    0.0048       8.5       8      44 ..     256     294 ..     249     347 .. 0.75

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 7.4e-14
                          DUF11   1 ltKtvdksevrpGdtvtytltvtNtgpasangvvvtDtlP.aglayvsvsasqgtasaltsv.gsLeagesatlsftvrv 78 
                                    + K++dk++v+ Gd+v++t+tv+N g+ +a ++ v D++P a +ay+ +           ++  +L +ge+    + +r+
  gi|116753559|ref|YP_842677.1| 136 VEKSFDKTTVNYGDEVKVTVTVKNIGTEAARNIEVYDIPPlAEFAYIAGYPP--------KIkSELGPGETDSAVYVMRA 207
                                    68**************************************999999998888........33458888888888888888 PP

                          DUF11  79 trt 81 
                                     ++
  gi|116753559|ref|YP_842677.1| 208 VKE 210
                                    765 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0048
                          DUF11   8 sevrpGdtvtytltvtNtgpasangvvvtDtl..Pagla 44 
                                    ++v++G+t    +   Ntg+a+a+ v v+  +  P+gl+
  gi|116753559|ref|YP_842677.1| 256 TNVTSGETAPIEVRIENTGQATATMVEVSSEVkpPEGLR 294
                                    58999******************9999986665555554 PP

>> TRAP_beta  Translocon-associated protein beta (TRAPB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.3   1.2e-11   2.2e-08      16     116 ..     130     229 ..     121     260 .. 0.87
   2 !    7.9   0.0     0.001       1.9      33     111 ..     260     335 ..     248     355 .. 0.76

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 1.2e-11
                      TRAP_beta  16 asarvlvkKkilnrllvegedltveytiyNvGssaAldVslvDdsfpeeaFevvsgslsakwerlapgenvshsfvvepk 95 
                                    a++ ++v+K++ +  +  g ++ v++t+ N+G++aA++++++D   p  +F  + g   +    l pge+ s ++v+++ 
  gi|116753559|ref|YP_842677.1| 130 AAPNLVVEKSFDKTTVNYGDEVKVTVTVKNIGTEAARNIEVYDIP-PLAEFAYIAGYPPKIKSELGPGETDSAVYVMRAV 208
                                    57899*************************************943.8899****************************** PP

                      TRAP_beta  96 ksgsfngtaavvtYresekga 116
                                    k+g  +    +v Yr++++  
  gi|116753559|ref|YP_842677.1| 209 KEGLVKVPQIEVRYRDAKDRI 229
                                    **************9888733 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.001
                      TRAP_beta  33 egedltveytiyNvGssaAldVslvDdsfpeeaFevvsgslsakwerlapgenvshsfvvepkksgsfngtaavvtYre 111
                                     ge   +e+ i N G+++A+ V+++ +  p+e     +  l+  +  ++pg+   ++ +++   sg++ ++  +v+Yr+
  gi|116753559|ref|YP_842677.1| 260 SGETAPIEVRIENTGQATATMVEVSSEVKPPEGLRCTG--LDQLIPEIPPGSAKIYTGEMRGERSGNYTIS-LTVSYRS 335
                                    5788899*****************99888888766543..6667777888888888888888888877664.5677754 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   3.7e-08   6.6e-05       2      40 ..     132     170 ..     131     211 .. 0.95
   2 !   15.6   0.0     8e-06     0.014       3      84 ..     248     331 ..     246     336 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 3.7e-08
                                    --EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEE CS
                          CARDB   2 pDLtvtntlnpseafvgeentitvtvkNqGtaasgatkv 40 
                                    p+L+v++++  +++++g+e+++tvtvkN Gt+a+++++v
  gi|116753559|ref|YP_842677.1| 132 PNLVVEKSFDKTTVNYGDEVKVTVTVKNIGTEAARNIEV 170
                                    99*********************************9987 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 8e-06
                                    -EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE.....EEEEESEE-CTEEEEEEEEEE-S-S-CE CS
                          CARDB   3 DLtvtntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelv.....gtvtvpsLaagesttvsftwtteatege 77 
                                    +L+    +n+++++ ge+  i+v ++N+G+a+++ ++v+  +   +       ++ +p++ +g+ +  +  +  e  +g+
  gi|116753559|ref|YP_842677.1| 248 NLVA--RINVTNVTSGETAPIEVRIENTGQATATMVEVSSEVKPPEGlrctgLDQLIPEIPPGSAKIYTGEMRGE-RSGN 324
                                    5555..78999***********************99999888876666677777888999998888888888887.8888 PP

                                    EEEEEEE CS
                          CARDB  78 vtltvvv 84 
                                    +t++++v
  gi|116753559|ref|YP_842677.1| 325 YTISLTV 331
                                    8887776 PP

>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       5.7     1e+04      57      71 ..      31      45 ..      29      48 .. 0.82
   2 !   10.6   0.0    0.0003      0.54       2      26 ..     146     170 ..     145     176 .. 0.89
   3 !   13.0   0.1   5.3e-05     0.094       1      52 [.     258     310 ..     258     334 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 5.7
                    NPCBM_assoc 57 vkVtppagaaaGdye 71
                                   ++++++++ + Gdy+
  gi|116753559|ref|YP_842677.1| 31 FTMSIGDRVEIGDYR 45
                                   789999999999997 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0003
                    NPCBM_assoc   2 epGetvtltltvtndgtaaatnvsl 26 
                                    + G++v++t+tv+n gt+aa+n+++
  gi|116753559|ref|YP_842677.1| 146 NYGDEVKVTVTVKNIGTEAARNIEV 170
                                    569********************98 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 5.3e-05
                    NPCBM_assoc   1 vepGetvtltltvtndgtaaatnvslslsl..PeGWtvvevspasaaslapGet 52 
                                    v+ Get  +++ + n+g+a+at v++s ++  PeG + +    + +++++pG +
  gi|116753559|ref|YP_842677.1| 258 VTSGETAPIEVRIENTGQATATMVEVSSEVkpPEGLRCTGL-DQLIPEIPPGSA 310
                                    578******************99999987776999884444.456778888766 PP

>> BatD  Oxygen tolerance
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   6.7   5.5e-07   0.00099     269     384 ..     132     260 ..     122     381 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 5.5e-07
                           BatD 269 gsfslsaslskdelkvgepltltvtisGtG.....NlkllqlPelnfpegfevYdpkpedntkktgnglsGsrteeyalv 343
                                     ++ ++ s++k++++ g+ + +tvt++  G     N++   +P+l + + +  Y+pk + +  + +     + +  y++ 
  gi|116753559|ref|YP_842677.1| 132 PNLVVEKSFDKTTVNYGDEVKVTVTVKNIGteaarNIEVYDIPPLAEFAYIAGYPPKIKSELGPGE-----TDSAVYVMR 206
                                    567789999*****************977766666888899999999999999****776666655.....566779999 PP

                           BatD 344 PrkaGkytipaiefsyFDtatkkyetatlpeitikVekga..............a 384
                                    + k+G +++p+ie+ y D  +++ +t t+++++i V++ +              +
  gi|116753559|ref|YP_842677.1| 207 AVKEGLVKVPQIEVRYRDA-KDRIKTNTTEPLEIIVAPPKrpnlvarinvtnvtS 260
                                    99**************995.6899************5444334443333322221 PP

>> Arrestin_C  Arrestin (or S-antigen), C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1      0.01        18       7      41 ..     136     170 ..     133     172 .. 0.88
   2 ?    6.2   0.0    0.0075        13       5      41 ..     247     283 ..     243     287 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.01
                                    EEEEES-SEEETT--EEEEEEEEE-SSSEEEEEEE CS
                     Arrestin_C   7 leaslpkkgyvpGetipvtvkidndskkkvkkikv 41 
                                    +e s++k+ +  G++++vtv+++n      ++i+v
  gi|116753559|ref|YP_842677.1| 136 VEKSFDKTTVNYGDEVKVTVTVKNIGTEAARNIEV 170
                                    56799*******************99999998887 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0075
                                    EEEEEEES-SEEETT--EEEEEEEEE-SSSEEEEEEE CS
                     Arrestin_C   5 vsleaslpkkgyvpGetipvtvkidndskkkvkkikv 41 
                                     +l a ++ + ++ Get p++v i+n  + +   ++v
  gi|116753559|ref|YP_842677.1| 247 PNLVARINVTNVTSGETAPIEVRIENTGQATATMVEV 283
                                    567889999*****************88777666665 PP

>> DUF4352  Domain of unknown function (DUF4352)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.4    0.0048       8.7      40      54 ..     151     165 ..     134     170 .. 0.84
   2 ?    4.4   0.0     0.024        43      36      63 ..     260     287 ..     212     295 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0048
                                    EEEEEEEEE-SSS-E CS
                        DUF4352  40 livdvtvkNkgkeal 54 
                                    ++v+vtvkN+g ea 
  gi|116753559|ref|YP_842677.1| 151 VKVTVTVKNIGTEAA 165
                                    89*********9975 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.024
                                    .SEEEEEEEEEEE-SSS-EEEEGGGEEE CS
                        DUF4352  36 ggeflivdvtvkNkgkealtvnssqfkL 63 
                                     ge + ++v+++N+g+ + t+ + + ++
  gi|116753559|ref|YP_842677.1| 260 SGETAPIEVRIENTGQATATMVEVSSEV 287
                                    4677789*********999987776655 PP

>> BsuPI  Intracellular proteinase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       3.3   5.9e+03      77      93 ..      32      48 ..      22      51 .. 0.69
   2 ?    3.9   0.2      0.03        55       4      27 ..     141     164 ..     138     167 .. 0.86
   3 ?   -0.4   0.1      0.68   1.2e+03       5      30 ..     255     280 ..     251     284 .. 0.81
   4 ?    5.6   0.0    0.0087        16      67      96 ..     304     332 ..     302     336 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.3
                                   EEEE.S---SEEEEEEE CS
                          BsuPI 77 eetwdedlepGeYtlea 93
                                   + ++ +++e G+Y++e 
  gi|116753559|ref|YP_842677.1| 32 TMSIGDRVEIGDYRAEL 48
                                   33333689999999875 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.03
                                    EEEEEE-SS-EEEEEEEEE-SSS- CS
                          BsuPI   4 aleaeasgeavelaltvtNesdea 27 
                                    ++++ + g++v++++tv+N ++ea
  gi|116753559|ref|YP_842677.1| 141 DKTTVNYGDEVKVTVTVKNIGTEA 164
                                    678888899***********9987 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.68
                                    EEEEE-SS-EEEEEEEEE-SSS-EEE CS
                          BsuPI   5 leaeasgeavelaltvtNesdeavtl 30 
                                    ++  +sge+  ++++++N+++ + t+
  gi|116753559|ref|YP_842677.1| 255 VTNVTSGETAPIEVRIENTGQATATM 280
                                    56667889999999999999988775 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.0087
                                    EE-TT-EEEEEEEE.S---SEEEEEEEEE- CS
                          BsuPI  67 tlepgesatyeetwdedlepGeYtleaelv 96 
                                    ++ pg +++y+ ++ +  ++G+Yt+  ++ 
  gi|116753559|ref|YP_842677.1| 304 EIPPGSAKIYTGEM-RGERSGNYTISLTVS 332
                                    589***********.899******998875 PP

>> TTc_toxin_rep  Tripartite Tc toxins repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.6   0.00028       0.5       3      21 ..     324     342 ..     322     350 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00028
                  TTc_toxin_rep   3 nYTtdiTVSnrSNRAVlss 21 
                                    nYT+++TVS rS  A+  +
  gi|116753559|ref|YP_842677.1| 324 NYTISLTVSYRSGDAMSIT 342
                                    9***********8887544 PP

>> Cohesin  Cohesin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.7   0.00013      0.23       4      28 ..     139     163 ..     136     172 .. 0.83
   2 ?   -2.4   0.2       2.8   5.1e+03       7      27 ..     255     275 ..     250     284 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                                    EESEEEE-TTSEEEEEEEEESECTT CS
                        Cohesin   4 kidkvsakvGdtvtvpvtvsnvskk 28 
                                    ++dk++++ Gd+v+v+vtv+n+ + 
  gi|116753559|ref|YP_842677.1| 139 SFDKTTVNYGDEVKVTVTVKNIGTE 163
                                    789*******************885 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.8
                                    EEEE-TTSEEEEEEEEESECT CS
                        Cohesin   7 kvsakvGdtvtvpvtvsnvsk 27 
                                     +++  G+t  + v+++n  +
  gi|116753559|ref|YP_842677.1| 255 VTNVTSGETAPIEVRIENTGQ 275
                                    444466777777777777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); 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: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.38
# Mc/sec: 3029.65
//
Query:       gi|116753560|ref|YP_842678.1|  [L=272]
Description: nicotinate-nucleotide pyrophosphorylase [Methanosaeta thermophila PT]
Scores for 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-58  197.9   0.3    1.3e-58  197.5   0.3    1.1  1  QRPTase_C       Quinolinate phosphoribosyl transferase, C-ter
    8.6e-25   86.6   0.0    1.8e-24   85.6   0.0    1.5  1  QRPTase_N       Quinolinate phosphoribosyl transferase, N-ter
    0.00014   21.3   0.3    0.00024   20.5   0.3    1.4  1  TMP-TENI        Thiamine monophosphate synthase
  ------ inclusion threshold ------
      0.034   13.9   0.2      0.058   13.2   0.2    1.3  1  KDGP_aldolase   KDGP aldolase
      0.037   13.4   0.4        1.7    8.0   0.0    2.2  2  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
      0.061   13.0   0.0       0.15   11.8   0.0    1.6  1  Fis1_TPR_N      Fis1 N-terminal tetratricopeptide repeat


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 !  197.5   0.3   4.3e-62   1.3e-58       1     169 []     101     268 ..     101     268 .. 0.98

  Alignments for each domain:
  == domain 1  score: 197.5 bits;  conditional E-value: 4.3e-62
                                    HHHHHHHHHHHHHCTSSEEEE-S---TTTHHHHHHHHHHTTSB--TSSTTTSEEE-HHHHHHHSSHHHHHHHHHHHHTTT CS
                      QRPTase_C   1 iAtltarmveaaksakvrildTRkttPglrllekyAvliGGgdnhrlgLsdmvlikdnhiaaagsiveavksvreavdke 80 
                                    iAtlt+++v +a+++  r+++TRkttPg+r++ek+AvliGGgd+hr++Ls +v+ikdnhia++g +++a+k++r+ ++++
  gi|116753560|ref|YP_842678.1| 101 IATLTRECVLRAQKV--RVACTRKTTPGFRYFEKKAVLIGGGDTHRFNLSGAVMIKDNHIAIMG-LEDAIKEARKRASFT 177
                                    9********999877..9*********************************************9.*************** PP

                                    SEEEEEESSHHHHHHHHHHT-SEEEEES--HHHHHHHHHHHHHHSTT..SEEEEESS--TTTHHHHHCTT-SEEEECHHC CS
                      QRPTase_C  81 vkievevesleeleevleaeadiimLDnfsveelkkaveelkeknkr..vlievSGgvtlenveeyaksgvdvisvgalt 158
                                    + ieveve l+ + +++e +adiim+Dn+++ee+k+ v +l+e+  r  v++e+SGg++  n+e+ya++gvdvis+galt
  gi|116753560|ref|YP_842678.1| 178 KMIEVEVEDLDTMIRAAELGADIIMFDNMNPEEIKRGVAMLEEMGVRsgVILEASGGINPGNLEAYASTGVDVISMGALT 257
                                    99***************************************99999999******************************* PP

                                    HTB----EEEE CS
                      QRPTase_C 159 hsvkalDislk 169
                                     +++++D+s++
  gi|116753560|ref|YP_842678.1| 258 RGARWMDFSME 268
                                    *********95 PP

>> QRPTase_N  Quinolinate phosphoribosyl transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.6   0.0     6e-28   1.8e-24       5      89 .]      19      99 ..      14      99 .. 0.95

  Alignments for each domain:
  == domain 1  score: 85.6 bits;  conditional E-value: 6e-28
                                   -HHHHHHGCTTSEEEEEEEESSSEEE-SHHHHHHHHHHHTTTEEEESS-TT-EEETTEEEEEEEEEHHHHHHHHHHHHHHHH CS
                      QRPTase_N  5 DlttealipeekkakaeiiakeegvvaGlevaeevfellpglevellvkDGervekgdvlleieGnarallsaERvaLnllq 86
                                   D t+   i ++ ++ a ii+ke++++aGle++ e+fe+l +++ e+l++DGe++++g+ ++ i+G+ar++l++ERvaLn+l 
  gi|116753560|ref|YP_842678.1| 19 DSTS---IVPDLNVDAAIISKEDCILAGLEEVSELFEYL-DVNSEPLFDDGEYATAGAEVMSIQGSARNILRGERVALNILG 96
                                   4444...999*****************************.****************************************** PP

                                   HHH CS
                      QRPTase_N 87 rlS 89
                                   r+S
  gi|116753560|ref|YP_842678.1| 97 RMS 99
                                   **9 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.3   8.2e-08   0.00024      69     177 ..     148     253 ..     133     255 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 8.2e-08
                       TMP-TENI  69 alavgadgvHlgq..ddlpvaearellgpdliiGlSvhsleeaeeaealgadYigvGpifpTdtKkdaeplgleglkela 146
                                      av ++  H+     + +++ear+     ++i + v++l+ + +a++lgad i++  + p + K     +g++ l+e+ 
  gi|116753560|ref|YP_842678.1| 148 SGAVMIKDNHIAImgLEDAIKEARKRASFTKMIEVEVEDLDTMIRAAELGADIIMFDNMNPEEIK-----RGVAMLEEMG 222
                                    55555555566553234478999999999****************************99877777.....6889999999 PP

                       TMP-TENI 147 ealeiPvvaiGGitlenvaevleagadgvav 177
                                     ++ + + a GGi++ n+++ + +g+d +++
  gi|116753560|ref|YP_842678.1| 223 VRSGVILEASGGINPGNLEAYASTGVDVISM 253
                                    999999*********************9987 PP

>> KDGP_aldolase  KDGP aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   1.9e-05     0.058     130     194 ..     177     243 ..     166     252 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.9e-05
                                    SS--EEEHHHHHHHHH..HCT--EEEE---TTTTTHHHHHHHHHHHHHCT-EEEEBSS--TTTHHHH CS
                  KDGP_aldolase 130 kekaivsvetaiallk..dmggssvkffpmeGlkrleelaavakaaakkgltlePtGGidldnfeei 194
                                    ++ ++v+ve   ++++  ++g++ + f  m+ ++ +  +a++ ++ +++g++le +GGi+  n+e+ 
  gi|116753560|ref|YP_842678.1| 177 TKMIEVEVEDLDTMIRaaELGADIIMFDNMNPEEIKRGVAMLEEMGVRSGVILEASGGINPGNLEAY 243
                                    566778888776676433899***************************************9999875 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 ?    8.0   0.0   0.00058       1.7      64     113 ..     182     230 ..     156     232 .. 0.83
   2 ?    5.5   0.1    0.0033       9.7     169     195 ..     229     255 ..     227     257 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00058
                                    EESSSHHHCHHHHHHCT-SEEEEE-ST-TTHHHHHHHHHHTTSEEEEEE- CS
                 Ribul_P_3_epim  64 LmveevdrivpefaeagasiisvHaEalehlkrtiqeikeaGakaglvln 113
                                    + ve++d ++ + ae+ga+ii++   + e++kr ++ + e+G+++g++l+
  gi|116753560|ref|YP_842678.1| 182 VEVEDLDTMIRA-AELGADIIMFDNMNPEEIKRGVAMLEEMGVRSGVILE 230
                                    457777777765.89********************************996 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0033
                                    EEEESS--TTTCHHHHHHT--EEEESH CS
                 Ribul_P_3_epim 169 ievDGGvkldnieqiaeagadvlVags 195
                                    +e+ GG++  n e+ a+ g+dv+ +g 
  gi|116753560|ref|YP_842678.1| 229 LEASGGINPGNLEAYASTGVDVISMGA 255
                                    7899*******************9985 PP

>> Fis1_TPR_N  Fis1 N-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   4.9e-05      0.15      15      28 ..     207     220 ..     207     221 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.9e-05
                     Fis1_TPR_N  15 nredqqeGiaLLee 28 
                                    n+e++++G+a+Lee
  gi|116753560|ref|YP_842678.1| 207 NPEEIKRGVAMLEE 220
                                    79***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1989.21
//
Query:       gi|116753561|ref|YP_842679.1|  [L=269]
Description: aspartate dehydrogenase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-30  105.9   0.3      1e-30  105.9   0.3    1.5  1  DUF108           Domain of unknown function DUF108
    2.7e-23   82.8   0.1    5.9e-23   81.7   0.1    1.6  1  NAD_binding_3    Homoserine dehydrogenase, NAD binding domain
    2.6e-07   30.8   0.0    5.7e-07   29.7   0.0    1.6  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
    4.4e-06   27.2   0.8    9.1e-06   26.2   0.8    1.5  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    1.8e-05   25.5   0.1    3.4e-05   24.6   0.1    1.4  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
    0.00075   18.9   0.0     0.0012   18.2   0.0    1.3  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
     0.0026   18.0   0.1     0.0065   16.7   0.1    1.7  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0066   16.9   0.0      0.011   16.2   0.0    1.4  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
     0.0073   17.0   0.3      0.013   16.2   0.3    1.4  1  CoA_binding      CoA binding domain
  ------ inclusion threshold ------
      0.014   15.5   0.1      0.023   14.9   0.1    1.4  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
      0.045   13.6   0.5      0.083   12.7   0.5    1.5  1  Rossmann-like    Rossmann-like domain
       0.13   12.5   0.0       0.22   11.8   0.0    1.3  1  NAD_Gly3P_dh_C   NAD-dependent glycerol-3-phosphate dehydroge
       0.17   12.3   1.3       0.23   11.9   0.2    1.8  2  DUF2122          RecB-family nuclease (DUF2122)


Domain annotation for each model (and alignments):
>> DUF108  Domain of unknown function DUF108
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.9   0.3   7.5e-34     1e-30       2      89 .]     170     255 ..     169     255 .. 0.98

  Alignments for each domain:
  == domain 1  score: 105.9 bits;  conditional E-value: 7.5e-34
                                    SS-EEEEEEEHHHHHHHSTTS-CHHHHHHHHHH.CCGEEEEEEEETT-SSEEEEEEEEETTEEEEEEEEE-EETTEEEEE CS
                         DUF108   2 teptvlFeGsareaikkfPknvNvaaalaLaalgfdrvkvelvadpnldkniheieveGsfgefslevenkpspenPkts 81 
                                    +ept+++eG+a+ea+++fP+nvNvaa+l+L     +++ v++v+dp+++ n+he+ +eG+fg++ ++ven+psp+nP+ts
  gi|116753561|ref|YP_842679.1| 170 REPTLIYEGPASEAVRAFPANVNVAATLSLTY--GQDAWVRIVVDPKATVNVHEVVAEGDFGRMVTRVENVPSPRNPRTS 247
                                    69*****************************9..79******************************************** PP

                                    HHHHHHHH CS
                         DUF108  82 alaalsvi 89 
                                    +laals+i
  gi|116753561|ref|YP_842679.1| 248 YLAALSAI 255
                                    ******86 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.7   0.1   4.3e-26   5.9e-23       1     117 []       9     121 ..       9     121 .. 0.94

  Alignments for each domain:
  == domain 1  score: 81.7 bits;  conditional E-value: 4.3e-26
                                    --SHHHHHHHHHHHH---SSEEEEEEEEESSEEE-TTHHHHHT--CB---HHHHHHHHS-EEEEE-S--HHHHTTHHHHH CS
                  NAD_binding_3   1 GlGaiGsavleqlkrqqseielelvavadrdsllskdrkallasealtldlddliahldpdvvVEcasseavaelvlkaL 80 
                                    G+GaiG +++++++r+    +++l+av dr+++  ++  + +++++++ +l++l++    d+vVE+as++av +++++aL
  gi|116753561|ref|YP_842679.1|   9 GCGAIGFEIASAIDRGDV--NADLAAVFDRNPKNMNRLIEAMRNKPEVVELEELAE--LSDIVVEAASQAAVPQVAEAAL 84 
                                    9****************8..8**********555555667888999999*******..********************** PP

                                    HTTEEEE-S--CGGG-HHHHHHHTSSSTTS--.EE-G CS
                  NAD_binding_3  81 kagkdvvtankgaladealyeeLreaaeangakiyve 117
                                    k+gkd++++++gal+d +ly+++ + ae++g ++y++
  gi|116753561|ref|YP_842679.1|  85 KRGKDIMIMSVGALMDRELYRRICSMAESSGGRVYIP 121
                                    **********************************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 !   29.7   0.0   4.1e-10   5.7e-07       1     101 [.       3      97 ..       3     121 .. 0.85

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 4.1e-10
                                    EEEEEETTTSHHHHHHHHHHHH.STTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH-SEEEE-S-HHH CS
                         DapB_N   1 ikvavvGasGrmGkevvkavee.aedlelvaavdrkeselegkdagellglgklgvavtddleevlekadvliDFTtpea 79 
                                    ikv++vG+ G +G e+++a+++ + ++ l+a++dr++     k++ +l++  +++ +v  +lee++e +d++++  + +a
  gi|116753561|ref|YP_842679.1|   3 IKVGLVGC-GAIGFEIASAIDRgDVNADLAAVFDRNP-----KNMNRLIEAMRNKPEVV-ELEELAELSDIVVEAASQAA 75 
                                    79******.***********996789**********9.....67778888877777776.89****************** PP

                                    HHHHHHHHHHTT-EEEE--SS- CS
                         DapB_N  80 vlenlklalekgvklViGTTGl 101
                                    v +++++al++g+++ i + G 
  gi|116753561|ref|YP_842679.1|  76 VPQVAEAALKRGKDIMIMSVGA 97 
                                    *************999877765 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 !   26.2   0.8   6.6e-09   9.1e-06       1      83 [.       4      85 ..       4      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 6.6e-09
                                   EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHCG CS
                  F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevlsela 82
                                   k+g++G+G +g+ +as + + ++++     + +rnp+ ++ l e++  k + v+ ee+ae +d+vv a   ++v++v++++ 
  gi|116753561|ref|YP_842679.1|  4 KVGLVGCGAIGFEIASAIDRGDVNADLAA-VFDRNPKNMNRLIEAMRNKPEVVELEELAELSDIVVEAASQAAVPQVAEAAL 84
                                   79**************7777775555555.56**********************************************9883 PP

                                   H CS
                  F420_oxidored 83 k 83
                                   k
  gi|116753561|ref|YP_842679.1| 85 K 85
                                   3 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 !   24.6   0.1   2.5e-08   3.4e-05       1      91 [.       3      92 ..       3      94 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.5e-08
                                   EEEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHE.EESSHHHHHTCTTESEEEE-S-GGGHHHHHHH CS
                   GFO_IDH_MocA  1 lrvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgve.aysdleelladpeidavivatpngtheelaka 81
                                   ++v+++G+G ig + + ++ + + +++++a++d+++++  ++ e+++ +  + +leel++    d+v+ a       ++a+a
  gi|116753561|ref|YP_842679.1|  3 IKVGLVGCGAIGFEIASAIDRGDVNADLAAVFDRNPKNMNRLIEAMRNKpEVVELEELAE--LSDIVVEAASQAAVPQVAEA 82
                                   68**************9****99999****************888888778999999999..7789999999999******* PP

                                   HHHTT-EEEE CS
                   GFO_IDH_MocA 82 aleagkhvll 91
                                   al++gk++++
  gi|116753561|ref|YP_842679.1| 83 ALKRGKDIMI 92
                                   ******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 !   18.2   0.0     9e-07    0.0012      38      97 ..       4      69 ..       3      89 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 9e-07
                                   EEEEES-SHHHHHHHHHHHHTT-E..E.EEESSSHHHHH...CHHHHTCEECSHHHHHHH-SEEEE CS
                   2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmk..v.iaydrskkkee...eeeelgvelvsleellaesDivsl 97
                                   +vG++G+G+IG ++a  +   +++  +  ++dr++k+ +   e+ +++ e+v+leel + sDiv+ 
  gi|116753561|ref|YP_842679.1|  4 KVGLVGCGAIGFEIASAIDRGDVNadLaAVFDRNPKNMNrliEAMRNKPEVVELEELAELSDIVVE 69
                                   69*****************7766522325678888877788766666779**************85 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 !   16.7   0.1   4.7e-06    0.0065       1     101 [.       5      95 ..       5     113 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.7e-06
                                    EEEE--SHHHHHHHHHHHCTCCT-G.EEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SSG CS
                Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvda.eitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnlspp 79 
                                    v ++G+G++G  +a  + r + v a   +v dr+ +++++l++++          ++ ++ + L++l +  d+vv ++ +
  gi|116753561|ref|YP_842679.1|   5 VGLVGCGAIGFEIASAIDRGD-VNAdLAAVFDRNPKNMNRLIEAM---------RNKPEVVE-LEELAELSDIVVEAASQ 73 
                                    6789**************975.5565999********99998643.........34444445.6666666899******* PP

                                    GGHHHHHHHHHHHT-EEEESS- CS
                Sacchrp_dh_NADP  80 issldvlkaCietgvhyvdtsi 101
                                        +v++a++++g + +  s+
  gi|116753561|ref|YP_842679.1|  74 AAVPQVAEAALKRGKDIMIMSV 95 
                                    ************9998776555 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 !   16.2   0.0   7.7e-06     0.011       1      93 [.       4      90 ..       4     130 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.7e-06
                                   EEEEETTTSHHHHHHHHHHHC.TSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGCTT-SEEEE-SCHHHHHH CS
                 Semialdhyde_dh  1 kvaivGatGyvGqellrlLee.hpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeelkevdivflalpagvske 81
                                   kv++vG  G++G e++  +++ + +++l++++ ++ ++ ++l ea++  ++ + +++e+      +  div+ a+++ +  +
  gi|116753561|ref|YP_842679.1|  4 KVGLVG-CGAIGFEIASAIDRgDVNADLAAVFDRNPKNMNRLIEAMR--NKPEVVELEE----LAELSDIVVEAASQAAVPQ 78
                                   79****.9*************************99955555555544..3333333433....44669************** PP

                                   HHHHHHHTTSEE CS
                 Semialdhyde_dh 82 lapklaeagvkv 93
                                   +a++++++g  +
  gi|116753561|ref|YP_842679.1| 79 VAEAALKRGKDI 90
                                   ********9854 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.3   9.3e-06     0.013       4      87 ..       3      88 ..       1      96 [. 0.91

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 9.3e-06
                                   EEEEEETTTSHHHHHH.HHHHHHHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHCT.TTEEEEES-HHHHHHHHHHHH CS
                    CoA_binding  4 tkviviGagglgiagl.yhfkeklkygikavfgvnprkvgtevlglpvyksvdeleekte.vdvavitvPaesaqeavdelv 83
                                    kv+++G g  g +++    + + +  + avf+ np+ + + ++ +  +++v elee  e  d+ v +++++++ +++++++
  gi|116753561|ref|YP_842679.1|  3 IKVGLVGCGAIGFEIAsAIDRGDVNADLAAVFDRNPKNMNRLIEAMRNKPEVVELEELAElSDIVVEAASQAAVPQVAEAAL 84
                                   69**************999999************************************98899999999********99999 PP

                                   HTT- CS
                    CoA_binding 84 eagi 87
                                   + g 
  gi|116753561|ref|YP_842679.1| 85 KRGK 88
                                   9764 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 ?   14.9   0.1   1.6e-05     0.023       1      79 [.       4      86 ..       4     129 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.6e-05
                                   EEEEE--SHHHHHHHHHHHHTT-E...EEEE-SSHHHHHHHHHTT..EEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHC CS
                  NAD_binding_2  1 kigfiGlGvMGsnmalnllkagyk...vavynrtkekveelvaeg..akaaesieelvasldvvitmvkagkavdeviegll 77
                                   k+g++G G +G ++a+ + + + +    av++r+++++++l+++      + ++eel++  d+v +   +++av +v e  l
  gi|116753561|ref|YP_842679.1|  4 KVGLVGCGAIGFEIASAIDRGDVNadlAAVFDRNPKNMNRLIEAMrnKPEVVELEELAELSDIV-VEAASQAAVPQVAEAAL 84
                                   69****************77665522258*************9974433333444444444444.44455666777766644 PP

                                   CC CS
                  NAD_binding_2 78 ea 79
                                   ++
  gi|116753561|ref|YP_842679.1| 85 KR 86
                                   43 PP

>> Rossmann-like  Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.5   6.1e-05     0.083      11      86 ..       3      81 ..       1      98 [. 0.74

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.1e-05
                  Rossmann-like 11 lsvGiisaGrvGtalgaaleraghv..vvgisaisaas.reraerrlPdvpvlevedvaaraellllavPdaelpglvk 86
                                   ++vG+++ G +G  ++ a++r +    + ++        +++ e++  + +v+e+e++a+ +++++ a   a +p++ +
  gi|116753561|ref|YP_842679.1|  3 IKVGLVGCGAIGFEIASAIDRGDVNadLAAVFDRNPKNmNRLIEAMRNKPEVVELEELAELSDIVVEAASQAAVPQVAE 81
                                   68******************976441144444433333034455555667899***************99999998765 PP

>> NAD_Gly3P_dh_C  NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00016      0.22      16      73 ..      12      73 ..       9      94 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00016
                                   HHHHHHHHHTTH-H.HH.HHHHHHHHHHHHHHHHHHHTSSGGGGG..STTTHHHHHHHHHSC CS
                 NAD_Gly3P_dh_C 16 AiaaGivdglglgd.nt.kaalitrglaEmarlakalgakpetfl..glaglgDlivtctsg 73
                                   Ai++ i+++++ gd n+  aa++ r  + m rl++a+ +kpe +   +la l D++v + s+
  gi|116753561|ref|YP_842679.1| 12 AIGFEIASAIDRGDvNAdLAAVFDRNPKNMNRLIEAMRNKPEVVEleELAELSDIVVEAASQ 73
                                   89999999**9999888569*****************9999944335999999999988876 PP

>> DUF2122  RecB-family nuclease (DUF2122)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       5.1     7e+03      17      35 ..      49      67 ..      46      68 .. 0.71
   2 ?   11.9   0.2   0.00017      0.23       2      25 ..      70      93 ..      69     100 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 5.1
                        DUF2122 17 klgksllvlpdlkDalell 35
                                   +++ +++ l++l +  +++
  gi|116753561|ref|YP_842679.1| 49 RNKPEVVELEELAELSDIV 67
                                   5555888899988887765 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00017
                        DUF2122  2 aAAqsGipevlklalklgksllvl 25
                                   aA+q  +p+v + alk+gk ++++
  gi|116753561|ref|YP_842679.1| 70 AASQAAVPQVAEAALKRGKDIMIM 93
                                   699******************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2072.46
//
Query:       gi|116753562|ref|YP_842680.1|  [L=152]
Description: hypothetical protein Mthe_0243 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-53  179.3   0.0    5.5e-53  179.1   0.0    1.0  1  DUF1890   Domain of unknown function (DUF1890)


Domain annotation for each model (and alignments):
>> DUF1890  Domain of unknown function (DUF1890)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.1   0.0   3.1e-57   5.5e-53       1     139 []       7     147 ..       7     147 .. 0.99

  Alignments for each domain:
  == domain 1  score: 179.1 bits;  conditional E-value: 3.1e-57
                                    EEE---S-STTHHHHHHHHHHHHHCTTEEEEEEE-HHHHHHHHHHSTT-SS-SEEEEHHHHHHH--TT..S-SEEEEEES CS
                        DUF1890   1 lillGCPevPvqtplalylanklkkkgievvvagnpaalkLlkvaDpekhYvkelvdldkaleeieek..dvdlllgfvh 78 
                                    l+l+GCPevPvq++l+lyl+ +l++kg++v++agnpaal+L +vaD +++Y+++l++l++++++i+e+  ++ ++++f+h
  gi|116753562|ref|YP_842680.1|   7 LLLMGCPEVPVQMSLVLYLSGALRDKGLKVFIAGNPAALNLARVADRKRCYLGRLIELERTIADIVEGrrSFGICFAFAH 86 
                                    79******************************************************************99********** PP

                                    SHHHHHHHHHHHHHH-.SEEEEEEE-S-HHHHHHHHHH--EEEEE--SS--HHHHHHHHHH CS
                        DUF1890  79 nDagvsyavtlkavlnkakliaivfgkdaeelaeliefdaeviaaravHnpkplkkkldev 139
                                    nDag++ya+t++a+l++a++++i+fg++aeela +++fdae+ia+ravHnp  lkkk+dev
  gi|116753562|ref|YP_842680.1|  87 NDAGITYAATVRALLPEARFFVIIFGRNAEELAGTVDFDAEKIAERAVHNPLGLKKKIDEV 147
                                    ***********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 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:                        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: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 1092.62
//
Query:       gi|116753563|ref|YP_842681.1|  [L=102]
Description: hypothetical protein Mthe_0244 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.7e-34  115.9   0.0      9e-34  115.7   0.0    1.0  1  DUF1894   Domain of unknown function (DUF1894)


Domain annotation for each model (and alignments):
>> DUF1894  Domain of unknown function (DUF1894)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.7   0.0     5e-38     9e-34       1      88 []       1      88 [.       1      88 [. 0.98

  Alignments for each domain:
  == domain 1  score: 115.7 bits;  conditional E-value: 5e-38
                                   B---HHH--S-SS-EEESSHHHHHHHHTTSEEEEES--EEESSS---SS----EEEE--.S-EEEE---SS-EEEEE-SS-G CS
                        DUF1894  1 maCleklkyeillkeasfkeceeyikkkakevyevepgykilgvrliGvppipvgidee.kilfpytkPCyGtfvlkvkese 81
                                   m+C+e lk +ill+++sf+e++eyi++ ++e+y+++pg++++g ++iG ppi+vgi+++ +i+fpytkPC+Gtfvlk  ++e
  gi|116753563|ref|YP_842681.1|  1 MGCIEMLKPQILLRGISFREAREYIESSCDECYHFQPGFRLFGEYIIGAPPIAVGIMKDgSIVFPYTKPCHGTFVLKH-RDE 81
                                   89****************************************************************************.899 PP

                                   GGHHHHH CS
                        DUF1894 82 eeieklr 88
                                   +e+e++r
  gi|116753563|ref|YP_842681.1| 82 AEAERVR 88
                                   9999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.29s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 725.28
//
Query:       gi|116753564|ref|YP_842682.1|  [L=189]
Description: flavoprotein [Methanosaeta thermophila PT]
Scores for complete 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   56.8   0.0    2.6e-15   56.5   0.0    1.2  1  Flavoprotein  Flavoprotein


Domain annotation for each model (and alignments):
>> Flavoprotein  Flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.5   0.0   1.4e-19   2.6e-15       2     119 ..       7     139 ..       6     175 .. 0.81

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 1.4e-19
                                    EEEEEE-SSCGGGCH.HHHHHHHHH...TTEEEEEEESCHHHHCCHHGGS..........TCSSHHHHHHCT........ CS
                   Flavoprotein   2 killgiTGsvaaika.lellekLkk...egievqvvltkaAkkfiskeklklaa......redpilhielrr........ 63 
                                    k+++giTGs + + + +++++++++   + ++++v++++a+ ++++  ++kl +                 +        
  gi|116753564|ref|YP_842682.1|   7 KVAWGITGSGDRLPEiVDMMKNVQEmyrDAVDIRVYISRAGDQVVK--YYKLFNeleasfD----------Kiwveanan 74 
                                    799********998889999999999989*****************..6666553333330..........244444666 PP

                                    ...........TESEEEEEEEEHHHHHHHHTT--SSHHHHHHHT..HCCTTEEEEE.--HHCCTCSTCH CS
                   Flavoprotein  64 ...........wadllviaPasantlakianGiadnlltlilra..takkpiliaPamnpamyenpqtl 119
                                               ++ +l+iaPa+ nt+aki + +ad+llt+ + +  +a +p +i+P    + ye+ +t+
  gi|116753564|ref|YP_842682.1|  75 apflagqlqlgKFAFLIIAPATSNTVAKISLRLADTLLTNAAIMaqKAYVPLYIMP----SDYEEGVTI 139
                                    77777777779****************************99944366666777777....566665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); 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: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1310.94
//
Query:       gi|116753565|ref|YP_842683.1|  [L=157]
Description: hypothetical protein Mthe_0246 [Methanosaeta thermophila PT]
Scores for complete 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   20.6   0.0    0.00022   20.4   0.0    1.2  1  S-layer   S-layer protein


Domain annotation for each model (and alignments):
>> S-layer  S-layer protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   1.2e-08   0.00022     113     163 ..      28      75 ..      23     122 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.2e-08
                        S-layer 113 tlksgssleLeegYeleikqiDvdgdkvwleLtkdgeevdskvissskads 163
                                    +l++g+sl+ + + +l ++++D +  +vwl+L+  g+ v s+v+      +
  gi|116753565|ref|YP_842683.1|  28 MLTTGESLQFAGNLTLVVEDVDPQAGRVWLSLYTSGSPVASSVLGI---GD 75 
                                    689****************************************988...33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1171.66
//
Query:       gi|116753566|ref|YP_842684.1|  [L=324]
Description: putative DNA-binding/iron metalloprotein/AP endonuclease [Methanosaeta thermophila PT]
Scores for 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-87  291.1   0.0    1.2e-86  290.8   0.0    1.0  1  Peptidase_M22  Glycoprotease family


Domain annotation for each model (and alignments):
>> Peptidase_M22  Glycoprotease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  290.8   0.0   6.5e-91   1.2e-86       9     271 .]      27     291 ..      22     291 .. 0.96

  Alignments for each domain:
  == domain 1  score: 290.8 bits;  conditional E-value: 6.5e-91
                                    EEEEE....SSSSHHHHHHHHHHHHHHHHHHHHHHH.TSTGGGEEEEEEEEESS-HHHHHHHHHHHHHHHHHCT--EEEE CS
                  Peptidase_M22   9 sqkelhakyGGvvPelasraHserllplieealaea.glsledldaIavtkgPGlftgLrvGvsfAkglalalnkPlvgV 87 
                                      ++++++ GG++P++a+++Hse++ pl++e+++ a +l ++ +d++a+++gPGl+++Lr ++++A+ lal+ln+PlvgV
  gi|116753566|ref|YP_842684.1|  27 RAATYTPARGGIHPREAAQHHSEHIGPLLREVIQGArDLGIK-IDGVAFSQGPGLGPCLRTVATAARVLALKLNVPLVGV 105
                                    445667888*************************99666665.************************************* PP

                                    EHHHHHHHCCHCTSECSSCEEEEESSSTEEEEEECTTEEEEEEEESSSEHHHHHHHHHHHHT..SSCCHHHHHHHCTC.S CS
                  Peptidase_M22  88 nhleahalaarleekeefPvvllvsGghtqvylvkegryeilgetlddaagealdkvarllglpypggpkieklakeg.k 166
                                    nh++ah++ ++ +++ ++P vl+vsGg++qv++ + gry+i+getld+ +g++ldk+ar +glp+pggp ie+la+++ +
  gi|116753566|ref|YP_842684.1| 106 NHCIAHIEIGKWKTGARDPAVLYVSGGNSQVLALRRGRYRIFGETLDISVGNMLDKFARSVGLPHPGGPRIEELARNAkE 185
                                    ***********999889*****************99****************************************9988 PP

                                    .......EETTEEE.CHHHHHHHHHHST.THHHHHHHHHHHHHHHHHHHHHHHHHHCTBSEEEEESGGGGXHHHHHCHCC CS
                  Peptidase_M22 167 kiefprplkgldfsfsGlktavlkelek.evedlaasfqeavvdhlvekteralklpkakelvilGGvaankrLrealee 245
                                    +i +p+++kg+dfsfsGl+ta+++++++ + ed+++s+qe+++++lve+tera+++ ++ke +++GGv+an+rL e+l+ 
  gi|116753566|ref|YP_842684.1| 186 YIPLPYTVKGMDFSFSGLATAAAEAARRyDLEDVCYSLQETAFAMLVEVTERAMAHAEKKEAMLVGGVGANRRLGEMLRL 265
                                    8*************************7777************************************************** PP

                                    HHHHTTSEEEXXXHHHHSSXCHHHHH CS
                  Peptidase_M22 246 eaeelglkliiPplkyctdnaamiaw 271
                                    ++ee+g++++ P+ +++ dn+ mia+
  gi|116753566|ref|YP_842684.1| 266 MCEERGARFYLPERRFMGDNGSMIAY 291
                                    ************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2395.36
//
Query:       gi|116753567|ref|YP_842685.1|  [L=468]
Description: phosphoribosylamine--glycine ligase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-58  197.8   0.0    2.3e-58  197.2   0.0    1.3  1  GARS_A       Phosphoribosylglycinamide synthetase, ATP-grasp 
      5e-26   91.3   0.0    8.3e-26   90.6   0.0    1.4  1  GARS_N       Phosphoribosylglycinamide synthetase, N domain
    2.7e-22   78.8   0.4    8.1e-22   77.3   0.1    1.9  2  GARS_C       Phosphoribosylglycinamide synthetase, C domain
  ------ inclusion threshold ------
      0.015   14.5   0.0      0.046   13.0   0.0    1.7  2  ATPgrasp_ST  Sugar-transfer associated ATP-grasp
      0.015   14.8   0.0      0.024   14.2   0.0    1.2  1  ATP-grasp    ATP-grasp domain
      0.036   14.1   0.0         10    6.1   0.0    2.2  2  ATP-grasp_3  ATP-grasp domain
       0.16   11.5   0.0       0.44   10.1   0.0    1.6  2  ATP-grasp_2  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 !  197.2   0.0   9.1e-62   2.3e-58       1     194 []     107     327 ..     107     327 .. 0.96

  Alignments for each domain:
  == domain 1  score: 197.2 bits;  conditional E-value: 9.1e-62
                                    HBHHHHHHHHHHTT--B--EEEESSHHHHHHHHHHHSSSE....EEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS.-T CS
                         GARS_A   1 asKsfakdllkkagiptaeyeaftdpeeakeyieeataka....lVvKadglaagKgvivakseeealkavkeilek.kk 75 
                                    +sK+++kdll+++g+p + y++f+dp+eake+++++ +      lV+KadglaagKg +v++s++eal++v+ i+++ + 
  gi|116753567|ref|YP_842685.1| 107 GSKCWTKDLLSEIGVPVPPYRNFDDPDEAKEFVDQFYDTHpgenLVIKADGLAAGKGSVVCSSRDEALSTVERIMVEpRI 186
                                    69*******************************998765555669*****************************987478 PP

                                    TCCCCSSEEEEE---SEEEEEEEEECTTEEEE---BEEEEEEECCCE..................EEEECECEEEES-TT CS
                         GARS_A  76 fGeagekvviEelleGeEvsllalvdgktvkplplaqdhkrvlegDk..................gpnTGGmGayspapv 137
                                    fG+ag+++ iE +leG E+ ++a+ dgk++ pl++a d+k+++  D+                  +pnTGGmG +sp+p+
  gi|116753567|ref|YP_842685.1| 187 FGDAGNRIEIERRLEGRELMFFAIADGKNILPLESAMDYKQAFAPDEitairlfnrlsgnpnlenNPNTGGMGGFSPHPW 266
                                    ******************************************************************************** PP

                                    S-HHHHHHHHHHTHHHHHHHHHCTT---EEEEEEEEEEE.TTE...EEEEEEESS--TTCH CS
                         GARS_A 138 vteellekikeeileptveglkkegipfkGvLyaglmlv.edg...pkvlefnvRfgDpet 194
                                    + ++l e+i+++i +pt+  + + g  ++G++y glm++ +dg   p+vle+nvR gDpe+
  gi|116753567|ref|YP_842685.1| 267 LDDDLRETIMSRIARPTMRRIYDMGLRYRGFIYFGLMIMeRDGerePYVLEINVRLGDPEA 327
                                    ***************************************666699**************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 !   90.6   0.0   3.2e-29   8.3e-26       2      90 .]       5     106 ..       4     106 .. 0.95

  Alignments for each domain:
  == domain 1  score: 90.6 bits;  conditional E-value: 3.2e-29
                                    EEEEEESSHHHHHHHHHHTTSTTESEEEEEE--CGG..............TTHHHHHHHHHHCTESEEEE-SHHHHHTTH CS
                         GARS_N   2 kvLvvGsGGRehalawklaqspkvekvyvapgNagt..............edlealvefakeekidlvvvGpeapLvaGv 67 
                                    ++Lvv  GGR +a+a+++++sp+vekv+vapgNag               ++++++++fa++++idl++vGpe  L aG+
  gi|116753567|ref|YP_842685.1|   5 RILVVDAGGRGNAIAHAFSRSPSVEKVFVAPGNAGSsllqkcsqadgaqiKSIDEMLSFAERNRIDLTFVGPEGYLSAGI 84 
                                    79**********************************9**9999988887766789************************* PP

                                    HHHHHHHHT-EEES--CCCCHHH CS
                         GARS_N  68 adaleeekgikvfGpskeaAqlE 90 
                                    +da+ee+ g+ ++Gp+++aA lE
  gi|116753567|ref|YP_842685.1|  85 VDAFEER-GLDIVGPERRAALLE 106
                                    ****888.************999 PP

>> GARS_C  Phosphoribosylglycinamide synthetase, C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0         6   1.5e+04      30      49 ..     362     379 ..     359     381 .. 0.72
   2 !   77.3   0.1   3.2e-25   8.1e-22      10      79 ..     385     465 ..     383     466 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 6
                                    ESSEEEEE-SSEEEEEEEEE CS
                         GARS_C  30 hagtklvtsGGRvlavvavg 49 
                                    h g  + + +GRv+  v+ g
  gi|116753567|ref|YP_842685.1| 362 HLG--VCAVSGRVVKPVSSG 379
                                    556..677789999877766 PP

  == domain 2  score: 77.3 bits;  conditional E-value: 3.2e-25
                                    TTTSS--ST-EEBS.....TTEEEEESSEE......EEE-SSEEEEEEEEESSHHHHHHHHHHHHTTCB-TTEE--STTT CS
                         GARS_C  10 GYPgsyekgkeitg.....egvkvfhagtk......lvtsGGRvlavvavgetleeArakayeavkkikfeglfyRkDIG 78 
                                    GYPg+  ++ +i+g      +v v+h+gt+      ++t+GGRvl++va g++l+eAr+kay+++++i+f+g+ yRkDIG
  gi|116753567|ref|YP_842685.1| 385 GYPGAHYTNIPIRGldkvdPDVLVYHNGTAfgdsgkIYTTGGRVLTLVAKGSSLAEARSKAYDNIRRIRFNGMRYRKDIG 464
                                    9***********99*****8899*******9999999******************************************9 PP

                                    H CS
                         GARS_C  79 a 79 
                                     
  gi|116753567|ref|YP_842685.1| 465 L 465
                                    5 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 ?   13.0   0.0   1.8e-05     0.046      13      85 ..     100     173 ..      97     183 .. 0.87
   2 ?   -2.4   0.0      0.86   2.2e+03     253     266 ..     309     322 ..     304     327 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.8e-05
                    ATPgrasp_ST  13 raefplvddKlkfkelalraglkvpkllgvikeqaeiseleafvkeleeg..vviKpakgsgGkGilviteredq 85 
                                    r+++ l  +K  +k+l+++ g++vp  +  ++  +e++e+ +   + ++g  +viK+    +GkG +v+++r+++
  gi|116753567|ref|YP_842685.1| 100 RRAALLEGSKCWTKDLLSEIGVPVPP-YRNFDDPDEAKEFVDQFYDTHPGenLVIKADGLAAGKGSVVCSSRDEA 173
                                    55556667899***************.9999999****9998888888999******************987664 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.86
                    ATPgrasp_ST 253 eekgplllElNarp 266
                                     e++p++lE+N r 
  gi|116753567|ref|YP_842685.1| 309 GEREPYVLEINVRL 322
                                    5788*******875 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   9.5e-06     0.024       2      61 ..     117     180 ..     116     201 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.5e-06
                                    HTTT--B-EEEEECCHHHHHHHHHHH.....-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC CS
                      ATP-grasp   2 eklglpvprflaveskeeleeaaeel.....glpvvvKarrlgydGkGqsvvrseedleqaleal 61 
                                    ++ g+pvp++   ++ +e++e+++++     g  +v+K + +   GkG+ v+ s++++ +++e +
  gi|116753567|ref|YP_842685.1| 117 SEIGVPVPPYRNFDDPDEAKEFVDQFydthpGENLVIK-ADGLAAGKGSVVCSSRDEALSTVERI 180
                                    6789************************9999******.566668*********99987777655 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0041        10       4      89 ..     109     219 ..     107     246 .. 0.80
   2 ?    5.8   0.0    0.0049        13     139     158 ..     301     322 ..     270     325 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0041
                                    HHHHHHHHTTT.S---..........-EESS--............SSSEEEEESS-------B--SS--TTE........ CS
                    ATP-grasp_3   4 KlktykkLkeagvkvP......tkleaeeleee............ekklvvKprdGaggesvrvveekeeaeaaieeve. 64 
                                    K  t + L+e gv+vP      +  e      +             ++lv+K    a+g++ +v   ++ea +++e +  
  gi|116753567|ref|YP_842685.1| 109 KCWTKDLLSEIGVPVPpyrnfdDPDE------AkefvdqfydthpGENLVIKADGLAAGKGSVVCSSRDEALSTVERIMv 182
                                    77788899999*****6655543333......33344558888889******99999**************999999877 PP

                                    ............EEEE---SEEEEEEEEE.SSSEEEE CS
                    ATP-grasp_3  65 ............lvqefieGkplSvsllsdgekvlvl 89 
                                                 + + +eG++l   +++dg+++l+l
  gi|116753567|ref|YP_842685.1| 183 eprifgdagnriEIERRLEGRELMFFAIADGKNILPL 219
                                    7888888888855677788888888888888877777 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0049
                                    EEEEEESS...SEEEEEEESS- CS
                    ATP-grasp_3 139 GvDlvlkd..eepyviEvNPRl 158
                                    G  ++ +d   epyv+E+N Rl
  gi|116753567|ref|YP_842685.1| 301 GLMIMERDgeREPYVLEINVRL 322
                                    555555556689*********8 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.1   2.8e+03      48      65 ..       9      26 ..       8      59 .. 0.56
   2 ?   10.1   0.0   0.00017      0.44       7      75 ..     112     180 ..     110     214 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.1
                                   -SSSTCCCTTCEEEESSH CS
                    ATP-grasp_2 48 vlaGGRGKagGvklvksk 65
                                   v aGGRG a    + +s+
  gi|116753567|ref|YP_842685.1|  9 VDAGGRGNAIAHAFSRSP 26
                                   679999998544444444 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00017
                                    HHHHHHCTT----SEEEESSHHHHHHHHHHHT....SSSEEEEE--SSSTCCCTTCEEEESSHHHHHHHHHCC CS
                    ATP-grasp_2   7 akeilakygvkvpegevaesaeeaeeaakklg....ekelvvKaQvlaGGRGKagGvklvkskeeakeaakel 75 
                                    +k++l++ gv+vp  +  ++++ea+e ++++     +++lv+Ka  la G+G      +++s +ea ++++++
  gi|116753567|ref|YP_842685.1| 112 TKDLLSEIGVPVPPYRNFDDPDEAKEFVDQFYdthpGENLVIKADGLAAGKGS----VVCSSRDEALSTVERI 180
                                    589************************9999622224679*****99988764....3455555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (468 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); 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: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 3362.12
//
Query:       gi|116753568|ref|YP_842686.1|  [L=433]
Description: glutamine synthetase, type I [Methanosaeta thermophila PT]
Scores for complete 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-132  439.8   0.0   7.3e-132  439.5   0.0    1.0  1  Gln-synt_C    Glutamine synthetase, catalytic domain
    1.7e-32  111.0   0.0    2.7e-32  110.3   0.0    1.3  1  Gln-synt_N    Glutamine synthetase, beta-Grasp domain
  ------ inclusion threshold ------
      0.035   13.9   0.0       0.14   12.0   0.0    2.0  1  Gln-synt_N_2  Glutamine synthetase N-terminal domain


Domain annotation for each model (and alignments):
>> Gln-synt_C  Glutamine synthetase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  439.5   0.0  1.2e-135  7.3e-132       2     345 .]      98     429 ..      97     429 .. 0.99

  Alignments for each domain:
  == domain 1  score: 439.5 bits;  conditional E-value: 1.2e-135
                                    T-HHHHHHHHHHHHHHTTCEEEEEEEEEEEEESEECCCESSEEEEEEE.TB...B.TSS-TTBHCCCCCTCCHHHHHHHH CS
                     Gln-synt_C   2 rdPRsvlkralarlaeeGltvvvgpElEFflfdkeedkeasksllevdseekgrpaekggyfsvapvdeaedlrreivea 81 
                                    +dPR+vlkr l+ +a++G+t++vgpElEFflf++e+              ++++p++ ggyf++ pvd aed+ reiv++
  gi|116753568|ref|YP_842686.1|  98 GDPRYVLKRNLEVAAKMGYTMNVGPELEFFLFERENG-------------SGTKPHDFGGYFDLGPVDLAEDVKREIVRV 164
                                    79*******************************9977.............4678999*********************** PP

                                    HHHTT--EECCEEECCCTEEEEEE--EECHHHHHHHHHHHHHHHHHHHHTT-EEE-SSSSSTTS---BEEEEEEEEECTT CS
                     Gln-synt_C  82 lealgieveashhEvatgQvEinlkfadalkaaDnvvtfKrvvkevArkhgltatFmpKplegdnGsgmHvhlSlwdkdg 161
                                    l ++g++vea+hhEva gQ+Ei++ +++al+ aD+vvtfK+v+k++A k++l+atFmpKp++g++GsgmHv++Sl+  +g
  gi|116753568|ref|YP_842686.1| 165 LIEMGFTVEAAHHEVARGQHEIDFVYDEALRNADKVVTFKYVTKTIALKNNLRATFMPKPIYGQAGSGMHVNISLF-RKG 243
                                    ****************************************************************************.*** PP

                                    EESSB-TTSGGGB-HHHHHHHHHHHHHHHHHHHHHS-SCCHHHHCSSSTTSSSBEEEESS-TTCSEEEE-TSGGCSTEEE CS
                     Gln-synt_C 162 knlfadeddeyalselarhfigGllkhakaltaltaptvnSYkRlvpgyeaPvalawgarNRsallRipaskekakrvEl 241
                                    +n f+d++++y+ls+++r+f+gGll+ha+a+ta+++p +nSYkRlv+g+eaPv+++w+  NRs l+R+pa+++ ++r+E+
  gi|116753568|ref|YP_842686.1| 244 ENTFFDPERPYNLSDVGRYFVGGLLEHAPAITAVANPLINSYKRLVSGFEAPVYISWSGPNRSSLIRVPAARGLSTRIEF 323
                                    ******************************************************************************** PP

                                    ECEBTTS-HHHHHHHHHHHHHHHHHTT--------S-SSSS-TTTH..TSS-B--SSHHHHHHHHHCSHHHCCSS-HHHH CS
                     Gln-synt_C 242 RlpdasaNPYLalAallaAgldGienklepgepvekdlyelspeer..kgieelPasleeAlealeedellkevlgeevi 319
                                    R+pd+s+NPYLa+Aa+laAgldGi+++++pgep++ +ly ls++e   +g++ lP++l+eAl aleed++++++lge+v+
  gi|116753568|ref|YP_842686.1| 324 RSPDPSCNPYLAFAAILAAGLDGIRKGIDPGEPLDLNLYGLSQAELdqLGVRMLPSNLHEALVALEEDKVIRDALGEHVV 403
                                    ********************************************99999******************************* PP

                                    HHHHHHHHHCHHHHHCT--HHHHHHH CS
                     Gln-synt_C 320 eaylalkraEleeleeevsdwelery 345
                                    ++ l+l + E+++++++v++we++ry
  gi|116753568|ref|YP_842686.1| 404 NNLLRLGKLEWRNYNTYVHQWEIDRY 429
                                    ***********************998 PP

>> Gln-synt_N  Glutamine synthetase, beta-Grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.3   0.0   4.5e-36   2.7e-32       1      82 [.       8      90 ..       8      91 .. 0.97

  Alignments for each domain:
  == domain 1  score: 110.3 bits;  conditional E-value: 4.5e-36
                                   T--EEEEEEE-SSS-EEEEEEEHHHHHHHTTTT-EEEETTSSTTT------EEEEEEEGGGEEE-SS-SS-...EEEEEEEE CS
                     Gln-synt_N  1 evkfvdlqFtDikgklkhvtipadelsedaleegvsFDGSsiegfaeieeSDmlLkPdlstavidPfreek..ktarvicdv 80
                                   +v+f++lqFtDi+g +k+v+ip+++l  +a++ g+sFDGSsiegfa+i+eSDm+LkPdl+t++i+P+r+    + ar+icdv
  gi|116753568|ref|YP_842686.1|  8 NVEFIRLQFTDIQGIVKNVAIPVTQL-GKAFKTGISFDGSSIEGFARIQESDMVLKPDLDTFCILPWRSMGgtNEARLICDV 88
                                   69************************.******************************************77789******** PP

                                   E- CS
                     Gln-synt_N 81 yd 82
                                   y+
  gi|116753568|ref|YP_842686.1| 89 YT 90
                                   *7 PP

>> Gln-synt_N_2  Glutamine synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.3e-05      0.14       8      51 ..       2      45 ..       1     109 [. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.3e-05
                                   ...------EEEEEEE-TTS-EEEEEEEGGGHHHHHTT-EEE-G CS
                   Gln-synt_N_2  8 eqleekqveLieflyvdlaGvtrGkalplasLeekLasGiGltk 51
                                   e ++ ++ve+i++ ++d +G+++  a+p ++L + +  Gi +  
  gi|116753568|ref|YP_842686.1|  2 EIIRDRNVEFIRLQFTDIQGIVKNVAIPVTQLGKAFKTGISFDG 45
                                   668899*****************************999997643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); 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: 00:00:00.43
# Mc/sec: 2990.39
//
Query:       gi|116753569|ref|YP_842687.1|  [L=132]
Description: protein tyrosine phosphatase [Methanosaeta thermophila PT]
Scores for complete 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   79.7   0.0    3.8e-22   79.2   0.0    1.3  1  LMWPc     Low molecular weight phosphotyrosine protein phosph


Domain annotation for each model (and alignments):
>> LMWPc  Low molecular weight phosphotyrosine protein phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.2   0.0   2.1e-26   3.8e-22       1     139 [.      12     129 ..      12     132 .] 0.92

  Alignments for each domain:
  == domain 1  score: 79.2 bits;  conditional E-value: 2.1e-26
                                    EEEEESSSSSHHHHHHHHHHHHHHHTT-CCCEEEEEEESTSTTT-B--HHHHHHHHHTTS--TT-BB-BS-HHHHHHSSE CS
                          LMWPc   1 vlfvClgNicRSpmAealfrkelekagleekvevdSaGtgalvgkradpravevlkekgislsghvarqlskeelaelDl 80 
                                    vlfvC+ N++RS+mAeal+r++  k   +++ e++SaG++     ++dp+av++++e gi++s+++++ l      ++D 
  gi|116753569|ref|YP_842687.1|  12 VLFVCVHNSARSQMAEALLRAL--K---GDNYEAYSAGIE---PTEVDPNAVSAMAEIGIDISEQRSKGLDSMRDIHFDT 83 
                                    89*******************9..2...57899*******...789**************************99999*** PP

                                    EEESSHHHHHHHHHHCCTTGGGGEEEGGGGSSTSS---HTTSSHHHHHHHHHHHHHHHH CS
                          LMWPc  81 ilamdeenkreleslapekekakvkllgeyteqldieDPyygeieafeevldeieeavk 139
                                    i+++++++    ++  p+          +   + + +DP++g+i+af++v+d+i++ ++
  gi|116753569|ref|YP_842687.1|  84 IVTLCDAAD--SCPYIPG-V--------H--MHRAFPDPAGGGINAFRRVRDDIKRWIE 129
                                    *****9887..9******.3........2..38899******************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); 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 0.27s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 950.33
//
Query:       gi|116753570|ref|YP_842688.1|  [L=372]
Description: radical SAM domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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-08   33.5   0.1    2.4e-07   31.3   0.0    2.2  2  Radical_SAM  Radical SAM superfamily
    1.6e-07   31.4   0.0    6.7e-07   29.5   0.0    1.9  2  HHH_3        Helix-hairpin-helix motif
    4.3e-05   23.2   0.0    0.00011   21.9   0.0    1.7  1  HHH          Helix-hairpin-helix motif
     0.0016   19.0   0.0     0.0039   17.8   0.0    1.7  1  HHH_5        Helix-hairpin-helix domain
  ------ inclusion threshold ------
      0.013   15.6   0.0      0.026   14.6   0.0    1.4  1  HHH_2        Helix-hairpin-helix motif
      0.048   13.9   0.1       0.13   12.6   0.1    1.7  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 !   31.3   0.0   8.1e-11   2.4e-07       3     157 ..      61     218 ..      59     245 .. 0.71
   2 ?   -2.0   0.0       1.3     4e+03      23      42 ..     270     289 ..     265     319 .. 0.72

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 8.1e-11
                                    EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTC......C CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx......x RF
                    Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlakla......v 75 
                                    +t+ C ++C +C++      +  g s ++ee+ ++v +l+ + g +++++l++g   + +   e++++ +++       +
  gi|116753570|ref|YP_842688.1|  61 FTNECYHQCGYCPNA----GTSNGCSYTPEELSNIVSSLR-REGlIDGLFLSSGAGRDEDSTMEEMLETVRILrerhgfS 135
                                    8999***********....58******************6.9999*******7755555444444444444434557766 PP

                                    CTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHH.......HHHHHHHHHHHHTTSET.... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxx.... RF
                    Radical_SAM  76 pgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtf.......eevlealeklreagikr.... 144
                                      i++ +     ++    +e+ +el  drvs+++ea++ ++ ++l  +++++       + +++ + +       r    
  gi|116753570|ref|YP_842688.1| 136 GYIHLKILPGTSRH---LIEEAVELA-DRVSINIEAPSMDVMHELS-PTKDYerdildrQMYIRDILAR------Rsrgs 204
                                    77777776666666...*********.*************777777.6666644444333333333322......13333 PP

                                    .EEEEEEEBTTTSH CS
                                    .xxxxxxxxxxxxx RF
                    Radical_SAM 145 .vvdrivglpGend 157
                                     ++  +vg  Ge+d
  gi|116753570|ref|YP_842688.1| 205 qTTQLVVGAAGETD 218
                                    47777777777776 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.3
                                    HHHHHHHHHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  23 egrgrslsveeileevkelk 42 
                                     +r++ ls+e+i++ ++ + 
  gi|116753570|ref|YP_842688.1| 270 LYRVYRLSPEQIKNVFDDYG 289
                                    67888999999999998887 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.7   4.9e+03      46      58 ..     270     282 ..     262     284 .. 0.74
   2 !   29.5   0.0   2.2e-10   6.7e-07       6      47 ..     309     349 ..     307     361 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.7
                          HHH_3  46 Llkvkglgpktfe 58 
                                    L +v++l+p+++ 
  gi|116753570|ref|YP_842688.1| 270 LYRVYRLSPEQIK 282
                                    6788888888765 PP

  == domain 2  score: 29.5 bits;  conditional E-value: 2.2e-10
                          HHH_3   6 vdiNtAsaeeLqklpGlgpklAknIvayReknGpfksreeLl 47 
                                     d+N A+ + L ++pG+gp  A++I+ yR  + +++s+ +L 
  gi|116753570|ref|YP_842688.1| 309 LDVNEADFQSLIRVPGIGPESARRIISYR-RRERIESPSDLI 349
                                    69***************************.666999999986 PP

>> HHH  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   3.7e-08   0.00011       5      30 .]     311     336 ..     309     336 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 3.7e-08
                                    HHTSSHHHHHTSTT-SHHHHHHHHHH CS
                            HHH   5 lipasreeLlalPGVGpktAeaIlsy 30 
                                    +++a++  L  +PG+Gp+ A++I+sy
  gi|116753570|ref|YP_842688.1| 311 VNEADFQSLIRVPGIGPESARRIISY 336
                                    789*********************98 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.3e-06    0.0039      34      53 ..     316     335 ..     298     356 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.3e-06
                                    HHHHHTSTTS-HHHHHHHHH CS
                          HHH_5  34 veeLakipGiGkktAeriil 53 
                                     + L ++pGiG++ A+rii 
  gi|116753570|ref|YP_842688.1| 316 FQSLIRVPGIGPESARRIIS 335
                                    55555555555555555553 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   8.8e-06     0.026      30      59 ..     312     341 ..     308     344 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.8e-06
                          HHH_2  30 kkasleeLlevddiGeeiAqsivefFenek 59 
                                     +a+++ L+ v++iG+e A+ i+++ + e+
  gi|116753570|ref|YP_842688.1| 312 NEADFQSLIRVPGIGPESARRIISYRRRER 341
                                    68*********************9977665 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   4.3e-05      0.13       4      61 ..      52     109 ..      49     160 .. 0.71
   2 ?   -2.5   0.0         2   5.8e+03     121     137 ..     250     266 ..     222     267 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.3e-05
                        Fer4_12   4 eGvrl..slfvsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesi.egltllGG 61 
                                      vrl  +lf++ C ++C +C n  t    +g  +t e l +i+ +l  e   +gl l+ G
  gi|116753570|ref|YP_842688.1|  52 CHVRLfkTLFTNECYHQCGYCPNAGTS---NGCSYTPEELSNIVSSLRREGLiDGLFLSSG 109
                                    44665559**************99886...5677887888888888866443366666655 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2
                        Fer4_12 121 esledeslrfrgssnqr 137
                                    ++ ++++lr+r s++++
  gi|116753570|ref|YP_842688.1| 250 FEGKQPQLRWRESRLYQ 266
                                    55677889999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); 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: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2973.27
//
Query:       gi|116753571|ref|YP_842689.1|  [L=319]
Description: N(5),N(10)-methenyltetrahydromethanopterin cyclohydrolase [Methanosaeta thermophila PT]
Scores for 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-126  419.5   0.1   9.3e-126  419.3   0.1    1.0  1  MCH       Cyclohydrolase (MCH)


Domain annotation for each model (and alignments):
>> MCH  Cyclohydrolase (MCH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  419.3   0.1  5.2e-130  9.3e-126       1     311 []       2     314 ..       2     314 .. 0.99

  Alignments for each domain:
  == domain 1  score: 419.3 bits;  conditional E-value: 5.2e-130
                                    -HHHHHHHHHHHHHHTHHHHT-EEEE-TTS-EEEESSSSS---HHHHHHHHHHHTTT-EEEEEEEEEETTEEEEEEEEEE CS
                            MCH   1 SvnelalelveellekaeelrieveelengatviDaGveaeGgleAGlllaeiclggLaevslelsevkgaklpavevst 80 
                                    S+ne+++e++ee+l+ a++lr++v elenga viDaGv+a+Ggl AG+ +++ic+++La++++ +   kg+++p ++v+t
  gi|116753571|ref|YP_842689.1|   2 SINEMGFEVFEEMLDLADDLRVDVIELENGAVVIDAGVKAPGGLWAGIFISRICMADLADIQIVPYGLKGISVPGIQVTT 81 
                                    8******************************************************************************* PP

                                    SSHHHHHTTTTS--EEEEETTEEEEEESTTHHHHTS.HHHHHHHT-----S-EEEEEESSS---HHHHHHHHHHHTS-GG CS
                            MCH  81 dhPvlacLasqkAgWelsaekffalgsGPaRalaak.eelfeelgyedeadaavlvlesdklPdeevvekvaeecgvepe 159
                                    dhP+++c++sq+A W+++++k+fa+gsGPaRala+k ++l+e++g+ + +d++++vle++++Pd++v++++ae cg+ep+
  gi|116753571|ref|YP_842689.1|  82 DHPAISCMGSQCAMWQIKVDKYFAMGSGPARALARKtKDLYERIGFDEYSDVGAIVLEASRIPDAAVAARIAEMCGIEPS 161
                                    ******************************************************************************** PP

                                    GEEEEEE-SSSHHHHHHHHTTHHHHHHHHHHHTT--GGGEEEEEEEEE-----SSHHHHHHHHHHHHHHH-EEEEEES.. CS
                            MCH 160 nvtllvaptaSlaGsvqvaaRvvevalhkleelgfdlekivsavgtaPiapvakdelkamgrtndailYggrvhltve.a 238
                                    ++ ++vapt+S+aG+vqv+aR+ve+++hkl+++gfd++ki+s++g+aPiapva+d++ +mg++ndai+Ygg++++t+e +
  gi|116753571|ref|YP_842689.1| 162 DLRIAVAPTDSVAGMVQVSARIVETGMHKLFTMGFDITKIKSGWGVAPIAPVAGDATMCMGASNDAIIYGGDTYYTIEyE 241
                                    ******************************************************************************77 PP

                                    ..TTHHHHHHHSSGGGSTTTTS-HHHHHHHTTTTGGGS-GGGSS-SEEEEEETTT--EEEEE---HHHHHHHT CS
                            MCH 239 edeeaedlakklpssaskdygkpFaeifkeaeydfykidkalFspAevtvndletgktfkaGelneellaesf 311
                                    + ee++d+++k+pssas+dyg pF++ fk+a++df+k+d+++F+pA+v++n+l + +t++ G+ln+++l+esf
  gi|116753571|ref|YP_842689.1| 242 NLEELKDYVRKMPSSASRDYGVPFYSAFKAAGFDFFKVDHNIFAPARVVMNELISRTTIVSGRLNHDVLMESF 314
                                    889*********************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); 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: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2305.57
//
Query:       gi|116753572|ref|YP_842690.1|  [L=233]
Description: hypothetical protein Mthe_0253 [Methanosaeta thermophila PT]
Scores for complete 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-64  215.9   0.0    5.5e-64  215.7   0.0    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 !  215.7   0.0     3e-68   5.5e-64       1     200 [.       5     211 ..       5     212 .. 0.97

  Alignments for each domain:
  == domain 1  score: 215.7 bits;  conditional E-value: 3e-68
                                    EEEESSSS-EEEEEE-TT-EEEE-CCGEEEEETTEEEEE...--------------EEEEEEES.SS-.EEEEE--SSSE CS
                          AIM24   1 fevlgepssllsvtLspgeelyaerGalvamsgkvemet...gllkalkrlltgeslfllkftakiss.gtvllapklpg 76 
                                    +++lg++ ++l+v+++pge++  e+Ga+++m+++++m++   g+ k+lkr+++ge+lf+++ft+++++    ++++++pg
  gi|116753572|ref|YP_842690.1|   5 YTILGDDLQVLEVQMAPGESIRSEAGAMLFMDDEIDMSAstgGIIKGLKRAVAGEGLFITSFTNRSDDmKRMAFSAPFPG 84 
                                    789************************************************************9988899********** PP

                                    EEEEEEG.GTT.EEEEEGGGEEEEETT-EEEEEEEE--.SSGGGTS-EEEEEEESSSEEEEEEECSEEEEEEE.EEEEEE CS
                          AIM24  77 tivtlel.gggdwlivqkdafLAatgnveldikfqkgl.kglfggeglflqkltGrGlvalsgyGaiyeielkageelvv 154
                                    +i++l+l + g +l++q++afL+ +++ve++++f+k+l +g+fggeg++lq+l+GrG+v+++++Ga+++ +l+++e + v
  gi|116753572|ref|YP_842690.1|  85 KILPLNLdEFGGQLLCQRGAFLCGESGVEIELAFTKRLgAGFFGGEGFVLQRLRGRGMVFIHAGGALITRDLQEEEVINV 164
                                    *******665559***********************99****************************************** PP

                                    EGGGEEEEETTEEEEEEEETT---STTTTS-E.EEEEEEEEEEEEES CS
                          AIM24 155 dpghlvafsgslkfdiervgglkrrligGegl.flkltGpgtvllqs 200
                                    d+g+lvafs  +++di+ vgg++++l+gGeg+ +++l+Gpg+v+lqs
  gi|116753572|ref|YP_842690.1| 165 DTGCLVAFSRDVDYDIRFVGGIRNALFGGEGIfLARLKGPGRVYLQS 211
                                    ********************************99************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       176  (0.0098165); expected 358.6 (0.02)
Passed bias filter:                      172  (0.0095934); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1793.90
//
Query:       gi|116753573|ref|YP_842691.1|  [L=610]
Description: glycogen debranching enzyme, putative [Methanosaeta thermophila PT]
Scores for 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-113  377.1   0.0   1.6e-112  376.2   0.0    1.3  2  GDE_C            Amylo-alpha-1,6-glucosidase
    7.5e-66  221.7   0.0    1.3e-65  220.9   0.0    1.4  1  GDE_N            Glycogen debranching enzyme N terminal
    0.00017   20.4   0.0       0.45    9.1   0.0    2.1  2  Glyco_hydro_100  Alkaline and neutral invertase
  ------ inclusion threshold ------
      0.011   14.5   0.0      0.045   12.5   0.0    1.8  2  Glyco_hydro_63   Glycosyl hydrolase family 63 C-terminal doma


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 ?   -3.8   0.0      0.99   4.4e+03      92     127 ..      85     123 ..      83     130 .. 0.71
   2 !  376.2   0.0  3.7e-116  1.6e-112       2     383 .]     254     601 ..     252     601 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 0.99
                          GDE_C  92 lieaiekYleyagdaeilrriyp...vlqeilqkyvqGt 127
                                     +e + +Yl+ a+  e++++i+        +++ ++ G 
  gi|116753573|ref|YP_842691.1|  85 TAEPVPTYLYRANGIEVVKQIFMvhgENTTVVKYHISGD 123
                                    567788999999999999999983332344677777765 PP

  == domain 2  score: 376.2 bits;  conditional E-value: 3.7e-116
                          GDE_C   2 asdqflvrrkseslkeeekgvsliAGlpwFsdWGRDtfIaLsGllLvtgrfeeAreilltFaktlrhGliPNlldegqea 81 
                                    a+d+flvrr          g+s+iAG++wF+dWGRD++IaL+GllL tgrf++Ar++l+tF++++++GliPN l +g   
  gi|116753573|ref|YP_842691.1| 254 AADSFLVRRG--------SGMSIIAGYHWFDDWGRDAMIALPGLLLCTGRFDDARAVLRTFSEQMQDGLIPNDLGAG--- 322
                                    5677777765........799*****************************************************776... PP

                          GDE_C  82 lyntvdaslwlieaiekYleyagdaeilrriypvlqeilqkyvqGtkykigldeedglisagerlnqlTWmDakvkgepv 161
                                     yntvdasl +i+a+ +Y + + d +++r+ +p+l  i++ y+  t    ++d +d lis  e     TWmDa+v+g+ v
  gi|116753573|ref|YP_842691.1| 323 SYNTVDASLLFIRAVCEYHRFSSDSSFIRELWPTLMGIIECYTTMTP-VGYMD-SDCLISSSE---GATWMDARVDGRCV 397
                                    5*******************************************999.88999.******999...99************ PP

                          GDE_C 162 tPRdGkaveinaLwyaaLkileelaekalgeakkssykelaekikesfekkFwdeaaaavakreilaDvlksseekdlsl 241
                                    tPR+Gk ve+naLwy+aL++leel+e a  e   ++++ lae+++ sf++ Fw+         ++l+D++++    d s+
  gi|116753573|ref|YP_842691.1| 398 TPRAGKCVEVNALWYEALRSLEELSEAAGLE---WRWHGLAERVRRSFRR-FWN-------PAGYLYDTIDP---YDGSV 463
                                    **************************66666...**************99.***.......789******99...789** PP

                          GDE_C 242 RpNflialslapellseekakkvlekaeeeLltplGlktLdpedpeYkgnYdgsedsrdaaYHqGtvWvwllgsyveall 321
                                    RpN+++a++  + lls e++++v+++a+eeLltp+Gl+tL+p+dp+Y g+Y+gs  +rd+aYHqGtvW+wl+g y++a+l
  gi|116753573|ref|YP_842691.1| 464 RPNQVVAVAFSHGLLSLERTRAVVRNATEELLTPYGLRTLSPRDPAYIGRYEGSPRERDQAYHQGTVWPWLIGPYITAYL 543
                                    ******************************************************************************** PP

                          GDE_C 322 kfgeklgkskea.leevkalLeglekhleeaglgslsElfdgdaellpkgciaQAWSvaellr 383
                                    ++++   +s+ + ++++++lLe       + g+g+++E++dgd+++ p gci QAWSvae++r
  gi|116753573|ref|YP_842691.1| 544 RASRYSKRSRMHaISLLRPLLE-----ERRYGIGTIAEVYDGDPPHRPGGCISQAWSVAEVIR 601
                                    **99733332223566666666.....35789****************************997 PP

>> GDE_N  Glycogen debranching enzyme N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  220.9   0.0   2.9e-69   1.3e-65       1     213 [.      10     210 ..      10     214 .. 0.95

  Alignments for each domain:
  == domain 1  score: 220.9 bits;  conditional E-value: 2.9e-69
                          GDE_N   1 REwllTNglGGYasgtvagantRryhGlLvaalnppsgRtlllskldeslevsgkvfeLstneypgeiepeGyeyLesFe 80 
                                    REw++TNg+GGYas+t +gantR yhGlL+a+l+pp++R+llls+lde++      +eL+ ++ypg+++p+G+ yLesF+
  gi|116753573|ref|YP_842691.1|  10 REWIVTNGIGGYASSTSIGANTRAYHGLLIASLSPPVDRWLLLSSLDETVNG----IELANHQYPGVVHPRGFMYLESFT 85 
                                    9*************************************************98....************************ PP

                          GDE_N  81 lepvptwtyrvgdvllekqivmpkgentvliaYrlenadepatLrlrpllafRdfheltkanellqksqeeglveiqase 160
                                     epvpt+ yr++++++ kqi+m++gent++++Y++++   + ++r+ pl++ R fh+ +   e  q+  e+     +  +
  gi|116753573|ref|YP_842691.1|  86 AEPVPTYLYRANGIEVVKQIFMVHGENTTVVKYHISG---DSHIRIMPLVTSRCFHAVSGRPEIRQEIMER----GTLLR 158
                                    *************************************...67******************87766666553....34568 PP

                          GDE_N 161 aepslrlqaskegefqeepvwyynveypeEaerGlddredlyspgyfevelkp 213
                                    ++++l+l ++ ++++++++vwy+n+ey+ E+ rGl + edl++pg fe+++++
  gi|116753573|ref|YP_842691.1| 159 SRCNLHLFSD-RARYVRNEVWYHNFEYEIERVRGLGWVEDLLCPGWFEADVEN 210
                                    999******9.99************************************9986 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 !    9.1   0.0    0.0001      0.45     109     203 ..     322     424 ..     301     446 .. 0.78
   2 !    9.1   0.0    0.0001      0.46     349     423 ..     518     597 ..     509     605 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0001
                                    GG---HHHHHHHHHHHHHHHHHH---HHHHS..HHHHHHHHHHHHHHT---SSSSSS--B-SS-SSS-S-SS...-...- CS
                Glyco_hydro_100 109 gRvapvDsslWWiillraYvkatgdlslaee..eevqkgiklilelvlaerfdeaPtllvpdgafmidRrlg...v...y 180
                                    g   +vD+sl +i  +  Y++ + d+s+ +e  +++   i+   ++      d    +  ++ga+ +d r++   v   +
  gi|116753573|ref|YP_842691.1| 322 GSYNTVDASLLFIRAVCEYHRFSSDSSFIRElwPTLMGIIECYTTMTPVGYMDSDCLISSSEGATWMDARVDgrcVtprA 401
                                    455789**********************987334555556666666666677777788899*******999855533336 PP

                                    BSBHHHHHHHHHHHHHHHHHS-S CS
                Glyco_hydro_100 181 gapleiqaLlyaalrsakellee 203
                                    g+ +e++aL+y alrs +el e 
  gi|116753573|ref|YP_842691.1| 402 GKCVEVNALWYEALRSLEELSEA 424
                                    999*************9998655 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0001
                                    GGG-TTBTTBT-B-GGGHHHHHHHHHHTT-HHHHHHHHHH.......HHTTHTTTT--S-EESTTS-EE-TT--SSBHHH CS
                Glyco_hydro_100 349 pkntpwsYhngGsWpvllWllvaaalkterkelaekaiel.......aekrlskdewaeYydgktgrlvgkqarkyqtwt 421
                                    p+ +  +Yh g  Wp l+   ++a l+++r +  ++++++        e+r+   + ae ydg   +  g   +  q+w+
  gi|116753573|ref|YP_842691.1| 518 PRERDQAYHQGTVWPWLIGPYITAYLRASRYSKRSRMHAIsllrpllEERRYGIGTIAEVYDGDPPHRPG--GCISQAWS 595
                                    7788899**********************96555554443101111134444555568888887665554..35556666 PP

                                    HH CS
                Glyco_hydro_100 422 ia 423
                                    +a
  gi|116753573|ref|YP_842691.1| 596 VA 597
                                    65 PP

>> Glyco_hydro_63  Glycosyl hydrolase family 63 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.22   9.9e+02     415     473 ..     408     464 ..     404     475 .. 0.71
   2 ?   12.5   0.0     1e-05     0.045     367     411 ..     482     531 ..     468     540 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.22
                                    HHHHHHHHHHH---SS-.--HHHHHHHHHHHHHHHHHHHHHHHTSS--SEE-TTT--EE CS
                 Glyco_hydro_63 415 nylilsalkhyskvegpykekakeiykeLrsnlvnnivkqyketGfvweqYddktGkgk 473
                                    n l  +al+  ++ +  +++ ++  ++ L + + +   + ++ +G++++  d+ +G+ +
  gi|116753573|ref|YP_842691.1| 408 NALWYEALRSLEELS--EAAGLEWRWHGLAERVRRSFRRFWNPAGYLYDTIDPYDGSVR 464
                                    555555555555332..23455566777888888888899999******9999999765 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 1e-05
                                    HHHHHHH-.TTTTEETTEEBSB-TTSTTTT-.........TT-SSSS-B- CS
                 Glyco_hydro_63 367 klldlikd.peelwsdyGlrslskksslygkrn....tehdenYWrgpiW 411
                                    ++ + +++ +eel ++yGlr ls +++ y  r      e d++Y +g++W
  gi|116753573|ref|YP_842691.1| 482 RTRAVVRNaTEELLTPYGLRTLSPRDPAYIGRYegspRERDQAYHQGTVW 531
                                    555566652589****************987642323699********** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (610 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 4149.91
//
Query:       gi|116753574|ref|YP_842692.1|  [L=495]
Description: Alpha-amylase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-59  202.3   0.1    1.7e-59  201.7   0.1    1.3  1  Glyco_hydro_57   Glycosyl hydrolase family 57
    0.00013   21.8   0.0    0.00032   20.6   0.0    1.7  2  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 !  201.7   0.1   1.9e-63   1.7e-59       2     324 ..      10     300 ..       9     301 .. 0.93

  Alignments for each domain:
  == domain 1  score: 201.7 bits;  conditional E-value: 1.9e-63
                                    EEEEE-----TTS-SSSSSHHHHHHH...HHHTHHHHHHHHHHHHHTT----EEEEE-HHHHHHHT-HHHHHHHHHHHHH CS
                 Glyco_hydro_57   2 fvfhqHqplykkpgkgeytlpwvreh...aaedYiklalilekfpkvhvtfeLsgsLiaqLeeylngekksylpateell 78 
                                    + f++Hqp++ k++   ++   ++ +     + Y++++ + + f++v+                    +k+ylpa++++l
  gi|116753574|ref|YP_842692.1|  10 ISFEVHQPFRLKKE--FFWSGSIFRRtrpHHDFYFDDIENRNVFERVA--------------------EKCYLPANRIML 67 
                                    6799******9777..77777666652223456***************....................************ PP

                                    HHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHT.TT-HHHHHHHHHHCTSEEEEEE-TT-B-GGG-S-HHHHHHHHH CS
                 Glyco_hydro_57  79 elieeglerctelkldlavlfnlaisgplleqiqkwlnkevlelfrelqesgqvElltspyyHpllpllpdsedieaqvk 158
                                    eli+++ +  + +k      +++++sg ++eq++++  ++vl+ f e++++g+vE+l ++yyH+l++l+ + +++++qv+
  gi|116753574|ref|YP_842692.1|  68 ELIKRFSDTDRPFK------VAYSLSGVFVEQCRRY-RPDVLDTFIEMVDTGNVEILDQTYYHSLTSLFDR-KEFREQVR 139
                                    **************......****************.**********************************.******** PP

                                    HHHHHHHHHHSS--SBEE-GGG-B--SHHHHHHHTT--EEEE-C------------TTS-EE-TTS..-EEEE--CHH-T CS
                 Glyco_hydro_57 159 karelyeeyfgqePrgfwlpElavspeileilaelGfeylftdelaeiledkskespyrpyllkngg.iavffRdreLsd 237
                                    ++rel+ ++fg++P+ f ++El++++ei+++ +++G++ +f++++      +   +p+ +y+++  + i++++R+++L d
  gi|116753574|ref|YP_842692.1| 140 MHRELMWDIFGVKPTIFENTELIYNDEIAAMAEDMGYRGIFAEGVI-----A---DPNHVYRPEGCRsISLLLRNYQLTD 211
                                    *******************************************953.....3...5678888888888************ PP

                                    TTSGGG-................TTSB..........-TT---TTT-..-BB-TT-S---HHHHHHHHHHHHHHHHHHHH CS
                 Glyco_hydro_57 238 digFrys....eqypleavddfinwlkkvkkaksevvtialdgEnwg..hypetgkkeFleklyeeleenglielvtpse 311
                                    digFr+s    e +pl ++d+++ wl  +   +++++++++d+E++g  h+petg++eFl+ l+ e+ + + +++ tp e
  gi|116753574|ref|YP_842692.1| 212 DIGFRFSsrnwEEFPL-TADKYAAWLAAT---PGRCINLFMDYETFGehHWPETGIFEFLRCLPGEILKWKNLRFSTPAE 287
                                    *******9999999**.**********98...************************************************ PP

                                    HHHHHSS-EEEEE CS
                 Glyco_hydro_57 312 fikklkpkglikl 324
                                    ++++++p +++++
  gi|116753574|ref|YP_842692.1| 288 IVERVEPSRTVSV 300
                                    *******998876 PP

>> Polysacc_deac_1  Polysaccharide deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   3.6e-08   0.00032      48     122 ..     102     177 ..      34     179 .. 0.92
   2 ?   -3.4   0.0      0.94   8.4e+03      31      58 ..     380     407 ..     365     410 .. 0.61

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.6e-08
                                    HHHHHHHHHTT.EEEEE--SS--EGGGSHHHHHHHHHHHHHHHHHHHHS----EEE-GGGEE-HHHHHHHHHTT.E CS
                Polysacc_deac_1  48 pdevremaasG.veignHtinhsnlkrlseeevrreierakdalrkalgreprlfryPygsasatvlevarelgfa 122
                                     d   em++ G vei   t+ hs  +   ++e+r+++ + ++ + +++g +p+ f    + +++++ ++a+++g++
  gi|116753574|ref|YP_842692.1| 102 LDTFIEMVDTGnVEILDQTYYHSLTSLFDRKEFREQVRMHRELMWDIFGVKPTIFENTELIYNDEIAAMAEDMGYR 177
                                    577789********************************************************************98 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.94
                                    CT--EEEEE-HHHHCH-HHHHHHHHHTT CS
                Polysacc_deac_1  31 ykvkatffvigglvedypdevremaasG 58 
                                    y++  t f + +   +  +e+  ma+++
  gi|116753574|ref|YP_842692.1| 380 YDAAVTYFSVLSDLHRRLSEILDMADHP 407
                                    5666666666665555557777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 3635.15
//
Query:       gi|116753575|ref|YP_842693.1|  [L=298]
Description: prenyltransferase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-18   65.2  21.4    1.1e-17   64.2  21.5    1.4  1  UbiA      UbiA prenyltransferase family
  ------ inclusion threshold ------
        1.3    8.6   4.2         13    5.3   0.4    2.3  2  Ycf4      Ycf4


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 !   64.2  21.5   1.2e-21   1.1e-17      21     230 ..      60     269 ..      30     275 .. 0.79

  Alignments for each domain:
  == domain 1  score: 64.2 bits;  conditional E-value: 1.2e-21
                           UbiA  21 lllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilgllllalllnpltallgllal 100
                                        ++++++l+++++++l+ ++D + D    + p R   + + s++  +++ ++++ l+++l ++++ p ++ l+++ +
  gi|116753575|ref|YP_842693.1|  60 PSMMICFAVFLVSFSVYTLDKLVDLDRDIS--NMPAR--KQFLYSRRRFFLVLALSAYLAAALIMVYVRPAALPLVFVPV 135
                                    4456778899********************..98888..67788877777755555555555555*************99 PP

                           UbiA 101 llyvvYt.......glrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavflltwaialandlrdregDrk 173
                                    ++  +Y        + rlK+++++++vv+g a++l+ +l  ++ +g  s++al+l+++++  ++ + l+ d+rd+ gDr 
  gi|116753575|ref|YP_842693.1| 136 IANAFYGmrllpwiP-RLKDIPVMKNVVVGSAWALVTVLIPVFHSGYGSPWALVLYFIFIKTFIDTVLY-DIRDVAGDRI 213
                                    999***999998555.9**************************99999888888888856666665555.9********* PP

                           UbiA 174 agiktlpvvlGrkaarillalllavllla.llllllalllllylllalllaalallra 230
                                     g++t+pv+lG+  ++   +ll++ + ++ + l+l+++   ++l+l+l+  a++ +  
  gi|116753575|ref|YP_842693.1| 214 SGVRTMPVILGETPTVL--VLLILNTTILpVSLFLPGGSREIALALTLYGYAYIAYLR 269
                                    ****************9..555555555555688999999999999888888887763 PP

>> Ycf4  Ycf4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.3    0.0025        22       3      39 ..      19      55 ..      18      78 .. 0.82
   2 ?    5.3   0.4    0.0014        13      30      66 ..     105     143 ..      78     148 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0025
                           Ycf4  3 vlrqevlgsrrlsnylwavvvllGglgfllagissyl 39
                                   v r+ +  + rl  +l  + +++Gg+gf+ + ++s l
  gi|116753575|ref|YP_842693.1| 19 VCRDAIDAVERLLAFLAVTSLFIGGTGFFKTYMASLL 55
                                   5677788889999999999**********98777764 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0014
                           Ycf4  30 fllagissylkvnllpisepse...lvfiPqGlvllfYgv 66 
                                    fl+ ++s+yl   l+++        lvf+P  ++ +fYg+
  gi|116753575|ref|YP_842693.1| 105 FLVLALSAYLAAALIMVYVRPAalpLVFVPV-IANAFYGM 143
                                    8889**********99875444466999995.88899997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2364.36
//
Query:       gi|116753576|ref|YP_842694.1|  [L=144]
Description: CMP/dCMP deaminase, zinc-binding [Methanosaeta thermophila PT]
Scores for complete 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  105.4   1.4    1.4e-30  105.1   1.4    1.1  1  dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-
      1e-20   73.9   0.4    1.3e-20   73.6   0.4    1.1  1  MafB19-deam      MafB19-like deaminase
    0.00014   21.9   0.4    0.00031   20.8   0.4    1.6  1  Bd3614-deam      Bd3614-like deaminase
     0.0022   17.9   1.2      0.009   15.9   1.2    1.9  1  APOBEC_N         APOBEC-like N-terminal domain
  ------ inclusion threshold ------
      0.054   13.4   1.2      0.054   13.4   1.2    2.0  2  zf-C3HC4         Zinc finger, C3HC4 type (RING finger)
      0.062   13.4   0.6        0.2   11.8   0.6    1.8  1  SNAD4            Secreted Novel AID/APOBEC-like Deaminase 4
       0.14   12.3   0.0       0.17   12.0   0.0    1.3  1  APOBEC3          APOBEC3
       0.14   12.2   0.9       0.25   11.4   0.7    1.5  2  NAD1             Novel AID APOBEC clade 1
       0.34   10.9   1.2       0.98    9.4   1.2    1.8  1  APOBEC2          APOBEC2


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 !  105.1   1.4   7.1e-34   1.4e-30       4      99 ..       7     121 ..       4     123 .. 0.98

  Alignments for each domain:
  == domain 1  score: 105.1 bits;  conditional E-value: 7.1e-34
                                    HHHHHHHHHHHHHHHHTTTSCSEEEEEEETTEEEEEEESBHHCCTG.....................TTB-HHHHHHHHH CS
                dCMP_cyt_deam_1   4 dekllelalkaakeaqkcsnfkVGavivkngeiistgyngepaggs.....................ktiHAEvnAilka 62 
                                    de+++e+a  +ak++ +c + +VGaviv++++i+stgyng p+g +                     + +HAE+nAi++a
  gi|116753576|ref|YP_842694.1|   7 DEYFMEIASVVAKRS-TCLRNRVGAVIVRDKRILSTGYNGAPTGLEhcdvagclrekvesgtrhelcRAVHAEQNAIIQA 85 
                                    89*************.**************************************************************** PP

                                    HHHTSSCETTEEEEEEE--BHHHHHHHHHHT-SEEEE CS
                dCMP_cyt_deam_1  63 aknggsklegatlyvtlePCsmCakaiiqsgikkvvv 99 
                                    a   g+++egatly+t++PC  Cak++i+++i++vv+
  gi|116753576|ref|YP_842694.1|  86 ALH-GVSIEGATLYCTHQPCILCAKMMINARIRRVVY 121
                                    *88.99******************************9 PP

>> MafB19-deam  MafB19-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.6   0.4   6.5e-24   1.3e-20       4     107 ..       7     131 ..       6     144 .] 0.87

  Alignments for each domain:
  == domain 1  score: 73.6 bits;  conditional E-value: 6.5e-24
                    MafB19-deam   4 ekafrkalaevekatkikedkigavivkdkkviargsn.......................ekelnakataHaEiaalqq 60 
                                    +++f+++++ v k++ +    +gaviv dk+++ +g+n                       ++  +     HaE +a+ q
  gi|116753576|ref|YP_842694.1|   7 DEYFMEIASVVAKRSTCLRNRVGAVIVRDKRILSTGYNgaptglehcdvagclrekvesgtRH--ELCRAVHAEQNAIIQ 84 
                                    589**************************************************9999774333..445667********* PP

                    MafB19-deam  61 AakklkskrlddatlyvtlepCdmCagaivqaglkklvygagnpks..l 107
                                    Aa  + s+  ++atly t++pC  Ca+++++a+++++vy  ++p+   l
  gi|116753576|ref|YP_842694.1|  85 AALHGVSI--EGATLYCTHQPCILCAKMMINARIRRVVYRNQYPDEgaL 131
                                    *6655555..********************************9997662 PP

>> Bd3614-deam  Bd3614-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.4   1.6e-07   0.00031      76     119 ..      93     131 ..      76     140 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.6e-07
                    Bd3614-deam  76 egarllvtlqcCkmCAalvvaaadapgrevllkvvYle..edkGaL 119
                                    ega+l+ t+q+C +CA ++++a         ++vvY +  +d+GaL
  gi|116753576|ref|YP_842694.1|  93 EGATLYCTHQPCILCAKMMINARI-------RRVVYRNqyPDEGAL 131
                                    79****************998866.......456665422577776 PP

>> APOBEC_N  APOBEC-like N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   1.2   4.5e-06     0.009      46      95 ..      52     114 ..      11     143 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.5e-06
                                    S.....................TBCHHHHHHHHHHHHT--.TTEEEEEEEEESS-S-HH....HHHHHHHH CS
                       APOBEC_N  46 a.....................skHaEelflediedqelrepkkkyeitlYvswsPChessdeCaeklaaf 95 
                                    +                       HaE+    +i +++l    +    tlY++ +PC      Ca+++ ++
  gi|116753576|ref|YP_842694.1|  52 HcdvagclrekvesgtrhelcrAVHAEQN---AIIQAALH-GVSIEGATLYCTHQPCIL----CAKMMINA 114
                                    04444444444444557788889999998...44444555.6889999***********....***99875 PP

>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       6.4   1.3e+04      24      28 ..      22      26 ..      21      28 .. 0.65
   2 ?   13.4   1.2   2.7e-05     0.054       4      32 ..      72     114 ..      70     125 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 6.4
                                   HHHHH CS
                       zf-C3HC4 24 kCirk 28
                                   +C+r+
  gi|116753576|ref|YP_842694.1| 22 TCLRN 26
                                   67776 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 2.7e-05
                                    T-S--SS-E...............E-TTS--B-CHHHHHHHHC CS
                       zf-C3HC4   4 Cleeakepn..............elleCkHsfCskCirkilks 32 
                                    C  + +e+n               +l C+H+ C  C + +++ 
  gi|116753576|ref|YP_842694.1|  72 CRAVHAEQNaiiqaalhgvsiegATLYCTHQPCILCAKMMINA 114
                                    6666666666666667777777789*************99994 PP

>> SNAD4  Secreted Novel AID/APOBEC-like Deaminase 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.6    0.0001       0.2      20      62 ..      72     113 ..      55     144 .] 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0001
                          SNAD4  20 kke.haEllflekikseldpsqeyrvtwylswsPCaeCaekiae 62 
                                    ++  haE + + +    l+       t+y +  PC  Ca+ +++
  gi|116753576|ref|YP_842694.1|  72 CRAvHAEQNAIIQA--ALHGVSIEGATLYCTHQPCILCAKMMIN 113
                                    23369999988777..7887777889**************9986 PP

>> APOBEC3  APOBEC3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   8.7e-05      0.17      30      72 ..      74     113 ..      54     139 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.7e-05
                        APOBEC3  30 kkHAEerfidkirslnldslkqykitcylswsPcpkCaeelve 72 
                                      HAE+ +i + +   +        t+y +  Pc  Ca+ +++
  gi|116753576|ref|YP_842694.1|  74 AVHAEQNAIIQAALHGV---SIEGATLYCTHQPCILCAKMMIN 113
                                    679***99977666444...44559**************9997 PP

>> NAD1  Novel AID APOBEC clade 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.7   0.00012      0.25      48      91 ..      74     113 ..      49     120 .. 0.71
   2 ?   -2.4   0.0       2.2   4.3e+03     116     130 ..     127     141 ..     116     143 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                           NAD1  48 kcHaEllflnkikslklldpsqkykvtwylswSPCseCasklae 91 
                                    ++HaE+  + +    +l +  ++   t+y+++ PC  Ca+ +++
  gi|116753576|ref|YP_842694.1|  74 AVHAEQNAIIQA---AL-HGVSIEGATLYCTHQPCILCAKMMIN 113
                                    248888765444...33.55578889**************9987 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.2
                           NAD1 116 nqegLrsLasagvkl 130
                                     + +Lr L++ag+++
  gi|116753576|ref|YP_842694.1| 127 DEGALRFLEQAGIEV 141
                                    567899999999875 PP

>> APOBEC2  APOBEC2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   1.2   0.00049      0.98      51      91 ..      76     113 ..      46     143 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00049
                        APOBEC2  51 HaEllflskvkkkkleekkeykvtwyvswsPCaeCaeevae 91 
                                    HaE   + +      +  +    t+y+++ PC  Ca+ + +
  gi|116753576|ref|YP_842694.1|  76 HAEQNAIIQAAL---HGVSIEGATLYCTHQPCILCAKMMIN 113
                                    555443333222...222334569************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); 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:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1055.43
//
Query:       gi|116753577|ref|YP_842695.1|  [L=425]
Description: nucleotidyl transferase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-35  122.4   0.0    5.4e-35  121.2   0.0    1.6  2  NTP_transferase  Nucleotidyl transferase
    3.1e-13   48.9   5.1    1.4e-06   27.8   1.2    3.5  3  Hexapep          Bacterial transferase hexapeptide (six repea
     0.0077   14.4   0.4      0.012   13.8   0.4    1.3  1  DUF4954          Domain of unknown function (DUF4954)
  ------ inclusion threshold ------
      0.016   14.9   0.8       0.28   11.0   0.1    2.8  2  Hexapep_2        Hexapeptide repeat of succinyl-transferase
      0.023   15.0   0.0      0.043   14.2   0.0    1.5  1  NTP_transf_3     MobA-like NTP transferase domain


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.2   0.0   1.5e-38   5.4e-35       6     246 ..       9     251 ..       4     253 .. 0.87
   2 ?   -2.7   0.0      0.97   3.5e+03      75     114 ..     324     363 ..     309     369 .. 0.74

  Alignments for each domain:
  == domain 1  score: 121.2 bits;  conditional E-value: 1.5e-38
                                    --S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETT.THHHHHHHHTTSGGGT........SEEE CS
                NTP_transferase   6 aGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqe.hsflveeqlkegskfg........vevl 76 
                                    +GG GtRL+PLt  ++k+lv v ++  +i   +  la +g+++ i+ +  + +   + +++k+g+ f          e +
  gi|116753577|ref|YP_842695.1|   9 VGGGGTRLYPLTLCQPKPLVEVCDT-AIIAVLFRVLAIQGCRRFILGSKGFeNTLALSNYFKAGEGFFkrlgidehEEFS 87 
                                    69***********************.*****************5555554413444566666666554899988666666 PP

                                    EEEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTT.SEEEEEEESS-.CTTSEEEEEC CS
                NTP_transferase  77 ialepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakg.tvtfgivpvee.ateyGviead 154
                                    +  + e  g+Ad+++  +++++ +++   vlv++gD li+ ++ee+++ ++ ++  + tv++   p+ee  ++yGv+e +
  gi|116753577|ref|YP_842695.1|  88 YQPQYEDHGSADSLRYCINYFNLNDD---VLVVSGDNLIDIDLEEFIAYHRRRNP-IlTVALKELPREEsVSQYGVAELE 163
                                    66677777*****************7...**************************.55998888776651699******* PP

                                    TTSBEEEEECS-SSHSH.CSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEEXS CS
                NTP_transferase 155 eegrverfvEKPkeaka.selassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsDvG 233
                                    ++ r++rfvEKPk+ +  s ++++  Y+f +e+ + la+     ++++d ++d++p+++e+g++   +  k+  yW D+G
  gi|116753577|ref|YP_842695.1| 164 SDMRIRRFVEKPKAGTEpSRMINTAFYLFSPEIRDVLAE---MGDKSRDIGGDLIPYLTENGYDVCGYPLKG--YWIDIG 238
                                    ************98766599*****************65...88999*************************..9***** PP

                                    SHHHHHHHHHHHH CS
                NTP_transferase 234 tldslleanekla 246
                                    t++ ll+a+++++
  gi|116753577|ref|YP_842695.1| 239 TPERLLQATMNVL 251
                                    ********99876 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.97
                                    EEEEEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEE CS
                NTP_transferase  75 vlialepegkgtAdAvalaaelledeksdelvlvLggDhl 114
                                    +  +  ++  ++ + v+l++ ++++++ +e   vL +D++
  gi|116753577|ref|YP_842695.1| 324 IRNSAVMSISNIMHGVRLNRAIVGRYSTIEAHSVLDADQF 363
                                    4444444555889999999999999999999999999986 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   1.2   3.8e-10   1.4e-06       1      36 []     292     326 ..     292     331 .. 0.92
   2 !   13.1   0.0   1.7e-05     0.062       9      34 ..     334     358 ..     329     360 .. 0.90
   3 !    7.7   0.0   0.00083         3       3      22 ..     371     390 ..     370     392 .. 0.75

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 3.8e-10
                                    TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                        Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36 
                                    s++IG ++ I p++vi +n ++G  + I+++v i++
  gi|116753577|ref|YP_842695.1| 292 SVFIGRDCRIEPGVVI-ENSHVGHTCMIERNVEIRN 326
                                    69**********9999.9999999999999999975 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 1.7e-05
                                    EE-TTEEEETTEEE-TTEEEETTEEE CS
                        Hexapep   9 lIgpfaviggnVkIGdnvkIgagvvi 34 
                                     I++++ + + +++G++++I+a++v+
  gi|116753577|ref|YP_842695.1| 334 NIMHGVRL-NRAIVGRYSTIEAHSVL 358
                                    59999999.***************98 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.00083
                                    EEETTEEE-TTEEEETTEEE CS
                        Hexapep   3 vIGsnvlIgpfaviggnVkI 22 
                                    v+G+nv + + +v+g+++ +
  gi|116753577|ref|YP_842695.1| 371 VVGDNVRLQKESVVGPGTRV 390
                                    77888888888888888766 PP

>> DUF4954  Domain of unknown function (DUF4954)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.4   3.3e-06     0.012     175     243 ..     294     358 ..     281     391 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.3e-06
                        DUF4954 175 eigekvkilnaglikNvkigdyatiegasklengtinSskeapveiGegViledfiissGskikdgavi 243
                                     ig++++i+   +i+N ++g++++ie   +++n +++S     ++i +gV l+ +i+   s+i+  +v+
  gi|116753577|ref|YP_842695.1| 294 FIGRDCRIEPGVVIENSHVGHTCMIERNVEIRNSAVMSI----SNIMHGVRLNRAIVGRYSTIEAHSVL 358
                                    588999999999999999999999999999999888875....56778888888888887777765544 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 ?   11.0   0.1   7.8e-05      0.28      18      33 ..     293     308 ..     287     309 .. 0.88
   2 ?    1.2   0.1     0.089   3.2e+02      17      29 ..     373     387 ..     368     390 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7.8e-05
                                    EEE-TT-EE-TT-EE- CS
                      Hexapep_2  18 vslGdncvvgaGvvit 33 
                                    v +G++c +++Gvvi 
  gi|116753577|ref|YP_842695.1| 293 VFIGRDCRIEPGVVIE 308
                                    669***********95 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.089
                                    S..EEE-TT-EE-TT CS
                      Hexapep_2  17 G..vslGdncvvgaG 29 
                                    G  v l +++vvg+G
  gi|116753577|ref|YP_842695.1| 373 GdnVRLQKESVVGPG 387
                                    333666666677666 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 ?   14.2   0.0   1.2e-05     0.043       6     100 ..      10     124 ..       8     205 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.2e-05
                                    ESS-TTTT.....TTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH.CHHHH..........HHTTCTS-....EEE- CS
                   NTP_transf_3   6 GGrSsRmg.....gdKallplggkpllervldalraagvdevvvvggd.eevla..........alarlgvr....vved 65 
                                    GG ++R+      ++K+l++++++ +++ +++ l+ +g+++ ++  +  e+ la           ++rlg++    + ++
  gi|116753577|ref|YP_842695.1|  10 GGGGTRLYpltlcQPKPLVEVCDTAIIAVLFRVLAIQGCRRFILGSKGfENTLAlsnyfkagegFFKRLGIDeheeFSYQ 89 
                                    899****5444447*************************99999876657666655555555553344443322224444 PP

                                    TTS.S-SHHHHHHHHHHHH.SSSCEEEEETT-TT-- CS
                   NTP_transf_3  66 edp.gkgplaslaaalraaadadavlvlacDmPllt 100
                                    +++ + g + sl+  ++  + +d vlv+++D  l++
  gi|116753577|ref|YP_842695.1|  90 PQYeDHGSADSLRYCINYFNLNDDVLVVSGDN-LID 124
                                    444269************999**********8.444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); 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: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3159.88
//
Query:       gi|116753578|ref|YP_842696.1|  [L=689]
Description: MCM family protein [Methanosaeta thermophila PT]
Scores for complete 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-96  321.2   0.0    3.3e-96  320.7   0.0    1.2  1  MCM              MCM P-loop domain
    1.8e-37  128.0   0.0    2.8e-37  127.4   0.0    1.3  1  MCM_OB           MCM OB domain
    4.1e-28   97.6   0.1    1.2e-27   96.1   0.1    1.9  1  MCM_lid          MCM AAA-lid domain
    1.2e-08   34.6   0.1    3.1e-06   26.7   0.0    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    9.8e-08   32.1   0.0    2.3e-07   30.9   0.0    1.7  1  AAA_5            AAA domain (dynein-related subfamily)
    2.3e-07   31.3   0.1    2.9e-06   27.8   0.0    2.7  3  MCM_N            MCM N-terminal domain
    6.3e-06   26.1   0.0      2e-05   24.5   0.0    1.8  1  AAA_3            ATPase family associated with various cellul
    0.00025   21.1   0.2     0.0019   18.3   0.1    2.6  3  AbiEi_4          Transcriptional regulator, AbiEi antitoxin
      0.001   18.8   0.0     0.0094   15.7   0.0    2.1  1  Sigma54_activat  Sigma-54 interaction domain
     0.0055   17.1   0.5      0.019   15.4   0.0    2.1  2  AAA_16           AAA ATPase domain
  ------ inclusion threshold ------
       0.03   13.9   0.0       0.29   10.7   0.1    2.3  2  HTH_47           winged helix-turn-helix
      0.077   13.4   0.0        0.3   11.5   0.0    2.0  1  AAA              ATPase family associated with various cellul
       0.11   12.7   3.0       0.25   11.5   3.0    1.6  1  Zn-ribbon_8      Zinc ribbon domain


Domain annotation for each model (and alignments):
>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  320.7   0.0   2.4e-99   3.3e-96       2     223 ..     260     482 ..     259     483 .. 0.98

  Alignments for each domain:
  == domain 1  score: 320.7 bits;  conditional E-value: 2.4e-99
                                    HHHHHHHHTSSTHHHHHHHHSSTTSSS-HHHHHHHHHHHH---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHHHHS CS
                            MCM   2 veeikelakekdiieklvksiapsiyghedvkkaillqlfggvkkkledktklrgdinvllvgdpgtaKsqlLkyvekla 81 
                                    +++i el+++++i+ek+v+siapsiyg+edvk+a++lql++g +k+l+d++++rgdi++llvgdpg+aKsqlL+y++kl+
  gi|116753578|ref|YP_842696.1| 260 EKRILELSRDPNIYEKIVRSIAPSIYGYEDVKEALALQLVSGFSKRLPDGARIRGDIHILLVGDPGVAKSQLLRYMAKLS 339
                                    7899**************************************************************************** PP

                                    SSEEEEESSSSSSSHSSSEEEEESSSSS.EEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEE CS
                            MCM  82 pravytsgkgssaagLtaavvrdeetge.fvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaGivat 160
                                    pr++ytsgk+s++agLta+  +de  +  +++eaGalvladkG++++De+dkm+ +drsalhEamEqqtis+aKaG++at
  gi|116753578|ref|YP_842696.1| 340 PRGIYTSGKSSTSAGLTATAIKDELGDGrWTIEAGALVLADKGIAAVDEMDKMSPDDRSALHEAMEQQTISVAKAGVMAT 419
                                    ***********************986555*************************************************** PP

                                    EE--EEEEEEE--SSSSCCTTS-HHHHSSSSHHHHHHSSEEEEE-SSTTHHHHHHHHHHHHHH CS
                            MCM 161 LnartsvlaAanpkagrydkkksvaeninlsaalLsrFDlifvllDkvdeekDeelaehivsl 223
                                    L++r+++laAanpk+gr+d+ +++a +inl++al+srFDlifvl D+++ e+D+++a+hi+++
  gi|116753578|ref|YP_842696.1| 420 LKSRCALLAAANPKMGRFDRYEPIAPQINLTPALMSRFDLIFVLTDEPNVERDSHIATHILKS 482
                                    ************************************************************985 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.4   0.0     2e-40   2.8e-37       2     125 ..      94     222 ..      91     223 .. 0.96

  Alignments for each domain:
  == domain 1  score: 127.4 bits;  conditional E-value: 2e-40
                                    XGG--GGGTTSEEEEEEEEEEE---EEEEEEEEEEETTT-.-EEE.....S----SB-..TTT-HHH-EEE-GGGSEEEE CS
                         MCM_OB   2 lRdlrsehigklvkveGivtrasevkpklkkavfeckkcgktvev.....eleePrkCeekeCeskdpfkletekskfvd 76 
                                    +Rdlrs+higkl+ +eG v +a+ev+pk+++a++ec++cg++  v     ++ eP +C++++C++++pf+l +++s+fvd
  gi|116753578|ref|YP_842696.1|  94 TRDLRSDHIGKLIAIEGQVRTATEVRPKIVRAAYECQRCGHVFYVdqsgtKFIEPYECPNEACDRRGPFRLLPKRSQFVD 173
                                    6***************************************97777788888889************************** PP

                                    EEEEEEE-------------EEEEEEEGGGTT---TT-EEEEEEEEEEE CS
                         MCM_OB  77 fqklklQEspeevpaGelPrslevileddlvdkvkPGdrvevtGiyral 125
                                     qk+++QEspe++  Ge P++l+v l ddlv ++ PGdrv + Gi+r++
  gi|116753578|ref|YP_842696.1| 174 AQKVRVQESPEDLRGGEQPQTLDVELGDDLVGRIFPGDRVIINGILRSY 222
                                    **********************************************986 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.1   0.1   8.7e-31   1.2e-27       1      86 [.     516     600 ..     516     601 .. 0.96

  Alignments for each domain:
  == domain 1  score: 96.1 bits;  conditional E-value: 8.7e-31
                                    HHHHHHHHHHHHTT--BETCHHHHHHHHHHHHHHHHHTSSTSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHHHHHH CS
                        MCM_lid   1 ellrkYiayarekikPklseeakeklseaYvelRkeeedskrksipitvRqLesliRLseAlAklrlsevvteedveeai 80 
                                    ellrkY+ayar++++P+l+  a+e ++e+Y++lR++ +d  +k +p+t+RqLe+liRL eA+A+lrls+ +teedv+++i
  gi|116753578|ref|YP_842696.1| 516 ELLRKYVAYARKNVFPMLTRVAMERFKEYYINLRSQGQD-GNKPVPVTARQLEALIRLGEASARLRLSNWITEEDVDRVI 594
                                    68*********************************9965.59************************************** PP

                                    HHHHHH CS
                        MCM_lid  81 rllkes 86 
                                    ++++++
  gi|116753578|ref|YP_842696.1| 595 KIVESC 600
                                    ***987 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.0     0.007       9.6      21      48 ..     314     341 ..     310     353 .. 0.88
   2 !   26.7   0.0   2.2e-09   3.1e-06      92     159 ..     365     433 ..     349     460 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.007
                   Mg_chelatase  21 GgHnlllvGppGsGKtmlakrlpsllpp 48 
                                    G  ++llvG pG  K+ l + +++l p+
  gi|116753578|ref|YP_842696.1| 314 GDIHILLVGDPGVAKSQLLRYMAKLSPR 341
                                    7889***************999998775 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 2.2e-09
                   Mg_chelatase  92 Gggs.kpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpc 159
                                    G g+ +++ G++ la +G+  +DE+ +++ +   +L e +e++++++++a   ++  +r+ l+aa+Np 
  gi|116753578|ref|YP_842696.1| 365 GDGRwTIEAGALVLADKGIAAVDEMDKMSPDDRSALHEAMEQQTISVAKAGVMATLKSRCALLAAANPK 433
                                    55555899***********************************************************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 !   30.9   0.0   1.6e-10   2.3e-07       1     137 [.     317     456 ..     317     457 .. 0.80

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 1.6e-10
                                    EEEEE--SSSSHHHHHHHGGGGBS--EEE...EE--TT--HHHHH--B--.........--------G-SEEEEESGGG- CS
                          AAA_5   1 dvlLvGppGtgKselaerlaaalnrevey...vqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEvera 77 
                                    ++lLvG+pG++Ks+l +++a++  r + +      ++++t++ +k ++   +g+   + ++lv     + i+ +DE +++
  gi|116753578|ref|YP_842696.1| 317 HILLVGDPGVAKSQLLRYMAKLSPRGIYTsgkSSTSAGLTATAIKDELG--DGRWTIEAGALV--LADKGIAAVDEMDKM 392
                                    79*********************66555522256778888999998888..999999******..88999********** PP

                                    -HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--..........-TT-TTHHHHTT CS
                          AAA_5  78 esevlnsLlslleerrllleeggelvkaknddllerfrviatanpld.........rslnelspalrsR 137
                                    +++  ++L+  +e++++++++ g     k+        ++a+anp +           + +l+pal sR
  gi|116753578|ref|YP_842696.1| 393 SPDDRSALHEAMEQQTISVAKAGVMATLKSR-----CALLAAANPKMgrfdryepiAPQINLTPALMSR 456
                                    ******************9988888877775.....999*****9996654444443444555555555 PP

>> MCM_N  MCM N-terminal 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   2.9e-06       7      81 ..      12      76 ..       6     100 .. 0.83
   2 ?   -2.0   0.0       3.9   5.3e+03      62      85 ..     527     550 ..     512     578 .. 0.69
   3 ?   -1.2   0.0       2.2     3e+03      53      80 ..     581     609 ..     572     636 .. 0.72

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 2.1e-09
                          MCM_N  7 FLeefkddsededgekkYrdqlqemaer..ekttLevdlddLaafdeeLaeailenpkeylplleealkevvkklep 81
                                   F+++             Y d l ++ae     ++L vd+ dL  +d e+a+ +lenp  +l++   al+e+v  ++ 
  gi|116753578|ref|YP_842696.1| 12 FIRS------------RYWDDLLKLAESypSTRSLIVDFADLDRYDTEFADDLLENPDVMLDAAHTALQEIVLPVDV 76
                                   4443............49999999998866789*************************************9977665 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.9
                          MCM_N  62 keylplleealkevvkklepsykd 85 
                                    k + p+l +++ e +k+++ +   
  gi|116753578|ref|YP_842696.1| 527 KNVFPMLTRVAMERFKEYYINLRS 550
                                    456688888888888888775443 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 2.2
                          MCM_N  53 Laeail.enpkeylplleealkevvkkle 80 
                                    L+++i+ e+  +++++ e++lk+v  + e
  gi|116753578|ref|YP_842696.1| 581 LSNWITeEDVDRVIKIVESCLKKVGVDPE 609
                                    555554156899*********99975554 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   1.5e-08     2e-05       1     112 [.     317     432 ..     317     441 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.5e-08
                          AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeeke.kefefkkGpvf.an..llladeinrapp 76 
                                    h+ll g PG+ak +l + +ak     +           + ++ t + +e    ++++++G+++ a+  +  +de+++ +p
  gi|116753578|ref|YP_842696.1| 317 HILLVGDPGVAKSQLLRYMAKLSPRGIYT--SGKSSTSAGLTATAIKDELGdGRWTIEAGALVlADkgIAAVDEMDKMSP 394
                                    9******************9875544332..22344667889999888754499******976333338888******** PP

                          AAA_3  77 ktqsalleameerqvtveg..ethklpepflvlatqnP 112
                                      +sal eame+++++v++     +l++   +la+ nP
  gi|116753578|ref|YP_842696.1| 395 DDRSALHEAMEQQTISVAKagVMATLKSRCALLAAANP 432
                                    *************9998751157799***********9 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       6.7   9.2e+03      42      47 ..     340     345 ..     336     346 .. 0.74
   2 ?   -3.1   0.0       6.9   9.5e+03      10      32 ..     380     403 ..     376     405 .. 0.79
   3 !   18.3   0.1   1.4e-06    0.0019      19      45 ..     655     685 ..     647     685 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 6.7
                        AbiEi_4  42 rrGvYa 47 
                                    +rG+Y+
  gi|116753578|ref|YP_842696.1| 340 PRGIYT 345
                                    4****7 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6.9
                        AbiEi_4  10 qvGlfttrelea.aGispsalrrL 32 
                                    ++G++ ++e  + +  ++sal+++
  gi|116753578|ref|YP_842696.1| 380 DKGIAAVDEMDKmSPDDRSALHEA 403
                                    568888888888888899999986 PP

  == domain 3  score: 18.3 bits;  conditional E-value: 1.4e-06
                        AbiEi_4  19 leaaGisp.sa...lrrLvrkGwLvrlrrGv 45 
                                    +ea Gi++ +a   ++rL+++G L++  rG+
  gi|116753578|ref|YP_842696.1| 655 AEAEGIDRdRAeeiISRLRQEGSLIQTSRGT 685
                                    477*****999*******************7 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   6.8e-06    0.0094      21     145 ..     314     434 ..     306     440 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 6.8e-06
                                    SSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-E.EEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BEHHHHHTTTSEEEE CS
                Sigma54_activat  21 tdlsvlitGesGtGKellaraiheaskrkekpf.vavncaaipeelleseLFGhekGaFtGAekekkGlfekadgGtlfL 99 
                                     d+++l++G+ G+ K+ l r + + s+r       +   a ++++ ++ eL    +G +t     ++G++  ad+G+  +
  gi|116753578|ref|YP_842696.1| 314 GDIHILLVGDPGVAKSQLLRYMAKLSPRGIYTSgKSSTSAGLTATAIKDEL---GDGRWT----IEAGALVLADKGIAAV 386
                                    578888888888888888888888888764433034444556777777776...345554....578************* PP

                                    ETGGGS-HHHHHHHHHHHHHSEE..ESBTSSSEEE--EEEEEEESS-H CS
                Sigma54_activat 100 DeigelplelQekLlrvlqegev..ervGsskeikvdvriiaatnedl 145
                                    De+ +++++  + L ++++++++   + G  ++ k  + ++aa+n ++
  gi|116753578|ref|YP_842696.1| 387 DEMDKMSPDDRSALHEAMEQQTIsvAKAGVMATLKSRCALLAAANPKM 434
                                    *******************99762269999*************99765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       5.7   7.9e+03     117     150 ..      15      47 ..       6      66 .. 0.71
   2 !   15.4   0.0   1.3e-05     0.019      26     125 ..     317     406 ..     305     417 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 5.7
                         AAA_16 117 srllellkrllallsrderplvlvlDdlqwadea 150
                                    sr ++ l +l++ ++++++ l++ + dl++ d++
  gi|116753578|ref|YP_842696.1|  15 SRYWDDLLKLAESYPSTRS-LIVDFADLDRYDTE 47 
                                    7888888888844444255.66666688887775 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.3e-05
                         AAA_16  26 lvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqllde...aesaeleawrekle 102
                                     +ll+G++Gv Ks l+r  +  l+ + gi+++gk   +            l++ + ++++l +   + +a +   ++k  
  gi|116753578|ref|YP_842696.1| 317 HILLVGDPGVAKSQLLRYMA-KLSPR-GIYTSGKSSTS----------AGLTA-TAIKDELGDgrwTIEAGALVLADKGI 383
                                    689*****************.68888.78888888888..........66645.77777777756644445555555566 PP

                         AAA_16 103 ealaavpelagaeasrllellkr 125
                                    +a+ + ++++++++s+l+e++ +
  gi|116753578|ref|YP_842696.1| 384 AAVDEMDKMSPDDRSALHEAMEQ 406
                                    66667888888888999988876 PP

>> HTH_47  winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.52   7.2e+02      10      27 ..     430     447 ..     424     463 .. 0.77
   2 ?   10.7   0.1   0.00021      0.29      24      74 ..     621     676 ..     618     680 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.52
                                    S---TTS----------- CS
                         HTH_47  10 gEPqLGrrGLYrtiggkn 27 
                                      P++Gr + Y+ i+ + 
  gi|116753578|ref|YP_842696.1| 430 ANPKMGRFDRYEPIAPQI 447
                                    57*********9998665 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00021
                                    ---------HHHHHHH...HHH-EEEE..EHHHHHHHHT--HHHHHHHHHHHHHTT CS
                         HTH_47  24 ggkntakqaemallwv...LnlaDGkr..sLldiAeriglpfdrvaaiaraLaeag 74 
                                    g  ++++++++++l++   L   DG++  ++ld Ae  g++ dr ++i+ +L+++g
  gi|116753578|ref|YP_842696.1| 621 GISKSTRDKTKQMLNIikeLGGKDGAHidDVLDRAEAEGIDRDRAEEIISRLRQEG 676
                                    555656777777777722245679987779**********************9987 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00021       0.3       1     125 [.     318     438 ..     318     444 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00021
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHH....HHTS....TSEEEEEETGGGHHH CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkea....keka....kpsilfiDEidalak 72 
                                    +ll+G pG+ K+ l + +ak  + + + +sg++ +    g ++  i++ + +     ++ a    ++ i  +DE+d++ +
  gi|116753578|ref|YP_842696.1| 318 ILLVGDPGVAKSQLLRYMAKL-SPRGIYTSGKSST--SAGLTATAIKDELGDGrwtiEAGAlvlaDKGIAAVDEMDKMSP 394
                                    69****************998.5556666777666..3445555555444443111122236666779************ PP

                                    HHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS.GGGSTHHHHS.TTSS CS
                            AAA  73 srsgseseeeervvnqLlteldgvkkkeskvivigatnr.pdkldpallr.gRfd 125
                                    ++            ++L +++++++ + +k  v+++ ++    l  a  + gRfd
  gi|116753578|ref|YP_842696.1| 395 DD-----------RSALHEAMEQQTISVAKAGVMATLKSrCALLAAANPKmGRFD 438
                                    *9...........777777777777774444444433332333333333444444 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   3.0   0.00018      0.25       6      30 ..     127     152 ..     126     157 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00018
                    Zn-ribbon_8   6 YrCeeCghefevlqsisdaplta.CP 30 
                                    Y+C++Cgh+f v qs ++  ++  CP
  gi|116753578|ref|YP_842696.1| 127 YECQRCGHVFYVDQSGTKFIEPYeCP 152
                                    *************9988555667799 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (689 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.42
# Mc/sec: 4933.44
//
Query:       gi|116753579|ref|YP_842697.1|  [L=434]
Description: phenylacetate--CoA ligase [Methanosaeta thermophila PT]
Scores for complete 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-35  119.1   0.1    1.6e-34  118.1   0.1    1.6  1  AMP-binding_C_2  AMP-binding enzyme C-terminal domain
    2.9e-17   62.4   1.3    3.4e-17   62.1   0.1    1.6  2  AMP-binding      AMP-binding enzyme
     0.0004   19.4   0.0       0.14   11.0   0.0    2.2  2  GH3              GH3 auxin-responsive promoter


Domain annotation for each model (and alignments):
>> AMP-binding_C_2  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.1   0.1   2.7e-38   1.6e-34       1      96 []     336     432 ..     336     432 .. 0.99

  Alignments for each domain:
  == domain 1  score: 118.1 bits;  conditional E-value: 2.7e-38
                                    TEEE-HHHHHHHHHT-TTEEEEEEEEEEEETTEEEEEEEEEE-T.T----HHHHHHHHHHHHHHHHHHHSS--EEEEE-T CS
                AMP-binding_C_2   1 GvnvfPsqieevlkeieevepeYqivvtregelDelevkvEvke.gfsdelkelealekkiakklksklgvsvkvelvep 79 
                                    G+nvfPsqie+vl++i+ev+p+Yqi+v+reg lD+++v+vE+++ gfsd++ +l al+++i+k+lk++l++ ++velvep
  gi|116753579|ref|YP_842697.1| 336 GINVFPSQIESVLMNIPEVGPHYQIIVSREGALDVMKVRVELTDrGFSDRIGDLMALNRRISKELKNVLNIFAEVELVEP 415
                                    99******************************************99********************************** PP

                                    T-S---------EEE-S CS
                AMP-binding_C_2  80 gtlprsegKakrviDkR 96 
                                    g +prsegKakrviD+R
  gi|116753579|ref|YP_842697.1| 416 GVIPRSEGKAKRVIDTR 432
                                    ***************99 PP

>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.1   0.1   5.8e-21   3.4e-17     167     370 ..      92     287 ..      57     294 .. 0.86
   2 ?   -1.7   0.1      0.14   8.2e+02     410     423 .]     322     335 ..     315     335 .. 0.86

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 5.8e-21
                                    E--SSSS-EEEEEEHHHHHHHHHHHH.HHHCSCCTTT-EE.EESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGC.CHHH CS
                    AMP-binding 167 TSGTTGkPKGVmlshrnlvanvaslk.letrfklkeddvv.lsilplahifglilelllallsGatvvllpkdaa.ldpk 243
                                    +SGTTGkP  V ++ + + a + sl+   t  +l+++dv+ + +    +  gl    ++a   Gatv   ++ ++ +   
  gi|116753579|ref|YP_842697.1|  92 SSGTTGKPTVVGYTKGDIEAWTESLArALTSIGLGRNDVIqVGYGYGLFTGGL-GLHYGAERIGATVLPTSTGNTeR--- 167
                                    8*****************88888887533346677899996666666777776.999********998877776633... PP

                                    HHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTCEEEEEEEEGGGSS CS
                    AMP-binding 244 lllelieklkvtviagvPrvlealle.sgalkaakkakdlsslrlvllggeplspellrffralfgeevlegYGlTEttg 322
                                      +el+++l+ t ia++P+ + +++e +++    ++ +d  +lr+ ++g+ep s e+ r++++++g + +++YG +E +g
  gi|116753579|ref|YP_842697.1| 168 -QIELMQDLESTAIACTPSYFLHIAEvAERMG--VSIRDDTKLRVGIFGAEPWSIETRRRIEDITGIKAYDIYGTSEISG 244
                                    .48*********************99776555..56668788************************************** PP

                                    ECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEE CS
                    AMP-binding 323 vvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvr 370
                                     ++  +++++    g +        ++ivD++tge v+dge+Gel+v 
  gi|116753579|ref|YP_842697.1| 245 PLF-TECQHQ---NG-IHVWADMFLIEIVDPKTGEQVEDGEQGELVVT 287
                                    *98.564444...33.666667889*********************96 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.14
                                    EEEEEECCCEEEET CS
                    AMP-binding 410 leivgRkkdliklr 423
                                    ++i+gR++d++++r
  gi|116753579|ref|YP_842697.1| 322 MRILGRTDDMLVIR 335
                                    68********9985 PP

>> GH3  GH3 auxin-responsive promoter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.0   0.00057       3.4      76     112 ..      86     121 ..      79     197 .. 0.81
   2 !   11.0   0.0   2.3e-05      0.14     348     418 ..     270     349 ..     247     365 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.00057
                                    -SEEEEECCEETTEEEEEEESHHHHHHHHHH.HHHHH CS
                            GH3  76 iklfalsSGTtsgksKliPvteeslkelallvlalla 112
                                    ++++  sSGTt gk+ ++ +t+   + ++  ++++l 
  gi|116753579|ref|YP_842697.1|  86 VVRYHVSSGTT-GKPTVVGYTKGDIEAWTESLARALT 121
                                    78999******.**********999988776555444 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 2.3e-05
                                    SEECCCS-TTSEEEEEEES....TTS-SSEEECEEE....EEEEEETTEE.EEEEEECCTEEE-SSSS-CCHHHHHHHHH CS
                            GH3 348 tvdleevevGkeYelvvTt....faGLyRYrigDvv....rvtgfynkaP.rleFvgRknvvlsidgeklteeelqkave 418
                                    + + e+ve G++ elvvTt    +  L RYrigD+     +  +   + P +++++gR++ +l i+g  +  +++++++ 
  gi|116753579|ref|YP_842697.1| 270 PKTGEQVEDGEQGELVVTTlnkwAMPLIRYRIGDLTikesEPCECGRTHPrIMRILGRTDDMLVIRGINVFPSQIESVLM 349
                                    56679**************5444468********7422223344556789888999999999999998888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 3137.54
//
Query:       gi|116753580|ref|YP_842698.1|  [L=144]
Description: amino acid-binding ACT domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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   69.8   0.2    1.1e-09   37.9   0.0    2.2  2  ACT         ACT domain
    4.2e-08   33.7   0.2     0.0023   18.5   0.0    2.2  2  ACT_4       ACT domain
    6.2e-07   29.1   0.1     0.0087   15.8   0.0    2.7  2  ACT_7       ACT domain
  ------ inclusion threshold ------
      0.017   15.1   0.0        0.3   11.1   0.0    2.3  2  ACT_6       ACT domain
       0.04   14.0   0.0      0.061   13.4   0.0    1.3  1  DUF4840     Domain of unknown function (DUF4840)
       0.12   12.2   0.0       0.84    9.5   0.0    2.3  3  ACT_5       ACT domain
       0.12   12.6   0.0       0.52   10.5   0.0    2.0  1  Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygena


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 !   37.9   0.0   4.1e-13   1.1e-09       3      52 ..       7      53 ..       5      62 .. 0.85
   2 !   30.1   0.0   1.2e-10     3e-07       3      57 ..      73     123 ..      72     133 .. 0.76

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 4.1e-13
                                   EEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEH CS
                            ACT  3 lrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvde 52
                                   ++++v++rPG +a+v+ +l+d+g+Ni+ +++++ +d     v+ ++v d+
  gi|116753580|ref|YP_842698.1|  7 ISLFVENRPGRMAKVSKTLSDAGVNIRAMTIAEAGD---FGVIRMVVDDP 53
                                   8899*******************************9...66666666665 PP

  == domain 2  score: 30.1 bits;  conditional E-value: 1.2e-10
                                    EEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTT.ECEEEEEEEEEEHHHHHH CS
                            ACT   3 lrvgvpDrPGlLarvfgaladrgiNidsieqrssedk.vagivfvvivvdeedlee 57 
                                    l v+++D PG L ++ +al++++iNid +  + +  +  a++++ v+ +d     +
  gi|116753580|ref|YP_842698.1|  73 LAVEMRDTPGGLYEIVSALGENNINIDYAYAFVTAKSeKAMLIMRVDDID-----A 123
                                    6699******************************6654444444444443.....3 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0     9e-07    0.0023       8      53 ..       6      49 ..       5      51 .. 0.87
   2 !   13.3   0.0   3.7e-05     0.094       9      43 ..      73     107 ..      65     126 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 9e-07
                          ACT_4  8 rleveaedrkglLaditqviseekanivsvnaktrkkdglaeikit 53
                                   ++++ +e+r+g +a++++++s++++ni+++++ +  +  +  i++ 
  gi|116753580|ref|YP_842698.1|  6 QISLFVENRPGRMAKVSKTLSDAGVNIRAMTIAE--AGDFGVIRMV 49
                                   58999***************************99..4557777665 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 3.7e-05
                          ACT_4   9 leveaedrkglLaditqviseekanivsvnaktrk 43 
                                    l ve++d +g L +i++++ e+++ni    a  + 
  gi|116753580|ref|YP_842698.1|  73 LAVEMRDTPGGLYEIVSALGENNINIDYAYAFVTA 107
                                    789***********************876665544 PP

>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   3.4e-06    0.0087      20      42 ..      14      36 ..       6      47 .. 0.85
   2 !   10.8   0.0   0.00013      0.33      19      40 ..      79     100 ..      65     130 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.4e-06
                                   S--HHHHHHHHHHTTT---EEEE CS
                          ACT_7 20 vtGivaklaspLaeagIsifqiS 42
                                    +G++ak+++ L++ag++i +++
  gi|116753580|ref|YP_842698.1| 14 RPGRMAKVSKTLSDAGVNIRAMT 36
                                   69*****************8877 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00013
                                    SS--HHHHHHHHHHTTT---EE CS
                          ACT_7  19 dvtGivaklaspLaeagIsifq 40 
                                    d++G + +++s+L e++I+i +
  gi|116753580|ref|YP_842698.1|  79 DTPGGLYEIVSALGENNINIDY 100
                                    6999***************954 PP

>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00012       0.3       5      49 ..       7      51 ..       3      63 .. 0.83
   2 ?    1.8   0.0     0.094   2.4e+02      11      30 ..      79      98 ..      75     118 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00012
                          ACT_6  5 itvtGpdrpGltasLtsvlaefgvnilDieqavihgrlsLgllvs 49
                                   i+++ ++rpG  a+++++l++ gvni     a  ++  ++ ++v+
  gi|116753580|ref|YP_842698.1|  7 ISLFVENRPGRMAKVSKTLSDAGVNIRAMTIAEAGDFGVIRMVVD 51
                                   6666689*******************9998888888777777776 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.094
                          ACT_6 11 drpGltasLtsvlaefgvni 30
                                   d pG + ++ s+l e+++ni
  gi|116753580|ref|YP_842698.1| 79 DTPGGLYEIVSALGENNINI 98
                                   89999***********9998 PP

>> DUF4840  Domain of unknown function (DUF4840)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.4e-05     0.061      37      93 ..      61     115 ..      49     121 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.4e-05
                        DUF4840  37 kdstltienfPvkdLaksivdeeeelkeaieavgdvtlkvkyefvlndekdsiyfli 93 
                                    +ds +t++   +++La ++ d+++ l e+++a g+++++++y  ++ ++k+ +++li
  gi|116753580|ref|YP_842698.1|  61 RDSGFTVSM--TDVLAVEMRDTPGGLYEIVSALGENNINIDYAYAFVTAKSEKAMLI 115
                                    555555554..578************************************9998876 PP

>> ACT_5  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00033      0.84       2      49 ..      14      60 ..      13      62 .. 0.80
   2 ?   -1.7   0.0         1   2.7e+03      12      21 ..      59      68 ..      57      74 .. 0.84
   3 ?   -0.1   0.0      0.33   8.5e+02      29      51 ..     107     130 ..      79     137 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00033
                          ACT_5  2 apgvLeRvlrvvrrrgFevkslnmsttedggtvrieltVes.ersvelL 49
                                   +pg   +v  +++  g++++++++ + +d g   i ++V++ ++  + L
  gi|116753580|ref|YP_842698.1| 14 RPGRMAKVSKTLSDAGVNIRAMTIAEAGDFG--VIRMVVDDpQKGYDVL 60
                                   899999*******************966665..6777777766666655 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1
                          ACT_5 12 vvrrrgFevk 21
                                   v+r  gF+v+
  gi|116753580|ref|YP_842698.1| 59 VLRDSGFTVS 68
                                   8999999985 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.33
                          ACT_5  29 edggtvrieltVes.ersvelLsn 51 
                                     +++++ + ++V++ + +  +Ls+
  gi|116753580|ref|YP_842698.1| 107 AKSEKAMLIMRVDDiDAARRTLSS 130
                                    456667777777776666666654 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 ?   10.5   0.0    0.0002      0.52      24     103 ..      64     137 ..       6     140 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0002
                                    TSEEEEEEEE...EEST.EEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSCTSEEEEEEEEEHCHHHHHHHHHHHTTG CS
                     Glyoxalase  24 Gfklvkktdn...teet.eglriaffhaggghielvlneapsgaakhvkkieetvhhvafialdvedvgkaldrlkeagv 99 
                                    Gf+++  ++    +  t +gl  ++   g++ i++ ++ a  +a++            a +   v+d+++a + l+++gv
  gi|116753580|ref|YP_842698.1|  64 GFTVSMTDVLaveMRDTpGGLYEIVSALGENNINIDYAYAFVTAKSEK----------AMLIMRVDDIDAARRTLSSRGV 133
                                    444444444433322223444444455555555555555555555555..........888999**************** PP

                                    EEEE CS
                     Glyoxalase 100 kvva 103
                                    k+ +
  gi|116753580|ref|YP_842698.1| 134 KIAT 137
                                    *976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); 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: 0.37u 0.29s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 1017.25
//
Query:       gi|116753581|ref|YP_842699.1|  [L=305]
Description: replication factor C small subunit [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-22   79.3   0.0    5.3e-22   78.0   0.0    1.7  1  Rep_fac_C        Replication factor C C-terminal domain
    1.7e-16   60.8   0.0    3.2e-16   59.9   0.0    1.5  1  AAA              ATPase family associated with various cellul
    2.8e-13   49.9   0.0    2.7e-09   37.0   0.0    2.4  2  DNA_pol3_delta2  DNA polymerase III, delta subunit
    1.1e-05   25.9   0.2       0.01   16.2   0.0    2.9  3  AAA_16           AAA ATPase domain
    3.8e-05   24.0   0.2    9.8e-05   22.6   0.2    1.7  1  AAA_assoc_2      AAA C-terminal domain
    6.6e-05   22.7   0.1     0.0011   18.8   0.0    2.6  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00078   18.9   0.0       0.27   10.6   0.0    2.5  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    0.00084   18.6   0.0      0.013   14.7   0.0    2.2  2  TIP49            TIP49 P-loop domain
    0.00092   19.3   0.0      0.014   15.4   0.0    2.2  2  ResIII           Type III restriction enzyme, res subunit
      0.001   18.9   0.0     0.0021   17.9   0.0    1.5  1  AAA_3            ATPase family associated with various cellul
     0.0016   18.0   0.0       0.11   12.0   0.0    2.3  2  AAA_7            P-loop containing dynein motor region
     0.0035   17.1   0.0      0.021   14.6   0.0    2.2  3  IstB_IS21        IstB-like ATP binding protein
     0.0062   16.3   0.0       0.01   15.6   0.0    1.4  1  DNA_pol3_delta   DNA polymerase III, delta subunit
     0.0063   15.3   0.0       0.04   12.6   0.0    1.9  2  SNF2_N           SNF2 family N-terminal domain
     0.0074   16.6   0.2        6.9    6.9   0.0    2.6  3  AAA_22           AAA domain
  ------ inclusion threshold ------
      0.016   15.2   0.1       0.33   11.0   0.1    2.5  1  AAA_5            AAA domain (dynein-related subfamily)
      0.017   14.8   0.0        3.5    7.3   0.0    2.3  2  Sigma54_activat  Sigma-54 interaction domain
      0.083   12.6   0.0        0.2   11.4   0.0    1.6  1  AAA_24           AAA domain
      0.085   12.4   0.1       0.39   10.2   0.0    2.0  2  AAA_25           AAA domain
       0.12   12.8   0.0        0.3   11.5   0.0    1.7  1  RNA_helicase     RNA helicase
       0.15   12.2   0.0       0.47   10.6   0.0    1.8  2  Torsin           Torsin


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 !   78.0   0.0   6.2e-25   5.3e-22       2      87 ..     208     292 ..     207     293 .. 0.97

  Alignments for each domain:
  == domain 1  score: 78.0 bits;  conditional E-value: 6.2e-25
                                    -HHHHHHHHHHHHHT-HHHHHHHHHHHHHHC---HHHHHHHHHHHGCCS..S-HHHHHHHHHHHHHHHHHHHCTH-HHHH CS
                      Rep_fac_C   2 hpteieeileaclngdfeeaykklrellvekGysaediltqlhrvvkeqeelpeaqkleilellgeiekrlveGasehlq 81 
                                    +p++i+++++ + +gdf+ a+++l++ll  +G+s++d++ q+hr + +  ++p+a k++++ ++gei++r++eGa+e++q
  gi|116753581|ref|YP_842699.1| 208 RPEQIRNLIKMAISGDFAGARNELDDLLLVQGLSGQDVVVQIHREMLDL-DVPDADKVRMINRIGEIDFRITEGANERIQ 286
                                    79**********99**********************************6.7***************************** PP

                                    HHHHHH CS
                      Rep_fac_C  82 lsalla 87 
                                    l+al+a
  gi|116753581|ref|YP_842699.1| 287 LEALIA 292
                                    *****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 !   59.9   0.0   3.8e-19   3.2e-16       1     127 [.      22     137 ..      22     142 .. 0.89

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 3.8e-19
                                    EEEESSTTSSHHHHHHHHHHHH.....THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHH CS
                            AAA   1 vllyGppGtGKTllakavakel.....gvefleisgsellskyvgesekkirelfkeakeka.kpsilfiDEidalaksr 74 
                                    +l++GppG+GKT++a ++++e+       +f+e+++s+ +   +     k++++ + a     + +++f+DE+dal+++ 
  gi|116753581|ref|YP_842699.1|  22 LLFSGPPGVGKTAAAISIVREIfgegwRDNFIELNASDER--GIDVVRTKVKDFARMAPLGGaEFKVIFLDEADALTSDA 99 
                                    69*******************765544699**********..99999999999999886666556***********9999 PP

                                    TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEE CS
                            AAA  75 sgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrk 127
                                               +++L + +++++    ++ +i+ +n+ +k+ +++  +R+ + 
  gi|116753581|ref|YP_842699.1| 100 -----------QSALRRTMERYSA---TCRFILSCNYSSKIIEPIQ-SRCAVY 137
                                    ...........************9...69*****************.9*9875 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 !   10.8   0.0   0.00038      0.32       1      46 [.       2      46 ..       2      56 .. 0.91
   2 !   37.0   0.0   3.1e-12   2.7e-09      84     162 ..      62     142 ..      49     143 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00038
                DNA_pol3_delta2  1 gqeealkilskalksgrlahayLfeGdegigkkelalnlakallce 46
                                   gq+e+++ l++ +++ +l h +Lf+G+ g+gk ++a  ++++++ e
  gi|116753581|ref|YP_842699.1|  2 GQPEIVRRLKSYVATRNLPH-LLFSGPPGVGKTAAAISIVREIFGE 46
                                   689999*********99999.8*******************99977 PP

  == domain 2  score: 37.0 bits;  conditional E-value: 3.1e-12
                DNA_pol3_delta2  84 kldqirelieelsrk.pre.skkkiiiiedaekmtksAaNalLktlEEPsenaifiLitsdtnklLktirSRcqelkfsp 161
                                     +d +r   +++ r+ p   ++ k+i +++a+ +t+ A+ al +t+E  s+   fiL  + ++k++++i+SRc +++f++
  gi|116753581|ref|YP_842699.1|  62 GIDVVRTKVKDFARMaPLGgAEFKVIFLDEADALTSDAQSALRRTMERYSATCRFILSCNYSSKIIEPIQSRCAVYRFRA 141
                                    78999966666655515555789*******************************************************98 PP

                DNA_pol3_delta2 162 l 162
                                    l
  gi|116753581|ref|YP_842699.1| 142 L 142
                                    6 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.2e-05      0.01       9      52 ..       7      47 ..       2      82 .. 0.74
   2 ?    6.6   0.0     0.011       9.5     122     163 ..      69     111 ..      48     119 .. 0.71
   3 ?   -0.1   0.0       1.2     1e+03      71     113 ..     202     242 ..     141     268 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.2e-05
                         AAA_16  9 leqLlsalervrsgrpelvllsGesGvGKsslvrellralekdg 52
                                   +++L+s++    +   + +l+sG++GvGK++ + ++ r++ ++g
  gi|116753581|ref|YP_842699.1|  7 VRRLKSYVA---TRNLPHLLFSGPPGVGKTAAAISIVREIFGEG 47
                                   566666665...334489*************9988888877774 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.011
                         AAA_16 122 llkrllallsrderp.lvlvlDdlqwadeaslqllaaLlrlle 163
                                    ++k++++ ++ ++    v++lD+++ + ++ +++l+ ++++ +
  gi|116753581|ref|YP_842699.1|  69 KVKDFARMAPLGGAEfKVIFLDEADALTSDAQSALRRTMERYS 111
                                    55555533333333337*******************9998755 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 1.2
                         AAA_16  71 alaqalareellrqlldeaesaeleawrekleealaavpelag 113
                                    ++++++ r e +r l  +a s +++ +r +l++ l  v+ l+g
  gi|116753581|ref|YP_842699.1| 202 QITSMA-RPEQIRNLIKMAISGDFAGARNELDDLLL-VQGLSG 242
                                    455555.33555666666666666666666666655.444444 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.2   1.2e-07   9.8e-05       3      40 ..     158     195 ..     156     223 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.2e-07
                                    X.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX. CS
                    AAA_assoc_2   3 kklkleddalealaeladGDaRkaLnlLElaaeaaeak 40 
                                    + +++++d +ea+  +a GD+Rka+n+L++aa  +++ 
  gi|116753581|ref|YP_842699.1| 158 EGVEVTEDGIEAINYVARGDMRKAINALQAAALISDKV 195
                                    6799*************************999887653 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 !   18.8   0.0   1.3e-06    0.0011      30      58 ..      16      44 ..       1     125 [. 0.57
   2 ?   -1.9   0.0       2.8   2.4e+03      14      40 ..     211     239 ..     169     251 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.3e-06
                         RuvB_N 30 eealdhvllyGpPGlGkttlakiiakelg 58
                                   +++l h+l++GpPG+Gkt+ a  i +e+ 
  gi|116753581|ref|YP_842699.1| 16 TRNLPHLLFSGPPGVGKTAAAISIVREIF 44
                                   35789***************998888863 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.8
                         RuvB_N  14 kvkeklkifiea..akkreealdhvllyG 40 
                                    ++++ +k++i+   a +r+e  d +l++G
  gi|116753581|ref|YP_842699.1| 211 QIRNLIKMAISGdfAGARNELDDLLLVQG 239
                                    44444444443322556666656555555 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00032      0.27      17      42 ..      14      39 ..       1      70 [. 0.72
   2 !    6.0   0.0    0.0081       6.9     108     135 ..      85     112 ..      76     136 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00032
                   Mg_chelatase 17 iaaaGgHnlllvGppGsGKtmlakrl 42
                                   +a     +ll+ GppG GKt  a  +
  gi|116753581|ref|YP_842699.1| 14 VATRNLPHLLFSGPPGVGKTAAAISI 39
                                   55555679************988554 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0081
                   Mg_chelatase 108 GvLfLDElpefkrkvlevLRePledgev 135
                                     v+fLDE+  +++++  +LR+ +e+ + 
  gi|116753581|ref|YP_842699.1|  85 KVIFLDEADALTSDAQSALRRTMERYSA 112
                                    599********************98765 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.5e-05     0.013      53      96 ..      22      68 ..      11      77 .. 0.79
   2 ?    1.2   0.0      0.19   1.6e+02     281     315 ..      86     121 ..      71     133 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.5e-05
                                   XXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49 53 vLlaGpsgtGktalaiaiskel...gedvpfvalsgsevyslevkkt 96
                                   +L++Gp+g Gkta ai+i +e+   g    f+ l++s+    +v +t
  gi|116753581|ref|YP_842699.1| 22 LLFSGPPGVGKTAAAISIVREIfgeGWRDNFIELNASDERGIDVVRT 68
                                   899******************94222456799999998666666555 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.19
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXX CS
                          TIP49 281 vlfiDevhmlDiecfsylnraleselaPi.vilatn 315
                                    v+f+De+  l  ++ s l r++e   a    il+ n
  gi|116753581|ref|YP_842699.1|  86 VIFLDEADALTSDAQSALRRTMERYSATCrFILSCN 121
                                    9**********************8665432566666 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 !   15.4   0.0   1.6e-05     0.014       8      58 ..       3      53 ..       1      78 [. 0.90
   2 ?    1.2   0.0      0.37   3.2e+02     129     161 ..      80     114 ..      71     124 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.6e-05
                                   HHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EE CS
                         ResIII  8 QeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekfl 58
                                   Q e++++l++ +  ++  ++l+  + G+GKT  a++++++++ +g++++f+
  gi|116753581|ref|YP_842699.1|  3 QPEIVRRLKSYVATRNLPHLLFSGPPGVGKTAAAISIVREIFGEGWRDNFI 53
                                   899999999999877777****************************99997 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.37
                                    HTTT-SEEEEETGGGTTS...TTTHHHHHT---SE CS
                         ResIII 129 lrdrfdviiiDEaHrlgak..kswreilekfkeav 161
                                    +  +f+vi+ DEa  l+++  ++ r+ +e +++ +
  gi|116753581|ref|YP_842699.1|  80 GGAEFKVIFLDEADALTSDaqSALRRTMERYSATC 114
                                    56789999999998888763335555555555554 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 !   17.9   0.0   2.5e-06    0.0021       1      92 [.      21     113 ..      21     119 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.5e-06
                          AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkk..Gpvfanllladeinrappkt 78 
                                    h+l+ g PG++kt ++ ++ + +  e  r  f  +l  sd  G++v+++k k+f   +  G    ++++ de +  ++ +
  gi|116753581|ref|YP_842699.1|  21 HLLFSGPPGVGKTAAAISIVREIFGEGWRDNFI-ELNASDERGIDVVRTKVKDFARMAplGGAEFKVIFLDEADALTSDA 99 
                                    99*********************99999*9996.799**************9997653346777789999********** PP

                          AAA_3  79 qsalleameerqvt 92 
                                    qsal  +me    t
  gi|116753581|ref|YP_842699.1| 100 QSALRRTMERYSAT 113
                                    ********987666 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 !   12.0   0.0   0.00013      0.11      34      72 ..      20      58 ..       9      99 .. 0.87
   2 ?    3.7   0.0     0.045        38     119     167 ..     184     233 ..     178     238 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                          AAA_7 34 kpvllvGptGtGKtviikdllkkldkekylsltinfsaq 72
                                    ++l+ Gp G+GKt+ + ++++++  e +  ++i+++a+
  gi|116753581|ref|YP_842699.1| 20 PHLLFSGPPGVGKTAAAISIVREIFGEGWRDNFIELNAS 58
                                   5899***************99999999999999999985 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.045
                          AAA_7 119 aqppiellRqlldyggwYdrkkl.efkeikdvqlvaamgppgggrneitp 167
                                    a ++ +l+   +d++ +Y+ + +   ++i++++ +a  g  +g rne++ 
  gi|116753581|ref|YP_842699.1| 184 ALQAAALISDKVDMNTIYQITSMaRPEQIRNLIKMAISGDFAGARNELDD 233
                                    66788999999*********8876999*******************9876 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   2.4e-05     0.021      39      86 ..      11      58 ..       2     123 .. 0.68
   2 ?   -1.1   0.0       1.6   1.3e+03       3      41 ..     180     218 ..     178     229 .. 0.81
   3 ?   -3.1   0.0       6.3   5.4e+03      13      34 ..     264     285 ..     261     293 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.4e-05
                      IstB_IS21 39 atlsfiekkenivllGpsGvGKshlaialgveavraglsvlfvrvedL 86
                                    +   +++   +++ Gp+GvGK+  ai++ +e   +g++  f+ +++ 
  gi|116753581|ref|YP_842699.1| 11 KSYVATRNLPHLLFSGPPGVGKTAAAISIVREIFGEGWRDNFIELNAS 58
                                   444445555678999************************999987654 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.6
                      IstB_IS21   3 rletrlrlaklpaqktledidfraarsldkrkvkeLatl 41 
                                    +  + l++a+l   k+  +  ++ + ++ ++++++L+++
  gi|116753581|ref|YP_842699.1| 180 KAINALQAAALISDKVDMNTIYQITSMARPEQIRNLIKM 218
                                    555778889999889888999999999999999988765 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 6.3
                      IstB_IS21  13 lpaqktledidfraarsldkrk 34 
                                    +++ + + +idfr ++++++r+
  gi|116753581|ref|YP_842699.1| 264 VRMINRIGEIDFRITEGANERI 285
                                    5666778899999999998874 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 !   15.6   0.0   1.2e-05      0.01      57     170 ..      83     186 ..      39     190 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.2e-05
                                    SEEEEEEE--.....TT-S-TTHHHHHHHHTTT--SSEEEEEEES.S--HHHHHHHHHTTTEEEEEE----TTTHHHHHH CS
                 DNA_pol3_delta  57 dkrivvlknpklltkesklnekllkeLeeylsnlpedtlLiliapkklderkklvklLkkkatvveaktlkeeelkkwiq 136
                                    + ++++l+ +      + l+ + + +L ++++++++++ +il ++       k++  ++++  v ++  l+ + + k i 
  gi|116753581|ref|YP_842699.1|  83 EFKVIFLDEA------DALTSDAQSALRRTMERYSATCRFILSCN----YSSKIIEPIQSRCAVYRFRALTPDAIEKRIR 152
                                    4577777777......66899999*********************....55789************************** PP

                                    HHHHHTT-EE-HHHHHHHHHHHTT-HHHHHHHHH CS
                 DNA_pol3_delta 137 kraqelglkiekealelLlelvennlsaikqele 170
                                    ++a+++g++ +++ +e + +   ++++ + ++l+
  gi|116753581|ref|YP_842699.1| 153 YIAEQEGVEVTEDGIEAINYVARGDMRKAINALQ 186
                                    *****************************99998 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.31   2.7e+02      60      77 ..      24      41 ..      10      50 .. 0.84
   2 !   12.6   0.0   4.7e-05      0.04     158     212 ..      64     119 ..      61     121 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.31
                                   E---TTS--HHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxx RF
                         SNF2_N 60 LaDemGLGKTvqvlalil 77
                                   ++  +G+GKT  +++++ 
  gi|116753581|ref|YP_842699.1| 24 FSGPPGVGKTAAAISIVR 41
                                   56679**********996 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 4.7e-05
                                    HHHHHHT......TTS-S-S-SEEEES-GGGT--T.TSHHHHHHHH---S-EEEE- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                         SNF2_N 158 dvlsreaelqkkrsvlkqvewkrvvlDEghtlkns.tskaaeavskLstsnrwilt 212
                                    dv++++++ ++++ +l   e k + lDE+  l +  +s ++ +++++s+  r il+
  gi|116753581|ref|YP_842699.1|  64 DVVRTKVKDFARMAPLGGAEFKVIFLDEADALTSDaQSALRRTMERYSATCRFILS 119
                                    56777788889999*********************99******************8 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0    0.0081       6.9       7      22 ..      21      36 ..      16      44 .. 0.84
   2 ?    6.6   0.0      0.01       8.6      87     118 ..      81     109 ..      52     123 .. 0.70
   3 ?   -2.8   0.0       8.4   7.2e+03      82     115 ..     178     218 ..     174     229 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0081
                         AAA_22  7 ilvvtGesGtGKTtll 22
                                   +l+  G++G+GKT  +
  gi|116753581|ref|YP_842699.1| 21 HLLFSGPPGVGKTAAA 36
                                   68899********976 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.01
                         AAA_22  87 raravielliiDEaqhlrseealeeLrsllnl 118
                                     a +  +++ +DEa+ l + +a + Lr+ ++ 
  gi|116753581|ref|YP_842699.1|  81 GAEF--KVIFLDEADAL-TSDAQSALRRTMER 109
                                    3444..5**********.88888888777773 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 8.4
                         AAA_22  82 leqalraravielliiDEaqhlr.....s...eealeeLrsl 115
                                    +++a++a ++ ++li D ++  +     s   +e++++L ++
  gi|116753581|ref|YP_842699.1| 178 MRKAINALQA-AALISDKVDMNTiyqitSmarPEQIRNLIKM 218
                                    5666666666.7777776666323444313345555555544 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 ?   11.0   0.1   0.00039      0.33       1      90 [.      21     108 ..      21     114 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00039
                                    EEEEE--SSSSHHHHHHHGGGGB...S--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG- CS
                          AAA_5   1 dvlLvGppGtgKselaerlaaal...nreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEvera 77 
                                    ++l  GppG+gK+  a ++ + +   +++ + + l+++ + +  +  +++ + +   +  pl   + e ++++lDE + +
  gi|116753581|ref|YP_842699.1|  21 HLLFSGPPGVGKTAAAISIVREIfgeGWRDNFIELNASDE-RG-IDVVRT-KVKDFARMAPLG--GAEFKVIFLDEADAL 95 
                                    68999*********99999988888866666666666222.22.222221.334444444554..559999999999999 PP

                                    -HHHHHHHHHHHH CS
                          AAA_5  78 esevlnsLlslle 90 
                                     s+++++L + +e
  gi|116753581|ref|YP_842699.1|  96 TSDAQSALRRTME 108
                                    9999999877666 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0041       3.5      14      59 ..       9      58 ..       3      63 .. 0.72
   2 ?    5.1   0.0      0.02        17      92     119 ..      82     109 ..      74     114 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0041
                                   HHHHHCTSS..S-EEEECSTTSSHHHHHHHHHH..HSTTTTS-EEEEETT CS
                Sigma54_activat 14 qikkvaktd..lsvlitGesGtGKellaraihe..askrkekpfvavnca 59
                                   ++k++++t+   ++l  G  G+GK+  a +i +    +  + +f+++n +
  gi|116753581|ref|YP_842699.1|  9 RLKSYVATRnlPHLLFSGPPGVGKTAAAISIVReiFGEGWRDNFIELNAS 58
                                   4555444443467899************9998844455667789988876 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.02
                                    TTTSEEEEETGGGS-HHHHHHHHHHHHH CS
                Sigma54_activat  92 adgGtlfLDeigelplelQekLlrvlqe 119
                                    a+  ++fLDe   l+ ++Q+ L r +++
  gi|116753581|ref|YP_842699.1|  82 AEFKVIFLDEADALTSDAQSALRRTMER 109
                                    556689****************999986 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   0.00023       0.2       6      88 ..      23     106 ..      20     113 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00023
                         AAA_24   6 liyGpsgiGKTtlakel.........gpkplfidtekGlksldadkfpdieswedfldevvelaaeladyktlviDtide 76 
                                    l  Gp+g+GKT  a ++          ++++ ++  +  + +d+ +        +++d++   +   a++k++++D +d 
  gi|116753581|ref|YP_842699.1|  23 LFSGPPGVGKTAAAISIvreifgegwRDNFIELNASD-ERGIDVVRT-------KVKDFARMAPLGGAEFKVIFLDEADA 94 
                                    557***********99977778774444444444433.234566664.......47788888899*************** PP

                         AAA_24  77 leelclaevirq 88 
                                    l + +   ++r 
  gi|116753581|ref|YP_842699.1|  95 LTSDAQSALRRT 106
                                    *99988877665 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   0.00046      0.39      37      64 ..      23      49 ..      20      66 .. 0.84
   2 ?   -2.1   0.0       2.9   2.4e+03      29      50 ..     284     305 .]     281     305 .] 0.84

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00046
                         AAA_25 37 llaGapgtGKttlaldlalavatGkpwl 64
                                   l+ G+pg+GKt++a++++ ++  G+ w 
  gi|116753581|ref|YP_842699.1| 23 LFSGPPGVGKTAAAISIVREIF-GEGWR 49
                                   678***************9999.45554 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.9
                         AAA_25  29 llpagelallaGapgtGKttla 50 
                                     + +++l++ ++ +g  K+t++
  gi|116753581|ref|YP_842699.1| 284 RIQLEALIAYMALTGLSKSTAT 305
                                    5678899999*********975 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   0.00035       0.3       2      40 ..      23      58 ..      22      66 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00035
                   RNA_helicase  2 wlyGpsgeGKStlakeLakallkklklkkkdsvysrnpe 40
                                   +++Gp+g+GK+ +a ++++++    ++ ++d+++  n++
  gi|116753581|ref|YP_842699.1| 23 LFSGPPGVGKTAAAISIVREIF---GEGWRDNFIELNAS 58
                                   799***************9999...55577777665555 PP

>> Torsin  Torsin
   #    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      36      89 ..       5      55 ..       1      65 [. 0.86
   2 ?   -2.2   0.0         5   4.3e+03      12      41 ..     220     249 ..     216     256 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00055
                                   HHHHHHHHHHT-SS-SS-EEEEEEE-TTSSHHHHHHHHHHHHSTTGGGSTTEEE CS
                         Torsin 36 lvvksvkaylenekpkkpLvlsfhGwtGtGknfvaeiiaenlyrdGlrsdyvkk 89
                                    +v+ +k+y+++ +      l f G +G Gk   a  i+ +++ +G r ++++ 
  gi|116753581|ref|YP_842699.1|  5 EIVRRLKSYVATRNLP---HLLFSGPPGVGKTAAAISIVREIFGEGWRDNFIEL 55
                                   6899999999887654...46699**************************9975 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5
                                    .---HHHHHHHHHHH--S-HHHHHHHHHHH CS
                         Torsin  12 isanleeLekdlekklfGqhlvkklvvksv 41 
                                    is ++ + +++l++ l  q l  + vv  +
  gi|116753581|ref|YP_842699.1| 220 ISGDFAGARNELDDLLLVQGLSGQDVVVQI 249
                                    666777777888888888888877776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 2085.82
//
Query:       gi|116753582|ref|YP_842700.1|  [L=199]
Description: GPR1/FUN34/yaaH family protein [Methanosaeta thermophila PT]
Scores for complete 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-41  141.9  19.5    2.5e-41  141.5  19.5    1.0  1  Gpr1_Fun34_YaaH  GPR1/FUN34/yaaH family
  ------ inclusion threshold ------
       0.64   10.5   6.0       0.15   12.5   1.9    2.0  2  DUF983           Protein of unknown function (DUF983)


Domain annotation for each model (and alignments):
>> Gpr1_Fun34_YaaH  GPR1/FUN34/yaaH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.5  19.5   2.8e-45   2.5e-41      16     201 ..      16     194 ..       7     198 .. 0.94

  Alignments for each domain:
  == domain 1  score: 141.5 bits;  conditional E-value: 2.8e-45
                Gpr1_Fun34_YaaH  16 kfaNPaPlgllafalttfvlslvnlgargitepnvvvglalfyGGlvqllaGiwefavgntFgatalssYGgFwlsy.aa 94 
                                    + aNPaPlgl++f++tt +l+l+n+g  ++ +  +++++ +fyGG++q++aGi+e+  gntFg+ta++sYG Fwl++ ++
  gi|116753582|ref|YP_842700.1|  16 TTANPAPLGLMGFGMTTVLLNLHNAGYFELGS--MILAMGIFYGGIAQIIAGIMEWKKGNTFGTTAFTSYGLFWLTLvGL 93 
                                    68*************************99987..9****************************************95499 PP

                Gpr1_Fun34_YaaH  95 ilipgfgilaaYeedeeelnnalglyllgwfiftfllllatlrstvalfllfffldltflllaigeltgsakvlkAggvf 174
                                    i+ipg++  ++          a+  yl++w +ft ++++ tlr++ al ++f+ l + f+lla+ + tgsa + + +g+ 
  gi|116753582|ref|YP_842700.1|  94 IMIPGMNLGEKT------SLPAMTAYLFMWGLFTAVMFFGTLRANRALQFVFLSLAILFFLLAARDATGSAAIGTLAGYE 167
                                    *******98887......4679999******************************************************* PP

                Gpr1_Fun34_YaaH 175 giiaaflawYnalaglatkensyftlp 201
                                    gii+++ a Y+ala+++++ +  ++lp
  gi|116753582|ref|YP_842700.1| 168 GIICGLSAIYTALAQVLNEAHGRVILP 194
                                    *****************9987766666 PP

>> DUF983  Protein of unknown function (DUF983)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1      0.38   3.4e+03      32      78 ..      25      72 ..      12      78 .. 0.54
   2 ?   12.5   1.9   1.6e-05      0.15      30      79 ..      86     135 ..      80     141 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.38
                         DUF983 32 ilivghlvvplallvevayep.plwvhlliwlpltlllsllllrplKG 78
                                   ++  g+  v l l  + ++e+ ++ + + i+   ++ ++ +++   KG
  gi|116753582|ref|YP_842700.1| 25 LMGFGMTTVLLNLHNAGYFELgSMILAMGIFYGGIAQIIAGIMEWKKG 72
                                   444455555554444444444455555555555555555555555555 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 1.6e-05
                         DUF983  30 fvilivghlvvplallvevayepplwvhlliwlpltlllsllllrplKGa 79 
                                    f +++vg +++p + l e +  p +   l +w ++t+++ +++lr  +++
  gi|116753582|ref|YP_842700.1|  86 FWLTLVGLIMIPGMNLGEKTSLPAMTAYLFMWGLFTAVMFFGTLRANRAL 135
                                    77899****************************************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1447.21
//
Query:       gi|116753583|ref|YP_842701.1|  [L=275]
Description: hypothetical protein Mthe_0264 [Methanosaeta thermophila PT]
Scores for complete 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   41.5   0.0    1.5e-08   35.0   0.0    2.2  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    5.1e-05   23.9   0.1    0.00012   22.6   0.1    1.7  1  Metallophos    Calcineurin-like phosphoesterase


Domain annotation for each model (and alignments):
>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.0   1.7e-12   1.5e-08       3     147 ..       2     253 ..       1     268 [. 0.82

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 1.7e-12
                  Metallophos_2   3 laiiSDlH..............snldaleav.........lealkevgvdaiihaGD............leeeepevlee 47 
                                    ++++SD+H              +                  ++l++    +++++GD            l e+ep +l +
  gi|116753583|ref|YP_842701.1|   2 IIAVSDVHmaerpsdrqvkaddA-------RflefldctaSDQLSSG--GHLVLLGDivdlwrrdfvraLIESEP-ALSR 71 
                                    789*****987777744333322.......35566666444444444..9*******888888887664245555.8888 PP

                  Metallophos_2  48 llela...pvlaVrGNnDeev.veedvlreaaelgtdlpeeaelelagekvlliHgdpl..................... 102
                                    l+e+     v+++ GN+D    + +++  +++++  ++++  +le + +k+++iHg +l                     
  gi|116753583|ref|YP_842701.1|  72 LIEISrkaTVHYIAGNHD--FhMLRMWELANNRFPFEVTKPLRLEDGMTKLFFIHGYQLevlanpycksvsayetfsegl 149
                                    88888888**********..558999999999999999999999967777*******99********************* PP

                  Metallophos_2 103 .............................................................gvkdalaellkeaeegsdv 121
                                                                                                 +++ ++a++++ ++e++++
  gi|116753583|ref|YP_842701.1| 150 ciagddtgnaadklwdtfnvaksaldgikrlpsdlkgaidsmmqsqgirmtgphntramaeQLASSMARVVYLGMEPDEF 229
                                    *****************************************************9999888888888888888899999** PP

                  Metallophos_2 122 vvcGHtHvpevekeggvlvvnPGsvg 147
                                    +++GHtH+p +  e+  ++ n Gs  
  gi|116753583|ref|YP_842701.1| 230 LISGHTHRPFCNPEE--RIANTGSWN 253
                                    *********988874..666777765 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.1   1.4e-08   0.00012       3     123 ..       2     126 ..       1     238 [. 0.56

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.4e-08
                                    EEEEESBTB......TTCCTHHHHHHHHHHHH....HHHTTESEEEEESTSSSSS.........HHHHHHHHHHHHHHHH CS
                    Metallophos   3 ilvigDlHl......algggqlddllkllddl....lreekpdlvllaGDlvdrg.........dlekellellaalvky 63 
                                    i+ ++D+H           ++ +++l++ld +    l++ ++ ++l  GD+vd           + e +    l++l++ 
  gi|116753583|ref|YP_842701.1|   2 IIAVSDVHMaerpsdRQVKADDARFLEFLDCTasdqLSSGGHLVLL--GDIVDLWrrdfvraliESEPA----LSRLIEI 75 
                                    7899****99999985555677777777744433224444666666..*****9967665543322222....3333333 PP

                                    ..TSEEEEEC-TTS..............CHHH.HHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESE CS
                    Metallophos  64 ..pipvylllGNHe..............gfee.ellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGg 123
                                      +  v+ ++GNH+               fe  + l++++  ++                          ++++hG 
  gi|116753583|ref|YP_842701.1|  76 srKATVHYIAGNHDfhmlrmwelannrfPFEVtKPLRLEDGMTK--------------------------LFFIHGY 126
                                    666889********555544444444443333222222222222..........................3333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); 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 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2070.04
//
Query:       gi|116753584|ref|YP_842702.1|  [L=337]
Description: transcription initiation factor IIB [Methanosaeta thermophila PT]
Scores for complete 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  149.2   3.5    6.3e-22   77.4   1.2    2.3  2  TFIIB            Transcription factor TFIIB repeat
    7.2e-19   67.0   1.2    7.2e-19   67.0   1.2    1.8  1  TF_Zn_Ribbon     TFIIB zinc-binding
     0.0033   17.2   0.0       0.14   11.9   0.0    2.3  2  Cyclin_N         Cyclin, N-terminal domain
     0.0044   16.8   2.1      0.036   13.9   0.1    3.1  3  HTH_AsnC-type    AsnC-type helix-turn-helix domain
     0.0057   16.7   0.0        2.8    8.0   0.0    2.4  2  Cyclin_C         Cyclin, C-terminal domain
     0.0064   16.8   0.4       0.18   12.2   0.2    2.5  2  Lar_restr_allev  Restriction alleviation protein Lar
     0.0082   15.6   7.6      0.072   12.6   0.0    3.9  4  Sigma70_r4       Sigma-70, region 4
  ------ inclusion threshold ------
      0.011   15.6   0.3      0.029   14.3   0.3    1.7  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.018   14.4   0.2        1.7    8.2   0.1    2.4  2  zf-ribbon_3      zinc-ribbon domain
      0.031   14.3   0.1      0.087   12.9   0.0    1.8  1  RB_B             Retinoblastoma-associated protein B domain
      0.034   12.7   0.2      0.049   12.2   0.2    1.2  1  Terminase_GpA    Phage terminase large subunit (GpA)
      0.036   14.6   0.0        2.5    8.7   0.0    2.5  2  RPA_interact_C   Replication protein A interacting C-terminal
      0.041   13.9   0.1        3.7    7.7   0.0    3.7  4  HTH_3            Helix-turn-helix
      0.046   13.7   0.6       0.38   10.8   0.2    2.3  2  DZR              Double zinc ribbon
      0.053   13.2   0.1       0.15   11.8   0.1    1.7  1  Ribosomal_S27e   Ribosomal protein S27
      0.059   13.4   2.7        8.4    6.5   0.0    3.5  3  HTH_Crp_2        Crp-like helix-turn-helix domain
      0.059   13.7   1.7       0.09   13.1   0.1    2.1  2  Prim_Zn_Ribbon   Zinc-binding domain of primase-helicase
      0.076   13.1   3.9        3.8    7.7   2.2    2.9  2  zf-ACC           Acetyl-coA carboxylase zinc finger domain
       0.11   12.5   0.3       0.11   12.5   0.3    1.9  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
       0.12   12.8   6.4        5.6    7.4   0.1    4.0  3  HTH_31           Helix-turn-helix domain
       0.14   12.2   1.7        1.5    8.8   0.6    2.5  2  HypA             Hydrogenase/urease nickel incorporation, met
       0.16   11.8   1.0        7.4    6.4   0.1    2.7  2  zinc_ribbon_2    zinc-ribbon domain
       0.26   11.4   5.3       0.59   10.3   0.3    3.0  4  Zn-ribbon_8      Zinc ribbon domain
       0.28   10.9   1.1        1.8    8.4   1.1    2.2  1  A2L_zn_ribbon    A2L zinc ribbon domain
       0.36   11.0   1.9         33    4.7   0.3    3.7  4  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
        0.6   10.3   2.4        4.1    7.6   0.9    2.3  2  Auto_anti-p27    Sjogren's syndrome/scleroderma autoantigen 1
       0.68   10.1   2.4         37    4.5   0.0    2.8  2  SR1P             SR1 protein
        2.6    7.9   7.0          1    9.2   0.1    3.6  3  HTH_23           Homeodomain-like domain
        2.8    7.6   5.0         21    4.8   0.0    2.8  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
        8.3    6.4   6.6        1.6    8.7   1.5    2.5  2  Nudix_N_2        Nudix N-terminal


Domain annotation for each model (and alignments):
>> TFIIB  Transcription factor TFIIB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.4   1.2     1e-24   6.3e-22       2      71 .]     157     226 ..     156     226 .. 0.98
   2 !   72.1   0.0   4.9e-23   2.9e-20       1      71 []     250     320 ..     250     320 .. 0.99

  Alignments for each domain:
  == domain 1  score: 77.4 bits;  conditional E-value: 1e-24
                                    HHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                          TFIIB   2 krfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                     r+a+al+L+  V++ A  ++++a+e++++ Grs +g+aAA+ly Acr+++v rt+ ei++v++Vs k+i
  gi|116753584|ref|YP_842702.1| 157 DRMASALGLSRNVRETAAVIYRRAVEKNLIRGRSIEGVAAAALYAACRQCNVPRTLDEIAEVSRVSRKEI 226
                                    69*****************************************************************997 PP

  == domain 2  score: 72.1 bits;  conditional E-value: 4.9e-23
                                    HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                          TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                    i+rf++ l+L+  V+ +  e++++a+e+++++Gr p+g+aAA++yiA+ +++ +rtq+e+++v+ V+e+ti
  gi|116753584|ref|YP_842702.1| 250 IPRFCSGLNLKGDVQAKGIEILRQAAEKELTSGRGPTGVAAAAIYIASILCNDRRTQREVADVAGVTEVTI 320
                                    89*******************************************************************98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.0   1.2   1.2e-21   7.2e-19       3      43 .]      41      81 ..      39      81 .. 0.98

  Alignments for each domain:
  == domain 1  score: 67.0 bits;  conditional E-value: 1.2e-21
                                   ETTTTCEECHEETSTTCEEESSSSBEEEECCCCCCCHHHHH CS
                   TF_Zn_Ribbon  3 CPnCgstnlveDpergelvCtdCGlVlednsidegpewref 43
                                   CP+Cgs+ lv+D+er+elvC++CGlV+++n id gpewr+f
  gi|116753584|ref|YP_842702.1| 41 CPECGSRALVRDYERAELVCSECGLVIDENFIDQGPEWRAF 81
                                   ***************************************98 PP

>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00023      0.14      38     113 ..     156     228 ..     123     242 .. 0.81
   2 ?    3.0   0.0      0.13        81      34      90 ..     246     302 ..     232     334 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00023
                                    HHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSSS---HHHHHHHTTTSS-HHHHHH CS
                       Cyclin_N  38 lvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveeisppkledlvyitdeafteeeile 113
                                    l ++a+ + l++++  +a++++ R ++k+ ++ + ++ v+a++L+ A++  ++ p +l++++ ++   ++++ei +
  gi|116753584|ref|YP_842702.1| 156 LDRMASALGLSRNVRETAAVIYRRAVEKNLIRGRSIEGVAAAALYAACRQCNV-PRTLDEIAEVS--RVSRKEIGR 228
                                    5567788899999999*********************************9888.88888888774..355666655 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.13
                                    HHHHHHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSS CS
                       Cyclin_N  34 lidwlvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveei 90 
                                     id++ + ++ ++l+ ++ +  +++l +  +k+ ++ +    v+a+++++A+ + ++
  gi|116753584|ref|YP_842702.1| 246 PIDYIPRFCSGLNLKGDVQAKGIEILRQAAEKELTSGRGPTGVAAAAIYIASILCND 302
                                    589999999999999999999999999999999999999999*********977444 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0         2   1.2e+03      23      31 ..     159     167 ..     156     169 .. 0.85
   2 ?   -0.0   0.0       1.3     8e+02      15      36 ..     207     228 ..     205     231 .. 0.73
   3 !   13.9   0.1     6e-05     0.036      17      41 ..     303     327 ..     297     328 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 2
                  HTH_AsnC-type  23 LAervGlSe 31 
                                    +A ++GlS+
  gi|116753584|ref|YP_842702.1| 159 MASALGLSR 167
                                    799*****8 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.3
                  HTH_AsnC-type  15 daRisyaeLAervGlSestvlr 36 
                                    +  ++  e+Ae   +S+ ++ r
  gi|116753584|ref|YP_842702.1| 207 NVPRTLDEIAEVSRVSRKEIGR 228
                                    5667888999988888887766 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 6e-05
                  HTH_AsnC-type  17 RisyaeLAervGlSestvlrRvrrL 41 
                                    R++ +e+A+  G++e t+++R++ L
  gi|116753584|ref|YP_842702.1| 303 RRTQREVADVAGVTEVTIRNRYKEL 327
                                    99********************988 PP

>> Cyclin_C  Cyclin, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.019        11      47      83 ..     194     230 ..     191     240 .. 0.88
   2 !    8.0   0.0    0.0047       2.8      47      89 ..     288     330 ..     283     334 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.019
                                    HHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHH CS
                       Cyclin_C  47 iAaaalllarstlnspewtetlehytgyskedlkpcv 83 
                                    +Aaaal++a+++ n p   +++ +++++s +++   +
  gi|116753584|ref|YP_842702.1| 194 VAAAALYAACRQCNVPRTLDEIAEVSRVSRKEIGRTY 230
                                    7***************999999999999998886665 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0047
                                    HHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHHHHH CS
                       Cyclin_C  47 iAaaalllarstlnspewtetlehytgyskedlkpcvelilel 89 
                                    +Aaaa+++a+   n+   ++++  + g+++  +++ ++ ++e 
  gi|116753584|ref|YP_842702.1| 288 VAAAAIYIASILCNDRRTQREVADVAGVTEVTIRNRYKELAEE 330
                                    8************************************999986 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.2   0.00031      0.18       5      37 ..      40      67 ..      36      89 .. 0.77
   2 ?    2.1   0.0      0.44   2.7e+02      27      36 ..     193     208 ..     165     227 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00031
                Lar_restr_allev  5 pCPfCggravlersqrvvaeigqcvyCadCga.s 37
                                    CP Cg+ra +   +r          C +Cg   
  gi|116753584|ref|YP_842702.1| 40 ECPECGSRALVRDYERAE------LVCSECGLvI 67
                                   6********998887774......89*****942 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.44
                Lar_restr_allev  27 q......cvyCadCga 36 
                                           + +C +C++
  gi|116753584|ref|YP_842702.1| 193 GvaaaalYAACRQCNV 208
                                    144555699******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 ?   -1.9   0.7       4.1   2.4e+03      35      43 ..       5      13 ..       4      20 .. 0.76
   2 ?   -2.3   0.1       5.5   3.3e+03      34      47 ..     170     183 ..     158     183 .. 0.65
   3 ?    5.3   0.0     0.024        14      20      35 ..     209     224 ..     202     231 .. 0.86
   4 !   12.6   0.0   0.00012     0.072      20      43 ..     303     326 ..     294     333 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 4.1
                                   HHHHHHHHH CS
                     Sigma70_r4 35 erVrqiekr 43
                                   er+r ie+ 
  gi|116753584|ref|YP_842702.1|  5 ERIREIERT 13
                                   89****986 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.5
                                    HHHHHHHHHHHHHH CS
                     Sigma70_r4  34 rerVrqiekrAlrk 47 
                                    re++  i +rA++k
  gi|116753584|ref|YP_842702.1| 170 RETAAVIYRRAVEK 183
                                    46666777777765 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.024
                                    T--HHHHHHHHTS-HH CS
                     Sigma70_r4  20 glTleEIgerlgiSre 35 
                                    ++Tl EI+e+  +Sr 
  gi|116753584|ref|YP_842702.1| 209 PRTLDEIAEVSRVSRK 224
                                    79*********99996 PP

  == domain 4  score: 12.6 bits;  conditional E-value: 0.00012
                                    T--HHHHHHHHTS-HHHHHHHHHH CS
                     Sigma70_r4  20 glTleEIgerlgiSrerVrqiekr 43 
                                     +T+ E++++ g+++ ++r + k+
  gi|116753584|ref|YP_842702.1| 303 RRTQREVADVAGVTEVTIRNRYKE 326
                                    68*******************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 ?   14.3   0.3   4.9e-05     0.029      29      57 ..      39      68 ..      17      71 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.9e-05
                 OrfB_Zn_ribbon 29 ktCseCgsknke.alsgrtfkCpnCgfead 57
                                    +C+eCgs+    + ++ +++C++Cg+++d
  gi|116753584|ref|YP_842702.1| 39 VECPECGSRALVrDYERAELVCSECGLVID 68
                                   68******9877799***********9987 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1    0.0028       1.7       2      10 ..      38      46 ..      38      52 .. 0.85
   2 ?    3.6   0.0     0.077        46      18      25 ..      59      66 ..      54      69 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0028
                    zf-ribbon_3  2 tvrCPnCGa 10
                                   tv+CP+CG+
  gi|116753584|ref|YP_842702.1| 38 TVECPECGS 46
                                   799*****7 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.077
                    zf-ribbon_3 18 vCpyCGtk 25
                                   vC  CG +
  gi|116753584|ref|YP_842702.1| 59 VCSECGLV 66
                                   56666655 PP

>> RB_B  Retinoblastoma-associated protein B domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00015     0.087      10      96 ..     149     233 ..     141     241 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00015
                           RB_B  10 yklaavrlrdLcerLklsselrekiwtlfehvlveetellkdRhlDqillcavYvvakvtkeelsFkeiikaYrkqpqas 89 
                                    +  a + l ++ + L ls+++re +  + ++++  e++l++ R ++ +  +a+Y+ ++ ++  +++ ei +  r + ++ 
  gi|116753584|ref|YP_842702.1| 149 LAFALSELDRMASALGLSRNVRETAAVIYRRAV--EKNLIRGRSIEGVAAAALYAACRQCNVPRTLDEIAEVSRVSRKEI 226
                                    66788899999999*****99999987777766..578*********************************999999999 PP

                           RB_B  90 skvyrsv 96 
                                     ++yr v
  gi|116753584|ref|YP_842702.1| 227 GRTYRFV 233
                                    9988877 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 ?   12.2   0.2   8.3e-05     0.049     195     240 ..      35      70 ..      17     103 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.3e-05
                  Terminase_GpA 195 rryyvpCphCgelqelsferlkwpegeaeekaryvCphcgslieeh 240
                                     +y v+Cp+Cg+   ++          + e a++vC++cg +i+e+
  gi|116753584|ref|YP_842702.1|  35 DKYTVECPECGSRALVR----------DYERAELVCSECGLVIDEN 70 
                                    38************999..........4678************997 PP

>> RPA_interact_C  Replication protein A interacting C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0    0.0041       2.5       2      27 ..      41      69 ..      40     125 .. 0.82
   2 ?    3.4   0.0      0.19   1.2e+02      65      78 ..     195     208 ..     166     211 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0041
                 RPA_interact_C  2 CPvCkkrklkets..evifCe.Cglrlet 27
                                   CP C +r l ++     ++C+ Cgl ++ 
  gi|116753584|ref|YP_842702.1| 41 CPECGSRALVRDYerAELVCSeCGLVIDE 69
                                   *******9988543477***99***9987 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.19
                 RPA_interact_C  65 gveaLlaeCeeCdf 78 
                                      +aL+a C++C++
  gi|116753584|ref|YP_842702.1| 195 AAAALYAACRQCNV 208
                                    5689********86 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       3.5   2.1e+03      39      51 ..     154     166 ..     150     168 .. 0.76
   2 ?    0.4   0.0       1.2   7.2e+02      11      27 ..     211     227 ..     202     228 .. 0.85
   3 ?    7.7   0.0    0.0061       3.7      11      27 ..     305     321 ..     300     323 .. 0.92
   4 ?   -1.6   0.0       4.9   2.9e+03      13      21 ..     325     333 ..     322     334 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 3.5
                                    HHHHHHHHHHTSE CS
                          HTH_3  39 etlkklakaLgvs 51 
                                    + l ++a aLg+s
  gi|116753584|ref|YP_842702.1| 154 SELDRMASALGLS 166
                                    5678888888876 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.2
                                    HHHHHHHHHTSSHHHHH CS
                          HTH_3  11 sqeeLAeklGvsrstis 27 
                                    ++ e+Ae++ vsr  i 
  gi|116753584|ref|YP_842702.1| 211 TLDEIAEVSRVSRKEIG 227
                                    67899999999998876 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0061
                                    HHHHHHHHHTSSHHHHH CS
                          HTH_3  11 sqeeLAeklGvsrstis 27 
                                    +q+e+A+++Gv+  ti+
  gi|116753584|ref|YP_842702.1| 305 TQREVADVAGVTEVTIR 321
                                    9*************997 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 4.9
                                    HHHHHHHTS CS
                          HTH_3  13 eeLAeklGv 21 
                                    +eLAe+l++
  gi|116753584|ref|YP_842702.1| 325 KELAEELNI 333
                                    899999986 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   0.00063      0.38      13      41 ..      39      70 ..      30      72 .. 0.74
   2 ?    0.3   0.0       1.2   7.2e+02      30      36 ..     202     208 ..     188     216 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00063
                            DZR 13 rfCseCgtk..lkavaa.edrCpsCgekvdpe 41
                                     C+eCg++  ++ +++ e +C++Cg  +d++
  gi|116753584|ref|YP_842702.1| 39 VECPECGSRalVRDYERaELVCSECGLVIDEN 70
                                   56999999986666665899999999877765 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.2
                            DZR  30 rCpsCge 36 
                                    +C +C+ 
  gi|116753584|ref|YP_842702.1| 202 ACRQCNV 208
                                    4555543 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00025      0.15       8      36 ..      39      67 ..      37      69 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00025
                                   EE-TTTS-EEEEESS-SS-EEESSSTCEE CS
                 Ribosomal_S27e  8 vkCpdCenetvvFshaatvvkCisCgkvL 36
                                   v Cp+C+    v +       C  Cg v+
  gi|116753584|ref|YP_842702.1| 39 VECPECGSRALVRDYERAELVCSECGLVI 67
                                   99************************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 ?    1.9   0.5      0.38   2.3e+02      26      58 ..     158     192 ..     127     202 .. 0.67
   2 ?    3.1   0.0      0.16        95      12      42 ..     203     230 ..     194     236 .. 0.77
   3 ?    6.5   0.0     0.014       8.4      23      48 ..     305     330 ..     291     335 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.38
                                    HHHHHTTSSH...HHHHHHHHHHHHTTSEEETEEEE CS
                      HTH_Crp_2  26 elAsmlGltr...etvsrilseLkreglisrgrrir 58 
                                     +As lGl+r   et   i ++  +++li+ +  i+
  gi|116753584|ref|YP_842702.1| 158 RMASALGLSRnvrETAAVIYRRAVEKNLIRGRS-IE 192
                                    589999998533377777777777777777554.55 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.16
                                    CTTTCEEEEEHHHHHHHHHTTSSHHHHHHHH CS
                      HTH_Crp_2  12 eraggeielpltqeelAsmlGltretvsril 42 
                                    +r   ++++p t +e+A+   ++r  + r+ 
  gi|116753584|ref|YP_842702.1| 203 CR---QCNVPRTLDEIAEVSRVSRKEIGRTY 230
                                    33...478999*************9998875 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.014
                                    HHHHHHHHTTSSHHHHHHHHHHHHHT CS
                      HTH_Crp_2  23 tqeelAsmlGltretvsrilseLkre 48 
                                    tq+e A+  G+t +t+    +eL +e
  gi|116753584|ref|YP_842702.1| 305 TQREVADVAGVTEVTIRNRYKELAEE 330
                                    9***************9999999876 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 ?   13.1   0.1   0.00015      0.09       1      33 [.      36      64 ..      36      70 .. 0.89
   2 ?   -2.0   0.2       7.5   4.5e+03      28      31 ..     203     206 ..     201     209 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00015
                                   EEEE--TTTT-TTTEE.ETT....S-EEETTTTB CS
                 Prim_Zn_Ribbon  1 gkhspCPvCGGrDrFr.fddkdgrGtwfCrqCgg 33
                                   ++ ++CP CG+r   r +++       +C++C g
  gi|116753584|ref|YP_842702.1| 36 KYTVECPECGSRALVRdYER----AELVCSEC-G 64
                                   599**********9999999....999**999.4 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 7.5
                                    ETTT CS
                 Prim_Zn_Ribbon  28 CrqC 31 
                                    CrqC
  gi|116753584|ref|YP_842702.1| 203 CRQC 206
                                    **** 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 ?    7.7   2.2    0.0064       3.8       3      26 .]      40      63 ..      39      63 .. 0.95
   2 ?    3.9   0.0     0.093        56       9      20 ..     174     185 ..     173     185 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0064
                         zf-ACC  3 KCpsCgemlykkeLernlyVCPkC 26
                                    Cp+Cg+  + ++ er   VC +C
  gi|116753584|ref|YP_842702.1| 40 ECPECGSRALVRDYERAELVCSEC 63
                                   6*********************** PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.093
                         zf-ACC   9 emlykkeLernl 20 
                                    +++y++ +e+nl
  gi|116753584|ref|YP_842702.1| 174 AVIYRRAVEKNL 185
                                    79*********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 ?   12.5   0.3   0.00018      0.11      19      44 ..      39      64 ..      34      65 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00018
                  Zn_Tnp_IS1595 19 fvCPhCgsr.kayriktrglfqCkeCr 44
                                   + CP Cgsr  ++ ++ r  + C+eC+
  gi|116753584|ref|YP_842702.1| 39 VECPECGSRaLVRDYE-RAELVCSECG 64
                                   67*******6566666.599******7 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1     0.073        44      44      62 ..     153     171 ..     131     173 .. 0.83
   2 ?    1.5   0.1      0.63   3.8e+02      16      33 ..     211     228 ..     187     231 .. 0.81
   3 ?    7.4   0.1    0.0094       5.6      10      32 ..     272     321 ..     269     322 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.073
                         HTH_31  44 pavlealaralgldpaera 62 
                                    ++ l+++a algl+++ r+
  gi|116753584|ref|YP_842702.1| 153 LSELDRMASALGLSRNVRE 171
                                    5799**********99887 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.63
                         HTH_31  16 sqeevAerlgvsestlsr 33 
                                    +++e Ae ++vs+  ++r
  gi|116753584|ref|YP_842702.1| 211 TLDEIAEVSRVSRKEIGR 228
                                    778899999999888877 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0094
                         HTH_31  10 Rera...........................GLsqeevAerlgvsestls 32 
                                    R++a                           + +q+evA+ +gv+e t++
  gi|116753584|ref|YP_842702.1| 272 RQAAekeltsgrgptgvaaaaiyiasilcndRRTQREVADVAGVTEVTIR 321
                                    555555566666666666666666667777788************99986 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.6    0.0026       1.5      65      93 ..      33      64 ..       8      77 .. 0.75
   2 ?    1.7   0.0      0.43   2.5e+02      40      79 ..     169     209 ..     141     225 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0026
                                   EEE--EEEETTTS-EEECHH..H.HHS-TTTS CS
                           HypA 65 eevpvkvrCreCgkefelee..k.alrCpkCg 93
                                   e  + +v+C eCg++  +++  + +l C +Cg
  gi|116753584|ref|YP_842702.1| 33 ELDKYTVECPECGSRALVRDyeRaELVCSECG 64
                                   55678899999999988666443678999998 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.43
                                    -HHHHHHHHHHHHCC.TTTT-EEE.EEEE--EEEETTTS-E CS
                           HypA  40 epeaLefafellaegtvlegaeLe.ieevpvkvrCreCgke 79 
                                    + e+ + +++ + e+++++g ++e +    + + Cr+C+  
  gi|116753584|ref|YP_842702.1| 169 VRETAAVIYRRAVEKNLIRGRSIEgVAAAALYAACRQCNVP 209
                                    45556667777777778888888767788889999999854 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1     0.012       7.4       8      21 ..      33      46 ..      32      47 .. 0.78
   2 ?    2.9   0.1      0.16        98       2      12 ..      60      70 ..      59      71 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.012
                  zinc_ribbon_2  8 elqdnakFCpyCGt 21
                                   el++  + Cp+CG+
  gi|116753584|ref|YP_842702.1| 33 ELDKYTVECPECGS 46
                                   77788888999996 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.16
                  zinc_ribbon_2  2 CpnCGaelqdn 12
                                   C++CG  +++n
  gi|116753584|ref|YP_842702.1| 60 CSECGLVIDEN 70
                                   99999777665 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.3   0.00099      0.59      27      38 ..      38      51 ..      23      53 .. 0.74
   2 ?    8.8   2.4     0.003       1.8       4      33 ..      37      64 ..      37      71 .. 0.66
   3 ?    1.8   0.1      0.45   2.7e+02       6      13 ..      58      65 ..      52      77 .. 0.68
   4 ?   -0.9   0.0       3.2   1.9e+03      28      33 ..     201     207 ..     191     212 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00099
                    Zn-ribbon_8 27 ta.CPeCgs.evrr 38
                                   t+ CPeCgs ++ r
  gi|116753584|ref|YP_842702.1| 38 TVeCPECGSrALVR 51
                                   555******88887 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.003
                    Zn-ribbon_8  4 YeYrCeeCghefevlqsisdapltaCPeCg 33
                                   Y  +C eCg    +l++  ++++ +C eCg
  gi|116753584|ref|YP_842702.1| 37 YTVECPECG--SRALVRDYERAELVCSECG 64
                                   666777777..3344433467777777776 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.45
                    Zn-ribbon_8  6 YrCeeCgh 13
                                     C eCg 
  gi|116753584|ref|YP_842702.1| 58 LVCSECGL 65
                                   34666665 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 3.2
                    Zn-ribbon_8  28 a.CPeCg 33 
                                    a C +C+
  gi|116753584|ref|YP_842702.1| 201 AaCRQCN 207
                                    4477774 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   1.1    0.0029       1.8       5      30 ..      40      66 ..      38      67 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0029
                  A2L_zn_ribbon  5 vCsvCggngiln.seqgylvCieCgas 30
                                   +C  Cg+  ++   e+++lvC eCg++
  gi|116753584|ref|YP_842702.1| 40 ECPECGSRALVRdYERAELVCSECGLV 66
                                   6778888888877799*********86 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 ?    4.7   0.3     0.056        33       9      23 ..      31      45 ..      25      50 .. 0.78
   2 ?    2.1   2.3      0.36   2.2e+02       2      25 ..      41      66 ..      40      70 .. 0.73
   3 ?   -1.2   0.0       3.8   2.3e+03      17      26 ..     201     210 ..     188     216 .. 0.78
   4 ?   -0.2   0.0       1.9   1.1e+03      24      53 ..     250     277 ..     249     278 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.056
                       zf-Mss51  9 qtapkhvdfeCpdCG 23
                                   +++  + ++eCp+CG
  gi|116753584|ref|YP_842702.1| 31 EEELDKYTVECPECG 45
                                   456678899*****9 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.36
                       zf-Mss51  2 CPvpkhkqt..apkhvdfeCpdCGip 25
                                   CP + ++    + ++ ++ C +CG++
  gi|116753584|ref|YP_842702.1| 41 CPECGSRALvrDYERAELVCSECGLV 66
                                   77776665556677888999999986 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 3.8
                       zf-Mss51  17 feCpdCGipt 26 
                                      C +C +p 
  gi|116753584|ref|YP_842702.1| 201 AACRQCNVPR 210
                                    5799999996 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 1.9
                       zf-Mss51  24 iptycseehwedDyeahleicdtLrqvned 53 
                                    ip +cs    + D +   + ++ Lrq+ e 
  gi|116753584|ref|YP_842702.1| 250 IPRFCSGLNLKGDVQ--AKGIEILRQAAEK 277
                                    688899999999988..788999**98776 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.9    0.0069       4.1      17      40 .]      40      64 ..      38      64 .. 0.87
   2 ?    1.5   0.0      0.55   3.3e+02      16      25 ..     201     210 ..     197     217 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0069
                  Auto_anti-p27 17 tCpvC.gvPLmrdrkggkvyCvaCd 40
                                    Cp+C +  L+rd ++ +++C  C+
  gi|116753584|ref|YP_842702.1| 40 ECPECgSRALVRDYERAELVCSECG 64
                                   6****777899998899******96 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.55
                  Auto_anti-p27  16 etCpvCgvPL 25 
                                    + C +C+vP 
  gi|116753584|ref|YP_842702.1| 201 AACRQCNVPR 210
                                    46******96 PP

>> SR1P  SR1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1     0.062        37       5      14 ..      59      68 ..      58      71 .. 0.92
   2 ?    4.5   0.0     0.062        37      22      32 ..     197     207 ..     190     210 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.062
                           SR1P  5 vCqtCnatId 14
                                   vC++C+ +Id
  gi|116753584|ref|YP_842702.1| 59 VCSECGLVID 68
                                   9********9 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.062
                           SR1P  22 ttLYgtCnqce 32 
                                    + LY+ C qc+
  gi|116753584|ref|YP_842702.1| 197 AALYAACRQCN 207
                                    579****9775 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.9       7.4   4.4e+03      30      40 ..     125     135 ..     124     142 .. 0.74
   2 ?    0.0   0.1       1.3     8e+02      17      27 ..     220     230 ..     210     238 .. 0.52
   3 ?    9.2   0.1    0.0017         1      15      40 ..     301     326 ..     295     333 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 7.4
                         HTH_23  30 srrTvyrwlkr 40 
                                    +r ++yr +k+
  gi|116753584|ref|YP_842702.1| 125 NRAQLYRLRKW 135
                                    57788888887 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.3
                         HTH_23  17 GlsvreIAreL 27 
                                    + s++eI r +
  gi|116753584|ref|YP_842702.1| 220 RVSRKEIGRTY 230
                                    45555555554 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0017
                         HTH_23  15 aeGlsvreIAreLgvsrrTvyrwlkr 40 
                                     ++ ++re+A+  gv++ T+++  k 
  gi|116753584|ref|YP_842702.1| 301 NDRRTQREVADVAGVTEVTIRNRYKE 326
                                    4588*****************65554 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.046        27       2      12 ..      38      48 ..      38      54 .. 0.78
   2 ?    4.8   0.0     0.035        21       4      14 ..      59      69 ..      56      73 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.046
                         zf_UBZ  2 tylCerCgkei 12
                                   t+ C++Cg++ 
  gi|116753584|ref|YP_842702.1| 38 TVECPECGSRA 48
                                   678*****975 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.035
                         zf_UBZ  4 lCerCgkeipe 14
                                   +C++Cg  i e
  gi|116753584|ref|YP_842702.1| 59 VCSECGLVIDE 69
                                   8*****99987 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   1.5    0.0027       1.6       3      31 ..      41      66 ..      41      67 .. 0.82
   2 ?   -1.9   0.3       5.6   3.3e+03      25      28 ..     203     206 ..     201     210 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0027
                                   -TTT--B-EEE--TT-SS-EEEETTTTEE CS
                      Nudix_N_2  3 CsqCGtpvelripdgDnreRlvCpaCgti 31
                                   C++CG++   ++  + +r  lvC+ Cg +
  gi|116753584|ref|YP_842702.1| 41 CPECGSR---ALVRDYERAELVCSECGLV 66
                                   *****99...4445568999*******87 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.6
                                    ETTT CS
                      Nudix_N_2  25 CpaC 28 
                                    C +C
  gi|116753584|ref|YP_842702.1| 203 CRQC 206
                                    5555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1490  (0.0831056); expected 358.6 (0.02)
Passed bias filter:                      939  (0.0523733); expected 358.6 (0.02)
Passed Vit filter:                       114  (0.00635841); 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: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 2461.60
//
Query:       gi|116753585|ref|YP_842703.1|  [L=85]
Description: hypothetical protein Mthe_0266 [Methanosaeta thermophila PT]
Scores for complete 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    1.9e-14   53.7   0.0    1.0  1  Gar1      Gar1/Naf1 RNA binding region
  ------ inclusion threshold ------
      0.072   13.2   0.1       0.12   12.5   0.1    1.5  1  PRC       PRC-barrel domain


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 !   53.7   0.0   2.1e-18   1.9e-14      21     102 ..       2      77 ..       1      84 [. 0.91

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 2.1e-18
                                    EEEEEEEEEETTEEEEEE---S--B--BTT-EEEETT--EEEE--EEES-SSS-EEEEE--GGHHHHHHHTTTTSEEEEE CS
                           Gar1  21 leiGtvssivenevviksttsgekkvldfnsilflenktqiGkVdEifGpvnepyysVklnsseeikaksfkvgdkvyia 100
                                    + +Gt  ++v+n+++++ ++    + + ++s++ + + t++GkV +ifGp++ py+ V++    ++ a  ++vg+ +y+ 
  gi|116753585|ref|YP_842703.1|   2 KRLGTALHVVQNKLIVRRDAA---DPPRIGSVVVDRKSTKVGKVSDIFGPLERPYVIVRPA--RGVDA-TVHVGSMLYVK 75 
                                    579***************944...89***********************************..99999.999*****998 PP

                                    -X CS
                           Gar1 101 pd 102
                                      
  gi|116753585|ref|YP_842703.1|  76 SP 77 
                                    76 PP

>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   1.3e-05      0.12      10      38 ..      27      53 ..      27      78 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.3e-05
                                   TT-EEEETTSSEEEEEEEEEEETTTTEEE CS
                            PRC 10 iGkeVytedGeklGkVkDvvidekegrvr 38
                                   iG  V++++ +k+GkV+D+ + +   r++
  gi|116753585|ref|YP_842703.1| 27 IGSVVVDRKSTKVGKVSDI-FGP-LERPY 53
                                   5777***************.876.55555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       149  (0.00831056); expected 358.6 (0.02)
Passed bias filter:                      132  (0.00736237); 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: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 614.25
//
Query:       gi|116753586|ref|YP_842704.1|  [L=306]
Description: nucleolar GTP-binding 1 [Methanosaeta thermophila PT]
Scores for 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-35  119.9   0.0    1.7e-34  119.1   0.0    1.4  1  NOG1_N      NOG1 N-terminal helical domain
    1.4e-22   79.2   0.0    2.4e-22   78.5   0.0    1.4  1  NOG1        Nucleolar GTP-binding protein 1 (NOG1)
    2.9e-19   69.2   0.0    4.8e-19   68.5   0.0    1.4  1  MMR_HSR1    50S ribosome-binding GTPase
    2.4e-10   40.2   0.0    3.8e-10   39.5   0.0    1.4  1  FeoB_N      Ferrous iron transport protein B
  ------ inclusion threshold ------
      0.022   14.6   0.0       0.17   11.6   0.0    2.1  2  ATP_bind_1  Conserved hypothetical ATP binding protein
      0.026   14.0   0.0      0.066   12.6   0.0    1.7  1  SRPRB       Signal recognition particle receptor beta subunit


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 !  119.1   0.0   5.6e-38   1.7e-34       1     160 []       2     143 ..       2     143 .. 0.97

  Alignments for each domain:
  == domain 1  score: 119.1 bits;  conditional E-value: 5.6e-38
                         NOG1_N   1 FekiptvptseelidkalrrakraakttkkkkneikrlrnlearkvrtasntlsdkLeeivkkfPnldelhpFyrelldv 80 
                                    Fe++ tvp+++el+++a+rr ++a k+  ++            + v ta  +l++ L++iv++fP +++l+ Fy++l+d+
  gi|116753586|ref|YP_842704.1|   2 FERLSTVPDAQELLERAFRRGSKAVKAAGDDA-----------AFVGTAGGVLATALSSIVRRFPTFEKLPEFYYDLVDA 70 
                                    9*************************999983...........35899******************************** PP

                         NOG1_N  81 lvdkdelkksLaqvkwarklirkigkeyvnklkkaddkkeakelrreafgrvasvlkkvdkaldfLedvrkkLrkLpaiD 160
                                    +v++d+l++sL++v wa+k ir i++ey+++ + a++       rr+a+gr+asv+k++d++l+fL+++   Lr++p iD
  gi|116753586|ref|YP_842704.1|  71 VVGVDQLRISLSRVGWAAKQIRRISREYMRSPRGAGE-------RRSALGRMASVVKSIDEDLAFLNEASARLREIPGID 143
                                    ***********************************99.......99*********************************9 PP

>> NOG1  Nucleolar GTP-binding protein 1 (NOG1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.5   0.0   7.9e-26   2.4e-22       1      58 []     213     269 ..     213     269 .. 0.99

  Alignments for each domain:
  == domain 1  score: 78.5 bits;  conditional E-value: 7.9e-26
                           NOG1   1 eIEkqAiaALkhladavlFllDpseecgysleeQlsLleeikelfankpvivvlnKiD 58 
                                    eIE+qAiaA++hl+++vlFl+Dp+++cgy+l+ Q +Lleeik+ ++  pv+v++nK+D
  gi|116753586|ref|YP_842704.1| 213 EIERQAIAAMRHLRGVVLFLIDPTGHCGYPLDAQHRLLEEIKSWLE-LPVVVAYNKSD 269
                                    6********************************************9.9*********9 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.5   0.0   1.6e-22   4.8e-19       2     114 .]     149     267 ..     148     267 .. 0.79

  Alignments for each domain:
  == domain 1  score: 68.5 bits;  conditional E-value: 1.6e-22
                                    EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSS..HHHHHH.HHHHHHHHHHCT.S CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGlie..gaseek.glgkaflaleea.d 77 
                                    ++i+G+pNvGKS+++   t+++ +++++p+tT+  + g++++k+k+++++DtpGl++    se++  +++a++a++    
  gi|116753586|ref|YP_842704.1| 149 IIIAGYPNVGKSSFLAMVTRARPEIASYPFTTQGLIVGHITMKDKRYQILDTPGLLDrpL-SERNeIERQAIAAMRHLrG 227
                                    89****************************************************986432.2333245566666555339 PP

                                    EEEEEEETT.......TTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                       MMR_HSR1  78 lillvvdas.......eeklkpldeeleelleeakkplilvlnk 114
                                    ++l+++d +       +   ++l ee++++l   + p+++++nk
  gi|116753586|ref|YP_842704.1| 228 VVLFLIDPTghcgyplD-AQHRLLEEIKSWL---ELPVVVAYNK 267
                                    9******6677666641.2345568888887...5999999998 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 !   39.5   0.0   1.3e-13   3.8e-10       2     116 ..     148     269 ..     147     302 .. 0.76

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 1.3e-13
                                    EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHHCTS..S CS
                         FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardflleee..p 79 
                                    t++++G pnvGk++++  +t a+ +++ +p +t     g++++k+k+++i+D PG  +  + se +++ r+ ++  +   
  gi|116753586|ref|YP_842704.1| 148 TIIIAGYPNVGKSSFLAMVTRARPEIASYPFTTQGLIVGHITMKDKRYQILDTPGLLD-RPLSERNEIERQAIAAMRhlR 226
                                    6899***************************************************987.789999999999987544115 PP

                                    SEEEEEEEGG.G....HHHHHHHHHHHHH.TTSSEEEEEETHH CS
                         FeoB_N  80 dvvvnvvdat.n....lernLyLtlqlle.lgvpvvlalnmid 116
                                     vv+ ++d t +    l+ +  L+ ++   l++pvv+a n++d
  gi|116753586|ref|YP_842704.1| 227 GVVLFLIDPTgHcgypLDAQHRLLEEIKSwLELPVVVAYNKSD 269
                                    6777777755221111333333333333235566666666666 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.13   3.9e+02       1      23 [.     151     173 ..     151     179 .. 0.85
   2 ?   11.6   0.0   5.7e-05      0.17      85     173 ..     187     275 ..     172     294 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.13
                     ATP_bind_1   1 vvGpaGsGKttfvgalseilelr 23 
                                    ++G + +GK++f   ++  ++++
  gi|116753586|ref|YP_842704.1| 151 IAGYPNVGKSSFLAMVTRARPEI 173
                                    68999********9999887765 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 5.7e-05
                     ATP_bind_1  85 elekeeddyllfDtPGQie..lfthseslakiveeLesefalvvvyLvDsq.rltdptkfisgllsalsamlrlelPhvv 161
                                     +  +++ y ++DtPG +   l    e  ++ + ++  + + vv++L+D++  +  p +  ++  +   +   lelP vv
  gi|116753586|ref|YP_842704.1| 187 HITMKDKRYQILDTPGLLDrpLSERNEIERQAIAAMR-HLRGVVLFLIDPTgHCGYPLDAQHR--LLEEIKSWLELPVVV 263
                                    55556889********764225555566666777777.7999*******87245558888888..445677789****** PP

                     ATP_bind_1 162 vlnkfDllkekl 173
                                    ++nk D+ +++ 
  gi|116753586|ref|YP_842704.1| 264 AYNKSDIPSDHP 275
                                    *******88663 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 ?   12.6   0.0   2.2e-05     0.066       4     124 ..     147     270 ..     144     282 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.2e-05
                                    -EEEEE-STTSSHHHHHHHHHHS..S---B---SS-EEETTG...GGTT-SEEEETT-..G..CCSHHHHHHHHH.HGGE CS
                          SRPRB   4 pavllvGlsdsGKTslftrLttd..svkktvtSqessaalkvksekgskltliDfPGh..e..klrqklleklka.kssl 76 
                                    p+++++G  + GK s++  +t    ++ +     +  ++ ++ + k+++ +++D PG      + r+++  + +a  ++l
  gi|116753586|ref|YP_842704.1| 147 PTIIIAGYPNVGKSSFLAMVTRArpEIASYPFTTQGLIVGHI-TMKDKRYQILDTPGLldRplSERNEIERQAIAaMRHL 225
                                    89****************999984433333334466777777.899***********52221144778876655504559 PP

                                    EEEE.EEEETTS-HHH.HHHHHHHHHHHHHHHHHHTT---EEEEEE-TTS CS
                          SRPRB  77 kglv.fvvDStidpke.vkevAEllyeilliteklkdavdiliACnKqel 124
                                    +g+v f++D t      +     ll ei +  e     +++++A nK+++
  gi|116753586|ref|YP_842704.1| 226 RGVVlFLIDPTGHCGYpLDAQHRLLEEIKSWLE-----LPVVVAYNKSDI 270
                                    986549999886543313334445555555554.....666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); 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: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2235.18
//
Query:       gi|116753587|ref|YP_842705.1|  [L=134]
Description: hypothetical protein Mthe_0268 [Methanosaeta thermophila PT]
Scores for complete 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-54  182.1   0.0    3.6e-54  181.9   0.0    1.0  1  DUF1699   Protein of unknown function (DUF1699)
  ------ inclusion threshold ------
      0.026   14.4   0.0        0.5   10.3   0.0    2.3  2  DUF433    Protein of unknown function (DUF433)
      0.065   13.0   0.1       0.33   10.8   0.0    2.1  2  HTH_38    Helix-turn-helix domain


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 !  181.9   0.0     6e-58   3.6e-54       1     128 [.       1     128 [.       1     130 [. 0.99

  Alignments for each domain:
  == domain 1  score: 181.9 bits;  conditional E-value: 6e-58
                        DUF1699   1 mkirvvsskeeietlnenekivHlafrpsntdilslvkkcpklkaiqvpeSykktlsksakmfleiqgiellegdvwghr 80 
                                    m+irvvs+k+eie+ln++e +vHlafr+sn di++l+++cp+lkaiqvp+Sy++tls++ kmfl+i+g++l+egdvwghr
  gi|116753587|ref|YP_842705.1|   1 MRIRVVSTKSEIERLNRDEMFVHLAFRASNADIFRLLQRCPQLKAIQVPASYYRTLSQAGKMFLQIHGVTLIEGDVWGHR 80 
                                    9******************************************************************************* PP

                        DUF1699  81 kdineyyevseevierikelkseglseeeiaeklsketklspdlikfl 128
                                    kd++ey  ++e+ ++ri+el s+g+s e+iae+l +++k+sp l++f+
  gi|116753587|ref|YP_842705.1|  81 KDLSEYLIIEEQDLRRISELLSSGMSPEDIAESLCDDMKVSPGLVRFI 128
                                    ***********************************************9 PP

>> DUF433  Protein of unknown function (DUF433)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.038   2.3e+02      27      50 ..      26      49 ..      21      53 .. 0.81
   2 ?   10.3   0.0   8.4e-05       0.5      22      40 ..      95     113 ..      93     117 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.038
                                   HHHTT--HHHHHHHH.TS-HHHHH CS
                         DUF433 27 llaaGesieeiledyPdLtlediq 50
                                     a+ ++i ++l+  P+L++ ++ 
  gi|116753587|ref|YP_842705.1| 26 FRASNADIFRLLQRCPQLKAIQVP 49
                                   56788889999*******998885 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 8.4e-05
                                    HHHHHHHHTT--HHHHHHH CS
                         DUF433  22 etilellaaGesieeiled 40 
                                    ++i ell++G+s+e+i+e 
  gi|116753587|ref|YP_842705.1|  95 RRISELLSSGMSPEDIAES 113
                                    57899***********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 ?   -1.0   0.0      0.27   1.6e+03      22      35 ..      29      42 ..      27      43 .. 0.75
   2 ?   10.8   0.0   5.5e-05      0.33       8      30 ..      92     114 ..      85     117 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.27
                         HTH_38 22 slreIArrLgrsps 35
                                   s+++I r+L r p+
  gi|116753587|ref|YP_842705.1| 29 SNADIFRLLQRCPQ 42
                                   77788888888875 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 5.5e-05
                         HTH_38   8 eeReeIerllaeGlslreIArrL 30 
                                    ++ ++I  ll+ G+s  +IA  L
  gi|116753587|ref|YP_842705.1|  92 QDLRRISELLSSGMSPEDIAESL 114
                                    66689***************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); 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: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1047.31
//
Query:       gi|116753588|ref|YP_842706.1|  [L=481]
Description: hypothetical protein Mthe_0269 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.9e-22   76.8  50.8    1.1e-08   35.1   7.8    6.4  7  Pentapeptide_3  Pentapeptide repeats (9 copies)
  ------ inclusion threshold ------
       0.15   12.2  10.9        1.7    8.9   0.1    4.2  3  Pentapeptide_4  Pentapeptide repeats (9 copies)
        1.2    8.9   9.5        6.1    6.6   0.1    5.7  5  Pentapeptide    Pentapeptide repeats (8 copies)


Domain annotation for each model (and alignments):
>> Pentapeptide_3  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.0    0.0019        12      24      46 ..      69      91 ..      64      93 .. 0.88
   2 !   13.0   1.1   1.5e-05     0.088       3      31 ..      80     107 ..      78     109 .. 0.85
   3 !   35.1   7.8   1.8e-12   1.1e-08       1      45 [.      99     144 ..      99     147 .. 0.95
   4 !    6.0   3.0    0.0022        13      11      41 ..     153     184 ..     144     186 .. 0.84
   5 !   22.3  10.4   1.8e-08   0.00011       3      45 ..     189     232 ..     189     235 .. 0.95
   6 !   24.2   2.5   4.7e-09   2.8e-05       4      47 ..     234     278 ..     231     279 .. 0.93
   7 ?    1.3   0.1     0.063   3.8e+02      24      38 ..     286     303 ..     280     307 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0019
                 Pentapeptide_3 24 snadFgsadFsgarFtgdvdFsg 46
                                   +n+ +g++d+sg  F+++vd++ 
  gi|116753588|ref|YP_842706.1| 69 TNSEMGDVDLSGLVFEDAVDLTS 91
                                   7999************8899976 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 1.5e-05
                 Pentapeptide_3   3 ganFsgaadFrgatFsgaasFsnadFgsa 31 
                                    g +F++a+d++ + F+g+ +F +a+F++ 
  gi|116753588|ref|YP_842706.1|  80 GLVFEDAVDLTSTKFDGM-NFASAVFSDG 107
                                    558***************.9******643 PP

  == domain 3  score: 35.1 bits;  conditional E-value: 1.8e-12
                 Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadF.gsadFsgarFtgdvdFs 45 
                                    F  a+Fs+ a+F++ + sg+asF++a+F ++++Fsg+rF gd++++
  gi|116753588|ref|YP_842706.1|  99 FASAVFSDGAFFDRIVVSGDASFEGAHFkQDVSFSGSRFLGDAEMN 144
                                    789*************************99************9875 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.0022
                 Pentapeptide_3  11 dFrgatFsgaasFsnadF.gsadFsgarFtgd 41 
                                    +F ++ F g+   s++ F g adF g+ ++gd
  gi|116753588|ref|YP_842706.1| 153 YFADSAFLGDLHISSSSFqGFADFYGVCISGD 184
                                    78999999999999999988999999999987 PP

  == domain 5  score: 22.3 bits;  conditional E-value: 1.8e-08
                 Pentapeptide_3   3 ganFsgaadFrgatFsgaasFsnadF.gsadFsgarFtgdvdFs 45 
                                    ++ F + a F  + F+g+a+F  + F g  +F+g+ F gd++F 
  gi|116753588|ref|YP_842706.1| 189 NTKFGDGAGFMSTEFDGDANFGMSSFaGYTSFDGSVFRGDANFA 232
                                    789****************************************5 PP

  == domain 6  score: 24.2 bits;  conditional E-value: 4.7e-09
                 Pentapeptide_3   4 anFsgaadFrgatFsgaasFsnadF.gsadFsgarFtgdvdFsga 47 
                                    a+F++a++F + +F+g+a F  + F g a+F+g+ F  d++++ a
  gi|116753588|ref|YP_842706.1| 234 ARFDKAVYFGDIRFEGDAIFGLTEFeGLANFAGTYFAEDLNLNSA 278
                                    89***********************88**************9876 PP

  == domain 7  score: 1.3 bits;  conditional E-value: 0.063
                 Pentapeptide_3  24 snadF...gsadFsgarF 38 
                                    +n++F   +++++ ga F
  gi|116753588|ref|YP_842706.1| 286 DNTTFgraSGINLKGAEF 303
                                    566665544555555555 PP

>> Pentapeptide_4  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.1   0.00028       1.7      35      70 ..      70     106 ..      61     115 .. 0.58
   2 ?    2.5   0.1     0.028   1.7e+02       6      25 ..     119     139 ..     116     173 .. 0.62
   3 ?    2.0   2.5     0.041   2.4e+02       8      44 ..     253     291 ..     184     309 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00028
                 Pentapeptide_4  35 nvnFdecnlsdvdfae.vdlkrasFsgcnlknvnfsd 70 
                                    n ++ + +ls + f++ vdl+++ F g+n+++++fsd
  gi|116753588|ref|YP_842706.1|  70 NSEMGDVDLSGLVFEDaVDLTSTKFDGMNFASAVFSD 106
                                    4445555555555554246666666666666666643 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.028
                 Pentapeptide_4   6 csfnncklsn.vnFsearlrd 25 
                                    +sf+++ +++ v+Fs +r+ +
  gi|116753588|ref|YP_842706.1| 119 ASFEGAHFKQdVSFSGSRFLG 139
                                    345555555445555554443 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.041
                 Pentapeptide_4   8 fnncklsn.vnFsearlrd.cnFtecrlsnvnFdecnls 44 
                                    f  + +++ +nF+ +++ +  n++++r+++ ++d++++ 
  gi|116753588|ref|YP_842706.1| 253 FGLTEFEGlANFAGTYFAEdLNLNSARIDAFVLDNTTFG 291
                                    444445554555555553335555555555555555543 PP

>> Pentapeptide  Pentapeptide repeats (8 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1     0.001       6.1       6      24 ..      87     105 ..      85     107 .. 0.77
   2 ?   -2.1   0.0      0.53   3.1e+03      21      29 ..     174     182 ..     173     183 .. 0.38
   3 ?   -0.6   0.2      0.19   1.1e+03      15      15 ..     228     228 ..     206     240 .. 0.61
   4 ?   -2.1   0.0      0.55   3.3e+03       6      13 ..     262     269 ..     262     271 .. 0.36
   5 ?    1.4   0.0     0.043   2.6e+02      14      24 ..     294     304 ..     285     307 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.001
                                    -B-CCSCCEECCCESEEEC CS
                   Pentapeptide   6 AnLsganLsganlsgAnLt 24 
                                    ++L+ ++++g n+  A+++
  gi|116753588|ref|YP_842706.1|  87 VDLTSTKFDGMNFASAVFS 105
                                    6888888888888888876 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.53
                                    EEECT-B-T CS
                   Pentapeptide  21 AnLtgAnls 29 
                                    A+++g+ +s
  gi|116753588|ref|YP_842706.1| 174 ADFYGVCIS 182
                                    344444333 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.19
                                    E CS
                   Pentapeptide  15 g 15 
                                    +
  gi|116753588|ref|YP_842706.1| 228 D 228
                                    2 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 0.55
                                    -B-CCSCC CS
                   Pentapeptide   6 AnLsganL 13 
                                    An+ g+++
  gi|116753588|ref|YP_842706.1| 262 ANFAGTYF 269
                                    33333333 PP

  == domain 5  score: 1.4 bits;  conditional E-value: 0.043
                                    EECCCESEEEC CS
                   Pentapeptide  14 sganlsgAnLt 24 
                                    sg nl+gA ++
  gi|116753588|ref|YP_842706.1| 294 SGINLKGAEFR 304
                                    45555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (481 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); 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: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 3733.76
//
Query:       gi|116753589|ref|YP_842707.1|  [L=210]
Description: hypothetical protein Mthe_0270 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.034   14.1   0.0      0.064   13.2   0.0    1.4  1  RL               RL domain
      0.083   12.7   0.1       0.13   12.1   0.1    1.4  1  Selenoprotein_S  Selenoprotein S (SelS)


Domain annotation for each model (and alignments):
>> RL  RL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   7.1e-06     0.064      35      59 ..      70      94 ..      68     102 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.1e-06
                             RL 35 sqhGkinkhFfYeskgvyavvEFse 59
                                   s++G++  +FfY s  + av+ Fse
  gi|116753589|ref|YP_842707.1| 70 SEQGRVAGYFFYISGCLLAVILFSE 94
                                   899********************97 PP

>> Selenoprotein_S  Selenoprotein S (SelS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   1.5e-05      0.13      15      59 ..      13      57 ..       2      77 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.5e-05
                Selenoprotein_S 15 paleaeglrflqetvgallskyGWylllgivllllliqklrkrlr 59
                                    +++ ++++    +v  +l k+GWy+ +g+v+ +ll+  + + lr
  gi|116753589|ref|YP_842707.1| 13 KEIRRKSIHLTGLSVPIILLKAGWYVTVGFVATALLVAVVLEALR 57
                                   567888899999999****************99999876655544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       820  (0.045736); 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:                         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: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1587.84
//
Query:       gi|116753590|ref|YP_842708.1|  [L=577]
Description: glycyl-tRNA synthetase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-23   82.2   1.4    1.5e-22   79.6   0.0    2.8  3  HGTP_anticodon  Anticodon binding domain
    6.3e-11   42.6   0.0    2.1e-10   40.8   0.0    1.9  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
     0.0012   19.0   0.1       0.12   12.5   0.0    2.7  2  Zn-ribbon_8     Zinc ribbon domain
  ------ inclusion threshold ------
      0.068   13.4   2.1       0.12   12.7   0.2    2.3  3  DUF2382         Domain of unknown function (DUF2382)
       0.28   11.7   2.5        2.3    8.8   0.1    3.2  3  zf-C2H2         Zinc finger, C2H2 type
       0.36   10.3   1.4       0.51    9.8   0.1    2.0  2  zf-ribbon_3     zinc-ribbon domain


Domain annotation for each model (and alignments):
>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       2.1   6.3e+03      66      88 ..     232     257 ..     210     259 .. 0.59
   2 ?    0.1   0.1      0.29   8.8e+02      45      73 ..     384     414 ..     368     421 .. 0.64
   3 !   79.6   0.0   4.9e-26   1.5e-22       1      93 [.     470     560 ..     470     561 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.1
                                    HTEEEEEETTTCEE...EEEETTHHH CS
                 HGTP_anticodon  66 kgtvtvrdrdtreq...ervsldelv 88 
                                    +  + + +r+ +e+   e++s+ e+v
  gi|116753590|ref|YP_842708.1| 232 DLRLRLYSREAQERgqvEEMSVGEAV 257
                                    34444455533333333677777766 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.29
                                    HHHHHHTT-SEEEEE-HHHHH..HTEEEEEE CS
                 HGTP_anticodon  45 ireadllgipfavvvGekele..kgtvtvrd 73 
                                    ++ adl+g  + ++v+ +++e  ++ v+v++
  gi|116753590|ref|YP_842708.1| 384 MSVADLKGDTIKITVDGETYEieRRLVSVEE 414
                                    4456677777777777776642235555544 PP

  == domain 3  score: 79.6 bits;  conditional E-value: 4.9e-26
                                    SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEEE CS
                 HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtreqe 80 
                                    +v+++pl +k+e l e a+++ +e+r+ g+ +e+d  ++sig+++r+ d++g+p++++v++++le+gtvtvrdrdt++q+
  gi|116753590|ref|YP_842708.1| 470 DVAILPLMDKDE-LVEPARRIFDEFRRCGMLAEFD-TSGSIGRRYRRNDEIGTPYCITVDYQTLEDGTVTVRDRDTMQQI 547
                                    69*******555.*********************8.8******************************************* PP

                                    EEETTHHHHHHHH CS
                 HGTP_anticodon  81 rvsldelveklke 93 
                                    r++ d +v+++++
  gi|116753590|ref|YP_842708.1| 548 RIEADRAVDIIRD 560
                                    *********9986 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 !   40.8   0.0   7.1e-14   2.1e-10      10     178 ..     155     445 ..     147     446 .. 0.68

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 7.1e-14
                                    EEEE-SSSHHHHHHHHHHHEEEBGG..SSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEES.GGGHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                   tRNA-synt_2b  10 eyiLkPtneetfvelirdevlrskr..LPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfha.easlddslrdlika 86 
                                      +L+P+  +++   ++   lr +r  LP+  +qi++ yR+E s  +G++R+reF q +++vf    ++    ++++  +
  gi|116753590|ref|YP_842708.1| 155 PGYLRPETAQGMFINFQRL-LRYYRdsLPFGAVQIGRSYRNEISPRQGVIRLREFSQAEAEVFIDpRNKQHPRFSEVKDL 233
                                    56899*9999998888855.9995558****************9566******************77999999******* PP

                                    HHHHHHHTT.SCEEEEEEGTTSC......................................................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxx......................................................... RF
                   tRNA-synt_2b  87 isriferlglefraiielmsaks......................................................... 109
                                      r+++r   e  +++e+ s ++                                                         
  gi|116753590|ref|YP_842708.1| 234 RLRLYSREAQERGQVEEM-SVGEavergiiaheilayfvartyeyllavgvdrerlrfrqhkademahyaadcwdaevll 312
                                    ********9876666555.4333456777888888888888888888888888887777777666666666666666666 PP

                                    .....................BTTSEEEEEEEEETT............................................ CS
                                    .....................xxxxxxxxxxxxxxx............................................ RF
                   tRNA-synt_2b 110 .....................adykdkkefeavses............................................ 124
                                                                                                                    
  gi|116753590|ref|YP_842708.1| 313 drlgwieivgiadrtdydlrsH-------------Malskanlsvfvhypepvrrkrvavkpdmkvlgprfkgrakaiad 379
                                    6666666644444433333330.............255555555555556666666666666666666666666666666 PP

                                    ................TSEEEEEEEEEEEETHHHHHTTEEEECTTSSEEEEEEEEEEEEHHHHHHHHHHH CS
                                    ................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2b 125 ................ltkgieigtiqklgtrlserlgatvldennreksvimicaaigveRllsaileq 178
                                                    +t  +e+  i+ +    +e+++ ++    +++  +++i  ++g+ R+l  +le+
  gi|116753590|ref|YP_842708.1| 380 alqamsvadlkgdtikITVDGETYEIERR-LVSVEEIEEEI---RGEYVVPHVIEPSFGIDRILYTVLEH 445
                                    66666664443333333333333333333.33333333333...56788899999999999999988886 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.028        83      21      34 ..      81      93 ..      69      98 .. 0.76
   2 !   12.5   0.0     4e-05      0.12      16      39 ..     114     137 ..     112     138 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.028
                    Zn-ribbon_8 21 isdapltaCPeCgs 34
                                   +  +plt+C+eC++
  gi|116753590|ref|YP_842708.1| 81 F-SDPLTECKECKE 93
                                   3.468999****75 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 4e-05
                    Zn-ribbon_8  16 evlqsisdapltaCPeCgsevrrv 39 
                                    e++ ++ ++++++CPeCg+e+  v
  gi|116753590|ref|YP_842708.1| 114 EEIYRMIKENDITCPECGGELSEV 137
                                    56777888899********98765 PP

>> DUF2382  Domain of unknown function (DUF2382)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       3.1   9.2e+03      34      52 ..     280     298 ..     273     304 .. 0.71
   2 ?   12.7   0.2   3.9e-05      0.12      36      88 ..     351     416 ..     334     424 .. 0.74
   3 ?   -2.5   0.1       2.1   6.2e+03      10      30 ..     526     546 ..     524     552 .. 0.70

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.1
                        DUF2382  34 eVpverEevvverepvdre 52 
                                     V v rE+++  ++++d+ 
  gi|116753590|ref|YP_842708.1| 280 AVGVDRERLRFRQHKADEM 298
                                    6778888888877777665 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 3.9e-05
                        DUF2382  36 pverEevvver.............epvdrevaaaeaareeeetievplyeErvvvekeavvvEeVr 88 
                                    pv+r +v v+              ++++++ +a + a+ +++ti++++  E+ ++e+++v vEe++
  gi|116753590|ref|YP_842708.1| 351 PVRRKRVAVKPdmkvlgprfkgraKAIADALQAMSVADLKGDTIKITVDGETYEIERRLVSVEEIE 416
                                    555555555555444444444434556666666677799*************************96 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 2.1
                        DUF2382  10 vgkervetGeVrvrkevvtee 30 
                                    v+ ++ e G+V+vr + + ++
  gi|116753590|ref|YP_842708.1| 526 VDYQTLEDGTVTVRDRDTMQQ 546
                                    777888888998887766655 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1   0.00077       2.3       2      20 ..      87     104 ..      86     106 .. 0.94
   2 ?    0.2   0.1      0.41   1.2e+03       2       7 ..     126     131 ..     125     141 .. 0.83
   3 ?   -0.2   0.0      0.57   1.7e+03      14      21 ..     329     336 ..     326     337 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00077
                                    EETTTTEEESSHHHHHHHH CS
                        zf-C2H2   2 kCpdCgksFkrksnLkrHi 20 
                                    +C++C++ + r ++L +Hi
  gi|116753590|ref|YP_842708.1|  87 ECKECKEIY-RADHLIKHI 104
                                    6********.********8 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.41
                                    EETTTT CS
                        zf-C2H2   2 kCpdCg 7  
                                    +Cp+Cg
  gi|116753590|ref|YP_842708.1| 126 TCPECG 131
                                    8****9 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.57
                                    HHHHHHHH CS
                        zf-C2H2  14 snLkrHir 21 
                                    ++L++H+ 
  gi|116753590|ref|YP_842708.1| 329 YDLRSHMA 336
                                    89****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 ?   -3.5   0.1       2.7   7.9e+03       5       9 ..      88      92 ..      86      94 .. 0.54
   2 ?    9.8   0.1   0.00017      0.51      12      26 .]     120     134 ..     119     134 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.7
                    zf-ribbon_3  5 CPnCG 9 
                                   C +C+
  gi|116753590|ref|YP_842708.1| 88 CKECK 92
                                   55554 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00017
                    zf-ribbon_3  12 lssddnvCpyCGtkl 26 
                                    +++ d++Cp CG++l
  gi|116753590|ref|YP_842708.1| 120 IKENDITCPECGGEL 134
                                    57889*******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (577 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); 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: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 3948.28
//
Query:       gi|116753591|ref|YP_842709.1|  [L=141]
Description: hypothetical protein Mthe_0272 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.018   14.9   0.0      0.044   13.7   0.0    1.6  2  TrmB      Sugar-specific transcriptional regulator TrmB


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.29   5.3e+03      19      32 ..      13      26 ..      11      30 .. 0.76
   2 ?   13.7   0.0   2.5e-06     0.044      26      60 ..      79     113 ..      73     120 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.29
                                   HHCCCHHCHHCCCT CS
                           TrmB 19 klgpatadeiaeel 32
                                   k+ p ta++i  ++
  gi|116753591|ref|YP_842709.1| 13 KNAPRTATTIKVRS 26
                                   67888999987666 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 2.5e-06
                                    CHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTT CS
                           TrmB  26 deiaeelgvprskvYevLrsLedkGlVerekgrpk 60 
                                    + + +elg++rs  Y + ++L+ +Gl+ ++ g+++
  gi|116753591|ref|YP_842709.1|  79 ESLIRELGISRSAFYAMRNKLLGAGLISIRGGEYR 113
                                    678899***********************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); 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: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 995.65
//
Query:       gi|116753592|ref|YP_842710.1|  [L=93]
Description: hypothetical protein Mthe_0273 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.031   14.2   0.1      0.065   13.2   0.1    1.6  1  FixQ      Cbb3-type cytochrome oxidase component FixQ
       0.17    9.8   0.1       0.19    9.7   0.1    1.0  1  IgaA      Intracellular growth attenuator protein IgaA


Domain annotation for each model (and alignments):
>> FixQ  Cbb3-type cytochrome oxidase component FixQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   7.2e-06     0.065      13      37 ..      39      63 ..      35      68 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.2e-06
                           FixQ 13 wgllflvllfygvviyafrpgnrkd 37
                                   ++l ++++l y vv+y+ r++++++
  gi|116753592|ref|YP_842710.1| 39 LMLPVFFVLNYLVVVYMARSRRERE 63
                                   5899*****************9654 PP

>> IgaA  Intracellular growth attenuator protein IgaA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   2.1e-05      0.19     646     689 ..      26      67 ..      16      79 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 2.1e-05
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                           IgaA 646 davtlwrylgttlLllvlllllilnavlllrrlrknrqRleeiq 689
                                     a+ +w++l  +lL+l ++++l + +v+ + r r++  R + ++
  gi|116753592|ref|YP_842710.1|  26 HAMEMWKILLICLLMLPVFFVLNYLVVVYMARSRRE--REMRVE 67 
                                    67999********99988776666665555555554..444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       849  (0.0473534); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 672.03
//
Query:       gi|116753593|ref|YP_842711.1|  [L=113]
Description: ribonucleoprotein complex SRP, Srp19 component [Methanosaeta thermophila PT]
Scores for complete 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-23   81.4   0.1    8.9e-23   81.1   0.1    1.2  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 !   81.1   0.1     5e-27   8.9e-23       1      92 [.      27     109 ..      27     112 .. 0.87

  Alignments for each domain:
  == domain 1  score: 81.1 bits;  conditional E-value: 5e-27
                                    EEECCCCBTTS-CCCT--S-CCCSBSS--HHHHHHHHHHCTSCEEEEEEECTTSSTTCC.EEEEEC-..........SS- CS
                          SRP19   1 viYPvYldskktrkeGRrvpkelavenPtaqeiaealkalglevvvepeksyPrdwanp.GrVrvklkedgkevnekikn 79 
                                    vi+P+Y+d +++r +GRrv+  +av+nP++++i +a k lgl+ vve+ek+yP++w+++ GrV v +k           +
  gi|116753593|ref|YP_842711.1|  27 VIWPAYFDLERSRGQGRRVATANAVRNPKLEDIIRASKDLGLDPVVETEKCYPKNWYEQpGRVLVLKK----------GS 96 
                                    7******************************************************99655******85..........45 PP

                                    CHHHHHHHHHHHH CS
                          SRP19  80 kkellkkiaellk 92 
                                    k++ l++ia+ lk
  gi|116753593|ref|YP_842711.1|  97 KTKTLRSIARALK 109
                                    5555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); 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: 00:00:00.45
# Mc/sec: 755.68
//
Query:       gi|116753594|ref|YP_842712.1|  [L=105]
Description: hypothetical protein Mthe_0275 [Methanosaeta thermophila PT]
Scores for complete 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-39  131.9   2.6    7.8e-39  131.7   2.6    1.0  1  DUF211    Uncharacterized ArCR, COG1888
  ------ inclusion threshold ------
      0.054   13.4   0.0      0.072   13.0   0.0    1.3  1  DUF86     Protein of unknown function DUF86
       0.11   12.2   0.0       0.15   11.9   0.0    1.3  1  YfmQ      Uncharacterised protein from bacillus cereus group


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 !  131.7   2.6   1.3e-42   7.8e-39       2      88 ..      13      99 ..      12     100 .. 0.98

  Alignments for each domain:
  == domain 1  score: 131.7 bits;  conditional E-value: 1.3e-42
                                   EEEEEEEEEEESSS-HHHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHCTT-EEEEEEEEEEESS CS
                         DUF211  2 irrlvLDvlkphepsivelakklaelegvdgvnitvkevDketenlkitieGenidyeeieeaieelggvihSiDevvaGkk 83
                                   irr+vLDvlkph+p+i+ela+ l++l+gv+gvn+++ evD++te++k+tieG+nidy+++e+ i+e+gg++hSiD+vvaG++
  gi|116753594|ref|YP_842712.1| 13 IRRIVLDVLKPHKPTIIELANVLSDLKGVKGVNMSLFEVDRQTETVKVTIEGDNIDYHAVERLIQEFGGAVHSIDQVVAGRE 94
                                   9********************************************************************************* PP

                                   ----- CS
                         DUF211 84 iveev 88
                                   +vee+
  gi|116753594|ref|YP_842712.1| 95 MVEEI 99
                                   ***86 PP

>> DUF86  Protein of unknown function DUF86
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.2e-05     0.072      17      51 ..      59      93 ..      27     102 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.2e-05
                                   STSCCGSHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          DUF86 17 eeeflsdeleydavernlqvigEaaidiakhlakk 51
                                   + +++ d+++y+aver +q  g a+  i + +a +
  gi|116753594|ref|YP_842712.1| 59 KVTIEGDNIDYHAVERLIQEFGGAVHSIDQVVAGR 93
                                   566778**********************9886655 PP

>> YfmQ  Uncharacterised protein from bacillus cereus group
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.4e-05      0.15      24      69 ..      40      83 ..      24      94 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.4e-05
                           YfmQ 24 gvvesliskfevhakleeenvtitlegknlegeekskviqefneai 69
                                   gv +  +s fev ++   e v++t+eg n++ +  +++iqef  a+
  gi|116753594|ref|YP_842712.1| 40 GVKGVNMSLFEVDRQ--TETVKVTIEGDNIDYHAVERLIQEFGGAV 83
                                   556666788888775..678999*******************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 753.72
//
Query:       gi|116753595|ref|YP_842713.1|  [L=369]
Description: myo-inositol-1-phosphate synthase [Methanosaeta thermophila PT]
Scores for 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-33  112.8   0.0    1.9e-32  111.8   0.0    1.6  2  Inos-1-P_synth  Myo-inositol-1-phosphate synthase
  ------ inclusion threshold ------
      0.035   13.5   0.0      0.058   12.8   0.0    1.5  1  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 ?   -3.5   0.0       1.3   1.2e+04      66      77 ..     130     141 ..     114     148 .. 0.71
   2 !  111.8   0.0   2.1e-36   1.9e-32       1     109 []     196     304 ..     196     304 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.3
                                    ....EEEEE-GG CS
                 Inos-1-P_synth  66 vdhevvikYvpy 77 
                                       e+ i+Y+p+
  gi|116753595|ref|YP_842713.1| 130 SGAEILINYMPV 141
                                    445788999986 PP

  == domain 2  score: 111.8 bits;  conditional E-value: 2.1e-36
                                    SHHHHHHHHHHHHHHTT-EEEEEEEEEEE-HHHHHHTTSHHHHHHHHHHHHHHHHHHHSS--EEE....EEE...EE-GG CS
                 Inos-1-P_synth   1 GqTklksvLaellverglkvksivslNilGnnDgknlseeerfksKkisKssvvddivkanellyvdhevvi...kYvpy 77 
                                    G+T+++++La+l+++rg++++++++lN++Gn+D++n+ +++r++sKkisK+++v+++++a +l+    +++i   +Y+p+
  gi|116753595|ref|YP_842713.1| 196 GATIVHRTLAKLFMDRGCRLDRTYQLNVGGNTDFLNMLSRDRLRSKKISKTEAVQSVLDA-PLDP--ENIHIgpcDYIPW 272
                                    9**********************************************************9.5543..57999999***** PP

                                    GTTEEEEEEEEEEEEGGGEEEEEEEEEEEEH. CS
                 Inos-1-P_synth  78 lgDsKvaldeieseiflggkntielkleceDS 109
                                     +D+Kv++ ++e++if+++++++el+l++eDS
  gi|116753595|ref|YP_842713.1| 273 QKDNKVCFLRMEGRIFGDVPINLELRLSVEDS 304
                                    *******************************9 PP

>> NAD_binding_5  Myo-inositol-1-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   6.5e-06     0.058     207     252 ..     148     252 ..     119     355 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.5e-06
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxx................................ RF
                  NAD_binding_5 207 tiyavAailegvpyingsPqntlvpglvelA...ekkgvfiaGdDfKt................................ 251
                                      ya Aa+ +gv++in  P   ++ +  e A   +++g++++GdD+K+                                
  gi|116753595|ref|YP_842713.1| 148 RFYAQAALDAGVAFINCMPV--FIASDREWAtkfQERGIPVVGDDIKSqigativhrtlaklfmdrgcrldrtyqlnvgg 225
                                    67*****************6..5666666662235689**********77766666666666666666666666666666 PP

                                    ..........................x RF
                  NAD_binding_5 252 ..........................l 252
                                                              +
  gi|116753595|ref|YP_842713.1| 226 ntdflnmlsrdrlrskkiskteavqsV 252
                                    666666666666555555555555553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2666.72
//
Query:       gi|116753596|ref|YP_842714.1|  [L=286]
Description: hypothetical protein Mthe_0277 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 2185.66
//
Query:       gi|116753597|ref|YP_842715.1|  [L=164]
Description: hypothetical protein Mthe_0278 [Methanosaeta thermophila PT]
Scores for complete 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   82.4   0.1    6.7e-21   75.3   0.0    2.1  2  DUF45          Protein of unknown function DUF45
     0.0026   17.8   0.1      0.029   14.5   0.0    2.1  2  WLM            WLM domain
  ------ inclusion threshold ------
       0.03   14.3   0.0        0.1   12.6   0.0    1.8  1  DUF4980        Domain of unknown function (DUF4980)
      0.049   13.2   0.0      0.063   12.9   0.0    1.2  1  Peptidase_M57  Dual-action HEIGH metallo-peptidase
       0.17   11.8   0.2       0.56   10.1   0.0    2.0  2  SprT-like      SprT-like family


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 !    5.9   0.0    0.0033        12       1      38 [.      13      49 ..      13      71 .. 0.83
   2 !   75.3   0.0   1.9e-24   6.7e-21     130     193 ..      76     141 ..      49     151 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0033
                          DUF45  1 knlrlrvepdgsvevsaPkgvseeeiedfvkkkakwie 38
                                   k++ +r ++ +++ev aP ++s+ ++++ +++ ++ +e
  gi|116753597|ref|YP_842715.1| 13 KTIEIRLRE-DKIEVLAPADISDGDLNAHIARFRSRME 49
                                   7899*****.*****************99998666655 PP

  == domain 2  score: 75.3 bits;  conditional E-value: 1.9e-24
                          DUF45 130 kprsvsik.dmktrWGsc.sskgkirlnwrLvkappevidYVvvHElaHlleknHskrFwalvekl 193
                                    +++s+s + +m++r+Gsc +s+g+ir++ rL  +p  v dYV+vHElaH++e+nH++rFw+lv+++
  gi|116753597|ref|YP_842715.1|  76 SWKSISYSdKMERRYGSCtPSNGTIRISPRLRSMPVWVEDYVIVHELAHMIEPNHGPRFWSLVNRY 141
                                    5556665526999*****99*******************************************997 PP

>> WLM  WLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.12   4.4e+02      60      73 ..      11      24 ..       8      32 .. 0.84
   2 !   14.5   0.0     8e-06     0.029      86     108 ..     117     139 ..     113     149 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.12
                            WLM 60 kGekieLrLRtdkd 73
                                   +++ ie+rLR+dk 
  gi|116753597|ref|YP_842715.1| 11 RKKTIEIRLREDKI 24
                                   5789******9985 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 8e-06
                            WLM  86 tllHELaHnvygpHdakFyallk 108
                                    +++HELaH++  +H  +F++l++
  gi|116753597|ref|YP_842715.1| 117 VIVHELAHMIEPNHGPRFWSLVN 139
                                    689*****************987 PP

>> DUF4980  Domain of unknown function (DUF4980)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.9e-05       0.1      29      93 ..       3      87 ..       1      90 [. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.9e-05
                        DUF4980 29 vkviknnkavkelnvrLavdkvdYyvPldldeykgakevtldikvkge.....................lkdalcwkelkls 89
                                   v++ + ++ +k++++rL +dk++   P d+++  + ++   +++   e                     l  ++ wk++++s
  gi|116753597|ref|YP_842715.1|  3 VEIRRSKRRKKTIEIRLREDKIEVLAPADISD-GDLNAHIARFRSRMEmrksrddsyleqramrlnmkyLGGVISWKSISYS 83
                                   778888999*********************99.3334444444444335677889999999999999988899999999999 PP

                        DUF4980 90 dtfd 93
                                   d+++
  gi|116753597|ref|YP_842715.1| 84 DKME 87
                                   9875 PP

>> Peptidase_M57  Dual-action HEIGH metallo-peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.8e-05     0.063     116     149 ..      97     130 ..      65     136 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.8e-05
                  Peptidase_M57 116 ykviqigtglesysvdvnehvithelGhtvGlRh 149
                                    +++i+i+  l s++v v ++vi hel h +   h
  gi|116753597|ref|YP_842715.1|  97 NGTIRISPRLRSMPVWVEDYVIVHELAHMIEPNH 130
                                    579*************************997666 PP

>> SprT-like  SprT-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       1.7   6.3e+03      42      53 ..      10      21 ..       4      26 .. 0.61
   2 ?   10.1   0.0   0.00016      0.56      21      76 ..      78     126 ..      59     148 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.7
                      SprT-like 42 tvrhhasIeLse 53
                                   +++++ +I+L e
  gi|116753597|ref|YP_842715.1| 10 RRKKTIEIRLRE 21
                                   356666777765 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00016
                      SprT-like  21 vkiiwskrlnttaGranlkratvrhhasIeLseklldsrsedrllntLaHElcHla 76 
                                     +i+ s+++++  G ++ ++       +I++s++l    +      +++HEl+H++
  gi|116753597|ref|YP_842715.1|  78 KSISYSDKMERRYGSCTPSN------GTIRISPRLRSM-PVWVEDYVIVHELAHMI 126
                                    46788899************......9******99888.777777899******86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1248.23
//
Query:       gi|116753598|ref|YP_842716.1|  [L=185]
Description: putative methylase [Methanosaeta thermophila PT]
Scores for complete 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-10   39.7   0.0    8.5e-08   31.9   0.0    2.2  2  MTS              Methyltransferase small domain
    2.9e-06   27.2   0.0    4.9e-06   26.4   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
    4.9e-06   26.1   0.4    7.2e-06   25.6   0.4    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    4.9e-05   23.2   0.0    0.00044   20.1   0.0    2.2  1  Methyltransf_23  Methyltransferase domain
    0.00017   22.2   0.0    0.00049   20.7   0.0    1.9  1  Methyltransf_25  Methyltransferase domain
      0.002   18.8   0.1      0.012   16.3   0.0    2.2  2  Methyltransf_12  Methyltransferase domain
     0.0036   17.9   0.0       0.02   15.5   0.0    2.1  2  Methyltransf_11  Methyltransferase domain
     0.0056   16.6   0.0      0.009   15.9   0.0    1.2  1  UPF0146          Uncharacterised protein family (UPF0146)
     0.0091   15.9   0.1      0.026   14.5   0.1    1.6  2  Methyltransf_18  Methyltransferase domain
  ------ inclusion threshold ------
      0.021   13.9   0.0      0.029   13.3   0.0    1.2  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
       0.18   11.4   0.1       0.38   10.3   0.0    1.5  2  NodS             Nodulation protein S (NodS)
       0.22   11.2   0.0       0.39   10.4   0.0    1.3  1  Met_10           Met-10+ like-protein


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 !   31.9   0.0   5.7e-11   8.5e-08      27     107 ..      19      91 ..       9      99 .. 0.84
   2 !    5.7   0.0    0.0066       9.8     112     159 ..     116     166 ..     112     173 .. 0.75

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 5.7e-11
                                    CHCC.TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEEE-- CS
                            MTS  27 lpke.lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdlivsNP 105
                                    ++++ + ++v+ +GcG Gv++a+l  +  +  + ++d++ +A+++a        l + +v  d+++ ++  kfdli+ NP
  gi|116753598|ref|YP_842716.1|  19 ISEAsAGDSVIEIGCGSGVISASLIGKVRS--ILATDINPHAVRAAA------SLGIPAVRADLFHGIN-SKFDLILFNP 89 
                                    444446778***************998877..9**********9764......5678999*********.********** PP

                                    -S CS
                            MTS 106 Pf 107
                                    P+
  gi|116753598|ref|YP_842716.1|  90 PY 91 
                                    *7 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0066
                                    HCHHHHHHHHHHHHHHHEEEEEEEEEEEETTSCHHHH..HHHHHS.--EEE CS
                            MTS 112 atelavaeeliaeAkeaLkegGeLliVanrklgyesl..leelfg.nvevv 159
                                    a   +v+e++++  k+++++ G+Ll+ +++  g +++  l++  g n+e+v
  gi|116753598|ref|YP_842716.1| 116 ADGREVIERFLKGVKNIMSPRGRLLLLISSLTGLDEVqeLARRSGfNTEIV 166
                                    566789**********************99988887766665555344444 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   3.3e-09   4.9e-06       3     125 ..      24     159 ..      22     176 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 3.3e-09
                Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDlilsn 81 
                                     g +v+++GCG+G ++  l  ++++   +   Di+++a++ A +         +   ++d ++ ++     +kfDlil n
  gi|116753598|ref|YP_842716.1|  24 AGDSVIEIGCGSGVISASLIGKVRS---ILATDINPHAVRAAASL-------GIPAVRADLFHgIN-----SKFDLILFN 88 
                                    5779****************99988...***************95.......56688999999899.....78******* PP

                Methyltransf_31  82 .....................evlnaladpdkile....eiervlkpggilliedpr..llaelpakveee 125
                                                          +l+  ad  +++e    ++++ ++p g+ll+   +  +l+e+ + ++++
  gi|116753598|ref|YP_842716.1|  89 ppylptedgldlnpeddrwlsTALDGGADGREVIErflkGVKNIMSPRGRLLLLISSltGLDEVQELARRS 159
                                    99999999999999999999878899999999999888899999*****9876554433666666665555 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.4   4.8e-09   7.2e-06     159     201 ..      22      63 ..       9      70 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 4.8e-09
                           PrmA 159 vkegeevlDvGtGSGiLaiaaakLg.akkvvavDiDevAvkvak 201
                                      +g++v+ +G+GSG+++  a+++g  ++++a+Di++ Av++a+
  gi|116753598|ref|YP_842716.1|  22 ASAGDSVIEIGCGSGVIS--ASLIGkVRSILATDINPHAVRAAA 63 
                                    56789***********76..666662689************997 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   2.9e-07   0.00044      15      87 ..      21      86 ..       9     163 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.9e-07
                Methyltransf_23 15 rllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae..kakkaqkdqfdeqeaaepqgkfdlIv 87
                                   +      ag +v++iGcG+G  + +l  ++ s+ + D++p+av  a+  +++  + d f        + kfdlI 
  gi|116753598|ref|YP_842716.1| 21 E----ASAGDSVIEIGCGSGVISASLIGKVRSILATDINPHAVRAAAslGIPAVRADLF-----HGINSKFDLIL 86
                                   2....45789**********88877777778************9998885555555555.....22233666665 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   3.3e-07   0.00049       1      41 [.      28      66 ..      28      98 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 3.3e-07
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHH CS
                Methyltransf_25  1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaarera 41
                                   v+++GcG+G +++ l  ++   +++++Di++ +++aa++  
  gi|116753598|ref|YP_842716.1| 28 VIEIGCGSGVISASLIGKV--RSILATDINPHAVRAAASLG 66
                                   89**************998..9*************998754 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   8.1e-06     0.012       2      38 ..      30      63 ..      29      88 .. 0.82
   2 ?   -0.3   0.0       1.2   1.8e+03      81      99 .]     121     139 ..     111     139 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8.1e-06
                Methyltransf_12  2 eiGcGtGsllralleklpdieytgvDispsaiedake 38
                                   eiGcG+G +++ l  k    +++++Di+p+a+ +a++
  gi|116753598|ref|YP_842716.1| 30 EIGCGSGVISASLIGK--VRSILATDINPHAV-RAAA 63
                                   9***************..99999*********.4444 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.2
                Methyltransf_12  81 direvldnirklLkpgGrl 99 
                                     i+++l+ +++ ++p Grl
  gi|116753598|ref|YP_842716.1| 121 VIERFLKGVKNIMSPRGRL 139
                                    688999**********997 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   1.4e-05      0.02       2      52 ..      30      74 ..      29      89 .. 0.76
   2 ?   -0.2   0.0       1.1   1.7e+03      77      95 ..     122     140 ..      97     141 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.4e-05
                                   EET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEEC CS
                Methyltransf_11  2 dvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvada 52
                                   ++GcG+G +++ l  ++++++++D+++ ++++a + + ++      v+ad+
  gi|116753598|ref|YP_842716.1| 30 EIGCGSGVISASLIGKVRSILATDINPHAVRAAASLGIPA------VRADL 74
                                   89************888*************8886554333......45555 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.1
                                    HHHHHHHHHHHEEEEEEEE CS
                Methyltransf_11  77 pekalkeiaRvLkpgGllv 95 
                                     e++lk ++ ++ p G+l+
  gi|116753598|ref|YP_842716.1| 122 IERFLKGVKNIMSPRGRLL 140
                                    5899999999999999986 PP

>> UPF0146  Uncharacterised protein family (UPF0146)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0     6e-06     0.009       8      62 ..      19      76 ..      13      83 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 6e-06
                                   HHHHS-SSEEEEET-TT--HHHHHHHHHS-EEEEE-SS-S........STTEE---SSS CS
                        UPF0146  8 iaeenargkvvEvGiGrkldvaealakrgvdlvatDikek....kakegvrivrDDvtd 62
                                   i e +a   v+E+G G  +  a+++ k    ++atDi+++     a +g+ +vr D+++
  gi|116753598|ref|YP_842716.1| 19 ISEASAGDSVIEIGCGSGVISASLIGKV-RSILATDINPHavraAASLGIPAVRADLFH 76
                                   444455559**********999999998.89********97754445888899999885 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   1.7e-05     0.026       8      55 ..      18      63 ..      14      67 .. 0.88
   2 ?   -1.7   0.0       1.6   2.4e+03      94     134 ..     120     162 ..     114     174 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.7e-05
                Methyltransf_18  8 iaslvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekak 55
                                    +s  + g++v+ iG+  g++++ l+  gk+++++a+Din++++++a 
  gi|116753598|ref|YP_842716.1| 18 AISEASAGDSVIEIGCGSGVISASLI--GKVRSILATDINPHAVRAAA 63
                                   556667899****************9..99************999886 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.6
                Methyltransf_18  94 elileILeeakeklkkikk..lilqpnseaeelRkylvengfk 134
                                    e+i + L+  k++++   +  l++++ +  +e+++   ++gf+
  gi|116753598|ref|YP_842716.1| 120 EVIERFLKGVKNIMSPRGRllLLISSLTGLDEVQELARRSGFN 162
                                    5666667766666665555446677888888888888888776 PP

>> tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     2e-05     0.029     199     240 ..      21      63 ..      11      73 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2e-05
                tRNA_U5-meth_tr 199 qeskg.dllelycGnGnfslalarnfekvlateiakssveaaq 240
                                    + s g  ++e+ cG G  s +l  +++ +lat+i   +v aa 
  gi|116753598|ref|YP_842716.1|  21 EASAGdSVIEIGCGSGVISASLIGKVRSILATDINPHAVRAAA 63 
                                    445551589***************************9999875 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00025      0.38      34      81 ..      14      62 ..       8      88 .. 0.83
   2 ?   -2.6   0.0       2.4   3.6e+03      97     123 ..     151     177 ..     148     182 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00025
                           NodS 34 ilrlslaqgsiad.alevGcaaGalterlapyckrltvvdvveeaiara 81
                                   ++r ++++ s++d ++e+Gc +G ++  l    +++   d+ ++a+  a
  gi|116753598|ref|YP_842716.1| 14 LMRAAISEASAGDsVIEIGCGSGVISASLIGKVRSILATDINPHAVRAA 62
                                   6888899988875389************************999998654 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.4
                           NodS  97 dvqqfstdekfdlivvaevlyyiedva 123
                                    +vq++     f++ +va   y+ e++ 
  gi|116753598|ref|YP_842716.1| 151 EVQELARRSGFNTEIVAMERYFFEELY 177
                                    578888888899988888888888765 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00026      0.39      97     138 ..      21      60 ..      14      64 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00026
                                    T--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHH CS
                         Met_10  97 lveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvk 138
                                     ++ g+ V+++  G G   i+++  +k + +la d+nP++v+
  gi|116753598|ref|YP_842716.1|  21 EASAGDSVIEIGCGSGV--ISASLIGKVRSILATDINPHAVR 60 
                                    56789999998777776..55556679************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1453.83
//
Query:       gi|116753599|ref|YP_842717.1|  [L=319]
Description: NAD-dependent epimerase/dehydratase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-53  181.5   0.1    2.2e-53  181.2   0.1    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    4.6e-48  164.3   0.0    1.5e-47  162.6   0.0    1.7  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    1.5e-18   66.9   0.0    1.9e-18   66.6   0.0    1.1  1  RmlD_sub_bind    RmlD substrate binding domain
    7.6e-18   64.7   0.0    6.4e-17   61.6   0.0    1.9  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
      1e-17   64.1   0.0    1.3e-17   63.8   0.0    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    4.5e-12   46.2   0.0    1.5e-11   44.5   0.0    1.8  2  NAD_binding_10   NAD(P)H-binding
    6.8e-10   38.5   0.4    3.4e-05   23.1   0.0    2.7  2  NAD_binding_4    Male sterility protein
    0.00023   21.4   0.0    0.00052   20.3   0.0    1.6  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    0.00065   19.3   0.0      0.023   14.3   0.0    2.1  2  NmrA             NmrA-like family
     0.0022   17.5   0.0       0.13   11.7   0.0    2.3  2  adh_short        short chain dehydrogenase
  ------ inclusion threshold ------
       0.15   11.7   0.0       0.19   11.4   0.0    1.2  1  DUF4292          Domain of unknown function (DUF4292)


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 !  181.2   0.1   1.3e-56   2.2e-53       1     241 []       9     243 ..       9     243 .. 0.97

  Alignments for each domain:
  == domain 1  score: 181.2 bits;  conditional E-value: 1.3e-56
                                    EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.....EEEE--TT-HHHHHHHHHHHT-SEEEE--S-- CS
                      Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl.....elveldltdrsalerlfkeeqpdavihlAavg 75 
                                    ilVtG++GfiGs+lv+al +++ +v+++d+ls+++++ ++++      +l+e+dl+dr ++ +++k  + d+v+hlAa  
  gi|116753599|ref|YP_842717.1|   9 ILVTGGAGFIGSHLVDALIKHN-DVTVIDNLSTGKREYLRAHEpnprfRLIEADLLDRLEVYDAVK--DKDIVFHLAANP 85 
                                    8******************986.9************9999999***********************..67********** PP

                                    -HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHH CS
                      Epimerase  76 gvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklvea 155
                                    +va+  +d    +e+n+  t+nllea+r+a v+r+ f s+s+vYG+ + +p+ e+   gplkp s Y+a+Kla e ++ +
  gi|116753599|ref|YP_842717.1|  86 SVAVGETDTRVHLEQNALTTYNLLEAMRRARVRRIAFTSTSTVYGEAKIIPTPEDY--GPLKPISLYGASKLACEAMISS 163
                                    **********************************************9999977777..8********************* PP

                                    HHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT-STT CS
                      Epimerase 156 yaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvdagdkg 235
                                    y ++++++a i r  n++G+r     +++vi  +irk+ ++ +e+ +lg+g ++  +l+v+D+++a+++ +eh d+  + 
  gi|116753599|ref|YP_842717.1| 164 YCHTFDMQAWIYRFANIVGER----GNHGVIVDFIRKLRANPNELEILGSGAQRKSYLDVRDCVDAMIHCVEHADE--QV 237
                                    *********************....99*************99*******************************776..45 PP

                                    EEEEES CS
                      Epimerase 236 eiyniG 241
                                    +iyniG
  gi|116753599|ref|YP_842717.1| 238 NIYNIG 243
                                    7****9 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.6   0.0   9.4e-51   1.5e-47       1     330 [.      10     309 ..      10     311 .. 0.86

  Alignments for each domain:
  == domain 1  score: 162.6 bits;  conditional E-value: 9.4e-51
                                    EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEE CS
                  GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevy 80 
                                    L+TG+aGfiGs+l++ L++   +v++i+++s    tg+ e l+ +   e +++++l+++Dl D+ ++ +++++   d v+
  gi|116753599|ref|YP_842717.1|  10 LVTGGAGFIGSHLVDALIKH-NDVTVIDNLS----TGKREYLRAH---EPNPRFRLIEADLLDRLEVYDAVKDK--DIVF 79 
                                    9*****************86.7788887664....4455555542...34689********************9..89** PP

                                    E--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TT.S-----SHHHHHHHH CS
                  GDP_Man_Dehyd  81 nLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEt.tpfyPrsPYaaaKly 159
                                    +LAA   V+v  ++    +e n+l t++LLea+r++ ++   r+ ++Sts+vYG+++ +p  E+  p++P s Y+a+Kl+
  gi|116753599|ref|YP_842717.1|  80 HLAANPSVAVGETDTRVHLEQNALTTYNLLEAMRRARVR---RIAFTSTSTVYGEAKIIPTPEDyGPLKPISLYGASKLA 156
                                    ***********************************9875...9999**************988768************** PP

                                    HHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHHC CS
                  GDP_Man_Dehyd 160 adwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyveamwlmlqq 239
                                    ++ ++ +y ++++++a + ++ n  + r g++     i++++ +  ++ +e  +lG + ++++++ v+D v+am   +++
  gi|116753599|ref|YP_842717.1| 157 CEAMISSYCHTFDMQAWIYRFANIVGER-GNHG---VIVDFIRKLRANPNELEILGSGAQRKSYLDVRDCVDAMIHCVEH 232
                                    **************************99.6665...5999********999999***********************998 PP

                                    ..SS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB--B-THHHHHHH CS
                  GDP_Man_Dehyd 240 ..dkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlllgdaskakeeL 317
                                      ++ + y+i++++t  vre++++ ++ +g + +                + +  +d +   +g+v+l++  ++ ++  L
  gi|116753599|ref|YP_842717.1| 233 adEQVNIYNIGSQDTIDVREIADIVVKTMGLDGVRY--------------RFTGGIDGRGW-KGDVKLMCLSTDAIR-AL 296
                                    545668899**************9999999764322..............23334665555.577766666655554.88 PP

                                    ----SS-HHHHHH CS
                  GDP_Man_Dehyd 318 gWkpkvsfeelvr 330
                                    gW+p+ s +e v+
  gi|116753599|ref|YP_842717.1| 297 GWRPRLSSREAVA 309
                                    8888888777765 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 !   66.6   0.0   1.2e-21   1.9e-18       1     235 [.       7     265 ..       7     277 .. 0.88

  Alignments for each domain:
  == domain 1  score: 66.6 bits;  conditional E-value: 1.2e-21
                                    EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT....................T--TTSHHHHHHHHHHH--SEEEE--- CS
                  RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeglevlaltre....................eldltdaeavaellkeakpdvvvnaAA 60 
                                    m ilvtG+ G +Gs+L+++l +++ +v+ +++                     e+dl d+ +v +++k+  +d+v ++AA
  gi|116753599|ref|YP_842717.1|   7 MSILVTGGAGFIGSHLVDALIKHN-DVTVIDNLstgkreylrahepnprfrliEADLLDRLEVYDAVKD--KDIVFHLAA 83 
                                    88***************9998766.66666444567889*****************************9..899****** PP

                                    ---HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-E.EEEEEEGGGS-S-TTS-B-TT.S----SSHHHHHHHHHHHHHHH CS
                  RmlD_sub_bind  61 ytavDkaEseeeaayavnaeavealAeaaaavgal.LihvStDyVFdGekkrpYeed.detsPlnvYGrtKlaGEqavla 138
                                       v   E++ +   + na  + +l ea +++ +  + + St  V+  +k  p  ed  + +P+++YG++Kla E ++ +
  gi|116753599|ref|YP_842717.1|  84 NPSVAVGETDTRVHLEQNALTTYNLLEAMRRARVRrIAFTSTSTVYGEAKIIPTPEDyGPLKPISLYGASKLACEAMISS 163
                                    *****************************99998627789******999999966652688******************* PP

                                    H-S....SEEEEEE-SEESSSSS-..HHHHHHHHHHH-SEEEEES..S-EE--EEHHHHHHHHHHHHHHCHH.GGG-EEE CS
                  RmlD_sub_bind 139 agk....kalivRtswvygekgkn..fvktmlrlakereelkvva..DqlgsPTsardlAevllqllekaaeekelagvy 210
                                    +++    +a+i R++ + ge+g+    v  + +l ++ +el++     q  s   +rd  +++++ +e+a e   +  +y
  gi|116753599|ref|YP_842717.1| 164 YCHtfdmQAWIYRFANIVGERGNHgvIVDFIRKLRANPNELEILGsgAQRKSYLDVRDCVDAMIHCVEHADE---QVNIY 240
                                    776444489***********888633567788888********9622588888899***********99997...688** PP

                                    E---BS-EEHHHHHHHHHHHHCHTT CS
                  RmlD_sub_bind 211 HlanegetswlefArailkeagads 235
                                     +++++++   e+A+ ++k++g d+
  gi|116753599|ref|YP_842717.1| 241 NIGSQDTIDVREIADIVVKTMGLDG 265
                                    *****************99998876 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   0.0   3.9e-20   6.4e-17       1     250 [.       9     264 ..       9     277 .. 0.80

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 3.9e-20
                                    EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SE CS
                Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdv 80 
                                    +lvtG++G iGs+lv+ ++k++   + ++++  +   e  + +     + ++  +   + +d+ d+ ++ +a++  + d+
  gi|116753599|ref|YP_842717.1|   9 ILVTGGAGFIGSHLVDALIKHN--DVTVIDNLSTGKREYLRAH---EPNPRF--R--LIEADLLDRLEVYDAVK--DKDI 77 
                                    89****************9986..5566665554444433333...234333..3..4469*************..9*** PP

                                    EEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEG......GGS.........S--SHHHHHHHHH CS
                Polysacc_synt_2  81 vfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStD......KAv.........nPtnvmGatKrla 145
                                    vfh AA   V + e+ +   +++N l t n++ea  +a+v+++ + St       K +         +P++++Ga+K+++
  gi|116753599|ref|YP_842717.1|  78 VFHLAANPSVAVGETDTRVHLEQNALTTYNLLEAMRRARVRRIAFTSTStvygeaKIIptpedygplKPISLYGASKLAC 157
                                    **********************************************9962222223323333333338************ PP

                                    HHHHHHGGG--SSS--EEEEEEE-EETTGTTS..SHHHHHHHHHTT.SSEEES-TT-EE.EEE-HHHHHHHHHHHHHH-- CS
                Polysacc_synt_2 146 ekllqalakeseekktkfvvvRfGNVlgSrGS..viplFkkqikeg.gpvtvTdpemtR.yfmtieeavqLvlqalalak 221
                                    e ++ ++ ++    +++  + Rf N++g rG   vi  F ++++++ +++ +  +   R  ++ +++ v+ +++++++a+
  gi|116753599|ref|YP_842717.1| 158 EAMISSYCHTF---DMQAWIYRFANIVGERGNhgVIVDFIRKLRANpNELEILGSGAQRkSYLDVRDCVDAMIHCVEHAD 234
                                    ****9999887...899999**********955599999999988879****99988884689*************9986 PP

                                    SS-EEEE--...-EEEHHHHHHHH....... CS
                Polysacc_synt_2 222 ggeifvldmG..epvkivdlakalielsgle 250
                                    + ++ + ++G  +++ ++++a  +++++gl+
  gi|116753599|ref|YP_842717.1| 235 E-QVNIYNIGsqDTIDVREIADIVVKTMGLD 264
                                    5.56666666225688899999999999874 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 !   63.8   0.0   7.7e-21   1.3e-17       1     226 [.      10     227 ..      10     247 .. 0.75

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 7.7e-21
                      3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlD...lrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslv 77 
                                    +vtGgaGF+G++lv +L++ ++   v v+D     +++ l+ +  + + + +ie+D++d  ++ +a+++ d+v+hla+  
  gi|116753599|ref|YP_842717.1|  10 LVTGGAGFIGSHLVDALIKHND---VTVIDnlsTGKREYLRAHEPNPRFR-LIEADLLDRLEVYDAVKDKDIVFHLAANP 85 
                                    69*****************996...7777742144444444444444444.*************************9988 PP

                      3Beta_HSD  78 dvag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKalaEkl 156
                                     va  ++ +    + n   T n+lea ++a vr++ +tS+  v g+   +++i     e + + ++ + y  sK   E++
  gi|116753599|ref|YP_842717.1|  86 SVAVgETDTRVHLEQNALTTYNLLEAMRRARVRRIAFTSTSTVYGE---AKIIP-TP-EDYGPLKPISLYGASKLACEAM 160
                                    876536777778899******************************9...66666.44.456788999************9 PP

                      3Beta_HSD 157 vlkaNgrtlknggrlyTcaLRpagiyGegdk..llvpllkqlaklglalfkigdeevlsdrvYvgNvawahi 226
                                    + +          ++     R a i Ge+ +  ++v ++++l  + ++l  +g+  + +++  v   ++a i
  gi|116753599|ref|YP_842717.1| 161 ISSYCH-----TFDMQAWIYRFANIVGERGNhgVIVDFIRKLRANPNELEILGSGAQRKSYLDVRDCVDAMI 227
                                    977655.....3356666667777777754312466677777666666666666666666666666666665 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 !   44.5   0.0   9.5e-15   1.5e-11       1     105 [.      13     132 ..      13     167 .. 0.78
   2 ?   -1.2   0.0         1   1.6e+03      46      90 ..     217     266 ..     194     277 .. 0.68

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 9.5e-15
                                    TTTSHHHHHHHHHHHHC-T-EE..EEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC..... CS
                 NAD_binding_10   1 GAtGkvGrllvkellargghev..talvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggk..... 73 
                                    G+ G +G++lv+ l+++++++v   + + + e l + e +++ +++e+d++d  ++ +a+k+ d+V+  +++ +      
  gi|116753599|ref|YP_842717.1|  13 GGAGFIGSHLVDALIKHNDVTVidNLSTGKREYLRAHEPNPRFRLIEADLLDRLEVYDAVKDKDIVFHLAANPSVavget 92 
                                    99**************9865552222333456666677789*************************99995555455544 PP

                                    HHHH........HHHHHHHHHHCT--EEEEEEETTTTSGC CS
                 NAD_binding_10  74 deeg........aknivdaakeagvkRfvlvsaigvgdev 105
                                    d+++        + n+++a+++a v+R+ + s+  v+ e+
  gi|116753599|ref|YP_842717.1|  93 DTRVhleqnaltTYNLLEAMRRARVRRIAFTSTSTVYGEA 132
                                    444466777899************************9764 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1
                                    --TT-.CCHHHHHHTT-S.EE.EES---TCC..HHHHHHHHHHHHHHCT- CS
                 NAD_binding_10  46 gdvtd.vedlaealkgad.aV.vsalggggk..deegaknivdaakeagv 90 
                                    +dv d v+++ + +++ad  V + ++g++++   +e+a+ +v+ +   gv
  gi|116753599|ref|YP_842717.1| 217 LDVRDcVDAMIHCVEHADeQVnIYNIGSQDTidVREIADIVVKTMGLDGV 266
                                    56666567777777777754557777777777656667777777777777 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   2.9e-05     0.047       1      25 [.      11      34 ..      11      50 .. 0.88
   2 !   23.1   0.0   2.1e-08   3.4e-05      82     214 ..      69     189 ..      52     226 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.9e-05
                                   EE-TTSHHHHHHHHHHHHHS-.TEE CS
                  NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpevki 25
                                   +TG+ GF+G++L+  L++ ++ v++
  gi|116753599|ref|YP_842717.1| 11 VTGGAGFIGSHLVDALIKHND-VTV 34
                                   7****************9985.544 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 2.1e-08
                                    HHHHHH--EEEE--SS-S.ST...TSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H..... CS
                  NAD_binding_4  82 qelaeevdviihsaAtvnfde...pykellrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegeke 158
                                     + ++  d+++h aA+ ++     ++++ l+ N + t ++le  ++ +    + + ST++v+ge +  +           
  gi|116753599|ref|YP_842717.1|  69 YDAVKDKDIVFHLAANPSVAVgetDTRVHLEQNALTTYNLLEAMRRARVR-RIAFTSTSTVYGEAK--I----------- 134
                                    5566788********87664333488999*************88877666.*************99..3........... PP

                                    .HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE--SSS.T- CS
                  NAD_binding_4 159 ekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitgeskt.Gw 214
                                        + e     +    Y  sK + E ++ ++ +  ++++ i+R  +i+ge  + G+
  gi|116753599|ref|YP_842717.1| 135 --IPTPEDYGPLKPISLYGASKLACEAMISSYCHTFDMQAWIYRFANIVGERGNhGV 189
                                    ..67788888888899*********************************97655354 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   3.2e-07   0.00052       3      80 ..      11      85 ..       9      90 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 3.2e-07
                                   EE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHH.HHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SSGG CS
                Sacchrp_dh_NADP  3 iiGa.GsvGqavaellarhfdvdaeitvadrskekl.ealaakalgvrfeaialdaenyeavLaallkegdlvvnlsppi 80
                                   + G+ G++G+ +++ l +h+dv    tv+d   ++  e l a++ ++rf  i+ d  ++ + +  ++k++d+v +l+ + 
  gi|116753599|ref|YP_842717.1| 11 VTGGaGFIGSHLVDALIKHNDV----TVIDNLSTGKrEYLRAHEPNPRFRLIEADLLDRLE-VYDAVKDKDIVFHLAANP 85
                                   55555***************87....888876555404555556*****************.88889********99775 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   1.4e-05     0.023       1      99 [.       9     122 ..       9     133 .. 0.72
   2 ?    3.0   0.0      0.04        65     165     231 ..     202     268 ..     188     270 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.4e-05
                                    EEESSTTSHHHHHHHHHHHHHT-EEEE.EES-S.-SHHHHHHHHSTT.EEEES-TT-HHHHHHHHTT-SEEEE---GG.. CS
                           NmrA   1 IlviGaTGrqGksvvrallkaghkvra.lvRdt.kselakslkeaGv.elvkgdlddkeslvealkgvdvvfsvtgfy.. 75 
                                    Ilv+G++G +G+++v+al+k++  + +  +  t k+e +++ + ++   l+++dl d+  +  a+k+ d vf   +    
  gi|116753599|ref|YP_842717.1|   9 ILVTGGAGFIGSHLVDALIKHNDVTVIdNLS-TgKREYLRAHEPNPRfRLIEADLLDRLEVYDAVKDKDIVFHLAANPsv 87 
                                    9*******************76544430333.2588888888888862577********************987764355 PP

                                    ...........S-HHHHHHHHHHHHHHHS-SEEEE CS
                           NmrA  76 ...........skeiedgkklvdAakeaGvkhfiy 99 
                                               +++     +l +A  +a v+++ +
  gi|116753599|ref|YP_842717.1|  88 avgetdtrvhlEQNALTTYNLLEAMRRARVRRIAF 122
                                    66666665554444445556666666666666665 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.04
                                    .-EEEEESS-TTS-EE-HHHHHHHHHHHHHHHHHHHTTEEEEE-SEEE-HHHHHHHHHHHHTS-.EEE CS
                           NmrA 165 dkvtllgpgnpkavlldaeeDiGafvikilkdprklkgkriklagntlsgneivelfekkigkt.vkY 231
                                    + +++lg g     +l +++D   ++i+ +++ ++  + +   +++t+ + ei+++  k +g   v+Y
  gi|116753599|ref|YP_842717.1| 202 NELEILGSGAQRKSYL-DVRDCVDAMIHCVEHADEQVNIYNIGSQDTIDVREIADIVVKTMGLDgVRY 268
                                    3688888898888888.***************999877777789***************999654666 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0     8e-05      0.13       3      69 ..       9      73 ..       7      82 .. 0.81
   2 ?    3.5   0.0     0.026        42     145     165 ..     146     166 ..     102     172 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8e-05
                                   EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHH CS
                      adh_short  3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealve 69
                                   +lvtG+++ IG  ++++l+k + +v+v+d+ +   +e +   +  + ++  i++D+ dr ev ++v+
  gi|116753599|ref|YP_842717.1|  9 ILVTGGAGFIGSHLVDALIKHN-DVTVIDNLSTGKREYLRAHEP-NPRFRLIEADLLDRLEVYDAVK 73
                                   89******************96.566666665555555555444.589*********9999998887 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.026
                                    TBHHHHHHHHHHHHHHHHHHH CS
                      adh_short 145 gvaaYsAsKaavagltrslak 165
                                      + Y+AsK a +++++s  +
  gi|116753599|ref|YP_842717.1| 146 PISLYGASKLACEAMISSYCH 166
                                    5789*********99998765 PP

>> DUF4292  Domain of unknown function (DUF4292)
   #    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      31      66 ..       3      39 ..       1     105 [. 0.92

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                        DUF4292 31 mekdeaiwlsa.apflGievaralitpdsvlvydkln 66
                                   + +d+ i++   a+f+G   ++ali  + v+v+d+l+
  gi|116753599|ref|YP_842717.1|  3 ILRDMSILVTGgAGFIGSHLVDALIKHNDVTVIDNLS 39
                                   569*******************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); 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: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2134.34
//
Query:       gi|116753600|ref|YP_842718.1|  [L=78]
Description: hypothetical protein Mthe_0281 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 586.70
//
Query:       gi|116753601|ref|YP_842719.1|  [L=302]
Description: NOL1/NOP2/sun family RNA methylase [Methanosaeta thermophila PT]
Scores for complete 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-52  177.5   0.0    2.9e-52  177.2   0.0    1.1  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    2.8e-11   43.8   0.0    4.7e-11   43.0   0.0    1.4  1  Methyltr_RsmF_N  N-terminal domain of 16S rRNA methyltransfer
     0.0001   22.5   0.0    0.00021   21.4   0.0    1.5  1  FtsJ             FtsJ-like methyltransferase
     0.0026   17.5   0.0     0.0039   17.0   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
     0.0036   17.1   0.0     0.0048   16.7   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
  ------ inclusion threshold ------
      0.023   15.4   0.0        0.1   13.3   0.0    2.0  1  Methyltransf_25  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 !  177.2   0.0   9.7e-56   2.9e-52       2     200 .]      94     295 ..      93     295 .. 0.90

  Alignments for each domain:
  == domain 1  score: 177.2 bits;  conditional E-value: 9.7e-56
                                    HHH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC..EE CS
                Methyltr_RsmB-F   2 llLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfD 81 
                                    ++L+pq++e+ilDlcaaPGgK + i+  m+nkg vvA+d ++ R+  + +nl+rLg  n+ v+++D+r+++++     fD
  gi|116753601|ref|YP_842719.1|  94 VVLDPQPGERILDLCAAPGGKAAQISMQMSNKGLVVANDSSSARIVPLRANLERLGAVNVVVTSYDGRRFPQY----NFD 169
                                    68********************************************************************886....49* PP

                                    EEEEEE--CCGGGTTT-TCHHHH--HHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEES--STTTTHHHHHHHHHH-TTEE CS
                Methyltr_RsmB-F  82 riLlDaPCsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaLkkredve 161
                                    r+L+DaPCs+ g+ rr p+v  r + k  a l++lq  ll  ai+l+k+gGv+vYsTC+ ++eEne v+ ++L   +   
  gi|116753601|ref|YP_842719.1| 170 RALVDAPCSSEGTARRYPEVIARCSAKRSADLQNLQVSLLRRAIQLTKPGGVVVYSTCTFAPEENEGVVSRVLDLADLES 249
                                    ********************9999*************************************************9875444 PP

                                    EESSBSTTSTTSSECEEC.......TSEEE-TTTTSS-SEEEEEEE CS
                Methyltr_RsmB-F 162 lvetelsepkglklgeea.......gtlrllPhtenkdgffiaklk 200
                                     +   l +++g++  +         + +r++Ph++++ gff+akl+
  gi|116753601|ref|YP_842719.1| 250 FTIQGLRSSQGIASWNSIdygeelvKCRRYYPHENDTGGFFVAKLR 295
                                    4444455555544333336666778899****************96 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 !   43.0   0.0   1.6e-14   4.7e-11       4      90 .]       4      90 ..       1      90 [. 0.91

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 1.6e-14
                                   HHHHHHHHHHGGGHHHHHHHHH-----EEE--TTS..TTHHHHHHH..-SS--B-TT-TTEEES---...TTSHHHHTTS-E CS
                Methyltr_RsmF_N  4 eFiekmkellgeeaeaflaaleeprkkglRvNtlKisveeleklse..efelepvpwceeGfyleeeerpgkhplheaGlyY 83
                                   e +e+++++++ +++afl+ +++p ++ +R+NtlK+sv el +  +  ++  e+  w + G  l++e +pg+ +++++Gl++
  gi|116753601|ref|YP_842719.1|  4 EHLERYRDIIP-DFDAFLDFMSRPLPVTIRINTLKTSVPELLSRLDrlGIGYERMRWYPLGLRLDAE-KPGRLMEFHMGLIH 83
                                   66788888886.79***********************999887666699****************99.9************* PP

                                   E--TTTH CS
                Methyltr_RsmF_N 84 iQEpSam 90
                                   +QE  +m
  gi|116753601|ref|YP_842719.1| 84 VQEELSM 90
                                   ***8877 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   7.1e-08   0.00021       9     141 ..      81     234 ..      78     252 .. 0.66

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 7.1e-08
                                    HHHHHHHHT-S.....-..TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS......HHHTTEEEECS-CCCSSH CS
                           FtsJ   9 Lleidekfklf.....k..pgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm......aplpgvttiqgditdpet 75 
                                    L++++e+ +++     +  pg++++Dl+aaPGg +  ++ ++ +kg vva D  +       a+l+++  ++  +t+ + 
  gi|116753601|ref|YP_842719.1|  81 LIHVQEELSMLppvvlDpqPGERILDLCAAPGGKAAQISMQMSNKGLVVANDSSSArivplrANLERLGAVNVVVTSYDG 160
                                    77777777755222222336799***********99999999999********998554443333455555555555555 PP

                                    HHHHCHCHHHSSEEEEEE--S-SS-CH.HHHHHHHH..........CCCCHHHHCCHCCCCECCCEEEECCCH..CCCH CS
                           FtsJ  76 iekikealserkvdlvvsDgapdvsgv.hdldeylq..........sqLllaalelalkllkpggtfvlkifr..geet 141
                                    ++  +     + +d  + D   + +g+ +  +e+++           +L  + l+ a++l kpgg++v  +++   ee 
  gi|116753601|ref|YP_842719.1| 161 RRFPQ-----YNFDRALVDAPCSSEGTaRRYPEVIArcsakrsadlQNLQVSLLRRAIQLTKPGGVVVYSTCTfaPEEN 234
                                    55544.....467777777766555554555555556666666554455555555577789999999988877433333 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.3e-06    0.0039      72     135 ..      99     162 ..      89     178 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.3e-06
                                    -TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGG CS
                           PCMT  72 kkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrk 135
                                    ++g+r+L++ +  G ++a +++ + +kg+vv+ + +   +   ++nl++l++ nv+v+  DGr 
  gi|116753601|ref|YP_842719.1|  99 QPGERILDLCAAPGGKAAQISMQMSNKGLVVANDSSSARIVPLRANLERLGAVNVVVTSYDGRR 162
                                    799***********************************999*********************96 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.6e-06    0.0048       3     113 ..     100     228 ..      98     274 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.6e-06
                Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsn. 81 
                                     g r+lDl ++ G ++ ++  ++  k+ vv  D s   i   r+n+++lg  nv +   d   +++     +fD  l + 
  gi|116753601|ref|YP_842719.1| 100 PGERILDLCAAPGGKAAQISMQMSNKGLVVANDSSSARIVPLRANLERLGAVNVVVTSYDGRRFPQY----NFDRALVDa 175
                                    6789****************99999999*************************************74....377755553 PP

                Methyltransf_31  82 ............evl.........naladpdkileeiervlkpggilliedpr 113
                                                ev+         ++++ + + l++++++ kpgg+++ +++ 
  gi|116753601|ref|YP_842719.1| 176 pcssegtarrypEVIarcsakrsaDLQNLQVSLLRRAIQLTKPGGVVVYSTCT 228
                                    3333444444442225555588989999999*******************998 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.5e-05       0.1       1      70 [.     104     173 ..     104     220 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.5e-05
                                    EEEET-TTSHHHHHHHCTS.TSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEE CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrl.gkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvs 70 
                                    +Ldl++ +G  +++++ ++ +k+ v++ D s++ +   r+++e+ g+ nv +   d +++p  +  fD  ++
  gi|116753601|ref|YP_842719.1| 104 ILDLCAAPGGKAAQISMQMsNKGLVVANDSSSARIVPLRANLERLGAvNVVVTSYDGRRFP--QYNFDRALV 173
                                    8***************999769********************9988667777777777776..334554443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2261.09
//
Query:       gi|116753602|ref|YP_842720.1|  [L=160]
Description: hypothetical protein Mthe_0283 [Methanosaeta thermophila PT]
Scores for complete 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-13   48.5   0.0    2.6e-12   46.5   0.0    1.8  2  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 ?   -0.6   0.0     0.076   1.4e+03       3      15 ..      73      85 ..      71      86 .. 0.85
   2 !   46.5   0.0   1.5e-16   2.6e-12       1      50 []      87     136 ..      87     136 .. 0.98

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.076
                Methyltranf_PUA  3 rYlkGetielepd 15
                                   rY++++ i l+++
  gi|116753602|ref|YP_842720.1| 73 RYARKNVIDLDDE 85
                                   9******999975 PP

  == domain 2  score: 46.5 bits;  conditional E-value: 1.5e-16
                Methyltranf_PUA   1 alrYlkGetielepdlkkGwvlVcydgyplGwgKlvggrlKNkyPkglRr 50 
                                    a+r+++Ge++el  + ++G+v+V++ g ++G+g ++ grl++++P+++R+
  gi|116753602|ref|YP_842720.1|  87 ARRFFAGESLELRAPVERGYVVVTHMGSVIGCGLYTPGRLISQLPRERRI 136
                                    79**********************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1245.10
//
Query:       gi|116753603|ref|YP_842721.1|  [L=358]
Description: radical SAM domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-12   47.9   0.1    3.7e-12   46.9   0.1    1.5  1  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.9   0.1   2.1e-16   3.7e-12       1     165 [.      61     229 ..      61     231 .. 0.81

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 2.1e-16
                                    EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESS.TGGGS.TTHHHHHHHHHHTCCCTE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx.xxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilggg.eplly.pdfvellerlaklavpgi 78 
                                    +++t+ C +rC+fCa+++      +g++l+ eei++ +ke+ +  g+ e+ l gg  p l   d+ e+le l+ +  p +
  gi|116753603|ref|YP_842721.1|  61 INFTNICVGRCRFCAFRK-----SDGYILTHEEIVQRAKEA-EQLGATEICLQGGlAPGLTvEDYCEILEVLKSN-FPRM 133
                                    689**************6.....7*****************.9***66666555505544433444444444444.5777 PP

                                    EEEEEECSSCHG.........HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEE CS
                                    xxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  79 ritvetngtlpd.........eeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdr 148
                                    +++  ++  +            e l+ l++ g+d +  ++  +  + v+k ++  + + +e+   ++++++ gi+ ++++
  gi|116753603|ref|YP_842721.1| 134 HLHAYSPMEVMHmsrcsgvdvHEALRSLRDSGLDSMPGTAAELLVDSVRKVICpEKLSTSEWSFIIKAAHAMGIP-TTST 212
                                    777777777766777888778***********999999999999999******99999*****************.8999 PP

                                    EEEBTTTSHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxx RF
                    Radical_SAM 149 ivglpGendeeleelle 165
                                    ++ ++ e++e++  +le
  gi|116753603|ref|YP_842721.1| 213 MLYGHIESFEDRLSHLE 229
                                    99888899999877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        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 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 2500.68
//
Query:       gi|116753604|ref|YP_842722.1|  [L=646]
Description: aconitate hydratase [Methanosaeta thermophila PT]
Scores for 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-112  374.5   0.7   8.7e-110  367.9   0.7    2.4  1  Aconitase      Aconitase family (aconitate hydratase)
    3.3e-19   69.5   0.0    6.1e-19   68.6   0.0    1.4  1  Aconitase_C    Aconitase C-terminal domain
     0.0022   16.8   0.0     0.0032   16.2   0.0    1.2  1  DUF521         Protein of unknown function (DUF521)
     0.0056   16.3   0.0       0.01   15.5   0.0    1.5  1  Aconitase_2_N  Aconitate hydratase 2 N-terminus


Domain annotation for each model (and alignments):
>> Aconitase  Aconitase family (aconitate hydratase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  367.9   0.7  1.9e-113  8.7e-110       2     461 .]       8     407 ..       7     407 .. 0.91

  Alignments for each domain:
  == domain 1  score: 367.9 bits;  conditional E-value: 1.9e-113
                      Aconitase   2 kiwdahlvee.....egiayvpdrvllqdvtgvqalvdlaaareavrrlggtlatidhlvpvdlvidhsvgaeealeknl 76 
                                     i+++hlv+      ++i    d+ l+qd+tg +a  ++++++ +  +++ +++ +dh          +          +
  gi|116753604|ref|YP_842722.1|   8 RILRDHLVDGkyepgSEIGIRIDQTLTQDATGTMAYLQFESMGLEGIATELSVSYVDH----------NT---------I 68 
                                    6788888833344333355568************************555555555554..........44.........3 PP

                      Aconitase  77 edefernkeryefLksaakafgirvvppgqGIvHqvnlEyglalpgktvvgtDSHTtmigglGvlaiGvGgieaeavllg 156
                                    +  fe+ +   + L+s+a+++gi +  pg+GI+Hqv lE  +  pgkt++g+DSHT++ gglG++aiG Gg +++ ++ g
  gi|116753604|ref|YP_842722.1|  69 QVGFEN-ADDHRYLQSVAERYGIYFSRPGNGICHQVHLER-FGRPGKTLLGSDSHTPTGGGLGMIAIGAGGLDVAVAMGG 146
                                    334444.5667899**************************.*************************************** PP

                      Aconitase 157 qplelkipkvvgvkltGklkegvtakDlvlavigklrkkgvvgkvvEffGegvesLsledraTiaNMaaEvGAttglfpv 236
                                     p++l++pkv++v+ltG+l+++vt+kD++l+v ++l++kg  g v E++G+gv+ L++ draTi+NM+aE+G tt++fp 
  gi|116753604|ref|YP_842722.1| 147 GPYYLTAPKVMEVHLTGELQPWVTPKDVILKVLQILTTKGNIGWVCEYTGDGVAGLTVPDRATITNMGAETGVTTSIFPS 226
                                    ******************************************************************************** PP

                      Aconitase 237 dektleYLkatgreeaavlveaydkaqalfelaadedaeydkvleldlstlepsvagpkrPqdavplselvkkefkeele 316
                                    de+t ++L+a+gr+e+             + la d+da+ydk +e+dls+lep va p++P +++pls+ v         
  gi|116753604|ref|YP_842722.1| 227 DEQTRRFLAAQGRAEHW------------VPLAPDRDATYDKSIEIDLSELEPLVAAPHSPGNVIPLSRVV--------- 285
                                    *********99994333............25889*********************************5555......... PP

                      Aconitase 317 keaaekaleyklkegtklkdgkvdiaaigSCTNssnedvraaagllakavekglkvkpgvktsvaPGSevvkayleaeGl 396
                                                        ++vd++++gSCTNss+ d++ +a++++     g++  p+v++ vaPGS++v + + ++G 
  gi|116753604|ref|YP_842722.1| 286 -------------------GTPVDQVLVGSCTNSSYTDMMTVASMVK-----GKHLPPNVSFGVAPGSRQVLRMMARSGA 341
                                    ...................34699***********************.....**************************** PP

                      Aconitase 397 leiLekaGfevvgagCstCignsdrleegeaivsssNRNFegRqg.pntrayLaSPelvvaaAlaG 461
                                    l++L + G+ +++++C+ Cigns    ++ +++ +sNRNF+gR g p+++ yL+SP +++aaA++G
  gi|116753604|ref|YP_842722.1| 342 LDDLIAFGARILESACGFCIGNSMSPGTDAVSIRTSNRNFKGRSGtPSANVYLTSPVVAAAAAIKG 407
                                    *************************88999**************9566777*************98 PP

>> Aconitase_C  Aconitase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.6   0.0   1.4e-22   6.1e-19      60     130 ..     511     581 ..     469     582 .. 0.84

  Alignments for each domain:
  == domain 1  score: 68.6 bits;  conditional E-value: 1.4e-22
                                    EEHHHHHHHHHHTT--EEEE--SSBTBS---THHHHHHHHTTEEEEEES-B-HHHHHHHHHTT-EEEEEST CS
                    Aconitase_C  60 edvvdaaerykkegaklvviagknfGeGSSRehAAkalrllGikaviaeSFerIfennliknglLplefke 130
                                    +++   a + +++g +  ++ag  +G+GSSRehAA+ +  lG+kav+a+S erI+  nl++ g+Lpl f +
  gi|116753604|ref|YP_842722.1| 511 PEFSRRAAELRDKGLHNFIVAGVSYGQGSSREHAAMCPMYLGVKAVVAKSIERIHAANLVNFGILPLYFVR 581
                                    4788888899999999999************************************************9865 PP

>> DUF521  Protein of unknown function (DUF521)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   7.2e-07    0.0032     289     363 ..     287     365 ..     254     379 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.2e-07
                         DUF521 289 ekvdlvalG.cPhlsleElrelaellkgkkkkvkvelwvt.tsrevkeeaerlglveklekaGvkvlsdtCmvv..spl 363
                                    ++vd v++G c   s+ +++++a+++kgk+  ++v + v   sr+v +++ r+g ++ l ++G+++l++ C ++  + +
  gi|116753604|ref|YP_842722.1| 287 TPVDQVLVGsCTNSSYTDMMTVASMVKGKHLPPNVSFGVApGSRQVLRMMARSGALDDLIAFGARILESACGFCigNSM 365
                                    567888887688999**********************98835899**************************66555444 PP

>> Aconitase_2_N  Aconitate hydratase 2 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.3e-06      0.01       2      73 ..     472     545 ..     471     607 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.3e-06
                                    EEEEEEEEEEHHHHS-GGGG.GGTTSHHHHHCCTT-S-BTTSHHHHHHHHTTSS-EEEEEEE.EEES---THHH CS
                  Aconitase_2_N   2 tvfkveGetntDdlsPasdA.wsRsDiplHakamlkkkaeeelkaieelkkkgvplayvgdv.vGtGssRksav 73 
                                    + +kve ++ tD + Pa      Rs++p +++ ++++  +e  ++ +el++kg++   v +v  G GssR  a 
  gi|116753604|ref|YP_842722.1| 472 VAIKVEDNITTDHIMPAGSRlKYRSNVPKYSTFVFEPLDPEFSRRAAELRDKGLHNFIVAGVsYGQGSSREHAA 545
                                    5689************9765167*****************************987655555538******9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (646 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:01.59
# Mc/sec: 1233.49
//
Query:       gi|116753605|ref|YP_842723.1|  [L=132]
Description: hypothetical protein Mthe_0286 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-19   69.4   0.1    3.4e-19   69.0   0.1    1.2  1  4HBT      Thioesterase superfamily
    6.1e-12   45.8   0.0    8.1e-12   45.4   0.0    1.1  1  DUF4442   Domain of unknown function (DUF4442)
    8.9e-10   39.2   0.1      1e-09   39.0   0.1    1.1  1  4HBT_3    Thioesterase-like superfamily


Domain annotation for each model (and alignments):
>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.0   0.1   5.7e-23   3.4e-19       1      77 [.      41     114 ..      41     116 .. 0.97

  Alignments for each domain:
  == domain 1  score: 69.0 bits;  conditional E-value: 5.7e-23
                                    TSSB-HHHHHHHHHHHHHHHHHHTTSTTEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEETTSCE CS
                           4HBT   1 gGvvhgGvylallDeaagaalrslggrgilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrdedgrl 77 
                                    +G+vhgG++++l+D+a gaa++s+g    ++v+++ ++d+lrp+ ++++l++ear +   r++ ++ +evr+++g+l
  gi|116753605|ref|YP_842723.1|  41 FGTVHGGAIFSLIDQAFGAAANSHGA---VAVAISVTVDYLRPASPDETLYAEAREVSRTRRISTYNIEVRNQEGQL 114
                                    79***********************7...9********************************************987 PP

>> DUF4442  Domain of unknown function (DUF4442)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   0.0   1.4e-15   8.1e-12      13     121 ..       9     113 ..       4     122 .. 0.85

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 1.4e-15
                                    SGGGGGG--EEEEEETTEEEEEE---GGGB-TTSSB-HHHHHHHHHHHHHHHHHHHS-TTEEEEEEEEEEEE-S---S-E CS
                        DUF4442  13 aPYfgtvgprieelepgraevrlkkrrrvrNhigtvHAiAicnlaElamGllaeatlpdthrwipkgmevdYlakatgdl 92 
                                     P+ + +g+r  el+ g+ +v ++  +++rN +gtvH++Ai++l + a+G+ a+    ++++ +  +++vdYl++a  d 
  gi|116753605|ref|YP_842723.1|   9 QPFARRLGMRLVELDEGYSKVVMEPSWENRNFFGTVHGGAIFSLIDQAFGAAANS---HGAVAVAISVTVDYLRPASPDE 85 
                                    599999********************************************98764...788999999**********999 PP

                                    EEEEE-TTS-TT--EEEEEEEEEEETTE. CS
                        DUF4442  93 tavaelepedvgekeelvvevevrdekge 121
                                    t  ae+ +  ++++   + ++evr+++g+
  gi|116753605|ref|YP_842723.1|  86 TLYAEAREVSRTRR-ISTYNIEVRNQEGQ 113
                                    99999998777643.34455556666665 PP

>> 4HBT_3  Thioesterase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.1   1.7e-13     1e-09       3      87 ..      33     126 ..      31     131 .. 0.80

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 1.7e-13
                                    GGGECTTC....-HHHHHHHHHHHHHHT......-S.SS.EEEEEEE-S---SE.EEEEEEEEEE--SS-EEEEEEEE.E CS
                         4HBT_3   3 ppwtpgga..g.yGGyvlAlalraaqrtv.....pdprl.hslhvyFlrpgdag.pviyhvervrdGrsfstrtvels.q 71 
                                    p+w +       +GG++ +l+ +a  ++          +  s++v++lrp++++  +  ++++v ++r++st+ +e++ q
  gi|116753605|ref|YP_842723.1|  33 PSWENRNFfgTvHGGAIFSLIDQAFGAAAnshgaV--AVaISVTVDYLRPASPDeTLYAEAREVSRTRRISTYNIEVRnQ 110
                                    677777444334********999999887544321..2366************************************626 PP

                                    TTEEEEEEEEEEE--- CS
                         4HBT_3  72 ggrpiftatasfgrae 87 
                                    +g+  +t++a   r++
  gi|116753605|ref|YP_842723.1| 111 EGQLKATCLAMAYRRD 126
                                    6***999999877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); 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: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 942.94
//
Query:       gi|116753606|ref|YP_842724.1|  [L=470]
Description: acetyl-CoA decarbonylase/synthase complex subunit gamma [Methanosaeta thermophila PT]
Scores for 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-128  427.1   0.1   6.1e-128  426.8   0.1    1.1  1  CdhD         CO dehydrogenase/acetyl-CoA synthase delta subun
      3e-15   55.6   1.7    5.8e-15   54.7   1.7    1.5  1  FeS          Putative Fe-S cluster
  ------ inclusion threshold ------
      0.023   14.4   0.1        1.6    8.4   0.0    2.2  2  Pterin_bind  Pterin binding enzyme


Domain annotation for each model (and alignments):
>> CdhD  CO dehydrogenase/acetyl-CoA synthase delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  426.8   0.1    1e-131  6.1e-128       2     385 ..      70     462 ..      69     463 .. 0.97

  Alignments for each domain:
  == domain 1  score: 426.8 bits;  conditional E-value: 1e-131
                                    EEESSGCG-EEEE----SSTTTS---S--EEEEEEESSS-HHHHHHHHHHHTT-EEE....ETTEEEE--EEEEE--SSS CS
                           CdhD   2 vvlGaeekavkiGgeevLyrfeltffnptaiaidvsDelseellkalaerieevvddwakkrvgekltldaiairlistd 81 
                                    v +G++ek+ k+Gge+v+yr++ tffn++ +a+dv D+++e    al+er++++   w+k+++g+   +++ia+r +s+d
  gi|116753606|ref|YP_842724.1|  70 VYVGTGEKEQKVGGEDVMYRHQMTFFNKPPFAYDVTDTMEE---AALVERVKKIST-WKKFYIGKWERVEMIAVRSTSGD 145
                                    789**********************************9998...5***********.********99************* PP

                                    T.HHHHHHHHHHHCC--SEEEEE-SSHHHHHHHHTTTCCC--EEEEE-TTTHHHHHHHHHHTT--EEEE-.SSHHHHHHH CS
                           CdhD  82 PakkfakavekvakavkvplvlggsdpevlkaalevvederpllyaAtkddykeiaelaleykvpvvllsindleelkel 161
                                    P +kfa+ v+kv++ ++ p++l+++dp+vl+a+lev++  rpl+yaA+kd+++e+a+l  e++vpvvl++  dl+ lk++
  gi|116753606|ref|YP_842724.1| 146 P-AKFAACVKKVMETTDYPMILCSFDPKVLRAGLEVAAKTRPLVYAANKDNWQEVAKLVHEFNVPVVLSVPFDLDGLKSM 224
                                    *.****************************************************************************** PP

                                    HHHHHCTT---EEEE---SH.....HHHHHHHHHHHHHHHHS.-TTS-S-BEEE---SSHHHHHHHHH...........H CS
                           CdhD 162 arkllkagvkdivldPttaalGegleetidnvvriRraaikg.dkdlafPilslttnawlaresdeve...........l 229
                                    a ++ ++g++d++ld +ta+ G+ l+e+++n++++Rraa+++  kd+a+P ++l++naw +  +d v+           +
  gi|116753606|ref|YP_842724.1| 225 ALTFEQMGIHDLILDFGTAPNGKKLQESLHNLLKLRRAALEEgQKDIAYPTIALPINAWFTT-KDPVRaaywesvltatF 303
                                    *****************************************99******************6.88888899999999*** PP

                                    HHTT-SEEEES---HHHHHHHHHHHHHHTS-SSS--B--SSEEEESS--TTS-EEEEESBHHHHHHHHHHHHHTTS-EEE CS
                           CdhD 230 vvrYadililrslekeellPvltlrqniYtDPrkPvavdpglyeigdrdensPvflttnfsLtyYtvegdlesdkitayL 309
                                    v+r a+i+i + +e + ++P ++lr niYtDPr Pv+v+pg+y++g++ e+sPvf+ttnf+LtyYtve+d+ s++i ay+
  gi|116753606|ref|YP_842724.1| 304 VIRGASIMIKHCIEPHCVMPDMHLRYNIYTDPRRPVQVKPGIYKVGNPTEESPVFVTTNFALTYYTVESDVASNNIDAYI 383
                                    ******************************************************************************** PP

                                    EEE-SSS--HHHHHHTTSSSHHHHHHHHHHTTHH.HHSSS-EEEE-GGGGGGHHHHHHHHTSEE..EE--SSGGGHHHH CS
                           CdhD 310 LvldteGlgvevslaggqleaekvkdlieetgie.ekvkhrflilPglvavlkgkiedltgwkv..lvgprdsseivav 385
                                    ++++t+G+gv++s+aggql+ +k+ ++++e++++  k+k   ++lPg++a+ +g++edl+g kv  lvgp+ds++iv++
  gi|116753606|ref|YP_842724.1| 384 MSINTDGIGVQASVAGGQLNPQKIVEAFKEADFDfTKMKYPSIVLPGMAAKFSGELEDLFGGKVkiLVGPEDSGRIVEW 462
                                    **********************************6689***********************9873369********998 PP

>> FeS  Putative Fe-S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.7   1.7   9.6e-19   5.8e-15       1      33 []      13      45 ..      13      45 .. 0.99

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 9.6e-19
                            FeS  1 LPgtNCgaCGypgCmafAealvegeaqledCpp 33
                                   LP+tNCg+CG+++CmafA+al+  ++++e+C+p
  gi|116753606|ref|YP_842724.1| 13 LPQTNCGKCGFQTCMAFAAALIDRSKRVEECTP 45
                                   9******************************98 PP

>> Pterin_bind  Pterin binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0   0.00026       1.6      54     122 ..     142     212 ..     133     215 .. 0.84
   2 ?    3.8   0.0    0.0066        39     151     192 ..     222     262 ..     218     279 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00026
                                    HHHHHHHHHHHHHHHHHHCTSEEEEE-S-HHHHHHHHHT...TSEEEEETTTTSSSTTHHHHHHHHT-EEEE CS
                    Pterin_bind  54 eeeelervvpvlealrdeadvpisiDttkaevaeaAlka...gadivNdvsgeerdpkmlelvaeagaavvv 122
                                       + ++++  ++++ +++d p+ + +++++v++a+l++    + +v   +  +  +++++lv e++++vv+
  gi|116753606|ref|YP_842724.1| 142 TSGDPAKFAACVKKVMETTDYPMILCSFDPKVLRAGLEVaakTRPLVYAANKDN-WQEVAKLVHEFNVPVVL 212
                                    55667889999******99*******************9654446676666666.99*************98 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.0066
                                    HHHHHHHHHTT--GGGEEEETTTTS.STTHHHHHHHHHTHHHH CS
                    Pterin_bind 151 earveaaeeaGvaperillDpgigf.gkteehnlellrrldel 192
                                    ++++  +e++G+++  ++lD g+ + gk+ +++l+ l +l + 
  gi|116753606|ref|YP_842724.1| 222 KSMALTFEQMGIHD--LILDFGTAPnGKKLQESLHNLLKLRRA 262
                                    667778999***76..*********999999999888777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (470 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 3505.74
//
Query:       gi|116753607|ref|YP_842725.1|  [L=452]
Description: acetyl-CoA decarbonylase/synthase complex subunit delta [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      1e-82  277.9   0.3      1e-77  261.5   0.0    3.2  2  CdhD         CO dehydrogenase/acetyl-CoA synthase delta subun
     0.0041   16.8   0.1      0.064   12.9   0.1    2.3  1  Pterin_bind  Pterin binding enzyme
  ------ inclusion threshold ------
      0.053   11.7   0.0       0.09   10.9   0.0    1.3  1  HSP70        Hsp70 protein


Domain annotation for each model (and alignments):
>> CdhD  CO dehydrogenase/acetyl-CoA synthase delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  261.5   0.0   1.7e-81     1e-77       1     228 [.     129     380 ..     129     414 .. 0.94
   2 !    7.0   0.1   0.00034         2     350     383 ..     415     449 ..     411     452 .] 0.86

  Alignments for each domain:
  == domain 1  score: 261.5 bits;  conditional E-value: 1.7e-81
                                    EEEESS.......GCG-EEEE----S.STTTS---S--EEEEEEESSS-HHHHHHHHHHHTT-EEE.......ETTEEEE CS
                           CdhD   1 evvlGa.......eekavkiGgeevL.yrfeltffnptaiaidvsDelseellkalaerieevvdd...wakkrvgeklt 69 
                                    ev+lGa       +++++kiGge++L + +++++++++++++dv+D++  + +ka+++++e+v +d   wakk+v + ++
  gi|116753607|ref|YP_842725.1| 129 EVTLGAtkadggsRGHTIKIGGEKALpFFYDAPMPHRPVVTMDVFDMPI-GMAKAVKMHYEDVINDpgeWAKKAVTK-FG 206
                                    677777777777799***********666*****************888.68*************************.** PP

                                    --EEEEE--SSST.......HHHHHHHHHHHCC--SEEEEE-S.....SHHHHHHHHTTTCCC--EEEEE-TT.THHHHH CS
                           CdhD  70 ldaiairlistdP......akkfakavekvakavkvplvlggs.....dpevlkaalevvederpllyaAtkd.dykeia 137
                                    +d+++i+listdP      ++++ak+ve+v++av+vp+++ggs     dpevlkaa+ev+++er l+++A+++ d+++i 
  gi|116753607|ref|YP_842725.1| 207 ADLVTIHLISTDPllkdtpPREAAKTVEEVLQAVDVPICIGGSgnpdkDPEVLKAAAEVAQGERALIASANLNmDWEKIG 286
                                    ******************************************************************************** PP

                                    HHHHHTT--EEEE-.SSHHHHHHHHHHHHC.TT-..--EEEE---SH.....HHHHHHHHHHHHHHHHS-TTS-S-BEEE CS
                           CdhD 138 elaleykvpvvllsindleelkelarkllk.agv..kdivldPttaalGegleetidnvvriRraaikgdkdlafPilsl 214
                                    ++ +++++  +++++ +++++kel+rkl+k agv  ++iv+dPttaal +gl+++++n++riR+ a+kgd++l+fP++s+
  gi|116753607|ref|YP_842725.1| 287 RACVDNGHVCLAWTQLEINSQKELNRKLMKvAGVprESIVMDPTTAALAYGLDFAYTNMERIRLGALKGDEELTFPMSSG 366
                                    ******************************9999********************************************** PP

                                    ---SSHHHHHHHHH CS
                           CdhD 215 ttnawlaresdeve 228
                                    ttnaw++re+++v+
  gi|116753607|ref|YP_842725.1| 367 TTNAWGVREAWMVR 380
                                    ************97 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00034
                                    EEEE.-GGGGGGHHHHHHHHTSEEEE--SSGGGHH CS
                           CdhD 350 flil.Pglvavlkgkiedltgwkvlvgprdsseiv 383
                                    f+++ P +va l++++++l+g   ++ p+ +++++
  gi|116753607|ref|YP_842725.1| 415 FMMMhPLAVAYLQEITQTLMGLIDAETPDITNWVK 449
                                    89999****************99998888888776 PP

>> Pterin_bind  Pterin binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.1   1.1e-05     0.064      26     173 ..     197     331 ..     183     350 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.1e-05
                                    HHHHHHHT.T-SEEEEESS-TSTT--CCHHHHHHHHHHHHHHHHHHHCTSEEEEE-S.....-HHHHHHHHHT..TS.EE CS
                    Pterin_bind  26 qarkmvee.GAdilDiggestrPgaervdeeeelervvpvlealrdeadvpisiDtt.....kaevaeaAlka..ga.di 96 
                                    +a+k v++ GAd++ i   st P  +  +++e+ + v +vl+     +dvpi+i  +     ++ev++aA ++  g  ++
  gi|116753607|ref|YP_842725.1| 197 WAKKAVTKfGADLVTIHLISTDPLLKDTPPREAAKTVEEVLQ----AVDVPICIGGSgnpdkDPEVLKAAAEVaqGErAL 272
                                    666665544*********************************....779*****87644444799*****999995449* PP

                                    EEETTTTSSSTTHHHHHHHHT-EEEEESECSSTTTHCCCCCCCSSHHHHHHHHHHHHHHHHHHTT--GGGEEEETTT CS
                    Pterin_bind  97 vNdvsgeerdpkmlelvaeagaavvvmhmrgtpktmqeeegqyedvveeveaflearveaaeeaGvaperillDpgi 173
                                    + + ++ ++ +k+ + ++++g   v++++          +        e++++ e  ++ ++ aGv++e i++Dp +
  gi|116753607|ref|YP_842725.1| 273 IASANLNMDWEKIGRACVDNGH--VCLAWT---------Q-------LEINSQKELNRKLMKVAGVPRESIVMDPTT 331
                                    ********99999999998874..444444.........2.......357777777777788888888888888865 PP

>> HSP70  Hsp70 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   1.5e-05      0.09     156     180 ..     315     339 ..     305     349 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 1.5e-05
                                    HHHTTXEEEEEEEHHHHHHHHHHTC CS
                          HSP70 156 gkiAGLnvlRivNepTAaalaYGld 180
                                     k+AG+    iv +pT aalaYGld
  gi|116753607|ref|YP_842725.1| 315 MKVAGVPRESIVMDPTTAALAYGLD 339
                                    689*********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.23s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 3461.18
//
Query:       gi|116753608|ref|YP_842726.1|  [L=253]
Description: cobyrinic acid a,c-diamide synthase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-19   70.9   0.1    1.3e-19   70.5   0.1    1.1  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    5.1e-14   52.6   0.0    1.3e-13   51.2   0.0    1.7  1  AAA_31           AAA domain
    2.1e-10   40.3   1.5    3.2e-09   36.4   0.3    2.5  2  ArsA_ATPase      Anion-transporting ATPase
    7.8e-07   28.8   0.1     0.0017   17.9   0.0    2.2  2  Fer4_NifH        4Fe-4S iron sulfur cluster binding proteins,
    1.9e-06   27.7   0.0    3.5e-06   26.9   0.0    1.4  1  AAA_24           AAA domain
    7.5e-06   25.6   0.0    0.00034   20.2   0.0    2.1  2  CBP_BcsQ         Cellulose biosynthesis protein BcsQ
    4.7e-05   23.0   0.2    0.00019   21.0   0.2    2.0  1  ParA             NUBPL iron-transfer P-loop NTPase
    7.5e-05   22.9   0.4    0.00018   21.7   0.4    1.9  1  DUF87            Helicase HerA, central domain
    0.00018   22.0   0.0    0.00038   20.9   0.0    1.3  1  AAA_16           AAA ATPase domain
    0.00025   20.9   1.3       0.17   11.7   0.3    2.5  2  AAA_26           AAA domain
    0.00077   19.1   0.2      0.082   12.5   0.1    2.3  2  SRP54            SRP54-type protein, GTPase domain
     0.0019   18.1   0.4       0.85    9.5   0.2    2.3  2  NTPase_1         NTPase
     0.0027   17.6   0.0      0.005   16.7   0.0    1.5  1  APS_kinase       Adenylylsulphate kinase
     0.0035   17.4   0.0     0.0063   16.5   0.0    1.4  1  ResIII           Type III restriction enzyme, res subunit
     0.0039   16.9   0.0     0.0057   16.4   0.0    1.3  1  AAA_30           AAA domain
     0.0093   15.0   0.3      0.017   14.1   0.3    1.5  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
  ------ inclusion threshold ------
      0.011   16.0   0.1      0.042   14.1   0.1    2.1  2  AAA_22           AAA domain
      0.015   15.1   0.0      0.028   14.2   0.0    1.4  1  CLP1_P           mRNA cleavage and polyadenylation factor CLP
      0.015   14.5   0.0      0.027   13.7   0.0    1.5  1  DUF2075          Uncharacterized conserved protein (DUF2075)
       0.02   15.4   0.0      0.092   13.3   0.0    2.0  2  AAA_18           AAA domain
      0.028   14.1   0.1       0.89    9.2   0.0    2.6  3  Thymidylate_kin  Thymidylate kinase
       0.03   14.2   0.1       0.14   12.0   0.0    2.1  3  Helicase_RecD    Helicase
      0.032   13.5   0.6        1.5    8.1   0.1    2.2  2  MipZ             ATPase MipZ
      0.033   13.5   0.0      0.075   12.4   0.0    1.7  2  ATPase           KaiC
      0.076   12.1   0.3       0.13   11.4   0.3    1.3  1  LpxK             Tetraacyldisaccharide-1-P 4'-kinase
      0.079   12.4   0.2       0.25   10.8   0.0    1.9  2  RecA             recA bacterial DNA recombination protein
      0.097   11.8   0.1       0.18   11.0   0.1    1.6  1  NB-ARC           NB-ARC domain
      0.097   12.2   0.0       0.15   11.6   0.0    1.4  1  AAA_25           AAA domain
       0.11   12.8   0.0       0.21   11.9   0.0    1.6  1  AAA_19           AAA domain
       0.12   12.1   0.0        0.2   11.4   0.0    1.4  1  PRK              Phosphoribulokinase / Uridine kinase family


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 !   70.5   0.1   2.2e-22   1.3e-19       2     126 ..       5     228 ..       4     230 .. 0.91

  Alignments for each domain:
  == domain 1  score: 70.5 bits;  conditional E-value: 2.2e-22
                                    EEEESSTTSSHHHHHHHHHHHHHH..TT--EEEEEEEESSCCCCHHTTEB-HHHH......................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................... RF
                           CbiA   2 aiastkGGvGKTtlaanLaralar..rglrVllvDaDpqannlaileglendiep......................... 54 
                                    +++ +kGG+GKT +aa L r+l +  r++rVl++DaDp++n++  + g+e  +                           
  gi|116753608|ref|YP_842726.1|   5 IAITGKGGTGKTAVAALLVRYLIKsgRKYRVLVIDADPDSNLAD-ALGVEVTKTVgdmrefmqearyttppetdkerlfe 83 
                                    6789******************997779*************999.555555555567777******************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                           CbiA  55 ................................................................................ 54 
                                                                                                                    
  gi|116753608|ref|YP_842726.1|  84 akifeilveengydllvmgkpegsgcycfvnnllrgimdrlidqyditiidtaaglehfsrkvipdldslivvtdssrrg 163
                                    ******************************************************************************** PP

                                    ..CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS CS
                                    ..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA  55 ..dlkrllellealgkkkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeaparge 126
                                      + +r+ el+++lg k     + + v++n+v ++n +++++e+ + +     ++v+g ip+de++a  +  g+
  gi|116753608|ref|YP_842726.1| 164 ltTGERIRELASELGLK----YNNLYVIANKVTENN-KEKIIENARSV----SLNVIGTIPYDERLANFDLVGD 228
                                    *9999999*******99....568********9985.66666766666....9************998776665 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.2   0.0   2.2e-16   1.3e-13       2     162 ..       3     172 ..       2     187 .. 0.72

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 2.2e-16
                         AAA_31   2 kvIaianqKGGvGKTTtsvnlaaalaklgkk..vLlvDlDpQanattglgiekneiektlyevlieeknikeaiiktkve 79 
                                    +vIai+  KGG GKT+ +  l   l k+g k  vL++D+Dp +n++ +lg+e +++  ++ e +  e+++        ++
  gi|116753608|ref|YP_842726.1|   3 RVIAIT-GKGGTGKTAVAALLVRYLIKSGRKyrVLVIDADPDSNLADALGVEVTKTVGDMREFMQ-EARYTTPPE---TD 77 
                                    788875.6*****************98875433*****************976666666666643.333322222...22 PP

                         AAA_31  80 nldlipssid...Laeaeielvelekk.........eeilkellekvkdeYDyiiiDcpPsLglltenaLvasdsviipv 147
                                    +  l  ++i    + e   +l+ + k          ++ l+ +++++ d+YD+ iiD+   L+ + ++ +   ds+i+++
  gi|116753608|ref|YP_842726.1|  78 KERLFEAKIFeilVEENGYDLLVMGKPegsgcycfvNNLLRGIMDRLIDQYDITIIDTAAGLEHFSRKVIPDLDSLIVVT 157
                                    3344444332110333334444444444478888877779**************************************** PP

                         AAA_31 148 qaeayaleGleqllk 162
                                    +++ + l + e++ +
  gi|116753608|ref|YP_842726.1| 158 DSSRRGLTTGERIRE 172
                                    998888776666555 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.3   5.4e-12   3.2e-09       2      59 ..       3      62 ..       2     142 .. 0.82
   2 ?    2.8   0.2      0.09        54     204     271 ..     148     214 ..     115     233 .. 0.73

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 5.4e-12
                                   EEEEEEESTTSSHHHHHHHHHHHHHHTT..S-EEEEE-STTTHHHHHHTS--BSS-EEET CS
                    ArsA_ATPase  2 kvilvgGKGGVGKttvsaatavklsekg..kkvllistDPAhslsDsfdqklgkeptkvk 59
                                   +vi ++GKGG GKt+v+a +  +l ++g  ++vl+i  DP  +l+D++  +++k++  ++
  gi|116753608|ref|YP_842726.1|  3 RVIAITGKGGTGKTAVAALLVRYLIKSGrkYRVLVIDADPDSNLADALGVEVTKTVGDMR 62
                                   799**************999999866651167*******************999876665 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.09
                                    TTTEEEEEEEESSHHHHHHHHHHHHHHHHTT-EEEE..EEEEEE-TTCSSSTSHHHHHHHHHHHHHHHHH CS
                    ArsA_ATPase 204 pertsfrlVvipEklslkEteRaikeLkkygikvda..vivNkllpeeeqenCeflearkkiqkkylkei 271
                                    p+  s+++V+ + +  l   eR  +  +++g+k ++  vi Nk+ +++++   +++e+ +++  +++  i
  gi|116753608|ref|YP_842726.1| 148 PDLDSLIVVTDSSRRGLTTGERIRELASELGLKYNNlyVIANKVTENNKE---KIIENARSVSLNVIGTI 214
                                    45567888888888888888888888888888888644688888766666...67777777777666665 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   2.8e-06    0.0017       1      58 [.       3      61 ..       3     109 .. 0.85
   2 !    9.3   0.0    0.0012      0.71     179     233 ..     186     239 ..     150     250 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.8e-06
                      Fer4_NifH  1 rkiaiyGkGGiGksttsqnlsaalaemgkk..vlivGCDPkaDstrlllggkaqetvldt 58
                                   r iai GkGG Gk+  ++ l+  l + g+k  vl++  DP ++ +   lg  +++tv d+
  gi|116753608|ref|YP_842726.1|  3 RVIAITGKGGTGKTAVAALLVRYLIKSGRKyrVLVIDADPDSNLA-DALGVEVTKTVGDM 61
                                   569************************974449*******88766.45666666666555 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0012
                      Fer4_NifH 179 liinsrkvddereliekfaeelgtkvlevvPrdeivrkaelrkktvieyapeseq 233
                                    +i n + +++++e i + a++++++v+ ++P de + + +l    +i+  ++++ 
  gi|116753608|ref|YP_842726.1| 186 VIAN-KVTENNKEKIIENARSVSLNVIGTIPYDERLANFDLVGDPLINLPDDAPS 239
                                    4566.7789999**********************999888877777776666555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   5.9e-09   3.5e-06       2      80 ..       2     142 ..       1     158 [. 0.89

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 5.9e-09
                         AAA_24   2 klkiliyGpsgiGKTtlakel.........gpkplfidtekGlksldadkfpdieswedfldevvel............. 59 
                                    ++ i+i+G+ g+GKT +a+ l         ++++l+id +  ++  da  ++  +++ d++++++e              
  gi|116753608|ref|YP_842726.1|   2 GRVIAITGKGGTGKTAVAALLvryliksgrKYRVLVIDADPDSNLADALGVEVTKTVGDMREFMQEAryttppetdkerl 81 
                                    678**************************************77666666666666999999999999999********** PP

                         AAA_24  60 ........................................aaeladyktlviDtideleel 80 
                                                                            ++  ++y++ +iDt+  le +
  gi|116753608|ref|YP_842726.1|  82 feakifeilveengydllvmgkpegsgcycfvnnllrgimDRLIDQYDITIIDTAAGLEHF 142
                                    ********99999999999999999999999999999999999999999999999887665 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   5.7e-07   0.00034       3      66 ..       4      68 ..       2      76 .. 0.83
   2 ?    3.4   0.0     0.077        46     105     146 ..     117     158 ..      93     165 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 5.7e-07
                       CBP_BcsQ  3 vlalqGvRGGvGttsllaaLawalhelg..esvlviDlspdnlLrlhFnvdieqregwaraeldga 66
                                   v+a++G +GG+G+t+++a L + l + g  ++vlviD+ pd  L+    v+++++ g +r  +++a
  gi|116753608|ref|YP_842726.1|  4 VIAITG-KGGTGKTAVAALLVRYLIKSGrkYRVLVIDADPDSNLADALGVEVTKTVGDMREFMQEA 68
                                   678888.8****************87642279************9999999999888877666655 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.077
                       CBP_BcsQ 105 llaalkelkeqyrwillDlpagasaltrellaladlvllvve 146
                                    l   +++l  qy+  ++D  ag ++  r+++   d+ + v+ 
  gi|116753608|ref|YP_842726.1| 117 LRGIMDRLIDQYDITIIDTAAGLEHFSRKVIPDLDSLIVVTD 158
                                    555688999***********************8888888875 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 !   21.0   0.2   3.2e-07   0.00019       7     238 ..       5     243 ..       1     251 [. 0.62

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3.2e-07
                           ParA   7 avlSgKGGVGKStvavnlAlaLakkg..lkvgllDaD.......iyGpsiprllgveeekpeqsekkliPvea...kgik 74 
                                    + + gKGG GK+ va+ l   L k+g  ++v ++DaD         G  + + +g  +e  +q+++  +P e+   +  +
  gi|116753608|ref|YP_842726.1|   5 IAITGKGGTGKTAVAALLVRYLIKSGrkYRVLVIDADpdsnladALGVEVTKTVGDMRE-FMQEARYTTPPETdkeRLFE 83 
                                    3457******************9877225677888762222111455555555554443.55666567788875533356 PP

                           ParA  75 vmSigfllesedeavvwrGpmksk....aikqllkdve...wgelDyLiiDlPPGtgDeqltvaqklplagaviVttpqe 147
                                    +  +++l+e++   ++  G    +    ++++ll+ +     ++ D+ iiD+  G    +  v+   +l+  ++Vt   +
  gi|116753608|ref|YP_842726.1|  84 AKIFEILVEENGYDLLVMGKPEGSgcycFVNNLLRGIMdrlIDQYDITIIDTAAGLEHFSRKVIP--DLDSLIVVTDSSR 161
                                    66677888877777666654333211115555554433111567788888887666544444444..4578888888888 PP

                           ParA 148 valadvkkaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdegkplvl 227
                                      l+  ++  e+++++ +k      N  +++ +k +e+    +k++  + a++++++++g+ip d+++++    g+pl+ 
  gi|116753608|ref|YP_842726.1| 162 RGLTTGERIRELASELGLKY-----NNLYVIANKVTEN----NKEKIIENARSVSLNVIGTIPYDERLANFDLVGDPLIN 232
                                    88888888888888766654.....3344444444443....45666677888888888888888888887777777776 PP

                           ParA 228 kepeseaakal 238
                                      ++++  k++
  gi|116753608|ref|YP_842726.1| 233 LPDDAPSVKEI 243
                                    66565555554 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.4   2.9e-07   0.00018      26      62 ..       5      42 ..       1     219 [. 0.87

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.9e-07
                          DUF87 26 lAilgsTGsGKSntvavLleelle.kkgatililDpHG 62
                                   +Ai g+ G+GK+  +a+L++ l++  +++++l++D++ 
  gi|116753608|ref|YP_842726.1|  5 IAITGKGGTGKTAVAALLVRYLIKsGRKYRVLVIDADP 42
                                   8**********************988888******875 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   6.4e-07   0.00038      25      96 ..       3      69 ..       1      84 [. 0.84

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 6.4e-07
                         AAA_16 25 elvllsGesGvGKsslvrellralekd....ggiflrgkcdqlesaipysalaqalareellrqlldeaesaelea 96
                                   +++ ++G  G+GK++++  l r+l k+    +++++ ++ d++        la+al   e+ + ++d+ e  + ++
  gi|116753608|ref|YP_842726.1|  3 RVIAITGKGGTGKTAVAALLVRYLIKSgrkyRVLVIDADPDSN--------LADAL-GVEVTKTVGDMREFMQEAR 69
                                   6799***********************99977999********........99999.6688888888866655544 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0035       2.1      10      33 ..      11      34 ..       3      54 .. 0.85
   2 !   11.7   0.3   0.00028      0.17     160     196 ..     184     222 ..     116     223 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0035
                         AAA_26 10 tgvGKTvvslgLvralkrkgvkvg 33
                                    g GKT+v+++Lvr+l + g k +
  gi|116753608|ref|YP_842726.1| 11 GGTGKTAVAALLVRYLIKSGRKYR 34
                                   479*************98877755 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00028
                         AAA_26 160 lGvilNkvrnpenvetlekksgi..pvlGvvPylpdlea 196
                                    l vi+Nkv++ ++ + +e++ ++  +v+G++Py+++l +
  gi|116753608|ref|YP_842726.1| 184 LYVIANKVTENNKEKIIENARSVslNVIGTIPYDERLAN 222
                                    669****999988888888877555**********9975 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.1   0.00014     0.082       3      37 ..       4      40 ..       2      43 .. 0.81
   2 ?    4.7   0.0     0.035        21      81     116 ..     125     161 ..      99     209 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                                   EEEEEESTTSSHHHHHHHHHHHHHHT..TS-EEEEEE CS
                          SRP54  3 villvGlqGaGKTttlaKLaallkke..gkkvllvaa 37
                                   vi++ G  G+GKT  +a L ++l k+  +++vl++ a
  gi|116753608|ref|YP_842726.1|  4 VIAITGKGGTGKTAVAALLVRYLIKSgrKYRVLVIDA 40
                                   899**********************944444555544 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.035
                                    HTTSSEEEEEE-.-SSTTHHHHHHHHHHHHHHHSSSE CS
                          SRP54  81 eekidvvlvDTa.Grlqndkelmeelkkikkvvkpde 116
                                     +++d+ ++DTa G  +  ++++ +l+++  v+++ +
  gi|116753608|ref|YP_842726.1| 125 IDQYDITIIDTAaGLEHFSRKVIPDLDSLIVVTDSSR 161
                                    5689******954999999999999999888775554 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.2    0.0014      0.85       2      30 ..       5      33 ..       4      40 .. 0.90
   2 ?    6.5   0.0     0.012       7.1      87     165 ..     119     201 ..     102     203 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0014
                                   EEEE--TTSSHHHHHHHHHHHH...GGGE CS
                       NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkv 30
                                   ++iTG+ G+GKt +   +++ l +sg k+
  gi|116753608|ref|YP_842726.1|  5 IAITGKGGTGKTAVAALLVRYLIKSGRKY 33
                                   89******************999998775 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.012
                                    HHHHHHHHHH-EEEE---STTGGG-HHHHHHHHHHHT...TTSEEEEE--SS--SHHHHHHHT-TT...-EEEE--TTTT CS
                       NTPase_1  87 ealrkalseadviviDEiGkmElkskkfkeaveevLk...sekpvlavihrrkdlalveeirerkd...vkvfevteenr 160
                                     ++++ + + d+ +iD    +E +s+k++  ++ ++    s++  l++  r +  +l  e+  + +   v   +vte+n+
  gi|116753608|ref|YP_842726.1| 119 GIMDRLIDQYDITIIDTAAGLEHFSRKVIPDLDSLIVvtdSSRRGLTTGERIR--ELASELGLKYNnlyVIANKVTENNK 196
                                    4566777999********************99987633237777777777664..3444443322212133334888888 PP

                                    TTHHH CS
                       NTPase_1 161 dalle 165
                                    +++ e
  gi|116753608|ref|YP_842726.1| 197 EKIIE 201
                                    88766 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   8.4e-06     0.005       2      39 ..       2      39 ..       1      70 [. 0.78

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 8.4e-06
                                   -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHH CS
                     APS_kinase  2 gvvvwltGlsgsGKstianalekkLvekgisvylLdGd 39
                                   g v+ +tG  g+GK+++a  l ++L ++g++  +L  d
  gi|116753608|ref|YP_842726.1|  2 GRVIAITGKGGTGKTAVAALLVRYLIKSGRKYRVLVID 39
                                   67999***********************9766655333 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 !   16.5   0.0   1.1e-05    0.0063      29      60 ..       7      38 ..       3      93 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.1e-05
                                   EEESTTSTHHHHHHHHHHHH-S.....-EEEE CS
                         ResIII 29 ikmaTGtGKTlvaaklierllkkgkeekflfl 60
                                   i    GtGKT vaa l+++l k+g++ ++l++
  gi|116753608|ref|YP_842726.1|  7 ITGKGGTGKTAVAALLVRYLIKSGRKYRVLVI 38
                                   55667*******************99999998 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   9.5e-06    0.0057      19      73 ..       3      58 ..       1     100 [. 0.78

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 9.5e-06
                         AAA_30 19 rvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgi.easti 73
                                   rv ++tG  GtGKt + + l++ + ++g++  +l   +    +La++lg+  ++t+
  gi|116753608|ref|YP_842726.1|  3 RVIAITGKGGTGKTAVAALLVRYLIKSGRKYRVLVIDADPDSNLADALGVeVTKTV 58
                                   5889****************999999998888887777777788887777334444 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 !   14.1   0.3   2.8e-05     0.017      30      70 ..       3      45 ..       1      62 [. 0.82

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.8e-05
                                   EEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE..----- CS
                           MeaB 30 qvvGltGvPGaGkstlvealglelrrrGkrvavlav..DPssp 70
                                   +v+ +tG  G+Gk  +   l+  l++ G++  vl +  DP s+
  gi|116753608|ref|YP_842726.1|  3 RVIAITGKGGTGKTAVAALLVRYLIKSGRKYRVLVIdaDPDSN 45
                                   5899*********9999999*******9865555551167776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1     7e-05     0.042       6      56 ..       3      49 ..       2     162 .. 0.69
   2 ?   -0.9   0.0         3   1.8e+03      51      71 ..     162     192 ..     120     232 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7e-05
                         AAA_22  6 gilvvtGesGtGKTtllrrlleqldeeakaee.erpevvfvtlpsstsskdl 56
                                   +++++tG  GtGKT +++ l++ l     ++  ++ +v+ +++  +++++d 
  gi|116753608|ref|YP_842726.1|  3 RVIAITGKGGTGKTAVAALLVRYL-----IKSgRKYRVLVIDADPDSNLADA 49
                                   689******************988.....22245555555555555544433 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 3
                         AAA_22  51 t..sskdllrellralglelka........e 71 
                                       +  +  rel+++lgl+ ++         
  gi|116753608|ref|YP_842726.1| 162 RglTTGERIRELASELGLKYNNlyviankvT 192
                                    3455555566677777666655555544433 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 ?   14.2   0.0   4.7e-05     0.028       1      33 [.       9      43 ..       9      47 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.7e-05
                         CLP1_P  1 GpkdsGKSTlarlLlNyalrkgr..kpvyvDlDvG 33
                                   G+  +GK+++a+lL+ y++++gr  +++++D+D+ 
  gi|116753608|ref|YP_842726.1|  9 GKGGTGKTAVAALLVRYLIKSGRkyRVLVIDADPD 43
                                   66789****************9755899*****95 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.5e-05     0.027       2      36 ..       3      35 ..       2      85 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.5e-05
                        DUF2075  2 avvlVtGvaGtGKtvvllnllaeleddeeertavy 36
                                   +v+ +tG+ GtGKt v+  l+  l   +++r+  +
  gi|116753608|ref|YP_842726.1|  3 RVIAITGKGGTGKTAVAALLVRYLI--KSGRKYRV 35
                                   6899*****************9993..33333333 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   0.00015     0.092       1      37 [.       5      42 ..       5      81 .. 0.78
   2 ?   -0.6   0.0       3.1   1.9e+03      25      44 ..     167     186 ..     150     218 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00015
                         AAA_18  1 IlltGtpGvGKttlakeLskrl.gfgvnlrdvakengl 37
                                   I++tG+ G+GKt +a  L + l ++g+++r ++ + ++
  gi|116753608|ref|YP_842726.1|  5 IAITGKGGTGKTAVAALLVRYLiKSGRKYRVLVIDADP 42
                                   89****************99886666655555554444 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 3.1
                         AAA_18  25 gvnlrdvakenglllevdpe 44 
                                    g+++r++a+e gl + +   
  gi|116753608|ref|YP_842726.1| 167 GERIRELASELGLKYNNLYV 186
                                    77777777777777776666 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0    0.0015      0.89       3      27 ..       9      35 ..       7      64 .. 0.82
   2 ?    1.6   0.0      0.32   1.9e+02      38      86 ..     113     158 ..      84     162 .. 0.68
   3 ?   -0.6   0.0       1.5     9e+02      36     183 ..     164     197 ..     152     207 .. 0.51

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0015
                                   ESTTSSHHHHHHHHHHHHHHTTE...E CS
                Thymidylate_kin  3 GlDGaGKttqaellkerlkeegik..v 27
                                   G  G+GKt +a+ll+++l ++g+k  v
  gi|116753608|ref|YP_842726.1|  9 GKGGTGKTAVAALLVRYLIKSGRKyrV 35
                                   6679*****************998644 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.32
                                    HHHHHHHHHHTCS---HHHHHHHHHHHHHHTTHHHHHHHHHTT-EEEEE CS
                Thymidylate_kin  38 iGekirelllkeeeleeqteallfaadriehleekikpalkqgktvivd 86 
                                    + +++r+++   + ++++ + +  +a+  eh+++k++p+l++  +v++d
  gi|116753608|ref|YP_842726.1| 113 VNNLLRGIMD--RLIDQYDITIIDTAAGLEHFSRKVIPDLDS-LIVVTD 158
                                    4456666644..677777788888999999999999999998.677766 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.5
                                    SHHHHHHHHHHHTCS---HHHHHHHHHHHHHHTTHHHHHHHHHTT-EEEEES-HHHHHHHHHTTTTTTCHHHHHHGGGTT CS
                Thymidylate_kin  36 teiGekirelllkeeeleeqteallfaadriehleekikpalkqgktvivdRylfSslaYqgakegvdldlvlslnedvl 115
                                     ++Ge irel +                                                                    
  gi|116753608|ref|YP_842726.1| 164 LTTGERIRELAS-------------------------------------------------------------------- 175
                                    455566665544.................................................................... PP

                                    SE-SEEEEEESSHHHHHTSCCTTSSTTTSHHHHHHHHHHHHHHHHHHHHTTSTEEEEETTS-HHHHHH CS
                Thymidylate_kin 116 lkPdltflldvdpevalkRlakrdeldeeeeeqldflrkvrerylelakederiliidasksieevhe 183
                                                                                 el  + +++++i a+k +e+ +e
  gi|116753608|ref|YP_842726.1| 176 ---------------------------------------------ELGLKYNNLYVI-ANKVTENNKE 197
                                    .............................................333222222333.3333333333 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00023      0.14       2      34 ..       7      40 ..       6     101 .. 0.82
   2 ?   -0.9   0.0       2.2   1.3e+03      88     103 ..     125     140 ..     119     160 .. 0.77
   3 ?   -2.5   0.0       6.6   3.9e+03      29      58 ..     154     189 ..     135     208 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00023
                  Helicase_RecD  2 ltAdRGRGKSaalGlalaaliaegk.snilvtap 34
                                   +t++ G+GK+a+++l++  li++g+  ++lv   
  gi|116753608|ref|YP_842726.1|  7 ITGKGGTGKTAVAALLVRYLIKSGRkYRVLVIDA 40
                                   899********************99766665433 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.2
                  Helicase_RecD  88 keqadllvvDEAAaip 103
                                     +q d+ ++D AA ++
  gi|116753608|ref|YP_842726.1| 125 IDQYDITIIDTAAGLE 140
                                    4567999999999876 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 6.6
                  Helicase_RecD  29 ilvtapskenvktlfeflakglealglke.......e 58 
                                    i+vt  s++ ++t  e++++  ++lglk+       +
  gi|116753608|ref|YP_842726.1| 154 IVVTDSSRRGLTT-GERIRELASELGLKYnnlyviaN 189
                                    4455444444433.34444555555555533333331 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.1    0.0024       1.5       7      39 ..       8      40 ..       3      48 .. 0.78
   2 ?    3.4   0.1     0.064        38      89     127 ..     117     155 ..     112     162 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0024
                                   -SSTTSSHHHHHHHHHHHHHTTT--EEEEE--T CS
                           MipZ  7 nekGGsGksttavhvavaLlkkGarvaaidldl 39
                                     kGG+Gk+++a  ++  L+k+G +  ++ +d+
  gi|116753608|ref|YP_842726.1|  8 TGKGGTGKTAVAALLVRYLIKSGRKYRVLVIDA 40
                                   57*********************8755544443 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.064
                                    HHHHHHHHHHH-SEEEEE--SS--HHHHHHHHT-SEEEE CS
                           MipZ  89 leelvadleaeldfividtPGsdsalsrlahsladtlvt 127
                                    l+ ++++l  ++d+ +idt    ++ sr +    d+l+ 
  gi|116753608|ref|YP_842726.1| 117 LRGIMDRLIDQYDITIIDTAAGLEHFSRKVIPDLDSLIV 155
                                    56789999************9999999999999999875 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00012     0.075      19      57 ..       2      41 ..       1      79 [. 0.78
   2 ?   -2.7   0.0       5.1     3e+03      56      68 ..     192     204 ..     147     211 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                         ATPase 19 grvvlitGepGtGKtifal...qFlikgaekygepgvfvtve 57
                                   grv+ itG+ GtGKt +a+   ++lik+ +k  ++++ +  +
  gi|116753608|ref|YP_842726.1|  2 GRVIAITGKGGTGKTAVAAllvRYLIKSGRK--YRVLVIDAD 41
                                   89*************9885344899998555..777777655 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.1
                         ATPase  56 veepaedlrenak 68 
                                    +e ++e+++ena+
  gi|116753608|ref|YP_842726.1| 192 TENNKEKIIENAR 204
                                    3444455555555 PP

>> LpxK  Tetraacyldisaccharide-1-P 4'-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3   0.00021      0.13      46      71 ..      11      36 ..       4      38 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00021
                                   S-HSHHHHHHHHHHHTTTS..-EEEE CS
                           LpxK 46 GGtGKTPlvialvkllqarglkvgvl 71
                                   GGtGKT +++ lv++l ++g k  vl
  gi|116753608|ref|YP_842726.1| 11 GGTGKTAVAALLVRYLIKSGRKYRVL 36
                                   9*******************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 ?   10.8   0.0   0.00042      0.25      53     107 ..       2      56 ..       1      68 [. 0.89
   2 ?   -2.3   0.0       4.2   2.5e+03      98     133 ..     174     209 ..     171     212 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00042
                                    TSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEESS----HHHHHHTT--GGG CS
                           RecA  53 GriieiyGpessGkttlalhaiaeaqkkggvaafidaehaldpkyakklGvdide 107
                                    Gr+i i G   +Gkt++a  ++    k+g     +  +   d++ a +lGv++ +
  gi|116753608|ref|YP_842726.1|   2 GRVIAITGKGGTGKTAVAALLVRYLIKSGRKYRVLVIDADPDSNLADALGVEVTK 56 
                                    9*********************99999999876666666679*********9976 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.2
                                    HHHTT--GGG-EEE--SSHHHHHHHHHHHHTTT--S CS
                           RecA  98 akklGvdidellvsqpdtGeqaleiadalvrsgaid 133
                                    a +lG++ ++l+v      e+  e +    rs +++
  gi|116753608|ref|YP_842726.1| 174 ASELGLKYNNLYVIANKVTENNKEKIIENARSVSLN 209
                                    678888888888877777777666554445555555 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   0.1    0.0003      0.18      22      59 ..       4      37 ..       1     101 [. 0.72

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0003
                                   EEEEEESTTSSHHHHHHHHCCSHCCCCCCBTEEEEEEE CS
                         NB-ARC 22 vvalvGmgGvGKttlakqilnksdevegrFdsvawvvv 59
                                   v+a+ G+gG GKt +a+  ++ + +  +++ ++    v
  gi|116753608|ref|YP_842726.1|  4 VIAITGKGGTGKTAVAALLVRYLIKSGRKYRVL----V 37
                                   89***************9999988888888644....3 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00025      0.15      33      81 ..       2      42 ..       1     100 [. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00025
                         AAA_25 33 gelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEd 81
                                   g +++++G +gtGKt++a  l+  +  +G+         + +Vl+++a+ 
  gi|116753608|ref|YP_842726.1|  2 GRVIAITGKGGTGKTAVAALLVRYLIkSGR---------KYRVLVIDADP 42
                                   7899**************999887775555.........33666666665 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00035      0.21      11      45 ..       3      35 ..       1      97 [. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00035
                         AAA_19 11 kvllvtaGpGtGKTrvlkhivallvelggvkpeei 45
                                   +v+++t+  GtGKT v    v++l++ g+    ++
  gi|116753608|ref|YP_842726.1|  3 RVIAITGKGGTGKTAVAALLVRYLIKSGRK--YRV 35
                                   7899*********************99854..444 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00033       0.2       1      28 [.       4      31 ..       4      70 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00033
                            PRK  1 vIgvagsSGaGkttvarklekifgrekv 28
                                   vI+++g+ G Gkt+va+ l+  + + + 
  gi|116753608|ref|YP_842726.1|  4 VIAITGKGGTGKTAVAALLVRYLIKSGR 31
                                   8******************999876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      668  (0.0372581); expected 358.6 (0.02)
Passed Vit filter:                       130  (0.00725082); 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: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 1796.06
//
Query:       gi|116753609|ref|YP_842727.1|  [L=469]
Description: acetyl-CoA decarbonylase/synthase complex subunit beta [Methanosaeta thermophila PT]
Scores for complete 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-60  202.1   0.9      6e-60  201.6   0.1    1.7  2  CdhC      CO dehydrogenase/acetyl-CoA synthase complex beta s
  ------ inclusion threshold ------
        0.2   11.6   0.8        1.6    8.7   0.1    2.5  3  DUF4945   Domain of unknown function (DUF4945)


Domain annotation for each model (and alignments):
>> CdhC  CO dehydrogenase/acetyl-CoA synthase complex beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.6   0.1   6.7e-64     6e-60       1     155 []       5     159 ..       5     159 .. 0.99
   2 ?   -2.5   0.1      0.47   4.2e+03     122     152 ..     417     443 ..     406     446 .. 0.63

  Alignments for each domain:
  == domain 1  score: 201.6 bits;  conditional E-value: 6.7e-64
                           CdhC   1 ipvevspafeGeriRkedlyvelggkktkafElvkvkeadevedgkieviGpdideveegsrlplailvevaGkkleedl 80 
                                    i++++sp++eGeriRk+dl+ve+gg k+++fEl  ++++devedgk+++iGpd+++v+egs++p++++++vaG+k+e+dl
  gi|116753609|ref|YP_842727.1|   5 IQLDISPMYEGERIRKDDLWVEMGGPKADGFELTLAASMDEVEDGKVTIIGPDLKDVKEGSTIPFGMIFKVAGEKIEKDL 84 
                                    6789*********************99***************************************************** PP

                           CdhC  81 EpvlERriHeflnyieGvmHlgqRdiiwvRiskeavekGl.rlkhigevlyaklkeefeaivdkvevtlitdeekv 155
                                    E+++ERr+H++l+yi G+mHl+qR++iw+R++k+  +kG+ ++++i + +++++k+e+ ++++k+evt++td++kv
  gi|116753609|ref|YP_842727.1|  85 ESIIERRNHALLSYISGLMHLNQRYDIWMRLGKSLQKKGVtSWEQIFKPVINLYKAEM-PFIEKMEVTIVTDPAKV 159
                                    ****************************************99****************.**************997 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.47
                           CdhC 122 lkhigevlyaklkeefeaivdkvevtlitde 152
                                    +++i    ++ lke++ a+++k e ++ td+
  gi|116753609|ref|YP_842727.1| 417 FEEI----TDELKEQVIAFIEKYEGEIDTDN 443
                                    4444....44566666778888887777776 PP

>> DUF4945  Domain of unknown function (DUF4945)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0     0.096   8.6e+02      73     107 ..      97     131 ..      63     134 .. 0.78
   2 ?   -2.5   0.0      0.53   4.7e+03      38      52 ..     156     170 ..     139     177 .. 0.53
   3 ?    8.7   0.1   0.00018       1.6      14      70 ..     395     452 ..     389     463 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.096
                        DUF4945  73 efeyeikdaekkyrivvklqGslkvkevgisseiy 107
                                    +++  ++  +++y i ++l  sl+ k v   ++i+
  gi|116753609|ref|YP_842727.1|  97 SYISGLMHLNQRYDIWMRLGKSLQKKGVTSWEQIF 131
                                    566678889999*9999999999999888777776 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.53
                        DUF4945  38 PdniPeeierPlevf 52 
                                    P  + ee+e+ ++v+
  gi|116753609|ref|YP_842727.1| 156 PAKVKEELEKAMQVY 170
                                    334444444444444 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.00018
                        DUF4945  14 slPkvedlksslvddndvkltWkiPdniPeeierPlevfvqvkeiavlekvis...lene 70 
                                      P v+++    vd++++   Wk  ++i +e++  +  f++++e+++ ++++    l +e
  gi|116753609|ref|YP_842727.1| 395 DHPVVTGVVRP-VDNKKITEGWKF-EEITDELKEQVIAFIEKYEGEIDTDNVKnelLMSE 452
                                    56888888776.9**********8.68*******************99998875544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); 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: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 3409.30
//
Query:       gi|116753610|ref|YP_842728.1|  [L=182]
Description: acetyl-CoA decarbonylase/synthase complex subunit epsilon [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-36  125.0   0.2    2.9e-36  124.8   0.2    1.0  1  CO_dh         CO dehydrogenase beta subunit/acetyl-CoA syntha
     0.0003   20.5   0.0    0.00074   19.3   0.0    1.6  1  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain


Domain annotation for each model (and alignments):
>> CO_dh  CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.8   0.2   3.2e-40   2.9e-36       3     167 ..       7     176 ..       5     177 .. 0.94

  Alignments for each domain:
  == domain 1  score: 124.8 bits;  conditional E-value: 3.2e-40
                                    XXXXXXXXXXXXXXX--EEE--SHHHHHHHHHSSSEEEEE-S--.-HH.HHHHHHHHHT.SSSEEEEET.....HHHTT- CS
                          CO_dh   3 lekiPfdeaaianskkatleealkvvakmikkakrPllivGpqvlkaeneeakekkile.kklkvvata.....lkeagl 76 
                                    +++iPf+ a+i+++++a++    kv+  +ikkakrPll+vG ++  + +++ k+  i++ k+++++ata     ++e+g 
  gi|116753610|ref|YP_842728.1|   7 KNPIPFEMAQIPGPEMAKAYPV-KVIGAIIKKAKRPLLVVGAELFDDPVMFDKAIEIAKaKNMTIAATAhtikgFIERGY 85 
                                    5689**************9866.****************************99988765499*******99999999999 PP

                                    G..GGSE..-HHHHHHHHHSTT--TTTSS---SEEEEES--HHHHHHHHHHHHHH-TT-EEEE-SSS--TTSSEEE---G CS
                          CO_dh  77 kdyekkn..klveltkllkdpepkgfdgegeydlvlfiGviyYyasqalsslkkftdkittiaidkyyhpdAdvslanls 154
                                        +++   l+ lt+ l  +++kg dg+g yd+v+f+G+ y  a+ + s+lk+f   i+ ++id+yyh +Ad++++nl 
  gi|116753610|ref|YP_842728.1|  86 T--TNVYqiGLHPLTNYLRFKDWKGLDGQGHYDVVIFMGIFYKFANAMFSALKHFNRDIKRVSIDRYYHVNADMTFGNLA 163
                                    9..66665699********************************************************************* PP

                                    GGHHHHHHHHHHH CS
                          CO_dh 155 keeeeylemleel 167
                                     +   y e ++el
  gi|116753610|ref|YP_842728.1| 164 FDSAGYHEAIDEL 176
                                    ********99997 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   8.2e-08   0.00074       6     110 ..      33     148 ..      28     159 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 8.2e-08
                                    HHHHH-SSEEEEE-CHHCHT.TGHHHHHHHHHHHT-EEEEEGGG.TTSS-TTSTTEEEESGGGS........CHHHHHHH CS
                   TPP_enzyme_M   6 ellkaakrpvilvGggvars.gaseelrelaeklgiPvvttlmg.kgvipedhplylgmlglhg........skaaneal 75 
                                    +++k+akrp+++vG +  ++    +++ e a++ ++ ++ t +  kg+i++    ++  +glh         + ++ +  
  gi|116753610|ref|YP_842728.1|  33 AIIKKAKRPLLVVGAELFDDpVMFDKAIEIAKAKNMTIAATAHTiKGFIERGYTTNVYQIGLHPltnylrfkDWKGLDGQ 112
                                    68**************988768****************9998888****************9976545444444444445 PP

                                    HH-SEEEEES-SSSTCCCTT.TTT.TTTTT-EEEEEE CS
                   TPP_enzyme_M  76 eeaDlvlalGarfddirttg.sep.efapeakiihid 110
                                     + D+v++ G  +++ +    s   +f+++ k + id
  gi|116753610|ref|YP_842728.1| 113 GHYDVVIFMGIFYKFANA-MfSALkHFNRDIKRVSID 148
                                    569999999966666433.324332454443555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1416.15
//
Query:       gi|116753611|ref|YP_842729.1|  [L=805]
Description: acetyl-CoA decarbonylase/synthase complex subunit alpha [Methanosaeta thermophila PT]
Scores for complete 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-93  313.6   7.8    1.1e-79  268.4   0.0    2.0  2  Prismane  Prismane/CO dehydrogenase family
    3.8e-06   27.3   9.4     0.0036   17.8   0.3    3.3  3  Fer4_17   4Fe-4S dicluster domain
    4.8e-06   26.9   6.8      0.048   14.1   3.0    3.2  3  Fer4_8    4Fe-4S dicluster domain
    9.3e-06   25.7   9.0    9.3e-06   25.7   9.0    2.7  3  Fer4_10   4Fe-4S dicluster domain
    5.1e-05   23.3  10.1    5.1e-05   23.3  10.1    3.3  4  Fer4_9    4Fe-4S dicluster domain
    0.00015   22.3  10.1    0.00015   22.3  10.1    3.2  3  Fer4_7    4Fe-4S dicluster domain
    0.00062   19.5  20.3     0.0031   17.2   3.7    3.0  2  Fer4      4Fe-4S binding domain
  ------ inclusion threshold ------
      0.013   15.6   8.6      0.032   14.4   0.8    2.8  2  Fer4_18   4Fe-4S dicluster domain
      0.038   14.9  14.0        2.8    9.0   4.3    3.0  3  Fer4_16   4Fe-4S double cluster binding domain
       0.12   13.3  15.9      0.044   14.6   4.4    2.9  2  Fer4_22   4Fe-4S dicluster domain
       0.43   10.7  22.6      0.085   13.0   2.5    3.4  3  Fer4_6    4Fe-4S binding domain
       0.96   10.1  14.3       0.94   10.1   5.0    3.5  2  Fer4_4    4Fe-4S binding domain
        6.2    7.1  27.3       0.41   10.9   4.1    4.4  4  Fer4_2    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Prismane  Prismane/CO dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   7.3     1e-14   1.4e-11       2      54 ..      66     118 ..      65     135 .. 0.89
   2 !  268.4   0.0   8.3e-83   1.1e-79     119     511 .]     146     691 ..     132     691 .. 0.87

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 1e-14
                                    EE-SSTCT-ECSCS.SS-TTS-BHHHHHHHHHHHHHHHHHHHHHHHHHHCHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Prismane   2 fCrqCengpCritknkrGvCGkdadtavardlliavlkgaaahaahareladt 54 
                                     C +C++gpC++t+nkrG+CG+d+++   + +l+a+l+g++ah+ah+r+l++ 
  gi|116753611|ref|YP_842729.1|  66 TCTLCTFGPCDLTGNKRGACGIDMAGTCGKIVLVACLMGTCAHTAHGRHLYHW 118
                                    7************************************************9443 PP

  == domain 2  score: 268.4 bits;  conditional E-value: 8.3e-83
                                    CCCHHHHHHHHHHHCHHTT-HHHHHHHHHHHCCCCTTSTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---....--EE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxx RF
                       Prismane 119 ellpkglkglyaehaivlgyadeevveflaktlaglesdpldllskalrlGlldlkgmelldeantslfGtP....eppl 194
                                    ++ pk+l    ++ +++l+y +e+++++la+t++g+e++++d++skal++G++d  g e++d +++++++ P    ++pl
  gi|116753611|ref|YP_842729.1| 146 GIRPKSL----KDFGKALEYCEEQITQLLAATHTGQEGSYVDFESKALHAGMIDSLGKEICDMLQIVAYNMPrgdpNAPL 221
                                    3444444....555*******************************************************9998888999* PP

                                    EEECGCG-.SSSEEEEEESS-HHHHHHHHHHHCTTCCCCCCCGCCCCCCHHHHHH.HHHCC.............EEEEEC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx.............xxxxxx RF
                       Prismane 195 tevnlgvldkdkvnIlvsGHdladleelleqtegkglnvythgemLpghcctalk.lkyrh.............lvgnvG 260
                                    +e+++g+ld++k +++  GH+la+ +e + +te+++l ++++   + g+ccta + +++ +              ++++G
  gi|116753611|ref|YP_842729.1| 222 VEIGMGTLDQNKAVLIAYGHNLAAGAEAMFYTETNNLWDKVD---IGGVCCTAIDlTRIGEgmgekkvpdmigtKAKVAG 298
                                    ******************************************...**********777777******************* PP

                                    SSGGGHHHHHCCHECEEEESSSS--TTHHHHHHCHCCEEEEECTTB-TTSEEE-.-CTTCH................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx................... RF
                       Prismane 261 nawqqekaeftgavdaivvdtnCivpplasvaekyktrlittsevakpgakhie.eeekad................... 320
                                       + +k++++g++d ++vd++C+  +  +  e+ k++li+t++++ +g+k+   ++ + +                   
  gi|116753611|ref|YP_842729.1| 299 AVGWWRKMVRAGIMDTVMVDEQCVWCDALKDCEERKIPLIATNDKILYGLKDRTnDPVD-Eivddlvnfrvpgvvildpv 377
                                    *************************999999999*******************943333.13445677888888888898 PP

                                    HHHHHHHHHHHCCHCCTTCGG.-......................................................HHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxx......................................................xxx RF
                       Prismane 321 kdaseiiekAielakareekkve......................................................ida 346
                                    k+ +  +++Ai+++++r++ +                                                           
  gi|116753611|ref|YP_842729.1| 378 KAGEVGVKTAIAVKPKRADIRNRivltedefkklvssctkcnecafvcpphirisnlmeeaakgnlepfsstyevcvG-C 456
                                    999999***********8833336788888888888888888888777777777776666666666666666555550.0 PP

                                    ..................................................HHTTSS-EEEEE-B---TTCGCCHHHHHHH CS
                                    ..................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Prismane 347 ..................................................iksGtIkgvvlvvGCdnakkgrdyytelak 376
                                                                                      i+ GtI+gv+++vGC+n+++g++  +++ak
  gi|116753611|ref|YP_842729.1| 457 grceqvcrqnipilkmyeyanreyirnqkfkmragrgpirdteiravgapIVLGTIPGVIALVGCSNYPNGTKECYDIAK 536
                                    55555555556666666666667777777777888888888888889999****************************** PP

                                    HCHHTTEEEEEECHHHHHC...CCTTTTEC...GHHHHSTHCEESEEEEESCCCHHHHHHHHHHHHHHT.......TS.S CS
                                    xxxxxxxxxxxxxxxxxxx...xxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xx.x RF
                       Prismane 377 elikrdvlvltaGCakyal...nklglgti...eaaelagegiPrvLdvGsCvdnyrivvialklaeal.......gv.d 442
                                    e++ r ++v+t+GC+++++    +++++ti   ++  ++g +   + +vGsCv+n++i+++a+k+a ++       ++ d
  gi|116753611|ref|YP_842729.1| 537 EFVDRGYIVVTTGCMAMDMslyTDAEGKTIweqYPGAFDGRN---ICNVGSCVANAHIHGAAIKVATIFahrnhraNYdD 613
                                    ******************99999*********9*******99...******************************9999* PP

                                    GGGSSE...EEEECC-..-SHHHHHHHHHHHHTT-CEEECSS-TTTT-HHHHHHHHCH....HHHHHCEEEECHCHHH CS
                                    xxxxxx...xxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxx RF
                       Prismane 443 indLpl...aalalew..yeqKAvailltllalGinihlgptlpafgspnvlkvlved....fedriggivtveedpe 511
                                    i+d++l   +a+ ++w  y+qKA++i+++++++G+++++ p+  +++++++ +    +    +++r g++v++e++pe
  gi|116753611|ref|YP_842729.1| 614 IADYILskvGACGIAWgaYSQKAASIATGVNRIGVPVVVQPHSVIYRRAFLGRADLPEdwmvIDARDGSKVRIEPAPE 691
                                    ********9*****************************************9987554448888889999999998875 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       7.9   1.1e+04      34      53 ..     312     331 ..     293     333 .. 0.53
   2 !   17.8   0.3   2.6e-06    0.0036      35      60 ..     404     429 ..     385     430 .. 0.76
   3 !   14.0   0.7     4e-05     0.055      41      60 ..     448     467 ..     431     468 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 7.9
                        Fer4_17  34 leeaekeekaslCieCgeCe 53 
                                    +++++ +e++  C   + Ce
  gi|116753611|ref|YP_842729.1| 312 MDTVMVDEQCVWCDALKDCE 331
                                    44443333444444444555 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 2.6e-06
                        Fer4_17  35 eeaekeekaslCieCgeCerkCPqgl 60 
                                    +e e ++ +s+C++C+eC+ +CP ++
  gi|116753611|ref|YP_842729.1| 404 TEDEFKKLVSSCTKCNECAFVCPPHI 429
                                    344556899**************987 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 4e-05
                        Fer4_17  41 ekaslCieCgeCerkCPqgl 60 
                                    ++ + C++Cg+Ce++C q++
  gi|116753611|ref|YP_842729.1| 448 STYEVCVGCGRCEQVCRQNI 467
                                    67899************998 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.4       6.2   8.6e+03      45      59 ..     318     332 ..     292     334 .. 0.67
   2 !   14.1   3.0   3.5e-05     0.048      44      65 .]     399     429 ..     318     429 .. 0.72
   3 !   12.8   0.1   9.1e-05      0.13       4      65 .]     452     467 ..     435     505 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 6.2
                         Fer4_8  45 eealwsCttcgaCte 59 
                                    +e    C + + C+e
  gi|116753611|ref|YP_842729.1| 318 DEQCVWCDALKDCEE 332
                                    445556777777765 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 3.5e-05
                         Fer4_8  44 e.........eealwsCttcgaCtevCpvgi 65 
                                    +         ++ + sCt c++C+ vCp +i
  gi|116753611|ref|YP_842729.1| 399 NrivltedefKKLVSSCTKCNECAFVCPPHI 429
                                    0333334566899***************886 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 9.1e-05
                         Fer4_8   4 kCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvgi 65 
                                     C++Cg+C++ C                                               ++i
  gi|116753611|ref|YP_842729.1| 452 VCVGCGRCEQVC----------------------------------------------RQNI 467
                                    366666666666..............................................4443 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   1.7       3.9   5.4e+03       6      13 ..      64      71 ..      62      85 .. 0.78
   2 ?   -3.4   0.2       8.1   1.1e+04      38      51 ..     317     330 ..     303     332 .. 0.54
   3 !   25.7   9.0   6.8e-09   9.3e-06       7      55 ..     413     463 ..     409     464 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3.9
                        Fer4_10  6 ddtCirCg 13
                                   ddtC+ C+
  gi|116753611|ref|YP_842729.1| 64 DDTCTLCT 71
                                   68888886 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 8.1
                        Fer4_10  38 vrkkvekCtgcgaC 51 
                                    v++ +  C++   C
  gi|116753611|ref|YP_842729.1| 317 VDEQCVWCDALKDC 330
                                    34444444444455 PP

  == domain 3  score: 25.7 bits;  conditional E-value: 6.8e-09
                        Fer4_10   7 dtCirCgkCvkaCPadl..tsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                    ++C++C++C  +CP ++  ++   ++++ + e+ +  +e C gcg C ++C
  gi|116753611|ref|YP_842729.1| 413 SSCTKCNECAFVCPPHIriSNLMEEAAKGNLEPFSSTYEVCVGCGRCEQVC 463
                                    68*************998666666667777778888*************** PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       4.3     6e+03      34      39 ..      65      70 ..      39      76 .. 0.67
   2 ?   -0.4   0.1      0.96   1.3e+03      27      43 ..     313     331 ..     287     333 .. 0.67
   3 !   12.8   1.8   7.2e-05     0.099      18      49 ..     391     428 ..     386     429 .. 0.72
   4 !   23.3  10.1   3.7e-08   5.1e-05       2      49 ..     415     466 ..     414     468 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4.3
                         Fer4_9 34 eaCigC 39
                                   + C+ C
  gi|116753611|ref|YP_842729.1| 65 DTCTLC 70
                                   456666 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.96
                         Fer4_9  27 rlraaseeaCigCga...Cv 43 
                                       + + e+C+ C a   C+
  gi|116753611|ref|YP_842729.1| 313 DTVMVD-EQCVWCDAlkdCE 331
                                    333333.5899998766665 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 7.2e-05
                         Fer4_9  18 vedaaerkarlraase......eaCigCgaCveaCpkg 49 
                                    ++++a   +r+  +++      ++C++C++C+ +Cp +
  gi|116753611|ref|YP_842729.1| 391 KPKRADIRNRIVLTEDefkklvSSCTKCNECAFVCPPH 428
                                    555555556665555577788889************87 PP

  == domain 4  score: 23.3 bits;  conditional E-value: 3.7e-08
                         Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase....eaCigCgaCveaCpkg 49 
                                    Ct+C++C  +Cp ++ +    e+ a+ + +      e C+gCg+C+++C ++
  gi|116753611|ref|YP_842729.1| 415 CTKCNECAFVCPPHIRISNLMEEAAKGNLEPFsstyEVCVGCGRCEQVCRQN 466
                                    *************9999888888888766555889999***********998 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.4       8.2   1.1e+04      36      42 ..      65      71 ..      54      87 .. 0.74
   2 ?    2.4   0.1      0.18   2.5e+02      17      46 ..     300     332 ..     281     333 .. 0.81
   3 !   22.3  10.1   1.1e-07   0.00015       1      51 [.     414     466 ..     414     467 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 8.2
                         Fer4_7 36 ekClgCg 42
                                   ++C+ C+
  gi|116753611|ref|YP_842729.1| 65 DTCTLCT 71
                                   6777774 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.18
                         Fer4_7  17 ieldeeenekgtekveidpekClgCga...Cva 46 
                                    + ++ + + +g+++++++ e+C+ C+a   C++
  gi|116753611|ref|YP_842729.1| 300 VGWWRKMVRAGIMDTVMVDEQCVWCDAlkdCEE 332
                                    5555556667889999*********98777876 PP

  == domain 3  score: 22.3 bits;  conditional E-value: 1.1e-07
                         Fer4_7   1 rCigCgaCvaaCpvkaield.eeenekgt.ekveidpekClgCgaCvavCPtg 51 
                                    +C++C+ C+ +Cp + +  +  ee +kg+ e     +e C+gCg+C++vC  +
  gi|116753611|ref|YP_842729.1| 414 SCTKCNECAFVCPPHIRISNlMEEAAKGNlEPFSSTYEVCVGCGRCEQVCRQN 466
                                    5************66554441223445553445667999***********876 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   2.3   5.6e-05     0.077       6      19 ..     413     426 ..     410     429 .. 0.91
   2 !   17.2   3.7   2.3e-06    0.0031       5      21 ..     450     466 ..     449     468 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.6e-05
                                    TTSSS-THHHHHST CS
                           Fer4   6 ekCigCGaCvevCP 19 
                                    + C++C++C+ vCP
  gi|116753611|ref|YP_842729.1| 413 SSCTKCNECAFVCP 426
                                    67************ PP

  == domain 2  score: 17.2 bits;  conditional E-value: 2.3e-06
                                    TTTSSS-THHHHHSTTT CS
                           Fer4   5 eekCigCGaCvevCPvg 21 
                                    +e C+gCG+C++vC  +
  gi|116753611|ref|YP_842729.1| 450 YEVCVGCGRCEQVCRQN 466
                                    689***********776 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.8   2.3e-05     0.032      49      79 ..     403     433 ..     389     439 .. 0.78
   2 ?    4.2   1.6     0.035        48      59      79 ..     451     471 ..     435     477 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.3e-05
                        Fer4_18  49 ekeerkekgagdcidcescvkvcPtgidirk 79 
                                     +e++ +k ++ c++c+ c  vcP +i i +
  gi|116753611|ref|YP_842729.1| 403 LTEDEFKKLVSSCTKCNECAFVCPPHIRISN 433
                                    45556678899****************9976 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.035
                        Fer4_18  59 gdcidcescvkvcPtgidirk 79 
                                      c+ c+ c +vc  +i i k
  gi|116753611|ref|YP_842729.1| 451 EVCVGCGRCEQVCRQNIPILK 471
                                    56***********99998865 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   4.3     0.002       2.8       2      13 ..     415     426 ..     386     428 .. 0.73
   2 ?    5.2  15.1     0.031        43       2      66 ..     415     465 ..     414     466 .. 0.60
   3 ?    8.1   2.9    0.0037       5.1       2      16 ..     453     467 ..     452     499 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.002
                        Fer4_16   2 CgtCgkCaevCP 13 
                                    C++C++Ca vCP
  gi|116753611|ref|YP_842729.1| 415 CTKCNECAFVCP 426
                                    666666666666 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.031
                        Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCPa 66 
                                    C++C++Ca vCP +   ++    +e    +++ + + + ++ ++      e + gC++C++vC  
  gi|116753611|ref|YP_842729.1| 415 CTKCNECAFVCPPHIRISN---LME----EAA-KGNLEPFSSTY------EVCVGCGRCEQVCRQ 465
                                    ************7653333...222....111.11122333333......4577*********65 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0037
                        Fer4_16   2 CgtCgkCaevCPtna 16 
                                    C++Cg+C +vC +n 
  gi|116753611|ref|YP_842729.1| 453 CVGCGRCEQVCRQNI 467
                                    999999999998876 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   3.1     0.072        99       2      13 ..     415     426 ..     414     444 .. 0.86
   2 ?   14.6   4.4   3.2e-05     0.044      78      96 .]     449     467 ..     430     467 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.072
                        Fer4_22   2 ClsCgaCtlvCp 13 
                                    C +C++C++vCp
  gi|116753611|ref|YP_842729.1| 415 CTKCNECAFVCP 426
                                    ***********9 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 3.2e-05
                        Fer4_22  78 gesgCvGCgRCieacpvki 96 
                                      ++CvGCgRC+++c ++i
  gi|116753611|ref|YP_842729.1| 449 TYEVCVGCGRCEQVCRQNI 467
                                    5679***********9987 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   1.2       6.6     9e+03       7      13 ..      65      71 ..      64      75 .. 0.73
   2 ?   13.0   2.5   6.1e-05     0.085       7      20 ..     413     426 ..     412     433 .. 0.90
   3 ?    9.5   4.0   0.00079       1.1       9      19 ..     453     463 ..     450     467 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 6.6
                         Fer4_6  7 dkCigCg 13
                                   d C+ C 
  gi|116753611|ref|YP_842729.1| 65 DTCTLCT 71
                                   7899994 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 6.1e-05
                         Fer4_6   7 dkCigCgdCvrvCP 20 
                                    ++C+ C++C+ vCP
  gi|116753611|ref|YP_842729.1| 413 SSCTKCNECAFVCP 426
                                    68************ PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00079
                         Fer4_6   9 CigCgdCvrvC 19 
                                    C+gCg+C+ vC
  gi|116753611|ref|YP_842729.1| 453 CVGCGRCEQVC 463
                                    *********** PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   1.8      0.13   1.8e+02       3      15 ..     414     426 ..     413     436 .. 0.90
   2 ?   10.1   5.0   0.00068      0.94       2      16 ..     451     465 ..     450     466 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.13
                         Fer4_4   3 rCigCgsCvaaCP 15 
                                    +C+ C  C  +CP
  gi|116753611|ref|YP_842729.1| 414 SCTKCNECAFVCP 426
                                    7*******99999 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00068
                         Fer4_4   2 erCigCgsCvaaCPq 16 
                                    e C+gCg+C+ +C q
  gi|116753611|ref|YP_842729.1| 451 EVCVGCGRCEQVCRQ 465
                                    78***********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 ?    2.1   0.3      0.18   2.5e+02       8      16 ..      65      75 ..      57      78 .. 0.81
   2 ?   -2.7   0.7       6.2   8.6e+03       5      14 ..     317     325 ..     315     331 .. 0.69
   3 ?    8.5   2.4    0.0016       2.3       8      21 ..     413     426 ..     407     427 .. 0.90
   4 ?   10.9   4.1   0.00029      0.41       8      20 ..     451     463 ..     448     465 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.18
                         Fer4_2  8 drCigC..gaC 16
                                   d+C+ C  g+C
  gi|116753611|ref|YP_842729.1| 65 DTCTLCtfGPC 75
                                   69****88899 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6.2
                         Fer4_2   5 vdtdrCigCg 14 
                                    vd++ C+ C 
  gi|116753611|ref|YP_842729.1| 317 VDEQ-CVWCD 325
                                    5666.99995 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0016
                         Fer4_2   8 drCigCgaCvsaCP 21 
                                     +C+ C+ C  +CP
  gi|116753611|ref|YP_842729.1| 413 SSCTKCNECAFVCP 426
                                    57***********9 PP

  == domain 4  score: 10.9 bits;  conditional E-value: 0.00029
                         Fer4_2   8 drCigCgaCvsaC 20 
                                    + C+gCg C ++C
  gi|116753611|ref|YP_842729.1| 451 EVCVGCGRCEQVC 463
                                    79*********** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (805 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); 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):              13  [number of targets reported over threshold]
# CPU time: 0.68u 0.25s 00:00:00.93 Elapsed: 00:00:00.40
# Mc/sec: 5981.87
//
Query:       gi|116753612|ref|YP_842730.1|  [L=316]
Description: cobalamin biosynthesis protein CobD [Methanosaeta thermophila PT]
Scores for 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-82  274.3   2.9    1.1e-81  274.1   2.9    1.1  1  CobD_Cbib  CobD/Cbib protein


Domain annotation for each model (and alignments):
>> CobD_Cbib  CobD/Cbib protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  274.1   2.9     6e-86   1.1e-81       1     275 [.      11     296 ..      11     304 .. 0.89

  Alignments for each domain:
  == domain 1  score: 274.1 bits;  conditional E-value: 6e-86
                      CobD_Cbib   1 lllAlllDlllgdprrllhPvvligklisalekrlrkakkerlaGvllalllvllallvalllllla.laa.ll...... 72 
                                    l+lAll+D++lg+p+++lhPvv+ig+++++l++++ +   ++++G+++ +l++ +a+l++++l+++a + +  l      
  gi|116753612|ref|YP_842730.1|  11 LILALLIDIVLGEPPAALHPVVIIGTAVDRLRRMMPR---RKISGMIISVLVISGAVLAGFALIRIAyA-TgSLagssem 86 
                                    699****************************998854...579**********************8852.3222577788 PP

                      CobD_Cbib  73 ....glvlealllkltlalrsLleevrkvakalkgdleaaReavsmiVgRdtseldeeeiarAavEsvaENlsDgvvaPl 148
                                        +l+++++llk+t+a +sL+ ++r++ + +++dl+aa++ +  +V+R++ +l++++ ++A++Es++EN +D +v+Pl
  gi|116753612|ref|YP_842730.1|  87 gdilALIISSYLLKSTFAFKSLIMTSREIGNLIDEDLDAAKHLLPALVSRNPLNLTHAQARSAVIESLSENYVDTIVSPL 166
                                    88777799*************************99********************************************* PP

                      CobD_Cbib 149 fyflll.....glpgalaykavnTlDsmvGYkneryedfGwaaArlDDllnyiPARltalllala......aalriarrd 217
                                    fy++l+     g+ +ala+kav+T+Dsm+GYk++ ++++G+++ArlDD+ln+iPARl+  l+++a       +l++++r+
  gi|116753612|ref|YP_842730.1| 167 FYYVLFscaglGVEAALAFKAVSTMDSMLGYKSDDLREIGYVPARLDDILNWIPARLSLPLIMIAsprksmDILKACMRY 246
                                    *****9888888899********************************************99999767766677******* PP

                      CobD_Cbib 218 arkhpSpNsgwpeaalAgalgvrLggpnvYlgkleekptlgdkkrpleaedieralrl 275
                                    ++ +pSpNsgwp+aa+Agalg r+++p+vY   l+e        r++e ed++ a++l
  gi|116753612|ref|YP_842730.1| 247 HSVTPSPNSGWPMAAAAGALGTRMAKPGVYTI-LDE-------GRDPESEDVSSAISL 296
                                    ******************************43.222.......233355566555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); 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 0.23s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2577.12
//
Query:       gi|116753613|ref|YP_842731.1|  [L=550]
Description: hypothetical protein Mthe_0296 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.028   15.2   3.6      0.084   13.6   0.8    2.6  2  GPI-anchored     Ser-Thr-rich glycosyl-phosphatidyl-inositol-
      0.029   13.3   0.1      0.041   12.8   0.1    1.1  1  Chondroitinas_B  Chondroitinase B
        1.9    8.9   4.5        1.8    9.0   0.7    2.7  2  GspH             Type II transport protein GspH


Domain annotation for each model (and alignments):
>> GPI-anchored  Ser-Thr-rich glycosyl-phosphatidyl-inositol-anchored membrane family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1       0.1     6e+02      13      77 ..     254     324 ..     248     334 .. 0.62
   2 ?   13.6   0.8   1.4e-05     0.084       2      66 ..     426     488 ..     425     517 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.1
                   GPI-anchored  13 kpvtitWkdsg...tdpgtvtlvLcagssnnlksvktiasgiknsd.gsytwtv...paslesggaYflqiv 77 
                                    +++t t++d +     + + +l+++ gs+ ++   +t +  ++n+  g+++ +    ++   +g++Y ++i 
  gi|116753613|ref|YP_842731.1| 254 ATITATYADADlayVAENSLNLYVWDGSN-WIAATDTAVNAAENRVsGKFSASLltgSPIALAGKDYSVTIE 324
                                    45777777766655445899999999999.777776666666554336666655222333345566777776 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 1.4e-05
                   GPI-anchored   2 sPssgevvtagkpvtitWkdsgtdpgtvt.lvLcagssnnlksvktiasgiknsdgsytwtvpasl 66 
                                    +P  gev++   pvtitW+  +  + +v+ +vL   +++  +   tias +   ++s+tw +p+  
  gi|116753613|ref|YP_842731.1| 426 TPNGGEVLKRQIPVTITWTMPS--SASVSgVVLSYSTDGGKTYPHTIASIMGP-ATSFTWRPPNIA 488
                                    7999****************75..45555144444444555666777755555.5*******8744 PP

>> Chondroitinas_B  Chondroitinase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   6.8e-06     0.041       3      62 ..      37      99 ..      36     146 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.8e-06
                                   SHHHHHHHHHH--TT-EEEE-SEEEET-EE...EE-S--BTTB-EEEEESSTTS.EEEEES-EE CS
                Chondroitinas_B  3 sakeleeavkeakpGdeivlknGvykdvql...kfkgeGteekPivlkaetaGk.vfieGeskl 62
                                   s++ +++a+++a pGd+iv+  G+y++  +   ++k  G  ++P + +a+ +G+ v i+G+  +
  gi|116753613|ref|YP_842731.1| 37 SKSSIQDAINNASPGDTIVVYSGTYNENVVvdkTLKLVGI-NNPTINAANPSGNaVSITGSGVV 99
                                   56789********************985541213455565.56666666666643888886543 PP

>> GspH  Type II transport protein GspH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.7    0.0003       1.8      20      98 ..      26     112 ..      22     121 .. 0.74
   2 ?   -0.2   0.2      0.23   1.3e+03      79      96 ..     426     446 ..     351     503 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0003
                                    SS-EEEECTTEEEESCEESSSCCCCEETTTCSSEEEEEESSSSTTESSEC..............TT--SCEEE-TTSSCB CS
                           GspH  20 grpvtlcpssgwqggWrvfvdanangtldggedvlrrgaaldggdtltga..............akgtpqitFnpsGgel 85 
                                     +++t+cps+  +++  ++ da +n++++++  ++  ++++++++++ ++              + + ++++++ sG  l
  gi|116753613|ref|YP_842731.1|  26 AATYTVCPSG--CSKSSIQ-DAINNASPGDT--IVVYSGTYNENVVVDKTlklvginnptinaaNPSGNAVSITGSGVVL 100
                                    5788999888..4555555.66666666666..7777777777777777789999999999999999**********999 PP

                                    --EEEEEETTCTC CS
                           GspH  86 tpgtltlctsasa 98 
                                    t++t+t + s+++
  gi|116753613|ref|YP_842731.1| 101 TGFTITGA-STGN 112
                                    ****9955.3333 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.23
                                    -TTS....SCB--EEEEEETTC CS
                           GspH  79 npsG....geltpgtltlctsa 96 
                                    +p+G        p t+t +  +
  gi|116753613|ref|YP_842731.1| 426 TPNGgevlKRQIPVTITWT-MP 446
                                    2344444433344444444.22 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (550 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.24s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3969.35
//
Query:       gi|116753614|ref|YP_842732.1|  [L=214]
Description: hypothetical protein Mthe_0297 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.25   11.6   0.3       0.46   10.8   0.0    1.6  2  zf-H2C2   H2C2 zinc finger


Domain annotation for each model (and alignments):
>> zf-H2C2  H2C2 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   2.6e-05      0.46       8      32 ..     112     136 ..     112     138 .. 0.90
   2 ?   -4.1   0.1         1   1.8e+04      13      20 ..     177     184 ..     175     185 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 2.6e-05
                        zf-H2C2   8 inkltallarkYhwlgiketvseVi 32 
                                    +nk+ +++ + Y+++++k + + Vi
  gi|116753614|ref|YP_842732.1| 112 ENKMVQKILEDYYLPRLKSIYKPVI 136
                                    59****************9977776 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 1
                        zf-H2C2  13 allarkYh 20 
                                    + +ar Yh
  gi|116753614|ref|YP_842732.1| 177 DVIARLYH 184
                                    56788888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); 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: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1633.95
//
Query:       gi|116753615|ref|YP_842733.1|  [L=263]
Description: hypothetical protein Mthe_0298 [Methanosaeta thermophila PT]
Scores for complete 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-61  205.7   0.2    7.9e-61  205.5   0.2    1.1  1  DNA_alkylation  DNA alkylation repair enzyme
  ------ inclusion threshold ------
      0.095   13.0   1.1       0.16   12.3   0.2    1.9  2  YvbH_ext        YvbH-like oligomerisation region


Domain annotation for each model (and alignments):
>> DNA_alkylation  DNA alkylation repair enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.5   0.2   8.9e-65   7.9e-61       1     213 []      36     252 ..      36     252 .. 0.99

  Alignments for each domain:
  == domain 1  score: 205.5 bits;  conditional E-value: 8.9e-65
                 DNA_alkylation   1 ikaeLealadpekaeemqryfkegdeflGvkvpelrklakeffkelkle..eelqelaeeLwksperEerllAldlltqa 78 
                                    i+aeL ++ad++++e+ qr+f+e  +++Gv++p +r++a++ f+++++   +e++el+e+L+k++++E+ ++A+d+ +  
  gi|116753615|ref|YP_842733.1|  36 IRAELLQNADAQTQESAQRFFREPVRLYGVRTPVVREIARRHFRSIRHLekTEIFELCEALLKTDYNEDAIVAFDWSYAL 115
                                    789*********************************************9999**************************** PP

                 DNA_alkylation  79 kkklaeadlelyeklve.tinnWdlvDslaskivgalladkperrdllkeWaksenlWerRaAivatlklikk.tdlell 156
                                    ++++a+ d++++e++v  +innW  +D+++s+ +g +++++p+  ++lk Wa+sen+W+rRaA+v++++ +++   l ++
  gi|116753615|ref|YP_842733.1| 116 RRSYAPRDFQVFERWVAsYINNWVKCDTFCSRSLGTFVEMYPAYIQNLKGWATSENRWVRRAAAVTMVPSARRgRFLGEM 195
                                    *************************************************************************9999*** PP

                 DNA_alkylation 157 leiaeelladkedfiqkAiGwaLrelsktdpdlveeFlekhakrmprlslreAiekl 213
                                    lei+++ll+d+ed +qk++Gw+L+e+s+ ++++v++++++++ +m+r++lr+Aiek+
  gi|116753615|ref|YP_842733.1| 196 LEIVDLLLGDPEDIVQKGCGWLLKEASRCHQQEVFSYIMSRKGEMARIVLRYAIEKM 252
                                    *******************************************************97 PP

>> YvbH_ext  YvbH-like oligomerisation region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   1.8e-05      0.16      27      61 .]     100     137 ..      94     137 .. 0.82
   2 ?   -3.0   0.0       1.1   9.6e+03      51      61 .]     152     162 ..     152     162 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.8e-05
                                    HHHHHHHHHHHHHHHHHHHHS-S--HHHHHH....HH-X CS
                       YvbH_ext  27 efkelnefaFnWLedarkkynkKDFgevFek....YInN 61 
                                    +++e + +aF+W    r+ y  +DF +vFe+    YInN
  gi|116753615|ref|YP_842733.1| 100 DYNEDAIVAFDWSYALRRSYAPRDF-QVFERwvasYINN 137
                                    556666789****************.6***966667777 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.1
                                    -HHHHHHHH-X CS
                       YvbH_ext  51 FgevFekYInN 61 
                                    F e++  YI+N
  gi|116753615|ref|YP_842733.1| 152 FVEMYPAYIQN 162
                                    6678999**99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1765.62
//
Query:       gi|116753616|ref|YP_842734.1|  [L=410]
Description: LOR/SDH bifunctional protein [Methanosaeta thermophila PT]
Scores for complete 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-37  126.5   0.0    8.9e-37  125.5   0.0    1.5  1  Saccharop_dh_N  LOR/SDH bifunctional enzyme conserved region
     0.0028   17.4   0.4       0.41   10.4   0.0    2.5  2  TPP_enzyme_M    Thiamine pyrophosphate enzyme, central domain
  ------ inclusion threshold ------
       0.14   11.6   0.1       0.58    9.7   0.0    2.1  2  Sirohm_synth_M  Sirohaem biosynthesis protein central


Domain annotation for each model (and alignments):
>> Saccharop_dh_N  LOR/SDH bifunctional enzyme conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.5   0.0   1.5e-40   8.9e-37       3     100 .]       6     103 ..       4     103 .. 0.99

  Alignments for each domain:
  == domain 1  score: 125.5 bits;  conditional E-value: 1.5e-40
                                    EEEEEEXXTTSSHHHHHHHHHHHTTXEEEEEEEEXXSSTTSXEEEEEEEEESSHHHHHHHHHHHHHHHHHSCCCCEEEEC CS
                 Saccharop_dh_N   3 eveleGhliDsgilnkvldlileaggsfevlefevGkkkkdtSyaelevsaedeevLeeileeltelgaelveeedvkle 82 
                                     +e+eGhliDs+il+k+ld+i+++gg+fe++ef+vGk+k+++S+++l++ ++d ++L++il+el++lga+lv++edv+le
  gi|116753616|ref|YP_842734.1|   6 DIEMEGHLIDSLILTKALDKIMDMGGEFEIKEFTVGKRKDEPSHVRLTLIGKDPAHLNQILDELNALGARLVDSEDVRLE 85 
                                    69****************************************************************************** PP

                                    ESSCTTB--TTB----SS CS
                 Saccharop_dh_N  83 kaekdgvlpedFYsttnh 100
                                    +a++d+v+p++FYsttnh
  gi|116753616|ref|YP_842734.1|  86 PAPSDMVVPRGFYSTTNH 103
                                    *****************8 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 !    4.7   0.1    0.0039        23      13      66 ..     200     253 ..     184     260 .. 0.84
   2 !   10.4   0.0   6.8e-05      0.41      67     136 ..     325     395 ..     306     396 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0039
                                    SEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEEESGGG CS
                   TPP_enzyme_M  13 rpvilvGggvarsgaseelrelaeklgiPvvttlmgkgvipedhplylgmlglh 66 
                                    r++ ++G  v   ga+ +l++l++   i v+ + ++  v + + +l+  +lg+ 
  gi|116753616|ref|YP_842734.1| 200 RIAAICGPAVVHTGAAPALAQLIRDGYIDVLLSGNALAVHDIERQLFGTSLGMD 253
                                    8899**********************************9999999998899985 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 6.8e-05
                                    SCHHHHHHHHH-SEEEEES-SSSTCCCTTTTTTTTTT-EEEEEESSCCCCTTCC....--SEEEECTHHHHHHH CS
                   TPP_enzyme_M  67 gskaanealeeaDlvlalGarfddirttgsepefapeakiihididpaeigkny....qvdlaivgdvketlea 136
                                    +++a  eal+  D  l+  + ++ i t++  p +    k + +di+pa++ k        ++++v dv+++l  
  gi|116753616|ref|YP_842734.1| 325 AKDAMAEALKGVDMALMMATMLHSIATGNLLPSYV---KTLCVDINPATVTKLMdrgtAQAIGLVTDVGTFLPM 395
                                    4678899*****************98877666665...68*********9999844433569999999999875 PP

>> Sirohm_synth_M  Sirohaem biosynthesis protein central
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   9.7e-05      0.58      12      23 ..     213     224 ..     212     224 .. 0.95
   2 ?   -2.4   0.0      0.55   3.3e+03      15      23 ..     394     402 ..     394     402 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 9.7e-05
                 Sirohm_synth_M  12 GksPrLAaliRr 23 
                                    G++P+LA+liR+
  gi|116753616|ref|YP_842734.1| 213 GAAPALAQLIRD 224
                                    9**********7 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.55
                 Sirohm_synth_M  15 PrLAaliRr 23 
                                    P LA  iR+
  gi|116753616|ref|YP_842734.1| 394 PMLAEEIRK 402
                                    99*****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2715.53
//
Query:       gi|116753617|ref|YP_842735.1|  [L=373]
Description: ATP dependent DNA ligase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-41  140.9   1.3    4.1e-41  139.9   1.3    1.5  1  Lig_C           Ligase Pab1020 C-terminal region
    3.4e-18   66.5   0.0    7.8e-18   65.3   0.0    1.6  2  RNA_ligase      RNA ligase
  ------ inclusion threshold ------
      0.018   14.7   0.1        6.7    6.3   0.0    2.6  3  DNA_ligase_A_M  ATP dependent DNA ligase domain


Domain annotation for each model (and alignments):
>> Lig_C  Ligase Pab1020 C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.9   1.3   6.8e-45   4.1e-41       2     125 .]     248     371 ..     247     371 .. 0.99

  Alignments for each domain:
  == domain 1  score: 139.9 bits;  conditional E-value: 6.8e-45
                                    HCCSCCGS-STSCHHHHHHHHHHHHHH--SHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---EEEEEEE-SSHHHHHHHH CS
                          Lig_C   2 afsylfelgrdFlfsRviReafqavefeeseeelrerakeLGesiLepmvetikkvkeeekvkeefrvrfkdeenieell 81 
                                    af+y++++++dF+fsRv+Re+fq+ve++e+e+ lrera +LGesiL p+++ti++  ++e++++++++r+++ +++++++
  gi|116753617|ref|YP_842735.1| 248 AFRYYNDYAQDFFFSRVVREGFQSVEWNEDEAALRERALRLGESILVPLTDTIRRRMQGEQIMQQVQIRVRSIQTARDFE 327
                                    9******************************************************************************* PP

                                    HHHHCTT--EEEEEEE..TTEEEEE..EE-HHHHHHHHHHHTT- CS
                          Lig_C  82 ehLrrlgvkaeveekekedgelvvkfkkiaqsttdkikslLeGg 125
                                    +hLrr+g ka+++ +e++++++vv++ k ++st+dk+ +++eG+
  gi|116753617|ref|YP_842735.1| 328 QHLRRMGTKAIFDIPEQDGDRYVVRILKQVMSTNDKTLAVIEGQ 371
                                    ***************************************99996 PP

>> RNA_ligase  RNA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.3   0.0   1.3e-21   7.8e-18       2     156 ..      81     231 ..      80     236 .. 0.74
   2 ?   -2.4   0.0      0.85   5.1e+03      56      69 ..     300     310 ..     250     353 .. 0.53

  Alignments for each domain:
  == domain 1  score: 65.3 bits;  conditional E-value: 1.3e-21
                                    EEEEEEE-SSEEEEEEEETT.EEEEETTCEB.CTTTHHHHHHTHHHHHHHHHHHHH...ECCEEEEEEEES...SS...T CS
                     RNA_ligase   2 evvvtEKlDGtnfriylvke.vgvasRsqil.pfgeekfkefkrwaaalrkklkekla.neelilyGElig..hsi.kyg 75 
                                    +v v+EK++G+n+r + v++ v++ +R++++ p        +++ ++++ +  ++ ++ +++++l+GE++g  +++ + +
  gi|116753617|ref|YP_842735.1|  81 RVAVEEKMNGYNIRAVSVDGdVYALTRGGYIcP-------FSTEIVRERIS--PDLFEdHPDIVLCGEMVGpeNPYvPKD 151
                                    689************999556**********43.......23333344443..344447788*********753334545 PP

                                    TSS....EEEEEEEEEEECTTBECE--HHHHHHHHHCCT..B..EEEEE.SS.HHHHHCCC.H.HHHTC--EEEEEESSS CS
                     RNA_ligase  76 glpk...efyvFdifdirdkeeqrylspdevealakglg..tvpvlyegkfl.aaeellelll.skgnkrEGlVikpese 148
                                     +p    +fy+Fdi    +k+ +  +   +++ala+++    vp+++e++++ aaee+ ++++    + rEG+Vik++++
  gi|116753617|ref|YP_842735.1| 152 VYPVesiDFYLFDIS---KKNCRSMMGVHATHALAEEYSikVVPFFGEFPVErAAEEIFRIIKrLGRSGREGVVIKDPEN 228
                                    577744566666666...7779999***********99999*****99999766666666632568889*******9988 PP

                                    SBETTEBS CS
                     RNA_ligase 149 lyknkgra 156
                                    +       
  gi|116753617|ref|YP_842735.1| 229 R-----TS 231
                                    6.....44 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.85
                                    ..ECCEEEEEEEES CS
                     RNA_ligase  56 laneelilyGElig 69 
                                    ++    +++GE i 
  gi|116753617|ref|YP_842735.1| 300 IR---RRMQGEQIM 310
                                    22...345555555 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 ?    5.3   0.0    0.0023        14      20      82 ..      80     142 ..      72     151 .. 0.85
   2 ?    6.3   0.0    0.0011       6.7     163     189 ..     202     228 ..     156     238 .. 0.86
   3 ?   -2.8   0.0      0.67     4e+03       7      36 ..     323     352 ..     318     359 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0023
                                    SEEEEEEEESSEEEEEEEETTEEEEEETTS-B-GGGCHHHHHHHHHHBSTTESEEEEEEEEEE CS
                 DNA_ligase_A_M  20 kafivEiKyDGeRaqvhkegdkvklfSRrlkditaakpelvkalkeafkkdeksvilDGElva 82 
                                    + + vE+K++G+ ++    +++v+ ++R +   + + + + ++++  +++d  +++l GE+v 
  gi|116753617|ref|YP_842735.1|  80 DRVAVEEKMNGYNIRAVSVDGDVYALTRGGYICPFSTEIVRERISPDLFEDHPDIVLCGEMVG 142
                                    45569********9999999**********999998888889999999999999******995 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0011
                                    SHHHHHHHHHHHHHTTECEEEEEETT- CS
                 DNA_ligase_A_M 163 dveeleelleeaiseglEGlvvKnpds 189
                                     +ee+ +++++  ++g EG+v+K+p+ 
  gi|116753617|ref|YP_842735.1| 202 AAEEIFRIIKRLGRSGREGVVIKDPEN 228
                                    6799999*****************976 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 0.67
                                    ESCHHHHHHHTTTSEEEEEE.EESSEEEEEE CS
                 DNA_ligase_A_M   7 lksiekalkkleekafivEi.KyDGeRaqvh 36 
                                    ++++e+ l+++ ++++i++i   DG+R  v+
  gi|116753617|ref|YP_842735.1| 323 ARDFEQHLRRM-GTKAIFDIpEQDGDRYVVR 352
                                    45778888888.5666666635789886655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2513.68
//
Query:       gi|116753618|ref|YP_842736.1|  [L=262]
Description: CBS domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-41  140.6  12.0    7.4e-12   45.5   0.4    4.1  4  CBS       CBS domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   0.1   1.2e-14   2.1e-10       1      55 [.       3      55 ..       3      56 .. 0.93
   2 !   19.2   0.1   7.1e-08    0.0013       9      53 ..      78     119 ..      70     123 .. 0.86
   3 !   41.4   0.3   8.1e-15   1.5e-10       3      55 ..     129     179 ..     126     181 .. 0.89
   4 !   45.5   0.4   4.1e-16   7.4e-12       1      56 [.     200     255 ..     200     256 .. 0.95

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 1.2e-14
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                            CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55
                                   V+dimt+++ t++ ++ l+ al+lm+++g +rl+V+ ++gkl Gi+t+r ++r+l
  gi|116753618|ref|YP_842736.1|  3 VKDIMTPPI-TIDKSERLGHALDLMEKHGTRRLLVT-NNGKLGGIITMRQIARVL 55
                                   89***8877.***************9999****888.6***99*********987 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 7.1e-08
                                    CEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                            CBS   9 vvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                                    v+ v+p++ +eea+ l+ +    +++VV  +++++G v  r +l 
  gi|116753618|ref|YP_842736.1|  78 VIPVHPEMGVEEAILLLQK--T-SVLVVTQNDEILGWVRPREILA 119
                                    799**************55..5.7769988999*********996 PP

  == domain 3  score: 41.4 bits;  conditional E-value: 8.1e-15
                                    HHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                            CBS   3 dimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                    d m++ + tv+p + l  a ++m +++++rlPV+ + gklvGi+t+rD++ral
  gi|116753618|ref|YP_842736.1| 129 DAMRSAL-TVSPRDRLIHARRMMMDRDIGRLPVL-DGGKLVGILTERDIARAL 179
                                    6676666.**************87999*******.6999************98 PP

  == domain 4  score: 45.5 bits;  conditional E-value: 4.1e-16
                                    HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                            CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                    V+d+mt+dv +v+ dt+lee+ +++ e++ ++lPV+++dg l G++t+r l+++l+
  gi|116753618|ref|YP_842736.1| 200 VSDVMTHDVKYVYVDTPLEEVRRIILEENRGGLPVLNSDGTLAGMITRRCLIDYLV 255
                                    89**********************778888*********************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); 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 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1847.94
//
Query:       gi|116753619|ref|YP_842737.1|  [L=282]
Description: signal transduction protein [Methanosaeta thermophila PT]
Scores for complete 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-43  145.1   9.2    4.2e-15   55.9   0.1    4.2  4  CBS       CBS domain
  ------ inclusion threshold ------
       0.13   12.8   0.1       0.66   10.5   0.0    2.1  2  B_lectin  D-mannose binding lectin
       0.13   12.2   0.0         68    3.5   0.0    3.5  4  GCV_T_C   Glycine cleavage T-protein C-terminal 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 !   41.1   0.0   2.9e-14   1.7e-10       1      55 [.       3      56 ..       3      58 .. 0.92
   2 !   55.9   0.1     7e-19   4.2e-15       4      55 ..      76     126 ..      68     128 .. 0.93
   3 !   33.8   0.3   5.8e-12   3.5e-08       1      52 [.     135     186 ..     135     188 .. 0.92
   4 !   17.8   0.4   5.5e-07    0.0033       1      54 [.     226     278 ..     225     281 .. 0.90

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 2.9e-14
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                            CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55
                                   V+d+m ++v +v  ++++  a +lm ++++srlPV+ + gklvGivt+ D+ + l
  gi|116753619|ref|YP_842737.1|  3 VKDYMATPVWVVERNEPIQRARNLMFKHDISRLPVM-DKGKLVGIVTKYDISNRL 56
                                   89**********************65888*******.6************97665 PP

  == domain 2  score: 55.9 bits;  conditional E-value: 7e-19
                                    HSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                            CBS   4 imtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                    +mt++++t++pd+tl +a+elm e+++++lPV ++dg+lvGi+t rDll++ 
  gi|116753619|ref|YP_842737.1|  76 VMTENPITIYPDATLTQAAELMMENEIDGLPV-EKDGELVGIITSRDLLKYF 126
                                    6********************87999******.79***************96 PP

  == domain 3  score: 33.8 bits;  conditional E-value: 5.8e-12
                                    HHHHSBSSCEEEETTSBHHHHHHHHHH.HTSSEEEEEETTTBEEEEEEHHHHH CS
                            CBS   1 Vgdimtrdvvtvppdttleealelmre.kgvsrlPVVdedgklvGivtlrDll 52 
                                    Vgd+m + +v+v+   t++ ++e+m + +gvsr++V +++ ++vG++t++ l 
  gi|116753619|ref|YP_842737.1| 135 VGDLMAEGMVSVHRHHTIAHVVEQM-NlHGVSRVLVYEDNMRPVGVITRSNLT 186
                                    89***********************.6478****9998888********9885 PP

  == domain 4  score: 17.8 bits;  conditional E-value: 5.5e-07
                                    HHHHSBSSCEEEETTSB.HHHHHHHHHHHT.SSEEEEEETTTBEEEEEEHHHHHHH CS
                            CBS   1 Vgdimtrdvvtvppdtt.leealelmrekg.vsrlPVVdedgklvGivtlrDllra 54 
                                    ++dim+++++ ++ d+  + +a  l  ek  + ++PV+ e++  vG ++ r ++  
  gi|116753619|ref|YP_842737.1| 226 AEDIMSSPIIAARVDDKaVDDAKVLV-EKSiC-GMPVI-ENDSMVGFFSTREIVAE 278
                                    469***********************.88878.*****.7888********99876 PP

>> B_lectin  D-mannose binding lectin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00011      0.66       1      33 [.       9      41 ..       9      60 .. 0.66
   2 ?   -0.4   0.0      0.29   1.7e+03      64      79 ..     182     197 ..      93     217 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00011
                       B_lectin  1 TvvWVaNrekPikdssgvlkise.dgnLvllnes 33
                                   T vWV +r++Pi+++ + l +++  ++L ++++ 
  gi|116753619|ref|YP_842737.1|  9 TPVWVVERNEPIQRARN-LMFKHdISRLPVMDKG 41
                                   89**********66655.3333313456555554 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.29
                       B_lectin  64 sssnseevlWqsfdhp 79 
                                    +s+ + + +++sfd+p
  gi|116753619|ref|YP_842737.1| 182 RSNLTFAGIFDSFDQP 197
                                    3344444556666666 PP

>> GCV_T_C  Glycine cleavage T-protein C-terminal barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.011        68      20      41 ..      36      57 ..      25      59 .. 0.89
   2 ?    3.2   0.0     0.014        85      18      33 ..     104     119 ..      92     122 .. 0.86
   3 ?    0.0   0.0      0.14   8.2e+02      21      35 ..     169     184 ..     149     188 .. 0.73
   4 ?   -1.9   0.0      0.55   3.3e+03      18      30 ..     257     269 ..     236     275 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.011
                        GCV_T_C 20 pilrdgevvGhvTSgaysptlg 41
                                   p+++ g+ vG vT    s +l 
  gi|116753619|ref|YP_842737.1| 36 PVMDKGKLVGIVTKYDISNRLA 57
                                   78899*********99999886 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.014
                        GCV_T_C  18 gepilrdgevvGhvTS 33 
                                    g p+ +dge vG +TS
  gi|116753619|ref|YP_842737.1| 104 GLPVEKDGELVGIITS 119
                                    568899*********9 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.14
                        GCV_T_C  21 ilr.dgevvGhvTSga 35 
                                    +++ + ++vG +T++ 
  gi|116753619|ref|YP_842737.1| 169 VYEdNMRPVGVITRSN 184
                                    44435599*****986 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 0.55
                        GCV_T_C  18 gepilrdgevvGh 30 
                                    g+p+++++ +vG+
  gi|116753619|ref|YP_842737.1| 257 GMPVIENDSMVGF 269
                                    6788888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 2070.11
//
Query:       gi|116753620|ref|YP_842738.1|  [L=320]
Description: signal transduction protein [Methanosaeta thermophila PT]
Scores for complete 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  161.5   9.7    3.7e-12   46.5   0.1    4.2  4  CBS       CBS domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.0   3.6e-12   6.5e-08       4      55 ..      44      96 ..      39      98 .. 0.89
   2 !   44.6   0.6     8e-16   1.4e-11       1      55 [.     121     175 ..     121     177 .. 0.95
   3 !   46.5   0.1   2.1e-16   3.7e-12       1      56 [.     184     238 ..     184     239 .. 0.96
   4 !   41.3   0.2   8.6e-15   1.5e-10       2      56 ..     260     313 ..     251     314 .. 0.89

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 3.6e-12
                                   HSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTT..BEEEEEEHHHHHHHH CS
                            CBS  4 imtrdvvtvppdttleealelmrekgvsrlPVVdedg..klvGivtlrDllral 55
                                   i +++vvt+pp+tt+  a+++m ++g++rlP+  + g  +l+G vt  D++++l
  gi|116753620|ref|YP_842738.1| 44 IASTEVVTAPPTTTIIGAIKIMNSYGFRRLPIA-DAGtnRLLGFVTCVDIVDFL 96
                                   5899******************9999******9.466669***********998 PP

  == domain 2  score: 44.6 bits;  conditional E-value: 8e-16
                                    HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                            CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                    +++im+++++++p ++++ eal++m e++v++lP+Vde  ++  ivt++D ++++
  gi|116753620|ref|YP_842738.1| 121 IREIMSTKLISAPDTASVDEALRIMYERNVGGLPIVDERSRIKAIVTEEDFVEVV 175
                                    589**********************9************************99875 PP

  == domain 3  score: 46.5 bits;  conditional E-value: 2.1e-16
                                    HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                            CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                    V+d+m+++vvt+p ++++e+  +++++kg++rlP++  dg l Gi+t +D++++++
  gi|116753620|ref|YP_842738.1| 184 VSDYMSPNVVTAPASMSIEKTSRMIVQKGFRRLPII-QDGILTGIITASDIMKYMA 238
                                    89**********************************.7**999**********986 PP

  == domain 4  score: 41.3 bits;  conditional E-value: 8.6e-15
                                    HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                            CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                    +++  r +++ +p t l++a++lm+ek+v++lPV+ e g  vGi+t+rD lral+
  gi|116753620|ref|YP_842738.1| 260 KSLIKRSLIMTDPRTRLKDAANLMVEKDVGSLPVM-EGGSMVGIITERDFLRALA 313
                                    455667789**************************.8999*************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2268.54
//
Query:       gi|116753621|ref|YP_842739.1|  [L=261]
Description: signal transduction protein [Methanosaeta thermophila PT]
Scores for complete 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  155.3  16.1    5.4e-16   58.8   0.4    4.1  4  CBS       CBS domain
    0.00043   20.3   0.2        1.1    9.4   0.0    2.9  2  PRC       PRC-barrel domain
  ------ inclusion threshold ------
      0.026   14.8   0.1        9.8    6.5   0.0    2.9  3  IF3_N     Translation initiation factor IF-3, N-terminal doma
      0.052   14.0   0.0      0.085   13.3   0.0    1.4  1  MAGP      Microfibril-associated glycoprotein (MAGP)


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   0.3   2.8e-14   1.3e-10       1      53 [.       3      55 ..       3      58 .. 0.97
   2 !   21.5   0.1   5.1e-08   0.00023       9      55 ..      72     120 ..      65     122 .. 0.81
   3 !   58.8   0.4   1.2e-19   5.4e-16       1      53 [.     130     182 ..     130     184 .. 0.96
   4 !   43.1   0.6   9.7e-15   4.4e-11       1      56 [.     204     258 ..     204     259 .. 0.96

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 2.8e-14
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                            CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53
                                   V+dim+rd+++v  ++    a +l+r+++v++lPV+d +g+++Givt  D lr
  gi|116753621|ref|YP_842739.1|  3 VADIMSRDPLYVEKTDFATRARQLIRDNHVRGLPVIDPEGRVIGIVTNQDMLR 55
                                   89***********************9999*********************998 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 5.1e-08
                                    CEEEETTSBHHHHHHHHHHHTSSEEEEE..ETTTBEEEEEEHHHHHHHH CS
                            CBS   9 vvtvppdttleealelmrekgvsrlPVV..dedgklvGivtlrDllral 55 
                                    v+ +++++++ +a++lm +++v+ lPVV  +++  l G+v+l D+++ l
  gi|116753621|ref|YP_842739.1|  72 VPLITEEMDMMDAARLMFQEKVTLLPVVdsPSSRMLRGVVSLLDIFKHL 120
                                    67899***********65777*888***544444588*********987 PP

  == domain 3  score: 58.8 bits;  conditional E-value: 1.2e-19
                                    HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                            CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                                    V +im+rdv+t++pd++++++ ++m e+++++lPVV+e+g+++Gi+t+ D+l+
  gi|116753621|ref|YP_842739.1| 130 VDAIMSRDVITARPDDPISKVWDRMLEEDITGLPVVNESGRPIGIITRFDILK 182
                                    5689***********************************************98 PP

  == domain 4  score: 43.1 bits;  conditional E-value: 9.7e-15
                                    HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                            CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                    V+ +m++++ +++ d++l++a+e m +++++r+ VV e++ lvGiv + Dl++a+l
  gi|116753621|ref|YP_842739.1| 204 VEKLMSTPLYSIKRDAPLRQAVEVMLKHDIGRISVV-ENDVLVGIVDRYDLIKAVL 258
                                    7789********************************.8**9************986 PP

>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0   0.00084       3.7       4      27 ..      27      50 ..      25      54 .. 0.89
   2 !    9.4   0.0   0.00024       1.1       8      28 ..     158     178 ..     152     184 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00084
                                   CCS---TT-EEEETTSSEEEEEEE CS
                            PRC  4 frasdliGkeVytedGeklGkVkD 27
                                   +r + ++G++V++ +G+ +G V++
  gi|116753621|ref|YP_842739.1| 27 IRDNHVRGLPVIDPEGRVIGIVTN 50
                                   677889***************975 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00024
                                    --TT-EEEETTSSEEEEEEEE CS
                            PRC   8 dliGkeVytedGeklGkVkDv 28 
                                    d+ G++V++e+G+ +G ++ +
  gi|116753621|ref|YP_842739.1| 158 DITGLPVVNESGRPIGIITRF 178
                                    899*************99865 PP

>> IF3_N  Translation initiation factor IF-3, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0    0.0069        31       8      33 ..      33      58 ..      25      64 .. 0.81
   2 ?   -2.1   0.0       1.1   4.8e+03      12      12 ..      98      98 ..      74     122 .. 0.55
   3 ?    6.5   0.0    0.0022       9.8      12      56 ..     164     210 ..     158     219 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0069
                                   SEEEEE-SSS-EEEEEEHHHHHHHHH CS
                          IF3_N  8 revrlvdedGeqlGvistreAlrlae 33
                                   r   ++d +G  +G+++ ++ lr+  
  gi|116753621|ref|YP_842739.1| 33 RGLPVIDPEGRVIGIVTNQDMLRITS 58
                                   44459*****************9875 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.1
                                   E CS
                          IF3_N 12 l 12
                                   +
  gi|116753621|ref|YP_842739.1| 98 V 98
                                   3 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0022
                                    EE-SSS-EEEEEEHHHHHHH..HHHHTSEEEEEESSSSS-EEEEE-H CS
                          IF3_N  12 lvdedGeqlGvistreAlrl..aeekgldLVevspnaepPVcrimdy 56 
                                    +v+e G  +G+i++ ++l++  a+  + d+   + +a+  V ++m+ 
  gi|116753621|ref|YP_842739.1| 164 VVNESGRPIGIITRFDILKRgwARLGKEDMYRSKDTAKIRVEKLMST 210
                                    89****************95338888889999999999988888865 PP

>> MAGP  Microfibril-associated glycoprotein (MAGP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.9e-05     0.085      73     124 ..     195     248 ..     163     256 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.9e-05
                           MAGP  73 dknasaeCreekypCtrlysvhk..PvkqClkqlcfyslrrvYiinkeiCvrlv 124
                                      + +a+ r ek+  t lys+++  P++q ++ +    + r+ ++ +++ v +v
  gi|116753621|ref|YP_842739.1| 195 RSKDTAKIRVEKLMSTPLYSIKRdaPLRQAVEVMLKHDIGRISVVENDVLVGIV 248
                                    45678999*************97779**********************988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1824.66
//
Query:       gi|116753622|ref|YP_842740.1|  [L=185]
Description: signal-transduction protein [Methanosaeta thermophila PT]
Scores for complete 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-33  115.0   6.1    7.9e-18   64.7   0.3    2.3  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 !   52.9   1.1   2.1e-18   3.7e-14       1      55 [.       7      60 ..       7      62 .. 0.92
   2 !   64.7   0.3   4.4e-22   7.9e-18       1      53 [.      72     124 ..      72     126 .. 0.97

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 2.1e-18
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                            CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55
                                   V++im+r+v+tv+ dt++ +a+++m++++v++l VV    k++Gi+t+rDl++++
  gi|116753622|ref|YP_842740.1|  7 VREIMSRPVLTVDADTDVLDAANRMISANVGSLIVVQ-GAKPIGIITERDLVKKV 60
                                   89*******************************9994.447**********9986 PP

  == domain 2  score: 64.7 bits;  conditional E-value: 4.4e-22
                                    HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                            CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                                    Vgd+m+++++ ++pd++l++a+elm ++gv rlPV+ +dgklvGi+t++Dl++
  gi|116753622|ref|YP_842740.1|  72 VGDVMNSPLIKIHPDASLRDAAELMLKSGVKRLPVISDDGKLVGIITDTDLVS 124
                                    89**********************************99************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); 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: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1323.08
//
Query:       gi|116753623|ref|YP_842741.1|  [L=162]
Description: molybdenum cofactor synthesis domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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   95.4   0.1    2.7e-27   95.2   0.1    1.0  1  MoCF_biosynth  Probable molybdopterin binding domain


Domain annotation for each model (and alignments):
>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.2   0.1   1.5e-31   2.7e-27       3     144 .]       6     154 ..       4     154 .. 0.94

  Alignments for each domain:
  == domain 1  score: 95.2 bits;  conditional E-value: 1.5e-31
                                    EEE-HHHH........TTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTS.SEEEEESS-SSSTT-- CS
                  MoCF_biosynth   3 itvGdell........sgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleea.dviittGGtGptpdDv 73 
                                    itv+++++        + ++eD +g+ ++e++++ g++ + y+++pD  + ++ all+++e++ d++i++GGtG++p D+
  gi|116753623|ref|YP_842741.1|   6 ITVSTSRFmqygavsgPDDAEDVSGKAIVEKITASGHDFR-YRLIPDGVMPVRIALLESIERKsDAVIFCGGTGLSPSDL 84 
                                    89999999999999999999*****************987.99*************88888888**************** PP

                                    HHHHHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EE.....TTEEEEE-SSHHHHHHHHHHHHHGGHHH CS
                  MoCF_biosynth  74 tpealaklfekelegfeeafrrvslkpgkpvgvapgailsrav.....gktiigLPGspkavkealeeillpaleh 144
                                    t ea+++l ek+++gf+e+fr  s+++     v++ ++l ra      g +++++PGsp a+  ++e+il ++leh
  gi|116753623|ref|YP_842741.1|  85 TIEAIEPLVEKSIPGFGEIFRLKSMEQ-----VGTRVMLTRASagiisGVPVFAIPGSPAAASLGIELIL-QELEH 154
                                    **************************8.....999999**99999**7777******************9.88876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 1158.91
//
Query:       gi|116753624|ref|YP_842742.1|  [L=81]
Description: hypothetical protein Mthe_0307 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 586.73
//
Query:       gi|116753625|ref|YP_842743.1|  [L=98]
Description: hypothetical protein Mthe_0308 [Methanosaeta thermophila PT]
Scores for complete 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   90.1   0.8      7e-26   90.0   0.8    1.0  1  Thiamine_BP  Thiamine-binding protein


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 !   90.0   0.8   3.9e-30     7e-26       1      91 [.       4      94 ..       4      95 .. 0.98

  Alignments for each domain:
  == domain 1  score: 90.0 bits;  conditional E-value: 3.9e-30
                                   EEEEEEECSSSSSGHHHHHHHHHHHHHTTSSEEEEETTEEEEEEE.HHHHHHHHHHHHHHHHCTTSSEEEEEEEEEEESSS- CS
                    Thiamine_BP  1 veisviPlgtegesvskyVakvvevlkesglkyeltpmgTtiege.ldevmevvkkahealfeaGakRvstvikiddrrdke 81
                                   +e+sviP+g  g+s  +y+ +v+e+l++sg+++  ++m+Ttie+e +++v+ +v++a+++l +++++Rv+t++ id+r dk 
  gi|116753625|ref|YP_842743.1|  4 AEFSVIPMGA-GTSAGRYIRAVHEMLRNSGIRFVPGAMSTTIEAEsIEQVCMIVERANKILTDMEVQRVITTVTIDYRLDKV 84
                                   69*******9.*********************************************************************** PP

                                   --HHHHHHHH CS
                    Thiamine_BP 82 qtleeKvksv 91
                                    +++ K+k++
  gi|116753625|ref|YP_842743.1| 85 ISIDTKLKAL 94
                                   *******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 754.86
//
Query:       gi|116753626|ref|YP_842744.1|  [L=510]
Description: Na+/solute symporter [Methanosaeta thermophila PT]
Scores for complete 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  185.9  37.3    1.4e-54  185.6  37.3    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 !  185.6  37.3   7.7e-59   1.4e-54       1     406 []      33     447 ..      33     447 .. 0.94

  Alignments for each domain:
  == domain 1  score: 185.6 bits;  conditional E-value: 7.7e-59
                            SSF   1 yflagrsltgfvlglslaasnisaasfvGlaGavaasGlavvllelgalllvlllllllaerlr....nagalTlpdyls 76 
                                    +++agr+l+ + l l + as  s+  ++G +G+++  G  +++ ++ + l + +++l+ + +l     ++g +T+ dyl+
  gi|116753626|ref|YP_842744.1|  33 FIVAGRNLGFWLLTLMIVASICSGMTILGTSGLGYIGGWPTIWEQIFVPLSAAFVILVYGTKLHaiseRMGYITIQDYLA 112
                                    89*************************************99998888888888888888888888999************ PP

                            SSF  77 kRfkgkrilvylsalslllvitlklsvdlvggaklielalGlnyetavlllaaltalYtviGGllAvvytdtiqavlmlv 156
                                    +Rf ++r l+ lsa++ +lv  ++l  + v+  + +  +l ++y+ a+l++a+++++Yt++GGl A+ +   +q++++l+
  gi|116753626|ref|YP_842744.1| 113 QRFYSQRGLRGLSAVAGILVSLIYLVGQYVAISMVLSWMLKISYTDALLIGAIIVMIYTILGGLYAIAWISLVQGLMILI 192
                                    ******************************************************************************** PP

                            SSF 157 galilliivllevGgleslveklkeaapkvvdl....lt.pdslkllrdpltalslwlglvlGvaglphilvRflaakda 231
                                    g li++ + + ++Ggl ++ + l+ ++p+ v++    ++ p+++  ++ p+   s+  +l +G+a +ph++  +l+a + 
  gi|116753626|ref|YP_842744.1| 193 GVLIVSPFIIQSAGGLTHVNNVLAGIDPNYVKIwypqMHpPYAKYAFLTPMYLVSFFFLLTFGLASAPHVINNVLSARSR 272
                                    *****************************98886666446999999********************************** PP

                            SSF 232 kailkgvlkltivlilvligmisiilfaiklagavp..kavgtevgvsniaypeLvvkllpnllaGlllavmlAaimstl 309
                                    +    + l + ++ ++v+ + i i  fa +++   +  ++ +++ +++++a++  +++++p+    l+  ++l+a+mst 
  gi|116753626|ref|YP_842744.1| 273 SFFKWSPLAAFVLYLIVMYL-IKISGFASRVMVEEGmiALPTNVSNAQDYAFVVAAMHIFPHTAGPLVAVIVLSAVMSTT 351
                                    **********9999999999.889899999999999655566777899***************9999999********** PP

                            SSF 310 tslllsassaftkDlYkkirrkasakekelvgvsriivlvvislaillavqeeqkgvlklvelafaglasavlavillal 389
                                    + l+l   s +  D+Yk ++ k+ a+++ +  vsr++++  + l ++la+ ++ + +++l+ + ++++ + ++  il +l
  gi|116753626|ref|YP_842744.1| 352 DRLMLTIGSYVGWDIYKMFFNKK-ASDRSITLVSRLAIVFSVILTLILAWRKPPELLAFLIWMGIGIMLATFVVPILSGL 430
                                    ********************999.99999999999999888888899999888877************************ PP

                            SSF 390 fwkrvneqGAlagliiG 406
                                    +w r++++GA+a++ +G
  gi|116753626|ref|YP_842744.1| 431 YWRRATREGAIASMSLG 447
                                    *************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (510 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1077  (0.0600703); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.46
# Mc/sec: 3311.95
//
Query:       gi|116753627|ref|YP_842745.1|  [L=204]
Description: CDP-alcohol phosphatidyltransferase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-12   47.4   2.5    2.4e-12   47.4   2.5    2.3  2  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase


Domain annotation for each model (and alignments):
>> CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.4   2.5   1.4e-16   2.4e-12       2      66 .]      27      95 ..      26      95 .. 0.87
   2 ?   -0.4   1.2      0.11     2e+03      11      24 ..     153     165 ..     100     197 .. 0.62

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 1.4e-16
                                   -HHHHHHHHHHHHHHHHHGGGS-H........HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
                CDP-OH_P_transf  2 lPnaiTllrlllsvlailllltyyp......lvlailllliasltDalDGklARrlnqvstlGkllDslaD 66
                                   +Pn++++l+l++s+la++++ ++        l+ a++++++ +l+Da+DG lARr++   + G++lD+++D
  gi|116753627|ref|YP_842745.1| 27 TPNMLSVLSLCFSFLAFVFY-YI-SasdqrmLLGAAIMVMLNGLADAVDGALARRMGHADQRGDFLDHVID 95
                                   8****************744.33.357***8888888889****************99666********99 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.11
                                    HHHHHHHHHGGGS- CS
                CDP-OH_P_transf  11 lllsvlaillllty 24 
                                    l++ ++a+ l +++
  gi|116753627|ref|YP_842745.1| 153 LVFLIIAT-LANAL 165
                                    33333333.23333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       780  (0.0435049); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1459.65
//
Query:       gi|116753628|ref|YP_842746.1|  [L=173]
Description: hypothetical protein Mthe_0311 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      9e-26   91.0   0.0    1.1e-25   90.6   0.0    1.1  1  AAA_18        AAA domain
    0.00021   21.7   0.1    0.00057   20.3   0.1    1.9  1  AAA_17        AAA domain
     0.0005   20.3   0.5     0.0013   19.0   0.4    1.9  1  AAA_28        AAA domain
     0.0026   17.9   0.0        1.2    9.2   0.0    2.2  2  AAA_33        AAA domain
  ------ inclusion threshold ------
      0.086   13.1   0.3       0.19   12.0   0.3    1.5  1  ABC_tran_CTD  ABC transporter C-terminal domain
      0.097   12.6   0.1       0.22   11.4   0.1    1.7  2  NTPase_1      NTPase
       0.21   11.3   0.0       0.33   10.7   0.0    1.3  1  AAA_24        AAA domain
       0.31   10.4   1.5        1.3    8.3   0.8    2.2  3  ATPase        KaiC
       0.49   10.8   2.6        4.6    7.6   2.6    2.0  1  AAA_16        AAA ATPase domain
          3    7.4   5.9        4.5    6.8   0.9    2.5  3  AAA_25        AAA domain


Domain annotation for each model (and alignments):
>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.6   0.0   6.2e-29   1.1e-25       1     130 []       3     117 ..       3     117 .. 0.97

  Alignments for each domain:
  == domain 1  score: 90.6 bits;  conditional E-value: 6.2e-29
                         AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegknlvid 80 
                                    I+ltGtpG+GKtt++  L  r   +vnl+d++++ g++ ++dpe  +e++++d+d l++ ++++e+++      ++l+i+
  gi|116753628|ref|YP_842746.1|   3 IALTGTPGTGKTTVSGLLPFR---VVNLNDLIRD-GMSAGFDPE--RECLEADMDALEEKIEEIERSCG----DDVLIIE 72 
                                    89****************999...9********9.9********..********************998....8999*** PP

                         AAA_18  81 ghlaeleseaakdikkvvLtaspeelleRlekRgyeeakikeneeaeild 130
                                    gh a+++ ++a     +vL+++p++l++Rle+Rgy+  ki+en eae++d
  gi|116753628|ref|YP_842746.1|  73 GHFAHHFADEA-----IVLRLHPNVLRRRLEARGYSASKIRENVEAEAID 117
                                    *********99.....9******************************975 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   3.2e-07   0.00057       1      81 [.       6      76 ..       6     146 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 3.2e-07
                                   EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE-SE CS
                         AAA_17  1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemrklpleekkelqkeaaekiaeeakkkgvlvdghpr 81
                                   +G PG GK+t++      + f +++  dl+r+ ++  g +++r+      le + + ++e +e+i++ ++++ ++++gh+ 
  gi|116753628|ref|YP_842746.1|  6 TGTPGTGKTTVS----GLLPFRVVNLNDLIRDGMS-AGFDPERE-----CLEADMDALEEKIEEIERSCGDDVLIIEGHFA 76
                                   69**********....668*************985.55555555.....567788888889999***************96 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.4   7.1e-07    0.0013       1      63 [.       2      61 ..       2     121 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 7.1e-07
                         AAA_28  1 kivitGgestGKTtlleaLaargypvv..pEaareileeklakgedalpwvedllafaervleeq 63
                                   +i++tG+++tGKTt++  L  r   vv   +  r+ ++ + + +++ l++  d+ a++e+++e +
  gi|116753628|ref|YP_842746.1|  2 RIALTGTPGTGKTTVSGLLPFR---VVnlNDLIRDGMSAGFDPERECLEA--DMDALEEKIEEIE 61
                                   79*************9888633...3333666677766666666665554..6666666666554 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0   0.00069       1.2       4      32 ..       5      29 ..       3      64 .. 0.73
   2 !    6.8   0.0    0.0039       7.1      95     134 ..      77     117 ..      71     122 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00069
                         AAA_33  4 lvGlpGsGKstlaerllkklgavllssdt 32
                                   l G pG+GK+t++  l    ++ +++ ++
  gi|116753628|ref|YP_842746.1|  5 LTGTPGTGKTTVSGLL----PFRVVNLND 29
                                   78*********98643....355555555 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0039
                         AAA_33  95 lgvpvrivvvetdeetlkeRlakRaang.ddrsevpeeald 134
                                    ++++++++v++  + +l++Rl++R  +  + r +v+ ea+d
  gi|116753628|ref|YP_842746.1|  77 HHFADEAIVLRLHPNVLRRRLEARGYSAsKIRENVEAEAID 117
                                    68899*******************99754667777777776 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.3    0.0001      0.19      11      29 ..      44      62 ..      40      68 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0001
                   ABC_tran_CTD 11 eeleaeIeaLEeeiaelea 29
                                   e lea+++aLEe+i+e+e 
  gi|116753628|ref|YP_842746.1| 44 ECLEADMDALEEKIEEIER 62
                                   679**************97 PP

>> NTPase_1  NTPase
   #    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       1      15 [.       2      16 ..       2      37 .. 0.88
   2 ?   -2.5   0.0       2.3   4.1e+03      44      44 ..     113     113 ..      85     152 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                                   EEEEE--TTSSHHHH CS
                       NTPase_1  1 kvfiTGppGvGKtTl 15
                                   ++++TG pG+GKtT+
  gi|116753628|ref|YP_842746.1|  2 RIALTGTPGTGKTTV 16
                                   689***********8 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.3
                                    - CS
                       NTPase_1  44 r 44 
                                     
  gi|116753628|ref|YP_842746.1| 113 A 113
                                    2 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00018      0.33       4      20 ..       2      18 ..       1      35 [. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00018
                         AAA_24  4 kiliyGpsgiGKTtlak 20
                                   +i+++G +g+GKTt+  
  gi|116753628|ref|YP_842746.1|  2 RIALTGTPGTGKTTVSG 18
                                   89************875 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.8   0.00072       1.3      22      36 ..       3      17 ..       1      72 [. 0.66
   2 ?    1.0   0.0      0.13   2.3e+02     100     126 ..      46      72 ..      27     122 .. 0.71
   3 ?   -1.1   0.0      0.53   9.5e+02      60      94 ..      90     124 ..      83     155 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00072
                         ATPase 22 vlitGepGtGKtifa 36
                                   + +tG+pGtGKt+++
  gi|116753628|ref|YP_842746.1|  3 IALTGTPGTGKTTVS 17
                                   689*********987 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.13
                         ATPase 100 dkedleelieelaeaikeikakrvviD 126
                                     ++d+++l e+++e+ ++ +   ++i 
  gi|116753628|ref|YP_842746.1|  46 LEADMDALEEKIEEIERSCGDDVLIIE 72 
                                    567788888888888888777777774 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.53
                         ATPase  60 aedlrenakslGwdlekleeegklaiidasesaee 94 
                                    ++ lr++ ++ G    k++e+ +   id+   ++ 
  gi|116753628|ref|YP_842746.1|  90 PNVLRRRLEARGYSASKIRENVEAEAIDLILVEAL 124
                                    56677777777777777777777777776555444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   2.6    0.0025       4.6      27      45 ..       3      21 ..       2     158 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0025
                         AAA_16 27 vllsGesGvGKsslvrell 45
                                   + l+G +G+GK+++   l+
  gi|116753628|ref|YP_842746.1|  3 IALTGTPGTGKTTVSGLLP 21
                                   579**********987776 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.9    0.0025       4.5      36      49 ..       3      16 ..       1      30 [. 0.89
   2 ?    3.1   0.1     0.035        63     124     147 ..      42      70 ..      19      82 .. 0.73
   3 ?   -1.9   0.0       1.1     2e+03     134     147 ..     108     120 ..      89     154 .. 0.49

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0025
                         AAA_25 36 allaGapgtGKttl 49
                                   ++l+G pgtGKtt+
  gi|116753628|ref|YP_842746.1|  3 IALTGTPGTGKTTV 16
                                   68***********8 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.035
                         AAA_25 124 tl..ltadvdaleaaieeveg...vrlvv 147
                                    ++  l+ad+dale++iee+e+    ++++
  gi|116753628|ref|YP_842746.1|  42 ERecLEADMDALEEKIEEIERscgDDVLI 70 
                                    44458899999999999987654455555 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.1
                         AAA_25 134 eaaieevegvrlvv 147
                                    ++ +e+ e ++l+ 
  gi|116753628|ref|YP_842746.1| 108 RENVEA-EAIDLIL 120
                                    333333.3333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      619  (0.0345251); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 1262.31
//
Query:       gi|116753629|ref|YP_842747.1|  [L=352]
Description: histidinol-phosphate aminotransferase [Methanosaeta thermophila PT]
Scores for complete 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-49  168.4   0.0    3.1e-49  168.1   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    1.5e-05   24.1   0.0    0.00031   19.7   0.0    2.0  2  Alliinase_C      Allinase
      0.007   14.9   0.0       0.01   14.4   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
  ------ inclusion threshold ------
      0.085   11.6   0.0       0.11   11.3   0.0    1.1  1  Aminotran_MocR   Alanine-glyoxylate amino-transferase


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.1   0.0   6.8e-53   3.1e-49       2     362 ..      36     346 ..      35     346 .. 0.93

  Alignments for each domain:
  == domain 1  score: 168.1 bits;  conditional E-value: 6.8e-53
                                    EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHH CS
                  Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagali 81 
                                     +++Lgsne++++    ++p+v++a +e      +ln y+ +    +l e +a++ +        +e++v+ gsG + +i
  gi|116753629|ref|YP_842747.1|  36 RIVKLGSNENPYG----PSPAVRRAIAE-----APLNLYPETV---DLIESIARYTN-------FPEGQVLIGSGMDGVI 96 
                                    579**********....*********98.....9*********...***********.......8999************ PP

                                    HHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT CS
                  Aminotran_1_2  82 ealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPt 161
                                    ++l +l+ l++g + l+p+pt++ y+ +  l+g+  v ++       +    +++e l++   ++  + +++++sp+NPt
  gi|116753629|ref|YP_842747.1|  97 DTLSRLF-LDHGVRALIPTPTFSYYEIVTILCGADPVFVR-------RTEPGEMIERLRD---KS--IGMVFICSPNNPT 163
                                    *******.********************************.......8899999999998...44..59*********** PP

                                    --B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHH CS
                  Aminotran_1_2 162 GtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvs 241
                                    G v ++e l+ +   +++  +++f+DeaY +f+  s+     + +v+e+ nl++ +++sKafGlaG R+Gy+l+ +++++
  gi|116753629|ref|YP_842747.1| 164 GEVVDEELLRSI---IESTDAVVFLDEAYVEFAERSM-----VDLVNEYENLVVGRTMSKAFGLAGVRLGYALAPEWIAE 235
                                    ************...888899**************65.....9************************************* PP

                                    HHHHHHHHHTS.SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEEEEETHHCHHHH CS
                  Aminotran_1_2 242 qlrklsrpfls.ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmflltdlsaetakel 320
                                    + r ++ pf   ++++ aa  aalsd +    ++  +++ ++++r+ l +e+    ++  +s ++++++   +++  + +
  gi|116753629|ref|YP_842747.1| 236 AYRMAAPPFFGvTTPAVAAGIAALSDLE----HMRRSVEMIKRERELLLSEI----VEASPSWGNFLYIETSERS--DVI 305
                                    **********9***************88....9******************9....6677777777777666555..555 PP

                                    HHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHHH CS
                  Aminotran_1_2 321 skkLleevgvyvtpgtsftv..pgrlRitvAglteeeleelvea 362
                                     + +l + g++v+ ++sf+     ++R+tv  +t+e++ +++ea
  gi|116753629|ref|YP_842747.1| 306 TERMLRK-GIIVRDCRSFRDagDHHIRVTV--GTPEQNARFLEA 346
                                    6668888.***********999999*****..*****9999986 PP

>> Alliinase_C  Allinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0     7e-08   0.00031     142     208 ..     155     229 ..     127     239 .. 0.75
   2 ?    2.3   0.0     0.014        63     282     345 ..     268     334 ..     257     346 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 7e-08
                                    EEESS-TTT--.....-------TT-EEEEEE-TT-.STTTS---..S-B--SEEEEEHHHHHS-GGG-EEEEEE CS
                    Alliinase_C 142 lvtsPnnPdgl.....lreavvkgseakviyDlayY.WPhytpit..skadedimLftlskltGhaGsrlGWalv 208
                                    ++ sPnnP g      l ++++++++a v  D ay  + + + +   ++ ++ ++  t+sk  G aG rlG+al 
  gi|116753629|ref|YP_842747.1| 155 FICSPNNPTGEvvdeeLLRSIIESTDAVVFLDEAYVeFAERSMVDlvNEYENLVVGRTMSKAFGLAGVRLGYALA 229
                                    579*****87522222678899*****9******97345545444104444556668****************95 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.014
                                    E-----EEEETTTTSEEE---SEE.EEEESSSS..-H.HHHHHTTTEEEEEGGGG.TS-TTEEEEES CS
                    Alliinase_C 282 slqklkseyCnyfkkvrepsPaya.Wlkcekeededc.aevlrekkiltrsGevf.eaesryvrlsl 345
                                    s++ +k+e+   + +++e+sP+++ +l +e +e +d+ +e + +k+i+ r+ + f +a+ +++r+++
  gi|116753629|ref|YP_842747.1| 268 SVEMIKRERELLLSEIVEASPSWGnFLYIETSERSDViTERMLRKGIIVRDCRSFrDAGDHHIRVTV 334
                                    66666777777788999*****974667788787775256677778888888777367889999875 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 !   14.4   0.0   2.3e-06      0.01      71     176 ..      86     189 ..      66     193 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.3e-06
                                    EEESSHHHHHHHHHHTTS.-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEESTTSHHHHHHHCCT.TEEEEEEESS-T CS
                Cys_Met_Meta_PP  71 lavssGmaAiaaailall.kaGdeivvsddlYggtqrllkkvlkklgievkfvdtsdleelekaike.ntklvylEtptn 148
                                    +++ sGm  +  ++ +l+  +G + ++      +t+++ + v+   g +  fv  +++ e+ + +++    +v++ +p n
  gi|116753629|ref|YP_842747.1|  86 VLIGSGMDGVIDTLSRLFlDHGVRALIP----TPTFSYYEIVTILCGADPVFVRRTEPGEMIERLRDkSIGMVFICSPNN 161
                                    5666777776666665541446655555....467888888889999999999999998877776663789********* PP

                                    TTT----HHHHHHHHHHTT-EEEEEGTT CS
                Cys_Met_Meta_PP 149 pllkvvDiekiaklakkagvlvvvDntf 176
                                    p+ +vvD e + +++ + +++v++D ++
  gi|116753629|ref|YP_842747.1| 162 PTGEVVDEELLRSIIESTDAVVFLDEAY 189
                                    ************************9876 PP

>> Aminotran_MocR  Alanine-glyoxylate amino-transferase
   #    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     105     217 ..      88     190 ..      54     212 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.4e-05
                                    HHHHHC--TT-SS-GGGG.--EEEEEES--HHHHHHHHHHT-EEEEEEEETTEE-HHHHHHHHHC-TTEEEEEE-SSS-T CS
                 Aminotran_MocR 105 tlallhGvrdsegpwvkeekvkllvtvpGydrhfllleelGielltvdlqddGpdvdaveklvaedasvkGilavpkysn 184
                                      + + Gv d+      ++ v+ l+++p +  + +++   G + + v   + G   +++e+l  +d s+ G++++    n
  gi|116753629|ref|YP_842747.1|  88 IGSGMDGVIDTLSRLFLDHGVRALIPTPTFSYYEIVTILCGADPVFVRRTEPG---EMIERL--RDKSI-GMVFICSPNN 161
                                    55556777777766666778888888888888888888888888888777766...568888..58888.9********* PP

                                    TT-----HHHHHHHHT---SSTT-EEEEE-TTS CS
                 Aminotran_MocR 185 ptGetiseevarrlaalkaaapdfrifaddaya 217
                                    ptGe++ ee  r ++     + d  +f d+ay 
  gi|116753629|ref|YP_842747.1| 162 PTGEVVDEELLRSIIE----STDAVVFLDEAYV 190
                                    ************9976....5677899***996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2724.80
//
Query:       gi|116753630|ref|YP_842748.1|  [L=380]
Description: acetylornithine aminotransferase [Methanosaeta thermophila PT]
Scores for complete 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-117  393.1   0.0   1.4e-117  392.8   0.0    1.0  1  Aminotran_3      Aminotransferase class-III
    1.5e-05   24.3   0.0    2.2e-05   23.8   0.0    1.3  1  Aminotran_1_2    Aminotransferase class I and II
    5.5e-05   22.6   0.0    9.4e-05   21.8   0.0    1.4  1  Beta_elim_lyase  Beta-eliminating lyase
     0.0033   16.8   0.0     0.0059   15.9   0.0    1.4  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
     0.0048   15.9   0.0     0.0097   14.9   0.0    1.5  2  Aminotran_5      Aminotransferase class-V
     0.0085   16.1   0.3       0.13   12.2   0.0    2.6  3  ADH_zinc_N       Zinc-binding dehydrogenase
  ------ inclusion threshold ------
       0.15   11.7   0.0        0.3   10.7   0.0    1.5  1  Zot              Zonular occludens toxin (Zot)


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 !  392.8   0.0  5.4e-121  1.4e-117       8     402 ..      20     376 ..      14     380 .] 0.97

  Alignments for each domain:
  == domain 1  score: 392.8 bits;  conditional E-value: 5.4e-121
                                    -SCEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT-.. CS
                    Aminotran_3   8 nlllvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapkgl 87 
                                      +++i ++ G++++d+dg++y+D+v++iav+n+Gh+hP+vv+a+k q + l h+s +++ +e++++lae+l +l +   
  gi|116753630|ref|YP_842748.1|  20 RQPVLIARGSGARVWDQDGREYIDFVAGIAVNNVGHCHPRVVEAIKRQCELLIHTS-NLYYTENQVRLAEELKSLSGM-- 96 
                                    44699***************************************************.******************999.. PP

                                    SEEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-TTBGGG CS
                    Aminotran_3  88 dkvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlkypdeev 167
                                    dkvf++nsG+e+ve+AlKl r+      at + +i+a +g+fHGrtlgal++t + + y++ f p+  e ++++y+d   
  gi|116753630|ref|YP_842748.1|  97 DKVFFCNSGTESVEAALKLTRR------ATGRIEIVAATGSFHGRTLGALGLTYK-QSYREPFRPL-NEATFVPYND--- 165
                                    **********************......***************************.********96.67899****9... PP

                                    TB-HHHHHHHHHHHHHHHHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTTTTTSSSSGG CS
                    Aminotran_3 168 lkeneeeeaalleelealekkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEvqtGfGrTGklfAl 247
                                                  leal+ + ++e+aAvi+Ep+qge+Gv++as+e+l+++re+c++ ++lli+DEvqtGfGrTG +fA 
  gi|116753630|ref|YP_842748.1| 166 --------------LEALKSAVTKETAAVILEPVQGEAGVYPASNEYLRAAREICDDRGALLIFDEVQTGFGRTGRWFAK 231
                                    ..............99**************************************************************** PP

                                    GGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTSB--TTTT-HHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHH CS
                    Aminotran_3 248 ehagvspDlmtlaKaltgGlplsavlataevmqalapgshgsTfgGnplacavalavleiieeekllenaqelgaalkeg 327
                                    eh gv pD+mtlaKa++gGlp+ a+l ++++   ++ g+h+sTfgG pl ca+ala++ +i +e+l+++ +e+g++l  +
  gi|116753630|ref|YP_842748.1| 232 EHSGVMPDIMTLAKAIAGGLPMGAMLSNENISGCFQRGDHASTFGGGPLVCAAALASISAIRDENLVRRSEEMGSYLLRE 311
                                    ******************************************************************************** PP

                                    HHHHCTT-TTEEEEEEETTEEEEEEBCCCETTCHHHHHHHHHCTEE-EEETTTEEEE---TT--HHHHHHHHHHH CS
                    Aminotran_3 328 LeelqkkyevikevRgkGlmiaielkeeaevkekeilkkakekGvlilsaGdnvirllppliitdeeidelleil 402
                                    L++l  +       Rg+Glm+++++ ++a+    +++++a++ Gvl+ s+G++++rl+ppl++t+eeid +++ +
  gi|116753630|ref|YP_842748.1| 312 LSRLPVS------ARGLGLMVGVDIDKDAR----AVVDAARADGVLLNSTGEHTLRLVPPLVVTKEEIDRVVDVI 376
                                    ***9955......6****************....8***********************************99987 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 !   23.8   0.0   8.6e-09   2.2e-05      22     361 ..      59     374 ..      42     376 .. 0.64

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 8.6e-09
                                    HHHHHHHH.HHHHHTSTTST-BTTHHHHHHHHHHHHHC.....TCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-E CS
                  Aminotran_1_2  22 evakaeke.galaggtlneygpidglpeleealakflg.....rseklklkreaavvvgsGagaliealifllklnpgde 95 
                                    +v++a k+   l  +t n y +   +  l e+l ++ g      ++  ++  eaa+ ++  a+  ie++++    ++g+ 
  gi|116753630|ref|YP_842748.1|  59 RVVEAIKRqCELLIHTSNLYYTEN-QVRLAEELKSLSGmdkvfFCNSGTESVEAALKLTRRATGRIEIVAATG-SFHGRT 136
                                    444444444335555555555555.567777777666622222222223333333333333333333333333.444444 PP

                                    EEEEESS-T.HHHHHHH.HTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B-.-HHHHHH CS
                  Aminotran_1_2  96 ilvpdptya.syknilr.lsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtva.tleelek 172
                                      +  +ty  sy + +r l+ +++v+y+         dleal+ a+++      +t  +++e ++   G+ + + e l++
  gi|116753630|ref|YP_842748.1| 137 LGALGLTYKqSYREPFRpLNEATFVPYN---------DLEALKSAVTK------ETAAVILEPVQGEAGVYPaSNEYLRA 201
                                    4444444431344444435555666666.........99999999999......999*************9725566888 PP

                                    HHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTT..SSGGG-EEEEEEEHHHHHHHHHHHHHH CS
                  Aminotran_1_2 173 lldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKaf..GlaGeRvGyilgnaavvsqlrklsrpf 250
                                      ++++ +++ll++De+  gf  +   +++ +++v++++      +l+Ka   Gl+    G+ l+n+++  + ++   + 
  gi|116753630|ref|YP_842748.1| 202 AREICDDRGALLIFDEVQTGFGRTGRWFAKEHSGVMPDIM-----TLAKAIagGLPM---GAMLSNENISGCFQRGDHAS 273
                                    899********************988777779****9988.....*****9556666...****************9997 PP

                                    TSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEEEEETHHCHHHHHHHHHHTCTE CS
                  Aminotran_1_2 251 lsssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmflltdlsaetakelskkLleevgv 330
                                    ++   ++ ++aaal     +  + e+ ++r +++  +l  eL    l+v a   g+ + +d+++  a ++ ++ +   gv
  gi|116753630|ref|YP_842748.1| 274 TF-GGGPLVCAAALASISAI--RDENLVRRSEEMGSYLLRELS--RLPVSARGLGLMVGVDIDKD-ARAVVDAARAD-GV 346
                                    77.44444555555544444..457788888888888888884..45555555677777777766.66666666666.66 PP

                                    EEEEGGGGTSTTEEEEEC.TTS-HHHHHHHHH CS
                  Aminotran_1_2 331 yvtpgtsftvpgrlRitv.Aglteeeleelve 361
                                    ++      t +  lR+ +   +t+ee++++v+
  gi|116753630|ref|YP_842748.1| 347 LLNS----TGEHTLRLVPpLVVTKEEIDRVVD 374
                                    6666....235566666655666666666666 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   3.7e-08   9.4e-05      32     167 ..      81     216 ..      61     260 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 3.7e-08
                                    HHHHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH-.-TTEEEEEETT-HHHHSSTTHHHHC.C--EEEEE-.EBTTTB CS
                Beta_elim_lyase  32 ktvnrLedavaelfgkeaalfvpqGtaAnsillkill.qrgeevivtepahihfdetgaiael.agvklrdlk.nkeaGk 108
                                    ++  rL+++++ l g+++++f+ +Gt + + +lk+     g   iv  ++ +h ++ ga+    +++   +++  +ea  
  gi|116753630|ref|YP_842748.1|  81 ENQVRLAEELKSLSGMDKVFFCNSGTESVEAALKLTRrATGRIEIVAATGSFHGRTLGALGLTyKQSYREPFRpLNEATF 160
                                    45679***********************999999887455666799999**********998877776666662444467 PP

                                    E-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEE CS
                Beta_elim_lyase 109 mdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlD 167
                                    +  ++lea+  +v +   ++++++l+     ag  + s e+lr++++i++++g  l++D
  gi|116753630|ref|YP_842748.1| 161 VPYNDLEALKSAVTK---ETAAVILEPVQGEAGVYPASNEYLRAAREICDDRGALLIFD 216
                                    778899988888666...9999*****99999*9********************99999 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.3e-06    0.0059      15     144 ..      73     216 ..      60     227 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.3e-06
                                    TSS-SSSSHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHH.TTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-.. CS
                DegT_DnrJ_EryC1  15 ksgwltsgpeveeFEkafaaylgvkhaiavssGtaAlhlaLra.lgvgpgdeVIvpsltFvatanavlelgakpvfvD.. 91 
                                    ++  l   ++  +++++++   g++ +  ++sGt++++ aL+    ++ + e++ ++ +F +    +l l +k  + +  
  gi|116753630|ref|YP_842748.1|  73 HTSNLYYTENQVRLAEELKSLSGMDKVFFCNSGTESVEAALKLtRRATGRIEIVAATGSFHGRTLGALGLTYKQSYREpf 152
                                    444444456677899****************************544445669999999****999999999888766622 PP

                                    ..B-TTTSSB..-GGGCGGG--TTEEEEEEB-GGGB-......-.-HHHHHHHHHHCT-EEEEE CS
                DegT_DnrJ_EryC1  92 ..vdpdtyni..dpaaieaaitertkaIlpVhlyGqv......a.dmdalkaiaakhglkvieD 144
                                       +++t+ +  d +a+++a+t++t+a+++  + G++      +  + a ++i+++ g  +i D
  gi|116753630|ref|YP_842748.1| 153 rpLNEATFVPynDLEALKSAVTKETAAVILEPVQGEAgvypasNeYLRAAREICDDRGALLIFD 216
                                    226899998766899**************86666654111211335778888888888888887 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   3.8e-06    0.0097      61     179 ..      96     220 ..      65     225 .. 0.82
   2 ?   -3.7   0.0       1.7   4.4e+03     261     295 ..     282     316 ..     280     318 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.8e-06
                                    GGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBE...GGGHHHH-- CS
                    Aminotran_5  61 eeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeld...ldeleklln 137
                                     +++ f+ ++te+++++++  + +   + eiv  +   h+ ++ +  l  ++ ++  + pl+e   +    l++l+++++
  gi|116753630|ref|YP_842748.1|  96 MDKVFFCNSGTESVEAALKLTR-RATGRIEIVAATGSFHGRTLGALGLTYKQSYREPFRPLNEATFVPyndLEALKSAVT 174
                                    467************9988875.478888999999999******************999**9999875445999999*** PP

                                    TTEEEEEEESBETTTTEB--HHHHHHHHHH....TT-EEEEE-TTT CS
                    Aminotran_5 138 ektklvaithvsnvtGtiqpveeigklakk....kgalvlvDaaqa 179
                                    ++t++v++  v+ + G+    +e  ++a++    +gal++ D +q+
  gi|116753630|ref|YP_842748.1| 175 KETAAVILEPVQGEAGVYPASNEYLRAAREicddRGALLIFDEVQT 220
                                    *****************877666665555443227*********97 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 1.7
                                    HHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTST CS
                    Aminotran_5 261 lgaaleyleeigleaiekhekelaeyllerlkslp 295
                                    ++aal  +++i  e+  ++++e+ +yll +l+ lp
  gi|116753630|ref|YP_842748.1| 282 CAAALASISAIRDENLVRRSEEMGSYLLRELSRLP 316
                                    68899999999999999999999999999999876 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   5.2e-05      0.13      41      95 ..      80     135 ..      48     150 .. 0.80
   2 ?   -2.4   0.0       1.7   4.3e+03      68      83 ..     195     210 ..     160     218 .. 0.54
   3 ?    0.5   0.1      0.22   5.7e+02      16      67 ..     324     377 ..     318     379 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.2e-05
                                    TTTC.HHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCEEEE.EEEEECSC..TSSEE CS
                     ADH_zinc_N  41 ykea.dlverikeltggegvdvvfecvGsgatleaalkllkpg.GrlvvvGg..gkgee 95 
                                    +++  +l e++k+l    g d vf c    +++eaalkl+++  Gr+ +v++  ++++ 
  gi|116753630|ref|YP_842748.1|  80 TENQvRLAEELKSLS---GMDKVFFCNSGTESVEAALKLTRRAtGRIEIVAAtgSFHGR 135
                                    35666899*******...99999999877*************99******986655544 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.7
                                    SHHHHHHHHHCEEEEE CS
                     ADH_zinc_N  68 sgatleaalkllkpgG 83 
                                    s++ l+aa ++++ +G
  gi|116753630|ref|YP_842748.1| 195 SNEYLRAAREICDDRG 210
                                    2333333333333333 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.22
                                    EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHT.....TTSSEEEEEESSC CS
                     ADH_zinc_N  16 eviavdsseeklelakklGadevinykeadlverikelt.....ggegvdvvfecvG 67 
                                      ++vd++++ ++ +    ad v+ +   +  e+  +l       +e +d v++++G
  gi|116753630|ref|YP_842748.1| 324 LMVGVDIDKDARAVVDAARADGVLLN---STGEHTLRLVpplvvTKEEIDRVVDVIG 377
                                    56889999999999999999999887...2233333333333333556666666666 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00012       0.3      68     107 ..     198     237 ..     164     263 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00012
                            Zot  68 tlkefakwatidkgallviDEcqeifp.vrakegrkdpevi 107
                                     l +++  +  d+gall++DE+q+ f  + +++ ++  +v+
  gi|116753630|ref|YP_842748.1| 198 YLRAAREICD-DRGALLIFDEVQTGFGrTGRWFAKEHSGVM 237
                                    4444444455.6************99625677666655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); 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: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2595.52
//
Query:       gi|116753631|ref|YP_842749.1|  [L=214]
Description: beta-lactamase domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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   94.9   0.2    7.8e-27   94.6   0.2    1.0  1  Lactamase_B    Metallo-beta-lactamase superfamily
    1.2e-06   28.2   0.0    1.4e-06   28.0   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 !   94.6   0.2   8.7e-31   7.8e-27       6     197 .]      14     191 ..      11     191 .. 0.92

  Alignments for each domain:
  == domain 1  score: 94.6 bits;  conditional E-value: 8.7e-31
                                    SEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCH CS
                    Lactamase_B   6 vnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfme 85 
                                    +n+yl+   ++ +LiD+G+ +e +       ++ ++p++++ +ilTH H+DH ++++ ++e+t++++   +ee     ++
  gi|116753631|ref|YP_842749.1|  14 GNAYLV-MAERPVLIDAGMFAEPTIRNI---RRFIDPEELEMIILTHCHHDHSAAAPAIKERTGAKIMLSKEEIGLVGDD 89 
                                    799**9.9************99999875...9************************************************ PP

                                    HHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTS.SHHCCCCCC.T CS
                    Lactamase_B  86 eaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDall.agetgridltl 164
                                     a  a+ ++     +++++ +d ++e++ + ++g+++l+v+++pgh++g+++++ + +++lf+GD+++  g++gr+dl  
  gi|116753631|ref|YP_842749.1|  90 LATVAYLFGD----TAPEFEVDMPLEDGMVLDLGDLRLEVIHTPGHSPGSMCFYERREGMLFSGDTVFpDGNIGRTDL-- 163
                                    **99999975....7*****************************************************5566666666.. PP

                                    TCEEE-SHCHHHHHHHHHHHHHHHCHSEEEE.SS CS
                    Lactamase_B 165 rgaevrdpsdaekyldsllklaglkaevlvp.gH 197
                                          ++++ e++ +s+++l +l++  +++ gH
  gi|116753631|ref|YP_842749.1| 164 ------FGGSTEDLVRSIERLLELDDVSCMYpGH 191
                                    ......************9999998766555588 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   1.6e-10   1.4e-06       3     151 ..      25     159 ..      23     204 .. 0.75

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.6e-10
                                    EEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEE....HHHHHHCCTTCGHHH CS
                  Lactamase_B_2   3 iLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyap....kgvlavleanfvyla 78 
                                    +LiDag   ++   ++ ++ ++  +++++++++lth+H DH a ++ ++e+++   +++ +      v+++l++   yl+
  gi|116753631|ref|YP_842749.1|  25 VLIDAGMF-AE---PTIRNIRRFIDPEELEMIILTHCHHDHSAAAPAIKERTGA--KIMLSkeeiGLVGDDLATV-AYLF 97 
                                    78999886.33...4443445567899***********************7665..4554412323466677777.4555 PP

                                    CHTTTTEEE.EEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HHHH CS
                  Lactamase_B_2  79 leeepavnv.heldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipeeig 151
                                     + +p+ +v  +l+ g+ ++lg  +l+++++  ++ s+           ++++ + ++ ++++gDt + ++ ig
  gi|116753631|ref|YP_842749.1|  98 GDTAPEFEVdMPLEDGMVLDLG--DLRLEVIHTPGHSPG----------SMCFYERREGMLFSGDTVFPDGNIG 159
                                    5555233331355555555555..799999999999999..........9999999999*******98777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       208  (0.0116013); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1527.46
//
Query:       gi|116753632|ref|YP_842750.1|  [L=426]
Description: thiamine biosynthesis protein ThiC [Methanosaeta thermophila PT]
Scores for complete 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-171  568.4   0.1   8.9e-171  568.3   0.1    1.0  1  ThiC_Rad_SAM  Radical SAM ThiC family
     0.0013   18.2   0.2      0.052   13.0   0.1    2.8  3  PEP_mutase    Phosphoenolpyruvate phosphomutase
  ------ inclusion threshold ------
       0.11   12.6   0.1       0.35   11.0   0.1    1.9  1  AbiEi_4       Transcriptional regulator, AbiEi antitoxin
       0.12   11.8   0.4        3.3    7.1   0.1    2.2  2  PcrB          PcrB family


Domain annotation for each model (and alignments):
>> ThiC_Rad_SAM  Radical SAM ThiC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  568.3   0.1    2e-174  8.9e-171       1     417 [.       2     415 ..       2     416 .. 0.98

  Alignments for each domain:
  == domain 1  score: 568.3 bits;  conditional E-value: 2e-174
                   ThiC_Rad_SAM   1 tqleaarkgiiteemeevaekenvepefvreevaeGrivipanknh.kekpvaiGkglrtkvnaniGtsadasdieeEve 79 
                                    t +e+a++g+i ++++++ae e+v+pe +r+ +a+Gr+v+p+n ++ +e++v+iG+ l tkvn+n+Gts + s+ieeEve
  gi|116753632|ref|YP_842750.1|   2 TLMEDAKNGRIPDALRSAAEIEGVDPEALRRLLAAGRVVVPMNARRmRERAVGIGELLCTKVNVNVGTSPSLSNIEEEVE 81 
                                    789*******************************************5566****************************** PP

                   ThiC_Rad_SAM  80 KlkvalkagadtvmdLstggdideirekileespvpvgtvpiYqaleekekkveelteeellevieeqaedGvdfltiHa 159
                                    K+ +a++agadt+mdLstggd+deir++il++++vpvgtvpiYqa++e     e+lt++ +++++e++a+dGvdf+t+H+
  gi|116753632|ref|YP_842750.1|  82 KALAAVNAGADTIMDLSTGGDLDEIRRSILKKVDVPVGTVPIYQAAVE-----ENLTSQGMFNALEKHAKDGVDFVTVHV 156
                                    **********************************************85.....589************************ PP

                   ThiC_Rad_SAM 160 gvtlellellkkekRltgivSrgGsllaawmlanekenplyeefdelleilkeydvtlSlgdglRpGsiaDatdeaqlae 239
                                    gv++e++++l ++ Rl+g+vSrgGsl++++++++++enp+yeefd+llei+ke+d+tlSlgdglRpG+i+Da+d+a+++e
  gi|116753632|ref|YP_842750.1| 157 GVNKESMRRLCRDPRLMGVVSRGGSLTMKYITETGEENPYYEEFDYLLEIAKEHDLTLSLGDGLRPGCIEDASDRAKYME 236
                                    ******************************************************************************** PP

                   ThiC_Rad_SAM 240 livlgelvkrareagvqvmveGPGHvpldeieanvklqkklckeaPfyvlGplvtDiapgYDhitsaiGaalaaaaGadl 319
                                    +i lge+v rareagvq+mveGPGHvp deie++v+++k+l+++aP+y+lGp+vtD+apgYDhit+a+G+ +a++aGad+
  gi|116753632|ref|YP_842750.1| 237 FILLGEMVARAREAGVQAMVEGPGHVPADEIETSVRAMKHLTDGAPLYLLGPIVTDVAPGYDHITAAMGGLIAGMAGADF 316
                                    ******************************************************************************** PP

                   ThiC_Rad_SAM 320 lCyvtpaEHlglPdeedvkeGviaakiaahaadlakg..lkkarerdkalskaRkeldwekqfelaldpekareireekl 397
                                    lC  tp+EHl lP+ ed+ eG +++kiaahaadl+k   +++ar++d+++++aR++ldwe+qf+ a+dp+kar+ir+++ 
  gi|116753632|ref|YP_842750.1| 317 LCATTPSEHLDLPTLEDIIEGTVVTKIAAHAADLTKPgvRERARAWDRRMADARANLDWEAQFREAIDPTKARRIRHRRG 396
                                    ************************************766899***********************************998 PP

                   ThiC_Rad_SAM 398 peeeeaCsmCgekCavkive 417
                                      + e+C+mC+e Ca++i++
  gi|116753632|ref|YP_842750.1| 397 I-DVETCTMCSELCAIRIAR 415
                                    6.99*************986 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.1   1.2e-05     0.052     154     204 ..      75     127 ..      65     155 .. 0.80
   2 ?    1.5   0.0     0.039   1.7e+02     165     207 ..     144     185 ..     139     193 .. 0.73
   3 ?   -1.5   0.0      0.31   1.4e+03      51      88 ..     261     305 ..     244     321 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.2e-05
                     PEP_mutase 154 gleeaieRaraYaeAGAdgvfvpglqkdae.i.aelvaavdvplnvvplkgtl 204
                                    ++ee +e a a ++AGAd+++  +   d + i ++++++vdvp+  vp  ++ 
  gi|116753632|ref|YP_842750.1|  75 NIEEEVEKALAAVNAGADTIMDLSTGGDLDeIrRSILKKVDVPVGTVPIYQAA 127
                                    68999****************9999777666967899999****999943333 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.039
                     PEP_mutase 165 YaeAGAdgvfvpglqkdaeiaelvaavdvplnvvplkgtlsva 207
                                     a+ G d v+v+ + +++++++l++  +++ +v   +g+l+++
  gi|116753632|ref|YP_842750.1| 144 HAKDGVDFVTVHVGVNKESMRRLCRDPRLMGVVSR-GGSLTMK 185
                                    578899******************98755444444.3345555 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.31
                     PEP_mutase  51 elpleellaavraiaevvs.......lPlivDledGygespeeva 88 
                                    ++p++e+ + vra+ + ++        P+  D+  Gy    + + 
  gi|116753632|ref|YP_842750.1| 261 HVPADEIETSVRAMKHLTDgaplyllGPIVTDVAPGYDHITAAMG 305
                                    677778888888888888777777777888888888866555555 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   7.9e-05      0.35      20      39 ..      20      40 ..      11      42 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7.9e-05
                        AbiEi_4 20 ea.aGispsalrrLvrkGwLv 39
                                   ++  G++p alrrL+ +G++v
  gi|116753632|ref|YP_842750.1| 20 AEiEGVDPEALRRLLAAGRVV 40
                                   6669**************997 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1   0.00073       3.3      14      61 ..      71     118 ..      67     134 .. 0.81
   2 ?    2.5   0.0     0.018        83     176     224 ..     207     257 ..     176     259 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00073
                                    TTSS-CHHHHHHH...HCTT-SEEEEECSTCHHHHHHHHHHHHHCTSSS-E CS
                           PcrB  14 PeeenpdEiveiv...iesgtDavmigGsqsvtldntvrllkkvsriklPi 61 
                                    P   n++E ve +   ++ g+D++m   s++ +ld+++r + k   +++P+
  gi|116753632|ref|YP_842750.1|  71 PSLSNIEEEVEKAlaaVNAGADTIM-DLSTGGDLDEIRRSILKK--VDVPV 118
                                    667889999997767789*****99.678899*******99887..79997 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.018
                                    HHHSSSEEEEESS--SH..HHHHHHHCCSSEEEE-CHHHHHHHCHHHHHHH CS
                           PcrB 176 kklekarlivGGGirsa..EkAkevveaADvivvGnvveekderkidaile 224
                                    +k ++ +l  G G+r +  E+A + +++ + i+ G++v    e  ++a++e
  gi|116753632|ref|YP_842750.1| 207 AKEHDLTLSLGDGLRPGciEDASDRAKYMEFILLGEMVARAREAGVQAMVE 257
                                    33456788999999975559*******************999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.29s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3068.51
//
Query:       gi|116753633|ref|YP_842751.1|  [L=340]
Description: hypothetical protein Mthe_0316 [Methanosaeta thermophila PT]
Scores for complete 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   34.0   0.1    7.1e-05   22.6   0.2    2.1  2  NurA          NurA domain
  ------ inclusion threshold ------
      0.082   12.7   1.4        5.7    6.6   0.0    2.3  2  Amidohydro_2  Amidohydrolase


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 !   22.6   0.2     8e-09   7.1e-05       2     128 ..      47     193 ..      46     197 .. 0.83
   2 !    9.6   0.0   7.5e-05      0.68     178     241 ..     236     299 ..     200     300 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 8e-09
                                    EEEEEEEEEEEEEETTCEEEEEEEEEEECCEEECCCEEEECEBTCCHHEEEEE........................... CS
                           NurA   2 rvaAvDGSngvvrlsggilyilsayavvgggkerleealslasvdsispsdel........................... 54 
                                    r++AvDGSn +v   +++    +++++v   ++r e++++  +  ++   d++                           
  gi|116753633|ref|YP_842751.1|  47 RIFAVDGSNVKVCDLSVVKANHIRAGYVVYRGRRWERTAVTYDDLFVA--DRRdymewfreplerlemgeidlsglrgse 124
                                    89**********888888888888888888888888887777777766..444479************************ PP

                                    .HHHHHHHHHHHHHH.HHHHHCGGCCSCEEEEECSHHCCCHHHHHHHHHHHHHHHHHHHHHHTT-....TTCEEEEESS- CS
                           NurA  55 .errirllmetlElk.lgallleekgedllllDGsligslvefdelheeleyeeylyslsrllea....glnlvgvaKsf 128
                                     +r+   ++e+ E+  l+a l e ++ dl+l+DG +  +             +   + +++++++    g++l+gv+Ks 
  gi|116753633|ref|YP_842751.1| 125 lDRISTYFRELQEYVaLDAALSESEEGDLILYDGGFAIWKD-----------RPFGRVVDEIIKRaakrGVDLLGVSKST 193
                                    **************99999999999***********99999...........4444444444444444699999999986 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 7.5e-05
                                    HHHHHH-EEEEEEESSTTTTEEEEEHHHHHHCCHHHHHHHHHH....TTB-SSSBCCHHHHHHHHC CS
                           NurA 178 ealidkeiyfaYvrlegggsilrleipaevstakdedvlslla..sqrlsisGYprpLalAhelak 241
                                    e + +  iy+   +  + ++ +r+++p      ++ + ls++a  s   +++GYp++L +Ah+  k
  gi|116753633|ref|YP_842751.1| 236 EGRWEGSIYMVLFHP-EADRAFRVDVPSYM-NGRVTSALSKAAafSGSSESPGYPHALFRAHHDLK 299
                                    555566666666665.78888999988754.59999999999999999999************987 PP

>> Amidohydro_2  Amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0   0.00063       5.7      21      80 ..      40      99 ..      21     105 .. 0.91
   2 ?    4.8   0.4    0.0023        20      86     169 ..     159     297 ..     158     320 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.00063
                                   GCTSCCCHHHHHCHHTSSECCCEHCHHHHHHHHTSHHCHHHHHHHHHHHHHHHHHHHHHH CS
                   Amidohydro_2 21 ngfdpeerlafmkragvdpqlaspeallvlnaaagiaravivaalcrgannrvlaeaakr 80
                                   ++   e+r+ + +  +v++ ++s++ ++  +a  ++ r+ ++++++ ++++ ++a+  ++
  gi|116753633|ref|YP_842751.1| 40 EPQPFEGRIFAVDGSNVKVCDLSVVKANHIRAGYVVYRGRRWERTAVTYDDLFVADRRDY 99
                                   56678999999********************************************98775 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0023
                                    ECEEECTSSHCHHHHHHHHHHHHTTECEEEEESSTTTCCTTTCGGH...........HHHHHHHHHH...T-EEEEE... CS
                   Amidohydro_2  86 ggaavvpldpedaaaeleraveelgfkGvrlnphvggddllgdrld...........rpifealeel...glpvdihtGp 151
                                    g+a + ++ + ++++e++++++++g+  + ++++   ++    +              p+++ +++l   +++ d++ G 
  gi|116753633|ref|YP_842751.1| 159 GFAIWKDRPFGRVVDEIIKRAAKRGVDLLGVSKSTTISWGEISMPLvyhvsrlgknlLPGMAWCVDLggkNVHPDLQEGR 238
                                    78999999******************997777777543333333333344444445558888888873333555555555 PP

                                    ..........................................CHHHCHHHHHHHHHHHH CS
                   Amidohydro_2 152 s.........................................pewlfggpqettraiqp 169
                                    +                                         +++++g+p++ +ra+++
  gi|116753633|ref|YP_842751.1| 239 WegsiymvlfhpeadrafrvdvpsymngrvtsalskaaafsgSSESPGYPHALFRAHHD 297
                                    55555555555555555555555555555555555555556666666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2455.15
//
Query:       gi|116753634|ref|YP_842752.1|  [L=402]
Description: TraB family protein [Methanosaeta thermophila PT]
Scores for complete 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  107.0   0.1    2.8e-30  106.1   0.0    1.4  2  TraB       TraB family
  ------ inclusion threshold ------
        5.7    5.6   7.1        5.1    5.7   5.3    1.8  1  DUF2207    Predicted membrane protein (DUF2207)


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 !  106.1   0.0   3.2e-34   2.8e-30       7     249 ..      11     224 ..       6     229 .. 0.85
   2 ?   -3.6   0.0      0.89   7.9e+03     183     197 ..     329     347 ..     322     362 .. 0.47

  Alignments for each domain:
  == domain 1  score: 106.1 bits;  conditional E-value: 3.2e-34
                           TraB   7 kggttsyLfGTiHvskksvyplspeveealeksdtvvvEldlsddtdeatqkelaklkllp..dgktlsdllseelyarl 84 
                                    ++ +++ ++GT+Hvs+ksv ++++++e+   ++d v+vEl+++++ + + q++  + k+ +  +g+ +  +l + l+a +
  gi|116753634|ref|YP_842752.1|  11 DARNEILVIGTAHVSEKSVAEVREAIEQ--TRPDIVAVELCQRRYLALTGQDRDEDIKVSEllSGGRIYLVLVQWLLAYI 88 
                                    455669999*******************..8**************7777777777766666666**************** PP

                           TraB  85 qkalakrglplaaldkmkPwllalllslaelakkkagldpelvDrylaktakragkpvgglEtveeqlsll.sslpdeeq 163
                                    q+ + + ++++      +P  +a++l+++e  ++  +   +lvDr++++t +r + +++ +E+++ ++sl+ ++l   ++
  gi|116753634|ref|YP_842752.1|  89 QRQIGS-EMGV------RP--GAEMLAAIEA-ARVVNARVALVDRDISITIQRFWSAMSIWEKLKMLWSLVvAALGFGKE 158
                                    ******.9***......**..7777777776.3555666777*****************************444666666 PP

                           TraB 164 lealeetldeleeakdlleelveaykegdlealeleaeaeeefpelkevlldeRnrrwaekieallkepgsvfvaVGagH 243
                                    +  ++ ++    +++d +++l++              e+++++p   ++l+deR+++ a+++   l++ g+v+++VGagH
  gi|116753634|ref|YP_842752.1| 159 DLDID-SV----TDSDVVSQLMA--------------EFRKIAPSAARALVDERDAYIARNLYD-LSRYGKVLAVVGAGH 218
                                    66665.33....35889******..............**************************9.5566*********** PP

                           TraB 244 laGedg 249
                                      G+  
  gi|116753634|ref|YP_842752.1| 219 REGIMR 224
                                    988765 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 0.89
                           TraB 183 elveayke....gdleale 197
                                     +vea+k+    gd+++l+
  gi|116753634|ref|YP_842752.1| 329 GMVEAWKRkptmGDVKRLA 347
                                    4666666522223444442 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   5.3   0.00057       5.1     369     427 ..     235     291 ..     216     337 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.00057
                        DUF2207 369 rgyfdkkgkkklkklsalglgliilglilillallllvlllvfllilllillliaiivl 427
                                     + fd+ ++k++    a+g+++++l+++ ++++l++ +  +++ ++l++++++++ + l
  gi|116753634|ref|YP_842752.1| 235 TQIFDAPPEKRFSLGKAFGIIVTLLIILTFVYILVAGY--SSGVVLLAFGIWFLVTGGL 291
                                    57899999999999999999999999999999988855..3444444444443333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1018  (0.0567795); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); 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):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 2969.16
//
Query:       gi|116753635|ref|YP_842753.1|  [L=370]
Description: CBS domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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-28   97.9   6.3    2.3e-15   56.7   0.7    2.4  2  CBS             CBS domain
    1.3e-13   50.8  12.2    2.3e-06   27.1   3.5    3.2  3  Peptidase_M50   Peptidase family M50
    0.00015   21.5   3.9    0.00015   21.5   3.9    2.4  2  Peptidase_M50B  Peptidase M50B-like
  ------ inclusion threshold ------
          5    6.8  10.4        0.7    9.6   0.2    3.0  3  DUF21           Cyclin M transmembrane N-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 !   43.9   0.5   5.3e-15   2.4e-11       1      53 [.     247     298 ..     247     302 .. 0.86
   2 !   56.7   0.7   5.2e-19   2.3e-15       1      55 [.     309     362 ..     309     364 .. 0.97

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 5.3e-15
                                    HHHHSBSSCEEEETTSBHHHHHHH.HHHHTSSEEEE.EETTTBEEEEEEHHHHHH CS
                            CBS   1 Vgdimtrdvvtvppdttleealel.mrekgvsrlPV.VdedgklvGivtlrDllr 53 
                                    V++im++dv +vpp++tl+e+++l + ek ++++PV V  +++lvGivt +Dl r
  gi|116753635|ref|YP_842753.1| 247 VRHIMSKDVRVVPPEMTLAELMRLmFYEK-HRGYPVmV--NDELVGIVTITDLQR 298
                                    799*********************55444.69****77..566*********976 PP

  == domain 2  score: 56.7 bits;  conditional E-value: 5.2e-19
                                    HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                            CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                    Vgd+mtr++ ++ pd+    a+++m +k+++rlPV+ edg+lvGi++++Dllra+
  gi|116753635|ref|YP_842753.1| 309 VGDVMTRNIYVIGPDDEATAAIKIMGDKKIRRLPVI-EDGRLVGIISREDLLRAI 362
                                    89***********************9999*******.9***************98 PP

>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   2.5   7.1e-10   3.2e-06       2     109 ..      62     134 ..      61     145 .. 0.78
   2 !   27.1   3.5   5.2e-10   2.3e-06     175     247 ..     132     204 ..     111     209 .. 0.68
   3 ?   -1.3   0.1      0.23     1e+03      97     129 ..     214     249 ..     200     326 .. 0.53

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 7.1e-10
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M50   2 filllgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallpLGGyVkmageepeeelseeeakaflk 81 
                                    f++ll+i+v +HElGH +vAk+ g+++++                    i+l+ +GG+ +m++                 
  gi|116753635|ref|YP_842753.1|  62 FAVLLFICVGLHELGHSYVAKRYGIEIRS--------------------ITLYFFGGVASMEEIP--------------- 106
                                    89*************************99....................5566677777777766............... PP

                                    XXXXXXXXXXXXXXXXXXXXXXXXXXX- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M50  82 kspwqrllivlAGplanfilailvfvvp 109
                                    ++p  +l++++AGp++   l+++ +++ 
  gi|116753635|ref|YP_842753.1| 107 RNPSMELRMAIAGPAVSAALGVMSILLY 134
                                    5667777777777777777777777665 PP

  == domain 2  score: 27.1 bits;  conditional E-value: 5.2e-10
                                    XXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                    xxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M50 175 siaqlaseaaeagls..sflqllalisvnLgilNLlPipvLDGghllfalleairrkplserkeevanlvglall 247
                                     ++  +++ + +g     +l++l +++++L i+NL+P +++DGg++l+a ++     p  + ++++a l  ++ +
  gi|116753635|ref|YP_842753.1| 132 LLYTQSESILGEGHPfsILLWTLGIMNIILMIFNLIPAFPMDGGRVLRAWFSTRM--PYVVATKNAAALGKIFAV 204
                                    44444444554443343788999**************************999766..666666666555444444 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.23
                                    XXXXXXXXXXXX........-EEECECTTTSCEE-SEEEC- CS
                                    xxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M50  97 anfilailvfvv........pkkskeseeekrgviGvspkp 129
                                     nf+  i+ +++              s + + ++ G++  +
  gi|116753635|ref|YP_842753.1| 214 LNFLTLIIGIFLyiaaseedR-----STTIEDSLRGIKVRH 249
                                    455555555555433332220.....333344444443333 PP

>> Peptidase_M50B  Peptidase M50B-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   3.9   3.3e-08   0.00015      19     107 ..      64     162 ..      46     171 .. 0.72
   2 ?    2.0   2.4     0.031   1.4e+02      91     125 ..     192     227 ..     177     232 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 3.3e-08
                 Peptidase_M50B  19 pfkllvvffHElGHalaalLtGgrvkgielhsdesGvtvtrg.pgglgqil.tllaGYlgpallGlllillsasgka... 93 
                                    ++  + v +HElGH  +a+  G ++ +i+l+   +Gv+ ++  p+ +++ l +++aG+  +a lG++ ill +++     
  gi|116753635|ref|YP_842753.1|  64 VLLFICVGLHELGHSYVAKRYGIEIRSITLYFF-GGVASMEEiPRNPSMELrMAIAGPAVSAALGVMSILLYTQSESilg 142
                                    46677899***********************95.79999999977777654399*************9999855333122 PP

                 Peptidase_M50B  94 .....rlllv.llvllllvl 107
                                         ++ll+ l+++ ++++
  gi|116753635|ref|YP_842753.1| 143 eghpfSILLWtLGIMNIILM 162
                                    22224456663333333333 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.031
                 Peptidase_M50B  91 gkarlllv.llvllllvllllvrnlfglvlllllga 125
                                    +k +++l+ +++++l++l l++ n+++l++ ++l +
  gi|116753635|ref|YP_842753.1| 192 TKNAAALGkIFAVFLIFLGLFTLNFLTLIIGIFLYI 227
                                    333445554888888888888888888888887765 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 ?    1.7   0.7      0.04   1.8e+02      51     123 ..      16      95 ..       3     101 .. 0.69
   2 ?    0.6   0.4      0.09     4e+02     108     133 ..     141     166 ..     112     172 .. 0.69
   3 ?    9.6   0.2   0.00016       0.7     102     160 ..     184     243 ..     177     250 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.04
                          DUF21  51 rlLstlligntlvnillsalatalfvellae.......galavviatvivtllilvfgEilPkslalkyaekialalapp 123
                                    rl +t l+ +  v  l +++ +++f++l++         ++   + ++++ ++ + + E+    +a++y  +i +++ ++
  gi|116753635|ref|YP_842753.1|  16 RLHVTFLLIIPWVAYLFGSVSATVFGKLYGFgavepplVRWIYSLLFAVLLFICVGLHELGHSYVAKRYGIEIRSITLYF 95 
                                    66778888888888888888888888888777777676333333444555777777778888888888888777777766 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.09
                          DUF21 108 lalkyaekialalapplrvlmvllyP 133
                                    l+  ++ +i+l++ +++ ++++++  
  gi|116753635|ref|YP_842753.1| 141 LGEGHPFSILLWTLGIMNIILMIFNL 166
                                    55567778888888888888877765 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00016
                          DUF21 102 EilPkslalkyaekialalapplrvlmvllyPlvwllskllnlil.esesepavseeelk 160
                                      +P  +a+k+a ++ +++a++l +l  ++  ++ l+  ++ +i  ++e+++++ e+ l+
  gi|116753635|ref|YP_842753.1| 184 TRMPYVVATKNAAALGKIFAVFLIFLGLFTLNFLTLIIGIFLYIAaSEEDRSTTIEDSLR 243
                                    557999************************999999999999999777777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); 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):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2781.40
//
Query:       gi|116753636|ref|YP_842754.1|  [L=215]
Description: N-glycosylase/DNA lyase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.072   13.5   0.3       0.13   12.7   0.3    1.4  1  DUF1690          Protein of Unknown function (DUF1690)
        0.2   11.5   0.8        5.9    6.7   0.1    2.9  3  PolyA_pol_RNAbd  Probable RNA and SrmB- binding site of polym


Domain annotation for each model (and alignments):
>> DUF1690  Protein of Unknown function (DUF1690)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.3   1.5e-05      0.13      83     134 ..       7      63 ..       1      66 [. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.5e-05
                        DUF1690  83 ekieeLrkkleefkkkeeekl.....peeveeareevveClrenkgkpLdCweevee 134
                                    e+++eL++kle++ + + ++      +++ e+  ee+v Cl++ ++++  Cw  ve+
  gi|116753636|ref|YP_842754.1|   7 EQLKELHRKLEDVVEARLREFdqlwlDADEERLFEELVFCLLTPQSRARSCWAAVEK 63 
                                    5677777787776555553335667678888899*********************97 PP

>> PolyA_pol_RNAbd  Probable RNA and SrmB- binding site of polymerase A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.03   2.7e+02      10      29 ..       7      26 ..       6      30 .. 0.91
   2 ?    6.7   0.1   0.00066       5.9       5      41 ..      17      53 ..      15      56 .. 0.80
   3 ?    1.2   0.0     0.036   3.2e+02       9      31 ..      58      82 ..      54      85 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.03
                PolyA_pol_RNAbd 10 aairklaplLkkispeRife 29
                                   +++++l+  L+++  +R++e
  gi|116753636|ref|YP_842754.1|  7 EQLKELHRKLEDVVEARLRE 26
                                   67899*************97 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.00066
                PolyA_pol_RNAbd  5 epeTaaairklaplLkkispeRifeEllKlLlsghpe 41
                                   e  ++a +r+  +l  +   eR+feEl+  Ll+++++
  gi|116753636|ref|YP_842754.1| 17 EDVVEARLREFDQLWLDADEERLFEELVFCLLTPQSR 53
                                   66667777777777788899********999999876 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.036
                PolyA_pol_RNAbd  9 aaairklap..lLkkispeRifeEl 31
                                   +aa +kl++  +L+   p+Ri++El
  gi|116753636|ref|YP_842754.1| 58 WAAVEKLSSmgELRCPVPARIQMEL 82
                                   677777777777888889******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1583.32
//
Query:       gi|116753637|ref|YP_842755.1|  [L=388]
Description: beta-lactamase domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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-08   32.8   0.0    1.5e-07   31.6   0.0    1.7  1  Lactamase_B    Metallo-beta-lactamase superfamily
  ------ inclusion threshold ------
      0.024   14.2   0.1      0.068   12.7   0.1    1.8  1  Lactamase_B_2  Beta-lactamase superfamily domain
       0.11   12.7   0.0       0.18   12.0   0.0    1.4  1  Flavodoxin_1   Flavodoxin
       0.19   12.0   0.0       0.31   11.3   0.0    1.3  1  Flavodoxin_5   Flavodoxin domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   3.4e-11   1.5e-07       4     197 .]      32     216 ..      29     216 .. 0.91

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 3.4e-11
                                    CSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCH CS
                    Lactamase_B   4 dpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalf 83 
                                    ++ nsyli g +++ LiD+  ++ ++ + +   +  l ++++d++i  H+  DH G+ + l e++d  v   ++  + l+
  gi|116753637|ref|YP_842755.1|  32 TSYNSYLIKGSEKTALIDAVDPGKKDVLID--NLDSLRIDRIDYIISQHAEQDHSGAIKFLLERYDSTVLGSQKCIELLL 109
                                    567*************************97..778888899*************************************** PP

                                    CHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC. CS
                    Lactamase_B  84 meeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetgridl. 162
                                    +++              vs+d   ++ + + + +g++ +  +    +h ++ +  +++++++lft D+l a+   ++ + 
  gi|116753637|ref|YP_842755.1| 110 DFGI-------------VSKDRTRAVSDNELLSLGDMTLEFISAPWVHWPDTIFTYLRERRMLFTCDFLGAHLATSDLFa 176
                                    ****.............88888889999999999999999999999************************8888888889 PP

                                    ......TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                    Lactamase_B 163 .....tlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                           r  + +     +++++ l+++++l +e+++p+H
  gi|116753637|ref|YP_842755.1| 177 wnpesAKRYYAEIMMPFRANARRHLERIRALGPEIIAPSH 216
                                    9888877777777777788888899999999999999999 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 ?   12.7   0.1   1.5e-05     0.068      25     115 ..      67     147 ..      46     216 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.5e-05
                                    S--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEECSTTEE CS
                  Lactamase_B_2  25 rdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeepavnvheldwgesfelgdggle 104
                                    r  +++id ++  ha+ DH   + +l e+++   ++++++++++ l + ++        + +++ +  +e ++lgd  le
  gi|116753637|ref|YP_842755.1|  67 R--IDRIDYIISQHAEQDHSGAIKFLLERYD--STVLGSQKCIELLLDFGIVS------KDRTRAVSDNELLSLGDMTLE 136
                                    4..459**********************655..5899******9999997643......334567888888888876666 PP

                                    EEEEEE-EE-- CS
                  Lactamase_B_2 105 itatparhksg 115
                                    +   p  h+  
  gi|116753637|ref|YP_842755.1| 137 FISAPWVHWPD 147
                                    66666666544 PP

>> Flavodoxin_1  Flavodoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.1e-05      0.18       3      56 ..     246     301 ..     244     359 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.1e-05
                                    EETSSSHHHHHHHHHHHHHHHTTTEEEEEEEEGTTSC..GGGGGTHSEEEEEEEEE CS
                   Flavodoxin_1   3 YgSetGnteklAkqlaeelgehgfnadvvslsdydes..lseieeealllvvtsTf 56 
                                    + S+ G+tek+  +l + l ++g++++ ++l + d    + ++ + a ++++t+ f
  gi|116753637|ref|YP_842755.1| 246 FVSMHGSTEKMVSHLVDALIDRGVSVERFDLTKTDTGalAASLVDAATVVFGTPAF 301
                                    89*********************************77999999999******9976 PP

>> Flavodoxin_5  Flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   6.9e-05      0.31       2      54 ..     244     301 ..     243     326 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.9e-05
                   Flavodoxin_5   2 ilYsSrdGqTkkiaeriaeelree...gelvdvedvekese..dlesydavvigasvy 54 
                                    + + S +G+T+k ++++ ++l ++   +e +d+++ ++ +   +l ++  vv+g++ +
  gi|116753637|ref|YP_842755.1| 244 VPFVSMHGSTEKMVSHLVDALIDRgvsVERFDLTKTDTGALaaSLVDAATVVFGTPAF 301
                                    6799********************5555555666544333323677777899998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2708.19
//
Query:       gi|116753638|ref|YP_842756.1|  [L=76]
Description: hypothetical protein Mthe_0321 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); 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: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 590.77
//
Query:       gi|116753639|ref|YP_842757.1|  [L=648]
Description: periplasmic copper-binding [Methanosaeta thermophila PT]
Scores for 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-51  174.6  27.1    3.3e-47  160.8  21.1    2.2  2  NosD        Periplasmic copper-binding protein (NosD)
    8.8e-19   67.9  32.1    2.5e-18   66.4  21.3    3.2  3  Beta_helix  Right handed beta helix region
  ------ inclusion threshold ------
       0.06   13.2   0.0       0.17   11.8   0.0    1.7  1  PKD         PKD domain


Domain annotation for each model (and alignments):
>> NosD  Periplasmic copper-binding protein (NosD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.2   1.1e-07   0.00066      21     107 ..      52     152 ..      35     154 .. 0.58
   2 !  160.8  21.1   5.6e-51   3.3e-47      36     240 ..     148     362 ..     144     363 .. 0.97

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.1e-07
                           NosD  21 lens........egseisnneisnsrdgi..lldnssnntitgntienl.....ryGihlensesntiedntlssnesGi 85 
                                     e++        +g++ s+  + n   +      + ++++itg +   +     ++Gi++++ ++ ++ d+++s+n++Gi
  gi|116753639|ref|YP_842757.1|  52 SERIvvdksliiRGNTTSGYPVVNAGGSGtaVTISGDDIQITGIRAIGSgmaprDAGIFVTGRNN-RVMDCQVSGNRYGI 130
                                    33333332244433333333333322222233446777777777555555777788888888776.99999999999999 PP

                           NosD  86 almsssnntlenNtisnnenyG 107
                                    +l+  +++tlen  +  ++++G
  gi|116753639|ref|YP_842757.1| 131 VLSFAEGCTLENILAEASSEAG 152
                                    9999999999776665555555 PP

  == domain 2  score: 160.8 bits;  conditional E-value: 5.6e-51
                           NosD  36 nsrdgilldnssnntitgntienlryGihlensesntiedntlssne.sGialmsssnn.tlenNtisnnenyGillsds 113
                                    +s++g+lldns++n+i g+++en+ +Gi+l++sesnti++n++s+++ ++++l++ssn+  +e+N+i+ n++ Gi+l++s
  gi|116753639|ref|YP_842757.1| 148 SSEAGMLLDNSTKNSIIGCKLENNIHGIRLVSSESNTIRGNIISNTTfEALSLERSSNRnLIEDNIIRFNQI-GISLETS 226
                                    68999****************************************************888************.******* PP

                           NosD 114 snntisnNtisnnnkGiflensssntitgNriesnqkiGil..................llsssegntiynNyFinnsen 175
                                    ++n+i++N +snn+ Gi++ n +++t + + ie+ +k+G +                   lss+++ntiynN++inn+en
  gi|116753639|ref|YP_842757.1| 227 RGNNITRNLASNNSVGIKIAN-HNDTESISPIENPGKYGGVsikykpnsdiksydvrdkDLSSYTTNTIYNNTLINNEEN 305
                                    *********************.9********************************************************* PP

                           NosD 176 vkydgsnnneWnttktsgtniiggpylgGNyWsdydg.....eDadgDGigDtpYeindgv.iDylplvnp 240
                                    + +dg  nn+W++ +             GN++sd+d      +D+++DGi+D+++ei++g+ +D++pl+++
  gi|116753639|ref|YP_842757.1| 306 AIDDG--NNQWDNGT------------LGNHYSDFDEpeegcRDRNRDGICDSAHEIEGGMsTDRHPLSPK 362
                                    *****..9***9999............*****************************************976 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 !   15.8   3.0   1.6e-06    0.0098      43     121 ..      37     133 ..      15     136 .. 0.76
   2 !   66.4  21.3   4.2e-22   2.5e-18       1     149 [.     107     250 ..     107     259 .. 0.94
   3 ?    1.8   8.2     0.032   1.9e+02      46     123 ..     263     312 ..     251     341 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.6e-06
                                    S.-SS-SEEE-TT.........-S-EEES-EEE---.....SEEE-TT.--S--EEES-EEES-....SS-SEE-TT-S- CS
                     Beta_helix  43 n.nsgsGiyilgs.........snntisnntisdnn.....gggialf.gasnnlienneitdn....ggsGiylnyssn 102
                                    + +sg+ i+i+g+         +  +i++nt s+       g+g a++  ++   i + + +      +++Gi+++   n
  gi|116753639|ref|YP_842757.1|  37 SaSSGDAIEIQGGiyserivvdKSLIIRGNTTSGYPvvnagGSGTAVTiSGDDIQITGIRAIGSgmapRDAGIFVT-GRN 115
                                    36788888888888886668878888888888755588888777777768888889999999988888888**887.7** PP

                                    -EEES-EEESTT--SEE-- CS
                     Beta_helix 103 ntienNiidnnagsGivid 121
                                    n++ ++++++n+ +Giv++
  gi|116753639|ref|YP_842757.1| 116 NRVMDCQVSGNR-YGIVLS 133
                                    ************.***986 PP

  == domain 2  score: 66.4 bits;  conditional E-value: 4.2e-22
                                    -SEEE-SS-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES.-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S- CS
                     Beta_helix   1 sgisingssnvtiknntisnsggyGiylrgssnvvienneian.nsgsGiyilgssnntisnntisdnngggialfgasn 79 
                                    +gi+++g +n  + ++++s+ ++yGi l  ++++++e n +a  +s+ G+ + +s++n i +++ ++n   gi l  +  
  gi|116753639|ref|YP_842757.1| 107 AGIFVTGRNN-RVMDCQVSG-NRYGIVLSFAEGCTLE-NILAEaSSEAGMLLDNSTKNSIIGCKLENNI-HGIRLVSSES 182
                                    5999******.*********.6***************.777777*************************.********** PP

                                    -EEES-EEES-SS-SEE-T.T-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS CS
                     Beta_helix  80 nlienneitdnggsGiyln.yssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsss 149
                                    n+i++n i+++    ++l+ +s++n ie+Nii+ n+  Gi+++ s  ++++t N ++nn+ +Gi+++++++
  gi|116753639|ref|YP_842757.1| 183 NTIRGNIISNTTFEALSLErSSNRNLIEDNIIRFNQ-IGISLETSR-GNNITRNLASNNS-VGIKIANHND 250
                                    ***********999*****66777************.*********.8889********8.*****99876 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.032
                                    S-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---T CS
                     Beta_helix  46 gsGiyilgssnntisnntisdnngggialfgasnnlienneitdnggsGiylnyssnntienNiidnnagsGividds 123
                                    + G++i++ +n+ i+   ++d       l+    n+i+nn+ ++n+++ i                          ++
  gi|116753639|ref|YP_842757.1| 263 YGGVSIKYKPNSDIKSYDVRDKD-----LSSYTTNTIYNNTLINNEENAIDDG-----------------------NN 312
                                    44555555555555555555555.....5555555555555555555555333.......................22 PP

>> PKD  PKD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.8e-05      0.17      39      66 ..     516     543 ..     481     547 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.8e-05
                                    EEEETTEEEEEE-SSEEEEEEEEEE-SS CS
                            PKD  39 qvlseptvthtYlspGeYeVtvtasnav 66 
                                    +++ ++ v +t+++pG+Y+V++ a + +
  gi|116753639|ref|YP_842757.1| 516 GSTNGSLVLYTPSTPGTYNVRMFADDGY 543
                                    57889999**************999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (648 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 4456.57
//
Query:       gi|116753640|ref|YP_842758.1|  [L=472]
Description: major facilitator transporter [Methanosaeta thermophila PT]
Scores for complete 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  219.6  77.0    3.5e-52  177.5  51.6    2.3  2  MFS_1       Major Facilitator Superfamily
    3.8e-08   32.6  19.3    3.8e-08   32.6  19.3    3.3  3  Sugar_tr    Sugar (and other) transporter
    3.9e-05   22.7  24.6    0.00057   18.8  10.6    2.8  2  MFS_1_like  MFS_1 like family
    9.4e-05   21.0  23.3    0.00018   20.1  12.0    2.2  2  MFS_3       Transmembrane secretion effector
  ------ inclusion threshold ------
        8.6    4.5  21.7       0.55    8.4   1.4    3.2  3  OATP        Organic Anion Transporter Polypeptide (OATP) fami


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 !  177.5  51.6   9.7e-56   3.5e-52       3     352 ..      23     408 ..      21     409 .. 0.87
   2 !   56.2  17.4   7.6e-19   2.7e-15       3     172 ..     271     457 ..     269     472 .] 0.90

  Alignments for each domain:
  == domain 1  score: 177.5 bits;  conditional E-value: 9.7e-56
                          MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.f 81 
                                    ++ fl+a+++s +++alp a++++l +++  ++++ t++ l+aav+ +p+Grl+d +Gr+r++  g++lf l+  +l+ +
  gi|116753640|ref|YP_842758.1|  23 IGSFLTAFMSSSINIALP-AIGSELSMDAVMLSWISTAFLLAAAVFLVPFGRLADIYGRKRIFGYGIALFTLA-SILApV 100
                                    899***************.******************************************************.555534 PP

                          MFS_1  82 asslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaiv 160
                                     s +  +++++r++qG+ga+++f +++a+++ +fp ++rgr+ig+ +a++ lG  lgp+lgg+l+++lgWr++f++  ++
  gi|116753640|ref|YP_842758.1| 101 -SRSAsMIIAARFVQGVGAAMIFGTAVAILTSVFPLRKRGRVIGINAASVYLGLSLGPVLGGILTQYLGWRSLFVATVPI 179
                                    .88888************************************************************************** PP

                          MFS_1 161 sllafvlfllll.....peepperkrkspkeee..........................................kgtgp 193
                                    ++la+ l   l+     +++++ ++ +     +                                          + +++
  gi|116753640|ref|YP_842758.1| 180 GALALAL---LMnlrgeWADARGERFD-----LsgslvygisimalvygmsllpssagrfvtvaglaglvlflylETKAE 251
                                    ****663...33222443333333333.....1455669999999999999999999999999999*********99999 PP

                          MFS_1 194 aplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgr 273
                                     p+++   ++++++v+ +  +a+l++  +++++ +ll lylq    l+   +agl+l +  l++ il++l+grlsdr+ +
  gi|116753640|ref|YP_842758.1| 252 NPVIE-VDLFKSNRVFALSNLAALINYSATFATGFLLSLYLQYIKALD-PRSAGLVLLAQPLMMTILSPLTGRLSDRMEP 329
                                    99999.88888899886677777777779999****************.8***************************777 PP

                          MFS_1 274 rrrlllallllllaalglallavt..ssavllll.vlvliGfglgfvfpsllalasdlappeeagtasglfntagslgga 350
                                       +l+a +++++++l+++++ +    ++v+++  vl+l+Gfgl++++p+ ++++++++ +++ g as+  +t++ lg +
  gi|116753640|ref|YP_842758.1| 330 ---RLVASAGMAITLLSIVPFVFLdeRTPVWFIGaVLLLLGFGLALFTPPNTNAIMSSVERKYYGIASATLGTMRLLGQM 406
                                    ...555555555555555555555444899998878888***************************************99 PP

                          MFS_1 351 lg 352
                                    l+
  gi|116753640|ref|YP_842758.1| 407 LS 408
                                    97 PP

  == domain 2  score: 56.2 bits;  conditional E-value: 7.6e-19
                          MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.f 81 
                                    laa++++ a +++g++l+l+l+    ++p ++gl+l +  l + ++s+++Grlsdr+ +r v  +g+++++l+ ++++ f
  gi|116753640|ref|YP_842758.1| 271 LAALINYSATFATGFLLSLYLQYIKALDPRSAGLVLLAQPLMMTILSPLTGRLSDRMEPRLVASAGMAITLLS-IVPFvF 349
                                    6889999999999999999******************************************************.666657 PP

                          MFS_1  82 a...sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllgglla.sslg........ 149
                                        +++w++ ++ +l G+g ++++p    +i   + ++  g a + l+++  lG +l + l+ ++   ++g        
  gi|116753640|ref|YP_842758.1| 350 LderTPVWFIGAVLLLLGFGLALFTPPNTNAIMSSVERKYYGIASATLGTMRLLGQMLSMSLAMVIFaIYIGrveitpdt 429
                                    577899998999999*************************************************99967777******** PP

                          MFS_1 150 .......Wravfyilaivsllafvlfllll 172
                                            r +f i+ ++++++  +f+ l 
  gi|116753640|ref|YP_842758.1| 430 yssliesSRIAFAIFSVLCFIG--IFASLA 457
                                    ****999999999999999998..444554 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6  19.3   1.1e-11   3.8e-08      43     190 ..      48     189 ..       5     193 .. 0.87
   2 ?   -0.7   0.7      0.14     5e+02     326     414 ..     211     295 ..     199     320 .. 0.68
   3 ?   -1.7   1.3      0.28     1e+03     324     364 ..     406     454 ..     390     457 .. 0.55

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 1.1e-11
                                    H...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHH CS
                       Sugar_tr  43 essvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvl 122
                                      +v +++i  +fl+ a++  + +g l+d++GRk ++  +++lf  +++l  ++    s  ++i++R++ G+g+ ++ ++
  gi|116753640|ref|YP_842758.1|  48 MDAVMLSWISTAFLLAAAVFLVPFGRLADIYGRKRIFGYGIALFTLASILAPVSR---SASMIIAARFVQGVGAAMIFGT 124
                                    367899*************************************************...99******************** PP

                                    HHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGG CS
                       Sugar_tr 123 vPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilllf 190
                                    +   +  + p ++Rg++++++  ++ +G  ++ ++g +l ++ +   wr l+  ++ +  l l+ll+ 
  gi|116753640|ref|YP_842758.1| 125 AVAILTSVFPLRKRGRVIGINAASVYLGLSLGPVLGGILTQYLG---WRSLFVATVPIGALALALLMN 189
                                    **************************************999999...*****9999999888888775 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.14
                                    HHHHHHHHHH..HHHHTTSS...CHHHHHHHH.HHHHHHHTTTTHHHHHHHHHHSHTTTHHHHHHHHHHHHHHHHHHHHH CS
                       Sugar_tr 326 gmaicfvilgivalllvakskaasivaivfia.lfialfalgwgpvpwvlvsElfpqsvRskalaiavavnwlanflisl 404
                                    g +i+++++g  + ll+++  a  +v ++++a l+++l+  + +  p v+  +lf ++   + + +a+ +n  a+f++++
  gi|116753640|ref|YP_842758.1| 211 GISIMALVYG--MSLLPSS--AGRFVTVAGLAgLVLFLYLETKAENP-VIEVDLFKSNRVFALSNLAALINYSATFATGF 285
                                    5677888887..6666666..35666666665344566777777777.77888888877777777888888888888888 PP

                                    HHHHHHCHHH CS
                       Sugar_tr 405 lfpiiteaig 414
                                    l    ++ i+
  gi|116753640|ref|YP_842758.1| 286 LLSLYLQYIK 295
                                    8777777666 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.28
                                    HHHHHHHHHHHH.....HHHHTTSS........CHHHHHHHHHHHHHHH CS
                       Sugar_tr 324 aagmaicfvilg...ivalllvaks.....kaasivaivfialfialfa 364
                                    ++ m++++vi++   + + +++++      ++    ai+ ++ fi +fa
  gi|116753640|ref|YP_842758.1| 406 MLSMSLAMVIFAiyiGRVEITPDTYsslieSSRIAFAIFSVLCFIGIFA 454
                                    4555555555553222333333333655555555556666666666665 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8  10.6   1.6e-07   0.00057     242     384 ..      21     174 ..      14     175 .. 0.77
   2 !   10.1   4.7   7.2e-05      0.26      22      86 ..     287     351 ..     274     462 .. 0.59

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.6e-07
                     MFS_1_like 242 giienFlflYL.kelgasntllGslvalgvva...........eiplfffaeklleklGhvklliiallayilrfllyai 309
                                    ++i++Fl+ ++ ++ +     +Gs + + +v+             ++++   +l +++G  ++   ++ +++l  +l  +
  gi|116753640|ref|YP_842758.1|  21 SVIGSFLTAFMsSSINIALPAIGSELSMDAVMlswistafllaAAVFLVPFGRLADIYGRKRIFGYGIALFTLASILAPV 100
                                    5566665555555555555555555555444321111111111556777788999*******************999999 PP

                     MFS_1_like 310 ienawlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsglyfglGralGsliGGllwdlksaiflFr 384
                                     ++a++++ + + +g+  ++++++av     ++p + +++++g+ ++  + lG  lG ++GG+l ++ + + lF 
  gi|116753640|ref|YP_842758.1| 101 SRSASMIIAARFVQGVGAAMIFGTAVAILTSVFPLRKRGRVIGINAAS-VYLGLSLGPVLGGILTQYLGWRSLFV 174
                                    9*******************************************7654.669999*********99999999886 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 7.2e-05
                     MFS_1_like  22 ltiylk.skglkaseigiitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavlflsllfip 86 
                                    l++yl+  k l+++  g+++l+ pl+  + +p++g l+Dr++ r  v+++++ + +++ + ++f+ 
  gi|116753640|ref|YP_842758.1| 287 LSLYLQyIKALDPRSAGLVLLAQPLMMTILSPLTGRLSDRMEPRL-VASAGMAITLLSIVPFVFLD 351
                                    789***6678******************************98774.66666655555555444443 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1  12.0     5e-08   0.00018      36     176 ..      42     177 ..       8     216 .. 0.83
   2 !    6.7   3.5   0.00054       1.9      45     136 ..     300     389 ..     262     417 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 5e-08
                          MFS_3  36 lmtdisasplmvAlvqaaatLPifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligi 115
                                    + +++s   +m   +  a  L   ++ ++ G laD++ r++++  + +l  l+s+l+ v+      s ++++a  ++ g+
  gi|116753640|ref|YP_842758.1|  42 IGSELSMDAVMLSWISTAFLLAAAVFLVPFGRLADIYGRKRIFGYGIALFTLASILAPVSR-----SASMIIAARFVQGV 116
                                    4456788888889999999999999*****************************9998875.....6789********** PP

                          MFS_3 116 GaalndPaWqAsvgelvkrrdvpaAvaLnsvginiaRsvGPAlgGvlvaavGaalafavna 176
                                    Gaa+   +  A++  + + r+    + +n+  + +  s GP lgG+l   +G    f +++
  gi|116753640|ref|YP_842758.1| 117 GAAMIFGTAVAILTSVFPLRKRGRVIGINAASVYLGLSLGPVLGGILTQYLGWRSLFVATV 177
                                    ****************************************************999988765 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.00054
                          MFS_3  45 lmvAlvqaaatLPifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalglls.pwlllaltlligiGaalndPa 123
                                        lv  a  L + +ls l+G l+D ++ R v  a++++ +   + ++ +++l+  + +w + a+ ll+g G al +P 
  gi|116753640|ref|YP_842758.1| 300 RSAGLVLLAQPLMMTILSPLTGRLSDRMEPRLVASAGMAITL---LSIVPFVFLDERTpVWFIGAVLLLLGFGLALFTPP 376
                                    45569999999*******************976666655544...4455555665555056666778899******9998 PP

                          MFS_3 124 WqAsvgelvkrrd 136
                                       ++   v+r+ 
  gi|116753640|ref|YP_842758.1| 377 NTNAIMSSVERKY 389
                                    8888888888764 PP

>> OATP  Organic Anion Transporter Polypeptide (OATP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   2.8     0.033   1.2e+02       3      82 ..      18      97 ..      16     102 .. 0.93
   2 ?    8.4   1.4   0.00015      0.55     133     193 ..     105     165 ..      98     176 .. 0.92
   3 ?    6.8   2.4    0.0005       1.8     134     216 ..     358     438 ..     343     457 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.033
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           OATP  3 lvllsllglvqamvsgyfkstittiEkrFklpsstsgliassneignillilfvsYfggrghrPrwigigallmalgsll 82
                                   lv+ ++ +++ a++s+ +++++  i  + +++     +i++++ ++++++++  + +++   r r+ g+g+ l++l+s+l
  gi|116753640|ref|YP_842758.1| 18 LVVSVIGSFLTAFMSSSINIALPAIGSELSMDAVMLSWISTAFLLAAAVFLVPFGRLADIYGRKRIFGYGIALFTLASIL 97
                                   677778889999999**************************************************************998 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00015
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           OATP 133 llfflaqlllGiGatpiytlGisYidDnvkkknsplylgilyalrilGpalGfllGslllk 193
                                     ++++a +++G+Ga++i+  +++ +      ++    +gi  a   lG  lG +lG++l++
  gi|116753640|ref|YP_842758.1| 105 SMIIAARFVQGVGAAMIFGTAVAILTSVFPLRKRGRVIGINAASVYLGLSLGPVLGGILTQ 165
                                    4799*****************************************************9887 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0005
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                           OATP 134 lfflaqlllGiGatpiytlGisYidDnvkkknsplylgilyalrilGpalGfllGslllklyvdidseisltp.kdprWv 212
                                    ++ +  lllG+G +++ +  +  i  +v++k   +  ++l ++r+lG +l   l+ ++  +y+     +++tp + ++ +
  gi|116753640|ref|YP_842758.1| 358 FIGAVLLLLGFGLALFTPPNTNAIMSSVERKYYGIASATLGTMRLLGQMLSMSLAMVIFAIYIGR---VEITPdTYSSLI 434
                                    555667899*****************************************************987...777873233344 PP

                                    xxxx RF
                           OATP 213 gaWW 216
                                        
  gi|116753640|ref|YP_842758.1| 435 ESSR 438
                                    4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       723  (0.0403257); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.23s 00:00:00.86 Elapsed: 00:00:00.41
# Mc/sec: 3464.78
//
Query:       gi|116753641|ref|YP_842759.1|  [L=442]
Description: acetylornithine deacetylase or succinyl-diaminopimelate desuccinylase [Methanosaeta thermophila PT]
Scores for complete 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-36  125.8   0.0    2.4e-36  125.4   0.0    1.2  1  Peptidase_M20  Peptidase family M20/M25/M40
    1.6e-19   69.8   0.0    4.1e-19   68.5   0.0    1.7  2  M20_dimer      Peptidase dimerisation domain
    8.7e-05   22.3   0.0    0.00013   21.7   0.0    1.2  1  Peptidase_M28  Peptidase family M28
  ------ inclusion threshold ------
      0.035   14.0   0.0       0.11   12.5   0.0    1.8  1  HetR_C         Heterocyst differentiation regulator C-termina


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 !  125.4   0.0   5.4e-40   2.4e-36       2     205 ..     126     441 ..     125     442 .] 0.85

  Alignments for each domain:
  == domain 1  score: 125.4 bits;  conditional E-value: 5.4e-40
                                    EEEES-BSSTTCGGGSSS.TTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTT.THHH CS
                                    xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                  Peptidase_M20   2 lgsHlDvVpeeetdgwtt.pfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggr.gGak 79 
                                    ++ HlDvVp+++  gw+t pfslt++dG+ yGrG++d kg v+a+++alr + +e  kpk++++ll+++dEE+g+ +G  
  gi|116753641|ref|YP_842759.1| 126 IYTHLDVVPPGD--GWSTdPFSLTIRDGRAYGRGVSDSKGAVAAMIAALRGILRER-KPKYNLRLLLTTDEEVGGySGLC 202
                                    899******555..5****************************************6.99*************98889999 PP

                                    HHHH.HHH.TTTCESEEEEEEEESSSBTCHSTETEEEE.......................................... CS
                                    xxxx.xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................................... RF
                  Peptidase_M20  80 alle.gle.erekvdavfelhieepgileagklaigvv.......................................... 115
                                    +l++ g + +++k+ +      +++   +     + ++                                          
  gi|116753641|ref|YP_842759.1| 203 YLADsG-MvKGDKMLC------MDGFSDD-----VVIGsngiitwevtvngraahsgssflgdnaiekslpvidailrhk 270
                                    999942.334333322......3333333.....111122333444446688888889999999999************* PP

                                    ............................................................................EEEE CS
                                    ............................................................................xxxx RF
                  Peptidase_M20 116 ............................................................................kvev 119
                                                                                                                ++++
  gi|116753641|ref|YP_842759.1| 271 revekkssslpassvlrdkgiahmmpilninvihggikenivpdrcvfrgdrrvipeermedamseleeivkrfgsDIDI 350
                                    ***************************************************************************77*** PP

                                    EEEEEESHEEEC.CHHHHHHHHHHHHHHHTSCEEEEEESSSBHTHHHH...TTTEEE.EEEESS.GGCTTSTTTEEEHHH CS
                                    xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxx.xxxxxx.xxxxxxxxxxxxxxx RF
                  Peptidase_M20 120 elleggapvtln.dsplvkalaeaaeelfgekvelivsgpggtdarff...agiptv.mifgpg.sglaHspnEyvdled 193
                                    + + g++p++++ ++p+v  ++ea+++++g +++l+ ++ g+ d ++     +ip++ +++g+  +++aH+ +E+v++ed
  gi|116753641|ref|YP_842759.1| 351 RMWPGYPPMRMDpEHPWVLEVKEAVRRATGTEPHLSGTQ-GSLDQAYAteiTKIPAAvYGVGRQlESNAHGIDENVSVED 429
                                    *99************************99*777776666.99999999676777977244776646************** PP

                                    HHHHHHHHHHHH CS
                                    xxxxxxxxxxxx RF
                  Peptidase_M20 194 lekgikvlarll 205
                                    l+ +++++ +ll
  gi|116753641|ref|YP_842759.1| 430 LVSYMRFVGELL 441
                                    *******99887 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       2.2   9.9e+03      92     108 ..     167     183 ..     155     194 .. 0.68
   2 !   68.5   0.0   9.3e-23   4.1e-19       1     103 [.     227     343 ..     227     348 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.2
                                    HHHHHHHHHHTSCCSTT CS
                      M20_dimer  92 evleeieeilekeaped 108
                                    + +++++ il++++p++
  gi|116753641|ref|YP_842759.1| 167 AMIAALRGILRERKPKY 183
                                    44555566666665554 PP

  == domain 2  score: 68.5 bits;  conditional E-value: 9.3e-23
                                    SEB-EEEEEEEEEE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC...................TCCTCCCCCEECCE- CS
                      M20_dimer   1 ighkGlaggkitvkgkagHsgapgagaNAieklarllaeledeegdia..............eerslprttlnvtgiegG 66 
                                    ig  G++++++tv+g+a+Hsg    g+NAiek   +++++  ++++++              ++     + ln+++i+gG
  gi|116753641|ref|YP_842759.1| 227 IGSNGIITWEVTVNGRAAHSGSSFLGDNAIEKSLPVIDAILRHKREVEkkssslpassvlrdKGIAHMMPILNINVIHGG 306
                                    5789************************************99999988************9888888889********** PP

                                    CCCCEESSEEEEEEEEEHHHHHHHHHHHHHHHHHHTS CS
                      M20_dimer  67 saknvipdeaeakidiRllpgedpeevleeieeilek 103
                                     + n++pd++ +  d+R+ p+e  e+++ e+eei+++
  gi|116753641|ref|YP_842759.1| 307 IKENIVPDRCVFRGDRRVIPEERMEDAMSELEEIVKR 343
                                    **********************************986 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   2.9e-08   0.00013       1      78 [.     111     200 ..     111     231 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.9e-08
                                    EEEEEESTTCESEEEEEEEE--B-TTT.............TCC.T---TTTTHHHHHHHHHHHHHCHHGGCCSSEEEEEE CS
                  Peptidase_M28   1 NviatlegkatdevlllgAHyDsvgvg.............rgp.ifvGAdDnAsgvaalLelarvlaasgsrpkrgvrfl 66 
                                    N+ia++  +  +e l++  H+D v+ g             +g     G+ D+   vaa++  +r + ++  +pk+++r+l
  gi|116753641|ref|YP_842759.1| 111 NLIADMDLRR-PEWLVIYTHLDVVPPGdgwstdpfsltirDGRaYGRGVSDSKGAVAAMIAALRGILRER-KPKYNLRLL 188
                                    8999999889.9*************99***99999999883335578******************99755.9******** PP

                                    EESSCSGSSHHH CS
                  Peptidase_M28  67 ffdaEEagllGS 78 
                                    +++ EE g +  
  gi|116753641|ref|YP_842759.1| 189 LTTDEEVGGYSG 200
                                    ******976644 PP

>> HetR_C  Heterocyst differentiation regulator C-terminal Hood domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.4e-05      0.11      39      59 ..     325     345 ..     317     349 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.4e-05
                         HetR_C  39 ippekleqaleeldeiirewa 59 
                                    ip+e++e+a++el+ei++ ++
  gi|116753641|ref|YP_842759.1| 325 IPEERMEDAMSELEEIVKRFG 345
                                    9****************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 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:                        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: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 3454.13
//
Query:       gi|116753642|ref|YP_842760.1|  [L=134]
Description: molybdopterin-guanine dinucleotide biosynthesis protein B [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-19   69.6   0.5    2.9e-19   69.3   0.5    1.1  1  MobB             Molybdopterin guanine dinucleotide synthesis
     0.0013   18.3   0.7     0.0019   17.8   0.7    1.4  1  GTP_EFTU         Elongation factor Tu GTP binding domain
     0.0013   18.7   0.1     0.0014   18.7   0.1    1.4  1  MMR_HSR1         50S ribosome-binding GTPase
     0.0035   17.4   0.1     0.0051   16.9   0.1    1.2  1  Dynamin_N        Dynamin family
     0.0064   16.9   0.1     0.0078   16.6   0.1    1.3  1  AAA_16           AAA ATPase domain
     0.0069   16.9   0.0      0.008   16.7   0.0    1.3  1  AAA_18           AAA domain
     0.0096   16.4   0.1      0.014   16.0   0.1    1.3  1  ABC_tran         ABC transporter
  ------ inclusion threshold ------
      0.012   15.2   0.1      0.014   15.0   0.1    1.3  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
      0.013   14.5   0.1      0.017   14.1   0.1    1.1  1  DUF463           YcjX-like family, DUF463
      0.019   15.1   0.3      0.027   14.7   0.3    1.4  1  AAA_33           AAA domain
      0.047   13.7   0.1      0.073   13.1   0.1    1.3  1  AAA_14           AAA domain
      0.071   12.5   2.6        0.1   11.9   2.6    1.2  1  Glyco_hydro_3    Glycosyl hydrolase family 3 N terminal domai
      0.088   12.6   0.0       0.16   11.7   0.0    1.5  1  AAA_29           P-loop containing region of AAA domain
      0.088   13.1   0.1       0.15   12.3   0.1    1.4  1  AAA_22           AAA domain
      0.097   12.4   0.1       0.19   11.4   0.0    1.6  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
       0.11   12.7   0.1       0.19   11.9   0.1    1.5  1  Roc              Ras of Complex, Roc, domain of DAPkinase
       0.12   12.0   0.0       0.16   11.6   0.0    1.2  1  Thymidylate_kin  Thymidylate kinase
       0.13   11.9   0.0       0.16   11.6   0.0    1.2  1  Peripla_BP_6     Periplasmic binding protein


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 !   69.3   0.5   2.9e-22   2.9e-19       1     112 [.       3     107 ..       3     125 .. 0.81

  Alignments for each domain:
  == domain 1  score: 69.3 bits;  conditional E-value: 2.9e-22
                           MobB   1 vlgivgksgsGKTtLleklipelkarglrvgtiKhahhgfdvdkpgkDsyrhrkAGAkevlvaskerlalikeleeaels 80 
                                    v+++vg+ +sGKTtL+e l++ lk++g rvgt+Kh    ++vd  + D++rh  AGA+ v+  +  ++ ++ +      s
  gi|116753642|ref|YP_842760.1|   3 VVAVVGHHKSGKTTLIEALVKSLKRHG-RVGTVKHMPG-HHVD--QGDTHRHLMAGADVVIGLGLGQIVVTPK-G----S 73 
                                    689********************9998.9******864.4455..46***********999888888887777.3....4 PP

                           MobB  81 leellarlse..vDlvlvEGfkkealpkievlra 112
                                    le  l+ +++  +D+v+ EGfk++++pki++   
  gi|116753642|ref|YP_842760.1|  74 LESALEEMRSrgIDFVILEGFKSSQYPKIVIGGI 107
                                    555555553335*****************99655 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 !   17.8   0.7   1.9e-06    0.0019       6      37 ..       4      35 ..       1      58 [. 0.82

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.9e-06
                                   EEEEESTTSSHHHHHHHHHHHTTSSCHHHHHH CS
                       GTP_EFTU  6 igiighvDhGKtTLtdrLlyktgaiskkgeka 37
                                   ++++gh  +GKtTL+++L++++++  + g+++
  gi|116753642|ref|YP_842760.1|  4 VAVVGHHKSGKTTLIEALVKSLKRHGRVGTVK 35
                                   89******************999988877776 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   1.4e-06    0.0014       2      31 ..       4      39 ..       3     125 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.4e-06
                                   EEEEESTTSSHHHHHHHHHTS......TEEESSSTT CS
                       MMR_HSR1  2 vaivGrpNvGKStLinaltge......kaivsdkpg 31
                                   va+vG+  +GK+tLi al+++      +  v+++pg
  gi|116753642|ref|YP_842760.1|  4 VAVVGHHKSGKTTLIEALVKSlkrhgrVGTVKHMPG 39
                                   89*****************85332221335555555 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   5.1e-06    0.0051       1      20 [.       4      23 ..       4      33 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5.1e-06
                                   EEEEEBTTTTHHHHHHHHHT CS
                      Dynamin_N  1 iavvGsqSsGKSSvlnaLlg 20
                                   +avvG+ +sGK+++++aL++
  gi|116753642|ref|YP_842760.1|  4 VAVVGHHKSGKTTLIEALVK 23
                                   89****************97 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   7.8e-06    0.0078      26      62 ..       3      43 ..       2      95 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 7.8e-06
                         AAA_16 26 lvllsGesGvGKsslvrellralekdg.gif...lrgkcdq 62
                                   +v ++G+  +GK++l+++l ++l+++g + +   + g+ ++
  gi|116753642|ref|YP_842760.1|  3 VVAVVGHHKSGKTTLIEALVKSLKRHGrVGTvkhMPGHHVD 43
                                   589***********************534443444444444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0     8e-06     0.008       1      28 [.       4      44 ..       4     114 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 8e-06
                         AAA_18  1 IlltGtpGvGKttlakeLskrlgf.............gvnl 28
                                   +++ G + +GKttl ++L k+l+              +v  
  gi|116753642|ref|YP_842760.1|  4 VAVVGHHKSGKTTLIEALVKSLKRhgrvgtvkhmpghHVDQ 44
                                   6899**************99985556666666666553333 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   1.4e-05     0.014      12      51 ..       2      44 ..       1      62 [. 0.73

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.4e-05
                                   SEEEEEESTTSSHHHHHHHHTTSS--..SEEEEEET.TCEGGG CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx.xxxxxx RF
                       ABC_tran 12 ekvaivGenGaGKStLlkllagllkp..teGeilld.gkdlke 51
                                   ++va+vG+  +GK+tL+++l + lk     G+++   g+++++
  gi|116753642|ref|YP_842760.1|  2 KVVAVVGHHKSGKTTLIEALVKSLKRhgRVGTVKHMpGHHVDQ 44
                                   689*******************998544445553333555544 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 ?   15.0   0.1   1.4e-05     0.014       2      89 ..       3      92 ..       2     127 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.4e-05
                                   EEEEEESTTCCHHHHHHHHH.CT--SS-EEEEESS-SSCHCCCCCCHCCCT.....EEEETTTTECCHCTT-HHHHHHHHHH CS
                           cobW  2 vtvltGflGsGKTtLlnhll.enraglklavivNefgevsiDaellretgve....ivelenGciCctlredllkelealee 78
                                   v+ ++G   sGKTtL+++l+ + +++ ++  +    g  ++D+   +++       ++ l  G i  t +  l  +le++ +
  gi|116753642|ref|YP_842760.1|  3 VVAVVGHHKSGKTTLIEALVkSLKRHGRVGTVKHMPG-HHVDQGDTHRHLMAgadvVIGLGLGQIVVTPKGSLESALEEMRS 83
                                   677899999***********86777888888877666.77776655555222334599999999999999999999999999 PP

                                   HHTT-SEEEEE CS
                           cobW 79 reerldviliE 89
                                   r   +d +++E
  gi|116753642|ref|YP_842760.1| 84 RG--IDFVILE 92
                                   98..8998888 PP

>> DUF463  YcjX-like family, DUF463
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   1.7e-05     0.017       3      37 ..       4      41 ..       3      55 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.7e-05
                         DUF463  3 lavTGLsraGKtvfitsLvnqLlaaek...karlplfe 37
                                   +av G  ++GKt++i +Lv+ L ++ +    +++p  +
  gi|116753642|ref|YP_842760.1|  4 VAVVGHHKSGKTTLIEALVKSLKRHGRvgtVKHMPGHH 41
                                   69********************9666554455555554 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.3   2.7e-05     0.027       1      25 [.       3      32 ..       3      99 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.7e-05
                         AAA_33  1 lvllvGlpGsGKstlaerllkklg.....a 25
                                   +v +vG+  sGK+tl+e l+k l+     +
  gi|116753642|ref|YP_842760.1|  3 VVAVVGHHKSGKTTLIEALVKSLKrhgrvG 32
                                   799****************99887644440 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   7.3e-05     0.073       3      27 ..       2      26 ..       1      42 [. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.3e-05
                         AAA_14  3 kilvitGaRrvGKTtllkqlikell 27
                                   k+++++G  ++GKTtl++ l+k+l 
  gi|116753642|ref|YP_842760.1|  2 KVVAVVGHHKSGKTTLIEALVKSLK 26
                                   799*****************98876 PP

>> Glyco_hydro_3  Glycosyl hydrolase family 3 N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   2.6    0.0001       0.1     150     187 ..      15      52 ..       8      56 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0001
                                    HHHHHHHHHHHHHTT-EEEEEEETTGTT-SSETTTSEE CS
                  Glyco_hydro_3 150 aalaaamvkGlqgagvaatvKHFpghGdgavdshkelp 187
                                    ++l +a vk l++ g + tvKH pgh   + d+h++l 
  gi|116753642|ref|YP_842760.1|  15 TTLIEALVKSLKRHGRVGTVKHMPGHHVDQGDTHRHLM 52 
                                    5788999*******************777889999975 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00016      0.16      25      43 ..       4      22 ..       1      30 [. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00016
                         AAA_29 25 tlltGpsGsGKSTllDAiq 43
                                   + ++G+  sGK+Tl+ A+ 
  gi|116753642|ref|YP_842760.1|  4 VAVVGHHKSGKTTLIEALV 22
                                   6799***********9986 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00015      0.15       7      32 ..       3      28 ..       2      58 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00015
                         AAA_22  7 ilvvtGesGtGKTtllrrlleqldee 32
                                   +++v+G+  +GKTtl++ l+++l+++
  gi|116753642|ref|YP_842760.1|  3 VVAVVGHHKSGKTTLIEALVKSLKRH 28
                                   679******************99765 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00019      0.19       1      23 [.       1      23 [.       1      44 [. 0.88
   2 ?   -2.9   0.0       5.3   5.3e+03     122     140 ..     112     130 ..     103     131 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00019
                      PduV-EutP  1 mkkilliGkvgsGKttLtqalkg 23
                                   mk + ++G+ +sGKttL +al +
  gi|116753642|ref|YP_842760.1|  1 MKVVAVVGHHKSGKTTLIEALVK 23
                                   89999*************99965 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.3
                      PduV-EutP 122 kifevsavekegieellky 140
                                    ki  v  v++  +e+l+++
  gi|116753642|ref|YP_842760.1| 112 KICDVHDVNDAAVEHLVEM 130
                                    6677777777777777665 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00019      0.19       2      24 ..       4      26 ..       2      49 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00019
                                   EEEESSTTSSHHHHHHCHCT-CC CS
                            Roc  2 vvlvGdsgvGKtsllkrfvedkf 24
                                   v +vG +++GKt+l++ +v++  
  gi|116753642|ref|YP_842760.1|  4 VAVVGHHKSGKTTLIEALVKSLK 26
                                   5689**************98755 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00016      0.16       3      33 ..       8      39 ..       6      56 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00016
                                   ESTTSSHHHHHHHHHHHHHHTTE..EEEESSS CS
                Thymidylate_kin  3 GlDGaGKttqaellkerlkeegik.vvltrep 33
                                   G  ++GKtt +e+l++ lk+ g+  +v   + 
  gi|116753642|ref|YP_842760.1|  8 GHHKSGKTTLIEALVKSLKRHGRVgTVKHMPG 39
                                   6679*****************98755555555 PP

>> Peripla_BP_6  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00016      0.16     136     203 ..       2      67 ..       1      95 [. 0.92

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00016
                                    CEEEEEEESSHHHHHHHHHHHHHHHCCTEEEEEEEEE-TTH.HHHHHHHHHHHTTT-SEEEEESSHHHH CS
                   Peripla_BP_6 136 kkvalvyadyafgregiaalkaaakaaGgevvgeepvplgt.tdfsaqvlqikaagadavllagtgadl 203
                                    k va+v++  +  + +i+al +++k++G   vg++++ +g   d+    + ++a gad+v++ g g+ +
  gi|116753642|ref|YP_842760.1|   2 KVVAVVGHHKSGKTTLIEALVKSLKRHG--RVGTVKHMPGHhVDQGDTHRHLMA-GADVVIGLGLGQIV 67 
                                    6799***********************9..67*******999***********9.******99988755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); 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: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1032.29
//
Query:       gi|116753643|ref|YP_842761.1|  [L=190]
Description: hypothetical protein Mthe_0327 [Methanosaeta thermophila PT]
Scores for 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-39  132.2  18.5    4.3e-21   75.0   5.7    2.1  2  UPF0016   Uncharacterized protein family UPF0016
    0.00079   19.1  15.1      0.012   15.3   0.8    2.6  3  TauE      Sulfite exporter TauE/SafE


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 !   63.5   4.9   1.9e-21   1.7e-17       4      75 .]      15      87 ..      12      87 .. 0.98
   2 !   75.0   5.7   4.8e-25   4.3e-21       2      75 .]     111     184 ..     110     184 .. 0.98

  Alignments for each domain:
  == domain 1  score: 63.5 bits;  conditional E-value: 1.9e-21
                        UPF0016  4 flliflaElGDkTqlaaalLaary.kplpVflGavlAlalmtvlsvllGsslakrlperlielvaavlFllfG 75
                                   f++i++aElGDkTql ++lL++r+ + ++ ++G++ A+++++++++llG+++++++p ++++++++ +FllfG
  gi|116753643|ref|YP_842761.1| 15 FITIAIAELGDKTQLSVLLLSTRTkEHFKLLIGVMSAFLIVDGFAILLGAWITEVVPASILKIISGGIFLLFG 87
                                   99**********************99999*******************************************9 PP

  == domain 2  score: 75.0 bits;  conditional E-value: 4.8e-25
                        UPF0016   2 aaflliflaElGDkTqlaaalLaarykplpVflGavlAlalmtvlsvllGsslakrlperlielvaavlFllfG 75 
                                    + fl+iflaE+GDkTq+a a++a++y+p+ V+ G++lAl++ ++ +++lG+++ +++++r+i+l+a+++F+++G
  gi|116753643|ref|YP_842761.1| 111 SGFLVIFLAEWGDKTQIASAVFATQYNPWLVLGGTMLALFILSISAIYLGRFILGYINRRTITLAAGLIFMAMG 184
                                    679*********************************************************************98 PP

>> TauE  Sulfite exporter TauE/SafE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1     0.034     3e+02      80     105 ..      30      55 ..       9      59 .. 0.70
   2 !   15.3   0.8   1.3e-06     0.012      68     128 ..      51     111 ..      35     122 .. 0.73
   3 !    9.1   5.7    0.0001      0.91     187     235 ..     134     186 ..     124     188 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.034
                           TauE  80 Gallllllpsellkllfgvlllllal 105
                                     +lll+   +e++kll+gv+ ++l++
  gi|116753643|ref|YP_842761.1|  30 SVLLLSTRTKEHFKLLIGVMSAFLIV 55 
                                    45555544445779999998888765 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.3e-06
                           TauE  68 llllgsliGallGallllllpsellkllfgvlllllallmllrkkrsrakgrerrptaill 128
                                     +l++   ++llGa++  ++p+++lk++ g + ll+++ +l+     +++gr+  +++ l+
  gi|116753643|ref|YP_842761.1|  51 AFLIVDGFAILLGAWITEVVPASILKIISGGIFLLFGIITLRDLDGDEGDGRKFDESPFLS 111
                                    45555567899******************************97665455544444444433 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0001
                           TauE 187 agavdwpllll....llpgallGallGarlarrlsertlrrlfallllvlgvk 235
                                    + +  w +l+     l + ++  ++lG  +  ++++rt+ ++ +l+ +++g+ 
  gi|116753643|ref|YP_842761.1| 134 TQYNPWLVLGGtmlaLFILSISAIYLGRFILGYINRRTITLAAGLIFMAMGIV 186
                                    23333443333566688889999999999999999999999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.68
# Mc/sec: 843.86
//
Query:       gi|116753644|ref|YP_842762.1|  [L=298]
Description: cation diffusion facilitator family transporter [Methanosaeta thermophila PT]
Scores for complete 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-46  157.4  16.9      5e-46  156.9  16.9    1.1  1  Cation_efflux  Cation efflux family
  ------ inclusion threshold ------
      0.031   14.4   0.7      0.056   13.6   0.7    1.4  1  ZT_dimer       Dimerisation domain of Zinc Transporter
      0.034   14.3   0.1      0.054   13.7   0.1    1.3  1  GerPE          Spore germination protein GerPE
       0.04   14.4   0.0       0.11   13.0   0.0    1.7  2  Ubiquitin_2    Ubiquitin-like domain
          8    6.9   7.5        2.9    8.3   0.9    2.7  3  DUF3165        Protein of unknown function (DUF3165)


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 !  156.9  16.9   1.4e-49     5e-46       3     199 .]      15     205 ..      14     205 .. 0.95

  Alignments for each domain:
  == domain 1  score: 156.9 bits;  conditional E-value: 1.4e-49
                  Cation_efflux   3 lsllanlilalvelivglltnSlalladafhslsdlvsllllllalklsrkppderfpfGygrlevlgalvsgllllgla 82 
                                    l+++++++++++el + ++t+Slall+da h ++dl++l l+++a+++s  p++er+++G++r+ev++al +gl+l ++a
  gi|116753644|ref|YP_842762.1|  15 LAMILTISILIAELLGSWWTGSLALLSDAAHVFLDLFALGLSWFAIRISALPASERYSYGFHRFEVIAALANGLTLGFVA 94 
                                    689999************************************************************************** PP

                  Cation_efflux  83 vfllleaiqklikegereihaglalvvalvslvvnlalllilrragrklrsaalkaaalhvlgDaltslgvlvsalvill 162
                                    + +l+ea+ +l+   ++ +    +l++a ++l+vnl++++ l r g ++ + +l++a lhvlgDa++slgv+ +alvi+ 
  gi|116753644|ref|YP_842762.1|  95 LVILIEAYRRLL--QPEPVKGLDLLLIATFGLIVNLIVAFVLSRDG-HMDDLNLRSAILHVLGDAAASLGVIAAALVIWR 171
                                    ************..566666666788899***************98.7******************************** PP

                  Cation_efflux 163 fnlksgplaDpvaslligliilysalkllkeslseLl 199
                                    +     + aDp++slli+++i+  +++l+k+s++ ++
  gi|116753644|ref|YP_842762.1| 172 TGW---YPADPIISLLISVMIFAGSYRLIKDSFRLIM 205
                                    944...66*************************9876 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 ?   13.6   0.7   1.6e-05     0.056       7      77 ..     215     282 ..     212     284 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.6e-05
                                    HHHHHHHTT-SS-EEEEEEEEE.-S----EEEEEEEE-TTS-HHHHHHHHHHHHHHHHHH-TT--EEEEEEE CS
                       ZT_dimer   7 eeireiiksvpgvkgvhdlrtr.ksGskifvdlhievdgdlsvkeaHeiadevekrikeefpgvadvliHve 77 
                                    +e+ + i++  gv++vhdl++     s+i+ + h++v+++   ++  +   e+++++ + f g+++ +i +e
  gi|116753644|ref|YP_842762.1| 215 DEVVDQISTASGVIQVHDLHIWgVCSSNILLSAHVVVSPE---SDHQRTLSEIRDKLSSIF-GIEHATIQLE 282
                                    56777788899***********67779*************...8999999*******9999.9999999987 PP

>> GerPE  Spore germination protein GerPE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   1.5e-05     0.054      49      95 ..     198     244 ..     185     270 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.5e-05
                          GerPE  49 kkefeiftepiplllpetdvklavlhekPvikvrsikiegvssssvv 95 
                                    k++f++  e +p   ++++v  ++   + vi+v+ ++i gv ss ++
  gi|116753644|ref|YP_842762.1| 198 KDSFRLIMEGVPECIRTDEVVDQISTASGVIQVHDLHIWGVCSSNIL 244
                                    6899****************************************996 PP

>> Ubiquitin_2  Ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       2.9     1e+04      14      24 ..       7      17 ..       3      20 .. 0.77
   2 ?   13.0   0.0   3.1e-05      0.11      21      48 ..     256     283 ..     240     295 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.9
                                   SEEEEEEETTS CS
                    Ubiquitin_2 14 vsserrfsksl 24
                                   ++ errfs+ +
  gi|116753644|ref|YP_842762.1|  7 RVIERRFSLAM 17
                                   6789**99876 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 3.1e-05
                                    ETTSBHHHHHHHHHHHH---TTCEEEEE CS
                    Ubiquitin_2  21 sksltieelKekLelitGtspasmrLql 48 
                                    + + t++e+++kL  i+G++ a+ +L+ 
  gi|116753644|ref|YP_842762.1| 256 DHQRTLSEIRDKLSSIFGIEHATIQLEN 283
                                    7789*********************985 PP

>> DUF3165  Protein of unknown function (DUF3165)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1      0.08   2.9e+02      28      71 ..      17      61 ..      11      70 .. 0.73
   2 ?    8.3   0.9   0.00082       2.9       4      45 ..      93     135 ..      90     136 .. 0.89
   3 ?   -2.3   0.1       1.7     6e+03      57      71 ..     184     198 ..     160     205 .. 0.59

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.08
                        DUF3165 28 lialv.allalllvlavlsflkilqlPkeifvgllmillgyfalk 71
                                   +i  + +l+a ll     + l +l+    +f+ l+ + l++fa++
  gi|116753644|ref|YP_842762.1| 17 MILTIsILIAELLGSWWTGSLALLSDAAHVFLDLFALGLSWFAIR 61
                                   444331455666666677889999999999999999999999997 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00082
                        DUF3165   4 lilailillyYlfiaPksvkn.tlnlialvallalllvlavls 45 
                                    + l ili  y   + P+ vk+  l lia  +l++ l+v+ vls
  gi|116753644|ref|YP_842762.1|  93 VALVILIEAYRRLLQPEPVKGlDLLLIATFGLIVNLIVAFVLS 135
                                    557899999999********945999**************997 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.7
                        DUF3165  57 fvgllmillgyfalk 71 
                                     +++++++ +y  +k
  gi|116753644|ref|YP_842762.1| 184 LISVMIFAGSYRLIK 198
                                    333444444444455 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); 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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2160.55
//
Query:       gi|116753645|ref|YP_842763.1|  [L=116]
Description: hypothetical protein Mthe_0329 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       212  (0.0118244); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 922.45
//
Query:       gi|116753646|ref|YP_842764.1|  [L=291]
Description: hypothetical protein Mthe_0330 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 2021.59
//
Query:       gi|116753647|ref|YP_842765.1|  [L=122]
Description: 50S ribosomal protein L7Ae [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.7e-25   87.5   0.2    4.3e-25   87.3   0.2    1.1  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil
    3.6e-05   23.6   0.0      5e-05   23.1   0.0    1.2  1  PELOTA_1        PELOTA RNA binding domain


Domain annotation for each model (and alignments):
>> Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.3   0.2   4.8e-29   4.3e-25       3      94 ..      19     110 ..      17     111 .. 0.96

  Alignments for each domain:
  == domain 1  score: 87.3 bits;  conditional E-value: 4.8e-29
                                    HHHHHHHHHHHTEEEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHHHTTEEEEEESCHHHHHHHTTSSSECSE CS
                 Ribosomal_L7Ae   3 ieevlkkakkagklvlGlkevtkalergeaklvilAedvepeekkkllealckekevpyvkvkskkeLGelvgkkrpvsa 82 
                                      e+l++a+++g++++G++e+tka+erg aklvi+ edvep+e++++l+ lc+ek+ pyv+vk + + G+++g+++ ++a
  gi|116753647|ref|YP_842765.1|  19 SLEALELARDTGRIKKGTNEATKAVERGVAKLVIIGEDVEPPEIVAHLPPLCEEKNTPYVYVKKQSDVGAAAGLSVKSAA 98 
                                    56899*************************************************************************** PP

                                    EEEEESTTTHHH CS
                 Ribosomal_L7Ae  83 laikdegdskdl 94 
                                    +ai+++g+ k+l
  gi|116753647|ref|YP_842765.1|  99 AAIIEPGKGKEL 110
                                    ******987775 PP

>> PELOTA_1  PELOTA RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   5.6e-09     5e-05      17      71 ..      27      83 ..      16      92 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 5.6e-09
                       PELOTA_1 17 edinliKPgigEaTRvlLRRvPekvlvrdeee..pdlahlllLakekgvpveevpdl 71
                                   +d+ +iK g  EaT+++ R v + v++ ++ e  + +ahl  L++ek++p++ v+++
  gi|116753647|ref|YP_842765.1| 27 RDTGRIKKGTNEATKAVERGVAKLVIIGEDVEppEIVAHLPPLCEEKNTPYVYVKKQ 83
                                   6899***********************9988865679*************9988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); 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: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 914.23
//
Query:       gi|116753648|ref|YP_842766.1|  [L=70]
Description: 30S ribosomal protein S28e [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-31  107.1   1.2    3.5e-31  107.0   1.2    1.0  1  Ribosomal_S28e  Ribosomal protein S28e


Domain annotation for each model (and alignments):
>> Ribosomal_S28e  Ribosomal protein S28e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.0   1.2   1.9e-35   3.5e-31       2      64 .]       5      67 ..       4      67 .. 0.97

  Alignments for each domain:
  == domain 1  score: 107.0 bits;  conditional E-value: 1.9e-35
                                   --EEEEEEEEEE---SSSSEEEEEEEE-S-SS-S-EEEEEEES---TT-EEEES--S--TT-- CS
                 Ribosomal_S28e  2 eaklAeVikvlgrtGsrGevtqVrvellegkdkgriiiRnVkGPvreGDiLtLlEterEArrL 64
                                   + ++AeVi+v+g tG++Ge+tq+++++leg++kgrii+Rn++GPvr+GD+L+LlEt+rEA++L
  gi|116753648|ref|YP_842766.1|  5 NGVPAEVIEVIGVTGMHGEATQIKCRILEGSNKGRIITRNCMGPVRVGDVLMLLETAREAKKL 67
                                   6789*********************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       249  (0.0138881); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.40
# Mc/sec: 523.88
//
Query:       gi|116753649|ref|YP_842767.1|  [L=56]
Description: ribosomal protein L24E [Methanosaeta thermophila PT]
Scores for complete 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   68.1   2.9    6.4e-19   68.0   2.9    1.0  1  Ribosomal_L24e  Ribosomal protein L24e
    2.5e-05   24.1   2.3    3.3e-05   23.7   2.3    1.2  1  zf-FCS          MYM-type Zinc finger with FCS sequence motif
    3.3e-05   23.9   1.2    4.5e-05   23.4   1.2    1.2  1  YHS             YHS domain
     0.0024   16.7   0.0     0.0024   16.7   0.0    1.0  1  SerH            Cell surface immobilisation antigen SerH
  ------ inclusion threshold ------
        0.2   11.2   3.7       0.62    9.6   3.7    1.7  1  zf-FLZ          zinc-finger of the FCS-type, C2-C2
       0.24   11.3   5.7       0.66    9.9   5.7    1.6  1  VATC            Vms1-associating treble clef domain


Domain annotation for each model (and alignments):
>> Ribosomal_L24e  Ribosomal protein L24e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.0   2.9   2.1e-22   6.4e-19       1      53 [.       1      53 [.       1      55 [. 0.96

  Alignments for each domain:
  == domain 1  score: 68.0 bits;  conditional E-value: 2.1e-22
                                   XXX-B-TTT-SB--SS--EEEE-TTS-EEEESSHHHHHHHHTT--GGGSTTST CS
                 Ribosomal_L24e  1 mktekCsFsgykiyPGhGkrfvrnDgkvfrFlssKceklfkqkrnPrklkWTk 53
                                   m+ ++CsF+  +i PG+Gk++ ++Dg+v+ F+ssKcek+++  r  rk+kW +
  gi|116753649|ref|YP_842767.1|  1 MEERRCSFCNTRITPGTGKLYAKKDGTVYYFCSSKCEKNMRLGRVSRKIKWAR 53
                                   77899**********************************************86 PP

>> zf-FCS  MYM-type Zinc finger with FCS sequence motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   2.3   1.1e-08   3.3e-05       4      37 ..       4      36 ..       2      38 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.1e-08
                         zf-FCS  4 krCwfCkkyikgkpeftyvlendgvvgqFCStsC 37
                                   +rC+fC++ i+ ++    +  +dg v++FCS+ C
  gi|116753649|ref|YP_842767.1|  4 RRCSFCNTRITPGT-GKLYAKKDGTVYYFCSSKC 36
                                   69********9999.68999************99 PP

>> YHS  YHS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   1.2   1.5e-08   4.5e-05       6      35 ..       9      38 ..       8      41 .. 0.95

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.5e-08
                            YHS  6 cgmkvdkekaeekseYkGkeYyFcSegCkd 35
                                   c +++++++ + + + +G+ YyFcS +C+ 
  gi|116753649|ref|YP_842767.1|  9 CNTRITPGTGKLYAKKDGTVYYFCSSKCEK 38
                                   999*************************85 PP

>> SerH  Cell surface immobilisation antigen SerH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   8.2e-07    0.0024     239     276 ..       4      41 ..       1      53 [. 0.58

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 8.2e-07
                           SerH 239 sdCnaCattaspstkllfAnaagssCvassascttssr 276
                                      C  C t  +p t +l+A+++g++    s +c+ + r
  gi|116753649|ref|YP_842767.1|   4 RRCSFCNTRITPGTGKLYAKKDGTVYYFCSSKCEKNMR 41 
                                    45555555555555555555555555555555555544 PP

>> zf-FLZ  zinc-finger of the FCS-type, C2-C2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   3.7   0.00021      0.62      15      45 ..       5      38 ..       4      43 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00021
                         zf-FLZ 15 aCflCkkkLgegk.DiymYrGdka..FCSeeCRq 45
                                    C++C+ ++++g    y  +  +   FCS+ C +
  gi|116753649|ref|YP_842767.1|  5 RCSFCNTRITPGTgKLYAKKDGTVyyFCSSKCEK 38
                                   7***********96677766444245******65 PP

>> VATC  Vms1-associating treble clef domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   5.7   0.00022      0.66       4      31 ..       4      36 ..       2      41 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00022
                           VATC  4 lrCsiCgeslegkv..yFekfd...frYCstkC 31
                                   +rCs+C++++ + +   + k d   + +Cs kC
  gi|116753649|ref|YP_842767.1|  4 RRCSFCNTRITPGTgkLYAKKDgtvYYFCSSKC 36
                                   79*********85445666655455889***** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.32u 0.26s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 429.98
//
Query:       gi|116753650|ref|YP_842768.1|  [L=143]
Description: nucleoside-diphosphate kinase [Methanosaeta thermophila PT]
Scores for complete 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  189.1   0.0    3.5e-56  189.0   0.0    1.0  1  NDK       Nucleoside diphosphate kinase
  ------ inclusion threshold ------
       0.16   11.9   0.4       0.37   10.7   0.2    1.7  2  ACT_5     ACT domain


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 !  189.0   0.0   3.8e-60   3.5e-56       6     135 .]       1     130 [.       1     130 [. 0.99

  Alignments for each domain:
  == domain 1  score: 189.0 bits;  conditional E-value: 3.8e-60
                                    EE-HHHHHTT-HHHHHHHHHHHT-EEEEEEEECE-HHHHHHHTGGGTTSTTHHHHHHHHTSSEEEEEEEESTTHHHHHHH CS
                            NDK   6 liKPdavkrgligeiisrleekglkivalkmlrlteeqaeehYaehkgkpffeelvefmtsgpvvalvlegedaiekvre 85 
                                    +iKPd+v+rgl+g+ii+r+eekg+kiva+++  +++e+ae+hYaeh+gkpf+ +lvef+tsgp v +v+eg+ +i+++r+
  gi|116753650|ref|YP_842768.1|   1 MIKPDGVQRGLVGRIIQRIEEKGFKIVAMRLSVMDKERAEKHYAEHAGKPFYGDLVEFITSGPSVQMVVEGKGVISAIRK 80 
                                    8******************************************************************************* PP

                                    HH--SSTTTSSTTSHHHHH-SSSTT-SEEE-SSHHHHHHHHHHHSTGGGS CS
                            NDK  86 liGatnpaeaapgtiRadfgvslgeNlvHgSdseesaereiklfFkeeei 135
                                    + GatnpaeaapgtiR+dfg+++g+N++HgSds+esa+rei+l F+++ei
  gi|116753650|ref|YP_842768.1|  81 MNGATNPAEAAPGTIRGDFGIETGRNVIHGSDSPESAAREIALHFSDSEI 130
                                    **********************************************9986 PP

>> ACT_5  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   4.2e-05      0.37       3      28 ..       9      34 ..       8      42 .. 0.84
   2 ?   -2.5   0.0      0.51   4.6e+03      36      47 ..      65      76 ..      64      85 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 4.2e-05
                          ACT_5  3 pgvLeRvlrvvrrrgFevkslnmstt 28
                                    g++ R+++ ++ +gF++ ++ +s  
  gi|116753650|ref|YP_842768.1|  9 RGLVGRIIQRIEEKGFKIVAMRLSVM 34
                                   58999*****************9983 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.51
                          ACT_5 36 ieltVesersve 47
                                   ++++Ve++  ++
  gi|116753650|ref|YP_842768.1| 65 VQMVVEGKGVIS 76
                                   677777755444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 1143.26
//
Query:       gi|116753651|ref|YP_842769.1|  [L=217]
Description: hypothetical protein Mthe_0335 [Methanosaeta thermophila PT]
Scores for complete 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-66  221.9   0.1    4.9e-66  221.6   0.1    1.0  1  DUF99     Protein of unknown function DUF99


Domain annotation for each model (and alignments):
>> DUF99  Protein of unknown function DUF99
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.6   0.1   2.7e-70   4.9e-66       2     182 ..      33     208 ..      32     209 .. 0.98

  Alignments for each domain:
  == domain 1  score: 221.6 bits;  conditional E-value: 2.7e-70
                                    GSEEEEEEEEE.....-SS-EEEEEEEEETT.EEEEEEEEEE-TT-S-HHHHHHHHHCC-TTTTEEEEEESSSEETTTEE CS
                          DUF99   2 eirvlGiddsfferkkkdgksvlvGvvmradrvvdgvafgrvtvdGtDateaiielvkrleredirvvlldGitiagFNv 81 
                                    +ir+lGi++sf++   +d+ s+l+G vmr+d ++dgva++++tv+G+Dat+ +++++++l redi++++l+G +i++FN+
  gi|116753651|ref|YP_842769.1|  33 GIRALGIAESFVR---SDSLSTLAGLVMRGDMRIDGVALAEITVGGMDATDGVLSIYRKLGREDINILMLSGNVISWFNI 109
                                    79*********66...49************************************************************** PP

                                    --HHHHHHHH---EEEEESS---HHHHHHCCT.TSTTHHHHHHHHHHC.---EEETT....EEEEEESS-HHHHHHHHHH CS
                          DUF99  82 vDlerlheetglPviavtreepdlgklekaLrkhfpdeeeRlelieklgerieevektgeelyvravGieleeaaklvrk 161
                                    +D+er+h+etglPvi+vt+ee+d g le++++++fp++ eRl  +++lger +++ ktg++l+vra+Gi+l+e+++++++
  gi|116753651|ref|YP_842769.1| 110 IDPERIHRETGLPVISVTYEESD-G-LERYIEEYFPGDVERLMKYRALGERSAIRLKTGYDLFVRAHGISLKETRAVLNR 187
                                    ***********************.8.****************************************************** PP

                                    C-SSSSS-HHHHHHHHHHHHH CS
                          DUF99 162 ltlegriPEPlRvAhliAsal 182
                                    +t+egriPEP+RvA+l+A+a+
  gi|116753651|ref|YP_842769.1| 188 FTIEGRIPEPVRVARLVARAA 208
                                    *******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       237  (0.0132188); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1610.30
//
Query:       gi|116753652|ref|YP_842770.1|  [L=353]
Description: pyruvate carboxyltransferase [Methanosaeta thermophila PT]
Scores for complete 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   78.7   0.0    6.6e-22   78.3   0.0    1.1  1  HMGL-like  HMGL-like


Domain annotation for each model (and alignments):
>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.3   0.0   3.7e-26   6.6e-22      64     261 ..       7     210 ..       2     213 .. 0.86

  Alignments for each domain:
  == domain 1  score: 78.3 bits;  conditional E-value: 3.7e-26
                                    -B..--EE-SSHHHHHHHHH....TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHH.HHHHHHHHHTT-ETTT-BTTTBS CS
                      HMGL-like  64 karilalvrarekdikaavealkgagakrvhvfiatselhlkaklkkdreevakka.eeavkaarslgkdvelsledasr 142
                                    +++++++ ra+ +di+   e     g ++  + +++s+ h+ +k++    e+a+++  +a+++a ++g +++  led +r
  gi|116753652|ref|YP_842770.1|   7 NPEVTGWSRANTNDIDLVLE---MDGIRETGILMSISDPHILIKMGLPGREAAREMyLDALQYAVDHGLRTRAHLEDITR 83 
                                    56799***************...999********************9866666555279********************* PP

                                    --HH.HHHHHHHHHHHHT-SE.EEEEETTS---HHHHHH...HHHHHHHHS-...GGGEEEEEB-TTS-HHHHHHHHHHT CS
                      HMGL-like 143 tdle.flaevveaaeeaGatr.iniaDtvGvltPneaae...lisalkervk..dkvilsvHcHndlGlAvantlaAvea 215
                                    +dle f++ +v +++++  ++ i+i Dt+G+  P+e  +   +i  +++r+       +++H H+d+G ++ n+++++  
  gi|116753652|ref|YP_842770.1|  84 ADLEgFVYPLVREIIDIDRDCtIRICDTLGYGLPFEGMNdpySIPNMVRRLReiGVKNIETHIHDDFGFGTVNSIVGYWY 163
                                    ***967899********776449*********99886542446777777777555579********************** PP

                                    T--EEEEBTTS--SSBBB-BHHHHHHHHHHTT.-B----HHHHHHHH CS
                      HMGL-like 216 GadrvdgtvnGlGeraGnaaleelvaalealg.vdtgldlqklrsia 261
                                    Ga++ + t +G+GeraGna le++ + l+++     ++dl+ l++ a
  gi|116753652|ref|YP_842770.1| 164 GANWSNLTFLGIGERAGNAELEKVLLFLKTRVeGFEKYDLSCLTEFA 210
                                    ****************************9986555666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 2596.74
//
Query:       gi|116753653|ref|YP_842771.1|  [L=63]
Description: hypothetical protein Mthe_0337 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0065   16.1   0.0     0.0075   15.9   0.0    1.0  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 !   15.9   0.0   4.2e-07    0.0075       2      34 ..      20      52 ..      19      55 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.2e-07
                                   -EEEE-TTTHHHHTSSS---HHHHHHHHHHHHH CS
                      HMGL-like  2 vkivdttLRDGeqalkaalsveeklaiakaLde 34
                                   v i+d+tLRDG q ++  +++ + l+i + L +
  gi|116753653|ref|YP_842771.1| 20 VFISDSTLRDGAQMPGIVINLRDRLRIYEYLHR 52
                                   679************************999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       223  (0.0124379); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 470.69
//
Query:       gi|116753654|ref|YP_842772.1|  [L=187]
Description: hypothetical protein Mthe_0338 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); 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:                         0  (0); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 1380.67
//
Query:       gi|116753655|ref|YP_842773.1|  [L=221]
Description: metallophosphoesterase [Methanosaeta thermophila PT]
Scores for complete 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   56.9   0.0    5.5e-15   55.9   0.0    1.5  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    1.7e-14   53.8   0.0    6.7e-14   51.8   0.0    1.8  1  Metallophos_3  Metallophosphoesterase, calcineurin superfamil
    2.1e-13   51.3   0.1    3.2e-13   50.6   0.1    1.3  1  Metallophos    Calcineurin-like phosphoesterase


Domain annotation for each model (and alignments):
>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.9   0.0   9.2e-19   5.5e-15       1     157 [.       1     205 [.       1     213 [. 0.75

  Alignments for each domain:
  == domain 1  score: 55.9 bits;  conditional E-value: 9.2e-19
                  Metallophos_2   1 MklaiiSDlHsnldaleavlealkevgvdaiihaGDl.eeeepevleellela.....pvlaVrGNnD............ 62 
                                    M+l+ i+D+H+  +  + ++ + +++  d+++ aGDl ++++p++  ++l+++       l+++GN+D            
  gi|116753655|ref|YP_842773.1|   1 MRLICIADVHD--APSRLWFLEGRSA--DLMVIAGDLhNDGTPDTAVRVLDQLsrfpqMKLIIPGNMDprtfaedlwrsh 76 
                                    9*********3..3344455555666..**********9999*96666666666877656799***************** PP

                  Metallophos_2  63 ............................eev.veedvlreaaelgtdlpeeaelel..agekvlliHgdpl......... 102
                                                                +++    +  ++ ++l + l++  +  +   +++v ++H+ p          
  gi|116753655|ref|YP_842773.1|  77 glipihrstfvigkvgfvgmggmvarnpKRIgDPARYYHSDEDLYRTLTDLLRS-IrdLDRRVVVVHQPPRgvrdrlyng 155
                                    ************999988766555544322223333334444444444322222.2333445******988999999999 PP

                  Metallophos_2 103 ..gvkdalaellkeaeegsdvvvcGHtHvp.evekeggvlvvnPGsvgeprdgdpety 157
                                      +++ +l+++++e   + d+v+cGH+H+  ++ + gg+lvvn G+++++       +
  gi|116753655|ref|YP_842773.1| 156 elSGSSGLRRVIEE--LQPDLVICGHIHEDrGALNLGGTLVVNVGEARMG------YA 205
                                    98889999999988..8889*********9788899**********9987......44 PP

>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.8   0.0   1.1e-17   6.7e-14      58     253 ..      20     216 ..       2     219 .. 0.74

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 1.1e-17
                                    TT----THHHHHHHHHHHHHHHHHHHHHHTT...-SEEEEE--TTS--HHHHHHHHHHTTTT-TTEEE-SSEEEEETTTE CS
                  Metallophos_3  58 errepdkkeileekneiiklldklfrelgel...dvpafvvPGkrDaPlevflreayeaevvfpnlkvvhesfaekeGev 134
                                    e+r  d  +i  + +++  + d + r l++l   +   +++PG++D    +f  +++  + + p    +h s  +  G+v
  gi|116753655|ref|YP_842773.1|  20 EGRSADLMVIAGDLHNDG-TPDTAVRVLDQLsrfPQMKLIIPGNMDP--RTFAEDLWRSHGLIP----IHRST-FVIGKV 91 
                                    566666666666666552.3455555555542115667899****95..578888888444444....44443.456889 PP

                                    EEEEE-SEEESS--BS.SSS-EEEHHHHHHH..GGGGGGS--.-EEEEEESS--S-SST.BTTBS---S-HHHHHHHHHH CS
                  Metallophos_3 135 liaGmGGeivdgekee.efrLkYPaweveyr..Lkvlkelkd.rrkvlllatpPigelv.adkglkekgsevvaelvktl 209
                                     ++GmGG +  + k   +    Y   e  yr    +l+ ++d  r+v+++++pP g  + + +g +  gs  +  ++ +l
  gi|116753655|ref|YP_842773.1|  92 GFVGMGGMVARNPKRIgDPARYYHSDEDLYRtlTDLLRSIRDlDRRVVVVHQPPRGVRDrLYNG-ELSGSSGLRRVIEEL 170
                                    9*******99887776344445555565676431345555553699**********99966666.999************ PP

                                    --SEEEE-SS--EE..EEETTEEEEE--BGGGTEEEEEETTTTEEE CS
                  Metallophos_3 210 nPevvvvghavkeh..eelgktlvvnPGaleeGdfavvdleekkve 253
                                    +P++v++gh + ++   +lg tlvvn G+ + G  a++dl++ +ve
  gi|116753655|ref|YP_842773.1| 171 QPDLVICGHIHEDRgaLNLGGTLVVNVGEARMGYAALIDLDDLDVE 216
                                    ***********99977789*********************999887 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6   0.1   5.4e-17   3.2e-13       1     204 []       1     183 [.       1     183 [. 0.74

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 5.4e-17
                                    EEEEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTSCHHHH CS
                    Metallophos   1 lrilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNHegfeee 80 
                                    +r+++i+D+H        ++l+ l         +dl+++aGDl ++g +++  ++ l++l ++p+ + +++GN +     
  gi|116753655|ref|YP_842773.1|   1 MRLICIADVH-----DAPSRLWFLE-----GRSADLMVIAGDLHNDGTPDT-AVRVLDQLSRFPQMKLIIPGNMD----- 64 
                                    7999******.....4444433333.....3377*************9999.888889999999999********..... PP

                                    HHHHHHHHHHH.HHHHEHHHCEEETSEEEE....EETTEEEEEEEESECEEETHHHHHHHHHHHSCHHHHCC...HHHHH CS
                    Metallophos  81 llnkygylgif.sepwrsdaevfnnlplas....lgsgslkvlllhGgspellvsldklgslnleleapepg...dewlk 152
                                      +      +f  ++wrs     + +p+      +g+    ++ + G          + +++  + ++ +++   +  l 
  gi|116753655|ref|YP_842773.1|  65 --P-----RTFaEDLWRSH----GLIPIHRstfvIGKV--GFVGMGGM------VARNPKRIGDPARYYHSDedlYRTLT 125
                                    ..1.....12225566666....555555522214444..66666666......34444444445555555545566666 PP

                                    H.HHHHTTCSEEEEEESSESS.....CSSSCSCCHHHHHHHHHHTTESEEEEESSSSE CS
                    Metallophos 153 d.lekrekadwvivlgHsply.....rgsgylfgdealedllkkygvdlvisGHtHvy 204
                                    d l+  ++ d  +v+ H p+       ++g l g+  l+++ ++ ++dlvi+GH+H++
  gi|116753655|ref|YP_842773.1| 126 DlLRSIRDLDRRVVVVHQPPRgvrdrLYNGELSGSSGLRRVIEELQPDLVICGHIHED 183
                                    67777999******************9*****************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1492.92
//
Query:       gi|116753656|ref|YP_842774.1|  [L=120]
Description: signal-transduction protein [Methanosaeta thermophila PT]
Scores for 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-25   86.8   0.8    2.8e-16   59.7   0.3    2.0  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 !   26.0   0.0   5.3e-10   9.5e-06       5      55 ..       1      53 [.       1      55 [. 0.87
   2 !   59.7   0.3   1.6e-20   2.8e-16       1      53 [.      65     117 ..      65     120 .] 0.95

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 5.3e-10
                                   SBSSCEEEETTSBHHHHHHHHHHHT.SSEEEEEETTT...BEEEEEEHHHHHHHH CS
                            CBS  5 mtrdvvtvppdttleealelmrekg.vsrlPVVdedg...klvGivtlrDllral 55
                                   m+ +v+tvpp++ + +a++lm  +g  +++ +V e g   ++ Givt + +++++
  gi|116753656|ref|YP_842774.1|  1 MSYPVLTVPPNAKVIDAIKLM-ASGpKGCV-IVAEGGllkEVEGIVTTSRIFKKV 53
                                   7889*****************.55556888.8978889978*********99875 PP

  == domain 2  score: 59.7 bits;  conditional E-value: 1.6e-20
                                    HHHHSBS.SCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                            CBS   1 Vgdimtr.dvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                                    V+dimt+ ++vt++p++t +ea+elm++++++rlPVV +dg lvGi+t +Dll+
  gi|116753656|ref|YP_842774.1|  65 VADIMTPaPLVTISPEATTREAAELMVRHNIRRLPVV-KDGVLVGIITSKDLLQ 117
                                    89*****8889**************************.8*************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); 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: 0.37u 0.29s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 840.62
//
Query:       gi|116753657|ref|YP_842775.1|  [L=304]
Description: metallophosphoesterase [Methanosaeta thermophila PT]
Scores for complete 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   48.9   0.0    1.5e-10   41.5   0.0    2.3  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    6.1e-08   33.4   0.1    1.3e-07   32.4   0.1    1.5  1  Metallophos    Calcineurin-like phosphoesterase


Domain annotation for each model (and alignments):
>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   0.0   1.7e-14   1.5e-10       1     161 [.       1     284 [.       1     287 [. 0.75

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 1.7e-14
                  Metallophos_2   1 MklaiiSDlH...........snldaleavlealkevgvdaiihaGD......l.eeeepevleellela.....pvlaV 57 
                                    M +a+iSD+H           +n+d+    l +    g+d ++++GD      + +e++      +++++      v +V
  gi|116753657|ref|YP_842775.1|   1 MSIAVISDTHfglkssvlsrrDNVDYFIWELWRYG-DGIDEVVLLGDildlwrVrMESAIRDASYFFRRLdelglGVSYV 79 
                                    9*************988855555555554455544.459********666555243344443334444334555****** PP

                  Metallophos_2  58 rGNnD......................eevveedvlreaaelgtdl..................p.eeaelelagekvll 96 
                                     GN+D                      +                 +                     + e+e++ +++ +
  gi|116753657|ref|YP_842775.1|  80 VGNHDhhmtvicqelslleraargelfS-----------------VylpnlrwamnlaglrmtfHyPTYEMEIGSRRFMF 142
                                    *****88766666655555555554442.................0334444444444444444335668899******* PP

                  Metallophos_2  97 iHgdpl.......................................................................... 102
                                    +Hg++l                                                                          
  gi|116753657|ref|YP_842775.1| 143 THGHHLdgikslpvqifegirrlsgepvlpadlermmayayesiyrscylgeaveieeslwrvtsifdkvrsgvlrtlry 222
                                    ****88********************************************************************999999 PP

                  Metallophos_2 103 .....gvkdalaellkeaeegsdvvvcGHtHvpevekeg.gvlvvnPGsvgeprdgdpetyaild 161
                                         ++++ ++  ++++  ++d++++G tH++ + +++ ++lv n+Gs++ +  gd+ ty+il+
  gi|116753657|ref|YP_842775.1| 223 spvesQYDAIIKFIRERHPGKVDCFIYGDTHQAAIYRRNeDLLVANAGSLADG--GDN-TYLILT 284
                                    98875555555555555555566**********887775277777******99..777.999886 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.1   1.4e-11   1.3e-07       1     203 [.       1     254 [.       1     255 [. 0.68

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 1.4e-11
                                    EEEEEEESBTB.......TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSS.........HHHHHHHHHHHHHHHHT CS
                    Metallophos   1 lrilvigDlHl.......algggqlddllkllddllreekpdlvllaGDlvdrg.........dlekellellaalvkyp 64 
                                    ++i+vi+D+H+       ++++   + +++l++      ++d v+l+GD+ d           d ++ + + l++l+   
  gi|116753657|ref|YP_842775.1|   1 MSIAVISDTHFglkssvlSRRDNVDYFIWELWRYG---DGIDEVVLLGDILDLWrvrmesairDASY-FFRRLDELGL-- 74 
                                    78***********9999877777777778888666...577999999******99999976655555.4444466666.. PP

                                    SEEEEEC-TTS..................CHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEE..EETTEEEEEEEESEC CS
                    Metallophos  65 ipvylllGNHe..................gfeeellnkygylgifsepwrsdaevfnnlplas..lgsgslkvlllhGgs 124
                                      v  + GNH+                  g   el++ y  + +++++      +f ++p  +  +gs   ++ + hG+ 
  gi|116753657|ref|YP_842775.1|  75 -GVSYVVGNHDhhmtvicqelslleraarG---ELFSVYLPNLRWAMNLAGLRMTF-HYPTYEmeIGSR--RFMFTHGH- 146
                                    .89*************99988888874443...88888888777766666667777.555555347777..********. PP

                                    EEETHHHHHHHHHHHSCHHHHCC...HHHHHHHHHHTTCSEEEEEESSESS............................. CS
                    Metallophos 125 pellvsldklgslnleleapepg...dewlkdlekrekadwvivlgHsply............................. 172
                                         +ld ++sl+ +  +   +   +      + +++ +  ++ ++  +y                             
  gi|116753657|ref|YP_842775.1| 147 -----HLDGIKSLPVQIFEGIRRlsgE-----PVLPADLERMMAYAYESIYrscylgeaveieeslwrvtsifdkvrsgv 216
                                    .....7777777766655544222221.....444444555555555555544444444444444444444444444777 PP

                                    ....CSSSCSCCHHHHHHH.HHHTT..ESEEEEESSSS CS
                    Metallophos 173 ....rgsgylfgdealedl.lkkyg..vdlvisGHtHv 203
                                        r+s     ++a+ ++  +++   vd  i+G+tH+
  gi|116753657|ref|YP_842775.1| 217 lrtlRYSPVESQYDAIIKFiRERHPgkVDCFIYGDTHQ 254
                                    77777777777777777775555557788889998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); 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: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2230.18
//
Query:       gi|116753658|ref|YP_842776.1|  [L=267]
Description: periplasmic binding protein [Methanosaeta thermophila PT]
Scores for 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-23   82.2   0.0    5.1e-23   81.9   0.0    1.1  1  Peripla_BP_2  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.9   0.0   2.8e-27   5.1e-23       1     206 [.      44     248 ..      44     258 .. 0.89

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 2.8e-27
                                    EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT..TS-BSBESSSB-HHHHHHH--SEEEE-GGG....GGGHHHH CS
                   Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadkleeaivevgadgeidvEklaalkPDlvilskgl.gltdedeell 79 
                                    i++lsp+ +e+l alG +dk+++v + +  p+  + l e+  +  +++++d+E++++lkPDlvi+++g   + ++++ l 
  gi|116753658|ref|YP_842776.1|  44 IVCLSPAAAEVLCALGMSDKIAAVTEDCIIPSLCRCLQEKERVGTSGRNADLERILELKPDLVIAKTGSlFPEESEKVLV 123
                                    9*********************************999966666677889*******************988888899999 PP

                                    HHHS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT...-EEEEEEEETTE..EEEE-TT CS
                   Peripla_BP_2  80 ksgiptvivessntgeslkeqiralgellgledeaeklvaeidsklaaaksaidse..kpkpvlvfggadeggyvvagsn 157
                                    + gip++ ++     + l  +i  lg +++ ed+ ++++ +i + +  + ++++     ++p+++f++    +   ag++
  gi|116753658|ref|YP_842776.1| 124 SCGIPVLRYRALHI-DALIPMINDLGRIVNAEDKSHEIIGWITKYYNTILERVSLVpeSERPTVYFMSMGH-FDWTAGNQ 201
                                    99**********97.************************************99999555566666654444.55788999 PP

                                    STTTHHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEHHHHT CS
                   Peripla_BP_2 158 syigdlldalgieniaaeskkseyeeisaEqilasdpdvifvsgraead 206
                                    s +   ++++g++nia +  ++    +++E++  ++p++i++s+  +++
  gi|116753658|ref|YP_842776.1| 202 SAGDIRISEAGGRNIAGNL-TETVPHVDMEWVIQQNPQIIIFSMA-SNQ 248
                                    999999*********9999.***********************99.443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1955.07
//
Query:       gi|116753659|ref|YP_842777.1|  [L=289]
Description: transposase, IS4 family protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.2e-33  113.1   0.0    3.2e-31  107.9   0.0    2.2  2  DDE_Tnp_1_5  Transposase DDE domain
      9e-21   74.5   0.1    1.6e-20   73.7   0.1    1.4  1  DDE_Tnp_1    Transposase DDE domain


Domain annotation for each model (and alignments):
>> DDE_Tnp_1_5  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.9   0.0   3.6e-35   3.2e-31       2     111 ..      18     125 ..      17     126 .. 0.95
   2 ?    2.8   0.0     0.016   1.4e+02      40      67 ..     252     281 ..     246     287 .. 0.82

  Alignments for each domain:
  == domain 1  score: 107.9 bits;  conditional E-value: 3.6e-35
                    DDE_Tnp_1_5   2 kRGsltiwldeeaiaawkek...kkngkrgrpqvysdaaiqtcltvkvlfklplRqlqGfvqsllklaglellvpdystl 78 
                                    +RG  +++l+++++++w+e+    +++k+grp++y++++iq+c +++++++lp+Rql+Gf+q+l+ ++   ll++dystl
  gi|116753659|ref|YP_842777.1|  18 RRG--WFYLSTDFVNNWDEEllkMNKNKNGRPYRYPETFIQFCGLAYAFLHLPYRQLEGFIQALSGFVPG-LLAADYSTL 94 
                                    799..************9987745569******************************************9.99******* PP

                    DDE_Tnp_1_5  79 srraktlevkipvkrkskglhlvvdstGlkvlg 111
                                    ++r ++le++ip+ +++  l+++vdstG+kv++
  gi|116753659|ref|YP_842777.1|  95 WQRITNLELNIPIPDND--LVVAVDSTGMKVTN 125
                                    **************999..99**********97 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.016
                    DDE_Tnp_1_5  40 tcltvkvlfklplRql..qGfvqsllklag 67 
                                    ++  +k++f+ ++R++  +G+++ + ++ +
  gi|116753659|ref|YP_842777.1| 252 VFSAIKRIFGETVRATskEGMIREVRRMFT 281
                                    56789*********9855699999988876 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.7   0.1   1.8e-24   1.6e-20       5     200 ..     112     271 ..     108     285 .. 0.83

  Alignments for each domain:
  == domain 1  score: 73.7 bits;  conditional E-value: 1.8e-24
                      DDE_Tnp_1   5 evlivDattvrvpgtkedarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrprkgklvlaDa 84 
                                     v++vD+t ++v+  + ++r++++  + + ++k+hiavd +++ ++ ++it+  v d++ +k+ll+ +   k    l+D+
  gi|116753659|ref|YP_842777.1| 112 LVVAVDSTGMKVTNRGDWMRESHGVER-RGWIKVHIAVDVETRKPVTFEITDETVTDHEMVKPLLEDV---KLEDSLMDG 187
                                    699******************888666.79************************************99...89******* PP

                      DDE_Tnp_1  85 GYasaelldtleekgvd.yiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgdvyyvtntnsells 163
                                    +Y++++++d+++ekgvd + i+++kn+ ++        r +    +++  +  +++ +++                    
  gi|116753659|ref|YP_842777.1| 188 AYDKEGVFDFMKEKGVDmPGIKIRKNAIVKAG----SSRAEPVLEFMKYGYHSWKIVHGY-------------------- 243
                                    ****************9568899999988866....344445555555555555555555.................... PP

                      DDE_Tnp_1 164 aeevaelyrlRwqiErvFkwlkrkfgldrlryrglnr 200
                                             +Rw  E+vF+ +kr fg + +r+ ++++
  gi|116753659|ref|YP_842777.1| 244 --------GRRWAAESVFSAIKRIFG-ETVRATSKEG 271
                                    ........***************998.6666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 2202.81
//
Query:       gi|116753660|ref|YP_842778.1|  [L=84]
Description: periplasmic binding protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
        0.2   11.2   0.0       0.27   10.8   0.0    1.1  1  Peripla_BP_2  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   1.5e-05      0.27     211     235 ..       5      29 ..       2      31 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 1.5e-05
                                    HHHHT-SHHHHTSHHHHTT-EEEE- CS
                   Peripla_BP_2 211 leflkenpllaelpAvkngrVyald 235
                                     +++++ +++ ++ Avk+grVy +d
  gi|116753660|ref|YP_842778.1|   5 RDEIMSLTGFDSIDAVKSGRVYVMD 29 
                                    58999999**************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       247  (0.0137766); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 580.17
//
Query:       gi|116753661|ref|YP_842779.1|  [L=166]
Description: hypothetical protein Mthe_0345 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1200.52
//
Query:       gi|116753662|ref|YP_842780.1|  [L=227]
Description: histidine biosynthesis [Methanosaeta thermophila PT]
Scores for complete 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-28   97.5   0.1    8.9e-28   97.3   0.1    1.1  1  His_biosynth  Histidine biosynthesis protein
    2.6e-05   23.6   0.3      4e-05   23.0   0.3    1.3  1  ThiG          Thiazole biosynthesis protein ThiG


Domain annotation for each model (and alignments):
>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.3   0.1   9.9e-32   8.9e-28       2     227 ..       3     219 ..       2     221 .. 0.92

  Alignments for each domain:
  == domain 1  score: 97.3 bits;  conditional E-value: 9.9e-32
                                    EEEEEEEETTEEEEECTTCS........TCEEEETTSHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-S CS
                   His_biosynth   2 iipalDlkdGkvVrlvkGdr........fqelryagdpvelakryeeegadelhvvDldaakegreanldlveeiaeevf 73 
                                     i+++D+ + kvV+ v+G+r        f++ +   dp+e+++ +     +e++v+Dl+   +g++ nl+ +e+i ++  
  gi|116753662|ref|YP_842780.1|   3 CIFVMDIYNSKVVHAVRGERsryrsintFSRVVSTPDPIEIIEIL---APKEVYVADLNRL-SGSGDNLKTIERISSK-- 76 
                                    699*****************9999999999999999****99998...789*******876.7***************.. PP

                                    SEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEECEEEEETTTTEEEEEEHHHHH CS
                   His_biosynth  74 ipvqvGGGIrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarrgykvaikgwreetgldavela 153
                                    +  + + GI++l+d+  l e      ++gt+++ + +li+++++      ivv+iD+++  kv  + +  +    ++el+
  gi|116753662|ref|YP_842780.1|  77 AITMADIGISTLSDLSLLPEP--TTPVLGTETA-SLDLISDASDL---RDIVVSIDMKHR-KVISHSGLLD----PLELI 145
                                    77889********98766665..8889999986.688******94...57*********9.9999999877....***** PP

                                    HHHHHTT-SEEEEEETTTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHHHHTTCSEEEESHHHHTTS CS
                   His_biosynth 154 kkleelgageilltdidrdGtlsGpdleltkelaeavkipviasGGvgsledlkelksegvdavivgsalyege 227
                                    k++++l +  i+l + dr+Gt +G+d+e++++  ++ ++pv+++GGv+ l+d+++l++ gv++v+v++a +++ 
  gi|116753662|ref|YP_842780.1| 146 KEMNDLDLLGIILLELDRVGTSAGVDIEFLSSAVASSDHPVLVGGGVRGLSDVHALEEIGVHGVLVATAVHSRA 219
                                    ***********************************************************************876 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.3   4.5e-09     4e-05     155     217 ..     164     225 ..     147     227 .] 0.91

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 4.5e-09
                                    TTS----S-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHH CS
                           ThiG 155 iGsglGllnkealkiiieeakvPvivDAGigspsdaaqamelGadavllntavaeakdpvamA 217
                                    +G++ G+   e+l+  +++ + Pv+v  G++  sd+ +  e+G+ +vl++tav + + p++m 
  gi|116753662|ref|YP_842780.1| 164 VGTSAGVD-IEFLSSAVASSDHPVLVGGGVRGLSDVHALEEIGVHGVLVATAVHSRAMPIEMI 225
                                    67777764.57899999999****************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); 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: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1686.72
//
Query:       gi|116753663|ref|YP_842781.1|  [L=234]
Description: hypothetical protein Mthe_0348 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-88  296.7   0.0    1.4e-88  296.5   0.0    1.0  1  4HFCP_synth  4-HFC-P synthase
     0.0054   16.5   0.0       0.14   12.0   0.0    2.3  2  QRPTase_C    Quinolinate phosphoribosyl transferase, C-termin


Domain annotation for each model (and alignments):
>> 4HFCP_synth  4-HFC-P synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  296.5   0.0   1.5e-92   1.4e-88       1     227 [.       5     230 ..       5     231 .. 0.99

  Alignments for each domain:
  == domain 1  score: 296.5 bits;  conditional E-value: 1.5e-92
                                    EEE--SSHHHHHHHHHHT-SEEEE--GGG-TT----HHHHHHHHHHS-TTSEEEEEEEEE-S-HHHHHHHHHHHHHTT-S CS
                    4HFCP_synth   1 LLvSvrnleEaelalaggadiiDvKnPaeGsLGalfpevireivevvpgsvpvSaaiGdlpekpgtvslaalgaaaagvd 80 
                                    LLvS+++leEa +al+ggadiiDvKnP+eGsLGa+fp+ ir++ve+v+g++pvSa+iGdlp+kpgt+slaalgaa++g+d
  gi|116753663|ref|YP_842781.1|   5 LLVSPMDLEEAVAALDGGADIIDVKNPREGSLGANFPWAIRSVVELVAGRTPVSATIGDLPFKPGTASLAALGAAVSGAD 84 
                                    8******************************************************************************* PP

                                    EEEEEE-S--SHHHHHHHHHHHHHHHHHH-TTSEEEEEEETTGGGTT---GGGHHHHHHHHT-SEEEEE-SS-SS--HHH CS
                    4HFCP_synth  81 yvKvGlaglkkeeealealkavvkavkeedkekkvvavlyaDaervasvsplellelaaeagaagvmlDTadKdgkslld 160
                                    y+K Gl g+++ eea+e+l+++v++v+++d+++k+va++y+D++r++s++pl l+e+aae+ga++vm+DTa+Kdg+s+l+
  gi|116753663|ref|YP_842781.1|  85 YIKAGLLGVSEPEEAIELLRPIVRSVRDYDSRRKIVAAAYSDFRRAGSLPPLVLPEIAAECGADVVMVDTAIKDGRSTLE 164
                                    ******************************************************************************** PP

                                    HS-HHHHHHHHHHHHHTT-EEEE-SS--GGGHHHHHHTT-SEEEESGGGBTTSSTTSSB-HHHHHHH CS
                    4HFCP_synth 161 flseeelaefveeareaglltaLAGslkledlpaLkklkpdilGvRgavCeegdRngkidaelvekl 227
                                    f+s+eel++fve+a+++g++ aLAG+l ++dl+a+++++pdilGvRgavC +gdRn++i+aelv++l
  gi|116753663|ref|YP_842781.1| 165 FMSVEELKHFVESAHDLGMEAALAGNLGVRDLEAIRAASPDILGVRGAVC-GGDRNSRIRAELVRSL 230
                                    **************************************************.*************998 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 ?    2.2   0.0     0.015   1.4e+02      84     110 ..       6      40 ..       1      61 [. 0.70
   2 !   12.0   0.0   1.5e-05      0.14      96     154 ..     142     209 ..     138     216 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.015
                                    EEEESSHHHHHHHHHHT-SEEEEES-........- CS
                      QRPTase_C  84 evevesleeleevleaeadiimLDnf........s 110
                                     v    lee+ ++l  +adii + n+         
  gi|116753663|ref|YP_842781.1|   6 LVSPMDLEEAVAALDGGADIIDVKNPregslganF 40 
                                    566667999************99998544444433 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 1.5e-05
                                    HHHHT-SEEEEES-...........-HHHHHHHHHHHHHHSTTSEEEEESS--TTTHHHHHCTT-SEEEE CS
                      QRPTase_C  96 vleaeadiimLDnf...........sveelkkaveelkeknkrvlievSGgvtlenveeyaksgvdvisv 154
                                    ++e +ad++m+D+            sveelk++ve  ++++  ++   +G++   ++e+++    d+++v
  gi|116753663|ref|YP_842781.1| 142 AAECGADVVMVDTAikdgrstlefmSVEELKHFVE--SAHDLGMEAALAGNLGVRDLEAIRAASPDILGV 209
                                    67899******************9999********..66777799999**********999887777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1726.80
//
Query:       gi|116753664|ref|YP_842782.1|  [L=181]
Description: hypothetical protein Mthe_0349 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.15   11.4   0.0       0.34   10.2   0.0    1.5  2  DUF3747   Protein of unknown function (DUF3747)


Domain annotation for each model (and alignments):
>> DUF3747  Protein of unknown function (DUF3747)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   1.9e-05      0.34     134     170 ..      56      92 ..      38      97 .. 0.79
   2 ?   -1.7   0.0     0.089   1.6e+03      20      51 ..      98     130 ..      90     132 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 1.9e-05
                        DUF3747 134 igrtkglasgflkieLepgWrltkrtyegktlgHvYl 170
                                     g ++g a  ++ i+++ +W+++ rt ++k++g v l
  gi|116753664|ref|YP_842782.1|  56 TGGATGSATTYTSIDIRGNWSFELRTLDDKMVGTVNL 92 
                                    45566677999*********************98866 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.089
                        DUF3747  20 kaalfgeqevdqskfvavaapl.genkyqLlvl 51 
                                     +++fg+  v  s+ ++ a     +n  +L+++
  gi|116753664|ref|YP_842782.1|  98 GTVVFGAGTVRGSNAIVTANGAiVDNMLTLNIV 130
                                    567899999999999999886657777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1337.80
//
Query:       gi|116753665|ref|YP_842783.1|  [L=359]
Description: radical SAM domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.5e-14   53.5   0.0    4.7e-14   53.1   0.0    1.2  1  Radical_SAM  Radical SAM superfamily
    3.1e-10   40.4   1.0    8.9e-10   39.0   0.4    2.0  2  SPASM        Iron-sulfur cluster-binding domain
    0.00017   21.8   0.0    0.00031   21.0   0.0    1.3  1  Fer4_12      4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.026   14.6   0.0      0.043   13.9   0.0    1.4  1  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.1   0.0   1.1e-17   4.7e-14       1     166 [.      70     223 ..      70     224 .. 0.85

  Alignments for each domain:
  == domain 1  score: 53.1 bits;  conditional E-value: 1.1e-17
                                    EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiri 80 
                                    ++v+rgC++ C++C+ p+     + g +l  + +++ + e+  + g   v++ ggep+l+ d+ +l++    +    i +
  gi|116753665|ref|YP_842783.1|  70 ISVFRGCPNSCIHCSAPS-----RSGDVLEGDVVKRVISEA-LDLGSYLVTFDGGEPMLRLDLPDLVASVDDR---AIAT 140
                                    6899*************7.....555555555555555555.5666**************************8...7888 PP

                                    EEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  81 tvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglpGendee 159
                                    ++++ + l  e+ + +l+++g+  + ++++++ +e  +++++ r++ f + + + +++ +ag+  v  ++v+ p +n ++
  gi|116753665|ref|YP_842783.1| 141 CFTSGYALS-EKLALELKKRGLYAIRVSIDSPVEE-QHDHFRgRRGAFGDAISGARNALQAGLL-VDLFMVVSP-YNIDQ 216
                                    887777776.*************************.8888888*********************.777777777.99999 PP

                                    HHHHHHH CS
                                    xxxxxxx RF
                    Radical_SAM 160 leellel 166
                                    le+ ++l
  gi|116753665|ref|YP_842783.1| 217 LEDAYSL 223
                                    9998876 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.1     5e+03      37      52 ..     244     264 ..     235     272 .. 0.67
   2 !   39.0   0.4     2e-13   8.9e-10       1      57 [.     289     338 ..     289     349 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.1
                          SPASM  37 eesleeIwnseeyqe.....f 52 
                                    e+ l+e+++s+ +++     +
  gi|116753665|ref|YP_842783.1| 244 EDHLDEVLSSKDIERlaefhM 264
                                    568999999998888444222 PP

  == domain 2  score: 39.0 bits;  conditional E-value: 2e-13
                          SPASM   1 CfapsrslfInsdGdVvpCcvdkktyveelklGnireesleeIwnse.eyqefrkskk 57 
                                    Cfa++r + +++ Gd +pC ++      ++++Gn+++ sl++Iw+   +y +fr+  +
  gi|116753665|ref|YP_842783.1| 289 CFAGRRWIHVDPSGDAMPCAYM------PISFGNVKKSSLKNIWRRMsRYSWFRH--R 338
                                    9******************333......7***************8888******4..2 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 !   21.0   0.0     7e-08   0.00031      12     123 ..      73     176 ..      66     184 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 7e-08
                        Fer4_12  12 vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdiwly 91 
                                    + gC+ sC  C ++     +sg+  + ++ +++i ++ +     +t+ GGEP+l   + +l +lv +v  +++  ++  +
  gi|116753665|ref|YP_842783.1|  73 FRGCPNSCIHCSAP----SRSGDVLEGDVVKRVISEALDLGSYLVTFDGGEPML---RLDLPDLVASVDDRAIA-TC-FT 143
                                    689*******9955....467888899999999999999999************...999*************3.55.55 PP

                        Fer4_12  92 tgytleelskk.ekeellkeidvlvdGkfeesl 123
                                    +gy l e ++   k++ l  i v +d + ee+ 
  gi|116753665|ref|YP_842783.1| 144 SGYALSEKLALeLKKRGLYAIRVSIDSPVEEQH 176
                                    677666655433667778889999999988664 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 ?   13.9   0.0   9.7e-06     0.043       5      92 ..      73     149 ..      70     171 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.7e-06
                        Fer4_14   5 lsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekkiw 84 
                                    + gC+ sC  C   +    ++g + + +++++++   ++ +     +++ GGeP++     +l +lv  + ++   +   
  gi|116753665|ref|YP_842783.1|  73 FRGCPNSCIHCSAPS----RSGDVLEGDVVKRVI--SEALDLGSYLVTFDGGEPMLR---LDLPDLVASVDDRA--IATC 141
                                    679********9887....777777777777777..44445555779********66...56777888888887..6666 PP

                        Fer4_14  85 letngtle 92 
                                    + +++ l 
  gi|116753665|ref|YP_842783.1| 142 FTSGYALS 149
                                    66666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); 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: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2651.87
//
Query:       gi|116753666|ref|YP_842784.1|  [L=289]
Description: polyprenyl synthetase [Methanosaeta thermophila PT]
Scores for complete 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-47  162.3   0.0    1.4e-47  161.9   0.0    1.1  1  polyprenyl_synt  Polyprenyl synthetase


Domain annotation for each model (and alignments):
>> polyprenyl_synt  Polyprenyl synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.9   0.0   7.8e-52   1.4e-47       5     240 ..      28     241 ..      25     255 .. 0.90

  Alignments for each domain:
  == domain 1  score: 161.9 bits;  conditional E-value: 7.8e-52
                                    HHHHHHHHHSSS--HHHHHHHHHHHHHSCGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEETTEE-HHHCTCHHHHH CS
                polyprenyl_synt   5 eealeylveagGKrlRpllvllaaealkeeeeelekaavlawivellhaasLvhDDimDdsetRRGqpcahrlvGnklAi 84 
                                     e++ey++ ++GKr+Rpl++l ++ea++ ++   + a+++a +vel haasL+hDDi D    RRG+p+a r++G+++++
  gi|116753666|ref|YP_842784.1|  28 GEVIEYVLMSPGKRVRPLILLFSSEAFGCDP---RYALNAALAVELAHAASLIHDDILDCGVERRGAPSAFRRFGMEASL 104
                                    6899************************666...789******************************************* PP

                                    HHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHTTTTTCCC.SHHHHHHHHHHHTHHHCHHHHHHHHH CS
                polyprenyl_synt  85 ndgdfllarafellaklfekslellelfsevllqtveGqlldleeekdddlskfsleeyleivkyKTaylfalpvalaal 164
                                    ++gd+l +++  l++++  ++  +++lfs+++++++eG+++dl ++    ++  s +ey + +++KTa+lfa++++l+++
  gi|116753666|ref|YP_842784.1| 105 LAGDYLISMSIGLISSY--GE-PAIRLFSKACMDMAEGEIIDL-SR----IA--SPQEYYQCITKKTASLFAASARLGCM 174
                                    *****************..76.89*******************.23....44..589*********************** PP

                                    HTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHSS-TSHHHHTT---HHHHHHHHCT-HHHHHHHHHHTT CS
                polyprenyl_synt 165 lagasdeelealkdiglelGlaFQiqDDylDlfgdpevlgKpagtDiqegkctlpilkalelaspeqrkvlkeilg 240
                                    +aga++e+   ++++glelGla+Qi+DD+  l g   + gK      +++ +tlp ++al+ + pe+  +l+ ++ 
  gi|116753666|ref|YP_842784.1| 175 IAGADREDQILYERYGLELGLAYQIVDDLEELIGI--DQGKR----STKKSMTLPRIYALR-SGPEE--TLRMCVD 241
                                    ****99999************************87..55788....89999**********.55663..4555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 2123.06
//
Query:       gi|116753667|ref|YP_842785.1|  [L=157]
Description: TspO and MBR like proteins [Methanosaeta thermophila PT]
Scores for complete 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  152.3  17.2    8.4e-45  152.1  17.2    1.0  1  TspO_MBR  TspO/MBR family
  ------ inclusion threshold ------
        1.9    8.9  14.9         51    4.3  14.9    2.5  1  DUF805    Protein of unknown function (DUF805)


Domain annotation for each model (and alignments):
>> TspO_MBR  TspO/MBR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.1  17.2   9.3e-49   8.4e-45       2     135 .]      11     155 ..      10     155 .. 0.98

  Alignments for each domain:
  == domain 1  score: 152.1 bits;  conditional E-value: 9.3e-49
                                    HHHHHHHHHHHHHHHHHCCH.HHHHHS---TTS--HHHHTTHHHHHHHHHHHHHHHHHHH..........HHHHHHHHHH CS
                       TspO_MBR   2 alalpllvgllgglftksee.ewykslrkPpwaPpdwvfppvWtvlyilmgvaaylvwka..........lalyavqlvl 70 
                                    ++ ++ l+g+lg++ft++++ +wy  l kP+++Pp+w++++vW vly+lmg++++lv+++          l+ ++vql+l
  gi|116753667|ref|YP_842785.1|  11 CITVCQLAGVLGSYFTDMSVsTWYPMLIKPSYTPPGWLIGVVWVVLYTLMGISLFLVLDSkpesgtlksaLIPFGVQLLL 90 
                                    688999***********8889*************************************************77******** PP

                                    HHTSGGCTTTTTSGGGHHHHHHHHHHHHHHHHHHCCCC-HHHHHHHCHHHHHHHHHHHHHHHHHH CS
                       TspO_MBR  71 nllwsplffglkspvlalvdivallglvvalilafskvdklaallllpyllWllfatylnasiwr 135
                                    n++ws +ffgl+sp+ alv+i+al++++++++++f+ v+++a++ll+py++W++fa+yln++iwr
  gi|116753667|ref|YP_842785.1|  91 NISWSGAFFGLRSPLYALVVIAALWLSIIITMRRFYDVSRIAGVLLIPYIMWVSFAAYLNYTIWR 155
                                    ****************************************************************5 PP

>> DUF805  Protein of unknown function (DUF805)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3  14.9    0.0057        51      36      85 ..      69     147 ..       1     155 [. 0.72

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0057
                         DUF805  36 a.............................aavasalsvvlallllvpslavtvRRlHDtgrsgwllllllvplialll 85 
                                    +                               + s l  ++++++l +s+ +t+RR+ D+ r + +ll+ ++ ++++ +
  gi|116753667|ref|YP_842785.1|  69 DskpesgtlksalipfgvqlllniswsgafFGLRSPLYALVVIAALWLSIIITMRRFYDVSRIAGVLLIPYIMWVSFAA 147
                                    2455557777777777777666677767766677778888888999999*************99987777776554433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1287.76
//
Query:       gi|116753668|ref|YP_842786.1|  [L=121]
Description: hypothetical protein Mthe_0353 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.14   12.4   0.0       0.23   11.7   0.0    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 ?   11.7   0.0   1.3e-05      0.23      14      49 ..      68     103 ..      60     116 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.3e-05
                        DUF4157  14 fgadlsdVrvhtgsaaaraaralgAqAfTlgndivf 49 
                                    +g+++++V  h+ ++ +r  r+++A A+T+ n + +
  gi|116753668|ref|YP_842786.1|  68 VGTEVGRVSSHNKDEVRRIIREIKAGAYTMSNPVKV 103
                                    78999*************************998866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 893.80
//
Query:       gi|116753669|ref|YP_842787.1|  [L=261]
Description: hypothetical protein Mthe_0354 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 1894.37
//
Query:       gi|116753670|ref|YP_842788.1|  [L=322]
Description: GTP cyclohydrolase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-83  279.1   0.8      4e-83  278.9   0.8    1.0  1  GCHY-1        Type I GTP cyclohydrolase folE2
  ------ inclusion threshold ------
       0.03   13.8   0.3      0.081   12.4   0.0    1.8  2  Dot_icm_IcmQ  Dot/Icm secretion system protein (dot_icm_IcmQ)


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 !  278.9   0.8   4.5e-87     4e-83       1     259 []       4     295 ..       4     295 .. 0.95

  Alignments for each domain:
  == domain 1  score: 278.9 bits;  conditional E-value: 4.5e-87
                                    .XXXXXXXXXX----SEEEEEEEEEEEEE--TTTS-EEEEEEEEEEEES-SS--GGGGGHHHHHHH.HS-SSEEG..GGH CS
                         GCHY-1   1 lpDvqsekderkipldrVGvkgvklpvkvkdkekkaqtlvaevdlfvdLpaekkGihmSRlvevle.eaeeelee..ksl 77 
                                    lpDvq+ +++++i+l+rVGv+gvk++vkv++++++++ l++++++fvdLp+++kG+++SR++e+++   eee++   +++
  gi|116753670|ref|YP_842788.1|   4 LPDVQACHPAYPINLTRVGVTGVKKLVKVERSGERPIVLISNFEVFVDLPSSRKGANLSRNTEAIDeVLEEEISRpvYEI 83 
                                    79****************************************************************66678888678777 PP

                                    HH....HHHHHHHHTT.-SEEEEEEEEEEEEEEE-TTT--EEEEEEEEEEEEEE...TT.EEEEEEEEEEEEEEE-HHHH CS
                         GCHY-1  78 ee....ileellekleyaeraevelkfeyfiekkapvsgkeglesyevtleaeler.ke.evkltvgvevpvttlCPCsk 151
                                    ee    i+ +lle++eya+raev++k+ey++++++p+++++++e +++++ea +++  + +vk++vg+ev +tt+CPC++
  gi|116753670|ref|YP_842788.1|  84 EElcgkIALRLLERHEYATRAEVKMKSEYIVKRQTPATRVNCQEVVDIFAEAMATSgPDpHVKKIVGAEVIGTTACPCAQ 163
                                    777778************************************************9854456******************* PP

                                    HHS.........................SS---EEEEEEEEEEEE......--HHHHHHHHHHHSSEE--S---HHHHHH CS
                         GCHY-1 152 eisrell.....................eagaHnQRsvvtvkvelaeeekeveiedlielvessassevyellKReDEka 210
                                    ei+re++                     ++++HnQR++ ++++e+ +++k v+i+++i+++e+s+ss+vy llKR+DE+ 
  gi|116753670|ref|YP_842788.1| 164 EIVREQMrrdllnlglsedaiegflkkvPVATHNQRGRGSISIEV-RDRKCVPIDRIIRIIEESMSSKVYGLLKRPDEAL 242
                                    *****99*************************************5.68999***************************** PP

                                    HHHHHHTS---HHHHHHHHHHHHHS-TTEEEE.........EEEEEEE-TTTSSEEEE CS
                         GCHY-1 211 vtekayenpkFvEDvvRevaaaleeeerveef.........sveveneESiHnHnavA 259
                                    v+ +a+ np+FvED+vRe+a+++     v++f         ++++ neESiH+Hna+A
  gi|116753670|ref|YP_842788.1| 243 VVSRAHMNPMFVEDCVREMAQRV-----VATFvelpddavvTLKQINEESIHRHNAFA 295
                                    ***********************.....7777777999999****************8 PP

>> Dot_icm_IcmQ  Dot/Icm secretion system protein (dot_icm_IcmQ)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     9e-06     0.081      48     107 ..      31      90 ..      15     126 .. 0.69
   2 ?   -1.9   0.1      0.23     2e+03      27      61 ..     279     313 ..     276     315 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9e-06
                   Dot_icm_IcmQ  48 kldselanrialrsnkqeiyvslyss.dGsdlksWeriiaslprqmisrPiyaneedvkai 107
                                    k++      i l sn  e++v l ss +G +l+     i ++ +  isrP+y+ ee   +i
  gi|116753670|ref|YP_842788.1|  31 KVERSGERPIVLISN-FEVFVDLPSSrKGANLSRNTEAIDEVLEEEISRPVYEIEELCGKI 90 
                                    555555555666665.69*****98857************************988866554 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.23
                   Dot_icm_IcmQ  27 nlkeireeflkkvnaasqekekldselanrialrs 61 
                                     lk+i ee +++ na ++   k+    a+ +a+++
  gi|116753670|ref|YP_842788.1| 279 TLKQINEESIHRHNAFAERVAKMGELRAELAAIHE 313
                                    57899999999999988888888887777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2315.58
//
Query:       gi|116753671|ref|YP_842789.1|  [L=91]
Description: hypothetical protein Mthe_0356 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.69   10.3   5.9        2.5    8.5   1.4    2.1  2  UPF0184   Uncharacterised protein family (UPF0184)


Domain annotation for each model (and alignments):
>> UPF0184  Uncharacterised protein family (UPF0184)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.2    0.0023        41      47      60 ..      26      39 ..       7      50 .. 0.82
   2 ?    8.5   1.4   0.00014       2.5      37      62 ..      50      75 ..      45      87 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0023
                        UPF0184 47 ernDdlnskLrELl 60
                                   +  Dd++ +LrEL+
  gi|116753671|ref|YP_842789.1| 26 HDPDDIERQLRELM 39
                                   5569*********9 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00014
                        UPF0184 37 qinsaLDalEernDdlnskLrELles 62
                                   +++s+LD ++er   +   L ELle 
  gi|116753671|ref|YP_842789.1| 50 ELESILDGINERDCRISEMLDELLEE 75
                                   689*********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 657.03
//
Query:       gi|116753672|ref|YP_842790.1|  [L=294]
Description: permease [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-54  183.8  23.9    4.4e-54  183.6  23.9    1.0  1  ArsP_1           Predicted permease
  ------ inclusion threshold ------
        5.6    6.5  12.8       0.18   11.4   4.6    2.5  2  ABC_membrane     ABC transporter transmembrane region


Domain annotation for each model (and alignments):
>> ArsP_1  Predicted permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.6  23.9     5e-58   4.4e-54       4     291 ..       8     290 ..       5     293 .. 0.93

  Alignments for each domain:
  == domain 1  score: 183.6 bits;  conditional E-value: 5e-58
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         ArsP_1   4 ealtlfasilleallaLvlgflisgaiqvfvkeekiielLgprnrlisllvaallGfllpvCscsavPlarrllkkGapl 83 
                                     + ++f  i+le  ++ +   +++g+i  +v+ +++++ Lg r+ +++++++a++G+l+p+Cscs +P+  ++l +G+p+
  gi|116753672|ref|YP_842790.1|   8 IVINFFVKIALELTVLFIGVSFLVGLIHEYVSDDAVKRALGGRHIVAGSVLGAAFGALTPFCSCSTIPMLLGMLNAGVPF 87 
                                    5778999999998777777779********************************************************** PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         ArsP_1  84 gaavaFlvaaPainiiaiiltlillgwqllvarivlalivaiviglvleylfkeeelekaarevaeaglekltlkpklea 163
                                    +a ++Fl+++P +n++++ l ++llgw ++++++ ++++va+ +glvl  l  +++++  a+ +++  l+ +    ++++
  gi|116753672|ref|YP_842790.1|  88 AACMSFLFSSPLLNPVILSLFVVLLGWRVALLYLAVTFLVAVSAGLVLDALGFKSQVKSVAFVRDD--LPAQDAGSRIRR 165
                                    *************************************************************97655..444444444444 PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         ArsP_1 164 lkafaknevkewlelgkyLiiGvaiagviqaflpesvllsllggnsvsssllamligvvlyvcslgevpfiaalfesgla 243
                                        a+ ++  + +l++yL++G+ i+++i +f+p + +++++g+++  +++ a++ig++ly+ +++ +p+  al+e+g++
  gi|116753672|ref|YP_842790.1| 166 ---SADFALTLFCQLMPYLLLGAGIGAFIYGFVPSDLVVQIAGQDNTLAIPAAAIIGIPLYIRTETILPIGLALIEKGMS 242
                                    ...788889999******************************************************************** PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         ArsP_1 244 lGsalAfLlagpllslpellillkvlkkklvavllglvvvsvvlaglv 291
                                    +G +lA+ + g+  s+pel +l++++ +kl+a+++++++ ++v+ag +
  gi|116753672|ref|YP_842790.1| 243 VGAVLALVIGGAGASIPELSLLSAIFERKLLAAFVLTIFTIAVAAGFM 290
                                    ********************************************9975 PP

>> ABC_membrane  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   1.1      0.17   1.5e+03     223     249 ..       3      29 ..       1      39 [. 0.81
   2 ?   11.4   4.6     2e-05      0.18     120     162 ..      93     135 ..      88     148 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.17
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   ABC_membrane 223 anglligitqllgllsyalalwfGttl 249
                                    +++l+i+i++++  ++ + +l++G+++
  gi|116753672|ref|YP_842790.1|   3 YDSLMIVINFFVKIALELTVLFIGVSF 29 
                                    678888899999999999999998876 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 2e-05
                                    HHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHH CS
                   ABC_membrane 120 glffqslltfvgglivmfylgwkltlvllailpliilvsavia 162
                                    +lf+ +ll+ v++ +++++lgw+++l+ la+++l+++++ ++ 
  gi|116753672|ref|YP_842790.1|  93 FLFSSPLLNPVILSLFVVLLGWRVALLYLAVTFLVAVSAGLVL 135
                                    789*********************************9988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2096.07
//
Query:       gi|116753673|ref|YP_842791.1|  [L=84]
Description: hypothetical protein Mthe_0358 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       398  (0.0221987); 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:                         0  (0); expected 0.2 (1e-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 0.28s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 607.33
//
Query:       gi|116753674|ref|YP_842792.1|  [L=413]
Description: peptide chain release factor 1 [Methanosaeta thermophila PT]
Scores for complete 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  152.0   0.0      2e-44  151.1   0.0    1.5  1  eRF1_2          eRF1 domain 2
    1.8e-31  109.0   0.0    5.7e-31  107.3   0.0    1.8  2  eRF1_3          eRF1 domain 3
      2e-14   53.7   0.0    5.7e-14   52.2   0.0    1.8  3  eRF1_1          eRF1 domain 1
    3.9e-14   53.1   0.0    7.1e-14   52.2   0.0    1.4  1  baeRF_family10  Bacterial archaeo-eukaryotic release factor f
    2.5e-11   44.0   0.0    6.7e-11   42.6   0.0    1.7  2  acVLRF1         Actinobacteria/chloroflexi VLRF1 release fact
    0.00072   19.5   0.9       0.11   12.5   0.1    2.6  2  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
  ------ inclusion threshold ------
      0.028   14.5   3.2       0.13   12.4   1.3    2.4  2  Zn-ribbon_8     Zinc ribbon domain
      0.078   13.6   0.0       0.18   12.4   0.0    1.6  1  baeRF_family12  Bacterial archaeo-eukaryotic release factor f
      0.086   12.7   1.5       0.52   10.2   0.0    3.0  4  Rad50_zn_hook   Rad50 zinc hook motif
        1.6    8.7   6.7        2.2    8.3   0.4    2.3  2  DUF1936         Domain of unknown function (DUF1936)


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 !  151.1   0.0   1.1e-47     2e-44       2     132 ..     140     270 ..     139     271 .. 0.98

  Alignments for each domain:
  == domain 1  score: 151.1 bits;  conditional E-value: 1.1e-47
                                    EEEEEEETTEEEEEEEESSCEEEEEEEE------BSTTBSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCHTTTESEEE CS
                         eRF1_2   2 vglivldegeAtigllkgsrtevlkkievsvPkKhkrGgqsarrfeRlreekleeflkkvaeaankafllvdkdklkgii 81 
                                    +glivld++eAtig+lkg+r+e lk+++++vP+K+++Ggqs++rf+ lr  +++ f+k+++eaan+afl++d+++l+gi+
  gi|116753674|ref|YP_842792.1| 140 FGLIVLDRREATIGILKGKRIEPLKHLTSTVPGKQRKGGQSSHRFQQLRLIAIHDFYKRIGEAANDAFLSIDQKELQGIL 219
                                    89****************************************************************************** PP

                                    EEESSTHHHHHHHHHHHHHHHHTCCEEEEE-S-TSCHHHHHHHHCCHHHHC CS
                         eRF1_2  82 lagpgfvkeefldkdlldaelkkkviklvdvsyggesglnevlekaaevlk 132
                                    ++gp+++keef+ +++l++el+ k+++ +dvsy++e+gl+e++e+a+++l 
  gi|116753674|ref|YP_842792.1| 220 IGGPSPTKEEFIAGNFLHHELQRKIVDAFDVSYTDEAGLSELVEAAQDRLL 270
                                    ***********************************************9985 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       2.3   4.1e+03      59      95 ..      48      86 ..      12      93 .. 0.61
   2 !  107.3   0.0   3.2e-34   5.7e-31       2     112 ..     275     409 ..     274     410 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.3
                                   -HHH-HHHHHH..HHHHHHHHHHHTT-EEEEE-TTSHHH CS
                         eRF1_3 59 ketgeelelve..lieelvenveesgakveiisseseeG 95
                                   +e+g+ +++ +  +  ++ +  e+  a++ +i+   e+G
  gi|116753674|ref|YP_842792.1| 48 EEHGQAANIKSklTRTNVQSALESAMARLRLIPRAPENG 86
                                   445555544445333344444566667777777666666 PP

  == domain 2  score: 107.3 bits;  conditional E-value: 3.2e-34
                                    HHHHHHHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSHHHHHS.....................-H CS
                         eRF1_3   2 iqekklleefleelakdtgkavYGveevlkalemgAvetLLvseelersrdtlkekv.....................ke 60 
                                     qek ++ +f++el  d g+a YG++ev++ l +gAv+ LL+seel+++r +++++                      ++
  gi|116753674|ref|YP_842792.1| 275 TQEKLAMRRFMKELVSDRGLASYGEKEVRHNLALGAVDLLLLSEELRKTRAKVRCQNqscdyseemtrtpsspaigtcPK 354
                                    699***********************************************999998899********************* PP

                                    HH-HHHHHH...HHHHHHHHHHHTT-EEEEE-TTSHHHHHHHHHTTTEEEEESS- CS
                         eRF1_3  61 tgeelelve...lieelvenveesgakveiisseseeGeqlvkafgGiaaiLRyk 112
                                    +g+ l++ e   li el + +e+sga v+iis+++eeG+ql++afgGiaa+LRyk
  gi|116753674|ref|YP_842792.1| 355 CGSPLTITEevdLITELSQLAEQSGAAVKIISTDFEEGAQLLHAFGGIAAVLRYK 409
                                    **9998888888******************************************9 PP

>> eRF1_1  eRF1 domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   0.0   3.2e-17   5.7e-14       2     128 ..      13     133 ..      12     134 .. 0.94
   2 ?   -3.8   0.0       6.7   1.2e+04      59      76 ..     266     283 ..     253     302 .. 0.74
   3 ?   -3.5   0.0       5.5   9.9e+03      67      87 ..     382     402 ..     372     404 .. 0.79

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 3.2e-17
                                    EEEEE..CTBTTSCCEEEEEE-SCHHHHHHHHHCHTTHEEEEEEEECHHH.......--CEEEEEEEEEEEEEEECTT.. CS
                         eRF1_1   2 kllkr..dlekdgsgsvtLipeddedlwhlynliapgdsvrastvrkvqresstgsreservklkLtikvekvdfdkd.. 77 
                                    +ll +  + +++g+++++L++++d+++++++  ++++++++a++++k +r         ++v+++L++ + ++++ ++  
  gi|116753674|ref|YP_842792.1|  13 RLLDElrSKSGRGTELISLYIPPDKQISDVMAQLREEHGQAANIKSKLTR---------TNVQSALESAMARLRLIPRap 83 
                                    66666657889*************************************99.........9***************99988 PP

                                    .SSEEEEEEEEEEGGGG--TTSEEEEEE-TTSEEEEEECE.ESHHHHHHHHHH CS
                         eRF1_1  78 .agvlrisGkvieenehvklgafhtldlelkrpftiikee.wdsfalerLkea 128
                                     +gv+ + G v  + +    + + t  +e+++p+t+++++ ++sf l +L+e+
  gi|116753674|ref|YP_842792.1|  84 eNGVVLFIGAVDIGGN---RTDMYTKVIEPPEPITTYRYHcDSSFLLTPLEEM 133
                                    89*********99999...79*****************999**********98 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 6.7
                                    CEEEEEEEEEEEEEEECT CS
                         eRF1_1  59 ervklkLtikvekvdfdk 76 
                                    +  +l L++++ek+ +  
  gi|116753674|ref|YP_842792.1| 266 QDRLLDLELTQEKLAMRR 283
                                    556677777777776655 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 5.5
                                    EEEEEEEECTTSSEEEEEEEE CS
                         eRF1_1  67 ikvekvdfdkdagvlrisGkv 87 
                                    +k+ ++df++ a++l+  G +
  gi|116753674|ref|YP_842792.1| 382 VKIISTDFEEGAQLLHAFGGI 402
                                    677788899999999888765 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 !   52.2   0.0     4e-17   7.1e-14       3     135 ..     127     265 ..     126     269 .. 0.88

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 4e-17
                 baeRF_family10   3 lapLlealdeyerygvvlvdreraRlfevylgeleeveevegevpgrtktggwksqdrfqrreeeqaerhlkevAellak 82 
                                    l+pL e l e + +g++++dr++a +    + ++e  +++++ vpg++++gg+ s +rfq+ +   ++ ++k+++e++++
  gi|116753674|ref|YP_842792.1| 127 LTPLEEMLSEKKTFGLIVLDRREATIGILKGKRIEPLKHLTSTVPGKQRKGGQ-SSHRFQQLRLIAIHDFYKRIGEAAND 205
                                    79***************************************************.************************** PP

                 baeRF_family10  83 ll...eergverlvlgGdeeetaal..ldrlpkalrarvvgtlplpvda..saaaVleka 135
                                    ++   ++++++ +++gG+   ++++   + l+ +l++++v+ ++++ ++    ++++e+a
  gi|116753674|ref|YP_842792.1| 206 AFlsiDQKELQGILIGGPSPTKEEFiaGNFLHHELQRKIVDAFDVSYTDeaGLSELVEAA 265
                                    984445777*********7777776225689***********998884434667776666 PP

>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       5.8     1e+04     108     124 ..      60      76 ..      39      81 .. 0.53
   2 !   42.6   0.0   3.7e-14   6.7e-11       4     126 ..     142     267 ..     139     271 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 5.8
                        acVLRF1 108 dvpdprravLedavrra 124
                                     +   ++++Le a++r 
  gi|116753674|ref|YP_842792.1|  60 LTRTNVQSALESAMARL 76 
                                    34445567777777665 PP

  == domain 2  score: 42.6 bits;  conditional E-value: 3.7e-14
                        acVLRF1   4 gvllvrrggfavgvveggelvaskvgtrdvqgrtaaGGwSqqRfaRrrenqadalleavaeaaarll....aeesae... 76 
                                    +++l+rr + ++g+++g++++  k+ t+ v g+ ++GG+S  Rf++ r   + + ++++ eaa++ +    +    +   
  gi|116753674|ref|YP_842792.1| 142 LIVLDRREA-TIGILKGKRIEPLKHLTSTVPGKQRKGGQSSHRFQQLRLIAIHDFYKRIGEAANDAFlsidQ----Kelq 216
                                    5899*****.********************************************************954444....3455 PP

                        acVLRF1  77 .vvlgGdrslvaevledarlap.latlareelldvpdprravLedavrrara 126
                                     +++gG+  + +e+ + + l++ l++  ++ ++dv   ++a L + v+ a++
  gi|116753674|ref|YP_842792.1| 217 gILIGGPSPTKEEFIAGNFLHHeLQRKIVD-AFDVSYTDEAGLSELVEAAQD 267
                                    6***************96643324444444.668888888888888887765 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1     0.013        23      16      25 ..     325     334 ..     317     335 .. 0.86
   2 !   12.5   0.1   6.3e-05      0.11       1      16 [.     351     365 ..     351     382 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.013
                 DNA_ligase_ZBD  16 aiyRCtnlsC 25 
                                    a  RC n sC
  gi|116753674|ref|YP_842792.1| 325 AKVRCQNQSC 334
                                    889******* PP

  == domain 2  score: 12.5 bits;  conditional E-value: 6.3e-05
                 DNA_ligase_ZBD   1 hCPvCGsavvReegea 16 
                                    +CP CGs++  +e e+
  gi|116753674|ref|YP_842792.1| 351 TCPKCGSPLTITE-EV 365
                                    7********9887.44 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.23     4e+02       3      10 ..     116     123 ..     115     136 .. 0.89
   2 ?   12.4   1.3   7.1e-05      0.13       7      36 ..     328     359 ..     326     361 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.23
                    Zn-ribbon_8   3 iYeYrCee 10 
                                    +Y Y+C++
  gi|116753674|ref|YP_842792.1| 116 TYRYHCDS 123
                                    8*****86 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 7.1e-05
                    Zn-ribbon_8   7 rCee..Cghefevlqsisdaplta.CPeCgsev 36 
                                    rC++  C+   e++ +   +p +  CP+Cgs++
  gi|116753674|ref|YP_842792.1| 328 RCQNqsCD-YSEEMTRTPSSPAIGtCPKCGSPL 359
                                    788777**.6777777665555555*****976 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 ?   12.4   0.0   9.9e-05      0.18      43     130 ..     166     256 ..     158     264 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.9e-05
                 baeRF_family12  43 gssdrpGrsssggagrsameetdfke..q.eeerFakeladeLkk...rakegkferlvlvappetlgelr..khlhkev 114
                                    ++s+ pG+++ gg++     ++ f++  + + ++F+k++ ++ ++    + +++ + + + +p +t +e+   + lh e+
  gi|116753674|ref|YP_842792.1| 166 LTSTVPGKQRKGGQS-----SHRFQQlrLiAIHDFYKRIGEAANDaflSIDQKELQGILIGGPSPTKEEFIagNFLHHEL 240
                                    677889998888888.....44444433568999*******99993334567889999999*********83357***** PP

                 baeRF_family12 115 kkrlvgeiaknltkhp 130
                                    ++++v  ++  +t++ 
  gi|116753674|ref|YP_842792.1| 241 QRKIVDAFDVSYTDEA 256
                                    *********9999875 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 ?   -1.5   0.1       1.3   2.4e+03       4      18 ..       7      21 ..       5      24 .. 0.64
   2 ?   -2.0   0.0       1.8   3.3e+03      30      44 ..      34      49 ..      33      52 .. 0.81
   3 ?   -1.9   0.1       1.8   3.2e+03      34      49 ..     258     273 ..     253     288 .. 0.69
   4 ?   10.2   0.0   0.00029      0.52      21      47 ..     351     377 ..     347     380 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.3
                                   HHHHHHHHHHHHTT- CS
                  Rad50_zn_hook  4 eteelnkkieelkea 18
                                   e+ e+++ ++el ++
  gi|116753674|ref|YP_842792.1|  7 EKYEFKRLLDELRSK 21
                                   556777777777665 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.8
                                   -HHH.HHHHHHHHHHH CS
                  Rad50_zn_hook 30 deeh.rseLikelqsk 44
                                   ++++  s+++ +l+++
  gi|116753674|ref|YP_842792.1| 34 PPDKqISDVMAQLREE 49
                                   5677799999999988 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.8
                                    HHHHHHHHHHHHHHHH CS
                  Rad50_zn_hook  34 rseLikelqsklerlp 49 
                                     seL++  q++l +l+
  gi|116753674|ref|YP_842792.1| 258 LSELVEAAQDRLLDLE 273
                                    6777777777777664 PP

  == domain 4  score: 10.2 bits;  conditional E-value: 0.00029
                                    E-TTT--EE-HHHHHHHHHHHHHHHHH CS
                  Rad50_zn_hook  21 cCPlCgReldeehrseLikelqskler 47 
                                     CP Cg++l+  +  +Li el++  e+
  gi|116753674|ref|YP_842792.1| 351 TCPKCGSPLTITEEVDLITELSQLAEQ 377
                                    8*******************9998775 PP

>> DUF1936  Domain of unknown function (DUF1936)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.4    0.0012       2.2      24      34 .]     328     338 ..     325     338 .. 0.92
   2 ?    3.1   1.3      0.05        89       2       7 ..     352     357 ..     351     359 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0012
                                    EES-TT---EE CS
                        DUF1936  24 RCdredCdYiE 34 
                                    RC+++ CdY E
  gi|116753674|ref|YP_842792.1| 328 RCQNQSCDYSE 338
                                    *********98 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.05
                                    -TTTSS CS
                        DUF1936   2 CPKCnv 7  
                                    CPKC++
  gi|116753674|ref|YP_842792.1| 352 CPKCGS 357
                                    ****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       806  (0.0449551); expected 358.6 (0.02)
Passed bias filter:                      720  (0.0401584); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); 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 0.27s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2814.80
//
Query:       gi|116753675|ref|YP_842793.1|  [L=137]
Description: hypothetical protein Mthe_0360 [Methanosaeta thermophila PT]
Scores for complete 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   34.2   0.0    7.5e-07   29.4   0.0    2.0  1  RNA_binding  RNA binding


Domain annotation for each model (and alignments):
>> RNA_binding  RNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   4.2e-11   7.5e-07       1     117 [.       3     107 ..       3     108 .. 0.74

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 4.2e-11
                                    EEEEEEEE-TTC-HHHHHHHHHTTSTTSE---EEEEEE-CCC-EEEEEEEEESSHHHHHHHHHHHHHHCCCCH..HHHHH CS
                    RNA_binding   1 kievrafvhaTEdeekVlealsnllpeeeveieeeeaeGhygnpitileaelekkkakkvlkkllellreeei..keLlk 78 
                                    +++vr+ v++TE  ekV  a+++++p    +i+   ++G+ g  i               l+ +++ lr+e+i  +  + 
  gi|116753675|ref|YP_842793.1|   3 EVTVRTLVRPTERVEKVVAAIERIFPGLTLDIRDDLVQGYGG--ISS-------------LRVFRKVLRDERIldTARSV 67 
                                    599***********************9977788888888887..222.............33333334444442211122 PP

                                    CCHCCB-TTSEEEEEEEHHHHHTT---BESSSS...EEEEEE CS
                    RNA_binding  79 eleervdekgklylrldKQaaylgklslvegdd...vIkvki 117
                                     l +r+   ++  +r++K  a++g++ ++ +++   +I+v+i
  gi|116753675|ref|YP_842793.1|  68 MLAGRIG--DSYQFRISKPGAFMGRVGFPPEEEplgSIHVEI 107
                                    3333333..6888*****************9999999**998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       231  (0.0128842); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); 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: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1010.38
//
Query:       gi|116753676|ref|YP_842794.1|  [L=253]
Description: xylose isomerase domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-32  112.1   0.2    2.9e-32  111.8   0.2    1.1  1  AP_endonuc_2  Xylose isomerase-like TIM barrel


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.8   0.2   1.6e-36   2.9e-32       3     210 .]      19     216 ..      17     216 .. 0.94

  Alignments for each domain:
  == domain 1  score: 111.8 bits;  conditional E-value: 1.6e-36
                                    HHHHCT-SEEEEECCTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCS.HHHHHHHHHHHHHHHHH CS
                   AP_endonuc_2   3 aaaeaGfdgvElfgrdlvpvselsdeelrelrkaldelglriaslslftrfgypdederear.reesvdalkraielaaa 81 
                                    +++++G++g E+ + + +  +e   ++++e r++++ ++l i+++ ++++ +   ++  +   +eesv+++k+++ laa+
  gi|116753676|ref|YP_842794.1|  19 QLEDLGYTGWEIVCEGMQRLTE---DNVDEARRIAETTDLVITLHLPYSDLNLASVN--Q-PiWEESVRQMKSCLTLAAD 92 
                                    6789****************96...8************************9998884..4.3599*************** PP

                                    HTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTC..HHHHHHHHHHTTTTEEEE CS
                   AP_endonuc_2  82 LGapllvlhpGtagagpkgseeeawerlaeslneladyaekegvklalEtlagsgvelgd..eelarlldavdspnvgvc 159
                                    + ++l v+hpG+ + ++ + +e awe+ + +++ ++d+ae+ g+++a+E++ + ++ lg+   e++ ++d vd++n+g++
  gi|116753676|ref|YP_842794.1|  93 F-TELAVVHPGHLSPLGAQVPERAWEQNILGIRSICDHAEDLGITIAVENMVNIPTLLGRapFEIVGIMDTVDRENLGFT 171
                                    *.**********9999****************************************9999******************** PP

                                    EEHHHHHHHTTTHHHHHHHHHGGEEEEEE.EESSTTTTSSTTEESTTSSSS CS
                   AP_endonuc_2 160 lDtgHlliaeedvddalraladrikhvHikDakgdlgagrdrhvpigeGei 210
                                    lD+gH++ + +++ ++l +l +ri h+Hi+D+ g     rd+h+p+g G++
  gi|116753676|ref|YP_842794.1| 172 LDVGHANTN-GNLKEFL-QLRERITHIHIHDNHG----ERDEHLPVGSGTV 216
                                    *******99.6666666.79**************....***********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1885.11
//
Query:       gi|116753677|ref|YP_842795.1|  [L=223]
Description: translin family protein [Methanosaeta thermophila PT]
Scores for complete 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-12   45.7   1.2    2.8e-10   40.5   1.2    2.1  1  Translin  Translin family
  ------ inclusion threshold ------
      0.074   13.2   2.3        3.5    7.8   0.9    2.5  3  HEPN      HEPN domain


Domain annotation for each model (and alignments):
>> Translin  Translin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   1.2   3.1e-14   2.8e-10       3     193 ..      30     191 ..      28     193 .. 0.87

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 3.1e-14
                                    HHHHHHHHHHHHHHHHHHHHHHHTTGSSTTTHHHHHHH.HHHHHHHHHHHTTSS..........GHHHHGGGTH.HHHHH CS
                       Translin   3 reriikasrditaaskkiifllhrvrsekteaqdkkakikkeakeklkeiakllasvaeelqgsnayrYqrqisgglqel 82 
                                    re+  ++sr + ++s ++i + hr +        +++++ k+a+e+l++i++ll        +++  rY+  +  + qe+
  gi|116753677|ref|YP_842795.1|  30 REEALRLSRIVIRLSSTAIRATHRRE------RREAESLLKDAREHLTTIKDLL-------VEHQDVRYSGFVDDAEQEF 96 
                                    88899999999999999999999944......335677779*************.......557889************* PP

                                    HHHHHHHHHHHHSS---HHHHHHHTT.---SSSSSS---HHHHHHHHHHHHHHHHHHHHHHHCTT--S.HHHHHHHHHHH CS
                       Translin  83 iealsfahYletqtLitleevqkilealkeneedafhltpedYllGlfdLtgELmRfainsvalgdkeekplqilkflre 162
                                    +ea  +++ + ++++ t+e++               +++p  Yl Gl dLtgEL R     + +g  e +    l+ ++e
  gi|116753677|ref|YP_842795.1|  97 VEASVLYSLIFEGRMPTHEDL---------------EVDPVSYLSGLGDLTGELRRNILELIRNGRPE-DGEVLLEIMEE 160
                                    **********99999998764...............578999************99988888888866.999999***** PP

                                    HHHHHHTS----HH....HHHHHTTHHHHHHH CS
                       Translin 163 lragfellnlknds.akdlrkKldvlkqsvkK 193
                                    ++ ++  ++ +  + ++ lr+K d +++ +++
  gi|116753677|ref|YP_842795.1| 161 IYHMLMRFDYPD-AlMRGLRRKTDLTRSMIER 191
                                    ***999999994.44999********998876 PP

>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.9   0.00038       3.5      52     117 ..       8      75 ..       3      76 .. 0.78
   2 ?   -2.9   0.0      0.79   7.1e+03      33      38 ..      95     100 ..      80     118 .. 0.51
   3 ?    4.2   0.0    0.0051        46      57      95 ..     140     176 ..     122     204 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00038
                                    SCCHHHHHHCCHHHT...-HHHHHHHHHHHCCCHHCCCTSS--S..--HHHHHHHHHHHHHHHHHHHH CS
                           HEPN  52 kthdlreLleelkkelkeseelreeleeLekayiesrYpdakee..yteedaeealkdaeevlelvee 117
                                      +dl +L+  l k+  e +  ree+ +L+++ i     + +     ++++ae++lkda+e l+ +++
  gi|116753677|ref|YP_842795.1|   8 NRSDLDDLIDALLKHFDEKDAAREEALRLSRIVIRLSSTAIRAThrRERREAESLLKDAREHLTTIKD 75 
                                    678899999955555555999999998898888888887777777889************98887765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.79
                                    HHHHHH CS
                           HEPN  33 qaaeka 38 
                                    + +e +
  gi|116753677|ref|YP_842795.1|  95 EFVEAS 100
                                    222222 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.0051
                                    HHHHCCHHHT...-HHHHHHHHHHHCCCHHCCCTSS--S CS
                           HEPN  57 reLleelkkelkeseelreeleeLekayiesrYpdakee 95 
                                    +eL+++ + e+   e l e++ee+ ++    +Ypda   
  gi|116753677|ref|YP_842795.1| 140 LELIRNGRPED--GEVLLEIMEEIYHMLMRFDYPDALMR 176
                                    33333333333..46777777888888888888887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 1785.94
//
Query:       gi|116753678|ref|YP_842796.1|  [L=545]
Description: O-phosphoseryl-tRNA synthetase [Methanosaeta thermophila PT]
Scores for complete 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-53  180.8   0.0    5.3e-49  166.9   0.0    2.1  2  tRNA-synt_2d     tRNA synthetases class II core domain (F)
    5.8e-15   55.1   0.2    1.1e-14   54.2   0.2    1.5  1  SepRS_C          O-phosphoseryl-tRNA synthetase C-terminal do
    4.6e-10   39.3   0.0    2.2e-06   27.3   0.0    2.4  2  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
  ------ inclusion threshold ------
       0.15   11.1   0.0         19    4.2   0.0    2.7  3  tRNA-synt_2      tRNA synthetases class II (D, K and N)
       0.16   11.9   0.0       0.48   10.4   0.0    1.8  1  tRNA-synt_2b     tRNA synthetase class II core domain (G, H, 


Domain annotation for each model (and alignments):
>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   3.9e-05      0.14       7      45 ..      37      75 ..      32      86 .. 0.88
   2 !  166.9   0.0   1.5e-52   5.3e-49      16     240 ..     121     355 ..     106     358 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.9e-05
                                   CTSCTSHSB-SHHHHHHHHHHHHHHCTTCEESSTTSEEE CS
                   tRNA-synt_2d  7 pgkrieagklhpltkvleeikeiflelgfeevegpeves 45
                                   p +++ +g+ hp+ +++++++e +l++gf+e+ +p + +
  gi|116753678|ref|YP_842796.1| 37 PRRSYPHGRPHPVFETIQRLREAYLRMGFTEMMNPVIVD 75
                                   5678899**************************998855 PP

  == domain 2  score: 166.9 bits;  conditional E-value: 1.5e-52
                                    -SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-ECESEEE-SSTHHHHHHHH CS
                   tRNA-synt_2d  16 lhpltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpekaveekllLRthttavqirtl 95 
                                    ++ +++ +e ++ei++++++ +veg+++     + +a+n ++++    ++ +F+  ++ +++ ++++LR+h+t+ ++++l
  gi|116753678|ref|YP_842796.1| 121 KELTAEEIEALREILHSYKKGAVEGDDL--VPEISKAINASDSQVSMMLESVFPEFRELRPEPTSRTLRSHMTSGWFISL 198
                                    566677899***************8888..567899******************************************** PP

                                    ....TTS-SSEEEEEEEEEEBSST.-SSSB-SEEEEEEEEEEETT--HHHHHHHHHHHHHHHCTST.EEEEEEECEETTE CS
                   tRNA-synt_2d  96 ....ekkkppikiisigrvfRrda.vDathlaeFhqveglvvdenvsladlkgvleellkklfgae.vkvrfrpsyfpft 169
                                         +  +p++++s++r+fRr++ +Da +l+++h+++++v+de++s+++ k++ e ll+++ g+e +++r +++ ++++
  gi|116753678|ref|YP_842796.1| 199 snlwYRMPLPVRLFSVDRCFRREQsEDAARLMSYHSASCVVMDEDMSVDEGKAISEGLLSQF-GFEnFRFRPDEKRSKYY 277
                                    88888889****************99************************************.999788888889***** PP

                                    EEEEEEEEEE.........CCSSSSEEEEEEEEEE-HHHHHHTT-.TTSEEEEEEEEHHHHHHHHHT-SSGHHHHTT.HH CS
                   tRNA-synt_2d 170 ePsaevdvyl.........vekkkkwlEllgaGmvrpevleavgideevsgfafGlGveRlamlkygieDiRelvendlr 240
                                     P+++++vy+         ++ +++w+E++++G+++p++l++++i   ++++++GlGveRlam+ yg +D+R+l +++l+
  gi|116753678|ref|YP_842796.1| 278 IPGTQIEVYAyhpglvgseTKYGSGWVEIATFGVYSPTALAQYDI--PYPVLNLGLGVERLAMILYGSKDLRALSYPQLQ 355
                                    *********9********999************************..***************************998775 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 !   54.2   0.2   3.2e-18   1.1e-14       1      31 []     435     465 ..     435     465 .. 1.00

  Alignments for each domain:
  == domain 1  score: 54.2 bits;  conditional E-value: 3.2e-18
                                    EEEEEETTEEEEEES-TTTCCHHHHSEEEEE CS
                        SepRS_C   1 NEvyVYdGnIlGvPdtekwkearenGvsTGI 31 
                                    NE++VY++ IlG+P+t+kw+ a+e+Gv+TGI
  gi|116753678|ref|YP_842796.1| 435 NEIVVYRNEILGIPRTPKWEAAFEEGVQTGI 465
                                    ******************************9 PP

>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0   0.00016      0.59       4      49 ..      35      80 ..      32      90 .. 0.89
   2 !   27.3   0.0   6.2e-10   2.2e-06      74     208 ..     186     327 ..     181     331 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00016
                tRNA_synthFbeta  4 tlPkapttegelnkeqklrrklrdllagaGlnEvitysfvsekeld 49
                                     P+ + ++g++++ +++ ++lr++   +G++E+++   v+++e+ 
  gi|116753678|ref|YP_842796.1| 35 IYPRRSYPHGRPHPVFETIQRLREAYLRMGFTEMMNPVIVDAQEVH 80
                                   6799999*****************************9999988775 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 6.2e-10
                tRNA_synthFbeta  74 lRtsLlpglLevlarNl.argnedvrlFEigkvflkd..seeelpeeerhlaivltgkreeeswsekaravdfydlkgiv 150
                                    lR+ +++g    l++   +  ++ vrlF + ++f+ +  ++  +    +  ++v++ ++           +++ + k+i 
  gi|116753678|ref|YP_842796.1| 186 LRSHMTSGWFISLSNLWyRMPLP-VRLFSVDRCFRREqsEDAARLMSYHSASCVVMDED-----------MSVDEGKAIS 253
                                    66666666666665544144555.*************5222233455555555666666...........9********* PP

                tRNA_synthFbeta 151 ealleslgiekvefep..aehpalhpgrsAeikvdgk..............evGvlGelhpevleafdlkqrvy 208
                                    e ll+++g+e+++f+p  +  +++ pg + e+++                 e+  +G  +p  l+++d++++v 
  gi|116753678|ref|YP_842796.1| 254 EGLLSQFGFENFRFRPdeKRSKYYIPGTQIEVYAYHPglvgsetkygsgwvEIATFGVYSPTALAQYDIPYPVL 327
                                    ****************766699**********7744445666678888889********************985 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 ?   -1.4   0.0      0.26   9.4e+02      29      59 ..      53      81 ..      50      98 .. 0.76
   2 ?    3.3   0.0      0.01        37      93     112 ..     210     229 ..     199     248 .. 0.85
   3 ?    4.2   0.0    0.0052        19     287     308 ..     329     350 ..     319     355 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.26
                                   HHHHHHHHHHTT-EE----SEESS--SSSS- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2 29 tkavrkyleengfieietPiLsksdteegar 59
                                   ++ +r+ + + gf+e+  P+++++  +e  r
  gi|116753678|ref|YP_842796.1| 53 IQRLREAYLRMGFTEMMNPVIVDA--QEVHR 81
                                   677888888999999999999987..44444 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.01
                                    EEEEEEEEE--S--BTTB-S CS
                                    xxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2  93 rvfqiaraFRaEdsrtdrhl 112
                                    r f++ r+FR E+s+    l
  gi|116753678|ref|YP_842796.1| 210 RLFSVDRCFRREQSEDAARL 229
                                    78***********9876655 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.0052
                                    EEEEHHHHHHHHCT-SSGGGCS CS
                                    xxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2 287 lglGldRlvmlllgsesIrdvi 308
                                    lglG++Rl m+l gs++ r ++
  gi|116753678|ref|YP_842796.1| 329 LGLGVERLAMILYGSKDLRALS 350
                                    79***************99764 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00014      0.48      35      73 ..     207     243 ..     177     344 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00014
                                    SSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESG CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2b  35 LPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhae 73 
                                    LP++l+ + +++R+E+s+     R+  +h   ++v+  +
  gi|116753678|ref|YP_842796.1| 207 LPVRLFSVDRCFRREQSEDA--ARLMSYHSASCVVMDED 243
                                    9***************9333..37777777776666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (545 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); 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: 4042.26
//
Query:       gi|116753679|ref|YP_842797.1|  [L=206]
Description: ribose-5-phosphate isomerase A [Methanosaeta thermophila PT]
Scores for 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-61  204.6   0.1    9.7e-61  204.3   0.1    1.0  1  Rib_5-P_isom_A  Ribose 5-phosphate isomerase A (phosphoribois


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 !  204.3   0.1   5.4e-65   9.7e-61       2     168 ..      30     192 ..      29     197 .. 0.95

  Alignments for each domain:
  == domain 1  score: 204.3 bits;  conditional E-value: 5.4e-65
                                    EEESSHHHHHHHHHTT--BE-GGCCSSEEEEEE--SEEETTS-EE--TTS-HHHHHHHHHTEEEEEEEEEGGGBESSTTS CS
                 Rib_5-P_isom_A   2 gvptSeqteelaeelgipllsldeveeidlaiDGaDevdedlnliKGgGgallrEKivaaaakkfiviadesKlveklgk 81 
                                    +vptS+q+e+la e+gipl++l++ + +dlaiDG+D++d ++n+iKGgG+a++rEK+v  aa++f+v+ad sK ve l+ 
  gi|116753679|ref|YP_842797.1|  30 AVPTSYQSEALAIECGIPLTTLSQNPVLDLAIDGVDQIDIRMNAIKGGGAAHTREKVVSIAARRFVVVADGSKRVEVLN- 108
                                    7**************************************************************************9996. PP

                                    S-EEEEE-GGGHHHHHHHHHHTTT-EEEE-TETTTTEE-B-TTS-EEEEEESSSBSSSHHHHHHHHHTSTTEEEESEE-S CS
                 Rib_5-P_isom_A  82 fpvPveVlpfaleavarelekllggkpelReakgkdgpvvTdngnlilDvkfeekiedpeelekelksipGVvetGlFlg 161
                                     pvPveVlpfa++ v rel + +gg p++R+a++kdgpv+Tdngn+++Dv+f+ +i+dp++l++e+++ipGVv++G+F++
  gi|116753679|ref|YP_842797.1| 109 RPVPVEVLPFAAMVVERELVR-IGGYPVVRQARMKDGPVITDNGNFVMDVSFG-EIRDPATLAQEISQIPGVVDHGIFTK 186
                                    9******************96.6*****************************5.677**********************9 PP

                                    --SEEEE CS
                 Rib_5-P_isom_A 162 ladkvlv 168
                                    + d++ +
  gi|116753679|ref|YP_842797.1| 187 I-DELHI 192
                                    8.44444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1518.19
//
Query:       gi|116753680|ref|YP_842798.1|  [L=339]
Description: translation initiation factor IF-2B subunit alpha [Methanosaeta thermophila PT]
Scores for complete 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-80  269.6   0.0    3.7e-80  269.2   0.0    1.1  1  IF-2B     Initiation factor 2 subunit family


Domain annotation for each model (and alignments):
>> IF-2B  Initiation factor 2 subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  269.2   0.0     2e-84   3.7e-80       1     281 [.      45     330 ..      45     331 .. 0.99

  Alignments for each domain:
  == domain 1  score: 269.2 bits;  conditional E-value: 2e-84
                                    SS-SHHHHHHHHHHHHHHHHHHCCCSTHHHHHHHHHHHHHHHHTSSTS-HHHHHHHHHHHHHHHCCTTTSSHHHHHHHHH CS
                          IF-2B   1 kvrGspaiaiaalevllevikdaktskvaeLkeelrkaidlLkkarPtavslgnairrllkeiselksssdvkeakksli 80 
                                    k+rG+pa++ a+ ++++ ++ ++k ++ +   +e++ a++++k++rPtav+l++ ++r+l+   + ++ +  +e+++ ++
  gi|116753680|ref|YP_842798.1|  45 KIRGAPALGAAGGYGIALAAMRSKFQERDGVLHEMEIAAEMIKNSRPTAVNLSWGVDRVLR---AAQEGEIADEVREIAL 121
                                    69***********************************************************...789************* PP

                                    HHHHHHHHHHHHHHHHHHHHHHTTC-TTEEEEEES--SH........HHHHHHHHHHTTEEEEEEEEEXTTTTHH.HTHH CS
                          IF-2B  81 ekikelikeieeadekigdiaaelikdgdtilTicnskt........vlevlraaakekkkfkVivvEsrPrlqG.rlta 151
                                    ++++++++e++ +++ ig+++a+l++dgd +lT+cn++         +l+v+r+a+ ++k+++V+++E+rP +qG rlt 
  gi|116753680|ref|YP_842798.1| 122 REAERIAEEDLIINKMIGRHGAKLLNDGDSVLTHCNAGRlacvgwgtALGVIRQAVMDGKEIHVYACETRPLNQGsRLTS 201
                                    ******************************************************************************** PP

                                    HHHHHTTXEEEEEEGGGHHHHHHC.TESEEEEEXSEEETTSEEEEETTHHHHHHHHHHTTXEEEEEXXGGGBESTSSSGG CS
                          IF-2B 152 keLvqagipvtlitdsavayvmse.evdkvivGAdrilenGaiankiGTsslAvlAkefnipvlvvaeslkfservqlde 230
                                    +eL++++i+vtl+ dsa +++m++ ++d vivGAdri+++  ++nkiGT++ AvlAk++ ip++v+a++++f+   + ++
  gi|116753680|ref|YP_842798.1| 202 WELMEDNIDVTLVCDSASGILMRRgMIDSVIVGADRITRDA-VFNKIGTYTHAVLAKAHGIPFYVAAPLSTFDAS-HDES 279
                                    ****************************************9.********************************9.8899 PP

                                    GSSXXBEXTHHHHEETTEESSTTTEEEEEBSEEEEEGGGXSEEEETTEEEX CS
                          IF-2B 231 difieerdpeellnitgeriaeeelkvvnpafDvtPpelItliITevGvlp 281
                                    +i+ieerd +el +   +r a+  +kv+npafD tP +l++++ITe+Gv+ 
  gi|116753680|ref|YP_842798.1| 280 EIVIEERDGDELRRLGVTRLAPDGVKVYNPAFDATPIDLVSAMITEKGVFR 330
                                    9************************************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2441.79
//
Query:       gi|116753681|ref|YP_842799.1|  [L=102]
Description: translation initiation factor Sui1 [Methanosaeta thermophila PT]
Scores for complete 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   78.3   0.7      7e-22   77.7   0.7    1.2  1  SUI1      Translation initiation factor SUI1
     0.0062   16.8   0.3       0.01   16.1   0.3    1.5  1  Img2      Mitochondrial large subunit ribosomal protein (Img2
     0.0068   16.1   1.1     0.0085   15.8   1.1    1.1  1  DTW       DTW domain


Domain annotation for each model (and alignments):
>> SUI1  Translation initiation factor SUI1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.7   0.7   1.2e-25     7e-22       2      76 ..      25      95 ..      24      96 .. 0.97

  Alignments for each domain:
  == domain 1  score: 77.7 bits;  conditional E-value: 1.2e-25
                           SUI1  2 kpkihirleqrggrKkvTtvsgleafgidlkklakelkkkfacsgsvvkdggeeiqvQGdqrkkvaelLtekygv 76
                                   +++i +++ +r+ +K vT+++g+++ +idl++l+  lk+k+ac+g+v kdg  +i++QG+++ ++++lL +k g+
  gi|116753681|ref|YP_842799.1| 25 QQRIVVKIHKRRYGKEVTVIQGIDPHEIDLQDLCTYLKSKLACGGTV-KDG--VIELQGNHIGRIKDLLSKK-GF 95
                                   899*******************************************8.999..9*****************9.87 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 !   16.1   0.3   1.7e-06      0.01      19      80 .]      33      95 ..      13      95 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.7e-06
                           Img2 19 vkrggtkkltvirkieG...DiaalredLrkaleelvkvnevtgkieikGdrveevkkfLeskgF 80
                                    kr+  k++tvi+ i+    D+++l + L++ l+  +  + + g ie++G++  ++k+ L++kgF
  gi|116753681|ref|YP_842799.1| 33 HKRRYGKEVTVIQGIDPheiDLQDLCTYLKSKLA--CGGTVKDGVIELQGNHIGRIKDLLSKKGF 95
                                   5666778899999997543478888888888888..8888899*********************9 PP

>> DTW  DTW domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   1.1   1.4e-06    0.0085       2      35 ..       4      34 ..       3      47 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.4e-06
                            DTW  2 elCerCllpaevclcsslppleklpikvlilqhp 35
                                   e+C+ C lp+e+c+c+++ + e++  ++++  h+
  gi|116753681|ref|YP_842799.1|  4 EMCTVCGLPKELCICEEVAK-EQQ--RIVVKIHK 34
                                   68******************.766..55555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       859  (0.0479112); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); 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: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 738.15
//
Query:       gi|116753682|ref|YP_842800.1|  [L=446]
Description: Na+/solute symporter [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-26   92.7  33.6    1.1e-24   87.0  33.6    2.6  1  SSF       Sodium:solute symporter family


Domain annotation for each model (and alignments):
>> SSF  Sodium:solute symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.0  33.6   6.4e-29   1.1e-24       1     324 [.      42     337 ..      42     409 .. 0.84

  Alignments for each domain:
  == domain 1  score: 87.0 bits;  conditional E-value: 6.4e-29
                            SSF   1 yflagrsltgfvlglslaasnisaasfvGlaGavaasGlavvllelgalllvlllllllaerlrnagalTlpdylskRfk 80 
                                    +fl+gr  + + +  sl a+ ++a+s +Gl G+++  Gl ++++ l   l++l+l   +a+  r++ga Tlpd++   ++
  gi|116753682|ref|YP_842800.1|  42 FFLGGRGFGTLHITGSLVATILGASSTIGLVGLGYSRGLPGAWWLLSGALGLLVLS-KVAHAVRRTGARTLPDLIGIFYG 120
                                    8*********************************************9999987765.57999***************999 PP

                            SSF  81 gkrilvylsalslllvitlklsvdlvggaklielalGlnyetavlllaaltalYtviGGllAvvytdtiqavlmlvgali 160
                                    ++   +  +++ +l+     +++++v++++++  ++G +    + ++a++++ Yt+ GG +Avv td  q  ++l+g ++
  gi|116753682|ref|YP_842800.1| 121 SSA--KKTASILILISWLGVIAAQIVAAGRIMGALFGHDWFW-MSAMAVVLVAYTAHGGQRAVVRTDLWQIYVILAGVIL 197
                                    999..555666678889999*******************865.6788899999*************************99 PP

                            SSF 161 lliivllevG.gleslveklkeaapkvvdlltpdslkllrdpltalslwlglvlGvagl..philvRflaakdakailkg 237
                                    +  i l ++  +l+         +     + ++ s   l+d ++     + +v G + l  p i  R+l+a + ++++ +
  gi|116753682|ref|YP_842800.1| 198 MFAICLRSAPeALN-------RLEF---PMSEQMS---LQDIIS-----MVVVVGSMYLigPDIYSRVLSARNPESARVA 259
                                    99998876542222.......2222...1222223...333333.....455566665556***********99999988 PP

                            SSF 238 vlkltivlilvligmisiilfaiklagavpkavgtevgvsniaypeLvvkllpnllaGlllavmlAaimstltslllsas 317
                                     + + +++i + + + si++fa++l              ++ a+p L+  +lp++  G++ a+ lAa+ms+ ++ ll as
  gi|116753682|ref|YP_842800.1| 260 AIFSAMIIIPLAFVITSIGIFAQHLLPD---------IRPEDALPLLITDILPPWAGGVVAAAFLAAVMSSADTSLLTAS 330
                                    88877777777777799******99765.........46889************************************** PP

                            SSF 318 saftkDl 324
                                    s++t Dl
  gi|116753682|ref|YP_842800.1| 331 SILTLDL 337
                                    ******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 3061.72
//
Query:       gi|116753683|ref|YP_842801.1|  [L=432]
Description: tryptophanyl-tRNA synthetase [Methanosaeta thermophila PT]
Scores for complete 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-40  137.4   0.0    2.3e-22   79.7   0.0    2.1  2  tRNA-synt_1b  tRNA synthetases class I (W and Y)
  ------ inclusion threshold ------
      0.068   13.5   0.1       0.21   11.9   0.1    1.8  1  DUF2383       Domain of unknown function (DUF2383)
        0.3   11.7   1.8        0.5   11.0   0.1    2.2  3  YbjQ_1        Putative heavy-metal-binding


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 !   79.7   0.0   3.9e-26   2.3e-22       2     182 ..      62     235 ..      60     250 .. 0.88
   2 !   55.8   0.0   7.1e-19   4.2e-15     177     293 .]     294     412 ..     283     412 .. 0.91

  Alignments for each domain:
  == domain 1  score: 79.7 bits;  conditional E-value: 3.9e-26
                                    HHS--EEEEEEETSSS-BGGGHHHHHHHHHHHHTTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHHHHHHHHHHHHTCH CS
                   tRNA-synt_1b   2 kerplrvysGidPTgklHlGylvplkklvelqkaghevffliaDlhAiigdpskaeerklrkreevlenaikaqlakgld 81 
                                    ++rp++v+sG++P+gk H G++++++ +++ qk+g ++f+ ia+++A  ++   +  r  +   +++  +   ++a g++
  gi|116753683|ref|YP_842801.1|  62 EHRPFAVMSGFMPSGKAHFGHMMVMNEIIWHQKHGADAFVAIANMEAHAVRGI-SWQRCRELGINDYILS---LIALGFE 137
                                    489************************************************99.4555555566777777...99***** PP

                                    TTTEEEEETHHHHTTHHHHHHHHHHHTTCBHHHHHHHHHCCHHCSS.S.C--BHHHHHHHHHHHHHHHHTCHSEEEEEGG CS
                   tRNA-synt_1b  82 pekaevvlqsewlehlelaellrdlgklgslnrmlqfksvkkrlee.g.egislgeftYplLqaaDilllkadlvpgGsD 159
                                    p   ++++qse +   +la  l+  +++ +++ ++ f   ++++ + +    + +++++p+L  +     k+ +vp+GsD
  gi|116753683|ref|YP_842801.1| 138 P-TGHIYFQSENYRMRDLAFELAAEANFSEVSAIYGFSG-ETSIGHmEsVMAQSADILHPQLPDYGGP--KPVVVPVGSD 213
                                    *.789**********************************.8888885444557899****99888777..********** PP

                                    GHHHHHHHHHHHHHHHHHSTTSS CS
                   tRNA-synt_1b 160 Qkqnielgrdlarrfnkkevfkk 182
                                    Q+ +++l+rdla r++k  + ++
  gi|116753683|ref|YP_842801.1| 214 QDAHMRLTRDLAYRMRKF-LVEQ 235
                                    ***************997.4444 PP

  == domain 2  score: 55.8 bits;  conditional E-value: 7.1e-19
                                    H...STTSS-EEEEET-BBSTTSSSBTTCETTCGC-BTTCCHHHHHHHHHHCHCSTTC..SHHHHHHHHHTHHHCHHHHH CS
                   tRNA-synt_1b 177 k...evfkkpegltvplltgldGekKmSKSagnsaIfLddekesvkkkiqkavtdsde..evekllklktelsnelierl 251
                                    +     f +p +++++++tgl+G+ KmS+S ++s+I L+++++++  ki ka+t  ++    ++ + + +e +  ++e l
  gi|116753683|ref|YP_842801.1| 294 NngeFGFIPPASIYHRFMTGLTGG-KMSSSRPESYIALTEDPDEAANKIMKAITGGKQslAEHRRYGGEPERCA-VYEFL 371
                                    44435799****************.*********************************8888899999999999.99999 PP

                                    HHHCCSEEESSHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH CS
                   tRNA-synt_1b 252 eavsgkkpkreaeellaeevtklvhggdlkkalaealnelle 293
                                      ++ +++ +e+eel++e+++++ ++g +kk +a+ ++e+l+
  gi|116753683|ref|YP_842801.1| 372 LFHLAEDD-SELEELYKECRSGRQMCGSCKKIAAARIREFLK 412
                                    99999998.9*****************************995 PP

>> DUF2383  Domain of unknown function (DUF2383)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   3.5e-05      0.21       5      52 ..     381     427 ..     378     430 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.5e-05
                                    HHHHHHHHHHHHHHHHHHHHHT--SHHHHHHHHHHHHHHHHHHHHHHH CS
                        DUF2383   5 aLndLietlkdgeegykeaaekvkdpqlktlleriaeereeaaeeLqs 52 
                                    +L++L + +++g++ + ++++ +  ++++++l++++ +r++a+ +L++
  gi|116753683|ref|YP_842801.1| 381 ELEELYKECRSGRQMCGSCKKIAA-ARIREFLKEHQSARRDAINRLKE 427
                                    799****************98777.*********************97 PP

>> YbjQ_1  Putative heavy-metal-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       1.6   9.3e+03      71      81 ..      94     104 ..      92     115 .. 0.62
   2 ?   -2.9   0.0       1.9   1.1e+04      56      85 ..     150     178 ..     144     188 .. 0.62
   3 ?   11.0   0.1   8.4e-05       0.5      30      67 ..     390     427 ..     383     431 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.6
                         YbjQ_1  71 elGAnAvvgvr 81 
                                    + GA+A v++ 
  gi|116753683|ref|YP_842801.1|  94 KHGADAFVAIA 104
                                    56777777664 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.9
                         YbjQ_1  56 eareeAlerlkeeAeelGAnAvvgvrldts 85 
                                    ++r+ A+ +l++eA+     A+ g++ +ts
  gi|116753683|ref|YP_842801.1| 150 RMRDLAF-ELAAEANFSEVSAIYGFSGETS 178
                                    4555555.4777777777777777766554 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 8.4e-05
                         YbjQ_1  30 nvlkdilaglrslvGGelkayeeeleeareeAlerlke 67 
                                      ++++  + ++++ ++++++ +e ++ar++A++rlke
  gi|116753683|ref|YP_842801.1| 390 RSGRQMCGSCKKIAAARIREFLKEHQSARRDAINRLKE 427
                                    56899999****************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); 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: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 3004.44
//
Query:       gi|116753684|ref|YP_842802.1|  [L=444]
Description: signal recognition particle protein Srp54 [Methanosaeta thermophila PT]
Scores for complete 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-70  235.3   3.7    7.4e-70  234.6   3.7    1.3  1  SRP54            SRP54-type protein, GTPase domain
    8.1e-30  103.4   2.2    1.7e-29  102.4   1.4    2.0  1  SRP_SPB          Signal peptide binding domain
    3.1e-21   75.4   1.8    1.3e-20   73.4   0.1    2.8  3  SRP54_N          SRP54-type protein, helical bundle domain
    1.5e-07   31.5   0.0    1.1e-06   28.7   0.0    2.6  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    1.1e-05   25.1   1.6    0.00019   21.1   1.6    2.3  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
    0.00011   22.2   0.1    0.00051   20.0   0.1    2.2  2  APS_kinase       Adenylylsulphate kinase
    0.00044   19.6   0.3     0.0014   18.0   0.0    1.9  2  6PF2K            6-phosphofructo-2-kinase
    0.00049   19.4   0.0      0.001   18.4   0.0    1.5  1  Zeta_toxin       Zeta toxin
    0.00052   20.4   0.0     0.0011   19.4   0.0    1.6  1  AAA_16           AAA ATPase domain
    0.00062   18.8   0.2     0.0021   17.1   0.2    1.9  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
     0.0012   19.0   0.9      0.014   15.5   0.9    2.5  1  MMR_HSR1         50S ribosome-binding GTPase
     0.0013   18.7   0.0     0.0035   17.2   0.0    1.8  1  MobB             Molybdopterin guanine dinucleotide synthesis
     0.0013   18.2   0.2       0.46    9.9   0.0    2.4  2  SRPRB            Signal recognition particle receptor beta su
     0.0027   17.9   0.0      0.006   16.8   0.0    1.7  1  AAA_33           AAA domain
     0.0035   16.7   0.1       0.48    9.7   0.0    2.4  2  AAA_8            P-loop containing dynein motor region D4
      0.004   17.7   0.0      0.012   16.1   0.0    1.9  1  AAA_18           AAA domain
  ------ inclusion threshold ------
      0.012   14.5   0.1      0.022   13.7   0.1    1.3  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
      0.013   15.0   0.0      0.026   14.0   0.0    1.4  1  KTI12            Chromatin associated protein KTI12
      0.014   15.0   0.1      0.064   12.9   0.1    2.1  2  Thymidylate_kin  Thymidylate kinase
      0.017   14.9   0.0      0.037   13.8   0.0    1.6  1  AAA_24           AAA domain
       0.02   15.2   0.0      0.049   13.9   0.0    1.8  1  AAA_22           AAA domain
      0.028   14.2   2.0      0.036   13.8   0.6    2.0  1  AAA_30           AAA domain
      0.033   14.1   0.1        0.1   12.5   0.1    1.9  1  AAA_31           AAA domain
      0.044   13.1   0.3        1.3    8.2   0.3    2.3  1  MipZ             ATPase MipZ
      0.053   13.8   0.8       0.16   12.2   0.5    2.1  2  AAA_28           AAA domain
      0.057   13.3   0.3       0.43   10.5   0.1    2.2  2  NTPase_1         NTPase
      0.059   13.4   0.0      0.092   12.7   0.0    1.5  1  ResIII           Type III restriction enzyme, res subunit
      0.068   13.1   0.1       0.15   12.0   0.1    1.6  1  NACHT            NACHT domain
      0.077   12.2   5.1        1.1    8.4   0.1    2.9  3  ArsA_ATPase      Anion-transporting ATPase
      0.078   13.4   0.4       0.35   11.3   0.4    2.4  1  AAA              ATPase family associated with various cellul
       0.12   12.4   0.0       0.35   10.8   0.0    1.8  1  AAA_5            AAA domain (dynein-related subfamily)
       0.18   11.6   1.2        3.1    7.5   0.2    2.5  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
       0.25   11.8   0.8        0.7   10.4   0.8    1.9  1  AAA_23           AAA domain


Domain annotation for each model (and alignments):
>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  234.6   3.7   1.4e-72   7.4e-70       2     196 .]      98     290 ..      97     290 .. 0.99

  Alignments for each domain:
  == domain 1  score: 234.6 bits;  conditional E-value: 1.4e-72
                                    EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHHHHH CS
                          SRP54   2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeavekake 81 
                                    + i+lvGlqG+GKTtt+aKLa +++++g ++++++aDtfRa+A++QLk+l ++ g+ ++++k ++++ +vak+++e+ k+
  gi|116753684|ref|YP_842802.1|  98 QTIMLVGLQGSGKTTTAAKLATYFQRRGLRTAVICADTFRAGAYDQLKALCDRQGIFFYGEKGNENAPEVAKNGLEATKK 177
                                    579*************************************************************************9998 PP

                                    TTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSSSSTTHHHH CS
                          SRP54  82 ekidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltklDgdakgGaals 161
                                      +dv +vDTaGr++ +++l++e+k+i+ vv++d++llv+da++gq+a +qa+aF+eavgitgvi+tklDg+akgG+als
  gi|116753684|ref|YP_842802.1| 178 --YDVRIVDTAGRHALESDLIQEMKDIHAVVNADHKLLVMDAAIGQQASEQARAFNEAVGITGVIITKLDGTAKGGGALS 255
                                    ..****************************************************************************** PP

                                    HHHHHTS-EEEEE-SSSTTGEEE--HHHHHHHHHT CS
                          SRP54 162 iaaelklPikfigvGekiedleefdperlvsrllg 196
                                    ++ae+k+ ++figvGe+  dle+f+++r++srllg
  gi|116753684|ref|YP_842802.1| 256 AVAETKTSVAFIGVGETASDLEKFEADRFISRLLG 290
                                    *********************************95 PP

>> SRP_SPB  Signal peptide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.4   1.4   3.1e-32   1.7e-29       1      98 [.     319     419 ..     319     420 .. 0.90

  Alignments for each domain:
  == domain 1  score: 102.4 bits;  conditional E-value: 3.1e-32
                                    SSCTHHHHHHHHHHHCCCCCCHHHHCCC............H...CCCCCHHHHHHHHHTTSBHHHHHSGCG-..HHHHHH CS
                        SRP_SPB   1 eftlrdlleqlqqikkmGplskllsmiP..gmsae.....akaeeeaekklkrieaiidSMTkeErdspekllkesRkrR 73 
                                    +ftl+d+++ql+ ++kmGpl+++++m+P  g          k+ + ++++l+ + +i+dSMT+eE+++p+ ++++sR++R
  gi|116753684|ref|YP_842802.1| 319 KFTLKDMYKQLEAMNKMGPLKQIMQMLPfgG---IgielsDKEYQVTKERLEAYRFIMDSMTDEELEDPK-IINASRIKR 394
                                    6***************************533...235565444488899*********************.999****** PP

                                    HHHHTTS-HHHHHHHHHHHHHHHHH CS
                        SRP_SPB  74 iArGsGtsvqevnellkqfeqmkkm 98 
                                    iArGsGt+ + v+ellk++  m+k 
  gi|116753684|ref|YP_842802.1| 395 IARGSGTRPELVKELLKSHAAMQKA 419
                                    **********************996 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 !   73.4   0.1   2.3e-23   1.3e-20       1      75 []       6      83 ..       6      83 .. 0.97
   2 ?   -0.4   0.0       2.6   1.4e+03      35      46 ..     306     317 ..     292     335 .. 0.80
   3 ?   -2.2   0.0       9.6   5.2e+03      55      63 ..     405     412 ..     385     421 .. 0.51

  Alignments for each domain:
  == domain 1  score: 73.4 bits;  conditional E-value: 2.3e-23
                                   HHHHHHHHHHHHCCSSCGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTS...S-HHHHHHHHHHHHH CS
                        SRP54_N  1 LgkklnsalkklsgkskideedleealkeleeaLleaDVgvkvvkklienvkkkavgekk...lkpkqqvkkivkdeL 75
                                   Lg++l++alkk+ +++++d++++++a++++++aLl+aDV+vk+v++l ++++++a++ek    ++p+++v++iv++eL
  gi|116753684|ref|YP_842802.1|  6 LGGSLRGALKKIASATRVDKALVDDAVRDIQRALLQADVNVKLVMSLSNRIRERALNEKPpagMNPREHVINIVYQEL 83
                                   799******************************************************666*****************8 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2.6
                                    HHTT--HHHHHH CS
                        SRP54_N  35 leaDVgvkvvkk 46 
                                    +e+DV v++ +k
  gi|116753684|ref|YP_842802.1| 306 IESDVDVDAMMK 317
                                    899999988765 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 9.6
                                    HHCTTSS-H CS
                        SRP54_N  55 avgekklkp 63 
                                     v+ + lk+
  gi|116753684|ref|YP_842802.1| 405 LVK-ELLKS 412
                                    222.23444 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 !   28.7   0.0   2.1e-09   1.1e-06       9     101 ..     107     261 ..     102     371 .. 0.81

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 2.1e-09
                                    TSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH......HTTEB-HHHH............................ CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxx............................ RF
                           CbiA   9 GvGKTtlaanLaralarrglrVllvDaDpqannlai......leglendiep............................ 54 
                                    G+GKTt+aa+La++++rrglr++++ aD+ +  +                 +                            
  gi|116753684|ref|YP_842802.1| 107 GSGKTTTAAKLATYFQRRGLRTAVICADTFRAGAYDqlkalcD--------Rqgiffygekgnenapevakngleatkky 178
                                    99**************************985544313333330........14566666666666799999999999999 PP

                                    ........................................CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCH CS
                                    ........................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA  55 ........................................dlkrllellealgkkkalllkiagvvlnrvdgeneetllk 94 
                                                                                 ++ +++  + ++ ++ i gv++++ dg +      
  gi|116753684|ref|YP_842802.1| 179 dvrivdtagrhalesdliqemkdihavvnadhkllvmdaaI----GQQASEQARAFNEAVGITGVIITKLDGTAKGGGAL 254
                                    99999999999999999999999999998888888774441....23333333333333788899999999887776666 PP

                                    HHHHHHH CS
                                    xxxxxxx RF
                           CbiA  95 ealeelk 101
                                    +a++e+k
  gi|116753684|ref|YP_842802.1| 255 SAVAETK 261
                                    6666655 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   1.6   3.5e-07   0.00019       2     157 ..      99     252 ..      98     265 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.5e-07
                                    EEEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCCHCCCT...EEEETTTTECCHCTT-HHHHHHHHH CS
                           cobW   2 vtvltGflGsGKTtLlnhll..enraglklavivNefgevsiDaellretgve..ivelenGciCctlredllkeleale 77 
                                    +++l+G  GsGKTt   +l    +r+gl++avi  +    +   +l + ++ +   +  e+G      +e++ +++++ +
  gi|116753684|ref|YP_842802.1|  99 TIMLVGLQGSGKTTTAAKLAtyFQRRGLRTAVICADTFRAGAYDQLKALCDRQgiFFYGEKG------NENAPEVAKNGL 172
                                    5789*************99988899***********99888777777766555223333333......456777777766 PP

                                    HHHTT-SEEEEEECT.TTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHHHCHC CS
                           cobW  78 ereerldviliEttG.laePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDlldee 156
                                    e  +++dv ++ t G  a    ++ + +++++ +++d+++ v+Da ++ ++ +++++ +++ +  + + +++K D   + 
  gi|116753684|ref|YP_842802.1| 173 EATKKYDVRIVDTAGrHALESDLIQEMKDIHAVVNADHKLLVMDA-AIGQQASEQARAFNEAVGITGV-IITKLDGTAKG 250
                                    66679**********877777777789******************.7779999999999999999876.57899977665 PP

                                    .. CS
                           cobW 157 .a 157
                                      
  gi|116753684|ref|YP_842802.1| 251 gG 252
                                    44 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   9.4e-07   0.00051       3      49 ..      98     144 ..      96     151 .. 0.92
   2 ?   -2.2   0.0       6.1   3.3e+03     118     133 ..     293     308 ..     291     315 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 9.4e-07
                                    EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT- CS
                     APS_kinase   3 vvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdL 49 
                                     +++l Gl gsGK+t a +l+++ +++g ++ ++  d+ R g + +L
  gi|116753684|ref|YP_842802.1|  98 QTIMLVGLQGSGKTTTAAKLATYFQRRGLRTAVICADTFRAGAYDQL 144
                                    699*************************************9987776 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.1
                                    TTTSHHHHHHTTSSSS CS
                     APS_kinase 118 DpkglYkkareGeike 133
                                    D kgl +ka+e +i++
  gi|116753684|ref|YP_842802.1| 293 DIKGLIEKAQEVQIES 308
                                    89*******9998875 PP

>> 6PF2K  6-phosphofructo-2-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.6e-06    0.0014      12      59 ..      96     143 ..      89     187 .. 0.67
   2 ?   -1.6   0.1       2.5   1.4e+03     166     193 ..     363     390 ..     354     396 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.6e-06
                                    S-EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHHHHHHSS CS
                          6PF2K  12 sklvivlvGLpargKtyiskkltrylkwlgvrtkvFnvgkyrreaska 59 
                                    +k  i+lvGL   gKt+++ kl  y +  g+rt v  +  +r  a  +
  gi|116753684|ref|YP_842802.1|  96 KKQTIMLVGLQGSGKTTTAAKLATYFQRRGLRTAVICADTFRAGAYDQ 143
                                    57789**********************888888775555555444333 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.5
                                    HHHHHHHHTT-----TTTTTTSEEEEEE CS
                          6PF2K 166 lkRlenyekqyeplddeedeelsyIkvi 193
                                    ++Rle y+   ++++dee e+ + I+  
  gi|116753684|ref|YP_842802.1| 363 KERLEAYRFIMDSMTDEELEDPKIINAS 390
                                    6899999999999998888877777665 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   1.9e-06     0.001      15      56 ..      96     138 ..      89     151 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.9e-06
                     Zeta_toxin  15 rPklillgGqpGAGKselaellkdele.rqgnvvrldpDdlRe 56 
                                    ++  i+l+G +G+GK+++a++l+++++ r+ +  ++ +D++R+
  gi|116753684|ref|YP_842802.1|  96 KKQTIMLVGLQGSGKTTTAAKLATYFQrRGLRTAVICADTFRA 138
                                    67789**********************88889*********97 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0     2e-06    0.0011      25     141 ..      98     215 ..      72     234 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2e-06
                         AAA_16  25 elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekleea 104
                                    + ++l+G +G+GK++ + +l+++++++g  ++   +d + +a +y++l  +++r + +   +++ ++ ++++ ++  +ea
  gi|116753684|ref|YP_842802.1|  98 QTIMLVGLQGSGKTTTAAKLATYFQRRGLRTAVICADTF-RAGAYDQLKALCDRQG-IFFYGEKGNE-NAPEVAKNGLEA 174
                                    6799***********************888888888888.4446666666665533.3333333344.333333334444 PP

                         AAA_16 105 la....avpelagaea..srllellkrllallsrderplvlvl 141
                                    ++     + + ag +a  s+l +++k++ a    d++  +lv+
  gi|116753684|ref|YP_842802.1| 175 TKkydvRIVDTAGRHAleSDLIQEMKDIHAVVNADHK--LLVM 215
                                    4457553333333333667777777777766666344..4444 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.2   3.9e-06    0.0021      30      67 ..      98     135 ..      82     211 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.9e-06
                                    EEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE-- CS
                           MeaB  30 qvvGltGvPGaGkstlvealglelrrrGkrvavlavDP 67 
                                    q + l G+ G+Gk t+  +l++ ++rrG r av+  D 
  gi|116753684|ref|YP_842802.1|  98 QTIMLVGLQGSGKTTTAAKLATYFQRRGLRTAVICADT 135
                                    678899****************************9884 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.9   2.6e-05     0.014       2      95 ..     100     225 ..      99     243 .. 0.54

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.6e-05
                                    EEEEESTTSSHHHHHHHHHT......STEEESSSTTSSSSE.EEEEEE....ETTEE....................... CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltg......ekaivsdkpgtTrdi.negrvk....lkgke....................... 47 
                                    +++vG   +GK+t   +l           +++ +   T     + ++k        +                       
  gi|116753684|ref|YP_842802.1| 100 IMLVGLQGSGKTTTAAKLATyfqrrgL--RTAVICADTFRAgAYDQLKalcdR---Qgiffygekgnenapevaknglea 174
                                    778888888888888888753322220..222222222222122222222120...133333333444455555555555 PP

                                    .....EEEEECGGCSSHHHHHH.HHHHHHHHHHCTSEEEEEEETT..TTCSHHHHH CS
                       MMR_HSR1  48 .....ielvDtpGliegaseek.glgkaflaleeadlillvvdas..eeklkplde 95 
                                         +++vDt+G  +  +++  ++ k+++a+ +ad+ llv+da+  +    +  e
  gi|116753684|ref|YP_842802.1| 175 tkkydVRIVDTAG-RHALESDLiQEMKDIHAVVNADHKLLVMDAAigQ----QASE 225
                                    55555********.55333344588999999999*********87542....2222 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 !   17.2   0.0   6.5e-06    0.0035       2      33 ..     100     131 ..      99     142 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 6.5e-06
                           MobB   2 lgivgksgsGKTtLleklipelkarglrvgti 33 
                                    + +vg +gsGKTt   kl + +++rglr ++i
  gi|116753684|ref|YP_842802.1| 100 IMLVGLQGSGKTTTAAKLATYFQRRGLRTAVI 131
                                    789***************************98 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0   0.00084      0.46       2      26 ..      96     120 ..      95     149 .. 0.84
   2 ?    5.8   0.0     0.015       8.1      44      90 ..     173     222 ..     161     239 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00084
                                    ---EEEEE-STTSSHHHHHHHHHHS CS
                          SRPRB   2 skpavllvGlsdsGKTslftrLttd 26 
                                    +k++++lvGl+ sGKT+   +L t 
  gi|116753684|ref|YP_842802.1|  96 KKQTIMLVGLQGSGKTTTAAKLATY 120
                                    5789*************99999886 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.015
                                    ...GGTT-SEEEETT-GCCSHHHHHHHHHHGG...EEEEEEEEETTS-HH CS
                          SRPRB  44 ksekgskltliDfPGheklrqklleklkakss...lkglvfvvDStidpk 90 
                                    +++k+  ++++D  G + l ++l++++k+ +    +   + v+D++i ++
  gi|116753684|ref|YP_842802.1| 173 EATKKYDVRIVDTAGRHALESDLIQEMKDIHAvvnADHKLLVMDAAIGQQ 222
                                    6789999*******************998776322445678888888776 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   1.1e-05     0.006       2      38 ..     100     141 ..     100     233 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.1e-05
                         AAA_33   2 vllvGlpGsGKstlaerl...lkklg..avllssdtlrrrlf 38 
                                    ++lvGl+GsGK+t a +l    +++g  + ++  dt+r   +
  gi|116753684|ref|YP_842802.1| 100 IMLVGLQGSGKTTTAAKLatyFQRRGlrTAVICADTFRAGAY 141
                                    79***************9444455557777777777666544 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 !    9.7   0.0   0.00088      0.48      24      58 ..      97     132 ..      82     154 .. 0.74
   2 ?    4.5   0.0     0.035        19     101     144 ..     284     327 ..     257     352 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00088
                          AAA_8  24 rghaLlvGvgGsGrqs.ltkLAafiaelelfqievt 58 
                                    +  ++lvG++GsG+ +  +kLA++ ++  l++  + 
  gi|116753684|ref|YP_842802.1|  97 KQTIMLVGLQGSGKTTtAAKLATYFQRRGLRTAVIC 132
                                    5678**********862679****998877766554 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.035
                          AAA_8 101 dinnlLntGevpnLfskeekeeiieelrkeakkqgvedskesll 144
                                     i+ lL  G++  L +k ++ +i +++  +a ++g+ + k+   
  gi|116753684|ref|YP_842802.1| 284 FISRLLGMGDIKGLIEKAQEVQIESDVDVDAMMKGKFTLKDMYK 327
                                    6999************************9998876554444443 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   2.2e-05     0.012       1      88 [.     100     224 ..     100     238 .. 0.51

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.2e-05
                         AAA_18   1 IlltGtpGvGKttlakeL....skrlgf.................................gvnlrdvakenglllevdp 43 
                                    I+l G +G+GKtt a  L    ++r g+                                 g +    +++ngl+ +   
  gi|116753684|ref|YP_842802.1| 100 IMLVGLQGSGKTTTAAKLatyfQRR-GLrtavicadtfragaydqlkalcdrqgiffygekGNENAPEVAKNGLEATKKY 178
                                    89****************5555444.236678888855555544444444433333333333333333333333333333 PP

                         AAA_18  44 ealdeskrldedkldklldaleenss..............aleegknlvidghlaeles 88 
                                    +     +++d+  +++                         ++++k lv+d  +++  s
  gi|116753684|ref|YP_842802.1| 179 D----VRIVDTAGRHA---------LesdliqemkdihavVNADHKLLVMDAAIGQQAS 224
                                    3....22222222222.........2222222223444444556666666666665555 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 ?   13.7   0.1   4.1e-05     0.022      15      49 ..      97     131 ..      91     143 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.1e-05
                  TrwB_AAD_bind  15 tqhilivGttGsGKtqalekllrairargdraivl 49 
                                    +q i++vG +GsGKt+++ kl +  ++rg r  v+
  gi|116753684|ref|YP_842802.1|  97 KQTIMLVGLQGSGKTTTAAKLATYFQRRGLRTAVI 131
                                    6889*************************664432 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   4.8e-05     0.026       4      41 ..     100     137 ..      98     147 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.8e-05
                                    EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH CS
                          KTI12   4 vvltGlPssGKstrakeLakaleeekrsvvviddeslg 41 
                                    ++l Gl  sGK+t a++La++++ ++ +  vi  ++++
  gi|116753684|ref|YP_842802.1| 100 IMLVGLQGSGKTTTAAKLATYFQRRGLRTAVICADTFR 137
                                    7899************************9999888876 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   0.00012     0.064       3      27 ..     104     129 ..     102     133 .. 0.90
   2 ?   -1.8   0.0       3.9   2.1e+03      16      86 ..     144     216 ..     140     220 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
                                    ESTTSSHHHHHHHHHHHHHHTTE..E CS
                Thymidylate_kin   3 GlDGaGKttqaellkerlkeegik.v 27 
                                    Gl G+GKtt a++l+ +++++g++ +
  gi|116753684|ref|YP_842802.1| 104 GLQGSGKTTTAAKLATYFQRRGLRtA 129
                                    99*******************98743 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.9
                                    HHHHHHHTTE.EEEESSSTTSHHHHHHHHHHHTCS---HHH....HHHHHHHHHHHTTHHHHHHHHHTT-EEEEE CS
                Thymidylate_kin  16 lkerlkeegikvvltrepggteiGekirelllkeeeleeqt....eallfaadriehleekikpalkqgktvivd 86 
                                    lk+ ++++gi  ++  e+g+ +  e++++ l+ +++++           +  d i+++ + +   +++ k++++d
  gi|116753684|ref|YP_842802.1| 144 LKALCDRQGI--FFYGEKGNENAPEVAKNGLEATKKYDVRIvdtaGRHALESDLIQEMKDIHAVVNADHKLLVMD 216
                                    6777777774..688888888888888887776666555543433223345566666666666666666666666 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   6.8e-05     0.037       2      75 ..      97     187 ..      96     218 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.8e-05
                         AAA_24   2 klkiliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdieswedfldevvel............... 59 
                                    k+ i+++G +g+GKTt+a++l       g           ++ + ad f  + ++++++  ++                 
  gi|116753684|ref|YP_842802.1|  97 KQTIMLVGLQGSGKTTTAAKLatyfqrrGL---------RTAVICADTFR-AGAYDQLKALCDRQgiffygekgnenape 166
                                    789******************555544422.........33333333332.22334444444444555555555555666 PP

                         AAA_24  60 .....aaeladyktlviDtid 75 
                                          ++ ++y++ ++Dt++
  gi|116753684|ref|YP_842802.1| 167 vakngLEATKKYDVRIVDTAG 187
                                    666565666667777777765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0     9e-05     0.049       5      33 ..      97     125 ..      95     218 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9e-05
                         AAA_22   5 agilvvtGesGtGKTtllrrlleqldeea 33 
                                    ++ ++++G  G+GKTt++++l+  ++++ 
  gi|116753684|ref|YP_842802.1|  97 KQTIMLVGLQGSGKTTTAAKLATYFQRRG 125
                                    67899****************99887654 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.6   6.7e-05     0.036      19      59 ..      98     139 ..      94     215 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.7e-05
                         AAA_30  19 rvavltGpAGtGKttalkalreaweaag.grviglAptgkaA 59 
                                    ++ +l+G  G+GKtt+ ++l+  ++++g ++ +++A t +a 
  gi|116753684|ref|YP_842802.1|  98 QTIMLVGLQGSGKTTTAAKLATYFQRRGlRTAVICADTFRAG 139
                                    56789**********************857777889887774 PP

>> AAA_31  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       0.1      12      47 ..     107     169 ..      98     235 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00018
                         AAA_31  12 GvGKTTtsvnlaaalaklgkkvLlvDlDpQanatt...........................g 47 
                                    G GKTTt+ +la  + ++g ++ ++ +D+  + +                            +
  gi|116753684|ref|YP_842802.1| 107 GSGKTTTAAKLATYFQRRGLRTAVICADTFRAGAYdqlkalcdrqgiffygekgnenapevaK 169
                                    89***********************99987665555566666666655555555555444443 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.3    0.0024       1.3      11      40 ..     107     136 ..     100     217 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0024
                                    TSSHHHHHHHHHHHHHTTT--EEEEE--TT CS
                           MipZ  11 GsGksttavhvavaLlkkGarvaaidldlr 40 
                                    GsGk+tta  +a+ + ++G+r a+i  d+ 
  gi|116753684|ref|YP_842802.1| 107 GSGKTTTAAKLATYFQRRGLRTAVICADTF 136
                                    9**********************9988864 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.5    0.0003      0.16       2      33 ..     100     138 ..      99     218 .. 0.83
   2 ?   -2.2   0.0       7.8   4.2e+03      23      67 ..     179     226 ..     170     234 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0003
                         AAA_28   2 ivitGgestGKTtlleaLa....ar..gypvv.pEaare 33 
                                    i+++G +++GKTt++++La    +r   + v+ ++++r 
  gi|116753684|ref|YP_842802.1| 100 IMLVGLQGSGKTTTAAKLAtyfqRRglRTAVIcADTFRA 138
                                    899****************66633333344556666665 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 7.8
                         AAA_28  23 gypvvpEaareileeklakgedalpwv...edllafaervleeqleee 67 
                                    ++++v  a+r  le+ l ++ +++++v   + +l + ++ + +q++e+
  gi|116753684|ref|YP_842802.1| 179 DVRIVDTAGRHALESDLIQEMKDIHAVvnaDHKLLVMDAAIGQQASEQ 226
                                    566677777777777776666656655322233333333333333333 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00079      0.43       2      39 ..     100     137 ..      99     142 .. 0.85
   2 ?    0.2   0.0       1.1   6.2e+02      87     128 ..     170     212 ..     160     236 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00079
                                    EEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE- CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgGfyteevr 39 
                                    +++ G +G+GKtT   k++   +++g++ + + +   r
  gi|116753684|ref|YP_842802.1| 100 IMLVGLQGSGKTTTAAKLATYFQRRGLRTAVICADTFR 137
                                    7899**********************998766666555 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.1
                                    HHHHHHHHHH-EEEE---STTGGG-HHHHH..HHHHHHTTTSEE CS
                       NTPase_1  87 ealrkalseadviviDEiGkmElkskkfke..aveevLksekpv 128
                                    + l+ a ++ dv ++D  G+  l+s  ++e   ++ v++ +  +
  gi|116753684|ref|YP_842802.1| 170 NGLE-ATKKYDVRIVDTAGRHALESDLIQEmkDIHAVVNADHKL 212
                                    4454.568999999999998777777666411577777744433 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   0.00017     0.092      22      58 ..      95     130 ..      54     227 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00017
                                    .TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EE CS
                         ResIII  22 krdkrglikmaTGtGKTlvaaklierllkkgkeekfl 58 
                                     +++ ++++   G+GKT +aakl+ ++++ g  + ++
  gi|116753684|ref|YP_842802.1|  95 LKKQTIMLVGLQGSGKTTTAAKLATYFQRRGL-RTAV 130
                                    4667889999*************999887644.3444 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00028      0.15       2      29 ..      99     126 ..      98     134 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00028
                                    CEEEEC-TTTCHHHHHHHHHHHHCTS-S CS
                          NACHT   2 lvilqGeaGsGKTtLlqklalawaegkl 29 
                                    +++l G +GsGKTt ++kla+  +++ l
  gi|116753684|ref|YP_842802.1|  99 TIMLVGLQGSGKTTTAAKLATYFQRRGL 126
                                    899*****************98888765 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1    0.0021       1.1       3      38 ..      99     134 ..      97     138 .. 0.93
   2 ?   -2.1   0.0         3   1.7e+03     122     133 ..     175     186 ..     169     219 .. 0.83
   3 ?    4.7   0.5     0.026        14     151     205 ..     324     380 ..     315     390 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0021
                                    EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                    ArsA_ATPase   3 vilvgGKGGVGKttvsaatavklsekgkkvllistD 38 
                                     i++ G  G GKtt +a +a++  + g ++ +i  D
  gi|116753684|ref|YP_842802.1|  99 TIMLVGLQGSGKTTTAAKLATYFQRRGLRTAVICAD 134
                                    68999999************************9988 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3
                                    CSSSSEEEEESB CS
                    ArsA_ATPase 122 eeeydvvvlDta 133
                                    +++ydv ++Dta
  gi|116753684|ref|YP_842802.1| 175 TKKYDVRIVDTA 186
                                    578999999998 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.026
                                    HHHHHHHHHHHHHHHHHHHCCCSHCHHHHHH...HHHHHHHHHHHHHHHHHHHHTSTT CS
                    ArsA_ATPase 151 lleklvklkeklsplakqlvkllglggvsie...ealeeleetkeeikkveeiltdpe 205
                                     + k ++  +k++pl++ + ++l++gg  ie   +  +  +e++e ++ + + +td+e
  gi|116753684|ref|YP_842802.1| 324 DMYKQLEAMNKMGPLKQIM-QMLPFGGIGIElsdKEYQVTKERLEAYRFIMDSMTDEE 380
                                    3455566666778877666.99****99999777777888888888888888899987 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.4   0.00065      0.35       1      25 [.     100     124 ..     100     289 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00065
                                    EEEESSTTSSHHHHHHHHHHHHTHE CS
                            AAA   1 vllyGppGtGKTllakavakelgve 25 
                                    ++l+G  G GKT++a  +a+ ++++
  gi|116753684|ref|YP_842802.1| 100 IMLVGLQGSGKTTTAAKLATYFQRR 124
                                    689****************998654 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00065      0.35       2      27 ..     100     126 ..      99     138 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00065
                                    EEEE--SSSSHHHHHHHGGGGB.S--E CS
                          AAA_5   2 vlLvGppGtgKselaerlaaal.nrev 27 
                                    ++LvG +G+gK++ a +la  + +r +
  gi|116753684|ref|YP_842802.1| 100 IMLVGLQGSGKTTTAAKLATYFqRRGL 126
                                    79*****************99954444 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.2    0.0058       3.1       2      21 ..      98     117 ..      97     123 .. 0.87
   2 ?    2.0   0.0      0.29   1.6e+02      38     102 ..     180     247 ..     172     272 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0058
                      PduV-EutP   2 kkilliGkvgsGKttLtqal 21 
                                    + i+l+G  gsGKtt + +l
  gi|116753684|ref|YP_842802.1|  98 QTIMLVGLQGSGKTTTAAKL 117
                                    579************98887 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.29
                      PduV-EutP  38 deviDtPGeylenrklysalivt..saeadvialvqdateeesvfppgfasvfnkeviG.iitkidla 102
                                     +++Dt G ++ +  l + ++ +   ++ad   lv+da   ++   ++ a   +  + G iitk+d +
  gi|116753684|ref|YP_842802.1| 180 VRIVDTAGRHALESDLIQEMKDIhaVVNADHKLLVMDAAIGQQASEQARAFNEAVGITGvIITKLDGT 247
                                    46899999999999999998654216789999999988876665444433333334566357998865 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.8    0.0013       0.7      11      55 ..      89     145 ..      82     421 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0013
                         AAA_23  11 rdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrks..............g 55 
                                    r+++i ++k    ++G  G+GKTT   A kla+y + ++l++                +
  gi|116753684|ref|YP_842802.1|  89 RGTDIPLKKQTIMLVGLQGSGKTTT--AAKLATYFQRRGLRTAVicadtfragaydqlK 145
                                    5678999*****************6..66777777777666554555555555555550 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       723  (0.0403257); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                        33  (0.00184059); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              33  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.46
# Mc/sec: 2917.21
//
Query:       gi|116753685|ref|YP_842803.1|  [L=65]
Description: hypothetical protein Mthe_0370 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.098   13.2   0.6       0.13   12.9   0.6    1.2  1  DUF2627    Protein of unknown function (DUF2627)
       0.12   12.6   1.7        6.2    7.0   0.3    2.0  2  DUF872     Eukaryotic protein of unknown function (DUF872)
       0.24   11.0   6.9       0.94    9.1   6.9    1.8  1  DUF3098    Protein of unknown function (DUF3098)


Domain annotation for each model (and alignments):
>> DUF2627  Protein of unknown function (DUF2627)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.6   2.1e-05      0.13       9      56 ..       1      56 [.       1      64 [. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.1e-05
                        DUF2627  9 LvipgllaayGiklmrd.alfgilsspfssl.......wlqflaGlllfaiglgfi 56
                                   ++i +l+a++Gi  m + a+fg+ s  +          ++++ +G ll+++g+ ++
  gi|116753685|ref|YP_842803.1|  1 MIIGILVAVVGIWTMANpAWFGHNSWMYGLNwwsytasIIKGSIGPLLILVGIVIV 56
                                   689999******99987589*99999987665677777888888999999988776 PP

>> DUF872  Eukaryotic protein of unknown function (DUF872)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1    0.0027        16      53      79 ..       1      28 [.       1      31 [. 0.87
   2 ?    7.0   0.3     0.001       6.2      42      68 ..      31      57 ..      29      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0027
                         DUF872 53 lllGlvLlllgvvilvep.seGvssavf 79
                                   +++G+++ ++g++ +++p   G++s+++
  gi|116753685|ref|YP_842803.1|  1 MIIGILVAVVGIWTMANPaWFGHNSWMY 28
                                   589***************5679999998 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.001
                         DUF872 42 nrkvvlaallLlllGlvLlllgvvilv 68
                                   n+ +  a+++   +G +L+l+g+vi+ 
  gi|116753685|ref|YP_842803.1| 31 NWWSYTASIIKGSIGPLLILVGIVIVW 57
                                   8999999****************9975 PP

>> DUF3098  Protein of unknown function (DUF3098)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   6.9   0.00016      0.94      10      62 ..       1      59 [.       1      60 [. 0.77

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00016
                        DUF3098 10 lliglaviilGfiLmsGggsddpnvFnedi....F..sfrRirlAPivvliGfvieiya 62
                                   ++ig++v ++G++ m+      +n++ + +    +  s+ +  ++P+++l+G+vi  +a
  gi|116753685|ref|YP_842803.1|  1 MIIGILVAVVGIWTMANPAWFGHNSWMYGLnwwsYtaSIIKGSIGPLLILVGIVIVWIA 59
                                   89**************999988888877543322322444557***********98766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); 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: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 507.82
//
Query:       gi|116753686|ref|YP_842804.1|  [L=252]
Description: hypothetical protein Mthe_0371 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-06   28.9  19.9      0.033   14.5   1.7    3.3  3  Alanine_zipper  Alanine-zipper, major outer membrane lipoprot
    1.5e-06   28.3   7.3        0.4   10.9   0.3    3.3  3  DUF3175         Protein of unknown function (DUF3175)
    7.9e-05   22.7   8.5        0.4   10.6   0.4    3.1  3  DUF3907         Protein of unknown function (DUF3907)
    0.00034   19.7   5.0        1.5    7.7   0.1    3.1  3  TTKRSYEDQ       Predicted coiled-coil domain-containing prote
    0.00047   20.6   0.0         15    6.1   0.0    3.2  3  DUF5498         Family of unknown function (DUF5498)
  ------ inclusion threshold ------
      0.062   13.0   2.6      0.083   12.6   2.6    1.1  1  CiPC            Clock interacting protein circadian


Domain annotation for each model (and alignments):
>> Alanine_zipper  Alanine-zipper, major outer membrane lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   1.7   1.1e-05     0.033      13      56 ..      90     133 ..      73     138 .. 0.77
   2 !   13.0   2.1   3.3e-05     0.099      22      55 ..     155     188 ..     148     195 .. 0.70
   3 !   12.1   1.6   6.5e-05      0.19       9      38 ..     212     241 ..     205     247 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.1e-05
                 Alanine_zipper  13 aeqdaaaaksaadeAkskAdeAaarAenAeaaAeeAqkaAeean 56 
                                    + +  +  +++a  A++ A  A++ Ae Ae  A +A+  A e++
  gi|116753686|ref|YP_842804.1|  90 ILSIYNLTRKMAVYASENASIARSMAESAEMNARRAETSAYECR 133
                                    55555566778888888888888888888888888888888875 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 3.3e-05
                 Alanine_zipper  22 saadeAkskAdeAaarAenAeaaAeeAqkaAeea 55 
                                    ++a  A++ A  A++ Ae Ae  A +A+  A e+
  gi|116753686|ref|YP_842804.1| 155 KMAVYASENASIARSMAESAEMNARRAETSAYEC 188
                                    5566677777777777777777777777777766 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 6.5e-05
                 Alanine_zipper   9 kadqaeqdaaaaksaadeAkskAdeAaarA 38 
                                    +a  a+++a+ a+s+a++A++ A+ A++ A
  gi|116753686|ref|YP_842804.1| 212 MAVYASENASIARSMAESAEMNARRAETSA 241
                                    444456666666666666666666666544 PP

>> DUF3175  Protein of unknown function (DUF3175)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.2   0.00023       0.7      19      47 ..     102     130 ..      92     137 .. 0.74
   2 !   10.2   0.1   0.00022      0.65      19      47 ..     158     186 ..     145     193 .. 0.75
   3 !   10.9   0.3   0.00013       0.4      19      51 ..     214     246 ..     201     250 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00023
                        DUF3175  19 vfksddpkkiakslkrsaekskrRka.epf 47 
                                    v++s + ++ia+s+ +sae ++rR   +++
  gi|116753686|ref|YP_842804.1| 102 VYAS-ENASIARSMAESAEMNARRAEtSAY 130
                                    5554.5578************999641555 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00022
                        DUF3175  19 vfksddpkkiakslkrsaekskrRka.epf 47 
                                    v++s + ++ia+s+ +sae ++rR   +++
  gi|116753686|ref|YP_842804.1| 158 VYAS-ENASIARSMAESAEMNARRAEtSAY 186
                                    5554.5578************999641555 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00013
                        DUF3175  19 vfksddpkkiakslkrsaekskrRk.aepfrsam 51 
                                    v++s + ++ia+s+ +sae ++rR  ++++   m
  gi|116753686|ref|YP_842804.1| 214 VYAS-ENASIARSMAESAEMNARRAeTSAYEFRM 246
                                    5554.5578************9996245555444 PP

>> DUF3907  Protein of unknown function (DUF3907)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.4   0.00013       0.4      24      79 ..      76     131 ..      63     135 .. 0.90
   2 !    8.1   0.2   0.00081       2.4      29      79 ..     137     187 ..     132     190 .. 0.88
   3 !    8.4   0.2   0.00064       1.9      29      79 ..     193     243 ..     188     250 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00013
                        DUF3907  24 lesllkeeeeeeeyykgllsdlRrllvfseegleklrvllrrekFrkeaAekaLyk 79 
                                     esll+e + e++ + ++ +  R+++v++ e +  +r + ++++ +   Ae   y+
  gi|116753686|ref|YP_842804.1|  76 AESLLSEMKRERDEILSIYNLTRKMAVYASENASIARSMAESAEMNARRAETSAYE 131
                                    57899999999999999**********************************99886 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00081
                        DUF3907  29 keeeeeeeyykgllsdlRrllvfseegleklrvllrrekFrkeaAekaLyk 79 
                                    +e+e+ ++ + ++ +  R+++v++ e +  +r + ++++ +   Ae   y+
  gi|116753686|ref|YP_842804.1| 137 NETESVRSEILSIYNLTRKMAVYASENASIARSMAESAEMNARRAETSAYE 187
                                    45677788888999999*****************************99886 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.00064
                        DUF3907  29 keeeeeeeyykgllsdlRrllvfseegleklrvllrrekFrkeaAekaLyk 79 
                                    +e+e+ ++ + ++ +  R+++v++ e +  +r + ++++ +   Ae   y+
  gi|116753686|ref|YP_842804.1| 193 NETESVRSEILSIYNLTRKMAVYASENASIARSMAESAEMNARRAETSAYE 243
                                    45677788888999999*****************************99987 PP

>> TTKRSYEDQ  Predicted coiled-coil domain-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7   0.1    0.0021       6.2      37      65 ..      91     119 ..      76     139 .. 0.85
   2 !    7.7   0.1    0.0005       1.5      32      64 ..     142     174 ..     127     186 .. 0.80
   3 !    7.7   0.1   0.00051       1.5      32      64 ..     198     230 ..     183     241 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0021
                      TTKRSYEDQ  37 etlsplnqkfsqYLhenaayvRpleesll 65 
                                     ++ +l++k++ Y  ena+  R++ es +
  gi|116753686|ref|YP_842804.1|  91 LSIYNLTRKMAVYASENASIARSMAESAE 119
                                    578899******************99865 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0005
                      TTKRSYEDQ  32 vdsaietlsplnqkfsqYLhenaayvRpleesl 64 
                                    v s+i ++ +l++k++ Y  ena+  R++ es 
  gi|116753686|ref|YP_842804.1| 142 VRSEILSIYNLTRKMAVYASENASIARSMAESA 174
                                    4466778899*******************9986 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.00051
                      TTKRSYEDQ  32 vdsaietlsplnqkfsqYLhenaayvRpleesl 64 
                                    v s+i ++ +l++k++ Y  ena+  R++ es 
  gi|116753686|ref|YP_842804.1| 198 VRSEILSIYNLTRKMAVYASENASIARSMAESA 230
                                    4466778899*******************9986 PP

>> DUF5498  Family of unknown function (DUF5498)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.015        45      29      53 ..      87     111 ..      72     132 .. 0.86
   2 !    6.1   0.0    0.0051        15      25      53 ..     139     167 ..     130     179 .. 0.84
   3 !    6.1   0.0    0.0052        16      25      52 ..     195     222 ..     184     232 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.015
                        DUF5498  29 ydefikifgtdkkfgifpsenfskp 53 
                                     de++ i+   +k+ ++ sen s  
  gi|116753686|ref|YP_842804.1|  87 RDEILSIYNLTRKMAVYASENASIA 111
                                    599******************9854 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0051
                        DUF5498  25 neavydefikifgtdkkfgifpsenfskp 53 
                                     e+v  e++ i+   +k+ ++ sen s  
  gi|116753686|ref|YP_842804.1| 139 TESVRSEILSIYNLTRKMAVYASENASIA 167
                                    36899********************9854 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0052
                        DUF5498  25 neavydefikifgtdkkfgifpsenfsk 52 
                                     e+v  e++ i+   +k+ ++ sen s 
  gi|116753686|ref|YP_842804.1| 195 TESVRSEILSIYNLTRKMAVYASENASI 222
                                    36899********************985 PP

>> CiPC  Clock interacting protein circadian
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   2.6   2.8e-05     0.083      78     259 ..      51     232 ..      47     247 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.8e-05
                           CiPC  78 vqpslevvpaqpqlvflqpvvspsasstskesaekkkrskkYlPilnSYpkIAPhPgkksss.....ssslsasersssh 152
                                    +++s  ++pa pq++ l  +    ++++++  +e k+++++ l i n   k A + ++++s      +s+  + +r +++
  gi|116753686|ref|YP_842804.1|  51 FGTSGFAAPASPQVMALSTSA--MVHQAESLLSEMKRERDEILSIYNLTRKMAVYASENASIarsmaESAEMNARRAETS 128
                                    566677788889998887665..4444444568999***********************887444432333333333444 PP

                           CiPC 153 ssskrvcterkkeklses...sasstsesssatpekealpsspstssplsaklasesaretsssllatpaserpssssse 229
                                    + + rv  +++++  s +     + t +++  + e+ +++ s + s++++a++a++sa e+   l +t++++++  s  +
  gi|116753686|ref|YP_842804.1| 129 AYECRVALNETESVRS-EilsIYNLTRKMAVYASENASIARSMAESAEMNARRAETSAYECRVALNETESVRSEILSIYN 207
                                    4455555444443322.223233444455566666777777777777777777777777777777666666666666665 PP

                           CiPC 230 lslssaslsssataskasalssaspasses 259
                                    l+ + a + +s++as a++++++    +e 
  gi|116753686|ref|YP_842804.1| 208 LTRKMAVY-ASENASIARSMAES----AEM 232
                                    55543333.33344444444433....333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       689  (0.0384294); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1766.45
//
Query:       gi|116753687|ref|YP_842805.1|  [L=339]
Description: hypothetical protein Mthe_0372 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-42  144.3  30.2    6.5e-42  143.8  30.2    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 !  143.8  30.2   3.6e-46   6.5e-42       3     324 ..       9     324 ..       7     327 .. 0.88

  Alignments for each domain:
  == domain 1  score: 143.8 bits;  conditional E-value: 3.6e-46
                AI-2E_transport   3 lilvllllllalypfiselllplliAlvlayllnpvvkfL.kkrgvkrvlavllvlllllvllvllvlllvplliaqltq 81 
                                    +  vl+++++++y++++ l+  ++++ v+ay+  p+ + +  ++++   +a++ +++ ++++l+l v+ ++    + +  
  gi|116753687|ref|YP_842805.1|   9 IAVVLIAFIAIAYFMFP-LVDGIILGTVFAYIGRPIRDMFgPRKRLGSAIATIGIIVPISLVLILGVMEIA----NFFMW 83 
                                    67899************.**********************7777777777777776666666666666666....88888 PP

                AI-2E_transport  82 lvkslpayidslqnilnelpslleelenliqalkqslskilsnilssi.lnsllsllasllglilslvlvllllffllld 160
                                    + ++   +  + ++ ++ l+ + +e +     +  sl++ils + +    + ll++ + ++ l++++++ + +++fll d
  gi|116753687|ref|YP_842805.1|  84 IAQNPGSMAREMSSTISGLE-IPDEIY---TLITGSLQSILSFVADVAaRMPLLDYGRRVVLLAVNIIVAIPVCYFLLCD 159
                                    88887777788777777776.445553...457777777777777776456699************************** PP

                AI-2E_transport 161 geklrqgilkllpervrervkailrelektlsgylrgqvlvaliigvlvfigllilgvpyalllailvglanliPyiGav 240
                                    ge++++  + ++pe+  + ++a++++++++lsg++ g++ +a++ +v+++i+++++ vp ++ +a lv++a l+P + a+
  gi|116753687|ref|YP_842805.1| 160 GERFVDSWFTIVPEESLDTYRAYFNRIDRILSGIFLGSMYTAIVGSVISAIVFYAFDVPRPFAMASLVFIAGLVPALTAW 239
                                    ******************************************************************************** PP

                AI-2E_transport 241 ivlipiaiialltggikevlivlivvllvqlie.gnilePklmgkrlglhplvillsllaggklfGlvGlilavpltavi 319
                                     v++p++i+ +++ g++e+l++++v+ ++ ++  + i++P+l+  r ++hpl+++ls+l+g++++G+ G++la+ +++vi
  gi|116753687|ref|YP_842805.1| 240 AVIVPVSIYRYIHMGPAEALMFFAVASALIYLPsELIVRPYLVAARSSIHPLLVMLSFLGGAMVAGIGGFFLAPAVMGVI 319
                                    *********************99999887777615688*****************************************9 PP

                AI-2E_transport 320 kaile 324
                                      i++
  gi|116753687|ref|YP_842805.1| 320 VGIYQ 324
                                    98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1009  (0.0562775); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2336.35
//
Query:       gi|116753688|ref|YP_842806.1|  [L=411]
Description: MiaB-like tRNA modifying enzyme [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      7e-21   75.3   0.0    1.9e-20   73.9   0.0    1.7  2  Radical_SAM  Radical SAM superfamily
    1.1e-13   51.0   0.1    2.3e-13   50.0   0.1    1.5  1  UPF0004      Uncharacterized protein family UPF0004
    3.9e-11   42.8   0.0    7.7e-11   41.8   0.0    1.5  1  TRAM         TRAM domain
  ------ inclusion threshold ------
       0.12   12.3   0.0       0.25   11.3   0.0    1.5  1  SeqA         SeqA protein C-terminal domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.2   5.2e+03      28      67 ..      49      84 ..      41      95 .. 0.80
   2 !   73.9   0.0   4.2e-24   1.9e-20       1     163 [.     125     293 ..     125     297 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.2
                                   HHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM 28 slsveeileevkelkaekgvkevilgggepllypdfvell 67
                                   s++ ++ l+ + elk    ++ +i+ g  p + p+++e +
  gi|116753688|ref|YP_842806.1| 49 SRTERNMLRRIGELK----GRRLIVAGCLPAAIPELIESV 84
                                   677888888888888....888888888888888887766 PP

  == domain 2  score: 73.9 bits;  conditional E-value: 4.2e-24
                                    EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS.....TTHHHHHHHHHHTC. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxx. RF
                    Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly.....pdfvellerlakla. 74 
                                    v++++gC ++C +C++++    +g+ rs+ + ei++ v +l  + g+ e+ l++++  +y     + + ell+ l+ ++ 
  gi|116753688|ref|YP_842806.1| 125 VNISEGCLGACAYCIVKR---ARGTLRSREPHEIEKDVMRL-ISSGAVEIQLTSQDAGAYgcdigASLPELLDLLSDIDg 200
                                    6899*************8...8*******************.8******************9999777777777777754 PP

                                    CCTEEEEEEECSSCHG..HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET...EEEE CS
                                    xxxxxxxxxxxxxxxx..xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxx RF
                    Radical_SAM  75 vpgiritvetngtlpd..eeklerllelg.vdrvslgleaaddekvlklmnrghtfeevlealeklreagikr...vvdr 148
                                       ir+ +  +  ++   ++ l+  ++      ++l+l++++d+ vl++m+rg+t +++++++ ++r++  ++   ++d+
  gi|116753688|ref|YP_842806.1| 201 AFMIRVGMMNPNSVLKilDDLLDSYKNEKiYRFIHLPLQSGSDR-VLERMRRGYTSDDFVNVVSAFRSR-YPEislTTDV 278
                                    35666666666666558899999999988***************.************************.8888****** PP

                                    EEEBTTTSHHHHHHH CS
                                    xxxxxxxxxxxxxxx RF
                    Radical_SAM 149 ivglpGendeeleel 163
                                    i+g+pGe+d++++ +
  gi|116753688|ref|YP_842806.1| 279 ITGFPGESDQDFRMT 293
                                    ***********9987 PP

>> UPF0004  Uncharacterized protein family UPF0004
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.0   0.1   5.1e-17   2.3e-13       1      86 [.       2      81 ..       2      89 .. 0.89

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 5.1e-17
                                   XEEEE--S-CCCCHHHHHHHHHTTTSSS----SSS--SEEEEEE--SSSSHHHHTHHHHHHHHTTST.--EEEEEEHHHHS- CS
                        UPF0004  1 kvaietlGCqmNevdseelaslLkkegyelvedeeeAdvvlvnTCavrekaekkviqalrelkalkkpekkvvvlGCmaqre 82
                                   ++ iet+GC+ N+ +s el ++L ++g+++ +  + ++vv++nTCav++++e++++++++elk  +     ++v+GC++ + 
  gi|116753688|ref|YP_842806.1|  2 RFCIETYGCTSNTGNSMELRGALIAHGHQESD-LDGSEVVILNTCAVTSRTERNMLRRIGELKGRR-----LIVAGCLPAAI 77
                                   6889***********************99865.589*******************99999998866.....9******9877 PP

                                   HHHH CS
                        UPF0004 83 keel 86
                                   +e +
  gi|116753688|ref|YP_842806.1| 78 PELI 81
                                   6655 PP

>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   0.0   1.7e-14   7.7e-11       1      60 [.     349     406 ..     349     408 .. 0.97

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 1.7e-14
                                    XXXXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT-.-T..TEEEEEEEEEE-SSEEEEE CS
                           TRAM   1 rsyvGstqeVlveglsksegegiGrtdngkvvfvpgd.lpgIGdfVeVkItkvkrqyLrGe 60 
                                    r+y+G+t++Vlv++++ + g++ +rt n+  v+v+g  +p  G++V+++  +++++y +++
  gi|116753688|ref|YP_842806.1| 349 RRYIGETLDVLVTEQG-RAGTMKARTRNYTGVVVHGLsSP--GKWVKARAIDATPFYVKAR 406
                                    69**************.********************9**..****************997 PP

>> SeqA  SeqA protein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   5.5e-05      0.25      43      79 ..     368     404 ..     348     408 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.5e-05
                           SeqA  43 kvkGrtRvYfakdeetllasgkstkpkqipetpfWVi 79 
                                    ++k rtR Y +   + l + gk +k++ i  tpf+V 
  gi|116753688|ref|YP_842806.1| 368 TMKARTRNYTGVVVHGLSSPGKWVKARAIDATPFYVK 404
                                    6899*******************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 3100.94
//
Query:       gi|116753689|ref|YP_842807.1|  [L=180]
Description: hypothetical protein Mthe_0374 [Methanosaeta thermophila PT]
Scores for complete sequence (score 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   14.9   0.0      0.093   12.7   0.0    2.1  2  DASH_Dad4  DASH complex subunit Dad4
      0.023   14.8   0.2      0.058   13.5   0.2    1.7  1  MbeD_MobD  MbeD/MobD like
      0.033   13.8   0.0      0.075   12.6   0.0    1.6  1  HTH_24     Winged helix-turn-helix DNA-binding
      0.033   14.0   0.0      0.073   12.9   0.0    1.6  1  HTH_IclR   IclR helix-turn-helix domain


Domain annotation for each model (and alignments):
>> DASH_Dad4  DASH complex subunit Dad4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.46   2.1e+03      16      26 ..      29      39 ..      21      41 .. 0.73
   2 ?   12.7   0.0   2.1e-05     0.093      10      38 ..      46      74 ..      43      84 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.46
                      DASH_Dad4 16 IiknvekLnes 26
                                   +i+ v++L+es
  gi|116753689|ref|YP_842807.1| 29 LITAVNRLTES 39
                                   67888888887 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 2.1e-05
                      DASH_Dad4 10 salLsRIiknvekLnesvvelnkeleein 38
                                     lL R+i  v++L++ v++l+++l+   
  gi|116753689|ref|YP_842807.1| 46 VELLGRLIDQVDRLSKEVADLKTQLRARH 74
                                   579*********************98654 PP

>> MbeD_MobD  MbeD/MobD like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   1.3e-05     0.058      12      66 ..       2      71 ..       1      75 [. 0.90

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.3e-05
                      MbeD_MobD 12 lEqLQqdYeqrlqeWesafaelqrmfeltqrena...............aLseqvtgLsqQVesLseqvr 66
                                   +E+L + Y+ r  e e    e q+m+el    n                 L  qv++Ls+ V +L  q+r
  gi|116753689|ref|YP_842807.1|  2 FEELLEVYKNRAAETERKLREEQAMIELITAVNRltesagygrdvellgRLIDQVDRLSKEVADLKTQLR 71
                                   79999999******************998877666788899999999999***************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 ?   12.6   0.0   1.7e-05     0.075       2      41 ..      90     130 ..      89     133 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.7e-05
                         HTH_24   2 detdrkILelLqknpr.isqreLAerlglSpstvnrrlkrL 41 
                                    d+  r+++e++ + p+  + +eL ++lgl ++tv   +kr 
  gi|116753689|ref|YP_842807.1|  90 DRHARALIEIMSERPGeYTTAELVDMLGLNKTTVISVMKRA 130
                                    77789999***************************999985 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 ?   12.9   0.0   1.6e-05     0.073       7      35 ..      95     123 ..      88     127 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.6e-05
                                    HHHCT-CTTBSS-BHHHHHHHHTS-HHHH CS
                       HTH_IclR   7 aiLdalaeapqeltlselArrtglpkStv 35 
                                    a++++ +e+p+e t +el + +gl+k+tv
  gi|116753689|ref|YP_842807.1|  95 ALIEIMSERPGEYTTAELVDMLGLNKTTV 123
                                    78999***********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       959  (0.0534888); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1431.37
//
Query:       gi|116753690|ref|YP_842808.1|  [L=265]
Description: hydrolase [Methanosaeta thermophila PT]
Scores for 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-15   55.5   0.0      2e-13   51.1   0.0    2.1  2  Hydrolase    haloacid dehalogenase-like hydrolase
    0.00019   21.3   0.0     0.0071   16.1   0.0    2.4  3  Hydrolase_3  haloacid dehalogenase-like hydrolase
    0.00057   20.0   0.0       0.01   16.0   0.0    2.2  1  HAD_2        Haloacid dehalogenase-like hydrolase
     0.0067   16.5   0.0      0.042   13.9   0.0    2.1  2  Hydrolase_6  Haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.032   13.7   0.0      0.049   13.1   0.0    1.2  1  SRPRB        Signal recognition particle receptor beta subuni
      0.094   12.6   0.0       0.18   11.7   0.0    1.4  1  DUF2399      Protein of unknown function C-terminus (DUF2399)


Domain annotation for each model (and alignments):
>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.059   1.8e+02       3      26 ..       5      28 ..       4      47 .. 0.83
   2 !   51.1   0.0   6.6e-17     2e-13     113     210 .]     138     226 ..     112     226 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.059
                                   EEEEESBTTTBCHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase  3 tvvfDkdGTLttgepsvedvivsa 26
                                   +vv+D+ GTL++  ++  d+i  +
  gi|116753690|ref|YP_842808.1|  5 AVVLDVAGTLLRMYRVANDLIHGR 28
                                   79*********9888888777655 PP

  == domain 2  score: 51.1 bits;  conditional E-value: 6.6e-17
                                    HHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTTGGGESEEEEHHCES.STTTSHHHHHHHHHHHTSTGG CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 113 iadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlGddyfdaviasdiet.vakpspegkvaaireLqgkpe 191
                                    ++    ++p+++ ++ +L+++g ++++++gd+ +   +  +  G         +d +   + ++p  k++++++L+++ +
  gi|116753690|ref|YP_842808.1| 138 VSTGGVPFPGVRSVLDELRDMGADIYIASGDSARSLIHMVDY-G---------IDPKNiYSVADPMRKREIVKRLKENHR 207
                                    55566799***********************97666655554.4.........3344477777***************** PP

                                    GEEEEESSHHHHHHHHHTT CS
                                    xxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 192 evamVGDgvnDaaalaaAg 210
                                     v+mVGDg+nD+ al++A+
  gi|116753690|ref|YP_842808.1| 208 AVVMVGDGLNDIYALEEAD 226
                                    *****************98 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       2.2   6.6e+03       1      11 [.       6      16 ..       6      23 .. 0.85
   2 ?    2.6   0.0     0.031        93      20      50 ..     148     178 ..     137     189 .. 0.84
   3 !   16.1   0.0   2.4e-06    0.0071     194     227 ..     197     230 ..     194     254 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.2
                                   EEEEIIIIIS- CS
                    Hydrolase_3  1 ialDlDGTLln 11
                                   ++lD+ GTLl+
  gi|116753690|ref|YP_842808.1|  6 VVLDVAGTLLR 16
                                   689******97 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.031
                                    HHHHHHHHHHTTSEEEEE-SS-HHHHHHHHH CS
                    Hydrolase_3  20 tkeaikklkekgikvviATGRslravlpvle 50 
                                     ++++ +l++ g  + iA+G s r+++++++
  gi|116753690|ref|YP_842808.1| 148 VRSVLDELRDMGADIYIASGDSARSLIHMVD 178
                                    678999**************99999988876 PP

  == domain 3  score: 16.1 bits;  conditional E-value: 2.4e-06
                                    HHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEE CS
                    Hydrolase_3 194 klakelnisleeviafGDgeNDieMLeaaglgvA 227
                                    +++k+l+ ++  v+ +GDg NDi  Le a+lgv 
  gi|116753690|ref|YP_842808.1| 197 EIVKRLKENHRAVVMVGDGLNDIYALEEADLGVL 230
                                    78999***************************96 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   3.4e-06      0.01      80     174 ..     144     228 ..     139     232 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.4e-06
                          HAD_2  80 pydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekaleklklkkeeviyvG 159
                                    p++gv+++L+eL+++g  + i++  s++++ ++++  gi+   + i++  d  +k       ++++++lk ++  v++vG
  gi|116753690|ref|YP_842808.1| 144 PFPGVRSVLDELRDMGADIYIASGDSARSLIHMVD-YGIDP--KNIYSVADPMRK-------REIVKRLKENHRAVVMVG 213
                                    89*********************999999988776.56643..566666665565.......6999************** PP

                          HAD_2 160 DsptDieaakkagik 174
                                    D  +Di a  +a + 
  gi|116753690|ref|YP_842808.1| 214 DGLNDIYALEEADLG 228
                                    ******998888765 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.46   1.4e+03       1      14 [.       6      19 ..       6      35 .. 0.84
   2 !   13.9   0.0   1.4e-05     0.042      11      94 ..     140     219 ..     129     226 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.46
                                   EEEESTTTSEETTE CS
                    Hydrolase_6  1 flfDidGvLwrgdk 14
                                   +++D+ G+L+r ++
  gi|116753690|ref|YP_842808.1|  6 VVLDVAGTLLRMYR 19
                                   689******98665 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1.4e-05
                                    ETTEE-TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHHHHHHTT----GGGEEEHHHHHH..HHHHHHSXXXEEEEESX CS
                    Hydrolase_6  11 rgdkaipgaaealnalraagkpvvllTNnsskseeeyakkleklgvditeeqvvtsataaa..eylkkrkadkkvlvige 88 
                                     g+ ++pg+  +l+ lr++g ++++ +  s +s       ++ +++ i+++++++ a++++  e++k+ k++++ +v+++
  gi|116753690|ref|YP_842808.1| 140 TGGVPFPGVRSVLDELRDMGADIYIASGDSARS------LIHMVDYGIDPKNIYSVADPMRkrEIVKRLKENHRAVVMVG 213
                                    5889**************************999......45778888999999999999862246777788888888888 PP

                                    HHHHHH CS
                    Hydrolase_6  89 eglree 94 
                                    +gl ++
  gi|116753690|ref|YP_842808.1| 214 DGLNDI 219
                                    888765 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 ?   13.1   0.0   1.6e-05     0.049      71     101 ..     165     195 ..     141     213 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.6e-05
                                    HHHGGEEEEEEEEETTS-HHHHHHHHHHHHH CS
                          SRPRB  71 kaksslkglvfvvDStidpkevkevAEllye 101
                                       +s+++l+++vD  idpk++ +vA+ + +
  gi|116753690|ref|YP_842808.1| 165 ASGDSARSLIHMVDYGIDPKNIYSVADPMRK 195
                                    34567*********************87654 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 ?   11.7   0.0   5.9e-05      0.18      33      72 ..     125     164 ..     118     178 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.9e-05
                        DUF2399  33 aaadrlgakaaplvctsGqpsaaalelldklaaagarlrY 72 
                                     ++d+++++ + +v+t+G p   + ++ld+l++ ga ++ 
  gi|116753690|ref|YP_842808.1| 125 LIVDAVDMTVPYIVSTGGVPFPGVRSVLDELRDMGADIYI 164
                                    6899********************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); 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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2047.70
//
Query:       gi|116753691|ref|YP_842809.1|  [L=294]
Description: hypothetical protein Mthe_0376 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00084   19.3   0.0     0.0014   18.5   0.0    1.5  1  Lactamase_B_3  Beta-lactamase superfamily domain
     0.0015   18.1   0.2     0.0027   17.3   0.2    1.5  1  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
       0.66    9.9   6.7        7.6    6.5   6.9    2.2  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 !   18.5   0.0   2.4e-07    0.0014      11      67 ..      19      96 ..      13     192 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.4e-07
                  Lactamase_B_3 11 lletagarilvDPf..........kanlgyeppa...................eeaDlvlisqaledHahletlkqlaenvk 63
                                    le +g r+++DP                    +                   e+ D++++++ + dH +++       ++ 
  gi|116753691|ref|YP_842809.1| 19 CLEARGLRVMIDPAvslgprryglP--------PhpieldrlnttwqdvrglaESSDILIVTHYHYDHHNPNDPDLYRGKIV 92
                                   6899*********966665544440........34455666666666666777***************99885444344555 PP

                  Lactamase_B_3 64 vlee 67
                                   ++++
  gi|116753691|ref|YP_842809.1| 93 YIKD 96
                                   5554 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 !   17.3   0.2   4.5e-07    0.0027      24     164 ..      59     195 ..      26     234 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.5e-07
                                    SS--..SEEEEE-SS--HHHH..GGGGCCCCC--EEEEEE.EEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEECS CS
                  Lactamase_B_2  24 lrdelppidaVllthaHyDHl..aglltlrelrpkklply.apkgvlavleanfvylaleeepavnvheldwgesfelgd 100
                                     r   ++ d +++th HyDH   ++ ++l +++   + +y  +++ + + +++  ++ +    + +  +++ g++f  g+
  gi|116753691|ref|YP_842809.1|  59 VRGLAESSDILIVTHYHYDHHnpND-PDLYRGK---I-VYiKDPKNRINFSQKRRAHYFLSRIEDADIQIADGGEFGHGP 133
                                    344455789************8555.8888843...3.442445555544444444443333223334556688888886 PP

                                    TTEEEEEE.EE-EE--CTCCE-TTTSEEEEEE....CTTEEEEEESS-S..---HHHHHHHCT.-SEEEEE- CS
                  Lactamase_B_2 101 ggleitat.parhksgrrldrnagdtlGlrie....gggkrvyyigDtg..yipeeigerlgg.adlllldi 164
                                      l+i++  p+ h++g+         lG++ie     g+ +v+y+ D++   +++++   l+  +  l+ld+
  gi|116753691|ref|YP_842809.1| 134 --LTIRFSqPVYHGTGN--------RLGYVIEasisCGEDKVVYTSDVEgpAMDDQVTFILEEsPRTLILDG 195
                                    ..555553288888888........8999999888778899******9955566776666665456666664 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   6.9    0.0013       7.6      46     153 ..      67     173 ..      13     196 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0013
                                    EEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHHCCHH..TTCHCGCCEEEEETTTEECCCTEEEE CS
                    Lactamase_B  46 davilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeaddaasrkgll..lagvsadkpdvdeeeldgnaggrral 123
                                    d +i+TH+H+DH   ++    + +++ ++ ++   ++    +  ++     +  +a   + + +++ ++  +++++ + +
  gi|116753691|ref|YP_842809.1|  67 DILIVTHYHYDHHNPNDPDLYRGKIVYIKDPKNRINFSQKRRAHYFLS---RieDADIQIADGGEFGHGPLTIRFSQPVY 143
                                    7789********877777777777777777777777777777554444...23344455555555555555566666666 PP

                                    EHECTTSTSCCEEEEEETTCCEEEECTTTS CS
                    Lactamase_B 124 yvtggpghghghgvveygggkvlftGDall 153
                                    + tg  +   + +++++g++kv++t D+  
  gi|116753691|ref|YP_842809.1| 144 HGTGNRLGYVIEASISCGEDKVVYTSDVEG 173
                                    666666666666677777777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1984.44
//
Query:       gi|116753692|ref|YP_842810.1|  [L=309]
Description: ABC transporter related [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.9e-28   97.5   0.0    2.2e-27   96.2   0.0    1.6  2  ABC_tran  ABC transporter
    2.9e-14   53.6   0.9    1.8e-07   31.3   0.0    2.2  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    5.2e-06   27.1   0.1    7.6e-06   26.6   0.1    1.3  1  AAA_23    AAA domain
    3.8e-05   24.3   0.0    6.3e-05   23.6   0.0    1.4  1  DUF4162   Domain of unknown function (DUF4162)
    8.5e-05   22.4   0.1       0.39   10.4   0.3    2.1  2  AAA_15    AAA ATPase domain
    0.00048   19.8   0.1    0.00094   18.9   0.1    1.4  1  AAA_29    P-loop containing region of AAA domain
    0.00055   19.4   0.0        0.5    9.8   0.0    2.8  3  SMC_N     RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
      0.029   14.4   0.0        1.8    8.6   0.0    2.4  2  AAA_14    AAA domain
      0.049   12.7   0.0      0.078   12.0   0.0    1.3  1  T2SSE     Type II/IV secretion system protein
      0.077   12.8   0.0       0.15   11.9   0.0    1.4  1  DEAD      DEAD/DEAH box helicase
       0.13   12.3   0.0       0.46   10.5   0.0    1.9  1  AAA_5     AAA domain (dynein-related subfamily)
       0.16   11.7   0.0       0.37   10.5   0.0    1.6  1  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 !   96.2   0.0   1.5e-30   2.2e-27       1     136 [.      25     168 ..      25     169 .. 0.98
   2 ?   -1.9   0.0       2.9   4.4e+03      62      80 ..     218     262 ..     210     295 .. 0.56

  Alignments for each domain:
  == domain 1  score: 96.2 bits;  conditional E-value: 1.5e-30
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                    lk+++l +   e+ +i+G+nG+GK+tLl++++ l  p++Ge+++ g d ++ +++++rk i + + +p++   ltv+en 
  gi|116753692|ref|YP_842810.1|  25 LKDINLLIDGEEIFGILGPNGSGKTTLLSIFSTLIYPDSGELTILGIDARR-NTHEVRKLINISTGKPNFPWSLTVKENl 103
                                    799***********************************************9.9999************************ PP

                                    ............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    ............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                e d+ ++  +++++l + +dt+     ++LS G kqr++la+a+l+ pkll+lDEpt
  gi|116753692|ref|YP_842810.1| 104 rhsgmlyglhgrELDRAVDWSMESFELYQYQDTRF----ENLSTGVKQRLSLAKAMLNGPKLLFLDEPT 168
                                    ***********999999*****************9....*****************************9 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.9
                                    EEE-SS..--S-TTSBHHHH........................H CS
                                    xxxxxx..xxxxxxxxxxxx........................x RF
                       ABC_tran  62 gvlpqe..pqlfpeltvren........................e 80 
                                    +++ q+  ++l+++l+++e+                         
  gi|116753692|ref|YP_842810.1| 218 RIIAQDtpARLKRNLKIGERmrirysgnidcdalrsipglisaeI 262
                                    555666666666666666666666655555554444444444441 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 !   20.8   1.0   1.9e-07   0.00028       2      24 ..      38      60 ..      37     119 .. 0.72
   2 !   31.3   0.0   1.2e-10   1.8e-07     219     298 ..     102     200 ..      70     203 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.9e-07
                         AAA_21  2 nvliGpNgsGKSnLLdaldllar 24
                                    ++ GpNgsGK++LL +++ l  
  gi|116753692|ref|YP_842810.1| 38 FGILGPNGSGKTTLLSIFSTLIY 60
                                   689***************88843 PP

  == domain 2  score: 31.3 bits;  conditional E-value: 1.2e-10
                         AAA_21 219 r.....................gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHP...kl 274
                                    +                      +  +e  ++q++ + +lS G+k+ l l+ a+l  +   +ll++DEp +gL+P   ++
  gi|116753692|ref|YP_842810.1| 102 NlrhsgmlyglhgreldravdwSMESFELYQYQDTRFENLSTGVKQRLSLAKAMLNGP---KLLFLDEPTTGLDPqmaQR 178
                                    3444455555555555567777888999999************************988...9*************66666 PP

                         AAA_21 275 lrrllellkelsrngaQviltTHS 298
                                    +r l++ + +    g+ v++tTH 
  gi|116753692|ref|YP_842810.1| 179 TRALVKRIHRD--MGVSVVMTTHY 200
                                    67777777444..4699******5 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.1   5.1e-09   7.6e-06       5      65 ..      12      84 ..      10     157 .. 0.67

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 5.1e-09
                         AAA_23  5 enfrsf....rd..qeidF...skgltlItGpNGaGKTTildAiklaLygetprlsrks.grgfeksdve..i 65
                                   ++f+ +    ++  ++i++   +  ++ I GpNG+GKTT+l  +    y ++++l     + + ++++v+  i
  gi|116753692|ref|YP_842810.1| 12 KGFNTIfrgkKEvlKDINLlidGEEIFGILGPNGSGKTTLLSIFSTLIYPDSGELTILGiDARRNTHEVRklI 84
                                   5666666642222234888999999*******************99999988777654343344455555443 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   4.2e-08   6.3e-05      13      80 ..     236     307 ..     224     308 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 4.2e-08
                                    SEEEEE....-------..---EEEE-TTS-EEEEE--.---------------EEEEEEEE---HHHHHHHH CS
                        DUF4162  13 nrieve....adaeelleepgveeveeeggelelkled.eeaanellkaltsgveirsFeeeePsLndIFiek 80 
                                    +r++++     d ++l+++pg+ + e  +g++ l +++ e++ ++++++  + +ei ++e+eeP L+d+Fie+
  gi|116753692|ref|YP_842810.1| 236 ERMRIRysgnIDCDALRSIPGLISAEISKGRADLVVDKnEATFSRVMRTF-QSAEILELELEEPDLEDVFIEL 307
                                    566666655445789999*********9*9*******889**********.9*******************97 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   0.3   0.00026      0.39      25      47 ..      37      59 ..      24      88 .. 0.78
   2 !   10.0   0.0   0.00034      0.51     291     364 ..     135     199 ..      82     200 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00026
                         AAA_15 25 ltvliGkNnsGKSsilealdlFl 47
                                   +  + G+N+sGK+++l ++  ++
  gi|116753692|ref|YP_842810.1| 37 IFGILGPNGSGKTTLLSIFSTLI 59
                                   66789************998776 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00034
                         AAA_15 291 elplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                    ++ +++ ++Gv++ l+l+   l+          +++l+++EP + L pq+ +    l k++ +d    v++tTH
  gi|116753692|ref|YP_842810.1| 135 DTRFENLSTGVKQRLSLAKAMLN---------GPKLLFLDEPTTGLDPQMAQRTRALVKRIHRDMGVSVVMTTH 199
                                    66778888888888877644433.........3577************************************** 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 !   18.9   0.1   6.3e-07   0.00094      22      50 ..      35      63 ..      24      67 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 6.3e-07
                         AAA_29 22 kgatlltGpsGsGKSTllDAiqalLvpak 50
                                   ++++ + Gp+GsGK+Tll  +++l++p++
  gi|116753692|ref|YP_842810.1| 35 EEIFGILGPNGSGKTTLLSIFSTLIYPDS 63
                                   447789********************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 !    9.8   0.0   0.00034       0.5      26      41 ..      37      52 ..      23      59 .. 0.85
   2 !    6.2   0.0     0.004         6     136     211 ..     140     210 ..      75     218 .. 0.81
   3 ?   -0.7   0.0      0.53   7.9e+02     105     133 ..     263     291 ..     257     295 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00034
                                   EEEEEESTTSSHHHHH CS
                                   xxxxxxxxxxxxxxxx RF
                          SMC_N 26 ftaivGpNGSGKsnll 41
                                   +  i+GpNGSGK+ ll
  gi|116753692|ref|YP_842810.1| 37 IFGILGPNGSGKTTLL 52
                                   5679*********987 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.004
                                    CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklvgv 211
                                    +LS G k+     L +A  + +   l +lDe    LD +  ++   l+k+ + ++ + v+  ++ m  +a++l+g+
  gi|116753692|ref|YP_842810.1| 140 NLSTGVKQ----RLSLAKAMLNGPKLLFLDEPTTGLDPQMAQRTRALVKRIHRDMGVSVVMTTHYM-PEAEELCGM 210
                                    66666555....455677788899999**********************99999999888766555.556666665 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.53
                                    TTSEEEEEETTEEE-HHHHHHHHHCTT-S CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 105 rkgeseykingkevtkkevsellesagis 133
                                    +kg+ +  ++++e+t++ v++ ++sa+i 
  gi|116753692|ref|YP_842810.1| 263 SKGRADLVVDKNEATFSRVMRTFQSAEIL 291
                                    577889999*************9999985 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0    0.0012       1.8       3      27 ..      36      59 ..      34      89 .. 0.71
   2 ?    3.3   0.0     0.054        81      49      90 ..     138     190 ..     109     198 .. 0.55

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0012
                         AAA_14  3 kilvitGaRrvGKTtllkqlikell 27
                                   +i  i G+  +GKTtll  ++++l+
  gi|116753692|ref|YP_842810.1| 36 EIFGILGPNGSGKTTLLS-IFSTLI 59
                                   6889************85.445555 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.054
                         AAA_14  49 pekllelilek..lke....ekktylflDEi......qevpewekalkslvdeg 90 
                                    +e+l + ++++  l +    ++ ++lflDE       q++++ +  +k+++++ 
  gi|116753692|ref|YP_842810.1| 138 FENLSTGVKQRlsL-AkamlNGPKLLFLDEPttgldpQMAQRTRALVKRIHRDM 190
                                    33444444444222.13466799*******622222244466666666666554 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 ?   12.0   0.0   5.2e-05     0.078     122     197 ..      28     104 ..      15     106 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.2e-05
                          T2SSE 122 lrkavrerglilvsGgTgsGKttllyallkeinksderivtvE.DpvEiqleganqvqlnakkakvtfadllraaLR 197
                                    ++  +  + ++ + G+ gsGKttll +  + i  ++ ++ ++  D++    e  + +++ + k + + +  +++ LR
  gi|116753692|ref|YP_842810.1|  28 INLLIDGEEIFGILGPNGSGKTTLLSIFSTLIYPDSGELTILGiDARRNTHEVRKLINISTGKPNFPWSLTVKENLR 104
                                    55566667777789**************9999888555544422666666666777777766666666666666666 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   9.8e-05      0.15       8     110 ..      28     230 ..      22     244 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.8e-05
                                    HHHHHTTCEEE.EEESTTSSHHHHHHHHHHHHHHHS...TTSTS.................................... CS
                                    xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx...xxxxx.................................... RF
                           DEAD   8 iplilgggdvl.vaaeTGsGKTlaflipvlqivyet...kgktg.................................... 47 
                                    i+l+++g++++ + ++ GsGKT+  +i     +y +       +                                    
  gi|116753692|ref|YP_842810.1|  28 INLLIDGEEIFgILGPNGSGKTTLLSIFST-LIYPDsgeL---Tilgidarrnthevrklinistgkpnfpwsltvkenl 103
                                    6777788888757899********999888.444432440...2666666666789999999****************** PP

                                    .......................................................-EEEEE.ESSHHHHHHHHHHHHHHT CS
                                    .......................................................xxxxxx.xxxxxxxxxxxxxxxxxx RF
                           DEAD  48 .......................................................pkaliv.ePtreLaeqtlnnlkkfk 71 
                                                                                           pk l++ ePt+ L  q++++++ + 
  gi|116753692|ref|YP_842810.1| 104 rhsgmlyglhgreldravdwsmesfelyqyqdtrfenlstgvkqrlslakamlngPKLLFLdEPTTGLDPQMAQRTRALV 183
                                    *******************************************************88888769***************** PP

                                    TTST..SEEEEEETTSSHHHHHHHH.......HTTCSEEEEEHHHHHH CS
                                    xxxx..xxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxx RF
                           DEAD  72 kyid..lrvlliiggvaardqlskl.......dngvdivvgtpgrldd 110
                                    k i+  + v+++++ + +  + ++l       ++g  i   tp rl +
  gi|116753692|ref|YP_842810.1| 184 KRIHrdMGVSVVMT-THYMPEAEELcgmiaflKEGRIIAQDTPARLKR 230
                                    *8764444443333.344444444423233324555555666666655 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00031      0.46       4      50 ..      40      89 ..      38     101 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00031
                                   EE--SSSSHHHHHHHGGGGB...S--EEEEE--TT--HHHHH--B--... CS
                          AAA_5  4 LvGppGtgKselaerlaaal...nreveyvqltrdtteedlkgrreikng 50
                                   ++Gp G+gK++l   ++ ++     e+++  + ++ ++ +++  ++i+ g
  gi|116753692|ref|YP_842810.1| 40 ILGPNGSGKTTLLSIFSTLIypdSGELTILGIDARRNTHEVRKLINISTG 89
                                   68******************988888888888888888888888887655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00025      0.37       6      43 ..      39      83 ..      36     106 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00025
                         AAA_24  6 liyGpsgiGKTtlakel.......gpkplfidtekGlksldadkf 43
                                    i Gp+g+GKTtl++ +         +  ++ +++  +  +++k+
  gi|116753692|ref|YP_842810.1| 39 GILGPNGSGKTTLLSIFstliypdSGELTILGIDARRNTHEVRKL 83
                                   699************995555555555555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); 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: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2149.59
//
Query:       gi|116753693|ref|YP_842811.1|  [L=261]
Description: ABC-2 type transporter [Methanosaeta thermophila PT]
Scores for complete 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   42.5  24.5    4.8e-11   42.5  24.5    1.7  2  ABC2_membrane  ABC-2 type transporter
  ------ inclusion threshold ------
       0.21   11.1   0.2        0.3   10.6   0.2    1.2  1  ADC            Acetoacetate decarboxylase (ADC)


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 !   42.5  24.5   5.4e-15   4.8e-11       9     208 ..      16     217 ..       9     219 .. 0.81
   2 ?   -0.8   0.1     0.092   8.3e+02      53      82 ..     227     256 ..     216     259 .. 0.60

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 5.4e-15
                  ABC2_membrane   9 reflqrwrdpslgllwrliqplllalvfgtvfgnlg..nsedglnrpgllffsvlflafsaltsvapvferergvlerel 86 
                                    ++++  +r+ ++  +  ++ pl+ +l +g++   lg    + ++  +g+++ ++l ++ ++  + +++f++  ++++  +
  gi|116753693|ref|YP_842811.1|  16 KNWIISKRNVFTV-FELVFWPLISLLSIGLMTRFLGvgGDTVAFLLVGAIGLTILQIC-QIDVAYVLLFDMWSKSIKNTF 93 
                                    5566566666444.77788888888888888888776333333357************.5555566************** PP

                  ABC2_membrane  87 vsplyslsayvlakvlvelpvsllqalifllivyflvgldls..rf..flflllllltalaasslgllisalapsfedas 162
                                    vsp+ +    vl+ +l+ +++++++ +i+++i+ +l+g+d     f  +l++l+ ++ + a++++ ++is+l+  ++  +
  gi|116753693|ref|YP_842811.1|  94 VSPV-RGYHLVLGALLFGMVRGTFAFTILVVISRILFGFDFLagGFhtVLIFLAGVFAVSAIIGMIVCISILLFGQKADV 172
                                    ****.************************************986446677777777777777778888888886655544 PP

                  ABC2_membrane 163 qlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrsn 208
                                         +  +++l sG+++p++ +p+ lq +a++ Plty++e +rs+
  gi|116753693|ref|YP_842811.1| 173 AA-WSLSGVIMLISGIYYPVSVLPEPLQLMARAVPLTYFLEYYRSA 217
                                    44.556667789***********99*****************9987 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.092
                  ABC2_membrane  53 pgllffsvlflafsaltsvapvferergvl 82 
                                    +g+l+ ++ ++a +++ ++ + + r+ g+l
  gi|116753693|ref|YP_842811.1| 227 IGVLMVAAYMIAGLIVLEMTIERARKTGIL 256
                                    566666666666666666666666666665 PP

>> ADC  Acetoacetate decarboxylase (ADC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2   3.3e-05       0.3      35      76 ..     192     233 ..     191     250 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 3.3e-05
                                    TTSBTTEEECSTSEEEEEEEEEEEECTTTCEEEEEEEEEEEE CS
                            ADC  35 allPepLelaerplvavyfaeypdssfgggqYneagivvpvr 76 
                                    ++lPepL+l +r++   yf ey  s++g+g++n ++ v++v 
  gi|116753693|ref|YP_842811.1| 192 SVLPEPLQLMARAVPLTYFLEYYRSAYGFGDHNIVIGVLMVA 233
                                    58****************************888777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       979  (0.0546043); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); 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: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1939.52
//
Query:       gi|116753694|ref|YP_842812.1|  [L=885]
Description: ATPase, P-type (transporting), HAD superfamily, subfamily IC [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-52  176.1   0.4    4.9e-52  176.1   0.4    3.6  4  E1-E2_ATPase     E1-E2 ATPase
    3.7e-40  137.6   2.8    3.7e-40  137.6   2.8    2.4  4  Cation_ATPase_C  Cation transporting ATPase, C-terminus
    4.8e-22   79.3   0.6    7.2e-21   75.4   0.6    2.3  1  Hydrolase        haloacid dehalogenase-like hydrolase
    2.2e-20   72.1   0.2    1.8e-18   66.0   0.0    2.6  2  Cation_ATPase_N  Cation transporter/ATPase, N-terminus
    1.2e-18   66.9   0.0    2.7e-18   65.8   0.0    1.6  1  Cation_ATPase    Cation transport ATPase (P-type)
    7.9e-05   23.1   0.1    0.00016   22.1   0.1    1.5  1  HAD              haloacid dehalogenase-like hydrolase
    0.00082   19.2   1.2     0.0058   16.4   0.8    2.2  2  Hydrolase_3      haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.049   13.1   0.0          3    7.3   0.0    2.2  2  Peptidase_A3     Cauliflower mosaic virus peptidase (A3)


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.3      0.37   8.2e+02     111     141 ..      49      76 ..      42      95 .. 0.58
   2 !  176.1   0.4   2.2e-55   4.9e-52       2     181 .]     111     302 ..     110     302 .. 0.99
   3 ?   -1.4   0.3      0.63   1.4e+03      94     140 ..     660     701 ..     654     719 .. 0.50
   4 ?    0.1   0.9      0.22   4.9e+02     106     157 ..     816     868 ..     751     870 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.37
                                    HHHHHHHHHHHHHHHHHHHHHHHHHS-STTT CS
                   E1-E2_ATPase 111 lqkkldklgkvlvpvvlliallvflialllg 141
                                    +   l+++ +++v+v +++a++ +l     +
  gi|116753694|ref|YP_842812.1|  49 VRILLRQFENYMVIVLMAAAVISWLSG---E 76 
                                    556667777777777777766666654...3 PP

  == domain 2  score: 176.1 bits;  conditional E-value: 2.2e-55
                                    SS--EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-S.EEE-TTTS---S-EE-............G-TT CS
                   E1-E2_ATPase   2 llpptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsa.evdesaLTGEslpvek............ekgd 68 
                                    + +p+a+v+r+g++ + +a++lvpGD++ l+agd++paD+ri++  a +  es+LTGEs+pv+k            ++ +
  gi|116753694|ref|YP_842812.1| 111 MVAPEARVFRSGKLITLPARDLVPGDLIYLEAGDIIPADARILDAAAlKTVESSLTGESTPVRKspdpveegaplaDRSS 190
                                    7899***********************************************************************99*** PP

                                    EE-TT-EEEE-EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHH CS
                   E1-E2_ATPase  69 mvfsGtvvvsgeakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeal 148
                                    mvf+Gt+v+ g+ kavVt tg+dte+g+i  +++e+ ++++pl+  l++l+k l+++v+++al+vf i++++g ++ ++l
  gi|116753694|ref|YP_842812.1| 191 MVFMGTMVIYGNGKAVVTSTGSDTEIGRISGMIQET-PAEPPLKIRLQQLSKSLAVLVFIAALVVFSIQVYRGYPVLDTL 269
                                    ***********************************9.******************************************* PP

                                    HHHHHHHHHHS-TTHHHHHHHHHHHHHHHHHHT CS
                   E1-E2_ATPase 149 lralallvaaiPcaLplavplalalgarrlakk 181
                                    l a al+va iP+aLp +v+lala+g++++a++
  gi|116753694|ref|YP_842812.1| 270 LIAAALAVAGIPEALPFVVTLALAYGTQSMARR 302
                                    *******************************96 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.63
                                    TTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STT CS
                   E1-E2_ATPase  94 lgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialll 140
                                    +++i+++vee +    ++ ++++k ++++ +v ++ +++++ ia+l+
  gi|116753694|ref|YP_842812.1| 660 FATIVAAVEEGR----RIYENIRKASSYMLAVTFAEVAVIL-IAVLV 701
                                    556666666664....3444444444444433333322222.22222 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.22
                                    ----HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTT.HHHHHHHHHHHH CS
                   E1-E2_ATPase 106 skktplqkkldklgkvlvpvvlliallvflialllgksla.eallralallva 157
                                     +++ l  ++++l++vl+++ + ++  +f +++l+ +s+   +l+++++++va
  gi|116753694|ref|YP_842812.1| 816 GNRKLLAGIVTSLASVLMVIYVPVFQGAFETLPLTMNSWLqVWLVSTIVIVVA 868
                                    56666777888999999999999999998888887777775777778877776 PP

>> Cation_ATPase_C  Cation transporting ATPase, C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.3         2   4.5e+03     123     139 ..      77      93 ..      57     100 .. 0.59
   2 ?   -3.7   0.4       3.8   8.4e+03      63     142 ..     249     256 ..     236     290 .. 0.56
   3 ?   -2.3   0.1       1.4     3e+03     120     145 ..     675     701 ..     660     703 .. 0.66
   4 !  137.6   2.8   1.7e-43   3.7e-40       1     181 [.     704     873 ..     704     874 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2
                Cation_ATPase_C 123 fsnkllllaillslllq 139
                                    +sn +++l+ill ++++
  gi|116753694|ref|YP_842812.1|  77 RSNAIVVLGILLFIAIL 93 
                                    45555555555555444 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3.8
                Cation_ATPase_C  63 lvtllvffltlllfgisekenklssnyaqtmaFitlvlsqifnalnlrsrreslfkfsglfsnkllllaillslllqvli 142
                                    +++                                                                        l+v+ 
  gi|116753694|ref|YP_842812.1| 249 IAA------------------------------------------------------------------------LVVFS 256
                                    111........................................................................11111 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.4
                Cation_ATPase_C 120 sglf.snkllllaillslllqvlivyv 145
                                    ++++  + ++l +++++++++++ v+v
  gi|116753694|ref|YP_842812.1| 675 ENIRkASSYMLAVTFAEVAVILIAVLV 701
                                    455545678888888888777776665 PP

  == domain 4  score: 137.6 bits;  conditional E-value: 1.7e-43
                Cation_ATPase_C   1 plplsaiqiLwinLvtDllpalaLaleppekdimkrpPrkkkepliskkmlrriliqgllqalvtllvffltlllfgise 80 
                                    p pl a+qiLwin+v + +pa+ La+ep+ ++im+++Pr++kep++s+ +l+++++ ++ +++ tl +f+l++       
  gi|116753694|ref|YP_842812.1| 704 PAPLLALQILWINVVAEDFPAIGLAVEPARSGIMNERPRNPKEPILSRDLLIYTIGTSAAMLIGTLGLFLLNID---GGL 780
                                    78*******************************************************************98887...333 PP

                Cation_ATPase_C  81 kenklssnyaqtmaFitlvlsqifnalnlrsrreslfkfsglfsnkllllaillslllqvlivyvpglnavfgtaplsle 160
                                            ya+t+aF +l ++ i na+++rs ++s+++ ++   n+ ll +i+ sl+ +++++yvp+++ +f+t pl+++
  gi|116753694|ref|YP_842812.1| 781 G-------YARTVAFASLGICAIYNAYSSRSFHHSVLQ-MNPMGNRKLLAGIVTSLASVLMVIYVPVFQGAFETLPLTMN 852
                                    3.......5*****************************.77779************************************ PP

                Cation_ATPase_C 161 ewlialllalvvllvdelvKl 181
                                    +wl + l++ +v++v+e++K+
  gi|116753694|ref|YP_842812.1| 853 SWLQVWLVSTIVIVVAEVLKR 873
                                    ******************995 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.4   0.6   3.2e-24   7.2e-21       2     210 .]     319     634 ..     318     634 .. 0.67

  Alignments for each domain:
  == domain 1  score: 75.4 bits;  conditional E-value: 3.2e-24
                                    SEEEEESBTTTBCHHHHHHHHHHHH..........................CHHHHHHHHHH................HH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx..........................xxxxxxxxxxx................xx RF
                      Hydrolase   2 ktvvfDkdGTLttgepsvedvivsa..........................alalaaaletg................se 39 
                                    ++++ Dk+GTLt+ge+ v++v++                            + a ++ + tg                  
  gi|116753694|ref|YP_842812.1| 319 TVICTDKTGTLTRGEMTVREVWCGCrvevtgsgyvpegvfrvngseidlgsDAAVRETIITGalcnnseivfedgwhvV- 397
                                    5899*********************666666665555555555555544443333333333333333333333333332. PP

                                    CHHHHHHHHHHHHHHHHHHHHHHETTTE............HHHHTHHHHHHHH....HCHHHHHHHHHHHHHHCHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxx............xxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase  40 hpigkalvaaakarsgaltgfatfigrg............ayaigkpewltal....dippdlgaaigsaqsqgrtvall 103
                                                               g            ++    +e+ ++       ++  ++++  + + g  v ++
  gi|116753694|ref|YP_842812.1| 398 ---------------------------GdptegalivlarKAGLDVREMCREVteypFASDTRRMTTVHECDSGLRVSMK 450
                                    ...........................03344455544443333333333333333222222222222222222222222 PP

                                    ................................................................TTHHHHHHHHHHTHHB CS
                                    ................................................................xxxxxxxxxxxxxxxx RF
                      Hydrolase 104 ................................................................qaralavftiadplkv 119
                                                                                                    +    ++f + dp  +
  gi|116753694|ref|YP_842812.1| 451 gavevvlercaymmdstglkpltdvdrrrileiademagralrvlaaafkrieseepdrevlesDLIFTGLFGMMDP--P 528
                                    555555555555555555555555555666666666666666666666888888888888887777888899999**..* PP

                                    HTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT...........GGGE.SEEEEHHCES...STTTSHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxx.xxxxxxxxxx...xxxxxxxxxxxxxx RF
                      Hydrolase 120 kpeaaeavasLkaagievvlltgdnpetaeraanqlG...........ddyf.daviasdiet...vakpspegkvaair 184
                                    ++e+  a+   k+agi+ v++tgd+++tae++a++l             d + d +++  ie    ++ +  e+k ++i+
  gi|116753694|ref|YP_842812.1| 529 RDEVCGAIDVCKKAGIRPVMITGDHKRTAEAIASELRmlngevldgseLDSMsDQELSDRIERisvFSRATAEHKMRIIK 608
                                    ************************************99*9999999994455599999999999**************** PP

                                    HHTSTGGGEEEEESSHHHHHHHHHTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 185 eLqgkpeevamVGDgvnDaaalaaAg 210
                                     L++ ++ vam GDgvnDa+al+ A+
  gi|116753694|ref|YP_842812.1| 609 ALKEHGHVVAMTGDGVNDAPALRSAD 634
                                    ************************98 PP

>> Cation_ATPase_N  Cation transporter/ATPase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.0   0.0   8.1e-22   1.8e-18       1      69 []       4      71 ..       4      71 .. 0.99
   2 ?    3.3   0.3     0.029        65      38      68 ..     223     253 ..     222     254 .. 0.89

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 8.1e-22
                Cation_ATPase_N  1 ehalsleevlekLetdlenGLtqaeaaerlkkyGpNelkekkkkslwvkllkqftnplvilLlvaalvs 69
                                   +hal++ee+l+ L+ + ++GLt+aeaa rl+++GpN l+    +  +++ll+qf n +vi+L++aa++s
  gi|116753694|ref|YP_842812.1|  4 WHALPPEEALKLLN-SGPDGLTDAEAASRLERFGPNDLARISGPGPVRILLRQFENYMVIVLMAAAVIS 71
                                   9************9.9***************************************************98 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.029
                Cation_ATPase_N  38 lkekkkkslwvkllkqftnplvilLlvaalv 68 
                                    ++e + ++ +++ l+q++  l  l ++aalv
  gi|116753694|ref|YP_842812.1| 223 IQETPAEPPLKIRLQQLSKSLAVLVFIAALV 253
                                    578899***********99999999999987 PP

>> Cation_ATPase  Cation transport ATPase (P-type)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.8   0.0   1.2e-21   2.7e-18       1      90 [.     381     462 ..     381     463 .. 0.92

  Alignments for each domain:
  == domain 1  score: 65.8 bits;  conditional E-value: 1.2e-21
                  Cation_ATPase   1 ilcNsaafsensekdevkllGnktEsALlvlaeklgldteelreetkkvqeipFnssrKrmsvvlklepekkvrlyvKGA 80 
                                    +lcN++++     +d ++++G++tE AL+vla+k+gld+   re   +v e+pF s+ +rm++v++ +  +++r+ +KGA
  gi|116753694|ref|YP_842812.1| 381 ALCNNSEI---VFEDGWHVVGDPTEGALIVLARKAGLDV---REMCREVTEYPFASDTRRMTTVHECD--SGLRVSMKGA 452
                                    69**9999...999*********************8886...5567789*****************76..********** PP

                  Cation_ATPase  81 peiilkrCth 90 
                                     e++l+rC +
  gi|116753694|ref|YP_842812.1| 453 VEVVLERCAY 462
                                    ********87 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.1   7.2e-08   0.00016      84     188 .]     518     631 ..     459     631 .. 0.63

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 7.2e-08
                            HAD  84 k.....lldp......galellaahraaGdrvvvvSgglrplvepllaelg..adevlat.elevdd..rltgelglegk 147
                                           +dp      ga ++++   +aG+r v+++g +++ +e+++ el     evl+  el++     l+ +  +e  
  gi|116753694|ref|YP_842812.1| 518 FtglfgMMDPprdevcGAIDVCK---KAGIRPVMITGDHKRTAEAIASELRmlNGEVLDGsELDSMSdqELSDR--IERI 592
                                    13444346666775667788888...*********************888867566666657766667788888..6666 PP

                            HAD 148 pvrgegkv....aalrewlaaegegidleevvay.GDspsDlpllr 188
                                    +v+ ++++    + +++ l+++g+      vva  GD+++D p+lr
  gi|116753694|ref|YP_842812.1| 593 SVFSRATAehkmRIIKA-LKEHGH------VVAMtGDGVNDAPALR 631
                                    66665555211144444.333443......78888*********98 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.098   2.2e+02      22      94 ..     534     613 ..     528     619 .. 0.64
   2 !   16.4   0.8   2.6e-06    0.0058     196     248 ..     607     660 ..     604     667 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.098
                                    HHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEEEGGGTEEECTTTEEEEE--B-.........HHHHHHHHHHHH CS
                    Hydrolase_3  22 eaikklkekgikvviATGRslravlpvleelgldlpvialNGaliddekgkilykstis.........kedvkeiikllk 92 
                                     ai  +k++gi  v  TG + r+++ ++ el +      l G+  d  +++ l++ +i+          e+ ++iik+lk
  gi|116753694|ref|YP_842812.1| 534 GAIDVCKKAGIRPVMITGDHKRTAEAIASELRML-NGEVLDGSELDSMSDQELSD-RIErisvfsratAEHKMRIIKALK 611
                                    589999*****************99999999944.33335677666666666532.222222444444555555555555 PP

                                    HT CS
                    Hydrolase_3  93 en 94 
                                    e+
  gi|116753694|ref|YP_842812.1| 612 EH 613
                                    55 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 2.6e-06
                                    HHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETT.S-HHHHHHSSEEE--GGG CS
                    Hydrolase_3 196 akelnisleeviafGDgeNDieMLeaaglgvAmgn.aseevkkaAdyvtksnne 248
                                    +k l+ +   v+  GDg ND + L  a++g+Amg  +++  k+a+d+v ++ n 
  gi|116753694|ref|YP_842812.1| 607 IKALKEHGHVVAMTGDGVNDAPALRSADIGIAMGRtGTDVSKEASDMVLADDNF 660
                                    56666666778889*******************962777778888888887775 PP

>> Peptidase_A3  Cauliflower mosaic virus peptidase (A3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0013         3      27      92 ..     379     446 ..     371     452 .. 0.86
   2 ?    3.4   0.0      0.02        45     110     150 ..     844     882 ..     823     885 .] 0.75

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0013
                   Peptidase_A3  27 tGaslciakkkvipeenWvilkrPke...vkiadkskitiskvikdvd.lkienkifliPivylqesGld 92 
                                    tGa lc  +  v  e+ W ++  P e   +++a k+   +++++++v     +++  ++ +v+  +sGl 
  gi|116753694|ref|YP_842812.1| 379 TGA-LCNNSEIVF-EDGWHVVGDPTEgalIVLARKAGLDVREMCREVTeYPFASDTRRMTTVHECDSGLR 446
                                    665.999999888.*********986555999**************96267999999**********985 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.02
                   Peptidase_A3 110 lervilrkkklyPkeiaklsrkvlvktevlkeslkkrsktl 150
                                     e++ l+ +     ++  +s+ v v +evlk s+ k skt 
  gi|116753694|ref|YP_842812.1| 844 FETLPLTMNSW--LQVWLVSTIVIVVAEVLKRSMLKASKTC 882
                                    46666666554..4566799*****************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (885 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.42
# Mc/sec: 6398.62
//
Query:       gi|116753695|ref|YP_842813.1|  [L=297]
Description: aldolase [Methanosaeta thermophila PT]
Scores for complete 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  165.6   0.0    1.7e-48  165.3   0.0    1.1  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 !  165.3   0.0   9.3e-53   1.7e-48       2     235 .]      32     267 ..      31     267 .. 0.98

  Alignments for each domain:
  == domain 1  score: 165.3 bits;  conditional E-value: 9.3e-53
                                    EEEEECCSHHHHHHHHCTSS..HHHHHHHHHHHHHHGGGSSEEEEETTTHHHHHHCSCTTSEEEEETECSSCCTTSTTEE CS
                           DeoC   2 vilavDqrvankddtasaqn..eqledlkalvkealtpgasavlldpgviasaskeyakdiallvkldkgtyllkskqrd 79 
                                    +++a Dq+v++ +d++  +   e+ +d+++l++ a ++ ++++++++g+ia++ ++y  ++++lvkl+++t l+k++q+d
  gi|116753695|ref|YP_842813.1|  32 MLFAGDQKVEHLNDDFYGPGisEDDADPEHLFRIASRGRIGVFATQLGLIARYGMDYP-EVPYLVKLNSKTNLVKTSQAD 110
                                    789**************999**************************************.9******************** PP

                                    EE.....TTCHHHHHHHTT-SEEEEEEEEHTTTTCHHHHHHHHHHHHHHHHHHHTEEEEEEEEE-CTTBSSTTCHHHHHH CS
                           DeoC  80 vd.....evasveeakalGAdavkvvvyyradgseeeqqklaeikrvkeacheeglplilelylrdeaikdekvdpdlva 154
                                    ++     +v +v e+ + ++  +  v y+ + gse e  +l+e ++v  ++h +gl+++l++y+r++a+kde+ dp+l+a
  gi|116753695|ref|YP_842813.1| 111 PLsrawlDVSQVMEFRRESGLRILGVGYTVYPGSEHEVVMLREAAQVVHEAHRHGLVVVLWMYPRGKAVKDER-DPHLIA 189
                                    *************************************************************************.****** PP

                                    HHHHHHTCCT-SEEEE--SSCC.B.HHHHHHHHHHHHHCHSSTEEEEETTS..SHHHHHHHHHHHHHHHTHCEEEESHHH CS
                           DeoC 155 eAarvsaelGaDiiKvevpkevvnateedaevfkdvikaapvpgvvlsGGv..seedfletvedAvkeagasGvlsGRai 232
                                     A  v+a lG+D++Kv++p     + e+ a +f++++ aa   +v+++GG+  + e+fl+ ++++++ +gasG+++GR+i
  gi|116753695|ref|YP_842813.1| 190 GACGVAAALGSDFVKVNYP-----KAENPALAFREAVMAAGRTKVICAGGSseDPELFLQRLHEQIHISGASGNATGRNI 264
                                    *******************.....6699999*********9999*******88889************************ PP

                                    HTT CS
                           DeoC 233 fqk 235
                                    +qk
  gi|116753695|ref|YP_842813.1| 265 HQK 267
                                    *97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 2111.27
//
Query:       gi|116753696|ref|YP_842814.1|  [L=244]
Description: hypothetical protein Mthe_0381 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); 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: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1915.02
//
Query:       gi|116753697|ref|YP_842815.1|  [L=211]
Description: hypothetical protein Mthe_0382 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.41    8.9   1.3       0.55    8.5   1.3    1.1  1  RAP1      Rhoptry-associated protein 1 (RAP-1)


Domain annotation for each model (and alignments):
>> RAP1  Rhoptry-associated protein 1 (RAP-1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   1.3     3e-05      0.55     104     158 ..     123     177 ..     110     186 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 3e-05
                           RAP1 104 sasaaaileeddskddlefkasqsvvktskpkststeslksssdskskasaksnv 158
                                    s    ail + d+ +    k +qs + t++p+st+t+s+ +s ds+    + +++
  gi|116753697|ref|YP_842815.1| 123 SGEFDAILINPDTSGYTPVKEAQSDIVTTQPESTTTSSNTTSVDSSETQGTGAQS 177
                                    56677999999*******************************9998776555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); 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 0.28s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1509.62
//
Query:       gi|116753698|ref|YP_842816.1|  [L=205]
Description: cyclase family protein [Methanosaeta thermophila PT]
Scores for complete 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   60.9   0.0    2.4e-16   60.2   0.0    1.3  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 !   60.2   0.0   1.3e-20   2.4e-16       1     135 [.       7     139 ..       7     140 .. 0.90

  Alignments for each domain:
  == domain 1  score: 60.2 bits;  conditional E-value: 1.3e-20
                        Cyclase   1 idLshplsedtpvwp.dp....................islsehtGTHlDapgHfae..ktidelpleelvgpavvldvs 57 
                                    +d +h++s++ pv+p dp                    ++ls h+GTH+Dap+Hf++  ++++e+p+e+l+  ++++d  
  gi|116753698|ref|YP_842816.1|   7 YDVTHTMSSSLPVYPgDPgfsrdvlksldrgdpytlsaLHLSAHAGTHIDAPSHFISsgRSVHEIPIERLIMMVALIDS- 85 
                                    799***********6566788899999****************************99999******************9. PP

                        Cyclase  58 akaaaedyeiitaedleaalakqgveikpgdivlirTgwskrledkekyrnpglseeaaewlaekgvkavGvDtlsvD 135
                                          ++ ++++e+l         + +p + v++rTg               +se+aa+  ++ ++k+vG+D+lsvD
  gi|116753698|ref|YP_842816.1|  86 ------GM-VVSPENLSGL------N-PPAEGVMFRTGSLM----------GEISESAARACVDLKLKLVGTDALSVD 139
                                    ......45.67*****554......4.79999*****9753..........24************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       226  (0.0126053); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.29s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 1426.86
//
Query:       gi|116753699|ref|YP_842817.1|  [L=1692]
Description: multi-sensor hybrid histidine kinase [Methanosaeta thermophila PT]
Scores for 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-59  196.2   0.0    8.4e-22   77.4   0.0    7.2  6  PAS_9            PAS domain
    1.3e-52  176.5   0.5    2.4e-11   43.6   0.0    7.6  7  PAS              PAS fold
    9.1e-49  164.3   0.3      1e-13   51.5   0.0    7.8  6  PAS_4            PAS fold
    1.9e-34  117.1   0.2    9.5e-06   25.5   0.0    6.8  6  PAS_8            PAS domain
    2.5e-31  108.5   0.0    5.5e-31  107.4   0.0    1.6  1  HATPase_c        Histidine kinase-, DNA gyrase B-, and HSP90-
    1.7e-27   95.8   0.1    5.6e-27   94.1   0.1    2.0  1  Response_reg     Response regulator receiver domain
    3.4e-25   88.1   1.7    4.8e-10   39.6   0.1    6.8  6  PAS_3            PAS fold
    3.1e-18   65.6   0.2    3.1e-18   65.6   0.2    3.4  3  HisKA            His Kinase A (phospho-acceptor) domain
    8.8e-13   48.3   0.5    3.9e-12   46.3   0.5    2.3  1  Hpt              Hpt domain
    5.5e-12   46.5   0.0    1.8e-05   25.4   0.0    3.4  2  GAF              GAF domain
    2.3e-08   34.2   0.2       0.11   12.7   0.0    5.6  4  PAS_7            PAS fold
      3e-08   34.0   0.5       0.01   16.2   0.0    4.2  3  GAF_2            GAF domain
    0.00036   20.2   0.0        1.4    8.5   0.0    3.1  3  PAS_12           UPF0242 C-terminal PAS-like domain
    0.00052   20.6   0.2          5    7.8   0.0    4.6  4  PAS_10           PAS domain
  ------ inclusion threshold ------
       0.02   15.0   0.0        0.6   10.2   0.0    2.7  2  MLTR_LBD         MmyB-like transcription regulator ligand bin
       0.02   14.7   0.0       0.23   11.3   0.0    2.6  2  PAS_6            YheO-like PAS domain
      0.061   12.5   0.0       0.11   11.6   0.0    1.3  1  Sugar-bind       Putative sugar-binding domain
       0.17   10.8   0.0       0.33    9.8   0.0    1.4  1  PARP_regulatory  Poly A polymerase regulatory subunit


Domain annotation for each model (and alignments):
>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.28   2.8e+02       9      89 ..      13      83 ..       6      93 .. 0.52
   2 !   20.7   0.0   3.8e-07   0.00038       4      85 ..     120     198 ..     117     209 .. 0.70
   3 !   30.1   0.1   4.4e-10   4.4e-07       2     104 .]     402     508 ..     401     508 .. 0.90
   4 !   37.1   0.0   2.9e-12   2.9e-09       1     104 []     531     649 ..     531     649 .. 0.83
   5 !   77.4   0.0   8.4e-25   8.4e-22       2     104 .]     842     949 ..     841     949 .. 0.94
   6 !   19.0   0.0   1.2e-06    0.0012       5     104 .]     976    1078 ..     972    1078 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.28
                          PAS_9  9 pdgrilyaNeaalrllG.....yspeevlgksitdlf..vtdpeanerlraaleqgrkkerevevvlirkngetfwvlltas 83
                                   ++gri y +++a+ l G      s  evlg s+++ +  + +++a +r+ra                i  +g++++  l+++
  gi|116753699|ref|YP_842817.1| 13 EKGRIRYLSRTAEMLSGgiskcRSIHEVLGVSCSESLasAIASDAPSRIRA---------------RIGCSGSEIP--LSVI 77
                                   777777777777777776533333666777777776633222222222222...............2333455555..5555 PP

                          PAS_9 84 pvkddd 89
                                   p++d+d
  gi|116753699|ref|YP_842817.1| 78 PLRDAD 83
                                   555555 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 3.8e-07
                          PAS_9   4 ilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwvlltas 83 
                                    +++  ++ ril+aN  + +llGy pee+    + d++   ++++e+++++++   + e e    +++ +g+ +  + ++s
  gi|116753699|ref|YP_842817.1| 120 FFVEAESRRILDANAVFQELLGYPPEEIHSLTLYDIM---EQDREEIDEIIRHAMSRETESIQAYRTIDGSSIQMKGRFS 196
                                    455668889****************************...6666666666665553444555566666777777666666 PP

                          PAS_9  84 pv 85 
                                    p 
  gi|116753699|ref|YP_842817.1| 197 PT 198
                                    66 PP

  == domain 3  score: 30.1 bits;  conditional E-value: 4.4e-10
                          PAS_9   2 dgili.dnpdgrilyaNeaalrllGyspeevlgksitdlf.....vtdpeanerlraaleqgrkkerevevvlirknget 75 
                                    ++i++  +  g++ ++Ne a +++Gys+ e+lgk +  ++     +t  + +  ++++l++ +   r+  +++++k+ge+
  gi|116753699|ref|YP_842817.1| 402 NSIILrLDRRGNVRFINEFAQQFFGYSESEILGKCVMGTLvpeveSTGRDLRGMIAEILKAPE-DYRTNVNENMKKSGER 480
                                    577878889************************998877789999999999999999999999.5566777899****** PP

                          PAS_9  76 fwvlltaspvkdddgelvgiivilrDite 104
                                    +w+  t  +v +++ge+  i+++ +Dite
  gi|116753699|ref|YP_842817.1| 481 VWIAWTNKTVSSESGEME-ILCVGNDITE 508
                                    **********9**99999.79*******8 PP

  == domain 4  score: 37.1 bits;  conditional E-value: 2.9e-12
                          PAS_9   1 pdgilidnpdgrilyaNeaalrllGyspeevlgks...itdlf...............vtdpeanerlraaleqgrk.ke 61 
                                    pd++l+++ dgr+  +N+a+++++G ++ e+lgk    +   +                 d++ ++  +++ ++g++  +
  gi|116753699|ref|YP_842817.1| 531 PDATLVVDADGRVMAWNRAMEEMTGIQKSEMLGKGdfaY--ALpfhgcrrpmlidlvmRYDEHIASLYENLERRGDTlYA 608
                                    68999999*************************986441..226677777778888866677777777777777776877 PP

                          PAS_9  62 revevvlirkngetfwvlltaspvkdddgelvgiivilrDite 104
                                    + +   l+   g ++w  ++asp+kd+dg++vg+i  +rDite
  gi|116753699|ref|YP_842817.1| 609 YVYVPSLYSGRGAYLW--VKASPLKDSDGRIVGAIESMRDITE 649
                                    7778888888889999..************************8 PP

  == domain 5  score: 77.4 bits;  conditional E-value: 8.4e-25
                          PAS_9   2 dgili...dnpdg..rilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.kerevevvlirknget 75 
                                    d+i+i   d +dg  +i+y+N a+ r++Gy +eevlg++ + l  +++ +++++ ++le+ r+ ++ ++e+v++rk+g++
  gi|116753699|ref|YP_842817.1| 842 DAIVIaapDPSDGmpKIIYVNSAFTRMTGYAREEVLGRYPDFLE-GPETDRSKIMEILEAVRNaQPVNQELVNYRKDGSR 920
                                    67787777777889999********************9988888.*********************************** PP

                          PAS_9  76 fwvlltaspvkdddgelvgiivilrDite 104
                                    fwv+l+++pv+d  ge++++++i+rD te
  gi|116753699|ref|YP_842817.1| 921 FWVELNIFPVRDHMGEVTHWVSIQRDTTE 949
                                    ***************************98 PP

  == domain 6  score: 19.0 bits;  conditional E-value: 1.2e-06
                          PAS_9    5 li.dnpdgrilyaNeaalrllGys..pee.....vlgksitdlf....vtdpeanerlraaleqgrkkerevevvlir 70  
                                      + +   g+ ly N  +++llG    +e+     + g  +   f    + +p+a + lr+++++ +    e e+++++
  gi|116753699|ref|YP_842817.1|  976 YVlNRATGKSLYLNHRFCELLGVEdlEEDlrcgrLDGSAL---FsrigSMHPDAGDSLREIYNRTD----EAEIEIRT 1046
                                     43377889999***********665566644444444444...25559*****************9....99****** PP

                          PAS_9   71 kngetfwvlltaspvkdddgelvgiivilrDite 104 
                                      +g+ +   + a+ ++d++g+++g ++i++D+t+
  gi|116753699|ref|YP_842817.1| 1047 ADGRVIK--VFATDIRDKSGKYFGRLGIFEDVTK 1078
                                     ***5555..***********************95 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.022        22      12      35 ..       6      29 ..       1      33 [. 0.91
   2 !   27.4   0.0   2.5e-09   2.5e-06       3      97 ..     108     199 ..     107     209 .. 0.81
   3 !   41.1   0.1   1.5e-13   1.5e-10       1     113 []     392     506 ..     392     506 .. 0.86
   4 !   36.8   0.0   3.1e-12     3e-09       5      44 ..     525     564 ..     523     647 .. 0.67
   5 !   43.6   0.0   2.5e-14   2.4e-11      22     112 ..     857     946 ..     833     947 .. 0.86
   6 !   11.6   0.0   0.00021      0.21       3      38 ..     964    1000 ..     962    1007 .. 0.91
   7 ?   -2.3   0.0       4.4   4.4e+03      75     113 .]    1040    1076 ..    1020    1076 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.022
                                   SEEEEEETTSBEEEECHHHHHHHS CS
                            PAS 12 dpifvvDedgrilyvNaaaeellG 35
                                   +++ v De+gri y +++ae l G
  gi|116753699|ref|YP_842817.1|  6 PAVYVFDEKGRIRYLSRTAEMLSG 29
                                   7899***************98877 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 2.5e-09
                                    HHHHHHHSSSEEEEEE.TTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEEC CS
                            PAS   3 lraileslpdpifvvD.edgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfkl 81 
                                    +r+ l+  ++++f v  e+ ril +Na ++ellG+++ee+ + +l+d + e+d++e  e+++ +++  +es +  +++  
  gi|116753699|ref|YP_842817.1| 108 YRTALDRCREAVFFVEaESRRILDANAVFQELLGYPPEEIHSLTLYDIM-EQDREEIDEIIRHAMSRETESIQAYRTI-- 184
                                    67778888899999999*****************************655.7788899999999999888888887765.. PP

                                    TTSSEEEEEEEEEEEE CS
                            PAS  82 rdgrpihlevraspvr 97 
                                     dg+ i++  r sp+ 
  gi|116753699|ref|YP_842817.1| 185 -DGSSIQMKGRFSPTE 199
                                    .557777766666655 PP

  == domain 3  score: 41.1 bits;  conditional E-value: 1.5e-13
                                    HHHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHH...HHHHHHHHHHHHTT-ECCCCE CS
                            PAS   1 edlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheedda...elaelleqlleqgeesragei 77 
                                    e++r+++es+ + i+ +D++g++ ++N+ a++++G+s++e+lgk +++ +++e ++   +l+  + + l++ e+ r+   
  gi|116753699|ref|YP_842817.1| 392 ERYRELVESANSIILRLDRRGNVRFINEFAQQFFGYSESEILGKCVMGTLVPEVEStgrDLRGMIAEILKAPEDYRT--- 468
                                    68***************************************************999666555555555555555544... PP

                                    EEEC...TTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                            PAS  78 sfkl...rdgrpihlevraspvrdaggeilgflgvlrdi 113
                                    +++    + g+ +++  ++++v +++ge+ ++l+v++di
  gi|116753699|ref|YP_842817.1| 469 NVNEnmkKSGERVWIAWTNKTVSSESGEM-EILCVGNDI 506
                                    33333367********************9.********8 PP

  == domain 4  score: 36.8 bits;  conditional E-value: 3.1e-12
                                    HHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTS CS
                            PAS   5 aileslpdpifvvDedgrilyvNaaaeellGlsreevlgk 44 
                                    +i+e lpd+++vvD+dgr++ +N+a+ee++G++ +e+lgk
  gi|116753699|ref|YP_842817.1| 525 EIIEFLPDATLVVDADGRVMAWNRAMEEMTGIQKSEMLGK 564
                                    58999**********************************9 PP

  == domain 5  score: 43.6 bits;  conditional E-value: 2.5e-14
                                    BEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEECTTSSEEEEEEEEEEEEETTE CS
                            PAS  22 rilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfklrdgrpihlevraspvrdagg 101
                                    +i+yvN+a+++++G++reevlg+    l  +e+d+    +++++ +++++ +++ ++ ++ dg+ +++e++  pvrd+ g
  gi|116753699|ref|YP_842817.1| 857 KIIYVNSAFTRMTGYAREEVLGRYPDFLEGPETDRSKIMEILEAVRNAQPVNQELVNYRK-DGSRFWVELNIFPVRDHMG 935
                                    79*********************7654444555557778888899999999999999999.******************* PP

                                    EEEEEEEEEEE CS
                            PAS 102 eilgflgvlrd 112
                                    e+++++ + rd
  gi|116753699|ref|YP_842817.1| 936 EVTHWVSIQRD 946
                                    ******99998 PP

  == domain 6  score: 11.6 bits;  conditional E-value: 0.00021
                                     HHHHHHHSSSEEEEEE.TTSBEEEECHHHHHHHSSTH CS
                            PAS    3 lraileslpdpifvvD.edgrilyvNaaaeellGlsr 38  
                                     +r++ es+p +  v++ + g+ ly N+ ++ellG + 
  gi|116753699|ref|YP_842817.1|  964 MRSMTESIPFGFYVLNrATGKSLYLNHRFCELLGVED 1000
                                     899*******************************876 PP

  == domain 7  score: -2.3 bits;  conditional E-value: 4.4
                                     CCEEEECTTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                            PAS   75 geisfklrdgrpihlevraspvrdaggeilgflgvlrdi 113 
                                      ei +++     + + v a+ +rd++g+  g lg++ d+
  gi|116753699|ref|YP_842817.1| 1040 AEIEIRT--ADGRVIKVFATDIRDKSGKYFGRLGIFEDV 1076
                                     3444455..444556788999999999888888888776 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.019        19       2      28 ..       2      28 ..       1      94 [. 0.60
   2 !   24.1   0.0   3.4e-08   3.4e-05       6      71 ..     117     182 ..     112     208 .. 0.80
   3 !   27.4   0.0   3.1e-09   3.1e-06       1     110 []     398     511 ..     398     511 .. 0.93
   4 !   51.5   0.0     1e-16     1e-13       4     109 ..     530     651 ..     527     652 .. 0.89
   5 !   39.0   0.0   7.7e-13   7.7e-10      16     109 ..     857     951 ..     839     952 .. 0.85
   6 ?    5.7   0.0     0.017        17       2     106 ..     969    1077 ..     968    1080 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.019
                          PAS_4  2 dslpdalavldpdgrvlyaNaaaaelf 28
                                   d+ + a++v+d+ gr++y++++a+ l 
  gi|116753699|ref|YP_842817.1|  2 DADQPAVYVFDEKGRIRYLSRTAEMLS 28
                                   56778999************9955422 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 3.4e-08
                          PAS_4   6 dalavl.dpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepieflee 71 
                                    +a++++  +  r+l+aNa ++el+g+ppee+   tl++++ + d++++++++r++++ e+  +++  
  gi|116753699|ref|YP_842817.1| 117 EAVFFVeAESRRILDANAVFQELLGYPPEEIHSLTLYDIMEQ-DREEIDEIIRHAMSRETESIQAYR 182
                                    667777577889**************************9887.**************9876666554 PP

  == domain 3  score: 27.4 bits;  conditional E-value: 3.1e-09
                          PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktla.ellpee..daarleralrrvlegeepiefleelll..p 75 
                                    ++s + +++ ld+ g+v+++N+ a++ fg++  e+lGk++   l+pe    +++l+  +++ l+  e +++    +   +
  gi|116753699|ref|YP_842817.1| 398 VESANSIILRLDRRGNVRFINEFAQQFFGYSESEILGKCVMgTLVPEVesTGRDLRGMIAEILKAPEDYRTNVNENMkkS 477
                                    57889999*********************************8899998*9***************99998877666677* PP

                          PAS_4  76 geerhyelrllPlrdesGevigvlvisrDiTerrr 110
                                    ge++++ ++   +  esGe + +l+++ DiTe+rr
  gi|116753699|ref|YP_842817.1| 478 GERVWIAWTNKTVSSESGE-MEILCVGNDITELRR 511
                                    *******************.************997 PP

  == domain 4  score: 51.5 bits;  conditional E-value: 1e-16
                          PAS_4   4 lpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpee.......daarleralrrvlegeepiefleelll.. 74 
                                    lpda++v+d+dgrv+++N+a++e+ g++  e+lGk ++ ++ +        + + ++r++++ ++  e +e+   +l   
  gi|116753699|ref|YP_842817.1| 530 LPDATLVVDADGRVMAWNRAMEEMTGIQKSEMLGKGDFAYALPFhgcrrpmLIDLVMRYDEHIASLYENLERRGDTLYay 609
                                    8*************************************988888788888877777777777777777777766666688 PP

                          PAS_4  75 .......pgeerhyelrllPlrdesGevigvlvisrDiTerr 109
                                           +g++ ++ + ++Pl+d++G+++g+++ +rDiTe r
  gi|116753699|ref|YP_842817.1| 610 vyvpslySGRGAYLWVKASPLKDSDGRIVGAIESMRDITESR 651
                                    88999***********************************87 PP

  == domain 5  score: 39.0 bits;  conditional E-value: 7.7e-13
                          PAS_4  16 rvlyaNaaaaelfgappeellGktla..ellpeedaarleralrrvlegeepiefleelllpgeerhyelrllPlrdesG 93 
                                    +++y+N a+ ++ g+++ee+lG+ +   e  pe d+  ++++l++v   + + ++l  ++ +g++ ++el+++P+rd+ G
  gi|116753699|ref|YP_842817.1| 857 KIIYVNSAFTRMTGYAREEVLGRYPDflE-GPETDRSKIMEILEAVRNAQPVNQELVNYRKDGSRFWVELNIFPVRDHMG 935
                                    69*********************999544.3555********9988777655555566666******************* PP

                          PAS_4  94 evigvlvisrDiTerr 109
                                    ev +++ i rD+Terr
  gi|116753699|ref|YP_842817.1| 936 EVTHWVSIQRDTTERR 951
                                    ***************8 PP

  == domain 6  score: 5.7 bits;  conditional E-value: 0.017
                          PAS_4    2 dslpdalavl.dpdgrvlyaNaaaaelfgapp.......eellGktla....ellpeedaarleralrrvlegeepie 67  
                                     +s+p++++vl  + g+ ly+N +++el+g+++        +l G+ l+    +++p+ +++ l+++++r  e e  i+
  gi|116753699|ref|YP_842817.1|  969 ESIPFGFYVLnRATGKSLYLNHRFCELLGVEDleedlrcGRLDGSALFsrigSMHPD-AGDSLREIYNRTDEAEIEIR 1045
                                     567777777744567777777777775555543322222334455555444456665.77777777777777753333 PP

                          PAS_4   68 fleelllpgeerhyelrllPlrdesGevigvlvisrDiT 106 
                                     +        ++r++ ++++ +rd sG+  g l+i+ D+T
  gi|116753699|ref|YP_842817.1| 1046 T-------ADGRVIKVFATDIRDKSGKYFGRLGIFEDVT 1077
                                     3.......369***************************9 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.86   8.6e+02      13      35 ..       7      29 ..       3      52 .. 0.78
   2 !   21.4   0.0   1.9e-07   0.00019       3      58 ..     108     165 ..     106     175 .. 0.84
   3 !   25.5   0.0   9.6e-09   9.5e-06       1      56 [.     392     449 ..     392     459 .. 0.86
   4 !   23.1   0.0   5.6e-08   5.6e-05       6      40 ..     526     561 ..     514     581 .. 0.79
   5 !   22.6   0.0   7.9e-08   7.9e-05       3      54 ..     833     886 ..     831     902 .. 0.70
   6 !   14.2   0.0   3.4e-05     0.034       4      48 ..     965    1009 ..     963    1021 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.86
                          PAS_8 13 giavvdlgdrivdvNqaalellG 35
                                   ++ v+d+ +ri++  ++a++l G
  gi|116753699|ref|YP_842817.1|  7 AVYVFDEKGRIRYLSRTAEMLSG 29
                                   6788995557***********99 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 1.9e-07
                          PAS_8   3 lralfesspdgiavvd.lgd.rivdvNqaalellGys.adlkgellgqllpvlrplled 58 
                                    +r++++  +++++ v  +   ri+d+N  ++ellGy+ +++   +l +++++ r+++++
  gi|116753699|ref|YP_842817.1| 108 YRTALDRCREAVFFVEaE-SrRILDANAVFQELLGYPpEEIHSLTLYDIMEQDREEIDE 165
                                    89***********99954.359***************9888888888999999988874 PP

  == domain 3  score: 25.5 bits;  conditional E-value: 9.6e-09
                          PAS_8   1 erlralfesspdgiavvd.lgdrivdvNqaalellGys.adlkgell.gqllpvlrpll 56 
                                    er+r l+es++  i+ +d +g+ ++++N+ a++++Gys  +++g+ + g+l+p++++  
  gi|116753699|ref|YP_842817.1| 392 ERYRELVESANSIILRLDrRGN-VRFINEFAQQFFGYSeSEILGKCVmGTLVPEVESTG 449
                                    7*****************7777.******************999999668888877655 PP

  == domain 4  score: 23.1 bits;  conditional E-value: 5.6e-08
                          PAS_8   6 lfesspdgiavvdlgdrivdvNqaalellGys.adl 40 
                                    ++e +pd+ +vvd+++r++ +N+a++e++G    ++
  gi|116753699|ref|YP_842817.1| 526 IIEFLPDATLVVDADGRVMAWNRAMEEMTGIQkSEM 561
                                    6999*********8888*************553333 PP

  == domain 5  score: 22.6 bits;  conditional E-value: 7.9e-08
                          PAS_8   3 lralfesspdgiavv..d.lgd..rivdvNqaalellGysadlkgellgqllpvlrp 54 
                                    l++++ +s+d+i+++  d  ++  +i++vN a+ +++Gy    ++e+lg++++ l++
  gi|116753699|ref|YP_842817.1| 833 LESAVVNSNDAIVIAapDpSDGmpKIIYVNSAFTRMTGYA---REEVLGRYPDFLEG 886
                                    7788889******973445444889*************88...44444444444433 PP

  == domain 6  score: 14.2 bits;  conditional E-value: 3.4e-05
                          PAS_8    4 ralfesspdgiavvd..lgdrivdvNqaalellGysadlkgellg.ql 48  
                                     r++ es+p g  v++  +g + ++ N +++ellG++  +++e+l+  +
  gi|116753699|ref|YP_842817.1|  965 RSMTESIPFGFYVLNraTG-KSLYLNHRFCELLGVE--DLEEDLRcGR 1009
                                     8999**********96444.6*************88..9999886544 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 !  107.4   0.0   5.6e-34   5.5e-31       1     110 [.    1211    1325 ..    1211    1327 .. 0.94

  Alignments for each domain:
  == domain 1  score: 107.4 bits;  conditional E-value: 5.6e-34
                                     EHHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEE...EE..TEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCHTST CS
                      HATPase_c    1 gdekrLrqiisnlvdNavkfatkageieveika...se..ddlvisveDnGiGipkedlkklfekfsq.ddstkrggg 72  
                                     gd +rLrq++ nl++Na+kf t+ ge+++++     +e   +l++ v+D+GiGip+e++++lf  fsq d+s +r++g
  gi|116753699|ref|YP_842817.1| 1211 GDATRLRQVLVNLLENAIKF-TERGEVFLRVICqymDEdlSELHFFVRDTGIGIPPEKMDRLFHTFSQvDSSITRRYG 1287
                                     799*****************.******999998766336789************************************ PP

                                     SSSHHHHHHHHHHHHTTTEEEEEEETTTEEEEEEEEES CS
                      HATPase_c   73 gtGlGlsivkklvelmgGeiwvesepgrGttftftlpl 110 
                                     gtGlGl+i+k lve+mgG+iw es pg G+tf+ft++ 
  gi|116753699|ref|YP_842817.1| 1288 GTGLGLAISKHLVEMMGGRIWAESIPGAGSTFHFTIKA 1325
                                     ***********************************986 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.1   0.1   5.6e-30   5.6e-27       1     112 []    1462    1574 ..    1462    1574 .. 0.98

  Alignments for each domain:
  == domain 1  score: 94.1 bits;  conditional E-value: 5.6e-30
                                     EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCT..TTSEEEE CS
                   Response_reg    1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireed..pelpvii 76  
                                     +l+++D+p++++++  +l + gy + ++a++g e+l  l+++++dl+++D++mp+mdGle++++ir+ +  + +++++
  gi|116753699|ref|YP_842817.1| 1462 ILVAEDNPVNLKVVLMMLSHLGY-RADSARNGLEVLSALEHRDYDLVFMDVQMPDMDGLEAARRIRDMKgyEGPRIVA 1538
                                     89*********************.*******************************************99988999*** PP

                                     EESSTSHHHHHHHHHCTESEEEESSG-HHHHHHHHH CS
                   Response_reg   77 ltahseeedavealkagaddflsKpfdpeeLlkale 112 
                                     +ta++ e d+ +++ ag+dd++sKp+++e+L++a+e
  gi|116753699|ref|YP_842817.1| 1539 ITAYALEGDRDRCIAAGMDDYISKPVTMEKLKAAIE 1574
                                     ********************************9985 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.5e-05     0.015       2      83 ..     130     205 ..     129     209 .. 0.84
   2 !   14.7   0.0   2.8e-05     0.028       3      82 ..     416     497 ..     414     502 .. 0.83
   3 !    7.5   0.0    0.0049       4.9       2      29 ..     544     571 ..     543     611 .. 0.89
   4 ?   -1.1   0.0       2.4   2.4e+03      63      84 ..     620     639 ..     614     642 .. 0.77
   5 !   39.6   0.1   4.8e-13   4.8e-10       1      88 [.     858     943 ..     858     944 .. 0.91
   6 ?    2.8   0.0      0.15   1.5e+02      25      82 ..    1017    1066 ..     985    1073 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.5e-05
                          PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirdengk 81 
                                    + +++ ++e+lGy pee+ +   +++d++  +Dre++ e + +a+++ +  e    +r+ dG+ + ++ r +++   +g 
  gi|116753699|ref|YP_842817.1| 130 LDANAVFQELLGYPPEEIHSL--TLYDIME-QDREEIDEIIRHAMSRET--ESIQAYRTIDGSSIQMKGRFSPT-EGDGT 203
                                    678999***************..****985.688********9998888..66667788899999999999888.66666 PP

                          PAS_3  82 pv 83 
                                     +
  gi|116753699|ref|YP_842817.1| 204 LC 205
                                    55 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2.8e-05
                          PAS_3   3 yvserveeilGyspeellgkveswldlvhpeD...rervrealqealkkgepy.egeyRirrkdGeyrwveararvirde 78 
                                    +++e  ++ +Gys++e+lgk   ++  + pe       +r  ++e+lk  e+y +     ++k+Ge +w+ ++ + + +e
  gi|116753699|ref|YP_842817.1| 416 FINEFAQQFFGYSESEILGK--CVMGTLVPEVestGRDLRGMIAEILKAPEDYrTNVNENMKKSGERVWIAWTNKTVSSE 493
                                    567778899***********..9999999999444444555677999******66669*******************999 PP

                          PAS_3  79 ngkp 82 
                                    +g+ 
  gi|116753699|ref|YP_842817.1| 494 SGEM 497
                                    8875 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0049
                          PAS_3   2 iyvserveeilGyspeellgkveswldl 29 
                                    + +++++ee++G++++e+lgk ++ + l
  gi|116753699|ref|YP_842817.1| 544 MAWNRAMEEMTGIQKSEMLGKGDFAYAL 571
                                    67*******************8877765 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 2.4
                          PAS_3  63 Geyrwveararvirdengkpvr 84 
                                    G y wv+a+  +++d++g++v 
  gi|116753699|ref|YP_842817.1| 620 GAYLWVKAS--PLKDSDGRIVG 639
                                    566666665..*******9986 PP

  == domain 5  score: 39.6 bits;  conditional E-value: 4.8e-13
                          PAS_3   1 iiyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirdeng 80 
                                    iiyv+ ++ +++Gy +ee+lg++ ++l+     Dr++++e l+ a+++ +p+++e    rkdG+ +wve  ++++rd  g
  gi|116753699|ref|YP_842817.1| 858 IIYVNSAFTRMTGYAREEVLGRYPDFLEGP-ETDRSKIMEILE-AVRNAQPVNQELVNYRKDGSRFWVELNIFPVRDHMG 935
                                    69********************88888764.4569****9998.667999****************************** PP

                          PAS_3  81 kpvrvigv 88 
                                    ++++++++
  gi|116753699|ref|YP_842817.1| 936 EVTHWVSI 943
                                    *****986 PP

  == domain 6  score: 2.8 bits;  conditional E-value: 0.15
                          PAS_3   25 swldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirdengkp 82  
                                     s +  +hp+  + +re +++        e e+ ir++dG ++ v   a+ ird++gk 
  gi|116753699|ref|YP_842817.1| 1017 SRIGSMHPDAGDSLREIYNRT----D--EAEIEIRTADGRVIKV--FATDIRDKSGKY 1066
                                     445567777777777777633....2..5789999999988544..445677888775 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.3       4.7   4.7e+03      27      52 ..     387     409 ..     379     410 .. 0.69
   2 !   65.6   0.2   3.1e-21   3.1e-18       1      67 []    1099    1164 ..    1099    1164 .. 0.96
   3 ?   -2.0   0.1       3.7   3.7e+03      35      53 ..    1666    1684 ..    1618    1692 .] 0.56

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 4.7
                                    HHC..T-HSSCHHHHHHHHHHHHHHH CS
                          HisKA  27 Lkregklteelkeyletiesearrld 52 
                                    L+r     e+ +e++e++ s + rld
  gi|116753699|ref|YP_842817.1| 387 LRR---SEERYRELVESANSIILRLD 409
                                    444...67999999998888777776 PP

  == domain 2  score: 65.6 bits;  conditional E-value: 3.1e-21
                                     HHHHHHHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH CS
                          HisKA    1 slgrflagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdlsrieag 67  
                                     s+ +fla+++HE+rtPL+ai+g++ +L r+ + t+e++ y+  i+s+++ l++++ d+Ldlsrie+g
  gi|116753699|ref|YP_842817.1| 1099 SKAEFLANMSHEIRTPLNAIIGMSGLLLRT-NVTPEQRSYVSAIQSSGNALLEMLADILDLSRIEEG 1164
                                     689************************997.889*******************************87 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 3.7
                                     SSCHHHHHHHHHHHHHHHH CS
                          HisKA   35 eelkeyletiesearrldh 53  
                                     + + e+l  + +e +r+++
  gi|116753699|ref|YP_842817.1| 1666 DGVDEMLSALDEEFERVRR 1684
                                     3333344444444444444 PP

>> Hpt  Hpt domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3   0.5   3.9e-15   3.9e-12       4      84 ..    1605    1684 ..    1602    1685 .. 0.94

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 3.9e-15
                                     HHHHHHHHHHHHHHHHHHSCCHHHHHHHHHHHHHHHHHHTTBHHHHHHHHHHHHHHHHCTSCHHHHHHHHHHHHHHHH CS
                            Hpt    4 elfleeaeelleqleqaldqedlqelaraaHtLKGsagmlGltelaelahelEdlldragelelepellealkallea 81  
                                     e+fl +a+ +++++ +al+++d  +l raaH++K++++++G+ +l+++++e+E+l+ r+ +l+  +e+l al+++ e+
  gi|116753699|ref|YP_842817.1| 1605 EIFLSNAPLRIASMYEALKRNDPYALHRAAHSMKSASASIGALRLSRICAEIEELV-REARLDGVDEMLSALDEEFER 1681
                                     89****************************************************77.8999999999999*****999 PP

                                     HHH CS
                            Hpt   82 lra 84  
                                     +r+
  gi|116753699|ref|YP_842817.1| 1682 VRR 1684
                                     986 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   5.9e-06    0.0059       6     125 ..     245     370 ..     241     378 .. 0.70
   2 !   25.4   0.0   1.8e-08   1.8e-05       7     132 ..     685     820 ..     679     821 .. 0.60

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.9e-06
                                    HHHHHHHHHHHHTESEEEEEEEEETTEEECEEEEECC........EEEETTSHHHH............HHHHHSSSEEES CS
                            GAF   6 ldtvveelrellgadrvalylpdydGlhydipqasrw........lfmkngrgicg............qvlatgqplvip 65 
                                    l +++e l+++ ++drv +y+++ +G ++      rw        l         +            + + +++p++  
  gi|116753699|ref|YP_842817.1| 245 LMNALEFLGSAADVDRVYVYQNTDSG-DE-AVLRFRWergsvharL---------DerirydvlprwrERFLNDRPVHGI 313
                                    66788999999**********77777.33.3334444333322220.........2222232444444778888888888 PP

                                    TGGTSTTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS..CSHHHHHHHHHHH CS
                            GAF  66 dstpdprfaqynrrdllenmgirsslvvPlvndgelwGllvlhnpsp..pftreelellqvl 125
                                        ++  +q  +r+ll+  g rs+l  P++  ++ wG + + ++ +  +++ +e+ +l+  
  gi|116753699|ref|YP_842817.1| 314 ---VEEMPLQ--ERELLKCRGARSVLIFPITIADRFWGFIGFEDCERerSWSWNEISILMLG 370
                                    ...7888888..89******************************666677888888777654 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 1.8e-08
                                    HHHHHHHHHHHTESEEEEEE...EEETTEEE.......CEEEEECC....EEEETTSHHHH...........HHHHHSSS CS
                            GAF   7 dtvveelrellgadrvalyl...pdydGlhy.......dipqasrw....lfmkngrgicg...........qvlatgqp 61 
                                    +++++ l+ + ++drv ++    +d++           +    ++w    +fm       g           +vl++g++
  gi|116753699|ref|YP_842817.1| 685 NEAMQILGLISDVDRVYVFEnheEDELC--LrfewcrdG---IRSWmddqIFM-------GlsysrffpgwyEVLSSGKV 752
                                    5667777777777777777643211122..122332221...22222222222.......12222233345577777765 PP

                                    EEESTGGTSTTHHTTHHHHHHHHTTESEEEEEEEEETTEEEEEEEEEESSS..CSHHHHHHHHHHHHHHHHHH CS
                            GAF  62 lvipdstpdprfaqynrrdllenmgirsslvvPlvndgelwGllvlhnpsp..pftreelellqvladqvava 132
                                    +    +++ p   +    ++le++g+ s l vP++++g+ wG + +++++   +++++e+ +l + a+ ++ a
  gi|116753699|ref|YP_842817.1| 753 IKGL-VRDLPPSVK----EILEPYGVLSILIVPITVGGRFWGFVGFDDTTYerEWSDAEISILVASASTIGEA 820
                                    5433.333333333....699***************************444567**********999999876 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0      0.03        30      14      93 ..     126     194 ..     112     204 .. 0.61
   2 ?    0.6   0.0      0.59   5.9e+02       7      39 ..     404     436 ..     398     514 .. 0.72
   3 !   12.7   0.0   0.00011      0.11       5      35 ..     531     561 ..     527     655 .. 0.67
   4 !    8.3   0.0    0.0025       2.5      16     114 ..     984    1083 ..     969    1084 .. 0.59

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.03
                          PAS_7  14 dlrLvawNrrylelldlpeelvqvgvpleellrynaergefgagdveaeverrlaaaragkphsfererpdgrvievrgn 93 
                                    + r++  N  ++ell++p+e +    +l ++++    r+e++     + +++ +   ++++++    ++ dg  i+++g+
  gi|116753699|ref|YP_842817.1| 126 SRRILDANAVFQELLGYPPEEI-HSLTLYDIMEQD--REEID-----EIIRHAM---SRETESIQAYRTIDGSSIQMKGR 194
                                    4577889999999999999999.778888888765..33333.....3333333...33333444444456666666655 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.59
                          PAS_7   7 GisvfDadlrLvawNrrylelldlpeelvqvgv 39 
                                     i+ +D++++++++N+  ++ ++++e+ +   +
  gi|116753699|ref|YP_842817.1| 404 IILRLDRRGNVRFINEFAQQFFGYSESEILGKC 436
                                    57779999**************99998774444 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 0.00011
                          PAS_7   5 sqGisvfDadlrLvawNrrylelldlpeelv 35 
                                    +++ +v+Dad+r++awNr + e+ ++ ++ +
  gi|116753699|ref|YP_842817.1| 531 PDATLVVDADGRVMAWNRAMEEMTGIQKSEM 561
                                    56678******************99987655 PP

  == domain 4  score: 8.3 bits;  conditional E-value: 0.0025
                          PAS_7   16 rLvawNrrylelldlpeelvqvgvpleellrynaergefgagdveaeverrlaaaragkphsfererpdgrvievrgn 93  
                                     + +  N+r++ell++ +      +   +  +  ++ g++ +++  + +    + +++ ++  +e +++dgrvi+v ++
  gi|116753699|ref|YP_842817.1|  984 KSLYLNHRFCELLGVEDLEEDLRCGRLDGSALFSRIGSMHPDA-GDSL---REIYNRTDEAEIEIRTADGRVIKVFAT 1057
                                     5556677777776665433333333333333333444444222.2222...234456678899***********9999 PP

                          PAS_7   94 plpdg.....GfVttytDiTerrrae 114 
                                      + d+     G + +++D+T+ ++a+
  gi|116753699|ref|YP_842817.1| 1058 DIRDKsgkyfGRLGIFEDVTKDIKAA 1083
                                     996533344499*********99886 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.1   0.00012      0.12      13     137 ..     247     378 ..     236     379 .. 0.69
   2 ?   -0.7   0.0       1.7   1.6e+03      95     109 ..     627     642 ..     517     660 .. 0.63
   3 !   16.2   0.0     1e-05      0.01      59     137 ..     743     821 ..     684     822 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00012
                                    HHHHHSS......EEEEEEE-TTS-EEEEEEEES-TTSTT-S-B--..-TTH.HHHHHHHTS-EE.ES-GGG-S-HHHHH CS
                          GAF_2  13 delvelg.aa...lgyillvdddgglrlaawgeaeeefgaaldrpl..gegl.vgealrtgrpvi.lndleedpdkkglp 84 
                                    ++l+ lg aa    +y++   d g+  ++ ++ +++++ a+ld ++  +  + + e + + rpv  +  +ee+p + ++ 
  gi|116753699|ref|YP_842817.1| 247 NALEFLGsAAdvdRVYVYQNTDSGDEAVLRFRWERGSVHARLDERIryDVLPrWRERFLNDRPVHgI--VEEMPLQEREL 324
                                    4444455333333446666555555224445555555555555544323334599999999999955..99999999999 PP

                                    HHHHTT--EEEEEE-TTS---EEEEES.......--HHHHHHHHHHHHHHHHHH CS
                          GAF_2  85 aghaglrsflavPlisegrvvGvlnlyankppa.fdeedlelLeelaeqiaiai 137
                                    +  +g rs l++P++  +r  G++++   ++++ +++ ++++L +  + i+ ai
  gi|116753699|ref|YP_842817.1| 325 LKCRGARSVLIFPITIADRFWGFIGFEDCERERsWSWNEISILMLGVASIGGAI 378
                                    **************8877********877777779******9988777777776 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.7
                                    EEEE-T.TS---EEEE CS
                          GAF_2  95 avPlis.egrvvGvln 109
                                    a Pl + +gr+vG+++
  gi|116753699|ref|YP_842817.1| 627 ASPLKDsDGRIVGAIE 642
                                    5588887888888877 PP

  == domain 3  score: 16.2 bits;  conditional E-value: 1e-05
                                    HHHHHHHTS-EEES-.GGG-S-HHHHHHHHHTT--EEEEEE-TTS---EEEEE.S......--HHHHHHHHHHHHHHHHH CS
                          GAF_2  59 vgealrtgrpvilnd.leedpdkkglpaghaglrsflavPlisegrvvGvlnl.yankppafdeedlelLeelaeqiaia 136
                                    + e+l +g+  ++   +++ p +  + ++  g+ s+l+vP++ +gr  G++++  ++ +++++++++++L + a++i+ a
  gi|116753699|ref|YP_842817.1| 743 WYEVLSSGK--VIKGlVRDLPPSVKEILEPYGVLSILIVPITVGGRFWGFVGFdDTTYEREWSDAEISILVASASTIGEA 820
                                    667777776..445668888888888899999*********************65666666*****************99 PP

                                    H CS
                          GAF_2 137 i 137
                                    +
  gi|116753699|ref|YP_842817.1| 821 V 821
                                    7 PP

>> PAS_12  UPF0242 C-terminal PAS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0031         3      59     112 ..     119     173 ..     112     193 .. 0.75
   2 ?   -1.4   0.0       1.6   1.6e+03      58      88 ..     403     433 ..     394     437 .. 0.78
   3 !    8.5   0.0    0.0014       1.4      29      97 ..     814     886 ..     806     924 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0031
                         PAS_12  59 ilvysqkenkllfaNaqirallGwssdkflq.dfseivqegleeWkralaklssk 112
                                    +++     +++l aNa +++llG+ ++++ +    +i+++  ee  + + +  s+
  gi|116753699|ref|YP_842817.1| 119 VFFVEAESRRILDANAVFQELLGYPPEEIHSlTLYDIMEQDREEIDEIIRHAMSR 173
                                    4555556789******************987356788888888877777554444 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.6
                         PAS_12  58 ailvysqkenkllfaNaqirallGwssdkfl 88 
                                    +i++   +   + f+N+  +++ G+s+ ++l
  gi|116753699|ref|YP_842817.1| 403 SIILRLDRRGNVRFINEFAQQFFGYSESEIL 433
                                    5555555666789*************98876 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0014
                         PAS_12  29 ksrfrdlsldnyaldlRrLfDsLrsEnlgailvysqken....kllfaNaqirallGwssdkflqdfseivqe 97 
                                    +s+  +  ++  +++  rL +s     + ai++ ++       k++++N+ + +++G++ +++l ++ + ++ 
  gi|116753699|ref|YP_842817.1| 814 ASTIGEAVAKKDSIERMRLLESAVVNSNDAIVIAAPDPSdgmpKIIYVNSAFTRMTGYAREEVLGRYPDFLEG 886
                                    55666666677777777777777777777777776543222339********************999998764 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0         5   4.9e+03       9      37 ..     531     559 ..     523     561 .. 0.82
   2 !    7.8   0.0     0.005         5      76     106 .]     618     648 ..     588     648 .. 0.81
   3 ?    3.7   0.0     0.093        93      48      95 ..     887     937 ..     857     946 .. 0.80
   4 ?    2.7   0.0      0.19   1.9e+02      66     106 .]    1036    1077 ..    1023    1077 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 5
                         PAS_10   9 pieltflDdnlqirrFtpaakklfklipa 37 
                                    p +++ +D + +++ +++a +++  ++++
  gi|116753699|ref|YP_842817.1| 531 PDATLVVDADGRVMAWNRAMEEMTGIQKS 559
                                    557999************99988777665 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.005
                         PAS_10  76 kngkwvlvrylpyrdedgeiaGvvetfvDit 106
                                     +g +  v+ +p++d dg+i G++e + Dit
  gi|116753699|ref|YP_842817.1| 618 GRGAYLWVKASPLKDSDGRIVGAIESMRDIT 648
                                    67889999**********************7 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.093
                         PAS_10  48 pkkavknveeviealrtgekdevevvvp...kngkwvlvrylpyrdedgei 95 
                                    p+   +++ e++ea+r+ + +++e v      +  wv ++++p+rd  ge+
  gi|116753699|ref|YP_842817.1| 887 PETDRSKIMEILEAVRNAQPVNQELVNYrkdGSRFWVELNIFPVRDHMGEV 937
                                    4566677889999****999999988855334466999********98875 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.19
                         PAS_10   66 ekdevevvv.pkngkwvlvrylpyrdedgeiaGvvetfvDit 106 
                                     ++de e+++ + +g+++ v    +rd+ g++ G + +f D+t
  gi|116753699|ref|YP_842817.1| 1036 RTDEAEIEIrTADGRVIKVFATDIRDKSGKYFGRLGIFEDVT 1077
                                     445555555269*********************999999986 PP

>> MLTR_LBD  MmyB-like transcription regulator ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.33   3.3e+02       7      41 ..     110     144 ..     108     157 .. 0.87
   2 ?   10.2   0.0    0.0006       0.6      14      72 ..     531     604 ..     520     612 .. 0.59

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.33
                       MLTR_LBD   7 rlLdalepvPAlVldrrwdvlaaNraaraLlgdpa 41 
                                    + Ld+  ++  +V +    +l+aN++++ Llg p+
  gi|116753699|ref|YP_842817.1| 110 TALDRCREAVFFVEAESRRILDANAVFQELLGYPP 144
                                    678999999999999*****************954 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0006
                       MLTR_LBD  14 pvPAlVldrrwdvlaaNraaraLlgd.paalpe.............perNllrlvfl.dpglrpliedweevar 72 
                                    p + lV+d++  v+a+Nra++ + g   +++++             +++ l+ lv+  d+++++l+e+ e+  +
  gi|116753699|ref|YP_842817.1| 531 PDATLVVDADGRVMAWNRAMEEMTGIqKSEMLGkgdfayalpfhgcRRPMLIDLVMRyDEHIASLYENLERRGD 604
                                    55789******************998622222222233333334434445555555444455555555555544 PP

>> PAS_6  YheO-like PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.4   1.4e+03      88     113 ..     489     513 ..     447     514 .. 0.56
   2 ?   11.3   0.0   0.00023      0.23      70     108 ..    1040    1078 ..    1023    1085 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.4
                          PAS_6  88 firdekgkliglLCiNldlskleaae 113
                                     +  e+g  + +LC+  d+++l++a+
  gi|116753699|ref|YP_842817.1| 489 TVSSESG-EMEILCVGNDITELRRAK 513
                                    3444444.5679*********99875 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00023
                          PAS_6   70 vnyktktkdgkilksstifirdekgkliglLCiNldlsk 108 
                                     ++ + +t+dg+ +k   + ird++gk++g L+i  d++k
  gi|116753699|ref|YP_842817.1| 1040 AEIEIRTADGRVIKVFATDIRDKSGKYFGRLGIFEDVTK 1078
                                     477899***************************999997 PP

>> Sugar-bind  Putative sugar-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00011      0.11     186     233 ..       8      55 ..       5      58 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                                    TEEEETTS-BCCHCHCCCBSB--HHHHTTSSEEEEE--SGGGHHHHHH CS
                     Sugar-bind 186 grffDaeGevvetelnerviglsledlrkipkviavAggesKaeAila 233
                                     ++fD++G++ + + + ++++  +++ r+i +v++v+++es a+Ai +
  gi|116753699|ref|YP_842817.1|   8 VYVFDEKGRIRYLSRTAEMLSGGISKCRSIHEVLGVSCSESLASAIAS 55 
                                    689******************************************975 PP

>> PARP_regulatory  Poly A polymerase regulatory subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00033      0.33      89     138 ..    1368    1417 ..    1354    1444 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00033
                PARP_regulatory   89 iDgrdhdesleglknvklvtrfvdesyleklkkklrksklvlisDirskr 138 
                                     +D+  hdesl   +   ++  f d+s+++k+k++l +++++li+D++ + 
  gi|116753699|ref|YP_842817.1| 1368 VDAPFHDESLLTGNFDFVIAEFADDSDIMKIKSALPDTRILLITDLQRQG 1417
                                     566666666654432245689************************95443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1692 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       735  (0.040995); expected 358.6 (0.02)
Passed bias filter:                      675  (0.0376485); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); 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: 1.05u 0.30s 00:00:01.35 Elapsed: 00:00:00.46
# Mc/sec: 11011.08
//
Query:       gi|116753700|ref|YP_842818.1|  [L=490]
Description: cobyric acid synthase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.3e-50  169.8   0.1    1.4e-49  168.4   0.0    1.7  2  GATase_3   CobB/CobQ-like glutamine amidotransferase domain
    3.7e-21   75.8   0.0    1.7e-20   73.7   0.0    1.9  1  AAA_26     AAA domain
    1.3e-19   70.5   0.0    3.2e-19   69.3   0.0    1.6  1  CbiA       CobQ/CobB/MinD/ParA nucleotide binding domain
    0.00026   20.9   0.0    0.00047   20.1   0.0    1.4  1  SNO        SNO glutamine amidotransferase family
    0.00037   20.4   0.2     0.0093   15.9   0.0    2.6  3  MobB       Molybdopterin guanine dinucleotide synthesis prote
    0.00071   19.4   0.2     0.0017   18.1   0.0    1.8  2  GATase     Glutamine amidotransferase class-I
  ------ inclusion threshold ------
      0.085   12.6   0.1       0.76    9.6   0.0    2.1  2  DJ-1_PfpI  DJ-1/PfpI family


Domain annotation for each model (and alignments):
>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.78     2e+03      11      46 ..     103     131 ..      96     141 .. 0.59
   2 !  168.4   0.0   5.3e-53   1.4e-49       1     196 []     255     437 ..     255     437 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.78
                       GATase_3  11 snytdldpLeaepevrvrfvplkdeslgedadlvil 46 
                                      y+d+d L++  +          e+l +d+d +i+
  gi|116753700|ref|YP_842818.1| 103 DYYKDIDSLKEVVDSA-------IEELSRDYDYIIV 131
                                    4566999998744433.......3344455555555 PP

  == domain 2  score: 168.4 bits;  conditional E-value: 5.3e-53
                       GATase_3   1 kiavirlpaisnytdldpLeaepevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlg 80 
                                    +ia+i+lp+isn+td++pLe+ +  rvr+v+  +++lg+ +d+vi+pG+k+t++dla +r++g+d++i ++  +++p++g
  gi|116753700|ref|YP_842818.1| 255 EIAIIKLPRISNFTDFEPLERYA--RVRYVD-LKDDLGN-PDAVIIPGTKNTVSDLAEMRRHGMDRKILSL--KNVPIIG 328
                                    69*****************9966..999***.7888987.*****************************97..57***** PP

                       GATase_3  81 iCGGlqmLGeeiedpegvegeageveglglLdietefek.ekltgqvegevel......aaegeevkGyEiHsGrtilke 153
                                    iCGG+q+LG+ei+d  g+e+  g+++glgl+d+ t+f   ek+t qv++ev          +ge vkGyEiH+G t ++e
  gi|116753700|ref|YP_842818.1| 329 ICGGYQILGREIIDC-GIEDICGSIPGLGLIDAVTRFDAyEKRTVQVTKEVTGdgpilgRIKGEYVKGYEIHMGITESRE 407
                                    **************6.9**********************9****9****9777****998899***********777654 PP

                       GATase_3 154 kakpllkvkvggnngekdGavkksedgnvlGtYlHglfdnrna 196
                                      +   ++       ++dGav    dg v+GtYlHglf+n+n+
  gi|116753700|ref|YP_842818.1| 408 --RS--AF-------GDDGAVA--GDGMVIGTYLHGLFENENF 437
                                    ..44..44.......67****5..5***************986 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.7   0.0   6.5e-24   1.7e-20       3     192 ..       5     228 ..       3     232 .. 0.81

  Alignments for each domain:
  == domain 1  score: 73.7 bits;  conditional E-value: 6.5e-24
                         AAA_26   3 ifvtgtdtgvGKTvvslgLvralkrkgvkvgyfKPiqtgie.....................ededselikellgldqty 61 
                                    +++ gt+ ++GK+++ ++L+r+lk++g +v+ fK  +  ++                       e s l+  +l  ++  
  gi|116753700|ref|YP_842818.1|   5 LIILGTTSHSGKSILVTALCRMLKNRGLRVAPFKSQNMSLNswvttsggeigiaqavqawaaGVEPSVLMNPILLKPKGD 84 
                                    7899*******************************998888888887776666655555542233555555566555555 PP

                         AAA_26  62 elpeplalsaplspelaarqegedidlekiv....kelekdadivvVEGagglgvp.itee.llnadiaknlgapvilVa 135
                                       + +++ +p++++ aa+  +    l+++v    +el+ d+d ++VEGagg  +  +++    n+++a +l+ap+ilV+
  gi|116753700|ref|YP_842818.1|  85 RTSQVIIMGRPVADKSAADYYKDIDSLKEVVdsaiEELSRDYDYIIVEGAGGAAEInLFDRdIANIYVASRLRAPIILVG 164
                                    55677788899999999988775555999999999*******************7624444588**************** PP

                         AAA_26 136 rggl.gtinqllltiealrqknvr.vlGvilNkvrnp.e....nvetlekksgipvlGvvPylp 192
                                     +++ g ++ l+ t+++l  +  + v+G+++Nk+r + +     +++le+ +gipvlG++Pyl+
  gi|116753700|ref|YP_842818.1| 165 DIERgGVFASLYGTVKLLPPEIRElVKGMVINKFRGDpTilqpGIKMLEELTGIPVLGILPYLD 228
                                    **994589**********9865557*********9986255569*****************975 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.3   0.0   1.2e-22   3.2e-19       1     116 [.       5     228 ..       5     240 .. 0.97

  Alignments for each domain:
  == domain 1  score: 69.3 bits;  conditional E-value: 1.2e-22
                                    EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH.HTTEB-HHHH......................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx......................... RF
                           CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai.leglendiep......................... 54 
                                    ++i +t++ +GK+ l+++L+r l++rglrV++++ ++++ n+ +   g e+ i++                         
  gi|116753700|ref|YP_842818.1|   5 LIILGTTSHSGKSILVTALCRMLKNRGLRVAPFKSQNMSLNSWVtTSGGEIGIAQavqawaagvepsvlmnpillkpkgd 84 
                                    589**************************************999999********************************* PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                           CbiA  55 ................................................................................ 54 
                                                                                                                    
  gi|116753700|ref|YP_842818.1|  85 rtsqviimgrpvadksaadyykdidslkevvdsaieelsrdydyiivegaggaaeinlfdrdianiyvasrlrapiilvg 164
                                    ******************************************************************************** PP

                                    CCHCCCHHHHHHCHCHHHH.......EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--C CS
                                    xxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA  55 dlkrllellealgkkkall.....lkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprde 116
                                    d++r ++++++l+++++ll      +++g+v+n+++g+   t l+ +++ l++ +g+pvlg++p+ +
  gi|116753700|ref|YP_842818.1| 165 DIER-GGVFASLYGTVKLLppeirELVKGMVINKFRGD--PTILQPGIKMLEELTGIPVLGILPYLD 228
                                    ****.**********9999*******************..9999*9*99999888*********976 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   1.8e-07   0.00047      24     153 ..     281     416 ..     268     445 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.8e-07
                                    EE-SGGGGCC-SEEEE-SS-HHHHHHH.HHHTT-HHHHHHHHHTT.--EEEETHHHHHHCCEETTB.......SS-SS-- CS
                            SNO  24 tvkrkedlaevdaliiPGGestamskl.iertglyedllefvknsekvvlGtCaGlillskelene.......lvktlel 95 
                                     v  k+dl + da+iiPG   t   +  + r g ++     +k  + +++G C G  +l +e+           ++ l+l
  gi|116753700|ref|YP_842818.1| 281 YVDLKDDLGNPDAVIIPGTKNTVSDLAeMRRHG-MDRKILSLK--NVPIIGICGGYQILGREIIDCgiedicgSIPGLGL 357
                                    577899************998865554233444.555444455..559************99854333367778899*** PP

                                    CCEEEETTTT-SCCGEEEEEEEETTTC.SEEEEEESS--EEEEE-.TTTCEEEEECTTE CS
                            SNO  96 lkvkvkrnafGrqvdsfekeldfknli.ekftavfiraPvieeilddeavkvlyeldge 153
                                    ++ + + +a+ ++    +ke++  + i   +++ +++   i+  + +  ++++   dg 
  gi|116753700|ref|YP_842818.1| 358 IDAVTRFDAYEKRTVQVTKEVTGDGPIlGRIKGEYVKGYEIHMGITESRERSAFGDDGA 416
                                    **********9999999999987775556777777777777776666666666666654 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   3.6e-06    0.0093       5      38 ..       9      42 ..       4      52 .. 0.85
   2 ?    1.4   0.0      0.11   2.8e+02      73      98 ..     107     133 ..      94     142 .. 0.73
   3 ?   -2.6   0.0       1.9   4.8e+03      88     119 ..     288     319 ..     276     329 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.6e-06
                           MobB  5 vgksgsGKTtLleklipelkarglrvgtiKhahh 38
                                     +s sGK  L++ l ++lk+rglrv+  K ++ 
  gi|116753700|ref|YP_842818.1|  9 GTTSHSGKSILVTALCRMLKNRGLRVAPFKSQNM 42
                                   3569***********************9998765 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.11
                           MobB  73 eleeaelsleellarl.sevDlvlvEG 98 
                                    ++++ +  ++  ++ l +++D ++vEG
  gi|116753700|ref|YP_842818.1| 107 DIDSLKEVVDSAIEELsRDYDYIIVEG 133
                                    4555455677778888456*******9 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.9
                           MobB  88 lsevDlvlvEGfkkealpkievlraelgkeel 119
                                    l + D v++ G k++  +  e+ r+ ++++ l
  gi|116753700|ref|YP_842818.1| 288 LGNPDAVIIPGTKNTVSDLAEMRRHGMDRKIL 319
                                    45579999999999999988988888777444 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1         2   5.2e+03      61      77 ..     209     223 ..     199     223 .. 0.67
   2 !   18.1   0.0   6.8e-07    0.0017      39      88 ..     287     340 ..     268     409 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2
                                    HHHHHHHCTSTS-EEEE CS
                         GATase  61 ieaikearenkiPiLGI 77 
                                    i++++e+ +  iP+LGI
  gi|116753700|ref|YP_842818.1| 209 IKMLEELTG--IPVLGI 223
                                    566666555..*****9 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 6.8e-07
                                    THHSTSEEEEEEESSCTT...TTTHHHHHHHHCT.STS-EEEETHHHHHHHHHT CS
                         GATase  39 llknpdgilvsgGpgspg...vegkieaikeare.nkiPiLGICLGmQllaief 88 
                                     l npd+++++g  ++++         + +++++ +++Pi+GIC G Q+l+ e+
  gi|116753700|ref|YP_842818.1| 287 DLGNPDAVIIPGTKNTVSdlaEMRRHGMDRKILSlKNVPIIGICGGYQILGREI 340
                                    4789*********999999743334557778877799************99875 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 ?    0.2   0.0      0.22   5.6e+02      45      70 ..     110     134 ..      88     148 .. 0.77
   2 ?    9.6   0.0    0.0003      0.76      59     109 ..     288     338 ..     273     342 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.22
                                    SEEEE-SEEGGGCTCCG-SEEEE--B CS
                      DJ-1_PfpI  45 GlkvtvdaslddvkaaeyDalvlpGG 70 
                                     lk +vd ++++++ + yD +++ G 
  gi|116753700|ref|YP_842818.1| 110 SLKEVVDSAIEELSRD-YDYIIVEGA 134
                                    4677899****98777.****99763 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0003
                                    CCG-SEEEE--BHHHHHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHHHH CS
                      DJ-1_PfpI  59 aaeyDalvlpGGragperlrenekvvelvkefaekgklvaaICagpqlLaa 109
                                     ++ Da+++pG ++   +l+e  + +   k    k+ ++  IC g q+L +
  gi|116753700|ref|YP_842818.1| 288 LGNPDAVIIPGTKNTVSDLAEMRRHGMDRKILSLKNVPIIGICGGYQILGR 338
                                    4589****************9999998889999**************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (490 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 3409.63
//
Query:       gi|116753701|ref|YP_842819.1|  [L=382]
Description: molybdenum cofactor synthesis domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-38  131.8   0.0    2.7e-38  131.2   0.0    1.3  1  MoeA_N         MoeA N-terminal region (domain I and II)
    1.8e-24   86.1   0.0      3e-24   85.3   0.0    1.4  1  MoCF_biosynth  Probable molybdopterin binding domain
      1e-16   60.8   0.5    3.5e-15   55.9   0.1    3.1  3  MoeA_C         MoeA C-terminal region (domain IV)


Domain annotation for each model (and alignments):
>> MoeA_N  MoeA N-terminal region (domain I and II)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.2   0.0   4.6e-42   2.7e-38       2     157 .]       7     153 ..       6     153 .. 0.88

  Alignments for each domain:
  == domain 1  score: 131.2 bits;  conditional E-value: 4.6e-42
                                    -HHHHHHHHHHH-.HH-EEE.EEGGCG-TT-BBSS-EE-SS-BSSS-EESSSEEEEEEBTTB--...........-S--- CS
                         MoeA_N   2 sveealaiilaal.eleeee.vplaaealgrvlaedvvApedvPpfdnSamDGYAvraeagsgaseeepsaageeperll 79 
                                    s++ al+++l+++ +lee e +++ ++a grvla dv +pe++P f+++amDGYAvr+ +++gas+         ++++ 
  gi|116753701|ref|YP_842819.1|   7 SLSYALERLLDLCnPLEEREkIQI-KDACGRVLASDVLSPENLPSFNRAAMDGYAVRSHETRGASQ---------SSPVR 76 
                                    577899*******88888888***.99************************************954.........44455 PP

                                    TT-EEEE-TTSB--TT--EEEEGGGE..E....EETTE.S--STTTTEE-TTSSB-TTSEEE-TTBB--CCCHHHHHHCT CS
                         MoeA_N  80 pggavrimTGaplPegadaVvpvEdte.eeeaketvev.kavkpgenvrraGedikaGevllragtrltpaeigllasvG 157
                                      + vr+ TGa+lPeg+daVv++Ed   +    +  e+ ++ +p +nv r+Ged+++G+++l+  +rl+p +++ll +vG
  gi|116753701|ref|YP_842819.1|  77 ITEYVRVRTGAALPEGFDAVVMLEDSFlR---GNVLEItAELTPYRNVSRIGEDVRSGDIVLSCEHRLRPPDLALLGAVG 153
                                    566**********************7442...22222248999*********************************9998 PP

>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.3   0.0     5e-28     3e-24       1     143 [.     166     301 ..     166     302 .. 0.95

  Alignments for each domain:
  == domain 1  score: 85.3 bits;  conditional E-value: 5e-28
                                    EEEEE-HHHH.......TTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSSTT-- CS
                  MoCF_biosynth   1 avitvGdell.......sgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGptpdDv 73 
                                    avi +Gdel+       +g+++  n+ ++++++k  g e +  +v+pD+ ++ikea+ + + ++d+i+++GGt+++++D+
  gi|116753701|ref|YP_842819.1| 166 AVIPTGDELVprscvpaPGEAREINSIMICSYVKLWGGEPQLSGVIPDERDAIKEAI-KRCTGSDLILVSGGTSVGDRDY 244
                                    79*******************************************************.667999**************** PP

                                    HHHHHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EETTEEEEE-SSHHHHHHHHHHHHHGGHH CS
                  MoCF_biosynth  74 tpealaklfekelegfeeafrrvslkpgkpvgvapgailsravgktiigLPGspkavkealeeillpale 143
                                     p +l +++e         +++++l pg+p+ ++++   +++   +i++LPG+p+a+ + l ++++pa++
  gi|116753701|ref|YP_842819.1| 245 APGVLDEMGE-------LMVHGIRLSPGRPTALGAI---NGT---PIVCLPGYPVAALASLYLLVRPAVK 301
                                    **********.......8***********9888888...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 ?   -1.0   0.0      0.33     2e+03       3      29 ..      37      59 ..      36      73 .. 0.78
   2 ?    1.0   0.0     0.084     5e+02      13      34 ..     240     260 ..     237     266 .. 0.85
   3 !   55.9   0.1   5.9e-19   3.5e-15       2      72 .]     315     381 ..     314     381 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.33
                                   EESS-EE--SSS-EEEEEEEES-S-EE CS
                         MoeA_C  3 rlaedlksdpgrreflRvilteedgey 29
                                   +la+d+ s+++ ++f R+ ++    +y
  gi|116753701|ref|YP_842819.1| 37 VLASDVLSPENLPSFNRAAMD----GY 59
                                   588999999999999999988....34 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.084
                                    SS-EEEEEEEES-S-EEEEEE- CS
                         MoeA_C  13 grreflRvilteedgeyvaept 34 
                                    g r++ +++l+ e ge++++ +
  gi|116753701|ref|YP_842819.1| 240 GDRDYAPGVLD-EMGELMVHGI 260
                                    5799*******.7899999876 PP

  == domain 3  score: 55.9 bits;  conditional E-value: 5.9e-19
                                    EEESS-EE--SSS-EEEEEEEES-S-EEEEEE-S---TT-GGGCTT--EEEEE-TT--EE-TT-EEEEEE- CS
                         MoeA_C   2 arlaedlksdpgrreflRvilteedgeyvaeptgkqgSglLsslaeAnglivipegtegleaGeeVevill 72 
                                    arl+++++s pg  +f Rv+l+    + +aep+  +g g+Lss a+A+g++ +pe+ egl++Ge+Vev+++
  gi|116753701|ref|YP_842819.1| 315 ARLSRKIPSRPGYITFARVSLR----DGIAEPVMVSGAGILSSVARADGFVLVPEDLEGLDEGEKVEVHIF 381
                                    9*********************....66****************************************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2840.41
//
Query:       gi|116753702|ref|YP_842820.1|  [L=160]
Description: hypothetical protein Mthe_0387 [Methanosaeta thermophila PT]
Scores for complete 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   19.5  10.1       0.26   12.1   0.4    3.1  3  TraD_N    F sex factor protein N terminal
     0.0044   17.3   2.4         23    5.4   0.1    3.5  3  DUF4277   Domain of unknown function (DUF4277)


Domain annotation for each model (and alignments):
>> TraD_N  F sex factor protein N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.4   2.9e-05      0.26       4      57 ..       9      66 ..       7      71 .. 0.75
   2 !    5.5   0.2    0.0033        30      27      57 ..      72     102 ..      67     110 .. 0.82
   3 !    7.4   0.7   0.00083       7.4      18      55 ..     111     148 ..     105     152 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.9e-05
                         TraD_N  4 vllflvLtglllwlrlsqevflnglyY.....waieeyvslknligsaafydiktikit 57
                                   +ll++vL++++l  ++sqe + ++  Y     ++ + +   +    ++++ydi+++  t
  gi|116753702|ref|YP_842820.1|  9 LLLIVVLSAMVL-TTTSQENLQVAQGYnvdqyFRQKPLYDVQAYFMQKPTYDIQQFVKT 66
                                   677777777655.6677777766655555555999999999999999******998776 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0033
                         TraD_N  27 glyYwaieeyvslknligsaafydiktikit 57 
                                    + +Y++ + +   +    ++++ydi+++  t
  gi|116753702|ref|YP_842820.1|  72 VEMYFRQKPLYDVQAYFMQKPTYDIQQFVKT 102
                                    5679999999999999999999999888766 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.00083
                         TraD_N  18 rlsqevflnglyYwaieeyvslknligsaafydiktik 55 
                                    +  q+ ++ + +Y+  +    +++ ++   +ydik++ 
  gi|116753702|ref|YP_842820.1| 111 YFRQKPLYDVQAYFMQKPTYDIQQFVKTRDTYDIKQYS 148
                                    34556666667777777777777777777777776664 PP

>> DUF4277  Domain of unknown function (DUF4277)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.1   0.1    0.0031        28      53      71 ..      40      58 ..      20      74 .. 0.88
   2 !    5.3   0.1    0.0027        24      53      71 ..      76      94 ..      72     105 .. 0.87
   3 !    5.4   0.1    0.0026        23      53      71 ..     112     130 ..     108     143 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0031
                        DUF4277 53 fvsrpLylfpeffedkple 71
                                   f ++pLy ++ +f +kp+ 
  gi|116753702|ref|YP_842820.1| 40 FRQKPLYDVQAYFMQKPTY 58
                                   78999********999985 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0027
                        DUF4277 53 fvsrpLylfpeffedkple 71
                                   f ++pLy ++ +f +kp+ 
  gi|116753702|ref|YP_842820.1| 76 FRQKPLYDVQAYFMQKPTY 94
                                   899************9985 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.0026
                        DUF4277  53 fvsrpLylfpeffedkple 71 
                                    f ++pLy ++ +f +kp+ 
  gi|116753702|ref|YP_842820.1| 112 FRQKPLYDVQAYFMQKPTY 130
                                    899************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1212.87
//
Query:       gi|116753703|ref|YP_842821.1|  [L=126]
Description: hypothetical protein Mthe_0388 [Methanosaeta thermophila PT]
Scores for complete sequence (score 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   13.3   0.0      0.058   13.1   0.0    1.2  1  BamHI     Restriction endonuclease BamHI
      0.088   13.0   0.0       0.18   12.0   0.0    1.5  1  HTH_34    Winged helix DNA-binding domain


Domain annotation for each model (and alignments):
>> BamHI  Restriction endonuclease BamHI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   6.5e-06     0.058      48      98 ..      47      98 ..      16     119 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.5e-06
                          BamHI 48 trkGnGvk.PikeelmirlkedgwklekrlalkaeakPGkvdavkliegkaf 98
                                    + G G++ P   + m  l+++gw+ e+ ++ +++ +P kv  +k+  +  +
  gi|116753703|ref|YP_842821.1| 47 IEMGTGLRqPEVSIGMRYLRQNGWIDERDVKGEGKGRPMKVYTLKVSIDDII 98
                                   556777643777889***************************9998665544 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     2e-05      0.18       4      59 ..      31      88 ..      30      91 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2e-05
                         HTH_34  4 avlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievd..kefkgkkprtll 59
                                   a+++yL+ ++e++ +e+   +++ + + s+ ++ L ++g+i  +  k+  +++p+ ++
  gi|116753703|ref|YP_842821.1| 31 ALVTYLSNTKEVSSREIEMGTGLRQPEVSIGMRYLRQNGWIDERdvKGEGKGRPMKVY 88
                                   6899*************************************75522333334466655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       838  (0.0467399); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); 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: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 938.58
//
Query:       gi|116753704|ref|YP_842822.1|  [L=508]
Description: hypothetical protein Mthe_0389 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.2e-37  127.9   0.0    9.5e-37  127.3   0.0    1.3  1  DUF87            Helicase HerA, central domain
    3.3e-08   33.6   0.4      7e-08   32.5   0.1    1.8  2  HAS-barrel       HAS barrel domain
    3.9e-07   29.0   0.0      0.013   14.2   0.0    2.1  2  DUF853           Bacterial protein of unknown function (DUF85
    6.4e-05   22.0   0.0    0.00074   18.5   0.0    2.0  2  AAA_10           AAA-like domain
    6.7e-05   22.0   0.0      0.019   13.9   0.0    2.3  2  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
  ------ inclusion threshold ------
      0.035   14.1   0.0      0.093   12.7   0.0    1.6  2  ResIII           Type III restriction enzyme, res subunit
      0.038   13.6   0.0       0.13   11.9   0.0    1.8  2  Zot              Zonular occludens toxin (Zot)
      0.051   12.4   0.0       0.14   10.9   0.0    1.7  2  T4SS-DNA_transf  Type IV secretory system Conjugative DNA tra
      0.084   13.1   0.1         19    5.5   0.0    3.0  2  AAA_22           AAA domain
       0.11   12.2   0.0        5.8    6.6   0.0    2.5  2  DEAD             DEAD/DEAH box helicase


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 !  127.3   0.0   5.3e-40   9.5e-37       2     225 ..     120     335 ..     119     337 .. 0.89

  Alignments for each domain:
  == domain 1  score: 127.3 bits;  conditional E-value: 5.3e-40
                          DUF87   2 eiGrllsgsevpvyldlnklvtrHlAilgsTGsGKSntvavLleellekkgatililDpHGEYgkal............e 69 
                                    +iG l +g +++v ld+n lv++H+ +l++TGsGKS+t+av+leell +kg+ +l++D HGEYg+++             
  gi|116753704|ref|YP_842822.1| 120 YIGIL-KGHDLRVELDANTLVQKHCSVLAKTGSGKSYTAAVILEELL-DKGVALLVIDTHGEYGSMRypnrdgdfnrfrV 197
                                    58878.999**************************************.*******************6666666666554 PP

                          DUF87  70 kllsekvkvitpspsa....kdkelkinpwsldpeelldlleeddkpaaavqrsvleealdqakakeekeklssdepvek 145
                                    k    ++ v+tp++ a     d++++++  +l+ ++++++l+    + ++ + ++l+ea++ ++   e+e+++ +++++ 
  gi|116753704|ref|YP_842822.1| 198 KPKGYNITVYTPANLAinprADRPFRFDGLNLSARDIARMLPD---DPTNGSVALLYEAIAALR--SERESYDLEDIIK- 271
                                    4444555556665555***************************...5556799**********9..9*********999. PP

                          DUF87 146 lleelkkekeelrklknqaiarlldkledllrkggsfsnsstdliallleklekegkitiidlsgvdelaqqlvvsvilr 225
                                              +++k++++++++l+ +le+ll+ g +   ++t++++ll     + g+ ++id+ gv+++ q ++v+ +l 
  gi|116753704|ref|YP_842822.1| 272 ----------QVEKANSKSKWTLIGQLEQLLEMGLFS-GEPTRPEELL-----QRGHASVIDMTGVPQEMQPMIVAKLLT 335
                                    ..........5779999***************99998.**********.....********************9999986 PP

>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.1   3.9e-11     7e-08       1      50 [.       5      52 ..       5      80 .. 0.90
   2 ?   -3.8   0.0       8.2   1.5e+04      55      74 ..     262     281 ..     255     286 .. 0.52

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 3.9e-11
                     HAS-barrel  1 iGevigestssslifrvegskdvkvGeyVeielpdgeivlGmvtdirrgn 50
                                   +G+++ge+++  + f ++g   v+ G+yV++++++++++l +v+ irr n
  gi|116753704|ref|YP_842822.1|  5 VGVIVGETSPLQFKFMIHG--AVGRGDYVKVRGDGRSWILAQVEEIRRSN 52
                                   79*****************..***************************65 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 8.2
                     HAS-barrel  55 ndlalvlsleeleeangdde 74 
                                      ++l++ +++ e an+ ++
  gi|116753704|ref|YP_842822.1| 262 ESYDLEDIIKQVEKANSKSK 281
                                    33444555555555555555 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 !   14.2   0.0     7e-06     0.013      18      81 ..     137     200 ..     124     214 .. 0.84
   2 !   12.8   0.0   1.8e-05     0.032     289     374 ..     382     460 ..     328     478 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7e-06
                         DUF853  18 klanrhGliaGatGtGktvtLqvlaeslseaGvpvfladvkGdLsgiakaGevkdklaarleei 81 
                                    +l+ +h  +   tG Gk  t  v+ e+l + Gv+ ++ d  G+  ++  + +  d    r++  
  gi|116753704|ref|YP_842822.1| 137 TLVQKHCSVLAKTGSGKSYTAAVILEELLDKGVALLVIDTHGEYGSMRYPNRDGDFNRFRVKPK 200
                                    56789999***********************************999888877777776666655 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 1.8e-05
                         DUF853 289 rskGvGvyfvtqnPldlPdtvLaqLGnrvqhalraftpkdqkavkaaadtfranpefdveeaiteLgvGealvsvLdekG 368
                                    r  G+G+  ++q P+ + ++vL+q  +  q  +r   p+d ka+ +  +++ +    ++ee i+ L  G a++   +e  
  gi|116753704|ref|YP_842822.1| 382 RKFGMGLMIISQRPARVDKNVLSQCNT--QIIMRVTNPNDLKALSKGLEGMST----ELEEEIKRLPPGTAMIV-SNEIE 454
                                    6669********************876..5579***************99976....67888899999999884.46666 PP

                         DUF853 369 aPsive 374
                                    +P +v+
  gi|116753704|ref|YP_842822.1| 455 RPIVVN 460
                                    776664 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   4.1e-07   0.00074      22     164 ..     141     288 ..     131     298 .. 0.79
   2 ?    1.2   0.0     0.076   1.4e+02     260     323 ..     372     437 ..     342     448 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 4.1e-07
                         AAA_10  22 sasliiGdlGnGKSvlakllvlyisllggkaliiDpkkerekfketlpeiakkinvvtLdseeenegvLdPlvllkeeke 101
                                     ++ ++ ++G GKS++a ++   ++  g  +l+iD   e   ++   p+  + +n+ +++++  n  v  P  l+ ++++
  gi|116753704|ref|YP_842822.1| 141 KHCSVLAKTGSGKSYTAAVILEELLDKGVALLVIDTHGEYGSMR--YPNRDGDFNRFRVKPKGYNITVYTPANLAINPRA 218
                                    6889999********************************54443..356679**************************** PP

                         AAA_10 102 aeslaedilel....llgvkkke..sekkaalseaveavl.egkqrgllavieelrkedekvareiarhl 164
                                       +  d l+l    +  + +++  +  +a+l ea++a   e++  +l+++i++++k ++k    +   l
  gi|116753704|ref|YP_842822.1| 219 DRPFRFDGLNLsardIARMLPDDptNGSVALLYEAIAALRsERESYDLEDIIKQVEKANSKSKWTLIGQL 288
                                    **9999999996444222223331133467899***998747999**********999887665555555 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.076
                         AAA_10 260 kllkelvRiGRsynaavylvtqsadDvlkeelknniglklaFr...etdkeeikkvLeflgldvede 323
                                     +++ +   GR++   +++++q +  v+k+ l++   ++++ r   ++d ++  k+Le +  + e+e
  gi|116753704|ref|YP_842822.1| 372 SIIRTIAAEGRKFGMGLMIISQRPARVDKNVLSQC-NTQIIMRvtnPNDLKALSKGLEGMSTELEEE 437
                                    455666668******************99986543.3334444001345555566666666666544 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 !   13.9   0.0   1.1e-05     0.019      14      57 ..     139     182 ..     132     192 .. 0.88
   2 !    5.7   0.0    0.0033       5.9     261     323 ..     374     429 ..     370     453 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.1e-05
                  TrwB_AAD_bind  14 etqhilivGttGsGKtqalekllrairargdraivlDltGafvs 57 
                                     ++h  ++  tGsGK+ ++  +l+++  +g   +v+D++G++ s
  gi|116753704|ref|YP_842822.1| 139 VQKHCSVLAKTGSGKSYTAAVILEELLDKGVALLVIDTHGEYGS 182
                                    688999999********************************965 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0033
                  TrwB_AAD_bind 261 lksllaegRkfGgavvlglqsiaqlrevYGedaaqsilslvntklilrvsdaetAeelsell.G 323
                                    + +++aegRkfG+ + +  q  a++         +++ls +nt++i+rv++ +  + ls+ l G
  gi|116753704|ref|YP_842822.1| 374 IRTIAAEGRKFGMGLMIISQRPARVD--------KNVLSQCNTQIIMRVTNPNDLKALSKGLeG 429
                                    67789999999999999999999987........47999999***9999999988888887755 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   5.2e-05     0.093      24      63 ..     140     176 ..     123     212 .. 0.86
   2 ?   -3.1   0.0       3.8   6.8e+03     135     145 ..     350     360 ..     331     378 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.2e-05
                                    TSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESS CS
                         ResIII  24 dkrglikmaTGtGKTlvaaklierllkkgkeekflflvpr 63 
                                    +k+  + + TG+GK+++aa + e+ll kg    +l+++++
  gi|116753704|ref|YP_842822.1| 140 QKHCSVLAKTGSGKSYTAAVILEELLDKGV---ALLVIDT 176
                                    566678889*****************9965...5666665 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.8
                                    EEEEETGGGTT CS
                         ResIII 135 viiiDEaHrlg 145
                                    +++i EaH++ 
  gi|116753704|ref|YP_842822.1| 350 MVVIEEAHNYI 360
                                    89999999875 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.4   2.5e+03      10      18 ..     150     158 ..     145     210 .. 0.65
   2 ?   11.9   0.0   7.1e-05      0.13      82     139 ..     349     407 ..     327     416 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.4
                            Zot  10 GsgKtsgav 18 
                                    GsgK++ a 
  gi|116753704|ref|YP_842822.1| 150 GSGKSYTAA 158
                                    666666553 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 7.1e-05
                            Zot  82 allviDEcqeifpvrakegrkdpevi.naftehRhlgwDivlltqdiskihkevralae 139
                                    +++vi E+++  p+r +  +    +i    +e R++g  ++++ q +++++k+v   ++
  gi|116753704|ref|YP_842822.1| 349 GMVVIEEAHNYIPERGTGRAASTSIIrTIAAEGRKFGMGLMIISQRPARVDKNVLSQCN 407
                                    799*******99999995555566667778899*******************9976665 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   7.9e-05      0.14      44      90 ..     136     188 ..      98     212 .. 0.70
   2 ?   -1.9   0.0      0.62   1.1e+03     321     344 ..     374     397 ..     372     439 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 7.9e-05
                T4SS-DNA_transf  44 f....ehvlvvAptrsgK..gvgvviPnllkwkqsiVvlDpkgElaeltskiR 90 
                                         +h +v A t+sgK  +++v++  ll ++ ++ v+D  gE   + +  R
  gi|116753704|ref|YP_842822.1| 136 NtlvqKHCSVLAKTGSGKsyTAAVILEELLDKGVALLVIDTHGEYGSMRYPNR 188
                                    134459************55589999*****************9877766555 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.62
                T4SS-DNA_transf 321 leealatiagYgirltlIiQsisq 344
                                    + +  a ++++g+ l++I Q  + 
  gi|116753704|ref|YP_842822.1| 374 IRTIAAEGRKFGMGLMIISQRPAR 397
                                    566667788888888888886543 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.011        19       5      29 ..     140     164 ..     137     185 .. 0.84
   2 ?    4.4   0.0     0.023        41      70     115 ..     314     377 ..     232     423 .. 0.66

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.011
                         AAA_22   5 agilvvtGesGtGKTtllrrlleql 29 
                                    ++++ v + +G+GK+++++ +le+l
  gi|116753704|ref|YP_842822.1| 140 QKHCSVLAKTGSGKSYTAAVILEEL 164
                                    67888999**********9999887 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.023
                         AAA_22  70 a........erlsseellealeqalrarav....ielliiDEaqhlr..s....eealeeLrsl 115
                                    +        ++ +   + ++l++ ++ar+     +++++i+Ea++ +  +    ++  + +r++
  gi|116753704|ref|YP_842822.1| 314 SvidmtgvpQEMQPMIVAKLLTDLFEARKLgrvcPGMVVIEEAHNYIpeRgtgrAASTSIIRTI 377
                                    055555543333444555777777777777889999********95545134434444444444 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0033       5.8      13      35 ..     139     161 ..     130     184 .. 0.78
   2 ?    2.9   0.0     0.047        84     107     137 ..     333     364 ..     267     392 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0033
                                    TTCEEEEEESTTSSHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  13 gggdvlvaaeTGsGKTlaflipv 35 
                                     ++++ v a+TGsGK+  +++ +
  gi|116753704|ref|YP_842822.1| 139 VQKHCSVLAKTGSGKSYTAAVIL 161
                                    4678999********99876544 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.047
                                    HHHHHHHCTSSHCTTE..EEEEEETHHHHHHT.T CS
                                    xxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx.x RF
                           DEAD 107 rlddllstgklnlsqv..rflVlDEadrlldq.g 137
                                     l dl++ +k  l +v   ++V+ Ea+++  + g
  gi|116753704|ref|YP_842822.1| 333 LLTDLFEARK--LGRVcpGMVVIEEAHNYIPErG 364
                                    4667778888..66666699*******9987754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (508 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); 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: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.42
# Mc/sec: 3589.59
//
Query:       gi|116753705|ref|YP_842823.1|  [L=255]
Description: hypothetical protein Mthe_0390 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1837.12
//
Query:       gi|116753706|ref|YP_842824.1|  [L=153]
Description: hypothetical protein Mthe_0391 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       226  (0.0126053); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1171.73
//
Query:       gi|116753707|ref|YP_842825.1|  [L=156]
Description: ribosomal-protein-alanine acetyltransferase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-15   57.6   0.0    1.7e-15   57.3   0.0    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    5.7e-13   49.1   0.0    8.1e-13   48.6   0.0    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    7.5e-12   45.3   0.0      9e-12   45.0   0.0    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    1.1e-05   25.3   0.0    1.5e-05   24.8   0.0    1.2  1  FR47             FR47-like protein
    5.4e-05   23.9   0.1    0.00021   22.0   0.1    1.8  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
     0.0018   18.4   0.0     0.0022   18.1   0.0    1.3  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
     0.0063   16.2   0.0      0.015   15.0   0.0    1.5  2  Acetyltransf_8   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
       0.12   12.5   0.0          2    8.5   0.0    2.1  1  Acetyltransf_9   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.3   0.0   7.4e-19   1.7e-15      22     117 .]      41     133 ..      21     133 .. 0.85

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 7.4e-19
                                    HH...HHHHHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTE.SEE CS
                 Acetyltransf_1  22 ee...feesfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegi.kki 97 
                                    e    f+e+   ++ + lvae dg+++G + ++k ++    ++ +  laV+ +y+g+G+G+ Ll a+++++ + g+  + 
  gi|116753707|ref|YP_842825.1|  41 ELfmtFHEY---HPQTMLVAEIDGKVVGVAIGFKPTP---FEGRVFWLAVRQAYQGHGIGRSLLSAILRIFSRLGAlSA- 113
                                    332236666...999********************99...8899999**********************9999999566. PP

                                    EEEEETTEHHHHHHHHHTTE CS
                 Acetyltransf_1  98 vlaveedndaairlYeklGF 117
                                     l+v+  n++a++lY  +GF
  gi|116753707|ref|YP_842825.1| 114 TLEVRIGNRRAQKLYASMGF 133
                                    ***************77**9 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   0.0   3.6e-16   8.1e-13       3      75 ..      52     134 ..      50     135 .. 0.71

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 3.6e-16
                                    EEEEEEEETTEEEEEEEEEEES...TCTEEEEE-GGGTTSSHHHHHHHH..TT...SEEEEE.EEEE..THHHHHHHHHH CS
                 Acetyltransf_7   3 gevfVaeddgkivGfialslld...aeitrlaVdpeyrgkGiGraLlea..ae...kgiile.qlel..naekaikfYek 71 
                                    ++++Vae dgk+vG ++        +   +laV+++y+g+GiGr Ll a  ++    g  l+ +le+   +++a+k+Y++
  gi|116753707|ref|YP_842825.1|  52 QTMLVAEIDGKVVGVAIGFKPTpfeGRVFWLAVRQAYQGHGIGRSLLSAilRIfsrLG-ALSaTLEVriGNRRAQKLYAS 130
                                    5799**********6665555477666666******************8442244444.23333333333339******* PP

                                    TTEE CS
                 Acetyltransf_7  72 lGFe 75 
                                    +GF+
  gi|116753707|ref|YP_842825.1| 131 MGFV 134
                                    ***8 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   0.0     4e-15     9e-12      30     125 ..      51     154 ..      37     156 .] 0.84

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 4e-15
                Acetyltransf_10  30 ealllvaeeggkivGvi.elrdgs...hisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavpfYek 103
                                      ++lvae +gk+vGv+ + + +    ++  l+V+++y+g Gig++Ll a+++ +++ g    +l+v+  +  a+++Y +
  gi|116753707|ref|YP_842825.1|  51 PQTMLVAEIDGKVVGVAiGFKPTPfegRVFWLAVRQAYQGHGIGRSLLSAILRIFSRLGALSaTLEVRIGNrRAQKLYAS 130
                                    5689************96665554578***************************999999989*******99******** PP

                Acetyltransf_10 104 lGFkav..geeqeenGirfvpMek 125
                                    +GF++    +  + +G   + M+k
  gi|116753707|ref|YP_842825.1| 131 MGFVVDnvIPTYYSDGEAALIMRK 154
                                    ****98545666666666666665 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   6.8e-09   1.5e-05      22      79 ..      77     135 ..      61     142 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 6.8e-09
                                    SSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S.-EEEEEETT-HHHHHHHHHHT-EE CS
                           FR47  22 gelgalqvlpehrrrGlgsrlvkalakeiaergk.tvllvvvasNtpsirlyeklGfek 79 
                                    g ++ l v++  ++ G g++l +a+ +  ++ g   ++l v+++N ++++ly ++Gf +
  gi|116753707|ref|YP_842825.1|  77 GRVFWLAVRQAYQGHGIGRSLLSAILRIFSRLGAlSATLEVRIGNRRAQKLYASMGFVV 135
                                    88999**************************876378999*****************76 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.1   9.3e-08   0.00021      55     137 ..      53     133 ..      13     134 .. 0.71

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 9.3e-08
                 Acetyltransf_3  55 gwaivlkdtgviGsv.glrdleeedeeaelgymla.psfwgkGyateavralleyafeelglerlvavidkeNeaSirvl 132
                                    + ++ + d++v+G++ g+ + + e   + + ++   ++++g+G+++  ++a+l+++ ++lg+     ++   N++ ++++
  gi|116753707|ref|YP_842825.1|  53 TMLVAEIDGKVVGVAiGFKPTPFE---GRVFWLAVrQAYQGHGIGRSLLSAILRIF-SRLGALSATLEVRIGNRRAQKLY 128
                                    355666777789999666666665...78887765266*****************9.777788899************** PP

                 Acetyltransf_3 133 eklGf 137
                                     ++Gf
  gi|116753707|ref|YP_842825.1| 129 ASMGF 133
                                    ****9 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   9.9e-07    0.0022      53     135 ..      55     134 ..      16     146 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 9.9e-07
                 Acetyltransf_4  53 lvae.sdrivGyaylgqfkkrakdwkaelsvyla.erdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhk 130
                                    lvae ++++vG a + ++ +   ++ +   ++la +++ +  g+gr l+ a+  ++++ + ++ + e+   n  ++++++
  gi|116753707|ref|YP_842825.1|  55 LVAEiDGKVVGVAIGFKPTP--FEGRV---FWLAvRQAYQGHGIGRSLLSAILRIFSRLGALSATLEVRIGNRRAQKLYA 129
                                    67778888888888777777..44443...555558899*****************************99********** PP

                 Acetyltransf_4 131 alGFe 135
                                    ++GF 
  gi|116753707|ref|YP_842825.1| 130 SMGFV 134
                                    ****6 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.1   2.5e+03      42      58 ..      50      66 ..      42      74 .. 0.76
   2 !   15.0   0.0   6.6e-06     0.015      88     141 ..      85     137 ..      76     141 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.1
                                   TTEEEEEEEETTEEEEE CS
                 Acetyltransf_8 42 phsepliglldgepvgy 58
                                   + ++ l++++dg+ vg 
  gi|116753707|ref|YP_842825.1| 50 HPQTMLVAEIDGKVVGV 66
                                   56778889999988876 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 6.6e-06
                                    SHHHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-EEEE CS
                 Acetyltransf_8  88 eaeargkglttallralvhylfadprtrrvvvEPdvrNerairllekaGfekek 141
                                     +++ g+g++++ll+a+++ +f++ ++ +  +E ++ N+ra +l++++Gf+   
  gi|116753707|ref|YP_842825.1|  85 RQAYQGHGIGRSLLSAILR-IFSRLGALSATLEVRIGNRRAQKLYASMGFVVDN 137
                                    56789***********996.79999*************************9876 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0   0.00091         2       3     101 ..      17     104 ..      15     134 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00091
                                    EEE-GGGHHHHHHHHHHHTT----H..HHHHHHHHHHTTSEEEEEEETTEEEEEEEEEEEEEEETTEEEEE.EEEEEEEE CS
                 Acetyltransf_9   3 relteedldevlellkyaFqdeespleeireyfrklleesrvlgaedngelvgqlallplelnvpGktlka.agvtgVav 81 
                                    r+ + +dl+e +e+ +++ +   ++l    +     + ++ +l+ae +g++vg++  +        k ++  + v + av
  gi|116753707|ref|YP_842825.1|  17 RQFEIKDLPELMEIDREVGGGYSPEL----FMTFHEYHPQTMLVAEIDGKVVGVAIGF--------KPTPFeGRVFWLAV 84 
                                    55666666666666666666655554....3445556666677777777777765443........34444356788999 PP

                                    -CCGTTS-HHHHHHHHHHHH CS
                 Acetyltransf_9  82 apehrgrgvlskLlaralee 101
                                       ++g+g+ ++Ll + l+ 
  gi|116753707|ref|YP_842825.1|  85 RQAYQGHGIGRSLLSAILRI 104
                                    99999999999999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1226.92
//
Query:       gi|116753708|ref|YP_842826.1|  [L=168]
Description: hypothetical protein Mthe_0393 [Methanosaeta thermophila PT]
Scores for complete 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   54.1   0.0    2.4e-14   53.6   0.0    1.2  1  LTD       Lamin Tail Domain


Domain annotation for each model (and alignments):
>> LTD  Lamin Tail Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.6   0.0   1.3e-18   2.4e-14       4     107 ..      21     124 ..      19     127 .. 0.83

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 1.3e-18
                            LTD   4 aagdvvIsevmedgagnnan..efvelyNtsskavdLsgwkledasge.....ytfpngt.......gtlaageyvvvws 69 
                                    a+g+vvI+e+  ++++++    e++el N+++++vd++gw+    s+      ++fp +        ++l+agey v++ 
  gi|116753708|ref|YP_842826.1|  21 AEGSVVINEFELNPPSDQPYavEWIELLNSGEEDVDIGGWQAVIISTVpgetgAQFPWSGkitvplgTVLKAGEYRVLTG 100
                                    689***********998888*********************999995566677444444477777777************ PP

                            LTD  70 gsgttsasngskasssavwnn.ggdavaLydasgevvds 107
                                    ++               +w+   + +v+Lyd+ g++vd+
  gi|116753708|ref|YP_842826.1| 101 DQ---------------RWDHgFNATVILYDQVGNEVDR 124
                                    94...............45554566999*********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 1412.15
//
Query:       gi|116753709|ref|YP_842827.1|  [L=322]
Description: radical SAM domain-containing protein [Methanosaeta thermophila PT]
Scores for 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-14   52.3   1.1    9.3e-13   48.9   0.2    2.1  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 !   48.9   0.2   5.2e-17   9.3e-13       1     158 [.      92     242 ..      92     251 .. 0.80
   2 ?    2.3   0.0     0.011   1.9e+02     119     143 ..     272     295 ..     244     305 .. 0.78

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 5.2e-17
                                    EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTC.CCTE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                    Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlakla.vpgi 78 
                                    ++v++ C ++C+fCa+p+       g ++s+e+++e v+++ a  g  k + l++g      ++ve ++++a+     ++
  gi|116753709|ref|YP_842827.1|  92 ITVSERCIYDCRFCAVPK-----LMGPTKSKEKVIEMVRRA-AMTGrLKAISLTSGVEVSPEHEVERIAEIARALkTFNV 165
                                    67999************6.....899***************.78898999999988444444444444444443245566 PP

                                    EEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHH.TTSETEEEEEEEBTTTSH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  79 ritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklre.agikrvvdrivglpGend 157
                                     i +++++t    +  e l+++g   v  +le++d++ ++  + +g +fe++++al  +    gi+rv+++++++ Ge+d
  gi|116753709|ref|YP_842827.1| 166 PIGISVCPTE---RSNEILRRAGAVEVKYNLETLDPDIFQTVC-PGLSFEDIKNALADAVGvFGINRVFTNVIVGLGESD 241
                                    6666666555...5779999999**************999999.************99887256666***********99 PP

                                    H CS
                                    x RF
                    Radical_SAM 158 e 158
                                    +
  gi|116753709|ref|YP_842827.1| 242 R 242
                                    7 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.011
                                    HHHTCTSHHHHHHHHHHHHHHTTSE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM 119 klmnrghtfeevlealeklreagik 143
                                    +l +r+++ e++l++ e lr+a ++
  gi|116753709|ref|YP_842827.1| 272 DLEMRRPSAERILRLAEHLRRA-LD 295
                                    444599*************998.55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); 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: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2350.93
//
Query:       gi|116753710|ref|YP_842828.1|  [L=475]
Description: betaine-aldehyde dehydrogenase [Methanosaeta thermophila PT]
Scores for complete 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-171  570.8   0.0     2e-171  570.6   0.0    1.0  1  Aldedh    Aldehyde dehydrogenase family
     0.0011   18.4   0.1     0.0097   15.4   0.0    2.3  2  DUF1487   Protein of unknown function (DUF1487)


Domain annotation for each model (and alignments):
>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  570.6   0.0  2.3e-175    2e-171      11     462 .]      23     471 ..      13     471 .. 0.98

  Alignments for each domain:
  == domain 1  score: 570.6 bits;  conditional E-value: 2.3e-175
                                    EEETTTCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH---HHHHHHHH CS
                         Aldedh  11 vinPatgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaeletletGkplaearaev 90 
                                     +nPa++e +a+v+ ++  d+ +a+++A++af++w+++pa++R+ +L+ aa++++er++++a+l+t+e+Gkp++++r+ev
  gi|116753710|ref|YP_842828.1|  23 IHNPANQEAVAEVAIGDVIDAVKALESAQRAFPGWSSIPATKRCTLLHDAAEIVRERADNIAKLLTMEMGKPIRDSRREV 102
                                    579***************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHSEEEEEECTTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-EEEEEE-TTSHHHHH CS
                         Aldedh  91 eeaidvlryyaelaeklegevlpssegklalvrrePlGvvgaItPWNfPlllaawklapalaaGNtvvlKPaeetplsal 170
                                     +a+d l+y+ae+  +  ge ++   +++++v+r+P+Gvv++ItPWN+P+ l+awk+ palaaG+t v KP++ +p+ a+
  gi|116753710|ref|YP_842828.1| 103 LSAADSLDYFAEEGLRNIGEWISA-GDTRSIVVRQPVGVVSLITPWNYPVELLAWKVGPALAAGCTAVAKPSSLAPVAAT 181
                                    ****************99999888.58***************************************************** PP

                                    HHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTTSEEEEEE---EEEEE-TTSHH CS
                         Aldedh 171 llaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknlkrvtlElGGknplivledaDl 250
                                     ++ ++++aglP+gv+n+v+gsg+++g++lv++p  +k+sftG+t++gr i+ +aa+ lkr++lElGG++p+iv++daD+
  gi|116753710|ref|YP_842828.1| 182 EFVMAINDAGLPPGVMNIVHGSGDTIGAELVKNPIPRKISFTGETSTGRWIMGTAAEYLKRISLELGGHAPMIVFDDADI 261
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT-SB---SSHHHHHHHHHHHHHHHHT CS
                         Aldedh 251 dkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpldedtdvGPliseaqlekvekyveeakee 330
                                    d a+ a+v+ afgn+GQvCi+++r++v esi+++f+ek++ ++ +l++gdpld+d+d+GP++seaq++k ++++e+a+++
  gi|116753710|ref|YP_842828.1| 262 DTAAGACVRRAFGNMGQVCISVNRVYVDESIAEDFTEKVIRRTLELRIGDPLDPDVDLGPMVSEAQRRKTREHIEDAVDR 341
                                    ******************************************************************************** PP

                                    TSEEEE-TTE.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEESSHHHHHHHHHSSSEESEEEEE-SBHHHHH CS
                         Aldedh 331 gaklllGgereeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfkdeeeaieiaNdteyGLaagvftkdlerae 410
                                    ga++l+Gg re +g  +gy++ Ptvl++v++ mri++eE+FGPV+++++f+deeea+++aNdteyGLaa+v+t++l+ra 
  gi|116753710|ref|YP_842828.1| 342 GANILCGG-REPEGFTRGYYFMPTVLTDVDHTMRIMREETFGPVAPIMRFRDEEEAVRLANDTEYGLAAYVYTNSLSRAV 420
                                    ********.7799******************************************************************* PP

                                    HHHHHS-SSEEEESSSST--TTTSEB--CGGGEES-BSHHHHHHHTEEEEEE CS
                         Aldedh 411 rvaerleaGnvyiNdsttgaaealpfgGvkqSglGreggkegleeytevktv 462
                                    r aerleaG+v++N  ++ + +a pfgG+kqSg+Gre ++ g+eey+e+k++
  gi|116753710|ref|YP_842828.1| 421 RTAERLEAGSVGVNVGSVIDRHA-PFGGWKQSGIGRELSHRGIEEYMEIKHI 471
                                    ***********************.**************************86 PP

>> DUF1487  Protein of unknown function (DUF1487)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.32   2.8e+03      26      45 ..      22      41 ..      20      43 .. 0.84
   2 !   15.4   0.0   1.1e-06    0.0097       8      57 ..     253     305 ..     249     439 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.32
                        DUF1487 26 slkePfaegavatvlveesi 45
                                    +++P +++ava v++ + i
  gi|116753710|ref|YP_842828.1| 22 LIHNPANQEAVAEVAIGDVI 41
                                   589***********997765 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.1e-06
                        DUF1487   8 mvifedgDlnsalealveslkePfa..egavatvlveesirdefverv.rskl 57 
                                    m++f+d+D+++a+ a v+     ++  + +v  v v+esi+++f e+v r++l
  gi|116753710|ref|YP_842828.1| 253 MIVFDDADIDTAAGACVRRAFGNMGqvCISVNRVYVDESIAEDFTEKViRRTL 305
                                    9*************9999887777622467889************98724444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3578.05
//
Query:       gi|116753711|ref|YP_842829.1|  [L=457]
Description: TrkA domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      6e-42  142.6   2.2      4e-23   81.9   0.3    2.3  2  TrkA_N         TrkA-N domain
    2.8e-14   52.8   9.8    2.8e-14   52.8   9.8    2.2  2  Ion_trans_2    Ion channel
    1.6e-08   34.3   0.0    5.3e-08   32.6   0.0    1.9  1  TrkA_C         TrkA-C domain
    1.3e-06   28.9   0.3     0.0045   17.5   0.1    2.3  2  XdhC_C         XdhC Rossmann domain
    6.1e-06   26.5   0.2    0.00061   20.0   0.0    2.3  2  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd
    0.00012   22.5   0.4     0.0027   18.1   0.1    2.4  2  NAD_binding_7  Putative NAD(P)-binding
     0.0011   19.1   0.0       0.12   12.4   0.0    2.5  2  Shikimate_DH   Shikimate / quinate 5-dehydrogenase
     0.0016   18.0   0.0      0.035   13.7   0.0    2.2  2  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
     0.0074   15.5   5.5      0.013   14.8   5.5    1.2  1  Ion_trans      Ion transport protein
     0.0079   15.6   0.0       0.17   11.3   0.0    2.2  2  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
  ------ inclusion threshold ------
      0.021   14.1   0.0      0.094   11.9   0.0    1.9  2  FAD_binding_3  FAD binding domain
      0.024   15.2   0.0         13    6.5   0.0    2.9  3  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
       0.54   10.2   2.2       0.89    9.5   2.2    1.2  1  DUF5090        Domain of unknown function (DUF5090)


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 !   60.5   0.1   1.3e-19   1.7e-16       1     116 []     116     228 ..     116     228 .. 0.93
   2 !   81.9   0.3   2.9e-26     4e-23       1     115 [.     339     448 ..     339     449 .. 0.92

  Alignments for each domain:
  == domain 1  score: 60.5 bits;  conditional E-value: 1.3e-19
                                    EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHHHHH CS
                         TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeanilav 80 
                                    i+i+G+G + ++l+e+L e g+++ +++++e++++++  + + +v gd++d +vL++a+i++a++v++    de+n+ ++
  gi|116753711|ref|YP_842829.1| 116 ILICGYGPMVERLTERLDEMGIEFAIVESRESVARSIF-KRYITVWGDPSDVQVLRNANISTARMVMVNY-TDEVNADVI 193
                                    79*****************7767******999999976.5566999**********************97.99******* PP

                                    HHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEEEEH CS
                         TrkA_N  81 llakelnpkkkiiaraqdpehaellkklgadvvisp 116
                                    l+++e     +iia ++d  h + l+ +ga +v+sp
  gi|116753711|ref|YP_842829.1| 194 LTIREVSR-VEIIAMVEDLRHSRFLSYAGASRVLSP 228
                                    ****9666.79**********************998 PP

  == domain 2  score: 81.9 bits;  conditional E-value: 2.9e-26
                                    EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHHHHH CS
                         TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeanilav 80 
                                    ++++G+G+vG++l++ L e+g   vv+d++      l+ + +e v gd+ +e+vL +ag+++a ++++++++d + i+a+
  gi|116753711|ref|YP_842829.1| 339 FLVVGYGDVGQRLVRVLCEHGVVPVVVDRR-----DLATDRFEHVRGDGYSEDVLVRAGVKEATCIMIMLNNDHDAIYAT 413
                                    68*****************77335777775.....45556789************************************* PP

                                    HHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEEEE CS
                         TrkA_N  81 llakelnpkkkiiaraqdpehaellkklgadvvis 115
                                    l+a++lnp++ iiara++ ++ e+l+++gad+v s
  gi|116753711|ref|YP_842829.1| 414 LVARNLNPDAFIIARANHLKTTEKLYRAGADYVAS 448
                                    ********************************976 PP

>> Ion_trans_2  Ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.8   9.8     2e-17   2.8e-14       2      70 ..      17      88 ..      14      94 .. 0.87
   2 ?   -0.6   0.0      0.98   1.3e+03      39      44 ..     342     347 ..     339     355 .. 0.85

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 2e-17
                                   HHHHTCHHHHHHHHT........T---HHHHHHHHHHHHTTS----SSTT-----HHHHHHHHHHHHHHHHHH CS
                    Ion_trans_2  2 vlllvlifgaviysl...eeg.wekwsfldalYfsfvtltTiGYGdivpetdagrlftivyillGlalfalfl 70
                                   ++++v +++a++ +l   e g +e    ++a+Y++++t+tT+GYGdiv  + +grlf+iv+ l G+al+++f+
  gi|116753711|ref|YP_842829.1| 17 TVVIVAVYSAIYMILmryE-GrSELAHPMNAVYWVVMTITTVGYGDIVFSSSLGRLFSIVVSLSGIALVFAFV 88
                                   4567777777777779953.447889************************9999*****************98 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.98
                                    S----S CS
                    Ion_trans_2  39 iGYGdi 44 
                                    +GYGd+
  gi|116753711|ref|YP_842829.1| 342 VGYGDV 347
                                    9****7 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.0   3.9e-11   5.3e-08       1      68 [.     261     329 ..     261     329 .. 0.94

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 3.9e-11
                                    CEEEEEE--GGGTTSBHHHHTHHHHS-EEEEE.E-T-EEES--TT-B--TT-EEEEEEEHHHHHHHHHH CS
                         TrkA_C   1 lvevtvpagsplvGktlkelnlrargvlvvai.rRggeliipsgdtvLeeGDvllvvgspsdlaelrel 68 
                                    lvev v +gspl  + +++  l + g+ ++++ +Rg++++ p g+ ++  G v+l vg++++l +lr+l
  gi|116753711|ref|YP_842829.1| 261 LVEVPVLPGSPLSEREISDPLLIQTGAAIAGLwKRGEFMPRPAGTERISTGSVVLAVGDSEQLMRLRSL 329
                                    69*****************666666*******99******************************99975 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0     0.001       1.4       2      45 ..     117     177 ..     116     224 .. 0.67
   2 !   17.5   0.1   3.2e-06    0.0045       2      75 ..     340     425 ..     339     452 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.001
                                    EEE--STTHHHHHHHHHHHTEEEEEEES-GGGG....................-GGG-TT-SE.....- CS
                         XdhC_C   2 vifGaghvaqalarlaaalgfrvtvvdpreefa....................tkerfpeade.....t 45 
                                    +i+G g++++ l + + ++g++  +v++re++a                    +        +     +
  gi|116753711|ref|YP_842829.1| 117 LICGYGPMVERLTERLDEMGIEFAIVESRESVArsifkryitvwgdpsdvqvlR--------NanistA 177
                                    89****************************977666666666666444333321........1334432 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 3.2e-06
                                    EEE--STTHHHHHHHHHHHTEEEEEEES-GGGG-GGG-TT-SE................-EEEE--S-HHHHHHHHHHHS CS
                         XdhC_C   2 vifGaghvaqalarlaaalgfrvtvvdpreefatkerfpeade................tavvvlthdhklDaealeaal 65 
                                    +++G g+v+q l+r++ + g+  +vvd r+   +++rf++++                 t+++++ ++ ++Da + ++++
  gi|116753711|ref|YP_842829.1| 340 LVVGYGDVGQRLVRVLCEHGVVPVVVDRRDL--ATDRFEHVRGdgysedvlvragvkeaTCIMIMLNN-DHDAIY-ATLV 415
                                    79****************************5..46788866547889999999999966555555443.344333.3333 PP

                                    SS--SEEEES CS
                         XdhC_C  66 rkkaayigll 75 
                                    +++++  + +
  gi|116753711|ref|YP_842829.1| 416 ARNLNPDAFI 425
                                    2344444444 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 ?    4.3   0.1      0.03        41       4      71 ..     118     190 ..     115     208 .. 0.82
   2 !   20.0   0.0   4.4e-07   0.00061       4      96 ..     341     434 ..     338     450 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.03
                                    EE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHH..HHHHHC...SEEEE-SSSHHHHHH CS
                  NAD_binding_2   4 fiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesie..elvasl...dvvitmvkagkavde 71 
                                    + G G M + + ++l + g++ a+++ +++ ++++ ++ +++  +++  ++++++    + ++mv+ +++v++
  gi|116753711|ref|YP_842829.1| 118 ICGYGPMVERLTERLDEMGIEFAIVESRESVARSIFKRYITVWGDPSdvQVLRNAnisTARMVMVNYTDEVNA 190
                                    6799**********************************99999998833455666777778889999888875 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 4.4e-07
                                    EE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SS...HHHHHHHCSEEEE-SSSHHHHHHHHHS.HCCC CS
                  NAD_binding_2   4 fiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaes...ieelvasldvvitmvkagkavdevieg.llea 79 
                                    ++G G  G+ +++ l ++g   +v++r+  +++++ + + +++++   +++ v+++ ++++m++++   d+++   ++++
  gi|116753711|ref|YP_842829.1| 341 VVGYGDVGQRLVRVLCEHGVVPVVVDRRDLATDRFEHVRGDGYSEdvlVRAGVKEATCIMIMLNND--HDAIYATlVARN 418
                                    89**************************99999998887555554111556677778888888885..567888868899 PP

                                    --TT-EEEE-S---HHH CS
                  NAD_binding_2  80 lkkgdilidgstssped 96 
                                    l++++++i  ++   ++
  gi|116753711|ref|YP_842829.1| 419 LNPDAFIIARANHL-KT 434
                                    ****9999988854.34 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.21   2.9e+02       9      75 ..     115     190 ..     112     216 .. 0.62
   2 !   18.1   0.1   1.9e-06    0.0027       7      72 ..     336     406 ..     333     436 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.21
                  NAD_binding_7   9 kvlvvGgGevAarkvrklleagakvtvvapevkeele.....elvkl..aeeel....ekdlegadlviaatddreln 75 
                                    ++l+ G G++ +r  ++l e g +  +v  +    +      + +++   ++++    +++++ a +v++  +d+   
  gi|116753711|ref|YP_842829.1| 115 HILICGYGPMVERLTERLDEMGIEFAIVESRE--SVArsifkRYITVwgDPSDVqvlrNANISTARMVMVNYTDEVNA 190
                                    78999999999999999999999988887772..21122222222221223333333345577777777777554444 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 1.9e-06
                  NAD_binding_7   7 gkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvkl.aeeelekd......legadlviaatddr 72 
                                    +k+ lvvG G+v++r vr l+e g   +vv+ +  + + +++++ + + +++d      +++a +++++ +++
  gi|116753711|ref|YP_842829.1| 336 EKRFLVVGYGDVGQRLVRVLCEHGVVPVVVDRR--DLATDRFEHvRGDGYSEDvlvragVKEATCIMIMLNND 406
                                    699*********************999999999..44455566414555655556555577777776666554 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     0.038        53       7      44 ..     108     145 ..     103     171 .. 0.82
   2 !   12.4   0.0     9e-05      0.12      11      46 ..     335     370 ..     327     387 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.038
                                    HS..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEES CS
                   Shikimate_DH   7 leslkekkvlliGaGemaelvakhLlakgvkkvvvaNR 44 
                                    ++++ + ++l+ G G m e++++ L + g++  +v  R
  gi|116753711|ref|YP_842829.1| 108 VPEWMSGHILICGYGPMVERLTERLDEMGIEFAIVESR 145
                                    56677889********************9995555555 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 9e-05
                                    TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSH CS
                   Shikimate_DH  11 kekkvlliGaGemaelvakhLlakgvkkvvvaNRtl 46 
                                     ek+ l++G G +++++++ L+++gv  vvv  R+l
  gi|116753711|ref|YP_842829.1| 335 MEKRFLVVGYGDVGQRLVRVLCEHGVVPVVVDRRDL 370
                                    47999**********************999988875 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.11   1.5e+02       6      77 ..     115     193 ..     112     206 .. 0.72
   2 !   13.7   0.0   2.6e-05     0.035       4      91 ..     336     425 ..     335     444 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.11
                                    -EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-......HHHHHHHHTT-EEEEHHHH.HHT-SEEEE-S-HHHHHHHH CS
                           IlvN   6 kiaviGyGsqGhaqalnlrdsgldvvvglregs......ksvkkAkeegfevltvaea.vkkadvvmiliPDelqkevy 77 
                                    +i + GyG   +  ++ l + g++ ++   ++s      k + +   +  +v+ +++a +++a +vm+   De++++v+
  gi|116753711|ref|YP_842829.1| 115 HILICGYGPMVERLTERLDEMGIEFAIVESRESvarsifKRYITVWGDPSDVQVLRNAnISTARMVMVNYTDEVNADVI 193
                                    5789999999999999999999998888777775544443344444555566655555367889999999999988886 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 2.6e-05
                                    TS-EEEES-SHHHHHHHHHHHHTT-.-EEEEE-TT-H.HHHHHHHTT-EE.EEHHHHHHT-SEEEE-S-HHHHHHHHHHH CS
                           IlvN   4 gkkiaviGyGsqGhaqalnlrdsgl.dvvvglregsk.svkkAkeegfev.ltvaeavkkadvvmiliPDelqkevyeee 80 
                                    +k+  v+GyG  G+   + l + g+  vvv  r+ ++  +++ + +g++  + v+  vk+a  +mi++ +  ++++y + 
  gi|116753711|ref|YP_842829.1| 336 EKRFLVVGYGDVGQRLVRVLCEHGVvPVVVDRRDLATdRFEHVRGDGYSEdVLVRAGVKEATCIMIMLNN-DHDAIYATL 414
                                    68889*******************956777777766448999*****97516678889*******99965.5789***** PP

                                    TGGG--TT-EE CS
                           IlvN  81 iepnlkegkal 91 
                                    ++ nl+ ++ +
  gi|116753711|ref|YP_842829.1| 415 VARNLNPDAFI 425
                                    *****988765 PP

>> Ion_trans  Ion transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   5.5   9.1e-06     0.013     134     226 ..      14      84 ..      10      94 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 9.1e-06
                                    HHHHHHHHHHHHHHHHHHHTTSCCCCCCSCCSTSSSTTTSSSSSSHHHHHHHHHHHHTTSSHHHHHHHHHHHSHHHHHHH CS
                      Ion_trans 134 lllllvvlfifaligvqlfkgklreknecaktwenpnngntnFdnfftallwlfrlmttegwgdilyatldekskvaliy 213
                                    +++++v++ +++ i + l                   +g+++    ++a++w++ ++tt+g+gdi+     ++      +
  gi|116753711|ref|YP_842829.1|  14 VFFTVVIVAVYSAIYMILM----------------RYEGRSELAHPMNAVYWVVMTITTVGYGDIVFSSSLGR------L 71 
                                    6777888888888888888................35578889999***************************......7 PP

                                    HHHHHHHHHHHHH CS
                      Ion_trans 214 fvifiilgsflll 226
                                    f i++ l+++ l+
  gi|116753711|ref|YP_842829.1|  72 FSIVVSLSGIALV 84 
                                    7777777666543 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 ?    1.9   0.0     0.088   1.2e+02      38      70 ..     115     147 ..     101     172 .. 0.85
   2 !   11.3   0.0   0.00012      0.17      36      79 ..     336     379 ..     319     440 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.088
                                    EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHH CS
                   2-Hacid_dh_C  38 tvGiiGlGrIGqavakrlkafgmkviaydrskk 70 
                                     + i G+G + +++ +rl ++g++  +++ +++
  gi|116753711|ref|YP_842829.1| 115 HILICGYGPMVERLTERLDEMGIEFAIVESRES 147
                                    688*********************999988766 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00012
                                    TSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHT CS
                   2-Hacid_dh_C  36 gktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelg 79 
                                    +k+  ++G+G++Gq++ ++l + g+  +++dr+  +++++e+++
  gi|116753711|ref|YP_842829.1| 336 EKRFLVVGYGDVGQRLVRVLCEHGVVPVVVDRRDLATDRFEHVR 379
                                    78999********************9999999998887555433 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.47   6.4e+02       4      35 ..     116     147 ..     115     154 .. 0.89
   2 ?   11.9   0.0   6.8e-05     0.094       5      47 ..     340     385 ..     336     432 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.47
                                    EEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                  FAD_binding_3   4 VlIVGaGpaGlmlallLseaGvrvvlvekrst 35 
                                    +lI G Gp    l+  L e G++  +ve r++
  gi|116753711|ref|YP_842829.1| 116 ILICGYGPMVERLTERLDEMGIEFAIVESRES 147
                                    68999999999999**************9986 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 6.8e-05
                                    EEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSS...S--EEEH CS
                  FAD_binding_3   5 lIVGaGpaGlmlallLseaGvrvvlvekrsttvvlp...radglnq 47 
                                    l+VG G +G  l ++L+e+Gv  v+v++r+ +++ +   r+dg ++
  gi|116753711|ref|YP_842829.1| 340 LVVGYGDVGQRLVRVLCEHGVVPVVVDRRDLATDRFehvRGDGYSE 385
                                    8***************************987776554447777655 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 ?    6.5   0.0    0.0092        13       3      47 ..     117     157 ..     115     200 .. 0.77
   2 ?    5.4   0.0      0.02        27       4      23 ..     341     360 ..     338     381 .. 0.81
   3 ?   -2.8   0.0       7.3     1e+04      14      38 ..     410     434 ..     388     443 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0092
                                    EEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC CS
                  F420_oxidored   3 giiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg 47 
                                     i G+G m e l+++l + g    e+ ++ ++ ++ a+++ +++ 
  gi|116753711|ref|YP_842829.1| 117 LICGYGPMVERLTERLDEMG---IEFAIV-ESRESVARSIFKRYI 157
                                    456*****************...999988.666666777777764 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.02
                                    EETTSHHHHHHHHHHHHTTS CS
                  F420_oxidored   4 iiGaGnmgealasgllaaga 23 
                                    ++G+G++g+ l++ l ++g+
  gi|116753711|ref|YP_842829.1| 341 VVGYGDVGQRLVRVLCEHGV 360
                                    78****************93 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 7.3
                                    HHHHHHHTTS-GGCEEEEEESSCCC CS
                  F420_oxidored  14 lasgllaagaqpheivvansrnpek 38 
                                    +   l+a++ +p  +++a  ++ ++
  gi|116753711|ref|YP_842829.1| 410 IYATLVARNLNPDAFIIARANHLKT 434
                                    4444555555555555565554444 PP

>> DUF5090  Domain of unknown function (DUF5090)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   2.2   0.00065      0.89      56     133 ..      16      89 ..       3      94 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00065
                        DUF5090  56 itlllkavllipiyllviaengnkldflksksriifltlikivlsilvdlvvyfselsslfkvflllkiikllitliv 133
                                    +t+++ av   +iy++ ++++g   + +   + +++ +++ +++ + +  +v+ s l+ lf +++ l++i l++++++
  gi|116753711|ref|YP_842829.1|  16 FTVVIVAVY-SAIYMILMRYEGRS-ELA-HPMNAVYWVVM-TITTVGYGDIVFSSSLGRLFSIVVSLSGIALVFAFVL 89 
                                    344443433.389****9999996.333.33333333332.46788899999*********************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.56u 0.23s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3296.39
//
Query:       gi|116753712|ref|YP_842830.1|  [L=96]
Description: TrkA domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-15   56.1   0.1    3.3e-15   55.7   0.1    1.2  1  TrkA_C    TrkA-C domain


Domain annotation for each model (and alignments):
>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   0.1   1.8e-19   3.3e-15       1      70 []      22      93 ..      22      93 .. 0.96

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 1.8e-19
                                   CEEEEEE--GGGTTSBHHHHTHHHH.S-EEEEEE-T.-EEES--TT-B--TT-EEEEEEEHHHHHHHHHHHH CS
                         TrkA_C  1 lvevtvpagsplvGktlkelnlrar.gvlvvairRg.geliipsgdtvLeeGDvllvvgspsdlaelrellg 70
                                   l++++v+  s+++ +tl+el l +r g+ vvai R  + l++ sg+t+  +GDvl+++g+p +++++ +++g
  gi|116753712|ref|YP_842830.1| 22 LRRYEVRRRSHMARRTLRELALIERfGCAVVAINRAgDALLSLSGETEVLPGDVLILLGPPGSMDRFSRVFG 93
                                   6899*****************************888799999999***********************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); 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: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 714.56
//
Query:       gi|116753713|ref|YP_842831.1|  [L=433]
Description: tRNA pseudouridine synthase D [Methanosaeta thermophila PT]
Scores for 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-165  550.7   0.0   2.2e-165  550.5   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 !  550.5   0.0  1.2e-169  2.2e-165       2     416 .]      14     424 ..      13     424 .. 0.98

  Alignments for each domain:
  == domain 1  score: 550.5 bits;  conditional E-value: 1.2e-169
                           TruD   2 lgielyvtdtegigGrlrespeDFiVeEieefsgeeeadegeylvlrvekrnwdtldlvrelaralgisrkrvgfaGtKD 81 
                                    lg+e+y+t t+gigG +r+speDF+VeEi    +e + + g+ylv++vekr+wdt++lvre+aral+is++r++faGtKD
  gi|116753713|ref|YP_842831.1|  14 LGMEIYITRTPGIGGVIRKSPEDFVVEEI---FDEDHYEGGRYLVVEVEKRDWDTHKLVREIARALRISQRRISFAGTKD 90 
                                    89***************************...5556899***************************************** PP

                           TruD  82 krAvTtQlisirkvepeelealeikdvelevvgrarrklrlGdLaGNkFeirvrdv.aeeeeaakraeeileeleekggv 160
                                    +rAvT+Q ++i++++++el +l+i+d++++v+gr++r+l lGdL+GN+F+i++rd+  + ++a++r+e+i++e+ e ggv
  gi|116753713|ref|YP_842831.1|  91 RRAVTRQRMAIMNLDEDELIDLRIPDLKISVLGRTNRPLGLGDLKGNRFRIVIRDLaVDVDSARERMERITSEILEIGGV 170
                                    ********************************************************999********************* PP

                           TruD 161 PNyfGvQRFGsrrpvthlvGkaivkgdleeAvelyvgkpfeeesedtreareavaetgdleealeelpkslryErallkr 240
                                    PNyfGvQRFG++rpvthlvG+aiv+gdle+Av +y++ pf+ e+e+tr+are ++e+gd+++al+++p++l+yE a+l++
  gi|116753713|ref|YP_842831.1| 171 PNYFGVQRFGEIRPVTHLVGEAIVRGDLERAVFTYLSMPFDGEPEETRAAREELWESGDVRAALRRYPRHLTYELAMLNH 250
                                    ******************************************************************************** PP

                           TruD 241 LaekpkdykkAlealpknLqrlFvhAyqSylFNrvlseRlerglpldepveGDvvifaeerlpdtdrlqlvteknveevk 320
                                    L+++p+d ++Al +lp+nL+r+FvhAyqSylFNr+ls+Rl+r l++ epveGD+v+f+++ +pd +r+++vt++n+e+vk
  gi|116753713|ref|YP_842831.1| 251 LVSSPGDHAGALMVLPDNLRRMFVHAYQSYLFNRMLSMRLRRCLTF-EPVEGDIVCFSKDGMPDVSRIERVTAENIEAVK 329
                                    *******************************************998.8******************************** PP

                           TruD 321 rliergrafvtaplvGtetelaegevgeierevleeegleledFklpklpelsskGtrRaillrvedlelsaeedeltle 400
                                    rl++r+rafvt+pl+G+e+ela+ge+geier++le+eg+++e+F+++++p+lss G+rR++ll+v+ + ++   ++++++
  gi|116753713|ref|YP_842831.1| 330 RLFDRKRAFVTLPLIGYESELADGEQGEIERSILESEGISRESFSVKTCPDLSSPGARRPALLQVDPV-FELGAESACIR 408
                                    ******************************************************************63.46677889*** PP

                           TruD 401 FsLpkGsYATvvlrEi 416
                                    FsLp+GsYATvvlrE+
  gi|116753713|ref|YP_842831.1| 409 FSLPPGSYATVVLREY 424
                                    ***************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        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 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 3054.13
//
Query:       gi|116753714|ref|YP_842832.1|  [L=422]
Description: Bcr/CflA subfamily drug resistance transporter [Methanosaeta thermophila PT]
Scores for 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-40  138.3  38.8      3e-40  138.3  38.8    1.8  2  MFS_1     Major Facilitator Superfamily
    2.3e-11   42.9  29.1    8.7e-07   27.8  10.9    3.1  3  MFS_2     MFS/sugar transport protein
      1e-10   41.1   5.6      1e-10   41.1   5.6    2.5  2  Sugar_tr  Sugar (and other) transporter
  ------ inclusion threshold ------
       0.05   13.9   2.9      0.093   13.0   0.1    2.8  3  DUF2499   Protein of unknown function (DUF2499)


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 !  138.3  38.8   6.6e-44     3e-40       2     353 .]      34     371 ..      33     371 .. 0.88
   2 ?   -0.2   0.1     0.081   3.6e+02     249     270 ..     385     406 ..     374     421 .. 0.73

  Alignments for each domain:
  == domain 1  score: 138.3 bits;  conditional E-value: 6.6e-44
                          MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllf 81 
                                    +l+ +++ l+ ++++palp  +a+ + +s + ++l lt+++l +++++l++G+lsdr+Grr++ll+gl l+++++l+++f
  gi|116753714|ref|YP_842832.1|  34 SLLSAFVPLSTDLYLPALP-GMADYFCVSSDLANLTLTMFFLSFGAGTLLWGPLSDRYGRRPMLLIGLSLYSIASLACAF 112
                                    57788999***********.******************************************************999999 PP

                          MFS_1  82 asslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaiv 160
                                     s+   ll+++r+l G+g++++f+++ a+i d++  + r   ++++++++ ++++ +p++g++l+    Wr++f +la++
  gi|116753714|ref|YP_842832.1| 113 -STDIhLLIAFRALEGIGGSSGFAVATAMIKDVYDVRSREPILAVVQTMVLISPVSAPVIGAILLKFTTWRGLFEALAFI 191
                                    .77777************************************************************************** PP

                          MFS_1 161 sllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsg.lltllplylqevlg 239
                                    +lla  l++   ++e  er+ + +         ++l   +  + ++p + +ll+ + l +++  + + + + +y    +g
  gi|116753714|ref|YP_842832.1| 192 GLLA--LAGSIALQETLERRCSGSLL-------HSLGR-LYVVARNPAFASLLLLFSLPSICALAfIASSSYIY-IRGFG 260
                                    ****..66777766666666665544.......46666.77777888776444444444444444377777778.99999 PP

                          MFS_1 240 lsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGfglgfvfp 319
                                    ls  l+ ++++a+ a++++ +  +  +ls+r+ rr + ++ +++++l+  ++++l++  s+++++++l+  ++++g v++
  gi|116753714|ref|YP_842832.1| 261 LS-ELEYSYFFAFNAIGMISSPTIYLKLSRRMCRRSFVTMCFGVMILSGTLILILGTW-SPWIFAVALLPSTIAAGAVRT 338
                                    99.8999999999999999999999999999999888888888888888888888888.88888888888999******* PP

                          MFS_1 320 sllalasdlappeeagtasglfntagslggalgp 353
                                    + ++l+ +   +e +g+a++l++ +g ++g++g+
  gi|116753714|ref|YP_842832.1| 339 PGTNLMLEQQ-REDTGSAAALMSCFGIIAGSIGM 371
                                    ********98.5******************9996 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.081
                          MFS_1 249 llallalvgailallagrlsdr 270
                                    l ++++l+g i a+l+ ++s++
  gi|116753714|ref|YP_842832.1| 385 LGMMYMLIGTICAILWHYISKK 406
                                    4566666666668888888887 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   1.2   6.9e-10   3.1e-06     252     345 ..      56     147 ..      20     152 .. 0.88
   2 !   27.8  10.9   1.9e-10   8.7e-07     167     328 ..     180     333 ..     150     346 .. 0.79
   3 ?   -0.3   2.2     0.067     3e+02     294     331 ..     362     399 ..     348     406 .. 0.47

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 6.9e-10
                          MFS_2 252 tyvlgngsaasvfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvlllqpsnlllflvllviagfgvgva 331
                                    +y+  + + a++ l+++++s  +g++lw pl  r+g++ + l+g++l+ + ++ + +   +++ l++++ ++ g+g  + 
  gi|116753714|ref|YP_842832.1|  56 DYFCVSSDLANLTLTMFFLSFGAGTLLWGPLSDRYGRRPMLLIGLSLYSIASLACAFS--TDIHLLIAFRALEGIGGSSG 133
                                    5666677888888999999999********************9999999988888887..9******************* PP

                          MFS_2 332 allpwsmladvvDy 345
                                    + ++++m+ dv+D+
  gi|116753714|ref|YP_842832.1| 134 FAVATAMIKDVYDV 147
                                    ************97 PP

  == domain 2  score: 27.8 bits;  conditional E-value: 1.9e-10
                          MFS_2 167 erkgylifaliialLmllgviivvlgtkervemrkkekteqkeklslleqlkevfrnraflillllfllaalalgvlngl 246
                                    + +g + ++++i lL+l+g i++      +   ++ e+ ++ + l+ l+ l  v rn+af  llllf+l + + +   + 
  gi|116753714|ref|YP_842832.1| 180 TWRGLFEALAFIGLLALAGSIAL------Q---ETLERRCSGSLLHSLGRLYVVARNPAFASLLLLFSLPSICALAFIAS 250
                                    33344444444444444444444......2...34466799*******************************99999999 PP

                          MFS_2 247 llYyltyvlg.ngsaasvfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvlllqpsnlllflvllviag 325
                                    + Y +    g ++ ++s+f+++  i+++ +  +  +l +r++++  + +++ ++i+ ++l+l+l++++ ++f v+l+ + 
  gi|116753714|ref|YP_842832.1| 251 SSYIYIRGFGlSELEYSYFFAFNAIGMISSPTIYLKLSRRMCRRSFVTMCFGVMILSGTLILILGTWSPWIFAVALLPST 330
                                    99988888888**************************************************************9987666 PP

                          MFS_2 326 fgv 328
                                    +++
  gi|116753714|ref|YP_842832.1| 331 IAA 333
                                    655 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.067
                          MFS_2 294 lgalltivllvlvlllqpsnlllflvllviagfgvgva 331
                                    +g+++  ++++l+ + +++ + ++ ++++++g++ +++
  gi|116753714|ref|YP_842832.1| 362 FGIIAGSIGMTLISMTRENMIPALGMMYMLIGTICAIL 399
                                    23333333333333333333333444555555554443 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   5.6   2.3e-14     1e-10      48     194 ..      65     205 ..      14     208 .. 0.92
   2 ?   -6.6  12.9         4   1.8e+04      48     166 ..     266     379 ..     249     403 .. 0.61

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 2.3e-14
                                    HHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHH CS
                       Sugar_tr  48 sglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyi 127
                                      l++ +f++   +G l+ g+l+dr+GR++ lli+  l++i+++ +a+++    + +li+ R l Gig     ++++  i
  gi|116753714|ref|YP_842832.1|  65 ANLTLTMFFLSFGAGTLLWGPLSDRYGRRPMLLIGLSLYSIASLACAFST---DIHLLIAFRALEGIGGSSGFAVATAMI 141
                                    45666677777778************************************...9************************** PP

                                    HTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS--- CS
                       Sugar_tr 128 sEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilllflPES 194
                                    + +   + R  +  + q+++ +  + a ++g++l k++    wr l+   +++ ll l++ + l E+
  gi|116753714|ref|YP_842832.1| 142 KDVYDVRSREPILAVVQTMVLISPVSAPVIGAILLKFTT---WRGLFEALAFIGLLALAGSIALQET 205
                                    ***************************************...*******************999998 PP

  == domain 2  score: -6.6 bits;  conditional E-value: 4
                                    HHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHH.HHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHH CS
                       Sugar_tr  48 sglivsiflvGaiiGslfagllgdrfGRkkslli.aavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmy 126
                                    ++ ++++  +G i +  +  +l+ r+ R++   + ++v+ + g+++ ++ +  +s ++++v+ + + i++G++ +  + +
  gi|116753714|ref|YP_842832.1| 266 YSYFFAFNAIGMISSPTIYLKLSRRMCRRSFVTMcFGVMILSGTLILILGT--WSPWIFAVALLPSTIAAGAVRTPGTNL 343
                                    555666666666666666667777777776655523444444444444444..888888888777777777776666555 PP

                                    HHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS- CS
                       Sugar_tr 127 isEiApkklRgalvslyqlaitfGilvaaifglglnktsn 166
                                    + E    + R   +s   l+  fGi+ ++i ++ +++t++
  gi|116753714|ref|YP_842832.1| 344 MLE----QQREDTGSAAALMSCFGIIAGSIGMTLISMTRE 379
                                    554....567777777777777777777777766666666 PP

>> DUF2499  Protein of unknown function (DUF2499)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.1   4.7e+03      65      87 ..     116     138 ..     106     166 .. 0.72
   2 ?   -1.2   0.1      0.55   2.5e+03      37      52 ..     320     335 ..     305     339 .. 0.78
   3 ?   13.0   0.1   2.1e-05     0.093      35      68 ..     379     412 ..     357     421 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.1
                        DUF2499  65 lellvtlqalltllGnltlllaa 87 
                                    ++ll++ +al  + G+  +++a+
  gi|116753714|ref|YP_842832.1| 116 IHLLIAFRALEGIGGSSGFAVAT 138
                                    56666666666666666666665 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.55
                        DUF2499  37 rvlalamlPalvsalc 52 
                                     ++a+a+lP+ ++a +
  gi|116753714|ref|YP_842832.1| 320 WIFAVALLPSTIAAGA 335
                                    5688999998888755 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 2.1e-05
                        DUF2499  35 elrvlalamlPalvsalcaltwHlfdnaeslell 68 
                                    e  + al+m+ +l++++ca+ wH+++ ++ ++ +
  gi|116753714|ref|YP_842832.1| 379 ENMIPALGMMYMLIGTICAILWHYISKKPYVSHV 412
                                    4555689*****************9999877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       737  (0.0411066); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.24s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 3035.12
//
Query:       gi|116753715|ref|YP_842833.1|  [L=351]
Description: hypothetical protein Mthe_0400 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       232  (0.0129399); expected 358.6 (0.02)
Passed bias filter:                      198  (0.0110436); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.21s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 2766.69
//
Query:       gi|116753716|ref|YP_842834.1|  [L=1213]
Description: hypothetical protein Mthe_0401 [Methanosaeta thermophila PT]
Scores for complete 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   70.4   1.7    0.00014   22.1   0.0    7.9  5  DUF11            Domain of unknown function DUF11
    1.7e-08   34.7   8.8        5.4    7.3   0.0    8.2  8  CARDB            CARDB
    0.00025   20.9   1.1        6.9    6.7   0.0    3.9  4  Lep_receptor_Ig  Ig-like C2-type domain
     0.0012   19.0   0.7         20    5.5   0.0    6.3  7  NPCBM_assoc      NPCBM-associated, NEW3 domain of alpha-galac
  ------ inclusion threshold ------
        0.1   13.0   0.0         72    3.8   0.0    4.3  4  Arrestin_C       Arrestin (or S-antigen), C-terminal domain


Domain annotation for each model (and alignments):
>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0     4e-08   0.00014       8      82 ..      65     165 ..      56     230 .. 0.88
   2 ?    4.0   0.0     0.017        62       6      34 ..     277     305 ..     274     307 .. 0.86
   3 !    7.4   0.0    0.0015       5.4       4      49 ..     372     427 ..     369     455 .. 0.80
   4 !   11.3   1.0   8.8e-05      0.31      11      44 ..     477     517 ..     468     637 .. 0.72
   5 !   11.7   0.2   6.8e-05      0.24       4      81 ..     665     811 ..     662     822 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 4e-08
                          DUF11   8 sevrpGdtvtytltvtNtgpasangvvvtDtl..........................Paglayvsvsasqgtasaltsv 61 
                                    ++v++Gd ++yt +++Ntg ++++++ vtD                            P+ +++  +s ++  as ++s+
  gi|116753716|ref|YP_842834.1|  65 TDVAAGDVLDYTCILRNTGDRTLSNISVTDGTreigfrdtlppgdvfsiraktppilsPSRFKLTASSDGRELASQEFSI 144
                                    489***************************999********999999999999888887888888888888888888888 PP

                          DUF11  62 gsLeagesatlsftvrvtrta 82 
                                    g +e  e+ t   ++r+t+++
  gi|116753716|ref|YP_842834.1| 145 GVVEKEERSTPYPALRATVES 165
                                    888888888887777777765 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.017
                          DUF11   6 dksevrpGdtvtytltvtNtgpasangvv 34 
                                    +++++r+G++++y  tv N+  +  ++v 
  gi|116753716|ref|YP_842834.1| 277 STTRARAGENISYRCTVINSCSDVIYNVD 305
                                    4678****************999888875 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0015
                          DUF11   4 tvdksevrpGdtvtytltvtNtgpasangvvvtDtl..........Paglayvsvs 49 
                                    + d++++ +G+ ++ t+ + N+g + + ++vv+D            P  ++ vs +
  gi|116753716|ref|YP_842834.1| 372 SADPPKIISGGVTNITVKLENSGSDLLRDIVVEDSFghigeikelkPGEVSHVSRK 427
                                    567888999*************************8766666666666666666655 PP

  == domain 4  score: 11.3 bits;  conditional E-value: 8.8e-05
                          DUF11  11 rpGdtvtytltvtNtgpasangvvvtDtl.......Pagla 44 
                                     pG+++++  tv Ntg +s+ +v++  +        P+g++
  gi|116753716|ref|YP_842834.1| 477 YPGEETEVLCTVENTGEVSLRNVTLAGIRsarigeiPPGTE 517
                                    69**********************98776777777744444 PP

  == domain 5  score: 11.7 bits;  conditional E-value: 6.8e-05
                          DUF11   4 tvdksevrpGdtvtytltvtNtgpasangvvvtDtl............................................ 39 
                                    +v+++++r+Gd+v+   tv N g+++++++ vt  +                                            
  gi|116753716|ref|YP_842834.1| 665 SVSPEAARFGDKVRISCTVENVGGVPLQEIFVTSRVigpmgsidflapkqrktvtmtipltmdisdtvtaegltpsrghv 744
                                    78999****************************99999999999999888888888888888888888888888888888 PP

                          DUF11  40 .................Paglayvsvsas..qgtasaltsv.....gsLeages.atlsftvrvtrt 81 
                                                     P+g +  s+ a+   g++  ++sv     + L+ +es a l+ tv+ ++t
  gi|116753716|ref|YP_842834.1| 745 ldreplsirllkgleprPSGKSQNSAPAAskAGVYVNDSSVkeigaNALNESESiASLAKTVTSNTT 811
                                    8888777777777777766666555555554555555555544454555555542455555555554 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.087   3.1e+02       2      40 ..      54      92 ..      53     136 .. 0.84
   2 ?    0.7   0.0      0.18   6.3e+02      23      65 ..     174     213 ..     161     218 .. 0.76
   3 ?    1.2   0.0      0.13   4.5e+02       3      30 ..     271     296 ..     269     340 .. 0.88
   4 ?    2.9   0.0     0.037   1.3e+02       2      40 ..     365     403 ..     364     445 .. 0.75
   5 !    7.3   0.0    0.0016       5.6      15      81 ..     476     535 ..     468     550 .. 0.67
   6 !    4.8   0.0     0.009        32      16      76 ..     573     627 ..     558     642 .. 0.74
   7 !    7.3   0.0    0.0015       5.4       6      72 ..     662     725 ..     657     736 .. 0.80
   8 ?    3.2   0.7     0.029     1e+02      35      75 ..     771     811 ..     767     832 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.087
                                   --EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEE CS
                          CARDB  2 pDLtvtntlnpseafvgeentitvtvkNqGtaasgatkv 40
                                   p L+ t+ +  +++ +g+ +  t+ ++N+G+ +  +++v
  gi|116753716|ref|YP_842834.1| 54 PELEMTVRTDFTDVAAGDVLDYTCILRNTGDRTLSNISV 92
                                   7888999999999******************99888876 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.18
                                    EEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEE CS
                          CARDB  23 itvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttv 65 
                                     ++ ++N+G+ + + +k+   +d+ +    ++p+La+ges t 
  gi|116753716|ref|YP_842834.1| 174 HRIRIANTGKTELRRVKI---VDRRNSVLGIIPALAPGESHTL 213
                                    567899999999888876...455554446899*****99886 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.13
                                    -EEE.EEEC-SEEETTSEEEEEEEEEE- CS
                          CARDB   3 DLtvtntlnpseafvgeentitvtvkNq 30 
                                    DL++  +++ + a +ge+++ ++tv N+
  gi|116753716|ref|YP_842834.1| 271 DLIL--ETSTTRARAGENISYRCTVINS 296
                                    7777..8888999**************7 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.037
                                    --EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEE CS
                          CARDB   2 pDLtvtntlnpseafvgeentitvtvkNqGtaasgatkv 40 
                                    p L ++ ++ p +   g   +itv+++N+G++  +++ v
  gi|116753716|ref|YP_842834.1| 365 PELNISASADPPKIISGGVTNITVKLENSGSDLLRDIVV 403
                                    8899999999999999999***********987666554 PP

  == domain 5  score: 7.3 bits;  conditional E-value: 0.0016
                                    EETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S-S-CEEEEE CS
                          CARDB  15 afvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtteategevtlt 81 
                                    +++gee ++ +tv+N+G+ + +++++a + +          ++ +g++t + +++  +  +++vt+t
  gi|116753716|ref|YP_842834.1| 476 LYPGEETEVLCTVENTGEVSLRNVTLAGIRSARI------GEIPPGTETRIAASISSD-ISKDVTIT 535
                                    5899*****************9999886655544......444444444444444444.33333333 PP

  == domain 6  score: 4.8 bits;  conditional E-value: 0.009
                                    ETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S-S-C CS
                          CARDB  16 fvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtteateg 76 
                                     +g+e+++++ v+N+Gt+   +++++    g++   +++  La+ge +tv+ ++ ++   +
  gi|116753716|ref|YP_842834.1| 573 PAGDEFNVSCLVSNSGTDLLHDVQISESEIGTV---ASLGDLAPGEFRTVTPSISVN---K 627
                                    4689999**********9998887765555555...569999999999999888776...3 PP

  == domain 7  score: 7.3 bits;  conditional E-value: 0.0015
                                    E.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S CS
                          CARDB   6 vtntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtte 72 
                                    ++ +++p++a  g++++i++tv+N G    +++ v+  + g   g  ++  La+++ +tv++t++ +
  gi|116753716|ref|YP_842834.1| 662 LKISVSPEAARFGDKVRISCTVENVGGVPLQEIFVTSRVIGPM-G--SIDFLAPKQRKTVTMTIPLT 725
                                    456999********************99998888888887777.3..56778888888888888765 PP

  == domain 8  score: 3.2 bits;  conditional E-value: 0.029
                                    EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S-S- CS
                          CARDB  35 sgatkvalyldgelvgtvtvpsLaagesttvsftwtteate 75 
                                      a+k+ +y+++++v+++  ++L+ +es+   ++ +t+ t+
  gi|116753716|ref|YP_842834.1| 771 PAASKAGVYVNDSSVKEIGANALNESESIASLAKTVTSNTT 811
                                    5678999********99999999999998877777776333 PP

>> Lep_receptor_Ig  Ig-like C2-type domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       2.4   8.5e+03      13      29 ..      67      83 ..      60      89 .. 0.79
   2 !    4.7   0.1    0.0079        28       9      34 ..     277     302 ..     270     316 .. 0.80
   3 !    5.1   0.0    0.0061        22       9      29 ..     567     588 ..     563     599 .. 0.78
   4 !    6.7   0.0    0.0019       6.9       5      27 ..     663     685 ..     662     704 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.4
                Lep_receptor_Ig 13 vslGsnvtasCilkenC 29
                                   v +G+    +Cil+++ 
  gi|116753716|ref|YP_842834.1| 67 VAAGDVLDYTCILRNTG 83
                                   778999999****9865 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0079
                Lep_receptor_Ig   9 espvvslGsnvtasCilkenCshlsv 34 
                                    ++   ++G+n++  C++ ++Cs+   
  gi|116753716|ref|YP_842834.1| 277 STTRARAGENISYRCTVINSCSDVIY 302
                                    4444899**************87655 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.0061
                Lep_receptor_Ig   9 espv.vslGsnvtasCilkenC 29 
                                    ++ v +++G+++++sC ++++ 
  gi|116753716|ref|YP_842834.1| 567 PTRVvTPAGDEFNVSCLVSNSG 588
                                    5556599***********9966 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.0019
                Lep_receptor_Ig   5 visvespvvslGsnvtasCilke 27 
                                    +isv+++  ++G++v +sC++++
  gi|116753716|ref|YP_842834.1| 663 KISVSPEAARFGDKVRISCTVEN 685
                                    599*****************987 PP

>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.4   4.9e+03       3      26 ..      69      92 ..      67      93 .. 0.86
   2 ?   -3.8   0.0       4.5   1.6e+04      10      26 ..     175     191 ..     171     191 .. 0.83
   3 ?   -0.2   0.0      0.35   1.2e+03       2      26 ..     282     306 ..     281     308 .. 0.90
   4 ?   -3.5   0.0       3.7   1.3e+04       6      26 ..     383     403 ..     380     404 .. 0.81
   5 !    5.5   0.0    0.0057        20       3      27 ..     478     502 ..     476     504 .. 0.93
   6 ?    3.3   0.0     0.028     1e+02       3      29 ..     574     600 ..     572     631 .. 0.73
   7 ?    0.6   0.0      0.19   6.6e+02       4      29 ..     674     699 ..     671     705 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.4
                    NPCBM_assoc  3 pGetvtltltvtndgtaaatnvsl 26
                                   +G+   +t  + n+g+++++n+s+
  gi|116753716|ref|YP_842834.1| 69 AGDVLDYTCILRNTGDRTLSNISV 92
                                   78888899999**********998 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 4.5
                    NPCBM_assoc  10 tltvtndgtaaatnvsl 26 
                                    ++ ++n+g++ +++v++
  gi|116753716|ref|YP_842834.1| 175 RIRIANTGKTELRRVKI 191
                                    66789******999986 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.35
                    NPCBM_assoc   2 epGetvtltltvtndgtaaatnvsl 26 
                                    ++Ge  +++ tv n++++ + nv l
  gi|116753716|ref|YP_842834.1| 282 RAGENISYRCTVINSCSDVIYNVDL 306
                                    689999************9999976 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 3.7
                    NPCBM_assoc   6 tvtltltvtndgtaaatnvsl 26 
                                     +++t+ + n+g++ ++++ +
  gi|116753716|ref|YP_842834.1| 383 VTNITVKLENSGSDLLRDIVV 403
                                    578999999999999988876 PP

  == domain 5  score: 5.5 bits;  conditional E-value: 0.0057
                    NPCBM_assoc   3 pGetvtltltvtndgtaaatnvsls 27 
                                    pGe++++  tv n+g+ +++nv l+
  gi|116753716|ref|YP_842834.1| 478 PGEETEVLCTVENTGEVSLRNVTLA 502
                                    8*********************985 PP

  == domain 6  score: 3.3 bits;  conditional E-value: 0.028
                    NPCBM_assoc   3 pGetvtltltvtndgtaaatnvslsls 29 
                                    +G++ ++   v+n+gt+ +++v++s s
  gi|116753716|ref|YP_842834.1| 574 AGDEFNVSCLVSNSGTDLLHDVQISES 600
                                    699999999999999999999999854 PP

  == domain 7  score: 0.6 bits;  conditional E-value: 0.19
                    NPCBM_assoc   4 Getvtltltvtndgtaaatnvslsls 29 
                                    G++v++  tv n g+ +++++ ++ +
  gi|116753716|ref|YP_842834.1| 674 GDKVRISCTVENVGGVPLQEIFVTSR 699
                                    99****************99987655 PP

>> Arrestin_C  Arrestin (or S-antigen), C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.42   1.5e+03       5      41 ..      56      92 ..      53      93 .. 0.93
   2 ?   -0.5   0.0      0.43   1.5e+03       5      41 ..     367     403 ..     365     404 .. 0.85
   3 ?    1.8   0.0     0.084     3e+02      17      45 ..     477     505 ..     464     568 .. 0.81
   4 ?    3.8   0.0      0.02        72       4      41 ..     659     696 ..     657     699 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.42
                                   EEEEEEES-SEEETT--EEEEEEEEE-SSSEEEEEEE CS
                     Arrestin_C  5 vsleaslpkkgyvpGetipvtvkidndskkkvkkikv 41
                                   +++++ ++ + ++ G+ ++ t  ++n   +++ +i+v
  gi|116753716|ref|YP_842834.1| 56 LEMTVRTDFTDVAAGDVLDYTCILRNTGDRTLSNISV 92
                                   7899*******************************98 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.43
                                    EEEEEEES-SEEETT--EEEEEEEEE-SSSEEEEEEE CS
                     Arrestin_C   5 vsleaslpkkgyvpGetipvtvkidndskkkvkkikv 41 
                                    ++++as +   ++ G  +++tvk++n  +  ++ i v
  gi|116753716|ref|YP_842834.1| 367 LNISASADPPKIISGGVTNITVKLENSGSDLLRDIVV 403
                                    67888999999999************99888887765 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.084
                                    ETT--EEEEEEEEE-SSSEEEEEEEEEEE CS
                     Arrestin_C  17 vpGetipvtvkidndskkkvkkikvslvq 45 
                                    +pGe+++v  +++n   ++++++++  ++
  gi|116753716|ref|YP_842834.1| 477 YPGEETEVLCTVENTGEVSLRNVTLAGIR 505
                                    79*********************987665 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.02
                                    -EEEEEEES-SEEETT--EEEEEEEEE-SSSEEEEEEE CS
                     Arrestin_C   4 kvsleaslpkkgyvpGetipvtvkidndskkkvkkikv 41 
                                     ++l++s++ ++  +G++++++ +++n  ++ +++i v
  gi|116753716|ref|YP_842834.1| 659 ALNLKISVSPEAARFGDKVRISCTVENVGGVPLQEIFV 696
                                    689****************************9999866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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 0.27s 00:00:00.97 Elapsed: 00:00:00.42
# Mc/sec: 8655.50
//
Query:       gi|116753717|ref|YP_842835.1|  [L=483]
Description: indolepyruvate ferredoxin oxidoreductase [Methanosaeta thermophila PT]
Scores for 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-07   29.9   0.1    9.6e-07   28.7   0.1    1.7  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    0.00033   20.3   0.2     0.0018   17.9   0.1    2.1  2  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-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 !   28.7   0.1   1.1e-10   9.6e-07      26      92 ..     363     429 ..     352     472 .. 0.88

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1.1e-10
                                    TTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEEEEEEE-SBCCCHHHHH CS
                   TPP_enzyme_C  26 glgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpitvvvlnNegygmtggqq 92 
                                    g + m ygl+ +iG++    +++ +aivGD +++++ +q l++a+  + +++v v+ N++ +mtg q+
  gi|116753717|ref|YP_842835.1| 363 GAVDMVYGLGSSIGVASGF-REKGIAIVGDYALAHTgIQGLINAIWSRKNVLVGVIWNRVAAMTGFQE 429
                                    5667889999999999864.3499*****************************************995 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 !   17.9   0.1     2e-07    0.0018       5     169 ..       6     158 ..       3     161 .. 0.89
   2 ?   -0.8   0.0      0.11     1e+03      79     128 ..     398     445 ..     378     469 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2e-07
                                    HHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-C.HHHHHHCHHHH CS
                   TPP_enzyme_N   5 ealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvts.gpGatnaltal 83 
                                    e + +aL++ gv +v  vpG  i++l  +l +e       a++E +a   A g   atg +  v+v   g +++     +
  gi|116753717|ref|YP_842835.1|   6 EQIYKALRDVGVGYVAYVPGYPITDLAQSLGAE------IAVNEKVAFECALGA-SATGIRSLVIVKQlGMNILADPLVI 78 
                                    67999****************************......8*************7.78888888888888*****999999 PP

                                    HHHHHHT--EEEEEEE--CCCHHS..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EEEEEEEHHH CS
                   TPP_enzyme_N  84 aeAkvdriPllvlsgdrptslrgqgvlqqeldqlalfrpvtkyaervtspeelpealrrAirtalsgrpgPvylelpkdv 163
                                       ++++  ++vl+gd    + +    q     + ++ p+t+  +    +  l +a+ +A+r++ ++   Pv l +  dv
  gi|116753717|ref|YP_842835.1|  79 SATHTTGAGIVVLVGDDLGPRGS----Q-IEMDSRFYGPLTELPVLDPAAPGLYRAVTEAFRVS-EEYFIPVILRVTSDV 152
                                    999************97766666....6.445678899***99888888889999*********.*************** PP

                                    CC-EEE CS
                   TPP_enzyme_N 164 lleevd 169
                                    l+++ +
  gi|116753717|ref|YP_842835.1| 153 LEDAST 158
                                    999876 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.11
                                    CHHHHHHHHHHT--EEEEEEE--CCCHHS..TC--T-CCHHHCCCSSEEE CS
                   TPP_enzyme_N  79 altalaeAkvdriPllvlsgdrptslrgqgvlqqeldqlalfrpvtkyae 128
                                    ++ +l++A  +r  +lv + ++ ++     ++q+++d +++++ +  + +
  gi|116753717|ref|YP_842835.1| 398 GIQGLINAIWSRKNVLVGVIWNRVAAMT--GFQEVFDLEHVLKALMPEMR 445
                                    5678888888888888888888777777..78877798888876654433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (483 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); 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 0.23s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 3777.97
//
Query:       gi|116753718|ref|YP_842836.1|  [L=303]
Description: hypothetical protein Mthe_0403 [Methanosaeta thermophila PT]
Scores for complete 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   40.4   0.0      9e-08   32.2   0.0    3.2  2  DUF1743   Domain of unknown function (DUF1743)


Domain annotation for each model (and alignments):
>> DUF1743  Domain of unknown function (DUF1743)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.0     5e-12     9e-08       1     113 [.     152     240 ..     152     242 .. 0.91
   2 ?    0.9   0.0     0.025   4.5e+02       1      12 [.     274     285 ..     274     297 .. 0.86

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 5e-12
                                    TTHHHHHHHHHH-..-TTS-EEEEEEEE-GGGTT---EEHHHHHHHHHHHTTCECTSEBTTTTCECCS-STTSS...... CS
                        DUF1743   1 grgiiGAtaalganialedstyEllaYreperwgerevdeesvieadektypetfdnvDlshklvvlvPhtpdp...... 74 
                                    +++++GAt++l++ni+++  +y       + r+                          +sh+lv+l+P +p++      
  gi|116753718|ref|YP_842836.1| 152 DSKTTGATWSLVHNISEKVDRY-------EARY--------------------------ISHSLVQLFP-VPTKtqncvs 197
                                    68999**********9885556.......2232..........................9*********.********** PP

                                    ..EEEEEEES-HHHHHHHHHCSEE..S-EEC..EEEEEESTTS CS
                        DUF1743  75 ..vlfGirgedpeallkaakeilskeeesee..mavfrtnqgt 113
                                      v+f++ + ++  +++ ++++l+++++s+e  m+v r+++++
  gi|116753718|ref|YP_842836.1| 198 taVEFACIPGRERGMIEDFRNLLERYTVSDEtgMVVCRSFDPS 240
                                    ***************************************9876 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.025
                                    TTHHHHHHHHHH CS
                        DUF1743   1 grgiiGAtaalg 12 
                                    g+g+iGA+aa+ 
  gi|116753718|ref|YP_842836.1| 274 GQGLIGAVAAVP 285
                                    789*******85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 2227.55
//
Query:       gi|116753719|ref|YP_842837.1|  [L=129]
Description: hypothetical protein Mthe_0404 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-05   23.1   0.1    0.00021   21.1   0.1    1.9  2  MarR_2    MarR family
    0.00024   20.9   0.2      0.003   17.4   0.1    2.3  2  TrmB      Sugar-specific transcriptional regulator TrmB
     0.0061   16.2   0.1     0.0094   15.6   0.1    1.5  1  SMC_ScpB  Segregation and condensation complex subunit ScpB
  ------ inclusion threshold ------
      0.013   15.4   0.1      0.023   14.6   0.1    1.5  1  PadR      Transcriptional regulator PadR-like family
      0.034   14.0   0.0       0.17   11.8   0.0    2.1  2  HTH_5     Bacterial regulatory protein, arsR family
      0.045   13.1   2.1      0.087   12.1   1.1    1.7  2  DUF1978   Domain of unknown function (DUF1978)
      0.064   13.1   0.0        2.4    8.0   0.0    2.4  2  HTH_IclR  IclR helix-turn-helix domain
      0.065   13.4   0.0       0.11   12.6   0.0    1.4  1  HTH_34    Winged helix DNA-binding 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 ?    1.1   0.0      0.17   3.8e+02      18      35 ..      10      27 ..       5      29 .. 0.84
   2 !   21.1   0.1   9.5e-08   0.00021       2      59 ..      24      79 ..      23      83 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.17
                                   TTSEEEHHHHHHHHTSSH CS
                         MarR_2 18 pgrdltvgelarrlglsk 35
                                   + rd+ v e+ r lg+++
  gi|116753719|ref|YP_842837.1| 10 DSRDMQVVEILRSLGVPR 27
                                   567899*********986 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 9.5e-08
                                   T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE..ESSSS CS
                         MarR_2  2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr..pgpeD 59
                                   g+++     La+L++ ++   t ++++r  +l ++ vs +l+ L ++ ++e++  +  +D
  gi|116753719|ref|YP_842837.1| 24 GVPRKVSNMLAYLANVEE--ATSRDIERGSDLRQPEVSIALRTLRKHNWIEESvrR--ND 79
                                   677777889********9..9******************************99444..44 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.041        92      22      46 ..      13      36 ..       5      39 .. 0.80
   2 !   17.4   0.1   1.3e-06     0.003      14      63 ..      33      89 ..      20      93 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.041
                                   CCHHCHHCCCTTSSCHCHHHHHHHH CS
                           TrmB 22 patadeiaeelgvprskvYevLrsL 46
                                    +++ ei + lgvpr kv ++L  L
  gi|116753719|ref|YP_842837.1| 13 DMQVVEILRSLGVPR-KVSNMLAYL 36
                                   578999********9.677777666 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 1.3e-06
                                   CHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.......TTEEE CS
                           TrmB 14 YlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.......pklYr 63
                                    ++L + ++at ++i + +++ ++ v  +Lr L +  ++e + +r        k+Yr
  gi|116753719|ref|YP_842837.1| 33 LAYLANVEEATSRDIERGSDLRQPEVSIALRTLRKHNWIEESVRRndgtgrpVKVYR 89
                                   5678899*********************************99877778888555776 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 !   15.6   0.1   4.2e-06    0.0094      86     140 ..      30      89 ..       3     109 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.2e-06
                       SMC_ScpB  86 letLaiIaykqpvtraeie...eiRGvnsdsvvrtLlerglieekgrkee.pgrpil.Yg 140
                                      +La+ a  +  t+ +ie   ++R  +++ ++rtL + ++iee+ r++  +grp+  Y+
  gi|116753719|ref|YP_842837.1|  30 SNMLAYLANVEEATSRDIErgsDLRQPEVSIALRTLRKHNWIEESVRRNDgTGRPVKvYR 89 
                                    568999999999999999744469*******************98666544***986465 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1     1e-05     0.023      37      65 ..      61      90 ..      48      99 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1e-05
                                   HHHHHHHTTSEEEEEE-S.TSSS-EEEEEE CS
                           PadR 37 aLkrLekeglvesewees.gegpprkyYrl 65
                                   aL++L+k++++e++ +++ g+g+p k+Yrl
  gi|116753719|ref|YP_842837.1| 61 ALRTLRKHNWIEESVRRNdGTGRPVKVYRL 90
                                   79*************9999**********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 ?   -0.7   0.0      0.62   1.4e+03      17      26 ..      15      24 ..       9      29 .. 0.60
   2 ?   11.8   0.0   7.7e-05      0.17       5      43 ..      30      69 ..      26      73 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.62
                                   EHHHHHHHHT CS
                          HTH_5 17 cvcelaeelg 26
                                    v e+ + lg
  gi|116753719|ref|YP_842837.1| 15 QVVEILRSLG 24
                                   4555555555 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 7.7e-05
                                   HHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTT CS
                          HTH_5  5 lkILklLae.gelcvcelaeelglsqstvShHLkkLreaG 43
                                   + +L +La+ +e+++ ++ +  +l q+ vS  L+ Lr+ +
  gi|116753719|ref|YP_842837.1| 30 SNMLAYLANvEEATSRDIERGSDLRQPEVSIALRTLRKHN 69
                                   67899****9***************************965 PP

>> DUF1978  Domain of unknown function (DUF1978)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.27   6.1e+02     172     212 ..       4      44 ..       2      73 .. 0.57
   2 ?   12.1   1.1   3.9e-05     0.087      98     130 ..      91     123 ..      86     128 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.27
                        DUF1978 172 dywKeeekkelersaElrekgtkvkseEleeqlesleellk 212
                                    +y+ + ++++++    lr  g + k   +  +l   ee   
  gi|116753719|ref|YP_842837.1|   4 SYVMKFDSRDMQVVEILRSLGVPRKVSNMLAYLANVEEATS 44 
                                    56666666665555555555555554444444444444433 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 3.9e-05
                        DUF1978  98 eeaekellkalkdlkdqeierveeRlkelealY 130
                                    +   +e lk+ ++ k +e +r+ eR+++l+al 
  gi|116753719|ref|YP_842837.1|  91 KASIDEILKYYEEEKLKEANRAMERIQKLRALL 123
                                    566799*************************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 ?    3.1   0.0     0.036        82      17      32 ..      12      27 ..      10      38 .. 0.82
   2 ?    8.0   0.0    0.0011       2.4       9      49 ..      33      72 ..      27      74 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.036
                                   SS-BHHHHHHHHTS-H CS
                       HTH_IclR 17 qeltlselArrtglpk 32
                                   +++ + e+ r +g+p+
  gi|116753719|ref|YP_842837.1| 12 RDMQVVEILRSLGVPR 27
                                   68999**********8 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0011
                                   HCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                       HTH_IclR  9 LdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                   L +la   ++ t +++ r ++l  + v+  L+tL ++ ++e
  gi|116753719|ref|YP_842837.1| 33 LAYLANVEEA-TSRDIERGSDLRQPEVSIALRTLRKHNWIE 72
                                   6677777776.999*************************98 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.1e-05      0.11       5      49 ..      32      76 ..      30      92 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.1e-05
                         HTH_34  5 vlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdke 49
                                   +l+yLa v+ea+ +++     + + + s+ l++L k ++ie +  
  gi|116753719|ref|YP_842837.1| 32 MLAYLANVEEATSRDIERGSDLRQPEVSIALRTLRKHNWIEESVR 76
                                   699*************************************85544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1169  (0.0652016); expected 358.6 (0.02)
Passed bias filter:                      643  (0.0358637); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 996.62
//
Query:       gi|116753720|ref|YP_842838.1|  [L=281]
Description: phosphate binding protein [Methanosaeta thermophila PT]
Scores for complete 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-38  131.1   0.1    1.7e-37  129.6   0.1    1.6  1  PBP_like_2  PBP superfamily domain
    8.1e-20   70.8   0.0    1.1e-19   70.3   0.0    1.1  1  PBP_like    PBP superfamily domain
     0.0097   15.7   0.0      0.044   13.5   0.0    2.0  2  SBP_bac_11  Bacterial extracellular solute-binding protein


Domain annotation for each model (and alignments):
>> PBP_like_2  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.6   0.1   2.9e-41   1.7e-37       8     280 ..      28     266 ..      24     268 .. 0.89

  Alignments for each domain:
  == domain 1  score: 129.6 bits;  conditional E-value: 2.9e-41
                     PBP_like_2   8 svgeifgaGsttpapalrkladafekaapgakvnyastGSgagikalrngdvdfagsdrplteseiaagwaangaggliq 87 
                                    sv+ i+++Gstt+ p+ +  a+ f+  +  + v+++++GSg gi + ++g +d+a+s+r ++ se  a ++    +++ +
  gi|116753720|ref|YP_842838.1|  28 SVDRIRVSGSTTVMPLAELCAEEFNFMYREYMVTVTAGGSGVGIIDAAEGRADIAMSSREIKPSER-ALYERPD-RKFKE 105
                                    5677*******************9999999**********************************99.5666665.***** PP

                     PBP_like_2  88 vpvaigaialvvnkd...npln.lsreaLakIfsgkItnWndvlglpadgpIkvvhrsdgsgttflfstalaeqgpwtas 163
                                    + v+++ai++vv+++   + ++ l++++++kI+sg+I+nW+  +g+p d  I vv r+ gsgt+++f + ++  + +++ 
  gi|116753720|ref|YP_842838.1| 106 ILVGYDAIIVVVSPQiynSSVRsLTATEVKKIYSGEIRNWKS-VGGP-DREIMVVGRKAGSGTRDTFNEIIMGSAAAETP 183
                                    *************9999777779******************9.6666.**************************888877 PP

                     PBP_like_2 164 gigasg..segvasav.snngaigyvsvaywlavkgysladvtngagkfvlptaataasalkvakiasnplawslqpvee 240
                                    g++ +   s++v++a+   + aigy+ ++y +              ++ v p       al             + p+++
  gi|116753720|ref|YP_842838.1| 184 GVSIEAldSSEVKTAIlGSDRAIGYLGYSYVR--------------TGGVVPL------ALDG-----------VYPTMD 232
                                    77744466*******9677*********9888..............2233333......3444...........9***** PP

                     PBP_like_2 241 niadgayPlsrftyiivyqpyayhgnnaalakaFldylls 280
                                    ni  g y l r +y+++  ++       a+akaF+d++l 
  gi|116753720|ref|YP_842838.1| 233 NIRGGNYTLARKLYFYTFGEP------TAGAKAFIDFVLG 266
                                    *******************99......**********986 PP

>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.3   0.0   1.8e-23   1.1e-19       1     155 [.      48     215 ..      48     231 .. 0.78

  Alignments for each domain:
  == domain 1  score: 70.3 bits;  conditional E-value: 1.8e-23
                                    HHHHHHH-TTCEEEEEES-HHHHHHHHHTTS-SEEEESS---CCCH..HCCCCCEEEEEEEEEEEE-CC-HCHCCCCHCC CS
                       PBP_like   1 aeelaeknpgvrvavanvGsggGlkalrageadiagshlldketee..ynapalrkaldgievvlvnlarreqglvvakg 78 
                                    aee++   +++ v+v+  Gsg G+   ++g+adia+s++ +k +e+  y+        +++++ ++ + ++++ +vv ++
  gi|116753720|ref|YP_842838.1|  48 AEEFNFMYREYMVTVTAGGSGVGIIDAAEGRADIAMSSREIKPSERalYER-------PDRKFKEILVGYDAIIVVVSPQ 120
                                    6888888999*****************************999887755333.......3334444444444554555444 PP

                                    HHHS.................--BGGGC..-S-B-EEEEE-TTSHHHHHHHHHHC-CEECTE-SSTTSEEESSHHHHHCC CS
                       PBP_like  79 npkk.................itnwkdl..adaplrlvnRetGSGtrdlfdellkkegiskssikgyaqearshlavaaa 139
                                      +                  i+nwk +  +d+++ +v+R++GSGtrd f+e + +   + ++ +g++ ea ++++v++a
  gi|116753720|ref|YP_842838.1| 121 IYNSsvrsltatevkkiysgeIRNWKSVggPDREIMVVGRKAGSGTRDTFNEIIMG--SAAAETPGVSIEALDSSEVKTA 198
                                    333222333333344445555*********************************55..68899***************** PP

                                    HCCETTCCEC.CCGG-H CS
                       PBP_like 140 Vaagradvgv.gieava 155
                                    +   + ++g+ g + v 
  gi|116753720|ref|YP_842838.1| 199 ILGSDRAIGYlGYSYVR 215
                                    *********87777665 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 ?   -0.2   0.0      0.11   6.7e+02      92     107 ..     141     156 ..      32     191 .. 0.57
   2 !   13.5   0.0   7.3e-06     0.044     206     229 ..     255     278 ..     224     279 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.11
                                    ---SHHHHHHSS--EE CS
                     SBP_bac_11  92 kikgwadLlkpglkla 107
                                     i++w+++++p+ ++ 
  gi|116753720|ref|YP_842838.1| 141 EIRNWKSVGGPDREIM 156
                                    4556666666655554 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 7.3e-06
                                    HHHHHHHHHTTSHHHHHHHHHTT- CS
                     SBP_bac_11 206 eaAraFlafLrspeaqailrkyGf 229
                                    + A+aF++f+++pe+++i++ +Gf
  gi|116753720|ref|YP_842838.1| 255 AGAKAFIDFVLGPEGRRIAETNGF 278
                                    679********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2197.55
//
Query:       gi|116753721|ref|YP_842839.1|  [L=291]
Description: apurinic endonuclease Apn1 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-36  124.9   0.0    3.4e-36  124.7   0.0    1.1  1  AP_endonuc_2  Xylose isomerase-like TIM barrel


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.7   0.0   1.9e-40   3.4e-36       2     210 .]      28     244 ..      27     244 .. 0.95

  Alignments for each domain:
  == domain 1  score: 124.7 bits;  conditional E-value: 1.9e-40
                                    HHHHHCT-SEEEEECCTCSHHHHC..HHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHHHHHHH CS
                   AP_endonuc_2   2 aaaaeaGfdgvElfgrdlvpvsel..sdeelrelrkaldelglriaslslftrfgypdederearreesvdalkraiela 79 
                                    ++a e+G d+ ++f+++++ +  +  sd+ +++++++l + g+  ++ ++++ ++      re++  +sv+alk+++ ++
  gi|116753721|ref|YP_842839.1|  28 RRAIELGCDTYQIFTSNPRGWHTKqlSDDVIEAFKSQLSRSGIWPVVGHMPYLPNLASP--RESVYSRSVQALKDELMRC 105
                                    67889*****************99********************999988888777666..45557889*********** PP

                                    HHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTC..HHHHHHHHHHTTTTEE CS
                   AP_endonuc_2  80 aaLGapllvlhpGtagagpkgseeeawerlaeslneladyaekegvklalEtlagsgvelgd..eelarlldavdspnvg 157
                                    +aLG+p+lv+h G   ++ ++++++ + r++ +++++++    +g k++lEt+ gs ++ g+  e+la++l++v+s+ +g
  gi|116753721|ref|YP_842839.1| 106 SALGIPYLVTHMG---SHLGSGRDSGISRIVGAIEAALPD--SNGTKILLETTSGSKNSIGGrfEDLADVLERVGSDLLG 180
                                    *************...************************..99**************9999****************** PP

                                    EEEEHHHHHHH......TTTHHHHHHHHHGG.....EEEEEE.EESSTTTTSSTTEESTTSSSS CS
                   AP_endonuc_2 158 vclDtgHllia......eedvddalraladr.....ikhvHikDakgdlgagrdrhvpigeGei 210
                                    +clDt+H ++a      e  +d++lra+++      + ++H++D++gdlg+g drh+ ig+G i
  gi|116753721|ref|YP_842839.1| 181 ICLDTCHVFAAgydlrdEKSLDATLRAFDSTaglkdLMLIHLNDSVGDLGSGLDRHEHIGMGKI 244
                                    **************************************************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); 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 0.22s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 2304.46
//
Query:       gi|116753722|ref|YP_842840.1|  [L=142]
Description: response regulator receiver protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-21   76.4   0.1    2.1e-21   76.1   0.1    1.1  1  Response_reg    Response regulator receiver domain
  ------ inclusion threshold ------
      0.095   12.9   0.0       0.14   12.4   0.0    1.2  1  H_lectin        H-type lectin domain
       0.11   11.7   0.0       0.14   11.3   0.0    1.2  1  Methyltransf_3  O-methyltransferase


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.1   0.1   3.6e-25   2.1e-21       1     108 [.      18     134 ..      18     138 .. 0.90

  Alignments for each domain:
  == domain 1  score: 76.1 bits;  conditional E-value: 3.6e-25
                                    EEEESSSHHHHHHHHHHHHHTTE.EEEEEESSHHHHHHHHHHHH......ESEEEEESSCSSSEHHHHHHHHHHCT..TT CS
                   Response_reg   1 vlivdDdplvrellrqlleeegy.eevaeaedgkealellkeek......vdlillDinmpgmdGlellkeireed..pe 71 
                                    +l+v+D+p  + l+r++l+++g+  + + + dg+eal++l+ +       +dlillDin+p+m G+ +lk i+ +   + 
  gi|116753722|ref|YP_842840.1|  18 ILLVEDNPEDVFLTRKVLRKSGLdGDMQITGDGAEALRILEDMLragehlPDLILLDINLPDMGGMAVLKSIKGDArfSR 97 
                                    89*******************994466799**********5444445556**********************9888789* PP

                                    SEEEEEESSTSHHHHHHHHHCTESEEEESSG-HHHHH CS
                   Response_reg  72 lpviiltahseeedavealkagaddflsKpfdpeeLl 108
                                    +pv++lt  ++++d+++ +++ga+ +l+Kp+++++++
  gi|116753722|ref|YP_842840.1|  98 IPVVMLTCSNADSDIQKSYDLGASTYLVKPVSRDAMI 134
                                    ********************************99987 PP

>> H_lectin  H-type lectin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.3e-05      0.14       8      35 ..      93     120 ..      87     131 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.3e-05
                                    S--SS--EEEEEEEEEEEBTT.EEEEEE CS
                       H_lectin   8 kpFssiPkVflslnkidmdkgqnlrvsv 35 
                                      Fs+iP V+l+ ++ d+d +++++  +
  gi|116753722|ref|YP_842840.1|  93 ARFSRIPVVMLTCSNADSDIQKSYDLGA 120
                                    67****************9988766544 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.4e-05      0.14      74     130 ..      17      74 ..       5      79 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.4e-05
                                    EEEEEES-HHHHHHHHHHHHHTT-GGGEEEE..ES-HHHHHHHHHTSSS---EEEEEE- CS
                 Methyltransf_3  74 kilaididreayeialkfiqkagvaekieli..egdalkvLeelvkdkklpefDfifvD 130
                                    +il ++ ++e + +++k+++k+g++  +++    ++al++Le++++  +    D+i++D
  gi|116753722|ref|YP_842840.1|  17 RILLVEDNPEDVFLTRKVLRKSGLDGDMQITgdGAEALRILEDMLRAGE-HLPDLILLD 74 
                                    68999*******************9887775226799*******99885.344777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       236  (0.013163); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1062.56
//
Query:       gi|116753723|ref|YP_842841.1|  [L=299]
Description: tRNA-modifying enzyme [Methanosaeta thermophila PT]
Scores for 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-23   81.3   0.0    2.7e-22   79.9   0.0    1.7  1  Radical_SAM   Radical SAM superfamily
    1.1e-21   76.9   0.0    2.2e-21   75.9   0.0    1.5  1  Wyosine_form  Wyosine base formation


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.9   0.0     3e-26   2.7e-22       3     166 ..      53     226 ..      51     227 .. 0.83

  Alignments for each domain:
  == domain 1  score: 79.9 bits;  conditional E-value: 3e-26
                                    EESEESS--TTTSCCTT....................HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTT CS
                                    xxxxxxxxxxxxxxxxx....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   3 vtrgCnlrCsfCarpet....................vrregrgrslsveeileevkelkaekgvkevilgggepllypd 62 
                                    ++  Cn+ C +C+rp +                     ++++        ++++ ++   a+  +++ i+++gep++yp+
  gi|116753723|ref|YP_842841.1|  53 PVLHCNHLCLHCWRPVDdsfplperwtepedlldlvlREQRRILSGYWGSDVVDRARLQDASTPKHVAISLMGEPTFYPH 132
                                    5667*************999988777777777777774444444455555555555555455558888888********* PP

                                    HHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  63 fvellerlaklavpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagi 142
                                    +  l++++ ++   g++ +++tngt p     + l++  +++++++++a+d++++++   +g ++ ++le+l ++r++++
  gi|116753723|ref|YP_842841.1| 133 LRGLIKAINER---GMTSFLVTNGTNP-----DVLKDVDPTQLYISINAPDEDTYRRVS-GGRDWNRILESLAMMRDLRC 203
                                    *9999999998...*************.....*********************666666.99****************** PP

                                    ETEEEEEEEBTTTSHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM 143 krvvdrivglpGendeeleellel 166
                                    + +v+ri++++G+n+   +++++l
  gi|116753723|ref|YP_842841.1| 204 R-TVVRITLIRGVNMFNPDAYARL 226
                                    *.************9877777776 PP

>> Wyosine_form  Wyosine base formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.9   0.0   2.5e-25   2.2e-21       2      63 .]     229     289 ..     228     289 .. 0.97

  Alignments for each domain:
  == domain 1  score: 75.9 bits;  conditional E-value: 2.5e-25
                                    HT-SEEEEEE------------------HHHHHHHHHHHHTSSS.EEEEEEETTTTEEEEEE CS
                   Wyosine_form   2 aepdFvEvKaytyvGssrsrLtmknvPwheevadfakrlegsaedYellaehrhSrvvllar 63 
                                    aepdFvEvKay+++G sr+rL+++++P+heev++fa +l++s + Y+l ++   Srv+ll+r
  gi|116753723|ref|YP_842841.1| 229 AEPDFVEVKAYMHLGRSRYRLSRDAMPSHEEVVSFASALAESMG-YTLEDQVSLSRVALLTR 289
                                    89******************************************.**************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 2320.97
//
Query:       gi|116753724|ref|YP_842842.1|  [L=403]
Description: malate dehydrogenase [Methanosaeta thermophila PT]
Scores for 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-31  106.9   0.1    3.9e-28   98.5   0.1    2.3  1  malic          Malic enzyme, N-terminal domain
    1.7e-21   76.7   2.1      3e-20   72.6   2.1    2.5  1  Malic_M        Malic enzyme, NAD binding domain
     0.0028   17.4   0.0     0.0048   16.7   0.0    1.3  1  ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydro
  ------ inclusion threshold ------
      0.014   14.8   1.0      0.026   13.9   1.0    1.4  1  ThiF           ThiF family


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 !   98.5   0.1   8.7e-32   3.9e-28       4     182 .]       4     134 ..       1     134 [. 0.94

  Alignments for each domain:
  == domain 1  score: 98.5 bits;  conditional E-value: 8.7e-32
                                    ECCCCCCHHCCCHHHHHHHHSTTCHHHHHHHHHHHGGCHHSCCCEGGGETCHHHHHTTSS.SS..EEEEE-SSSBTTTBS CS
                          malic   4 netlfykllkekleellpivYtPtvgeacqeyseeyrkarglylsikdkekikeilknlpeedvkvivvtdgeriLGlGd 83 
                                    + ++   +lk+   e+l+++YtP+v+e+  ++s+++++++ ly+s++++                v+vvtdg+++LGlGd
  gi|116753724|ref|YP_842842.1|   4 IAISSRVVLKDA--EDLSLAYTPGVAEPSLAISRNPDDVY-LYTSKGNM----------------VAVVTDGTAVLGLGD 64 
                                    555666677777..**************************.********................*************** PP

                                    -G.HHHHHHHHHHHHHHHHHHS-EGGGEEEEEECS-BS.HHHHC.TT..S.SSB...SHHHHHHHHHHHHHHHHHHGCTS CS
                          malic  84 lG.vagvgimvGKlaLytalagidPekvlpvvldvgtnneelledplYlGlrkkRvkgeeydefvdefveavkelfppka 162
                                    +G +a++++m+GK+ L++++agid   ++p++l ++                           +  e+ve+v ++ p ++
  gi|116753724|ref|YP_842842.1|  65 IGpLASIPVMEGKALLFKKFAGID---AFPIALSTK---------------------------DPAEIVETVVRISPVFG 114
                                    ************************...*********...........................889************** PP

                                    EEEE-S--CCHHHHHHHHHC CS
                          malic 163 liqfEDfkaknafeileryr 182
                                    +i++ED++a+++fei+e ++
  gi|116753724|ref|YP_842842.1| 115 GINLEDISAPRCFEIEEELK 134
                                    ****************9875 PP

>> Malic_M  Malic enzyme, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.6   2.1   6.8e-24     3e-20       3     257 ..     148     366 ..     146     368 .. 0.87

  Alignments for each domain:
  == domain 1  score: 72.6 bits;  conditional E-value: 6.8e-24
                                    HHHHHHHHHHHHHHHHH-S-GGG--EEEEC-SHHHHHHHHHHHHHHHTTTS-HHHHHTTEEEEETTEE-BTT-S---TTT CS
                        Malic_M   3 gTaavalagllaalkitgkklseqkivvlGaGsagiGiaeqivealvkeGlseeeakkkiylvDrkGLltedrekleeek 82 
                                    gTa+v++a+l++alk+ gk++++  i v GaG+ag+ +++ +++  v          ++i + DrkG+++++re+l++ k
  gi|116753724|ref|YP_842842.1| 148 GTAVVVVAALINALKLVGKSFKDISIAVSGAGAAGVAVTKFLLDFGV----------RDIRVCDRKGIIHRGREDLSPIK 217
                                    9*************************************999988755..........56899****************** PP

                                    GGGSBS--SS--S....SHHHHHHHH--SEEEE-SSSSS-S-HHHHHHHHHHSSS-EEEE--SSGGGSSS-HHHHHHHTT CS
                        Malic_M  83 kpfakkkeelkeakdkltLeevvkkvkptvliGlsgvagafteeivremaksterPiilplSNPtskaEataedvlkwtd 162
                                    +++a+ ++       + tL ++++   ++v iGls v+g+ ++++v+ m +    P+++++ NP    E +++++ k   
  gi|116753724|ref|YP_842842.1| 218 RMLAELTNPEGI---TGTLRDAMRG--ADVFIGLS-VGGIVSRDMVEGMGR---DPVVFAMANPVP--EIMPDEARK--A 284
                                    **9998877663...579***9997..69*****8.89*********9975...7*********86..889999987..5 PP

                                    T-SEEEESS----EEETSEEE--EE--GGGTHHHHHHHHHHTT-SS--HHHHHHHHHHHHTT--HHHHHTT-SS--GGGH CS
                        Malic_M 163 gkalvasGsPfkpvelngktyeigQaNNayifPglglgvivarakritdemllaaaealaelvseeelkegsllPelsei 242
                                    g+ +va+G          +  +++Q NNa+ fPg+  g++ +ra+ i+++m  aaa a+a+lv++ +   + + P+  + 
  gi|116753724|ref|YP_842842.1| 285 GARVVATG----------RSDYPNQVNNALGFPGIFRGALDVRASDINERMKRAAAFAIASLVDPVRE--DCIIPSPLD- 351
                                    78889987..........67799****************************************98775..477775433. PP

                                    HHHHHHHHHHHHHHH CS
                        Malic_M 243 revslkvavavakaa 257
                                    r v  +va ava aa
  gi|116753724|ref|YP_842842.1| 352 RRVVPAVAEAVAAAA 366
                                    445556666666555 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 !   16.7   0.0   1.1e-06    0.0048       7      70 ..     146     208 ..     142     233 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.1e-06
                                    TTHHHHHHHHHHHHHHHHTTTS-STTEEEEEE--SHHHHHHHHHHHHCT-EEEEEEESSEEEEE CS
                  ELFV_dehydrog   7 peaTglGvvyyveemlkklkldslegkrvaisGsGnvgsyaallltelgakvvavsDssGviyd 70 
                                    ++ T++ vv+++ ++lk   ++s+++ ++a+sG G  g ++ ++l + g + + v D +G+i+ 
  gi|116753724|ref|YP_842842.1| 146 QHGTAVVVVAALINALKL-VGKSFKDISIAVSGAGAAGVAVTKFLLDFGVRDIRVCDRKGIIHR 208
                                    555666666666677766.4557***************************************95 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   1.0   5.8e-06     0.026      14      50 ..     166     202 ..     150     205 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.8e-06
                                    HHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEEES CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF  14 ekLrdskvllvGaGglGsellknLalsGvgkltlvDn 50 
                                    +  +d ++++ GaG+ G  + k L   Gv+ +++ D 
  gi|116753724|ref|YP_842842.1| 166 KSFKDISIAVSGAGAAGVAVTKFLLDFGVRDIRVCDR 202
                                    567899*****************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); 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: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2881.67
//
Query:       gi|116753725|ref|YP_842843.1|  [L=312]
Description: nucleoside recognition domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0083   16.4  24.8      0.029   14.7   3.3    3.2  3  Gate             Nucleoside recognition
  ------ inclusion threshold ------
      0.079   13.0   0.3      0.079   13.0   0.3    3.2  3  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe


Domain annotation for each model (and alignments):
>> Gate  Nucleoside recognition
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   3.3   3.2e-06     0.029       4     108 ..      15     114 ..      12     118 .. 0.73
   2 !   13.6   5.3   6.7e-06      0.06       7     102 ..     186     274 ..     180     284 .. 0.83
   3 ?   -0.4   0.2      0.15   1.3e+03       3      18 ..     284     299 ..     282     308 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.2e-06
                           Gate   4 agpiillasiliwflssssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtlytsalgellqgfdtpk 83 
                                    ++ +++l+++l ++l + ++l+r++ l +p+++     l+  ++ s+l+++++  ++ ++++++       +   +d+++
  gi|116753725|ref|YP_842843.1|  15 VLVTVFLGLFLAGMLMELGVLDRLSVLSKPLVSMAN--LPSISASSFLVSLGSAVAANSMIAEFK------MRGAIDDRE 86 
                                    78899*****************************77..**************7777777777775......444444444 PP

                           Gate  84 salafllfvllyt....pcvatlavivre 108
                                    + + + +++++ +    +  ++++v+v  
  gi|116753725|ref|YP_842843.1|  87 T-VLCAMMNSIPVyireIFTYQIPVVVPL 114
                                    4.444444443332266666666666655 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 6.7e-06
                           Gate   7 iillasiliwflssssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtlytsalgellqgfdtpks.a 85 
                                    + +++++l+  l++++++++++ l  p+ + +g   + +a v+l+t +a+  +++++l+ +        ++g  t+++ a
  gi|116753725|ref|YP_842843.1| 186 TYMAMTLLVLSLNDHGFFDKLSVL--PIAQTFG--ISPEALVPLTTYVASPLIGLSMLSPMI-------QSGSLTEIQaA 254
                                    55678888888999********99..*******..***********************8885.......99******956 PP

                           Gate  86 lafllfvllytpcvat...l 102
                                     +++l ++++ p +a    +
  gi|116753725|ref|YP_842843.1| 255 TVLMLGSMFMLPIFAMksmV 274
                                    68888888888998874444 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.15
                           Gate   3 kagpiillasiliwfl 18 
                                    ++g +i+++s+ ++++
  gi|116753725|ref|YP_842843.1| 284 RVGLMIVAISTGLSVM 299
                                    7899999999999987 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 ?   -0.6   1.5      0.15   1.3e+03      71      85 ..      17      32 ..       4      78 .. 0.58
   2 ?   13.0   0.3   8.8e-06     0.079      53     113 .]     119     174 ..     107     174 .. 0.76
   3 ?   -1.2   5.4      0.23     2e+03      42      80 ..     253     309 ..     245     312 .] 0.57

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.15
                Phage_holin_3_6 71 i.vaavllvlagvlal 85
                                   + v++ l+++++++ l
  gi|116753725|ref|YP_842843.1| 17 VtVFLGLFLAGMLMEL 32
                                   2122222222222222 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 8.8e-06
                Phage_holin_3_6  53 lllval.alalaalwlaalivaavllvlagvlalvglkklkkakplpertieelkedvaalk 113
                                    + l+ + ++++      + iv ++++++ g l+l+g++ +  +  +p+r i++l +++++l+
  gi|116753725|ref|YP_842843.1| 119 VGLFYAgVFII------TAIVKVLMVIILGRLILRGRNGAEISWEAPRRNINSLDATLKILR 174
                                    22222224444......6779*****************9999888***********999885 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.23
                Phage_holin_3_6  42 aagvlallalllllvala................lalaa...lwlaalivaavllvla 80 
                                    aa vl+l ++++l ++++                l++ +     l+ ++ a++ll+l 
  gi|116753725|ref|YP_842843.1| 253 AATVLMLGSMFMLPIFAMksmvpnytaifgprvgLMI-VaisTGLSVMVRAVFLLALL 309
                                    6777777777777777766667777776666633222.22334444444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 2195.40
//
Query:       gi|116753726|ref|YP_842844.1|  [L=282]
Description: ribose-phosphate pyrophosphokinase [Methanosaeta thermophila PT]
Scores for complete 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   86.2   0.0    1.5e-19   70.0   0.0    2.4  2  Pribosyltran_N  N-terminal domain of ribose phosphate pyropho
    2.5e-20   72.6   0.3    4.2e-20   71.9   0.3    1.3  1  Pribosyltran    Phosphoribosyl transferase domain
      3e-07   30.6   1.0      7e-07   29.5   0.4    1.8  2  Pribosyl_synth  Phosphoribosyl synthetase-associated domain
    1.4e-06   27.9   0.1    2.5e-06   27.1   0.1    1.4  1  UPRTase         Uracil phosphoribosyltransferase
  ------ inclusion threshold ------
      0.061   12.8   0.1       0.13   11.7   0.1    1.6  1  PRTase_2        Phosphoribosyl transferase
       0.21    9.4   0.0       0.28    9.0   0.0    1.1  1  DUF5396         Family of unknown function (DUF5396)


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 !   70.0   0.0     5e-23   1.5e-19       3     113 ..       2     107 ..       1     109 [. 0.95
   2 !   13.8   0.0   1.3e-05      0.04       8      82 ..     163     234 ..     156     246 .. 0.79

  Alignments for each domain:
  == domain 1  score: 70.0 bits;  conditional E-value: 5e-23
                 Pribosyltran_N   3 ifagssskeLaekiakrlgvelgkakvsrfadgEikveieesvrgkdvfiiqslskpvndnlmelllmidalrrasakri 82 
                                    i+ g ss+ La ++a+ lg +++ ++ ++f+dgE++ ++++++  +dv++iqs+ ++   +++ ll ++d +r    ++i
  gi|116753726|ref|YP_842844.1|   2 IIGGPSSQLLAGRVASILGERVALCEYRTFPDGEAYTQLQSEID-DDVVVIQSTPSD--RDIVYLLQLLDIVR---ERNI 75 
                                    89999*************************************95.79******9877..99***********9...899* PP

                 Pribosyltran_N  83 taViPylgysrqdrk.ksrepisaklvaklLe 113
                                    t+ViPy+gy+rqd+  k+ ep++a+ +a+ L+
  gi|116753726|ref|YP_842844.1|  76 TLVIPYFGYARQDKIfKPGEPLTARAIASALN 107
                                    ****************************9885 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.3e-05
                 Pribosyltran_N   8 sskeLaekiakrlgvelgkakvsrfadgEikveiee.svrgkdvfiiqslskpvndnlmelllmidalrrasakri 82 
                                     + ++a++ ++ lg+   + + +r +  E+++  +e +vrg+dv+i+ ++ +        +   i+ lrr+ a+++
  gi|116753726|ref|YP_842844.1| 163 GAMAMASRASEILGCDFDHLEKTRHSGTEVSIAPKEiDVRGRDVVIMDDMIATG----GTMATAISMLRRQGARSV 234
                                    567889999999************************9***********998762....234456666777777665 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.9   0.3   1.4e-23   4.2e-20      11     141 ..     136     260 ..     132     275 .. 0.85

  Alignments for each domain:
  == domain 1  score: 71.9 bits;  conditional E-value: 1.4e-23
                                    EEEEEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----TTSEE CS
                   Pribosyltran  11 ildavarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledpagkkV 90 
                                    +lda  +la+ei++  + + +vv+ +++g++ +a++ +  L++ ++ ++k+++++   + a+        +++d++g+ V
  gi|116753726|ref|YP_842844.1| 136 SLDATPHLAEEIRRL-DLRDPVVISPDKGAMAMASRASEILGCDFDHLEKTRHSGTEVSIAP--------KEIDVRGRDV 206
                                    566777888888888.**************************99999998888877777776........9********* PP

                                    EEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEE...E-HHHHHHHHHH-TTS. CS
                   Pribosyltran  91 liVDDildtGgTllaalelLkekgpeevriavlv...dkpateeevdknakrvf 141
                                    +i+DD+++tGgT+  a+  L+++g+ +v++a+++   + +a  +   ++++rv 
  gi|116753726|ref|YP_842844.1| 207 VIMDDMIATGGTMATAISMLRRQGARSVHLAAVHpvlTGNALLKLYHAGVDRVT 260
                                    ********************************9977777776666666666665 PP

>> Pribosyl_synth  Phosphoribosyl synthetase-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.3     4e+03     130     149 ..      39      58 ..      30      66 .. 0.72
   2 !   29.5   0.4   2.4e-10     7e-07      80     150 ..     200     270 ..     194     279 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.3
                                    HHHHSS--EEEEESSS--HH CS
                 Pribosyl_synth 130 lleesaidevvvtntiphei 149
                                    +l++   d+vvv  + p + 
  gi|116753726|ref|YP_842844.1|  39 QLQSEIDDDVVVIQSTPSDR 58 
                                    55544446899999999875 PP

  == domain 2  score: 29.5 bits;  conditional E-value: 2.4e-10
                                    --TTSEEEEEEEEE-S-HHHHHHHHHHHHTT--EEEEEEEEE---TTHHHHHHHSS--EEEEESSS--HHH CS
                 Pribosyl_synth  80 dvgGriaiivddliddvesfvaaaevlkerGaykiyvlathGllssdaprlleesaidevvvtntipheiq 150
                                    dv Gr  +i+dd+i    ++  a  +l+ +Ga  ++  a h +l+ +a  +l ++ +d v  t+t+ + + 
  gi|116753726|ref|YP_842844.1| 200 DVRGRDVVIMDDMIATGGTMATAISMLRRQGARSVHLAAVHPVLTGNALLKLYHAGVDRVTATDTLDRGVS 270
                                    9****************************************************************987765 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.1   8.4e-10   2.5e-06     116     166 ..     196     248 ..     164     274 .. 0.70

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 8.4e-10
                        UPRTase 116 Pkki..aertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegv 166
                                    Pk+i  + r v+++D +iaTGg++a+ai++L+++g+++ +   +  +   +++
  gi|116753726|ref|YP_842844.1| 196 PKEIdvRGRDVVIMDDMIATGGTMATAISMLRRQGARSVHLAAVHPVLTGNAL 248
                                    7777667889***********************99876655555544444433 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   4.4e-05      0.13     120     150 ..     202     232 ..     170     247 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.4e-05
                       PRTase_2 120 aakelvLvDDEistGktalnliralqeklpr 150
                                    + + +v++DD i+tG t++  i+ l+++  r
  gi|116753726|ref|YP_842844.1| 202 RGRDVVIMDDMIATGGTMATAISMLRRQGAR 232
                                    5688*******************99998766 PP

>> DUF5396  Family of unknown function (DUF5396)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   9.4e-05      0.28     283     340 ..     107     164 ..     103     174 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 9.4e-05
                        DUF5396 283 enyknkndsvftlyiteaypytfgllskeyfaalphtnqkiknihlksgtpisyeksa 340
                                    + + n n  vft+ i  +   t  +   e + a ph  ++i+ ++l+    is +k a
  gi|116753726|ref|YP_842844.1| 107 NPFLNDNSRVFTVNIHAPSVLTHFMCRAESLDATPHLAEEIRRLDLRDPVVISPDKGA 164
                                    66899******************************************98888766654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2138.20
//
Query:       gi|116753727|ref|YP_842845.1|  [L=450]
Description: peptidase U62, modulator of DNA gyrase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.3e-52  177.7   0.5    5.7e-52  177.3   0.5    1.2  1  PmbA_TldD  Putative modulator of DNA gyrase


Domain annotation for each model (and alignments):
>> PmbA_TldD  Putative modulator of DNA gyrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.3   0.5   3.2e-56   5.7e-52       1     279 []      33     320 ..      33     320 .. 0.84

  Alignments for each domain:
  == domain 1  score: 177.3 bits;  conditional E-value: 3.2e-56
                                    EEEEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEEEEETTEEEEEE...ESSHHHHHHHHHHHHHHCCS---TT-..... CS
                      PmbA_TldD   1 eaevrleesestsvrfengevetnsssedsglgvrvikggrlgfastldtsdealeeaveraveiaklapedpea..... 75 
                                    eaev+ + s+++++++++++ve++s s  +glg+r+i +g +gf+st+d+s   +++++e+av++a+  ++d  +     
  gi|116753727|ref|YP_842845.1|  33 EAEVFGVWSRNLTLELRRDRVESISASVLRGLGLRAIIKGGVGFSSTSDLS--RIDDVAEAAVSAARIFGPDRLWrglpg 110
                                    69*********************************777899*****99999..**********************87766 PP

                                    ...............GGS-HHHHHHHHHHHHHH.CHCST......TEEEEE......EE..EEE......EEE.EEEEEE CS
                      PmbA_TldD  76 ...............eevsaeekielleelekalrsadp......kiensk......ga..risgvsaslsaskeeklia 126
                                                   +                   ++++      +    +      ga  ++  vs+ +s +++  +++
  gi|116753727|ref|YP_842845.1| 111 ksrmpsvdgvfdrriA-------------------DVQTdtlleiS----EellggcGAvgGVEPVSGGVSCTHSLEILI 167
                                    6555444333322222...................22222222221....111223322459999*************** PP

                                    ETTSEEEEEEEEEEEEEEEEEE..STCSETEEEEEEEE...SSHHH..S..SSHHHHHHHHHHCTTT-B---SEEEEEEE CS
                      PmbA_TldD 127 nSeGldveqtrtrvslslsvia.ddggsgdgmgggsgy...edlee..edleeiaeeaaekalasleakplppgkypVvl 200
                                    nS Gld++++ t+++l l+ ia  ++    g  +gs++   +   +   ++++++e+aa+ a++sl+  ++++ +y+Vvl
  gi|116753727|ref|YP_842845.1| 168 NSSGLDLSEEGTSIHLALETIArGSS----GVATGSEFdnsR---SfsVNARAVGEKAADLARRSLDGISIETDTYDVVL 240
                                    **********************3332....445566654421...23468899*************************** PP

                                    -HHHHHHHHHGHHHHHTBHHHHHTT--TTTT-TTSB-S-TT--EEEETT-......-SB-TTSBB---EEEEETTEE--- CS
                      PmbA_TldD 201 speavgsllheavghaleadavlegrSflkdklGekvaselltivddpts.gglgsypfDdEGvptqrtvlIenGvLkny 279
                                    sp a+++ll+ ++ ++l+a++v++grS l+++l++ v +  l++vdd+    g+gs++fD+EGvp+qr+vl e+GvL++y
  gi|116753727|ref|YP_842845.1| 241 SPVAFAELLESTFIPSLSAENVQKGRSTLAGMLNKSVSDLRLQVVDDGALpAGMGSSAFDGEGVPSQRNVLLEDGVLRSY 320
                                    *****************************889*****************99***************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       212  (0.0118244); expected 358.6 (0.02)
Passed bias filter:                      186  (0.0103743); 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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 3586.99
//
Query:       gi|116753728|ref|YP_842846.1|  [L=255]
Description: hypothetical protein Mthe_0414 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-53  180.8   0.1    3.9e-53  180.6   0.1    1.0  1  PAC2      PAC2 family


Domain annotation for each model (and alignments):
>> PAC2  PAC2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.6   0.1   2.2e-57   3.9e-53       1     212 [.      19     233 ..      19     234 .. 0.91

  Alignments for each domain:
  == domain 1  score: 180.6 bits;  conditional E-value: 2.2e-57
                                    EEEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETT..EEE-SEEEEEE..TTT.SEEEEEEE.. CS
                           PAC2   1 LilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveeg..relepprlyak..dsgsrdllvlqg.. 74 
                                    L++G+pg+G+Vg+l++++Lie+l+aek+ ei+s++ +p     p+vlv+++  ++   +++ya    +g+ dll+l+g  
  gi|116753728|ref|YP_842846.1|  19 LVEGLPGVGHVGKLVAEHLIEELKAEKIIEIYSPH-FP-----PQVLVQSDgtVRQVRNEIYAYkgADGEPDLLILVGdy 92 
                                    89*********************************.**.....********766666677787767667*********77 PP

                                    ..E-HSCHHHHHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHHH.......CT.-CEEEE CS
                           PAC2  75 ..repilqyeefakalldwaeelgvkevvvLggldageradvphtrpekvtgaatdeelleele.......es.eyggiv 144
                                       + +++ye ++   ld+aee+gv+++++Lgg+++g+       +p +v+ga ++ el+ee++       e+ ++ggi+
  gi|116753728|ref|YP_842846.1|  93 qsATNEGHYE-LTGIFLDIAEEFGVRRIYTLGGYGTGQFV-----EP-QVIGATNRSELVEEMKslgvvfhENePGGGII 165
                                    7777777777.************************99874.....66.9**************64666655227****** PP

                                    HHHHHHHHHHHHTT-EEEEEEEEEECCC--HHHHHHHHHHHHHHHT---HCHHHHHHHHHHHHHHHHH CS
                           PAC2 145 gitglLlsaakergipavgllaevphylpdPkaaaalleflskllglevdtedLeedaeeleeqleel 212
                                    g++glL+++++ rgi+av+l++ +++yl+dPk+a a+l++l k++g+ev t+ Lee+a+e+e+ +++l
  gi|116753728|ref|YP_842846.1| 166 GVSGLLVGLGGLRGIDAVCLMGTTSGYLVDPKSAHAVLKVLCKAIGIEVRTQALEERAAEMERIVSKL 233
                                    ***************************************************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       757  (0.0422221); expected 358.6 (0.02)
Passed bias filter:                      692  (0.0385967); 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: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.36
# Mc/sec: 2122.61
//
Query:       gi|116753729|ref|YP_842847.1|  [L=60]
Description: nucleolar RNA-binding protein Nop10p [Methanosaeta thermophila PT]
Scores for complete 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   79.5   2.9    1.5e-22   79.3   2.9    1.1  1  Nop10p        Nucleolar RNA-binding protein, Nop10p family
    0.00045   19.7   1.3    0.00057   19.4   1.3    1.2  1  RecR          RecR protein
     0.0075   14.2   0.2     0.0075   14.2   0.2    1.0  1  PolC_DP2      DNA polymerase II large subunit DP2
  ------ inclusion threshold ------
      0.012   15.7   0.5      0.014   15.5   0.5    1.3  1  NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
      0.037   13.7   0.8      0.044   13.5   0.8    1.1  1  TackOD1       Thaumarchaeal output domain 1
      0.049   12.4   0.4      0.047   12.5   0.4    1.0  1  NRDD          Anaerobic ribonucleoside-triphosphate reductase
       0.13   12.3   1.1       0.15   12.1   1.1    1.1  1  HypA          Hydrogenase/urease nickel incorporation, metall
        0.3   11.0   8.4       0.44   10.5   1.0    2.3  2  zf-FPG_IleRS  Zinc finger found in FPG and IleRS
       0.82    9.3   3.4        2.5    7.8   0.2    2.2  2  zf_UBZ        Ubiquitin-Binding Zinc Finger


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 !   79.3   2.9   7.7e-26   1.5e-22       2      48 ..       3      49 ..       2      53 .. 0.95

  Alignments for each domain:
  == domain 1  score: 79.3 bits;  conditional E-value: 7.7e-26
                                   ----EE-TTT--EESSSB-TTT-SB-B-SS--S--TT-TTCHHHHHC CS
                         Nop10p  2 ksylrkcgkcrvYTLkkvcpecggptksahPaRFSPdDkyskyRral 48
                                   +s++ +c++cr YTLk++cp+cg++t+ ++PaRFSP+D+y++yRral
  gi|116753729|ref|YP_842847.1|  3 RSKILRCERCRLYTLKETCPRCGSHTTGTKPARFSPEDRYGRYRRAL 49
                                   7899*****************************************98 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   1.3   2.9e-07   0.00057      12      36 ..       2      26 ..       1      28 [. 0.91

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.9e-07
                                   HHHH-EE-TTT--EESSSS-CCCCS CS
                           RecR 12 akekvrhCsrCgnlteedlCaICsd 36
                                   +++k+ +C+rC+ +t ++ C+ C +
  gi|116753729|ref|YP_842847.1|  2 VRSKILRCERCRLYTLKETCPRCGS 26
                                   6899*******************76 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 !   14.2   0.2   3.8e-06    0.0075     618     642 ..       6      30 ..       1      57 [. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.8e-06
                       PolC_DP2 618 rrkCkkCgketlearCeeCgektee 642
                                      +C++C   tl+ +C++Cg++t+ 
  gi|116753729|ref|YP_842847.1|   6 ILRCERCRLYTLKETCPRCGSHTTG 30 
                                    579*******************986 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.5   7.1e-06     0.014       4      33 ..       2      28 ..       1      50 [. 0.86

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.1e-06
                   NOB1_Zn_bind  4 vkswvlrChaCfkvtkdmtkkFCpkCGnkt 33
                                   v+s +lrC  C   t    k+ Cp+CG++t
  gi|116753729|ref|YP_842847.1|  2 VRSKILRCERCRLYTL---KETCPRCGSHT 28
                                   7999*******99876...555******98 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.8   2.2e-05     0.044      71     100 ..       4      31 ..       1      34 [. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.2e-05
                        TackOD1  71 drirlCpsCksghlnvrevCpkCkSidiee 100
                                     +i  C++C+ + l  +e+Cp C+S  + +
  gi|116753729|ref|YP_842847.1|   4 SKILRCERCRLYTL--KETCPRCGSHTTGT 31 
                                    58899****98876..79*******98765 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.4   2.4e-05     0.047     506     530 ..       5      29 ..       2      49 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.4e-05
                                    -EEEETT.--EESSSB-TTT--BE. CS
                           NRDD 506 kidvCnecgykgeiekCpkCgseee 530
                                    ki +C++c    ++e+Cp+Cgs+ +
  gi|116753729|ref|YP_842847.1|   5 KILRCERCRLYTLKETCPRCGSHTT 29 
                                    6779******999999*****8864 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   1.1   7.6e-05      0.15      70      97 ..       6      29 ..       2      35 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.6e-05
                                   EEEETTTS-EEECHHHHHS-TTTSSS-E CS
                           HypA 70 kvrCreCgkefeleekalrCpkCgsadv 97
                                    +rC++C+  ++l+   ++Cp+Cgs+ +
  gi|116753729|ref|YP_842847.1|  6 ILRCERCR-LYTLK---ETCPRCGSHTT 29
                                   579****9.44444...37******875 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 ?    5.7   1.2    0.0067        13       3      13 ..       8      18 ..       7      20 .. 0.79
   2 ?   10.5   1.0   0.00022      0.44       2      11 ..      19      28 ..      18      32 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0067
                                   B-TTT--BBEE CS
                   zf-FPG_IleRS  3 pCpRCwryier 13
                                   +C+RC+ y+ +
  gi|116753729|ref|YP_842847.1|  8 RCERCRLYTLK 18
                                   7****988765 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00022
                                   SB-TTT--BB CS
                   zf-FPG_IleRS  2 epCpRCwryi 11
                                   e CpRC+ ++
  gi|116753729|ref|YP_842847.1| 19 ETCPRCGSHT 28
                                   88*****997 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.3     0.065   1.3e+02       5       9 ..       9      13 ..       7      16 .. 0.84
   2 ?    7.8   0.2    0.0013       2.5       4      11 ..      20      27 ..      18      30 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.065
                         zf_UBZ  5 CerCg 9 
                                   CerC 
  gi|116753729|ref|YP_842847.1|  9 CERCR 13
                                   ****6 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0013
                         zf_UBZ  4 lCerCgke 11
                                   +C+rCg++
  gi|116753729|ref|YP_842847.1| 20 TCPRCGSH 27
                                   8*****86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.33u 0.26s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 454.39
//
Query:       gi|116753730|ref|YP_842848.1|  [L=257]
Description: translation initiation factor IF-2 subunit alpha [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.4e-23   81.9   0.7    5.2e-23   81.3   0.2    1.6  2  EIF_2_alpha  Eukaryotic translation initiation factor 2 alpha
    1.8e-10   41.0   0.9    3.7e-10   40.0   0.2    1.8  2  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 ?   -3.2   0.0      0.95   8.5e+03      72      84 ..      49      61 ..      33      81 .. 0.61
   2 !   81.3   0.2   5.9e-27   5.2e-23       3     116 .]     117     226 ..     116     226 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.95
                                   HHHHHHHHHHHST CS
                    EIF_2_alpha 72 veaIkeaLkagee 84
                                   ++ I++  ++g++
  gi|116753730|ref|YP_842848.1| 49 IKYIRDHVREGQK 61
                                   6677777776665 PP

  == domain 2  score: 81.3 bits;  conditional E-value: 5.9e-27
                                    HCTHHHHTTTTS-HHHHH.HHHHSTTHHHHHTTS-TTTHHHHHHCTHHHHHHT-EEEEEEEEEEE-STTHHHHHHHHHHH CS
                    EIF_2_alpha   3 eevgwklyekyghaydaF.klaitdeevldkleipeeveeaLveiikkklkpqkvkiradieltcftkdGveaIkeaLka 81 
                                    ++v   l++ y+++y a+ + ai++ee l++ +++ee ++ +   +k+++k++ v+i+++++l++f++dG+e Ik+aLk+
  gi|116753730|ref|YP_842848.1| 117 KRVKDALMKSYNSLYGALeETAISGEESLSDSGLTEEDIKIISRLAKENVKIPMVEISGYVDLRSFAPDGIEIIKKALKQ 196
                                    5678899************************************************************************8 PP

                                    HST.S..TTSSSEEEEEEEESSSSEEEEEEEES.. CS
                    EIF_2_alpha  82 geeasneeeveeeeevkikliapPeYvltvetldk 116
                                    +++  ++     + +++ik++++P+Y+++v ++d+
  gi|116753730|ref|YP_842848.1| 197 AKRIRDK-----DATLEIKYVGAPRYRIKVIAPDY 226
                                    8886555.....59****************99997 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.2   4.1e-14   3.7e-10       2      75 .]       7      81 ..       7      81 .. 0.95
   2 ?   -1.8   0.0      0.46   4.1e+03      13      56 ..     159     200 ..     157     203 .. 0.69

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 4.1e-14
                                   STTTCEEEEEEEEEETTEEEEEET..TTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEEEEEC CS
                             S1  2 pekgevveGeVtsvtkgGafVelg..ngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrriilsik 75
                                   pe g+ v  +V +v ++GafV l+   + +gf+++se+++   ++ + +++++G+++  kvl+vdk +  i+ls+k
  gi|116753730|ref|YP_842848.1|  7 PEPGDLVVCTVDQVLDFGAFVTLDeyVDKKGFIHISEVASG-WIKYIRDHVREGQKIVCKVLNVDKSKHHIDLSLK 81
                                   577888889999999**********99*************9.9999****************************86 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.46
                                    EEEETTEEEEEETTTEEEEEEGGGSSSSCEESCHHHCEETTEEE CS
                             S1  13 tsvtkgGafVelgngvegfvpaselsrdarvedpdevlkvGdev 56 
                                    +++ k+++ + ++ +++g+v + + + d  +e +++ lk+ +++
  gi|116753730|ref|YP_842848.1| 159 SRLAKENVKIPMV-EISGYVDLRSFAPD-GIEIIKKALKQAKRI 200
                                    5556666666666.89999988888888.777777777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1038  (0.057895); expected 358.6 (0.02)
Passed bias filter:                      639  (0.0356406); 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: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1878.50
//
Query:       gi|116753731|ref|YP_842849.1|  [L=56]
Description: 30S ribosomal protein S27e [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.7e-26   90.6   0.5    3.9e-26   90.5   0.5    1.0  1  Ribosomal_S27e  Ribosomal protein S27
  ------ inclusion threshold ------
      0.023   14.7   0.9      0.033   14.2   0.9    1.2  1  zinc_ribbon_6   Zinc-ribbon
       0.03   14.0   0.3      0.032   13.9   0.3    1.1  1  TackOD1         Thaumarchaeal output domain 1
       0.11   12.4   1.2       0.14   12.1   1.2    1.1  1  eIF-5_eIF-2B    Domain found in IF2B/IF5
       0.15   12.1   1.9        1.4    9.0   0.0    2.1  2  zf-BED          BED zinc finger
       0.25   10.9   0.1       0.25   10.9   0.1    2.0  2  Sgf11           Sgf11 (transcriptional regulation protein)


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 !   90.5   0.5   1.3e-29   3.9e-26       3      54 ..       4      55 ..       2      56 .] 0.97

  Alignments for each domain:
  == domain 1  score: 90.5 bits;  conditional E-value: 1.3e-29
                                   --EEEEE-TTTS-EEEEESS-SS-EEESSSTCEEEEECSSSEEESSCEEEEE CS
                 Ribosomal_S27e  3 skFldvkCpdCenetvvFshaatvvkCisCgkvLvePtGGkaklkaqilerl 54
                                   skFl+vkC dCen +v+Fs+aatvvkC+ Cg++L+eP+GGka +k +ile+l
  gi|116753731|ref|YP_842849.1|  4 SKFLRVKCNDCENVQVIFSRAATVVKCLVCGRTLAEPRGGKADIKTEILEVL 55
                                   89***********************************************997 PP

>> zinc_ribbon_6  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.9   1.1e-05     0.033      26      54 ..       5      34 ..       2      35 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.1e-05
                  zinc_ribbon_6 26 kkvkilCnDCekksevkfh.vlglkCkeCg 54
                                   k  ++ CnDCe+ + +  +    +kC  Cg
  gi|116753731|ref|YP_842849.1|  5 KFLRVKCNDCENVQVIFSRaATVVKCLVCG 34
                                   56789******9988554415678999996 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.3   1.1e-05     0.032     147     173 ..       9      38 ..       5      49 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.1e-05
                        TackOD1 147 ykCnsCks...lfsepevkarClsCekese 173
                                    +kCn+C++   +fs +++ ++Cl C+++ +
  gi|116753731|ref|YP_842849.1|   9 VKCNDCENvqvIFSRAATVVKCLVCGRTLA 38 
                                    6799997633369************99865 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 ?   12.1   1.2   4.5e-05      0.14      88     116 ..       9      35 ..       2      36 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.5e-05
                                    TSTSSSTSTCEEECCSSSCEEEEESSSTC CS
                   eIF-5_eIF-2B  88 VlCkeCkspetelekeerllvlkCkaCga 116
                                    V C+ C++ ++ +++  +++  kC  Cg+
  gi|116753731|ref|YP_842849.1|   9 VKCNDCENVQVIFSRAATVV--KCLVCGR 35 
                                    89******999877766555..*****96 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   0.4     0.032        96      16      25 ..       8      17 ..       4      23 .. 0.87
   2 ?    9.0   0.0   0.00047       1.4      12      27 ..      23      38 ..      18      44 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.032
                                   --EETTTTEE CS
                         zf-BED 16 kavCryCgki 25
                                   +++C+ C+++
  gi|116753731|ref|YP_842849.1|  8 RVKCNDCENV 17
                                   79*****986 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00047
                                   GGSS--EETTTTEE-- CS
                         zf-BED 12 lkeqkavCryCgkils 27
                                   +  ++++C  Cg++l+
  gi|116753731|ref|YP_842849.1| 23 RAATVVKCLVCGRTLA 38
                                   55799********987 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.9      0.27   7.9e+02       5      11 ..       9      15 ..       8      16 .. 0.80
   2 ?   10.9   0.1   8.5e-05      0.25       3      16 ..      26      39 ..      24      41 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.27
                                   EE-TTTS CS
                          Sgf11  5 vtCpnCg 11
                                   v+C+ C+
  gi|116753731|ref|YP_842849.1|  9 VKCNDCE 15
                                   7899995 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 8.5e-05
                                   -EEE-TTTSSEEEG CS
                          Sgf11  3 eyvtCpnCgRqiaa 16
                                   + v+C+ CgR+ a 
  gi|116753731|ref|YP_842849.1| 26 TVVKCLVCGRTLAE 39
                                   679********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.38
# Mc/sec: 438.33
//
Query:       gi|116753732|ref|YP_842850.1|  [L=93]
Description: 50S ribosomal protein L44e [Methanosaeta thermophila PT]
Scores for complete 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   84.4   6.2    6.9e-24   84.1   6.2    1.1  1  Ribosomal_L44  Ribosomal protein L44
  ------ inclusion threshold ------
      0.053   14.0   7.4        1.7    9.2   0.1    2.5  2  zf-H2C2_2      Zinc-finger double domain
      0.072   13.1   2.1        1.5    8.9   0.3    2.2  2  Zn_Tnp_IS1595  Transposase zinc-ribbon domain
        0.1   13.1   1.1        0.1   13.1   1.1    2.1  2  Ribosomal_L33  Ribosomal protein L33
       0.12   12.2   1.3        1.9    8.5   0.1    2.2  2  PyrI_C         Aspartate carbamoyltransferase regulatory chai
       0.18   11.7   1.6         10    6.1   0.1    2.2  2  zf-C4_ClpX     ClpX C4-type zinc finger
        1.7    8.5   7.3        5.6    6.8   0.5    2.5  2  Zn_Tnp_IS1     InsA N-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_L44  Ribosomal protein L44
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.1   6.2   2.7e-27   6.9e-24       1      76 []      16      91 ..      16      91 .. 0.98

  Alignments for each domain:
  == domain 1  score: 84.1 bits;  conditional E-value: 2.7e-27
                                   EEEEEEEEE-------SSSHHHHHHHH.H-SSS..GGGGS----.--SSBB--EEEEETTT--EEE----BBS--EEE CS
                  Ribosomal_L44  1 kHtehkveqykkgkdselaqgkRrydrkqsgyg..GqtkpvfkkkaKttKKivlrleCteCkkkrlkalkRakkfelv 76
                                   kHt+h+ve++++g+++++++++R+++r  +g g  G++++v+++ +K+tK+++lr++C+ Ckk++ ++++R++kfelv
  gi|116753732|ref|YP_842850.1| 16 KHTTHTVERVRRGQARSMTRIARQKAR-ANGTGnqGKFSKVPGG-DKPTKRVNLRYRCSLCKKAHNRKGIRLGKFELV 91
                                   8**************************.8899999*********.*******************************96 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 ?    6.5   3.3    0.0048        12      16      26 .]      10      20 ..       2      20 .. 0.78
   2 ?    9.2   0.1   0.00068       1.7      14      23 ..      68      77 ..      57      80 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0048
                      zf-H2C2_2 16 eCplCdkaFkt 26
                                   +Cp+C+k +++
  gi|116753732|ref|YP_842850.1| 10 HCPFCKKHTTH 20
                                   8******9987 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00068
                      zf-H2C2_2 14 pyeCplCdka 23
                                   +y C+lC+ka
  gi|116753732|ref|YP_842850.1| 68 RYRCSLCKKA 77
                                   59*******8 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.3   0.00058       1.5      19      35 ..       9      27 ..       4      41 .. 0.83
   2 ?    4.1   0.1     0.017        45      37      45 ..      68      76 ..      49      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00058
                  Zn_Tnp_IS1595 19 fvCPhCgsrkayrikt..r 35
                                    +CP+C++ + +++++  r
  gi|116753732|ref|YP_842850.1|  9 AHCPFCKKHTTHTVERvrR 27
                                   57*****998888888432 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.017
                  Zn_Tnp_IS1595 37 lfqCkeCrk 45
                                   +++C+ C+k
  gi|116753732|ref|YP_842850.1| 68 RYRCSLCKK 76
                                   8******97 PP

>> Ribosomal_L33  Ribosomal protein L33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.1   3.9e-05       0.1      33      43 ..      10      20 ..       6      23 .. 0.86
   2 ?   -0.2   0.3      0.54   1.4e+03       6      12 ..      70      76 ..      60      85 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.9e-05
                                   EETTTTEEEEE CS
                  Ribosomal_L33 33 Ycprcrkhtlh 43
                                   +cp+c+kht+h
  gi|116753732|ref|YP_842850.1| 10 HCPFCKKHTTH 20
                                   8********** PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.54
                                   EET.... CS
                  Ribosomal_L33  6 eCtecks 12
                                   +C+ ck+
  gi|116753732|ref|YP_842850.1| 70 RCSLCKK 76
                                   3444444 PP

>> PyrI_C  Aspartate carbamoyltransferase regulatory chain, metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.2     0.041   1.1e+02      30      45 ..       5      20 ..       2      22 .. 0.81
   2 ?    8.5   0.1   0.00074       1.9      28      47 ..      63      82 ..      58      83 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.041
                                   TTTEEEETTT--EEEH CS
                         PyrI_C 30 ekvklkCkYCekeise 45
                                   ++++ +C +C k  ++
  gi|116753732|ref|YP_842850.1|  5 KEIEAHCPFCKKHTTH 20
                                   567889****998776 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00074
                                   ETTTTEEEETTT--EEEHHH CS
                         PyrI_C 28 dkekvklkCkYCekeiseee 47
                                   ++ +++++C  C k ++++ 
  gi|116753732|ref|YP_842850.1| 63 KRVNLRYRCSLCKKAHNRKG 82
                                   567899**********9986 PP

>> zf-C4_ClpX  ClpX C4-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1    0.0082        21       2      11 ..      10      19 ..       9      29 .. 0.82
   2 ?    6.1   0.1     0.004        10       2      11 ..      70      79 ..      69      83 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0082
                     zf-C4_ClpX  2 rCSFCgkses 11
                                   +C FC k  +
  gi|116753732|ref|YP_842850.1| 10 HCPFCKKHTT 19
                                   8*****9765 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.004
                     zf-C4_ClpX  2 rCSFCgkses 11
                                   rCS C k ++
  gi|116753732|ref|YP_842850.1| 70 RCSLCKKAHN 79
                                   8******876 PP

>> Zn_Tnp_IS1  InsA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   1.4    0.0095        24       6      21 ..       9      29 ..       6      35 .. 0.60
   2 ?    6.8   0.5    0.0022       5.6      28      35 .]      68      75 ..      60      75 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0095
                     Zn_Tnp_IS1  6 ihCPrC..sstd.V..yRhGk 21
                                    hCP C  + t  V  +R G+
  gi|116753732|ref|YP_842850.1|  9 AHCPFCkkHTTHtVerVRRGQ 29
                                   6*****442333332255665 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0022
                     Zn_Tnp_IS1 28 RfrCrdCk 35
                                   R+rC+ Ck
  gi|116753732|ref|YP_842850.1| 68 RYRCSLCK 75
                                   9******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       745  (0.0415528); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); 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: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 769.47
//
Query:       gi|116753733|ref|YP_842851.1|  [L=198]
Description: hypothetical protein Mthe_0419 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.2e-05   23.4   1.8      9e-05   22.9   0.3    1.9  2  Sld5      GINS complex protein
  ------ inclusion threshold ------
      0.056   13.3   0.4        0.1   12.5   0.1    1.5  2  CK2S      Casein Kinase 2 substrate
        0.1   12.8   0.1       0.18   12.0   0.1    1.3  1  DUF2652   Protein of unknown function (DUF2652)
       0.13   12.3   1.7          3    7.9   0.0    3.0  2  DUF61     Protein of unknown function DUF61


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 !   22.9   0.3     2e-08     9e-05      30     108 ..       5     100 ..       3     101 .. 0.83
   2 ?   -1.0   0.1      0.53   2.4e+03      69      87 ..     106     124 ..     104     148 .. 0.67

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 2e-08
                                    HHHCCCHHTTSSSSTTTTTTHHHHHHH.HHHHHT...................HCHHHHHHHHHHHHHHHHHHHTHCHHH CS
                           Sld5  30 leailedetkssdlpslpphflelavk.llelard..................ldelkrllrdllevRlakirkfaenle 90 
                                    l+++l  e++s++l+ l+ +f++la + + +l+rd                  l+  ++ + +l+++R++ki k a+  +
  gi|116753733|ref|YP_842851.1|   5 LANVLRGERQSAELQHLEGDFYRLAGRhIASLERDlekledhfsveaqiiedeLKSSRKSISKLMDLRIKKIAKKAMMQA 84 
                                    667788899999*************55477888876666667777777775555555599******************** PP

                                    HHHHTS-TCCHCCS-HHH CS
                           Sld5  91 daagggggellsglseeE 108
                                    +++  ++g+  +g++eeE
  gi|116753733|ref|YP_842851.1|  85 SSS--TPGKPPDGMTEEE 100
                                    ***..9***********9 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.53
                                    HHHHHHHHHHHHHHHHTHC CS
                           Sld5  69 rllrdllevRlakirkfae 87 
                                     +l++l ++R + +  ++ 
  gi|116753733|ref|YP_842851.1| 106 TILEALTRCREEILAHLSY 124
                                    6777888888665555443 PP

>> CK2S  Casein Kinase 2 substrate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   2.3e-05       0.1      44     120 ..      12      89 ..       5      90 .. 0.88
   2 ?   -3.1   0.0       1.4   6.1e+03      65      70 ..     112     117 ..      98     130 .. 0.48

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.3e-05
                           CK2S  44 klygtplrdfpdlqerLrekqlealeevlakLrekle.elqkvrdsleklvrdalqlyeekadklslkeliersavtP 120
                                    ++++++l+++++   rL  +++++le+ l+kL++  + e q + d+l++ +++  +l++   +k+ +k+++++s+ tP
  gi|116753733|ref|YP_842851.1|  12 ERQSAELQHLEGDFYRLAGRHIASLERDLEKLEDHFSvEAQIIEDELKSSRKSISKLMDLRIKKIAKKAMMQASSSTP 89 
                                    556666777777777********************7648999**********************************99 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.4
                           CK2S  65 lealee 70 
                                    +   ee
  gi|116753733|ref|YP_842851.1| 112 TRCREE 117
                                    222222 PP

>> DUF2652  Protein of unknown function (DUF2652)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   3.9e-05      0.18       8      84 ..       8      80 ..       2      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.9e-05
                        DUF2652  8 iidanklglklseieGDAvlfyklgealtleelleqveamrkaFhkklkllekdrickckacaqaekLslKlvaHsG 84
                                   ++  +++  +l+++eGD   fy+l  +  + +l + +e++  +F+ + + +e +  ++ k+  +  +L +K +a + 
  gi|116753733|ref|YP_842851.1|  8 VLRGERQSAELQHLEGD---FYRLAGRHIA-SLERDLEKLEDHFSVEAQIIEDELKSSRKSISKLMDLRIKKIAKKA 80
                                   56666778899******...9999888776.8***************************************999765 PP

>> DUF61  Protein of unknown function DUF61
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.5      0.04   1.8e+02      22      22 ..      54      54 ..       2     116 .. 0.56
   2 ?    7.9   0.0   0.00066         3      26      59 ..     146     179 ..     134     196 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.04
                                   H CS
                          DUF61 22 L 22
                                   +
  gi|116753733|ref|YP_842851.1| 54 I 54
                                   2 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00066
                                    HHT--EEEB.TTS-EEE--HHHHHHHHTTS-GGG CS
                          DUF61  26 Leeekptivtkdgsehrfdkeeleklkeilpeel 59 
                                    L e  p++v+ dg+++ ++k+++ +l ei  ++l
  gi|116753733|ref|YP_842851.1| 146 LLETVPMFVGVDGKRYALRKDDVVMLPEIHARNL 179
                                    678899********************99877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       906  (0.0505327); expected 358.6 (0.02)
Passed bias filter:                      604  (0.0336884); 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: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1452.48
//
Query:       gi|116753734|ref|YP_842852.1|  [L=395]
Description: DNA primase small subunit [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.4e-20   72.2   0.0    1.8e-19   70.5   0.0    1.8  1  DNA_primase_S  DNA primase small subunit


Domain annotation for each model (and alignments):
>> DNA_primase_S  DNA primase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.5   0.0   9.9e-24   1.8e-19       1     175 [.      94     330 ..      94     332 .. 0.77

  Alignments for each domain:
  == domain 1  score: 70.5 bits;  conditional E-value: 9.9e-24
                                    EEEEEETTT-....TT--HHHHHHHHHHHHHHHHHHHH-----GG..GEEEEE--SEEEEEEE--TTEEES-HHHHHHHH CS
                  DNA_primase_S   1 FDiDmddydd...cseatvcekcwkfvsvavkvldellredfgfk..dilwvfsgrrGfHcwvsdkdarpltdeeraaiv 75 
                                    FD+D+d++ +   + ++++ e++ ++  +++k+l+ ll  dfgf+   i + fsg+rG+H++v+dk +  l +  r++iv
  gi|116753734|ref|YP_842852.1|  94 FDLDADHLAEyrgSGIRDFREMLERVKGETMKLLEFLL-SDFGFDerMISVAFSGGRGYHIHVRDKSVLKLRSDARREIV 172
                                    9*********************************9998.******7556678**************************** PP

                                    HH..........................................................HCHHHHCT--------.... CS
                  DNA_primase_S  76 nylnly..................rplhpflsrsmlkivkpvveeiileeqdpf......eikkllrllpdkslre.... 127
                                    +yl+                     +++++l +                + + +      +i+++  +l++ ++ e    
  gi|116753734|ref|YP_842852.1| 173 DYLTGRgldperfihkigvdgdagVERARSLRGP-------------ASDAPGWggrinkAIESMVMHLRELDDEEalrl 239
                                    *655557888877777777666662244444444.............455555566666655555555555555554444 PP

                                    .............................................................-----------------.. CS
                  DNA_primase_S 128 kkkw...........................................eakedivlvllyprldeqvtkgikhllkapfci 164
                                     k++                                            +  ++ ++ l  ++de+vt+++++l++ p ++
  gi|116753734|ref|YP_842852.1| 240 LKNVkgigkqkarlflsqireenaiksiragnldffkhasgiwnliiPYIMEETVRALGGETDEPVTADVHRLIRFPESL 319
                                    222244455555666666666667777778888888999999999996677788999*********************** PP

                                    ..--------- CS
                  DNA_primase_S 165 hgktgnvcvpl 175
                                    hg+tg +++ l
  gi|116753734|ref|YP_842852.1| 320 HGGTGLRVTSL 330
                                    *****888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 2890.58
//
Query:       gi|116753735|ref|YP_842853.1|  [L=245]
Description: Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase [Methanosaeta thermophila PT]
Scores for 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-35  120.3   0.0    1.1e-34  119.9   0.0    1.1  1  CN_hydrolase  Carbon-nitrogen hydrolase


Domain annotation for each model (and alignments):
>> CN_hydrolase  Carbon-nitrogen hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.9   0.0   6.3e-39   1.1e-34       1     260 [.       2     231 ..       2     232 .. 0.91

  Alignments for each domain:
  == domain 1  score: 119.9 bits;  conditional E-value: 6.3e-39
                                    EEEEEEBB-STTHHHHHHHHHHHHHHHHHHTTESEEEEETTTTTBSSSHHHHHHHHBHSSSHHHHHHHHHHHHHTEEEEE CS
                   CN_hydrolase   1 rvAvvQlpqkaadleanlqklleliaeAarkgadLivlPElfitgykeeahfleaAeaglgetlallaalarkngiavvi 80 
                                    r+A+vQl+ + +d   n  ++l+l++ +a++gad+ivlPElf+tg+ + +   e    ++ ++l  ++al+ + g ++v+
  gi|116753735|ref|YP_842853.1|   2 RAACVQLSVRECDVGDNKRRALQLSSDVADIGADIIVLPELFLTGF-CYDLKPE---SIPYPSLMSFRALSLDSGAILVG 77 
                                    79********************************************.5555554...7899******************* PP

                                    EEEEEECCTTEEEEEEEEEEEETTSEEEEEEE-SS--EECTTSCECCGHHTSCS-SSS-EEEETTEEEEEEEGGGGGSHH CS
                   CN_hydrolase  81 gliereltngklqayntavlldldgklvgkyrKlhLfpgeprpptaverelfepgdgipvfdtpvgkiGaaiCyeigfpe 160
                                     ++ +   +      n ++++      +g y K+h f          e++ f pg+ i+++++ +  iG++iCy+i+fpe
  gi|116753735|ref|YP_842853.1|  78 SIMAS--SDRGP--INMGFCMAGAE--TGFYCKTHPF--------GDEKKHFIPGEIIAPVKVGGLSIGLEICYDIRFPE 143
                                    *****..77777..8*****95444..5*******66........89*********9999999999************** PP

                                    HHHHHHHTT-SEEEEBH.GCCCTCHHHHHHHHHHHHHHHHHHTSEEEEEEBEEEHCETTEEEE--EEEE-TTS-EEEECC CS
                   CN_hydrolase 161 llralalkgaeilvnlserapvpksmgppqwellgraralengcfviaanqvggyeqlilwpvghSaiidpdGrilaglg 240
                                    ++r+l + ga++lv+ +  a++p  +   +w +l  ara+en++  ia+n  g         +g+S+i++p G++la++g
  gi|116753735|ref|YP_842853.1| 144 VARKLCASGADLLVT-I--AQFPAERI-HHWRALVTARAIENQIHHIACNASGS-------AGGSSMIVGPAGEVLAEAG 212
                                    ***************.4..45666555.566999********************.......******************* PP

                                    SSSTEEEEEEEEHHHHHHHH CS
                   CN_hydrolase 241 eeeegvliaeidladvratr 260
                                     ee  v++a++dl++  ++r
  gi|116753735|ref|YP_842853.1| 213 VEEC-VITADLDLDERDRVR 231
                                    *995.********9987776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1908.78
//
Query:       gi|116753736|ref|YP_842854.1|  [L=299]
Description: radical SAM domain-containing protein [Methanosaeta thermophila PT]
Scores for 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-24   84.7   0.1    1.6e-23   83.9   0.1    1.5  1  Radical_SAM  Radical SAM superfamily
    9.1e-06   25.8   0.0    2.1e-05   24.6   0.0    1.6  1  Fer4_14      4Fe-4S single cluster domain
    0.00021   21.6   0.0    0.00057   20.2   0.0    1.7  1  Fer4_12      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.9   0.1   2.6e-27   1.6e-23       2     165 ..      44     224 ..      43     247 .. 0.91

  Alignments for each domain:
  == domain 1  score: 83.9 bits;  conditional E-value: 2.6e-27
                                    EEESEESS--TTTSCCTT....HHHHHHHHHHHHHHHHHHHHHHH.HHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCC CS
                                    xxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   2 vvtrgCnlrCsfCarpet....vrregrgrslsveeileevkelk.aekg.vkevilgggepllypdfvellerlaklav 75 
                                    +v + Cn +C++C+r ++    +r+++++r+l+++e le v+e+  +++  + + + g gepl++ +  e l+   ++  
  gi|116753736|ref|YP_842854.1|  44 PVAPKCNIQCKYCIRDFDcvneSRPGVTSRVLTPQEALERVDEVLsKYHYiKVVAVAGPGEPLANEETFETLRLVGEK-Y 122
                                    57899***************************************99999988899999******99776666666666.5 PP

                                    CTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHH................HHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................xxxxxxxxxxxx RF
                    Radical_SAM  76 pgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtf................eevlealeklre 139
                                    p + ++++tng+l+ ++ +e l++ gv+ ++++l+a+d+  + + +   + +                + +l+++e + +
  gi|116753736|ref|YP_842854.1| 123 PHLILCISTNGLLL-PDRIEDLDRIGVTNITVTLNAVDPT-IGEQI-YDYVIykgeryegleaakillDNQLKGIEEAVR 199
                                    **************.************************9.88888.6555588888899999999999999****9999 PP

                                    TTSETEEEEEEEBTTTSHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM 140 agikrvvdrivglpGendeeleelle 165
                                    +  k v++++v++pG nd+++ ++++
  gi|116753736|ref|YP_842854.1| 200 R-KKIVKVNTVLIPGINDKHVFDIAR 224
                                    9.555***************988876 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 !   24.6   0.0   3.6e-09   2.1e-05       7      92 ..      48     136 ..      45     157 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 3.6e-09
                        Fer4_14   7 gCnlsCkgCd......nketwkselgkpqteelleqilkdlkkseikiqglvltG.GePLhyenkkellklvkrlkeeyp 79 
                                    +Cn++Ck C       n++    ++     +e le+ ++++  ++  i+ + + G GePL  +n +e ++ ++ + e+yp
  gi|116753736|ref|YP_842854.1|  48 KCNIQCKYCIrdfdcvNESRPGVTSRVLTPQEALER-VDEVLSKYHYIKVVAVAGpGEPL--AN-EETFETLRLVGEKYP 123
                                    8******88765555566666666666666666643.44444444446889*********..44.556677899999*** PP

                        Fer4_14  80 ekkiwletngtle 92 
                                    ++   + tng+l 
  gi|116753736|ref|YP_842854.1| 124 HLILCISTNGLLL 136
                                    *********9875 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   9.5e-08   0.00057      14      98 ..      48     138 ..      39     158 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 9.5e-08
                        Fer4_12  14 gCnlsCkgCfnketwsfk.......sgkeftkelleeiiedlkk.esiegltllG.GEPllpenaeallelvkevkeekp 84 
                                     Cn++Ck+C+ ++  +++       s   +++e+le++ e l+k ++i+ + + G GEPl+ e+     e ++ v e++p
  gi|116753736|ref|YP_842854.1|  48 KCNIQCKYCI-RDFDCVNesrpgvtSRVLTPQEALERVDEVLSKyHYIKVVAVAGpGEPLANEE---TFETLRLVGEKYP 123
                                    7*******98.45554443444442555557*******999999677899999999*****333...3444555666666 PP

                        Fer4_12  85 .ekdiwlytgytlee 98 
                                        +++++g  l +
  gi|116753736|ref|YP_842854.1| 124 hLILCISTNGLLLPD 138
                                    445888899887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); 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):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2174.05
//
Query:       gi|116753737|ref|YP_842855.1|  [L=537]
Description: hypothetical protein Mthe_0423 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (537 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 4134.47
//
Query:       gi|116753738|ref|YP_842856.1|  [L=480]
Description: hypothetical protein Mthe_0424 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.025   15.3   0.3      0.025   15.3   0.3    2.8  3  Big_9     Bacterial Ig domain


Domain annotation for each model (and alignments):
>> Big_9  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.19   3.5e+03      73      87 ..     160     184 ..      99     186 .. 0.71
   2 ?   15.3   0.3   1.4e-06     0.025      11      79 ..     210     286 ..     203     303 .. 0.69
   3 ?   -0.1   0.3     0.089   1.6e+03      63      83 ..     374     408 ..     344     420 .. 0.61

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.19
                          Big_9  73 a..........gfsgtdsftYtvsD 87 
                                    +            +g++sf ++ +D
  gi|116753738|ref|YP_842856.1| 160 KfpeitdlrdlKKTGNVSFRIRYTD 184
                                    3335555555567888888888888 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.4e-06
                          Big_9  11 vndaPvavddsvtvt..edsv.....landtdpdgdaltvtsltvtlvtapanGtvtin..adgtltytpna.gfsgtd 79 
                                    +n +P ++ ++vt +     +     +a  +dpdgd+l+vt   +++++ ++   vt    + gt+++  ++ gf+g d
  gi|116753738|ref|YP_842856.1| 210 INNPPLVNYTNVTYKprY--SdpieyVAEISDPDGDTLNVTLHILEADNRTERMNVTQElvGGGTVRFKNSEyGFFGKD 286
                                    699999999999998552..3336889************9988888877777666665544888888888878444444 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.089
                          Big_9  63 adgtltytpna..............gfsgtdsftY 83 
                                    ++ t+t tp+               +++  ++f+Y
  gi|116753738|ref|YP_842856.1| 374 GSKTITVTPERqtvsfetsfdvsdcNQTFAYRFSY 408
                                    44456666655444444444444455555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (480 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); 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 0.25s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 3459.35
//
Query:       gi|116753739|ref|YP_842857.1|  [L=193]
Description: hypothetical protein Mthe_0425 [Methanosaeta thermophila PT]
Scores for complete sequence (score 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   13.9   9.5      0.065   12.0   1.1    2.1  2  DUF2207          Predicted membrane protein (DUF2207)
      0.056   13.7   0.0      0.093   13.0   0.0    1.3  1  Lipoprotein_Ltp  Host cell surface-exposed lipoprotein
        2.5    7.9   8.1         14    5.4   8.1    2.0  1  VIT1             VIT family
        5.2    7.4   0.0        5.2    7.4   0.0    4.7  5  YiaAB            yiaA/B two helix domain


Domain annotation for each model (and alignments):
>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.1   1.5e-05     0.065     348     437 ..      20     117 ..      14     124 .. 0.62
   2 ?    6.8   1.8   0.00055       2.5     379     430 ..     132     183 ..     128     193 .] 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.5e-05
                        DUF2207 348 kkakkfkkalkkwksavkkkergyfdkkgkkklkklsalglgliilglilillallllvll................lvf 411
                                    ++ +++++ l+++ ++v k   ++++     + + +sa  +  +++++i++++ l     +                 ++
  gi|116753739|ref|YP_842857.1|  20 MNFERIYRRLSELSDSVSK--DKLYEVLYIDHGANFSAMVFSSWVAFFIAFMYYL-----IpsttpwllrsgfpiatDYG 92 
                                    5778888999999999999..3444444333334444444444444444444333.....233344699*******7777 PP

                        DUF2207 412 llilllillliaiivlllfsrllgrr 437
                                    l++++++++++a+i+l+ + r+l+ +
  gi|116753739|ref|YP_842857.1|  93 LAFFAILVAVLASILLWAI-RRLPVW 117
                                    7777777777777776665.667766 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.00055
                        DUF2207 379 klkklsalglgliilglilillallllvlllvfllilllillliaiivlllf 430
                                    + k l+a+ ++++ ++ i++++ ++ + +++  l   +++l+++a+i+l+++
  gi|116753739|ref|YP_842857.1| 132 NEKNLCAATVLVLAFSAIFSIYNFVNYPFVNKTLEAASWVLIIVAVILLFIP 183
                                    5678999999999999999999999999999999999999999999988887 PP

>> Lipoprotein_Ltp  Host cell surface-exposed lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.1e-05     0.093      18      38 ..      35      55 ..      25      56 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.1e-05
                Lipoprotein_Ltp 18 nmSkqglydqLtseyGekFte 38
                                   ++Sk++ly+ L+ ++G +F++
  gi|116753739|ref|YP_842857.1| 35 SVSKDKLYEVLYIDHGANFSA 55
                                   69*****************86 PP

>> VIT1  VIT family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   8.1    0.0032        14     129     187 ..     131     189 ..      14     193 .] 0.85

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0032
                           VIT1 129 eelasplkaAlssalsf.liGgliPllpylfvesvglalvvsiavtllalllfGavkall 187
                                    ++++  l aA +  l+f +i+++   + y fv++  +a  +++++++++ll++ +vk ++
  gi|116753739|ref|YP_842857.1| 131 RNEK-NLCAATVLVLAFsAIFSIYNFVNYPFVNKTLEAASWVLIIVAVILLFIPVVKEFV 189
                                    3443.4455555555553899********************************9999886 PP

>> YiaAB  yiaA/B two helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0     0.098   4.4e+02      13      27 ..       8      21 ..       2      27 .. 0.71
   2 ?    3.5   2.2     0.019        87       3      18 ..      58      73 ..      57      73 .. 0.88
   3 ?   -1.1   0.9       0.5   2.3e+03       6      15 ..      95     104 ..      91     118 .. 0.54
   4 ?    7.4   0.0    0.0012       5.2      24      45 ..     128     149 ..     123     151 .. 0.90
   5 ?    2.9   1.2     0.029   1.3e+02       4      18 ..     168     182 ..     167     186 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.098
                          YiaAB 13 lvlllvGlwylpldl 27
                                   lvlll+Gl+ l+  +
  gi|116753739|ref|YP_842857.1|  8 LVLLLIGLV-LHKMN 21
                                   78999**99.74444 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.019
                          YiaAB  3 gqswlsfllalvlllv 18
                                   + sw++f++a++ +l+
  gi|116753739|ref|YP_842857.1| 58 FSSWVAFFIAFMYYLI 73
                                   679********99986 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.5
                          YiaAB   6 wlsfllalvl 15 
                                     ++ l+a+++
  gi|116753739|ref|YP_842857.1|  95 FFAILVAVLA 104
                                    3444444433 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.0012
                          YiaAB  24 pldlseKgfyamgllfllfsaf 45 
                                    p+  +eK  +a+++l+l fsa+
  gi|116753739|ref|YP_842857.1| 128 PISRNEKNLCAATVLVLAFSAI 149
                                    8999****************98 PP

  == domain 5  score: 2.9 bits;  conditional E-value: 0.029
                          YiaAB   4 qswlsfllalvlllv 18 
                                    +sw++ ++a++ll++
  gi|116753739|ref|YP_842857.1| 168 ASWVLIIVAVILLFI 182
                                    89**********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1196  (0.0667076); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1313.45
//
Query:       gi|116753740|ref|YP_842858.1|  [L=509]
Description: hypothetical protein Mthe_0426 [Methanosaeta thermophila PT]
Scores for complete 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-06   28.1   0.1    0.00036   20.8   0.2    2.9  2  Tubulin    Tubulin/FtsZ family, GTPase domain
     0.0012   18.1   0.0      0.068   12.4   0.0    2.3  2  Tubulin_2  Tubulin like


Domain annotation for each model (and alignments):
>> Tubulin  Tubulin/FtsZ family, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.7   0.0    0.0069        62       3      20 ..       4      21 ..       2      85 .. 0.82
   2 !   20.8   0.2     4e-08   0.00036     111     193 ..     146     237 ..     121     240 .. 0.61

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.0069
                                   EEEEEHHHHHHHHHHHHH CS
                        Tubulin  3 ivigvGqcGnqignelwe 20
                                   +++g+G+cG+++++ + +
  gi|116753740|ref|YP_842858.1|  4 CCVGIGGCGGKMLEVFLK 21
                                   579*********998887 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 4e-08
                                    TT-SE.SEEEEEEETTSSHHHHHHHHHHHHHHHTS.TTSEEEEEEEE--...GG.G-HHHHHH...HHHH.....HHHHH CS
                        Tubulin 111 ekcdslqgffitaslgGGTGSGlgpvilevlkeey.pkalvvtvvvlPs...efsevvvepyn...aila.....lkeli 178
                                     +cd+   ++++ slgGGTG+G+ + i+ +++    ++ +v+   +l     + +++v e++    a+ +     +k+  
  gi|116753740|ref|YP_842858.1| 146 GECDN---ILFIVSLGGGTGTGFINPIVNYIRSGGrREFPVFVLGILTEegeDSRTGVSEEQRglaAAISiydllTKNKD 222
                                    46777...***********************9885344444444444444442222332222211122221111123333 PP

                                    HT-SEEEEEEHHHHH CS
                        Tubulin 179 eesdavividNdaLl 193
                                    e +da+i+idN+ L+
  gi|116753740|ref|YP_842858.1| 223 EGVDALIPIDNQILI 237
                                    447777777777665 PP

>> Tubulin_2  Tubulin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.2   0.0    0.0045        41       2      35 ..       5      37 ..       4      63 .. 0.76
   2 !   12.4   0.0   7.5e-06     0.068     135     185 ..     128     178 ..     116     197 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.0045
                      Tubulin_2  2 viGLGGtGgkvlaelrrrlreelgslelpdkvqF 35
                                   ++G+GG Ggk+l+ + + l   l +++ p+ v+F
  gi|116753740|ref|YP_842858.1|  5 CVGIGGCGGKMLEVFLKPLDIYL-PFRDPEPVAF 37
                                   8***********99888875444.6666666655 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 7.5e-06
                      Tubulin_2 135 irealrdaikrlrgsageeeglnvfVvgSLaGGTGSGiflDvayllrkilk 185
                                    i++a  daikr ++ a++ e  n+  ++SL GGTG G + +++ ++r   +
  gi|116753740|ref|YP_842858.1| 128 ILDATWDAIKRYTTLAESGECDNILFIVSLGGGTGTGFINPIVNYIRSGGR 178
                                    44555556666666433356679999********************97655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (509 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 3544.12
//
Query:       gi|116753741|ref|YP_842859.1|  [L=294]
Description: hypothetical protein Mthe_0427 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00048   20.4   0.0     0.0074   16.6   0.0    2.5  2  DUF4352   Domain of unknown function (DUF4352)


Domain annotation for each model (and alignments):
>> DUF4352  Domain of unknown function (DUF4352)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0     0.028     5e+02      89     116 ..      99     123 ..      73     128 .. 0.62
   2 !   16.6   0.0   4.1e-07    0.0074       2     102 ..     132     218 ..     131     240 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.028
                                    E-TT-EEEEEEEEEESTT-CGEEEEE.H CS
                        DUF4352  89 lnpGkkvtGklvFdvpkgkkkleLeyqt 116
                                    ++pG +    l+F+vp+++ + +L++++
  gi|116753741|ref|YP_842859.1|  99 VSPGREL---LAFVVPREAIPKSLVVDS 123
                                    4444443...788888888888888755 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 4.1e-07
                                    STCEEECCTTEEEEEEEEEEEEEETTS-CEETT-.SEEEEEEEEEEE-SSS-EEEEGGGEEEEETTEEE-BEEESCCCCT CS
                        DUF4352   2 kvgetvkvgdlevtVnsveytksvgkneylqpdaggeflivdvtvkNkgkealtvnssqfkLkdgdgkeydadlsasska 81 
                                    ++ge+ +++d ++tV+ +     +g++   ++    + l +d++v+N+++ ++ +++ + +L+d+ g  y+a+ +     
  gi|116753741|ref|YP_842859.1| 132 DLGEPLNYSDENITVTYY---GIMGSRLDYNR----KALDIDISVRNNSSNPMRISPENCTLVDQWGWGYRATDG----- 199
                                    578888888888888888...66663333333....4599*************************9999998766..... PP

                                    TB--EEEE-TT-EEEEEEEEE CS
                        DUF4352  82 ddlflgtlnpGkkvtGklvFd 102
                                      +   tln++++++G++ F 
  gi|116753741|ref|YP_842859.1| 200 --FETRTLNANESIRGVVRFR 218
                                    ..5567899999999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2121.06
//
Query:       gi|116753742|ref|YP_842860.1|  [L=375]
Description: periplasmic binding protein [Methanosaeta thermophila PT]
Scores for complete 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-34  118.6   0.0    8.4e-34  117.2   0.0    1.7  2  Peripla_BP_2  Periplasmic binding protein
  ------ inclusion threshold ------
       0.13   12.3   0.0        1.5    8.9   0.0    2.3  2  LysM          LysM domain


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.2   0.0   9.4e-38   8.4e-34       1     234 [.      47     305 ..      47     308 .. 0.93
   2 ?   -2.1   0.0      0.26   2.3e+03     159     176 ..     342     360 ..     340     369 .. 0.82

  Alignments for each domain:
  == domain 1  score: 117.2 bits;  conditional E-value: 9.4e-38
                                    EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT....................TS-BSBESSSB-HHHHHHH--SE CS
                   Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadklee..................aivevgadgeidvEklaalkPDl 62 
                                    i++ sp+ ++i +alGa dk+ + + +t+++l                         + +e++++ +i +Ek+aal PD+
  gi|116753742|ref|YP_842860.1|  47 IITRSPDEARIIIALGAGDKLIASEQATKYCLCPMTFGDtsegcvncfetiiegrmpDLPEISTRYDIYFEKIAALNPDI 126
                                    77889999*********************998776555567779999998888888888********************9 PP

                                    EEE-GGG...GGGHHHHHHHS-EEE----TTS...HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT.-EE CS
                   Peripla_BP_2  63 vilskglgltdedeellksgiptvivessntg...eslkeqiralgellgledeaeklvaeidsklaaaksaidsekpkp 139
                                    ++  +     d++  ++k g+p+v+   + +    e++ ++i++ g++l++e+ea++l+ +i+sk++++ks +d+ ++++
  gi|116753742|ref|YP_842860.1| 127 IFCGSLK---DAEAFEDKIGCPVVVLGGRGWNfsdEGYFNSIEVAGKALDKEEEAKELIDFIKSKIDRVKSVTDEMDDSE 203
                                    9998877...666667899**********999************************************************ PP

                                    EEEEEETTE..EEEE-TTSTTTHHHHT.S--EESTTT--.......STT-EEE-HHHHHHH--SEEEEEEHHHHT-S--H CS
                   Peripla_BP_2 140 vlvfggadeggyvvagsnsyigdllda.lgieniaaesk.......kseyeeisaEqilasdpdvifvsgraeadnktgl 211
                                     + +++a +g+   +++  +++d++++   +++++ +++        ++  +++ Eqi a++pd+if++++ +  n t l
  gi|116753742|ref|YP_842860.1| 204 KPKVYFASRGASAAFYDPKEGRDFTRTePEYDPLTVAGGinvasdiPGSTVNVGLEQIIAWNPDYIFIASS-DPGNYTAL 282
                                    **************************9999999977777789998899***********************.******** PP

                                    HHHT-SHHHHTSHHHHTT-EEEE CS
                   Peripla_BP_2 212 eflkenpllaelpAvkngrVyal 234
                                     f+k++p+l++++A+kng+Vy++
  gi|116753742|ref|YP_842860.1| 283 NFIKNSPELQSVNAIKNGNVYYC 305
                                    *********************98 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.26
                                    TTTHHHHT.S--EESTTT- CS
                   Peripla_BP_2 159 yigdllda.lgieniaaes 176
                                    +++++++a lg++n++ e+
  gi|116753742|ref|YP_842860.1| 342 EGNEIFRAfLGVDNVFTEY 360
                                    5789999999999999887 PP

>> LysM  LysM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00017       1.5      12      29 ..     108     126 ..     105     135 .. 0.84
   2 ?    0.2   0.0     0.087   7.8e+02      17      28 ..     255     270 ..     246     277 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00017
                                    HHHHCTCHHHHHHHHC.TC CS
                           LysM  12 IAkrygitveklleaN.nl 29 
                                    I+ ry+i +ek++++N  +
  gi|116753742|ref|YP_842860.1| 108 ISTRYDIYFEKIAALNpDI 126
                                    9***************654 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.087
                                    TCHHHHHHHHC....T CS
                           LysM  17 gitveklleaN....n 28 
                                    ++ +e+++++N     
  gi|116753742|ref|YP_842860.1| 255 NVGLEQIIAWNpdyiF 270
                                    8999*******55444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      637  (0.035529); 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: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2730.85
//
Query:       gi|116753743|ref|YP_842861.1|  [L=275]
Description: methyltransferase type 12 [Methanosaeta thermophila PT]
Scores for complete 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   51.0   0.1    6.9e-13   49.1   0.0    1.9  2  Methyltransf_25  Methyltransferase domain
    2.3e-10   41.0   0.0    5.7e-10   39.7   0.0    1.7  1  Methyltransf_11  Methyltransferase domain
    3.2e-10   40.0   0.0    4.5e-10   39.5   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    3.5e-08   32.9   0.0    4.8e-08   32.4   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
    2.1e-07   30.9   0.0    2.8e-07   30.5   0.0    1.1  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    2.4e-06   28.2   0.0    6.2e-06   26.9   0.0    1.7  1  Methyltransf_12  Methyltransferase domain
    2.6e-06   27.1   0.0    3.9e-06   26.5   0.0    1.2  1  MTS              Methyltransferase small domain
    5.6e-06   25.9   0.0    8.2e-06   25.3   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    9.6e-06   25.5   0.0    1.4e-05   25.0   0.0    1.2  1  Met_10           Met-10+ like-protein
    1.2e-05   25.2   0.0      2e-05   24.5   0.0    1.4  1  Methyltransf_23  Methyltransferase domain
    6.3e-05   22.8   0.0    9.2e-05   22.2   0.0    1.2  1  Methyltransf_16  Lysine methyltransferase
    9.6e-05   22.0   0.0    0.00013   21.5   0.0    1.2  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    0.00014   21.3   0.0    0.00021   20.8   0.0    1.3  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    0.00015   21.5   0.0    0.00022   20.9   0.0    1.2  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    0.00024   20.5   0.0    0.00039   19.8   0.0    1.3  1  GidB             rRNA small subunit methyltransferase G
    0.00028   20.3   0.0    0.00041   19.8   0.0    1.2  1  TehB             Tellurite resistance protein TehB
    0.00033   20.0   0.0    0.00046   19.6   0.0    1.3  1  CMAS             Mycolic acid cyclopropane synthetase
     0.0016   18.1   0.0     0.0025   17.5   0.0    1.2  1  Cons_hypoth95    Conserved hypothetical protein 95
     0.0089   15.5   0.0      0.015   14.8   0.0    1.3  1  Methyltransf_4   Putative methyltransferase
  ------ inclusion threshold ------
      0.014   15.4   0.0      0.026   14.5   0.0    1.4  1  Methyltransf_18  Methyltransferase domain
      0.021   13.9   0.0      0.032   13.3   0.0    1.3  1  DREV             DREV methyltransferase
      0.043   13.6   0.0      0.093   12.5   0.0    1.6  2  DUF938           Protein of unknown function (DUF938)
       0.11   12.2   0.0       0.16   11.7   0.0    1.3  1  PAXX             PAXX, PAralog of XRCC4 and XLF, also called 
       0.11   11.4   0.1       0.28   10.1   0.0    1.6  2  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.0   9.3e-16   6.9e-13       1      94 [.      62     152 ..      62     154 .. 0.90
   2 ?   -1.1   0.0       4.4   3.3e+03      65      84 ..     219     238 ..     195     247 .. 0.67

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 9.3e-16
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTT.TEEEEEEESTGGGSS CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedg.sfDlvvssgalhhls 78 
                                    vLd+G+GtGrl++ +a+    ++vt++D s +ml+  ++++++eg+ n++++q d e++  ++    D+v+ss++l +++
  gi|116753743|ref|YP_842861.1|  62 VLDIGAGTGRLAIPMARMA--KSVTALDRSGGMLKCLKANMQAEGIsNITCIQRDWEEIGVDEIpPHDVVLSSNSLGVVD 139
                                    9***************996..9*************************************97544499*****98888875 PP

                                    HHHHHHHHHHHHHHEE CS
                Methyltransf_25  79 dedlekalkeiarvLk 94 
                                       l++al+++ ++ k
  gi|116753743|ref|YP_842861.1| 140 ---LRTALAKMDQLAK 152
                                    ...8889988877765 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 4.4
                                    EEEEEEESTGGGSSHHHHHH CS
                Methyltransf_25  65 fDlvvssgalhhlsdedlek 84 
                                     D+v s+ ++h +sde+++k
  gi|116753743|ref|YP_842861.1| 219 DDAVASWKEMHDISDEKVPK 238
                                    47888887788888777654 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.0   7.7e-13   5.7e-10       1      90 [.      63     153 ..      63     159 .. 0.93

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 7.7e-13
                                    EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-T.T-EEEEEEES-CCC-CCHH CS
                Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl.kvefvvadaeklpfed.nsfDlvvssevlhhvedpe 78 
                                    Ld+G+GtGrla ++a+ +++v+++D s  mlk+ k++ + eg+ ++++++ d e++ + +    D+v+ss++l  v d++
  gi|116753743|ref|YP_842861.1|  63 LDIGAGTGRLAIPMARMAKSVTALDRSGGMLKCLKANMQAEGIsNITCIQRDWEEIGVDEiPPHDVVLSSNSLGVV-DLR 141
                                    8*******************************************************9999679***********99.799 PP

                                    HHHHHHHHHEEE CS
                Methyltransf_11  79 kalkeiaRvLkp 90 
                                     al+++ ++ k 
  gi|116753743|ref|YP_842861.1| 142 TALAKMDQLAKR 153
                                    999999988876 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.0     6e-13   4.5e-10       4     107 ..      59     157 ..      56     199 .. 0.88

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 6e-13
                Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieelekl.ledekfDlilsne 82 
                                    + +vlD+G+GtG+l++ +a +  + + v+ +D+s  +++  ++n q  g++n++  q d+ee+  + +   + D++ls +
  gi|116753743|ref|YP_842861.1|  59 HETVLDIGAGTGRLAIPMA-R--MAKSVTALDRSGGMLKCLKANMQAEGISNITCIQRDWEEIGVDeIP--PHDVVLSSN 133
                                    679****************.4..3556***********************************9966555..7******99 PP

                Methyltransf_31  83 vlnaladpdkileeiervlkpggil 107
                                     l  + d+  +l ++ ++ k   ++
  gi|116753743|ref|YP_842861.1| 134 SL-GVVDLRTALAKMDQLAKRAVYI 157
                                    99.9999999999999888876654 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.0   6.4e-11   4.8e-08       4      85 ..      32     115 ..      29     124 .. 0.89

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 6.4e-11
                                    CXXGCG--EE--HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT..TCCCEEEE CS
                         RrnaAD   4 lrksygqnflknkkvineIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls..kdeklkvv 81 
                                    + k + q  +k +  ++  +  l+l++  tvl+ig+G+G l  ++a +ak+v++l     ++k l+++++    ++++ +
  gi|116753743|ref|YP_842861.1|  32 KAKAFNQRVMKHREWAEMQVASLKLQPHETVLDIGAGTGRLAIPMARMAKSVTALDRSGGMLKCLKANMQaeGISNITCI 111
                                    5567777778888888888999*********************************************999777899999* PP

                                    -S-C CS
                         RrnaAD  82 hqDf 85 
                                    ++D 
  gi|116753743|ref|YP_842861.1| 112 QRDW 115
                                    9996 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 !   30.5   0.0   3.7e-10   2.8e-07      62     149 ..      47     132 ..      12     154 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 3.7e-10
                                    HHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GG.GTTGGG CS
                           PCMT  62 valalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGr.kGyeek 140
                                      + +  l+l++ + vL++G+G+G l+  +ar+ ++++   +++r+  + +  k+n+++++++n++ +  D +  G++e 
  gi|116753743|ref|YP_842861.1|  47 AEMQVASLKLQPHETVLDIGAGTGRLAIPMARMAKSVT---ALDRSGGMLKCLKANMQAEGISNITCIQRDWEeIGVDEI 123
                                    445677899************************99988...9*****************************7527***** PP

                                    -SEEEEEES CS
                           PCMT 141 aPYdaihvg 149
                                     P+d+++ +
  gi|116753743|ref|YP_842861.1| 124 PPHDVVLSS 132
                                    ****99865 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   8.2e-09   6.2e-06       1      94 [.      63     152 ..      63     156 .. 0.92

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 8.2e-09
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlk 80 
                                    L+iG+GtG+l+ ++++    +++t++D s  +++  k+ +++++  n ++++ + ++++ ++ +   D+v++sn l ++ 
  gi|116753743|ref|YP_842861.1|  63 LDIGAGTGRLAIPMARM--AKSVTALDRSGGMLKCLKANMQAEGISNITCIQRDWEEIGVDEIP-PHDVVLSSNSLGVV- 138
                                    8****************..**************9999999999999999999999998877766.*************9. PP

                Methyltransf_12  81 direvldnirklLk 94 
                                    d+r +l+++ +l k
  gi|116753743|ref|YP_842861.1| 139 DLRTALAKMDQLAK 152
                                    99999999998876 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   5.2e-09   3.9e-06      26      90 ..      53     116 ..      47     131 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 5.2e-09
                                    HCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STT CS
                            MTS  26 tlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvl 90 
                                     l+ + +++vlD+G+G+G l++ +a++ ++  vt++d +   l++ k+n++a++++ ++++++d  
  gi|116753743|ref|YP_842861.1|  53 SLKLQPHETVLDIGAGTGRLAIPMARMAKS--VTALDRSGGMLKCLKANMQAEGISnITCIQRDWE 116
                                    567777889*****************9988..9**********************99999988864 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   1.1e-08   8.2e-06      31     141 ..      42     149 ..      34     162 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.1e-08
                                    THHHHHHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT- CS
                Ubie_methyltran  31 ihrlWkkfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeL 110
                                     hr W ++       ++ ++vlD+ +Gtg la+ +++++++   v+ lD +  mLk  ++ ++ eg +ni  +q + ee+
  gi|116753743|ref|YP_842861.1|  42 KHREWAEMQVASLKLQPHETVLDIGAGTGRLAIPMARMAKS---VTALDRSGGMLKCLKANMQAEGISNITCIQRDWEEI 118
                                    79****9888888888999****************998875...899********************************9 PP

                                    TTS-.T-EEEEEEES-GGG-S-HHHHHHHHHH CS
                Ubie_methyltran 111 pfed.dsfDvvtvsfGlrnvtDklkaLkeayr 141
                                      ++    Dvv  s  l  v D  +aL ++ +
  gi|116753743|ref|YP_842861.1| 119 GVDEiPPHDVVLSSNSL-GVVDLRTALAKMDQ 149
                                    99986677777666555.46677777777765 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   1.8e-08   1.4e-05      92     164 ..      49     119 ..      27     157 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.8e-08
                                    HHHHTT.--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG-- CS
                         Met_10  92 erlakl.veegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevi 164
                                    +++a+l  ++ e+V+d+ AG G +aip+a+   ak v a d      k lk n++   ++++   i+ D +e+ 
  gi|116753743|ref|YP_842861.1|  49 MQVASLkLQPHETVLDIGAGTGRLAIPMAR--MAKSVTALDRSGGMLKCLKANMQAEGISNIT-CIQRDWEEIG 119
                                    345555589*********************..88889*********************99876.9999988875 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   2.7e-08     2e-05      18     127 ..      54     182 ..      33     230 .. 0.68

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 2.7e-08
                Methyltransf_23  18 pklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae.........kakkaqkdqfdeqeaae........pq 80 
                                     kl++   vLdiG+GtG+l+  +++  +svt+ D s  + + ++         ++ + q d + e+  +e        ++
  gi|116753743|ref|YP_842861.1|  54 LKLQPHETVLDIGAGTGRLAIPMARMAKSVTALDRSGGMLKCLKanmqaegisNITCIQRDWE-EIGVDEipphdvvlSS 132
                                    4588999*****************************988887756666666665555555555.3333335545555555 PP

                Methyltransf_23  81 gkfdlIvlrevlehvpdpp...ellrqiatllkpgGylllseplaslked 127
                                    ++  ++ lr  l  ++ ++    ++ ++ ++ ++gG +++++p  s  + 
  gi|116753743|ref|YP_842861.1| 133 NSLGVVDLRTALAKMDQLAkraVYIFTFTDHRRDGGFMEFLMPEHSRRSP 182
                                    56666666666666665444446777777777788888888875544333 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   1.2e-07   9.2e-05      47     150 ..      59     154 ..      33     175 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.2e-07
                Methyltransf_16  47 klsvlELGsGtGlvGlavaellpeakviltDlee.llellkknielnknalkskvkvevLdWgeeleedllekeevDlil 125
                                    + +vl++G+GtG   + +a++    +v+  D++  +l++lk n+++++    s+++  + dW+e +  d + ++  D++l
  gi|116753743|ref|YP_842861.1|  59 HETVLDIGAGTGRLAIPMARM--AKSVTALDRSGgMLKCLKANMQAEG---ISNITCIQRDWEE-IGVDEIPPH--DVVL 130
                                    568******************..999*****9988***********55...7899999****65.666776666..9*** PP

                Methyltransf_16 126 aaDcvYledslelLvkvLkellkke 150
                                     +  +   d  ++L+k +++l k  
  gi|116753743|ref|YP_842861.1| 131 SSNSLGVVDLRTALAK-MDQLAKRA 154
                                    **99988888888876.45555555 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 !   21.5   0.0   1.8e-07   0.00013       2      78 ..      60     132 ..      59     159 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.8e-07
                Methyltransf_15   2 rvilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfe........llaklklekikvd 73 
                                    +++lD+ +G+G  +i +a++ ++v a++ +   l+c + N ++ g+s +it+++ d++e        +           d
  gi|116753743|ref|YP_842861.1|  60 ETVLDIGAGTGRLAIPMARMAKSVTALDRSGGMLKCLKANMQAEGIS-NITCIQRDWEEigvdeippH-----------D 127
                                    679*****************************************996.6********99333333330...........4 PP

                Methyltransf_15  74 lvflS 78 
                                    +v+ S
  gi|116753743|ref|YP_842861.1| 128 VVLSS 132
                                    44444 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   0.0   2.9e-07   0.00021     159     220 ..      56     116 ..      39     144 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.9e-07
                           PrmA 159 vkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalsee 220
                                    ++++e+vlD+G+G+G Lai  a++ ak+v+a+D     +k  k+N++  ++++   ++   e
  gi|116753743|ref|YP_842861.1|  56 LQPHETVLDIGAGTGRLAIPMARM-AKSVTALDRSGGMLKCLKANMQAEGISNITCIQRDWE 116
                                    78999*****************98.799*********************9999775654433 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 !   20.9   0.0     3e-07   0.00022       3      71 ..      53     118 ..      51     129 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 3e-07
                                    HH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCC CS
                Methyltr_RsmB-F   3 lLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarki 71 
                                     L++q++et+lD+ a+ G     +a +   ++ v+A+d++   lk +++n++  g+ n+++++ D  +i
  gi|116753743|ref|YP_842861.1|  53 SLKLQPHETVLDIGAGTGRLAIPMARM---AKSVTALDRSGGMLKCLKANMQAEGISNITCIQRDWEEI 118
                                    699**************9999999988...899*******************************98775 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   5.3e-07   0.00039      45     121 ..      56     131 ..      34     162 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5.3e-07
                                    S-CCC-.EEEETSTTTTTHHHHHHH-TTSEEEEEES-HHHHHHHHHHHHHCT-SSEEEEES-CCC..TTTTT-EEEEEE CS
                           GidB  45 lkekrdkviDvGsGaGlPGipLaiarpelkltLleslekkiaFLeevkeelklenveivearaee..kqeeekydvvts 121
                                    l+ ++ +v+D+G+G G  +ip+a  r  +++t l+++    + L+  +++ +++n++ ++ + ee   +e  + dvv+s
  gi|116753743|ref|YP_842861.1|  56 LQPHE-TVLDIGAGTGRLAIPMA--RMAKSVTALDRSGGMLKCLKANMQAEGISNITCIQRDWEEigVDEIPPHDVVLS 131
                                    33334.7**********999987..5566788*********************************99899999999986 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   5.5e-07   0.00041       9     104 ..      36     134 ..      28     156 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5.5e-07
                                    HHHHHT-----HHHHHHCCCS-S-.EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--G CS
                           TehB   9 fskkynltathsevveavkivkpg.kvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistalydi 87 
                                    f+++    +  +e+  a   ++p   vld+g g gr ++ ++ +   vta+d+    ++ l+  ++ e ++ni++   d 
  gi|116753743|ref|YP_842861.1|  36 FNQRVMKHREWAEMQVASLKLQPHeTVLDIGAGTGRLAIPMARMAKSVTALDRSGGMLKCLKANMQAEGISNITCIQRDW 115
                                    5555555566667777777777762589**************************************************** PP

                                    GG----S..-EEEEEEESS CS
                           TehB  88 neaklde..rydfilstvv 104
                                    +e+ +de   +d +ls+  
  gi|116753743|ref|YP_842861.1| 116 EEIGVDEipPHDVVLSSNS 134
                                    **99998434788888755 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   6.2e-07   0.00046      51     125 ..      47     119 ..      25     169 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 6.2e-07
                                    HHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-- CS
                           CMAS  51 ldlileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedld 125
                                     ++ +  l+l+p +t+LdiG+G G l++ +++    +v +l  S    k  k++++++++++ + ++  d+e++ 
  gi|116753743|ref|YP_842861.1|  47 AEMQVASLKLQPHETVLDIGAGTGRLAIPMARM-AKSVTALDRSGGMLKCLKANMQAEGISNITCIQ-RDWEEIG 119
                                    4677889*********************99988.889999*******************98877765.7999874 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   3.3e-06    0.0025      41      99 ..      58     114 ..      45     131 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.3e-06
                                    CC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES CS
                  Cons_hypoth95  41 egarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelked 99 
                                     +++vLD+ aG+G l++  + R ak++++++++  ++k lk+n+++ ++++ ++ +++d
  gi|116753743|ref|YP_842861.1|  58 PHETVLDIGAGTGRLAIP-MARMAKSVTALDRSGGMLKCLKANMQAEGISN-ITCIQRD 114
                                    4678*************5.89*************************99997.5555555 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0     2e-05     0.015       4      60 ..      61     115 ..      58     128 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2e-05
                                    EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-C CS
                 Methyltransf_4   4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgda 60 
                                    +vl+iG G G++ + +A +   k++ +++ +  +++ + ++++a++++N+ +++ d 
  gi|116753743|ref|YP_842861.1|  61 TVLDIGAGTGRLAIPMARMA--KSVTALDRSGGMLKCLKANMQAEGISNITCIQRDW 115
                                    79***************996..5667889999999999999************9985 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   3.4e-05     0.026      12      70 ..      56     111 ..      49     130 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.4e-05
                Methyltransf_18  12 vekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievr 70 
                                    ++++++v+DiG+  g l+i ++  ++ak+v+a D + g l+  k+n++ +g+++ i+++
  gi|116753743|ref|YP_842861.1|  56 LQPHETVLDIGAGTGRLAIPMA--RMAKSVTALDRSGGMLKCLKANMQAEGISN-ITCI 111
                                    566889***************9..68899********************99964.6665 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.2e-05     0.032      93     135 ..      57      99 ..      36     146 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.2e-05
                           DREV  93 qedkklldlGaGdGeitkrvaptfeevyatelsetmrdrlkkk 135
                                    q ++++ld+GaG G ++  +a + + v a + s  m + lk  
  gi|116753743|ref|YP_842861.1|  57 QPHETVLDIGAGTGRLAIPMARMAKSVTALDRSGGMLKCLKAN 99 
                                    44679*****************************999888753 PP

>> DUF938  Protein of unknown function (DUF938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00012     0.093      22     120 ..      56     143 ..      42     171 .. 0.70
   2 ?   -2.9   0.0       6.3   4.7e+03      49      78 ..     206     235 ..     201     239 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                         DUF938  22 lakttervLEiasGtGqHAvffApalpnlkwqpsdqdeelresiaawadelalsnlkpPleldvtaevapvereappapa 101
                                    l+ +++ vL+i++GtG+ A+ +A   + ++  + d    + + ++a +++ ++sn++      ++++++++  +   +  
  gi|116753743|ref|YP_842861.1|  56 LQPHET-VLDIGAGTGRLAIPMARMAKSVT--ALDRSGGMLKCLKANMQAEGISNITC-----IQRDWEEIGVD---EIP 124
                                    455555.****************9887765..67888889999************975.....44444444433...334 PP

                         DUF938 102 sidailsinllHispwsav 120
                                    + d++ls+n l +  + ++
  gi|116753743|ref|YP_842861.1| 125 PHDVVLSSNSLGVVDLRTA 143
                                    5677777777776666554 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.3
                         DUF938  49 nlkwqpsdqdeelresiaawadelalsnlk 78 
                                      ++ +s++  +l +++a w++   +s  k
  gi|116753743|ref|YP_842861.1| 206 IHRFESSEYYANLDDAVASWKEMHDISDEK 235
                                    567899999999999999998877766655 PP

>> PAXX  PAXX, PAralog of XRCC4 and XLF, also called C9orf142
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00021      0.16      61     107 ..      37      83 ..       6     103 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00021
                                    --SHHHHHHHHHHT-EEEEEETTEEEEEE-SSSS-EEEEEEE--HHH CS
                           PAXX  61 edyalrfraaceqqavsltlqedrasltlsggpsaLtleLskledpe 107
                                    ++ +++ r  +e q +sl+lq  + +l++++g+  L++ ++++ ++ 
  gi|116753743|ref|YP_842861.1|  37 NQRVMKHREWAEMQVASLKLQPHETVLDIGAGTGRLAIPMARMAKSV 83 
                                    5678999***********************************98764 PP

>> tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00037      0.28     200     261 ..      57     118 ..      28     121 .. 0.82
   2 ?   -2.3   0.1       2.2   1.7e+03      68     149 ..     229     262 ..     198     272 .. 0.45

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00037
                tRNA_U5-meth_tr 200 eskgdllelycGnGnfslalarnfekvlateiakssveaaqyniaankidnvqiirlsaeel 261
                                    + ++ +l++  G G +++++ar+ + v a + +   ++  ++n++a+ i n+  i+   ee+
  gi|116753743|ref|YP_842861.1|  57 QPHETVLDIGAGTGRLAIPMARMAKSVTALDRSGGMLKCLKANMQAEGISNITCIQRDWEEI 118
                                    44568999*********************************************998887775 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.2
                tRNA_U5-meth_tr  68 fdaaselinelmkallaalkqdeklreklfqvdflstlsgellvsllyhkklddewkeaaealkdkleaqeldvnligra 147
                                    +d+++e++ +l                                                 e l++kl   +  +++  r+
  gi|116753743|ref|YP_842861.1| 229 HDISDEKVPKLR------------------------------------------------EFLSQKLIPTDQGLQMHRRS 260
                                    223333333332................................................33334444444445555555 PP

                tRNA_U5-meth_tr 148 rk 149
                                    + 
  gi|116753743|ref|YP_842861.1| 261 KI 262
                                    55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); 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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2095.41
//
Query:       gi|116753744|ref|YP_842862.1|  [L=261]
Description: band 7 protein [Methanosaeta thermophila PT]
Scores for 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-35  120.3   1.2    1.1e-34  120.0   1.2    1.1  1  Band_7    SPFH domain / Band 7 family
  ------ inclusion threshold ------
      0.016   14.9   0.1      0.032   13.9   0.1    1.6  1  Band_7_1  SPFH domain-Band 7 family


Domain annotation for each model (and alignments):
>> Band_7  SPFH domain / Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.0   1.2   1.2e-38   1.1e-34       2     177 ..      24     193 ..      23     194 .. 0.99

  Alignments for each domain:
  == domain 1  score: 120.0 bits;  conditional E-value: 1.2e-38
                         Band_7   2 iieegevgvvvrfGklsrvlepGlhfilPfgrsvtvvsvrvqtldvsvsltvptkDglpvtidvtviyrvpddapklvaa 81 
                                    ++++ e++vv+r Gkl++ ++pG+ f lP+++++++v++rv++ldv++ +tv+++D++ + +d++++y+v +da+k++ +
  gi|116753744|ref|YP_842862.1|  24 VVRQYERAVVFRLGKLHGEKGPGILFLLPLIDRMIRVDMRVRELDVPK-QTVISSDNVTLEVDAVIYYKV-SDASKAIIE 101
                                    799*********************************************.*********************.********* PP

                         Band_7  82 veresanldnlirrvlesalrevisemtleellsnreelaeelknelneqlrkyGvevldvritdidpppevaqalaakq 161
                                    v    +++++    +++ +lr v++++ l+++ls+r++l++++++ l      +G  v+ v+ +d+ +p++  +a+a+ +
  gi|116753744|ref|YP_842862.1| 102 V----EDYEAATLLLAQTTLRDVLGQNQLDTILSDRDDLNKKIQEILDTITGPWGMRVVMVTMRDVALPENMLRAIARQA 177
                                    *....9************************************************************************** PP

                         Band_7 162 aaeaeaqaeiaraeae 177
                                    +ae+e++a+i  ae+e
  gi|116753744|ref|YP_842862.1| 178 EAEREKRARIILAEGE 193
                                    *************998 PP

>> Band_7_1  SPFH domain-Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   3.6e-06     0.032     142     209 ..     114     179 ..      80     181 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.6e-06
                       Band_7_1 142 vtrlsdvlaeskipvldlaakseelaeklkealkeelaeyGlelekleienislpeevekaldkrasm 209
                                    +t+l dvl+++++  +   +  ++l +k++e l++     G+ +  +++++++lpe++ +a+ ++a++
  gi|116753744|ref|YP_842862.1| 114 QTTLRDVLGQNQLDTI--LSDRDDLNKKIQEILDTITGPWGMRVVMVTMRDVALPENMLRAIARQAEA 179
                                    4567888888888765..578899***************************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       991  (0.0552736); expected 358.6 (0.02)
Passed bias filter:                      641  (0.0357521); 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 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1813.82
//
Query:       gi|116753745|ref|YP_842863.1|  [L=374]
Description: transport system permease protein [Methanosaeta thermophila PT]
Scores for complete 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-88  296.1  34.5    3.1e-88  295.8  34.5    1.0  1  FecCD       FecCD transport family
  ------ inclusion threshold ------
      0.079   12.4  19.7       0.13   11.7  19.7    1.4  1  ABC-3       ABC 3 transport family
       0.26   11.1   0.1       0.26   11.1   0.1    2.6  3  Cortexin    Cortexin of kidney


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 !  295.8  34.5   5.1e-92   3.1e-88       2     312 .]      49     366 ..      44     366 .. 0.97

  Alignments for each domain:
  == domain 1  score: 295.8 bits;  conditional E-value: 5.1e-92
                          FecCD   2 lllllllslllgavkispsevfeallgka.......dsleaeivlelrlprvlaallvGaaLavaGallQtvtrNpLadP 74 
                                    llll+ + ++lg+ +is+ + ++all++        d l + +v+++r+pr++ +l++G++L+++G+++Q+v++NpLa+P
  gi|116753745|ref|YP_842863.1|  49 LLLLTGFVITLGPLNISMYDAYSALLERFlpsyfqvDALTSRVVWNIRFPRIVGGLMAGFGLGMCGCVMQAVLKNPLASP 128
                                    4566677799****************9999999999999999************************************** PP

                          FecCD  75 silGissgaalgavlallll.lgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsallsaltsllll 153
                                     +lGis+ga +g+ +a++++ +   + + ++  af++all +ll+++la   kga+++ l+LaGiav+++++a+++ll++
  gi|116753745|ref|YP_842863.1| 129 FTLGISAGAQFGISVAAVIGfAIFGGPYFIIGNAFICALLCSLLIVALA-AIKGATSENLVLAGIAVNYFFTAMSQLLKY 207
                                    *****************999777788999********************.****************************** PP

                          FecCD 154 llneealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrllllllvallta 233
                                    ++++e+l+ +++w +G+l+  sw +  +ll ++l++++ll+  + +l++++ gd+ Aks+Gv+ er+r++++++++ll+a
  gi|116753745|ref|YP_842863.1| 208 FASDEQLRIMTNWGMGDLAAFSWANSRILLGIFLICFPLLISRSWDLNIMTAGDDAAKSIGVDAERTRIFIMVISSLLVA 287
                                    ******************************************************************************** PP

                          FecCD 234 vavalvGpigFvGLivPhiarllvgadhrkllplsallGallllladllarlllsptelpvgivtaliGapffiylllr 312
                                    ++v++vG+igFvGL++Ph+ar+++g dhr l+p+s+ lG+l+l+ ad ++ ++++pt +p+gi+t++iG+pff+yl+l+
  gi|116753745|ref|YP_842863.1| 288 TIVCFVGTIGFVGLVAPHMARMVIGGDHRFLIPASGALGSLVLVSADAVGMNAIAPTIIPTGIMTSIIGVPFFMYLMLK 366
                                    ****************************************************************************986 PP

>> ABC-3  ABC 3 transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7  19.7   2.2e-05      0.13      27     226 ..     120     331 ..      94     367 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.2e-05
                          ABC-3  27 vlrr..qsllgdalsHaalpGvalayllgvn.......lllgailvgliaavalellkrktklked..taigivlsvfla 95 
                                    vl+   +s +  ++s  a  G+ +a ++g+        ++  a++++l++++ +++l++ +   ++  ++ gi +  f+ 
  gi|116753745|ref|YP_842863.1| 120 VLKNplASPFTLGISAGAQFGISVAAVIGFAifggpyfIIGNAFICALLCSLLIVALAAIKGATSEnlVLAGIAVNYFFT 199
                                    5554335677778888888888888888888778888444568999***********998766666234569*9999986 PP

                          ABC-3  96 lglvlvslikk.skvd.ldsyLfGniltisqedliliaiieavvllllllfwkelllitfdeelAkveglsvkllkllll 173
                                        l+++  +  +   ++++ +G++++ s  +  +++ i ++++ ll+    +l ++t   + Ak++g+  ++ ++ ++
  gi|116753745|ref|YP_842863.1| 200 AMSQLLKYFASdEQLRiMTNWGMGDLAAFSWANSRILLGIFLICFPLLISRSWDLNIMTAGDDAAKSIGVDAERTRIFIM 279
                                    5555555555434444156899********************************************************** PP

                          ABC-3 174 alialavvvalqavGviLvialliiPaatArrltrslesllivAillglvsvv 226
                                    ++ +l v++++ +vG i  +  l++P ++ + ++ + + l+  + +lg + +v
  gi|116753745|ref|YP_842863.1| 280 VISSLLVATIVCFVGTIGFVG-LVAPHMARMVIGGDHRFLIPASGALGSLVLV 331
                                    ***************998777.4678777777777777777777676665554 PP

>> Cortexin  Cortexin of kidney
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   4.4e-05      0.26       5      51 ..      16      62 ..      12      72 .. 0.88
   2 ?   -5.0   1.2         3   1.8e+04      35      47 ..     236     247 ..     235     250 .. 0.57
   3 ?    1.0   0.0     0.063   3.8e+02      13      38 ..     264     289 ..     253     295 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.4e-05
                       Cortexin  5 alapsgnevsavsldleqktvfafvilLlifLglLivrCfriLLDPY 51
                                   ++a  +++ s++ l  eq   f  + +L i+L lL++  f i L P 
  gi|116753745|ref|YP_842863.1| 16 PIARRTGKKSGMQLAHEQFKLFRSIFVLAILLFLLLLTGFVITLGPL 62
                                   567778999999******************************99996 PP

  == domain 2  score: -5.0 bits;  conditional E-value: 3
                       Cortexin  35 fLglLivrCfriL 47 
                                    +Lg+ ++ Cf +L
  gi|116753745|ref|YP_842863.1| 236 LLGIFLI-CFPLL 247
                                    5666655.66555 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.063
                       Cortexin  13 vsavsldleqktvfafvilLlifLgl 38 
                                     +++++d+e+   f+ vi  l++ ++
  gi|116753745|ref|YP_842863.1| 264 AKSIGVDAERTRIFIMVISSLLVATI 289
                                    44567888888888888765555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       826  (0.0460706); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.27s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2627.11
//
Query:       gi|116753746|ref|YP_842864.1|  [L=262]
Description: ABC transporter related [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-34  118.8   0.0    3.3e-34  118.3   0.0    1.2  1  ABC_tran         ABC transporter
    3.2e-10   40.3   0.3    7.8e-06   25.9   0.0    2.2  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    1.6e-07   31.0   0.4    1.9e-06   27.5   0.4    2.1  1  SMC_N            RecF/RecN/SMC N terminal domain
    6.7e-07   30.0   0.0    8.1e-07   29.7   0.0    1.2  1  AAA_23           AAA domain
    2.1e-06   27.3   0.0    4.4e-06   26.4   0.0    1.5  1  AAA_29           P-loop containing region of AAA domain
    5.8e-06   26.3   0.0    9.5e-06   25.6   0.0    1.2  1  AAA_15           AAA ATPase domain
    0.00033   19.6   0.5       0.69    8.6   0.0    2.8  2  ABC_ATPase       Predicted ATPase of the ABC class
    0.00035   21.0   0.0    0.00059   20.3   0.0    1.4  1  AAA_16           AAA ATPase domain
     0.0024   16.7   0.2     0.0077   15.0   0.0    1.7  2  RNA12            RNA12 protein
     0.0048   16.8   0.1      0.082   12.8   0.0    2.1  2  Rad17            Rad17 P-loop domain
     0.0048   17.2   1.0      0.044   14.1   1.0    2.1  1  AAA_22           AAA domain
     0.0079   15.8   0.0      0.013   15.1   0.0    1.3  1  AAA_27           AAA domain
      0.009   15.3   0.0      0.014   14.7   0.0    1.3  1  Zeta_toxin       Zeta toxin
     0.0099   15.8   0.0      0.022   14.7   0.0    1.7  1  RsgA_GTPase      RsgA GTPase
  ------ inclusion threshold ------
      0.011   15.1   0.0      0.023   14.1   0.0    1.4  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.019   14.2   4.4       0.15   11.2   4.4    2.0  1  NB-ARC           NB-ARC domain
       0.02   15.0   0.0      0.065   13.4   0.0    1.8  2  AAA_33           AAA domain
      0.022   14.5   0.0      0.064   13.0   0.0    1.8  2  AAA_30           AAA domain
      0.023   14.7   0.1          1    9.4   0.0    2.5  2  AAA_5            AAA domain (dynein-related subfamily)
      0.049   12.3   0.1       0.88    8.1   0.0    2.0  2  AAA_13           AAA domain
      0.067   12.9   0.0       0.14   11.9   0.0    1.5  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.12   12.4   0.1        0.6   10.1   0.0    2.0  2  AAA_14           AAA domain
       0.14   12.5   0.9        1.1    9.6   0.9    2.5  1  AAA_19           AAA domain
       0.14   12.1   0.3        0.3   11.0   0.3    1.8  1  NACHT            NACHT domain
       0.14   12.6   0.0       0.48   10.8   0.0    1.9  1  RNA_helicase     RNA helicase
       0.15   11.2   0.0       0.25   10.4   0.0    1.3  1  G-alpha          G-protein alpha subunit
       0.16   11.1   0.4       0.39    9.8   0.0    1.8  3  DUF815           Protein of unknown function (DUF815)


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 !  118.3   0.0     5e-37   3.3e-34       1     137 []      20     167 ..      20     167 .. 0.96

  Alignments for each domain:
  == domain 1  score: 118.3 bits;  conditional E-value: 5e-37
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvren 79 
                                    l+++s+++ ++++v ivG+nG+GKStL+k++ + l+p++G+il+d k+l++ +++++ + ++++pq   ++fp+  v ++
  gi|116753746|ref|YP_842864.1|  20 LNDLSFEIPPSNLVTIVGPNGSGKSTLIKCIDRILSPQKGSILIDRKELTRMNRREVARYLSYVPQSsVRVFPTN-VFDT 98 
                                    799****************************************************************98999998.8888 PP

                                    ...............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    ...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ...............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                                   ++++++ ++l+ l++++l+ ++      +LSgGq+q+v +aral+++++++llDEpt+
  gi|116753746|ref|YP_842864.1|  99 ilmgrrphigwlgsqDDERKVWDVLRLLDIEHLAMKNF----DELSGGQQQKVLIARALVQEAEVMLLDEPTS 167
                                    99999********9888888************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 !   25.9   0.0   1.2e-08   7.8e-06       2      24 ..      33      55 ..      32      90 .. 0.75
   2 !   12.6   0.0   0.00013     0.087     233     298 ..     135     198 ..     101     203 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 1.2e-08
                         AAA_21  2 nvliGpNgsGKSnLLdaldllar 24
                                     ++GpNgsGKS+L++++d + +
  gi|116753746|ref|YP_842864.1| 33 VTIVGPNGSGKSTLIKCIDRILS 55
                                   579****************9964 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00013
                         AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHS 298
                                    +++elS G+++   ++ al + +    + l+DEp ++L+ + +  ++ ++ ++ +++++  i++ H+
  gi|116753746|ref|YP_842864.1| 135 NFDELSGGQQQKVLIARALVQEA---EVMLLDEPTSNLDIWHQIDVMNVIrDIVKSRDITAIMALHD 198
                                    68999*******77777777777...9************9988888888843333366666666555 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.4   2.8e-09   1.9e-06      25     189 ..      31     187 ..      19     216 .. 0.71

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 2.8e-09
                                    SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrvk 104
                                    ++  ivGpNGSGKs l+  i  +L+         +k s li + ke  ++++ ev+ +++   ++ +++   +++  ++ 
  gi|116753746|ref|YP_842864.1|  31 NLVTIVGPNGSGKSTLIKCIDRILS--------PQKGSILIDR-KELTRMNRREVARYLSYVPQS-SVRVFPTNVFDTIL 100
                                    5778****************77777........4566899998.999999999999999877666.45555566666666 PP

                                    TTSEEEEEETTEEE-H...HHHHHHHHCTT-STT...CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHH CS
                                    xxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 105 rkgeseykingkevtk...kevsellesagiske...lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkk 178
                                     + + ++   g++  +    +v +ll  +++ ++   +LSgG+++     +l+A   v+ a ++llDe  ++LD  +   
  gi|116753746|ref|YP_842864.1| 101 MGRRPHIGWLGSQDDErkvWDVLRLLDIEHLAMKnfdELSGGQQQK----VLIARALVQEAEVMLLDEPTSNLDIWHQID 176
                                    66665555544444440025666666666655444448****8763....3344455699999***************** PP

                                    HHHHHHHHCTT CS
                                    xxxxxxxxxxx RF
                          SMC_N 179 vaellkekskn 189
                                    v ++++   k+
  gi|116753746|ref|YP_842864.1| 177 VMNVIRDIVKS 187
                                    ***99975554 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   1.2e-09   8.1e-07      12      49 ..      22      60 ..      12     159 .. 0.80

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 1.2e-09
                         AAA_23 12 dqeidF.skgltlItGpNGaGKTTildAiklaLygetpr 49
                                   d +++   ++l+ I+GpNG+GK+T++ +i  +L  +++ 
  gi|116753746|ref|YP_842864.1| 22 DLSFEIpPSNLVTIVGPNGSGKSTLIKCIDRILSPQKGS 60
                                   5555555569*******************9999877644 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   6.6e-09   4.4e-06      15      50 ..      23      58 ..      13      61 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 6.6e-09
                         AAA_29 15 htieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                    ++ei +++ + ++Gp+GsGKSTl+  i  +L p+k
  gi|116753746|ref|YP_842864.1| 23 LSFEIPPSNLVTIVGPNGSGKSTLIKCIDRILSPQK 58
                                   678899999999**********************97 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   1.4e-08   9.5e-06      17      69 ..      25      72 ..      22      81 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.4e-08
                         AAA_15 17 veidlseeltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleife 69
                                   +ei+ s+ l +++G+N+sGKS++++ +d +l+ +    k  i i+ ++l  ++
  gi|116753746|ref|YP_842864.1| 25 FEIPPSN-LVTIVGPNGSGKSTLIKCIDRILSPQ----KGSILIDRKELTRMN 72
                                   7888889.************************88....677788777776665 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0     0.001      0.69     244     266 ..      30      52 ..      25      55 .. 0.87
   2 !    7.4   0.5    0.0025       1.7     323     363 ..     139     179 ..     133     245 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.001
                                    SSEEEEEE-TTSSHHHHHHHHHH CS
                     ABC_ATPase 244 kGvtlIvGggfhGKsTLLeAlek 266
                                      +++IvG++  GKsTL++ +++
  gi|116753746|ref|YP_842864.1|  30 SNLVTIVGPNGSGKSTLIKCIDR 52 
                                    45899**************9975 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0025
                                    --HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHH CS
                     ABC_ATPase 323 ASGStsqAanimealeagakllLiDEDtsAtNlmirDermq 363
                                     SG   q + i++al  +a+++L+DE ts   + ++ + m+
  gi|116753746|ref|YP_842864.1| 139 LSGGQQQKVLIARALVQEAEVMLLDEPTSNLDIWHQIDVMN 179
                                    59999999*******************99777766544443 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   8.9e-07   0.00059      25      59 ..      31      66 ..      20     150 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 8.9e-07
                         AAA_16 25 elvllsGesGvGKsslvrellralekdg.giflrgk 59
                                   +lv ++G+ G+GKs+l++++ r l+ ++  i++  k
  gi|116753746|ref|YP_842864.1| 31 NLVTIVGPNGSGKSTLIKCIDRILSPQKgSILIDRK 66
                                   8999******************99999624444333 PP

>> RNA12  RNA12 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.2e-05    0.0077      17      55 ..      30      70 ..      25      86 .. 0.87
   2 ?   -1.1   0.1      0.87   5.8e+02     307     379 ..     146     218 ..     118     229 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.2e-05
                          RNA12 17 ntFivvkGPrGSGkkeLv..ldrvlkdrkkvlvidCdelvk 55
                                   +  +++ GP GSGk+ L+  +dr+l+ +k  + id +el+ 
  gi|116753746|ref|YP_842864.1| 30 SNLVTIVGPNGSGKSTLIkcIDRILSPQKGSILIDRKELTR 70
                                   56799************8778**************999976 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.87
                          RNA12 307 eeiieqsaeeilkmflldseeakkakwtkeqaWklikklskkgsieynellleelfkgsaesalkaLekaeli 379
                                    + +i ++ ++  +++lld+  ++ + w++ ++ ++i+ + k+  i++ + l++  + ++  + +  + k  ++
  gi|116753746|ref|YP_842864.1| 146 KVLIARALVQEAEVMLLDEPTSNLDIWHQIDVMNVIRDIVKSRDITAIMALHDLNLASAYSDRIIMMHKGRIV 218
                                    4467777777777777778888888888888888888888888888777777766666666666555555555 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   0.00012     0.082      41      72 ..      26      57 ..      17      86 .. 0.87
   2 ?    2.0   0.0      0.25   1.7e+02     107     176 ..     134     200 ..     113     208 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00012
                          Rad17 41 esrkkriLLisGPsGCgkstvvkvLskelgik 72
                                   e  + +++ i GP G gkst +k + ++l+++
  gi|116753746|ref|YP_842864.1| 26 EIPPSNLVTIVGPNGSGKSTLIKCIDRILSPQ 57
                                   555677999***************99999887 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.25
                          Rad17 107 esfkeleLkdakylklqklGddlrtdkklilvedlPnkfyrds.dalrevirkylrssealplilviteie 176
                                    + f el   + + +k+      l  + +++l+++  ++  +     + +vir  ++s++  + i+ + +++
  gi|116753746|ref|YP_842864.1| 134 KNFDEL--SGGQQQKVL-IARALVQEAEVMLLDEPTSNLDIWHqIDVMNVIRDIVKSRDI-TAIMALHDLN 200
                                    556665..333333333.3456667778888888777777655467899*******9998.7888887766 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   1.0   6.6e-05     0.044       7      43 ..      32      77 ..      29     203 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.6e-05
                         AAA_22  7 ilvvtGesGtGKTtllrrlleqldeeakaee.........erpevv 43
                                   +++++G+ G+GK+tl++ + + l  ++             +r+ev+
  gi|116753746|ref|YP_842864.1| 32 LVTIVGPNGSGKSTLIKCIDRILSPQKGSILidrkeltrmNRREVA 77
                                   689**************99998865544444666666666555555 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0     2e-05     0.013      18      50 ..      22      54 ..      19      56 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2e-05
                         AAA_27 18 sldfsaeeadlhliyGpNEAGKstalrAisdll 50
                                    l+f+   ++l  i+GpN +GKst+++ i ++l
  gi|116753746|ref|YP_842864.1| 22 DLSFEIPPSNLVTIVGPNGSGKSTLIKCIDRIL 54
                                   57788889******************9998765 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   2.1e-05     0.014      18      60 ..      32      74 ..      26     104 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.1e-05
                     Zeta_toxin 18 lillgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPe 60
                                   l+ ++G  G+GKs+l++ +++ l +q++ + +d+ +l ++ ++
  gi|116753746|ref|YP_842864.1| 32 LVTIVGPNGSGKSTLIKCIDRILSPQKGSILIDRKELTRMNRR 74
                                   68899****************************9998777654 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   3.3e-05     0.022      79     121 ..       9      52 ..       2      88 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.3e-05
                                    EEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase  79 vllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                     l+ s +++  l++l+ ++   +++++vG+ G GKStLi+ ++ 
  gi|116753746|ref|YP_842864.1|   9 NLTFSYNSHPILNDLSFEIPPsNLVTIVGPNGSGKSTLIKCIDR 52 
                                    5667777778889999999887999**************99875 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   3.5e-05     0.023      25      60 ..      33      68 ..      30      86 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.5e-05
                   Mg_chelatase 25 lllvGppGsGKtmlakrlpsllpplseeealevaki 60
                                   + +vGp GsGK+ l+k++  +l+p + +  ++ +++
  gi|116753746|ref|YP_842864.1| 33 VTIVGPNGSGKSTLIKCIDRILSPQKGSILIDRKEL 68
                                   5689*******************9887766666555 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   4.4   0.00023      0.15      19     117 ..      29     176 ..      14     208 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00023
                                    CSEEEEEEESTTSSHHHHHHHHCCSHCCCCCCBTEEEEE......................................... CS
                         NB-ARC  19 qslvvalvGmgGvGKttlakqilnksdevegrFdsvawv......................................... 57 
                                     s +v++vG  G+GK+tl+k i + ++  +g     + +                                         
  gi|116753746|ref|YP_842864.1|  29 PSNLVTIVGPNGSGKSTLIKCIDRILSPQKGS----ILIdrkeltrmnrrevarylsyvpqssvrvfptnvfdtilmgrr 104
                                    4579***************9998775554442....22223334577888999999999999999999999999999999 PP

                                    ....EEESXXHHHHHHHXXHHHHHCCCTTSSSS-STTS...HHHHHHHHCCCTTEEEEEE......EE-SHHH CS
                         NB-ARC  58 ....vvsktdkseeiletilkeLslseddleekeeves...lkrklvrlLltkrfllvlD......DVweeed 117
                                         ++ +d+++++++ +l+ L  ++  +++++e       k  + r+L +   +++lD      D+w++ d
  gi|116753746|ref|YP_842864.1| 105 phigWLGSQDDERKVWD-VLRLLDIEHLAMKNFDELSGgqqQKVLIARALVQEAEVMLLDeptsnlDIWHQID 176
                                    99999999999999999.9999998888888888877676678889999999999999995555555555544 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   9.8e-05     0.065       1      18 [.      32      49 ..      32     101 .. 0.73
   2 ?   -1.4   0.0       3.7   2.4e+03      16      89 ..     150     178 ..     127     197 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.8e-05
                         AAA_33  1 lvllvGlpGsGKstlaer 18
                                   lv +vG++GsGKstl++ 
  gi|116753746|ref|YP_842864.1| 32 LVTIVGPNGSGKSTLIKC 49
                                   7899***********874 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.7
                         AAA_33  16 aerllkklgavllssdtlrrrlfgtdqqsktdytrvldrlyqilnelarkalsagrnvildat..nlsrrerarfl 89 
                                    a+ l+++  + ll                                               d +  nl+ +++ +++
  gi|116753746|ref|YP_842864.1| 150 ARALVQEAEVMLL-----------------------------------------------DEPtsNLDIWHQIDVM 178
                                    3333333333333...............................................4443344444444444 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   9.7e-05     0.064      19      49 ..      31      61 ..      27      76 .. 0.87
   2 ?   -2.9   0.0       6.9   4.6e+03      83      96 ..     151     164 ..     132     186 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.7e-05
                         AAA_30 19 rvavltGpAGtGKttalkalreaweaaggrv 49
                                    +++++Gp G+GK+t++k + +++  ++g++
  gi|116753746|ref|YP_842864.1| 31 NLVTIVGPNGSGKSTLIKCIDRILSPQKGSI 61
                                   4789****************99988775554 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.9
                         AAA_30  83 rarlepgtllivDE 96 
                                    ra ++++++++ DE
  gi|116753746|ref|YP_842864.1| 151 RALVQEAEVMLLDE 164
                                    33444556666666 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0    0.0015         1       3      25 ..      34      57 ..      32     141 .. 0.88
   2 ?    3.2   0.0      0.13        83      19      58 ..     149     188 ..     144     222 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0015
                                   EEE--SSSSHHHHHHHGGGGB.S- CS
                          AAA_5  3 lLvGppGtgKselaerlaaal.nr 25
                                    +vGp G+gKs+l++ + + l  +
  gi|116753746|ref|YP_842864.1| 34 TIVGPNGSGKSTLIKCIDRILsPQ 57
                                   689***********9999988633 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.13
                                    GGGGBS--EEEEE--TT--HHHHH--B--.........-- CS
                          AAA_5  19 laaalnreveyvqltrdtteedlkgrreikngttslvdsp 58 
                                    +a+al +e e+++l + t+  d+  +++++n  +  v+s 
  gi|116753746|ref|YP_842864.1| 149 IARALVQEAEVMLLDEPTSNLDIWHQIDVMNVIRDIVKSR 188
                                    78999999*****************999998777776664 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0013      0.88      21      66 ..      35      91 ..      29     119 .. 0.61
   2 ?    2.0   0.3     0.092        61     524     564 ..     154     193 ..     146     213 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0013
                         AAA_13 21 iYGwNGaGKTtLSrllrslelgetepkfangsieitnge.................eldirVf 66
                                   i G NG+GK+tL + ++ + +       ++gsi i ++e                 +  +rVf
  gi|116753746|ref|YP_842864.1| 35 IVGPNGSGKSTLIKCIDRILSP------QKGSILIDRKEltrmnrrevarylsyvpQSSVRVF 91
                                   77***********999987332......23444333333223333445555555555566666 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.092
                         AAA_13 524 igkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQl 564
                                    +++ ++  +D P S LD  ++  v++ i++ + k+ ++  +
  gi|116753746|ref|YP_842864.1| 154 VQEAEVMLLDEPTSNLDIWHQIDVMNVIRDIV-KSRDITAI 193
                                    5678999**********************998.66666555 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 ?   11.9   0.0   0.00021      0.14       5      74 ..      37     102 ..      33     109 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00021
                Viral_helicase1   5 GvpGcGKStlirkllrtsliltvnrptaelltegk..pklpnlsvrtvdsflmalvkstkgkililDEylll 74 
                                    G  G+GKStli+ + r    l++ +    +l ++k   + ++++v +  s+ ++ + +  + ++++D +l++
  gi|116753746|ref|YP_842864.1|  37 GPNGSGKSTLIKCIDRI---LSPQKG--SILIDRKelTRMNRREVARYLSYVPQSSVR-VFPTNVFDTILMG 102
                                    556*********99988...666666..334444323666666666666666665554.6999999988886 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00091       0.6       3      40 ..      31      67 ..      29      95 .. 0.68
   2 ?   -0.2   0.1       1.5   9.8e+02      55      76 ..     148     168 ..     121     195 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00091
                         AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldd 40
                                   ++++i+G+  +GK+tl+k + ++ l +++  + i+ ++
  gi|116753746|ref|YP_842864.1| 31 NLVTIVGPNGSGKSTLIKCI-DRILSPQKGSILIDRKE 67
                                   5799************9654.45453555555555444 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.5
                         AAA_14  55 lileklkeekktylflDEiqev 76 
                                    li + l  ++ ++++lDE    
  gi|116753746|ref|YP_842864.1| 148 LIARALV-QEAEVMLLDEPTSN 168
                                    2222222.36788999996544 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.9    0.0017       1.1      10      39 ..      30      59 ..      24     229 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0017
                         AAA_19 10 ekvllvtaGpGtGKTrvlkhivallvelgg 39
                                   ++++ ++++ G+GK++++k+i ++l  ++g
  gi|116753746|ref|YP_842864.1| 30 SNLVTIVGPNGSGKSTLIKCIDRILSPQKG 59
                                   6789999*************9998887765 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.3   0.00045       0.3       2      20 ..      32      50 ..      31     178 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00045
                                   CEEEEC-TTTCHHHHHHHH CS
                          NACHT  2 lvilqGeaGsGKTtLlqkl 20
                                   lv + G++GsGK+tL++ +
  gi|116753746|ref|YP_842864.1| 32 LVTIVGPNGSGKSTLIKCI 50
                                   689************9877 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   0.00072      0.48       2      34 ..      34      61 ..      33      80 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00072
                   RNA_helicase  2 wlyGpsgeGKStlakeLakallkklklkkkdsv 34
                                    ++Gp+g GKStl+k + + +l    +++k+s+
  gi|116753746|ref|YP_842864.1| 34 TIVGPNGSGKSTLIKCIDR-IL----SPQKGSI 61
                                   689************9443.33....3555554 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00038      0.25      27     150 ..      34     197 ..      29     240 .. 0.46

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00038
                                    EEEESTTSSHHHHHHHHHHHCS--.....--HHHHHCCHHHHHHHHHHHHHHHHHHHHHTT................... CS
                        G-alpha  27 lllGqseSGKsTilkqlkllykkg.....fseeelatwraviqlnivrsiktilealesleselsesf............ 89 
                                     ++G ++SGKsT++k + ++  ++     +   ++++++ + +  + r ++ + +   +  ++    f            
  gi|116753746|ref|YP_842864.1|  34 TIVGPNGSGKSTLIKCIDRILSPQkgsilI---DRKELTRMNRREVARYLSYVPQSSVRVFPTNV--Fdtilmgrrphig 108
                                    579***************887666566652...22334444444444444444444444211111..0112333334444 PP

                                    .....HHHC-SS-SCCCS-HCHHHH............................HHCCHHC..........-HCHHHHHHH CS
                        G-alpha  90 .....elqelkerldplkkveasliaklssateee..................qeiefnp..........raevgedika 136
                                         +++    ++ +l+++e+  ++++++ +  +                        +          +++v + i++
  gi|116753746|ref|YP_842864.1| 109 wlgsqDDERKVWDVLRLLDIEHLAMKNFDELSGGQqqkvliaralvqeaevmlL-----DeptsnldiwhQIDVMNVIRD 183
                                    445432222222333333444433333333333222225554444433333330.....023333344445666666666 PP

                                    HCCSHHHHHHHCCG CS
                        G-alpha 137 Lwndpgiqelyerr 150
                                    ++++  i ++++  
  gi|116753746|ref|YP_842864.1| 184 IVKSRDITAIMALH 197
                                    66666666666644 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00058      0.39      52      95 ..      29      71 ..      20      90 .. 0.76
   2 ?   -3.1   0.0       5.3   3.5e+03      18      37 ..     127     146 ..     119     164 .. 0.60
   3 ?   -3.8   0.1       8.7   5.8e+03      92     117 ..     175     200 ..     173     204 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00058
                         DUF815 52 pannvLLwGarGtGKSslvkallneyaeegLrlievekedlkel 95
                                   p+n v ++G  G+GKS+l+k + + ++ ++   i +++++l+ +
  gi|116753746|ref|YP_842864.1| 29 PSNLVTIVGPNGSGKSTLIKCIDRILSPQKGS-ILIDRKELTRM 71
                                   6788999*************998877766633.44666666655 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.3
                         DUF815  18 pveevdevklddLvgidkqk 37 
                                     +e++   ++d+L g ++qk
  gi|116753746|ref|YP_842864.1| 127 DIEHLAMKNFDELSGGQQQK 146
                                    34444455555555555554 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 8.7
                         DUF815  92 lkelpklvellrerperfilfvDDLs 117
                                    ++ ++ + +++++r+   i+ + DL 
  gi|116753746|ref|YP_842864.1| 175 IDVMNVIRDIVKSRDITAIMALHDLN 200
                                    66677788888888888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); 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: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 1779.29
//
Query:       gi|116753747|ref|YP_842865.1|  [L=365]
Description: radical SAM domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      4e-15   56.6   0.0    1.1e-14   55.2   0.0    1.6  2  Radical_SAM  Radical SAM superfamily
      9e-07   29.2   0.0    1.8e-06   28.3   0.0    1.5  2  Fer4_12      4Fe-4S single cluster domain
    6.4e-06   26.3   0.0    2.5e-05   24.4   0.0    1.9  2  Fer4_14      4Fe-4S single cluster domain
    1.9e-05   25.0   0.2    3.9e-05   24.1   0.2    1.5  1  SPASM        Iron-sulfur cluster-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 !   55.2   0.0   2.4e-18   1.1e-14       4     147 ..      31     170 ..      30     179 .. 0.90
   2 ?   -3.3   0.0       2.3     1e+04     108     143 ..     285     317 ..     283     323 .. 0.73

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 2.4e-18
                                    ESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   4 trgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritve 83 
                                    t  CnlrC++C+ +     ++  +++ ++  ++ ++ +++  ++  v l ggepll+  ++e +  +++   ++ +i + 
  gi|116753747|ref|YP_842865.1|  31 TTDCNLRCVYCYAN----GGDNKAYMGWDVAKRAIDLVAEGADCFKVQLAGGEPLLNFGLIERIVFYIHDLGADASIQLQ 106
                                    778***********....69******************76666**************999888888888779******** PP

                                    ECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHH.HHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  84 tngtlpdeeklerllelgvdrvslgleaadde.kvlklmn.rghtfeevlealeklreagikrvvd 147
                                    tn+tl+++ ++ rl+ lg   v ++l+ +    ++l+++  + ++   v++++++lr+agi  v  
  gi|116753747|ref|YP_842865.1| 107 TNATLISPAIASRLRALG-IGVGVSLDGVPAInDHLRPFAdGHGSTHSVINGIRNLRDAGIS-VGM 170
                                    ******************.999999999998888999999999999***************9.444 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.3
                                    EEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM 108 gleaaddekvlklmnrghtfeevlealeklreagik 143
                                    +l+++d +   +++  +  ++ + e l+ +r++ ik
  gi|116753747|ref|YP_842865.1| 285 SLHHPDFR-LGNIL-EPRFWDTISERLRDARRS-IK 317
                                    56777777.77777.557888888888888887.66 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0     4e-10   1.8e-06       8      91 ..      26     106 ..      18     150 .. 0.80
   2 ?   -3.9   0.0       3.5   1.6e+04      55      72 ..     233     250 ..     222     256 .. 0.66

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 4e-10
                        Fer4_12   8 lslf.vsgCnlsCkgCfnketwsfk.sgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpe 85 
                                    l+l+ +++Cnl+C +C+++   +    g+++ k +++ + e +     +++ l GGEPll  n   + ++v ++   + +
  gi|116753747|ref|YP_842865.1|  26 LILWvTTDCNLRCVYCYANGGDNKAyMGWDVAKRAIDLVAEGA---DCFKVQLAGGEPLL--NFGLIERIVFYIHDLGAD 100
                                    4677678**********87766544268888888888777655...88************..*******99999888776 PP

                        Fer4_12  86 kdiwly 91 
                                     +i l 
  gi|116753747|ref|YP_842865.1| 101 ASIQLQ 106
                                    555554 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 3.5
                        Fer4_12  55 gltllGGEPllpenaeal 72 
                                     l  +GG P+   ++e +
  gi|116753747|ref|YP_842865.1| 233 YLAGSGGNPVRFREVERM 250
                                    566689999876665555 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 !   24.4   0.0   5.5e-09   2.5e-05       5      91 ..      31     111 ..      28     132 .. 0.77
   2 ?   -2.0   0.0      0.87   3.9e+03      50      71 ..     233     254 ..     219     256 .. 0.67

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 5.5e-09
                        Fer4_14   5 lsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekkiw 84 
                                    +  Cnl C+ C+ +   ++ +   ++ +   + +    ++ +   ++ l GGePL   n   + ++v ++++ + + +i+
  gi|116753747|ref|YP_842865.1|  31 TTDCNLRCVYCYANGGDNKAYMGWDVAKRAIDLV-AEGADCF---KVQLAGGEPL--LNFGLIERIVFYIHDLGADASIQ 104
                                    789*********6665555554444444443444.2344444...577*******..99********************* PP

                        Fer4_14  85 letngtl 91 
                                    l+tn+tl
  gi|116753747|ref|YP_842865.1| 105 LQTNATL 111
                                    *****97 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.87
                        Fer4_14  50 glvltGGePLhyenkkellklv 71 
                                     l  +GG+P  + + + +  l+
  gi|116753747|ref|YP_842865.1| 233 YLAGSGGNPVRFREVERMRCLL 254
                                    366689***9998877766555 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.2   8.6e-09   3.9e-05       1      67 [.     264     325 ..     264     326 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 8.6e-09
                          SPASM   1 C.fapsrslfInsdGdVvpCcvdkktyveelklGnireesleeIwnseeyqefrkskkfplielCrnC 67 
                                    C f  ++sl + ++Gd +pC    +  + +++lGni e  + + + se++++ r+s k   ++ C +C
  gi|116753747|ref|YP_842865.1| 264 CyFDAYQSLMVCPNGDAYPC---ASLHHPDFRLGNILEPRFWDTI-SERLRDARRSIKT--PHKCMTC 325
                                    77888999************...4556566********9988886.9999998843333..3569999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); 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: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2592.70
//
Query:       gi|116753748|ref|YP_842866.1|  [L=1244]
Description: cobaltochelatase, CobN subunit [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
          0 1370.3   0.0          0 1370.0   0.0    1.0  1  CobN-Mg_chel  CobN/Magnesium Chelatase


Domain annotation for each model (and alignments):
>> CobN-Mg_chel  CobN/Magnesium Chelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1370.0   0.0         0         0       2    1087 ..     121    1226 ..     120    1228 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1370.0 bits;  conditional E-value: 0
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel    2 aYlkeggveNlknllryladkllgkkeeeveppvelpeegiyhpdakelfesleeylewykkakkekaptvgilfyra 79  
                                     +Y+++gg+eN++nl+ yla++++g  + ++++p++  +egiyhp+  + + sleey+   +k+ +e++ tvgi+fy +
  gi|116753748|ref|YP_842866.1|  121 EYISYGGRENFRNLVLYLANRFAG-AKYAFRDPEKSVWEGIYHPEF-DHVPSLEEYM---QKRCREDRLTVGIWFYHS 193 
                                     7**********************8.66689*************983.3455555555...5689************** PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...x...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel   80 hllagntavidaliraleerglnvlpvfvssl...d...seaqealeelftkegeekvdalinttsfalvkgpaeeee 151 
                                      +++gnta++d++ir++e++g+nv+pvf++sl   d   + a+  +e++f+++g++ +d+lin ++f++++ + +e +
  gi|116753748|ref|YP_842866.1|  194 FWQSGNTAFVDEMIREVERAGANVIPVFMYSLkdeDlgtRGAEWVIENYFMQNGRPIIDVLINPLMFSISMRSCTEGS 271 
                                     ********************************965266789999*************************998865554 PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxx.xxxxxxxxx RF
                   CobN-Mg_chel  152 eeaeeealkelnvPvlqailssqsreeWeessqGlspldlamsvalpEldGriepvvisfke...eee.eetevekye 225 
                                     +      +++l vP+++ai++++s ++W+es+ Gl+p+d+++sva+pE+dG +++v++++ke   +++ +  +v++ e
  gi|116753748|ref|YP_842866.1|  272 S-----IFSRLRVPIIKAIITYNSLKDWQESQCGLTPMDITLSVAMPEFDGDLITVPVAAKErteRDPlTGVTVTRLE 344 
                                     3.....58******************************************************87544489999***** PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  226 pipervervadlaarwarLrrkpnaekkvaiilanyppgegrlgnavgLdvpaSlvnlLkalkeeGYdveelpesgde 303 
                                     piperv+++++l  +warLr+kpn+ek+vaiil+nypp+++r+g+a gLd+paS++n+++ lk++GY++ e+pesgd+
  gi|116753748|ref|YP_842866.1|  345 PIPERVRKLVQLSLNWARLRHKPNDEKRVAIILHNYPPRDDRIGTAFGLDIPASVLNIMRVLKAAGYRIYEIPESGDA 422 
                                     *********************************************************************888****** PP

                                     xxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  304 Liellleggtndpew...eelkvgaaallpaeeYeewfeeLpeelreeveerWgeppgemveeeksgekklvipglql 378 
                                     Li+ ++++ tnd++    ee+k +a+a+++ e+Y +wf+eLp ++r+++++ Wg+ppg    e   +++ ++ipg+  
  gi|116753748|ref|YP_842866.1|  423 LIRDIKKHLTNDNRLrspEEMKSRAVASVSRERYMKWFDELPINIRRRMVKSWGNPPG----ELFVHRGGILIPGIIN 496 
                                     **************988988888***********************************....5666799********* PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  379 GnvfvgvQPargyeedpsklyhdpdlpPthqYlAfYlWlreefgadavvHvGkHGtlEwlPGKqvglseecyPdillg 456 
                                     Gn+f+g+QP+rg+ e+  ++yh+pdlp +h+Y+A+Y+W+r+ f+ad ++H+GkHG+lEwlPGK+vgls++c+Pdi++ 
  gi|116753748|ref|YP_842866.1|  497 GNIFIGLQPPRGFLENAAAIYHSPDLPIPHHYYAYYRWIRDIFRADLIMHIGKHGSLEWLPGKSVGLSDSCFPDIAIS 574 
                                     ****************************************************************************** PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  457 dlPhlYpYivnnpgEGtqAKRRsyAviidHltPpmtraelygelaeLeelideYeeaesldperlkalreqilelvee 534 
                                     dlP++YpYi+nnpgEGtqAKRRsy++iidHl+P+m ra+ly++laeLe ++++Y++a+s+dp +l+++++ ++e+v++
  gi|116753748|ref|YP_842866.1|  575 DLPNIYPYIINNPGEGTQAKRRSYCCIIDHLVPVMHRANLYDHLAELEVMLRDYHHAASEDPGKLESMKRIVWEKVVQ 652 
                                     ****************************************************************************** PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  535 lnldkdlgleeakeeeeeefeellekldgyleelkeaqirdglhilGeapegeqlvdlvvailrleneegeslteala 612 
                                     ++ld+dlg +  ++++ ++f++ll +l++yl+e++++qirdglh+lG +p++++l +++v+++rl+n+e +sl+e la
  gi|116753748|ref|YP_842866.1|  653 ARLDRDLGID--ENTALSDFDQLLVRLHDYLNEIADTQIRDGLHVLGVPPKDTRLDEFLVSLTRLQNGEVPSLRETLA 728 
                                     *******888..47789************************************************************* PP

                                     xxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............. RF
                   CobN-Mg_chel  613 ealgldlde..leeksekelrtagdalealeeeaeelveelleeeaeeeeaeaeeleeeeeeeee............. 675 
                                       +g+d+++    + +   ++t g++le+++e + +lv++l e+++++e++ + e+e   +++++             
  gi|116753748|ref|YP_842866.1|  729 LIMGYDYSSlmAGRGRYFGMKTGGELLEDIDELSLHLVAKLRENGFDPESIPKVEDEILGRRDARlelvlnyiiklsq 806 
                                     ********94444455567899***************************999999998888887799*********** PP

                                     ...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  676 ...eteeEitallraLdGeyippgpsGdptrgraevLPTGrNfysvDpraiPteaAwevGkklaeellerylqehgey 750 
                                        +te+E+++ll+a +G y+p+gpsG+ptrg+a++LPTGrNfysvDp+aiPt+aAw+vG + a++ll+ry +e+g+y
  gi|116753748|ref|YP_842866.1|  807 kitSTEDELNNLLAASEGCYVPSGPSGAPTRGMADILPTGRNFYSVDPQAIPTPAAWNVGVANADALLRRYIREEGRY 884 
                                     **8888************************************************************************ PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  751 PekvglslwgtetmrteGediAqiLallGvrPvwdaa.grvvdlelipleeLgRPRiDVtvriSGffRDafpnliell 827 
                                     Pe +g+++wg++tmrt+G+diA++L+l+GvrP+wd++ grv++le+ipleeL+RPRiDV++riSG+fRDafpn+++l+
  gi|116753748|ref|YP_842866.1|  885 PEAIGMVIWGSSTMRTKGDDIAEALYLIGVRPIWDRRnGRVQGLEVIPLEELKRPRIDVLIRISGLFRDAFPNIVHLI 962 
                                     ****************************************************************************** PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  828 dkavelvaeldEpeedNfvrkhvleeeaelee....keeaeeratyRvFgskpGaYgagvqeliessnWedeedLaea 901 
                                     d+ave+va+ldEp+++N++++hv e+ +e  +    ++ a+ +a+yR+Fg +pGaYgagv e+++s+nW+d +dLae+
  gi|116753748|ref|YP_842866.1|  963 DEAVEMVASLDEPHDMNYLARHVAEDVNEKLDdgidPKLARIEASYRIFGCRPGAYGAGVCEAVDSKNWRDLKDLAEI 1040
                                     ***************************9999945433355599*********************************** PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  902 YlnwssyaYgkgaegeeaeeafearLkrvdvvvqnqdsrehdlldsddyyqflGGltaavrslsgkkpeayfgdssnp 979 
                                     Y++w++yaY+++++g+  +e f++ L r++++v+n+d+re+d+ldsdd+y+++GG++aavr+ +g++p++y+gdss+p
  gi|116753748|ref|YP_842866.1| 1041 YVTWGGYAYTRQEYGTIVPESFKKCLCRLELTVKNEDTREYDMLDSDDFYSYHGGMIAAVRAFRGDRPRSYCGDSSDP 1118
                                     ****************************************************************************** PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  980 enpkvrtlkeeiarelrsrvlNPkWiegmmrhGykGafelaatvdnlfgwdatadvvddwvyeevaetYvlDeevref 1057
                                     e++kvr+++ee+ + +r+r+lNPkWie+m+rhGykGa +l++tvd +fgwdat++v+++w+yee+a++Y+lD++++e+
  gi|116753748|ref|YP_842866.1| 1119 ERVKVRSISEETMHIFRARILNPKWIESMKRHGYKGAGDLSRTVDVVFGWDATSEVIEEWMYEELANRYALDKDMQEW 1196
                                     ****************************************************************************** PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel 1058 leekNpwAlreiaerLlEaarrglWeasee 1087
                                     l+e Np+Al++i+erLlEa++rg+W+a+e 
  gi|116753748|ref|YP_842866.1| 1197 LKEVNPHALQNIVERLLEAIERGMWRATES 1226
                                     **************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); 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: 0.84u 0.32s 00:00:01.15 Elapsed: 00:00:00.47
# Mc/sec: 7900.85
//
Query:       gi|116753749|ref|YP_842867.1|  [L=362]
Description: periplasmic binding protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.3e-22   79.2   0.0    5.2e-22   78.6   0.0    1.2  1  Peripla_BP_2  Periplasmic binding protein
  ------ inclusion threshold ------
       0.13   12.2   0.1        9.5    6.1   0.1    2.2  2  DUF3855       Domain of Unknown Function with PDB structure (


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 !   78.6   0.0   5.8e-26   5.2e-22       1     236 [.      47     307 ..      47     308 .. 0.85

  Alignments for each domain:
  == domain 1  score: 78.6 bits;  conditional E-value: 5.8e-26
                                    EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT..TS-BSBESSSB-HHHHHH.......H--SEEEE-GGG.... CS
                   Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadkleeaivevgadgeidvEklaa.......lkPDlvilskgl.glt 72 
                                    i++ + + ++ l al+a+dkvvgv+ +   + + + l+ ++ +vg+ +++d+E + +         PD+++l++++ g  
  gi|116753749|ref|YP_842867.1|  47 IIVQNGGAARALMALDAADKVVGVADFIPKNPELYPLLTDKQVVGTWKSFDYELVGEiakrgdtITPDIIVLCYYYkGMS 126
                                    56677788999***************9999999998888*************98865222233357**********9777 PP

                                    GGGHHHHHHHS-E.....EE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT.-EEEEEEEETT CS
                   Peripla_BP_2  73 dedeellksgipt.....vivessntgeslkeqiralgellgledeaeklvaeidsklaaaksaidsekpkpvlvfggad 147
                                     +++ ++k  +p+     ++ +++n  e+l++++  lg +lg+e++a+++ ++ ++ ++ +ksa++ + p p ++  +++
  gi|116753749|ref|YP_842867.1| 127 FSIDSFEKGFAPFenitlIALDFTNP-ENLTDSLYKLGVILGKEEKAREINEWRQKQIELVKSAVEGQ-PMPRVYIESGA 204
                                    77777777655543332255566666.*****************************************.44444444444 PP

                                    E.....EEEE-TTSTTTHHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEH............HHHT-S--HH CS
                   Peripla_BP_2 148 e...ggyvvagsnsyigdlldalgieniaaeskkseyeeisaEqilasdpdvifvsgr............aeadnktgle 212
                                    +   g+ + +g  s++g l+ ++g++nia +  ++ + ++s+E++++++pdvi+v  +            ++ +   +l 
  gi|116753749|ref|YP_842867.1| 205 SkglGELTAFGPESGMGTLVKIAGGDNIAGSL-GEVFPKVSWEWVVSQNPDVILVWYSadsvgwepspseDTVELERKLN 283
                                    4479************************9999.********************9988889*******9999999999*** PP

                                    HHT-SHHHHTSHHHHTT-EEEE-H CS
                   Peripla_BP_2 213 flkenpllaelpAvkngrVyalds 236
                                    +++ +p+ a++ Av   rV+ ++s
  gi|116753749|ref|YP_842867.1| 284 EVLDRPGGASISAVNAERVFLCHS 307
                                    ********************9976 PP

>> DUF3855  Domain of Unknown Function with PDB structure (DUF3855)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1    0.0011       9.5       5      59 ..     114     170 ..     111     191 .. 0.86
   2 ?    3.7   0.0    0.0061        55      21      65 ..     278     321 ..     271     349 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0011
                                    X-EEEEEEETT---HH..HHHHHHHHHHHHS--------SSEEEEEEEEEEE-TT-- CS
                        DUF3855   5 dileilyykkgkefgi..lekkmkeifnetgvslepvnseligriflkisvleegee 59 
                                    di+ + yy kg  f i  +ek +    n t ++l+  n e +   + k+ v+   ee
  gi|116753749|ref|YP_842867.1| 114 DIIVLCYYYKGMSFSIdsFEKGFAPFENITLIALDFTNPENLTDSLYKLGVILGKEE 170
                                    89999*********9966799999999*************99999999999765554 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0061
                                    HHHHHHHHHHH.HS--------SSEEEEEEEEEEE-TT.----SEEE CS
                        DUF3855  21 lekkmkeifne.tgvslepvnseligriflkisvleeg.eevpsfai 65 
                                    le+k++e+++   g s+  vn+e   r+fl  s++  g e+v  +a 
  gi|116753749|ref|YP_842867.1| 278 LERKLNEVLDRpGGASISAVNAE---RVFLCHSMMLSGlENVVGLAY 321
                                    89******99725799*****98...889988877666355665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 2364.39
//
Query:       gi|116753750|ref|YP_842868.1|  [L=55]
Description: CopG/Arc/MetJ family transcriptional regulator [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); 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: 0.32u 0.27s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 433.37
//
Query:       gi|116753751|ref|YP_842869.1|  [L=120]
Description: putative 6-pyruvoyl tetrahydropterin synthase [Methanosaeta thermophila PT]
Scores for complete 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  112.4   0.1    1.4e-32  112.2   0.1    1.0  1  PTPS             6-pyruvoyl tetrahydropterin synthase
  ------ inclusion threshold ------
      0.085   12.3   0.0        6.1    6.2   0.0    2.1  2  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 


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 !  112.2   0.1   1.6e-36   1.4e-32       6     121 ..       7     119 ..       3     120 .] 0.94

  Alignments for each domain:
  == domain 1  score: 112.2 bits;  conditional E-value: 1.6e-36
                                    EEEEEEE--TTTTGGGGSTEEEEEEEEEEEEEC-STCTTBSS-HHHHHHHHHHHHHCTTTEECCCC-CCHHCCS.--HHH CS
                           PTPS   6 feFdaaHrlrkhegkcrnlHGHnykvevtvegeeldetgmvvdfgelkealkeileelDhkflnaddpeleellspTaEn 85 
                                     eFdaaH+l+ h+gkc+++HGH+y+vev ++g+   ++gm++df  lk+++ ++++elDh++ln     l+   +pTaE+
  gi|116753751|ref|YP_842869.1|   7 MEFDAAHHLPMHDGKCSRIHGHTYRVEVVLQGD-PGDDGMIIDFYMLKKIVGRVIQELDHNNLN---TVLQ---NPTAEM 79 
                                    69*******************************.999***************************...3444...4***** PP

                                    HHHHHHHHHHHHH....GCCCGCEEEEEEEEETTEEEEEE CS
                           PTPS  86 laklifeelkerl....qekevklskvrvwEtpnswaeyr 121
                                    +a++i+++l e+l     +++++l +vr+wE +++w+ ++
  gi|116753751|ref|YP_842869.1|  80 IASHIHRRLHEELkmtgLSDKATLLSVRLWEGRDKWVMVD 119
                                    ***************99999****************9875 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 ?    6.2   0.0   0.00068       6.1     157     181 ..       3      26 ..       1      38 [. 0.87
   2 ?    4.5   0.0    0.0024        21     139     163 ..      45      69 ..      29      89 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.00068
                tRNA_synthFbeta 157 lgiekvefepaehpalhpgrsAeik 181
                                    +g+ ++ef++a+h ++h g++ +i+
  gi|116753751|ref|YP_842869.1|   3 MGL-SMEFDAAHHLPMHDGKCSRIH 26 
                                    677.89******************8 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0024
                tRNA_synthFbeta 139 ravdfydlkgivealleslgiekve 163
                                       dfy lk+iv ++ ++l  +++ 
  gi|116753751|ref|YP_842869.1|  45 MIIDFYMLKKIVGRVIQELDHNNLN 69 
                                    558***************9986654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); 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 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 868.00
//
Query:       gi|116753752|ref|YP_842870.1|  [L=224]
Description: exsB protein [Methanosaeta thermophila PT]
Scores for complete 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-60  204.1   0.0    1.9e-60  204.0   0.0    1.0  1  QueC           Queuosine biosynthesis protein QueC
    1.9e-09   37.4   0.1    2.6e-07   30.4   0.1    2.5  2  ThiI           Thiamine biosynthesis protein (ThiI)
    0.00043   20.1   0.1     0.0016   18.1   0.0    1.8  2  Asn_synthase   Asparagine synthase
     0.0032   16.3   0.0     0.0037   16.1   0.0    1.3  1  tRNA_Me_trans  tRNA methyl transferase
     0.0045   16.5   0.1      0.017   14.6   0.1    1.8  1  AP_endonuc_2   Xylose isomerase-like TIM barrel
  ------ inclusion threshold ------
       0.02   14.7   0.0      0.053   13.3   0.0    1.6  2  ATP_bind_3     PP-loop family


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 !  204.0   0.0   6.4e-64   1.9e-60       1     209 [.       3     214 ..       3     215 .. 0.95

  Alignments for each domain:
  == domain 1  score: 204.0 bits;  conditional E-value: 6.4e-64
                                    EEEEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-T.TSHHHHHHHHHHHHT--.-EEEEE-GGGGGGSCGGG------- CS
                           QueC   1 kavvllSGGlDSttvlalakkegkevealtfdYgqr.hkkeleaakkiakelgveehkildldllkelggsaLtdeeiev 79 
                                    +av+l SGGlDSt+++++a+++g  v++++++Ygq+ +++e+ea ++ia+++g ++     +dl++++  saLt++ +++
  gi|116753752|ref|YP_842870.1|   3 RAVCLCSGGLDSTVAATIARRSGMDVYLIHVSYGQQaERREIEAIERIADAIGASDLMCSRIDLFRNI--SALTTQGARI 80 
                                    69**********************************99****************9*********9998..79******** PP

                                    --...--...--------TTHHHHHHHHHHHHHHHHT-SEEEE---S-STT--GGGSHHHHHHHHHHHHHH...HTS--E CS
                           QueC  80 pk...eeleeeelpntfVpaRNliflslaasyaealgaeaiiiGvneedfsgYPDcrdefvkalnkalnlg...edkkie 153
                                    p+    +l++e++p t+V  RN+++ls+aa+yae lga++i++G+n+e++  YPD+r+efv+++n++l+ +    +++ +
  gi|116753752|ref|YP_842870.1|  81 PRgeeVSLDSESTPPTWVYCRNTVLLSMAAAYAEYLGAHSIYVGFNAEEAMSYPDNRPEFVEQFNALLEKAvasFSRPPK 160
                                    *975555677************************************************************988877999* PP

                                    EE-TTTT--HHHHHHHHHHTTHHHHH-B-STTS.-BTTTTSSSHHHHHHHHHHHHH CS
                           QueC 154 ieaPlidlsKaeivklgkelgvpleetlsCYegeeegkaCgeCdaCalRkkgfeea 209
                                    ++aPl+d+ K++iv+lg+++++ple+t+sCY ++e   +Cg+C++C+ R++gf ea
  gi|116753752|ref|YP_842870.1| 161 VVAPLVDMRKKDIVRLGADIKAPLELTWSCYLNGEI--HCGTCESCQHRRRGFVEA 214
                                    *******************************99555..***************986 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.1   8.7e-11   2.6e-07       4      62 ..       2      60 ..       1     128 [. 0.68
   2 !    4.4   0.0    0.0079        24     139     159 ..     160     180 ..     148     198 .. 0.88

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 8.7e-11
                           ThiI  4 gkvlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellaeyqts 62
                                   g++++L SgG+DS Vaa ++ + G+ v l+h++     + ++ie +e++a+ +   +  
  gi|116753752|ref|YP_842870.1|  2 GRAVCLCSGGLDSTVAATIARRSGMDVYLIHVSYGQQAERREIEAIERIADAIGASDLM 60
                                   899*****************************877888888999999999887666643 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0079
                           ThiI 139 lilrPLigldKeeiiklAkei 159
                                     ++ PL+ + K++i++l  +i
  gi|116753752|ref|YP_842870.1| 160 KVVAPLVDMRKKDIVRLGADI 180
                                    5899************98877 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   5.5e-07    0.0016      22      88 ..       6      70 ..       3     101 .. 0.81
   2 ?   -0.5   0.0      0.26   7.8e+02      61      96 ..     107     142 ..     106     155 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 5.5e-07
                   Asn_synthase 22 alLSGGlDSSliaalaarqsksplktFsigf.eekgsdeakyakevaehlgtehtelvlteeelldal 88
                                   +l SGGlDS++ a +a+r    ++   ++ + ++++  e+++ +++a+++g    +l +++ +l++ +
  gi|116753752|ref|YP_842870.1|  6 CLCSGGLDSTVAATIARRSGM-DVYLIHVSYgQQAERREIEAIERIADAIGAS--DLMCSRIDLFRNI 70
                                   677******999999999775.888888888556****************988..4666666666555 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.26
                   Asn_synthase  61 kyakevaehlgtehtelvlteeelldalpdviyhle 96 
                                    ++a++ ae+lg   + + +++ee++++ +  ++++e
  gi|116753752|ref|YP_842870.1| 107 SMAAAYAEYLGAHSIYVGFNAEEAMSYPDNRPEFVE 142
                                    578999999999999999999999987555555555 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.2e-06    0.0037       3      54 ..       4      53 ..       2     142 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.2e-06
                  tRNA_Me_trans  3 vvvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkda 54
                                    v++ SgG DS+vaa++ ++ g +v  +++   +++++ +    a e ++da
  gi|116753752|ref|YP_842870.1|  4 AVCLCSGGLDSTVAATIARRSGMDVYLIHVSYGQQAERRE--IEAIERIADA 53
                                   58999*********************99999887744433..4444444444 PP

>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   5.7e-06     0.017       2     120 ..      19     151 ..      18     154 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.7e-06
                                    HHHHHCT-SEEEEECCTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHC.....................H CS
                   AP_endonuc_2   2 aaaaeaGfdgvElfgrdlvpvselsdeelrelrkaldelglriaslslftrfgypded.....................e 60 
                                    ++a++ G+d   ++ ++++++ +++ e++++++ a+ + +l ++ + lf + +++ ++                      
  gi|116753752|ref|YP_842870.1|  19 TIARRSGMDVYLIHVSYGQQAERREIEAIERIADAIGASDLMCSRIDLFRNISALTTQgariprgeevsldsestpptwV 98 
                                    6899*****************999******************************9999*****99999887776666664 PP

                                    TTCSHHHHHHHHHHHHHHHHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHH CS
                   AP_endonuc_2  61 rearreesvdalkraielaaaLGapllvlhpGtagagpkgseeeawerlaeslneladya 120
                                     +++       l  a+ +a+ LGa+ + +++    a +  s+++++  ++e +n+l+++a
  gi|116753752|ref|YP_842870.1|  99 YCRN----TVLLSMAAAYAEYLGAHSIYVGFN---AEEAMSYPDNRPEFVEQFNALLEKA 151
                                    4444....7799999**************955...**********************998 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.8e-05     0.053       6      81 ..       8      79 ..       3      85 .. 0.73
   2 ?   -1.8   0.0      0.76   2.3e+03     138     154 ..     159     175 ..     136     180 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.8e-05
                                   --SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT.-EEEEEE--HHHCTTSTCCCHHH CS
                     ATP_bind_3  6 vSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckkln.ikleiekvdvakkkgknleeaAR 81
                                    SgGlDS++   ++ ++    g+++ +ihv +g ++e ++e e+++++++ ++  +l  +++d+ ++ +  + + AR
  gi|116753752|ref|YP_842870.1|  8 CSGGLDSTVAATIARRS----GMDVYLIHVSYGQQAE-RREIEAIERIADAIGaSDLMCSRIDLFRNISALTTQGAR 79
                                   6******9876666655....789*********8766.577889999999887456777777775555555555555 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.76
                                    CCEE-CCCT--HHHHHH CS
                     ATP_bind_3 138 irlvRPlLkvskeelee 154
                                     ++v Pl++++k+++ +
  gi|116753752|ref|YP_842870.1| 159 PKVVAPLVDMRKKDIVR 175
                                    57888999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); 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: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1680.70
//
Query:       gi|116753753|ref|YP_842871.1|  [L=124]
Description: hypothetical protein Mthe_0440 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.011   15.2   0.1      0.012   15.0   0.1    1.1  1  Rab5-bind  Rabaptin-like protein


Domain annotation for each model (and alignments):
>> Rab5-bind  Rabaptin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   6.9e-07     0.012     142     205 ..      22      85 ..      12     117 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 6.9e-07
                      Rab5-bind 142 veeLqelvlklrEeliesRtakdHlEekLkaEillLkeqiqaEkalkEnlEetlqleierlkee 205
                                    v  ++elv k+  +l++ R+  d + e  + Eil+L+ ++   k++   + e+l   +e+ k +
  gi|116753753|ref|YP_842871.1|  22 VSVIRELVEKFEVDLVKRRARVDVIGEVDEREILVLRGDLDTIKQAEKYMFEALDRKLEEWKRD 85 
                                    67899***********************************999999999999999999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       954  (0.0532099); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); 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 0.25s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 854.93
//
Query:       gi|116753754|ref|YP_842872.1|  [L=1192]
Description: cobaltochelatase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
          0 1180.4   0.0          0 1174.8   0.0    2.0  1  CobN-Mg_chel  CobN/Magnesium Chelatase


Domain annotation for each model (and alignments):
>> CobN-Mg_chel  CobN/Magnesium Chelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1174.8   0.0         0         0       2    1088 ..      99    1138 ..      98    1139 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1174.8 bits;  conditional E-value: 0
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel    2 aYlkeggveNlknllryladkllgkkeeeveppvelpeegiyhpdakelfesleeylewykkakkekaptvgilfyra 79  
                                     aY+ +gg eN+kn+l y+ +++lg  +  +++p+e+ ++giyhpd+++ f+++eeylew   +  +++ tvgilf r+
  gi|116753754|ref|YP_842872.1|   99 AYVVYGGLENIKNMLLYIGREVLG-LDLPCREPQETLWQGIYHPDSRKAFSTIEEYLEW---RPFRHEHTVGILFFRT 172 
                                     79*********************8.66689*****************************...5889999********* PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel   80 hllagntavidaliraleerglnvlpvfvssl...dseaqealeelftkegeekvdalinttsfalvkgpaeeeeeea 154 
                                     ++ +g+++++d lir+le++ +nv+++f  +    ++  ++ +++++++  + +vd++in++s+  +++ +       
  gi|116753754|ref|YP_842872.1|  173 YWANGDLEIVDRLIRSLERE-FNVIAAFGLGSvgsKQTDAKPIDQVVRDFLSGRVDLIINLQSVFHAGSVEV------ 243 
                                     *****************987.99999997776676577888889998888899********99888766642...... PP

                                     xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                   CobN-Mg_chel  155 eeealkelnvPvlqa.ilssqsreeWeessqGlspldlamsvalpEldGriepvvisfkeeee.eetevekyepiper 230 
                                     + ++l+e++vPvl++ +l+++++eeW+e+ +G++p ++ +svalpE++G ie ++i++  ++e   +eve+++pi+er
  gi|116753754|ref|YP_842872.1|  244 SLRSLEEIDVPVLHPlTLYHKTEEEWREDIKGMDPGEIGWSVALPEFEGLIENIPIGVAYRKEmWGDEVEVHHPIEER 321 
                                     23458**********99*****************************************8766679999********** PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  231 vervadlaarwarLrrkpnaekkvaiilanypp..gegrlgnavgLdvpaSlvnlLkalkeeGYdveelpesgdeLie 306 
                                     +e++++++++w+rLr+kp++e+++a+il+n+p+   e+++g+a++Ld+++S+++++++l+e GY++++ p +g+eLie
  gi|116753754|ref|YP_842872.1|  322 IEKLVRRIRAWIRLRSKPRSERRIAFILHNSPCasVEATVGAAAHLDSLESVARIMSRLAELGYTLDSFPGNGKELIE 399 
                                     *********************************8889*****************************999********* PP

                                     xxxxxxx.xxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxx RF
                   CobN-Mg_chel  307 llleggt.ndpeweelkv.....gaaallpaeeYeewfeeLpeelreeveerWgeppge........mveeeksgekk 370 
                                      +l++++ ++++w++++      ga+al+++e+Y ewf+eL+ee r+++  +Wg ppge        m       ++k
  gi|116753754|ref|YP_842872.1|  400 DILNHKAiSEFRWTTVQEivsrgGALALVDQEKYSEWFNELTEESRSKICSAWGMPPGEpregapapM-----VYQGK 472 
                                     *******99****5554456667************************************999544444.....568** PP

                                     xxxxxxxxxxxxxxxxxxxx...xxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  371 lvipglqlGnvfvgvQParg...yeedps..klyhdpdlpPthqYlAfYlWlreefgadavvHvGkHGtlEwlPGKqv 443 
                                     +v++g ++Gnv+v+vQP+rg   +++d +  +++hdp++pP+hqYlA+Y++l+++fgad+++HvG+HG+lE+lPGK+v
  gi|116753754|ref|YP_842872.1|  473 IVVTGRRYGNVVVCVQPKRGcagARCDGQacRILHDPEIPPPHQYLATYRYLQKDFGADIIIHVGTHGNLEFLPGKSV 550 
                                     ********************88877775557*********************************************** PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  444 glseecyPdillgdlPhlYpYivnnpgEGtqAKRRsyAviidHltPpmtraelygelaeLeelideYeeaesldperl 521 
                                     +ls++c Pdi++gd+PhlY+Y+ +np EGt AKRRs Avi+dH++++mt+a+lygel+eL++ i+eY++ae+  + r+
  gi|116753754|ref|YP_842872.1|  551 ALSQNCLPDIAIGDTPHLYIYNSDNPPEGTVAKRRSCAVIVDHMQTVMTTAGLYGELKELDDRIAEYRKAED--HGRK 626 
                                     *********************************************************************965..589* PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  522 kalreqilelveelnldkdlgleeakeeeeeefeellekldgyleelkeaqirdglhilGeapegeqlvdlvvailrl 599 
                                     +al++ ilel+e+ nl  +lg+     +++++fee+le+ ++ l+e+ ++ i+dg+hi+Ge+pege++v+++ ai+  
  gi|116753754|ref|YP_842872.1|  627 HALKHIILELLERSNLAGELGAG----HDHDNFEEILERAHAKLSEIYSSYIPDGMHIFGEVPEGEKRVEMISAIA-- 698 
                                     ********************777....5789*********************************************.. PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  600 eneegesltealaealgldldeleeksekelrtagdalealeeeaeelveelleeeaeeeeaeaeeleeeeeeeeeet 677 
                                          ++l ++ a+                               +++v+++l+ + ++ e+ + +l  +++    + 
  gi|116753754|ref|YP_842872.1|  699 -----KPLVNSSADL------------------------------KDAVRAVLSGGDADPEIGELVLDISRRM---DE 738 
                                     .....5666666555..............................6899999998776666655444444433...44 PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  678 eeEitallraLdGeyippgpsGdptrgraevLPTGrNfysvDpraiPteaAwevGkklaeellerylqehgeyPekvg 755 
                                     ++E+ +l++a+dG++++pgpsG +trg++evLPTGrN+ys+Dp ++Pt+aA  +Gk+lae+llery++eh+++Pe+v+
  gi|116753754|ref|YP_842872.1|  739 SDEMGSLMHAIDGGFVRPGPSGLITRGKPEVLPTGRNMYSLDPGNVPTQAAALIGKQLAEKLLERYRSEHKRWPENVA 816 
                                     58**************************************************************************** PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  756 lslwgtetmrteGediAqiLallGvrPvwdaagrvvdlelipleeLgRPRiDVtvriSGffRDafpnlielldkavel 833 
                                     +++++++ m+++Ge++Aq+++llGv+Pvw + grv++++++ple L+RPRiD tvr+SG+ RD f+ +ielld+a++ 
  gi|116753754|ref|YP_842872.1|  817 MYWMASDIMWSDGEQLAQMFYLLGVEPVWRG-GRVSGYRIMPLEDLKRPRIDLTVRVSGITRDCFMGCIELLDSAIQD 893 
                                     *****************************77.********************************************** PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  834 vaeldEpeedNfvrkhvleeeaeleekeeaeeratyRvFgskpGaYgagvqeliessnWedeedLaeaYlnwssyaYg 911 
                                     va+ldEp+e+N+vrkh+ e  +            ++R+F s+pG+Yg+gv+ ++ +s+W+de+dL +++++w+syaYg
  gi|116753754|ref|YP_842872.1|  894 VASLDEPPEMNYVRKHMIESGDG----------RALRIFASPPGTYGSGVNLAVYASAWKDEKDLTDVFMQWNSYAYG 961 
                                     *****************998644..........479****************************************** PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  912 kgaegeeaeeafearLkrvdvvvqnqdsrehdlldsddyyqflGGltaavrslsgkkpeayfgdssnpenpkvrtlke 989 
                                     k+  g +a+ a+++ L++vdv+++++ ++e+dll +++y+ + GGlt+a++slsg+k ++y+gd++++e++++rtl++
  gi|116753754|ref|YP_842872.1|  962 KDIFGDPAPGALKKMLSSVDVAFNKTVTDEYDLLGCCCYFGTYGGLTNAAESLSGHKISTYYGDTRDSERIEIRTLAD 1039
                                     ****************************************************************************** PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  990 eiarelrsrvlNPkWiegmmrhGykGafelaatvdnlfgwdatadvvddwvyeevaetYvlDeevrefleekNpwAlr 1067
                                     ei+r++r+++lNPkWieg++rhGykGa +++++v  ++gw+at++ vddw+++++a+t+vlDe++r+f+e++NpwAl+
  gi|116753754|ref|YP_842872.1| 1040 EIRRVVRTKLLNPKWIEGIKRHGYKGAGDISKRVGRVYGWEATTREVDDWIFDDIARTFVLDEDMRRFFEDSNPWALE 1117
                                     ****************************************************************************** PP

                                     xxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel 1068 eiaerLlEaarrglWeaseet 1088
                                     ei +rLlEa++rglW+a+ e 
  gi|116753754|ref|YP_842872.1| 1118 EIGRRLLEAHQRGLWDADPEV 1138
                                     *****************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); 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: 0.86u 0.32s 00:00:01.18 Elapsed: 00:00:00.49
# Mc/sec: 7350.89
//
Query:       gi|116753755|ref|YP_842873.1|  [L=261]
Description: ABC transporter related [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-31  109.5   0.0    2.5e-31  109.0   0.0    1.3  1  ABC_tran      ABC transporter
    1.4e-12   48.1   1.4      9e-06   25.7   0.1    2.3  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    4.9e-07   29.4   0.6    2.5e-05   23.8   0.6    2.1  1  SMC_N         RecF/RecN/SMC N terminal domain
    5.5e-05   23.6   0.1    0.00011   22.6   0.1    1.7  1  AAA_16        AAA ATPase domain
    5.9e-05   23.7   0.1    8.8e-05   23.1   0.1    1.3  1  AAA_23        AAA domain
      0.001   19.5   0.0     0.0068   16.8   0.0    2.0  1  AAA           ATPase family associated with various cellular 
     0.0012   18.5   0.1     0.0026   17.5   0.1    1.5  1  AAA_29        P-loop containing region of AAA domain
     0.0014   18.4   1.0     0.0033   17.2   0.1    1.8  2  AAA_15        AAA ATPase domain
      0.002   17.5   0.1      0.044   13.2   0.0    2.1  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
     0.0026   18.0   2.3      0.049   13.9   2.3    2.1  1  AAA_22        AAA domain
     0.0037   17.5   0.1      0.072   13.3   0.1    2.2  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
     0.0098   15.1   0.4      0.048   12.8   0.0    1.9  2  NB-ARC        NB-ARC domain
  ------ inclusion threshold ------
      0.015   15.0   0.1      0.034   13.9   0.0    1.8  1  AAA_30        AAA domain
      0.024   13.6   0.0       0.04   12.9   0.0    1.3  1  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
      0.037   14.2   0.0       0.12   12.5   0.0    1.8  2  AAA_33        AAA domain
      0.049   13.5   0.3       0.37   10.7   0.0    2.1  2  NTPase_1      NTPase
      0.057   12.1   0.1        2.7    6.5   0.0    2.0  2  AAA_13        AAA domain
      0.076   12.9   0.1       0.27   11.1   0.0    1.8  2  Rad17         Rad17 P-loop domain
      0.078   12.9   0.1       0.17   11.8   0.1    1.6  1  MobB          Molybdopterin guanine dinucleotide synthesis pr
      0.084   12.8   0.7       0.68    9.8   0.0    2.1  2  NACHT         NACHT domain
       0.11   12.5   0.0        1.4    9.0   0.0    2.3  2  AAA_14        AAA domain
       0.11   12.5   0.1       0.88    9.6   0.0    2.1  2  AAA_5         AAA domain (dynein-related subfamily)
       0.13   11.8   0.1       0.26   10.9   0.1    1.5  1  cobW          CobW/HypB/UreG, nucleotide-binding domain
       0.14   10.9   0.3        7.3    5.3   0.0    2.3  2  ABC_ATPase    Predicted ATPase of the ABC class
       0.26   11.6   1.4       0.81   10.0   1.4    2.0  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 !  109.0   0.0   3.6e-34   2.5e-31       1     137 []      19     165 ..      19     165 .. 0.91

  Alignments for each domain:
  == domain 1  score: 109.0 bits;  conditional E-value: 3.6e-34
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                    l++++l +  +e++++vG+nG+GK+tL+k++ + lkp  G+illdg+dl++ e ++  +eig++pq  +   ++tv e+ 
  gi|116753755|ref|YP_842873.1|  19 LNDLNLVVGDSEILGLVGPNGSGKTTLIKCIDRILKP-RGSILLDGRDLSSMEGSEIAREIGYVPQSGSSAMGTTVFETi 97 
                                    7899********************************8.9****************************99999999***** PP

                                    ...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                                sd+++e + + ++l +l+d  + ++  +LSgGqkq+v +aral+++p++lllDEpt+
  gi|116753755|ref|YP_842873.1|  98 lmgrrphiswrVSDRDLEIVTEVIELLHLEDLAM-RDFGQLSGGQKQKVLIARALAQEPSVLLLDEPTS 165
                                    ******9999877777777766677766544444.666*****************************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 !   25.7   0.1   1.3e-08     9e-06       2      24 ..      32      54 ..      31      86 .. 0.76
   2 !   21.8   0.2   1.9e-07   0.00014     217     285 ..     114     182 ..      54     201 .. 0.71

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.3e-08
                         AAA_21  2 nvliGpNgsGKSnLLdaldllar 24
                                    +l+GpNgsGK++L++++d +  
  gi|116753755|ref|YP_842873.1| 32 LGLVGPNGSGKTTLIKCIDRILK 54
                                   579***************98853 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 1.9e-07
                         AAA_21 217 rer...gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkel 285
                                    +e     + +l+ +d   +++ +lS G+k+   ++ al++ +   s+ll+DEp ++L+ k + +++e+++e 
  gi|116753755|ref|YP_842873.1| 114 LEIvteVIELLHLEDLAMRDFGQLSGGQKQKVLIARALAQEP---SVLLLDEPTSNLDMKHQLEVMEIIREM 182
                                    3335556777888888889999*********55555555555...**************7776666666443 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 !   23.8   0.6   3.4e-08   2.5e-05      25     188 ..      30     184 ..      21     200 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 3.4e-08
                                    SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrvk 104
                                    ++  +vGpNGSGK+ l+  i  +L  r +  l  ++ls++     ++ + + ++v      ++++     + v  +  + 
  gi|116753755|ref|YP_842873.1|  30 EILGLVGPNGSGKTTLIKCIDRILKPRGSILLDGRDLSSME---GSEIAREIGYVPQ----SGSS--AMGTTVFETILMG 100
                                    56679***************999998877666666666652...3455555566655....3333..2334445555566 PP

                                    TTSEEEEEETTEEE-H.HHHHHHHHCTT-STT...CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHH CS
                                    xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 105 rkgeseykingkevtk.kevsellesagiske...lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkva 180
                                    r  + ++++ +++ +  +ev ell+ +++ +    +LSgG+k+ v +a  +A    +  ++ llDe  ++LD k+  +v 
  gi|116753755|ref|YP_842873.1| 101 RRPHISWRVSDRDLEIvTEVIELLHLEDLAMRdfgQLSGGQKQKVLIARALA----QEPSVLLLDEPTSNLDMKHQLEVM 176
                                    66678899999999988********99998865669*****99766655544....5667889***************** PP

                                    HHHHHHCT CS
                                    xxxxxxxx RF
                          SMC_N 181 ellkeksk 188
                                    e+++e  +
  gi|116753755|ref|YP_842873.1| 177 EIIREMVQ 184
                                    ***98654 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   0.1   1.5e-07   0.00011      22      63 ..      27      68 ..      16     189 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.5e-07
                         AAA_16 22 grpelvllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                   g++e++ l+G+ G+GK++l++++ r l+ +g i+l g+  ++
  gi|116753755|ref|YP_842873.1| 27 GDSEILGLVGPNGSGKTTLIKCIDRILKPRGSILLDGRDLSS 68
                                   6679999******************99999999998887777 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.1   1.2e-07   8.8e-05      15      43 ..      22      53 ..       3      81 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.2e-07
                         AAA_23 15 idF...skgltlItGpNGaGKTTildAiklaL 43
                                   +++   ++ +  ++GpNG+GKTT++ +i  +L
  gi|116753755|ref|YP_842873.1| 22 LNLvvgDSEILGLVGPNGSGKTTLIKCIDRIL 53
                                   3336677788999***************7665 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 !   16.8   0.0   9.4e-06    0.0068       3      66 ..      34     162 ..      32     192 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 9.4e-06
                                    EESSTTSSHHHHHHHHHHHH.........THEEEEEETTTCSSS.................................... CS
                            AAA   3 lyGppGtGKTllakavakel.........gvefleisgsellsk.................................... 37 
                                    l+Gp G GKT+l+k + + l         g+++ +++gse+  +                                    
  gi|116753755|ref|YP_842873.1|  34 LVGPNGSGKTTLIKCIDRILkprgsilldGRDLSSMEGSEIAREigyvpqsgssamgttvfetilmgrrphiswrvsdrd 113
                                    89*****************9444433444466888888888866888888888888888888888888888888888888 PP

                                    .....................STTHHHHHHHHHHHHHHHTSTSEEEEEET CS
                            AAA  38 .....................yvgesekkirelfkeakekakpsilfiDE 66 
                                                          +  + +k + l+++a ++ +ps+l++DE
  gi|116753755|ref|YP_842873.1| 114 leivteviellhledlamrdfGQLSGGQKQKVLIARALAQ-EPSVLLLDE 162
                                    8888888888888888888654444444444445444444.488888888 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   3.6e-06    0.0026      25      50 ..      32      57 ..      20      60 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.6e-06
                         AAA_29 25 tlltGpsGsGKSTllDAiqalLvpak 50
                                     l+Gp+GsGK+Tl+  i  +L p+ 
  gi|116753755|ref|YP_842873.1| 32 LGLVGPNGSGKTTLIKCIDRILKPRG 57
                                   5599************9999999875 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   0.1   4.6e-06    0.0033      25      50 ..      31      56 ..      17      79 .. 0.80
   2 ?   -0.7   0.1       1.2   8.8e+02     322     355 ..     153     186 ..     142     188 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.6e-06
                         AAA_15 25 ltvliGkNnsGKSsilealdlFlnnk 50
                                   +  l+G+N+sGK+++++ +d +l+  
  gi|116753755|ref|YP_842873.1| 31 ILGLVGPNGSGKTTLIKCIDRILKPR 56
                                   6679****************999865 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.2
                         AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandn 355
                                    +++ +ll++EP  +L  ++q ++++ ++e+++ +
  gi|116753755|ref|YP_842873.1| 153 QEPSVLLLDEPTSNLDMKHQLEVMEIIREMVQRK 186
                                    577899**********************999875 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   6.1e-05     0.044      25      48 ..      31      55 ..      20      81 .. 0.80
   2 ?    2.2   0.0      0.14     1e+02     107     150 ..     155     203 ..     134     212 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.1e-05
                   Mg_chelatase 25 ll.lvGppGsGKtmlakrlpsllpp 48
                                   +l lvGp GsGKt l+k++  +l p
  gi|116753755|ref|YP_842873.1| 31 ILgLVGPNGSGKTTLIKCIDRILKP 55
                                   4449******************977 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.14
                   Mg_chelatase 107 nGvLfLDElp.....efkrkvlevLRePledgevtisrakakvefparf 150
                                      vL+LDE +     + + +v+e++Re +++++++   a ++++  arf
  gi|116753755|ref|YP_842873.1| 155 PSVLLLDEPTsnldmKHQLEVMEIIREMVQRKSISAVMAVHDLNLAARF 203
                                    3689999964222114566799999**9999999999999988888887 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   2.3   6.8e-05     0.049       7     132 ..      31     198 ..      27     203 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.8e-05
                         AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaee..............................erpevv......fvtlpss 50 
                                    il ++G+ G+GKTtl++ + + l+ + ++                                   e++      ++   +s
  gi|116753755|ref|YP_842873.1|  31 ILGLVGPNGSGKTTLIKCIDRILKPRGSILLdgrdlssmegseiareigyvpqsgssamgtTVFETIlmgrrpHISWRVS 110
                                    6679******************9755444447777777755555555555555555543332222223333333444444 PP

                         AAA_22  51 tsskdllrellralglelkaerlsseell.ealeqalrarav...ielliiDEaqh.lr...seealeeLrsllnlsrkg 122
                                        ++ +e+ + l+le  a   +  +l   + ++ l ara    +++l++DE    l+   + e++e +r+++   rk+
  gi|116753755|ref|YP_842873.1| 111 DRDLEIVTEVIELLHLEDLA-MRDFGQLSgGQKQKVLIARALaqePSVLLLDEPTSnLDmkhQLEVMEIIREMVQ--RKS 187
                                    44444455555555555555.555555555555555555555888899999999888988755999999999999..999 PP

                         AAA_22 123 vqliLvGtp.e 132
                                    ++ +++ +  +
  gi|116753755|ref|YP_842873.1| 188 ISAVMAVHDlN 198
                                    99988766555 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 !   13.3   0.1    0.0001     0.072      27      89 ..     131     180 ..     125     181 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.0001
                        SbcCD_C  27 srssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                     r++g+lSGG+kq++    +a ala    +       +++++LDE  s+lD + + +++e+++
  gi|116753755|ref|YP_842873.1| 131 MRDFGQLSGGQKQKV---LIARALA----Q------EPSVLLLDEPTSNLDMKHQLEVMEIIR 180
                                    589999******654...4443333....3......3788***************99999987 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   6.7e-05     0.048      16      40 ..      27      49 ..      16      55 .. 0.84
   2 ?    0.1   0.1      0.51   3.7e+02      67     111 ..     115     162 ..      92     192 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.7e-05
                                   TTSCSEEEEEEESTTSSHHHHHHHH CS
                         NB-ARC 16 delqslvvalvGmgGvGKttlakqi 40
                                   ++++  +++lvG  G+GKttl+k i
  gi|116753755|ref|YP_842873.1| 27 GDSE--ILGLVGPNGSGKTTLIKCI 49
                                   5666..***************9876 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.51
                                    HHHHXXHHHHHCCCTTSSSS-STTS...HHHHHHHHCCCTTEEEEEEE CS
                         NB-ARC  67 eiletilkeLslseddleekeeves...lkrklvrlLltkrfllvlDD 111
                                    ei+ ++++ L+l++  +  + +       k  + r+L +  ++l+lD 
  gi|116753755|ref|YP_842873.1| 115 EIVTEVIELLHLEDLAMRDFGQLSGgqkQKVLIARALAQEPSVLLLDE 162
                                    566666677766665555555544454467778899999999999985 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.7e-05     0.034      19      46 ..      30      57 ..      22     188 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.7e-05
                         AAA_30 19 rvavltGpAGtGKttalkalreaweaag 46
                                    +  l+Gp G+GKtt++k + ++++ +g
  gi|116753755|ref|YP_842873.1| 30 EILGLVGPNGSGKTTLIKCIDRILKPRG 57
                                   47889***************99998776 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 ?   12.9   0.0   5.5e-05      0.04      15      57 ..      15      57 ..       3      60 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.5e-05
                                   HHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT CS
                           MeaB 15 akellerllakaGraqvvGltGvPGaGkstlvealglelrrrG 57
                                   ++ +l+ l    G ++ +Gl G  G+Gk tl++ +   l+ rG
  gi|116753755|ref|YP_842873.1| 15 SNLILNDLNLVVGDSEILGLVGPNGSGKTTLIKCIDRILKPRG 57
                                   66789999999**********************9999998888 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       4      30 ..      34      63 ..      31     122 .. 0.83
   2 ?   -0.8   0.0       2.2   1.6e+03      16      38 ..     148     183 ..     144     219 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00017
                         AAA_33  4 lvGlpGsGKstlaerl...lkklgavllss 30
                                   lvG++GsGK+tl++ +   lk++g +ll+ 
  gi|116753755|ref|YP_842873.1| 34 LVGPNGSGKTTLIKCIdriLKPRGSILLDG 63
                                   79**********874333377777777765 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.2
                         AAA_33  16 aerllkklgavllssdt.............lrrrlf 38 
                                    a+ l+++  + ll+++t             ++r ++
  gi|116753755|ref|YP_842873.1| 148 ARALAQEPSVLLLDEPTsnldmkhqlevmeIIREMV 183
                                    666777777888888886666555555555444444 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00052      0.37       4      27 ..      34      57 ..      31      71 .. 0.89
   2 ?    0.6   0.1      0.63   4.5e+02      94     152 ..     153     215 ..     141     223 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00052
                                   EE--TTSSHHHHHHHHHHHH...G CS
                       NTPase_1  4 iTGppGvGKtTlvkkvlellkssg 27
                                   + Gp G+GKtTl+k + + lk +g
  gi|116753755|ref|YP_842873.1| 34 LVGPNGSGKTTLIKCIDRILKPRG 57
                                   78**************99999877 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.63
                                    HHH-EEEE--.-STTGGG-H.HHHHHHHHHHT.TTSEEEEE--SS-.-SHHHHHHHT-TT-EE CS
                       NTPase_1  94 seadviviDE.iGkmElksk.kfkeaveevLk.sekpvlavihrrk.dlalveeirerkdvkv 152
                                    +e+ v+++DE   ++ +k + ++ e ++e+++ ++   ++ +h  +   ++v+++   k++++
  gi|116753755|ref|YP_842873.1| 153 QEPSVLLLDEpTSNLDMKHQlEVMEIIREMVQrKSISAVMAVHDLNlAARFVDKLAVLKNGRI 215
                                    555666666633456665553578889999997778888899988778889998887777665 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0038       2.7      23      38 ..      36      51 ..      34      59 .. 0.86
   2 ?    3.5   0.0     0.032        23     526     561 ..     154     188 ..     146     199 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0038
                         AAA_13 23 GwNGaGKTtLSrllrs 38
                                   G NG+GKTtL + ++ 
  gi|116753755|ref|YP_842873.1| 36 GPNGSGKTTLIKCIDR 51
                                   99********999876 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.032
                         AAA_13 526 kdkivviDDPvSSLDsnslfivfsliksrllkkkka 561
                                    +  +  +D P S LD +++  v+  i++ + ++k++
  gi|116753755|ref|YP_842873.1| 154 EPSVLLLDEPTSNLDMKHQLEVMEIIREMV-QRKSI 188
                                    678999*********************998.56655 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00037      0.27      45      72 ..      29      56 ..      18      97 .. 0.88
   2 ?   -0.8   0.0       1.7   1.2e+03     131     174 ..     153     196 ..     127     201 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00037
                          Rad17 45 kriLLisGPsGCgkstvvkvLskelgik 72
                                    +iL + GP G gk+t +k + ++l ++
  gi|116753755|ref|YP_842873.1| 29 SEILGLVGPNGSGKTTLIKCIDRILKPR 56
                                   46999***************99998765 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.7
                          Rad17 131 tdkklilvedlPnkfyrds.dalrevirkylrssealplilvite 174
                                     + +++l+++  ++  +     + e+ir++++ +  ++ ++ + +
  gi|116753755|ref|YP_842873.1| 153 QEPSVLLLDEPTSNLDMKHqLEVMEIIREMVQRKS-ISAVMAVHD 196
                                    45566777775566655543567788888887554.477777665 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00024      0.17       1      27 [.      31      57 ..      31      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00024
                           MobB  1 vlgivgksgsGKTtLleklipelkarg 27
                                   +lg+vg +gsGKTtL++ + ++lk rg
  gi|116753755|ref|YP_842873.1| 31 ILGLVGPNGSGKTTLIKCIDRILKPRG 57
                                   799*************99888888877 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00094      0.68       5      22 ..      34      51 ..      30      61 .. 0.82
   2 ?    1.2   0.1      0.42     3e+02      72     121 ..     145     191 ..     109     198 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00094
                                   EEC-TTTCHHHHHHHHHH CS
                          NACHT  5 lqGeaGsGKTtLlqklal 22
                                   l G++GsGKTtL++ + +
  gi|116753755|ref|YP_842873.1| 34 LVGPNGSGKTTLIKCIDR 51
                                   89**********997755 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.42
                                    CHHHHCCSCCCEEEEEE-STT-SS-TCH.........HHHHHCTTTTT-- CS
                          NACHT  72 vwavllelperlLlilDglDelvtdlgqkekqpvrtlLselirkkllpea 121
                                    v + ++  +e  +l+l   De  + l+ k++ +v + ++e++++k+++ +
  gi|116753755|ref|YP_842873.1| 145 VLIARALAQEPSVLLL---DEPTSNLDMKHQLEVMEIIREMVQRKSISAV 191
                                    4444444444444554...4555555555667777778887777776655 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0    0.0019       1.4       3      22 ..      30      49 ..      28      80 .. 0.77
   2 ?    1.1   0.0      0.54   3.9e+02      51     107 ..     174     227 ..     119     235 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0019
                         AAA_14  3 kilvitGaRrvGKTtllkql 22
                                   +il ++G+  +GKTtl+k +
  gi|116753755|ref|YP_842873.1| 30 EILGLVGPNGSGKTTLIKCI 49
                                   7999************9644 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.54
                         AAA_14  51 kllelileklkeekktylflDEiqevpewekalkslvdegknldvivtGSnskllsk 107
                                    +++e+i+e+++  +k++     ++ ++ + +++ +l   + n++++++G +s+ll  
  gi|116753755|ref|YP_842873.1| 174 EVMEIIREMVQ--RKSISAVMAVHDLNLAARFVDKLAVLK-NGRIWAAGDASSLLTP 227
                                    34444444432..333333334445555555666665555.6667766666666655 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0    0.0012      0.88       4      24 ..      34      54 ..      31      74 .. 0.84
   2 ?    0.5   0.0      0.76   5.5e+02      19      56 ..     147     184 ..     137     229 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0012
                                   EE--SSSSHHHHHHHGGGGBS CS
                          AAA_5  4 LvGppGtgKselaerlaaaln 24
                                   LvGp G+gK++l++ + + l+
  gi|116753755|ref|YP_842873.1| 34 LVGPNGSGKTTLIKCIDRILK 54
                                   9************99988883 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.76
                                    GGGGBS--EEEEE--TT--HHHHH--B--......... CS
                          AAA_5  19 laaalnreveyvqltrdtteedlkgrreikngttslvd 56 
                                    +a+al +e  + +l + t+  d+k ++e+++  +++v+
  gi|116753755|ref|YP_842873.1| 147 IARALAQEPSVLLLDEPTSNLDMKHQLEVMEIIREMVQ 184
                                    67778888888888888888888888888755555554 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00036      0.26       3      19 ..      32      48 ..      30      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00036
                                   EEEEESTTCCHHHHHHH CS
                           cobW  3 tvltGflGsGKTtLlnh 19
                                   ++l+G+ GsGKTtL++ 
  gi|116753755|ref|YP_842873.1| 32 LGLVGPNGSGKTTLIKC 48
                                   789***********975 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.03        21     247     266 ..      32      51 ..      27      67 .. 0.79
   2 ?    5.3   0.0      0.01       7.3     323     362 ..     137     176 ..     129     222 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.03
                                    EEEEE-TTSSHHHHHHHHHH CS
                     ABC_ATPase 247 tlIvGggfhGKsTLLeAlek 266
                                      +vG++  GK+TL++ +++
  gi|116753755|ref|YP_842873.1|  32 LGLVGPNGSGKTTLIKCIDR 51 
                                    5579*************987 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.01
                                    --HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHH CS
                     ABC_ATPase 323 ASGStsqAanimealeagakllLiDEDtsAtNlmirDerm 362
                                     SG   q + i++al  + ++lL+DE ts   + ++ e m
  gi|116753755|ref|YP_842873.1| 137 LSGGQKQKVLIARALAQEPSVLLLDEPTSNLDMKHQLEVM 176
                                    599999*********************9976665555555 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.4    0.0011      0.81      10      38 ..      29      57 ..      24     202 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0011
                         AAA_19 10 ekvllvtaGpGtGKTrvlkhivallvelg 38
                                   +++l ++++ G+GKT+++k+i ++l+ +g
  gi|116753755|ref|YP_842873.1| 29 SEILGLVGPNGSGKTTLIKCIDRILKPRG 57
                                   5678899*************998887666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); 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: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 1766.91
//
Query:       gi|116753756|ref|YP_842874.1|  [L=355]
Description: transport system permease protein [Methanosaeta thermophila PT]
Scores for complete 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-94  316.0  35.5    2.6e-94  315.7  35.5    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 !  315.7  35.5   1.5e-98   2.6e-94       3     312 .]      33     349 ..      29     349 .. 0.98

  Alignments for each domain:
  == domain 1  score: 315.7 bits;  conditional E-value: 1.5e-98
                          FecCD   3 llllllslllgavkispsevfeallgka.......dsleaeivlelrlprvlaallvGaaLavaGallQtvtrNpLadPs 75 
                                    +++  +s +lg++++s+ ev++a+l++a       + ++++iv+ lrl r+l+++++Ga+L+vaGa +Q++++NpLa+P 
  gi|116753756|ref|YP_842874.1|  33 VIIAGISATLGSANLSVFEVYSAILARAfpgyfetTWFADTIVWGLRLHRILMGVVAGAGLGVAGAAMQGILKNPLASPF 112
                                    566778899****************9999*99998889999*************************************** PP

                          FecCD  76 ilGissgaalgavlallll.lgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsallsaltslllll 154
                                    +lGiss+a++ga+la++l+  ++ +++ ++  af++ lla++ v+ la k kg++p+++iLaGia+ +++sa+ts+l+++
  gi|116753756|ref|YP_842874.1| 113 TLGISSAASFGAALAIILGaGFAGGEYLIIGNAFVFTLLATFAVYGLA-KYKGITPETMILAGIAIMYFFSAMTSFLQYV 191
                                    *******************989999***********************.******************************* PP

                          FecCD 155 lneealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrllllllvalltav 234
                                      +e++++++fw++Gsl++ sw+kv+ ++++++++l++l+l + +++++  gdetAkslGvnver+r+l +++++l+ta+
  gi|116753756|ref|YP_842874.1| 192 GRAEQVQEVVFWMMGSLGRSSWDKVYASALMIIICLPYLILKSWDINAIGAGDETAKSLGVNVERIRVLSMIFASLITAS 271
                                    ******************************************************************************** PP

                          FecCD 235 avalvGpigFvGLivPhiarllvgadhrkllplsallGallllladllarlllsptelpvgivtaliGapffiylllr 312
                                    +++++G+igF+GL++Ph+ r+++g dhr l+p sal+G+++ll+ad+lar++l+p+ lpvgi+t+++G+pff+yl+++
  gi|116753756|ref|YP_842874.1| 272 VICFTGTIGFIGLVAPHMTRMVIGGDHRFLIPGSALMGSVILLAADTLARTVLAPVILPVGIMTSFLGVPFFVYLFMK 349
                                    ***************************************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2416.83
//
Query:       gi|116753757|ref|YP_842875.1|  [L=356]
Description: periplasmic binding protein [Methanosaeta thermophila PT]
Scores for 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-25   87.7   0.5    4.3e-24   85.4   0.5    1.8  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 !   85.4   0.5   2.4e-28   4.3e-24       1     234 [.      45     301 ..      45     303 .. 0.85

  Alignments for each domain:
  == domain 1  score: 85.4 bits;  conditional E-value: 2.4e-28
                                    EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT..TS-BSBESSSB-HHHHHHH-.......-SEEEE-GGG.... CS
                   Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadkleeaivevgadgeidvEklaalk.......PDlvilskgl.... 69 
                                    i++l+++ +e +  lGa+dk+vg++ ++++ + +  ++++  +vg+ +e+d+E++ +         P +++ s+++    
  gi|116753757|ref|YP_842875.1|  45 IIVLNSDAAEAVTILGAADKIVGISDSVKNKAYYFPALKNRQSVGKWNEPDYEMIGEIArsgdeivPNIIVISYTYpdkp 124
                                    89*************************999999954444*************99987544444444**********6555 PP

                                    ......GGGHHHHHHHS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT.-EEEEEEEET CS
                   Peripla_BP_2  70 ...gltdedeellksgiptvivessntgeslkeqiralgellgledeaeklvaeidsklaaaksaidsekpkpvlvfgga 146
                                         +++  e    +     + +++  e+ +++i+ lg +lg+e+ea+ +++++++k a++++a+++ + ++v v  ++
  gi|116753757|ref|YP_842875.1| 125 ygiVEVAKRLEPFTGITAIGLDFYKP--ENMTREIELLGRILGKEAEAQRFIEWYEEKQADVENAVANRNVPKVYVEWTS 202
                                    53333333333333333333344444..*****************************************44444444446 PP

                                    TE..EEEE-TTSTTTHHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEH............HHHT-S--HHHH CS
                   Peripla_BP_2 147 deggyvvagsnsyigdlldalgieniaaeskkseyeeisaEqilasdpdvifvsgr............aeadnktglefl 214
                                     +g+ + +g++s+  +l++ +++ ++a +  k++y +i++E++ + +pdvi+ +++            ++ +    l ++
  gi|116753757|ref|YP_842875.1| 203 KGGELTTMGTGSGAAQLVSMARGYSVANDL-KDAYPKIGWEWVISKNPDVIIKRSTstqlgwekppslDSTNLENTLNEV 281
                                    668***************************.************************************9999999999*** PP

                                    T-SHHHHTSHHHHTT-EEEE CS
                   Peripla_BP_2 215 kenpllaelpAvkngrVyal 234
                                    +++ ++a+++Avkn rVy +
  gi|116753757|ref|YP_842875.1| 282 LSRSGAAAVNAVKNDRVYIV 301
                                    ******************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2638.16
//
Query:       gi|116753758|ref|YP_842876.1|  [L=328]
Description: hypothetical protein Mthe_0445 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2340.67
//
Query:       gi|116753759|ref|YP_842877.1|  [L=266]
Description: ABC transporter related [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-29  103.1   0.0    2.2e-29  102.7   0.0    1.2  1  ABC_tran      ABC transporter
    1.3e-13   51.5   0.0    1.9e-06   28.0   0.0    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    1.6e-06   27.8   0.1     0.0046   16.4   0.0    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
     0.0002   21.8   0.0     0.0036   17.7   0.0    2.3  2  AAA           ATPase family associated with various cellular 
    0.00022   21.2   0.0     0.0071   16.4   0.0    2.3  2  AAA_14        AAA domain
    0.00034   20.1   0.0     0.0006   19.3   0.0    1.4  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
     0.0013   18.5   0.0     0.0067   16.2   0.0    1.8  2  AAA_15        AAA ATPase domain
     0.0017   18.0   0.1     0.0081   15.9   0.0    2.1  2  AAA_29        P-loop containing region of AAA domain
      0.005   16.8   0.0     0.0076   16.2   0.0    1.2  1  ATPase_2      ATPase domain predominantly from Archaea
     0.0062   16.8   0.0      0.027   14.8   0.0    1.9  2  AAA_22        AAA domain
      0.007   16.3   0.1      0.013   15.4   0.1    1.3  1  Rad17         Rad17 P-loop domain
     0.0079   16.2   0.0        0.1   12.6   0.0    2.2  2  AAA_5         AAA domain (dynein-related subfamily)
     0.0086   16.6   0.1      0.014   15.9   0.1    1.2  1  AAA_23        AAA domain
  ------ inclusion threshold ------
      0.012   15.5   0.1      0.097   12.6   0.0    2.0  2  RsgA_GTPase   RsgA GTPase
      0.014   14.6   0.0      0.054   12.7   0.0    1.8  2  NB-ARC        NB-ARC domain
      0.015   15.1   0.0       0.17   11.6   0.0    2.5  3  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
      0.016   14.4   0.0       0.56    9.3   0.0    2.1  2  PIF1          PIF1-like helicase
      0.019   15.4   0.1      0.034   14.5   0.1    1.6  1  AAA_16        AAA ATPase domain
      0.023   14.6   0.1      0.046   13.6   0.1    1.5  1  NACHT         NACHT domain
      0.033   13.5   0.0      0.048   12.9   0.0    1.2  1  Zeta_toxin    Zeta toxin
      0.051   12.4   0.0        3.9    6.2   0.0    2.2  2  ABC_ATPase    Predicted ATPase of the ABC class
      0.095   12.9   0.0       0.18   12.0   0.0    1.5  1  AAA_28        AAA domain
       0.12   11.9   0.0       0.29   10.7   0.0    1.5  1  AAA_25        AAA domain
       0.13   11.9   0.0       0.29   10.8   0.0    1.5  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 !  102.7   0.0     3e-32   2.2e-29       1     137 []      22     171 ..      22     171 .. 0.92

  Alignments for each domain:
  == domain 1  score: 102.7 bits;  conditional E-value: 3e-32
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvren 79 
                                    l+n+ +++++g+++ ++G+nG+GK+tLlk++ gll pt+G++ +d +d+++ +  ++ +++g +pq   + fp + v + 
  gi|116753759|ref|YP_842877.1|  22 LNNICMEIERGRVITLLGPNGCGKTTLLKIINGLLPPTSGRVYVDCRDTRSMKPGEMARRMGHVPQAqRSTFPFT-VLDV 100
                                    799***********************************************99999999*********55556655.8888 PP

                                    .................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    .................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 .................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                                      + e++++al+ +g  +++d++     +++SgG++q  ++aral+++p++lllDEpt+
  gi|116753759|ref|YP_842877.1| 101 vltgrfsyisplskpgeRDVEKAYRALEMVGALHIADRPY----NHVSGGERQLAMIARALAQEPSFLLLDEPTS 171
                                    999**********999655666999999999999999999....*****************************96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0     2e-07   0.00015       3      23 ..      36      56 ..      34      76 .. 0.86
   2 !   28.0   0.0   2.5e-09   1.9e-06     231     283 ..     137     186 ..     112     204 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2e-07
                         AAA_21  3 vliGpNgsGKSnLLdaldlla 23
                                    l GpNg+GK++LL+++ +l 
  gi|116753759|ref|YP_842877.1| 36 TLLGPNGCGKTTLLKIINGLL 56
                                   699**************9994 PP

  == domain 2  score: 28.0 bits;  conditional E-value: 2.5e-09
                         AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellk 283
                                    ++p++++S G ++l a+++  l++ +  s+ll+DEp + L+ + + r+l+ ++
  gi|116753759|ref|YP_842877.1| 137 DRPYNHVSGGERQL-AMIARALAQEP--SFLLLDEPTSYLDFRNQIRILKTVR 186
                                    689***********.*******9998..9********************9883 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0   0.00085      0.63      25      44 ..      33      52 ..      15      62 .. 0.81
   2 !   16.4   0.0   6.1e-06    0.0046     136     199 ..     142     202 ..     108     222 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00085
                                   SEEEEEESTTSSHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 25 sftaivGpNGSGKsnlldAi 44
                                   ++  ++GpNG+GK+ ll  i
  gi|116753759|ref|YP_842877.1| 33 RVITLLGPNGCGKTTLLKII 52
                                   466799********999866 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 6.1e-06
                                    CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                          SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislre 199
                                      SgGe++L+++a  +A    +  ++ llDe  + LD++n  ++ + ++   ++    +v+sl++
  gi|116753759|ref|YP_842877.1| 142 HVSGGERQLAMIARALA----QEPSFLLLDEPTSYLDFRNQIRILKTVRGFAESgLMTVVMSLHD 202
                                    68*********998877....5678*********************9997665535566666665 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   4.8e-06    0.0036       2      54 ..      36      90 ..      35     102 .. 0.82
   2 ?    1.1   0.0      0.66   4.9e+02      41      66 ..     145     168 ..     122     184 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.8e-06
                                   EEESSTTSSHHHHHHHHHHHH..THEEEEEETTTCSSSSTTHHHHHHHHHHHHHH CS
                            AAA  2 llyGppGtGKTllakavakel..gvefleisgsellskyvgesekkirelfkeak 54
                                    l Gp G+GKT+l k +   l   +  + +++ + +s+  ge+++++ ++ ++ +
  gi|116753759|ref|YP_842877.1| 36 TLLGPNGCGKTTLLKIINGLLppTSGRVYVDCRDTRSMKPGEMARRMGHVPQAQR 90
                                   689**************99995446679999999999999999999988887654 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.66
                                    HHHHHHHHHHHHHHHTSTSEEEEEET CS
                            AAA  41 esekkirelfkeakekakpsilfiDE 66 
                                     +e++++++ +++ +  +ps l++DE
  gi|116753759|ref|YP_842877.1| 145 GGERQLAMIARALAQ--EPSFLLLDE 168
                                    556666666655433..489999999 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   9.5e-06    0.0071       2      44 ..      32      73 ..      31      94 .. 0.84
   2 ?    2.4   0.0      0.19   1.4e+02      56      87 ..     153     183 ..     132     199 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 9.5e-06
                         AAA_14  2 rkilvitGaRrvGKTtllkqlikellvkkesilyinldderdk 44
                                   ++++++ G+  +GKTtll ++i+ ll + +  +y+++ d r  
  gi|116753759|ref|YP_842877.1| 32 GRVITLLGPNGCGKTTLL-KIINGLLPPTSGRVYVDCRDTRSM 73
                                   5899*************7.777888878899999999998764 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.19
                         AAA_14  56 ileklkeekktylflDEiqevpewekalkslv 87 
                                    i + l + + ++l+lDE   + ++++ ++ l 
  gi|116753759|ref|YP_842877.1| 153 IARALAQ-EPSFLLLDEPTSYLDFRNQIRILK 183
                                    4444444.7899*********99999998765 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   8.1e-07    0.0006      25      65 ..      35      75 ..      25     104 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 8.1e-07
                   Mg_chelatase 25 lllvGppGsGKtmlakrlpsllpplseeealevakiasvag 65
                                   + l+Gp G+GKt l k +++llpp s +  ++++  +s++ 
  gi|116753759|ref|YP_842877.1| 35 ITLLGPNGCGKTTLLKIINGLLPPTSGRVYVDCRDTRSMKP 75
                                   789************************99999999999876 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0     9e-06    0.0067      20      47 ..      28      56 ..      21      76 .. 0.81
   2 ?   -0.2   0.0      0.83   6.2e+02     322     366 ..     159     203 ..     137     205 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 9e-06
                         AAA_15 20 dlsee.ltvliGkNnsGKSsilealdlFl 47
                                   +++   + +l G+N++GK+++l++++ +l
  gi|116753759|ref|YP_842877.1| 28 EIERGrVITLLGPNGCGKTTLLKIINGLL 56
                                   333334899****************8766 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.83
                         AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSp 366
                                    +++ +ll++EP  +L   +q  + k+ +  a+++ + v+++ H p
  gi|116753759|ref|YP_842877.1| 159 QEPSFLLLDEPTSYLDFRNQIRILKTVRGFAESGLMTVVMSLHDP 203
                                    56799****************999999999999877777777766 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 ?   -1.0   0.0         2   1.5e+03      33      43 ..       3      13 ..       2      24 .. 0.86
   2 !   15.9   0.0   1.1e-05    0.0081      16      50 ..      26      60 ..      15      64 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2
                         AAA_29 33 sGKSTllDAiq 43
                                   sGK  l+D ++
  gi|116753759|ref|YP_842877.1|  3 SGKGILIDGVS 13
                                   89999999876 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.1e-05
                         AAA_29 16 tieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                    +ei++  ++ l Gp+G GK+Tll  i+ lL p++
  gi|116753759|ref|YP_842877.1| 26 CMEIERGRVITLLGPNGCGKTTLLKIINGLLPPTS 60
                                   577875559999************88888887765 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 !   16.2   0.0     1e-05    0.0076      16      59 ..      28      70 ..      20      93 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1e-05
                       ATPase_2 16 erepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialre 59
                                   e e+ +++ + Gp g+GKt+Llk ii+ l+     ++y++   +
  gi|116753759|ref|YP_842877.1| 28 EIERGRVITLLGPNGCGKTTLLK-IINGLLPPTSGRVYVDCRDT 70
                                   5677899999***********97.77777777778888876555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   3.6e-05     0.027       4      51 ..      31      71 ..      27      90 .. 0.82
   2 ?   -0.6   0.0         2   1.5e+03      80     117 ..     151     190 ..     123     202 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.6e-05
                         AAA_22  4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst 51
                                   + +++++ G+ G+GKTtll+ +   l+       + ++ v+v++    
  gi|116753759|ref|YP_842877.1| 31 RGRVITLLGPNGCGKTTLLKIINGLLP-------PTSGRVYVDCRDTR 71
                                   6789****************9998887.......37777788887665 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2
                         AAA_22  80 ealeqalraravielliiDEaqh.lr...seealeeLrslln 117
                                    +++++al +    ++l++DE    l+   + ++l+++r +++
  gi|116753759|ref|YP_842877.1| 151 AMIARALAQEP--SFLLLDEPTSyLDfrnQIRILKTVRGFAE 190
                                    44444444444..58999987666655433555555555554 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   1.7e-05     0.013      38      66 ..      25      53 ..      19      63 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.7e-05
                          Rad17 38 dvLesrkkriLLisGPsGCgkstvvkvLs 66
                                     +e ++ r++ + GP GCgk+t +k++ 
  gi|116753759|ref|YP_842877.1| 25 ICMEIERGRVITLLGPNGCGKTTLLKIIN 53
                                   5567777799999*************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 !   12.6   0.0   0.00013       0.1       3      32 ..      36      67 ..      34      91 .. 0.79
   2 ?    1.2   0.0      0.46   3.4e+02      19      64 ..     153     198 ..     146     232 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00013
                                   EEE--SSSSHHHHHHHGGGGB..S--EEEEE- CS
                          AAA_5  3 lLvGppGtgKselaerlaaal..nreveyvql 32
                                    L+Gp G+gK++l + +  +l  ++  +yv +
  gi|116753759|ref|YP_842877.1| 36 TLLGPNGCGKTTLLKIINGLLppTSGRVYVDC 67
                                   59****************99997555555555 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.46
                                    GGGGBS--EEEEE--TT--HHHHH--B--.........-------- CS
                          AAA_5  19 laaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar 64 
                                    +a+al +e    +l + t++ d++ +++i +  + + +s l++ + 
  gi|116753759|ref|YP_842877.1| 153 IARALAQEPSFLLLDEPTSYLDFRNQIRILKTVRGFAESGLMTVVM 198
                                    6888888888899999999999999999999999999999987665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   1.9e-05     0.014      23      40 ..      36      53 ..      27      62 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.9e-05
                         AAA_23 23 lItGpNGaGKTTildAik 40
                                    + GpNG+GKTT+l  i 
  gi|116753759|ref|YP_842877.1| 36 TLLGPNGCGKTTLLKIIN 53
                                   578***********9886 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00013     0.097      87     121 ..      19      54 ..       6      71 .. 0.79
   2 ?    0.5   0.0      0.67     5e+02      19      41 ..     194     216 ..     176     248 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00013
                                    HTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase  87 kegleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                    ++ l+++  +++  ++++l+G+ G GK+tL++ +++
  gi|116753759|ref|YP_842877.1|  19 RAVLNNICMEIERgRVITLLGPNGCGKTTLLKIING 54 
                                    556667777777669***************987765 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.67
                                    EEEEEESTTTT--HHHHHHHHHH CS
                    RsgA_GTPase  19 llivvslkepelslnlldrfLvl 41 
                                    + +v+sl++p+  l + dr+++l
  gi|116753759|ref|YP_842877.1| 194 MTVVMSLHDPNHALMFSDRVVLL 216
                                    67899999999888888887654 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   7.3e-05     0.054       8      41 ..      21      53 ..      15      62 .. 0.80
   2 ?   -0.7   0.0      0.86   6.4e+02      85     111 ..     142     168 ..     126     234 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.3e-05
                                   HHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHC CS
                         NB-ARC  8 viekLlekdelqslvvalvGmgGvGKttlakqil 41
                                   v ++   + e +  v++l G  G+GKttl+k i+
  gi|116753759|ref|YP_842877.1| 21 VLNNICMEIERG-RVITLLGPNGCGKTTLLKIIN 53
                                   556666566666.79**************99776 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.86
                                    SS-STTSHHHHHHHHCCCTTEEEEEEE CS
                         NB-ARC  85 ekeeveslkrklvrlLltkrfllvlDD 111
                                    + + +e    ++ r+L +  + l+lD 
  gi|116753759|ref|YP_842877.1| 142 HVSGGERQLAMIARALAQEPSFLLLDE 168
                                    555555567788888888877777775 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00022      0.17       4      23 ..      35      54 ..      32      82 .. 0.86
   2 ?   -1.6   0.0       2.7     2e+03     105     123 ..     117     135 ..      87     139 .. 0.82
   3 ?   -0.1   0.0      0.95   7.1e+02      41      78 ..     166     205 ..     157     240 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00022
                      PduV-EutP  4 illiGkvgsGKttLtqalkg 23
                                   i l+G+ g+GKttL + ++g
  gi|116753759|ref|YP_842877.1| 35 ITLLGPNGCGKTTLLKIING 54
                                   789*************9987 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.7
                      PduV-EutP 105 eenieaveelLksaGaeki 123
                                    e ++e++ + L+++Ga +i
  gi|116753759|ref|YP_842877.1| 117 ERDVEKAYRALEMVGALHI 135
                                    6789999999999999877 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.95
                      PduV-EutP  41 iDtPGeylenrklysalivts..aeadvialvqdateees 78 
                                    +D P  yl+ r+  + l+++   ae+ ++++v++ +++++
  gi|116753759|ref|YP_842877.1| 166 LDEPTSYLDFRNQIRILKTVRgfAESGLMTVVMSLHDPNH 205
                                    7888888888888888877643366667777776665543 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00076      0.56       2      50 ..      14      60 ..      13      66 .. 0.83
   2 ?    3.0   0.0     0.063        47     129     163 ..      85     119 ..      77     127 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00076
                                   --HHHHHHHHHH......HCTS-EEEEESTTSSCHHHHHHHHHHCHCTC CS
                           PIF1  2 LneeQkkvfdaiieavlnekgklfFvtGsgGtgKtflwkallkklrseg 50
                                   L+ + ++v+++i   +  e+g+++ + G  G gKt l+k +   l ++ 
  gi|116753759|ref|YP_842877.1| 14 LSYNGRAVLNNI--CMEIERGRVITLLGPNGCGKTTLLKIINGLLPPTS 60
                                   666778899999..566699*******************9998887765 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.063
                                    HCT-...-SCCCC-EEEEE--TTS-----SSSSS- CS
                           PIF1 129 ilkekeidkpFGGktvvlgGDfrQilPviekgsra 163
                                    + +++  + pF    vvl G f  i P+++ g+r 
  gi|116753759|ref|YP_842877.1|  85 VPQAQRSTFPFTVLDVVLTGRFSYISPLSKPGERD 119
                                    5566667889999****************999986 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   4.6e-05     0.034      23      51 ..      31      59 ..      19     168 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.6e-05
                         AAA_16 23 rpelvllsGesGvGKsslvrellralekd 51
                                   r++++ l G+ G+GK++l++ +   l  +
  gi|116753759|ref|YP_842877.1| 31 RGRVITLLGPNGCGKTTLLKIINGLLPPT 59
                                   448999*************8776544444 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   6.1e-05     0.046       1      20 [.      33      52 ..      33      57 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.1e-05
                                   SCEEEEC-TTTCHHHHHHHH CS
                          NACHT  1 rlvilqGeaGsGKTtLlqkl 20
                                   r++ l G++G+GKTtLl+ +
  gi|116753759|ref|YP_842877.1| 33 RVITLLGPNGCGKTTLLKII 52
                                   7899*************866 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.5e-05     0.048      12      63 ..      28      79 ..      19     109 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.5e-05
                     Zeta_toxin 12 sqerPklillgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPeyee 63
                                   + er  +i l G  G+GK++l++ ++  l ++++ v +d  d R++ P   +
  gi|116753759|ref|YP_842877.1| 28 EIERGRVITLLGPNGCGKTTLLKIINGLLPPTSGRVYVDCRDTRSMKPGEMA 79
                                   55777789999***********************************998333 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 ?    6.2   0.0    0.0052       3.9     240     265 ..      27      53 ..      16      85 .. 0.91
   2 ?    4.1   0.0     0.021        16     322     351 ..     142     171 ..     136     178 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0052
                                    EEE-SS.EEEEEE-TTSSHHHHHHHHH CS
                     ABC_ATPase 240 mgipkG.vtlIvGggfhGKsTLLeAle 265
                                    m i +G v+++ G++  GK+TLL+ ++
  gi|116753759|ref|YP_842877.1|  27 MEIERGrVITLLGPNGCGKTTLLKIIN 53 
                                    8899**99***************9775 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.021
                                    S--HHHHHHHHHHHHHHTT-SEEEEEGGGS CS
                     ABC_ATPase 322 dASGStsqAanimealeagakllLiDEDts 351
                                      SG   q a i++al  + + lL+DE ts
  gi|116753759|ref|YP_842877.1| 142 HVSGGERQLAMIARALAQEPSFLLLDEPTS 171
                                    679999*********************998 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00024      0.18       2      47 ..      35      86 ..      34     104 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00024
                         AAA_28  2 ivitGgestGKTtlleaLa.....argypvv.pEaareileeklakgedalp 47
                                   i ++G+ ++GKTtll+ ++       g ++v  +  r +   ++a++ ++ p
  gi|116753759|ref|YP_842877.1| 35 ITLLGPNGCGKTTLLKIINgllppTSGRVYVdCRDTRSMKPGEMARRMGHVP 86
                                   7899***********9887443332265555555555555555555555555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00039      0.29      29      50 ..      29      49 ..      19      51 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00039
                         AAA_25 29 llpagelallaGapgtGKttla 50
                                   +  +g ++ l G+ g+GKttl+
  gi|116753759|ref|YP_842877.1| 29 I-ERGRVITLLGPNGCGKTTLL 49
                                   4.89****************96 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   0.00039      0.29      17      46 ..      31      60 ..      19      83 .. 0.83
   2 ?   -2.9   0.0       6.4   4.8e+03      90     111 ..     162     184 ..     142     197 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00039
                         AAA_30 17 gdrvavltGpAGtGKttalkalreaweaag 46
                                   + rv +l Gp G GKtt+lk ++ ++    
  gi|116753759|ref|YP_842877.1| 31 RGRVITLLGPNGCGKTTLLKIINGLLPPTS 60
                                   4469999*************9988776654 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.4
                         AAA_30  90 tllivDE.agmvdtkqlaallka 111
                                    + l+ DE ++ +d+++  ++lk 
  gi|116753759|ref|YP_842877.1| 162 SFLLLDEpTSYLDFRNQIRILKT 184
                                    55555553344555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1786.14
//
Query:       gi|116753760|ref|YP_842878.1|  [L=340]
Description: transport system permease protein [Methanosaeta thermophila PT]
Scores for 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-93  311.5  31.3      6e-93  311.3  31.3    1.0  1  FecCD     FecCD transport family
    2.3e-05   24.0  17.4    2.3e-05   24.0  17.4    1.7  2  ABC-3     ABC 3 transport family


Domain annotation for each model (and alignments):
>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  311.3  31.3   6.7e-97     6e-93       3     311 ..      22     332 ..      18     333 .. 0.98

  Alignments for each domain:
  == domain 1  score: 311.3 bits;  conditional E-value: 6.7e-97
                          FecCD   3 llllllslllgavkispsevfeallgka.......dsleaeivlelrlprvlaallvGaaLavaGallQtvtrNpLadPs 75 
                                    l++++lsl++g+++isp +++++++ +         s  +++v+e+rlpr+l+++lvGa+L+vaGa +Q+++rNpL++P+
  gi|116753760|ref|YP_842878.1|  22 LIVMVLSLFIGKFTISPDDIIQLVIFNLmgaetphPSVYKTVVFEVRLPRILLGMLVGASLSVAGAAFQGIFRNPLVSPY 101
                                    6889*******************998889999999999999*************************************** PP

                          FecCD  76 ilGissgaalgavlalllllgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsallsaltsllllll 155
                                    ilG+ssgaa+ga+l+l++    +++f + l a++++lla+++ + +a++r+++  ++l+L+G++vsa++ +l s++++ +
  gi|116753760|ref|YP_842878.1| 102 ILGLSSGAAFGAALSLAV----APQFPVQLSALFFSLLAVGFAYYIATSRGSTPVISLLLSGVIVSAVFDSLLSIIQMAV 177
                                    ***************998....69999***************************************************** PP

                          FecCD 156 neealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrllllllvalltava 235
                                    ne+al+si++wl+Gsl++aswsk+   l+l+l+++++++ll+ +l++la+gde+A+s+G+n+e ++ +++++++l+++++
  gi|116753760|ref|YP_842878.1| 178 NERALQSIVYWLMGSLATASWSKIHSTLPLALAGCAVIFLLRWRLNVLAMGDEEARSVGMNPELYKAVFVVAASLAASSV 257
                                    ******************************************************************************** PP

                          FecCD 236 valvGpigFvGLivPhiarllvgadhrkllplsallGallllladllarlllsptelpvgivtaliGapffiylll 311
                                    v++vG+igFvGL++Ph++r+++g+dh++l+pl++ +Ga++++l+d +ar  +  +e+pvg++t+liGapff+yll+
  gi|116753760|ref|YP_842878.1| 258 VSVVGIIGFVGLVIPHMMRMIFGPDHTHLIPLCITFGAAFMVLVDDIARAGM-GFEVPVGVITTLIGAPFFAYLLR 332
                                    *************************************************997.8********************97 PP

>> ABC-3  ABC 3 transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.4      0.51   4.5e+03     131     149 ..      17      35 ..      10      49 .. 0.59
   2 !   24.0  17.4   2.6e-09   2.3e-05      44     227 ..     111     300 ..      70     331 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.51
                          ABC-3 131 aiieavvllllllfwkell 149
                                    +i++ +++++l lf  +++
  gi|116753760|ref|YP_842878.1|  17 LILSPLIVMVLSLFIGKFT 35 
                                    4555555555555544444 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 2.6e-09
                          ABC-3  44 pGvalayll..gvnlllgailvgliaavalellkrktklk....edtaigivlsvfla..lglvlvslikkskvdldsyL 115
                                     G al +++  ++++ l+a++++l+a  +  +++ +++ +    +  + g+++s+++   l+++ +  ++++ +++  +L
  gi|116753760|ref|YP_842878.1| 111 FGAALSLAVapQFPVQLSALFFSLLAVGFAYYIA-TSRGStpviSLLLSGVIVSAVFDslLSIIQMAVNERALQSIVYWL 189
                                    4555444441145588888888887655555554.4444401104456799999999733566666666669999***** PP

                          ABC-3 116 fGniltisqedliliaiieavvllllllfwkelllitfdeelAkveglsvkllkllllalialavvvalqavGviLvial 195
                                    +G+++t s   + +++ +++   ++++l++  l ++ +  e A++ g++++l+k ++++  +la + ++ +vG+i  +  
  gi|116753760|ref|YP_842878.1| 190 MGSLATASWSKIHSTLPLALAGCAVIFLLRWRLNVLAMGDEEARSVGMNPELYKAVFVVAASLAASSVVSVVGIIGFVG- 268
                                    *********************99999999999******************************************98888. PP

                          ABC-3 196 liiPaatArrltrslesllivAillglvsvva 227
                                    l+iP ++ + ++ + ++l+ + i +g+ ++v+
  gi|116753760|ref|YP_842878.1| 269 LVIPHMMRMIFGPDHTHLIPLCITFGAAFMVL 300
                                    578****************9999999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2464.51
//
Query:       gi|116753761|ref|YP_842879.1|  [L=345]
Description: periplasmic binding protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-20   73.8   0.3    1.9e-20   73.4   0.3    1.2  1  Peripla_BP_2  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.4   0.3   1.1e-24   1.9e-20      11     236 ..      54     291 ..      44     293 .. 0.80

  Alignments for each domain:
  == domain 1  score: 73.4 bits;  conditional E-value: 1.1e-24
                                    HHHHTT-GGGEEE..B-GGG--GGGGGGT........TS-BSBESSSB-HHHHHHH--SEEEE-GGG....GGGHHHHHH CS
                   Peripla_BP_2  11 illalGatdkvvg..vdtttsdpldadklee......aivevgadgeidvEklaalkPDlvilskgl.gltdedeellks 81 
                                    + +a+G+++++v+  +d + +  ld+           + ++  +++ +d+E+la + PDlv+l ++  +++     ++ +
  gi|116753761|ref|YP_842879.1|  54 TYYAVGDPENIVAlkDDRWMRKLLDDIFPVIdpdfekKLTVSVSGDRVDLESLARANPDLVVLWATTpDDANLKAIEETL 133
                                    55677777777753355666666666555446666656677888999********************9999999999*** PP

                                    HS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT...-EEEEEEEETTE..EEEE-TTST CS
                   Peripla_BP_2  82 giptvivessntgeslkeqiralgellgledeaeklvaeidsklaaaksaidse..kpkpvlvfggadeggyvvagsnsy 159
                                    g+p+++   +++ +++  q+ + g++ ++ ++a ++ + + + +    + ++++   ++p +++++ d      ag ns+
  gi|116753761|ref|YP_842879.1| 134 GVPVFAIFVRSV-DDVLHQVDTMGTISDRMERAAEVKEIMHDYMNTTTNVTSNIpeSERPKVYWMWTDV--LGTAGVNSG 210
                                    **********98.****************9888776666666666666666666444777778887776..78899**** PP

                                    TTHHHHTS--EESTTT--.....STT-EEE-HHHHHHH--SEEEEEEHHHHT-S--HHHHT-S...HHHHTSHHHHTT-E CS
                   Peripla_BP_2 160 igdlldalgieniaaesk.....kseyeeisaEqilasdpdvifvsgraeadnktgleflken...pllaelpAvkngrV 231
                                    i+dl++ +g+ n+ +        + e   ++ E++ + +pdvi++  +     + ++e++++     ++++++AvkngrV
  gi|116753761|ref|YP_842879.1| 211 INDLIELAGGVNVMKFAEnetamTMEHPVVNLETLIKLNPDVIYMWYN----ENLDPEDILTGddfNGWKDINAVKNGRV 286
                                    *************6555557*********************9976555....7888888887634569************ PP

                                    EEE-H CS
                   Peripla_BP_2 232 yalds 236
                                    y++ +
  gi|116753761|ref|YP_842879.1| 287 YEIRN 291
                                    *9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2447.36
//
Query:       gi|116753762|ref|YP_842880.1|  [L=669]
Description: magnesium chelatase [Methanosaeta thermophila PT]
Scores for complete 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   77.4   2.7    5.5e-22   77.4   2.7    2.1  2  AAA_lid_2        AAA lid domain
    5.1e-15   56.0   0.0    2.9e-14   53.6   0.0    2.2  2  VWA_2            von Willebrand factor type A domain
    4.9e-10   39.5   0.1      2e-06   27.8   0.0    2.8  3  AAA_5            AAA domain (dynein-related subfamily)
    1.8e-08   34.9   0.0    3.1e-08   34.1   0.0    1.3  1  VWA              von Willebrand factor type A domain
    1.5e-07   31.0   0.0    1.5e-07   31.0   0.0    3.1  4  Mg_chelatase     Magnesium chelatase, subunit ChlI
    2.5e-06   26.8   0.1    5.7e-05   22.3   0.0    2.5  2  MCM              MCM P-loop domain
      1e-05   25.0   4.0    2.7e-05   23.7   4.0    1.7  1  VWA_CoxE         VWA domain containing CoxE-like protein
      0.004   16.9   0.0        0.2   11.4   0.0    2.3  2  Sigma54_activat  Sigma-54 interaction domain
  ------ inclusion threshold ------
      0.011   16.2   0.0       0.28   11.6   0.0    3.3  4  AAA              ATPase family associated with various cellul
      0.012   15.9   2.6      0.017   15.5   0.1    2.5  2  AAA_16           AAA ATPase domain
      0.025   14.5   0.0        2.1    8.2   0.0    2.8  2  AAA_3            ATPase family associated with various cellul
      0.025   15.1   2.2      0.047   14.2   2.2    1.5  1  DUF2894          Protein of unknown function (DUF2894)
      0.081   13.6   2.4       0.14   12.9   0.6    2.4  1  Mg_chelatase_C   Magnesium chelatase, subunit ChlI C-terminal
      0.094   13.2   7.6      0.054   14.0   4.0    2.4  3  UreE_C           UreE urease accessory protein, C-terminal do
       0.73    9.2  10.9        1.2    8.5  10.9    1.2  1  SelP_N           Selenoprotein P, N terminal region
       0.83    9.7   3.9         11    6.0   2.4    2.3  2  Peptidase_S49_N  Peptidase family S49 N-terminal


Domain annotation for each model (and alignments):
>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.4   2.7   4.9e-25   5.5e-22       3      72 ..     269     338 ..     267     339 .. 0.95
   2 ?   -2.4   0.1         4   4.5e+03      12      31 ..     430     447 ..     425     467 .. 0.55

  Alignments for each domain:
  == domain 1  score: 77.4 bits;  conditional E-value: 4.9e-25
                      AAA_lid_2   3 trahlaielgvsgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlrrepeaegetteeivee 72 
                                     +a+++ie+gv ++Ra+++++r+Ar++Aa+egr+ Vt+eDv++a  l+L+HR+r +p++++  ++e++e+
  gi|116753762|ref|YP_842880.1| 269 LIARTCIEMGVRTHRAEIVTARTARTIAAFEGRNDVTEEDVRRAMILALPHRMRSKPFEPPSMAQEKLEQ 338
                                    6899*********************************************************999999886 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4
                      AAA_lid_2  12 gvsgrRadlallraArAlAa 31 
                                     v+gr  d+a+  + rA A 
  gi|116753762|ref|YP_842880.1| 430 PVDGR--DIAFDATIRAAAP 447
                                    56666..6666666666663 PP

>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       3.5   3.9e+03      45      72 ..     228     256 ..     227     295 .. 0.71
   2 !   53.6   0.0   2.6e-17   2.9e-14       1     106 [.     478     584 ..     478     585 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 3.5
                          VWA_2  45 fsdgpevli.pltkdkakilnalrnleak 72 
                                    f+++pe +i  +++ ++ +++++r+ +++
  gi|116753762|ref|YP_842880.1| 228 FESDPEAFIsEWSDEQNLLRERIRRAKQM 256
                                    67777766636889999999999988877 PP

  == domain 2  score: 53.6 bits;  conditional E-value: 2.6e-17
                          VWA_2   1 lvfvlDtSgSmrngdygptrleaakdaveallk.slp.gdrvglvtfsd.gpevlipltkdkakilnalrnleakgggtn 77 
                                    ++fv+D SgSm++     +r+e ak av +ll  s++ +dr+g v+f++ ++ +l+p++++ +  +++l +l + gg t 
  gi|116753762|ref|YP_842880.1| 478 VLFVVDASGSMGAM----RRMESAKGAVLSLLMdSYQkRDRIGMVAFRGnDADLLLPPCSSVDLAMKRLAELPT-GGRTP 552
                                    79***********9....6*********8877646655***********77**********************7.7**** PP

                          VWA_2  78 laaaLqlarkalkkrr...kgekrvivlitDg 106
                                    l a+L++a  +++ +    k ++  ivl++Dg
  gi|116753762|ref|YP_842880.1| 553 LSAGLSKALRVIQGELiknKETRPMIVLVSDG 584
                                    ************98878889999********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 !    8.7   0.0    0.0014       1.6       2      23 ..      36      57 ..      35      73 .. 0.89
   2 !   27.8   0.0   1.8e-09     2e-06      28     138 .]      99     203 ..      91     203 .. 0.81
   3 ?   -3.5   0.0       8.3   9.3e+03      16      46 ..     284     314 ..     280     323 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0014
                                   EEEE--SSSSHHHHHHHGGGGB CS
                          AAA_5  2 vlLvGppGtgKselaerlaaal 23
                                   vl+ G++Gt+Ks+ ++ la +l
  gi|116753762|ref|YP_842880.1| 36 VLIRGDKGTAKSTAVRALADLL 57
                                   8999***************998 PP

  == domain 2  score: 27.8 bits;  conditional E-value: 1.8e-09
                                    EEEE--TT--HHHHH--B--.............--------G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SSSEE CS
                          AAA_5  28 eyvqltrdtteedlkgrreik....ngttslvdsplvraaregeilvlDEveraesevlnsLlslleerrllleeggelv 103
                                     +v l+ + te+ ++g+++++    +g ++l++++l   a +  il++DEv+ ++++v+++Ll         +e  g  v
  gi|116753762|ref|YP_842880.1|  99 PVVDLPLGATEDRVVGSLDVEraikEGIKALEPGILA--AANRGILYIDEVNLLDDHVADVLLDAAAMGVNIVEREGVSV 176
                                    5667777889*********999999***********9..55667******************777766666655544444 PP

                                    E---......-EEEEEESS--.-TT-TTHHHHTT- CS
                          AAA_5 104 kaknddllerfrviatanpldrslnelspalrsRf 138
                                     +++     rf++++t+np +    e+ p+l++Rf
  gi|116753762|ref|YP_842880.1| 177 AHPS-----RFMLVGTMNPEE---GEIRPQLLDRF 203
                                    4444.....3*********99...78899999999 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 8.3
                                    HHHGGGGBS--EEEEE--TT--HHHHH--B- CS
                          AAA_5  16 aerlaaalnreveyvqltrdtteedlkgrre 46 
                                    ae + a++ r++    ++ d teed++  + 
  gi|116753762|ref|YP_842880.1| 284 AEIVTARTARTIAAFEGRNDVTEEDVRRAMI 314
                                    5566677777777788888888888887665 PP

>> VWA  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0   2.8e-11   3.1e-08       2     139 ..     478     615 ..     478     657 .. 0.79

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 2.8e-11
                                    EEEEEE-STTS.CHHHHHHHHHHHHHHHHHHTBTTTTEEEEEEEESSS.EEEEEETTSHCHHHHHHHHHHTGSGGGGSSC CS
                            VWA   2 ivfvlDgSgsm.geenfekvkefikklveklevgpegtrvglvqfsse.vktefslndysskeellsalnnlkysgggtt 79 
                                    + fv+D+Sgsm   +++e++k ++ +l+ + +  ++++r+g+v f ++ +    +  +  s + +++ l +l   +gg t
  gi|116753762|ref|YP_842880.1| 478 VLFVVDASGSMgAMRRMESAKGAVLSLLMDSY--QKRDRIGMVAFRGNdADLLLPPCS--SVDLAMKRLAEL--PTGGRT 551
                                    68*********4458899*****999998888..9**********9876999999999..679********8..667777 PP

                                    -HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CSS...HTHHHHHHHHGC..TEEEEEEEE CS
                            VWA  80 ntgkalkyaleklfkssagaRenakkviilltdGksndg...dpkeaaneakeq..gikvfavGv 139
                                     + ++l++al+ ++ +  +++e ++ +i+l++dG+ n +   dpk+++ ++ e+  ++ v++v +
  gi|116753762|ref|YP_842880.1| 552 PLSAGLSKALRVIQGELIKNKE-TRPMIVLVSDGRANVSissDPKKEIVQIAEEarRLGVHTVVI 615
                                    7**********88888888555.999**********99889*66665554443223444444433 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.061        68       2      48 ..      11      59 ..      10      66 .. 0.85
   2 !   31.0   0.0   1.3e-10   1.5e-07      93     158 ..     125     190 ..     115     198 .. 0.93
   3 ?   -2.0   0.0       1.7   1.9e+03     187     202 ..     197     212 ..     191     216 .. 0.81
   4 ?   -3.9   2.6       6.4   7.1e+03      47      87 ..     328     368 ..     321     370 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.061
                   Mg_chelatase  2 lkdvkGqeeakraleiaaaGgH..nlllvGppGsGKtmlakrlpsllpp 48
                                   +++++Gq+  k al + a+      +l+ G  G+ K+   ++l+ ll +
  gi|116753762|ref|YP_842880.1| 11 FTSIVGQDLMKLALVLNAINPRigGVLIRGDKGTAKSTAVRALADLLDE 59
                                   57899999999999999986542279******************99976 PP

  == domain 2  score: 31.0 bits;  conditional E-value: 1.3e-10
                   Mg_chelatase  93 ggskpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNp 158
                                    g +  +pG ++ a++G+L++DE+  ++ +v +vL +    g   ++r   +v +p+rf+lv +mNp
  gi|116753762|ref|YP_842880.1| 125 GIKALEPGILAAANRGILYIDEVNLLDDHVADVLLDAAAMGVNIVEREGVSVAHPSRFMLVGTMNP 190
                                    667889***********************************************************9 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.7
                   Mg_chelatase 187 gplldRidlqvevkkl 202
                                      lldR+ lqv+v+ +
  gi|116753762|ref|YP_842880.1| 197 PQLLDRFGLQVNVEVI 212
                                    579*********9765 PP

  == domain 4  score: -3.9 bits;  conditional E-value: 6.4
                   Mg_chelatase  47 pplseeealevakiasvagkkeeekllkrrpfraphhsask 87 
                                    pp   +e le a+ +   +k++++++ ++ + r p + +s+
  gi|116753762|ref|YP_842880.1| 328 PPSMAQEKLEQAMAKHQEQKHQHKHQHEHHEERRPQEESSD 368
                                    78889999999999988888888888888888888877775 PP

>> MCM  MCM P-loop domain
   #    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      60      80 ..      36      56 ..      10      64 .. 0.84
   2 !   22.3   0.0   5.1e-08   5.7e-05     102     205 ..     119     222 ..      84     233 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.12
                                   EEEEESSTSTHHHHHHHHHHH CS
                            MCM 60 vllvgdpgtaKsqlLkyvekl 80
                                   vl+ gd gtaKs+ ++++++l
  gi|116753762|ref|YP_842880.1| 36 VLIRGDKGTAKSTAVRALADL 56
                                   8999********988877665 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 5.1e-08
                                    EEESSSSSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--SSSSCCTT CS
                            MCM 102 vrdeetgefvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaGivatLnartsvlaAanpkagrydkk 181
                                     r  ++g  +le G l  a++G+++iDe++  +++  ++l++a       + + G+ +  ++r  ++  +np++g+  ++
  gi|116753762|ref|YP_842880.1| 119 ERAIKEGIKALEPGILAAANRGILYIDEVNLLDDHVADVLLDAAAMGVNIVEREGVSVAHPSRFMLVGTMNPEEGEIRPQ 198
                                    5555666679**********************************9999999************************99999 PP

                                    S-HHHHSSSSHHHHHHSSEEEEE- CS
                            MCM 182 ksvaeninlsaalLsrFDlifvll 205
                                          ++++ +++s  Dl + + 
  gi|116753762|ref|YP_842880.1| 199 LLDRFGLQVNVEVISDVDLRVEIA 222
                                    888888888888888888876665 PP

>> VWA_CoxE  VWA domain containing CoxE-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   4.0   2.4e-08   2.7e-05      14     179 ..     418     608 ..     401     619 .. 0.68

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2.4e-08
                       VWA_CoxE  14 rrr....rrrkrrrrgrriDlrrtlranlrhgge..........lvelvrrkprerkprelvllvDvSgSmaaysai... 76 
                                    +rr     r k    gr+i + +t+ra+  h ++          + ++  +++ +++++ ++++vD SgSm a  ++   
  gi|116753762|ref|YP_842880.1| 418 MRRsgryLRSKLPVDGRDIAFDATIRAAAPHQHMrerrfavtilPQDIREKERVRKTSATVLFVVDASGSMGAMRRMesa 497
                                    3333113566777789*****************99*******97777777777566667999********9885543222 PP

                       VWA_CoxE  77 ...flallhAllqqlprtevfaFdtrlvdlTral.rerDpaeaLarvsaaved.lgGgTrigaalaeflelvtrpaLsr. 150
                                       +l+ll    q+++r+ ++aF  + +dl   l   ++ + a++r++   e   gG T ++a+l ++l++++ + +++ 
  gi|116753762|ref|YP_842880.1| 498 kgaVLSLLMDSYQKRDRIGMVAFRGNDADL--LLpPCSSVDLAMKRLA---ELpTGGRTPLSAGLSKALRVIQGELIKNk 572
                                    2226666666777888*******9887776..4522234455555555...6669****************998877642 PP

                       VWA_CoxE 151 ..ravvvlvsD.....glergdreellaelarlvrr 179
                                      r ++vlvsD        +++++e+++  ++ +r 
  gi|116753762|ref|YP_842880.1| 573 etRPMIVLVSDgranvSISSDPKKEIVQIAEEARRL 608
                                    22789******3333323344444444444444444 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.071        80      23      44 ..      34      55 ..      16      78 .. 0.76
   2 !   11.4   0.0   0.00018       0.2      83     142 ..     128     189 ..     118     203 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.071
                                   S-EEEECSTTSSHHHHHHHHHH CS
                Sigma54_activat 23 lsvlitGesGtGKellaraihe 44
                                     vli+G++Gt K++  ra+ +
  gi|116753762|ref|YP_842880.1| 34 GGVLIRGDKGTAKSTAVRALAD 55
                                   569***********99998866 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00018
                                    S-BEHHHHHTTTSEEEEETGGGS-HHHHHHHHHH..HHHSEEESBTSSSEEE--EEEEEEES CS
                Sigma54_activat  83 kekkGlfekadgGtlfLDeigelplelQekLlrv..lqegevervGsskeikvdvriiaatn 142
                                    + + G + +a+ G+l++De++ l+ ++   Ll +  +  + ver G s  ++  ++++ + n
  gi|116753762|ref|YP_842880.1| 128 ALEPGILAAANRGILYIDEVNLLDDHVADVLLDAaaMGVNIVEREGVSVAHPSRFMLVGTMN 189
                                    5567***********************99999752255567888888887777777776655 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 ?   11.6   0.0   0.00025      0.28       1     131 [.      36     210 ..      36     211 .. 0.66
   2 ?   -0.9   0.0       1.8     2e+03      39      65 ..     239     264 ..     221     289 .. 0.77
   3 ?   -3.0   0.0         8     9e+03      99     128 ..     376     407 ..     339     410 .. 0.66
   4 ?   -2.8   0.0         7   7.9e+03      56      98 ..     468     511 ..     448     534 .. 0.49

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00025
                                    EEEESSTTSSHHHHHHHHHHHHT....HE........EEEEETTTCSSS............................... CS
                            AAA   1 vllyGppGtGKTllakavakelg....ve........fleisgsellsk............................... 37 
                                    vl+ G +Gt K+++++a+a  l+    v+        f e ++ +                                   
  gi|116753762|ref|YP_842880.1|  36 VLIRGDKGTAKSTAVRALADLLDeipvVDgcpfncnpFSEDEMCD---Icyqksqngdlqvlmrrmpvvdlplgatedrv 112
                                    68899****************844333222222233333333333...03334667777777777777777777777776 PP

                                    .STTHHHHHHHHHHHHHHHTS....TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS. CS
                            AAA  38 .yvgesekkirelfkeakeka....kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnr. 111
                                        + e+ i+e +k+++       +  il iDE+  l  +  +   + +   vn   +e   v +  s+++++g+ n  
  gi|116753762|ref|YP_842880.1| 113 vGSLDVERAIKEGIKALEPGIlaaaNRGILYIDEVNLLDDHVADVLLDAAAMGVNIVEREGVSVAH-PSRFMLVGTMNPe 191
                                    6444556666666666544446665569********997666555555555555555554444444.688********98 PP

                                    GGGSTHHHHSTTSSEEEETT CS
                            AAA 112 pdkldpallrgRfdrkieie 131
                                    + ++ p+ll +Rf  ++++e
  gi|116753762|ref|YP_842880.1| 192 EGEIRPQLL-DRFGLQVNVE 210
                                    99*******.***9988876 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.8
                                    TTHHHHHHHHHHHHHHHTSTSEEEEEE CS
                            AAA  39 vgesekkirelfkeakekakpsilfiD 65 
                                    +++ ++ +re +++ak++  p +++ D
  gi|116753762|ref|YP_842880.1| 239 WSDEQNLLRERIRRAKQML-PGVVMDD 264
                                    56778899999****9999.9888755 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 8
                                    S..SSTEEEEEEESSGGGSTHHHHSTTSSEEE CS
                            AAA  99 k..eskvivigatnrpdkldpallrgRfdrki 128
                                    +  e+ v+ ig   ++++l + l+r+R+ r++
  gi|116753762|ref|YP_842880.1| 376 StpEESVFGIGSPIDVKQLRDTLRRDRVLRRM 407
                                    23344577777777788888888888877765 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 7
                                    TS.....TSEEEEE.ETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTT CS
                            AAA  56 ka.....kpsilfi.DEidalaksrsgseseeeervvnqLlteldgvkk 98 
                                    k+     + ++lf+ D   +++  r     + e+   ++L   +d ++k
  gi|116753762|ref|YP_842880.1| 468 KErvrktSATVLFVvDASGSMGAMR-----RMESAKGAVLSLLMDSYQK 511
                                    4444443235555414444444444.....2222222333333444444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.1   1.5e-05     0.017      14     155 ..      24     159 ..      16     171 .. 0.56
   2 ?   -1.8   0.6       3.1   3.4e+03     124     124 ..     399     399 ..     287     508 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.5e-05
                         AAA_16  14 salervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipy......salaqalareellrqlld 87 
                                     +l+ +  +r + vl++G++G+ Ks+ vr+l+  l ++ + ++ g    +    p+      ++  q   +++ l+ l +
  gi|116753762|ref|YP_842880.1|  24 LVLN-AINPRIGGVLIRGDKGTAKSTAVRALA-DLLDE-IPVVDGCPFNC---NPFsedemcDICYQKS-QNGDLQVLMR 96 
                                    4444.44567799*******************.56666.55555555555...2322222223344444.3344444444 PP

                         AAA_16  88 eaesaeleawrekleealaavpelagaea..srllellkrll.allsrderplvlvlDdlqwadeaslql.l 155
                                    +       +  ++ +++++   +l       +++ e +k+l    l+   r  +l +D++  +d++ +++ l
  gi|116753762|ref|YP_842880.1|  97 RMPV-VDLPLGATEDRVVG---SL----DveRAIKEGIKALEpGILAAANR-GILYIDEVNLLDDHVADVlL 159
                                    4222.22223332333333...22....13366666666666655555333.78888888888888777744 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.1
                         AAA_16 124 k 124
                                    +
  gi|116753762|ref|YP_842880.1| 399 R 399
                                    2 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.077        86       2      24 ..      36      58 ..      35      62 .. 0.92
   2 ?    8.2   0.0    0.0019       2.1      65     116 ..     141     194 ..     126     204 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.077
                          AAA_3  2 vllegvPGlaktllvkalakald 24
                                   vl++g  G+ak ++v+ala+ ld
  gi|116753762|ref|YP_842880.1| 36 VLIRGDKGTAKSTAVRALADLLD 58
                                   7999***************9987 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0019
                          AAA_3  65 llladeinrappktqsallea..meerqvtvegethklpepflvlatqnPieqe 116
                                    +l  de+n    ++   ll+a  m  + v  eg + + p+ f+++ t nP e e
  gi|116753762|ref|YP_842880.1| 141 ILYIDEVNLLDDHVADVLLDAaaMGVNIVEREGVSVAHPSRFMLVGTMNPEEGE 194
                                    7889***************853388899999999****************8755 PP

>> DUF2894  Protein of unknown function (DUF2894)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   2.2   4.2e-05     0.047      13      82 ..     307     394 ..     295     454 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.2e-05
                        DUF2894  13 dpvrfrfleaLarRaaaqsgevrrlleaklaalldayaarlerae............kaaaealaeaaakapaa...... 74 
                                    + vr +++ aL  R++ ++ e   + ++kl++++++ +++ ++++            +++++a +e+++++p++      
  gi|116753762|ref|YP_842880.1| 307 EDVRRAMILALPHRMRSKPFEPPSMAQEKLEQAMAKHQEQKHQHKhqhehheerrpqEESSDAPSEQSESTPEEsvfgig 386
                                    569999**********************************9999855555555322222222222222222222333333 PP

                        DUF2894  75 spstLaaL 82 
                                    sp   ++L
  gi|116753762|ref|YP_842880.1| 387 SPIDVKQL 394
                                    33333333 PP

>> Mg_chelatase_C  Magnesium chelatase, subunit ChlI C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.6   0.00012      0.14      42      90 ..     264     313 ..     215     315 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
                 Mg_chelatase_C  42 eeaeellee.aierlglsaRaydrilkvArTiADLegseeieeehlaeAl 90 
                                    ++  +l+ +  ie +  + Ra   + + ArTiA  eg+++++ee++ +A+
  gi|116753762|ref|YP_842880.1| 264 DSLLRLIARtCIEMGVRTHRAEIVTARTARTIAAFEGRNDVTEEDVRRAM 313
                                    4444444440445555578999999**********************997 PP

>> UreE_C  UreE urease accessory protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       5.8   6.5e+03      33      54 ..     145     168 ..     142     175 .. 0.72
   2 ?   14.0   4.0   4.8e-05     0.054      13      87 .]     268     356 ..     259     357 .. 0.66
   3 ?   -2.2   0.0       5.4   6.1e+03      30      50 ..     391     411 ..     388     451 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 5.8
                         UreE_C  33 delrieddhvledmlrt..lgaev 54 
                                    de+ + ddhv + +l++  +g+++
  gi|116753762|ref|YP_842880.1| 145 DEVNLLDDHVADVLLDAaaMGVNI 168
                                    6788889***99999983334444 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 4.8e-05
                         UreE_C  13 e.laraayhLGNrHvpleikedelrie......ddhvledmlrt...lgaeveevlapfepeggAy....eaakghghhe 78 
                                    + +ar++ ++G r   +ei + +          ++ v e+ +r+   l +  +  ++pfep + A+    +a  +h+ ++
  gi|116753762|ref|YP_842880.1| 268 RlIARTCIEMGVRTHRAEIVTARTARTiaafegRNDVTEEDVRRamiLALPHRMRSKPFEPPSMAQekleQAMAKHQEQK 347
                                    44899999999998888885333222223567888888888887665567778888999999888854434444455566 PP

                         UreE_C  79 hehghehsH 87 
                                    h+h+h+h+H
  gi|116753762|ref|YP_842880.1| 348 HQHKHQHEH 356
                                    777777776 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 5.4
                         UreE_C  30 ikedelrieddhvledmlrtl 50 
                                    +k+ +  +++d+vl++m r+ 
  gi|116753762|ref|YP_842880.1| 391 VKQLRDTLRRDRVLRRMPRGR 411
                                    555555678999999998874 PP

>> SelP_N  Selenoprotein P, N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5  10.9     0.001       1.2     173     224 ..     327     376 ..     312     383 .. 0.54

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.001
                         SelP_N 173 ekpaeaeektehehahshkqghkhhekhghhHkekeelsesqqeepeeeekp 224
                                    e p+ a+ek e++ a++++q+h+h+++h+  H+e+++ +e+++++p+e+++ 
  gi|116753762|ref|YP_842880.1| 327 EPPSMAQEKLEQAMAKHQEQKHQHKHQHE--HHEERRPQEESSDAPSEQSES 376
                                    55555656665555555556666655555..455444444444444443332 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 ?    6.0   2.4    0.0099        11      53      89 ..     332     368 ..     327     387 .. 0.72
   2 ?    2.5   0.0      0.12   1.3e+02      88     111 ..     469     492 ..     440     516 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0099
                Peptidase_S49_N  53 lkeeleealldeeelkaaekkekkeekeekkaekkka 89 
                                     +e+le+a+ +++e+k+++k++++++ e++ +e ++ 
  gi|116753762|ref|YP_842880.1| 332 AQEKLEQAMAKHQEQKHQHKHQHEHHEERRPQEESSD 368
                                    5789999999999999999998888877777763322 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.12
                Peptidase_S49_N  88 kakeeeekkrvfvldFkGdikAse 111
                                    ++ ++++ + +fv+d +G++ A +
  gi|116753762|ref|YP_842880.1| 469 ERVRKTSATVLFVVDASGSMGAMR 492
                                    22236778899*********9964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (669 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1889  (0.10536); expected 358.6 (0.02)
Passed bias filter:                     1163  (0.064867); expected 358.6 (0.02)
Passed Vit filter:                       164  (0.00914719); 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: 0.89u 0.33s 00:00:01.22 Elapsed: 00:00:00.48
# Mc/sec: 4224.12
//
Query:       gi|116753763|ref|YP_842881.1|  [L=304]
Description: dihydroorotate dehydrogenase 1B [Methanosaeta thermophila PT]
Scores for 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-59  199.0   0.2    1.1e-58  198.8   0.2    1.0  1  DHO_dh        Dihydroorotate dehydrogenase
      5e-08   32.4   1.4    0.00012   21.2   0.0    2.1  2  Dus           Dihydrouridine synthase (Dus)
    4.9e-05   22.9   6.3    7.6e-05   22.2   6.3    1.4  1  NMO           Nitronate monooxygenase
     0.0024   17.4   0.4     0.0071   15.8   0.1    1.8  2  His_biosynth  Histidine biosynthesis protein
      0.006   15.8   1.2      0.009   15.2   0.2    1.7  2  DUF561        Protein of unknown function (DUF561)
  ------ inclusion threshold ------
        0.6    9.1   6.3        1.1    8.2   5.0    2.0  3  IMPDH         IMP dehydrogenase / GMP reductase domain


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 !  198.8   0.2   3.6e-62   1.1e-58       2     295 .]       4     281 ..       3     281 .. 0.95

  Alignments for each domain:
  == domain 1  score: 198.8 bits;  conditional E-value: 3.6e-62
                                    G-EEETTEEESSSEEE-TTSSTTSSSHHHHHCTT.SSEEEEEEE-SS-B--S-S--EEEETTCTEEEE---S-BS-HHHH CS
                         DHO_dh   2 latkvlglkfknpiglAaGfdkegeeilkllklg.fgaieigsvtpkpqeGnpkPrvfrlkedrsvlNslGlnneGldav 80 
                                    l+ +v gl+++np++lAaG+ + + +  + ++l  +ga+ ++sv+++p++G+p P+v+rl  +  ++N++Gl+n+   a 
  gi|116753763|ref|YP_842881.1|   4 LSGDVGGLRLENPLILAAGILGTTGASMRRVALAgAGAVVTKSVGLEPRNGHPGPTVVRLGVG--LINAMGLPNPSYRAF 81 
                                    5667889****************999999999988****************************..*************** PP

                                    HHHHHHHHHHHHCC.CEEEEEEE-TTSS.HHHHHHHHHHHHGGGESEEEEES-SCTCC.TSCCCGCHHHHHHHHHHHHHH CS
                         DHO_dh  81 lekllkrrkeqeekkelginlskakktenavddyvevvrkigpfadilelNvSsPntp.glrdlqekeelkaillkvvke 159
                                     +++   r+       +++++s+ +++    ++++e++  ++  +d +elN+S+P++  ++ +++ +++  ++++++v+ 
  gi|116753763|ref|YP_842881.1|  82 QDEIDIAREG-----GVPVVASIFGSC---PEEFAEIASALD--VDGFELNLSCPHAGgYGMEIGCDPANVEEITRAVRR 151
                                    ***9999866.....69*********9...9*******9997..8*************889******************* PP

                                    HHSSEEEEEE-SSSSHHHHHHHHHHHH.HHTECEEEE...BSEE--CTTCCGCCCCTTSSEEEEEGGGHHHHHHHHHHHH CS
                         DHO_dh 160 vskvpvlvKlaPdltdeekkdiadvll.elkldgiivtNttvqrlaidlkseknvkanktGGlsGkalkdialkvirely 238
                                    + +vpv+vKl+P++td+    ia++   +  + +i+    t++ +aid++s  ++  n  GGlsG+a+k++al+ ++el+
  gi|116753763|ref|YP_842881.1| 152 AVNVPVWVKLTPNVTDIRVLGIAAQRGgANAVVAIN----TLKAMAIDVESGYPILGNVIGGLSGPAIKPVALRCVYELS 227
                                    ***********************9998676677777....788888********************************** PP

                                    HHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHHHHHHHHHHH CS
                         DHO_dh 239 krlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpkiakkikkeleelL 295
                                     +l+  ip+IgvGG++  +Da+e+i+aGA+ vq++tal   g  ++++i  ++ ++L
  gi|116753763|ref|YP_842881.1| 228 GVLE--IPVIGVGGVSCWQDAVEMIMAGAAGVQIGTAL-MGGLEVIRDITSGIIRFL 281
                                    ****..********************************.9**********9998765 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   4.2e-08   0.00012      66     130 ..     105     162 ..      81     184 .. 0.82
   2 !   10.2   0.2   9.3e-05      0.28     172     217 ..     220     264 ..     214     276 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 4.2e-08
                                    HHHHHHHHHHHHTT-SCEEEEESSTTEEETTEEEGGGGGGSHHHHHHHHHHHHCCSSS-EEEEEE CS
                            Dus  66 allaeaAklvadlgadeIdlNvGCPskkvtrggaGaaLlrkpdlvaqivkavvkaveiPvtvkir 130
                                    +   e+A+++ +l++d+ +lN+ CP     + ++G+    +p+ v++i +av++av++Pv vk  
  gi|116753763|ref|YP_842881.1| 105 E---EFAEIASALDVDGFELNLSCPHAGGYGMEIGC----DPANVEEITRAVRRAVNVPVWVKLT 162
                                    3...6788889999***********98666666666....9*********************975 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 9.3e-05
                                    CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHC CS
                            Dus 172 weaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgal 217
                                    ++ ++e+   ++ipvi+ G++  ++da +++   Ga gv ig +  
  gi|116753763|ref|YP_842881.1| 220 LRCVYELSGVLEIPVIGVGGVSCWQDAVEMIMA-GAAGVQIGTALM 264
                                    5678999999********************999.*******98765 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   6.3   2.6e-08   7.6e-05     131     227 ..     174     265 ..      87     270 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 2.6e-08
                            NMO 131 rlkeagvvliptissvkearkvearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavdiPviAaGGiidrrgvaa 210
                                    + +++g+ +++ i + k++ +  ++G  +l   G   GG  G p+++    ++ v +   +++iPvi  GG+   ++   
  gi|116753763|ref|YP_842881.1| 174 AAQRGGANAVVAINTLKAMAIDVESGYPIL---GNVIGGLSG-PAIK-PVALRCVYELSGVLEIPVIGVGGVSCWQDAVE 248
                                    556677777788888888888888887766...999999999.6664.5678999999********************** PP

                            NMO 211 aLalGAsgvqigtrfLl 227
                                    ++ +GA+gvqigt++++
  gi|116753763|ref|YP_842881.1| 249 MIMAGAAGVQIGTALMG 265
                                    **************987 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       0.4   1.2e+03     181     194 ..     144     157 ..     132     197 .. 0.65
   2 !   15.8   0.1   2.4e-06    0.0071      60     115 ..     218     273 ..     208     279 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.4
                                    HHHHHHHHHHSSEE CS
                   His_biosynth 181 eltkelaeavkipv 194
                                    e+t+++++av++pv
  gi|116753763|ref|YP_842881.1| 144 EITRAVRRAVNVPV 157
                                    34555555555554 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 2.4e-06
                                    HHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHH CS
                   His_biosynth  60 anldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknpelikel 115
                                    + l +v e+   ++ipv   GG++  +d+ e++ aga  v igta +   e+i+++
  gi|116753763|ref|YP_842881.1| 218 VALRCVYELSGVLEIPVIGVGGVSCWQDAVEMIMAGAAGVQIGTALMGGLEVIRDI 273
                                    45566677777777777777777777777777777777777777777777777666 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      0.57   1.7e+03      49      66 ..     142     159 ..     136     185 .. 0.74
   2 !   15.2   0.2     3e-06     0.009     174     218 ..     219     264 ..     206     283 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.57
                         DUF561  49 dpklvkkvksvsniPiCv 66 
                                     +++ + v+ ++n+P+ v
  gi|116753763|ref|YP_842881.1| 142 VEEITRAVRRAVNVPVWV 159
                                    567778888888888877 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 3e-06
                         DUF561 174 tlastyeiskkvslPvicasGlsdvtvpla.lslgasGiGigsavs 218
                                    +l ++ye+s ++++Pvi   G+s     +  + +ga+G+ ig a+ 
  gi|116753763|ref|YP_842881.1| 219 ALRCVYELSGVLEIPVIGVGGVSCWQDAVEmIMAGAAGVQIGTALM 264
                                    799********************98877752578********9864 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0      0.98   2.9e+03      52      63 ..      85      96 ..      68     101 .. 0.62
   2 ?   -0.9   0.1      0.21   6.4e+02      17      74 ..     138     194 ..     133     198 .. 0.74
   3 ?    8.2   5.0   0.00037       1.1     186     244 ..     208     268 ..     157     276 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.98
                                   HHHHHTTSEEEE CS
                                   xxxxxxxxxxxx RF
                          IMPDH 52 ialareGgigvi 63
                                   i +areGg+ v+
  gi|116753763|ref|YP_842881.1| 85 IDIAREGGVPVV 96
                                   445566665554 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.21
                                    -GGGSB--EESSTTEEESSSEEE-SSTTT-SHHHHHHHHHTTSEEEE-SSS-HHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH  17 lpkevdlktkltkkiklniPlvsaamdtvtesemAialareGgigvihknlsieeqae 74 
                                     p++v+  t+ +++  +n+P+       vt+ ++    a++Gg   +    + ++ a 
  gi|116753763|ref|YP_842881.1| 138 DPANVEEITRAVRR-AVNVPVWVKLTPNVTDIRVLGIAAQRGGANAVVAINTLKAMAI 194
                                    56667766777666.7999999999999999999888899998877776666666555 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.00037
                                    CSB---HHH..HHHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCCCTTBTT CS
                                    xxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 186 agvGvpqlt..AvaevaeaakkagvpviaDGGikysgdivkAlaaGadavmlGsllagteE 244
                                     g+  p +   A+  v+e     ++pvi  GG++  +d v  + aGa  v +G  l g  E
  gi|116753763|ref|YP_842881.1| 208 GGLSGPAIKpvALRCVYELSGVLEIPVIGVGGVSCWQDAVEMIMAGAAGVQIGTALMGGLE 268
                                    555555554114445666777789******************************9988666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2151.67
//
Query:       gi|116753764|ref|YP_842882.1|  [L=257]
Description: oxidoreductase FAD/NAD(P)-binding subunit [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-09   37.2   4.2    3.2e-09   36.4   4.2    1.4  1  DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydr
      7e-05   23.4   0.0    0.00035   21.2   0.0    2.0  1  NAD_binding_1    Oxidoreductase NAD-binding domain
  ------ inclusion threshold ------
      0.015   15.3   0.4      0.057   13.4   0.8    1.7  2  Fer2_3           2Fe-2S iron-sulfur cluster binding domain
       0.16   12.3   0.0        1.1    9.7   0.0    2.1  1  FAD_binding_6    Oxidoreductase FAD-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 !   36.4   4.2   7.2e-13   3.2e-09       1      41 [.     203     237 ..     203     238 .. 0.92

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 7.2e-13
                                    ----SSSSSSS-TTEEEETTCTT.CEEETTTT-CEEECCCB CS
                DHODB_Fe-S_bind   1 eerMaCGvGaClgCvvktkggdggeykrvCkdGPvFdadev 41 
                                    +++ +C+vG+C++C+++ +g       rvC++GPv+++d++
  gi|116753764|ref|YP_842882.1| 203 NRYFKCAVGICGSCCLDPDG------IRVCVEGPVITGDRL 237
                                    5899**************65......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 !   21.2   0.0   7.8e-08   0.00035       1     105 [.      97     185 ..      97     189 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 7.8e-08
                                    EEEEGGGGHHHHHHHHHHHHHCTTCSEEEEEEEESSGCGSTTHHHHHHHHHHCTTEEEEEEEESSCTTTSSSEESSHHHH CS
                  NAD_binding_1   1 miagGtGiaPvrsvlraileeakdktkvvlvyGnrteedllyreeleelakklpgrlkvvavvsreeagweggkgrvqda 80 
                                    +i+gG+G+aP+  + + + +   +   v+ + G r +ed+++ +++++l     g   ++++    ++g++g +gr ++ 
  gi|116753764|ref|YP_842882.1|  97 LIGGGVGVAPLAFLGEDVKK---RGIDVTSLIGFRCREDIIFLDRFRRL-----GD-VILTT----DDGSAGIEGRASAG 163
                                    79********8766666666...5799*********************9.....42.34444....55566679999988 PP

                                    HHHHHHHHSSTTEEEEEECSHHHHH CS
                  NAD_binding_1  81 lleellslkkeethvyvCGppgMik 105
                                    l  e+++  ++ +++y+CGp+ M+ 
  gi|116753764|ref|YP_842882.1| 164 L-SEIDP--EDYSQIYLCGPEMMMI 185
                                    8.88999..9**********99985 PP

>> Fer2_3  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.81   3.6e+03      78     101 ..     112     134 ..      92     138 .. 0.72
   2 ?   13.4   0.8   1.3e-05     0.057      27      66 ..     180     222 ..     168     228 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.81
                         Fer2_3  78 dlakqkseieleplpkfpvirDLv 101
                                    +  k+   i +++l +f+   D++
  gi|116753764|ref|YP_842882.1| 112 EDVKKR-GIDVTSLIGFRCREDII 134
                                    444444.39999999999999987 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1.3e-05
                         Fer2_3  27 eedtvldaLlkikeev...dptlafrasCregiCGscavainG 66 
                                    +e++++d++ + +e+    + +++ + +C  giCGsc +  +G
  gi|116753764|ref|YP_842882.1| 180 PEMMMIDIIRRCREHAsriQASINRYFKCAVGICGSCCLDPDG 222
                                    789999999999998777799****************988777 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 ?    9.7   0.0   0.00024       1.1      70      96 ..      60      86 ..       7      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00024
                                   -TT-HHHHHHHCS-TT-EEEEEEEE-S CS
                  FAD_binding_6 70 ypgGkmsqaLdelkigdtleikGPlGk 96
                                    + G+ + aL  l++gd++ i+GP+G+
  gi|116753764|ref|YP_842882.1| 60 HAVGEATRALCDLRPGDSVGIRGPFGN 86
                                   46799********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); 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:                         4  (0.000223102); expected 0.2 (1e-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 0.28s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1834.45
//
Query:       gi|116753765|ref|YP_842883.1|  [L=240]
Description: 5-carboxymethyl-2-hydroxymuconate delta-isomerase [Methanosaeta thermophila PT]
Scores for complete 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-73  247.5   0.0    1.3e-73  247.2   0.0    1.0  1  FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family
  ------ inclusion threshold ------
       0.29   12.1   5.5        2.1    9.3   2.6    3.1  2  DUF2437        Domain of unknown function (DUF2437)


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 !  247.2   0.0   1.5e-77   1.3e-73       1     216 [.      43     238 ..      43     240 .] 0.97

  Alignments for each domain:
  == domain 1  score: 247.2 bits;  conditional E-value: 1.5e-77
                                    .EEEEEEE--SHHHHHTTT.-SS-EEEEEEGGGE.EETTE..EE-TTSSSS-EE......EEEEEEEESS-B--T--HHH CS
                  FAA_hydrolase   1 kivcdglnyaehvreagkaaeeppdrhiplepvfflkrasslvgpgdpirrPagsekldyEvELavvigkplrevlsvee 80 
                                    k+vc+glny eh+re++   ++ pd     ep++flk++s++vg++d+i +P+ s+++dyE+ELavvi++++r++ s++e
  gi|116753765|ref|YP_842883.1|  43 KVVCVGLNYLEHARELR---MDLPD-----EPIIFLKPPSAVVGHDDEIILPEMSRRVDYEGELAVVISRRCRRI-SADE 113
                                    689************96...78999.....888******************************************.9*** PP

                                    HHTTEEEEEEEEEEE-SBGGG---.HHHHHHTGGGEEEEEE-B--B-.STT---SS-EEEEEETTEEEEEEEGGGTTTSH CS
                  FAA_hydrolase  81 AedaiaGytllnDvsaRdlqaeekaplgwflgksfdtftpiGpwivtpdeledpedlelrlrvngeevqdsntkdmifsp 160
                                    A+d+i+Gyt +nDv+aRdlq+++    +w+++ksfdtf+p+Gpw+    ++ed edl++++rvnge++q+snt+d+if++
  gi|116753765|ref|YP_842883.1| 114 ADDYILGYTCFNDVTARDLQQKDG---QWTRSKSFDTFAPVGPWV-AQMSVEDAEDLSISTRVNGETRQRSNTSDLIFGV 189
                                    ************************...*****************8.778999**************************** PP

                                    HHHHHHHHHHH-B-TT-EEEEEES.......S--EE--TT-EEEEEETTTEEEEEE CS
                  FAA_hydrolase 161 aeliahlsagltLepGdliltGTpsgvgaeeeslkflkdgDeveveieglGelrnr 216
                                    ael++ +s+++tLepGd+i+tGTp+gvg  +     l+ gD veveieg+G lrnr
  gi|116753765|ref|YP_842883.1| 190 AELVEFVSSIMTLEPGDVIATGTPPGVG--R-----LESGDIVEVEIEGIGLLRNR 238
                                    **************************98..4.....******************97 PP

>> DUF2437  Domain of unknown function (DUF2437)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   2.6   0.00024       2.1       3      50 .]       2      38 ..       1      38 [. 0.85
   2 ?   -0.3   0.0      0.23   2.1e+03       8      25 ..     210     227 ..     208     230 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00024
                                   EEEEEETTEEEEEEEE.EEEEEESS-TTSS-EEEEEEEEGGGSEEE-S CS
                        DUF2437  3 iaRFshgggpryGvlegdtvvvlagdpfgavqpTGervpLadVrLLAP 50
                                   iaRF++g+++  G ++gd++v  +g           ++ L++V+LL+P
  gi|116753765|ref|YP_842883.1|  2 IARFRYGDRVFDGDVDGDRIV-SDG----------VSYELEEVKLLPP 38
                                   899999999999999999986.355..........699********99 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.23
                                    ETTEEEEEEEE.EEEEEE CS
                        DUF2437   8 hgggpryGvlegdtvvvl 25 
                                    +g  p+ G le++ +v++
  gi|116753765|ref|YP_842883.1| 210 TGTPPGVGRLESGDIVEV 227
                                    5667999****9888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1787.25
//
Query:       gi|116753766|ref|YP_842884.1|  [L=314]
Description: rhodanese domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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-26   90.8   0.0    2.8e-18   66.4   0.0    2.6  3  Rhodanese  Rhodanese-like domain
  ------ inclusion threshold ------
       0.14   12.4   0.2       0.38   11.0   0.2    1.7  1  DCR        Dppa2/4 conserved region


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       0.3   2.7e+03      20      55 ..      43      77 ..      42      87 .. 0.65
   2 !   66.4   0.0   3.2e-22   2.8e-18      15     106 ..      88     179 ..      73     180 .. 0.84
   3 !   21.6   0.0   2.6e-08   0.00023       2     102 ..     208     304 ..     207     306 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.3
                      Rhodanese 20 RppeeYekghIpgAvnvskdtlsrakkseapllelp 55
                                   R++e+Y+++ +p A+   ++   + +   a+  + +
  gi|116753766|ref|YP_842884.1| 43 RQKEAYSQSQLPPALRT-AQQNETLQVKSAEKRYEV 77
                                   78899999999999988.444444444444444444 PP

  == domain 2  score: 66.4 bits;  conditional E-value: 3.2e-22
                      Rhodanese  15 a...llDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdgggraaaaaallkklGy 91 
                                    a    +D R+peeY++ghIpgA+n+  +++s  + +  +  +l+e+l+e g++  +++vvy+++g+  + + ++l++ G+
  gi|116753766|ref|YP_842884.1|  88 AgavPVDSRSPEEYAAGHIPGARNI--WWRSVRSGESINASALVEALRENGVNTTDRIVVYGEEGDA-SYLFWALEYIGH 164
                                    244579*******************..777888888889999*************************.666777777**7 PP

                      Rhodanese  92 knvsvldGGfkawke 106
                                     nvs+l+GG++aw++
  gi|116753766|ref|YP_842884.1| 165 RNVSLLNGGVDAWAK 179
                                    77***********86 PP

  == domain 3  score: 21.6 bits;  conditional E-value: 2.6e-08
                      Rhodanese   2 akelkellekgkvallDvR.ppeeYekghIpgAvnv.skdtlsrakkseapllelpeellelgidnkktvvvycdgggra 79 
                                    +++l++ +++ +  ++D+R +++++ +++I+gA+ +  ++ + +++ ++a +le + + +  g+d ++  +vy+d  +  
  gi|116753766|ref|YP_842884.1| 208 PEDLEDVIGAAQ--IIDTReSFADFGRSRIQGAIQIpISTVIADNSVRDAASLESIFSGR--GLDGGRLQIVYGDMPDA- 282
                                    577777776654..*****88899************555555555555555555554444..56**********99888. PP

                      Rhodanese  80 aaaaallkklGyknvsvldGGfk 102
                                    +  ++ l+ +G ++  ++dG ++
  gi|116753766|ref|YP_842884.1| 283 SIMYYCLRLMG-YRAALMDGNWR 304
                                    777999999**.79999999776 PP

>> DCR  Dppa2/4 conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2   4.2e-05      0.38      38      63 ..       7      32 ..       4      34 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.2e-05
                            DCR 38 visLfLlPacifpppgleDNlLCpec 63
                                   v  L+LlPa   +  g eD   Cp+c
  gi|116753766|ref|YP_842884.1|  7 VLILLLLPALFGALAGTEDGSFCPTC 32
                                   6679********************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2406.00
//
Query:       gi|116753767|ref|YP_842885.1|  [L=279]
Description: diaminopimelate epimerase [Methanosaeta thermophila PT]
Scores for complete 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  192.4   0.2      7e-34  116.6   0.0    2.0  2  DAP_epimerase  Diaminopimelate epimerase
    0.00028   20.0   0.0     0.0034   16.5   0.0    2.0  2  Pro_racemase   Proline racemase


Domain annotation for each model (and alignments):
>> DAP_epimerase  Diaminopimelate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.6   0.0   7.8e-38     7e-34       1     119 [.       6     128 ..       6     130 .. 0.96
   2 !   74.0   0.3   1.3e-24   1.1e-20       2     120 ..     154     264 ..     153     265 .. 0.89

  Alignments for each domain:
  == domain 1  score: 116.6 bits;  conditional E-value: 7.8e-38
                                    EEEECSSEEEEEEECCTTCSSHHH...HHHHHHHHTTTTSTT-SEEEEEEEEETTEEEEEEEETTTEEESTTHCCHHHHH CS
                  DAP_epimerase   1 fakshGnpndvvvvddveaelvle...aelvaalcdreagpgadgvlfvkpsgeediklryfnrdgseaemCGnGvrvfa 77 
                                    f+k hGn+nd++++d++++e + e   +e+ ++lc+r++g+g+dgvlf +ps+++di +r f  dgseaemCGnG+r+ a
  gi|116753767|ref|YP_842885.1|   6 FVKLHGNGNDFILIDELNGERIPEdekSEASRILCHRNFGIGGDGVLFLVPSERADIGMRLFQPDGSEAEMCGNGIRCLA 85 
                                    799****************9999988899*************************************************** PP

                                    HHHHCTTS-S-SEEEEEETTEEEEEEEECTTSS..EEEEEE--E CS
                  DAP_epimerase  78 aylreggletkkevtvetlgGeleievkddgek..vkvdmGkas 119
                                    + ++e+g +  ++++vetl+G ++i+v++d +    +v+mG ++
  gi|116753767|ref|YP_842885.1|  86 KHAWESGYV-GERFSVETLAGVIPIQVRRDRKGfwARVEMGIPR 128
                                    *******77.********************98899999999776 PP

  == domain 2  score: 74.0 bits;  conditional E-value: 1.3e-24
                                    EEECSSEEEEEEECCTTCSSHHHHHHHHHHHTTTTSTT-SEEEEEEEEETTEEEEEEEETT.TEEESTTHCC.HHHHHHH CS
                  DAP_epimerase   2 akshGnpndvvvvddveaelvleaelvaalcdreagpgadgvlfvkpsgeediklryfnrd.gseaemCGnG.vrvfaay 79 
                                    a+++G+p++v++v++++   v++  +++++ +  ++p++ +v+fv     +++++r+f+r+ + e+ +CG+G v+++a++
  gi|116753767|ref|YP_842885.1| 154 AVNTGVPHAVIFVENLD-IPVEQ--IAPKIRHSSCFPEGANVNFVRL--GNHLEVRTFERGvEAETLSCGTGsVAAAAVA 228
                                    79***************.57777..*********************5..99*****77765378********88888888 PP

                                    HHCTTS-S-SEEEEEETTEEEEEEEECTTSSEEEEEE--EE CS
                  DAP_epimerase  80 lreggletkkevtvetlgGeleievkddgekvkvdmGkasl 120
                                     r g  +  ++v+v t+gG+l i+   +++   ++ G+a+ 
  gi|116753767|ref|YP_842885.1| 229 RRLGL-V-GETVEVMTKGGPLRISFAGEKA---FMEGPAVT 264
                                    88887.4.8****************99985...99999986 PP

>> Pro_racemase  Proline racemase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   3.7e-07    0.0034      59     133 ..      54     123 ..      45     133 .. 0.80
   2 ?    1.1   0.1     0.018   1.6e+02      82     103 ..     216     237 ..     210     258 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.7e-07
                                    EE--SSTTSSEEEEEEESSSB-.SSTHHHHHHHHHHHHHTTSS-SEEEECEEEEEETTEEEEEEEECTST.SEEEEE CS
                   Pro_racemase  59 lvppkepdadlgvifletsgyl.pmcGsntigvvtvlletGlvevqepetklsletpaGlvevtaecrdg.kvervs 133
                                    lvp  +++ad+g+ +++++g    mcG++  ++++ + e+G v       ++s+et aG++ ++++ + +    rv+
  gi|116753767|ref|YP_842885.1|  54 LVP--SERADIGMRLFQPDGSEaEMCGNGIRCLAKHAWESGYVGE-----RFSVETLAGVIPIQVRRDRKgFWARVE 123
                                    444..47899********998626******************975.....4677********999865442556655 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.018
                                    STHHHHHHHHHHHHHTTSS-SE CS
                   Pro_racemase  82 mcGsntigvvtvlletGlvevq 103
                                    +cG +++++++v+   Glv  +
  gi|116753767|ref|YP_842885.1| 216 SCGTGSVAAAAVARRLGLVGET 237
                                    6999999999999999998654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       220  (0.0122706); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.20s 00:00:00.60 Elapsed: 00:00:01.13
# Mc/sec: 748.37
//
Query:       gi|116753768|ref|YP_842886.1|  [L=428]
Description: bifunctional hexulose-6-phosphate synthase/ribonuclease regulator [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-43  149.0   2.9    2.5e-43  147.8   2.9    1.6  1  RraA-like      Aldolase/RraA
    6.8e-24   84.7   3.6    1.6e-23   83.5   2.8    1.9  2  OMPdecase      Orotidine 5'-phosphate decarboxylase / HUMPS f
    7.9e-07   28.4   5.9    8.4e-06   25.1   3.4    2.3  2  NanE           Putative N-acetylmannosamine-6-phosphate epime
    2.1e-06   27.4   3.7    3.5e-06   26.6   3.7    1.3  1  NMO            Nitronate monooxygenase
    5.5e-05   22.5   0.3    0.00021   20.5   0.3    2.0  1  DUF561         Protein of unknown function (DUF561)
    6.1e-05   22.6   0.7    0.00031   20.3   0.2    2.1  2  His_biosynth   Histidine biosynthesis protein
    0.00019   21.2   7.7      0.005   16.5   1.8    2.8  2  Pterin_bind    Pterin binding enzyme
    0.00026   20.6   2.7     0.0082   15.7   0.3    2.6  2  HMGL-like      HMGL-like
     0.0003   20.2   3.0     0.0022   17.3   3.0    2.5  1  TMP-TENI       Thiamine monophosphate synthase
     0.0014   17.9   2.3     0.0029   16.9   0.4    2.4  3  PEP_hydrolase  Phosphoenolpyruvate hydrolase-like
      0.003   17.0   2.2      0.012   15.1   0.1    2.6  2  PEP_mutase     Phosphoenolpyruvate phosphomutase
     0.0031   16.9   4.2     0.0045   16.3   2.2    2.1  2  ThiG           Thiazole biosynthesis protein ThiG
     0.0059   15.7   0.2      0.033   13.3   0.0    2.2  2  PdxJ           Pyridoxal phosphate biosynthesis protein PdxJ
  ------ inclusion threshold ------
      0.038   13.1   0.8      0.087   11.9   0.1    2.0  2  Dus            Dihydrouridine synthase (Dus)
       0.05   12.6   8.3       0.13   11.3   7.0    2.2  1  FMN_dh         FMN-dependent dehydrogenase
       0.15   10.8   5.3        1.4    7.7   2.1    2.9  3  Trp_syntA      Tryptophan synthase alpha chain
        1.7    8.5   5.9       0.28   11.0   1.1    2.2  2  DUF3983        Protein of unknown function (DUF3983)


Domain annotation for each model (and alignments):
>> RraA-like  Aldolase/RraA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.8   2.9   2.3e-46   2.5e-43       1     150 []     237     383 ..     237     383 .. 0.92

  Alignments for each domain:
  == domain 1  score: 147.8 bits;  conditional E-value: 2.3e-46
                                    HHHHHHHCEE-SSBSTB.TT.EE.S.EEEEEEEEEESS.BGHHHHHHHTS--TTEEEEEESTT.SSSSSECE-HHHHHHH CS
                      RraA-like   1 tadvsDalkklggrsggirpler.s.fvGpavTvkvveadnslvkealeeagpgdvlVvdgggdeslraallGgllataa 78 
                                    t+++ Da++  +g  ++i p+ + + +vG+a+Tv+++e+d++++ ea++eagpg+v+V+ +g+  +  a + Ggl + ++
  gi|116753768|ref|YP_842886.1| 237 TPNITDAMH-RKGAMRDILPIIPgTkIVGTAITVQTFEGDWAKTVEAIDEAGPGKVIVIYNGS--RYVAPW-GGLATLSC 312
                                    789******.444444799966644699*******************************9888..558888.******** PP

                                    HHTTBSEEEEEEEES-HHHHTTSSSEEEEEEE-SSB-B-S.STSEESS-EEETTEEE-TTSEEEEETTEEEE CS
                      RraA-like  79 kangvaGvvvdGavRDvaelreldfpvfargvtprkkpkkkgkgevnvpveiggvtvkpgdlivaDedGvvv 150
                                    +++gv+Gvv+dGavRDv+e+r+l++pvfa ++ p + + k g ge+nv++ +gg++v+pgd+iv+D+ Gvvv
  gi|116753768|ref|YP_842886.1| 313 MQKGVEGVVIDGAVRDVDEIRRLNYPVFASAIAPTAGEPK-GMGEINVEIVCGGQVVRPGDYIVGDDCGVVV 383
                                    ***********************************96666.******************************8 PP

>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.5   2.8   1.5e-26   1.6e-23       3     225 .]       7     207 ..       5     207 .. 0.93
   2 ?   -0.9   0.0      0.96     1e+03      14      54 ..     278     315 ..     266     345 .. 0.76

  Alignments for each domain:
  == domain 1  score: 83.5 bits;  conditional E-value: 1.5e-26
                                    EEEEE-SSSHHHHHHHHHHHGG.GSSEEEEEHHHHHHHTHH.HHTHHHHHHHHHT..SEEEEEEEE-S-HHHHHHHHHST CS
                      OMPdecase   3 LclalDvatarelleladkvgp.sivvlKthydlvegwgfegtgaklaalarkhg..flifeDrKfaDIGntvekqatag 79 
                                    L++alD+ + ++++e+a+++ +  +++++ +++l++++g     +++++++r+    + i++D+K++D G+ + ++a   
  gi|116753768|ref|YP_842886.1|   7 LQVALDLLEIDRAVEIAKEAIAgGADWIEAGTPLIKSEG-----MDAVRELRRTLpgVRIVADMKTVDTGAMEVEMA--- 78 
                                    9*******************999****************.....*********9666********************... PP

                                    CHHHHTTESEEEEEGTGHHHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHH..H..SHHHHHHHHHHHHHHHTTESEE CS
                      OMPdecase  80 sarikewadivtvhavaGkasvkalaeaaekwgnrgllilaqmsskgnlmlqe..k..gytqacveaarehkaedfvmGf 155
                                       +k++adiv   a  ++++++ +++aa+k+g    ++++ +s ++  ++++  +  g+++ cv+   +++       +
  gi|116753768|ref|YP_842886.1|  79 ---AKAGADIVALLAISDDSTIQDAIRAARKYG--VEIMVDLLSAPDPVKRARelEelGVDYICVHVGIDQQ-------M 146
                                    ...69***************************9..9****************987379************99.......3 PP

                                    ECCCHTHHHHHHTTCSCEEEHHHTTEEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSHHHHHHHH CS
                      OMPdecase 156 vaqetlnateedaddfihltpgigleqggdgkgqqyntpekligiagadiiivGRgIlkagdpveeaery 225
                                    v ++t        d +  +++ + +   + ++g+     +++i   ga+i+ivG  I++++d    a+r+
  gi|116753768|ref|YP_842886.1| 147 VGKST-I------DLLREVVQVVSI-PVAAAGGIDASSGKDAIF-YGASIVIVGGNITRSADVTGSARRI 207
                                    44444.3......689999999998.*********997777777.99******************99996 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.96
                                    HHHHHHHHHGG.GSSEEEEEHHHHHHHTHH.HHTHHHHHHHH CS
                      OMPdecase  14 elleladkvgp.sivvlKthydlvegwgfegtgaklaalark 54 
                                    + +e +d++gp +++v+  +  +v+ wg    g  +++ ++k
  gi|116753768|ref|YP_842886.1| 278 KTVEAIDEAGPgKVIVIYNGSRYVAPWG----GLATLSCMQK 315
                                    5678899999999999999999999999....5555555555 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 !   25.1   3.4   7.9e-09   8.4e-06      16     183 ..      41     201 ..      24     212 .. 0.74
   2 ?    3.6   0.0     0.032        34     119     182 ..     261     332 ..     220     341 .. 0.69

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 7.9e-09
                                    EEEESHHHHHHHHTT--S-EEEE-B---TTS---BS-SHHHHHHHHTTT-SEEEEE--SS--T--HHHHHHHHHHH--EE CS
                           NanE  16 iriegvedikaikavvdlPiiGivkrdlpdsevritatlkdideLaaagadiialDatdrerpvtieelikkikekyqll 95 
                                    i+ eg++ ++++++  +lP + iv     d +   t    +++  a+agadi+al a + +   ti++ i++ ++ ++ +
  gi|116753768|ref|YP_842886.1|  41 IKSEGMDAVRELRR--TLPGVRIVA----DMKTVDTGA-MEVEMAAKAGADIVALLAISDD--STIQDAIRAARKYGVEI 111
                                    55555555555554..355555542....333333444.479999**********999876..6899************* PP

                                    EEE-.SSHHHHHHH...HHTT-SEEE-TTTTSSTTS-.SS--HHHHHHHHH.TT--EEEES---SHHHHHHHHTT--SEE CS
                           NanE  96 maDi.stleeglva...kklGvdivGttlsGytkeeekaepDfalvkalse.aglkviaeGrintPekakkaieiGvdav 170
                                    m D+ s+ +  + a   ++lGvd++   + G ++++   +  ++l++++++   + v a G i++    k+ai  G+  v
  gi|116753768|ref|YP_842886.1| 112 MVDLlSAPDPVKRArelEELGVDYICVHV-G-IDQQMVGKSTIDLLREVVQvVSIPVAAAGGIDAS-SGKDAIFYGASIV 188
                                    ***73666666655222679*****8765.5.455555677889999988725789*******985.6899999****** PP

                                    EE-HHHH-HHHHH CS
                           NanE 171 vvGsaitrleeia 183
                                    +vG+ itr ++++
  gi|116753768|ref|YP_842886.1| 189 IVGGNITRSADVT 201
                                    *********9987 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.032
                                    TTTTSSTTS-.SS--H.HHHHHHHHTT...--EEEES.---SH...HHHHHHHTT--SEEEE-HHHH-HHHH CS
                           NanE 119 tlsGytkeeekaepDf.alvkalseag...lkviaeG.rintP...ekakkaieiGvdavvvGsaitrleei 182
                                     + G + + +  e D+ + v+a+ eag   + vi +G r+ +P       ++++ Gv+ vv+ +a+  ++ei
  gi|116753768|ref|YP_842886.1| 261 KIVGTAITVQTFEGDWaKTVEAIDEAGpgkVIVIYNGsRYVAPwggLATLSCMQKGVEGVVIDGAVRDVDEI 332
                                    44444444444333431356666665422255776765888884323456899************9888877 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   3.7   3.3e-09   3.5e-06      96     224 ..      65     193 ..      34     210 .. 0.68

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 3.3e-09
                            NMO  96 ieegvrfyrkvevvldekvevvsfgf...glpteevvarlkeagvvliptiss....vkearkvearGaDalivqGpeaG 168
                                    +++ ++    ve+ ++ ++++v + +   +   ++++ +  + gv +++   s    vk ar++e++G D + v      
  gi|116753768|ref|YP_842886.1|  65 MKTVDTGAMEVEMAAKAGADIVALLAisdDSTIQDAIRAARKYGVEIMVDLLSapdpVKRARELEELGVDYICVH----- 139
                                    555555555666666666666553321114444666666666665444433321344899**********99995..... PP

                            NMO 169 GhqG.tpevgdkglfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtr 224
                                       G + ++ +k+++ L+ +v+++v+iPv AaGGi    g +a++ +GAs v +g  
  gi|116753768|ref|YP_842886.1| 140 --VGiDQQMVGKSTIDLLREVVQVVSIPVAAAGGIDASSGKDAIF-YGASIVIVGGN 193
                                    ..44333333489**********************9999988876.9***9999965 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.3     2e-07   0.00021     129     235 ..     116     212 ..     107     219 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2e-07
                         DUF561 129 LkleeqvkLakkLeslgvdliqteGkitsiskakkvndliekslstlastyeiskkvslPvicasGlsdvtvplalslga 208
                                    L+  + vk a++Le+lgvd+i    +i         ++++ k  st+    e++++vs+Pv +a G+  ++ + a+ +ga
  gi|116753768|ref|YP_842886.1| 116 LSAPDPVKRARELEELGVDYICVHVGI--------DQQMVGK--STIDLLREVVQVVSIPVAAAGGIDASSGKDAIFYGA 185
                                    666677888888999999988766533........3455555..46666789**************************** PP

                         DUF561 209 sGiGigsavsklndeeemvallseikk 235
                                    s + +g ++++  d +     ++e ++
  gi|116753768|ref|YP_842886.1| 186 SIVIVGGNITRSADVTGSARRIREAID 212
                                    ***********9998777766666555 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.69   7.3e+02      84     132 ..      19      69 ..      18     101 .. 0.72
   2 !   20.3   0.2   2.9e-07   0.00031      26     112 ..     116     201 ..      99     215 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.69
                                    SHHHHHHHHHCT-SEEEESHHHHH-..THHHHHHHHHHCGGGEEEEEEEEE CS
                   His_biosynth  84 sledveelleagadkviigtaavkn..pelikelaekfgsqkivvaiDarr 132
                                     +e ++e++  gad +  gt  +k+   + ++el +  ++ +iv+   + +
  gi|116753768|ref|YP_842886.1|  19 AVEIAKEAIAGGADWIEAGTPLIKSegMDAVRELRRTLPGVRIVADMKTVD 69 
                                    567788899999999999999987733567999999999888887665554 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 2.9e-07
                                    EETTSHHHHHHHHHHHT-SEEEE.EEHHHHCTTHHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHH CS
                   His_biosynth  26 ryagdpvelakryeeegadelhv.vDldaakegreanldlveeiaeevfipvqvGGGIrsledveelleagadkviigta 104
                                      a dpv+ a+++ee g+d+++v v +d  + g +  +dl++e+++ v+ipv   GGI   +  ++++  ga+ vi+g  
  gi|116753768|ref|YP_842886.1| 116 LSAPDPVKRARELEELGVDYICVhVGIDQQMVG-KSTIDLLREVVQVVSIPVAAAGGIDASS-GKDAIFYGASIVIVGGN 193
                                    5688*****************986889988755.5679********************9888.88899999******988 PP

                                    HHH-THHH CS
                   His_biosynth 105 avknpeli 112
                                      ++ ++ 
  gi|116753768|ref|YP_842886.1| 194 ITRSADVT 201
                                    88777765 PP

>> Pterin_bind  Pterin binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   1.8   4.7e-06     0.005      18      97 ..      14      86 ..       9      87 .. 0.90
   2 !    6.7   0.5    0.0047         5      75     207 ..      90     222 ..      86     250 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.7e-06
                                   THHHHHHHHHHHHHHTT-SEEEEESS-TSTT--CCHHHHHHHHHHHHHHHHHHHCTSEEEEE-S-HHHHHHHHHTTSEEE CS
                    Pterin_bind 18 edldkalaqarkmveeGAdilDiggestrPgaervdeeeelervvpvlealrdeadvpisiDttkaevaeaAlkagadiv 97
                                   +++d+a++ a++ ++ GAd +  g      ++e +d+ +el+r +p ++ ++d       +Dt  +ev e+A kagadiv
  gi|116753768|ref|YP_842886.1| 14 LEIDRAVEIAKEAIAGGADWIEAGTPLI--KSEGMDAVRELRRTLPGVRIVADM----KTVDTGAMEV-EMAAKAGADIV 86
                                   5789********************9999..789****************88884....379***9998.78889***998 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0047
                                    EEEEE-S-HHHHHHHHHTTSEEEEETTTTSSSTTHHHHHHHHT-EEEEESECSSTTTHCCCCCCCSSHHHHHHHHHHHHH CS
                    Pterin_bind  75 pisiDttkaevaeaAlkagadivNdvsgeerdpkmlelvaeagaavvvmhmrgtpktmqeeegqyedvveeveaflearv 154
                                     is D+t  ++++aA k g++i  d     +  k ++ + e g+ +++ h+   +++m      + d+ +ev + ++  v
  gi|116753768|ref|YP_842886.1|  90 AISDDSTIQDAIRAARKYGVEIMVDLLSAPDPVKRARELEELGVDYICVHVG-IDQQMVG--KSTIDLLREVVQVVSIPV 166
                                    6888*********************99999999******************9.3333322..346777777777766444 PP

                                    HHHHHTT--GGG....EEEETTTTS.STTHHHHHHHHHTHHHHHHTTSSEBEEEGTTG CS
                    Pterin_bind 155 eaaeeaGvaper....illDpgigf.gkteehnlellrrldelrealevpvllGvSrk 207
                                    +aa   G++++     i+    i + g++   + ++     ++rea +     G+Sr 
  gi|116753768|ref|YP_842886.1| 167 AAAG--GIDASSgkdaIFYGASIVIvGGNITRSADVTGSARRIREAIDHVEGAGTSRR 222
                                    4443..4433211122555555555555555555555555555555555555555555 PP

>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.3   7.7e-06    0.0082      14     123 ..       8     116 ..       2     119 .. 0.85
   2 ?    5.3   0.1     0.012        13      20      65 ..     116     165 ..     112     251 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 7.7e-06
                                    HTSSS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B..--EE-SSHHHHHHHHH....TT-SEE CS
                      HMGL-like  14 qalkaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkarilalvrarekdikaavealkgagakrv 93 
                                    q + + l++++ ++iak+  + g d iE+g p    + +++vr++ ++++  ri+a ++ ++    + ve + +aga++v
  gi|116753768|ref|YP_842886.1|   8 QVALDLLEIDRAVEIAKEAIAGGADWIEAGTPLIKSEGMDAVRELRRTLPGVRIVADMKTVDTGA-MEVEMAAKAGADIV 86 
                                    67778899*********************************************999888877664.34555677****** PP

                                    EEEEES-HHHHHHHHSSTHHHHHHHHHHHH CS
                      HMGL-like  94 hvfiatselhlkaklkkdreevakkaeeav 123
                                     +     +  ++  ++  r++ ++++++++
  gi|116753768|ref|YP_842886.1|  87 ALLAISDDSTIQDAIRAARKYGVEIMVDLL 116
                                    999888888899999888888888877765 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.012
                                    --HHHHHHHHHHHHHHT-SEE--....TSGGGT.THHHHHHHS---TT-B CS
                      HMGL-like  20 lsveeklaiakaLdeagvdeiEv....gfpaaseddfevvraiakavkka 65 
                                    ls+++ ++ a++L+e+gvd+i v       + ++  ++ +r+++++v ++
  gi|116753768|ref|YP_842886.1| 116 LSAPDPVKRARELEELGVDYICVhvgiDQQMVGKSTIDLLREVVQVVSIP 165
                                    6677778889***********99774323457888999999999999776 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   3.0   2.1e-06    0.0022     101     177 ..     116     190 ..      15     194 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.1e-06
                       TMP-TENI 101 lSvhslee.aeeaealgadYigvGpifpTdtKkdaeplgleglkelaealeiPvvaiGGitlenvaevleagadgvav 177
                                    lS+ ++ + a+e+e+lg+dYi+v   +     ++     +++l+e+++ ++iPv a GGi++++ ++++ +ga+ v v
  gi|116753768|ref|YP_842886.1| 116 LSAPDPVKrARELEELGVDYICV---HVGIDQQMVGKSTIDLLREVVQVVSIPVAAAGGIDASSGKDAIFYGASIVIV 190
                                    466666556999*********97...4466677889999*********************************999877 PP

>> PEP_hydrolase  Phosphoenolpyruvate hydrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.6   1.7e+03     162     174 ..      75      87 ..      67     104 .. 0.70
   2 !   16.9   0.4   2.7e-06    0.0029     160     260 ..     123     231 ..      99     237 .. 0.82
   3 ?   -1.0   0.0      0.76     8e+02      30      49 ..     284     302 ..     261     344 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.6
                  PEP_hydrolase 162 aramaeaGadviv 174
                                     +  a+aGad++ 
  gi|116753768|ref|YP_842886.1|  75 VEMAAKAGADIVA 87 
                                    4445667777654 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 2.7e-06
                  PEP_hydrolase 160 eearamaeaGadvivahlGlttggsigaktalsleeavelvqeiadaakevn....pdvi.....vlvhGGpiaepedae 230
                                    + ar++ e G+d i++h+G+ +  ++g++t   l+e+v+ v+  ++aa  ++    +d i     +++ GG+i++  d++
  gi|116753768|ref|YP_842886.1| 123 KRARELEELGVDYICVHVGIDQ-QMVGKSTIDLLREVVQVVSIPVAAAGGIDassgKDAIfygasIVIVGGNITRSADVT 201
                                    679****************976.589***************9999999877655555554333337899**********9 PP

                  PEP_hydrolase 231 yvlertkgvkGfigassleRlpvekaiket 260
                                       +r +++  ++ +    R  +e+ + ++
  gi|116753768|ref|YP_842886.1| 202 GSARRIREAIDHVEGAGTSRRSLEEEMISI 231
                                    999999999888888888888888777665 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.76
                  PEP_hydrolase  30 aeaggaDliliynsGrfrma 49 
                                     eag   +i+iyn  r+  a
  gi|116753768|ref|YP_842886.1| 284 DEAGPGKVIVIYNGSRYV-A 302
                                    467788899999999994.3 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   1.2e-05     0.012     163     225 ..      76     144 ..      59     151 .. 0.78
   2 ?    0.7   0.1      0.28     3e+02      55      74 ..     149     168 ..     140     207 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.2e-05
                     PEP_mutase 163 raYaeAGAdgvfvpglqkdaeiaelvaav.dvplnvvp.l...kgt..lsvaelaelGvarislgnhllr 225
                                    ++ a+AGAd v    +++d++i++ ++a  +  + +++ l   + +     +el+elGv  i ++  + +
  gi|116753768|ref|YP_842886.1|  76 EMAAKAGADIVALLAISDDSTIQDAIRAArKYGVEIMVdLlsaP-DpvKRARELEELGVDYICVHVGIDQ 144
                                    6789*******************999999565566665333322.2558999**********99876655 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.28
                     PEP_mutase  55 eellaavraiaevvslPliv 74 
                                    +++++++r++++vvs+P+ +
  gi|116753768|ref|YP_842886.1| 149 KSTIDLLREVVQVVSIPVAA 168
                                    45677778888888888754 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   2.2   4.3e-06    0.0045     118     233 ..     103     220 ..      67     238 .. 0.74
   2 ?   -0.5   0.0       0.6   6.3e+02     192     215 ..     311     334 ..     307     350 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.3e-06
                                    HHHHTT-EEEEEE..-S-HH.HHHHHHHTT-SEBEEBSSSTTS----S-HHHHHHHHHH-SS-BEEES---SHHHHHHHH CS
                           ThiG 118 iLvkeGFevlpYv..sdDlv.larrleevGcaavmPlaapiGsglGllnkealkiiieeakvPvivDAGigspsdaaqam 194
                                    +  k G e+++ +   +D+v  ar lee+G+  +           G ++   l+ +++ +++Pv    Gi  +s    a+
  gi|116753768|ref|YP_842886.1| 103 AARKYGVEIMVDLlsAPDPVkRARELEELGVDYICVHVGIDQQMVGKSTIDLLREVVQVVSIPVAAAGGID-ASSGKDAI 181
                                    444555555543211456663699******99985554444444566666666666777789998877775.677889** PP

                                    HTT-SEEEESHHHHTSSSHHHHHHHHHHHHHHHHHHHHH CS
                           ThiG 195 elGadavllntavaeakdpvamArafklaveaGrlayla 233
                                     +Ga+ v++   +++++d    Ar ++ a++    a ++
  gi|116753768|ref|YP_842886.1| 182 FYGASIVIVGGNITRSADVTGSARRIREAIDHVEGAGTS 220
                                    *****************************9865555554 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.6
                                    HHHHTT-SEEEESHHHHTSSSHHH CS
                           ThiG 192 qamelGadavllntavaeakdpva 215
                                      m+ G+++v+++ av   +++ +
  gi|116753768|ref|YP_842886.1| 311 SCMQKGVEGVVIDGAVRDVDEIRR 334
                                    5799************98887655 PP

>> PdxJ  Pyridoxal phosphate biosynthesis protein PdxJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.64   6.7e+02     131     150 ..      69      88 ..      61     114 .. 0.66
   2 !   13.3   0.0   3.1e-05     0.033      19      63 ..     117     161 ..      99     168 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.64
                                    -S-HHHHHHHHHCT-SEEEE CS
                           PdxJ 131 dpdkeqieaaaelgadvvEL 150
                                    d+ + ++e+aa++gad+v L
  gi|116753768|ref|YP_842886.1|  69 DTGAMEVEMAAKAGADIVAL 88 
                                    45555566666666666544 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 3.1e-05
                                    S-S-HHHHHHHHHCCT.SEEEEE--TT-SSS-HHHHHHHHHH-SS CS
                           PdxJ  19 nePdvveaaelaeeaGAdgitvhlreDrRhiqdeDveelkelvkt 63 
                                    + Pd+v+ a+  ee G+d i vh+  D++ + ++ +  l+e+v++
  gi|116753768|ref|YP_842886.1| 117 SAPDPVKRARELEELGVDYICVHVGIDQQMVGKSTIDLLREVVQV 161
                                    58**************************************99975 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   8.2e-05     0.087     141     213 ..     122     191 ..      97     258 .. 0.78
   2 ?   -2.0   0.0       1.5   1.5e+03     173     212 ..     278     322 ..     268     326 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.2e-05
                                    HHHHHHHHHCT-SEEEEESSECCCTT-CG--CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEES CS
                            Dus 141 lelakiveaaGaqaltvHgRtraqnyegtadweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmig 213
                                    ++ a+ +e+ G++ + vH    +q+  g+  ++  +ev q vsipv a G+I    + ++++ + Ga  v++g
  gi|116753768|ref|YP_842886.1| 122 VKRARELEELGVDYICVHVGIDQQMV-GKSTIDLLREVVQVVSIPVAAAGGIDAS-SGKDAIFY-GASIVIVG 191
                                    778999************98887776.566677899****************754.44444444.55555555 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.5
                                    HHHHHHHHH-S..S-EEEESS--SH....HHHHHHHHHH--SEEEE CS
                            Dus 173 eaIkevkqavs..ipviaNGdIkda....edaqaileetGadgvmi 212
                                    ++++++ +a +  + vi NG  + a     +   ++++ G++gv+i
  gi|116753768|ref|YP_842886.1| 278 KTVEAIDEAGPgkVIVIYNGSRYVApwggLATLSCMQK-GVEGVVI 322
                                    35778888888889999999866665676777888888.9999987 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   7.0   0.00012      0.13     228     313 ..     123     204 ..      50     216 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
                                    HHHHHHHHTTESEEEE--GGG.TSSTT---HHHCHHHHHHHH..SS-EEEESS-..-SHHHHHHHHHTT-SEEEESHHHH CS
                         FMN_dh 228 edakraveaGvdgivvSNHGG.RqldgapatidvLpeiveavggrievlvDgGi..rrGsDvlkAlalGAdavllGRpfl 304
                                    + a+++ e+Gvd i v  H G  q     +tid L e+v+ v   i+v + gGi  ++G+D   A+  GA++v++G  + 
  gi|116753768|ref|YP_842886.1| 123 KRARELEELGVDYICV--HVGiDQQMVGKSTIDLLREVVQVVS--IPVAAAGGIdaSSGKD---AIFYGASIVIVGGNIT 195
                                    3455556789999988..65536777889*************8..*********4446777...899**********999 PP

                                    HHHHHHHHH CS
                         FMN_dh 305 yglaagGee 313
                                      + + G +
  gi|116753768|ref|YP_842886.1| 196 RSADVTGSA 204
                                    888887765 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.055        58      22      46 ..      15      39 ..       6      44 .. 0.87
   2 ?    0.2   0.0      0.26   2.8e+02     120     164 ..      61     105 ..      56     109 .. 0.62
   3 ?    7.7   2.1    0.0013       1.4     135     234 ..     103     199 ..      75     222 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.055
                                   -HHHHHHHHHHHHHCT-SSEEEE-- CS
                      Trp_syntA 22 dleqsleilkalekagadviElGlp 46
                                   ++++ +ei k+  ++gad iE G p
  gi|116753768|ref|YP_842886.1| 15 EIDRAVEIAKEAIAGGADWIEAGTP 39
                                   678999*****************99 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.26
                                    EETTSBCCCHHHH.HHHHHHTT-EEEEEE-TTS-HHHHHHHHHH-- CS
                      Trp_syntA 120 ivpDlPleeaeel.veaakkkglelvflvapttsderlkevveqae 164
                                    iv+D+ + +   + ve+a k+g ++v l+a  ++d++++  +++a+
  gi|116753768|ref|YP_842886.1|  61 IVADMKTVDTGAMeVEMAAKAGADIVALLAI-SDDSTIQDAIRAAR 105
                                    5555555555444246667777777777777.66666666666655 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0013
                                    HHHHTT-EE.EEEE-TTS-HHHHHHHHHH--S-EEEESTTC-SSTTSSB-TTHHHHHHHHHHCTSS-EEEESSS-SHHHH CS
                      Trp_syntA 135 aakkkglel.vflvapttsderlkevveqaegfvYvvsraGvTgaenavaaevdelverlkkltavPvavGFGistkeqv 213
                                    aa+k+g+e+ v l++   + +r +e+ e +  ++ v    G+   ++ v +++ +l++++ ++   Pva   Gi + +  
  gi|116753768|ref|YP_842886.1| 103 AARKYGVEImVDLLSAPDPVKRARELEELGVDYICV--HVGI--DQQMVGKSTIDLLREVVQVVSIPVAAAGGIDASSGK 178
                                    555666664244554446666666666665555533..4455..56778888999************************* PP

                                    HHHHTT-SEEEE-HHHHHHHH CS
                      Trp_syntA 214 kqvakvadGvivGSalvkkie 234
                                    +++  +a+ vivG  + +  +
  gi|116753768|ref|YP_842886.1| 179 DAIFYGASIVIVGGNITRSAD 199
                                    **************9988655 PP

>> DUF3983  Protein of unknown function (DUF3983)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.3       4.6   4.9e+03       3       9 ..     205     211 ..     204     212 .. 0.87
   2 ?   11.0   1.1   0.00026      0.28       9      18 ..     392     401 ..     388     403 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4.6
                        DUF3983   3 RKvRKAI 9  
                                    R++R AI
  gi|116753768|ref|YP_842886.1| 205 RRIREAI 211
                                    8999998 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00026
                        DUF3983   9 IARRAKdVEK 18 
                                    IARRAK+VEK
  gi|116753768|ref|YP_842886.1| 392 IARRAKEVEK 401
                                    9********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       729  (0.0406604); expected 358.6 (0.02)
Passed bias filter:                      588  (0.032796); 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):              17  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 2817.50
//
Query:       gi|116753769|ref|YP_842887.1|  [L=125]
Description: helix-turn-helix, type 11 domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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-07   29.0   0.0      1e-06   28.2   0.0    1.5  1  HTH_24           Winged helix-turn-helix DNA-binding
    2.6e-06   27.7   0.0    4.1e-06   27.1   0.0    1.2  1  FaeA             FaeA-like protein
      6e-06   26.0   0.0      1e-05   25.3   0.0    1.3  1  HTH_IclR         IclR helix-turn-helix domain
    0.00016   21.6   0.1    0.00031   20.6   0.0    1.5  1  HTH_11           HTH domain
    0.00035   20.3   0.1    0.00074   19.2   0.0    1.6  2  HTH_23           Homeodomain-like domain
    0.00063   19.5   0.7     0.0022   17.8   0.4    1.9  2  LacI             Bacterial regulatory proteins, lacI family
    0.00066   19.5   0.1    0.00094   19.0   0.1    1.3  1  TrmB             Sugar-specific transcriptional regulator Trm
     0.0027   18.1   0.0     0.0042   17.5   0.0    1.5  1  HTH_40           Helix-turn-helix domain
      0.003   17.5   0.0     0.0044   17.0   0.0    1.3  1  HTH_29           Winged helix-turn helix
     0.0032   17.4   0.1     0.0047   16.8   0.1    1.3  1  TBPIP            TBPIP/Hop2 winged helix domain
     0.0032   17.3   0.0     0.0091   15.8   0.0    1.7  1  HTH_5            Bacterial regulatory protein, arsR family
     0.0052   17.0   0.3     0.0094   16.1   0.3    1.4  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
     0.0072   16.8   0.0       0.01   16.3   0.0    1.3  1  LZ_Tnp_IS481     leucine-zipper of insertion element IS481
     0.0098   15.3   0.0      0.024   14.0   0.0    1.6  2  HTH_Tnp_ISL3     Helix-turn-helix domain of transposase famil
  ------ inclusion threshold ------
       0.01   16.1   0.0      0.019   15.2   0.0    1.5  1  HTH_Tnp_1        Transposase
      0.011   15.8   1.0      0.042   13.9   0.3    2.2  3  HTH_7            Helix-turn-helix domain of resolvase
      0.026   14.3   0.0      0.055   13.3   0.0    1.5  1  TetR_N           Bacterial regulatory proteins, tetR family
      0.026   14.3   0.0      0.045   13.5   0.0    1.4  1  PheRS_DBD1       PheRS DNA binding domain 1
      0.031   14.1   0.0       0.08   12.8   0.0    1.7  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
      0.047   14.1   0.0      0.091   13.1   0.0    1.5  1  HTH_31           Helix-turn-helix domain
      0.049   12.5   0.0      0.063   12.1   0.0    1.1  1  HTH_micro        HTH-like
      0.052   13.8   0.0      0.092   13.0   0.0    1.3  1  Antifungal_prot  Antifungal protein
      0.069   12.1   0.0        0.1   11.6   0.0    1.3  1  TnsD             Tn7-like transposition protein D
      0.099   12.2   0.0       0.16   11.5   0.0    1.4  1  GerE             Bacterial regulatory proteins, luxR family
       0.12   12.6   0.2       0.42   10.8   0.1    1.9  2  HTH_17           Helix-turn-helix domain
       0.12   12.0   0.1       0.44   10.2   0.0    1.9  2  CENP-B_N         CENP-B N-terminal DNA-binding domain
       0.13   12.3   0.1       0.31   11.1   0.1    1.7  2  z-alpha          Adenosine deaminase z-alpha domain
       0.18   11.9   0.0       0.28   11.3   0.0    1.3  1  HTH_20           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 !   28.2   0.0   1.6e-09     1e-06       6      45 ..      14      54 ..      11      55 .. 0.95

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 1.6e-09
                         HTH_24  6 rkILelLqk.nprisqreLAerlglSpstvnrrlkrLeeeG 45
                                    kIL+++q+ + +++  e+A++ g+S++tv ++l  L +eG
  gi|116753769|ref|YP_842887.1| 14 EKILRAIQDsKDGLTTVEVARQAGVSKTTVIKYLSVLRSEG 54
                                   69************************************999 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   6.4e-09   4.1e-06       2      59 ..      13      68 ..      12      70 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 6.4e-09
                                   HHHHHHHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEEEE--SSSSS-EEE CS
                           FaeA  2 keeIleylnsikapckTreiAdalglsaYQaRyYLeqLekegkikrspvrrGvstlWe 59
                                   ke+Il  +++ k + +T e+A  +g+s   +  YL  L+ egk + + v  G s lW+
  gi|116753769|ref|YP_842887.1| 13 KEKILRAIQDSKDGLTTVEVARQAGVSKTTVIKYLSVLRSEGKCEYVEV--GPSKLWR 68
                                   89*******99**********************************9988..5667775 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   1.6e-08     1e-05       8      46 ..      16      54 ..      15      59 .. 0.96

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.6e-08
                                   HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTT CS
                       HTH_IclR  8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelG 46
                                   iL+a+     +lt  e+Ar++g++k+tv  +L+ L  +G
  gi|116753769|ref|YP_842887.1| 16 ILRAIQDSKDGLTTVEVARQAGVSKTTVIKYLSVLRSEG 54
                                   9**********************************9887 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   4.9e-07   0.00031       3      44 ..      14      57 ..      13      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 4.9e-07
                         HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg..v 44
                                   ++il+ + ++++ ++  e A++ +vS++tv +++  L++ g   
  gi|116753769|ref|YP_842887.1| 14 EKILRAIQDSKDGLTTVEVARQAGVSKTTVIKYLSVLRSEGkcE 57
                                   799****888877**************************99653 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.2e-06   0.00074       8      42 ..      17      51 ..      10      57 .. 0.82
   2 ?   -2.8   0.0       9.8   6.3e+03      19      25 ..      72      78 ..      65      79 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.2e-06
                         HTH_23  8 lrillllaeGlsvreIAreLgvsrrTvyrwlkryr 42
                                   lr+++  ++Gl++ e+Ar+ gvs+ Tv ++l+  r
  gi|116753769|ref|YP_842887.1| 17 LRAIQDSKDGLTTVEVARQAGVSKTTVIKYLSVLR 51
                                   568888888******************99987655 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 9.8
                         HTH_23 19 svreIAr 25
                                   +++eI++
  gi|116753769|ref|YP_842887.1| 72 PKKEICK 78
                                   6789987 PP

>> LacI  Bacterial regulatory proteins, lacI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0         3   1.9e+03      31      39 ..      13      21 ..      10      23 .. 0.83
   2 !   17.8   0.4   3.4e-06    0.0022       4      20 ..      31      47 ..      28      52 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 3
                                   HHHHHHHHH CS
                           LacI 31 rerVeaame 39
                                   +e++++a++
  gi|116753769|ref|YP_842887.1| 13 KEKILRAIQ 21
                                   899*99997 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 3.4e-06
                                   HHHHHCTS-HHHHHHHC CS
                           LacI  4 DVArlAGVSkaTVSrvL 20
                                   +VAr+AGVSk+TV ++L
  gi|116753769|ref|YP_842887.1| 31 EVARQAGVSKTTVIKYL 47
                                   8************7666 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   0.1   1.5e-06   0.00094      20      67 ..      24      72 ..      11      73 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.5e-06
                                   HCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.TTEEEE--H CS
                           TrmB 20 lgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.pklYravdp 67
                                   ++ +t+ e+a+++gv++++v ++L+ L + G  e ++    kl rav p
  gi|116753769|ref|YP_842887.1| 24 KDGLTTVEVARQAGVSKTTVIKYLSVLRSEGKCEYVEVGpSKLWRAVTP 72
                                   67899***************************99999662569999987 PP

>> HTH_40  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   6.6e-06    0.0042      10      48 ..      24      61 ..      12      93 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 6.6e-06
                         HTH_40 10 eeglsieeIAkerglkesTIegHLaelieegeeidlerl 48
                                   ++gl+  e+A++ g++++T++++L  l  eg+  ++ ++
  gi|116753769|ref|YP_842887.1| 24 KDGLTTVEVARQAGVSKTTVIKYLSVLRSEGK-CEYVEV 61
                                   79************************999997.444333 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   6.9e-06    0.0044       3      40 ..      18      54 ..      17      72 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.9e-06
                         HTH_29  3 qallllaeGvstvsqiAkllglsrrtvyrwlkrfeegG 40
                                   +a++ +++G+ t+ ++A++ g+s++tv ++l   + +G
  gi|116753769|ref|YP_842887.1| 18 RAIQDSKDGL-TTVEVARQAGVSKTTVIKYLSVLRSEG 54
                                   699*******.9*****************997666666 PP

>> TBPIP  TBPIP/Hop2 winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   7.3e-06    0.0047      27      59 ..      35      67 ..      13      69 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7.3e-06
                          TBPIP 27 qkklgKtavqkaLdeLvdegkiieKeyGKqkiY 59
                                   q +++Kt+v k L  L++egk+ + e G +k++
  gi|116753769|ref|YP_842887.1| 35 QAGVSKTTVIKYLSVLRSEGKCEYVEVGPSKLW 67
                                   679*********************999988775 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 !   15.8   0.0   1.4e-05    0.0091       6      43 ..      15      54 ..      13      54 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.4e-05
                                   HHHHHHTT.SS.EEHHHHHHHHTS-HHHHHHHHHHHHHTT CS
                          HTH_5  6 kILklLae.ge.lcvcelaeelglsqstvShHLkkLreaG 43
                                   kIL++ ++ +  l+  e a++ g+s+ tv  +L++Lr +G
  gi|116753769|ref|YP_842887.1| 15 KILRAIQDsKDgLTTVEVARQAGVSKTTVIKYLSVLRSEG 54
                                   7999999963369************************988 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.3   1.5e-05    0.0094       9      55 ..      12      59 ..       6      65 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.5e-05
                                   HHHHHHHHHH.HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                 Fe_dep_repress  9 YLetIYtlse.ekkvvktkdlaerLnvspssVsemlkkLekdGyveye 55
                                   Y e I+++   +k+  +t ++a+  +vs+ +V + l+ L+++G  ey+
  gi|116753769|ref|YP_842887.1| 12 YKEKILRAIQdSKDGLTTVEVARQAGVSKTTVIKYLSVLRSEGKCEYV 59
                                   5566777766699****************************9966654 PP

>> LZ_Tnp_IS481  leucine-zipper of insertion element IS481
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.6e-05      0.01      24      55 ..      25      56 ..      13      78 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.6e-05
                   LZ_Tnp_IS481 24 drrtvaqvarelGvslrtaykwlarfraeGld 55
                                   d  t  +var++Gvs+ t  k+l+ +r+eG  
  gi|116753769|ref|YP_842887.1| 25 DGLTTVEVARQAGVSKTTVIKYLSVLRSEGKC 56
                                   4457889**********************965 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 !   14.0   0.0   3.7e-05     0.024      24      47 ..      23      46 ..      12      48 .. 0.80
   2 ?   -2.4   0.0       5.2   3.3e+03      35      48 ..      57      70 ..      56      71 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.7e-05
                   HTH_Tnp_ISL3 24 llesrsvkavArqlgvSwtTVwri 47
                                   ++++ +  +vArq gvS tTV+ +
  gi|116753769|ref|YP_842887.1| 23 SKDGLTTVEVARQAGVSKTTVIKY 46
                                   56668999*************865 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.2
                   HTH_Tnp_ISL3 35 rqlgvSwtTVwril 48
                                   + + v+++ +wr++
  gi|116753769|ref|YP_842887.1| 57 EYVEVGPSKLWRAV 70
                                   56778999999976 PP

>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0     3e-05     0.019      10      39 ..      14      42 ..      12      59 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3e-05
                      HTH_Tnp_1 10 efKariVreslepgksvsevArrhgvspnq 39
                                   e ++r+++ s + g +++evAr+ gvs+ +
  gi|116753769|ref|YP_842887.1| 14 EKILRAIQDS-KDGLTTVEVARQAGVSKTT 42
                                   7899******.****************876 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   0.3   6.6e-05     0.042       7      43 ..      13      48 ..      10      49 .. 0.85
   2 ?   -2.1   0.0       6.7   4.3e+03      22      30 ..      71      79 ..      65      79 .. 0.79
   3 ?   -1.1   0.0       3.3   2.1e+03      11      25 ..     108     122 ..     101     123 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.6e-05
                                   -HHHHGGGGSSTTTT--STTTSSSS---SSSS--SS- CS
                          HTH_7  7 skndinrvvkLleeGisiskIAkevnisRsTvYRyla 43
                                   ++ +i r+++  ++G +  ++A++ ++s++Tv +yl+
  gi|116753769|ref|YP_842887.1| 13 KE-KILRAIQDSKDGLTTVEVARQAGVSKTTVIKYLS 48
                                   44.6777777788999999***************995 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 6.7
                                   --STTTSSS CS
                          HTH_7 22 isiskIAke 30
                                   +++++I+k+
  gi|116753769|ref|YP_842887.1| 71 TPKKEICKR 79
                                   688999996 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 3.3
                                    HGGGGSSTTTT--ST CS
                          HTH_7  11 inrvvkLleeGisis 25 
                                     +++ +Ll++ +si+
  gi|116753769|ref|YP_842887.1| 108 ADQLSALLRQIQSIN 122
                                    689999999988887 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 ?   13.3   0.0   8.5e-05     0.055      15      36 ..      25      46 ..      21      46 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.5e-05
                                   TT--HHHHHHHHTSSHHHHHHH CS
                         TetR_N 15 dattvreIAkrAGvskgalYry 36
                                   d++t+ e+A++AGvsk ++ +y
  gi|116753769|ref|YP_842887.1| 25 DGLTTVEVARQAGVSKTTVIKY 46
                                   679999************9877 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 ?   13.5   0.0   7.1e-05     0.045       4      35 ..      11      43 ..       8      44 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.1e-05
                     PheRS_DBD1  4 dlaeqlLqrLek.kgevdslelAaelgvdHqkv 35
                                   + +e++L+++++ k+++++ e+A++ gv+  +v
  gi|116753769|ref|YP_842887.1| 11 SYKEKILRAIQDsKDGLTTVEVARQAGVSKTTV 43
                                   5689********9*************9976655 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00012      0.08       7      35 ..      15      44 ..      14      45 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00012
                  HTH_AsnC-type  7 kILeaLqed.aRisyaeLAervGlSestvl 35
                                   kIL+a+q     ++  e+A++ G+S +tv+
  gi|116753769|ref|YP_842887.1| 15 KILRAIQDSkDGLTTVEVARQAGVSKTTVI 44
                                   899999998878999*************97 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00014     0.091      14      35 ..      26      47 ..      12      56 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00014
                         HTH_31 14 GLsqeevAerlgvsestlsrlE 35
                                   GL+  evA+++gvs++t+ ++ 
  gi|116753769|ref|YP_842887.1| 26 GLTTVEVARQAGVSKTTVIKYL 47
                                   9****************98776 PP

>> HTH_micro  HTH-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   9.9e-05     0.063     195     239 ..      14      58 ..       6      63 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.9e-05
                      HTH_micro 195 dqikkkienteeGitskdlkdkfGislkqglklLnklieeeedsi 239
                                    ++i + i+ +++G+t+ ++ ++ G+s     k+L  l  e + ++
  gi|116753769|ref|YP_842887.1|  14 EKILRAIQDSKDGLTTVEVARQAGVSKTTVIKYLSVLRSEGKCEY 58 
                                    678899****************************99988776655 PP

>> Antifungal_prot  Antifungal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00014     0.092       9      47 ..      52      90 ..      50      92 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00014
                Antifungal_prot  9 kkneCkYkkdGkdvivkCpsaankrCtkDrnkCeyDsvs 47
                                   ++ +C+Y + G + + +  +     C++D ++Ce++svs
  gi|116753769|ref|YP_842887.1| 52 SEGKCEYVEVGPSKLWRAVTPKKEICKRDIEPCEVESVS 90
                                   5678***************999**************997 PP

>> TnsD  Tn7-like transposition protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00016       0.1     196     227 ..      23      54 ..       9      68 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00016
                           TnsD 196 eeeglslkeiAkelgvdiktVlryakklgllk 227
                                    +++gl+  e+A+++gv+  tV++y++ l ++ 
  gi|116753769|ref|YP_842887.1|  23 SKDGLTTVEVARQAGVSKTTVIKYLSVLRSEG 54 
                                    3399*********************9887776 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   0.0   0.00025      0.16      16      39 ..      25      48 ..      13      52 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00025
                                   TTS-HHHHHHHHTS-HHHHHHHHH CS
                           GerE 16 eGksnkeIAeelniSekTVkvhks 39
                                   +G+++ e+A++ ++S++TV  ++s
  gi|116753769|ref|YP_842887.1| 25 DGLTTVEVARQAGVSKTTVIKYLS 48
                                   69*****************87776 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00065      0.42       2      22 ..      27      47 ..      27      68 .. 0.80
   2 ?   -0.4   0.0       2.1   1.3e+03       8      23 ..      56      71 ..      49      81 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00065
                         HTH_17  2 ltveEaAelLgvsrstvyrli 22
                                   lt+ E+A+  gvs++tv +++
  gi|116753769|ref|YP_842887.1| 27 LTTVEVARQAGVSKTTVIKYL 47
                                   8999*************9997 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2.1
                         HTH_17  8 AelLgvsrstvyrlir 23
                                   +e+  v++s++ r + 
  gi|116753769|ref|YP_842887.1| 56 CEYVEVGPSKLWRAVT 71
                                   8999999999988775 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 ?   10.2   0.0   0.00069      0.44      10      40 ..      13      44 ..      10      48 .. 0.89
   2 ?   -1.7   0.0       3.6   2.3e+03      21      39 ..      61      66 ..      56      79 .. 0.48

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00069
                                   HHHH.HHHHHHHCTT-HHHHHHHHT--CCHHH CS
                       CENP-B_N 10 reKi.evIqrleegeSkaelarrfnvpestls 40
                                   +eKi ++Iq + +g    e+ar+ +v ++t+ 
  gi|116753769|ref|YP_842887.1| 13 KEKIlRAIQDSKDGLTTVEVARQAGVSKTTVI 44
                                   788659************************96 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.6
                                   CTT-HHHHHHHHT--CCHH CS
                       CENP-B_N 21 egeSkaelarrfnvpestl 39
                                    g+Sk             l
  gi|116753769|ref|YP_842887.1| 61 VGPSK-------------L 66
                                   44443.............3 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 ?   11.1   0.1   0.00048      0.31       2      49 ..       9      54 ..       8      74 .. 0.80
   2 ?   -1.6   0.0       4.6     3e+03      33      39 ..      71      77 ..      64      81 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00048
                                   HHHHHHHHHHHHHHC-TTCECCHHHHHHHHCC-HHHHHHHHHHHHHTT CS
                        z-alpha  2 aqeqaekilelLeelgekkaatalalergLstpkreiNrvLydlerkg 49
                                   a + +ekil +++++ ++  + ++a++ g+s  k  + + L  l  +g
  gi|116753769|ref|YP_842887.1|  9 AMSYKEKILRAIQDSKDGLTTVEVARQAGVS--KTTVIKYLSVLRSEG 54
                                   66889***********************999..666666666555555 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.6
                                   C-HHHHH CS
                        z-alpha 33 tpkreiN 39
                                   tpk+ei 
  gi|116753769|ref|YP_842887.1| 71 TPKKEIC 77
                                   5888885 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00044      0.28      14      51 ..      15      53 ..      13      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00044
                                   HHHHHH.STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHC CS
                         HTH_20 14 rilraL.araegltaselaerldlskntlsyHLrvLeea 51
                                   +ilra+  +++glt  e+a++ ++sk+t+ + L vL++ 
  gi|116753769|ref|YP_842887.1| 15 KILRAIqDSKDGLTTVEVARQAGVSKTTVIKYLSVLRSE 53
                                   69999999********************99999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 902.18
//
Query:       gi|116753770|ref|YP_842888.1|  [L=454]
Description: GvpD gas vesicle [Methanosaeta thermophila PT]
Scores for complete 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  132.1   0.0    3.3e-32  111.8   0.0    2.2  2  GvpD         GvpD gas vesicle protein
    2.9e-10   39.9   0.1    1.2e-07   31.4   0.0    2.7  2  ATPase       KaiC
     0.0015   18.9   0.0      0.003   18.0   0.0    1.5  1  AAA_16       AAA ATPase domain
     0.0019   17.6   0.0          2    7.7   0.0    2.4  2  DnaB_C       DnaB-like helicase C terminal domain
     0.0027   17.5   0.2      0.018   14.7   0.1    2.4  2  AAA_24       AAA domain
     0.0028   18.1   0.0      0.014   15.8   0.0    2.2  2  AAA          ATPase family associated with various cellular a
     0.0077   16.8   0.0      0.018   15.6   0.0    1.6  1  AAA_18       AAA domain
  ------ inclusion threshold ------
      0.019   14.2   0.0      0.059   12.6   0.0    1.7  2  Zeta_toxin   Zeta toxin
      0.023   14.4   0.0      0.028   14.1   0.0    1.5  1  ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-bindi
      0.028   14.2   0.0      0.045   13.5   0.0    1.3  1  AAA_11       AAA domain
      0.031   13.8   0.0      0.068   12.7   0.0    1.5  1  AAA_25       AAA domain
      0.033   14.3   0.0       0.23   11.6   0.0    2.1  2  AAA_33       AAA domain
      0.037   14.0   0.0      0.069   13.1   0.0    1.5  1  AAA_5        AAA domain (dynein-related subfamily)
      0.049   13.7   0.0        0.1   12.6   0.0    1.6  1  AAA_14       AAA domain
      0.057   12.7   0.0      0.085   12.1   0.0    1.2  1  DUF2075      Uncharacterized conserved protein (DUF2075)
       0.12   11.6   0.0        0.2   10.8   0.0    1.3  1  NB-ARC       NB-ARC domain
       0.14   11.9   0.1        2.6    7.7   0.0    2.2  2  IstB_IS21    IstB-like ATP binding protein
       0.16   12.5   0.0       0.59   10.7   0.0    1.8  2  ABC_tran     ABC transporter


Domain annotation for each model (and alignments):
>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.8   0.0   3.3e-35   3.3e-32       1     296 [.       7     310 ..       7     322 .. 0.78
   2 !   18.2   0.0   7.7e-07   0.00077     380     468 ..     348     441 ..     342     451 .. 0.88

  Alignments for each domain:
  == domain 1  score: 111.8 bits;  conditional E-value: 3.3e-35
                           GvpD   1 leqffdgeaGktllikGaPGtGktlftlrgldvlrresdvlyvstrvddetvseay......fsgeaeld..ktalldll 72 
                                    +++ff+   G+tllikG PGtGkt+++ + l+v+ ++ + +y+strvd + ++  +      +  +  ++  + +ll  l
  gi|116753770|ref|YP_842888.1|   7 IHRFFEIGEGQTLLIKGLPGTGKTTLAFEILNVMCEKRNGMYISTRVDPDRLYRTFpwikeiVPPRNVVNatQSKLLQTL 86 
                                    679****************************************************9776665444444442233455444 PP

                           GvpD  73 kd.pleldl.dvdvPiekldlesllefvdeiaaiatkliialdswelvyeylaerydsPediktvkndlvvlaresgvrl 150
                                    ++ + ++++ d ++ +       l+e v+      + +ii +dsw+ +++y++   ++ ++++    ++  +ar+ g+++
  gi|116753770|ref|YP_842888.1|  87 RNiAGGIPTyDTVLDF----FRVLFEDVE----DMESPIIVFDSWDALMNYISPIIKEQQSFEQ---NICEFARDMGIHI 155
                                    4312345441233334....455666666....5689****************99988888875...566677******* PP

                           GvpD 151 vlvletaansrleyivdGvvtl...........nvked.drgrlrrdlrleklrGvrignrlqPftladGkfksitr.ve 217
                                    + v+e+a   +l+yivdGvv +            v++   r r  r++rleklrGv i +r +  tl +G+f++ t+ ve
  gi|116753770|ref|YP_842888.1| 156 IFVSESADLMPLDYIVDGVVYMehyriagtpssAVRDSgMRTRYAREIRLEKLRGVEILQRTFTATLHGGRFQCFTPcVE 235
                                    ********************9987766666655566652477889*******************************9344 PP

                           GvpD 218 lvtidtvtdeakyePlandkakfsvglrdldkllseGtdrGsvvildlgkdlsrdawsvlvlaairdflsqemgvavvp 296
                                       +  + d+ +    ++d a  s+g+  ld+++ +G + Gs  +l++ +  ++  + +l+  a  + l +   v+++p
  gi|116753770|ref|YP_842888.1| 236 DGDARIGGDHVRISDPKEDCA--STGIPQLDEIT-GGLKYGSCNVLEINHGVGKRYYHILTALA-SNALKNGRAVCIIP 310
                                    445555555555544444444..8********97.89***********9999999999988655.45566677777766 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 7.7e-07
                           GvpD 380 vervreesegPllyvismdtayeafetr.lgdfanyva....lrndavilivkdgtelrtradrvadmhirlelsgdaiv 454
                                     ++ re+s  P+l +i md +  af+ r l + an ++      nd  +l+vk g e    a  vad+++ ++    ++ 
  gi|116753770|ref|YP_842888.1| 348 WDELRERSGRPILNIIGMDAMEFAFGYRqLLNIANRLInqwkETNDINLLVVKTGQESINMAIHVADTYFVVNELNGGLC 427
                                    56789*********************87588999999988777899***************************9999999 PP

                           GvpD 455 lygenkltsllgig 468
                                    +yg  + t l  + 
  gi|116753770|ref|YP_842888.1| 428 IYGVIPRTELYNMS 441
                                    99999998887665 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.0   1.2e-10   1.2e-07      17     214 ..      14     217 ..       4     225 .. 0.81
   2 ?    5.4   0.0      0.01        10       2      32 ..     257     286 ..     256     306 .. 0.87

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 1.2e-10
                         ATPase  17 pegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslG..wdlekleeegklaiidasesaee 94 
                                     eg++ li G pGtGKt++a + l   +ek  ++g+++++  ++  l++ +  +   +  +++ +  +  ++++ ++ ++
  gi|116753770|ref|YP_842888.1|  14 GEGQTLLIKGLPGTGKTTLAFEILNVMCEK--RNGMYISTRVDPDRLYRTFPWIKeiVPPRNVVNATQSKLLQTLRNIAG 91 
                                    5899****************9999999888..***************998875542233344444445555555555444 PP

                         ATPase  95 saeekdkedleelieelaeaikeikakrvviDsitgl.ayeekeavaReilrqlvrvl.kklgvTailvsekssseeaag 172
                                     +   + + +  + + l e +++++   +v Ds ++l +y++   +  + + q + ++ +++g+  i+vse   s   a 
  gi|116753770|ref|YP_842888.1|  92 GI--PTYDTVLDFFRVLFEDVEDMESPIIVFDSWDALmNYISPIIKEQQSFEQNICEFaRDMGIHIIFVSE---S---AD 163
                                    33..56788999*************************8898888888888987666666************...3...22 PP

                         ATPase 173 gygveefivdgvivLdlkeiee.............elvRtleivkmRgtkhskke 214
                                          +ivdgv+ +++ +i++             +  R ++  k+Rg ++ +++
  gi|116753770|ref|YP_842888.1| 164 LMP-LDYIVDGVVYMEHYRIAGtpssavrdsgmrtRYAREIRLEKLRGVEILQRT 217
                                    333.468*********9999999999999999999999*********99987766 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.01
                         ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGK 32 
                                    +tgI+ lDei+ gG+  g+   +  + G GK
  gi|116753770|ref|YP_842888.1| 257 STGIPQLDEIT-GGLKYGSCNVLEINHGVGK 286
                                    7*********7.***9998877777777776 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0     3e-06     0.003      21      63 ..      13      56 ..       5     126 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3e-06
                         AAA_16 21 sgrpelvllsGesGvGKsslvrellralekdg.giflrgkcdql 63
                                    g+++ +l+ G +G+GK++l+ e+l+ +++++ g +++++ d  
  gi|116753770|ref|YP_842888.1| 13 IGEGQTLLIKGLPGTGKTTLAFEILNVMCEKRnGMYISTRVDPD 56
                                   477799********************999996688888877776 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0027       2.7      18      48 ..      15      45 ..      10      62 .. 0.83
   2 !    7.7   0.0     0.002         2       3      52 ..     257     307 ..     256     321 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0027
                                   TTXEEEEEEXTTSSHHHHHHHHHHHHHHCST CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         DnaB_C 18 kgdliiiAarpsmGktalalniaenaavkek 48
                                   +g+ ++i + p++Gkt+la++i + +++k++
  gi|116753770|ref|YP_842888.1| 15 EGQTLLIKGLPGTGKTTLAFEILNVMCEKRN 45
                                   57788999***************99887554 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.002
                                    XSSTHHHHHHCTSBXTTXEEEEEEXTTSSHHHHHHHHH..HHHHHCSTSEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxx RF
                         DnaB_C   3 stgfkdLDkltsGlqkgdliiiAarpsmGktalalnia..enaavkeklpva 52 
                                    stg  +LD++t+Gl+ g   ++    ++Gk    +  a  +na + +   v+
  gi|116753770|ref|YP_842888.1| 257 STGIPQLDEITGGLKYGSCNVLEINHGVGKRYYHILTAlaSNALK-NGRAVC 307
                                    68999*************************986554442155544.443444 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   1.8e-05     0.018       3      92 ..      17     141 ..      15     152 .. 0.69
   2 ?   -1.2   0.0       1.4   1.4e+03      98     128 ..     368     399 ..     350     408 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.8e-05
                         AAA_24   3 lkiliyGpsgiGKTtlakelgpkplfidtekGl...ksldadkfpdie................................ 47 
                                    + +li G +g+GKTtla e+  ++ +    +G+    ++d+d++ +                                  
  gi|116753770|ref|YP_842888.1|  17 QTLLIKGLPGTGKTTLAFEI-LNVMCE-KRNGMyisTRVDPDRLYRTFpwikeivpprnvvnatqskllqtlrniaggip 94 
                                    678999**************.443333.3333311134444444333366667777777777777777777777777777 PP

                         AAA_24  48 swedfldevvel..aaeladyktlviDtideleelclaevirqneka 92 
                                    +++++ld++  l  + e+ +  ++v+D+ d l+++++  +++q++ +
  gi|116753770|ref|YP_842888.1|  95 TYDTVLDFFRVLfeDVEDMESPIIVFDSWDALMNYISPIIKEQQSFE 141
                                    777777777777765555566789************99999998864 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.4
                         AAA_24  98 kgdgkGygelaeefrrllkklqelrk.nvifi 128
                                      +++Gy +l +  +rl+++ +e+++ n  ++
  gi|116753770|ref|YP_842888.1| 368 MEFAFGYRQLLNIANRLINQWKETNDiNLLVV 399
                                    568999**************999999865554 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   1.4e-05     0.014       1      72 [.      19     128 ..      19     165 .. 0.75
   2 ?   -1.7   0.0       3.8   3.8e+03      48     108 ..     346     401 ..     334     410 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.4e-05
                                    EEEESSTTSSHHHHHHHHHHHH.....THE..........................EEEEETTTCSSS.........STT CS
                            AAA   1 vllyGppGtGKTllakavakel.....gve..........................fleisgsellsk.........yvg 40 
                                    +l+ G pGtGKT+la  + + +     g                            +++   s+ll+          +  
  gi|116753770|ref|YP_842888.1|  19 LLIKGLPGTGKTTLAFEILNVMcekrnG-MyistrvdpdrlyrtfpwikeivpprnVVNATQSKLLQTlrniaggipTYD 97 
                                    5889****************97654441.034444555555566666666666666788888888766888888888888 PP

                                    HHHHHHHHHHHHHHHTSTSEEEEEETGGGHHH CS
                            AAA  41 esekkirelfkeakekakpsilfiDEidalak 72 
                                       + +r lf++++ ++   i+++D  dal++
  gi|116753770|ref|YP_842888.1|  98 TVLDFFRVLFEDVEDME-SPIIVFDSWDALMN 128
                                    88888888888888887.88999999998876 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.8
                                    HHHHHHHHTS.TS..EEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEE CS
                            AAA  48 elfkeakeka.kp..silfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskviviga 108
                                    ++++e++e + +p   i+ +D ++  ++ r      +  +++n L++++++ ++   +++v+ +
  gi|116753770|ref|YP_842888.1| 346 GIWDELRERSgRPilNIIGMDAMEFAFGYR------QLLNIANRLINQWKETNDI--NLLVVKT 401
                                    566666666663334677777777777777......6777888888888877763..4666555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.8e-05     0.018       2      88 ..      20     109 ..      19     128 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.8e-05
                         AAA_18   2 lltGtpGvGKttlakeL.....skrlgfgvnlrdvakenglllevdpe.aldeskrldedkldklldaleenss....al 71 
                                    l+ G pG+GKttla e+     +kr+  g  ++  +  ++l+ ++ +  ++ + + ++   + kll++l++++       
  gi|116753770|ref|YP_842888.1|  20 LIKGLPGTGKTTLAFEIlnvmcEKRN--GMYISTRVDPDRLYRTFPWIkEIVPPRNVVNATQSKLLQTLRNIAGgiptY- 96 
                                    688**************555554444..444444444444444444444333444444444477777777766522220. PP

                         AAA_18  72 eegknl.vidghlaeles 88 
                                           v+d +++ +e+
  gi|116753770|ref|YP_842888.1|  97 -----DtVLDFFRVLFED 109
                                    .....1255555555554 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.9e-05     0.059      19      77 ..      19      79 ..      14      89 .. 0.80
   2 ?   -2.5   0.0       2.7   2.7e+03      81     100 ..     138     157 ..     133     159 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.9e-05
                     Zeta_toxin 19 illgGqpGAGKselaellkdele..rqgnvv..rldpDdlRelhPeyeeilkadpkkaseltq 77
                                   +l+ G pG GK++la ++ + +   r+g ++  r+dpD+l + +P  +ei    p+++++ tq
  gi|116753770|ref|YP_842888.1| 19 LLIKGLPGTGKTTLAFEILNVMCekRNGMYIstRVDPDRLYRTFPWIKEIVP--PRNVVNATQ 79
                                   678899***************9966666666558*************99765..666666665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.7
                     Zeta_toxin  81 selvekllqeaiengyniiv 100
                                    + + +++++ a ++g++ii+
  gi|116753770|ref|YP_842888.1| 138 QSFEQNICEFARDMGIHIIF 157
                                    5678999***********97 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.8e-05     0.028       6      49 ..       8     130 ..       5     410 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.8e-05
                                    HHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEE..................................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..................................... RF
                    ATP-synt_ab   6 DalfpivqGqrtlipgafgvGktvisqslskqsnsddaiiyvg..................................... 48 
                                      +f i++Gq++li g  g+Gkt+++ ++++ + +++   y+                                      
  gi|116753770|ref|YP_842888.1|   8 HRFFEIGEGQTLLIKGLPGTGKTTLAFEILNVMCEKRNGMYIStrvdpdrlyrtfpwikeivpprnvvnatqskllqtlr 87 
                                    56899*********************999888765544444433355555555555555555555555555555555555 PP

                                    ..........................................E CS
                                    ..........................................x RF
                    ATP-synt_ab  49 ..........................................i 49 
                                                                              i
  gi|116753770|ref|YP_842888.1|  88 niaggiptydtvldffrvlfedvedmespiivfdswdalmnyI 130
                                    5555555555555555555555555555555555555555550 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   4.5e-05     0.045      16      44 ..      15      43 ..       7      82 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.5e-05
                         AAA_11 16 eseitliqGPPGtgKTktivellsqllsr 44
                                   e +  li+G PGtgKT+   e+l+++ ++
  gi|116753770|ref|YP_842888.1| 15 EGQTLLIKGLPGTGKTTLAFEILNVMCEK 43
                                   555789*******************9744 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   6.8e-05     0.068      31     157 ..      14     129 ..      12     161 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.8e-05
                         AAA_25  31 pagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgealrddarllvldlag 110
                                     +g + l+ G pgtGKttla ++   +++ +           + +y+s+  + d+l r + ++ e ++++  + +++  +
  gi|116753770|ref|YP_842888.1|  14 GEGQTLLIKGLPGTGKTTLAFEILNVMCEKR-----------NGMYISTRVDPDRLYRTFPWIKEIVPPRNVVNATQS-K 81 
                                    57899999***************99999655...........778888888888888888866666643333333332.2 PP

                         AAA_25 111 v..eslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralgg 157
                                       + ++++  +    ++  +++ l +++e++e    +v+D+ +++++ 
  gi|116753770|ref|YP_842888.1|  82 LlqTLRNIAGGIPTYDTVLDFFRVLFEDVEDME-SPIIVFDSWDALMNY 129
                                    111112222222222335567788888888865.778888887777765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00023      0.23       3      33 ..      20      58 ..      19      95 .. 0.70
   2 ?   -0.4   0.0       1.2   1.2e+03      51      74 ..     284     308 ..     270     311 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00023
                         AAA_33  3 llvGlpGsGKstlaerl....lkklg....avllssdtl 33
                                   l+ GlpG+GK+tla ++    ++k+      ++++ d l
  gi|116753770|ref|YP_842888.1| 20 LIKGLPGTGKTTLAFEIlnvmCEKRNgmyiSTRVDPDRL 58
                                   567***********8874444333333555555555554 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.2
                         AAA_33  51 vldrlyqilnelarkalsagrn.vi 74 
                                    v +r y il +la  al+ gr+ +i
  gi|116753770|ref|YP_842888.1| 284 VGKRYYHILTALASNALKNGRAvCI 308
                                    5678899**************9555 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   6.9e-05     0.069       2      40 ..      19      57 ..      18      85 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.9e-05
                                   EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHH CS
                          AAA_5  2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteed 40
                                   +l++G pGtgK++la +++ +++ + + + ++ +  ++ 
  gi|116753770|ref|YP_842888.1| 19 LLIKGLPGTGKTTLAFEILNVMCEKRNGMYISTRVDPDR 57
                                   799*******************77777666666666665 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0    0.0001       0.1       3      49 ..      17      62 ..      15      86 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0001
                         AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladp 49
                                   + l+i+G+  +GKTtl++++++    +k++ +yi+   ++d+ ++++
  gi|116753770|ref|YP_842888.1| 17 QTLLIKGLPGTGKTTLAFEILNVMC-EKRNGMYISTRVDPDRLYRTF 62
                                   6789*****************7666.99999**99988888776655 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   8.6e-05     0.085       3      25 ..      18      40 ..      16      57 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.6e-05
                        DUF2075  3 vvlVtGvaGtGKtvvllnllael 25
                                    +l++G +GtGKt +++++l+ +
  gi|116753770|ref|YP_842888.1| 18 TLLIKGLPGTGKTTLAFEILNVM 40
                                   689****************9877 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    0.0002       0.2      16      44 ..      14      40 ..       6      53 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0002
                                   TTSCSEEEEEEESTTSSHHHHHHHHCCSH CS
                         NB-ARC 16 delqslvvalvGmgGvGKttlakqilnks 44
                                   +e q   + + G +G GKttla +iln +
  gi|116753770|ref|YP_842888.1| 14 GEGQ--TLLIKGLPGTGKTTLAFEILNVM 40
                                   5555..7899***************9975 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0026       2.6      44      74 ..      13      43 ..       6      54 .. 0.82
   2 ?    1.4   0.0      0.22   2.2e+02      55      79 ..     281     307 ..     271     312 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0026
                      IstB_IS21 44 iekkenivllGpsGvGKshlaialgveavra 74
                                   i + + +++ G +G+GK+ la  +    +++
  gi|116753770|ref|YP_842888.1| 13 IGEGQTLLIKGLPGTGKTTLAFEILNVMCEK 43
                                   5678999**************9887777764 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.22
                      IstB_IS21  55 psGvGKs..hlaialgveavraglsvl 79 
                                      GvGK   h+ +al+ +a ++g +v 
  gi|116753770|ref|YP_842888.1| 281 NHGVGKRyyHILTALASNALKNGRAVC 307
                                    5799996448999**********9986 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   0.00059      0.59       6      31 ..      11      36 ..       9      88 .. 0.83
   2 ?   -1.6   0.0       3.6   3.6e+03     105     126 ..     366     387 ..     354     389 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00059
                                   EEEETTSEEEEEESTTSSHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  6 lklkegekvaivGenGaGKStLlkll 31
                                   +++ eg+++ i G  G+GK+tL+  +
  gi|116753770|ref|YP_842888.1| 11 FEIGEGQTLLIKGLPGTGKTTLAFEI 36
                                   7899*****************96444 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.6
                                    TSGGS-HHHHHHHHHHHHHHHT CS
                                    xxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran 105 spssLSgGqkqrvalarallkk 126
                                    ++ ++  G +q + +a+ l+++
  gi|116753770|ref|YP_842888.1| 366 DAMEFAFGYRQLLNIANRLINQ 387
                                    55678889********999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); 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: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 3279.28
//
Query:       gi|116753771|ref|YP_842889.1|  [L=404]
Description: proteasome-activating nucleotidase [Methanosaeta thermophila PT]
Scores for 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-45  152.4   0.0    2.1e-44  151.1   0.0    1.7  1  AAA              ATPase family associated with various cellul
    1.1e-13   50.8   0.9      3e-13   49.5   0.6    1.9  2  Prot_ATP_ID_OB   Proteasomal ATPase OB C-terminal domain
    1.3e-13   50.5   0.5    2.8e-13   49.4   0.5    1.6  1  AAA_lid_3        AAA+ lid domain
    1.5e-06   28.3   0.1    1.4e-05   25.1   0.1    2.8  2  AAA_5            AAA domain (dynein-related subfamily)
    4.6e-06   27.1   5.3    0.00022   21.7   0.1    3.0  2  AAA_16           AAA ATPase domain
    6.7e-06   26.3   0.0    1.9e-05   24.9   0.0    1.7  1  AAA_2            AAA domain (Cdc48 subfamily)
    5.6e-05   22.9   0.0    0.00015   21.6   0.0    1.6  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    5.6e-05   23.4   0.2     0.0092   16.3   0.0    2.6  2  AAA_22           AAA domain
    5.7e-05   22.7   0.5    5.7e-05   22.7   0.5    2.1  1  Prot_ATP_OB_N    Proteasomal ATPase OB N-terminal domain
    9.2e-05   21.7   0.0    0.00016   21.0   0.0    1.3  1  DUF815           Protein of unknown function (DUF815)
     0.0035   17.7   0.0     0.0061   16.9   0.0    1.4  1  RNA_helicase     RNA helicase
     0.0046   17.5   0.0      0.023   15.2   0.0    2.1  2  AAA_18           AAA domain
     0.0055   15.9   0.0       0.01   15.1   0.0    1.4  1  TIP49            TIP49 P-loop domain
     0.0056   16.9   0.0     0.0056   16.9   0.0    1.9  1  AAA_28           AAA domain
     0.0056   16.4   0.0      0.013   15.2   0.0    1.6  1  IstB_IS21        IstB-like ATP binding protein
     0.0081   15.9   0.0      0.041   13.6   0.0    2.0  2  AAA_24           AAA domain
     0.0081   15.6   0.0      0.018   14.5   0.0    1.5  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.032   14.1   0.0    1.7  1  AAA_3            ATPase family associated with various cellul
      0.016   15.2   0.0       0.46   10.4   0.0    2.5  2  ATPase_2         ATPase domain predominantly from Archaea
      0.025   14.1   0.0       0.05   13.1   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
      0.027   14.2   0.2      0.078   12.7   0.0    1.9  2  AAA_30           AAA domain
      0.029   14.2   0.5       0.84    9.4   0.0    2.2  2  AAA_11           AAA domain
      0.033   14.4   1.3      0.034   14.3   0.0    1.7  1  AAA_33           AAA domain
      0.045   13.1   0.0       0.12   11.6   0.0    1.7  1  ATPase           KaiC
      0.058   12.5   0.0        0.1   11.6   0.0    1.3  1  Parvo_NS1        Parvovirus non-structural protein NS1
      0.075   12.9   0.0        0.3   11.0   0.0    2.0  2  NTPase_1         NTPase
      0.077   12.7   0.0       0.22   11.2   0.0    1.7  1  Sigma54_activat  Sigma-54 interaction domain
        0.1   12.6   0.0       0.18   11.8   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.12   11.9   0.5       0.38   10.3   0.0    2.2  3  AAA_25           AAA domain
       0.12   11.8   0.1       0.22   11.0   0.1    1.3  1  PhoH             PhoH-like protein
       0.18   11.1   1.0       0.31   10.3   0.0    1.8  2  Zeta_toxin       Zeta toxin
       0.22   11.6   0.0       0.46   10.6   0.0    1.4  1  Torsin           Torsin


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 !  151.1   0.0   3.8e-47   2.1e-44       1     132 []     182     315 ..     182     315 .. 0.96

  Alignments for each domain:
  == domain 1  score: 151.1 bits;  conditional E-value: 3.8e-47
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH...TTC CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr...sgs 77 
                                    vllyGppGtGKTllakava++++++fl++ gse+++ky+ge+++ +relf+ ak+ a p i+fiDE+da++++r    +s
  gi|116753771|ref|YP_842889.1| 182 VLLYGPPGTGKTLLAKAVANSTEATFLRVVGSEFVQKYIGEGARLVRELFDLAKSRA-PAIIFIDELDAIGSRRidgATS 260
                                    79******************************************************9.*****************88777 PP

                                    CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETTS CS
                            AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieiel 132
                                     ++e +r++ qLl+e+dg++ + ++v +igatnrpd+ldpallr gRfdr i+++l
  gi|116753771|ref|YP_842889.1| 261 GDREVQRTLMQLLAEMDGFDPR-GEVKIIGATNRPDMLDPALLRpGRFDRAIYVPL 315
                                    889999***************7.66****************************985 PP

>> Prot_ATP_ID_OB  Proteasomal ATPase OB C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5   0.6   5.3e-16     3e-13       1      57 []      70     124 ..      70     124 .. 0.97
   2 ?   -2.3   0.0       7.8   4.3e+03       1      10 [.     154     163 ..     154     218 .. 0.56

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 5.3e-16
                                    EEEEEEE-TTSSEEEEE-TTS-EEEEEE-GGGSSST--TTEEEEEETTTTEEEEEE- CS
                 Prot_ATP_ID_OB   1 VatVsEvlddteraiVktssdeevvvslagavpremLrpgDlVavdkdtgfifEkLP 57 
                                    V+tV+Evld+  r+iVk+s++   vvs++  +  e+Lrpg +V+++++t++++ +LP
  gi|116753771|ref|YP_842889.1|  70 VGTVVEVLDE-SRVIVKSSTGPRLVVSVSQFIE-EELRPGVQVGLNQQTFAVMCVLP 124
                                    9*********.*********************9.66********************9 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 7.8
                                    EEEEEEE-TT CS
                 Prot_ATP_ID_OB   1 VatVsEvldd 10 
                                    +a+++E+++ 
  gi|116753771|ref|YP_842889.1| 154 IAELREIVEL 163
                                    5677777765 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.4   0.5     5e-16   2.8e-13       1      44 [.     337     380 ..     337     381 .. 0.98

  Alignments for each domain:
  == domain 1  score: 49.4 bits;  conditional E-value: 5e-16
                      AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitmedfe 44 
                                    dvdl  +A +Te+ SGADl+a++ eA++ A+r+ ++++ ++dfe
  gi|116753771|ref|YP_842889.1| 337 DVDLRSIADLTENASGADLKAIVTEAGMSAIREERTQVLQRDFE 380
                                    9******************************************8 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       6.2   3.5e+03      79     102 ..      67      90 ..      42     123 .. 0.74
   2 !   25.1   0.1   2.6e-08   1.4e-05       1     135 [.     181     302 ..     181     304 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 6.2
                                    HHHHHHHHHHHHSSEEE..-SSSE CS
                          AAA_5  79 sevlnsLlslleerrllleeggel 102
                                    + +++++  +l+e r+ + ++++ 
  gi|116753771|ref|YP_842889.1|  67 PMIVGTVVEVLDESRVIVKSSTGP 90 
                                    667777777777777777666654 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 2.6e-08
                                    EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG--HH CS
                          AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEveraese 80 
                                    +vlL GppGtgK+ la+ +a  ++++++ v ++++ ++    g r +      ++   l  + r ++i+++DE++ + s 
  gi|116753771|ref|YP_842889.1| 181 GVLLYGPPGTGKTLLAKAVANSTEATFLRVVGSEFVQKYIGEGARLV------RELFDLA-KSRAPAIIFIDELDAIGSR 253
                                    59******************************997666655555555......4444444.5569999999999999966 PP

                                    HHHHHHHHHHSSEEE..-SSSEEE---........-EEEEEESS--.-TT-TTHHHH CS
                          AAA_5  81 vlnsLlslleerrllleeggelvkaknddller..frviatanpldrslnelspalr 135
                                     ++   s   e ++ l+++  +++     + +r  + +i+++n++d     l+pal+
  gi|116753771|ref|YP_842889.1| 254 RIDGATSGDREVQRTLMQLLAEMDG----FDPRgeVKIIGATNRPD----MLDPALL 302
                                    5555544444444444444433322....22333488999999888....6677775 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1   3.9e-07   0.00022      16      55 ..     171     207 ..     149     220 .. 0.71
   2 ?    7.0   0.0     0.013       7.2     121     146 ..     225     257 ..     221     283 .. 0.68

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 3.9e-07
                         AAA_16  16 lervrsgrpelvllsGesGvGKsslvrellralekdggif 55 
                                    +++v    p  vll+G++G+GK+ l+++++++ e++   f
  gi|116753771|ref|YP_842889.1| 171 FHAVGIEPPKGVLLYGPPGTGKTLLAKAVANSTEAT---F 207
                                    34444444599*******************876655...3 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.013
                         AAA_16 121 ellkrllallsrderplvlvlDdlq........w 146
                                    +l+++l++l+++ + p ++++D+l+         
  gi|116753771|ref|YP_842889.1| 225 RLVRELFDLAKS-RAPAIIFIDELDaigsrridG 257
                                    567888899999.777*********666665552 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   3.4e-08   1.9e-05       6     103 ..     182     273 ..     178     285 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 3.4e-08
                                    EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG---- CS
                          AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpk 83 
                                    +ll gp g+Gkt+laka+a+  ++    ++ r+  se+ +    + + +     ++    a+ +   i+++DE+d i ++
  gi|116753771|ref|YP_842889.1| 182 VLLYGPPGTGKTLLAKAVANSTEA----TFLRVVGSEFVQ----KYIGEGARLVRELFDLAKSRApaIIFIDELDAIGSR 253
                                    6889****************9985....9**********9....55544455555555555555455************8 PP

                                    ---------HHHHHHHHHHH CS
                          AAA_2  84 essgadvSregVqrdLLqil 103
                                    +  ga     +Vqr L+q+l
  gi|116753771|ref|YP_842889.1| 254 RIDGATSGDREVQRTLMQLL 273
                                    7778888889********98 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   2.6e-07   0.00015      34      95 ..     180     249 ..     174     256 .. 0.68

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.6e-07
                         RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvkl.kitsgPvleka.gd...laalltnleek...dvlfideihr 95 
                                      vllyGpPG Gkt lak +a+  ++++ ++  +  ++k  g+   l+  l +l ++    ++fide+  
  gi|116753771|ref|YP_842889.1| 180 KGVLLYGPPGTGKTLLAKAVANSTEATFlRVVGSEFVQKYiGEgarLVRELFDLAKSrapAIIFIDELDA 249
                                    569********************99986255555556653244111444455554432226899999865 PP

>> AAA_22  AAA 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    0.0092       8      30 ..     182     204 ..     177     215 .. 0.86
   2 ?    5.5   0.0     0.033        19      52     104 ..     203     251 ..     200     290 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.6e-05
                         AAA_22   8 lvvtGesGtGKTtllrrlleqld 30 
                                    ++++G++GtGKT+l++ ++++ +
  gi|116753771|ref|YP_842889.1| 182 VLLYGPPGTGKTLLAKAVANSTE 204
                                    689***************99874 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.033
                         AAA_22  52 sskdllrellralglelkaerlsseellealeqalraravielliiDEaqhlr 104
                                    + +++lr + +++ ++  +   +  +l++ l + +++ra  +++ iDE + + 
  gi|116753771|ref|YP_842889.1| 203 TEATFLRVVGSEFVQKYIG---EGARLVRELFDLAKSRAP-AIIFIDELDAIG 251
                                    5667777788888877777...8899999999********.*********995 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 !   22.7   0.5     1e-07   5.7e-05       2      52 ..      70     119 ..      69     126 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1e-07
                  Prot_ATP_OB_N   2 yGtflavnsqdgtadVlvggrrmrVavsPlvdaeeLrpGqeVlLnEalvvV 52 
                                    +Gt+++v ++ + +  ++ g r++V+vs  ++ eeLrpG +V Ln++  +V
  gi|116753771|ref|YP_842889.1|  70 VGTVVEVLDESRVIVKSSTGPRLVVSVSQFIE-EELRPGVQVGLNQQTFAV 119
                                    79******99999999****************.9***********998777 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   2.8e-07   0.00016      51     116 ..     177     247 ..     131     249 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.8e-07
                         DUF815  51 lpannvLLwGarGtGKSslvkallneyaeegLrli..evekedlkelpklvellr...erperfilfvDDL 116
                                    +p + vLL+G  GtGK  l ka+ n+++++ Lr++  e  ++ + e  +lv++l    +++   i+f+D L
  gi|116753771|ref|YP_842889.1| 177 EPPKGVLLYGPPGTGKTLLAKAVANSTEATFLRVVgsEFVQKYIGEGARLVRELFdlaKSRAPAIIFIDEL 247
                                    57789******************************777788999999999887652226667799***988 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.1e-05    0.0061       1      61 [.     182     233 ..     182     252 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.1e-05
                   RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvvidDfgqv 61 
                                    ++lyGp+g+GK++lak            ++++ ++ r + ++f+++Y g+ + ++ ++   
  gi|116753771|ref|YP_842889.1| 182 VLLYGPPGTGKTLLAKA---------VANSTEATFLRVVGSEFVQKYIGEGARLVRELFDL 233
                                    689**************.........34566788889999999999998887777776655 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       3.8   2.1e+03      53      92 ..      16      55 ..       7      74 .. 0.68
   2 !   15.2   0.0   4.2e-05     0.023       1      25 [.     182     227 ..     182     288 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 3.8
                         AAA_18 53 dedkldklldaleenssaleegknlvidghlaeleseaak 92
                                   d++k+ +  ++  +  ++++eg+  +i+ +  ++e ea+k
  gi|116753771|ref|YP_842889.1| 16 DRMKQLEERNLALREQKDRAEGEKRLIENQKLKYEREARK 55
                                   4444444444444444467888888888888888877766 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 4.2e-05
                         AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....................g 25 
                                    +ll G+pG+GKt lak+++++++                      +
  gi|116753771|ref|YP_842889.1| 182 VLLYGPPGTGKTLLAKAVANSTEAtflrvvgsefvqkyigegarlV 227
                                    799***************9997444676666544444444444444 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.8e-05      0.01      51      90 ..     180     217 ..     176     231 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.8e-05
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevys 90 
                                    ++vLl Gp+gtGkt la a++++   +  f  ++gse+ +
  gi|116753771|ref|YP_842889.1| 180 KGVLLYGPPGTGKTLLAKAVANST--EATFLRVVGSEFVQ 217
                                    89*******************975..58899999999865 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0     1e-05    0.0056       2      40 ..     182     225 ..     181     269 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1e-05
                         AAA_28   2 ivitGgestGKTtlleaLaar....gypvv.pEaareileekla 40 
                                    + + G+++tGKT l++a a+       +vv  E++ +++ e+++
  gi|116753771|ref|YP_842889.1| 182 VLLYGPPGTGKTLLAKAVANSteatFLRVVgSEFVQKYIGEGAR 225
                                    6799***************5444447788899999999987764 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 !   15.2   0.0   2.4e-05     0.013      46      71 ..     178     203 ..     168     216 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.4e-05
                      IstB_IS21  46 kkenivllGpsGvGKshlaialgvea 71 
                                      ++++l Gp+G+GK+ la a++ ++
  gi|116753771|ref|YP_842889.1| 178 PPKGVLLYGPPGTGKTLLAKAVANST 203
                                    56789****************99765 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.8     1e+03      63     120 ..       7      65 ..       4      91 .. 0.73
   2 !   13.6   0.0   7.3e-05     0.041       5      22 ..     182     199 ..     179     262 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.8
                         AAA_24  63 ladyktlviDtideleelclaevirqnekaeskedkgdgkG.ygelaeefrrllkklqe 120
                                     +d++ +++D   +lee  la   ++++++ +k  + ++k  y + a+++r+ l++l+ 
  gi|116753771|ref|YP_842889.1|   7 GPDFSKYILDRMKQLEERNLALREQKDRAEGEKRLIENQKLkYEREARKLRSELERLRV 65 
                                    56888899999999999988888888888666655555565677777777777777765 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 7.3e-05
                         AAA_24   5 iliyGpsgiGKTtlakel 22 
                                    +l+yGp+g+GKT lak  
  gi|116753771|ref|YP_842889.1| 182 VLLYGPPGTGKTLLAKAV 199
                                    89*************987 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   3.2e-05     0.018      25      43 ..     182     200 ..     173     208 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.2e-05
                   Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                    +ll+GppG+GKt+lak+++
  gi|116753771|ref|YP_842889.1| 182 VLLYGPPGTGKTLLAKAVA 200
                                    89*************9875 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   5.7e-05     0.032       2      30 ..     182     210 ..     181     217 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.7e-05
                          AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                    vll g PG++ktll+ka+a++ +++f r+
  gi|116753771|ref|YP_842889.1| 182 VLLYGPPGTGKTLLAKAVANSTEATFLRV 210
                                    7999**********************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 ?   10.4   0.0   0.00082      0.46      16      45 ..     175     204 ..     165     223 .. 0.81
   2 ?    1.9   0.0      0.32   1.8e+02     112     139 ..     232     259 ..     224     277 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00082
                       ATPase_2  16 erepneiyfiYGpegsGKtaLlkeiienle 45 
                                      ep + +++YGp g GKt L k +++  e
  gi|116753771|ref|YP_842889.1| 175 GIEPPKGVLLYGPPGTGKTLLAKAVANSTE 204
                                    557777899**********99999988775 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.32
                       ATPase_2 112 kikkkgkkiiiiiDelqklidlglngae 139
                                    ++ k++   ii+iDel  +++  ++ga+
  gi|116753771|ref|YP_842889.1| 232 DLAKSRAPAIIFIDELDAIGSRRIDGAT 259
                                    455555668999****999988887654 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 ?   13.1   0.0   8.9e-05      0.05      33      59 ..     179     205 ..     167     220 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.9e-05
                          AAA_7  33 kkpvllvGptGtGKtviikdllkkldk 59 
                                     k vll+Gp GtGKt+++k + ++ + 
  gi|116753771|ref|YP_842889.1| 179 PKGVLLYGPPGTGKTLLAKAVANSTEA 205
                                    5789****************9998874 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   0.00014     0.078      21      51 ..     182     212 ..     171     256 .. 0.91
   2 ?   -2.4   0.1       5.9   3.3e+03      92     104 ..     357     369 ..     338     389 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00014
                         AAA_30  21 avltGpAGtGKttalkalreaweaaggrvig 51 
                                    ++l Gp+GtGKt + ka+++  ea   rv+g
  gi|116753771|ref|YP_842889.1| 182 VLLYGPPGTGKTLLAKAVANSTEATFLRVVG 212
                                    5789****************99999888876 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.9
                         AAA_30  92 livDEagmvdtkq 104
                                     iv Eagm ++++
  gi|116753771|ref|YP_842889.1| 357 AIVTEAGMSAIRE 369
                                    4777888876554 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.3      0.16        88     151     199 ..      23      83 ..       5      88 .. 0.54
   2 ?    9.4   0.0    0.0015      0.84      19      39 ..     181     201 ..     160     238 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.16
                         AAA_11 151 klkkskekskskleqerrklkkerkelskeleeaeesle............eevldeaeiv 199
                                    +++ + +++k+++e e+r +++++ ++++e ++ +++le             evlde++++
  gi|116753771|ref|YP_842889.1|  23 ERNLALREQKDRAEGEKRLIENQKLKYEREARKLRSELErlrvgpmivgtvVEVLDESRVI 83 
                                    2333334444444444444444444455555555555544444444677777777777776 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0015
                         AAA_11  19 itliqGPPGtgKTktivells 39 
                                     +l+ GPPGtgKT    ++ +
  gi|116753771|ref|YP_842889.1| 181 GVLLYGPPGTGKTLLAKAVAN 201
                                    4799*********65555544 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   6.1e-05     0.034       2      29 ..     182     209 ..     182     242 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.1e-05
                         AAA_33   2 vllvGlpGsGKstlaerllkklgavlls 29 
                                    vll G+pG+GK+ la+ +++ + a++l+
  gi|116753771|ref|YP_842889.1| 182 VLLYGPPGTGKTLLAKAVANSTEATFLR 209
                                    7899***************988866665 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00022      0.12      13      37 ..     169     197 ..     146     204 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00022
                         ATPase  13 k....gGipegrvvlitGepGtGKtifal 37 
                                    +     Gi   + vl++G pGtGKt++a+
  gi|116753771|ref|YP_842889.1| 169 ElfhaVGIEPPKGVLLYGPPGTGKTLLAK 197
                                    0444578888999**************97 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00019       0.1     117     138 ..     182     203 ..     177     210 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00019
                      Parvo_NS1 117 vwfyGpantGktnlaeaIakav 138
                                    v++yGp+ tGkt la+a a+ +
  gi|116753771|ref|YP_842889.1| 182 VLLYGPPGTGKTLLAKAVANST 203
                                    89****************9976 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00054       0.3       2      56 ..     182     237 ..     181     256 .. 0.85
   2 ?   -1.9   0.0       4.9   2.8e+03      66      92 ..     364     390 ..     344     395 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00054
                                    EEEE--TTSSHHHHHHHHHHHH...GGGEEEE.EEEEE-------EEEEEET.T-- CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgGf.yteevreggrrigFkivdlasge 56 
                                    v++ GppG+GKt l k v++  +   ++v G   ++++  +g r   ++ dla+ +
  gi|116753771|ref|YP_842889.1| 182 VLLYGPPGTGKTLLAKAVANSTEATFLRVVGSeFVQKYIGEGARLVRELFDLAKSR 237
                                    6788********************99999997357778899999999999997655 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.9
                                    --SSEETTEEE-HHHHHHHHHHHHHHH CS
                       NTPase_1  66 kreprvgkyvvdvesfeelalealrka 92 
                                     + +r ++ +v   +fe+ ++++l+ +
  gi|116753771|ref|YP_842889.1| 364 MSAIREERTQVLQRDFERAIAKVLQAE 390
                                    566677777777777777777777654 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00039      0.22      23      47 ..     180     204 ..     169     220 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00039
                                    S-EEEECSTTSSHHHHHHHHHHHST CS
                Sigma54_activat  23 lsvlitGesGtGKellaraiheask 47 
                                      vl+ G  GtGK+lla+a+ ++++
  gi|116753771|ref|YP_842889.1| 180 KGVLLYGPPGTGKTLLAKAVANSTE 204
                                    579****************987655 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   0.00032      0.18      20      48 ..     180     210 ..     153     227 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00032
                                    EEEEEEESTTSSHHHHHHHHHHHTT--..-- CS
                           TsaE  20 dvilLeGdLGaGKTtlvrglakalgve..ev 48 
                                    + +lL+G+ G+GKT l++++a++ + +  +v
  gi|116753771|ref|YP_842889.1| 180 KGVLLYGPPGTGKTLLAKAVANSTEATflRV 210
                                    349******************9988765544 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00067      0.38      36      54 ..     182     200 ..     149     218 .. 0.90
   2 ?   -2.8   0.0         7   3.9e+03     130     155 ..     227     251 ..     223     275 .. 0.70
   3 ?   -3.0   0.1       8.1   4.5e+03     116     139 ..     365     388 ..     344     391 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00067
                         AAA_25  36 allaGapgtGKttlaldla 54 
                                    +ll+G+pgtGKt la  +a
  gi|116753771|ref|YP_842889.1| 182 VLLYGPPGTGKTLLAKAVA 200
                                    69************97666 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 7
                         AAA_25 130 vdaleaaieevegvrlvviDplsral 155
                                    v++l + +++   ++ + iD l+++ 
  gi|116753771|ref|YP_842889.1| 227 VRELFDLAKS-RAPAIIFIDELDAIG 251
                                    5677777788.459999999988764 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 8.1
                         AAA_25 116 Lfakdrggtlltadvdaleaaiee 139
                                     +  + + ++l++d+++ +a++ +
  gi|116753771|ref|YP_842889.1| 365 SAIREERTQVLQRDFERAIAKVLQ 388
                                    344566667788888887777766 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00039      0.22      22      41 ..     182     201 ..     172     214 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00039
                                    EEEE--TTSSTTHHHHHHHH CS
                           PhoH  22 vfaiGpaGtGKtylavalav 41 
                                    v   Gp GtGKt+la a+a 
  gi|116753771|ref|YP_842889.1| 182 VLLYGPPGTGKTLLAKAVAN 201
                                    6789***********98874 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.4       3.2   1.8e+03     142     193 ..      28      83 ..      19      88 .. 0.63
   2 ?   10.3   0.0   0.00056      0.31      14      49 ..     177     210 ..     168     220 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 3.2
                     Zeta_toxin 142 dRyeeevae..gRlvpkeeh..deafeglresvealeeekqldrvkikdrdgktvl 193
                                     R++++ ae   Rl++ ++   ++  ++lr+++e+l +   ++ +++   d+++v+
  gi|116753771|ref|YP_842889.1|  28 LREQKDRAEgeKRLIENQKLkyEREARKLRSELERLRVGPMIVGTVVEVLDESRVI 83 
                                    45556533322599887654115778889999999988887777777666665555 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00056
                     Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrl 49 
                                    e Pk +ll G pG GK+ la+++++++  +  ++r+
  gi|116753771|ref|YP_842889.1| 177 EPPKGVLLYGPPGTGKTLLAKAVANST--EATFLRV 210
                                    56999*******************998..5555555 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00082      0.46      57      92 ..     183     221 ..     174     224 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00082
                                    EEEE-TTSSHHHHHHHHHH...HHSTTGGGSTTEEEEEH CS
                         Torsin  57 sfhGwtGtGknfvaeiiae...nlyrdGlrsdyvkkfva 92 
                                     ++G +GtGk  +a+ +a+   +++ + + s++v+k+++
  gi|116753771|ref|YP_842889.1| 183 LLYGPPGTGKTLLAKAVANsteATFLRVVGSEFVQKYIG 221
                                    5789*************9722257999999*******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       904  (0.0504211); expected 358.6 (0.02)
Passed bias filter:                      700  (0.0390429); expected 358.6 (0.02)
Passed Vit filter:                       127  (0.0070835); expected 17.9 (0.001)
Passed Fwd filter:                        33  (0.00184059); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              32  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.42
# Mc/sec: 2858.38
//
Query:       gi|116753772|ref|YP_842890.1|  [L=165]
Description: XRE family transcriptional regulator [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-05   24.6   2.4    3.1e-05   24.0   2.4    1.3  1  HTH_3     Helix-turn-helix
    0.00017   21.4   1.4    0.00043   20.1   1.4    1.7  1  HTH_25    Helix-turn-helix domain
     0.0003   20.8   4.0    0.00048   20.1   4.0    1.4  1  HTH_19    Helix-turn-helix domain
  ------ inclusion threshold ------
      0.026   14.8   0.0      0.034   14.4   0.0    1.2  1  DUF4443   Domain of unknown function (DUF4443)
      0.044   13.8   0.1      0.066   13.3   0.1    1.2  1  DZR       Double zinc ribbon
      0.062   13.7   0.0        0.1   13.0   0.0    1.4  1  HTH_31    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   2.4     1e-08   3.1e-05       1      54 [.      85     138 ..      85     138 .. 0.97

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1e-08
                                    HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEHHH CS
                          HTH_3   1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvslde 54 
                                    +k +R+  +ls+e+LA ++  + s +++iE+ e  P  ++ kkl+k L+++l+e
  gi|116753772|ref|YP_842890.1|  85 IKNARESMNLSLEDLALRIKEKASLLRKIEREELVPEDDVRKKLEKELKIKLTE 138
                                    899**********************************************99976 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   1.4   1.4e-07   0.00043       2      34 ..      85     117 ..      84     122 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.4e-07
                                    HHHHHHTTT--HHHHHHHSS--HHHHHHHHCT- CS
                         HTH_25   2 LraaRearglsleevaketkIrkdylealEedd 34 
                                     ++aRe+++lsle++a ++k ++++l+++E+++
  gi|116753772|ref|YP_842890.1|  85 IKNARESMNLSLEDLALRIKEKASLLRKIEREE 117
                                    589***************************986 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   4.0   1.6e-07   0.00048       1      58 [.      82     138 ..      82     145 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.6e-07
                         HTH_19   1 GerLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgidley 58 
                                    G  +k aRe  +l++e+la r++   s +++iE ++  vp+ ++ +k+ ++l+i l++
  gi|116753772|ref|YP_842890.1|  82 GNIIKNARESMNLSLEDLALRIKEKASLLRKIEREEL-VPEDDVRKKLEKELKIKLTE 138
                                    7789*****************************7766.67666668888889988775 PP

>> DUF4443  Domain of unknown function (DUF4443)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.1e-05     0.034       4      63 ..      69     125 ..      67     155 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.1e-05
                        DUF4443   4 ahfvgkvdgmpayaivvknppqfksielrdeairffakgamilivkngepvfpederplr 63 
                                     hf   v+ +p y  ++kn  +   + l d a+r+  k +++  ++    ++ped+   r
  gi|116753772|ref|YP_842890.1|  69 DHFRDLVEVVPDYGNIIKNARESMNLSLEDLALRIKEKASLLRKIERE-ELVPEDDV--R 125
                                    599999*****************************9999888777665.56677763..2 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   2.2e-05     0.066      11      42 ..       5      44 ..       2      49 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.2e-05
                            DZR 11 darfCseCgtklkavaa........edrCpsCgekvdpea 42
                                   ++r C+ Cg++++  ++         ++C sC +  +pe+
  gi|116753772|ref|YP_842890.1|  5 SDRQCEICGADISGSPErividgsvLEVCKSCARFGKPED 44
                                   6899*********9999***************98777766 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.4e-05       0.1       7      49 ..      86     127 ..      80     140 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.4e-05
                         HTH_31   7 ralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlea 49 
                                    + +Re  +Ls+e++A r+   +s l+++E+ +  +p  +v  +
  gi|116753772|ref|YP_842890.1|  86 KNARESMNLSLEDLALRIKEKASLLRKIEREEL-VPEDDVRKK 127
                                    679*****************************9.686665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1181  (0.0658709); expected 358.6 (0.02)
Passed bias filter:                      723  (0.0403257); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
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 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1184.79
//
Query:       gi|116753773|ref|YP_842891.1|  [L=198]
Description: Sua5/YciO/YrdC/YwlC family protein [Methanosaeta thermophila PT]
Scores for complete 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  164.1   0.0    2.6e-48  163.9   0.0    1.0  1  Sua5_yciO_yrdC  Telomere recombination


Domain annotation for each model (and alignments):
>> Sua5_yciO_yrdC  Telomere recombination
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.9   0.0   1.4e-52   2.6e-48       2     179 .]      15     186 ..      14     186 .. 0.96

  Alignments for each domain:
  == domain 1  score: 163.9 bits;  conditional E-value: 1.4e-52
                                    HHHTTSEEEEE-SSSEEEEEETTSHHHHHHHHHHHTSHCCC--EEEESSCCCCCCCC-TC--HHHHHHHHCT-SSSCEEE CS
                 Sua5_yciO_yrdC   2 alrkGgivaiptetvYgLacdatneeaverlreiKgrpsdkplavlvasledlkklaeseveeealkllerfwPGpitll 81 
                                    ++ +Ggiv++ptetvYg++++a +e+++ r+++iK+rp dkp+++ v+s+e+l ++a+  v  e l ++++++PGp+t+l
  gi|116753773|ref|YP_842891.1|  15 CILSGGIVVYPTETVYGIGANALDESSIVRVYAIKRRPLDKPISIAVSSFEMLCDVAH--VRPEDLDMMRKLLPGPVTFL 92 
                                    5789*****************************************************8..9999999************* PP

                                    EE..E-TS-HHHHTTTTEEEEEE-SSHHHHHHHHHCTS-EEEEES-STTS-S-SSHHHHHHHC-TTSECB-SS---SSS- CS
                 Sua5_yciO_yrdC  82 lkrskeklpkevapglktvGvrlPdtplarlLlealgeplvaTSanlsgepsitdaeeveeelgeivdlildggeiavgv 161
                                    +++ ++ +p+ +++g+  vGvr Pd+++a++L+e +g p+++TSan+ g p++ d++e++ e+ ++vd+++dgg+++ +v
  gi|116753773|ref|YP_842891.1|  93 VRK-RSIVPDMLTAGSPLVGVRYPDHEMALRLIEMTG-PITSTSANITGAPPPSDPKEIDPEILSRVDMLIDGGRCRYAV 170
                                    **6.444****************************98.****************************************** PP

                                    --EEEETTSSTSSECEXX CS
                 Sua5_yciO_yrdC 162 dstVvdltegkpkilRrG 179
                                    +st vdl+    +ilR G
  gi|116753773|ref|YP_842891.1| 171 PSTLVDLST--RRILRMG 186
                                    *******96..8999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       234  (0.0130515); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1440.01
//
Query:       gi|116753774|ref|YP_842892.1|  [L=311]
Description: DNA polymerase beta subunit [Methanosaeta thermophila PT]
Scores for 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   25.7   0.0    2.2e-05   24.7   0.0    1.6  1  NTP_transf_2  Nucleotidyltransferase domain
  ------ inclusion threshold ------
      0.038   14.1   0.0       0.06   13.4   0.0    1.3  1  Polbeta       Polymerase beta, Nucleotidyltransferase
       0.05   13.8   0.0      0.095   12.9   0.0    1.5  1  DUF2007       Putative prokaryotic signal transducing protein


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 !   24.7   0.0   3.7e-09   2.2e-05       3      67 ..     102     160 ..     100     186 .. 0.67

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 3.7e-09
                                    HHHHHHHHHTT.TSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECT CS
                   NTP_transf_2   3 klleelkelep.vakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleell 67 
                                    +++e+l+e       + ++GS   G++ + SDiDl+v+++++       +++++ + + k   ++ 
  gi|116753774|ref|YP_842892.1| 102 RIAEILEEHGIpERCIGITGSMLLGLHSRSSDIDLVVYGNAW-------WKARDVIADAKRSGSIQ 160
                                    567777776666777999***********************9.......44444444444444433 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     1e-05      0.06       3      42 ..     103     143 ..     101     173 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1e-05
                                    TTTTHHHHHHH..HSTTEEEEEE-S------EEEEEEEESS- CS
                        Polbeta   3 ikeilekekei..elaylFGSrakgkareeSDiDlavllkek 42 
                                    i eile++ +i  + + + GS++ g + ++SDiDl v+ +  
  gi|116753774|ref|YP_842892.1| 103 IAEILEEH-GIpeRCIGITGSMLLGLHSRSSDIDLVVYGNAW 143
                                    77888888.4433466789*******************9876 PP

>> DUF2007  Putative prokaryotic signal transducing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.6e-05     0.095      12      66 ..      99     153 ..      93     154 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.6e-05
                        DUF2007  12 eaelikslLeeagIeavvkdeftssileGalgelp.vrilVaeedleeAreileea 66 
                                    ++++i ++Lee+gI+ ++ +   +s+l G  +  + +++ V    + +Ar ++++a
  gi|116753774|ref|YP_842892.1|  99 RVGRIAEILEEHGIPERCIGIT-GSMLLGLHSRSSdIDLVVYGNAWWKARDVIADA 153
                                    6899***************995.9999999544447****************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); 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: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2200.02
//
Query:       gi|116753775|ref|YP_842893.1|  [L=512]
Description: thymidine phosphorylase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-12   47.0   1.4    1.5e-11   44.4   1.4    1.9  1  Glycos_transf_3  Glycosyl transferase family, a/b domain
      4e-11   42.6   0.1    1.6e-10   40.7   0.0    2.1  2  Glycos_trans_3N  Glycosyl transferase family, helical bundle 
    3.5e-09   36.2   0.0    7.1e-09   35.2   0.0    1.5  1  PYNP_C           Pyrimidine nucleoside phosphorylase C-termin
    1.6e-05   24.9   0.0    3.5e-05   23.8   0.0    1.5  1  Molydop_binding  Molydopterin dinucleotide binding domain
     0.0031   16.4   0.0     0.0049   15.8   0.0    1.2  1  DUF2254          Predicted membrane protein (DUF2254)


Domain annotation for each model (and alignments):
>> Glycos_transf_3  Glycosyl transferase family, a/b domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   1.4   4.3e-15   1.5e-11       3     252 ..     157     384 ..     155     385 .. 0.91

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 4.3e-15
                                    TBEEEEESS-SSSTHHHHHHHHHHHHHHTT-BEEEEE-STCTTCS-HHHHHCTST--ST--HHHHHHHHHHHSEEEE..E CS
                Glycos_transf_3   3 dlvDivgTGGdgantfNiStaaaivvAaaGvkvakhgnrsvssksGsaDvLealgvnleltpeeveklleevgvgfl..f 80 
                                    ++vD+++ GG+  n   +S    ++vAa G+ ++k + r+++  +G+aD++e l   +e t++e++++ e+vg ++   +
  gi|116753775|ref|YP_842893.1| 157 PVVDKHSIGGVPGNK--VSMLVVPIVAASGLLIPKTSSRAITGAGGTADLMEVL-APVEFTADEIKEITETVGGVIAwgG 233
                                    79***********99..9**********************************99.589*************996665226 PP

                                    HHSSSSHHHHHHHHHHHHTT.-SSHHHCHHHHHT..SEEEEHHHHHHHHTCHSEEEEEEEESTTSSCCSTSHHHHHHHHH CS
                Glycos_transf_3  81 apeyhkamkhvapvrrelgirTvfnlLGPLinparvkkqllgvyskelaeklaevlkelgveralvvhgdGldevsllak 160
                                    a++  +a +  +++  +l i            p   ++ l ++++k+ a ++++v+ +++++ +  +++   +++++lak
  gi|116753775|ref|YP_842893.1| 234 ATNIAPADDRLIKAEYALAI-----------DP--YSQMLASIMAKKGAVGADAVVVDMPTGPGTKLET--PEKARVLAK 298
                                    88888888888888888877...........55..5666889***************************..********* PP

                                    HHHHHHH.TTEEEEEEEEEGSSTSSSEEESHHHHSSHHHHHHHHTTHHTSCHHHHHHHHHHHHHHHHHHHTTSSSSHHHH CS
                Glycos_transf_3 161 ttvaelk.dgeiteytlepedfglkraelealeggepkenaeilkavlegkksaakrdlvllnagaalvlagkadslkeg 239
                                     +    +  g + e +++    +++r  + ale+   +e++++l+   eg++s   r+  l++ag +l + g +    eg
  gi|116753775|ref|YP_842893.1| 299 DLTDLGErLGIRVECAMTFGGSPVGRTVGPALEV---REALKMLETG-EGPNSL--REKSLALAGILLEMGG-VAARGEG 371
                                    ***999999*************************...9******987.788887..8999999999999888.89999** PP

                                    HHHHHHHHHTSHH CS
                Glycos_transf_3 240 vakaeevidsGkA 252
                                     + aee++ sGkA
  gi|116753775|ref|YP_842893.1| 372 YRAAEEILVSGKA 384
                                    ************9 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 !   40.7   0.0   4.4e-14   1.6e-10       2      63 .]      87     148 ..      86     148 .. 0.97
   2 ?   -1.8   0.1      0.81   2.9e+03      12      21 ..     212     221 ..     206     225 .. 0.74

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 4.4e-14
                                    HHHHHHHTT.---HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH---HHHHHHHHHHHHHHS CS
                Glycos_trans_3N   2 diikklrdgeeLtaeeirfaihgilkgevtdaqiaAfLmAlrlkGetaeEiaalaeAmresg 63 
                                    ++ik l+d+++L++++ir ++++i+ +++++++++A  +A ++  ++++E+  l++Am+e g
  gi|116753775|ref|YP_842893.1|  87 SYIKMLMDRQKLSEDQIRSIVRDIVYNNLSEIELSAYITASYIHNLDPQETEWLTRAMIETG 148
                                    69********************************************************9976 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.81
                                    ---HHHHHHH CS
                Glycos_trans_3N  12 eLtaeeirfa 21 
                                    e+ta+ei+++
  gi|116753775|ref|YP_842893.1| 212 EFTADEIKEI 221
                                    7888888876 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 !   35.2   0.0     2e-12   7.1e-09       1      67 [.     422     481 ..     422     486 .. 0.91

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 2e-12
                                    EEEEE-HHHHHHHHHHTTTSBSSTTS---TT-EEEES--TT-EEBTTSEEEEEEESSSCHHHHHHHH CS
                         PYNP_C   1 yvseidareiGlaaveLGAGRakkeDpidlavGielhkklGdkVkkGeplatiYankeekleeavkk 67 
                                    yv ++ +++i  +a+++GA       p d+++G+ +hkk+G+ VkkGepl+ti +++ ++le avk 
  gi|116753775|ref|YP_842893.1| 422 YVVAFYNKRIIEIARAAGA-------PGDKRAGVIIHKKMGEIVKKGEPLLTICSSTDWELECAVKM 481
                                    5677788999999******.......*********************************99999886 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   9.8e-09   3.5e-05      31      75 ..      15      60 ..      10      78 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 9.8e-09
                                   EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESS.B-TTEEE CS
                Molydop_binding 31 vveinpedAaalGikdGdlVevesrrGsvevrakvter.vrpGvvf 75
                                    v++n +dA+a+G++ Gd+V+v++r  s+++   vt + + +G+v 
  gi|116753775|ref|YP_842893.1| 15 KVMLNIADARAMGLNPGDRVRVRTRGASLTAILDVTGQmIGQGQVG 60
                                   599******************************9998856777765 PP

>> DUF2254  Predicted membrane protein (DUF2254)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.4e-06    0.0049     185     245 ..     405     471 ..     377     490 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.4e-06
                        DUF2254 185 eeseeeeatpiraersGylqaidveaLvklaeehd......lvielevrpGdfvvkgeplakvwgee 245
                                    + +  e +++i ++++Gy+ a + ++++++a++++      + + +++++G+ v kgepl+++ + +
  gi|116753775|ref|YP_842893.1| 405 DIQIGEHQKQILSPTNGYVVAFYNKRIIEIARAAGapgdkrAGVIIHKKMGEIVKKGEPLLTICSST 471
                                    3456778999*********************987522222268*******************98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (512 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); 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: 00:00:00.41
# Mc/sec: 3743.63
//
Query:       gi|116753776|ref|YP_842894.1|  [L=284]
Description: histone deacetylase superfamily protein [Methanosaeta thermophila PT]
Scores for complete 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-39  136.4   0.2      3e-38  132.0   0.2    2.0  2  Hist_deacetyl  Histone deacetylase domain


Domain annotation for each model (and alignments):
>> Hist_deacetyl  Histone deacetylase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    1.8   0.0    0.0073   1.3e+02       7      52 ..      25      70 ..      21      73 .. 0.80
   2 !  132.0   0.2   1.7e-42     3e-38      88     306 ..      75     277 ..      71     278 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.0073
                                   HHHHHHHHHHHT.THHHHCCE..EE-----HHHHTTTS-HHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Hist_deacetyl  7 Rlsaileslaesvglldelel.liqpseatkeellkvHskeYlelle 52
                                   R++   ++l +s gl+d +e+ +++p++a  e ++++H+++++++++
  gi|116753776|ref|YP_842894.1| 25 RIRPSFDALMNS-GLVDGVEVqVFRPQPAPVELVAEAHTENHMQNMR 70
                                   666667788887.8888777668899999999**********99876 PP

  == domain 2  score: 132.0 bits;  conditional E-value: 1.7e-42
                                    CHHHHHHHHHHHHHHHHHHTTSSSEEEETTSS--TT-BTTB-BTTBSS-HHHHHHHHHHHCC-SS-EEEEE-SSS--HHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Hist_deacetyl  88 lkaallavgavleavdavlsgsvkaafvlvrPpgHHakaseasGFClvNnvaiaikylqakhelkrvailDvDvHhGnGt 167
                                    +++all++g+vl+a+++v+sg++++af+    +gHHa ++ + GFC++N+vai+i +l++  +lkr++i+DvD H+G+Gt
  gi|116753776|ref|YP_842894.1|  75 WNVALLSAGSVLMAAELVVSGKAESAFAYTGTAGHHASRGSCWGFCYFNDVAITILKLRK-MGLKRFLIIDVDPHFGDGT 153
                                    789********************************************************9.99***************** PP

                                    HHHCTT-TTEEEEEEEE-CCTSTTSS--TT---SGGGTTSEEEEEE-TT-BHHHHHHHHHHCHHHHHCCH--SEEEEEE- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Hist_deacetyl 168 eeafysdpdvltlSiHryegifyPgtgaledlgegkgkgfnlnvpleegtgdeeylkvfeeilrpvleefkPdlilvsaG 247
                                     ++f +dpdv+++ +H          g++++      + +n  + +  + +de++l+ +e++l +++e f+ ++  v  G
  gi|116753776|ref|YP_842894.1| 154 RDFFGNDPDVFHINFHS---------GSQKEFD---HERNNYDFGIGWNANDETFLREMENAL-KLAEGFDYEVCFVIFG 220
                                    ****************9.........7777774...4457788888888999*********99.888************* PP

                                    STTBTTSTT-S-BB-HHHHHHHHHHHCCCHGS-G.EEEEE-S---HHHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Hist_deacetyl 248 fDalkgdplgelnlsvegykeltkklaeladkvkkvvllleGGYnlealaravtavlsa 306
                                     D++ +  +g+++l+ + y ++ +++++  d   ++v++l GG n++ ++ra+  v+++
  gi|116753776|ref|YP_842894.1| 221 HDSHTD-DYGGFDLTLNAYPKMASMIKKAVDGK-PLVFVLSGGSNPDVARRAIPDVIAV 277
                                    ***975.5799*******************954.****************999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        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 0.28s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 2006.02
//
Query:       gi|116753777|ref|YP_842895.1|  [L=284]
Description: hypothetical protein Mthe_0464 [Methanosaeta thermophila PT]
Scores for 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-37  126.9   0.0    2.6e-36  125.3   0.0    1.7  1  DUF89     Protein of unknown function DUF89
     0.0095   16.0   0.0      0.024   14.7   0.0    1.7  1  MetOD2    Metanogen output domain 2


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 !  125.3   0.0   2.9e-40   2.6e-36       2     351 ..       2     277 ..       1     279 [. 0.88

  Alignments for each domain:
  == domain 1  score: 125.3 bits;  conditional E-value: 2.9e-40
                                    HHTHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHCTTCGHHH-HHHHT-BTTBSBHHHHHHHHHHHHHHHHT CS
                          DUF89   2 leerlpciltqviddlekakdekeeelkkiieelselkeelqtdkpltpledeeekrswfnapwlfaecylyrrllelfg 81 
                                    +  ++ cil+++  ++e  +   e+++ +++e l ++++e+  d p t                    ++    l+++ g
  gi|116753777|ref|YP_842895.1|   2 ASSCYICILERAGFECELLSLP-EDRRLELVEGLLQFMAEHMRDVPATVG------------------TEREIMLKRISG 62 
                                    5689999999999999997777.789999999999999888887777777..................555667888888 PP

                                    HSGGGTTS-TTHHHHHHHHHHHHHHHHHHHHHHHHCCSHHHHHHHHHHHHHHHCG--CCCHTSHHCHHHHHHHHHHHHHH CS
                          DUF89  82 lskelknyDpFkeqKeesnksalkaveelakrleeledekelfkellkislwGNaiDlsllateediqkdqeeearkale 161
                                            Dp++++Keesn+ a+++++  ++ ++ +ed+   +++l++i+ + N + +++++  +++ + + +++ +++ 
  gi|116753777|ref|YP_842895.1|  63 ------VADPYSKLKEESNDVARELLPVAERFYDLSEDK---MEALVRIAAAANSMEFGVRG--HEFDNRSFSSVFEDTL 131
                                    ......99******************************9...********************..8888888888888888 PP

                                    CTESEE-HHHHHHHHCTCHTSEEEEE--BTTHHHHHHHHHHHHHHHCTTTSEEEEEEBSS--TTTB-BHHHHHHHHHHHH CS
                          DUF89 162 knilvddleklweklkkkkakrvdivlDNaGfElvfDlllaeeLlesglatkVvlhvkaiPwfvsDvtpeDfewlleqla 241
                                    ++ lv dl++l + l   +++r+++++DNaG E+vfDl+++e+L+e  ++++V++ +ka P +++Dvt +++e       
  gi|116753777|ref|YP_842895.1| 132 REDLVGDLDALKKLL--ARSSRIFYLTDNAG-EVVFDLFVMEKLRE--MGKRVIIGPKAEP-VLNDVTADELE------- 198
                                    8889***********..**************.**************..*************.***********....... PP

                                    -TTTSHHHHCHTTHHHHHHTSEEEEESSCGGSSS--CCGSSSHHHHHHH.HHC-SEEEEEHHHHHHHHTTSCTTTTTSEH CS
                          DUF89 242 dsksfelsalgagldellkegklvlrgssfwttglsysempeapelyee.lekadLvifKGdlNyrkLtgdrkwppttpf 320
                                                g++     +++v +g     +g+s++++  +pe ++  ++   Lvi+KG++N++++++ +++ +    
  gi|116753777|ref|YP_842895.1| 199 ------------GMTD----AEIVPTGGV---VGISLDRI--NPEARRLlFDPEWLVIAKGMGNFETISEFEEALR---- 253
                                    ............6666....889999877...9*******..5555555055788*************98888875.... PP

                                    HHHTGTSS--EEEEEE--SHHHHHHH.STTTH CS
                          DUF89 321 ttalgfspvpvlaLrtvKadvvagll.egege 351
                                             ++++++++K+++va+   +++g+
  gi|116753777|ref|YP_842895.1| 254 --------GRLIYIFRAKCEPVARANcVRQGS 277
                                    ........78*************998777775 PP

>> MetOD2  Metanogen output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   2.7e-06     0.024      25      79 ..      67     122 ..      49     130 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.7e-06
                         MetOD2  25 YarLa.ksvevnkrllslLsqtydidddkaevseeieaalknlekkleaqeerlkq 79 
                                    Y +L   s +v + ll + ++ yd+++dk+e+   i aa  ++e +++ +e + + 
  gi|116753777|ref|YP_842895.1|  67 YSKLKeESNDVARELLPVAERFYDLSEDKMEALVRIAAAANSMEFGVRGHEFDNRS 122
                                    6666515789*************************************999977665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2020.21
//
Query:       gi|116753778|ref|YP_842896.1|  [L=245]
Description: hypothetical protein Mthe_0465 [Methanosaeta thermophila PT]
Scores for 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-31  107.6   0.2    1.1e-30  107.3   0.2    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 !  107.3   0.2   5.9e-35   1.1e-30       2     210 ..      27     230 ..      26     231 .. 0.89

  Alignments for each domain:
  == domain 1  score: 107.3 bits;  conditional E-value: 5.9e-35
                                    EEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETT.EEE-SEEEEEETTT.SEEEEEEEE-HSCH CS
                           PAC2   2 ilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveeg.relepprlyakdsgsrdllvlqgrepilq 80 
                                    ++ fpgiG+Vg++avd+Li+ ++ + + ++  ++ +p     p+vl+++g  +l  + ++ +++g +d+l+l++ +++l 
  gi|116753778|ref|YP_842896.1|  27 VVSFPGIGSVGKVAVDYLISCTNSRMIMTLPFSG-FP-----PQVLIQDGvARLFTVDVF-SPEGREDILLLTSDAQPLE 99 
                                    788*******************************.**.....********7766666665.57789********666655 PP

                                    HH...HHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHHHCT.....-CEEEEHHHHHHHH CS
                           PAC2  81 ye...efakalldwaeelgvkevvvLggldageradvphtrpekvtgaatdeelleelees.....eyggivgitglLls 152
                                         ++a ++l+ ++e++v+ vv+L+++            +e v g+atd + +e l+++     + ++i+g++g++ +
  gi|116753778|ref|YP_842896.1| 100 VLgmnRLAGEILSDMREMDVRDVVTLAAYV----GA----VHENVVGTATDADGVELLKSAgiavmPSSIIGGMNGIIAG 171
                                    555588************************....53....456899*********99974457789************** PP

                                    HHHHTT-EEEEEEEEEECCC.--HHHHHHHHHHHHHHHT---HCHHHHHHHHHHHHHHH CS
                           PAC2 153 aakergipavgllaevphyl.pdPkaaaalleflskllglevdtedLeedaeeleeqle 210
                                    +a  +g+ + ++l+ ++++  +d +aa+ ll  +++ll++e+d+++Le + ee +e++e
  gi|116753778|ref|YP_842896.1| 172 MAPLYGLRGFCILGTTSGERlVDLNAARNLLLSIKNLLQMEIDVSQLEIEEEEEAEEIE 230
                                    ******************8669*************************999999888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 1778.30
//
Query:       gi|116753779|ref|YP_842897.1|  [L=192]
Description: hypothetical protein Mthe_0466 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       445  (0.0248201); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1378.22
//
Query:       gi|116753780|ref|YP_842898.1|  [L=383]
Description: radical SAM domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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   56.3   0.0    4.2e-14   53.3   0.0    2.2  2  Radical_SAM  Radical SAM superfamily
      6e-07   29.9   2.0    1.4e-06   28.7   2.0    1.7  1  SPASM        Iron-sulfur cluster-binding domain
     0.0023   18.2   0.0      0.006   16.9   0.0    1.8  1  Fer4_12      4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.064   13.4   0.8       0.13   12.4   0.0    1.9  2  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.3   0.0   9.3e-18   4.2e-14       1     150 [.      11     154 ..      11     171 .. 0.82
   2 ?    0.4   0.0      0.17   7.4e+02       3      20 ..     309     328 ..     308     378 .. 0.71

  Alignments for each domain:
  == domain 1  score: 53.3 bits;  conditional E-value: 9.3e-18
                                    EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHH.HHTTSEEEEEESSTGGGS......TTHHHHHHHHHHT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxx RF
                    Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelk.aekgvkevilgggeplly......pdfvellerlakl 73 
                                    +++t gC+ +Cs+C+ +e     + + ++s++ ++e+v++lk ++++  +++++ggepll       + +  l++ l++l
  gi|116753780|ref|YP_842898.1|  11 IIPTLGCPSKCSYCWSSE-----EGSPVMSIDTVKEIVEWLKlFRDDPVTFTFHGGEPLLAgvefyrKALPLLADGLSHL 85 
                                    57999************6.....788888888888888888877777*************75555555555555555555 PP

                                    CCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  74 avpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdriv 150
                                         ++++ tn  ++++e +e l+e+    +  +l+ + +  + +l +  + +++++++  ++r++g+   v +i 
  gi|116753780|ref|YP_842898.1|  86 ---TPSFALQTNLWRLTPELAEVLKEYD-VPIGSSLDGPKE--INDLQRSEGYYDRTMRGYGIARDHGLS--VQFIC 154
                                    ...9************************.999999999999..677777889***************998..33333 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.17
                                    EESEESS--TTTSCCTT..H CS
                                    xxxxxxxxxxxxxxxxx..x RF
                    Radical_SAM   3 vtrgCnlrCsfCarpet..v 20 
                                    ++r C+++C++ a+++t  +
  gi|116753780|ref|YP_842898.1| 309 HLRYCRGGCPYNAISHTdgE 328
                                    5789******9888876442 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   2.0   3.2e-10   1.4e-06       4      67 ..     246     307 ..     240     315 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 3.2e-10
                          SPASM   4 psrslfInsdGdVvpCcvdkktyvee.lklGnirees.leeIwnseeyqefrkskkfplielCrnC 67 
                                    + +++++ +dG ++pC   ++ +  + +++G++r+++ ++++ +se+ +++  ++++  +  Cr+C
  gi|116753780|ref|YP_842898.1| 246 MDNTFAVGPDGSIYPC---YRFVGMPdYVMGDVRDHPsMDDLKRSEAWRRMN-RFRECVEVHCRKC 307
                                    68899***********...44555558******9998699999***999966.3434444559999 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.3e-06     0.006      12      65 ..      14      65 ..       4     130 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.3e-06
                        Fer4_12 12 vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPll 65
                                   + gC+ +C++C   e  s+  + ++ ke+ e  ++ +  +    +t+ GGEPll
  gi|116753780|ref|YP_842898.1| 14 TLGCPSKCSYCWSSEEGSPVMSIDTVKEIVEW-LKLF-RDDPVTFTFHGGEPLL 65
                                   569*******9988887777777777666544.4455.4555789********9 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.8e-05      0.13       6      60 ..      15      65 ..      10      75 .. 0.72
   2 ?   -2.7   0.6       1.4   6.1e+03       9      16 ..     301     308 ..     294     358 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.8e-05
                        Fer4_14  6 sgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLh 60
                                    gC+ +C  C  +e    e  ++ + +++++i++ lk  + ++   ++ GGePL+
  gi|116753780|ref|YP_842898.1| 15 LGCPSKCSYCWSSE----EGSPVMSIDTVKEIVEWLKLFRDDPVTFTFHGGEPLL 65
                                   69********9999....45555555555555555555555555799*******5 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.4
                        Fer4_14   9 nlsCkgCd 16 
                                    +++C+ C 
  gi|116753780|ref|YP_842898.1| 301 EVHCRKCR 308
                                    46666553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); 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: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 2635.51
//
Query:       gi|116753781|ref|YP_842899.1|  [L=528]
Description: Na+/solute symporter [Methanosaeta thermophila PT]
Scores for complete 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-59  200.6  40.4    4.9e-59  200.2  40.4    1.2  1  SSF            Sodium:solute symporter family
  ------ inclusion threshold ------
        0.2   11.5   0.0       0.36   10.7   0.0    1.3  1  LapD_MoxY_N    LapD/MoxY periplasmic domain
       0.42   10.5   2.3        1.4    8.8   0.3    2.8  2  Herpes_US9     Alphaherpesvirus tegument protein US9


Domain annotation for each model (and alignments):
>> SSF  Sodium:solute symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.2  40.4   8.3e-63   4.9e-59       1     406 []      34     451 ..      34     451 .. 0.86

  Alignments for each domain:
  == domain 1  score: 200.2 bits;  conditional E-value: 8.3e-63
                            SSF   1 yflagrsltgfvlglslaasnisaasfvGlaGavaasGlavvllel.galllvlllllllaerlr....nagalTlpdyl 75 
                                    y++agr++ ++ +++s +a+ is + +vG  G++ + G++ ++l + ++ +++ +++++ ++r r    n+ga+Tlp+++
  gi|116753781|ref|YP_842899.1|  34 YMVAGRKIHPYIMAMSYGATFISTSAIVGFGGMAGLFGMGLLWLTFlNIFVGIFIAFIIYGKRTRrmgyNLGAMTLPELM 113
                                    99*****************************************99626667777777788888889************** PP

                            SSF  76 skRfkgkrilvylsalslllvitlklsvdlvggaklielalGlnyetavlllaaltalYtviGGllAvvytdtiqavlml 155
                                      Rf+++  + ++s l+++l + l+ sv l+g+a+++e++l++++++a+l+  +++a Y+v GGl  v+ytd +q+++m 
  gi|116753781|ref|YP_842899.1| 114 GRRFDSQF-IQWFSGLVIFLGMPLYASVVLIGAARFMETTLSIDFNLALLIYSLIIAAYVVWGGLKGVMYTDAMQGTVMF 192
                                    *******9.99********************************************************************* PP

                            SSF 156 vgalilliivllevGgleslveklkeaapkvvdl...........ltpdslkllrdpltalslwlglvlGvaglphilvR 224
                                    +g ++lli++ l++Gg+ ++ + l+ +a+ v +            + + +       +++ +  lg+++Gv  +p  +vR
  gi|116753781|ref|YP_842899.1| 193 LGMIFLLIMTYLHLGGVTAAHQALTDMANLVPQSlaaqghrgwtsMPALGSAWWWTLVSTVV--LGVGIGVLAMPQLAVR 270
                                    ***********************999999885552455555544333334333444444444..4778888888****** PP

                            SSF 225 flaakdakailkgvlkltivlilvligmisiilfaiklagavp...kavgt.evgvsniaypeLvvkllpnllaGlllav 300
                                    f+++ +++++ +gvl++  v+il + g ++  ++a + ++++    k++++ + g+++ ++p  +++ +p+++  l++  
  gi|116753781|ref|YP_842899.1| 271 FMTVRSGRELNRGVLIGG-VFILAMTG-VAFDVGALSNVFFHAtqgKIAIEvAKGNADSIIPVYINAAMPEWFVYLFMLT 348
                                    ****************95.66666776.55555555555555445766665156899*********************** PP

                            SSF 301 mlAaimstltslllsassaftkDlYkkirrkasakekelvgvsriivlvvislaillavqeeqkgvlklvelafaglasa 380
                                     lAa mst +s++ +  +a+ +D+Y+ +  k+  +   lv ++ iiv vvi++++   + +e+  ++   ++ f+  a+a
  gi|116753781|ref|YP_842899.1| 349 LLAAAMSTSSSQFHAQGTAIGRDIYETLTGKK-GTGSILVTRAGIIVAVVIAVVLGY-ILPENI-IARGTSIFFGLCAAA 425
                                    *****************************999.788888888888888888776554.445666.899999999****** PP

                            SSF 381 vlavillalfwkrvneqGAlagliiG 406
                                    +l++   alfw r+++ GA+agl++G
  gi|116753781|ref|YP_842899.1| 426 FLPMYTCALFWRRATRAGAIAGLVTG 451
                                    ***********************998 PP

>> LapD_MoxY_N  LapD/MoxY periplasmic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0     6e-05      0.36      45      93 ..     293     349 ..     288     362 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 6e-05
                                    HHHHHHHHHS-ESEEEEEETT--EEEEEE------........-S-HHHHHHH--S- CS
                    LapD_MoxY_N  45 llinalfDsgyyssirltdldgkvlverenetkie........gvPqWFirlvplea 93 
                                     +  + fD g  s++ +++++gk  +e  + +  +        + P+WF+ l+ l  
  gi|116753781|ref|YP_842899.1| 293 AMTGVAFDVGALSNVFFHATQGKIAIEVAKGNADSiipvyinaAMPEWFVYLFMLTL 349
                                    567789*********************9999999677788888*******9998865 PP

>> Herpes_US9  Alphaherpesvirus tegument protein US9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.3   0.00024       1.4      40      59 ..     288     307 ..     273     309 .. 0.80
   2 ?   -0.5   0.1       0.2   1.2e+03      40      57 ..     390     406 ..     368     408 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00024
                     Herpes_US9  40 ivllvAvlsaaFalGallsq 59 
                                     v+++A+++ aF +Gal   
  gi|116753781|ref|YP_842899.1| 288 GVFILAMTGVAFDVGALSNV 307
                                    49**************9765 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.2
                     Herpes_US9  40 ivllvAvlsaaFalGall 57 
                                    + ++vAv+ a   lG++l
  gi|116753781|ref|YP_842899.1| 390 AGIIVAVVIAVV-LGYIL 406
                                    556777777766.88876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (528 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1097  (0.0611858); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.70u 0.32s 00:00:01.02 Elapsed: 00:00:00.50
# Mc/sec: 3197.99
//
Query:       gi|116753782|ref|YP_842900.1|  [L=62]
Description: hypothetical protein Mthe_0469 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       880  (0.0490825); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); 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: 0.36u 0.28s 00:00:00.64 Elapsed: 00:00:00.87
# Mc/sec: 215.29
//
Query:       gi|116753783|ref|YP_842901.1|  [L=467]
Description: replication factor C large subunit [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-15   58.1   0.1      4e-14   53.2   0.0    2.6  2  AAA              ATPase family associated with various cellul
    2.5e-06   27.3   0.0    5.3e-06   26.3   0.0    1.5  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    5.1e-06   26.7   0.5    1.5e-05   25.2   0.1    2.1  2  AAA_assoc_2      AAA C-terminal domain
    5.6e-06   26.7   0.1       0.05   13.9   0.0    3.6  4  AAA_22           AAA domain
    3.6e-05   24.2   0.8    0.00046   20.6   0.0    2.8  2  AAA_16           AAA ATPase domain
    5.1e-05   23.3   0.0    8.9e-05   22.5   0.0    1.4  1  Rad17            Rad17 P-loop domain
    0.00046   20.2   0.0       0.01   15.8   0.0    2.4  2  AAA_5            AAA domain (dynein-related subfamily)
    0.00055   19.7   0.1     0.0024   17.6   0.0    2.1  2  AAA_30           AAA domain
     0.0021   17.7   0.1      0.017   14.7   0.0    2.4  2  AAA_25           AAA domain
     0.0025   17.6   0.0     0.0071   16.1   0.0    1.8  1  IstB_IS21        IstB-like ATP binding protein
     0.0032   17.5   0.0     0.0079   16.2   0.0    1.7  1  AAA_14           AAA domain
     0.0052   16.0   0.0     0.0088   15.3   0.0    1.3  1  TIP49            TIP49 P-loop domain
     0.0085   16.3   0.0      0.015   15.4   0.0    1.4  1  RFC1             Replication factor RFC1 C terminal domain
  ------ inclusion threshold ------
      0.012   15.4   0.0        1.4    8.7   0.0    2.3  2  DNA_pol3_delta2  DNA polymerase III, delta subunit
      0.012   16.1   0.0          1   10.0   0.0    2.7  2  TipAS            TipAS antibiotic-recognition domain
      0.021   15.4   0.0      0.059   13.9   0.0    1.8  1  AAA_18           AAA domain
      0.027   14.9   0.0      0.052   13.9   0.0    1.5  1  RNA_helicase     RNA helicase
      0.065   12.9   0.0       0.12   12.1   0.0    1.4  1  AAA_24           AAA domain
      0.087   12.9   0.0        1.5    8.9   0.0    2.4  2  AAA_2            AAA domain (Cdc48 subfamily)
       0.11   12.3   0.1        0.3   10.8   0.0    1.8  2  AAA_11           AAA domain
       0.11   12.9   0.2        0.8   10.1   0.0    2.5  3  AAA_17           AAA domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.2   0.0   4.6e-17     4e-14       1     126 [.      43     153 ..      43     159 .. 0.86
   2 ?    2.0   0.1      0.31   2.7e+02      17      65 ..     383     428 ..     347     455 .. 0.75

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 4.6e-17
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS....TSEEEEEETGGGHHHHHTT CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakeka....kpsilfiDEidalaksrsg 76 
                                    ++lyGppG+GKT++a a+a+e++ +++e+++s+ +      +++ i+ +   a++ +    +   +++DE+d+l+++   
  gi|116753783|ref|YP_842901.1|  43 LILYGPPGVGKTSAALALASEMDWDYIELNASDQR------TAEIIKSIAGPASQVStfsgRRRLVILDEADNLHGTY-- 114
                                    58*********************************......55555666555555555556669***********999.. PP

                                    CCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSE CS
                            AAA  77 seseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdr 126
                                         ++  ++++l+++++ ++      vi+++n++ +++++l+ + +  
  gi|116753783|ref|YP_842901.1| 115 -----DRGGAAAILRVIKNATQ-----PVILIANEYYNIEKPLR-DACRG 153
                                    .....88999***********9.....69999***********9.77765 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.31
                                    HHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS.TSEEEEEE CS
                            AAA  17 avakelgvefleisgsellskyvgesekkirelfkeakeka.kpsilfiD 65 
                                    ava +lg ++ ei + +      + + kk+++lf++a++   +  i +iD
  gi|116753783|ref|YP_842901.1| 383 AVAASLGLNIEEIALLTGS----SPTTKKVQKLFEDAQKIIeAEQIAMID 428
                                    5666666666666655555....678999999999998876444777777 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 !   26.3   0.0   6.2e-09   5.3e-06       2      60 ..       9      67 ..       8      94 .. 0.92

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 6.2e-09
                         RuvB_N  2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvk 60
                                   rPk+l+  +g +k  ++l+    a +k + ++  ++lyGpPG+Gkt+ a  +a+e++ +
  gi|116753783|ref|YP_842901.1|  9 RPKNLDGILGNAKAVSELRAWAMAWEKGRPEVKCLILYGPPGVGKTSAALALASEMDWD 67
                                   9********************99999999999************************865 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 !   25.2   0.1   1.8e-08   1.5e-05       4      46 ..     176     219 ..     173     246 .. 0.80
   2 ?   -2.4   0.0       7.3   6.2e+03      55      55 ..     427     427 ..     388     463 .. 0.55

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.8e-08
                                    .XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXX CS
                    AAA_assoc_2   4 klkleddalealaeladGDaRkaLnlLElaaeaaeak.egkiei 46 
                                     +++e++a+ ++a++++GD R+a+n LE+aa+  ++   +++  
  gi|116753783|ref|YP_842901.1| 176 GIECEPEAVMHIAAMSGGDLRSAINDLEAAARGLKHLrLEDVAT 219
                                    6899**************************99887644333333 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 7.3
                                    X CS
                    AAA_assoc_2  55 l 55 
                                    +
  gi|116753783|ref|YP_842901.1| 427 I 427
                                    2 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   5.8e-05      0.05       6      30 ..      41      65 ..      39      86 .. 0.79
   2 !    8.3   0.0     0.003       2.6      90     117 ..      93     128 ..      68     145 .. 0.65
   3 ?   -0.7   0.0       1.8   1.6e+03      38      64 ..     240     266 ..     160     284 .. 0.70
   4 ?   -1.7   0.0       3.8   3.3e+03      70      87 ..     392     420 ..     334     435 .. 0.47

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.8e-05
                         AAA_22  6 gilvvtGesGtGKTtllrrlleqld 30
                                   ++l+++G++G+GKT  +  l+++ d
  gi|116753783|ref|YP_842901.1| 41 KCLILYGPPGVGKTSAALALASEMD 65
                                   699**************99998864 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.003
                         AAA_22  90 av....ielliiDEaqhlr....seealeeLrslln 117
                                    ++    ++l+i+DEa++l     +  a   Lr + n
  gi|116753783|ref|YP_842901.1|  93 STfsgrRRLVILDEADNLHgtydRGGAAAILRVIKN 128
                                    44556679**********654433666666666666 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.8
                         AAA_22  38 erpevvfvtlpsstsskdllrellral 64 
                                     +++ ++ t + ++s++dl +++ ++l
  gi|116753783|ref|YP_842901.1| 240 DSRSALEATYQLDESPEDLIHWIDENL 266
                                    344455666666667777777777766 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 3.8
                         AAA_22  70 a...........erlsseellealeqalr 87 
                                                 +++ + l+e  ++ ++
  gi|116753783|ref|YP_842901.1| 392 IeeialltgsspTTKKVQKLFEDAQKIIE 420
                                    02232222322223444444444444444 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   5.3e-07   0.00046      11      63 ..      25      76 ..      17     259 .. 0.81
   2 ?    1.1   0.1      0.52   4.5e+02      36      88 ..     336     377 ..     333     427 .. 0.62

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 5.3e-07
                         AAA_16 11 qLlsalervrsgrp..elvllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                   +L++   ++ +grp   +++l+G++GvGK+s + +l+ ++  d   +++ ++ + 
  gi|116753783|ref|YP_842901.1| 25 ELRAWAMAWEKGRPevKCLILYGPPGVGKTSAALALASEMDWD---YIELNASDQ 76
                                   5555555788999999****************99999766655...344444444 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.52
                         AAA_16  36 GKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqllde 88 
                                    G ++ +r++++++ ++    ++++c+ +   ++y   a+      ++ +ll+ 
  gi|116753783|ref|YP_842901.1| 336 GQTRKARSVRDSAARK----IAAHCHVS---TSY---ARSELL-NFVGALLRS 377
                                    88999999*******9....99999999...444...222211.333333333 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0     1e-07   8.9e-05       8      76 ..       3      71 ..       1      98 [. 0.90

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1e-07
                          Rad17  8 lWfekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklrew 76
                                    W eky+P+ ++ +    k ++e++ w  a    + + + L++ GP+G gk+ +   L+ e+  +++e 
  gi|116753783|ref|YP_842901.1|  3 SWAEKYRPKNLDGILGNAKAVSELRAWAMAWEKGRPEVKCLILYGPPGVGKTSAALALASEMDWDYIEL 71
                                   7**************************999999999999**********************99999884 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.2e-05      0.01       2      43 ..      43      84 ..      42     112 .. 0.81
   2 ?    1.7   0.0      0.28   2.4e+02      48      90 ..     191     233 ..     173     245 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.2e-05
                                   EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH- CS
                          AAA_5  2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkg 43
                                   ++L GppG+gK++ a  la+ + + + + + +++ t+e +k 
  gi|116753783|ref|YP_842901.1| 43 LILYGPPGVGKTSAALALASEMDWDYIELNASDQRTAEIIKS 84
                                   79**********************999998888877766654 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.28
                                    .........--------G-SEEEEESGGG--HHHHHHHHHHHH CS
                          AAA_5  48 kngttslvdsplvraaregeilvlDEveraesevlnsLlslle 90 
                                    ++g+ +   + l  aar  ++l+l++v + e++v +s  ++l+
  gi|116753783|ref|YP_842901.1| 191 SGGDLRSAINDLEAAARGLKHLRLEDVATSERDVKASIFRVLD 233
                                    45666666677888999999**************999999998 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   2.8e-06    0.0024      20     181 ..      42     202 ..      37     208 .. 0.71
   2 ?   -1.7   0.0       2.4   2.1e+03      50      74 ..     399     425 ..     342     443 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.8e-06
                         AAA_30  20 vavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieastiakllkrlkgrarlepgtllivDEagm 99 
                                    + +l Gp+G GKt a  al+  ++     + + A+ ++ A+ ++ ++  +as +  +     g     +++l+i DEa  
  gi|116753783|ref|YP_842901.1|  42 CLILYGPPGVGKTSAALALASEMDW--DYIELNASDQRTAEIIK-SIAGPASQVSTFS----G-----RRRLVILDEADN 109
                                    56899********987666555543..458999******99999.8888********9....5.....679******976 PP

                         AAA_30 100 v....dtkqlaallkaaekagakvilvGDe.....rQlasVeaGgvlrdlveaagigtaeLtevvRqke.seeraaa... 166
                                    +    d   +aa+l+ +++a   vil+  e     + l    +G ++r++   a++ +  L+e+ R +  + e +a+   
  gi|116753783|ref|YP_842901.1| 110 LhgtyDRGGAAAILRVIKNATQPVILIANEyynieKPLRDACRGVQFRSI--RAQTIASLLREICRSEGiECEPEAVmhi 187
                                    666669999***********9****9988622222346666677777777..5677777777887775334444443000 PP

                         AAA_30 167 lalregdaeealeal 181
                                     a++ gd ++a++ l
  gi|116753783|ref|YP_842901.1| 188 AAMSGGDLRSAINDL 202
                                    344455555555555 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.4
                         AAA_30  50 iglAptgkaAkvLaeelg..ieastia 74 
                                     g +pt k  ++L e+++  iea+ ia
  gi|116753783|ref|YP_842901.1| 399 TGSSPTTKKVQKLFEDAQkiIEAEQIA 425
                                    234455555555544444333444444 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0     2e-05     0.017      31      57 ..      38      64 ..      19      65 .. 0.86
   2 ?   -0.5   0.0      0.91   7.8e+02     144     172 ..     100     129 ..      72     132 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2e-05
                         AAA_25 31 pagelallaGapgtGKttlaldlalav 57
                                   p+ +  +l+G+pg+GKt +al la ++
  gi|116753783|ref|YP_842901.1| 38 PEVKCLILYGPPGVGKTSAALALASEM 64
                                   777889*****************9875 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.91
                         AAA_25 144 rlvviDplsralgg.densnsdvgalveal 172
                                    rlv++D  + ++g  d   ++++ ++++++
  gi|116753783|ref|YP_842901.1| 100 RLVILDEADNLHGTyDRGGAAAILRVIKNA 129
                                    89********99998888888888888876 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 !   16.1   0.0   8.4e-06    0.0071      48     136 ..      41     128 ..      19     141 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.4e-06
                      IstB_IS21  48 enivllGpsGvGKshlaialgveavra..glsvlfvrvedLveelkrarrdgklaralkrllkvdllilDdlgll..pld 123
                                    ++++l Gp+GvGK+  a al+ e   +  +l+ + +r++++++++      g +++  +   + +l+ilD+   l  + d
  gi|116753783|ref|YP_842901.1|  41 KCLILYGPPGVGKTSAALALASEMDWDyiELNASDQRTAEIIKSI-----AGPASQVSTFSGRRRLVILDEADNLhgTYD 115
                                    799*****************9875332002222223333333333.....344444445556667777777654422456 PP

                      IstB_IS21 124 qaeaellfeviek 136
                                    +  a+ +++vi++
  gi|116753783|ref|YP_842901.1| 116 RGGAAAILRVIKN 128
                                    6666666666665 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   9.2e-06    0.0079       3      78 ..      41     112 ..      39     142 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 9.2e-06
                         AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevpe 78 
                                    k l++ G+  vGKT  +  l++e      +++++n  d+r++++ ++   +    + +++ ++++++lDE+ ++ +
  gi|116753783|ref|YP_842901.1|  41 KCLILYGPPGVGKTSAALALASEMD---WDYIELNASDQRTAEIIKSIAGPASQVSTFSG-RRRLVILDEADNLHG 112
                                    6799*****************9888...89999999999998766553233333333556.999*******99865 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0     1e-05    0.0088      25      95 ..      15      83 ..       5      86 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1e-05
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49 25 glvGqkkareaagvivelikekklaGravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkk 95
                                   g++G  ka           ++++   ++++l Gp+g Gkt+ a+a++ e+     ++ l++s+  ++e+ k
  gi|116753783|ref|YP_842901.1| 15 GILGNAKAVSELRAWAMAWEKGRPEVKCLILYGPPGVGKTSAALALASEMD--WDYIELNASDQRTAEIIK 83
                                   556666655555555555556666779**********************97..778999999988888776 PP

>> RFC1  Replication factor RFC1 C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.8e-05     0.015       1      87 [.     282     370 ..     282     385 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.8e-05
                                    HHHHHHHHHHHTTSS-GGGHHHHHHHHTHHHHHTT-EE-SS-----..SHHHHHHHHHHHHHHHHHHHTTTTT------H CS
                           RFC1   1 isdgDlvdkkirseqnWsLlpthavlssvlPaslvrgslegrisFp..swLGknSktnKnkRllqelqshlrlktsasks 78 
                                    +s++D++  ++r++qn+ L ++ a+l +     + ++ ++g ++F   s+  +  +t K + + +  + +++++++ s+s
  gi|116753783|ref|YP_842901.1| 282 LSRADIFLGRVRRRQNYTLWRYAAFLMTGGVRAVSSKVRRGYTQFRppSLWKRLGQTRKARSVRDSAARKIAAHCHVSTS 361
                                    599**********************9976654444444445666655555555555666666666666666666666666 PP

                                    HHHHTTTHH CS
                           RFC1  79 elrldylpl 87 
                                    + r + l++
  gi|116753783|ref|YP_842901.1| 362 YARSELLNF 370
                                    666555544 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 ?    4.3   0.0     0.036        31      20      42 ..      41      63 ..      24      76 .. 0.84
   2 ?    8.7   0.0    0.0016       1.4      88     161 ..      82     158 ..      65     160 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.036
                DNA_pol3_delta2 20 hayLfeGdegigkkelalnlaka 42
                                   ++++++G+ g+gk ++al+la++
  gi|116753783|ref|YP_842901.1| 41 KCLILYGPPGVGKTSAALALASE 63
                                   67899***************986 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0016
                DNA_pol3_delta2  88 irelieelsr.kpreskkkiiiiedaekmt....ksAaNalLktlEEPsenaifiLitsdtnklLktirSRcqelkfsp 161
                                    i+++   +s+ +++ ++++++i+++a++++    +  a a+L+++ +    + +iLi+++  ++ k++r  c  ++f++
  gi|116753783|ref|YP_842901.1|  82 IKSIAGPASQvSTFSGRRRLVILDEADNLHgtydRGGAAAILRVIKNA--TQPVILIANEYYNIEKPLRDACRGVQFRS 158
                                    55555555551556699***********97333356899******998..566799**************999999987 PP

>> TipAS  TipAS antibiotic-recognition domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0    0.0012         1      35      94 ..     138     196 ..     135     214 .. 0.84
   2 ?    3.1   0.0      0.15   1.3e+02      45      71 ..     396     420 ..     376     438 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0012
                                    XXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXX CS
                          TipAS  35 aelkelfaklaaalaagkdpdseeaqelaeehralieefwg.ecskeilaglgqmYvadpr 94 
                                    +e+ ++ + l++a+ +g++  s +aq +a  +r++++   g ec++e++ +++ m   d r
  gi|116753783|ref|YP_842901.1| 138 NEYYNIEKPLRDAC-RGVQFRSIRAQTIASLLREICRS-EGiECEPEAVMHIAAMSGGDLR 196
                                    67778999999999.9*********************5.5558**********99766655 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.15
                                    XXX..XXXXXXXXXXXXXXXXXXXXXX CS
                          TipAS  45 aaalaagkdpdseeaqelaeehralie 71 
                                    a +  +g +p+ +++q+l+e  +++ie
  gi|116753783|ref|YP_842901.1| 396 ALL--TGSSPTTKKVQKLFEDAQKIIE 420
                                    333..799****************998 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   6.9e-05     0.059       2      22 ..      44      64 ..      43     105 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.9e-05
                         AAA_18  2 lltGtpGvGKttlakeLskrl 22
                                   +l G+pGvGKt+ a +L++++
  gi|116753783|ref|YP_842901.1| 44 ILYGPPGVGKTSAALALASEM 64
                                   799**************9885 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   6.1e-05     0.052       2      84 ..      44     133 ..      43     143 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.1e-05
                   RNA_helicase   2 wlyGpsgeGKStlakeLakallkkl......klkkkdsvys.rnpeddfwdgYt.gqevvvidDfgqvkdeenpsdlael 73 
                                    +lyGp+g+GK+++a  La+++  ++      ++ +++ + s  +p++++ + ++ +   v+ d+  + + +++    a +
  gi|116753783|ref|YP_842901.1|  44 ILYGPPGVGKTSAALALASEMDWDYielnasDQRTAEIIKSiAGPASQV-STFSgRRRLVILDEADNLHGTYDRGGAAAI 122
                                    79*****************998444455554444444455544444444.444425556666666665555466677777 PP

                   RNA_helicase  74 irlvsstpypl 84 
                                    +r++++++ p+
  gi|116753783|ref|YP_842901.1| 123 LRVIKNATQPV 133
                                    77777766665 PP

>> AAA_24  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      0.12       4      22 ..      42      60 ..      39     108 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                         AAA_24  4 kiliyGpsgiGKTtlakel 22
                                    +++yGp+g+GKT+ a+ l
  gi|116753783|ref|YP_842901.1| 42 CLILYGPPGVGKTSAALAL 60
                                   5789***********9987 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0017       1.5       7      82 ..      44     112 ..      37     125 .. 0.79
   2 ?    1.1   0.2      0.45   3.9e+02      53      97 ..     408     458 ..     380     459 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0017
                                    EEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS.EEEEETGGG--- CS
                          AAA_2   7 lllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG.ivllDEidKihp 82 
                                    +l gp gvGkt +a ala+ ++       i ++as+  +    ++++++  g +     +  +   v lDE d  h 
  gi|116753783|ref|YP_842901.1|  44 ILYGPPGVGKTSAALALASEMDW----DYIELNASDQRT----AEIIKSIAGPASQVSTFSGRRrLVILDEADNLHG 112
                                    578*******************7....899999999999....7788777776666666554446999999999887 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.45
                                    HHHHHHHTTT-HHHHTTS.....EEEEE.TGGG-------------HHHHH CS
                          AAA_2  53 vsrligappgyvgaeegG.....ivllD.EidKihpkessgadvSregVqr 97 
                                    v++l   ++ +++ae+          +D Ei+K   k  + a vS+e Vq+
  gi|116753783|ref|YP_842901.1| 408 VQKLFEDAQKIIEAEQIAmidrgLKIVDrEIEKPEDKAMKYASVSKEIVQE 458
                                    455555555555555544444442233448888888888888888888875 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00036       0.3      15      42 ..      34      65 ..      23     144 .. 0.77
   2 ?   -2.0   0.2       2.9   2.5e+03     134     157 ..     413     439 ..     334     463 .. 0.50

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00036
                         AAA_11 15 sese....itliqGPPGtgKTktivellsqll 42
                                   ++        ++ GPPG gKT++ ++l s++ 
  gi|116753783|ref|YP_842901.1| 34 EKGRpevkCLILYGPPGVGKTSAALALASEMD 65
                                   4443444477899***************9995 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.9
                         AAA_11 134 eklakelrafeeeeek..........eklkkske 157
                                    e+ +k ++                  ++++++ e
  gi|116753783|ref|YP_842901.1| 413 EDAQKIIE-------AeqiamidrglKIVDREIE 439
                                    22222221.......1122222233322222222 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00094       0.8       1      31 [.      46      78 ..      46     109 .. 0.78
   2 ?   -2.2   0.0       6.2   5.3e+03      29      48 ..     167     186 ..     162     225 .. 0.61
   3 ?   -1.9   0.1       4.8   4.1e+03      77      77 ..     428     428 ..     383     462 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00094
                                   EE-TTSSHHHHHHHHHHHHTEEE..EEHHHHHH CS
                         AAA_17  1 lGgPGsGKgtqceklvekygfth..lsaGdllr 31
                                   +G+PG+GK+ ++  l+ +++  +  l+a+d   
  gi|116753783|ref|YP_842901.1| 46 YGPPGVGKTSAALALASEMDWDYieLNASDQRT 78
                                   7*****************965551156677655 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.2
                                    HHHHHHHTTTSHSSHHHHCT CS
                         AAA_17  29 llreeakrgglakardemrk 48 
                                    llre ++++g + + ++++ 
  gi|116753783|ref|YP_842901.1| 167 LLREICRSEGIECEPEAVMH 186
                                    67777777765444444433 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 4.8
                                    E CS
                         AAA_17  77 d 77 
                                    d
  gi|116753783|ref|YP_842901.1| 428 D 428
                                    1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (467 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 3193.60
//
Query:       gi|116753784|ref|YP_842902.1|  [L=142]
Description: pyridoxamine 5'-phosphate oxidase-related, FMN-binding [Methanosaeta thermophila PT]
Scores for 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-23   82.9   0.0    2.1e-23   82.9   0.0    1.1  1  Pyridox_ox_2    Pyridoxamine 5'-phosphate oxidase
    1.1e-07   32.0   0.0    1.3e-07   31.6   0.0    1.1  1  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase


Domain annotation for each model (and alignments):
>> Pyridox_ox_2  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.9   0.0   2.3e-27   2.1e-23       3     111 ..       9     109 ..       7     139 .. 0.87

  Alignments for each domain:
  == domain 1  score: 82.9 bits;  conditional E-value: 2.3e-27
                                    HHHHHHHHC-SEEEEEEEETTEEEEEEEEEEEETTEEEEEEETTSHCCHCCC.T--ECEEEEEEEEEEE-SEGGEEEEEE CS
                   Pyridox_ox_2   3 eeilalLdegevgrlafvddgepvilPvnyvvdgdslyfhgakgsrlaaalr.gapvcvvvtevdglvlarsfnslnyrS 81 
                                    +e+++lL+++++grla++ +++p+++P++yv+ ++++++h+ +++++++ +r +++vc++v e++g    ++     +rS
  gi|116753784|ref|YP_842902.1|   9 DECEDLLRRCRYGRLALSYEDRPYVIPMSYVYVDNTVILHSRPSGKKIEIARrNSNVCFEVDELEG----QR-----WRS 79 
                                    8***************************************************6666*********9....55.....*** PP

                                    EEEEEEEEEE--HHHHHHHCCCHHHHHSTT CS
                   Pyridox_ox_2  82 VvvrGraeevtdeeekaealellvekivpg 111
                                    V+v+Grae+  ++e k++ +++++++ + g
  gi|116753784|ref|YP_842902.1|  80 VIVYGRAELSGSQESKRRMFDAFMKSGIGG 109
                                    *********************999876555 PP

>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   1.5e-11   1.3e-07       3      84 ..       9      89 ..       7      93 .. 0.92

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 1.5e-11
                                   HHHHHHHHHSSEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETT..GSEEEEEEEEEE CS
                 Putative_PNPOx  3 eelreflaeskavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallfldde..lgrgvrieGtae 82
                                   +e++++l+++++++lA   ed  P+v p+++++ d +   ++++    +k +  ++n++v++ +++ e    r+v ++G+ae
  gi|116753784|ref|YP_842902.1|  9 DECEDLLRRCRYGRLALSYEDR-PYVIPMSYVYVDNT--VILHSRPSGKKIEIARRNSNVCFEVDELEgqRWRSVIVYGRAE 87
                                   789*************996666.**************..*****************************988899999***** PP

                                   EE CS
                 Putative_PNPOx 83 lv 84
                                   l 
  gi|116753784|ref|YP_842902.1| 88 LS 89
                                   86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1110.24
//
Query:       gi|116753785|ref|YP_842903.1|  [L=327]
Description: farnesyltranstransferase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-63  214.4   0.0    1.6e-63  214.1   0.0    1.1  1  polyprenyl_synt  Polyprenyl synthetase
  ------ inclusion threshold ------
        0.1   12.9   0.0       0.13   12.5   0.0    1.4  1  Asparaginase_C   Glutaminase/Asparaginase C-terminal domain
       0.12   12.4   0.1       0.22   11.5   0.1    1.4  1  DUF615           Protein of unknown function (DUF615)


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 !  214.1   0.0   2.7e-67   1.6e-63       4     255 ..      36     278 ..      33     279 .. 0.94

  Alignments for each domain:
  == domain 1  score: 214.1 bits;  conditional E-value: 2.7e-67
                                    HHHHHHHHHHSSS--HHHHHHHHHHHHHSCGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEETTEE-HHHCTCHHHH CS
                polyprenyl_synt   4 leealeylveagGKrlRpllvllaaealkeeeeelekaavlawivellhaasLvhDDimDdsetRRGqpcahrlvGnklA 83 
                                    l++a+++l+ agGKrlRp l+l a e ++ +     ++  +a+++el+h+++L+hDDimD++++RRG+p++h ++G++ A
  gi|116753785|ref|YP_842903.1|  36 LYDAARHLLGAGGKRLRPSLLLIAGESVGCDA---ARLVPAAVAIELVHNFTLIHDDIMDNASLRRGKPAVHVIWGTSGA 112
                                    78999************************444...899****************************************** PP

                                    HHHHHHHHHHHHHHHHHHH...STTHHHHHHHHHHHHHHHHHHHHHHHHTTTTTCCC.SHHHHHHHHHHHTHHHCHHHHH CS
                polyprenyl_synt  84 indgdfllarafellaklf...ekslellelfsevllqtveGqlldleeekdddlskfsleeyleivkyKTaylfalpva 160
                                    i++gd l+++afe+l+ +    e+ l ++++++++++ ++eGq  dle e+ ++++   ++eyle++++KT++l+ +++ 
  gi|116753785|ref|YP_842903.1| 113 ILAGDTLYSKAFEMLSMVDappERVLAAMDMLARTCTSICEGQWQDLEFERAESVT---EKEYLEMIEKKTGVLYGASAW 189
                                    ****************9998755559*********************999888888...********************* PP

                                    HHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHSS-TSHHHHTT---HHHHHHHHCT-HHHHHHHHHHTT CS
                polyprenyl_synt 161 laallagasdeelealkdiglelGlaFQiqDDylDlfgdpevlgKpagtDiqegkctlpilkalelaspeqrkvlkeilg 240
                                    ++a l+ga +e++  l+++g+  G+ FQi+DD+lDl+  ++vlgK +g Di egk t++i+ al    +    v  ei+g
  gi|116753785|ref|YP_842903.1| 190 IGATLGGAPPEVAGGLEEFGRLTGMGFQIHDDILDLTVPEDVLGKRLGGDILEGKKTMIIIDALS---KG---VKLEIFG 263
                                    ********99*******************************************************...22...5688999 PP

                                    SSHHHHHHHHHHHHH CS
                polyprenyl_synt 241 kkaekeedvkealel 255
                                    k ++++e+++ea+++
  gi|116753785|ref|YP_842903.1| 264 KGQASQEQLREAISA 278
                                    999999999988875 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 ?   12.5   0.0   2.2e-05      0.13      19      49 ..     249     280 ..     119     305 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.2e-05
                                    HHHTT--EEEEEEBTTTB--H.HHHHHHHHHH CS
                 Asparaginase_C  19 llkkgakGvvlegtGvGnlps.allealkeak 49 
                                    +++++ kGv le++G G++++ +l+ea++ ++
  gi|116753785|ref|YP_842903.1| 249 IIDALSKGVKLEIFGKGQASQeQLREAISALR 280
                                    468999**************978999888774 PP

>> DUF615  Protein of unknown function (DUF615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   3.7e-05      0.22      36      70 ..     269     303 ..     264     318 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.7e-05
                         DUF615  36 deelldalleakrikshrearrRqlqyigkllRea 70 
                                    +e+l++a+ + +r +s   arrR  +++g+  R  
  gi|116753785|ref|YP_842903.1| 269 QEQLREAISALRRCGSIDYARRRAEEFVGRGKRAL 303
                                    699*************99***********976665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 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:                        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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2593.37
//
Query:       gi|116753786|ref|YP_842904.1|  [L=446]
Description: beta-lactamase domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.1e-09   35.5   0.5      1e-07   31.8   0.1    2.5  2  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
    1.1e-08   34.8   0.9    4.9e-08   32.7   0.2    2.1  2  Lactamase_B_2  Beta-lactamase superfamily domain
    7.3e-08   32.6   0.8    1.9e-07   31.3   0.6    1.7  1  Lactamase_B    Metallo-beta-lactamase superfamily
  ------ inclusion threshold ------
      0.099   12.9   0.1       0.64   10.3   0.0    2.3  2  NUMOD3         NUMOD3 motif (2 copies)


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 ?    0.8   0.1      0.11   4.8e+02      31      54 ..      75      97 ..      69     106 .. 0.81
   2 !   31.8   0.1   2.3e-11     1e-07       9      51 ..     381     423 ..     375     436 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.11
                          RMMBL 31 prnvilvHGeeeatsalarllkee 54
                                    r ++  HG+ +++ a  +l+  +
  gi|116753786|ref|YP_842904.1| 75 VRAIVCTHGHLDHIGAVSKLA-HK 97
                                   56799********99999888.55 PP

  == domain 2  score: 31.8 bits;  conditional E-value: 2.3e-11
                          RMMBL   9 eeidfSgHadknellelirklkprnvilvHGeeeatsalarll 51 
                                    +++++SgHa ++++ el+r+++p++vi+ HG  ++  ++  l+
  gi|116753786|ref|YP_842904.1| 381 DNVHVSGHACREDHWELLRMINPEHVIPSHGNLNSHGQYLMLA 423
                                    3556***************************887766665555 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 !   32.7   0.2   1.1e-11   4.9e-08      28     143 ..      72     175 ..      59     185 .. 0.85
   2 ?   -0.1   0.0      0.12   5.4e+02     169     200 ..     382     410 ..     340     410 .. 0.74

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 1.1e-11
                                    ..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEECSTTEEEEE CS
                  Lactamase_B_2  28 lppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeepavnvheldwgesfelgdggleita 107
                                     +++ a++ th+H DH+  +  l++ +  ++p++a++ +++ ++++++++   +  + +v  l +ge+ +++ +++e+++
  gi|116753786|ref|YP_842904.1|  72 ASKVRAIVCTHGHLDHIGAVSKLAHKY--RAPIIATPFTADLVNQEIKAERIFRV-NNEVISLRAGERYQVT-PDIELEF 147
                                    4699*************8888888843..389**************999999999.99*************8.69***** PP

                                    EEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS- CS
                  Lactamase_B_2 108 tparhksgrrldrnagdtlGlriegggkrvyyigDt 143
                                    + ++h+           ++  ++ +++ +++y+ D 
  gi|116753786|ref|YP_842904.1| 148 IRVQHSIVD--------CVFAALHTKHGTILYANDF 175
                                    *****8776........6666666667777777665 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.12
                                    TTHHHHHHT---STSHHHHCTTSSSSEEEEES CS
                  Lactamase_B_2 169 ddemirhmgHltpeeaveaaadlgakrlvliH 200
                                    +       gH+  e+ +e++++++++ +++ H
  gi|116753786|ref|YP_842904.1| 382 NVH---VSGHACREDHWELLRMINPEHVIPSH 410
                                    333...567888899**************999 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.6   4.3e-11   1.9e-07      43      81 ..      73     111 ..      13     144 .. 0.76

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 4.3e-11
                                    GGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHC CS
                    Lactamase_B  43 kdvdavilTHlHlDHiGglgglveatdvpvgavaeeapa 81 
                                     +v+a++ TH+HlDHiG++ +l++++ +p++a + +a  
  gi|116753786|ref|YP_842904.1|  73 SKVRAIVCTHGHLDHIGAVSKLAHKYRAPIIATPFTADL 111
                                    68***************************9987766655 PP

>> NUMOD3  NUMOD3 motif (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       0.6   2.7e+03      15      26 ..     260     271 ..     253     273 .. 0.75
   2 ?   10.3   0.0   0.00014      0.64       3      20 ..     365     382 ..     364     387 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.6
                         NUMOD3  15 alkGennpfyGK 26 
                                     ++G++++++G+
  gi|116753786|ref|YP_842904.1| 260 RKMGRKPILLGR 271
                                    3459**999997 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00014
                         NUMOD3   3 khSeetKaKmsealkGen 20 
                                     h+ etK Km+ a+ ++n
  gi|116753786|ref|YP_842904.1| 365 RHTVETKLKMKGARIYDN 382
                                    6**********9987865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); 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: 0.47u 0.21s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 3627.34
//
Query:       gi|116753787|ref|YP_842905.1|  [L=357]
Description: isopentenyl pyrophosphate isomerase [Methanosaeta thermophila PT]
Scores for 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-23   80.9   0.2    7.1e-16   58.2   0.2    2.2  2  FMN_dh        FMN-dependent dehydrogenase
    0.00015   20.9   1.2       0.13   11.3   0.7    3.1  3  IMPDH         IMP dehydrogenase / GMP reductase domain
  ------ inclusion threshold ------
      0.018   14.2   0.2       0.11   11.6   0.1    2.1  2  Glu_synthase  Conserved region in glutamate synthase


Domain annotation for each model (and alignments):
>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   2.7e-08   0.00016      27      96 ..      23      94 ..       5     112 .. 0.86
   2 !   58.2   0.2   1.2e-19   7.1e-16     214     344 ..     178     331 ..     128     335 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.7e-08
                                   HHGGGGEEE---SSSS-SS-B..--EEETTEEESSSEEE--BSTGGGTSTTHHHHHHHHHHHHTS-EEEETT CS
                         FMN_dh 27 raaferirlrprvlrdvskvd..lsttllGqklslPvliaPvglaklahpdgelalaraaakagipfvlstv 96
                                    + f+++ l +r+l ++ + d  +++t+l ++ls+P++i+++      +++ + +la aa+++gi ++++++
  gi|116753787|ref|YP_842905.1| 23 YRPFDDLILLHRALPEIDESDvcTECTFLNRRLSAPLIISAMTGGHPDAREINANLATAAQETGIAIGVGSQ 94
                                   56799999*******9999863378899**************998888899**************9999887 PP

  == domain 2  score: 58.2 bits;  conditional E-value: 1.2e-19
                                    HHSSEEEEEEE...-SHHHHHHHHHTTESEEEE--GGG..........TSSTT---HHHCH................... CS
                         FMN_dh 214 qtklplvvKGv...ltaedakraveaGvdgivvSNHGG..........RqldgapatidvL................... 261
                                    + +lp+++K+    +  eda+++v+ G++ i v+  GG                      L                   
  gi|116753787|ref|YP_842905.1| 178 RFRLPIIIKETgcgIPFEDARMLVDSGIQLIDVAGTGGtswsmvesyrA----------ELrgdpeskeigmlfaewgip 247
                                    6789*****98777889*********************66666666652..........443333321111224444443 PP

                                    ..HHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-SBHH CS
                         FMN_dh 262 ..peiveavggrievlvDgGirrGsDvlkAlalGAdavllGRpflyglaagGeeGvervleilraelertmallGvksva 339
                                       ++ e  +  ++v+ +gG+r+G Dv++ +alGA + + + p+l + a+ G   v rvl+ + +el+ +m l+G +s++
  gi|116753787|ref|YP_842905.1| 248 tpVSVIECSRAGAQVISSGGVRSGIDVARSIALGAFMAGAALPLL-APATRGSVDVVRVLQRFVRELRISMFLTGSRSLQ 326
                                    323334444667*****************************9995.6699****************************** PP

                                    HHHCG CS
                         FMN_dh 340 eldrs 344
                                    el+r+
  gi|116753787|ref|YP_842905.1| 327 ELSRA 331
                                    **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 ?    0.3   0.0     0.044   2.7e+02       4      43 ..      26      65 ..      24      91 .. 0.82
   2 !   11.3   0.7   2.1e-05      0.13     195     235 ..     251     285 ..     240     297 .. 0.78
   3 !    5.5   0.0    0.0012       7.4     298     328 ..     301     331 ..     292     345 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.044
                                   GGGEEEE---B.-S-GGGSB--EESSTTEEESSSEEE-SST CS
                                   xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH  4 fddvllvpaks.evlpkevdlktkltkkiklniPlvsaamd 43
                                   fdd++l+ ++  e+  ++v ++ ++ ++ +l+ Pl+ +am 
  gi|116753787|ref|YP_842905.1| 26 FDDLILLHRALpEIDESDVCTECTFLNR-RLSAPLIISAMT 65
                                   9998888776548888888888888765.9******99995 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 2.1e-05
                                    HHHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 195 AvaevaeaakkagvpviaDGGikysgdivkAlaaGadavml 235
                                    +v+e+    ++ag +vi+ GG+++  d+++++a+Ga   m 
  gi|116753787|ref|YP_842905.1| 251 SVIEC----SRAGAQVISSGGVRSGIDVARSIALGAF--MA 285
                                    45544....567899********************94..44 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.0012
                                    -HHHHHHHHHHHHHHHHHHHT-SSHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 298 svkevveqlvgglrsgmgylGaktieelkek 328
                                    +v +v++++v +lr +m  +G+++++el + 
  gi|116753787|ref|YP_842905.1| 301 DVVRVLQRFVRELRISMFLTGSRSLQELSRA 331
                                    456899**********************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 ?   -0.8   0.0      0.11   6.5e+02      61     100 ..      52      92 ..      31     106 .. 0.79
   2 ?   11.6   0.1   1.8e-05      0.11     196     298 ..     173     283 ..     165     294 .. 0.64

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.11
                                    HHHHHTTEE---B-TTTS.-HHHHHHHHHHHHHHT-B-EET CS
                   Glu_synthase  61 alkikkriltsamSyGal.seeahealakamnrlgtksntG 100
                                    + +++ ++++sam  G   ++e +  la+a+++ g+++  G
  gi|116753787|ref|YP_842905.1|  52 NRRLSAPLIISAMTGGHPdAREINANLATAAQETGIAIGVG 92 
                                    46788999999999997625667778999999999887766 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 1.8e-05
                                    HHHHH-TTSEEEEE.EE-STTHHHHHHHHHHTT-SEEEEE-TT---SSEEHHH..HHHB---..HHHHHHHHHHHH.... CS
                   Glu_synthase 196 dLkevnkeakvsvK.lvaeagvetiaagvakanadiilidGleGGTGAspkss..ikhaGlP..lelalaevdqtl.... 266
                                    +L+e+  + ++ +K  +++ + e+ ++ +++++  +i + G+ GGT  s  +s  ++  G P   e+++  ++  +    
  gi|116753787|ref|YP_842905.1| 173 SLREARFRLPIIIKeTGCGIPFEDARM-LVDSGIQLIDVAGT-GGTSWSMVESyrAELRGDPesKEIGMLFAEWGIptpv 250
                                    577777777777774467777777777.77777888888775.6666665554223456666332344443332221111 PP

                                    .HHTT-GGG-EEEEESS--SHHHHHHHHHHT-S CS
                   Glu_synthase 267 .keeglrdrvsliadGglktgadvvkalalGAd 298
                                     + e  r   ++i +Gg+++g dv+ ++alGA 
  gi|116753787|ref|YP_842905.1| 251 sVIECSRAGAQVISSGGVRSGIDVARSIALGAF 283
                                    1234457778899******************94 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2428.89
//
Query:       gi|116753788|ref|YP_842906.1|  [L=248]
Description: aspartate/glutamate/uridylate kinase [Methanosaeta thermophila PT]
Scores for complete 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  131.0   2.3    5.7e-38  130.9   2.3    1.0  1  AA_kinase  Amino acid kinase family


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.9   2.3   3.2e-42   5.7e-38       1     241 []       1     225 [.       1     225 [. 0.95

  Alignments for each domain:
  == domain 1  score: 130.9 bits;  conditional E-value: 3.2e-42
                                    TEEEEEE-TTCCCCTCC......HHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC....E..HHHH CS
                      AA_kinase   1 krvVvKlGGssltdkee......aslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaaglrstleeag 74 
                                    ++ ++KlGGs++tdk++      + + r+a +i+ +    ++l+vVhG+gsf++ +++   gl+++++          +g
  gi|116753788|ref|YP_842906.1|   1 MLKILKLGGSIITDKSRlatarlDQISRIAHEISGI----ENLIVVHGAGSFGHIHAKN-FGLPERFSG---------EG 66 
                                    6789*************9**7777777777777777....99*****************.********9.........79 PP

                                    HHHHHHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETTTE CS
                      AA_kinase  75 evatrdalaslgerlvaallaaglpavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvltgfigldeege 154
                                     + t+ ++  l++++v+al +ag++a +l++ ++ + ++gr       + + ++e i e+l ++vvpvl+g++++d  ++
  gi|116753788|ref|YP_842906.1|  67 LLKTHLSVSDLNRIVVEALHDAGVDALPLHPLSSVVLRDGR-------IHHMSTEVITEMLRRDVVPVLHGDVAMDLSKG 139
                                    9999*******************************998888.......******************************** PP

                                    EEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHH.......CSSS.TTTHHHHCHHHHH CS
                      AA_kinase 155 lgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaee.......saselatgGmkvkhpaal 227
                                     g++s+D++ ++ A  lgA ++   tdVdGV+ +       +r+l+ i+ +++ +        ++ ++tgGm+ k+ + +
  gi|116753788|ref|YP_842906.1| 140 AGIVSGDQLVSYMARTLGAGMVAMGTDVDGVMID-------GRVLSCITPNDMHSleshllpAKGVDVTGGMRGKLAELV 212
                                    *******************************954.......5************************************** PP

                                    HHHHCTT-EEEEEE CS
                      AA_kinase 228 aaarrggipvvItn 241
                                    ++a  g i+ +I+n
  gi|116753788|ref|YP_842906.1| 213 ELAGIG-IDSRIFN 225
                                    *****9.****998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1979.19
//
Query:       gi|116753789|ref|YP_842907.1|  [L=321]
Description: mevalonate kinase [Methanosaeta thermophila PT]
Scores for complete 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-18   66.0   2.2    2.6e-18   66.0   2.2    1.9  2  GHMP_kinases_N   GHMP kinases N terminal domain
    4.4e-12   46.2   0.7    4.4e-12   46.2   0.7    2.1  2  GHMP_kinases_C   GHMP kinases C terminal
    0.00053   19.5   0.1     0.0014   18.1   0.1    1.7  1  GalKase_gal_bdg  Galactokinase galactose-binding signature


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 ?   -3.3   0.4       1.9   1.2e+04      21      22 ..      78      79 ..      69      91 .. 0.45
   2 !   66.0   2.2   4.4e-22   2.6e-18       1      66 []      95     163 ..      95     163 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.9
                                   HH CS
                 GHMP_kinases_N 21 av 22
                                   a+
  gi|116753789|ref|YP_842907.1| 78 AA 79
                                   32 PP

  == domain 2  score: 66.0 bits;  conditional E-value: 4.4e-22
                                    EEEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHH...HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                 GHMP_kinases_N   1 divikseiPvgaGLGSSAAlavalvaAllallglslee...aklaleaerlaqggngsggDvaasvyGg 66 
                                    +i+++seiPv++GLGSSAA++va++aAl ++ g+++e    a  a ++e+ +qgg gs++D a ++yGg
  gi|116753789|ref|YP_842907.1|  95 RITVSSEIPVASGLGSSAAIVVATLAALSHHMGIDMEVksiAAEAHRIEKTVQGGLGSPMDTALAAYGG 163
                                    699******************************9974433577788888888****************8 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1      0.93   5.6e+03      64      82 ..      68      85 ..      66      88 .. 0.75
   2 !   46.2   0.7   7.4e-16   4.4e-12       6      67 ..     229     289 ..     224     304 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.93
                 GHMP_kinases_C 64 alfkdkdeaeqvaralree 82
                                    l+ + dea+++ar +++ 
  gi|116753789|ref|YP_842907.1| 68 SLG-SSDEAAAAARYVSAV 85
                                   566.789999999999876 PP

  == domain 2  score: 46.2 bits;  conditional E-value: 7.4e-16
                 GHMP_kinases_C   6 ergdlellgellnlsqrselkavvgilppeleellealselG.algaklsGaGgGptvfalfk 67 
                                    +  dl++lg+l+n ++   l++ +g+ ++el el+ a++ +G algakl+GaGgG++ +al k
  gi|116753789|ref|YP_842907.1| 229 KDLDLKELGRLMNINHG--LLEAIGVGTRELSELVYAARGAGmALGAKLTGAGGGGCMIALPK 289
                                    44599************..899***************************************84 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 !   18.1   0.1   2.4e-07    0.0014      13      47 ..       3      37 ..       2      38 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.4e-07
                                   EEEEEEEEEEE--S-TTTT-EEEEEEEEEEEEEEE CS
                GalKase_gal_bdg 13 vasAPGRvnLiGEHtDYngGfVlpmAieqdiyiav 47
                                   +asAPG v L GEH   +g   l +Ai+++  + v
  gi|116753789|ref|YP_842907.1|  3 AASAPGKVILFGEHAVVSGAPALGTAIDLRARVLV 37
                                   589**************************988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.24s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2523.20
//
Query:       gi|116753790|ref|YP_842908.1|  [L=269]
Description: hypothetical protein Mthe_0477 [Methanosaeta thermophila PT]
Scores for complete 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-68  230.1   0.0      3e-68  229.9   0.0    1.0  1  Memo      Memo-like protein
    0.00092   18.4   0.0     0.0014   17.7   0.0    1.3  1  LigB      Catalytic LigB subunit of aromatic ring-opening dio


Domain annotation for each model (and alignments):
>> Memo  Memo-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  229.9   0.0   3.3e-72     3e-68       2     270 ..       4     266 ..       3     267 .. 0.90

  Alignments for each domain:
  == domain 1  score: 229.9 bits;  conditional E-value: 3.3e-72
                           Memo   2 aavAGsfYpedeeelkkqleeflekntgkkei.arviisPHagyvysgevaakayaelesskvervvilGpsHtilgskv 80 
                                    +a AG fYp+++e+l + l + ++    + ++     ++PHagy+ysg vaa++ya+l ++  e+ v++Gp+Ht+lg +v
  gi|116753790|ref|YP_842908.1|   4 PAAAGMFYPARAEALLAELSSAFRGLKRE-PMpVIGAVVPHAGYIYSGYVAAEVYARLPER--ETYVLIGPNHTGLGLPV 80 
                                    899*****************777654433.333555667*******************999..9**************** PP

                           Memo  81 svlaaseleTPlGdlkvDeelveeLvkkeeiadldetaalaEHSlEvqlpfLkellkekkfkivPilvsaqseetakevg 160
                                    +v++ ++++TPlG++ vD el+ +L     i+++de+a+++EHS+EvqlpfL++ +    f+i+Pi++++q++eta evg
  gi|116753790|ref|YP_842908.1|  81 AVSR-ETWRTPLGSVPVDLELADALEG--TIVASDEMAHMEEHSIEVQLPFLQRCFSG--FRILPICMGMQDQETAIEVG 155
                                    ****.********************99..59***************************..******************** PP

                           Memo 161 ealakvikdes..nlviiSsDlsHygrrFgspqeiaesieDrevikaleelneeelkeylek.....tnnticGekpiav 233
                                    ea+a++i +      vi+SsDl+Hy        e a++  D  +++ + +++ ++l+ ++e      ++  +cG++p+a+
  gi|116753790|ref|YP_842908.1| 156 EAVANAILKLGrsCTVIASSDLTHYL-----RYETARQL-DTSILESVIRMDIDDLYSKIEMldsryYGHGVCGYGPMAA 229
                                    *******99987899***********.....66777777.8888999999999999998876111224578********* PP

                           Memo 234 ilkalkklgakkakllkYaqssdvtsdtdsvVsyasl 270
                                    ++ a++ lga  +kll+Ya+s+dv++d+ +vV+y+++
  gi|116753790|ref|YP_842908.1| 230 TIAASRRLGASMGKLLRYATSGDVSGDRGQVVGYGAV 266
                                    **********************************976 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 !   17.7   0.0   1.6e-07    0.0014     144     247 ..     141     233 ..     132     254 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.6e-07
                           LigB 144 vaypllsferlykLGeAlrkaveeldknvlilgsGglsHqlegdeaakadaqtlllneefdeelldllkegrveelckms 223
                                    + +++ + e   ++GeA+++a+ +l +   +++s +l+H+l+ + a            ++d  +l+  + +++++l +  
  gi|116753790|ref|YP_842908.1| 141 ICMGMQDQETAIEVGEAVANAILKLGRSCTVIASSDLTHYLRYETAR-----------QLDTSILESVIRMDIDDLYSKI 209
                                    45667899999*******************************99865...........6666666666666666666666 PP

                           LigB 224 keelsaaagheeeelvplvvalGa 247
                                    ++  s+ +gh+ ++  p+++  +a
  gi|116753790|ref|YP_842908.1| 210 EMLDSRYYGHGVCGYGPMAATIAA 233
                                    566666666666666666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.20s 00:00:00.59 Elapsed: 00:00:00.35
# Mc/sec: 2325.11
//
Query:       gi|116753791|ref|YP_842909.1|  [L=206]
Description: 30S ribosomal protein S2 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.1e-25   87.5   0.3    4.8e-15   55.4   0.1    2.0  2  Ribosomal_S2  Ribosomal protein S2
  ------ inclusion threshold ------
       0.14   11.7   0.2       0.29   10.7   0.2    1.5  2  Peripla_BP_4  Periplasmic binding protein domain


Domain annotation for each model (and alignments):
>> Ribosomal_S2  Ribosomal protein S2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0     2e-11   1.8e-07       2      95 ..      23     113 ..      22     119 .. 0.92
   2 !   55.4   0.1   5.4e-19   4.8e-15     148     213 ..     121     186 ..     118     188 .. 0.96

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 2e-11
                   Ribosomal_S2   2 LeagvhfGhqtrrwnpkmkpyIyger.ngihiidlektlaalrraykvvkevaakggkilfvgtkkqakeavkeaakran 80 
                                    L+agvh+G q++  + +m +yIy +r +g +++d++ t + +r a k++ +   + +kil v+ ++  ++  +  ak ++
  gi|116753791|ref|YP_842909.1|  23 LAAGVHIGTQQK--TSDMMKYIYRVRtDGLYVLDVQATDKRIRLAGKFLAN--YEPSKILVVSARQYGQRPATMFAKAVG 98 
                                    89******7666..899******999569********************87..57899********99999999****** PP

                   Ribosomal_S2  81 gyyvnerWlgGtLTN 95 
                                    +     r+++ tLTN
  gi|116753791|ref|YP_842909.1|  99 ARANVGRFIPNTLTN 113
                                    99999********** PP

  == domain 2  score: 55.4 bits;  conditional E-value: 5.4e-19
                   Ribosomal_S2 148 lPdlvvvldpkkekiavkEakklgipviaivDtnvdpdlvdypIpaNddsirsiklilgvladaie 213
                                     Pd+++v+dp  +  avkEa   gipv+a++Dtn  +++vd +Ip N++  ++++li+ +la+++ 
  gi|116753791|ref|YP_842909.1| 121 EPDVLLVTDPAGDGQAVKEAVDIGIPVVALCDTNNMTSNVDLVIPTNNKGRKALTLIYWLLARQVL 186
                                    59************************************************************9875 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 ?   -3.2   0.0      0.54   4.8e+03     105     126 ..      83     103 ..      69     115 .. 0.75
   2 ?   10.7   0.2   3.3e-05      0.29      58     105 ..     124     169 ..     117     171 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.54
                                    HHHHHHHHHHHHHHCTTH.EEE CS
                   Peripla_BP_4 105 eaaGelqaeylaeklggkkgkv 126
                                     ++G+  a + a+++g++ ++v
  gi|116753791|ref|YP_842909.1|  83 RQYGQRPATMFAKAVGAR-ANV 103
                                    577888888888888877.666 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 3.3e-05
                                    EEEE--SSHHHHHHHHHHHHHTT-EEEEESTTGCTTT-CEEEEEC-HH CS
                   Peripla_BP_4  58 giivapvdstalapalkkakaaGIpVvafdsddapsgerlayvgfdne 105
                                    +++v+  d+++  +a+k+a + GIpVva    ++ +++++ ++ ++n+
  gi|116753791|ref|YP_842909.1| 124 VLLVT--DPAGDGQAVKEAVDIGIPVVALCDTNNMTSNVDLVIPTNNK 169
                                    55554..7777779**************65554999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); 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: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1670.82
//
Query:       gi|116753792|ref|YP_842910.1|  [L=60]
Description: RNA polymerase Rpb6 [Methanosaeta thermophila PT]
Scores for complete 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-12   47.3   0.1    1.7e-12   47.0   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 !   47.0   0.1   9.7e-17   1.7e-12       8      49 .]       7      52 ..       4      52 .. 0.84

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 9.7e-17
                                   -HHHHHHHHHHHHHHH....HT........SS-SSSSTTCHHHHTT-S-- CS
                   RNA_pol_Rpb6  8 trYelvriaakRArQieegesl........etqkpvviAlrEiaegkipi 49
                                   tr+e +ri+++RA+Qi     +        ++ +p+ iAl+E+  g ipi
  gi|116753792|ref|YP_842910.1|  7 TRFERARIVGARALQI----FMgapvlirtDSIDPLEIALEEMRLGVIPI 52
                                   9***************....6666666653235***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       183  (0.0102069); expected 358.6 (0.02)
Passed bias filter:                      168  (0.00937029); 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: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.42
# Mc/sec: 433.79
//
Query:       gi|116753793|ref|YP_842911.1|  [L=61]
Description: DNA-directed RNA polymerase subunit N [Methanosaeta thermophila PT]
Scores for 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   99.4   0.5    1.1e-28   99.3   0.5    1.0  1  RNA_pol_N       RNA polymerases N / 8 kDa subunit
  ------ inclusion threshold ------
       0.01   16.1   0.2      0.012   15.9   0.2    1.1  1  Chordopox_RPO7  Chordopoxvirus DNA-directed RNA polymerase 7 


Domain annotation for each model (and alignments):
>> RNA_pol_N  RNA polymerases N / 8 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.3   0.5   1.3e-32   1.1e-28       2      58 ..       1      56 [.       1      57 [. 0.96

  Alignments for each domain:
  == domain 1  score: 99.3 bits;  conditional E-value: 1.3e-32
                                   ---SS-TTT--B-STHHHHHHHHHHTT--HHHHHHHHT--SHHHHHHHHTB--THHH CS
                      RNA_pol_N  2 iiPVrCFtCGkvigekweeylellekgeepkdaLdaLglkryCCrrmllthvdliek 58
                                   +iPVrCF+CGkvi+++weey+e+++ +  p++++d+Lg++ryCCrrmll+hv+++e 
  gi|116753793|ref|YP_842911.1|  1 MIPVRCFSCGKVISSVWEEYRERIKSE-PPGKVMDDLGIERYCCRRMLLSHVEVVEM 56
                                   8***********************987.99***********************9985 PP

>> Chordopox_RPO7  Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide (RPO7)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.9   0.2   1.3e-06     0.012       4      49 ..       3      52 ..       1      58 [. 0.82

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.3e-06
                 Chordopox_RPO7  4 plvCstCGrDlse..eryrLlvkkkkLkdvlat..vkrkCCrlkLstqie 49
                                   p+ C +CG+ +s   e yr  +k +   +v++   ++r CCr  L   +e
  gi|116753793|ref|YP_842911.1|  3 PVRCFSCGKVISSvwEEYRERIKSEPPGKVMDDlgIERYCCRRMLLSHVE 52
                                   678*********84468**************9733589***988877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); 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: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 449.26
//
Query:       gi|116753794|ref|YP_842912.1|  [L=132]
Description: 30S ribosomal protein S9P [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.2e-32  110.7   0.7    6.9e-32  110.5   0.7    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 !  110.5   0.7   3.9e-36   6.9e-32       1     121 []       8     132 .]       8     132 .] 0.92

  Alignments for each domain:
  == domain 1  score: 110.5 bits;  conditional E-value: 3.9e-36
                                    EECTTEEEEEEEEESSSEEEETTEECCHHSTTSCHHHHHCHHHHHTTTS.SSEEEEEEEESS-HHHHHHHHHHHHHHHHH CS
                   Ribosomal_S9   1 GrrKesvArvwikegkgkilvngksleeYfkeeaarekvleplkltgll.gkfdvfvkvkgGGlsgqaeAirlgiaraLv 79 
                                    G++K+++Ar++ kegkg+i++n+++le  ++   ar+k++ep+ ++ +  +++dv v+v gGG++gqa+A+r+++ar+++
  gi|116753794|ref|YP_842912.1|   8 GKKKTAIARATFKEGKGRIRINNVPLEI-IEPALARMKMMEPVIMAAEAfSSVDVDVSVMGGGVMGQADAVRTALARGIL 86 
                                    89**************************.8779*********8877655157**************************** PP

                                    HHHHHHHHHHC......TCCCTS-B--------TTSSCTTB----S-- CS
                   Ribosomal_S9  80 alekeekkeLk......kaglltrDpRvvErkKtgkkkARkkyqwskR 121
                                    +++     +Lk      +++ll++D R++E+kK+g  +AR+kyq+s+R
  gi|116753794|ref|YP_842912.1|  87 EWTG--DAALKeayaeyDRNLLVSDHRQKEKKKFGGLGARAKYQKSYR 132
                                    **88..577776677889****************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1013.20
//
Query:       gi|116753795|ref|YP_842913.1|  [L=136]
Description: 50S ribosomal protein L13 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-09   37.1   0.2    5.1e-07   30.0   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 !   30.0   0.2   2.9e-11   5.1e-07       6     114 ..       4      98 ..       1     103 [. 0.73

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 2.9e-11
                                    EETTSBHHHHHHHHHHHHHTTTSTT--TTS--S-EEEEEEGGCBB-SSTHHTT-EEEEE-SSTTSEEEEEHHHHHCCSHH CS
                  Ribosomal_L13   6 DAegqvlgrlaskiakvLrGkhkptytphvdcGdyvvvinaekvaltgkkleqkvyyrhtgypgglkevtakellekkpe 85 
                                    DA+g v+grlas  ak L              G+ + ++naek  ++g+k +    yr+    g  ++        k+p+
  gi|116753795|ref|YP_842913.1|   4 DATGLVMGRLASITAKCL------------LQGEEIRIVNAEKAIISGSKESVLREYREMLERGTREK---GPYYPKRPD 68 
                                    555555555555555554............46888999***********9886555555544444444...3457899** PP

                                    HHHHHHHHCCS-.SSHHHHHHGCTEEEESS CS
                  Ribosomal_L13  86 eilekaVkgmLp.knklgrrrlkrLkvyag 114
                                    +il+++V+gmLp k++ gr+ + rL+vy g
  gi|116753795|ref|YP_842913.1|  69 RILKRTVRGMLPyKTSRGREAMARLRVYVG 98 
                                    ************5667899999******88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       241  (0.0134419); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 999.00
//
Query:       gi|116753796|ref|YP_842914.1|  [L=120]
Description: 50S ribosomal protein L18e [Methanosaeta thermophila PT]
Scores for complete 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   45.8   0.1    4.9e-12   45.6   0.1    1.1  1  Ribosomal_L18   Ribosomal protein 60S L18 and 50S L18e
    9.6e-08   32.8   0.3    3.7e-07   30.9   0.3    1.9  1  Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27
  ------ inclusion threshold ------
      0.077   13.5   0.0       0.15   12.5   0.0    1.5  1  RuvA_C          RuvA, C-terminal domain


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 !   45.6   0.1   8.2e-16   4.9e-12      18     139 ..       5     120 .]       1     120 [] 0.88

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 8.2e-16
                  Ribosomal_L18  18 ksenvylklLvklyrfLarRtdskFnkvvlkrLfmsrinrpplslsrlvkkvkkkeeekkiavvvgtvtdDvrllevPkl 97 
                                    k +n+ l  L+   +  +r +++   + v  rL + r+n +++ ls++ +++ +    + ++ v g+v+    + +  ++
  gi|116753796|ref|YP_842914.1|   5 KKTNPRLVRLISDLKAASRESKAAIWRDVAERLEKPRRNYAAVNLSKINRHTGD----DDTVLVAGKVLGAGEIDH--RV 78 
                                    556666666666667788999999999**********************99985....5899*******9988875..79 PP

                  Ribosomal_L18  98 svaALrftetararilkaGGeiltlDqLalraPtGkntvLlr 139
                                    +vaAL f+e+a ++i+ aGG ++ +++L   +P+G+   +lr
  gi|116753796|ref|YP_842914.1|  79 TVAALGFSEQAASKIISAGGRCMKIEELIRLHPKGTGIKILR 120
                                    ***********************************9998886 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 !   30.9   0.3   6.2e-11   3.7e-07      71     127 ..      43     101 ..      19     102 .. 0.72

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 6.2e-11
                                    ---EEEGGGTTTTSSS......SE..EEE--S---.--EEEESEE-HHHHHHHHHTT-EEE CS
                 Ribosomal_L27A  71 eaeeidleelaeaglikk..kdgv..KvlgkgeltkklkvkaskfSkkAkekIeaaGGkve 127
                                    + + ++l+++ ++       +  v  Kvlg ge+ + ++v a  fS++A +kI +aGG+++
  gi|116753796|ref|YP_842914.1|  43 NYAAVNLSKINRHTG--DddTVLVagKVLGAGEIDHRVTVAALGFSEQAASKIISAGGRCM 101
                                    334566666622222..234333336********************************995 PP

>> RuvA_C  RuvA, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.6e-05      0.15      12      41 ..      82     109 ..      81     109 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.6e-05
                                    HCTS-HHHHHHHHHHHHC-TTS-HHHHHHH CS
                         RuvA_C  12 aLGYkekeaekAvakvlanpgasveelIra 41 
                                    aLG++e+ a k++++   +  + +eelIr+
  gi|116753796|ref|YP_842914.1|  82 ALGFSEQAASKIISAG--GRCMKIEELIRL 109
                                    8**************9..999999999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); 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: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 928.79
//
Query:       gi|116753797|ref|YP_842915.1|  [L=116]
Description: XRE family transcriptional regulator [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-05   24.4   0.0    4.6e-05   23.4   0.0    1.5  1  HTH_3           Helix-turn-helix
     0.0021   17.8   0.6     0.0071   16.1   0.1    1.9  2  HTH_23          Homeodomain-like domain
     0.0066   16.6   0.1      0.011   15.8   0.1    1.4  1  HTH_28          Helix-turn-helix domain
     0.0068   16.7   0.1      0.011   16.0   0.1    1.4  1  HTH_31          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.024   14.6   0.2       0.25   11.3   0.0    2.2  2  DUF438          Family of unknown function (DUF438)
       0.04   13.8   0.2       0.11   12.4   0.0    1.9  2  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
      0.058   13.4   0.1       0.12   12.4   0.0    1.5  2  HTH_37          Helix-turn-helix domain
      0.074   13.1   0.0       0.36   10.9   0.0    2.0  1  HTH_19          Helix-turn-helix domain
       0.08   12.8   0.1       0.15   11.9   0.1    1.5  1  MarR_2          MarR family
       0.12   12.6   0.0       0.21   11.8   0.0    1.4  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
       0.13   11.7   0.2       0.23   10.9   0.2    1.4  1  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family
       0.14   12.3   0.2       0.35   11.0   0.1    1.7  2  Trp_repressor   Trp repressor protein
       0.18   10.7   0.0       0.21   10.5   0.0    1.1  1  Pacs-1          PACS-1 cytosolic sorting protein


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   3.4e-08   4.6e-05       1      34 [.      20      53 ..      20      54 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 3.4e-08
                                   HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSS CS
                          HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnGer 34
                                   +++ +  +g sq+e++++++v+++++s++ +G+r
  gi|116753797|ref|YP_842915.1| 20 IAQELVRRGVSQREVSRLMDVTPAAVSQYVSGKR 53
                                   56778899************************97 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   5.2e-06    0.0071       7      39 ..      17      50 ..      15      55 .. 0.90
   2 ?   -0.4   0.0      0.81   1.1e+03      18      28 ..      81      91 ..      60      94 .. 0.59

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.2e-06
                         HTH_23  7 Rlrillllae.GlsvreIAreLgvsrrTvyrwlk 39
                                   R+ i++ l + G s+re++r+++v++  v+++++
  gi|116753797|ref|YP_842915.1| 17 RATIAQELVRrGVSQREVSRLMDVTPAAVSQYVS 50
                                   88888888888*******************9976 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.81
                         HTH_23 18 lsvreIAreLg 28
                                   + +++I++++ 
  gi|116753797|ref|YP_842915.1| 81 DLIKRICEICK 91
                                   55667777665 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   8.3e-06     0.011       2      32 ..      17      48 ..      16      54 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8.3e-06
                         HTH_28  2 Rleiiklla.aGhsvreaArelgisrrtvyrW 32
                                   R++i ++l  +G+s+re++r++ +++  v++ 
  gi|116753797|ref|YP_842915.1| 17 RATIAQELVrRGVSQREVSRLMDVTPAAVSQY 48
                                   899**99886799**************99875 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   0.1   8.3e-06     0.011      12      40 ..      26      54 ..      21      72 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 8.3e-06
                         HTH_31 12 raGLsqeevAerlgvsestlsrlEqGrrg 40
                                   r+G+sq+ev ++  v+++ +s++ +G+rg
  gi|116753797|ref|YP_842915.1| 26 RRGVSQREVSRLMDVTPAAVSQYVSGKRG 54
                                   89************************996 PP

>> DUF438  Family of unknown function (DUF438)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00018      0.25      35      56 ..      19      40 ..       3      50 .. 0.88
   2 ?    0.8   0.1      0.35   4.8e+02      31      55 ..      65      88 ..      55      93 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00018
                         DUF438 35 qaEqeLieeGipveeiqkLCdv 56
                                    + qeL++ G++++e+ +L dv
  gi|116753797|ref|YP_842915.1| 19 TIAQELVRRGVSQREVSRLMDV 40
                                   678******************9 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.35
                         DUF438 31 eEIsqaEqeLieeGipveeiqkLCd 55
                                   eEIs + + L++     + i++ C+
  gi|116753797|ref|YP_842915.1| 65 EEISRLAEDLMNGD-ADDLIKRICE 88
                                   68888888888643.4456666666 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   7.9e-05      0.11      10      35 ..      30      55 ..      22      72 .. 0.89
   2 ?   -2.9   0.1       4.6   6.4e+03      45      45 ..      91      91 ..      83     105 .. 0.48

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.9e-05
                 YdaS_antitoxin 10 gqkaLAealgvsqqaVsqWlkgkkqv 35
                                   +q+++ ++ +v+++aVsq ++gk++ 
  gi|116753797|ref|YP_842915.1| 30 SQREVSRLMDVTPAAVSQYVSGKRGY 55
                                   799999*****************984 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.6
                 YdaS_antitoxin 45 k 45
                                   k
  gi|116753797|ref|YP_842915.1| 91 K 91
                                   2 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   8.5e-05      0.12      21      51 ..      18      48 ..      13      54 .. 0.89
   2 ?   -3.3   0.0       6.9   9.5e+03       3      12 ..      72      81 ..      70      85 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.5e-05
                                   HHHHHHHHHCT--HHHHHHHHT--HHHHHHH CS
                         HTH_37 21 laiaeliekrelsqseaaqllgiaqPkvsrl 51
                                   ++ia+ + +r+ sq+e+ +l+ ++ + vs+ 
  gi|116753797|ref|YP_842915.1| 18 ATIAQELVRRGVSQREVSRLMDVTPAAVSQY 48
                                   46999***********************986 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 6.9
                                   XXXX--HHHH CS
                         HTH_37  3 aDlgeedaee 12
                                   +Dl+  da+ 
  gi|116753797|ref|YP_842915.1| 72 EDLMNGDADD 81
                                   6777777765 PP

>> HTH_19  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   0.00026      0.36      10      39 ..      26      54 ..      20      92 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00026
                         HTH_19 10 elgltqeelaerlgisrskisaiEngkkdv 39
                                    +g +q+e+++  +++++  s++ +gk+  
  gi|116753797|ref|YP_842915.1| 26 RRGVSQREVSRLMDVTPAAVSQYVSGKR-G 54
                                   689***********************76.2 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00011      0.15      12      42 ..      22      49 ..      13      51 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                                   HHHHCTTTSEEEHHHHHHHHTSSHHHHHHHH CS
                         MarR_2 12 aaLgrrpgrdltvgelarrlglsksavsril 42
                                    +L rr+   ++++e+ r ++++++avs+ +
  gi|116753797|ref|YP_842915.1| 22 QELVRRG---VSQREVSRLMDVTPAAVSQYV 49
                                   5788888...9*****************977 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 ?   11.8   0.0   0.00015      0.21      20      44 ..      26      50 ..      20      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                                   HSSB-HHHHHHHHTS-HHHHHHHHH CS
                 Fe_dep_repress 20 kkvvktkdlaerLnvspssVsemlk 44
                                   +  v++ ++++ ++v p+ Vs+ ++
  gi|116753797|ref|YP_842915.1| 26 RRGVSQREVSRLMDVTPAAVSQYVS 50
                                   5668999***************886 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 ?   10.9   0.2   0.00017      0.23      17      45 ..      17      46 ..      16      50 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00017
                   HTH_Tnp_ISL3 17 eayilellles.rsvkavArqlgvSwtTVw 45
                                   +a i+++l ++  s ++v+r+++v++  V 
  gi|116753797|ref|YP_842915.1| 17 RATIAQELVRRgVSQREVSRLMDVTPAAVS 46
                                   678999999999************998875 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   0.00026      0.35      38      67 ..      17      46 ..      15      60 .. 0.90
   2 ?   -2.3   0.0       3.7   5.1e+03      66      76 ..      67      77 ..      63      88 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00026
                  Trp_repressor 38 RlqvvkeLLkeelsqreIaeelgvSiAtIt 67
                                   R  +++eL + ++sqre++  ++v  A ++
  gi|116753797|ref|YP_842915.1| 17 RATIAQELVRRGVSQREVSRLMDVTPAAVS 46
                                   899****************99999877765 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.7
                  Trp_repressor 66 ItRvsrsLktg 76
                                   I+R +  L +g
  gi|116753797|ref|YP_842915.1| 67 ISRLAEDLMNG 77
                                   55555555433 PP

>> Pacs-1  PACS-1 cytosolic sorting protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00015      0.21     122     181 ..      45     103 ..      37     115 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00015
                         Pacs-1 122 varyLgsldsrysslfldeawrdlferleaktsadaadvvtrisqYltgansvlqlpiae 181
                                    v++y++   + y+ +f d+   ++ + +e+ ++ da d+++ri +  ++a+    +p++e
  gi|116753797|ref|YP_842915.1|  45 VSQYVSG-KRGYNIVFRDDIREEISRLAEDLMNGDADDLIKRICEICKKARGEELCPVEE 103
                                    5666654.678********777777777777888****************9999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      608  (0.0339115); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); 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: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 930.16
//
Query:       gi|116753798|ref|YP_842916.1|  [L=349]
Description: hypothetical protein Mthe_0485 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       846  (0.0471861); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 2839.45
//
Query:       gi|116753799|ref|YP_842917.1|  [L=134]
Description: hypothetical protein Mthe_0486 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 1022.84
//
Query:       gi|116753800|ref|YP_842918.1|  [L=215]
Description: methyltransferase type 11 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-17   62.4   0.0    1.1e-16   61.3   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
    1.2e-14   54.8   0.1    3.8e-14   53.2   0.1    1.8  1  Methyltransf_25  Methyltransferase domain
    9.8e-11   41.8   0.0    1.3e-10   41.3   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    2.8e-09   36.9   0.0    1.2e-08   34.9   0.0    1.8  1  Methyltransf_31  Methyltransferase domain
    6.7e-09   36.4   0.0    1.2e-08   35.6   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
    2.6e-05   23.7   0.0    9.1e-05   21.9   0.0    1.7  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    0.00019   21.2   0.0    0.00027   20.7   0.0    1.1  1  TPMT             Thiopurine S-methyltransferase (TPMT)
    0.00028   20.5   0.9      0.023   14.3   0.1    2.1  2  MetW             Methionine biosynthesis protein MetW
     0.0055   16.0   0.3     0.0092   15.3   0.3    1.6  1  CMAS             Mycolic acid cyclopropane synthetase
  ------ inclusion threshold ------
      0.031   14.0   0.0      0.044   13.5   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      0.034   13.1   0.2      0.075   11.9   0.1    1.5  2  Methyltransf_9   Protein of unknown function (DUF1698)
       0.17   12.3   0.0       0.35   11.3   0.0    1.5  2  HsbA             Hydrophobic surface binding protein A


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 !   61.3   0.0   7.2e-20   1.1e-16       1      96 []      27     141 ..      27     141 .. 0.87

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 7.2e-20
                                    EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-.................EEEETTEECCCTSS-TT-EE CS
                Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl.................kvefvvadaeklpfednsfD 63 
                                    L++GcG+G+  + +  +g r+v++D+s ++++++++ + +  +                 +ve++ ad + lpf+d+ fD
  gi|116753800|ref|YP_842918.1|  27 LELGCGSGKTIRGMIGKGWRIVAIDISRRAVEISRSIKDGVTVasqlgnpstnsskgiteEVELLTADGRLLPFRDEVFD 106
                                    89*************99**************777554444444445555555588999999999**************** PP

                                    EEEEES-CCC-..CCHHHHHHHHHHHEEEEEEEEE CS
                Methyltransf_11  64 lvvssevlhhv..edpekalkeiaRvLkpgGllvi 96 
                                    +v++++vl h+   +++ + +ei Rv + gGl+++
  gi|116753800|ref|YP_842918.1| 107 AVFAFHVLGHLleTQRSVVTREIIRVTRSGGLVFF 141
                                    ***********99899999*************986 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.2   0.1   2.5e-17   3.8e-14       1      97 []      26     137 ..      26     137 .. 0.91

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 2.5e-17
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHH...............HHHHHTTT..TEEEEESBCCGBSSSTT CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaar...............eraeeegl..nvefvqgdaedlpfedg 63 
                                    vL+lGcG+G++++ +  ++   +++++Dis +++e+ r               + ++++g+  +ve++++d + lpf d+
  gi|116753800|ref|YP_842918.1|  26 VLELGCGSGKTIRGMIGKG--WRIVAIDISRRAVEISRsikdgvtvasqlgnpSTNSSKGIteEVELLTADGRLLPFRDE 103
                                    9***************995..***************998889988887777765555577799***************** PP

                                    TEEEEEEESTGGGSSHHHHHHHHHHHHHHEEEEE CS
                Methyltransf_25  64 sfDlvvssgalhhlsdedlekalkeiarvLkpgG 97 
                                     fD+v+++++l hl + ++  + +ei rv++ gG
  gi|116753800|ref|YP_842918.1| 104 VFDAVFAFHVLGHLLETQRSVVTREIIRVTRSGG 137
                                    *******888***888999**************9 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.0   8.8e-14   1.3e-10      22     155 ..      22     181 ..       5     183 .. 0.72

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 8.8e-14
                Methyltransf_23  22 aggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae.............kakkaqkdqfdeqeaaepqg....... 81 
                                     g+rvL++GcG+G + + +  +g+ ++++D+s++avei +             +++++ ++           g       
  gi|116753800|ref|YP_842918.1|  22 CGSRVLELGCGSGKTIRGMIGKGWRIVAIDISRRAVEISRsikdgvtvasqlgNPSTNSSK-----------Giteevel 90 
                                    578***********************************98887777766555522222222...........13333333 PP

                Methyltransf_23  82 .............kfdlIvlrevlehvpd..ppellrqiatllkpgGylllseplasl..kedrllldwlylvpagrhis 144
                                                  fd + +++vl+h+       + r i + ++ gG+++++ +  ++  +    ++  ++++ +g+  +
  gi|116753800|ref|YP_842918.1|  91 ltadgrllpfrdeVFDAVFAFHVLGHLLEtqRSVVTREIIRVTRSGGLVFFRGFSFDDfrAGGDEIERGTFIRGDGTITH 170
                                    3333445555555***************5336688899*************99755543334444566666777767778 PP

                Methyltransf_23 145 ffsarslkell 155
                                    +f+++++ +l+
  gi|116753800|ref|YP_842918.1| 171 YFTEDEVLDLF 181
                                    88887776665 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.0   7.8e-12   1.2e-08       5     113 ..      24     145 ..      22     182 .. 0.85

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 7.8e-12
                Methyltransf_31   5 lrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielAre................naqklgldnveFeqgdieelek 68 
                                     rvl+lGCG+G+ +  +    g++ ++v iDis +a+e +r+                n++k   ++ve+  +d   l+ 
  gi|116753800|ref|YP_842918.1|  24 SRVLELGCGSGKTIRGMI---GKGWRIVAIDISRRAVEISRSikdgvtvasqlgnpstNSSKGITEEVELLTADGRLLP- 99 
                                    68***************9...77889****************99****9999999996655555559************. PP

                Methyltransf_31  69 lledekfDlilsnevl.naladpdkile.eiervlkpggilliedpr 113
                                     + de fD ++++ vl ++l  + ++   ei+rv ++gg +  + ++
  gi|116753800|ref|YP_842918.1| 100 -FRDEVFDAVFAFHVLgHLLETQRSVVTrEIIRVTRSGGLVFFRGFS 145
                                    .99*************9666666665544**********99876655 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.0   7.9e-12   1.2e-08       1      98 [.      27     138 ..      27     139 .. 0.76

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 7.9e-12
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg................ 64 
                                    Le+GcG+G ++r +  k  +++++++Dis++a+   ++ +++ +   ++++ +  +++++   g                
  gi|116753800|ref|YP_842918.1|  27 LELGCGSGKTIRGMIGK--GWRIVAIDISRRAV-EISRSIKD-GVTVASQLGNPSTNSSK---Giteevelltadgrllp 99 
                                    8****************..**************.22222222.22344444444444443...246699999999***** PP

                Methyltransf_12  65 ...ssfDlvvasnvlhhl.kdir.evldnirklLkpgGr 98 
                                       + fD+v+a++vl hl ++ r  v ++i ++ + gG 
  gi|116753800|ref|YP_842918.1| 100 frdEVFDAVFAFHVLGHLlETQRsVVTREIIRVTRSGGL 138
                                    ******************854442777799999999996 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   6.1e-08   9.1e-05      33     154 ..       8     144 ..       4     149 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 6.1e-08
                                    HHHHHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS.............. CS
                Ubie_methyltran  33 rlWkkfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki.............. 98 
                                    r W   + ++     g++vl++ +G+g     +  ++g+  ++v +Di+   +++++      ++               
  gi|116753800|ref|YP_842918.1|   8 RSWGGVTRDIPDLPCGSRVLELGCGSGKT---IRGMIGKGWRIVAIDISRRAVEISRSIKDGVTVAsqlgnpstnsskgi 84 
                                    567777777777788999********974...667899999999999999998887653222222234455566677788 PP

                                    ..TEEEEE--TTT-TTS-T-EEEEEEES-GGG-..S-HHHHHHHHHHHEEEEEEEEEEEE CS
                Ubie_methyltran  99 ..nieflqanaeeLpfeddsfDvvtvsfGlrnv..tDklkaLkeayrvlkpGGrlvvlef 154
                                      ++e+l+a++  Lpf d+ fD v   + l  +  t ++ + +e+ rv + GG ++   f
  gi|116753800|ref|YP_842918.1|  85 teEVELLTADGRLLPFRDEVFDAVFAFHVLGHLleTQRSVVTREIIRVTRSGGLVFFRGF 144
                                    899********************9887777666225666788***********9986555 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   1.8e-07   0.00027      36     152 ..      21     140 ..      15     151 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.8e-07
                                    S--EEEEEET-TT-HHHHHH-BTTEEEEEE-S-HHHHHHHHHHHTT........SGGGGGEEEE--...........-TT CS
                           TPMT  36 kaglrvlvPlCGkaldlvwlAeqgrevvGvelselAvekffeeanl........epkvkelsgvkeysageiellcgdvF 107
                                    + g rvl  +CG++  +  +  +g+++v++++s  Ave   + ++         +p  ++ +g  e    e+ell++d  
  gi|116753800|ref|YP_842918.1|  21 PCGSRVLELGCGSGKTIRGMIGKGWRIVAIDISRRAVEISRSIKDGvtvasqlgNPSTNSSKGITE----EVELLTADGR 96 
                                    567899999***************************986432222233544444555555555555....9999999988 PP

                                    T---SS-..EEEEEEESSTTTS-GGGHHHHHHHHHHHEEEEEE.. CS
                           TPMT 108 tlraeelgkfdliydraalvAlppelreryakslaelLkpdgegl 152
                                     l+ ++   fd+++   +l  l +  r+   +++ ++ + +g ++
  gi|116753800|ref|YP_842918.1|  97 LLPFRDE-VFDAVFAFHVLGHLLETQRSVVTREIIRVTRSGGLVF 140
                                    8875543.4999999988888888888888888877777777766 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1   1.6e-05     0.023      12      62 ..      21      72 ..      14      81 .. 0.79
   2 ?    5.0   0.0     0.011        16      63     115 ..      92     147 ..      78     152 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.6e-05
                           MetW 12 kpgsrvldlGcGdGellell.keekqvdgrGleldeegvaecvakGlsviqg 62
                                   + gsrvl+lGcG G+ ++ +  +   + +  +   +  + ++++ G++v  +
  gi|116753800|ref|YP_842918.1| 21 PCGSRVLELGCGSGKTIRGMiGKGWRIVAIDISRRAVEISRSIKDGVTVASQ 72
                                   679***********99985504555666666666677788999999999865 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.011
                           MetW  63 dldkdlenfedksfdyvvlsqtlqatrnpk..evldellrigrra.ivsfPnfGhW 115
                                     +d  l  f+d+ fd v     l  + +++   v +e++r++r   +v f  f + 
  gi|116753800|ref|YP_842918.1|  92 TADGRLLPFRDEVFDAVFAFHVLGHLLETQrsVVTREIIRVTRSGgLVFFRGFSFD 147
                                    57888999*******998888887765554116889*****997426777777765 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   0.3   6.1e-06    0.0092      60     104 ..      20      63 ..      13     163 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.1e-06
                                    --TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHH CS
                           CMAS  60 lkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkr 104
                                    l  G+++L++GcG G+++r ++ + + ++v++ +S+   + ++  
  gi|116753800|ref|YP_842918.1|  20 LPCGSRVLELGCGSGKTIRGMIGK-GWRIVAIDISRRAVEISRSI 63 
                                    678*********************.**********9988887765 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 ?   13.5   0.0     3e-05     0.044      71     116 ..      20      62 ..      13     108 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3e-05
                                    --TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHH CS
                           PCMT  71 lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakr 116
                                    l  g+rvLe+G+GsG     +  ++g+  r+v+i+ +++ ve ++ 
  gi|116753800|ref|YP_842918.1|  20 LPCGSRVLELGCGSGKT---IRGMIGKGWRIVAIDISRRAVEISRS 62 
                                    66799**********64...7899************9999998864 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1     5e-05     0.075     101     145 ..       7      51 ..       3      70 .. 0.84
   2 ?   -1.9   0.0      0.83   1.2e+03     181     194 ..     103     116 ..      84     123 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5e-05
                                    HHHHHHHGGGS.--T.T-EEEEET-TTSHHHHHHHHCT-SEEEEE- CS
                 Methyltransf_9 101 dwkWdrvlphlsdlk.grtildvGcgnGyhlwrmvgegaklvvGid 145
                                     + W  v++ ++dl  g ++l++Gcg+G  +  m+g+g ++ v id
  gi|116753800|ref|YP_842918.1|   7 GRSWGGVTRDIPDLPcGSRVLELGCGSGKTIRGMIGKGWRI-VAID 51 
                                    678999********54899*****************99765.4565 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.83
                                    --EEEEEEES-GGG CS
                 Methyltransf_9 181 eafdtvfsmGvlyh 194
                                    e fd+vf+  vl h
  gi|116753800|ref|YP_842918.1| 103 EVFDAVFAFHVLGH 116
                                    789****9999988 PP

>> HsbA  Hydrophobic surface binding protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00024      0.35      31      76 ..      49      94 ..      35      98 .. 0.88
   2 ?   -3.3   0.0       7.8   1.2e+04      58      74 ..     172     188 ..     168     191 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00024
                                   HHHHHHHHHHHHHHHHHHHHHHHTS----HHHHHHHHHHHHHCHHH CS
                           HsbA 31 alpilsasnalvsaikkattdaqasapltdeealalaqavqtLepd 76
                                   a+ i   + ++ ++ik++ t a++ ++ + + ++ ++++v+ L+ d
  gi|116753800|ref|YP_842918.1| 49 AIDISRRAVEISRSIKDGVTVASQLGNPSTNSSKGITEEVELLTAD 94
                                   78999999*******************************9988776 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 7.8
                                    --HHHHHHHHHHHHHCH CS
                           HsbA  58 ltdeealalaqavqtLe 74 
                                    +t++e l+l  ++ +L 
  gi|116753800|ref|YP_842918.1| 172 FTEDEVLDLFKPLLNLS 188
                                    89999999999988886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1639.37
//
Query:       gi|116753801|ref|YP_842919.1|  [L=319]
Description: ADP-ribosylation/crystallin J1 [Methanosaeta thermophila PT]
Scores for 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-69  232.4   0.2      1e-68  232.2   0.2    1.0  1  ADP_ribosyl_GH  ADP-ribosylglycohydrolase
  ------ inclusion threshold ------
       0.15   12.2   0.0       0.53   10.4   0.0    1.9  2  DUF531          Protein of unknown function (DUF531)


Domain annotation for each model (and alignments):
>> ADP_ribosyl_GH  ADP-ribosylglycohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  232.2   0.2   1.2e-72     1e-68       1     291 []       9     290 ..       9     290 .. 0.95

  Alignments for each domain:
  == domain 1  score: 232.2 bits;  conditional E-value: 1.2e-72
                                    HHHHHHHHHHHHHGGGTT--HHHHHHHTSS--S.-----STTTTTS-TT---HHHHHHHHHHHTEET.TEE-HHHHHHHH CS
                 ADP_ribosyl_GH   1 GallGaavGDAlGlpvefwsydeirrrygelge.tpdktgfghfglkpgewtddtqmalllleslleaggldpedlarrf 79 
                                    G+llG+a+GDAlG+p+e++s  ei+r +g+  e  p +  + h+gl++g++tddt+ ++ l+esllea+g++ + +a+r+
  gi|116753801|ref|YP_842919.1|   9 GCLLGSALGDALGMPLEGLSALEIQRSFGRVVEmLPAPDHHFHHGLQAGQYTDDTEETIILAESLLEAQGFSGDLFAERL 88 
                                    9*******************************9767777788999**********************************8 PP

                                    HH.HHT......T--SS--HHHHHHHHHTTTT-...-S-B...---BTTTGGG-HHHHHHTSS-HHHHHHHHHHHHHTTB CS
                 ADP_ribosyl_GH  80 laeWleep..gdteprgignttrealrnlksgepppeaganangsagngalmRaaplgllyagdpeeaaelaeeaarlTH 157
                                    ++ W  ++  +++ +rg+g ttr+a++n+ sg+p+++ag       ++ga+mRaap+gl+y++d+  + +++e ++ +TH
  gi|116753801|ref|YP_842919.1|  89 VR-WGSTWilDERLDRGVGITTRSAIENMLSGKPWQDAGVD---IETCGAAMRAAPIGLVYHWDLSMVSRYSELQSIVTH 164
                                    87.999845899***************************98...************************************ PP

                                    --HHHHHHHHHHHHHHHHHHTT--STHHHHHH..HHHHTTT-HHHHHHHGGGGG---HHH........HHHHH--SSBHH CS
                 ADP_ribosyl_GH 158 nhpeavagaaayaaliaaalrgksleealdaaeeelavapaeeelaaalrkalaladsdkdvdvdaeeavdelgsggyav 237
                                    ++  a aga+a+a  +a  l   +  ++l+       +   + el +++++++ + +sd+    d +++++ lg++ +++
  gi|116753801|ref|YP_842919.1| 165 RSRGARAGAVAVAVGVALSLLDLPRMKILEIS--TDIASRISPELGRKMDEVRIFLESDR----DPSDVLELLGTSPSVH 238
                                    *******************9999999999999..4555566689****************....9*************** PP

                                    HHHHHHHHHHHH.-SSHHHHHHHHHTS-SSHHHHHHHHHHHHHHHH-GGGS-HH CS
                 ADP_ribosyl_GH 238 ealaaalyallhaaddfeeallaavnlGgDtdttgaiaGallGalyGleaiPee 291
                                    +a+++a+y++ +   d+e+al +avn GgDtd+++++aGal+Ga+yG+++ Pe+
  gi|116753801|ref|YP_842919.1| 239 DAVPSAFYCFVR-L-DPEDALVEAVNAGGDTDSVASMAGALAGARYGTSWMPER 290
                                    ************.4.9************************************86 PP

>> DUF531  Protein of unknown function (DUF531)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.05   4.4e+02      24      40 ..     136     152 ..     130     163 .. 0.88
   2 ?   10.4   0.0   5.9e-05      0.53       4      50 ..     149     194 ..     146     222 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.05
                         DUF531  24 ARaapicyafdfnLall 40 
                                     Raapi  +++++L+++
  gi|116753801|ref|YP_842919.1| 136 MRAAPIGLVYHWDLSMV 152
                                    69************986 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 5.9e-05
                         DUF531   4 lglvntYDkkklheaHkRaiARaapicyafdfnLalldFplkkeeke 50 
                                    l +v  Y + +   +H+   ARa+ +++a ++ L+lld p  k   e
  gi|116753801|ref|YP_842919.1| 149 LSMVSRYSELQSIVTHRSRGARAGAVAVAVGVALSLLDLPRMK-ILE 194
                                    678888999999999**99********************9764.334 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2441.73
//
Query:       gi|116753802|ref|YP_842920.1|  [L=341]
Description: N-acetyl-gamma-glutamyl-phosphate reductase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-34  117.6   0.0    7.9e-34  116.7   0.0    1.4  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
    3.1e-21   76.3   0.0    4.1e-21   75.9   0.0    1.2  1  Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation dom
    0.00059   20.4   0.0     0.0013   19.3   0.0    1.6  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
      0.068   13.3   0.2       0.15   12.2   0.2    1.5  1  TypeIII_RM_meth  Type III restriction/modification enzyme met
       0.12   13.3   0.0        0.2   12.5   0.0    1.4  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 


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 !  116.7   0.0   2.2e-37   7.9e-34       2     117 ..       4     134 ..       3     137 .. 0.97

  Alignments for each domain:
  == domain 1  score: 116.7 bits;  conditional E-value: 2.2e-37
                                    EEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGC.TT-SEEEE-SCHHHHH CS
                 Semialdhyde_dh   2 vaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeel.kevdivflalpagvsk 80 
                                    ++ivG++Gy+G ellrlL+ hp++++v+++s++  aGk++++++++l++  dl++e+++++e+ +++d+vf+a+p+g+++
  gi|116753802|ref|YP_842920.1|   4 IGIVGGSGYTGGELLRLLSVHPSANVVCVTSRKL-AGKPVTSVHQHLRGLLDLRFEAPSPAEIaQRCDVVFTAVPHGTAM 82 
                                    89********************************.**********************8888887**************** PP

                                    HHHHHHHHTTSEEEESSSTTTTST...............TSEBE-HHHHGGG CS
                 Semialdhyde_dh  81 elapklaeagvkviDlssdfRlkd...............davyvlpevnrea 117
                                    +++p+l+++g+kviDls+d+Rl                 dav++lpe+++e 
  gi|116753802|ref|YP_842920.1|  83 DWVPELLDNGAKVIDLSADYRLPVdvfektygikhraprDAVFGLPELHPEV 134
                                    **********************889************************985 PP

>> Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.9   0.0   1.1e-24   4.1e-21       2     184 .]     155     312 ..     154     312 .. 0.91

  Alignments for each domain:
  == domain 1  score: 75.9 bits;  conditional E-value: 1.1e-24
                                    HHHHHCTT.EEEEEEEEEEEGGGCHHHHHHHHHHHHHHHHHSTTS.CTTTSSHHTTSEESTCSTBTTTTCHCBHHHHHHH CS
                Semialdhyde_dhC   2 kPLldalgelervivatyqavSGaGkkgvreLlkqvaelqrsdeakpgvfgvpiagNlipyidkeedkgepetreelkav 81 
                                    +PL++a g ++rv++++++++SGaG++                 +++  ++ ++a N+  y ++  +++ pe+++el+ +
  gi|116753802|ref|YP_842920.1| 155 APLAKA-GMVDRVVFDSKSGISGAGAE-----------------PTETSHYPNLAENIRCYRVT-NHRHVPEIKQELSRL 215
                                    8****8.99*****************7.................999*****************.9************** PP

                                    HHHHHHCTESCSEEEEEEEESBSSEEEEEEEEEES.......SSHHHHHHHHHHHHCSTTEEEEESSHCHHSSHHHHTTC CS
                Semialdhyde_dhC  82 aetkkileftekvsatcvrVPvlrGhseavtiklk.......lkdveveeveellaaapevkvvvneeedrPtpaavagg 154
                                    ++   +++ft+      + +P++rG+++++++ +k       ++++ +++ ++ +++   ++v+  e   +P++ +v+  
  gi|116753802|ref|YP_842920.1| 216 QN-DIRISFTP------HVIPAVRGILTTAHVFVKdsfqdtiQDREFISKLYSDFYRN-AKFVRLVE--GVPMLGNVRC- 284
                                    *9.67788899......78*****************9966665666666666666666.99999995..*********8. PP

                                    SSSEEEEEEEEETTCTTEEEEEEEEETTTT CS
                Semialdhyde_dhC 155 tnsvsVGRirkdemgdeglklvvvgDNllk 184
                                    +n++++G ++  +  d+ +++++++DNl+k
  gi|116753802|ref|YP_842920.1| 285 SNFCDIG-FEIEKNSDR-IVVISAIDNLVK 312
                                    9******.*99998897.**********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 !   19.3   0.0   3.5e-07    0.0013       2      96 ..       4     100 ..       3     101 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 3.5e-07
                                    EEEE.TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCC..HHHHHHHHC....-EEECECHHHHHHH-SEEEE-S-HHHH CS
                  F420_oxidored   2 igii.GaGnmgealasgllaagaqpheivvansrnpek..aeelaeelg....vkvtavdneeaaeeadvvvlavkpedv 74 
                                    igi+ G+G  g  l++ l+ +     ++v ++sr+     +++ +++l      + +a + +e a+++dvv+ av+   +
  gi|116753802|ref|YP_842920.1|   4 IGIVgGSGYTGGELLRLLSVHP--SANVVCVTSRKLAGkpVTSVHQHLRglldLRFEAPSPAEIAQRCDVVFTAVPHGTA 81 
                                    99**99**********888885..777777889997542267777777788889999999******************** PP

                                    HHHHHHCGHHHHTTSEEEEESS CS
                  F420_oxidored  75 eevlselakdalkgklvisvla 96 
                                     + + el   +++g  vi+ +a
  gi|116753802|ref|YP_842920.1|  82 MDWVPEL---LDNGAKVIDLSA 100
                                    ******9...788888998776 PP

>> TypeIII_RM_meth  Type III restriction/modification enzyme methylation subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   4.1e-05      0.15      25      50 ..     238     263 ..     231     266 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.1e-05
                TypeIII_RM_meth  25 vlvFdkekFaefienkeflpdSYTkf 50 
                                    + vF k+ F+++i+++ef+ + Y  f
  gi|116753802|ref|YP_842920.1| 238 AHVFVKDSFQDTIQDREFISKLYSDF 263
                                    57******************999887 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.7e-05       0.2       2      90 ..       3      96 ..       2      97 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.7e-05
                                   EEEEETT.SHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHE.......EESSHHHHHTCTTESEEEE-S-GGGH CS
                   GFO_IDH_MocA  2 rvaiiGa.Gkigskhlrplnesqrleevvalldpdaeraeavaesfgve.......aysdleelladpeidavivatpngth 75
                                    ++i+G+ G+ g + lr l  + + ++vv++ +++ +     + + ++           + +e+++  ++d+v+ a+p gt 
  gi|116753802|ref|YP_842920.1|  3 DIGIVGGsGYTGGELLRLLSVH-PSANVVCVTSRKLAGKPVTSVHQHLRglldlrfEAPSPAEIAQ--RCDVVFTAVPHGTA 81
                                   6899999777788888666666.*************999988777777743344233333667777..9************* PP

                                   HHHHHHHHHTT-EEE CS
                   GFO_IDH_MocA 76 eelakaaleagkhvl 90
                                   ++ + ++l +g +v+
  gi|116753802|ref|YP_842920.1| 82 MDWVPELLDNGAKVI 96
                                   ***********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 2439.37
//
Query:       gi|116753803|ref|YP_842921.1|  [L=158]
Description: signal transduction protein [Methanosaeta thermophila PT]
Scores for 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-38  128.5   2.8    1.1e-18   67.4   0.3    2.4  3  CBS          CBS domain
     0.0088   16.7   0.0        3.4    8.3   0.0    2.1  2  GAF          GAF domain
  ------ inclusion threshold ------
      0.091   12.7   0.2          4    7.3   0.0    2.3  2  MreC         rod shape-determining protein MreC
       0.26   11.1   0.5        6.4    6.6   0.0    2.4  2  Regnase_1_C  Endoribonuclease Regnase 1/ ZC3H12 C-terminal do


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 !   61.3   0.1     2e-20     9e-17       1      56 [.       3      57 ..       3      58 .. 0.95
   2 ?   -3.6   0.0       3.6   1.6e+04      48      53 ..      78      83 ..      76      88 .. 0.63
   3 !   67.4   0.3   2.4e-22   1.1e-18       1      53 [.      99     150 ..      99     154 .. 0.93

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 2e-20
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                            CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56
                                   V+dim+r++v++  +++++ea++l+re+++s++PV+d+d+ lvG+++++Dllr+l+
  gi|116753803|ref|YP_842921.1|  3 VKDIMNRNPVSCQASDPIAEAARLLRENRISGMPVLDGDE-LVGVISESDLLRLLS 57
                                   89***********************9999*******8777.************985 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 3.6
                                   HHHHHH CS
                            CBS 48 lrDllr 53
                                    rD++r
  gi|116753803|ref|YP_842921.1| 78 VRDVIR 83
                                   466665 PP

  == domain 3  score: 67.4 bits;  conditional E-value: 2.4e-22
                                    HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                            CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                                    V+d+m+r+++tv+pd+++eea+ +m++++++rlPVV e  +lvGivt+ D+++
  gi|116753803|ref|YP_842921.1|  99 VADVMSRKPITVSPDASIEEAAAIMTKHRINRLPVV-EGSRLVGIVTRGDIIS 150
                                    89**********************************.4557**********97 PP

>> GAF  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.0    0.0025        11      87     105 ..      32      47 ..       3      52 .. 0.70
   2 !    8.3   0.0   0.00075       3.4      17     106 ..      58     144 ..      50     147 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0025
                                    ESEEEEEEEEETTEEEEEE CS
                            GAF  87 irsslvvPlvndgelwGll 105
                                    i    ++P+++++el+G++
  gi|116753803|ref|YP_842921.1|  32 I---SGMPVLDGDELVGVI 47 
                                    3...69************8 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00075
                                    HTESEEEEEEEEETTEEE.CEEEEECCEEEET.....TSHHHHHHHHHSSSEEESTGGTSTTHHTTHHHHHHHHTTESEE CS
                            GAF  17 lgadrvalylpdydGlhy.dipqasrwlfmkn.....grgicgqvlatgqplvipdstpdprfaqynrrdllenmgirss 90 
                                    ++ dr+ l+lp+   + + ++ +  rw +mk       +++++ v++ ++p++++   pd    +     +++ + i+  
  gi|116753803|ref|YP_842921.1|  58 TEDDRGGLWLPSPFEIFEiPVRDVIRWERMKRsldeiTKMRVADVMS-RKPITVS---PDASIEE--AAAIMTKHRIN-- 129
                                    56699999998777764445666888855555544447777776666.*******...8888777..44566677776.. PP

                                    EEEEEEETTEEEEEEE CS
                            GAF  91 lvvPlvndgelwGllv 106
                                      +P+v + +l+G+++
  gi|116753803|ref|YP_842921.1| 130 -RLPVVEGSRLVGIVT 144
                                    .899999999999985 PP

>> MreC  rod shape-determining protein MreC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0   0.00089         4      26      41 ..      34      49 ..      29      52 .. 0.90
   2 ?    3.0   0.0     0.019        86      27      41 ..     131     145 ..     124     147 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00089
                                   T-EEEETTEEEEEEEE CS
                           MreC 26 gmpVvsgkglVGkVte 41
                                   gmpV++g++lVG+++e
  gi|116753803|ref|YP_842921.1| 34 GMPVLDGDELVGVISE 49
                                   9*************97 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.019
                                    -EEEETTEEEEEEEE CS
                           MreC  27 mpVvsgkglVGkVte 41 
                                     pVv+g+ lVG+Vt+
  gi|116753803|ref|YP_842921.1| 131 LPVVEGSRLVGIVTR 145
                                    69****99*****86 PP

>> Regnase_1_C  Endoribonuclease Regnase 1/ ZC3H12 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0014       6.4      21      45 ..       2      29 ..       1      30 [. 0.78
   2 ?    2.6   0.1     0.025   1.1e+02      22      43 ..      99     123 ..      97     126 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0014
                    Regnase_1_C 21 LVraVMarnP...hllDaQeLAAeILve 45
                                   LV+ +M+rnP   +  D+   AA  L+e
  gi|116753803|ref|YP_842921.1|  2 LVKDIMNRNPvscQASDPIAEAARLLRE 29
                                   8*********666667777777777765 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.025
                    Regnase_1_C  22 VraVMarnPhllDaQ...eLAAeIL 43 
                                    V  VM+r P  + +    e AA+I+
  gi|116753803|ref|YP_842921.1|  99 VADVMSRKPITVSPDasiEEAAAIM 123
                                    778******8876642234566665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1163.62
//
Query:       gi|116753804|ref|YP_842922.1|  [L=388]
Description: arginine biosynthesis bifunctional protein ArgJ [Methanosaeta thermophila PT]
Scores for complete 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-132  442.4   0.5   1.3e-132  442.1   0.5    1.0  1  ArgJ      ArgJ family


Domain annotation for each model (and alignments):
>> ArgJ  ArgJ family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  442.1   0.5  7.1e-137  1.3e-132       6     376 .]      16     388 .]      12     388 .] 0.96

  Alignments for each domain:
  == domain 1  score: 442.1 bits;  conditional E-value: 7.1e-137
                                    XXSSS..SXXEEEEEEEEEEEEEEEEEXXSSXXHHHHHHHHHHH.HHS.EEEEEEEEEEXXXSXHHHHHHHHHHHHHHHH CS
                           ArgJ   6 aagikkkkkdlalivseepasaaavfTknkvkAapvkvsrevlkkkkg.aravvvnsgnANavtgeqGledaeemaeava 84 
                                    a+gik+ +  +a+i++  +  aa+vfT+n+v+Aap++v+ ++l+++ g ++++++nsg ANa+tg +G++dae+ma  +a
  gi|116753804|ref|YP_842922.1|  16 ACGIKRGRYGVAMIAC--SGYAAGVFTRNRVRAAPIEVTIDHLRRSGGrTEGIIANSGSANAYTGVRGIRDAERMAGIMA 93 
                                    79***99*******99..6789*********************998878******************************* PP

                                    HHHTSXGGGEEEEEEEESSXXXXHHHHHHHHHHX....X......HHHHHHHXSSXSSXXEEEEEEEETEEEEEEEEEEX CS
                           ArgJ  85 ealgikeeevlvasTGviGerlpmekieagieklvekle......eeaaeAimTTDtvpKlaavevelgkevtiagiaKG 158
                                      lg+++e + vasTGviG+ l+++ i +  +++v +l+      ++aa+AimTTDt  K++ave e    ++++gi+KG
  gi|116753804|ref|YP_842922.1|  94 GILGCSPEMISVASTGVIGRYLDLDLISSLAKEVVPSLRtspdasSDAARAIMTTDTRVKEIAVEHE---GFHMGGICKG 170
                                    ***********************************99977788889******************985...9********* PP

                                    SSSXXXXEE--EEEEEE-----HHHHHHHHHHHHHHTGGGB-SSS---SS-EEEEEE--TTTT.STTHHHHHHHHHHHHH CS
                           ArgJ 159 aGmihPnmaTmLafittDaavsaealqellkeavdksFnsisvDgdtSTnDtvlllAngaaeeeeedleefeealtevlq 238
                                    aGmi+P+maTmLafi+tDa+v +  l  +lkeavd sFn+++vDgdtSTnDtvll +++++   e d ++f+ea++ v+ 
  gi|116753804|ref|YP_842922.1| 171 AGMIEPDMATMLAFIYTDADVGPG-LYPFLKEAVDVSFNMLTVDGDTSTNDTVLLTSTRMV---ECDPDSFKEAMEYVCV 246
                                    *********************987.789********************************9...6799************ PP

                                    HHHHHHHHTSTT-S-EEEEEEEEESSHHHHHHHHHHHHT-HHHHHHHHTT---HHHHHHHHHHSSS---TTS-EE..... CS
                           ArgJ 239 eLakqivrDGEGatklveveVkgakseeeAkkvaksvanssLvKtAlfGeDanwGRilaavGyagaeldpekvsv....l 314
                                    +La++i+rDGEGatk +eveV+ga+s+e+A+++aks+a+s+LvK+Al+GeD+nwGRi++a+G++gae+dp+k+s+    +
  gi|116753804|ref|YP_842922.1| 247 SLARMIARDGEGATKAMEVEVTGAASSEDARRAAKSIARSNLVKAALYGEDPNWGRIVCAAGRSGAEFDPTKISLsissS 326
                                    ***************************************************************************87877 PP

                                    .TTEEEEETTEE----HHHHHHHHH-SSEEEEEE--SSSEEEEEEEE---HHHHHHHTT-XX CS
                           ArgJ 315 lgevkvlekgepeevdeerakeilkeeeveievdlgegeeeatvwtcDLsyeYvkiNadYrt 376
                                    +g+v ++++g  ++   e+ak++++++e+ i++dlg+g+++a+ ++cDLs+eYv+iNa+Y+t
  gi|116753804|ref|YP_842922.1| 327 IGSVLLVDRGIIVDGVLEEAKKVMSSDEIFIHIDLGAGAGSARSFGCDLSHEYVNINAKYTT 388
                                    788********999999*******************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2898.63
//
Query:       gi|116753805|ref|YP_842923.1|  [L=487]
Description: argininosuccinate lyase [Methanosaeta thermophila PT]
Scores for complete 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-59  201.7   0.0    2.7e-59  201.1   0.0    1.2  1  Lyase_1   Lyase
    6.5e-17   62.1   0.3    2.3e-16   60.3   0.0    2.2  2  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 !  201.1   0.0     3e-63   2.7e-59      39     312 .]      43     295 ..      19     295 .. 0.93

  Alignments for each domain:
  == domain 1  score: 201.1 bits;  conditional E-value: 3e-63
                                    HHHTTSSTHHHHHHHHHHHHHHHCHCHHCGGHHHBSSSSSHHHHHHHHHHHHHHHHTTHSSGIIIIITTT--HHHHHHHH CS
                        Lyase_1  39 aakanvdlkeeaaaiikaldevleegklddqfvlkviqegsgtavnmnlnevigellgekvepndkvhtgqSsnDqvpTa 118
                                    + + ++++ e  a i+ al+e+l+     + f +    e+++ a+++ + e +g        + +  ht++S+nD v+T 
  gi|116753805|ref|YP_842923.1|  43 LYERGLIPREDCARILTALKELLA-----EGFGVLGEGEDIHEAIEAYVIERVG-------PAGGRMHTARSRNDEVATC 110
                                    566777888999999999999999.....35899999**********9999999.......999**************** PP

                                    HHHHHHHHHHHTHHHHHHHHHHHHHHHHHHTTT-EEEEEETTEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHTCEET CS
                        Lyase_1 119 lrlalkkalsekLlpaleqLidalkekakefkdvvkiGrThlqdAtPvtlgqelsayaealerdrerlkellkrllvell 198
                                    +r+al++++   L+++l q+idal++ a e ++ + +G+Thlq+A+P+tl++ l a+a+al rd+er++ +++r+++++l
  gi|116753805|ref|YP_842923.1| 111 IRIALREQMLG-LMDELIQMIDALVRIADETRERIIPGYTHLQHAQPTTLAHHLLAHADALIRDLERFESTYERVNLSPL 189
                                    *********55.******************************************************************** PP

                                    TTTTTTSSTTTSCCTHHHHHHHHHHHHHCSTEESSSHHHHHHC-HHHHHHHHHHHHHHHHHHHHHHHHHHHTSTTTSSEE CS
                        Lyase_1 199 gggtavgtglnadpefaelvakelakvtglpvkapnsfeavsdrDavvellgalkllatsLskfaeDlrllssgeaglve 278
                                    g+++ + tg+++d+    + ++ l+ ++g     +ns++avs+rD+ +e+l+  ++l+++Ls++ae+++l s++e+g+ve
  gi|116753805|ref|YP_842923.1| 190 GAAAFASTGFDIDRY---MTCELLG-FSG---LVENSMDAVSSRDFALEVLSDTSILMINLSRIAEEIILWSTSEFGYVE 262
                                    ***************...9******.999...9*********************************************** PP

                                    EEGCCTSSC-TTSTTTEBTHHHHHHHHHHHHHHH CS
                        Lyase_1 279 lslaesepGSSiMPgKvNPvqlElltgvagrvvG 312
                                    +++   +  SSiMP+K+NP+++El++ ++g ++G
  gi|116753805|ref|YP_842923.1| 263 VNDLFAS-TSSIMPQKKNPDTAELVRAKSGTAIG 295
                                    **99998.8********************99887 PP

>> ASL_C2  Argininosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       1.4   1.2e+04      21      31 ..     160     170 ..     159     194 .. 0.59
   2 !   60.3   0.0   2.6e-20   2.3e-16       1      68 [.     358     430 ..     358     431 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.4
                                    HHHHHHHHHHH CS
                         ASL_C2  21 AHeivgravrl 31 
                                    AH++ ++a +l
  gi|116753805|ref|YP_842923.1| 160 AHHLLAHADAL 170
                                    56666655433 PP

  == domain 2  score: 60.3 bits;  conditional E-value: 2.6e-20
                                    STTHHHHHHHHHHC.TS-HHHHHHHHHHHHHHHHHTT--.GGG--HHHHHHH-.....TT.--.GGGGGGSSHHHHT CS
                         ASL_C2   1 FstATdlADyLvrk.GlpFReAHeivgravrlaeekgke.leeltleelkeis.....pl.le.edveeaLdpeasV 68 
                                    F+tAT+lAD +vr  G+pFR+AH+ivgr++rl    gk+ le+l+ +++  ++     ++ ++ ed+e+aLdp++ +
  gi|116753805|ref|YP_842923.1| 358 FTTATELADSMVRItGIPFRTAHQIVGRLARL---PGKPsLEDLDRAAMV-VAdlrlsQMgFTaEDLERALDPRTNI 430
                                    99***********99*****************...222225555555544.2234333449999*********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (487 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); 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: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 3482.13
//
Query:       gi|116753806|ref|YP_842924.1|  [L=145]
Description: alkylhydroperoxidase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.4e-16   58.4   0.6    8.3e-16   57.8   0.6    1.4  1  CMD              Carboxymuconolactone decarboxylase family
  ------ inclusion threshold ------
      0.029   14.3   0.1      0.034   14.1   0.1    1.2  1  tRNA-synt_2b     tRNA synthetase class II core domain (G, H, 
        0.5   11.2   4.6        1.4    9.8   1.0    2.2  2  Tnp_zf-ribbon_2  DDE_Tnp_1-like zinc-ribbon


Domain annotation for each model (and alignments):
>> CMD  Carboxymuconolactone decarboxylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.8   0.6   1.4e-19   8.3e-16      10      76 ..      52     117 ..      43     126 .. 0.84

  Alignments for each domain:
  == domain 1  score: 57.8 bits;  conditional E-value: 1.4e-19
                                    HHHHHCCGSSTS-HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHSHHHH CS
                            CMD  10 lreallareggLdpkereLialavsaangceyCvdaHtraAleaGvteeeiaevlaqaaayagwpaa 76 
                                    +++a++ r+++Ld k+ eLi++avsaa +c +C+ +H+r A ++G ++eeia+++  aa      ++
  gi|116753806|ref|YP_842924.1|  52 HNNAIV-RNSKLDMKTIELISIAVSAAIRCSHCLEMHIRVASRMGISDEEIAAAMFLAANLVNASVL 117
                                    556666.5***********************************************999876665555 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 ?   14.1   0.1   5.7e-06     0.034      73     148 ..      11      97 ..       2     135 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.7e-06
                                    GGGHHHHHHHHHHHHHHHHHHTT.SC...........EEEEEEGTTSCBTTSEEEEEEEEETTTSEEEEEEEEEEEETHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2b  73 easlddslrdlikaisriferlglef...........raiielmsaksadykdkkefeavsesltkgieigtiqklgtrl 141
                                    e+ ++ s +d+ik+i++i+ ++   f            +i++ + +   +  d k +e++s  ++++i ++++ +   r 
  gi|116753806|ref|YP_842924.1|  11 EKGVERSAEDMIKTIEEIYGEVPYIFhfmkdspellvTKILHNNAIVRNSKLDMKTIELISIAVSAAIRCSHCLEMHIRV 90 
                                    55688899*************954443466677766666666677777888899999*******************99** PP

                                    HHHTTEE CS
                                    xxxxxxx RF
                   tRNA-synt_2b 142 serlgat 148
                                    ++r+g++
  gi|116753806|ref|YP_842924.1|  91 ASRMGIS 97 
                                    *****95 PP

>> Tnp_zf-ribbon_2  DDE_Tnp_1-like zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1     0.037   2.2e+02       2      11 ..      79      88 ..      78      94 .. 0.75
   2 ?    9.8   1.0   0.00024       1.4      18      30 ..     130     142 ..     125     142 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.037
                Tnp_zf-ribbon_2  2 RCkvClkkki 11
                                   RC +Cl   i
  gi|116753806|ref|YP_842924.1| 79 RCSHCLEMHI 88
                                   8999987555 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00024
                Tnp_zf-ribbon_2  18 iCqeCdvplCrnh 30 
                                     C +C+v++C +h
  gi|116753806|ref|YP_842924.1| 130 VCRACQVGTCEVH 142
                                    7*********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       766  (0.0427241); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1079.56
//
Query:       gi|116753807|ref|YP_842925.1|  [L=307]
Description: hypothetical protein Mthe_0494 [Methanosaeta thermophila PT]
Scores for complete 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-122  406.8   0.2   3.7e-122  406.6   0.2    1.0  1  MCR_C     Methyl-coenzyme M reductase operon protein C


Domain annotation for each model (and alignments):
>> MCR_C  Methyl-coenzyme M reductase operon protein C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  406.6   0.2  2.1e-126  3.7e-122       1     271 []       2     270 ..       2     270 .. 0.99

  Alignments for each domain:
  == domain 1  score: 406.6 bits;  conditional E-value: 2.1e-126
                          MCR_C   1 lepltyeGGvykhdellelieDlGGyilqknvialevvltllvPkedvelieelakellgklteaPlagteiavvsptLa 80 
                                    lep++++GGvykhd+++el+eDlGGy+lqknv+++ev+l llvP ed++++e+l+kel+g+lt+aPlagte+avv+ptLa
  gi|116753807|ref|YP_842925.1|   2 LEPVMFTGGVYKHDLVIELVEDLGGYLLQKNVTQSEVILLLLVPAEDLRILEDLTKELRGELTRAPLAGTEVAVVTPTLA 81 
                                    689***************************************************************************** PP

                          MCR_C  81 rhhlPhsaCDvaeylrraGaktnmiGlarGvgkriaqikeeekrlinehDlavfvlGnfkdCikkkkeklfedievPvvv 160
                                    +hhlPh+aCD+aeylrr+Gak+nmiGlarGvg++iaqi+e+e++linehD+avf++Gnf +Ci k ke+l++++++Pvvv
  gi|116753807|ref|YP_842925.1|  82 IHHLPHTACDIAEYLRRNGAKSNMIGLARGVGREIAQINEYETALINEHDAAVFIFGNFVKCIIK-KEELYKGVNIPVVV 160
                                    ****************************************************************9.9************* PP

                          MCR_C 161 tggPeelkleevpgaeayvgglGriahrlrkeeeiealdelveeveevldkkreelakDpllvsparvkkeieeqveeie 240
                                    tggP e+   e+p+a +yv+++Griahr +k++ei +ld++v +v++ ldk+r++++kDpl++sp rv++ ++eqv++ie
  gi|116753807|ref|YP_842925.1| 161 TGGP-EIPKGEMPYAFEYVSSVGRIAHRSKKANEIGNLDRIVAAVGRALDKMRADIEKDPLTTSPPRVMDVVREQVPDIE 239
                                    ****.9************************************************************************** PP

                          MCR_C 241 evlsPapitlqldglrvklpydeyaekieev 271
                                    +++sP pi+l+l+g+r+klpydey+++i +v
  gi|116753807|ref|YP_842925.1| 240 RSYSPLPIALNLNGCRIKLPYDEYHDAIGNV 270
                                    ****************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 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:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2360.35
//
Query:       gi|116753808|ref|YP_842926.1|  [L=189]
Description: hypothetical protein Mthe_0495 [Methanosaeta thermophila PT]
Scores for 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  209.9   0.1    2.4e-62  209.6   0.1    1.0  1  DUF2113   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2113  Uncharacterized protein conserved in archaea (DUF2113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  209.6   0.1   1.3e-66   2.4e-62       6     184 ..      13     186 ..       8     187 .. 0.97

  Alignments for each domain:
  == domain 1  score: 209.6 bits;  conditional E-value: 1.3e-66
                        DUF2113   6 tdeegaeaYeeiirdilqDlnllrsierlkvyidpeeplFiiavllrktsspiklgdvaeveedkeegkvkikiedEtyl 85 
                                     +e ga++Y+eii dilqDl+l+rsi+rl+vyid+e p+F++++llr +++p+++gdva+v +  +++ ++ik+++E++l
  gi|116753808|ref|YP_842926.1|  13 GEEFGAAKYREIILDILQDLGLVRSIGRLYVYIDMERPYFAVYGLLRGSLPPLRVGDVADVVR--TQEGYQIKVNEEEHL 90 
                                    5789***********************************************************..9************** PP

                        DUF2113  86 pelLkkLwekygrenveqpdRfeiiiesdedleeleelvVaDpkeelkkkvidaliriaPEGfrvrkealednsfvfvAs 165
                                    +++L++Lwekygr++veqpdR  ++i+sd ++   ++l+V+D ++e++++++daliriaPEGfr+r++ ++++sf+f+As
  gi|116753808|ref|YP_842926.1|  91 ADMLRVLWEKYGRDRVEQPDRDLLTIASDVSP---ADLIVTDVDAEFRRDLTDALIRIAPEGFRNRRNEMTEDSFLFIAS 167
                                    ****************************9988...********************************************* PP

                        DUF2113 166 eetlkeewieeakelkeel 184
                                    eet+++e+iee++e+++ +
  gi|116753808|ref|YP_842926.1| 168 EETITPELIEEVREKIRGM 186
                                    **************99877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.37
# Mc/sec: 1520.34
//
Query:       gi|116753809|ref|YP_842927.1|  [L=408]
Description: putative CoA-substrate-specific enzyme activase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-59  201.3   3.6    2.5e-59  201.0   3.6    1.1  1  BcrAD_BadFG    BadF/BadG/BcrA/BcrD ATPase family
    5.9e-05   23.4   0.2     0.0015   18.9   0.2    2.6  1  FtsA           Cell division protein FtsA
     0.0017   17.3   0.2     0.0048   15.8   0.2    1.8  2  MreB_Mbl       MreB/Mbl protein
     0.0029   17.2   0.6        0.1   12.1   0.1    2.3  2  FGGY_N         FGGY family of carbohydrate kinases, N-termina
     0.0069   16.1   0.0        1.1    8.9   0.0    2.2  2  Peptidase_M22  Glycoprotease family
     0.0077   16.0   0.8     0.0077   16.0   0.8    2.8  4  Hydant_A_N     Hydantoinase/oxoprolinase N-terminal region
     0.0084   14.8   1.5      0.065   11.8   0.1    2.3  2  MutL           MutL protein
  ------ inclusion threshold ------
      0.014   15.1   0.2      0.039   13.7   0.2    1.7  1  FGGY_C         FGGY family of carbohydrate kinases, C-termina
        0.1   12.9   0.1       0.23   11.8   0.1    1.5  1  Jag_N          Jag N-terminus


Domain annotation for each model (and alignments):
>> BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.0   3.6   1.3e-62   2.5e-59       2     266 ..     149     401 ..     148     402 .. 0.96

  Alignments for each domain:
  == domain 1  score: 201.0 bits;  conditional E-value: 1.3e-62
                                    EEEE-SSEEEEEEEETTTEEEEEEEE--TTS-HHH.........HHHHHHHHHHT--GGGECEE..EEESTTCCCTCTTB CS
                    BcrAD_BadFG   2 GiDgGsTttkavlmdekgevlgrgitnsanlesvrfeaaekvleealtealerageeeadieetylvgtgyGratlpekf 81 
                                    GiD+GsTttkav+m++++ + + ++ +++ ++s+         eea+++al+++g ++++i+ +  ++tgyGr  ++++f
  gi|116753809|ref|YP_842927.1| 149 GIDSGSTTTKAVIMRDNQIIGTGWVPTTEVIKSA---------EEAFQQALQESGVKREEIQGI--GVTGYGRFLVGKHF 217
                                    9****************77777777777777755.........59*****************99..************** PP

                                    SEEE-..HHHHHHHHHHHH-TT--...EEEEEETTEEEEEEEETTEEEEEEEESS--TTSHHHHHHHHHHHT--TTTHHH CS
                    BcrAD_BadFG  82 ekeiirseilvhgdGavalypgtr...tvldigGqdskgiqidkgkvenfqmndrcaageGrylgiiadelnmglreldg 158
                                    +++ i++ei+v+++Gav+l+ +++   tv+digG+d+k+i +++g +  f+m++ ca+ +Gr+l+++a++l++ + +l+ 
  gi|116753809|ref|YP_842927.1| 218 DAKLIQEEITVNSKGAVFLANAQKgpaTVIDIGGMDNKAISVQDGVPGSFTMGGICAGASGRFLELTARRLGVNITDLGK 297
                                    ******************************************************************************** PP

                                    HHTT--.S-------SHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHHHHHTT---SS.EEEESGGGG-HHHHHHH. CS
                    BcrAD_BadFG 159 laekat.kkarinstcavfaeaelrdalsggekaedIlaglhraialrvialisrsggvtdevtltGGvakneaavkelr 237
                                    la +++ k+  +ns+c vf  + l++ ls+g+  ed+   +++++a++v +++ ++ +v++ v+++GG++  e++ +++ 
  gi|116753809|ref|YP_842927.1| 298 LALRGSyKSVPMNSYCIVFGTQSLVNSLSKGARPEDVAMAACHSVAEQVFEQQLQEVEVKQPVIMVGGTSLIEGLPRAM- 376
                                    *****96669*********************************************************************. PP

                                    ....HHHH-S-EE--GGGGGHHHHHHHHH CS
                    BcrAD_BadFG 238 klvkenygevkininpdsiytgalGAalf 266
                                        e+ ++ k+ ++ +++y ga+GAal+
  gi|116753809|ref|YP_842927.1| 377 ----EDLLGIKVIVPNHAQYIGAVGAALL 401
                                    ....9999*******************97 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.2   7.8e-07    0.0015       1      87 [.     148     386 ..     148     397 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 7.8e-07
                                    EEEEE-SSSEEEEEEETTEEEEEEEES--HHHHHHHHHHHHT--HHHH....HHHHHHH--S--............EEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxx............xxxx RF
                           FtsA   1 alvDiGagktdvavaedgalvhlrvigvggngitkdiakalrtaveeA....erikikyGsala............ekei 64 
                                    a++D G+++t++++++d++++ +  +++    + k++++a+++a++e     e+i    G  +                 
  gi|116753809|ref|YP_842927.1| 148 AGIDSGSTTTKAVIMRDNQIIGTGWVPT--TEVIKSAEEAFQQALQESgvkrEEIQ---GIGVTgygrflvgkhfdA--- 219
                                    79***************99888888866..45666666666555555522114554...222223344444555542... PP

                                    EHHHHH.......................................................................... CS
                                    xxxxxx.......................................................................... RF
                           FtsA  65 grkels.......................................................................... 70 
                                      k ++                                                                          
  gi|116753809|ref|YP_842927.1| 220 --KLIQeeitvnskgavflanaqkgpatvidiggmdnkaisvqdgvpgsftmggicagasgrfleltarrlgvnitdlgk 297
                                    ..222233337777788888888888888888888999999999999999999999999999999999999999999999 PP

                                    ...................................................................GGGGSTTHHHHHH CS
                                    ...................................................................xxxxxxxxxxxxx RF
                           FtsA  71 ...................................................................ggsalpnleelae 83 
                                                                                                       g+s +++l +++e
  gi|116753809|ref|YP_842927.1| 298 lalrgsyksvpmnsycivfgtqslvnslskgarpedvamaachsvaeqvfeqqlqevevkqpvimvgGTSLIEGLPRAME 377
                                    99999999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                                    HHH.....T CS
                                    xxx.....x RF
                           FtsA  84 ral.....s 87 
                                    + l      
  gi|116753809|ref|YP_842927.1| 378 DLLgikviV 386
                                    886433333 PP

>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       1.5   2.9e+03     265     301 ..      70     107 ..      22     111 .. 0.78
   2 !   15.8   0.2   2.4e-06    0.0048     273     318 ..     356     401 ..     333     407 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.5
                                    -HHHHHHHHHH-EEEESGGGGSBT.HHHHHHHHHSS-E CS
                       MreB_Mbl 265 ppeLaadivdrgivltGGgallkg.ldkllseetglpv 301
                                     p+La  ++  + + +  ga+++g ++++++e+ +lpv
  gi|116753809|ref|YP_842927.1|  70 NPDLADAVFVATCFRCAEGAIIRGeVRRYIHEHSRLPV 107
                                    57888888888888888888888657778888888877 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 2.4e-06
                                    HHH-EEEESGGGGSBTHHHHHHHHHSS-EEE-SSTTTHHHHHHHHT CS
                       MreB_Mbl 273 vdrgivltGGgallkgldkllseetglpvkvaedpltcvakGtgkv 318
                                    v++ ++++GG++l++gl + +++ +g++v+v +++    a G++ +
  gi|116753809|ref|YP_842927.1| 356 VKQPVIMVGGTSLIEGLPRAMEDLLGIKVIVPNHAQYIGAVGAALL 401
                                    67889****************************9999988888765 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 ?    3.4   0.1     0.024        49       3      22 ..     148     166 ..     146     177 .. 0.78
   2 !   12.1   0.1   5.2e-05       0.1      46      81 ..     176     211 ..     164     231 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.024
                                    EEEEEESSEEEEEEEETTS- CS
                         FGGY_N   3 lglDcGttstkaivldekgk 22 
                                     g+D G t tka+++    +
  gi|116753809|ref|YP_842927.1| 148 AGIDSGSTTTKAVIMRD-NQ 166
                                    69***********9953.34 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 5.2e-05
                                    HHHHHHHHHHHHHHHHHCT.-GCCEEEEEEEE-SS- CS
                         FGGY_N  46 eeiwqalaeairkvleqagisekqikaIgisgqreg 81 
                                     e++++  ea +++l+++g++ ++i++Ig++g +  
  gi|116753809|ref|YP_842927.1| 176 TEVIKSAEEAFQQALQESGVKREEIQGIGVTGYGRF 211
                                    58899999***********************98765 PP

>> Peptidase_M22  Glycoprotease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.1   0.0    0.0081        16      32      57 ..     181     206 ..     162     208 .. 0.86
   2 !    8.9   0.0   0.00057       1.1     160     267 ..     297     398 ..     215     400 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0081
                                    HHHHHHHHHHHHHTSTGGGEEEEEEE CS
                  Peptidase_M22  32 rllplieealaeaglsledldaIavt 57 
                                       ++ ++al+e+g++ e++++I vt
  gi|116753809|ref|YP_842927.1| 181 SAEEAFQQALQESGVKREEIQGIGVT 206
                                    567889*****************999 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00057
                                    HHHCTCS.......EETTEEE.CHHHHHHHHHHST.T.HHHHHHHHHHHHHHHHHHHHHHHHHHCTBSEEEE.ESGGGGX CS
                  Peptidase_M22 160 klakegkkiefprplkgldfsfsGlktavlkelek.e.vedlaasfqeavvdhlvekteralklpkakelvi.lGGvaan 236
                                    kla +g +++ + p+ +  ++  G+++ v ++  k +  ed+a++  ++v+++   + e+ l++ ++k+ vi +GG +  
  gi|116753809|ref|YP_842927.1| 297 KLALRG-SYK-SVPM-NSYCIVFGTQSLVNSLS-KgArPEDVAMAACHSVAEQ---VFEQQLQEVEVKQPVImVGGTSLI 369
                                    444444.333.2233.33355667766555555.4335999999999998777...445555667777765505566666 PP

                                    HHHHHCHCCHHHHTTSEEEXXXHH.HHSSXCH CS
                  Peptidase_M22 237 krLrealeeeaeelglkliiPplk.yctdnaa 267
                                    ++L +a+e   + lg+k+i+P+++ y+   +a
  gi|116753809|ref|YP_842927.1| 370 EGLPRAME---DLLGIKVIVPNHAqYIGAVGA 398
                                    66555554...4599******98778877666 PP

>> Hydant_A_N  Hydantoinase/oxoprolinase N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.47   9.4e+02     101     125 ..      26      50 ..      14      81 .. 0.78
   2 ?   -3.5   0.0       3.7   7.3e+03      80      96 ..     127     143 ..     112     144 .. 0.76
   3 !   16.0   0.8   3.8e-06    0.0077       3      60 ..     149     203 ..     147     207 .. 0.92
   4 ?   -1.5   0.0      0.86   1.7e+03     151     173 ..     332     354 ..     317     358 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.47
                     Hydant_A_N 101 lfelrikkplvlyeevvevdervea 125
                                    +   ++ +p+v  e+v+ev++r  +
  gi|116753809|ref|YP_842927.1|  26 IVGAKMISPEVSLEDVMEVEKRFGV 50 
                                    44556779999********999766 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.7
                     Hydant_A_N  80 aLittkgfrdlleigrq 96 
                                    aL+tt ++r ll+ +rq
  gi|116753809|ref|YP_842927.1| 127 ALVTTARMRGLLARERQ 143
                                    78899999988888777 PP

  == domain 3  score: 16.0 bits;  conditional E-value: 3.8e-06
                     Hydant_A_N   3 gIDvGGTfTDavaldekeeevavlKllstpdavaegirealeevleesiprtskidvv 60 
                                    gID G+T T av+++++ + + +  +++t  +v++   ea++++l+es+ ++++i+ +
  gi|116753809|ref|YP_842927.1| 149 GIDSGSTTTKAVIMRDN-QIIGTGWVPTT--EVIKSAEEAFQQALQESGVKREEIQGI 203
                                    9**************87.9**********..999999999999999999999999866 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 0.86
                     Hydant_A_N 151 esiavvllhSylnpehElrvaei 173
                                    e +a +  hS++    E++ +e+
  gi|116753809|ref|YP_842927.1| 332 EDVAMAACHSVAEQVFEQQLQEV 354
                                    56888999999999999988775 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.1   3.3e-05     0.065       4      50 ..     150     192 ..     148     213 .. 0.79
   2 ?    1.5   0.1     0.044        88     235     269 ..     233     264 ..     227     271 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.3e-05
                           MutL   4 iDiGSttTkvtlvdlekvderllgqaeapTtveeedvleGleealee 50 
                                    iD GSttTk++++++     +++g++  pTt   +   e++++al+e
  gi|116753809|ref|YP_842927.1| 150 IDSGSTTTKAVIMRD----NQIIGTGWVPTTEVIKSAEEAFQQALQE 192
                                    799**********99....46**********8556666666666665 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.044
                           MutL 235 vellaeeeekglgdllvvDvGGaTTdvhsvaegsp 269
                                    + +la+  +k  g + v+D+GG+    +sv +g p
  gi|116753809|ref|YP_842927.1| 233 AVFLAN-AQK--GPATVIDIGGMDNKAISVQDGVP 264
                                    556777.344..7999************9977755 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 ?   13.7   0.2     2e-05     0.039     112     193 ..     323     401 ..     311     403 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2e-05
                         FGGY_C 112 tglsssttlahiarAaleavalqlra.ilealekdsgkpldrlavdGGgskndllmqllAdilgvpVerpkt.aeatalG 189
                                     +ls++  ++++a+Aa+ +va q+ +  l++         ++++++GG s  + l + + d+lg++V +p   + ++a+G
  gi|116753809|ref|YP_842927.1| 323 NSLSKGARPEDVAMAACHSVAEQVFEqQLQEV-----EVKQPVIMVGGTSLIEGLPRAMEDLLGIKVIVPNHaQYIGAVG 397
                                    56788888999999999999988754033333.....33589******************************999***** PP

                         FGGY_C 190 aAil 193
                                    aA+l
  gi|116753809|ref|YP_842927.1| 398 AALL 401
                                    **97 PP

>> Jag_N  Jag N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00012      0.23       4      24 ..     180     200 ..     180     203 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                          Jag_N   4 kTveeAiekAlkeLgvsrdev 24 
                                    k+ eeA ++Al+e gv+r+e+
  gi|116753809|ref|YP_842927.1| 180 KSAEEAFQQALQESGVKREEI 200
                                    789****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.39
# Mc/sec: 3156.43
//
Query:       gi|116753810|ref|YP_842928.1|  [L=145]
Description: hypothetical protein Mthe_0497 [Methanosaeta thermophila PT]
Scores for complete 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-63  211.1   0.0    7.2e-63  210.9   0.0    1.0  1  DUF2112   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2112  Uncharacterized protein conserved in archaea (DUF2112)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.9   0.0     4e-67   7.2e-63       1     143 []       2     144 ..       2     144 .. 0.99

  Alignments for each domain:
  == domain 1  score: 210.9 bits;  conditional E-value: 4e-67
                        DUF2112   1 mkvaviPdnsliladlverfgheplslakeikekvktaeldspplniteedpkkGlkyaavevPsGvrGRlsligpliee 80 
                                    +kv+v+P++s iladlv+r+gh+pl++a+ei++k++t++l+spplnit+edpkkGlkyaav+vPsGvrGR+sligp+i+e
  gi|116753810|ref|YP_842928.1|   2 VKVIVYPPTSTILADLVDRMGHTPLVMANEIRKKIDTPSLESPPLNITPEDPKKGLKYAAVDVPSGVRGRMSLIGPMIDE 81 
                                    69****************************************************************************** PP

                        DUF2112  81 aeaaiiveeadilfgcvGCartnelvkalirkkdiPileleyPkseeeaielvkkineFLksl 143
                                    aeaaiive++++l+gc+GCartnel++ li+ k+iP++el+yP+++ ea+++v++i+ FL++l
  gi|116753810|ref|YP_842928.1|  82 AEAAIIVEDNNCLVGCTGCARTNELTRLLIKIKGIPFIELKYPRDDGEARRFVHEIRMFLEGL 144
                                    ************************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 1183.51
//
Query:       gi|116753811|ref|YP_842929.1|  [L=141]
Description: hypothetical protein Mthe_0498 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-43  145.7   0.0    3.9e-43  145.4   0.0    1.1  1  DUF2102   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2102  Uncharacterized protein conserved in archaea (DUF2102)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.4   0.0   2.2e-47   3.9e-43       1     103 []       6     109 ..       6     109 .. 0.99

  Alignments for each domain:
  == domain 1  score: 145.4 bits;  conditional E-value: 2.2e-47
                        DUF2102   1 lvvieseaevtpselvrkvyeleedvtiketCfGllvegeeeevekvveevrkldpnkifvkeRgfppgderrCRakr.g 79 
                                    +v+ ++e+e++ps++++++y +++dv++ketCfG++++ge++e+e++v+e+r++dpn if+k+Rgfppgd+rrCR++r g
  gi|116753811|ref|YP_842929.1|   6 YVITSPESEILPSDIAMHIYGSKRDVHVKETCFGVIINGEKDEIEDLVREIRAMDPNGIFIKDRGFPPGDPRRCRGHRgG 85 
                                    7999**************************************************************************99 PP

                        DUF2102  80 gaRpGfhqlekEvelleliskaLe 103
                                    g+RpGf +le E ++l++is+aLe
  gi|116753811|ref|YP_842929.1|  86 GPRPGFFMLECESKMLPMISRALE 109
                                    **********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); 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 0.23s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1070.01
//
Query:       gi|116753812|ref|YP_842930.1|  [L=509]
Description: hypothetical protein Mthe_0499 [Methanosaeta thermophila PT]
Scores for complete 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   18.3   0.0     0.0051   16.6   0.0    1.9  1  PASTA          PASTA domain
     0.0082   16.4   0.0         22    5.3   0.0    3.9  4  Pro_isomerase  Cyclophilin type peptidyl-prolyl cis-trans iso


Domain annotation for each model (and alignments):
>> PASTA  PASTA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   5.7e-07    0.0051       6      59 ..     320     370 ..     319     372 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.7e-07
                                    TTTSBHHHHHHHHHHTT--CCCEEEECTCCGTTB...EEEECS-TTSEECTTS-EEE CS
                          PASTA   6 vtGmsvdeAkatLkalGlkiktveetsddvpeGt...VisQsPeaGtevskgskvtl 59 
                                    v Gm++++A++++++ G+      e+s+d  +G+   Vi+Q+P+   ev+k  kv l
  gi|116753812|ref|YP_842930.1| 320 VLGMPLSDAMELARSRGI------EPSVDGYTGDdavVIEQNPPTTMEVLKAGKVSL 370
                                    78****************......3444444444467************99999988 PP

>> Pro_isomerase  Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.028   2.5e+02     123     141 ..     150     168 ..     125     181 .. 0.86
   2 ?   -0.2   0.0      0.12     1e+03      10      35 ..     203     227 ..     198     245 .. 0.82
   3 ?    2.9   0.0     0.014   1.2e+02     112     135 ..     278     301 ..     259     317 .. 0.80
   4 !    5.3   0.0    0.0025        22      11      40 ..     378     418 ..     370     427 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.028
                  Pro_isomerase 123 vFGkVveGmdvvekiekve 141
                                    +F +Vv G ++++++ek +
  gi|116753812|ref|YP_842930.1| 150 IFARVVGGKNILDRLEKSD 168
                                    8***************974 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.12
                  Pro_isomerase  10 GrivieLfadkaPktvenFlklvkeg 35 
                                     r+++eL +d  Pk +e Fl+ +k+g
  gi|116753812|ref|YP_842930.1| 203 SRFEVELIQDA-PKGAEFFLAATKDG 227
                                    57999999887.********999988 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.014
                  Pro_isomerase 112 keaphldgkytvFGkVveGmdvve 135
                                    k+    + ++ v G+V+ G+d+++
  gi|116753812|ref|YP_842930.1| 278 KADRTSNPGHSVVGRVTAGLDLLK 301
                                    334567889************996 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.0025
                  Pro_isomerase  11 rivieLfadkaPktvenFlklvkeg...........fYdgt 40 
                                     + ieL++d aPkt + F+++v  +           +Y++t
  gi|116753812|ref|YP_842930.1| 378 LVRIELYDDLAPKTLDYFRHVVGLKerpvgplpvffVYENT 418
                                    578****************9985445556666665555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (509 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); 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 0.25s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 3566.48
//
Query:       gi|116753813|ref|YP_842931.1|  [L=533]
Description: ABC transporter related [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.4e-49  167.4   0.0    2.5e-25   89.6   0.0    2.5  2  ABC_tran     ABC transporter
    4.7e-06   26.6   0.6      0.044   13.6   0.1    3.2  3  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    0.00012   21.7   0.3       0.33   10.7   0.0    2.5  2  AAA_29       P-loop containing region of AAA domain
    0.00059   19.8   0.2       0.43   10.5   0.0    2.6  2  RsgA_GTPase  RsgA GTPase
    0.00061   19.3   4.0       0.18   11.2   0.0    3.6  4  SMC_N        RecF/RecN/SMC N terminal domain
     0.0037   17.4   1.8       0.31   11.1   0.0    2.4  2  DUF87        Helicase HerA, central domain
     0.0047   16.1   0.8        1.3    8.2   0.1    2.4  2  NB-ARC       NB-ARC domain
  ------ inclusion threshold ------
      0.013   15.8   0.0         14    6.0   0.0    3.3  2  SbcCD_C      Putative exonuclease SbcCD, C subunit
      0.032   14.0   1.1         33    4.2   0.0    3.6  3  IstB_IS21    IstB-like ATP binding protein
      0.054   13.2   0.8        9.7    5.9   0.0    2.7  2  AAA_30       AAA domain
      0.058   13.9   0.4        3.9    7.9   0.3    2.2  2  AAA_23       AAA domain
      0.071   13.2   2.6        1.8    8.6   0.0    3.1  3  MMR_HSR1     50S ribosome-binding GTPase
      0.075   12.9   0.2        3.3    7.6   0.1    2.7  2  MobB         Molybdopterin guanine dinucleotide synthesis pro
       0.11   13.1   2.0        2.5    8.6   0.2    2.6  2  AAA_18       AAA domain
       0.16   10.9   0.0       0.24   10.3   0.0    1.3  1  mTERF        mTERF
       0.21   11.3   0.9       0.36   10.6   0.0    1.8  2  zf-CSL       CSL zinc finger
       0.24   11.8   0.8          9    6.6   0.0    2.8  3  AAA_16       AAA ATPase domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.4   0.0   5.7e-24     6e-21       1     136 [.      20     199 ..      20     200 .. 0.79
   2 !   89.6   0.0   2.4e-28   2.5e-25       1     136 [.     303     458 ..     303     459 .. 0.91

  Alignments for each domain:
  == domain 1  score: 75.4 bits;  conditional E-value: 5.7e-24
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--..SEEEE..................................EE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxx..................................xx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp..teGei..................................ll 44 
                                    l+nv+l+++ege v+i+G++GaGKS L+ +l g ++    +G++                                   +
  gi|116753813|ref|YP_842931.1|  20 LSNVNLEIEEGESVGILGRSGAGKSVLMHVLRGVEEFpgISGSViyhiaicdrcghveppsrvggqcrcggtfkaseaDF 99 
                                    78*******************************9987789****999999999999999999999999999886665544 PP

                                    TTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHH...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HH CS
                                    xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  45 dgkdlkeqeleslrkeigvlpqe.pqlfpeltvren...........esdeeiekalsklglkelkdtvvksspssLSgG 112
                                     +  +++  ++ + ++i+++ q    l  + +v  n            s  +++++l++++l++   +v+    ++LSgG
  gi|116753813|ref|YP_842931.1| 100 AKLGINDPLRRAVARRIAIMLQRtFALYGDERVIVNvmravedagetISVHKAADLLDEVNLSHRMMHVA----RELSGG 175
                                    4444444667778888888888844455555566667888766654444444666666666666444444....****** PP

                                    HHHHHHHHHHHHHTSSEEEEESTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran 113 qkqrvalarallkkpkllllDEpt 136
                                    +kqrv+lar l+k p lll+DEpt
  gi|116753813|ref|YP_842931.1| 176 EKQRVVLARQLAKSPMLLLADEPT 199
                                    ***********************9 PP

  == domain 2  score: 89.6 bits;  conditional E-value: 2.4e-28
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEET.TCEGGG......B-HHHCCHCEEEE-SS--S-TT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx......xxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilld.gkdlke......qeleslrkeigvlpqepqlfpe 73 
                                    ++nvs++++e e+ +ivG +G GK+tL k+++gl +pt+G   ++ g+++ +      + + ++ k igvl+qe +l p 
  gi|116753813|ref|YP_842931.1| 303 VDNVSFEVYEREIFGIVGVSGGGKTTLSKIISGLITPTSGFAFVRvGDEWVDmtllgaDGRGRATKYIGVLHQEYTLYPY 382
                                    58***************************************97777777777778887********************** PP

                                    SBHHHH............HHHTCHHHHHHHSTTGGTTCBGESTTS.GGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    xxxxxx............xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  74 ltvren............esdeeiekalsklglkelkdtvvkssp.ssLSgGqkqrvalarallkkpkllllDEpt 136
                                     tv en              ++++ + l+++g +e++++ + ++   +LS+G++ rva+a++l+k+p++++lDEpt
  gi|116753813|ref|YP_842931.1| 383 RTVIENlteaiglslpyeLGERKAIHTLTTVGFTEDEAEMILNKYpDELSEGERHRVAMAQVLIKEPRIVVLDEPT 458
                                    ***************99766777999******99988776655545*****************************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 ?    3.1   0.0     0.063        67       3      22 ..      34      53 ..      32      72 .. 0.82
   2 !   13.6   0.1   4.2e-05     0.044       1      82 [.     315     390 ..     315     405 .. 0.87
   3 !    6.4   0.0    0.0065       6.9     234     299 ..     428     491 ..     415     495 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.063
                         AAA_21  3 vliGpNgsGKSnLLdaldll 22
                                   ++ G+ g+GKS L+  l+++
  gi|116753813|ref|YP_842931.1| 34 GILGRSGAGKSVLMHVLRGV 53
                                   799***********999876 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 4.2e-05
                         AAA_21   1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrler 80 
                                    + +++G  g GK++L +++++l      ++++  ++  ++g  +++  l + d +++++  i  ++++ + y y+  +e+
  gi|116753813|ref|YP_842931.1| 315 IFGIVGVSGGGKTTLSKIISGL------ITPTSGFAFVRVGDEWVDMTLLGADGRGRATKYIGVLHQEYTLYPYRTVIEN 388
                                    578****************888......7899999999999999999999999999999999888888888888877777 PP

                         AAA_21  81 sq 82 
                                      
  gi|116753813|ref|YP_842931.1| 389 LT 390
                                    65 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0065
                         AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHP....kllrrllellkelsrngaQviltTHSp 299
                                    ++elS+G ++  a++  l+  +   +++++DEp   ++P    ++ +++l   +el++    +++++H+ 
  gi|116753813|ref|YP_842931.1| 428 PDELSEGERHRVAMAQVLIKEP---RIVVLDEPTGTMDPitkiEVSKSILSAREELEE---TFVIVSHDM 491
                                    5789*****9999999999988...**************8888888888877788888...899999986 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 !   10.7   0.0   0.00032      0.33      15      39 ..      23      47 ..      18      51 .. 0.82
   2 !    8.3   0.1    0.0017       1.8      13      50 ..     304     341 ..     300     346 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00032
                         AAA_29 15 htieidlkgatlltGpsGsGKSTll 39
                                     +ei++ +++ + G+sG+GKS l+
  gi|116753813|ref|YP_842931.1| 23 VNLEIEEGESVGILGRSGAGKSVLM 47
                                   567787666999**********997 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0017
                         AAA_29  13 dghtieidlkgatlltGpsGsGKSTllDAiqalLvpak 50 
                                    d+ ++e+ +++++ ++G sG GK+Tl   i+ l++p++
  gi|116753813|ref|YP_842931.1| 304 DNVSFEVYEREIFGIVGVSGGGKTTLSKIISGLITPTS 341
                                    55677777788999************888888888876 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   0.00041      0.43      90     121 ..      20      52 ..       5      60 .. 0.77
   2 !    6.5   0.0     0.007       7.4      88     120 ..     301     334 ..     275     344 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00041
                                    HHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase  90 leelkellkd.ktsvlvGqSGvGKStLinallp 121
                                    l++++ ++++ + + ++G SG+GKS L+ +l++
  gi|116753813|ref|YP_842931.1|  20 LSNVNLEIEEgESVGILGRSGAGKSVLMHVLRG 52 
                                    5566666666578889*************9987 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.007
                                    TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHC CS
                    RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLinall 120
                                    +++++++ ++ + ++  +vG SG GK+tL + + 
  gi|116753813|ref|YP_842931.1| 301 KAVDNVSFEVYErEIFGIVGVSGGGKTTLSKIIS 334
                                    66777776666658999************88765 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   0.1      0.23   2.4e+02      27      43 ..      33      49 ..      20      53 .. 0.77
   2 !   11.2   0.0   0.00017      0.18     115     208 ..     144     242 ..     101     251 .. 0.74
   3 ?   -0.3   0.1      0.57     6e+02      23      43 ..     312     332 ..     298     348 .. 0.83
   4 ?    5.4   0.0      0.01        11     134     205 ..     428     497 ..     354     509 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.23
                                   EEEEESTTSSHHHHHHH CS
                                   xxxxxxxxxxxxxxxxx RF
                          SMC_N 27 taivGpNGSGKsnlldA 43
                                     i+G+ G+GKs l+  
  gi|116753813|ref|YP_842931.1| 33 VGILGRSGAGKSVLMHV 49
                                   469*********99865 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00017
                                    TEEE-HHHHHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCT CS
                                    xxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 115 gkevtkkevsellesagiske......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksk 188
                                    g++++ ++ ++ll ++++s        +LSgGek+ v     +A q +k   l l De    LD +  + v + +k++  
  gi|116753813|ref|YP_842931.1| 144 GETISVHKAADLLDEVNLSHRmmhvarELSGGEKQRVV----LARQLAKSPMLLLADEPTGTLDPATAAVVHDSIKRAVR 219
                                    4555566666666666666666666668******9665....55566666667778********************8877 PP

                                    T..SEEEEE-SSHH.HCCC-SCE CS
                                    x..xxxxxxxxxxx.xxxxxxxx RF
                          SMC_N 189 n..aQfivislree.mlekadkl 208
                                    +  + ++++s+ ++ m+  ad+ 
  gi|116753813|ref|YP_842931.1| 220 DfkMTMVITSHWQDvMVDLADRA 242
                                    63355677777554155556665 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.57
                                    TSSEEEEEESTTSSHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  23 sksftaivGpNGSGKsnlldA 43 
                                    ++++  ivG  G GK+ l   
  gi|116753813|ref|YP_842931.1| 312 EREIFGIVGVSGGGKTTLSKI 332
                                    567788*********998765 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.01
                                    TTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx RF
                          SMC_N 134 kelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislreemleka 205
                                    +++LS Ge+  va+a ++    +k   +++lDe    +D     +v++ + +++++    f+++s++ ++++++
  gi|116753813|ref|YP_842931.1| 428 PDELSEGERHRVAMAQVL----IKEPRIVVLDEPTGTMDPITKIEVSKSILSAREEleETFVIVSHDMDFVSNV 497
                                    4589*****999999884....5666799************99999999988877744789999**99998876 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0    0.0003      0.31      24      43 ..      31      50 ..      16      53 .. 0.89
   2 ?    4.7   0.7     0.027        28      26      43 ..     316     333 ..     311     342 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0003
                          DUF87 24 rHlAilgsTGsGKSntvavL 43
                                   ++++ilg++G+GKS ++ vL
  gi|116753813|ref|YP_842931.1| 31 ESVGILGRSGAGKSVLMHVL 50
                                   679**************998 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.027
                          DUF87  26 lAilgsTGsGKSntvavL 43 
                                    ++i+g +G GK+++ +++
  gi|116753813|ref|YP_842931.1| 316 FGIVGVSGGGKTTLSKII 333
                                    89**********998876 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.0     0.006       6.3      22      38 ..      32      48 ..      17      58 .. 0.83
   2 !    8.2   0.1    0.0012       1.3      16      40 ..     311     333 ..     298     358 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.006
                                   EEEEEESTTSSHHHHHH CS
                         NB-ARC 22 vvalvGmgGvGKttlak 38
                                    v++ G+ G GK++l++
  gi|116753813|ref|YP_842931.1| 32 SVGILGRSGAGKSVLMH 48
                                   699************96 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0012
                                    TTSCSEEEEEEESTTSSHHHHHHHH CS
                         NB-ARC  16 delqslvvalvGmgGvGKttlakqi 40 
                                     e +  + ++vG  G GKttl+k i
  gi|116753813|ref|YP_842931.1| 311 YERE--IFGIVGVSGGGKTTLSKII 333
                                    4555..99*************9865 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 ?    5.4   0.0      0.02        22      25      42 ..     164     181 ..     151     216 .. 0.68
   2 ?    6.0   0.0     0.013        14      62      78 ..     447     463 ..     411     472 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.02
                        SbcCD_C  25 elsrssgtlSGGekqfla 42 
                                    ++ + +++lSGGekq ++
  gi|116753813|ref|YP_842931.1| 164 RMMHVARELSGGEKQRVV 181
                                    567788999****97655 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.013
                        SbcCD_C  62 palrlvfLDEAFsklDe 78 
                                    + +r+v+LDE  +++D+
  gi|116753813|ref|YP_842931.1| 447 KEPRIVVLDEPTGTMDP 463
                                    469*************7 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 ?    4.2   0.0     0.031        33      44      65 ..      27      48 ..      18      64 .. 0.89
   2 ?    1.9   0.1      0.15   1.6e+02      81     147 ..     150     229 ..     136     246 .. 0.54
   3 ?    4.1   0.0     0.033        35      30      67 ..     295     333 ..     289     372 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.031
                      IstB_IS21 44 iekkenivllGpsGvGKshlai 65
                                   ie+ e++ +lG sG+GKs l  
  gi|116753813|ref|YP_842931.1| 27 IEEGESVGILGRSGAGKSVLMH 48
                                   788999************9865 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.15
                      IstB_IS21  81 vrvedLveelkrarrdgklaral...........krllkvdllilDdlgllpldqaeaellfeviekrye..rrsiiits 147
                                     +++dL+ e+++ +r  ++ar+l           ++l+k+ +l+l d  + +ld a a+++ + i++++   + +++its
  gi|116753813|ref|YP_842931.1| 150 HKAADLLDEVNLSHRMMHVARELsggekqrvvlaRQLAKSPMLLLADEPTGTLDPATAAVVHDSIKRAVRdfKMTMVITS 229
                                    55555555555555555555544111110000115566666666666666777777777777777665542245555555 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.033
                      IstB_IS21  30 ldkrkvkeLatlsf.iekkenivllGpsGvGKshlaial 67 
                                    +d+  vk++ + sf + ++e + ++G sG GK+ l+  +
  gi|116753813|ref|YP_842931.1| 295 IDRGVVKAVDNVSFeVYEREIFGIVGVSGGGKTTLSKII 333
                                    56667777777888678899999**********998654 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0    0.0092       9.7      21      41 ..      33      53 ..      24      68 .. 0.82
   2 ?    4.9   0.4     0.018        19      19      46 ..     314     342 ..     307     456 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0092
                         AAA_30 21 avltGpAGtGKttalkalrea 41
                                   + + G+ G+GK+ ++ +lr +
  gi|116753813|ref|YP_842931.1| 33 VGILGRSGAGKSVLMHVLRGV 53
                                   5688************99876 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.018
                         AAA_30  19 rvavltGpAGtGKttalkalreaweaa.g 46 
                                     +  ++G+ G GKtt+ k +  +++   g
  gi|116753813|ref|YP_842931.1| 314 EIFGIVGVSGGGKTTLSKIISGLITPTsG 342
                                    57789***********9999888776655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.073        77      21      39 ..      32      50 ..       7      53 .. 0.77
   2 ?    7.9   0.3    0.0037       3.9      13      37 ..     306     331 ..     300     342 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.073
                         AAA_23 21 ltlItGpNGaGKTTildAi 39
                                    + I G  GaGK+ ++  +
  gi|116753813|ref|YP_842931.1| 32 SVGILGRSGAGKSVLMHVL 50
                                   568**********998655 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0037
                         AAA_23  13 qeidF.skgltlItGpNGaGKTTild 37 
                                    ++++  ++ ++ I+G  G GKTT+  
  gi|116753813|ref|YP_842931.1| 306 VSFEVyEREIFGIVGVSGGGKTTLSK 331
                                    444447889**************965 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0    0.0017       1.8       2      21 ..      33      52 ..      32      72 .. 0.86
   2 ?    3.2   0.1     0.085        89       3      22 ..     317     336 ..     315     354 .. 0.80
   3 ?   -3.2   0.0       8.1   8.6e+03      28      38 ..     455     465 ..     432     501 .. 0.51

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0017
                                   EEEEESTTSSHHHHHHHHHT CS
                       MMR_HSR1  2 vaivGrpNvGKStLinaltg 21
                                   v+i+Gr+ +GKS L+  l g
  gi|116753813|ref|YP_842931.1| 33 VGILGRSGAGKSVLMHVLRG 52
                                   89************998865 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.085
                                    EEEESTTSSHHHHHHHHHTS CS
                       MMR_HSR1   3 aivGrpNvGKStLinaltge 22 
                                    +ivG +  GK+tL + ++g 
  gi|116753813|ref|YP_842931.1| 317 GIVGVSGGGKTTLSKIISGL 336
                                    8************9988874 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 8.1
                                    SSTTSSSSEEE CS
                       MMR_HSR1  28 dkpgtTrdine 38 
                                    d+p  T d+++
  gi|116753813|ref|YP_842931.1| 455 DEPTGTMDPIT 465
                                    33333333322 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 ?    2.5   0.0      0.12   1.2e+02       2      22 ..      33      53 ..      32      68 .. 0.75
   2 ?    7.6   0.1    0.0032       3.3       1      21 [.     315     334 ..     315     361 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.12
                           MobB  2 lgivgksgsGKTtLleklipe 22
                                   +gi g+sg+GK  L++ l  +
  gi|116753813|ref|YP_842931.1| 33 VGILGRSGAGKSVLMHVLRGV 53
                                   789***********9877555 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0032
                           MobB   1 vlgivgksgsGKTtLleklip 21 
                                    ++givg sg GKTtL  k+i+
  gi|116753813|ref|YP_842931.1| 315 IFGIVGVSGGGKTTLS-KIIS 334
                                    689***********84.4554 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1      0.12   1.3e+02       1      24 [.      33      56 ..      33      74 .. 0.73
   2 ?    8.6   0.2    0.0024       2.5       3      21 ..     318     336 ..     317     369 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.12
                         AAA_18  1 IlltGtpGvGKttlakeLskrlgf 24
                                   +++ G +G+GK+ l + L+  ++f
  gi|116753813|ref|YP_842931.1| 33 VGILGRSGAGKSVLMHVLRGVEEF 56
                                   6899**********9999544344 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0024
                         AAA_18   3 ltGtpGvGKttlakeLskr 21 
                                    + G++G GKttl+k +s +
  gi|116753813|ref|YP_842931.1| 318 IVGVSGGGKTTLSKIISGL 336
                                    89************99755 PP

>> mTERF  mTERF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00023      0.24     200     244 ..     384     431 ..     357     456 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00023
                          mTERF 200 rvikkyPqilsls...eekilksvetLlglGfskeevakmvkrfpqll 244
                                     vi+++ + ++ls   e   +k ++tL+ +Gf+++e  ++  ++p+ l
  gi|116753813|ref|YP_842931.1| 384 TVIENLTEAIGLSlpyELGERKAIHTLTTVGFTEDEAEMILNKYPDEL 431
                                    688888888888887777778889999999999999999999999765 PP

>> zf-CSL  CSL zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.2       7.4   7.8e+03      21      24 ..      70      74 ..      66      75 .. 0.73
   2 ?   10.6   0.0   0.00034      0.36      20      36 ..      85     101 ..      84     116 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 7.4
                                   E.TTS CS
                         zf-CSL 21 C.RCg 24
                                   C RCg
  gi|116753813|ref|YP_842931.1| 70 CdRCG 74
                                   77887 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00034
                                    EETTSSEEEEEHHHHHT CS
                         zf-CSL  20 pCRCgdeFelteedlee 36 
                                    +CRCg++F+ +e+d+ +
  gi|116753813|ref|YP_842931.1|  85 QCRCGGTFKASEADFAK 101
                                    6************9876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0085         9      23      45 ..      29      51 ..      17      80 .. 0.83
   2 ?   -1.9   0.1       3.6   3.8e+03     106     106 ..     161     161 ..      93     224 .. 0.54
   3 ?    2.7   0.0      0.14   1.5e+02      27      48 ..     316     337 ..     307     456 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0085
                         AAA_16 23 rpelvllsGesGvGKsslvrell 45
                                   ++e+v + G sG GKs l+  l+
  gi|116753813|ref|YP_842931.1| 29 EGESVGILGRSGAGKSVLMHVLR 51
                                   458999************96654 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.6
                         AAA_16 106 a 106
                                     
  gi|116753813|ref|YP_842931.1| 161 L 161
                                    0 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.14
                         AAA_16  27 vllsGesGvGKsslvrellral 48 
                                      ++G sG GK++l + +   +
  gi|116753813|ref|YP_842931.1| 316 FGIVGVSGGGKTTLSKIISGLI 337
                                    5589*********977665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (533 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      614  (0.0342462); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); 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: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.44
# Mc/sec: 3652.65
//
Query:       gi|116753814|ref|YP_842932.1|  [L=196]
Description: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-24   86.8   0.0    2.4e-24   85.9   0.0    1.3  1  Flavoprotein  Flavoprotein


Domain annotation for each model (and alignments):
>> Flavoprotein  Flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.9   0.0   1.3e-28   2.4e-24       1     125 [.       1     162 [.       1     171 [. 0.86

  Alignments for each domain:
  == domain 1  score: 85.9 bits;  conditional E-value: 1.3e-28
                                    EEEEEEE-SSCGGGCHHHHHHHHHHTTEEEEEEESCHHHHCCHHG..GS....TCSSHHHHHHCT............... CS
                   Flavoprotein   1 kkillgiTGsvaaikalellekLkkegievqvvltkaAkkfiske..klklaaredpilhielrr............... 63 
                                    ++i+lgi+G+++++++ +lle L++  + v++++t+aA+k+++ e  ++ +++       i+l++               
  gi|116753814|ref|YP_842932.1|   1 MEIVLGISGASGVVYGTRLLEVLRE-RCFVNLIVTEAARKILEIEcdRSYKDI-------ISLADrvfepgdltapiasg 72 
                                    68**********************7.*****************8854222222.......45544566666677777777 PP

                                    ..TESEEEEEEEEHHHHHHHHTT--SSHH..............................HHHHHTHCCTTEEEEE.--HH CS
                   Flavoprotein  64 ..wadllviaPasantlakianGiadnll..............................tlilratakkpiliaPamnpa 111
                                       +d++v+aP+s+ t+a+ia+G++d+l+                              +    a+++++ +++P ++p+
  gi|116753814|ref|YP_842932.1|  73 syLFDAMVVAPCSMRTMAAIAYGMSDTLItrvadvclkqrrplvlvpresplslihlrnMV---AVSEAGGIVLP-ASPS 148
                                    77*************************************************9999864433...579********.**** PP

                                    CCTCSTCHHHHHHH CS
                   Flavoprotein 112 myenpqtlknlekl 125
                                    +y++p ++ +l++ 
  gi|116753814|ref|YP_842932.1| 149 FYSRPLKVGDLVDT 162
                                    *******9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1421.72
//
Query:       gi|116753815|ref|YP_842933.1|  [L=387]
Description: major facilitator transporter [Methanosaeta thermophila PT]
Scores for complete 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  181.9  52.2    3.2e-36  125.0  25.0    2.0  2  MFS_1        Major Facilitator Superfamily
      1e-06   27.9  21.9      8e-06   24.9   9.2    2.1  2  MFS_1_like   MFS_1 like family
    3.2e-06   26.3  12.2    3.2e-06   26.3  12.2    2.8  2  Sugar_tr     Sugar (and other) transporter
     0.0071   14.8  23.7     0.0078   14.6  23.7    1.1  1  MFS_3        Transmembrane secretion effector
  ------ inclusion threshold ------
       0.19   10.0  18.6      0.036   12.4   2.3    3.2  3  OATP         Organic Anion Transporter Polypeptide (OATP) fam


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.0  25.0   8.8e-40   3.2e-36       1     221 [.      11     220 ..      11     230 .. 0.84
   2 !   60.4  23.3   3.8e-20   1.4e-16       3     167 ..     216     380 ..     209     386 .. 0.85

  Alignments for each domain:
  == domain 1  score: 125.0 bits;  conditional E-value: 8.8e-40
                          MFS_1   1 lllaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalg.llll 79 
                                    l+l++f+s l++++++p++p ++  d g+++  +g+++++y+++++++++p+Grlsd  Gr++vll+gll+f ++ ll++
  gi|116753815|ref|YP_842933.1|  11 LYLSVFVSVLGFAVVAPIFP-LYVLDMGATHLMLGMIISIYGAVQLLTQMPAGRLSDQRGRKPVLLIGLLTFTIMpLLYI 89 
                                    5799****************.7889**************************************************55555 PP

                          MFS_1  80 lfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilai 159
                                      as+ + ll+ r++ G+ga++++p+ +ali+d + +++rg+a+g+++a+f  ++++gp++g+ll+ s+g  a+f++  +
  gi|116753815|ref|YP_842933.1|  90 Y-ASNAYQLLLIRIFGGIGASMVWPVTMALIVDCVDPSHRGLAMGWYNASFYSAVAVGPVIGSLLYGSFGINAPFIFWSL 168
                                    5.677779************************************************************************ PP

                          MFS_1 160 vsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfff 221
                                    +++ +++++ ++++e+p++ +  s+ +      ++p +    +++    +   +i+++++ +
  gi|116753815|ref|YP_842933.1| 169 FAVASLIMVTFVVREPPVRGEVLSTNTP-----RTPKAR---LIVDGSMI--TFIICCSVVM 220
                                    *****99755555555555555544444.....333333...33333322..4444444444 PP

  == domain 2  score: 60.4 bits;  conditional E-value: 3.8e-20
                          MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalglllllf 81 
                                    ++++++   ++ ++++l + la + g+ +s++g+l+ +ya   a+a++ +Gr++d  G+rr ++  g l+ +lg+l+l  
  gi|116753815|ref|YP_842933.1| 216 CSVVMVPGIIGGFNMTLLPELALSVGVGVSQLGILYMAYAGSNALANIYFGRVADL-GHRRlLISGGSLGCVLGFLVLG- 293
                                    555566666666666666699**********************************6.9999666666666666666666. PP

                          MFS_1  82 a.sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaiv 160
                                    + +++ + l++  + Gl +g+ +pa+ ++++ ++++e+rg  +g+++++  lG+++gp+++gl a+++g  ++  ++ +v
  gi|116753815|ref|YP_842933.1| 294 HgQGILPQLIALTILGLSSGICTPAATVVVSYITSPERRGEIFGIFNTSRMLGVVIGPIIAGLTADLGGLAGAITAFLAV 373
                                    35889989999999*******************************************************99998888888 PP

                          MFS_1 161 sllafvl 167
                                    sll   +
  gi|116753815|ref|YP_842933.1| 374 SLLISAM 380
                                    8887554 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 !   24.9   9.2   2.2e-09     8e-06     232     379 ..      13     159 ..       5     166 .. 0.87
   2 !    8.5   5.7   0.00023      0.82     189     378 ..     169     362 ..     159     372 .. 0.65

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 2.2e-09
                     MFS_1_like 232 lvalilgmswgiienFlflYLkelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaiie 311
                                    l +++    ++++   + lY  ++ga++ +lG+++ +  + ++ + + a +l ++ G   +l+i+ll++++  lly + +
  gi|116753815|ref|YP_842933.1|  13 LSVFVSVLGFAVVAPIFPLYVLDMGATHLMLGMIISIYGAVQLLTQMPAGRLSDQRGRKPVLLIGLLTFTIMPLLYIYAS 92 
                                    5555555566677777899************************************************************* PP

                     MFS_1_like 312 nawlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsglyfglGralGsliGGllwdlksa 379
                                    na  +l+i ++ gi   ++w + +  + + + +s+++  +g +++ ++++  a+G +iG ll++ ++ 
  gi|116753815|ref|YP_842933.1|  93 NAYQLLLIRIFGGIGASMVWPVTMALIVDCVDPSHRGLAMGWYNASFYSA-VAVGPVIGSLLYGSFGI 159
                                    *******************************************9988774.67777777777766665 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00023
                     MFS_1_like 189 llvisllvvl.ilnetekesklkvtkslqvl.lnilknpeviifllvalilgmswgiienFlflYLkel....gasntll 262
                                    + v+sl++v  ++ e     ++  t++++    +++ + ++i+f++ +  + m+ gii+ F    L el    g   + l
  gi|116753815|ref|YP_842933.1| 169 FAVASLIMVTfVVREPPVRGEVLSTNTPRTPkARLIVDGSMITFIICCS-VVMVPGIIGGFNMTLLPELalsvGVGVSQL 247
                                    3344433322012222222333333444443055666666666666555.568999999998888733300113334445 PP

                     MFS_1_like 263 GslvalgvvaeiplfffaeklleklGhvklliialla.yilrfllyaiienawlvlpievLhgisfgllwaaaveyvski 341
                                    G+l +  + ++    ++  + +  lGh++lli + ++  +l fl+++  +     l++ ++ g+s g++  aa+ +vs i
  gi|116753815|ref|YP_842933.1| 248 GILYMAYAGSNALANIYFGR-VADLGHRRLLISGGSLgCVLGFLVLGHGQGILPQLIALTILGLSSGICTPAATVVVSYI 326
                                    55544444444333333333.4678****9998765516788************************************** PP

                     MFS_1_like 342 apksleatgqgllsglyfglGralGsliGGllwdlks 378
                                    ++++ ++ + g++++    lG  +G +i+Gl+ dl +
  gi|116753815|ref|YP_842933.1| 327 TSPERRGEIFGIFNTS-RMLGVVIGPIIAGLTADLGG 362
                                    *************987.67************987654 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3  12.2   8.9e-10   3.2e-06      44     191 ..      39     180 ..      12     186 .. 0.84
   2 ?    0.9  18.1     0.046   1.6e+02      47     182 ..     246     379 ..     166     385 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 8.9e-10
                                    ...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHH CS
                       Sugar_tr  44 ssvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlv 123
                                    + + +g+i si+ ++++++++ ag l+d  GRk++lli+ + f i  +l + a    + ++l++ R++ Gig+ ++  ++
  gi|116753815|ref|YP_842933.1|  39 THLMLGMIISIYGAVQLLTQMPAGRLSDQRGRKPVLLIGLLTFTIMPLLYIYAS---NAYQLLLIRIFGGIGASMVWPVT 115
                                    56789*************************************************...99********************* PP

                                    HHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS CS
                       Sugar_tr 124 PmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilllfl 191
                                      +i     +++Rg  +++y+ +      v+ ++g  l  + +      ++ + +++a++ li+++f+
  gi|116753815|ref|YP_842933.1| 116 MALIVDCVDPSHRGLAMGWYNASFYSAVAVGPVIGSLLYGSFG---INAPFIFWSLFAVASLIMVTFV 180
                                    *********************9888887777777777633333...4566666666666666666553 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.046
                                    HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHH CS
                       Sugar_tr  47 lsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmy 126
                                    ++g++  ++    ++  +++g ++d   R+  +  +++ +v g ++ +  +    +   +++  ++G++ G+++  +++ 
  gi|116753815|ref|YP_842933.1| 246 QLGILYMAYAGSNALANIYFGRVADLGHRRLLISGGSLGCVLGFLVLGHGQ---GILPQLIALTILGLSSGICTPAATVV 322
                                    455555555555678889999999988888888889999999998888888...566666667899************** PP

                                    HHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-.TTHHHHHHHCCHHHHH CS
                       Sugar_tr 127 isEiApkklRgalvslyqlaitfGilvaaifglglnktsn.adgwrillglqlvpal 182
                                    +s i+ ++ Rg + ++++++  +G +++ i+   +++ ++ a     +l+++l+++ 
  gi|116753815|ref|YP_842933.1| 323 VSYITSPERRGEIFGIFNTSRMLGVVIGPIIAGLTADLGGlAGAITAFLAVSLLISA 379
                                    ******************************999998888867777777777776664 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6  23.7   2.2e-06    0.0078      34     390 ..      30     382 ..       1     387 [] 0.76

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.2e-06
                          MFS_3  34 sWlmtdisasplmvAlvqaaatLPifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlli 113
                                       + d+ a+ lm  ++        +l  ++aG l+D+  r+ vll++ l        ++ l ++   + + ll + ++ 
  gi|116753815|ref|YP_842933.1|  30 PLYVLDMGATHLMLGMIISIYGAVQLLTQMPAGRLSDQRGRKPVLLIGLLTFT-----IMPLLYIYASNAYQLLLIRIFG 104
                                    55566777777888877766666678889****************99976544.....444555556678889999999* PP

                          MFS_3 114 giGaalndPaWqAsvgelvkrrdvpaAvaLnsvginiaRsvGPAlgGvlvaavGaalafavnalsylalivallrwkrev 193
                                    giGa++  P   A + + v+ ++   A+      +  a +vGP +g +l  ++G  + f + +l  +a    l+ +   v
  gi|116753815|ref|YP_842933.1| 105 GIGASMVWPVTMALIVDCVDPSHRGLAMGWYNASFYSAVAVGPVIGSLLYGSFGINAPFIFWSLFAVA---SLIMVTFVV 181
                                    *******************************************************9999887664444...333444445 PP

                          MFS_3 194 rksslprEklleal..raglRftaasreikavlvRaalF..glsasavlaLLPlvardqldgdalvyGillgalGvGAil 269
                                    r+ ++  E l +    +  +R     + i  ++  +++   g+     ++LLP +a   ++ + +  Gil  a      l
  gi|116753815|ref|YP_842933.1| 182 REPPVRGEVLSTNTprTPKARLIVDGSMITFIICCSVVMvpGIIGGFNMTLLPELALS-VGVGVSQLGILYMAYAGSNAL 260
                                    55555555554443113446666677777777777665533566667799****9975.78889999**98777666667 PP

                          MFS_3 270 galllsrLRerlsserlvllaavalAlvllslalasslwvavlvlllgG.aaWitalstlnvavqlavPrWvvgRalavY 348
                                    + +   r+ +  +   l++  ++++ l  l+l+  + +   +++l ++G ++ i + +   v   +++P+  +g  + ++
  gi|116753815|ref|YP_842933.1| 261 ANIYFGRVADLGHRRLLISGGSLGCVLGFLVLGHGQGILPQLIALTILGlSSGICTPAATVVVSYITSPE-RRGEIFGIF 339
                                    8999999998888888999*************************99999345566666666666667776.69******* PP

                          MFS_3 349 ltvlaGglaaGsllWGavaealsvtlaLla.aaaalllaaail 390
                                     t  + g+  G ++ G +a+  +++ a++a  a++ll++a++l
  gi|116753815|ref|YP_842933.1| 340 NTSRMLGVVIGPIIAGLTADLGGLAGAITAfLAVSLLISAMTL 382
                                    **************************99862577788877665 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 ?   12.4   2.3     1e-05     0.036     137     187 ..      99     153 ..      86     165 .. 0.78
   2 ?    3.2   2.1     0.006        21       5      83 ..     213     292 ..     209     299 .. 0.88
   3 ?    4.0   0.6    0.0034        12     140     191 ..     306     357 ..     294     360 .. 0.50

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1e-05
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxx RF
                           OATP 137 laqlllGiGatpiytlGisYidDnvkkknsplyl....gilyalrilGpalGfll 187
                                    l  ++ GiGa++++++ ++ i D v++++  l +    + +y++ ++Gp++G ll
  gi|116753815|ref|YP_842933.1|  99 LIRIFGGIGASMVWPVTMALIVDCVDPSHRGLAMgwynASFYSAVAVGPVIGSLL 153
                                    556788**********************998766111155678888888888776 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.006
                                    xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           OATP   5 llsllglvq.amvsgyfkstittiEkrFklpsstsgliassneignillilfvsYfggrghrPrwigigallmalgslll 83 
                                    ++++ +++  ++++g+  + + ++    +   s+ g++ +++  +n+l+ +  + +++ ghr  +i  g+l + lg l+l
  gi|116753815|ref|YP_842933.1| 213 IICCSVVMVpGIIGGFNMTLLPELALSVGVGVSQLGILYMAYAGSNALANIYFGRVADLGHRRLLISGGSLGCVLGFLVL 292
                                    444444444499999999999*******************************************************9986 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.0034
                                    xxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           OATP 140 lllGiGa...tpiytlGisYidDnvkkknsplylgilyalrilGpalGfllGsll 191
                                    ++lG+ +   tp  t+ +sYi   +++++    +gi+ + r+lG+++G ++++l+
  gi|116753815|ref|YP_842933.1| 306 TILGLSSgicTPAATVVVSYI---TSPERRGEIFGIFNTSRMLGVVIGPIIAGLT 357
                                    344443311133333333333...5555666666666666666666666655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 2694.07
//
Query:       gi|116753816|ref|YP_842934.1|  [L=77]
Description: AsnC family transcriptional regulator [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-10   40.8   0.1    1.9e-10   40.5   0.1    1.0  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
  ------ inclusion threshold ------
      0.069   13.1   0.0      0.069   13.1   0.0    1.1  1  GYD             GYD domain


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   0.1   2.1e-14   1.9e-10       1      73 [.       5      73 ..       5      74 .. 0.96

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 2.1e-14
                                   EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEE CS
                 AsnC_trans_reg  1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivl 73
                                   +++++epg+    +e+ + l+++  ++e+  v G+yd+++++ v+ + +l+r +   ++++p v++t+t + +
  gi|116753816|ref|YP_842934.1|  5 IMINVEPGS---EKEVFDSLQKIRDIKEVVPVYGEYDFIAIADVEAISDLNRMVLS-VREIPSVTNTRTILGM 73
                                   789******...********************************************.************9876 PP

>> GYD  GYD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   7.7e-06     0.069      38      79 ..      28      70 ..       7      76 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.7e-06
                            GYD 38 eslyatlGeyDvvvivEapDdetaaalslalaasGtvrt.etl 79
                                   +++  + GeyD+++i +++  +   ++ l++++  +v++ +t+
  gi|116753816|ref|YP_842934.1| 28 KEVVPVYGEYDFIAIADVEAISDLNRMVLSVREIPSVTNtRTI 70
                                   6677789************************999888886665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 594.67
//
Query:       gi|116753817|ref|YP_842935.1|  [L=169]
Description: TPR repeat-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-32  108.6   0.9    7.2e-13   47.8   0.2    4.2  4  TPR_1            Tetratricopeptide repeat
    7.3e-30  100.7   1.0    2.5e-10   39.7   0.1    4.2  4  TPR_2            Tetratricopeptide repeat
    7.2e-22   75.7   0.5    1.5e-07   31.0   0.0    4.3  4  TPR_8            Tetratricopeptide repeat
    4.3e-20   72.1   0.0    1.7e-08   35.0   0.0    3.1  3  TPR_16           Tetratricopeptide repeat
    2.3e-19   68.8   1.3    1.4e-06   27.9   0.1    4.3  4  TPR_11           TPR repeat
    3.5e-18   65.9   0.1    3.4e-07   30.7   0.1    3.1  3  TPR_19           Tetratricopeptide repeat
    5.1e-18   64.2   0.7     0.0011   19.5   0.0    4.1  4  TPR_14           Tetratricopeptide repeat
    7.1e-18   64.7   6.7    4.9e-10   39.6   0.5    3.7  3  TPR_12           Tetratricopeptide repeat
    4.1e-17   61.3   2.4    1.3e-07   31.5   0.1    3.8  4  TPR_17           Tetratricopeptide repeat
      9e-17   59.8   1.8      0.014   15.4   0.0    4.2  4  TPR_7            Tetratricopeptide repeat
    3.7e-15   55.8   7.0    1.3e-08   34.8   0.1    3.1  3  TPR_9            Tetratricopeptide repeat
    1.1e-11   44.2   4.4     0.0009   19.0   0.1    4.2  4  TPR_10           Tetratricopeptide repeat
      5e-10   39.4   0.1      0.086   13.5   0.0    4.1  4  TPR_6            Tetratricopeptide repeat
    1.6e-08   34.5   0.1       0.01   15.9   0.0    3.3  3  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
    5.2e-08   33.0   0.3    0.00029   21.0   0.0    2.1  2  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    5.9e-05   22.2   0.1       0.12   11.3   0.0    2.1  2  NARP1            NMDA receptor-regulated protein 1
      9e-05   22.5   0.0      0.069   13.2   0.0    2.4  2  SRP_TPR_like     Putative TPR-like repeat
     0.0001   22.3   1.0        2.5    8.5   0.0    4.1  4  PPR              PPR repeat
    0.00028   21.2   0.0        6.3    7.7   0.0    3.7  3  TPR_4            Tetratricopeptide repeat
    0.00033   20.0   0.0      0.005   16.1   0.0    1.9  2  TPR_15           Tetratricopeptide repeat
    0.00049   20.2   0.2       0.19   11.8   0.0    2.8  2  DUF3856          Domain of Unknown Function (DUF3856)
    0.00079   19.9   0.5      0.012   16.1   0.1    2.4  2  BTAD             Bacterial transcriptional activator domain
     0.0012   18.8   1.3        8.6    6.5   0.1    3.8  4  MIT              MIT (microtubule interacting and transport) 
     0.0017   17.8   0.0       0.43    9.9   0.0    2.8  2  TPR_MalT         MalT-like TPR region
     0.0041   17.1   0.0        1.3    9.1   0.0    3.7  4  TPR_3            Tetratricopeptide repeat
     0.0083   16.4   0.0      0.016   15.4   0.0    1.5  1  TPR_5            Tetratrico peptide repeat
     0.0088   15.8   0.3       0.37   10.5   0.2    3.0  3  RPN7             26S proteasome subunit RPN7
  ------ inclusion threshold ------
      0.014   15.5   0.0         11    6.2   0.0    3.1  3  Rapsyn_N         Rapsyn N-terminal myristoylation and linker 
      0.024   14.4   0.0          6    6.7   0.0    2.4  2  SGTA_dimer       Homodimerisation domain of SGTA
      0.045   14.1   0.2       0.32   11.4   0.1    2.1  2  TPR_20           Tetratricopeptide repeat
      0.088   12.8   0.0         12    5.9   0.0    2.9  3  DUF627           Protein of unknown function (DUF627)
       0.11   12.9   0.0          4    7.9   0.0    2.4  2  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   2.4e-09   1.4e-06      13      33 ..      17      37 ..       8      38 .. 0.95
   2 !   47.8   0.2   1.3e-15   7.2e-13       2      34 .]      40      72 ..      39      72 .. 0.96
   3 !   16.9   0.0   7.4e-06    0.0042       3      29 ..      75     101 ..      74     102 .. 0.90
   4 !   11.6   0.0   0.00035       0.2       7      30 ..     112     135 ..     111     139 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 2.4e-09
                                   HTT-HHHHHHHHHHHHHHSTT CS
                          TPR_1 13 klgkydeAleyyekALelnPn 33
                                   k g+y++A+ey+++ALe+nP+
  gi|116753817|ref|YP_842935.1| 17 KRGMYEKAVEYCDRALEINPD 37
                                   78******************8 PP

  == domain 2  score: 47.8 bits;  conditional E-value: 1.3e-15
                                   HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                          TPR_1  2 kalynlGnayfklgkydeAleyyekALelnPnn 34
                                   +a++n+G+a+++l + deAle+y++ALe++P n
  gi|116753817|ref|YP_842935.1| 40 DAWNNKGVALYNLDRIDEALECYNRALEIDPGN 72
                                   8******************************87 PP

  == domain 3  score: 16.9 bits;  conditional E-value: 7.4e-06
                                    HHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                          TPR_1   3 alynlGnayfklgkydeAleyyekALe 29 
                                    a  n++ +++ lg++++Ale ye  +e
  gi|116753817|ref|YP_842935.1|  75 AMRNIAFVHRDLGELEKALELYETIIE 101
                                    5679*******************9887 PP

  == domain 4  score: 11.6 bits;  conditional E-value: 0.00035
                                    HHHHHHHTT-HHHHHHHHHHHHHH CS
                          TPR_1   7 lGnayfklgkydeAleyyekALel 30 
                                    ++ ++  lg++++A+e+  +A e 
  gi|116753817|ref|YP_842935.1| 112 KATILVALGRFQDAIECIGRAYEM 135
                                    5778899**********9999776 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   5.6e-08   3.1e-05       3      33 ..       7      37 ..       5      38 .. 0.90
   2 !   39.7   0.1   4.4e-13   2.5e-10       2      34 .]      40      72 ..      39      72 .. 0.96
   3 !   17.1   0.0   7.2e-06    0.0041       3      29 ..      75     101 ..      73     103 .. 0.91
   4 !   16.2   0.0   1.4e-05     0.008       4      33 ..     109     138 ..     106     139 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 5.6e-08
                          TPR_2  3 alynlGlayyklgdyeeAleafekAleldPn 33
                                   +l   G    k+g ye+A+e++++Ale++P+
  gi|116753817|ref|YP_842935.1|  7 ILIHKGIDMVKRGMYEKAVEYCDRALEINPD 37
                                   5777889999********************8 PP

  == domain 2  score: 39.7 bits;  conditional E-value: 4.4e-13
                          TPR_2  2 ealynlGlayyklgdyeeAleafekAleldPnn 34
                                   +a++n G a+y+l++ +eAle++++Ale+dP+n
  gi|116753817|ref|YP_842935.1| 40 DAWNNKGVALYNLDRIDEALECYNRALEIDPGN 72
                                   79*****************************97 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 7.2e-06
                          TPR_2   3 alynlGlayyklgdyeeAleafekAle 29 
                                    a  n++ +++ lg++e+Ale++e  +e
  gi|116753817|ref|YP_842935.1|  75 AMRNIAFVHRDLGELEKALELYETIIE 101
                                    7899*******************9876 PP

  == domain 4  score: 16.2 bits;  conditional E-value: 1.4e-05
                          TPR_2   4 lynlGlayyklgdyeeAleafekAleldPn 33 
                                    l + + ++ +lg++++A+e+  +A e  P+
  gi|116753817|ref|YP_842935.1| 109 LEAKATILVALGRFQDAIECIGRAYEMTPD 138
                                    567889999*****************9997 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   8.7e-06    0.0049      14      33 ..      18      37 ..      16      38 .. 0.92
   2 !   31.0   0.0   2.7e-10   1.5e-07       2      33 ..      40      71 ..      39      72 .. 0.95
   3 !   10.8   0.0   0.00086      0.48       6      29 ..      78     101 ..      73     102 .. 0.90
   4 !   12.4   0.0   0.00025      0.14       7      33 ..     112     138 ..     109     139 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 8.7e-06
                                   TT-HHHHHHHHHHHHHHHHH CS
                          TPR_8 14 lgdyeeAkeyyekaleldpd 33
                                    g ye+A+ey+ +ale++pd
  gi|116753817|ref|YP_842935.1| 18 RGMYEKAVEYCDRALEINPD 37
                                   589****************8 PP

  == domain 2  score: 31.0 bits;  conditional E-value: 2.7e-10
                                   CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                          TPR_8  2 eayynlgsiylklgdyeeAkeyyekaleldpd 33
                                   +a++n+g ++ +l +++eA e+y++ale+dp 
  gi|116753817|ref|YP_842935.1| 40 DAWNNKGVALYNLDRIDEALECYNRALEIDPG 71
                                   79****************************96 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00086
                                    HHHHHHHHTT-HHHHHHHHHHHHH CS
                          TPR_8   6 nlgsiylklgdyeeAkeyyekale 29 
                                    n++ ++++lg++e+A e ye  +e
  gi|116753817|ref|YP_842935.1|  78 NIAFVHRDLGELEKALELYETIIE 101
                                    79999***************9887 PP

  == domain 4  score: 12.4 bits;  conditional E-value: 0.00025
                                    HHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                          TPR_8   7 lgsiylklgdyeeAkeyyekaleldpd 33 
                                    ++ i+  lg+++ A+e++ +a e+ pd
  gi|116753817|ref|YP_842935.1| 112 KATILVALGRFQDAIECIGRAYEMTPD 138
                                    7899********************998 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.0     3e-11   1.7e-08       8      67 ..      16      72 ..      11      72 .. 0.94
   2 !   30.0   0.1   1.1e-09   6.1e-07       8      64 ..      50     103 ..      49     108 .. 0.91
   3 !   16.2   0.0   2.2e-05     0.013       2      41 ..     111     150 ..     110     158 .. 0.86

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 3e-11
                         TPR_16  8 lragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67
                                   +++g y++A+++ ++al+ +   Pd  +A++++g+a++ + r +eA++ y++al+ +p++
  gi|116753817|ref|YP_842935.1| 16 VKRGMYEKAVEYCDRALEIN---PDSSDAWNNKGVALYNLDRIDEALECYNRALEIDPGN 72
                                   67888***************...99999******************************86 PP

  == domain 2  score: 30.0 bits;  conditional E-value: 1.1e-09
                         TPR_16   8 lragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraa 64 
                                    +++ + d+A++ +++al+ d   P + +A+ + + ++  +g+l++A++ly+  ++ +
  gi|116753817|ref|YP_842935.1|  50 YNLDRIDEALECYNRALEID---PGNLDAMRNIAFVHRDLGELEKALELYETIIERG 103
                                    778899**************...****************************998665 PP

  == domain 3  score: 16.2 bits;  conditional E-value: 2.2e-05
                         TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllg 41 
                                    a+a++++++g+++dA++   +a ++ p++ + +e++   g
  gi|116753817|ref|YP_842935.1| 111 AKATILVALGRFQDAIECIGRAYEMTPDPRFEVEMAAIIG 150
                                    6899**********************99988888776665 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.1     9e-09     5e-06       5      41 ..      16      52 ..      14      53 .. 0.95
   2 !   27.9   0.1   2.5e-09   1.4e-06       3      38 ..      48      83 ..      48      86 .. 0.91
   3 !    8.6   0.1    0.0027       1.5       4      19 ..      83      98 ..      82     101 .. 0.88
   4 ?    5.7   0.0     0.021        12       3      26 ..     115     138 ..     113     138 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 9e-09
                         TPR_11  5 yeqGkyeeAieaYkkAlkldPdnaeayynLGlayykq 41
                                   +++G ye+A+e   +Al+++Pd+ +a++n G+a+y++
  gi|116753817|ref|YP_842935.1| 16 VKRGMYEKAVEYCDRALEINPDSSDAWNNKGVALYNL 52
                                   589********************************86 PP

  == domain 2  score: 27.9 bits;  conditional E-value: 2.5e-09
                         TPR_11  3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlay 38
                                   a+y + +++eA+e+Y++Al++dP n +a  n+++++
  gi|116753817|ref|YP_842935.1| 48 ALYNLDRIDEALECYNRALEIDPGNLDAMRNIAFVH 83
                                   5788889**********************9999987 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0027
                         TPR_11  4 yyeqGkyeeAieaYkk 19
                                    +++G++e+A+e Y++
  gi|116753817|ref|YP_842935.1| 83 HRDLGELEKALELYET 98
                                   689***********85 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.021
                         TPR_11   3 ayyeqGkyeeAieaYkkAlkldPd 26 
                                    +++++G++ +Aie+  +A + +Pd
  gi|116753817|ref|YP_842935.1| 115 ILVALGRFQDAIECIGRAYEMTPD 138
                                    789**********98888877776 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.1   6.1e-10   3.4e-07       2      52 ..      16      66 ..      15      67 .. 0.95
   2 !   29.7   0.1   1.2e-09   6.7e-07       7      57 ..      55     105 ..      54     113 .. 0.92
   3 !   13.1   0.0   0.00019       0.1      32      61 ..     113     141 ..     106     148 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 6.1e-10
                         TPR_19  2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalp 52
                                   +++g y+ A+++  +al+ +p++++a+ +   al++l ++deA ++ ++++
  gi|116753817|ref|YP_842935.1| 16 VKRGMYEKAVEYCDRALEINPDSSDAWNNKGVALYNLDRIDEALECYNRAL 66
                                   5789******************************************99987 PP

  == domain 2  score: 29.7 bits;  conditional E-value: 1.2e-09
                         TPR_19   7 yaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                     +eAl+ + +al+ dp+n++a  + A ++  lg+l++A +l +++ e   d
  gi|116753817|ref|YP_842935.1|  55 IDEALECYNRALEIDPGNLDAMRNIAFVHRDLGELEKALELYETIIERGGD 105
                                    69*********************************************9998 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 0.00019
                         TPR_19  32 AeallalgqldeAealLdalpeedpddary 61 
                                    A +l+alg++++A++++ ++ e++pd +r 
  gi|116753817|ref|YP_842935.1| 113 ATILVALGRFQDAIECIGRAYEMTPD-PRF 141
                                    889***********************.775 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   2.3e-06    0.0013      13      40 ..      17      44 ..      11      48 .. 0.89
   2 !   19.5   0.0     2e-06    0.0011      10      42 ..      48      80 ..      45      82 .. 0.89
   3 !   12.2   0.1   0.00047      0.27       7      34 ..      79     106 ..      73     112 .. 0.85
   4 !   10.8   0.0    0.0013      0.73       7      34 ..     112     139 ..     106     148 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.3e-06
                         TPR_14 13 alGdpdeAiallrralalaPddaeawll 40
                                    +G +++A+++++ral+ +Pd+ +aw  
  gi|116753817|ref|YP_842935.1| 17 KRGMYEKAVEYCDRALEINPDSSDAWNN 44
                                   689**********************965 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 2e-06
                         TPR_14 10 allalGdpdeAiallrralalaPddaeawllla 42
                                   al++l++ deA+++++ral+ +P++++a +  a
  gi|116753817|ref|YP_842935.1| 48 ALYNLDRIDEALECYNRALEIDPGNLDAMRNIA 80
                                   8999*********************99987665 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 0.00047
                         TPR_14   7 laeallalGdpdeAiallrralalaPdd 34 
                                    +a +++ lG++++A++l++ +++++ d 
  gi|116753817|ref|YP_842935.1|  79 IAFVHRDLGELEKALELYETIIERGGDA 106
                                    577999*****************98774 PP

  == domain 4  score: 10.8 bits;  conditional E-value: 0.0013
                         TPR_14   7 laeallalGdpdeAiallrralalaPdd 34 
                                     a +l alG++++Ai++  ra +  Pd+
  gi|116753817|ref|YP_842935.1| 112 KATILVALGRFQDAIECIGRAYEMTPDP 139
                                    57899******************99995 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.2   6.4e-10   3.6e-07       9      75 ..      11      69 ..       4      70 .. 0.89
   2 !   39.6   0.5   8.7e-13   4.9e-10       3      73 ..      39     101 ..      37     103 .. 0.92
   3 !    9.8   0.0    0.0017      0.93       9      32 ..     112     135 ..     105     138 .. 0.79

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 6.4e-10
                         TPR_12  9 laavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75
                                    +    ++g y++A e++++alei      pd+   + + +n g +++ l+r +eAle +++al+i+
  gi|116753817|ref|YP_842935.1| 11 KGIDMVKRGMYEKAVEYCDRALEIN-----PDS---SDAWNNKGVALYNLDRIDEALECYNRALEID 69
                                   555666899****************.....997...89***************************96 PP

  == domain 2  score: 39.6 bits;  conditional E-value: 8.7e-13
                         TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                                    + a+nn +++l+ l r deAle++++alei      p +   + ++rn++ ++r lg++e+Alel+e  ++
  gi|116753817|ref|YP_842935.1|  39 SDAWNNKGVALYNLDRIDEALECYNRALEID-----PGN---LDAMRNIAFVHRDLGELEKALELYETIIE 101
                                    6799***************************.....656...779*********************98766 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.0017
                         TPR_12   9 laavlrrlgrydeAlellekalei 32 
                                     a++l +lgr+++A+e+  +a+e+
  gi|116753817|ref|YP_842935.1| 112 KATILVALGRFQDAIECIGRAYEM 135
                                    688888888888888888888875 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       3.6     2e+03       1       9 [.      20      28 ..      20      30 .. 0.85
   2 !   31.5   0.1   2.4e-10   1.3e-07       2      34 .]      28      60 ..      27      60 .. 0.95
   3 !   25.1   0.0   2.5e-08   1.4e-05       1      34 []      61      94 ..      61      94 .. 0.97
   4 ?    2.1   0.0      0.57   3.2e+02      18      34 .]     111     127 ..     104     127 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 3.6
                         TPR_17  1 lylkaleld 9 
                                   +y+ka+e++
  gi|116753817|ref|YP_842935.1| 20 MYEKAVEYC 28
                                   69***9986 PP

  == domain 2  score: 31.5 bits;  conditional E-value: 2.4e-10
                         TPR_17  2 ylkaleldPnnadaynnLAelllknGdlmtArq 34
                                   + +ale++P+++da+nn++++l+++ + ++A++
  gi|116753817|ref|YP_842935.1| 28 CDRALEINPDSSDAWNNKGVALYNLDRIDEALE 60
                                   89****************************985 PP

  == domain 3  score: 25.1 bits;  conditional E-value: 2.5e-08
                         TPR_17  1 lylkaleldPnnadaynnLAelllknGdlmtArq 34
                                   +y +ale+dP n da+ n A +++ +G+l++A++
  gi|116753817|ref|YP_842935.1| 61 CYNRALEIDPGNLDAMRNIAFVHRDLGELEKALE 94
                                   8******************************985 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.57
                         TPR_17  18 nLAelllknGdlmtArq 34 
                                     +A++l  +G++++A++
  gi|116753817|ref|YP_842935.1| 111 AKATILVALGRFQDAIE 127
                                    67999*********986 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   6.8e-05     0.038      11      34 ..      17      40 ..      16      41 .. 0.85
   2 !   13.9   0.1   7.6e-05     0.042       1      31 [.      41      71 ..      41      76 .. 0.85
   3 !   13.7   0.1   8.9e-05      0.05       4      24 ..      78      98 ..      75     106 .. 0.86
   4 !   15.4   0.0   2.5e-05     0.014       5      32 ..     112     139 ..     109     142 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.8e-05
                          TPR_7 11 rlGdyeeAielyeqsLaltkdped 34
                                   ++G ye+A+e++ ++L++  d +d
  gi|116753817|ref|YP_842935.1| 17 KRGMYEKAVEYCDRALEINPDSSD 40
                                   689***********9999877665 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 7.6e-05
                          TPR_7  1 aLlnLarlysrlGdyeeAielyeqsLaltkd 31
                                   a++n +++  +l + +eA+e+y ++L+++  
  gi|116753817|ref|YP_842935.1| 41 AWNNKGVALYNLDRIDEALECYNRALEIDPG 71
                                   799*********************6666543 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 8.9e-05
                          TPR_7  4 nLarlysrlGdyeeAielyeq 24
                                   n+a ++++lG+ e+A+elye 
  gi|116753817|ref|YP_842935.1| 78 NIAFVHRDLGELEKALELYET 98
                                   66668**************97 PP

  == domain 4  score: 15.4 bits;  conditional E-value: 2.5e-05
                          TPR_7   5 LarlysrlGdyeeAielyeqsLaltkdp 32 
                                     a + ++lG++++Aie+  ++ ++t dp
  gi|116753817|ref|YP_842935.1| 112 KATILVALGRFQDAIECIGRAYEMTPDP 139
                                    588999***************9**9998 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.1   2.4e-11   1.3e-08      10      65 ..      20      75 ..      15      77 .. 0.93
   2 !   24.9   0.4     3e-08   1.7e-05       9      66 ..      53     110 ..      51     112 .. 0.93
   3 !   11.5   0.1   0.00044      0.25      14      62 ..      92     139 ..      88     147 .. 0.82

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 2.4e-11
                          TPR_9 10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65
                                    +e+a ++++r l ++Pd+ + +   G++l+ l+++ +Al++ +++l+++p + da
  gi|116753817|ref|YP_842935.1| 20 MYEKAVEYCDRALEINPDSSDAWNNKGVALYNLDRIDEALECYNRALEIDPGNLDA 75
                                   589************************************************77666 PP

  == domain 2  score: 24.9 bits;  conditional E-value: 3e-08
                          TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapdae 66 
                                    ++ ++al++++r l ++P   +  r  ++++  lG l++Al+  e+ ++  +da d e
  gi|116753817|ref|YP_842935.1|  53 DRIDEALECYNRALEIDPGNLDAMRNIAFVHRDLGELEKALELYETIIERGGDAYDLE 110
                                    6889********************************************9999988776 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00044
                          TPR_9  14 alavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapda 62 
                                    al+ +e ++     d++++   + +l+ lG+++ A+++  ++ +++pd+
  gi|116753817|ref|YP_842935.1|  92 ALELYETIIERG-GDAYDLEAKATILVALGRFQDAIECIGRAYEMTPDP 139
                                    555555555543.5789999***************************86 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.039        22      16      31 ..      19      34 ..      12      38 .. 0.75
   2 !   14.3   0.4   4.9e-05     0.028       6      31 ..      43      68 ..      41      68 .. 0.96
   3 !   19.0   0.1   1.6e-06    0.0009       3      30 ..      74     101 ..      73     103 .. 0.92
   4 ?    4.3   0.0     0.071        40       9      31 ..     113     135 ..     112     136 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.039
                         TPR_10 16 grydeAealleealai 31
                                   g y++A++++++al+i
  gi|116753817|ref|YP_842935.1| 19 GMYEKAVEYCDRALEI 34
                                   5577888888888876 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 4.9e-05
                         TPR_10  6 nNLanalrqrgrydeAealleealai 31
                                   nN ++al+++ r deA++ + +al+i
  gi|116753817|ref|YP_842935.1| 43 NNKGVALYNLDRIDEALECYNRALEI 68
                                   899*********************97 PP

  == domain 3  score: 19.0 bits;  conditional E-value: 1.6e-06
                         TPR_10   3 sslnNLanalrqrgrydeAealleeala 30 
                                     ++ N+a ++r++g++++A++l+e  ++
  gi|116753817|ref|YP_842935.1|  74 DAMRNIAFVHRDLGELEKALELYETIIE 101
                                    79**********************9887 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.071
                         TPR_10   9 analrqrgrydeAealleealai 31 
                                    a +l ++gr+++A +   +a+++
  gi|116753817|ref|YP_842935.1| 113 ATILVALGRFQDAIECIGRAYEM 135
                                    678899*******9999988876 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0    0.0021       1.2      12      33 .]      17      38 ..      10      38 .. 0.90
   2 !   10.4   0.0    0.0015      0.84       7      32 ..      46      71 ..      44      72 .. 0.91
   3 !   13.5   0.0   0.00015     0.086       1      29 [.      74     102 ..      74     102 .. 0.94
   4 ?   -0.6   0.0       4.9   2.8e+03      10      22 ..     116     128 ..     107     135 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0021
                                   HHHHHHHHHHHHHHHHHH-TT- CS
                          TPR_6 12 klgdtdkAlealerlikeYPdS 33
                                   k g ++kA+e+ +r ++  PdS
  gi|116753817|ref|YP_842935.1| 17 KRGMYEKAVEYCDRALEINPDS 38
                                   5679*****************9 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0015
                                   HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                          TPR_6  7 alsyrklgdtdkAlealerlikeYPd 32
                                   + ++++l++ d+Ale ++r ++  P+
  gi|116753817|ref|YP_842935.1| 46 GVALYNLDRIDEALECYNRALEIDPG 71
                                   8899**99*************99886 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 0.00015
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          TPR_6   1 dAlyklalsyrklgdtdkAlealerlike 29 
                                    dA+ ++a  +r lg+ +kAle++e +i++
  gi|116753817|ref|YP_842935.1|  74 DAMRNIAFVHRDLGELEKALELYETIIER 102
                                    78899*******99************986 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 4.9
                                    HHHHHHHHHHHHH CS
                          TPR_6  10 yrklgdtdkAlea 22 
                                    + +lg+ ++A+e 
  gi|116753817|ref|YP_842935.1| 116 LVALGRFQDAIEC 128
                                    5566788888875 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.8e-05      0.01      13      37 ..      17      41 ..      13      43 .. 0.88
   2 !   13.4   0.0   0.00011      0.06       9      37 ..      47      75 ..      45      77 .. 0.93
   3 ?    1.0   0.0      0.83   4.6e+02      11      29 ..      83     101 ..      78     103 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.8e-05
                                   HHT-HHHHHHHHHHHHHHTTS-HHH CS
                     Fis1_TPR_C 13 klgeYseArryvdalLeiEPenrQa 37
                                   k g Y++A +y+d+ Lei P+ + a
  gi|116753817|ref|YP_842935.1| 17 KRGMYEKAVEYCDRALEINPDSSDA 41
                                   7799****************97665 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00011
                                   HHHHHHT-HHHHHHHHHHHHHHTTS-HHH CS
                     Fis1_TPR_C  9 lGhyklgeYseArryvdalLeiEPenrQa 37
                                   ++ y l + +eA+++ ++ Lei+P+n  a
  gi|116753817|ref|YP_842935.1| 47 VALYNLDRIDEALECYNRALEIDPGNLDA 75
                                   8999**********************988 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.83
                                    HHHHT-HHHHHHHHHHHHH CS
                     Fis1_TPR_C  11 hyklgeYseArryvdalLe 29 
                                    h  lge ++A+++ ++++e
  gi|116753817|ref|YP_842935.1|  83 HRDLGELEKALELYETIIE 101
                                    5569999****99998875 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   1.1e-05    0.0059      34      80 ..      16      63 ..      11      65 .. 0.90
   2 !   21.0   0.0   5.2e-07   0.00029       5      81 ..      55     131 ..      54     132 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.1e-05
                                   HHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                         ANAPC3 34 ylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80
                                    ++g y++A e++++a ++n+ s  ++  ++ +l+ L++++eA+ ++ 
  gi|116753817|ref|YP_842935.1| 16 VKRGMYEKAVEYCDRAlEINPDSSDAWNNKGVALYNLDRIDEALECYN 63
                                   5789999*********9**************************99876 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 5.2e-07
                                    HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                         ANAPC3   5 yknAiflaerllaaetespedayllAlclylngqykrAyellrkaklnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                    +++A+ +++r+l+ ++ ++++    A ++  +g+ ++A+el+++  +++ +   +  +A  l++L+++++Ai ++++
  gi|116753817|ref|YP_842935.1|  55 IDEALECYNRALEIDPGNLDAMRNIAFVHRDLGELEKALELYETIIERGGDAYDLEAKATILVALGRFQDAIECIGR 131
                                    799******************999*********************999999999999*****************987 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00021      0.12     205     256 ..      18      69 ..       5      72 .. 0.80
   2 !    8.3   0.0    0.0016      0.91      13      66 ..      82     134 ..      72     141 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00021
                                    HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
                          NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                                     g +ekA+ey d+a+e +p + + + +K+  l     +++A e+ ++a ++D
  gi|116753817|ref|YP_842935.1|  18 RGMYEKAVEYCDRALEINPDSSDAWNNKGVALYNLDRIDEALECYNRALEID 69 
                                    4568899999999999999999999999988888888888888888887777 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0016
                                    HHHHHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                          NARP1  13 iieeagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLle 66 
                                    + ++ g+le+Ale  e+  ++  D    +e+ka +l++Lgr+++A + + +  e
  gi|116753817|ref|YP_842935.1|  82 VHRDLGELEKALELYETIIERGGDAYD-LEAKATILVALGRFQDAIECIGRAYE 134
                                    455666667777766666666666655.35667777777777766665544444 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 !    7.4   0.0    0.0077       4.3      30      70 ..      21      64 ..       3      95 .. 0.52
   2 !   13.2   0.0   0.00012     0.069       3      51 ..      94     143 ..      91     160 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0077
                   SRP_TPR_like 30 yeeaLkllkkgs...alsedvrfEkaYvlYklkkykkalkilkk 70
                                   ye a+++++ +      s+d    k  +lY l +  +al+  ++
  gi|116753817|ref|YP_842935.1| 21 YEKAVEYCDRALeinPDSSDAWNNKGVALYNLDRIDEALECYNR 64
                                   55555555544311122344444555555555555555544443 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00012
                   SRP_TPR_like   3 eeyekilrlegkelk.kfkvvaliklekyeeaLkllkkgsalsedvrfEk 51 
                                    e ye i++  g+ ++ + k++ l+ l+++++a++ +  + +++ d rfE 
  gi|116753817|ref|YP_842935.1|  94 ELYETIIERGGDAYDlEAKATILVALGRFQDAIECIGRAYEMTPDPRFEV 143
                                    57999********99456******************99999999988874 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1      0.05        28      11      25 ..      16      30 ..      15      35 .. 0.84
   2 ?    3.6   0.0      0.17        94      12      25 ..      51      64 ..      48      69 .. 0.80
   3 !    8.5   0.0    0.0045       2.5      13      30 ..      86     103 ..      83     104 .. 0.92
   4 ?   -0.2   0.0       2.7   1.5e+03      11      23 ..     117     129 ..     114     132 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.05
                            PPR 11 cknGkleeAlelfke 25
                                   +k G++e+A+e+ ++
  gi|116753817|ref|YP_842935.1| 16 VKRGMYEKAVEYCDR 30
                                   699********9887 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.17
                            PPR 12 knGkleeAlelfke 25
                                      +++eAle++++
  gi|116753817|ref|YP_842935.1| 51 NLDRIDEALECYNR 64
                                   56799*******98 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0045
                            PPR  13 nGkleeAlelfkeMkekG 30 
                                     G+le+Alel++ ++e+G
  gi|116753817|ref|YP_842935.1|  86 LGELEKALELYETIIERG 103
                                    599***********9998 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 2.7
                            PPR  11 cknGkleeAlelf 23 
                                    +  G++++A+e++
  gi|116753817|ref|YP_842935.1| 117 VALGRFQDAIECI 129
                                    66899****9986 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.062        35       6      23 ..      44      61 ..      41      64 .. 0.84
   2 ?    7.7   0.0     0.011       6.3       8      25 ..      80      97 ..      74      98 .. 0.89
   3 ?    3.8   0.0      0.21   1.2e+02       7      20 ..     112     125 ..     109     131 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.062
                          TPR_4  6 aLArallalGdldeAral 23
                                   + + al+ l + deA++ 
  gi|116753817|ref|YP_842935.1| 44 NKGVALYNLDRIDEALEC 61
                                   5689***********986 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.011
                          TPR_4  8 ArallalGdldeAralle 25
                                   A ++ +lG+l+ A++l e
  gi|116753817|ref|YP_842935.1| 80 AFVHRDLGELEKALELYE 97
                                   889************987 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.21
                          TPR_4   7 LArallalGdldeA 20 
                                     A  l alG++ +A
  gi|116753817|ref|YP_842935.1| 112 KATILVALGRFQDA 125
                                    58899******999 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.21   1.2e+02     158     182 ..      17      41 ..      13      45 .. 0.89
   2 !   16.1   0.0   8.9e-06     0.005     160     250 ..      53     141 ..      42     156 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.21
                         TPR_15 158 qegqtdaAlrdyreAlalapdssel 182
                                    ++g  ++A++   +Al+ +pdss++
  gi|116753817|ref|YP_842935.1|  17 KRGMYEKAVEYCDRALEINPDSSDA 41 
                                    678899***************9986 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 8.9e-06
                         TPR_15 160 gqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkara..esdasLwgplaaAlllLgrpkkALeyl 237
                                    ++ d+Al++y +Al+ +p++ ++  ++ ++  Dlg   eL ++l+ ++       da   ++ a+ l++Lgr + A e +
  gi|116753817|ref|YP_842935.1|  53 DRIDEALECYNRALEIDPGNLDAMRNIAFVHRDLG---ELEKALELYETIIerGGDAYDLEAKATILVALGRFQDAIECI 129
                                    56799******************************...6668**9999999433355555789999999*******9999 PP

                         TPR_15 238 rkqakenrkdplw 250
                                     + ++ +  dp  
  gi|116753817|ref|YP_842935.1| 130 GRAYE-MTPDPRF 141
                                    99887.6666655 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00035      0.19      79     129 ..      22      68 ..      19      75 .. 0.93
   2 ?    5.7   0.0     0.025        14      41      82 ..      92     133 ..      74     162 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00035
                                    HHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                        DUF3856  79 dkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagem 129
                                    +ka++y +r  e++ d    W     +++val +l r deal+ ++ a e+
  gi|116753817|ref|YP_842935.1|  22 EKAVEYCDRALEINPDSSDAW----NNKGVALYNLDRIDEALECYNRALEI 68 
                                    7899**************999....58********************9985 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.025
                                    TS-TTS---HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                        DUF3856  41 tipaeeafdheGfdalchaglsealaklgrydealesadkal 82 
                                    ++   e+    G da    + +  l+ lgr+++a+e++ +a 
  gi|116753817|ref|YP_842935.1|  92 ALELYETIIERGGDAYDLEAKATILVALGRFQDAIECIGRAY 133
                                    445555555566666666666666666666666666666554 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   2.1e-05     0.012      73     124 ..      16      67 ..       8      78 .. 0.92
   2 ?    2.1   0.1      0.42   2.4e+02      92     136 ..      69     113 ..      64     121 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.1e-05
                                    HHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           BTAD  73 lrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                    ++ G +e+a+++ +++++ +P   +++     Al+ ++r  eALe Y+r+ +
  gi|116753817|ref|YP_842935.1|  16 VKRGMYEKAVEYCDRALEINPDSSDAWNNKGVALYNLDRIDEALECYNRALE 67 
                                    567999******************************************9855 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.42
                                    STT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----H CS
                           BTAD  92 hPlrErlhrqlmrAlarsGrqaeALevYerlrrlLaeeLgvepgp 136
                                    +P + +++r +    + +G+ ++ALe Ye++ ++  +  ++e+++
  gi|116753817|ref|YP_842935.1|  69 DPGNLDAMRNIAFVHRDLGELEKALELYETIIERGGDAYDLEAKA 113
                                    555666666666677788888899999998887777777776665 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.029        16      26      40 ..      20      34 ..       8      45 .. 0.73
   2 ?    6.5   0.1     0.015       8.6      16      32 ..      51      67 ..      43      68 .. 0.79
   3 ?    2.9   0.0      0.21   1.2e+02      18      29 ..      87      98 ..      78     102 .. 0.84
   4 ?   -0.9   0.0       3.1   1.7e+03      24      34 ..     119     129 ..     105     140 .. 0.60

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.029
                            MIT 26 lYkealelLlqalke 40
                                   +Y++a+e++  al  
  gi|116753817|ref|YP_842935.1| 20 MYEKAVEYCDRALEI 34
                                   688888888888862 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.015
                            MIT 16 nagnyeeAlelYkeale 32
                                   n   ++eAle+Y  ale
  gi|116753817|ref|YP_842935.1| 51 NLDRIDEALECYNRALE 67
                                   556789*********98 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.21
                            MIT 18 gnyeeAlelYke 29
                                   g+ e+AlelY++
  gi|116753817|ref|YP_842935.1| 87 GELEKALELYET 98
                                   899*******85 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 3.1
                            MIT  24 lelYkealelL 34 
                                    l  +++a+e +
  gi|116753817|ref|YP_842935.1| 119 LGRFQDAIECI 129
                                    44444444443 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0   0.00077      0.43      10     107 ..      14     100 ..       5     106 .. 0.71
   2 !    7.2   0.0    0.0049       2.8     124     207 ..      75     152 ..      52     164 .. 0.52

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00077
                       TPR_MalT  10 laiasgdaeralelArqALallpe..ddllariaatavlGeasllqGdleaAlqalqeaeklarqadslhvallallqqa 87 
                                      +++g  e+a+e++ +AL++ p+  d++  +++a+++         + ++Al+ ++ a ++    ++    l a++ +a
  gi|116753817|ref|YP_842935.1|  14 DMVKRGMYEKAVEYCDRALEINPDssDAWNNKGVALYN-------LDRIDEALECYNRALEID--PGN----LDAMRNIA 80 
                                    56889999*************99722556666777776.......457777777776655543..444....44778888 PP

                       TPR_MalT  88 eilvaqGrLheAletyeqal 107
                                     +++  G+L++Ale+ye ++
  gi|116753817|ref|YP_842935.1|  81 FVHRDLGELEKALELYETII 100
                                    88888888888888888877 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0049
                       TPR_MalT 124 llvlladllyEwndLeeAeqhlqeGielleqlepeaaldayvllarialaqGdleeAetllekaeelaresnfhvdwlan 203
                                    +++  a ++++ ++Le+A +  +  ie + +      l+a    a i  a G+ ++A + + +a e++   +f v + a 
  gi|116753817|ref|YP_842935.1|  75 AMRNIAFVHRDLGELEKALELYETIIERGGDA---YDLEA---KATILVALGRFQDAIECIGRAYEMTPDPRFEVEMAAI 148
                                    34444555555666666666555444333333...22222...3445555566666666666665555555555555555 PP

                       TPR_MalT 204 aeev 207
                                    + +v
  gi|116753817|ref|YP_842935.1| 149 IGKV 152
                                    5555 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       2.6   1.5e+03      17      23 ..      21      27 ..      18      29 .. 0.86
   2 !    9.1   0.0    0.0023       1.3      10      34 ..      48      70 ..      46      72 .. 0.81
   3 ?    2.2   0.0      0.33   1.8e+02      15      27 ..      87      97 ..      85      99 .. 0.84
   4 ?   -0.5   0.0       2.3   1.3e+03      15      22 ..     120     127 ..     118     128 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 2.6
                                   HHHHHHH CS
                          TPR_3 17 yqeArel 23
                                   y++A+e+
  gi|116753817|ref|YP_842935.1| 21 YEKAVEY 27
                                   9****99 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0023
                                   HHHHTT-HHHHHHH..HHHHHHH-T CS
                          TPR_3 10 efynkkkyqeArelfsYallaildk 34
                                   ++yn ++++eA+e   Y  +  +d+
  gi|116753817|ref|YP_842935.1| 48 ALYNLDRIDEALEC--YNRALEIDP 70
                                   79************..667777765 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.33
                                   T-HHHHHHH..HH CS
                          TPR_3 15 kkyqeArelfsYa 27
                                   +++++A+el  Y+
  gi|116753817|ref|YP_842935.1| 87 GELEKALEL--YE 97
                                   889******..64 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 2.3
                                    T-HHHHHH CS
                          TPR_3  15 kkyqeAre 22 
                                    +++q+A+e
  gi|116753817|ref|YP_842935.1| 120 GRFQDAIE 127
                                    89****98 PP

>> TPR_5  Tetratrico peptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   2.9e-05     0.016      17      96 ..      55     128 ..      40     141 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.9e-05
                          TPR_5  17 edkavplYrraLaeGLagarrrratiqLassLRnlGeaeealaLLraeleapsdelddalaaflaLvLsdlgrereavsi 96 
                                     d+a + Y+raL+       +  a+  +a   R lGe+e+al+L ++ +e+++d +d       a +L++lgr ++a+  
  gi|116753817|ref|YP_842935.1|  55 IDEALECYNRALEID---PGNLDAMRNIAFVHRDLGELEKALELYETIIERGGDAYDLEA---KATILVALGRFQDAIEC 128
                                    588999999999854...33444555678889************************9654...45567777777777764 PP

>> RPN7  26S proteasome subunit RPN7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       3.1   1.7e+03      48      64 ..      17      33 ..      11      48 .. 0.78
   2 !   10.5   0.2   0.00066      0.37      41     136 ..      44     129 ..      33     134 .. 0.64
   3 ?    3.0   0.0      0.13        74      40      75 ..     110     145 ..     106     155 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 3.1
                                   HCT-HHHHHHHHHTCCC CS
                           RPN7 48 kigdleeAlkaysrire 64
                                   k g +e+A++++ r++e
  gi|116753817|ref|YP_842935.1| 17 KRGMYEKAVEYCDRALE 33
                                   55677777777777654 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00066
                                    HHHHHHHHCT-HHHHHHHHHTCCCC--SHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHCSSS---.HHHHHHHHHHHH CS
                           RPN7  41 dlaehYlkigdleeAlkaysrireyctslkhkidmllnlirvaiffndwdlvskylekakellekggdwerknrlkvyeG 120
                                    +++   ++   ++eAl++y+r++e        +d +     +a+   d + ++k le  ++++e+ggd         +++
  gi|116753817|ref|YP_842935.1|  44 NKGVALYNLDRIDEALECYNRALEIDPG---NLDAMR---NIAFVHRDLGELEKALELYETIIERGGDAYDLE----AKA 113
                                    5555555555667777777776554333...233333...367888888888888888888888888866655....666 PP

                                    HHHHHTT-HHHHHHHH CS
                           RPN7 121 lallairkfkeAaell 136
                                    ++l+a ++f++A e++
  gi|116753817|ref|YP_842935.1| 114 TILVALGRFQDAIECI 129
                                    7777777777776665 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.13
                                    HHHHHHHHHCT-HHHHHHHHHTCCCC--SHHHHHHH CS
                           RPN7  40 ldlaehYlkigdleeAlkaysrireyctslkhkidm 75 
                                    +++a   +  g ++ A+++  r++e +  +   ++m
  gi|116753817|ref|YP_842935.1| 110 EAKATILVALGRFQDAIECIGRAYEMTPDPRFEVEM 145
                                    789999999999999999999999988777766666 PP

>> Rapsyn_N  Rapsyn N-terminal myristoylation and linker region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.032        18       7      42 ..       6      41 ..       1      44 [. 0.83
   2 ?    6.2   0.0     0.019        11      11      65 ..      44      95 ..      41     110 .. 0.80
   3 ?    0.8   0.0      0.95   5.3e+02      51      64 ..     114     127 ..      85     136 .. 0.53

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.032
                       Rapsyn_N  7 krkiekGLklyesndtekalrvWrkvLkktsdregk 42
                                   k  i+kG+ + +    eka++   ++L+   d+++ 
  gi|116753817|ref|YP_842935.1|  6 KILIHKGIDMVKRGMYEKAVEYCDRALEINPDSSDA 41
                                   44579*********************9998888775 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.019
                       Rapsyn_N 11 ekGLklyesndtekalrvWrkvLkktsdregkfrvLGcLitahsemGkykealef 65
                                   +kG+ ly+ +  ++al+ + ++L+    + + +r + +    h ++G   +ale+
  gi|116753817|ref|YP_842935.1| 44 NKGVALYNLDRIDEALECYNRALEIDPGNLDAMRNIAF---VHRDLGELEKALEL 95
                                   69*********************987777676665544...57777777777765 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.95
                       Rapsyn_N  51 tahsemGkykeale 64 
                                    t    +G++++a+e
  gi|116753817|ref|YP_842935.1| 114 TILVALGRFQDAIE 127
                                    33344666666665 PP

>> SGTA_dimer  Homodimerisation domain of SGTA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.026        14      26      64 ..      51      89 ..      31      92 .. 0.87
   2 ?    6.7   0.0     0.011         6      33      47 ..     125     139 ..     124     151 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.026
                     SGTA_dimer 26 daESleVAiqCIaeaFevdkedkaavkkakfggqsLlei 64
                                   + + ++ A +C   a e+d+ + +a+ + +f +++L e+
  gi|116753817|ref|YP_842935.1| 51 NLDRIDEALECYNRALEIDPGNLDAMRNIAFVHRDLGEL 89
                                   5678899*******************9999999999775 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.011
                     SGTA_dimer  33 AiqCIaeaFevdked 47 
                                    Ai+CI+ a+e +++ 
  gi|116753817|ref|YP_842935.1| 125 AIECIGRAYEMTPDP 139
                                    9**********9975 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0       1.2   6.9e+02       9      43 ..      26      60 ..      21      63 .. 0.86
   2 ?   11.4   0.1   0.00057      0.32      11      66 ..      62     117 ..      56     125 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1.2
                         TPR_20  9 aeleaalaanpddldarldlAlallaagryeeAle 43
                                   +  ++al+ npd  da  +   al+   r +eAle
  gi|116753817|ref|YP_842935.1| 26 EYCDRALEINPDSSDAWNNKGVALYNLDRIDEALE 60
                                   5567899999**99999999999999999999997 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00057
                         TPR_20  11 leaalaanpddldarldlAlallaagryeeAleqLleilkrdrkweddaarkqllk 66 
                                      +al+ +p +lda+ + A +    g+ e+Ale+  +i++r  ++ d +a+ ++l 
  gi|116753817|ref|YP_842935.1|  62 YNRALEIDPGNLDAMRNIAFVHRDLGELEKALELYETIIERGGDAYDLEAKATILV 117
                                    568999***************************************99999999885 PP

>> DUF627  Protein of unknown function (DUF627)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.022        12      90     106 ..      18      34 ..       3      36 .. 0.80
   2 ?   -1.3   0.0       3.9   2.2e+03      62      74 ..      58      70 ..      55      88 .. 0.70
   3 ?    3.8   0.0       0.1        58       9      46 ..      87     120 ..      79     136 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.022
                         DUF627  90 klyYkkavkkakraLsv 106
                                    +  Y+kav+ + raL +
  gi|116753817|ref|YP_842935.1|  18 RGMYEKAVEYCDRALEI 34 
                                    557************98 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.9
                         DUF627 62 svecfseavelsr 74
                                   ++ec+++a e+  
  gi|116753817|ref|YP_842935.1| 58 ALECYNRALEIDP 70
                                   7889998888764 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.1
                         DUF627   9 gnhikALeiiedlisrhgedeksallhrlqGtifvkla 46 
                                    g+  kALe+ e +i r g+    a   ++++ti+v+l 
  gi|116753817|ref|YP_842935.1|  87 GELEKALELYETIIERGGD----AYDLEAKATILVALG 120
                                    6677**********99998....455677888887776 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0071         4      70     118 ..       6      54 ..       1      65 [. 0.82
   2 ?    3.3   0.0      0.19   1.1e+02      79     118 ..      83     121 ..      48     165 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0071
                                    HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHH CS
                Alkyl_sulf_dimr  70 ekvlekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgy 118
                                    + ++ k  + +k+g y+ a+e ++ +++ +p+ ++a + k  al +l +
  gi|116753817|ref|YP_842935.1|   6 KILIHKGIDMVKRGMYEKAVEYCDRALEINPDSSDAWNNKGVALYNLDR 54 
                                    55678888999**********************9999988777766655 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.19
                                    HHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHH CS
                Alkyl_sulf_dimr  79 alkegdyrwaaellnhlvfadpenaeakelkadaleqlgy 118
                                    +++ g+++ a+el + +++   + a   e+ka +l +lg+
  gi|116753817|ref|YP_842935.1|  83 HRDLGELEKALELYETIIERGGD-AYDLEAKATILVALGR 121
                                    34445555555555555544332.3333344444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); 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: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1077.94
//
Query:       gi|116753818|ref|YP_842936.1|  [L=113]
Description: hypothetical protein Mthe_0505 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-17   63.0   0.0      3e-17   62.6   0.0    1.1  1  DUF3467   Protein of unknown function (DUF3467)


Domain annotation for each model (and alignments):
>> DUF3467  Protein of unknown function (DUF3467)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.6   0.0   1.6e-21     3e-17      14      90 ..       8      95 ..       4      96 .. 0.83

  Alignments for each domain:
  == domain 1  score: 62.6 bits;  conditional E-value: 1.6e-21
                        DUF3467 14 alrie.vdesvaggsYsngaivmtspsEfiidF....lqlv.pgrpearvksr.....vvlspaaakqlvaaLqknldlyet 84
                                   +++ie  ++  ++++Y++gai  +sp++f+i F    ++ + +g ++    +r     v+lsp aak+l+++L +++++ye+
  gi|116753818|ref|YP_842936.1|  8 EVSIEvTRSPAFRQVYAIGAIGGHSPYDFRISFyndsPRAFiEGGKQLSTVERsmeveVILSPLAAKELAEWLMNHIKEYEK 89
                                   68999666799**********************7777556666666555444444444************************ PP

                        DUF3467 85 rfGeik 90
                                    fGeik
  gi|116753818|ref|YP_842936.1| 90 LFGEIK 95
                                   *****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.28s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 815.71
//
Query:       gi|116753819|ref|YP_842937.1|  [L=110]
Description: hypothetical protein Mthe_0506 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); 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: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 827.76
//
Query:       gi|116753820|ref|YP_842938.1|  [L=139]
Description: hypothetical protein Mthe_0507 [Methanosaeta thermophila PT]
Scores for complete 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-28   98.6   0.0    2.7e-28   98.3   0.0    1.1  1  DUF123    Domain of unknown function DUF123


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 !   98.3   0.0   1.5e-32   2.7e-28       3      94 .]      27     117 ..      25     117 .. 0.91

  Alignments for each domain:
  == domain 1  score: 98.3 bits;  conditional E-value: 1.5e-32
                         DUF123   3 lkkgvylYvGsalgsgglasRvkrHaslskkkekklhWhiDyLleseeaelaevvv.aseerlEcalaeal.eaeapvag 80 
                                    +++g+y+Y+Gsa g+gg+ +R++rH+++ ++++++++WhiDyLl  ++a+l+ v++ a++ +lEc+ a+++ +   +v++
  gi|116753820|ref|YP_842938.1|  27 FPEGYYAYTGSARGPGGF-KRISRHVAVMNGDNSTRRWHIDYLL--PHATLRDVITtATDMDLECEAAKRIgAYCISVPR 103
                                    89****************.*************************..667788888845*************55555999* PP

                         DUF123  81 fGasDckcesHLlk 94 
                                    fG++Dc+c sHL++
  gi|116753820|ref|YP_842938.1| 104 FGCTDCRCPSHLHY 117
                                    ************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1075.12
//
Query:       gi|116753821|ref|YP_842939.1|  [L=413]
Description: hypothetical protein Mthe_0508 [Methanosaeta thermophila PT]
Scores for complete 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   49.2  10.5    4.3e-12   46.7   6.7    3.0  2  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
       0.16   12.2   0.0       0.53   10.6   0.0    1.9  2  Cobl         Cordon-bleu ubiquitin-like 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 !   46.7   6.7   4.8e-16   4.3e-12       9     162 ..      51     198 ..      18     200 .. 0.85
   2 ?   -1.1   0.1      0.25   2.2e+03      81      91 ..     344     364 ..     272     407 .. 0.68

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 4.8e-16
                                    S--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   9 lrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlaklavpgiritvetngt 87 
                                     +C +C+r      eg++ +++++ ++  v ++++     k+ i+ggg+ + yp++ +l++ l ++ +  i++ +++  +
  gi|116753821|ref|YP_842939.1|  51 KGCDYCTRAI---IEGYPGFKPLDAVVFDVAQASYGATpEKVTISGGGDLSCYPNLLKLVRILGQK-NVPIHLGYTSGKG 126
                                    3466666665...8*******************9555559999999*******************9.5999999999999 PP

                                    CHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  88 lpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGendeelee 162
                                      + + +++l+++gv  vs+++ a+d+e  +++ +  + +e+ l +l+++ e+ ++ v+   v+l+G+nd e+ e
  gi|116753821|ref|YP_842939.1| 127 FKRGDEADELVDAGVREVSFTVFATDPE-LRRKYMHDKHPEAALSNLRIFCER-CD-VYAAAVLLKGVNDGEVLE 198
                                    988*************************.66666688****************.**.*************99866 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.25
                                    EEEECSSCHG..........H CS
                                    xxxxxxxxxx..........x RF
                    Radical_SAM  81 tvetngtlpd..........e 91 
                                    tv+++g ++           +
  gi|116753821|ref|YP_842939.1| 344 TVVIPGRMLAherevkkelsR 364
                                    333333333333333333334 PP

>> Cobl  Cordon-bleu ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   5.9e-05      0.53      29      81 ..     164     215 ..     155     223 .. 0.79
   2 ?   -3.6   0.0       1.6   1.4e+04       4      18 ..     230     244 ..     229     246 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5.9e-05
                                    -SSS-HHHHHHHHHHHTT--TTSEEEES-SS---B--TT.S-HHHHT-SEEEEE CS
                           Cobl  29 sPevplqellpvicekcefdpehvlllkdsiskeeldla.kslkdlgikelyal 81 
                                     Pe++l +l  + ce+c++  +  +llk     e l+ + + l+d+g k l  +
  gi|116753821|ref|YP_842939.1| 164 HPEAALSNL-RIFCERCDVYAAA-VLLKGVNDGEVLERTcQDLEDMGAKGLILM 215
                                    689999996.699******8765.678999999999865378999998888665 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.6
                                    XXXXX-S-EEEEEEE CS
                           Cobl   4 aPkiPektvrlvvny 18 
                                    aP+iP + v  v ++
  gi|116753821|ref|YP_842939.1| 230 APIIPGQDVHTVEEF 244
                                    899999999887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); 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 0.23s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 3291.79
//
Query:       gi|116753822|ref|YP_842940.1|  [L=363]
Description: hypothetical protein Mthe_0509 [Methanosaeta thermophila PT]
Scores for complete 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   79.4   0.0    1.2e-18   67.5   0.0    2.3  2  FmdE      FmdE, Molybdenum formylmethanofuran dehydrogenase o


Domain annotation for each model (and alignments):
>> FmdE  FmdE, Molybdenum formylmethanofuran dehydrogenase operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0   4.6e-05      0.83      11      88 ..      29     117 ..      25     154 .. 0.75
   2 !   67.5   0.0   6.4e-23   1.2e-18       1      96 [.     192     301 ..     192     330 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 4.6e-05
                                    HHHHHHHHHHHCC....-TTSSSEEEEES-S.........TCHHHHHHHHCS--TTTTSEEE--...SS-SEEEEEETTT CS
                           FmdE  11 lGyrmakaalkelgpkeeegdeelvaivetd.........sCldDAiqvltgctlGkgnlivmd...ygkkaltfkkrkt 78 
                                    +G+++a+ a+ el+ +  +gde++ ++++           + +  +i  + gc+ G gnl+ +    +    + f ++++
  gi|116753822|ref|YP_842940.1|  29 IGVKAAEKAMSELSFQ--KGDENILVLTNAGyaivsgmttQKALKGITETAGCSHGDGNLFQVLrphWKPLWFYFFDKNS 106
                                    8************984..468999999999999999988877888999999*********86643334445558999999 PP

                                    -EEEEEEE-.C CS
                           FmdE  79 gkavrlklk.e 88 
                                    ++a+ l +k e
  gi|116753822|ref|YP_842940.1| 107 KEALYLEVKpE 117
                                    99998888831 PP

  == domain 2  score: 67.5 bits;  conditional E-value: 6.4e-23
                                    HHSS--CHHHHHHHHHHHHHHCC....-TTSSSEEEEES-STCHHHHHHHHCS--TTTTSEEE--............SS- CS
                           FmdE   1 fHGHlCpglvlGyrmakaalkelgpkeeegdeelvaivetdsCldDAiqvltgctlGkgnlivmd............ygk 68 
                                    fH+HlCpg+++Gy++ak++ +el+++   + e + +i+   +C+dDA+q+l+++t+Gk  ++vm             y++
  gi|116753822|ref|YP_842940.1| 192 FHDHLCPGVTSGYMIAKYVERELPINS--SAESYKVIAVPPWCKDDALQILWDATVGKSGIFVMAltdteknalkakYNQ 269
                                    9***********************963..358999999999*****************8888888777555555555444 PP

                                    SEE..EEEET.....TT-EEEEEEE-CCTHHHHHH CS
                           FmdE  69 kal..tfkkr.....ktgkavrlklkeelpelrek 96 
                                    + +   f+ r     k+g+a+ l+++  + ++ e 
  gi|116753822|ref|YP_842940.1| 270 SDVagIFV-RwndtaKQGDALVLSFN--WTRMYEL 301
                                    44443333.35888888888888888..4443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 2966.14
//
Query:       gi|116753823|ref|YP_842941.1|  [L=510]
Description: extracellular solute-binding protein [Methanosaeta thermophila PT]
Scores for complete 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-83  278.8   1.6    8.2e-83  278.4   1.6    1.1  1  SBP_bac_5  Bacterial extracellular solute-binding proteins, f


Domain annotation for each model (and alignments):
>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  278.4   1.6   4.6e-87   8.2e-83       2     364 ..      70     417 ..      69     429 .. 0.89

  Alignments for each domain:
  == domain 1  score: 278.4 bits;  conditional E-value: 4.6e-87
                                    EEESSEEEEEEEETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHCTCTEEEEEEEETTEEEEE CS
                      SBP_bac_5   2 vvpaLAeswwevsdDgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyaslleedqdikkveavddytvrft 81 
                                    +vpaLAes we  +D   y+f+L++++k++DG+p+tA+Dvvf++++++++++++  +s+       +++e++dd+tv+++
  gi|116753823|ref|YP_842941.1|  70 FVPALAES-WEYLKDENAYIFNLNPNAKWHDGEPFTADDVVFTINYIKEHPYQWVDSSTV------DRAEKIDDHTVKIY 142
                                    79******.799******************************************998875......8************* PP

                                    ESSETTTTTTHCHHHHHHHGC.CHTCTCTTTTTGTTTSE-BSSSEEEEEEETTT.EEEEEE-TTSTTTSCSSSSEEEEEE CS
                      SBP_bac_5  82 lkkpnalfltllaavpasiak.kaaekeddkdkdtnekpvgtGPYklkefkpgq.kivlernpdYwgggkpkldriefkv 159
                                    l+kp+a+fl  +a + + +++    + ++ +d + ++++ gtGP+kl+++++ q +  +e+n+dY+ +g+pk+++++f  
  gi|116753823|ref|YP_842941.1| 143 LAKPYAPFLDQVAGTLPILPEhIYIDVTKPEDFQDAKALTGTGPFKLVDYNKAQgTYLYEANEDYY-QGAPKVKQLKFVK 221
                                    ******99999999999888844445566667777888888***********995666*******9.************* PP

                                    -.SHHHHHHHHHTTSSSEEESTTCCTHCHHHHHTTEEEEEEEEEEEEEEEEETTTSTGGGSHHHHHHHHHHS-HHHHHHH CS
                      SBP_bac_5 160 ipdsdaraaalqsGeiddvaepppsdieqlkeakglkvlyespgggvtylafNtkkppfddkrvRqAlsyAiDreeivka 239
                                      +++ +  al+ Ge+ d+a +pp+ +e l+ +    v  e++  +   l++N+kk+pf+d+r+RqAl+y iDre++v++
  gi|116753823|ref|YP_842941.1| 222 L-SEEMAGPALKRGEV-DAAAVPPEVAEGLRGSF--VV-LEGAHDWLAKLMINHKKEPFSDVRFRQALAYSIDREKLVEI 296
                                    *.999999999*****.99999**9999985554..55.56*************************************** PP

                                    CTTTSSEEESSS.STTTSTTCCSCHCCCSHHSHHHHHHHHHHHTT-BCSSTSCEETCEEEEEEEEETTSHHHHHHHHHHH CS
                      SBP_bac_5 240 vlegyatpansl.lppsspgadeeykpaykaydpekAkklLkeaGykdgdggglrekklkltlllasgspaekaiaeliq 318
                                    + +gy++pa    ++p s +++++ +++  a+dpekA +lLke Gy++++   +++++++l ++l   ++ ++++ eli+
  gi|116753823|ref|YP_842941.1| 297 AQRGYGVPASPGlFAPDSEWYNPDVEQY--AHDPEKAGELLKELGYEKKG-VFFEKDGKTLEVELLV-TSSNERAGELIK 372
                                    *********9999********9999987..77***************995.5666664444444333.3345789***** PP

                                    HHHHHTTEEEEEEEECHHHHHHHHHHCTTESEEEEEEECTTSTTHH CS
                      SBP_bac_5 319 qqlkkiGikvevktvdwaatylervkdgdfdmillgwgadypdpdn 364
                                     +l+++Gikv++++vd+ +t +++v++++fd++l+g g+  +dp  
  gi|116753823|ref|YP_842941.1| 373 RDLEEAGIKVNMRSVDS-KTLDNAVNEWNFDLALSGHGGMGGDPAI 417
                                    *****************.*********************9999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (510 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); 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: 0.55u 0.23s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 3857.55
//
Query:       gi|116753824|ref|YP_842942.1|  [L=249]
Description: cobyrinic acid a,c-diamide synthase [Methanosaeta thermophila PT]
Scores for complete 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   53.5   0.0    3.9e-14   52.8   0.0    1.4  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
    1.8e-09   37.8   0.0    3.3e-09   36.9   0.0    1.4  1  AAA_31         AAA domain
    1.3e-08   34.6   0.0    3.4e-08   33.2   0.0    1.7  2  ParA           NUBPL iron-transfer P-loop NTPase
    3.8e-06   26.6   0.0      0.002   17.7   0.0    2.1  2  CBP_BcsQ       Cellulose biosynthesis protein BcsQ
    9.7e-06   25.0   0.3    1.6e-05   24.3   0.3    1.3  1  ArsA_ATPase    Anion-transporting ATPase
    1.5e-05   24.9   0.0      3e-05   24.0   0.0    1.6  1  APS_kinase     Adenylylsulphate kinase
    3.7e-05   23.3   1.0    0.00017   21.1   0.0    2.2  2  Fer4_NifH      4Fe-4S iron sulfur cluster binding proteins, N
    4.7e-05   23.6   0.0     0.0001   22.5   0.0    1.7  1  DUF87          Helicase HerA, central domain
    9.4e-05   21.8   0.1     0.0011   18.3   0.1    2.1  2  Zeta_toxin     Zeta toxin
    0.00012   21.9   0.0     0.0059   16.4   0.0    2.1  2  CLP1_P         mRNA cleavage and polyadenylation factor CLP1 
    0.00038   20.7   0.3       0.43   10.8   0.0    2.5  2  TrkA_N         TrkA-N domain
    0.00046   19.6   0.0      0.004   16.5   0.0    2.0  2  MipZ           ATPase MipZ
    0.00076   19.2   0.0     0.0068   16.1   0.0    2.0  2  SRP54          SRP54-type protein, GTPase domain
     0.0032   17.6   0.0      0.013   15.6   0.0    1.8  2  AAA_33         AAA domain
     0.0035   17.9   0.4      0.008   16.7   0.3    1.7  1  AAA_18         AAA domain
     0.0039   16.7   0.0     0.0056   16.2   0.0    1.3  1  KTI12          Chromatin associated protein KTI12
     0.0045   16.7   0.0      0.012   15.3   0.0    1.7  2  AAA_24         AAA domain
      0.005   16.4   0.4        1.6    8.3   0.1    2.7  2  cobW           CobW/HypB/UreG, nucleotide-binding domain
     0.0058   15.6   0.1      0.011   14.7   0.1    1.4  1  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
     0.0062   16.1   0.0      0.014   14.9   0.0    1.7  2  AAA_25         AAA domain
     0.0071   16.7   0.2      0.018   15.5   0.2    2.0  1  AAA_16         AAA ATPase domain
  ------ inclusion threshold ------
      0.023   13.6   0.1      0.064   12.2   0.0    1.8  2  AAA_10         AAA-like domain
      0.031   13.2   0.1      0.052   12.5   0.1    1.3  1  MeaB           Methylmalonyl Co-A mutase-associated GTPase Me
      0.031   14.8   0.0      0.037   14.5   0.0    1.7  1  ABC_tran       ABC transporter
      0.041   14.2   0.0      0.072   13.4   0.0    1.5  1  AAA_22         AAA domain
      0.066   13.6   0.0       0.13   12.7   0.0    1.6  1  RNA_helicase   RNA helicase
       0.15   12.5   0.0       0.32   11.4   0.0    1.5  1  DUF3964        Protein of unknown function (DUF3964)
       0.19   11.0   0.1       0.44    9.8   0.1    1.6  1  VirC1          VirC1 protein
        0.2   11.7   0.2         20    5.3   0.1    2.4  2  MMR_HSR1       50S ribosome-binding GTPase
        0.3   10.9   0.6       0.49   10.2   0.6    1.3  1  AAA_29         P-loop containing region of AAA domain


Domain annotation for each model (and alignments):
>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.8   0.0   6.5e-17   3.9e-14       4     125 ..       5     231 ..       2     234 .. 0.85

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 6.5e-17
                                    EESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH............................. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................. RF
                           CbiA   4 astkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep............................. 54 
                                    + +kGG+GK+t++a Lar +a rg rVl+vDaD    n   ++   ++ +p                             
  gi|116753824|ref|YP_842942.1|   5 ICGKGGSGKSTVSALLAREIAGRGTRVLVVDADES--NFG-IYRMLGFDQPkdfmeslggkralserlmrfirserreal 81 
                                    569****************************9988..766.5666666666677888*********************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                           CbiA  55 ................................................................................ 54 
                                                                                                                    
  gi|116753824|ref|YP_842942.1|  82 siipeefqikdippevvvgdemvklvaigkihnfgegcacpmgalarefleklrtngeyvivdtdagiehfgrgvetgcd 161
                                    *****************************************************************************777 PP

                                    ..............CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCC CS
                                    ..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA  55 ..............dlkrllellealgkkkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavae 120
                                                    +++ e+ e++        k +++++nr+d++  ++ + ++++      +++v+gvip+++++ +
  gi|116753824|ref|YP_842942.1| 162 kivavidpcyesvqLSEKIAEMGEKI-------GKDVFFIVNRIDED--SEDILDMID------RDRVIGVIPKRKDLFR 226
                                    77777766665333333333333333.......567*********99..444444333......689***********99 PP

                                    CCHHT CS
                                    xxxxx RF
                           CbiA 121 aparg 125
                                    a  +g
  gi|116753824|ref|YP_842942.1| 227 ASLTG 231
                                    98766 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.0   5.5e-12   3.3e-09       9     160 ..       7     180 ..       2     195 .. 0.73

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 5.5e-12
                         AAA_31   9 qKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanatt..glgiekneiektlyevl....ieeknikeaiiktkvenld 82 
                                     KGG GK+T s  la  +a +g +vL+vD+D  +n  +   lg+   +  k+++e l    + ++++   i +++ e l+
  gi|116753824|ref|YP_842942.1|   7 GKGGSGKSTVSALLAREIAGRGTRVLVVDADE-SNFGIyrMLGF---DQPKDFMESLggkrALSERLMRFIRSERREALS 82 
                                    6******************************7.56555124454...334455555433225566777777788899999 PP

                         AAA_31  83 lipssidLaeaeielvelekk..............eei......l.kellekvkdeYDyiiiDcpPsLglltenaLvasd 141
                                    +ip + ++ ++  e+v  ++                        l +e+lek++ +  y+i+D+   ++ + +   +  d
  gi|116753824|ref|YP_842942.1|  83 IIPEEFQIKDIPPEVVVGDEMvklvaigkihnfgeG-CacpmgaLaREFLEKLRTNGEYVIVDTDAGIEHFGRGVETGCD 161
                                    999999999999998877666666666666555550.05555555499****************9999998888888888 PP

                         AAA_31 142 sviipvqaeayaleGleql 160
                                    +++ ++++ + +++  e++
  gi|116753824|ref|YP_842942.1| 162 KIVAVIDPCYESVQLSEKI 180
                                    8888888876666554444 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 !   33.2   0.0   5.7e-11   3.4e-08       8      57 ..       4      53 ..       1      84 [. 0.90
   2 ?   -1.1   0.0       1.8   1.1e+03     134     171 ..     158     195 ..      85     201 .. 0.65

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 5.7e-11
                           ParA  8 vlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeek 57
                                    + gKGG GKStv++ lA ++a +g++v ++DaD   + i r+lg ++ k
  gi|116753824|ref|YP_842942.1|  4 LICGKGGSGKSTVSALLAREIAGRGTRVLVVDADESNFGIYRMLGFDQPK 53
                                   468******************************************98854 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.8
                           ParA 134 lplagaviVttpqevaladvkkaiemfkkvkvkvlGvv 171
                                       +++v V  p   +++  +k +em +k+  +v+ +v
  gi|116753824|ref|YP_842942.1| 158 TGCDKIVAVIDPCYESVQLSEKIAEMGEKIGKDVFFIV 195
                                    34455566666666666666666666666666665555 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   3.3e-06     0.002      10      43 ..       8      41 ..       1      85 [. 0.73
   2 !    7.2   0.0    0.0054       3.2     106     157 ..     128     178 ..     111     210 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.3e-06
                       CBP_BcsQ 10 RGGvGttsllaaLawalhelgesvlviDlspdnl 43
                                   +GG G+++++a La+ +   g +vlv+D+  +n+
  gi|116753824|ref|YP_842942.1|  8 KGGSGKSTVSALLAREIAGRGTRVLVVDADESNF 41
                                   7****************************99994 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0054
                       CBP_BcsQ 106 laalkelkeqyrwillDlpagasaltrellaladlvllvvepdanchvrLhq 157
                                     ++l++l+++ +++++D  ag ++  r + + +d+ ++v+ p   + v+L +
  gi|116753824|ref|YP_842942.1| 128 REFLEKLRTNGEYVIVDTDAGIEHFGRGVETGCDKIVAVIDPCYES-VQLSE 178
                                    567899**********************************997665.44444 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.3   2.7e-08   1.6e-05       4      38 ..       3      37 ..       1      40 [. 0.94

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 2.7e-08
                                   EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                    ArsA_ATPase  4 ilvgGKGGVGKttvsaatavklsekgkkvllistD 38
                                   il+ GKGG GK+tvsa +a +++  g +vl++  D
  gi|116753824|ref|YP_842942.1|  3 ILICGKGGSGKSTVSALLAREIAGRGTRVLVVDAD 37
                                   899*****************************988 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   5.1e-08     3e-05       5      53 ..       3      51 ..       1      80 [. 0.94

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 5.1e-08
                                   EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT--SSH CS
                     APS_kinase  5 vwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLgfse 53
                                   +++ G  gsGKst++  l++++  +g++v ++d d+  +g+++ Lgf++
  gi|116753824|ref|YP_842942.1|  3 ILICGKGGSGKSTVSALLAREIAGRGTRVLVVDADESNFGIYRMLGFDQ 51
                                   8899*******************************************87 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 !   21.1   0.0   2.8e-07   0.00017       1      39 [.       1      39 [.       1      71 [. 0.85
   2 ?    0.9   0.3      0.43   2.5e+02     179     221 ..     193     231 ..      76     247 .. 0.52

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.8e-07
                      Fer4_NifH  1 rkiaiyGkGGiGksttsqnlsaalaemgkkvlivGCDPk 39
                                   +ki i GkGG+Gkst s+ l+  +a +g +vl+v  D  
  gi|116753824|ref|YP_842942.1|  1 MKILICGKGGSGKSTVSALLAREIAGRGTRVLVVDADES 39
                                   5899******************************99865 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.43
                      Fer4_NifH 179 liinsrkvddereliekfaeelgtkvlevvPrdeivrkaelrk 221
                                     i+n r +d+++e i +++++   +v+ v+P+ +++ +a+l  
  gi|116753824|ref|YP_842942.1| 193 FIVN-R-IDEDSEDILDMIDR--DRVIGVIPKRKDLFRASLTG 231
                                    3444.3.44444444444433..35666666666666666655 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   1.7e-07    0.0001      26      61 ..       3      37 ..       1      94 [. 0.84

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.7e-07
                          DUF87 26 lAilgsTGsGKSntvavLleellekkgatililDpH 61
                                   ++i g+ GsGKS+  a+L +e++  +g+++l++D++
  gi|116753824|ref|YP_842942.1|  3 ILICGKGGSGKSTVSALLAREIA-GRGTRVLVVDAD 37
                                   7899*******************.**********97 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   1.8e-06    0.0011      19      53 ..       3      38 ..       1      43 [. 0.95
   2 ?    0.8   0.0      0.41   2.5e+02      31      52 ..     125     146 ..     123     150 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.8e-06
                     Zeta_toxin 19 illgGqpGAGKselaellkdele.rqgnvvrldpDd 53
                                   il+ G  G+GKs++++ll++e++ r+ +v+++d+D+
  gi|116753824|ref|YP_842942.1|  3 ILICGKGGSGKSTVSALLAREIAgRGTRVLVVDADE 38
                                   899*******************99999*******97 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.41
                     Zeta_toxin  31 elaellkdelerqgnvvrldpD 52 
                                    +la+++ ++l+++g++v +d+D
  gi|116753824|ref|YP_842942.1| 125 ALAREFLEKLRTNGEYVIVDTD 146
                                    68999999************99 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 !   16.4   0.0   9.9e-06    0.0059       1      31 [.       7      37 ..       7      50 .. 0.92
   2 ?    3.5   0.0      0.09        54      86     119 ..     125     154 ..     120     198 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 9.9e-06
                         CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlD 31
                                   G+  sGKST+++lL+ +++ +g ++++vD+D
  gi|116753824|ref|YP_842942.1|  7 GKGGSGKSTVSALLAREIAGRGTRVLVVDAD 37
                                   6778**************************9 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.09
                         CLP1_P  86 elareveekleenkkakasgliIntpGwvkglga 119
                                    +lare+ ekl++    + + +i++t+  ++ +g+
  gi|116753824|ref|YP_842942.1| 125 ALAREFLEKLRT----NGEYVIVDTDAGIEHFGR 154
                                    567777766666....488888888888887664 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   0.00073      0.43       1      34 [.       3      41 ..       3      50 .. 0.89
   2 !    7.5   0.0    0.0079       4.7       6      31 ..     123     147 ..     120     184 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00073
                                   EEEES-SHHHHHHHHHHHHTT.....EEEEEEESSHHHH CS
                         TrkA_N  1 iiiiGlGrvGrslaeeLsegg.....kdvvvidkdeerv 34
                                   i+i+G G  G+s +  L +++      +v+v+d de+++
  gi|116753824|ref|YP_842942.1|  3 ILICGKGGSGKSTVSALLAREiagrgTRVLVVDADESNF 41
                                   79*****************88899**77*******9875 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0079
                                    -SHHHHHHHHHHHHTTEEEEEEESSH CS
                         TrkA_N   6 lGrvGrslaeeLseggkdvvvidkde 31 
                                    +G ++r+ +e+L+++g+ +v++d+d 
  gi|116753824|ref|YP_842942.1| 123 MGALAREFLEKLRTNGE-YVIVDTDA 147
                                    8999**********995.******97 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   6.8e-06     0.004       8      43 ..       7      42 ..       2      57 .. 0.87
   2 ?    0.7   0.0      0.43   2.6e+02      91     137 ..     129     175 ..     122     195 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.8e-06
                                   SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-H CS
                           MipZ  8 ekGGsGksttavhvavaLlkkGarvaaidldlrqrt 43
                                    kGGsGkst++  +a  ++ +G+rv ++d d     
  gi|116753824|ref|YP_842942.1|  7 GKGGSGKSTVSALLAREIAGRGTRVLVVDADESNFG 42
                                   69***************************9986655 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.43
                                    HHHHHHHHH-SEEEEE--SS--HHHHHHHHT-SEEEEEEESSHHHHC CS
                           MipZ  91 elvadleaeldfividtPGsdsalsrlahsladtlvtPlndsfvdfd 137
                                    e +++l ++ +++++dt    ++  r + +  d +v+ ++  +  + 
  gi|116753824|ref|YP_842942.1| 129 EFLEKLRTNGEYVIVDTDAGIEHFGRGVETGCDKIVAVIDPCYESVQ 175
                                    56788899999******999999999999999999988776665555 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   0.0   1.1e-05    0.0068       4      52 ..       3      56 ..       1      70 [. 0.82
   2 ?    1.0   0.0      0.46   2.7e+02      73     115 ..     128     170 ..     105     203 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.1e-05
                                   EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES.....TSSTTHHHHHHHHH CS
                          SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvllvaaD.....tfRaaAveQLktla 52
                                   il++G  G+GK t  a La+ +  +g++vl+v aD     ++R+  ++Q k + 
  gi|116753824|ref|YP_842942.1|  3 ILICGKGGSGKSTVSALLAREIAGRGTRVLVVDADesnfgIYRMLGFDQPKDFM 56
                                   89********************************94444446777777766555 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.46
                                    HHHHHHHHHTTSSEEEEEE.--SSTTHHHHHHHHHHHHHHHSSS CS
                          SRP54  73 keavekakeekidvvlvDT.aGrlqndkelmeelkkikkvvkpd 115
                                    +e +ek +  + ++v+vDT aG  +  + + +  +ki  v++p 
  gi|116753824|ref|YP_842942.1| 128 REFLEKLRT-NGEYVIVDTdAGIEHFGRGVETGCDKIVAVIDPC 170
                                    444445444.669999**97888887777777777777777665 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   2.2e-05     0.013       2      69 ..       3      79 ..       3      86 .. 0.62
   2 ?   -0.7   0.0       2.4   1.4e+03      17      33 ..     128     148 ..     125     189 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.2e-05
                         AAA_33  2 vllvGlpGsGKstlaerllkklg.....avllssdtlrrrlfg....tdqqsktdytrvldrlyqilnelarkalsa 69
                                   +l++G  GsGKst++  l+++ +     + +++ d+  + ++     +++++  ++   +  l ++l +++r+ +++
  gi|116753824|ref|YP_842942.1|  3 ILICGKGGSGKSTVSALLAREIAgrgtrVLVVDADESNFGIYRmlgfDQPKDFMESLGGKRALSERLMRFIRSERRE 79
                                   689***************99988888777778888744444333222333333333334444555555666655555 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.4
                         AAA_33  17 erllkklg....avllssdtl 33 
                                    ++ l+kl     +v++++d+ 
  gi|116753824|ref|YP_842942.1| 128 REFLEKLRtngeYVIVDTDAG 148
                                    555555555556777777763 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.3   1.3e-05     0.008       1      24 [.       3      27 ..       3      74 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.3e-05
                         AAA_18  1 IlltGtpGvGKttlakeLskrl.gf 24
                                   Il++G+ G+GK+t++  L+++  g 
  gi|116753824|ref|YP_842942.1|  3 ILICGKGGSGKSTVSALLAREIaGR 27
                                   99****************9986444 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   9.4e-06    0.0056       4      41 ..       3      40 ..       1      76 [. 0.91

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 9.4e-06
                                   EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH CS
                          KTI12  4 vvltGlPssGKstrakeLakaleeekrsvvviddeslg 41
                                   ++++G   sGKst+++ La++++ ++ +v v+d +  +
  gi|116753824|ref|YP_842942.1|  3 ILICGKGGSGKSTVSALLAREIAGRGTRVLVVDADESN 40
                                   89*******************************77665 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   2.1e-05     0.012       4      34 ..       2      39 ..       1      69 [. 0.89
   2 ?   -2.0   0.0       4.2   2.5e+03      23      36 ..     137     150 ..     127     158 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.1e-05
                         AAA_24  4 kiliyGpsgiGKTtlakel.......gpkplfidtekG 34
                                   kili G+ g+GK+t+ + l       g ++l++d +++
  gi|116753824|ref|YP_842942.1|  2 KILICGKGGSGKSTVSALLareiagrGTRVLVVDADES 39
                                   9**************99999***************996 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.2
                         AAA_24  23 gpkplfidtekGlk 36 
                                      + +++dt++G  
  gi|116753824|ref|YP_842942.1| 137 NGEYVIVDTDAGIE 150
                                    37789999999976 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 ?    5.1   0.1     0.025        15       3      38 ..       3      38 ..       1      45 [. 0.82
   2 !    8.3   0.1    0.0026       1.6      12     155 ..      61     203 ..      58     222 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.025
                                   EEEEESTTCCHHHHHHHHHCT--SS-EEEEESS-SS CS
                           cobW  3 tvltGflGsGKTtLlnhllenraglklavivNefge 38
                                   ++++G  GsGK+t+   l ++ ag+ + v+v +  e
  gi|116753824|ref|YP_842942.1|  3 ILICGKGGSGKSTVSALLAREIAGRGTRVLVVDADE 38
                                   679999*******98877798899988888888766 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0026
                                    CHHHHHHHHH...CT--SS-EEEEESS-SSCHCCCCCCHCCCT........EEEETTTTECCHCTT-HHHHHHHHHHHHT CS
                           cobW  12 GKTtLlnhll...enraglklavivNefgevsiDaellretgve.......ivelenGciCctlredllkelealeeree 81 
                                    GK +L ++l+   + ++ + l +i  ef+  +i  e++  ++         i ++ +Gc C      l +e+ + ++   
  gi|116753824|ref|YP_842942.1|  61 GKRALSERLMrfiRSERREALSIIPEEFQIKDIPPEVVVGDEMVklvaigkIHNFGEGCACPM--GALAREFLEKLR--T 136
                                    677776666666688899999999999998889999987774334778888999999999988..333333332223..3 PP

                                    T-SEEEEEE.CTTTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHHHCH CS
                           cobW  82 rldviliEt.tGlaePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDllde 155
                                    + +++++ t  G+ +             ++  d +vav+D    + + +++  ++++++ +  ++++n +D  +e
  gi|116753824|ref|YP_842942.1| 137 NGEYVIVDTdAGIEHFGRG--------VETGCDKIVAVIDPCYESVQLSEKIAEMGEKIGKDVFFIVNRIDEDSE 203
                                    3588888873466554443........478889999999985556677777788888888888889999886555 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   1.8e-05     0.011      17      51 ..       2      36 ..       1      45 [. 0.94

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.8e-05
                  TrwB_AAD_bind 17 hilivGttGsGKtqalekllrairargdraivlDl 51
                                   +ili G  GsGK+++   l r+i  rg r++v+D+
  gi|116753824|ref|YP_842942.1|  2 KILICGKGGSGKSTVSALLAREIAGRGTRVLVVDA 36
                                   699*******************************7 PP

>> AAA_25  AAA 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     0.014      36      86 ..       3      43 ..       2     107 .. 0.89
   2 ?   -2.0   0.0       3.7   2.2e+03     147     159 ..     166     178 ..     139     225 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.4e-05
                         AAA_25 36 allaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsedel 86
                                   +l++G +g+GK+t+   la ++a +G            +Vl+v+a++s+ ++
  gi|116753824|ref|YP_842942.1|  3 ILICGKGGSGKSTVSALLAREIAgRG-----------TRVLVVDADESNFGI 43
                                   6899*******************444...........489999999887665 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.7
                         AAA_25 147 viDplsralggde 159
                                    viDp+++ ++ +e
  gi|116753824|ref|YP_842942.1| 166 VIDPCYESVQLSE 178
                                    5555555444443 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2   2.9e-05     0.018      27      63 ..       3      39 ..       2     207 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.9e-05
                         AAA_16 27 vllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                   +l+ G  G+GKs++   l+r++ ++g  +l  ++d++
  gi|116753824|ref|YP_842942.1|  3 ILICGKGGSGKSTVSALLAREIAGRGTRVLVVDADES 39
                                   6999*********************988877777776 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00011     0.064      24      62 ..       3      41 ..       1      80 [. 0.87
   2 ?   -1.7   0.0       1.7     1e+03      52      75 ..     164     187 ..     158     209 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                         AAA_10 24 sliiGdlGnGKSvlakllvlyisllggkaliiDpkkere 62
                                    li G+ G GKS ++ ll   i+ +g ++l++D  + + 
  gi|116753824|ref|YP_842942.1|  3 ILICGKGGSGKSTVSALLAREIAGRGTRVLVVDADESNF 41
                                   689******************************876654 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.7
                         AAA_10  52 aliiDpkkerekfketlpeiakki 75 
                                    + +iDp  e  +  e++ e+ +ki
  gi|116753824|ref|YP_842942.1| 164 VAVIDPCYESVQLSEKIAEMGEKI 187
                                    558899999999999887755542 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 ?   12.5   0.1   8.7e-05     0.052      32      68 ..       3      39 ..       1      44 [. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.7e-05
                                   EEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE--- CS
                           MeaB 32 vGltGvPGaGkstlvealglelrrrGkrvavlavDPs 68
                                   + + G  G+Gkst+   l+ e++ rG+rv v+  D s
  gi|116753824|ref|YP_842942.1|  3 ILICGKGGSGKSTVSALLAREIAGRGTRVLVVDADES 39
                                   558899*************************988865 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   6.2e-05     0.037      13      42 ..       2      31 ..       1     244 [. 0.88

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.2e-05
                                   EEEEEESTTSSHHHHHHHHTTSS--SEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran 13 kvaivGenGaGKStLlkllagllkpteGei 42
                                   k+ i G+ G+GKSt+ +lla++      ++
  gi|116753824|ref|YP_842942.1|  2 KILICGKGGSGKSTVSALLAREIAGRGTRV 31
                                   5789****************9987655555 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   0.00012     0.072       8      91 ..       3      78 ..       2     136 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00012
                         AAA_22  8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka..erlsseellealeqalr 87
                                   ++++G  G+GK+t+ + l+++         ++ +v+ v++ +s+    ++r+l  +    ++   + + +++l e+l + +r
  gi|116753824|ref|YP_842942.1|  3 ILICGKGGSGKSTVSALLAREIA------GRGTRVLVVDADESN--FGIYRMLGFDQP--KDFmeSLGGKRALSERLMRFIR 74
                                   79******************974......457777777777776..444444432222..2223344445555555555555 PP

                         AAA_22 88 arav 91
                                   + ++
  gi|116753824|ref|YP_842942.1| 75 SERR 78
                                   5555 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   0.00021      0.13       1      25 [.       3      27 ..       3      74 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00021
                   RNA_helicase  1 iwlyGpsgeGKStlakeLakallkk 25
                                   i+++G+ g GKSt++  La++++++
  gi|116753824|ref|YP_842942.1|  3 ILICGKGGSGKSTVSALLAREIAGR 27
                                   689******************9965 PP

>> DUF3964  Protein of unknown function (DUF3964)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00053      0.32      14      60 ..      61     115 ..      53     120 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00053
                        DUF3964  14 dkrelaeqvlkl...ekkeql.ylpdefeikqvvgy.eige...kevilgrleef 60 
                                     kr l+e+++++   e++e l  +p+ef+ik++++   +g+   k v +g++++f
  gi|116753824|ref|YP_842942.1|  61 GKRALSERLMRFirsERREALsIIPEEFQIKDIPPEvVVGDemvKLVAIGKIHNF 115
                                    588899988765333777777368*********9861568844445679999998 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00073      0.44       9      41 ..       7      39 ..       1      44 [. 0.87

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00073
                          VirC1  9 lkGGaGkttalmglcsalasdgkrvalfeaden 41
                                    kGG+Gk+t    l   +a +g+rv + +ade 
  gi|116753824|ref|YP_842942.1|  7 GKGGSGKSTVSALLAREIAGRGTRVLVVDADES 39
                                   39*******999999****************96 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1     0.033        20       1      23 [.       2      24 ..       2      40 .. 0.83
   2 ?    4.0   0.0     0.083        49      49     113 ..     141     196 ..     127     197 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.033
                                   EEEEEESTTSSHHHHHHHHHTST CS
                       MMR_HSR1  1 evaivGrpNvGKStLinaltgek 23
                                   +++i G+  +GKSt+   l +e 
  gi|116753824|ref|YP_842942.1|  2 KILICGKGGSGKSTVSALLAREI 24
                                   589***********998888764 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.083
                                    EEEEC.GGCSSHHHHHHHHHHHHHHHHC.TSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEE CS
                       MMR_HSR1  49 elvDt.pGliegaseekglgkaflalee.adlillvvdaseeklkpldeeleelleeakkplilvln 113
                                    ++vDt +G ie       +g+ ++     +d i+ v+d   e   +l e+++e+ e+ +k++++++n
  gi|116753824|ref|YP_842942.1| 141 VIVDTdAG-IE------HFGRGVE---TgCDKIVAVIDPCYE-SVQLSEKIAEMGEKIGKDVFFIVN 196
                                    55555444.44......3344433...34899*****94444.346779999999989999999998 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   0.6   0.00081      0.49      25      38 ..       3      16 ..       1      21 [. 0.89

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00081
                         AAA_29 25 tlltGpsGsGKSTl 38
                                   +l+ G+ GsGKST+
  gi|116753824|ref|YP_842942.1|  3 ILICGKGGSGKSTV 16
                                   69***********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                       121  (0.00674884); 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: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 1696.27
//
Query:       gi|116753825|ref|YP_842943.1|  [L=151]
Description: hypothetical protein Mthe_0512 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-33  115.9   0.0    1.4e-33  115.6   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 !  115.6   0.0   7.8e-38   1.4e-33       2     119 .]      23     133 ..      22     133 .. 0.90

  Alignments for each domain:
  == domain 1  score: 115.6 bits;  conditional E-value: 7.8e-38
                                    S-SSGGG--.-EEEEEE-HHH..HGGGTTGGG-SEEEEEEE-TTS...-.SS--E-TT-.SS-E.EGGGS--S-SSS-EE CS
                           TrmO   2 iPrqpglaeeaeaeielepeynseealegleefshlwllfvfhenaekklkakvrpprlggnervGvfatRsphRpnpig 81 
                                    +P+q+++++   +eie++pe+  e++l ++e+++hl++l++++++  +++k   +pp  +g+ + GvfatRsp Rpnp++
  gi|116753825|ref|YP_842943.1|  23 APHQGRVSR-EICEIEIFPEF--EDGLMDIEKCTHLIVLYWLDRA--DRTKLRAVPP-HDGRVH-GVFATRSPDRPNPVA 95 
                                    79***9999.79*********..********************99..3323444555.567666.*************** PP

                                    EEEEEEEEEETTEEEEES----TT-EEEEEEE--HHHH CS
                           TrmO  82 lsvvklekvegnvlevsgvDlldgtpvlDiKPYvpyaD 119
                                    +sv++l +veg++l+v+g+D+ldgtp++DiKPY + +D
  gi|116753825|ref|YP_842943.1|  96 FSVAELLSVEGRKLRVRGLDALDGTPLIDIKPYSAGID 133
                                    *********************************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       184  (0.0102627); expected 358.6 (0.02)
Passed bias filter:                      176  (0.0098165); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1093.09
//
Query:       gi|116753826|ref|YP_842944.1|  [L=385]
Description: FAD dependent oxidoreductase [Methanosaeta thermophila PT]
Scores for complete 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   41.1   0.1    4.2e-10   39.2   0.0    1.7  2  Lycopene_cycl   Lycopene cyclase protein
    6.6e-07   29.2   1.3     0.0049   16.5   0.0    3.8  4  DAO             FAD dependent oxidoreductase
    1.7e-06   27.5   0.1    0.00071   18.9   0.0    2.2  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    3.7e-05   23.3   0.9    3.7e-05   23.3   0.9    1.8  2  FAD_oxidored    FAD dependent oxidoreductase
    0.00012   21.5   0.0     0.0048   16.2   0.0    2.1  2  FAD_binding_3   FAD binding domain
    0.00012   21.4   0.2     0.0053   16.0   0.0    2.4  2  Thi4            Thi4 family
    0.00017   20.6   0.1    0.00043   19.3   0.0    1.6  2  Trp_halogenase  Tryptophan halogenase
    0.00026   20.2   0.0     0.0012   18.0   0.1    1.8  2  GIDA            Glucose inhibited division protein A
     0.0022   16.8   0.0     0.0041   15.9   0.0    1.4  1  HI0933_like     HI0933-like protein
  ------ inclusion threshold ------
      0.022   15.0   0.2       0.15   12.3   0.1    2.5  3  NAD_binding_8   NAD(P)-binding Rossmann-like domain
      0.022   13.8   0.4      0.055   12.5   0.4    1.6  1  FAD_binding_2   FAD binding domain
      0.073   12.3   0.0       0.23   10.7   0.0    1.7  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
       0.11   12.4   0.0        1.1    9.3   0.0    2.5  2  NAD_binding_9   FAD-NAD(P)-binding


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 !   39.2   0.0     3e-13   4.2e-10       1     145 [.       4     146 ..       4     178 .. 0.83
   2 ?   -0.7   0.0      0.42   5.8e+02     276     346 ..     277     346 ..     255     351 .. 0.76

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 3e-13
                  Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfpnnyvWsdefedlga...leecvehsWsgtivylddgkkill 77 
                                    Dv+v+Ga pAgls Aa +  a+++ + vli+    ++  +n   +   ++  a    e +  h+ +g+++  + g++ ++
  gi|116753826|ref|YP_842944.1|   4 DVAVVGASPAGLSAAASS--ARTDARTVLIDRDLTSVPNANTIFEGMASA--AclnVEPFSIHQVRGMRLISPSGHSLEI 79 
                                    9*****************..**********87666643444455544444..233599********************** PP

                  Lycopene_cycl  78 graYgrvsskrlkeellerlvengvklleakvesveeeeageslvvleggrkirarlvvdarglaslk 145
                                    +   + + +k + ++ l++ ++ g++  e+ v sv  + +      l+ g  i+ar+v+da g+ s+ 
  gi|116753826|ref|YP_842944.1|  80 DAGGHFLDRKGFYAHYLNSAADYGAEIIESEVRSVSRSAD-GMELFLSTGDVIDARIVIDAAGVDSQL 146
                                    *999***********************************9.778899999*************55443 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.42
                  Lycopene_cycl 276 varslaeapllasaiaaalresslsarawatlwprerkrqreffrllglalllkldiegrrrfldaFfrlp 346
                                    +a s+++ +++ ++  +a+  +    r+  + + r  +r+ +f  +lg+a l +l+      + ++F  l+
  gi|116753826|ref|YP_842944.1| 277 LAYSMRAGEICGDVAGRAAL-ERDPSRERLSEYSRRWWRELGFEYILGRASLERLRSMSDDEIDRLFISLS 346
                                    56677777755554444444.44445555667778888888886699999999999999999999998886 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   0.1    0.0055       7.6       1      29 [.       4      34 ..       4      51 .. 0.91
   2 !   16.5   0.0   3.6e-06    0.0049     133     212 ..      75     149 ..      49     161 .. 0.74
   3 ?    2.0   0.0     0.088   1.2e+02     316     351 ..     171     204 ..     158     205 .. 0.84
   4 ?    0.4   0.0      0.27   3.7e+02      51      72 ..     296     317 ..     246     362 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0055
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEESS CS
                            DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekg 29
                                   dv+++G+  +Gls+A   ar    ++l++++
  gi|116753826|ref|YP_842944.1|  4 DVAVVGASPAGLSAAASSARTDarTVLIDRD 34
                                   8*****************998789*****98 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 3.6e-06
                                    EEEEETTEEEE.EHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEE.EEEEEEEE--GGGHHHHHTT CS
                            DAO 133 galfypdtgqv.dpakltaalaraaealGveilegtevtgleeedgkvwgverttpgen.daadavVnaaGawsdllgll 210
                                     +l  + +g++ d   + a +++ a++ G+ei+e  ev+++++   ++++++  t g + da + v+ aaG+ s+l+   
  gi|116753826|ref|YP_842944.1|  75 HSLEIDAGGHFlDRKGFYAHYLNSAADYGAEIIES-EVRSVSRSA-DGMELFLST-GDViDA-RIVIDAAGVDSQLA--- 147
                                    5566677788889999999***************8.*****8753.345665444.766233.66********9977... PP

                                    CT CS
                            DAO 211 ke 212
                                      
  gi|116753826|ref|YP_842944.1| 148 SS 149
                                    22 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.088
                                    SEEEEEEETEE.EEEEEEECTTTHHHHHHHHHHHHHH CS
                            DAO 316 lpligetpgvk.glylatGhsghGltlapatGkllae 351
                                     p ige+   +  +++ + + g+  t++pa G+ +a 
  gi|116753826|ref|YP_842944.1| 171 HPGIGEED--RfEYWVGSIAPGWKATFSPA-GEDMAT 204
                                    68899963..4599****************.**9995 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 0.27
                                    HHSTHHHHHHHHHHHHHHHHHH CS
                            DAO  51 lpeaselarlslealeelrele 72 
                                    l+      rls+++++++rel 
  gi|116753826|ref|YP_842944.1| 296 LERDPSRERLSEYSRRWWRELG 317
                                    2222223389999999998886 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 !   18.9   0.0   5.2e-07   0.00071       1      32 [.       3      35 ..       3      60 .. 0.77
   2 !    6.2   0.0    0.0038       5.2     185     252 ..      91     154 ..      78     159 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 5.2e-07
                                   CSEEEE--SHHHHHHHHHHHHHTS-EEEEE.TT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                    Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlve.le 32
                                   +dv+v+G+ pAGl+aa   a+  a+++l++ + 
  gi|116753826|ref|YP_842944.1|  3 FDVAVVGASPAGLSAAASSARTDARTVLIDrDL 35
                                   69***************************7522 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0038
                                    HHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 185 lsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrpstelleeklglel 252
                                    + a + +   + G e+  +++v  + +  + +e+ l++g++ida+ v+ a+Gv  +  l+  +lg+++
  gi|116753826|ref|YP_842944.1|  91 FYAHYLNSAADYGAEII-ESEVRSVSRSADGMELFLSTGDVIDARIVIDAAGVDSQ--LA-SSLGIKT 154
                                    55566666666677777.889999999999999*******************9876..34.5666665 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.9   2.7e-08   3.7e-05       1      31 [.       4      34 ..       4      36 .. 0.96
   2 ?   -1.7   0.1      0.99   1.4e+03     130     144 ..     127     141 ..     103     154 .. 0.70

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 2.7e-08
                   FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveer 31
                                   Dv VvG+ paG+ AA ++ar +a+++L++++
  gi|116753826|ref|YP_842944.1|  4 DVAVVGASPAGLSAAASSARTDARTVLIDRD 34
                                   9***************************985 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.99
                   FAD_oxidored 130 grktirAkvfiDATg 144
                                     + +i A+++iDA g
  gi|116753826|ref|YP_842944.1| 127 TGDVIDARIVIDAAG 141
                                    477899******987 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   3.5e-06    0.0048       2      39 ..       3      40 ..       2      45 .. 0.91
   2 ?    3.4   0.0     0.027        37     152     185 ..     130     163 ..      98     235 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.5e-06
                                   EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCS CS
                  FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvl 39
                                    dV++VGa+paGl++a   ++   r+vl+++  t v++
  gi|116753826|ref|YP_842944.1|  3 FDVAVVGASPAGLSAAASSARTDARTVLIDRDLTSVPN 40
                                   69*****************************9887765 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.027
                                    EEEEEEEEE--GTT-HHHHHHTGG.EEEEEEEEEE CS
                  FAD_binding_3 152 tvrakYlvGaDGgrStvrktlgie.fegeetvyea 185
                                     ++a+ ++ a G+ S+ +++lgi+ ++ +++v  +
  gi|116753826|ref|YP_842944.1| 130 VIDARIVIDAAGVDSQLASSLGIKtMRHPDDV-AW 163
                                    589*********************67666665.22 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   3.9e-06    0.0053      17      52 ..       2      36 ..       1      49 [. 0.92
   2 ?    2.8   0.0     0.042        57     156     175 ..     130     149 ..     122     162 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.9e-06
                                   EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS CS
                           Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailersvs 52
                                   + Dv++vGa ++GL+aa   a+  d ++++++r ++
  gi|116753826|ref|YP_842944.1|  2 KFDVAVVGASPAGLSAAASSART-DARTVLIDRDLT 36
                                   67********************9.*******99875 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.042
                                    EEEEEEEEE--GSSSTTTTH CS
                           Thi4 156 virakvvvdatGhdgeivav 175
                                    vi+a++v+da+G d+++ + 
  gi|116753826|ref|YP_842944.1| 130 VIDARIVIDAAGVDSQLASS 149
                                    89************998764 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.82   1.1e+03       1      22 [.       4      25 ..       4      34 .. 0.80
   2 !   19.3   0.0   3.1e-07   0.00043     151     238 ..      86     166 ..      46     175 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.82
                                   EEEEE--SHHHHHHHHHHHHHT CS
                 Trp_halogenase  1 kivivGGGtaGwlaAaalakal 22
                                   ++ +vG+ +aG  aAa  a++ 
  gi|116753826|ref|YP_842944.1|  4 DVAVVGASPAGLSAAASSARTD 25
                                   589*********9999877765 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 3.1e-07
                                    E-HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGGG-IIIIIIT---EEE-TTT-- CS
                 Trp_halogenase 151 ldaalyakfLrrvaearGvtrvegkvvevqldedgrveslrledgreveadlfiDcsGfrgllieqaLktgfedwsdvLl 230
                                    ld++ +  +  + a + G +++e +v +v   +dg   +l l++g +++a+++iD+ G  + l ++    g++++ +  +
  gi|116753826|ref|YP_842944.1|  86 LDRKGFYAHYLNSAADYGAEIIESEVRSVSRSADGM--ELFLSTGDVIDARIVIDAAGVDSQLASSL---GIKTMRH--P 158
                                    68877766666778899******************6..888899******************99884...5555555..4 PP

                                    --EEEEEE CS
                 Trp_halogenase 231 tdrAlavq 238
                                     d A+a++
  gi|116753826|ref|YP_842944.1| 159 DDVAWAIE 166
                                    46666655 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1     9e-07    0.0012       1      34 [.       4      43 ..       4      60 .. 0.80
   2 ?   -0.3   0.0      0.32   4.3e+02      93     150 ..      87     142 ..      74     156 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 9e-07
                                   CEEEE-SSHHHHHHHHHHHHTT--EEEE......ES-GGG CS
                           GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi......thkldt 34
                                   dv V+G+  AG+ AA+ +ar  a+++Li      +++ +t
  gi|116753826|ref|YP_842944.1|  4 DVAVVGASPAGLSAAASSARTDARTVLIdrdltsVPNANT 43
                                   79**************************666665444444 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.32
                                    -HHHHHHHHHHHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT CS
                           GIDA  93 drelyskevteklenepnleiieeeveeliveekkvkgvvtedgetikakavviatGt 150
                                    dr+ + +++ +   +    eiie ev +++  +     + +++g +i a++v+ a+G 
  gi|116753826|ref|YP_842944.1|  87 DRKGFYAHYLNSAAD-YGAEIIESEVRSVSR-SADGMELFLSTGDVIDARIVIDAAGV 142
                                    555555555555444.567999999*99955.677777999************99996 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0     3e-06    0.0041       1      31 [.       3      33 ..       3      37 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3e-06
                                   -SEEEE--SHHHHHHHHHHHHTT--EEEE-S CS
                    HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllek 31
                                   +dv+v+G+ +AGl aA+s a++++r++l+++
  gi|116753826|ref|YP_842944.1|  3 FDVAVVGASPAGLSAAASSARTDARTVLIDR 33
                                   59***************************97 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 ?   12.3   0.1   0.00011      0.15       1      27 [.       7      33 ..       7      36 .. 0.95
   2 ?   -1.7   0.0       2.6   3.6e+03      43      52 ..      98     107 ..      71     115 .. 0.57
   3 ?   -3.0   0.0       6.6   9.1e+03      30      53 ..     289     314 ..     285     320 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                                   EE--SHHHHHHHHHHHCCTEEEEEE-S CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllek 27
                                   +vGa  +Gl+aA+  a+ +++ +l+++
  gi|116753826|ref|YP_842944.1|  7 VVGASPAGLSAAASSARTDARTVLIDR 33
                                   8*********************99997 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.6
                                    CEECTS---E CS
                  NAD_binding_8  43 vrvdygahif 52 
                                     ++dyga i+
  gi|116753826|ref|YP_842944.1|  98 SAADYGAEII 107
                                    4455555554 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 6.6
                                    SSSGGG-EECETT..CEECTS---EE CS
                  NAD_binding_8  30 rlGGraasyevpg..vrvdygahifh 53 
                                    ++ Graa +++p   +  +y  ++++
  gi|116753826|ref|YP_842944.1| 289 DVAGRAALERDPSreRLSEYSRRWWR 314
                                    56688888887654466667777765 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.4     4e-05     0.055       1      30 [.       4      33 ..       4      38 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4e-05
                                   SEEEE--SHHHHHHHHHHHHTTT-EEEEES CS
                  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvek 30
                                   Dv V+G+  AGL+AA++ a+  +++++++ 
  gi|116753826|ref|YP_842944.1|  4 DVAVVGASPAGLSAAASSARTDARTVLIDR 33
                                   9*************************9985 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 ?   10.7   0.0   0.00017      0.23       2     134 ..       7     142 ..       6     159 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00017
                    Pyr_redox_3   2 IiGaGPaGlaaaielkkagledylilEkg.nignsiyrypkemtfispsftsekleip...dlnaiseet.spafslkee 76 
                                    ++Ga PaGl+aa    + +  + + ++++ + +       + m     + + e ++i+   ++  is++  s ++    +
  gi|116753826|ref|YP_842944.1|   7 VVGASPAGLSAAASSARTDA-RTVLIDRDlTSVPNANTIFEGMASAA-CLNVEPFSIHqvrGMRLISPSGhSLEIDAGGH 84 
                                    8******************9.67899999766655555555555543.45566666651115667777652566667788 PP

                    Pyr_redox_3  77 klsrke.aleYlrevaksfelpiklfeeVesvkkedegfevetske.tyeAkkviiAtGe 134
                                     l rk  +++Yl++ a+ +  +i  ++eV+sv+++++g e+  s++ ++ A+ vi A+G 
  gi|116753826|ref|YP_842944.1|  85 FLDRKGfYAHYLNSAAD-YGAEII-ESEVRSVSRSADGMELFLSTGdVIDARIVIDAAGV 142
                                    88888625666666655.566665.578******999999887776599******99996 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 ?   -0.4   0.0      0.73     1e+03       1      19 [.       6      24 ..       6      56 .. 0.83
   2 ?    9.3   0.0   0.00078       1.1     106     154 ..      94     141 ..      82     143 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.73
                  NAD_binding_9  1 aivGaGprGlavlerLlar 19
                                   a+vGa p+Gl++++  ++ 
  gi|116753826|ref|YP_842944.1|  6 AVVGASPAGLSAAASSART 24
                                   79*********99876555 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00078
                  NAD_binding_9 106 ellarlpegvtvevhraevvdleeradgqavlladgaslaadaVvLAlG 154
                                    + l+++ ++   e++++ev +++++adg+++ l++g+ ++a+ V+ A G
  gi|116753826|ref|YP_842944.1|  94 HYLNSA-ADYGAEIIESEVRSVSRSADGMELFLSTGDVIDARIVIDAAG 141
                                    444444.34567899*****************************98888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2481.22
//
Query:       gi|116753827|ref|YP_842945.1|  [L=299]
Description: hypothetical protein Mthe_0514 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00046   19.5   2.6      0.059   12.6   0.1    2.4  2  DUF5050   Domain of unknown function (DUF5050)
      0.007   16.4   0.9      0.074   13.1   0.1    2.3  2  DUF5038   Domain of unknown function (DUF5038)
  ------ inclusion threshold ------
      0.093   12.9   0.0        2.3    8.4   0.0    2.3  2  DP-EP     DP-EP family
       0.42   11.2   2.4        3.3    8.3   0.0    3.3  4  PQQ_3     PQQ-like domain


Domain annotation for each model (and alignments):
>> DUF5050  Domain of unknown function (DUF5050)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.3    0.0008       3.6     149     247 ..      47     158 ..      10     164 .. 0.54
   2 !   12.6   0.1   1.3e-05     0.059     135     175 ..     215     253 ..     181     263 .. 0.57

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0008
                                    EEEE-T.TT-.-EEEEETTTTEEEEEE-S-EEEEEE...EETTEEEEEGGGTT-EEEE-SSS---.....EE-S-S-.EE CS
                        DUF5050 149 iYytgesedh.slykldtdgksiskvseenlyllvv...egdyiYyidlsknyaLyrvklsgsek.....evltedk.vd 218
                                    +Yyt+  e+  s+y+  t      +  ++n+y++     + +++Y+++  +++++yr+++ ++       +v t+d+ v 
  gi|116753827|ref|YP_842945.1|  47 LYYTDARESPgSVYHAGT---PNYTRRSGNIYSFAFhpgVPEKLYFVN-ANENKIYRTHMRSDGYyfpeeTVYTHDTyV- 121
                                    566666333224444433...333334455555444122457888877.566678887777664311110333333321. PP

                                    E...EEEE...TTEEEEEE-SSS-E...EEEEETTS- CS
                        DUF5050 219 n...yNvt...gnwiYyqkesdeeka..lyrikldGs 247
                                        + ++   +  +Y++++++ +++  +yr++++G+
  gi|116753827|ref|YP_842945.1| 122 RdiaFALDdsgDLRLYFSEATGAGANgmIYRLETNGT 158
                                    1212222211144677777776655555777777776 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 1.3e-05
                                    ESS----SEEETTEEEEE-T.TT--EEEEETTTTEEEEEE- CS
                        DUF5050 135 sdeaieplsvkdgwiYytgesedhslykldtdgksiskvse 175
                                    ++e+i+ l vkdg iYy++   ++ +ykl++ ++s+ +++ 
  gi|116753827|ref|YP_842945.1| 215 NTEPIKGLVVKDGAIYYANW--RNTIYKLNLTDGSKIDIYT 253
                                    34466666677777777776..5567777766655555543 PP

>> DUF5038  Domain of unknown function (DUF5038)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.068     3e+02      48      77 ..      22      51 ..      12      67 .. 0.75
   2 !   13.1   0.1   1.7e-05     0.074      45      95 ..      96     148 ..      84     169 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.068
                        DUF5038 48 rtdvtsaeylpdetgypdtttvelhfllsd 77
                                   ++dvt+a+ l   t yp    + + +  +d
  gi|116753827|ref|YP_842945.1| 22 QADVTAAQSLEAGTNYPIPVDIVIDLYYTD 51
                                   689*************97766555544444 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 1.7e-05
                        DUF5038  45 rigrtdvtsae.ylpdetgyp.dtttvelhfllsddstlpvfydtmtgafsfg 95 
                                    +i rt + s   y+p+et y  dt   ++ f l d   l +++   tga + g
  gi|116753827|ref|YP_842945.1|  96 KIYRTHMRSDGyYFPEETVYThDTYVRDIAFALDDSGDLRLYFSEATGAGANG 148
                                    78899998865279******825555689*******************97766 PP

>> DP-EP  DP-EP family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.046     2e+02      48      86 ..     102     140 ..      88     159 .. 0.84
   2 ?    8.4   0.0   0.00052       2.3      39     103 ..     208     272 ..     182     280 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.046
                                    XSSSXXEEEEEEESSTTSSSSXEE.EEXTTSSEEEEEES CS
                          DP-EP  48 esakglafvgaaietedDgnndivlslsengktlvlidk 86 
                                      ++g+ f +  ++t d   +di + l ++g ++ ++ +
  gi|116753827|ref|YP_842945.1| 102 MRSDGYYFPEETVYTHDTYVRDIAFALDDSGDLRLYFSE 140
                                    4568999***99**9999*************99766655 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00052
                                    EEEEEEEEEXSSSXXEEEEEEESSTTSSSSXEE.EEXTTSSEEEEEESSX.SXEEEEEEEEEEXS CS
                          DP-EP  39 vdiiyvltdesakglafvgaaietedDgnndivlslsengktlvlidkdkdsdesigfklvlaak 103
                                    v+++y+++ e  kgl+ ++ ai+  + +n   +l+l+++ k  +++d+d +   ++gf+ vl+a 
  gi|116753827|ref|YP_842945.1| 208 VEVVYTDNTEPIKGLVVKDGAIYYANWRNTIYKLNLTDGSKIDIYTDSDRTWLSDVGFRRVLSAD 272
                                    579********************88889999999****9999*****************999976 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.9   8.6e+03      28      36 ..      63      77 ..      55      78 .. 0.64
   2 ?   -1.1   0.1      0.67     3e+03      27      37 ..     144     154 ..     113     156 .. 0.73
   3 ?    0.3   0.1      0.24   1.1e+03       9      30 ..     170     192 ..     165     205 .. 0.76
   4 ?    8.3   0.0   0.00074       3.3      12      39 ..     218     244 ..     202     245 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.9
                          PQQ_3 28 tg......dGtlyAl 36
                                   ++       G++y++
  gi|116753827|ref|YP_842945.1| 63 GTpnytrrSGNIYSF 77
                                   444666667888876 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.67
                          PQQ_3  27 gtgdGtlyAlD 37 
                                    ++ +G +y l+
  gi|116753827|ref|YP_842945.1| 144 AGANGMIYRLE 154
                                    33488888876 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.24
                          PQQ_3   9 lpgpvnsspavdg.glvyvgtgd 30 
                                    ++g   +  a+d  g +y ++g+
  gi|116753827|ref|YP_842945.1| 170 VGGSWAGDFAFDTeGNLYLSSGN 192
                                    55555566678744999999985 PP

  == domain 4  score: 8.3 bits;  conditional E-value: 0.00074
                          PQQ_3  12 pvnsspavdgglvyvgtgdGtlyAlDae 39 
                                    p+  +++v +g +y + + +t+y l+ +
  gi|116753827|ref|YP_842945.1| 218 PI-KGLVVKDGAIYYANWRNTIYKLNLT 244
                                    56.689*******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 2227.12
//
Query:       gi|116753828|ref|YP_842946.1|  [L=418]
Description: major facilitator transporter [Methanosaeta thermophila PT]
Scores for complete 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  70.5    1.9e-27   96.1  38.9    2.1  2  MFS_1     Major Facilitator Superfamily
  ------ inclusion threshold ------
        8.9    6.2   9.4          4    7.3   0.2    2.7  3  DUF412    Protein of unknown function, DUF412
        9.6    4.5  21.7       0.46    8.8   4.6    2.5  2  MFS_3     Transmembrane secretion effector


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.1  38.9   3.1e-31   1.9e-27      21     308 ..      38     331 ..      15     340 .. 0.81
   2 !   50.8  23.6   1.9e-17   1.1e-13       1     177 [.     236     416 ..     236     418 .] 0.89

  Alignments for each domain:
  == domain 1  score: 96.1 bits;  conditional E-value: 3.1e-31
                          MFS_1  21 l.alaedlg.....ispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fasslw.lllvlr 92 
                                       l+++++     +s+  + l ++++ +++a+a+++ G  ++++G+r+v ++g +l +lg +ll+  ass+  l     
  gi|116753828|ref|YP_842946.1|  38 VkPLTDHFQamgqvVSANDVLLPFSIFLAVFAIAMPLSGKYIEKYGPRKVTMVGGVLCGLG-WLLAsTASSVQmLYPTYG 116
                                    22566777766677777778889**************************************.88884349999888999* PP

                          MFS_1  93 vlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafv...lfl 169
                                    ++ Glg g+++   +a++a+wfp+ +rg+a+gl  +gf+++a +++ ++g+l+++ g   +f ++++++++ +v   + l
  gi|116753828|ref|YP_842946.1| 117 IIGGLGVGIAYGCPVAVAARWFPD-RRGLAVGLTVLGFGFSAFFTANIAGYLIAAQGVMNTFRVFGVAFIIIIVllsMPL 195
                                    ************************.********************************99999999999999988666666 PP

                          MFS_1 170 lllpeepperkrkspkeeekgtgpaplvp..awkallkdpvlw.illialllfffgfsglltllplylqevlglsgllla 246
                                    ++ p+ ++++++ +p+++     +a+++     +++lk p ++ ++l+ +++  +g++++++  p+   e   ++   la
  gi|116753828|ref|YP_842946.1| 196 VFPPAGYKPPGWTPPAPK----PGAAVTHefRREEMLKTPTFYgLWLCYFIGCLAGLMAISVSKPV-GTEIVQID-PELA 269
                                    777888888888888888....66666667767788888877644555555555555557777777.799999**.7*** PP

                          MFS_1 247 glllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlv 308
                                    ++l++++a+++ ++++l+g+l d+l +r++ +++++l+++a++++a +a ++ + +++++++
  gi|116753828|ref|YP_842946.1| 270 TFLVGFFAIFNGGGRPLFGYLTDKLTPRNAAIVSFVLIFIACMMMATMAKPTASEIYVVAFA 331
                                    ************************************************99944433333333 PP

  == domain 2  score: 50.8 bits;  conditional E-value: 1.9e-17
                          MFS_1   1 lllaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll 80 
                                    l+l++f+ +la  +++++  +  +e  +i+p  + +l++++a++ + + +++G+l+d++ +r   +++++l ++++++++
  gi|116753828|ref|YP_842946.1| 236 LWLCYFIGCLAGLMAISVSKPVGTEIVQIDPELATFLVGFFAIFNGGGRPLFGYLTDKLTPRNAAIVSFVLIFIACMMMA 315
                                    6889999998888877777767788899***********************************99999999999956666 PP

                          MFS_1  81 .fa.sslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllgglla.sslgWravfyi 156
                                     +a ++   + +v+ +   l+ g+ ++++ + +a  f  ++ +r +g++ +++++Gai+gp l+g++  s +++ +vf  
  gi|116753828|ref|YP_842946.1| 316 tMAkPTASeIYVVAFAALWLCLGGWLAIAPTSTATFFGTTDYPRNYGVVFLAYGAGAIVGPQLAGFIKtSTGSYMGVFNY 395
                                    6889777779999999****************************************************66666******* PP

                          MFS_1 157 laivsllafvlfllllpeepp 177
                                    +a++++++++++++l++ +++
  gi|116753828|ref|YP_842946.1| 396 VAALAIIGIIIAYVLMRPPKK 416
                                    ********9987777655544 PP

>> DUF412  Protein of unknown function, DUF412
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.2   0.00068         4      46      80 ..      44      78 ..      31      82 .. 0.85
   2 ?    4.6   0.3    0.0047        28      40      76 ..     159     195 ..     135     196 .. 0.81
   3 ?   -3.1   0.5       1.1   6.4e+03      43      66 ..     304     326 ..     294     339 .. 0.48

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00068
                         DUF412 46 vltlvlqlylagsealpqailtalfllsLPlQGly 80
                                    ++++ q++ a+   lp +i++a+f++ +Pl G y
  gi|116753828|ref|YP_842946.1| 44 HFQAMGQVVSANDVLLPFSIFLAVFAIAMPLSGKY 78
                                   577788888888889****************9966 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0047
                         DUF412  40 vmpalavltlvlqlylagsealpqailtalfllsLPl 76 
                                    ++  +a   ++ q +++    + +a +++++lls+Pl
  gi|116753828|ref|YP_842946.1| 159 FTANIAGYLIAAQGVMNTFRVFGVAFIIIIVLLSMPL 195
                                    55667777788888888888****************8 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 1.1
                         DUF412  43 alavltlvlqlylagsealpqail 66 
                                    ++ ++++++ ++++++   ++ i 
  gi|116753828|ref|YP_842946.1| 304 FVLIFIACMMMATMAKP-TASEIY 326
                                    44444444444444322.222333 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   9.1     0.017     1e+02      58     186 ..      67     191 ..      47     196 .. 0.74
   2 ?    8.8   4.6   7.6e-05      0.46      44     190 ..     256     412 ..     227     418 .] 0.71

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.017
                          MFS_3  58 ifllsi.laGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaalndPaWqAsvgelvkrrd 136
                                    +f +++ l+G   +++  Rkv +++ +l  l+ +l+ + + +++l p   ++    +g+G a   P   A+     + r 
  gi|116753828|ref|YP_842946.1|  67 VFAIAMpLSGKYIEKYGPRKVTMVGGVLCGLGWLLASTASSVQMLYPTYGIIGG--LGVGIAYGCPV--AVAARWFPDR- 141
                                    455555346777777778888888888888888888888888888877644433..45666666665..3333444333. PP

                          MFS_3 137 vpaAvaLnsvginiaRsvGPAlgGvlvaavGaalafavnalsylalival 186
                                       Av L+ +g+  +      ++G l+aa G + +f v  ++++++iv l
  gi|116753828|ref|YP_842946.1| 142 RGLAVGLTVLGFGFSAFFTANIAGYLIAAQGVMNTFRVFGVAFIIIIVLL 191
                                    3469***************************************9999876 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 7.6e-05
                          MFS_3  44 plmvAlvqaaatLPifl...lsila.......GalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlli 113
                                    p+   +vq+   L +fl   ++i+        G l+D++  R+  ++  +l+ ++ ++++++a     + +++   +l++
  gi|116753828|ref|YP_842946.1| 256 PVGTEIVQIDPELATFLvgfFAIFNgggrplfGYLTDKLTPRNAAIVSFVLIFIACMMMATMAKPTASEIYVVAFAALWL 335
                                    4445555555555555411145543222222278******************************9999999999999999 PP

                          MFS_3 114 giGaaln.dPaWqAsvgelvkrrdvpaAvaLnsvginiaRsvGPAlgGvlvaavGaal.afa.vnalsylalivallrwk 190
                                     +G  l  +P+  A    +    d p    +  + +     vGP l+G + ++ G+ + +f  v+al+ + +i+a + ++
  gi|116753828|ref|YP_842946.1| 336 CLGGWLAiAPTSTA---TFFGTTDYPRNYGVVFLAYGAGAIVGPQLAGFIKTSTGSYMgVFNyVAALAIIGIIIAYVLMR 412
                                    99999862576555...5778889999999999999999****************9863453367777777777766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1018  (0.0567795); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 2847.84
//
Query:       gi|116753829|ref|YP_842947.1|  [L=329]
Description: hypothetical protein Mthe_0516 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); 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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2347.14
//
Query:       gi|116753830|ref|YP_842948.1|  [L=265]
Description: oxidoreductase FAD/NAD(P)-binding subunit [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-11   45.2   0.0      2e-11   44.5   0.0    1.3  1  NAD_binding_1    Oxidoreductase NAD-binding domain
    1.9e-10   40.4   1.6    3.6e-10   39.5   1.6    1.5  1  DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydr
      6e-06   26.5   0.0    9.6e-06   25.9   0.0    1.3  1  FAD_binding_6    Oxidoreductase FAD-binding domain
     0.0078   16.3   0.0      0.013   15.6   0.0    1.3  1  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 !   44.5   0.0   4.4e-15     2e-11       3     108 ..     112     211 ..     110     212 .. 0.91

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 4.4e-15
                                    EEGGGGHHHHHHHHHHHHHCTTCSEEEEEEEESSGCGSTTHHHHHHHHHHCTTEEEEEEEESSCTTTSSSEESSHHHHHH CS
                  NAD_binding_1   3 agGtGiaPvrsvlraileeakdktkvvlvyGnrteedllyreeleelakklpgrlkvvavvsreeagweggkgrvqdall 82 
                                    +gG+G+a +rs+++ i+++ +   +v + yG+rt++dl++ +e +++  k++g +++  +v+  +++w+g+ g v + l 
  gi|116753830|ref|YP_842948.1| 112 GGGSGFATLRSLINYIVDRRDEFEEVFVAYGARTRQDLYFMQEYKSW--KMEG-IEIELTVDVGDESWRGNVGMVPELLD 188
                                    79*****************9999************************..8888.677777899*************9995 PP

                                    HHHHHHSSTTEEEEEECSHHHHHHHH CS
                  NAD_binding_1  83 eellslkkeethvyvCGppgMikavr 108
                                    ++ +   ++ + + +CGp +Mi+av+
  gi|116753830|ref|YP_842948.1| 189 RMDI---SPPASAAICGPLPMIRAVA 211
                                    5444...59**************996 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 !   39.5   1.6     8e-14   3.6e-10       1      41 [.     229     261 ..     229     262 .. 0.95

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 8e-14
                                    ----SSSSSSS-TTEEEETTCTT.CEEETTTT-CEEECCCB CS
                DHODB_Fe-S_bind   1 eerMaCGvGaClgCvvktkggdggeykrvCkdGPvFdadev 41 
                                    e++M+CG+G C +C++           rvCk+GPvF+++ +
  gi|116753830|ref|YP_842948.1| 229 ERHMKCGIGKCEHCTIGP--------YRVCKEGPVFPYNTI 261
                                    89****************........79*********9976 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 !   25.9   0.0   2.1e-09   9.6e-06       2      96 ..       9      97 ..       8      99 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 2.1e-09
                                   EEEEEEEECCTTEEEEEEEESTTTS-----TT-EEEEEECETTCCEEEEEE.BSSTTECCEEEEEEE--TT-HHHHHHHCS- CS
                  FAD_binding_6  2 lkltekeevsedtrifrfklpsekqklglpvGqhvflrlkikgeaviRsYtpissenekGelellvkvypgGkmsqaLdelk 83
                                   +++++  +v++d   +++++ +++ ++ +++Gq+v+++l   ge    + +++ss  +++ l+l +++   G++++ +    
  gi|116753830|ref|YP_842948.1|  9 AEIVDIDRVTHDSYLISLQILDRDVSFTYRPGQFVMVSLFGMGE---CPISIASS-PTRNVLQLCIRR--AGRITNGIMDSM 84
                                   57888999********************************9998...56775554.5789*******7..6*******9999 PP

                                   TT-EEEEEEEE-S CS
                  FAD_binding_6 84 igdtleikGPlGk 96
                                   igd+l i+GPlG+
  gi|116753830|ref|YP_842948.1| 85 IGDVLGIRGPLGN 97
                                   ***********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 !   15.6   0.0   2.8e-06     0.013      13      81 ..      20      83 ..       8     111 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.8e-06
                  FAD_binding_8 13 eedliklkvskpkkslkykaGqyvyinipslsklfwqsHPFtiasapeddklslvikvksgltkklakk 81
                                   ++ li+l++     s+ y +Gq+v +++  + +      P +ias+p  + l+l+i+  + +t+ +   
  gi|116753830|ref|YP_842948.1| 20 DSYLISLQILDRDVSFTYRPGQFVMVSLFGMGEC-----PISIASSPTRNVLQLCIRRAGRITNGIMDS 83
                                   456788888777778***********99888866.....************************988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); 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:                         4  (0.000223102); expected 0.2 (1e-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 0.24s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1823.81
//
Query:       gi|116753831|ref|YP_842949.1|  [L=524]
Description: cation transporter [Methanosaeta thermophila PT]
Scores for complete 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-62  209.7  15.4    1.1e-54  185.7  15.1    2.7  2  TrkH      Cation transport protein


Domain annotation for each model (and alignments):
>> TrkH  Cation transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   2.2e-09   3.9e-05      11     118 ..      44     149 ..      35     155 .. 0.83
   2 !  185.7  15.1   6.2e-59   1.1e-54      75     489 ..     147     516 ..     126     523 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2.2e-09
                           TrkH  11 itialgavllfldkeskyplalkddfqivkaaeialsvdgtlklllesaslafldalfeavsgltttglsvivveeslpr 90 
                                     +ia+  ++ f+++ +   l +kd+f  v   ++a   +g+++ +     ++++d+lfe++sg+tttg+sv ++++s ++
  gi|116753831|ref|YP_842949.1|  44 SMIAMMIGSFFRRHGEIGDLSIKDGFALVAFGWLAAAMIGAIPYM--MLGMGSIDSLFESMSGFTTTGASVLTDSNSEGY 121
                                    4556666677777766688999*********************98..677888*************************** PP

                           TrkH  91 sgltlraqlqqiGglgvvvlaylslptl 118
                                    ++   + + q++  +   ++ yl ++t 
  gi|116753831|ref|YP_842949.1| 122 WIIDGELANQSVAFIVAGSVEYLLWATT 149
                                    *988888888777776678888888775 PP

  == domain 2  score: 185.7 bits;  conditional E-value: 6.2e-59
                           TrkH  75 tttglsvivveeslprs..gltlraqlqqiGglgvvvlaylslptlgrgsaflylseaqkeelggkelrslselikilvv 152
                                    +tt ++v    ++ p++   l++r++ q++Gg+g++ l  ++lp+lg  + +ly++e++++e++ + ++++++++ +l+ 
  gi|116753831|ref|YP_842949.1| 147 ATTNTTVSAMIPEHPTYygLLFWRSFSQWLGGMGIILLFIAILPRLGVAGRQLYRAEVPGPEKE-SLTPRIRQTAELLWG 225
                                    555555555555555441169*****************************************97.789************ PP

                           TrkH 153 yyvgleilafvllvvliytakaysevvdstgvsplwwaffhsmSafnnlGfsltpnSlasfnknivillvaiifiilGni 232
                                    +y++l i+ ++ll           +++      pl++a++ ++ ++ ++Gfs  + S++ + + ++i+ ++++f++l + 
  gi|116753831|ref|YP_842949.1| 226 IYLSLSIIEVILL---------KVAGM------PLYDALCNTFATVATGGFSPQSMSIEAYGS-PMIEYIIVLFMFLAGA 289
                                    *************.........57899......******************************.**************** PP

                           TrkH 233 gFpillrviiaikkkilrdlkqikeslsflldlprrcftLllasgfvwllllelavlnvtdnilfilldegslvvksipk 312
                                    +F +++ +i +   +             +++d+++r+       +f++++++ ++              +   +++++p 
  gi|116753831|ref|YP_842949.1| 290 NFALHYMTIHQDR-R------------CLIRDPEFRFY------SFIIVVSTLFI-------------AATAGMMSPLP- 336
                                    *****98875432.2............4789*******......77777777766.............45568999999. PP

                           TrkH 313 gsrvlkalFqsvstrta.GFsvvdlsnlhpaikvllvlmmyigglpgStaggIrrtnvyeefslgkyeieqekepkavsk 391
                                     +r++ alFq+vs  t+ GFs+  ++ + pa k++l+l m++g+++gSt g I+ ++v+++ + + +e+    +pkav +
  gi|116753831|ref|YP_842949.1| 337 -DRIRCALFQVVSIMTTtGFSTTNFDTWYPAAKIVLLLLMFVGACAGSTGGAIKVVRVLVILKYVHRELMLAMHPKAVIQ 415
                                    .************99999************************************************************** PP

                           TrkH 392 ksidgkhlerqllvdlwslflvlliilileglklsdv..qepdfsffdiLfevvSaygtvGLSlGa.knaslsaqlttis 468
                                    +++   +++++++++  s+f v+++ + l + +l      +  +++ +i+ +v+S++g+vG+++G+      +a++ +++
  gi|116753831|ref|YP_842949.1| 416 VKLHDITVKEEIVRSTISFFGVYMLTFALASIVLAAIsySDQAMNLEAIISAVASCLGNVGPGFGPvGPYMNFAEIHPLG 495
                                    ***********************99999999888654114557**********************9899999******** PP

                           TrkH 469 klvlialmirGrlrglpvlld 489
                                    klvli+ m++Grl++++vl++
  gi|116753831|ref|YP_842949.1| 496 KLVLILCMWMGRLEIMTVLVL 516
                                    ******************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (524 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       850  (0.0474092); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.24s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 3568.69
//
Query:       gi|116753832|ref|YP_842950.1|  [L=289]
Description: transposase, IS4 family protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.2e-33  113.1   0.0    3.2e-31  107.9   0.0    2.2  2  DDE_Tnp_1_5  Transposase DDE domain
      9e-21   74.5   0.1    1.6e-20   73.7   0.1    1.4  1  DDE_Tnp_1    Transposase DDE domain


Domain annotation for each model (and alignments):
>> DDE_Tnp_1_5  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.9   0.0   3.6e-35   3.2e-31       2     111 ..      18     125 ..      17     126 .. 0.95
   2 ?    2.8   0.0     0.016   1.4e+02      40      67 ..     252     281 ..     246     287 .. 0.82

  Alignments for each domain:
  == domain 1  score: 107.9 bits;  conditional E-value: 3.6e-35
                    DDE_Tnp_1_5   2 kRGsltiwldeeaiaawkek...kkngkrgrpqvysdaaiqtcltvkvlfklplRqlqGfvqsllklaglellvpdystl 78 
                                    +RG  +++l+++++++w+e+    +++k+grp++y++++iq+c +++++++lp+Rql+Gf+q+l+ ++   ll++dystl
  gi|116753832|ref|YP_842950.1|  18 RRG--WFYLSTDFVNNWDEEllkMNKNKNGRPYRYPETFIQFCGLAYAFLHLPYRQLEGFIQALSGFVPG-LLAADYSTL 94 
                                    799..************9987745569******************************************9.99******* PP

                    DDE_Tnp_1_5  79 srraktlevkipvkrkskglhlvvdstGlkvlg 111
                                    ++r ++le++ip+ +++  l+++vdstG+kv++
  gi|116753832|ref|YP_842950.1|  95 WQRITNLELNIPIPDND--LVVAVDSTGMKVTN 125
                                    **************999..99**********97 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.016
                    DDE_Tnp_1_5  40 tcltvkvlfklplRql..qGfvqsllklag 67 
                                    ++  +k++f+ ++R++  +G+++ + ++ +
  gi|116753832|ref|YP_842950.1| 252 VFSAIKRIFGETVRATskEGMIREVRRMFT 281
                                    56789*********9855699999988876 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.7   0.1   1.8e-24   1.6e-20       5     200 ..     112     271 ..     108     285 .. 0.83

  Alignments for each domain:
  == domain 1  score: 73.7 bits;  conditional E-value: 1.8e-24
                      DDE_Tnp_1   5 evlivDattvrvpgtkedarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrprkgklvlaDa 84 
                                     v++vD+t ++v+  + ++r++++  + + ++k+hiavd +++ ++ ++it+  v d++ +k+ll+ +   k    l+D+
  gi|116753832|ref|YP_842950.1| 112 LVVAVDSTGMKVTNRGDWMRESHGVER-RGWIKVHIAVDVETRKPVTFEITDETVTDHEMVKPLLEDV---KLEDSLMDG 187
                                    699******************888666.79************************************99...89******* PP

                      DDE_Tnp_1  85 GYasaelldtleekgvd.yiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgdvyyvtntnsells 163
                                    +Y++++++d+++ekgvd + i+++kn+ ++        r +    +++  +  +++ +++                    
  gi|116753832|ref|YP_842950.1| 188 AYDKEGVFDFMKEKGVDmPGIKIRKNAIVKAG----SSRAEPVLEFMKYGYHSWKIVHGY-------------------- 243
                                    ****************9568899999988866....344445555555555555555555.................... PP

                      DDE_Tnp_1 164 aeevaelyrlRwqiErvFkwlkrkfgldrlryrglnr 200
                                             +Rw  E+vF+ +kr fg + +r+ ++++
  gi|116753832|ref|YP_842950.1| 244 --------GRRWAAESVFSAIKRIFG-ETVRATSKEG 271
                                    ........***************998.6666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 2140.94
//
Query:       gi|116753833|ref|YP_842951.1|  [L=323]
Description: aliphatic sulfonate ABC transporter periplasmic ligand-binding protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-38  131.9   0.0    4.5e-38  131.4   0.0    1.2  1  NMT1_2          NMT1-like family
    1.8e-18   67.3   0.0    2.5e-18   66.8   0.0    1.2  1  NMT1            NMT1/THI5 like
    1.1e-06   28.3   0.0    4.7e-05   23.0   0.0    2.4  3  NMT1_3          NMT1-like family
     0.0017   18.0   0.0     0.0022   17.6   0.0    1.2  1  Phosphonate-bd  ABC transporter, phosphonate, periplasmic sub
  ------ inclusion threshold ------
       0.09   12.3   0.0       0.18   11.3   0.0    1.4  1  VitK2_biosynth  Menaquinone biosynthesis


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 !  131.4   0.0   1.2e-41   4.5e-38       3     249 ..      23     257 ..      21     260 .. 0.93

  Alignments for each domain:
  == domain 1  score: 131.4 bits;  conditional E-value: 1.2e-41
                         NMT1_2   3 pekeqlklGfialtdaaplvvakekglfake....Glt.velekqaswaelrdkllagelDaahv.ltpapllidlGigg 76 
                                    +e+ +l++G+++ t+    +va ekg+  +     G+t ve  ++ s++  ++++lag+lD+a+v  +p +++i+ G+  
  gi|116753833|ref|YP_842951.1|  23 SENITLRIGYQPSTHQIAEMVAMEKGWWLEDlkpfGVTaVEEYEFPSGPPEMQAMLAGSLDVAYVgTAPPISAISGGL-- 100
                                    677799**********9999999999987777999***99*************************999999******9.. PP

                         NMT1_2  77 akadmkvlaslnlnGqaitlsnklkdkkvsdakalkdlvakkkaskplkiavtfpgsthdlllrywLaaaGldpeadvkl 156
                                       d k++a +n+nG a++l+ +      ++ ++ ++l       k++ ia+  pgs +d+ l+ wL+++G+d+ ++vk+
  gi|116753833|ref|YP_842951.1| 101 ---DAKIVAGVNTNGSALVLAPD------KEYSGPESL-------KGMSIATFPPGSIQDTVLKKWLRENGVDT-SEVKV 163
                                    ...*****************975......444444444.......789**************************.***** PP

                         NMT1_2 157 vvvpppqmvanlkagtidgfcvgePwnaqavaegiGvtaltsqelwkdhPekvlgvredfveknpntaralvkalleAtk 236
                                    + + p ++v ++ ag++dg++ +eP +++ ++ + G  ++ s+e w++h ++ l+v+ +++ ++p++++++vk++++At+
  gi|116753833|ref|YP_842951.1| 164 LPMGPGDAVTAMFAGQVDGTFLPEPSPSVIEMSNKGKVVVYSGEMWPNHACCSLVVSGKLIREHPELVEQIVKTHIKATE 243
                                    ******************************************************************************** PP

                         NMT1_2 237 wlda.kkenraeaa 249
                                    ++ a  +e++++ a
  gi|116753833|ref|YP_842951.1| 244 YVYAhPDEAARIYA 257
                                    ***97777777666 PP

>> NMT1  NMT1/THI5 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.8   0.0     7e-22   2.5e-18       8     216 .]      42     252 ..      35     252 .. 0.84

  Alignments for each domain:
  == domain 1  score: 66.8 bits;  conditional E-value: 7e-22
                                    HHHHHTTHHHHT....TEEE..EEE--SSTTHHHHHHHCTS-SEEEE-HHHHHHHHHTT--EEEEEEEE-S--EEEEEEC CS
                           NMT1   8 yvAkekGYFkee....GldV..eivepadpsdatelvasgkadfgvsyqesllaarakglpvvsvaallqeplsglivlk 81 
                                    +vA ekG++ e     G+    e+  p++    ++++ +g  d++   +   + a + gl+ + va ++ ++ s+l+   
  gi|116753833|ref|YP_842951.1|  42 MVAMEKGWWLEDlkpfGVTAveEYEFPSG-PPEMQAMLAGSLDVAYVGTAPPISAISGGLDAKIVAGVN-TNGSALVLAP 119
                                    66777777654322224432344555555.44567788899999999999999999*****99999887.999******* PP

                                    CC--SSGGGGTTSEEEE-S.-TTHHHHHHHHHHHTT--GGG-EEEE-.TT-HHHHHHCTSSSEEECEETTTHHHHHHHTT CS
                           NMT1  82 dsgikspkDLkGkrigyvg.spfekallkallakdggdpsdvtlvnvggtslakalltgkvDaaiggyenwegveleseg 160
                                    d++ + p++LkG  i++++ +++++++lk+ l+++g+d s+v+++++g  ++++a+ +g+vD ++       ++e+ ++ 
  gi|116753833|ref|YP_842951.1| 120 DKEYSGPESLKGMSIATFPpGSIQDTVLKKWLRENGVDTSEVKVLPMGPGDAVTAMFAGQVDGTFLPEPSPSVIEMSNK- 198
                                    ****************8887999*****************************************977777777777655. PP

                                    --EEEE-GGGTT-----SEEEEEEHHHHHH-HHHHHHHHHHHHHHHHHHHHSHHHH CS
                           NMT1 161 kelrifaladlgvpdyyslvlitnekllkenpelvkkFlrAlkkGyeyalahPeea 216
                                       +++ ++   +p+     l+++ kl++e+pelv+++++   k++ey++ahP+ea
  gi|116753833|ref|YP_842951.1| 199 --GKVVVYSGEMWPNHACCSLVVSGKLIREHPELVEQIVKTHIKATEYVYAHPDEA 252
                                    ..5667777777889999999**********************************8 PP

>> NMT1_3  NMT1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.019        68     150     176 ..      71      97 ..      47     106 .. 0.85
   2 !   23.0   0.0   1.3e-08   4.7e-05      84     184 ..     104     201 ..      99     207 .. 0.90
   3 ?   -2.9   0.0         1   3.6e+03     152     176 ..     230     254 ..     226     271 .. 0.65

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.019
                         NMT1_3 150 gesadalkdgqldgaalvaGvPvsavt 176
                                     + ++a+  g ld+a + +++P+sa++
  gi|116753833|ref|YP_842951.1|  71 PPEMQAMLAGSLDVAYVGTAPPISAIS 97 
                                    56789********************96 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 1.3e-08
                         NMT1_3  84 aitmlyaevfqlvvskdsgigsiadlkgkrvsvGpegsGtegsarailealglsekdlklleelgygesadalkdgqldg 163
                                    +++ ++++  +lv++ d++ +  + lkg++++  p+gs +++   + l++ g++ +++k+   +g+g++++a+  gq+dg
  gi|116753833|ref|YP_842951.1| 104 IVAGVNTNGSALVLAPDKEYSGPESLKGMSIATFPPGSIQDTVLKKWLRENGVDTSEVKV-LPMGPGDAVTAMFAGQVDG 182
                                    56678888899999999999999***********************************97.688**************** PP

                         NMT1_3 164 aalvaGvPvsavtqlaasedi 184
                                    ++l+   P+ +v +++++ ++
  gi|116753833|ref|YP_842951.1| 183 TFLP--EPSPSVIEMSNKGKV 201
                                    ****..788899999887665 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1
                         NMT1_3 152 sadalkdgqldgaalvaGvPvsavt 176
                                     ++++ + +++++ +v ++P  a  
  gi|116753833|ref|YP_842951.1| 230 LVEQIVKTHIKATEYVYAHPDEAAR 254
                                    5677777888888888888876544 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 !   17.6   0.0   6.3e-07    0.0022      43     165 ..      74     187 ..      64     249 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 6.3e-07
                                    HHHHHTTS-SEEE--HHHHHHHHHHS-EEEEEEEEETT--SEEEEEEEEETTSS--SHHHHGG-EEEE--TT-TTTTHHH CS
                 Phosphonate-bd  43 vealragqvDiaflgplayvqardqagveplatrvrsdGsasyrsviivradsdiqsledLkgktiafvspsStsGylvp 122
                                    ++a+ ag++D+a++g+ + + a    g++  a+ v+  G ++  s+++ ++d ++   e Lkg +ia   p S     v 
  gi|116753833|ref|YP_842951.1|  74 MQAMLAGSLDVAYVGTAPPISAISG-GLD--AKIVA--GVNTNGSALVLAPDKEYSGPESLKGMSIATFPPGSIQ-DTVL 147
                                    69********************975.433..34443..55799********************************.6777 PP

                                    HHHTCCCCT--HHHHSSEEEE--HHHHHHHHHTTSSSEEEEEH CS
                 Phosphonate-bd 123 aalLvkeagldpeddfsevfsgshdaavlavlsgdadaaavsa 165
                                    + +L +e+g+d+++  +   +g    av a ++g++d  ++++
  gi|116753833|ref|YP_842951.1| 148 KKWL-RENGVDTSEV-KVLPMG-PGDAVTAMFAGQVDGTFLPE 187
                                    889*.8*****9875.443666.55566777999999888655 PP

>> VitK2_biosynth  Menaquinone biosynthesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0     5e-05      0.18     166     229 ..     202     263 ..     191     274 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5e-05
                                    EEEHHHHHHHHHSS-EEEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHCCSTTS CS
                 VitK2_biosynth 166 vlDLgelWeeltglPlvlglwvvrrdlaaeaakeleealreSveyalahldevaeyaaeraqem 229
                                    v+  ge+W +++   lv  + ++r+   +e ++++++  +++ ey +ah+de+a+  a+r++ +
  gi|116753833|ref|YP_842951.1| 202 VVYSGEMWPNHACCSLVVSGKLIREH--PELVEQIVKTHIKATEYVYAHPDEAARIYANRTKQD 263
                                    44449*******************99..6999**********************9988777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2192.60
//
Query:       gi|116753834|ref|YP_842952.1|  [L=239]
Description: binding-protein-dependent transport systems inner membrane component [Methanosaeta thermophila PT]
Scores for complete 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   69.3  13.9    5.3e-19   68.7  13.9    1.4  1  BPD_transp_1  Binding-protein-dependent transport system inne
     0.0061   16.1   0.9     0.0061   16.1   0.9    2.1  3  YibE_F        YibE/F-like protein


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.7  13.9   5.9e-23   5.3e-19       2     165 ..      51     215 ..      47     232 .. 0.83

  Alignments for each domain:
  == domain 1  score: 68.7 bits;  conditional E-value: 5.9e-23
                   BPD_transp_1   2 illGilaa......lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraa 75 
                                    i++G+++a      +  ++ ldk+++p+++v++ +P+++++++ +       ++g +  ++ ++++++a+++++++++ +
  gi|116753834|ref|YP_842952.1|  51 IFAGMIIAmplgmgMGWSRSLDKIIDPIVEVVRPIPPLAWIPFAI------VWFGLTHESAGFIVFIGAVFPILINTYVG 124
                                    5566666666666677*****************************......9**************************** PP

                   BPD_transp_1  76 lrslpkdlveaaralGasr.wqifrkvvlPnalppiitglilafggllggavlleflg.swpGlgtllleailgydysei 153
                                    +r+lp+ +ve a +lGa+r + ++r+v+lP alp+i++g+++a+g+++   v++e++g s +Glg+++++ +    +   
  gi|116753834|ref|YP_842952.1| 125 FRNLPRVYVESAMVLGATRdRDLIRYVALPYALPSIAAGIRIAMGIAWMCLVAAEMFGvSTSGLGYRIWSYYYLHKMEHV 204
                                    *****************9835699*********************************94556799999887777777744 PP

                   BPD_transp_1 154 snggvlalviav 165
                                    +  ++++l+ + 
  gi|116753834|ref|YP_842952.1| 205 L-LYMIVLGMLG 215
                                    4.3333333333 PP

>> YibE_F  YibE/F-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0     0.072   6.5e+02      77      93 ..      47      63 ..      20      81 .. 0.63
   2 ?   -2.6   0.2      0.34     3e+03      32      43 ..     108     119 ..      91     140 .. 0.62
   3 !   16.1   0.9   6.8e-07    0.0061      77     142 ..     156     221 ..     150     225 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.072
                         YibE_F 77 allgtllgvllalllal 93
                                    +lg+++g+++a+ l++
  gi|116753834|ref|YP_842952.1| 47 FFLGIFAGMIIAMPLGM 63
                                   34555555555554444 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.34
                         YibE_F  32 lvlilvllplll 43 
                                    +v+i +++p+l+
  gi|116753834|ref|YP_842952.1| 108 IVFIGAVFPILI 119
                                    222222222222 PP

  == domain 3  score: 16.1 bits;  conditional E-value: 6.8e-07
                         YibE_F  77 allgtllgvllalllallviklakltGlnseeaeellylplqgldlsglllagiligalGAvmDva 142
                                    al ++ +g+ +a+++a++++ +a++ G++++ + + + +++   +++++ll +i++g+lG  +D a
  gi|116753834|ref|YP_842952.1| 156 ALPSIAAGIRIAMGIAWMCLVAAEMFGVSTSGLGYRIWSYYYLHKMEHVLLYMIVLGMLGLFIDKA 221
                                    67788999*************************999666655679****************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1839.39
//
Query:       gi|116753835|ref|YP_842953.1|  [L=567]
Description: adenine deaminase [Methanosaeta thermophila PT]
Scores for complete 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-67  225.0   0.1    7.9e-67  223.8   0.1    1.6  1  Adenine_deam_C  Adenine deaminase C-terminal domain
    1.5e-32  113.3   0.5    2.7e-31  109.2   0.5    2.2  1  Amidohydro_1    Amidohydrolase family
    6.4e-08   32.5   0.8    2.6e-05   23.9   0.0    2.3  2  Amidohydro_3    Amidohydrolase family


Domain annotation for each model (and alignments):
>> Adenine_deam_C  Adenine deaminase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  223.8   0.1   1.3e-70   7.9e-67       1     168 [.     393     559 ..     393     560 .. 0.99

  Alignments for each domain:
  == domain 1  score: 223.8 bits;  conditional E-value: 1.3e-70
                                    .SS-EEEEEEEEEETTEEE-..-TTEEEEEEE--SSSS--EEEEEEESS--BSSEEEES--TTT--EEEEESSHHHHHHH CS
                 Adenine_deam_C   1 qliTkelevelpvkdgvvvadlekdllkiavveRhgktgnvgvgfvkgfglkkgAiAssvahDshniivvGtndedmalA 80 
                                    q++T+ + ++ +v++g+v +d+++d+lk+avveRh++tgnvg+g+v+gfglk+gAiAssv+hDshniivvG+++e+m++A
  gi|116753835|ref|YP_842953.1| 393 QILTETIAARPEVRNGEVISDTRNDILKVAVVERHRATGNVGLGLVSGFGLKRGAIASSVSHDSHNIIVVGEDEESMVRA 472
                                    689***************************************************************************** PP

                                    HHHHHHTTSEEEEEETTEEEEEEE-TBTTTBBSS-HHHHHHHHHHHHHHHHTTS-TTTBSGGGGGSTT-TTSSSEEEETT CS
                 Adenine_deam_C  81 vnrvielgGGivvvedgkvlaelpLpiaGlmSdepaeevaekleeleaalkelgvkledpfmtlsflalpviPelkltdk 160
                                    v+ +i++gGG v v dg+++a+lpLpiaGl+S++++e+v+e+ e++ aa ++lg++led fmtlsflalpviPel++td+
  gi|116753835|ref|YP_842953.1| 473 VESLISMGGGWVSV-DGTTIASLPLPIAGLLSERRVEDVVEEAENVIAASHSLGSELEDSFMTLSFLALPVIPELRITDR 551
                                    **************.999************************************************************** PP

                                    SEEETTTT CS
                 Adenine_deam_C 161 Glvdvkkf 168
                                    Glvdv++f
  gi|116753835|ref|YP_842953.1| 552 GLVDVREF 559
                                    *****987 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.2   0.5   4.5e-35   2.7e-31       2     344 .]      64     343 ..      63     343 .. 0.85

  Alignments for each domain:
  == domain 1  score: 109.2 bits;  conditional E-value: 4.5e-35
                                    EEE-EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHHHHHHHHHHTSSSEEEEEE CS
                   Amidohydro_1   2 vlPGlIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattstgiealleaaeelplglrilg 81 
                                    + PG IDaHvH+e+s+l         +p e+a++++ +g+ t + +++++++  g     gi+ ll+ ae +p+ + + +
  gi|116753835|ref|YP_842953.1|  64 IAPGSIDAHVHIESSML---------MPSEYARAVVPRGTLTVIADPHEIANVLGVD---GISYLLRCAEGIPMRFLVTA 131
                                    78***********9988.........******************************7...******************** PP

                                    ESSEGGS.GCCCSHHHHHHHHHHHHHHHHHHCTTTCEE.EEEEECGTCCSHHHHHHHHHHHHHHHTTEEEEEE..TSSCH CS
                   Amidohydro_1  82 gkvsldr.gsaetskasreklkagaaetikgkadgvvk.valapheapafsdeelkealkeakkrdlpvaiHa..letkg 157
                                    +++++++  +++     + ++++       +++  vv   +++ ++ +   d  + + lk+a+ +++ ++ Ha  l+ + 
  gi|116753835|ref|YP_842953.1| 132 PSCVPAThLETSGAALGVSEIASLL-----DDH-RVVGlGEMMNYPGVIHRDKPVLAKLKVAASKNKTICGHApgLGGRD 205
                                    *****97655565555555665553.....444.455569**************************************** PP

                                    HHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHHHHHHHCEEHHHHHHHHSEHHHHHHHHHHH CS
                   Amidohydro_1 158 evedaeaafgetiehgthlevaeslglldeiklilahgvhltpteaellkerlkeagvahcpfsnsilrsgrealrkald 237
                                     +++a a + +++e++   e +e+          l  g++++                      + + + +++ l k ++
  gi|116753835|ref|YP_842953.1| 206 LHAYAAALIEDDHECTRAEEAMEQ----------LRAGICIMIR--------------------EGSAARNLDELVKIIR 255
                                    ***************877777777..........9999999966....................3446677777777777 PP

                                    H.TSC.EEEEEECT.......TSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-T CS
                   Amidohydro_1 238 e.Gvk.vglgtDga.......asgnslnlleelrlalklqrgllyedeegglslkealrmaTingAkalglddkvGsiev 308
                                    e ++  ++l+tD+         +++ +     +r  +           e+g ++  a++maTin+A+++gl +++G++++
  gi|116753835|ref|YP_842953.1| 256 EyNTPnIMLCTDDLdprdivhRHIDHM-----IRRII-----------EAGTDPVAAIQMATINPARHFGL-RRTGAVAP 318
                                    766656999999555555433333333.....66666...........899********************.6******* PP

                                    TSB--EEEECCCTCGGGTTTCTSEEEEEEEETTEEE CS
                   Amidohydro_1 309 GkdADlvvvdldilaafvglkkdgnvkkvivkGklv 344
                                    G++AD++v+            +d+nv++vi  G+ v
  gi|116753835|ref|YP_842953.1| 319 GYRADIIVM-----------DHDFNVRRVIFEGEEV 343
                                    *********...........*************976 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.2   0.00065       3.9       2      50 ..      56     100 ..      55     113 .. 0.80
   2 !   23.9   0.0   4.4e-09   2.6e-05     412     449 ..     295     331 ..     261     348 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.00065
                   Amidohydro_3   2 viDakGrlvlPGFvDsHtHlagggvnl.rllrlpdarvtslegvltavrd 50 
                                    vi  +  l +PG +D+H H     ++  +l+++++ar+    g+lt+++d
  gi|116753835|ref|YP_842953.1|  56 VISVEDHLIAPGSIDAHVH-----IESsMLMPSEYARAVVPRGTLTVIAD 100
                                    677788899**********.....66656888888888777777777776 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 4.4e-09
                   Amidohydro_3 412 ealalyTrgpAkalgledrkGtLevGadADlvvldadp 449
                                    +a+++ T +pA+ +gl+ + G +++G++AD++v d d 
  gi|116753835|ref|YP_842953.1| 295 AAIQMATINPARHFGLRRT-GAVAPGYRADIIVMDHDF 331
                                    79****************8.**************9664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (567 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.23s 00:00:00.77 Elapsed: 00:00:00.39
# Mc/sec: 4333.76
//
Query:       gi|116753836|ref|YP_842954.1|  [L=371]
Description: radical SAM domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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-18   65.6   0.6    1.9e-13   51.1   0.2    2.4  2  Radical_SAM  Radical SAM superfamily
    1.3e-11   44.6   0.0    2.2e-11   43.9   0.0    1.3  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 !   12.6   0.0   1.5e-05      0.13      29      73 ..      46      90 ..      35     115 .. 0.88
   2 !   51.1   0.2   2.1e-17   1.9e-13       1     162 [.     149     313 ..     149     338 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.5e-05
                                   HHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHT CS
                                   xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM 29 lsveeileevkelkaekg.vkevilgggepllypdfvellerlakl 73
                                    + ee+ +ev++++ + g + ++i gg +p+++p++v   + ++ +
  gi|116753836|ref|YP_842954.1| 46 PQAEEVYREVDAAR-NSGmKSVFIAGGPHPSARPEEVLRHFDYVVI 90
                                   678**********6.9999*****************9998877665 PP

  == domain 2  score: 51.1 bits;  conditional E-value: 2.1e-17
                                    EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS........TTHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxx RF
                    Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly........pdfvellerlak 72 
                                    +++trgC+ +C +C++p+    + + r++s+ +il +++          + +++ + ++y         + vell+r   
  gi|116753836|ref|YP_842954.1| 149 IEITRGCPWGCAYCQTPRL--CGSVMRHRSIPSILSHARMHM------DLRFTSPNAFAYgsdglkprLERVELLLRTLS 220
                                    689**************74..666666666666666665553......45666666666666666556666666666666 PP

                                    TCCCTEEEEEEECSSCHG.....HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEE CS
                                    xxxxxxxxxxxxxxxxxx.....xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  73 lavpgiritvetngtlpd.....eeklerllelg.vdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvv 146
                                    +   g+ i + t +  ++      + le++  +    ++s+g ++++d+ +l+ +nrgh + ++  a+e++ ++ i ++v
  gi|116753836|ref|YP_842954.1| 221 E--LGRPIYFGTFPSEVRpdfisGKALELITTYCtNRTLSIGGQSGSDR-ILRDINRGHCVHDIEMACEICLDHEIVPNV 297
                                    6..47777777766666666**************999************.****************************** PP

                                    EEEEEBTTTSHHHHHH CS
                                    xxxxxxxxxxxxxxxx RF
                    Radical_SAM 147 drivglpGendeelee 162
                                    d i+ lpGe++e+   
  gi|116753836|ref|YP_842954.1| 298 DLILCLPGETEEDQML 313
                                    ************9554 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.0   2.4e-15   2.2e-11      50     121 .]      33     101 ..      26     101 .. 0.89

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 2.4e-15
                    B12-binding  50 e.kpdvvglSalltsqleavkelvellkrirprvkvvvGGahpsldpeetleaklgiddvvvgegedaleala 121
                                    + +p + + S+  t q e+v + v++++  + +   ++GG+hps+ pee+l++   +d+vv+gege++l++l+
  gi|116753836|ref|YP_842954.1|  33 RpRPGIMLYSI-ATPQAEEVYREVDAARNSGMKSVFIAGGPHPSARPEEVLRH---FDYVVIGEGEETLPELI 101
                                    43788888898.**************99999999*****************85...8*************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.36
# Mc/sec: 3085.86
//
Query:       gi|116753837|ref|YP_842955.1|  [L=111]
Description: hypothetical protein Mthe_0524 [Methanosaeta thermophila PT]
Scores for complete sequence (score 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       0.21   11.9   0.0    1.2  1  FCH       Fes/CIP4, and EFC/F-BAR homology domain
       0.38   10.6   2.4       0.36   10.7   0.7    1.8  2  BH4       Bcl-2 homology region 4


Domain annotation for each model (and alignments):
>> FCH  Fes/CIP4, and EFC/F-BAR homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.4e-05      0.21      17      45 ..      12      40 ..       6      62 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.4e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHHCT--- CS
                            FCH 17 edlqeflkeRaeiEkeYakkLqkLakkyl 45
                                   e++++fl eR  +E   + +L+kL+  +l
  gi|116753837|ref|YP_842955.1| 12 EEIRDFLLERLRLEGKCGEALDKLSLPFL 40
                                   89**********************97665 PP

>> BH4  Bcl-2 homology region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.51   4.5e+03       6      10 ..       5       9 ..       4       9 .. 0.85
   2 ?   10.7   0.7     4e-05      0.36      14      25 ..      65      76 ..      65      76 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.51
                                   HHHHH CS
                            BH4  6 ReLVv 10
                                   ReLV+
  gi|116753837|ref|YP_842955.1|  5 RELVI 9 
                                   9**96 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 4e-05
                                   HHHHHHTT---T CS
                            BH4 14 sYKLsQrGyeWe 25
                                   +YK+ QrGy W+
  gi|116753837|ref|YP_842955.1| 65 KYKIPQRGYIWY 76
                                   6**********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       234  (0.0130515); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 843.31
//
Query:       gi|116753838|ref|YP_842956.1|  [L=295]
Description: tungsten formylmethanofuran dehydrogenase, subunit C-like [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-07   30.8  13.9    6.1e-05   22.7   4.4    2.5  2  GXGXG     GXGXG motif
  ------ inclusion threshold ------
      0.077   12.9   0.2         12    5.8   0.0    3.0  3  XPB_DRD   Xeroderma pigmentosum group B helicase damage recog
      0.089   12.6   0.3       0.15   11.9   0.3    1.3  1  DUF2807   Putative auto-transporter adhesin, head GIN domain
        1.3    7.5   4.8        2.2    6.8   0.1    2.1  2  FapA      Flagellar Assembly Protein A


Domain annotation for each model (and alignments):
>> GXGXG  GXGXG motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   2.0   1.4e-05     0.061     104     166 ..      52     111 ..      44     124 .. 0.80
   2 !   22.7   4.4   1.4e-08   6.1e-05      33     122 ..     174     250 ..     153     257 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.4e-05
                                    EEESSB--SSTTTT-SS-EEEESEB-SSTTTT-EEEEEEE-S-B-SSBTTT--EEEEEEE.-SS CS
                          GXGXG 104 lfirgkageRfavrnsgatavvegvgdhgceYmtGGvvvvLgktgrnfaaGmsgGiayvl.ded 166
                                    + i g++g+R +  + +  +  +g g      + GG+v+v g++g  ++ +m +G++yv   ++
  gi|116753838|ref|YP_842956.1|  52 VRILGDVGSRLCSSMGVDLMRLGGSGGA----VDGGKVIVDGDVGPRMGISMIRGAIYVSgRVE 111
                                    5577888999998888888888888655....57*************************84444 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 1.4e-08
                                    EEEEEEEE-TTTTTT--TTEEEEEEEEE-STTTTT-ESSEEEEE--TT-SS-GGGSB-S-SSTTTT--SEEEEESSB--S CS
                          GXGXG  33 kiklkGsaGqslgaflakGltleleGdandyvGkglsgGkivikpskeskfkaeeniivGnvvlygatgGklfirgkage 112
                                    +i++ G+aG s g+ + +G  le++G +   +G  lsgG++++++++             + ++  +++G++f++g+ag 
  gi|116753838|ref|YP_842956.1| 174 RIEVFGNAGMSAGILMRSG-DLEIHGCSGRNTGVLLSGGTVIVHGDT------------EDFTATEMRSGEIFVKGSAGG 240
                                    6788888888888888555.788888888888888888888888888............367777888888888888888 PP

                                    STTTT-SS-E CS
                          GXGXG 113 Rfavrnsgat 122
                                     ++ r++g  
  gi|116753838|ref|YP_842956.1| 241 FACSRMRGGC 250
                                    8888887765 PP

>> XPB_DRD  Xeroderma pigmentosum group B helicase damage recognition domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0    0.0028        12      35      50 ..      35      50 ..      31      52 .. 0.85
   2 ?    3.4   0.0     0.016        72       6      16 ..     211     221 ..     208     233 .. 0.82
   3 ?   -1.6   0.0      0.58   2.6e+03      34      43 ..     284     293 ..     281     295 .] 0.84

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0028
                                   EGGGHHHHHHHHHCTT CS
                        XPB_DRD 35 pAlrYrdlveaLraag 50
                                    ++ Yr+lv+aLr+ +
  gi|116753838|ref|YP_842956.1| 35 DGWSYRALVDALRRGE 50
                                   5799*********865 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.016
                                    TEEEECSSSTT CS
                        XPB_DRD   6 GTllidgdprg 16 
                                    GT++++gd ++
  gi|116753838|ref|YP_842956.1| 211 GTVIVHGDTED 221
                                    ********997 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.58
                                    EEGGGHHHHH CS
                        XPB_DRD  34 apAlrYrdlv 43 
                                    + A+ Yr+++
  gi|116753838|ref|YP_842956.1| 284 IHAMMYRKIL 293
                                    689****997 PP

>> DUF2807  Putative auto-transporter adhesin, head GIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3   3.3e-05      0.15     105     180 ..     162     237 ..     154     238 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.3e-05
                                    EEEEEEEEECCEEEEEEEEEEEEEEEEECCEEEEEEEEEEEEEEEEEECCEEEEEEEEEEEEEEEECCEEEEEES- CS
                        DUF2807 105 aeelsveasgsgdielsGtadrlevsvaGsGeleardlkasevevevaGsgdaevnaseslkasisgsGdvrykGn 180
                                     e++ +++++ g ie+ G+a+     +  sG+le  ++  +++ v ++G+  +    +e+ +a+   sG++ +kG+
  gi|116753838|ref|YP_842956.1| 162 RETIGARNESPGRIEVFGNAGMSAGILMRSGDLEIHGCSGRNTGVLLSGGTVIVHGDTEDFTATEMRSGEIFVKGS 237
                                    56777899999****************************************99999*******************8 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   1.1     0.012        55     201     228 ..      83     111 ..      75     114 .. 0.86
   2 ?    6.8   0.1   0.00049       2.2     216     259 ..     170     214 ..     164     224 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.012
                           FapA 201 GsViikGnVeegmkVka.sgditikGvve 228
                                    G+Vi+ G+V + m ++   g i ++G ve
  gi|116753838|ref|YP_842956.1|  83 GKVIVDGDVGPRMGISMiRGAIYVSGRVE 111
                                    69************985379999999997 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.00049
                           FapA 216 kasgditikGvv.esatieA.ggnItikgGiigkgkskikAggnis 259
                                    ++ g+i++ G+   sa i   +g+++i+ G+ g++++++ +gg++ 
  gi|116753838|ref|YP_842956.1| 170 ESPGRIEVFGNAgMSAGILMrSGDLEIH-GCSGRNTGVLLSGGTVI 214
                                    6789********999999999*******.*********99999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.21s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 2335.70
//
Query:       gi|116753839|ref|YP_842957.1|  [L=363]
Description: glycosyl transferase, group 1 [Methanosaeta thermophila PT]
Scores for 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-33  113.1   0.0    1.5e-32  112.5   0.0    1.2  1  Glycos_transf_1  Glycosyl transferases group 1
    4.6e-28   98.3   0.1    7.3e-28   97.7   0.1    1.3  1  Glyco_trans_1_4  Glycosyl transferases group 1
    1.1e-24   87.3   0.1    2.7e-23   82.8   0.1    2.1  2  Glyco_transf_4   Glycosyltransferase Family 4
    4.1e-13   50.1   0.1    1.6e-12   48.1   0.0    1.9  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    5.9e-06   26.6   0.0    1.1e-05   25.8   0.0    1.4  1  Glyco_trans_1_2  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.5   0.0   4.2e-36   1.5e-32      12     163 ..     190     337 ..     182     345 .. 0.87

  Alignments for each domain:
  == domain 1  score: 112.5 bits;  conditional E-value: 4.2e-36
                                    TTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHH CS
                Glycos_transf_1  12 nekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleellk 91 
                                    ++ +  +++ grl  +K+++ l++a+all     ++v l+i+G+g+e  +l++la +l++ ++v+f g++++ed ++l+k
  gi|116753839|ref|YP_842957.1| 190 ADSEHDLVFAGRLISHKNLHMLLEAIALL-----SDVSLLIIGEGPEASRLHSLARSLGVDNRVRFSGFLKYEDTIALIK 264
                                    56777899*******************87.....79******************************************** PP

                                    CESEEEEEESSBSS-HHHHHHHHTT--EEEET..TTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSH.HHHH CS
                Glycos_transf_1  92 nadifvlpsisEgfGivllEAmaaglpviasn..aggpaevvkdgetGllvkpnnaealaeairkllede.elre 163
                                    ++ +fvlps++EgfG+++lEAma+g+pv+a+   +  ++++++++  G++ +   ++++a+ai+ +l+ + +  +
  gi|116753839|ref|YP_842957.1| 265 SSRAFVLPSTREGFGMAALEAMACGVPVVAVRhrMNAACDLLTPET-GVISELS-PASMADAIQAALDLSrKAGQ 337
                                    *******************************954556677777765.7777766.99999999999988754444 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.7   0.1     2e-31   7.3e-28       2     132 ..     194     329 ..     193     330 .. 0.89

  Alignments for each domain:
  == domain 1  score: 97.7 bits;  conditional E-value: 2e-31
                                    EEEEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---..HHHHHHHT..T-T.TEEEE---..THHHHHHHH-SEEE CS
                Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkkdvrlvivGdgprpeeleelaa..gleerveftGfv..edlaellaaadvfv 77 
                                    ++++f Grl  + k++++llea++ll   dv l+i+G+gp++++l++la+  g+++rv+f Gf+  ed  +l+++++ fv
  gi|116753839|ref|YP_842957.1| 194 HDLVFAGRLISH-KNLHMLLEAIALLS--DVSLLIIGEGPEASRLHSLARslGVDNRVRFSGFLkyEDTIALIKSSRAFV 270
                                    689******555.**************..89*********666999988779**99*********9************** PP

                                    E--..---SHHHHHHHHTT-EEEE-TG..GGTTT--.TTSSEE--TT-HHHHHHHHHHHH CS
                Glyco_trans_1_4  78 aPs..egfglkllEamaaglpvVatdv..ggiaevv.gengllvppgdpealaeailrLl 132
                                    +Ps  egfg+++lEama+g+pvVa +    ++++++  e+g++ +  +p+++a+ai++ l
  gi|116753839|ref|YP_842957.1| 271 LPStrEGFGMAALEAMACGVPVVAVRHrmNAACDLLtPETGVISE-LSPASMADAIQAAL 329
                                    ****99*******************87223567777879997775.68********9877 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.8   0.1   7.5e-27   2.7e-23       2     168 ..      16     181 ..      15     183 .. 0.92
   2 ?    2.6   0.0     0.034   1.2e+02      84     108 ..     278     301 ..     234     351 .. 0.79

  Alignments for each domain:
  == domain 1  score: 82.8 bits;  conditional E-value: 7.5e-27
                 Glyco_transf_4   2 GGverhvleLaraLarrGheVtvv.tpgddgpleeev.elvvrvprvplpllkrllrslaflrrlrrllkre...kpDvv 76 
                                    GG+er v+eL+++LarrGh+V+ + ++++dg+ e +  ++++ ++++p+pl+++++rs+  ++ ++  + r+   ++Dv+
  gi|116753839|ref|YP_842957.1|  16 GGAERRVYELSQRLARRGHDVHCYgARWWDGEREIKLgDVWHHGVCPPHPLYNKNKRSVKQALLFALGVLRNlegGFDVI 95 
                                    9***********************9999999999999*99999**********9999998877766544444488***** PP

                 Glyco_transf_4  77 HahspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeatadelrerygvpp 156
                                     ++ +++l +   +lr   g+ + +t H  +   ++  +l+   +l  a+e+ ++  +   iavSe t++el++ +g   
  gi|116753839|ref|YP_842957.1|  96 DCQEFPYLSCFSTRLRS-GGASFFITWHEIW-GDYWIEYLGVSGYLGMAVEKATATLTGNNIAVSEMTRRELLK-LGAG- 171
                                    *******9999999998.*************.89****************************************.**55. PP

                 Glyco_transf_4 157 ekitVipnGvDl 168
                                        V+pnG+D 
  gi|116753839|ref|YP_842957.1| 172 --SIVVPNGIDY 181
                                    ..58******95 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.034
                 Glyco_transf_4  84 lgaallalrrrlgiplVltvHglye 108
                                    +g a+l +++  g+p+V+  H + +
  gi|116753839|ref|YP_842957.1| 278 FGMAALEAMA-CGVPVVAVRHRMNA 301
                                    4445555554.8*********9875 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 !   48.1   0.0   4.6e-16   1.6e-12       1     160 []      16     178 ..      16     178 .. 0.77
   2 ?   -0.8   0.0      0.51   1.8e+03      87     105 ..     281     304 ..     267     352 .. 0.60

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 4.6e-16
                Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgapeleedgvrvhrl....pvprrpspladla.alralrrllrqrrerpd 75 
                                    gG++r+v+el+++La+rGh+V+++ +++  g++e+  + v+ h++    p++ + +  ++++ al  + ++lr  + ++d
  gi|116753839|ref|YP_842957.1|  16 GGAERRVYELSQRLARRGHDVHCYGARWWDGEREIKLGDVWHHGVcpphPLYNKNK--RSVKqALLFALGVLRNLEGGFD 93 
                                    8********************************99988999888633222333322..22221222233344667***** PP

                Glyco_trans_4_4  76 vvhahs.ptaglaarlarrrrgiplvvtlhglllr...rgsgavrrlyralerrllrradavlvvseaeaeelralgvpa 151
                                    v+ +++ p+++ +  ++r   g+ +++t+h+ +++   ++ g ++ l  a+e+++++     ++vse  ++el  lg+  
  gi|116753839|ref|YP_842957.1|  94 VIDCQEfPYLSCFSTRLR-SGGASFFITWHEIWGDywiEYLGVSGYLGMAVEKATATLTGNNIAVSEMTRRELLKLGAG- 171
                                    ******767888888888.99*********866552224467887777999*************************976. PP

                Glyco_trans_4_4 152 drvvvvpng 160
                                        vvpng
  gi|116753839|ref|YP_842957.1| 172 -S-IVVPNG 178
                                    .3.567887 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.51
                Glyco_trans_4_4  87 aarlarrrrgiplvvtlh......g 105
                                    aa+ a  + g+p+v   h      +
  gi|116753839|ref|YP_842957.1| 281 AALEAM-ACGVPVVAVRHrmnaacD 304
                                    333333.667777766664433321 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 !   25.8   0.0     3e-09   1.1e-05       3      63 ..     270     333 ..     265     355 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 3e-09
                Glyco_trans_1_2   3 LnpsrsespnlrlfEaaacGafaltdda..egleelftpgkevilfe.dleelaekirylla.np 63 
                                    + ps +e++ +  +Ea+acG+++++ +    +  +l+tp+ ++++ e +++++a++i+++l+ ++
  gi|116753839|ref|YP_842957.1| 270 VLPSTREGFGMAALEAMACGVPVVAVRHrmNAACDLLTPE-TGVISElSPASMADAIQAALDlSR 333
                                    568999*******************9889999*******9.8889999***********997333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); 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: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.36
# Mc/sec: 3017.61
//
Query:       gi|116753840|ref|YP_842958.1|  [L=374]
Description: glycosyl transferase family protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-28   98.7   0.0    4.2e-28   98.3   0.0    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
    3.6e-11   43.4   0.0    5.3e-11   42.9   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
     0.0019   17.8   0.0     0.0027   17.2   0.0    1.2  1  Glyco_tranf_2_2  Glycosyltransferase like family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.3   0.0   7.1e-32   4.2e-28       1     168 [.       5     165 ..       5     167 .. 0.96

  Alignments for each domain:
  == domain 1  score: 98.3 bits;  conditional E-value: 7.1e-32
                                    EEEEEESS-TTTHHHHHHHHHHH..GGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH- CS
                Glycos_transf_2   1 svviptyNeektlletlesllaq..dpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraa 78 
                                    s +ipt Ne++t+ e++++ +a     ++ +eiiv+D ++ Det+ i+e++     + rv+r e   G+++a+ +g++ a
  gi|116753840|ref|YP_842958.1|   5 SLIIPTLNEADTIGECIRRSRAVlqSVASVWEIIVIDSSD-DETPRIAESH-----GARVVRSE-ALGYGRAYLKGFEVA 77 
                                    78****************9888888899999999999888.**********.....9*******.66************* PP

                                    -SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTCSTCC CS
                Glycos_transf_2  79 tgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfeigsa 158
                                    +gdyi+++D D++++p++++kl++ l++ gad+++g+r r + +++ ++  +r +  ++  + + ++ + + +s+ +++ 
  gi|116753840|ref|YP_842958.1|  78 SGDYIVLMDGDLTYAPEDIPKLLKLLDD-GADLAMGSRLRGRIHPGAMPALHR-YIGNPALTWILNHLYSIRVSDAHCGL 155
                                    ****************************.********************9998.6999999999**************** PP

                                    CEEEEHHHHH CS
                Glycos_transf_2 159 allrrealee 168
                                    +++rr+al++
  gi|116753840|ref|YP_842958.1| 156 RAIRRDALKK 165
                                    ********87 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 !   42.9   0.0   8.8e-15   5.3e-11       4     177 ..       4     201 ..       2     241 .. 0.63

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 8.8e-15
                Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqey..prvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralne 81 
                                    +++++pt+ne+d++ge+++   a      +v  ++v d sd+et + ae     +   + rvv +++ lg   + ra+  
  gi|116753840|ref|YP_842958.1|   4 VSLIIPTLNEADTIGECIRRSRAVLQsvASVWEIIVIDSSDDETPRIAES----H---GARVV-RSEALG---YGRAYLK 72 
                                    89****************99887643235555555558899999998864....4...45766.556567...67788** PP

                Glyco_tranf_2_3  82 alravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfl.l.nrstl...............vsalgalefaer 144
                                    +++ +++d+++l+D+D    P+ +++ll ++ +++++ + ++++  + ++ ++               ++ l+ +++ + 
  gi|116753840|ref|YP_842958.1|  73 GFEVASGDYIVLMDGDLTYAPEDIPKLLKLL-DDGADLAMGSRLRgRiHPGAMpalhryignpaltwiLNHLYSIRVSDA 151
                                    ******************************9.999999888875524344444455555555555555555555555555 PP

                Glyco_tranf_2_3 145 hlrflaar.ralgvltlnGsgslirrevlkele................g 177
                                    h   +a r +al+ + l+++g+ +  e+l e                  +
  gi|116753840|ref|YP_842958.1| 152 HCGLRAIRrDALKKMRLRTAGMEFASEMLVEASrrglriaespidyyprR 201
                                    55333322144444555555555555555444455555555555555541 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   4.5e-07    0.0027       1     106 [.       5     103 ..       5     109 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.5e-07
                Glyco_tranf_2_2   1 svviplraseerhyieervlqkakyy...deeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGa 77 
                                    s++ip  ++ ++  i e +++ +          e+iv+d  Ss++   e   i + ++   ++ e   a + ++a  +G+
  gi|116753840|ref|YP_842958.1|   5 SLIIPTLNEADT--IGECIRRSRAVLqsvASVWEIIVID--SSDD---ETPRIAESHGARVVRSE---ALGYGRAYLKGF 74 
                                    689999999888..9999988877764445677888887..6666...45566666555554555...8999******** PP

                Glyco_tranf_2_2  78 skaesdlvlFlDaDcfissDkfekilkli 106
                                    + a +d+++ +D+D  ++++ + k+lkl+
  gi|116753840|ref|YP_842958.1|  75 EVASGDYIVLMDGDLTYAPEDIPKLLKLL 103
                                    **************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); 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:                         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 0.23s 00:00:00.69 Elapsed: 00:00:00.36
# Mc/sec: 3079.24
//
Query:       gi|116753841|ref|YP_842959.1|  [L=361]
Description: periplasmic binding protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-27   95.8   0.0    5.7e-27   94.8   0.0    1.4  1  Peripla_BP_2  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.8   0.0   3.2e-31   5.7e-27       1     234 [.      46     306 ..      46     309 .. 0.95

  Alignments for each domain:
  == domain 1  score: 94.8 bits;  conditional E-value: 3.2e-31
                                    EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT..TS-BSBESSSB-HHHHHHH-.......-SEEEE-GGG.... CS
                   Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadkleeaivevgadgeidvEklaalk.......PDlvilskgl.... 69 
                                    i++l+++ +e ++ lG +d++vgv+ t+++ + +  +++    vg+ +e+d+E++a+         P +++  ++     
  gi|116753841|ref|YP_842959.1|  46 IVVLNSDAAEAVAILGCADEIVGVSDTVKNKEYYFPQLKGAQLVGTWKEPDYEMIAEIAkvgdevvPNILVITYTSpgkl 125
                                    9************************9999999886555599***************8655555555***9999999999* PP

                                    ....GGGHHHHHHHS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT.-EEEEEEEETTE CS
                   Peripla_BP_2  70 .gltdedeellksgiptvivessntgeslkeqiralgellgledeaeklvaeidsklaaaksaidsekpkpvlvfggade 148
                                     g+ +++ +l+  gi++v  + ++  e    +i +lg++l++e+ea  +v++++s  +++++a++ e  ++v v +++ +
  gi|116753841|ref|YP_842959.1| 126 yGVEEAAAKLEPFGIKVVGLDLNKP-ETMISEILTLGKILDREEEASRYVEWYKSVQEEVEDAVKDESVPKVYVESTSKG 204
                                    *************************.*****************************************9999999999999 PP

                                    ..EEEE-TTSTTTHHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEH.................HHHT-S--H CS
                   Peripla_BP_2 149 ggyvvagsnsyigdlldalgieniaaeskkseyeeisaEqilasdpdvifvsgr.................aeadnktgl 211
                                    g+y+  g +s++ +l++++++ niaa+   ++y  +++E++ + +pd+i+   +                 ++ +   +l
  gi|116753841|ref|YP_842959.1| 205 GSYTTHGPGSGVDQLVSIARGHNIAADL-REAYPVVDWEWVISKNPDIIIKKVSytdrtpypfgweippsqDSVKLENIL 283
                                    ****************************.*********************999999**************99999999** PP

                                    HHHT-SHHHHTSHHHHTT-EEEE CS
                   Peripla_BP_2 212 eflkenpllaelpAvkngrVyal 234
                                     +++++p+ +++ A+kn rVy +
  gi|116753841|ref|YP_842959.1| 284 NEIISRPGSESISAIKNSRVYLM 306
                                    *********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 2696.08
//
Query:       gi|116753842|ref|YP_842960.1|  [L=307]
Description: ABC transporter related [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-33  115.5   0.0    3.9e-33  114.9   0.0    1.3  1  ABC_tran  ABC transporter
    8.4e-17   61.9   0.0    9.3e-09   35.5   0.0    2.5  3  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    0.00075   20.1   0.3     0.0013   19.2   0.3    1.5  1  AAA_23    AAA domain
     0.0032   17.2   0.0        1.4    8.6   0.0    2.1  2  AAA_15    AAA ATPase domain
      0.004   16.6   0.0      0.013   14.9   0.0    1.7  1  SMC_N     RecF/RecN/SMC N terminal domain
     0.0061   16.2   0.0      0.014   15.1   0.0    1.5  1  SRP54     SRP54-type protein, GTPase domain
  ------ inclusion threshold ------
      0.014   15.1   0.1      0.045   13.5   0.1    1.8  1  AAA_30    AAA domain
       0.03   14.8   0.0      0.052   14.1   0.0    1.5  1  AAA_18    AAA domain
      0.089   13.0   0.0       0.17   12.2   0.0    1.5  1  SbcCD_C   Putative exonuclease SbcCD, C subunit
        0.1   12.3   0.1       0.17   11.6   0.1    1.3  1  AAA_29    P-loop containing region of AAA domain
       0.16   12.3   0.6        1.6    9.0   0.6    2.4  1  AAA_22    AAA domain
       0.19   11.7   0.0       0.41   10.5   0.0    1.5  2  Rad17     Rad17 P-loop domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.9   0.0   2.6e-36   3.9e-33       2     136 ..      42     184 ..      41     185 .. 0.96

  Alignments for each domain:
  == domain 1  score: 114.9 bits;  conditional E-value: 2.6e-36
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                    ++++l++ +ge+ +++G+nGaGK+t +++++ l+kp +G++l++g d+ +   +++++e+gv++q+ +l+++lt++en  
  gi|116753842|ref|YP_842960.1|  42 DDLNLHVARGELFGFLGPNGAGKTTTIRIITTLTKPSSGRVLINGIDVVR-HPSRVKAEFGVVQQHMSLNRDLTIEENle 120
                                    899**********************************************9.78899************************ PP

                                    ...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                               e++e+i+++l+ +gl+e +d  +      +SgG+k+r ++arall +p+ll+lDEpt
  gi|116753842|ref|YP_842960.1| 121 lharlhhiprsERRERISELLEYVGLEEHADYLI----DDVSGGMKRRAMIARALLHRPRLLILDEPT 184
                                    ********99888889************888888....*****************************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 !   23.7   0.0   2.5e-08   3.7e-05       2      97 ..      54     135 ..      53     148 .. 0.89
   2 !   35.5   0.0   6.2e-12   9.3e-09     234     297 ..     154     214 ..     149     218 .. 0.91
   3 ?   -2.5   0.0       2.3   3.4e+03      58      82 ..     250     273 ..     241     291 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2.5e-08
                         AAA_21   2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrlers 81 
                                     ++ GpNg+GK++ ++++  l              ++ ++ r+ ++ +d     ++++ e+  +++q++  +  l++e++
  gi|116753842|ref|YP_842960.1|  54 FGFLGPNGAGKTTTIRIITTL--------------TKPSSGRVLINGIDVVRHPSRVKAEFG-VVQQHMSLNRDLTIEEN 118
                                    5789**************766..............889************************.***************** PP

                         AAA_21  82 qv.eeklssvetllesg 97 
                                        ++l + ++ +++ 
  gi|116753842|ref|YP_842960.1| 119 LElHARLHHIPRSERRE 135
                                    **977777777776654 PP

  == domain 2  score: 35.5 bits;  conditional E-value: 6.2e-12
                         AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                    ++++S G+kr  a+++  l  ++  +ll++DEp  gL+ +  rr+++l+++ ++ ga v+ltTH
  gi|116753842|ref|YP_842960.1| 154 IDDVSGGMKRR-AMIARALLHRP--RLLILDEPTVGLDVQTRRRVWDLIRRVNSDGATVFLTTH 214
                                    6899*******.88888887666..************************999889********* PP

  == domain 3  score: -2.5 bits;  conditional E-value: 2.3
                         AAA_21  58 fefeieeflsqgvryryglrlersq 82 
                                    ++ e+   +s+g+ryry+ + +  +
  gi|116753842|ref|YP_842960.1| 250 VTVEVQ-NNSNGTRYRYFPDRDAAA 273
                                    556666.788999999987766655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.3   8.9e-07    0.0013      20      43 ..      52      75 ..      38     155 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 8.9e-07
                         AAA_23 20 gltlItGpNGaGKTTildAiklaL 43
                                    l+ + GpNGaGKTT ++ i+  +
  gi|116753842|ref|YP_842960.1| 52 ELFGFLGPNGAGKTTTIRIITTLT 75
                                   6999**************999754 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0   0.00093       1.4      28      50 ..      56      78 ..      43     121 .. 0.79
   2 !    6.9   0.0    0.0031       4.6     288     364 ..     148     214 ..     104     215 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00093
                         AAA_15 28 liGkNnsGKSsilealdlFlnnk 50
                                   + G+N++GK++ ++++  + + +
  gi|116753842|ref|YP_842960.1| 56 FLGPNGAGKTTTIRIITTLTKPS 78
                                   88**************9998877 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0031
                         AAA_15 288 ddeelplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                    +  +  +++++ G++r   ++  +l+  +          l+++EP + L  q  + +++l++++ +d+   v++tTH
  gi|116753842|ref|YP_842960.1| 148 EHADYLIDDVSGGMKRRAMIARALLHRPRL---------LILDEPTVGLDVQTRRRVWDLIRRVNSDGA-TVFLTTH 214
                                    666667888888888888887777666555.........************************999997.9****** 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 !   14.9   0.0   8.8e-06     0.013      30     212 ..      57     229 ..      45     235 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 8.8e-06
                                    EESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEETTSEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  30 vGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrvkrkges 109
                                    +GpNG+GK+  +  i  +L + s+  +  + + d++ +  ++ +++++ v+ +++ + + + +  e++++  r+ +  +s
  gi|116753842|ref|YP_842960.1|  57 LGPNGAGKTTTIRII-TTLTKPSSGRVLINGI-DVVRH-PSRVKAEFGVVQQHMSLNRDLTIE--ENLELHARLHHIPRS 131
                                    799******999998.6777655544444443.55555.567777777777776554444222..233333333333332 PP

                                    EEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 110 eykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn 189
                                    e    ++  +  e+  l e+a+  ++  SgG k  +++a        ++  l +lDe    LD + +++v +l+++ +++
  gi|116753842|ref|YP_842960.1| 132 ER--RERISELLEYVGLEEHADYLIDDVSGGMKRRAMIARA----LLHRPRLLILDEPTVGLDVQTRRRVWDLIRRVNSD 205
                                    22..23333445555555566666669****9976666533....23555699**********************76555 PP

                                    .SEEEEE-SSHHHCCC-SCEEEEE CS
                                    .xxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 190 .aQfivislreemlekadklvgvt 212
                                     a ++ +++  e  e   + vg++
  gi|116753842|ref|YP_842960.1| 206 gATVFLTTHYIEEAEALCNRVGIM 229
                                    499999999877777766666665 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   9.1e-06     0.014       6      42 ..      56      92 ..      52      97 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 9.1e-06
                                   EEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSST CS
                          SRP54  6 lvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRa 42
                                   ++G++GaGKTtt+  +  l k +  +vl+   D+ R 
  gi|116753842|ref|YP_842960.1| 56 FLGPNGAGKTTTIRIITTLTKPSSGRVLINGIDVVRH 92
                                   79********************************995 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1     3e-05     0.045      20      99 ..      53     185 ..      45     214 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3e-05
                         AAA_30  20 vavltGpAGtGKttalkalreaweaaggrviglApt.gkaAkvLaeelgi........eastiakllkrlk......... 81 
                                    +    Gp G+GKtt+++ ++ + + + grv++      +   ++++e+g+        +  ti++ l+ ++         
  gi|116753842|ref|YP_842960.1|  53 LFGFLGPNGAGKTTTIRIITTLTKPSSGRVLINGIDvVRHPSRVKAEFGVvqqhmslnRDLTIEENLELHArlhhiprse 132
                                    55678*****************9999655554332202223333333333221111122222222222222444444555 PP

                         AAA_30  82 ...................................grarlepgtllivDEagm 99 
                                                                       +ra l++ +lli DE  +
  gi|116753842|ref|YP_842960.1| 133 rreriselleyvgleehadyliddvsggmkrramiARALLHRPRLLILDEPTV 185
                                    56666666666666667777777777777766666555666667777777554 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   3.5e-05     0.052       4      92 ..      57     167 ..      55     217 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.5e-05
                         AAA_18   4 tGtpGvGKttlakeLskrl.gf......................gvnlrdvakenglllevdpe.aldeskrldedkldk 59 
                                     G+ G+GKtt  + +  ++  +                      gv+ +++  +++l +e++ e   + +++ + +++++
  gi|116753842|ref|YP_842960.1|  57 LGPNGAGKTTTIRIITTLTkPSsgrvlingidvvrhpsrvkaefGVVQQHMSLNRDLTIEENLElHARLHHIPRSERRER 136
                                    69*************66653335666777788899999999999*****************9997778888888888888 PP

                         AAA_18  60 lldaleenssaleegknlvidghlaeleseaak 92 
                                    ++++le     lee+ +++id++ + +   a++
  gi|116753842|ref|YP_842960.1| 137 ISELLEYVG--LEEHADYLIDDVSGGMKRRAMI 167
                                    888888875..7999999****99988877766 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00011      0.17      62      89 ..     173     200 ..     158     201 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                        SbcCD_C  62 palrlvfLDEAFsklDeesiatllelle 89 
                                    +++rl++LDE   +lD ++++++ +l++
  gi|116753842|ref|YP_842960.1| 173 HRPRLLILDEPTVGLDVQTRRRVWDLIR 200
                                    789*********************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 ?   11.6   0.1   0.00012      0.17      18      50 ..      47      79 ..      40      87 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
                         AAA_29 18 eidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                   ++ + + + + Gp+G+GK+T +  i++l  p++
  gi|116753842|ref|YP_842960.1| 47 HVARGELFGFLGPNGAGKTTTIRIITTLTKPSS 79
                                   55544477799**********988888887776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.6    0.0011       1.6      12     102 ..      58     185 ..      51     246 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0011
                         AAA_22  12 GesGtGKTtllrrlleqldeeakaee...........erpevvfvtlpsstsskdllrellralglelka.......... 70 
                                    G+ G+GKTt++r ++   +  ++              ++p+ v+ +  +     +l r+l  + +lel+a          
  gi|116753842|ref|YP_842960.1|  58 GPNGAGKTTTIRIITTLTK--PS--SgrvlingidvvRHPSRVKAEFGVVQQHMSLNRDLTIEENLELHArlhhiprser 133
                                    99**********9998863..22..1346787888886666666666666666666666666666666666666666666 PP

                         AAA_22  71 ............erlsseellealeqalrarav........ielliiDEaqh 102
                                                 +   + l++ +   +++ra+        ++lli+DE   
  gi|116753842|ref|YP_842960.1| 134 reriselleyvgLEEHADYLIDDVSGGMKRRAMiarallhrPRLLILDEPTV 185
                                    6666666655552222233333333333333334444444444777777555 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00027      0.41      47      93 ..      53     101 ..      40     128 .. 0.71
   2 ?   -3.3   0.0       4.8   7.2e+03      69      84 ..     250     265 ..     243     275 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00027
                          Rad17  47 iLLisGPsGCgkstvvkvLskelgikl.rewlnpvsl.kepdnqksdfk 93 
                                    +    GP G gk+t++++++    ++  r  +n++ + ++p+  k +f 
  gi|116753842|ref|YP_842960.1|  53 LFGFLGPNGAGKTTTIRIITTLTKPSSgRVLINGIDVvRHPSRVKAEFG 101
                                    55567*************9988776652667899875266666666664 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.8
                          Rad17  69 lgiklrewlnpvslke 84 
                                     ++++++++n++ ++ 
  gi|116753842|ref|YP_842960.1| 250 VTVEVQNNSNGTRYRY 265
                                    5678899999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); 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 0.27s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2159.61
//
Query:       gi|116753843|ref|YP_842961.1|  [L=251]
Description: ABC-2 type transporter [Methanosaeta thermophila PT]
Scores for complete 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-24   84.8  19.7    5.4e-24   84.8  19.7    1.9  2  ABC2_membrane    ABC-2 type transporter
    3.2e-10   39.7  24.8    3.2e-10   39.7  24.8    1.7  2  ABC2_membrane_3  ABC-2 family transporter protein
  ------ inclusion threshold ------
        5.6    5.1  17.1        7.8    4.7  17.1    1.2  1  DUF2070          Predicted membrane protein (DUF2070)


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 !   84.8  19.7   9.1e-28   5.4e-24       3     208 ..      10     217 ..       8     219 .. 0.90
   2 ?   -0.2   1.1     0.091   5.4e+02     105     123 ..     223     241 ..     212     246 .. 0.59

  Alignments for each domain:
  == domain 1  score: 84.8 bits;  conditional E-value: 9.1e-28
                  ABC2_membrane   3 ikallkreflqrwrdpslgllwrliqplllalvfgtvfgn.lg.nsedglnr..pgllffsvlflafsaltsvapvfere 78 
                                    i+ +l+ ++ + +r+++ +l++ l++pll+++ fg   g+ ++ n  ++l++  pg+++ ++++ +f+++    +v    
  gi|116753843|ref|YP_842961.1|  10 ICSILWSDLVTLKRRWARYLITTLMSPLLYLMAFGWGLGRgINmNGMSYLEFviPGIIALTAMNASFNGAGIRLNVDRLY 89 
                                    7899***********************************754344444444489************88888887777778 PP

                  ABC2_membrane  79 rgvlerelvsplyslsayvlakvlvelpvsllqalifllivyflv.gldlsrfflflllllltalaasslgllisalaps 157
                                     +++++ l +p+ s  + ++++ ++ ++++l+ + +f+++++ +  +++++    fll+ll+t +++ s+g+l + la+s
  gi|116753843|ref|YP_842961.1|  90 FRSFDESLMAPV-SDVSLLIGRSMIGMVRGLISSSVFVMLALAIApSMHIE--PVFLLILLITCMTFASMGVLAALLARS 166
                                    99**********.**************************998874466665..6789*********************** PP

                  ABC2_membrane 158 fedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrsn 208
                                    +ed+++++sl+l+p+++l+G f++++++p+wl+ + y++Plt+    lr++
  gi|116753843|ref|YP_842961.1| 167 HEDMATFSSLILMPMTFLGGTFFSLSQVPEWLRLVLYILPLTHSSACLRAA 217
                                    ****************************99*************99888875 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.091
                  ABC2_membrane 105 lpvsllqalifllivyflv 123
                                    +p+s ++a+i+++ v++++
  gi|116753843|ref|YP_842961.1| 223 VPWSSFIAIIMFMSVFLVT 241
                                    4555555555555444443 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 ?   -1.3   0.8      0.15   8.9e+02       3      20 ..      28      45 ..      25      86 .. 0.62
   2 !   39.7  24.8   5.3e-14   3.2e-10     196     337 ..      97     240 ..      50     246 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.15
                ABC2_membrane_3  3 fliitlllPiilvlllgl 20
                                   +li+tl++P++++  +g+
  gi|116753843|ref|YP_842961.1| 28 YLITTLMSPLLYLMAFGW 45
                                   455666666655554444 PP

  == domain 2  score: 39.7 bits;  conditional E-value: 5.3e-14
                ABC2_membrane_3 196 lvsgvsplqywlskilgdflvyllqlllilllafglgipfg.nlglll.llfllfglayialgyllsslfknsetaqili 273
                                    l+++vs  ++++++  + ++ +l+++ +++ la++  i  + ++  ++ l +l+ +++++++g l   l +++e++ ++ 
  gi|116753843|ref|YP_842961.1|  97 LMAPVSDVSLLIGRSMIGMVRGLISSSVFVMLALA--IAPSmHIEPVFlLILLITCMTFASMGVLAALLARSHEDMATFS 174
                                    589*****************************999..888889988875777778************************* PP

                ABC2_membrane_3 274 fivilllsgffgglfp.ledlpsalkwifsiiPffapglgllrlitgd.plwe.illsliilalfav 337
                                    +++++ ++ f+gg+f+ l+++p++l+ +++i+P+++ +  l   + g+  +w+ ++  ++++ +f v
  gi|116753843|ref|YP_842961.1| 175 SLILM-PMTFLGGTFFsLSQVPEWLRLVLYILPLTHSSACLRAAALGQpVPWSsFIAIIMFMSVFLV 240
                                    *****.77777777655****************************9998555515566666666554 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7  17.1    0.0013       7.8       7     149 ..      17     223 ..      12     249 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0013
                        DUF2070   7 yifrlPswkvsllliillalligllaflssk.......lfgillfglpalvaflltlpvlrilggrltykrs.......l 72 
                                     +++l + +   l++ l++ l+ l+af  +         +++l f +p ++a+ + +   + +g+rl++ r         
  gi|116753843|ref|YP_842961.1|  17 DLVTLKRRWARYLITTLMSPLLYLMAFGWGLgrginmnGMSYLEFVIPGIIALTAMNASFNGAGIRLNVDRLyfrsfdeS 96 
                                    677888877999999999999999998888899999998899************************99888844433344 PP

                        DUF2070  73 flalltelivviisllaillsall....qalvllalvls................lalvfalrllvlvavsdesllkavl 132
                                    ++a ++ + ++i   +  +    +    +++v+ +l+l+                ++ +++ ++ vl a+  +s+  ++ 
  gi|116753843|ref|YP_842961.1|  97 LMAPVSDVSLLIGRSMIGM----VrgliSSSVFVMLALAiapsmhiepvfllillITCMTFASMGVLAALLARSHEDMAT 172
                                    4444555555544444444....255555555555555566***********9999999999999***999999999999 PP

                        DUF2070 133 paliqpllailllvly..................................f 149
                                     ++++++ + +l   +                                  +
  gi|116753843|ref|YP_842961.1| 173 FSSLILMPMTFLGGTFfslsqvpewlrlvlyilplthssaclraaalgqpV 223
                                    999998888888888856666655555555555555555555555544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       808  (0.0450667); 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:                         3  (0.000167327); expected 0.2 (1e-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: 1834.60
//
Query:       gi|116753844|ref|YP_842962.1|  [L=719]
Description: AAA family ATPase, CDC48 subfamily protein [Methanosaeta thermophila PT]
Scores for complete 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-98  325.0   0.0    4.4e-48  163.1   0.0    2.3  2  AAA              ATPase family associated with various cellul
    7.1e-33  112.2   3.5    2.4e-16   59.2   0.4    2.8  2  AAA_lid_3        AAA+ lid domain
    1.8e-28   98.5   0.3    8.7e-28   96.3   0.3    2.2  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
    1.1e-15   58.4   0.9    1.1e-06   29.1   0.0    3.5  2  AAA_16           AAA ATPase domain
    1.7e-15   57.1   0.0    9.3e-08   32.0   0.0    2.9  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    2.1e-15   57.2   0.0    3.8e-07   30.4   0.0    2.4  2  AAA_2            AAA domain (Cdc48 subfamily)
    6.9e-13   48.8   0.2    1.3e-05   25.2   0.1    3.7  2  AAA_5            AAA domain (dynein-related subfamily)
    2.4e-12   47.2   0.0    8.8e-07   29.2   0.0    2.8  2  AAA_33           AAA domain
    3.5e-12   45.9   0.0      1e-11   44.4   0.0    1.9  1  CDC48_2          Cell division protein 48 (CDC48), domain 2
      1e-11   45.3   1.1     0.0014   18.9   0.0    3.9  4  AAA_22           AAA domain
    5.6e-11   42.2   0.1    0.00044   19.6   0.0    2.8  3  TIP49            TIP49 P-loop domain
    1.7e-08   34.6   0.0     0.0043   17.1   0.0    2.3  2  AAA_14           AAA domain
    3.1e-08   33.6   0.0     0.0079   15.9   0.0    2.4  2  IstB_IS21        IstB-like ATP binding protein
    3.9e-08   33.7   0.1     0.0033   17.7   0.0    2.7  2  AAA_28           AAA domain
    5.6e-08   33.4   0.0       0.01   16.4   0.0    2.9  2  AAA_18           AAA domain
    6.4e-08   33.0   0.0      0.012   16.0   0.0    2.6  2  RNA_helicase     RNA helicase
    2.3e-07   30.4   0.1       0.02   14.3   0.0    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    5.2e-07   29.7   0.0      0.047   13.7   0.0    2.5  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    2.1e-06   27.6   0.0       0.04   13.8   0.0    2.7  2  AAA_3            ATPase family associated with various cellul
    2.8e-06   27.1   0.1       0.14   11.9   0.0    3.3  2  Sigma54_activat  Sigma-54 interaction domain
    3.8e-06   26.5   0.3       0.25   10.8   0.0    3.5  3  PhoH             PhoH-like protein
      6e-06   25.7   0.0      0.053   12.8   0.0    2.4  2  Zeta_toxin       Zeta toxin
    9.2e-06   25.7   0.0       0.33   10.7   0.0    3.3  2  Bac_DnaA         Bacterial dnaA  protein
      1e-05   25.4   0.0      0.061   13.0   0.0    2.5  2  AAA_24           AAA domain
    1.1e-05   25.0   0.4       0.78    9.0   0.0    3.5  3  ATPase           KaiC
    1.1e-05   25.4   0.3       0.16   11.9   0.0    3.4  3  NACHT            NACHT domain
    1.1e-05   25.4   0.2       0.04   13.7   0.0    2.7  2  AAA_11           AAA domain
    1.3e-05   24.9   7.1       0.49    9.9   0.7    4.3  3  AAA_25           AAA domain
    1.3e-05   24.7   0.0       0.17   11.4   0.0    2.5  2  AAA_7            P-loop containing dynein motor region
    3.3e-05   23.8   0.4       0.24   11.5   0.1    2.7  2  Vps4_C           Vps4 C terminal oligomerisation domain
    3.5e-05   24.3   0.0       0.35   11.4   0.0    2.6  2  ABC_tran         ABC transporter
      9e-05   22.3   0.2       0.55    9.9   0.0    2.7  2  AAA_30           AAA domain
    0.00014   21.1   0.0       0.11   11.7   0.0    2.6  2  DUF815           Protein of unknown function (DUF815)
    0.00016   21.1   0.0        0.4    9.9   0.0    2.2  2  DUF2075          Uncharacterized conserved protein (DUF2075)
    0.00028   20.1   0.0       0.36    9.9   0.0    2.2  2  Parvo_NS1        Parvovirus non-structural protein NS1
    0.00042   19.8   0.0          2    7.8   0.0    3.4  3  TniB             Bacterial TniB protein
    0.00053   19.2   0.0          1    8.5   0.0    2.4  2  NB-ARC           NB-ARC domain
    0.00065   20.1   0.8        1.2    9.4   0.0    3.1  3  AAA_19           AAA domain
    0.00069   19.7   0.0       0.54   10.4   0.0    2.7  2  Sigma54_activ_2  Sigma-54 interaction domain
     0.0011   19.5   0.0          2    8.8   0.0    2.9  2  AAA_17           AAA domain
     0.0017   18.4   0.0        1.3    8.8   0.0    2.8  3  ATPase_2         ATPase domain predominantly from Archaea
     0.0024   16.8   0.0        1.7    7.4   0.0    2.4  2  AFG1_ATPase      AFG1-like ATPase
     0.0026   17.6   0.0        1.5    8.5   0.0    2.2  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
     0.0048   16.6   0.1        3.5    7.3   0.0    2.6  2  Cytidylate_kin   Cytidylate kinase
     0.0095   15.9   0.6          4    7.3   0.0    3.4  3  NTPase_1         NTPase
  ------ inclusion threshold ------
       0.01   14.9   0.0        1.8    7.6   0.0    2.3  2  T2SSE            Type II/IV secretion system protein
      0.011   15.8   0.0        4.6    7.2   0.0    2.7  2  ResIII           Type III restriction enzyme, res subunit
      0.018   14.9   0.0        5.6    6.8   0.0    2.6  2  CPT              Chloramphenicol phosphotransferase-like prot
      0.035   14.0   0.0         17    5.3   0.0    2.9  2  Rad17            Rad17 P-loop domain
       0.05   13.2   0.0        5.6    6.6   0.0    3.3  2  Zot              Zonular occludens toxin (Zot)
      0.069   12.6   0.0        6.7    6.1   0.0    2.3  2  SRPRB            Signal recognition particle receptor beta su
      0.072   12.3   0.0        3.9    6.6   0.0    2.5  2  KAP_NTPase       KAP family P-loop domain
      0.073   12.8   0.0         12    5.7   0.0    2.5  2  AAA_29           P-loop containing region of AAA domain
      0.085   13.0   0.0        6.4    6.9   0.0    2.4  2  Torsin           Torsin
       0.11   11.7   0.0        3.6    6.7   0.0    2.2  2  DAP3             Mitochondrial ribosomal death-associated pro
       0.12   12.1   0.1         47    3.6   0.0    3.5  3  Guanylate_kin    Guanylate kinase
       0.14   11.9   0.0       0.35   10.7   0.0    1.6  1  cIII             cIII protein family
       0.17   11.6   0.0         27    4.5   0.0    2.6  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
       0.19   10.8   0.0        9.3    5.3   0.0    2.2  2  PIF1             PIF1-like helicase


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.1   0.0   1.4e-50   4.4e-48       1     131 [.     215     344 ..     215     345 .. 0.98
   2 !  159.8   0.0   1.4e-49   4.4e-47       1     131 [.     488     619 ..     488     620 .. 0.96

  Alignments for each domain:
  == domain 1  score: 163.1 bits;  conditional E-value: 1.4e-50
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCH CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgsese 80 
                                    vll+GppGtGKTlla+a+a+e++++f ++sg+e++sky gese+++r+lfk+a+e+a psi++iDEid++a++r++ + e
  gi|116753844|ref|YP_842962.1| 215 VLLHGPPGTGKTLLARALASETNAHFETLSGPEIMSKYYGESEERLRQLFKTAEENA-PSIILIDEIDSIAPKREEVTGE 293
                                    79******************************************************9.********************** PP

                                    HHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                            AAA  81 eeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                    +e+rvv+qLl+ +dg++++ +kv++igatnrpd ldpal+r gRfdr+iei+
  gi|116753844|ref|YP_842962.1| 294 VERRVVAQLLALMDGLESR-GKVVIIGATNRPDALDPALRRpGRFDREIEIG 344
                                    ******************6.77***************************996 PP

  == domain 2  score: 159.8 bits;  conditional E-value: 1.4e-49
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH..TTCC CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr..sgse 78 
                                    +llyGppGtGKTllakava+e++++f++++g+e+lsk+vgese+ +re+f++ak+ a p ++f+DEida+a+ r    ++
  gi|116753844|ref|YP_842962.1| 488 ILLYGPPGTGKTLLAKAVATESQANFISVKGPEFLSKWVGESERAVRETFRKAKQAA-PAVVFFDEIDAIAPMRssGAAD 566
                                    69******************************************************9.****************855559 PP

                                    CHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                            AAA  79 seeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                    s ++erv++q+l+e+dg++   ++vivi+atnrpd +dpallr gRfdr iei+
  gi|116753844|ref|YP_842962.1| 567 SHVTERVISQILSEMDGLEPL-HNVIVIAATNRPDIIDPALLRpGRFDRMIEIG 619
                                    99******************7.66***************************986 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   0.2   7.2e-17   2.2e-14       1      44 [.     367     427 ..     367     428 .. 0.78
   2 !   59.2   0.4   7.9e-19   2.4e-16       1      45 []     642     699 ..     642     699 .. 0.80

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 7.2e-17
                      AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrr.................gikeitmedfe 44 
                                    dvdl +LA  T+G++GADlaal reA+++Alrr                 +  e+tm+df+
  gi|116753844|ref|YP_842962.1| 367 DVDLGKLADITHGFVGADLAALAREAGMRALRRvlpeldlevesipaeilNKIEVTMADFM 427
                                    9********************************6665555555555554333357777776 PP

  == domain 2  score: 59.2 bits;  conditional E-value: 7.9e-19
                      AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrr...........gik..eitmedfee 45 
                                    dvdl+e+A+rTe+ySGADlaa+c eA++lA+r+            ik   ++ ++fee
  gi|116753844|ref|YP_842962.1| 642 DVDLAEIAKRTENYSGADLAAVCSEAVMLAIREyvlagkpqdeeAIKnlRVERRHFEE 699
                                    9********************************6666666655523332477777775 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.3   0.3   2.9e-30   8.7e-28       2      84 ..       7      89 ..       6      91 .. 0.97

  Alignments for each domain:
  == domain 1  score: 96.3 bits;  conditional E-value: 2.9e-30
                                   EEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEEEEEE CS
                        CDC48_N  2 LrVaeapqedvgrgivridpedmeelglepgdvveiegkrkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVtVrka 83
                                   L+V ea+ +dvgrgi+r+dp++++e g++ gdv+ i+gk++T+a+ wp++ped+g+giIrmdg +R+nagv+i+++V Vr +
  gi|116753844|ref|YP_842962.1|  7 LKVGEARASDVGRGIARVDPAVIKERGWQAGDVISIRGKKQTAALLWPGYPEDTGTGIIRMDGTLRRNAGVTIDERVPVRIV 88
                                   99*****99**********************************************************************988 PP

                                   - CS
                        CDC48_N 84 e 84
                                   +
  gi|116753844|ref|YP_842962.1| 89 Q 89
                                   6 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   3.7e-09   1.1e-06      16     140 ..     204     318 ..     199     319 .. 0.67
   2 !   24.9   0.0   7.2e-08   2.2e-05      16     125 ..     477     579 ..     475     594 .. 0.61

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 3.7e-09
                         AAA_16  16 lervrsgrpelvllsGesGvGKsslvrellralekdggif..lrgkcdqlesaipysa.laqalareellrqlldeaesa 92 
                                    +er+    p  vll+G++G+GK+ l+r+l+    +++++f  l+g    +     y+    + l r +l++  +++   a
  gi|116753844|ref|YP_842962.1| 204 FERLGVEAPKGVLLHGPPGTGKTLLARALAS---ETNAHFetLSGPEIMS----KYYGeSEERL-R-QLFKTAEEN---A 271
                                    66666667899*******************6...3335563233333333....3322255555.4.555555544...4 PP

                         AAA_16  93 eleawrekleealaavpelagaeasrllellkrllallsrderplvlv 140
                                          +++++ +    e++g+ ++r+ ++l +l++ l+++++ +v++
  gi|116753844|ref|YP_842962.1| 272 PSIILIDEIDSIAPKREEVTGEVERRVVAQLLALMDGLESRGK-VVII 318
                                    444455556666667778888888***********99999888.8875 PP

  == domain 2  score: 24.9 bits;  conditional E-value: 7.2e-08
                         AAA_16  16 lervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaele 95 
                                    +e  +++ p  +ll+G++G+GK+ l+++++++ +++   f++ k  ++     +s ++   +r  + +    ++++a + 
  gi|116753844|ref|YP_842962.1| 477 FEHMKASPPKGILLYGPPGTGKTLLAKAVATESQAN---FISVKGPEF-----LSKWVGESER-AVRETFRKAKQAAPAV 547
                                    5666666679********************988888...999999999.....4446666633.5555555555555555 PP

                         AAA_16  96 awrekleealaavpelagaea......srllellkr 125
                                     + +++++ +     +++++a      +r+  ++ +
  gi|116753844|ref|YP_842962.1| 548 VFFDEIDAIAP----MRSSGAadshvtERVISQILS 579
                                    55555444433....333333233344444444444 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 !   32.0   0.0     3e-10   9.3e-08      31     104 ..     210     291 ..     188     339 .. 0.78
   2 !   21.9   0.0   3.9e-07   0.00012      33      69 ..     485     521 ..     477     564 .. 0.75

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 3e-10
                         RuvB_N  31 ealdhvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsravee 102
                                    ea   vll+GpPG Gkt la+ +a+e ++++++ sgP +      e +  l  l+++ ee+   +++idei  ++++ ee
  gi|116753844|ref|YP_842962.1| 210 EAPKGVLLHGPPGTGKTLLARALASETNAHFETLSGPEImskyygESEERLRQLFKTAEENapSIILIDEIDSIAPKREE 289
                                    566789*******************************994333333345677777776665337*************999 PP

                         RuvB_N 103 vl 104
                                    v 
  gi|116753844|ref|YP_842962.1| 290 VT 291
                                    85 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 3.9e-07
                         RuvB_N  33 ldhvllyGpPGlGkttlakiiakelgvklkitsgPvl 69 
                                       +llyGpPG Gkt lak +a+e ++++ +  gP  
  gi|116753844|ref|YP_842962.1| 485 PKGILLYGPPGTGKTLLAKAVATESQANFISVKGPEF 521
                                    5679**************************9999964 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.0   1.2e-09   3.8e-07       6     105 ..     215     308 ..     212     314 .. 0.89
   2 !   24.2   0.0   9.7e-08     3e-05       6      89 ..     488     566 ..     484     584 .. 0.76

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 1.2e-09
                                    EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG---- CS
                          AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpk 83 
                                    +ll gp g+Gkt+la+ala+  ++    ++ ++   e++     + + ++++  ++  + aee+   i+l+DEid i+pk
  gi|116753844|ref|YP_842962.1| 215 VLLHGPPGTGKTLLARALASETNA----HFETLSGPEIMS----KYYGESEERLRQLFKTAEENApsIILIDEIDSIAPK 286
                                    5789******************96....999999999999....99999999999999999999999************9 PP

                                    .---------HHHHHHHHHHHH- CS
                          AAA_2  84 .essgadvSregVqrdLLqileg 105
                                     e+ + +v r  V+  LL +++g
  gi|116753844|ref|YP_842962.1| 287 rEEVTGEVERR-VVAQLLALMDG 308
                                    88888888886.66678888887 PP

  == domain 2  score: 24.2 bits;  conditional E-value: 9.7e-08
                                    EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG---- CS
                          AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpk 83 
                                    ill gp g+Gkt+laka+a   ++    ++i +   e+l     + + +++   ++   +a++    +v++DEid i+p 
  gi|116753844|ref|YP_842962.1| 488 ILLYGPPGTGKTLLAKAVATESQA----NFISVKGPEFLS----KWVGESERAVRETFRKAKQAApaVVFFDEIDAIAPM 559
                                    8999****************9995....************....66666666677777777777799************8 PP

                                    .------ CS
                          AAA_2  84 .essgad 89 
                                     +s  ad
  gi|116753844|ref|YP_842962.1| 560 rSSGAAD 566
                                    5443333 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 !   25.2   0.1   4.2e-08   1.3e-05       1     136 [.     214     333 ..     214     334 .. 0.67
   2 !   18.8   0.0   4.2e-06    0.0013       2     124 ..     488     600 ..     487     610 .. 0.66

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 4.2e-08
                                    EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG-- CS
                          AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEverae 78 
                                    +vlL GppGtgK+ la+ la+ +n+ +e+  +++ +++          +++++l    l + a+   ++i+++DE++ + 
  gi|116753844|ref|YP_842962.1| 214 GVLLHGPPGTGKTLLARALASETNAHFETLSGPEIMSKYYG-------ESEERL--RQLFKTAEenAPSIILIDEIDSIA 284
                                    59******************************997765322.......222333..333333443589999999999887 PP

                                    ...HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHT CS
                          AAA_5  79 ...sevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrs 136
                                        ev++++ +    + l l++g e  ++        + +i+++n++d     l+palr+
  gi|116753844|ref|YP_842962.1| 285 pkrEEVTGEVERRVVAQLLALMDGLESRGK--------VVIIGATNRPD----ALDPALRR 333
                                    222345555544444444444444444433........88888888888....78888876 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 4.2e-06
                                    EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG--. CS
                          AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEverae. 78 
                                    +lL GppGtgK+ la+ +a   ++++  v +++++++     +r +          +  r+a+   ++++++DE++ +  
  gi|116753844|ref|YP_842962.1| 488 ILLYGPPGTGKTLLAKAVATESQANFISVKGPEFLSKWVGESERAV---------RETFRKAKqaAPAVVFFDEIDAIAp 558
                                    89*****************************998876555555554.........4444444446789999999998774 PP

                                    HHHHHHHHHHHHSSEEE....-SSSEEE---......-EEEEEESS-- CS
                          AAA_5  79 sevlnsLlslleerrll..leeggelvkaknddllerfrviatanpld 124
                                        ++  s   er ++  l e+++l+         ++ via++n++d
  gi|116753844|ref|YP_842962.1| 559 MRSSGAADSHVTERVISqiLSEMDGLEPLH------NVIVIAATNRPD 600
                                    455556666666666651112222222222......277777777776 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   2.9e-09   8.8e-07       2      80 ..     215     323 ..     215     359 .. 0.81
   2 !   15.2   0.0   5.9e-05     0.018       2      39 ..     488     527 ..     488     643 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 2.9e-09
                         AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt............................dytrv 51 
                                    vll+G+pG+GK+ la+ l+ ++   +++ls ++++++++g+ +++++                               +v
  gi|116753844|ref|YP_842962.1| 215 VLLHGPPGTGKTLLARALASETNahFETLSGPEIMSKYYGESEERLRqlfktaeenapsiilideidsiapkreeVTGEV 294
                                    799****************99999****************8888777777888888888888888888888665433346 PP

                         AAA_33  52 ldrlyqilnelarkalsagrnvildatnl 80 
                                    + r+ ++l +l +   s+g+ vi+ atn+
  gi|116753844|ref|YP_842962.1| 295 ERRVVAQLLALMDGLESRGKVVIIGATNR 323
                                    66677788888888888888888888875 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 5.9e-05
                         AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfg 39 
                                    +ll G+pG+GK+ la+ ++ + +  ++ +  ++++++ +g
  gi|116753844|ref|YP_842962.1| 488 ILLYGPPGTGKTLLAKAVATESQanFISVKGPEFLSKWVG 527
                                    6789***************999966666666665555555 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 !   44.4   0.0   3.4e-14     1e-11       2      63 ..     106     167 ..     105     168 .. 0.93

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 3.4e-14
                                    .SCCCCHHHHCCCTTEEE-TTEEEEECCTCCCEEEEEEEECCCCSC.EEECTSCCEEESTTCC CS
                        CDC48_2   2 idgdemaylkrqFlgrpvtkGdlvvfefkgqeiklvVvstePkgpv.gitetTeielgtkpve 63 
                                    i g+ ++ylkr+ +gr+++ Gd++  +++g+ i+lv+v ++P  ++ +i + T+ie+++kp++
  gi|116753844|ref|YP_842962.1| 106 ITGG-EEYLKRYMEGRVISRGDVIELNVMGRKIDLVAVRITPPRDAlVIGDRTKIEISEKPAK 167
                                    7788.88**********************************999555**************98 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   4.8e-06    0.0014       8      56 ..     215     263 ..     210     270 .. 0.70
   2 ?    7.2   0.0     0.019       5.7      73     132 ..     255     322 ..     241     327 .. 0.67
   3 !   16.0   0.0   3.6e-05     0.011       8      40 ..     488     511 ..     482     525 .. 0.81
   4 ?   -0.8   0.0       5.7   1.7e+03      83     104 ..     534     557 ..     522     586 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 4.8e-06
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee.erpevv.fvtlpsstsskdl 56 
                                    ++++G++GtGKT+l+r l+++ +++ +  +  +pe++ +++  s++ +++l
  gi|116753844|ref|YP_842962.1| 215 VLLHGPPGTGKTLLARALASETNAHFE--TlSGPEIMsKYYGESEERLRQL 263
                                    689*****************9865433..2345555555555555555555 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.019
                         AAA_22  73 lsseellealeqalraravielliiDEaqhlr..s........eealeeLrsllnlsrkgvqliLvGtpe 132
                                     s+e+l++++  a +++   ++++iDE++ +   +         +++ +L  l++  ++  +++++G ++
  gi|116753844|ref|YP_842962.1| 255 ESEERLRQLFKTAEENAP--SIILIDEIDSIApkReevtgeveRRVVAQLLALMDGLESRGKVVIIGATN 322
                                    444555555554444444..6**********886245556677778888878888767777777777765 PP

  == domain 3  score: 16.0 bits;  conditional E-value: 3.6e-05
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerp 40 
                                    ++++G++GtGKT+l++ ++ +          ++
  gi|116753844|ref|YP_842962.1| 488 ILLYGPPGTGKTLLAKAVATES---------QA 511
                                    89****************9987.........33 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 5.7
                         AAA_22  83 eqalrarav..ielliiDEaqhlr 104
                                    ++ +r+++   ++++  DE++ + 
  gi|116753844|ref|YP_842962.1| 534 RETFRKAKQaaPAVVFFDEIDAIA 557
                                    3333333334567********985 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       4.6   1.4e+03     170     238 ..     121     189 ..     111     207 .. 0.66
   2 !   19.3   0.0   1.8e-06   0.00054      50     103 ..     212     264 ..     204     269 .. 0.83
   3 !   19.6   0.0   1.4e-06   0.00044      51     106 ..     486     540 ..     475     544 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 4.6
                                    T--TT-EEEEETTT--EEE-S.SS-SS------S--------S---S----XXXXXXXXXXXXXXXXXXX CS
                          TIP49 170 kvkegDviviekesGkvkklG.rsearakefDiekdefvelPkGevekkkevvqevtLhdlDvanarpqd 238
                                     +++gDvi ++    k+  +  r +  ++   i + + +e+ +    k+ +++q+vt  d+    a+ + 
  gi|116753844|ref|YP_842962.1| 121 VISRGDVIELNVMGRKIDLVAvRITPPRDALVIGDRTKIEISEKP-AKEEKMIQRVTYEDIGGLSAEIKK 189
                                    567778887777777777665244555555666777777777654.566667888888888766666554 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 1.8e-06
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXX CS
                          TIP49  50 GravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte.vltqal 103
                                     ++vLl Gp+gtGkt la a++ e +   +f +lsg e+ s     +e  l q +
  gi|116753844|ref|YP_842962.1| 212 PKGVLLHGPPGTGKTLLARALASETN--AHFETLSGPEIMSKYYGESEeRLRQLF 264
                                    699********************977..89**********998776651455554 PP

  == domain 3  score: 19.6 bits;  conditional E-value: 1.4e-06
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXX CS
                          TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte.vltqalrks 106
                                    +++Ll Gp+gtGkt la a++ e   +  f++++g e+ s  v  +e ++ +++rk+
  gi|116753844|ref|YP_842962.1| 486 KGILLYGPPGTGKTLLAKAVATES--QANFISVKGPEFLSKWVGESErAVRETFRKA 540
                                    89*******************985..689**************99985788999998 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.4e-05    0.0043       4      88 ..     214     307 ..     211     336 .. 0.72
   2 !   15.1   0.0   5.7e-05     0.017       5      77 ..     488     557 ..     485     581 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.4e-05
                         AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe.kllelileklkeekktylflDEiqev...... 76 
                                     +++ G+  +GKT l++ l++e      ++  ++  +   k + ++e +l +l++  ++e+  +++++DEi  +      
  gi|116753844|ref|YP_842962.1| 214 GVLLHGPPGTGKTLLARALASETN---AHFETLSGPEIMSKYYGESEeRLRQLFKT-AEENAPSIILIDEIDSIapkree 289
                                    5899****************9988...88888888888887777655245555555.4556999********99666666 PP

                         AAA_14  77 ......pewekalkslvd 88 
                                          +++   l  l+d
  gi|116753844|ref|YP_842962.1| 290 vtgeveRRVVAQLLALMD 307
                                    665555555555555555 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 5.7e-05
                         AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe.kllelileklkeekktylflDEiqevp 77 
                                    +++ G+  +GKT l+k ++ e+     +++ ++  +   k   ++e  + e +++ +k+    ++f+DEi  + 
  gi|116753844|ref|YP_842962.1| 488 ILLYGPPGTGKTLLAKAVATESQ---ANFISVKGPEFLSKWVGESErAVRETFRK-AKQAAPAVVFFDEIDAIA 557
                                    7899**************98877...55555555554444444554234455555.4456899*******8875 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    0.0079      44      71 ..     209     236 ..     190     249 .. 0.89
   2 !   15.0   0.0   5.1e-05     0.016      49      77 ..     487     515 ..     480     553 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.6e-05
                      IstB_IS21  44 iekkenivllGpsGvGKshlaialgvea 71 
                                    +e+ ++++l Gp+G+GK+ la al+ e+
  gi|116753844|ref|YP_842962.1| 209 VEAPKGVLLHGPPGTGKTLLARALASET 236
                                    6677899*****************9875 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 5.1e-05
                      IstB_IS21  49 nivllGpsGvGKshlaialgveavragls 77 
                                    +i+l Gp+G+GK+ la a+++e  ++ +s
  gi|116753844|ref|YP_842962.1| 487 GILLYGPPGTGKTLLAKAVATESQANFIS 515
                                    799****************9987666555 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.1e-05    0.0033       2      44 ..     215     262 ..     214     301 .. 0.79
   2 !   13.3   0.0   0.00024     0.073       2      39 ..     488     530 ..     487     571 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.1e-05
                         AAA_28   2 ivitGgestGKTtlleaLaar...gypvv..pEaareileeklakged 44 
                                    + + G+++tGKT l++aLa++    ++++  pE++ +++ e  ++ ++
  gi|116753844|ref|YP_842962.1| 215 VLLHGPPGTGKTLLARALASEtnaHFETLsgPEIMSKYYGESEERLRQ 262
                                    6799***************54456666666899999999887776665 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00024
                         AAA_28   2 ivitGgestGKTtlleaLaar....gypvv.pEaareileekl 39 
                                    i + G+++tGKT l++a a +     ++v  pE+  + + e  
  gi|116753844|ref|YP_842962.1| 488 ILLYGPPGTGKTLLAKAVATEsqanFISVKgPEFLSKWVGESE 530
                                    7899***************544453233335565555544433 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   3.4e-05      0.01       1      25 [.     215     257 ..     215     321 .. 0.64
   2 !   13.9   0.0    0.0002     0.061       1      22 [.     488     509 ..     488     592 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.4e-05
                         AAA_18   1 IlltGtpGvGKttlakeLskrlgf..................g 25 
                                    +ll G+pG+GKt la++L+++++                    
  gi|116753844|ref|YP_842962.1| 215 VLLHGPPGTGKTLLARALASETNAhfetlsgpeimskyygesE 257
                                    7899**************9997445555555555554444441 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 0.0002
                         AAA_18   1 IlltGtpGvGKttlakeLskrl 22 
                                    Ill G+pG+GKt lak+++ + 
  gi|116753844|ref|YP_842962.1| 488 ILLYGPPGTGKTLLAKAVATES 509
                                    99****************7764 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0     4e-05     0.012       1      36 [.     215     250 ..     215     262 .. 0.86
   2 !   14.4   0.0   0.00012     0.037       1      27 [.     488     520 ..     488     597 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4e-05
                   RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvys 36 
                                    ++l+Gp+g+GK++la+ La++   ++++ + ++++s
  gi|116753844|ref|YP_842962.1| 215 VLLHGPPGTGKTLLARALASETNAHFETLSGPEIMS 250
                                    689********************9998777776665 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 0.00012
                   RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl......k 27 
                                    i+lyGp+g+GK++lak +a++ + ++      +
  gi|116753844|ref|YP_842962.1| 488 ILLYGPPGTGKTLLAKAVATESQANFisvkgpE 520
                                    789**************8777665553333321 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   0.00011     0.032      25      44 ..     215     234 ..     208     260 .. 0.91
   2 !   14.3   0.0   6.6e-05      0.02      24      43 ..     487     506 ..     479     546 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00011
                   Mg_chelatase  25 lllvGppGsGKtmlakrlps 44 
                                    +ll GppG+GKt+la++l+s
  gi|116753844|ref|YP_842962.1| 215 VLLHGPPGTGKTLLARALAS 234
                                    89**************9975 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 6.6e-05
                   Mg_chelatase  24 nlllvGppGsGKtmlakrlp 43 
                                     +ll+GppG+GKt+lak+++
  gi|116753844|ref|YP_842962.1| 487 GILLYGPPGTGKTLLAKAVA 506
                                    589*************9975 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0    0.0002     0.061      11      49 ..     204     244 ..     188     263 .. 0.75
   2 !   13.7   0.0   0.00016     0.047      19      53 ..     485     521 ..     455     524 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.0002
                                    HHHHHHCHTEEEEEEESTTSSHHHHHHHHHHHTT--..--- CS
                           TsaE  11 gkklakalgdvilLeGdLGaGKTtlvrglakalgve..evk 49 
                                     ++l+ ++ + +lL+G+ G+GKT l+r+la++ + +  + +
  gi|116753844|ref|YP_842962.1| 204 FERLGVEAPKGVLLHGPPGTGKTLLARALASETNAHfeTLS 244
                                    44555444567*******************99987663343 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00016
                                    TEEEEEEESTTSSHHHHHHHHHHHTT--..----TTT CS
                           TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve..evkSPTF 53 
                                     + ilL+G+ G+GKT l++++a + + +  +vk P F
  gi|116753844|ref|YP_842962.1| 485 PKGILLYGPPGTGKTLLAKAVATESQANfiSVKGPEF 521
                                    3459********************9999889999988 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   0.00013      0.04       2      37 ..     215     249 ..     214     301 .. 0.69
   2 !   11.1   0.0   0.00087      0.27       2      91 ..     488     574 ..     487     614 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00013
                          AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdll 37 
                                    vll+g PG++ktll++ala+  +++f+ +   p+++
  gi|116753844|ref|YP_842962.1| 215 VLLHGPPGTGKTLLARALASETNAHFETLS-GPEIM 249
                                    89***********************99764.45555 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00087
                          AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanllladeinrapp.ktqs 80 
                                    +ll g PG++ktll+ka+a+  +++f  ++  p++l    +G +     +++f+  k      +++ dei+  +p ++  
  gi|116753844|ref|YP_842962.1| 488 ILLYGPPGTGKTLLAKAVATESQANFISVK-GPEFLSKW-VGESERA-VRETFRKAKQ-AAPAVVFFDEIDAIAPmRSSG 563
                                    7999******************99998886.56666544.4443222.2222322222.223456666666433313333 PP

                          AAA_3  81 alleameerqv 91 
                                    a    + er +
  gi|116753844|ref|YP_842962.1| 564 AADSHVTERVI 574
                                    33334444444 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00079      0.24      21      47 ..     211     237 ..     192     248 .. 0.85
   2 !   11.9   0.0   0.00045      0.14      22      56 ..     485     516 ..     475     600 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00079
                                    SSS-EEEECSTTSSHHHHHHHHHHHST CS
                Sigma54_activat  21 tdlsvlitGesGtGKellaraiheask 47 
                                     +  vl++G  GtGK+llara+ ++++
  gi|116753844|ref|YP_842962.1| 211 APKGVLLHGPPGTGKTLLARALASETN 237
                                    56789****************987655 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00045
                                    SS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEE CS
                Sigma54_activat  22 dlsvlitGesGtGKellaraiheaskrkekpfvav 56 
                                    +  +l+ G  GtGK+lla+a+ ++s+   ++f++v
  gi|116753844|ref|YP_842962.1| 485 PKGILLYGPPGTGKTLLAKAVATESQ---ANFISV 516
                                    4679****************998876...455555 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00081      0.25      22      43 ..     215     236 ..     205     317 .. 0.85
   2 ?    0.6   0.0       1.1   3.3e+02      63     106 ..     406     449 ..     395     455 .. 0.79
   3 !   10.4   0.0    0.0011      0.33      23      43 ..     489     509 ..     477     516 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00081
                                    EEEE--TTSSTTHHHHHHHHHH CS
                           PhoH  22 vfaiGpaGtGKtylavalavea 43 
                                    v   Gp GtGKt+la ala e 
  gi|116753844|ref|YP_842962.1| 215 VLLHGPPGTGKTLLARALASET 236
                                    6789************999775 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.1
                                    ----SS---------TTTHHHHHHHTTTS-TTCHHHHHHTTSEE CS
                           PhoH  63 eelGflpgdleekvdpylrplydaLkdllgaekvekllekgkie 106
                                     e+   p ++ +k+++ ++ ++daL+dl  ++  e l+e+ +++
  gi|116753844|ref|YP_842962.1| 406 LEVESIPAEILNKIEVTMADFMDALRDLEPSAMREVLVESPNVH 449
                                    56667899999****************98888777777777666 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.0011
                                    EEE--TTSSTTHHHHHHHHHH CS
                           PhoH  23 faiGpaGtGKtylavalavea 43 
                                       Gp GtGKt+la a+a e 
  gi|116753844|ref|YP_842962.1| 489 LLYGPPGTGKTLLAKAVATES 509
                                    578*************99875 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    0.0011      0.34      14      41 ..     210     237 ..     201     243 .. 0.87
   2 !   12.8   0.0   0.00017     0.053      13      51 ..     482     518 ..     474     523 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0011
                     Zeta_toxin  14 erPklillgGqpGAGKselaellkdele 41 
                                    e Pk +ll G pG GK+ la++l+ e++
  gi|116753844|ref|YP_842962.1| 210 EAPKGVLLHGPPGTGKTLLARALASETN 237
                                    89*********************99975 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00017
                     Zeta_toxin  13 qerPklillgGqpGAGKselaellkdelerqgnvvrldp 51 
                                     + Pk ill G pG GK+ la+++++e   q n++ +++
  gi|116753844|ref|YP_842962.1| 482 ASPPKGILLYGPPGTGKTLLAKAVATES--QANFISVKG 518
                                    4679***********************8..899998875 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0    0.0011      0.33      37     176 ..     215     356 ..     209     370 .. 0.73
   2 !   10.5   0.0    0.0013       0.4      37     176 ..     488     631 ..     479     656 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0011
                                    EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHT.T-SEEEEE-GGGGTT-HH. CS
                       Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklr.kvDvLliDDiqflagkek. 114
                                    ++++g+ G Gkt L +a++ e+ +++       l++ e +++     +++  + fk     +  ++liD+i  +a k + 
  gi|116753844|ref|YP_842962.1| 215 VLLHGPPGTGKTLLARALASETNAHF-----ETLSGPEIMSKYYGESEERLRQLFKTAEEnAPSIILIDEIDSIAPKREe 289
                                    79************999988776655.....56899999999999999999999998877255899********988532 PP

                                    ........HHHHHHHHHHHHHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHH CS
                       Bac_DnaA 115 ........tqeelfhtfnalleegkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailk 176
                                            +  +l+ +++ l   gk v++ +   P +l+    r   rf++ +  +i  p+++ rl+il+
  gi|116753844|ref|YP_842962.1| 290 vtgeverrVVAQLLALMDGLESRGKVVIIGATNRPDALDPAL-RRPGRFDREI--EIGVPNRDARLEILQ 356
                                    211111113345667777777889999999999999987644.3356787755..455577777777775 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0013
                                    EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHTT-.SEEEEE-GGGGTT-HH. CS
                       Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklrkv.DvLliDDiqflagkek. 114
                                    +++yg+ G Gkt L ka++ e ++n+       +++ eFl++ v   +    e+f++  +++  v+  D+i  +a   + 
  gi|116753844|ref|YP_842962.1| 488 ILLYGPPGTGKTLLAKAVATESQANFI-----SVKGPEFLSKWVGESERAVRETFRKAKQAApAVVFFDEIDAIAPMRSs 562
                                    79***************9988776664.....567999999999999999999998877654156677888877643320 PP

                                    .......HHHHHHHHHHHH...HTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHH CS
                       Bac_DnaA 115 .......tqeelfhtfnal...leegkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailk 176
                                           t+  + +++ ++      ++ +v+++   P  ++    r   rf++  +++i ppd+e rl+ilk
  gi|116753844|ref|YP_842962.1| 563 gaadshvTERVISQILSEMdglEPLHNVIVIAATNRPDIIDPALLR-PGRFDR--MIEIGPPDEESRLEILK 631
                                    1111111222333333333110333456677777777666543322.245554..56777777777777775 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0    0.0021      0.63       4      29 ..     214     240 ..     211     291 .. 0.63
   2 !   13.0   0.0    0.0002     0.061       5      22 ..     488     505 ..     485     562 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0021
                         AAA_24   4 kiliyGpsgiGKTtlakel.gpkplfi 29 
                                     +l+ Gp+g+GKT la+ l  ++ + +
  gi|116753844|ref|YP_842962.1| 214 GVLLHGPPGTGKTLLARALaSETNAHF 240
                                    5899************99954444444 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.0002
                         AAA_24   5 iliyGpsgiGKTtlakel 22 
                                    il+yGp+g+GKT lak  
  gi|116753844|ref|YP_842962.1| 488 ILLYGPPGTGKTLLAKAV 505
                                    89*************987 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0    0.0041       1.2      15      38 ..     208     231 ..     201     242 .. 0.81
   2 ?    3.4   0.0      0.14        42     108     154 ..     260     309 ..     241     318 .. 0.69
   3 !    9.0   0.0    0.0026      0.78      22      43 ..     488     509 ..     484     538 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0041
                         ATPase  15 GipegrvvlitGepGtGKtifalq 38 
                                    G+   + vl+ G pGtGKt++a  
  gi|116753844|ref|YP_842962.1| 208 GVEAPKGVLLHGPPGTGKTLLARA 231
                                    55566779*************975 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.14
                         ATPase 108 ieelaeaikeikakrvviDsitgl...ayeekeavaReilrqlvrvlkkl 154
                                    +++l +  +e   + ++iD i+++    +e + +v R+ + ql+  + +l
  gi|116753844|ref|YP_842962.1| 260 LRQLFKTAEENAPSIILIDEIDSIapkREEVTGEVERRVVAQLLALMDGL 309
                                    44455555555667788888887743244555667899999999999765 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0026
                         ATPase  22 vlitGepGtGKtifalqFlikg 43 
                                    +l++G pGtGKt++a+  + ++
  gi|116753844|ref|YP_842962.1| 488 ILLYGPPGTGKTLLAKAVATES 509
                                    89************99766655 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00052      0.16       3      24 ..     215     236 ..     213     311 .. 0.92
   2 ?   -0.1   0.0       2.5   7.7e+02      63     115 ..     254     308 ..     240     343 .. 0.62
   3 !    9.2   0.0    0.0036       1.1       3      23 ..     488     508 ..     486     515 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00052
                                    EEEEC-TTTCHHHHHHHHHHHH CS
                          NACHT   3 vilqGeaGsGKTtLlqklalaw 24 
                                    v+l+G++G GKT L++ la++ 
  gi|116753844|ref|YP_842962.1| 215 VLLHGPPGTGKTLLARALASET 236
                                    79****************9875 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 2.5
                                    TS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH.............HHHHHCT CS
                          NACHT  63 pepaapvsevwavllelperlLlilDglDelvtdlgq....kekqpvrtlLselirk 115
                                     e++++ ++ ++   e++ ++ +++D +D ++ + ++     e++ v + L  l+ +
  gi|116753844|ref|YP_842962.1| 254 GESEERLRQLFKTAEENAPSI-ILIDEIDSIAPKREEvtgeVERRVVAQ-LLALMDG 308
                                    555556666555555555554.567999999887777777433444444.4466655 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0036
                                    EEEEC-TTTCHHHHHHHHHHH CS
                          NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                    ++l G++G GKT L++ +a++
  gi|116753844|ref|YP_842962.1| 488 ILLYGPPGTGKTLLAKAVATE 508
                                    7899*************9987 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   0.00013      0.04      16      44 ..     211     239 ..     198     278 .. 0.71
   2 !    8.9   0.1    0.0038       1.1      20      41 ..     488     509 ..     478     716 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00013
                         AAA_11  16 eseitliqGPPGtgKTktivellsqllsr 44 
                                     ++ +l++GPPGtgKT    +l s+ + +
  gi|116753844|ref|YP_842962.1| 211 APKGVLLHGPPGTGKTLLARALASETNAH 239
                                    555689**********9999999998744 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0038
                         AAA_11  20 tliqGPPGtgKTktivellsql 41 
                                     l+ GPPGtgKT    ++  + 
  gi|116753844|ref|YP_842962.1| 488 ILLYGPPGTGKTLLAKAVATES 509
                                    5899********6665555555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.1    0.0027      0.81      36      56 ..     215     235 ..     208     246 .. 0.89
   2 ?    5.8   0.1     0.029       8.9     128     176 ..     258     306 ..     250     325 .. 0.89
   3 !    9.9   0.7    0.0016      0.49      36      56 ..     488     508 ..     484     593 .. 0.52

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0027
                         AAA_25  36 allaGapgtGKttlaldlala 56 
                                    +ll G+pgtGKt la  la +
  gi|116753844|ref|YP_842962.1| 215 VLLHGPPGTGKTLLARALASE 235
                                    69*************999865 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.029
                         AAA_25 128 advdaleaaieevegvrlvviDplsralggdensnsdv.galvealeria 176
                                    + +++l +++ee + +  + iD ++++ +  e+   +v +++v++l  + 
  gi|116753844|ref|YP_842962.1| 258 ERLRQLFKTAEE-NAPSIILIDEIDSIAPKREEVTGEVeRRVVAQLLALM 306
                                    5678999*****.77******************9*9999*****998776 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.0016
                         AAA_25  36 allaGapgtGKttlaldlala 56 
                                    +ll+G+pgtGKt la  +a +
  gi|116753844|ref|YP_842962.1| 488 ILLYGPPGTGKTLLAKAVATE 508
                                    69**********998665543 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 !   11.4   0.0   0.00055      0.17      30      58 ..     209     237 ..     201     246 .. 0.83
   2 !   10.4   0.0    0.0011      0.33      34      60 ..     486     511 ..     473     523 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00055
                          AAA_7  30 lknkkpvllvGptGtGKtviikdllkkld 58 
                                    +++ k vll Gp GtGKt++++ l ++ +
  gi|116753844|ref|YP_842962.1| 209 VEAPKGVLLHGPPGTGKTLLARALASETN 237
                                    677899***************99988876 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0011
                          AAA_7  34 kpvllvGptGtGKtviikdllkkldke 60 
                                    k +ll+Gp GtGKt+++k + ++ +  
  gi|116753844|ref|YP_842962.1| 486 KGILLYGPPGTGKTLLAKAVATESQ-A 511
                                    679***************9877766.3 PP

>> Vps4_C  Vps4 C terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.1   0.00077      0.24      16      45 ..     408     437 ..     403     445 .. 0.85
   2 !    9.6   0.0     0.003      0.91      22      46 ..     685     709 ..     677     714 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00077
                         Vps4_C  16 wmdipsdkllePpvtlkDflkalkkarptV 45 
                                    ++ ip++ l + +vt+ Df++al+   p+ 
  gi|116753844|ref|YP_842962.1| 408 VESIPAEILNKIEVTMADFMDALRDLEPSA 437
                                    678998888899*************99985 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.003
                         Vps4_C  22 dkllePpvtlkDflkalkkarptVs 46 
                                    + +++  v++++f++alkk+rp+  
  gi|116753844|ref|YP_842962.1| 685 EAIKNLRVERRHFEEALKKVRPSLK 709
                                    5677789***************976 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0    0.0012      0.35       7      42 ..     208     243 ..     206     313 .. 0.76
   2 !   10.2   0.0    0.0027      0.81      11      51 ..     485     523 ..     479     594 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0012
                                    EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkpteGei 42 
                                     +++ + v + G+ G+GK+ L+++la +++   +++
  gi|116753844|ref|YP_842962.1| 208 GVEAPKGVLLHGPPGTGKTLLARALASETNAHFETL 243
                                    567777899******************999876666 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0027
                                    TSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  11 gekvaivGenGaGKStLlkllagllkpteGeilldgkdlke 51 
                                     + + + G+ G+GK+ L+k++a +++  +  i ++g ++ +
  gi|116753844|ref|YP_842962.1| 485 PKGILLYGPPGTGKTLLAKAVATESQ--ANFISVKGPEFLS 523
                                    5667899***************9986..5666667666666 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.1     0.002      0.62      21      43 ..     215     237 ..     202     319 .. 0.89
   2 !    9.9   0.0    0.0018      0.55      10      42 ..     477     509 ..     474     519 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.002
                         AAA_30  21 avltGpAGtGKttalkalreawe 43 
                                    ++l+Gp+GtGKt + +al+   +
  gi|116753844|ref|YP_842962.1| 215 VLLHGPPGTGKTLLARALASETN 237
                                    689***********999976555 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0018
                         AAA_30  10 vealltsgdrvavltGpAGtGKttalkalreaw 42 
                                    +e++ +s+ +  +l Gp+GtGKt + ka++   
  gi|116753844|ref|YP_842962.1| 477 FEHMKASPPKGILLYGPPGTGKTLLAKAVATES 509
                                    67777888888899***********99997655 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.012       3.8      54      81 ..     213     240 ..     170     323 .. 0.80
   2 !   11.7   0.0   0.00036      0.11      24      80 ..     447     512 ..     431     520 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.012
                         DUF815  54 nnvLLwGarGtGKSslvkallneyaeeg 81 
                                    + vLL G  GtGK  l +al +e++++ 
  gi|116753844|ref|YP_842962.1| 213 KGVLLHGPPGTGKTLLARALASETNAHF 240
                                    679******************9988764 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00036
                         DUF815  24 evklddLvgidkqkealvente.........qfleglpannvLLwGarGtGKSslvkallneyaee 80 
                                    +v+++d+ g+ + k++l+e +e         ++++  p + +LL+G  GtGK  l ka+ +e +++
  gi|116753844|ref|YP_842962.1| 447 NVHWSDIGGLAQAKQELMEAVEwpltypklfEHMKASPPKGILLYGPPGTGKTLLAKAVATESQAN 512
                                    56666777777777777766543333332225678888899******************9998876 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0    0.0013       0.4       4      25 ..     215     236 ..     212     287 .. 0.79
   2 !    9.1   0.0    0.0022      0.68       4      37 ..     488     514 ..     485     556 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0013
                        DUF2075   4 vlVtGvaGtGKtvvllnllael 25 
                                    vl +G +GtGKt+++ +l+ e 
  gi|116753844|ref|YP_842962.1| 215 VLLHGPPGTGKTLLARALASET 236
                                    6889**************9998 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0022
                        DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavyl 37 
                                    +l  G +GtGKt+++ ++++e        +a+++
  gi|116753844|ref|YP_842962.1| 488 ILLYGPPGTGKTLLAKAVATES-------QANFI 514
                                    6789************999998.......34444 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 !    7.8   0.0    0.0049       1.5     117     136 ..     215     234 ..     212     239 .. 0.89
   2 !    9.9   0.0    0.0012      0.36     117     137 ..     488     508 ..     479     512 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0049
                      Parvo_NS1 117 vwfyGpantGktnlaeaIak 136
                                    v+++Gp+ tGkt la+a+a 
  gi|116753844|ref|YP_842962.1| 215 VLLHGPPGTGKTLLARALAS 234
                                    7899**************97 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0012
                      Parvo_NS1 117 vwfyGpantGktnlaeaIaka 137
                                    +++yGp+ tGkt la+a a+ 
  gi|116753844|ref|YP_842962.1| 488 ILLYGPPGTGKTLLAKAVATE 508
                                    89***************9975 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.023         7      25      62 ..     202     239 ..     190     249 .. 0.84
   2 ?    1.5   0.0      0.54   1.6e+02     108     133 ..     260     285 ..     241     339 .. 0.67
   3 !    7.8   0.0    0.0067         2      25      59 ..     475     509 ..     461     518 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.023
                           TniB  25 eLleypkrkrmpnlllvGdsnnGKtmivekFarlhppe 62 
                                    eL+e+   + ++ +ll+G++ +GKt +++  a++ +++
  gi|116753844|ref|YP_842962.1| 202 ELFERLGVEAPKGVLLHGPPGTGKTLLARALASETNAH 239
                                    5777777888999**************99988877665 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.54
                           TniB 108 eqqvlrllrelkvrvLiiDEihnlla 133
                                     +q  ++ +e  + +++iDEi+++  
  gi|116753844|ref|YP_842962.1| 260 LRQLFKTAEENAPSIILIDEIDSIAP 285
                                    34455666777899********9963 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0067
                           TniB  25 eLleypkrkrmpnlllvGdsnnGKtmivekFarlh 59 
                                    +L+e+ k++ ++ +ll+G++ +GKt +++  a + 
  gi|116753844|ref|YP_842962.1| 475 KLFEHMKASPPKGILLYGPPGTGKTLLAKAVATES 509
                                    68999999999***************999877665 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0042       1.3      22      52 ..     214     241 ..     201     256 .. 0.80
   2 !    8.5   0.0    0.0034         1      22      45 ..     487     510 ..     473     526 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0042
                                    EEEEEESTTSSHHHHHHHHCCSHCCCCCCBT CS
                         NB-ARC  22 vvalvGmgGvGKttlakqilnksdevegrFd 52 
                                     v l+G +G GKt la+   ++   ++ +F+
  gi|116753844|ref|YP_842962.1| 214 GVLLHGPPGTGKTLLARALASE---TNAHFE 241
                                    4789***********9988777...555665 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0034
                                    EEEEEESTTSSHHHHHHHHCCSHC CS
                         NB-ARC  22 vvalvGmgGvGKttlakqilnksd 45 
                                     + l+G +G GKt lak +  +s+
  gi|116753844|ref|YP_842962.1| 487 GILLYGPPGTGKTLLAKAVATESQ 510
                                    5789**************998844 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.2     0.021       6.5      11      31 ..     213     233 ..     208     249 .. 0.81
   2 ?   -1.2   0.0       7.7   2.3e+03      98     125 ..     267     294 ..     250     307 .. 0.66
   3 !    9.4   0.0    0.0041       1.2       7      32 ..     482     507 ..     478     555 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.021
                         AAA_19  11 kvllvtaGpGtGKTrvlkhiv 31 
                                    k +l+ ++pGtGKT + ++  
  gi|116753844|ref|YP_842962.1| 213 KGVLLHGPPGTGKTLLARALA 233
                                    55899*********8776655 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 7.7
                         AAA_19  98 kklqeeellivDEfqdvdelqyrLlkal 125
                                     + ++  ++++DE+  + +   ++  ++
  gi|116753844|ref|YP_842962.1| 267 AEENAPSIILIDEIDSIAPKREEVTGEV 294
                                    333345699****999987766665555 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0041
                         AAA_19   7 alkekvllvtaGpGtGKTrvlkhiva 32 
                                    a++ k +l+ ++pGtGKT + k++ +
  gi|116753844|ref|YP_842962.1| 482 ASPPKGILLYGPPGTGKTLLAKAVAT 507
                                    6677889***********87776654 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0    0.0018      0.54      22      47 ..     213     238 ..     202     289 .. 0.71
   2 ?    6.4   0.0     0.029         9      24      48 ..     488     512 ..     476     563 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0018
                                    S-EEEEEETT--HHHHHHCC--TTS- CS
                Sigma54_activ_2  22 lpvfltGekGsgkelvArlLhknsgp 47 
                                      v+l G++G+gk+l Ar+L+++   
  gi|116753844|ref|YP_842962.1| 213 KGVLLHGPPGTGKTLLARALASETNA 238
                                    569*****************987654 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.029
                                    EEEEEETT--HHHHHHCC--TTS-E CS
                Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpw 48 
                                    ++l G++G+gk+l A++ + +s+ +
  gi|116753844|ref|YP_842962.1| 488 ILLYGPPGTGKTLLAKAVATESQAN 512
                                    89***************99887653 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0     0.017       5.2       2      53 ..     219     271 ..     218     300 .. 0.69
   2 !    8.8   0.0    0.0066         2       1      57 [.     491     548 ..     491     613 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.017
                                    E-TTSSHHHHHHHHHHHH..TEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHH CS
                         AAA_17   2 GgPGsGKgtqceklveky..gfthlsaGdllreeakrgglakardemrklplee 53 
                                    G+PG GK+ +++ l+ +   +f+ ls  +++ +   +++ ++ r+ +++++++ 
  gi|116753844|ref|YP_842962.1| 219 GPPGTGKTLLARALASETnaHFETLSGPEIMSKYYGESE-ERLRQLFKTAEENA 271
                                    9**************887447888997777766554443.34455555555444 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0066
                                    EE-TTSSHHHHHHHHHHHHTEEEEEH.HHHHH.HHHHTTTSHSSHHHHCTSHHHHHHHH CS
                         AAA_17   1 lGgPGsGKgtqceklvekygfthlsa.Gdllr.eeakrgglakardemrklpleekkel 57 
                                    +G+PG GK+ +++ ++ + +  ++s  G  +  + + +++    r+ +rk+++     +
  gi|116753844|ref|YP_842962.1| 491 YGPPGTGKTLLAKAVATESQANFISVkGPEFLsKWVGESER-AVRETFRKAKQAAPAVV 548
                                    7***********99999886666665444444044444343.45666776666655555 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 ?    5.7   0.0     0.039        12      22     122 ..     214     318 ..     202     321 .. 0.60
   2 !    8.8   0.0    0.0044       1.3      15      45 ..     480     510 ..     474     544 .. 0.82
   3 ?   -1.2   0.0         5   1.5e+03     104     136 ..     531     562 ..     508     594 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.039
                       ATPase_2  22 iyfiYGpegsGKtaLlkeiienledkdk.......yviyyialreesiskldefieeeeekkklekalgiavpkaeleei 94 
                                     +++ Gp g GKt L + ++++ + + +          yy + +e+  + +++  ee+  +  l + + +  pk   ee+
  gi|116753844|ref|YP_842962.1| 214 GVLLHGPPGTGKTLLARALASETNAHFEtlsgpeiMSKYYGESEERLRQLFKTA-EENAPSIILIDEIDSIAPK--REEV 290
                                    57889************9999984433335555533334444444433333333.4444444444444444444..4456 PP

                       ATPase_2  95 lkeksklvfkaielllekikkkgkkiii 122
                                      e  + v +++ +l++ ++ +gk +ii
  gi|116753844|ref|YP_842962.1| 291 TGEVERRVVAQLLALMDGLESRGKVVII 318
                                    6677888888888888888888875554 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0044
                       ATPase_2  15 lerepneiyfiYGpegsGKtaLlkeiienle 45 
                                    ++ +p + +++YGp g GKt L k ++++++
  gi|116753844|ref|YP_842962.1| 480 MKASPPKGILLYGPPGTGKTLLAKAVATESQ 510
                                    5566777899*************99998774 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 5
                       ATPase_2 104 kaielllekikkkgkk...iiiiiDelqklidlgln 136
                                    +a+ + ++k k    +    ++++De+  +  + + 
  gi|116753844|ref|YP_842962.1| 531 RAVRETFRKAK----QaapAVVFFDEIDAIAPMRSS 562
                                    44444444444....345478999**9998877665 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0    0.0089       2.7      52      78 ..     204     228 ..     161     243 .. 0.81
   2 !    7.4   0.0    0.0057       1.7      49      79 ..     474     502 ..     452     510 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0089
                    AFG1_ATPase  52 fgrkrksvepvrglYlwGgvGrGKtyl 78 
                                    f r    ve+++g+ l+G+ G GKt l
  gi|116753844|ref|YP_842962.1| 204 FER--LGVEAPKGVLLHGPPGTGKTLL 228
                                    443..3589****************88 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0057
                    AFG1_ATPase  49 gklfgrkrksvepvrglYlwGgvGrGKtylm 79 
                                     klf +   +  p++g+ l+G+ G GKt l 
  gi|116753844|ref|YP_842962.1| 474 PKLFEHM--KASPPKGILLYGPPGTGKTLLA 502
                                    5677744..688****************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 ?    6.9   0.0     0.015       4.6       2      71 ..     216     280 ..     215     285 .. 0.73
   2 !    8.5   0.0    0.0051       1.5       4      71 ..     491     553 ..     488     566 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.015
                Viral_helicase1   2 vvhGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                    + hG pG GK+ l r l+++   ++ + +   e+ ++   +++ +    ++++++++       i+++DE+
  gi|116753844|ref|YP_842962.1| 216 LLHGPPGTGKTLLARALASETnAHFETLSG-PEIMSKYYGESEERLRQLFKTAEENAP-----SIILIDEI 280
                                    68****************996655555555.566666666777777777777777654.....48888986 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0051
                Viral_helicase1   4 hGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                     G pG GK+ l + ++ +s  ++ +++   e l++++ ++++   +t++++ +a+ +     ++++DE+
  gi|116753844|ref|YP_842962.1| 491 YGPPGTGKTLLAKAVATESqANFISVKG-PEFLSKWVGESERAVRETFRKAKQAAPA-----VVFFDEI 553
                                    588*************999977767776.8*******99999999999998888764.....89***98 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0     0.011       3.5       3      26 ..     217     240 ..     215     245 .. 0.90
   2 ?    6.6   0.0     0.019       5.9       3      28 ..     490     515 ..     488     517 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.011
                                    EE-STTSSHHHHHHHHHHHHT-EE CS
                 Cytidylate_kin   3 iDGPagsGKssvaralaeklglky 26 
                                    + GP g+GK  +arala++ ++++
  gi|116753844|ref|YP_842962.1| 217 LHGPPGTGKTLLARALASETNAHF 240
                                    68*****************99876 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.019
                                    EE-STTSSHHHHHHHHHHHHT-EEEE CS
                 Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyld 28 
                                    + GP g+GK  +a+a+a++ ++++++
  gi|116753844|ref|YP_842962.1| 490 LYGPPGTGKTLLAKAVATESQANFIS 515
                                    67*******************99986 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.25        75       2      21 ..     215     234 ..     214     245 .. 0.83
   2 ?    1.6   0.1      0.75   2.3e+02      82     117 ..     257     293 ..     232     306 .. 0.70
   3 ?    7.3   0.0     0.013         4       2      32 ..     488     518 ..     487     553 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.25
                                    EEEE--TTSSHHHHHHHHHH CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvle 21 
                                    v++ GppG+GKt l + +++
  gi|116753844|ref|YP_842962.1| 215 VLLHGPPGTGKTLLARALAS 234
                                    6789********99887766 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.75
                                    HHHHHHHHHHHH.HHH-EEEE---STTGGG-HHHHHH CS
                       NTPase_1  82 eelalealrkal.seadviviDEiGkmElkskkfkea 117
                                    ee   + +++a  + + +i+iDEi ++  k +++  +
  gi|116753844|ref|YP_842962.1| 257 EERLRQLFKTAEeNAPSIILIDEIDSIAPKREEVTGE 293
                                    44555556666635667*******7766665555555 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.013
                                    EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                    +++ GppG+GKt l k v+ + + + ++v+G
  gi|116753844|ref|YP_842962.1| 488 ILLYGPPGTGKTLLAKAVATESQANFISVKG 518
                                    6788***************999998888888 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 ?    7.6   0.0    0.0058       1.8     125     156 ..     208     239 ..     141     246 .. 0.74
   2 ?    4.8   0.0     0.041        12     130     153 ..     486     509 ..     434     518 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0058
                          T2SSE 125 avrerglilvsGgTgsGKttllyallkeinks 156
                                     v++ + +l+ G+ g+GKt l+ al +e n++
  gi|116753844|ref|YP_842962.1| 208 GVEAPKGVLLHGPPGTGKTLLARALASETNAH 239
                                    46677889******************999987 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.041
                          T2SSE 130 glilvsGgTgsGKttllyallkei 153
                                    + il+ G+ g+GKt l+ a+ +e 
  gi|116753844|ref|YP_842962.1| 486 KGILLYGPPGTGKTLLAKAVATES 509
                                    6799************99987765 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   0.0     0.015       4.6      21      48 ..     200     236 ..     168     244 .. 0.75
   2 ?    5.7   0.0     0.045        14      17      47 ..     478     508 ..     455     553 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.015
                                    ...........TTSEEEEEESTTSTHHHHHHHHHHHH CS
                         ResIII  21 s.........krdkrglikmaTGtGKTlvaaklierl 48 
                                    +         +  k +l++ + GtGKTl+a +l+ + 
  gi|116753844|ref|YP_842962.1| 200 HpelferlgvEAPKGVLLHGPPGTGKTLLARALASET 236
                                    05555555557789999************98887665 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.045
                                    ......TTSEEEEEESTTSTHHHHHHHHHHH CS
                         ResIII  17 eklkskrdkrglikmaTGtGKTlvaaklier 47 
                                    e++k+   k +l+  + GtGKTl+a +++ +
  gi|116753844|ref|YP_842962.1| 478 EHMKASPPKGILLYGPPGTGKTLLAKAVATE 508
                                    5556577788999**********99665554 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0     0.019       5.6       4      31 ..     215     242 ..     213     329 .. 0.90
   2 ?    5.4   0.0     0.048        15       4      40 ..     488     524 ..     486     565 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.019
                                    EEEEE-TTSSHHHHHHHHHHHSSS-EEE CS
                            CPT   4 ilLnGgsssGKsslaralqevldepwlh 31 
                                    +lL+G + +GK+ laral + +++ +  
  gi|116753844|ref|YP_842962.1| 215 VLLHGPPGTGKTLLARALASETNAHFET 242
                                    89****************9988877755 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.048
                                    EEEEE-TTSSHHHHHHHHHHHSSS-EEEEEHHHHHHH CS
                            CPT   4 ilLnGgsssGKsslaralqevldepwlhlgvDafvea 40 
                                    ilL G + +GK+ la+a+ + +++ ++ ++  +f+ +
  gi|116753844|ref|YP_842962.1| 488 ILLYGPPGTGKTLLAKAVATESQANFISVKGPEFLSK 524
                                    89************************99987777765 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.068        21      48      79 ..     215     246 ..     189     280 .. 0.79
   2 ?    5.3   0.0     0.056        17      45      79 ..     485     519 ..     455     595 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.068
                          Rad17  48 LLisGPsGCgkstvvkvLskelgiklrewlnp 79 
                                    +L+ GP+G gk+   + L+ e   +++  + p
  gi|116753844|ref|YP_842962.1| 215 VLLHGPPGTGKTLLARALASETNAHFETLSGP 246
                                    5889**************99988877766655 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.056
                          Rad17  45 kriLLisGPsGCgkstvvkvLskelgiklrewlnp 79 
                                     + +L+ GP+G gk+   k ++ e   +++    p
  gi|116753844|ref|YP_842962.1| 485 PKGILLYGPPGTGKTLLAKAVATESQANFISVKGP 519
                                    3456789********99999988877777665555 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.018       5.6       4      62 ..     216     280 ..     215     305 .. 0.73
   2 ?    2.4   0.1      0.35   1.1e+02      28      88 ..     517     552 ..     488     613 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.018
                            Zot   4 lvtGapGsgKtsga..vkkdllp..alkegRkiitnidGlrlerieqvlgekvs.tarlirid.n 62 
                                    l +G+pG+gKt+ a  +  + +      +g +i+ +  G   er++q+++++ + ++ +i id +
  gi|116753844|ref|YP_842962.1| 216 LLHGPPGTGKTLLAraLASETNAhfETLSGPEIMSKYYGESEERLRQLFKTAEEnAPSIILIDeI 280
                                    679********865114444444333337999999999999999999999999888999988841 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.35
                            Zot  28 egRkiitnidGlrlerieqvlgekvstarliridnpegaetlkefakwatidkgallviDE 88 
                                    +g ++  +  G   ++++  ++++++                         +  a++++DE
  gi|116753844|ref|YP_842962.1| 517 KGPEFLSKWVGESERAVRETFRKAKQ-------------------------AAPAVVFFDE 552
                                    33333333333333333333333333.........................2334444444 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.022       6.7       5      43 ..     214     252 ..     210     264 .. 0.77
   2 ?    4.0   0.0     0.096        29       5      29 ..     487     511 ..     483     533 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.022
                                    EEEEE-STTSSHHHHHHHHHHSS---B---SS-EEETTG CS
                          SRPRB   5 avllvGlsdsGKTslftrLttdsvkktvtSqessaalkv 43 
                                     vll G+  +GKT+l   L +++  +  t   +++  k+
  gi|116753844|ref|YP_842962.1| 214 GVLLHGPPGTGKTLLARALASETNAHFETLSGPEIMSKY 252
                                    699****************99987776666666666666 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.096
                                    EEEEE-STTSSHHHHHHHHHHSS-- CS
                          SRPRB   5 avllvGlsdsGKTslftrLttdsvk 29 
                                     +ll G+  +GKT+l + + t+s  
  gi|116753844|ref|YP_842962.1| 487 GILLYGPPGTGKTLLAKAVATESQA 511
                                    589************9999888654 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 ?    6.6   0.0     0.013       3.9     139     196 ..     217     294 ..     150     301 .. 0.64
   2 ?    2.9   0.0      0.18        55      13      45 ..     478     510 ..     472     583 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.013
                     KAP_NTPase 139 s.....................raaklkeeaplkklqteveelladmektLdalqkrlVvviDdLDrceteevlqllea 196
                                                              l+  + + k   e ee l +++kt ++ + + +++iD++D++ +++   + e+
  gi|116753844|ref|YP_842962.1| 217 LhgppgtgktllaralasetnaHFETLSGPEIMSKYYGESEERLRQLFKTAEE-NAPSIILIDEIDSIAPKREEVTGEV 294
                                    05555555555555555555333334555566666667788888888888888.9999**********99987776665 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.18
                     KAP_NTPase  13 septlatpivvgLygkWGsGKssllnkledelk 45 
                                     ++++++p  + Lyg+ G+GK+ l + +  e +
  gi|116753844|ref|YP_842962.1| 478 EHMKASPPKGILLYGPPGTGKTLLAKAVATESQ 510
                                    56677899999***********99988777655 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 ?    4.3   0.0      0.11        34      21      38 ..     212     228 ..     204     240 .. 0.82
   2 ?    5.7   0.0     0.039        12      21      42 ..     485     505 ..     465     509 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.11
                         AAA_29  21 lkgatlltGpsGsGKSTl 38 
                                    +kg +ll Gp G+GK+ l
  gi|116753844|ref|YP_842962.1| 212 PKG-VLLHGPPGTGKTLL 228
                                    567.9**********865 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.039
                         AAA_29  21 lkgatlltGpsGsGKSTllDAi 42 
                                    +kg +ll Gp G+GK+ l  A+
  gi|116753844|ref|YP_842962.1| 485 PKG-ILLYGPPGTGKTLLAKAV 505
                                    456.9**********8776665 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0     0.021       6.4      56      77 ..     215     236 ..     205     246 .. 0.86
   2 ?    3.2   0.0      0.28        87      50      75 ..     482     507 ..     470     526 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.021
                                    EEEEE-TTSSHHHHHHHHHHHH CS
                         Torsin  56 lsfhGwtGtGknfvaeiiaenl 77 
                                    + +hG +GtGk  +a+ +a ++
  gi|116753844|ref|YP_842962.1| 215 VLLHGPPGTGKTLLARALASET 236
                                    569**************99875 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.28
                                    -SS-EEEEEEE-TTSSHHHHHHHHHH CS
                         Torsin  50 pkkpLvlsfhGwtGtGknfvaeiiae 75 
                                    ++ p  + ++G +GtGk  +a+ +a 
  gi|116753844|ref|YP_842962.1| 482 ASPPKGILLYGPPGTGKTLLAKAVAT 507
                                    4455667799***********99986 PP

>> DAP3  Mitochondrial ribosomal death-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.22        68      25      39 ..     214     228 ..     203     240 .. 0.81
   2 ?    6.7   0.0     0.012       3.6      16      53 ..     478     514 ..     467     539 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.22
                                    EEEEE-SSSSSTTTT CS
                           DAP3  25 rlvltGekgsGKSvl 39 
                                     ++l+G +g+GK++l
  gi|116753844|ref|YP_842962.1| 214 GVLLHGPPGTGKTLL 228
                                    579*********975 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.012
                                    TS-SSS---EEEEE-SSSSSTTTTHHHHHHHGGGS--E CS
                           DAP3  16 kadkkkkvkrlvltGekgsGKSvlLlqalayAlekgwv 53 
                                    +  k+++ k ++l+G +g+GK++ L++a+a   +++++
  gi|116753844|ref|YP_842962.1| 478 EHMKASPPKGILLYGPPGTGKTL-LAKAVATESQANFI 514
                                    55678899999**********86.67776665555555 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0      0.16        47       3      31 ..     213     241 ..     211     248 .. 0.86
   2 ?   -0.3   0.0       2.4   7.2e+02      75      95 ..     249     269 ..     244     287 .. 0.80
   3 ?    3.3   0.0      0.19        58       4      30 ..     487     513 ..     485     519 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.16
                                    SEEEEESTTTSSHHHHHHHHHHHSTTTEE CS
                  Guanylate_kin   3 rpvvlvgpsgaGksslkkaLlselpekfg 31 
                                    + v l gp g+Gk  l  aL se + +f 
  gi|116753844|ref|YP_842962.1| 213 KGVLLHGPPGTGKTLLARALASETNAHFE 241
                                    56899*****************9999985 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 2.4
                                    TTEEEEEEHHHHHHHHHTTSE CS
                  Guanylate_kin  75 sgnlygtsveaieevlekgki 95 
                                     +++yg+s e  ++ ++++ +
  gi|116753844|ref|YP_842962.1| 249 MSKYYGESEERLRQLFKTAEE 269
                                    579************999876 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.19
                                    EEEEESTTTSSHHHHHHHHHHHSTTTE CS
                  Guanylate_kin   4 pvvlvgpsgaGksslkkaLlselpekf 30 
                                     + l gp g+Gk  l ka+ +e + +f
  gi|116753844|ref|YP_842962.1| 487 GILLYGPPGTGKTLLAKAVATESQANF 513
                                    6899***************99998887 PP

>> cIII  cIII protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0    0.0012      0.35       5      32 ..     243     267 ..     241     270 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0012
                           cIII   5 LaGsGvMSAYYPtESELskkiRrLIRAA 32 
                                    L+G  +MS YY  ESE   ++R+L + A
  gi|116753844|ref|YP_842962.1| 243 LSGPEIMSKYY-GESE--ERLRQLFKTA 267
                                    9**********.5888..899**99877 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     0.088        27       2      25 ..     213     236 ..     212     244 .. 0.85
   2 ?    4.2   0.0      0.11        34       2      24 ..     486     508 ..     485     514 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.088
                      PduV-EutP   2 kkilliGkvgsGKttLtqalkgee 25 
                                    k +ll G+ g+GKt L++al  e+
  gi|116753844|ref|YP_842962.1| 213 KGVLLHGPPGTGKTLLARALASET 236
                                    5699****************8875 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.11
                      PduV-EutP   2 kkilliGkvgsGKttLtqalkge 24 
                                    k ill G+ g+GKt L++a+  e
  gi|116753844|ref|YP_842962.1| 486 KGILLYGPPGTGKTLLAKAVATE 508
                                    6699**************99765 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.14        41      20      45 ..     210     235 ..     200     243 .. 0.81
   2 ?    5.3   0.0     0.031       9.3      14      45 ..     477     508 ..     471     516 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.14
                                    HCTS-EEEEESTTSSCHHHHHHHHHH CS
                           PIF1  20 ekgklfFvtGsgGtgKtflwkallkk 45 
                                    e +k + ++G  GtgKt l +al + 
  gi|116753844|ref|YP_842962.1| 210 EAPKGVLLHGPPGTGKTLLARALASE 235
                                    67788899*************99876 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.031
                                    ......HCTS-EEEEESTTSSCHHHHHHHHHH CS
                           PIF1  14 ieavlnekgklfFvtGsgGtgKtflwkallkk 45 
                                     e ++++ +k + ++G  GtgKt l ka+ + 
  gi|116753844|ref|YP_842962.1| 477 FEHMKASPPKGILLYGPPGTGKTLLAKAVATE 508
                                    56677788999**************9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (719 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); expected 17.9 (0.001)
Passed Fwd filter:                        59  (0.00329076); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              59  [number of targets reported over threshold]
# CPU time: 0.80u 0.29s 00:00:01.09 Elapsed: 00:00:00.43
# Mc/sec: 4975.96
//
Query:       gi|116753845|ref|YP_842963.1|  [L=265]
Description: fructose-bisphosphate aldolase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.2e-59  200.9   0.1    2.6e-59  200.7   0.1    1.0  1  DeoC         DeoC/LacD family aldolase
     0.0036   16.9   0.0      0.004   16.8   0.0    1.3  1  OMPdecase    Orotidine 5'-phosphate decarboxylase / HUMPS fam
  ------ inclusion threshold ------
       0.05   14.0   0.0      0.096   13.1   0.0    1.5  1  Radical_SAM  Radical SAM superfamily


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 !  200.7   0.1   4.3e-63   2.6e-59       1     234 [.      21     236 ..      21     237 .. 0.99

  Alignments for each domain:
  == domain 1  score: 200.7 bits;  conditional E-value: 4.3e-63
                                    EEEEEECCSHHHHHHHHCTSSHHHHHHHHHHHHHHGGGSSEEEEETTTHHHHHHCSCTTSEEEEETECSSCCTTSTTEEE CS
                           DeoC   1 ivilavDqrvankddtasaqneqledlkalvkealtpgasavlldpgviasaskeyakdiallvkldkgtyllkskqrdv 80 
                                    +vi+++D++   +++ +       +dl+a v++++++ga+avl + g+ + ++++y+kd++l+++l+++t l ++++++v
  gi|116753845|ref|YP_842963.1|  21 TVIVPMDHGLTVGPIPGL------IDLAAAVDKVAEGGANAVLGHMGLPLYGHRGYGKDVGLIIHLSASTSLGPDANHKV 94 
                                    69****************......9******************************************************* PP

                                    ETTCHHHHHHHTT-SEEEEEEEEHTTTTCHHHHHHHHHHHHHHHHHHHTEEEEEEEEE-CTTBSSTTCHHHHHHHHHHHH CS
                           DeoC  81 devasveeakalGAdavkvvvyyradgseeeqqklaeikrvkeacheeglplilelylrdeaikdekvdpdlvaeAarvs 160
                                    + v+ ve a++ GAd v+++v++   g+e+e+++l+++++v+ +c+ +g+pl++++y+r++++  e+ + + v++Aarv+
  gi|116753845|ref|YP_842963.1|  95 L-VTRVEDAIRVGADGVSIHVNV---GAEDEAEMLRDLGMVARRCDLWGMPLLAMMYPRGAKVRSEH-SVEYVKHAARVG 169
                                    *.*********************...*****************************************.************ PP

                                    TCCT-SEEEE--SSCC.B.HHHHHHHHHHHHHCHSSTEEEEETTS...SHHHHHHHHHHHHHHHTHCEEEESHHHHT CS
                           DeoC 161 aelGaDiiKvevpkevvnateedaevfkdvikaapvpgvvlsGGv...seedfletvedAvkeagasGvlsGRaifq 234
                                    aelG+Di+K++++        ++ e+f++v++++p p vv++GG+   +e+d+l++v dA+ +aga+G+++GR+ifq
  gi|116753845|ref|YP_842963.1| 170 AELGVDIVKTNYT--------GSPETFREVVRGCPAP-VVIAGGPkmdTEADLLQMVYDAM-QAGAAGISIGRNIFQ 236
                                    *************........****************.***********************.**************9 PP

>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   6.8e-07     0.004      83     219 ..     103     241 ..      28     247 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6.8e-07
                                    HHTTESEEEEEGTGH....HHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHHHSHHHHHHHHHHHHHHHTTESEEECC CS
                      OMPdecase  83 ikewadivtvhavaG....kasvkalaeaaekwgnrgllilaqmsskgnlmlqekgytqacveaarehkaedfvmGfvaq 158
                                    i  +ad v +h+ +G     ++++ l  +a++++  g+ +la+m   g+  + e     + v++a++  ae    G+   
  gi|116753845|ref|YP_842963.1| 103 IRVGADGVSIHVNVGaedeAEMLRDLGMVARRCDLWGMPLLAMMYPRGAKVRSE--HSVEYVKHAARVGAE---LGVDIV 177
                                    555666666666665333357888888899998888999999999999999999..999********9999...677666 PP

                                    CHTHHHHHHTTCSCEEEHHHTT......EEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSHH CS
                      OMPdecase 159 etlnateedaddfihltpgigl......eqggdgkgqqyntpekligiagadiiivGRgIlkagdpv 219
                                    +t   t  + ++f  +++g+ +        + d+++   +++ +++ +aga  i +GR I++a++p 
  gi|116753845|ref|YP_842963.1| 178 KTNY-T-GSPETFREVVRGCPApvviagGPKMDTEADLLQMVYDAM-QAGAAGISIGRNIFQAENPT 241
                                    6644.2.22469**********999555444444444444455554.599***************96 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.6e-05     0.096      35     160 ..      42     191 ..      29     193 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.6e-05
                                    HHHHHHHHHHTTSEEEEEESSTGGGS.....................TTHHHHHHHHHHTC...CCTEEEEEEECSSCHG CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx.....................xxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx RF
                    Radical_SAM  35 leevkelkaekgvkevilgggeplly.....................pdfvellerlakla...vpgiritvetngtlpd 90 
                                    ++ v+++ ae g++ v+ ++g pl+                      pd   +++  + ++   v    +++ +n +   
  gi|116753845|ref|YP_842963.1|  42 AAAVDKV-AEGGANAVLGHMGLPLYGhrgygkdvgliihlsastslgPDANHKVLVTRVEDairVGADGVSIHVNVGA-- 118
                                    5566666.5767888888888888886666655555555555555554444444444444344434444444444444.. PP

                                    HHHHHHHHHTT.....-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHH CS
                                    xxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  91 eeklerllelg.....vdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGendeel 160
                                    e+ +e l++lg     +d   ++l a  +     +++  h++e v+ a +  +e+g++ v+++++g p e+++e+
  gi|116753845|ref|YP_842963.1| 119 EDEAEMLRDLGmvarrCDLWGMPLLAMMYP-RGAKVRSEHSVEYVKHAARVGAELGVDIVKTNYTGSP-ETFREV 191
                                    788999999999999999999999999997.66666699*****************************.887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 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:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2023.65
//
Query:       gi|116753846|ref|YP_842964.1|  [L=870]
Description: ATP-dependent helicase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.4e-49  166.9   0.0      9e-49  165.9   0.0    1.6  1  DEAD_assoc  DEAD/H associated
      2e-29  102.6   0.0    1.4e-28   99.9   0.0    2.3  2  DEAD        DEAD/DEAH box helicase
    6.9e-19   68.2   0.0    2.5e-17   63.2   0.0    2.5  2  Helicase_C  Helicase conserved C-terminal domain
    3.9e-05   23.7   0.0    0.00021   21.4   0.0    2.0  2  ResIII      Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
       0.13   12.6   0.0       0.53   10.6   0.0    2.0  2  AAA_19      AAA domain
       0.15   12.3   0.2          2    8.7   0.2    2.8  1  AAA_22      AAA domain


Domain annotation for each model (and alignments):
>> DEAD_assoc  DEAD/H associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.9   0.0     3e-52     9e-49       1     191 []     644     832 ..     644     832 .. 0.97

  Alignments for each domain:
  == domain 1  score: 165.9 bits;  conditional E-value: 3e-52
                     DEAD_assoc   1 lPtdrtllvErfrdelgdwrlvvhspfGrrvnealalllaarlsrrfgidvqvaanDdgivlllpleerlpllldellel 80 
                                    ++tdr+++vE++rd  g++ +++ + +G r+n+++++++a+ lsr+  ++v v+++D g++l++p++++++    ++l++
  gi|116753846|ref|YP_842964.1| 644 ISTDRRIVVEETRDTKGKMVYYFLTNYGLRFNDGFSRMVAYLLSREGRSNVLVSIADTGFMLSIPEKSKAD--PIAALKS 721
                                    689***********************************************************998777765..456899* PP

                     DEAD_assoc  81 lspdeleedleaalnaselfkrrFrevAaralllprrypgkrkplwqqrlraaqLldvareypdfpllleavrevledql 160
                                    ++p++ e++l++a+++++l+kr Fr +A+r+++++r+y g+rk++++q+++a++L+  a++++df +l+e +re++ed++
  gi|116753846|ref|YP_842964.1| 722 IRPEMCEDLLRRAVENTNLLKRVFRINATRFFMILRNYMGHRKSARRQQVSADMLIGLAKRLEDFAVLKESYREIIEDKF 801
                                    ******************************************************************************** PP

                     DEAD_assoc 161 DlerlaellrriaageirvvevetprpSpfA 191
                                    +l++++ +++ i++g+i++v+ ++p+p p+A
  gi|116753846|ref|YP_842964.1| 802 ELDNIKSVVEAISTGDIEIVKKRSPSPGPMA 832
                                    *********************9999999998 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.9   0.0   4.6e-32   1.4e-28       1     170 [.      32     220 ..      32     227 .. 0.88
   2 ?   -0.9   0.0      0.41   1.2e+03      82     125 ..     759     809 ..     725     810 .. 0.62

  Alignments for each domain:
  == domain 1  score: 99.9 bits;  conditional E-value: 4.6e-32
                                    -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHS....TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                           DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyet....kgktgpkalivePtreLaeqtlnnlkkfkkyid. 75 
                                    t+ Q+ a+pli  g++vl++ +TGsGKTl ++i ++++++        ++   +l+v+P+r+La+++++nl++ + +i+ 
  gi|116753846|ref|YP_842964.1|  32 TPPQRLAVPLIHAGRSVLISSPTGSGKTLSAFISIINSLFILsrtdGLENSVYCLYVSPLRSLANDIHRNLERPLTEIQe 111
                                    688*********************************988766667778999************************97777 PP

                                    ...........SEEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSH..CTTEEEEEEETHHHHHHTTTHHHH CS
                                    ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  76 ...........lrvlliiggvaardqlskldngvdivvgtpgrlddllstgkln..lsqvrflVlDEadrlldqgfsdfi 142
                                               +r     g+v+ ++  + l+++++i+ +tp+ l+ ll++ +++  l+ +r++V+DE++ l  ++++ ++
  gi|116753846|ref|YP_842964.1| 112 iaaerriesveIRHAIRHGDVSSSERAKMLRKTPHILNTTPESLALLLNSPRFRekLRTIRWVVVDEIHSLAGSKRGVHL 191
                                    778877777666666667889999999999999*************9965555555************************ PP

                                    HHHHHHSHHHCTTST.TTSEEEEEESSBS CS
                                    xxxxxxxxxxxxxxx.xxxxxxxxxxxxx RF
                           DEAD 143 nrilnqlpqitcdgk.lqrqvivlSATlp 170
                                    +  l++l++ + ++  ++   i +SAT++
  gi|116753846|ref|YP_842964.1| 192 SLSLERLEELKRETGgESFVRIGCSATIE 220
                                    *******9999999877777*******96 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.41
                                    ETTSSHHHHHHHHHTTCSEEEEEHHHHHHHH.........HCTSSHCTTEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxx RF
                           DEAD  82 iggvaardqlskldngvdivvgtpgrlddll.........stgklnlsqvrfl 125
                                    + g++++  ++++  ++d+++g  +rl d+           + k++l++++ +
  gi|116753846|ref|YP_842964.1| 759 YMGHRKSARRQQV--SADMLIGLAKRLEDFAvlkesyreiIEDKFELDNIKSV 809
                                    4455555555555..799*********99655666655543445556666655 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 ?    2.1   0.0     0.079   2.4e+02      39      62 ..     117     144 ..      94     154 .. 0.78
   2 !   63.2   0.0   8.4e-21   2.5e-17       5     108 ..     269     379 ..     265     381 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.079
                                    T....TSTEEEESTTSTHHHHHHHHHHH CS
                     Helicase_C  39 k....gikvavlhgelpqnereeileqf 62 
                                    +    +i+ a+ hg+ +++er ++l++ 
  gi|116753846|ref|YP_842964.1| 117 RiesvEIRHAIRHGDVSSSERAKMLRKT 144
                                    2333489****************99986 PP

  == domain 2  score: 63.2 bits;  conditional E-value: 8.4e-21
                                    HHHHHH.HHTTTTSEEEEEESSHHHHHHHHHH........HHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGG CS
                     Helicase_C   5 allell.kleeeggkilifvntidrlekvkll........lekkgikvavlhgelpqnereeileqfnkgesdvLiatdv 75 
                                    al+e l +l +e++++l+f+nt++ +e  ++l         + ++ ++ ++hg++ + +r+++ e+ ++g+ +v+ +++ 
  gi|116753846|ref|YP_842964.1| 269 ALYETLdELIQEHRNTLVFTNTRNGAE--RILynlrarypDRYNESNSGCHHGSMGKTSRLDVEERLKSGDLKVVTSSTS 346
                                    56777777779*************887..4443322333255559*********************************** PP

                                    GTSSSTSTTESEEEESSSSSSHHHHHHHHTTSS CS
                     Helicase_C  76 aerGidipkvnlVinfdlprnvtsyiqriGRtg 108
                                    +e Gid+p ++lV +++ p++v+ + qriGR+g
  gi|116753846|ref|YP_842964.1| 347 LELGIDMPHLDLVLQIGSPKSVAALLQRIGRAG 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 !   21.4   0.0     7e-08   0.00021      25     170 ..      46     220 ..      20     221 .. 0.72
   2 ?   -1.0   0.0      0.51   1.5e+03      45      85 ..     274     318 ..     268     346 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 7e-08
                                    SEEEEEESTTSTHHHHH.HHHHHHH-S...........-EEEEESSHHHHHHHHHHGGGGTGG...............GE CS
                         ResIII  25 krglikmaTGtGKTlva.aklierllkkgkee......kflflvprkslleqtleefkkflseayke...........ig 86 
                                    + +li  +TG+GKTl a +++i +l+   + +       +l + p +sl +   +++++ l e ++              
  gi|116753846|ref|YP_842964.1|  46 RSVLISSPTGSGKTLSAfISIINSLFILSRTDglensvYCLYVSPLRSLANDIHRNLERPLTEIQEIaaerriesveiR- 124
                                    5789*************99******998777799999999**************9997777765444433432222221. PP

                                    EEESSS-B--................-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T.......TT CS
                         ResIII  87 kkvsgdkkka.........kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk.......sw 150
                                          + ++          +  +++ +il tt +sl   +   ++ + + +  ++  +++DE H l+++k       s 
  gi|116753846|ref|YP_842964.1| 125 ------HAIRhgdvssserAKMLRKTPHILNTTPESLALLL---NSPRFREKLRTIRWVVVDEIHSLAGSKrgvhlslSL 195
                                    ......22224433333433345677777777777777777...6666666666777************85666666666 PP

                                    HHHHHT---......SEEEEEESS-S CS
                         ResIII 151 reilekfke......avllglTATpe 170
                                    +++ e   +      +v++g +AT+e
  gi|116753846|ref|YP_842964.1| 196 ERLEELK-RetggesFVRIGCSATIE 220
                                    6643333.335666699999999985 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.51
                                    HHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG..........G CS
                         ResIII  45 ierllkkgkeekflflvprkslleqtleefkkflseayke......i 85 
                                     ++l ++++  ++l++ ++++  e+ l +++  +++ y+e      +
  gi|116753846|ref|YP_842964.1| 274 LDELIQEHR--NTLVFTNTRNGAERILYNLRARYPDRYNEsnsgchH 318
                                    566777655..99*******999999999999999988775544431 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00018      0.53       1     113 [.      35     181 ..      35     191 .. 0.63
   2 ?   -4.0   0.0       5.5   1.6e+04      42      62 ..     281     301 ..     269     339 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00018
                         AAA_19   1 qreave.alkekvllvtaGpGtGKTr..vlkhivall..velgg.vkpeeillvaftgrAakelrerlaalgaeatTiHr 74 
                                    qr av   ++ + +l+  + G+GKT    +  i +l+   ++ g ++   +l v++ +  a+ ++ +l   +++ t i +
  gi|116753846|ref|YP_842964.1|  35 QRLAVPlIHAGRSVLISSPTGSGKTLsaFISIINSLFilSRTDGlENSVYCLYVSPLRSLANDIHRNL---ERPLTEIQE 111
                                    7788877888999999999******62233333333300333331334779999***********999...566444444 PP

                         AAA_19  75 lal.................................ldfddlltealelleeaeeekklqeeellivDEfqd 113
                                    +a                                  l+++++    + ll++ + ++kl+   +++vDE+  
  gi|116753846|ref|YP_842964.1| 112 IAAerriesveirhairhgdvssserakmlrktphiLNTTPES--LALLLNSPRFREKLRTIRWVVVDEIHS 181
                                    4444455555555555555555555555555554444555544..445677888999996666******876 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 5.5
                         AAA_19  42 peeillvaftgrAakelrerl 62 
                                     ++ l+ + t+  a+++  +l
  gi|116753846|ref|YP_842964.1| 281 HRNTLVFTNTRNGAERILYNL 301
                                    367788888888888876555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.2   0.00065         2       6     113 ..      46     202 ..      42     221 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00065
                         AAA_22   6 gilvvtGesGtGKTtllr.rlleqldeeakaeeerpevv..fvtlpsstsskdllrellralglelka............ 70 
                                    +++++  ++G+GKT+++   + ++l         r + +  +v++   + +++l++++ r+l+++l +            
  gi|116753846|ref|YP_842964.1|  46 RSVLISSPTGSGKTLSAFiSIINSLF-----ILSRTDGLenSVYCLYVSPLRSLANDIHRNLERPLTEiqeiaaerries 120
                                    67788889999999987413344431.....1123333347777777777899999999999999999999999999999 PP

                         AAA_22  71 .............................erlsseellealeqalrarav.................ielliiDEaqhlr 104
                                                                  +                                    i+ +++DE++ l 
  gi|116753846|ref|YP_842964.1| 121 veirhairhgdvssserakmlrktphilnTTP-----------------EslalllnsprfreklrtIRWVVVDEIHSLA 183
                                    99999999999977777777666666433111.................122222222333444556899*********8 PP

                         AAA_22 105 ...s.......eealeeLr 113
                                       +        e leeL+
  gi|116753846|ref|YP_842964.1| 184 gskRgvhlslsLERLEELK 202
                                    8651455544466666663 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (870 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.66u 0.27s 00:00:00.93 Elapsed: 00:00:00.44
# Mc/sec: 5957.20
//
Query:       gi|116753847|ref|YP_842965.1|  [L=235]
Description: phosphoesterase, putative [Methanosaeta thermophila PT]
Scores for complete 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   18.7   1.1     0.0046   17.5   0.4    1.7  1  Metallophos  Calcineurin-like phosphoesterase
  ------ inclusion threshold ------
       0.15   11.8   0.3       0.48   10.3   0.2    1.8  2  DBD_HTH      Putative DNA-binding 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 !   17.5   0.4   5.2e-07    0.0046       4      87 ..      29     123 ..      27     154 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 5.2e-07
                                    EEEESBTB...........TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSS.SHHHHHHHHHHHHHHHH...TSEEE CS
                    Metallophos   4 lvigDlHl...........algggqlddllkllddllreekpdlvllaGDlvdr.gdlekellellaalvky...pipvy 68 
                                     v++D+H+                  ++ll+ ++ +l++ +p  ++laGD+v+  g  ++++ + l+a ++    +  ++
  gi|116753847|ref|YP_842965.1|  29 CVLSDIHIgleeellaqglVFPLREKEELLRRIEIILAKLNPKRFVLAGDVVHSfGRADQRIRRKLDAILNTirsRCDLV 108
                                    589***********99777555556666666666668888*************95699999999999999999888888* PP

                                    EEC-TTSCHHHHHHHHHHH CS
                    Metallophos  69 lllGNHegfeeellnkygy 87 
                                    l+ G H+    ++l+  g+
  gi|116753847|ref|YP_842965.1| 109 LISGTHD----GMLPYMGF 123
                                    *******....44443333 PP

>> DBD_HTH  Putative DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0      0.94   8.5e+03       6      16 ..      59      69 ..      59      73 .. 0.80
   2 ?   10.3   0.2   5.3e-05      0.48       4      30 ..      90     117 ..      90     118 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.94
                        DBD_HTH  6 rqLdklLDsld 16
                                   r+++ +L +l+
  gi|116753847|ref|YP_842965.1| 59 RRIEIILAKLN 69
                                   89998887776 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 5.3e-05
                        DBD_HTH   4 rRrqLdklLDsldDk.eLsiieatakGI 30 
                                    +Rr+Ld++L++   + +L++i +t +G 
  gi|116753847|ref|YP_842965.1|  90 IRRKLDAILNTIRSRcDLVLISGTHDGM 117
                                    5***********8766********9885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); 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 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1761.21
//
Query:       gi|116753848|ref|YP_842966.1|  [L=403]
Description: SufBD protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-51  174.2   0.0    3.8e-51  173.9   0.0    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 !  173.9   0.0   2.1e-55   3.8e-51       2     218 .]     152     374 ..     151     374 .. 0.96

  Alignments for each domain:
  == domain 1  score: 173.9 bits;  conditional E-value: 2.1e-55
                        UPF0051   2 qfertlivveegaevtiieeyagc............gvveifvgenAklkyvkvqnwsedavnlstkraeegrdaklelt 69 
                                    q ++++i++eeg+e+++i   +gc            gv+e+f++++A++++++++nw++++ + +++++  ++ a+l+ +
  gi|116753848|ref|YP_842966.1| 152 QRVHNIIIAEEGSELHVI---TGCttpshvqrglhlGVSEFFIKKGAHVSFTMIHNWGREVEVRPRTAIYMEGGATLSNN 228
                                    789***************...999999999999999*********************************9999******* PP

                        UPF0051  70 tvslggkltrk.epsvelkgegaeaelnglylakgkqhldtrtkvdhngpntssrilskgvlkdearavfrgkikvrkga 148
                                    ++ l  + t++ +p++ l+g+ga a++n++++ak++ hldt+++v +++p++s++ ++++v+  +++++ rgk+ v +  
  gi|116753848|ref|YP_842966.1| 229 YICLTPAKTLQtYPKAILDGPGAVASFNTVLYAKEG-HLDTGSEVVLRAPGCSADSITRAVSV-GGEIITRGKM-VGE-V 304
                                    **99988775559*********************95.9*************************.599*******.555.9 PP

                        UPF0051 149 qktdahqenrnLllsdkaradtiPeleidaddvkasHgAtvGkideeqlfYLmsRGlseeeArrlivrgf 218
                                       +ah e+  L+ls+k+r+d+iPel  + +   +sH+A+vGki+e++l YLm+RGl++++A+ +ivrgf
  gi|116753848|ref|YP_842966.1| 305 PDVKAHLECVGLILSEKGRIDSIPELDGRCGGLDMSHEAAVGKISEQELEYLMARGLTKDQATGVIVRGF 374
                                    *********************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); 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 0.23s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2994.24
//
Query:       gi|116753849|ref|YP_842967.1|  [L=245]
Description: ABC transporter related [Methanosaeta thermophila PT]
Scores for complete 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   93.9   0.0    1.7e-26   93.4   0.0    1.2  1  ABC_tran     ABC transporter
      5e-09   36.4   0.6     0.0023   17.8   0.1    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    0.00012   21.6   0.2       0.31   10.4   0.2    2.2  2  SMC_N        RecF/RecN/SMC N terminal domain
     0.0028   18.2   1.4     0.0035   17.9   0.4    1.5  2  AAA_23       AAA domain
     0.0038   16.9   0.0     0.0071   16.1   0.0    1.4  1  AAA_29       P-loop containing region of AAA domain
      0.009   16.4   0.0      0.013   15.9   0.0    1.3  1  AAA_16       AAA ATPase domain
  ------ inclusion threshold ------
      0.013   16.0   0.1       0.05   14.0   0.0    1.9  2  AAA          ATPase family associated with various cellular a
      0.015   15.2   0.0      0.031   14.2   0.0    1.5  1  ATPase_2     ATPase domain predominantly from Archaea
      0.019   15.3   0.1       0.41   10.9   0.0    2.3  2  AAA_22       AAA domain
       0.03   14.2   0.0      0.049   13.5   0.0    1.3  1  RsgA_GTPase  RsgA GTPase
      0.034   14.2   0.0       0.72    9.9   0.0    2.5  2  AAA_14       AAA domain
      0.043   13.1   0.0        1.3    8.2   0.0    2.1  2  Zeta_toxin   Zeta toxin
      0.065   13.5   0.0        0.1   12.8   0.0    1.3  1  AAA_28       AAA domain
      0.081   13.5   0.0        8.6    6.9   0.0    2.2  2  AAA_18       AAA domain
        0.1   12.1   0.0        0.2   11.2   0.0    1.4  1  AAA_25       AAA domain
       0.11   12.6   0.0       0.18   11.9   0.0    1.4  1  MMR_HSR1     50S ribosome-binding GTPase
       0.12   12.3   0.0       0.22   11.4   0.0    1.4  1  NACHT        NACHT domain
       0.17   11.5   0.0       0.32   10.6   0.0    1.2  1  ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-bindi
        0.2   11.4   0.0       0.26   11.0   0.0    1.3  1  AAA_24       AAA domain
       0.22   10.6   0.1        2.3    7.4   0.0    2.0  2  NB-ARC       NB-ARC domain
       0.24   10.2   0.0       0.31    9.8   0.0    1.1  1  DLIC         Dynein light intermediate chain (DLIC)


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 !   93.4   0.0   1.9e-29   1.7e-26       1     136 [.      20     159 ..      20     160 .. 0.96

  Alignments for each domain:
  == domain 1  score: 93.4 bits;  conditional E-value: 1.9e-29
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--..SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp..teGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvr 77 
                                    lk ++lk+++ge +a++G+nG+GK+tLl+++ag  +   + G+il++g+d+++    e++r  ig+ +q p   ++l+++
  gi|116753849|ref|YP_842967.1|  20 LKGINLKINRGENHALFGPNGCGKTTLLNTIAGVPRYivERGRILFKGNDITHlSMDERARMGIGIAFQSPPAIRGLKLK 99 
                                    789******************************877767**************99999*******************999 PP

                                    HH....HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    xx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  78 en....esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                    +     + ++++ek+l++++  e++d+ v    + +SgG+ +r +la++l+++p+l++lDEp 
  gi|116753849|ref|YP_842967.1| 100 DLiklcNPEVNPEKVLKEVNFLEFADREV---NRGFSGGEIKRSELAQLLAQRPELVMLDEPD 159
                                    99***************************...799**************************95 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   2.7e-06    0.0023       3      22 ..      34      53 ..      33      79 .. 0.76
   2 !   17.5   0.1   3.3e-06    0.0028     224     288 ..     119     186 ..      64     201 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.7e-06
                         AAA_21  3 vliGpNgsGKSnLLdaldll 22
                                   +l GpNg+GK++LL ++ ++
  gi|116753849|ref|YP_842967.1| 34 ALFGPNGCGKTTLLNTIAGV 53
                                   799**************887 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 3.3e-06
                         AAA_21 224 lengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr......n 288
                                    +  ++      r +S G  +   l+ +l++++    l+ +DEp++g + + ++ + + +++l++      +
  gi|116753849|ref|YP_842967.1| 119 NFLEFADREVNRGFSGGEIKRSELAQLLAQRP---ELVMLDEPDSGVDLENIKLIGRAINKLTEkdtkpsK 186
                                    55555556666677777777767777777777...9***********************888885555554 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.2   0.00037      0.31      27      44 ..      33      50 ..      20      53 .. 0.83
   2 !    9.1   0.0   0.00091      0.78     137     188 ..     132     179 ..      84     187 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00037
                                   EEEEESTTSSHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxx RF
                          SMC_N 27 taivGpNGSGKsnlldAi 44
                                    a+ GpNG+GK+ ll+ i
  gi|116753849|ref|YP_842967.1| 33 HALFGPNGCGKTTLLNTI 50
                                   5899**********9988 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00091
                                    S-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 137 LSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksk 188
                                    +SgGe + + la l+A    ++  l++lDe d+  D +n+k + + +++ ++
  gi|116753849|ref|YP_842967.1| 132 FSGGEIKRSELAQLLA----QRPELVMLDEPDSGVDLENIKLIGRAINKLTE 179
                                    6999999999998877....445699*********************99876 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.4   4.2e-06    0.0035      23      40 ..      34      51 ..      19      53 .. 0.85
   2 ?   -2.5   0.0       7.2   6.2e+03     127     127 ..     155     155 ..     109     191 .. 0.52

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 4.2e-06
                         AAA_23 23 lItGpNGaGKTTildAik 40
                                   +++GpNG+GKTT+l+ i 
  gi|116753849|ref|YP_842967.1| 34 ALFGPNGCGKTTLLNTIA 51
                                   689***********9885 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 7.2
                         AAA_23 127 s 127
                                     
  gi|116753849|ref|YP_842967.1| 155 L 155
                                    1 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   8.3e-06    0.0071      16      42 ..      24      50 ..      18      53 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.3e-06
                         AAA_29 16 tieidlkgatlltGpsGsGKSTllDAi 42
                                    ++i++ +++ l Gp+G GK+Tll  i
  gi|116753849|ref|YP_842967.1| 24 NLKINRGENHALFGPNGCGKTTLLNTI 50
                                   57888777***************9766 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.5e-05     0.013      22      88 ..      28     107 ..      20     184 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.5e-05
                         AAA_16  22 grpelvllsGesGvGKsslvrell...ralekdggiflrgkcdql.esa........ipy.sa.laqalareellrqlld 87 
                                    +r+e+  l G+ G+GK++l+++++   r++ ++g i+++g+   + +++        i++ s+  ++ l+  + l +l++
  gi|116753849|ref|YP_842967.1|  28 NRGENHALFGPNGCGKTTLLNTIAgvpRYIVERGRILFKGNDITHlSMDerarmgigIAFqSPpAIRGLKL-KDLIKLCN 106
                                    455777899***********888733358888877777777666653333334444444465557777744.44444444 PP

                         AAA_16  88 e 88 
                                    +
  gi|116753849|ref|YP_842967.1| 107 P 107
                                    4 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   5.8e-05      0.05       3      20 ..      35      52 ..      33      93 .. 0.87
   2 ?   -0.4   0.0       1.6   1.4e+03      57      71 ..     147     162 ..      99     195 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.8e-05
                                   EESSTTSSHHHHHHHHHH CS
                            AAA  3 lyGppGtGKTllakavak 20
                                   l+Gp G+GKT+l + +a 
  gi|116753849|ref|YP_842967.1| 35 LFGPNGCGKTTLLNTIAG 52
                                   89***********99996 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.6
                                    S.TSEEEEEETGGGHH CS
                            AAA  57 a.kpsilfiDEidala 71 
                                    a +p  +++DE d+ +
  gi|116753849|ref|YP_842967.1| 147 AqRPELVMLDEPDSGV 162
                                    2347889999988755 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   3.6e-05     0.031      16      41 ..      28      51 ..      18      58 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.6e-05
                       ATPase_2 16 erepneiyfiYGpegsGKtaLlkeii 41
                                   +r++n+   ++Gp g+GKt+Ll+ i+
  gi|116753849|ref|YP_842967.1| 28 NRGENH--ALFGPNGCGKTTLLNTIA 51
                                   554444..578***********9986 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   0.00048      0.41       9      25 ..      34      50 ..      28      57 .. 0.89
   2 ?    1.9   0.0       0.3   2.5e+02      38     112 ..     148     170 ..     122     235 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00048
                         AAA_22  9 vvtGesGtGKTtllrrl 25
                                   +++G+ G+GKTtll+++
  gi|116753849|ref|YP_842967.1| 34 ALFGPNGCGKTTLLNTI 50
                                   79***********9986 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.3
                         AAA_22  38 erpevvfvtlpsstsskdllrellralglelkaerlsseellealeqalraravielliiDEaqhlrseealeeL 112
                                    +rpe+v  + p s+                                                   +   e+++ +
  gi|116753849|ref|YP_842967.1| 148 QRPELVMLDEPDSG---------------------------------------------------V-DLENIKLI 170
                                    34444444444444...................................................3.22222222 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   5.8e-05     0.049      96     121 ..      26      52 ..       5      71 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.8e-05
                                    HCTT.SEEEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase  96 llkd.ktsvlvGqSGvGKStLinallp 121
                                    +++  +  +l G+ G GK+tL+n++++
  gi|116753849|ref|YP_842967.1|  26 KINRgENHALFGPNGCGKTTLLNTIAG 52 
                                    555448899***************987 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00085      0.72       6      23 ..      34      51 ..      30      82 .. 0.79
   2 ?    1.7   0.0      0.29   2.5e+02      91     105 ..     213     227 ..      98     237 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00085
                         AAA_14  6 vitGaRrvGKTtllkqli 23
                                   ++ G+  +GKTtll++++
  gi|116753849|ref|YP_842967.1| 34 ALFGPNGCGKTTLLNTIA 51
                                   678***********9997 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.29
                         AAA_14  91 knldvivtGSnskll 105
                                     ++ +++tGS   +l
  gi|116753849|ref|YP_842967.1| 213 MEGTIVCTGSPREIL 227
                                    245677777766666 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.08        68      23      37 ..      37      51 ..      32      64 .. 0.86
   2 ?    8.2   0.0    0.0015       1.3      87     127 ..     200     240 ..     173     243 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.08
                     Zeta_toxin 23 GqpGAGKselaellk 37
                                   G  G+GK++l++ ++
  gi|116753849|ref|YP_842967.1| 37 GPNGCGKTTLLNTIA 51
                                   789********9876 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0015
                     Zeta_toxin  87 llqeaiengyniivegtlrspdvvkklaealkkaGYevevv 127
                                    +l+++   + ++ +egt+  +  ++++ e++k +GYe  v+
  gi|116753849|ref|YP_842967.1| 200 ILDYISVDKAHVMMEGTIVCTGSPREILEQIKTRGYEGCVR 240
                                    78899999****************************97776 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00012       0.1       2      21 ..      33      52 ..      32      83 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00012
                         AAA_28  2 ivitGgestGKTtlleaLaa 21
                                    +++G+ ++GKTtll+ +a 
  gi|116753849|ref|YP_842967.1| 33 HALFGPNGCGKTTLLNTIAG 52
                                   5899************9984 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0      0.01       8.6       3      18 ..      35      50 ..      34      81 .. 0.87
   2 ?    4.6   0.0     0.053        46      37     116 ..     152     236 ..     122     237 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.01
                         AAA_18  3 ltGtpGvGKttlakeL 18
                                   l G+ G+GKttl + +
  gi|116753849|ref|YP_842967.1| 35 LFGPNGCGKTTLLNTI 50
                                   88*********98765 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.053
                         AAA_18  37 lllevdpealdeskrldedkldklldaleenss..aleegknlvidghlaeleseaakdikk.....vvLtaspeelleR 109
                                    l+  ++p+  +  + ++++   +++++l e +   + +  + +vi  +   l + +  +++      +v t sp e le 
  gi|116753849|ref|YP_842967.1| 152 LVMLDEPD--SGVDLENIKLIGRAINKLTEKDTkpSKRIRSGIVITHFGHILDYISVDKAHVmmegtIVCTGSPREILEQ 229
                                    55555555..555556666677777777777666655556665666554444444444444478999************* PP

                         AAA_18 110 lekRgye 116
                                    +++Rgye
  gi|116753849|ref|YP_842967.1| 230 IKTRGYE 236
                                    *****97 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00024       0.2      30      50 ..      27      47 ..      19      53 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00024
                         AAA_25 30 lpagelallaGapgtGKttla 50
                                   + +ge ++l+G+ g+GKttl+
  gi|116753849|ref|YP_842967.1| 27 INRGENHALFGPNGCGKTTLL 47
                                   679999*************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 ?   11.9   0.0   0.00021      0.18       3      40 ..      34      74 ..      32     119 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00021
                                   EEEESTTSSHHHHHHHHHTS...TEEESSSTTSSSSEEEEE CS
                       MMR_HSR1  3 aivGrpNvGKStLinaltge...kaivsdkpgtTrdinegr 40
                                   a++G    GK+tL+n++ g     ++ +++ ++  di++  
  gi|116753849|ref|YP_842967.1| 34 ALFGPNGCGKTTLLNTIAGVpryIVERGRILFKGNDITHLS 74
                                   899***************96623344466666666666655 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   0.00025      0.22       5      21 ..      35      51 ..      32      53 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00025
                                   EEC-TTTCHHHHHHHHH CS
                          NACHT  5 lqGeaGsGKTtLlqkla 21
                                   l G++G+GKTtLl  +a
  gi|116753849|ref|YP_842967.1| 35 LFGPNGCGKTTLLNTIA 51
                                   67************997 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 ?   10.6   0.0   0.00037      0.32      11      35 ..      27      51 ..      19      76 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00037
                                   EBTT-EEEEEESTTSSHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab 11 ivqGqrtlipgafgvGktvisqsls 35
                                   i +G++ +++g +g+Gkt+++++++
  gi|116753849|ref|YP_842967.1| 27 INRGENHALFGPNGCGKTTLLNTIA 51
                                   779******************9997 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00031      0.26       5      23 ..      33      53 ..      29     115 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00031
                         AAA_24  5 iliyGpsgiGKTtlakel..g 23
                                    +++Gp+g GKTtl++++   
  gi|116753849|ref|YP_842967.1| 33 HALFGPNGCGKTTLLNTIagV 53
                                   689*************99442 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0026       2.3      24      40 ..      34      50 ..      25      55 .. 0.89
   2 ?    0.9   0.0      0.24   2.1e+02      90     122 ..     136     168 ..     108     181 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0026
                                   EEEESTTSSHHHHHHHH CS
                         NB-ARC 24 alvGmgGvGKttlakqi 40
                                   al G  G+GKttl++ i
  gi|116753849|ref|YP_842967.1| 34 ALFGPNGCGKTTLLNTI 50
                                   689**********9987 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.24
                                    TSHHHHHHHHCCCTTEEEEEEEE-SHHHH.... CS
                         NB-ARC  90 eslkrklvrlLltkrfllvlDDVweeedwdkig 122
                                    e +  +l +lL ++  l++lD     +d+++i+
  gi|116753849|ref|YP_842967.1| 136 EIKRSELAQLLAQRPELVMLDEPDSGVDLENIK 168
                                    337789***************877777777776 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00036      0.31      21      74 ..      26      80 ..       8      90 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00036
                           DLIC 21 klPsgksvlvlGedgsGkttliaklqGveeekkGrG.leylyldvkdedrddltr 74
                                   k+  g +  ++G +g+Gkttl+  + Gv  +   rG + +   d+    +d+ +r
  gi|116753849|ref|YP_842967.1| 26 KINRGENHALFGPNGCGKTTLLNTIAGVPRYIVERGrILFKGNDITHLSMDERAR 80
                                   777888999*******************998777662334444555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 1816.14
//
Query:       gi|116753850|ref|YP_842968.1|  [L=117]
Description: hypothetical protein Mthe_0537 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00042   20.0   0.3     0.0014   18.4   0.3    1.8  1  SprB      SprB repeat
  ------ inclusion threshold ------
      0.028   14.4   0.0      0.038   14.0   0.0    1.2  1  BiPBP_C   Penicillin-Binding Protein C-terminus Family
      0.034   14.9   0.1       0.12   13.1   0.1    2.0  1  Big_7     Bacterial Ig domain


Domain annotation for each model (and alignments):
>> SprB  SprB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.3   2.3e-07    0.0014      19      32 ..      55      68 ..      54      72 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.3e-07
                           SprB 19 vtvsGGtapYtYsw 32
                                   +++sGG +pYtY+w
  gi|116753850|ref|YP_842968.1| 55 ASASGGRGPYTYEW 68
                                   79***********8 PP

>> BiPBP_C  Penicillin-Binding Protein C-terminus Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   6.4e-06     0.038       5      86 ..      28     109 ..      24     114 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.4e-06
                        BiPBP_C   5 assaasplrIafPadGailaldpdipkrqrlqlkarggea..plrWll.dgeplaetkrgrelawqp...epGrhrLtv. 77 
                                    + s++ + +I++P++Ga+l   p       +  +a+gg++  +++W+   +++l   ++g+++++++   ++G+h + v 
  gi|116753850|ref|YP_842968.1|  28 TGSTELAAKIISPKAGAVLSGGP-----VVMEASASGGRGpyTYEWWSsMNRYL---GSGSKIKVDSsglKKGEHLIVVk 99 
                                    55678899************998.....45999999997769565555267888...8888888888889*****98776 PP

                        BiPBP_C  78 .vDaaGrvdd 86 
                                      D +G+ ++
  gi|116753850|ref|YP_842968.1| 100 vRDSTGKEVQ 109
                                    6899998765 PP

>> Big_7  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   2.1e-05      0.12       4      28 ..      36      60 ..      34      98 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.1e-05
                                   EEEE--TT--EBTSEEEEEEEEE-S CS
                          Big_7  4 titsPangatvsggtvtisasAsdd 28
                                   +i+sP++ga++sgg+v  +asAs  
  gi|116753850|ref|YP_842968.1| 36 KIISPKAGAVLSGGPVVMEASASGG 60
                                   79********************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.26s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 832.23
//
Query:       gi|116753851|ref|YP_842969.1|  [L=187]
Description: hypothetical protein Mthe_0538 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-07   32.1   0.0    2.3e-07   31.4   0.0    1.3  1  TIR_2        TIR domain
  ------ inclusion threshold ------
        0.1   12.1   0.3        2.5    7.7   0.1    2.4  2  zf-ribbon_3  zinc-ribbon domain
       0.12   12.4   0.6       0.79    9.8   0.8    2.0  2  CpXC         CpXC protein
       0.64   10.1   3.1       0.55   10.3   0.2    2.3  2  DZR          Double zinc ribbon


Domain annotation for each model (and alignments):
>> TIR_2  TIR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.0   5.2e-11   2.3e-07       1     117 [.       5     120 ..       5     121 .. 0.89

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 5.2e-11
                          TIR_2   1 VFiSyssedkewaeklaeaLeaagirvwldrwdlkpgedweeeieeaiessdvvlvvlspaylesewcreeleaaleaae 80 
                                    +++S++++d + a +l++aL +  i+ + ++     g +  ++   +i+ss++++ +++++++ s+ ++ e+  a++   
  gi|116753851|ref|YP_842969.1|   5 IYVSHCHSDADLAGDLCTALYRICIESLTSQFRYTCGISRTAWASFGIRSSECIVPIVTSNSIFSRTVNMEIGFAKA--- 81 
                                    79******************9999**99999899******************************************8... PP

                          TIR_2  81 egkkrlipvlle.pekppl.aslqyidlskk.deealerL 117
                                      ++ +ip+  +  e p + +++  i +s++ +++a++ L
  gi|116753851|ref|YP_842969.1|  82 -IDHLIIPIAEDgVEMPFFiEDVVPITFSSGgFANAVADL 120
                                    .4677*****99535565369******9977887777666 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1   0.00055       2.5       3      10 ..     135     142 ..     134     146 .. 0.84
   2 ?    2.1   0.0     0.031   1.4e+02       3      11 ..     166     175 ..     164     180 .. 0.58

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00055
                    zf-ribbon_3   3 vrCPnCGa 10 
                                    vrCP CG+
  gi|116753851|ref|YP_842969.1| 135 VRCPICGE 142
                                    79999997 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.031
                    zf-ribbon_3   3 vrCPnCGa.p 11 
                                    + C+ C a +
  gi|116753851|ref|YP_842969.1| 166 TACSFCEAeI 175
                                    4566665544 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1     0.019        84      32      47 ..     129     144 ..     118     150 .. 0.74
   2 ?    9.8   0.8   0.00018      0.79       1      50 [.     135     178 ..     135     183 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.019
                           CpXC  32 dgslfeatCpkCgata 47 
                                      + ++++Cp Cg++ 
  gi|116753851|ref|YP_842969.1| 129 RLEWLRVRCPICGEEM 144
                                    5566788999999875 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00018
                           CpXC   1 ltCpaCgkefeaeiwtsidadedpelkeklldgslfeatCpkCgatakle 50 
                                    ++Cp Cg+e +  + +  +      +  ++++++++e+ C  C+a+++l+
  gi|116753851|ref|YP_842969.1| 135 VRCPICGEEMTQYLTPQEN------VDRAIRENRYLETACSFCEAEISLD 178
                                    6799999987766555444......4589****************99987 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.3      0.32   1.4e+03      34      45 ..      10      21 ..       8      46 .. 0.64
   2 ?   10.3   0.2   0.00012      0.55      15      41 ..     137     178 ..     131     182 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.32
                            DZR 34 CgekvdpearfC 45
                                   C++++d+    C
  gi|116753851|ref|YP_842969.1| 10 CHSDADLAGDLC 21
                                   444444444444 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00012
                            DZR  15 CseCgtklkavaa...............edrCpsCgekvdpe 41 
                                    C+ Cg+++ ++ +               e++C+ C+++++++
  gi|116753851|ref|YP_842969.1| 137 CPICGEEMTQYLTpqenvdrairenrylETACSFCEAEISLD 178
                                    *******9988889999*******************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 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:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1302.71
//
Query:       gi|116753852|ref|YP_842970.1|  [L=392]
Description: 3-dehydroquinate synthase [Methanosaeta thermophila PT]
Scores for complete 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-148  494.7   1.3   1.4e-148  494.6   1.3    1.0  1  DHQS            3-dehydroquinate synthase II
    0.00061   19.5   0.2       0.57   10.0   0.2    2.8  2  DUF1953         Domain of unknown function (DUF1953)
     0.0063   16.6   0.0        2.1    8.5   0.0    2.7  3  OapA            Opacity-associated protein A LysM-like domain
  ------ inclusion threshold ------
      0.068   12.6   0.0        0.1   12.0   0.0    1.3  1  Peripla_BP_1    Periplasmic binding proteins and sugar bindin
       0.08   12.9   0.9        1.5    8.8   0.0    3.1  3  Prot_ATP_ID_OB  Proteasomal ATPase OB C-terminal domain
        0.1   12.1   0.1         12    5.4   0.0    2.5  2  Hint            Hint module
        0.2   11.8   1.0        5.3    7.3   0.1    3.0  3  TOBE_2          TOBE domain


Domain annotation for each model (and alignments):
>> DHQS  3-dehydroquinate synthase II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  494.6   1.3  5.4e-152  1.4e-148       1     352 []      32     392 .]      32     392 .] 0.98

  Alignments for each domain:
  == domain 1  score: 494.6 bits;  conditional E-value: 5.4e-152
                           DHQS   1 kevwikadeeeweerkelvtaaleagvdavlveeedaekvkelgkikviakeed.........davlvgkddleklkka. 70 
                                    ke w++a ++ew++ k l+t+ale+g+d+v+v++++ e v+elg+i+++ + ++         d+ +  ++++++++k  
  gi|116753852|ref|YP_842970.1|  32 KEKWLMALASEWDDVKPLITTALESGFDCVVVSRDHIELVRELGSIRIACFGRErgsedllimDTSVPRENQIKSVEKIg 111
                                    789**********************************************9996667887888877788888899998889 PP

                           DHQS  71 kkvaalveikskeeeeeaaeaakeadyvivelkdwtvIPlEnliAalqgeetkiiaavksaeeAklaletLEkGadgvll 150
                                    + ++ +vei+ske+e +a+e++k++dy++v ++dw+vIPlEn+iAalqg + kii++v+s+eeA++al+tLE+Gadgvll
  gi|116753852|ref|YP_842970.1| 112 RPIGGYVEIRSKEDELFATELGKHVDYLLVVGTDWKVIPLENMIAALQGYDCKIISCVRSSEEAEVALSTLEHGADGVLL 191
                                    99****************************************************************************** PP

                           DHQS 151 ktedveeikelaelleeaeeekleLkeaevtkveevgmgdRvcvDtcslmkegeGmLvGsssrglfLvhsEtlespYvas 230
                                    +t+d++eik++++++e+   ++++Lk+a+v++v++vgmgdRvcvDtcslm++geGmLvGs+sr++fLv+sE++espYva+
  gi|116753852|ref|YP_842970.1| 192 DTRDPSEIKRVQAAAERLGMSRIDLKTATVVAVKPVGMGDRVCVDTCSLMRRGEGMLVGSQSRAFFLVQSEAEESPYVAA 271
                                    ******************************************************************************** PP

                           DHQS 231 RPFRVNAGavhaYvlvpggkTkYLseLkaGdevlvvdkkGktreavvGRvKiEkRPlllveaeaegkkvstilQnaetir 310
                                    RPFRVNAGavhaY++v g+kT+YLseLk+Gdev++vdk+G tr+avvGRvKiE+RP++lveae++g++vst+lQnaeti+
  gi|116753852|ref|YP_842970.1| 272 RPFRVNAGAVHAYIRV-GDKTRYLSELKSGDEVTIVDKDGMTRSAVVGRVKIERRPMILVEAEVDGERVSTLLQNAETIK 350
                                    ****************.*************************************************************** PP

                           DHQS 311 lvtedgkaisvteLkeGdevlvyleekaRHfGikieEtiiEk 352
                                    lv++dg++isv+eLk+Gd+vlv++e++aRHfG++ieEtiiE+
  gi|116753852|ref|YP_842970.1| 351 LVSHDGTPISVAELKPGDKVLVHVETSARHFGMSIEETIIER 392
                                    *****************************************7 PP

>> DUF1953  Domain of unknown function (DUF1953)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.2   0.00022      0.57      41      62 ..     309     330 ..     298     331 .. 0.89
   2 !    6.4   0.0    0.0029       7.5      17      36 ..     367     386 ..     361     390 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00022
                                    ETTTTEEEEEEEEE-SS-EEEE CS
                        DUF1953  41 dvitdetvrGrvkvdklplilv 62 
                                    d +t  +v Grvk+++ p+ilv
  gi|116753852|ref|YP_842970.1| 309 DGMTRSAVVGRVKIERRPMILV 330
                                    6789999**************9 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0029
                                    TTTEEEEEESSSS-EEEEEE CS
                        DUF1953  17 Gdkvlvivktlnrdydieid 36 
                                    Gdkvlv v t  r + + i+
  gi|116753852|ref|YP_842970.1| 367 GDKVLVHVETSARHFGMSIE 386
                                    9************9998875 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 ?   -3.0   0.0       3.1     8e+03      34      65 ..     184     215 ..     172     222 .. 0.60
   2 !    8.5   0.0    0.0008       2.1      24      58 ..     278     311 ..     271     337 .. 0.76
   3 !    5.1   0.0    0.0093        24      25      66 ..     346     387 ..     340     390 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.1
                           OapA  34 eGadkplSnlksGqkvriklnaqgkvdelqle 65 
                                    +Gad +l + +   +++  ++a  ++ + +++
  gi|116753852|ref|YP_842970.1| 184 HGADGVLLDTRDPSEIKRVQAAAERLGMSRID 215
                                    36666666666666666666666666555555 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0008
                           OapA  24 lsdvnalakveGadkplSnlksGqkvriklnaqgk 58 
                                       v+a  +v  + + lS+lksG++v+i  +++g+
  gi|116753852|ref|YP_842970.1| 278 AGAVHAYIRVGDKTRYLSELKSGDEVTIV-DKDGM 311
                                    566889999999999***********994.44443 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.0093
                           OapA  25 sdvnalakveGadkplSnlksGqkvriklnaqgkvdelqlek 66 
                                    ++  +l+  +G+  ++++lk G+kv ++++++ +   +++e+
  gi|116753852|ref|YP_842970.1| 346 AETIKLVSHDGTPISVAELKPGDKVLVHVETSARHFGMSIEE 387
                                    55667777888888899**************99999999986 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 ?   12.0   0.0   4.1e-05       0.1      28      92 ..     157     223 ..     153     257 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.1e-05
                                    HHHTEEEEEEE-SSHHHHHHHHHHHHHTT-SEEEEE-S-GG.HHHHHHHHHH.T-EEEEESS--B-T CS
                   Peripla_BP_1  28 kehgvdvlllaageeedlakaidllkakgidgliiatsdts.fdditakaes.gipvialedaidap 92 
                                    + +g+d +++     ++ a+ + + +++g+dg+++ t+d+s   +++a ae  g+  i l+ a + +
  gi|116753852|ref|YP_842970.1| 157 ALQGYDCKIISCVRSSEEAEVALSTLEHGADGVLLDTRDPSeIKRVQAAAERlGMSRIDLKTATVVA 223
                                    5689999***99999999988888889**************99999999999999999999887776 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 ?    0.3   0.0      0.26   6.7e+02      31      47 ..     221     237 ..     214     241 .. 0.79
   2 ?   -1.5   0.0         1   2.6e+03      36      45 ..     296     305 ..     287     311 .. 0.78
   3 ?    8.8   0.0   0.00058       1.5      31      49 ..     358     376 ..     335     378 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.26
                                    GGSSST--TTEEEEEET CS
                 Prot_ATP_ID_OB  31 avpremLrpgDlVavdk 47 
                                     v+ +++  gD+V vd+
  gi|116753852|ref|YP_842970.1| 221 VVAVKPVGMGDRVCVDT 237
                                    577888999******98 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1
                                    T--TTEEEEE CS
                 Prot_ATP_ID_OB  36 mLrpgDlVav 45 
                                    +L+ gD V +
  gi|116753852|ref|YP_842970.1| 296 ELKSGDEVTI 305
                                    6999999963 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.00058
                                    GGSSST--TTEEEEEETTT CS
                 Prot_ATP_ID_OB  31 avpremLrpgDlVavdkdt 49 
                                    ++  ++L+pgD V+v+  t
  gi|116753852|ref|YP_842970.1| 358 PISVAELKPGDKVLVHVET 376
                                    556678*********9766 PP

>> Hint  Hint module
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0    0.0046        12      24      47 ..     289     312 ..     280     341 .. 0.83
   2 ?    3.9   0.0     0.013        33      22      41 ..     354     373 ..     345     383 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0046
                                    XXXXXXXXXXXXXXXXXXXXXXXX CS
                           Hint  24 geqkslseLepGdkVlavdesgev 47 
                                    ++++ lseL+ Gd+V  vd++g +
  gi|116753852|ref|YP_842970.1| 289 DKTRYLSELKSGDEVTIVDKDGMT 312
                                    45889**************98864 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.013
                                    XXXXXXXXXXXXXXXXXXXX CS
                           Hint  22 edgeqkslseLepGdkVlav 41 
                                    +dg+ +s+ eL+pGdkVl  
  gi|116753852|ref|YP_842970.1| 354 HDGTPISVAELKPGDKVLVH 373
                                    6888999**********974 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.4   3.7e+03      20      38 ..     218     236 ..     201     239 .. 0.72
   2 ?    7.3   0.1    0.0021       5.3      20      51 ..     278     309 ..     265     319 .. 0.87
   3 ?    1.6   0.0      0.13   3.2e+02      43      70 ..     347     376 ..     329     381 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.4
                         TOBE_2  20 sGtVedveylGsstryvve 38 
                                    ++tV+ v   G   r+ v+
  gi|116753852|ref|YP_842970.1| 218 TATVVAVKPVGMGDRVCVD 236
                                    5788888887777777766 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0021
                         TOBE_2  20 sGtVedveylGsstryvvelaggqlvvvrqpn 51 
                                    +G V+  +  G+ try+ el +g +v+++  +
  gi|116753852|ref|YP_842970.1| 278 AGAVHAYIRVGDKTRYLSELKSGDEVTIVDKD 309
                                    799999*******************9987655 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.13
                         TOBE_2  43 qlvvvrqpnadr.d.salapGdtVelswdp 70 
                                    + ++++ ++++  + + l+pGd+V +++++
  gi|116753852|ref|YP_842970.1| 347 ETIKLVSHDGTPiSvAELKPGDKVLVHVET 376
                                    455566666666666889999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); 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: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2765.30
//
Query:       gi|116753853|ref|YP_842971.1|  [L=226]
Description: 3-dehydroquinate dehydratase, type I [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-44  152.6   0.0    2.3e-44  152.4   0.0    1.0  1  DHquinase_I  Type I 3-dehydroquinase
  ------ inclusion threshold ------
       0.21   10.7   0.1       0.41    9.8   0.0    1.4  2  ALAD         Delta-aminolevulinic acid dehydratase


Domain annotation for each model (and alignments):
>> DHquinase_I  Type I 3-dehydroquinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.4   0.0   2.5e-48   2.3e-44      17     229 .]      31     220 ..      17     220 .. 0.89

  Alignments for each domain:
  == domain 1  score: 152.4 bits;  conditional E-value: 2.5e-48
                                    HHHTT.S-SEEEEEGGG-.TT.THHHHHHHHHHHHHHTTS-EEEE---GGGT-S.SSS-HHHHHHHHHHHHHCT-SEEEE CS
                    DHquinase_I  17 esgke.kaDlvElRlDllketseaedvseeleelrstsdlpliftlrtkaeggrfkrkseeeylellrtaielgadyvDv 95 
                                     ++++ +aD++E+RlDll+++ +       ++ +rst +lpli+t r+++egg+f r+see ++++lr a ++  d++D+
  gi|116753853|ref|YP_842971.1|  31 SRAESeGADIIEVRLDLLADP-D------VIRDIRSTVSLPLIATNRIASEGGSF-RGSEERRISILRDASRF-SDIIDI 101
                                    3344459***********876.3......8999999999****************.9***************7.7***** PP

                                    EGG-.HHGHHHHHHHHHHHTT-EEEEEEEESS----HHHHHHHHHHHHHTT-SEEEEEE--SSHHHHHHHHHHHHHHHHH CS
                    DHquinase_I  96 ElteapeeskkrlieekreggtkvIvSyhdfegtpsaeelkallekmqalgaDivKiavmaksieDvlrllsltseakee 175
                                    El+ ap    + l +++   ++   +Syhdf+g p++  lk+++e + + gaD+vKiav+++s+++ l++l++       
  gi|116753853|ref|YP_842971.1| 102 ELM-APG--RDMLLKNI---SCPALISYHDFSGVPDN--LKSIIEDAMRAGADLVKIAVTPHSMQEALAILRILL----- 168
                                    **5.664..45678887...9**************66..**********************************94..... PP

                                    T-SS-EEEEE-TTTTGHHHCHHHHHTB-EEEEESSS-..SSTT-EEHHHHHHHH CS
                    DHquinase_I 176 kdeaplIamamGelGkiSRilgevfGspvtfasleeakasapGqltarelreil 229
                                    + + pl+ + mG  G+  R +++++Gs +t++ ++ +  +apGq+++rel ++l
  gi|116753853|ref|YP_842971.1| 169 DVDCPLCIIGMGAVGRHLRAVAPLYGSLLTYGYVTGP--TAPGQMSVRELDTAL 220
                                    5679*****************************9999..***********9875 PP

>> ALAD  Delta-aminolevulinic acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   4.6e-05      0.41     225     267 ..      25      68 ..      19      74 .. 0.85
   2 ?   -3.5   0.0      0.49   4.4e+03     298     306 ..     140     148 ..     130     155 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 4.6e-05
                                    HHHHHHHHHHHTT-SBEEEES-.TTGHHHHHHHHTT-SS-EEEE CS
                           ALAD 225 ealreveldleeGADivmvKPa.laylDiirevkeefdlpvaay 267
                                    +a r +++  +eGADi+ v+   la  D+ir+++++++lp++a 
  gi|116753853|ref|YP_842971.1|  25 DAERVASRAESEGADIIEVRLDlLADPDVIRDIRSTVSLPLIAT 68 
                                    5778888999*********97615678*************9985 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 0.49
                                    HHHTT-SEE CS
                           ALAD 298 ikRAGadli 306
                                      RAGadl+
  gi|116753853|ref|YP_842971.1| 140 AMRAGADLV 148
                                    457777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1648.46
//
Query:       gi|116753854|ref|YP_842972.1|  [L=156]
Description: hypothetical protein Mthe_0541 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
        0.1   12.2   0.0        3.5    7.2   0.0    2.0  2  F_actin_cap_B  F-actin capping protein, beta subunit


Domain annotation for each model (and alignments):
>> F_actin_cap_B  F-actin capping protein, beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0    0.0025        45      30      64 ..      37      71 ..      23      72 .. 0.88
   2 ?    7.2   0.0    0.0002       3.5      50      70 ..      73      93 ..      69     115 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0025
                  F_actin_cap_B 30 laedllssvdqplkvakdkeegkeyllcdyNrdgd 64
                                    +  l+s+v   +  + + +e+ + +lcd+N   d
  gi|116753854|ref|YP_842972.1| 37 ATPSLVSRVIRTIARIDCATEHERVILCDFNEISD 71
                                   5678999999999999***************9876 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0002
                  F_actin_cap_B 50 egkeyllcdyNrdgdsYRSpw 70
                                   eg+ y+l  y r gd YR+ +
  gi|116753854|ref|YP_842972.1| 73 EGRGYVLTSYARSGDMYRAIF 93
                                   6899**************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1190.07
//
Query:       gi|116753855|ref|YP_842973.1|  [L=367]
Description: aminotransferase, class I and II [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.6e-65  219.3   0.0    9.7e-65  219.1   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    3.2e-11   43.1   0.0    4.9e-11   42.5   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    6.7e-08   31.9   0.0      1e-07   31.3   0.0    1.1  1  Aminotran_5      Aminotransferase class-V
    7.1e-07   28.1   0.0      1e-06   27.5   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
      0.001   18.4   0.0     0.0015   17.9   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
      0.027   13.1   0.0       0.06   12.0   0.0    1.5  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 !  219.1   0.0   3.2e-68   9.7e-65       4     362 ..      27     362 ..      24     363 .. 0.96

  Alignments for each domain:
  == domain 1  score: 219.1 bits;  conditional E-value: 3.2e-68
                                    EESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHH CS
                  Aminotran_1_2   4 inLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliea 83 
                                    +nL+++++++d    t+ ++++a+++  +  ++ + y+p+ g pel+ a+++ l+r+++l++ ++ ++ v+sGa++++ +
  gi|116753855|ref|YP_842973.1|  27 VNLSIGQPDFD----TPGHIKEAAIK--AIEQGMTGYTPNLGIPELRAAICEKLRRENGLTFSPD-QIMVTSGASEALFL 99 
                                    8**********....**********9..999999*******************************.************** PP

                                    HHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT-- CS
                  Aminotran_1_2  84 lifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGt 163
                                    +i++    pgde+l+pdp + sy + ++++ g  v ++l+   + +l ++ + e ++       kt  i+v+sp NPtG+
  gi|116753855|ref|YP_842973.1| 100 AIAAV-TSPGDEVLMPDPGFVSYRPLVQAANGRPVGVHLD--HELKLSVDTVAEHITP------KTSAIIVNSPANPTGA 170
                                    *****.7*******************************99..9999***********9......9*************** PP

                                    B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTT.EEEEEESSSTTSSGGG-EEEEEEEHHHHHH CS
                  Aminotran_1_2 164 vatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepn.llivgslsKafGlaGeRvGyilgnaavvsq 242
                                    v ++ e++ l++la+ +++ l++De+Y++f ++ +     ++  +++ + +++v+ +sK ++++G+R+Gy+++ ++ ++ 
  gi|116753855|ref|YP_842973.1| 171 VQSESEIRGLAELADDKGIALISDEVYEHFIYEGE-----HVSPARYGEnVITVNAVSKTYAMTGWRLGYLAAPPEAIDV 245
                                    *********************************65.....5555555555****************************** PP

                                    HHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEEEEETHHCHHHH CS
                  Aminotran_1_2 243 lrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmflltdlsaetakel 320
                                    + k+++ +    ss+ qaa++aa+  +++    + emr+ + +rr+ +  +L++lgl+ + ++++++ + ++     +e+
  gi|116753855|ref|YP_842973.1| 246 MLKIHQYIQAcaSSISQAAALAAITGPQD---CVREMRESFRRRRDMMIRGLRDLGLDLVVPKGAFYIFPRVGDG--DEF 320
                                    *****9877677****************7...9**************************************9977..9** PP

                                    HHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHHH CS
                  Aminotran_1_2 321 skkLleevgvyvtpgtsftv..pgrlRitvAglteeeleelvea 362
                                    +  L    gv+ +pg+ f+v  + ++Ri++ +++e++l+ ++e+
  gi|116753855|ref|YP_842973.1| 321 AARLGAA-GVITVPGSAFGVngKPHIRISY-AVSEDNLRLALER 362
                                    *******.*************9889*****.*********9997 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 !   42.5   0.0   1.6e-14   4.9e-11      43     144 ..      89     194 ..      60     198 .. 0.88

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 1.6e-14
                                    EESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEE...EB- CS
                DegT_DnrJ_EryC1  43 avssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaaieaaitertkaIl...pVh 119
                                     +s +++Al la+ a+  +pgdeV++p  +Fv+    v+ ++ +pv v  d + + ++++++++ it++t+aI+   p++
  gi|116753855|ref|YP_842973.1|  89 VTSGASEALFLAIAAVT-SPGDEVLMPDPGFVSYRPLVQAANGRPVGVHLD-HELKLSVDTVAEHITPKTSAIIvnsPAN 166
                                    34556789999999976.57*******************************.88*******************9555578 PP

                                    GGGB--...-HHHHHHHHHHCT-EEEEE CS
                DegT_DnrJ_EryC1 120 lyGqva...dmdalkaiaakhglkvieD 144
                                      G+v    ++  l ++a+++g+ +i+D
  gi|116753855|ref|YP_842973.1| 167 PTGAVQsesEIRGLAELADDKGIALISD 194
                                    888875445899999***********99 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.0   3.4e-11     1e-07      61     175 ..      84     194 ..      77     199 .. 0.85

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 3.4e-11
                                    GGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTE CS
                    Aminotran_5  61 eeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnekt 140
                                     ++i++tsG++ea+ l++ ++    +pgde+++ + +  + + p +++a+ + + v    ld+e +l +d++++++++kt
  gi|116753855|ref|YP_842973.1|  84 PDQIMVTSGASEALFLAIAAV---TSPGDEVLMPDPGFVSYR-PLVQAANGRPVGV---HLDHELKLSVDTVAEHITPKT 156
                                    589******************...99****************.9999996666555...89******************* PP

                                    EEEEEESBETTTTEB--HHHH...HHHHHHTT-EEEEE CS
                    Aminotran_5 141 klvaithvsnvtGtiqpveei...gklakkkgalvlvD 175
                                    ++++++   n tG +q   ei   ++la +kg+ ++ D
  gi|116753855|ref|YP_842973.1| 157 SAIIVNSPANPTGAVQSESEIrglAELADDKGIALISD 194
                                    **************997766611155556667666666 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 !   27.5   0.0   3.5e-10     1e-06      71     176 ..      87     197 ..      77     223 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 3.5e-10
                                    EEESSHHH.HHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHH.TTCEEEEESTTSHHHHHHHCCTTEEEEEEESS-T CS
                Cys_Met_Meta_PP  71 lavssGma.AiaaailallkaGdeivvsddlYggtqrllkkvlkk.lgievkfvdtsdleelekaikentklvylEtptn 148
                                    ++v+sG + A+++ai a+ + Gde+++ d  + + + l++    + +g++ ++  + +++ ++++i+++t+++ + +p+n
  gi|116753855|ref|YP_842973.1|  87 IMVTSGASeALFLAIAAVTSPGDEVLMPDPGFVSYRPLVQAANGRpVGVHLDHELKLSVDTVAEHITPKTSAIIVNSPAN 166
                                    566777655999***********************99*999998889********************************* PP

                                    TTT--...--HHHHHHHHHHTT-EEEEEGTT CS
                Cys_Met_Meta_PP 149 pllkv...vDiekiaklakkagvlvvvDntf 176
                                    p+  v     i+ +a+la ++g+ ++ D ++
  gi|116753855|ref|YP_842973.1| 167 PTGAVqseSEIRGLAELADDKGIALISDEVY 197
                                    *97762226899999*******999999765 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   5.1e-07    0.0015      18     167 ..      46     194 ..      37     196 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 5.1e-07
                                    H.HCS----CCCT--HHHHHHHHHHHHHTT-SEEE.E......ES-HHHHHHHHH..HHH--TTEEEEEETT-HHHHSST CS
                Beta_elim_lyase  18 q.aaamlGdesYgedktvnrLedavaelfgkeaal.f......vpqGtaAnsill..killqrgeevivtepahihfdet 87 
                                       a+++G   Y  + ++ +L +a++e +  e +l f      v++G a++++ l  ++++ +g+ev++ +p+ +     
  gi|116753855|ref|YP_842973.1|  46 AiKAIEQGMTGYTPNLGIPELRAAICEKLRRENGLtFspdqimVTSG-ASEALFLaiAAVTSPGDEVLMPDPGFV---SY 121
                                    44677788888888888888999999988888887547777745555.56665552277789*********9855...56 PP

                                    THHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEE CS
                Beta_elim_lyase  88 gaiaelagvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlD 167
                                    + +++ a  +++ +  +++ k++++ ++++i++      k+++i++    n   G v s  e+r +a++a+++gi l+ D
  gi|116753855|ref|YP_842973.1| 122 RPLVQAANGRPVGVHLDHELKLSVDTVAEHITP------KTSAIIVNSPANP-TGAVQSESEIRGLAELADDKGIALISD 194
                                    77888888889999999999************9......4666666665553.6***********************988 PP

>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     2e-05      0.06     181     234 ..     144     196 ..     117     201 .. 0.84
   2 ?   -3.1   0.0      0.74   2.2e+03     362     405 ..     319     366 ..     276     367 .] 0.63

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2e-05
                                    HHHHHHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-T CS
                    Aminotran_3 181 elealekkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEv 234
                                     +  + + ++++++A+iv       G  v+s++ +++l+el+++++++li DEv
  gi|116753855|ref|YP_842973.1| 144 SVDTVAEHITPKTSAIIVNSPANPTGA-VQSESEIRGLAELADDKGIALISDEV 196
                                    566777899999******987767776.5677779******************9 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.74
                                    HHHHHHHHCTEE-EEETT....TEEEE---TT--HHHHHHHHHHHHHH CS
                    Aminotran_3 362 eilkkakekGvlilsaGd....nvirllppliitdeeidelleilkka 405
                                    e+++++ ++Gv++ +           ++ ++ +++++++ +le++k++
  gi|116753855|ref|YP_842973.1| 319 EFAARLGAAGVITVPGSAfgvnGKPHIRISYAVSEDNLRLALERMKEV 366
                                    566666666766654222211222234457888888888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2686.22
//
Query:       gi|116753856|ref|YP_842974.1|  [L=180]
Description: CopG/DNA-binding domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-11   42.7   0.6    6.4e-11   41.8   0.6    1.4  1  RHH_1          Ribbon-helix-helix protein, copG family
     0.0032   17.4   0.1     0.0058   16.6   0.1    1.4  1  RHH_3          Ribbon-helix-helix domain
  ------ inclusion threshold ------
      0.025   15.3   0.1      0.059   14.1   0.0    1.7  2  PSK_trans_fac  Rv0623-like transcription factor
       0.15   12.1   0.4       0.35   10.9   0.1    1.7  2  HTH_19         Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   0.6   1.4e-14   6.4e-11       1      36 [.       6      41 ..       6      42 .. 0.98

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 1.4e-14
                                   EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHH CS
                          RHH_1  1 rvsirldeellerLdelarrrgrSrSelIReAlrey 36
                                   r++i++dee+++++++l++++g+S+Se++ReAlr+y
  gi|116753856|ref|YP_842974.1|  6 RITISMDEETARLFRKLRDELGVSQSEMMREALRFY 41
                                   8*********************************98 PP

>> RHH_3  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   1.3e-06    0.0058       3      37 ..       5      39 ..       4      44 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.3e-06
                          RHH_3  3 trttvsidpelaekLkaLSekTrIprSklldeAie 37
                                   +r+t+s+d+e a   + L  ++++ +S+  +eA+ 
  gi|116753856|ref|YP_842974.1|  5 ERITISMDEETARLFRKLRDELGVSQSEMMREALR 39
                                   69*******************************95 PP

>> PSK_trans_fac  Rv0623-like transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.3e-05     0.059       7      35 ..      12      40 ..       7      60 .. 0.92
   2 ?   -2.5   0.0       2.1   9.3e+03      38      38 ..     108     108 ..      88     133 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.3e-05
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                  PSK_trans_fac  7 dpeverlareLarltgeskteAvrrAlee 35
                                   d+e+ rl r+L +  g+s+ e  r+Al+ 
  gi|116753856|ref|YP_842974.1| 12 DEETARLFRKLRDELGVSQSEMMREALRF 40
                                   99*************************85 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.1
                                    X CS
                  PSK_trans_fac  38 e 38 
                                    +
  gi|116753856|ref|YP_842974.1| 108 R 108
                                    2 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   7.8e-05      0.35       2      22 ..      17      37 ..      16      44 .. 0.91
   2 ?   -3.2   0.0         2   8.9e+03      42      53 ..     114     125 ..     109     127 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 7.8e-05
                         HTH_19  2 erLkeaReelgltqeelaerl 22
                                   + ++++R elg +q e+++++
  gi|116753856|ref|YP_842974.1| 17 RLFRKLRDELGVSQSEMMREA 37
                                   679***************975 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2
                         HTH_19  42 aelllkiaealg 53 
                                    a+++l+++ea++
  gi|116753856|ref|YP_842974.1| 114 ADVILRRLEACN 125
                                    788899999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1366.90
//
Query:       gi|116753857|ref|YP_842975.1|  [L=246]
Description: UBA/THIF-type NAD/FAD binding protein [Methanosaeta thermophila PT]
Scores for complete 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-59  199.6   0.0    6.2e-59  199.3   0.0    1.0  1  ThiF             ThiF family
  ------ inclusion threshold ------
      0.027   13.6   0.0       0.45    9.6   0.0    2.1  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
       0.14   12.4   0.1       0.26   11.5   0.1    1.4  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
       0.16   11.6   0.1       0.25   11.0   0.1    1.4  1  ApbA             Ketopantoate reductase PanE/ApbA
       0.25   10.6   0.4       0.33   10.2   0.4    1.1  1  FAD_binding_3    FAD binding domain


Domain annotation for each model (and alignments):
>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.3   0.0   1.7e-62   6.2e-59       1     240 [.      10     233 ..      10     238 .. 0.91

  Alignments for each domain:
  == domain 1  score: 199.3 bits;  conditional E-value: 1.7e-62
                                    THHHHHHHHHHHHHHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEEESSB--GGGGGTBTTS-GGGTTSBHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF   1 ysrqlallgedgqekLrdskvllvGaGglGsellknLalsGvgkltlvDnDkielsNlnRqflfreediGkpKaevaaea 80 
                                    ysrq+ llg +gqe+Lr+s vl+ GaGglGs    +La++Gvg++++vD D ++lsNlnRq+l+r    G  Ka +a+e 
  gi|116753857|ref|YP_842975.1|  10 YSRQIPLLGIEGQERLRRSGVLIAGAGGLGSVSSYYLAAAGVGRIRIVDSDIVDLSNLNRQILHRI--PGVRKAVSAEET 87 
                                    89*************************************************************664..4999******** PP

                                    HHHT-TTSEEEEEES-CCGCCS-HHHHTT-SEEEEESSSHHHHHHHHHHHHHHT-EEEEEEEETTEEEEEEEEECCS-EC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF  81 lqeinpdveveavteritdetvleellesvDlVvdalDniearrlvnracvkkgiplieagtlgfegqvvviipgktgcy 160
                                    l+++np +eve v  +i++++  ++l+ ++Dl+vda+D++e+r+++n+a+ k+g+pl++++++g++gqv++iipg+t+c+
  gi|116753857|ref|YP_842975.1|  88 LRSLNPTIEVEGVDICISESS-IDDLVDDIDLIVDAMDSFEVRYILNSAALKHGLPLVHGAVSGLDGQVTTIIPGRTACL 166
                                    *******************87.69******************************************************** PP

                                    TSS-TGGS.EECCCCEEHHHHHHCTE-B-HHHHHHHHHHHHHHHHHHHTTBCGGGCCEEEECCTTTTEEEEECCEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF 161 eCldpsstedptekkvplctsiagnipaiatttavvaglaalellkllsgkeklenslltqvdllesrfenvelerakks 240
                                    +C +p   + p+++  p +         i++t++++++++a+e++k+l g  +l  ++l   d+   +++++ +er++ +
  gi|116753857|ref|YP_842975.1| 167 RCVFP---RPPPRDA-PPV---------IGATCGIIGSIQATEAIKMLTGVGELLLNRLLIWDGRCAQMDEISIERDAGC 233
                                    ****9...6666665.555.........69******************77666666666678887777788777776644 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00013      0.45      59      93 ..     108     144 ..      30     157 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00013
                                    .E--.TT-HHHHHHHTT..T-SEEEE------.HHHH CS
                Polysacc_synt_2  59 vigd.vrdkerlekaleelkvdvvfhaAAlKh.VPlv 93 
                                     i d v d + + +a+++++v +++++AAlKh +Plv
  gi|116753857|ref|YP_842975.1| 108 SIDDlVDDIDLIVDAMDSFEVRYILNSAALKHgLPLV 144
                                    4445367789999******************955665 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 ?   11.5   0.1   7.2e-05      0.26       1      94 [.      30     141 ..      30     163 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.2e-05
                                    EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH...................TTTCEEEEE--TTTHHH CS
                Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka...................lgvrfeaialdaenyea 61 
                                    vli GaG+ G++   +la+ +    +i ++d +   l +l  ++                   l++++e + +d+   e+
  gi|116753857|ref|YP_842975.1|  30 VLIAGAGGLGSVSSYYLAAAGVG--RIRIVDSDIVDLSNLNRQIlhripgvrkavsaeetlrsLNPTIEVEGVDICISES 107
                                    7999***************9976..********99999999999999999999999999999999999999999999999 PP

                                    HHHHHHTTSSEEEE-SSGGGHHHHH.HHHHHHT- CS
                Sacchrp_dh_NADP  62 vLaallkegdlvvnlsppissldvl.kaCietgv 94 
                                     ++ l+ + dl+v+++ +++ + +l  a++++g 
  gi|116753857|ref|YP_842975.1| 108 SIDDLVDDIDLIVDAMDSFEVRYILnSAALKHGL 141
                                    9999999999999999999666555145666665 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   6.9e-05      0.25       1      23 [.      30      52 ..      30     104 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.9e-05
                                   EEEES-SHHHHHHHHHHHHHTHC CS
                           ApbA  1 iailGaGaiGsllaakLakagad 23
                                   ++i+GaG++Gs+  ++La+ag  
  gi|116753857|ref|YP_842975.1| 30 VLIAGAGGLGSVSSYYLAAAGVG 52
                                   68*****************9975 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.4   9.1e-05      0.33       3      32 ..      29      59 ..      27      73 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 9.1e-05
                                   EEEEE--SHHHHHHHHHHHHTTHH.EEEEES CS
                  FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvr.vvlvek 32
                                    VlI GaG  G +++  L+ aGv   ++v+ 
  gi|116753857|ref|YP_842975.1| 29 GVLIAGAGGLGSVSSYYLAAAGVGrIRIVDS 59
                                   59*********************64778876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1793.76
//
Query:       gi|116753858|ref|YP_842976.1|  [L=392]
Description: proposed homoserine kinase [Methanosaeta thermophila PT]
Scores for 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   0.0    1.5e-56  190.9   0.0    1.4  1  PhosphMutase   2,3-bisphosphoglycerate-independent phosphogly
      8e-39  133.5   0.0    9.2e-39  133.3   0.0    1.0  1  Metalloenzyme  Metalloenzyme superfamily


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 !  190.9   0.0   1.7e-60   1.5e-56       1     170 []      37     196 ..      37     196 .. 0.97

  Alignments for each domain:
  == domain 1  score: 190.9 bits;  conditional E-value: 1.7e-60
                                    HHTSEEEEEE-----------TCHHHHTT--HHCH---HHHHHHHHTT----TT-EEEEEEEEEEC..TTCEEETTGGG- CS
                   PhosphMutase   1 AkkGetGlldtvpegiapgSdvAnlsilGydpkkyytGRGplEAlgiGlelkpgdvafRcnlvtvdeedgiiidrragri 80 
                                    A+ G++Gl++tvpeg++pgSdvAnlsi+Gydp++yytGR+plEA+++ + l++++vafRcn+vtv   dgi+ d++ag+i
  gi|116753858|ref|YP_842976.1|  37 ARIGRCGLARTVPEGMTPGSDVANLSIMGYDPRRYYTGRAPLEAAAMRIPLGEKEVAFRCNFVTV--MDGIMDDYSAGHI 114
                                    789**************************************************************..59*********** PP

                                    .-TTHHHHHHHT-EEE.TTEEEEEEE-STTEEEEEE--S-B--S--..SSTTS------BS.SGGGHHHHHHHHHHHHHH CS
                   PhosphMutase  81 steeakeLikalneeleegvevkfypgveyrhllvllsdkitdtdpphdkegkeikellplkseeaketaellnelieks 160
                                    ++ee++e++++l++ +      ++ypgv+yr+++vl+  +   ++pphd+ gk+i+++lp +    +++a +l +++e++
  gi|116753858|ref|YP_842976.1| 115 TSEEGAEIAESLKKVIP---GGRIYPGVSYRNIVVLKVCRDAVCTPPHDIMGKPISDHLP-R----GDDAHILIDIMERA 186
                                    ****************6...68**************666679******************.7....99************ PP

                                    HHHHHHSHHH CS
                   PhosphMutase 161 qeiLedhpvN 170
                                    + +Le+hpvN
  gi|116753858|ref|YP_842976.1| 187 RPLLEEHPVN 196
                                    *********9 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.3   0.0     1e-42   9.2e-39       1     241 [.       1     385 [.       1     391 [. 0.97

  Alignments for each domain:
  == domain 1  score: 133.3 bits;  conditional E-value: 1e-42
                                    -EEEEEEETTBB----GGGTT...HHHS--HHHHHHHHH.......SEEEEEESSSTT----HHHHHHHH.......... CS
                                    xxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......... RF
                  Metalloenzyme   1 kkvvlvvlDGlGeapadelna...ihvAktPtldkLkkeaPerwlikahgtavglpeddmgnsevgHlel.......... 67 
                                    +k+v+++ DG++++p++ l++   ++vA++P++d+++         + +g+a ++pe+++++s+v++l++          
  gi|116753858|ref|YP_842976.1|   1 MKYVVLLGDGMADWPMEALGGrtpLQVARKPNMDSIARI-------GRCGLARTVPEGMTPGSDVANLSImgydprryyt 73 
                                    58899*******************************998.......89******************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                  Metalloenzyme  68 ................................................................................ 67 
                                                                                                                    
  gi|116753858|ref|YP_842976.1|  74 grapleaaamriplgekevafrcnfvtvmdgimddysaghitseegaeiaeslkkvipggriypgvsyrnivvlkvcrda 153
                                    ******************************************************************************** PP

                                    ............................................HHHHTT-----EEEEEEEE-S---SSHHHHHT--EE CS
                                    ............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Metalloenzyme  68 ............................................lrisetvkfahvtffwnggrsgyfnpleereeipsd 103
                                                                                 r+s++ k+a+++++w++g  ++++ + e ++++++
  gi|116753858|ref|YP_842976.1| 154 vctpphdimgkpisdhlprgddahilidimerarplleehpvnrRRVSMGLKPANMIWLWGQGPAPSMPRFHEIYGLKGA 233
                                    ********************************************99********************************** PP

                                    EE--SHH....................STT--HHHHHHHHHHHH.CC.-SEEEEEE-HHHHHHHTT-HHHHHHHHHHHHH CS
                                    xxxxxxx....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Metalloenzyme 104 tvitfdl....................qpemkavevaekaldailsgkfdlvvvniknaDmvGHtgdleatiaaieaaDe 163
                                    ++ ++dl                    + ++++  ++++al+a+  g+ dlv+++i+ +D+++H+gd+e++i+aie +De
  gi|116753858|ref|YP_842976.1| 234 VISAVDLlkglgvcagwrvidvpgatgTIDTNYAGKVRAALEAL--GSVDLVYLHIEAPDEAAHSGDVEQKIRAIELFDE 311
                                    ********************************************..779******************************* PP

                                    .HHHHHHTTS-TTTE..EEEEE-SSB--TTTSS........-----EEEEEESTT----S--S.SHHHHTT-TTEEEEGG CS
                                    .xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                  Metalloenzyme 164 .avkeildaieqvdg..ilvvtADHgnaedmvkrdkqplTsHtlepVPilivgkglapdkvke.gakfrekggLanvaat 239
                                      v+ +++ +e +++   +++++DH+++ ++ +        H+++pVP++i+g g+  d+v   ++ ++++gg + +++ 
  gi|116753858|ref|YP_842976.1| 312 rVVGPMIHGLERSGEawRVLLLPDHPTPIEIRT--------HSTDPVPFAIAGSGVCVDSVDAfDEISASEGGYGMIEGN 383
                                    67899******99983357999***********........*****************9999999999999999999877 PP

                                    GH CS
                                    xx RF
                  Metalloenzyme 240 ll 241
                                     l
  gi|116753858|ref|YP_842976.1| 384 DL 385
                                    65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       249  (0.0138881); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2949.79
//
Query:       gi|116753859|ref|YP_842977.1|  [L=209]
Description: methyl-coenzyme M reductase operon protein C [Methanosaeta thermophila PT]
Scores for complete 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-08   33.0   0.6    1.7e-07   30.6   0.4    2.1  1  MCR_C     Methyl-coenzyme M reductase operon protein C


Domain annotation for each model (and alignments):
>> MCR_C  Methyl-coenzyme M reductase operon protein C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.4   9.7e-12   1.7e-07      72     169 ..      37     145 ..      22     159 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 9.7e-12
                          MCR_C  72 iavvsptLarhhlPhsaCDvaeylrraGaktnmiGlarGvg.........kr...iaqikeeekrlinehDlavfvlGnf 139
                                    +  ++++  r+h+  ++C+++  lrr+G +t ++ l  G+g         +    +  ++ +e + i+ h +av  lGn 
  gi|116753859|ref|YP_842977.1|  37 VIAIAMSPGRRHITKPVCEITYGLRREGIQTSVLVLEAGTGvpdsfpqasRGygpTFGLTPKEIEQIQRHKIAVIHLGNV 116
                                    556789999*************************9988877332221111111112347889****************** PP

                          MCR_C 140 kdCikkkkeklfedievPvvvtggPeelkl 169
                                    k+ +  k++ ++  +++P vv++    ++ 
  gi|116753859|ref|YP_842977.1| 117 KSHVIYKTRDILAYVDIPAVVVSQC-PVDF 145
                                    ******************8887654.3444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1567.73
//
Query:       gi|116753860|ref|YP_842978.1|  [L=654]
Description: hypothetical protein Mthe_0547 [Methanosaeta thermophila PT]
Scores for complete 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-50  168.5   0.0      2e-49  166.9   0.0    1.9  2  DUF460          Protein of unknown function (DUF460)
    0.00033   19.1   2.7    0.00033   19.1   2.7    1.6  2  CCD48           Coiled-coil domain-containing protein 48
     0.0029   17.4   1.5     0.0029   17.4   1.5    2.9  2  PKcGMP_CC       Coiled-coil N-terminus of cGMP-dependent prot
  ------ inclusion threshold ------
      0.019   14.4   3.4      0.034   13.5   3.4    1.5  1  FAM76           FAM76 protein
      0.036   14.4   0.1      0.036   14.4   0.1    2.7  2  acVLRF1         Actinobacteria/chloroflexi VLRF1 release fact
      0.093   11.1   1.2       0.83    8.0   1.1    2.1  2  Hydantoinase_B  Hydantoinase B/oxoprolinase
       0.17   11.1   7.6       0.27   10.5   7.6    1.3  1  MPS2            Monopolar spindle protein 2
       0.18   10.4   3.8       0.28    9.8   3.8    1.2  1  AAA_13          AAA domain
        0.2   11.8   3.9       0.58   10.3   3.9    1.8  1  Fib_alpha       Fibrinogen alpha/beta chain family
        0.2   11.6   1.3       0.68    9.9   0.9    2.1  1  Noelin-1        Neurogenesis glycoprotein
       0.32   10.6  10.3        5.6    6.5  10.1    2.5  1  DUF4795         Domain of unknown function (DUF4795)
       0.36    9.3   4.4       0.57    8.6   4.4    1.2  1  Herpes_UL6      Herpesvirus UL6 like
       0.44   10.9   9.2        0.8   10.1   1.0    3.3  3  Csm1_N          Csm1 N-terminal domain
       0.46   10.8  13.2      0.061   13.7   1.3    3.1  3  DUF641          Plant protein of unknown function (DUF641)
        0.5   10.4   7.2       0.74    9.9   1.7    3.2  3  Bap31_Bap29_C   Bap31/Bap29 cytoplasmic coiled-coil domain
       0.72   10.7   6.3          2    9.3   5.2    2.2  2  Csm2_III-A      Csm2 Type III-A
       0.79   10.2   3.1        4.8    7.6   0.5    3.2  3  FlaC_arch       Flagella accessory protein C (FlaC)
        2.2    6.8   6.1        4.4    5.8   6.1    1.4  1  FapA            Flagellar Assembly Protein A
        2.9    8.6   5.3         14    6.4   5.3    2.2  1  YabA            Initiation control protein YabA
          7    5.9   9.7        0.3   10.4   1.8    2.1  2  DUF4407         Domain of unknown function (DUF4407)
        8.1    5.2  14.7       0.52    9.1   7.6    2.2  2  Spc7            Spc7 kinetochore protein


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 ?   -2.9   0.0         6   5.1e+03      61      83 ..      38      59 ..      32      61 .. 0.82
   2 !  166.9   0.0   2.3e-52     2e-49       3     141 .]     215     346 ..     213     346 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 6
                         DUF460 61 eldreevieliselGkpvivAtD 83
                                    ++r+++i++i e  kp i+A+D
  gi|116753860|ref|YP_842978.1| 38 MVSRQKLIRFIREK-KPDIIAVD 59
                                   57899999999886.89999998 PP

  == domain 2  score: 166.9 bits;  conditional E-value: 2.3e-52
                         DUF460   3 kskdvkvevesvekdkiefeplkkkrkkklivGiDPGittgiavldldgevlalkssreldreevieliselGkpvivAt 82 
                                    ++ dv+++v ++ +++++f+pl ++r+++livG+DPG+ttgia+l+l+ge+++l s r++++++vie+i++ G+p+ivAt
  gi|116753860|ref|YP_842978.1| 215 SRGDVQIRVAPIPRQRLQFVPL-QQRRDYLIVGMDPGTTTGIAALNLRGELVDLISARTMSSSDVIEWIAARGRPLIVAT 293
                                    678*******************.9******************************************************** PP

                         DUF460  83 DvspppetvkklarslkavlyvPeedlsveeKeelaeklsekekvkykddHeRDalaAA 141
                                    Dvsp+p +v+k++r+++avly+P edl++e+K+ la+       ++y++dHeRDalaAA
  gi|116753860|ref|YP_842978.1| 294 DVSPAPGAVEKIKRAFNAVLYSPGEDLAAEDKIMLARP------FDYRNDHERDALAAA 346
                                    **************************************......999***********9 PP

>> CCD48  Coiled-coil domain-containing protein 48
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   2.7   3.8e-07   0.00033     179     273 ..     411     507 ..     397     524 .. 0.79
   2 ?   -3.1   0.9         2   1.7e+03     238     263 ..     610     635 ..     590     653 .. 0.47

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 3.8e-07
                          CCD48 179 deervarleeensslrelvedlraalqssdarclalqvglwksqaslkeaargepea..aarelrqaqgalaaaeararr 256
                                      e +  l e+   lre vedlra + s d     l+  l k q+ + ++ + + e     +e+ + ++ l a ++r rr
  gi|116753860|ref|YP_842978.1| 411 RPEELRLLTEQVRNLREYVEDLRAEISSKDKEISELKGQLEKLQDRAYREMKRDHEIriRDKEIERLRNLLRAERKRMRR 490
                                    5566677899999*******************************9987777665554115699***************** PP

                          CCD48 257 lrrgqaevrrraeearq 273
                                    lr +   +r+       
  gi|116753860|ref|YP_842978.1| 491 LRSEAKRIRKAERIEAM 507
                                    **997777764433334 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2
                          CCD48 238 relrqaqgalaaaeararrlrrgqae 263
                                    +e    q    +ae+ra+rlr    e
  gi|116753860|ref|YP_842978.1| 610 KERWAEQRRAYEAEKRAERLRSIIEE 635
                                    33333333333333333333333222 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 !   17.4   1.5   3.4e-06    0.0029      12      35 .]     431     454 ..     427     454 .. 0.91
   2 ?    1.1   2.4      0.44   3.7e+02      16      29 ..     466     479 ..     459     481 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.4e-06
                      PKcGMP_CC  12 ELEkrlaekdeEIqELrskLDKfQ 35 
                                    +L + ++ kd+EI EL+ +L K Q
  gi|116753860|ref|YP_842978.1| 431 DLRAEISSKDKEISELKGQLEKLQ 454
                                    78999*****************88 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.44
                      PKcGMP_CC  16 rlaekdeEIqELrs 29 
                                     ++ +d+EI+ Lr 
  gi|116753860|ref|YP_842978.1| 466 EIRIRDKEIERLRN 479
                                    68889******996 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   3.4     4e-05     0.034     224     295 ..     418     491 ..     338     502 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4e-05
                          FAM76 224 Lkeeiaslkkqleqkdqellekdkkitelkaellekekelreklke..lekeakekieklekkirellkevael 295
                                    L e++++l+  +e    e+++kdk+i+elk++l++ + +  + +k+    +  +++ie+l++  r+ +k + +l
  gi|116753860|ref|YP_842978.1| 418 LTEQVRNLREYVEDLRAEISSKDKEISELKGQLEKLQDRAYREMKRdhEIRIRDKEIERLRNLLRAERKRMRRL 491
                                    67788888888888888888888888888887776655544444430033445566666666666555555444 PP

>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   4.2e-05     0.036      38      64 ..     149     175 ..     122     188 .. 0.76
   2 ?   -0.6   0.1       1.8   1.5e+03      57     125 ..     355     423 ..     345     429 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.2e-05
                        acVLRF1  38 aaGGwSqqRfaRrrenqadalleavae 64 
                                     +GGwSq+R+ R++ + ++   +++++
  gi|116753860|ref|YP_842978.1| 149 GRGGWSQNRYSRKIHGNVKLISRDIEQ 175
                                    46***********99988876666655 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.8
                        acVLRF1  57 alleavaeaaarllaeesae.vvlgGd..rslvaevledarlaplatlareelldvpdprravLedavrrar 125
                                    + +++v++++ r +++++ + +v+ G   ++++ae+le+ +  p+a + ++   ++p pr + L+   ++ r
  gi|116753860|ref|YP_842978.1| 355 NKFSQVEKKVSRDVNPDEVKaLVVRGYsiEKAMAELLESDE-MPVASAEEP--PQIPPPRPEELRLLTEQVR 423
                                    56677888888888666666688888522466666666633.566666655..4566665555554444444 PP

>> Hydantoinase_B  Hydantoinase B/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   1.1   0.00097      0.83     162     210 ..     415     463 ..     408     504 .. 0.79
   2 ?    0.3   0.0      0.21   1.8e+02      72      99 ..     529     554 ..     512     556 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00097
                 Hydantoinase_B 162 lelllanvRtpednlgDlkAqiaanqvgerrlkelieeyGldtveaamd 210
                                    l+ll+++vR++++ + Dl+A+i++ ++ +++lk  +e+    +++++ +
  gi|116753860|ref|YP_842978.1| 415 LRLLTEQVRNLREYVEDLRAEISSKDKEISELKGQLEKLQDRAYREMKR 463
                                    699*****************************99999988888877655 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.21
                 Hydantoinase_B  72 ekfegelkpGDvlltNdPyaggtHlpDi 99 
                                     k+  ++ +GD++l+ dP  gg  + D+
  gi|116753860|ref|YP_842978.1| 529 SKW--SIGRGDLILLQDPSGGGPNTADL 554
                                    222..67788888888888777677665 PP

>> MPS2  Monopolar spindle protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   7.6   0.00031      0.27     105     223 ..     363     481 ..     347     508 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00031
                           MPS2 105 kisslelkeevkrlvvlssknsekdslstprkkilldllkkqesPeklrrsnrklkaLevrveslkdELeakdevlreke 184
                                    k+s+ +  +evk lvv     +++  +    ++  +     +e P+ ++ + + l+ L  +v +l++ +e+    +  k+
  gi|116753860|ref|YP_842978.1| 363 KVSRDVNPDEVKALVVRGYSIEKAMAELLESDE--MPVASAEEPPQIPPPRPEELRLLTEQVRNLREYVEDLRAEISSKD 440
                                    555555556777776666555555555555555..55667788899999999**************************** PP

                           MPS2 185 RelleLkkrlseykek.Yellqrefs.lykarrveksqnsl 223
                                    +e++eLk +l++++++ Y  ++r+++   +++++e  +n l
  gi|116753860|ref|YP_842978.1| 441 KEISELKGQLEKLQDRaYREMKRDHEiRIRDKEIERLRNLL 481
                                    ***************779******99445777777777764 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   3.8   0.00033      0.28     327     454 ..     340     503 ..     304     508 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00033
                         AAA_13 327 kaeaealeeqLkglqraleaKrkepfksvelesvkakie......................................sik 368
                                    ++++ a  +++k+ +++ ++  k+++++v+ ++vka ++                                       ++
  gi|116753860|ref|YP_842978.1| 340 RDALAAAMSAFKKYRNKFSQVEKKVSRDVNPDEVKALVVrgysiekamaellesdempvasaeeppqippprpeelrLLT 419
                                    34556667789999999999999999999999999999888999999999999999999999999999999999999999 PP

                         AAA_13 369 klvaeineliakhNekvanleeekeeakkklelhlveeleseldeykkkykklekaieklekelkeeeaelkkleeeike 448
                                    ++v ++ e +++  + +++ ++e +e+k +le+     ++ e++  +++++  +k+ie l + l++e ++++ l+ e+k 
  gi|116753860|ref|YP_842978.1| 420 EQVRNLREYVEDLRAEISSKDKEISELKGQLEKLQDR-AYREMK-RDHEIRIRDKEIERLRNLLRAERKRMRRLRSEAKR 497
                                    ********************************95555.555654.567899999************************99 PP

                         AAA_13 449 Lekqlr 454
                                    ++k  r
  gi|116753860|ref|YP_842978.1| 498 IRKAER 503
                                    999765 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   3.9   0.00068      0.58      44     125 ..     415     495 ..     412     501 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00068
                                    CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHH CS
                      Fib_alpha  44 leeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvlesneqkiqkLeq 123
                                    l+ ++++ ++ +e+v++++  + +k k+ ++ +  ++k++++   + ++ +++i    ++i+ L+n+l++ ++++ +L++
  gi|116753860|ref|YP_842978.1| 415 LRLLTEQVRNLREYVEDLRAEISSKDKEISELKGQLEKLQDRAY-REMKRDHEIRIRDKEIERLRNLLRAERKRMRRLRS 493
                                    66677888899999999999999999999999999999999999.8888899999999********************98 PP

                                    HH CS
                      Fib_alpha 124 di 125
                                    + 
  gi|116753860|ref|YP_842978.1| 494 EA 495
                                    76 PP

>> Noelin-1  Neurogenesis glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.9    0.0008      0.68      36      90 ..     410     465 ..     408     476 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0008
                       Noelin-1  36 arsrqlrqllekvqnlsqsievldlRtsrdlqyvrktetllktlesk.lkvveedr 90 
                                    +r ++lr l+e+v+nl + +e l    s+  +++++ + +l++l+++ +++++ d+
  gi|116753860|ref|YP_842978.1| 410 PRPEELRLLTEQVRNLREYVEDLRAEISSKDKEISELKGQLEKLQDRaYREMKRDH 465
                                    67889*******************999999999********999887245555554 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5  10.1    0.0065       5.6      88     167 ..     420     512 ..     357     514 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0065
                        DUF4795  88 eakkeLekmleellekleeqeealkkaldtLq.......eelkekld....rlelepLkeqle...erlkelqkelqeam 153
                                    e +  L++ +e+l+  ++++++++ ++  +L+       +e+k   +     +e+e+L++ l    +r++ l+ e + ++
  gi|116753860|ref|YP_842978.1| 420 EQVRNLREYVEDLRAEISSKDKEISELKGQLEklqdrayREMKRDHEirirDKEIERLRNLLRaerKRMRRLRSEAK-RI 498
                                    4445556666666666665555555554444455566666666555566669**********999999999998887.55 PP

                        DUF4795 154 ekedkedeaaglrk 167
                                    +k +  +++ag rk
  gi|116753860|ref|YP_842978.1| 499 RKAERIEAMAGYRK 512
                                    66666679999997 PP

>> Herpes_UL6  Herpesvirus UL6 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   4.4   0.00066      0.57     369     454 ..     417     501 ..     414     506 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00066
                     Herpes_UL6 369 cleeqineqfdtiekLkkenelllkklkelekeLerlreeakkeakarevdlltsstdaslenlpessalsklkkvidts 448
                                     l+eq+ ++ + +e+L++e +   k ++el+ +Le+l+++a +e k+ +      + ++ l nl + +   +++++   +
  gi|116753860|ref|YP_842978.1| 417 LLTEQVRNLREYVEDLRAEISSKDKEISELKGQLEKLQDRAYREMKRDHEIRIRDKEIERLRNLLRAERK-RMRRLRSEA 495
                                    79************************************99999999999888999999999999544443.336666666 PP

                     Herpes_UL6 449 ksvddd 454
                                    k + + 
  gi|116753860|ref|YP_842978.1| 496 KRIRKA 501
                                    666655 PP

>> Csm1_N  Csm1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       2.8   2.4e+03      41      59 ..     413     431 ..     411     434 .. 0.59
   2 ?   10.1   1.0   0.00094       0.8      32      61 ..     432     461 ..     430     466 .. 0.83
   3 ?    4.0   1.2     0.073        63      34      64 ..     465     495 ..     460     502 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.8
                         Csm1_N  41 qeiesLkeqlaeleekvke 59 
                                    +e+  L eq+ +l+e v++
  gi|116753860|ref|YP_842978.1| 413 EELRLLTEQVRNLREYVED 431
                                    5566666666666666554 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00094
                         Csm1_N  32 LsqkletkdqeiesLkeqlaeleekvkele 61 
                                    L+ ++++kd+ei++Lk ql++l+ +  +  
  gi|116753860|ref|YP_842978.1| 432 LRAEISSKDKEISELKGQLEKLQDRAYREM 461
                                    667899****************99876555 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.073
                         Csm1_N  34 qkletkdqeiesLkeqlaeleekvkeleerr 64 
                                     +++ +d+eie+L++ l + ++++++l +++
  gi|116753860|ref|YP_842978.1| 465 HEIRIRDKEIERLRNLLRAERKRMRRLRSEA 495
                                    57889************99999998877665 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 ?   13.7   1.3   7.1e-05     0.061      85     122 ..     420     457 ..     403     463 .. 0.85
   2 ?    3.6   1.0     0.093        80      98     125 ..     464     491 ..     458     497 .. 0.78
   3 ?   -0.7   0.2         2   1.7e+03      59      92 ..     604     638 ..     583     652 .. 0.48

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.1e-05
                         DUF641  85 sllktyeitvkkleaelkakdseieeLkekLeeaeksn 122
                                    + ++ +   v++l+ae+++kd+ei+eLk +Le+++ + 
  gi|116753860|ref|YP_842978.1| 420 EQVRNLREYVEDLRAEISSKDKEISELKGQLEKLQDRA 457
                                    5677888899**********************999875 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.093
                         DUF641  98 eaelkakdseieeLkekLeeaeksnkkl 125
                                    + e++ +d+eie+L++ L++++k+ ++l
  gi|116753860|ref|YP_842978.1| 464 DHEIRIRDKEIERLRNLLRAERKRMRRL 491
                                    5688999999999999998888777665 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 2
                         DUF641  59 lyrkkqkkkas.eaeeseleaeiqeqrsllktyei 92 
                                      +k  k++ + + +  e e++++++rs+++ y +
  gi|116753860|ref|YP_842978.1| 604 EMLKAAKERWAeQRRAYEAEKRAERLRSIIEEYRA 638
                                    44444333322113333344444445555555543 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 ?   -0.2   0.0       1.2     1e+03      30      41 ..     106     117 ..     105     126 .. 0.81
   2 ?    9.9   1.7   0.00087      0.74       3      28 ..     429     454 ..     427     466 .. 0.90
   3 ?    0.9   0.4      0.55   4.7e+02       1      26 [.     472     497 ..     472     501 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.2
                  Bap31_Bap29_C  30 EYDrLadehskl 41 
                                    ++DrL++ h++ 
  gi|116753860|ref|YP_842978.1| 106 AFDRLNPMHEAE 117
                                    59*******975 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00087
                  Bap31_Bap29_C   3 iekLkkeLkkkkkDlealKkQaegla 28 
                                    +e L++e+ +k+k++  lK Q e l+
  gi|116753860|ref|YP_842978.1| 429 VEDLRAEISSKDKEISELKGQLEKLQ 454
                                    899*********************98 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.55
                  Bap31_Bap29_C   1 keiekLkkeLkkkkkDlealKkQaeg 26 
                                    keie+L++ L +++k +  l++ a+ 
  gi|116753860|ref|YP_842978.1| 472 KEIERLRNLLRAERKRMRRLRSEAKR 497
                                    79*********999777777666654 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 ?   -1.5   0.0       5.3   4.6e+03      29      49 ..     160     180 ..     158     207 .. 0.81
   2 ?    9.3   5.2    0.0023         2      22      92 ..     416     492 ..     411     514 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 5.3
                                    HHHHHHHHHHHHHHHHTHHHH CS
                     Csm2_III-A  29 Rkfydevkrieekikkkkeee 49 
                                    Rk++++vk i+++i+++ +e 
  gi|116753860|ref|YP_842978.1| 160 RKIHGNVKLISRDIEQRLKES 180
                                    999******999998876665 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0023
                                    TS-STTTHHHHHHHHHHHHHHHHTHHHHHHHTHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHHHHH--SH. CS
                     Csm2_III-A  22 klktsqiRkfydevkrieekikkkkeeeseeilrklkllkpklaYaagr.......eeavkelsevlkkaidkvkksk 92 
                                    +l t q+R++ ++v++++++i++k++e  +e++ +l+ l+ ++  + +r       +++++ l++ l++  +   + +
  gi|116753860|ref|YP_842978.1| 416 RLLTEQVRNLREYVEDLRAEISSKDKEI-SELKGQLEKLQDRAYREMKRdheirirDKEIERLRNLLRAERKRMRRLR 492
                                    57899***************98887776.9************999999966665554555555555544444444333 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 ?    0.5   0.0      0.94     8e+02      44      51 ..      36      43 ..      35      44 .. 0.91
   2 ?   -2.2   0.0       6.7   5.7e+03      47      53 ..     364     370 ..     351     370 .. 0.80
   3 ?    7.6   0.5    0.0057       4.8       3      36 ..     423     456 ..     421     462 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.94
                      FlaC_arch 44 YEvVsnqv 51
                                   YE+Vs+q+
  gi|116753860|ref|YP_842978.1| 36 YEMVSRQK 43
                                   ******96 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.7
                      FlaC_arch  47 VsnqvNP 53 
                                    Vs++vNP
  gi|116753860|ref|YP_842978.1| 364 VSRDVNP 370
                                    7888887 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0057
                      FlaC_arch   3 delEnklsklsteletvkkeneelsksveelken 36 
                                     +l + +++l  e+++  ke++el+ ++e+l+++
  gi|116753860|ref|YP_842978.1| 423 RNLREYVEDLRAEISSKDKEISELKGQLEKLQDR 456
                                    6777889999999999999999999999999986 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   6.1    0.0051       4.4     333     419 ..     423     506 ..     410     515 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0051
                           FapA 333 pelkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletk.eklkeeleeleeelkelkeelesk 411
                                     +l+e +++l+ e+ +  +e+ +lk +++kl++ +a   + + k++   +++ +  e+l++ l++ ++++ +l +e ++ 
  gi|116753860|ref|YP_842978.1| 423 RNLREYVEDLRAEISSKDKEISELKGQLEKLQD-RA---YREMKRDHEIRIRDKEiERLRNLLRAERKRMRRLRSEAKRI 498
                                    47889999************************9.33...33444444444444443888889999999999999999998 PP

                           FapA 412 keeakikv 419
                                    +++++i++
  gi|116753860|ref|YP_842978.1| 499 RKAERIEA 506
                                    65557775 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   5.3     0.017        14       5      58 ..     431     487 ..     413     514 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.017
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHXXXXXX CS
                           YabA   5 elfdkleeleeqleelleeleelkeelaelleenaeLel...eneklrerleeeekk 58 
                                    +l +++++ +++++el+ +le+l+++ ++ +++++e+++   e e+lr++l+ e+k+
  gi|116753860|ref|YP_842978.1| 431 DLRAEISSKDKEISELKGQLEKLQDRAYREMKRDHEIRIrdkEIERLRNLLRAERKR 487
                                    556677777788888888888888888888888888887333466677777333333 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.8   0.00035       0.3     126     208 ..     421     499 ..     337     516 .. 0.69
   2 ?   -0.4   1.2      0.66   5.7e+02     191     233 ..     605     647 ..     597     652 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00035
                        DUF4407 126 qlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqaelaelkak 205
                                    q++ +l++ +++l+a+i++ ++ei++++ +l++l++ a +e++ +       ++ + ++ ++ ++ l a ++++  l+++
  gi|116753860|ref|YP_842978.1| 421 QVR-NLREYVEDLRAEISSKDKEISELKGQLEKLQDRAYREMKRDHE-----IRIRDKEIERLRNLLRAERKRMRRLRSE 494
                                    332.3566666666677777777777777777777777666665332.....3334455566666666666666666655 PP

                        DUF4407 206 ld..a 208
                                     +  +
  gi|116753860|ref|YP_842978.1| 495 AKriR 499
                                    33221 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.66
                        DUF4407 191 qldaaqaelaelkakldatarlaalraelaeleaerakeraas 233
                                    +l+aa++++ae ++  +a++r ++lr+ ++e +aer +e++  
  gi|116753860|ref|YP_842978.1| 605 MLKAAKERWAEQRRAYEAEKRAERLRSIIEEYRAERLREERLE 647
                                    6778888888888888899999999999999888888877654 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   7.6   0.00061      0.52     199     280 ..     420     500 ..     411     510 .. 0.73
   2 ?   -0.7   0.6      0.59     5e+02     196     226 ..     601     630 ..     586     652 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00061
                           Spc7 199 eeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkal 278
                                    e++++lre +++l aei++k ke++el+ qle+l+++     ++ +e++ + +e er+++  +  +++  +rl++e k++
  gi|116753860|ref|YP_842978.1| 420 EQVRNLREYVEDLRAEISSKDKEISELKGQLEKLQDRAYREMKRDHEIRIRDKEIERLRNLLR-AERKRMRRLRSEAKRI 498
                                    678899999999999999999999999999999999887666666777666666666666444.4555666666666665 PP

                           Spc7 279 ee 280
                                     +
  gi|116753860|ref|YP_842978.1| 499 RK 500
                                    55 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.59
                           Spc7 196 idkeeLeelreelaelkaeieekkkelaelq 226
                                    +d+e L++++e+ ae+   +e+ k+  ++l+
  gi|116753860|ref|YP_842978.1| 601 VDPEMLKAAKERWAEQRRAYEAEKR-AERLR 630
                                    7888888888888888888874443.33333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (654 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1605  (0.0895198); expected 358.6 (0.02)
Passed bias filter:                      913  (0.0509231); expected 358.6 (0.02)
Passed Vit filter:                       171  (0.00953762); 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):              21  [number of targets reported over threshold]
# CPU time: 0.90u 0.31s 00:00:01.21 Elapsed: 00:00:00.44
# Mc/sec: 4422.64
//
Query:       gi|116753861|ref|YP_842979.1|  [L=288]
Description: protein of unknown function RIO1 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-40  139.4   0.1    1.4e-40  139.0   0.1    1.1  1  RIO1      RIO1 family
    6.1e-23   80.9   0.0    1.1e-22   80.0   0.0    1.4  1  Rio2_N    Rio2, N-terminal
    2.1e-05   24.6   3.1      0.073   13.0   0.3    2.9  2  APH       Phosphotransferase enzyme family
     0.0014   18.4   0.1      0.022   14.6   0.0    2.3  2  HTH_IclR  IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.011   15.6   0.0       0.22   11.4   0.0    2.5  2  TrmB      Sugar-specific transcriptional regulator TrmB


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 !  139.0   0.1   3.8e-44   1.4e-40       2     180 ..     107     270 ..     106     278 .. 0.91

  Alignments for each domain:
  == domain 1  score: 139.0 bits;  conditional E-value: 3.8e-44
                                    EEEEEETTTEEEEEEEE-S---SS-HHHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEEEETT CS
                           RIO1   2 VyhavsedgkevaiKiyktstteFkkrkkyvsgekrfkdrksktnprklvklwaekEfrnLkrleeagvpvPkpielkrh 81 
                                    Vy+a   d+  ++iK+++ ++t+F ++++ +++ ++    + k  + + + l+a+ Ef+ +++l+ + v+vPkpi+  rh
  gi|116753861|ref|YP_842979.1| 107 VYEAL--DDIPLVIKFHREGRTSFSRVRRVRDYLRD----RPKVAWIYAAALAARTEFDVMRKLYPH-VSVPKPIARSRH 179
                                    67764..46689*********************999....689************************.************ PP

                                    EEEEE--EETTEEGGBHHHCG-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETTEEEE--GTTEEETTSTTHH CS
                           RIO1  82 vlvmefigedgvaapklkdveeeeeaeelyeevleemrklykeaglvHaDLSeyNvlvdedkvviIDvsQaveldhpnal 161
                                    ++vme +   gv ++k  d++   + + +++ +lee+ k+y + g++HaD+SeyNv+v +d ++iID++Qav  dh++a+
  gi|116753861|ref|YP_842979.1| 180 AVVMERVP--GVLLTKT-DLD---DPAFYLNRILEEIGKAY-RLGVIHADMSEYNVIVADD-IIIIDWPQAVGSDHESAE 251
                                    *******9..8877764.344...4667999**********.***************9987.****************** PP

                                    HHHHHHHHHHHHHHHTTC- CS
                           RIO1 162 efLerDveniikfFrrkgv 180
                                    e+L+rD++ni k+F+r++ 
  gi|116753861|ref|YP_842979.1| 252 ELLNRDISNILKYFKRRYK 270
                                    ***************9976 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.0   0.0     3e-26   1.1e-22       3      82 .]      10      89 ..       8      89 .. 0.98

  Alignments for each domain:
  == domain 1  score: 80.0 bits;  conditional E-value: 3e-26
                         Rio2_N  3 yLskedfrvLtavEmgmrnhevVptelieeisrlkeeevkkrlsrllkaklisrktakydGYkLtyeGyDyLALktlvkr 82
                                   +L +ed  +L+a+E gmr+ e+Vp e+i+ is++ +++ ++ l+ l ++kl+++++++y+GY++ +++yD LAL+ lv+r
  gi|116753861|ref|YP_842979.1| 10 SLRSEDVTLLRAIEAGMRRREWVPIEEISAISGIPASKADYYLRLLSDRKLVAHTNVPYEGYQIEFAAYDLLALHDLVRR 89
                                   6999************************************************************************9987 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.3     2e-05     0.073      27      96 ..     140     208 ..      96     215 .. 0.75
   2 !   11.9   0.1   4.3e-05      0.15     163     196 ..     213     242 ..     194     246 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2e-05
                                    EE-TT....S-HHHHHHHHHHHHHHHHTT-B--B-CTTBS-EEETTEEEEEEE----EE-SS...HHHHHHHHHHHH CS
                            APH  27 rnppa....raaeeirrevallrlLakagvpvPevlagdtddeeigllfalieyvpgrsllr...klsaaqlpelle 96 
                                    + p+      aa  +r e++++r L  + v+vP+++a       + ++++++e+vpg  l+     + a  l ++le
  gi|116753861|ref|YP_842979.1| 140 DRPKVawiyAAALAARTEFDVMRKLYPH-VSVPKPIA-------RSRHAVVMERVPGVLLTKtdlDDPAFYLNRILE 208
                                    4444445545678889999999999999.99******.......77799*********9999655444555555555 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 4.3e-05
                                    SS-EEEE-SS-SGGGEEEC..TTEEEEE---TT- CS
                            APH 163 elptvllHgDlhpgNllvdpddgrvtGviDfeda 196
                                    + + +++H D +  N++v   d+ +  +iD+  a
  gi|116753861|ref|YP_842979.1| 213 AYRLGVIHADMSEYNVIVA--DDII--IIDWPQA 242
                                    56789**************..99**..****655 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   6.1e-06     0.022       7      49 ..      17      62 ..      16      64 .. 0.91
   2 ?    1.2   0.0     0.091   3.3e+02      39      49 ..      83      93 ..      82      96 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.1e-06
                                   HHHCT-CTTBSS...-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                       HTH_IclR  7 aiLdalaeapqe...ltlselArrtglpkStvhRlLqtLvelGyve 49
                                    +L+a++++ ++   + + e+++ +g+p S++  +L+ L  +++v 
  gi|116753861|ref|YP_842979.1| 17 TLLRAIEAGMRRrewVPIEEISAISGIPASKADYYLRLLSDRKLVA 62
                                   5899999998888878***************************996 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.091
                                   HHHHHHTTSEE CS
                       HTH_IclR 39 LqtLvelGyve 49
                                   L+ Lv++G+v 
  gi|116753861|ref|YP_842979.1| 83 LHDLVRRGFVA 93
                                   899******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 ?   11.4   0.0   6.1e-05      0.22      25      60 ..      34      69 ..      28      80 .. 0.87
   2 ?    1.4   0.0     0.083     3e+02      42      64 ..      82     110 ..      76     112 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.1e-05
                                   HCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTT CS
                           TrmB 25 adeiaeelgvprskvYevLrsLedkGlVerekgrpk 60
                                   ++ei+ ++g+p sk+  +Lr L+d+ lV      + 
  gi|116753861|ref|YP_842979.1| 34 IEEISAISGIPASKADYYLRLLSDRKLVAHTNVPYE 69
                                   589*************************98776654 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.083
                                    HHHHHHHCTSEEEESST......TTEEEE CS
                           TrmB  42 vLrsLedkGlVerekgr......pklYra 64 
                                    +L  L+++G+V     r        +Y+a
  gi|116753861|ref|YP_842979.1|  82 ALHDLVRRGFVASLGDRlgvgkeSVVYEA 110
                                    578999****9877666666655556655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); 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: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2149.37
//
Query:       gi|116753862|ref|YP_842980.1|  [L=375]
Description: isocitrate dehydrogenase (NAD(+)) [Methanosaeta thermophila PT]
Scores for 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-68  232.0   0.0    1.6e-68  231.4   0.0    1.2  1  Iso_dh    Isocitrate/isopropylmalate dehydrogenase


Domain annotation for each model (and alignments):
>> Iso_dh  Isocitrate/isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  231.4   0.0     9e-73   1.6e-68       2     319 ..      18     327 ..      17     339 .. 0.91

  Alignments for each domain:
  == domain 1  score: 231.4 bits;  conditional E-value: 9e-73
                                    EEEEEESTTHHHHHHHHHHHHHHHHHHHT-EEEEEE---THHHHHHHS...SSS-HHHHHHHHHSSEEEEEE---CS... CS
                         Iso_dh   2 iallegdgiGpevveaalkvlkaakekaglelefeevdvGgaaidetg...eplpeetleaikeadvvllgavgtpk... 75 
                                    i  + gdgiGp ++ +a++vl+++ + +  + ++e +++ g +i+e     ++lp+++l+a+k+ +v+l+g+++tpk   
  gi|116753862|ref|YP_842980.1|  18 IGYVDGDGIGPYITGEAIRVLQSLLRDELERGDVEFRKIEGLSIEERAramKALPDDALDALKKCHVILKGPLTTPKkgd 97 
                                    66789********************9999888888888888888876656699************************776 PP

                                    .SSSSSHHHHHHHHHHHTTEEEEEEEEE-BCCTTCCSSBTHHHHCT-EEEEEEE-SSCGGCSSEEEEETTG.GGGEEEEE CS
                         Iso_dh  76 .ekevrpengLlaLrkeldlfanlrpvkvfeklkvksplkrevveevdlvivReltggiYfgeekekkgsifteevavdt 154
                                       ++++ n  +a+r+eldlfan+rpv +           +   e++d v +Re+t+g Y+   k  +    t++ avd 
  gi|116753862|ref|YP_842980.1|  98 pWPNLESAN--VAMRRELDLFANVRPVSIP----------S---EGIDWVFFRENTEGEYVLGSKGFNV---TDDLAVDF 159
                                    556777777..****************987..........2...689*************988887766...589***** PP

                                    EEEEHHHHHHHHHHHHHHHHHTTTSEEEEEESTTTTHHHH.HHHHHHHHHHCCTTTTSEEEEEEHHHHHHHHHHSG..GG CS
                         Iso_dh 155 klyseeeieriaraafelAlkrgkkkvtlvdKanvlksse.lwrkiveevaeeeypdielehqlvDsaamqlvksp..kq 231
                                    k+++++++eri+r+af++A++++ ++v +v+Kanv k+++  + +i+  + + eyp+i++++ +vD +a++lv     + 
  gi|116753862|ref|YP_842980.1| 160 KVITTQGSERIIRLAFDYARRNNINRVSVVTKANVVKTTDgKFLEIARAISK-EYPEITFDDWFVDIMAAKLVDTKrrRD 238
                                    ****************************************888888888888.********************8773356 PP

                                    GSEEEE-HHHHHHHHHHHHHHTTSGCC-EEEEEETSS-EEEEESS---CCCTTSS-...S-THHHHHHHHHHHHHTTT-H CS
                         Iso_dh 232 fdVivtkNlfGDilSDeaaalvGslGllpSaslgekkvaifEavHGsapdiagkdk...aNpiavilSaalmLryslgle 308
                                    f Viv +Nl+GDil Deaa   G++G + Sa++g k+ a+fEa+HGsap++   +    a p++ + + +++Lr+ +g+ 
  gi|116753862|ref|YP_842980.1| 239 FRVIVLPNLYGDILTDEAAEFQGGVGTAGSANIG-KRYAMFEAIHGSAPRMVQEGRaqyADPSSIMRASTMLLRH-VGMI 316
                                    77********************************.79*************9876665569***************.**** PP

                                    HHHHHHHHHHH CS
                         Iso_dh 309 eaAdkiekAve 319
                                    ++A+k+e A++
  gi|116753862|ref|YP_842980.1| 317 DKARKLEMALD 327
                                    *******9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2823.73
//
Query:       gi|116753863|ref|YP_842981.1|  [L=243]
Description: hypothetical protein Mthe_0550 [Methanosaeta thermophila PT]
Scores for complete 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-70  234.9   0.0    8.4e-70  234.7   0.0    1.0  1  DUF166    Domain of unknown function
  ------ inclusion threshold ------
       0.11   12.7   0.0       0.31   11.1   0.0    1.8  2  DapB_N    Dihydrodipicolinate reductase, N-terminus


Domain annotation for each model (and alignments):
>> DUF166  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  234.7   0.0   9.4e-74   8.4e-70       2     219 ..       5     219 ..       4     220 .. 0.99

  Alignments for each domain:
  == domain 1  score: 234.7 bits;  conditional E-value: 9.4e-74
                         DUF166   2 vltsgeyGervvenilnepdferslivavvevpeeldefiedpeelLpe......lkeaDiviaytlhpDlllelaekak 75 
                                    v+t+g+yGer++++il+++df+    v++++vpe+l+ fiedp+e+L++      ++++D++++ytlhpDl+ ++a++a 
  gi|116753863|ref|YP_842981.1|   5 VITRGKYGERLIDTILRHTDFD----VVHAAVPETLPGFIEDPDEFLRSidlnedVFSSDLIVMYTLHPDLTPAIARIAG 80 
                                    9*********************....**********************9999999************************* PP

                         DUF166  76 ekkvkalivpaeapkaglrkelkekleelgievavpkpfCsleeegkpkideFleefGkPelevevkdgkikkVeVlrsa 155
                                    e++vkal++p   ++ag ++el++ +e++++ ++v++++C+le++g + +d+F+e++G+Pel+ve+++g+i +V+V+r++
  gi|116753863|ref|YP_842981.1|  81 ERGVKALLIPGGIGRAGSIEELRSISERYNVYIEVDEICCTLEKVGVDAVDQFAEHLGRPELRVELNSGRIGRVDVVRGS 160
                                    ******************************************************************************** PP

                         DUF166 156 pCGstwyvakklkGkeveeaeekageahqsYpClAsmerdfelketklhkAgyihkeavekAlk 219
                                    pCGstw+va++l+Gk+v ea++ ag+a+q+YpC+A+++     + +++h++g++hk+a+e+Al+
  gi|116753863|ref|YP_842981.1| 161 PCGSTWHVARELIGKSVAEAPSLAGLACQQYPCRAVRG-----TPGGIHTSGDLHKNAMERALG 219
                                    **************************************.....99*****************98 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   3.5e-05      0.31       1     115 [.       1     108 [.       1     115 [. 0.76
   2 ?   -3.3   0.0         1   9.3e+03      86     100 ..     187     201 ..     186     213 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.5e-05
                                    EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH-SEEEE-S.-HHH CS
                         DapB_N   1 ikvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavtddleevlekadvliDFT.tpea 79 
                                    ++v+v+  +G+ G+++++++ +++d+ +v a   ++ +   +d        + ++  + dl+e + ++d ++ +T +p+ 
  gi|116753863|ref|YP_842981.1|   1 MRVGVIT-RGKYGERLIDTILRHTDFDVVHAAVPETLPGFIED--------PDEFLRSIDLNEDVFSSDLIVMYTlHPDL 71 
                                    6888886.5*********************9999874333344........44555567888888889999999989999 PP

                                    HHHHHHHHHHTT-EEEE--SS-.-HHHHHHHHHHTTT CS
                         DapB_N  80 vlenlklalekgvklViGTTGl.seeelaeleelakk 115
                                    + + +++a e+gvk+ +   G+  +  ++el++++++
  gi|116753863|ref|YP_842981.1|  72 TPAIARIAGERGVKALLIPGGIgRAGSIEELRSISER 108
                                    9999999999999987666666455566666666655 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1
                                    HHHHTT-EEEE--SS CS
                         DapB_N  86 lalekgvklViGTTG 100
                                    ++ +++ ++V GT G
  gi|116753863|ref|YP_842981.1| 187 ACQQYPCRAVRGTPG 201
                                    578889999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 1722.19
//
Query:       gi|116753864|ref|YP_842982.1|  [L=271]
Description: tartrate/fumarate subfamily Fe-S type hydro-lyase alpha subunit [Methanosaeta thermophila PT]
Scores for complete 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-84  281.3   0.0    8.5e-84  281.2   0.0    1.0  1  Fumerase  Fumarate hydratase (Fumerase)


Domain annotation for each model (and alignments):
>> Fumerase  Fumarate hydratase (Fumerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  281.2   0.0   4.7e-88   8.5e-84       3     269 ..       4     261 ..       2     262 .. 0.94

  Alignments for each domain:
  == domain 1  score: 281.2 bits;  conditional E-value: 4.7e-88
                       Fumerase   3 aveealkeastelpedvlealkkalekEesenakevleqlleNaeiAaeeklplCqDTGiavvfvkigeevevetgdlee 82 
                                    a+e +  + +++lp +v++ +++al++E+se+a++ l+++l+N++iA+ + +p+CqDTG++v++v+ige ++  + +l e
  gi|116753864|ref|YP_842982.1|   4 ATEAVACKSQISLPGWVVRLIENALRSERSEIARYHLNAILNNIRIAEADARPVCQDTGLPVFHVEIGEGCS-FDFNLWE 82 
                                    6677788999*************************************************************7.999**** PP

                       Fumerase  83 aineGvreaykegplRksvvadplerkntgd....nlPavihielvpgdeleitvlakGgGsenksklkmlnpsdglegv 158
                                    ai+eGv  a+++g lR +vv dpl+r ntgd    ++P ++ ++ v gd+l+it+++kG+Gsen+s+l mlnp+d   + 
  gi|116753864|ref|YP_842982.1|  83 AIAEGVTIATRKGMLRSNVV-DPLSRLNTGDntgpGMP-YLIVDHVTGDSLRITAFPKGAGSENMSFLGMLNPAD---DP 157
                                    ********************.**********7777778.77788889**************************76...9* PP

                       Fumerase 159 kkfvletvkeagtnaCpPlvlgvgiGgtseeaallakkallrelgeenpdeelaeleeellekinklgiGpqGlGGkttv 238
                                     +++le+++e  +naCpP+++g+giGgt+++aa lak+a+   +g  ++    ++ e  ll++in+lgiGp+GlGG+tt+
  gi|116753864|ref|YP_842982.1| 158 FEYILENLAERVSNACPPVFVGIGIGGTFDQAAALAKRAI---IGLPGE----SKEELLLLKRINDLGIGPMGLGGDTTA 230
                                    ****************************************...666673....345999********************* PP

                       Fumerase 239 ldvkierlprhiAslpvavnvsCsadRrakv 269
                                    l+vkier+ +h+Aslpvavn++C+a+Rra++
  gi|116753864|ref|YP_842982.1| 231 LGVKIERAFCHTASLPVAVNLQCWANRRATA 261
                                    ****************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       235  (0.0131073); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); 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: 00:00:00.43
# Mc/sec: 1897.93
//
Query:       gi|116753865|ref|YP_842983.1|  [L=176]
Description: tartrate/fumarate subfamily Fe-S type hydro-lyase beta subunit [Methanosaeta thermophila PT]
Scores for complete 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-29  100.8   0.0    8.3e-29  100.4   0.0    1.1  1  Fumerase_C  Fumarase C-terminus


Domain annotation for each model (and alignments):
>> Fumerase_C  Fumarase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.4   0.0   4.6e-33   8.3e-29      37     205 ..      10     165 ..       3     166 .. 0.89

  Alignments for each domain:
  == domain 1  score: 100.4 bits;  conditional E-value: 4.6e-33
                     Fumerase_C  37 teeelskykvgtrlllsGkllvaRDaaHkrlkerlekgeelpeyvklkdrviYyaGPvktpedeavgsaGPTTatRmdky 116
                                     e ++sk+ +g+ + lsG +++aRD aH+rl e       +   ++l++ viY++GP    +d++v saGPT + R  +y
  gi|116753865|ref|YP_842983.1|  10 SEGDVSKLSAGDIVWLSGVIYTARDKAHQRLGE-------VK--FDLRGGVIYHCGPL--IRDTTVVSAGPTSSVRLARY 78 
                                    567899*************************94.......44..8999*********8..6788999************* PP

                     Fumerase_C 117 vekllkktgllimlaKgnrskkvleaikkhggvYLgaiGG.aAilakkaikkvevvefeelGm.EAiyeievedf.pafv 193
                                    + ++l+  g++ +++Kg++  +  + + + ++vYL   GG +A  a+++  +v+ v  +elGm EA++e+e +d+ p +v
  gi|116753865|ref|YP_842983.1|  79 TPQVLD-LGVRCIIGKGGMPGA--AELMRGRAVYLAYPGGcGA-AAARS-LSVRGVCLSELGMaEAVWEFEATDLgPMVV 153
                                    *****8.79********99765..468899**********544.45555.4899********************978999 PP

                     Fumerase_C 194 vvddkGndlfke 205
                                    ++d++G dl++e
  gi|116753865|ref|YP_842983.1| 154 AIDSHGRDLYRE 165
                                    **********87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       220  (0.0122706); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); 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 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 1251.32
//
Query:       gi|116753866|ref|YP_842984.1|  [L=186]
Description: hypothetical protein Mthe_0553 [Methanosaeta thermophila PT]
Scores for 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-47  159.0   0.1    1.1e-46  158.6   0.1    1.2  1  DUF5616   Domain of unknown function (DUF5616)
    1.7e-05   24.4   0.3    4.2e-05   23.1   0.3    1.7  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 !  158.6   0.1   1.3e-50   1.1e-46       2     139 ..      36     173 ..      35     174 .. 0.98

  Alignments for each domain:
  == domain 1  score: 158.6 bits;  conditional E-value: 1.3e-50
                        DUF5616   2 eelkgkelliDGfNvlitlesalsgevlllcdDgviRDlagvrgkyklveeteealelilellkelkvkkvifllDkpvS 81 
                                    e+l g  l+iDG+Nvlit+es+++ge ++lcdDg+iRD++ +++ky+++  t+ea++l+++++++++++ v +llDk++S
  gi|116753866|ref|YP_842984.1|  36 ENLMGGVLHIDGYNVLITIESIITGEDIFLCDDGFIRDMRCLFRKYRRSGATDEAVQLMIDVISRARPSDVLLLLDKQIS 115
                                    6889999************************************************************************* PP

                        DUF5616  82 nSgelaklireileeaglegevelvknvDkeLkeseeivatsDsvildkvksvldlaa 139
                                    +Sgela+ i e +++ag++g+++++++vD+ Lk+s+++vatsD++i+d+v+s ld++a
  gi|116753866|ref|YP_842984.1| 116 RSGELASDIGEAFSAAGIPGTARTARDVDRGLKSSSAVVATSDGIIIDHVSSALDIPA 173
                                    *******************************************************986 PP

>> DUF434  Protein of unknown function (DUF434)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.3   4.7e-09   4.2e-05      27      56 .]       2      31 ..       1      31 [. 0.94

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 4.7e-09
                         DUF434 27 gnhYqLskrqRlaLaRcvssdeeiearksK 56
                                   ++hY+ +k+ R++L+R+v sd+ + +r+ K
  gi|116753866|ref|YP_842984.1|  2 ADHYRIDKEYRNILSRAVLSDDVARSRRLK 31
                                   79*************************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1431.55
//
Query:       gi|116753867|ref|YP_842985.1|  [L=689]
Description: CoA-binding domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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-74  250.4   0.0    1.8e-74  249.9   0.0    1.2  1  ATP-grasp_5    ATP-grasp domain
    3.1e-42  143.7   0.1    1.1e-41  141.9   0.1    2.0  1  Succ_CoA_lig   Succinyl-CoA ligase like flavodoxin domain
    1.5e-24   86.7   0.1    5.7e-24   84.9   0.1    2.1  1  CoA_binding_2  CoA binding domain
    5.5e-14   52.6   0.4    2.4e-13   50.6   0.0    2.3  3  CoA_binding    CoA binding domain
     0.0024   17.4   0.1     0.0052   16.4   0.1    1.5  1  ATP-grasp_2    ATP-grasp domain
  ------ inclusion threshold ------
       0.12   12.1   0.2          1    9.1   0.0    2.5  3  TPP_enzyme_M   Thiamine pyrophosphate enzyme, central domain


Domain annotation for each model (and alignments):
>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  249.9   0.0   6.1e-78   1.8e-74       1     222 []      11     226 ..      11     226 .. 0.99

  Alignments for each domain:
  == domain 1  score: 249.9 bits;  conditional E-value: 6.1e-78
                    ATP-grasp_5   1 kalaegrtlLteaeakelleaygipvvetrlassaeeaveaaeeigypvvlKivspdilhKtdvgGvrlnlkdaeevraa 80 
                                    +al+egrt+L e+e+k++l ++g++++  +lassa++av++a+++gypvvlK+ s++++hK+d+gGvrlnl+ ae+vr+a
  gi|116753867|ref|YP_842985.1|  11 QALEEGRTYLMEHESKRILMDVGLETTGAHLASSADDAVRIANQLGYPVVLKVLSKEVIHKSDAGGVRLNLQGAEAVRSA 90 
                                    699***************************************************************************** PP

                    ATP-grasp_5  81 aeeilervkekspeariegvlVqemakrggrElivgvteDpvFGpvilfGlGGtavevlkdvavalpplnstlarelier 160
                                    ++e+ + ++e      + gv+Vq+ma   g+E+i+gvt+Dp+FGpv++fGlGG+ ve+l+dv+++  p+++++a+++i++
  gi|116753867|ref|YP_842985.1|  91 YHEMEKIFRE----RGMIGVSVQRMAS-PGIEVIIGVTRDPTFGPVLMFGLGGVFVEILRDVSFRSIPISEEDAESMIRE 165
                                    *******988....789********99.9*************************************************** PP

                    ATP-grasp_5 161 tkaskllkgvrgekkadlaaleellvrlsqLvvdlpeIreldinPllveeegvvalDarirl 222
                                    ++ ++ll+g+rg    d++a++++l+r+s+Lv+++  I+e+d+nP++v++ g +++Dari l
  gi|116753867|ref|YP_842985.1| 166 IRGYPLLRGYRGI-SGDIDAIKSILLRVSDLVEKHSIIKEMDLNPVFVYPMGYTIADARIIL 226
                                    *************.*********************************************976 PP

>> Succ_CoA_lig  Succinyl-CoA ligase like flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.9   0.1   3.5e-45   1.1e-41       1     138 []     394     530 ..     394     530 .. 0.96

  Alignments for each domain:
  == domain 1  score: 141.9 bits;  conditional E-value: 3.5e-45
                   Succ_CoA_lig   1 pGkialisqSGalalalldwaasrglgfskvvslGneadvdvadlleylaedpetkvillylEsirdgrkflsaarraar 80 
                                    +G+++li+q G +a+  l w  ++ l+f  ++++Gn++d++++d+le+++ d++++v+++ylE+++ gr+f+++ar++++
  gi|116753867|ref|YP_842985.1| 394 RGNVGLIAQAGVYAAGYL-WGLRKVLDFGIIATIGNKLDLNETDMLEAIGMDENIDVVCMYLEDVKGGRRFIDVAREVSK 472
                                    69*********9998876.666667******************************************************* PP

                   Succ_CoA_lig  81 kkpvvvlksGrseagaraaashtgalagsdavvdaafrqaGvlrvdsleelfdaaell 138
                                    +kp+vvlk Gr+eag++a++sht++lag+d++++a+f+qaG++r+++ + +f++a+++
  gi|116753867|ref|YP_842985.1| 473 RKPIVVLKTGRTEAGKKAVSSHTASLAGNDQIYSAVFKQAGLIRARDNDHMFALARAF 530
                                    ******************************************************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 !   84.9   0.1   1.9e-27   5.7e-24       2     115 ..     252     377 ..     251     378 .. 0.95

  Alignments for each domain:
  == domain 1  score: 84.9 bits;  conditional E-value: 1.9e-27
                                    -EEEET--S-TTSHHHHHHHHHHHHT-..-EEEESSS-SEETTEES----T....T--EEEE-S-HHHHGGGHHHHHHH- CS
                  CoA_binding_2   2 tiaVvGasdnpgkfgykvlryllehgl..pvvpVnpkeeeilgekvyaslaedpepvdlvdvftppeatpeivkealalg 79 
                                    +iaV+Gas+++gk g  v+ +ll hg+  + +pVnp++ e++g+k+y+s+ + pepvd+++v++p+  tp++v++++a+g
  gi|116753867|ref|YP_842985.1| 252 SIAVIGASNTKGKLGWNVFYNLLTHGYrgRLYPVNPNAAEVQGVKAYPSIRDVPEPVDVAVVLVPAGMTPQVVQDCCAAG 331
                                    8***********************8874479********************758************************** PP

                                    -SEEEE-TT..........---HHHHHHHHHTT-EEE.ES-HHHHH CS
                  CoA_binding_2  80 akavwlqpg..........sedeeaaelaeeagirvvgdrCilveg 115
                                    +k +++ ++            ++e++++++++g r++g++C ++++
  gi|116753867|ref|YP_842985.1| 332 VKYIVVESAgfaelgdegkRIEREILSIVRRHGCRLLGPNCSGIIN 377
                                    ********9*********************************9975 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.0         6   1.8e+04      22      37 ..     108     123 ..     104     125 .. 0.65
   2 !   50.6   0.0     8e-17   2.4e-13       3      94 ..     250     339 ..     248     341 .. 0.96
   3 ?   -2.1   0.0       2.1   6.3e+03      42      58 ..     659     675 ..     636     680 .. 0.67

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 6
                                    HHHHHHECEEEEEEC- CS
                    CoA_binding  22 fkeklkygikavfgvn 37 
                                    ++++ + gi++++gv+
  gi|116753867|ref|YP_842985.1| 108 VQRMASPGIEVIIGVT 123
                                    5566666777777776 PP

  == domain 2  score: 50.6 bits;  conditional E-value: 8e-17
                                    TEEEEEETTTSHHHHHH.HHHHHHHHECEE.EEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHHH CS
                    CoA_binding   3 dtkviviGagglgiagl.yhfkeklkygik.avfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqeavd 80 
                                    + +++viGa+++ ++++  +f + l  g +  +++vnp+  + ev+g+++y+s+++++e   vdvav++vPa    ++v+
  gi|116753867|ref|YP_842985.1| 250 PQSIAVIGASNTKGKLGwNVFYNLLTHGYRgRLYPVNPN--AAEVQGVKAYPSIRDVPEP--VDVAVVLVPAGMTPQVVQ 325
                                    679***************************9********..*******************..****************** PP

                                    HHHHTT-SEEEEES CS
                    CoA_binding  81 elveagikgiviit 94 
                                    ++ +ag+k iv+ +
  gi|116753867|ref|YP_842985.1| 326 DCCAAGVKYIVVES 339
                                    ***********865 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 2.1
                                    TCEETTEEEESCHHHHH CS
                    CoA_binding  42 gtevlglpvyksvdele 58 
                                      e  g+pvy + +++ 
  gi|116753867|ref|YP_842985.1| 659 KMERAGIPVYSTPEQAA 675
                                    34455888886655555 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   1.7e-06    0.0052       2      72 ..      20      90 ..      19     111 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.7e-06
                                   E-HHHHHHHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--.SSSTCCCTTCEEEESSHHHHHHHH CS
                    ATP-grasp_2  2 lhEyqakeilakygvkvpegevaesaeeaeeaakklgekelvvKaQv.laGGRGKagGvklvkskeeakeaa 72
                                   l E+++k il + g++++ +++a+sa++a ++a++lg  + v+K     +  +  agGv+l  +  ea + a
  gi|116753867|ref|YP_842985.1| 20 LMEHESKRILMDVGLETTGAHLASSADDAVRIANQLGYPV-VLKVLSkEVIHKSDAGGVRLNLQGAEAVRSA 90
                                   79***********************************999.8886441455678889998876655555444 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 ?    9.1   0.0   0.00034         1      20      77 ..      37      93 ..      23      99 .. 0.80
   2 ?   -1.4   0.0      0.61   1.8e+03      69      90 ..     546     567 ..     538     616 .. 0.80
   3 ?   -2.8   0.0       1.6   4.9e+03      36      47 ..     661     672 ..     660     675 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00034
                                   CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEE.ESGGGSCHHHHHHHHH CS
                   TPP_enzyme_M 20 ggvarsgaseelrelaeklgiPvvttlmgkgvipedhplylg.mlglhgskaanealee 77
                                    g++ +  ++++++ a++lg Pvv  +  k vi +++    g +l l g++a++ a +e
  gi|116753867|ref|YP_842985.1| 37 TGAHLASSADDAVRIANQLGYPVVLKVLSKEVIHKSDA--GGvRLNLQGAEAVRSAYHE 93
                                   4777888999***********************98887..5668888888888888776 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.61
                                    HHHHHHHHH-SEEEEES-SSST CS
                   TPP_enzyme_M  69 kaanealeeaDlvlalGarfdd 90 
                                    +a++  ++ aD +++ G+r+ +
  gi|116753867|ref|YP_842985.1| 546 YAGSLGVAAADAIVMNGMRLAE 567
                                    5666678899999999999877 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.6
                                    HHHT-EEEEEGG CS
                   TPP_enzyme_M  36 eklgiPvvttlm 47 
                                    e+ giPv +t+ 
  gi|116753867|ref|YP_842985.1| 661 ERAGIPVYSTPE 672
                                    899******997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (689 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); 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: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 4797.42
//
Query:       gi|116753868|ref|YP_842986.1|  [L=96]
Description: hypothetical protein Mthe_0555 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); 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:                         0  (0); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 726.86
//
Query:       gi|116753869|ref|YP_842987.1|  [L=127]
Description: hypothetical protein Mthe_0556 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-21   77.0   0.0    1.8e-21   76.5   0.0    1.2  1  DUF134        Protein of unknown function  DUF134
    0.00043   19.9   1.5    0.00052   19.6   0.1    1.8  2  Sigma70_r4_2  Sigma-70, region 4


Domain annotation for each model (and alignments):
>> DUF134  Protein of unknown function  DUF134
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.5   0.0     2e-25   1.8e-21      20      97 ..       2      78 ..       1      79 [. 0.95

  Alignments for each domain:
  == domain 1  score: 76.5 bits;  conditional E-value: 2e-25
                         DUF134 20 rifkPeaveetgkvaisldeleairlvdyedlkqeeaaklmGiskatlwrlltearkkiakalveGraiilkGGeykr 97
                                   r f Pe+ e++  v+++l+elea+rlvd  dl+qeeaa  mG+s+++lw+ l +ar+k+a+alv G  i ++GG y+ 
  gi|116753869|ref|YP_842987.1|  2 RCFLPESGENAS-VVLTLEELEALRLVDLLDLEQEEAALYMGVSRKALWNDLVSARRKVAAALVYGMGIRIEGGSYIL 78
                                   8899**877777.**************************************************************975 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 !   19.6   0.1   5.8e-08   0.00052      15      53 ..      20      58 ..      15      59 .. 0.91
   2 ?   -1.8   0.1      0.29   2.6e+03       3      13 ..     103     113 ..     101     114 .. 0.65

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 5.8e-08
                                   HHHHHHHHHTS---HHHHHHHHT--HHHHHHHHHHHHHH CS
                   Sigma70_r4_2 15 qreifllryleglsykEIAellgisegtVksrlsRArkk 53
                                   + e++ l +l +l ++E+A ++g+s ++  + l  Ar+k
  gi|116753869|ref|YP_842987.1| 20 ELEALRLVDLLDLEQEEAALYMGVSRKALWNDLVSARRK 58
                                   5689********************************998 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.29
                                    HHHHHHTTS-H CS
                   Sigma70_r4_2   3 alrealaeLpe 13 
                                     l + l++L+ 
  gi|116753869|ref|YP_842987.1| 103 ILKRRLDQLSR 113
                                    56677777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); 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: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 934.30
//
Query:       gi|116753870|ref|YP_842988.1|  [L=281]
Description: MRP/NBP35 family ATP-binding protein [Methanosaeta thermophila PT]
Scores for complete 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-96  322.3   0.1    2.1e-96  322.1   0.1    1.0  1  ParA             NUBPL iron-transfer P-loop NTPase
    7.9e-13   48.6   0.0    1.5e-12   47.7   0.0    1.6  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    1.2e-09   37.8   0.0    1.8e-09   37.3   0.0    1.3  1  MipZ             ATPase MipZ
    3.6e-06   27.0   1.0      2e-05   24.6   1.0    2.1  1  AAA_31           AAA domain
    2.9e-05   23.4   3.9    0.00014   21.2   1.3    2.4  2  ArsA_ATPase      Anion-transporting ATPase
     0.0015   18.5   0.0     0.0023   17.9   0.0    1.3  1  APS_kinase       Adenylylsulphate kinase
      0.003   17.4   0.0     0.0054   16.5   0.0    1.4  1  CLP1_P           mRNA cleavage and polyadenylation factor CLP
     0.0049   15.9   0.1      0.008   15.2   0.1    1.3  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
     0.0053   16.2   0.0      0.014   14.8   0.1    1.6  2  Fer4_NifH        4Fe-4S iron sulfur cluster binding proteins,
     0.0058   16.2   0.4      0.011   15.3   0.4    1.4  1  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
     0.0063   16.4   0.1        1.3    8.8   0.1    2.2  2  AAA_26           AAA domain
  ------ inclusion threshold ------
      0.012   15.1   0.0      0.019   14.4   0.0    1.3  1  PhoH             PhoH-like protein
      0.017   14.6   0.1      0.069   12.6   0.0    1.8  2  CBP_BcsQ         Cellulose biosynthesis protein BcsQ
      0.031   13.9   0.1      0.055   13.1   0.1    1.3  1  SRP54            SRP54-type protein, GTPase domain
      0.037   13.3   0.1      0.055   12.7   0.1    1.2  1  Zeta_toxin       Zeta toxin
      0.056   13.5   0.0      0.093   12.8   0.0    1.3  1  zf-Sec23_Sec24   Sec23/Sec24 zinc finger
      0.067   13.2   0.2       0.13   12.2   0.2    1.5  1  DUF1610          Domain of unknown function (DUF1610)
       0.11   12.1   0.0       0.18   11.3   0.0    1.3  1  AAA_25           AAA domain
       0.17   11.0   0.1       0.33   10.0   0.1    1.4  1  LpxK             Tetraacyldisaccharide-1-P 4'-kinase
       0.17   11.3   0.0        0.3   10.5   0.0    1.4  1  KTI12            Chromatin associated protein KTI12
       0.18   11.5   0.1       0.31   10.8   0.1    1.3  1  AAA_30           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 !  322.1   0.1   2.5e-99   2.1e-96       2     245 ..      30     271 ..      29     276 .. 0.96

  Alignments for each domain:
  == domain 1  score: 322.1 bits;  conditional E-value: 2.5e-99
                           ParA   2 vkkviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqsekkliPveakgikvmSigfl 81 
                                    +k++i++ SgKGG GKStv++nlA++L+++g++vg+lDaDi+Gp+ip+llg+e+ek ++s++++ P +a+gikv+S+++l
  gi|116753870|ref|YP_842988.1|  30 IKHKIVIGSGKGGTGKSTVSANLAVSLKRRGYSVGILDADITGPDIPKLLGIEDEKLTASSEGIEPADARGIKVVSMALL 109
                                    8***********************************************************99****************** PP

                           ParA  82 lesedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqkl.plagaviVttpqevaladvkkaiemf 160
                                    les+d+avvwrGp+k++a+kq++ dv+wg+lD+L++DlPPGt+De ++ +q l  ++ga++Vttpq+val d++ka++mf
  gi|116753870|ref|YP_842988.1| 110 LESRDSAVVWRGPVKMAALKQFVFDVNWGDLDFLVVDLPPGTSDEPISAVQLLsGMDGAIVVTTPQDVALLDTRKAVNMF 189
                                    *****************************************************889************************ PP

                           ParA 161 kkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdegkplvlkepeseaakalee 240
                                      + v+vlG++eNmsgf cp+cg+ ++if+kgggek+a++lgv++lg +p+dp+i++++d gk +v++   s+a  a+e+
  gi|116753870|ref|YP_842988.1| 190 LMMGVRVLGIIENMSGFRCPNCGTVVNIFSKGGGEKAARDLGVDFLGYLPIDPRIVSMCDMGKAFVEN---SDAGGAFEK 266
                                    ***************************************************************99966...556666666 PP

                           ParA 241 iaekv 245
                                    i++k+
  gi|116753870|ref|YP_842988.1| 267 IVDKL 271
                                    66654 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 !   47.7   0.0   1.7e-15   1.5e-12       1      55 [.      34     193 ..      34     254 .. 0.71

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 1.7e-15
                                    EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH.......................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................... RF
                           CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep.......................... 54 
                                    i+i s+kGG+GK+t++anLa++l+rrg+ V  +DaD  ++    l g e ++ +                          
  gi|116753870|ref|YP_842988.1|  34 IVIGSGKGGTGKSTVSANLAVSLKRRGYSVGILDADITGPDIPKLLGIEDEKLTassegiepadargikvvsmalllesr 113
                                    7899*************************************985555555554488888888888888888888888888 PP

                                    ...............................................................................C CS
                                    ...............................................................................x RF
                           CbiA  55 ...............................................................................d 55 
                                                                                                                   +
  gi|116753870|ref|YP_842988.1| 114 dsavvwrgpvkmaalkqfvfdvnwgdldflvvdlppgtsdepisavqllsgmdgaivvttpqdvalldtrkavnmflmmG 193
                                    88888888888888888888888888888888888877777777777777666666666666666664444444443332 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.0   2.1e-12   1.8e-09       1     114 [.      32     156 ..      32     182 .. 0.70

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 2.1e-12
                                    EEEEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHH..HHHHHHHHHHT------E......EE-SSS CS
                           MipZ   1 hvivlgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlaryl..enraataerkglsLplpe......alalse 72 
                                    h iv+g  kGG+Gkst++  +av+L ++G +v+ +d d+    + + l  e+ + ta+++g++ + ++      +  l e
  gi|116753870|ref|YP_842988.1|  32 HKIVIGSGKGGTGKSTVSANLAVSLKRRGYSVGILDADITGPDIPKLLgiEDEKLTASSEGIEPADARgikvvsMALLLE 111
                                    78***************************************999998622566667777777754433111000333444 PP

                                    -HHHHTTS-HHHHHHHHHHHHHHHH.HH-SEEEEE--.S.S--HH CS
                           MipZ  73 aeeaeveeeeeaevaeleelvadle.aeldfividtP.G.sdsal 114
                                    +  + v      ++a+l++ v d++  +ldf+v+d P G sd+++
  gi|116753870|ref|YP_842988.1| 112 SRDSAVVWRGPVKMAALKQFVFDVNwGDLDFLVVDLPpGtSDEPI 156
                                    45555555566777899888777762689******8734234444 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   1.0   2.4e-08     2e-05       3      40 ..      33      70 ..      31     192 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.4e-08
                         AAA_31  3 vIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDp 40
                                    I+i   KGG GK+T s nla++l ++g+ v + D+D 
  gi|116753870|ref|YP_842988.1| 33 KIVIGSGKGGTGKSTVSANLAVSLKRRGYSVGILDADI 70
                                   689999******************************96 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   1.3   1.6e-07   0.00014       1      38 [.      32      69 ..      32      72 .. 0.90
   2 ?    1.8   0.0      0.13   1.1e+02     210     243 ..     169     202 ..     160     207 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.6e-07
                                   -EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                    ArsA_ATPase  1 lkvilvgGKGGVGKttvsaatavklsekgkkvllistD 38
                                   +k+++ +GKGG GK+tvsa +av l + g++v ++  D
  gi|116753870|ref|YP_842988.1| 32 HKIVIGSGKGGTGKSTVSANLAVSLKRRGYSVGILDAD 69
                                   588999***********************999877665 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.13
                                    EEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEE CS
                    ArsA_ATPase 210 rlVvipEklslkEteRaikeLkkygikvdavivN 243
                                    ++V++p  ++l +t++a++ +  +g++v  +i N
  gi|116753870|ref|YP_842988.1| 169 IVVTTPQDVALLDTRKAVNMFLMMGVRVLGIIEN 202
                                    6899************************999987 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   2.7e-06    0.0023       5      55 ..      35      85 ..      31      94 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.7e-06
                                   EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT--SSHHH CS
                     APS_kinase  5 vwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLgfseed 55
                                   v  +G  g+GKst++ +l+ +L+++g+sv +Ld d    ++ k Lg ++e+
  gi|116753870|ref|YP_842988.1| 35 VIGSGKGGTGKSTVSANLAVSLKRRGYSVGILDADITGPDIPKLLGIEDEK 85
                                   5668999****************************9999999999988775 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 !   16.5   0.0   6.3e-06    0.0054       1      36 [.      39      74 ..      39      81 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.3e-06
                         CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGqse 36
                                   G+  +GKST++++L+  + r+g+++ ++D+D+  ++
  gi|116753870|ref|YP_842988.1| 39 GKGGTGKSTVSANLAVSLKRRGYSVGILDADITGPD 74
                                   66789**************************97665 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   9.4e-06     0.008      33      68 ..      37      71 ..      12      76 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 9.4e-06
                                   EEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE--- CS
                           MeaB 33 GltGvPGaGkstlvealglelrrrGkrvavlavDPs 68
                                   G  G  G+Gkst+  +l+++l+rrG+ v++l  D +
  gi|116753870|ref|YP_842988.1| 37 G-SGKGGTGKSTVSANLAVSLKRRGYSVGILDADIT 71
                                   4.6999*************************98865 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   1.7e-05     0.014       6      34 ..      38      66 ..      32      76 .. 0.85
   2 ?   -2.6   0.0       3.4   2.9e+03     195     216 ..     225     246 ..     211     278 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.7e-05
                      Fer4_NifH  6 yGkGGiGksttsqnlsaalaemgkkvliv 34
                                    GkGG Gkst s+nl+ +l+++g  v i+
  gi|116753870|ref|YP_842988.1| 38 SGKGGTGKSTVSANLAVSLKRRGYSVGIL 66
                                   59*******************99887665 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.4
                      Fer4_NifH 195 kfaeelgtkvlevvPrdeivrk 216
                                    k a++lg++ l  +P d  +  
  gi|116753870|ref|YP_842988.1| 225 KAARDLGVDFLGYLPIDPRIVS 246
                                    5566777777777777765543 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.4   1.3e-05     0.011       5      25 ..     204     224 ..     201     225 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.3e-05
                                    -EEE-TTT--EEEECC--SS- CS
                Desulfoferrod_N   5 evYkCevCGniVeVleaGgGe 25 
                                      ++C  CG +V++  +GgGe
  gi|116753870|ref|YP_842988.1| 204 SGFRCPNCGTVVNIFSKGGGE 224
                                    569*****************7 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.1    0.0015       1.3       3      34 ..      34      65 ..      32      77 .. 0.88
   2 ?    5.6   0.0     0.014        12     132     194 ..     169     244 ..     104     247 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0015
                         AAA_26  3 ifvtgtdtgvGKTvvslgLvralkrkgvkvgy 34
                                   i++ +   g GK++vs+ L+ +lkr+g++vg 
  gi|116753870|ref|YP_842988.1| 34 IVIGSGKGGTGKSTVSANLAVSLKRRGYSVGI 65
                                   6677777799*******************985 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.014
                         AAA_26 132 ilVargglgtinqllltiealrqknvrvlGvilNk....vrnpenvetlekksg.........ipvlGvvPylpdl 194
                                    i+V+++++ ++ ++  +++++   +vrvlG+i N     ++n  +v ++++k+g         ++ lG +P +p++
  gi|116753870|ref|YP_842988.1| 169 IVVTTPQDVALLDTRKAVNMFLMMGVRVLGIIENMsgfrCPNCGTVVNIFSKGGgekaardlgVDFLGYLPIDPRI 244
                                    6677777778888888999999999*******98755445555688888888777777777778999999988876 PP

>> PhoH  PhoH-like protein
   #    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      14      46 ..      25      59 ..      16      67 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.3e-05
                                   HHHH..H-SEEEEE--TTSSTTHHHHHHHHHHHHT CS
                           PhoH 14 ealk..kndivfaiGpaGtGKtylavalavealkk 46
                                   + lk  k++iv++ G+ GtGK+ ++  lav++ ++
  gi|116753870|ref|YP_842988.1| 25 DRLKriKHKIVIGSGKGGTGKSTVSANLAVSLKRR 59
                                   55666699**********************97665 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   8.1e-05     0.069      10      38 ..      40      68 ..      32      97 .. 0.91
   2 ?   -0.6   0.0      0.88   7.6e+02     111     148 ..     134     175 ..     121     189 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.1e-05
                       CBP_BcsQ 10 RGGvGttsllaaLawalhelgesvlviDl 38
                                   +GG+G+++++a La +l++ g+sv ++D+
  gi|116753870|ref|YP_842988.1| 40 KGGTGKSTVSANLAVSLKRRGYSVGILDA 68
                                   8***********************99997 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.88
                       CBP_BcsQ 111 elk.eqyrwillDlpagasal...trellaladlvllvvepd 148
                                     ++ ++ +++++Dlp g+s+    + +ll+  d  + v++p+
  gi|116753870|ref|YP_842988.1| 134 DVNwGDLDFLVVDLPPGTSDEpisAVQLLSGMDGAIVVTTPQ 175
                                    44557789999***9987764111445666677788888775 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   6.4e-05     0.055       7      39 ..      38      70 ..      32      74 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.4e-05
                                   EESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                          SRP54  7 vGlqGaGKTttlaKLaallkkegkkvllvaaDt 39
                                    G  G+GK t  a La  lk++g++v +  aD+
  gi|116753870|ref|YP_842988.1| 38 SGKGGTGKSTVSANLAVSLKRRGYSVGILDADI 70
                                   6889************************99996 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   6.5e-05     0.055      12      70 ..      28      87 ..      18     101 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.5e-05
                     Zeta_toxin 12 sqerPklillgGqpGAGKselaellkdelerqgnvv.rldpDdlRelhPeyeeilkadpk 70
                                   ++ + k+++ +G  G GKs++++ l+ +l+r+g  v  ld+D   + +P+  +i++++ +
  gi|116753870|ref|YP_842988.1| 28 KRIKHKIVIGSGKGGTGKSTVSANLAVSLKRRGYSVgILDADITGPDIPKLLGIEDEKLT 87
                                   45677889999*******************777766257888888888888777665544 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 ?   12.8   0.0   0.00011     0.093       3      16 ..     207     220 ..     206     225 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00011
                 zf-Sec23_Sec24   3 rCrrCraylNpfck 16 
                                    rC +C++++N+f+k
  gi|116753870|ref|YP_842988.1| 207 RCPNCGTVVNIFSK 220
                                    9***********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 ?   12.2   0.2   0.00015      0.13      12      23 ..     201     212 ..     199     213 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                        DUF1610  12 EravvFpCPNCG 23 
                                    E+ + F CPNCG
  gi|116753870|ref|YP_842988.1| 201 ENMSGFRCPNCG 212
                                    55678******9 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00022      0.18      32      57 ..      31      56 ..      18      65 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00022
                         AAA_25 32 agelallaGapgtGKttlaldlalav 57
                                   ++++++  G +gtGK+t+  +la+++
  gi|116753870|ref|YP_842988.1| 31 KHKIVIGSGKGGTGKSTVSANLAVSL 56
                                   78899999***************986 PP

>> LpxK  Tetraacyldisaccharide-1-P 4'-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00039      0.33      39      71 ..      35      66 ..      25      68 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00039
                                   EEEESBSS-HSHHHHHHHHHHHTTTS..-EEEE CS
                           LpxK 39 vVGNitvGGtGKTPlvialvkllqarglkvgvl 71
                                   v+G    GGtGK  + + l+  l++rg+ vg+l
  gi|116753870|ref|YP_842988.1| 35 VIGS-GKGGTGKSTVSANLAVSLKRRGYSVGIL 66
                                   5555.35************************97 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00035       0.3       4      40 ..      35      71 ..      33      92 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00035
                                   EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHH CS
                          KTI12  4 vvltGlPssGKstrakeLakaleeekrsvvviddesl 40
                                   v+ +G   +GKst++++La  l+ +++sv ++d +  
  gi|116753870|ref|YP_842988.1| 35 VIGSGKGGTGKSTVSANLAVSLKRRGYSVGILDADIT 71
                                   566788899**********************998765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00036      0.31      18      50 ..      32      64 ..      25      69 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00036
                         AAA_30 18 drvavltGpAGtGKttalkalreaweaaggrvi 50
                                   +++++  G  GtGK+t+ + l+  ++++g++v 
  gi|116753870|ref|YP_842988.1| 32 HKIVIGSGKGGTGKSTVSANLAVSLKRRGYSVG 64
                                   678999******************999999986 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:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                       114  (0.00635841); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2018.85
//
Query:       gi|116753871|ref|YP_842989.1|  [L=430]
Description: radical SAM domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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  105.2   0.0      7e-30  104.6   0.0    1.3  1  Radical_SAM  Radical SAM superfamily
    3.1e-05   24.0   0.7     0.0018   18.3   0.1    3.3  3  B12-binding  B12 binding domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.6   0.0   7.8e-34     7e-30       2     166 ..     156     324 ..     155     325 .. 0.95

  Alignments for each domain:
  == domain 1  score: 104.6 bits;  conditional E-value: 7.8e-34
                                    EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS........TTHHHHHHHHHHT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxx RF
                    Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly........pdfvellerlakl 73 
                                    ++ rgC ++C+fC++p+    ++  rs+s+e+i+eev+el+ ++gvk v ++gg+ +l         + f++ l +l+ +
  gi|116753871|ref|YP_842989.1| 156 ETHRGCLGGCTFCQVPRF--FGRNIRSRSLENIVEEVRELR-RMGVKRVAVSGGTASLFgyrnaldkDAFIRMLQELSGI 232
                                    6789*************8..********************5.************99999999997777777777777777 PP

                                    CCCTEEEEEEECSSCHG...HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEE CS
                                    xxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  74 avpgiritvetngtlpd...eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdriv 150
                                         r  ++++ +++d   +e+le+++e+ + ++ +g+e+++d+  lklm++g t+ + ++a+e++r++g+k+  ++iv
  gi|116753871|ref|YP_842989.1| 233 ---LGRKNLSVPDMRVDlvdDEILEAIREYTIGWLFFGIESGSDR-MLKLMRKGVTVLDNIRAVELARSHGVKVGGSFIV 308
                                    ...99****************************************.********************************** PP

                                    EBTTTSHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxx RF
                    Radical_SAM 151 glpGendeeleellel 166
                                    g pGe++e++e++l++
  gi|116753871|ref|YP_842989.1| 309 GYPGESREDFEQTLDF 324
                                    **************98 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1     2e-07    0.0018      13     120 ..      11     102 ..       4     103 .. 0.80
   2 ?   -2.0   0.0      0.39   3.5e+03      42      89 ..     185     207 ..     177     228 .. 0.52
   3 ?   -0.9   0.0      0.18   1.6e+03      22      54 ..     231     263 ..     225     313 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2e-07
                    B12-binding  13 hplGlavlaaalrdagfeVqllganvenedivaairaekpdvvglSalltsqleavkelvellkrirprvkvvvGGahps 92 
                                    +++G +vl ++lrd+g++V +            +  +++ dv+ lS+ +t ql    ++ e++ +++p  +v +GG+ + 
  gi|116753871|ref|YP_842989.1|  11 YTYGSMVLGGILRDRGHSVNIS-----------KDLRHDGDVIILSLFSTLQL-LDPAIREFVSKAGP--PVYCGGP-VG 75 
                                    5677777788888888877433...........2236889******9555555.55889999988867..9*****8.6* PP

                    B12-binding  93 ldpeetleaklgiddvvvgegedaleal 120
                                    + pe++l + l +d v + ege  +++l
  gi|116753871|ref|YP_842989.1|  76 ICPEMVLGE-LDVDAVAMCEGEGIIARL 102
                                    ********9.************998887 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.39
                    B12-binding  42 divaairaekpdvvglSalltsqleavkelvellkrirprvkvvvGGa 89 
                                    +iv+++r+                         l+r++ +   v GG+
  gi|116753871|ref|YP_842989.1| 185 NIVEEVRE-------------------------LRRMGVKRVAVSGGT 207
                                    34444444.........................444444423333333 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.18
                    B12-binding  22 aalrdagfeVqllganvenedivaairaekpdv 54 
                                    ++l +++ +V ++ ++  +++i++air+     
  gi|116753871|ref|YP_842989.1| 231 GILGRKNLSVPDMRVDLVDDEILEAIREYTIGW 263
                                    556666666666666666699999999876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 3428.35
//
Query:       gi|116753872|ref|YP_842990.1|  [L=119]
Description: dinitrogenase iron-molybdenum cofactor biosynthesis [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.8e-24   84.8   0.0    4.6e-24   84.6   0.0    1.1  1  Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor


Domain annotation for each model (and alignments):
>> Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.6   0.0   2.5e-28   4.6e-24       2      94 ..      14     101 ..      13     102 .. 0.96

  Alignments for each domain:
  == domain 1  score: 84.6 bits;  conditional E-value: 2.5e-28
                                    TSCB-STCCC-SEEEEEEESSSCEEEEEEEE.GCCCTSSCSSTHHHHHHHHTT-SEEEESSSCHHHHHHHCTTTSEEEES CS
                  Nitro_FeMo-Co   2 gsrvdqhFGrapyFaiyeveegevkivenrveeaadaegggggklaqllaeegvdvvivgkiGpralakleaagievykg 81 
                                    ++ ++qhFGr+p+F+i+++e+g+++i+ n      +++ gg g +++ l+ +gv+vvi+g+ Gp+a+ ++++ gi+v++g
  gi|116753872|ref|YP_842990.1|  14 DEYISQHFGRSPTFTIVDTETGAIEIIGNN-----STHMGGNGLPVDALHGKGVQVVIAGGLGPKAISAFQQLGIRVFVG 88 
                                    6789**************************.....888899*************************************** PP

                                    -SSBHHHHHHHHH CS
                  Nitro_FeMo-Co  82 aggtveealkevl 94 
                                    a+gtv++a+++++
  gi|116753872|ref|YP_842990.1|  89 AAGTVKDAIDDWM 101
                                    **********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 1007.04
//
Query:       gi|116753873|ref|YP_842991.1|  [L=141]
Description: dinitrogenase iron-molybdenum cofactor biosynthesis [Methanosaeta thermophila PT]
Scores for complete 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   0.0    3.1e-24   85.1   0.0    1.2  1  Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
     0.0018   18.0   1.7     0.0025   17.5   1.7    1.1  1  TMP_2          Prophage tail length tape measure protein
  ------ inclusion threshold ------
      0.052   13.8   0.0      0.067   13.4   0.0    1.1  1  DUF5304        Family of unknown function (DUF5304)
      0.077   12.4   2.3       0.11   11.8   2.3    1.2  1  DUF3482        Domain of unknown function (DUF3482)


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   0.0     7e-28   3.1e-24       2      94 ..      13     102 ..      12     103 .. 0.97

  Alignments for each domain:
  == domain 1  score: 85.1 bits;  conditional E-value: 7e-28
                                    TSCB-STCCC-SEEEEEEESSSCEEEEEEEE.GCCCTSSCSSTHHHHHHHHTT-SEEEESSSCHHHHHHHCTTTSEEEES CS
                  Nitro_FeMo-Co   2 gsrvdqhFGrapyFaiyeveegevkivenrveeaadaegggggklaqllaeegvdvvivgkiGpralakleaagievykg 81 
                                    +  vd++FGr+p+F+++++++ +++ ++n    aa+a+gg+g+++aql+++ g++v+i+g++Gp+a++ l++agie+y+ 
  gi|116753873|ref|YP_842991.1|  13 DAPVDPRFGRCPFFVVVDLDSMSESSMQNT---AAGAAGGAGIQAAQLVSQLGASVLITGNVGPNAMQVLSSAGIEIYQS 89 
                                    578***************************...*********************************************** PP

                                    -SSBHHHHHHHHH CS
                  Nitro_FeMo-Co  82 aggtveealkevl 94 
                                    +ggtv++a+++++
  gi|116753873|ref|YP_842991.1|  90 QGGTVRDAVERFR 102
                                    **********985 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 !   17.5   1.7   5.6e-07    0.0025     110     177 ..      34     103 ..      32     109 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 5.6e-07
                          TMP_2 110 lTasqLeamaesiaeagg.tqaa.aaealaalastGkiggeqlervakaaaelekatGqsvdetakelak 177
                                    +++s++++ a+ +a+ +g + a+ ++++ a ++ tG++g+++++ +++a +e+ +  G +v ++++ + +
  gi|116753873|ref|YP_842991.1|  34 MSESSMQNTAAGAAGGAGiQAAQlVSQLGASVLITGNVGPNAMQVLSSAGIEIYQSQGGTVRDAVERFRR 103
                                    7899999999999998887655525666678999********************************9975 PP

>> DUF5304  Family of unknown function (DUF5304)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.5e-05     0.067      47     129 ..      37     116 ..      27     130 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.5e-05
                        DUF5304  47 sglqspllgavaspaaqqvvrqvveqakaavepviernPdvfdhLaaaGsellaaYRsavegqerrwterekkakeagde 126
                                    s++q+  +ga a++a    + q+v+q  a v    +  P+ ++ L++aG e+  +   +v++  +r+ ++e  ak +g +
  gi|116753873|ref|YP_842991.1|  37 SSMQNTAAGA-AGGA-GIQAAQLVSQLGASVLITGNVGPNAMQVLSSAGIEIYQSQGGTVRDAVERFRRGE-LAKVSGPT 113
                                    5677777665.4444.4556799********7777888***************999999999999988864.45555554 PP

                        DUF5304 127 eda 129
                                    + +
  gi|116753873|ref|YP_842991.1| 114 APP 116
                                    444 PP

>> DUF3482  Domain of unknown function (DUF3482)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   2.3   2.6e-05      0.11     151     198 ..      39      87 ..      30      99 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.6e-05
                        DUF3482 151 gaGaaaGAaaGagiDlavgGltLGaaaaiGalaGg.laatlkrygkrll 198
                                    ++  aaGAa Gagi +a +   LGa  +i + +G  ++++l+++g +++
  gi|116753873|ref|YP_842991.1|  39 MQNTAAGAAGGAGIQAAQLVSQLGASVLITGNVGPnAMQVLSSAGIEIY 87 
                                    5678*****************************9525677777766666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1056.35
//
Query:       gi|116753874|ref|YP_842992.1|  [L=294]
Description: beta-lactamase domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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-11   44.2   1.1    3.8e-11   43.4   0.7    1.8  2  Lactamase_B    Metallo-beta-lactamase superfamily
    2.5e-09   37.0   0.6    6.2e-09   35.7   0.6    2.0  1  Lactamase_B_2  Beta-lactamase superfamily domain
     0.0028   17.1   0.1     0.0045   16.5   0.1    1.2  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 !   43.4   0.7   6.4e-15   3.8e-11       7      67 ..      38     100 ..      33     214 .. 0.84
   2 ?   -2.6   0.0      0.76   4.5e+03     178     197 .]     246     265 ..     227     265 .. 0.77

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 6.4e-15
                                    EEEEEE....ETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTH CS
                    Lactamase_B   7 nsylie....gdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglvea 67 
                                     s+lie     +  +iL DtG s++  +    +  lg++ +d+d ++l+H+H+DH+Ggl+gl ++
  gi|116753874|ref|YP_842992.1|  38 LSVLIEadlgSESMCILMDTGASSDVLLHN--MDVLGIDSDDIDLIFLSHGHYDHTGGLMGLLKH 100
                                    57888888888899**************96..8*****************************996 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.76
                                    HHHHHHHHHHHCHSEEEESS CS
                    Lactamase_B 178 yldsllklaglkaevlvpgH 197
                                     ++++  l +l++e++ pgH
  gi|116753874|ref|YP_842992.1| 246 IRRTAGALLDLDPEIVRPGH 265
                                    56778888899999998888 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.6     1e-12   6.2e-09       3      68 ..      53     115 ..      52     283 .. 0.85

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 1e-12
                                    EEES--TT...HHHHHTCGGS--S.SS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHH CS
                  Lactamase_B_2   3 iLiDagpd...lrqqalralqPve.lrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvla 68 
                                    iL D+g +   l       l++   l  + ++id+++l+h+HyDH+ gl+ l + +++++p++a++g+ a
  gi|116753874|ref|YP_842992.1|  53 ILMDTGASsdvL-------LHNMDvLGIDSDDIDLIFLSHGHYDHTGGLMGLLKHMKRHVPILAHPGIFA 115
                                    566666663322.......2344445666689**********************88888*******9876 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 !   16.5   0.1   7.5e-07    0.0045       5      63 ..      49     105 ..      45     115 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 7.5e-07
                  Lactamase_B_6   5 dnvkiLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayallyakfkskl 63 
                                    ++++iL+D G ++  +   + ++ l    +++dli Lsh   +h G+++ l++++k+++
  gi|116753874|ref|YP_842992.1|  49 ESMCILMDTGASSDVL--LHNMDVLGIDSDDIDLIFLSHGHYDHTGGLMGLLKHMKRHV 105
                                    6899*******98633..356677777789*****************999998876653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2133.85
//
Query:       gi|116753875|ref|YP_842993.1|  [L=311]
Description: radical SAM domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.4e-13   50.3   0.0    4.7e-13   49.9   0.0    1.2  1  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.9   0.0   2.6e-17   4.7e-13       3     159 ..      22     181 ..      20     191 .. 0.87

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 2.6e-17
                                    EESEESS--TTTSCCTT.....HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEE.SSTGGGSTTHHHHHHHHHHTCCC CS
                                    xxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   3 vtrgCnlrCsfCarpet.....vrregrgrslsveeileevkelkaekgvkevilg.ggepllypdfvellerlaklavp 76 
                                    + + C++ C++C++++t     +rr+ ++  + + e+++++  +  + +v++++++  gep+l+ ++ ++++ l+ l   
  gi|116753875|ref|YP_842993.1|  22 PPKICTYSCIYCQVGRTlglsvERRGFYPPARVLNEVERKISDAG-DVRVDYITFVpDGEPTLDLNIGKEIDLLRTL--- 97 
                                    5678*************************************9995.777*******99*******************... PP

                                    TEEEEEEECSSCHG.HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHH...HHHHHHHHHHHHTTSETEEEEEEEB CS
                                    xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  77 giritvetngtlpd.eeklerllelgvdrvslgleaaddekvlklmnrghtf...eevlealeklreagikrvvdrivgl 152
                                    g+r++v++n+ l+  +++ e l     d vs+ ++aadd    +++nr+h       +l++++ +++    r ++  +++
  gi|116753875|ref|YP_842993.1|  98 GLRVAVISNASLLWrPDVREDLMS--ADLVSIKIDAADDG-MWRRINRPHHSlklRTILDGIREFAADYSGRLITESMLI 174
                                    *************97777777777..59************.566665444433669999***9999888888******** PP

                                    TTTSHHH CS
                                    xxxxxxx RF
                    Radical_SAM 153 pGendee 159
                                    +  nd +
  gi|116753875|ref|YP_842993.1| 175 KDMNDCD 181
                                    **99965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 2374.18
//
Query:       gi|116753876|ref|YP_842994.1|  [L=205]
Description: hypothetical protein Mthe_0563 [Methanosaeta thermophila PT]
Scores for complete sequence (score 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   0.1       0.15   12.1   0.1    1.5  1  Bile_Hydr_Trans  Acyl-CoA thioester hydrolase/BAAT N-terminal
       0.13   11.9   0.0       0.24   11.1   0.0    1.4  1  SAD_SRA          SAD/SRA domain
       0.15   12.0   0.1       0.27   11.2   0.1    1.4  1  Deltameth_res    Deltamethrin resistance


Domain annotation for each model (and alignments):
>> Bile_Hydr_Trans  Acyl-CoA thioester hydrolase/BAAT N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   2.5e-05      0.15      53      72 ..     181     200 ..     176     205 .] 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.5e-05
                Bile_Hydr_Trans  53 lgGsYtgvepmGLfwsmkpe 72 
                                    l+GsY g +p GL+ws + +
  gi|116753876|ref|YP_842994.1| 181 LQGSYYGYSPQGLIWSGQAR 200
                                    79**************8765 PP

>> SAD_SRA  SAD/SRA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0     4e-05      0.24      12      53 ..      83     124 ..      79     148 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4e-05
                                    -EESSHHHHHHTTSS--SS-SEEEE-GGGEEEEEE-S-STT- CS
                        SAD_SRA  12 dtfksraelleagvHrplqagIsgskeegAvSivlsggYedd 53 
                                    +t+++  +l ++g  r ++ g+++ + +g + +vls+gY  d
  gi|116753876|ref|YP_842994.1|  83 HTWEYLETLQRWGYTRGYVPGVQTLRMDGSWHLVLSEGYTAD 124
                                    79*************************************987 PP

>> Deltameth_res  Deltamethrin resistance
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   4.5e-05      0.27      24      48 ..      27      51 ..      15      53 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.5e-05
                  Deltameth_res 24 vLaaGiviligTialakesglinln 48
                                    La G++il++T+++  +s++i+l 
  gi|116753876|ref|YP_842994.1| 27 LLAWGLAILCITLIAHSQSDVIDLR 51
                                   4899******************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); 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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1568.55
//
Query:       gi|116753877|ref|YP_842995.1|  [L=286]
Description: cobyrinic acid a,c-diamide synthase [Methanosaeta thermophila PT]
Scores for 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-19   67.7   0.0    1.2e-18   67.4   0.0    1.1  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    1.3e-11   43.8  12.2    1.3e-06   27.9   2.7    2.7  2  Fer4         4Fe-4S binding domain
    1.4e-08   34.5   0.1     0.0026   17.3   0.0    2.7  2  ParA         NUBPL iron-transfer P-loop NTPase
    5.2e-08   33.4   5.1     0.0008   19.9   1.2    2.6  2  Fer4_7       4Fe-4S dicluster domain
      1e-06   28.5  12.4     0.0025   17.8   2.1    2.7  2  Fer4_6       4Fe-4S binding domain
    1.5e-06   28.2   9.5    4.4e-06   26.7   9.5    1.8  1  Fer4_21      4Fe-4S dicluster domain
    4.6e-06   26.6   0.3      0.068   13.1   0.0    2.2  2  AAA_31       AAA domain
    5.2e-06   27.1   6.0     0.0099   16.6   0.1    2.6  2  Fer4_15      4Fe-4S single cluster domain
    5.4e-06   26.2  14.7     0.0056   16.7   3.3    2.8  2  Fer4_2       4Fe-4S binding domain
    0.00016   21.7  13.3      0.004   17.3  13.7    2.4  2  Fer4_9       4Fe-4S dicluster domain
    0.00034   20.6   1.3       0.22   11.4   0.0    2.8  3  RsgA_GTPase  RsgA GTPase
    0.00037   20.9   3.5       0.18   12.3   0.8    2.6  2  Fer4_8       4Fe-4S dicluster domain
     0.0014   19.1   0.1      0.006   17.0   0.0    2.0  2  AAA_16       AAA ATPase domain
     0.0024   18.0  14.2      0.087   13.0  15.2    2.5  2  Fer4_10      4Fe-4S dicluster domain
     0.0036   18.2  10.9       0.22   12.5   2.2    2.5  3  Fer4_16      4Fe-4S double cluster binding domain
  ------ inclusion threshold ------
      0.012   14.8   2.5      0.026   13.7   2.5    1.5  1  ArsA_ATPase  Anion-transporting ATPase
      0.027   14.2   0.0      0.042   13.6   0.0    1.3  1  AAA_24       AAA domain
      0.028   13.6   0.8          2    7.5   0.4    2.4  2  NB-ARC       NB-ARC domain
      0.079   13.9  15.1       0.14   13.2   2.4    2.8  2  Fer4_3       4Fe-4S binding domain
       0.12   11.8   0.0        6.2    6.2   0.0    2.1  2  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
       0.13   12.8   0.0       0.18   12.3   0.0    1.2  1  AAA_23       AAA domain
       0.17   11.5   0.3       0.65    9.5   0.2    1.9  2  AAA_25       AAA domain
       0.37   11.4  11.7        1.4    9.5   3.1    2.4  2  Fer4_17      4Fe-4S dicluster domain
       0.59    9.8   1.6        1.1    9.0   0.4    1.8  2  AAA_30       AAA domain
        0.6   10.8  19.2        1.8    9.3   3.6    2.9  2  Fer4_4       4Fe-4S binding domain
        5.9    7.5  16.2        3.2    8.4   4.3    2.9  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 !   67.4   0.0   1.8e-21   1.2e-18       1     128 []       4     262 ..       4     262 .. 0.96

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 1.8e-21
                                    EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH.......................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................... RF
                           CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep.......................... 54 
                                    i+++s+kGG+GKT+++a++a++ +    r +  D+D++a+ l+i+   + ++++                          
  gi|116753877|ref|YP_842995.1|   4 IVVISGKGGTGKTSIVASFAACASG---RAVIADCDVDAPDLHIILNPVVRERReffglrrafidkerctecgaciercr 80 
                                    79**********************9...9**************9888888777789999999999*************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                           CbiA  55 ................................................................................ 54 
                                                                                                                    
  gi|116753877|ref|YP_842995.1|  81 fdainnfevdqsacegcgvctlvcgsdavrmvehlsgyayisdtrygplvhaemfpaeeasgklvtmvreiarnlaeslr 160
                                    ******************************************************************************** PP

                                    ......................................CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHH CS
                                    ......................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA  55 ......................................dlkrllellealgkkkalllkiagvvlnrvdgeneetllkea 96 
                                                                          dl+r+l l+e+++++       a+v +nr+d +   + ++++
  gi|116753877|ref|YP_842995.1| 161 memvlidgspgigcpvisslagadlalvvteptisgvhDLDRILDLAEHFRIR-------AMVCINRYDIN---EDISKN 230
                                    ****************************************************9.......**********9...778888 PP

                                    HHHHHHHCTS-EEEEEE--CCHCCCCHHTS-H CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA  97 leelkqrygvpvlgviprdeavaeapargepv 128
                                    +e+ +   g + +g ip+d +v++a  rg pv
  gi|116753877|ref|YP_842995.1| 231 IERACDGRGTEMVGRIPFDMNVIDAMVRGVPV 262
                                    88888666********************9886 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   2.7     2e-09   1.3e-06       2      23 ..      63      84 ..      62      85 .. 0.94
   2 !   20.6   2.1   3.8e-07   0.00027       2      23 ..      88     109 ..      87     110 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 2e-09
                                   EEETTTSSS-THHHHHSTTTEE CS
                           Fer4  2 videekCigCGaCvevCPvgAI 23
                                    id+e+C+ CGaC+e C ++AI
  gi|116753877|ref|YP_842995.1| 63 FIDKERCTECGACIERCRFDAI 84
                                   69*******************9 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 3.8e-07
                                    EEETTTSSS-THHHHHSTTTEE CS
                           Fer4   2 videekCigCGaCvevCPvgAI 23 
                                    ++d++ C gCG C  vC  +A 
  gi|116753877|ref|YP_842995.1|  88 EVDQSACEGCGVCTLVCGSDAV 109
                                    69***************99996 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   3.7e-06    0.0026       5      51 ..       3      46 ..       1      56 [. 0.76
   2 !   14.1   0.0   3.5e-05     0.024     111     243 ..     160     278 ..     141     281 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.7e-06
                           ParA  5 viavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprll 51
                                    i+v+SgKGG GK+++ +++A+    +g +  + D D+  p++  +l
  gi|116753877|ref|YP_842995.1|  3 QIVVISGKGGTGKTSIVASFAACA--SG-RAVIADCDVDAPDLHIIL 46
                                   699************999998764..33.344788888887776666 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 3.5e-05
                           ParA 111 elDyLiiDlPPGtgDeqltvaqklplagaviVttpqevaladvkkaiemfkkvkvkvlGvveNmsgfvcpkcgekteifg 190
                                     +++++iD  PG g   ++ +     + a++Vt p    ++d  + ++++++ +++ +  ++        + +e      
  gi|116753877|ref|YP_842995.1| 160 RMEMVLIDGSPGIGCPVISSLAGA--DLALVVTEPTISGVHDLDRILDLAEHFRIRAMVCINR------YDINED----I 227
                                    578899******999888766655..6799**********************99886544433......333333....2 PP

                           ParA 191 kgggeklaeelgvpllgeipldpeireasdegkplvlkepeseaakaleeiae 243
                                    +++ e++++  g++++g+ip+d+++ +a+ +g p+v+ +  ++a+ ++++i +
  gi|116753877|ref|YP_842995.1| 228 SKNIERACDGRGTEMVGRIPFDMNVIDAMVRGVPVVELN--TPASYSIKQIWS 278
                                    467899****************************99765..666767766665 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   1.2   1.2e-06    0.0008      21      52 .]      48      83 ..      23      83 .. 0.69
   2 !   14.7   0.1   5.2e-05     0.036       1      21 [.      93     113 ..      87     143 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.2e-06
                         Fer4_7 21 eeenek....gtekveidpekClgCgaCvavCPtga 52
                                   ++ +e+    g +++ id e+C+ CgaC+++C ++a
  gi|116753877|ref|YP_842995.1| 48 PVVRERreffGLRRAFIDKERCTECGACIERCRFDA 83
                                   3433332233448899****************9886 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 5.2e-05
                         Fer4_7   1 rCigCgaCvaaCpvkaielde 21 
                                    +C gCg C+ +C ++a+++ e
  gi|116753877|ref|YP_842995.1|  93 ACEGCGVCTLVCGSDAVRMVE 113
                                    488888888888888888876 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   2.9   2.3e-05     0.016       2      24 .]      62      84 ..      61      84 .. 0.91
   2 !   17.8   2.1   3.6e-06    0.0025       3      23 ..      88     108 ..      87     109 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.3e-05
                         Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                   + id+++C+ Cg+C+  C ++ai
  gi|116753877|ref|YP_842995.1| 62 AFIDKERCTECGACIERCRFDAI 84
                                   679************99998887 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 3.6e-06
                         Fer4_6   3 eidpdkCigCgdCvrvCPega 23 
                                    e+d+++C gCg C+ vC  +a
  gi|116753877|ref|YP_842995.1|  88 EVDQSACEGCGVCTLVCGSDA 108
                                    89***************8766 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   9.5   6.3e-09   4.4e-06       1      59 []      62     111 ..      62     111 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 6.3e-09
                        Fer4_21   1 AridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedciem 59 
                                    A+id+++C +Cg C+  C+    +ai+      ++v ++ C GC +C+ vC  +d+++m
  gi|116753877|ref|YP_842995.1|  62 AFIDKERCTECGACIERCR---FDAIN-----NFEVDQSACEGCGVCTLVCG-SDAVRM 111
                                    89*****************...67776.....5899***************9.588887 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.2   0.00028      0.19       1      27 [.       1      27 [.       1      40 [. 0.83
   2 !   13.1   0.0   9.8e-05     0.068     118     166 ..     161     209 ..     129     220 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00028
                         AAA_31  1 gkvIaianqKGGvGKTTtsvnlaaala 27
                                   +k I+++  KGG GKT  +  +aa+ +
  gi|116753877|ref|YP_842995.1|  1 MKQIVVISGKGGTGKTSIVASFAACAS 27
                                   799***************999999865 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 9.8e-05
                         AAA_31 118 YDyiiiDcpPsLglltenaLvasdsviipvqaeayaleGleqllktiee 166
                                      +++iD +P +g+ ++++L+ +d  +++++++   ++ l+++l+  e+
  gi|116753877|ref|YP_842995.1| 161 MEMVLIDGSPGIGCPVISSLAGADLALVVTEPTISGVHDLDRILDLAEH 209
                                    579*****************************98888888888876665 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 !   11.6   2.0   0.00052      0.36       3      18 ..      64      79 ..      63      86 .. 0.89
   2 !   16.6   0.1   1.4e-05    0.0099       2      33 ..      88     122 ..      87     142 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00052
                        Fer4_15  3 vDrdaCigcglCvaea 18
                                   +D+++C+ cg+C++++
  gi|116753877|ref|YP_842995.1| 64 IDKERCTECGACIERC 79
                                   9*************99 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1.4e-05
                        Fer4_15   2 vvDrdaCigcglCvaea.pevfelde..dglasvl 33 
                                    +vD++aC+gcg+C  ++ ++ +++ e   g+a++ 
  gi|116753877|ref|YP_842995.1|  88 EVDQSACEGCGVCTLVCgSDAVRMVEhlSGYAYIS 122
                                    69**************9844443333226777655 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   3.3   8.1e-06    0.0056       2      20 ..      61      79 ..      60      80 .. 0.89
   2 !   14.2   3.6   5.1e-05     0.035       4      20 ..      88     104 ..      86     104 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 8.1e-06
                         Fer4_2  2 pvvvdtdrCigCgaCvsaC 20
                                   ++++d +rC++CgaC+  C
  gi|116753877|ref|YP_842995.1| 61 RAFIDKERCTECGACIERC 79
                                   689************8766 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 5.1e-05
                         Fer4_2   4 vvdtdrCigCgaCvsaC 20 
                                    +vd  +C gCg C+ +C
  gi|116753877|ref|YP_842995.1|  88 EVDQSACEGCGVCTLVC 104
                                    7999************* PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   3.1   1.6e-05     0.011      33      51 .]      59      84 ..      23      84 .. 0.75
   2 !   17.3  13.7   5.8e-06     0.004       1      50 [.      68     108 ..      68     109 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.6e-05
                         Fer4_9 33 e.......eaCigCgaCveaCpkgai 51
                                           e+C++CgaC+e+C  +ai
  gi|116753877|ref|YP_842995.1| 59 LrrafidkERCTECGACIERCRFDAI 84
                                   0444555679***********98876 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 5.8e-06
                         Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                    +Ct+CgaC+e C ++++++ ++ +          aC gCg C+ +C ++a
  gi|116753877|ref|YP_842995.1|  68 RCTECGACIERCRFDAINNFEVDQS---------ACEGCGVCTLVCGSDA 108
                                    6******************999998.........6***********9886 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.3      0.01       6.9      99     120 ..       2      23 ..       1      32 [. 0.86
   2 ?   -0.6   0.0       1.6   1.1e+03      89     111 ..     151     173 ..     141     183 .. 0.82
   3 !   11.4   0.0   0.00032      0.22      20      68 ..     187     231 ..     160     245 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.01
                                    TSEEEEECSTTSSHHHHHHHHC CS
                    RsgA_GTPase  99 dktsvlvGqSGvGKStLinall 120
                                    ++++v+ G+ G GK++++ +++
  gi|116753877|ref|YP_842995.1|   2 KQIVVISGKGGTGKTSIVASFA 23 
                                    5899*************98766 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.6
                                    THHHHHHHCTTSEEEEECSTTSS CS
                    RsgA_GTPase  89 gleelkellkdktsvlvGqSGvG 111
                                     +++l+e l+ +++++ G+ G+G
  gi|116753877|ref|YP_842995.1| 151 IARNLAESLRMEMVLIDGSPGIG 173
                                    56789999999999999999999 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00032
                                    EEEEESTTTT--.HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHH CS
                    RsgA_GTPase  20 livvslkepels.lnlldrfLvlaeekgiepvivlnKiDlleeeeeleel 68 
                                    l+v+   ep++s ++ ldr+L lae+ +i+ ++++n+ D+ e+ +  +++
  gi|116753877|ref|YP_842995.1| 187 LVVT---EPTISgVHDLDRILDLAEHFRIRAMVCINRYDINEDIS--KNI 231
                                    4443...344442678***********************998876..444 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.8   0.00026      0.18       3      15 ..      67      79 ..      24      88 .. 0.84
   2 !    8.9   0.1     0.003       2.1       3      16 ..      92     105 ..      90     158 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00026
                         Fer4_8  3 ekCieCgaCqsaC 15
                                   e+C+eCgaC + C
  gi|116753877|ref|YP_842995.1| 67 ERCTECGACIERC 79
                                   4566666665555 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.003
                         Fer4_8   3 ekCieCgaCqsaCp 16 
                                    ++C +Cg C+  C 
  gi|116753877|ref|YP_842995.1|  92 SACEGCGVCTLVCG 105
                                    67888888888883 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   8.7e-06     0.006      25      63 ..       3      38 ..       1      71 [. 0.79
   2 ?   -0.9   0.0       2.8   1.9e+03      23      36 ..     160     173 ..     142     173 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 8.7e-06
                         AAA_16 25 elvllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                   ++v++sG  G+GK+s+v +++  ++++   ++ ++cd  
  gi|116753877|ref|YP_842995.1|  3 QIVVISGKGGTGKTSIVASFAACASGR---AVIADCDVD 38
                                   589*****************9644444...455666655 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.8
                         AAA_16  23 rpelvllsGesGvG 36 
                                    r e+vl+ G +G+G
  gi|116753877|ref|YP_842995.1| 160 RMEMVLIDGSPGIG 173
                                    23899999999998 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0  15.2   0.00013     0.087       3      55 ..      63     104 ..      61     105 .. 0.84
   2 !   10.4   2.0   0.00081      0.56       4      20 ..      89     105 ..      86     127 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00013
                        Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                     id+++C++Cg+C + C             + ++  +++ ++C+gcg C+ +C
  gi|116753877|ref|YP_842995.1|  63 FIDKERCTECGACIERC-----------RFDAINNFEVDQSACEGCGVCTLVC 104
                                    69***************...........3455556666789*********999 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00081
                        Fer4_10   4 idddtCirCgkCvkaCP 20 
                                    +d++ C +Cg C+ +C 
  gi|116753877|ref|YP_842995.1|  89 VDQSACEGCGVCTLVCG 105
                                    68899999999999994 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   2.2   0.00031      0.22       1      20 [.      68      87 ..      68      93 .. 0.87
   2 !    8.9   1.7    0.0043       2.9      51      64 ..      91     104 ..      86     107 .. 0.79
   3 !   10.0   1.6    0.0019       1.3       2      20 ..      94     112 ..      93     124 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00031
                        Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                   rC++Cg+C+e C  +ai++ 
  gi|116753877|ref|YP_842995.1| 68 RCTECGACIERCRFDAINNF 87
                                   6****************875 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0043
                        Fer4_16  51 qeaitgCdiCqdvC 64 
                                    q a+ gC++C+ vC
  gi|116753877|ref|YP_842995.1|  91 QSACEGCGVCTLVC 104
                                    67899999999999 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.0019
                        Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                    C +Cg C+ vC ++a+++ 
  gi|116753877|ref|YP_842995.1|  94 CEGCGVCTLVCGSDAVRMV 112
                                    9999999999999998865 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   2.5   3.8e-05     0.026       2      25 ..       3      26 ..       2      32 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.8e-05
                                   EEEEEEESTTSSHHHHHHHHHHHH CS
                    ArsA_ATPase  2 kvilvgGKGGVGKttvsaatavkl 25
                                   ++++++GKGG GKt++ a++a+  
  gi|116753877|ref|YP_842995.1|  3 QIVVISGKGGTGKTSIVASFAACA 26
                                   6899****************9765 PP

>> AAA_24  AAA 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     0.042       1      32 [.       1      36 [.       1      71 [. 0.88

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.1e-05
                         AAA_24  1 kklkiliyGpsgiGKTtlakel....gpkplfidte 32
                                   +k+ ++i G+ g+GKT++++++      ++++ d++
  gi|116753877|ref|YP_842995.1|  1 MKQIVVISGKGGTGKTSIVASFaacaSGRAVIADCD 36
                                   57889*****************99999999999998 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.4    0.0029         2      21      39 ..       3      21 ..       1      27 [. 0.87
   2 ?    4.1   0.0     0.032        22       3      40 ..     146     181 ..     144     191 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0029
                                   EEEEEEESTTSSHHHHHHH CS
                         NB-ARC 21 lvvalvGmgGvGKttlakq 39
                                    +v ++G+gG GKt ++++
  gi|116753877|ref|YP_842995.1|  3 QIVVISGKGGTGKTSIVAS 21
                                   499***********99875 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.032
                                    HHHHHHHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHH CS
                         NB-ARC   3 ksvekviekLlekdelqslvvalvGmgGvGKttlakqi 40 
                                    ++v++++ +L e+  ++  +v + G +G+G  ++++ +
  gi|116753877|ref|YP_842995.1| 146 TMVREIARNLAESLRME--MVLIDGSPGIGCPVISSLA 181
                                    6999*******998888..***********99998755 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   2.4    0.0002      0.14       1      15 []      69      83 ..      69      83 .. 0.95
   2 ?    5.5   5.1     0.057        39       1      15 []      94     108 ..      94     108 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.0002
                         Fer4_3  1 CtgCgaCvevCPvgA 15
                                   Ct CgaC e C+ +A
  gi|116753877|ref|YP_842995.1| 69 CTECGACIERCRFDA 83
                                   ***********9987 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.057
                         Fer4_3   1 CtgCgaCvevCPvgA 15 
                                    C gCg C  vC ++A
  gi|116753877|ref|YP_842995.1|  94 CEGCGVCTLVCGSDA 108
                                    99*********7766 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0    0.0089       6.2       1      24 [.       1      24 [.       1      72 [. 0.83
   2 ?    3.8   0.0     0.048        33     109     181 ..     152     231 ..     114     270 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0089
                       CBP_BcsQ  1 mkvlalqGvRGGvGttsllaaLaw 24
                                   mk++++   +GG+G+ts++a+ a 
  gi|116753877|ref|YP_842995.1|  1 MKQIVVISGKGGTGKTSIVASFAA 24
                                   7777777779**********9875 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.048
                       CBP_BcsQ 109 lkelk..eqyrwillDlpagasaltrellaladlvllvvepdanchvrLhq.....qalpaaellLiNqfeaasqlqqDl 181
                                     ++l+   + +++l+D   g    + + la adl l v+ep  +    L++     +++  ++++ iN+++++  + + +
  gi|116753877|ref|YP_842995.1| 152 ARNLAesLRMEMVLIDGSPGIGCPVISSLAGADLALVVTEPTISGVHDLDRildlaEHFRIRAMVCINRYDINEDISKNI 231
                                    3344444567899***999999888888889**********987755555411111457778888999999988877665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00026      0.18      20      46 ..       3      29 ..       2      71 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00026
                         AAA_23 20 gltlItGpNGaGKTTildAiklaLyge 46
                                    +++I+G+ G+GKT+i+  +  +  g+
  gi|116753877|ref|YP_842995.1|  3 QIVVISGKGGTGKTSIVASFAACASGR 29
                                   689*****************9999886 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.2   0.00095      0.65      34      58 ..       3      27 ..       1      39 [. 0.86
   2 ?   -1.1   0.0       1.7   1.2e+03     119     149 ..     138     167 ..     119     168 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00095
                         AAA_25 34 elallaGapgtGKttlaldlalava 58
                                    ++++ G +gtGKt ++ + a++ +
  gi|116753877|ref|YP_842995.1|  3 QIVVISGKGGTGKTSIVASFAACAS 27
                                   57899***************99865 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.7
                         AAA_25 119 kdrggtlltadvdaleaaieevegvrlvviD 149
                                    +++ g+l+t  v+++++ + e  + ++v iD
  gi|116753877|ref|YP_842995.1| 138 EEASGKLVT-MVREIARNLAESLRMEMVLID 167
                                    333444443.345666666665556666666 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   3.1     0.002       1.4       1      21 [.      68      88 ..      68      93 .. 0.80
   2 ?    6.3   1.5     0.021        15       1      14 [.      93     106 ..      93     140 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.002
                        Fer4_17  1 rCiqCgyClpeCpsyeaydne 21
                                   rC++Cg+C++ C + +++++e
  gi|116753877|ref|YP_842995.1| 68 RCTECGACIERCRFDAINNFE 88
                                   699999999999988777765 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.021
                        Fer4_17   1 rCiqCgyClpeCps 14 
                                    +C +Cg C+ +C s
  gi|116753877|ref|YP_842995.1|  93 ACEGCGVCTLVCGS 106
                                    59999999999976 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.4    0.0015       1.1      19      42 ..       3      26 ..       1      34 [. 0.83
   2 ?   -0.7   0.0       1.5     1e+03      90     115 ..     185     210 ..     137     217 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0015
                         AAA_30 19 rvavltGpAGtGKttalkalreaw 42
                                   +++v+ G  GtGKt ++++ ++ +
  gi|116753877|ref|YP_842995.1|  3 QIVVISGKGGTGKTSIVASFAACA 26
                                   689**************9987765 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.5
                         AAA_30  90 tllivDEagmvdtkqlaallkaaeka 115
                                      l+v E    + ++l+++l+ ae+ 
  gi|116753877|ref|YP_842995.1| 185 LALVVTEPTISGVHDLDRILDLAEHF 210
                                    45788888888888888888888774 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   4.6    0.0027       1.9       1      14 [.      66      79 ..      66      82 .. 0.84
   2 ?    9.3   3.6    0.0026       1.8       1      14 [.      91     104 ..      91     107 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0027
                         Fer4_4  1 qerCigCgsCvaaC 14
                                   +erC++Cg+C+  C
  gi|116753877|ref|YP_842995.1| 66 KERCTECGACIERC 79
                                   69********8666 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0026
                         Fer4_4   1 qerCigCgsCvaaC 14 
                                    q+ C gCg+C+ +C
  gi|116753877|ref|YP_842995.1|  91 QSACEGCGVCTLVC 104
                                    578*********** PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   4.3    0.0046       3.2       1      16 [.      64      79 ..      64      80 .. 0.94
   2 ?    5.0   2.7      0.05        35       1      16 [.      89     104 ..      89     106 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0046
                        Fer4_13  1 VDrdtCiacgaCvela 16
                                   +D+++C++cgaC e +
  gi|116753877|ref|YP_842995.1| 64 IDKERCTECGACIERC 79
                                   8************988 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.05
                        Fer4_13   1 VDrdtCiacgaCvela 16 
                                    VD++ C +cg+C  ++
  gi|116753877|ref|YP_842995.1|  89 VDQSACEGCGVCTLVC 104
                                    9***********9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                       108  (0.00602376); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 2080.32
//
Query:       gi|116753878|ref|YP_842996.1|  [L=277]
Description: cobyrinic acid a,c-diamide synthase [Methanosaeta thermophila PT]
Scores for complete 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   53.9   0.0    2.5e-14   53.4   0.0    1.2  1  CbiA       CobQ/CobB/MinD/ParA nucleotide binding domain
      1e-13   50.5  13.3    5.3e-07   29.2   2.7    2.7  2  Fer4       4Fe-4S binding domain
    4.1e-13   48.8  13.8    3.2e-06   27.0   3.7    2.6  2  Fer4_6     4Fe-4S binding domain
    3.1e-10   39.9   0.0    0.00099   18.6   0.0    3.0  2  ParA       NUBPL iron-transfer P-loop NTPase
    1.8e-08   35.2   5.2    0.00058   20.7   0.1    2.4  2  Fer4_16    4Fe-4S double cluster binding domain
    5.6e-08   32.8  10.7    1.1e-07   31.9  10.7    1.5  1  Fer4_21    4Fe-4S dicluster domain
    3.7e-07   30.6  35.6    2.1e-05   25.0  13.1    2.3  3  Fer4_7     4Fe-4S dicluster domain
    4.2e-07   30.0  20.9    7.5e-05   22.8  12.7    2.4  2  Fer4_10    4Fe-4S dicluster domain
    9.2e-06   25.7  13.2    3.2e-05   24.0  12.2    2.2  2  Fer4_9     4Fe-4S dicluster domain
    2.8e-05   24.1   0.1        0.1   12.5   0.0    2.2  2  AAA_31     AAA domain
    5.1e-05   23.6   6.9       0.02   15.3   0.4    2.4  2  Fer4_8     4Fe-4S dicluster domain
    6.5e-05   22.8  16.2     0.0014   18.6   2.7    2.9  3  Fer4_2     4Fe-4S binding domain
    8.9e-05   22.7  12.8     0.0068   16.8   2.0    2.8  2  Fer4_4     4Fe-4S binding domain
    0.00069   20.1   8.3      0.079   13.5   0.4    2.4  2  Fer4_17    4Fe-4S dicluster domain
     0.0024   18.7   9.0      0.056   14.3   1.3    2.4  2  Fer4_22    4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.036   15.0   6.1      0.036   15.0   6.1    3.2  3  Fer4_3     4Fe-4S binding domain
      0.059   12.9   0.1       0.46   10.0   0.1    2.0  2  AAA_25     AAA domain
       0.14   11.6   0.1        1.3    8.4   0.0    2.1  2  Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/


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 !   53.4   0.0   2.5e-17   2.5e-14       1     125 [.       3     251 ..       3     254 .. 0.97

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 2.5e-17
                                    EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH...HTTEB-HHHH....................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxx....................... RF
                           CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai...leglendiep....................... 54 
                                    +++as+kGG+GKT +a+++ ++ +      +l+D+D++ +n+++    ++l  ++e+                       
  gi|116753878|ref|YP_842996.1|   3 VSVASGKGGTGKTLVATSITASVKG----AQLLDCDVEEPNAFLffpEMKLLDRKECtvpvpqideklcvhcgrcaevca 78 
                                    579******************9998....99************98777777777777*********************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                           CbiA  55 ................................................................................ 54 
                                                                                                                    
  gi|116753878|ref|YP_842996.1|  79 fnaiaviptravvfpelchgcgacmiscpekaisevlrrigwisrarsedheivwgelepgearptplirdvrrhanadt 158
                                    ******************************************************************************** PP

                                    ...................................CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHH CS
                                    ...................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA  55 ...................................dlkrllellealgkkkalllkiagvvlnrvdgeneetllkealee 99 
                                                                       dl+  l+lle+l+++        gv++n+ +    ++++++ le+
  gi|116753878|ref|YP_842996.1| 159 vivdcppgascsvvesvrdtdfcllvaeptpfglyDLDLALKLLERLSIP-------RGVLVNKSGIG--TREIYSYLEK 229
                                    ************************************************99.......9**********..9********9 PP

                                    HHHHCTS-EEEEEE--CCHCCCCHHT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA 100 lkqrygvpvlgviprdeavaeaparg 125
                                    +     vpvl +ip + ++ae+++rg
  gi|116753878|ref|YP_842996.1| 230 R----DVPVLMEIPMSREIAELYSRG 251
                                    8....9*****************998 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   3.1   4.7e-09   4.7e-06       1      23 [.      60      82 ..      60      83 .. 0.94
   2 !   29.2   2.7   5.3e-10   5.3e-07       2      24 .]      90     112 ..      89     112 .. 0.94

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 4.7e-09
                                   EEEETTTSSS-THHHHHSTTTEE CS
                           Fer4  1 vvideekCigCGaCvevCPvgAI 23
                                   ++ide +C++CG+C+evC ++AI
  gi|116753878|ref|YP_842996.1| 60 PQIDEKLCVHCGRCAEVCAFNAI 82
                                   68****************99998 PP

  == domain 2  score: 29.2 bits;  conditional E-value: 5.3e-10
                                    EEETTTSSS-THHHHHSTTTEEE CS
                           Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                    v+ +e+C gCGaC+  CP  AI+
  gi|116753878|ref|YP_842996.1|  90 VVFPELCHGCGACMISCPEKAIS 112
                                    799******************96 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   3.7   3.2e-09   3.2e-06       1      24 []      59      82 ..      59      82 .. 0.96
   2 !   26.9   2.5   3.5e-09   3.5e-06       2      24 .]      89     111 ..      88     111 .. 0.95

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 3.2e-09
                         Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                   v++id+ +C++Cg+C+ vC ++ai
  gi|116753878|ref|YP_842996.1| 59 VPQIDEKLCVHCGRCAEVCAFNAI 82
                                   699*******************98 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 3.5e-09
                         Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                    +++ p++C gCg+C++ CPe+ai
  gi|116753878|ref|YP_842996.1|  89 AVVFPELCHGCGACMISCPEKAI 111
                                    6899*****************98 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 !   18.6   0.0   9.9e-07   0.00099       5      46 ..       2      39 ..       1      69 [. 0.79
   2 !   16.4   0.0   4.6e-06    0.0046     103     243 ..     146     270 ..     124     273 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 9.9e-07
                           ParA  5 viavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGps 46
                                   ++ v+SgKGG GK+ va++++++++       llD D+  p+
  gi|116753878|ref|YP_842996.1|  2 IVSVASGKGGTGKTLVATSITASVKGA----QLLDCDVEEPN 39
                                   689***************999988543....47899987776 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 4.6e-06
                           ParA 103 llkdve.wgelDyLiiDlPPGtgDeqltvaqkl.plagaviVttpqevaladvkkaiemfkkvkvkvlGvveNmsgfvcp 180
                                    l++dv+ + + D +i+D+PPG +    +v++++ +++ +++V+ p    l d   a++++++++++  Gv+ N sg+ + 
  gi|116753878|ref|YP_842996.1| 146 LIRDVRrHANADTVIVDCPPGAS---CSVVESVrDTDFCLLVAEPTPFGLYDLDLALKLLERLSIPR-GVLVNKSGIGTR 221
                                    56666425689**********87...6788888666789**************************95.888888887655 PP

                           ParA 181 kcgekteifgkgggeklaeelgvpllgeipldpeireasdegkplvlkepeseaakaleeiae 243
                                                +  ++ e+ +vp+l eip++ ei+e   +g  +v      e  + ++++ae
  gi|116753878|ref|YP_842996.1| 222 ------------EIYSYLEKRDVPVLMEIPMSREIAELYSRGVIFVNML--GEWRERFTNLAE 270
                                    ............3446778889999999999999999999998766543..555666666665 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   1.7   2.6e-05     0.025       2      18 ..      67      83 ..      66      92 .. 0.89
   2 !   20.7   0.1   5.8e-07   0.00058       2      20 ..      96     114 ..      95     150 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.6e-05
                        Fer4_16  2 CgtCgkCaevCPtnaik 18
                                   C+ Cg+CaevC  nai 
  gi|116753878|ref|YP_842996.1| 67 CVHCGRCAEVCAFNAIA 83
                                   ***************96 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 5.8e-07
                        Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                    C++Cg+C+ +CP++ai+e 
  gi|116753878|ref|YP_842996.1|  96 CHGCGACMISCPEKAISEV 114
                                    ****************997 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9  10.7   1.1e-10   1.1e-07       2      57 ..      61     111 ..      60     113 .. 0.89

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 1.1e-10
                        Fer4_21   2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57 
                                    +ide+ C++Cg+C+ +C     +ai + + +   v  + C GC  C++ CP e++i
  gi|116753878|ref|YP_842996.1|  61 QIDEKLCVHCGRCAEVCA---FNAIAVIPTRA-VVFPELCHGCGACMISCP-EKAI 111
                                    69***************9...79999887665.789***************.6877 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   4.2     5e-06     0.005      27      52 .]      56      81 ..      33      81 .. 0.76
   2 !   25.0  13.1   2.1e-08   2.1e-05       2      52 .]      67     110 ..      66     110 .. 0.93
   3 !   14.4   2.6   4.3e-05     0.043       2      18 ..      96     112 ..      95     137 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5e-06
                         Fer4_7 27 gtekveidpekClgCgaCvavCPtga 52
                                   +++ ++id+  C++Cg+C++vC ++a
  gi|116753878|ref|YP_842996.1| 56 TVPVPQIDEKLCVHCGRCAEVCAFNA 81
                                   3477899***************9987 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 2.1e-08
                         Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                    C++Cg+C+++C  +ai + +        ++++ pe C gCgaC+  CP +a
  gi|116753878|ref|YP_842996.1|  67 CVHCGRCAEVCAFNAIAVIPT-------RAVVFPELCHGCGACMISCPEKA 110
                                    ******************986.......57899***************876 PP

  == domain 3  score: 14.4 bits;  conditional E-value: 4.3e-05
                         Fer4_7   2 CigCgaCvaaCpvkaie 18 
                                    C gCgaC+  Cp kai+
  gi|116753878|ref|YP_842996.1|  96 CHGCGACMISCPEKAIS 112
                                    99**********99986 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8  12.7   7.5e-08   7.5e-05       3      56 .]      61     107 ..      59     107 .. 0.89
   2 !   19.5   1.1   7.7e-07   0.00077       6      29 ..      93     116 ..      88     133 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 7.5e-08
                        Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                    +id++ C++Cg+C ++C a       +++a +  +  + +e C+gcgaC+ +CP
  gi|116753878|ref|YP_842996.1|  61 QIDEKLCVHCGRCAEVC-A------FNAIAVIPTRAVVFPELCHGCGACMISCP 107
                                    699**************.4......578888888888899*************9 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 7.7e-07
                        Fer4_10   6 ddtCirCgkCvkaCPadltsvgak 29 
                                    ++ C +Cg+C+ +CP ++ s + +
  gi|116753878|ref|YP_842996.1|  93 PELCHGCGACMISCPEKAISEVLR 116
                                    789*************77544444 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   3.9   5.4e-05     0.054      29      51 .]      60      82 ..      33      82 .. 0.76
   2 !   24.0  12.2   3.2e-08   3.2e-05       2      51 .]      67     111 ..      66     111 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.4e-05
                         Fer4_9 29 raaseeaCigCgaCveaCpkgai 51
                                    + +e+ C++Cg+C+e+C  +ai
  gi|116753878|ref|YP_842996.1| 60 PQIDEKLCVHCGRCAEVCAFNAI 82
                                   3444479***********98876 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 3.2e-08
                         Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                    C+ Cg+C e+C ++++     +  +  +      C+gCgaC+  Cp++ai
  gi|116753878|ref|YP_842996.1|  67 CVHCGRCAEVCAFNAIAVIPTRAVVFPE-----LCHGCGACMISCPEKAI 111
                                    ***************9998888888764.....6*************987 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0   0.00086      0.86       3      32 ..       2      29 ..       1      50 [. 0.82
   2 !   12.5   0.0    0.0001       0.1     117     165 ..     155     203 ..     137     208 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00086
                         AAA_31  3 vIaianqKGGvGKTTtsvnlaaalaklgkk 32
                                   ++++a  KGG GKT  ++ + a++  +g +
  gi|116753878|ref|YP_842996.1|  2 IVSVASGKGGTGKTLVATSITASV--KGAQ 29
                                   799***********9999888765..4444 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.0001
                         AAA_31 117 eYDyiiiDcpPsLglltenaLvasdsviipvqaeayaleGleqllktie 165
                                    + D +i+DcpP  ++ ++ ++   d ++ + +++++ l+ l+  lk +e
  gi|116753878|ref|YP_842996.1| 155 NADTVIVDCPPGASCSVVESVRDTDFCLLVAEPTPFGLYDLDLALKLLE 203
                                    569**********************************999887777665 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   1.4   0.00039      0.38      50      62 ..      66      78 ..      47      86 .. 0.77
   2 !   15.3   0.4     2e-05      0.02       5      20 ..      96     117 ..      93     172 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00039
                         Fer4_8 50 sCttcgaCtevCp 62
                                    C++cg+C+evC 
  gi|116753878|ref|YP_842996.1| 66 LCVHCGRCAEVCA 78
                                   4666666666664 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2e-05
                         Fer4_8   5 CieCgaCqsaCp......vlrr 20 
                                    C++CgaC+ +Cp      vlrr
  gi|116753878|ref|YP_842996.1|  96 CHGCGACMISCPekaiseVLRR 117
                                    9999999999997766543333 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   2.7   1.4e-06    0.0014       1      20 [.      58      77 ..      58      79 .. 0.93
   2 !   12.1   2.5   0.00017      0.16       4      22 .]      90     108 ..      87     108 .. 0.84
   3 ?   -2.8   0.1       9.3   9.3e+03       6      10 ..     177     181 ..     175     182 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.4e-06
                         Fer4_2  1 apvvvdtdrCigCgaCvsaC 20
                                   +++++d+  C++Cg C  +C
  gi|116753878|ref|YP_842996.1| 58 PVPQIDEKLCVHCGRCAEVC 77
                                   579***************** PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00017
                         Fer4_2   4 vvdtdrCigCgaCvsaCPa 22 
                                    vv ++ C gCgaC  +CP+
  gi|116753878|ref|YP_842996.1|  90 VVFPELCHGCGACMISCPE 108
                                    556889************5 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 9.3
                         Fer4_2   6 dtdrC 10 
                                    dtd C
  gi|116753878|ref|YP_842996.1| 177 DTDFC 181
                                    89999 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   3.3   0.00088      0.88       3      15 ..      66      78 ..      64      80 .. 0.85
   2 !   16.8   2.0   6.9e-06    0.0068       1      16 [.      93     108 ..      93     114 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00088
                         Fer4_4  3 rCigCgsCvaaCP 15
                                    C++Cg+C  +C 
  gi|116753878|ref|YP_842996.1| 66 LCVHCGRCAEVCA 78
                                   6**********95 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 6.9e-06
                         Fer4_4   1 qerCigCgsCvaaCPq 16 
                                    +e C gCg+C+++CP 
  gi|116753878|ref|YP_842996.1|  93 PELCHGCGACMISCPE 108
                                    588************5 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   2.2     0.001         1      44      57 ..      65      78 ..      48      82 .. 0.85
   2 !   13.5   0.4   7.9e-05     0.079       2      15 ..      96     109 ..      92     169 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.001
                        Fer4_17 44 slCieCgeCerkCP 57
                                   +lC++Cg+C+++C 
  gi|116753878|ref|YP_842996.1| 65 KLCVHCGRCAEVCA 78
                                   57999999999995 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 7.9e-05
                        Fer4_17   2 CiqCgyClpeCpsy 15 
                                    C++Cg+C+ +Cp  
  gi|116753878|ref|YP_842996.1|  96 CHGCGACMISCPEK 109
                                    66666666666654 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   1.3   5.6e-05     0.056      75      93 ..      60      78 ..      47      81 .. 0.83
   2 !    8.3   1.3    0.0042       4.1      81      95 ..      95     109 ..      87     111 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.6e-05
                        Fer4_22 75 ekfgesgCvGCgRCieacp 93
                                    +++e+ Cv CgRC e+c 
  gi|116753878|ref|YP_842996.1| 60 PQIDEKLCVHCGRCAEVCA 78
                                   67899*************7 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0042
                        Fer4_22  81 gCvGCgRCieacpvk 95 
                                     C GCg C+ +cp+k
  gi|116753878|ref|YP_842996.1|  95 LCHGCGACMISCPEK 109
                                    799999999999975 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   6.3   0.00045      0.45       1      15 []      67      81 ..      67      81 .. 0.93
   2 ?   15.0   6.1   3.7e-05     0.036       1      15 []      96     110 ..      96     110 .. 0.97
   3 ?   -1.2   1.1       5.4   5.4e+03      11      15 .]     163     167 ..     163     167 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00045
                         Fer4_3  1 CtgCgaCvevCPvgA 15
                                   C++Cg+C evC  +A
  gi|116753878|ref|YP_842996.1| 67 CVHCGRCAEVCAFNA 81
                                   ***********8887 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 3.7e-05
                         Fer4_3   1 CtgCgaCvevCPvgA 15 
                                    C+gCgaC+ +CP++A
  gi|116753878|ref|YP_842996.1|  96 CHGCGACMISCPEKA 110
                                    ************998 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 5.4
                         Fer4_3  11 CPvgA 15 
                                    CP+gA
  gi|116753878|ref|YP_842996.1| 163 CPPGA 167
                                    ****9 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00046      0.46      35      65 ..       3      32 ..       1      46 [. 0.79
   2 ?    0.5   0.0      0.39   3.9e+02     122     149 ..     139     162 ..      87     164 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00046
                         AAA_25 35 lallaGapgtGKttlaldlalavatGkpwlg 65
                                   +++  G +gtGKt +a+++ ++v  G ++l+
  gi|116753878|ref|YP_842996.1|  3 VSVASGKGGTGKTLVATSITASVK-GAQLLD 32
                                   67889***************9996.555555 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.39
                         AAA_25 122 ggtlltadvdaleaaieevegvrlvviD 149
                                    g+++ t+    l+++++++++++ v++D
  gi|116753878|ref|YP_842996.1| 139 GEARPTP----LIRDVRRHANADTVIVD 162
                                    3334444....66777777777889988 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 ?    0.7   0.1      0.29   2.8e+02       6      24 ..       7      25 ..       2      37 .. 0.81
   2 ?    8.4   0.0    0.0013       1.3     178     247 ..     210     275 ..     203     277 .] 0.87

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.29
                      Fer4_NifH  6 yGkGGiGksttsqnlsaal 24
                                    GkGG Gk+  ++ ++a++
  gi|116753878|ref|YP_842996.1|  7 SGKGGTGKTLVATSITASV 25
                                   59******99888877765 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0013
                      Fer4_NifH 178 GliinsrkvddereliekfaeelgtkvlevvPrdeivrkaelrkktvieyapeseqakeyrelarkilen 247
                                    G+++n  k   ++  i  + e+ +++vl  +P++ ++ +   r  + +++  e++  + + +la++i e 
  gi|116753878|ref|YP_842996.1| 210 GVLVN--KSGIGTREIYSYLEKRDVPVLMEIPMSREIAELYSRGVIFVNMLGEWR--ERFTNLAERIREM 275
                                    67777..345567778999******************999999999999999999..9********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); 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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2197.01
//
Query:       gi|116753879|ref|YP_842997.1|  [L=83]
Description: hypothetical protein Mthe_0566 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-11   45.1   0.4    1.1e-09   39.3   0.4    2.0  1  DUF5320   Family of unknown function (DUF5320)
  ------ inclusion threshold ------
       0.33   11.2   0.2       0.33   11.2   0.2    1.5  2  XhlA      Haemolysin XhlA


Domain annotation for each model (and alignments):
>> DUF5320  Family of unknown function (DUF5320)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.4   1.2e-13   1.1e-09       1      99 []       1      79 [.       1      79 [. 0.79

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 1.2e-13
                        DUF5320  1 MPrgdgtGpmGlGpmtGrglGyCagadapgyansagfGrgrggrglgrgfgrrrraggarlaaaetaeaskeeekelLeeqa 82
                                   MP+gd tGp++l  +     G    + apg+ n   + r    r++ rgfg+      a++++a+++e++++ee ++Le+ a
  gi|116753879|ref|YP_842997.1|  1 MPWGDCTGPWWLPGR-----G----YRAPGFWN--PWCR---ARWFWRGFGM------AGYPYAPFREPTPDEEVRYLEDVA 62
                                   999999999998433.....3....33456654..3555...6788888888......444456899*************** PP

                        DUF5320 83 eaLeeeleaikkrlkel 99
                                   + Leeel+ai++rl++l
  gi|116753879|ref|YP_842997.1| 63 ADLEEELKAIRERLERL 79
                                   **************986 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.7         1   9.2e+03      49      53 ..      30      34 ..      29      36 .. 0.85
   2 ?   11.2   0.2   3.7e-05      0.33      18      46 ..      53      81 ..      50      83 .] 0.90

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1
                           XhlA 49 kWlir 53
                                    W++r
  gi|116753879|ref|YP_842997.1| 30 RWFWR 34
                                   6***9 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 3.7e-05
                           XhlA 18 ervdkleekaaeaeekiknleedlkkles 46
                                   e+v  le+ aa  ee++k + e+l++l s
  gi|116753879|ref|YP_842997.1| 53 EEVRYLEDVAADLEEELKAIRERLERLRS 81
                                   46889*********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       780  (0.0435049); expected 358.6 (0.02)
Passed bias filter:                      625  (0.0348597); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 607.87
//
Query:       gi|116753880|ref|YP_842998.1|  [L=402]
Description: cation diffusion facilitator family transporter [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-30  106.6  15.6    1.8e-30  106.2  15.6    1.2  1  Cation_efflux  Cation efflux family
    6.9e-17   61.4   1.5    1.3e-16   60.4   1.5    1.5  1  ZT_dimer       Dimerisation domain of Zinc Transporter
      7e-13   48.7   0.0    1.3e-12   47.8   0.0    1.4  1  Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor


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 !  106.2  15.6     3e-34   1.8e-30       2     199 .]      16     204 ..      15     204 .. 0.95

  Alignments for each domain:
  == domain 1  score: 106.2 bits;  conditional E-value: 3e-34
                  Cation_efflux   2 ilsllanlilalvelivglltnSlalladafhslsdlvsllllllalklsrkppderfpfGygrlevlgalvsgllllgl 81 
                                    i+sll+n++l  ++l++  l++Sl+l ada+hs++d++++l l+++l++s ++ +e+fp+G++++e+++++  ++ll++ 
  gi|116753880|ref|YP_842998.1|  16 IYSLLLNIFLVGAKLVLSELSGSLSLRADAIHSMVDVLASLALIVGLVISTRK-SENFPYGLYKVENVVSVAISILLFLS 94 
                                    789***********************************************665.69************************ PP

                  Cation_efflux  82 avfllleaiqklikegereihaglalvvalvslvvnlalllilrragrklrsaalkaaalhvlgDaltslgvlvsalvil 161
                                    a+ +++ a+         + ++g+ l+ + + + + +++ ++ +r g++ +s+++ a+  ++  D+lts +vl+++l+++
  gi|116753880|ref|YP_842998.1|  95 AYEIVMAALRGEQ---IFLTYSGWQLLAVMALVPIPFIFGRYQIRIGERFGSPSMIADGAQHQADVLTSSIVLIAFLGQM 171
                                    ********86544...4499************************************************************ PP

                  Cation_efflux 162 lfnlksgplaDpvaslligliilysalkllkeslseLl 199
                                     +       +D va+++i+l+++ +++++l + +++Ll
  gi|116753880|ref|YP_842998.1| 172 AG-----VQLDRVAAVVIALFVIRAGWDILESGMRVLL 204
                                    *7.....56**************************997 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 !   60.4   1.5   2.2e-20   1.3e-16       2      78 ..     209     284 ..     208     285 .. 0.97

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 2.2e-20
                                    ...HHHHHHHHHTT-SS-EEEEEEEEE-S----EEEEEEEE-TTS-HHHHHHHHHHHHHHHHHH-TT--EEEEEEEE CS
                       ZT_dimer   2 deeeeeeireiiksvpgvkgvhdlrtrksGskifvdlhievdgdlsvkeaHeiadevekrikeefpgvadvliHveP 78 
                                    d e++e+ir+ii++ p+v++v+++ +r+sG+++fv+  +++  +  +++aH+ a+++e++ik+e+p v +++iH+eP
  gi|116753880|ref|YP_842998.1| 209 DRETLERIRSIIEEAPEVVSVKEVVARNSGRYLFVEANLVFRLR-DLQRAHASATRIEESIKREVPAVDRIIIHYEP 284
                                    789**************************************999.******************************** 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 !   47.8   0.0   2.2e-16   1.3e-12       4      93 ..     302     395 ..     300     397 .. 0.95

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 2.2e-16
                                    CB-STCCC-SEEEEEEESSSCEEEEEEE..E.GCCCTSSCSSTHHHHHHHHTT-SEEEESSS..CHHHHHHHCTTTSEEE CS
                  Nitro_FeMo-Co   4 rvdqhFGrapyFaiyeveegevkivenr..veeaadaegggggklaqllaeegvdvvivgki..Gpralakleaagievy 79 
                                    +v  hFG++pyFai ++++ e+k+  ++   +++ + e+g+g+k+a+ll +++ d+v++++   G+++  ++++ag+e +
  gi|116753880|ref|YP_842998.1| 302 DVGTHFGESPYFAILDIDNVERKVKRQEivANPYLGLEKGKGIKVAELLLKHKPDIVLTKESlrGRGPGYAFAEAGVETL 381
                                    5789**************99999999999999*****************************999**************** PP

                                    ES-SSBHHHHHHHH CS
                  Nitro_FeMo-Co  80 kgaggtveealkev 93 
                                    + +  +++e ++++
  gi|116753880|ref|YP_842998.1| 382 QIQTDSLKELIDDL 395
                                    *********99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2818.57
//
Query:       gi|116753881|ref|YP_842999.1|  [L=252]
Description: zinc transporter ZupT [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-22   78.8  22.6    2.3e-18   66.5   8.6    2.1  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 !   18.2   5.4   6.6e-08    0.0012     246     332 ..       9      83 ..       2      84 .. 0.69
   2 !   66.5   8.6   1.3e-22   2.3e-18     174     331 ..      95     244 ..      84     245 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 6.6e-08
                            Zip 246 vllnllfaltaplGiliGilvrsisessgaeivsgillalsaGtflYvalvellphEllnekgssslkqsllqllglllG 325
                                    +ll ll ++++ +G li          + +    ++ l++++G+++Yva+v+l         gs+++    +++l++++G
  gi|116753881|ref|YP_842999.1|   9 LLLTLLAGSATGIGSLISYI-----VPRPDMRYLSLSLGFASGVMIYVAFVDLFC-------GSREVAGLAYSNLFFITG 76 
                                    34444455555555555544.....3333344556779****************8.......3346677789******** PP

                            Zip 326 falmlll 332
                                    ++lm +l
  gi|116753881|ref|YP_842999.1|  77 VLLMYIL 83 
                                    ****997 PP

  == domain 2  score: 66.5 bits;  conditional E-value: 1.3e-22
                            Zip 174 edkeklaslkvraiilllglilHsfidGLAlG..vssssstgislfiAvllHelpeelglgaiLlkaglsrkkavllnll 251
                                    + + ++++l   +i+  +g+ +H++++G+A++    s+   g+++ +A+ +H++pe+++  ++ + a  +r    l++++
  gi|116753881|ref|YP_842999.1|  95 QADAHCSTLYRSSIMSAIGIAIHNLPEGMAVAlvSLSDIHLGVPIALAIAIHNIPEGIACSVPFYCATNKRGRSCLISFA 174
                                    345788899999********************9778999***************************************** PP

                            Zip 252 faltaplGiliGilvrsisessgaeivsgillalsaGtflYvalvellphEllnekgssslkqsllqllglllGfalmll 331
                                     ++t plG+++++l         ++++ +  lal +G+++ +   el+p    +++     + ++l +lg+++Gfa+m++
  gi|116753881|ref|YP_842999.1| 175 AGMTEPLGAVLALL---LLYPFLNQWILSAALALVSGIMVFICIDELIP---IANR----YGSEHLTNLGIIAGFAVMMI 244
                                    **************...445557899999999*****************...4444....4789**************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1846.21
//
Query:       gi|116753882|ref|YP_843000.1|  [L=559]
Description: coenzyme-B sulfoethylthiotransferase [Methanosaeta thermophila PT]
Scores for complete 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-149  496.7   0.0     2e-149  496.3   0.0    1.1  1  MCR_alpha_N  Methyl-coenzyme M reductase alpha subunit, N-ter
    4.1e-70  234.1   2.8    8.2e-70  233.2   2.8    1.5  1  MCR_alpha    Methyl-coenzyme M reductase alpha subunit, C-ter


Domain annotation for each model (and alignments):
>> MCR_alpha_N  Methyl-coenzyme M reductase alpha subunit, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  496.3   0.0  2.2e-153    2e-149       1     270 []       7     276 ..       7     276 .. 0.99

  Alignments for each domain:
  == domain 1  score: 496.3 bits;  conditional E-value: 2.2e-153
                                    XX--HHHHHHH-S.S.-TT--B---S-S-GGGG-HHHHHHHHHHHHHHHHH-S----TTS....S--S-SS---EEEBTT CS
                    MCR_alpha_N   1 eklflkalkkkfkke.dpeekktkfykfeGlkqserkrefveaakkiakkrgislynpdilhl.GvplGqrklmpykvsg 78 
                                    +klf++al+kkf k+ d +++kt++ k+ G +qs+rkref+e++kk++ krgis+ynp +lh+ GvplGqr+l+pyk+s+
  gi|116753882|ref|YP_843000.1|   7 KKLFVRALTKKFGKDfDLSSQKTEY-KRLGPEQSARKREFMEYSKKLEGKRGISFYNP-YLHCgGVPLGQRQLVPYKLSN 84 
                                    689**********9999*******9.********************************.88**9**************** PP

                                    S--EEEGGGSSGGG-HHHHHHHHHHHTEEEEE-HHHHHHHHHTT-----HHHHHHHHHHHHHHTTT--SS-TT-----TT CS
                    MCR_alpha_N  79 tdvlvegddlhfvnnaalqqlwddirrtvivgldtahevlekrlGkevtPetineylevlnhalPGgavvqehmvethPa 158
                                    t+++vegddlhfvnn+a+qq+wddirrtv+vgld+ahevlekrlGkevtPetin+yle+lnha+PG+avvqehmvethP+
  gi|116753882|ref|YP_843000.1|  85 TEYIVEGDDLHFVNNPAMQQMWDDIRRTVVVGLDMAHEVLEKRLGKEVTPETINNYLEILNHAMPGAAVVQEHMVETHPG 164
                                    ******************************************************************************** PP

                                    T-TT-EEEEEES-HHHHTTS-GGGB--HHHHS-HHHHHHHHHHH-S-EEEEEE--HHHHHHS-HHHHHHHHHHHHHHHHH CS
                    MCR_alpha_N 159 lvedcyvkvftGddeladeidkqflidinkefpeeqaeqlkkaiGkklyqvvriPtivsrtcdGgttsrwsamqigmsfi 238
                                    lvedc v+vftGdd+ladeid+q+lidink+fp++qaeqlk+aiGk+++q+++iPtiv+r+cdGgttsrwsamq++m+fi
  gi|116753882|ref|YP_843000.1| 165 LVEDCNVRVFTGDDDLADEIDPQYLIDINKLFPADQAEQLKAAIGKTTWQAIHIPTIVVRSCDGGTTSRWSAMQLSMTFI 244
                                    ******************************************************************************** PP

                                    HHHT--SS-TTHHHHHHHHHTTSEEES---B- CS
                    MCR_alpha_N 239 sayklcaGeaavadlayaakhaeviemgellP 270
                                    +ay++caGeaavadlayaakha+v++m+++lP
  gi|116753882|ref|YP_843000.1| 245 DAYNMCAGEAAVADLAYAAKHAAVLQMSDMLP 276
                                    *******************************9 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 !  233.2   2.8   9.2e-74   8.2e-70       1     127 []     324     450 ..     324     450 .. 1.00

  Alignments for each domain:
  == domain 1  score: 233.2 bits;  conditional E-value: 9.2e-74
                      MCR_alpha   1 dqiwlGsymsGGvGftqyataaytdnilddfvyygvdyvkdkygglakvkatlevvkdiatevtlyaleqyekyptlled 80 
                                    dqiwlGsymsGGvGftqyataayt+++lddf+yygvdy  +kygg+ak++a+levvkd+atevtlyaleqye++ptlled
  gi|116753882|ref|YP_843000.1| 324 DQIWLGSYMSGGVGFTQYATAAYTNDVLDDFSYYGVDYAVEKYGGFAKAPANLEVVKDLATEVTLYALEQYESFPTLLED 403
                                    9******************************************************************************* PP

                      MCR_alpha  81 hfGGsqraavlaaaagistalatgnsnaGlngwylsmllhkeahsrl 127
                                    hfGGsqra+v+aaa+gi++a+atgns+aGl+gwyls+llhkeah+rl
  gi|116753882|ref|YP_843000.1| 404 HFGGSQRAGVTAAASGITCAIATGNSQAGLAGWYLSQLLHKEAHGRL 450
                                    **********************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (559 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 4009.44
//
Query:       gi|116753883|ref|YP_843001.1|  [L=255]
Description: methyl-coenzyme M reductase, gamma subunit [Methanosaeta thermophila PT]
Scores for complete 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-121  402.1   0.0   8.2e-121  401.9   0.0    1.0  1  MCR_gamma  Methyl-coenzyme M reductase gamma subunit


Domain annotation for each model (and alignments):
>> MCR_gamma  Methyl-coenzyme M reductase gamma subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  401.9   0.0  4.6e-125  8.2e-121       1     246 []       5     253 ..       5     253 .. 0.99

  Alignments for each domain:
  == domain 1  score: 401.9 bits;  conditional E-value: 4.6e-125
                      MCR_gamma   1 aqyyPGeskvaenrrkfmdpeaeleklreisdedvvkilghraPGeeyksvhPPleemdepedpirelvePieGakaGdr 80 
                                    +qyyPG+++v++nrrk+m  + +leklr+i++ dvv+i+ghraPG++y+s+hPPl+em ep++pir+lveP++Ga aGdr
  gi|116753883|ref|YP_843001.1|   5 PQYYPGNTSVGANRRKHM--SGNLEKLRDIPEADVVAIMGHRAPGADYPSTHPPLKEMGEPDCPIRQLVEPTPGAAAGDR 82 
                                    7*****************..899********************************************************* PP

                      MCR_gamma  81 vryiqfadsmyfaPaqPyqrarlellryrgvdtGtlsGrqiievrerdlekiskelletelfdpartgirGatvhGhslr 160
                                    vry qfadsmyfaP+ Py+r++++++++rg+d+GtlsGrqiie+rerd+e ++k+l+++e++d+ar+++rG+tvhGhslr
  gi|116753883|ref|YP_843001.1|  83 VRYSQFADSMYFAPSIPYWRSYWAAINCRGADPGTLSGRQIIEARERDIEAYTKKLMDSEMTDVARCSMRGCTVHGHSLR 162
                                    ******************************************************************************** PP

                      MCR_gamma 161 ldenGlmfdalqrlvldeedgevkyvkdqvgvpldkkvdvGkpldedelkkkttiyrldgval......rddkevvevvk 234
                                    l+enGlmfd+l+r+ l  +dg+v yvkdqvg+pldkk++vGkp++edelkk+tti+r+d+v++      r+ +e++e+++
  gi|116753883|ref|YP_843001.1| 163 LEENGLMFDMLARTELG-ADGNVYYVKDQVGIPLDKKINVGKPMSEDELKKRTTIFRYDNVSFggkvgaRKFDEALEALH 241
                                    ****************8.9*******************************************9999999*********** PP

                      MCR_gamma 235 rihelrtklgfk 246
                                    +++e+rtk+gf+
  gi|116753883|ref|YP_843001.1| 242 HMWEYRTKWGFR 253
                                    **********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1903.32
//
Query:       gi|116753884|ref|YP_843002.1|  [L=170]
Description: methyl-coenzyme M reductase, protein D [Methanosaeta thermophila PT]
Scores for complete 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-56  189.7   0.0    2.4e-56  189.5   0.0    1.0  1  MCR_D     Methyl-coenzyme M reductase operon protein D


Domain annotation for each model (and alignments):
>> MCR_D  Methyl-coenzyme M reductase operon protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.5   0.0   1.3e-60   2.4e-56       1     142 [.      14     154 ..      14     155 .. 0.99

  Alignments for each domain:
  == domain 1  score: 189.5 bits;  conditional E-value: 1.3e-60
                          MCR_D   1 dveifpeRlLkpetteklLnelvelegikrvvihGprLPkkvpygpakGkevehkerkvievkgeeveLkvkvGrillel 80 
                                    +veifp+R+L+pett+klLnel++  gi+r++i+Gp+LP++v+ygp kG ++e++++ ++ev+ge +eL+vkvGri+lel
  gi|116753884|ref|YP_843002.1|  14 QVEIFPSRFLSPETTQKLLNELYKSGGIVRMMIQGPNLPRTVTYGPGKGLPIEEHRNLLVEVGGEVLELRVKVGRIRLEL 93 
                                    89****************************************************************************** PP

                          MCR_D  81 edeeviekieeiceevlpfsyeikegkfirkkktvsDyakyGeeeadkrllGlvDpksklee 142
                                    e ee+++ ie++ce++lpfs++ik+gkf+r+ +t+sDyakyG++ adkr+lGlvDp++k+e+
  gi|116753884|ref|YP_843002.1|  94 EGEEFLPGIEAACERALPFSFQIKRGKFFRDISTISDYAKYGKD-ADKRILGLVDPRAKKES 154
                                    ********************************************.**************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       232  (0.0129399); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 1234.51
//
Query:       gi|116753885|ref|YP_843003.1|  [L=434]
Description: methyl-coenzyme M reductase, beta subunit [Methanosaeta thermophila PT]
Scores for complete 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-136  452.6   7.5   5.6e-136  452.0   7.5    1.3  1  MCR_beta    Methyl-coenzyme M reductase beta subunit, C-termi
    5.5e-79  264.0   0.8    5.5e-79  264.0   0.8    1.7  2  MCR_beta_N  Methyl-coenzyme M reductase beta subunit, N-termi
  ------ inclusion threshold ------
       0.18   12.3   0.1       0.42   11.0   0.1    1.6  1  Rep_fac_C   Replication factor C C-terminal domain


Domain annotation for each model (and alignments):
>> MCR_beta  Methyl-coenzyme M reductase beta subunit, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  452.0   7.5  9.4e-140  5.6e-136       1     248 [.     186     433 ..     186     434 .] 0.99

  Alignments for each domain:
  == domain 1  score: 452.0 bits;  conditional E-value: 9.4e-140
                       MCR_beta   1 GyalrnikanhvvaitkknalnaaalssileqtavfemGdavGaferahllglayqGlnannlvydlvkengkegtvGtv 80 
                                    G+a rn++anh++aitk+na+naa+l++ileq++ femG+a+G fer++ll+la+qGlnann+vydlvk+ngk+gt+Gtv
  gi|116753885|ref|YP_843003.1| 186 GFAYRNVMANHIAAITKRNAMNAASLAAILEQMGEFEMGNAIGIFERHQLLALAFQGLNANNMVYDLVKKNGKTGTIGTV 265
                                    8******************************************************************************* PP

                       MCR_beta  81 veslveraiedkvikvekklpsgyklyetkdvalwnayaaaGllaavivnvgaaraaqavsstllyyndlleketglpGv 160
                                    v+s+vera+edkvik  kk+psgy +ye++dv++wnay aaG+laa++vn+ga r aqavsstllyyndl+eket+lpG+
  gi|116753885|ref|YP_843003.1| 266 VHSVVERALEDKVIKPGKKFPSGYVMYEANDVSMWNAYNAAGVLAATMVNCGALRGAQAVSSTLLYYNDLVEKETALPGC 345
                                    ******************************************************************************** PP

                       MCR_beta 161 dfGrveGtavGfsffshsiyGGGGpGifnGnhvvtrhskGfaipcvaaavaldaGtqlfspeatsglvgevfgeidefre 240
                                    dfGrv+GtavGfsffshsiyGGGGpG+fnGnh+vtrhs+G+aipcvaaavaldaGtq+f+pe+tsglvg ++gei+efre
  gi|116753885|ref|YP_843003.1| 346 DFGRVMGTAVGFSFFSHSIYGGGGPGVFNGNHIVTRHSRGMAIPCVAAAVALDAGTQMFTPEMTSGLVGAIYGEIKEFRE 425
                                    ******************************************************************************** PP

                       MCR_beta 241 plkavaea 248
                                    p+  vaea
  gi|116753885|ref|YP_843003.1| 426 PIVSVAEA 433
                                    *****986 PP

>> MCR_beta_N  Methyl-coenzyme M reductase beta subunit, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  264.0   0.8   9.1e-83   5.5e-79       1     182 []       3     184 ..       3     184 .. 1.00
   2 ?   -3.9   0.1       1.6   9.3e+03      51      74 ..     256     279 ..     252     282 .. 0.75

  Alignments for each domain:
  == domain 1  score: 264.0 bits;  conditional E-value: 9.1e-83
                     MCR_beta_N   1 DkidlyddkGkllesdvpleaisPlknpaikkivkdvkrtvavnlagiekalktgkvggkaskilGreldldivenadai 80 
                                    Dkid+y+d+G ll+sdv+l+aisPl+n+ai+k+ k+++rtvavnlagie+alktg+vgg  ++i+Grel++div+na a+
  gi|116753885|ref|YP_843003.1|   3 DKIDIYSDRGVLLKSDVDLSAISPLRNAAIQKLAKLTRRTVAVNLAGIENALKTGRVGGGRRQIKGRELNYDIVANASAL 82 
                                    9******************************************************************************* PP

                     MCR_beta_N  81 aekikelvqveedddtkvkllngGkqllvqvPskRleaaaeysvallataaavveaiidefdvdmfdasvvkaavlGryP 160
                                    aekik l+qv+ +ddt+v++l+gGkqllvq+Ps+R e+a+e+ v+++a+aaa+veaii++f+ + fda++++aav+G+yP
  gi|116753885|ref|YP_843003.1|  83 AEKIKALLQVTPGDDTNVQVLGGGKQLLVQIPSARAEIASEFVVGMTAAAAATVEAIIQHFKAGLFDAPMIHAAVWGEYP 162
                                    ******************************************************************************** PP

                     MCR_beta_N 161 qtvdlaggnvasilsipqkneG 182
                                    qtv ++ggnvas+l+ipq++eG
  gi|116753885|ref|YP_843003.1| 163 QTVGMNGGNVASVLNIPQNDEG 184
                                    *********************9 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 1.6
                     MCR_beta_N  51 alktgkvggkaskilGreldldiv 74 
                                      ktg++g+  +++  r l+ +++
  gi|116753885|ref|YP_843003.1| 256 NGKTGTIGTVVHSVVERALEDKVI 279
                                    557888888888888888887776 PP

>> 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 ?   11.0   0.1   7.1e-05      0.42      43      87 ..     197     240 ..     183     241 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7.1e-05
                                    HHHHGCCS..S-HHHHHHHHHHHHHHHHHHHCTH-HHHHHHHHHH CS
                      Rep_fac_C  43 lhrvvkeqeelpeaqkleilellgeiekrlveGasehlqlsalla 87 
                                    +  + k+ + +++a  + ile++ge+e+  + G  e+ ql+al +
  gi|116753885|ref|YP_843003.1| 197 IAAITKR-NAMNAASLAAILEQMGEFEMGNAIGIFERHQLLALAF 240
                                    4445555.569999999**************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 3226.27
//
Query:       gi|116753886|ref|YP_843004.1|  [L=363]
Description: radical SAM domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.1e-15   56.5   0.1    7.5e-15   55.7   0.1    1.5  1  Radical_SAM  Radical SAM superfamily
    0.00072   19.7   0.1     0.0013   18.8   0.1    1.4  1  Fer4_14      4Fe-4S single cluster domain
    0.00088   19.7   0.0      0.002   18.6   0.0    1.6  1  SPASM        Iron-sulfur cluster-binding domain
     0.0026   18.0   0.1     0.0055   17.0   0.1    1.5  1  Fer4_12      4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.041   14.1   0.2      0.086   13.1   0.2    1.5  1  TRP_2        Transient receptor ion channel II
       0.16   11.9   0.0        0.3   11.1   0.0    1.4  1  Rho_N        Rho termination factor, N-terminal domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   0.1   2.5e-18   7.5e-15       1     151 [.      91     229 ..      91     254 .. 0.90

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 2.5e-18
                                    EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiri 80 
                                    ++vtr C   C +C+  e       + +ls + i + ++++  ++g+  ++++ g+pll+pd++el++   k+   +  +
  gi|116753886|ref|YP_843004.1|  91 IEVTRRCGCSCEHCTLQE------AEDELSSDAIRNVIDQA-LDMGACIITFTEGDPLLRPDIIELVKYVDKE---KAVV 160
                                    689**************7......79999999999999999.8999*********************999998...9*** PP

                                    EEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  81 tvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivg 151
                                     + t+g+  ++e++++l+e+g+  + +g+ +ad++ +++ ++   + +e+ ++a+++  +ag+ +  ++ + 
  gi|116753886|ref|YP_843004.1| 161 NLFTPGLEMTPEIADALREAGLYNLIIGIYSADPR-IHDQIRgVVGAYERAVNAIRMGLKAGLLV--TMSTH 229
                                    ***********************************.999999999****************9994..44444 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   4.5e-07    0.0013       5      90 ..      94     167 ..      92     179 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 4.5e-07
                        Fer4_14   5 lsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekkiw 84 
                                    + +C +sC  C  +e     ++ + +++ + +++  +++ ++ +  +++t G+PL+    +++++lvk++ +e+    + 
  gi|116753886|ref|YP_843004.1|  94 TRRCGCSCEHCTLQE-----AEDELSSDAIRNVI--DQALDMGACIITFTEGDPLLR---PDIIELVKYVDKEK--AVVN 161
                                    569********9999.....44444555555666..44446666779********55...9***********99..7777 PP

                        Fer4_14  85 letngt 90 
                                    l t g+
  gi|116753886|ref|YP_843004.1| 162 LFTPGL 167
                                    777665 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   6.6e-07     0.002       1      48 [.     304     345 ..     304     359 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 6.6e-07
                          SPASM   1 CfapsrslfInsdGdVvpCcvdkktyveelklGnireesleeIwnsee 48 
                                    C+a++r l + +dG +  C +         + Gn+ +++l eIw+  +
  gi|116753886|ref|YP_843004.1| 304 CMAGRRWLHVGVDGGIRGCPYL------SRVYGNVLDTPLPEIWRAMR 345
                                    99*****************333......3899************7663 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   1.8e-06    0.0055      13      84 ..      95     158 ..      87     173 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.8e-06
                        Fer4_12  13 sgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekp 84 
                                     +C  sC+ C  +     ++++e ++++++++i+++ +     +t++ G+Pll   +++++elvk+v +ek 
  gi|116753886|ref|YP_843004.1|  95 RRCGCSCEHCTLQ-----EAEDELSSDAIRNVIDQALDMGACIITFTEGDPLL---RPDIIELVKYVDKEKA 158
                                    5788899998844.....4567778888899999999999*************...***********99986 PP

>> TRP_2  Transient receptor ion channel II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   2.9e-05     0.086       1      44 [.      99     143 ..      99     151 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.9e-05
                          TRP_2   1 CsCeeCkeereeDsLrlsksrlntYralaspayi.sltseDPilt 44 
                                    CsCe+C+ ++ eD+L+    r  + +al   a i + t+ DP+l+
  gi|116753886|ref|YP_843004.1|  99 CSCEHCTLQEAEDELSSDAIRNVIDQALDMGACIiTFTEGDPLLR 143
                                    ****************************88776515689999985 PP

>> Rho_N  Rho termination factor, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   9.9e-05       0.3       6      21 ..     237     252 ..     236     255 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.9e-05
                                    -HHHHHHHHHHTT-TT CS
                          Rho_N   6 tlseLraiAkelgien 21 
                                    tl+eL+++A+elg+  
  gi|116753886|ref|YP_843004.1| 237 TLPELYELARELGVHE 252
                                    89***********954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         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: 00:00:00.41
# Mc/sec: 2625.85
//
Query:       gi|116753887|ref|YP_843005.1|  [L=269]
Description: peptidylprolyl isomerase, FKBP-type [Methanosaeta thermophila PT]
Scores for complete 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-09   36.1   0.0    3.3e-08   33.7   0.0    2.1  2  FKBP_C    FKBP-type peptidyl-prolyl cis-trans isomerase
    8.4e-05   22.6   0.0    0.00018   21.5   0.0    1.6  1  FKBP26_C  FKBP26_C-terminal


Domain annotation for each model (and alignments):
>> FKBP_C  FKBP-type peptidyl-prolyl cis-trans isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.0   3.7e-12   3.3e-08       6      78 ..       4      88 ..       1     145 [. 0.89
   2 ?    0.2   0.0      0.11   9.6e+02      56      72 ..     171     187 ..     115     233 .. 0.73

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 3.7e-12
                                   -TTCEEEEEEEEEETTSSEEEEH..........CC...HTSEEEEETTSSSSCHHHHHHHTTSBTT-EEEEEEEGGGTTTTT CS
                         FKBP_C  6 kegdtVtvhykgkledgkvfdss..........rs...rakplefkvGsgqvikGfeealegmkvGekrtltippelaYgek 74
                                   ++gd+++++y+g + dg+vf s+          ++    + p  + +G+gq+++G+ee l g + G+   ++ ppe aYg +
  gi|116753887|ref|YP_843005.1|  4 NKGDIIKLEYTGIV-DGSVFTSTsadvakengiYDenvTYGPRIVILGAGQIVPGLEEELIGKEPGQSGSVELPPEKAYGVR 84
                                   79************.*******9999999999855667999***************************************98 PP

                                   TBCT CS
                         FKBP_C 75 glag 78
                                   + ++
  gi|116753887|ref|YP_843005.1| 85 DPEK 88
                                   7744 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.11
                                    BTT-EEEEEEEGGGTTT CS
                         FKBP_C  56 kvGekrtltippelaYg 72 
                                      ++ +++t+p e  Y 
  gi|116753887|ref|YP_843005.1| 171 ITDDVAEITVPWEISYF 187
                                    45667788888888885 PP

>> FKBP26_C  FKBP26_C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0     2e-08   0.00018       2      70 ..     152     215 ..     151     217 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2e-08
                                    HHHHHHHHHHH-TT--..--EEEEETTEEEEE--TTGGGSTTHHHHHHHHHHHHHHH-TTEEEEEEEEE CS
                       FKBP26_C   2 kekikelIkryiPnidlekfkieiedktvtIelpeeakFieniqlaklrIAkdilkrieevekVkFvde 70 
                                    +ek++++Ik     i+   ++  i+d +++I++p e ++ ++  ++++ +A+ +l+ + + ++V Fv+ 
  gi|116753887|ref|YP_843005.1| 152 EEKLRAMIKI-FSDIE---LESRITDDVAEITVPWEISYFKDWLMIRRWLADMALRTL-GLKEVRFVER 215
                                    8999999999.56777...7889********************************999.********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); 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: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 2056.48
//
Query:       gi|116753888|ref|YP_843006.1|  [L=326]
Description: PP-loop domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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      3e-13   49.9   0.0    1.3  1  ATP_bind_3     PP-loop family
    1.9e-09   36.8   0.0    2.5e-09   36.4   0.0    1.1  1  tRNA_Me_trans  tRNA methyl transferase
    4.1e-05   23.7   0.0    6.4e-05   23.1   0.0    1.2  1  PAPS_reduct    Phosphoadenosine phosphosulfate reductase fami
    5.4e-05   22.6   0.7    5.4e-05   22.6   0.7    3.0  3  zn-ribbon_14   Zinc-ribbon
     0.0004   20.2   0.0    0.00058   19.6   0.0    1.2  1  Asn_synthase   Asparagine synthase
    0.00054   19.2   0.0    0.00077   18.6   0.0    1.1  1  NAD_synthase   NAD synthase
     0.0031   17.1   0.0     0.0049   16.5   0.0    1.2  1  ThiI           Thiamine biosynthesis protein (ThiI)
  ------ inclusion threshold ------
       0.05   13.1   0.2       0.13   11.8   0.0    1.8  2  QueC           Queuosine biosynthesis protein QueC
        1.8    8.4   8.5         36    4.2   0.1    3.6  3  zinc_ribbon_2  zinc-ribbon domain
        2.3    7.9   8.4        0.7    9.5   1.3    3.0  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 !   49.9   0.0   1.7e-16     3e-13       2     156 ..      51     216 ..      50     224 .. 0.79

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 1.7e-16
                                    EEEE--SCHHHHHHHHHHHHHCTT.TTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H......HHCTTS CS
                     ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkk.lgiklvaihvdhglreeskeeaelvkelckklnikleiekvdv......akkkgk 74 
                                    v+vA+SgG DS +Ll+ l++  ++   i+l+a++vd g++   ++  +  ++l+++l++++++ +++       ++  ++
  gi|116753888|ref|YP_843006.1|  51 VAVALSGGKDSSVLLYTLKRIFSHrRDIELIALMVDEGISGYREDTLQNAAALADRLDVPHITLSFREefgitiDEIAER 130
                                    78*****************986651567**************************************99999999444444 PP

                                    TCCCH....HHHHHHHHHHHCHHCCT.CEEE---BHHHHHHHHHHHHCCT--CCHHH-S-SEEEETT.CCEE-CCCT--H CS
                     ATP_bind_3  75 nleea....ARelRYevlkealkkegievlllAhhadDqaEtfllrlargsglaglagikeaseias.irlvRPlLkvsk 149
                                     l++a       +R ++l++ +++ ++  l+++h+ dD a t+ll+  rg   + +  ++++   ++ +  + Pl  +  
  gi|116753888|ref|YP_843006.1| 131 DLHQApctyCGVMRKHLLNKRARELNAIALATGHNLDDEAQTILLNYLRGDVDRLFRLLPKRP-KEGlVYRIKPLRRIPE 209
                                    4444411116679************************************98765555444444.3332555667777766 PP

                                    HHHHHHH CS
                     ATP_bind_3 150 eeleeyl 156
                                     e+  y+
  gi|116753888|ref|YP_843006.1| 210 REVAIYA 216
                                    6666665 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.0   1.4e-12   2.5e-09       2     125 ..      50     165 ..      49     183 .. 0.83

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 1.4e-12
                  tRNA_Me_trans   2 kvvvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfekeykekvfee 81 
                                    +v+valSgG DSsv ++ lk+ + + + + l      de   +   e+ l++a + a++l++p+ +++f++e+  ++ e 
  gi|116753888|ref|YP_843006.1|  50 RVAVALSGGKDSSVLLYTLKRIFSHRRDIELIALMV-DEGI-SGYREDTLQNAAALADRLDVPHITLSFREEFGITIDEI 127
                                    79*********************9999998877766.3333.5688899************************9998777 PP

                  tRNA_Me_trans  82 fleeyeeGrTPnPdvlCNkeiKfgallekakeelgadalatGHY 125
                                      +++++     P+  C    K ++l ++a  el+a alatGH 
  gi|116753888|ref|YP_843006.1| 128 AERDLHQ----APCTYCGVMRK-HLLNKRAR-ELNAIALATGHN 165
                                    7667665....7*****86544.44555555.5**********5 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   3.6e-08   6.4e-05       2     153 ..      51     221 ..      50     224 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 3.6e-08
                                    EEEE--SSCTCHHHHHHHHHHCTTH.....EEEEEE-STB..-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S CS
                    PAPS_reduct   2 lvvsvsgGkdslVllhLalkafkpv.....pvvfvdtghe..fpetiefvdeleeryglrlkvyepeeevaekinaekhg 74 
                                    ++v+ sgGkds+Vll  + ++f  +       + vd g     ++t++   +l++r+++  ++ + +ee+   i +    
  gi|116753888|ref|YP_843006.1|  51 VAVALSGGKDSSVLLYTLKRIFSHRrdielIALMVDEGISgyREDTLQNAAALADRLDVPHITLSFREEFGITIDEIA-E 129
                                    6899************99999999778887799999998643688************999666666666666665555.3 PP

                                    -THHHC..HHHHHHTHHHHHHHHHCTTECEEE----CCCTTTTTTSSSEEECTTT-S.............CEEE-CCCT- CS
                    PAPS_reduct  75 sslyee..aaeriaKveplkkaLekldedalltGaRrdesksraklpiveidedfek.............slrvfPllnW 139
                                     +l++    ++ +++ + l+k  ++l++ al tG   d++++   l++++ d d  +             ++r+ Pl   
  gi|116753888|ref|YP_843006.1| 130 RDLHQApcTYCGVMRKHLLNKRARELNAIALATGHNLDDEAQTILLNYLRGDVD--RlfrllpkrpkeglVYRIKPLRRI 207
                                    578888999**************************************9998888..44588999999*9999******** PP

                                    -HHHHHHHHHHCT- CS
                    PAPS_reduct 140 teedvwqyilreni 153
                                     e++v  y+  ++i
  gi|116753888|ref|YP_843006.1| 208 PEREVAIYAMIHGI 221
                                    ****9999998887 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   0.3     0.085   1.5e+02       3      10 ..       4      11 ..       3      12 .. 0.85
   2 ?   -0.6   0.5      0.52   9.4e+02       3       9 ..     137     143 ..     136     145 .. 0.91
   3 !   22.6   0.7     3e-08   5.4e-05       2      23 ..     278     299 ..     277     303 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.085
                   zn-ribbon_14  3 CerCGylS 10
                                   C+rCG  S
  gi|116753888|ref|YP_843006.1|  4 CSRCGRPS 11
                                   *****766 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.52
                   zn-ribbon_14   3 CerCGyl 9  
                                    C+ CG +
  gi|116753888|ref|YP_843006.1| 137 CTYCGVM 143
                                    *****98 PP

  == domain 3  score: 22.6 bits;  conditional E-value: 3e-08
                   zn-ribbon_14   2 kCerCGylSSqkiCkACvLLeg 23 
                                    +CerCG  +  ++Ck C LLeg
  gi|116753888|ref|YP_843006.1| 278 RCERCGEPAGGSVCKTCQLLEG 299
                                    8********************9 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   3.2e-07   0.00058      19      88 ..      50     124 ..      43     162 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.2e-07
                   Asn_synthase  19 pvGalLSGGlDSSliaalaarqsk..splktFsigfee....kgsdeakyakevaehlgtehtelvlteeelldal 88 
                                    +v++ LSGG DSS++ ++++r     +++   ++  +e     + d ++ a+++a++l ++h++l + ee ++  +
  gi|116753888|ref|YP_843006.1|  50 RVAVALSGGKDSSVLLYTLKRIFShrRDIELIALMVDEgisgYREDTLQNAAALADRLDVPHITLSFREEFGIT-I 124
                                    6999*****************877668888888888666755778889****************9999986665.4 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   4.3e-07   0.00077      18     130 ..      48     165 ..      30     172 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 4.3e-07
                                    TSEEEEEE-SSHHHHHHHHHHHHHH...TCGEEEEEE--SSST..THHHHHHHHHHHHHHTSEEEE---HHHHHHHHHHH CS
                   NAD_synthase  18 akgvvlGlSGGvDSslvaalavkal...gkenvlalllPssvs..seedvedalalaenlgievktidikpivrafeqel 92 
                                       v + lSGG DSs+  +  ++++    + + +al++ +  s   e+ +++a ala++l++   t++ ++   +  +e+
  gi|116753888|ref|YP_843006.1|  48 GGRVAVALSGGKDSSVLLYTLKRIFshrRDIELIALMVDEGISgyREDTLQNAAALADRLDVPHITLSFREEFGITIDEI 127
                                    4578899******************4444445778888844432267889****************************** PP

                                    HHHH-HHHHHHHHHHHHHHHHHHHHHHHTEEEB---BH CS
                   NAD_synthase  93 keakedlakgNlkaRiRmailyaianklnllvlgTgnk 130
                                     e   + a    +  +R  +l + a +ln + l+Tg++
  gi|116753888|ref|YP_843006.1| 128 AERDLHQAPCTYCGVMRKHLLNKRARELNAIALATGHN 165
                                    999999999999***********************996 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   2.7e-06    0.0049       4     123 ..      49     171 ..      46     179 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.7e-06
                           ThiI   4 gkvlaLlSgGiDSpVaayll...lkRGcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlkeil 80 
                                    g+v + lSgG DS V  y l   ++    ++l+ l  + g s   ++ ++++a+l  + +  + +  +  +f  +++ei 
  gi|116753888|ref|YP_843006.1|  49 GRVAVALSGGKDSSVLLYTLkriFSHRRDIELIALMVDEGISGYREDTLQNAAALADRLDVPHITLSFREEFGITIDEIA 128
                                    788889*********99964111344456888888889999999**************9975554445678********* PP

                           ThiI  81 ekvkekltivllkrkmlriAekvaeeegakalvtGesLgqVaS 123
                                    e+  ++  +  +  +  ++ +k a+e +a al tG +L   a 
  gi|116753888|ref|YP_843006.1| 129 ERDLHQAPCTYCGVMRKHLLNKRARELNAIALATGHNLDDEAQ 171
                                    **************************************87664 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0     7e-05      0.13       3      61 ..      52     116 ..      50     172 .. 0.81
   2 ?   -1.9   0.1       1.1     2e+03     166     197 ..     265     295 ..     263     301 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7e-05
                                    EEE--SSHHHHHHHHHHHHH-.....SEEEEEEEESS-T..TSHHHHHHHHHHHHT--.-EEEEE- CS
                           QueC   3 vvllSGGlDSttvlalakkeg.....kevealtfdYgqr..hkkeleaakkiakelgveehkildl 61 
                                     v lSGG DS+++l++ k+ +      e++al +d g    ++ +l+ a+++a++l+v  h +l+ 
  gi|116753888|ref|YP_843006.1|  52 AVALSGGKDSSVLLYTLKRIFshrrdIELIALMVDEGISgyREDTLQNAAALADRLDV-PHITLSF 116
                                    5789***********9998774333346778888888775567778999999999999.7766654 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.1
                                    HHHHHHHTTHHHHH-B-STTS.-BTTTTSSSH CS
                           QueC 166 ivklgkelgvpleetlsCYegeeegkaCgeCd 197
                                    i +l+ ++ v+l+    C e+ + g+ C++C+
  gi|116753888|ref|YP_843006.1| 265 IRELAPDIHVDLHRCERCGEP-AGGSVCKTCQ 295
                                    566777888888888888888.5666666664 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.3     0.028        50      16      22 ..       4      10 ..       2      11 .. 0.64
   2 ?    4.2   0.1      0.02        36      13      20 ..     134     141 ..     128     142 .. 0.82
   3 ?    3.2   0.6     0.044        79      16      22 ..     279     285 ..     278     286 .. 0.63

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.028
                  zinc_ribbon_2 16 CpyCGtp 22
                                   C++CG p
  gi|116753888|ref|YP_843006.1|  4 CSRCGRP 10
                                   6777654 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.02
                  zinc_ribbon_2  13 akFCpyCG 20 
                                    +  C+yCG
  gi|116753888|ref|YP_843006.1| 134 QAPCTYCG 141
                                    568****9 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.044
                  zinc_ribbon_2  16 CpyCGtp 22 
                                    C++CG+p
  gi|116753888|ref|YP_843006.1| 279 CERCGEP 285
                                    6666665 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1      0.15   2.7e+02      18      23 ..       3       8 ..       1      12 [. 0.82
   2 ?   -1.2   0.1      0.86   1.5e+03      30      34 ..     136     140 ..     126     144 .. 0.64
   3 ?    9.5   1.3   0.00039       0.7      15      35 ..     275     295 ..     271     296 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.15
                                   E-TTT- CS
                           RecR 18 hCsrCg 23
                                   +CsrCg
  gi|116753888|ref|YP_843006.1|  3 PCSRCG 8 
                                   8****8 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.86
                                    S-CCC CS
                           RecR  30 lCaIC 34 
                                    +C+ C
  gi|116753888|ref|YP_843006.1| 136 PCTYC 140
                                    67777 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00039
                                    H-EE-TTT--EESSSS-CCCC CS
                           RecR  15 kvrhCsrCgnlteedlCaICs 35 
                                    ++++C+rCg  +   +C  C+
  gi|116753888|ref|YP_843006.1| 275 DLHRCERCGEPAGGSVCKTCQ 295
                                    579*****************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2303.63
//
Query:       gi|116753889|ref|YP_843007.1|  [L=125]
Description: hypothetical protein Mthe_0576 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.1   12.6   0.3        2.9    7.9   0.0    2.2  2  Cbl_N     CBL proto-oncogene N-terminal domain 1


Domain annotation for each model (and alignments):
>> Cbl_N  CBL proto-oncogene N-terminal domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0   0.00016       2.9      23      42 ..      71      90 ..      66     100 .. 0.81
   2 ?    3.0   0.1    0.0054        97      25      49 ..      98     124 ..      94     125 .] 0.78

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00016
                                   SSS---SSSS-HHHHHHHHH CS
                          Cbl_N 23 prlnLknspPylldllpdta 42
                                     +n+  spPy+ dl+ +t 
  gi|116753889|ref|YP_843007.1| 71 TSINMIYSPPYISDLVNNTL 90
                                   5678999*********9985 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.0054
                                    S---SSSS-H..HHHHHHHHHHHHHHH CS
                          Cbl_N  25 lnLknspPyl..ldllpdtaqlLreva 49 
                                    +n++ spPy+  +  +p+ta ++r+v+
  gi|116753889|ref|YP_843007.1|  98 MNVSISPPYIslNMSVPRTAYKIRHVI 124
                                    78899***9722456899999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 984.81
//
Query:       gi|116753890|ref|YP_843008.1|  [L=395]
Description: cobalt ABC transporter, ATPase subunit [Methanosaeta thermophila PT]
Scores for complete 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-33  116.2   0.0    4.5e-33  114.7   0.0    1.7  2  ABC_tran      ABC transporter
    1.8e-16   60.8   0.5    8.8e-11   42.2   0.0    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    6.1e-07   29.1   0.0    3.7e-06   26.5   0.0    2.0  1  SMC_N         RecF/RecN/SMC N terminal domain
     0.0018   18.1   0.0      0.032   14.0   0.0    2.0  2  AAA_15        AAA ATPase domain
      0.002   17.8   1.8      0.002   17.8   0.2    1.8  2  AAA_29        P-loop containing region of AAA domain
     0.0097   16.4   0.0      0.015   15.8   0.0    1.3  1  AAA_23        AAA domain
  ------ inclusion threshold ------
      0.017   15.0   0.1       0.04   13.8   0.0    1.6  2  RsgA_GTPase   RsgA GTPase
      0.017   15.4   0.0        0.1   12.8   0.0    2.2  1  AAA_22        AAA domain
      0.033   14.4   0.0       0.36   11.1   0.0    2.2  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
      0.037   13.8   0.2        5.6    6.7   0.0    2.5  3  IstB_IS21     IstB-like ATP binding protein
      0.038   14.4   0.0      0.067   13.6   0.0    1.5  1  AAA_16        AAA ATPase domain
      0.038   14.1   0.0        2.2    8.4   0.1    2.5  3  AAA_33        AAA domain
      0.058   12.7   0.0       0.18   11.1   0.0    1.8  2  Zeta_toxin    Zeta toxin
       0.07   12.9   0.4       0.27   10.9   0.1    1.9  2  AAA_24        AAA domain
      0.096   12.3   0.0       0.24   10.9   0.0    1.6  1  AAA_25        AAA domain
       0.23   11.4   1.2       0.32   11.0   0.1    1.9  2  BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette 
       0.25   11.4   0.7       0.79    9.8   0.2    2.0  2  MMR_HSR1      50S ribosome-binding GTPase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.7   0.0   4.2e-36   4.5e-33       1     137 []      21     169 ..      21     169 .. 0.94
   2 ?   -2.1   0.0       4.8     5e+03      22      39 ..     347     364 ..     346     380 .. 0.75

  Alignments for each domain:
  == domain 1  score: 114.7 bits;  conditional E-value: 4.2e-36
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG..B-HHHCCHCEEEE-SS..--S-TTSBH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx..xxxxxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke..qeleslrkeigvlpqe..pqlfpeltv 76 
                                    l+nv+l+++ g+kva+vG+nGaGKStLl +l g l+p +G++l++g+++++  ++l+  rk++gv++q+  +qlf  + v
  gi|116753890|ref|YP_843008.1|  21 LRNVTLSIESGSKVALVGPNGAGKSTLLLMLNGTLRPSSGTVLFKGEPMRYdsRSLRDIRKSVGVVFQNsdDQLFAPT-V 99 
                                    78*************************************************99999*************988888888.7 PP

                                    HHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    xxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  77 ren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                    ++              + ++ +  als +gl+e ++++     ++LSgG+k+rva+a +l+ +p++l+lDEpt+
  gi|116753890|ref|YP_843008.1| 100 EQDiafgplnlgypreKIERYVGYALSYVGLDEHRNRPP----HHLSGGEKKRVAIAGILVMEPEVLVLDEPTS 169
                                    7779********998777777999*********999998....*****************************96 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.8
                                    SSHHHHHHHHTTSS--SE CS
                                    xxxxxxxxxxxxxxxxxx RF
                       ABC_tran  22 aGKStLlkllagllkpte 39 
                                    aGKS+L+ +  g+++ +e
  gi|116753890|ref|YP_843008.1| 347 AGKSSLIITSGGMVEHAE 364
                                    799999977666666555 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 !   16.5   0.2   5.4e-06    0.0057       3      21 ..      35      53 ..      34     100 .. 0.74
   2 !   42.2   0.0   8.3e-14   8.8e-11     230     301 ..     134     202 ..     113     203 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.4e-06
                         AAA_21  3 vliGpNgsGKSnLLdaldl 21
                                   +l+GpNg+GKS+LL  l +
  gi|116753890|ref|YP_843008.1| 35 ALVGPNGAGKSTLLLMLNG 53
                                   79************98854 PP

  == domain 2  score: 42.2 bits;  conditional E-value: 8.3e-14
                         AAA_21 230 qelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpll 301
                                    +++p+++lS G k+  a++ +l   +    +l++DEp ++L+P+  ++++e+l+el+  g  v+++TH+ +l
  gi|116753890|ref|YP_843008.1| 134 RNRPPHHLSGGEKKRVAIAGILVMEP---EVLVLDEPTSNLDPATSEEIMEMLDELNLYGKTVVISTHDVEL 202
                                    689*********************99...9**************************************9776 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   3.5e-09   3.7e-06      26     199 ..      33     199 ..      20     213 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 3.5e-09
                                    EEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--.....BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  26 ftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk.....skekasvkkaeveitfdnedkklkiekeevsis 100
                                      a+vGpNG+GKs ll  +  +        lr ++ + l +       +++ +  + +v ++f+n+d++l   + e  i 
  gi|116753890|ref|YP_843008.1|  33 KVALVGPNGAGKSTLLLMLNGT--------LRPSSGTVLFKGepmryDSRSLRDIRKSVGVVFQNSDDQLFAPTVEQDIA 104
                                    4689**********99877544........5555555555445543335555666779********************** PP

                                    EEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 101 rrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkva 180
                                        + g  + ki++       +  l e+ +  ++ LSgGek+ va+a ++    ++p+   +lDe  ++LD +  +++ 
  gi|116753890|ref|YP_843008.1| 105 FGPLNLGYPREKIERYVGYALSYVGLDEHRNRPPHHLSGGEKKRVAIAGIL---VMEPEV-LVLDEPTSNLDPATSEEIM 180
                                    ***********************************************9885...456765.589**************** PP

                                    HHHHHHCTTSEEEEE-SSH CS
                                    xxxxxxxxxxxxxxxxxxx RF
                          SMC_N 181 ellkeksknaQfivislre 199
                                    e+l+e +     +vis ++
  gi|116753890|ref|YP_843008.1| 181 EMLDELNLYGKTVVISTHD 199
                                    *****99998888887654 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0     3e-05     0.032      14      44 ..      21      52 ..      20     103 .. 0.77
   2 ?    2.0   0.0      0.13   1.4e+02     325     365 ..     160     199 ..     157     203 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3e-05
                         AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsileald 44
                                   l++v++++++     l+G+N++GKS++l +l+
  gi|116753890|ref|YP_843008.1| 21 LRNVTLSIESGsKVALVGPNGAGKSTLLLMLN 52
                                   67777777777799**************9996 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.13
                         AAA_15 325 villiEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                     +l+++EP  +L p   +++++ l el   +k  v+i+TH 
  gi|116753890|ref|YP_843008.1| 160 EVLVLDEPTSNLDPATSEEIMEMLDELNLYGK-TVVISTHD 199
                                    6899***************************9.9******7 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 !   17.8   0.2   1.9e-06     0.002      15      39 ..      24      48 ..      19      62 .. 0.82
   2 ?   -2.7   0.1       4.9   5.1e+03      33      39 ..     347     353 ..     346     353 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.9e-06
                         AAA_29 15 htieidlkgatlltGpsGsGKSTll 39
                                    t++i+  + + l+Gp+G+GKSTll
  gi|116753890|ref|YP_843008.1| 24 VTLSIESGSKVALVGPNGAGKSTLL 48
                                   6777875559**************8 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.9
                         AAA_29  33 sGKSTll 39 
                                    +GKS+l+
  gi|116753890|ref|YP_843008.1| 347 AGKSSLI 353
                                    7****97 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.5e-05     0.015      22      37 ..      34      49 ..      16     121 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.5e-05
                         AAA_23 22 tlItGpNGaGKTTild 37
                                   ++++GpNGaGK+T+l 
  gi|116753890|ref|YP_843008.1| 34 VALVGPNGAGKSTLLL 49
                                   589**********994 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.8e-05      0.04      88     124 ..      19      56 ..       6      70 .. 0.77
   2 ?   -3.5   0.0       8.2   8.6e+03     110     117 ..     347     354 ..     347     369 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.8e-05
                                    TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-- CS
                    RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLinallpele 124
                                    ++l++++  +++ + ++lvG+ G+GKStL+ +l+++l+
  gi|116753890|ref|YP_843008.1|  19 AALRNVTLSIESgSKVALVGPNGAGKSTLLLMLNGTLR 56 
                                    55556666666658899*************99998765 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 8.2
                                    SSHHHHHH CS
                    RsgA_GTPase 110 vGKStLin 117
                                    +GKS+Li 
  gi|116753890|ref|YP_843008.1| 347 AGKSSLII 354
                                    59999985 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   9.9e-05       0.1       8      71 ..      34     134 ..      28     210 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.9e-05
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst....sskdllrellralglelka............. 70 
                                    ++++G+ G+GK+tll +l  +l        +++++v+++         s++d+++ +   ++++ +              
  gi|116753890|ref|YP_843008.1|  34 VALVGPNGAGKSTLLLMLNGTLR-------PSSGTVLFKGEPMRydsrSLRDIRKSVGVVFQNSDDQlfaptveqdiafg 106
                                    689***************99994.......35555533333333324444455444444444433334446666666666 PP

                         AAA_22  71 ...........................e 71 
                                                               +
  gi|116753890|ref|YP_843008.1| 107 plnlgyprekieryvgyalsyvgldehR 134
                                    6666665555555555555554444432 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00035      0.36      63      89 ..     158     184 ..     114     185 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00035
                        SbcCD_C  63 alrlvfLDEAFsklDeesiatllelle 89 
                                     +++++LDE  s+lD+ ++++++e+l+
  gi|116753890|ref|YP_843008.1| 158 EPEVLVLDEPTSNLDPATSEEIMEMLD 184
                                    3789********************986 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0053       5.6      44      65 ..      28      49 ..      19      65 .. 0.84
   2 ?    4.4   0.0     0.026        27     107     152 ..     157     203 ..     142     213 .. 0.80
   3 ?   -3.2   0.0       5.6   5.9e+03     133     152 ..     342     361 ..     341     367 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0053
                      IstB_IS21 44 iekkenivllGpsGvGKshlai 65
                                   ie+   ++l+Gp G+GKs l  
  gi|116753890|ref|YP_843008.1| 28 IESGSKVALVGPNGAGKSTLLL 49
                                   6778899***********9865 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.026
                      IstB_IS21 107 lkvdllilDdlgllpldqaeaellfeviek..ryerrsiiitsnlpfa 152
                                    +++++l+lD+  + +ld a +e+++e++++   y+++ +i t ++++a
  gi|116753890|ref|YP_843008.1| 157 MEPEVLVLDEP-TSNLDPATSEEIMEMLDElnLYGKTVVISTHDVELA 203
                                    5679*****96.689*************97336999988888777665 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 5.6
                      IstB_IS21 133 viekryerrsiiitsnlpfa 152
                                    v+++  +++s+iits   ++
  gi|116753890|ref|YP_843008.1| 342 VLKAIAGKSSLIITSGGMVE 361
                                    56677789999999976655 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   6.3e-05     0.067      19      63 ..      28      71 ..      18     195 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.3e-05
                         AAA_16 19 vrsgrpelvllsGesGvGKsslvrellralekdggif.lrgkcdql 63
                                   + sg  + v l+G+ G GKs+l+ +l   l+ + g + ++g+  ++
  gi|116753890|ref|YP_843008.1| 28 IESG--SKVALVGPNGAGKSTLLLMLNGTLRPSSGTVlFKGEPMRY 71
                                   3344..6699*************99999999985444366665555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1    0.0021       2.2       2      16 ..      34      48 ..      34      64 .. 0.87
   2 ?   -2.6   0.0       5.4   5.7e+03      75     112 ..     164     203 ..     152     207 .. 0.72
   3 ?    2.7   0.0      0.12   1.3e+02      55     104 ..     334     383 ..     307     394 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0021
                         AAA_33  2 vllvGlpGsGKstla 16
                                   v lvG++G+GKstl+
  gi|116753890|ref|YP_843008.1| 34 VALVGPNGAGKSTLL 48
                                   569**********96 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.4
                         AAA_33  75 ldat..nlsrrerarflklarrlgvpvrivvvetdeetlk 112
                                    ld +  nl++++ +++++++ +l+   + vv++t + +l+
  gi|116753890|ref|YP_843008.1| 164 LDEPtsNLDPATSEEIMEMLDELNLYGKTVVISTHDVELA 203
                                    5555557888888888888888888777777777666555 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.12
                         AAA_33  55 lyqilnelarkalsagrnvildatnlsrrerarflklarrlgvpvrivvv 104
                                     y+ + + + ka + + ++i+ ++   +++ +r+++ a+++g +++++++
  gi|116753890|ref|YP_843008.1| 334 SYGVVDKCVLKAIAGKSSLIITSGGMVEHAERRIRSYAEEFGIEIEVIIL 383
                                    566677777788888888888888777888889**********9998765 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00017      0.18      19      65 ..      34      80 ..      20     103 .. 0.84
   2 ?   -2.8   0.0       2.9   3.1e+03      83     128 ..     337     382 ..     332     387 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00017
                     Zeta_toxin 19 illgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPeyeeil 65
                                   + l+G  GAGKs+l+ +l+  l++ ++ v +++  +R   +  ++i+
  gi|116753890|ref|YP_843008.1| 34 VALVGPNGAGKSTLLLMLNGTLRPSSGTVLFKGEPMRYDSRSLRDIR 80
                                   6789*************************999999997666666655 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.9
                     Zeta_toxin  83 lvekllqeaiengyniivegtlrspdvvkklaealkkaGYevevvv 128
                                    +v+k + +ai  + ++i+ +     +  +++   +++ G e+ev++
  gi|116753890|ref|YP_843008.1| 337 VVDKCVLKAIAGKSSLIITSGGMVEHAERRIRSYAEEFGIEIEVII 382
                                    6677777777777777776666666666656666666666666655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00026      0.27       3      24 ..      32      52 ..      30      67 .. 0.85
   2 ?   -0.9   0.0         1   1.1e+03     109     130 ..     177     198 ..     174     201 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00026
                         AAA_24  3 lkiliyGpsgiGKTtlakelgp 24
                                    k++++Gp+g+GK+tl+++l +
  gi|116753890|ref|YP_843008.1| 32 SKVALVGPNGAGKSTLLLML-N 52
                                   699**************998.4 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1
                         AAA_24 109 eefrrllkklqelrknvifiah 130
                                    ee++++l+ l+ ++k+v++  h
  gi|116753890|ref|YP_843008.1| 177 EEIMEMLDELNLYGKTVVISTH 198
                                    7999999***999999999888 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00023      0.24      31      53 ..      29      51 ..      23      72 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00023
                         AAA_25 31 pagelallaGapgtGKttlaldl 53
                                     g+ ++l+G+ g+GK+tl+l l
  gi|116753890|ref|YP_843008.1| 29 ESGSKVALVGPNGAGKSTLLLML 51
                                   678999*************9976 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 ?   11.0   0.1   0.00031      0.32       5      19 ..     221     235 ..     221     235 .. 0.91
   2 ?   -2.7   0.1       5.7     6e+03      15      21 ..     242     248 ..     242     248 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00031
                   BCA_ABC_TP_C   5 eGtPaEvrndPrVie 19 
                                    +GtP+ v +dP+V++
  gi|116753890|ref|YP_843008.1| 221 TGTPERVFADPDVVR 235
                                    5************85 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.7
                   BCA_ABC_TP_C  15 PrVieAY 21 
                                    P+V e Y
  gi|116753890|ref|YP_843008.1| 242 PAVLEIY 248
                                    9****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 ?    9.8   0.2   0.00075      0.79       1      21 [.      33      53 ..      33      67 .. 0.84
   2 ?   -1.5   0.0       2.4   2.5e+03      10      16 ..     347     353 ..     346     364 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00075
                                   EEEEEESTTSSHHHHHHHHHT CS
                       MMR_HSR1  1 evaivGrpNvGKStLinaltg 21
                                   +va+vG   +GKStL+  l g
  gi|116753890|ref|YP_843008.1| 33 KVALVGPNGAGKSTLLLMLNG 53
                                   69*************977755 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.4
                                    SSHHHHH CS
                       MMR_HSR1  10 vGKStLi 16 
                                    +GKS+Li
  gi|116753890|ref|YP_843008.1| 347 AGKSSLI 353
                                    7*****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); 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 0.30s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2659.08
//
Query:       gi|116753891|ref|YP_843009.1|  [L=254]
Description: cobalt ABC transporter, inner membrane subunit CbiQ [Methanosaeta thermophila PT]
Scores for complete 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-41  141.5  10.9    4.4e-41  140.9  10.9    1.3  1  CbiQ      Cobalt transport protein


Domain annotation for each model (and alignments):
>> CbiQ  Cobalt transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.9  10.9   2.4e-45   4.4e-41       5     211 ..      14     216 ..      10     220 .. 0.89

  Alignments for each domain:
  == domain 1  score: 140.9 bits;  conditional E-value: 2.4e-45
                                    CCS-HHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHH..TTS---HHHHHHHCCCHCHHHHHHHHHHE.......EE CS
                           CbiQ   5 lhrldprvkliwlfllllalvlapnlvtlliiiallllll..llvilprvlaqalilpllflllgllillfqlittegef 82 
                                    l++++p++kl++  + ++a + +p++ ++l ++a l +++  l +i++r++  ++++pl f ll++ +++++    +ge 
  gi|116753891|ref|YP_843009.1|  14 LRDVSPKLKLAIGAFSIMACIASPTPAVPLAVSACLSAAVilLARIPWRLYIGIIAIPLSFALLSASVVALL-S--PGEE 90 
                                    78999*****99999999999999999998888877655411456666*******************99993.3..5555 PP

                                    CTTEEE...E-TTHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHCCCSS--HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           CbiQ  83 vfagggqisitseGllrglllalRiltllslllllalTTppeeltsslerlgvPlelalillLayRfiflLleevqrikq 162
                                    +++ g  +s+ +eGl  g+ll+ R++  +s l+++alTTp+ e++s l+++g P+ l+++ +L+yR+if+Llee+   + 
  gi|116753891|ref|YP_843009.1|  91 IMSLGA-LSLSREGLWLGMLLVSRTIGGTSSLFFIALTTPMTEIFSILRSMGLPETLVELSMLIYRYIFVLLEEAMLVHS 169
                                    555555.67*********************************************************************** PP

                                    HHHHTTTTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS-SS CS
                           CbiQ 163 AqklRlgdsklgirrslrslgkliaalflralkraervalAmeaRGYtg 211
                                    Aq++R+g++  +ir s++s ++l+  lf+ra++r+er+  Am++R+Y+g
  gi|116753891|ref|YP_843009.1| 170 AQEMRMGYT--SIRGSISSFAMLASVLFIRAWERGERLMVAMDSRCYSG 216
                                    *********..*************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 2001.25
//
Query:       gi|116753892|ref|YP_843010.1|  [L=94]
Description: cobalt transport protein CbiN [Methanosaeta thermophila PT]
Scores for complete 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-23   81.0   1.5    5.6e-23   80.7   1.5    1.1  1  CbiN      Cobalt transport protein component CbiN
  ------ inclusion threshold ------
       0.14   12.3   0.2         11    6.3   0.1    2.1  2  CbtB      Probable cobalt transporter subunit (CbtB)


Domain annotation for each model (and alignments):
>> CbiN  Cobalt transport protein component CbiN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.7   1.5   6.2e-27   5.6e-23       4      67 .]       6      73 ..       4      73 .. 0.86

  Alignments for each domain:
  == domain 1  score: 80.7 bits;  conditional E-value: 6.2e-27
                           CbiN  4 llllvvllavvplflvkgae...FgGaDdqaeevIeei.apdyepwfeplweppsGEiESlLFalQAA 67
                                   ++l+ +l+++v++++ +++    ++GaD +ae vIeei + +y+pw++plwepps+EiESl+F+lQAA
  gi|116753892|ref|YP_843010.1|  6 IALASILVFFVAFLWTSQSGlheWEGADAKAEGVIEEItGGSYTPWLQPLWEPPSSEIESLFFSLQAA 73
                                   56677777777777775554556***************999**************************8 PP

>> CbtB  Probable cobalt transporter subunit (CbtB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1    0.0012        11      17      37 ..       6      28 ..       4      29 .. 0.78
   2 ?    4.3   0.0    0.0047        42       8      30 ..      64      86 ..      57      90 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0012
                           CbtB 17 llLGlllvylvgfsqaaa..lHn 37
                                   ++L+ +lv++v f   +   lH+
  gi|116753892|ref|YP_843010.1|  6 IALASILVFFVAFLWTSQsgLHE 28
                                   789**********8666555665 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0047
                           CbtB  8 qrllqlvaAllLGlllvylvgfs 30
                                   ++l+  + A++ Gl++ y++g+ 
  gi|116753892|ref|YP_843010.1| 64 ESLFFSLQAAIGGLIIGYFLGYY 86
                                   56666677888888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 723.63
//
Query:       gi|116753893|ref|YP_843011.1|  [L=229]
Description: cobalt transport protein CbiM [Methanosaeta thermophila PT]
Scores for complete 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-56  191.7  17.3    1.5e-56  191.5  17.3    1.0  1  CbiM      Cobalt uptake substrate-specific transmembrane regi


Domain annotation for each model (and alignments):
>> CbiM  Cobalt uptake substrate-specific transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.5  17.3   8.5e-61   1.5e-56       1     206 [.       2     208 ..       2     209 .. 0.96

  Alignments for each domain:
  == domain 1  score: 191.5 bits;  conditional E-value: 8.5e-61
                           CbiM   1 HipdgiLspavllaayavalallalalrrlrkeldear..vpllallaafifaaqminipipggtslHllgavlaaiLlG 78 
                                    Hi++g+L+ +++ +++a++l+++a++++r+ + ++e+r  +plla+++afif+++++++p  +g+++H++g+++ aiL+G
  gi|116753893|ref|YP_843011.1|   2 HIMEGFLPHPWWEIWFAASLPFVAYGVSRISRMAREQRetLPLLAVAGAFIFVLSSLKLPSVTGSCSHPTGTGIGAILFG 81 
                                    *********************************9977779**************************************** PP

                           CbiM  79 pwaaflavavvlllqallfgdGGitaLGaNilnmavigvllaylvyrllsrlasskkrvalaaflaallsvvlaallval 158
                                    pw++ +  ++vll qal++++GG+++LGaN+++m+++g++++yl+yr+ +r      ++ +a+flaa+l+ ++++l+++l
  gi|116753893|ref|YP_843011.1|  82 PWITSVLSTIVLLYQALFLAHGGLSTLGANVFSMGIAGPVVGYLIYRATQRF-----NLYFAVFLAAALADLATYLVTSL 156
                                    ***********************************************88554.....89********************* PP

                           CbiM 159 elalsgleas....lsltaalaamllvhlpvgilEgviTaaivkalkkvrpe 206
                                    +lal+  +a+    lsl+a++a+++++++p++ +Egvi a+++k++ ++r++
  gi|116753893|ref|YP_843011.1| 157 QLALAFPAADggvlLSLKAFAAVFAITQVPLAGIEGVISALMFKYILQARSD 208
                                    *****7766689************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1706.43
//
Query:       gi|116753894|ref|YP_843012.1|  [L=74]
Description: deoxyribonuclease [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-14   54.2   0.9    1.2e-14   54.0   0.9    1.1  1  TRAM      TRAM domain


Domain annotation for each model (and alignments):
>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.0   0.9   6.9e-19   1.2e-14       3      62 .]      19      74 .]      17      74 .] 0.96

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 6.9e-19
                                   XXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEEEE CS
                           TRAM  3 yvGstqeVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGell 62
                                    vG++++V++e+ + +eg+gi+r++ g+v+fvp+++   Gd V +++++v r+++ G+l+
  gi|116753894|ref|YP_843012.1| 19 AVGTEYNVKIEDIA-REGDGIARVE-GFVIFVPDTKV--GDQVRIQVDRVMRRFAIGHLV 74
                                   69***********9.**********.*********99..******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 573.85
//
Query:       gi|116753895|ref|YP_843013.1|  [L=166]
Description: hypothetical protein Mthe_0582 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1339.75
//
Query:       gi|116753896|ref|YP_843014.1|  [L=228]
Description: hypothetical protein Mthe_0583 [Methanosaeta thermophila PT]
Scores for 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-05   22.9  12.4        1.7    8.4   0.2    4.8  4  Ribosomal_L12_N  Ribosomal protein L7/L12 dimerisation domain
    0.00012   21.7   0.1       0.24   10.9   0.0    2.2  2  SapC             SapC
     0.0031   17.4   7.7         12    5.9   0.1    4.2  4  DEK_C            DEK C terminal domain
  ------ inclusion threshold ------
      0.014   15.7  14.5        1.3    9.5   2.4    3.5  4  DUF1104          Protein of unknown function (DUF1104)
      0.023   14.1   0.3        3.6    7.0   0.0    2.1  2  Inj_translocase  DNA/protein translocase of phage P22 injecto
      0.084   13.4   6.1        5.4    7.7   0.8    3.1  2  CAAP1            Caspase activity and apoptosis inhibitor 1
      0.096   13.2   9.3        2.1    8.9   0.9    2.7  2  MerR-DNA-bind    MerR, DNA binding
      0.098   12.6  11.6         34    4.5   0.2    4.6  4  Rho_N            Rho termination factor, N-terminal domain
       0.18   11.8   4.9        6.9    6.7   0.5    2.4  2  HTH_37           Helix-turn-helix domain
       0.21   11.8   0.6         19    5.5   0.1    2.4  2  GP17             Superinfection exclusion gene product 17
        0.3   10.8   2.8         16    5.1   0.3    2.7  2  GDPD             Glycerophosphoryl diester phosphodiesterase 
       0.33   11.4   2.1         13    6.3   0.2    2.1  2  Sir1             Regulatory protein Sir1
       0.46   10.0   1.3         22    4.5   0.1    2.0  2  Topoisom_I_N     Eukaryotic DNA topoisomerase I, DNA binding 
       0.48   10.8   7.2        8.4    6.8   0.9    2.8  2  Prok-TraM        Prokaryotic Transcriptional repressor TraM
        0.7   10.0   4.4         41    4.4   0.7    3.5  3  Phage_TAC_7      Phage tail assembly chaperone proteins, E, o
        3.2    8.3   6.9         21    5.7   0.4    2.4  2  DUF2482          Hypothetical protein of unknown function (DU
        8.2    5.7  10.3         14    5.0   1.9    2.7  2  EURL             EURL protein


Domain annotation for each model (and alignments):
>> Ribosomal_L12_N  Ribosomal protein L7/L12 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.2    0.0037       3.9       7      20 ..      55      68 ..      53      71 .. 0.91
   2 ?    5.3   0.1     0.015        16       8      22 ..      75      89 ..      74      91 .. 0.89
   3 !    7.2   0.2    0.0037       3.9       7      20 ..     150     163 ..     148     166 .. 0.91
   4 !    8.4   0.2    0.0016       1.7       8      22 ..     170     184 ..     169     186 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0037
                                   HHHHTSBHHHHHHH CS
                Ribosomal_L12_N  7 eaikeltvLElseL 20
                                   e+++++t+ E+ eL
  gi|116753896|ref|YP_843014.1| 55 EDLENMTLAEIREL 68
                                   79***********9 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.015
                                   HHHTSBHHHHHHHHH CS
                Ribosomal_L12_N  8 aikeltvLElseLvk 22
                                   +++++t+ E+  L++
  gi|116753896|ref|YP_843014.1| 75 ELENMTLAEIRALKE 89
                                   89********99986 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0037
                                    HHHHTSBHHHHHHH CS
                Ribosomal_L12_N   7 eaikeltvLElseL 20 
                                    e+++++t+ E+ eL
  gi|116753896|ref|YP_843014.1| 150 EDLENMTLAEIREL 163
                                    79***********9 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.0016
                                    HHHTSBHHHHHHHHH CS
                Ribosomal_L12_N   8 aikeltvLElseLvk 22 
                                    +++++t+ E+ eL++
  gi|116753896|ref|YP_843014.1| 170 ELENMTLAEIRELKE 184
                                    89***********97 PP

>> SapC  SapC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00023      0.24     170     212 ..      74     116 ..      52     123 .. 0.79
   2 !    8.9   0.0   0.00097         1     171     210 ..     170     209 ..     146     215 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00023
                           SapC 170 ddgeklnlsglytideekLnaLsdealeelrkkgaLaliyahl 212
                                    ++ e+ +l+++ + +e++L+++++ +l+e+r kg+ ++ y+ +
  gi|116753896|ref|YP_843014.1|  74 AELENMTLAEIRALKEKRLAEMENTTLAEMRGKGYTECPYWPM 116
                                    34577889****************************9999865 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00097
                           SapC 171 dgeklnlsglytideekLnaLsdealeelrkkgaLaliya 210
                                    + e+ +l+++   +e++L+++++ +l+e+r kg+ ++ y+
  gi|116753896|ref|YP_843014.1| 170 ELENMTLAEIRELKEKRLAEMENTTLAEMRGKGYTECPYW 209
                                    356778999999**********************999887 PP

>> DEK_C  DEK C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1     0.012        12      16      30 ..      54      68 ..      52      73 .. 0.85
   2 ?    3.4   0.1     0.069        73      16      35 ..      73      92 ..      72      99 .. 0.86
   3 ?    5.9   0.1     0.012        12      16      30 ..     149     163 ..     147     168 .. 0.85
   4 ?    4.7   0.2     0.027        29      16      35 ..     168     187 ..     167     193 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.012
                          DEK_C 16 eaDLdtvTkkkvReq 30
                                   + DL+++T  ++Re 
  gi|116753896|ref|YP_843014.1| 54 QEDLENMTLAEIREL 68
                                   57***********96 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.069
                          DEK_C 16 eaDLdtvTkkkvReqLeekl 35
                                   +a L+++T  ++R+  e++l
  gi|116753896|ref|YP_843014.1| 73 RAELENMTLAEIRALKEKRL 92
                                   688**********9988887 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.012
                          DEK_C  16 eaDLdtvTkkkvReq 30 
                                    + DL+++T  ++Re 
  gi|116753896|ref|YP_843014.1| 149 QEDLENMTLAEIREL 163
                                    57***********96 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.027
                          DEK_C  16 eaDLdtvTkkkvReqLeekl 35 
                                    +a L+++T  ++Re  e++l
  gi|116753896|ref|YP_843014.1| 168 RAELENMTLAEIRELKEKRL 187
                                    688***********999988 PP

>> DUF1104  Protein of unknown function (DUF1104)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.2    0.0035       3.7      48      77 ..      49      78 ..      48      82 .. 0.88
   2 ?    9.5   2.4    0.0012       1.3      46      83 ..      66     104 ..      57     111 .. 0.84
   3 ?    8.5   0.3    0.0024       2.5      48      77 ..     144     173 ..     143     182 .. 0.82
   4 ?    9.4   3.0    0.0013       1.3      46      83 ..     161     199 ..     152     206 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0035
                                   HHHHHHHHHTTS-HHHHHHHHHHHHHHHHH CS
                        DUF1104 48 lkeaaeknlekmtvkefeklrkevrkalkk 77
                                   +++  ++ le+mt++e ++lr+  r++l++
  gi|116753896|ref|YP_843014.1| 49 MDDITQEDLENMTLAEIRELRESKRAELEN 78
                                   5677899****************9999987 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0012
                                    HHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHH.T----S CS
                        DUF1104  46 kklkeaaeknlekmtvkefeklrkevrkalkk.kikkms 83 
                                     +l+e+ +++le+mt++e ++l+++  +++++  + +m 
  gi|116753896|ref|YP_843014.1|  66 RELRESKRAELENMTLAEIRALKEKRLAEMENtTLAEMR 104
                                    5799*********************99999985556665 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0024
                                    HHHHHHHHHTTS-HHHHHHHHHHHHHHHHH CS
                        DUF1104  48 lkeaaeknlekmtvkefeklrkevrkalkk 77 
                                    +++  ++ le+mt++e ++lr+  r++l++
  gi|116753896|ref|YP_843014.1| 144 MDDITQEDLENMTLAEIRELRESKRAELEN 173
                                    56678999*************999999876 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.0013
                                    HHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHH.T----S CS
                        DUF1104  46 kklkeaaeknlekmtvkefeklrkevrkalkk.kikkms 83 
                                     +l+e+ +++le+mt++e ++l+++  +++++  + +m 
  gi|116753896|ref|YP_843014.1| 161 RELRESKRAELENMTLAEIRELKEKRLAEMENtTLAEMR 199
                                    5799*********************99999985556665 PP

>> Inj_translocase  DNA/protein translocase of phage P22 injectosome
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0034       3.6      19      50 ..      58      89 ..      46     108 .. 0.85
   2 ?    5.3   0.0     0.011        12      19      50 ..     153     184 ..     137     202 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0034
                Inj_translocase 19 inaaLglirdnnelarsGannlgLqaLsglkg 50
                                    n +L+ ir+  e +r+   n++L  +++lk+
  gi|116753896|ref|YP_843014.1| 58 ENMTLAEIRELRESKRAELENMTLAEIRALKE 89
                                   699**************************985 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.011
                Inj_translocase  19 inaaLglirdnnelarsGannlgLqaLsglkg 50 
                                     n +L+ ir+  e +r+   n++L  ++ lk+
  gi|116753896|ref|YP_843014.1| 153 ENMTLAEIRELRESKRAELENMTLAEIRELKE 184
                                    699*********************99999975 PP

>> CAAP1  Caspase activity and apoptosis inhibitor 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.4    0.0071       7.5      34      60 ..      67      93 ..      49     102 .. 0.78
   2 ?    7.7   0.8    0.0051       5.4      34      60 ..     162     188 ..     144     198 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0071
                          CAAP1 34 iLKklsleelkelCleqLeglskkrll 60
                                   +L++ +  el++++l +++ l++krl 
  gi|116753896|ref|YP_843014.1| 67 ELRESKRAELENMTLAEIRALKEKRLA 93
                                   577788889999999999999999986 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0051
                          CAAP1  34 iLKklsleelkelCleqLeglskkrll 60 
                                    +L++ +  el++++l ++++l++krl 
  gi|116753896|ref|YP_843014.1| 162 ELRESKRAELENMTLAEIRELKEKRLA 188
                                    567777788888888888888888875 PP

>> MerR-DNA-bind  MerR, DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.9     0.002       2.1      15      49 ..      60      96 ..      59     104 .. 0.85
   2 ?    8.0   1.9     0.004       4.2      15      49 ..     155     191 ..     154     199 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.002
                                   --HHHHHHHHHHHHS..TTTBHHHHHHHHHHHHHHHH CS
                  MerR-DNA-bind 15 FsLdeIrelLalydd..rappcqdvrallarklaele 49
                                   ++L+eIrel + +    ++ + ++ ral +++lae e
  gi|116753896|ref|YP_843014.1| 60 MTLAEIRELRESKRAelENMTLAEIRALKEKRLAEME 96
                                   89********775555899999999999999999987 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.004
                                    --HHHHHHHHHHHHS..TTTBHHHHHHHHHHHHHHHH CS
                  MerR-DNA-bind  15 FsLdeIrelLalydd..rappcqdvrallarklaele 49 
                                    ++L+eIrel + +    ++ + ++ r+l +++lae e
  gi|116753896|ref|YP_843014.1| 155 MTLAEIRELRESKRAelENMTLAEIRELKEKRLAEME 191
                                    89********664444777888888888888888776 PP

>> Rho_N  Rho termination factor, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.035        37       1      13 [.      56      68 ..      56      68 .. 0.92
   2 ?    4.3   0.3     0.036        38       1      13 [.      75      87 ..      75      94 .. 0.93
   3 ?    4.4   0.1     0.033        35       1      13 [.     151     163 ..     151     164 .. 0.92
   4 ?    4.5   0.2     0.032        34       1      13 [.     170     182 ..     170     186 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.035
                                   HHHHS-HHHHHHH CS
                          Rho_N  1 eLkektlseLrai 13
                                   +L+++tl+e r++
  gi|116753896|ref|YP_843014.1| 56 DLENMTLAEIREL 68
                                   8********9985 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.036
                                   HHHHS-HHHHHHH CS
                          Rho_N  1 eLkektlseLrai 13
                                   eL+++tl+e ra+
  gi|116753896|ref|YP_843014.1| 75 ELENMTLAEIRAL 87
                                   8********9986 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.033
                                    HHHHS-HHHHHHH CS
                          Rho_N   1 eLkektlseLrai 13 
                                    +L+++tl+e r++
  gi|116753896|ref|YP_843014.1| 151 DLENMTLAEIREL 163
                                    8********9985 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.032
                                    HHHHS-HHHHHHH CS
                          Rho_N   1 eLkektlseLrai 13 
                                    eL+++tl+e r++
  gi|116753896|ref|YP_843014.1| 170 ELENMTLAEIREL 182
                                    8********9986 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.4    0.0067         7      27      66 ..      63     102 ..      48     105 .. 0.89
   2 ?    6.7   0.5    0.0065       6.9      27      66 ..     158     197 ..     140     199 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0067
                                    HHHCT--HHHHHHHHT--HHHHHHHHTT--TT--HHHHHH CS
                         HTH_37  27 iekrelsqseaaqllgiaqPkvsrllrgklsrfsldkLln 66 
                                     e rel+ s+ a+l +++ +++ +l+  +l +++ ++L +
  gi|116753896|ref|YP_843014.1|  63 AEIRELRESKRAELENMTLAEIRALKEKRLAEMENTTLAE 102
                                    56789999999****************9999999988876 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0065
                                    HHHCT--HHHHHHHHT--HHHHHHHHTT--TT--HHHHHH CS
                         HTH_37  27 iekrelsqseaaqllgiaqPkvsrllrgklsrfsldkLln 66 
                                     e rel+ s+ a+l +++ +++ +l+  +l +++ ++L +
  gi|116753896|ref|YP_843014.1| 158 AEIRELRESKRAELENMTLAEIRELKEKRLAEMENTTLAE 197
                                    4567888888888888888888888888888887777765 PP

>> GP17  Superinfection exclusion gene product 17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.037        39      54      74 ..      44      64 ..      31      83 .. 0.88
   2 ?    5.5   0.1     0.018        19      53      74 ..     138     159 ..     128     183 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.037
                           GP17 54 glqlydedltdddledmgldd 74
                                   g+ l  +d+t++dle+m l +
  gi|116753896|ref|YP_843014.1| 44 GVWLLMDDITQEDLENMTLAE 64
                                   7788899**********9975 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.018
                           GP17  53 sglqlydedltdddledmgldd 74 
                                     g+ l  +d+t++dle+m l +
  gi|116753896|ref|YP_843014.1| 138 GGMWLLMDDITQEDLENMTLAE 159
                                    6888999***********9975 PP

>> GDPD  Glycerophosphoryl diester phosphodiesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.2     0.018        19      56      85 ..      54      80 ..      45     110 .. 0.57
   2 ?    5.1   0.3     0.016        16      58      85 ..     151     175 ..     142     206 .. 0.51

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.018
                                   H.BGGGS-HHHHHTST........ECCTTCCCCSCCCS CS
                           GDPD 56 rldvkdltleelkrld........kiakenkaqlsenr 85
                                   + d++++tl+e+++l+        +           ++
  gi|116753896|ref|YP_843014.1| 54 QEDLENMTLAEIRELReskraeleN-----------MT 80
                                   4568899999999999333333331...........22 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.016
                                    BGGGS-HHHHHTST........ECCTTCCCCSCCCS CS
                           GDPD  58 dvkdltleelkrld........kiakenkaqlsenr 85 
                                    d++++tl+e+++l+        +           ++
  gi|116753896|ref|YP_843014.1| 151 DLENMTLAEIRELReskraeleN-----------MT 175
                                    56777777777777222222221...........22 PP

>> Sir1  Regulatory protein Sir1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.035        36      25      60 ..      60      92 ..      47     102 .. 0.79
   2 ?    6.3   0.2     0.012        13      25      61 ..     155     188 ..     142     197 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.035
                           Sir1 25 pktkklkkltkeerekleklklvdldelkkysksdl 60
                                   +   ++++l++++r +le++ l +++ lk+   ++l
  gi|116753896|ref|YP_843014.1| 60 MTLAEIRELRESKRAELENMTLAEIRALKE---KRL 92
                                   55678999999************9999998...445 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.012
                           Sir1  25 pktkklkkltkeerekleklklvdldelkkysksdli 61 
                                    +   ++++l++++r +le++ l +++elk+   ++l 
  gi|116753896|ref|YP_843014.1| 155 MTLAEIRELRESKRAELENMTLAEIRELKE---KRLA 188
                                    566789999*******************99...5555 PP

>> Topoisom_I_N  Eukaryotic DNA topoisomerase I, DNA binding fragment
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.021        22      77     127 ..      53     103 ..      45     108 .. 0.84
   2 ?    4.5   0.1     0.021        22      77     127 ..     148     198 ..     140     203 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.021
                                    ----GGGEE-HHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHHHHEEEE CS
                   Topoisom_I_N  77 kikelekcdFskikeylekekekkkaltkeekkklkeekekleekygyall 127
                                    + ++le++   +i e  e+++++ +++t +e ++lke++ ++ e+ ++a +
  gi|116753896|ref|YP_843014.1|  53 TQEDLENMTLAEIRELRESKRAELENMTLAEIRALKEKRLAEMENTTLAEM 103
                                    56789999999**************************99998887776655 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.021
                                    ----GGGEE-HHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHHHHEEEE CS
                   Topoisom_I_N  77 kikelekcdFskikeylekekekkkaltkeekkklkeekekleekygyall 127
                                    + ++le++   +i e  e+++++ +++t +e ++lke++ ++ e+ ++a +
  gi|116753896|ref|YP_843014.1| 148 TQEDLENMTLAEIRELRESKRAELENMTLAEIRELKEKRLAEMENTTLAEM 198
                                    56789999999**************************99998887776655 PP

>> Prok-TraM  Prokaryotic Transcriptional repressor TraM
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.9     0.008       8.4      21      65 ..      49      94 ..      43     104 .. 0.69
   2 ?    6.3   0.7     0.011        12      20      44 ..     143     167 ..     137     198 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.008
                                   CTTS-HHHHHHHHHHHHHHHHHHHHHH.HHHHHCHHHSCHHHHTTS CS
                      Prok-TraM 21 lsslskseleaLaisAIrehRrllaaa.eavyeewvrasadekvse 65
                                   ++ +++++le+++   Ire R++  a+ e++  + +ra ++++ +e
  gi|116753896|ref|YP_843014.1| 49 MDDITQEDLENMTLAEIRELRESKRAElENMTLAEIRALKEKRLAE 94
                                   678899***************9854432444444456655555555 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.011
                                    HCTTS-HHHHHHHHHHHHHHHHHHH CS
                      Prok-TraM  20 llsslskseleaLaisAIrehRrll 44 
                                    l++ +++++le+++   Ire R++ 
  gi|116753896|ref|YP_843014.1| 143 LMDDITQEDLENMTLAEIRELRESK 167
                                    5678899999999999999999874 PP

>> Phage_TAC_7  Phage tail assembly chaperone proteins, E, or 41 or 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1     0.054        57      58      76 ..      52      70 ..      48      76 .. 0.87
   2 ?    4.4   0.7     0.039        41      57      76 ..     146     165 ..      67     170 .. 0.78
   3 ?    4.2   0.4     0.045        47      58      76 ..     147     165 ..     144     201 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.054
                    Phage_TAC_7 58 lppedlekLdlaDlarlqe 76
                                   +++edle+++la +++l+e
  gi|116753896|ref|YP_843014.1| 52 ITQEDLENMTLAEIRELRE 70
                                   899************9997 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.039
                    Phage_TAC_7  57 glppedlekLdlaDlarlqe 76 
                                     +++edle+++la +++l+e
  gi|116753896|ref|YP_843014.1| 146 DITQEDLENMTLAEIRELRE 165
                                    58899999999999999887 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.045
                    Phage_TAC_7  58 lppedlekLdlaDlarlqe 76 
                                    +++edle+++la +++l+e
  gi|116753896|ref|YP_843014.1| 147 ITQEDLENMTLAEIRELRE 165
                                    5667777777777777765 PP

>> DUF2482  Hypothetical protein of unknown function (DUF2482)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.4      0.02        21       2      25 ..      56      79 ..      55      94 .. 0.87
   2 ?    5.6   1.2     0.021        22       2      25 ..     151     174 ..     150     192 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.02
                        DUF2482  2 efKdmtqeeikdllaeKskeLyel 25
                                   ++ +mt  ei++l ++K  eL ++
  gi|116753896|ref|YP_843014.1| 56 DLENMTLAEIRELRESKRAELENM 79
                                   788*****************9765 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.021
                        DUF2482   2 efKdmtqeeikdllaeKskeLyel 25 
                                    ++ +mt  ei++l ++K  eL ++
  gi|116753896|ref|YP_843014.1| 151 DLENMTLAEIRELRESKRAELENM 174
                                    788******************875 PP

>> EURL  EURL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   1.5     0.017        18     207     234 ..      69      96 ..      46     104 .. 0.72
   2 ?    5.0   1.9     0.013        14     206     235 ..     163     192 ..     134     199 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.017
                           EURL 207 physreelnsmtleelkqlnekllkqiq 234
                                     +  r el++mtl+e++ l+ek l +++
  gi|116753896|ref|YP_843014.1|  69 RESKRAELENMTLAEIRALKEKRLAEME 96 
                                    3456889999999999999998877665 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.013
                           EURL 206 hphysreelnsmtleelkqlnekllkqiqe 235
                                      +  r el++mtl+e+++l+ek l ++++
  gi|116753896|ref|YP_843014.1| 163 LRESKRAELENMTLAEIRELKEKRLAEMEN 192
                                    334568999999999999999998877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 1647.50
//
Query:       gi|116753897|ref|YP_843015.1|  [L=355]
Description: transcriptional regulator, TrmB [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-07   30.3   0.1    5.8e-07   29.3   0.1    1.5  1  MarR_2          MarR family
      2e-06   27.5   0.1    4.6e-06   26.3   0.1    1.6  1  HTH_IclR        IclR helix-turn-helix domain
    4.8e-05   23.2   0.0    8.6e-05   22.4   0.0    1.4  1  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00063   19.8   0.0     0.0022   18.1   0.0    1.9  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
     0.0044   17.5   0.1     0.0086   16.6   0.1    1.5  1  HTH_27          Winged helix DNA-binding domain
     0.0069   16.3   0.1       0.08   12.9   0.2    2.5  2  MarR            MarR family
  ------ inclusion threshold ------
      0.023   14.5   0.1      0.037   13.9   0.1    1.3  1  TFIIE_alpha     TFIIE alpha subunit
      0.034   13.7   0.6      0.068   12.8   0.6    1.6  1  HTH_24          Winged helix-turn-helix DNA-binding
      0.049   13.0   0.2      0.078   12.3   0.2    1.2  1  RNA_pol_Rpc34   RNA polymerase Rpc34 subunit
      0.058   13.4   0.3       0.11   12.5   0.3    1.5  1  HTH_Crp_2       Crp-like helix-turn-helix domain
       0.15   12.1   1.1       0.25   11.4   1.1    1.3  1  Sulfolobus_pRN  Sulfolobus plasmid regulatory protein


Domain annotation for each model (and alignments):
>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.1   3.5e-10   5.8e-07       3      54 ..     284     334 ..     282     339 .. 0.94

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 3.5e-10
                                    --HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                         MarR_2   3 ltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54 
                                    lt  ++ v+  L r  gr +t+++l  ++g++ks++s il+ L+++ L+ +r
  gi|116753897|ref|YP_843015.1| 284 LTNRERTVIETLLRKSGR-MTQADLRYETGIPKSSLSGILNSLERRKLIKKR 334
                                    78999***********97.9*****************************988 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 !   26.3   0.1   2.8e-09   4.6e-06       8      50 ..     291     333 ..     287     335 .. 0.94

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 2.8e-09
                                    HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                       HTH_IclR   8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50 
                                    +++ l +  +++t ++l  +tg+pkS+ +++L++L++++++++
  gi|116753897|ref|YP_843015.1| 291 VIETLLRKSGRMTQADLRYETGIPKSSLSGILNSLERRKLIKK 333
                                    7899999*********************************997 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   5.3e-08   8.6e-05       6      61 ..     284     341 ..     283     347 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 5.3e-08
                                    HHHHCCCHCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES.STTTE CS
                           TrmB   6 LseyEakvYlaLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerek.grpkl 61 
                                    L+  E  v  +Ll k+g++t  ++  e+g+p+s+   +L+sLe++ l+++++ gr+++
  gi|116753897|ref|YP_843015.1| 284 LTNRERTVIETLLrKSGRMTQADLRYETGIPKSSLSGILNSLERRKLIKKREwGRTNV 341
                                    67788888899**9***********************************998555555 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 !   18.1   0.0   1.3e-06    0.0022      19      53 ..     302     336 ..     296     346 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.3e-06
                 B-block_TFIIIC  19 itqsdLakeskqdprslfyrlksLekkgLIvkqsi 53 
                                    +tq dL  e+++ ++sl ++l+sLe+ +LI+k++ 
  gi|116753897|ref|YP_843015.1| 302 MTQADLRYETGIPKSSLSGILNSLERRKLIKKREW 336
                                    689*****************************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 !   16.6   0.1   5.3e-06    0.0086       1      51 [.     284     334 ..     284     342 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.3e-06
                         HTH_27   1 ltrqqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvert 51 
                                    lt+ ++ v++++ +  +r+++adl+  + + +s+ s +l+ L+++ L+++ 
  gi|116753897|ref|YP_843015.1| 284 LTNRERTVIETLLRKSGRMTQADLRYETGIPKSSLSGILNSLERRKLIKKR 334
                                    7999********************************************654 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0       0.5   8.2e+02      31      51 ..      49      69 ..      47      74 .. 0.86
   2 !   12.9   0.2   4.9e-05      0.08      10      50 ..     294     334 ..     285     336 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.5
                                   HHHHHHHHHHHHHTTSEEEEE CS
                           MarR 31 kstvtrvldrLekkGlieRsk 51
                                   k+ +t  +d Le   ++++s+
  gi|116753897|ref|YP_843015.1| 49 KALITGYADSLEGLSFLTSSQ 69
                                   6789999*********99987 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 4.9e-05
                                    HHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                           MarR  10 rilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50 
                                    ++l+ +g +++++L    g+ ks+++ +l  Le++ li+++
  gi|116753897|ref|YP_843015.1| 294 TLLRKSGRMTQADLRYETGIPKSSLSGILNSLERRKLIKKR 334
                                    67999********************************9986 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   2.3e-05     0.037       8      62 ..     282     336 ..     275     351 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.3e-05
                                    HHCS-HHHHHHHHHHHCT.TSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEE CS
                    TFIIE_alpha   8 rkfygeeavlvldvLlek.gevteedlakelkidlnelrklLnrLyearlvkykrr 62 
                                        +     v++ Ll+k g +t  dl  e++i +  l  +Ln L   +l+k + +
  gi|116753897|ref|YP_843015.1| 282 ETLTN-RERTVIETLLRKsGRMTQADLRYETGIPKSSLSGILNSLERRKLIKKREW 336
                                    44444.445688888776269******************************98876 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   0.6   4.1e-05     0.068      11      48 .]     295     332 ..     284     332 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.1e-05
                         HTH_24  11 lLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                    lL+k +r++q++L  ++g+++s ++  l+ Le+  lIk
  gi|116753897|ref|YP_843015.1| 295 LLRKSGRMTQADLRYETGIPKSSLSGILNSLERRKLIK 332
                                    5667888**************************99997 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 ?   12.3   0.2   4.8e-05     0.078      74     135 ..     274     334 ..     272     336 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.8e-05
                                    -CCCHHHHHTSXHHHH.HHHHHHHHHXSSXEEHHHHHHTTGXXHHHHHHHHHHHHHTTXXEEE CS
                  RNA_pol_Rpc34  74 sreeAkkktslsedes.lVysiIeesGneGIwsrtiksklnLhksvvkkcLksLeskkyiksv 135
                                    +re A   ++l++ e   +    ++sG+    ++++++ ++++ks +  +L sLe +k+ik++
  gi|116753897|ref|YP_843015.1| 274 TREMAAVIETLTNRERtVIETLLRKSGR--MTQADLRYETGIPKSSLSGILNSLERRKLIKKR 334
                                    577788889999999966667789***9..59*****************************86 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 ?   12.5   0.3   6.5e-05      0.11      21      58 ..     301     343 ..     277     347 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.5e-05
                                    EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.E..TEE..EE CS
                      HTH_Crp_2  21 pltqeelAsmlGltretvsrilseLkreglis.r..grr..ir 58 
                                    ++tq++l    G+  +++s il+ L+r++li+ r  gr+  i+
  gi|116753897|ref|YP_843015.1| 301 RMTQADLRYETGIPKSSLSGILNSLERRKLIKkRewGRTnvIE 343
                                    89******************************65343434555 PP

>> Sulfolobus_pRN  Sulfolobus plasmid regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.1   0.00015      0.25       3      64 ..     283     348 ..     281     354 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00015
                 Sulfolobus_pRN   3 kltlsekill.il..srrcatleeleektGiekeellvyltrlykrGlis.rkWrkiaGkkvreyc 64 
                                     lt+ e+ ++ +l    + +t  +l+  tGi+k  l   l  l +r li  r+W +   + + e+ 
  gi|116753897|ref|YP_843015.1| 283 TLTNRERTVIeTLlrKSGRMTQADLRYETGIPKSSLSGILNSLERRKLIKkREWGRTNVIEIAEWF 348
                                    566666655522311346799***************************96488*999888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); 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: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 2767.83
//
Query:       gi|116753898|ref|YP_843016.1|  [L=402]
Description: hypothetical protein Mthe_0585 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.4e-31  108.5   0.5    5.4e-31  108.5   0.5    2.3  2  MacB_PCD         MacB-like periplasmic core domain
    3.9e-09   36.9   8.1    3.9e-09   36.9   8.1    3.2  3  FtsX             FtsX-like permease family
  ------ inclusion threshold ------
          4    6.6  10.9       0.33   10.1   2.2    2.8  3  Polysacc_synt_3  Polysaccharide biosynthesis protein
        7.7    6.1   5.9        5.5    6.6   3.1    1.9  2  RTX              N-terminal domain in RTX protein


Domain annotation for each model (and alignments):
>> MacB_PCD  MacB-like periplasmic core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.5   0.5   1.2e-34   5.4e-31       1     193 [.      21     245 ..      21     246 .. 0.77
   2 ?   -4.6   6.2         4   1.8e+04       4      21 ..     339     356 ..     337     359 .. 0.89

  Alignments for each domain:
  == domain 1  score: 108.5 bits;  conditional E-value: 1.2e-34
                       MacB_PCD   1 slltvLGiaiGvaaviaivslgeglqasvlsqisdlg.nlvtvtpgk...........gsgeslsdpdvealrrevp.ve 67 
                                    ++++ LGi+iGv+a+++++s+gegl + v+sq+s+l+ ++++v+pg+            +++ ++d d+++l +++p v+
  gi|116753898|ref|YP_843016.1|  21 TMMSSLGIIIGVMAIVVMLSVGEGLYSGVSSQFSALDlDVIHVSPGRftfggpptrspEEPAKFTDKDTKLL-ENIPgVR 99 
                                    67899*****************************88534889***988886665544444444999999655.679**** PP

                       MacB_PCD  68 avapvv....tvrgggsgeeevtvvgvdpdyfkvfglklaeGrffteadlrggpnvvvigeelaerlf....pvGdtirl 139
                                    +vap+     +v+++++ + ++t++gvdp+  + ++ k+++Grf+te+d +    ++vig+++a+ +f      G +ir+
  gi|116753898|ref|YP_843016.1| 100 NVAPQTstgvIVSFRNT-NASATLIGVDPEKEHDLKSKISQGRFLTESDYT----SIVIGSGVADGIFrmriSPGNRIRI 174
                                    ****9777654466665.44489***997444445555799******9877....8**************9989****** PP

                       MacB_PCD 140 ......kpftVvGvled.ppgsgsalg..ddavylp.........lttlqrrs......itvrlkdgadleaaaaele 193
                                           +++VvGvl + + +sg+  g  ++++y+                 +      + v+++d+++++++ ++++
  gi|116753898|ref|YP_843016.1| 175 yyednyMDLKVVGVLREeE-SSGMRAGniNTQMYVThkamkellgR------EnyyygtFQVTVDDPETVDEVVDRIK 245
                                    **999999*******6633.222222347999***95553333322......0234455***************9985 PP

  == domain 2  score: -4.6 bits;  conditional E-value: 4
                       MacB_PCD   4 tvLGiaiGvaaviaivsl 21 
                                    +++Gi++G+    ai+sl
  gi|116753898|ref|YP_843016.1| 339 SIIGIVLGIILSFAIGSL 356
                                    699*********999997 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8   0.2    0.0041        19       9      51 ..      11      53 ..       9      78 .. 0.70
   2 ?   -0.6   1.1      0.42   1.9e+03      19      46 ..     274     298 ..     267     305 .. 0.63
   3 !   36.9   8.1   8.6e-13   3.9e-09       2      93 ..     308     392 ..     307     395 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0041
                           FtsX  9 alGmkkkqvlllllteillitlvalviGlglgllaaqllsdvl 51
                                   ++G+k  +   ++ + +++i++ a+v+ l +g  +   +s+ +
  gi|116753898|ref|YP_843016.1| 11 SIGFKADRFKTMMSSLGIIIGVMAIVVMLSVGEGLYSGVSSQF 53
                                   7788888888888888888888888888777665555544444 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.42
                           FtsX  19 llllteillitlvalviGlglgllaaql 46 
                                     ++ + ++ i++++lv+G   g+ +a++
  gi|116753898|ref|YP_843016.1| 274 SMIKYALAGIGAISLVVG---GIGIANV 298
                                    555555566788888888...4444444 PP

  == domain 3  score: 36.9 bits;  conditional E-value: 8.6e-13
                           FtsX   2 reigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivlllllal 81 
                                    reig+++alG+++ +++ ++l+e+ l+++v+++iG++lg++++ ++ ++         l+  i++ ++li+++++ + ++
  gi|116753898|ref|YP_843016.1| 308 REIGVMKALGATTQDIRIQYLLEAGLLGVVSSIIGIVLGIILSFAIGSL-------AGLPSAIKIQSMLIGLLFGAISTI 380
                                    8**********************************99999998885555.......7899999999************** PP

                           FtsX  82 lagllsiskilk 93 
                                    +ag++++ k++ 
  gi|116753898|ref|YP_843016.1| 381 IAGVYPANKAAM 392
                                    ******999865 PP

>> Polysacc_synt_3  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.3     0.097   4.4e+02     117     146 ..      23      52 ..      11      63 .. 0.75
   2 ?   10.1   2.2   7.4e-05      0.33     104     156 ..     250     302 ..     244     362 .. 0.73
   3 ?    1.5   1.8     0.032   1.4e+02      18      94 ..     298     374 ..     291     392 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.097
                Polysacc_synt_3 117 itlvssvvgvivaivlAllglgvwALvigt 146
                                    ++ +++++gv++ +v+  +g g+++ v ++
  gi|116753898|ref|YP_843016.1|  23 MSSLGIIIGVMAIVVMLSVGEGLYSGVSSQ 52 
                                    344678899999999999999999977766 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 7.4e-05
                Polysacc_synt_3 104 llrrelkFkklfkitlvssvvgvivaivlAllglgvwALvigtllssllslvl 156
                                    +++++  +++++++++++s++++++ i  Al+g g+ +Lv+g +  + ++++ 
  gi|116753898|ref|YP_843016.1| 250 RYHKDEAYDATTARDMLTSLMSILSMIKYALAGIGAISLVVGGIGIANVMMLT 302
                                    6788999**********************************998655554443 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.032
                Polysacc_synt_3  18 lvvislanlfvdmGlssaliqke.dlteedlstvftfnlvlgllialvlfllapliasfynqpelvtvlrvlalvlil 94 
                                    ++++++ + + ++G+ +al  ++ d+  ++l  +  + +v++++  ++ ++l+ +i s+ + p ++++ ++l + l++
  gi|116753898|ref|YP_843016.1| 298 VMMLTVKERIREIGVMKALGATTqDIRIQYLLEAGLLGVVSSIIGIVLGIILSFAIGSLAGLPSAIKIQSML-IGLLF 374
                                    456788899999999999998887999999999999999999999999888888888888888887776655.34444 PP

>> RTX  N-terminal domain in RTX protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.19   8.6e+02      55      92 ..     258     295 ..     238     306 .. 0.60
   2 ?    6.6   3.1    0.0012       5.5      73     128 ..     329     394 ..     314     398 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.19
                            RTX  55 lgyegdslLaelyrekktieaaltaistvldvvsavvs 92 
                                      +++  +L++l+     i+ al++i ++  vv++++ 
  gi|116753898|ref|YP_843016.1| 258 DATTARDMLTSLMSILSMIKYALAGIGAISLVVGGIGI 295
                                    34455556666666666666666666666555555543 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0012
                            RTX  73 ieaalta.istvldvvsavvsaaaaasgVGaPval.....lvalitglisgile....askqaile 128
                                     ea+l + +s+++++v ++    a++s+ G P a+     l++l+ g+is+i+     a k a+l+
  gi|116753898|ref|YP_843016.1| 329 LEAGLLGvVSSIIGIVLGIILSFAIGSLAGLPSAIkiqsmLIGLLFGAISTIIAgvypANKAAMLD 394
                                    58888873599*********************7652222245555555555554111166666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       941  (0.0524848); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.22s 00:00:00.75 Elapsed: 00:00:00.38
# Mc/sec: 3204.06
//
Query:       gi|116753899|ref|YP_843017.1|  [L=286]
Description: hypothetical protein Mthe_0586 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1953.86
//
Query:       gi|116753900|ref|YP_843018.1|  [L=230]
Description: ABC transporter related [Methanosaeta thermophila PT]
Scores for 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-30  103.9   0.0    1.3e-29  103.5   0.0    1.2  1  ABC_tran       ABC transporter
    6.8e-09   36.0   0.1     0.0003   20.7   0.0    2.1  2  AAA_21         AAA domain, putative AbiEii toxin, Type IV TA 
    1.9e-06   27.5   0.1     0.0042   16.5   0.0    2.1  2  SMC_N          RecF/RecN/SMC N terminal domain
    0.00022   20.9   0.2    0.00047   19.8   0.2    1.5  1  AAA_29         P-loop containing region of AAA domain
     0.0016   18.4   0.1       0.28   11.1   0.0    2.2  2  NTPase_1       NTPase
      0.003   17.5   0.1     0.0053   16.7   0.1    1.4  1  RsgA_GTPase    RsgA GTPase
     0.0038   17.5   0.1      0.048   13.9   0.0    2.2  2  AAA_22         AAA domain
  ------ inclusion threshold ------
       0.03   14.5   0.0      0.063   13.4   0.0    1.7  1  AAA_33         AAA domain
      0.034   13.9   0.0        1.6    8.4   0.0    2.1  2  IstB_IS21      IstB-like ATP binding protein
      0.043   14.2   0.1      0.062   13.7   0.1    1.5  1  AAA_16         AAA ATPase domain
      0.062   13.0   0.2        3.7    7.2   0.1    2.0  2  AAA_15         AAA ATPase domain
      0.077   12.7   0.0       0.32   10.7   0.0    1.8  2  AAA_30         AAA domain
       0.12   11.6   0.0       0.14   11.3   0.0    1.1  1  G-alpha        G-protein alpha subunit
       0.12   12.8   0.1        0.2   12.2   0.1    1.3  1  AAA_23         AAA domain
       0.14   11.3   0.0       0.26   10.4   0.0    1.4  1  NB-ARC         NB-ARC domain
       0.18   11.6   0.0       0.25   11.1   0.0    1.1  1  KDGP_aldolase  KDGP aldolase
        0.2   11.3   0.0       0.46   10.2   0.0    1.5  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 !  103.5   0.0   1.2e-32   1.3e-29       1     136 [.      23     171 ..      23     172 .. 0.87

  Alignments for each domain:
  == domain 1  score: 103.5 bits;  conditional E-value: 1.2e-32
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS--S-TTSBH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke....qeleslrkeigvlpqepqlfpeltv 76 
                                    lk ++l++  g  +a++G++G+GKStL++++  l +pt+G+  l ++d+++    +   + r +ig+++q  +l  +++v
  gi|116753900|ref|YP_843018.1|  23 LKGINLSIDSGDFLALMGPSGSGKSTLMNIIGCLDRPTAGTYILLDRDVSRaseeELAMIRRDRIGFIFQAFNLIGRISV 102
                                    789**************************************9999999999777555567899***************** PP

                                    HHH..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    xxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  77 ren..........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                     +n           +de+ ++al+ l+ +++++ +++ sp ++SgG++qrva+aral+++p+++++DEpt
  gi|116753900|ref|YP_843018.1| 103 LKNvelpmmlkgmPRDERRDRALELLKSVGVAH-RADFSPLNISGGERQRVAIARALANNPEIIIADEPT 171
                                    *************55555555555555555333.446678*****************************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 !   13.6   0.1   4.1e-05     0.043       2      23 ..      36      57 ..      35      97 .. 0.78
   2 !   20.7   0.0   2.8e-07    0.0003     228     301 ..     135     205 ..      85     207 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.1e-05
                         AAA_21  2 nvliGpNgsGKSnLLdaldlla 23
                                    +l Gp gsGKS+L+ ++ +l 
  gi|116753900|ref|YP_843018.1| 36 LALMGPSGSGKSTLMNIIGCLD 57
                                   5799**************9993 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 2.8e-07
                         AAA_21 228 dgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpll 301
                                    ++ ++++ ++S G ++  a++ al+  +    +++ DEp  +L+ k +++++++l+ l+r+g  +i++TH+p++
  gi|116753900|ref|YP_843018.1| 135 HRADFSPLNISGGERQRVAIARALANNP---EIIIADEPTGNLDLKSTEEVMDILSGLNREGRTIIMVTHNPEI 205
                                    4556677778999999988888888877...9***********************999999***********98 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.1   0.00081      0.85      25      44 ..      34      53 ..      24      58 .. 0.85
   2 !   16.5   0.0     4e-06    0.0042     129     212 ..     136     216 ..      82     220 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00081
                                   SEEEEEESTTSSHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 25 sftaivGpNGSGKsnlldAi 44
                                    f a++Gp GSGKs l++ i
  gi|116753900|ref|YP_843018.1| 34 DFLALMGPSGSGKSTLMNII 53
                                   5889***********99865 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 4e-06
                                    CTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-SC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                          SMC_N 129 sagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemlekadk 207
                                    +a++s+ ++SgGe++ va+a  +A    +p  + + De   +LD k +++v ++l   + +   +i+++++ e+++ +++
  gi|116753900|ref|YP_843018.1| 136 RADFSPLNISGGERQRVAIARALAN---NP-EIIIADEPTGNLDLKSTEEVMDILSGLNREgRTIIMVTHNPEITKYCNR 211
                                    45566669**********9988773...34.48899********************766653788899************ PP

                                    EEEEE CS
                                    xxxxx RF
                          SMC_N 208 lvgvt 212
                                    ++g++
  gi|116753900|ref|YP_843018.1| 212 VIGMR 216
                                    **986 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.2   4.5e-07   0.00047      17      39 ..      28      50 ..      22      58 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 4.5e-07
                         AAA_29 17 ieidlkgatlltGpsGsGKSTll 39
                                   ++id  ++  l+GpsGsGKSTl+
  gi|116753900|ref|YP_843018.1| 28 LSIDSGDFLALMGPSGSGKSTLM 50
                                   6788666999************8 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.015        16       3      18 ..      37      52 ..      35      64 .. 0.84
   2 !   11.1   0.0   0.00026      0.28      84     152 ..     150     220 ..     123     227 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.015
                                   EEE--TTSSHHHHHHH CS
                       NTPase_1  3 fiTGppGvGKtTlvkk 18
                                   ++ Gp+G+GK+Tl++ 
  gi|116753900|ref|YP_843018.1| 37 ALMGPSGSGKSTLMNI 52
                                   678**********975 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00026
                                    HHHHHHHHHHHHH-EEEE--.-STTGGG-HHHHHHHHHHHT.TTSEEEEE--SS--SHHHHHHHT-TT-EE CS
                       NTPase_1  84 lalealrkalseadviviDE.iGkmElkskkfkeaveevLk.sekpvlavihrrkdlalveeirerkdvkv 152
                                      +++ r   +++++i+ DE  G++ lks +    +   L+ +++ +++v h+++  +  +++   +d+++
  gi|116753900|ref|YP_843018.1| 150 QRVAIARALANNPEIIIADEpTGNLDLKSTEEVMDILSGLNrEGRTIIMVTHNPEITKYCNRVIGMRDGRI 220
                                    334444444599********88*********9999999999999*********986666666666666665 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1     5e-06    0.0053     100     119 ..      34      53 ..      18      65 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5e-06
                                    SEEEEECSTTSSHHHHHHHH CS
                    RsgA_GTPase 100 ktsvlvGqSGvGKStLinal 119
                                    ++ +l+G+SG GKStL+n +
  gi|116753900|ref|YP_843018.1|  34 DFLALMGPSGSGKSTLMNII 53 
                                    7889**************86 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   4.6e-05     0.048       4      23 ..      32      51 ..      30      58 .. 0.89
   2 ?    1.0   0.0      0.44   4.7e+02      83     132 ..     155     204 ..     112     208 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.6e-05
                         AAA_22  4 tagilvvtGesGtGKTtllr 23
                                   +  +l+++G+sG+GK+tl++
  gi|116753900|ref|YP_843018.1| 32 SGDFLALMGPSGSGKSTLMN 51
                                   56799*************96 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.44
                         AAA_22  83 eqalrarav.....ielliiDEaqh.lr..seealeeLrsllnlsrkgvqliLvGtp.e 132
                                    +       +     +e++i DE    l+  s e + ++ s ln  r g ++i+v ++ e
  gi|116753900|ref|YP_843018.1| 155 A-------RalannPEIIIADEPTGnLDlkSTEEVMDILSGLN--REGRTIIMVTHNpE 204
                                    2.......22234667999999776686665666666666667..66666666655545 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     6e-05     0.063       4      33 ..      38     107 ..      36     212 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6e-05
                         AAA_33   4 lvGlpGsGKstlaerl..lkklg...avllssdt...................................l 33 
                                    l G++GsGKstl   +  l + +   ++ll+ d+                                   +
  gi|116753900|ref|YP_843018.1|  38 LMGPSGSGKSTLMNIIgcLDRPTagtYILLDRDVsraseeelamirrdrigfifqafnligrisvlknvE 107
                                    78**********9876545444477899999998666666666655555555555555555555444440 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0015       1.6      44      68 ..      30      54 ..      22      65 .. 0.87
   2 ?    3.3   0.0     0.057        61     107     154 ..     160     208 ..     139     217 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0015
                      IstB_IS21 44 iekkenivllGpsGvGKshlaialg 68
                                   i++ + ++l+GpsG GKs l   +g
  gi|116753900|ref|YP_843018.1| 30 IDSGDFLALMGPSGSGKSTLMNIIG 54
                                   6777889***********9977666 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.057
                      IstB_IS21 107 lkvdllilDdlgllpldqaeaellfevie..kryerrsiiitsnlpfaew 154
                                     +++++i D+  + +ld +++e+++++++  +r +r+ i++t n ++ ++
  gi|116753900|ref|YP_843018.1| 160 NNPEIIIADE-PTGNLDLKSTEEVMDILSglNREGRTIIMVTHNPEITKY 208
                                    3446666666.56789999999999**99445789999999999988877 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   5.9e-05     0.062      25      44 ..      34      53 ..      27     198 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.9e-05
                         AAA_16 25 elvllsGesGvGKsslvrel 44
                                     + l G+sG+GKs+l++ +
  gi|116753900|ref|YP_843018.1| 34 DFLALMGPSGSGKSTLMNII 53
                                   5789************9644 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1    0.0035       3.7      18      43 ..      29      53 ..      23      62 .. 0.80
   2 ?    4.0   0.0     0.032        34     322     368 ..     160     205 ..     149     206 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0035
                         AAA_15 18 eidlseeltvliGkNnsGKSsileal 43
                                   +id  + +  l G+ +sGKS++++++
  gi|116753900|ref|YP_843018.1| 29 SIDSGD-FLALMGPSGSGKSTLMNII 53
                                   344444.99**************998 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.032
                         AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSphi 368
                                    +++ i++ +EP  +L  +  +++++ l  l ++++  +i+ TH+p i
  gi|116753900|ref|YP_843018.1| 160 NNPEIIIADEPTGNLDLKSTEEVMDILSGLNREGR-TIIMVTHNPEI 205
                                    67889999999999999999**********99999.9********98 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    0.0003      0.32      16      38 ..      32      53 ..      26      80 .. 0.83
   2 ?   -0.5   0.0      0.83   8.8e+02      86     112 ..     159     186 ..     122     202 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0003
                         AAA_30 16 sgdrvavltGpAGtGKttalkal 38
                                   sgd + +l Gp G+GK+t+++ +
  gi|116753900|ref|YP_843018.1| 32 SGD-FLALMGPSGSGKSTLMNII 53
                                   565.8899************987 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.83
                         AAA_30  86 lepgtllivDE.agmvdtkqlaallkaa 112
                                     ++ +++i DE +g +d k+++++++++
  gi|116753900|ref|YP_843018.1| 159 ANNPEIIIADEpTGNLDLKSTEEVMDIL 186
                                    3334788888855666555555555443 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00013      0.14      26     120 ..      36     162 ..      31     222 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00013
                                    EEEEESTTSSHHHHHHHHHHHCS--.............--HHHHHCCHHHHHHHHHHHHHHHHHHHHHTT.......... CS
                        G-alpha  26 llllGqseSGKsTilkqlkllykkg.............fseeelatwraviqlnivrsiktilealesleselsesf... 89 
                                    l l+G s+SGKsT+++ + +l +++              seeela +r   +  i +++++i ++    + el   +   
  gi|116753900|ref|YP_843018.1|  36 LALMGPSGSGKSTLMNIIGCLDRPTagtyilldrdvsrASEEELAMIRRDRIGFIFQAFNLIGRISVLKNVELPM-Mlkg 114
                                    6799******************99999999999998888888887777777777777777776555554444422.2355 PP

                                    ..HHHC-SS-SCCCS-HCHHHH.........................H CS
                        G-alpha  90 ..elqelkerldplkkveasliaklssateee...............q 120
                                       ++ + ++l+ lk+v  ++ a +s+ + +                 
  gi|116753900|ref|YP_843018.1| 115 mpRDERRDRALELLKSVGVAHRADFSPLNISGgerqrvaiaralannP 162
                                    534444444444445555555444444444446654444444444431 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00019       0.2      20      39 ..      34      53 ..       5      55 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00019
                         AAA_23 20 gltlItGpNGaGKTTildAi 39
                                    + ++ Gp G+GK+T+++ i
  gi|116753900|ref|YP_843018.1| 34 DFLALMGPSGSGKSTLMNII 53
                                   456889***********987 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00025      0.26      19      39 ..      33      52 ..      23      61 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00025
                                   CSEEEEEEESTTSSHHHHHHH CS
                         NB-ARC 19 qslvvalvGmgGvGKttlakq 39
                                   + +++al+G  G+GK+tl++ 
  gi|116753900|ref|YP_843018.1| 33 G-DFLALMGPSGSGKSTLMNI 52
                                   3.59**************975 PP

>> KDGP_aldolase  KDGP aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00024      0.25     138     198 ..     122     186 ..     118     197 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00024
                                    HHHHHHHHHCT-.-EEEE---TTTTTHHHHHHHHHHHHHC.T-EE..EEBSS--TTTHHHHHHHH CS
                  KDGP_aldolase 138 etaiallkdmgg.ssvkffpmeGlkrleelaavakaaakk.gltl..ePtGGidldnfeeivqia 198
                                    + a++llk++g+ +   f p++    +   +a+a+a a++ ++++  ePtG +dl+ +ee++ i 
  gi|116753900|ref|YP_843018.1| 122 DRALELLKSVGVaHRADFSPLNISGGERQRVAIARALANNpEIIIadEPTGNLDLKSTEEVMDIL 186
                                    57999999999735789999998888888899999988763555568**************9986 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00043      0.46       6      22 ..      37      53 ..      34      84 .. 0.79
   2 ?   -2.9   0.0       4.3   4.5e+03     109     131 ..     180     202 ..     177     211 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00043
                         AAA_24  6 liyGpsgiGKTtlakel 22
                                   +++Gpsg+GK+tl++ +
  gi|116753900|ref|YP_843018.1| 37 ALMGPSGSGKSTLMNII 53
                                   79***********9877 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.3
                         AAA_24 109 eefrrllkklqelrknvifiahe 131
                                    ee++++l  l+  + ++i++ h 
  gi|116753900|ref|YP_843018.1| 180 EEVMDILSGLNREGRTIIMVTHN 202
                                    56666666666666788888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); 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: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1620.21
//
Query:       gi|116753901|ref|YP_843019.1|  [L=147]
Description: hypothetical protein Mthe_0588 [Methanosaeta thermophila PT]
Scores for complete 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-08   32.9   0.2    9.3e-08   32.4   0.2    1.2  1  LTD           Lamin Tail Domain
    0.00019   22.6   1.9    0.00039   21.6   1.3    1.7  2  Tad_C         Putative Tad-like Flp pilus-assembly
  ------ inclusion threshold ------
        0.1   12.2   0.0       0.13   11.9   0.0    1.1  1  LBP_BPI_CETP  LBP / BPI / CETP family, N-terminal domain


Domain annotation for each model (and alignments):
>> LTD  Lamin Tail Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.2   1.6e-11   9.3e-08       5     110 ..      47     143 ..      43     144 .. 0.81

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 1.6e-11
                            LTD   5 agdvvIsevmedgagnnanefvelyNtsskavdLsgwkledasge.ytfpngtgtlaageyvvvwsgsgttsasngskas 83 
                                    a+ + I+ v+ ++       +ve++N ++++ +L++++l+ + +e  t+ +    +++ ++v ++ g+g++        +
  gi|116753901|ref|YP_843019.1|  47 AAPLYIADVNIEE------GYVEIANDGNASQSLENYTLKIDENEpVTLGAI--EVQPASSVKLFLGAGEN-------TE 111
                                    5667777788777......8***********************887777665..6************7544.......33 PP

                            LTD  84 ssavwnn.....ggdavaLydasgevvdsvgy 110
                                    ++  +n+     +  +v+L+d++g++v++++y
  gi|116753901|ref|YP_843019.1| 112 TEIYLNTtiefaETGTVSLMDPEGNEVSTFAY 143
                                    455555566666677999**********9998 PP

>> Tad_C  Putative Tad-like Flp pilus-assembly
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   1.3   6.6e-08   0.00039       2      81 ..      17     107 ..      16     119 .. 0.84
   2 ?   -0.7   0.0      0.59   3.6e+03      40      57 ..     124     142 ..     115     144 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 6.6e-08
                          Tad_C   2 aAaelsdaeatsaaaaaaaqeaaalngfdaaagn.....saevetGhwspdaaapgpkrftagaa.........pinaVr 67 
                                    +Aa + d+ ++++a + +a+ea+a+n++  a+++     ++ +e G++++++++ +++ +  + +         +  a+ 
  gi|116753901|ref|YP_843019.1|  17 GAAYAEDTAENVTAENVTAEEAIAENVT--AEAAplyiaDVNIEEGYVEIANDG-NASQSLENYTlkidenepvTLGAIE 93 
                                    7999999999999999************..555569999***********4444.44555555556999***9999**** PP

                          Tad_C  68 VtvtrsvplfFasi 81 
                                    V+   sv+lf++++
  gi|116753901|ref|YP_843019.1|  94 VQPASSVKLFLGAG 107
                                    **********9986 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.59
                          Tad_C  40 etGhwsp.daaapgpkrft 57 
                                    etG++s  d+++++ ++f+
  gi|116753901|ref|YP_843019.1| 124 ETGTVSLmDPEGNEVSTFA 142
                                    7899999999999999985 PP

>> LBP_BPI_CETP  LBP / BPI / CETP family, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.2e-05      0.13       8     106 ..      16     126 ..      10     131 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.2e-05
                                    HHHHHHHHHHHTS-CCCEEEEEEETTTECEEEEEEEEEEEEEEEEEEEEEEETTTEEEEEEEEEEEEEEEEEEECECCEE CS
                   LBP_BPI_CETP   8 eglkvlqkeleklqlpdilgeekikllgkvkynisnlkIsnlqlpslslklspggglllliiplslkisgklpllgsfle 87 
                                    +g +  + + e+++ ++++ ee+i +  +v  +   l I ++++ + +++   +g+ +++  + +lki  + p++ + +e
  gi|116753901|ref|YP_843019.1|  16 LGAAYAEDTAENVTAENVTAEEAIAE--NVTAEAAPLYIADVNIEEGYVEIANDGNASQSLENYTLKIDENEPVTLGAIE 93 
                                    667777888999***********998..999*************************999999*************99998 PP

                                    E..............EEEEEEEEEEEEEEETTS CS
                   LBP_BPI_CETP  88 l..............avgvsitaelalerdeqG 106
                                    +                +++i+++ ++e  e+G
  gi|116753901|ref|YP_843019.1|  94 VqpassvklflgageNTETEIYLNTTIEFAETG 126
                                    877776666777777555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); 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: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1077.43
//
Query:       gi|116753902|ref|YP_843020.1|  [L=264]
Description: undecaprenyl diphosphate synthase [Methanosaeta thermophila PT]
Scores for complete 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-66  222.9   0.0    4.4e-66  222.6   0.0    1.0  1  Prenyltransf   Putative undecaprenyl diphosphate synthase
  ------ inclusion threshold ------
      0.051   13.4   0.1      0.095   12.6   0.1    1.4  1  SNN_cytoplasm  Stannin cytoplasmic


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 !  222.6   0.0     5e-70   4.4e-66       1     217 [.      35     255 ..      35     261 .. 0.91

  Alignments for each domain:
  == domain 1  score: 222.6 bits;  conditional E-value: 5e-70
                                    EE--HHHHHHHTT.S-HHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEEGGGGGS-HHHHHHHHHHHHHHHHHHH.HHHH CS
                   Prenyltransf   1 imDGNrRwAkkrgleereeGhkaGaealkeilelclelgvkvvtvYafSteNfkRskeevdalmellkeellkee.lkel 79 
                                    i DGNrR+A++++ +++++Gh+ Ga++ ++i ++clelg+k++tvYafSteNf+Rs+ e +++++l++e+ll+    +++
  gi|116753902|ref|YP_843020.1|  35 IQDGNRRYANRHN-MPVSNGHRLGAKTTEKISDWCLELGIKHLTVYAFSTENFSRSEPEKRYIFNLITEKLLELCsSEKI 113
                                    78***********.78888************************************************9766665434599 PP

                                    HHTTEEEEEESSGGGS-HHHHHHHHHHHHHHT.TTTSEEEEEEEEE-HHHHHHHHHHHHHHTT..SSSG.GGHSHHHHHC CS
                   Prenyltransf  80 lkegvrvrviGdlellpedvlealekaeeatkknnkklvlniavnYgsrdeiveavrelvkekseekkk.eeideetlek 158
                                    +k++vrvr+iG++++lpe +++a++++e+at+  ++ + ln+a++Yg++ e+++a+r+++++  +   + +++de+ + +
  gi|116753902|ref|YP_843020.1| 114 HKNRVRVRAIGRIDMLPEYLQNAIKEVEAATEGYSQ-MYLNVALAYGGQYELIDATRAMARDLRAGVIRiSDLDEDLVGR 192
                                    999*****************************5555.**********************999876666544568999*** PP

                                    TSTT..T..SSS-SEEEEESS--S-TTSSTTTTTT-E..EEEESSSGGG--HHHHHHHHHHHH CS
                   Prenyltransf 159 hlytaka..lpdpDlliRtsGeeRlSnFllwqlayse..lyfldvlWPdfskedllealleyq 217
                                    +ly +++  +p++Dl+iRt+Ge R SnFl wq+  se   yf+  +WP+f+k d+l+a+++ q
  gi|116753902|ref|YP_843020.1| 193 YLYPTTEtpVPKVDLIIRTGGEIRTSNFLPWQANGSEcaAYFCAPYWPEFRKIDFLRAIRTAQ 255
                                    ***6655689**********************99999999*******************8755 PP

>> SNN_cytoplasm  Stannin cytoplasmic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   1.1e-05     0.095       1      14 [.      18      31 ..      18      34 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.1e-05
                  SNN_cytoplasm  1 LLVQYSAkGPrVEr 14
                                   LL Q  A+GPrVE+
  gi|116753902|ref|YP_843020.1| 18 LLKQQLARGPRVEH 31
                                   677888******** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1966.66
//
Query:       gi|116753903|ref|YP_843021.1|  [L=116]
Description: nascent polypeptide-associated complex protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-16   59.7   0.7    3.2e-16   59.1   0.7    1.3  1  NAC       NAC domain
  ------ inclusion threshold ------
      0.024   14.5   0.0      0.041   13.7   0.0    1.3  1  UBA_4     UBA-like domain
      0.039   14.0   0.1      0.056   13.5   0.1    1.3  1  HOIP-UBA  HOIP UBA domain pair


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 !   59.1   0.7   5.3e-20   3.2e-16       1      56 [.      12      70 ..      12      70 .. 0.97

  Alignments for each domain:
  == domain 1  score: 59.1 bits;  conditional E-value: 5.3e-20
                            NAC  1 ekKlrkalkklgl..keipgieeVtirksdgkvlvfdnPkVq..kspgsntyvvfGeaee 56
                                   +kK++ +lk +g+   ei+g+eeV+ir+sd  ++v++n++V   +++g+ +y+++G++ e
  gi|116753903|ref|YP_843021.1| 12 PKKMKGMLKSMGIniDEIEGVEEVVIRTSD-REIVIKNASVAvmEAQGNRSYQISGDVTE 70
                                   7*****************************.**********999************9875 PP

>> UBA_4  UBA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   6.8e-06     0.041      11      33 ..      86     108 ..      82     109 .. 0.96

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.8e-06
                          UBA_4  11 TGadeekArqlLeannWdLerAi 33 
                                    TGa++e+Ar  L  +++dL  Ai
  gi|116753903|ref|YP_843021.1|  86 TGASPEEARAALMDCGGDLAEAI 108
                                    9*******************998 PP

>> HOIP-UBA  HOIP UBA domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   9.3e-06     0.056      69      95 ..      84     110 ..      42     114 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.3e-06
                       HOIP-UBA  69 evgklsraEakealleagGdvekAvkq 95 
                                    +    s +Ea+ al+++gGd+ +A+ +
  gi|116753903|ref|YP_843021.1|  84 SQTGASPEEARAALMDCGGDLAEAIIK 110
                                    5556799****************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.25s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 914.02
//
Query:       gi|116753904|ref|YP_843022.1|  [L=237]
Description: hypothetical protein Mthe_0591 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); 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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1754.67
//
Query:       gi|116753905|ref|YP_843023.1|  [L=343]
Description: putative transcriptional regulator [Methanosaeta thermophila PT]
Scores for complete 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  130.5   0.0      7e-38  129.8   0.0    1.3  1  SMC_ScpB  Segregation and condensation complex subunit ScpB
  ------ inclusion threshold ------
      0.015   15.3   0.2      0.093   12.8   0.0    2.3  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 !  129.8   0.0   7.8e-42     7e-38       2     154 ..       6     150 ..       5     154 .. 0.98

  Alignments for each domain:
  == domain 1  score: 129.8 bits;  conditional E-value: 7.8e-42
                       SMC_ScpB   2 iiEAiLfvageplsleeLakilelskeeveealeeLkeeyeeedrglelvevaggyrlvtkpelaevvkklvkekkktrL 81 
                                     +EA+Lf+ag+pls+ee++ + +l+ ++v +a ++L +ey++++ g+e++ v+g + ++++ +la+ v+ ++++    +L
  gi|116753905|ref|YP_843023.1|   6 LVEAMLFAAGRPLSVEEISGLSGLDAKDVLDAANSLLREYASRGGGIEVRAVEGSFVMQVRGDLAQSVAMVAPR----EL 81 
                                    79************************************************************************....** PP

                       SMC_ScpB  82 sqaaletLaiIaykqpvtraeieeiRGvnsdsvvrtLlerglieekgrkeepgrpilYgtTekFleyfglksl 154
                                    +++ ++tLa+Iay+qp++++e+++iRG +++++vr L ++gli+ ++    +gr+  ++tT+ F eyfgl+s 
  gi|116753905|ref|YP_843023.1|  82 DSSVIRTLAVIAYRQPIMQSELARIRGNKCYEHVRLLERMGLISASK----KGRTRELRTTRGFAEYFGLQSA 150
                                    ***********************************************....9******************995 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.21   1.9e+03      16      33 ..       8      26 ..       5      42 .. 0.77
   2 ?   12.8   0.0     1e-05     0.093      28      61 .]     101     131 ..      83     131 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.21
                                   HHHH.STCTTB-HHHHHHH CS
                         HTH_20 16 lraL.araegltaselaer 33
                                   +++L a +++l+++e+  +
  gi|116753905|ref|YP_843023.1|  8 EAMLfAAGRPLSVEEISGL 26
                                   5677789999****99765 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 1e-05
                                    HHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                         HTH_20  28 selaerldlskntlsyHLrvLeeagLvevvregr 61 
                                    sela   +++ n ++ H+r Le+ gL+   + gr
  gi|116753905|ref|YP_843023.1| 101 SELA---RIRGNKCYEHVRLLERMGLISASKKGR 131
                                    4444...59******************9877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2629.11
//
Query:       gi|116753906|ref|YP_843024.1|  [L=149]
Description: hypothetical protein Mthe_0593 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.1e-10   39.7   0.1    8.4e-10   39.0   0.1    1.3  1  Peptidase_M54  Peptidase family M54
    9.2e-06   25.6   0.0    1.3e-05   25.1   0.0    1.2  1  Peptidase_M10  Matrixin
    0.00099   19.6   0.0     0.0011   19.5   0.0    1.2  1  Reprolysin_3   Metallo-peptidase family M12B Reprolysin-like
      0.002   17.8   0.0     0.0024   17.5   0.0    1.1  1  Reprolysin_4   Metallo-peptidase family M12B Reprolysin-like
     0.0058   15.9   0.3     0.0082   15.4   0.3    1.1  1  DUF4953        Met-zincin
  ------ inclusion threshold ------
      0.011   15.9   0.0      0.012   15.8   0.0    1.2  1  Reprolysin_5   Metallo-peptidase family M12
      0.057   13.3   0.0      0.067   13.1   0.0    1.2  1  Reprolysin_2   Metallo-peptidase family M12B Reprolysin-like
      0.073   11.7   3.2      0.079   11.5   2.1    1.5  2  Metallopep     Putative peptidase family
      0.091   12.4   0.4       0.12   11.9   0.4    1.2  1  Astacin        Astacin (Peptidase family M12A)
       0.18   10.7   0.1       0.23   10.4   0.1    1.1  1  Peptidase_M66  Peptidase M66


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 !   39.0   0.1   4.7e-13   8.4e-10     148     189 ..      88     129 ..      80     134 .. 0.94

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 4.7e-13
                                    HHHHHHHHHTT----S-TSTTS--SSHHHHHHS-SS--HHHH CS
                  Peptidase_M54 148 evlhelGhlyGLshCkedCvmnfsndlkdvDrkapkyCksCl 189
                                     v+he+Gh++GL hC e C m+++ + ++v+r+    C++C 
  gi|116753906|ref|YP_843024.1|  88 VVMHEIGHILGLDHCIERCLMQPAMNEEEVERRPFALCEQCF 129
                                    589**************************************6 PP

>> Peptidase_M10  Matrixin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   7.3e-09   1.3e-05     110     140 ..      86     115 ..      71     123 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 7.3e-09
                                    HHHHHHHHHHHTTBESXSSTTSTTSSSCTXT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M10 110 flVaaHEiGHalGLeHssdkdalmyplykee 140
                                    + V++HEiGH+lGL+H   ++ lm+p ++ee
  gi|116753906|ref|YP_843024.1|  86 MNVVMHEIGHILGLDHC-IERCLMQPAMNEE 115
                                    6799************5.6667****99743 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 !   19.5   0.0   6.2e-07    0.0011      90     123 ..      74     101 ..      21     102 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 6.2e-07
                   Reprolysin_3  90 sskkagvnsgssvlgkvgadtvaHEiGHnfganH 123
                                     + ++g+++g        +++v+HEiGH +g++H
  gi|116753906|ref|YP_843024.1|  74 ITTTFGLSRGA------WMNVVMHEIGHILGLDH 101
                                    33334444333......358************** 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 !   17.5   0.0   1.4e-06    0.0024     132     154 ..      81     104 ..      53     126 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.4e-06
                   Reprolysin_4 132 srdey.difAHEiGHtfGaaHdls 154
                                    sr  + +++ HEiGH +G++H ++
  gi|116753906|ref|YP_843024.1|  81 SRGAWmNVVMHEIGHILGLDHCIE 104
                                    35577799*************876 PP

>> DUF4953  Met-zincin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.3   4.6e-06    0.0082      15      29 ..      87     101 ..      82     104 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4.6e-06
                        DUF4953  15 fvvaHEvGhtLGLrh 29 
                                     vv+HE+Gh+LGL+h
  gi|116753906|ref|YP_843024.1|  87 NVVMHEIGHILGLDH 101
                                    59************9 PP

>> Reprolysin_5  Metallo-peptidase family M12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   0.0   6.5e-06     0.012     136     158 ..      80     101 ..       8     116 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.5e-06
                   Reprolysin_5 136 vvstatevqvvaHElGHnfGavH 158
                                    ++  +  ++vv+HE+GH +G  H
  gi|116753906|ref|YP_843024.1|  80 LS-RGAWMNVVMHEIGHILGLDH 101
                                    33.445578*************9 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 ?   13.1   0.0   3.7e-05     0.067      85     146 ..      53     106 ..      14     121 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.7e-05
                   Reprolysin_2  85 ggvlGLayvgqicqkeassrktntglsttansgsaveetkeidvvaHEvGHaFGatHdndgs 146
                                    +g++ La vg+i    a++     +++tt            ++vv HE+GH+ G  H  +  
  gi|116753906|ref|YP_843024.1|  53 DGEIYLAGVGSIFGCAAGR----CAITTTFGLSRGA----WMNVVMHEIGHILGLDHCIERC 106
                                    5777899999997666666....5565533222222....3689**********99976644 PP

>> Metallopep  Putative peptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   2.1   4.4e-05     0.079     318     333 ..      89     104 ..      72     111 .. 0.86
   2 ?   -1.3   0.0      0.35   6.2e+02     141     163 ..     106     128 ..     104     143 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.4e-05
                     Metallopep 318 flHEiGHllglpHqed 333
                                    ++HEiGH+lgl H+ +
  gi|116753906|ref|YP_843024.1|  89 VMHEIGHILGLDHCIE 104
                                    8************965 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.35
                     Metallopep 141 aftaeklrrkglgrrtFrleeev 163
                                    ++ +  ++++ + rr F+l e++
  gi|116753906|ref|YP_843024.1| 106 CLMQPAMNEEEVERRPFALCEQC 128
                                    67788999999999999999999 PP

>> Astacin  Astacin (Peptidase family M12A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.4   6.8e-05      0.12      77      99 ..      83     105 ..      55     108 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.8e-05
                                    C-SHHHHHHHHHHHHTB--GGGS CS
                        Astacin  77 CeklgiivHElmHalGffHeqsR 99 
                                    ++ + +++HE++H lG+ H  +R
  gi|116753906|ref|YP_843024.1|  83 GAWMNVVMHEIGHILGLDHCIER 105
                                    45689*************97666 PP

>> Peptidase_M66  Peptidase M66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00013      0.23     191     209 ..      84     102 ..      60     110 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00013
                  Peptidase_M66 191 tltgefiHEqGHalGLpHy 209
                                       ++ +HE GH lGL H 
  gi|116753906|ref|YP_843024.1|  84 AWMNVVMHEIGHILGLDHC 102
                                    567899************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1105.92
//
Query:       gi|116753907|ref|YP_843025.1|  [L=285]
Description: chromosome partitioning ATPase protein-like [Methanosaeta thermophila PT]
Scores for 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-92  306.9   0.3    1.1e-91  306.7   0.3    1.0  1  ParA           NUBPL iron-transfer P-loop NTPase
    3.9e-13   49.6   0.0    5.8e-13   49.0   0.0    1.4  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
    1.7e-07   30.7   0.8    3.8e-06   26.3   0.3    2.2  2  ArsA_ATPase    Anion-transporting ATPase
      9e-07   29.0   1.0    1.1e-05   25.4   1.0    2.1  1  AAA_31         AAA domain
    7.6e-06   25.4   0.1    1.3e-05   24.6   0.1    1.5  1  MipZ           ATPase MipZ
    7.8e-05   22.6   0.2     0.0091   15.8   0.0    2.2  2  AAA_26         AAA domain
     0.0019   18.0   0.0     0.0031   17.4   0.0    1.3  1  CLP1_P         mRNA cleavage and polyadenylation factor CLP1 
  ------ inclusion threshold ------
       0.01   15.8   0.0      0.021   14.7   0.0    1.5  1  APS_kinase     Adenylylsulphate kinase
      0.013   15.1   0.1      0.029   14.0   0.1    1.5  1  SRP54          SRP54-type protein, GTPase domain
      0.025   13.5   0.3      0.052   12.5   0.1    1.5  2  MeaB           Methylmalonyl Co-A mutase-associated GTPase Me
      0.033   13.5   0.0      0.054   12.8   0.0    1.2  1  VirC1          VirC1 protein
      0.088   12.3   0.1       0.63    9.5   0.1    1.9  2  CBP_BcsQ       Cellulose biosynthesis protein BcsQ
       0.35   10.9   0.1       0.35   10.9   0.1    2.5  3  Zn_Tnp_IS1595  Transposase zinc-ribbon domain
       0.94    9.1   2.8        5.2    6.7   0.0    2.3  2  zf_UBZ         Ubiquitin-Binding Zinc Finger


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 !  306.7   0.3   8.5e-95   1.1e-91       2     218 ..      28     245 ..      27     272 .. 0.96

  Alignments for each domain:
  == domain 1  score: 306.7 bits;  conditional E-value: 8.5e-95
                           ParA   2 vkkviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqsekkliPveakgikvmSigfl 81 
                                    +k++++v SgKGGVGKStva+ lA+ Lak+g++vgllDaDi+Gp+ip+llg+e+e+ ++  ++++P ++ +ikv+S++++
  gi|116753907|ref|YP_843025.1|  28 IKRKMLVGSGKGGVGKSTVAAYLAIWLAKRGYSVGLLDADITGPNIPKLLGIEDERLTVGPDGIHPATVGNIKVVSMALI 107
                                    899*********************************************************99****************** PP

                           ParA  82 lesedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqkl.plagaviVttpqevaladvkkaiemf 160
                                    l+++ ++vvwrGpmk++aikq+l+dv wg+lDyLi+DlPPGt+De ++++q + +l+g+v+Vttpq+va++d+ k+i+mf
  gi|116753907|ref|YP_843025.1| 108 LPTSGTSVVWRGPMKMAAIKQFLSDVCWGDLDYLIVDLPPGTSDEPISLVQLIpDLDGVVVVTTPQDVAIIDTLKSIDMF 187
                                    *****************************************************889************************ PP

                           ParA 161 kkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeirea 218
                                    +k++v+++G+veNmsg+vcp+cg+++e fg+g+ge  a++++v++lg++p+dpe++  
  gi|116753907|ref|YP_843025.1| 188 RKMNVRIIGMVENMSGLVCPHCGKRVEAFGSGNGEVHARDMDVDFLGSVPVDPELSML 245
                                    *****************************************************99765 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 !   49.0   0.0   4.5e-16   5.8e-13       3      83 ..      34     201 ..      32     248 .. 0.84

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 4.5e-16
                                    EEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH............................ CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................ RF
                           CbiA   3 iastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep............................ 54 
                                    + s+kGGvGK+t+aa La+ la+rg+ V l+DaD  ++n   l g e ++ +                            
  gi|116753907|ref|YP_843025.1|  34 VGSGKGGVGKSTVAAYLAIWLAKRGYSVGLLDADITGPNIPKLLGIEDERLTvgpdgihpatvgnikvvsmalilptsgt 113
                                    779************************************99555555555559999999*****9999999999999999 PP

                                    ..............................................................CCHCCCHHHHHHCHCHHH CS
                                    ..............................................................xxxxxxxxxxxxxxxxxx RF
                           CbiA  55 ..............................................................dlkrllellealgkkkal 72 
                                                                                                   ++  l+++ +++k    
  gi|116753907|ref|YP_843025.1| 114 svvwrgpmkmaaikqflsdvcwgdldylivdlppgtsdepislvqlipdldgvvvvttpqdvAIIDTLKSIDMFRK---M 190
                                    9999999999999999999999999999999999999999999999999999999999997733333444444433...3 PP

                                    H..EEEEEEEE CS
                                    xxxxxxxxxxx RF
                           CbiA  73 llkiagvvlnr 83 
                                    +++i+g+v n+
  gi|116753907|ref|YP_843025.1| 191 NVRIIGMVENM 201
                                    36777777665 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.3     3e-09   3.8e-06       2      38 ..      31      67 ..      30      72 .. 0.89
   2 ?    2.5   0.0     0.051        66     122     186 ..     135     200 ..     120     207 .. 0.54

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 3e-09
                                   EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                    ArsA_ATPase  2 kvilvgGKGGVGKttvsaatavklsekgkkvllistD 38
                                   k+++ +GKGGVGK+tv+a +a++l++ g++v l+  D
  gi|116753907|ref|YP_843025.1| 31 KMLVGSGKGGVGKSTVAAYLAIWLAKRGYSVGLLDAD 67
                                   567779***********************99877665 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.051
                                    CSSSSEEEEESBSCC..HTCGGGGHHHHHHHHHHHHHHHHHHHHHHHHHHCCCSHCHHHHHHHHHHH CS
                    ArsA_ATPase 122 eeeydvvvlDtaPTG..htlrllslpevleklleklvklkeklsplakqlvkllglggvsieealee 186
                                      + d++++D +P    + + l++l   l+ ++   +    ++ + +k++ ++++ ++v i  ++e+
  gi|116753907|ref|YP_843025.1| 135 WGDLDYLIVDLPPGTsdEPISLVQLIPDLDGVVVVTTPQDVAIIDTLKSI-DMFRKMNVRIIGMVEN 200
                                    56667777777763212456666666666666553333333444555544.5555555555555555 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   1.0   8.8e-09   1.1e-05       6      42 ..      34      70 ..      29     195 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 8.8e-09
                         AAA_31  6 ianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQa 42
                                   +   KGGvGK+T +  la +lak+g+ v l D+D  +
  gi|116753907|ref|YP_843025.1| 34 VGSGKGGVGKSTVAAYLAIWLAKRGYSVGLLDADITG 70
                                   5678******************************754 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.1     1e-08   1.3e-05       3      46 ..      32      75 ..      30     191 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1e-08
                                   EEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHH CS
                           MipZ  3 ivlgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlar 46
                                   + +g  kGG Gkst+a ++a+ L+k+G +v+ +d d+    + +
  gi|116753907|ref|YP_843025.1| 32 MLVGSGKGGVGKSTVAAYLAIWLAKRGYSVGLLDADITGPNIPK 75
                                   67999******************************987665555 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1      0.02        25       5      33 ..      34      62 ..      30      67 .. 0.81
   2 !   15.8   0.0   7.1e-06    0.0091     131     195 ..     166     243 ..     148     244 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.02
                         AAA_26  5 vtgtdtgvGKTvvslgLvralkrkgvkvg 33
                                   v +   gvGK++v++ L+  l ++g++vg
  gi|116753907|ref|YP_843025.1| 34 VGSGKGGVGKSTVAAYLAIWLAKRGYSVG 62
                                   4455568***********99988999987 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 7.1e-06
                         AAA_26 131 vilVargglgtinqllltiealrqknvrvlGvilNk....vrnp..envetlekksg.........ipvlGvvPylpdle 195
                                    v++V+++++ +i ++l +i+++r+ nvr++G++ N     +  p   ++ +++ +++         ++ lG+vP +p+l+
  gi|116753907|ref|YP_843025.1| 166 VVVVTTPQDVAIIDTLKSIDMFRKMNVRIIGMVENMsglvC--PhcGKRVEAFGSGNgevhardmdVDFLGSVPVDPELS 243
                                    8999999999***********************99855432..234344444444444777777779********99985 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 !   17.4   0.0   2.4e-06    0.0031       1      36 [.      37      72 ..      37      79 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.4e-06
                         CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGqse 36
                                   G+  +GKST+a++L+ +++++g+++ ++D+D+  ++
  gi|116753907|ref|YP_843025.1| 37 GKGGVGKSTVAAYLAIWLAKRGYSVGLLDADITGPN 72
                                   66789**************************97665 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.7e-05     0.021       8      54 ..      36      82 ..      30      86 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.7e-05
                                   ESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT--SSHH CS
                     APS_kinase  8 tGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLgfsee 54
                                   +G  g GKst+a  l+  L ++g+sv lLd d    ++ k Lg ++e
  gi|116753907|ref|YP_843025.1| 36 SGKGGVGKSTVAAYLAIWLAKRGYSVGLLDADITGPNIPKLLGIEDE 82
                                   68899***************************988888888887765 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   2.3e-05     0.029       5      39 ..      32      68 ..      29      73 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.3e-05
                                   EEE..ESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                          SRP54  5 llv..GlqGaGKTttlaKLaallkkegkkvllvaaDt 39
                                   +lv  G  G+GK t +a La +l k+g++v l  aD+
  gi|116753907|ref|YP_843025.1| 32 MLVgsGKGGVGKSTVAAYLAIWLAKRGYSVGLLDADI 68
                                   555115679***********************99996 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 ?   12.5   0.1   4.1e-05     0.052      32      68 ..      34      69 ..      22      75 .. 0.84
   2 ?   -2.7   0.0       1.8   2.3e+03     136     164 ..     191     219 ..     174     224 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.1e-05
                                   EEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE--- CS
                           MeaB 32 vGltGvPGaGkstlvealglelrrrGkrvavlavDPs 68
                                   vG  G  G+Gkst+   l++ l++rG+ v++l  D +
  gi|116753907|ref|YP_843025.1| 34 VG-SGKGGVGKSTVAAYLAIWLAKRGYSVGLLDADIT 69
                                   44.6899************************988865 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.8
                                    HHHHHTT-SEEEEEEESSTTTTTTT--CC CS
                           MeaB 136 evdvaevvdtfvvlllpeaGDelqgikkG 164
                                    +v ++ +v+ +  l+ p+ G  + ++  G
  gi|116753907|ref|YP_843025.1| 191 NVRIIGMVENMSGLVCPHCGKRVEAFGSG 219
                                    68899999999999999999888887666 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.2e-05     0.054       7      40 ..      35      68 ..      30      74 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.2e-05
                          VirC1  7 cslkGGaGkttalmglcsalasdgkrvalfeade 40
                                    s kGG Gk+t    l  +la +g  v+l++ad 
  gi|116753907|ref|YP_843025.1| 35 GSGKGGVGKSTVAAYLAIWLAKRGYSVGLLDADI 68
                                   688*****************************96 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1   0.00049      0.63      10      38 ..      38      66 ..      31      74 .. 0.91
   2 ?    0.4   0.0      0.29   3.7e+02     105     147 ..     126     172 ..     119     185 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00049
                       CBP_BcsQ 10 RGGvGttsllaaLawalhelgesvlviDl 38
                                   +GGvG+++++a La+ l + g+sv ++D+
  gi|116753907|ref|YP_843025.1| 38 KGGVGKSTVAAYLAIWLAKRGYSVGLLDA 66
                                   7***********************99996 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.29
                       CBP_BcsQ 105 llaalkelk.eqyrwillDlpagasaltrellal...adlvllvvep 147
                                    ++++l+ +  ++ +++++Dlp g+s+   +l++l    d v+ v++p
  gi|116753907|ref|YP_843025.1| 126 IKQFLSDVCwGDLDYLIVDLPPGTSDEPISLVQLipdLDGVVVVTTP 172
                                    55666666668899********9887655554431115666666666 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.5       8.2   1.1e+04      21      25 ..       9      13 ..       7      24 .. 0.66
   2 ?    0.8   0.0       0.4   5.1e+02       5      17 ..     125     137 ..     124     138 .. 0.87
   3 ?   10.9   0.1   0.00027      0.35      18      29 ..     203     215 ..     201     220 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 8.2
                  Zn_Tnp_IS1595 21 CPhCg 25
                                   C +C 
  gi|116753907|ref|YP_843025.1|  9 CDRCD 13
                                   44554 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.4
                  Zn_Tnp_IS1595   5 earalLealrWpn 17 
                                    +++++L +++W++
  gi|116753907|ref|YP_843025.1| 125 AIKQFLSDVCWGD 137
                                    6789*******96 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00027
                  Zn_Tnp_IS1595  18 gfvCPhCgsr.ka 29 
                                    g vCPhCg+r +a
  gi|116753907|ref|YP_843025.1| 203 GLVCPHCGKRvEA 215
                                    789*****99665 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   1.0      0.14   1.8e+02       4      11 ..       8      15 ..       6      22 .. 0.77
   2 ?    6.7   0.0    0.0041       5.2       3      13 ..     204     214 ..     202     217 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.14
                         zf_UBZ  4 lCerCgke 11
                                    C+rC+++
  gi|116753907|ref|YP_843025.1|  8 ACDRCDAR 15
                                   5****987 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0041
                         zf_UBZ   3 ylCerCgkeip 13 
                                     +C+ Cgk+++
  gi|116753907|ref|YP_843025.1| 204 LVCPHCGKRVE 214
                                    68******997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); 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: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2066.74
//
Query:       gi|116753908|ref|YP_843026.1|  [L=744]
Description: DNA topoisomerase I [Methanosaeta thermophila PT]
Scores for complete 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-122  407.3   0.0     1e-121  406.9   0.0    1.2  1  Topoisom_bac    DNA topoisomerase
    1.2e-15   57.6   0.1    3.8e-15   56.0   0.1    2.0  2  Toprim          Toprim domain
    6.4e-15   54.7   0.8    6.4e-15   54.7   0.8    2.8  3  zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
    1.6e-09   38.2   1.2    4.8e-09   36.7   0.2    2.4  2  HHH_5           Helix-hairpin-helix domain
     0.0065   16.7   0.0      0.014   15.6   0.0    1.5  1  DUF4332         Domain of unknown function (DUF4332)
  ------ inclusion threshold ------
      0.052   13.8   0.0       0.11   12.8   0.0    1.5  1  Cdd1            Pathogenicity locus


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 !  406.9   0.0  3.4e-125    1e-121       2     412 ..     150     546 ..     149     547 .. 0.91

  Alignments for each domain:
  == domain 1  score: 406.9 bits;  conditional E-value: 3.4e-125
                   Topoisom_bac   2 inenlvdaaeaRrelDwliGinlsrlltkklkg..kkvlsaGRVqtptLaliveRereienFvpeeyweveatlkkekke 79 
                                    +++nl++++eaR+++D+++G++l+r+++ +  +  k++ls+GRVq+ptLaliv+Re+eie+F+p++ywe+ a+l+k+   
  gi|116753908|ref|YP_843026.1| 150 VDFNLAASGEARQIIDLVWGAALTRFISITSGRlgKEFLSVGRVQSPTLALIVDREKEIESFQPKPYWEIYADLEKGI-- 227
                                    689*************************94444569************************************975444.. PP

                   Topoisom_bac  80 kekkkkkkkerikdkeeaeaileklkkkeakvesvekkekkkppplpfdtttLqkeasrklglsakktlsiaqkLYekag 159
                                       + +++k+ri++++e+++il++l++  a+v+s++k e++++pp+pfdtt++ ++as++ g++a+++++ia++LY++ g
  gi|116753908|ref|YP_843026.1| 228 ---RVRHSKSRIWTRDEVDRILNSLSD-VARVRSISKGERRDRPPTPFDTTSFISAASSI-GFTAANAMRIAESLYTN-G 301
                                    ...3689******************66.5******************************8.****************7.* PP

                   Topoisom_bac 160 litYpRTdstrlseeaelkailealakkygkeylefaekllkktkkksvvknkkveaHeAIrPteelpklkelsddekkl 239
                                    +i+YpRTd+t+++++ +l+++le+l++   + ++e a +l k +  + + ++  +++H++I+Pt +++++++l++d++k+
  gi|116753908|ref|YP_843026.1| 302 YISYPRTDNTVYPPSIDLRSLLEMLSSG--P-FREDALELMKGSI-TPTKGKRSTTDHPPIYPT-SVADKDDLKEDQWKI 376
                                    ***************77********985..3.4444444443222.224455566*********.666569********* PP

                   Topoisom_bac 240 YelIvrrflaslmkdakyeettvkleveeeefkasgktilekGfkkvykeekkeeeeeelpelkegeevkvkeveleekk 319
                                    Yel+vrrf+a+l+ ++++e+t++ +++++e f+a+g++il+ G++++y+++++ee+   lp+l ege +kv + e+ +k+
  gi|116753908|ref|YP_843026.1| 377 YELVVRRFFATLSGECVWETTSISFDIGDEVFRANGSRILDLGWRRYYPYSRAEEN--VLPPLREGEGLKVLSHEVLSKE 454
                                    ************************************************99999976..5********************* PP

                   Topoisom_bac 320 TkppkryteasLikamekagiGtpaTraeiieklvergYverkkkslvptelGkalvellekf.kdlvspelTaeleekL 398
                                    T+pp+r+ +++L+k+m++ g+Gt++Tr++ii+kl+ r Y++ +   ++pt+++ a+v++l++  + +++pe+T+ le+++
  gi|116753908|ref|YP_843026.1| 455 TQPPARFGQGRLVKLMDELGLGTKSTRHDIISKLYARAYIHGNP--IRPTKTAYAVVDTLQRHaPAITKPEMTRTLENDM 532
                                    ******************************************66..**************7777**************** PP

                   Topoisom_bac 399 deIaegkadakevl 412
                                     +Iae k+++ ev+
  gi|116753908|ref|YP_843026.1| 533 LKIAERKITKGEVI 546
                                    *********99998 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.0   0.1   1.3e-18   3.8e-15       2     103 .]       3     135 ..       2     135 .. 0.89
   2 ?   -3.9   0.0       5.7   1.7e+04      24      44 ..     342     360 ..     335     376 .. 0.71

  Alignments for each domain:
  == domain 1  score: 56.0 bits;  conditional E-value: 1.3e-18
                                    EEEESSHHHHHHHHHTHT................STEEEEEEESSSSEEEHS..............TTEEEEE....ECT CS
                         Toprim   2 lvivEgpsdaktiakalg................sgfqavtaslGhildlet..............efkpvye....eie 47 
                                    l+i+E+  +ak i+++l                  ++ +v+ ++Ghi+ l+                +          ++
  gi|116753908|ref|YP_843026.1|   3 LIIAEKHDAAKRISEILAgkkptvtkvsgidtfrFDDRVVIGLSGHIVGLDYpecynnwhkvdyrdLI----RaeivSRP 78 
                                    8****************99**************98899**************8777766666444444....16665999 PP

                                    TTHHHHHHHHHHHHHHSEEEEECSSSHHHHHHHHHHHHHHTHHHTT.TEEEEEESSS CS
                         Toprim  48 dkkkvlkalkelakradeiilatDpDreGeaiawellevlkellen.kigrvefsei 103
                                    +++ +++al++l ++ad++ +atD DreGe i+ e+l+ l+e +++ k  rv+fs i
  gi|116753908|ref|YP_843026.1|  79 TQERIVSALRKLGREADRVTIATDYDREGELIGVEALCILQEVNPSiKADRVRFSAI 135
                                    9****************************************88888999****9976 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 5.7
                                    EEEEESSSSEEEHSTTEEEEE CS
                         Toprim  24 avtaslGhildletefkpvye 44 
                                     +t+++G+  + ++  +p+y 
  gi|116753908|ref|YP_843026.1| 342 SITPTKGKRSTTDH--PPIYP 360
                                    68999999999998..66666 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 ?   -1.3   0.3      0.63   1.9e+03      27      32 ..      54      59 ..      53      63 .. 0.81
   2 !   54.7   0.8   2.1e-18   6.4e-15       1      38 [.     581     619 ..     581     620 .. 0.96
   3 ?    0.2   0.1      0.22   6.5e+02       4      17 ..     652     666 ..     650     668 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.63
                                   T.T--- CS
                 zf-C4_Topoisom 27 YPeCkf 32
                                   YPeC +
  gi|116753908|ref|YP_843026.1| 54 YPECYN 59
                                   9***76 PP

  == domain 2  score: 54.7 bits;  conditional E-value: 2.1e-18
                                    -EE-SSS--EEEEEE-SSS.EEEEESST.T----EEB-G CS
                 zf-C4_Topoisom   1 vekCPkCggdLvlkrgkkG.kFvGCsnYPeCkftkklkk 38 
                                    v+kC  Cg+dL+++rg++G +FvGCs YPeC+ft +l++
  gi|116753908|ref|YP_843026.1| 581 VGKCRLCGSDLIIRRGRRGaRFVGCSGYPECRFTLPLPR 619
                                    589*********************************986 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.22
                                    -SSS-.-EEEEEE-S CS
                 zf-C4_Topoisom   4 CPkCg.gdLvlkrgk 17 
                                    CP C+ ++ + k+g 
  gi|116753908|ref|YP_843026.1| 652 CPYCNfNNWQAKKGS 666
                                    999998888888876 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       3.3   9.8e+03      26      43 ..      15      32 ..      10      33 .. 0.67
   2 !   36.7   0.2   1.6e-12   4.8e-09       3      56 ..     673     726 ..     672     727 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.3
                                   HHHHHHS-HHHHHTSTTS CS
                          HHH_5 26 vedlaaadveeLakipGi 43
                                   + +++a  + +++k+ Gi
  gi|116753908|ref|YP_843026.1| 15 ISEILAGKKPTVTKVSGI 32
                                   556666777777777777 PP

  == domain 2  score: 36.7 bits;  conditional E-value: 1.6e-12
                                    HHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHHH CS
                          HHH_5   3 eLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilelk 56 
                                    eL ++sGiGpk   +l saGi+++e+l++ d++ +++ +Gi+ k+  ++ ++++
  gi|116753908|ref|YP_843026.1| 673 ELDDISGIGPKSRERLESAGIKTLEALVSTDPASISESTGISIKKIISWQESAR 726
                                    699*******************************************99999987 PP

>> DUF4332  Domain of unknown function (DUF4332)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   4.7e-06     0.014       2      54 ..     679     726 ..     678     733 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.7e-06
                        DUF4332   2 gigkeeaekLkkaGikttedLlelgktekgrkalaeklgisernvlklanlAd 54 
                                    gig++ +e+L++aGikt e+L++  + ++++     ++gis +++ ++++ A+
  gi|116753908|ref|YP_843026.1| 679 GIGPKSRERLESAGIKTLEALVSTDPASISE-----STGISIKKIISWQESAR 726
                                    799*******************997777777.....*************9987 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.5e-05      0.11       3      43 ..     669     709 ..     667     716 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.5e-05
                           Cdd1   3 kalkelqdiPniGkalaedlvelGirsveelkgedpeelye 43 
                                    +++ el di +iG++  e l + Gi+++e l   dp+++ e
  gi|116753908|ref|YP_843026.1| 669 QRMPELDDISGIGPKSRERLESAGIKTLEALVSTDPASISE 709
                                    67889*******************************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (744 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.29s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 4790.53
//
Query:       gi|116753909|ref|YP_843027.1|  [L=437]
Description: peptidase U62, modulator of DNA gyrase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.4e-65  221.2   0.4    3.1e-65  220.8   0.4    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 !  220.8   0.4   1.7e-69   3.1e-65       3     279 .]       5     292 ..       3     292 .. 0.91

  Alignments for each domain:
  == domain 1  score: 220.8 bits;  conditional E-value: 1.7e-69
                                    EEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEEEEETTEEEEEE...ESSHHHHHHHHHHHHHHCCS---TT-....... CS
                      PmbA_TldD   3 evrleesestsvrfengevetnsssedsglgvrvikggrlgfastldtsdealeeaveraveiaklapedpea....... 75 
                                    + r++++++ s+ ++n++ve++s+s+ +g++vr++++g++gf+ +++++  +le+ +era  ia+  +  +         
  gi|116753909|ref|YP_843027.1|   5 DTRIVRGRRISIVVDNSKVEEISESIFQGVAVRALVDGAWGFVRSDSIE--DLERSIERACGIARAIGGREILnlaeser 82 
                                    6799**************************************9988888..*************999999999******* PP

                                    ............GGS-HHHHHHHHHHHHHH.CHCSTTEEEEEEEEEE......EEE.EEEEEEETTSEEEEEEEEEEEEE CS
                      PmbA_TldD  76 ............eevsaeekielleelekalrsadpkienskgarisgvsaslsaskeeklianSeGldveqtrtrvsls 143
                                                ++vs eek++l++e+e+a  ++ p        +is++++++++  +e+ + +S+G++++++ tr++++
  gi|116753909|ref|YP_843027.1|  83 glscrvpvkkdpSSVSLEEKVDLVREIERA--ARLP--------GISSTRVFYTDILTETEYSSSDGASLRSSVTRTGFG 152
                                    ****************************98..4455........99********************************** PP

                                    EEEEE...S..TCSETEEEEEEEE.......SSHHHS..SSHHHHHHHHHHCTTT-B---SEEEEEEE-HHHHHHHHHGH CS
                      PmbA_TldD 144 lsvia.d.d..ggsgdgmgggsgy.......edleeedleeiaeeaaekalasleakplppgkypVvlspeavgsllhea 212
                                    +s++a + +  +       + s+        e +e+ed+ e+a++aa++al++l+a+ ++ g++pVvl+ e  g+++hea
  gi|116753909|ref|YP_843027.1| 153 ISAVAmRsGllQ-------SSSEIragvcglELIEREDPFELARRAARTALDLLDARVPEGGRFPVVLDQELGGVFIHEA 225
                                    *****6633421.......1222244456655555688888****************99999****************** PP

                                    HHHHTBHHHHHTT--TTTT-TTSB-S-TT--EEEETT-.....-SB-TTSBB---EEEEETTEE--- CS
                      PmbA_TldD 213 vghaleadavlegrSflkdklGekvaselltivddptsgglgsypfDdEGvptqrtvlIenGvLkny 279
                                    vgha+e+d vleg S+l++++Ge+++sel+t+ ddp   ++g ypfDdEG ++++tvl+enG+L++y
  gi|116753909|ref|YP_843027.1| 226 VGHAAEGDIVLEGGSILQGRVGEQIGSELVTVKDDPSLMHYGHYPFDDEGSAARETVLVENGILRSY 292
                                    *****************88*****************659**************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       243  (0.0135535); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); 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: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 3175.70
//
Query:       gi|116753910|ref|YP_843028.1|  [L=635]
Description: ATP-dependent protease Lon [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-35  122.0   3.3    3.6e-35  121.4   3.3    1.3  1  Lon_C            Lon protease (S16) C-terminal proteolytic do
    2.9e-29  102.2   0.0    3.8e-22   78.8   0.0    2.4  2  AAA_32           AAA domain
    2.1e-15   56.7   0.1      7e-09   35.4   0.0    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    2.3e-14   53.5   0.0    3.1e-08   33.5   0.0    2.5  2  Sigma54_activat  Sigma-54 interaction domain
    1.1e-09   38.1   0.7    2.2e-09   37.2   0.7    1.5  1  ChlI             Subunit ChlI of Mg-chelatase
      3e-09   37.0   0.0     0.0047   16.9   0.0    2.9  2  AAA_5            AAA domain (dynein-related subfamily)
    2.3e-07   30.1   0.2     0.0049   16.0   0.0    2.7  3  MCM              MCM P-loop domain
    2.2e-05   24.7   0.0      0.002   18.4   0.0    2.7  2  AAA_22           AAA domain
    2.9e-05   24.5   0.0       0.22   11.9   0.0    2.9  2  AAA              ATPase family associated with various cellul
    0.00018   21.3   0.0      0.054   13.2   0.0    2.5  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00037   20.6   0.0       0.37   10.9   0.0    2.6  2  Sigma54_activ_2  Sigma-54 interaction domain
    0.00051   20.4   0.1     0.0058   17.0   0.1    2.4  1  AAA_19           AAA domain
    0.00076   19.0   0.0     0.0046   16.5   0.0    2.0  2  AAA_7            P-loop containing dynein motor region
    0.00084   18.6   0.0        1.4    8.0   0.0    2.4  2  TIP49            TIP49 P-loop domain
     0.0042   16.9   0.1        4.2    7.2   0.0    3.0  3  AAA_3            ATPase family associated with various cellul
     0.0069   16.8   0.0       0.48   10.8   0.0    2.8  2  AAA_16           AAA ATPase domain
  ------ inclusion threshold ------
      0.015   15.0   0.0      0.084   12.6   0.0    2.1  2  AAA_30           AAA domain
      0.045   13.6   2.9       0.17   11.7   0.3    2.8  3  Birna_VP4        Birnavirus VP4 protein
      0.052   14.1   0.0       0.13   12.8   0.0    1.7  1  AAA_18           AAA domain
      0.074   12.2   0.0       0.21   10.7   0.0    1.7  2  DUF815           Protein of unknown function (DUF815)
       0.11   13.0   0.0       0.32   11.5   0.0    1.8  1  ABC_tran         ABC transporter
       0.12   12.2   0.7        0.3   10.9   0.7    1.6  1  DUF4118          Domain of unknown function (DUF4118)
       0.13   12.4   0.0         11    6.2   0.0    2.5  2  MMR_HSR1         50S ribosome-binding GTPase


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 !  121.4   3.3   4.6e-38   3.6e-35       5     203 ..     404     599 ..     400     601 .. 0.87

  Alignments for each domain:
  == domain 1  score: 121.4 bits;  conditional E-value: 4.6e-38
                                    TTTHHHH-S-SS--SSSSS--BSSEEEEEEEETTEEEEEEEEEEEES....S-S-EEEEES--HHHHHHHHHHHHHHTSS CS
                          Lon_C   5 keleellGkkrfrseeaekedqvGvvtGlawtevGGdlltieavllp....gkgklkltGklgdvmkesaqaalsyvrsr 80 
                                    ++ +++l +++  s  +++ d+vG v Gla     G +l i a ++p     +g+++ tG+l ++ ke+++   +++++ 
  gi|116753910|ref|YP_843028.1| 404 QMADRYLERRKEYSMYKSSGDEVGRVNGLAVIGDSGIVLPIMAEVTPaqskEEGRVIATGRLQEIAKEAVTNVSALIKK- 482
                                    555667766665556667899********************99888722224689*************88776666654. PP

                                    -GGGSS-SS-TTT-EEEEEE-S-B-GGGGGGGHHHHHHHHHHHHTS--B-TTBEE--EE-TT-BEE--S-HHHHHHHHHH CS
                          Lon_C  81 aeelgidkevfekkdihihvPeGavPkdGPsaGvtlatalvslltgkkvrkdvamtGeitLrGrvlpiGGlkekllaakr 160
                                       l+ +    ++kd+hi +       +G sa +++ata+vs+l g++v++ vamtG +++rG vlp+GG+ +k+ aa +
  gi|116753910|ref|YP_843028.1| 483 ---LQGE--DITTKDVHIQFIGTYEGVEGDSASISIATAVVSALEGIPVKQSVAMTGSLSVRGDVLPVGGVTQKIEAAAQ 557
                                    ...4433..35689******9999999***************************************************** PP

                                    TT-SBEEEEGGGGGGTTTS-HHHHTS-B--EESBHHHHHHHHB CS
                          Lon_C 161 agikkvilPkenekdlediPeevreeleiilveevdevlkaal 203
                                    agik+v++Pk+n  d+  + e++r+++eii+v++++ev++  l
  gi|116753910|ref|YP_843028.1| 558 AGIKTVLIPKSNMGDVL-VDESIRDKIEIIPVSNISEVFEYSL 599
                                    ***************95.99*******************9887 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   1.8e-07   0.00014       7      90 ..      29     107 ..      25     122 .. 0.83
   2 !   78.8   0.0   4.8e-25   3.8e-22     280     509 ..     168     396 ..     162     400 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.8e-07
                         AAA_32   7 leeiigqeRAvealefglkikkkgYNifvlGesgtGrttlvkrlleeiakkeptpdDwcYvnnfdnpeePkalsLpaGkG 86 
                                    ++++igqe Ave ++ + +   +  ++ ++G++gtG+++l k + e      +  +D++  +n +++++P++  +paG+G
  gi|116753910|ref|YP_843028.1|  29 IDQVIGQEEAVEVIKKAAH---QRRHVMLIGSPGTGKSMLGKAMSELL-PV-EELQDILVYHNPEDNNNPRIRVVPAGRG 103
                                    5899***********8865...5569***********98877766554.44.446788888******************* PP

                         AAA_32  87 kelk 90 
                                    ++  
  gi|116753910|ref|YP_843028.1| 104 RQIV 107
                                    *975 PP

  == domain 2  score: 78.8 bits;  conditional E-value: 4.8e-25
                         AAA_32 280 vnvlvdnsetegaPVvvednptyanLfGkieyesemg..alvtdftlIkaGaLhkAnGGyLildaedlLeeplaWeaLkr 357
                                     ++lvdns ++ aP v  +  +   L+G + ++  +     +  +++++ Ga+h+A+ G+L +d  + L+ + + ++L  
  gi|116753910|ref|YP_843028.1| 168 PKLLVDNSGKKTAPFVDATGAHAGALLGDVRHDPFQSggLETPSHERVECGAIHRAHKGVLFIDEINTLRLE-SQQSLLT 246
                                    689****************************99754333555689**********************99865.6799*** PP

                         AAA_32 358 aLrskeikiesleeqlglistvsLkPepipldvKViLiGsrelYylLseyDpdfkklFkvkadFddemerteenekkyar 437
                                    aL+++   i       + +s    + ep+p++   ++ G+ +  + ++ +     k +  ++ + d+me t en +k++r
  gi|116753910|ref|YP_843028.1| 247 ALQEGMYPITGQ---SERSSGALVRTEPVPCSFIMVVAGNLDAVQGMHPALRSRIKGYGYEVYMRDTMEDTVENRDKLIR 323
                                    *********953...446788899******************99999999999999999********************* PP

                         AAA_32 438 fias.ivkkekllpfdrsavarlieyssrlaedqeklstrfseiadllrEAdywakkegaevveaehVekAle 509
                                    f+a+ +v++ k+++f+r+ava++i+++ r ++++ +l++ ++++  l+r A  +a++ega + ea+hV +A +
  gi|116753910|ref|YP_843028.1| 324 FVAQeVVRDGKIPHFTRDAVAEIIREAKRRSGRKGHLTLMLRDLGGLIRVAGDIARSEGAPLTEARHVIEAKK 396
                                    **863789999*********************************************************99965 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.0     9e-12     7e-09       3      55 ..      30      82 ..      28      90 .. 0.93
   2 !   18.9   0.0   9.9e-07   0.00077      96     139 ..     214     257 ..     205     300 .. 0.76

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 9e-12
                   Mg_chelatase  3 kdvkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsllpplseeeal 55
                                    +v+Gqeea ++++ aa  + +++l+G+pG+GK+ml k++++llp  + +++l
  gi|116753910|ref|YP_843028.1| 30 DQVIGQEEAVEVIKKAAHQRRHVMLIGSPGTGKSMLGKAMSELLPVEELQDIL 82
                                   68*******************************************98877766 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 9.9e-07
                   Mg_chelatase  96 kpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisr 139
                                    +++ G+i +ah+GvLf+DE+  ++ +  ++L + l++g   i+ 
  gi|116753910|ref|YP_843028.1| 214 RVECGAIHRAHKGVLFIDEINTLRLESQQSLLTALQEGMYPITG 257
                                    6788*****************99999999999888888776653 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   3.6e-06    0.0028       9      45 ..      36      72 ..      28      92 .. 0.86
   2 !   33.5   0.0   3.9e-11   3.1e-08      86     130 ..     215     261 ..     166     269 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.6e-06
                                   HHHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHH CS
                Sigma54_activat  9 kelleqikkvaktdlsvlitGesGtGKellaraihea 45
                                   +e++e ikk+a+++ +v++ G  GtGK++l +a+ e 
  gi|116753910|ref|YP_843028.1| 36 EEAVEVIKKAAHQRRHVMLIGSPGTGKSMLGKAMSEL 72
                                   67899***************************99875 PP

  == domain 2  score: 33.5 bits;  conditional E-value: 3.9e-11
                                    E..HHHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHSEEESBTSSSE CS
                Sigma54_activat  86 k..GlfekadgGtlfLDeigelplelQekLlrvlqegevervGsske 130
                                       G++++a++G+lf+Dei++l le Q+ Ll++lqeg +   G+s+ 
  gi|116753910|ref|YP_843028.1| 215 VecGAIHRAHKGVLFIDEINTLRLESQQSLLTALQEGMYPITGQSER 261
                                    335***********************************999888764 PP

>> ChlI  Subunit ChlI of Mg-chelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   0.7   2.8e-12   2.2e-09      14     121 .]     461     569 ..     447     569 .. 0.94

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 2.8e-12
                           ChlI  14 ivGlpdtavkeskervrsalkn.sgfefpakkitvnLaPadlkkeGsafDLpiAigilaaleqieaeeetlflGeLsldG 92 
                                     +G +++  ke+   v + +k+ +g ++ +k + +         eG + +++iA ++++ale i++++++ + G Ls  G
  gi|116753910|ref|YP_843028.1| 461 ATGRLQEIAKEAVTNVSALIKKlQGEDITTKDVHIQFIGTYEGVEGDSASISIATAVVSALEGIPVKQSVAMTGSLSVRG 540
                                    568889999************98899****************************************************** PP

                           ChlI  93 slrpvkgvlpialaakkegikkvivpken 121
                                    ++ pv gv++ + aa+++gik+v++pk+n
  gi|116753910|ref|YP_843028.1| 541 DVLPVGGVTQKIEAAAQAGIKTVLIPKSN 569
                                    **************************998 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0     6e-06    0.0047       1      24 [.      51      75 ..      51      97 .. 0.84
   2 !   16.8   0.0   6.4e-06     0.005      65     137 ..     224     297 ..     193     298 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6e-06
                                   EEEEE--SSSSHHHHHHHGGGGB.S CS
                          AAA_5  1 dvlLvGppGtgKselaerlaaal.n 24
                                   +v+L+G pGtgKs+l + ++++l  
  gi|116753910|ref|YP_843028.1| 51 HVMLIGSPGTGKSMLGKAMSELLpV 75
                                   79********************952 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 6.4e-06
                                    G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE---..........-EEEEEESS--.-TT-TTHHHHTT CS
                          AAA_5  65 egeilvlDEveraesevlnsLlslleerrllleeggelvkaknddller....frviatanpldrslnelspalrsR 137
                                    ++ +l++DE+++++ e ++sLl+ l e  +++    e+ + +   ++e+    f  + ++n     ++ + palrsR
  gi|116753910|ref|YP_843028.1| 224 HKGVLFIDEINTLRLESQQSLLTALQEGMYPITGQSERSSGALV-RTEPvpcsFIMVVAGNLDA--VQGMHPALRSR 297
                                    688***************************97777777766663.3444898766666666655..88889*****9 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   0.00019      0.15      41      83 ..      33      75 ..      10      81 .. 0.77
   2 !   16.0   0.0   6.3e-06    0.0049     111     147 ..     214     250 ..     175     257 .. 0.80
   3 ?   -3.5   0.0       5.7   4.5e+03      19      50 ..     476     507 ..     465     517 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00019
                                   H---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHHHHSSS CS
                            MCM 41 fggvkkkledktklrgdinvllvgdpgtaKsqlLkyveklapr 83
                                   +g  +  +  k+    + +v+l+g pgt+Ks l k++++l+p 
  gi|116753910|ref|YP_843028.1| 33 IGQEEAVEVIKKAAHQRRHVMLIGSPGTGKSMLGKAMSELLPV 75
                                   444444444455577889***************9999999886 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 6.3e-06
                                    EEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHH CS
                            MCM 111 vleaGalvladkGvcciDefdkmkeedrsalhEamEq 147
                                     +e+Ga+  a+kGv+ iDe++  + e +++l+ a+ +
  gi|116753910|ref|YP_843028.1| 214 RVECGAIHRAHKGVLFIDEINTLRLESQQSLLTALQE 250
                                    68****************************9999876 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 5.7
                                    HHHSSTTSSS-HHHHHHHHHHHH---EBBBSS CS
                            MCM  19 vksiapsiyghedvkkaillqlfggvkkkled 50 
                                    v+++++++ g++   k + +q +g+++  + d
  gi|116753910|ref|YP_843028.1| 476 VSALIKKLQGEDITTKDVHIQFIGTYEGVEGD 507
                                    35567778888888888888888877766555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   2.6e-06     0.002       4      38 ..      48      90 ..      44     121 .. 0.81
   2 ?    3.0   0.0      0.14   1.1e+02      86     109 ..     220     245 ..     208     262 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.6e-06
                         AAA_22  4 tagilvvtGesGtGKTtllrrlleqldeeakaee........e 38
                                   ++++++++G +GtGK++l + + e l+ e+ ++         +
  gi|116753910|ref|YP_843028.1| 48 QRRHVMLIGSPGTGKSMLGKAMSELLPVEELQDIlvyhnpedN 90
                                   899***********************99988877777666553 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.14
                         AAA_22  86 lraravielliiDEaqhlr..s.eeal 109
                                    ++++++ ++l iDE+  lr  s + +l
  gi|116753910|ref|YP_843028.1| 220 IHRAHK-GVLFIDEINTLRleSqQSLL 245
                                    677778.9**********776323333 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 !   11.9   0.0   0.00028      0.22       1      22 [.      52      73 ..      52     116 .. 0.89
   2 !    9.3   0.0    0.0018       1.4      58     124 ..     224     298 ..     211     302 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00028
                                   EEEESSTTSSHHHHHHHHHHHH CS
                            AAA  1 vllyGppGtGKTllakavakel 22
                                   v+l+G pGtGK++l ka+ + l
  gi|116753910|ref|YP_843028.1| 52 VMLIGSPGTGKSMLGKAMSELL 73
                                   68**************987765 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0018
                                    TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS...........SSTEEEEEEESS..GGGSTHHHHSTTS CS
                            AAA  58 kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk...........eskvivigatnr..pdkldpallrgRf 124
                                    ++ +lfiDEi  l  ++   +++  + +++ +++   + +++              +i+++a+n   ++ + pal+ +R+
  gi|116753910|ref|YP_843028.1| 224 HKGVLFIDEINTLRLES---QQSLLTALQEGMYPITGQSERSsgalvrtepvpC-SFIMVVAGNLdaVQGMHPALR-SRI 298
                                    359**********7777...4555555555555555555555999999999954.599999999999999999999.887 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0     7e-05     0.054       6      56 ..      29      72 ..      24      79 .. 0.78
   2 ?    5.3   0.0     0.019        15      84     111 ..     224     251 ..     217     282 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7e-05
                         RuvB_N  6 leeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiake 56
                                   +++ igqe+    ++++ +aa++r+    hv+l+G+PG Gk+ l k +++ 
  gi|116753910|ref|YP_843028.1| 29 IDQVIGQEEA---VEVIKKAAHQRR----HVMLIGSPGTGKSMLGKAMSEL 72
                                   5677888754...567778888886....9*************99988765 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.019
                         RuvB_N  84 ekdvlfideihrlsraveevlysamedf 111
                                    +k vlfidei  l+ + ++ l +a+++ 
  gi|116753910|ref|YP_843028.1| 224 HKGVLFIDEINTLRLESQQSLLTALQEG 251
                                    578***********99999999999765 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 !    6.9   0.0    0.0083       6.4      13      43 ..      41      71 ..      36      90 .. 0.87
   2 !   10.9   0.0   0.00048      0.37      41      96 ..     171     259 ..     163     288 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0083
                                   HHHHHHT-SS-EEEEEETT--HHHHHHCC-- CS
                Sigma54_activ_2 13 rLeqaaqsklpvfltGekGsgkelvArlLhk 43
                                    +++aa++   v l+G +G+gk++  +++++
  gi|116753910|ref|YP_843028.1| 41 VIKKAAHQRRHVMLIGSPGTGKSMLGKAMSE 71
                                   58999*******************9998876 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00048
                                    C--TTS-EE--SSTTHHHH-H.........................HHHHHHTTTSEEEEEE-TT--HHHHHHHHHHHHH CS
                Sigma54_activ_2  41 Lhknsgpwleifvverlaklp.........................ldlleqakggtLylkdiadlskaeqkeLlellak 95 
                                    L +nsg++ ++fv +++a++                             + +a+ g+L++ +i+ l  + q+ Ll +l++
  gi|116753910|ref|YP_843028.1| 171 LVDNSGKKTAPFVDATGAHAGallgdvrhdpfqsggletpsherveCGAIHRAHKGVLFIDEINTLRLESQQSLLTALQE 250
                                    55555555555555555553334445555555555555444444334456679*************************99 PP

                                    ........H CS
                Sigma54_activ_2  96 ........a 96 
                                            +
  gi|116753910|ref|YP_843028.1| 251 gmypitgqS 259
                                    555555553 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   7.5e-06    0.0058       6     126 ..      44     249 ..      35     256 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 7.5e-06
                         AAA_19   6 e.alkekvllvtaGpGtGKTrvlkhivallvelggvkp..........eeillvaftgrAakelrerlaalgaeatTiHr 74 
                                    + a++++++++++ pGtGK+ + k++ +ll  ++ ++           ++ + v ++gr  + +     ++ ++ +T   
  gi|116753910|ref|YP_843028.1|  44 KaAHQRRHVMLIGSPGTGKSMLGKAMSELLPVEELQDIlvyhnpednnNPRIRVVPAGRGRQIVDAHKMEARKKVQTRNM 123
                                    347999*************9888777777766664444778888888877778888888877777666555666666665 PP

                         AAA_19  75 lal............................................................................. 77 
                                    + +                                                                             
  gi|116753910|ref|YP_843028.1| 124 FFMlivmglivyayytgqllfgiiaaaliflsmrylipkedvfipkllvdnsgkktapfvdatgahagallgdvrhdpfq 203
                                    54477778888888888888888888888888888888888888888877777777777666666666666664444422 PP

                         AAA_19  78 ...ldfddlltealelle.....eaeeekklqeee.llivDEfqdvd.elqyrLlkall 126
                                       l             e     + e     ++++ +l++DE+  +  e q++Ll al 
  gi|116753910|ref|YP_843028.1| 204 sggL-------------EtpsheRVECGAIHRAHKgVLFIDEINTLRlESQQSLLTALQ 249
                                    2221.............244443222223334455799*********999****99997 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   5.9e-06    0.0046      25      63 ..      41      79 ..      27      90 .. 0.87
   2 ?   -0.8   0.0       1.2   9.2e+02     100     115 ..     224     239 ..     220     245 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.9e-06
                          AAA_7 25 llelllknkkpvllvGptGtGKtviikdllkkldkekyl 63
                                   ++++  +++++v+l+G+ GtGK+++ k + + l+ e+++
  gi|116753910|ref|YP_843028.1| 41 VIKKAAHQRRHVMLIGSPGTGKSMLGKAMSELLPVEELQ 79
                                   6788999******************99999988877766 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.2
                          AAA_7 100 kklvvFvDDlnmpake 115
                                    +k v+F+D++n  + e
  gi|116753910|ref|YP_843028.1| 224 HKGVLFIDEINTLRLE 239
                                    6789*******98777 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0     0.002       1.6      36      74 ..      38      73 ..      14      82 .. 0.76
   2 !    8.0   0.0    0.0018       1.4     279     309 ..     225     255 ..     217     266 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.002
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49 36 agvivelikekklaGravLlaGpsgtGktalaiaiskel 74
                                   a   ve+ik+     r v+l G +gtGk+ l  a+s+ l
  gi|116753910|ref|YP_843028.1| 38 A---VEVIKKAAHQRRHVMLIGSPGTGKSMLGKAMSELL 73
                                   2...678888888889***************99999765 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0018
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49 279 pGvlfiDevhmlDiecfsylnraleselaPi 309
                                    +GvlfiDe++ l +e+   l  al + + Pi
  gi|116753910|ref|YP_843028.1| 225 KGVLFIDEINTLRLESQQSLLTALQEGMYPI 255
                                    6*************************99998 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 ?    6.1   0.0     0.012       9.5       1      24 [.      51      74 ..      51      81 .. 0.90
   2 !    7.2   0.0    0.0054       4.2      64      97 ..     226     259 ..     211     281 .. 0.86
   3 ?   -1.6   0.0       2.9   2.3e+03      69      98 ..     466     495 ..     447     501 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.012
                          AAA_3  1 hvllegvPGlaktllvkalakald 24
                                   hv+l g PG++k +l ka+++ l 
  gi|116753910|ref|YP_843028.1| 51 HVMLIGSPGTGKSMLGKAMSELLP 74
                                   9******************99876 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0054
                          AAA_3  64 nllladeinrappktqsalleameerqvtveget 97 
                                     +l+ dein     +q +ll a++e    ++g++
  gi|116753910|ref|YP_843028.1| 226 GVLFIDEINTLRLESQQSLLTALQEGMYPITGQS 259
                                    68999********************988777765 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2.9
                          AAA_3  69 deinrappktqsalleameerqvtvegeth 98 
                                     ei + +    sal++ ++ +++t+++   
  gi|116753910|ref|YP_843028.1| 466 QEIAKEAVTNVSALIKKLQGEDITTKDVHI 495
                                    478888888889999999999999987665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00062      0.48      17      47 ..      43      72 ..      31     121 .. 0.68
   2 ?    2.7   0.0      0.19   1.5e+02     133     159 ..     222     249 ..     213     261 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00062
                         AAA_16 17 ervrsgrpelvllsGesGvGKsslvrellra 47
                                   ++++  + + v+l+G +G+GKs l ++  + 
  gi|116753910|ref|YP_843028.1| 43 KKAAH-QRRHVMLIGSPGTGKSMLGKAMSEL 72
                                   33333.3499************998777664 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.19
                         AAA_16 133 derplvlvlDdlqwadeaslql.laaLl 159
                                    ++++ vl++D++  ++ +s+q  l aL 
  gi|116753910|ref|YP_843028.1| 222 RAHKGVLFIDEINTLRLESQQSlLTALQ 249
                                    47778************99999555554 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00011     0.084       8      42 ..      40      73 ..      33      88 .. 0.74
   2 ?   -1.5   0.0       2.2   1.7e+03      87     114 ..     223     250 ..     188     253 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                         AAA_30  8 aavealltsgdrvavltGpAGtGKttalkalreaw 42
                                   ++++++++ ++r ++l G +GtGK+++ ka+ e++
  gi|116753910|ref|YP_843028.1| 40 EVIKKAAH-QRRHVMLIGSPGTGKSMLGKAMSELL 73
                                   33444554.556999************99999886 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.2
                         AAA_30  87 epgtllivDEagmvdtkqlaallkaaek 114
                                    +++ +l +DE+  +  ++ ++ll+a+++
  gi|116753910|ref|YP_843028.1| 223 AHKGVLFIDEINTLRLESQQSLLTALQE 250
                                    45689999**999999999999998876 PP

>> Birna_VP4  Birnavirus VP4 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.6   1.2e+03     212     245 ..      27      60 ..      11      69 .. 0.81
   2 ?    0.2   0.0      0.69   5.3e+02      13      30 ..     179     196 ..     175     209 .. 0.86
   3 ?   11.7   0.3   0.00021      0.17     180     238 ..     503     562 ..     440     582 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.6
                      Birna_VP4 212 evvddavgeiegvdl.klaaahelGlpLlGnsPGv 245
                                    +++d+ +g+ e v++ k aa ++  + L+G sPG 
  gi|116753910|ref|YP_843028.1|  27 SLIDQVIGQEEAVEViKKAAHQRRHVMLIG-SPGT 60 
                                    6788888999999986777777888999*9.9996 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.69
                      Birna_VP4  13 aaPligaideladallGD 30 
                                     aP++ a +  a allGD
  gi|116753910|ref|YP_843028.1| 179 TAPFVDATGAHAGALLGD 196
                                    79**************** PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00021
                      Birna_VP4 180 pvvGsssqLaiaaddllksdvdekvPi...vaftGevvdd.avgeiegvdlklaaahelGlpL 238
                                     v G s  ++i a  ++    +e++P+   va+tG++     v ++ gv  k+ aa + G++ 
  gi|116753910|ref|YP_843028.1| 503 GVEGDSASISI-ATAVVSA--LEGIPVkqsVAMTGSLSVRgDVLPVGGVTQKIEAAAQAGIKT 562
                                    57788888888.4455555..899**88889******66569*******************95 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00017      0.13       1      44 [.      52      94 ..      52     124 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00017
                         AAA_18  1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpe 44
                                   ++l G pG+GK+ l+k+ s++l  +++l+d++  +++++ ++p 
  gi|116753910|ref|YP_843028.1| 52 VMLIGSPGTGKSMLGKAMSELL-PVEELQDILVYHNPEDNNNPR 94
                                   789*****************95.377888888777777777776 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00027      0.21      52      82 ..      48      78 ..      26      87 .. 0.82
   2 ?   -3.3   0.0         5   3.9e+03      83     104 ..     464     485 ..     451     489 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00027
                         DUF815 52 pannvLLwGarGtGKSslvkallneyaeegL 82
                                   + ++v+L+G+ GtGKS l ka+ + +  e+L
  gi|116753910|ref|YP_843028.1| 48 QRRHVMLIGSPGTGKSMLGKAMSELLPVEEL 78
                                   4579*****************9877666655 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 5
                         DUF815  83 rlievekedlkelpklvellre 104
                                    rl e++ke ++++++l+++l+ 
  gi|116753910|ref|YP_843028.1| 464 RLQEIAKEAVTNVSALIKKLQG 485
                                    7889999999999999998876 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00041      0.32      10      38 ..      48      76 ..      40     121 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00041
                                   TTSEEEEEESTTSSHHHHHHHHTTSS--S CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran 10 egekvaivGenGaGKStLlkllagllkpt 38
                                   + + v ++G+ G+GKS L k++++ll  +
  gi|116753910|ref|YP_843028.1| 48 QRRHVMLIGSPGTGKSMLGKAMSELLPVE 76
                                   567899*****************998765 PP

>> DUF4118  Domain of unknown function (DUF4118)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.7   0.00038       0.3      26      61 ..     123     159 ..     113     162 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00038
                        DUF4118  26 nivllfllavllvallg.glgpgllaallsvllfnyf 61 
                                      ++l +++ ++ a+++  l+ g++aa+l +l   y+
  gi|116753910|ref|YP_843028.1| 123 MFFMLIVMGLIVYAYYTgQLLFGIIAAALIFLSMRYL 159
                                    4679999**********99*************99997 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.014        11       2      21 ..      52      71 ..      51     119 .. 0.85
   2 ?    3.5   0.0     0.095        74      15      59 ..     321     378 ..     320     421 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.014
                                   EEEEESTTSSHHHHHHHHHT CS
                       MMR_HSR1  2 vaivGrpNvGKStLinaltg 21
                                   v+++G p +GKS L +a+++
  gi|116753910|ref|YP_843028.1| 52 VMLIGSPGTGKSMLGKAMSE 71
                                   89************999875 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.095
                                    HHHHHHTSTEEESSSTTSSSSEEEEEEEETTEE........EEEEECGGCSS.....H CS
                       MMR_HSR1  15 LinaltgekaivsdkpgtTrdinegrvklkgke........ielvDtpGlie.....g 59 
                                    Li+   +e+++ +++p  Trd + + +++ +++        + l D+ Gli       
  gi|116753910|ref|YP_843028.1| 321 LIRFVAQEVVRDGKIPHFTRDAVAEIIREAKRRsgrkghltLMLRDLGGLIRvagdiA 378
                                    55666667888899********999998333223455555599******974221111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (635 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       921  (0.0513693); expected 358.6 (0.02)
Passed bias filter:                      757  (0.0422221); expected 358.6 (0.02)
Passed Vit filter:                       137  (0.00764125); 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: 0.74u 0.31s 00:00:01.05 Elapsed: 00:00:00.47
# Mc/sec: 4062.88
//
Query:       gi|116753911|ref|YP_843029.1|  [L=76]
Description: AsnC family transcriptional regulator [Methanosaeta thermophila PT]
Scores for complete 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   44.2   0.2    1.6e-11   44.0   0.2    1.0  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    0.00029   20.7   0.1    0.00031   20.7   0.1    1.1  1  GYD             GYD domain
    0.00063   19.7   0.5    0.00085   19.3   0.5    1.2  1  NapD            NapD protein
     0.0017   18.9   0.2      0.079   13.6   0.0    2.1  2  ACT_4           ACT domain


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.2   3.5e-15   1.6e-11       2      71 ..       7      72 ..       6      75 .. 0.96

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 3.5e-15
                                   EEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEE CS
                 AsnC_trans_reg  2 lvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsi 71
                                   +v++ pg+    + +  al++++ ++ +y+v G++d+++++ v  l  l+r++++ ++++++v+ t+t +
  gi|116753911|ref|YP_843029.1|  7 MVKVVPGQ---EKPVYNALRQVDGIKNVYHVFGEFDFVVIIEVDGLSTLNRLVDT-IREIENVTATQTVV 72
                                   69999999...*****************************************999.************76 PP

>> GYD  GYD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.1   6.8e-08   0.00031      27      79 ..      20      71 ..       4      75 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 6.8e-08
                            GYD 27 ealveslGgkleslyatlGeyDvvvivEapDdetaaalslalaasGtvrt.etl 79
                                    al ++++g ++++y ++Ge+D+vvi+E++  +t  +l  ++++  +v++ +t+
  gi|116753911|ref|YP_843029.1| 20 NAL-RQVDG-IKNVYHVFGEFDFVVIIEVDGLSTLNRLVDTIREIENVTAtQTV 71
                                   555.55544.689*********************99999999988888876665 PP

>> NapD  NapD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.5   1.9e-07   0.00085       7      70 ..       7      71 ..       1      74 [. 0.91

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.9e-07
                           NapD  7 vVqarperlaavkaalaalpgv.EvhasdeegklVvviEaesedeladtieaiealpgVlsaslv 70
                                    V++ p++ + v +al++++g+  v+++ +e   Vv+iE +   +l + +++i+++++V +++ v
  gi|116753911|ref|YP_843029.1|  7 MVKVVPGQEKPVYNALRQVDGIkNVYHVFGEFDFVVIIEVDGLSTLNRLVDTIREIENVTATQTV 71
                                   799******************9568999999*****************************99876 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.023     1e+02      65      79 ..      18      32 ..      14      32 .. 0.88
   2 !   13.6   0.0   1.8e-05     0.079      48      76 ..      38      66 ..      34      69 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.023
                          ACT_4 65 viakLraipgVisVe 79
                                   v ++Lr+++g+++V+
  gi|116753911|ref|YP_843029.1| 18 VYNALRQVDGIKNVY 32
                                   7899********996 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 1.8e-05
                          ACT_4 48 aeikitveVkdvehLsrviakLraipgVi 76
                                   +++ + +eV  ++ L+r+++ +r+i++V+
  gi|116753911|ref|YP_843029.1| 38 FDFVVIIEVDGLSTLNRLVDTIREIENVT 66
                                   677889**********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 533.99
//
Query:       gi|116753912|ref|YP_843030.1|  [L=613]
Description: DNA topoisomerase VI subunit B [Methanosaeta thermophila PT]
Scores for complete 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-63  212.5   0.0    4.6e-63  211.8   0.0    1.3  1  Topo-VIb_trans  Topoisomerase VI B subunit, transducer
    2.5e-32  111.4   0.0    9.4e-32  109.6   0.0    1.9  2  Top6b_C         Type 2 DNA topoisomerase 6 subunit B C-termin
    4.1e-10   40.2   0.0    8.2e-10   39.2   0.0    1.5  1  HATPase_c       Histidine kinase-, DNA gyrase B-, and HSP90-l
    1.2e-06   28.3   0.0    3.1e-06   27.0   0.0    1.6  1  HATPase_c_3     Histidine kinase-, DNA gyrase B-, and HSP90-l
     0.0016   17.3   0.0     0.0027   16.5   0.0    1.3  1  FbpA            Fibronectin-binding protein A N-terminus (Fbp
      0.004   17.1   0.0     0.0097   15.9   0.0    1.6  1  H2TH            Formamidopyrimidine-DNA glycosylase H2TH doma
  ------ inclusion threshold ------
      0.031   14.0   0.0      0.055   13.2   0.0    1.3  1  MAF_flag10      Protein of unknown function DUF115


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 !  211.8   0.0   1.8e-66   4.6e-63       1     159 []     309     472 ..     309     472 .. 0.98

  Alignments for each domain:
  == domain 1  score: 211.8 bits;  conditional E-value: 1.8e-66
                 Topo-VIb_trans   1 PstdclspigeeliekglkkelkpefvaavtrkpkvyeghpfivEvgiayGGelekeekaeilRfaNrvPLlydegadvi 80 
                                    P++dclspige+li++gl ke+k +f+a+v+r+++vy+g+pf+vE+gi++GGele++ +++ilRfaNrvPL+y++ga++i
  gi|116753912|ref|YP_843030.1| 309 PPADCLSPIGEDLIRSGLAKEYKLDFIATVSRPVSVYSGNPFVVEAGIGFGGELERSGRVDILRFANRVPLIYQQGACAI 388
                                    99****************************************************************************** PP

                 Topo-VIb_trans  81 tkavksinwkrYkleq.....pedpvvvlvhvastkvPfksegKeaiadveeiekeiklalqevarkLkkylskkekeke 155
                                    t+av+ ++wk+Y+l+q     p +p+v+lvhvast++Pf+se+K+aiad++ei +ei+lal+e++rkL+++l+ +e  +e
  gi|116753912|ref|YP_843030.1| 389 THAVEGVSWKSYGLDQpggglPVGPAVILVHVASTNIPFTSESKDAIADIPEILTEIDLALKEIGRKLRRFLALQETLSE 468
                                    ********************99***************************************************9999998 PP

                 Topo-VIb_trans 156 ekek 159
                                    ++ek
  gi|116753912|ref|YP_843030.1| 469 RREK 472
                                    8876 PP

>> Top6b_C  Type 2 DNA topoisomerase 6 subunit B C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.6   4.1e+03      45      71 ..     216     242 ..     205     243 .. 0.81
   2 !  109.6   0.0   3.7e-35   9.4e-32       3     114 .]     494     605 ..     493     605 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.6
                                    --EEE--EES-----------EEE-SS CS
                        Top6b_C  45 eefelheilpaeieeaspeakvvemdn 71 
                                    +  + +e+lp ++ e++p++  +e+++
  gi|116753912|ref|YP_843030.1| 216 RFERATELLPKRACEIKPHPAGIELGE 242
                                    4456799**************999985 PP

  == domain 2  score: 109.6 bits;  conditional E-value: 3.7e-35
                                    S---SHHHHHHHTT-EEEEEEE--SSS-.EEEEEEE---------EEE--EES-----------EEE-SSSEEE-EEE-- CS
                        Top6b_C   3 eepdidpvvArimgnvlvereveengdg.vevslkvkNfsdkkeefelheilpaeieeaspeakvvemdneydlkWelsv 81 
                                    e+pdi  vvArimgn+lv+r+++++ +g  +v ++++N+++ +++f+lheilp e+ee +p a+ v+m++ yd++W++ +
  gi|116753912|ref|YP_843030.1| 494 ERPDISMVVARIMGNILVRRDIKQE-NGrLRVCIEIENNTSAQRSFKLHEILPLEAEELDPPARRVDMGDRYDYQWRIAI 572
                                    79*********************99.777*************************************************** PP

                                    -TT-EEEE----SS-GGGS--B----------- CS
                        Top6b_C  82 sageskvleYsvdseaeeelsliveGveeekvT 114
                                    ++ge+ v++Y+++++ +   + +veG+e e+vT
  gi|116753912|ref|YP_843030.1| 573 RSGERMVIRYTIKNHLQRMPEAVVEGLEPEIVT 605
                                    *******************9***********99 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 !   39.2   0.0   3.2e-13   8.2e-10       4      89 ..      34     126 ..      31     178 .. 0.71

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 3.2e-13
                                    HHHHHHHHHHHHHHHHH...HSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCS.TTCH....HCSTCHTSTSSS CS
                      HATPase_c   4 krLrqiisnlvdNavkf...atkageieveikaseddlvisveDnGiGipkedlkklfe.kfsq....ddstkrggggtG 75 
                                    + L  +++++vdN++++   a+  ++i+v+ik++ + +++ veDnG+Gi +++++++f+  ++        ++rg++g G
  gi|116753912|ref|YP_843030.1|  34 RALITCVKEAVDNSLDAcedAGILPDIFVQIKRTGELYRVIVEDNGPGIVPSEIPRVFAmLLYGsrfhVLRQSRGQQGIG 113
                                    67899***********95444455599*****7668999****************9999744445877667778888888 PP

                                    HHHHHHHH.HHHHTT CS
                      HATPase_c  76 lGlsivkk.lvelmg 89 
                                    +++++  + l++  g
  gi|116753912|ref|YP_843030.1| 114 ISAAVLYSqLTS--G 126
                                    888887654544..3 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 !   27.0   0.0   1.2e-09   3.1e-06       6     102 ..      39     143 ..      35     170 .. 0.71

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 1.2e-09
                    HATPase_c_3   6 AlaelvdNsldAdaen.....vkievnknrgktgeivieDdGkGmseeelknalr.latsskeakrkstslGkkGiGlkl 79 
                                     + e vdNsldA         + +++++  g+  ++ +eD+G G+ ++e+ +++  l   s+  +  ++s+G+ GiG+  
  gi|116753912|ref|YP_843030.1|  39 CVKEAVDNSLDACEDAgilpdIFVQIKRT-GELYRVIVEDNGPGIVPSEIPRVFAmLLYGSRF-HVLRQSRGQQGIGISA 116
                                    589*********88888887755555553.5679******************77525555555.568**********888 PP

                    HATPase_c_3  80 Asl....slgkkltvitkkegesstlt 102
                                    A+l     +gk + ++++++ e+ +  
  gi|116753912|ref|YP_843030.1| 117 AVLysqlTSGKPARITSRTSPERPARY 143
                                    875222256788888888876666433 PP

>> FbpA  Fibronectin-binding protein A N-terminus (FbpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.1e-06    0.0027     149     238 ..     220     304 ..     195     313 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.1e-06
                                    SXXBSTTXBXXXSXXXSXBXTTSXXH.HHHHHHHHHS.XXXHHHHHHHBTTXXHHHHHHHHTTXSSSH............ CS
                           FbpA 149 vReilpgekYelPpsqdklnPleaeeleefkellskkekdlvkaLvkafqGlspllaeelleragldketsakelseedl 228
                                      e+lp++  e+ p   +++  e++++ + +e+     ++l+ +L ++f+ +++  a+e++++ gld+    ++l+ ++ 
  gi|116753912|ref|YP_843030.1| 220 ATELLPKRACEIKPHPAGIELGELTKMLRYTER-----RKLSSFLKESFTSIGNIAAQEVIHNSGLDPSMDPRSLNYDQS 294
                                    556777777777777666666666664455555.....89**************************************** PP

                                    ...HHHHHHH CS
                           FbpA 229 erlyealqel 238
                                    +rl+eal+++
  gi|116753912|ref|YP_843030.1| 295 KRLFEALRRI 304
                                    *******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 !   15.9   0.0   3.8e-06    0.0097      37      77 ..     264     304 ..     239     308 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.8e-06
                                    CS--HHHHHHHHHHTT--TTSBGGGS-HHHHHHHHHHHHHH CS
                           H2TH  37 aGlGNiyadEvLfrakihPerlakslskeelellhqeikev 77 
                                      +GNi a+Ev++ ++++P++  +sl+  + ++l ++++++
  gi|116753912|ref|YP_843030.1| 264 TSIGNIAAQEVIHNSGLDPSMDPRSLNYDQSKRLFEALRRI 304
                                    569*******************************9998765 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 ?   13.2   0.0   2.1e-05     0.055      55      96 ..      43      88 ..      31     125 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.1e-05
                     MAF_flag10 55 aadtalkaLlkegIkPDivvslDpqeasyevfkeaekkg....dip 96
                                   a+d +l a++++gI PDi+v + ++   y+v+ e +  g    +ip
  gi|116753912|ref|YP_843030.1| 43 AVDNSLDACEDAGILPDIFVQIKRTGELYRVIVEDNGPGivpsEIP 88
                                   899*********************9999999888777655555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (613 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); 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: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 4424.45
//
Query:       gi|116753913|ref|YP_843031.1|  [L=357]
Description: DNA topoisomerase VI subunit A [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-17   61.5   0.6    1.2e-16   60.4   0.1    1.9  2  TP6A_N    Type IIB DNA topoisomerase


Domain annotation for each model (and alignments):
>> TP6A_N  Type IIB DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0      0.56     1e+04      30      43 ..      39      55 ..      31      57 .. 0.68
   2 !   60.4   0.1   6.7e-21   1.2e-16       2      62 .]      65     130 ..      64     130 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 0.56
                                   HH...GGGS-SSHHHHH CS
                         TP6A_N 30 Yr...dvelFksQaesd 43
                                   Y+   dv ++++Q+ + 
  gi|116753913|ref|YP_843031.1| 39 YStkdDVWVYGDQESVR 55
                                   55555678889998775 PP

  == domain 2  score: 60.4 bits;  conditional E-value: 6.7e-21
                                    HHHHHHHHHHHH.HHHHHTT--EEHHHHHHH....GGGS-SSHHHHHHHHHHHHHHHTS-GGGGTE CS
                         TP6A_N   2 kfaqllkvleli.helleegkvvTkRdiYYr....dvelFksQaesdrliddievllgvsReeLnv 62 
                                    ++ +++++++l+ +e+l+ ++ +T+R+iYY     d ++F +Qaesdrli+d+e ++g++Ree++v
  gi|116753913|ref|YP_843031.1|  65 TLLKTVHLVDLLvKEHLRGNRASTLREIYYIsenwDLAKFAEQAESDRLIEDLEIITGLQREEFHV 130
                                    5677888888766******************99999*****************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2562.69
//
Query:       gi|116753914|ref|YP_843032.1|  [L=283]
Description: signal transduction protein [Methanosaeta thermophila PT]
Scores for complete 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  127.2  13.3    2.2e-14   53.6   0.9    4.2  4  CBS       CBS domain
  ------ inclusion threshold ------
      0.021   14.4   0.1      0.043   13.4   0.1    1.4  2  NS3       Non-structural protein NS3
      0.068   13.4   0.2       0.26   11.6   0.2    2.1  2  Clr5      Clr5 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 !   28.7   0.7   2.2e-10   1.3e-06       1      53 [.       5      56 ..       5      59 .. 0.91
   2 !   53.6   0.9   3.6e-18   2.2e-14       4      56 ..      66     117 ..      61     118 .. 0.94
   3 !   29.2   0.1   1.5e-10   9.2e-07       6      53 ..     130     177 ..     125     180 .. 0.88
   4 !   22.0   0.0   2.9e-08   0.00017      10      52 ..     232     274 ..     217     275 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 2.2e-10
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                            CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53
                                   V+d m rdv +v+   t  ++l+ + e++vs++PVV +   +vG+vt++Dllr
  gi|116753914|ref|YP_843032.1|  5 VRDAMVRDVAYVSLPGTRDKVLKVLNERHVSGVPVVKNC-TVVGMVTRTDLLR 56
                                   8999*********************7777*******544.5***********8 PP

  == domain 2  score: 53.6 bits;  conditional E-value: 3.6e-18
                                    HSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                            CBS   4 imtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                    +mtr++ +v+p++ l +a++l++ek+v+rlPVV ed++lvGi++  Dl+++++
  gi|116753914|ref|YP_843032.1|  66 LMTRNPYVVHPEDRLVDAAKLFVEKRVRRLPVV-EDERLVGIISVADLVKVIA 117
                                    5********************************.8999***********9986 PP

  == domain 3  score: 29.2 bits;  conditional E-value: 1.5e-10
                                    BSSCEEEETTSBHHHHHHHHHHHT.SSEEEEEETTTBEEEEEEHHHHHH CS
                            CBS   6 trdvvtvppdttleealelmrekg.vsrlPVVdedgklvGivtlrDllr 53 
                                     r+vv+v  +++l  +  +m e++ v + PV+d d +lvGi+t+rDl+ 
  gi|116753914|ref|YP_843032.1| 130 ERNVVVVWAEMPLPVVGAIM-EYAgVQACPVIDTDLQLVGIITDRDLIA 177
                                    689*****************.55559888***9888***********96 PP

  == domain 4  score: 22.0 bits;  conditional E-value: 2.9e-08
                                    EEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHH CS
                            CBS  10 vtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDll 52 
                                    +t+  ++ ++e++++m +k+++++PVV+   kl+G++ ++ ll
  gi|116753914|ref|YP_843032.1| 232 ITALRSSRVSECARTMSQKRIDQMPVVNAHRKLIGMLNDHNLL 274
                                    58889999********99*********98889*****999887 PP

>> NS3  Non-structural protein NS3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       1.2   7.1e+03     162     184 ..      56      78 ..      38      81 .. 0.58
   2 ?   13.4   0.1   7.2e-06     0.043      36     126 ..     165     255 ..     159     272 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 1.2
                            NS3 162 edsddyrytcdfsdnvtlldaed 184
                                     ++++ +     ++n+++ + ed
  gi|116753914|ref|YP_843032.1|  56 RNPEEDQIAMLMTRNPYVVHPED 78 
                                    45666666666788888888777 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 7.2e-06
                            NS3  36 klivcikdeevdiklevkedqlirkiykwdsvldswdwskqyklpkplyellelylkllkldertt.ipdwleesmlikc 114
                                    +l+  i d+++  k  v+e  l +        +d+w w  q+      y++ ++ lk +k++e  +     l +s + +c
  gi|116753914|ref|YP_843032.1| 165 QLVGIITDRDLIAKSVVEE-SLEKADADTAPEMDEWSWESQKEAISRYYQVSKITLKNVKVKEAMVqAITALRSSRVSEC 243
                                    5677788999988888888.777777778889*********99999***************996541456789******* PP

                            NS3 115 vryiknkriedi 126
                                     r + +kri+++
  gi|116753914|ref|YP_843032.1| 244 ARTMSQKRIDQM 255
                                    ********9986 PP

>> Clr5  Clr5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.84     5e+03      20      31 ..     139     150 ..     123     156 .. 0.76
   2 ?   11.6   0.2   4.3e-05      0.26       3      27 ..     199     223 ..     197     254 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.84
                           Clr5  20 nrsLkdvmeiMe 31 
                                    +++L  v+ iMe
  gi|116753914|ref|YP_843032.1| 139 EMPLPVVGAIME 150
                                    489999999997 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 4.3e-05
                           Clr5   3 edWeahkatIrrLYleenrsLkdvm 27 
                                     +We+ k+ I r+Y   + +Lk+v 
  gi|116753914|ref|YP_843032.1| 199 WSWESQKEAISRYYQVSKITLKNVK 223
                                    68************99999999764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); 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: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2195.31
//
Query:       gi|116753915|ref|YP_843033.1|  [L=147]
Description: UspA domain-containing protein [Methanosaeta thermophila PT]
Scores for 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-35  120.6   0.5    7.9e-35  120.4   0.5    1.0  1  Usp       Universal stress protein family
  ------ inclusion threshold ------
       0.15   12.3   0.0       0.28   11.4   0.0    1.4  1  SfsA_N    SfsA N-terminal OB 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 !  120.4   0.5   8.8e-39   7.9e-35       1     141 []       1     141 [.       1     141 [. 0.97

  Alignments for each domain:
  == domain 1  score: 120.4 bits;  conditional E-value: 8.8e-39
                                    S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTC CS
                            Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggv 80 
                                    m+++I++a+Dgs +s++A+++++ela++ ga++i+++v d+ + ++ +d++  ++     l+e e +    +  a ++gv
  gi|116753915|ref|YP_843033.1|   1 MIEKIMIATDGSVTSERAARFGVELARNLGARVIAVYVADTGRLSHLPDEMILVGIRDMLLKEGEDATSYVESIASEAGV 80 
                                    899****************************************************9999999998888889999999999 PP

                                    EEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                            Usp  81 kvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                      e  ++eg+p +eil++ +++++dl+V+Gs grsgl+r+llGSv+e+v++h+ +pVl V+
  gi|116753915|ref|YP_843033.1|  81 PCEKRIVEGKPTDEILKLSRDLSVDLLVMGSVGRSGLDRFLLGSVAEKVVQHSRVPVLTVP 141
                                    99999*****************************************************997 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 ?   11.4   0.0   3.1e-05      0.28       2      28 ..      16      47 ..      16      54 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.1e-05
                                   EEEETTEEEEEEE.......EE----S--TTT CS
                         SfsA_N  2 rRpnRFladveld.g.t...vHvpntGrlkel 28
                                   +R  RF ++   + g +   v+v++tGrl +l
  gi|116753915|ref|YP_843033.1| 16 ERAARFGVELARNlGaRviaVYVADTGRLSHL 47
                                   6999**99999887552456*********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.29s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1056.81
//
Query:       gi|116753916|ref|YP_843034.1|  [L=382]
Description: amidohydrolase [Methanosaeta thermophila PT]
Scores for complete 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-33  115.4   0.1    2.9e-20   72.9   0.1    3.0  2  Amidohydro_1  Amidohydrolase family
    9.2e-12   45.2   0.2    5.7e-10   39.3   0.0    2.2  2  Amidohydro_3  Amidohydrolase family
    5.5e-05   22.7   0.0      8e-05   22.1   0.0    1.2  1  A_deaminase   Adenosine/AMP deaminase


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.0   1.7e-12     1e-08       1      80 [.      79     173 ..      79     179 .. 0.90
   2 !   72.9   0.1   4.9e-24   2.9e-20     195     319 ..     240     354 ..     188     378 .. 0.77

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 1.7e-12
                                    EEEE-EEEEEEECETTECSSS...GHHHHH............STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHHHH CS
                   Amidohydro_1   1 ivlPGlIDaHvHleqsllrga...tledwl............vppetaaealesgiktalksGtttvadmgattstgiea 65 
                                    i++P++++aH+H+ +s  +++   +l d++            ++++ + e ++  ++++l  Gt  + d+++  s+g+e+
  gi|116753916|ref|YP_843034.1|  79 IICPAFVNAHTHVADSIAKDPpfmDLADLVgpgglkhrilesASDDLLVESMRFSVSEMLDTGTCVFGDFREGGSHGVEL 158
                                    699*************99999555555555************************************************** PP

                                    HHHHHHTSSSEEEEE CS
                   Amidohydro_1  66 lleaaeelplglril 80 
                                    ll+a+e l ++ ri+
  gi|116753916|ref|YP_843034.1| 159 LLRAIEGLGIQSRIF 173
                                    ******985555555 PP

  == domain 2  score: 72.9 bits;  conditional E-value: 4.9e-24
                                    TCEEE...HHHHHHHHHHHHHHCEEHHHHHHHHSEHHHHHHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHC CS
                   Amidohydro_1 195 gvhlt...pteaellkerlkeagvahcpfsnsilrsgrealrkaldeGvkvglgtDgaasgnslnlleelrlalklqrgl 271
                                     +hl+    ++++ ++e   +a+v+ cp+sn+  r g++++  +l+ G++v +gtD + ++ns n+++e+ l+       
  gi|116753916|ref|YP_843034.1| 240 LIHLSraeRSDLRDVAES--GASVVVCPRSNLFTRAGLPDVSSMLSLGINVCVGTD-NIMINSTNIFREMELLS------ 310
                                    4677754345999*****..************************************.************99999...... PP

                                    CTTTTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECC CS
                   Amidohydro_1 272 lyedeegglslkealrmaTingAkalglddkvGsievGkdADlvvvdl 319
                                        ++   +  +++ m+TingA+alg+d+++Gs+++Gk+A   v+d 
  gi|116753916|ref|YP_843034.1| 311 ----KALVRDDRQVFMMCTINGARALGMDERLGSVDPGKEARVMVFDR 354
                                    ....2333344679********************************76 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.6   0.1    0.0061        37      10      23 ..      80      93 ..      77     109 .. 0.83
   2 !   39.3   0.0   9.5e-14   5.7e-10     255     448 ..     193     355 ..     165     360 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0061
                   Amidohydro_3 10 vlPGFvDsHtHlag 23
                                     P+Fv +HtH+a 
  gi|116753916|ref|YP_843034.1| 80 ICPAFVNAHTHVAD 93
                                   57*********986 PP

  == domain 2  score: 39.3 bits;  conditional E-value: 9.5e-14
                   Amidohydro_3 255 tgwpdfedealaelvaaadergldvaihaigdaavddvldafeaaaekngnqdrrrlehaegvtesqiervaalqvaagv 334
                                    ++++d+++  + e+v+ a++ g ++aiha +++  d  +        ++++     l+h +    s++++va+ ++   v
  gi|116753916|ref|YP_843034.1| 193 SSTRDYDQSFVDEVVRIARKEGKRIAIHAGEAGRDD--I------DGALALDPD-ILIHLSRAERSDLRDVAESGASVVV 263
                                    4777777777*******************8877777..2......233444444.8************************ PP

                   Amidohydro_3 335 qpvfnf.edelldsrlgperargstpvkellnagvkvalgsDapvgpfdpwprigaavmrktrrggevlrpdeelsleea 413
                                    +p++n  +            + g++ v ++l+ g++v+ g+D   +++       +++ r+     e+l      + +++
  gi|116753916|ref|YP_843034.1| 264 CPRSNLfT------------RAGLPDVSSMLSLGINVCVGTD---NIMI----NSTNIFREM----ELLSKALVRDDRQV 320
                                    *****942............45789*****************...4433....344444444....777777777779** PP

                   Amidohydro_3 414 lalyTrgpAkalgledrkGtLevGadADlvvldad 448
                                    + ++T ++A+alg+++r G++ +G++A ++v+d++
  gi|116753916|ref|YP_843034.1| 321 FMMCTINGARALGMDERLGSVDPGKEARVMVFDRN 355
                                    *********************************87 PP

>> A_deaminase  Adenosine/AMP deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   1.3e-08     8e-05     180     314 ..     204     331 ..     189     338 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.3e-08
                                    HHHHCCCCHTT-EEEEEESSSS-CHHHHHHHHCS--SCECE-GGGGGSHHHHHHHHHCT-EEEE-HHHHCCCSST-TTTT CS
                    A_deaminase 180 lklraeagkstllltpHaGEagglehvveAllllkaerigHGvrlrkdpvLqyllalaqiplevcPlSNvalgafleyae 259
                                    +++ ++a+k++ ++++HaGEag  + +  Al+l + + + H ++ ++  +L  + a+    + vcP SN  ++a l++  
  gi|116753916|ref|YP_843034.1| 204 DEVVRIARKEGKRIAIHAGEAGR-DDIDGALAL-DPDILIH-LSRAERSDL-RDVAESGASVVVCPRSNLFTRAGLPD-- 277
                                    5677899*************986.679999998.9999999.555555566.568999************99665554.. PP

                                    -CHHHHHHTT-EEEE--BSCCCCT-SHHHHHHHHHHHH.T--HHHHHHHHHHHHHC CS
                    A_deaminase 260 nPlkeflerglnvslntDDPlqfgttLieeYaiaaqvf.klseedlaelarNsvkq 314
                                      +   l+ g+nv ++tD+ ++ +t++  e++ +++++ + +++ +   ++N++++
  gi|116753916|ref|YP_843034.1| 278 --VSSMLSLGINVCVGTDNIMINSTNIFREMELLSKALvRDDRQVFMMCTINGARA 331
                                    ..7899***************************99998344444455566666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2679.58
//
Query:       gi|116753917|ref|YP_843035.1|  [L=222]
Description: 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine 1-reductase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-53  181.1   0.0    2.5e-53  180.9   0.0    1.0  1  RibD_C    RibD C-terminal domain


Domain annotation for each model (and alignments):
>> RibD_C  RibD C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.9   0.0   1.4e-57   2.5e-53       1     199 [.       3     213 ..       3     214 .. 0.97

  Alignments for each domain:
  == domain 1  score: 180.9 bits;  conditional E-value: 1.4e-57
                                    -EEEEEEEEETTSBSSCTTSSGCTSS-HHHHHHHHHHHHTSSEEEEEHHHHHHHT--SS--SSCHSCHH.HTT.GSS-EE CS
                         RibD_C   1 pyvilklavSlDGklaaaggeskwitgeearadvhelraeadailvGrgtvladnpsltvrwvkkreae.adaearqpvr 79 
                                    pyv +++a+S+DGk++   + + +i+g+e+  +v++lrae+da++vG gtv+ad+p+l v+    r  + +++  ++p+r
  gi|116753917|ref|YP_843035.1|   3 PYVLINSAMSADGKISSFLRRQVRISGSEDLLRVERLRAESDAVMVGLGTVIADDPTLRVKSEALRSWRlERGVPENPLR 82 
                                    8*****************************************************************999999999***** PP

                                    EEEETTS-S-TTSHHHHSSS-EEEEESSCSCHHHHHHCC....E......SE-HHHHHHHHHHTT--EEEEEETHHHHHH CS
                         RibD_C  80 vVvdstlrvpldakvltddaptlvatteeadkekveklk....v......rvdlkelleeLkergirsllveGGatLags 149
                                    +V+ds+ r+p++a+vl  +   +va+++ a+++++++l+    +      rvdl elle L++rg+r+l+veGG+tL++s
  gi|116753917|ref|YP_843035.1|  83 IVADSRARTPPEARVLGPG--CIVAVSRYAPEDRLKELSerceIaicgedRVDLRELLEMLYRRGVRRLMVEGGGTLNWS 160
                                    *****************87..******************8877256899******************************* PP

                                    HHHTTT-SEEEEEEESCE--T.TSBCSSSSST-SS..EEEEEEEEEEETTEEE CS
                         RibD_C 150 llraglvDelrlyiaPkllGg.agktlfdgegfka..lklklvksealgegvv 199
                                    l+++glvDe+++++ P+++Gg +++tl+dg gf++   +l+l ++e++++g++
  gi|116753917|ref|YP_843035.1| 161 LIEQGLVDEICVFVGPMVIGGqDAPTLVDGRGFPEnfQRLELESAERIDDGLL 213
                                    *************************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       240  (0.0133861); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1719.62
//
Query:       gi|116753918|ref|YP_843036.1|  [L=232]
Description: hypothetical protein Mthe_0605 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-54  185.0   0.0      2e-54  184.7   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 !  184.7   0.0   1.1e-58     2e-54       2     204 ..      10     216 ..       9     217 .. 0.98

  Alignments for each domain:
  == domain 1  score: 184.7 bits;  conditional E-value: 1.1e-58
                         DUF169   2 LaealrlktePVavkfsdekpelpekkekieekkrlCqmvalarakgktvvftaetlgCpgGaaalGfkelpeklksg.. 79 
                                    L+ +l+l+ ePV+v ++++++++p++ ++ie++  +C mv+ ar +g+ +++  ++++C gGaa++G+   p+++ +g  
  gi|116753918|ref|YP_843036.1|  10 LKSTLGLDSEPVGVVLFKSEEDIPKDLKEIESPLPYCGMVQRAR-RGEVLFARSDKHACRGGAAGIGLHAFPDNIVQGkl 88 
                                    899*****************************************.*********************************9* PP

                         DUF169  80 ....egylkspeaakkfveslprleagevkyvvvapLekaefePdvvvffanpeqlmrLvqlalydrgggrlnvsfpgng 155
                                        ++++ +p + +++v++lp+++ag++ +++vapL+k++ +Pdvv+f++n+ q++r+vq++ly+rgg r+n +++g++
  gi|116753918|ref|YP_843036.1|  89 yfskLNKCATPTVGQRIVSNLPKIPAGSTVATLVAPLSKLNMNPDVVIFVGNALQARRIVQAVLYRRGG-RMNLDTAGIQ 167
                                    ***999*************************************************************99.********** PP

                         DUF169 156 aaCadivaypykegepniglgdpgarkfaklkddelafgiPyelleemv 204
                                    + C d++a p+ +g+ n++lg+ g+ k ++l d+ +++giP+e+le+++
  gi|116753918|ref|YP_843036.1| 168 SFCVDATASPILKGDVNVSLGCDGSAKKTGLTDNDVVVGIPFEMLEDIC 216
                                    **********************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1715.22
//
Query:       gi|116753919|ref|YP_843037.1|  [L=140]
Description: competence-like protein [Methanosaeta thermophila PT]
Scores for 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-23   81.9   0.6    4.9e-23   81.6   0.6    1.1  1  LTD       Lamin Tail Domain


Domain annotation for each model (and alignments):
>> LTD  Lamin Tail Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.6   0.6   2.7e-27   4.9e-23       3     107 ..      30     138 ..      28     139 .. 0.93

  Alignments for each domain:
  == domain 1  score: 81.6 bits;  conditional E-value: 2.7e-27
                            LTD   3 aaagdvvIsevmedgagnnan....efvelyNtsskavdLsgwkledasge.ytfpngtgtlaageyvvvwsgsgttsas 77 
                                    +++  v Is v   +++ + +    e+v+++N +  +vdL+gw+++d++++ y+fp+g  +l +g++v v++g+g+++++
  gi|116753919|ref|YP_843037.1|  30 SSETPVRISNVSFVAPSPERAnlneEWVKIENIGKIDVDLTGWSISDEQEHtYVFPDGF-ILRSGASVKVHTGTGNNTQE 108
                                    567788899888777777666789*************************99*******9.******************** PP

                            LTD  78 ngskasssavwnnggdavaLydasgevvds 107
                                    + ++++s +vwnn+gd+++L+d+sg+++ds
  gi|116753919|ref|YP_843037.1| 109 DLYWGRSVPVWNNDGDSATLRDSSGSIIDS 138
                                    ****************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1073.54
//
Query:       gi|116753920|ref|YP_843038.1|  [L=60]
Description: PUA domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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-09   35.8   0.2    6.4e-09   35.7   0.2    1.1  1  PUA       PUA domain
     0.0013   18.9   0.0     0.0015   18.8   0.0    1.1  1  UPF0113   UPF0113 PUA domain


Domain annotation for each model (and alignments):
>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.2   7.1e-13   6.4e-09       1      52 [.       8      59 ..       8      60 .] 0.96

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 7.1e-13
                                   CEEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEE CS
                            PUA  1 grvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGla 52
                                   ++vvv d Av ++++g  ++ + v++++ d+ +gd+V ++d++++++ v++a
  gi|116753920|ref|YP_843038.1|  8 KKVVVSDYAVPFVARGGRVFSKLVLRADPDVNPGDEVLVLDRNDRVITVAKA 59
                                   58*********************************************99876 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.7e-07    0.0015       1      51 [.       9      59 ..       9      60 .] 0.89

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.7e-07
                        UPF0113  1 kvvvkekaeklFLYGrdvlkesilkitesvkenqvvvVlnengeplGiGki 51
                                   kvvv+  a   +  G  v+ + +l+ +++v+ ++ v+Vl+ n++++ ++k+
  gi|116753920|ref|YP_843038.1|  9 KVVVSDYAVPFVARGGRVFSKLVLRADPDVNPGDEVLVLDRNDRVITVAKA 59
                                   56777777777777999*****************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       231  (0.0128842); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.21s 00:00:00.55 Elapsed: 00:00:00.38
# Mc/sec: 471.35
//
Query:       gi|116753921|ref|YP_843039.1|  [L=214]
Description: nuclease [Methanosaeta thermophila PT]
Scores for 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-09   35.7   0.0    1.4e-08   35.1   0.0    1.2  1  SNase           Staphylococcal nuclease homologue
    9.4e-05   22.4   1.2    0.00017   21.5   1.2    1.4  1  Ada_Zn_binding  Metal binding domain of Ada


Domain annotation for each model (and alignments):
>> SNase  Staphylococcal nuclease homologue
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.0   1.6e-12   1.4e-08       1      83 [.      61     145 ..      61     153 .. 0.93

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 1.6e-12
                                    EEEETTEE-STSSBTTTTTSTTHHHHHHHHHHHHHHCSSEEEEE-S.SBSTTSEEEEEEEET.......TEEHHHHHHHT CS
                          SNase   1 kvrLvgidaPetakpkktvqpfgkeAkeflkklvlqkkvvvleldk.kkDkygrllayvyln.......kknineeLvke 72 
                                    +vrL+++d+Pe         + g+ A++++ + +++++v+++++d   +D ygr +  vyl+       ++n+n  +v  
  gi|116753921|ref|YP_843039.1|  61 RVRLADVDCPEMD------TEAGRAAANYTISWLFGRTVWLDIDDLkGRDDYGRWICVVYLDengapdpEMNFNRMIVDS 134
                                    79***********......788**********************99899******************************* PP

                                    TSSEE---BTT CS
                          SNase  73 GlArvyevyek 83 
                                    G A+v  + ++
  gi|116753921|ref|YP_843039.1| 135 GHAVVRDFTDN 145
                                    ****8877765 PP

>> Ada_Zn_binding  Metal binding domain of Ada
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   1.2   1.9e-08   0.00017      17      64 ..     165     213 ..     160     214 .] 0.87

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.9e-08
                                    BEEEETTTTEEE-TT-S.SS-S-SCCEEEESSHHHHHHTT-EEETTTTT CS
                 Ada_Zn_binding  17 FvyavkttgiyCrpsCp.arlPkrenveFfdtaaeAeaagfrpCkrcrP 64 
                                     +++  + + y  p+C+ a++  + n   f++++eA+++g+ pC+ c+P
  gi|116753921|ref|YP_843039.1| 165 AYVGSVKSNKYHYPDCEwAQKISPVNLICFSSPSEARSKGYTPCRVCKP 213
                                    5788888889999***94555669************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1706.73
//
Query:       gi|116753922|ref|YP_843040.1|  [L=196]
Description: hypothetical protein Mthe_0609 [Methanosaeta thermophila PT]
Scores for complete 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  199.8   0.0      4e-59  199.7   0.0    1.0  1  Methyltrn_RNA_2  Putative SAM-dependent RNA methyltransferase


Domain annotation for each model (and alignments):
>> Methyltrn_RNA_2  Putative SAM-dependent RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.7   0.0   2.2e-63     4e-59       1     195 [.       1     191 [.       1     194 [. 0.95

  Alignments for each domain:
  == domain 1  score: 199.7 bits;  conditional E-value: 2.2e-63
                                    -EEEEEEESSEESSSHHHCCCTTTTTTSHHHHHHHHHHHHBESSSB-TTEEEEEEEEESSSS-EEEEEETTT--S--SSH CS
                Methyltrn_RNA_2   1 mrefvvlankapTdsdiplddlpGaagrldvlarcvsaalfvshgiRedvvvylvLegtpdpprtikieasevkkvspde 80 
                                    mr fv++++ a T++d++l+dlpG++gr+dvl+rcv+ a+ +shgiR+dv  +l+L+g+p+ p+++++++s +++ +pde
  gi|116753922|ref|YP_843040.1|   1 MRDFVIVGHIAKTTPDFSLEDLPGTSGRIDVLCRCVNSAFMLSHGIRRDVRCHLILMGGPE-PKILRFDGSRLRHLNPDE 79 
                                    9**********************************************************97.689*************** PP

                                    HHHHHHHHHHHCHCCTGCCSEEEEETTEEEE---HHHHHHHHHCT.SEEEEESTTSEEGGGS---SSEEEEEE-TT-SHH CS
                Methyltrn_RNA_2  81 rniailikkalkaveeikkqekkvrpgltVrkegfealleelsek.ksiillkekGedisnakielnPvFilgdHidlpe 159
                                    r+ a lik+al +      ++++++pg+++rk  ++ lle l+++ + +++l e+G   s+ + +   vF+lgdH +++ 
  gi|116753922|ref|YP_843040.1|  80 RSTAALIKRAL-SI-DASPSWRESTPGIYIRKGDLRSLLESLRDEgQRLYYLREDGAPLSESVSD--GVFVLGDHTGMTG 155
                                    ***********.55.5999************************99899********998887765..9************ PP

                                    HHHHHHHCTTSEEEES-SS---HHHHHHHHHHHHHH CS
                Methyltrn_RNA_2 160 eeekllerlkakrvslgPlsLhadhcvtlihneldk 195
                                    +ee+ll+ ++a+ vs+gPlsLhadhc++++  + d+
  gi|116753922|ref|YP_843040.1| 156 DEEHLLDSMGAETVSIGPLSLHADHCIVIVNWMCDN 191
                                    ******************************988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1457.82
//
Query:       gi|116753923|ref|YP_843041.1|  [L=323]
Description: pyridoxamine 5'-phosphate oxidase-related, FMN-binding [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-15   57.1   0.0    3.2e-15   56.6   0.0    1.2  1  Flavodoxin_5    Flavodoxin domain
    1.3e-07   31.7   0.0    2.3e-07   30.9   0.0    1.4  1  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
    5.5e-07   29.4   0.0    7.9e-07   28.9   0.0    1.2  1  Flavodoxin_3    Flavodoxin domain
    0.00031   20.7   0.0    0.00053   20.0   0.0    1.3  1  Pyridox_ox_2    Pyridoxamine 5'-phosphate oxidase
  ------ inclusion threshold ------
      0.018   14.8   0.0      0.029   14.1   0.0    1.3  1  FMN_red         NADPH-dependent FMN reductase
      0.036   14.3   0.0      0.066   13.4   0.0    1.5  1  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 !   56.6   0.0   1.1e-18   3.2e-15       1     123 [.       5     121 ..       5     135 .. 0.88

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 1.1e-18
                   Flavodoxin_5   1 lilYsSrdGqTkkiaeriaeelreegelvdvedvekesedlesydavvigasvyygkllpelakFvekhreaLstkpval 80 
                                    l++Y Sr+G+T+++a+++   l+ + + v+v++++   +++  ++ +v+ga+vy+g ++p+l +Fv++  + L++k++al
  gi|116753923|ref|YP_843041.1|   5 LVVYDSRYGSTEEVARTLSLILGPS-DAVKVDEIQ---PEHRRFELFVLGAPVYKGVISPKLWNFVRESLSWLREKRIAL 80 
                                    79*********************77.999999995...9***************************************** PP

                   Flavodoxin_5  81 fsvsltarkpeksyvrkflkeklrwqpklvgvfaGaldyskls 123
                                    f++s  +++ e  +++ +lk+ l++++ l + ++G+   ++ls
  gi|116753923|ref|YP_843041.1|  81 FTTSIDRKDGET-NLE-SLKKILGESVLLSRALGGRMCVERLS 121
                                    *****9887777.665.67777777777777777777777665 PP

>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0   7.6e-11   2.3e-07       4      87 ..     176     259 ..     173     260 .. 0.91

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 7.6e-11
                                    HHHHHHHHSSEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETT....GSEEEEEEE CS
                 Putative_PNPOx   4 elreflaeskavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallfldde....lgrgvrieG 79 
                                     + +fla++++++lAT     r+ ++p+ + + +g   +++  ++  +k++n+  n rv++ ++d+     +  g+++ G
  gi|116753923|ref|YP_843041.1| 176 LIDAFLASHNTCTLATG-YGSRVRATPLEYLYRNGA--MYIL-SEGGEKFANIVLNERVSVAVYDPYesmrDVAGIQLTG 251
                                    5789************6.7888*********99999..6666.78889***********************99******* PP

                                    EEEEESCH CS
                 Putative_PNPOx  80 taelvsdg 87 
                                    +a +v++g
  gi|116753923|ref|YP_843041.1| 252 RAGFVEEG 259
                                    **999987 PP

>> Flavodoxin_3  Flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   2.6e-10   7.9e-07       1      81 [.       5      88 ..       5     123 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 2.6e-10
                   Flavodoxin_3  1 lilysSltGNTkkvAeaikealeeekeivsikeakekveeadvvfvGfwvdkgtadeealkf....letlknkkillfgTlG 78
                                   l++y+S+ G T++vA++++  l   ++ v+++e++ +  +++++++G+ v+kg  + ++ +f    l+ l++k+i+lf T  
  gi|116753923|ref|YP_843041.1|  5 LVVYDSRYGSTEEVARTLSLILGP-SDAVKVDEIQPEHRRFELFVLGAPVYKGVISPKLWNFvresLSWLREKRIALFTTSI 85
                                   59*******************999.9*********99*******************99877633336779*********965 PP

                   Flavodoxin_3 79 agk 81
                                     k
  gi|116753923|ref|YP_843041.1| 86 DRK 88
                                   544 PP

>> Pyridox_ox_2  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   1.8e-07   0.00053       5      91 ..     177     256 ..     174     273 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.8e-07
                                    HHHHHHC-SEEEEEEEETTEEEEEEEEEEEETTEEEEEEETTSHCCHCCCT--ECEEEEEEEEEEE-SEGGEEEEEEEEE CS
                   Pyridox_ox_2   5 ilalLdegevgrlafvddgepvilPvnyvvdgdslyfhgakgsrlaaalrgapvcvvvtevdglvlarsfnslnyrSVvv 84 
                                    i+a+L+++ +++la+  ++++ ++P+ y ++++++y+ ++ g++ a+   + +v+v+v++  + + + +        +++
  gi|116753923|ref|YP_843041.1| 177 IDAFLASHNTCTLATGYGSRVRATPLEYLYRNGAMYILSEGGEKFANIVLNERVSVAVYDPYESMRDVA-------GIQL 249
                                    899************************************99999999888778*****99777555544.......6666 PP

                                    EEEEEEE CS
                   Pyridox_ox_2  85 rGraeev 91 
                                    +Gra  v
  gi|116753923|ref|YP_843041.1| 250 TGRAGFV 256
                                    6666555 PP

>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   9.7e-06     0.029      62     136 ..      33     102 ..      16     111 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9.7e-06
                                    HHHHHHHHHHH-SCEEEEEEECTTCE-HHHHHHHHCHT-.SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHH CS
                        FMN_red  62 dvaellekiaaadaliivtPeYngsysgllKnalDrlsrtrgkkelrgKpvalvavgggrrgglraeeqlrqvla 136
                                    +v e+    +  + ++++ P+Y+g +s+ l n+            lr K +al++++ +r+ g+   e+l+++l 
  gi|116753923|ref|YP_843041.1|  33 KVDEIQPEHRRFELFVLGAPVYKGVISPKLWNFVRES-----LSWLREKRIALFTTSIDRKDGETNLESLKKILG 102
                                    5678888888999********************9887.....78999***********************99997 PP

>> Flavodoxin_1  Flavodoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.2e-05     0.066       1      48 [.       6      52 ..       6      87 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.2e-05
                                   EEEETSSSHHHHHHHHHHHHHHHTTTEEEEEEEEGTTSC...GGGGGTHSE CS
                   Flavodoxin_1  1 ilYgSetGnteklAkqlaeelgehgfnadvvslsdydes...lseieeeal 48
                                   ++Y+S +G+te++A++l  +lg     +d+v++++++ +   ++ +   a 
  gi|116753923|ref|YP_843041.1|  6 VVYDSRYGSTEEVARTLSLILGP----SDAVKVDEIQPEhrrFELFVLGAP 52
                                   89*******************95....466777776643222444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); 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:                         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 0.28s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2245.63
//
Query:       gi|116753924|ref|YP_843042.1|  [L=417]
Description: hypothetical protein Mthe_0611 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-41  139.4   0.0    8.6e-41  138.7   0.0    1.4  1  DUF1743          Domain of unknown function (DUF1743)
  ------ inclusion threshold ------
      0.045   13.7   0.0      0.091   12.8   0.0    1.4  1  tRNA_anti-codon  OB-fold nucleic acid binding domain


Domain annotation for each model (and alignments):
>> DUF1743  Domain of unknown function (DUF1743)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.7   0.0   9.6e-45   8.6e-41       2     116 .]     137     248 ..     136     248 .. 0.98

  Alignments for each domain:
  == domain 1  score: 138.7 bits;  conditional E-value: 9.6e-45
                                    THHHHHHHHHH-..-TTS-EEEEEEEE-GGGTT.---EEHHHHHHHHHHHTTCECTSEBTTTTCECCS-STTSSEEEEEE CS
                        DUF1743   2 rgiiGAtaalganialedstyEllaYreperwg.erevdeesvieadektypetfdnvDlshklvvlvPhtpdpvlfGir 80 
                                    rg+iGA+aa+g   +++d+tyEl+aYr++  wg +r +de+s+++ad++typ+t+d+vD+s++++v  Ph+pdpvlfGir
  gi|116753924|ref|YP_843042.1| 137 RGLIGALAAVGS--EFDDHTYELIAYRRRGLWGtPRALDEDSIWNADRATYPATWDTVDYSNRRIVFSPHSPDPVLFGIR 214
                                    8***********..5568************************************************************** PP

                                    ES-HHHHHHHHHCSEE..S-EECEEEEEESTTS-TT CS
                        DUF1743  81 gedpeallkaakeilskeeeseemavfrtnqgtdah 116
                                    g+dp a+++a+++i+s  e  e+++++ tnqgtdah
  gi|116753924|ref|YP_843042.1| 215 GDDPGAIRRAFSMIRS--EAPERCVMYVTNQGTDAH 248
                                    ****************..****************99 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     1e-05     0.091      13      60 ..     277     326 ..     265     334 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1e-05
                                    EEETTEEEEEEEETTEEEEEEEET..HHHHHHHTTS-TTSEEEEEEEEEE CS
                tRNA_anti-codon  13 rsggkvifidlrDgtgriqvvlfr..eeatklaenlkeGdvvrvtGrvkr 60 
                                      +g+++f+ ++ g+ +i++ +f   + ++k+  +l +Gd+++v+G  k+
  gi|116753924|ref|YP_843042.1| 277 VIEGGHVFFPIDLGERKIECAAFEptKCFRKIVRSLIPGDLIEVYGSMKS 326
                                    5689******************************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 3113.97
//
Query:       gi|116753925|ref|YP_843043.1|  [L=204]
Description: ArsR family transcriptional regulator [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-15   56.0   2.1    1.2e-11   44.5   0.0    2.7  3  HTH_20          Helix-turn-helix domain
      5e-15   55.1   0.0    1.3e-08   34.6   0.0    2.4  2  HTH_5           Bacterial regulatory protein, arsR family
    5.1e-11   42.5   1.2    7.2e-06   26.0   0.0    2.6  2  DprA_WH         DprA winged helix domain
    1.9e-10   40.5   1.2    0.00058   19.7   0.1    2.7  2  MarR_2          MarR family
    2.6e-09   36.8   0.0    8.8e-05   22.3   0.0    2.3  2  TrmB            Sugar-specific transcriptional regulator TrmB
    5.9e-09   35.4   0.4       0.01   15.3   0.0    3.3  3  HTH_24          Winged helix-turn-helix DNA-binding
      5e-07   29.8   0.0    0.00041   20.5   0.0    2.3  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
    1.5e-06   27.8   0.2    0.00026   20.6   0.4    2.7  2  GntR            Bacterial regulatory proteins, gntR family
    2.7e-06   27.6   0.0      0.022   15.1   0.0    2.6  2  Rrf2            Transcriptional regulator
    1.9e-05   25.1   0.0       0.31   11.6   0.0    2.4  2  HTH_27          Winged helix DNA-binding domain
    3.5e-05   23.6   0.3      0.002   18.0   0.0    2.3  2  TFIIE_alpha     TFIIE alpha subunit
      4e-05   23.5   0.2        0.5   10.3   0.0    2.9  3  MarR            MarR family
    7.8e-05   22.6   0.3        0.2   11.6   0.1    2.6  2  HTH_Crp_2       Crp-like helix-turn-helix domain
    9.7e-05   22.1   0.1       0.94    9.3   0.0    3.1  3  LexA_DNA_bind   LexA DNA binding domain
     0.0018   18.3   0.0        3.1    8.0   0.0    2.5  2  DUF2250         Uncharacterized protein conserved in archaea 
     0.0031   17.4   0.0       0.61   10.1   0.0    2.7  2  HTH_11          HTH domain
     0.0046   16.7   1.9      0.047   13.5   0.1    2.8  3  HTH_IclR        IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.015   15.3   0.0       0.88    9.6   0.0    3.0  2  PadR            Transcriptional regulator PadR-like family
      0.021   15.5   2.2      0.038   14.6   2.2    1.4  1  Hemerythrin     Hemerythrin HHE cation binding domain
      0.041   13.8   0.2        4.7    7.3   0.0    3.0  4  Cdc6_C          CDC6, C terminal winged helix domain
      0.098   12.2   0.1         16    5.1   0.0    2.5  2  HTH_47          winged helix-turn-helix
       0.12   12.5   0.1         22    5.2   0.0    2.7  3  FeoC            FeoC like transcriptional regulator
       0.13   12.4   0.6       0.21   11.8   0.6    1.3  1  DUF4055         Domain of unknown function (DUF4055)
       0.13   12.1   0.0        1.7    8.5   0.0    2.4  2  IF2_N           Translation initiation factor IF-2, N-termina
       0.16   11.6   0.0        4.1    7.0   0.0    2.6  3  ArsR            ArsR transcriptional regulator
       0.16   12.1   0.0       0.55   10.4   0.0    1.8  2  HTH_9           RNA polymerase III subunit RPC82 helix-turn-h


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 !   44.5   0.0   1.7e-14   1.2e-11       2      60 ..       5      62 ..       4      63 .. 0.95
   2 ?   -2.2   0.1       6.7   4.6e+03      34      34 ..     120     120 ..     106     143 .. 0.58
   3 !   10.8   0.1   0.00058       0.4      22      55 ..     163     196 ..     153     202 .. 0.86

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 1.7e-14
                                   HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                         HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                   +++++L+++ Rrril++L + +++ ++e+a+rld+ ++ + +HL vLe agL+e  r +
  gi|116753925|ref|YP_843043.1|  5 ELLDVLGNENRRRILQLL-SFRPFYFNEIAKRLDVGPKAVIDHLGVLEAAGLIECYRDE 62
                                   6799**************.***********************************99876 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.7
                                    H CS
                         HTH_20  34 l 34 
                                    +
  gi|116753925|ref|YP_843043.1| 120 M 120
                                    2 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00058
                                    CTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                         HTH_20  22 aegltaselaerldlskntlsyHLrvLeeagLve 55 
                                     +  t + laerl ++++ ++  L+ Le+ gLv+
  gi|116753925|ref|YP_843043.1| 163 SGSSTEEMLAERLKMPPAVVRESLARLESRGLVR 196
                                    56668888*************************8 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.0   1.9e-11   1.3e-08       1      46 [.      12      57 ..      12      57 .. 0.97
   2 !   18.0   0.1   2.8e-06    0.0019       6      45 ..     156     195 ..     152     196 .. 0.94

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 1.9e-11
                                   SHHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_5  1 dptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                   +++R++IL+lL+ ++ ++ e+a+ l++ + +v  HL +L+ aGL+e
  gi|116753925|ref|YP_843043.1| 12 NENRRRILQLLSFRPFYFNEIAKRLDVGPKAVIDHLGVLEAAGLIE 57
                                   589*****************************************96 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 2.8e-06
                                    HHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_5   6 kILklLaegelcvcelaeelglsqstvShHLkkLreaGLV 45 
                                    ++L++L +g+ +   lae l+++++ v++ L++L+  GLV
  gi|116753925|ref|YP_843043.1| 156 ELLFSLLSGSSTEEMLAERLKMPPAVVRESLARLESRGLV 195
                                    689999999999999************************9 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0     1e-08   7.2e-06      12      57 ..      13      58 ..       5      61 .. 0.95
   2 !   14.5   0.6   4.3e-05     0.029       9      57 ..     149     197 ..     139     201 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 1e-08
                        DprA_WH 12 dlerrvLaaLgpePvhvDqLvrrtglpaaevsaaLleLELaGlver 57
                                   + +rr+L++L++ P  + ++++r+ + + +v  +L  LE aGl+e 
  gi|116753925|ref|YP_843043.1| 13 ENRRRILQLLSFRPFYFNEIAKRLDVGPKAVIDHLGVLEAAGLIEC 58
                                   679*****************************************85 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 4.3e-05
                        DprA_WH   9 plddlerrvLaaLgpePvhvDqLvrrtglpaaevsaaLleLELaGlver 57 
                                    ++d+ e+ +L  L + + +++ L++r+ +p+a+v   L  LE  Glv+ 
  gi|116753925|ref|YP_843043.1| 149 ATDEIEEELLFSLLSGSSTEEMLAERLKMPPAVVRESLARLESRGLVRF 197
                                    567777777766666778899************************9986 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   8.4e-07   0.00058       8      56 ..      16      61 ..       4     108 .. 0.81
   2 !   19.5   0.1     1e-06   0.00069      26      55 ..     170     199 ..     135     201 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 8.4e-07
                                   HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                         MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                   +r+L  L  rp   +  +e+a+rl++ + av  +l  L+aaGL+e  ++
  gi|116753925|ref|YP_843043.1| 16 RRILQLLSFRP---FYFNEIAKRLDVGPKAVIDHLGVLEAAGLIECYRD 61
                                   45555555555...9*****************************75444 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 1e-06
                                    HHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                         MarR_2  26 elarrlglsksavsrilkrLvaaGLverrp 55 
                                     la+rl+++++ v   l+rL+++GLv+ + 
  gi|116753925|ref|YP_843043.1| 170 MLAERLKMPPAVVRESLARLESRGLVRFEN 199
                                    59************************9875 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   0.00019      0.13      16      62 ..      20      67 ..      18      72 .. 0.85
   2 !   22.3   0.0   1.3e-07   8.8e-05       8      57 ..     152     200 ..     151     203 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00019
                                   HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.TTEE CS
                           TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.pklY 62
                                    Ll+  p   +eia++l+v    v + L  Le +Gl+e  + + +++Y
  gi|116753925|ref|YP_843043.1| 20 QLLSFRPFYFNEIAKRLDVGPKAVIDHLGVLEAAGLIECYRDErRRKY 67
                                   6999999999***************************98775434455 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 1.3e-07
                                    HHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
                           TrmB   8 eyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekg 57 
                                    e E +  + Ll +g++t + +ae+l+ p + v e+L +Le++GlV+ e g
  gi|116753925|ref|YP_843043.1| 152 EIEEELLFSLL-SGSSTEEMLAERLKMPPAVVRESLARLESRGLVRFENG 200
                                    56788888999.9********************************98876 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 ?    2.0   0.0      0.22   1.5e+02       2      12 ..      12      22 ..      11      23 .. 0.90
   2 !   14.5   0.0   2.7e-05     0.019      21      48 .]      30      57 ..      29      57 .. 0.96
   3 !   15.3   0.0   1.5e-05      0.01      23      48 .]     171     196 ..     151     196 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.22
                         HTH_24  2 detdrkILelL 12
                                   +e++r+IL+lL
  gi|116753925|ref|YP_843043.1| 12 NENRRRILQLL 22
                                   799******98 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 2.7e-05
                         HTH_24 21 reLAerlglSpstvnrrlkrLeeeGlIk 48
                                   +e+A+rl++ p +v  +l  Le +GlI+
  gi|116753925|ref|YP_843043.1| 30 NEIAKRLDVGPKAVIDHLGVLEAAGLIE 57
                                   79*************************7 PP

  == domain 3  score: 15.3 bits;  conditional E-value: 1.5e-05
                         HTH_24  23 LAerlglSpstvnrrlkrLeeeGlIk 48 
                                    LAerl ++p+ v++ l rLe+ Gl++
  gi|116753925|ref|YP_843043.1| 171 LAERLKMPPAVVRESLARLESRGLVR 196
                                    9***********************96 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0096       6.6      26      53 ..      30      57 ..      20      62 .. 0.92
   2 !   20.5   0.0     6e-07   0.00041      25      55 ..     168     198 ..     159     201 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0096
                                   HHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                 Fe_dep_repress 26 kdlaerLnvspssVsemlkkLekdGyve 53
                                    ++a+rL+v p  V   l  Le +G++e
  gi|116753925|ref|YP_843043.1| 30 NEIAKRLDVGPKAVIDHLGVLEAAGLIE 57
                                   58***********************997 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 6e-07
                                    HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                 Fe_dep_repress  25 tkdlaerLnvspssVsemlkkLekdGyveye 55 
                                      +laerL+  p+ V e+l +Le+ G+v  e
  gi|116753925|ref|YP_843043.1| 168 EEMLAERLKMPPAVVRESLARLESRGLVRFE 198
                                    689*************************876 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.063        44      28      55 ..      30      57 ..      29      62 .. 0.93
   2 !   20.6   0.4   3.7e-07   0.00026      26      59 ..     167     200 ..     149     201 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.063
                                   HHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                           GntR 28 reLaaefgVsrttvReALrrLeaeglve 55
                                   +e+a++++V+   v   L  Lea+gl+e
  gi|116753925|ref|YP_843043.1| 30 NEIAKRLDVGPKAVIDHLGVLEAAGLIE 57
                                   79************************98 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 3.7e-07
                                    -HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                           GntR  26 sereLaaefgVsrttvReALrrLeaeglverrqg 59 
                                    +e+ La++++    +vRe+L rLe++glv  ++g
  gi|116753925|ref|YP_843043.1| 167 TEEMLAERLKMPPAVVRESLARLESRGLVRFENG 200
                                    5899*************************99887 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0    0.0017       1.2      27      58 ..      28      59 ..      19      61 .. 0.90
   2 !   15.1   0.0   3.2e-05     0.022      27      60 ..     167     200 ..     158     202 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0017
                                   -HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                           Rrf2 27 sseeiaerqnispsylekilakLrkaglvksv 58
                                     +eia+r ++ p+ +   l  L+ agl++  
  gi|116753925|ref|YP_843043.1| 28 YFNEIAKRLDVGPKAVIDHLGVLEAAGLIECY 59
                                   578**************************965 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 3.2e-05
                                    -HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                           Rrf2  27 sseeiaerqnispsylekilakLrkaglvksvrG 60 
                                    + e +aer +++p +++  la+L+  glv+ + G
  gi|116753925|ref|YP_843043.1| 167 TEEMLAERLKMPPAVVRESLARLESRGLVRFENG 200
                                    66789*************************9988 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 !   11.6   0.0   0.00045      0.31      23      64 ..      31      70 ..      29      71 .. 0.92
   2 !   10.9   0.0    0.0007      0.48      13      48 ..     162     195 ..     153     201 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00045
                         HTH_27 23 dlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrl 64
                                   ++++rl+v+  +++  l  L+++GL+e  +de  rr+k +rl
  gi|116753925|ref|YP_843043.1| 31 EIAKRLDVGPKAVIDHLGVLEAAGLIECYRDE--RRRKYFRL 70
                                   899***********************999999..88888886 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0007
                         HTH_27  13 rhrrrrkkladlcgrlnvedshisyslkkLtekGLv 48 
                                        + +++++l++rl++  + + +sl +L+ +GLv
  gi|116753925|ref|YP_843043.1| 162 L--SGSSTEEMLAERLKMPPAVVRESLARLESRGLV 195
                                    5..677899*************************** PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.084        58      31      62 ..      30      61 ..       6      79 .. 0.79
   2 !   18.0   0.0   2.9e-06     0.002      16      59 ..     155     197 ..     141     200 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.084
                                   HHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEE CS
                    TFIIE_alpha 31 edlakelkidlnelrklLnrLyearlvkykrr 62
                                   +++ak l + ++ +   L  L  a+l+++ r 
  gi|116753925|ref|YP_843043.1| 30 NEIAKRLDVGPKAVIDHLGVLEAAGLIECYRD 61
                                   68**************************9875 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 2.9e-06
                                    HHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEE CS
                    TFIIE_alpha  16 vlvldvLlekgevteedlakelkidlnelrklLnrLyearlvky 59 
                                     + l++Ll  g  tee la+ lk+ + ++r+ L+rL + +lv +
  gi|116753925|ref|YP_843043.1| 155 EELLFSLL-SGSSTEEMLAERLKMPPAVVRESLARLESRGLVRF 197
                                    46788999.8999****************************976 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0    0.0011      0.74      17      53 ..      26      62 ..      13      66 .. 0.87
   2 ?   -1.5   0.0       3.6   2.5e+03      20      40 ..     113     133 ..     110     136 .. 0.82
   3 !   10.3   0.0   0.00073       0.5      19      49 ..     167     197 ..     163     200 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0011
                                   TEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEET CS
                           MarR 17 plsvseLakklgvskstvtrvldrLekkGlieRsksp 53
                                   p +  e+ak+l v + +v   l  Le +Glie ++++
  gi|116753925|ref|YP_843043.1| 26 PFYFNEIAKRLDVGPKAVIDHLGVLEAAGLIECYRDE 62
                                   566789**************************99986 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.6
                                    HHHHHHHHTS-HHHHHHHHHH CS
                           MarR  20 vseLakklgvskstvtrvldr 40 
                                    +s La  +   ++++  v++r
  gi|116753925|ref|YP_843043.1| 113 LSALAAEMDRLRMMMADVATR 133
                                    578999999999999888765 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00073
                                    EHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                           MarR  19 svseLakklgvskstvtrvldrLekkGlieR 49 
                                    +   La++l++ ++ v + l rLe +Gl++ 
  gi|116753925|ref|YP_843043.1| 167 TEEMLAERLKMPPAVVRESLARLESRGLVRF 197
                                    56679************************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 !    8.7   0.0    0.0025       1.7      25      53 ..      30      60 ..       6      72 .. 0.80
   2 !   11.6   0.1   0.00029       0.2      22      54 ..     166     199 ..     135     204 .] 0.83

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0025
                                   HHHHHHTTSSHHHHHHHHHHHHHTTSEE..E CS
                      HTH_Crp_2 25 eelAsmlGltretvsrilseLkreglis..r 53
                                    e+A +l + +  v   l+ L+ +gli+  r
  gi|116753925|ref|YP_843043.1| 30 NEIAKRLDVGPKAVIDHLGVLEAAGLIEcyR 60
                                   79**************************853 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00029
                                    HHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ET CS
                      HTH_Crp_2  22 ltqeelAsmlGltretvsrilseLkreglis.rg 54 
                                     t e lA++l + +  v   l++L+ +gl++  +
  gi|116753925|ref|YP_843043.1| 166 STEEMLAERLKMPPAVVRESLARLESRGLVRfEN 199
                                    68899*************************9543 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 !    8.9   0.0    0.0018       1.2      29      60 ..      30      60 ..      25      65 .. 0.88
   2 ?   -1.1   0.0       2.5   1.7e+03      38      51 ..     104     117 ..      89     119 .. 0.74
   3 !    9.3   0.0    0.0014      0.94      31      61 ..     171     200 ..     165     201 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0018
                                   HHHHHHHTS-.HHHHHHHHHHHHHTTSEE-GG CS
                  LexA_DNA_bind 29 reiaralglkSpsaveehLkaLerKGyierdp 60
                                    eia++l +  p+av  hL  Le  G+ie   
  gi|116753925|ref|YP_843043.1| 30 NEIAKRLDVG-PKAVIDHLGVLEAAGLIECYR 60
                                   69******99.*****************9765 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.5
                                    -.HHHHHHHHHHHH CS
                  LexA_DNA_bind  38 kSpsaveehLkaLe 51 
                                    +  +a++e L aL+
  gi|116753925|ref|YP_843043.1| 104 RDLRAIHEELSALA 117
                                    55579999999997 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0014
                                    HHHHHTS-.HHHHHHHHHHHHHTTSEE-GGG CS
                  LexA_DNA_bind  31 iaralglkSpsaveehLkaLerKGyierdpg 61 
                                    +a++l++  p+ v e L++Le +G+++ ++g
  gi|116753925|ref|YP_843043.1| 171 LAERLKMP-PAVVRESLARLESRGLVRFENG 200
                                    47778887.999***************9987 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 !    7.7   0.0    0.0056       3.9      20      56 ..      24      60 ..       9      74 .. 0.83
   2 !    8.0   0.0    0.0044       3.1      27      56 ..     170     199 ..     164     202 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0056
                        DUF2250 20 anvdYaksiakeleipleevrellkkLeelGLlerve 56
                                     + Y   iak+l++  + v + l  Le +GL+e + 
  gi|116753925|ref|YP_843043.1| 24 FRPFYFNEIAKRLDVGPKAVIDHLGVLEAAGLIECYR 60
                                   45668889*************************9876 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0044
                        DUF2250  27 siakeleipleevrellkkLeelGLlerve 56 
                                    ++a++l++p   vre l +Le+ GL+   +
  gi|116753925|ref|YP_843043.1| 170 MLAERLKMPPAVVRESLARLESRGLVRFEN 199
                                    7899*********************97655 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00088      0.61       2      43 ..      15      54 ..      14      60 .. 0.87
   2 ?    4.4   0.0     0.052        36      19      43 ..     169     193 ..     155     198 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00088
                         HTH_11  2 llqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg 43
                                   ++ il+lL + r+ +  +e+A++L+v  ++v  ++  Le++g
  gi|116753925|ref|YP_843043.1| 15 RRRILQLL-SFRP-FYFNEIAKRLDVGPKAVIDHLGVLEAAG 54
                                   57889998.6665.899***********************99 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.052
                         HTH_11  19 eeLAeeLnvSrrtvrrdIkaLeelg 43 
                                    e LAe+L++  ++vr  +++Le+ g
  gi|116753925|ref|YP_843043.1| 169 EMLAERLKMPPAVVRESLARLESRG 193
                                    67********************988 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 ?    1.9   0.0      0.29     2e+02      10      49 ..       8      57 ..       4      57 .. 0.66
   2 ?   -2.7   0.1       7.9   5.5e+03       9      25 ..     113     131 ..     113     133 .. 0.59
   3 !   13.5   0.1   6.8e-05     0.047      23      50 ..     170     197 ..     158     199 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.29
                                   CT-CTTBSS..........-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                       HTH_IclR 10 dalaeapqe..........ltlselArrtglpkStvhRlLqtLvelGyve 49
                                   d l+ ++++            + e+A+r+++ + +v  +L  L+  G++e
  gi|116753925|ref|YP_843043.1|  8 DVLGNENRRrilqllsfrpFYFNEIAKRLDVGPKAVIDHLGVLEAAGLIE 57
                                   55555555555555444443478999999988888888888888888875 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7.9
                                    HCT-CTTBSS..-BHHHHH CS
                       HTH_IclR   9 Ldalaeapqe..ltlselA 25 
                                    L ala++  +  +  +++A
  gi|116753925|ref|YP_843043.1| 113 LSALAAEMDRlrMMMADVA 131
                                    5677777777444666666 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 6.8e-05
                                    HHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                       HTH_IclR  23 elArrtglpkStvhRlLqtLvelGyveq 50 
                                     lA+r+ +p++ v+  L+ L+ +G+v+ 
  gi|116753925|ref|YP_843043.1| 170 MLAERLKMPPAVVRESLARLESRGLVRF 197
                                    69************************95 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0    0.0013      0.88      36      66 ..      45      71 ..      18      74 .. 0.73
   2 ?    1.2   0.0      0.51   3.5e+02      33      48 ..     181     196 ..     166     201 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0013
                                   HHHHHHHHTTSEEEEEE-STSSS-EEEEEES CS
                           PadR 36 paLkrLekeglveseweesgegpprkyYrlT 66
                                   + L  Le+ gl+e +++e    ++rky+rl+
  gi|116753925|ref|YP_843043.1| 45 DHLGVLEAAGLIECYRDE----RRRKYFRLA 71
                                   66888**********886....7******97 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.51
                                    HHHHHHHHHHHTTSEE CS
                           PadR  33 slYpaLkrLekeglve 48 
                                     +   L+rLe  glv 
  gi|116753925|ref|YP_843043.1| 181 VVRESLARLESRGLVR 196
                                    5556799******997 PP

>> Hemerythrin  Hemerythrin HHE cation binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   2.2   5.5e-05     0.038       5     101 ..     105     201 ..     101     203 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.5e-05
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHCCC.HCCHHHHHHHHHHHHHHHHHHHHHHCHHHHH.CCC.HHHHHHHHHHHHHH CS
                    Hemerythrin   5 aldeeHralrallerlraladaaaevhga.lrklaelldelvdeleaHhaaEEellfPlledrpggravldvlereHdei 83 
                                     l+++H++l al++++++l   +a+v+   l+  +++++++++   a  ++EEellf ll +++  +   ++l++  +++
  gi|116753925|ref|YP_843043.1| 105 DLRAIHEELSALAAEMDRLRMMMADVATReLELRQRAMRAIEEC--ATDEIEEELLFSLLSGSSTEEMLAERLKMPPAVV 182
                                    68999999999999886665555555555588888888888887..888************9999999999999999999 PP

                                    HHHHHHHH.HHCHTCGGST CS
                    Hemerythrin  84 relleelr.ellkgleeps 101
                                    re l +l+ + l ++e++s
  gi|116753925|ref|YP_843043.1| 183 RESLARLEsRGLVRFENGS 201
                                    9999999988888887665 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 ?    7.3   0.0    0.0068       4.7      39      73 ..      40      69 ..      29      78 .. 0.77
   2 ?   -2.5   0.0       7.4   5.1e+03      49      49 ..     120     120 ..     101     144 .. 0.58
   3 ?   -2.5   0.0       7.5   5.2e+03      12      24 ..     144     156 ..     135     157 .. 0.75
   4 ?    3.1   0.0      0.13        90      42      60 ..     182     200 ..     169     202 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0068
                                   HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEE CS
                         Cdc6_C 39 qrevsdllseLemlgileleksskGrregrtrkis 73
                                    + v d+l  Le+ g++e+ +  +     r ++++
  gi|116753925|ref|YP_843043.1| 40 PKAVIDHLGVLEAAGLIECYRDER-----RRKYFR 69
                                   56799**************99844.....444444 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 7.4
                                    H CS
                         Cdc6_C  49 L 49 
                                    +
  gi|116753925|ref|YP_843043.1| 120 M 120
                                    2 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 7.5
                                    SSS-EEHHHHHHH CS
                         Cdc6_C  12 gkeevttgevyev 24 
                                      ee+ t+e++e+
  gi|116753925|ref|YP_843043.1| 144 AIEECATDEIEEE 156
                                    5688999999885 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.13
                                    HHHHHHHHHHTTSEEEEEE CS
                         Cdc6_C  42 vsdllseLemlgileleks 60 
                                    v++ l++Le++g+++ e++
  gi|116753925|ref|YP_843043.1| 182 VRESLARLESRGLVRFENG 200
                                    67899**********9876 PP

>> HTH_47  winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.023        16      51      77 ..      31      57 ..      29      58 .. 0.95
   2 ?    4.7   0.0     0.033        23      52      77 ..     171     196 ..     142     197 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.023
                                   HHHHHHT--HHHHHHHHHHHHHTT-EE CS
                         HTH_47 51 diAeriglpfdrvaaiaraLaeaglla 77
                                   +iA+r++++ ++v++ +  L++agl++
  gi|116753925|ref|YP_843043.1| 31 EIAKRLDVGPKAVIDHLGVLEAAGLIE 57
                                   79***********************97 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.033
                                    HHHHHT--HHHHHHHHHHHHHTT-EE CS
                         HTH_47  52 iAeriglpfdrvaaiaraLaeaglla 77 
                                    +Aer+++p + v + + +L+  gl++
  gi|116753925|ref|YP_843043.1| 171 LAERLKMPPAVVRESLARLESRGLVR 196
                                    69*********************986 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.075        52      17      47 ..      29      59 ..      24      65 .. 0.90
   2 ?   -2.3   0.2       6.8   4.7e+03      23      36 ..     115     128 ..     107     132 .. 0.77
   3 ?    5.2   0.0     0.032        22      19      46 ..     170     197 ..     163     201 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.075
                           FeoC 17 lkeLsrhfkaspealeamLeqwvrkGrvekv 47
                                   ++e+++++++ p+a+ + L ++++ G +e+ 
  gi|116753925|ref|YP_843043.1| 29 FNEIAKRLDVGPKAVIDHLGVLEAAGLIECY 59
                                   79***********************999875 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 6.8
                           FeoC  23 hfkaspealeamLe 36 
                                    ++ a+++ l+ m++
  gi|116753925|ref|YP_843043.1| 115 ALAAEMDRLRMMMA 128
                                    47788999999987 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.032
                           FeoC  19 eLsrhfkaspealeamLeqwvrkGrvek 46 
                                     L+ ++k+ p+ ++  L+ ++ +G v+ 
  gi|116753925|ref|YP_843043.1| 170 MLAERLKMPPAVVRESLARLESRGLVRF 197
                                    599*********************9985 PP

>> DUF4055  Domain of unknown function (DUF4055)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.6    0.0003      0.21      65     118 ..     110     164 ..      89     178 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0003
                        DUF4055  65 geaiaagkealdrlekqmaalGarlle.ektateTatqaaieaeaenSvLallas 118
                                     e ++a+ +++drl+++ma ++ r le +++a ++ ++ a ++ +e+ + +ll +
  gi|116753925|ref|YP_843043.1| 110 HEELSALAAEMDRLRMMMADVATRELElRQRAMRAIEECATDEIEEELLFSLLSG 164
                                    57788999****************************9999998888777666654 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 ?    8.5   0.0    0.0025       1.7       7      24 ..      30      47 ..      30      50 .. 0.94
   2 ?    0.5   0.0      0.78   5.4e+02       9      22 ..     171     184 ..     169     189 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0025
                          IF2_N  7 yeLAkeLgvkskevikkL 24
                                   +e+Ak+L v +k vi++L
  gi|116753925|ref|YP_843043.1| 30 NEIAKRLDVGPKAVIDHL 47
                                   69**************99 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.78
                          IF2_N   9 LAkeLgvkskevik 22 
                                    LA++L+++++ v +
  gi|116753925|ref|YP_843043.1| 171 LAERLKMPPAVVRE 184
                                    9*******998755 PP

>> ArsR  ArsR transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0     0.006       4.1       8      58 ..       4      57 ..       1      61 [. 0.87
   2 ?    0.0   0.0      0.83   5.8e+02     109     141 ..     112     145 ..     104     151 .. 0.69
   3 ?    0.5   0.0       0.6   4.1e+02      16      57 ..     151     195 ..     142     199 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.006
                           ArsR  8 vpllqvfdsetkkkvyeelskeWlteeeleeklgee...veealklLkkikliE 58
                                   v ll v+++e+ +++++ ls +    +e++++l+     v + l +L+ ++liE
  gi|116753925|ref|YP_843043.1|  4 VELLDVLGNENRRRILQLLSFRPFYFNEIAKRLDVGpkaVIDHLGVLEAAGLIE 57
                                   78999*************************99875533688899999*****99 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.83
                           ArsR 109 lvekiekeveegntsisdls.rklglsplfiral 141
                                      + + +e+++ +++++d++ r+l+l +  +ra+
  gi|116753925|ref|YP_843043.1| 112 ELSALAAEMDRLRMMMADVAtRELELRQRAMRAI 145
                                    4455667777777777777436788888777776 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.6
                           ArsR  16 setkkkvyeelskeWlteeeleeklgee...veealklLkkikli 57 
                                    +e   +++ +l+++  tee l+e+l+     v+e+l+ L+  +l+
  gi|116753925|ref|YP_843043.1| 151 DEIEEELLFSLLSGSSTEEMLAERLKMPpavVRESLARLESRGLV 195
                                    555666777777777888888887776555678888888887776 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 ?   -2.4   0.0       7.6   5.3e+03      31      50 ..      30      49 ..      29      51 .. 0.70
   2 ?   10.4   0.0    0.0008      0.55      25      59 ..     163     197 ..     156     199 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 7.6
                                   HHHHHHHSSTHHHHHHHHHH CS
                          HTH_9 31 relvkktkLsldqVkksLvv 50
                                   +e++k++++ ++ V + L v
  gi|116753925|ref|YP_843043.1| 30 NEIAKRLDVGPKAVIDHLGV 49
                                   57888888888877766655 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0008
                                    HSSBEHHHHHHHHSSTHHHHHHHHHHHHHTTSEEE CS
                          HTH_9  25 kgrltlrelvkktkLsldqVkksLvvLiqhrlVqy 59 
                                    +g +t  +l++++k+++  V+ sL+ L  ++lV++
  gi|116753925|ref|YP_843043.1| 163 SGSSTEEMLAERLKMPPAVVRESLARLESRGLVRF 197
                                    5889999********************99999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       884  (0.0493056); expected 358.6 (0.02)
Passed bias filter:                      649  (0.0361983); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); 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: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1465.63
//
Query:       gi|116753926|ref|YP_843044.1|  [L=721]
Description: AAA family ATPase, CDC48 subfamily protein [Methanosaeta thermophila PT]
Scores for complete 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-97  321.5   0.0    1.9e-47  161.0   0.0    2.3  2  AAA              ATPase family associated with various cellul
    6.1e-33  112.4   0.2      2e-16   59.5   0.0    2.8  2  AAA_lid_3        AAA+ lid domain
    2.5e-27   94.9   0.3    1.5e-26   92.3   0.2    2.4  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
    5.1e-16   58.8   0.0    1.6e-08   34.4   0.0    2.7  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    7.4e-14   51.3   0.2    1.6e-13   50.2   0.2    1.6  1  CDC48_2          Cell division protein 48 (CDC48), domain 2
    9.5e-14   52.1   5.0    4.6e-06   27.1   0.5    3.7  2  AAA_16           AAA ATPase domain
    2.9e-13   50.3   0.0    2.6e-05   24.4   0.0    2.9  2  AAA_2            AAA domain (Cdc48 subfamily)
      3e-12   46.4   0.0    2.7e-05   23.5   0.0    2.6  2  TIP49            TIP49 P-loop domain
    3.1e-12   46.7   0.4    7.5e-06   26.0   0.0    3.5  2  AAA_5            AAA domain (dynein-related subfamily)
    3.9e-11   43.3   0.0    2.3e-05   24.6   0.0    2.5  2  AAA_33           AAA domain
      7e-11   42.5   1.3      0.017   15.4   0.1    3.9  3  AAA_22           AAA domain
    2.7e-08   33.9   0.0      0.011   15.8   0.0    2.4  2  AAA_14           AAA domain
    9.4e-08   31.9   0.2      0.054   13.2   0.1    3.8  2  Sigma54_activat  Sigma-54 interaction domain
    4.7e-07   30.4   0.0       0.02   15.5   0.0    2.7  2  AAA_18           AAA domain
    5.5e-07   29.2   1.0      0.013   14.9   0.1    2.7  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    1.2e-06   28.9   0.0      0.041   14.1   0.0    2.5  2  AAA_28           AAA domain
    2.8e-06   27.2   0.0      0.067   12.9   0.0    2.3  2  IstB_IS21        IstB-like ATP binding protein
    3.3e-06   27.0   0.0      0.065   13.1   0.0    2.5  2  AAA_3            ATPase family associated with various cellul
    7.1e-06   26.0   0.0       0.15   12.1   0.0    2.5  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    8.2e-06   25.5   5.0       0.61    9.6   0.0    4.2  4  AAA_25           AAA domain
    8.7e-06   25.4   0.0      0.077   12.5   0.0    2.6  2  AAA_7            P-loop containing dynein motor region
    2.7e-05   24.5   0.0       0.33   11.4   0.0    2.6  2  RNA_helicase     RNA helicase
    4.9e-05   23.3   0.7       0.95    9.4   0.0    3.9  4  NACHT            NACHT domain
    7.4e-05   22.2   0.5       0.87    8.9   0.0    3.2  3  ATPase           KaiC
    8.6e-05   22.3   0.0       0.16   11.7   0.0    2.4  2  AAA_24           AAA domain
    0.00014   21.7   0.0       0.25   11.1   0.0    2.3  2  AAA_11           AAA domain
    0.00026   20.5   0.4       0.81    9.1   0.1    2.4  2  PhoH             PhoH-like protein
    0.00027   20.1   0.1       0.26   10.3   0.0    2.2  2  Parvo_NS1        Parvovirus non-structural protein NS1
    0.00029   20.6   0.8       0.78    9.4   0.1    2.5  2  AAA_30           AAA domain
    0.00036   19.9   0.5        0.8    8.9   0.0    2.4  2  Zeta_toxin       Zeta toxin
    0.00047   20.3   0.0        1.6    8.9   0.0    2.5  2  Sigma54_activ_2  Sigma-54 interaction domain
    0.00053   20.4   0.0       0.36   11.3   0.0    2.7  2  AAA_17           AAA domain
    0.00081   18.7   0.0       0.45    9.7   0.0    2.2  2  DUF2075          Uncharacterized conserved protein (DUF2075)
    0.00082   19.9   0.0       0.88   10.1   0.0    2.7  2  ABC_tran         ABC transporter
    0.00085   19.7   3.3        1.4    9.3   0.1    3.3  3  AAA_19           AAA domain
     0.0013   18.0   0.0       0.91    8.6   0.0    2.8  3  NB-ARC           NB-ARC domain
     0.0015   18.0   0.0        2.9    7.3   0.0    3.8  4  TniB             Bacterial TniB protein
     0.0018   18.2   0.1        1.3    9.1   0.1    2.6  2  Vps4_C           Vps4 C terminal oligomerisation domain
     0.0021   17.3   0.0       0.79    8.8   0.0    2.6  2  DUF815           Protein of unknown function (DUF815)
     0.0035   17.1   0.1        2.4    7.8   0.0    2.4  2  Cytidylate_kin   Cytidylate kinase
     0.0044   16.9   0.0        0.5   10.2   0.0    2.6  2  CPT              Chloramphenicol phosphotransferase-like prot
     0.0094   16.1   0.0       0.28   11.3   0.0    2.5  2  Cytidylate_kin2  Cytidylate kinase-like family
  ------ inclusion threshold ------
      0.012   15.3   0.1          2    8.0   0.0    3.1  2  Zot              Zonular occludens toxin (Zot)
      0.021   13.7   0.0        6.2    5.6   0.0    2.5  2  AFG1_ATPase      AFG1-like ATPase
      0.022   14.7   0.0        5.2    7.0   0.0    2.5  2  ResIII           Type III restriction enzyme, res subunit
      0.024   14.5   0.2         30    4.4   0.0    3.6  3  ATPase_2         ATPase domain predominantly from Archaea
       0.03   14.0   0.0        7.7    6.2   0.0    2.2  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.033   13.6   0.3        1.3    8.4   0.0    2.3  2  IPT              Isopentenyl transferase
      0.039   13.9   0.0        4.7    7.1   0.0    3.0  3  Rad17            Rad17 P-loop domain
      0.047   13.4   0.3         52    3.4   0.0    3.7  4  Guanylate_kin    Guanylate kinase
      0.072   13.2   0.0          6    7.0   0.0    2.6  2  SKI              Shikimate kinase
        0.1   12.4   0.0         19    5.1   0.0    2.4  2  AAA_29           P-loop containing region of AAA domain
       0.22   11.6   0.0        7.9    6.6   0.0    2.4  2  Torsin           Torsin
       0.25   11.2   2.5         29    4.5   0.0    3.7  3  NTPase_1         NTPase
       0.46   10.7   1.1         13    6.0   0.1    2.3  2  Hydin_ADK        Hydin Adenylate kinase-like 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 !  158.4   0.0   3.7e-49   1.2e-46       1     131 [.     212     341 ..     212     342 .. 0.98
   2 !  161.0   0.0   5.8e-50   1.9e-47       1     131 [.     484     614 ..     484     615 .. 0.97

  Alignments for each domain:
  == domain 1  score: 158.4 bits;  conditional E-value: 3.7e-49
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCH CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgsese 80 
                                    vll+GppGtGKTl+a+ava+e++++f  isg+e++s y gese+++r++f++a+++a psi+fiDEid++a++r++   +
  gi|116753926|ref|YP_843044.1| 212 VLLHGPPGTGKTLIARAVASETDATFTAISGPEIMSRYYGESEQRLRQIFEDAQKSA-PSIIFIDEIDSIAPKREEVLGD 290
                                    79******************************************************9.****************99**** PP

                                    HHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                            AAA  81 eeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                     e+rvv+qLl+ +dg++++ ++vivi+atnrp+ ldpal+r gRfdr++ei+
  gi|116753926|ref|YP_843044.1| 291 LERRVVAQLLSLMDGLTSR-GEVIVIAATNRPNALDPALRRgGRFDREVEIG 341
                                    ******************7.66**************************9986 PP

  == domain 2  score: 161.0 bits;  conditional E-value: 5.8e-50
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.TTCCC CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr.sgses 79 
                                    vllyGppGtGKT++a+ava+e+g++f++i+g+el+sk+vgese+ +re+f++ak+ a p  +f+DEid+++++r sg++s
  gi|116753926|ref|YP_843044.1| 484 VLLYGPPGTGKTMIARAVATESGINFISIKGPELMSKWVGESERAVREVFRKAKQAA-PALIFFDEIDSIVPARdSGRDS 562
                                    79******************************************************9.****************9999** PP

                                    HHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                            AAA  80 eeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                     ++ervv+qLlte+dg+ +  ++v+v++atnrpd +dp llr gRfdr i+i+
  gi|116753926|ref|YP_843044.1| 563 HVTERVVSQLLTEIDGLVEL-KDVVVLAATNRPDLIDPSLLRpGRFDRMIYIQ 614
                                    *******************7.55***************************996 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1   0.0   5.2e-16   1.7e-13       2      36 ..     365     399 ..     364     424 .. 0.83
   2 !   59.5   0.0   6.1e-19     2e-16       1      36 [.     637     672 ..     637     694 .. 0.84

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 5.2e-16
                      AAA_lid_3   2 vdlkeLAerTeGySGADlaalcreAallAlrrgik 36 
                                    +dl+e+Ae+T+G++GADla+lc+eAa+++++r ++
  gi|116753926|ref|YP_843044.1| 365 LDLSEIAEMTHGFVGADLASLCKEAAMHTISRILP 399
                                    79*****************************9655 PP

  == domain 2  score: 59.5 bits;  conditional E-value: 6.1e-19
                      AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgik 36 
                                    dv+++eLA+rT+Gy+GAD++ +creA++lAlr++i+
  gi|116753926|ref|YP_843044.1| 637 DVNIDELAARTDGYTGADIEMICREAGMLALREKIQ 672
                                    9********************************876 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 !   92.3   0.2   4.7e-29   1.5e-26       2      84 ..       7      88 ..       6      89 .. 0.98

  Alignments for each domain:
  == domain 1  score: 92.3 bits;  conditional E-value: 4.7e-29
                                   EEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEEEEEE CS
                        CDC48_N  2 LrVaeapqedvgrgivridpedmeelglepgdvveiegkrkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVtVrka 83
                                   LrVaea+++d+g++i+ri+ +++++lgl++gdvvei+g++k +a++wp++p d  ++iIr+dg++R+n+gv+i+d+V Vr++
  gi|116753926|ref|YP_843044.1|  7 LRVAEAYHRDAGKSIARISLDVINRLGLKNGDVVEIQGRNKVCALAWPGNPGDA-PDIIRIDGNLRSNLGVGIDDRVFVRRT 87
                                   9***************************************************99.*************************98 PP

                                   - CS
                        CDC48_N 84 e 84
                                   e
  gi|116753926|ref|YP_843044.1| 88 E 88
                                   7 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 !   34.4   0.0     5e-11   1.6e-08      35     104 ..     211     288 ..     205     330 .. 0.85
   2 !   21.3   0.0   5.6e-07   0.00018      36      71 ..     484     519 ..     477     558 .. 0.79

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 5e-11
                         RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsraveevl 104
                                     vll+GpPG Gkt +a+ +a+e ++++ + sgP +      e ++ l  ++ + +++   ++fidei  ++++ eevl
  gi|116753926|ref|YP_843044.1| 211 GVLLHGPPGTGKTLIARAVASETDATFTAISGPEImsryygESEQRLRQIFEDAQKSapSIIFIDEIDSIAPKREEVL 288
                                    59*******************************984444444567899999888765337****************98 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 5.6e-07
                         RuvB_N  36 vllyGpPGlGkttlakiiakelgvklkitsgPvlek 71 
                                    vllyGpPG Gkt +a+ +a+e g+++ +  gP l  
  gi|116753926|ref|YP_843044.1| 484 VLLYGPPGTGKTMIARAVATESGINFISIKGPELMS 519
                                    9******************************98753 PP

>> CDC48_2  Cell division protein 48 (CDC48), domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2   0.2     5e-16   1.6e-13       7      63 ..     109     165 ..     104     166 .. 0.93

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 5e-16
                                    CHHHHCCCTTEEE-TTEEEEECCTCCCEEEEEEEECCCCSCEEECTSCCEEESTTCC CS
                        CDC48_2   7 maylkrqFlgrpvtkGdlvvfefkgqeiklvVvstePkgpvgitetTeielgtkpve 63 
                                    ++yl r ++grpvtkG+++++e  ++ +  vVvst+P gpv+it++T i++  ++ e
  gi|116753926|ref|YP_843044.1| 109 PQYLLRILEGRPVTKGEQIRIEMITNYLMMVVVSTTPPGPVVITRDTVINITSEQIE 165
                                    689************************************************998876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.5   1.4e-08   4.6e-06       8     139 ..     183     314 ..     179     316 .. 0.64
   2 !   24.1   0.0   1.2e-07   3.9e-05      15     124 ..     472     573 ..     471     589 .. 0.61

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 1.4e-08
                         AAA_16   8 eleqLlsale.rvrsgrp.........elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysa.laqal 76 
                                    e++++++++e ++r ++            vll+G++G+GK+ ++r+++ +     + f++    +      +s  + +  
  gi|116753926|ref|YP_843044.1| 183 EIRAIREMVElPLRHPEVfqklgitppKGVLLHGPPGTGKTLIARAVASETD---ATFTAISGPEI-----MSRyYGE-- 252
                                    55555555554444444455555555699*******************6333...55777777777.....2331222.. PP

                         AAA_16  77 areellrqllde.aesaeleawrekleealaavpelagaeasrllellkrllallsrderplvl 139
                                      e+ lrq+ ++ ++sa    + +++++ +    e+ g++++r+ ++l +l++ l+++++ +++
  gi|116753926|ref|YP_843044.1| 253 -SEQRLRQIFEDaQKSAPSIIFIDEIDSIAPKREEVLGDLERRVVAQLLSLMDGLTSRGE-VIV 314
                                    .2366666666623444455555666666668888999999***********66665566.333 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 1.2e-07
                         AAA_16  15 alervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqllde.aesae 93 
                                    a+e+v    p+ vll+G++G+GK+ ++r++++   ++g+ f++ k  +l     +s ++    + + +r++ ++ +++a 
  gi|116753926|ref|YP_843044.1| 472 AFEAVGIRPPRGVLLYGPPGTGKTMIARAVAT---ESGINFISIKGPEL-----MSKWVGES-E-RAVREVFRKaKQAAP 541
                                    56666666679********************7...66666999999999.....44455444.2.333333333133355 PP

                         AAA_16  94 leawrekleealaavpelagaea.srllellk 124
                                    +  + +++++ + a ++ ++++  +r+  +l 
  gi|116753926|ref|YP_843044.1| 542 ALIFFDEIDSIVPARDSGRDSHVtERVVSQLL 573
                                    55555656665553333333333644444444 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   8.1e-08   2.6e-05       6     105 ..     212     305 ..     208     319 .. 0.81
   2 !   22.5   0.0     3e-07   9.9e-05       6     103 ..     484     576 ..     479     581 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 8.1e-08
                                    EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG---- CS
                          AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpk 83 
                                    +ll gp g+Gkt++a+a+a+  ++    +++ +   e++     + + ++++  ++    a+++   i+++DEid i+pk
  gi|116753926|ref|YP_843044.1| 212 VLLHGPPGTGKTLIARAVASETDA----TFTAISGPEIMS----RYYGESEQRLRQIFEDAQKSApsIIFIDEIDSIAPK 283
                                    6889******************96....************....55555555555555555544488************9 PP

                                    .---------HHHHHHHHHHHH- CS
                          AAA_2  84 .essgadvSregVqrdLLqileg 105
                                     e+   d  r  V+  LL +++g
  gi|116753926|ref|YP_843044.1| 284 rEEVLGDLERR-VVAQLLSLMDG 305
                                    88888888776.66778899987 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 3e-07
                                    EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG---- CS
                          AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpk 83 
                                    +ll gp g+Gkt++a+a+a    +    ++i +   el+     + + +++   ++   +a++     +++DEid i p 
  gi|116753926|ref|YP_843044.1| 484 VLLYGPPGTGKTMIARAVATESGI----NFISIKGPELMS----KWVGESERAVREVFRKAKQAApaLIFFDEIDSIVPA 555
                                    6899*******************8....************....66666677777777777777799************9 PP

                                    ------.---HHHHHHHHHHH CS
                          AAA_2  84 essgad.vSregVqrdLLqil 103
                                    + sg+d    e V+  LL  +
  gi|116753926|ref|YP_843044.1| 556 RDSGRDsHVTERVVSQLLTEI 576
                                    555555145677777777655 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   1.1e-06   0.00037      51      97 ..     210     254 ..     202     267 .. 0.86
   2 !   23.5   0.0   8.3e-08   2.7e-05      51     106 ..     482     536 ..     478     539 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.1e-06
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte 97 
                                    ++vLl Gp+gtGkt +a a++ e   d  f+a+sg e+ s     +e
  gi|116753926|ref|YP_843044.1| 210 KGVLLHGPPGTGKTLIARAVASET--DATFTAISGPEIMSRYYGESE 254
                                    89*******************996..689*********998776666 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 8.3e-08
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXX CS
                          TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte.vltqalrks 106
                                    r+vLl Gp+gtGkt +a a++ e g  + f++++g e+ s  v  +e ++ + +rk+
  gi|116753926|ref|YP_843044.1| 482 RGVLLYGPPGTGKTMIARAVATESG--INFISIKGPELMSKWVGESErAVREVFRKA 536
                                    89********************987..****************99985688999997 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   2.3e-08   7.5e-06       1     136 [.     211     330 ..     211     333 .. 0.70
   2 !   16.6   0.1   1.8e-05    0.0058       1      34 [.     483     516 ..     483     603 .. 0.75

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 2.3e-08
                                    EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG-- CS
                          AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEverae 78 
                                    +vlL GppGtgK+ +a+ +a+ + ++++ + +++ +++             +++  +++   a+   ++i+++DE++ + 
  gi|116753926|ref|YP_843044.1| 211 GVLLHGPPGTGKTLIARAVASETDATFTAISGPEIMSRYYGES--------EQRLRQIFE-DAQksAPSIIFIDEIDSIA 281
                                    59*******************************9665432222........222234555.44447899********998 PP

                                    HHHHHHHHHHHHSSEEE..-SSSEEE---........-EEEEEESS--.-TT-TTHHHHT CS
                          AAA_5  79 sevlnsLlslleerrllleeggelvkaknddller..frviatanpldrslnelspalrs 136
                                    ++  ++L   le+r +   ++  l++       +r  + via++n+++     l+palr+
  gi|116753926|ref|YP_843044.1| 282 PKREEVL-GDLERRVVA--QLLSLMDGLT----SRgeVIVIAATNRPN----ALDPALRR 330
                                    7655555.334444443..4444443333....222399******999....88999986 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1.8e-05
                                    EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--T CS
                          AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltr 34 
                                    +vlL GppGtgK+++a+ +a   + ++  + +++
  gi|116753926|ref|YP_843044.1| 483 GVLLYGPPGTGKTMIARAVATESGINFISIKGPE 516
                                    59***************99876666655555555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0     7e-08   2.3e-05       2      79 ..     212     319 ..     212     356 .. 0.73
   2 !   16.2   0.0   2.7e-05    0.0087       2      43 ..     484     527 ..     484     611 .. 0.71

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 7e-08
                         AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt............................dytrv 51 
                                    vll+G+pG+GK+  a+ ++ +++  ++ +s +++++r++g+ +q+++                             + ++
  gi|116753926|ref|YP_843044.1| 212 VLLHGPPGTGKTLIARAVASETDatFTAISGPEIMSRYYGESEQRLRqifedaqksapsiifideidsiapkreeVLGDL 291
                                    799****************999998999************9888888667776777777777777777766444322223 PP

                         AAA_33  52 ldrlyqilnelarkalsagrnvildatn 79 
                                    + r+ ++l  l +   s+g  +++ atn
  gi|116753926|ref|YP_843044.1| 292 ERRVVAQLLSLMDGLTSRGEVIVIAATN 319
                                    3445555556665555555555556665 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 2.7e-05
                         AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqq 43 
                                    vll G+pG+GK+  a+ ++ + g  ++ +  ++l+++ +g+ ++
  gi|116753926|ref|YP_843044.1| 484 VLLYGPPGTGKTMIARAVATESGinFISIKGPELMSKWVGESER 527
                                    7899*******************988889999988877774433 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   5.1e-05     0.017       8      33 ..     212     237 ..     208     262 .. 0.75
   2 !    8.6   0.1    0.0064       2.1      72     116 ..     251     295 ..     238     317 .. 0.74
   3 !   15.3   0.1   5.4e-05     0.018       8      51 ..     484     518 ..     479     587 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.1e-05
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeea 33 
                                    ++++G++GtGKT+ +r ++++ d+  
  gi|116753926|ref|YP_843044.1| 212 VLLHGPPGTGKTLIARAVASETDATF 237
                                    589****************9987544 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0064
                         AAA_22  72 rlsseellealeqalraravielliiDEaqhlr..seealeeLrsll 116
                                    + s+++l++ +e+a +++    ++ iDE++ +   +ee+l +L +++
  gi|116753926|ref|YP_843044.1| 251 GESEQRLRQIFEDAQKSAPS--IIFIDEIDSIApkREEVLGDLERRV 295
                                    45677777777777777766..**********876588888884443 PP

  == domain 3  score: 15.3 bits;  conditional E-value: 5.4e-05
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst 51 
                                    ++++G++GtGKT+ +r ++ +          +  +++++ p+++
  gi|116753926|ref|YP_843044.1| 484 VLLYGPPGTGKTMIARAVATES---------GINFISIKGPELM 518
                                    689***************9997.........6666666666655 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   4.1e-05     0.013       5      76 ..     212     280 ..     209     319 .. 0.77
   2 !   15.8   0.0   3.3e-05     0.011       5      81 ..     484     557 ..     481     593 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.1e-05
                         AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76 
                                    +++ G+  +GKT +++ +++e       +  i+  +   + + ++e+ l+ i+e ++++  +++f+DEi  +
  gi|116753926|ref|YP_843044.1| 212 VLLHGPPGTGKTLIARAVASETD---ATFTAISGPEIMSRYYGESEQRLRQIFEDAQKSAPSIIFIDEIDSI 280
                                    7899***************9988...89999999998888777777666777776566699********988 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 3.3e-05
                         AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderd..kkladpekllelileklkeekktylflDEiqevpewek 81 
                                    +++ G+  +GKT++++ ++ e+      i +i+++ +++  k   ++e+  +++++k+k+    ++f+DEi  +  +++
  gi|116753926|ref|YP_843044.1| 484 VLLYGPPGTGKTMIARAVATESG-----INFISIKGPELmsKWVGESERAVREVFRKAKQAAPALIFFDEIDSIVPARD 557
                                    7899**************98888.....666666666662244445554555555555556899*******99855544 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.1   0.00017     0.054      23     143 ..     210     320 ..     199     332 .. 0.65
   2 !   10.8   0.0   0.00088      0.29      23      46 ..     482     505 ..     471     612 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00017
                                    S-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BEHHHHHTTT...SEEEE CS
                Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAekekkGlfekadg...GtlfL 99 
                                      vl++G  GtGK+l+ara+ +++   ++ f a+   +     ++s+ +G ++          +  fe a++   +++f+
  gi|116753926|ref|YP_843044.1| 210 KGVLLHGPPGTGKTLIARAVASET---DATFTAISGPE-----IMSRYYGESEQRL-------RQIFEDAQKsapSIIFI 274
                                    579****************97654...46666554433.....4566666544332.......23344333311167888 PP

                                    ETGGGS-HHHHHHHHHHHHHSEEESBTSSS...EEE--EEEEEEESS CS
                Sigma54_activat 100 DeigelplelQekLlrvlqegevervGssk...eikvdvriiaatne 143
                                    Dei ++ ++  e++l  l+++ v ++ s     + + +v +iaatn+
  gi|116753926|ref|YP_843044.1| 275 DEIDSIAPKR-EEVLGDLERRVVAQLLSLMdglTSRGEVIVIAATNR 320
                                    8888887764.566777888877776543211256677777777776 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00088
                                    S-EEEECSTTSSHHHHHHHHHHHS CS
                Sigma54_activat  23 lsvlitGesGtGKellaraiheas 46 
                                      vl+ G  GtGK+++ara+ ++s
  gi|116753926|ref|YP_843044.1| 482 RGVLLYGPPGTGKTMIARAVATES 505
                                    569****************98766 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    0.0006      0.19       1      23 [.     212     235 ..     212     318 .. 0.73
   2 !   15.5   0.0     6e-05      0.02       1      44 [.     484     525 ..     484     591 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0006
                         AAA_18   1 IlltGtpGvGKttlakeLskrl.g 23 
                                    +ll G+pG+GKt +a+++++++ +
  gi|116753926|ref|YP_843044.1| 212 VLLHGPPGTGKTLIARAVASETdA 235
                                    7899**************998633 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 6e-05
                         AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpe 44 
                                    +ll G+pG+GKt +a++++ +   g+n +++   + ++ +v + 
  gi|116753926|ref|YP_843044.1| 484 VLLYGPPGTGKTMIARAVATES--GINFISIKGPELMSKWVGES 525
                                    799***************9987..77777776655555554444 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.1    0.0003     0.099      25      43 ..     212     230 ..     204     238 .. 0.90
   2 !   14.9   0.1   3.9e-05     0.013      25      43 ..     484     502 ..     475     504 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0003
                   Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                    +ll GppG+GKt++a++++
  gi|116753926|ref|YP_843044.1| 212 VLLHGPPGTGKTLIARAVA 230
                                    89*************9875 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 3.9e-05
                   Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                    +ll+GppG+GKtm+a++++
  gi|116753926|ref|YP_843044.1| 484 VLLYGPPGTGKTMIARAVA 502
                                    89*************9875 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   0.00013     0.041       2      49 ..     212     264 ..     211     285 .. 0.79
   2 !   12.2   0.0   0.00048      0.15       2      34 ..     484     521 ..     483     548 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 0.00013
                         AAA_28   2 ivitGgestGKTtlleaLaar...gypvv..pEaareileeklakgedalpwv 49 
                                    + + G+++tGKT +++a a++    ++ +  pE++ +++ e  ++ +++ +++
  gi|116753926|ref|YP_843044.1| 212 VLLHGPPGTGKTLIARAVASEtdaTFTAIsgPEIMSRYYGESEQRLRQIFEDA 264
                                    6799***************5546544444599999999998888888777664 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00048
                         AAA_28   2 ivitGgestGKTtlleaLaar.gypvv....pEaarei 34 
                                    + + G+++tGKT +++a a + g++ +    pE + + 
  gi|116753926|ref|YP_843044.1| 484 VLLYGPPGTGKTMIARAVATEsGINFIsikgPELMSKW 521
                                    6799***************7667775533444444444 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 !   11.7   0.0   0.00049      0.16      48      70 ..     210     232 ..     201     244 .. 0.88
   2 !   12.9   0.0    0.0002     0.067      48      70 ..     482     504 ..     477     551 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00049
                      IstB_IS21  48 enivllGpsGvGKshlaialgve 70 
                                    ++++l Gp+G+GK+ +a a++ e
  gi|116753926|ref|YP_843044.1| 210 KGVLLHGPPGTGKTLIARAVASE 232
                                    6799***************9976 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.0002
                      IstB_IS21  48 enivllGpsGvGKshlaialgve 70 
                                     +++l Gp+G+GK+ +a a+++e
  gi|116753926|ref|YP_843044.1| 482 RGVLLYGPPGTGKTMIARAVATE 504
                                    5799***************9876 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0    0.0002     0.065       2      36 ..     212     245 ..     211     322 .. 0.76
   2 !   11.4   0.0   0.00066      0.22       2      43 ..     484     523 ..     483     604 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.0002
                          AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdl 36 
                                    vll+g PG++ktl+++a+a+  d++f+ i   p++
  gi|116753926|ref|YP_843044.1| 212 VLLHGPPGTGKTLIARAVASETDATFTAIS-GPEI 245
                                    89************************9885.4555 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00066
                          AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdllPsdilG 43 
                                    vll g PG++kt++++a+a+  +++f  i+  p+l+    +G
  gi|116753926|ref|YP_843044.1| 484 VLLYGPPGTGKTMIARAVATESGINFISIK-GPELMSKW-VG 523
                                    7999********************999887.57777543.34 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00079      0.26      19      51 ..     209     243 ..     185     260 .. 0.76
   2 !   12.1   0.0   0.00046      0.15      21      51 ..     483     515 ..     452     525 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00079
                                    TEEEEEEESTTSSHHHHHHHHHHHTT--..----T CS
                           TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve..evkSP 51 
                                     + +lL+G+ G+GKT ++r++a++ + +  +++ P
  gi|116753926|ref|YP_843044.1| 209 PKGVLLHGPPGTGKTLIARAVASETDATftAISGP 243
                                    3459*******************998877667766 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00046
                                    EEEEEESTTSSHHHHHHHHHHHTT--..----T CS
                           TsaE  21 vilLeGdLGaGKTtlvrglakalgve..evkSP 51 
                                     +lL+G+ G+GKT+++r++a + g++  ++k P
  gi|116753926|ref|YP_843044.1| 483 GVLLYGPPGTGKTMIARAVATESGINfiSIKGP 515
                                    39*********************9987777776 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1     0.017       5.5      36      54 ..     212     230 ..     205     233 .. 0.85
   2 ?    1.6   0.0      0.53   1.7e+02     128     176 ..     255     303 ..     234     318 .. 0.82
   3 !    9.6   0.0    0.0019      0.61      36      54 ..     484     502 ..     477     509 .. 0.87
   4 ?    6.4   0.1     0.018       5.9     127     172 ..     526     572 ..     515     590 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.017
                         AAA_25  36 allaGapgtGKttlaldla 54 
                                    +ll G+pgtGKt +a  +a
  gi|116753926|ref|YP_843044.1| 212 VLLHGPPGTGKTLIARAVA 230
                                    689**********997766 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.53
                         AAA_25 128 advdaleaaieevegvrlvviDplsralggdensnsdv.galvealeria 176
                                    + ++++ +++++   +  + iD ++++ +  e+   d  +++v++l ++ 
  gi|116753926|ref|YP_843044.1| 255 QRLRQIFEDAQK-SAPSIIFIDEIDSIAPKREEVLGDLeRRVVAQLLSLM 303
                                    456788888888.5699999999999999988888887699999988775 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0019
                         AAA_25  36 allaGapgtGKttlaldla 54 
                                    +ll+G+pgtGKt++a  +a
  gi|116753926|ref|YP_843044.1| 484 VLLYGPPGTGKTMIARAVA 502
                                    69***********997666 PP

  == domain 4  score: 6.4 bits;  conditional E-value: 0.018
                         AAA_25 127 tadvdaleaaieevegvrlvviDplsralgg.densnsdv.galveal 172
                                    +++v+++ +++++ + ++l+ +D +++++++ d+ ++s v +++v++l
  gi|116753926|ref|YP_843044.1| 526 ERAVREVFRKAKQ-AAPALIFFDEIDSIVPArDSGRDSHVtERVVSQL 572
                                    5789999******.66***************99999999777777765 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 !   12.5   0.0   0.00024     0.077      30      62 ..     206     237 ..     197     283 .. 0.83
   2 !   10.0   0.0    0.0014      0.45      34      55 ..     482     503 ..     476     513 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00024
                          AAA_7  30 lknkkpvllvGptGtGKtviikdllkkldkeky 62 
                                    ++  k vll Gp GtGKt+i++ + ++ d  ++
  gi|116753926|ref|YP_843044.1| 206 ITPPKGVLLHGPPGTGKTLIARAVASETD-ATF 237
                                    666789****************9999988.444 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0014
                          AAA_7  34 kpvllvGptGtGKtviikdllk 55 
                                    + vll+Gp GtGKt+i++ + +
  gi|116753926|ref|YP_843044.1| 482 RGVLLYGPPGTGKTMIARAVAT 503
                                    569*************998654 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0     0.001      0.33       1      36 [.     212     247 ..     212     280 .. 0.76
   2 !   10.5   0.0    0.0019      0.62       1      21 [.     484     504 ..     484     547 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.001
                   RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvys 36 
                                    ++l+Gp+g+GK+++a+ +a++   ++  ++ ++++s
  gi|116753926|ref|YP_843044.1| 212 VLLHGPPGTGKTLIARAVASETDATFTAISGPEIMS 247
                                    689**************8877766664444444433 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0019
                   RNA_helicase   1 iwlyGpsgeGKStlakeLaka 21 
                                    ++lyGp+g+GK+++a+ +a++
  gi|116753926|ref|YP_843044.1| 484 VLLYGPPGTGKTMIARAVATE 504
                                    689*************98776 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0    0.0084       2.7       3      23 ..     212     232 ..     210     237 .. 0.90
   2 ?   -0.5   0.0       3.1     1e+03      66     131 ..     254     320 ..     240     350 .. 0.63
   3 !    9.4   0.0    0.0029      0.95       3      23 ..     484     504 ..     482     506 .. 0.89
   4 ?    0.8   0.0       1.3   4.1e+02      64     113 ..     524     573 ..     515     619 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0084
                                    EEEEC-TTTCHHHHHHHHHHH CS
                          NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                    v+l+G++G GKT  ++ +a++
  gi|116753926|ref|YP_843044.1| 212 VLLHGPPGTGKTLIARAVASE 232
                                    79**************99986 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 3.1
                                    -SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH............HHHHHCTTTTT--EEEEEEECCC CS
                          NACHT  66 aapvsevwavllelperlLlilDglDelvtdlgq...kekqpvrtlLselirkkllpeasllltvrpra 131
                                    +++ +++++  ++ + ++ + +D +D ++ + ++   + +++v   L +l+ + l ++  +++++ +++
  gi|116753926|ref|YP_843044.1| 254 EQRLRQIFEDAQKSAPSIIF-IDEIDSIAPKREEvlgDLERRVVAQLLSLMDG-LTSRGEVIVIAATNR 320
                                    55555544444455555544.69999999888878884455555555588887.444444444443333 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0029
                                    EEEEC-TTTCHHHHHHHHHHH CS
                          NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                    v+l G++G GKT+ ++ +a++
  gi|116753926|ref|YP_843044.1| 484 VLLYGPPGTGKTMIARAVATE 504
                                    899*************99875 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 1.3
                                    S--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH..........HHHHH CS
                          NACHT  64 epaapvsevwavllelperlLlilDglDelvtdlgq.kekqpvrtlLseli 113
                                    e++++v+ev+   ++++  +L+ +D +D +v   +   +   ++++ s+l+
  gi|116753926|ref|YP_843044.1| 524 ESERAVREVFR-KAKQAAPALIFFDEIDSIVPARDSgRDSHVTERVVSQLL 573
                                    56666677444.36888899999******9987777633333444444444 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.1     0.004       1.3      14      37 ..     204     227 ..     198     237 .. 0.85
   2 ?    1.0   0.0       0.7   2.3e+02     109     153 ..     255     305 ..     234     318 .. 0.67
   3 !    8.9   0.0    0.0027      0.87      15      37 ..     477     499 ..     457     510 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.004
                         ATPase  14 gGipegrvvlitGepGtGKtifal 37 
                                     Gi   + vl+ G pGtGKt++a 
  gi|116753926|ref|YP_843044.1| 204 LGITPPKGVLLHGPPGTGKTLIAR 227
                                    58888889*************986 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.7
                         ATPase 109 eelaeaikeika...krvviDsitglayeekeav....aReilrqlvrvlkk 153
                                    ++l+++ ++ +    + + iD i+++   ++e+v     R+ + ql++ + +
  gi|116753926|ref|YP_843044.1| 255 QRLRQIFEDAQKsapSIIFIDEIDSI-APKREEVlgdlERRVVAQLLSLMDG 305
                                    45555555544433477889999998.3333333122268888888888865 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0027
                         ATPase  15 GipegrvvlitGepGtGKtifal 37 
                                    Gi   r vl++G pGtGKt++a 
  gi|116753926|ref|YP_843044.1| 477 GIRPPRGVLLYGPPGTGKTMIAR 499
                                    8888899*************986 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    0.0061         2       5      43 ..     212     245 ..     209     289 .. 0.61
   2 !   11.7   0.0   0.00048      0.16       5      22 ..     484     501 ..     481     553 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0061
                         AAA_24   5 iliyGpsgiGKTtlakelgpkplfidtekGlksldadkf 43 
                                    +l+ Gp+g+GKT +a+          t++ + ++ + ++
  gi|116753926|ref|YP_843044.1| 212 VLLHGPPGTGKTLIARAV-----ASETDATFTAISGPEI 245
                                    799*********999877.....5555555555555554 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00048
                         AAA_24   5 iliyGpsgiGKTtlakel 22 
                                    +l+yGp+g+GKT++a+  
  gi|116753926|ref|YP_843044.1| 484 VLLYGPPGTGKTMIARAV 501
                                    79***********99876 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00077      0.25      20      41 ..     212     233 ..     194     269 .. 0.81
   2 !    8.3   0.0    0.0055       1.8      20      38 ..     484     502 ..     458     540 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00077
                         AAA_11  20 tliqGPPGtgKTktivellsql 41 
                                    +l++GPPGtgKT    ++ s+ 
  gi|116753926|ref|YP_843044.1| 212 VLLHGPPGTGKTLIARAVASET 233
                                    79**********8777776655 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0055
                         AAA_11  20 tliqGPPGtgKTktivell 38 
                                    +l+ GPPGtgKT    ++ 
  gi|116753926|ref|YP_843044.1| 484 VLLYGPPGTGKTMIARAVA 502
                                    6999********7766655 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.1    0.0025      0.81      22      42 ..     212     232 ..     204     253 .. 0.89
   2 !    9.0   0.0    0.0028       0.9      22      42 ..     484     504 ..     477     509 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0025
                                    EEEE--TTSSTTHHHHHHHHH CS
                           PhoH  22 vfaiGpaGtGKtylavalave 42 
                                    v   Gp GtGKt++a a+a e
  gi|116753926|ref|YP_843044.1| 212 VLLHGPPGTGKTLIARAVASE 232
                                    6788***********999865 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0028
                                    EEEE--TTSSTTHHHHHHHHH CS
                           PhoH  22 vfaiGpaGtGKtylavalave 42 
                                    v   Gp GtGKt++a a+a e
  gi|116753926|ref|YP_843044.1| 484 VLLYGPPGTGKTMIARAVATE 504
                                    6789************99976 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 !    7.4   0.0    0.0065       2.1     117     137 ..     212     232 ..     205     237 .. 0.88
   2 !   10.3   0.0   0.00079      0.26     117     136 ..     484     503 ..     479     507 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0065
                      Parvo_NS1 117 vwfyGpantGktnlaeaIaka 137
                                    v+++Gp+ tGkt +a+a a  
  gi|116753926|ref|YP_843044.1| 212 VLLHGPPGTGKTLIARAVASE 232
                                    899**************9875 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00079
                      Parvo_NS1 117 vwfyGpantGktnlaeaIak 136
                                    v++yGp+ tGkt++a+a a+
  gi|116753926|ref|YP_843044.1| 484 VLLYGPPGTGKTMIARAVAT 503
                                    89***************986 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.1    0.0024      0.78      21      40 ..     212     231 ..     200     242 .. 0.84
   2 !    9.0   0.0    0.0033       1.1      19      39 ..     482     502 ..     471     508 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0024
                         AAA_30  21 avltGpAGtGKttalkalre 40 
                                    ++l+Gp+GtGKt + +a++ 
  gi|116753926|ref|YP_843044.1| 212 VLLHGPPGTGKTLIARAVAS 231
                                    689***********999975 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0033
                         AAA_30  19 rvavltGpAGtGKttalkalr 39 
                                    r ++l Gp+GtGKt++ +a++
  gi|116753926|ref|YP_843044.1| 482 RGVLLYGPPGTGKTMIARAVA 502
                                    567899**********99986 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.1    0.0033       1.1      16      41 ..     209     234 ..     201     243 .. 0.88
   2 !    8.9   0.0    0.0025       0.8      16      51 ..     481     514 ..     474     519 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0033
                     Zeta_toxin  16 PklillgGqpGAGKselaellkdele 41 
                                    Pk +ll G pG GK+ +a++++ e++
  gi|116753926|ref|YP_843044.1| 209 PKGVLLHGPPGTGKTLIARAVASETD 234
                                    999******************99986 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0025
                     Zeta_toxin  16 PklillgGqpGAGKselaellkdelerqgnvvrldp 51 
                                    P  +ll G pG GK+ +a+++++e   + n++ +++
  gi|116753926|ref|YP_843044.1| 481 PRGVLLYGPPGTGKTMIARAVATES--GINFISIKG 514
                                    77799******************98..888888765 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0    0.0048       1.6      24      83 ..     212     282 ..     207     295 .. 0.59
   2 !    8.7   0.0    0.0055       1.8      24      48 ..     484     508 ..     478     559 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0048
                                    EEEEEETT--HHHHHHCC--TTS-E.E-...-SSTTHHHH-H.......HHHHHHT...TTSEEEEEE-TT--H CS
                Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpw.le...ifvverlaklp.......ldlleqa...kggtLylkdiadlsk 83 
                                    v+l G++G+gk+l+Ar+ +++      +   + ++ r             +++e a    + ++++ +i+++ +
  gi|116753926|ref|YP_843044.1| 212 VLLHGPPGTGKTLIARAVASETDATfTAisgPEIMSRY---YgeseqrlRQIFEDAqksAPSIIFIDEIDSIAP 282
                                    9****************987654320220002222222...022223334444443333677777777777655 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0055
                                    EEEEEETT--HHHHHHCC--TTS-E CS
                Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpw 48 
                                    v+l G++G+gk+++Ar+ + +sg +
  gi|116753926|ref|YP_843044.1| 484 VLLYGPPGTGKTMIARAVATESGIN 508
                                    9****************99988763 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.036        12       2      30 ..     216     246 ..     215     294 .. 0.77
   2 !   11.3   0.0    0.0011      0.36       1      30 [.     487     517 ..     487     549 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.036
                                    E-TTSSHHHHHHHHHHHH..TEEEEEHHHHH CS
                         AAA_17   2 GgPGsGKgtqceklveky..gfthlsaGdll 30 
                                    G+PG GK+ +++ ++ +    ft +s  +++
  gi|116753926|ref|YP_843044.1| 216 GPPGTGKTLIARAVASETdaTFTAISGPEIM 246
                                    9**********99998773367777765555 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0011
                                    EE-TTSSHHHHHHHHHHHHTEEEEEH.HHHH CS
                         AAA_17   1 lGgPGsGKgtqceklvekygfthlsa.Gdll 30 
                                    +G+PG GK+ +++ ++ + g+ ++s  G  l
  gi|116753926|ref|YP_843044.1| 487 YGPPGTGKTMIARAVATESGINFISIkGPEL 517
                                    7*******************99998655444 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0    0.0014      0.45       4      25 ..     212     233 ..     209     284 .. 0.79
   2 !    7.0   0.0    0.0094       3.1       4      25 ..     484     505 ..     481     536 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0014
                        DUF2075   4 vlVtGvaGtGKtvvllnllael 25 
                                    vl +G +GtGKt+++ +++ e 
  gi|116753926|ref|YP_843044.1| 212 VLLHGPPGTGKTLIARAVASET 233
                                    6889***********9999987 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0094
                        DUF2075   4 vlVtGvaGtGKtvvllnllael 25 
                                    vl  G +GtGKt+++ ++++e 
  gi|116753926|ref|YP_843044.1| 484 VLLYGPPGTGKTMIARAVATES 505
                                    6789***********9999886 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0    0.0027      0.88       7      67 ..     205     263 ..     202     313 .. 0.78
   2 ?    7.0   0.0     0.024         8      10      36 ..     480     506 ..     475     586 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0027
                                    EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe 67 
                                     + + + v + G+ G+GK+ +++++a +++ t   i   g ++ ++   +++++++ ++++
  gi|116753926|ref|YP_843044.1| 205 GITPPKGVLLHGPPGTGKTLIARAVASETDATFTAI--SGPEIMSRYYGESEQRLRQIFED 263
                                    566677799********************9988777..56666665566666666666666 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.024
                                    TTSEEEEEESTTSSHHHHHHHHTTSS- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  10 egekvaivGenGaGKStLlkllagllk 36 
                                    + + v + G+ G+GK+ +++++a ++ 
  gi|116753926|ref|YP_843044.1| 480 PPRGVLLYGPPGTGKTMIARAVATESG 506
                                    5566889**************998864 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.3    0.0063         2      10      33 ..     209     232 ..     202     271 .. 0.84
   2 ?   -0.4   0.0         4   1.3e+03      98     126 ..     264     292 ..     244     302 .. 0.72
   3 !    9.3   0.1    0.0042       1.4       8      30 ..     479     501 ..     473     513 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0063
                         AAA_19  10 ekvllvtaGpGtGKTrvlkhival 33 
                                     k +l+ ++pGtGKT + +++ ++
  gi|116753926|ref|YP_843044.1| 209 PKGVLLHGPPGTGKTLIARAVASE 232
                                    56789**********998877655 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 4
                         AAA_19  98 kklqeeellivDEfqdvdelqyrLlkall 126
                                     +  +  ++++DE+  + +   ++l  l 
  gi|116753926|ref|YP_843044.1| 264 AQKSAPSIIFIDEIDSIAPKREEVLGDLE 292
                                    33334569********9998888887776 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0042
                         AAA_19   8 lkekvllvtaGpGtGKTrvlkhi 30 
                                     + + +l+ ++pGtGKT + +++
  gi|116753926|ref|YP_843044.1| 479 RPPRGVLLYGPPGTGKTMIARAV 501
                                    5567799**********987765 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0028      0.91      23      45 ..     212     234 ..     198     241 .. 0.82
   2 ?    5.9   0.0      0.02       6.4      23      43 ..     484     504 ..     481     511 .. 0.88
   3 ?   -2.2   0.0       5.7   1.8e+03      49      76 ..     605     632 ..     601     645 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0028
                                    EEEEESTTSSHHHHHHHHCCSHC CS
                         NB-ARC  23 valvGmgGvGKttlakqilnksd 45 
                                    v l+G +G GKt +a+ + ++ d
  gi|116753926|ref|YP_843044.1| 212 VLLHGPPGTGKTLIARAVASETD 234
                                    789**************999855 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.02
                                    EEEEESTTSSHHHHHHHHCCS CS
                         NB-ARC  23 valvGmgGvGKttlakqilnk 43 
                                    v l+G +G GKt +a+ +  +
  gi|116753926|ref|YP_843044.1| 484 VLLYGPPGTGKTMIARAVATE 504
                                    679*************99876 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 5.7
                                    CCBTEEEEEEEESXXHHHHHHHXXHHHH CS
                         NB-ARC  49 grFdsvawvvvsktdkseeiletilkeL 76 
                                    grFd+++++++ +    ++i+e  ++++
  gi|116753926|ref|YP_843044.1| 605 GRFDRMIYIQMPDLAARKKIFEIYMRKM 632
                                    69*****************999766665 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.041        13      34      60 ..     208     234 ..     195     246 .. 0.81
   2 ?   -1.0   0.0       3.1     1e+03     110     132 ..     259     281 ..     237     294 .. 0.71
   3 !    7.3   0.0    0.0089       2.9      36      56 ..     482     502 ..     457     509 .. 0.87
   4 ?   -1.5   0.0       4.4   1.4e+03     108     135 ..     529     556 ..     515     564 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.041
                           TniB  34 rmpnlllvGdsnnGKtmivekFarlhp 60 
                                     ++ +ll+G++ +GKt i++  a++  
  gi|116753926|ref|YP_843044.1| 208 PPKGVLLHGPPGTGKTLIARAVASETD 234
                                    56789*************998877665 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.1
                           TniB 110 qvlrllrelkvrvLiiDEihnll 132
                                    q+ +  ++  + ++ iDEi+++ 
  gi|116753926|ref|YP_843044.1| 259 QIFEDAQKSAPSIIFIDEIDSIA 281
                                    3344445667899******9986 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0089
                           TniB  36 pnlllvGdsnnGKtmivekFa 56 
                                    + +ll+G++ +GKtmi++  a
  gi|116753926|ref|YP_843044.1| 482 RGVLLYGPPGTGKTMIARAVA 502
                                    689*************98765 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 4.4
                           TniB 108 eqqvlrllrelkvrvLiiDEihnllags 135
                                     ++v r  ++  + ++ +DEi++++ ++
  gi|116753926|ref|YP_843044.1| 529 VREVFRKAKQAAPALIFFDEIDSIVPAR 556
                                    334444445667889999***9998655 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 !    9.1   0.1     0.004       1.3      18      45 ..     406     433 ..     401     443 .. 0.84
   2 ?    6.2   0.0     0.031        10      25      61 .]     683     719 ..     674     719 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.004
                         Vps4_C  18 dipsdkllePpvtlkDflkalkkarptV 45 
                                    +ip++ l + +v+++Dfl+a+kk  p+ 
  gi|116753926|ref|YP_843044.1| 406 EIPPEILDQLKVSREDFLAAMKKIEPSA 433
                                    6887778888***************996 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.031
                         Vps4_C  25 lePpvtlkDflkalkkarptVskeDLekheeFTkefG 61 
                                     + +v++++f++a ++ +p   +e L+++ +  + fG
  gi|116753926|ref|YP_843044.1| 683 SQIQVRRDHFERAYQNIKPHMPPETLKEYLRIMEMFG 719
                                    345999*********************9988777777 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.023       7.5      52      81 ..     208     237 ..     197     325 .. 0.68
   2 !    8.8   0.0    0.0024      0.79      21      85 ..     440     510 ..     422     551 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.023
                         DUF815  52 pannvLLwGarGtGKSslvkallneyaeeg 81 
                                    p + vLL G  GtGK  + +a+ +e+ ++ 
  gi|116753926|ref|YP_843044.1| 208 PPKGVLLHGPPGTGKTLIARAVASETDATF 237
                                    56789*****************99987765 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0024
                         DUF815  21 evdevklddLvgidkqkealvente.......qf..leglpannvLLwGarGtGKSslvkallneyaeegLrli 85 
                                    e+ ev+++d+ g+++ k+al e +e       +f  +  +p + vLL+G  GtGK  + +a+ +e    g+ +i
  gi|116753926|ref|YP_843044.1| 440 EIPEVHWSDIGGLEDAKQALREAVEwpimypeAFeaVGIRPPRGVLLYGPPGTGKTMIARAVATES---GINFI 510
                                    556677777777777777777766522211112211233566789****************98764...44444 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0     0.015         5       3      26 ..     214     237 ..     212     247 .. 0.89
   2 !    7.8   0.0    0.0073       2.4       4      28 ..     487     511 ..     484     513 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.015
                                    EE-STTSSHHHHHHHHHHHHT-EE CS
                 Cytidylate_kin   3 iDGPagsGKssvaralaeklglky 26 
                                    + GP g+GK  +ara+a++ ++++
  gi|116753926|ref|YP_843044.1| 214 LHGPPGTGKTLIARAVASETDATF 237
                                    68****************999877 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0073
                                    E-STTSSHHHHHHHHHHHHT-EEEE CS
                 Cytidylate_kin   4 DGPagsGKssvaralaeklglkyld 28 
                                     GP g+GK  +ara+a++ g+++++
  gi|116753926|ref|YP_843044.1| 487 YGPPGTGKTMIARAVATESGINFIS 511
                                    6*******************99985 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0    0.0015       0.5       4      34 ..     212     242 ..     210     299 .. 0.86
   2 ?    3.8   0.0      0.14        45       4      32 ..     484     512 ..     482     539 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0015
                                    EEEEE-TTSSHHHHHHHHHHHSSS-EEEEEH CS
                            CPT   4 ilLnGgsssGKsslaralqevldepwlhlgv 34 
                                    +lL+G + +GK+ +ara+ + +d+++ ++  
  gi|116753926|ref|YP_843044.1| 212 VLLHGPPGTGKTLIARAVASETDATFTAISG 242
                                    89************************99875 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.14
                                    EEEEE-TTSSHHHHHHHHHHHSSS-EEEE CS
                            CPT   4 ilLnGgsssGKsslaralqevldepwlhl 32 
                                    +lL G + +GK+ +ara+ + +   ++ +
  gi|116753926|ref|YP_843044.1| 484 VLLYGPPGTGKTMIARAVATESGINFISI 512
                                    89***************988777666665 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.71   2.3e+02       8      53 ..     218     265 ..     214     307 .. 0.74
   2 !   11.3   0.0   0.00086      0.28       8      55 ..     490     538 ..     486     590 .. 0.66

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.71
                Cytidylate_kin2   8 yGsgGetigeaLAekLglpfydreiieevakelglseeev.eevde.r 53 
                                     G+g++ i++a+A +    f     +e +++  g se+ + + +++ +
  gi|116753926|ref|YP_843044.1| 218 PGTGKTLIARAVASETDATFTAISGPEIMSRYYGESEQRLrQIFEDaQ 265
                                    69*************999999888888888888888888855555531 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00086
                Cytidylate_kin2   8 yGsgGetigeaLAekLglpfydreiieevakelglseeeveevde.rsr 55 
                                     G+g++ i++a+A++ g++f++ + +e ++k  g se  v+ev   ++ 
  gi|116753926|ref|YP_843044.1| 490 PGTGKTMIARAVATESGINFISIKGPELMSKWVGESERAVREVFRkAKQ 538
                                    59*******************************9999999554442222 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0063         2       4      63 ..     213     277 ..     212     297 .. 0.78
   2 ?    3.1   0.1       0.2        66      38      95 ..     523     555 ..     484     593 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0063
                            Zot   4 lvtGapGsgKts..gavkkdllpalk..egRkiitnidGlrlerieqvlgekvs.tarliridnp 63 
                                    l +G+pG+gKt+  +av  +        +g +i+ +  G   +r++q+++++ + ++ +i+id+ 
  gi|116753926|ref|YP_843044.1| 213 LLHGPPGTGKTLiaRAVASETDATFTaiSGPEIMSRYYGESEQRLRQIFEDAQKsAPSIIFIDEI 277
                                    789********722567665555433347********************999998999***9933 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.2
                            Zot  38 GlrlerieqvlgekvstarliridnpegaetlkefakwatidkgallviDEcqeifpv 95 
                                    G   ++                         + e++  a+ +  al+++DE   i p+
  gi|116753926|ref|YP_843044.1| 523 GESERA-------------------------VREVFRKAKQAAPALIFFDEIDSIVPA 555
                                    333333.........................333344444444555555555555555 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.019       6.2      59      78 ..     206     225 ..     179     266 .. 0.87
   2 ?    5.2   0.0     0.025       8.1      60      78 ..     479     497 ..     466     503 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.019
                    AFG1_ATPase  59 vepvrglYlwGgvGrGKtyl 78 
                                     +p++g+ l+G+ G GKt +
  gi|116753926|ref|YP_843044.1| 206 ITPPKGVLLHGPPGTGKTLI 225
                                    57****************76 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.025
                    AFG1_ATPase  60 epvrglYlwGgvGrGKtyl 78 
                                    +p+rg+ l+G+ G GKt++
  gi|116753926|ref|YP_843044.1| 479 RPPRGVLLYGPPGTGKTMI 497
                                    69***************97 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0     0.016       5.2      17      46 ..     202     231 ..     180     241 .. 0.75
   2 ?    4.9   0.0     0.075        24      24      45 ..     481     502 ..     436     513 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.016
                                    ......TTSEEEEEESTTSTHHHHHHHHHH CS
                         ResIII  17 eklkskrdkrglikmaTGtGKTlvaaklie 46 
                                    +kl ++  k +l++ + GtGKTl+a +++ 
  gi|116753926|ref|YP_843044.1| 202 QKLGITPPKGVLLHGPPGTGKTLIARAVAS 231
                                    444447788999************977665 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.075
                                    TSEEEEEESTTSTHHHHHHHHH CS
                         ResIII  24 dkrglikmaTGtGKTlvaakli 45 
                                     + +l+  + GtGKT++a +++
  gi|116753926|ref|YP_843044.1| 481 PRGVLLYGPPGTGKTMIARAVA 502
                                    5667889999*******95544 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 ?    3.6   0.0      0.16        52     103     162 ..     254     316 ..     238     320 .. 0.73
   2 ?    4.4   0.0     0.091        30      23      43 ..     484     504 ..     476     512 .. 0.85
   3 ?   -0.4   0.0       2.7   8.9e+02     107     131 ..     526     553 ..     507     593 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.16
                       ATPase_2 103 fkaielllekikkkgkkiiiiiDelqklidlgln......gaellvkeLlnliesltkekhlcvvi 162
                                    ++ + +++e+ +k++   ii+iDe+  +   + +       ++ +v++Ll+l++ lt++ +++v+ 
  gi|116753926|ref|YP_843044.1| 254 EQRLRQIFEDAQKSAP-SIIFIDEIDSIAP-K-ReevlgdLERRVVAQLLSLMDGLTSRGEVIVIA 316
                                    4556666666666644.7899***999872.2.123444478999***********9999999875 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.091
                       ATPase_2  23 yfiYGpegsGKtaLlkeiien 43 
                                    +++YGp g GKt + + ++++
  gi|116753926|ref|YP_843044.1| 484 VLLYGPPGTGKTMIARAVATE 504
                                    689*********999988765 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 2.7
                       ATPase_2 107 elllekikkkgkk...iiiiiDelqkli 131
                                    e++ +++ +k+k+     i++De+  ++
  gi|116753926|ref|YP_843044.1| 526 ERAVREVFRKAKQaapALIFFDEIDSIV 553
                                    445566666777777466778*999987 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 ?    5.6   0.0     0.034        11       2      71 ..     213     277 ..     212     282 .. 0.69
   2 ?    6.2   0.0     0.024       7.7       5      71 ..     488     549 ..     484     552 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.034
                Viral_helicase1   2 vvhGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                    + hG pG GK+ + r ++++    +t+++   e+ ++   +++++    ++++++++       i+++DE+
  gi|116753926|ref|YP_843044.1| 213 LLHGPPGTGKTLIARAVASETdATFTAISG-PEIMSRYYGESEQRLRQIFEDAQKSA-----PSIIFIDEI 277
                                    68**********999999996666666666.66666655555555555555555544.....458999997 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.024
                Viral_helicase1   5 GvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                    G pG GK+ + r ++ +s  ++ +++   el ++++ ++++   + ++++ +a+       ++++DE+
  gi|116753926|ref|YP_843044.1| 488 GPPGTGKTMIARAVATESgINFISIKG-PELMSKWVGESERAVREVFRKAKQAAP-----ALIFFDEI 549
                                    78*************999*99999999.9******97777766666666555543.....47888886 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1      0.21        67       5      28 ..     213     236 ..     210     241 .. 0.88
   2 ?    8.4   0.0     0.004       1.3       5      32 ..     485     512 ..     482     536 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.21
                            IPT   5 lifGatttGKtaeaiklaketgap 28 
                                    l++G+ +tGKt  a ++a et a 
  gi|116753926|ref|YP_843044.1| 213 LLHGPPGTGKTLIARAVASETDAT 236
                                    899****************99775 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.004
                            IPT   5 lifGatttGKtaeaiklaketgapvivl 32 
                                    l++G+ +tGKt  a ++a e g+  i++
  gi|116753926|ref|YP_843044.1| 485 LLYGPPGTGKTMIARAVATESGINFISI 512
                                    89********************999986 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.47   1.5e+02      48      69 ..     212     233 ..     202     248 .. 0.80
   2 ?   -0.3   0.0       2.7   8.8e+02     140     178 ..     244     280 ..     229     288 .. 0.74
   3 ?    7.1   0.0     0.014       4.7      46      82 ..     482     518 ..     472     555 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.47
                          Rad17  48 LLisGPsGCgkstvvkvLskel 69 
                                    +L+ GP+G gk+ + + ++ e 
  gi|116753926|ref|YP_843044.1| 212 VLLHGPPGTGKTLIARAVASET 233
                                    689*********9988887765 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 2.7
                          Rad17 140 dlPnkfyrds.dalrevirkylrssealplilviteiesl 178
                                    ++ +++y++s ++lr++   + +s  +   i+ i ei+s+
  gi|116753926|ref|YP_843044.1| 244 EIMSRYYGESeQRLRQIFEDAQKSAPS---IIFIDEIDSI 280
                                    566778887778888888887666544...6667777765 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.014
                          Rad17  46 riLLisGPsGCgkstvvkvLskelgiklrewlnpvsl 82 
                                    r +L+ GP+G gk+ + + ++ e gi+++    p ++
  gi|116753926|ref|YP_843044.1| 482 RGVLLYGPPGTGKTMIARAVATESGINFISIKGPELM 518
                                    557999********************99987776554 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.18        58       4      33 ..     211     241 ..     209     246 .. 0.87
   2 ?    1.6   0.0      0.58   1.9e+02      75      95 ..     246     266 ..     240     284 .. 0.81
   3 ?    3.4   0.0      0.16        52       3      30 ..     482     509 ..     480     514 .. 0.83
   4 ?   -1.6   0.0       5.7   1.9e+03      76      96 ..     519     539 ..     513     543 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.18
                                    EEEEESTTTSSHHHHHHHHHHHSTTTEE.E- CS
                  Guanylate_kin   4 pvvlvgpsgaGksslkkaLlselpekfg.vs 33 
                                     v l gp g+Gk  +  a+ se   +f+ +s
  gi|116753926|ref|YP_843044.1| 211 GVLLHGPPGTGKTLIARAVASETDATFTaIS 241
                                    68899*****************999997455 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.58
                                    TTEEEEEEHHHHHHHHHTTSE CS
                  Guanylate_kin  75 sgnlygtsveaieevlekgki 95 
                                     + +yg+s +  ++++e +++
  gi|116753926|ref|YP_843044.1| 246 MSRYYGESEQRLRQIFEDAQK 266
                                    5789************99876 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.16
                                    SEEEEESTTTSSHHHHHHHHHHHSTTTE CS
                  Guanylate_kin   3 rpvvlvgpsgaGksslkkaLlselpekf 30 
                                    r v l gp g+Gk ++  a+ +e   +f
  gi|116753926|ref|YP_843044.1| 482 RGVLLYGPPGTGKTMIARAVATESGINF 509
                                    6789*************99988776555 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 5.7
                                    TEEEEEEHHHHHHHHHTTSEE CS
                  Guanylate_kin  76 gnlygtsveaieevlekgkiv 96 
                                    ++  g+s  a++ev+ k+k++
  gi|116753926|ref|YP_843044.1| 519 SKWVGESERAVREVFRKAKQA 539
                                    567799***********9986 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0      0.22        73       1      20 [.     218     237 ..     218     266 .. 0.88
   2 ?    7.0   0.0     0.018         6       1      22 [.     490     511 ..     490     539 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.22
                                    TTSSHHHHHHHHHHHHTSEE CS
                            SKI   1 mGaGKstvGkllAkklglef 20 
                                    +G+GK+ +++++A + + +f
  gi|116753926|ref|YP_843044.1| 218 PGTGKTLIARAVASETDATF 237
                                    69************998887 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.018
                                    TTSSHHHHHHHHHHHHTSEEEE CS
                            SKI   1 mGaGKstvGkllAkklglefiD 22 
                                    +G+GK+ +++++A + g++fi 
  gi|116753926|ref|YP_843044.1| 490 PGTGKTMIARAVATESGINFIS 511
                                    69******************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 ?    4.5   0.0     0.086        28      21      38 ..     209     225 ..     199     231 .. 0.76
   2 ?    5.1   0.0     0.059        19      21      41 ..     481     500 ..     471     503 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.086
                         AAA_29  21 lkgatlltGpsGsGKSTl 38 
                                    +kg +ll Gp G+GK+ +
  gi|116753926|ref|YP_843044.1| 209 PKG-VLLHGPPGTGKTLI 225
                                    466.9**********755 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.059
                         AAA_29  21 lkgatlltGpsGsGKSTllDA 41 
                                    ++g +ll Gp G+GK+ +  A
  gi|116753926|ref|YP_843044.1| 481 PRG-VLLYGPPGTGKTMIARA 500
                                    356.9**********977655 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.024       7.9      57      76 ..     213     232 ..     205     240 .. 0.87
   2 ?    2.1   0.0      0.58   1.9e+02      58      75 ..     486     503 ..     478     508 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.024
                                    EEEE-TTSSHHHHHHHHHHH CS
                         Torsin  57 sfhGwtGtGknfvaeiiaen 76 
                                     +hG +GtGk  +a+ +a +
  gi|116753926|ref|YP_843044.1| 213 LLHGPPGTGKTLIARAVASE 232
                                    58*************99876 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.58
                                    EEE-TTSSHHHHHHHHHH CS
                         Torsin  58 fhGwtGtGknfvaeiiae 75 
                                    ++G +GtGk  +a+ +a 
  gi|116753926|ref|YP_843044.1| 486 LYGPPGTGKTMIARAVAT 503
                                    789**********99986 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.088        29       2      24 ..     212     234 ..     211     258 .. 0.83
   2 ?   -0.1   0.1       2.3   7.4e+02      82     105 ..     254     278 ..     244     300 .. 0.76
   3 ?    3.7   0.1      0.16        51       2      22 ..     484     504 ..     483     517 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.088
                                    EEEE--TTSSHHHHHHHHHHHH. CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvlellk 24 
                                    v++ GppG+GKt + + v+++ +
  gi|116753926|ref|YP_843044.1| 212 VLLHGPPGTGKTLIARAVASETD 234
                                    6789********99999988765 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 2.3
                                    HHHHHHHHHHHH.HHH-EEEE---S CS
                       NTPase_1  82 eelalealrkal.seadviviDEiG 105
                                    e+   ++++ a+ s + +i iDEi 
  gi|116753926|ref|YP_843044.1| 254 EQRLRQIFEDAQkSAPSIIFIDEID 278
                                    55666666777646667******95 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.16
                                    EEEE--TTSSHHHHHHHHHHH CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvlel 22 
                                    v++ GppG+GKt + + v+ +
  gi|116753926|ref|YP_843044.1| 484 VLLYGPPGTGKTMIARAVATE 504
                                    6788********999988765 PP

>> Hydin_ADK  Hydin Adenylate kinase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1     0.039        13       2      28 ..     212     238 ..     211     243 .. 0.86
   2 ?    3.1   0.1      0.31        99       2      30 ..     484     512 ..     483     515 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.039
                      Hydin_ADK   2 iivhGaPlsGKtatavtLakkYeaAll 28 
                                    +++hG+P +GKt +a ++a + +a + 
  gi|116753926|ref|YP_843044.1| 212 VLLHGPPGTGKTLIARAVASETDATFT 238
                                    689**************9998888765 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.31
                      Hydin_ADK   2 iivhGaPlsGKtatavtLakkYeaAllti 30 
                                    +++ G+P +GKt +a ++a + ++ +++i
  gi|116753926|ref|YP_843044.1| 484 VLLYGPPGTGKTMIARAVATESGINFISI 512
                                    5789**************99988888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (721 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        55  (0.00306766); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              55  [number of targets reported over threshold]
# CPU time: 0.77u 0.31s 00:00:01.08 Elapsed: 00:00:00.46
# Mc/sec: 4704.36
//
Query:       gi|116753927|ref|YP_843045.1|  [L=97]
Description: hypothetical protein Mthe_0614 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0085   15.9   0.1      0.014   15.2   0.1    1.3  1  RETICULATA-like  Protein RETICULATA-related
     0.0087   16.6   0.4     0.0094   16.5   0.4    1.1  1  Vac14_Fab1_bd    Vacuolar 14 Fab1-binding region


Domain annotation for each model (and alignments):
>> RETICULATA-like  Protein RETICULATA-related
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   1.6e-06     0.014      12      55 ..      41      84 ..      37      89 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.6e-06
                RETICULATA-like 12 kvllEevigvsasllaevekRkerfleEldlvladvvvgsvvnf 55
                                   k +l ++i+++++l++e+++R  ++++El l + +++v ++ ++
  gi|116753927|ref|YP_843045.1| 41 KNALSQIISIACNLIGEIATRAGEVISELSLEVFKILVKIASDM 84
                                   778899********************************998875 PP

>> Vac14_Fab1_bd  Vacuolar 14 Fab1-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.4     1e-06    0.0094      13      86 ..      15      90 ..       1      94 [. 0.81

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1e-06
                  Vac14_Fab1_bd 13 vaialekkikeyleei..vkpvlkcfsDkdsrvRyyacEslyniakvakgevlkllneifdalvklvaDsdesvks 86
                                   + i + ++++e l+++  ++ vl++ + + s++   ac  +  ia  a + + +l  e+f++lvk+++D+d+ ++s
  gi|116753927|ref|YP_843045.1| 15 LCICIWAQSSEKLNTVmpIAHVLEVSKNALSQIISIACNLIGEIATRAGEVISELSLEVFKILVKIASDMDTRIQS 90
                                   4566777778888887234579***********************999999888999**************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1170  (0.0652574); expected 358.6 (0.02)
Passed bias filter:                      666  (0.0371465); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 763.45
//
Query:       gi|116753928|ref|YP_843046.1|  [L=224]
Description: hypothetical protein Mthe_0615 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1829.85
//
Query:       gi|116753929|ref|YP_843047.1|  [L=263]
Description: hypothetical protein Mthe_0616 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); 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: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 2059.42
//
Query:       gi|116753930|ref|YP_843048.1|  [L=267]
Description: fructose-bisphosphate aldolase [Methanosaeta thermophila PT]
Scores for 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-63  212.0   0.0      1e-62  211.8   0.0    1.0  1  DeoC      DeoC/LacD family aldolase
    0.00059   19.2   0.6    0.00059   19.2   0.6    1.9  2  ThiG      Thiazole biosynthesis protein ThiG
  ------ inclusion threshold ------
       0.16   12.6   1.2        3.3    8.4   0.0    2.8  3  YbjQ_1    Putative heavy-metal-binding
        1.7    7.9   5.4       0.85    8.9   2.8    1.8  2  NMO       Nitronate monooxygenase


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 !  211.8   0.0   2.3e-66     1e-62       1     235 []      21     237 ..      21     237 .. 0.98

  Alignments for each domain:
  == domain 1  score: 211.8 bits;  conditional E-value: 2.3e-66
                                    EEEEEECCSHHHHHHHHCTSSHHHHHHHHHHHHHHGGGSSEEEEETTTHHHHHHCSCTTSEEEEETECSSCCTTSTTEEE CS
                           DeoC   1 ivilavDqrvankddtasaqneqledlkalvkealtpgasavlldpgviasaskeyakdiallvkldkgtyllkskqrdv 80 
                                    +vi+++D++++ +++++       ++l ++v++++++ga+avl ++g++++++++y++di+l+v+++++t l ++++ +v
  gi|116753930|ref|YP_843048.1|  21 TVIIPLDHGISVGPIQGL------ANLPEMVDKVAKGGANAVLQQKGMVRHGHRGYGRDIGLIVHMSASTSLGPDPNNKV 94 
                                    69****************......7***************************************************9999 PP

                                    ETTCHHHHHHHTT-SEEEEEEEEHTTTTCHHHHHHHHHHHHHHHHHHHTEEEEEEEEE-CTTBSSTTCHHHHHHHHHHHH CS
                           DeoC  81 devasveeakalGAdavkvvvyyradgseeeqqklaeikrvkeacheeglplilelylrdeaikdekvdpdlvaeAarvs 160
                                      va veea++lGAdav+v++++   gse+e+++l  +++v+e+c+ +g+pl++++y+r+++i++ + +pd+va+Aar++
  gi|116753930|ref|YP_843048.1|  95 Q-VAMVEEALKLGADAVSVHINI---GSETEAEQLHFLGMVSERCDFWGMPLVAMMYPRGKNITNPN-APDVVAHAARAG 169
                                    9.*********************...*************************************9999.************ PP

                                    TCCT-SEEEE--SSCC.B.HHHHHHHHHHHHHCHSSTEEEEETTS...SHHHHHHHHHHHHHHHTHCEEEESHHHHTT CS
                           DeoC 161 aelGaDiiKvevpkevvnateedaevfkdvikaapvpgvvlsGGv...seedfletvedAvkeagasGvlsGRaifqk 235
                                    aelGaDiiK++++        ++ ++f+dv++++pvp vv++GG+   ++ +fl+++e A+ +aga Gv++GR++fq+
  gi|116753930|ref|YP_843048.1| 170 AELGADIIKTNYT--------GSPDSFRDVVAGCPVP-VVIAGGPktaTDLEFLQMIEGAM-KAGARGVAIGRNVFQH 237
                                    *************........****************.*******9888889*********.**************97 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1      0.32   1.4e+03     191     207 ..     100     116 ..      95     125 .. 0.77
   2 !   19.2   0.6   1.3e-07   0.00059     164     236 ..     185     263 ..     159     267 .] 0.82

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.32
                                    HHHHHTT-SEEEESHHH CS
                           ThiG 191 aqamelGadavllntav 207
                                     +a++lGadav +   +
  gi|116753930|ref|YP_843048.1| 100 EEALKLGADAVSVHINI 116
                                    57999*****9887666 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 1.3e-07
                                    HHHHHHHHHH-SS-BEEES---SHHH......HHHHHHTT-SEEEESHHHHTSSSHHHHHHHHHHHHHHHHHHHHH--- CS
                           ThiG 164 kealkiiieeakvPvivDAGigspsd......aaqamelGadavllntavaeakdpvamArafklaveaGrlaylagri 236
                                    +  ++ +++ + vPv++  G  +++d      +  am+ Ga +v +   v + +dp +m ra+ + v+ Gr a +a  i
  gi|116753930|ref|YP_843048.1| 185 PDSFRDVVAGCPVPVVIAGGPKTATDleflqmIEGAMKAGARGVAIGRNVFQHRDPTRMTRAICAIVHHGRSAEEAASI 263
                                    556677888889*****9999999883333223569*************************************999765 PP

>> YbjQ_1  Putative heavy-metal-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1     0.083   3.7e+02      63      79 ..      42      58 ..      39      64 .. 0.88
   2 ?    8.4   0.0   0.00073       3.3      62      86 ..      95     120 ..      84     132 .. 0.77
   3 ?   -2.5   0.0       1.8   8.3e+03      64      77 ..     215     228 ..     210     237 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.083
                         YbjQ_1 63 erlkeeAeelGAnAvvg 79
                                    +++++ ++ GAnAv++
  gi|116753930|ref|YP_843048.1| 42 PEMVDKVAKGGANAVLQ 58
                                   5899***********85 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00073
                         YbjQ_1  62 lerlkeeAeelGAnAv.vgvrldtse 86 
                                       ++eeA +lGA+Av v +++ +++
  gi|116753930|ref|YP_843048.1|  95 QVAMVEEALKLGADAVsVHINIGSET 120
                                    568************96666665554 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.8
                         YbjQ_1  64 rlkeeAeelGAnAv 77 
                                    ++ e A + GA  v
  gi|116753930|ref|YP_843048.1| 215 QMIEGAMKAGARGV 228
                                    67888888888766 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.2     0.096   4.3e+02     106     136 ..      99     129 ..      37     137 .. 0.66
   2 ?    8.9   2.8   0.00019      0.85     108     223 ..     101     232 ..      79     241 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.096
                            NMO 106 vevvldekvevvsfgfglpteevvarlkeag 136
                                    ve  l+ ++++vs++++  +e   ++l+++g
  gi|116753930|ref|YP_843048.1|  99 VEEALKLGADAVSVHINIGSETEAEQLHFLG 129
                                    3444444555555555555555555555555 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00019
                            NMO 108 vvldekvevvsfgfglpteevvarlkeagvvl.iptissvkearkvearG.......aDalivqGpeaGGhqGtpevgdk 179
                                      l+ ++++vs++++  +e   ++l+++g+v  +     +  + ++  rG       a  +++    aG   G  ++ ++
  gi|116753930|ref|YP_843048.1| 101 EALKLGADAVSVHINIGSETEAEQLHFLGMVSeRCDFWGMPLVAMMYPRGknitnpnAPDVVAHAARAGAELG-ADIIKT 179
                                    5555566666666666666666666666655422223333333333333344444445556777778888888.444445 PP

                            NMO 180 glfaLvpqvldavd...iPviAaGGiidrrg......vaaaLalGAsgvqigt 223
                                    + +   ++ +d+v+   +Pv+ aGG  ++ +      ++ a+ +GA gv+ig 
  gi|116753930|ref|YP_843048.1| 180 NYTGSPDSFRDVVAgcpVPVVIAGGPKTATDleflqmIEGAMKAGARGVAIGR 232
                                    66666788899999999********9999884444445799**********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 2147.06
//
Query:       gi|116753931|ref|YP_843049.1|  [L=232]
Description: FkbM family methyltransferase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.8e-07   28.9   0.0      4e-06   27.0   0.0    1.8  1  Methyltransf_21  Methyltransferase FkbM domain
     0.0014   18.4   0.0     0.0021   17.8   0.0    1.2  1  Met_10           Met-10+ like-protein
     0.0044   16.4   0.0     0.0097   15.2   0.0    1.5  1  V_cholerae_RfbT  Vibrio cholerae RfbT protein
     0.0061   16.3   0.0      0.009   15.8   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
  ------ inclusion threshold ------
      0.061   12.5   0.0      0.085   12.0   0.0    1.2  1  Methyltransf_3   O-methyltransferase


Domain annotation for each model (and alignments):
>> Methyltransf_21  Methyltransferase FkbM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   1.1e-09     4e-06       1     152 [.      53     186 ..      53     205 .. 0.64

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 1.1e-09
                Methyltransf_21   1 dvGanigvwdsfanltarlcggggevlaiEPvpnslpkfeklranll........tlavgndvglyelivegksggkyfp 72 
                                    dvGa+ig  ++ ++++    g  g v+a+EP+++   ++e lr n+         ++a+++ +g+              +
  gi|116753931|ref|YP_843049.1|  53 DVGAHIG--SFALRAA-GMVGEDGLVVAVEPERS---NYELLRMNSEgmdsiiplRMALSDFRGT------------GRL 114
                                    9******..4444333.369999999********...******9944555444444444433333............333 PP

                Methyltransf_21  73 favgdtngfstssvlggedaryievpvvtldsfleeikksridllkiDvEGaElevLeGaqkglkrcqpnlivvEvhkfk 152
                                    f   +t  +s  +   ++ ++  evpv t   ++ee     +d++kiD+EGa l +L  +  +  rc+     +   +f+
  gi|116753931|ref|YP_843049.1| 115 FLAEGTVAHSLVF---RRSTSWDEVPVNTMNGLIEEL-GIGPDVVKIDAEGAALKIL--SCADRMRCRKIA--IAAYHFP 186
                                    3333333333332...3456679*******9888887.5679***************..444444444333..3555555 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   5.9e-07    0.0021      98     143 ..      45      91 ..      35     111 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5.9e-07
                                    --TT-EEEETT-TTTCCHHHC.CHHTTSSEEEEEES-HHHHHHHHHH CS
                         Met_10  98 veegevVvdvfAGiGpfaipi.akyskakrvlaidlnPesvkylken 143
                                    +++gevV dv A iG fa+ + +  +++  v+a++ + + +++l+ n
  gi|116753931|ref|YP_843049.1|  45 IRPGEVVFDVGAHIGSFALRAaGMVGEDGLVVAVEPERSNYELLRMN 91 
                                    689****************6515789*****************9988 PP

>> V_cholerae_RfbT  Vibrio cholerae RfbT protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   2.7e-06    0.0097      70     213 ..      38     173 ..      32     209 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.7e-06
                V_cholerae_RfbT  70 rhwivnhckhdttyidiganvgtfcgiaarhit.qgkiiaiepltemensirmnvqlnnplvefhhfgcaigenegenif 148
                                    rh+ +   +      d+ga +g+f+  aa  +  +g ++a+ep     + +rmn +  + ++ +     a+ +  g   +
  gi|116753931|ref|YP_843049.1|  38 RHYDLLDIRPGEVVFDVGAHIGSFALRAAGMVGeDGLVVAVEPERSNYELLRMNSEGMDSIIPL---RMALSDFRGTGRL 114
                                    566666666667789***********999998626999*******9999*****9998888876...5799999998876 PP

                V_cholerae_RfbT 149 evyefdnrvsslyfkkntdiadkvknsqvlvrklssldisptnsvvikidaegaeieilnqiyef 213
                                     + e      sl f++ t   +   n+  +   +  l i p    v+kidaega ++il     +
  gi|116753931|ref|YP_843049.1| 115 FLAEG-TVAHSLVFRRSTSWDEVPVNT--MNGLIEELGIGPD---VVKIDAEGAALKILSCADRM 173
                                    66664.456799****99876554443..3445667889996...89***********9866555 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   2.5e-06     0.009      66     110 ..      40      84 ..      29     107 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.5e-06
                                    HHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHH CS
                           PCMT  66 lellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikel 110
                                     +ll++++g+ v +vG+  G  +   a +vge+g+vv++e  ++ 
  gi|116753931|ref|YP_843049.1|  40 YDLLDIRPGEVVFDVGAHIGSFALRAAGMVGEDGLVVAVEPERSN 84 
                                    689************************************977654 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.4e-05     0.085      42      88 ..      42      88 ..      27     104 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.4e-05
                                   HHHHHT--EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHH CS
                 Methyltransf_3 42 LvklvnakrvleiGvftGyslLatalalPeDGkilaididreayeia 88
                                   L+++     v+++G + G  +L  a  + eDG ++a++ +r +ye+ 
  gi|116753931|ref|YP_843049.1| 42 LLDIRPGEVVFDVGAHIGSFALRAAGMVGEDGLVVAVEPERSNYELL 88
                                   56777778899*********************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       229  (0.0127726); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); 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 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1798.61
//
Query:       gi|116753932|ref|YP_843050.1|  [L=627]
Description: acetyl-CoA hydrolase/transferase [Methanosaeta thermophila PT]
Scores for complete 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-64  215.2   0.0    6.7e-64  214.5   0.0    1.4  1  AcetylCoA_hyd_C  Acetyl-CoA hydrolase/transferase C-terminal 
    3.7e-50  170.7   0.0    7.1e-50  169.7   0.0    1.5  1  AcetylCoA_hydro  Acetyl-CoA hydrolase/transferase N-terminal 
    2.2e-10   41.4   0.0    4.5e-10   40.3   0.0    1.6  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
    4.1e-10   39.9   0.1    9.5e-10   38.7   0.1    1.6  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    0.00017   21.9   0.2    0.00041   20.7   0.2    1.6  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    0.00021   21.5   0.1    0.00043   20.5   0.1    1.5  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    0.00043   18.8   0.3      0.039   12.3   0.1    2.1  2  Mal_decarbox_Al  Malonate decarboxylase, alpha subunit, trans
  ------ inclusion threshold ------
      0.021   14.7   0.1      0.051   13.5   0.1    1.7  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
      0.035   14.1   0.1      0.088   12.8   0.1    1.6  1  FR47             FR47-like protein
      0.054   13.6   0.1       0.38   10.9   0.1    2.2  2  Acetyltransf_CG  GCN5-related N-acetyl-transferase


Domain annotation for each model (and alignments):
>> AcetylCoA_hyd_C  Acetyl-CoA hydrolase/transferase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.5   0.0   3.7e-67   6.7e-64       1     154 []     284     437 ..     284     437 .. 0.99

  Alignments for each domain:
  == domain 1  score: 214.5 bits;  conditional E-value: 3.7e-67
                                    S-HHHHHHHTT-TTEEE-BHHHHT-HHHHTTSTTEEEEEE-SEEETTS-EESSECTTCCTCGGTTHHHHHHHHHHSTT-E CS
                AcetylCoA_hyd_C   1 GskklydfldenpkielrpveyvndpeviaqnkkvvsinsalevdltGqvnseslggrvvsGvGgqldFvrgaalskggk 80 
                                    G++k y+++++np+ie++ ++y+n+p +ia+n+++vsinsa+evdltGq+++eslg+ + sG+Ggq dF+rga ls+ggk
  gi|116753932|ref|YP_843050.1| 284 GTRKTYEYIHDNPAIEFKTIDYTNNPLIIAKNRNMVSINSAMEVDLTGQATAESLGTFFHSGIGGQADFMRGAVLSPGGK 363
                                    99****************************************************************************** PP

                                    EEEE--SEETTTTEESEESS-STTSSECE-TTT-SEEEETTEEEE-TT--HHHHHHHHHTTS-HHHHHHHHHHH CS
                AcetylCoA_hyd_C  81 siialpStakkgeiSrIvpslkegahvtttrhdvdyvvTEyGiadLrgkslreraealikiAhpdfreeLleea 154
                                    +i+alpSta++g+iSrIvp+l+ega+vt tr d++yvvTEyGia+L+gk++rera+ li++Ahp+fr++Lleea
  gi|116753932|ref|YP_843050.1| 364 AILALPSTAENGRISRIVPMLREGAGVTLTRGDLHYVVTEYGIAYLHGKNVRERAMDLIALAHPKFRPWLLEEA 437
                                    ***********************************************************************997 PP

>> AcetylCoA_hydro  Acetyl-CoA hydrolase/transferase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.7   0.0     4e-53   7.1e-50       2     192 ..       5     194 ..       4     200 .. 0.97

  Alignments for each domain:
  == domain 1  score: 169.7 bits;  conditional E-value: 4e-53
                AcetylCoA_hydro   2 qeeyekklke.peeaaelvkngshielsgftavgtakaipkylakrkvekenvkkkllidlavgavlsagPeeevleekd 80 
                                    ++ y  ++++ pe++++l + +shi+ ++++++gt +++p++l++   +++  ++k ++d + + v+++g ++++++ k+
  gi|116753932|ref|YP_843050.1|   5 EHYYSDLRAQwPEKFVSLERAFSHIHAGDRIFIGTGCGEPQFLVQALADYVREHPKAFFDTEILHVWTLG-AAPYTDIKF 83 
                                    56688899999***********************************************************.********* PP

                AcetylCoA_hydro  81 avlyrpapkqvgellrkainqglvsfvdkhlsevpqklekgfvpiDvalieataldedGylnlGvgvrakKviiEvaelv 160
                                      ++r + +++g+ +r a+n+ l+++++++ s +p+++ +g +piDvali++t++d++GylnlG++v+++K+++E a +v
  gi|116753932|ref|YP_843050.1|  84 RENFRLNTFFIGRSTRDAVNKELADYTPIFFSAIPDLIYRGRIPIDVALIQTTPPDRHGYLNLGISVDIVKAAVEKASVV 163
                                    ******************************************************************************** PP

                AcetylCoA_hydro 161 vivvkknpPrvngydelialdkvdyivvdpek 192
                                    ++++++n+Prv+g d++i++d v +++ ++e 
  gi|116753932|ref|YP_843050.1| 164 IAQINSNMPRVQG-DGFIHMDDVSFVIPHDEP 194
                                    *************.************999985 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.0   2.5e-13   4.5e-10       2     135 ..     473     608 ..     472     611 .. 0.81

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 2.5e-13
                 Acetyltransf_3   2 LlLrplteeD...lealfelrsdpe.vmrylpepltleeaeewlerawaeeseeegygwaivlkdtg.v.iGsvglrdle 75 
                                    +lLrp++ +D   l+++f  +sd++  +r+   ++   ++++ l+++   ++++e + +a++++d++ + iG   +  +e
  gi|116753932|ref|YP_843050.1| 473 ILLRPVKITDeplLKDFFYSLSDETmYQRFA--SARKGMSHKQLQDFVVIDYTREMVILAVIEEDDKeEvIGLGQYSIAE 550
                                    79********344444433477877666765..4567999999999977777778888888885554444****999888 PP

                 Acetyltransf_3  76 eedeeaelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvlekl 135
                                    + ++ ae+ +++++++++kG++ e ++ l+ +a +++gl +l a++  eN+a  r +e+l
  gi|116753932|ref|YP_843050.1| 551 GTHT-AEVAIVVRDDYQRKGVGMEILSYLVYLA-RKQGLFYLNAEVLVENQAVLRMFERL 608
                                    8766.***********************99999.8889********************98 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   0.1   5.3e-13   9.5e-10      26     115 ..     521     608 ..     489     610 .. 0.80

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 5.3e-13
                                    HHHHSTTC..EEEEEEET..TEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEE CS
                 Acetyltransf_1  26 esfsleae..gllvaeed..geliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlav 101
                                    ++   + e   l v+eed  +e+iG  ++++       +++   ++V+ +y++kG+G + l +l+  ar++g+ ++ ++v
  gi|116753932|ref|YP_843050.1| 521 DY---TREmvILAVIEEDdkEEVIGLGQYSIAEG---THTAEVAIVVRDDYQRKGVGMEILSYLVYLARKQGLFYLNAEV 594
                                    44...44432344488886677**********99...677777******************************55566** PP

                                    ETTEHHHHHHHHHT CS
                 Acetyltransf_1 102 eedndaairlYekl 115
                                     + n+a  r++e+l
  gi|116753932|ref|YP_843050.1| 595 LVENQAVLRMFERL 608
                                    ***********997 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.2   2.3e-07   0.00041       7      57 ..     531     593 ..     516     609 .. 0.65

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.3e-07
                                    EEEET..TEEEEEEEEEEES...TCTEE..EEE-GGGTTSSHHHHHHHH.....TTSEEE.EE.E CS
                 Acetyltransf_7   7 Vaedd..gkivGfialslld...aeitr..laVdpeyrgkGiGraLlea.....aekgii.le.q 57 
                                    V+e+d  ++++G   +s+ +   +   +  ++V+ +y++kG+G ++l +     +++g+  l  +
  gi|116753932|ref|YP_843050.1| 531 VIEEDdkEEVIGLGQYSIAEgthTA--EvaIVVRDDYQRKGVGMEILSYlvylaRKQGLFyLNaE 593
                                    6777777888887777777663333..36699****************75555322663322222 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   2.4e-07   0.00043      47     132 ..     524     608 ..     500     622 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.4e-07
                 Acetyltransf_4  47 ekeyvflvae...sdrivGyaylgqfkkrakdwkaelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspne 123
                                     +  ++ v+e   +++++G  +++  +    ++ ae+ + +   d + +g+g e++ +l+  +++q++ +l+ae+ ++n+
  gi|116753932|ref|YP_843050.1| 524 REMVILAVIEeddKEEVIGLGQYSIAE---GTHTAEVAIVVR-DDYQRKGVGMEILSYLVYLARKQGLFYLNAEVLVENQ 599
                                    555666676655567899999999555...5**********6.79*********************************99 PP

                 Acetyltransf_4 124 nsiqfhkal 132
                                    +   ++++l
  gi|116753932|ref|YP_843050.1| 600 AVLRMFERL 608
                                    887777765 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 !   12.3   0.1   2.1e-05     0.039     139     215 ..     129     204 ..     109     217 .. 0.81
   2 !    4.3   0.0    0.0056        10     448     478 ..     392     422 ..     384     427 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.1e-05
                Mal_decarbox_Al 139 nvalvaaekadreGnlytGantedtPaiveatafkdgiviaqvneivdklprvd....iPadwvdfvveadkpf..aiep 212
                                    +val+ ++  dr+G l  G + +    iv a+  k ++viaq+n    ++prv     i  d v+fv+  d+p   ++e+
  gi|116753932|ref|YP_843050.1| 129 DVALIQTTPPDRHGYLNLGISVD----IVKAAVEKASVVIAQINS---NMPRVQgdgfIHMDDVSFVIPHDEPLleYMES 201
                                    69******************986....999999999*******97...566665345588999*****999996335666 PP

                Mal_decarbox_Al 213 lft 215
                                    + t
  gi|116753932|ref|YP_843050.1| 202 VPT 204
                                    655 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0056
                Mal_decarbox_Al 448 iygddvthvvteeGiayllkaesleereqai 478
                                    +   d+ +vvte Giayl+  +  e  +++i
  gi|116753932|ref|YP_843050.1| 392 LTRGDLHYVVTEYGIAYLHGKNVRERAMDLI 422
                                    5567999***********8655544444444 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   2.9e-05     0.051      37      89 ..     535     592 ..     494     618 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.9e-05
                Acetyltransf_10  37 eeggkivGvi..elrdgshisll..fVdpeyrgqGigkaLleaveeeaekdgikl.el 89 
                                    +++++++G +  ++ +g h + +  +V+++y+++G+g ++l ++   a+k+g+     
  gi|116753932|ref|YP_843050.1| 535 DDKEEVIGLGqySIAEGTHTAEVaiVVRDDYQRKGVGMEILSYLVYLARKQGLFYlNA 592
                                    344677777744556666888776689******************9999997654433 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   4.9e-05     0.088      26      80 ..     558     613 ..     548     618 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.9e-05
                                    EEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EE.EEEETT-HHHHHHHHHHT-EEE CS
                           FR47  26 alqvlpehrrrGlgsrlvkalakeiaergktvl.lvvvasNtpsirlyeklGfeki 80 
                                    a+ v+++ +r+G g  + + l +  +++g   l + v  +N++  r++e+l+ +  
  gi|116753932|ref|YP_843050.1| 558 AIVVRDDYQRKGVGMEILSYLVYLARKQGLFYLnAEVLVENQAVLRMFERLNLRTE 613
                                    899************************998654388999************98865 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0         1   1.8e+03      44      56 ..      46      58 ..      25      61 .. 0.77
   2 ?   10.9   0.1   0.00021      0.38       8      58 ..     537     587 ..     531     590 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1
                Acetyltransf_CG 44 kLvkaalddaree 56
                                    Lv+a  d++re+
  gi|116753932|ref|YP_843050.1| 46 FLVQALADYVREH 58
                                   4999999999998 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00021
                Acetyltransf_CG   8 egeevafleYevrkegvldfthTeVpeelrGkGiAkkLvkaalddareegl 58 
                                    ++e ++  +Y+  ++ + +   ++V + +++kG+++++  + +  ar++gl
  gi|116753932|ref|YP_843050.1| 537 KEEVIGLGQYSIAEGTHTAEVAIVVRDDYQRKGVGMEILSYLVYLARKQGL 587
                                    5677888899977777888889**************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (627 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); 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: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.41
# Mc/sec: 4643.73
//
Query:       gi|116753933|ref|YP_843051.1|  [L=336]
Description: phosphate uptake regulator, PhoU [Methanosaeta thermophila PT]
Scores for 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-26   90.2  10.3    7.5e-18   64.8   3.2    2.3  2  PhoU            PhoU domain
    0.00033   20.5   0.1    0.00083   19.2   0.1    1.8  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an


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 !   64.8   3.2   8.4e-22   7.5e-18       1      88 [.     136     225 ..     136     226 .. 0.90
   2 !   29.7   0.7   7.3e-11   6.5e-07       1      88 [.     241     324 ..     241     325 .. 0.85

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 8.4e-22
                                    HHHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HGG-SHHHHHHHHHHHHHHHHHH CS
                           PhoU   1 lrrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealak...rqplaedlrellsllriardlER 77 
                                    lrr+  +v++m++da+++l    + la++vi+rdd++drl  +++r+ +e+l +   + + + d+ +++++  +a++lER
  gi|116753933|ref|YP_843051.1| 136 LRRLRTVVKSMIQDAIDSLIGMKKRLAQDVIQRDDDVDRLNLLVSRQFIEMLRTgalS-QSSLDVITAFNYALAASNLER 214
                                    689999*****************************************99999775642.333389999************ PP

                                    HHHHHHHHHHH CS
                           PhoU  78 igDhavniaer 88 
                                    i+Dha +ia+ 
  gi|116753933|ref|YP_843051.1| 215 IADHAHSIANL 225
                                    *********86 PP

  == domain 2  score: 29.7 bits;  conditional E-value: 7.3e-11
                                    HHHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..HGG-SHHHHHHHHHHHHHHHHHHH CS
                           PhoU   1 lrrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealak..rqplaedlrellsllriardlERi 78 
                                    l r+++i+   +d+a++al +++te+a+ +ie+ +ei r  ++  + ++   ++  +q++      +l  + i++++ R 
  gi|116753933|ref|YP_843051.1| 241 LTRISSIICGLIDEAISALLHRNTEIANSIIEQTKEIRREAMRSFEPVISSSSTgvNQEE------ILMRMVISSSIARF 314
                                    578999**************************************9999998877433333......44445599****** PP

                                    HHHHHHHHHH CS
                           PhoU  79 gDhavniaer 88 
                                     Dh++ni e 
  gi|116753933|ref|YP_843051.1| 315 LDHIKNIGEF 324
                                    *******986 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 !   19.2   0.1   9.3e-08   0.00083       2      44 ..       9      52 ..       8      54 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 9.3e-08
                                   EETTEEEEEE-CCCHHHCCEECTCEEEEEECTT.CCCCCCCHHS CS
                 MazE_antitoxin  2 kvGnsgavriPkevrfelgireGdevelevdgd.kiilrplksl 44
                                   ++ ++ +v++Pk ++   gi++G+ v +++ +   ++l+p ++ 
  gi|116753933|ref|YP_843051.1|  9 TGKSTFIVSLPKGWVVRSGIKPGSIVYITQGESgELVLSPERTS 52
                                   78899***********************9999999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       946  (0.0527637); expected 358.6 (0.02)
Passed bias filter:                      664  (0.037035); 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: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2429.23
//
Query:       gi|116753934|ref|YP_843052.1|  [L=226]
Description: phosphate uptake regulator, PhoU [Methanosaeta thermophila PT]
Scores for complete 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-41  139.2   9.5    1.5e-20   73.4   1.5    2.1  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 !   73.4   1.5   8.3e-25   1.5e-20       2      88 ..      27     113 ..      26     114 .. 0.98
   2 !   70.7   1.3     6e-24   1.1e-19       1      89 []     129     214 ..     129     214 .. 0.93

  Alignments for each domain:
  == domain 1  score: 73.4 bits;  conditional E-value: 8.3e-25
                                    HHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHHH CS
                           PhoU   2 rrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERigDh 81 
                                    r+++++v++ +++++eal ++d  larev++ d  +d+l  ++e +++e+la +qp+a+dlr+++++l+i  dlER gD 
  gi|116753934|ref|YP_843052.1|  27 RELSDLVSSSIERSVEALCRNDAILAREVVQGDYAVDDLSVKLESKCMELLALQQPMAKDLRMIIGILKIGIDLERAGDL 106
                                    799***************************************************************************** PP

                                    HHHHHHH CS
                           PhoU  82 avniaer 88 
                                    av+ia+ 
  gi|116753934|ref|YP_843052.1| 107 AVDIARV 113
                                    *****97 PP

  == domain 2  score: 70.7 bits;  conditional E-value: 6e-24
                                    HHHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHH CS
                           PhoU   1 lrrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERigD 80 
                                    l++ma i+ eml+ a+eale++d ++ar v + d  id l+ ++++ l+++ a++ +l   +++ + ll++ r++ERigD
  gi|116753934|ref|YP_843052.1| 129 LSKMAGIAVEMLSGAMEALEKGDPDMARNVTRHDYVIDSLYVKVRDVLMRMTAEDMNL---MDQTIPLLMVNRHIERIGD 205
                                    689*****************************************99999888887666...67899************** PP

                                    HHHHHHHHH CS
                           PhoU  81 havniaerv 89 
                                    h++ni+e++
  gi|116753934|ref|YP_843052.1| 206 HICNICESI 214
                                    ******975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1775.53
//
Query:       gi|116753935|ref|YP_843053.1|  [L=269]
Description: phosphate ABC transporter, ATPase subunit [Methanosaeta thermophila PT]
Scores for complete 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  109.4   0.0    3.1e-31  108.7   0.0    1.3  1  ABC_tran     ABC transporter
    7.4e-15   55.5   0.0    1.2e-07   31.9   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    5.7e-07   29.2   0.1    0.00015   21.3   0.1    2.2  1  SMC_N        RecF/RecN/SMC N terminal domain
    0.00048   20.7   0.1    0.00086   19.9   0.1    1.4  1  AAA_23       AAA domain
    0.00057   19.8   0.0     0.0012   18.8   0.0    1.5  1  RsgA_GTPase  RsgA GTPase
     0.0014   18.6   0.0     0.0023   17.9   0.0    1.4  1  Rad17        Rad17 P-loop domain
     0.0019   18.0   0.0     0.0021   17.8   0.0    1.3  1  AAA_15       AAA ATPase domain
      0.002   17.9   0.0     0.0034   17.1   0.0    1.3  1  AAA_29       P-loop containing region of AAA domain
     0.0022   18.4   0.0     0.0053   17.2   0.0    1.8  1  AAA_16       AAA ATPase domain
     0.0027   18.0   0.1     0.0082   16.4   0.1    2.0  1  AAA_22       AAA domain
  ------ inclusion threshold ------
      0.036   14.2   0.0      0.056   13.6   0.0    1.6  1  AAA_33       AAA domain
      0.037   13.6   0.0      0.097   12.2   0.1    1.7  1  AAA_25       AAA domain
      0.039   14.4   0.0       0.76   10.2   0.0    2.2  2  AAA          ATPase family associated with various cellular a
      0.052   12.9   0.4      0.091   12.1   0.1    1.5  2  ATPase       KaiC
      0.054   14.1   0.0       0.12   12.9   0.0    1.6  1  AAA_18       AAA domain
        0.1   12.8   0.2        3.6    7.8   0.0    2.3  2  AAA_28       AAA domain
       0.13   12.0   0.0        1.1    9.0   0.0    2.0  2  AAA_30       AAA domain
       0.16   10.7   0.1        4.5    5.9   0.0    2.1  2  ABC_ATPase   Predicted ATPase of the ABC class
       0.18   11.5   0.0        9.3    5.9   0.0    2.2  2  IstB_IS21    IstB-like ATP binding protein


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.7   0.0   3.3e-34   3.1e-31       1     136 [.      41     193 ..      41     194 .. 0.96

  Alignments for each domain:
  == domain 1  score: 108.7 bits;  conditional E-value: 3.3e-34
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--.....SEEEEEETTCEGGG..B-HHHCCHCEEEE-SS--S-TT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp.....teGeilldgkdlke..qeleslrkeigvlpqepqlfpe 73 
                                    lk ++l + e++++a++G++G+GKSt+++++ ++ +       eGeil+dgk++ +  ++   lrk+ig+++q+p+ fp 
  gi|116753935|ref|YP_843053.1|  41 LKSITLGIPENKITALIGPSGCGKSTFIRCINRMNDLipgvrIEGEILYDGKNIYDrdTDVVALRKKIGMVFQKPNPFPM 120
                                    7899******************************99888999*************98899999***************** PP

                                    SBHHHH...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    xxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  74 ltvren...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                    + +++n           + d+ +e+ l+   l e  ++++++ +  LSgGq+qr+++aral+ +p+++l+DEp+
  gi|116753935|ref|YP_843053.1| 121 S-IYDNiaygprihgykNIDRIVEQSLRDAALWEEVEDRLDQPAMGLSGGQQQRLCIARALAMRPEVILFDEPC 193
                                    *.9***********99888888******************9999*****************************7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   1.4e-07   0.00013       1      61 [.      53     113 ..      53     127 .. 0.81
   2 !   31.9   0.0   1.2e-10   1.2e-07     210     295 ..     139     221 ..     120     223 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.4e-07
                         AAA_21   1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefe 61 
                                    +++liGp g+GKS++++++  + +l++ v+ ++ +l +g++i + +       ++i ++f+
  gi|116753935|ref|YP_843053.1|  53 ITALIGPSGCGKSTFIRCINRMNDLIPGVRIEGEILYDGKNIYDRDTDVVALRKKIGMVFQ 113
                                    79********************999888888888888888887777777777777776665 PP

  == domain 2  score: 31.9 bits;  conditional E-value: 1.2e-10
                         AAA_21 210 asvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrng 289
                                    +++ e++++    ++e +d+ + pa  lS G+++ l+++ al+ ++    ++l+DEp + L+P  ++r+ el+++l+ + 
  gi|116753935|ref|YP_843053.1| 139 DRIVEQSLRDAALWEEVEDRLDQPAMGLSGGQQQRLCIARALAMRP---EVILFDEPCSALDPISTARIEELMESLRGKY 215
                                    33333444446678899******************9*******999...9*************99999999999999999 PP

                         AAA_21 290 aQvilt 295
                                    +Q+i+t
  gi|116753935|ref|YP_843053.1| 216 TQIIVT 221
                                    9*9998 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.1   1.6e-07   0.00015      23     205 ..      50     230 ..      38     243 .. 0.65

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.6e-07
                                    TSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCC..CC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  23 sksftaivGpNGSGKsnlldAilFvLGersakklrseklsd..lihkskekasvkkaeveitfdnedkklkiekeevsis 100
                                    ++++ta++Gp G+GKs ++  i  +        +  e l d   i+ +++   + + ++ ++f++++       +++   
  gi|116753935|ref|YP_843053.1|  50 ENKITALIGPSGCGKSTFIRCINRMNDLIPGVRIEGEILYDgkNIYDRDTDVVALRKKIGMVFQKPNPFPMSIYDNIAYG 129
                                    67899*****************5444444444444444433113555677778888899999999998855555555555 PP

                                    EEEETTSEEEEEETTEEE-H....HHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHH CS
                                    xxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 101 rrvkrkgeseykingkevtk....kevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknv 176
                                     r+   ++ + +i +++ +     +ev++ l +  +    LSgG+++ + +a  +A+   +p+ + l+De  +aLD   +
  gi|116753935|ref|YP_843053.1| 130 PRIHGYKNID-RIVEQSLRDaalwEEVEDRLDQPAM---GLSGGQQQRLCIARALAM---RPE-VILFDEPCSALDPIST 201
                                    5554444432.3444444440013455555555444...59*****99888888776...455.679************* PP

                                    HHHHHHHHHHCTT.SEEEEE-SSHHHCCC- CS
                                    xxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                          SMC_N 177 kkvaellkekskn.aQfivislreemleka 205
                                    +++ el+++ + + +Q+i ++++ ++ +++
  gi|116753935|ref|YP_843053.1| 202 ARIEELMESLRGKyTQII-VTHNMQQAARV 230
                                    ********9887735555.55655554443 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1   9.1e-07   0.00086      15      40 ..      44      72 ..      30      74 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 9.1e-07
                         AAA_23 15 idF...skgltlItGpNGaGKTTildAik 40
                                   i +   ++++t+++Gp G+GK+T++++i 
  gi|116753935|ref|YP_843053.1| 44 ITLgipENKITALIGPSGCGKSTFIRCIN 72
                                   555556899******************96 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.2e-06    0.0012      86     121 ..      37      73 ..      17      85 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.2e-06
                                    THTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase  86 tkegleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                    +k++l++++  + + k+++l+G+SG GKSt+i  ++ 
  gi|116753935|ref|YP_843053.1|  37 SKQALKSITLGIPEnKITALIGPSGCGKSTFIRCINR 73 
                                    556677777666665*****************98876 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   2.4e-06    0.0023      32      67 ..      38      73 ..      35     104 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.4e-06
                          Rad17 32 kewlkadvLesrkkriLLisGPsGCgkstvvkvLsk 67
                                   k++lk+ +L   +++i  + GPsGCgkst ++ + +
  gi|116753935|ref|YP_843053.1| 38 KQALKSITLGIPENKITALIGPSGCGKSTFIRCINR 73
                                   689999999999999****************98765 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.2e-06    0.0021      15      50 ..      42      78 ..      39     225 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.2e-06
                         AAA_15 15 kdveidlsee.ltvliGkNnsGKSsilealdlFlnnk 50
                                   k++++ + e+ +t liG+ ++GKS++++ ++ + +  
  gi|116753935|ref|YP_843053.1| 42 KSITLGIPENkITALIGPSGCGKSTFIRCINRMNDLI 78
                                   55555555555*******************9998854 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 !   17.1   0.0   3.6e-06    0.0034      19      39 ..      48      68 ..      27      74 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.6e-06
                         AAA_29 19 idlkgatlltGpsGsGKSTll 39
                                   i ++ +t l+GpsG GKST++
  gi|116753935|ref|YP_843053.1| 48 IPENKITALIGPSGCGKSTFI 68
                                   444559*************98 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   0.0   5.6e-06    0.0053      15      46 ..      40      73 ..      38     231 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.6e-06
                         AAA_16 15 alervrsgrp..elvllsGesGvGKsslvrellr 46
                                   al+++  g p   ++ l+G+sG+GKs+ +r++ r
  gi|116753935|ref|YP_843053.1| 40 ALKSITLGIPenKITALIGPSGCGKSTFIRCINR 73
                                   566666666666999****************986 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   8.7e-06    0.0082       5      30 ..      51      76 ..      49     231 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 8.7e-06
                         AAA_22  5 agilvvtGesGtGKTtllrrlleqld 30
                                    +i++++G+sG+GK+t +r + + +d
  gi|116753935|ref|YP_843053.1| 51 NKITALIGPSGCGKSTFIRCINRMND 76
                                   5799***************9988875 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   5.9e-05     0.056       3      36 ..      55      91 ..      53     189 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.9e-05
                         AAA_33  3 llvGlpGsGKstlaerllkklg...avllssdtlrrr 36
                                    l+G++G+GKst+++ + + ++   +v+++  +l++ 
  gi|116753935|ref|YP_843053.1| 55 ALIGPSGCGKSTFIRCINRMNDlipGVRIEGEILYDG 91
                                   589***********99887777778888888776664 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1    0.0001     0.097      30      50 ..      48      68 ..      36      72 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0001
                         AAA_25 30 lpagelallaGapgtGKttla 50
                                   +p++++++l+G++g+GK+t+ 
  gi|116753935|ref|YP_843053.1| 48 IPENKITALIGPSGCGKSTFI 68
                                   59*****************85 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    0.0008      0.76       3      21 ..      56      74 ..      54     122 .. 0.80
   2 ?    2.2   0.0      0.24   2.2e+02      44      66 ..     170     191 ..     131     228 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0008
                                   EESSTTSSHHHHHHHHHHH CS
                            AAA  3 lyGppGtGKTllakavake 21
                                   l+Gp G+GK+++++ + + 
  gi|116753935|ref|YP_843053.1| 56 LIGPSGCGKSTFIRCINRM 74
                                   89***********998665 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.24
                                    HHHHHHHHHHHHTSTSEEEEEET CS
                            AAA  44 kkirelfkeakekakpsilfiDE 66 
                                    ++ r ++++a ++ +p ++++DE
  gi|116753935|ref|YP_843053.1| 170 QQQRLCIARALAM-RPEVILFDE 191
                                    4455555555555.599*****9 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   9.6e-05     0.091      14      35 ..      46      67 ..      39      70 .. 0.90
   2 ?   -3.3   0.0       4.8   4.5e+03     145     167 ..     205     226 ..     201     235 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.6e-05
                         ATPase 14 gGipegrvvlitGepGtGKtif 35
                                    Gipe++++ + G +G+GK++f
  gi|116753935|ref|YP_843053.1| 46 LGIPENKITALIGPSGCGKSTF 67
                                   6*******************98 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.8
                         ATPase 145 rqlvrvlkklgvTailvseksss 167
                                     +l++ l++++ T i+v+   ++
  gi|116753935|ref|YP_843053.1| 205 EELMESLRGKY-TQIIVTHNMQQ 226
                                    56666666654.55555554444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00013      0.12       3      44 ..      56     100 ..      55     116 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00013
                         AAA_18   3 ltGtpGvGKttlakeLskrlgf...gvnlrdvakenglllevdpe 44 
                                    l G++G+GK+t+ + +++++ +   +++ +++++++   +++d +
  gi|116753935|ref|YP_843053.1|  56 LIGPSGCGKSTFIRCINRMNDLipgVRIEGEILYDGKNIYDRDTD 100
                                    89***************9986679766666777776666666655 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0    0.0038       3.6       3      21 ..      55      73 ..      53      88 .. 0.83
   2 ?    3.0   0.1      0.11   1.1e+02      98     138 ..     222     262 ..     133     267 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0038
                         AAA_28  3 vitGgestGKTtlleaLaa 21
                                   +++G++++GK+t ++ +++
  gi|116753935|ref|YP_843053.1| 55 ALIGPSGCGKSTFIRCINR 73
                                   79**********9987665 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.11
                         AAA_28  98 aeleaaarekrydlvfllppapeidddgeRredleereaid 138
                                     ++++aar + y+++f++ ++ e+ ++++  e ++er   d
  gi|116753935|ref|YP_843053.1| 222 HNMQQAARVSDYTAYFYMGEMIEFGETKQIFENPRERSTED 262
                                    34566999999*******99999966666667777776655 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0    0.0011       1.1      17      41 ..      50      74 ..      37      85 .. 0.83
   2 ?    0.8   0.0      0.37   3.5e+02      88     131 ..     183     230 ..     142     244 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0011
                         AAA_30 17 gdrvavltGpAGtGKttalkalrea 41
                                   ++++++l Gp G GK+t ++ ++++
  gi|116753935|ref|YP_843053.1| 50 ENKITALIGPSGCGKSTFIRCINRM 74
                                   56799**************999876 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.37
                         AAA_30  88 pgtllivDEagmv....dtkqlaallkaaekagakvilvGDerQlasV 131
                                    + ++++ DE   +    +t+ +++l+++++ + +++i+    +Q a V
  gi|116753935|ref|YP_843053.1| 183 RPEVILFDEPCSAldpiSTARIEELMESLRGKYTQIIVTHNMQQAARV 230
                                    347888888766667779999999999999988999988888887766 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 ?    5.9   0.0    0.0048       4.5     240     266 ..      46      73 ..      36      80 .. 0.89
   2 ?    2.7   0.0     0.045        43     324     355 ..     167     198 ..     163     232 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0048
                                    EEE-SS.EEEEEE-TTSSHHHHHHHHHH CS
                     ABC_ATPase 240 mgipkG.vtlIvGggfhGKsTLLeAlek 266
                                    +gip+  +t+++G+   GKsT ++ +++
  gi|116753935|ref|YP_843053.1|  46 LGIPENkITALIGPSGCGKSTFIRCINR 73 
                                    89*9988****************99976 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.045
                                    -HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHH CS
                     ABC_ATPase 324 SGStsqAanimealeagakllLiDEDtsAtNl 355
                                    SG   q   i++al ++ +++L+DE  sA   
  gi|116753935|ref|YP_843053.1| 167 SGGQQQRLCIARALAMRPEVILFDEPCSALDP 198
                                    888899999*****************999765 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 ?    5.9   0.0    0.0098       9.3      46      64 ..      50      68 ..      38      75 .. 0.81
   2 ?    3.4   0.0     0.059        55     102     151 ..     177     226 ..     151     235 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0098
                      IstB_IS21 46 kkenivllGpsGvGKshla 64
                                   +++  +l+GpsG GKs + 
  gi|116753935|ref|YP_843053.1| 50 ENKITALIGPSGCGKSTFI 68
                                   566679*********9765 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.059
                      IstB_IS21 102 alkrllkvdllilDd..lgllpldqaeaellfeviekryerrsiiitsnlpf 151
                                    a +  +++++++ D+   +l p++ a  e+l+e +  +y    ii+t n++ 
  gi|116753935|ref|YP_843053.1| 177 ARALAMRPEVILFDEpcSALDPISTARIEELMESLRGKYT--QIIVTHNMQQ 226
                                    4445678899999*95557999***********9999996..5899998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 2069.20
//
Query:       gi|116753936|ref|YP_843054.1|  [L=434]
Description: aspartyl-tRNA synthetase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-88  295.9   0.0    3.6e-88  295.7   0.0    1.0  1  tRNA-synt_2      tRNA synthetases class II (D, K and N)
    9.6e-11   41.5   0.1    1.6e-10   40.8   0.1    1.4  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
  ------ inclusion threshold ------
      0.023   14.9   0.0      0.053   13.7   0.0    1.5  1  tRNA_anti_2      OB-fold nucleic acid binding domain
      0.026   14.0   0.2          2    7.9   0.0    2.7  3  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 !  295.7   0.0   7.9e-92   3.6e-88       3     313 ..     119     428 ..     117     429 .. 0.95

  Alignments for each domain:
  == domain 1  score: 295.7 bits;  conditional E-value: 7.9e-92
                                    CHHHHTHHHHCCSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE....-E-S- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxx RF
                    tRNA-synt_2   3 elrlknryldlrtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeff....aLtqs 78 
                                    ++rl+ r+ldlr++   +v+++ s v++++r+ + e+gfie+ tP ++ ++te+g  lF +       ++f    +L+qs
  gi|116753936|ref|YP_843054.1| 119 DTRLDARFLDLRRPASMAVFKIESAVMRSLRNTFYEKGFIEVCTPKIVATATEGGTALFPI-------SYFereaFLNQS 191
                                    799**********************************************************.......44444445**** PP

                                    SHHHHHHHHHCTHSEEEEEEEEE--S--BTTB-S-CEEEEEEEEET-SCHHHHHHHHHHHHHHHHHHHHCSCCCCCHTTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2  79 pqlylellivagidrvfqiaraFRaEdsrtdrhlaEFtqieaemsfieeedimqvleelikslvkevlessakdiefvir 158
                                    pqly+++l++ g+drvf+i++ FRaE+++t+rhl+E +++++e+s++++ed+m++le+ ++s  + v e ++k+++    
  gi|116753936|ref|YP_843054.1| 192 PQLYKQILMATGLDRVFEIGPIFRAEEHDTRRHLNEAISVDVEVSYADHEDVMSLLENAVSSAYRYVSEICEKELQILGV 271
                                    *******************************************************************8888777665555 PP

                                    TTSEE-SSS-EEEEHHHHHHHHHTS.......-SS--HHHHHHHHHHS--SEEEEEEEBGGGSTTCBBBSTTSTTBBSEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2 159 rnskdlkkpfkrltykeaieklnei.......gkdldkaderalvkkeknepvfvtdfPaelkpFyarkeeddkkltesy 231
                                       + +k+pf+r+ty+ea+e ++e        g+d+d++ e +l    + e +f+td+P+++kp+y++  ed++++ +++
  gi|116753936|ref|YP_843054.1| 272 D-LDIPKTPFRRITYTEALEMASESgrksmewGDDIDTETEHYLGS-LIGEHYFLTDWPSSVKPYYTQPYEDKPEICKGF 349
                                    5.5677888************9888********************9.99******************************* PP

                                    EEEETTEEEEEEEEB--SHHHHHHHHHHCCHHSSSGGGGHHHHHHHHCT--SEEEEEEEHHHHHHHHCT-SSGGGCSSS- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2 232 DllingvElvgGslRiedpeeleeklkskgldeeaeekfswylealeyGapphgGlglGldRlvmlllgsesIrdviaFP 311
                                    Dl+ + +El++G++R++d+e+l  ++k+kgl+   +e+f++yl+ ++yG+pph+G+glGl Rlv+++lg+e+Ird+++FP
  gi|116753936|ref|YP_843054.1| 350 DLMHPSMELASGAQRVHDYELLISRIKEKGLN---PESFEFYLKPFRYGMPPHAGWGLGLARLVQTMLGLENIRDAVLFP 426
                                    ********************************...********************************************* PP

                                    XX CS
                                    xx RF
                    tRNA-synt_2 312 kl 313
                                    + 
  gi|116753936|ref|YP_843054.1| 427 RD 428
                                    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 !   40.8   0.1   3.7e-14   1.6e-10       1      76 []      20      99 ..      20      99 .. 0.87

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 3.7e-14
                                   EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET.HHHHHHHTTS-...TTSEEEEEEEEEEC...TTSSEEEEEEEEEE CS
                tRNA_anti-codon  1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfr.eeatklaenlk...eGdvvrvtGrvkrr...pggelelkveeiel 75
                                   Vt+aG v+ i  r+ g+++f++lrD++g  qv++    +++kl e+++   +++vv v+Grvk+    p+g +e+  e +e+
  gi|116753936|ref|YP_843054.1| 20 VTLAGHVHEI--RDLGGICFLVLRDREGLAQVTVLTkRADRKLVETVRgvsRESVVLVRGRVKAEpkaPNG-FEILPEAVEV 98
                                   89********..***************999998888756666666666666**************999999.***9999988 PP

                                   E CS
                tRNA_anti-codon 76 l 76
                                   l
  gi|116753936|ref|YP_843054.1| 99 L 99
                                   6 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 ?   13.7   0.0   1.2e-05     0.053      20      80 ..      18      81 ..       6      89 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.2e-05
                    tRNA_anti_2 20 kavwvrGeisnlkrkasghvYftLkDekakisavifrsra.aklkft...ledGmkVlvkgrlsv 80
                                   ++v++ G + ++ r   g +++ L+D +   ++++  +ra +kl  t   ++    Vlv+gr++ 
  gi|116753936|ref|YP_843054.1| 18 SEVTLAGHVHEI-RDLGGICFLVLRDREGLAQVTVLTKRAdRKLVETvrgVSRESVVLVRGRVKA 81
                                   569999******.64599********776666666665553444433457999*********975 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 ?   -2.0   0.0      0.44     2e+03      20      43 ..     142     165 ..     131     177 .. 0.78
   2 ?    2.9   0.0     0.014        64     103     142 ..     206     241 ..     189     262 .. 0.68
   3 ?    7.9   0.0   0.00044         2     212     234 ..     400     422 ..     390     431 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.44
                                    HHHHHHHHHHHHCTTCEESSTTSE CS
                   tRNA-synt_2d  20 tkvleeikeiflelgfeevegpev 43 
                                    + v++ ++++f e gf ev  p++
  gi|116753936|ref|YP_843054.1| 142 SAVMRSLRNTFYEKGFIEVCTPKI 165
                                    567888999999999998887776 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.014
                                    EEEEEEEEEBSST-SSSB-SEEEEEEEEEEETT--HHHHH CS
                   tRNA-synt_2d 103 kiisigrvfRrdavDathlaeFhqveglvvdenvsladlk 142
                                    +++ ig +fR ++ D ++    h  e + vd +vs ad  
  gi|116753936|ref|YP_843054.1| 206 RVFEIGPIFRAEEHDTRR----HLNEAISVDVEVSYADHE 241
                                    899**********66544....333555555555544444 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.00044
                                    EEEEEEHHHHHHHHHT-SSGHHH CS
                   tRNA-synt_2d 212 fafGlGveRlamlkygieDiRel 234
                                    +++GlG+ Rl   ++g+e+iR+ 
  gi|116753936|ref|YP_843054.1| 400 AGWGLGLARLVQTMLGLENIRDA 422
                                    68*******************84 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.36
# Mc/sec: 3632.10
//
Query:       gi|116753937|ref|YP_843055.1|  [L=216]
Description: hypothetical protein Mthe_0624 [Methanosaeta thermophila PT]
Scores for complete 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-30  104.2   0.0    7.6e-30  103.9   0.0    1.1  1  MAF_flag10     Protein of unknown function DUF115
      0.003   17.6   0.0     0.0059   16.6   0.0    1.5  1  TPK_catalytic  Thiamin pyrophosphokinase, catalytic domain


Domain annotation for each model (and alignments):
>> MAF_flag10  Protein of unknown function DUF115
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.9   0.0   8.5e-34   7.6e-30       7     169 ..      40     188 ..      33     190 .. 0.88

  Alignments for each domain:
  == domain 1  score: 103.9 bits;  conditional E-value: 8.5e-34
                     MAF_flag10   7 lkenlkpslkellnkfkgnkpaiivgaGPSLeknlellkelrdkaviiaadtalkaLlkegIkPDivvs.lDpqeasyev 85 
                                    ++++   +l+el++  +g ++++++g+ P L++++  +     + v++aad+a+++Ll+++++PDi+v+ lD+   ++ +
  gi|116753937|ref|YP_843055.1|  40 IDQI---TLDELKDAVRG-RDVVVCGNAPRLRDEIGGIT---PSDVVLAADGATSVLLEHDVIPDIIVTdLDG---CMPD 109
                                    3334...46888888889.*****************997...899****************************...**** PP

                     MAF_flag10  86 fkeaekkgdiplvfasgvnpellkkykgpki.flvtgstqa..lelleeekneilfgGgsvantaldlAvklgfkeIili 162
                                    + +a+++g++++v+a+g+n+++lk++ +++  +l  g+tqa  le++      ++fgG++++++a++lA+++  k+I li
  gi|116753937|ref|YP_843055.1| 110 IIDANRRGSAVVVHAHGDNIDKLKEHVPHLRrVL--GTTQAspLENV------HNFGGFTDGDRAVFLALEFMPKSIRLI 181
                                    *****************************99443..44554235555......9************************** PP

                     MAF_flag10 163 GqDlayt 169
                                    G+D+  +
  gi|116753937|ref|YP_843055.1| 182 GFDFDDE 188
                                    ****876 PP

>> TPK_catalytic  Thiamin pyrophosphokinase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   6.6e-07    0.0059       8      68 ..      76     130 ..      73     154 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.6e-07
                  TPK_catalytic   8 aslrvcaDgGanrlyeeekerlellpdvivGDlDSirpevkefyeskgteivkkpdqdstD 68 
                                    ++++++aDg++  l+     +++++pd+iv DlD   p++ +  +  g ++v + + d++D
  gi|116753937|ref|YP_843055.1|  76 SDVVLAADGATSVLL-----EHDVIPDIIVTDLDGCMPDIIDANRR-GSAVVVHAHGDNID 130
                                    6899***********.....999****************9997776.66666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.36
# Mc/sec: 1792.24
//
Query:       gi|116753938|ref|YP_843056.1|  [L=344]
Description: hypothetical protein Mthe_0625 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.36
# Mc/sec: 2879.87
//
Query:       gi|116753939|ref|YP_843057.1|  [L=351]
Description: putative translation factor pelota [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-29  101.3   0.0    5.9e-29  100.7   0.0    1.3  1  eRF1_1    eRF1 domain 1
    1.3e-21   77.2   0.1    4.8e-21   75.4   0.1    2.0  1  eRF1_3    eRF1 domain 3
    1.1e-08   35.5   0.0    2.5e-08   34.3   0.0    1.6  1  eRF1_2    eRF1 domain 2


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 !  100.7   0.0   9.9e-33   5.9e-29       1     128 [.       5     128 ..       5     129 .. 0.93

  Alignments for each domain:
  == domain 1  score: 100.7 bits;  conditional E-value: 9.9e-33
                                    HEEEEECTBTTSCCEEEEEE-SCHHHHHHHHHCHTTHEEEEEEEECHHH.......-...-CEEEEEEEEEEEEEEECTT CS
                         eRF1_1   1 mkllkrdlekdgsgsvtLipeddedlwhlynliapgdsvrastvrkvqresstgsre...servklkLtikvekvdfdkd 77 
                                    m+++kr+l++d +g ++L++e+ +dlwhl +l++pgd v a+t rk+    +t +      er +++L i+ve v+f++ 
  gi|116753939|ref|YP_843057.1|   5 MRVIKRNLRGD-EGEISLVAESLDDLWHLKHLVSPGDLVFATTQRKISG--ATDKLRpekAERRTVRLGISVEAVEFHTY 81 
                                    9********88.9**********************************66..3333334459******************* PP

                                    SSEEEEEEEEEEGGGG--TTSEEEEEE-TTSEEEEEECEESHHHHHHHHHH CS
                         eRF1_1  78 agvlrisGkvieenehvklgafhtldlelkrpftiikeewdsfalerLkea 128
                                    ++ lri+G + ++ +   +g++htl++e + +++iik +w    l+r++ea
  gi|116753939|ref|YP_843057.1|  82 SNWLRIHGVIKSGVD---IGSYHTLNIEAGSELSIIK-RWRPDELQRIEEA 128
                                    **********99998...*******************.9***********9 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.4   0.1     8e-25   4.8e-21       2     113 .]     256     347 ..     255     347 .. 0.96

  Alignments for each domain:
  == domain 1  score: 75.4 bits;  conditional E-value: 8e-25
                                    HHHHHHHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSHHHHHS-HHH-HHHHHHHHHHHHHHHHHT CS
                         eRF1_3   2 iqekklleefleelakdtgkavYGveevlkalemgAvetLLvseelersrdtlkekvketgeelelvelieelvenvees 81 
                                    ++e++l++++++e+a+d g+a+YG++ev++a+++gA+etL+++++l r  d                  +e+l+++v   
  gi|116753939|ref|YP_843057.1| 256 SRETRLMDDLMKEIATD-GRAAYGIREVREAANYGAIETLMIVDQLVRRGD------------------VESLIRDVAAG 316
                                    799**************.*****************************9852..................89********* PP

                                    T-EEEEE-TTSHHHHHHHHHTTTEEEEESS-- CS
                         eRF1_3  82 gakveiisseseeGeqlvkafgGiaaiLRykv 113
                                    +++v+i+s+e+e Ge+l +a+gG+aa+LR+++
  gi|116753939|ref|YP_843057.1| 317 RGRVVIFSTEFEPGERL-EALGGVAALLRFRI 347
                                    *****************.************96 PP

>> eRF1_2  eRF1 domain 2
   #    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       4     126 ..     139     243 ..     136     251 .. 0.88

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 4.3e-12
                                    EEEEETTEEEEEEEESSCEEEEEEEE------BSTTBSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCHTTTESEEEEE CS
                         eRF1_2   4 livldegeAtigllkgsrtevlkkievsvPkKhkrGgqsarrfeRlreekleeflkkvaeaankafllvdkdklkgiila 83 
                                    l +++egeAtig+l++  ++++++i +      ++G+ s+          ++ flk+va+++ +       ++ + ++la
  gi|116753939|ref|YP_843057.1| 139 LALVEEGEATIGVLRQFGVQTVAEIRGG----SGKGSGSSV---------RDDFLKEVADQIANS-----AGDDAYVVLA 200
                                    6789*******************99975....566777777.........499*******99999.....577789**** PP

                                    ESSTHHHHHHHHHHHHHHHHTCCEEEEE-S-TSCHHHHHHHHC CS
                         eRF1_2  84 gpgfvkeefldkdlldaelkkkviklvdvsyggesglnevlek 126
                                    gpgf+ke++ + + +++    k +++ d+s++g+sg++evl+ 
  gi|116753939|ref|YP_843057.1| 201 GPGFTKEDLRKVMEARYPDLLKRLTMDDASSTGRSGFQEVLRR 243
                                    ************999999999********************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.36
# Mc/sec: 2913.66
//
Query:       gi|116753940|ref|YP_843058.1|  [L=101]
Description: hypothetical protein Mthe_0627 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.4e-07   30.7   2.2    5.7e-07   30.0   2.2    1.4  1  Rubrerythrin  Rubrerythrin
     0.0023   17.0   0.2     0.0026   16.8   0.2    1.0  1  Mn_catalase   Manganese containing catalase
     0.0056   17.0   0.8       0.01   16.2   0.3    1.7  1  DUF2383       Domain of unknown function (DUF2383)
     0.0059   16.5   0.6     0.0059   16.5   0.6    1.6  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 !   30.0   2.2   1.3e-10   5.7e-07       5      66 ..      28      87 ..      24     101 .] 0.81

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 1.3e-10
                                   HHHHHHHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH..B.SS CS
                   Rubrerythrin  5 kAiagEssarrlYkelaekakegypqiaelFeelAeeEreHakilnklleklepele.levke 66
                                   + ia+E++a++lY+ lae ++   +  ++++ ++A+eE  Ha+ + +ll++lep +e l +ke
  gi|116753940|ref|YP_843058.1| 28 YVIAAEYEAIQLYTQLAESTD--DECARAVLIDIADEEVVHAGEFLRLLKELEPREEeL-YKE 87
                                   6699*****************..555699999*************************33.332 PP

>> Mn_catalase  Manganese containing catalase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.2   5.9e-07    0.0026     138     202 ..      21      85 ..      13      99 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.9e-07
                    Mn_catalase 138 nliaDlranlaaEakarlqverlyeltddpgvrdmlsfLlaRelvHqlafekAleeleeeetkvv 202
                                    +l+  +r  +aaE +a   +++l e tdd  +r  l  +   e+vH  +f + l+ele++e+++ 
  gi|116753940|ref|YP_843058.1|  21 ELVRAIRYVIAAEYEAIQLYTQLAESTDDECARAVLIDIADEEVVHAGEFLRLLKELEPREEELY 85 
                                    677788999**************************************************997665 PP

>> DUF2383  Domain of unknown function (DUF2383)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.3   2.3e-06      0.01       3      58 ..      23      78 ..      21      84 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.3e-06
                                   HHHHHHHHHHHHHHHHHHHHHHHT--SHHHHHHHHHHHHHHHHHHHHHHHHHHHCT CS
                        DUF2383  3 ieaLndLietlkdgeegykeaaekvkdpqlktlleriaeereeaaeeLqseiralg 58
                                   ++a+   i++++ +++ y++ ae  +d+  +++l +ia+e   +a e+   +++l 
  gi|116753940|ref|YP_843058.1| 23 VRAIRYVIAAEYEAIQLYTQLAESTDDECARAVLIDIADEEVVHAGEFLRLLKELE 78
                                   7889999**************************************99998888876 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.6   1.3e-06    0.0059      81     140 ..      22      78 ..       9      80 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.3e-06
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Ferritin  81 veevleaalehekkvteslrelielaeeegDpatadfledfleeqeeheweleallekle 140
                                    +  +++ ++++e+++++ + +l+e ++   D + +  l d+ +e++ h+ e+  ll++le
  gi|116753940|ref|YP_843058.1|  22 LVRAIRYVIAAEYEAIQLYTQLAESTD---DECARAVLIDIADEEVVHAGEFLRLLKELE 78 
                                    567889999************999999...56*****************99999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1014  (0.0565564); expected 358.6 (0.02)
Passed bias filter:                      619  (0.0345251); 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: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 749.70
//
Query:       gi|116753941|ref|YP_843059.1|  [L=213]
Description: HAD family hydrolase [Methanosaeta thermophila PT]
Scores for 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   55.4   0.0    2.9e-14   53.9   0.0    1.7  1  Hydrolase        haloacid dehalogenase-like hydrolase
    1.4e-14   54.5   0.0    4.1e-14   53.1   0.0    1.6  1  HAD_2            Haloacid dehalogenase-like hydrolase
    3.4e-05   24.3   0.1      6e-05   23.5   0.1    1.5  1  HAD              haloacid dehalogenase-like hydrolase
     0.0011   18.8   0.0       0.16   11.8   0.0    2.2  2  Acid_PPase       Acid Phosphatase
     0.0087   16.2   0.0       0.05   13.7   0.0    2.0  1  Hydrolase_6      Haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.012   15.0   0.0       0.04   13.3   0.0    1.7  2  Put_Phosphatase  Putative Phosphatase
      0.038   13.7   0.0        2.8    7.6   0.0    2.1  2  PNK3P            Polynucleotide kinase 3 phosphatase


Domain annotation for each model (and alignments):
>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   0.0   1.1e-17   2.9e-14       3     210 .]       4     181 ..       2     181 .. 0.71

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 1.1e-17
                                    EEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHH.HHHHHHHHHHHHHHHHETTTEHHHHTHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase   3 tvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkal.vaaakarsgaltgfatfigrgayaigkpewltald 81 
                                    ++ fD+dGTL+  +  v +v+ +                    +   +ak ++ +l++  + i  g+y++   + l++  
  gi|116753941|ref|YP_843059.1|   4 VISFDMDGTLVSPK-YVDRVWMEG-------------------IpELYAKRHGVELDNAKE-IVIGEYLKIGSDRLEWY- 61 
                                    789********777.555566665...................324477777777755555.44443333333344444. PP

                                    CHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHH.HHHHHTTGGGE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                      Hydrolase  82 ippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetae.raanqlGddyf 160
                                          +  + +++ +        ++l+++  + +  v+pe++e++ sL++ag+e+v+ ++  +e+ e ++   ++   f
  gi|116753941|ref|YP_843059.1|  62 ------DLGYWLEKFDLKIDKY--ELLEMYRSEIE--VYPEVEEVLDSLRDAGYELVVTSNAAREFIEmELDGLMD--RF 129
                                    ......2224444444444444..88999999988..*******************************44444455..55 PP

                                    SEEEEHHCES.STTTSHHHHHHHHHHHTSTGGGEEEEESSHH.HHHHHHHTT CS
                                    xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                      Hydrolase 161 daviasdiet.vakpspegkvaaireLqgkpeevamVGDgvn.DaaalaaAg 210
                                    + v++++ +    k sp+ +  ++r L+ kp ev+++GD    D +a  +Ag
  gi|116753941|ref|YP_843059.1| 130 SRVFSVTSDFrDVKKSPRSYILVCRALGRKPLEVLHIGDHYVyDYEAPIEAG 181
                                    4444444443456667************************999999988887 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.1   0.0   1.6e-17   4.1e-14       3     176 ..       7     185 ..       5     187 .. 0.73

  Alignments for each domain:
  == domain 1  score: 53.1 bits;  conditional E-value: 1.6e-17
                          HAD_2   3 FDlDgTlldte...eliiqafnelleey...glselseeelrkliglslrellrklgeseeeeekieellrkyne.ekkk 75 
                                    FD+DgTl+  +    ++++ + el+++    +l++ +e  + +++ + ++ l ++       e k++  ++ky+  e+++
  gi|116753941|ref|YP_843059.1|   7 FDMDGTLVSPKyvdRVWMEGIPELYAKRhgvELDNAKEIVIGEYLKIGSDRLEWYDLGYWL-E-KFDLKIDKYELlEMYR 84 
                                    99****9986412144555555555444333222333334445555555555444444322.2.5555566666414455 PP

                          HAD_2  76 kevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekaleklklkkeev 155
                                     e+++y++v+e+L++L++agy+l + ++  re +e++l+ l  +++  v  +++d+   K +p+++  +++ l+ k+ ev
  gi|116753941|ref|YP_843059.1|  85 SEIEVYPEVEEVLDSLRDAGYELVVTSNAAREFIEMELDGLM-DRFSRVFSVTSDFRDVKKSPRSYILVCRALGRKPLEV 163
                                    78**********************************999886.5666666778888888999****************** PP

                          HAD_2 156 iyvGDsp.tDieaakkagikvi 176
                                    + +GD+  +D ea  +ag++++
  gi|116753941|ref|YP_843059.1| 164 LHIGDHYvYDYEAPIEAGLDAL 185
                                    ******************9986 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.1   2.3e-08     6e-05       3     123 ..       7     126 ..       5     170 .. 0.66

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2.3e-08
                            HAD   3 fDfDgTLldgdslelllrfllrrgaprlwralreklllal........frellrldraglaelleallagls.eelaael 73 
                                    fD+DgTL+        ++ ++++ + +++ a r   +l+         + ++++++ ++++  ++   + ++   ++ el
  gi|116753941|ref|YP_843059.1|   7 FDMDGTLVSPKY----VD-RVWMEGIPELYAKRHGVELDNakeivigeYLKIGSDRLEWYDLGYWL--EKFDlKIDKYEL 79 
                                    9******99943....33.33333333333333333333311222444445555544444444443..333334456666 PP

                            HAD  74 erfvaevirpklldpgalellaahraaGdrvvvvSgglrplvepllaelg 123
                                     ++++++i+    +p++ e+l+  r+aG+++vv S++ r+++e  l+ l 
  gi|116753941|ref|YP_843059.1|  80 LEMYRSEIE---VYPEVEEVLDSLRDAGYELVVTSNAAREFIEMELDGLM 126
                                    666666665...56****************************98777555 PP

>> Acid_PPase  Acid Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.1   0.0    0.0071        18       2      17 ..       1      16 [.       1      42 [. 0.87
   2 !   11.8   0.0   6.1e-05      0.16      35      73 ..      78     116 ..      60     140 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0071
                                   --SEEEE-STTTSSSS CS
                     Acid_PPase  2 lpklivFDLDyTLWpf 17
                                   +p++i FD+D TL ++
  gi|116753941|ref|YP_843059.1|  1 MPEVISFDMDGTLVSP 16
                                   69**********9766 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 6.1e-05
                                    -EEETT--EE---TTHHHHHHHHHHTT--EEEEE--S-H CS
                     Acid_PPase  35 evvDrrgeelklypdveeileelkskevklavaSrtdep 73 
                                    e++  +  e+++yp+vee+l++l++++ +l+v S +++ 
  gi|116753941|ref|YP_843059.1|  78 ELLEMYRSEIEVYPEVEEVLDSLRDAGYELVVTSNAARE 116
                                    677788899*************************98875 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   1.9e-05      0.05       3      41 ..       7     115 ..       5     121 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.9e-05
                                    EESTTTSE......................................................................ET CS
                    Hydrolase_6   3 fDidGvLw......................................................................rg 12 
                                    fD+dG+L+                                                                       +
  gi|116753941|ref|YP_843059.1|   7 FDMDGTLVspkyvdrvwmegipelyakrhgveldnakeivigeylkigsdrlewydlgywlekfdlkidkyellemyrSE 86 
                                    78888888888888888888888888888888888888888888888888888888888888888888888777777667 PP

                                    TEE-TTHHHHHHHHHHTT-EEEEEE---S CS
                    Hydrolase_6  13 dkaipgaaealnalraagkpvvllTNnss 41 
                                     +++p+++e+l+ lr+ag+++v+ +N ++
  gi|116753941|ref|YP_843059.1|  87 IEVYPEVEEVLDSLRDAGYELVVTSNAAR 115
                                    899***********************875 PP

>> Put_Phosphatase  Putative Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.38   9.8e+02       2      15 ..       4      17 ..       3      30 .. 0.79
   2 ?   13.3   0.0   1.5e-05      0.04      68     125 ..      85     138 ..      67     144 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.38
                Put_Phosphatase  2 lvvfDFDktiided 15
                                   ++ fD D t+++ +
  gi|116753941|ref|YP_843059.1|  4 VISFDMDGTLVSPK 17
                                   789*******9854 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 1.5e-05
                Put_Phosphatase  68 rsiplspglvelikslakkkleldliiiSDaNsffieeileaagledlFseiftNPaa 125
                                     +i + p++ e++ sl  ++ +++l++ S+a + fie+ l+  gl d Fs++f+  + 
  gi|116753941|ref|YP_843059.1|  85 SEIEVYPEVEEVLDSL--RDAGYELVVTSNAAREFIEMELD--GLMDRFSRVFSVTSD 138
                                    468999**********..5789***************9886..899******997665 PP

>> PNK3P  Polynucleotide kinase 3 phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0011       2.8       2      16 ..       4      18 ..       3      33 .. 0.84
   2 ?    4.2   0.0     0.013        32      31      79 ..      90     138 ..      71     167 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0011
                          PNK3P  2 iaaFDlDstliktks 16
                                   +++FD+D+tl+ +k 
  gi|116753941|ref|YP_843059.1|  4 VISFDMDGTLVSPKY 18
                                   89*********9986 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.013
                          PNK3P  31 sesvlekLkklkeegykivifsNqggvvekktkkslekfkekieallke 79 
                                    +++v e L +l + gy++v+ sN      + + + l +  +++ +++++
  gi|116753941|ref|YP_843059.1|  90 YPEVEEVLDSLRDAGYELVVTSNAAREFIEMELDGLMDRFSRVFSVTSD 138
                                    577999*****************87655555666666666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1576.41
//
Query:       gi|116753942|ref|YP_843060.1|  [L=234]
Description: orotidine 5'-phosphate decarboxylase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.3e-36  126.4   0.0    1.6e-36  126.0   0.0    1.1  1  OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS famil


Domain annotation for each model (and alignments):
>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.0   0.0   9.1e-41   1.6e-36       1     224 [.      27     229 ..      27     230 .. 0.89

  Alignments for each domain:
  == domain 1  score: 126.0 bits;  conditional E-value: 9.1e-41
                                    SEEEEEE-SSSHHHHHHHHHHHGGGSSEEEEEHHHHHHHTHH.HHTHHHHHHHHHTSEEEEEEEE-S-HHHHHHHHHSTC CS
                      OMPdecase   1 snLclalDvatarelleladkvgpsivvlKthydlvegwgfegtgaklaalarkhgflifeDrKfaDIGntvekqatags 80 
                                    s+L+lalDv++++++ ++a + +  ++ +K++y+l+ ++g      ++++++    +++++D+K+aDI+nt  +++    
  gi|116753942|ref|YP_843060.1|  27 SRLILALDVESRDKANSIASETEGIFDAIKVGYPLMLSEG-----LSVIKELSNI-APVIADLKIADIPNTNHLICN--- 97 
                                    68**************************************.....*******998.7*******************8... PP

                                    HHHHTTESEEEEEGTGHHHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHHHSHHHHHHHHHHHHHHHTTESEEECCCH CS
                      OMPdecase  81 arikewadivtvhavaGkasvkalaeaaekwgnrgllilaqmsskgnlmlqekgytqacveaarehkaedfvmGfvaqet 160
                                      ++++a+ v++ha+ G +s++a++++a++w+   ++++++ms++g+l++    +++ +v  a  + a     G+va +t
  gi|116753942|ref|YP_843060.1|  98 RLFSAGAQGVIAHAFTGRDSLEACVDVAKRWS-GDVYAVTEMSHPGALEFMA-PVAERMVMLALVAGA----SGIVAPAT 171
                                    789****************************7.8******************.667777777766665....5******* PP

                                    TH....HHHHHTTCSCEEEHHHTTEEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSHHHHHHH CS
                      OMPdecase 161 ln....ateedaddfihltpgigleqggdgkgqqyntpekligiagadiiivGRgIlkagdpveeaer 224
                                    ++    a++++a  + ++ pg+g+ qgg   +           +agad++ivGR+++++++p+++ae+
  gi|116753942|ref|YP_843060.1| 172 RPerirALRRAAGGLTIISPGVGA-QGGSLRDA---------LEAGADYAIVGRSVYESANPRAAAEA 229
                                    **8666555558899999999997.44443333.........3579********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1758.72
//
Query:       gi|116753943|ref|YP_843061.1|  [L=713]
Description: multi-sensor signal transduction histidine kinase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.5e-26   91.9   0.0    6.1e-26   91.1   0.0    1.4  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
      4e-09   36.4   0.1      4e-09   36.4   0.1    3.0  3  HisKA        His Kinase A (phospho-acceptor) domain
    1.9e-08   34.3   0.1    2.5e-07   30.7   0.0    2.9  3  PAS          PAS fold
    8.7e-08   32.4   0.0      2e-07   31.2   0.0    1.7  1  PAS_4        PAS fold
    2.8e-06   27.5   0.0    1.1e-05   25.7   0.0    2.1  1  PAS_9        PAS domain
    6.5e-05   22.9   0.0    0.00023   21.1   0.0    2.0  1  PAS_8        PAS domain
    0.00065   20.3   0.0     0.0038   17.8   0.0    2.2  2  PAS_10       PAS domain
     0.0016   18.3   0.0     0.0031   17.4   0.0    1.5  1  HATPase_c_5  GHKL domain
     0.0059   16.4   0.0      0.012   15.5   0.0    1.4  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
  ------ inclusion threshold ------
      0.026   14.7   0.0        1.1    9.4   0.0    2.5  2  PAS_7        PAS fold
       0.45    9.0   4.2        1.1    7.8   0.4    2.0  2  Macoilin     Macoilin family
          4    7.6   5.9         27    4.9   0.3    2.3  2  CREPT        Cell-cycle alteration and expression-elevated pr


Domain annotation for each model (and alignments):
>> 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 !   91.1   0.0   4.1e-29   6.1e-26       2     111 ..     590     696 ..     589     697 .. 0.95

  Alignments for each domain:
  == domain 1  score: 91.1 bits;  conditional E-value: 4.1e-29
                                    HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHHH CS
                      HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsiv 81 
                                    d  r+ +++ nl+dN++k+++++++ ++ei  + +d  + v+DnGiGi+++ ++k+f+ f++    +r++ gtG Gl+iv
  gi|116753943|ref|YP_843061.1| 590 DRMRIGEMLANLIDNSIKYTANTDHPRIEIGWRPEDAAFFVKDNGIGIDPKYHDKVFDLFYR---IDRSTPGTGAGLAIV 666
                                    678999*************88**********86679**************************...88999********** PP

                                    HHHHHHTTTEEEEEEETTTEEEEEEEEESS CS
                      HATPase_c  82 kklvelmgGeiwvesepgrGttftftlple 111
                                    kk+ve +gG+iw+ese g+G+t+ ftlpl+
  gi|116753943|ref|YP_843061.1| 667 KKIVEVHGGRIWIESEGGKGCTVCFTLPLS 696
                                    ****************************86 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.5      0.67     1e+03      54      62 ..     317     325 ..     294     372 .. 0.61
   2 ?   -1.7   0.1       2.1   3.2e+03      27      43 ..     457     470 ..     439     477 .. 0.54
   3 !   36.4   0.1   2.7e-12     4e-09       2      65 ..     482     547 ..     481     548 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.67
                                    HHHHHHHHC CS
                          HisKA  54 lvedlLdls 62 
                                    ++++l++ +
  gi|116753943|ref|YP_843061.1| 317 MLKNLREEA 325
                                    222222222 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.1
                                    HHC..T-HSSCHHHHHH CS
                          HisKA  27 Lkregklteelkeylet 43 
                                    L    ++t el++++e+
  gi|116753943|ref|YP_843061.1| 457 L---RRYTTELERMVED 470
                                    1...2244444444444 PP

  == domain 3  score: 36.4 bits;  conditional E-value: 2.7e-12
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHH CS
                          HisKA   2 lgrflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdlsrie 65 
                                    ++rf+ +v+H+Lr PL +ilg++  L+++     t++++  ++ ie+++  +d+l+ + L+lsri+
  gi|116753943|ref|YP_843061.1| 482 MERFVYTVSHDLRSPLITILGFIGYLREDlrSGQTDKVESDIRFIENSVLKMDRLLTNTLELSRIG 547
                                    68************************98778666888888************************97 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       2.9   4.3e+03      49      78 ..     304     334 ..     295     336 .. 0.73
   2 !   30.7   0.0   1.7e-10   2.5e-07       3     113 .]     342     447 ..     340     447 .. 0.84
   3 ?   -2.0   0.0       2.3   3.4e+03      48      73 ..     548     573 ..     544     590 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.9
                                    GBSTTHHH.HHHHHHHHHHHHTT-ECCCCEE CS
                            PAS  49 liheedda.elaelleqlleqgeesrageis 78 
                                    l+ e+++  ++++ l++l+e++e++ a+e+s
  gi|116753943|ref|YP_843061.1| 304 LLREKQSLrTMHDMLKNLREEAERRAAMEKS 334
                                    4445544458999999999999998888876 PP

  == domain 2  score: 30.7 bits;  conditional E-value: 1.7e-10
                                    HHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEECT CS
                            PAS   3 lraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfklr 82 
                                    l++il+++ ++i+vvD+d +il++N+aa+++l  ++   l      +  e+       l   +++ g   +++e ++ + 
  gi|116753943|ref|YP_843061.1| 342 LESILSQAQCGILVVDADRKILFINDAARRILRKRPGGSLELRSHNSEDEP----EWNLCISRALRGAITESKEERVVV- 416
                                    789*********************************776655555555555....666666677777777777777888. PP

                                    TSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                            PAS  83 dgrpihlevraspvrdaggeilgflgvlrdi 113
                                    dg+ + l+++ +p+ d +g i g+++ ++di
  gi|116753943|ref|YP_843061.1| 417 DGESFDLLLNSAPLKDSSGGIVGAVVSFMDI 447
                                    ***************************9998 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 2.3
                                    GGBSTTHHHHHHHHHHHHHHHTT-EC CS
                            PAS  48 dliheeddaelaelleqlleqgeesr 73 
                                    ++i++++d ++ ++++++l++++ + 
  gi|116753943|ref|YP_843061.1| 548 RVISPPEDVYFSDIVREVLSDMNAKL 573
                                    6789999999********99998765 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   1.4e-10     2e-07       1     110 []     346     452 ..     346     452 .. 0.91

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 1.4e-10
                          PAS_4   1 ldslpdalavldpdgrvlyaNaaaae.lfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgeer 79 
                                    l++ +++++v+d+d ++l++N aa++ l ++p+ +l  ++  +    ed ++    + r+l+g  + + +e ++ +ge  
  gi|116753943|ref|YP_843061.1| 346 LSQAQCGILVVDADRKILFINDAARRiLRKRPGGSLELRSHNS----EDEPEWNLCISRALRGAITESKEERVVVDGESF 421
                                    568899********************77788888877777773....699*************99999999999999999 PP

                          PAS_4  80 hyelrllPlrdesGevigvlvisrDiTerrr 110
                                     ++l+  Pl+d+sG+++g++v + Di++r+r
  gi|116753943|ref|YP_843061.1| 422 DLLLNSAPLKDSSGGIVGAVVSFMDISDRKR 452
                                    999**************************97 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0     7e-09   1.1e-05       2     104 .]     351     449 ..     350     449 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 7e-09
                          PAS_9   2 dgilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwvllt 81 
                                    +gil+++ d +il++N+aa+r+l   p   l  + ++   ++pe n  +++al+      +++e   + + ge f  ll+
  gi|116753943|ref|YP_843061.1| 351 CGILVVDADRKILFINDAARRILRKRPGGSLELRSHNSE-DEPEWNLCISRALRGAI--TESKEERVVVD-GESFDLLLN 426
                                    799*999****************8778888887777777.88888999999999988..66666666655.89******* PP

                          PAS_9  82 aspvkdddgelvgiivilrDite 104
                                     +p+kd++g++vg++v + Di++
  gi|116753943|ref|YP_843061.1| 427 SAPLKDSSGGIVGAVVSFMDISD 449
                                    *********************96 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   1.5e-07   0.00023       2      42 ..     341     382 ..     340     407 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.5e-07
                          PAS_8   2 rlralfesspdgiavvdlgdrivdvNqaalellGys.adlkg 42 
                                     l++++ +++ gi+vvd++++i+++N+aa ++l  +  ++++
  gi|116753943|ref|YP_843061.1| 341 LLESILSQAQCGILVVDADRKILFINDAARRILRKRpGGSLE 382
                                    58999************9999************844444444 PP

>> PAS_10  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.5e-06    0.0038       1     105 [.     342     447 ..     342     448 .. 0.79
   2 ?   -1.1   0.0         2   2.9e+03      20      55 ..     456     498 ..     454     534 .. 0.53

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.5e-06
                         PAS_10   1 lnnlLnstpieltflDdnlqirrFtpaakklfklipadvGrpladi.hpkkavknveeviealrtgek...devevvvpk 76 
                                    l+ +L++++ +++ +D + +i++ ++aa+++++ +p   G +l+   h+++ +++ +  i +  +g     +e++vvv+ 
  gi|116753943|ref|YP_843061.1| 342 LESILSQAQCGILVVDADRKILFINDAARRILRKRP---GGSLELRsHNSEDEPEWNLCISRALRGAItesKEERVVVDG 418
                                    6789***********************998776555...66777653777999999998866665543222555555555 PP

                         PAS_10  77 ngkwvlvrylpyrdedgeiaGvvetfvDi 105
                                    +    l++  p++d  g i G+v+ f+Di
  gi|116753943|ref|YP_843061.1| 419 ESFDLLLNSAPLKDSSGGIVGAVVSFMDI 447
                                    6666899*********************9 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2
                         PAS_10  20 qirrFtp.......aakklfklipadvGrpladihpkkavknv 55 
                                    ++rr+t+       + ++ +++++a++ r + +++++ + + +
  gi|116753943|ref|YP_843061.1| 456 ELRRYTTelermveDRTREIERKNAEMERFVYTVSHDLRSPLI 498
                                    5677777333333223555666666666666666665444443 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   2.1e-06    0.0031       5      91 ..     593     683 ..     589     691 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.1e-06
                    HATPase_c_5   5 dlcvilgnlLdNAieacskieeekrfIrltvrekkksli.....isieNsyegekkkle.sskskkeehGiGlksireiv 78 
                                     +  +l nl+dN+i    +++  ++ I++  r ++ +++     i i+ +y+++   l+    +++   G Gl  +++iv
  gi|116753943|ref|YP_843061.1| 593 RIGEMLANLIDNSIKYTANTD--HPRIEIGWRPEDAAFFvkdngIGIDPKYHDKVFDLFyRIDRSTPGTGAGLAIVKKIV 670
                                    566799**************9..899**999977765441222244555566666444436688999************* PP

                    HATPase_c_5  79 kkykgnlsieaed 91 
                                    + ++g ++ie e 
  gi|116753943|ref|YP_843061.1| 671 EVHGGRIWIESEG 683
                                    *********9886 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   7.9e-06     0.012       7      55 ..     598     647 ..     593     662 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.9e-06
                    HATPase_c_3   7 laelvdNsld..Adaen..vkievnknrgktgeivieDdGkGmseeelknalr 55 
                                    la l+dNs+   A+  +  ++i +  +   ++ + ++D+G G++++  ++++ 
  gi|116753943|ref|YP_843061.1| 598 LANLIDNSIKytANTDHprIEIGWRPE---DAAFFVKDNGIGIDPKYHDKVFD 647
                                    899*****9844555546677777775...58************987666665 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00077       1.1       1      28 [.     346     373 ..     346     378 .. 0.90
   2 ?    2.5   0.0       0.1   1.6e+02      98     114 ..     438     454 ..     401     455 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00077
                          PAS_7   1 lenmsqGisvfDadlrLvawNrrylell 28 
                                    l++ + Gi+v+Dad +++++N+  +++l
  gi|116753943|ref|YP_843061.1| 346 LSQAQCGILVVDADRKILFINDAARRIL 373
                                    578899*****************99988 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.1
                          PAS_7  98 gGfVttytDiTerrrae 114
                                     G V+++ Di++r+r e
  gi|116753943|ref|YP_843061.1| 438 VGAVVSFMDISDRKRLE 454
                                    4899*********9976 PP

>> Macoilin  Macoilin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.4   0.00071       1.1     462     494 ..     308     340 ..     301     360 .. 0.81
   2 ?    2.5   0.3     0.029        43     525     559 ..     450     485 ..     445     501 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00071
                       Macoilin 462 qkdkqtlqqlekrLkeekearaslekqLaeekk 494
                                    ++  +t++ + k L+ee+e ra++ek Lae k 
  gi|116753943|ref|YP_843061.1| 308 KQSLRTMHDMLKNLREEAERRAAMEKSLAESKN 340
                                    2334467778899****************9886 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.029
                       Macoilin 525 kreleaeikkLekel.klkeeqirelelkvqelrky 559
                                    ++ le e+++ ++el ++ e++ re+e k  e++++
  gi|116753943|ref|YP_843061.1| 450 RKRLEDELRRYTTELeRMVEDRTREIERKNAEMERF 485
                                    678************89****************988 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 ?    4.8   0.9     0.019        29      54      96 ..     308     350 ..     303     360 .. 0.89
   2 ?    4.9   0.3     0.018        27      70     117 ..     446     494 ..     444     499 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.019
                          CREPT  54 eealellaeYnkrLeaeleeRkklakmledfleaqkellakae 96 
                                    +++l+ +++  k L +e e R  ++k l++ ++++ + l++a+
  gi|116753943|ref|YP_843061.1| 308 KQSLRTMHDMLKNLREEAERRAAMEKSLAESKNLLESILSQAQ 350
                                    5788899999********************9999999888876 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.018
                          CREPT  70 eleeRkklakmledfleaqkellakaeekleelkeklek.vksvrkelk 117
                                    ++++Rk+l+  l+ +++ +   +++  +++e+ +  +e+ v +v ++l+
  gi|116753943|ref|YP_843061.1| 446 DISDRKRLEDELRRYTTELERMVEDRTREIERKNAEMERfVYTVSHDLR 494
                                    689****************999999998888888777763556666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (713 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       983  (0.0548274); expected 358.6 (0.02)
Passed bias filter:                      682  (0.0380389); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.69u 0.27s 00:00:00.96 Elapsed: 00:00:00.44
# Mc/sec: 4861.88
//
Query:       gi|116753944|ref|YP_843062.1|  [L=205]
Description: hypothetical protein Mthe_0631 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
        0.1   11.0   0.0       0.13   10.6   0.0    1.1  1  Neurochondrin  Neurochondrin


Domain annotation for each model (and alignments):
>> Neurochondrin  Neurochondrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   7.3e-06      0.13     360     405 ..      11      56 ..       6      76 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 7.3e-06
                  Neurochondrin 360 dvkeekikdsvfvlAsvrvlgawLaeetsalrkevseLldfllkva 405
                                    + + ++++ s  v+A + vl+a L  ++++  + v +L++f +++ 
  gi|116753944|ref|YP_843062.1|  11 RSQSHSMRASRSVIALIIVLSAILLSQPTSAEPVVRDLGPFQVSFD 56 
                                    45679************************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1479.13
//
Query:       gi|116753945|ref|YP_843063.1|  [L=103]
Description: protein translocase SEC61 complex, gamma subunit [Methanosaeta thermophila PT]
Scores for complete 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-05   22.9   0.1    7.5e-05   22.6   0.1    1.1  1  SecE      SecE/Sec61-gamma subunits of protein translocation 


Domain annotation for each model (and alignments):
>> SecE  SecE/Sec61-gamma subunits of protein translocation complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.1   4.2e-09   7.5e-05       6      48 ..      55      97 ..      53     103 .] 0.91

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 4.2e-09
                                   HHHHHHHCCCCCHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           SecE  6 evkaElkKVtWPtrkEllkttvvVlvfvvimglflflvDlvfs 48
                                   e ++ lk   +Ptr+E++ + +v + +++++g ++f++  +++
  gi|116753945|ref|YP_843063.1| 55 EYIRVLKLARKPTREEFMMIGKVSITGIFLIGMIGFIIYALLT 97
                                   77899*********************************88876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 729.68
//
Query:       gi|116753946|ref|YP_843064.1|  [L=432]
Description: phenylacetate--CoA ligase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.7e-30  103.5   0.1    2.2e-29  101.6   0.3    1.9  2  AMP-binding_C_2  AMP-binding enzyme C-terminal domain
    3.9e-19   68.5   0.1    4.4e-18   65.1   0.1    2.0  1  AMP-binding      AMP-binding enzyme
  ------ inclusion threshold ------
      0.019   13.8   0.0       0.97    8.2   0.0    2.4  2  GH3              GH3 auxin-responsive promoter


Domain annotation for each model (and alignments):
>> AMP-binding_C_2  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.94   5.6e+03      30      41 ..     196     207 ..     179     230 .. 0.59
   2 !  101.6   0.3   3.6e-33   2.2e-29       1      96 []     333     430 ..     333     430 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.94
                                    ETTEEEEEEEEE CS
                AMP-binding_C_2  30 egelDelevkvE 41 
                                    +g +D+l++++ 
  gi|116753946|ref|YP_843064.1| 196 KGIMDKLKLRIG 207
                                    345777777664 PP

  == domain 2  score: 101.6 bits;  conditional E-value: 3.6e-33
                                    TEEE-HHHHHHHHHT-TTEEEEEEEEEEEET.TEEEEEEEEEE-T.T----HHHHHHHHHHHHHHHHHHHSS--EEEEE- CS
                AMP-binding_C_2   1 GvnvfPsqieevlkeieevepeYqivvtreg.elDelevkvEvke.gfsdelkelealekkiakklksklgvsvkvelve 78 
                                    G+nvfPsqie+vl +i+e+++++q++v+r++ +lDel+++vE+k+ +f+ el++l++l+kk++++lk++l+++ kvelve
  gi|116753946|ref|YP_843064.1| 333 GINVFPSQIEDVLLSIPEIGDYFQVIVDRKHhGLDELTIQVEMKDeAFTGELADLARLQKKVEERLKAVLNIRSKVELVE 412
                                    99***************************9637************78899****************************** PP

                                    TT-S---------EEE-S CS
                AMP-binding_C_2  79 pgtlprsegKakrviDkR 96 
                                    +g++pr+ gK+k+v+D R
  gi|116753946|ref|YP_843064.1| 413 KGSIPRTAGKSKKVVDLR 430
                                    ****************98 PP

>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.1   0.1   7.4e-22   4.4e-18     159     423 .]      83     332 ..      51     332 .. 0.80

  Alignments for each domain:
  == domain 1  score: 65.1 bits;  conditional E-value: 7.4e-22
                                    TSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHC...SCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-T CS
                    AMP-binding 159 ddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletr...fklkeddvvlsilplahifglilelllallsGatvvllp 235
                                    ++++ +  +SGTTGkP  V ++ r + +    ++  ++    +++++d +   + + + +g  l++ + + + +++ +++
  gi|116753946|ref|YP_843064.1|  83 EEIVRVHASSGTTGKPTVVGYTKRDIETWSDLMA--RDfvmVGVTRNDIFQNAVNYGFFTGG-LGVHYGIERMGAMAVPS 159
                                    556666669****************955433332..22244567789**************8.66666666666677777 PP

                                    TCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTCEEEEE CS
                    AMP-binding 236 kdaaldpklllelieklkvtviagvPrvlealle.sgalkaakkakdlsslrlvllggeplspellrffralfgeevleg 314
                                    ++  +  ++ le +++++vtvi+++P+ + +l+e ++a+       d  +lr+  +g+ep s e+ +++++ fg + +++
  gi|116753946|ref|YP_843064.1| 160 GTGNT--ERQLEIMADFGVTVIHCTPSYALYLAEtAKAKG----IMDKLKLRIGCFGAEPWSDEARQELEEAFGIKAYDS 233
                                    77773..3558*********************99665555....336677999889************************ PP

                                    EEEGGGSSECEECHCTTTCTSTTS-BEE-T..TEEEEEE-TTTSCBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEEET CS
                    AMP-binding 315 YGlTEttgvvtvlpleedkkklgsvGkplp..gvevkivDeetgepvpdgeeGellvrgpgvmkgYlkkpeataeafdse 392
                                    YGl+E+ g  + ++++e+       G  ++  +  v+i+D + g+p+++ge Gel++             ++t+ea+   
  gi|116753946|ref|YP_843064.1| 234 YGLSEMFGPGVAFECQEQ------NGLHIWedHFLVEILDGD-GNPCAPGERGELVLT------------SLTKEAMP-L 293
                                    *********984554444......36666445899******9.*************86............56888884.2 PP

                                    CCEEEEEEEEEEETTS.........EEEEEEECCCEEEET CS
                    AMP-binding 393 grwlrTGDlgrldedG.........yleivgRkkdliklr 423
                                       +rTGD+ +l edG           +++gR++d++++r
  gi|116753946|ref|YP_843064.1| 294 I-RYRTGDVTYLMEDGcscgrtsrkLHRFLGRADDMLVVR 332
                                    3.7********99999999999997789*******99875 PP

>> GH3  GH3 auxin-responsive promoter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0   0.00016      0.97      74     108 ..      83     116 ..      79     148 .. 0.84
   2 ?    3.0   0.0     0.006        36     370     474 ..     293     400 ..     274     415 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00016
                                    SS-SEEEEECCEETTEEEEEEESHHHHHHHHHH.H CS
                            GH3  74 epiklfalsSGTtsgksKliPvteeslkelallvl 108
                                    e+i++   sSGTt gk+ ++ +t++  ++++ l++
  gi|116753946|ref|YP_843064.1|  83 EEIVRVHASSGTT-GKPTVVGYTKRDIETWSDLMA 116
                                    789999*******.***********9999887744 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.006
                                    -SSEEECEEEEEEE...EETTEE.EE.EEEECCTEEE-SSSS-CCHHHHHHHHH.HHHHHTT-EEEEEEEEE.ESS.SSS CS
                            GH3 370 LyRYrigDvvrvtg...fynkaP.rl.eFvgRknvvlsidgeklteeelqkaveeaakeltglelvdftsfapdtsesep 444
                                    L RYr+gDv   ++    + ++  +l +F+gR + +l ++g  +  +++++++          e+ d+  +++d +++  
  gi|116753946|ref|YP_843064.1| 293 LIRYRTGDVTYLMEdgcSCGRTSrKLhRFLGRADDMLVVRGINVFPSQIEDVLL-SI-----PEIGDYFQVIVDRKHHGL 366
                                    788888888777652222222222332799999999999999999999999999.33.....346789988888888888 PP

                                    EEEEEEEEECS........S....HHHHHHHHHCS-S CS
                            GH3 445 ghyvlflElkkk...eepee....eecckeldesLed 474
                                       ++ +E+k++       e     ++ k+++e L+ 
  gi|116753946|ref|YP_843064.1| 367 DELTIQVEMKDEaftG---EladlARLQKKVEERLKA 400
                                    8899999998767653...123358999999999933 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 3033.98
//
Query:       gi|116753947|ref|YP_843065.1|  [L=444]
Description: glutamine synthetase, type I [Methanosaeta thermophila PT]
Scores for complete 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-133  443.1   0.0     7e-133  442.9   0.0    1.1  1  Gln-synt_C    Glutamine synthetase, catalytic domain
    1.5e-29  101.5   0.0    4.5e-29  100.0   0.0    1.8  1  Gln-synt_N    Glutamine synthetase, beta-Grasp domain
    0.00026   20.8   0.0     0.0032   17.3   0.0    2.3  1  Gln-synt_N_2  Glutamine synthetase N-terminal domain


Domain annotation for each model (and alignments):
>> Gln-synt_C  Glutamine synthetase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  442.9   0.0  1.2e-136    7e-133       2     345 .]     108     440 ..     107     440 .. 0.98

  Alignments for each domain:
  == domain 1  score: 442.9 bits;  conditional E-value: 1.2e-136
                                    T-HHHHHHHHHHHHHHTTCEEEEEEEEEEEEESEECCCESSEEEEEEE.TB...B.TSS-TTBHCCCCCTCCHHHHHHHH CS
                     Gln-synt_C   2 rdPRsvlkralarlaeeGltvvvgpElEFflfdkeedkeasksllevdseekgrpaekggyfsvapvdeaedlrreivea 81 
                                    +dPR+vlkr l+rl+e+G++++vgpElEFf f+++  +e                 + ggyf+++++d a+dlrr+ + a
  gi|116753947|ref|YP_843065.1| 108 GDPRYVLKRNLSRLKEKGYKFMVGPELEFFYFKSDCSTE---------------ILDTGGYFDLTTLDVASDLRRDTILA 172
                                    79*******************************887644...............5677********************** PP

                                    HHHTT--EECCEEECCCTEEEEEE--EECHHHHHHHHHHHHHHHHHHHHTT-EEE-SSSSSTTS---BEEEEEEEEECTT CS
                     Gln-synt_C  82 lealgieveashhEvatgQvEinlkfadalkaaDnvvtfKrvvkevArkhgltatFmpKplegdnGsgmHvhlSlwdkdg 161
                                    l+a+gi+ve shhEva++Q+Ei+l++adal++aDnv+t+K +vke+Arkhg +atFmpKp++g nGsgmHvh+Sl+ + +
  gi|116753947|ref|YP_843065.1| 173 LDAMGIDVEYSHHEVAPSQHEIDLRYADALTMADNVITYKITVKEIARKHGCYATFMPKPIFGVNGSGMHVHQSLF-QGK 251
                                    ****************************************************************************.888 PP

                                    EESSB-TTSGGGB-HHHHHHHHHHHHHHHHHHHHHS-SCCHHHHCSSSTTSSSBEEEESS-TTCSEEEE-...TSGGCST CS
                     Gln-synt_C 162 knlfadeddeyalselarhfigGllkhakaltaltaptvnSYkRlvpgyeaPvalawgarNRsallRipa...skekakr 238
                                    +n+++d+ dey+ls+ a+ +i+Gll+ha+++ta+t+++vnSYkRlvpgyeaPv+++w+ rNRsal+R+p+   +ke a+r
  gi|116753947|ref|YP_843065.1| 252 RNVMFDAADEYHLSDEAKWYIAGLLRHAPEITAVTNQWVNSYKRLVPGYEAPVYISWARRNRSALVRVPMykpGKEAATR 331
                                    ***********************************************************************9999***** PP

                                    EEEECEBTTS-HHHHHHHHHHHHHHHHHTT--------S-SSSS-TTTH..TSS-B--SSHHHHHHHHHCSHHHCCSS-H CS
                     Gln-synt_C 239 vElRlpdasaNPYLalAallaAgldGienklepgepvekdlyelspeer..kgieelPasleeAlealeedellkevlge 316
                                    vE+R+pd++aNPYLa++++l Agl Gi nk+e+++p e+d+y++s+ee+  +gi++lP sl+eA++  e++ +++e+lg+
  gi|116753947|ref|YP_843065.1| 332 VEYRSPDPAANPYLAFSVMLVAGLAGIANKYELPPPQERDIYHMSEEEKkaAGINSLPGSLNEAIQLAEQSYIVREALGD 411
                                    ************************************************9999**************************** PP

                                    HHHHHHHHHHHHCHHHHHCT--HHHHHHH CS
                     Gln-synt_C 317 evieaylalkraEleeleeevsdwelery 345
                                    +v+e+++a+k+aE++e++++vs+welery
  gi|116753947|ref|YP_843065.1| 412 HVFENFIAIKKAEWDEYRTNVSRWELERY 440
                                    ***************************98 PP

>> Gln-synt_N  Glutamine synthetase, beta-Grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.0   0.0   7.5e-33   4.5e-29       1      83 []      19     101 ..      19     101 .. 0.98

  Alignments for each domain:
  == domain 1  score: 100.0 bits;  conditional E-value: 7.5e-33
                                    T--EEEEEEE-SSS-EEEEEEEHHHHHHHTTTT-EEEETTSSTTT------EEEEEEEGGGEEE-SS-SS-..EEEEEEE CS
                     Gln-synt_N   1 evkfvdlqFtDikgklkhvtipadelsedaleegvsFDGSsiegfaeieeSDmlLkPdlstavidPfreek.ktarvicd 79 
                                    +v+fv+++FtDi g +k+++i++++l + a++eg++FDGSs++gfa+i eSD++ kPd+st+ i+P+r+++ ++ar++cd
  gi|116753947|ref|YP_843065.1|  19 NVRFVRIWFTDILGIPKSFAINTNQL-DGAFSEGMGFDGSSVRGFARIYESDLIAKPDPSTFRIVPWRQQEnAVARMFCD 97 
                                    699***********************.******************************************999******** PP

                                    EE-T CS
                     Gln-synt_N  80 vydp 83 
                                    +++p
  gi|116753947|ref|YP_843065.1|  98 ILNP 101
                                    *987 PP

>> Gln-synt_N_2  Glutamine synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   5.3e-07    0.0032       5     107 .]      10     106 ..       6     106 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.3e-07
                                    ......------EEEEEEE-TTS-EEEEEEEGGGHHHHHTT-EEE-GGGGG--TTS---TT-S-SSS--EEEEE-GGG-E CS
                   Gln-synt_N_2   5 avveqleekqveLieflyvdlaGvtrGkalplasLeekLasGiGltkatlalserdlidevedlgpvGelrLvpdPasav 84 
                                     v e +++++v++++  ++d  G+ +  a+   +L+  + +G+G+    +++     i e++       l   pdP+++ 
  gi|116753947|ref|YP_843065.1|  10 DVFEAIDKHNVRFVRIWFTDILGIPKSFAINTNQLDGAFSEGMGFDG--SSVRGFARIYESD-------LIAKPDPSTFR 80 
                                    689999**************************************975..6778888888875.......5556******* PP

                                    EE---SSTTS...EEEEEE-TTS-B- CS
                   Gln-synt_N_2  85 alpyaPdaaa...llgdlvevdgtPy 107
                                     +p   +  a   ++ d+ + dgtPy
  gi|116753947|ref|YP_843065.1|  81 IVPWRQQENAvarMFCDILNPDGTPY 106
                                    **97665333334************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 3200.33
//
Query:       gi|116753948|ref|YP_843066.1|  [L=95]
Description: CRISPR-associated Cas2 family protein [Methanosaeta thermophila PT]
Scores for 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   80.1   0.2    1.2e-22   79.9   0.2    1.1  1  CRISPR_Cas2  CRISPR associated protein Cas2
  ------ inclusion threshold ------
       0.14   12.0   0.0       0.23   11.3   0.0    1.3  1  AHD          ANC1 homology domain (AHD)


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 !   79.9   0.2   1.3e-26   1.2e-22       1      75 [.       1      73 [.       1      74 [. 0.98

  Alignments for each domain:
  == domain 1  score: 79.9 bits;  conditional E-value: 1.3e-26
                                   EEEEEEEECHCHHHHHHHHHHHHHHTTEEEEETTEEEEEESHHHHHHHHHHHHHHSHTTTCEEEEEEEETCHHHT CS
                    CRISPR_Cas2  1 mlvlvvYDikedrkrrrkvakilkkyGfqrvQySVFegelseaqleklkkrlkkiidpeedsiriykltekqfek 75
                                   mlv+v+YDi +d++ r++vaki+k+yG++rvQ+S F+g+l++++ + l+ +++++i++  ds+++++++e++f k
  gi|116753948|ref|YP_843066.1|  1 MLVWVIYDI-SDDRTRSRVAKICKNYGLYRVQKSAFLGDLNRNESDSLALECESVIEDT-DSVYVFPMCEDCFDK 73
                                   99*******.***********************************************88.*************87 PP

>> AHD  ANC1 homology domain (AHD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.6e-05      0.23      13      46 ..       6      39 ..       2      44 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.6e-05
                            AHD 13 lmsltdrkvlqrivdiIeetGlyeitestfDFDL 46
                                   + ++ d +   r+++i ++ Gly +++s+f  DL
  gi|116753948|ref|YP_843066.1|  6 IYDISDDRTRSRVAKICKNYGLYRVQKSAFLGDL 39
                                   7788999999*******************96666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 725.83
//
Query:       gi|116753949|ref|YP_843067.1|  [L=191]
Description: CRISPR-associated Cas4 family protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-15   57.8   1.7    1.6e-15   57.6   1.7    1.0  1  Cas_Cas4  Domain of unknown function DUF83
    1.8e-10   41.2   5.0    6.9e-10   39.3   3.0    1.9  2  PDDEXK_1  PD-(D/E)XK nuclease superfamily


Domain annotation for each model (and alignments):
>> Cas_Cas4  Domain of unknown function DUF83
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.6   1.7   1.8e-19   1.6e-15       2     160 ..       5     190 ..       4     191 .] 0.82

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 1.8e-19
                       Cas_Cas4   2 gtkiqyyliCkrklwlish.ei.tleensetvelGkllhe......esyerek.....kevel.se......sikiDvve 61 
                                    ++++  yl+C+r +++++  +i + ee+  +v  G+ lhe      +sy r++     kev++  +      ++++D v 
  gi|116753949|ref|YP_843067.1|   5 VSDVIEYLFCPRFIFFMHClNIpQREERYYKVLRGRELHEsrekvnTSYVRKRlrcvrKEVAVyMTsrryriKGEVDEVL 84 
                                    788999*********9998766355677789999******8777775666655788888988843378999999***998 PP

                       Cas_Cas4  62 .kekeklvvvEvKkskkk...eeaaklQllyY.lllLekkgveikeGvleypke.kkreevelteelreelekaikeiee 135
                                      +++++ ++++K  +     ++ +k+Ql  Y ll++e+ g  +++G++ y  + ++ eev + +++ +++ ++++ei +
  gi|116753949|ref|YP_843067.1|  85 fLDDGTAAPMDYKYAEYNdvvHRTHKYQLALYgLLIMEHFGAPVNRGFICYTRSdHHVEEVIFRRKDYHAALEIVNEILR 164
                                    89999999*****998765558889****9994455569************987255677******************** PP

                       Cas_Cas4 136 iissekppk.vkkkkiCkkCayaelC 160
                                     ++  ++p+ +k+k +C  C y+++C
  gi|116753949|ref|YP_843067.1| 165 TVQYGYYPEgTKQKARCVDCTYRNIC 190
                                    ***9966661566669********** PP

>> PDDEXK_1  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.8   0.1    0.0049        44       3      43 ..       4      45 ..       3      58 .. 0.80
   2 !   39.3   3.0   7.7e-14   6.9e-10     109     255 .]      53     191 .]      29     191 .] 0.70

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.0049
                       PDDEXK_1  3 SvsrletfleCplrfflryllglre.eeeleapdlGtlvHaa 43
                                   +vs +  +l Cp+  f+ + l++++ ee+  +  +G+ +H+ 
  gi|116753949|ref|YP_843067.1|  4 TVSDVIEYLFCPRFIFFMHCLNIPQrEERYYKVLRGRELHES 45
                                   6899999******99999*****6645555555999999986 PP

  == domain 2  score: 39.3 bits;  conditional E-value: 7.7e-14
                       PDDEXK_1 109 eakrgfrpvalelefg..gekvrLkGriDrvd.dkegelriiDyKtgsappkskelaelkeglQlllYllalaegeelke 185
                                      ++ +r v+ e+++   ++++r+kG +D v   ++g++  +DyK    ++  ++     +  Ql+lY l+++e+  ++ 
  gi|116753949|ref|YP_843067.1|  53 YVRKRLRCVRKEVAVYmtSRRYRIKGEVDEVLfLDDGTAAPMDYKYAEYNDVVHR----THKYQLALYGLLIMEHFGAPV 128
                                    222336777777555564699***********877779*******5554444443....5666************44443 PP

                       PDDEXK_1 186 egepagalylrleepkvkdeevvkkmalteeeleallqeleelaeeilagefparpskk..CeyCpyksvCr 255
                                    +  ++ + y r         + v+++   +++ +a+l+ ++e+++ ++ g +p    +k  C  C y+ +C+
  gi|116753949|ref|YP_843067.1| 129 N--RGFICYTRS-------DHHVEEVIFRRKDYHAALEIVNEILRTVQYGYYPEGTKQKarCVDCTYRNICD 191
                                    3..555555555.......5566666699*******************8877776666689**********5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1412.28
//
Query:       gi|116753950|ref|YP_843068.1|  [L=618]
Description: CRISPR-associated Csh1 family protein [Methanosaeta thermophila PT]
Scores for 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-178  592.9  11.1   9.7e-178  592.7  11.1    1.0  1  Cas_TM1802  CRISPR-associated protein TM1802 (cas_TM1802)
  ------ inclusion threshold ------
      0.098   13.5   0.1        4.3    8.2   0.0    2.5  2  FliT        Flagellar protein FliT
       0.45    8.7   1.5       0.64    8.2   1.5    1.1  1  K1377       Susceptibility to monomelic amyotrophy


Domain annotation for each model (and alignments):
>> Cas_TM1802  CRISPR-associated protein TM1802 (cas_TM1802)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  592.7  11.1  1.6e-181  9.7e-178       2     607 ..       6     601 ..       5     602 .. 0.96

  Alignments for each domain:
  == domain 1  score: 592.7 bits;  conditional E-value: 1.6e-181
                     Cas_TM1802   2 leaikeiGeillg...gegekdeleqltedpkae..kkhvliinfdtekekleykgveeidleefdekktakylYlkkgn 76 
                                    +ea+++iG+  +g   ++g++d l  ++e+p+ +  ++h l++++++++++++y+gve   lee ++   ++ylY k ++
  gi|116753950|ref|YP_843068.1|   6 IEAVARIGKQRIGehaQSGCEDILYYIVENPNLNggYNHALVVTLEEKDGDFSYRGVE---LEELKD--YRRYLY-KGKK 79 
                                    9*********6666999*****************************************...***999..99****.8888 PP

                     Cas_TM1802  77 angsnssqtykttkklekllskkipnlldleklgveknlseeekellkkiekelsknkekiakelekklkkiknekevvl 156
                                     n++++++t+k++k++ek+++kk++++    +   +++ls ee+ +lk+i+++l +nk+ki kel++k ++  +++e+++
  gi|116753950|ref|YP_843068.1|  80 GNATDATPTCKIAKDIEKTFEKKFLRW---FDGIDSSDLSGEERATLKNIKNVLFSNKDKIFKELQEKRSHL-KQRENCI 155
                                    89*************************...45555566*********************************9.5569*** PP

                     Cas_TM1802 157 ltlki....dgkylgdieeyrevllrklierlfekkkekkkkskegvCsvCgeekeevtgdvstklkfkfyttDkpgFas 232
                                    +tl++    d kyl+d++++r+vll+++++r+f+k   +++ +++++CsvC+e+k+ev++++     + f+t+DkpgF++
  gi|116753950|ref|YP_843068.1| 156 ITLGFvkdgDLKYLADYPAFRNVLLKNSCDRFFRK-YGGESRGTDALCSVCKEQKDEVYAYAIP---WPFHTFDKPGFIA 231
                                    *******9999******************999985.799*********************9978...************* PP

                     Cas_TM1802 233 g.fnkknawknfpiCeeCarkLeaGkkyleeklsfkfyglnyyvIPkfifslekvleeiidilsslkklkkleklekklk 311
                                    g f++++awkn+p+C +Ca +L+aGkky+ee l+f+fyg++y++IPk+i+   ++ +ei+dils +k   k+ k+++k++
  gi|116753950|ref|YP_843068.1| 232 GgFRQSDAWKNTPVCLNCAINLDAGKKYIEESLDFSFYGFRYLLIPKLII--GDDYQEILDILSGMK---KELKMSRKTR 306
                                    **************************************************..899**********99...99******** PP

                     Cas_TM1802 312 krldldeeeileeledekdvlllnfLFyerksqsafrilllieDVppsrlskilkakekvdekf...nklil.eekaslk 387
                                    +r+++de+eil++++d+kd+++ +++Fy+ k++sa+rill+i+ ++psrl+++++ake+v+  f   n+++l e+k++l 
  gi|116753950|ref|YP_843068.1| 307 NRITDDEDEILDMVKDQKDFFSNSLMFYK-KDNSAYRILLHIDGILPSRLRRLFEAKERVEGAFgiyNEMVLsEDKGRLI 385
                                    ****************************5.**********************************888888855999**** PP

                     Cas_TM1802 388 ftfgslykffpirkkkkkdddkykkfLeivnsifkgrpisyslLikqflelirksfkneekeekeiaykvlkanlllkFL 467
                                    f+fg+l++ff +r++++ ++dk+  fLeivn+if gr ++++lLi +++++ir++f++++    ++  ++l+ ++ll++L
  gi|116753950|ref|YP_843068.1| 386 FDFGVLRRFF-PRESGNVTHDKM--FLEIVNRIFVGRYVDRHLLISFMMKRIRDDFVHGR----STLMNTLNGFMLLHYL 458
                                    **********.6666********..***********************************....9*************** PP

                     Cas_TM1802 468 eelnllkg......gkkmdegelelkvedeekldeffkeyietlnyteqkkalFLlGvLlgellniQykkrkskPflkkL 541
                                    +elnllk       +  + + e+ + ++ ++++++ff+ + e+++ +++kka+FL GvL+++llniQ+ ++++kPf+ kL
  gi|116753950|ref|YP_843068.1| 459 KELNLLKDlevdrmSGIVLKREELEALPLDKRVERFFEANREFFD-SDAKKATFLEGVLVQKLLNIQWMEKNAKPFYTKL 537
                                    ******999988887777788888888888***************.********************************** PP

                     Cas_TM1802 542 nglgmderdikrllnevinKlrqYkknlykkkelleaiakyllesesnwklskdElnFyflsGysl 607
                                    +gl+m+e  ikrll+e++nKl++Y+kn+y  +el+ +ia++++ s++ wk+++dEl+Fyf++G++l
  gi|116753950|ref|YP_843068.1| 538 HGLKMNEALIKRLLPEIQNKLEEYEKNYY--RELEAIIAEHFVLSGRGWKETDDELSFYFVLGMNL 601
                                    **************************998..*********************************98 PP

>> FliT  Flagellar protein FliT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0   0.00073       4.3      29      70 ..     109     150 ..      95     152 .. 0.87
   2 ?    2.3   0.0      0.05     3e+02      19      70 ..     284     329 ..     281     341 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00073
                                    CS--ST--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           FliT  29 eldaaplspaereekrellrrilandaeirallqprldelqk 70 
                                     +d+++ls +er+ + ++++ +  n ++i + lq+++++l++
  gi|116753950|ref|YP_843068.1| 109 GIDSSDLSGEERATLKNIKNVLFSNKDKIFKELQEKRSHLKQ 150
                                    344666**********************************98 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.05
                                    HHHHHHHHHHCS--ST--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           FliT  19 erqqlverlreldaaplspaereekrellrrilandaeirallqprldelqk 70 
                                    ++q++++ l+ +        e +  r+  +ri ++++ei + ++ ++d  ++
  gi|116753950|ref|YP_843068.1| 284 DYQEILDILSGMK------KELKMSRKTRNRITDDEDEILDMVKDQKDFFSN 329
                                    5666666666666......555555555569999999999999999886665 PP

>> K1377  Susceptibility to monomelic amyotrophy
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   1.5   0.00011      0.64     520     555 ..      93     130 ..      88     154 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00011
                          K1377 520 aeipKt..ikKLRWfDeigkiekeaeeshslknrteis 555
                                     +i+Kt  +k LRWfD i+    + ee  +lkn +++ 
  gi|116753950|ref|YP_843068.1|  93 KDIEKTfeKKFLRWFDGIDSSDLSGEERATLKNIKNVL 130
                                    467787635559*********************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (618 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       882  (0.049194); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); 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: 0.66u 0.28s 00:00:00.94 Elapsed: 00:00:00.47
# Mc/sec: 3991.13
//
Query:       gi|116753951|ref|YP_843069.1|  [L=321]
Description: CRISPR-associated Csh2 family protein [Methanosaeta thermophila PT]
Scores for complete 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-58  196.3   0.0    7.4e-58  196.1   0.0    1.1  1  Cas_Cas7  CRISPR-associated protein Cas7


Domain annotation for each model (and alignments):
>> Cas_Cas7  CRISPR-associated protein Cas7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.1   0.0   4.1e-62   7.4e-58       1     250 [.       6     268 ..       6     270 .. 0.84

  Alignments for each domain:
  == domain 1  score: 196.1 bits;  conditional E-value: 4.1e-62
                       Cas_Cas7   1 nryefvllfdvkngNpNGDpdagnkPRidpetgeglvsDvclKrkiRnyvekakeekeiyvkekkv......lnekkeea 74 
                                    nr e ++++d+++gNpNGDp+++nkPR+d+etg +lv+Dv+lKr+iR+y+++ k+  ei+v+e         +++ k++a
  gi|116753951|ref|YP_843069.1|   6 NRSELLFIYDIRDGNPNGDPMDENKPRMDEETGVNLVTDVRLKRTIRDYLHNFKG-LEIFVREIIYdeengyIQDAKRRA 84 
                                    899*************************************************997.677777654433233244444444 PP

                       Cas_Cas7  75 ykdeekkelreamcenffDvRtFGavmstgvn................gqvr.GpVqltfarslepvlpeeqsitrmaat 137
                                    + d    e +e+++++++DvR+FG+v++ ++                 +++  GpVq++++rsl++v  + ++ t  +a+
  gi|116753951|ref|YP_843069.1|  85 K-DFG--EDQERILSECIDVRLFGGVIPLEKRrqnkqkdegegsskgdSITYtGPVQFKMGRSLHRVALKHIKGTGAFAS 161
                                    4.333..3589*****************9433455678899999999866667**************8888888999998 PP

                       Cas_Cas7 138 eekkekekkqrtmgrkhivpyglYrahgfinanlaektgfseeDlellkeallnmfehdrsaargemevrkllvfehesk 217
                                    +e  +   +q t+ +++++py+l+ ++g+in+n+a++t ++eeD+ ll e ++n++++  s+++ ++ +r ll +++   
  gi|116753951|ref|YP_843069.1| 162 KE--GM--TQATFREEYVLPYSLILFYGIINENAAKHTALTEEDVRLLLEGMWNGTKSLISRTKAGQVPRLLLKVNY--S 235
                                    88..33..79*******************************************************************..4 PP

                       Cas_Cas7 218 lgnapaaklfdlvkvekkdeveparsfedyeit 250
                                      n+    l +++k+ ++ ++e++r  ed+ ++
  gi|116753951|ref|YP_843069.1| 236 KANYHIGDLDRMIKLVSDVQHEAIRGPEDFCLD 268
                                    455556666666998887677888887777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 2185.83
//
Query:       gi|116753952|ref|YP_843070.1|  [L=233]
Description: CRISPR-associated Cas5 family Hmari subtype protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    8.9e-09   35.5   0.0    1.5e-08   34.8   0.0    1.3  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 !   34.8   0.0   8.2e-13   1.5e-08       1     131 [.       5     125 ..       5     149 .. 0.70

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 8.2e-13
                                    EEEEEEECCEE-EB-TTCCSCCCBESS--HHHHHHHHHHHHT--TTS-...-CCCCTTEEEEEEEEEEEEEEETEEEEEC CS
                      Cas_Cas5d   1 tLllrlegplasfgrpsrkveretydvPtkSavlGllaaalGirrddd...leelkpalrwgvrvdrrgellrgdyhtva 77 
                                    +L++ ++g++a f+  ++     ty +P+++a+ G+++a+ G++ +          +++++g r+ ++ + +r   + ++
  gi|116753952|ref|YP_843070.1|   5 VLVFDVWGDYAHFRKIYTTSSPLTYSFPPRTAISGIIGAIAGLSKESYfryF--SRDKASIGCRILEPVKKVRVGENLID 82 
                                    59******************************************99988553..44455555555555555552223333 PP

                                    T-GGGS--BSSS----CCEEEEEEEEEEEECEEEEEECCSCCHHHHHHHHHHHH CS
                      Cas_Cas5d  78 grtlperrkektadrkkraatvlseraYladahfevalegeeegklleelaral 131
                                         ++r+         +++  +  ++l d +f + l+  ++    ++l+++l
  gi|116753952|ref|YP_843070.1|  83 -----TKRS-----MHRIHNRTQVRFEFLKDPRFRIYLSHSDD-RFSRDLRDML 125
                                    .....1111.....22234555556667777777776666666.4455555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1702.02
//
Query:       gi|116753953|ref|YP_843071.1|  [L=804]
Description: CRISPR-associated helicase Cas3 [Methanosaeta thermophila PT]
Scores for complete 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   35.8   0.0    1.4e-08   35.0   0.0    1.4  1  ResIII      Type III restriction enzyme, res subunit
    2.8e-07   30.5   0.0      1e-06   28.6   0.0    1.9  2  DEAD        DEAD/DEAH box helicase
      6e-07   29.8   0.0    1.1e-06   28.9   0.0    1.3  1  HD_6        HD domain
    6.8e-05   23.2   0.2    0.00026   21.3   0.2    2.0  1  Helicase_C  Helicase conserved C-terminal domain
     0.0026   18.0   0.4     0.0074   16.5   0.2    1.9  2  HD          HD domain
     0.0075   15.7   0.0      0.089   12.2   0.0    2.2  2  PhoH        PhoH-like protein
  ------ inclusion threshold ------
        0.2   10.3   0.2       0.45    9.2   0.2    1.5  1  SNF2_N      SNF2 family N-terminal domain


Domain annotation for each model (and alignments):
>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.0   5.4e-12   1.4e-08      24     168 ..     286     460 ..     262     463 .. 0.76

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 5.4e-12
                                    TSEEE.EEESTTSTHHHHHHHHHHHH-S..........-EEEEESSHHHHHHHHHHGGGGTGG................. CS
                         ResIII  24 dkrgl.ikmaTGtGKTlvaaklierllkkgkee.....kflflvprkslleqtleefkkflseayke............. 84 
                                    ++r++ ++ +TGtGKTl++++++ rl++   +e     +++   p +s+++qt + f+++l++a  +             
  gi|116753953|ref|YP_843071.1| 286 NERIIsLNVPTGTGKTLTSLAMALRLRRRLMNErgvmpRIVYALPFLSIIDQTCDVFEDVLESAGIRadssvllkhhhls 365
                                    4455559*********************999999***********************99999886556666666655544 PP

                                    GEEEESSS-B--............-SEEEEEHHHHHHTH.........HHHTTT-SEEEEETG....GGTTS...TTTHH CS
                         ResIII  85 igkkvsgdkkka.....kekdstnkkilvttiqsldads.eeeeeeseellrdrfdviiiDEa....Hrlgak..kswre 152
                                      + ++gd++ +        +  n++i+vtt  +l   + +++++   ++ r ++ +ii+DE+    Hr+     +s + 
  gi|116753953|ref|YP_843071.1| 366 DITYTKGDEEFEsdvslLLMEGWNSEIVVTTFWQLFHTIfSNRNRRLRKFNRIANSIIIMDEVqavpHRYWHLlhDSLKM 445
                                    44446666666699999888889999999998777766603447777777777777******833445555545458888 PP

                                    HHHT---SEEEEEESS CS
                         ResIII 153 ilekfkeavllglTAT 168
                                    + ekf+ ++l+ +TAT
  gi|116753953|ref|YP_843071.1| 446 LCEKFN-SYLILVTAT 460
                                    888888.555556998 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   4.1e-10     1e-06      17     170 ..     290     462 ..     275     467 .. 0.70
   2 ?   -3.7   0.0       3.4   8.6e+03      96     112 ..     710     726 ..     689     735 .. 0.78

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 4.1e-10
                                    EEEEESTTSSHHHHHHHHHHHHHHHS...TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST.............SEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............xxxxx RF
                           DEAD  17 vlvaaeTGsGKTlaflipvlqivyet...kgktgpkalivePtreLaeqtlnnlkkfkkyid.............lrvll 80 
                                    + ++ +TG+GKTl  l  +l ++ ++   ++   p++++  P  +++ qt++ ++ +++ ++             l    
  gi|116753953|ref|YP_843071.1| 290 ISLNVPTGTGKTLTSLAMAL-RLRRRlmnERGVMPRIVYALPFLSIIDQTCDVFEDVLESAGiradssvllkhhhL---- 364
                                    56789********9777777.3333346588899*************************76644556665443332.... PP

                                    E.....ETTSSHHHHHHHHH.TT..CSEEEEEHHHHHHHH......HCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHH CS
                                    x.....xxxxxxxxxxxxxx.xx..xxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  81 i.....iggvaardqlskld.ng..vdivvgtpgrlddll......stgklnlsqvrflVlDEadrlldqgfsdfinril 146
                                           g+++ ++++s l  +g   +ivv+t  +l++ +      + +k+n    +++++DE++ +    +   ++  l
  gi|116753953|ref|YP_843071.1| 365 SditytKGDEEFESDVSLLLmEGwnSEIVVTTFWQLFHTIfsnrnrRLRKFNRIANSIIIMDEVQAVPHR-YWHLLHDSL 443
                                    1222213345557777777424478************966676533233344444499********9998.555555555 PP

                                    HHSHHHCTTSTTTSEEEEEESSBS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD 147 nqlpqitcdgklqrqvivlSATlp 170
                                    + l   +++ ++   +i+++AT p
  gi|116753953|ref|YP_843071.1| 444 KML---CEKFNS--YLILVTATQP 462
                                    555...555554..4999999976 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3.4
                                    TTCSEEEEEHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxx RF
                           DEAD  96 ngvdivvgtpgrlddll 112
                                     +vd++v t +r  d+ 
  gi|116753953|ref|YP_843071.1| 710 PRVDVFVETDERASDVW 726
                                    35999999999999965 PP

>> HD_6  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   4.3e-10   1.1e-06      15     138 ..      17     146 ..       9     180 .. 0.70

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 4.3e-10
                                    EHHHHHHHHHHHHHHHHHHTS-HHHHHC.TS-HHHHHHHHHHHHHCCCGGGSSHHHHTTS----TTS-.....-GGGT-- CS
                           HD_6  15 pLvaHllDvaavaealldkwlsllarllrgleeealrrllaflaalHDlGKaspaFqakvpelaekleeaglelekelek 94 
                                    +Lv Hl  v  ++++ ++++     r+l   + e l++++ ++ a HDlGKa+  Fq   +e  ek ++a l+ +   + 
  gi|116753953|ref|YP_843071.1|  17 LLVDHLRNVGEMCRRTVAESA----RNL--DDAEILKNVAYIIGATHDLGKATGFFQEYLRETDEKRRRA-LRSR---DV 86 
                                    788899888888877776554....666..67789*************************9988887766.3433...78 PP

                                    --HHHHHHHHHH................HHHHHHHHHHHTTTS---HHHHHTSS-HHHHT CS
                           HD_6  95 arHdslgaalle................evarslaaavggHHGkppkeeeekaekkssaa 138
                                    ++H+ l+ ++                  +     + av  HHG  +++ +e ++  ++++
  gi|116753953|ref|YP_843071.1|  87 TKHGLLSSLFTYaivrehlrkrgcempgALPLVSFIAVRRHHGDLTNALDEISAIYAERE 146
                                    9999999999445555555555555544444467778899***77776666555544444 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 !   21.3   0.2     1e-07   0.00026       8     109 ..     506     613 ..     500     614 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1e-07
                                    HHH...HHTTTTSEEEEEESSHHHHHH....HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHH...TTSSSEEEESGGGT CS
                     Helicase_C   8 ell...kleeeggkilifvntidrlek....vklllekkgikvavlhgelpqnereeileqfn...kgesdvLiatdvae 77 
                                    +ll    +++ +++ li++nti+++ +    +k l   ++ +  +l      ++r++ +++ +    g++++ ++t+ +e
  gi|116753953|ref|YP_843071.1| 506 ALLegeIHNNPEKDFLIVLNTIRSARNvysaIKAL-DLRDTELFYLSTHVVPRDRRDRIRRIRderGGRRKITVSTQLIE 584
                                    444555689999***********776554444444.34468888888888888999888888866458888********* PP

                                    SSSTSTTESEEEESSSSSSHHHHHHHHTTSSS CS
                     Helicase_C  78 rGidipkvnlVinfdlprnvtsyiqriGRtgR 109
                                     G+di +++ V++  +p  ++s++q +GR+ R
  gi|116753953|ref|YP_843071.1| 585 AGVDI-DADIVFRDLAP--LDSINQVAGRCNR 613
                                    *****.79999988888..6799999999988 PP

>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.2   2.9e-06    0.0074       3      92 ..      20     108 ..      18     154 .. 0.84
   2 ?   -4.0   0.0       6.4   1.6e+04      84      97 ..     358     371 ..     342     387 .. 0.60

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.9e-06
                                    HHHHHHHHHHHHHHHHHHH.....HHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHH CS
                             HD   3 eHsleVaklarrlaedlge.....eedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgld 77 
                                    +H ++V +++rr   + ++     e  ++++++++  HD+Gk +   +f+++ +e+++ +  +  ++ ++++ ++++   
  gi|116753953|ref|YP_843071.1|  20 DHLRNVGEMCRRTVAESARnlddaEILKNVAYIIGATHDLGKAT--GFFQEYLRETDEKRRRALRSRDVTKHGLLSSL-- 95 
                                    89*********9999999999*9*9*******************..58888977777778888888877776666663.. PP

                                    HHHHHHHHHTTCCHH CS
                             HD  78 ledvaklirehhesw 92 
                                        ++++reh+++ 
  gi|116753953|ref|YP_843071.1|  96 --FTYAIVREHLRKR 108
                                    ..5888888888765 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 6.4
                                    HHHTTCCHHHHHHH CS
                             HD  84 lirehheswegkkr 97 
                                    l ++hh s  ++++
  gi|116753953|ref|YP_843071.1| 358 LLKHHHLSDITYTK 371
                                    55566655554444 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   3.5e-05     0.089      18      50 ..     286     318 ..     268     338 .. 0.71
   2 ?    0.7   0.0      0.12   3.1e+02     118     132 ..     418     432 ..     413     440 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.5e-05
                                    H-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-S CS
                           PhoH  18 kndivfaiGpaGtGKtylavalavealkkkkvk 50 
                                    ++ i+    p+GtGKt+ ++a+a+++ ++   +
  gi|116753953|ref|YP_843071.1| 286 NERIISLNVPTGTGKTLTSLAMALRLRRRLMNE 318
                                    667889999***************976543333 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.12
                                    B-SEEEEE-SGGG-- CS
                           PhoH 118 lndafvilDEAQntt 132
                                    ++++++i+DE Q + 
  gi|116753953|ref|YP_843071.1| 418 IANSIIIMDEVQAVP 432
                                    689*********875 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.2   0.00018      0.45     134     214 ..     363     460 ..     295     464 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00018
                                    H...........-----------------EEEE-HHHHHHHT.........TTS-S-S-SEEEES-GGGT--T.....TS CS
                                    x...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxx.....xx RF
                         SNF2_N 134 k...........mkkkntkvapklladydvvittYdvlsreaelq...kkrsvlkqvewkrvvlDEghtlkns.....ts 194
                                    +           + ++ + ++    ++ ++v+tt+  l     ++    +  +++++    +++DE + +        + 
  gi|116753953|ref|YP_843071.1| 363 HlsditytkgdeEFESDVSLLLMEGWNSEIVVTTFWQLFHTI-FSnrnRRLRKFNRIANSIIIMDEVQAVPHRywhllHD 441
                                    12344444444466777778888899*********9998543.3345588999999*************99987666556 PP

                                    HHHHHHHH---S-EEEE-S- CS
                                    xxxxxxxxxxxxxxxxxxxx RF
                         SNF2_N 195 kaaeavskLstsnrwiltGT 214
                                    ++++ ++k++ s+ +++t+T
  gi|116753953|ref|YP_843071.1| 442 SLKMLCEKFN-SYLILVTAT 460
                                    6666666654.577777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (804 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); 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: 0.67u 0.27s 00:00:00.94 Elapsed: 00:00:00.44
# Mc/sec: 5468.48
//
Query:       gi|116753954|ref|YP_843072.1|  [L=280]
Description: hypothetical protein Mthe_0642 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.6e-42  142.5   0.0    8.7e-42  141.8   0.0    1.3  1  Cas6b_C   Cas6b C-terminal domain
      3e-33  114.0   0.0    4.6e-33  113.4   0.0    1.3  1  Cas6b_N   Cas6b N-terminal domain


Domain annotation for each model (and alignments):
>> Cas6b_C  Cas6b C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.8   0.0   9.7e-46   8.7e-42       2     112 ..     106     216 ..     105     218 .. 0.97

  Alignments for each domain:
  == domain 1  score: 141.8 bits;  conditional E-value: 9.7e-46
                        Cas6b_C   2 lseelieYkfltpwlaLnqenykkykklkseeekkellekiLvgnilsmakglgvtveekievkiteveekkvklkeqkm 81 
                                    ++ el++Y+f+tpwlaLnqeny +y+++ s+ e+ke+l+kiLvgnils+akglg+tv+e+i++++ +v+++ + lk++ +
  gi|116753954|ref|YP_843072.1| 106 CAGELHAYRFVTPWLALNQENYMRYADAASWYERKEILRKILVGNILSAAKGLGYTVDEQIRLELGRVRDEICILKGVMV 185
                                    67799*************************************************************************** PP

                        Cas6b_C  82 lafkgeFktnfliPdylGlGksvsrGfGtvk 112
                                    +++k+eF tnf+iPd++GlGksvsrGfG+v 
  gi|116753954|ref|YP_843072.1| 186 TGIKCEFLTNFHIPDLMGLGKSVSRGFGAVG 216
                                    ****************************995 PP

>> Cas6b_N  Cas6b N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.4   0.0   5.1e-37   4.6e-33       1     102 [.       1     102 [.       1     103 [. 0.96

  Alignments for each domain:
  == domain 1  score: 113.4 bits;  conditional E-value: 5.1e-37
                        Cas6b_N   1 mklktltlkfkeek.lkeseaeklRGafankfkeeellHnHkedkliYrYPliQYkvidgkplilgieegaellkeifkk 79 
                                    m+l++l+l++++++ +ke +a+klRG+fa++f+++ llH+H +d+liYrYPliQYk+i+g p+ilgi+ega++l+++++k
  gi|116753954|ref|YP_843072.1|   1 MDLRILRLRLRSDShVKE-DAAKLRGFFATSFNDQMLLHHHFTDRLIYRYPLIQYKIIQGVPVILGINEGADVLRDVYDK 79 
                                    789***********6666.************************************************************* PP

                        Cas6b_N  80 idelklgekklelkekelelkee 102
                                    + e++lg++++++ e++++l++e
  gi|116753954|ref|YP_843072.1|  80 FGEIRLGDRSYSVVERHICLRRE 102
                                    ******************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 2016.43
//
Query:       gi|116753955|ref|YP_843073.1|  [L=89]
Description: CRISPR-associated Csx3 family protein [Methanosaeta thermophila PT]
Scores for complete 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-25   87.2   0.3    5.8e-25   87.0   0.3    1.0  1  Cas_csx3       CRISPR-associated protein (Cas_csx3)
  ------ inclusion threshold ------
       0.17   11.6   0.1       0.21   11.3   0.1    1.2  1  Phage_Mu_Gp45  Bacteriophage Mu Gp45 protein


Domain annotation for each model (and alignments):
>> Cas_csx3  CRISPR-associated protein (Cas_csx3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.0   0.3   6.4e-29   5.8e-25       3      79 .]      10      85 ..       8      85 .. 0.94

  Alignments for each domain:
  == domain 1  score: 87.0 bits;  conditional E-value: 6.4e-29
                                   EE-SS--GGG.GGT-----.--TTSEEEEEESS-HHHHHHHHHHTTTSSE..EEEEETTT.EEEEEEESS.SS-TT-EE- CS
                       Cas_csx3  3 elereieped.LkklelPeeidlkqgvvisGrgPiWlygylvhelhetaw..iavydprLegavvvashtrevrvGqvik 79
                                    +e++i+p++ L+ l  P+ i + + vv++Gr+PiW+yg+ +h+lh +++  iav+dprL gavvvasht+++r+Gqv++
  gi|116753955|ref|YP_843073.1| 10 GVESPIAPDEpLPPL--PP-IPRGALVVVEGRAPIWRYGLALHRLHGSPAgaIAVFDPRL-GAVVVASHTPAYRPGQVVD 85
                                   67999***9999999..99.9*************************999777********.*****************95 PP

>> Phage_Mu_Gp45  Bacteriophage Mu Gp45 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   2.4e-05      0.21      35      75 ..      43      83 ..      31      85 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.4e-05
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--S---SS CS
                  Phage_Mu_Gp45 35 pyGftSvppaGaeaivlavgGdrshgvviavedrryRlkgl 75
                                    yG++ +   G+ a ++av + r  +vv+a+   +yR+ ++
  gi|116753955|ref|YP_843073.1| 43 RYGLALHRLHGSPAGAIAVFDPRLGAVVVASHTPAYRPGQV 83
                                   7************************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       168  (0.00937029); expected 358.6 (0.02)
Passed bias filter:                      140  (0.00780858); 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: 0.38u 0.21s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 677.49
//
Query:       gi|116753956|ref|YP_843074.1|  [L=404]
Description: hypothetical protein Mthe_0644 [Methanosaeta thermophila PT]
Scores for complete 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-135  450.2   0.0   5.4e-135  450.0   0.0    1.0  1  DUF1887       Domain of unknown function (DUF1887)
      1e-06   27.8   0.0    1.8e-06   27.0   0.0    1.3  1  Cas_Cas02710  CRISPR-associated protein (Cas_Cas02710)


Domain annotation for each model (and alignments):
>> DUF1887  Domain of unknown function (DUF1887)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  450.0   0.0    6e-139  5.4e-135       1     381 [.       1     365 [.       1     366 [. 0.99

  Alignments for each domain:
  == domain 1  score: 450.0 bits;  conditional E-value: 6e-139
                        DUF1887   1 mkvhvclvsaQdapnLlpalldkelkpehlvlivteaq..kekanrlekvlkekgidv....eifeledevdleeleesl 74 
                                    mk+++cl+s+Q++pnLl++   +el+p++lvl++te++  +e+anr+ k+l+++g+d+    ei++led++++ee+e++l
  gi|116753956|ref|YP_843074.1|   1 MKAMLCLISEQHVPNLLGV---HELRPDLLVLLETEGMkrREAANRFLKALAIGGQDYltrnEIVPLEDGDSIEETERAL 77 
                                    899****************...9***************999*************************************** PP

                        DUF1887  75 kglleelkaaeevvlNvtgGtklmalgayevfR.skhkrIfyvetasdkleflspeGkedievkdrisvsdylagygadv 153
                                    kg++e+++ ++e+++N+tgGtk+m++gay++fR +k++rI+yv +asd++++l+++G++di++++risv+++lagyg+dv
  gi|116753956|ref|YP_843074.1|  78 KGVYERYR-DAEWIVNITGGTKPMSIGAYGFFRqKKNARIIYV-SASDQSRALDFSGGADIPLSHRISVAEFLAGYGFDV 155
                                    ********.**********************************.************************************ PP

                        DUF1887 154 lraefsdkqkdeeadkrlkelaerlAsrakelgdilatLnalatts..Rkerrldvelsesdqgylrdlnllledladek 231
                                    l   + ++q++ee+++r+ +la+++A+r+++ g+il++L++l+++s  R++r++++++sesd+++l+d ++l+e++a+++
  gi|116753956|ref|YP_843074.1| 156 L--HYDKVQENEERSRRWLGLAAEIAARSQN-GAILGLLANLSRISkeRRGRYRGLKISESDGLFLND-GHLREMIASSF 231
                                    *..5999************************.************************************.*********** PP

                        DUF1887 232 llkleggi.vtfldeearrflnGeWLEvfvyktlrdiqdvqDvslnvevvrektekevrNeLDVvfivknklhiiECKtk 310
                                    +l+++gg+ +++ld++a+rfl+G+WLEvf+++ lr++++v+Dv+l+++++++ +ek ++N+LDVvf+++++l+i+ECK++
  gi|116753956|ref|YP_843074.1| 232 GLACDGGHfTGALDKYAVRFLTGGWLEVFTWGLLRGLDRVWDVHLGLQIGMK-NEK-LQNDLDVVFMTDQSLRIVECKSG 309
                                    ****************************************************.***.*********************** PP

                        DUF1887 311 gmendeedddtLyKleslrdllgglqarsmlVsfrPlrandivRAedlglaligddelkdlkehleewira 381
                                    g+e+d+e++dtLyK+e++r++lg+l++rs+lV+    ++++++           d+e++++kehle+++r 
  gi|116753956|ref|YP_843074.1| 310 GQEHDREGSDTLYKIEAIRKQLGALRVRSYLVT----TSDNVI-----------DSETGNIKEHLEDRSRL 365
                                    *********************************....99****...........**************986 PP

>> Cas_Cas02710  CRISPR-associated protein (Cas_Cas02710)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0     2e-10   1.8e-06       6     103 ..      18     122 ..      14     134 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 2e-10
                                    HHHHH--SEEEEEE-T..GGGGGHHHHHHHH-S-........EEEEE--TT-HHHHHHHHHHHHHHS.TTS-EEEE-SSS CS
                   Cas_Cas02710   6 sIaelrPerVvflase..kSekkleevkealgkklkq.....evlldedandllelykkikevlekaleeeevivDlTgG 78 
                                     ++elrP+  v+l +e  k ++ +++  +al+   ++     e+++ ed ++++e  + +k v+e++ ++ e iv++TgG
  gi|116753956|ref|YP_843074.1|  18 GVHELRPDLLVLLETEgmKRREAANRFLKALAIGGQDyltrnEIVPLEDGDSIEETERALKGVYERY-RDAEWIVNITGG 96 
                                    5788888888888887334455677777777777666777889************************.************ PP

                                    -HHHHHHHHHHHHHH...TEEEEEEE-- CS
                   Cas_Cas02710  79 tkeMtaglalagill...rvklsyVgge 103
                                    tk M++g+    +++    ++++yV   
  gi|116753956|ref|YP_843074.1|  97 TKPMSIGAYG--FFRqkkNARIIYVSAS 122
                                    ******9864..3333336778888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 3013.57
//
Query:       gi|116753957|ref|YP_843075.1|  [L=341]
Description: CRISPR-associated RAMP Cmr6 family protein [Methanosaeta thermophila PT]
Scores for 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-13   48.7   0.3    1.7e-11   44.5   0.3    2.7  2  RAMPs           RAMP superfamily
  ------ inclusion threshold ------
      0.037   13.4   0.0       0.06   12.7   0.0    1.3  1  ATPase          KaiC
       0.13   13.3   0.2         17    6.5   0.0    2.7  3  HK97-gp10_like  Bacteriophage HK97-gp10, putative tail-compon


Domain annotation for each model (and alignments):
>> RAMPs  RAMP superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5   0.3   2.9e-15   1.7e-11       3     212 ..      81     247 ..      79     248 .. 0.86
   2 ?    0.5   0.0      0.09   5.4e+02      38      52 ..     303     317 ..     298     338 .. 0.75

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 2.9e-15
                                    EESS-EE----..............---S----HHHHHHHHHHHHHHHHH.HHHTT-HHHHH.H.........HHHHHH- CS
                          RAMPs   3 etltPlhiGdgkisdekeespefrdkgglPyIPGSSlkGalRsalekllgsekkekkdeysrkkekqrvkkgdleeaiFG 82 
                                     t+ P  +G g +s++ e+  + +++ g Py+PGSS+kG +R +++ l++++++                    +++iFG
  gi|116753957|ref|YP_843075.1|  81 RTTAPFVTGLG-RSHPVENGFAWHHTLGIPYLPGSSVKGIVRGWAR-LWRNLDNG------------------EIRRIFG 140
                                    68889999999.******************************9998.55655543..................899**** PP

                                    -S...SS--SEEEEE.......................EEEEEEEEEEEEEEEEE--SSS-EEEEEE.....-TT-EEEE CS
                          RAMPs  83 neeeskiagrvffeDarpvkipgqileeskqikstpspklsgselrelldhsterrtrvaidrktktngk..kkgglftl 160
                                     + + ++ g v+f Da pv       e+++             +  + +  +  +++   ++ + +  +    +g+ f  
  gi|116753957|ref|YP_843075.1| 141 PD-GAGSVGSVIFLDALPVRPV----ELKAE-------IMTPHYGPYYRGDKPPEGWPADWHSPVPIPFLavAEGQEFLF 208
                                    **.*************886543....33333.......667778888888888888888888888777779888899*** PP

                                    EEEESS..............HHHHHHHHHHHHHH.HHH---STTTTBTTT-E CS
                          RAMPs 161 eaipaerikfsgrirlenlsdeelgallklLdlldlhflglGggkplGfGsv 212
                                     +ip +          +++ +++ g+l+++L+ +     g G+++ +G+G++
  gi|116753957|ref|YP_843075.1| 209 GVIPRK--------EATQDCEKVIGWLKEALQEI-----GAGAKTAVGYGRF 247
                                    ******........999*****************.....***********98 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.09
                                    HHHHHHHHHHHHHHH CS
                          RAMPs  38 SlkGalRsalekllg 52 
                                     lkG++R  +++++ 
  gi|116753957|ref|YP_843075.1| 303 ELKGMVRQEIMQIYQ 317
                                    69******9998887 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0     1e-05      0.06      63     152 ..     227     320 ..     217     324 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1e-05
                         ATPase  63 lrenakslGwdlekleeegklaiidasesaeesaee..kdkedleelieelaeaikeika..krvviDsitglayeekea 138
                                    l+e  +++G   +     g++a i+a + +e  +e    ++e le+l+ee+ + ++++     +v+ D  ++++++e + 
  gi|116753957|ref|YP_843075.1| 227 LKEALQEIGAGAKTAVGYGRFACIEAETPEEAAPEPmtPGREWLEKLAEEMGKSVEDFAKecPKVLADRWNAIENDELKG 306
                                    6778888888889999999********9998876668899*****************9985567999******99999** PP

                         ATPase 139 vaReilrqlvrvlk 152
                                    ++R++++q+++ ++
  gi|116753957|ref|YP_843075.1| 307 MVRQEIMQIYQCMN 320
                                    **********9997 PP

>> HK97-gp10_like  Bacteriophage HK97-gp10, putative tail-component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0028        17       7      39 ..      34      67 ..      31      83 .. 0.85
   2 ?   -2.8   0.0       2.2   1.3e+04      18      28 ..     226     236 ..     217     242 .. 0.58
   3 ?    3.7   0.0      0.02   1.2e+02       6      30 ..     269     292 ..     262     308 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0028
                 HK97-gp10_like  7 leklserevekaikkalkkaAkev.ldkakkrtp 39
                                   +++l ++  +++i+++++  ++e+ l+++k+r+ 
  gi|116753957|ref|YP_843075.1| 34 FNSLGDNGKKEWIRTVVRNVGDEAlLREIKERVI 67
                                   78999999**************9989****9975 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.2
                 HK97-gp10_like  18 aikkalkkaAk 28 
                                    ++k+al++ ++
  gi|116753957|ref|YP_843075.1| 226 WLKEALQEIGA 236
                                    55555555554 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.02
                 HK97-gp10_like   6 kleklserevekaikkalkkaAkev 30 
                                    +lekl+e e+ k +++++k++ k++
  gi|116753957|ref|YP_843075.1| 269 WLEKLAE-EMGKSVEDFAKECPKVL 292
                                    5566666.46666666665555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); 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: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2410.84
//
Query:       gi|116753958|ref|YP_843076.1|  [L=133]
Description: CRISPR-associated Cmr5 family protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-33  115.0   1.1    2.7e-33  114.8   1.1    1.0  1  Cas_Cmr5  CRISPR-associated protein (Cas_Cmr5)
     0.0025   17.0   0.1     0.0036   16.5   0.1    1.3  1  PDCD7     Programmed cell death protein 7


Domain annotation for each model (and alignments):
>> Cas_Cmr5  CRISPR-associated protein (Cas_Cmr5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.8   1.1     3e-37   2.7e-33       1     122 []       6     126 ..       6     126 .. 0.98

  Alignments for each domain:
  == domain 1  score: 114.8 bits;  conditional E-value: 3e-37
                                    HHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC.....SSCCCHHHHHHHHHHHHHHHH CS
                       Cas_Cmr5   1 leqqraadayekvkelkekskkkekkykslvkklPalIltnGLgqalAfllskg.....kkkkedahkkllehlaewlkk 75 
                                    leq+ra++a+e+v+++++  ++ ++k++s+v++lP  I++nGLgqa+A  l+ +      +++++ah+kl+e +a+w++ 
  gi|116753958|ref|YP_843076.1|   6 LEQERAKHALEAVNSIRG--ESWAGKFRSYVERLPPAIVMNGLGQAMAGELAAAgrageMSDDKKAHNKLYELVAGWIRT 83 
                                    69***************9..9****************************999999****9******************** PP

                                    CTSS...STTTCHHHHHHHHSTHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Cas_Cmr5  76 eksaskkkkgendllkelleadlseymratreaLallnWlkRfAeal 122
                                    +    +  ++e++l+k++++ d+++y++a++eaLa+l+Wlk+f++a+
  gi|116753958|ref|YP_843076.1|  84 R----RIYSAEENLMKAIVDGDQKQYVLAQAEALAYLEWLKKFSQAF 126
                                    *....99999***********************************96 PP

>> PDCD7  Programmed cell death protein 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1     4e-07    0.0036     169     215 ..      58     104 ..      50     130 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4e-07
                          PDCD7 169 gillekeadeafesklekLrkvlkkrteeyskEEkaLkvmLeeeqee 215
                                    g   e ++d++ ++kl +L+  + +  ++ys+EE  +k ++ + q++
  gi|116753958|ref|YP_843076.1|  58 GRAGEMSDDKKAHNKLYELVAGWIRTRRIYSAEENLMKAIVDGDQKQ 104
                                    66668899*********************************999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 986.96
//
Query:       gi|116753959|ref|YP_843077.1|  [L=267]
Description: CRISPR-associated RAMP Cmr4 family protein family protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-21   77.9   0.0    1.4e-21   77.5   0.0    1.1  1  RAMPs     RAMP superfamily


Domain annotation for each model (and alignments):
>> RAMPs  RAMP superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.5   0.0     8e-26   1.4e-21       4     212 ..      10     256 ..       8     257 .. 0.97

  Alignments for each domain:
  == domain 1  score: 77.5 bits;  conditional E-value: 8e-26
                                    ESS-EE----..............---S----HHHHHHHHHHHHHHHHH.HHHTT-HHHHH.H.........HHHHHH-- CS
                          RAMPs   4 tltPlhiGdgkisdekeespefrdkgglPyIPGSSlkGalRsalekllgsekkekkdeysrkkekqrvkkgdleeaiFGn 83 
                                    + t++h G+g++++  +++ +++ ++ +P+I GSSlkGalR a++    +++                      e iFG+
  gi|116753959|ref|YP_843077.1|  10 AETHIHSGAGRSEGFVDLPVAREAVTSYPVIAGSSLKGALRDAAR----ERG--------------------MDESIFGD 65 
                                    689**************************************9997....333....................9******* PP

                                    S...SS--SEEEEE.................................................................. CS
                          RAMPs  84 eeeskiagrvffeDarpvkipgqileeskqikstpsp........................................... 120
                                    +   ++ag v ++Dar++  p+++l +s+ ++++p                                             
  gi|116753959|ref|YP_843077.1|  66 Q---DRAGDVLVSDARLLLLPVRSLTGSYRWVTCPHIlerlsrdmrlcgisdgfegasvergkacctddlnqifleeref 142
                                    *...**************************************************************************** PP

                                    ................................EEEEEEEEEEEEEEEEE--SSS-EEEEEE...-TT-EEEEEEEESS.. CS
                          RAMPs 121 ................................klsgselrelldhsterrtrvaidrktktngkkkgglftleaipaeri 168
                                                                      s+ +++ +   ++ + +r+++d+ +k+++      +++ea+ ++  
  gi|116753959|ref|YP_843077.1| 143 qrsngidgalidalkkmvphkqtasrlerqlvIISDDDFGWFASYGLPVIARNKLDDNKKSKNL-----WYEEALAPD-- 215
                                    *********************************************************8877665.....*********.. PP

                                    ............HHHHHHHHHHHHHH..HHH---STTTTBTTT-E CS
                          RAMPs 169 kfsgrirlenlsdeelgallklLdll.dlhflglGggkplGfGsv 212
                                           +   +++++gal k+ + + +  +l+lGg +++G+G++
  gi|116753959|ref|YP_843077.1| 216 ----TLMYAMVFERKDGALGKVQSMFeTKPYLQLGGNETVGMGWF 256
                                    ....**********************999**************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); 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: 2088.86
//
Query:       gi|116753960|ref|YP_843078.1|  [L=358]
Description: CRISPR-associated Cmr3 family protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-88  297.2   0.0    2.5e-88  297.0   0.0    1.0  1  Cas_Cmr3  CRISPR-associated protein (Cas_Cmr3)


Domain annotation for each model (and alignments):
>> Cas_Cmr3  CRISPR-associated protein (Cas_Cmr3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  297.0   0.0   1.4e-92   2.5e-88       2     371 .]       5     358 .]       4     358 .] 0.97

  Alignments for each domain:
  == domain 1  score: 297.0 bits;  conditional E-value: 1.4e-92
                       Cas_Cmr3   2 llePlDplffrdgrpFedgeear.aasllfPlPsTlaGavrtalgekagldfgklleeekar..dgealgeiavrGpllv 78 
                                    +++P+D++ffrdgrpF+ ge+++ +  l++P+  T++Ga+r++l++ +g++ gk++ee ++   dg +l  +++rGpll+
  gi|116753960|ref|YP_843078.1|   5 RITPVDSWFFRDGRPFHLGEATSdVGGLFPPSAFTVVGAIRAHLARSMGWREGKWSEEICRVlgDGYDLAGLRFRGPLLC 84 
                                    79******************9999*************************************9****************** PP

                       Cas_Cmr3  79 repdgkeellfPaPadllvkekkeglvqllrlepr.dlpeglgplglpdreeveeprpkkkpkplpaylsleglskwLrg 157
                                    re d+  e+l+PaP++ll  +++++ ++++ l+p+ +++++lg+++lp++e      + + +k+l +y++ ++l+++Lrg
  gi|116753960|ref|YP_843078.1|  85 REGDRGPEMLYPAPLNLL-GKRNDSGYEMRLLRPGeEVECDLGRVRLPTAE------KIDGMKQLSGYVNGDQLKQVLRG 157
                                    ******************.9999************99999**********8......*********************** PP

                       Cas_Cmr3 158 elpesselvkeedlltkeeRigialdpetrtaeegalyqteglrlkedvrlallvelddpaeeeklepailrLGGerrla 237
                                    e+pe + +++ee l+ +e+ +g++++++trta+e++ly+++ +rl ++v+l+++ve+ d+   ekl+ a++++GGe+r+ 
  gi|116753960|ref|YP_843078.1| 158 EVPEGRVIPREE-LWGTEYAVGLERERDTRTAKEAHLYSINRIRLVRGVHLIMGVEGIDEGLLEKLDGAVMPIGGEGRMG 236
                                    **********98.******************************************************************* PP

                       Cas_Cmr3 238 lveeelseelesvpeeveaaiaeggrlrlvLlTPaifakgwrpgwldkekeleleelsaelvaaavkrpvavSgwdlark 317
                                    +ve+ +  +  s  +++  +i+ + r++lv++TPa+++++ rpg++       ++++++e+v+a+v+r+++++gwd +++
  gi|116753960|ref|YP_843078.1| 237 CVEMLSPGKGVSEIRQEIGPIDGRVRFTLVHITPAFLGRWPRPGES-------IPGVPGEVVSACVGRALRIGGWDSVNR 309
                                    ****77778888888888999***********************54.......999************************ PP

                       Cas_Cmr3 318 kpkptrravPaGsVyfleakeeeneeleelealtlsdaeqdrrdGfGlaligvw 371
                                    +p ++++++P+GsV+f+ea+++e ++ +++++     +++ +  GfG++++g w
  gi|116753960|ref|YP_843078.1| 310 RPVELKPFIPPGSVWFCEAEADELNDVMSVSR-----IGEYTGFGFGEIALGIW 358
                                    ********************************.....***************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       166  (0.00925874); expected 358.6 (0.02)
Passed bias filter:                      161  (0.00897987); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 2693.66
//
Query:       gi|116753961|ref|YP_843079.1|  [L=638]
Description: CRISPR-associated RAMP Crm2 family protein [Methanosaeta thermophila PT]
Scores for complete 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    5.6e-20   71.6   0.0    1.6  1  DUF3692   CRISPR-associated protein
      4e-05   23.9   0.1    0.00017   21.9   0.0    2.1  2  mCpol     minimal CRISPR polymerase domain


Domain annotation for each model (and alignments):
>> DUF3692  CRISPR-associated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.6   0.0   6.3e-24   5.6e-20       3     110 ..      11     113 ..      10     114 .. 0.93

  Alignments for each domain:
  == domain 1  score: 71.6 bits;  conditional E-value: 6.3e-24
                                    EEEEEESHHHHHS-SSHHHHHHHHHHHHHHHHHHHHHHHHHT-GGGEEES--TT-HHHHHHTS---GGGGGSB---SEEE CS
                        DUF3692   3 vvsigpVqefIaaaRktrDlWagSyllSylawkaikelvekyGpdvliyPslrgnplvdawllekleeeletalipnrfv 82 
                                    +++igpVq fIa+aR+trDlW gS+llSyl+  a+ e+ + +G   + +P+++g++l++ + ++ +   ++++++pnrfv
  gi|116753961|ref|YP_843079.1|  11 NFTIGPVQGFIAQARRTRDLWSGSFLLSYLSGCAMAEIRRCDGR--IKVPDVEGDQLLRWIESDGEGAPPRIGTLPNRFV 88 
                                    79***************************************999..99*******9999888889999************ PP

                                    EEEE.TTTHHHHHHHHHHHHHHHHHHHH CS
                        DUF3692  83 lilpkeeeaeelaeeveealkeawkeia 110
                                    + +++ +    +a+++ e ++++wk+ia
  gi|116753961|ref|YP_843079.1|  89 ASAEDPA---GAARSAAEGVRSRWKKIA 113
                                    ***9665...678888999*******98 PP

>> mCpol  minimal CRISPR polymerase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   1.8e-08   0.00017       3     101 ..     367     461 ..     365     469 .. 0.78
   2 ?   -3.5   0.0       1.4   1.3e+04      12      32 ..     566     586 ..     564     599 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.8e-08
                          mCpol   3 aiDGDdiGkklealllsndeeeleklskevkeaikklkkllkdelgasvifaaGDsilaksslee..dllvelsrvyqki 80 
                                     +DGD+ G+ +         e+ e++s  ++ + k ++++++d+    +++a+GD++la+ ++e+    +  ls  + + 
  gi|116753961|ref|YP_843079.1| 367 LMDGDNMGRLIR--------ESGEAVSRALASFAKDVERVVHDN-LGVLVYAGGDDVLAMLPVERamSCAYRLSVSFAES 437
                                    578888888775........456789999***************.7889***************9774444444444444 PP

                          mCpol  81 t...gltvSiGvGktlrealiaLk 101
                                        g+ ++i++G  ++++ ++L+
  gi|116753961|ref|YP_843079.1| 438 FeaqGMEATISAGLVFASHRVPLR 461
                                    456678888888889999999887 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.4
                          mCpol  12 klealllsndeeeleklskev 32 
                                     +e+ll  + +++le++s+  
  gi|116753961|ref|YP_843079.1| 566 DIETLLQAEYLNALEHRSEIT 586
                                    688888888888887777643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (638 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); 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: 00:00:00.40
# Mc/sec: 4768.79
//
Query:       gi|116753962|ref|YP_843080.1|  [L=421]
Description: CRISPR-associated RAMP Cmr1 family protein [Methanosaeta thermophila PT]
Scores for complete 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-14   52.2   0.4    6.5e-13   49.2   0.4    2.3  1  RAMPs     RAMP superfamily


Domain annotation for each model (and alignments):
>> RAMPs  RAMP superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   0.4   3.6e-17   6.5e-13       2     212 ..       6     165 ..       5     166 .. 0.84

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 3.6e-17
                                    EEESS-EE----..............---S----HHHHHHHHHHHHHHHHH.HHHTT-HHHHH.H.........HHHHHH CS
                          RAMPs   2 letltPlhiGdgkisdekeespefrdkgglPyIPGSSlkGalRsalekllgsekkekkdeysrkkekqrvkkgdleeaiF 81 
                                    +  +tPl++G++               + +P ++  ++kGalR+++++l++++ k + ++ ++           le +iF
  gi|116753962|ref|YP_843080.1|   6 FRIVTPLFMGGA--------------DQSTPELRVPGIKGALRFWWRALAWNWCKGDLSKIRD-----------LEGRIF 60 
                                    7789********..............****************************999999999...........****** PP

                                    --S...SS--SEEEEE.......................EEEEEEEEEEEEEEEEE--SSS-EEEEEE............ CS
                          RAMPs  82 GneeeskiagrvffeDarpvkipgqileeskqikstpspklsgselrelldhsterrtrvaidrktktngk......... 152
                                    G++    +     ++D                          g + +  +  ++e+r ++    +++ +++         
  gi|116753962|ref|YP_843080.1|  61 GST---EHGQSGVIMDL------------------------CGANAKFTNESFFEKRQGLMYLGYGPIEKGkltrdylkp 113
                                    ***...99999999998........................344445555555555555555555555555555555777 PP

                                    -TT-EEEEEEEESS..............HHHHHHHHHHHHHH.HHH---STTTTBTTT-E CS
                          RAMPs 153 kkgglftleaipaerikfsgrirlenlsdeelgallklLdlldlhflglGggkplGfGsv 212
                                    + +++ ++++ p++         ++  s+++ ++l k+L ++ + f+glG ++++GfGs+
  gi|116753962|ref|YP_843080.1| 114 PVDAILRIRIRPKN-------SDEKAPSESIADQLSKALIAM-GLFGGLGSRSRRGFGSF 165
                                    77888999999999.......99999****************.****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2884.66
//
Query:       gi|116753963|ref|YP_843081.1|  [L=583]
Description: CRISPR-associated TM1812 family protein [Methanosaeta thermophila PT]
Scores for complete 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-56  190.2   0.0      9e-56  190.0   0.0    1.1  1  Cas_DxTHG     CRISPR-associated (Cas) DxTHG family
     0.0066   15.2   0.0       0.64    8.6   0.0    2.3  2  DUF1887       Domain of unknown function (DUF1887)
  ------ inclusion threshold ------
      0.015   15.7   0.4        1.4    9.4   0.2    2.4  2  HEPN_Apea     Apea-like HEPN
       0.13   11.0   0.0       0.35    9.6   0.0    1.6  2  Cas_Cas02710  CRISPR-associated protein (Cas_Cas02710)


Domain annotation for each model (and alignments):
>> Cas_DxTHG  CRISPR-associated (Cas) DxTHG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.0   0.0     2e-59     9e-56       1     359 []      25     403 ..      25     403 .. 0.89

  Alignments for each domain:
  == domain 1  score: 190.0 bits;  conditional E-value: 2e-59
                      Cas_DxTHG   1 vlisflGtgnykevkYelkeeeeeeketsfvqeallellaekedpdkvvilltdtladkeaeekeeaaklkeeleelle. 79 
                                    vl++ lG  n ke++Y+    +++++++ ++++al++ll e+e +d+v++l+t+     e  ek +++ l+eel      
  gi|116753963|ref|YP_843081.1|  25 VLLTALGL-NPKETTYT---LGNRTCKSLLSPVALYNLLPEDERFDRVLALCTE-----EVLEK-TFPLLREELP---Vm 91 
                                    799*****.99******...67899*****************************.....99999.6777*****5...24 PP

                      Cas_DxTHG  80 iekvdveiipgggteeelweifekllekleendeiilDiThGfrylPvlallalaylrnvknltikgiyYgaf...keee 156
                                    +e+ +   +++g + ++l   ++++lek++e+ e+ilD+ThGfr++P+l+++a+ yl+ +k+++ik+i+Yg +   + ++
  gi|116753963|ref|YP_843081.1|  92 CEPTR---VHSGVSAGDLQATLHNMLEKIPEKAELILDVTHGFRHYPFLFFTACLYLKALKDVKIKKIWYGRLdakNPDG 168
                                    99***...*******************************************************************9999* PP

                      Cas_DxTHG 157 edPildlteflelsdwltaverflktgdaeklaellre.kkek.kkek....lkklkklkeklkkeleefskalelirpl 230
                                    ++P++dl+ +le+ dw + v++f + ++++ la+ l   k+ + k ++    +   kk  ++ +++ +ef++++ ++ p+
  gi|116753963|ref|YP_843081.1| 169 ATPFIDLSILLEMIDWFRVVQSFRDMSNPKALADKLLAyKRDViKPDTnippS--TKKKYSAVSSAAKEFAELFGIGLPV 246
                                    **********************************9977755556444466542..2333333566**************9 PP

                      Cas_DxTHG 231 ell.ekaeklekeiveklk..eeleeiesleeeesakplellldeikkklekf.................lkkq...ikw 287
                                    e+  + +++l++ ++e+l+   +l++i       ++   e ll ei++++e+f                 +++q   i+ 
  gi|116753963|ref|YP_843081.1| 247 EIGmA-SADLQR-LIEELRveGDLSAI-------KILLAEDLLLEIENAAERFrlpegvekkdlildigeIHRQeklIDA 317
                                    99955.445555.57776655777777.......3344456*****************9999999999997777899*** PP

                      Cas_DxTHG 288 clekgliqqaltllreliisl.lle....gedilnkkkrreeieeelknlskvekksseekeek..........lsniRN 352
                                    + e g+  +a+ l+reliis  +le     +++l+k +r e+ie+ +  l+ ++kk+s ++ ++          + + RN
  gi|116753963|ref|YP_843081.1| 318 YFEAGYHNNAIGLIRELIISRlMLEdedgRNSWLDKSQR-EKIERCIGALMDYSKKNSADLTKDrkelagiwssVIDARN 396
                                    *********************9999****99********.****************999999889*************** PP

                      Cas_DxTHG 353 diaHaGl 359
                                    +++H G+
  gi|116753963|ref|YP_843081.1| 397 KLHHYGM 403
                                    ******8 PP

>> DUF1887  Domain of unknown function (DUF1887)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.0   0.0    0.0037        16      61      98 ..      97     134 ..      54     148 .. 0.87
   2 !    8.6   0.0   0.00014      0.64      16     108 ..     455     543 ..     444     569 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0037
                        DUF1887  61 ledevdleeleeslkglleelkaaeevvlNvtgGtklm 98 
                                    ++ +v+   l+ +l+++le+++ ++e++l vt G ++ 
  gi|116753963|ref|YP_843081.1|  97 VHSGVSAGDLQATLHNMLEKIPEKAELILDVTHGFRHY 134
                                    566778888999***********************996 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00014
                        DUF1887  16 Llpalldkelkpehlvlivteaqkekanrlekvlkekg.idveifeledevdleeleeslkglleelkaaeevvlNvtgG 94 
                                    L +al  +++ pe+  +i +++  +  + l ++  + g  dv+ ++ +  +d + +  +  +ll +   ++evv N+tgG
  gi|116753963|ref|YP_843081.1| 455 LYTAL--RNVNPELCLVIASHETVGRWDELARMASYSGdFDVKEMDAHSFDDGKTIVVNSGELLVR---FDEVVCNLTGG 529
                                    55663..36999999999999999999999888877652677777777777777777776666665...56********* PP

                        DUF1887  95 tklmalgayevfRs 108
                                    t  m  ++ ++ R 
  gi|116753963|ref|YP_843081.1| 530 TAAMQYAVIQLARR 543
                                    *****999988874 PP

>> HEPN_Apea  Apea-like HEPN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.014        62      15      44 ..     156     195 ..     144     238 .. 0.70
   2 ?    9.4   0.2   0.00031       1.4      51      93 ..     356     405 ..     308     429 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.014
                      HEPN_Apea  15 ewfgeaireeddeda..ildlvialEaldll.........l 44 
                                     w+g+   ++ d  a  ++dl i lE++d +         +
  gi|116753963|ref|YP_843081.1| 156 IWYGRLDAKNPDG-AtpFIDLSILLEMIDWFrvvqsfrdmS 195
                                    5888877744443.336***********6557777665542 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00031
                      HEPN_Apea  51 tekislrsn.ayl...ke....dkeerkelkkkikklYdlRSkivHggkik 93 
                                    +eki +r+  a     k+      ++rkel   ++++ d R+k+ H g +k
  gi|116753963|ref|YP_843081.1| 356 REKI-ERCIgALMdysKKnsadLTKDRKELAGIWSSVIDARNKLHHYGMTK 405
                                    4555.3333322222211344446789*******************99777 PP

>> Cas_Cas02710  CRISPR-associated protein (Cas_Cas02710)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0      0.71   3.2e+03      58      78 ..     110     130 ..      67     142 .. 0.71
   2 ?    9.6   0.0   7.7e-05      0.35       5      88 ..     457     539 ..     454     557 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 0.71
                                    HHHHHHHS.TTS-EEEE-SSS CS
                   Cas_Cas02710  58 ikevlekaleeeevivDlTgG 78 
                                    ++++lek  e+ e i+D+T G
  gi|116753963|ref|YP_843081.1| 110 LHNMLEKIPEKAELILDVTHG 130
                                    444555555555555555555 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 7.7e-05
                                    HHHHHH--SEEEEEE-TGGGGGHHHHHHHH-S-...EEEEE--TT-HHHHHHHHHHHHHHS.TTS-EEEE-SSS-HHHHH CS
                   Cas_Cas02710   5 lsIaelrPerVvflasekSekkleevkealgkklkqevlldedandllelykkikevlekaleeeevivDlTgGtkeMta 84 
                                     ++++++Pe  +++as+++    +e+ + +  + +  v  + da ++    + + +  e  ++ +ev+ +lTgGt +M  
  gi|116753963|ref|YP_843081.1| 457 TALRNVNPELCLVIASHETVGRWDELARMASYSGDFDV-KEMDAHSFDDGKTIVVNSGELLVRFDEVVCNLTGGTAAMQY 535
                                    689999********************988777755443.3455555555555555555555566**************99 PP

                                    HHHH CS
                   Cas_Cas02710  85 glal 88 
                                    +++ 
  gi|116753963|ref|YP_843081.1| 536 AVIQ 539
                                    8765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (583 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 3985.69
//
Query:       gi|116753964|ref|YP_843082.1|  [L=289]
Description: transposase, IS4 family protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.2e-33  113.1   0.0    3.2e-31  107.9   0.0    2.2  2  DDE_Tnp_1_5  Transposase DDE domain
      9e-21   74.5   0.1    1.6e-20   73.7   0.1    1.4  1  DDE_Tnp_1    Transposase DDE domain


Domain annotation for each model (and alignments):
>> DDE_Tnp_1_5  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.9   0.0   3.6e-35   3.2e-31       2     111 ..      18     125 ..      17     126 .. 0.95
   2 ?    2.8   0.0     0.016   1.4e+02      40      67 ..     252     281 ..     246     287 .. 0.82

  Alignments for each domain:
  == domain 1  score: 107.9 bits;  conditional E-value: 3.6e-35
                    DDE_Tnp_1_5   2 kRGsltiwldeeaiaawkek...kkngkrgrpqvysdaaiqtcltvkvlfklplRqlqGfvqsllklaglellvpdystl 78 
                                    +RG  +++l+++++++w+e+    +++k+grp++y++++iq+c +++++++lp+Rql+Gf+q+l+ ++   ll++dystl
  gi|116753964|ref|YP_843082.1|  18 RRG--WFYLSTDFVNNWDEEllkMNKNKNGRPYRYPETFIQFCGLAYAFLHLPYRQLEGFIQALSGFVPG-LLAADYSTL 94 
                                    799..************9987745569******************************************9.99******* PP

                    DDE_Tnp_1_5  79 srraktlevkipvkrkskglhlvvdstGlkvlg 111
                                    ++r ++le++ip+ +++  l+++vdstG+kv++
  gi|116753964|ref|YP_843082.1|  95 WQRITNLELNIPIPDND--LVVAVDSTGMKVTN 125
                                    **************999..99**********97 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.016
                    DDE_Tnp_1_5  40 tcltvkvlfklplRql..qGfvqsllklag 67 
                                    ++  +k++f+ ++R++  +G+++ + ++ +
  gi|116753964|ref|YP_843082.1| 252 VFSAIKRIFGETVRATskEGMIREVRRMFT 281
                                    56789*********9855699999988876 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.7   0.1   1.8e-24   1.6e-20       5     200 ..     112     271 ..     108     285 .. 0.83

  Alignments for each domain:
  == domain 1  score: 73.7 bits;  conditional E-value: 1.8e-24
                      DDE_Tnp_1   5 evlivDattvrvpgtkedarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrprkgklvlaDa 84 
                                     v++vD+t ++v+  + ++r++++  + + ++k+hiavd +++ ++ ++it+  v d++ +k+ll+ +   k    l+D+
  gi|116753964|ref|YP_843082.1| 112 LVVAVDSTGMKVTNRGDWMRESHGVER-RGWIKVHIAVDVETRKPVTFEITDETVTDHEMVKPLLEDV---KLEDSLMDG 187
                                    699******************888666.79************************************99...89******* PP

                      DDE_Tnp_1  85 GYasaelldtleekgvd.yiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgdvyyvtntnsells 163
                                    +Y++++++d+++ekgvd + i+++kn+ ++        r +    +++  +  +++ +++                    
  gi|116753964|ref|YP_843082.1| 188 AYDKEGVFDFMKEKGVDmPGIKIRKNAIVKAG----SSRAEPVLEFMKYGYHSWKIVHGY-------------------- 243
                                    ****************9568899999988866....344445555555555555555555.................... PP

                      DDE_Tnp_1 164 aeevaelyrlRwqiErvFkwlkrkfgldrlryrglnr 200
                                             +Rw  E+vF+ +kr fg + +r+ ++++
  gi|116753964|ref|YP_843082.1| 244 --------GRRWAAESVFSAIKRIFG-ETVRATSKEG 271
                                    ........***************998.6666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); 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:                         2  (0.000111551); expected 0.2 (1e-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: 2015.80
//
Query:       gi|116753965|ref|YP_843083.1|  [L=257]
Description: HAD family hydrolase [Methanosaeta thermophila PT]
Scores for complete 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   75.8   0.0    4.8e-21   74.8   0.0    1.6  2  Hydrolase_6      Haloacid dehalogenase-like hydrolase
    7.5e-21   74.0   0.3    4.6e-20   71.5   0.0    2.2  2  Hydrolase_like   HAD-hyrolase-like
    2.3e-08   34.3   0.0    4.5e-06   26.9   0.0    2.5  3  HAD_2            Haloacid dehalogenase-like hydrolase
    7.4e-08   32.9   0.0    1.8e-06   28.4   0.0    2.7  1  Hydrolase        haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
       0.21   11.2   0.1       0.39   10.3   0.1    1.4  1  PGP_phosphatase  Mitochondrial PGP phosphatase


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 !   74.8   0.0   1.3e-24   4.8e-21       1     100 [.       8     106 ..       8     107 .. 0.98
   2 ?   -3.5   0.0       3.2   1.1e+04      44      64 ..     185     205 ..     181     206 .. 0.72

  Alignments for each domain:
  == domain 1  score: 74.8 bits;  conditional E-value: 1.3e-24
                                    EEEESTTTSEETTEE-TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHHHHHHTT----GGGEEEHHHHHHHHHHHHSXX CS
                    Hydrolase_6   1 flfDidGvLwrgdkaipgaaealnalraagkpvvllTNnsskseeeyakkleklgvditeeqvvtsataaaeylkkrkad 80 
                                    fl+D+dGvL+ g++++pga e+l+ ++++g+ + +++N++++ + ++ak+l+++g+ i++e+++t+++aa e +++  ++
  gi|116753965|ref|YP_843083.1|   8 FLMDLDGVLYVGRNPVPGARECLELMEEKGYSFRFISNSTRRCRASVAKRLSEMGYRIQPERIFTPSVAAIERIHR-SGK 86 
                                    79*************************************************************************8.9** PP

                                    XEEEEESXHHHHHHHHHTTX CS
                    Hydrolase_6  81 kkvlvigeeglreelkeagf 100
                                    +++++i + ++++ +++ag+
  gi|116753965|ref|YP_843083.1|  87 RRCYLISTGDVHRDFEDAGI 106
                                    ******************98 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.2
                                    HHHHHHHHHHTT----GGGEE CS
                    Hydrolase_6  44 eeeyakkleklgvditeeqvv 64 
                                    +e +   l+++gv+ ++  ++
  gi|116753965|ref|YP_843083.1| 185 PEFFSLALNDMGVNPQDAAMI 205
                                    555666789999998887776 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1      0.24   8.6e+02      16      30 ..     107     121 ..      74     123 .. 0.77
   2 !   71.5   0.0   1.3e-23   4.6e-20       2      75 .]     180     253 ..     179     253 .. 0.97

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.24
                                    HH---GGGEEEEES- CS
                 Hydrolase_like  16 vlgsdpeevlmiGDr 30 
                                    +l +d ++ ++iGD 
  gi|116753965|ref|YP_843083.1| 107 ALVEDEADFVVIGDA 121
                                    345667888999995 PP

  == domain 2  score: 71.5 bits;  conditional E-value: 1.3e-23
                                    .STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TTTHHHHHHHHT---SEEES- CS
                 Hydrolase_like   2 lgKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrpedleepehkptyvaddlaea 75 
                                    +gKP+pe++  al+++g++p++  miGD++ tD+ gA+++G+ ++LV+tG++rpe++e+   +p+ v+d++a++
  gi|116753965|ref|YP_843083.1| 180 VGKPSPEFFSLALNDMGVNPQDAAMIGDDIITDVGGAQRVGMLGILVRTGKYRPEHVERSGVRPDCVLDSIADL 253
                                    49********************************************************************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 ?   -2.5   0.0       1.3   4.6e+03       2      10 ..       9      17 ..       8      19 .. 0.87
   2 !    4.7   0.0     0.008        29      79     108 ..      21      50 ..      15      64 .. 0.85
   3 !   26.9   0.0   1.3e-09   4.5e-06     134     176 ..     181     224 ..     167     226 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.3
                          HAD_2  2 iFDlDgTll 10
                                   ++DlDg+l+
  gi|116753965|ref|YP_843083.1|  9 LMDLDGVLY 17
                                   79****996 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.008
                          HAD_2  79 kpydgvkelLeeLkeagyklgivTsksrea 108
                                    +p++g++e Le ++e+gy+   +++++r+ 
  gi|116753965|ref|YP_843083.1|  21 NPVPGARECLELMEEKGYSFRFISNSTRRC 50 
                                    699*********************999875 PP

  == domain 3  score: 26.9 bits;  conditional E-value: 1.3e-09
                          HAD_2 134 kKPdpeviekaleklklkkeeviyvGDsp.tDieaakkagikvi 176
                                     KP+pe +  al+ ++++++++ ++GD + tD+ +a+++g+  i
  gi|116753965|ref|YP_843083.1| 181 GKPSPEFFSLALNDMGVNPQDAAMIGDDIiTDVGGAQRVGMLGI 224
                                    5***************************************9655 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0     5e-10   1.8e-06       1     209 [.       5     219 ..       5     220 .. 0.60

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 5e-10
                                    SSEEEEESBTTTBCHH...HHHHHHHHHHCHHHHHHHHHH........HHCHHHHHHHHHHHHH..........HHHHHH CS
                                    xxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxx..........xxxxxx RF
                      Hydrolase   1 iktvvfDkdGTLttge...psvedvivsaalalaaaletg........sehpigkalvaaakar..........sgaltg 59 
                                    i ++++D+dG+L+ g+   p  +++++     + +    g        s++   + +++   ++          +++++ 
  gi|116753965|ref|YP_843083.1|   5 ISAFLMDLDGVLYVGRnpvPGARECLELM---EEK----GysfrfisnSTRRCRASVAKRLSEMgyriqperifTPSVAA 77 
                                    6799*********9997776667666666...222....12222445555555555555555556655666555555555 PP

                                    HHHETTTEHHHHTHHHHHHHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHH.HHHTTEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                      Hydrolase  60 fatfigrgayaigkpewltaldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavas.Lkaagievv 138
                                    +++         gk+++          g+   + +++g   +  +     v+  a +++ ++ +  a+++ L   g +++
  gi|116753965|ref|YP_843083.1|  78 IER-----IHRSGKRRCYLIS-----TGDVHRDFEDAGIALVE-DEADFVVIGDAGSNFTYERLNRAFNHvLE--GADMI 144
                                    555.....5555555544444.....23333333333333333.34445555555777788888877776355..77666 PP

                                    EEESSEH.HHHHHHHHHTT.GGGE.SEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHH.HHHHHHHT CS
                                    xxxxxxx.xxxxxxxxxxx.xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                      Hydrolase 139 lltgdnp.etaeraanqlG.ddyf.daviasdietvakpspegkvaaireLqgkpeevamVGDgvn.DaaalaaA 209
                                     l  d   +  e +   +G + +  +   ++  e v+kpspe +  a++ ++++p++ am+GD +  D+ +++++
  gi|116753965|ref|YP_843083.1| 145 ALEMDRYwRESEGLVLSAGpFVAAlEYATGKRAELVGKPSPEFFSLALNDMGVNPQDAAMIGDDIItDVGGAQRV 219
                                    66666553455555555884222224444444455****************************998898887766 PP

>> PGP_phosphatase  Mitochondrial PGP phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00011      0.39     135     166 ..     198     229 ..     187     231 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00011
                PGP_phosphatase 135 eadeiavvgDRllTdvllanmmGslgvwlrdg 166
                                    ++++ a++gD  +Tdv  a+++G lg+++r g
  gi|116753965|ref|YP_843083.1| 198 NPQDAAMIGDDIITDVGGAQRVGMLGILVRTG 229
                                    68999**********************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1858.42
//
Query:       gi|116753966|ref|YP_843084.1|  [L=159]
Description: hypothetical protein Mthe_0654 [Methanosaeta thermophila PT]
Scores for complete 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   0.0    1.4e-14   54.5   0.0    1.1  1  CGI-121   Kinase binding protein CGI-121
  ------ inclusion threshold ------
       0.09   13.0   0.0       0.22   11.7   0.0    1.7  2  PABP      Poly-adenylate binding protein, unique domain


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 !   54.5   0.0   1.6e-18   1.4e-14      24     161 ..      27     154 ..      12     155 .. 0.87

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 1.6e-18
                                    EEE-GGG---HHHHHHHHHHHHHHHHHS---SSSHHHHHHHHHSSSS-HHHHHHHHB--TT-S-EEEEEEESSS--HHHH CS
                        CGI-121  24 afldaslilskehllsAvlrallaaargklktktlhsEilfsLspnnnIgealkrfgisdkttsllvvkvssseadeeev 103
                                      lda++++s+ h+  A+ +a+ a ++g+   k l  Eil + s++++I++al   g+sd  +++ +  v++    e+++
  gi|116753966|ref|YP_843084.1|  27 QALDAAMVVSERHVFYAAEKAIAAFQEGRNVAKDLGIEILRYASGQRQIEKALS-LGVSDAAERVALLIVDDL---EDDE 102
                                    679**************************************************9.*******99*99999877...3333 PP

                                    HHHHHHHS-SEEE--SHHHHHH--HHHHHHHTT--..TT---SSHHH.HHHHHHHHHHT CS
                        CGI-121 104 lkslkevvegelvpleeeleeltdwkkikkiYklneleeekeeevke.ledlvvsaval 161
                                           + g l+++++ l+   d ++++++Y ++  ++e e++ ++ + dlv+++val
  gi|116753966|ref|YP_843084.1| 103 ----VRRITGMLIEPDD-LGIRFDAERVRRFYDIS--DAEIEAAGEDrIPDLVLERVAL 154
                                    ....3457788899999.99999************..55666666666*********97 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 ?   -2.5   0.0       0.7   6.2e+03      50      66 ..      18      34 ..      13      35 .. 0.74
   2 ?   11.7   0.0   2.5e-05      0.22      24      44 ..      95     115 ..      71     121 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.7
                           PABP 50 llesdeeLrekveeAie 66
                                    l s+  L++  + A+ 
  gi|116753966|ref|YP_843084.1| 18 NLRSKGYLIQALDAAMV 34
                                   56788888888888886 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 2.5e-05
                           PABP  24 iqklnpelAgKITGMLLemdn 44 
                                    +  l+ + + +ITGML+e d 
  gi|116753966|ref|YP_843084.1|  95 VDDLEDDEVRRITGMLIEPDD 115
                                    5667888999********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1295.50
//
Query:       gi|116753967|ref|YP_843085.1|  [L=198]
Description: hypothetical protein Mthe_0655 [Methanosaeta thermophila PT]
Scores for complete 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-66  223.5   0.8    2.5e-66  223.3   0.8    1.0  1  DUF2150        Uncharacterized protein conserved in archaea (
  ------ inclusion threshold ------
      0.023   12.8   0.2      0.029   12.5   0.2    1.0  1  Lant_dehydr_N  Lantibiotic dehydratase, N terminus


Domain annotation for each model (and alignments):
>> DUF2150  Uncharacterized protein conserved in archaea (DUF2150)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  223.3   0.8   2.7e-70   2.5e-66       1     188 []       4     189 ..       4     189 .. 0.99

  Alignments for each domain:
  == domain 1  score: 223.3 bits;  conditional E-value: 2.7e-70
                        DUF2150   1 eFYteeRwqNWlnrvkeedldleedseeleaavllnlqdDvilavlkiikaveeeelskeeAleeleevreivleeveed 80 
                                    eFYt++Rw NW+n+vke+++++ e+++++++av+++++dDvila+lk+++++e+++l+++eAle+++++r+iv +e+e+ 
  gi|116753967|ref|YP_843085.1|   4 EFYTQKRWLNWMNKVKESQFKFPESEQDAGGAVFVYIMDDVILACLKVLARLEKGMLTQDEALETIRSIRDIVSTEHESL 83 
                                    7*********************99999999************************************************** PP

                        DUF2150  81 deekeeliesvqtsllvvfaaaeeyieggvakekdieelvkaaaeaeaeedleaaleivaqiGakvidgeklpekvledl 160
                                     e+++ ++ s++tsl++vf+++++yi g+++k+++++e++++a++aeae+++e+al++v +iGa+vi+gek pe  + d+
  gi|116753967|ref|YP_843085.1|  84 GEDADLMLASLRTSLAAVFESCNSYILGDYDKDRRLDEMINEAVRAEAEGRIEDALAVVGNIGARVIAGEKPPE--IPDM 161
                                    **************************************************************************..69** PP

                        DUF2150 161 eyglvaewldgidslaaamsssesveee 188
                                    +y++vae+ldgid++aaam++++s++ee
  gi|116753967|ref|YP_843085.1| 162 DYCVVAELLDGIDAIAAAMVGDTSYKEE 189
                                    **************************97 PP

>> Lant_dehydr_N  Lantibiotic dehydratase, N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   3.2e-06     0.029     211     295 ..      50     140 ..      42     153 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.2e-06
                  Lant_dehydr_N 211 hllerL.eeipeaaellaelaalrdllarydaapegaaeaaleearrrmralsaaarrllqvDlrld.eaevvlpeeVlr 288
                                    ++l+rL + +  ++e+l++++ +rd +++  +   ++a++ l ++r++++a+ +++++++  D  +d   +  ++e+V++
  gi|116753967|ref|YP_843085.1|  50 KVLARLeKGMLTQDEALETIRSIRDIVSTEHESLGEDADLMLASLRTSLAAVFESCNSYILGDYDKDrRLDEMINEAVRA 129
                                    577888777889999************9888888777778************999************977777******* PP

                  Lant_dehydr_N 289 e....veraae 295
                                    e    +e+a+ 
  gi|116753967|ref|YP_843085.1| 130 EaegrIEDALA 140
                                    *5555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); 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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1535.36
//
Query:       gi|116753968|ref|YP_843086.1|  [L=287]
Description: methionine aminopeptidase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-41  142.2   0.0    5.3e-41  140.6   0.0    1.6  1  Peptidase_M24  Metallopeptidase family M24


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.6   0.0   2.9e-45   5.3e-41       2     209 .]       4     279 ..       3     279 .. 0.85

  Alignments for each domain:
  == domain 1  score: 140.6 bits;  conditional E-value: 2.9e-45
                                    HHHHHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBC..SSSB--TTEEEEE CS
                  Peptidase_M24   2 lirkaariasaaleavleaikpgvterelaaeieattlkrhgarglafppivasgenaavlhytp..ndrvlkegdlvli 79 
                                    ++r a+ri + +l ++ ++i  gv+   +a+ +e+t  +r+ ++++afp  + ++   +++hytp  nd+ +  +++v++
  gi|116753968|ref|YP_843086.1|   4 KYRTAGRILADVLGKASAKIDVGVSLLGVADYVENT--IREMGGEPAFP--CNISRDREAAHYTPkpNDDAVFGEEMVKL 79 
                                    79**************999***************99..5666689****..7788888888**887677778888***** PP

                                    EEEEEETTEEEEEEEEE.ECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTBCCGBSSCSEEEES CS
                  Peptidase_M24  80 dagaeydgyasDitrTv.lvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesaglakffphglGHgvG 158
                                    d+g+++dgy++D ++Tv l G  +p   el++a ++a++aai++v pGv++ ei++a++  +e  g+ k++ +++GHg+ 
  gi|116753968|ref|YP_843086.1|  80 DIGVHVDGYIADAAVTVdLSG--HP---ELVDASRAALDAAIELVGPGVSTCEIGRAIESAIEGFGF-KPVSNLTGHGLS 153
                                    *****************8899..66...6**********************************99**.************ PP

                                    S.SSSEEEEEESSSTT..CSSB--TTBEEEEEE.......EEEEETTT................................ CS
                  Peptidase_M24 159 l.evhdegpsvsresn..dgrkleeGmvftiEp.......giyfapge................................ 196
                                    + + h e p+v++ ++  +g++l++G+v++iEp                                               
  gi|116753968|ref|YP_843086.1| 154 RfNAHTE-PTVPN-RSctSGVELRPGDVIAIEPfatngsgR------Isdaplveifgltsrrpvrdrrarallseietr 225
                                    99****9.**986.335799*************66664441......033344444555555666667777777777888 PP

                                    .........................................EEEEEBEEEEEES CS
                  Peptidase_M24 197 .........................................ggvriedtvlvte 209
                                                                              + + e+tv+vte
  gi|116753968|ref|YP_843086.1| 226 fkglpfarrwlrgesidyslqrliragavhtypvlwevegaIVSQAEHTVIVTE 279
                                    888888888899999999999999999999999999999855999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2043.16
//
Query:       gi|116753969|ref|YP_843087.1|  [L=913]
Description: alanyl-tRNA synthetase [Methanosaeta thermophila PT]
Scores for 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-127  423.8   0.0   1.4e-126  423.2   0.0    1.2  1  tRNA-synt_2c  tRNA synthetases class II (A)
    9.4e-19   68.2   2.6      2e-18   67.1   2.6    1.5  1  DHHA1         DHHA1 domain
    3.5e-15   55.8   1.2    8.8e-15   54.5   1.2    1.8  1  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 !  423.2   0.0  2.3e-130  1.4e-126       2     551 ..      63     591 ..      62     592 .. 0.94

  Alignments for each domain:
  == domain 1  score: 423.2 bits;  conditional E-value: 2.3e-130
                                    HHHHHHHHHHCTT-EEE----SS-SSSTTCSS--SGGGGGHHHHTTSSCGGSSSEEEEEEEEE-EETTEEGGGGTTTSSS CS
                   tRNA-synt_2c   2 irekFldfFekkgHtvvksssvvpendptllfvnAgmaqfkpiflgkeakpklkravnsQkciRagGkhnDlenVGktar 81 
                                    +re++l+fFe++gHt+v++++vv+++++++++++A++a+f+p++++++  p+++++++sQ+ciR++    Dl++VG+ +r
  gi|116753969|ref|YP_843087.1|  63 MREHYLSFFEAHGHTRVQRYPVVARWRDDIYLTIASIADFQPFVTSGQVPPPANPLTISQPCIRLD----DLDSVGRSGR 138
                                    9*****************************************************************....********** PP

                                    --SEEEEEEEEESS.....SS-HHHHHHHHHHHHHTTTT--GGGEEEEEETTEH..HHHHHHHHTTTTEGGGEEEE-HH. CS
                   tRNA-synt_2c  82 HhTfFeMlGnfsfg.....dYfkeeaiefawelltkelgldkerlyvtvfeedd..eaveiweklvgvpeerilrfgek. 153
                                    H+T FeM++++ f+     +Y+k+ ++e++ ell   lg+d+e+++++++++++  +a++  e lvg+ e ++l+f ++ 
  gi|116753969|ref|YP_843087.1| 139 HLTTFEMMAHHVFNtkeheIYWKDRTVELCDELLL-GLGVDPESITYKESPWAGggNAGPSLEVLVGGLELATLVF-MNl 216
                                    ***********************************.9****************999*****************999.553 PP

                                    .....HHEEESSSSEEEEEEEEEEEECETTSHHCHCCCCTTCTCCHEEEEEEEEEEEEEEST....TSHEEEEEEEEEEE CS
                   tRNA-synt_2c 154 .....dnfwemgdtgpcgpcseiyydrgeeigkrkaaseveadddrvleiwnlvfmqfnree....dgtlkpLpkksidt 224
                                          ++   g+ +  ++++++++++g e++++++++ ++++d+ + +i+  +   +++e+     +  ++ +++++ +
  gi|116753969|ref|YP_843087.1| 217 rldssGEYVIKGERYSRMDNYIVDTGYGLERFVWASKGSPTIYDAVFPDIVRELSDLAGVEHdlhdPEYAEIFARNARLA 296
                                    44444677777888*****************************************999999966656778999******* PP

                                    EEEHHHHHHHHTTHSSGGGSCCTHHHHHHHHHHHT--TCSTCCHHHHHHHHHHHHHHHHHHHHTT--SSSSHHHHHHHHH CS
                   tRNA-synt_2c 225 GmglerlvavLqevrsnydtdlfvpvieaieeisgatyedkdetdealrviaDHvralafaladGvvpsnegrgYvlRrl 304
                                    Gm +    a L+++r++ ++++ ++ + +++ +++         +e++++iaDH+r+la++l+dG++psn+++gY++R++
  gi|116753969|ref|YP_843087.1| 297 GMIDLG-EASLRDLRKRIAESINTTPERLERIMAP---------MERIYAIADHTRCLAYMLGDGIIPSNVKAGYLARLV 366
                                    **9876.567***********************99.........89********************************** PP

                                    HHHHHHHHHHTT-SSTHHHHHHHHHHHHHTTTGCCHHCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCC.CSEEX CS
                   tRNA-synt_2c 305 lRravrhakkLglkekflaklvavvvevlgdvypelkekeekveeiieeEeerFakTlerGlklleelikklkk.kkels 383
                                    +Rr++r++k+L+l+ + l+++v+++++ l+  y + +e+ e+++ei++ Eeer+a+Tle+G++++++ +++ +k +  ++
  gi|116753969|ref|YP_843087.1| 367 IRRTLRMMKDLKLEIP-LSEIVEMQISKLD--YDDWRERMETISEILSLEEERYAETLEKGSRMVSKIASHYSKkGGRIP 443
                                    ****************.************9..**************************************9988799*** PP

                                    HHHHHHHHHCHXXXHHHHHHHHHCTTXEEXHHHHHHHHHHHHHHHCCHHSXSSXXXXXXXXTTSHCHHCCTSTTTXXXXX CS
                   tRNA-synt_2c 384 gedafkLydtyGfPvdltkeiaeekglkvdiegfekameeqrerskkekkekklikkdvealkelkkteeflgyeeleae 463
                                    + ++  Lydt+G+P+++ +e a   g++v+ ++++++ +++ ++  +e++e +      +    ++kte  ++y      
  gi|116753969|ref|YP_843087.1| 444 LTELVSLYDTHGIPPEIARETAGALGVDVELPDNFYSIVASTHSR-AEQREVE------TRSPPFEKTERLFYYRP---- 512
                                    ***************************************998877.3333333......46677788888777776.... PP

                                    XTSXXXXXXSEEEEEEEEEETTEEEESEEXXXXSSSSCSXXXEEEEESSEEEEESEEEEETTEEEEEXSS.XSXXXTTSE CS
                   tRNA-synt_2c 464 akvlallkdkefveeveegeevgvvLdrTpfYaesGGqigDeGliekegaefrvkdvqkakgvvlhkgkleegklkvgdk 543
                                            d+ef + v  + e+ vvLdrT fY+e+GGq +D+G++  +g+ f+v+dvq ++gvvlh+++ e   l+ gd+
  gi|116753969|ref|YP_843087.1| 513 -------FDQEFDATVLGIFEGSVVLDRTLFYPEGGGQPADRGVLVRDGQVFNVNDVQMIDGVVLHRVEQE--GLSPGDR 583
                                    .......589********************************************************99986..9****** PP

                                    EEEEEXHH CS
                   tRNA-synt_2c 544 vkaevdee 551
                                    v++++d +
  gi|116753969|ref|YP_843087.1| 584 VTGRIDMR 591
                                    ******76 PP

>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.1   2.6   3.4e-22     2e-18       3     132 ..     771     901 ..     769     905 .. 0.95

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 3.4e-22
                                    HHCHHHHHHHHHHHCHHHHHHHHHHHHHHHTCEEECTCEEEEEECHCCHHHHHHHHHHHHHHTHGBTTCEEEEEEEECT. CS
                          DHHA1   3 slneerkelekeleelkealaklkaeellekaeevkgvkvlvaevgeewdagalgiaadklksklkkpvivfvakeegd. 81 
                                    ++ ee+k+ +k +e lke++a + + +l ++a +v+gv++++  +  e d  +l  aa++l +   + ++++  + +g  
  gi|116753969|ref|YP_843087.1| 771 RFFEEWKDQQKVIEHLKEEIAGIRILTLSSEAVDVNGVSIVARDM-GESDGETLLKAATMLSE--RDITAILGGASGGAa 847
                                    6789*****************************************.999**************..889999999999999 PP

                                    EEEEEEEESSH..SS-HHHHHHHHHHHTTCCEEEE.TCEEEEEEEHCHHHHHHH CS
                          DHHA1  82 kvkvsarskkd..gvdagelakeaaaklgggGGGH.dlAaGagipaekleeale 132
                                    k+ vs++ ++   g++a++++++aa+ +gggGGG+ dlA+G+g + + l +a++
  gi|116753969|ref|YP_843087.1| 848 KIVVSVGRSGLerGLNAADIVRAAAKYIGGGGGGKpDLAQGGGPNVGGLRAAID 901
                                    ********988**********************************999888886 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 !   54.5   1.2   1.5e-18   8.8e-15       1      44 []     691     733 ..     691     733 .. 0.98

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 1.5e-18
                                    EEEEEETT.EEEEESS---SBGGGC-SEEEECCECCCTCEEEEE CS
                       tRNA_SAD   1 vrvvsiGdisvelCgGtHvpnTgeIgafkilseesiakglrRIy 44 
                                    +rvv++G+ ++e+C GtHv nTg+Ig +kil+ e++++g+ RI+
  gi|116753969|ref|YP_843087.1| 691 IRVVRVGS-DIEACAGTHVTNTGMIGPIKILRTERVQDGVERIE 733
                                    7******8.**********************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (913 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.68u 0.31s 00:00:00.99 Elapsed: 00:00:00.47
# Mc/sec: 5847.03
//
Query:       gi|116753970|ref|YP_843088.1|  [L=89]
Description: hypothetical protein Mthe_0658 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-10   41.3   0.2    2.3e-10   41.0   0.2    1.1  1  MJ1316    MJ1316 RNA cyclic group end recognition domain


Domain annotation for each model (and alignments):
>> MJ1316  MJ1316 RNA cyclic group end recognition domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   0.2   1.3e-14   2.3e-10       4      76 .]      12      82 ..      10      82 .. 0.86

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 1.3e-14
                         MJ1316  4 aqdvlnRirWdkeldkskfvvgyldR..fkgikevpleeiswied.flleeeegelaIPlHRiryikrkgevvWdR 76
                                    +++ln ++W   +d s++++ +l+R  +++ ++ +++ei   +  f++ ++     IP+HRi++i +kg+ v++R
  gi|116753970|ref|YP_843088.1| 12 PKHILNEMKWR-GFDLSDVEIEILHRgaPSNRIHARASEIALGRSfFTYMGT----DIPYHRIEKIVYKGRTVFSR 82
                                   5789******7.57************99999999999999998884444444....4*****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 656.63
//
Query:       gi|116753971|ref|YP_843089.1|  [L=487]
Description: DNA polymerase II small subunit [Methanosaeta thermophila PT]
Scores for complete 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   43.8   0.0    2.6e-11   43.3   0.0    1.2  1  DNA_pol_E_B      DNA polymerase alpha/epsilon subunit B
      5e-08   33.7   0.1    7.8e-08   33.1   0.1    1.3  1  Metallophos      Calcineurin-like phosphoesterase
    1.6e-07   31.7   0.0    3.8e-07   30.4   0.0    1.6  1  Metallophos_2    Calcineurin-like phosphoesterase superfamily
    4.7e-06   26.5   0.1    1.1e-05   25.3   0.1    1.7  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
  ------ inclusion threshold ------
       0.14   12.2   0.0       0.25   11.4   0.0    1.3  1  Frankia_peptide  Ribosomally synthesized peptide prototyped b


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 !   43.3   0.0   7.2e-15   2.6e-11       3     203 ..     235     431 ..     233     435 .. 0.85

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 7.2e-15
                                    EEES--S-TT---...-HHHHHHHHHHH...HTT--SEEEEES-SSBTTSHHHHHT---S--SSHHHHHHHHTHHHHTTS CS
                    DNA_pol_E_B   3 ivsglnldndnrs...leaLrkiLqgya..peesppdvlilaGnfvdaahkaiasskvstdekkenfdalalllsilesl 77 
                                    ++s+l++ ++++     + +  +++g +     s + ++++aG  vd      ++++  + e k+  +  +l  + ++++
  gi|116753971|ref|YP_843089.1| 235 FLSDLHVGSNKFLmdtWNRFVSWISGEDptGLSSDVGCIVIAGDIVDGIGVYPGQED--ELEIKDIYEQYQLAADLISQI 312
                                    7888999877777444455556666666777789999**********5555554443..468999999999999999999 PP

                                    -TTSEEEEE--TTBTT-S-SBSB----TTTTT--TTT...EEE--BSEEEEETTEEEEE--S-HHHH---EEESHHHHHS CS
                    DNA_pol_E_B  78 lekttvvlvPgpnDpanstvlPqqPlprlllsrikrvfkelklvtNPsrielnsvevvltsddivkdlkreslkesntdv 157
                                     + +++v+ Pg  D + + + Pq++lp+ + s    +   + +v NPs+i++ s  v+++ +  ++d+  ++   s    
  gi|116753971|ref|YP_843089.1| 313 PSWVKIVISPGNHDIVRQ-AEPQPALPKEIQSLFPGN---VMFVGNPSWITISSRPVLIYHGRSIDDFVLKIPGLSY--- 385
                                    999***************.********9988888887...99***************************99999999... PP

                                    -HHHHHHHHHHHHTBS---SS--B-GGGGGGGB-GGG---SEEE-- CS
                    DNA_pol_E_B 158 erlrklvktildqrhlaPlaptlrpvswdkddalvleplPdvlvlp 203
                                     + + ++  +l+ rhl+P++   ++v  +  d +v+++ P +l ++
  gi|116753971|ref|YP_843089.1| 386 REPELAMVEMLRRRHLCPIYGNRVSVAPEAEDHYVIDKPPAILHCG 431
                                    5777777889**************************999*999887 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.1   2.2e-11   7.8e-08       4     203 ..     234     435 ..     233     436 .. 0.67

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 2.2e-11
                                    EEEESBTBTTCCTHHHHHHHHHHHHHHH......TTESEEEEESTSSSSS.................HHHHHHHHHHHHH CS
                    Metallophos   4 lvigDlHlalgggqlddllkllddllre......ekpdlvllaGDlvdrg.................dlekellellaal 60 
                                    l+++DlH+ +    +d+ +++++++  e      +++  +++aGD+vd+                  +  +  ++l+++ 
  gi|116753971|ref|YP_843089.1| 234 LFLSDLHVGSNKFLMDTWNRFVSWISGEdptglsSDVGCIVIAGDIVDGIgvypgqedeleikdiyeQ-YQLAADLISQI 312
                                    789****75555666666666666644433445558899999*******9899999999888865532.22244444444 PP

                                    HHHTSEEEEEC-TTS..CHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESECEEETHHHHHHHHHH CS
                    Metallophos  61 vkypipvylllGNHe..gfeeellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGgspellvsldklgsln 138
                                     +  +++++ +GNH+        +++ +  ++ + ++  ++ +++n+  + + s    vl++hG s+++  ++ k+ +l+
  gi|116753971|ref|YP_843089.1| 313 PS-WVKIVISPGNHDivR---QAEPQPALPKEIQSLFPGNVMFVGNPSWITISSR--PVLIYHGRSIDD--FVLKIPGLS 384
                                    44.4778********430...3444444444445555555555555555555556..888999988777..888888888 PP

                                    HSCHHHHCCHHHHHHHHHHTTCSEEEEEESSESSCSSSCSCCHHHHHHHHHHTTESEEEEESSSS CS
                    Metallophos 139 leleapepgdewlkdlekrekadwvivlgHsplyrgsgylfgdealedllkkygvdlvisGHtHv 203
                                    ++ ++     e+l++             +  p+y g+  + ++ea + +  ++ + +  +GH+Hv
  gi|116753971|ref|YP_843089.1| 385 YREPELAM-VEMLRR------------RHLCPIY-GNRVSVAPEAEDHYVIDKPPAILHCGHVHV 435
                                    88887777.777777............6677888.888888888888886666667767799996 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 !   30.4   0.0   1.1e-10   3.8e-07       4     149 ..     234     455 ..     233     465 .. 0.73

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 1.1e-10
                  Metallophos_2   4 aiiSDlH..snldaleav..............lealkevgvdaiihaGD....................leeeepevlee 47 
                                    +++SDlH  sn ++ +++              l+      v  i+ aGD                    +  e+ +  ++
  gi|116753971|ref|YP_843089.1| 234 LFLSDLHvgSNKFLMDTWnrfvswisgedptgLSSD----VGCIVIAGDivdgigvypgqedeleikdiY--EQYQLAAD 307
                                    578999999888888888888888998885444443....566******666666655555555544422..33356777 PP

                  Metallophos_2  48 llela....pvlaVrGNnD.......eev.veedvlreaaelgtdlpeeaelelagekvlliHgdpl............. 102
                                    l+++     ++++ +GN+D       +   + ++++  + +    + +  ++++  + vl++Hg                
  gi|116753971|ref|YP_843089.1| 308 LISQIpswvKIVISPGNHDivrqaepQ-PaLPKEIQSLFPGNVMFVGNPSWITISSRPVLIYHGRSIddfvlkipglsyr 386
                                    77777887799999*****77655422.245556666666666666888889999999******977************* PP

                  Metallophos_2 103 ........................gvkdalaellkeaeegsdvvvcGHtHvpevekeggvlvvnPGsvgep 149
                                                             +++a ++ +   +++ +++ cGH Hv ++++ +gv+++n G  +++
  gi|116753971|ref|YP_843089.1| 387 epelamvemlrrrhlcpiygnrvsVAPEAEDHYVI--DKPPAILHCGHVHVVGITRYKGVTLINSGTWQGQ 455
                                    99999999999999999886665322333333333..47888************************98877 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 !   25.3   0.1   3.2e-09   1.1e-05       1      57 [.     147     202 ..     147     218 .. 0.94

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 3.2e-09
                                    EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET.HHHHHHHTTS-TTSEEEEEEE CS
                tRNA_anti-codon   1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfr.eeatklaenlkeGdvvrvtGr 57 
                                    V+v G+v++i  r+++++  ++l+D tg+++v + r + a++    l  + vv++tG+
  gi|116753971|ref|YP_843089.1| 147 VSVIGMVMAI--RNTSRARVVELEDPTGMVTVLFARdSPAYEDSMLLVTDEVVGITGT 202
                                    89********..************************8889999999***********8 PP

>> Frankia_peptide  Ribosomally synthesized peptide prototyped by Frankia Franean1_4349.
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   6.9e-05      0.25      26      60 ..       7      41 ..       3      43 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.9e-05
                Frankia_peptide 26 avkeagYdltpeElqalekadadsleavalglder 60
                                   + +e gY+ltpe l+ l k d+ s + +   ld++
  gi|116753971|ref|YP_843089.1|  7 MFAERGYQLTPEALEILSKKDTVSIDHLISSLDAS 41
                                   6689******************9999999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (487 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 3605.21
//
Query:       gi|116753972|ref|YP_843090.1|  [L=219]
Description: signal sequence peptidase [Methanosaeta thermophila PT]
Scores for complete 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   20.5   0.1    0.00068   19.6   0.1    1.5  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 !   19.6   0.1   3.8e-08   0.00068       2      39 ..      12      66 ..      11      74 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.8e-08
                                   XXSSTTCCTXXTTXEEEEECTS.................---TTSEEEEEETTCE CS
                  Peptidase_S24  2 vpGdSMeptlldGdlilVdkfs.................epkrGdivvfrlpgee 39
                                   v+++SM p +++Gd+i+V   s                   ++Gd++  r  g+e
  gi|116753972|ref|YP_843090.1| 12 VESGSMVPNMNIGDIIIVQGISrtdvitweegkargyrsFNNPGDVILYRPYGKE 66
                                   89*****************777788999999999999988889999988877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       224  (0.0124937); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1687.85
//
Query:       gi|116753973|ref|YP_843091.1|  [L=212]
Description: fibrillarin [Methanosaeta thermophila PT]
Scores for 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-62  208.5   0.0    7.6e-62  208.4   0.0    1.0  1  Fibrillarin      Fibrillarin
  ------ inclusion threshold ------
      0.047   13.7   0.0      0.081   12.9   0.0    1.5  1  Methyltransf_17  S-adenosyl-L-methionine methyltransferase


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 !  208.4   0.0   8.5e-66   7.6e-62       5     223 ..       3     209 ..       1     212 [] 0.93

  Alignments for each domain:
  == domain 1  score: 208.4 bits;  conditional E-value: 8.5e-66
                                    CSSTTEEEEETTSSEEEEEE-SSTT--SSSSEEEEETTEEEEEE-TTTSHHHHHHHTT-S--S--TTSEEEEESTTTSHH CS
                    Fibrillarin   5 eklegvyivkekgdarlatknlvpgekvYgEklikveeeEyRvWnpfrsKlaaailkglkelpikkgskvLYlGaasGtt 84 
                                    e l g+yi++ +   rlat    + e  YgEk+++      RvW+p+rsKlaa +l+      + +  kvLYlGaa Gtt
  gi|116753973|ref|YP_843091.1|   3 EILPGLYILRRD---RLATSP-PSQEPLYGEKIVD----GLRVWDPRRSKLAALLLRYPCLEGVVPSGKVLYLGAANGTT 74 
                                    566788888754...577755.456789*****97....58***************9988889999************** PP

                                    HHHHHHHHTTTSEEEEEESSHHHHHHHHHHHTTSTTEEEEES-TTSGGGGTTTS--EEEEEEESSSTTHHHHHHHHHHHH CS
                    Fibrillarin  85 vsHvsDivgeegvvyavefsprvlrelievakkRknivPileDArkPekYralvekvDvifaDvaqpdqarilaknaklf 164
                                    vs++ Di++  g++yave spr++r+l+ +a++R+ni+P+l+DA +Pe+Yr +ve vD++++Dvaq +qa+i+ +na+++
  gi|116753973|ref|YP_843091.1|  75 VSYLGDILT-GGMIYAVEISPRAMRDLLLLAEQRENIIPVLGDAARPETYRRIVEPVDLLYQDVAQRNQAEIASRNASIY 153
                                    ********9.9********************************************************************* PP

                                    EEEEEEEEEEEEHHHHHSSSSHHHHHHHHHHHHHHTTEEEEEEEE-TTTSTTEEEEEEE CS
                    Fibrillarin 165 lkeggyllisikarsidvtkepeevfkeeveklkeeglkvleqvklepyekdhalvvgk 223
                                    lk +g ++++ikarsid+t++++e+f ee+++l+  g++vl  v+l p+++dh++vv++
  gi|116753973|ref|YP_843091.1| 154 LKPNGLMVVMIKARSIDSTARSTEIFDEEIRRLS--GVEVLRRVDL-PHHRDHVAVVAR 209
                                    *******************************995..789******9.99********97 PP

>> Methyltransf_17  S-adenosyl-L-methionine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     9e-06     0.081      28      67 ..      60      99 ..      48     169 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9e-06
                                   --S-EEEE--TTSHHHHHHHHH--SS-EEEEESS--S-GG CS
                Methyltransf_17 28 ieGpvlelGLGnGRtydhlrellperriivfdralaahps 67
                                   ++G+vl lG  nG t ++l ++l++  i++++   +a  +
  gi|116753973|ref|YP_843091.1| 60 PSGKVLYLGAANGTTVSYLGDILTGGMIYAVEISPRAMRD 99
                                   68****************************9976655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1564.36
//
Query:       gi|116753974|ref|YP_843092.1|  [L=140]
Description: nickel responsive regulator [Methanosaeta thermophila PT]
Scores for complete 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-34  116.7   3.2    5.7e-34  116.1   3.2    1.3  1  NikR_C           NikR C terminal nickel binding domain
      8e-10   38.3   0.1    1.9e-09   37.1   0.1    1.6  1  RHH_1            Ribbon-helix-helix protein, copG family
     0.0043   17.2   0.0     0.0078   16.3   0.0    1.4  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit
  ------ inclusion threshold ------
      0.096   12.9   0.0       0.14   12.3   0.0    1.4  1  RHH_8            Ribbon-Helix-Helix transcriptional regulator


Domain annotation for each model (and alignments):
>> NikR_C  NikR C terminal nickel binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.1   3.2   1.3e-37   5.7e-34       1      77 []      58     134 ..      58     134 .. 0.99

  Alignments for each domain:
  == domain 1  score: 116.1 bits;  conditional E-value: 1.3e-37
                                    EEEEEEEEETTSTTHHHHHHHHHHHHSSEEEEEEEEEESSSEEEEEEEEEE-HHHHHHHHHHHHTSTTEEEEEEEEE CS
                         NikR_C   1 vGvitivydhhqrelserltdiqheyhdliisslhvhldhdncLevivlkGeaeeikelaeklralkgVkhvkltli 77 
                                    vGvitivy hhqr+l ++ltdiqhe+  +i sslhvhld+dncLev++l+Ge++++++ ae+++alkgVkhvklt++
  gi|116753974|ref|YP_843092.1|  58 VGVITIVYSHHQRGLVDSLTDIQHEFGSIINSSLHVHLDKDNCLEVVILRGEGKDVRRAAERMMALKGVKHVKLTTT 134
                                    7**************************************************************************86 PP

>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.1   4.3e-13   1.9e-09       1      37 [.       7      44 ..       7      45 .. 0.97

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 4.3e-13
                                   EEEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHHHHH CS
                          RHH_1  1 rvsirldeellerLdelarrrg.rSrSelIReAlreyl 37
                                   r+ ++l+e+ll r+de++  rg +SrSe IR+A+r+y+
  gi|116753974|ref|YP_843092.1|  7 RIGVSLPEKLLSRFDEIISQRGySSRSEGIRDAIRNYI 44
                                   899**********************************7 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 !   16.3   0.0   1.7e-06    0.0078      87     117 ..       3      34 ..       1      39 [. 0.86

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.7e-06
                HicB_lk_antitox  87 gkaeriNitlpervlkriDaavkaag.esRSg 117
                                    ++  ri ++lpe++l+r D++++++g +sRS 
  gi|116753974|ref|YP_843092.1|   3 QELMRIGVSLPEKLLSRFDEIISQRGySSRSE 34 
                                    56789*********************669997 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 ?   12.3   0.0   3.2e-05      0.14      13      46 ..      15      48 ..       3      82 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.2e-05
                          RHH_8 13 vDLgqiDlLveeGfYsnRtDlirtairaqLakhd 46
                                     L++ D ++ +  Ys+R++ ir air+ + +++
  gi|116753974|ref|YP_843092.1| 15 KLLSRFDEIISQRGYSSRSEGIRDAIRNYIIHYE 48
                                   55889999999999**************987664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1018.48
//
Query:       gi|116753975|ref|YP_843093.1|  [L=186]
Description: hypothetical protein Mthe_0663 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.21   10.7   0.0       0.31   10.1   0.0    1.2  1  BPL_N     Biotin-protein ligase, N terminal


Domain annotation for each model (and alignments):
>> BPL_N  Biotin-protein ligase, N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   1.7e-05      0.31      32      85 ..      24      79 ..      16      83 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 1.7e-05
                          BPL_N 32 avqtvsakvllkePWastcallVlPgG.aDlpYvreln..gegnrkikeyVekGGky 85
                                   +vq +++++l   P      +l++P G a+  Y r+l+  ++  + i+++V++GG  
  gi|116753975|ref|YP_843093.1| 24 DVQFIKPEMLC-SPFLPRFRALIIPTGfANQQYSRALRnlRACKEGIENFVRSGGVI 79
                                   57777777776.588999999****886899******977788999*********76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 1264.56
//
Query:       gi|116753976|ref|YP_843094.1|  [L=66]
Description: hypothetical protein Mthe_0664 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); 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: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 469.31
//
Query:       gi|116753977|ref|YP_843095.1|  [L=380]
Description: hypothetical protein Mthe_0665 [Methanosaeta thermophila PT]
Scores for 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-119  397.0  31.4   1.3e-118  396.4  31.4    1.2  1  DUF1646     Protein of unknown function (DUF1646)
  ------ inclusion threshold ------
       0.14   12.6   0.0       0.28   11.6   0.0    1.4  1  Phage_Gp19  Phage protein Gp19/Gp15/Gp42
        2.4    8.8   9.3       0.38   11.4   0.3    3.2  3  DUF2645     Protein of unknown function (DUF2645)
        5.6    6.8   5.0        2.6    7.9   0.6    2.7  2  DDDD        Putative mitochondrial precursor protein


Domain annotation for each model (and alignments):
>> DUF1646  Protein of unknown function (DUF1646)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  396.4  31.4  2.9e-122  1.3e-118       4     347 .]      12     372 ..      10     372 .. 0.90

  Alignments for each domain:
  == domain 1  score: 396.4 bits;  conditional E-value: 2.9e-122
                        DUF1646   4 llvilvlvlilPlvvrkveenlelfllimgvaavtvsglfslelliealktplaile........vg.....aipigitq 70 
                                    l++i+++vl+ P++vrk+e+nle+fl++mgv avt+sg  s e+l + + ++  ++e        v+     +i  gi+ 
  gi|116753977|ref|YP_843095.1|  12 LFAIVLIVLVGPFMVRKIEHNLEAFLFVMGVLAVTLSGFESKEVLEHLYANNPEMVEkigwhmelVMeavkePIIKGIVP 91 
                                    78999**********************************77777766665432222222222223111111134459*** PP

                        DUF1646  71 avllaGlvfellkkklksllaevldklalkvfvfllivilGlassvisaivaavilaeivallplerkekvklvviasfa 150
                                    avl+aGl+f++ +   +  +a+ l+ ++lkv+vfl++vilGl+ss+i+ai+a+++l+e+v+++pl+r++k+++v+ia+f+
  gi|116753977|ref|YP_843095.1|  92 AVLVAGLLFHYGRATAQRAMARILEVVPLKVIVFLMVVILGLSSSIITAIIASLLLVELVNCMPLDRQTKINVVIIACFS 171
                                    ******************************************************************************** PP

                        DUF1646 151 iGlGaaltPvGePlstiavskl.....nedflylidvlgeyiiiavlvlallaalslkrlskreelvevveyeeelkevl 225
                                    iGlGa ltPvGePlstia++kl     +++f++l++ l +yii++ l+++lla+++  + +k+       e++  l++v+
  gi|116753977|ref|YP_843095.1| 172 IGLGAVLTPVGEPLSTIAITKLqgppyHAGFFFLFNRLAVYIIPGCLAMGLLAMFFTGKAAKEA-CAVAAEEAAGLRDVF 250
                                    *********************955554589**************************99996555.5556789999***** PP

                        DUF1646 226 iravkvfvfilalellGegfkPlikayiaklkseilywvnlisavvdnatlaaaeisPelteeqirailmsllisGGlli 305
                                    +ra+kv++f++al llG g+k +i++y+  ++++ilywvn++sa++dnatl+aae+sP++   qi+a+lm+llisGG+li
  gi|116753977|ref|YP_843095.1| 251 VRALKVYIFVMALLLLGGGMKIVIDKYLLTIPPQILYWVNMVSAILDNATLTAAELSPSMEITQIQAVLMGLLISGGMLI 330
                                    ******************************************************************************** PP

                        DUF1646 306 PGniPnivsaGklkikskeWarvgvPlgiilliiyfivllvl 347
                                    PGniPni+saGkl+i+skeWar+gvPlg++l+++yfi ++++
  gi|116753977|ref|YP_843095.1| 331 PGNIPNIISAGKLNITSKEWARLGVPLGLVLMVLYFIWVFYI 372
                                    **************************************9986 PP

>> Phage_Gp19  Phage protein Gp19/Gp15/Gp42
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   6.3e-05      0.28      60     105 ..     299     355 ..     287     357 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.3e-05
                     Phage_Gp19  60 avltatdreP...mgqlSesalgysysgsalvsg........gklfikdselerLGl 105
                                    a lta++ +P   ++q     +g  +sg +l++g        gkl i+ +e++rLG+
  gi|116753977|ref|YP_843095.1| 299 ATLTAAELSPsmeITQIQAVLMGLLISGGMLIPGnipniisaGKLNITSKEWARLGV 355
                                    556777778865557777778999999*****************************8 PP

>> DUF2645  Protein of unknown function (DUF2645)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.2      0.07   3.1e+02      49      83 ..      11      45 ..       5      50 .. 0.78
   2 ?   -2.0   0.4       1.2   5.6e+03      20      20 ..     135     135 ..     105     172 .. 0.57
   3 ?   11.4   0.3   8.4e-05      0.38      60      96 ..     334     375 ..     284     376 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.07
                        DUF2645 49 dvaviaalllliPlllvlvkkklksaflvvialvi 83
                                    +++i+ ++l+ P+++  + + l+   +v+ +l++
  gi|116753977|ref|YP_843095.1| 11 GLFAIVLIVLVGPFMVRKIEHNLEAFLFVMGVLAV 45
                                   57899999******998888877777777777665 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.2
                        DUF2645  20 i 20 
                                    +
  gi|116753977|ref|YP_843095.1| 135 S 135
                                    1 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 8.4e-05
                        DUF2645  60 iPlll.....vlvkkklksaflvvialvillYiiWrFflRfa 96 
                                    iP ++      ++ k  +++ + + +++++lY+iW F++ f+
  gi|116753977|ref|YP_843095.1| 334 IPNIIsagklNITSKEWARLGVPLGLVLMVLYFIWVFYIPFH 375
                                    3443344444556677788888999999***********886 PP

>> DDDD  Putative mitochondrial precursor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.6   0.00057       2.6      28      61 ..       4      37 ..       1      43 [. 0.89
   2 ?   -1.0   0.3      0.35   1.5e+03      34      58 ..     120     143 ..      97     149 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00057
                           DDDD 28 kPkktpFgLlrvilvVipgllvGtliSknvAnlL 61
                                   +P+ +  gL++++l+V++g ++   i +n+ ++L
  gi|116753977|ref|YP_843095.1|  4 QPTPVDIGLFAIVLIVLVGPFMVRKIEHNLEAFL 37
                                   5666889***********************9998 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.35
                           DDDD  34 FgLlrvilvVipgllvGtliSknvA 58 
                                      ++  ++vVi+gl   + i   +A
  gi|116753977|ref|YP_843095.1| 120 LKVIVFLMVVILGLS-SSIITAIIA 143
                                    444555556666553.344455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       920  (0.0513135); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2800.83
//
Query:       gi|116753978|ref|YP_843096.1|  [L=362]
Description: hypothetical protein Mthe_0666 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00059   20.0   0.7     0.0018   18.5   0.7    1.8  1  NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosi
  ------ inclusion threshold ------
      0.057   13.2   0.0       0.11   12.3   0.0    1.4  1  DUF2807      Putative auto-transporter adhesin, head GIN doma


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 !   18.5   0.7     2e-07    0.0018       2      77 ..      75     149 ..      74     150 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2e-07
                    NPCBM_assoc   2 epGetvtltltvtndg.taaatnvslslsl.PeGWtvvevspasaa.slapGetveatvkVtppagaaaGdyevtakar 77 
                                    +pG+t  + + v n+g t  +  + +s ++   +W     + +s +  +++G +v+  ++Vtpp++a  Gdy+ +++a+
  gi|116753978|ref|YP_843096.1|  75 TPGKTLDYIVNVRNEGyTNVTATITVSPETcGMDWF----TWTSTEvFIPAGGEVSEPLQVTPPTNAMGGDYRFRVTAT 149
                                    677777777777777755555566777665466777....333333379************************999997 PP

>> DUF2807  Putative auto-transporter adhesin, head GIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.2e-05      0.11      44     127 ..     129     209 ..     124     212 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.2e-05
                                    EEEEE-TTTTSSB.EEEEEEES--SEEEEECCEEEEE-S-EEEEEEEEEEECSEEEEEEEEEEEEEEEEECCEEEEEEEE CS
                        DUF2807  44 LkirlekefestktlkvtvtvpnleelelsgsgsievegtlkadklelniagsgditlkldaeelsveasgsgdielsGt 123
                                    L++++ ++  + + ++++vt++   + + s+ ++++v+g    ++ e  i+gsg+++l+ d+++++  ++++ d+  sG+
  gi|116753978|ref|YP_843096.1| 129 LQVTPPTNAMGGD-YRFRVTATAPGAESSSDTEKFKVQG--YDYASETMISGSGQFQLSKDVRSMNSGIKSNKDVYFSGS 205
                                    6777777777777.8999999999999999999999999..788999999****************************** PP

                                    EEEE CS
                        DUF2807 124 adrl 127
                                    ++ l
  gi|116753978|ref|YP_843096.1| 206 VEAL 209
                                    9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2813.71
//
Query:       gi|116753979|ref|YP_843097.1|  [L=271]
Description: hypothetical protein Mthe_0667 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 2147.42
//
Query:       gi|116753980|ref|YP_843098.1|  [L=243]
Description: hypothetical protein Mthe_0668 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.035   14.4   0.1      0.087   13.1   0.1    1.6  1  DUF2850   Protein of unknown function (DUF2850)


Domain annotation for each model (and alignments):
>> DUF2850  Protein of unknown function (DUF2850)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   4.8e-06     0.087      10      67 ..      20      79 ..      18      84 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.8e-06
                        DUF2850 10 gvapYaaekltlsekGvvvngrlvsTsfefdGktl.eykvgseeyiyqllgeeks.qlkr 67
                                    +a+Y  ek t++  G    + ++sT++ + G++l e + gs+ +i + ++ e + ql+r
  gi|116753980|ref|YP_843098.1| 20 SAANYMYEKATIKGVGYKNVEMIISTQYGYAGAKLvEKESGSGNVIIERTELEAErQLNR 79
                                   589*************9999************9873667888888777666555557776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1854.84
//
Query:       gi|116753981|ref|YP_843099.1|  [L=314]
Description: hypothetical protein Mthe_0669 [Methanosaeta thermophila PT]
Scores for complete 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-73  246.3   0.0    3.1e-73  246.0   0.0    1.1  1  NRD1_2    NrpR regulatory domains NRD1 and 2
    1.1e-23   82.9   1.0    2.3e-23   81.9   0.6    1.8  2  HTH_12    Ribonuclease R winged-helix domain
     0.0095   15.7   0.6        3.3    7.6   0.1    3.5  3  HTH_IclR  IclR helix-turn-helix domain


Domain annotation for each model (and alignments):
>> NRD1_2  NrpR regulatory domains NRD1 and 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  246.0   0.0   5.1e-77   3.1e-73       1     237 [.      84     307 ..      84     308 .. 0.98

  Alignments for each domain:
  == domain 1  score: 246.0 bits;  conditional E-value: 5.1e-77
                                    ---HHHHHHHHHCC---BTTTTB-EEEEEEEEEEGGGHHHHHHHHHHHHHTT-SSSSEEEEEE-SSE........EEEEE CS
                         NRD1_2   1 vgfviskieelaykvtfdpetgkGkVivNlslidkedleealeilkeviksglsvsdrvkileegekelevpegkvgiat 80 
                                    +gfv++ iee+++++tfd ++  G+ ++N+slid++dle+alei++ v +sg+s +d+v++ ++++         ++i t
  gi|116753981|ref|YP_843099.1|  84 IGFVNTLIEEYMLRTTFDFAS--GDLVANISLIDRNDLERALEIMEMVAESGYS-GDLVRVHHKDDC--------AEIGT 152
                                    79***************9986..9*****************************6.9********999........***** PP

                                    E-CHHHHHHHHCTT--EEEEEEEEEEE-SS.-EEEEEEEESTT-SS-HHHHCGGG.........--SSSEEEEEEEEEET CS
                         NRD1_2  81 vCSitidgvLlknGIpvkpkyGGlleiedkepvrFtelIsYegtsidPlevfiskklTsvlevietgegkilAnlReipv 160
                                    vCSit+dg+Ll++GIpv+++++G+lei+++ep rF++lI+Y gtsidP+++f++++++ v++++++g+gk+lAn+Re+pv
  gi|116753981|ref|YP_843099.1| 153 VCSITVDGLLLRAGIPVNTTFAGVLEIRNGEPCRFSDLIAYAGTSIDPMRAFMARRIARVMDAVRSGSGKVLANVREVPV 232
                                    ******************************************************************************** PP

                                    TTHHHHHHHHHHH...T-TTEEEE--TT--BTTB---TTEEEEEEE-TTHHHHHHHHTT---EEEEEEEEEEGGGSE CS
                         NRD1_2 161 sarekveeileklkkagisgvleigepneevlgvpveeekvgivvvgGlnpiaalkeagikveikalsglidiselk 237
                                    sa e++ ++l+++  + i g +++g p+++vlg+pv +++vgi++++G+n+ +a+ e gi++++ ++s+li++ e++
  gi|116753981|ref|YP_843099.1| 233 SALEDAMRVLDRA--RSIVGRIAVGAPGDDVLGCPVAPGRVGIAICAGVNAPVAVAECGIRIRTCPISTLIPCGEMS 307
                                    ***********99..679999*****************************************************997 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 !   81.9   0.6   3.9e-27   2.3e-23       2      66 .]      11      75 ..      10      75 .. 0.99
   2 ?   -3.1   0.0       1.4   8.2e+03      42      53 ..     123     134 ..     121     137 .. 0.51

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 3.9e-27
                         HTH_12  2 eILkilaesdkpigakeiaeeLkkrgydigeravRyrLrkleergltrrvgyagreltEkGleeL 66
                                   eIL+++ae+++p+ga+ i + L  rgy++geravRy Lr+l+e g+trr gy+gr  t  Gl+eL
  gi|116753981|ref|YP_843099.1| 11 EILRVIAEAKRPVGARTISDMLSSRGYNLGERAVRYNLRILDELGFTRRYGYSGRIATSLGLKEL 75
                                   8**************************************************************98 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.4
                         HTH_12  42 leergltrrvgy 53 
                                    le ++++   gy
  gi|116753981|ref|YP_843099.1| 123 LEIMEMVAESGY 134
                                    444555555555 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 !    7.6   0.1   0.00055       3.3       4      26 ..       8      30 ..       7      33 .. 0.89
   2 !    4.1   0.0    0.0065        39       2      15 ..     119     132 ..     119     142 .. 0.89
   3 ?   -2.3   0.0       0.7   4.2e+03       4      17 ..     208     221 ..     206     230 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00055
                                   HHHHHHCT-CTTBSS-BHHHHHH CS
                       HTH_IclR  4 RalaiLdalaeapqeltlselAr 26
                                   + l+iL+ +aea ++++ + +++
  gi|116753981|ref|YP_843099.1|  8 KLLEILRVIAEAKRPVGARTISD 30
                                   789*************9999987 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0065
                                    HHHHHHHHCT-CTT CS
                       HTH_IclR   2 ldRalaiLdalaea 15 
                                    l+Ral+i++++ae 
  gi|116753981|ref|YP_843099.1| 119 LERALEIMEMVAES 132
                                    79*********997 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.7
                                    HHHHHHCT-CTTBS CS
                       HTH_IclR   4 RalaiLdalaeapq 17 
                                    R ++++da++++ +
  gi|116753981|ref|YP_843099.1| 208 RIARVMDAVRSGSG 221
                                    88999999987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2505.78
//
Query:       gi|116753982|ref|YP_843100.1|  [L=131]
Description: ribosomal protein S6e [Methanosaeta thermophila PT]
Scores for complete 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-43  147.9   0.0    1.5e-43  147.7   0.0    1.0  1  Ribosomal_S6e  Ribosomal protein S6e


Domain annotation for each model (and alignments):
>> Ribosomal_S6e  Ribosomal protein S6e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.7   0.0   8.6e-48   1.5e-43       2     124 ..      12     129 ..      11     130 .. 0.98

  Alignments for each domain:
  == domain 1  score: 147.7 bits;  conditional E-value: 8.6e-48
                                    EEEEEETTTTEEEEEE-CHHHCTTCTT-BSSEEEECCTTTSSSTS-EEEEEEEEETTC-BB-TTS-SSSEEEEEEETTSS CS
                  Ribosomal_S6e   2 klnisdpatgkqklievdekklrtligkrigeevdgdalGeelkgyvlkitggsdkqGfpmkqgvltpgrvrlLlskggv 81 
                                    +++isdp+tgk++++e+  k++ +ligk+ig+ v+gd+lG  l+gy + itggsd++Gfpm+ ++++ +r+rlLl++ gv
  gi|116753982|ref|YP_843100.1|  12 RVVISDPNTGKAYQVEL--KDAGKLIGKKIGDAVEGDLLG--LPGYAVTITGGSDRDGFPMRSDLPGMQRKRLLLAG-GV 86 
                                    79*************99..8899*****************..**********************************9.** PP

                                    SS-SSSSS-EEEEEEE-SB--SSEEEEEEEEEE--SS--TTTS CS
                  Ribosomal_S6e  82 gyrprrkGerkrksvrGcivsadisqlnlvivkkgekdieglt 124
                                    gyrpr kG ++rksv+G+++s +isq+n++i+++g+k+ie+l+
  gi|116753982|ref|YP_843100.1|  87 GYRPRVKGLKRRKSVCGREISPNISQINVKITEYGAKPIEELL 129
                                    *****************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 940.52
//
Query:       gi|116753983|ref|YP_843101.1|  [L=381]
Description: geranylgeranyl reductase [Methanosaeta thermophila PT]
Scores for complete 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   44.6   9.3    1.5e-09   37.6   1.3    2.9  2  FAD_binding_3   FAD binding domain
    1.5e-07   31.2   2.4    2.4e-07   30.5   2.4    1.5  1  FAD_oxidored    FAD dependent oxidoreductase
      4e-07   29.6   0.1    4.4e-06   26.1   0.1    2.1  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    8.2e-07   28.2   0.1      0.026   13.4   0.1    2.1  2  Trp_halogenase  Tryptophan halogenase
    3.1e-06   27.0   8.2     0.0079   15.8   1.6    2.4  2  DAO             FAD dependent oxidoreductase
      1e-05   24.8   0.6    1.8e-05   24.0   0.6    1.3  1  GIDA            Glucose inhibited division protein A
    1.1e-05   24.7   0.6    0.00048   19.3   0.1    2.3  2  Lycopene_cycl   Lycopene cyclase protein
    1.2e-05   24.3   0.6    1.6e-05   23.8   0.6    1.2  1  HI0933_like     HI0933-like protein
    1.9e-05   24.8   0.3    6.2e-05   23.2   0.3    1.9  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    3.4e-05   23.2   0.3    7.8e-05   22.1   0.3    1.6  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
    3.8e-05   23.0   0.6    8.6e-05   21.8   0.6    1.6  1  FAD_binding_2   FAD binding domain
    8.4e-05   23.1   0.3    0.00025   21.5   0.2    1.9  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    0.00018   20.9   1.2     0.0002   20.7   0.0    1.6  2  Thi4            Thi4 family
  ------ inclusion threshold ------
      0.019   14.3   0.3      0.027   13.7   0.3    1.2  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
      0.022   15.3   0.2        5.8    7.5   0.0    3.0  3  ATPgrasp_N      ATP-grasp N-terminal domain
       0.08   12.0   0.2       0.12   11.5   0.2    1.2  1  CoA_transf_3    CoA-transferase family III
       0.13   12.3   0.2         13    5.8   0.2    2.4  2  NAD_binding_9   FAD-NAD(P)-binding
       0.15   11.9   0.2       0.28   11.0   0.2    1.4  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 


Domain annotation for each model (and alignments):
>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   1.3   1.5e-12   1.5e-09       4     198 ..       3     187 ..       1     212 [. 0.78
   2 !    8.4   1.5    0.0011       1.1     281     308 ..     267     294 ..     261     311 .. 0.88

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 1.5e-12
                                    EEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEEEECCCC CS
                  FAD_binding_3   4 VlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradglnqrtmellrqlGledrilaegapnelmgealynelsdt 83 
                                    +++VGaGpaG ++a   ++ G +v+lve+r +     + +g+ ++  el r+l l d +l e+ ++   + +l+ +  ++
  gi|116753983|ref|YP_843101.1|   3 IIVVGAGPAGSTAAETAARLGADVILVERRMEIGSPVQCGGFIPEASEL-RDL-LPDAVLPETLVEIPERCILNRT--RI 78 
                                    78******************************99999*****9999985.554.6788888886666655555555..23 PP

                                    CEEEEEHH.CHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE-- CS
                  FAD_binding_3  84 pkaradle.lesspervtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrakYlvGaD 162
                                    ++  a        p +   +    ++r+L+++a+++g+q+  +te         g++  ++++++g +   +a+ ++GaD
  gi|116753983|ref|YP_843101.1|  79 QRLYAPSGrSAEFPVAGRCVDRRSFDRYLAHRAARAGAQLIVGTEAD-----VRGESIHLKGRREGII---DADIIIGAD 150
                                    222222221123344445678899****************9999865.....8899999999987765...********* PP

                                    GTT-HHHHHHTGG.EEEEEEEEEEEEEEEEEEC-SCC CS
                  FAD_binding_3 163 GgrStvrktlgie.fegeetvyeagvldvlfdadlsd 198
                                    G  S++++++g   + +++   e +++dv +d d ++
  gi|116753983|ref|YP_843101.1| 151 GPSSRIAEAIGAVqRDEPGICLEYEMVDVDIDRDAAE 187
                                    ***********87466777778899999999887663 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0011
                                    SEETTEEE-GGGTEEE-STTSHHHHHHH CS
                  FAD_binding_3 281 yrkgrvflaGDAaHihpPtgGqGlNtai 308
                                     ++gr +laGDAa  +  t G G+ +a+
  gi|116753983|ref|YP_843101.1| 267 IQSGRFLLAGDAAGHVMATSGGGVPLAM 294
                                    689**********999999999988887 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   2.4   2.4e-10   2.4e-07       2      35 ..       3      36 ..       2     140 .. 0.91

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 2.4e-10
                   FAD_oxidored  2 vvVvGGgpaGvaAAiaAaraGakvlLveergvlG 35
                                   ++VvG+gpaG +AA +Aar Ga v+Lve+r  +G
  gi|116753983|ref|YP_843101.1|  3 IIVVGAGPAGSTAAETAARLGADVILVERRMEIG 36
                                   89****************************9998 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.1   4.5e-09   4.4e-06       2      31 ..       2      31 ..       1      61 [. 0.87
   2 ?    0.9   0.0      0.22   2.2e+02     184     240 ..     102     155 ..      91     170 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 4.5e-09
                                   SEEEE--SHHHHHHHHHHHHHTS-EEEEET CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlvel 31
                                   +++v+G+GpAG +aa+t+a+ ga+v+lve+
  gi|116753983|ref|YP_843101.1|  2 RIIVVGAGPAGSTAAETAARLGADVILVER 31
                                   89**************************63 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.22
                                    HHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 184 elsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrps 240
                                    ++ ++l+++  + G ++ +gt++ +++g++   +++   +  idad ++ a G + +
  gi|116753983|ref|YP_843101.1| 102 SFDRYLAHRAARAGAQLIVGTEA-DVRGESI--HLKGRREGIIDADIIIGADGPSSR 155
                                    45666677777779999999999.8888875..788888888******999986655 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.1   2.6e-05     0.026       1      49 [.       2      48 ..       2      57 .. 0.75
   2 !   13.1   0.0   3.3e-05     0.033     151     279 ..      98     221 ..      78     309 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.6e-05
                                   EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-S.SS---SS-EE--THH CS
                 Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlvese.eigtvgvGeatipsi 49
                                   +i++vG+G+aG++aA + a+ +   ++v lve   eig      + ip+ 
  gi|116753983|ref|YP_843101.1|  2 RIIVVGAGPAGSTAAETAARLG---ADVILVERRmEIGSPVQCGGFIPEA 48
                                   69******************99...99****9742666544334555555 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 3.3e-05
                                    E-HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGGG-IIIIIIT---EEE-TTT-- CS
                 Trp_halogenase 151 ldaalyakfLrrvaearGvtrvegkvvevqldedgrveslrledgreveadlfiDcsGfrgllieqaLktgfedwsdvLl 230
                                    +d++ ++++L + a ++G + + g+ ++v    +g+  +l+   +  ++ad++i + G  +++ e  + +  +d   + l
  gi|116753983|ref|YP_843101.1|  98 VDRRSFDRYLAHRAARAGAQLIVGTEADV----RGESIHLKGRREGIIDADIIIGADGPSSRIAEA-IGAVQRDEPGICL 172
                                    79******************999988666....56667899999999************9997665.6888888888888 PP

                                    --EEEEEEEE--H---SSEEEEE-SSEEEEEEEETTEEEE.EEEE-TTTS CS
                 Trp_halogenase 231 tdrAlavqveseelvepytrataekaGWtWkiPLqhrlgn.Gyvyssaha 279
                                        + v+++++  +e y +      G  W iPL + + n G+ ++++++
  gi|116753983|ref|YP_843101.1| 173 EYEMVDVDIDRDA-AEMYFGERWAPGGYAWIIPLGDDIANvGVGVRRSYI 221
                                    8888888887765.89999999999*************999998888877 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   1.6   7.9e-06    0.0079       2      33 ..       3      36 ..       2      45 .. 0.91
   2 !   15.0   0.8   1.4e-05     0.014     110     227 ..      66     179 ..      38     303 .. 0.55

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.9e-06
                                   EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                            DAO  2 vviiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                                   ++++G+G +G+++A  +ar g  V+l+e++ ++g
  gi|116753983|ref|YP_843101.1|  3 IIVVGAGPAGSTAAETAARLGadVILVERRMEIG 36
                                   9****************9999*********8877 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.4e-05
                                    TTTEE.EEEHHHHHHHSTTSTTTSEEEEETTEEEE.EHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT CS
                            DAO 110 gldae.lldaeevrelepalpgllgalfypdtgqv.dpakltaalaraaealGveilegtevtgleeedgkvwgverttp 187
                                     ++++ +l++ ++++l+    +   +  +p +g++ d + + ++la++a+++G++++ gte+  ++ e++ ++g    + 
  gi|116753983|ref|YP_843101.1|  66 EIPERcILNRTRIQRLYA---PSGRSAEFPVAGRCvDRRSFDRYLAHRAARAGAQLIVGTEAD-VRGESIHLKGR--RE- 138
                                    456776899988999994...345556777777666***********************9985.43232222222..22. PP

                                    EEEEEEEEEEE--GGGHHHHHTTCTT..TSEEEEEEEEEEEE CS
                            DAO 188 gendaadavVnaaGawsdllgllkel..dlpispvrgqvlvl 227
                                    g++da d ++ a G+ s++++ ++ +  d p   +  +++ +
  gi|116753983|ref|YP_843101.1| 139 GIIDA-DIIIGADGPSSRIAEAIGAVqrDEPGICLEYEMVDV 179
                                    77544.66999*****99552221111223434445555555 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.6   1.8e-08   1.8e-05       2      31 ..       3      32 ..       2      44 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.8e-08
                                   EEEE-SSHHHHHHHHHHHHTT--EEEEES- CS
                           GIDA  2 viViGgGhAGceAAlaaarlGakvlLithk 31
                                   +iV+G+G AG+ AA +aarlGa+v+L+  +
  gi|116753983|ref|YP_843101.1|  3 IIVVGAGPAGSTAAETAARLGADVILVERR 32
                                   8*************************9544 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   4.8e-07   0.00048       2     149 ..       3     159 ..       2     190 .. 0.88
   2 ?    3.4   0.0     0.031        31     233     298 ..     248     318 ..     219     368 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 4.8e-07
                  Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlieaspsllfpnny.vWsdefedlga..............leecvehsWsgti 66 
                                    ++v+GaGpAg   A+    a+ g  v+l+e   ++  p +      e ++l                 e+c+  + +  +
  gi|116753983|ref|YP_843101.1|   3 IIVVGAGPAGSTAAETA--ARLGADVILVERRMEIGSPVQCgGFIPEASELRDllpdavlpetlveiPERCILNRTRIQR 80 
                                    79********9988888..************999999988888888888888899999*****9998899********** PP

                  Lycopene_cycl  67 vylddgkkillgraYgrvsskrlkeellerlvengvklleakvesveeeeageslvvleggr..kirarlvvdarglasl 144
                                    +y++ g++ +   a + v ++ + + l++r + +g++l  ++ + v+ e+       l+g r   i+a +++ a g +s+
  gi|116753983|ref|YP_843101.1|  81 LYAPSGRSAEFPVAGRCVDRRSFDRYLAHRAARAGAQLIVGTEADVRGESI-----HLKGRRegIIDADIIIGADG-PSS 154
                                    **********************************************99998.....8888887789********99.777 PP

                  Lycopene_cycl 145 kkarr 149
                                    + a +
  gi|116753983|ref|YP_843101.1| 155 RIAEA 159
                                    64443 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.031
                  Lycopene_cycl 233 kevveeEqgviPvtlggslprleqk.vlaiGaaaglvhPaTGYsvarslaeapllasaiaaalres.......s 298
                                     e+v   +g++P   gg ++ +++   l +G aag v  + G  v+ ++ + + +a  +aa+ ++        +
  gi|116753983|ref|YP_843101.1| 248 GEIVAVMRGIVPS--GGMPEIIQSGrFLLAGDAAGHVMATSGGGVPLAMVAGR-IAGEVAATHARGgdlnvytQ 318
                                    5777788999999..888777776568899******************98777.77777766664334444440 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.6   1.6e-08   1.6e-05       2      42 ..       2      42 ..       1      44 [. 0.91

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.6e-08
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHHHC CS
                    HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrKilis 42
                                   ++iv+G+G+AG  aA++aa+ g++V+l+e+  ++g+ ++  
  gi|116753983|ref|YP_843101.1|  2 RIIVVGAGPAGSTAAETAARLGADVILVERRMEIGSPVQCG 42
                                   69*******************************99877665 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   0.3   6.2e-08   6.2e-05       1      32 [.       5      36 ..       5      44 .. 0.95

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 6.2e-08
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSS CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlG 32
                                   +vGaG +G++aA ++a+ g+dv l+e+r  +G
  gi|116753983|ref|YP_843101.1|  5 VVGAGPAGSTAAETAARLGADVILVERRMEIG 36
                                   8***************************9998 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   0.3   7.8e-08   7.8e-05      30      62 ..       2      34 ..       1      48 [. 0.91

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 7.8e-08
                                   EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHH CS
                    AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrpa 62
                                   +++v+G+G aG  A++ta++lga+V +++ r++
  gi|116753983|ref|YP_843101.1|  2 RIIVVGAGPAGSTAAETAARLGADVILVERRME 34
                                   789*************************99987 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.6   8.6e-08   8.6e-05       2      36 ..       3      37 ..       2      46 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 8.6e-08
                                   EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                  FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36
                                   +iV+G+G AG +AA +aa+ G++v++ve   e g+
  gi|116753983|ref|YP_843101.1|  3 IIVVGAGPAGSTAAETAARLGADVILVERRMEIGS 37
                                   79**************************9877655 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.2   2.5e-07   0.00025       1      35 [.       2      36 ..       2      41 .. 0.93
   2 ?   -2.5   0.0       8.1     8e+03      14      46 ..     292     324 ..     288     330 .. 0.63

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.5e-07
                                   EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                      Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                   +++vvG+G  g  +A+++a+lg++V +ver+ ++ 
  gi|116753983|ref|YP_843101.1|  2 RIIVVGAGPAGSTAAETAARLGADVILVERRMEIG 36
                                   799****************************9887 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 8.1
                                    HHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHH CS
                      Pyr_redox  14 lAgalaelgkkVtvversdkllrllDeeaskil 46 
                                    lA ++ +++ +V   +++   l+++ + ++k+l
  gi|116753983|ref|YP_843101.1| 292 LAMVAGRIAGEVAATHARGGDLNVYTQRIEKEL 324
                                    566666666667666666666666666666655 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0     2e-07    0.0002      20      63 ..       3      45 ..       1      61 [. 0.92
   2 ?   -3.9   0.3       6.7   6.6e+03      16      29 ..     141     154 ..     139     161 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2e-07
                                   EEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTT CS
                           Thi4 20 vvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGql 63
                                   +++vGaG++G taa + a+  +  v+++er++ +G  +  GG +
  gi|116753983|ref|YP_843101.1|  3 IIVVGAGPAGSTAAETAARL-GADVILVERRMEIGSPVQCGGFI 45
                                   9***************9999.***************99999975 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 6.7
                                    TEEEEEEE--SHHH CS
                           Thi4  16 aesDvvivGaGssG 29 
                                    +++D++i   G+s 
  gi|116753983|ref|YP_843101.1| 141 IDADIIIGADGPSS 154
                                    67899998889885 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.3   2.7e-05     0.027       1      33 [.       4      36 ..       4      40 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.7e-05
                    Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg.nig 33
                                   i++GaGPaG +aa ++ ++g  d++ +E+  +ig
  gi|116753983|ref|YP_843101.1|  4 IVVGAGPAGSTAAETAARLGA-DVILVERRmEIG 36
                                   89*******************.899999975665 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 ?    7.5   0.0    0.0059       5.8       2      20 ..      17      35 ..      16      55 .. 0.87
   2 ?    4.0   0.1     0.076        76       2      56 ..     109     168 ..     108     177 .. 0.71
   3 ?   -0.8   0.0       2.4   2.3e+03      46      68 ..     336     359 ..     323     360 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0059
                                   HHHHHTT-EEEEEEETTS- CS
                     ATPgrasp_N  2 eaAkaLGikvvlvdeedew 20
                                   e A++LG +v+lv++++e 
  gi|116753983|ref|YP_843101.1| 17 ETAARLGADVILVERRMEI 35
                                   78*************9875 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.076
                                    HHHHHTT-EEEEEEETTS-.....---S-TT..EEEEEEE-TTT-HHHHHHHHHHHHHHS- CS
                     ATPgrasp_N   2 eaAkaLGikvvlvdeedew.....apeelae.lvekfipldlaqdpdaaleavralsrerp 56 
                                    ++A++ G ++++ +e d       ++ + +e ++++ i +  +  + ++ ea+ a++r++p
  gi|116753983|ref|YP_843101.1| 109 HRAARAGAQLIVGTEADVRgesihLKGR-REgIIDADIIIGADGPSSRIAEAIGAVQRDEP 168
                                    68***********999654422333333.34466666666666667899999999999876 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 2.4
                                    HHHHHHH.HHS--SEEE---GGGH CS
                     ATPgrasp_N  46 eavrals.rerpvdGivtftdlav 68 
                                    ++v+++  ++r +d i+++ d+++
  gi|116753983|ref|YP_843101.1| 336 RMVDRAMrSDRSIDMIFSLLDPMT 359
                                    556555426799******999875 PP

>> CoA_transf_3  CoA-transferase family III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   0.00012      0.12       4      35 ..       1      32 [.       1      38 [. 0.90

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                   CoA_transf_3  4 vrVldlsqvlaGplatslLAdlGAeVIkvEpp 35
                                   +r++ ++   aG +a+++ A lGA+VI vE++
  gi|116753983|ref|YP_843101.1|  1 MRIIVVGAGPAGSTAAETAARLGADVILVERR 32
                                   5788888889********************97 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 ?    5.8   0.2     0.013        13       2      33 ..       5      31 ..       4      40 .. 0.78
   2 ?    3.9   0.0     0.049        49      89     121 ..      96     128 ..      83     156 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.013
                  NAD_binding_9  2 ivGaGprGlavlerLlarakkkspleitlfdp 33
                                   +vGaGp+G +++e  ++        ++ l+++
  gi|116753983|ref|YP_843101.1|  5 VVGAGPAGSTAAETAARL-----GADVILVER 31
                                   8***********998888.....477777777 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.049
                  NAD_binding_9  89 dfvpRalyGrYlrdlfeellarlpegvtvevhr 121
                                    + v R+ + rYl+++++++ a+l  g++ +v  
  gi|116753983|ref|YP_843101.1|  96 RCVDRRSFDRYLAHRAARAGAQLIVGTEADVRG 128
                                    6789****************9997666666544 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 ?   11.0   0.2   0.00028      0.28       2      33 ..       3      34 ..       2      39 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00028
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HH CS
                        3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdisee 33
                                   + v+GaG  G+  a+ +a+ g +V lv+++ e
  gi|116753983|ref|YP_843101.1|  3 IIVVGAGPAGSTAAETAARLGADVILVERRME 34
                                   67*************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2661.07
//
Query:       gi|116753984|ref|YP_843102.1|  [L=633]
Description: Na+/solute symporter [Methanosaeta thermophila PT]
Scores for complete 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  116.4  32.8    1.8e-33  116.0  32.8    1.2  1  SSF       Sodium:solute symporter family
     0.0014   17.7  25.6     0.0031   16.5  25.6    1.6  1  Nramp     Natural resistance-associated macrophage protein


Domain annotation for each model (and alignments):
>> SSF  Sodium:solute symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.0  32.8   2.1e-37   1.8e-33       1     406 []      35     425 ..      35     425 .. 0.88

  Alignments for each domain:
  == domain 1  score: 116.0 bits;  conditional E-value: 2.1e-37
                            SSF   1 yflagrsltgfvlglslaasnisaasfvGlaGavaasGlavvllelgalllvlllllllaerlrnagalTlpdylskRfk 80 
                                    ++la+r+l+   lg s+aas + a+ ++   G+ ++ G++ +++ +   +++l ++ l+a+r  +  a+T p++l+ R++
  gi|116753984|ref|YP_843102.1|  35 FWLASRELGAASLGFSAAASWLTASALLLSTGLFMLIGVSSIWVWVFPNIAALAIIALIAGRIKRIPAMTQPELLEIRYD 114
                                    89***************************************99999999999999************************9 PP

                            SSF  81 gkrilvylsalslllvitlklsvdlvggaklielalGlnyetavlllaaltalYtviGGllAvvytdtiqavlmlvgali 160
                                        +  +++ +++++i +   vd++g    + + +G++   avl++a+++alY+ +GG++Avv+td +q  + l+g+ +
  gi|116753984|ref|YP_843102.1| 115 PMV-RAPVAVAITIMMILFS-VVDFIGFKLVLGTFFGVEPLYAVLIMAVSVALYVSLGGFRAVVWTDRVQY-IFLAGLAV 191
                                    887.7777777777766665.69***********************************************6.56777777 PP

                            SSF 161 lliivllevGgleslveklkeaapkvvdlltpdslkllrdpltalslwlglvlGvaglphilvRflaakdakailkgvlk 240
                                    ++ i  l++ +   +   + +aa  + +  +p     +   l al++ l+l+ G +  +   +R+ aa d ++++ g+l 
  gi|116753984|ref|YP_843102.1| 192 VVAILSLKLSADRGASIIAESAAL-GGEWWNPFM---MGGVLGALVFQLALLPGWIAEQDPWQRVWAARDERSARMGLLL 267
                                    666666677777766666666655.566666655...677899************************************* PP

                            SSF 241 ltivlilvligmisiilfaiklagavpkavgtevgvsniaypeLvvkllpnllaGlllavmlAaimstltslllsassaf 320
                                    + ++l++v+       l ai+l  + p   g+   ++++ y + + + +p+   +ll     Aa ms  ++   s++s +
  gi|116753984|ref|YP_843102.1| 268 GSMLLAIVYGA---CFLTAIALRAIYPLPEGE--VEAEMLYLRFISENVPPAAVALLTIGFAAASMSCTDTFATSGASCI 342
                                    99999988876...678899999998866555..5789******************99999999**************** PP

                            SSF 321 tkDlYkkirrkasakekelvgvsriivlvvislaillavqeeqkgvlklvelafaglasavlavillalfwkrvneqGAl 400
                                    ++D+++++++   a+ +e++ +sr++v+++is++ ++a++ e+   +  v +a+ + +   +  i+ +l+wkr+++ GAl
  gi|116753984|ref|YP_843102.1| 343 VRDIFQRFVKPD-ATMREMLIISRVLVVMMISISAFIALNVESI--MEAVIIATVIGTTSYFFPIVGGLYWKRATSWGAL 419
                                    ***********9.999***********************99987..555556665556666667899************* PP

                            SSF 401 agliiG 406
                                    a++i+G
  gi|116753984|ref|YP_843102.1| 420 AAVIVG 425
                                    ****99 PP

>> Nramp  Natural resistance-associated macrophage protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5  25.6   3.5e-07    0.0031      14     337 ..      74     394 ..      70     405 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.5e-07
                          Nramp  14 kLlwvlllstllaillqe.lsarLGlvTgkglaelirerlpkkvsillwilaelaiiatdlaeviGaAialnllfgipll 92 
                                    + +wv ++ +++a+++   ++ r+  +  ++ +el++ r+++ v++ +++++ +++i++++ ++iG  ++l ++fg+  l
  gi|116753984|ref|YP_843102.1|  74 SSIWVWVFPNIAALAIIAlIAGRIKRIPAMTQPELLEIRYDPMVRAPVAVAITIMMILFSVVDFIGFKLVLGTFFGVEPL 153
                                    55899999999887665515779********************************************************* PP

                          Nramp  93 vgvlitavlvllllfle.kggyrklEaliialvlvialsFiaelflvkpdw.gevlkglvvPslpg.keslllavgilGa 169
                                    ++vli+av v+l + l   + + +  ++  ++++ +a++ ++  + +  d  ++++++     l g   + +++ g+lGa
  gi|116753984|ref|YP_843102.1| 154 YAVLIMAVSVALYVSLGgFRAVVWTDRVQYIFLAGLAVVVAILSLKLSADRgASIIAESA--ALGGeWWNPFMMGGVLGA 231
                                    ***************554444556678888887777666655555555555144444444..4444447889999***** PP

                          Nramp 170 tvmphnlflhsslvqerkitidrsekeealkyeriDtiialivafli..nlailivaAavly..sggkdvesledaaeaL 245
                                     v   +l       q+ ++++   ++  + + +r+  +++ ++  ++  ++++ ++a +++y  ++g +ve      + +
  gi|116753984|ref|YP_843102.1| 232 LVFQLALLPGWIAEQDPWQRVW-AAR--DERSARMGLLLGSMLLAIVygACFLTAIALRAIYplPEG-EVEAEMLYLRFI 307
                                    **97777666666665553332.333..468888888887666555512556666667788874444.566666666889 PP

                          Nramp 246 epllGskaasvlFaigLlaaGlsStitgtlagqy.vmegflglrislwlrrlitralafvpalivilligaelelvkllv 324
                                    ++ +  +aa +l  ig  aa++s t t +++g+  ++ ++++  +++++     ++l +  +l+v++++ +++    +l 
  gi|116753984|ref|YP_843102.1| 308 SENVP-PAAVALLTIGFAAASMSCTDTFATSGAScIVRDIFQRFVKPDATM--REMLIISRVLVVMMISISAFI---ALN 381
                                    99999.7********************999997527899998888885544..666666666666666666666...444 PP

                          Nramp 325 lsqvllslllPfa 337
                                    +  ++ ++++  +
  gi|116753984|ref|YP_843102.1| 382 VESIMEAVIIATV 394
                                    4444444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (633 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       942  (0.0525406); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.43
# Mc/sec: 4460.21
//
Query:       gi|116753985|ref|YP_843103.1|  [L=548]
Description: dihydroxy-acid dehydratase [Methanosaeta thermophila PT]
Scores for complete 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-212  705.4   0.2   4.8e-212  705.2   0.2    1.0  1  ILVD_EDD  Dehydratase family


Domain annotation for each model (and alignments):
>> ILVD_EDD  Dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  705.2   0.2  2.7e-216  4.8e-212       1     516 [.      31     544 ..      31     545 .. 0.96

  Alignments for each domain:
  == domain 1  score: 705.2 bits;  conditional E-value: 2.7e-216
                       ILVD_EDD   1 kpiigiansyselvpchvhlkelaeavkegveeaggvpaefntigvsDgiamgeegmrysLpsReliadsvetmleaqll 80 
                                    +p+ig+ans +e+vp+h hl+++aeavk+g++ aggvp+ef+tigv+Dgiamg+ gmrysLpsRe+i ds+e+m++a++l
  gi|116753985|ref|YP_843103.1|  31 RPFIGVANSANEFVPGHIHLDRIAEAVKAGIRIAGGVPFEFQTIGVCDGIAMGHGGMRYSLPSREIIEDSIEIMAQAHQL 110
                                    7******************************************************************************* PP

                       ILVD_EDD  81 DalvlisgCDKivPgllmaaarlniPaifvsgGpmeagkkk..kldlssvfeavgalaagkiseeeleeleeaacpgaGs 158
                                    D+lvli++CDKivPg+lmaa rl++P+i+v+gGpm++g +   +ldl++vfe++++        e l+ le+ acpgaGs
  gi|116753985|ref|YP_843103.1| 111 DGLVLIPTCDKIVPGHLMAAGRLDLPTIVVTGGPMLPGFACdrELDLINVFEEWQK------GGESLSILEDLACPGAGS 184
                                    *************************************7633357888888877765......4688999*********** PP

                       ILVD_EDD 159 CsgmgTAntmaclaealGlslpgsasipatsaerkelaeeagkrivelvekdlkprdiltkeafeNAivvllalGGStNa 238
                                    C+g++TAn+mac+aealGlslpg+a+++a++a+++++a+ +g+ ivelv++ l++r+i+++e+feNA+ v++a+GGStN+
  gi|116753985|ref|YP_843103.1| 185 CAGLFTANSMACMAEALGLSLPGCATAHAVDAKKMRIAKLSGMMIVELVKRGLTARKIVSRESFENAVRVDMAIGGSTNT 264
                                    ******************************************************************************** PP

                       ILVD_EDD 239 vlHllAiAreagveltlddfdelsrkvpllaklkPsgkydmedlhraGGvpavlkeLlkagllhgdvltvtgktlaenle 318
                                    +lHl+AiA e++++l+ld fd+lsr++p+l++l+P g ++m dl+raGGv+av+++L+++  l+ +vltvtgktl+  l+
  gi|116753985|ref|YP_843103.1| 265 ALHLPAIAAEFDIDLELDVFDRLSRETPHLVNLRPGGPHHMLDLDRAGGVQAVMHRLSSK--LDLSVLTVTGKTLGAVLA 342
                                    **********************************************************65..*****************9 PP

                       ILVD_EDD 319 e.aev...keqdvirplekplskegglavLkGnLapeGavvKtsaveeellkfegpArvfdseeeaveailkgkikagdv 394
                                    e + v   ++ +vi +le+p+++egg+a+LkG+LapeG+vvK++av++++l+++gpA+v+dseee ++ il+g++kagdv
  gi|116753985|ref|YP_843103.1| 343 EfKPVnpkANAEVIATLERPVHPEGGIAILKGSLAPEGSVVKQTAVSKKMLVHKGPAVVYDSEEESMKGILSGEVKAGDV 422
                                    9733366699********************************************************************** PP

                       ILVD_EDD 395 vviryeGPkGgpGmpEmlkptsallgkglgkkvalitDGRfSGaskglvighvsPEAaegGpialvedGDiieidiekrt 474
                                    vviryeGPkGgpGm+E l+ptsa++g+gl+++valitDGRfSG+++g++ighvsPEAa+gGpialve+GD+i+idi++r+
  gi|116753985|ref|YP_843103.1| 423 VVIRYEGPKGGPGMRETLAPTSAIAGAGLSESVALITDGRFSGGTRGPCIGHVSPEAAVGGPIALVENGDMISIDIPNRR 502
                                    ******************************************************************************** PP

                       ILVD_EDD 475 lelevseeelaaRraawkp.ekkvktrgllakyaklvssaseG 516
                                    l+l+v+e  l++Rra+w+p e++v + g+l +y+k+v+sas+G
  gi|116753985|ref|YP_843103.1| 503 LDLLVDEGVLERRRASWRPpEPRV-RGGVLDRYRKSVTSASKG 544
                                    *******************55555.499**************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (548 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3904.06
//
Query:       gi|116753986|ref|YP_843104.1|  [L=177]
Description: 2'-5' RNA ligase [Methanosaeta thermophila PT]
Scores for complete 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  102.2   0.2    3.8e-16   59.0   0.0    2.0  2  LigT_PEase       LigT like Phosphoesterase
    6.6e-13   48.8   0.0    7.9e-13   48.6   0.0    1.1  1  2_5_RNA_ligase2  2'-5' RNA ligase superfamily


Domain annotation for each model (and alignments):
>> LigT_PEase  LigT like Phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.0   0.0   4.2e-20   3.8e-16       1      87 []       7      86 ..       7      86 .. 0.93
   2 !   41.5   0.0   1.3e-14   1.1e-10      11      87 .]      93     167 ..      88     167 .. 0.93

  Alignments for each domain:
  == domain 1  score: 59.0 bits;  conditional E-value: 4.2e-20
                                   EE-CHHHHHHHHHHHHHHHHHHCCTTEEETSGGGSEEEEEEEEEESHHHHHHHHHHHHHHHHTSBEEEEEEEEEEEEEECCS CS
                     LigT_PEase  1 lgppeeiaeelarlaaeleralaklglkpvrpfnpHiTLaflgevdeekvpellealaeiasgaepfelkvdgvglfpsrlr 82
                                   +++peei++ + ++++ ++      glk+v p  +HiTL+flgev+e++v+++++ala++  ++ pf+ +++gvg+fp r +
  gi|116753986|ref|YP_843104.1|  7 VDLPEEIKRGVPAIQQAFA----MNGLKLVDPNLVHITLKFLGEVEERRVDDIVNALARV--RFSPFQARITGVGAFPGR-S 81
                                   6788998888888888888....89***********************************..888************986.7 PP

                                   CCEEE CS
                     LigT_PEase 83 prviy 87
                                    rvi+
  gi|116753986|ref|YP_843104.1| 82 IRVIW 86
                                   99999 PP

  == domain 2  score: 41.5 bits;  conditional E-value: 1.3e-14
                                    HHHHHHHHHHHHCCTTEEETSGGGSEEEEEEEEEES.HHHHHHHHHHHHHHHHTSBEEEEEEEEEEEEEECC.SCCEEE CS
                     LigT_PEase  11 larlaaeleralaklglkpvrpfnpHiTLaflgevd.eekvpellealaeiasgaepfelkvdgvglfpsrl.rprviy 87 
                                     ++la+ ++ al  +g+  +++f  H TLa++++ +  + ++e l+ ++e++ ga    ++v++++l +s+l + +++y
  gi|116753986|ref|YP_843104.1|  93 FEELARAVDTALEPFGFERDKKFSAHATLARVKDPSlSRILAERLSGVSEVDLGA----FTVERFVLKKSTLtPRGPVY 167
                                    6899******************************999999999999999997775....*************9999998 PP

>> 2_5_RNA_ligase2  2'-5' RNA ligase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   0.0   8.8e-17   7.9e-13      19     144 ..      30     154 ..       9     160 .. 0.83

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 8.8e-17
                2_5_RNA_ligase2  19 kayprwppHitLlypfvededl.adlaellsrlaketepfevrldgfgvFehkks.vvylsvsdsealqalraallealp 96 
                                    k++    +HitL+++++ +e   +d++++l+r+  +++pf++r++g+g F++++  v++l +  + ++++l +a+ +al+
  gi|116753986|ref|YP_843104.1|  30 KLVDPNLVHITLKFLGEVEERRvDDIVNALARV--RFSPFQARITGVGAFPGRSIrVIWLGA--TGPFEELARAVDTALE 105
                                    45555559********9998877*********9..6****************7777******..**************** PP

                2_5_RNA_ligase2  97 eagdkedsgeftPHlTiaqsadstsaaelleklaqalpple...fevdeva 144
                                    + g  +d ++f  H+T+a+ +d+  ++ l e+l +   +++   f+v+++ 
  gi|116753986|ref|YP_843104.1| 106 PFGFERD-KKFSAHATLARVKDPSLSRILAERL-SGVSEVDlgaFTVERFV 154
                                    ****998.9*****************9999999.44444444447777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1383.28
//
Query:       gi|116753987|ref|YP_843105.1|  [L=401]
Description: tRNA CCA-pyrophosphorylase [Methanosaeta thermophila PT]
Scores for 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-42  141.9   0.0    1.3e-41  141.3   0.0    1.3  1  tRNA_NucTransf2  tRNA nucleotidyltransferase, second domain
    1.8e-13   50.5   0.0    5.4e-13   49.0   0.0    1.8  1  NTP_transf_2     Nucleotidyltransferase domain
  ------ inclusion threshold ------
      0.024   14.7   0.0      0.097   12.8   0.0    2.0  2  Polbeta          Polymerase beta, Nucleotidyltransferase


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 !  141.3   0.0   2.2e-45   1.3e-41       1     113 []     105     213 ..     105     213 .. 0.96

  Alignments for each domain:
  == domain 1  score: 141.3 bits;  conditional E-value: 2.2e-45
                                    HHHHHHHHHHHHTT-BSSSTTT-SB-HHHHHHHHHHHSSHHHHHHHHTT--TTEEEE......EEE..-SS-EEEETTEE CS
                tRNA_NucTransf2   1 devrllKkflkgigvYGselkvkGfsGYlaEllvleygsfeevleaaakwkpkvvidleekeallkkfdeplvviDPvDp 80 
                                    dev llK+f+kg+gvYGs+l++ GfsGYlaEllv++ygsf +vle a++w+p++ i+l       +++  plvviDPvDp
  gi|116753987|ref|YP_843105.1| 105 DEVLLLKQFMKGVGVYGSDLRTGGFSGYLAELLVIRYGSFLRVLEGASSWRPGTRINLAP----GANIMAPLVVIDPVDP 180
                                    89******************************************************7443....456999********** PP

                                    EEETTTTS-HHHHHHHHHHHHHHHHS--GGGGS CS
                tRNA_NucTransf2  81 kRNvaaalsleklaefilaareflkkpseefff 113
                                    kRNvaaal+l+++ +f++aar+fl++p+++fff
  gi|116753987|ref|YP_843105.1| 181 KRNVAAALTLDRMFQFVAAARCFLRSPDISFFF 213
                                    *******************************96 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   0.0     9e-17   5.4e-13      18      94 ..       6      91 ..       4      92 .. 0.96

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 9e-17
                                   EEEHHHHCTTSCTT.SSEEEEEEESTTCHHH........HHHEHHHHHHHHCCCEEECTTEEEEEECEEECCCCTEEEEEEC CS
                   NTP_transf_2 18 vlfGSyarGtalkg.SDiDllvvlpeevsre........kkeegleklaeiikfleellglevdlvtrekledpllvksile 90
                                   +l+GS+ar+t+l+g  DiD+++ +pe+ +          + ++++e++ae+ +++ ++ g  vdlv+++ ++dp+++ks+++
  gi|116753987|ref|YP_843105.1|  6 ILVGSAARNTWLSGdRDIDIFIAVPEDGNLGdaleiareIAPVHEERYAEHAYVHARIDGFDVDLVPCYDVRDPSKIKSAVD 87
                                   69*************************7777********99999************************************** PP

                                   EEEH CS
                   NTP_transf_2 91 erpl 94
                                   ++p+
  gi|116753987|ref|YP_843105.1| 88 RTPF 91
                                   *997 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.6e-05     0.097      18      58 ..       7      48 ..       5      62 .. 0.86
   2 ?   -2.5   0.0      0.96   5.7e+03      60      67 ..     274     281 ..     254     294 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.6e-05
                                   EEEEEE-S----.--EEEEEEEESS---HHHHHHHHHHHHHH CS
                        Polbeta 18 lFGSrakgkare.eSDiDlavllkekldleeelelaaeledi 58
                                   l GS a+++  + + DiD+++ + e+ +l + le+a e++ +
  gi|116753987|ref|YP_843105.1|  7 LVGSAARNTWLSgDRDIDIFIAVPEDGNLGDALEIAREIAPV 48
                                   679***99876449************************9987 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.96
                                    SSSEEEEE CS
                        Polbeta  60 lgkkvDlv 67 
                                    l+ +vDlv
  gi|116753987|ref|YP_843105.1| 274 LRSDVDLV 281
                                    34455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); 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 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2779.51
//
Query:       gi|116753988|ref|YP_843106.1|  [L=344]
Description: histone deacetylase superfamily protein [Methanosaeta thermophila PT]
Scores for 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-90  301.3   0.0    1.2e-89  300.9   0.0    1.2  1  Hist_deacetyl  Histone deacetylase domain


Domain annotation for each model (and alignments):
>> Hist_deacetyl  Histone deacetylase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  300.9   0.0   6.5e-94   1.2e-89       1     306 [.      25     309 ..      25     310 .. 0.96

  Alignments for each domain:
  == domain 1  score: 300.9 bits;  conditional E-value: 6.5e-94
                                    SCCGTHHHHHHHHHHHHT.THHHHCCE.EE-----HHHHTTTS-HHHHHHHHCHHHHCHHT.TTHCCHHHCCTSTSSSSS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Hist_deacetyl   1 hpenpkRlsaileslaesvglldelelliqpseatkeellkvHskeYlelleslsnelkkkeeakekeleeiaskllddd 80 
                                    hpe+++Rl+ai+e+++   gl ++    i+p++a+ +++++vHs++Y+e+++s++++ +                  d d
  gi|116753988|ref|YP_843106.1|  25 HPERKERLIAIMERIEAE-GLNPN---RIEPRPASLDKIEAVHSRRYIEQVRSICERGGGRL---------------DID 85 
                                    89*************996.98776...479*************************8876654...............568 PP

                                    THCTTTCCHHHHHHHHHHHHHHHHHHTTSSSEEEETTSS--TT-BTTB-BTTBSS-HHHHHHHHHHHCC-SS-EEEEE-S CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Hist_deacetyl  81 tpvspktlkaallavgavleavdavlsgsvkaafvlvrPpgHHakaseasGFClvNnvaiaikylqakhelkrvailDvD 160
                                    t++s++++++al+a+g+v+++vd+v+++  +  f+lvrPpgHHa++ + +GFC++Nnvai+++y+q+  +lk+v+i+D+D
  gi|116753988|ref|YP_843106.1|  86 TVLSKDSYDVALMAAGGVCAGVDHVMKK-PDPVFALVRPPGHHATPHRGMGFCVFNNVAIGARYAQS-LGLKKVLIVDWD 163
                                    9*************************88.6999**********************************.9*********** PP

                                    SS--HHHHHHCTT-TTEEEEEEEE-CCTSTTSS--TT---SGGGTTSEEEEEE-TT-BHHHHHHHHHHCHHHHHCCH--S CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Hist_deacetyl 161 vHhGnGteeafysdpdvltlSiHryegifyPgtgaledlgegkgkgfnlnvpleegtgdeeylkvfeeilrpvleefkPd 240
                                    vHhGnGt+++fy+d++vl++S+H++++  yPgtg ++++g gkgkgf++nvpl++g++d+ yl+v++eil pv+ ef+P+
  gi|116753988|ref|YP_843106.1| 164 VHHGNGTQAIFYEDNSVLYFSTHQHPH--YPGTGRVTEVGDGKGKGFTVNVPLPPGIDDSGYLAVYKEILVPVADEFRPE 241
                                    ************************766..*************************************************** PP

                                    EEEEEE-STTBTTSTT-S-BB-HHHHHHHHHHHCCCHGS-.G..EEEEE-S---HHHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Hist_deacetyl 241 lilvsaGfDalkgdplgelnlsvegykeltkklaeladkv.k.kvvllleGGYnlealaravtavlsa 306
                                    ++ vsaGfD ++ dplg+++l+++g++ l   ++++ad++ + ++v+ leGGY+le+l+++v +vl+a
  gi|116753988|ref|YP_843106.1| 242 IVFVSAGFDPHQMDPLGGMRLTENGFGALAGLVKDIADRHaGgRIVAALEGGYRLESLSESVVSVLRA 309
                                    ****************************************989*******************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 2346.72
//
Query:       gi|116753989|ref|YP_843107.1|  [L=720]
Description: S-layer-like domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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-179  593.5  34.8    3.9e-90  301.4  13.3    2.1  2  S-layer          S-layer protein
      3e-09   36.5   3.2      3e-09   36.5   3.2    2.1  2  PGF-CTERM        PGF-CTERM motif
    0.00026   21.2   1.2        1.1    9.6   0.1    2.7  2  PA-IIL           Fucose-binding lectin II (PA-IIL)
     0.0075   15.9   0.8        5.1    6.7   0.1    2.7  2  CAP_C            Adenylate cyclase associated (CAP) C termina
  ------ inclusion threshold ------
      0.015   15.4   0.5         12    6.2   0.1    3.1  2  PrcB_C           PrcB C-terminal
      0.033   13.6   0.0          5    6.4   0.0    2.7  3  ThiF             ThiF family
        1.4    9.1   3.9        3.8    7.7   3.9    1.7  1  Myco_arth_vir_N  Mycoplasma virulence signal region (Myco_art
        3.9    7.3  11.9         68    3.4   0.2    4.5  4  DUF3954          Protein of unknown function (DUF3954)


Domain annotation for each model (and alignments):
>> S-layer  S-layer protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  301.4  13.3   1.8e-93   3.9e-90       5     258 .]      37     307 ..      33     307 .. 0.96
   2 !  298.3  13.5   1.5e-92   3.4e-89       5     258 .]     341     611 ..     337     611 .. 0.96

  Alignments for each domain:
  == domain 1  score: 301.4 bits;  conditional E-value: 1.8e-93
                        S-layer   5 eeseeltwtasnFsgfyydiddglssEsltlelesksdrtieegelvYsttpvekefefeewgsYevigflaekYfagy. 83 
                                     + +++twt++nF+gfyydidd+l++E++t++++  +++  e ++++Y++t+++++f+fe+wg+Y+ igfl+e+Yfagy 
  gi|116753989|ref|YP_843107.1|  37 VDGATVTWTPQNFAGFYYDIDDDLGNEQITMTIT--GNKLEEPNGVKYTSTAQDNDFDFEDWGWYRSIGFLGENYFAGYs 114
                                    567899**************************76..6999999************************************7 PP

                        S-layer  84 dnsa............etsddvsllsdekLskvlidedeektlksgssleLeegYeleikqiDvdgdkvwleLtkdgeev 151
                                    +n++            ++s+d+++l de+L kvlid+d+e+t++sg+ l+L++gYel+ik+iDvdg+kv++eL+kdg++v
  gi|116753989|ref|YP_843107.1| 115 ENKPtvdgveidpelyKQSTDTNTLVDEQLLKVLIDDDTERTFTSGTPLKLADGYELMIKSIDVDGNKVYVELMKDGQSV 194
                                    5555789999999999999************************************************************* PP

                        S-layer 152 dskvissska.....dstyvyekdlgdeddvviiavhvdevfrgtedslvviegifqisddvleieegdefgkmevksvs 226
                                    d+kv+s+sk+     d+ty+y+kd+gd++d+vii vh++++frg+++++++++gifq+sd++++++ ++e++km+++sv+
  gi|116753989|ref|YP_843107.1| 195 DTKVVSPSKDgatmsDKTYYYKKDIGDTEDLVIIGVHFKNAFRGADQDIATVDGIFQVSDQPMDVSVDTEYDKMRISSVT 274
                                    *******9999********************************************************************* PP

                        S-layer 227 eneiemendds.itLsrdktieimddlkfkvaD 258
                                    +++iem+n+d+ itL+++k++++m  +++k+aD
  gi|116753989|ref|YP_843107.1| 275 RDTIEMDNKDNaITLNKNKDTTLMAGIHIKTAD 307
                                    *********999********************8 PP

  == domain 2  score: 298.3 bits;  conditional E-value: 1.5e-92
                        S-layer   5 eeseeltwtasnFsgfyydiddglssEsltlelesksdrtieegelvYsttpvekefefeewgsYevigflaekYfagy. 83 
                                     + +++tw++++F+gfyydidd+l++E++t++++  +++  e ++++Y++t+++++f+fe+wg+Y+ igfl+e+Yfagy 
  gi|116753989|ref|YP_843107.1| 341 VDGAQVTWDPKTFAGFYYDIDDDLGNEQITMTIT--GNKLEEPNGVKYTSTAQDNDFDFEDWGWYRSIGFLGENYFAGYs 418
                                    567899**************************76..6999999************************************7 PP

                        S-layer  84 dnsa............etsddvsllsdekLskvlidedeektlksgssleLeegYeleikqiDvdgdkvwleLtkdgeev 151
                                    +n++            ++s+d+++l de+L kvlid+d+e+t++sg+ l+L++gYel+ik+iDvdg+kv++eL+kdg++v
  gi|116753989|ref|YP_843107.1| 419 ENKPtvdgveidpelyKQSTDTNTLVDEQLLKVLIDDDTERTFTSGTPLKLADGYELMIKSIDVDGNKVYVELMKDGQSV 498
                                    5555789999999999999************************************************************* PP

                        S-layer 152 dskvissska.....dstyvyekdlgdeddvviiavhvdevfrgtedslvviegifqisddvleieegdefgkmevksvs 226
                                    d+kv+s+sk+     d+ty+y+kd+gd++d+vii vh++++frg+++++++++gifq+sd++++++ ++e++km+++sv+
  gi|116753989|ref|YP_843107.1| 499 DTKVVSPSKDgatmsDKTYYYKKDIGDTEDLVIIGVHFKNAFRGADQDIATVDGIFQVSDQPMDVSVDTEYDKMRISSVT 578
                                    *******9999********************************************************************* PP

                        S-layer 227 eneiemendds.itLsrdktieimddlkfkvaD 258
                                    +++iem+n+d+ itL+++k++++m  +++k+aD
  gi|116753989|ref|YP_843107.1| 579 RDTIEMDNKDNaITLNKNKDTTLMAGIHIKTAD 611
                                    *********999********************8 PP

>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   2.6       1.2   2.8e+03       7      18 ..       8      19 ..       7      22 .. 0.77
   2 !   36.5   3.2   1.4e-12     3e-09       1      23 []     697     719 ..     697     719 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.2
                      PGF-CTERM  7 vlAlaGLLaaal 18
                                   + Al++ La+a 
  gi|116753989|ref|YP_843107.1|  8 ITALVAVLATAM 19
                                   569999999885 PP

  == domain 2  score: 36.5 bits;  conditional E-value: 1.4e-12
                      PGF-CTERM   1 tPGFGavlAlaGLLaaalLaRRr 23 
                                    +PGF+av+A++GLLa+a+L++Rr
  gi|116753989|ref|YP_843107.1| 697 APGFEAVFAVTGLLAVAYLVTRR 719
                                    6*********************8 PP

>> PA-IIL  Fucose-binding lectin II (PA-IIL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.1   0.00049       1.1      19      71 ..     141     197 ..     130     212 .. 0.80
   2 !    9.6   0.1   0.00049       1.1      19      71 ..     445     501 ..     434     516 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00049
                                    EEEEEEEEETTEEEEEEEEEE....EEEEEEEEEEEE-TTSEEEEEEEETTEE-EEE CS
                         PA-IIL  19 eqqtikvyiddelkatftgkg....trdkvlgtkvlnsgsGkvrvevsanGkpsklr 71 
                                    ++q +kv+idd+++ tft+ +    ++   l  k ++    kv ve++ +G+  +++
  gi|116753989|ref|YP_843107.1| 141 DEQLLKVLIDDDTERTFTSGTplklADGYELMIKSIDVDGNKVYVELMKDGQSVDTK 197
                                    7899*************986632224456788999999999**********988765 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00049
                                    EEEEEEEEETTEEEEEEEEEE....EEEEEEEEEEEE-TTSEEEEEEEETTEE-EEE CS
                         PA-IIL  19 eqqtikvyiddelkatftgkg....trdkvlgtkvlnsgsGkvrvevsanGkpsklr 71 
                                    ++q +kv+idd+++ tft+ +    ++   l  k ++    kv ve++ +G+  +++
  gi|116753989|ref|YP_843107.1| 445 DEQLLKVLIDDDTERTFTSGTplklADGYELMIKSIDVDGNKVYVELMKDGQSVDTK 501
                                    7899*************986632224456788999999999**********988765 PP

>> CAP_C  Adenylate cyclase associated (CAP) C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.1    0.0023       5.3      29      64 ..     263     298 ..     247     312 .. 0.81
   2 !    6.7   0.1    0.0023       5.1      29      64 ..     567     602 ..     551     617 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0023
                          CAP_C  29 elkqsvyifkCknstiqikgKvnaitldnckkvsvv 64 
                                    +  +++ i++ +  ti++ +K naitl++ k+++++
  gi|116753989|ref|YP_843107.1| 263 TEYDKMRISSVTRDTIEMDNKDNAITLNKNKDTTLM 298
                                    44567899999*********************9987 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0023
                          CAP_C  29 elkqsvyifkCknstiqikgKvnaitldnckkvsvv 64 
                                    +  +++ i++ +  ti++ +K naitl++ k+++++
  gi|116753989|ref|YP_843107.1| 567 TEYDKMRISSVTRDTIEMDNKDNAITLNKNKDTTLM 602
                                    44567899999*********************9987 PP

>> PrcB_C  PrcB C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1    0.0052        12      12      48 ..     166     198 ..     161     213 .. 0.79
   2 ?    6.2   0.1    0.0052        12      12      48 ..     470     502 ..     465     517 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0052
                         PrcB_C  12 tgGYsievdkvyetenaiyvkttllgPepgeevtqal 48 
                                     +GY + ++++  ++n++yv++     ++g+ v  ++
  gi|116753989|ref|YP_843107.1| 166 ADGYELMIKSIDVDGNKVYVELM----KDGQSVDTKV 198
                                    58******************996....4455554444 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0052
                         PrcB_C  12 tgGYsievdkvyetenaiyvkttllgPepgeevtqal 48 
                                     +GY + ++++  ++n++yv++     ++g+ v  ++
  gi|116753989|ref|YP_843107.1| 470 ADGYELMIKSIDVDGNKVYVELM----KDGQSVDTKV 502
                                    58******************996....4455554444 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0         1   2.3e+03     112     130 ..      19      37 ..       9      55 .. 0.77
   2 ?    3.8   0.0     0.014        32      44      66 ..     302     324 ..     295     352 .. 0.82
   3 ?    6.4   0.0    0.0022         5      44      70 ..     606     632 ..     599     669 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1
                                    EEEEESSSHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxx RF
                           ThiF 112 lVvdalDniearrlvnrac 130
                                    +Vv a+D++e+r +v++++
  gi|116753989|ref|YP_843107.1|  19 MVVGAVDKVEIRGAVQEVV 37 
                                    6888999999998888775 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.014
                                    EEEEEESSB--GGGGGTBTTS-G CS
                                    xxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF  44 kltlvDnDkielsNlnRqflfre 66 
                                    +++ +D+D+i+ +N+ R ++++e
  gi|116753989|ref|YP_843107.1| 302 HIKTADQDVIDAENPLRFYIYKE 324
                                    89999**************9875 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0022
                                    EEEEEESSB--GGGGGTBTTS-GGGTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF  44 kltlvDnDkielsNlnRqflfreediG 70 
                                    +++ +D+D+i+ +N+ R ++++e+ i 
  gi|116753989|ref|YP_843107.1| 606 HIKTADQDVIDAENPLRFYIYKEATIE 632
                                    89999******************9985 PP

>> Myco_arth_vir_N  Mycoplasma virulence signal region (Myco_arth_vir_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   3.9    0.0017       3.8       7      29 ..       2      24 ..       2      24 .. 0.95

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0017
                Myco_arth_vir_N  7 KKikIltlalvaaLlaaltfgGV 29
                                   +K +I++ alva L++a  +g V
  gi|116753989|ref|YP_843107.1|  2 NKTAIMITALVAVLATAMVVGAV 24
                                   8*****************99987 PP

>> DUF3954  Protein of unknown function (DUF3954)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1     0.049   1.1e+02       4      13 ..     176     185 ..     174     194 .. 0.79
   2 ?    3.4   0.2      0.03        68       2      22 ..     278     298 ..     277     301 .. 0.92
   3 ?    2.7   0.1     0.049   1.1e+02       4      13 ..     480     489 ..     478     498 .. 0.79
   4 ?    3.4   0.2      0.03        68       2      22 ..     582     602 ..     581     605 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.049
                        DUF3954   4 iDvtDnkiyv 13 
                                    iDv  nk+yv
  gi|116753989|ref|YP_843107.1| 176 IDVDGNKVYV 185
                                    9********9 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.03
                        DUF3954   2 veiDvtDnkiyvvknGevtLL 22 
                                    +e+D  Dn i   kn + tL+
  gi|116753989|ref|YP_843107.1| 278 IEMDNKDNAITLNKNKDTTLM 298
                                    799****************97 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.049
                        DUF3954   4 iDvtDnkiyv 13 
                                    iDv  nk+yv
  gi|116753989|ref|YP_843107.1| 480 IDVDGNKVYV 489
                                    9********9 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.03
                        DUF3954   2 veiDvtDnkiyvvknGevtLL 22 
                                    +e+D  Dn i   kn + tL+
  gi|116753989|ref|YP_843107.1| 582 IEMDNKDNAITLNKNKDTTLM 602
                                    799****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (720 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); 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):               8  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.44
# Mc/sec: 4953.26
//
Query:       gi|116753990|ref|YP_843108.1|  [L=190]
Description: Mn2+-dependent serine/threonine protein kinase [Methanosaeta thermophila PT]
Scores for complete 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   44.5   0.0    1.9e-11   43.9   0.0    1.5  1  RIO1            RIO1 family
    1.7e-11   44.5   2.9      6e-06   26.3   0.4    2.3  2  APH             Phosphotransferase enzyme family
    1.2e-08   34.6   0.3    2.8e-07   30.1   0.3    2.2  1  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
    2.1e-08   33.9   0.1      4e-08   33.0   0.1    1.5  1  Pkinase         Protein kinase domain
    8.9e-06   25.5   0.1    1.1e-05   25.2   0.1    1.2  1  WaaY            Lipopolysaccharide core biosynthesis protein 
    0.00015   21.4   0.1      0.058   13.0   0.2    2.2  2  Choline_kinase  Choline/ethanolamine kinase
    0.00027   20.3   0.1     0.0012   18.2   0.1    1.9  1  Pkinase_Tyr     Protein tyrosine kinase
  ------ inclusion threshold ------
       0.04   14.1   1.0       0.04   14.1   1.0    2.1  2  TetR_C_31       Tetracyclin repressor-like, C-terminal domain
      0.047   13.0   0.0      0.047   13.0   0.0    1.2  1  EcKinase        Ecdysteroid kinase
      0.097   11.4   0.0       0.12   11.1   0.0    1.3  1  Pkinase_fungal  Fungal protein kinase
      0.098   11.5   0.0      0.098   11.5   0.0    1.1  1  DUF1679         Protein of unknown function (DUF1679)


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 !   43.9   0.0   1.2e-14   1.9e-11      55     152 ..      41     128 ..      16     174 .. 0.80

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 1.2e-14
                                    HHHHHHHHHHHHHTT--S--EEEEETTEEEEE--EETTEEGGBHHHCG-HHHHHHHHHHHHHHHHHHHHTSTEEESS-ST CS
                           RIO1  55 aekEfrnLkrleeagvpvPkpielkrhvlvmefigedgvaapklkdveeeeeaeelyeevleemrklykeaglvHaDLSe 134
                                    +  E r++ ++++agvp P   ++ r  lvme+++  g   +kl+d+  + e++e + e++      +++ag+vH+DL  
  gi|116753990|ref|YP_843108.1|  41 TVMEARIMAEARRAGVPTPIIRDVSRFELVMEYVD--G---KKLRDII-TPELSERVGELVG----RLHKAGIVHGDLTT 110
                                    45699******************************..5...5667766.3345555555555....56799********* PP

                                    TSEEEETTEEEE--GTTE CS
                           RIO1 135 yNvlvdedkvviIDvsQa 152
                                     N+l++++++++ID++ a
  gi|116753990|ref|YP_843108.1| 111 SNMLLKDNRIYFIDFGLA 128
                                    **************9854 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   4.4e-07   0.00071      32     108 ..      36     101 ..       8     102 .. 0.84
   2 !   26.3   0.4   3.7e-09     6e-06     166     199 ..     101     131 ..     100     182 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 4.4e-07
                                    S-HHHHHHHHHHHHHHHHTT-B--B-CTTBS-EEETTEEEEEEE----EE-SSHHHHHHHHHHHHHHHHHHCCHHCH CS
                            APH  32 raaeeirrevallrlLakagvpvPevlagdtddeeigllfalieyvpgrsllrklsaaqlpellealgeflaalhqv 108
                                      ae++  e+++++  ++agvp+P + +      +     +++eyv+g+ l++     ++pel e++ge+ ++lh +
  gi|116753990|ref|YP_843108.1|  36 LRAERTVMEARIMAEARRAGVPTPIIRD---VSRF----ELVMEYVDGKKLRD----IITPELSERVGELVGRLHKA 101
                                    45788999*************9998888...3333....56************....899***************87 PP

  == domain 2  score: 26.3 bits;  conditional E-value: 3.7e-09
                                    EEEE-SS-SGGGEEEC..TTEEEEE---TT-EEE CS
                            APH 166 tvllHgDlhpgNllvdpddgrvtGviDfedaglg 199
                                    ++++HgDl + N+l++  d+r+ ++iDf++a + 
  gi|116753990|ref|YP_843108.1| 101 AGIVHGDLTTSNMLLK--DNRI-YFIDFGLAYHD 131
                                    689*************..9**9.******99765 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.3   1.7e-10   2.8e-07     105     173 ..      69     132 ..      13     166 .. 0.73

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 1.7e-10
                            Kdo 105 LedllakwaelaeelkrallkavgrliaklhragvnHadlyaknillqqeeeeeaeiwliDldkarlrl 173
                                    L++ + ++++l +  + +l ++vg l+ +lh+ag+ H+dl   n+ll+ +      i++iD+  a++  
  gi|116753990|ref|YP_843108.1|  69 LVMEYVDGKKLRDIITPELSERVGELVGRLHKAGIVHGDLTTSNMLLKDNR-----IYFIDFGLAYHDQ 132
                                    34444445667777888999****************************995.....******8777654 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.1   2.4e-11     4e-08      43     147 ..      39     130 ..       3     149 .. 0.80

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 2.4e-11
                                    HHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-S CS
                        Pkinase  43 kkvlrEikilkklkhpnivrlyevfeekdelylvleyveggeladllerkgslseeeakkiakqilegleylHskgiiHr 122
                                    +++++E +i+++ +   + +   ++++ +++ lv+eyv+g++l d+++           ++ +++ e +  lH++gi+H 
  gi|116753990|ref|YP_843108.1|  39 ERTVMEARIMAEARRAGVPT--PIIRDVSRFELVMEYVDGKKLRDIITP----------ELSERVGELVGRLHKAGIVHG 106
                                    56677777777777777654..5688899999***************74..........566677788889********* PP

                                    S-SGGGEEEETTTEEEE-SGTTSEE CS
                        Pkinase 123 DlKpeNiLidekgelKitDFGlake 147
                                    Dl ++N+L++ ++ +  +DFGla +
  gi|116753990|ref|YP_843108.1| 107 DLTTSNMLLK-DNRIYFIDFGLAYH 130
                                    **********.9**********976 PP

>> WaaY  Lipopolysaccharide core biosynthesis protein (WaaY)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.1   6.8e-09   1.1e-05     111     178 ..      60     125 ..      33     143 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 6.8e-09
                           WaaY 111 ilryvkvyimiieyiegielvdmpeiddevkakikqsieklhqlgmvsgdphrgnfivkkdevriidl 178
                                    i+r v+ + +++ey++g +l d+  i+ e+ +++ + + +lh+ g+v gd    n+++k++ +  id+
  gi|116753990|ref|YP_843108.1|  60 IIRDVSRFELVMEYVDGKKLRDI--ITPELSERVGELVGRLHKAGIVHGDLTTSNMLLKDNRIYFIDF 125
                                    6788999**************96..8899999999*******************************97 PP

>> Choline_kinase  Choline/ethanolamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0022       3.5      36      81 ..      55     101 ..      27     105 .. 0.75
   2 !   13.0   0.2   3.6e-05     0.058     149     172 ..     105     126 ..     101     160 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0022
                                    SS-EEEEETTEEEE...E--TCEE--TTGGGCHHHHHHHHHHHHHHTTC CS
                 Choline_kinase  36 gpklygifenGrie...efiesrtlstedlrepeiskkiAkklaelHsl 81 
                                    g+ +  i + +r+e   e++++++l   d+ +pe+s+++++ +++lH+ 
  gi|116753990|ref|YP_843108.1|  55 GVPTPIIRDVSRFElvmEYVDGKKL--RDIITPELSERVGELVGRLHKA 101
                                    4455555555666655699999988..69******************86 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 3.6e-05
                                    -S--SGGGEEE.-CTTEEEE--GT CS
                 Choline_kinase 149 HnDlqegNillnkeekklvlIDFE 172
                                    H Dl  +N+ll  +++++++IDF 
  gi|116753990|ref|YP_843108.1| 105 HGDLTTSNMLL--KDNRIYFIDFG 126
                                    9**********..9*********5 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   7.5e-07    0.0012     111     153 ..      90     131 ..      25     145 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 7.5e-07
                                    HHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTTHEET CS
                    Pkinase_Tyr 111 qvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDfGLardi 153
                                     v + +  L++  +vH dl++ N+Ll++n+ +   DfGLa + 
  gi|116753990|ref|YP_843108.1|  90 RVGELVGRLHKAGIVHGDLTTSNMLLKDNR-IYFIDFGLAYHD 131
                                    5555566799*****************665.5666****9754 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 ?   14.1   1.0   2.4e-05      0.04      36     104 ..      28      98 ..       7     101 .. 0.83
   2 ?   -0.4   0.2      0.83   1.4e+03      39      62 ..     157     180 ..     147     186 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.4e-05
                                    CSCHHHHHHHHHHHHHHHHHHHHHHHHCSS-HH....HHHHHHHHHHHHHHHHHHHSGTS-HHHHHHHHHHHH CS
                      TetR_C_31  36 rrPeLraalarlrralrealaallaalGlpdpe....eaarllvaaldGllldrLagpaadpraevrellral 104
                                    r  eL + l++ r+ ++++++a  +++G+p p     ++ +l++ ++dG  l+ +++p  +  + v el+ +l
  gi|116753990|ref|YP_843108.1|  28 RMKELDERLRAERTVMEARIMAEARRAGVPTPIirdvSRFELVMEYVDGKKLRDIITP--ELSERVGELVGRL 98 
                                    7779*************************8664434479999****************..4456777777766 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.83
                                    HHHHHHHHHHHHHHHHHHHHHHHH CS
                      TetR_C_31  39 eLraalarlrralrealaallaal 62 
                                    +L +++ r++r+  +++ a+l+++
  gi|116753990|ref|YP_843108.1| 157 ALIESFKRGYRRAYQRADAVLTRV 180
                                    566667777777777777777764 PP

>> EcKinase  Ecdysteroid kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.9e-05     0.047     213     250 ..      99     130 ..      26     173 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.9e-05
                       EcKinase 213 efnvlnHGDlwvnNimfkydeegepedvilvDFQlsry 250
                                    + + ++HGDl ++N+++k +      +++++DF l+++
  gi|116753990|ref|YP_843108.1|  99 HKAGIVHGDLTTSNMLLKDN------RIYFIDFGLAYH 130
                                    556799***********886......79*****88865 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   7.6e-05      0.12     321     364 ..      97     133 ..      93     186 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 7.6e-05
                 Pkinase_fungal 321 sLflkagiLHrDiSenNilitdskkegerkglLiDLDlakelsd 364
                                    +L+ kagi+H D  + N+l+       +++   iD+ la + + 
  gi|116753990|ref|YP_843108.1|  97 RLH-KAGIVHGDLTTSNMLLK------DNRIYFIDFGLAYHDQS 133
                                    688.****************9......77888888888887664 PP

>> DUF1679  Protein of unknown function (DUF1679)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0     6e-05     0.098     240     285 ..      70     118 ..      42     183 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6e-05
                        DUF1679 240 lvdiveey.lkeililekaskvskvlGi..kkvlvhgDlwsaNiLfsee 285
                                    +++ v+   l +i++ e   +v +++G   k  +vhgDl  +N+L + +
  gi|116753990|ref|YP_843108.1|  70 VMEYVDGKkLRDIITPELSERVGELVGRlhKAGIVHGDLTTSNMLLKDN 118
                                    555554331456777788899******776889************9984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1271.63
//
Query:       gi|116753991|ref|YP_843109.1|  [L=340]
Description: pyruvate formate-lyase activating enzyme [Methanosaeta thermophila PT]
Scores for complete 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-91  306.4   0.0    1.5e-91  306.1   0.0    1.1  1  DUF1786   Putative pyruvate format-lyase activating enzyme (D
  ------ inclusion threshold ------
       0.14   11.2   0.2       0.37    9.7   0.1    1.7  2  DDR       Diol dehydratase reactivase ATPase-like domain


Domain annotation for each model (and alignments):
>> DUF1786  Putative pyruvate format-lyase activating enzyme (DUF1786)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  306.1   0.0   1.7e-95   1.5e-91       1     251 [.      59     304 ..      59     305 .. 0.97

  Alignments for each domain:
  == domain 1  score: 306.1 bits;  conditional E-value: 1.7e-95
                        DUF1786   1 MGGGavtkavkehlkaGlkvvateeaAltlrddlekvkemGieiveeapeeaekielkDvdlealkealeafglelpekv 80 
                                    MGGG++t+av++h+++Gl+v+ateeaAl+l+d+l++v++mG+ei+e++p+++++++++Dvdl al++a+++f+++lpe +
  gi|116753991|ref|YP_843109.1|  59 MGGGPLTAAVRRHIASGLRVYATEEAALSLHDNLQRVRSMGVEITEDPPKDCVDLQTCDVDLIALRTAFSSFDVDLPEAI 138
                                    ******************************************************************************** PP

                        DUF1786  81 avavqDHGyspgesnrkfRfelleelleeggkleelvfeeevpeeftRlkavaeslkeeg.kvvvmDtgaaavlGalldp 159
                                    avavqDHG+sp++snr +Rf++++  l++gg++e++v++e+ p  ++R++av + l+++g ++++mDtg+aav+Gal +p
  gi|116753991|ref|YP_843109.1| 139 AVAVQDHGFSPERSNRATRFDIIRASLKNGGRIEDFVYREP-PVVLSRMRAVWSYLHDQGmDILLMDTGPAAVFGALEEP 217
                                    *****************************************.***************9999******************* PP

                        DUF1786 160 eveklsgalvvnvGngHtlaalvkegrivgvfEhHTsaltkekleelieklaegeltneevfedgGHGvlaaaekeeaee 239
                                    + +   +alv+n+GngHt++alv+++ri+++fEhHTsal++ +l+ +++++++geltn e+fedgGHG ++++++    e
  gi|116753991|ref|YP_843109.1| 218 KCKM--PALVLNIGNGHTIGALVDDNRITAIFEHHTSALDPLRLNFILRRFCAGELTNSEIFEDGGHG-AHTEYV--PGE 292
                                    **96..**************************************************************.444444..589 PP

                        DUF1786 240 vekvvvtGPrre 251
                                    v++v+vtGPrr+
  gi|116753991|ref|YP_843109.1| 293 VRTVLVTGPRRR 304
                                    9*********96 PP

>> DDR  Diol dehydratase reactivase ATPase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.25   2.2e+03     137     148 ..       4      15 ..       2      23 .. 0.73
   2 ?    9.7   0.1   4.2e-05      0.37     120     157 ..     208     244 ..     198     254 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.25
                            DDR 137 ilDlGaGstDaa 148
                                     +D+GaG+ D  
  gi|116753991|ref|YP_843109.1|   4 AVDVGAGTQDIL 15 
                                    58******9944 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 4.2e-05
                            DDR 120 mAilGalttPGtekplailDlGaGstDaalieeegevk 157
                                    +A+ Gal  P  + p  +l++G G t  al+++++ ++
  gi|116753991|ref|YP_843109.1| 208 AAVFGALEEPKCKMPALVLNIGNGHTIGALVDDNR-IT 244
                                    79************************999998654.44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       241  (0.0134419); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2668.33
//
Query:       gi|116753992|ref|YP_843110.1|  [L=431]
Description: pyridoxal-5'-phosphate-dependent enzyme, beta subunit [Methanosaeta thermophila PT]
Scores for complete 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-28   98.1   0.0    8.8e-28   97.6   0.0    1.2  1  PALP      Pyridoxal-phosphate dependent enzyme
  ------ inclusion threshold ------
       0.28   11.1   1.2       0.59   10.1   0.4    1.9  2  HalOD2    Halobacterial output domain 2


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 !   97.6   0.0   9.8e-32   8.8e-28      24     294 .]     106     393 ..      83     393 .. 0.82

  Alignments for each domain:
  == domain 1  score: 97.6 bits;  conditional E-value: 9.8e-32
                                    EEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-EEEEEEETTS-HHHHHHHHHTT.- CS
                           PALP  24 lflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGlkvtivvpadaspekvallrllG.a 102
                                     +  +  l  t+SfK + a+  ++ l+  ++++t+v+as+GN++ra A +++    +++++vp ++  +++  + + G  
  gi|116753992|ref|YP_843110.1| 106 YWPERGALMRTCSFKELEAAPTMQMLRDRKAGETLVVASAGNTARAFAEVCSITDQPLILFVPVSSL-DRIWTTVEPGrV 184
                                    5556667788**********9999999999************************************9.**********33 PP

                                    EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHTTTTEEEEEEE-SSSHHHHHHHHHHHH.. CS
                           PALP 103 evvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileqlggkpdavvvpvGgGgliaGiaaglke.. 180
                                     vv v+gdy +a ++a  l ++  g+       n ++ +g+gt+ l  +++++  p++ + ++G+G    +++ + +   
  gi|116753992|ref|YP_843110.1| 185 LVVGVKGDYADAIKLADVLSSR-SGFRAEGGARNIARRDGMGTVLLDHVRRFNSLPNHYFQAIGSGTGGIAVWEASMRii 263
                                    44555**********7666666.6666666666*********************************99999999999988 PP

                                    ...HSTT..-EEEEEEECTTCGGTTCC.S..S.SS..B.SSS.CCSTCS.........CGTTCCHHHHSEEEEEEEEEEH CS
                           PALP 181 ...rrpd..vrvigvepegsdalarsl.ragrrvtvpvsdtiadglavg.........spselafelldrlvdeivtvsd 245
                                       r+++  +r+  ++++ ++++++ +   g++++   +  + +g++ +         ++   + +++  ++ +i+++++
  gi|116753992|ref|YP_843110.1| 264 edgRFGErlPRLHLAQNTPCAPVYNMWhGMGSEESDFDAYGCPEGMHDDvlfnrnppyAVPGGVRDAVISSGERIYGIDN 343
                                    877666689******************2223333333335566666666554454333333333444445555******* PP

                                    HHHHHHHHHHHHHHSB-B-HHHHHHHHHH.HHHHHHCCTTCEEEEEEE-B CS
                           PALP 246 eealeamrllarregivvepssaaalaal.klreagelkegdrvvviltg 294
                                      a++a++l+   egi + p++ +a+aal +++e g ++++d++++ +tg
  gi|116753992|ref|YP_843110.1| 344 SRAVSAQKLFEMSEGIDILPAASVAVAALvDAVESGFVENDDDILLNITG 393
                                    ***********************************************998 PP

>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.4   6.5e-05      0.59      26      47 ..      16      37 ..      11      39 .. 0.88
   2 ?   -3.3   0.0      0.96   8.6e+03       8      19 ..     283     294 ..     280     298 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 6.5e-05
                         HalOD2 26 qLGayvWkCtrCGevqaaAdpS 47
                                    +G y+ +C++CG+ + +  +S
  gi|116753992|ref|YP_843110.1| 16 SMGEYTLRCAGCGNLLIGGAAS 37
                                   589************9998887 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.96
                         HalOD2   8 CsldWttrhGdg 19 
                                    C   +  +hG g
  gi|116753992|ref|YP_843110.1| 283 CAPVYNMWHGMG 294
                                    666677889987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 3089.96
//
Query:       gi|116753993|ref|YP_843111.1|  [L=253]
Description: ABC transporter related [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      4e-13   50.0   0.0    5.7e-13   49.5   0.0    1.2  1  ABC_tran     ABC transporter
    2.7e-09   37.3   0.3     0.0022   17.9   0.1    2.7  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    0.00012   22.4   0.0    0.00043   20.6   0.0    1.8  1  AAA_22       AAA domain
    0.00016   21.2   0.1       0.14   11.6   0.0    2.2  2  SMC_N        RecF/RecN/SMC N terminal domain
    0.00062   20.2   0.0      0.001   19.5   0.0    1.4  1  AAA_16       AAA ATPase domain
     0.0066   16.2   0.1      0.015   15.0   0.1    1.5  1  AAA_29       P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.021   15.4   0.0       0.03   14.8   0.0    1.2  1  AAA_23       AAA domain
      0.022   14.5   0.1       0.44   10.2   0.0    2.3  3  AAA_30       AAA domain
      0.037   14.1   0.1       0.13   12.3   0.0    1.9  2  MMR_HSR1     50S ribosome-binding GTPase
      0.042   13.8   0.0      0.077   12.9   0.0    1.4  1  RsgA_GTPase  RsgA GTPase
      0.054   12.3   0.0       0.08   11.7   0.0    1.1  1  Adeno_IVa2   Adenovirus IVa2 protein
      0.068   12.9   0.0       0.12   12.1   0.0    1.4  1  ATP_bind_1   Conserved hypothetical ATP binding protein
      0.085   12.1   0.0       0.12   11.6   0.0    1.4  1  KAP_NTPase   KAP family P-loop domain
       0.11   13.0   0.0       0.23   12.0   0.0    1.6  2  AAA_18       AAA domain
       0.11   12.6   0.0        2.4    8.3   0.0    2.1  2  AAA_2        AAA domain (Cdc48 subfamily)
       0.14   12.1   0.0        3.3    7.6   0.0    2.1  2  ATPase_2     ATPase domain predominantly from Archaea
       0.17   10.7   0.0       0.29   10.0   0.0    1.4  1  AAA_PrkA     PrkA 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 !   49.5   0.0   5.4e-16   5.7e-13       5     135 ..      20     164 ..      17     166 .. 0.76

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 5.4e-16
                                    EEEEETTSEEEEEESTTSSHHHHHHHHTTSS--...SEEEEEETTCEGGGB-HHHCCHC.EEEE-SS--S-TTSBHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx. RF
                       ABC_tran   5 slklkegekvaivGenGaGKStLlkllagllkp...teGeilldgkdlkeqeleslrke.igvlpqepqlfpeltvren. 79 
                                    s++++ ge+++ivG++G+GKS+L++ l +  +        +l+dg + + + ++  rk+ ++ l+q+ ++  +++v +  
  gi|116753993|ref|YP_843111.1|  20 SVDVSSGEVIGIVGPTGSGKSSLISDLEQFAQGdtsSRRYVLIDGSPPDPEMRHDPRKKpVAQLSQNMHFLADMKVCDFi 99 
                                    789*********************999999888444555689****99997776666543999***********999999 PP

                                    .....HHHTC......HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHH.HHHHTSSEEEEEST CS
                                    .....xxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                       ABC_tran  80 .....esdee......iekalsklglkelkdtvvksspssLSgGqkqrvalar.allkkpkllllDEp 135
                                             +      ++k+l+  +    +  +++++ ++LSgGq + +++a  a++++++++l+DE 
  gi|116753993|ref|YP_843111.1| 100 cmharS---RgrdpglLSKVLEITNTLTGEPVHANDNLTELSGGQSRALMVADiAVISDSPIVLIDEI 164
                                    997642...23345554444444444443333444444**************737899********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 !   16.3   0.0   6.1e-06    0.0064       2      44 ..      29      64 ..      28      88 .. 0.73
   2 !   17.9   0.1   2.1e-06    0.0022     233     269 ..     133     167 ..     104     196 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6.1e-06
                         AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirk 44
                                    +++Gp gsGKS+L+  l+ +a+       + +++++++ i++
  gi|116753993|ref|YP_843111.1| 29 IGIVGPTGSGKSSLISDLEQFAQ-------GDTSSRRYVLIDG 64
                                   68****************98875.......4444444444444 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 2.1e-06
                         AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEng 269
                                    +++elS G+ r+  +++ ++   ++ +++liDE+En 
  gi|116753993|ref|YP_843111.1| 133 NLTELSGGQSRA-LMVADIAVISDS-PIVLIDEIENA 167
                                    67899*******.************.*********94 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   4.1e-07   0.00043       6     128 ..      27     187 ..      21     196 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 4.1e-07
                         AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee...................................erpevvfvtlpss 50 
                                     ++ ++G++G+GK+ l+  l + ++ + + ++                                   +  +++ + + s 
  gi|116753993|ref|YP_843111.1|  27 EVIGIVGPTGSGKSSLISDLEQFAQGDTSSRRyvlidgsppdpemrhdprkkpvaqlsqnmhfladmKVCDFICMHARSR 106
                                    56779******************988877777************************999999997777777778888888 PP

                         AAA_22  51 tsskdllrellralglelka...........erlsseellealeqalrarav........ielliiDEaqhlr..seeal 109
                                    +    ll+++l++++  + +           ++++s++l  +         v         ++++iDE+++    ++eal
  gi|116753993|ref|YP_843111.1| 107 GRDPGLLSKVLEITNTLTGEpvhandnltelSGGQSRAL--M---------VadiavisdSPIVLIDEIENAGirKKEAL 175
                                    877778888888888766666665555533222222222..3.........2333344445899*******854448888 PP

                         AAA_22 110 eeLrsllnlsrkgvqliLv 128
                                    + L       +   +++Lv
  gi|116753993|ref|YP_843111.1| 176 RLL-------SGEGKIVLV 187
                                    777.......444444444 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 !   11.6   0.0   0.00013      0.14      25      51 ..      27      54 ..      18      60 .. 0.75
   2 !    7.8   0.0    0.0019         2     136     170 ..     136     167 ..      72     190 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00013
                                   SEEEEEESTTSSHHHHHHHH.HHHCTT. CS
                                   xxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                          SMC_N 25 sftaivGpNGSGKsnlldAi.lFvLGer 51
                                   ++  ivGp GSGKs+l+  + +F  G++
  gi|116753993|ref|YP_843111.1| 27 EVIGIVGPTGSGKSSLISDLeQFAQGDT 54
                                   5678***********9976634666655 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0019
                                    CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaa 170
                                    +LSgG+   +++a    i  ++ +p++l+Dei+ a
  gi|116753993|ref|YP_843111.1| 136 ELSGGQSRALMVAD---IAVISDSPIVLIDEIENA 167
                                    89****88666554...677899*********976 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   9.5e-07     0.001      22     161 ..      24     181 ..      14     194 .. 0.63

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 9.5e-07
                         AAA_16  22 grpelvllsGesGvGKsslvrellralekd...ggif.lrgkcdqlesa.....ipy...sa.laqalareellrqllde 88 
                                    +++e++ ++G+ G+GKssl+  l + +++d   + ++ + g   + e+       p    s+    ++   +++  ++ +
  gi|116753993|ref|YP_843111.1|  24 SSGEVIGIVGPTGSGKSSLISDLEQFAQGDtssRRYVlIDGSPPDPEMRhdprkKPVaqlSQnMHFLA-DMKVCDFICMH 102
                                    4448999*****************99999888855565888888884444455544433355444444.44788888877 PP

                         AAA_16  89 aesaeleawrekleealaavpelagaea...........srllellkrllallsrderplvlvlDdlqwadeaslqllaa 157
                                    a+s  +++++  l ++l++++ l+g+              + ++l+ + +a +s   +  ++++D+++ a     ++l++
  gi|116753993|ref|YP_843111.1| 103 ARS--RGRDPGLLSKVLEITNTLTGEPVhandnltelsgGQSRALMVADIAVISD--S-PIVLIDEIENAGIRKKEALRL 177
                                    444..66666677777775555555444444445444334444444444444443..3.577788888888777777777 PP

                         AAA_16 158 Llrl 161
                                    L  +
  gi|116753993|ref|YP_843111.1| 178 LSGE 181
                                    7665 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   1.4e-05     0.015      16      39 ..      20      43 ..      14      54 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.4e-05
                         AAA_29 16 tieidlkgatlltGpsGsGKSTll 39
                                   +++++  +++ ++Gp+GsGKS+l+
  gi|116753993|ref|YP_843111.1| 20 SVDVSSGEVIGIVGPTGSGKSSLI 43
                                   56677555899***********98 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   2.8e-05      0.03      20      37 ..      27      44 ..      16      77 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.8e-05
                         AAA_23 20 gltlItGpNGaGKTTild 37
                                    +  I+Gp+G+GK++++ 
  gi|116753993|ref|YP_843111.1| 27 EVIGIVGPTGSGKSSLIS 44
                                   5789************96 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00042      0.44      15      43 ..      23      51 ..      16      64 .. 0.81
   2 ?    1.7   0.0      0.18   1.9e+02      82     109 ..     149     176 ..     111     195 .. 0.70
   3 ?   -3.0   0.0       4.7     5e+03     151     175 ..     223     246 ..     202     251 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00042
                         AAA_30 15 tsgdrvavltGpAGtGKttalkalreawe 43
                                    s+  v  ++Gp G+GK+ +++ l++ ++
  gi|116753993|ref|YP_843111.1| 23 VSSGEVIGIVGPTGSGKSSLISDLEQFAQ 51
                                   45556999**************9998776 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.18
                         AAA_30  82 grarlepgtllivDEagmvdtkqlaall 109
                                    + a ++++ ++++DE+  +++++ +al 
  gi|116753993|ref|YP_843111.1| 149 DIAVISDSPIVLIDEIENAGIRKKEALR 176
                                    4455667789*********999988764 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 4.7
                         AAA_30 151 LtevvRqkeseeraaalalregdae 175
                                     ++++R  +++  ++ + +r+g++ 
  gi|116753993|ref|YP_843111.1| 223 CDSLFRV-DTWLLSLRESIRRGEVL 246
                                    4556666.56777777777777765 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   0.00013      0.13       2      19 ..      29      46 ..      28      62 .. 0.87
   2 ?   -1.2   0.0         2   2.1e+03      80      82 ..     158     160 ..     112     206 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                                   EEEEESTTSSHHHHHHHH CS
                       MMR_HSR1  2 vaivGrpNvGKStLinal 19
                                   ++ivG + +GKS+Li+ l
  gi|116753993|ref|YP_843111.1| 29 IGIVGPTGSGKSSLISDL 46
                                   89*************987 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2
                                    EEE CS
                       MMR_HSR1  80 llv 82 
                                    +++
  gi|116753993|ref|YP_843111.1| 158 IVL 160
                                    222 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.3e-05     0.077      98     124 ..      25      51 ..      15      64 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.3e-05
                                    TTSEEEEECSTTSSHHHHHHHHCTT-- CS
                    RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpele 124
                                    +++++ +vG++G GKS+Li  l + ++
  gi|116753993|ref|YP_843111.1|  25 SGEVIGIVGPTGSGKSSLISDLEQFAQ 51 
                                    5678889*************9987555 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   7.6e-05      0.08      78     107 ..      18      46 ..      11      50 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.6e-05
                     Adeno_IVa2  78 lsslnyglqPviGviyGPtGsGksqllrnl 107
                                    + s+++    viG++ GPtGsGks l+ +l
  gi|116753993|ref|YP_843111.1|  18 VRSVDVSSGEVIGIV-GPTGSGKSSLISDL 46 
                                    56788888899**75.**********9876 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00011      0.12       1      30 [.      31      60 ..      31      67 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                     ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrsvavv 30
                                   +vGp GsGK+++++ l ++++    s ++v
  gi|116753993|ref|YP_843111.1| 31 IVGPTGSGKSSLISDLEQFAQGDTSSRRYV 60
                                   79*****************99776666665 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00011      0.12      15      81 ..      21      87 ..      14     179 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                     KAP_NTPase 15 ptlatpivvgLygkWGsGKssllnkledelkefakpvrflfaefnawsfkggddavaellaaLadal 81
                                    +++ + v+g+ g+ GsGKssl+  le+  +    ++r + ++ ++  ++ + d+ ++ +a+L++ +
  gi|116753993|ref|YP_843111.1| 21 VDVSSGEVIGIVGPTGSGKSSLISDLEQFAQGDTSSRRYVLIDGSPPDPEMRHDPRKKPVAQLSQNM 87
                                   55677889******************99877777677777777777777777777777777776655 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   0.00022      0.23       1      20 [.      29      48 ..      29      99 .. 0.73
   2 ?   -2.8   0.0       8.2   8.6e+03      71      89 ..     179     197 ..     158     221 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00022
                         AAA_18  1 IlltGtpGvGKttlakeLsk 20
                                   I++ G+ G+GK++l   L++
  gi|116753993|ref|YP_843111.1| 29 IGIVGPTGSGKSSLISDLEQ 48
                                   89**************9943 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 8.2
                         AAA_18  71 leegknlvidghlaelese 89 
                                    ++egk +++  h   l  +
  gi|116753993|ref|YP_843111.1| 179 SGEGKIVLVVTHDPLLALM 197
                                    4455555554444444433 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.14   1.5e+02       6      29 ..      29      52 ..      26      93 .. 0.79
   2 ?    8.3   0.0    0.0023       2.4      70      94 ..     148     182 ..     112     213 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.14
                                   EEEE--TTSSHHHHHHHHHHHTT- CS
                          AAA_2  6 illlgptgvGktelakalaellfv 29
                                   i ++gptg+Gk+ l   l+++ + 
  gi|116753993|ref|YP_843111.1| 29 IGIVGPTGSGKSSLISDLEQFAQG 52
                                   5689*********99999999874 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0023
                                    S.........EEEEETGGG----.---------HH CS
                          AAA_2  70 G.........ivllDEidKihpk.essgadvSreg 94 
                                              ivl+DEi+ +  + +++ +  S+eg
  gi|116753993|ref|YP_843111.1| 148 AdiavisdspIVLIDEIENAGIRkKEALRLLSGEG 182
                                    0444555556*********9887677777777776 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0031       3.3      19      39 ..      25      45 ..      18      62 .. 0.80
   2 ?    2.4   0.0      0.11   1.2e+02     112     137 ..     149     171 ..     113     180 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0031
                       ATPase_2 19 pneiyfiYGpegsGKtaLlke 39
                                   + e++ i Gp gsGK++L+  
  gi|116753993|ref|YP_843111.1| 25 SGEVIGIVGPTGSGKSSLISD 45
                                   5678899***********976 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.11
                       ATPase_2 112 kikkkgkkiiiiiDelqklidlglng 137
                                    +i      +i++iDe+ +++ +  ++
  gi|116753993|ref|YP_843111.1| 149 DIAVISDSPIVLIDEIENAG-I--RK 171
                                    555556679********998.3..33 PP

>> AAA_PrkA  PrkA AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00027      0.29      90     124 ..      28      66 ..      20     109 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00027
                       AAA_PrkA  90 ilyllGPvggGksslverlkklleaa...piyal.egsP 124
                                    ++ ++GP g+Gkssl+  l +  +       y+l +gsP
  gi|116753993|ref|YP_843111.1|  28 VIGIVGPTGSGKSSLISDLEQFAQGDtssRRYVLiDGSP 66 
                                    7779**************999877554456677666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1694.13
//
Query:       gi|116753994|ref|YP_843112.1|  [L=232]
Description: cobalamin synthesis protein, P47K [Methanosaeta thermophila PT]
Scores for 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-14   51.4   0.0    1.6e-13   50.6   0.0    1.4  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
    2.8e-05   23.2   0.0      0.011   14.8   0.0    2.3  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
     0.0002   21.7   0.0    0.00035   20.9   0.0    1.4  1  AAA_19           AAA domain
     0.0023   17.8   0.0     0.0041   17.0   0.0    1.4  1  MobB             Molybdopterin guanine dinucleotide synthesis
      0.004   16.5   0.0      0.011   15.0   0.0    1.7  2  Zeta_toxin       Zeta toxin
     0.0052   17.3   0.0     0.0077   16.8   0.0    1.5  1  AAA_18           AAA domain
     0.0057   16.3   0.0     0.0089   15.7   0.0    1.3  1  SRP54            SRP54-type protein, GTPase domain
     0.0094   15.2   0.0      0.012   14.9   0.0    1.1  1  DUF2075          Uncharacterized conserved protein (DUF2075)
  ------ inclusion threshold ------
      0.017   14.6   0.0      0.028   13.9   0.0    1.3  1  KTI12            Chromatin associated protein KTI12
      0.031   14.4   0.1      0.056   13.6   0.1    1.7  1  AAA_33           AAA domain
      0.036   14.4   0.0      0.067   13.6   0.0    1.5  1  AAA_16           AAA ATPase domain
       0.04   14.0   0.0      0.053   13.6   0.0    1.4  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
       0.04   13.8   0.1      0.067   13.1   0.0    1.5  1  TK               Thymidine kinase
      0.051   13.5   0.0      0.071   13.0   0.0    1.2  1  ATPase_2         ATPase domain predominantly from Archaea
      0.053   13.4   0.0       0.08   12.8   0.0    1.3  1  Ploopntkinase3   P-loop Nucleotide Kinase3
      0.056   12.7   0.0      0.065   12.5   0.0    1.2  1  MipZ             ATPase MipZ
       0.06   13.3   0.1       0.24   11.3   0.0    1.9  2  NACHT            NACHT domain
      0.078   12.9   0.1       0.13   12.2   0.1    1.3  1  NTPase_1         NTPase
      0.081   12.7   0.0        0.2   11.4   0.0    1.6  2  ATP_bind_1       Conserved hypothetical ATP binding protein
      0.088   11.9   0.4       0.17   10.9   0.2    1.5  2  LpxK             Tetraacyldisaccharide-1-P 4'-kinase
        0.1   11.5   0.0       0.14   11.0   0.0    1.2  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
       0.11   12.2   0.1       0.18   11.5   0.1    1.3  1  AAA_30           AAA domain
       0.11   11.8   0.0       0.16   11.3   0.0    1.2  1  DnaB_C           DnaB-like helicase C terminal domain
       0.14   11.8   0.0       0.21   11.3   0.0    1.2  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.15   11.8   0.0       0.21   11.3   0.0    1.4  1  AAA_11           AAA domain
       0.16   12.2   0.0       0.32   11.2   0.0    1.5  1  AAA_28           AAA domain
       0.17   12.2   0.0       0.29   11.4   0.0    1.4  1  AAA_22           AAA domain
       0.17   11.6   0.0       0.23   11.1   0.0    1.3  1  PRK              Phosphoribulokinase / Uridine kinase family
       0.21   10.3   0.0        0.3    9.8   0.0    1.1  1  RNA12            RNA12 protein


Domain annotation for each model (and alignments):
>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6   0.0   2.7e-16   1.6e-13       2     176 ..       3     164 ..       2     165 .. 0.89

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 2.7e-16
                                    EEEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCCHCCCT..EEEETTTTECCHCTT-HHHHHHHHHH CS
                           cobW   2 vtvltGflGsGKTtLlnhll..enraglklavivNefgevsiDaellretgve.ivelenGciCctlredllkelealee 78 
                                    ++v++G +GsGKT++l h++   ++ g + av+  +     +D +++++ gv+  v l+   ++   +   ++e+ + ++
  gi|116753994|ref|YP_843112.1|   3 MVVIAGTPGSGKTSVLMHTVknLQEMGIRPAVVKIDCL-WTEDDARINRLGVPvRVGLARDMCPDHYSIYNTEEMVSWAS 81 
                                    689*****************7666778899********.88888889999888679999999998888888888888888 PP

                                    HHTT-SEEEEEECT.TTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHHHCHC. CS
                           cobW  79 reerldviliEttG.laePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDlldeea 157
                                     +   dv+l Et G  +  ap                 v+v+D+    +++ +++ k++  l++ad++v +K Dl+++++
  gi|116753994|ref|YP_843112.1|  82 SQ-GADVLLNETAGlCLRCAPY----------PDRALAVCVIDV----TSGPNTPLKIGPLLTTADVVVATKGDLVSQAE 146
                                    88.7**********87888888..........4566789*****....99*****************************8 PP

                                    .HHHHHHHHHHHHTTS-EE CS
                           cobW 158 llekleerlrqlnpeakvl 176
                                      e+++er+ ++np+ +++
  gi|116753994|ref|YP_843112.1| 147 R-EVFRERVVEVNPKCRIV 164
                                    8.************99886 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 !   14.8   0.0   1.7e-05     0.011      31      66 ..       3      38 ..       1      45 [. 0.93
   2 !    6.2   0.0    0.0072       4.4     109     228 ..      72     184 ..      69     194 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.7e-05
                                   EEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE- CS
                           MeaB 31 vvGltGvPGaGkstlvealglelrrrGkrvavlavD 66
                                   +v + G+PG+Gk  ++ + + +l++ G r av+ +D
  gi|116753994|ref|YP_843112.1|  3 MVVIAGTPGSGKTSVLMHTVKNLQEMGIRPAVVKID 38
                                   57799******************************9 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0072
                                    HHHHHHHHHHHTT-SEEEEEEESSTTHHHHHHTT-SEEEEEEES..STTTTTTT--CC.CHHH-SEEEEE---.HHHHHH CS
                           MeaB 109 ktrevvllleaaGfDvvlietvGvGqsevdvaevvdtfvvlllp..eaGDelqgikkG.ileiaDiivvnkaD.kkeaek 184
                                    +t e+v    + G Dv+l et G        a   d  +++ +    +G +   +k G +l  aD++v  k D  ++ae+
  gi|116753994|ref|YP_843112.1|  72 NTEEMVSWASSQGADVLLNETAGLCL---RCAPYPDRALAVCVIdvTSGPN-TPLKIGpLLTTADVVVATKGDlVSQAER 147
                                    57888888899999999999999875...4555555555444320033444.45676658999*********94444444 PP

                                    HHHHHHHHHHHCSTTBTTB--EEEEEBCCCTBSHHHHHHHHHHH CS
                           MeaB 185 aarelraaleleeekekeWrpkvlktsavegeGidelvdaieeh 228
                                         +      +  e + + +++++ +++g+G  el+d i+  
  gi|116753994|ref|YP_843112.1| 148 EV-FRE------RVVEVNPKCRIVEANGLTGKGSRELADIIKYS 184
                                    32.222......22244456788899999999999998877654 PP

>> AAA_19  AAA 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   0.00035      11      40 ..       2      31 ..       1      45 [. 0.85

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 5.7e-07
                         AAA_19 11 kvllvtaGpGtGKTrvlkhivallvelggv 40
                                   k++++ + pG+GKT vl+h v+ l+e+g +
  gi|116753994|ref|YP_843112.1|  2 KMVVIAGTPGSGKTSVLMHTVKNLQEMGIR 31
                                   67899999*****************99854 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 !   17.0   0.0   6.7e-06    0.0041       2      35 ..       4      37 ..       3      46 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.7e-06
                           MobB  2 lgivgksgsGKTtLleklipelkarglrvgtiKh 35
                                   + i+g+ gsGKT+ l + ++ l++ g+r +++K 
  gi|116753994|ref|YP_843112.1|  4 VVIAGTPGSGKTSVLMHTVKNLQEMGIRPAVVKI 37
                                   7899****************************96 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.8e-05     0.011      17      42 ..       2      28 ..       2      47 .. 0.80
   2 ?   -2.8   0.0       5.3   3.3e+03      77      99 ..      73      88 ..      56      92 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.8e-05
                     Zeta_toxin 17 klillgGqpGAGKselaellkdele.r 42
                                   k+++++G pG+GK++++  + ++l+ +
  gi|116753994|ref|YP_843112.1|  2 KMVVIAGTPGSGKTSVLMHTVKNLQeM 28
                                   689**************9999998743 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5.3
                     Zeta_toxin 77 qkdaselvekllqeaiengynii 99
                                           e+++ +a ++g +++
  gi|116753994|ref|YP_843112.1| 73 T-------EEMVSWASSQGADVL 88
                                   3.......444555555555555 PP

>> AAA_18  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    0.0077       1      37 [.       4      46 ..       4      99 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.3e-05
                         AAA_18  1 IlltGtpGvGKttlakeLskrl.gf.....gvnlrdvakengl 37
                                   ++++GtpG+GKt++  +  k l ++     +v++ ++++e++ 
  gi|116753994|ref|YP_843112.1|  4 VVIAGTPGSGKTSVLMHTVKNLqEMgirpaVVKIDCLWTEDDA 46
                                   79***********987666666555668887777777776665 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.4e-05    0.0089       2      93 ..       2      94 ..       1      98 [. 0.92

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.4e-05
                                   EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEE.SSTTSCHHHHHHHHHHHHHHT CS
                          SRP54  2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvik.kkeeadpaavakeavekakee 82
                                   ++++++G+ G+GKT+ l    + l+++g ++++v  D+        ++ l+  ++v + + +  ++ ++  ++e v+ a ++
  gi|116753994|ref|YP_843112.1|  2 KMVVIAGTPGSGKTSVLMHTVKNLQEMGIRPAVVKIDCLWTEDDARINRLGVPVRVGLARdMCPDHYSIYNTEEMVSWASSQ 83
                                   57899**************************************99********99999886666677788889999****** PP

                                   TSSEEEEEE-- CS
                          SRP54 83 kidvvlvDTaG 93
                                   ++dv+l  TaG
  gi|116753994|ref|YP_843112.1| 84 GADVLLNETAG 94
                                   **********9 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.9e-05     0.012       2      26 ..       2      26 ..       1      47 [. 0.88

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.9e-05
                        DUF2075  2 avvlVtGvaGtGKtvvllnllaele 26
                                   ++v++ G +G+GKt vl++ + +l+
  gi|116753994|ref|YP_843112.1|  2 KMVVIAGTPGSGKTSVLMHTVKNLQ 26
                                   689*****************99983 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.5e-05     0.028       1      40 [.       1      40 [.       1      50 [. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.5e-05
                                   E.EEEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHH CS
                          KTI12  1 MpLvvltGlPssGKstrakeLakaleeekrsvvviddesl 40
                                   M +vv+ G P sGK+++  +  k l+e +++  v++ + l
  gi|116753994|ref|YP_843112.1|  1 MKMVVIAGTPGSGKTSVLMHTVKNLQEMGIRPAVVKIDCL 40
                                   889************************8888888776655 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   9.1e-05     0.056       1      25 [.       3      38 ..       3     167 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.1e-05
                         AAA_33  1 lvllvGlpGsGKstlaerllkklg...........a 25
                                   +v++ G pGsGK+ ++ + +k+l+            
  gi|116753994|ref|YP_843112.1|  3 MVVIAGTPGSGKTSVLMHTVKNLQemgirpavvkiD 38
                                   6899****************9999665554333333 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   0.00011     0.067      26      51 ..       3      28 ..       1      68 [. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00011
                         AAA_16 26 lvllsGesGvGKsslvrellralekd 51
                                   +v++ G +G+GK+s++ +  + l++ 
  gi|116753994|ref|YP_843112.1|  3 MVVIAGTPGSGKTSVLMHTVKNLQEM 28
                                   799*************9998888877 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   0.0   8.6e-05     0.053       2      37 ..       4      39 ..       3     158 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.6e-05
                                   EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA  2 aiastkGGvGKTtlaanLaralarrglrVllvDaDp 37
                                   ++++++ G+GKT+++ +  + l++ g r ++v+ D 
  gi|116753994|ref|YP_843112.1|  4 VVIAGTPGSGKTSVLMHTVKNLQEMGIRPAVVKIDC 39
                                   6889999**************************995 PP

>> TK  Thymidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00011     0.067       2      37 ..       2      37 ..       1      92 [. 0.71

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
                             TK  2 sielilgpmfaGKsteLlrrvkryqlaekkvvvika 37
                                   ++ +i g+  +GK++ L+++vk++q+   +  v+k 
  gi|116753994|ref|YP_843112.1|  2 KMVVIAGTPGSGKTSVLMHTVKNLQEMGIRPAVVKI 37
                                   677899999*******************99999884 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   0.00011     0.071      22      62 ..       3      45 ..       1      57 [. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00011
                       ATPase_2 22 iyfiYGpegsGKtaLlkeiienledkdk..yviyyialreesi 62
                                   +++i G  gsGKt++l++ ++nl++ +    v+ ++ l +e+ 
  gi|116753994|ref|YP_843112.1|  3 MVVIAGTPGSGKTSVLMHTVKNLQEMGIrpAVVKIDCLWTEDD 45
                                   689********************99987556666666655555 PP

>> Ploopntkinase3  P-loop Nucleotide Kinase3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00013      0.08       4      98 ..       2      96 ..       1     109 [. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                 Ploopntkinase3  4 rliylvGqPGaGkstlmaeltkgfdrskveqeeetvphdvlvdrttGev....vgaelGkrreafsGtdalassiidkavPw 81
                                   +++ + G+PG+Gk+ ++ +  k ++ + ++++  +v  d l  + +  +    v + +G  r++    d  +    +  v w
  gi|116753994|ref|YP_843112.1|  2 KMVVIAGTPGSGKTSVLMHTVKNLQEMGIRPA--VVKIDCLWTEDDARInrlgVPVRVGLARDMC--PDHYSIYNTEEMVSW 79
                                   7999**********9999999***99999955..5777777665555442212555667777764..466666667899999 PP

                 Ploopntkinase3 82 vetkPydlllaeGarla 98
                                    +++  d+ll e a l 
  gi|116753994|ref|YP_843112.1| 80 ASSQGADVLLNETAGLC 96
                                   99999999999999775 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    0.0001     0.065       4      61 ..       5      60 ..       2     135 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0001
                                   EE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHHHHHHHHHHHHT-- CS
                           MipZ  4 vlgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlarylenraataerkgls 61
                                   v+     GsGk+ + +h +  L ++G r a++ +d+          nr+ +  r gl+
  gi|116753994|ref|YP_843112.1|  5 VI-AGTPGSGKTSVLMHTVKNLQEMGIRPAVVKIDCLWTEDDA-RINRLGVPVRVGLA 60
                                   33.34569***************************96443332.23555555555555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0    0.0004      0.24       2      26 ..       3      27 ..       2      34 .. 0.88
   2 ?   -1.0   0.0       2.4   1.5e+03     117     149 ..     127     159 ..     122     171 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0004
                                   CEEEEC-TTTCHHHHHHHHHHHHCT CS
                          NACHT  2 lvilqGeaGsGKTtLlqklalawae 26
                                   +v++ G +GsGKT  l + +  ++e
  gi|116753994|ref|YP_843112.1|  3 MVVIAGTPGSGKTSVLMHTVKNLQE 27
                                   699*************999888876 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.4
                                    TTT--EEEEEEECCCHHHHCTTSSCE..EEEE- CS
                          NACHT 117 llpeasllltvrpralrdleeqleeaivleveg 149
                                    ll++a ++++++ + ++++e+ + +++v+ev++
  gi|116753994|ref|YP_843112.1| 127 LLTTADVVVATKGDLVSQAEREVFRERVVEVNP 159
                                    788999999999999999999999998999986 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00021      0.13       2      29 ..       4      31 ..       3      43 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00021
                                   EEEE--TTSSHHHHHHHHHHHH...GGG CS
                       NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvk 29
                                   v+i G pG+GKt ++   +++l++ g++
  gi|116753994|ref|YP_843112.1|  4 VVIAGTPGSGKTSVLMHTVKNLQEMGIR 31
                                   79*********************99975 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00032       0.2       1      33 [.       6      38 ..       6      41 .. 0.95
   2 ?   -2.4   0.0       5.4   3.4e+03     159     176 ..     132     150 ..     127     183 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00032
                     ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrsvavvNLD 33
                                   ++G++GsGKt+     ++ l++ g ++avv +D
  gi|116753994|ref|YP_843112.1|  6 IAGTPGSGKTSVLMHTVKNLQEMGIRPAVVKID 38
                                   79****************************998 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.4
                     ATP_bind_1 159 hvvvlnkfDllkek.leke 176
                                     vvv +k Dl+++  +e  
  gi|116753994|ref|YP_843112.1| 132 DVVVATKGDLVSQAeREVF 150
                                    5888888888884433322 PP

>> LpxK  Tetraacyldisaccharide-1-P 4'-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2   0.00028      0.17      47      71 ..      11      35 ..       4      36 .. 0.94
   2 ?   -3.1   0.0       5.1   3.1e+03     177     208 ..     129     160 ..     126     179 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00028
                                   -HSHHHHHHHHHHHTTTS..-EEEE CS
                           LpxK 47 GtGKTPlvialvkllqarglkvgvl 71
                                   G+GKT++ ++ vk lq+ g++++v+
  gi|116753994|ref|YP_843112.1| 11 GSGKTSVLMHTVKNLQEMGIRPAVV 35
                                   9**********************98 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.1
                                    GG-SEEEE..........-TTTSSSS-EEEEE CS
                           LpxK 177 kradlvilngakaeeeeaekaeeksipvlrmr 208
                                     +ad+v+ ++++  +++++++ ++++ +++ +
  gi|116753994|ref|YP_843112.1| 129 TTADVVVATKGDLVSQAEREVFRERVVEVNPK 160
                                    67888888777776666666655555444444 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 ?   11.0   0.0   0.00023      0.14      18      53 ..       4      39 ..       1      48 [. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00023
                  TrwB_AAD_bind 18 ilivGttGsGKtqalekllrairargdraivlDltG 53
                                   ++i+Gt GsGKt +l + ++++++ g r  v+   +
  gi|116753994|ref|YP_843112.1|  4 VVIAGTPGSGKTSVLMHTVKNLQEMGIRPAVVKIDC 39
                                   789********************9998877665555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1    0.0003      0.18      20      46 ..       3      29 ..       1      38 [. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0003
                         AAA_30 20 vavltGpAGtGKttalkalreaweaag 46
                                   ++v+ G +G+GKt +l + ++ +++ g
  gi|116753994|ref|YP_843112.1|  3 MVVIAGTPGSGKTSVLMHTVKNLQEMG 29
                                   789*************99988887766 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00026      0.16      20      45 ..       2      27 ..       1      45 [. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00026
                                   XEEEEEEXTTSSHHHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         DnaB_C 20 dliiiAarpsmGktalalniaenaav 45
                                   ++++iA+ p+ Gkt++ ++ ++n  +
  gi|116753994|ref|YP_843112.1|  2 KMVVIAGTPGSGKTSVLMHTVKNLQE 27
                                   589*****************999874 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 ?   11.3   0.0   0.00034      0.21       2      23 ..       5      25 ..       4      47 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00034
                Viral_helicase1  2 vvhGvpGcGKStlirkllrtsl 23
                                   v++G pG+GK++++ + +++ l
  gi|116753994|ref|YP_843112.1|  5 VIAGTPGSGKTSVLMHTVKN-L 25
                                   89************999988.3 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00034      0.21      19      43 ..       3      27 ..       1      85 [. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00034
                         AAA_11 19 itliqGPPGtgKTktivellsqlls 43
                                   +++i G PG+gKT+++++ +++l +
  gi|116753994|ref|YP_843112.1|  3 MVVIAGTPGSGKTSVLMHTVKNLQE 27
                                   689*****************99954 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00052      0.32       2      24 ..       4      30 ..       3      39 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00052
                         AAA_28  2 ivitGgestGKTtll....eaLaargy 24
                                   +vi G++++GKT++l    ++L+++g+
  gi|116753994|ref|YP_843112.1|  4 VVIAGTPGSGKTSVLmhtvKNLQEMGI 30
                                   8************98666677777765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00046      0.29       6      47 ..       2      39 ..       1      52 [. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00046
                         AAA_22  6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtl 47
                                   +++v+ G +G+GKT +l   +++l+e       rp vv++++
  gi|116753994|ref|YP_843112.1|  2 KMVVIAGTPGSGKTSVLMHTVKNLQEMG----IRPAVVKIDC 39
                                   5899**********99998888886432....3666666666 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00038      0.23       2      41 ..       4      43 ..       3      74 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00038
                            PRK  2 IgvagsSGaGkttvarklekifgrekvkaaeiegdsflrl 41
                                   + +ag  G+Gkt+v  + +k +++ ++++a+++ d + + 
  gi|116753994|ref|YP_843112.1|  4 VVIAGTPGSGKTSVLMHTVKNLQEMGIRPAVVKIDCLWTE 43
                                   569*************************999988766554 PP

>> RNA12  RNA12 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00049       0.3      20      50 ..       4      39 ..       2      50 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00049
                          RNA12 20 ivvkGPrGSGkkeLvldrvlkdrkk......vlvidC 50
                                   +v+ G +GSGk++++++ v k+ ++      v+ idC
  gi|116753994|ref|YP_843112.1|  4 VVIAGTPGSGKTSVLMHTV-KNLQEmgirpaVVKIDC 39
                                   9************987655.55444488998999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                       119  (0.00663729); 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: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 1696.85
//
Query:       gi|116753995|ref|YP_843113.1|  [L=203]
Description: Fe-S cluster domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-12   47.0   0.9    3.6e-12   45.7   0.3    2.0  2  FeS       Putative Fe-S cluster


Domain annotation for each model (and alignments):
>> FeS  Putative Fe-S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   0.3     2e-16   3.6e-12       1      33 []       6      37 ..       6      37 .. 0.97
   2 ?   -3.0   0.0      0.34   6.1e+03      25      31 ..      89      95 ..      86      96 .. 0.71

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 2e-16
                            FeS  1 LPgtNCgaCGypgCmafAealvegeaqledCpp 33
                                   LPg+NCg+CGy++C++fAe l++ e +l++Cp+
  gi|116753995|ref|YP_843113.1|  6 LPGYNCGECGYKSCRDFAEHLSSIE-DLSRCPY 37
                                   9***********************9.8****96 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.34
                            FeS 25 eaqledC 31
                                     +ledC
  gi|116753995|ref|YP_843113.1| 89 IHPLEDC 95
                                   5689999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 1585.60
//
Query:       gi|116753996|ref|YP_843114.1|  [L=183]
Description: carbonate dehydratase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.6e-12   46.6  11.4    0.00013   21.6   0.5    3.8  4  Hexapep     Bacterial transferase hexapeptide (six repeats)
    8.4e-12   44.6   3.6    3.2e-05   23.6   0.0    4.3  4  Hexapep_2   Hexapeptide repeat of succinyl-transferase
  ------ inclusion threshold ------
       0.13   11.2   0.0       0.41    9.5   0.0    1.7  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 !   19.6   0.3   8.6e-08   0.00051      10      35 ..      25      50 ..      22      51 .. 0.88
   2 ?   -2.1   0.1      0.64   3.8e+03       3      16 ..      58      71 ..      56      73 .. 0.56
   3 !   21.6   0.5   2.1e-08   0.00013       1      35 [.      78     112 ..      78     113 .. 0.95
   4 !   11.4   0.1   3.5e-05      0.21       2      34 ..     114     145 ..     113     147 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 8.6e-08
                                   E-TTEEEETTEEE-TTEEEETTEEEE CS
                        Hexapep 10 IgpfaviggnVkIGdnvkIgagvvig 35
                                   ++  av+ g+V IG++v++g+++ i+
  gi|116753996|ref|YP_843114.1| 25 VDETAVVIGDVRIGERVYVGPCASIR 50
                                   56679******************997 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.64
                                   EEETTEEE-TTEEE CS
                        Hexapep  3 vIGsnvlIgpfavi 16
                                   vI + + +  +a++
  gi|116753996|ref|YP_843114.1| 58 VISEECNVQDGAIF 71
                                   56666666666654 PP

  == domain 3  score: 21.6 bits;  conditional E-value: 2.1e-08
                                    TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                        Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                    s+++G++v + ++av++g+ +IGd + Ig ++v++
  gi|116753996|ref|YP_843114.1|  78 SIKLGKKVSVAHGAVVHGPMTIGDESFIGFNAVVH 112
                                    5789*****************************97 PP

  == domain 4  score: 11.4 bits;  conditional E-value: 3.5e-05
                                    EEEETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
                        Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvi 34 
                                    +++G+ ++Ig+ a +  +Vk+ d++ + +g+vi
  gi|116753996|ref|YP_843114.1| 114 STVGERCFIGHRALV-MGVKLKDGSFVPHGSVI 145
                                    579************.89************999 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.4     0.001         6       2      27 ..      35      66 ..      30      71 .. 0.79
   2 ?    1.6   0.3     0.039   2.3e+02      17      32 ..      78      93 ..      56      94 .. 0.83
   3 !   10.8   0.1   5.4e-05      0.32       1      16 [.      96     111 ..      96     116 .. 0.88
   4 !   23.6   0.0   5.3e-09   3.2e-05       3      33 ..     115     146 ..     114     147 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.001
                                   EEE-TT-EE-TT-EE......SEEE-TT-EE- CS
                      Hexapep_2  2 viIGdnCliGanagi......GvslGdncvvg 27
                                   v+IG+++ +G+ a i      ++ + ++c v+
  gi|116753996|ref|YP_843114.1| 35 VRIGERVYVGPCASIradeatPIVISEECNVQ 66
                                   78999999999988777667778888888776 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.039
                                   SEEE-TT-EE-TT-EE CS
                      Hexapep_2 17 GvslGdncvvgaGvvi 32
                                    ++lG+++ v+ G v+
  gi|116753996|ref|YP_843114.1| 78 SIKLGKKVSVAHGAVV 93
                                   4999999999999887 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 5.4e-05
                                    .EEE-TT-EE-TT-EE CS
                      Hexapep_2   1 pviIGdnCliGanagi 16 
                                    p +IGd ++iG na++
  gi|116753996|ref|YP_843114.1|  96 PMTIGDESFIGFNAVV 111
                                    669***********96 PP

  == domain 4  score: 23.6 bits;  conditional E-value: 5.3e-09
                                    EE-TT-EE-TT-EE.SEEE-TT-EE-TT-EE- CS
                      Hexapep_2   3 iIGdnCliGanagi.GvslGdncvvgaGvvit 33 
                                    ++G++C+iG +a + Gv+l d++ v  G+vi+
  gi|116753996|ref|YP_843114.1| 115 TVGERCFIGHRALVmGVKLKDGSFVPHGSVID 146
                                    59***********66***********999997 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.022   1.3e+02     287     349 ..      19      90 ..      12      96 .. 0.73
   2 ?    9.5   0.0   6.8e-05      0.41     271     330 ..      88     145 ..      51     152 .. 0.64

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.022
                     Fucokinase 287 vgegsviehsslk.gnvsigsnsivsglelessee........slelpddtilqtlslklskekeyvtvvfG 349
                                    v++++++ +  +  g+v+ig++ +v  +   + +e        +++++d  i ++l+ ++ k  ++v v+ G
  gi|116753996|ref|YP_843114.1|  19 VATTAYVDETAVViGDVRIGERVYVGPCASIRADEatpiviseECNVQDGAIFHGLKGSSIKLGKKVSVAHG 90 
                                    556666666555558899999999988888877778888888888888888888887776666666666655 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 6.8e-05
                     Fucokinase 271 kesavvinS.vlessvsvgegsviehsslkgnvsigsnsivsglelesseeslelpddtil 330
                                    +++avv+    +  +  +g ++v+  s++++++ ig + +v g++l+ ++    +p  +++
  gi|116753996|ref|YP_843114.1|  88 AHGAVVHGPmTIGDESFIGFNAVVHASTVGERCFIGHRALVMGVKLKDGSF---VPHGSVI 145
                                    333333322123355556677788899999999999999999999998755...6666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       250  (0.0139439); 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):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1484.02
//
Query:       gi|116753997|ref|YP_843115.1|  [L=208]
Description: superoxide dismutase [Methanosaeta thermophila PT]
Scores for complete 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  111.4   0.1    2.7e-32  110.9   0.1    1.2  1  Sod_Fe_C  Iron/manganese superoxide dismutases, C-terminal do
    2.4e-28   98.4   0.4    4.1e-28   97.7   0.4    1.4  1  Sod_Fe_N  Iron/manganese superoxide dismutases, alpha-hairpin


Domain annotation for each model (and alignments):
>> Sod_Fe_C  Iron/manganese superoxide dismutases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.9   0.1   3.1e-36   2.7e-32       1     102 []      99     201 ..      99     201 .. 0.94

  Alignments for each domain:
  == domain 1  score: 110.9 bits;  conditional E-value: 3.1e-36
                                    --HHHHHHHHHHHSSHHHHHHHHHHHHHHSSSSEEEEEEEETT.TEEEEEEEETTTBGGGGTTCEEEEEE-SGGGTHHHH CS
                       Sod_Fe_C   1 psgelaeaieedfgslekfkkefkaaalavfgsGwawLvldkk.kkLeivttknqdnplvkeakplLalDvwehAYyldy 79 
                                    p g+la++i+++fgs+e+f+kef+aaa++v+gsGwa L++  + ++  i++++++++++      lL+lDvwehAYyldy
  gi|116753997|ref|YP_843115.1|  99 PVGALADEIKDEFGSFERFRKEFTAAAVSVEGSGWAALAYCMQtRRPIIMQIEKHNTNICPMFRLLLVLDVWEHAYYLDY 178
                                    6799************************************8774577899999999999998999*************** PP

                                    TT-HHHHHHHHGGGBBHHHHHHH CS
                       Sod_Fe_C  80 qnkradYieafwnvvnWkeveer 102
                                    +n+ra+++eafw++ +W+e+++r
  gi|116753997|ref|YP_843115.1| 179 RNDRAKFVEAFWQIADWEEANRR 201
                                    *******************9986 PP

>> Sod_Fe_N  Iron/manganese superoxide dismutases, alpha-hairpin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.7   0.4   4.6e-32   4.1e-28       2      81 ..      12      91 ..      11      92 .. 0.99

  Alignments for each domain:
  == domain 1  score: 97.7 bits;  conditional E-value: 4.6e-32
                                   ------SS-TTTTTTTS-HHHHHHHHHTHHHHHHHHHHHHHHCHHHHCHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTB CS
                       Sod_Fe_N  2 yeLpeLpYaydaLePhisketlelHhdkHhktYvnnlNkalekleeakkkleelvlkklekalrnnagghvnHslfwknl 81
                                   y+LpeLpY  ++LeP+is+ +l+lHhdkHh +Yvn++N++lekl++a+++  ++++k++ k+l++++ggh++Hslfw n+
  gi|116753997|ref|YP_843115.1| 12 YTLPELPYGAKDLEPYISEAQLKLHHDKHHLAYVNGANAILEKLDKARREGADIDQKSTLKELSFHIGGHLLHSLFWANM 91
                                   9******************************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 1716.63
//
Query:       gi|116753998|ref|YP_843116.1|  [L=316]
Description: 1-phosphofructokinase [Methanosaeta thermophila PT]
Scores for 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-54  182.9   0.0      1e-53  182.7   0.0    1.0  1  PfkB          pfkB family carbohydrate kinase
    1.3e-06   28.0   0.0    1.9e-06   27.5   0.0    1.2  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase
     0.0038   16.7   0.0     0.0043   16.6   0.0    1.1  1  Carb_kinase   Carbohydrate kinase


Domain annotation for each model (and alignments):
>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.7   0.0   1.7e-57     1e-53       4     298 ..       8     296 ..       5     300 .. 0.90

  Alignments for each domain:
  == domain 1  score: 182.7 bits;  conditional E-value: 1.7e-57
                                    EEEEEEEE.EEEEEECSSHTTSEEEESEEEEEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHHHHHHTTEEETTE CS
                           PfkB   4 vvviGeal.idliavseklegelvevktveksaGGagaNvAvalarlgadvafigavGdDnfGeflleelkkegvdtdyv 82 
                                    +++i+ ++ ++ i++     +e+++  + e++aGG+ + v ++l++lg++++++g++G+   G +l+  l  eg+ td++
  gi|116753998|ref|YP_843116.1|   8 NPAIDRTMwVERIRD-----DEPNRIVREENYAGGKSIDVSKVLKNLGVESTALGFIGGFA-GMELEGRLLNEGIGTDFI 81 
                                    555666654455554.....4789*************************************.****************** PP

                                    EEESSSEEEEEEEEETTTSEEEEEEEEGGGGGHHHHHHHHHHHHHGCTSEEEEESEECTTSHHHHH....HHHHHHHHHT CS
                           PfkB  83 kidedtrtglalivvdedgertivfnrgaaadltkeeleededlleeadllyisgllsselpeavl....eelaeaakng 158
                                    +++++trt++ + +++ + + +++++ +++   +   l e+ + l   +++ i+g+l+++l+ av+    +e++++ +ng
  gi|116753998|ref|YP_843116.1|  82 RVSGETRTNIIIHEISTGRQLSFYAKGPDIRPHELVMLIEQIEGLRDPEIVTIGGSLPPGLSPAVYrrivTEAKKCEHNG 161
                                    ****************999****************9888****************9999999776611115677777777 PP

                                    TEEEEEECESSSHHHHHHHHHHH.CTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEEGGGEEEEEET CS
                           PfkB 159 gtfdpnlldplgaqfkeallell.aladllkpneeElealtgekledieealaalhklkakgaktvvvtlGkeGalvvek 237
                                     +   ++ld  g      l++ + a +d++kpn +El++l+g++l +i+e+laa+ +++ kg+++v+v++G +G ++v+ 
  gi|116753998|ref|YP_843116.1| 162 CK-AKVFLDVDGL----SLRSSIeAAPDVIKPNIYELSELVGRELREIDEVLAAAREINRKGVEVVLVSMGPRGIVLVSA 236
                                    75.88*******5....455555589****************************************************** PP

                                    TEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHTSSSSSTC CS
                           PfkB 238 dgelkvpavpkvkvvDttGAGDsfvggflaallegksleealrfanavAalvvqkkgaias 298
                                    ++e+++ + p+vkv +t+GAGDs v+gf+++ ++gksl+e+l +a+a++ +++ ++g++ +
  gi|116753998|ref|YP_843116.1| 237 HEEYHAIP-PQVKVENTVGAGDSSVAGFIYGMVNGKSLAECLIYAVAAGTATTLTEGTALA 296
                                    ********.99**********************************************9874 PP

>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   3.1e-10   1.9e-06     120     220 ..     183     276 ..     169     297 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 3.1e-10
                                    -SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHHTT-SEEEEEEGGS-SSSEEEEEEEETSSEEEEEEEE----S--BTH CS
                   Phos_pyr_kin 120 atvitPNlpEaeaLlgekikteedmkeaakkllklgakaVlikGghlegeeavvtdvlydgeeveeleaerietknthGt 199
                                     +vi PN+ E+++L+g+++++ +++ +aa+++ + g++ Vl+  g     +     vl++ +e+++   ++++ +nt G+
  gi|116753998|ref|YP_843116.1| 183 PDVIKPNIYELSELVGRELREIDEVLAAAREINRKGVEVVLVSMGP----RGI---VLVSAHEEYHAIPPQVKVENTVGA 255
                                    589***************************************9986....355...899999999999999999****** PP

                                    HHHHHHHHHHHHHCTSSHHHH CS
                   Phos_pyr_kin 200 GCtlssaiaaelakgesleeA 220
                                    G++  +     + +g+sl e 
  gi|116753998|ref|YP_843116.1| 256 GDSSVAGFIYGMVNGKSLAEC 276
                                    **9888888888888888775 PP

>> Carb_kinase  Carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   7.1e-07    0.0043      86     205 ..     151     272 ..      76     307 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 7.1e-07
                                    HCHHHCCCCS-....EEEEGGGGGSGGGG...TTTTSSEEEE--HHHHHHHCTTTCHHCCSHHHHHHHHHHHHTTEEEEE CS
                    Carb_kinase  86 lleevlekdep....lviDAdgLnllaqknelserkaeviLTPhkkEfkrLlkaivkkeddrlelarelaqklnavvllk 161
                                    + e +  ++++    + +D dgL l++       + a+ ++ P++ E + L++  + + d++l +are+ +k   vvl+ 
  gi|116753998|ref|YP_843116.1| 151 VTEAKKCEHNGckakVFLDVDGLSLRSSI-----EAAPDVIKPNIYELSELVGRELREIDEVLAAAREINRKGVEVVLVS 225
                                    444444555556677999******99985.....78999*****************9*************9987777765 PP

                                    .STTS.EEEECTTEEEEE----GGG-STTHHHH.HHHHHHHHHHCTS CS
                    Carb_kinase 162 .gekd.vivspegevlinstgssalakGGsGDv.LaGligalLaqne 205
                                     g    v+vs ++e  +++       + G GD   aG i ++   + 
  gi|116753998|ref|YP_843116.1| 226 mGPRGiVLVSAHEEYHAIPPQVKVENTVGAGDSsVAGFIYGMVNGKS 272
                                    25554145666999999999999*********648*****9987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2388.55
//
Query:       gi|116753999|ref|YP_843117.1|  [L=138]
Description: CoA-binding domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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  103.2   0.0    1.4e-29  103.0   0.0    1.1  1  CoA_binding_2  CoA binding domain
    5.8e-06   26.9   0.0    7.4e-06   26.6   0.0    1.2  1  CoA_binding    CoA binding domain


Domain annotation for each model (and alignments):
>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.0   0.0   1.5e-33   1.4e-29       1     115 [.      18     134 ..      18     135 .. 0.98

  Alignments for each domain:
  == domain 1  score: 103.0 bits;  conditional E-value: 1.5e-33
                                    --EEEET--S-TTSHHHHHHHHHHHHT--EEEESSS-..SEETTEES----T....T--EEEE-S-HHHHGGGHHHHHHH CS
                  CoA_binding_2   1 rtiaVvGasdnpgkfgykvlryllehglpvvpVnpke..eeilgekvyaslaedpepvdlvdvftppeatpeivkealal 78 
                                    rt+aV+Gas++p k+++ v   ++  g++++ Vnp++  eeilge+vyasl + p ++d+vdvf++p+a+ e+++e+ a+
  gi|116753999|ref|YP_843117.1|  18 RTVAVLGASTDPLKPSFFVSLVVRTYGFRMFFVNPNHvgEEILGEQVYASLRDIPVDIDIVDVFRRPSAAREVAEEIRAK 97 
                                    79**************************************************868************************* PP

                                    --SEEEE-TT---HHHHHHHHHTT-EEE.ES-HHHHH CS
                  CoA_binding_2  79 gakavwlqpgsedeeaaelaeeagirvvgdrCilveg 115
                                    g++ vw+qpg+ed ++a  ++++g  vv  rC++ve 
  gi|116753999|ref|YP_843117.1|  98 GCRIVWFQPGTEDVAVAGELADEGFYVVLGRCMKVEC 134
                                    ***********************************96 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   8.2e-10   7.4e-06       3      91 ..      17     103 ..      15     107 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 8.2e-10
                                    TEEEEEETTTSHHHHHH.HHHHHHHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHHHH CS
                    CoA_binding   3 dtkviviGagglgiagl.yhfkeklkygikavfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqeavde 81 
                                       v+v Ga+    +   +++   + yg+++ f vnp++vg+e+lg +vy s+++++ +  +d+  ++  + +a+e+++e
  gi|116753999|ref|YP_843117.1|  17 SRTVAVLGASTDPLKPSfFVSLVVRTYGFRMFF-VNPNHVGEEILGEQVYASLRDIPVD--IDIVDVFRRPSAAREVAEE 93 
                                    5689*************9************988.***********************99..8888888888999999998 PP

                                    HHHTT-SEEE CS
                    CoA_binding  82 lveagikgiv 91 
                                      ++g + ++
  gi|116753999|ref|YP_843117.1|  94 IRAKGCRIVW 103
                                    8888776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1099.19
//
Query:       gi|116754000|ref|YP_843118.1|  [L=450]
Description: beta-lactamase domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.7e-23   82.5   0.0    1.8e-12   47.7   0.0    2.4  2  Rhodanese    Rhodanese-like domain
    1.6e-05   25.0   2.8    9.8e-05   22.4   1.9    2.5  1  Lactamase_B  Metallo-beta-lactamase superfamily
  ------ inclusion threshold ------
       0.22   11.6   0.1       0.52   10.3   0.1    1.6  1  DUF1027      Protein of unknown function (DUF1027)


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.0   1.6e-11   9.6e-08       1     106 [.     251     338 ..     251     339 .. 0.88
   2 !   47.7   0.0     3e-16   1.8e-12       2     106 ..     351     441 ..     350     442 .. 0.94

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 1.6e-11
                      Rhodanese   1 sakelkellekgkvallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdgggraa 80 
                                    +++e++e l+++   ++D+R++++Y   hIpg+  +            + l++l   +l++    +k+v++++d+ +r  
  gi|116754000|ref|YP_843118.1| 251 TPEEVAEALDECV--IVDTRSDVAYGGAHIPGSQFI----------WADGLAALAGWYLSY----DKPVILVGDEIER-- 312
                                    6899*****8774..*********************..........888888899999998....********99999.. PP

                      Rhodanese  81 aaaallkklGykn.vsvldGGfkawke 106
                                    a+ +l++ +Gy +   +l GG+ aw  
  gi|116754000|ref|YP_843118.1| 313 ASRTLMR-MGYDEiSGYLGGGMLAWHM 338
                                    5555555.***9989999*****9975 PP

  == domain 2  score: 47.7 bits;  conditional E-value: 3e-16
                      Rhodanese   2 akelkellekgkva.llDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdgggraa 80 
                                    ++el ++l++g+ a +lDvR++ee +k +I+gA ++                +lp ++ e   +++k v+v+c +g+r++
  gi|116754000|ref|YP_843118.1| 351 VQELCRHLDQGGQAwILDVRSEEEVSKESITGAHHI-------------HVTQLPRRMDEV--SKEKAVYVFCGSGMRSM 415
                                    678888999998779*********************.............999999999998..***************** PP

                      Rhodanese  81 aaaallkklGyknvsvldGGfkawke 106
                                     aa +l+++G+ n+ v+ GG+++wk+
  gi|116754000|ref|YP_843118.1| 416 VAASFLRRHGWRNLAVVLGGLSGWKS 441
                                    **********999***********96 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   1.9   1.6e-08   9.8e-05       5     163 ..      12     179 ..       9     228 .. 0.71

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.6e-08
                                    SSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHC CS
                    Lactamase_B   5 pvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfm 84 
                                     ++sy++ + g++i+iD+ ++ +          + ++  ++++++ TH   D + g  +l   t++ v++   e+ +  +
  gi|116754000|ref|YP_843118.1|  12 AHYSYIVGDYGSAIVIDPRLDCDVYVDI-----ASRNKMRITDILETHRNEDYVTGSVELSALTGASVWHADPELDYRYG 86 
                                    6789999888****************98.....8************************************9999999999 PP

                                    HHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEE....EE..TTCCEEEECTTTSSHHCC CS
                    Lactamase_B  85 eeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvv....ey..gggkvlftGDallagetg 158
                                      a                         ++g ++ ++a+ +   p++gh+ g+      +  g    +ftGDa +ag+ g
  gi|116754000|ref|YP_843118.1|  87 APA-------------------------REGQVWKIGAWQIEAMPAPGHTLGSMayvlKDhaGVPHAVFTGDAMFAGDVG 141
                                    999.........................4455555555555555555555554400004422445799************ PP

                                    CCCC.................................. CS
                    Lactamase_B 159 ridl.................................t 163
                                    r+dl                                  
  gi|116754000|ref|YP_843118.1| 142 RVDLlgmdraeelagmlyesifqrilplgdgvllcpaH 179
                                    ****7666666666666655555555555555555550 PP

>> DUF1027  Protein of unknown function (DUF1027)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   8.7e-05      0.52      22      42 ..       3      23 ..       1      28 [. 0.88

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 8.7e-05
                        DUF1027 22 leeryseildkydYivGDigy 42
                                   +e+ +se l++y YivGD+g+
  gi|116754000|ref|YP_843118.1|  3 FERIVSEGLAHYSYIVGDYGS 23
                                   67778999***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); 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 0.27s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3188.78
//
Query:       gi|116754001|ref|YP_843119.1|  [L=291]
Description: rhodanese domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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  117.2   0.0    9.7e-18   64.7   0.0    2.2  2  Rhodanese  Rhodanese-like domain


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.5   0.0   1.4e-17   2.5e-13       1     106 [.      16     136 ..      16     137 .. 0.72
   2 !   64.7   0.0   5.4e-22   9.7e-18       4     106 ..     167     278 ..     165     279 .. 0.77

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 1.4e-17
                      Rhodanese   1 sakelkellekgkvallDvRppee.YekghIpgAvnv...skdtlsrakkseapllelpeellel.gidnkktvvvycdg 75 
                                    s+++l e++++ +  ++Dv p +  Y  ghIpgAv +     + +++ ++      e +e++ +  gi+++ +vvvy   
  gi|116754001|ref|YP_843119.1|  16 SPDWLDENMDDVR--IIDVQPNVHdYIMGHIPGAVYMnegILRVARGRQPASFVPPESIESVFSSmGISRDVPVVVYSGP 93 
                                    699******9987..*****66655************87733344444444444445555555556*************9 PP

                      Rhodanese  76 ggraaaa........aallkk....lGykn.vsvldGGfkawke 106
                                    g  ++ a        ++++ +     G ++ v++ldGG+++w e
  gi|116754001|ref|YP_843119.1|  94 GVYSRCAagigdgleQTMVAYalirFG-HQmVHILDGGIEGWME 136
                                    999555537776654334443455599.677***********86 PP

  == domain 2  score: 64.7 bits;  conditional E-value: 5.4e-22
                      Rhodanese   4 elkellekgkvallDvRppeeY......ek.ghIpgAvnvskdtlsrakkseapllelpeellelgid.nkktvvvycdg 75 
                                    el+ ++e ++++l+D+Rp + Y       k ghIpgA +++++ l ++k s     +   + +  g+d ++k+++vyc +
  gi|116754001|ref|YP_843119.1| 167 ELRSMMEGEDIILFDARPTPSYegqamwIKpGHIPGAHSLPWRNLMTEKNSRLLRSDVELRSMISGFDlDNKKIIVYCGT 246
                                    899*******99*****999976666666669********666655555555555555555544455524778******* PP

                      Rhodanese  76 ggraaaaaallkk.lGyknvsvldGGfkawke 106
                                    g  a++ + ++k+ lG+++v++++G+f++w++
  gi|116754001|ref|YP_843119.1| 247 GREATNEYLFFKYyLGHPDVRIYEGSFTEWSS 278
                                    99988888899966**999***********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 2046.58
//
Query:       gi|116754002|ref|YP_843120.1|  [L=122]
Description: hypothetical protein Mthe_0690 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-31  108.5   1.3    1.9e-31  108.3   1.3    1.0  1  DGC       DGC domain


Domain annotation for each model (and alignments):
>> DGC  DGC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.3   1.3   1.1e-35   1.9e-31       1     106 []      12     117 ..      12     117 .. 0.99

  Alignments for each domain:
  == domain 1  score: 108.3 bits;  conditional E-value: 1.1e-35
                            DGC   1 lvvsCsGasnvGqlaneaavklakegeakmiclagvgagveelvelaksarkiiaidGCpleCakkilekagvkpdehlv 80 
                                    ++++C+G+snvGqlan+a ++l+ +g+++++clag+ a + +++++a+ a+ ii idGC+leC++k le  g++pd h+v
  gi|116754002|ref|YP_843120.1|  12 AIFTCAGGSNVGQLANAAGRELTAQGYGRISCLAGITASIRGITASAQGADAIISIDGCSLECCRKSLEGCGFQPDVHVV 91 
                                    69****************************************************************************** PP

                            DGC  81 vtdlgikkeekldlseeeiekvveav 106
                                    +t+lg+kk+ +l++seee+++vv+a+
  gi|116754002|ref|YP_843120.1|  92 ITELGVKKSPDLSISEEELRSVVDAI 117
                                    **********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 852.26
//
Query:       gi|116754003|ref|YP_843121.1|  [L=77]
Description: redox-active disulfide protein 2 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-26   91.7   1.9    2.3e-26   91.6   1.9    1.0  1  Thioredoxin_3  Thioredoxin domain
     0.0013   18.9   0.0      0.023   14.9   0.0    1.9  2  Thioredoxin_4  Thioredoxin
  ------ inclusion threshold ------
      0.013   15.7   0.3      0.023   14.9   0.3    1.6  1  Glutaredoxin   Glutaredoxin
       0.02   14.9   0.0       0.02   14.9   0.0    1.1  1  Thioredoxin    Thioredoxin


Domain annotation for each model (and alignments):
>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.6   1.9   5.2e-30   2.3e-26       1      76 []       1      76 [.       1      76 [. 0.98

  Alignments for each domain:
  == domain 1  score: 91.6 bits;  conditional E-value: 5.2e-30
                                   EEEEEESSSSTTCHHHHHHHHHHCHCCTCECEEECCTTHHHHHHCT-SSSSEEECTTCEEEESS---CCHHHHHHH CS
                  Thioredoxin_3  1 meikvlgpgCakCpklekavkeaaaekgikaevekvtdfeeiekygVmsvPalvidgkvvvsGkvpseeeirklle 76
                                   m+i+vlg+gCakC+ le++v++a++e+gi+ae++kv  + ei+++gVm++Pal idg+ v++G+v s+eei+ ll+
  gi|116754003|ref|YP_843121.1|  1 MKIEVLGTGCAKCKGLENNVRQAVKEMGIDAEIVKVDSIMEIMDRGVMMTPALCIDGETVAVGRVLSVEEIKGLLK 76
                                   89**********************************************************************9985 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.1   0.00083       3.7      24      50 ..       9      36 ..       3      45 .. 0.83
   2 !   14.9   0.0   5.1e-06     0.023     113     165 ..      20      76 ..      17      77 .] 0.83

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00083
                                   T-HHHHHHHHHHH.HHHHHHHHTTSEEE CS
                  Thioredoxin_4 24 rCphCakfeeeve.klleeyidtGkvkf 50
                                    C  C+ +e++v  +++e  id++ vk+
  gi|116754003|ref|YP_843121.1|  9 GCAKCKGLENNVRqAVKEMGIDAEIVKV 36
                                   7***********9789999****98876 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 5.1e-06
                                    HTS-------HHHHHHHHHHH..HHHT--SS-EEEETTEE..E-TT--HHHHHHHHT CS
                  Thioredoxin_4 113 feacleeekldalveaeskea..kkagiestPtfiingek..veepqtyeelkalid 165
                                    + ++++e  +da++++ +  +    +g+ +tP + i+ge   v +  ++ee+k l++
  gi|116754003|ref|YP_843121.1|  20 VRQAVKEMGIDAEIVKVDSIMeiMDRGVMMTPALCIDGETvaVGRVLSVEEIKGLLK 76 
                                    56889999999999999998844556*************955689999999999886 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.3   5.2e-06     0.023      13      58 ..      18      58 ..       1      60 [. 0.79

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.2e-06
                                   HHHHHHHHHTTGGEEEEEGCCSHHHHHHHHHHHTSSSSSEEEETTE CS
                   Glutaredoxin 13 kkakrlLkelgvkfeeidvdkdeeireelkelsgvrtvPqvfidgk 58
                                   ++++++ ke+g++ e++ vd       e++++ gv+  P + idg+
  gi|116754003|ref|YP_843121.1| 18 NNVRQAVKEMGIDAEIVKVDSI----MEIMDR-GVMMTPALCIDGE 58
                                   489******************8....555556.8899999999987 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   4.5e-06      0.02      26      78 ..       6      55 ..       1      75 [. 0.81

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.5e-06
                                   E-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEE CS
                    Thioredoxin 26 yApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlkl 78
                                     + C++Ck l+  + ++ +e+  +  ++kvd   +     + +v + P+l +
  gi|116754003|ref|YP_843121.1|  6 LGTGCAKCKGLENNVRQAVKEMGIDAEIVKVDSIME---IMDRGVMMTPALCI 55
                                   5677*******************9*******98765...55567777777755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); 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: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 563.33
//
Query:       gi|116754004|ref|YP_843122.1|  [L=432]
Description: rhodanese domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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-17   63.2   0.0    2.7e-11   43.9   0.0    2.8  3  Rhodanese  Rhodanese-like domain
  ------ inclusion threshold ------
      0.019   14.8   0.8      0.038   13.9   0.2    1.7  2  FlgD_ig    FlgD Ig-like domain


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.7e-06     0.015      29      98 ..      67     137 ..      39     141 .. 0.84
   2 !   43.9   0.0     3e-15   2.7e-11      12      96 ..     175     254 ..     168     260 .. 0.82
   3 ?   -1.4   0.0      0.38   3.4e+03      55     103 ..     270     319 ..     255     323 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.7e-06
                      Rhodanese  29 hIpgAvnvskdtlsrakkseapllelpeellel....gidnkktvvvycdgggraaaa..aallkklGykn.vsvld 98 
                                     I+gA++v     +ra+++ +  l  + ++       g+++++ vvvy++  ++   +   +ll +lG ++ v+vld
  gi|116754004|ref|YP_843122.1|  67 YIQGAIHV-----PRAEFVADGRLRSVRDICGIlgshGVTRNDSVVVYGSCMECGDPTyiCWLLSYLG-QEdVRVLD 137
                                    5*******.....999999999999999999999999****************9555546779999**.666***98 PP

  == domain 2  score: 43.9 bits;  conditional E-value: 3e-15
                      Rhodanese  12 gkvallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellel.gidnkktvvvycdgggraaaaaallkklG 90 
                                    g+++l+D+R+++e+ + hIpgAvn+       ++   +  l++  el +l ++d++++vvvy  +gg+a+ ++ +l++lG
  gi|116754004|ref|YP_843122.1| 175 GAAQLVDARSADEFRAAHIPGAVNI-----ESSSVLSNGRLKNASELVPLfNLDHERPVVVYSLNGGQASLVWFALRSLG 249
                                    4556*********************.....55666666666777777777899***************888899****** PP

                      Rhodanese  91 yknvsv 96 
                                    y + ++
  gi|116754004|ref|YP_843122.1| 250 Y-DARL 254
                                    5.5554 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.38
                      Rhodanese  55 peellelgidnkktvvvycdgggr.aaaaaallkklGyknvsvldGGfka 103
                                      ++l+  +++++ vv+  + ++  ++++ +l+    ++ + ++ GG+++
  gi|116754004|ref|YP_843122.1| 270 ELSDLSAEVSPERAVVITARFSEIsKNESLNLMGCVTCEPITIYTGGLSG 319
                                    44444446777777888777777722222333333444559999999886 PP

>> FlgD_ig  FlgD Ig-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0      0.89   7.9e+03      18      31 ..      35      49 ..      27      54 .. 0.67
   2 ?   13.9   0.2   4.2e-06     0.038      23      74 ..     357     403 ..     337     406 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.89
                                   .ESSSEEE.EEEEE- CS
                        FlgD_ig 18 lpeaadev.tvtikD 31
                                   l++aa++v +v i D
  gi|116754004|ref|YP_843122.1| 35 LTSAASSVgVVDIGD 49
                                   788888875677766 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 4.2e-06
                                    EEEEEEEE-SS--EEEEEEEEESSSEEEEEEE-SB-TTS-B--SEEEEEEEE CS
                        FlgD_ig  23 devtvtikDasGevVrtidlgaqsaGvvsftWdGtdndGnkladGaYtvkvt 74 
                                      v   ++D+s e++++i l ++sa v++ tWd   ++G   + G Y+++v+
  gi|116754004|ref|YP_843122.1| 357 VDVLAVVTDSSDEEIERIMLHPESAYVYTGTWD---ASGV--PGGVYNLSVE 403
                                    4566789**************************...7776..9999*99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 3046.31
//
Query:       gi|116754005|ref|YP_843123.1|  [L=282]
Description: PP-loop domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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-07   29.8   0.0    5.1e-07   29.1   0.0    1.4  1  NAD_synthase     NAD synthase
  ------ inclusion threshold ------
      0.019   14.5   0.0       0.23   10.9   0.0    2.3  2  QueC             Queuosine biosynthesis protein QueC
      0.021   14.5   0.1      0.032   13.9   0.1    1.2  1  Asn_synthase     Asparagine synthase
      0.031   14.0   0.0       0.17   11.6   0.0    2.1  2  ATP_bind_3       PP-loop family
      0.041   13.4   0.0       0.12   11.9   0.0    1.8  2  Diphthami_syn_2  Diphthamide synthase
      0.042   12.6   0.1        1.3    7.7   0.4    2.5  2  tRNA_Me_trans    tRNA methyl transferase


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 !   29.1   0.0   1.7e-10   5.1e-07      19      77 ..      19      76 ..       3     108 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 1.7e-10
                                   SEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEE CS
                   NAD_synthase 19 kgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievk 77
                                   +++++  SGGvDSsl aa+++++lg + ++a++l s   +++++e+a+ +a+ lgi+  
  gi|116754005|ref|YP_843123.1| 19 ESMLVSFSGGVDSSLLAAISRDVLG-DGAVAVILDSPLMPRRELEHATSVAQLLGIRCI 76
                                   678899******************6.56789************************9965 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   7.6e-05      0.23       3      58 ..      22      76 ..      20      97 .. 0.80
   2 ?    0.8   0.0       0.1     3e+02     106     129 ..     108     131 ..     103     136 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 7.6e-05
                                   EEE--SSHHHHHHHHHHHHH.-SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEE CS
                           QueC  3 vvllSGGlDSttvlalakke.gkevealtfdYgqrhkkeleaakkiakelgveehki 58
                                   +v +SGG+DS+ ++a+ ++  g+   a+ +d     ++ele a+++a+ lg+  + i
  gi|116754005|ref|YP_843123.1| 22 LVSFSGGVDSSLLAAISRDVlGDGAVAVILDSPLMPRRELEHATSVAQLLGI--RCI 76
                                   799**********9999886268899999999999***************98..223 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.1
                                    HHHHHHHT-SEEEE---S-STT-- CS
                           QueC 106 asyaealgaeaiiiGvneedfsgY 129
                                      +a++lg++ ++ Gvn++d++ +
  gi|116754005|ref|YP_843123.1| 108 KKLANSLGISCVADGVNTTDYEDF 131
                                    6799****************9876 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   1.1e-05     0.032      22      78 ..      23      79 ..      17     107 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.1e-05
                   Asn_synthase 22 alLSGGlDSSliaalaarqsksplktFsigfee.kgsdeakyakevaehlgtehtelv 78
                                   + +SGG+DSSl+aa+ +  +   + ++ ++  +     e+++a  va+ lg++ +  v
  gi|116754005|ref|YP_843123.1| 23 VSFSGGVDSSLLAAISRDVLGDGAVAVILDS-PlMPRRELEHATSVAQLLGIRCIVAV 79
                                   568***************9986666666666.35889999999999999999933332 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.6e-05      0.17       2      68 ..      21      82 ..      20     127 .. 0.82
   2 ?   -0.7   0.0      0.34     1e+03     137     166 ..     140     171 ..     129     177 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.6e-05
                                   EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H CS
                     ATP_bind_3  2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikleiekvdv 68
                                   +lv +SgG+DS +L  +  +    lg  +va+ +d  l ++  +e e+  ++++ l+i+++++  dv
  gi|116754005|ref|YP_843123.1| 21 MLVSFSGGVDSSLLAAISRDV---LGDGAVAVILDSPLMPR--RELEHATSVAQLLGIRCIVAVHDV 82
                                   79**********999888777...44578888899888765..567788888899999998887776 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.34
                                    TCCEE-CCC..T--HHHHHHHHHHTT---B-- CS
                     ATP_bind_3 137 sirlvRPlL..kvskeeleeylkekkikwveD 166
                                    ++ ++ P++   +sk++++e+++  ++++ + 
  gi|116754005|ref|YP_843123.1| 140 EEGICHPFVdaGISKSDIREIARSIGLDFWNR 171
                                    56788899855589*******99999988765 PP

>> Diphthami_syn_2  Diphthamide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.1       2.5   7.4e+03       5      15 ..      23      33 ..      21      36 .. 0.80
   2 ?   11.9   0.0   3.9e-05      0.12      24     113 ..      80     167 ..      70     186 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 2.5
                Diphthami_syn_2  5 vlysGGkDsil 15
                                   v +sGG Ds l
  gi|116754005|ref|YP_843123.1| 23 VSFSGGVDSSL 33
                                   6699****976 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 3.9e-05
                Diphthami_syn_2  24 sevesLvsvisenke.symfhvvnvhlvellaesvGiplikletaGeeekevedLkgtlkkldveavviGaieseyqksr 102
                                    ++v  L svi++ +e  y      + +++ la+s+Gi  +     G++  + ed++  ++  d e+++   + +   ks 
  gi|116754005|ref|YP_843123.1|  80 HDVFELESVIENSPErCYHCKKSSAGILKKLANSLGISCVA---DGVNTTDYEDFRPGIRASDEEGICHPFVDAGISKSD 156
                                    78888999998887724666677899***********9885...56778999**************************** PP

                Diphthami_syn_2 103 iervCrelGlk 113
                                    i ++ r +Gl 
  gi|116754005|ref|YP_843123.1| 157 IREIARSIGLD 167
                                    *********85 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.4   0.00043       1.3       3      65 ..      21      75 ..      19      98 .. 0.63
   2 ?    1.6   0.0     0.032        95     170     194 ..     151     175 ..     141     181 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00043
                  tRNA_Me_trans  3 vvvalSgGVDSsvaaallkeq.gyevigvflklweeedeegkeccaeedlkdaervaeklgipl 65
                                   ++v +SgGVDSs+ aa+ ++  g   ++v+l               +++l++a++va+ lgi++
  gi|116754005|ref|YP_843123.1| 21 MLVSFSGGVDSSLLAAISRDVlGDGAVAVILDSPL---------MPRRELEHATSVAQLLGIRC 75
                                   6899********98877554313334444433222.........22345556666666666655 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.032
                  tRNA_Me_trans 170 eltKeevrkiAkeaglavaekkdSq 194
                                     + K+++r+iA+++gl+  +++ S 
  gi|116754005|ref|YP_843123.1| 151 GISKSDIREIARSIGLDFWNRPSSA 175
                                    578**************99999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); 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: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2171.94
//
Query:       gi|116754006|ref|YP_843124.1|  [L=155]
Description: PUA domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-24   85.3   0.1    5.6e-24   84.1   0.1    1.7  2  TGT_C2    Patch-forming domain C2 of tRNA-guanine transglycos
    1.9e-16   59.8   0.1    2.8e-16   59.2   0.1    1.3  1  PUA       PUA domain
    0.00029   21.0   0.0    0.00042   20.5   0.0    1.3  1  UPF0113   UPF0113 PUA domain


Domain annotation for each model (and alignments):
>> TGT_C2  Patch-forming domain C2 of tRNA-guanine transglycosylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.1   0.1   9.4e-28   5.6e-24       3      71 .]       5      73 ..       3      73 .. 0.97
   2 ?   -1.8   0.0      0.61   3.7e+03      41      41 ..     108     108 ..      88     126 .. 0.52

  Alignments for each domain:
  == domain 1  score: 84.1 bits;  conditional E-value: 9.4e-28
                         TGT_C2  3 lraiadYqFGagagdaLfpedvtitrsatgrirqvlvdgerlatlraqdgrltLsleGarrlheslppP 71
                                    r++ad qFG+gag+aLfp+d t+++s+t+r+r+++ ++er+at+ra+d  ltLs+ Ga+rlh ++++P
  gi|116754006|ref|YP_843124.1|  5 ARMLADIQFGRGAGAALFPDDTTFQLSSTQRLRYLISGNERIATVRARDSHLTLSMLGAKRLHVAFSHP 73
                                   699*************************************************************99988 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.61
                         TGT_C2  41 g 41 
                                    g
  gi|116754006|ref|YP_843124.1| 108 G 108
                                    2 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.2   0.1   4.7e-20   2.8e-16       2      71 ..      76     145 ..      75     148 .. 0.95

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 4.7e-20
                                    EEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEE CS
                            PUA   2 rvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveie 71 
                                    rvv    Av +++ g++L+a  v+ ++ ++++gd+V +vde+++l+a G++ +  +e+ +ik+g++v ++
  gi|116754006|ref|YP_843124.1|  76 RVVASPDAVPFVSAGKNLFARHVLYADPEIRAGDEVLVVDENDRLIATGRTVLAPDEMLQIKRGVAVSVR 145
                                    5777789************************************************************987 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0     7e-08   0.00042      15      52 ..      90     127 ..      77     142 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 7e-08
                        UPF0113  15 GrdvlkesilkitesvkenqvvvVlnengeplGiGkir 52 
                                    G++++  ++l+ +++++ ++ v+V++en+++++ G++ 
  gi|116754006|ref|YP_843124.1|  90 GKNLFARHVLYADPEIRAGDEVLVVDENDRLIATGRTV 127
                                    9**********************************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); 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 0.27s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1151.16
//
Query:       gi|116754007|ref|YP_843125.1|  [L=117]
Description: transposase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00012   22.3   0.0    0.00018   21.8   0.0    1.2  1  DDE_Tnp_IS240  DDE domain
     0.0013   18.8   0.0     0.0019   18.3   0.0    1.3  1  SpoIIID        Stage III sporulation protein D
     0.0021   17.8   0.0      0.003   17.3   0.0    1.2  1  HTH_23         Homeodomain-like domain
     0.0078   16.0   0.0      0.013   15.3   0.0    1.3  1  HTH_30         PucR C-terminal helix-turn-helix domain
  ------ inclusion threshold ------
      0.016   15.1   0.0      0.021   14.7   0.0    1.3  1  Terminase_5    Putative ATPase subunit of terminase (gpP-like


Domain annotation for each model (and alignments):
>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0     5e-08   0.00018       4      28 ..      79     103 ..      77     112 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 5e-08
                  DDE_Tnp_IS240   4 wrvDETyvkikGkwaYlyravDkeg 28 
                                      vDET +k +Gk++Yl++a+D e+
  gi|116754007|ref|YP_843125.1|  79 LDVDETILKYNGKKCYLFAAIDLES 103
                                    679*******************986 PP

>> SpoIIID  Stage III sporulation protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   5.2e-07    0.0019       8      42 ..      27      59 ..      20      73 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 5.2e-07
                        SpoIIID  8 vleiakyiveskatvRkaakvfgvskstvhkDvte 42
                                      ia+y+v s   vR++a v+gv ks vh  +t 
  gi|116754007|ref|YP_843125.1| 27 LFAIATYLVSS--SVRRTAAVLGVGKSSVHYWITR 59
                                   56799999975..7****************98886 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   8.4e-07     0.003       6      41 ..      25      60 ..      21      67 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 8.4e-07
                         HTH_23  6 eRlrillllaeGlsvreIAreLgvsrrTvyrwlkry 41
                                   ++l ++  +++  svr+ A+ Lgv ++ v  w+ r+
  gi|116754007|ref|YP_843125.1| 25 IKLFAIATYLVSSSVRRTAAVLGVGKSSVHYWITRF 60
                                   5667788888889**********************9 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 !   15.3   0.0   3.6e-06     0.013       6      46 ..      31      70 ..      28      80 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.6e-06
                                   HHHHHTTT-HHHHHHHHTS-HHHHHHHHHHHHHHHS--TTS CS
                         HTH_30  6 raylenggnisatAkaLhvHrnTlryRLrrieellgldldd 46
                                    +yl +  ++++tA+ L+v + +++y + r +  l++ +d+
  gi|116754007|ref|YP_843125.1| 31 ATYLVS-SSVRRTAAVLGVGKSSVHYWITRFKYSLDYKPDE 70
                                   578876.9***********************9988888776 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 ?   14.7   0.0     6e-06     0.021       1      38 [.      24      61 ..      24      79 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6e-06
                    Terminase_5  1 dvRrqArlLYwqGyrvaeIAeelglkeatVysWkkrde 38
                                   +++  A++ Y+   +v++ A+ lg+ + +V++W  r++
  gi|116754007|ref|YP_843125.1| 24 EIKLFAIATYLVSSSVRRTAAVLGVGKSSVHYWITRFK 61
                                   56788999999999*********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); 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: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 852.52
//
Query:       gi|116754008|ref|YP_843126.1|  [L=355]
Description: magnesium and cobalt transport protein CorA [Methanosaeta thermophila PT]
Scores for complete 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  239.8   6.2    4.4e-71  239.6   6.2    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 !  239.6   6.2   2.5e-75   4.4e-71       3     292 .]      63     351 ..      61     352 .. 0.94

  Alignments for each domain:
  == domain 1  score: 239.6 bits;  conditional E-value: 2.5e-75
                           CorA   3 gfvWldlssptee.eleeLaeelgldelaledlldseerprvedyddylllvlpsveldkseeeeeevplsillgdnfli 81 
                                    +++W+ ++   +  ++e+L + +++++l++ed++++ +rp++ed+++y+++vl+++ +d   +e +  ++s++++ nf+i
  gi|116754008|ref|YP_843126.1|  63 TVTWIKVNGIRDTeTMEKLGKIFDIHPLTIEDIITG-QRPKMEDFGEYIFIVLRVFYYDRIANEITSEQFSLIFSSNFVI 141
                                    579999998765559****************99987.***************************9999************ PP

                           CorA  82 tvrreplealdevikrlk..deggkpkspgellyrlldeivdrlfellekleeeldeledeledstkkeilrelaqlrrr 159
                                    t++++  ++++ + +r+k  + + +++    l y lld+ivd++f +le l ++++ le+ l ++ ++e lre+++l+ +
  gi|116754008|ref|YP_843126.1| 142 TFEESGGDVFKLIKERIKneKGKIRRRGTDYLAYVLLDAIVDNYFYILERLGDRIELLETVLVEEPSEENLREIYELKSS 221
                                    ******************9888899999**************************************************** PP

                           CorA 160 lvklrralapnrevlkrllakaddkllddedkeylrdlldelerllemlealrerleslqdtyssllserlNrvmkvLTv 239
                                    ++ lr++++p+rev+ ++l+++d +l+ +e   ylrd++d++ ++++ +e++r++l+ + +++ s  s++lN+++k+LT+
  gi|116754008|ref|YP_843126.1| 222 MIFLRKSVWPLREVI-TRLERGDSPLIHEETIIYLRDVYDHTIQVIDNIEIMRDMLSEMVSIHLSSASNELNNTIKILTS 300
                                    ***************.77888*********************************************************** PP

                           CorA 240 ltaif.lPlTlitGiyGmNfkglPelewsygypfvlllglmallailllfwfkr 292
                                    +t+if lP Tli++iyGmNf+++Pelew ygy+++  l+lma +++ ++++fkr
  gi|116754008|ref|YP_843126.1| 301 ITIIFmLP-TLIASIYGMNFRYMPELEWRYGYFAT--LILMASAVVTTVLYFKR 351
                                    *****999.**************************..55666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       708  (0.0394891); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2469.00
//
Query:       gi|116754009|ref|YP_843127.1|  [L=139]
Description: hypothetical protein Mthe_0697 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       296  (0.0165096); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 967.13
//
Query:       gi|116754010|ref|YP_843128.1|  [L=385]
Description: ATPase central domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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-36  124.7   0.0    4.8e-36  124.1   0.0    1.3  1  AAA              ATPase family associated with various cellul
    2.5e-07   30.4   0.1    5.3e-07   29.4   0.1    1.5  1  AAA_lid_3        AAA+ lid domain
    9.6e-07   29.1   0.0    1.9e-06   28.1   0.0    1.4  1  AAA_2            AAA domain (Cdc48 subfamily)
    1.2e-05   25.1   0.0    5.1e-05   23.1   0.0    2.0  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    1.3e-05   25.7   0.4    0.00037   20.9   0.4    2.8  1  AAA_16           AAA ATPase domain
    8.5e-05   22.5   0.0    0.00014   21.8   0.0    1.3  1  Bac_DnaA         Bacterial dnaA  protein
     0.0002   20.7   0.1    0.00065   19.0   0.0    1.8  2  TIP49            TIP49 P-loop domain
    0.00082   18.6   0.0     0.0055   15.9   0.0    2.0  2  DUF815           Protein of unknown function (DUF815)
    0.00089   19.3   0.0     0.0035   17.3   0.0    2.2  1  AAA_5            AAA domain (dynein-related subfamily)
     0.0013   19.0   0.5      0.059   13.6   0.0    2.5  2  AAA_22           AAA domain
     0.0013   18.5   0.0     0.0024   17.6   0.0    1.5  1  IstB_IS21        IstB-like ATP binding protein
     0.0044   16.4   0.0     0.0099   15.3   0.0    1.6  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0066   16.7   0.0      0.012   15.8   0.0    1.5  1  AAA_28           AAA domain
     0.0084   15.8   0.0      0.045   13.5   0.0    2.0  2  Sigma54_activat  Sigma-54 interaction domain
  ------ inclusion threshold ------
      0.013   15.5   0.0      0.024   14.6   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.014   14.9   0.0      0.088   12.3   0.0    2.0  2  AAA_7            P-loop containing dynein motor region
      0.015   15.5   0.0      0.028   14.6   0.0    1.5  1  AAA_33           AAA domain
      0.017   15.6   0.0      0.038   14.6   0.0    1.6  1  AAA_18           AAA domain
      0.034   14.5   0.0      0.057   13.8   0.0    1.4  1  RNA_helicase     RNA helicase
      0.044   13.2   0.1        0.4   10.1   0.0    2.3  2  TniB             Bacterial TniB protein
       0.06   13.1   0.2       0.16   11.6   0.1    1.8  2  AAA_24           AAA domain
      0.078   12.1   0.1        1.2    8.3   0.0    2.1  2  PIF1             PIF1-like helicase
      0.083   13.0   0.0       0.16   12.1   0.0    1.4  1  Torsin           Torsin
      0.084   12.8   0.0       0.18   11.7   0.0    1.6  1  NACHT            NACHT domain
       0.11   11.6   0.1       0.16   11.0   0.1    1.2  1  Parvo_NS1        Parvovirus non-structural protein NS1
       0.14   12.3   0.0       0.27   11.4   0.0    1.4  1  Sigma54_activ_2  Sigma-54 interaction domain
       0.15   11.9   0.1        1.5    8.7   0.0    2.1  2  CPT              Chloramphenicol phosphotransferase-like prot


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 !  124.1   0.0   7.2e-39   4.8e-36       1     131 [.     171     299 ..     171     300 .. 0.97

  Alignments for each domain:
  == domain 1  score: 124.1 bits;  conditional E-value: 7.2e-39
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.TTCCC CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr.sgses 79 
                                    +l+yG  GtGKT++a+a+a+e++v+++ ++ ++l+ ++vge++++i+ l ++a++ + p+i+fiDEida+a +r  ++ +
  gi|116754010|ref|YP_843128.1| 171 ILFYGASGTGKTMIARALATEANVSMMPVKSTSLIGEFVGEGARQIHSLYDRAEQLS-PCIIFIDEIDAIALDRrYQDLR 249
                                    69******************************************************9.****************99999* PP

                                    HHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEEEETT CS
                            AAA  80 eeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrkieie 131
                                    ++ +++vn+Llte+dg +++++ v+ i+atn+++ ldp ++ +Rf+++ie++
  gi|116754010|ref|YP_843128.1| 250 GDVSEIVNALLTEMDGISSRRG-VCTIAATNKIELLDPSIR-SRFEEEIEFK 299
                                    *******************866.******************.*******986 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.1   7.9e-10   5.3e-07       3      44 ..     324     366 ..     323     367 .. 0.95

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 7.9e-10
                      AAA_lid_3   3 dlkeLAerTeGySGADlaa.lcreAallAlrrgikeitmedfe 44 
                                    dl+e+A++TeG+SG Dl+  + + A + A+ ++   ++ ++++
  gi|116754010|ref|YP_843128.1| 324 DLAEIAKLTEGFSGRDLVDkILKVALHQAIIEDSRFVERRHLM 366
                                    9****************999*****************999997 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   2.9e-09   1.9e-06       5     105 ..     170     265 ..     168     282 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 2.9e-09
                                    -EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG--- CS
                          AAA_2   5 silllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihp 82 
                                    +il+ g +g+Gkt++a+ala   +v    +++ +  ++l+     e + +   + +  y +ae+    i+++DEid i+ 
  gi|116754010|ref|YP_843128.1| 170 NILFYGASGTGKTMIARALATEANV----SMMPVKSTSLIG----EFVGEGARQIHSLYDRAEQLSpcIIFIDEIDAIAL 241
                                    89**********************8....888888888888....78888888999999999999999***********9 PP

                                    -...---------HHHHHHHHHHHH- CS
                          AAA_2  83 k...essgadvSregVqrdLLqileg 105
                                        +  + dvS  +++++LL  ++g
  gi|116754010|ref|YP_843128.1| 242 DrryQDLRGDVS--EIVNALLTEMDG 265
                                    877888899999..899999987776 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 !   23.1   0.0   7.6e-08   5.1e-05       2      96 ..     133     239 ..     132     298 .. 0.70

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 7.6e-08
                         RuvB_N   2 rPksleeyigqekvkeklkifieaakk....reealdhvllyGpPGlGkttlakiiakelgvklk.itsgPvl.....ek 71 
                                     P s+++ +gq + k k+k++ +  ++     + a   +l+yG+ G Gkt +a+ +a+e +v++  + s+  +     e 
  gi|116754010|ref|YP_843128.1| 133 EPASFDDVVGQLDAKRKVKVIKRYLEEperfGSWAPRNILFYGASGTGKTMIARALATEANVSMMpVKSTSLIgefvgEG 212
                                    6999*************999754433311003457889***********************9864133333332122355 PP

                         RuvB_N  72 agdlaalltnleekd..vlfideihrl 96 
                                    a+++ +l  + e+    ++fidei  +
  gi|116754010|ref|YP_843128.1| 213 ARQIHSLYDRAEQLSpcIIFIDEIDAI 239
                                    677777776666543449999999865 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.4   5.6e-07   0.00037      13      63 ..     154     226 ..     147     380 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 5.6e-07
                         AAA_16  13 lsalervrsgrp...elvllsGesGvGKsslvrellralekd...................ggiflrgkcdql 63 
                                    +++le   + ++   +++l++G+sG+GK+ ++r+l+++++ +                    ++ l+ +++ql
  gi|116754010|ref|YP_843128.1| 154 KRYLEEPERFGSwapRNILFYGASGTGKTMIARALATEANVSmmpvkstsligefvgegarQIHSLYDRAEQL 226
                                    555665554444555*********************9888776666555555555555443244444444444 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   2.1e-07   0.00014      37     212 ..     171     347 ..     140     353 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 2.1e-07
                                    EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHT..T-HHHHHHHHTT-SEEEEE-GGGGTT-HH CS
                       Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrd..kkaeefkeklrkvDvLliDDiqflagkek 114
                                    +++yg +G Gkt + +a++ e+  +    + + l +e F+ e ++ +++  ++ae++     +  ++ iD+i  +a   +
  gi|116754010|ref|YP_843128.1| 171 ILFYGASGTGKTMIARALATEANVSMMPVKSTSLIGE-FVGEGARQIHSlyDRAEQL-----SPCIIFIDEIDAIALDRR 244
                                    799**************99998888777777777664.6666555555422333333.....334666666666665555 PP

                                    HHH...HHHHHHHHHHTTT-EE....EEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHHHHHHHTT---- CS
                       Bac_DnaA 115 tqe...elfhtfnalleegkqv....vlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailkkkieaeklevp 187
                                     q+   ++  ++nall e   +     +++  + +++e l+  +rsrfe  +  + + p +e rl+il++++++  lev+
  gi|116754010|ref|YP_843128.1| 245 YQDlrgDVSEIVNALLTEMDGIssrrGVCTIAATNKIELLDPSIRSRFEEEI--EFKLPSHEDRLEILRRNASKMPLEVR 322
                                    44322256667777766554441111577888999**************976..556689999****************9 PP

                                    TTHHHHHHHH--S-HHHHHHHHHHH CS
                       Bac_DnaA 188 eevlefiaervtdnvRelegalnrl 212
                                     +++e    +   + R+l   + ++
  gi|116754010|ref|YP_843128.1| 323 GDLAEIAKLTEGFSGRDLVDKILKV 347
                                    9987754333344566666555555 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   9.8e-07   0.00065      24      77 ..     138     195 ..     114     209 .. 0.82
   2 ?   -1.2   0.0       1.4   9.2e+02     276     293 ..     225     242 ..     214     283 .. 0.58

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 9.8e-07
                                    XXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49  24 eglvGqkkareaagvivelike....kklaGravLlaGpsgtGktalaiaiskelged 77 
                                    + +vGq +a++ + vi + ++e    +  a r +L+ G sgtGkt +a a++ e + +
  gi|116754010|ref|YP_843128.1| 138 DDVVGQLDAKRKVKVIKRYLEEperfGSWAPRNILFYGASGTGKTMIARALATEANVS 195
                                    579***************99883222345679********************998743 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.4
                                    XXXXXXXXXXXXXXXXXX CS
                          TIP49 276 eivpGvlfiDevhmlDie 293
                                    ++ p ++fiDe+  + ++
  gi|116754010|ref|YP_843128.1| 225 QLSPCIIFIDEIDAIALD 242
                                    566888888888765554 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   8.2e-06    0.0055      15     129 ..     125     249 ..     118     258 .. 0.64
   2 ?   -0.0   0.0      0.61     4e+02     181     216 ..     287     322 ..     276     338 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 8.2e-06
                         DUF815  15 alepveevdevklddLvgidkqkealventeqfle......glpannvLLwGarGtGKSslvkallneyaeeg.....Lr 83 
                                    ++ep + v++ ++dd+vg  + k++++  ++++le        + +n+L++Ga GtGK  + +al +e++ +        
  gi|116754010|ref|YP_843128.1| 125 RIEPAAVVEPASFDDVVGQLDAKRKVK-VIKRYLEeperfgSWAPRNILFYGASGTGKTMIARALATEANVSMmpvksTS 203
                                    567777777788888877665555543.2333333111111234589*******************99987775544433 PP

                         DUF815  84 li.evekedlkelpklvellrerperfilfvDDLsFeeeeeeyksLk 129
                                    li e   e  +++ +l++  ++    +i+f+D +   + +++y+ L+
  gi|116754010|ref|YP_843128.1| 204 LIgEFVGEGARQIHSLYDRAEQ-LSPCIIFIDEIDAIALDRRYQDLR 249
                                    4435555555555555555443.346888888887777777777776 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.61
                         DUF815 181 sLsdRFGlwlgFykldqeeYleiveklakklglele 216
                                    s+  RF   + F+ +++e+ lei+++ a+k+ le++
  gi|116754010|ref|YP_843128.1| 287 SIRSRFEEEIEFKLPSHEDRLEILRRNASKMPLEVR 322
                                    66789*********************9999888776 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   5.3e-06    0.0035       1      77 [.     170     239 ..     170     292 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.3e-06
                                    EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG- CS
                          AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEvera 77 
                                    ++l  G++GtgK+++a+ la    ++v ++  ++    + l+g+     g+ +++  +l++ a+  +++i+++DE++ +
  gi|116754010|ref|YP_843128.1| 170 NILFYGASGTGKTMIARALATE--ANVSMMPVKS----TSLIGEFV---GEGARQIHSLYDRAEqlSPCIIFIDEIDAI 239
                                    57999************99865..5555555544....44666666...45556668888888889**********965 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   8.9e-05     0.059       7      29 ..     170     192 ..     167     204 .. 0.86
   2 ?    3.0   0.1      0.18   1.2e+02      82     105 ..     219     244 ..     207     281 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.9e-05
                         AAA_22   7 ilvvtGesGtGKTtllrrlleql 29 
                                     ++ +G sGtGKT+ +r l+ ++
  gi|116754010|ref|YP_843128.1| 170 NILFYGASGTGKTMIARALATEA 192
                                    6889***************9987 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.18
                         AAA_22  82 leqalraravielliiDEaqhlr...s 105
                                    l++ +++ + + ++ iDE++ +    +
  gi|116754010|ref|YP_843128.1| 219 LYDRAEQLS-PCIIFIDEIDAIAldrR 244
                                    444444444.59*********854431 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 !   17.6   0.0   3.6e-06    0.0024      47     118 ..     168     237 ..     123     260 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.6e-06
                      IstB_IS21  47 kenivllGpsGvGKshlaialgveavraglsvlfvrvedLveel..krarrdgklaralkrllkvdllilDdlg 118
                                      ni++ G sG+GK+ +a al++ea    +s++ v+ + L+ e   + ar+  +l  ++++l  + ++ +D++ 
  gi|116754010|ref|YP_843128.1| 168 PRNILFYGASGTGKTMIARALATEAN---VSMMPVKSTSLIGEFvgEGARQIHSLYDRAEQLS-PCIIFIDEID 237
                                    469******************99874...4444445555554442234555555555555544.3345555555 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.5e-05    0.0099      23      43 ..     169     189 ..     136     203 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.5e-05
                   Mg_chelatase  23 HnlllvGppGsGKtmlakrlp 43 
                                     n+l++G++G+GKtm+a++l+
  gi|116754010|ref|YP_843128.1| 169 RNILFYGASGTGKTMIARALA 189
                                    69****************996 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.9e-05     0.012       1      28 [.     170     198 ..     170     245 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.9e-05
                         AAA_28   1 kivitGgestGKTtlleaLaar.gypvvp 28 
                                    +i + G+++tGKT +++aLa + +++++p
  gi|116754010|ref|YP_843128.1| 170 NILFYGASGTGKTMIARALATEaNVSMMP 198
                                    5899****************654555443 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   6.7e-05     0.045      22      48 ..     168     194 ..     146     205 .. 0.76
   2 ?   -0.2   0.0       1.1   7.1e+02      90     108 ..     224     242 ..     203     300 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.7e-05
                                    SS-EEEECSTTSSHHHHHHHHHHHSTT CS
                Sigma54_activat  22 dlsvlitGesGtGKellaraiheaskr 48 
                                    + ++l  G sGtGK+++ara+ ++ + 
  gi|116754010|ref|YP_843128.1| 168 PRNILFYGASGTGKTMIARALATEANV 194
                                    479*****************9876654 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.1
                                    HHTTTSEEEEETGGGS-HH CS
                Sigma54_activat  90 ekadgGtlfLDeigelple 108
                                    e+ +  ++f+Dei  + l+
  gi|116754010|ref|YP_843128.1| 224 EQLSPCIIFIDEIDAIALD 242
                                    5556678999999988776 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   3.6e-05     0.024      19      51 ..     168     202 ..     145     218 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.6e-05
                                    TEEEEEEESTTSSHHHHHHHHHHHTT--..----T CS
                           TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve..evkSP 51 
                                     + il++G  G+GKT+++r+la + +v+  +vkS 
  gi|116754010|ref|YP_843128.1| 168 PRNILFYGASGTGKTMIARALATEANVSmmPVKST 202
                                    4469**********************988889996 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 ?   12.3   0.0   0.00013     0.088      34      58 ..     169     193 ..     166     204 .. 0.82
   2 ?   -0.3   0.0         1   6.7e+02     101     115 ..     228     242 ..     222     246 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                          AAA_7  34 kpvllvGptGtGKtviikdllkkld 58 
                                    +++l++G +GtGKt+i++ l ++ +
  gi|116754010|ref|YP_843128.1| 169 RNILFYGASGTGKTMIARALATEAN 193
                                    689**************99887766 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1
                          AAA_7 101 klvvFvDDlnmpake 115
                                     +++F+D+++  a +
  gi|116754010|ref|YP_843128.1| 228 PCIIFIDEIDAIALD 242
                                    59*******988777 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   4.3e-05     0.028       2      65 ..     171     262 ..     171     294 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.3e-05
                         AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt..........................dytrvld 53 
                                    +l+ G++G+GK+  a+ l+ +    +  + s +l+   +g++ +++                           +y++++ 
  gi|116754010|ref|YP_843128.1| 171 ILFYGASGTGKTMIARALATEANvsMMPVKSTSLIGEFVGEGARQIHslydraeqlspciifideidaialdrRYQDLRG 250
                                    6899***************9999888889999999999997776665555555666666666666666666665566666 PP

                         AAA_33  54 rlyqilnelark 65 
                                    ++ +i+n+l+++
  gi|116754010|ref|YP_843128.1| 251 DVSEIVNALLTE 262
                                    666666666555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   5.6e-05     0.038       1      44 [.     171     225 ..     171     268 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.6e-05
                         AAA_18   1 IlltGtpGvGKttlakeLskrlgf...........gvnlrdvakenglllevdpe 44 
                                    Il  G++G+GKt +a++L+ + ++           g+ +++ a++ ++l+++ ++
  gi|116754010|ref|YP_843128.1| 171 ILFYGASGTGKTMIARALATEANVsmmpvkstsliGEFVGEGARQIHSLYDRAEQ 225
                                    8999**************9987667788888877877777666666666666655 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   8.7e-05     0.057       1      26 [.     171     196 ..     171     249 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.7e-05
                   RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                                    i++yG+sg+GK+++a+ La++   ++
  gi|116754010|ref|YP_843128.1| 171 ILFYGASGTGKTMIARALATEANVSM 196
                                    789****************9998666 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0    0.0006       0.4      34      58 ..     167     191 ..     138     203 .. 0.74
   2 ?    0.1   0.1      0.67   4.4e+02     116     181 ..     224     294 ..     212     301 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0006
                           TniB  34 rmpnlllvGdsnnGKtmivekFarl 58 
                                     ++n+l++G s +GKtmi++  a +
  gi|116754010|ref|YP_843128.1| 167 APRNILFYGASGTGKTMIARALATE 191
                                    468***************9987765 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.67
                           TniB 116 relkvrvLiiDEihnllagsark..qreflnalksLgnelk.i.pivlvGteealralr.tDpqlasRFep 181
                                    ++l++ ++ iDEi+ +   ++ +  +  + +++  L  e++ i +  +v t +a++ ++  Dp + sRFe+
  gi|116754010|ref|YP_843128.1| 224 EQLSPCIIFIDEIDAIALDRRYQdlRGDVSEIVNALLTEMDgIsSRRGVCTIAATNKIElLDPSIRSRFEE 294
                                    56667778888888775333222112334444444444443231234566666666665347777777775 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       7.8   5.2e+03     165     183 ..     139     157 ..     132     160 .. 0.86
   2 ?   11.6   0.1   0.00025      0.16       3      22 ..     169     188 ..     167     240 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 7.8
                         AAA_24 165 Dlvlranlkredkvgervl 183
                                    D+v++++ kr++kv +r+l
  gi|116754010|ref|YP_843128.1| 139 DVVGQLDAKRKVKVIKRYL 157
                                    8999999999999999987 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00025
                         AAA_24   3 lkiliyGpsgiGKTtlakel 22 
                                    ++il yG sg+GKT++a+ l
  gi|116754010|ref|YP_843128.1| 169 RNILFYGASGTGKTMIARAL 188
                                    689**************988 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0018       1.2      21      49 ..     167     195 ..     152     221 .. 0.81
   2 ?    1.5   0.0       0.2   1.3e+02     102     130 ..     349     377 ..     320     381 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0018
                                    CTS-EEEEESTTSSCHHHHHHHHHHCHCT CS
                           PIF1  21 kgklfFvtGsgGtgKtflwkallkklrse 49 
                                     ++++ ++G +GtgKt++ +al +  + +
  gi|116754010|ref|YP_843128.1| 167 APRNILFYGASGTGKTMIARALATEANVS 195
                                    578999***************99876655 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.2
                                    C-SEEEEECGGGSBHHHHHHHHHHHHHHC CS
                           PIF1 102 ktsliiwDEapmverecfealdrtlrdil 130
                                      ++ii D   +  r++++al+r+ rd+ 
  gi|116754010|ref|YP_843128.1| 349 LHQAIIEDSRFVERRHLMDALQRIKRDVK 377
                                    4578999999999**************97 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00024      0.16      28      76 ..     141     191 ..     125     208 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00024
                                    -S-HHHHHHHHHHHHHHHT-SS...-SS-EEEEEEE-TTSSHHHHHHHHHHH CS
                         Torsin  28 fGqhlvkklvvksvkaylenek...pkkpLvlsfhGwtGtGknfvaeiiaen 76 
                                    +Gq l +k  vk +k yle+++   +  p  + f+G +GtGk  +a+ +a +
  gi|116754010|ref|YP_843128.1| 141 VGQ-LDAKRKVKVIKRYLEEPErfgSWAPRNILFYGASGTGKTMIARALATE 191
                                    566.4445568999****9995233678999****************99875 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00028      0.18       2      29 ..     170     197 ..     169     209 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00028
                                    CEEEEC-TTTCHHHHHHHHHHHHCTS-S CS
                          NACHT   2 lvilqGeaGsGKTtLlqklalawaegkl 29 
                                     ++  G++G GKT+ ++ la+++  +  
  gi|116754010|ref|YP_843128.1| 170 NILFYGASGTGKTMIARALATEANVSMM 197
                                    57899***************99877655 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00024      0.16     113     136 ..     168     190 ..     164     197 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00024
                      Parvo_NS1 113 krntvwfyGpantGktnlaeaIak 136
                                    +rn ++fyG+  tGkt++a+a+a+
  gi|116754010|ref|YP_843128.1| 168 PRN-ILFYGASGTGKTMIARALAT 190
                                    555.89****************97 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 ?   11.4   0.0    0.0004      0.27      22      80 ..     169     238 ..     147     247 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0004
                                    S-EEEEEETT--HHHHHHCC--TTS-EE--SSTTHHH...........H-HHHHHHHTTTSEEEEEE-TT CS
                Sigma54_activ_2  22 lpvfltGekGsgkelvArlLhknsgpwleifvverla...........klpldlleqakggtLylkdiad 80 
                                     +++  G+ G+gk+++Ar+L+ ++   + +++  +l+           ++  d  eq+++ ++++ +i+ 
  gi|116754010|ref|YP_843128.1| 169 RNILFYGASGTGKTMIARALATEANVSMMPVKSTSLIgefvgegarqiHSLYDRAEQLSPCIIFIDEIDA 238
                                    578999******************9999999998888555444444444558888888999999999986 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0    0.0022       1.5       4      36 ..     171     203 ..     168     221 .. 0.85
   2 ?    0.8   0.0      0.57   3.8e+02      85     106 ..     352     373 ..     311     377 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0022
                                    EEEEE-TTSSHHHHHHHHHHHSSS-EEEEEHHH CS
                            CPT   4 ilLnGgsssGKsslaralqevldepwlhlgvDa 36 
                                    il  G+s +GK+ +aral + ++ + + +++ +
  gi|116754010|ref|YP_843128.1| 171 ILFYGASGTGKTMIARALATEANVSMMPVKSTS 203
                                    8999**************999988888776655 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.57
                                    EEEEEE--TTTHHHHHHHHHHH CS
                            CPT  85 nvivDdvilekewlvdllrrll 106
                                     +i D  ++e+++l+d+l+r+ 
  gi|116754010|ref|YP_843128.1| 352 AIIEDSRFVERRHLMDALQRIK 373
                                    6899999***********9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 2640.52
//
Query:       gi|116754011|ref|YP_843129.1|  [L=167]
Description: hypothetical protein Mthe_0699 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 1208.49
//
Query:       gi|116754012|ref|YP_843130.1|  [L=351]
Description: tRNA splicing endonuclease [Methanosaeta thermophila PT]
Scores for 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  168.7   5.6    8.4e-26   89.9   3.8    2.2  2  tRNA_int_endo    tRNA intron endonuclease, catalytic C-termin
    2.4e-41  139.2   1.4    7.6e-22   76.8   0.0    2.5  2  tRNA_int_endo_N  tRNA intron endonuclease, N-terminal domain
    0.00039   20.5   0.2       0.14   12.4   0.0    2.6  2  tRNA_int_end_N2  tRNA-splicing endonuclease subunit sen54 N-t
  ------ inclusion threshold ------
      0.062   13.6   0.0       0.12   12.7   0.0    1.4  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 !   78.6   0.0   6.2e-26   2.8e-22       1      85 []      80     163 ..      80     163 .. 0.98
   2 !   89.9   3.8   1.9e-29   8.4e-26       1      79 [.     258     339 ..     258     344 .. 0.95

  Alignments for each domain:
  == domain 1  score: 78.6 bits;  conditional E-value: 6.2e-26
                                    HHHHHHHHHHHHHTT-EEEECGGGTSSEEEE..TSCTTTSSCSEEEEEEETTSEEEHHHHHHHHHHHHHTTSEEEEEEET CS
                  tRNA_int_endo   1 falkyavyrdLrekGyvvrsGlkFGadFrvY..qrrpslehseylVvvvsedeeldwpdlsaavrlahsvkKklilaivd 78 
                                    f+ +y+vy+dLre+Gy+v++G     dFrvY  +++p+++ +e+ V+vvse+++l+++ +++ +rl+ +++++l+la+vd
  gi|116754012|ref|YP_843130.1|  80 FEFRYVVYKDLRERGYYVQPG---VPDFRVYprGGHPGKTPAEFYVFVVSERTPLPIERIVEPLRLSSQMRRRLMLAVVD 156
                                    899******************...67****************************************************** PP

                                    TTSCEEE CS
                  tRNA_int_endo  79 aegdvty 85 
                                    +e d+ty
  gi|116754012|ref|YP_843130.1| 157 EESDITY 163
                                    *****99 PP

  == domain 2  score: 89.9 bits;  conditional E-value: 1.9e-29
                                    HHHHHHHHHHHHHTT-EEEECGGGTSSEEEE...TSCTTTSSCSEEEEEEETTSEEEHHHHHHHHHHHHHTTSEEEEEEE CS
                  tRNA_int_endo   1 falkyavyrdLrekGyvvrsGlkFGadFrvY...qrrpslehseylVvvvsedeeldwpdlsaavrlahsvkKklilaiv 77 
                                    f++ky+vyrdLr++ +vv++G+kFG++FrvY   + +++ +hseylV++v+ d+ +++p ls+avrlahsv+K +++a+ 
  gi|116754012|ref|YP_843130.1| 258 FEMKYRVYRDLRDRKLVVKTGFKFGTHFRVYksvDAEKRGTHSEYLVHTVRVDHVFHLPVLSRAVRLAHSVRKMMVFAYS 337
                                    899****************************9999999*****************************************8 PP

                                    TT CS
                  tRNA_int_endo  78 da 79 
                                    d+
  gi|116754012|ref|YP_843130.1| 338 DD 339
                                    65 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 !   60.7   0.7   1.7e-20   7.7e-17       3      67 .]       8      70 ..       6      70 .. 0.95
   2 !   76.8   0.0   1.7e-25   7.6e-22       2      67 .]     183     248 ..     182     248 .. 0.97

  Alignments for each domain:
  == domain 1  score: 60.7 bits;  conditional E-value: 1.7e-20
                                   EEEETTEEEESSHHHHHHHHHTTT-SEECCTSSEEEEHHHHHHHHHTTSEEEETTSEEE-HHHHH CS
                tRNA_int_endo_N  3 geLsgdrvlvedeeaakrlyekgfYGkplidepLqLslvEAlYLlekGklevvkggeplsfeell 67
                                   g L++ +v++ + +a+k lye+g++G+   d+ L+L+lvEA+YLl++ +l+++++g+ lsf+ ++
  gi|116754012|ref|YP_843130.1|  8 GRLESGKVHLGK-DAVKVLYEQGYFGR-PLDDGLELTLVEAAYLLDRSRLRIEYDGHILSFRSFF 70
                                   78*********6.**************.7999*****************************9985 PP

  == domain 2  score: 76.8 bits;  conditional E-value: 1.7e-25
                                    EEEEETTEEEESSHHHHHHHHHTTT-SEECCTSSEEEEHHHHHHHHHTTSEEEE.TTSEEE-HHHHH CS
                tRNA_int_endo_N   2 egeLsgdrvlvedeeaakrlyekgfYGkplidepLqLslvEAlYLlekGklevv.kggeplsfeell 67 
                                    +++L++drv+++d +a++rl+++gfYGk +i+e+LqLslvE++YLle+G++++v ++g p+ ++el+
  gi|116754012|ref|YP_843130.1| 183 QATLLDDRVVLWDPKASERLHKHGFYGK-MIGERLQLSLVETAYLLERGMIQLVdRSGVPVPLDELM 248
                                    799*************************.9*********************************9996 PP

>> tRNA_int_end_N2  tRNA-splicing endonuclease subunit sen54 N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.0    0.0031        14      48      70 ..      35      57 ..      11      59 .. 0.80
   2 !   12.4   0.0   3.1e-05      0.14      39      70 ..     202     234 ..     107     236 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0031
                tRNA_int_end_N2 48 rrgrlwLlpeEaLYLvErGsldi 70
                                     + l+L+  Ea YL++r +l i
  gi|116754012|ref|YP_843130.1| 35 LDDGLELTLVEAAYLLDRSRLRI 57
                                   677899************99987 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 3.1e-05
                tRNA_int_end_N2  39 fktmGvsra.rrgrlwLlpeEaLYLvErGsldi 70 
                                    +++ G   +    rl L   E+ YL+ErG +++
  gi|116754012|ref|YP_843130.1| 202 LHKHGFYGKmIGERLQLSLVETAYLLERGMIQL 234
                                    5555655556789****************9997 PP

>> Sen15  Sen15 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.6e-05      0.12      59      92 ..     136     168 ..     101     171 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.6e-05
                          Sen15  59 vfkelkeekserkkrivLaivddDsTvvYYkvtd 92 
                                    +++ l  ++ +  +r++La+vd++s + YY+v +
  gi|116754012|ref|YP_843130.1| 136 IVEPLRLSS-QMRRRLMLAVVDEESDITYYEVRE 168
                                    444444333.4689****************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2533.51
//
Query:       gi|116754013|ref|YP_843131.1|  [L=384]
Description: hypothetical protein Mthe_0701 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2896.73
//
Query:       gi|116754014|ref|YP_843132.1|  [L=246]
Description: external DNA catabolism protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-13   49.7   0.0    3.6e-13   49.3   0.0    1.1  1  RsmJ      Ribosomal RNA large subunit methyltransferase D, Rl


Domain annotation for each model (and alignments):
>> RsmJ  Ribosomal RNA large subunit methyltransferase D, RlmJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.3   0.0     2e-17   3.6e-13       4     155 ..      33     172 ..      30     180 .. 0.86

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 2e-17
                                    -EEEESS--SSEEETTSHHHHHHSGGGGTGGGTTT-TT--GGGHHHHHHHHHTTTTSS--EEE-HHHHHHHHS-TT-EEE CS
                           RsmJ   4 favlDthaGvGrYdLsseeaektgeaeeGiaRliaqadlpaeleryldvvrklnkgeklryYpGspllarrllReqDrlv 83 
                                    +++ ++haG   Y L+ +     ge++ Gi+R ++  +  +  ++y  v++++n +e+l+ YpGs++++ rl R   r v
  gi|116754014|ref|YP_843132.1|  33 LVYAESHAGYTAYTLAPN-----GEWRWGIGRCWHLRSEIE--SPYFAVLEEMN-DEHLQIYPGSAKIILRLGRFFRRRV 104
                                    7899***********875.....9**********8765444..69********9.578********************** PP

                                    EE---TTHHHHHHHHTTT-TTEEEESS-HHHHHHHS-S-TTS-EEEEE----SSCCHHHHHHHHHHHHHHH- CS
                           RsmJ  84 lteLhpkdaalLkaelakdkrvrvkkadGfaalkaklppkekRglvliDPPyeakdeydrvvaalrealkRl 155
                                    ++eL +   ++  ++ + +  +  + +dGf+ +   l +++  gl+liDPP    d+ d+ ++ l++a  R 
  gi|116754014|ref|YP_843132.1| 105 VAELWDISEDV-GKSWSACPDIHFHLGDGFSGVMDLLNRRD-PGLLLIDPP--SPDDQDKAIELLKDASDRG 172
                                    *****988776.667999***************99998887.9********..5677777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); 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 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1936.37
//
Query:       gi|116754015|ref|YP_843133.1|  [L=572]
Description: small GTP-binding protein [Methanosaeta thermophila PT]
Scores for complete 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-51  171.7   0.2    1.1e-50  171.2   0.2    1.2  1  FeoB_N    Ferrous iron transport protein B
    2.5e-25   88.9  17.8    2.4e-13   50.3   6.1    2.7  2  Gate      Nucleoside recognition
    8.8e-19   67.7   0.0    1.3e-18   67.1   0.0    1.3  1  MMR_HSR1  50S ribosome-binding GTPase
    1.7e-12   46.8   1.7    7.7e-12   44.7   1.7    2.3  1  FeoB_C    Ferrous iron transport protein B C terminus
    1.6e-05   24.4   0.0    2.6e-05   23.7   0.0    1.3  1  SRPRB     Signal recognition particle receptor beta subunit
     0.0034   16.7   0.0     0.0055   16.1   0.0    1.3  1  AIG1      AIG1 family
  ------ inclusion threshold ------
       0.05   13.8   0.0       0.28   11.4   0.0    2.0  2  Roc       Ras of Complex, Roc, domain of DAPkinase


Domain annotation for each model (and alignments):
>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.2   0.2   4.3e-54   1.1e-50       2     156 .]       8     161 ..       7     161 .. 0.97

  Alignments for each domain:
  == domain 1  score: 171.2 bits;  conditional E-value: 4.3e-54
                                    EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHHCTSSSE CS
                         FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardflleeepdv 81 
                                    ++ l+GnpnvGk+++f +ltga+   +N+pG+tv  +eg++++ g+++ ++D+PG+Ysl++ s+ e+va+ ++le+ +d+
  gi|116754015|ref|YP_843133.1|   8 KILLMGNPNVGKSVIFSRLTGADAISSNYPGTTVSYTEGSINVLGRSAALIDVPGVYSLDPSSKAEEVAN-LILEQGADL 86 
                                    799*****************************************************************96.6678999** PP

                                    EEEEEEGGGHHHHHHHHHHHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBTHHHHHHHH CS
                         FeoB_N  82 vvnvvdatnlernLyLtlqllelgvpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkegieellkai 156
                                    +vnvvdatnlernL Ltl+l e g+p+v+aln++d+a ++g+eid+k+Lse+Lg++vv+t+a+++ gi++l++ai
  gi|116754015|ref|YP_843133.1|  87 IVNVVDATNLERNLNLTLELQERGIPMVVALNLWDVAVRRGLEIDVKRLSEELGIKVVPTVAASGLGIRDLVEAI 161
                                    ***********************************************************************9986 PP

>> Gate  Nucleoside recognition
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7   3.7   1.1e-14   2.7e-11       4     109 ..     293     384 ..     290     386 .. 0.96
   2 !   50.3   6.1   9.6e-17   2.4e-13       2     111 ..     449     546 ..     448     547 .. 0.95

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 1.1e-14
                           Gate   4 agpiillasiliwflssssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtlytsalgellqgfdtpk 83 
                                    ++p+++++ ++++fl++ ++l r++ l++ ++++lg  l++ a++++++g++   + v+ +  l+           ++ k
  gi|116754015|ref|YP_843133.1| 293 VLPFLIPFYLVLGFLEDLGYLPRVSVLMDALMHRLG--LHGAAIIPCVLGMG---CSVPGVLGLR---------VLESSK 358
                                    79**********************************..**************...*********9.........****** PP

                           Gate  84 salafllfvllytpcvatlavivrel 109
                                    +++ +  ++++++pc +++a+++++l
  gi|116754015|ref|YP_843133.1| 359 QRFLAATLMTMSIPCASQTAMVFGIL 384
                                    *********************99876 PP

  == domain 2  score: 50.3 bits;  conditional E-value: 9.6e-17
                           Gate   2 lkagpiillasiliwflssssllgrigkllepvfap.lgqeldwkatvslltgfaakevvvgtlgtlytsalgellqgfd 80 
                                      a+p+i ++++++++++ ++l+++ig l +p+++  lg  l+  a+++l++gf+ k +++g++  l             
  gi|116754015|ref|YP_843133.1| 449 SEAVPYIGIGIVVMNVFEITGLMKAIGELASPIVSGiLG--LPADAATALILGFLRKDIGIGMFVPL-----------GL 515
                                    5799*****************************999899..***********************555...........89 PP

                           Gate  81 tpksalafllfvllytpcvatlavivrelgs 111
                                    tp++ +++ +++++y+pcvatl v+++elg 
  gi|116754015|ref|YP_843133.1| 516 TPEQLVIAAVVLAMYFPCVATLTVLMKELGP 546
                                    ****************************995 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.1   0.0   5.2e-22   1.3e-18       1     113 [.       8     118 ..       8     119 .. 0.78

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 5.2e-22
                                    EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSS..HHHHHHHHHHHHHHHHC.TS CS
                       MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGlie..gaseekglgkaflalee.ad 77 
                                    +++++G+pNvGKS ++++ltg+ ai s++pgtT   +eg +++ g++  l+D+pG+++   +s+ +++++ +l  e+ ad
  gi|116754015|ref|YP_843133.1|   8 KILLMGNPNVGKSVIFSRLTGADAISSNYPGTTVSYTEGSINVLGRSAALIDVPGVYSldPSSKAEEVANLIL--EQgAD 85 
                                    5899**************************************999**********986422233334444444..4459* PP

                                    EEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEE CS
                       MMR_HSR1  78 lillvvdaseeklkpldeeleelleeakkplilvln 113
                                    li+ vvda+ + l+++ +   el +e+++p++++ln
  gi|116754015|ref|YP_843133.1|  86 LIVNVVDAT-N-LERNLNLTLEL-QERGIPMVVALN 118
                                    *******77.4.55553333333.567899999887 PP

>> FeoB_C  Ferrous iron transport protein B C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   1.7     3e-15   7.7e-12       1      53 []     392     443 ..     392     443 .. 0.97

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 3e-15
                         FeoB_C   1 lfslYllgilvallvalllkkttlkgepspfvmELPpYrlPslknvliktweR 53 
                                    +f++Y++ ++v+++++++l+++ ++ e++  +mE+P+Yr+P ++ +l+kt+ R
  gi|116754015|ref|YP_843133.1| 392 IFAVYATLLIVFIISGMILHRL-IREESPEIFMEIPQYRMPVIGALLKKTFVR 443
                                    69*******************8.***************************876 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 !   23.7   0.0     1e-08   2.6e-05       5      98 ..       8     106 ..       4     127 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1e-08
                                    EEEEE-STTSSHHHHHHHHHHS.S---B---SS-EEETTG...GGTT-SEEEETT-GCC....SHHHHHHHHHHGGEEEE CS
                          SRPRB   5 avllvGlsdsGKTslftrLttd.svkktvtSqessaalkvksekgskltliDfPGhekl....rqklleklkaksslkgl 79 
                                    ++ll+G  + GK  +f rLt   ++ + +     s ++   +  g + +liD+PG  +l    + + + +l+ ++ +  +
  gi|116754015|ref|YP_843133.1|   8 KILLMGNPNVGKSVIFSRLTGAdAISSNYPGTTVSYTEGSINVLGRSAALIDVPGVYSLdpssKAEEVANLILEQGADLI 87 
                                    699*****************763555555566777888778999************99944334556677888899**** PP

                                    EEEEETTS-HHHHHHHHHH CS
                          SRPRB  80 vfvvDStidpkevkevAEl 98 
                                    v vvD+t  +++++ + El
  gi|116754015|ref|YP_843133.1|  88 VNVVDATNLERNLNLTLEL 106
                                    ***********99988776 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   2.1e-06    0.0055       2      97 ..       8      97 ..       7     108 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.1e-06
                                   EEEEESSTTSSHHHHHHHHHTS--SS--TTTS---SS-EEEEEEETTEEEEEEE--SCCCTTCCHHCHHHHHHHHHHHCTT- CS
                           AIG1  2 tivlvGktgnGkSaTgNsilgkkaFesklsaqsvtkkcqkksrtwdgkkinViDTPglfdlsvsadkiskeivrclllseeg 83
                                   +i+l+G   +GkS     + g +a +s++   + t + ++ s  + g++   iD Pg+ +l+ s +   +e+ +  l+ e+g
  gi|116754015|ref|YP_843133.1|  8 KILLMGNPNVGKSVIFSRLTGADAISSNY--PGTTVSYTEGSINVLGRSAALIDVPGVYSLDPSSK--AEEVAN--LILEQG 83
                                   8***************************6..777888999999***************99998776..678887..777899 PP

                                   ESEEEEEEETTB-S CS
                           AIG1 84 ihalllvlslgrft 97
                                    + ++ v+++++++
  gi|116754015|ref|YP_843133.1| 84 ADLIVNVVDATNLE 97
                                   99999999887766 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00011      0.28       1      30 [.       8      37 ..       8      56 .. 0.76
   2 ?   -0.6   0.0      0.56   1.4e+03      55      64 ..     114     123 ..      88     128 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                                   EEEEESSTTSSHHHHHHCHCT-CCC-EEET CS
                            Roc  1 KvvlvGdsgvGKtsllkrfvedkfsekeks 30
                                   K++l+G+ +vGK+ +++r++  +  +++ +
  gi|116754015|ref|YP_843133.1|  8 KILLMGNPNVGKSVIFSRLTGADAISSNYP 37
                                   9******************98665544444 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.56
                                    CEEEEEEEE- CS
                            Roc  55 kvklniWDta 64 
                                     v ln+WD+a
  gi|116754015|ref|YP_843133.1| 114 VVALNLWDVA 123
                                    4889****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (572 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.39
# Mc/sec: 4345.87
//
Query:       gi|116754016|ref|YP_843134.1|  [L=290]
Description: phosphate ABC transporter, inner membrane subunit PstA [Methanosaeta thermophila PT]
Scores for complete 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   82.9  12.9    2.4e-23   82.9  12.9    2.5  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.8   0.4    0.0046        83      56     130 ..      21      48 ..      10      79 .. 0.70
   2 !   82.9  12.9   1.3e-27   2.4e-23       1     184 [.      84     289 ..      84     290 .] 0.87

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.0046
                   BPD_transp_1  56 viillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavllef 130
                                     ++l+++ +++++ +i+++++ +++ +                                               f
  gi|116754016|ref|YP_843134.1|  21 SAVLAIVILGGIFSVIIYNGIGAISIE-----------------------------------------------F 48 
                                    555555555555555555555554443...............................................3 PP

  == domain 2  score: 82.9 bits;  conditional E-value: 1.3e-27
                   BPD_transp_1   1 gillGilaa.lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrsl 79 
                                    gi++Gi++  ++r+ +l++++++ i +l ++Ps+v +++ ++  ++ s +g + l++ ++l l+++p+++l++++alrs+
  gi|116754016|ref|YP_843134.1|  84 GIGAGIYLNeYSRSHTLNRIITISISCLNGVPSVVYGLFGLA--FLVSTVGISLLAGSVILGLMNLPTIILTTQEALRSV 161
                                    899********************************8888775..4779******************************** PP

                   BPD_transp_1  80 pkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleail.gydyseis.... 154
                                    p +l+e + alGa++wq++ ++v+P+alp i+tgli+ ++++ g+++ + +++    ++ + + +   +  ++  +    
  gi|116754016|ref|YP_843134.1| 162 PNSLREGSVALGATKWQTILRIVIPSALPGILTGLIIGVARAAGETAPIMWTA----VTFTPVYVDKvYGVVPDVYqpvn 237
                                    ****************************************************9....44444433330333344447888 PP

                   BPD_transp_1 155 ......................nggvlalviavlllnlvadilqrlldprvr 184
                                                          +g++l+l  +vl++n++a ++  +  + +r
  gi|116754016|ref|YP_843134.1| 238 nlcyhllqliyflgawdvekraWGTALVLMGLVLAMNFLAIVVRNHYRKNIR 289
                                    8889999999999999999999999999999999999999988888777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 2181.56
//
Query:       gi|116754017|ref|YP_843135.1|  [L=301]
Description: phosphate ABC transporter, inner membrane subunit PstC [Methanosaeta thermophila PT]
Scores for complete 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-27   95.8  11.4    2.6e-27   95.8  11.4    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 ?    0.9   1.9     0.018   3.2e+02      58      77 ..      21      40 ..       3      89 .. 0.53
   2 !   95.8  11.4   1.4e-31   2.6e-27       1     184 [.      91     295 ..      91     299 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.018
                   BPD_transp_1 58 illllsaapyvrlirraalr 77
                                   +++++ ++++++li++  +r
  gi|116754017|ref|YP_843135.1| 21 LITAVASIAIMILIFAYLIR 40
                                   23333333333333222222 PP

  == domain 2  score: 95.8 bits;  conditional E-value: 1.4e-31
                   BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf......vilsilghlilpviillllsaapyvrlirra 74 
                                    gi+l+i++a  ++ +++ +l p +++l ++Ps+v ++l + ++       ++   g +il+++ill ++++p ++ i+++
  gi|116754017|ref|YP_843135.1|  91 GIPLAIYLAELSGPRTRAVLKPAVELLAGVPSIVYGFLGIIILvpylgnTFDMLTGRSILAGAILLGVMFIPSITTICED 170
                                    89********************************7777776667779**9999*************************** PP

                   BPD_transp_1  75 alrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis 154
                                    alr++p +++e + alGa+rwq++r+vvlP+a + i + ++l++g+++g++++++++ ++  + +  + ++  +d  ++ 
  gi|116754017|ref|YP_843135.1| 171 ALRAVPNEFKEGSMALGATRWQTIRYVVLPAASSGITAAVLLNIGNIIGETMAVLLVVGN--IARIPTPIYDVFDRGATF 248
                                    **********************************************************66..444444444444444444 PP

                   BPD_transp_1 155 .................nggvlalviavlllnlvadilqrlldprvr 184
                                                     + +++a+++++l ++ ++ ++ +l   r+r
  gi|116754017|ref|YP_843135.1| 249 tsviagemgevahgslhYHALFAVGLMLLTIVSILSVIGDLARERIR 295
                                    667888888999999**555555555555555555555555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2266.68
//
Query:       gi|116754018|ref|YP_843136.1|  [L=222]
Description: amino acid-binding ACT domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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-70  234.9   5.2    3.8e-70  234.3   5.2    1.3  1  DUF5612       Domain of unknown function (DUF5612)
    1.2e-09   37.7   0.1    3.8e-09   36.1   0.1    1.9  1  ACT           ACT domain
    5.4e-05   23.7   0.0    0.00016   22.2   0.0    1.8  1  ACT_4         ACT domain
    0.00016   21.6   0.0     0.0004   20.3   0.0    1.7  1  ACT_6         ACT domain
  ------ inclusion threshold ------
      0.038   13.4   0.1      0.065   12.6   0.1    1.4  1  Peripla_BP_1  Periplasmic binding proteins and sugar binding 
        0.2   12.0   0.3        7.6    6.9   0.0    2.1  2  DUF1178       Protein of unknown function (DUF1178)


Domain annotation for each model (and alignments):
>> DUF5612  Domain of unknown function (DUF5612)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  234.3   5.2   1.3e-73   3.8e-70       1     142 [.      80     220 ..      80     221 .. 0.98

  Alignments for each domain:
  == domain 1  score: 234.3 bits;  conditional E-value: 1.3e-73
                                    E--HHHHT-EEEEEEE-HHHHHHHHHHHHHHHHHHHCTSS-EEEEEEE--SHHHHHHHHHHGGGSTTEEEEEEESSB--T CS
                        DUF5612   1 hkslkeifGkrviilGGGaqvaqvalGaiseadrhnirGerisvdtiplvGeeelaeaveavsrlprvkvlvlaGslmGG 80 
                                    h s+++i+G+rvii+GGGaqvaq a+Ga+seadrhn+rGerisvdtiplvGe+++a+av+av rl+r+++l+laG+lmGG
  gi|116754018|ref|YP_843136.1|  80 HPSFNQIYGSRVIIIGGGAQVAQAAVGAVSEADRHNLRGERISVDTIPLVGEDAIADAVSAVGRLHRASILILAGALMGG 159
                                    5799**************************************************************************** PP

                                    HHHHHHHHHHHT.T-EEEEES-BSSHHHHSSEEESSHHHHHHHHHHHH-TTS---GGGCSS- CS
                        DUF5612  81 kiteavkklkeekdiivislnmaGsvtevadlvvtdpvqaGvlavmavadtavfdiervkgk 142
                                    +ite+v+kl++e +i+vi+l+maG+v+++adlvvtdp+qaG++avm+va+tavfdi+rv+g 
  gi|116754018|ref|YP_843136.1| 160 RITEEVAKLQKE-GIPVIALKMAGTVPKQADLVVTDPIQAGTFAVMHVARTAVFDINRVRGM 220
                                    ***********9.**********************************************985 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.1   1.3e-12   3.8e-09       3      40 ..       5      45 ..       3      71 .. 0.80

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 1.3e-12
                                   EEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTT...E CS
                            ACT  3 lrvgvpDrPGlLarvfgaladrgiNidsieqrssedk...v 40
                                   +++ ++DrPG+L +++g++ad+g Ni+  +q+  +++   +
  gi|116754018|ref|YP_843136.1|  5 INIICEDRPGMLRDIAGVVADHGGNIVYTQQFVLDRGvnkG 45
                                   99*************************99999887776542 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   5.2e-08   0.00016       8      78 ..       4      77 ..       1      78 [. 0.80

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 5.2e-08
                          ACT_4  8 rleveaedrkglLaditqviseekanivsvnaktrkk...dglaeikitveVkdvehLsrviakLraipgVisV 78
                                    +++++edr+g+L+di+ v++++++niv  +    ++   +g  ++ +++e   +  ++ ++++Lr++p V++V
  gi|116754018|ref|YP_843136.1|  4 AINIICEDRPGMLRDIAGVVADHGGNIVYTQQFVLDRgvnKGKGTVYMEIEGDVRGGIEGMVEALRSMPMVYEV 77
                                   699************************98776555444446666666666666677899999999999999998 PP

>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   1.4e-07    0.0004       5      40 ..       5      40 ..       2      45 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.4e-07
                          ACT_6  5 itvtGpdrpGltasLtsvlaefgvnilDieqavihg 40
                                   i+++ +drpG++ ++++v+a++g ni+  +q v+ +
  gi|116754018|ref|YP_843136.1|  5 INIICEDRPGMLRDIAGVVADHGGNIVYTQQFVLDR 40
                                   99****************************999875 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 ?   12.6   0.1   2.2e-05     0.065      55     109 ..     145     202 ..     119     211 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.2e-05
                                    TT-SEEEEE-..S-GG.HHHHHHHHHHT-EEEEESS--B-TTTS-EEEE-HHHHHHHH CS
                   Peripla_BP_1  55 kgidgliiat..sdts.fdditakaesgipvialedaidapdgvPcvipddtqagees 109
                                    +++  li+a+  ++++  +++ + +++gipvial+ a+  p++ ++v+ d  qag+ +
  gi|116754018|ref|YP_843136.1| 145 HRASILILAGalMGGRiTEEVAKLQKEGIPVIALKMAGTVPKQADLVVTDPIQAGTFA 202
                                    566666666422455656789999999***************************9865 PP

>> DUF1178  Protein of unknown function (DUF1178)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.036   1.1e+02     117     148 ..      98     129 ..      89     131 .. 0.86
   2 ?    6.9   0.0    0.0025       7.6     124     147 ..     157     180 ..     152     183 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.036
                        DUF1178 117 eaeeraIrGeataeeakeLleeGievlplpll 148
                                     + ++a  G  +++++++L+ e i+v ++pl+
  gi|116754018|ref|YP_843136.1|  98 AQVAQAAVGAVSEADRHNLRGERISVDTIPLV 129
                                    55667788*********************986 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0025
                        DUF1178 124 rGeataeeakeLleeGievlplpl 147
                                    +G   +ee+++L++eGi+v++l +
  gi|116754018|ref|YP_843136.1| 157 MGGRITEEVAKLQKEGIPVIALKM 180
                                    5667789*************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); 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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1628.80
//
Query:       gi|116754019|ref|YP_843137.1|  [L=81]
Description: glutaredoxin [Methanosaeta thermophila PT]
Scores for complete 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   36.3   0.0    6.1e-09   36.0   0.0    1.2  1  Glutaredoxin   Glutaredoxin
    0.00018   21.8   0.0    0.00022   21.5   0.0    1.1  1  DUF836         Glutaredoxin-like domain (DUF836)
    0.00031   20.8   0.0    0.00048   20.1   0.0    1.3  1  Thioredoxin_3  Thioredoxin domain
    0.00034   20.9   0.0    0.00041   20.6   0.0    1.1  1  GST_N          Glutathione S-transferase, N-terminal domain
    0.00074   19.9   0.0    0.00098   19.5   0.0    1.2  1  GST_N_3        Glutathione S-transferase, N-terminal domain
  ------ inclusion threshold ------
      0.062   13.5   0.0      0.067   13.4   0.0    1.1  1  SH3BGR         SH3-binding, glutamic acid-rich protein
       0.12   13.0   0.0       0.13   12.9   0.0    1.1  1  Pex14_N        Peroxisomal membrane anchor protein (Pex14p) c


Domain annotation for each model (and alignments):
>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.0   2.4e-12   6.1e-09       3      59 ..       8      64 ..       6      65 .. 0.84

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 2.4e-12
                                   EEESTSSHHHHHHHHHHHHTTGGEEEEEGCCSHHHHHHHHHHH.TSSSSSEEEETTEE CS
                   Glutaredoxin  3 lftkptCpyCkkakrlLkelgvkfeeidvdkdeeireelkels.gvrtvPqvfidgkh 59
                                   ++t+p Cp C + k++L+++gv+fee+d +   e+  el+ +    ++ P++  dg++
  gi|116754019|ref|YP_843137.1|  8 IYTTPDCPRCEQLKAFLESKGVSFEEVDMTTA-EALTELRVNGvFTMSAPVLEMDGRF 64
                                   8*****************************97.7777776665655788888888875 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   8.7e-08   0.00022       2      57 ..       6      62 ..       5      79 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 8.7e-08
                                   EEEEE-TT-HHHHHHHHHHHHHCCCTTEEEEEEETTT-CCCHC.....CCCTTTTEEEECT CS
                         DUF836  2 ltLyskpgChlCeqakekLkelkleegleleviDIakdeelea.....kYgleipvlaleg 57
                                   + +y++p C+ Ceq+k+ L+     +g++ e++D ++ e l +      +    pvl ++g
  gi|116754019|ref|YP_843137.1|  6 CRIYTTPDCPRCEQLKAFLE----SKGVSFEEVDMTTAEALTElrvngVFTMSAPVLEMDG 62
                                   569*****************....4678899*****9999888777889999999999988 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   1.9e-07   0.00048       5      74 ..       8      79 ..       4      80 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.9e-07
                                   E.ESSSSTTCHHHHHHHHHHCHCCTCEC...EEECCTTHHHHHHCT-..SSSSEEECTTCEEEESS---CCHHHHH CS
                  Thioredoxin_3  5 v.lgpgCakCpklekavkeaaaekgika...evekvtdfeeiekygV..msvPalvidgkvvvsGkvpseeeirkl 74
                                   +  +p C++C++l+++++    +kg+++   +++ ++ + e+  +gV  ms P l +dg++ ++G + +++ +++l
  gi|116754019|ref|YP_843137.1|  8 IyTTPDCPRCEQLKAFLE----SKGVSFeevDMTTAEALTELRVNGVftMSAPVLEMDGRFYTTGDLFDGDRLKEL 79
                                   655889*****9887765....556665333555555555554444444999******************999987 PP

>> GST_N  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.6e-07   0.00041       4      61 ..       7      62 ..       4      66 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.6e-07
                                   EEESSSTSHTHHHHHHHHHHTT-EEEEEEECSTTTCGGCHHHHHHCTT.S-SSEEEETT CS
                          GST_N  4 tlysirgsprahrirlllaakgveyevvpldfeageekspellklnpl.gkvPaLedng 61
                                   + y+ +++pr ++++++l+ kgv++e+v++++   +e+  el  +  +   +P+Le +g
  gi|116754019|ref|YP_843137.1|  7 RIYTTPDCPRCEQLKAFLESKGVSFEEVDMTT---AEALTELRVNGVFtMSAPVLEMDG 62
                                   689****************************8...444567776666688888888876 PP

>> GST_N_3  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   3.8e-07   0.00098       2      56 ..       9      64 ..       8      70 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 3.8e-07
                                   ES-TTSHHHHHHHHHHHHHT--EEEE---TTTTHHHHHHH-.TT--SSEEETTS-E CS
                        GST_N_3  2 ygfpaSpyarrvrlaLnekglpvevvevtpgehdeellakn.plgkvPvLeddgea 56
                                   y +p++p +   + +L+ kg+++e+v++t  e   el+     +  +PvLe dg+ 
  gi|116754019|ref|YP_843137.1|  9 YTTPDCPRCEQLKAFLESKGVSFEEVDMTTAEALTELRVNGvFTMSAPVLEMDGRF 64
                                   899*************************9999866654444556668**9999875 PP

>> SH3BGR  SH3-binding, glutamic acid-rich protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.6e-05     0.067      22      51 ..      19      48 ..      14      75 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.6e-05
                                   HHHHHHHHTT--EEEEETTT-HHHHHHHHH CS
                         SH3BGR 22 evlriLdakkiefdevDitkdeeerelmre 51
                                   +   +L++k ++f+evD+t+ e+  el  +
  gi|116754019|ref|YP_843137.1| 19 QLKAFLESKGVSFEEVDMTTAEALTELRVN 48
                                   56689***************9988776554 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 ?   12.9   0.0   5.2e-05      0.13      26      43 ..      21      38 ..      13      59 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.2e-05
                        Pex14_N 26 vaFLesKGLtqeEIeeaL 43
                                   +aFLesKG++ eE++   
  gi|116754019|ref|YP_843137.1| 21 KAFLESKGVSFEEVDMTT 38
                                   69************9655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       780  (0.0435049); expected 358.6 (0.02)
Passed bias filter:                      672  (0.0374812); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 601.41
//
Query:       gi|116754020|ref|YP_843138.1|  [L=110]
Description: hypothetical protein Mthe_0708 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); 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: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 852.67
//
Query:       gi|116754021|ref|YP_843139.1|  [L=164]
Description: hypothetical protein Mthe_0709 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.088   12.8   0.0       0.19   11.7   0.0    1.6  1  Hjc       Archaeal holliday junction resolvase (hjc)


Domain annotation for each model (and alignments):
>> Hjc  Archaeal holliday junction resolvase (hjc)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   1.1e-05      0.19      38      83 ..      47      97 ..      10     109 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.1e-05
                                   TTEEEEEEEEEESSS.EEEE....EHHHHHHHHHHHHHHTCEEEEEEEETT CS
                            Hjc 38 gdvvlviEvKsskke.riyl....kkeqvekllefarkaggelllavklqg 83
                                    + +l+iE+Ks + e ++y     + +q+++  +f + +g   +la+ ++g
  gi|116754021|ref|YP_843139.1| 47 PEYYLAIECKSLSMEgPLYFkqhfSPDQIDRESRFIELSGRTGVLAIEFRG 97
                                   5789******9877779**95555667999999999999999999999854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1172.13
//
Query:       gi|116754022|ref|YP_843140.1|  [L=215]
Description: thymidylate synthase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-21   76.5   0.0    2.3e-21   76.1   0.0    1.2  1  Thymidylat_synt  Thymidylate synthase


Domain annotation for each model (and alignments):
>> Thymidylat_synt  Thymidylate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.1   0.0   1.3e-25   2.3e-21      88     219 ..      81     205 ..      17     210 .. 0.83

  Alignments for each domain:
  == domain 1  score: 76.1 bits;  conditional E-value: 1.3e-25
                                    TB-SSSHHHHHHHBTSTTTSSB-HHHHHHHHHHHSTT-ST-EEE---GGGGGGSSS--SEEEEEEEE..SEETEEEEEEE CS
                Thymidylat_synt  88 gdlgpvYGkqwrkfkaeegkkidqlakvidqlkenpdsRriivsawnpaeldkmaLppChvlfqfyvkdkkegkLslqly 167
                                       +  YG  +r+++     ++dq+a+++++lk+np+ Rr     w p+  +k    pC+v++ f++++   ++L+l+++
  gi|116754022|ref|YP_843140.1|  81 PGFEYTYGERLRSWN----GEVDQIAEIVNRLKRNPRTRRATAVTWIPQVDHKREEVPCMVVCDFKIRS---SRLNLTVM 153
                                    357889********7....79**************************887545899***********54...46****** PP

                                    EEEEETTTHHHHHHHHHHHHHHHHHHHHT-EEEEEEEEEEEEEEEGGGHHHH CS
                Thymidylat_synt 168 qRSaDvflGvpFNiasyalLthmlaqvtglkpgelihtigdaHiYsnhveqv 219
                                     RS D++ + p N+ + + L+h + ++ g  pg+l+     aHiY+   + v
  gi|116754022|ref|YP_843140.1| 154 FRSHDFAGAYPANVYALSKLLHHVSRESGSVPGSLTTLSASAHIYEHDWDWV 205
                                    *********************************************9988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1637.79
//
Query:       gi|116754023|ref|YP_843141.1|  [L=138]
Description: thioredoxin [Methanosaeta thermophila PT]
Scores for complete 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   87.5   0.0    6.2e-25   87.2   0.0    1.2  1  Thioredoxin    Thioredoxin
    3.7e-08   33.8   0.1      5e-06   26.9   0.1    2.9  2  Thioredoxin_2  Thioredoxin-like domain
      3e-06   27.4   0.0     0.0013   19.0   0.0    2.3  2  Thioredoxin_8  Thioredoxin-like
    0.00024   20.9   0.0    0.00036   20.3   0.0    1.3  1  Thioredoxin_9  Thioredoxin
     0.0025   17.2   0.0     0.0031   16.9   0.0    1.1  1  OST3_OST6      OST3 / OST6 family, transporter family
     0.0078   16.2   0.0      0.013   15.5   0.0    1.5  1  HyaE           Hydrogenase-1 expression protein HyaE
  ------ inclusion threshold ------
      0.074   12.7   0.1       0.43   10.2   0.1    1.9  1  DUF953         Eukaryotic protein of unknown function (DUF953
      0.096   12.9   0.0        0.2   11.9   0.0    1.5  1  Thioredoxin_7  Thioredoxin-like
       0.12   12.2   0.0       0.42   10.5   0.0    1.7  2  AhpC-TSA       AhpC/TSA family
       0.13   11.9   0.0       0.26   11.0   0.0    1.6  2  Redoxin        Redoxin
       0.15   12.1   0.0       0.26   11.3   0.0    1.5  1  Thioredoxin_3  Thioredoxin domain


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.2   0.0   3.8e-28   6.2e-25       5     102 ..      38     134 ..      34     135 .. 0.92

  Alignments for each domain:
  == domain 1  score: 87.2 bits;  conditional E-value: 3.8e-28
                                    SSHHHHHHHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTEE CS
                    Thioredoxin   5 ltkenFeeevakekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkngke 84 
                                    +t+++ ++ +++    ++v+++A+wCg+C+a+aP+++++a+elk++v++ k++vd+n+ + +ky++++iPtl++f+ng+ 
  gi|116754023|ref|YP_843141.1|  38 VTDSSIDAGIRQ-YPVFVVDCWAEWCGPCRAIAPVIDEMARELKGRVVFGKLNVDQNPLTSRKYGITAIPTLLVFRNGRL 116
                                    566777777888.8899*************************************************************** PP

                                    EEEEESS-HHHHHHHHHH CS
                    Thioredoxin  85 vkkyegarekeklaaflk 102
                                    v++++ga +k+ l++ ++
  gi|116754023|ref|YP_843141.1| 117 VDRLVGAYPKQILMSRVR 134
                                    *********999887765 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.17   2.8e+02      72      89 ..      15      34 ..       3      41 .. 0.73
   2 !   26.9   0.1   3.1e-09     5e-06       8     105 ..      53     129 ..      47     132 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.17
                  Thioredoxin_2 72 larky..gvrgtPtivfldg 89
                                   l r++  + +gtPti ++d 
  gi|116754023|ref|YP_843141.1| 15 LKRELaaRSQGTPTIEYPDR 34
                                   4444444789*****99996 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 3.1e-09
                  Thioredoxin_2   8 vlvvftdpdCpyCkklkkelkel.ddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPt.iv 85 
                                    ++v+ ++++C+ C+++  +++e+ +++         k  +++   ++++++  +             rkyg+++ Pt +v
  gi|116754023|ref|YP_843141.1|  53 FVVDCWAEWCGPCRAIAPVIDEMaREL---------KGRVVFGKLNVDQNPLTS-------------RKYGITAIPTlLV 110
                                    467777*****************5555.........555888889999988775.............**********888 PP

                  Thioredoxin_2  86 fldgkeivarlpGyvpaeel 105
                                    f +g+  v+rl+G++p++ l
  gi|116754023|ref|YP_843141.1| 111 FRNGR-LVDRLVGAYPKQIL 129
                                    *****.*********98765 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   8.3e-07    0.0013       3      44 ..      52      91 ..      50      96 .. 0.84
   2 !    6.8   0.0     0.005       8.1      75      91 ..      97     113 ..      86     117 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 8.3e-07
                                   EEEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-S CS
                  Thioredoxin_8  3 vvlLyfgaswcppckaftpklkelyeklkkkkkveivyvsld 44
                                   v+++ ++a+wc pc+a+ p ++e+ ++lk   +v++  +++d
  gi|116754023|ref|YP_843141.1| 52 VFVVDCWAEWCGPCRAIAPVIDEMARELK--GRVVFGKLNVD 91
                                   6899***********************99..66666555555 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.005
                                    TT-S--TT-SEEEEE-T CS
                  Thioredoxin_8  75 kkkynvkaiPtlvvldk 91 
                                     +ky+++aiPtl+v ++
  gi|116754023|ref|YP_843141.1|  97 SRKYGITAIPTLLVFRN 113
                                    689**********9875 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   2.2e-07   0.00036      50     121 ..      59     128 ..      41     133 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.2e-07
                                    -TT-HHHHHHHHHHHHHH.HH-TTEEEEEE-HHHHHHHTTTTTT-SS--SSEEEEE-TT.--EEEEEESS-HHH CS
                  Thioredoxin_9  50 edwCgDaavnvPvlakia.elnpnievkillrdenlelmdqyltngaraiPtliildee.geelgvwgerPaev 121
                                    ++wCg ++++ Pv++++a el+ ++ +  l  d+n+ + ++y   g  aiPtl+++ ++   +    g +P+++
  gi|116754023|ref|YP_843141.1|  59 AEWCGPCRAIAPVIDEMArELKGRVVFGKLNVDQNPLTSRKY---GITAIPTLLVFRNGrL-VDRLVGAYPKQI 128
                                    68***************9455667777777777777777777...88******99988742.333467777765 PP

>> OST3_OST6  OST3 / OST6 family, transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.9e-06    0.0031      46     104 ..      62     113 ..      47     127 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.9e-06
                      OST3_OST6  46 CelCrefepefelvakswrkdekskskklfFakvdfdegkdvFqklglnsaPhlllfpp 104
                                    C +Cr ++p ++ +a+  +         ++F+k+++d+++ + +k+g++ +P ll+f  
  gi|116754023|ref|YP_843141.1|  62 CGPCRAIAPVIDEMARELKGR-------VVFGKLNVDQNPLTSRKYGITAIPTLLVFRN 113
                                    99************9998877.......9***************************976 PP

>> HyaE  Hydrogenase-1 expression protein HyaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   7.7e-06     0.013      48     101 ..      70     122 ..      37     127 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.7e-06
                                    HHHHHHHCT-TTS-EEEEEETHHHHHHHHHCCT-TSSSEEEEEETTEEEEEEES CS
                           HyaE  48 VvlpEllkaFpnalraavvadreqeealaerfgvlktPsllflrdgeylgvlak 101
                                     v+ E+ ++ + +     ++  +q+    +++g++  P+ll++r+g+++  l +
  gi|116754023|ref|YP_843141.1|  70 PVIDEMARELKGRVVFGKLN-VDQNPLTSRKYGITAIPTLLVFRNGRLVDRLVG 122
                                    57888888888887777777.888899999*****************9987765 PP

>> DUF953  Eukaryotic protein of unknown function (DUF953)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00027      0.43      36      99 ..      60     114 ..      56     130 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00027
                                    BSSHHHHHHHHHHHHHHHH-SS-EEEEEEE---HHHHT-TTSHHHH..TS---SSSEEEEETSS CS
                         DUF953  36 sWCPdCvkaepvieealkeapedvklvrvdvGdrevWkdpanpfRkdpklkltgvPtLlrwkgk 99 
                                     WC  C +  pvi e  +e+   v++ + +v + +       + R   k+ +t++PtLl + + 
  gi|116754023|ref|YP_843141.1|  60 EWCGPCRAIAPVIDEMARELKGRVVFGKLNVDQNPL------TSR---KYGITAIPTLLVFRNG 114
                                    5*******************9999998888866554......234...4889999999987653 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00012       0.2      16      81 ..      48     111 ..      45     113 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                                    HT--EEE.EE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S-GGG.-TT---...SSEEEEE CS
                  Thioredoxin_7  16 rgkpvlv.ffgaswcftCqalerdflsdeevkaalaekfvllrvdvterdanileldeqg...vPvvafl 81 
                                    r+ pv+v +  a+wc++C+a++ +  +    ++ l++++v+ +++v+++     +  ++g   +P+++++
  gi|116754023|ref|YP_843141.1|  48 RQYPVFVvDCWAEWCGPCRAIAPVIDEM--ARE-LKGRVVFGKLNVDQNPLTS-R--KYGitaIPTLLVF 111
                                    5678888799***********9988766..666.999***9999997766544.2..2223448888877 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00026      0.42      28      58 ..      53      82 ..      41      93 .. 0.87
   2 ?   -1.0   0.0      0.98   1.6e+03      88     116 ..      90     112 ..      86     118 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00026
                                   EEEEEESTST-CCHHHHHHHHHHCHHHCCCT CS
                       AhpC-TSA 28 vvlffypkdwcpvCttelpalaklyeefker 58
                                    v+ ++++ wc +C++ +p + +++ e+k r
  gi|116754023|ref|YP_843141.1| 53 FVVDCWAE-WCGPCRAIAPVIDEMARELKGR 82
                                   68999*99.***************9999854 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.98
                                    E-TTSHHHHHTT-EETTTTECSCEEEEE- CS
                       AhpC-TSA  88 sDeegkvakaygvlkeekglalratfvid 116
                                     D++  ++++yg+       a+++  v+ 
  gi|116754023|ref|YP_843141.1|  90 VDQNPLTSRKYGIT------AIPTLLVFR 112
                                    68888889999999......777777765 PP

>> Redoxin  Redoxin
   #    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      31      73 ..      53      93 ..      27     111 .. 0.79
   2 ?   -1.0   0.0       0.8   1.3e+03      92     133 ..      91     122 ..      85     131 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00016
                                   EEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSS CS
                        Redoxin 31 vvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadnd 73
                                    vv  ++  +c++C+a +p +++ a++lk + v +  +++d++
  gi|116754023|ref|YP_843141.1| 53 FVVDCWAE-WCGPCRAIAPVIDEMARELK-GRVVFGKLNVDQN 93
                                   58889999.***************99844.4355545555555 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.8
                                    -TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEEES CS
                        Redoxin  92 DgsaaftkalGlrleedaseglrtpryavidedgkvvyleve 133
                                    D++   ++++G++         ++p++ ++ ++g++v + v+
  gi|116754023|ref|YP_843141.1|  91 DQNPLTSRKYGIT---------AIPTL-LVFRNGRLVDRLVG 122
                                    6666667777755.........66655.45577777766555 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00016      0.26      10      59 ..      62     116 ..      46     131 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00016
                                    STTCHHHHHHHHHHCHCCTCECEEECC.TTHHHH..HHCT-SSSSEEEC..TTCE CS
                  Thioredoxin_3  10 CakCpklekavkeaaaekgikaevekv.tdfeei..ekygVmsvPalvi..dgkv 59 
                                    C  C++++ ++ e+a e++  + + k   d + +   kyg++++P+l++  +g++
  gi|116754023|ref|YP_843141.1|  62 CGPCRAIAPVIDEMARELKGRVVFGKLnVDQNPLtsRKYGITAIPTLLVfrNGRL 116
                                    999***************877755554433333336**********954236665 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:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1097.41
//
Query:       gi|116754024|ref|YP_843142.1|  [L=196]
Description: hypothetical protein Mthe_0712 [Methanosaeta thermophila PT]
Scores for complete 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   0.1    1.8e-29  102.9   0.1    1.2  1  DUF1638   Protein of unknown function (DUF1638)


Domain annotation for each model (and alignments):
>> DUF1638  Protein of unknown function (DUF1638)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.9   0.1   9.9e-34   1.8e-29       2     160 ..      34     183 ..      33     184 .. 0.94

  Alignments for each domain:
  == domain 1  score: 102.9 bits;  conditional E-value: 9.9e-34
                        DUF1638   2 leaglHnrpeeLrealqeeidrakadydqIllgYGlCggalaglrsdecpveilkgddCislllgseeayaeelkdekgt 81 
                                    l++glH +++eL  +l+e+++++k   + I+++YG C++++ +l  + ++ e++ +++Ci++l++++e   e+ ++e   
  gi|116754024|ref|YP_843142.1|  34 LDPGLHVDFDELALKLREALESCK--DNMIIVVYGACHPKMNDL-LEGYRAELIDCQNCIDALITRREV--ERIASEGLY 108
                                    89*********************8..899***************.*********************999..66566455* PP

                        DUF1638  82 ffltpgwvkewdrlv.lekygeelarmifgkllkgYkrlvyidtgltddpeleeraeefaarlglelevipgglgllekl 160
                                    f+ltpgw++ w++++  ++ g e+ar  +g     +k +++idt l + +++e+ + ef++++ l++ +ipg+l+++++l
  gi|116754024|ref|YP_843142.1| 109 FYLTPGWIECWRDIFrRLGWGMEEARLEMGC----FKGVIFIDT-LGNAEDYENDLLEFMDFTLLQYSIIPGKLDHFRSL 183
                                    **************8777777**********....*******99.9*******************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); 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 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1376.28
//
Query:       gi|116754025|ref|YP_843143.1|  [L=324]
Description: alanine dehydrogenase [Methanosaeta thermophila PT]
Scores for complete 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-111  371.5   0.0   3.1e-111  371.3   0.0    1.0  1  OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin famil
    2.7e-06   27.5   0.0    5.3e-06   26.5   0.0    1.5  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
  ------ inclusion threshold ------
      0.018   12.7   0.0      0.027   12.2   0.0    1.1  1  ACR_tran         AcrB/AcrD/AcrF family


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 !  371.3   0.0  5.2e-115  3.1e-111       6     316 ..       6     314 ..       1     316 [. 0.98

  Alignments for each domain:
  == domain 1  score: 371.3 bits;  conditional E-value: 5.2e-115
                                    E-HHHHHCCH-HCCCHHHHHHHHHHHHCC-CE----EEEEECCGTEEEEEEEEEETTTTEEEEEEEEEETTTCCCTSSSE CS
                OCD_Mu_crystall   6 ltaveveeelllddlakaveeafrrlasgkvkkpprvalevkdsrgelevmpaylagrellgvKlvnshpenkksglptv 85 
                                    l++ +v+++l ++d+++ave af++  +g+v++pp+ +l  ++  g+l+ mpay+++++++gvK+vnshp+n+++glp+v
  gi|116754025|ref|YP_843143.1|   6 LSEDDVKSILTMEDAIPAVESAFAEHGLGNVQMPPKSYLYYEH--GDLRTMPAYIKKLGATGVKIVNSHPGNPEKGLPSV 83 
                                    67899**************************************..*********************************** PP

                                    EEEEEEE-TTT--EEEEEE-HHHHHHHHHHHHHHHHHHHS-TT--EEEEE--SHHHHHHHHHHCCCS--SEEEEE-SSHH CS
                OCD_Mu_crystall  86 talvvLndpetGvplalmdatlltalRTaAvsavaakyLarkdasvlaiiGaGvqaetqlealkavldikevriydrdee 165
                                    +a+++Ln+ etG+plalm +t+lta+RT+A++++aakyLar++++ ++iiGaG+qa+tq++al +++d++ vr+ d ++ 
  gi|116754025|ref|YP_843143.1|  84 MAVIILNSFETGAPLALMGGTYLTAVRTGAAGGIAAKYLARRNSKAVGIIGAGAQARTQVMALAKIFDLDVVRVLDKSQA 163
                                    ******************************************************************************** PP

                                    HHHHHHHHCCS..CTT-EEECSCHHHHTTSSEEEE----SS-SB-GGGS-TT-EEEE-S--STT--SB-HHHHHCCEEEE CS
                OCD_Mu_crystall 166 aaekfaenlqef.efevsackseeeavegadivvtvTaakapilkaewvkpGahinavgadapgkteLdddilkradifv 244
                                     a +f++ ++ f + + + +++ ++a  ++di+vt+T++++p++  +wv +G+hina+gadapgk+eLd+ +l+ra+++v
  gi|116754025|ref|YP_843143.1| 164 RAMAFVSDARSFlDCDCVPVSDGRDAC-DCDILVTATPSREPVVRSDWVMEGTHINAIGADAPGKQELDPRLLRRAKVVV 242
                                    ***********66***********996.8*************************************************** PP

                                    SHHHHHHHCCCCHCHHHTTSSTCGGEEEEHHHHHCTSS-..-STTSEEEEE----HHHHHHHHHHHHHHHCC CS
                OCD_Mu_crystall 245 dseaqareeGeiqvaiekgvlaedakvaelgeviaGkkpGRtsdeeitlfdsvGlaveDvaaaklvyeraee 316
                                    d++ qa ++Ge++v+i++g  + d+++a+lge+iaGk+pGR++ +eit+fds+Gla++D+a+a lvy +a++
  gi|116754025|ref|YP_843143.1| 243 DDLSQAIHSGEVNVPISRGEYRSDEIHAQLGEIIAGKMPGREDVREITIFDSTGLAIQDIAVASLVYRKAKD 314
                                    ********************************************************************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 !   26.5   0.0   8.9e-10   5.3e-06       3      99 ..     118     215 ..     116     222 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 8.9e-10
                                    HHHHHS..TT-EEEEES-SHHHHHHHHHHHCC.T-CEEEEEESSHHHHHHHHHHH.T.ET-EEEEGCGHHHHHHT-SEEE CS
                   Shikimate_DH   3 akkkleslkekkvlliGaGemaelvakhLlak.gvkkvvvaNRtlerakelaeel.kgeeiealkleelkellaeadvvi 80 
                                    a k l + ++k v +iGaG  a+  + +L++   ++ v v+  +++ra +++++  +  ++  +++++ +++  ++d+++
  gi|116754025|ref|YP_843143.1| 118 AAKYLARRNSKAVGIIGAGAQARTQVMALAKIfDLDVVRVLDKSQARAMAFVSDArSFLDCDCVPVSDGRDA-CDCDILV 196
                                    6777788899*******************99779999***************99934457889999998865.579**** PP

                                    E-SSSSS-SB-HHHHHCCH CS
                   Shikimate_DH  81 sataseepilekeeveeal 99 
                                    +at s+ep++++++v+e  
  gi|116754025|ref|YP_843143.1| 197 TATPSREPVVRSDWVMEGT 215
                                    **************99876 PP

>> ACR_tran  AcrB/AcrD/AcrF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.5e-06     0.027     174     260 ..     217     304 ..     212     314 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.5e-06
                                    EEESS.-SEEEEEEE-HHHHHCTT--HHHHHHHHHHH..SSB-EEEEETT-SB-EEE..EESB---SHHHHHTSEEEETT CS
                       ACR_tran 174 vqliGgsekavriwldpqklaklgltltdvvsalkeq..nvnvaaGqlegqeeelli..raqgqlqsaediekiivknqd 249
                                    ++ iG ++   +  ldp  l++ ++ ++d+++a+++   nv ++ G+   +e ++++  ++ g++   ed+++i++   d
  gi|116754025|ref|YP_843143.1| 217 INAIG-ADAPGKQELDPRLLRRAKVVVDDLSQAIHSGevNVPISRGEYRSDEIHAQLgeIIAGKMPGREDVREITI--FD 293
                                    66666.444445589*******************9752266678999966665555533899**************..89 PP

                                    SCEEEHHHCEE CS
                       ACR_tran 250 gskvrlrDvAk 260
                                     + + ++D+A 
  gi|116754025|ref|YP_843143.1| 294 STGLAIQDIAV 304
                                    99999999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); 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 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2388.62
//
Query:       gi|116754026|ref|YP_843144.1|  [L=386]
Description: geranylgeranyl reductase [Methanosaeta thermophila PT]
Scores for 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   38.4   1.2    3.1e-05   23.4   0.3    3.1  3  FAD_binding_3   FAD binding domain
    6.9e-09   35.2   0.4    3.9e-08   32.8   0.4    2.0  1  Lycopene_cycl   Lycopene cyclase protein
    8.2e-09   35.1   0.2    0.00011   21.6   0.2    2.5  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    2.9e-08   32.9   2.1    1.2e-07   30.8   0.6    2.0  2  HI0933_like     HI0933-like protein
    1.8e-07   31.1   0.8     0.0024   17.5   0.0    2.3  2  DAO             FAD dependent oxidoreductase
    1.4e-05   24.5   0.1      0.004   16.5   0.6    2.2  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    2.7e-05   23.7   0.2    3.6e-05   23.3   0.2    1.4  1  FAD_oxidored    FAD dependent oxidoreductase
    3.4e-05   23.1   1.9    4.3e-05   22.8   1.1    1.6  2  FAD_binding_2   FAD binding domain
    8.8e-05   21.8   0.1    0.00013   21.2   0.1    1.3  1  GIDA            Glucose inhibited division protein A
    0.00015   21.1   0.3     0.0003   20.1   0.3    1.5  1  Thi4            Thi4 family
     0.0048   16.2   0.2     0.0091   15.3   0.2    1.4  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
     0.0064   15.4   0.2        1.2    7.9   0.3    2.5  3  Trp_halogenase  Tryptophan halogenase
  ------ inclusion threshold ------
       0.01   16.1   0.6      0.028   14.6   0.2    2.0  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
      0.049   14.2   0.4        1.1    9.9   0.1    2.8  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.3   2.5e-08   3.1e-05       2      34 ..       4      36 ..       3      48 .. 0.91
   2 !    6.4   0.0    0.0037       4.7     107     211 ..      98     206 ..      55     234 .. 0.71
   3 !    6.1   0.1    0.0045       5.8     283     304 ..     256     277 ..     252     312 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 2.5e-08
                                   EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                  FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrs 34
                                   +dV+++GaGpaGlm+a+  s+ G r++++e + 
  gi|116754026|ref|YP_843144.1|  4 YDVAVIGAGPAGLMAAKHASMCGARTIVLEEHM 36
                                   59****************************986 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0037
                                    HHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE--GTT-HHHHHHTGGEEEEEEEEEEE CS
                  FAD_binding_3 107 leriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrakYlvGaDGgrStvrktlgiefegeetvyeag 186
                                    ++r ++ +a+ +g+++  ++ v+sl++ ++     ++ +  g + ++ a+ ++ a+G+r  ++++ gi+   ++++    
  gi|116754026|ref|YP_843144.1|  98 FDRSMALAAVHHGVEITLNAHVRSLRRLGDL---MILHH--GDK-EIAARAVISAEGVRASIARRSGIP--PPKRLLSGA 169
                                    6677777788888888888888877777765...33333..444.79********************87..556666788 PP

                                    EEEEEEEC.-SCCCTTC...........CEEEEECCT CS
                  FAD_binding_3 187 vldvlfda.dlsdivep...........lvlilsaes 211
                                     ++v fd+ d++++  +           +v+ +s++s
  gi|116754026|ref|YP_843144.1| 170 QVEVPFDVdDIESVEVHlgkdiapglfaWVIPISRSS 206
                                    8888888877776655544444444444333334444 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0045
                                    ETTEEE-GGGTEEE-STTSHHH CS
                  FAD_binding_3 283 kgrvflaGDAaHihpPtgGqGl 304
                                     + ++++GDAa  + Pt G G+
  gi|116754026|ref|YP_843144.1| 256 ADGLLVVGDAAAHVKPTSGGGV 277
                                    6889***************997 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.4     3e-11   3.9e-08       1     312 [.       5     316 ..       5     343 .. 0.77

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 3e-11
                  Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfpnnyvWsdefedlga....leecvehsWsgtivylddgkkil 76 
                                    Dv+viGaGpAgl  A++   +  g + +++e    + +p +       ++l+a     e ++    +g++   ++g++  
  gi|116754026|ref|YP_843144.1|   5 DVAVIGAGPAGLMAAKHA--SMCGARTIVLEEHMAIGYPVQCAGLLGISALEAseiqTEGFLINPFKGAVFVSPNGSRLS 82 
                                    9***********999999..99********99999988887766666666665666678888889999988888888877 PP

                  Lycopene_cycl  77 lg...raYgrvsskrlkeellerlvengvk.lleakvesveeeeageslvvleggrkirarlvvdarglaslkkarrlgl 152
                                          +   v ++ + + ++   v++gv+  l+a v s +   +   ++  +g+++i ar+v+ a g  +++ arr g+
  gi|116754026|ref|YP_843144.1|  83 FKspnVRAWAVDRRLFDRSMALAAVHHGVEiTLNAHVRSLRRLGD--LMILHHGDKEIAARAVISAEG-VRASIARRSGI 159
                                    7767755567***************888751689*****998877..99999****************.77775555555 PP

                  Lycopene_cycl 153 ....QtfyGvevevdnppfdldkmvlMDfrveqklkgltFlYalPldsd..rllvEeTelaskpeLpadalkkrlaaylr 226
                                            G  vev   pfd+d ++     + +++    F +++P++++  r+ +  Te a +  L+  +   r+++++ 
  gi|116754026|ref|YP_843144.1| 160 pppkRLLSGAQVEV---PFDVDDIESVEVHLGKDIAPGLFAWVIPISRSsaRIGLCATERACHY-LKKFLSSDRIRNRI- 234
                                    22225667888877...6************999999999*******986226666677777766.77777777776665. PP

                  Lycopene_cycl 227 alglkvkevveeEqgviPvtlggslprleqkvlaiGaaaglvhPaTGYsvarslaeapllasaiaaalres....slsar 302
                                     lg  v+ vv    g +P+  g++ + ++   l +G aa  v+P+ G  v   +   + +a +iaa   +     ++++r
  gi|116754026|ref|YP_843144.1| 235 -LGSPVALVV----GGLPL--GPPDRTVADGLLVVGDAAAHVKPTSGGGVYPGIVCGR-IAGRIAAEHVLTggqlERYER 306
                                    .899999998....88***..666666666699**************98888776666.777777776666222255555 PP

                  Lycopene_cycl 303 awatlwprer 312
                                    +w++  +re+
  gi|116754026|ref|YP_843144.1| 307 EWRSAIGREI 316
                                    5555544444 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 !   21.6   0.2   8.6e-08   0.00011       1      35 [.       4      36 ..       4      70 .. 0.84
   2 !   10.9   0.0   0.00015      0.19     191     242 ..     104     154 ..      88     164 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 8.6e-08
                                   CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtc 35
                                   +dv+viG+GpAGl aa++++  ga+++++  e+++
  gi|116754026|ref|YP_843144.1|  4 YDVAVIGAGPAGLMAAKHASMCGARTIVL--EEHM 36
                                   69***********************9998..4433 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00015
                                    HHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES-H CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 191 ealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrpste 242
                                     a  ++Gve+ l++ v  +++ g+ l   +   +ei+a+ v+ a Gvr+s +
  gi|116754026|ref|YP_843144.1| 104 LAAVHHGVEITLNAHVRSLRRLGD-LMILHHGDKEIAARAVISAEGVRASIA 154
                                    556689*****************8.55445555559*************974 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.6   9.3e-11   1.2e-07       1      43 [.       4      46 ..       4      54 .. 0.94
   2 ?    1.2   0.0     0.091   1.2e+02     121     164 ..     108     149 ..     100     155 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 9.3e-11
                                   -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHHHCG CS
                    HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakklgrKilisG 43
                                   +dv+viG+G+AGlmaA +a+  g+r+++le+  ++g  ++ +G
  gi|116754026|ref|YP_843144.1|  4 YDVAVIGAGPAGLMAAKHASMCGARTIVLEEHMAIGYPVQCAG 46
                                   59********************************999888887 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.091
                                    HHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE---- CS
                    HI0933_like 121 eagvklrletevksvekeedgkfrvktkseeeleadklvlAtGG 164
                                    + gv++ l+ +v+s+++  d  + +++ +++e++a++++ A G 
  gi|116754026|ref|YP_843144.1| 108 HHGVEITLNAHVRSLRRLGDL-MILHH-GDKEIAARAVISAEGV 149
                                    689************886666.77777.9**********99985 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.5   9.8e-05      0.12       1      30 [.       5      36 ..       5      57 .. 0.89
   2 !   17.5   0.0   1.9e-06    0.0024     140     225 ..      90     171 ..      67     237 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.8e-05
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEESSS CS
                            DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgd 30
                                   dv++iG+G +Gl +A +++  g  +++le + 
  gi|116754026|ref|YP_843144.1|  5 DVAVIGAGPAGLMAAKHASMCGarTIVLEEHM 36
                                   8*****************88888999999984 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 1.9e-06
                                    EEEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEE.EEEEEEEE--GGGHHHHHTTCTTTSEEE CS
                            DAO 140 tgqvdpakltaalaraaealGveilegtevtgleeedgkvwgverttpgen.daadavVnaaGawsdllgllkeldlpis 218
                                    ++ vd + + +++a aa  +Gvei +++ v++l++  g+++ ++ +  g +  aa+av+ a G+ ++++++ ++ ++p +
  gi|116754026|ref|YP_843144.1|  90 AWAVDRRLFDRSMALAAVHHGVEITLNAHVRSLRR-LGDLMILH-H--GDKeIAARAVISAEGVRASIARRSGI-PPPKR 164
                                    4667999999***********************66.35667773.2..4443478*********9986633322.23335 PP

                                    EEEEEEE CS
                            DAO 219 pvrgqvl 225
                                     + g  +
  gi|116754026|ref|YP_843144.1| 165 LLSGAQV 171
                                    5555555 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 !   16.5   0.6   3.1e-06     0.004       2      31 ..       8      37 ..       7      42 .. 0.88
   2 !    5.5   0.0    0.0069       8.9      90     134 ..     105     149 ..      72     174 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.1e-06
                    Pyr_redox_3  2 IiGaGPaGlaaaielkkagledylilEkg.n 31
                                   +iGaGPaGl aa ++  +g  + ++lE + +
  gi|116754026|ref|YP_843144.1|  8 VIGAGPAGLMAAKHASMCGA-RTIVLEEHmA 37
                                   8*******************.688**99844 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0069
                    Pyr_redox_3  90 vaksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGe 134
                                     a ++ ++i l+ +V+s+ + ++  +++   +++ A+ vi A G 
  gi|116754026|ref|YP_843144.1| 105 AAVHHGVEITLNAHVRSLRRLGDLMILHHGDKEIAARAVISAEGV 149
                                    5678999***********************************996 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.2   2.8e-08   3.6e-05       1      35 [.       5      39 ..       5     160 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 2.8e-08
                   FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlG 35
                                   Dv V+G+gpaG++AA  A   Ga+++++ee+  +G
  gi|116754026|ref|YP_843144.1|  5 DVAVIGAGPAGLMAAKHASMCGARTIVLEEHMAIG 39
                                   9*****************************99998 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   1.1   3.3e-08   4.3e-05       1      33 [.       5      37 ..       5      61 .. 0.88
   2 ?   -2.4   0.0       1.5   1.9e+03     156     200 ..     111     148 ..      65     165 .. 0.56

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 3.3e-08
                                   SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSG CS
                  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqe 33
                                   Dv ViG+G AGL+AA  a+ +G++++v+e   +
  gi|116754026|ref|YP_843144.1|  5 DVAVIGAGPAGLMAAKHASMCGARTIVLEEHMA 37
                                   9***************************98766 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.5
                                    EEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE--- CS
                  FAD_binding_2 156 vdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatg 200
                                    v++  ++ +++L +      G+ +      ++ +i+a+av+ a+g
  gi|116754026|ref|YP_843144.1| 111 VEITLNAHVRSLRR-----LGDLMI--LHHGDKEIAARAVISAEG 148
                                    33333333333311.....222222..222333445555555544 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.1     1e-07   0.00013       1     149 [.       5     148 ..       5     172 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1e-07
                                    CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--SSSSEEE-T..THHHHHHH...HHHHT-SHHHHHHHHEEEEE CS
                           GIDA   1 dviViGgGhAGceAAlaaarlGakvlLithkldtiaelsCnpsiggi..akgllvrE...idalggliikaadkagiqfr 75 
                                    dv ViG+G AG+ AA +a+  Ga+++ + +++     + C   +g     ++++++E   i+ ++g +    + +++ f+
  gi|116754026|ref|YP_843144.1|   5 DVAVIGAGPAGLMAAKHASMCGARTIVLEEHMAIGYPVQCAGLLGISalEASEIQTEgflINPFKGAVFVSPNGSRLSFK 84 
                                    79**************************9888887788888776655445677777755556666777777777777444 PP

                                    EESTTS-CCC-EEEEEE-HHHHHHHHHHH.HHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--T CS
                           GIDA  76 ilNrskGpavralraqvdrelyskevtek.lenepnleiieeeveeliveekkvkgvvtedgetikakavviatG 149
                                           p vra   +vdr+l+ +++  + +++  ++++ ++ v +l         ++ + +++i a+av+ a G
  gi|116754026|ref|YP_843144.1|  85 ------SPNVRAW--AVDRRLFDRSMALAaVHHGVEITL-NAHVRSLRR--LGDLMILHHGDKEIAARAVISAEG 148
                                    ......4888888..999999998886440333333333.344555532..222446666666777777776666 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.3   2.3e-07    0.0003      18      58 ..       4      43 ..       1      53 [. 0.87

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.3e-07
                                   EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTT CS
                           Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailersvspGGGaw 58
                                    Dv+++GaG++GL aa+  +   + ++++le+++++G  + 
  gi|116754026|ref|YP_843144.1|  4 YDVAVIGAGPAGLMAAKHASMC-GARTIVLEEHMAIGYPVQ 43
                                   59***************98887.*************96655 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 !   15.3   0.2   7.1e-06    0.0091      31      62 ..       6      37 ..       3      61 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 7.1e-06
                                   EEEESTSHHHHHHHHHHHHTT-EEEEEESSHH CS
                    AlaDh_PNT_C 31 vlviGgGvaGlqAiatakglgakVtvlDvrpa 62
                                   v viG+G aGl A++ a+  ga++ vl+  +a
  gi|116754026|ref|YP_843144.1|  6 VAVIGAGPAGLMAAKHASMCGARTIVLEEHMA 37
                                   89**********************99987665 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.3   0.00093       1.2       1      30 [.       5      32 ..       5      42 .. 0.78
   2 !    4.6   0.0    0.0091        12     147     213 ..      89     153 ..      67     185 .. 0.85
   3 ?   -1.8   0.0      0.83   1.1e+03     313     341 ..     254     282 ..     196     314 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00093
                                   EEEEE--SHHHHHHHHHHHHHTTTSSEEEE CS
                 Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtl 30
                                   ++ ++G+G+aG +aA + ++ + +  ++ l
  gi|116754026|ref|YP_843144.1|  5 DVAVIGAGPAGLMAAKHASMCGAR--TIVL 32
                                   589**************9998844..4444 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0091
                                    -EEEE-HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGGG-II CS
                 Trp_halogenase 147 yAyhldaalyakfLrrvaearGvtrvegkvvevqldedgrveslrledgreveadlfiDcsGfrgll 213
                                     A+ +d++l+++ +   a ++Gv+++    v   l+  g+   l++  ++e+ a+ +i + G r+ +
  gi|116754026|ref|YP_843144.1|  89 RAWAVDRRLFDRSMALAAVHHGVEITLNAHV-RSLRRLGDLMILHH-GDKEIAARAVISAEGVRASI 153
                                    59**********************9876553.45677888888877.66779999999999998766 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.83
                                    SEETTEEE-CCCTEE--CCCS-HHHHHHH CS
                 Trp_halogenase 313 awvknvvalGlasgfvePlestsihliqa 341
                                    +   +++ +G+a++ v P  + +++   +
  gi|116754026|ref|YP_843144.1| 254 TVADGLLVVGDAAAHVKPTSGGGVYPGIV 282
                                    55667888999999999988888875544 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 ?   14.6   0.2   2.2e-05     0.028       1      32 [.       8      39 ..       8      46 .. 0.93
   2 ?   -3.0   0.0       6.8   8.8e+03      31      50 ..     297     321 ..     292     323 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.2e-05
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSS CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlG 32
                                   ++GaG +Gl aA +++  g++  +le +  +G
  gi|116754026|ref|YP_843144.1|  8 VIGAGPAGLMAAKHASMCGARTIVLEEHMAIG 39
                                   8*************************998887 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6.8
                                    SSGGG-EECE.....TTCEECTS-- CS
                  NAD_binding_8  31 lGGraasyev.....pgvrvdygah 50 
                                    +GG++ +ye+      g+ + +g++
  gi|116754026|ref|YP_843144.1| 297 TGGQLERYERewrsaIGREISLGMR 321
                                    6899999888543322366666665 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00082       1.1       2      32 ..       6      36 ..       5      45 .. 0.89
   2 ?    0.3   0.0      0.84   1.1e+03      52      67 ..     108     123 ..      95     131 .. 0.81
   3 ?   -1.4   0.0       2.8   3.5e+03      21      47 ..     312     339 ..     308     344 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00082
                                   EEEECSSHHHHHHHHHHHHTTSEEEEEESSS CS
                      Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversd 32
                                   v+v+G+G  gl++A+ ++  g+++ v+e + 
  gi|116754026|ref|YP_843144.1|  6 VAVIGAGPAGLMAAKHASMCGARTIVLEEHM 36
                                   89*********************99999875 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.84
                                    HTTEEEECSEEEEEEE CS
                      Pyr_redox  52 kngievllntkveeie 67 
                                    ++g+e+ ln+ v +++
  gi|116754026|ref|YP_843144.1| 108 HHGVEITLNAHVRSLR 123
                                    679*******999887 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 2.8
                                    TTSEEEEEESSSSSS.TTSSHHHHHHHH CS
                      Pyr_redox  21 lgkkVtvversdkll.rllDeeaskilq 47 
                                    +g ++++  r + +l r+ D+e+  +++
  gi|116754026|ref|YP_843144.1| 312 IGREISLGMRVNDILrRMSDKEIDMVIR 339
                                    6666666666677777888888876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 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:                        44  (0.00245412); 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: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2693.46
//
Query:       gi|116754027|ref|YP_843145.1|  [L=1039]
Description: Na+/solute symporter [Methanosaeta thermophila PT]
Scores for complete 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-55  187.1   0.0    9.4e-34  116.1   0.0    2.4  2  DUF835    Protein of unknown function (DUF835)
  ------ inclusion threshold ------
       0.27   11.5   8.6       0.26   11.5   0.2    4.3  4  DUF347    Repeat of Unknown Function (DUF347)


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 !   68.7   0.0   4.4e-23   3.9e-19       5     117 ..     634     752 ..     630     759 .. 0.91
   2 !  116.1   0.0     1e-37   9.4e-34       7     136 .]     902    1034 ..     896    1034 .. 0.95

  Alignments for each domain:
  == domain 1  score: 68.7 bits;  conditional E-value: 4.4e-23
                         DUF835   5 kekakeilsdlvkegvkvlaitRenpkkirekvkienvkviwltkvee..entvsPtnlekltetivkflkeaekgvvli 82 
                                     ++a+e+++d+v++g+++l++tR++p+++r+++++ ++++iwl +++e  e+++sPtnl+ l  ti++f++   kg++l+
  gi|116754027|ref|YP_843145.1| 634 AQNAYEVFTDQVTHGFEGLCVTRRPPEDVRSRYSLRKTPIIWLNQKREggEKQISPTNLPLLFLTIKTFVETCRKGIILL 713
                                    67889*****************************************975688**************************** PP

                         DUF835  83 DgleyLvlengF....esvlkflltlkDavllkngtlil 117
                                    D+le Lvl n+     e+ l+f+ +l   v  +n++lil
  gi|116754027|ref|YP_843145.1| 714 DNLEHLVLVNENvipaEDLLDFVNQLENLVHRTNTRLIL 752
                                    *******8887434447999999***9999999999998 PP

  == domain 2  score: 116.1 bits;  conditional E-value: 1e-37
                         DUF835    7 kakeilsdlvkegvkvlaitRenpkkirekvkienvkviwltkveeen...tvsPtnlekltetivkflkeaekgvvl 81  
                                     ++ ei+s+lv  g ++l+i+R np+++rek++i+  +viwlt++ ee+   +v+Ptn+++l  +i++fl++ e  v+l
  gi|116754027|ref|YP_843145.1|  902 RCFEIFSELVHAGLEGLCISRYNPESLREKYGISPETVIWLTQKTEEGkfrSVDPTNFPRLSSMISDFLRRTEYPVIL 979 
                                     5679****************************************9865566*************************** PP

                         DUF835   82 iDgleyLvlengFesvlkflltlkDavllkngtlilvidkealeekelalLkref 136 
                                     ++g+ yL++++++e+vl+f+++ +D v l++++++++id+  l++kel+ L+ e+
  gi|116754027|ref|YP_843145.1|  980 LEGIGYLITQSNYETVLRFIQSQRDEVSLRGAVMLVHIDPLSLDTKELHRLEGEM 1034
                                     ***************************************************9887 PP

>> DUF347  Repeat of Unknown Function (DUF347)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.2       0.1     9e+02      30      50 ..       7      27 ..       2      29 .. 0.79
   2 ?   11.5   0.2   2.9e-05      0.26      14      43 ..     100     129 ..     100     137 .. 0.91
   3 ?    1.1   0.4     0.053   4.8e+02      27      44 ..     154     171 ..     147     175 .. 0.53
   4 ?   -3.5   0.0       1.4   1.3e+04      16      30 ..     966     987 ..     965     988 .. 0.59

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.1
                         DUF347 30 vgaaifgalllvvvlaqfltk 50
                                     ++i++ lll+ ++a++  +
  gi|116754027|ref|YP_843145.1|  7 AFSIILTYLLLLSIIAYYADR 27
                                   557899999999999999766 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 2.9e-05
                         DUF347  14 ttaGDflsqglglgyavgaaifgalllvvv 43 
                                    t+++Df+s   g +ya+ga+++++ ++vv+
  gi|116754027|ref|YP_843145.1| 100 TSISDFISFRYGRSYAIGAIVTIVSMMVVI 129
                                    89************************9996 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.053
                         DUF347  27 gyavgaaifgalllvvvl 44 
                                    g+  + a+++a++++++ 
  gi|116754027|ref|YP_843145.1| 154 GTKLSVAVLLAVFAIIFG 171
                                    444455555555555554 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 1.4
                         DUF347  16 aGDflsqgl.......glgyav 30 
                                    ++Dfl ++        g+gy++
  gi|116754027|ref|YP_843145.1| 966 ISDFLRRTEypvilleGIGYLI 987
                                    7999998333333345777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1039 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       758  (0.0422779); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.69u 0.28s 00:00:00.97 Elapsed: 00:00:00.43
# Mc/sec: 7307.01
//
Query:       gi|116754028|ref|YP_843146.1|  [L=208]
Description: KaiC [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-34  119.1   0.0    2.2e-34  118.8   0.0    1.1  1  ATPase           KaiC
    0.00032   21.1   0.0    0.00051   20.5   0.0    1.4  1  AAA_16           AAA ATPase domain
    0.00073   19.8   0.0     0.0011   19.3   0.0    1.3  1  AAA_22           AAA domain
     0.0035   16.4   0.0     0.0047   16.0   0.0    1.2  1  T2SSE            Type II/IV secretion system protein
     0.0037   16.6   0.0      0.011   15.0   0.1    1.7  2  Rad51            Rad51
     0.0075   16.0   0.2      0.016   15.0   0.2    1.5  1  AAA_29           P-loop containing region of AAA domain
  ------ inclusion threshold ------
       0.01   15.4   0.1      0.027   14.0   0.1    1.9  1  AAA_25           AAA domain
      0.022   14.7   0.0      0.027   14.4   0.0    1.2  1  ATPase_2         ATPase domain predominantly from Archaea
      0.037   14.5   0.2      0.065   13.7   0.2    1.3  1  AAA_23           AAA domain
      0.052   13.3   0.0      0.067   13.0   0.0    1.3  1  DEAD             DEAD/DEAH box helicase
      0.062   12.8   0.0      0.088   12.3   0.0    1.2  1  AAA_7            P-loop containing dynein motor region
      0.068   12.9   0.0       0.11   12.2   0.0    1.3  1  Sigma54_activat  Sigma-54 interaction domain
      0.089   12.7   0.1       0.17   11.8   0.1    1.4  1  NACHT            NACHT domain
       0.19   11.0   0.1       0.35   10.1   0.1    1.4  1  Zeta_toxin       Zeta toxin


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 !  118.8   0.0   1.7e-37   2.2e-34      12     228 ..       2     206 ..       1     208 [] 0.88

  Alignments for each domain:
  == domain 1  score: 118.8 bits;  conditional E-value: 1.7e-37
                         ATPase  12 lkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvf.vtveepaedlrenakslG.wdlekleeegklaiidas 89 
                                    l+gGip  ++vli+Ge+G+GKt++++q+l+kgae  ge+g++  ++ epae + + +++   +d +++     + +id+ 
  gi|116754028|ref|YP_843146.1|   2 LEGGIPVPSSVLISGETGSGKTTLCMQYLFKGAEL-GERGIYfMALSEPAELMLRFISTYEfVDHRHFGTL--IRYIDLG 78 
                                    68******************************999.****9736888888877777776653566666655..99***** PP

                         ATPase  90 esaeesaeekdkedleelieelaeaikeikakrvviDsitglayeekeavaReilrqlvrvlkklgvTailvseksssee 169
                                    e  e       k d +e++e + + ++++  +r+viDs+  + ++  ++   + l++l  ++k ++   ++++e +ss  
  gi|116754028|ref|YP_843146.1|  79 EVIE-------KGDEDEILELMDREVRSFMPRRIVIDSLPFI-RTVLKDGYNRFLFRLGAIMKSWDSAVLITAESRSS-- 148
                                    9986.......5888999999*********************.66666666778999*****************6555.. PP

                         ATPase 170 aaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIteegikvle 228
                                    +   ++++  i dgvi+L ++ei  +++R+lei+km gt+h+  +h ++It++gi+v++
  gi|116754028|ref|YP_843146.1| 149 TPYPQDIAC-ITDGVIILYNMEIGRTRRRSLEILKMMGTSHRAGKHALDITSKGITVYP 206
                                    667789999.***********************************************98 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0     4e-07   0.00051      24      59 ..       9      48 ..       2     128 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 4e-07
                         AAA_16 24 pelvllsGesGvGKsslv.rellr..alekdggif.lrgk 59
                                   p++vl+sGe G+GK++l  + l++  +l ++g++f +  +
  gi|116754028|ref|YP_843146.1|  9 PSSVLISGETGSGKTTLCmQYLFKgaELGERGIYFmALSE 48
                                   599***************6666667688888888863333 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   8.5e-07    0.0011       6      98 ..      10     108 ..       8     134 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 8.5e-07
                         AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka............erl 73 
                                    +++++ Ge+G+GKTtl+ ++l +       e  +++++f+ l+++ ++   +    +++++++ +            e +
  gi|116754028|ref|YP_843146.1|  10 SSVLISGETGSGKTTLCMQYLFKGA-----ELGERGIYFMALSEPAELMLRFISTYEFVDHRHFGtliryidlgeviEKG 84 
                                    5789***********9988876642.....22477777888888888888888888888888888888899999998999 PP

                         AAA_22  74 sseellealeqalraravielliiD 98 
                                    +++e+le++ + +r+ +  + ++iD
  gi|116754028|ref|YP_843146.1|  85 DEDEILELMDREVRSFMP-RRIVID 108
                                    999999999999999888.888888 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 !   16.0   0.0   3.7e-06    0.0047     130     171 ..      10      54 ..       1      73 [. 0.71

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.7e-06
                          T2SSE 130 glilvsGgTgsGKttllyall...keinksderivtvEDpvEiql 171
                                     ++l+sG TgsGKttl    l   +e+ ++   ++ +  p+E+ l
  gi|116754028|ref|YP_843146.1|  10 SSVLISGETGSGKTTLCMQYLfkgAELGERGIYFMALSEPAELML 54 
                                    689************986655222345555555666666666655 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   8.8e-06     0.011      29      56 ..       1      28 [.       1      34 [. 0.94
   2 ?   -1.8   0.0       1.2   1.5e+03     163     188 ..     122     147 ..     118     161 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8.8e-06
                                   HHTSSEESSSEEEEEESTTSSHHHHHHH CS
                          Rad51 29 lLgGGietgsiteifGefrsGktqlcht 56
                                   +L+GGi++ s   i Ge +sGkt lc++
  gi|116754028|ref|YP_843146.1|  1 MLEGGIPVPSSVLISGETGSGKTTLCMQ 28
                                   69*************************8 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.2
                                    HHHHHHHHHHHHHH--EEEEEEE--- CS
                          Rad51 163 gkllrtLrkladefevavvitnqvva 188
                                    +++l +L  + + ++ av+it +  +
  gi|116754028|ref|YP_843146.1| 122 NRFLFRLGAIMKSWDSAVLITAESRS 147
                                    78999999999999999999987655 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2   1.2e-05     0.016      24      46 ..      11      31 ..       5      37 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.2e-05
                         AAA_29 24 atlltGpsGsGKSTllDAiqalL 46
                                   ++l++G++GsGK+Tl   +q+l+
  gi|116754028|ref|YP_843146.1| 11 SVLISGETGSGKTTLC--MQYLF 31
                                   48************97..66665 PP

>> AAA_25  AAA 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     0.027      29      61 ..       5      38 ..       1     137 [. 0.69

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.1e-05
                         AAA_25 29 llpagelallaGapgtGKttlaldlalava.tGk 61
                                    +p  + +l+ G +g+GKttl+++  ++ a +G+
  gi|116754028|ref|YP_843146.1|  5 GIPVPSSVLISGETGSGKTTLCMQYLFKGAeLGE 38
                                   56677889*****************999996555 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   0.0   2.1e-05     0.027      23      65 ..      12      54 ..       8     134 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.1e-05
                       ATPase_2 23 yfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskl 65
                                   ++i G  gsGKt+L ++ + +  +++++ iy++al+e ++  l
  gi|116754028|ref|YP_843146.1| 12 VLISGETGSGKTTLCMQYLFKGAELGERGIYFMALSEPAELML 54
                                   6899*******************************98776544 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   5.1e-05     0.065      22      35 ..      12      25 ..       9      27 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.1e-05
                         AAA_23 22 tlItGpNGaGKTTi 35
                                   +lI+G++G+GKTT+
  gi|116754028|ref|YP_843146.1| 12 VLISGETGSGKTTL 25
                                   69***********8 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   5.2e-05     0.067      16      38 ..      11      33 ..       2     106 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.2e-05
                                   EEEEEESTTSSHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD 16 dvlvaaeTGsGKTlaflipvlqi 38
                                   +vl+++eTGsGKT+  +  +++ 
  gi|116754028|ref|YP_843146.1| 11 SVLISGETGSGKTTLCMQYLFKG 33
                                   79************988877754 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 ?   12.3   0.0   6.9e-05     0.088      35      56 ..      11      33 ..       3      65 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.9e-05
                          AAA_7 35 pvllvGptGtGKtviikd.llkk 56
                                   +vl+ G+tG+GKt+++++ l+k 
  gi|116754028|ref|YP_843146.1| 11 SVLISGETGSGKTTLCMQyLFKG 33
                                   79**************9944444 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   8.6e-05      0.11      21      41 ..       8      28 ..       2      55 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.6e-05
                                   SSS-EEEECSTTSSHHHHHHH CS
                Sigma54_activat 21 tdlsvlitGesGtGKellara 41
                                    ++svli Ge+G+GK++l  +
  gi|116754028|ref|YP_843146.1|  8 VPSSVLISGETGSGKTTLCMQ 28
                                   6789***********987644 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00014      0.17       3      19 ..      12      28 ..      10      44 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00014
                                   EEEEC-TTTCHHHHHHH CS
                          NACHT  3 vilqGeaGsGKTtLlqk 19
                                   v++ Ge GsGKTtL  +
  gi|116754028|ref|YP_843146.1| 12 VLISGETGSGKTTLCMQ 28
                                   89***********9765 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00027      0.35      16      33 ..       9      26 ..       5      35 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00027
                     Zeta_toxin 16 PklillgGqpGAGKsela 33
                                   P ++l++G +G+GK++l 
  gi|116754028|ref|YP_843146.1|  9 PSSVLISGETGSGKTTLC 26
                                   899************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); 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: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 1638.97
//
Query:       gi|116754029|ref|YP_843147.1|  [L=482]
Description: dihydropteroate synthase-related protein [Methanosaeta thermophila PT]
Scores for complete 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   44.8   0.0    8.8e-11   41.9   0.0    2.1  2  DUF4346      Domain of unknown function (DUF4346)
    1.2e-07   31.6   0.1    3.4e-07   30.2   0.1    1.8  2  Pterin_bind  Pterin binding enzyme


Domain annotation for each model (and alignments):
>> DUF4346  Domain of unknown function (DUF4346)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.024   2.1e+02       5      30 ..     399     422 ..     395     432 .. 0.74
   2 !   41.9   0.0   9.8e-15   8.8e-11      62     118 .]     425     478 ..     403     478 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.024
                        DUF4346   5 klskRaielDpaGYflikvdreakli 30 
                                      s+R+  lDpaG f i +    ++i
  gi|116754029|ref|YP_843147.1| 399 ARSSRMFVLDPAGSFRIGL--CGDEI 422
                                    5699***********9877..34444 PP

  == domain 2  score: 41.9 bits;  conditional E-value: 9.8e-15
                        DUF4346  62 reaekvyrgrtakelcvkileeeeelpvtkldhaaYlGRelqraeaaLlsgkeYiqD 118
                                     + + v +grta+e+    ++      v++ldhaaYlGRel +ae+aL  gk+Y qD
  gi|116754029|ref|YP_843147.1| 425 VHDRMVIKGRTAREILDTAIDL---NLVSRLDHAAYLGRELEKAEIALRLGKSYTQD 478
                                    44567889*****987665554...67*****************************9 PP

>> Pterin_bind  Pterin binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.1   3.8e-11   3.4e-07      28     123 ..     166     250 ..     158     265 .. 0.84
   2 ?   -3.2   0.0       0.6   5.3e+03     195     240 ..     297     335 ..     286     336 .. 0.67

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 3.8e-11
                                    HHHHHTT-SEEEEESS-TSTT--CCHHHHHHHHHHHHHHHHHHHC.TSEEEEE-S-HHHHHHHHHTTSEEEEETTTTSSS CS
                    Pterin_bind  28 rkmveeGAdilDiggestrPgaervdeeeelervvpvlealrdea.dvpisiDttkaevaeaAlkagadivNdvsgeerd 106
                                    r   ++GAd++D+g              ++++rvv + +    ++ ++p+siDt +++ + a++++gad++ ++ g +  
  gi|116754029|ref|YP_843147.1| 166 RYYESQGADMIDLGFPLD-------ATTDDVRRVVRIAR----RFtELPVSIDTLRPDLILAGVESGADMILSIDGSN-M 233
                                    556679********8544.......34667778777666....55589******************************.9 PP

                                    TTHHHHHHHHT-EEEEE CS
                    Pterin_bind 107 pkmlelvaeagaavvvm 123
                                    ++++  + e +++ vv 
  gi|116754029|ref|YP_843147.1| 234 HAVADALLERDVPAVVI 250
                                    99999999999999986 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.6
                                    TTSSEBEEEGTTGHHHHHHHCTTCHGHHHHHHHHHHHHHHHTT-SE CS
                    Pterin_bind 195 alevpvllGvSrksflgrllelgkaeeRdagtaaflalaaaaGadi 240
                                    + + p++lGv ++  l++        + + ++a ++a++a+ Ga+i
  gi|116754029|ref|YP_843147.1| 297 HPDTPLFLGVGNVTELIDA-------DSQGVNAILAAIGAEVGASI 335
                                    4447888888888877763.......56667777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (482 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 3731.84
//
Query:       gi|116754030|ref|YP_843148.1|  [L=79]
Description: hypothetical protein Mthe_0718 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); 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: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 602.96
//
Query:       gi|116754031|ref|YP_843149.1|  [L=129]
Description: hypothetical protein Mthe_0719 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-43  147.6   0.1    1.4e-43  147.5   0.1    1.0  1  DUF473    Protein of unknown function (DUF473)
  ------ inclusion threshold ------
       0.12   12.9   0.0        1.1    9.7   0.0    2.3  3  HTH_26    Cro/C1-type HTH DNA-binding domain


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 !  147.5   0.1   1.6e-47   1.4e-43       1     117 [.       1     117 [.       1     118 [. 0.98

  Alignments for each domain:
  == domain 1  score: 147.5 bits;  conditional E-value: 1.6e-47
                         DUF473   1 MkvvaLtGiseevieeLkknklrtielrsahNvitllklevgdlvFlTsvsleDltkGteGiiaevlsveistkrvvess 80 
                                    M +vaLtGis++vi++L++n++rt+e+rs+ N+++l  +++gd +F+T++sl+D+++Gt G+ia+v +++i+t+r+++s+
  gi|116754031|ref|YP_843149.1|   1 MICVALTGISRNVIKDLVNNRVRTVEIRSPLNFFSLRGVNPGDRIFVTEASLKDIVNGTPGVIARVNEIQIMTHRMIQSN 80 
                                    99****************************************************************************** PP

                         DUF473  81 esfieErEttvarvqlkllglgrvrevkeeellkptk 117
                                    ++f+eE E+++ar+ql++lg+grvr++++ e ++p++
  gi|116754031|ref|YP_843149.1|  81 DFFYEEIESQAARAQLQFLGIGRVRRINTIEPYEPFV 117
                                    ****************************999998865 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 ?    9.7   0.0   0.00012       1.1      19      40 ..       6      27 ..       4      32 .. 0.89
   2 ?   -0.1   0.0      0.15   1.3e+03      22      35 ..      47      60 ..      36      66 .. 0.84
   3 ?   -1.9   0.0      0.54   4.8e+03       5      27 ..      71      96 ..      70     109 .. 0.49

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00012
                         HTH_26 19 gtgisaatlsrlvkgkpervsl 40
                                    tgis++ ++ lv++++++v +
  gi|116754031|ref|YP_843149.1|  6 LTGISRNVIKDLVNNRVRTVEI 27
                                   69**************999875 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.15
                         HTH_26 22 isaatlsrlvkgkp 35
                                   +++a+l+ +v+g+p
  gi|116754031|ref|YP_843149.1| 47 VTEASLKDIVNGTP 60
                                   57899999999998 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.54
                         HTH_26  5 lmadrgitkseL.argtg..isaatl 27
                                   +m +r i+++++  + ++    +a+l
  gi|116754031|ref|YP_843149.1| 71 IMTHRMIQSNDFfYEEIEsqAARAQL 96
                                   56667775544423333311444454 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.28s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 937.91
//
Query:       gi|116754032|ref|YP_843150.1|  [L=234]
Description: hypothetical protein Mthe_0720 [Methanosaeta thermophila PT]
Scores for complete 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-50  170.9   0.0    4.1e-50  170.8   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 !  170.8   0.0   2.3e-54   4.1e-50       1     213 []      12     215 ..      12     215 .. 0.94

  Alignments for each domain:
  == domain 1  score: 170.8 bits;  conditional E-value: 2.3e-54
                                    EEEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETTEEE-SEEEEEETTT.SEEEEEEE...E-H CS
                           PAC2   1 LilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveegrelepprlyakdsgsrdllvlqg...rep 77 
                                    L++GfpgiG+Vg +a ++Li++l++ ++g+  s+y +p     p +++ +g+  +p+r+y +d  + dl++l++   ++p
  gi|116754032|ref|YP_843150.1|  12 LVEGFPGIGLVGNIASQYLIHELKMNYLGAMTSRY-FP-----PLAVLLGGVVNMPVRIYERD--DLDLILLTSdipIHP 83 
                                    89*********************************.**.....*****************885..5********997777 PP

                                    SCHHHHHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHHH..CT..-CEEEEHHHHHHHHH CS
                           PAC2  78 ilqyeefakalldwaeelgvkevvvLggldageradvphtrpekvtgaatdeelleele..es..eyggivgitglLlsa 153
                                     + y+ +++++++wa +++ +e+v+L+g+  +       t++ +v+ga+++ elle+l   ++  e g+i+gi+g+++++
  gi|116754032|ref|YP_843150.1|  84 LASYD-MSREIVRWAASIKTREIVCLAGITLM-------TDQRRVFGAVSHAELLEKLRgvTEifELGTIAGISGSIMNE 155
                                    77777.***********************943.......56779**************6442268*************** PP

                                    HHHTT-EEEEEEEEEECCC--HHHHHHHHHHHHHHHT---HCHHHHHHHHHHHHHHHHHH CS
                           PAC2 154 akergipavgllaevphylpdPkaaaalleflskllglevdtedLeedaeeleeqleela 213
                                    ++ +gipav+ll+e+    pdP++aaa +++l++++gl+v+t +L e+a+e+e q+++la
  gi|116754032|ref|YP_843150.1| 156 CRLKGIPAVCLLGETMSDEPDPRSAAATIDALNRIYGLNVSTAKLLERAAEIEMQMQQLA 215
                                    *********************************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       679  (0.0378716); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); 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: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1753.72
//
Query:       gi|116754033|ref|YP_843151.1|  [L=756]
Description: AAA family ATPase, CDC48 subfamily protein [Methanosaeta thermophila PT]
Scores for complete 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-94  311.4   0.0    4.7e-47  159.7   0.0    2.3  2  AAA              ATPase family associated with various cellul
    1.2e-33  114.6   3.7    2.2e-16   59.4   0.7    3.0  2  AAA_lid_3        AAA+ lid domain
    7.1e-31  106.2   1.1      3e-30  104.2   0.6    2.3  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
    1.5e-16   59.9   0.0    4.5e-16   58.4   0.0    1.9  1  CDC48_2          Cell division protein 48 (CDC48), domain 2
    4.9e-16   59.6   0.0    8.6e-07   29.5   0.0    3.7  2  AAA_16           AAA ATPase domain
      4e-14   52.7   0.0    8.9e-06   25.5   0.0    2.6  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    8.3e-14   52.1   0.0    3.8e-07   30.4   0.0    2.3  2  AAA_2            AAA domain (Cdc48 subfamily)
    2.3e-12   47.3   0.1    0.00044   20.5   0.0    4.1  3  AAA_22           AAA domain
    6.5e-10   38.7   0.0     0.0012   18.2   0.0    2.5  2  TIP49            TIP49 P-loop domain
    7.7e-10   38.9   0.0    3.7e-05   23.8   0.0    2.3  2  AAA_14           AAA domain
    1.3e-09   38.2   1.0     0.0028   17.7   0.0    4.0  2  AAA_5            AAA domain (dynein-related subfamily)
    1.1e-08   35.3   0.0     0.0012   19.0   0.0    2.5  2  AAA_33           AAA domain
    1.1e-08   35.0   0.0     0.0065   16.2   0.0    2.6  2  AAA_24           AAA domain
    2.6e-08   33.5   1.0     0.0064   15.9   0.1    2.5  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    2.7e-08   34.4   0.0      0.012   16.1   0.0    2.6  2  AAA_18           AAA domain
    2.8e-08   33.7   0.0      0.012   15.3   0.0    3.0  2  IstB_IS21        IstB-like ATP binding protein
    2.7e-07   30.9   0.0      0.014   15.7   0.0    2.5  2  RNA_helicase     RNA helicase
    4.1e-07   30.4   0.0       0.01   16.1   0.0    2.5  2  AAA_28           AAA domain
    6.1e-07   29.3   0.0      0.031   14.0   0.0    2.9  2  Sigma54_activat  Sigma-54 interaction domain
    6.2e-07   29.5   0.2       0.23   11.3   0.0    4.0  3  NACHT            NACHT domain
      1e-06   28.4   0.0      0.025   14.1   0.0    2.5  2  AAA_7            P-loop containing dynein motor region
    1.3e-06   28.5   0.1       0.08   12.8   0.0    3.5  4  ATPase_2         ATPase domain predominantly from Archaea
    4.9e-06   25.8   0.0      0.057   12.5   0.0    2.2  2  Parvo_NS1        Parvovirus non-structural protein NS1
    7.5e-06   26.0   0.0        0.2   11.6   0.0    2.7  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    9.9e-06   26.1   0.0       0.13   12.8   0.0    2.4  2  ABC_tran         ABC transporter
    1.1e-05   24.8   0.0       0.11   11.6   0.0    2.4  2  DUF815           Protein of unknown function (DUF815)
    1.4e-05   24.8   6.4       0.34   10.5   0.7    4.1  3  AAA_25           AAA domain
    2.1e-05   23.9   0.1       0.16   11.2   0.0    2.5  2  Zeta_toxin       Zeta toxin
    7.6e-05   22.0   0.0       0.46    9.6   0.0    2.5  2  NB-ARC           NB-ARC domain
    8.8e-05   22.0   0.1       0.64    9.3   0.0    2.9  3  ATPase           KaiC
    0.00015   21.1   0.0       0.13   11.5   0.0    2.2  2  DUF2075          Uncharacterized conserved protein (DUF2075)
    0.00031   20.6   0.0       0.99    9.3   0.0    2.5  2  AAA_3            ATPase family associated with various cellul
    0.00046   19.7   0.1       0.98    8.8   0.0    2.4  2  PhoH             PhoH-like protein
    0.00073   19.3   0.3        1.6    8.4   0.1    2.5  2  AAA_30           AAA domain
     0.0008   18.9   0.0        2.1    7.7   0.0    3.2  2  TniB             Bacterial TniB protein
    0.00082   19.8   0.0        1.6    9.1   0.0    2.6  2  AAA_17           AAA domain
    0.00089   19.1   0.0        1.4    8.6   0.0    2.2  2  AAA_11           AAA domain
    0.00091   19.0   0.1         13    5.4   0.0    4.2  4  Guanylate_kin    Guanylate kinase
    0.00096   19.0   0.0        1.9    8.3   0.0    3.0  2  Bac_DnaA         Bacterial dnaA  protein
     0.0013   19.0   0.1        2.5    8.4   0.0    2.6  2  AAA_19           AAA domain
     0.0032   16.4   0.0        2.5    6.9   0.0    2.5  2  AFG1_ATPase      AFG1-like ATPase
     0.0035   17.4   0.0       0.87    9.6   0.0    2.3  2  ResIII           Type III restriction enzyme, res subunit
     0.0043   17.0   0.0        7.2    6.5   0.0    3.3  3  NTPase_1         NTPase
  ------ inclusion threshold ------
      0.011   15.9   0.0        7.1    6.8   0.0    2.5  2  Sigma54_activ_2  Sigma-54 interaction domain
      0.011   15.5   0.2        5.1    6.8   0.1    2.7  2  Cytidylate_kin   Cytidylate kinase
      0.014   14.5   0.0        3.1    6.8   0.0    2.7  2  T2SSE            Type II/IV secretion system protein
      0.016   14.5   0.3        4.5    6.4   0.0    3.3  4  KAP_NTPase       KAP family P-loop domain
      0.017   14.9   0.0        5.9    6.6   0.0    2.4  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
      0.018   15.2   0.0         11    6.1   0.0    3.2  3  SKI              Shikimate kinase
      0.021   13.9   0.0        1.3    8.0   0.0    2.3  2  MCM              MCM P-loop domain
      0.026   14.2   0.0        8.7    5.9   0.0    2.3  2  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
      0.041   13.3   0.2         12    5.2   0.0    2.6  2  IPT              Isopentenyl transferase
      0.045   13.5   0.0         15    5.4   0.0    2.5  2  AAA_29           P-loop containing region of AAA domain
      0.062   13.1   0.0         17    5.2   0.0    2.7  2  CPT              Chloramphenicol phosphotransferase-like prot
       0.09   12.4   0.0         14    5.2   0.0    2.4  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
       0.16   11.7   0.0         11    5.6   0.0    2.3  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.7   0.0   1.5e-49   4.7e-47       1     131 [.     244     373 ..     244     374 .. 0.97
   2 !  149.6   0.0     2e-46   6.4e-44       1     131 [.     517     648 ..     517     649 .. 0.96

  Alignments for each domain:
  == domain 1  score: 159.7 bits;  conditional E-value: 1.5e-49
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCH CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgsese 80 
                                    +llyGppGtGKT+lakava+e++++f++++g+e++sky gesek +r++f+ea+++a p i+f+DE+d++a++r + + e
  gi|116754033|ref|YP_843151.1| 244 ILLYGPPGTGKTMLAKAVANESDAYFISVNGPEIMSKYYGESEKALRDIFEEAEKNA-PAIIFLDELDSIAPKRGEVTGE 322
                                    69******************************************************9.****************999*** PP

                                    HHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                            AAA  81 eeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                    +e+rvv+qLl+ +dg+k++++ v+vig tnrp+ ld al+r gRfdr+ie++
  gi|116754033|ref|YP_843151.1| 323 VERRVVAQLLSLMDGLKERKN-VLVIGSTNRPEALDIALRRpGRFDREIELG 373
                                    ******************855.**************************9975 PP

  == domain 2  score: 149.6 bits;  conditional E-value: 2e-46
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH..TTCC CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr..sgse 78 
                                    +llyGppGtGKT+lakava+e++++f++ +gs llsk+ gesek+++e+f++a++ a p ++f+DE+dal++ r    +e
  gi|116754033|ref|YP_843151.1| 517 ILLYGPPGTGKTMLAKAVANESDANFITAKGSALLSKWYGESEKRVAEIFRKARQVA-PAVIFLDELDALVPVRggAVGE 595
                                    69******************************************************9.****************876679 PP

                                    CHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                            AAA  79 seeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                      ++er+vnqLl+eldg+++ ++ v+vigatnrpd +dpallr gRfd+ i ++
  gi|116754033|ref|YP_843151.1| 596 PHVTERIVNQLLSELDGLEELHG-VVVIGATNRPDIVDPALLRpGRFDELILVP 648
                                    9*******************755.*************************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 !   55.0   0.1   1.6e-17   5.2e-15       1      40 [.     396     435 ..     396     438 .. 0.95
   2 !   59.4   0.7   6.9e-19   2.2e-16       1      44 [.     671     716 ..     671     722 .. 0.94

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 1.6e-17
                      AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitm 40 
                                    dv+++e Ae+T G++GAD+aa+creAa++Alrr ++ei+ 
  gi|116754033|ref|YP_843151.1| 396 DVNIEEFAELTYGFVGADIAAVCREAAMNALRRILPEIDL 435
                                    9********************************9999875 PP

  == domain 2  score: 59.4 bits;  conditional E-value: 6.9e-19
                      AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgik.e.itmedfe 44 
                                    dvd+++L+e+Te+y+GAD+aa+cr+A++lAlr+++  e + +++f 
  gi|116754033|ref|YP_843151.1| 671 DVDIDALVELTEHYTGADIAAICRKAGRLALRESMSsEhVRERHFL 716
                                    9*********************************99637*****95 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 !  104.2   0.6   9.4e-33     3e-30       1      84 [.       6      89 ..       6      90 .. 0.99

  Alignments for each domain:
  == domain 1  score: 104.2 bits;  conditional E-value: 9.4e-33
                                   CEEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEEEEE CS
                        CDC48_N  1 rLrVaeapqedvgrgivridpedmeelglepgdvveiegkrkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVtVrk 82
                                   rL+Vaea q+dvg+gi+r++ + m+++g++p dv+ei+g+r+T+a+v++a+  d+g +iIrmdg++R+nag siG+ V+Vrk
  gi|116754033|ref|YP_843151.1|  6 RLKVAEADQRDVGKGIARVSDDFMKRMGVRPLDVIEITGDRRTAALVVSAYSADQGLDIIRMDGLIRSNAGSSIGQYVEVRK 87
                                   79******************************************************************************** PP

                                   E- CS
                        CDC48_N 83 ae 84
                                   ae
  gi|116754033|ref|YP_843151.1| 88 AE 89
                                   97 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 !   58.4   0.0   1.4e-18   4.5e-16       7      64 .]     111     196 ..     106     196 .. 0.85

  Alignments for each domain:
  == domain 1  score: 58.4 bits;  conditional E-value: 1.4e-18
                                    CHHHHCCCTTEEE-TTEEE.....................EECCT..........CCCEEEEEEEECCCCSCEEECTSCC CS
                        CDC48_2   7 maylkrqFlgrpvtkGdlv.....................vfefk..........gqeiklvVvstePkgpvgitetTei 55 
                                     + l+++F+grpv+kGd++                         +          ++eikl+V st P+g+v+it++Tei
  gi|116754033|ref|YP_843151.1| 111 SEVLTKVFQGRPVCKGDIIsttsvrrppsdtfgretmfeeI---FrgflgaqafgLGEIKLRVISTNPSGIVKITDATEI 187
                                    5689***************9999999988888777644443...15558889999************************* PP

                                    EEESTTCCE CS
                        CDC48_2  56 elgtkpvev 64 
                                    el +++vev
  gi|116754033|ref|YP_843151.1| 188 ELLPQAVEV 196
                                    ****99986 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0   2.7e-09   8.6e-07      16     140 ..     233     346 ..     230     348 .. 0.72
   2 !   24.5   0.1   9.3e-08     3e-05      14      91 ..     504     571 ..     501     622 .. 0.58

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 2.7e-09
                         AAA_16  16 lervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaes.ael 94 
                                    ++r+  + p  +ll+G++G+GK+ l++++++   +++++f++ +  +  ++  y          + lr++ +eae+ a +
  gi|116754033|ref|YP_843151.1| 233 FDRLGIDPPKGILLYGPPGTGKTMLAKAVAN---ESDAYFISVNGPEI-MSKYYGESE------KALRDIFEEAEKnAPA 302
                                    66666666799*******************6...6669**********.332332233......4445555553330455 PP

                         AAA_16  95 eawrekleealaavpelagaeasrllellkrllallsrderplvlv 140
                                      + ++l++ +   +e++g+ ++r+ ++l +l++ l++++   vlv
  gi|116754033|ref|YP_843151.1| 303 IIFLDELDSIAPKRGEVTGEVERRVVAQLLSLMDGLKERKN--VLV 346
                                    5566666666669999999999***********99999555..333 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 9.3e-08
                         AAA_16  14 salervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaes 91 
                                    s ++r+  + p  +ll+G++G+GK+ l+++++++  ++   f+++k   l     +s +      e+ ++++ ++a++
  gi|116754033|ref|YP_843151.1| 504 SNFKRLGINAPKGILLYGPPGTGKTMLAKAVANESDAN---FITAKGSAL-----LSKWYGES--EKRVAEIFRKARQ 571
                                    6788999999**********************977777...777666666.....22233333..2444444444333 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 !   25.5   0.0   2.8e-08   8.9e-06      35     102 ..     243     318 ..     232     327 .. 0.79
   2 !   24.1   0.0   7.4e-08   2.4e-05      34      96 ..     515     585 ..     500     593 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 2.8e-08
                         RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsravee 102
                                     +llyGpPG Gkt lak +a+e ++ + +  gP +      e ++ l  ++ + e++   ++f+de+  ++++  e
  gi|116754033|ref|YP_843151.1| 243 GILLYGPPGTGKTMLAKAVANESDAYFISVNGPEImskyygESEKALRDIFEEAEKNapAIIFLDELDSIAPKRGE 318
                                    59*******************************9843333334566777877776653369999999888776655 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 7.4e-08
                         RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrl 96 
                                      +llyGpPG Gkt lak +a+e ++++ ++ g +l      e ++ +a ++ + ++    v+f+de+  l
  gi|116754033|ref|YP_843151.1| 515 KGILLYGPPGTGKTMLAKAVANESDANFITAKGSALlskwygESEKRVAEIFRKARQVapAVIFLDELDAL 585
                                    569*************************9999988744333344566777777665532257888887655 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.0   1.2e-09   3.8e-07       6     105 ..     244     337 ..     239     346 .. 0.90
   2 !   19.2   0.0   3.1e-06     0.001       6     101 ..     517     608 ..     514     614 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 1.2e-09
                                    EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG---- CS
                          AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpk 83 
                                    ill gp g+Gkt+laka+a+  ++     +i ++  e++     + + ++++  ++   +ae++   i++lDE+d i+pk
  gi|116754033|ref|YP_843151.1| 244 ILLYGPPGTGKTMLAKAVANESDA----YFISVNGPEIMS----KYYGESEKALRDIFEEAEKNApaIIFLDELDSIAPK 315
                                    8999******************96....************....99999999999999999999999************9 PP

                                    .---------HHHHHHHHHHHH- CS
                          AAA_2  84 .essgadvSregVqrdLLqileg 105
                                     ++ + +v r  V+  LL +++g
  gi|116754033|ref|YP_843151.1| 316 rGEVTGEVERR-VVAQLLSLMDG 337
                                    88888888886.66778899987 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 3.1e-06
                                    EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG---- CS
                          AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpk 83 
                                    ill gp g+Gkt+laka+a+  ++    ++i+a  s+ll     + + ++++  ++   +a +    +++lDE+d   p 
  gi|116754033|ref|YP_843151.1| 517 ILLYGPPGTGKTMLAKAVANESDA----NFITAKGSALLS----KWYGESEKRVAEIFRKARQVApaVIFLDELDALVPV 588
                                    7999******************96....************....99999999999999999998888********99996 PP

                                    ..---------HHHHHHHHH CS
                          AAA_2  84 ..essgadvSregVqrdLLq 101
                                      +  g+    e +++ LL 
  gi|116754033|ref|YP_843151.1| 589 rgGAVGEPHVTERIVNQLLS 608
                                    66445555555666666665 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   1.4e-06   0.00044       8      59 ..     244     295 ..     239     301 .. 0.76
   2 ?    2.4   0.0      0.55   1.8e+02      73     118 ..     284     337 ..     275     354 .. 0.69
   3 !   19.2   0.0   3.6e-06    0.0012       8      38 ..     517     558 ..     512     623 .. 0.65

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.4e-06
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlpsstsskdllre 59 
                                    ++++G++GtGKT+l++ ++++ d++ ++  ++pe++ +++  s++ ++d+++e
  gi|116754033|ref|YP_843151.1| 244 ILLYGPPGTGKTMLAKAVANESDAY-FISVNGPEIMsKYYGESEKALRDIFEE 295
                                    89*******************8644.333367777767777777777777766 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.55
                         AAA_22  73 lsseellealeqalraravielliiDEaqhlr..s........eealeeLrsllnl 118
                                     s+++l++ +e+a +++ +  ++ +DE + +   +         +++ +L sl++ 
  gi|116754033|ref|YP_843151.1| 284 ESEKALRDIFEEAEKNAPA--IIFLDELDSIApkRgevtgeveRRVVAQLLSLMDG 337
                                    5666777777777777766..*********98762445566667777777777775 PP

  == domain 3  score: 19.2 bits;  conditional E-value: 3.6e-06
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee...........e 38 
                                    ++++G++GtGKT+l++ ++++ d+    ++            
  gi|116754033|ref|YP_843151.1| 517 ILLYGPPGTGKTMLAKAVANESDANFITAKgsallskwygeS 558
                                    89******************9976555544555555555543 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   4.9e-06    0.0016      51      97 ..     242     286 ..     239     297 .. 0.86
   2 !   18.2   0.0   3.7e-06    0.0012      50     107 ..     514     570 ..     507     574 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.9e-06
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte 97 
                                    +++Ll Gp+gtGkt la a+++e  +d  f++++g e+ s     +e
  gi|116754033|ref|YP_843151.1| 242 KGILLYGPPGTGKTMLAKAVANE--SDAYFISVNGPEIMSKYYGESE 286
                                    89*******************99..5799*********998766665 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 3.7e-06
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXX CS
                          TIP49  50 GravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkktev.ltqalrksi 107
                                     +++Ll Gp+gtGkt la a+++e  +d  f++ +gs + s     +e  + + +rk+ 
  gi|116754033|ref|YP_843151.1| 514 PKGILLYGPPGTGKTMLAKAVANE--SDANFITAKGSALLSKWYGESEKrVAEIFRKAR 570
                                    699*******************99..5799**********9988888753778889885 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   1.1e-07   3.7e-05       5     118 ..     244     367 ..     241     379 .. 0.83
   2 !   12.7   0.0    0.0003     0.097       5      75 ..     517     584 ..     513     622 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.1e-07
                         AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev........ 76 
                                    +++ G+  +GKT+l+k +++e+      ++ +n  +   k + ++ek l+ i+e+++++   ++flDE   +        
  gi|116754033|ref|YP_843151.1| 244 ILLYGPPGTGKTMLAKAVANESD---AYFISVNGPEIMSKYYGESEKALRDIFEEAEKNAPAIIFLDELDSIapkrgevt 320
                                    7899***************9888...889999998888888888888888888876666999****************** PP

                         AAA_14  77 ....pewekalkslvd..egknldvivtGSnskllskeiatslagrva 118
                                        +++   l sl+d  + ++ +v+v GS +     +ia +  gr +
  gi|116754033|ref|YP_843151.1| 321 geveRRVVAQLLSLMDglK-ERKNVLVIGSTNRPEALDIALRRPGRFD 367
                                    **99999999999999643.5669******998888788777777765 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.0003
                         AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe.kllelileklkeekktylflDEiqe 75 
                                    +++ G+  +GKT+l+k +++e+     +++  +      k + ++e ++ e++++  ++    ++flDE   
  gi|116754033|ref|YP_843151.1| 517 ILLYGPPGTGKTMLAKAVANESD---ANFITAKGSALLSKWYGESEkRVAEIFRKA-RQVAPAVIFLDELDA 584
                                    7899***************9988...899998888877777766553666777776.3447899*****865 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.2   4.8e-05     0.015       2      23 ..     244     265 ..     243     362 .. 0.76
   2 !   17.7   0.0   8.7e-06    0.0028       2      76 ..     517     584 ..     516     638 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.8e-05
                                    EEEE--SSSSHHHHHHHGGGGB CS
                          AAA_5   2 vlLvGppGtgKselaerlaaal 23 
                                    +lL GppGtgK++la+ +a   
  gi|116754033|ref|YP_843151.1| 244 ILLYGPPGTGKTMLAKAVANES 265
                                    89**************998755 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 8.7e-06
                                    EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG CS
                          AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEver 76 
                                    +lL GppGtgK++la+ +a    +++ +  +++      l+ ++    g+ + +  ++ r+ar   +++++lDE++ 
  gi|116754033|ref|YP_843151.1| 517 ILLYGPPGTGKTMLAKAVANESDANFITAKGSA------LLSKWY---GESEKRVAEIFRKARqvAPAVIFLDELDA 584
                                    89*****************99999998888877......666676...33344444444455557788888888775 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   3.7e-06    0.0012       2      49 ..     244     293 ..     244     352 .. 0.84
   2 !   13.8   0.0   0.00015     0.049       2      29 ..     517     544 ..     517     610 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 3.7e-06
                         AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqsktdyt 49 
                                    +ll G+pG+GK+ la+ ++++ +  ++ ++ ++++++++g+ ++ ++d  
  gi|116754033|ref|YP_843151.1| 244 ILLYGPPGTGKTMLAKAVANESDayFISVNGPEIMSKYYGESEKALRDIF 293
                                    6789***************9999877779999999999998777666443 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 0.00015
                         AAA_33   2 vllvGlpGsGKstlaerllkklgavlls 29 
                                    +ll G+pG+GK+ la+ ++++ +a +++
  gi|116754033|ref|YP_843151.1| 517 ILLYGPPGTGKTMLAKAVANESDANFIT 544
                                    6789***************999966665 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0     2e-05    0.0065       5      33 ..     244     274 ..     241     319 .. 0.66
   2 !   16.0   0.0   2.4e-05    0.0077       4      44 ..     516     557 ..     513     595 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2e-05
                         AAA_24   5 iliyGpsgiGKTtlakel..gpkplfidtek 33 
                                    il+yGp+g+GKT+lak    + ++ fi +++
  gi|116754033|ref|YP_843151.1| 244 ILLYGPPGTGKTMLAKAVanESDAYFISVNG 274
                                    89**************998888888887776 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 2.4e-05
                         AAA_24   4 kiliyGpsgiGKTtlakel.gpkplfidtekGlksldadkfp 44 
                                     il+yGp+g+GKT+lak    ++ + + t kG++ l  + ++
  gi|116754033|ref|YP_843151.1| 516 GILLYGPPGTGKTMLAKAVaNESDANFITAKGSALLSKWYGE 557
                                    699**************9984444444455666666666665 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   2.6e-05    0.0083      25      42 ..     244     261 ..     241     264 .. 0.90
   2 !   15.9   0.1     2e-05    0.0064      25      42 ..     517     534 ..     507     538 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.6e-05
                   Mg_chelatase  25 lllvGppGsGKtmlakrl 42 
                                    +ll+GppG+GKtmlak++
  gi|116754033|ref|YP_843151.1| 244 ILLYGPPGTGKTMLAKAV 261
                                    89*************987 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 2e-05
                   Mg_chelatase  25 lllvGppGsGKtmlakrl 42 
                                    +ll+GppG+GKtmlak++
  gi|116754033|ref|YP_843151.1| 517 ILLYGPPGTGKTMLAKAV 534
                                    89*************987 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   3.9e-05     0.012       1      25 [.     244     286 ..     244     354 .. 0.67
   2 !   15.7   0.0   5.1e-05     0.016       1      33 [.     517     546 ..     517     611 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.9e-05
                         AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.................g 25 
                                    Ill G+pG+GKt lak+++++  ++                  
  gi|116754033|ref|YP_843151.1| 244 ILLYGPPGTGKTMLAKAVANESdAYfisvngpeimskyygesE 286
                                    99****************9986555665554433333333332 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 5.1e-05
                         AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdvak 33 
                                    Ill G+pG+GKt lak+++++    +    +ak
  gi|116754033|ref|YP_843151.1| 517 ILLYGPPGTGKTMLAKAVANES---DANFITAK 546
                                    99****************9884...33333333 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0     6e-05     0.019      47      70 ..     241     264 ..     230     273 .. 0.86
   2 !   15.3   0.0   3.8e-05     0.012      45      70 ..     512     537 ..     508     585 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6e-05
                      IstB_IS21  47 kenivllGpsGvGKshlaialgve 70 
                                     ++i+l Gp+G+GK+ la a++ e
  gi|116754033|ref|YP_843151.1| 241 PKGILLYGPPGTGKTMLAKAVANE 264
                                    5789****************9976 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 3.8e-05
                      IstB_IS21  45 ekkenivllGpsGvGKshlaialgve 70 
                                    ++ ++i+l Gp+G+GK+ la a++ e
  gi|116754033|ref|YP_843151.1| 512 NAPKGILLYGPPGTGKTMLAKAVANE 537
                                    566789***************99876 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   4.5e-05     0.014       1      65 [.     244     299 ..     244     315 .. 0.76
   2 !   12.6   0.0   0.00042      0.13       1      23 [.     517     539 ..     517     563 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.5e-05
                   RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvvidDfgqvkdee 65 
                                    i+lyGp+g+GK++lak     +      +++d +++  +  +++++Y g+      D+ +  +++
  gi|116754033|ref|YP_843151.1| 244 ILLYGPPGTGKTMLAKA----V-----ANESDAYFISVNGPEIMSKYYGESEKALRDIFEEAEKN 299
                                    789**************....2.....34444555588899999999999888888888877664 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00042
                   RNA_helicase   1 iwlyGpsgeGKStlakeLakall 23 
                                    i+lyGp+g+GK++lak +a++  
  gi|116754033|ref|YP_843151.1| 517 ILLYGPPGTGKTMLAKAVANESD 539
                                    789**************887755 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   3.2e-05      0.01       2      51 ..     244     297 ..     243     316 .. 0.77
   2 !   11.8   0.0   0.00064      0.21       2      25 ..     517     541 ..     516     577 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.2e-05
                         AAA_28   2 ivitGgestGKTtlleaLaar....gypvv.pEaareileeklakgedalpwved 51 
                                    i + G+++tGKT l++a a++     ++v  pE++ +++ e  +  +d+ +++ +
  gi|116754033|ref|YP_843151.1| 244 ILLYGPPGTGKTMLAKAVANEsdayFISVNgPEIMSKYYGESEKALRDIFEEA-E 297
                                    7899***************7666545666699999999988877777776664.3 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00064
                         AAA_28   2 ivitGgestGKTtlleaLaar.gyp 25 
                                    i + G+++tGKT l++a a++ + +
  gi|116754033|ref|YP_843151.1| 517 ILLYGPPGTGKTMLAKAVANEsDAN 541
                                    7899**************9764444 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   9.8e-05     0.031      24      75 ..     243     286 ..     234     353 .. 0.76
   2 !   11.9   0.0   0.00044      0.14      21      52 ..     513     541 ..     501     559 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 9.8e-05
                                    -EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSS CS
                Sigma54_activat  24 svlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhek 75 
                                     +l+ G  GtGK++la+a+ ++s+   + f++vn  +i     +s+ +G ++
  gi|116754033|ref|YP_843151.1| 243 GILLYGPPGTGKTMLAKAVANESD---AYFISVNGPEI-----MSKYYGESE 286
                                    69****************998776...88999997765.....345555555 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00044
                                    SSS-EEEECSTTSSHHHHHHHHHHHSTTTTS- CS
                Sigma54_activat  21 tdlsvlitGesGtGKellaraiheaskrkekp 52 
                                     +  +l+ G  GtGK++la+a+ ++s+   ++
  gi|116754033|ref|YP_843151.1| 513 APKGILLYGPPGTGKTMLAKAVANESD---AN 541
                                    56779****************998876...44 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0     0.001      0.32       3      22 ..     244     263 ..     242     267 .. 0.89
   2 ?    2.1   0.0      0.49   1.6e+02      65     147 ..     285     374 ..     276     387 .. 0.63
   3 !   11.3   0.0   0.00073      0.23       3      23 ..     517     537 ..     515     617 .. 0.96

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.001
                                    EEEEC-TTTCHHHHHHHHHH CS
                          NACHT   3 vilqGeaGsGKTtLlqklal 22 
                                    ++l G++G GKT+L++ +a 
  gi|116754033|ref|YP_843151.1| 244 ILLYGPPGTGKTMLAKAVAN 263
                                    7899************9986 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.49
                                    --SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH............HHHHHCTTTTT--EEEEEEECCCHHHHCTTSSC CS
                          NACHT  65 paapvsevwavllelperlLlilDglDelvtdlgq...kekqpvrtlLselirkkllpeasllltvrpralrdleeqlee 141
                                    ++++ + ++++  +    + + lD lD ++ + g+   + +++v   L +l+ + l  +  +l++ ++++ + l   l++
  gi|116754033|ref|YP_843151.1| 285 SEKALRDIFEEAEK-NAPAIIFLDELDSIAPKRGEvtgEVERRVVAQLLSLMDG-LKERKNVLVIGSTNRPEALDIALRR 362
                                    55555554444433.44455668******9999999995555555555599999.6666667777777666666666666 PP

                                    E........EEE CS
                          NACHT 142 a......ivlev 147
                                    +      i l v
  gi|116754033|ref|YP_843151.1| 363 PgrfdreIELGV 374
                                    655554444545 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00073
                                    EEEEC-TTTCHHHHHHHHHHH CS
                          NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                    ++l G++G GKT+L++ +a +
  gi|116754033|ref|YP_843151.1| 517 ILLYGPPGTGKTMLAKAVANE 537
                                    7899************99876 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 !   11.7   0.0   0.00044      0.14      34      58 ..     242     266 ..     232     300 .. 0.85
   2 !   14.1   0.0   7.8e-05     0.025      28      62 ..     509     542 ..     486     550 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00044
                          AAA_7  34 kpvllvGptGtGKtviikdllkkld 58 
                                    k +ll+Gp GtGKt+++k + ++ d
  gi|116754033|ref|YP_843151.1| 242 KGILLYGPPGTGKTMLAKAVANESD 266
                                    679****************999887 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 7.8e-05
                          AAA_7  28 lllknkkpvllvGptGtGKtviikdllkkldkeky 62 
                                    l +++ k +ll+Gp GtGKt+++k + ++ d  ++
  gi|116754033|ref|YP_843151.1| 509 LGINAPKGILLYGPPGTGKTMLAKAVANESD-ANF 542
                                    44788899*****************999988.544 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   0.0   0.00025      0.08      20     116 ..     241     341 ..     231     347 .. 0.53
   2 ?    4.2   0.0      0.11        34     103     162 ..     286     347 ..     270     411 .. 0.75
   3 !    9.0   0.0    0.0038       1.2      23      45 ..     517     539 ..     509     546 .. 0.86
   4 ?   -1.8   0.0       7.6   2.4e+03     111     131 ..     563     586 ..     543     625 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00025
                       ATPase_2  20 neiyfiYGpegsGKtaLlkeiienledkdkyviyyialr..eesiskldefie......eeeekkklekal......... 82 
                                     + +++YGp g GKt L k ++++++       y+i+++  e+ ++++ e+ +      ee                   
  gi|116754033|ref|YP_843151.1| 241 PKGILLYGPPGTGKTMLAKAVANESDA------YFISVNgpEIMSKYYGESEKalrdifEEA--------Eknapaiifl 306
                                    556899****************99944......33333300444444444411333332222........2333333445 PP

                       ATPase_2  83 ..giavpkaeleeilkeksklvfkaielllekikkk 116
                                      ++ +  +++ e+  e  + v +++ +l++ +k++
  gi|116754033|ref|YP_843151.1| 307 deLDSIAPKRG-EVTGEVERRVVAQLLSLMDGLKER 341
                                    54333333333.444455555666666666666665 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.11
                       ATPase_2 103 fkaielllekikkkgkk...iiiiiDelqkli....dlglngaellvkeLlnliesltkekhlcvvi 162
                                    +ka+ +++e+ +    k    ii++Del  +     +++ + ++ +v++Ll+l++ l ++k++ +vi
  gi|116754033|ref|YP_843151.1| 286 EKALRDIFEEAE----KnapAIIFLDELDSIApkrgEVTGEVERRVVAQLLSLMDGLKERKNV-LVI 347
                                    445555555554....445478889***988622225555588999*******9996555554.454 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0038
                       ATPase_2  23 yfiYGpegsGKtaLlkeiienle 45 
                                    +++YGp g GKt L k ++++++
  gi|116754033|ref|YP_843151.1| 517 ILLYGPPGTGKTMLAKAVANESD 539
                                    689**************999874 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 7.6
                       ATPase_2 111 ekikkkgkk...iiiiiDelqkli 131
                                    ++i +k+++    +i++Del  l+
  gi|116754033|ref|YP_843151.1| 563 AEIFRKARQvapAVIFLDELDALV 586
                                    566677777775678889999887 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 !   12.5   0.0   0.00018     0.057     117     141 ..     244     268 ..     239     273 .. 0.91
   2 !   11.0   0.0   0.00053      0.17     117     138 ..     517     538 ..     514     541 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00018
                      Parvo_NS1 117 vwfyGpantGktnlaeaIakavply 141
                                    +++yGp+ tGkt+la+a a+ ++ y
  gi|116754033|ref|YP_843151.1| 244 ILLYGPPGTGKTMLAKAVANESDAY 268
                                    89*****************998876 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00053
                      Parvo_NS1 117 vwfyGpantGktnlaeaIakav 138
                                    +++yGp+ tGkt+la+a a+ +
  gi|116754033|ref|YP_843151.1| 517 ILLYGPPGTGKTMLAKAVANES 538
                                    899**************99865 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   0.00063       0.2      20      59 ..     242     281 ..     215     293 .. 0.76
   2 !   11.1   0.0   0.00096      0.31      19      45 ..     514     540 ..     500     560 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00063
                                    EEEEEEESTTSSHHHHHHHHHHHTT--..----TTTTSEEEE CS
                           TsaE  20 dvilLeGdLGaGKTtlvrglakalgve..evkSPTFtlveeY 59 
                                    + ilL+G+ G+GKT+l++++a++ +    +v+ P   ++++Y
  gi|116754033|ref|YP_843151.1| 242 KGILLYGPPGTGKTMLAKAVANESDAYfiSVNGP--EIMSKY 281
                                    459******************9987765667666..455555 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00096
                                    TEEEEEEESTTSSHHHHHHHHHHHTT- CS
                           TsaE  19 gdvilLeGdLGaGKTtlvrglakalgv 45 
                                     + ilL+G+ G+GKT+l++++a++ + 
  gi|116754033|ref|YP_843151.1| 514 PKGILLYGPPGTGKTMLAKAVANESDA 540
                                    4569*****************998765 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0    0.0017      0.54       8      67 ..     238     295 ..     235     348 .. 0.75
   2 !   12.8   0.0   0.00039      0.13       7      72 ..     510     574 ..     507     620 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0017
                                    EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe 67 
                                    + + + + + G+ G+GK+ L+k++a++++     i ++g ++ ++   +++k ++ +++e
  gi|116754033|ref|YP_843151.1| 238 IDPPKGILLYGPPGTGKTMLAKAVANESDA--YFISVNGPEIMSKYYGESEKALRDIFEE 295
                                    556667889*****************9975..4455577777776666777776666666 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00039
                                    EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-T CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                       ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfp 72 
                                     +++ + + + G+ G+GK+ L+k++a++++  +  i+ +g  l ++   +++k+++ ++ +  q+ p
  gi|116754033|ref|YP_843151.1| 510 GINAPKGILLYGPPGTGKTMLAKAVANESD--ANFITAKGSALLSKWYGESEKRVAEIFRKaRQVAP 574
                                    6777778899******************97..57777788888887777777777777776455555 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00068      0.22      54     116 ..     242     309 ..     236     357 .. 0.64
   2 !   11.6   0.0   0.00035      0.11      21      80 ..     473     541 ..     456     582 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00068
                         DUF815  54 nnvLLwGarGtGKSslvkallneyaeegLrl..ievekedlkelpklvellr...erperfilfvDDL 116
                                    + +LL+G  GtGK  l ka+ ne  +  + +   e+  +   e +k ++ +    e++   i+f+D L
  gi|116754033|ref|YP_843151.1| 242 KGILLYGPPGTGKTMLAKAVANESDAYFISVngPEIMSKYYGESEKALRDIFeeaEKNAPAIIFLDEL 309
                                    679*******************9988875542246666555554444444431113445578888877 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00035
                         DUF815  21 evdevklddLvgidkqkealvente...qfle.....glpa.nnvLLwGarGtGKSslvkallneyaee 80 
                                    ev +v++dd+ g+++ k+ l+e +e   ++++     g +a + +LL+G  GtGK  l ka+ ne  ++
  gi|116754033|ref|YP_843151.1| 473 EVPKVTWDDIGGLEDVKQLLIEAVEwplRYASnfkrlGINApKGILLYGPPGTGKTMLAKAVANESDAN 541
                                    566788888888888888888776533333331111233332679******************997665 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.1    0.0015      0.48      36      52 ..     244     260 ..     238     265 .. 0.87
   2 ?    3.2   0.1      0.17        56     128     176 ..     287     335 ..     259     348 .. 0.75
   3 !   10.5   0.7    0.0011      0.34      36      54 ..     517     535 ..     510     621 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0015
                         AAA_25  36 allaGapgtGKttlald 52 
                                    +ll+G+pgtGKt+la  
  gi|116754033|ref|YP_843151.1| 244 ILLYGPPGTGKTMLAKA 260
                                    69************965 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.17
                         AAA_25 128 advdaleaaieevegvrlvviDplsralggdensnsdv.galvealeria 176
                                     +++++ +++e+ + ++ + +D l+++ +   +   +v +++v++l ++ 
  gi|116754033|ref|YP_843151.1| 287 KALRDIFEEAEK-NAPAIIFLDELDSIAPKRGEVTGEVeRRVVAQLLSLM 335
                                    567889999999.77*************9966667776688887776654 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.0011
                         AAA_25  36 allaGapgtGKttlaldla 54 
                                    +ll+G+pgtGKt+la  +a
  gi|116754033|ref|YP_843151.1| 517 ILLYGPPGTGKTMLAKAVA 535
                                    79***********996554 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0    0.0013      0.41      15      44 ..     240     267 ..     232     281 .. 0.86
   2 !   11.2   0.0   0.00051      0.16      14      47 ..     512     543 ..     502     550 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0013
                     Zeta_toxin  15 rPklillgGqpGAGKselaellkdelerqg 44 
                                     Pk ill G pG GK+ la+++++e +   
  gi|116754033|ref|YP_843151.1| 240 PPKGILLYGPPGTGKTMLAKAVANESD--A 267
                                    5999*******************9984..4 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00051
                     Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvv 47 
                                    + Pk ill G pG GK+ la+++++e   + n++
  gi|116754033|ref|YP_843151.1| 512 NAPKGILLYGPPGTGKTMLAKAVANES--DANFI 543
                                    579**********************98..55555 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0    0.0014      0.46      23      45 ..     244     266 ..     231     270 .. 0.87
   2 !    9.5   0.0    0.0016      0.52      23      45 ..     517     539 ..     507     544 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0014
                                    EEEEESTTSSHHHHHHHHCCSHC CS
                         NB-ARC  23 valvGmgGvGKttlakqilnksd 45 
                                    + l+G +G GKt lak + n+sd
  gi|116754033|ref|YP_843151.1| 244 ILLYGPPGTGKTMLAKAVANESD 266
                                    779****************9976 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0016
                                    EEEEESTTSSHHHHHHHHCCSHC CS
                         NB-ARC  23 valvGmgGvGKttlakqilnksd 45 
                                    + l+G +G GKt lak + n+sd
  gi|116754033|ref|YP_843151.1| 517 ILLYGPPGTGKTMLAKAVANESD 539
                                    679****************9965 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0031      0.99      15      37 ..     237     259 ..     230     272 .. 0.83
   2 ?   -1.0   0.0       2.9   9.4e+02     125     154 ..     309     338 ..     261     351 .. 0.73
   3 !    9.3   0.0     0.002      0.64      15      38 ..     510     533 ..     484     542 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0031
                         ATPase  15 GipegrvvlitGepGtGKtifal 37 
                                    Gi   + +l++G pGtGKt++a+
  gi|116754033|ref|YP_843151.1| 237 GIDPPKGILLYGPPGTGKTMLAK 259
                                    67777889*************97 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.9
                         ATPase 125 iDsitglayeekeavaReilrqlvrvlkkl 154
                                    +Dsi++   e + +v R+ + ql++ + +l
  gi|116754033|ref|YP_843151.1| 309 LDSIAPKRGEVTGEVERRVVAQLLSLMDGL 338
                                    467777677777777888888888877554 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.002
                         ATPase  15 GipegrvvlitGepGtGKtifalq 38 
                                    Gi   + +l++G pGtGKt++a+ 
  gi|116754033|ref|YP_843151.1| 510 GINAPKGILLYGPPGTGKTMLAKA 533
                                    7888889**************975 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00039      0.13       4      54 ..     244     287 ..     241     317 .. 0.75
   2 !    7.5   0.0    0.0065       2.1       4      25 ..     517     538 ..     514     568 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00039
                        DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakk 54 
                                    +l  G +GtGKt+++ ++++e         a ++svN+p+++  +   ++k
  gi|116754033|ref|YP_843151.1| 244 ILLYGPPGTGKTMLAKAVANES-------DAYFISVNGPEIMSKYYGESEK 287
                                    6789************999998.......8899999*99987544433333 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0065
                        DUF2075   4 vlVtGvaGtGKtvvllnllael 25 
                                    +l  G +GtGKt+++ ++++e 
  gi|116754033|ref|YP_843151.1| 517 ILLYGPPGTGKTMLAKAVANES 538
                                    6789*************99998 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0    0.0045       1.4       2      28 ..     244     270 ..     243     279 .. 0.87
   2 !    9.3   0.0    0.0031      0.99       2      27 ..     517     542 ..     516     551 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0045
                          AAA_3   2 vllegvPGlaktllvkalakaldlefk 28 
                                    +ll g PG++kt+l+ka+a+  d+ f 
  gi|116754033|ref|YP_843151.1| 244 ILLYGPPGTGKTMLAKAVANESDAYFI 270
                                    7999***************99888775 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0031
                          AAA_3   2 vllegvPGlaktllvkalakaldlef 27 
                                    +ll g PG++kt+l+ka+a+  d++f
  gi|116754033|ref|YP_843151.1| 517 ILLYGPPGTGKTMLAKAVANESDANF 542
                                    7999****************999887 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0045       1.4      23      40 ..     245     262 ..     238     267 .. 0.87
   2 !    8.8   0.0    0.0031      0.98      22      41 ..     517     536 ..     507     543 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0045
                                    EEE--TTSSTTHHHHHHH CS
                           PhoH  23 faiGpaGtGKtylavala 40 
                                       Gp GtGKt+la a+a
  gi|116754033|ref|YP_843151.1| 245 LLYGPPGTGKTMLAKAVA 262
                                    578***********9998 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0031
                                    EEEE--TTSSTTHHHHHHHH CS
                           PhoH  22 vfaiGpaGtGKtylavalav 41 
                                    +   Gp GtGKt+la a+a 
  gi|116754033|ref|YP_843151.1| 517 ILLYGPPGTGKTMLAKAVAN 536
                                    5678***********99985 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0058       1.9      22      40 ..     245     263 ..     236     274 .. 0.86
   2 !    8.4   0.1     0.005       1.6      22      40 ..     518     536 ..     511     553 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0058
                         AAA_30  22 vltGpAGtGKttalkalre 40 
                                    +l Gp+GtGKt++ ka+++
  gi|116754033|ref|YP_843151.1| 245 LLYGPPGTGKTMLAKAVAN 263
                                    678***********99976 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.005
                         AAA_30  22 vltGpAGtGKttalkalre 40 
                                    +l Gp+GtGKt++ ka+++
  gi|116754033|ref|YP_843151.1| 518 LLYGPPGTGKTMLAKAVAN 536
                                    688***********99976 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0065       2.1      26      59 ..     232     265 ..     219     276 .. 0.83
   2 ?    7.0   0.0     0.011       3.4      35      60 ..     514     539 ..     504     550 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0065
                           TniB  26 LleypkrkrmpnlllvGdsnnGKtmivekFarlh 59 
                                    L+++   + ++ +ll+G++ +GKtm+++  a++ 
  gi|116754033|ref|YP_843151.1| 232 LFDRLGIDPPKGILLYGPPGTGKTMLAKAVANES 265
                                    566666667789**************99877665 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.011
                           TniB  35 mpnlllvGdsnnGKtmivekFarlhp 60 
                                    ++ +ll+G++ +GKtm+++  a++  
  gi|116754033|ref|YP_843151.1| 514 PKGILLYGPPGTGKTMLAKAVANESD 539
                                    5789**************98887665 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0     0.011       3.6       1      25 [.     247     271 ..     247     315 .. 0.79
   2 !    9.1   0.0    0.0051       1.6       1      32 [.     520     552 ..     520     577 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.011
                                    EE-TTSSHHHHHHHHHHHHTEEEEE CS
                         AAA_17   1 lGgPGsGKgtqceklvekygfthls 25 
                                    +G+PG GK+ +++ ++ + +  ++s
  gi|116754033|ref|YP_843151.1| 247 YGPPGTGKTMLAKAVANESDAYFIS 271
                                    7***********9999987666555 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0051
                                    EE-TTSSHHHHHHHHHHHHTEEEEEH.HHHHHH CS
                         AAA_17   1 lGgPGsGKgtqceklvekygfthlsa.Gdllre 32 
                                    +G+PG GK+ +++ ++ + +  +++a G+ l +
  gi|116754033|ref|YP_843151.1| 520 YGPPGTGKTMLAKAVANESDANFITAkGSALLS 552
                                    7***************99998888776666654 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0062         2      20      41 ..     244     265 ..     221     305 .. 0.81
   2 !    8.6   0.0    0.0045       1.4      18      41 ..     515     538 ..     504     570 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0062
                         AAA_11  20 tliqGPPGtgKTktivellsql 41 
                                     l+ GPPGtgKT    ++ ++ 
  gi|116754033|ref|YP_843151.1| 244 ILLYGPPGTGKTMLAKAVANES 265
                                    5899********8776666655 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0045
                         AAA_11  18 eitliqGPPGtgKTktivellsql 41 
                                    +  l+ GPPGtgKT    ++ ++ 
  gi|116754033|ref|YP_843151.1| 515 KGILLYGPPGTGKTMLAKAVANES 538
                                    45699*********8776666655 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.041        13       4      30 ..     243     269 ..     241     275 .. 0.85
   2 ?    1.3   0.0      0.76   2.4e+02      75      95 ..     278     298 ..     272     312 .. 0.79
   3 ?    5.2   0.0     0.046        15       3      30 ..     515     542 ..     513     549 .. 0.87
   4 ?    1.0   0.0      0.92     3e+02      75      96 ..     551     572 ..     538     581 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.041
                                    EEEEESTTTSSHHHHHHHHHHHSTTTE CS
                  Guanylate_kin   4 pvvlvgpsgaGksslkkaLlselpekf 30 
                                     + l gp g+Gk +l ka+ +e   +f
  gi|116754033|ref|YP_843151.1| 243 GILLYGPPGTGKTMLAKAVANESDAYF 269
                                    6899**************999988777 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.76
                                    TTEEEEEEHHHHHHHHHTTSE CS
                  Guanylate_kin  75 sgnlygtsveaieevlekgki 95 
                                     +++yg+s +a + ++e++ +
  gi|116754033|ref|YP_843151.1| 278 MSKYYGESEKALRDIFEEAEK 298
                                    679*************99876 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.046
                                    SEEEEESTTTSSHHHHHHHHHHHSTTTE CS
                  Guanylate_kin   3 rpvvlvgpsgaGksslkkaLlselpekf 30 
                                    + + l gp g+Gk +l ka+ +e   +f
  gi|116754033|ref|YP_843151.1| 515 KGILLYGPPGTGKTMLAKAVANESDANF 542
                                    66899**************999988777 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.92
                                    TTEEEEEEHHHHHHHHHTTSEE CS
                  Guanylate_kin  75 sgnlygtsveaieevlekgkiv 96 
                                     ++ yg+s + + e++ k+++v
  gi|116754033|ref|YP_843151.1| 551 LSKWYGESEKRVAEIFRKARQV 572
                                    5789***************995 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0     0.012       3.7      37      60 ..     244     267 ..     240     430 .. 0.72
   2 !    8.3   0.0     0.006       1.9      37      66 ..     517     546 ..     507     570 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.012
                                    EEEE-SSSSSHHHHHHHHHHHHHH CS
                       Bac_DnaA  37 lfiygevGlGktHLlkaignevle 60 
                                    +++yg+ G Gkt L ka++ne  +
  gi|116754033|ref|YP_843151.1| 244 ILLYGPPGTGKTMLAKAVANESDA 267
                                    799***************998654 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.006
                                    EEEE-SSSSSHHHHHHHHHHHHHHHSSSS- CS
                       Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelr 66 
                                    +++yg+ G Gkt L ka++ne  +n+  ++
  gi|116754033|ref|YP_843151.1| 517 ILLYGPPGTGKTMLAKAVANESDANFITAK 546
                                    79******************9988876665 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0     0.013       4.1      12      31 ..     243     262 ..     239     274 .. 0.83
   2 !    8.4   0.0    0.0079       2.5      12      32 ..     516     536 ..     511     576 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.013
                         AAA_19  12 vllvtaGpGtGKTrvlkhiv 31 
                                     +l+ ++pGtGKT + k++ 
  gi|116754033|ref|YP_843151.1| 243 GILLYGPPGTGKTMLAKAVA 262
                                    5899*********9877665 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0079
                         AAA_19  12 vllvtaGpGtGKTrvlkhiva 32 
                                     +l+ ++pGtGKT + k++ +
  gi|116754033|ref|YP_843151.1| 516 GILLYGPPGTGKTMLAKAVAN 536
                                    5899*********98877665 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.0    0.0091       2.9      59      79 ..     238     258 ..     223     268 .. 0.87
   2 !    6.9   0.0    0.0079       2.5      56      79 ..     508     531 ..     486     541 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0091
                    AFG1_ATPase  59 vepvrglYlwGgvGrGKtylm 79 
                                      p++g+ l+G+ G GKt+l 
  gi|116754033|ref|YP_843151.1| 238 IDPPKGILLYGPPGTGKTMLA 258
                                    579****************96 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0079
                    AFG1_ATPase  56 rksvepvrglYlwGgvGrGKtylm 79 
                                    r   ++++g+ l+G+ G GKt+l 
  gi|116754033|ref|YP_843151.1| 508 RLGINAPKGILLYGPPGTGKTMLA 531
                                    456789****************96 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 ?    5.5   0.0     0.049        16      11      46 ..     215     263 ..     212     310 .. 0.77
   2 !    9.6   0.0    0.0027      0.87       3      50 ..     458     540 ..     456     573 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.049
                                    HHHHHT...................TTSEEEEEESTTSTHHHHHHHHHH CS
                         ResIII  11 aienlleklks.............krdkrglikmaTGtGKTlvaaklie 46 
                                    ai++++e ++              +  k +l+  + GtGKT++a +++ 
  gi|116754033|ref|YP_843151.1| 215 AITKVREMIELplkhpelfdrlgiDPPKGILLYGPPGTGKTMLAKAVAN 263
                                    55555555544555566666666677889999**********9966655 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0027
                                    EE-HHHHHHHHHHT.........................................TTSEEEEEESTTSTHHHHHHHHHHH CS
                         ResIII   3 elreyQeeaienlleklks...................................krdkrglikmaTGtGKTlvaaklier 47 
                                     lre Q +a+++++ ++ +                                   +  k +l+  + GtGKT++a +++ +
  gi|116754033|ref|YP_843151.1| 458 ALREIQPSALREIMVEVPKvtwddiggledvkqllieavewplryasnfkrlgiNAPKGILLYGPPGTGKTMLAKAVANE 537
                                    578888888888886666677777777888888888889999999999999999999***************99777766 PP

                                    H-S CS
                         ResIII  48 llk 50 
                                       
  gi|116754033|ref|YP_843151.1| 538 SDA 540
                                    554 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.025       7.9       2      32 ..     244     274 ..     243     300 .. 0.86
   2 ?   -0.9   0.0       4.2   1.4e+03      83     119 ..     461     497 ..     445     505 .. 0.73
   3 ?    6.5   0.0     0.022       7.2       2      28 ..     517     543 ..     516     581 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.025
                                    EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                    +++ GppG+GKt l k v+++ +   ++v+G
  gi|116754033|ref|YP_843151.1| 244 ILLYGPPGTGKTMLAKAVANESDAYFISVNG 274
                                    6788**************9987665555555 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 4.2
                                    HHHHHHHHHHHHHH-EEEE---STTGGG-HHHHHHHH CS
                       NTPase_1  83 elalealrkalseadviviDEiGkmElkskkfkeave 119
                                    e+  +alr+ + e   +  D iG +E   + ++eave
  gi|116754033|ref|YP_843151.1| 461 EIQPSALREIMVEVPKVTWDDIGGLEDVKQLLIEAVE 497
                                    44555566666555566779************99998 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.022
                                    EEEE--TTSSHHHHHHHHHHHH...GG CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgv 28 
                                    +++ GppG+GKt l k v+++ + + +
  gi|116754033|ref|YP_843151.1| 517 ILLYGPPGTGKTMLAKAVANESDANFI 543
                                    6788*************9998765555 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 ?    6.4   0.0     0.028       8.8      24      47 ..     244     267 ..     240     317 .. 0.60
   2 ?    6.8   0.0     0.022       7.1      24      48 ..     517     541 ..     509     587 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.028
                                    EEEEEETT--HHHHHHCC--TTS- CS
                Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgp 47 
                                    ++l G++G+gk++ A++ +++s  
  gi|116754033|ref|YP_843151.1| 244 ILLYGPPGTGKTMLAKAVANESDA 267
                                    799*************99998754 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.022
                                    EEEEEETT--HHHHHHCC--TTS-E CS
                Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpw 48 
                                    ++l G++G+gk++ A++ +++s  +
  gi|116754033|ref|YP_843151.1| 517 ILLYGPPGTGKTMLAKAVANESDAN 541
                                    89****************9988663 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.029       9.2       3      28 ..     246     271 ..     244     274 .. 0.87
   2 ?    6.8   0.1     0.016       5.1       3      28 ..     519     544 ..     517     549 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.029
                                    EE-STTSSHHHHHHHHHHHHT-EEEE CS
                 Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyld 28 
                                    + GP g+GK  +a+a+a++ ++ +++
  gi|116754033|ref|YP_843151.1| 246 LYGPPGTGKTMLAKAVANESDAYFIS 271
                                    67****************99988775 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.016
                                    EE-STTSSHHHHHHHHHHHHT-EEEE CS
                 Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyld 28 
                                    + GP g+GK  +a+a+a++ +++++ 
  gi|116754033|ref|YP_843151.1| 519 LYGPPGTGKTMLAKAVANESDANFIT 544
                                    67*****************9999885 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.043        14     131     153 ..     243     265 ..     232     275 .. 0.85
   2 ?    6.8   0.0    0.0097       3.1     125     154 ..     510     539 ..     451     548 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.043
                          T2SSE 131 lilvsGgTgsGKttllyallkei 153
                                     il+ G+ g+GKt l+ a+ +e 
  gi|116754033|ref|YP_843151.1| 243 GILLYGPPGTGKTMLAKAVANES 265
                                    699*************9998775 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0097
                          T2SSE 125 avrerglilvsGgTgsGKttllyallkein 154
                                     +++ + il+ G+ g+GKt l+ a+ +e +
  gi|116754033|ref|YP_843151.1| 510 GINAPKGILLYGPPGTGKTMLAKAVANESD 539
                                    45567889*************999877644 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.69   2.2e+02      19      43 ..     240     264 ..     226     267 .. 0.80
   2 ?    6.4   0.0     0.014       4.5     156     196 ..     284     323 ..     272     330 .. 0.79
   3 ?    2.3   0.0      0.25        80      23      64 ..     517     553 ..     510     573 .. 0.78
   4 ?   -1.8   0.1       4.4   1.4e+03     171     185 ..     571     585 ..     545     590 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.69
                     KAP_NTPase  19 tpivvgLygkWGsGKssllnklede 43 
                                    +p  + Lyg+ G+GK+ l + + +e
  gi|116754033|ref|YP_843151.1| 240 PPKGILLYGPPGTGKTMLAKAVANE 264
                                    566699**********999887665 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.014
                     KAP_NTPase 156 eveelladmektLdalqkrlVvviDdLDrceteevlqllea 196
                                    e e+ l d++++ ++ + + ++++D+LD++ +++   + e+
  gi|116754033|ref|YP_843151.1| 284 ESEKALRDIFEEAEK-NAPAIIFLDELDSIAPKRGEVTGEV 323
                                    566678888888888.9*************99987777666 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.25
                     KAP_NTPase  23 vgLygkWGsGKssllnkledelkefakpvrflfaefnawsfk 64 
                                    + Lyg+ G+GK+ l + + +e + +     f+ a+ +a+++k
  gi|116754033|ref|YP_843151.1| 517 ILLYGPPGTGKTMLAKAVANESDAN-----FITAKGSALLSK 553
                                    88************99999988877.....666666666554 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 4.4
                     KAP_NTPase 171 lqkrlVvviDdLDrc 185
                                    +  + V+++D+LD +
  gi|116754033|ref|YP_843151.1| 571 QVAPAVIFLDELDAL 585
                                    46789********75 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.018       5.9       2      28 ..     242     268 ..     241     271 .. 0.88
   2 ?    5.7   0.0     0.036        11       2      24 ..     515     537 ..     514     543 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.018
                      PduV-EutP   2 kkilliGkvgsGKttLtqalkgeelkY 28 
                                    k ill G+ g+GKt L++a+ +e+  Y
  gi|116754033|ref|YP_843151.1| 242 KGILLYGPPGTGKTMLAKAVANESDAY 268
                                    6699****************9987555 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.036
                      PduV-EutP   2 kkilliGkvgsGKttLtqalkge 24 
                                    k ill G+ g+GKt L++a+ +e
  gi|116754033|ref|YP_843151.1| 515 KGILLYGPPGTGKTMLAKAVANE 537
                                    6699***************9987 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       6.5   2.1e+03      15      42 ..      59      86 ..      53     103 .. 0.82
   2 ?    5.1   0.0     0.073        23       1      24 [.     250     273 ..     250     300 .. 0.73
   3 ?    6.1   0.0     0.036        11       1      23 [.     523     545 ..     523     572 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 6.5
                                   HHTSEEEEHHHHHHHHHTS-HHHHHHHH CS
                            SKI 15 klglefiDlDeliekrtgksiaeifeee 42
                                     gl+ i +D li  ++g si +++e +
  gi|116754033|ref|YP_843151.1| 59 DQGLDIIRMDGLIRSNAGSSIGQYVEVR 86
                                   56889999**************999854 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.073
                                    TTSSHHHHHHHHHHHHTSEEEEHH CS
                            SKI   1 mGaGKstvGkllAkklglefiDlD 24 
                                    +G+GK+ ++k++A++ +  fi + 
  gi|116754033|ref|YP_843151.1| 250 PGTGKTMLAKAVANESDAYFISVN 273
                                    69***************9999764 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.036
                                    TTSSHHHHHHHHHHHHTSEEEEH CS
                            SKI   1 mGaGKstvGkllAkklglefiDl 23 
                                    +G+GK+ ++k++A++ + +fi +
  gi|116754033|ref|YP_843151.1| 523 PGTGKTMLAKAVANESDANFITA 545
                                    69******************987 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.12        38      60      88 ..     244     271 ..     238     277 .. 0.81
   2 ?    8.0   0.0    0.0041       1.3      23      92 ..     479     548 ..     458     552 .. 0.64

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.12
                                    EEEEESSTSTHHHHHHHHHHHSSSEEEEE CS
                            MCM  60 vllvgdpgtaKsqlLkyveklapravyts 88 
                                    +ll g pgt+K+ l k+v++  + a ++s
  gi|116754033|ref|YP_843151.1| 244 ILLYGPPGTGKTMLAKAVAN-ESDAYFIS 271
                                    89************999995.44555555 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0041
                                    STTSSS-HHHHHHHHHHHH---EBBBSSSSB..BCSS-EEEEEESSTSTHHHHHHHHHHHSSSEEEEESSSS CS
                            MCM  23 apsiyghedvkkaillqlfggvkkkledktk..lrgdinvllvgdpgtaKsqlLkyveklapravytsgkgs 92 
                                       i g edvk+  l+  +    + +++ ++  + +   +ll g pgt+K+ l k+v++  + a+++++kgs
  gi|116754033|ref|YP_843151.1| 479 WDDIGGLEDVKQL-LIEAVEWPLRYASNFKRlgINAPKGILLYGPPGTGKTMLAKAVAN-ESDANFITAKGS 548
                                    5566666666653.33333333333333222225566679*************999995.566777777776 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 ?    5.9   0.0     0.027       8.7      18      56 ..     245     327 ..     242     364 .. 0.60
   2 ?    5.7   0.0     0.032        10      17      64 ..     517     570 ..     512     591 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.027
                                    EEEESTTSSHHHHHHHHHHHSSTSSEEEEEE..............................................ESE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..............................................xxx RF
                    ATP-synt_ab  18 lipgafgvGktvisqslskqsnsddaiiyvg..............................................iGe 51 
                                    l+ g  g+Gkt+++++++++s  d + i v                                                Ge
  gi|116754033|ref|YP_843151.1| 245 LLYGPPGTGKTMLAKAVANES--DAYFISVNgpeimskyygesekalrdifeeaeknapaiifldeldsiapkrgevTGE 322
                                    678999**************7..435666666777777755555555555555555555555555555555554444444 PP

                                    EHHHH CS
                                    xxxxx RF
                    ATP-synt_ab  52 rgnev 56 
                                     ++ v
  gi|116754033|ref|YP_843151.1| 323 VERRV 327
                                    44444 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.032
                                    EEEEESTTSSHHHHHHHHHHHSSTS......SEEEEEEESEEHHHHHHHHHHCH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab  17 tlipgafgvGktvisqslskqsnsd......daiiyvgiGergnevaevleefp 64 
                                    +l+ g  g+Gkt+++++++++s+++      +a      Ge ++ vae++++ +
  gi|116754033|ref|YP_843151.1| 517 ILLYGPPGTGKTMLAKAVANESDANfitakgSALLSKWYGESEKRVAEIFRKAR 570
                                    5688999**************977766665336666668888888888877765 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.039        13       5      31 ..     245     271 ..     242     275 .. 0.88
   2 ?    5.2   0.0     0.038        12       5      30 ..     518     543 ..     515     546 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.039
                            IPT   5 lifGatttGKtaeaiklaketgapviv 31 
                                    l++G+ +tGKt  a ++a+e  a  i+
  gi|116754033|ref|YP_843151.1| 245 LLYGPPGTGKTMLAKAVANESDAYFIS 271
                                    89****************998877666 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.038
                            IPT   5 lifGatttGKtaeaiklaketgapvi 30 
                                    l++G+ +tGKt  a ++a+e  a  i
  gi|116754033|ref|YP_843151.1| 518 LLYGPPGTGKTMLAKAVANESDANFI 543
                                    89****************99887766 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.046        15      21      41 ..     241     260 ..     231     263 .. 0.75
   2 ?    5.4   0.0     0.048        15      21      41 ..     514     533 ..     494     536 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.046
                         AAA_29  21 lkgatlltGpsGsGKSTllDA 41 
                                    +kg +ll Gp G+GK+ l  A
  gi|116754033|ref|YP_843151.1| 241 PKG-ILLYGPPGTGKTMLAKA 260
                                    356.9**********988655 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.048
                         AAA_29  21 lkgatlltGpsGsGKSTllDA 41 
                                    +kg +ll Gp G+GK+ l  A
  gi|116754033|ref|YP_843151.1| 514 PKG-ILLYGPPGTGKTMLAKA 533
                                    456.9**********988655 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.054        17       4      33 ..     244     273 ..     242     303 .. 0.86
   2 ?    4.9   0.0     0.067        21       4      32 ..     517     545 ..     515     573 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.054
                                    EEEEE-TTSSHHHHHHHHHHHSSS-EEEEE CS
                            CPT   4 ilLnGgsssGKsslaralqevldepwlhlg 33 
                                    ilL G + +GK+ la+a+ + +d+ ++ ++
  gi|116754033|ref|YP_843151.1| 244 ILLYGPPGTGKTMLAKAVANESDAYFISVN 273
                                    89*******************999998876 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.067
                                    EEEEE-TTSSHHHHHHHHHHHSSS-EEEE CS
                            CPT   4 ilLnGgsssGKsslaralqevldepwlhl 32 
                                    ilL G + +GK+ la+a+ + +d+ ++  
  gi|116754033|ref|YP_843151.1| 517 ILLYGPPGTGKTMLAKAVANESDANFITA 545
                                    89******************999999865 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 ?    5.2   0.0     0.044        14       4      28 ..     245     269 ..     243     279 .. 0.82
   2 ?    4.5   0.0     0.075        24       4      24 ..     518     538 ..     516     545 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.044
                                    EEEESTTCCHHHHHHHHHCT--SS- CS
                           cobW   4 vltGflGsGKTtLlnhllenraglk 28 
                                    +l G++G+GKT+L +++ ++++ + 
  gi|116754033|ref|YP_843151.1| 245 LLYGPPGTGKTMLAKAVANESDAYF 269
                                    689**********999988777665 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.075
                                    EEEESTTCCHHHHHHHHHCT- CS
                           cobW   4 vltGflGsGKTtLlnhllenr 24 
                                    +l G++G+GKT+L +++ +++
  gi|116754033|ref|YP_843151.1| 518 LLYGPPGTGKTMLAKAVANES 538
                                    689*********998887554 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 ?    3.6   0.0      0.14        46       4      70 ..     247     308 ..     244     312 .. 0.64
   2 ?    5.6   0.0     0.035        11       4      70 ..     520     581 ..     517     587 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.14
                Viral_helicase1   4 hGvpGcGKStlirkllrts..liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDE 70 
                                     G pG GK+ l + ++++s  + ++vn p  e+ ++   ++++     ++++++++       i++lDE
  gi|116754033|ref|YP_843151.1| 247 YGPPGTGKTMLAKAVANESdaYFISVNGP--EIMSKYYGESEKALRDIFEEAEKNAP-----AIIFLDE 308
                                    588***************98655555555..55555554444444455555555543.....3566665 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.035
                Viral_helicase1   4 hGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDE 70 
                                     G pG GK+ l + ++++s  ++ + +   +ll+++  +++++  + ++++ + +       +++lDE
  gi|116754033|ref|YP_843151.1| 520 YGPPGTGKTMLAKAVANESdANFITAKG-SALLSKWYGESEKRVAEIFRKARQVAP-----AVIFLDE 581
                                    588***************9977766666.788999987777777777776555332.....4777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (756 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        56  (0.00312343); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              56  [number of targets reported over threshold]
# CPU time: 0.78u 0.30s 00:00:01.08 Elapsed: 00:00:00.44
# Mc/sec: 5166.45
//
Query:       gi|116754034|ref|YP_843152.1|  [L=438]
Description: DNA primase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-13   49.9   0.4    1.1e-12   48.3   0.2    2.0  2  Toprim_4  Toprim domain
    5.9e-06   26.6   0.0    1.6e-05   25.3   0.0    1.7  1  Toprim_2  Toprim-like
    0.00018   21.7   1.2     0.0033   17.6   0.2    3.1  2  Toprim    Toprim domain
  ------ inclusion threshold ------
        0.7   10.5   3.9        1.2    9.7   3.1    1.8  1  T5orf172  T5orf172 domain


Domain annotation for each model (and alignments):
>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       2.4   1.1e+04      25      44 ..      83     102 ..      75     118 .. 0.73
   2 !   48.3   0.2   2.3e-16   1.1e-12       2      77 ..     172     259 ..     171     276 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.4
                       Toprim_4  25 avlggalspldgirpeklkt 44 
                                    a+l  al++ d ++p   ++
  gi|116754034|ref|YP_843152.1|  83 AILAAALETIDRVGPCMARI 102
                                    67778888888888777666 PP

  == domain 2  score: 48.3 bits;  conditional E-value: 2.3e-16
                       Toprim_4   2 eiiiVEgyaDvlalekagiknvvavlggalspldgirpeklkt.enlve....aekkvkevilaldgDa.....eGeata 71 
                                    +i +VEg+aDvl+l k+gikn+vav g+++ p+   ++ ++k+ +++++    +e +vke++++ d D+     eG+ + 
  gi|116754034|ref|YP_843152.1| 172 AILVVEGRADVLNLLKYGIKNAVAVGGTNI-PPTITELCSKKIaTAFTDgdrgGELIVKELLQVADIDYvarapEGKCVE 250
                                    799***************************.999999999999889999********************77777777666 PP

                       Toprim_4  72 erlae...l 77 
                                    e   +   +
  gi|116754034|ref|YP_843152.1| 251 ELTQKeiiR 259
                                    655554443 PP

>> Toprim_2  Toprim-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   3.5e-09   1.6e-05       2      69 ..     175     236 ..     174     253 .. 0.79

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 3.5e-09
                       Toprim_2   2 vfEgaiDalSlaqlgikektnvvalgGtalteaalkllerypekkvvla.lDnDkaGrkaakrlaellr 69 
                                    v+Eg  D+l l+++gik   n+va+gGt+++++ ++l +++    +  a +D D+ G+  +k+l +++ 
  gi|116754034|ref|YP_843152.1| 175 VVEGRADVLNLLKYGIK---NAVAVGGTNIPPTITELCSKK----IATAfTDGDRGGELIVKELLQVAD 236
                                    9***************9...********8888777777666....55444************9998884 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.24   1.1e+03      20      60 ..      55     134 ..      20     144 .. 0.45
   2 !   17.6   0.2   7.4e-07    0.0033       2      91 ..     173     240 ..     172     250 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.24
                                    STEEEEEEESSSSEEEHS.......................................TTEEEEEECTTTHHHHHHHHHHH CS
                         Toprim  20 sgfqavtaslGhildlet.......................................efkpvyeeiedkkkvlkalkela 60 
                                    + ++++ +s G+ +   +                                         k++y++ + k+  +++++e++
  gi|116754034|ref|YP_843152.1|  55 RIDVQISSSGGKSMGTISipssfdkvetailaaaletidrvgpcmarihvtkiedvrAAKRKYIIDRAKRILVEMFDENL 134
                                    55555566666555555534333333333333333333333333333333333324444444445555555555555555 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 7.4e-07
                                    EEEESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHSTTEEEEEECTTTHHHHHHHHHHHHHHSEEEEE.CSSSHHHHHHH CS
                         Toprim   2 lvivEgpsdaktiakalgsgfqavtaslGhildletefkpvyeeiedkkkvlkalkelakradeiila.tDpDreGeaia 80 
                                    + +vEg +d+ ++ k+   g ++++a+ G+ +  +                     el    ++i  a tD+Dr Ge i 
  gi|116754034|ref|YP_843152.1| 173 ILVVEGRADVLNLLKY---GIKNAVAVGGTNIPPTI-------------------TELC--SKKIATAfTDGDRGGELIV 228
                                    78**************...9*********9997665...................4444..55666666*********** PP

                                    HHHHHHHT.HHH CS
                         Toprim  81 wellevlk.ell 91 
                                    +ell+v++ +++
  gi|116754034|ref|YP_843152.1| 229 KELLQVADiDYV 240
                                    ****99985444 PP

>> T5orf172  T5orf172 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   3.1   0.00026       1.2      44      97 ..     305     358 ..     280     362 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00026
                       T5orf172  44 levvaekevrkvpnahrvErlihkeLadrryrvkcdcgkehrEwFevsleevde 97 
                                     +vv   +++++   h++   +h++  + +y+ +  +g+e +EwF+ ++ee+d 
  gi|116754034|ref|YP_843152.1| 305 AQVVPIAHHAEIAPPHEIQTRVHQKEVHEHYEEPEIEGQEPEEWFKHHVEELDG 358
                                    344445778889999999999999999999999999999***********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.23s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3177.05
//
Query:       gi|116754035|ref|YP_843153.1|  [L=351]
Description: hypothetical protein Mthe_0723 [Methanosaeta thermophila PT]
Scores for complete 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-54  184.0   0.0    4.1e-54  183.6   0.0    1.1  1  NMD3            NMD3 family
  ------ inclusion threshold ------
       0.24   11.7   2.3        9.9    6.5   0.1    2.7  2  Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
        1.2    9.0   4.6         16    5.3   0.2    2.2  2  CxC4            CxC4 like cysteine cluster associated with KD
        3.8    7.7   8.2        5.4    7.2   0.6    3.1  3  Zn-ribbon_8     Zinc ribbon domain
          4    7.5   6.7        2.5    8.2   0.3    2.9  2  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
        7.2    6.6   8.1    1.6e+02    2.3   8.1    2.5  1  Prok-RING_1     Prokaryotic RING finger family 1


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 !  183.6   0.0   1.4e-57   4.1e-54       1     243 []      12     242 ..      12     242 .. 0.96

  Alignments for each domain:
  == domain 1  score: 183.6 bits;  conditional E-value: 1.4e-57
                           NMD3   1 CcrCGkeieelinglCedCllkevditegiekievevCkeCgrylpkgkWvkaeleseellaeclkklvekgLkvseeve 80 
                                    C+rCG +++   +glC +C+l++++++ ++++ie+ +C+ Cg++l +g+W     +s ++l+e++++++ k+++v++e+e
  gi|116754035|ref|YP_843153.1|  12 CPRCGGASD---DGLCLSCILETTEFMICPDQIEIVICPVCGSILDRGRW----RQSDSDLDELIRNALFKEISVHRELE 84 
                                    *******96...89************************************....7999*******************999 PP

                           NMD3  81 evkvelvdaefiwtephskrikvkvtvqgevrgenetilqqevevevkvkrqqCprCsriaggyyeaivQvRqk.relte 159
                                    +v++e++  +     ++ +r  + ++++g +rg   ti++ +++v+v+v+r++C+rCsriag+y+e+ivQvR + r ++e
  gi|116754035|ref|YP_843153.1|  85 DVELEILLHQ-----RGATRFVADIRLSGMFRG---TIVHADCQVRVRVSRRTCDRCSRIAGRYFEGIVQVRRRdRPPDE 156
                                    9999955554.....55899999*******977...8999**************************************** PP

                           NMD3 160 eehkrtfelleqli....lkhdahafiskikevkeGlDfyfgsksaArklveflksevggkvkeseklvsedkksgkevy 235
                                    ++  ++ e++++l     +k+d+ afi++ik+v+ G+D+ +gs++ +r++++ + +++gg+++es klv+  ++ gk+v+
  gi|116754035|ref|YP_843153.1| 157 SDLSEAREIAQSLAaagyKKGDRLAFIQDIKDVRGGIDIIVGSTQLGRHIAKTIAQRFGGRIQESVKLVGC-RD-GKDVF 234
                                    ***********************************************************************.88.***** PP

                           NMD3 236 rltysvrl 243
                                    r+t++vrl
  gi|116754035|ref|YP_843153.1| 235 RTTMLVRL 242
                                    ******97 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 ?    4.1   0.3     0.019        57       6      11 ..      12      17 ..       7      23 .. 0.63
   2 ?    6.5   0.1    0.0033       9.9       6      18 ..      46      59 ..      44      64 .. 0.66

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.019
                                   -TTTT- CS
                 Prim_Zn_Ribbon  6 CPvCGG 11
                                   CP CGG
  gi|116754035|ref|YP_843153.1| 12 CPRCGG 17
                                   666666 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0033
                                   -TTTT-.TTTEEET CS
                 Prim_Zn_Ribbon  6 CPvCGG.rDrFrfd 18
                                   CPvCG+  Dr r++
  gi|116754035|ref|YP_843153.1| 46 CPVCGSiLDRGRWR 59
                                   *****953555554 PP

>> CxC4  CxC4 like cysteine cluster associated with KDZ transposases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.8    0.0069        21      16      56 ..      11      53 ..       3      68 .. 0.66
   2 ?    5.3   0.2    0.0055        16      34      63 ..     112     138 ..     101     146 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0069
                           CxC4 16 rC.rCgtsldpsrptlekectvytl.tgalevrielqrCpaC...a 56
                                    C rCg+     ++ l  +c++ t+   +++ +ie++ Cp C    
  gi|116754035|ref|YP_843153.1| 11 ICpRCGGAS---DDGLCLSCILETTeFMICPDQIEIVICPVCgsiL 53
                                   577887655...55555689996663667899**********5441 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0055
                           CxC4  34 ctvytltgalevrielqrCpaCahtrrfiG 63 
                                     t+++  + ++vr+  ++C +C+   r +G
  gi|116754035|ref|YP_843153.1| 112 GTIVHADCQVRVRVSRRTCDRCS---RIAG 138
                                    588999999*************4...4444 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.2     0.019        56      28      34 ..      11      17 ..       3      20 .. 0.77
   2 ?    7.2   0.6    0.0018       5.4       8      34 ..      24      51 ..      23      55 .. 0.74
   3 ?   -1.3   0.1      0.85   2.5e+03      28      33 ..     129     134 ..     118     153 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.019
                    Zn-ribbon_8 28 aCPeCgs 34
                                    CP+Cg+
  gi|116754035|ref|YP_843153.1| 11 ICPRCGG 17
                                   4*****8 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0018
                    Zn-ribbon_8  8 CeeCghefevlqsisdaplta.CPeCgs 34
                                   C +C  e ++++   d  +++ CP Cgs
  gi|116754035|ref|YP_843153.1| 24 CLSCILETTEFMICPDQIEIViCPVCGS 51
                                   7777777777774447778999*****9 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.85
                    Zn-ribbon_8  28 aCPeCg 33 
                                    +C +C 
  gi|116754035|ref|YP_843153.1| 129 TCDRCS 134
                                    466664 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 ?    0.6   1.5       0.2     6e+02       2       8 ..      12      18 ..      12      18 .. 0.87
   2 ?    8.2   0.3   0.00084       2.5       2       9 ..      46      53 ..      46      57 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.2
                 DNA_ligase_ZBD  2 CPvCGsa 8 
                                   CP CG a
  gi|116754035|ref|YP_843153.1| 12 CPRCGGA 18
                                   *****75 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00084
                 DNA_ligase_ZBD  2 CPvCGsav 9 
                                   CPvCGs +
  gi|116754035|ref|YP_843153.1| 46 CPVCGSIL 53
                                   *****965 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   8.1     0.053   1.6e+02      18      35 ..      41      58 ..      10      63 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.053
                    Prok-RING_1 18 dDiVvCpeCgtpyHraCy 35
                                     iV+Cp+Cg+   r  +
  gi|116754035|ref|YP_843153.1| 41 IEIVICPVCGSILDRGRW 58
                                   57********87666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); 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):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2724.26
//
Query:       gi|116754036|ref|YP_843154.1|  [L=111]
Description: hypothetical protein Mthe_0724 [Methanosaeta thermophila PT]
Scores for complete 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-29  101.1   0.0    3.4e-29  101.0   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 !  101.0   0.0   1.9e-33   3.4e-29       1      92 []      21     111 .]      21     111 .] 0.99

  Alignments for each domain:
  == domain 1  score: 101.0 bits;  conditional E-value: 1.9e-33
                                    EEETTE.EEEEEEEGGGTT-EEEETTEEEE--HHHH--EEE-HHHHHHHHHHHEEEEEESHHHHHHHHHTTSS-GGG-EE CS
                         DUF424   1 yrtddllklvavcdkellgktfkegelllnvsegfyggelaseeeaikeLekatiaNivgeeavvlavkaGlvdpdsVlv 80 
                                    y+++++ +lvavcd+ellg++f+e+el+l+vs +f+g+elas++++  +Le+atiaN vge+av++a+  ++vd+++Vl+
  gi|116754036|ref|YP_843154.1|  21 YTIGGE-VLVAVCDSELLGQRFTEKELQLEVSVSFFGQELASAAMLEMALEEATIANFVGERAVAWAIAFEYVDRENVLR 99 
                                    789999.************************************************************************* PP

                                    ETTEEEEEEEE- CS
                         DUF424  81 idgvphaqigkl 92 
                                    idgvp aq++++
  gi|116754036|ref|YP_843154.1| 100 IDGVPCAQMVRM 111
                                    **********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 821.43
//
Query:       gi|116754037|ref|YP_843155.1|  [L=300]
Description: hypothetical protein Mthe_0725 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       241  (0.0134419); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); 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 0.22s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 2279.16
//
Query:       gi|116754038|ref|YP_843156.1|  [L=399]
Description: S-adenosylmethionine synthetase [Methanosaeta thermophila PT]
Scores for complete 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-177  590.1   2.2     2e-177  589.9   2.2    1.0  1  AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synt
  ------ inclusion threshold ------
      0.029   14.5   2.1       0.36   11.0   0.5    3.2  2  ZT_dimer         Dimerisation domain of Zinc Transporter


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 !  589.9   2.2  2.3e-181    2e-177       1     396 []       3     395 ..       3     395 .. 0.99

  Alignments for each domain:
  == domain 1  score: 589.9 bits;  conditional E-value: 2.3e-181
                                    --EEEEE-TTS-GTTSSEEEEEEE-TTSHHHHHHHHHHHHHHHHHHHHHHHHSS---EEEEEEEEE--EEEEETTEEEEE CS
                AdoMet_Synthase   1 rnivveelkkkpveeqevEivErKGiGHPDsiaDgiaeavsralskeylekfgailhhniDkvllvaGesepkfgGGevi 80 
                                    rni+veel+++pve+q++E+vErKG+GHPDs+aDgiae++sral+key+e+fg++lhhn+Dk ++vaG+s+p+fgGGevi
  gi|116754038|ref|YP_843156.1|   3 RNIRVEELTQRPVEKQKIEVVERKGLGHPDSVADGIAEEISRALCKEYIERFGRVLHHNTDKIQIVAGRSRPAFGGGEVI 82 
                                    79****************************************************************************** PP

                                    E-EEEEEEEEEEEEE.EEE--HHHHHHHHHHHHHHHH-SS--TTTSEEEEEEEEEEEEHHHHHHCH-SS..-BESSSEEE CS
                AdoMet_Synthase  81 epieillsgratkevegekipveeialeaakeylkenlraldlekdvivdvklgkgsadLkdvferkkkevplaNDtSfg 160
                                    +p +ill+grat+ +++ ++pv++ial++a+++lk+ lr+ldl+++vi+d+k+g+gsadL d+f+r++++vp+aNDtS+g
  gi|116754038|ref|YP_843156.1|  83 QPQYILLTGRATRVCGDVEVPVDAIALRTARNHLKRALRNLDLDTHVIIDCKIGTGSADLCDIFDRDASTVPSANDTSYG 162
                                    ******************************************************************************** PP

                                    EEEES--HHHHHHHHHHHHHTSHHHHHH-TTEEEEEEEEEEEETTEEEEEEEEEEEGGG--SHHHHHHHHHHHHHHHHHH CS
                AdoMet_Synthase 161 vgyaplseleklvleterllnskelkkklpevGeDiKvmglRekkkielTvavalvdrlvkdleeYlevkeeikeeveel 240
                                    vgyaplse+e++v++te+ l s  l++++p++GeDiKvmglRe+++i lT+a+a+vdr+++dl++Y+e+k+ei ee++  
  gi|116754038|ref|YP_843156.1| 163 VGYAPLSETERIVYSTEQELLS--LRSRIPAIGEDIKVMGLREDDTIYLTIACAMVDRYIDDLDHYVETKKEIVEEISAK 240
                                    *********************8..99****************************************************** PP

                                    HHHHSTTSEEEEEE-TT-BGGGTB--EESSSSGGGTT--EETTSS--TTSSB-TTS----S--TTS-TTT-HHHHHHHHH CS
                AdoMet_Synthase 241 akkltkerevevevNtaDkkeeesvyltvtGtsaEegDdGsvGRGNRvnGlitpnrpmslEAaaGKNPvsHvGKiYnvla 320
                                    a+++t+ r+v+v++N  D++ ++svy+tvtGtsaE+gDdG+vGRGNR+nGlitpnrpmslEA++GKNP++HvGKiYn+l+
  gi|116754038|ref|YP_843156.1| 241 AQSMTR-RRVDVQMNVGDNIATGSVYITVTGTSAEMGDDGAVGRGNRANGLITPNRPMSLEATSGKNPINHVGKIYNLLS 319
                                    **9999.************************************************************************* PP

                                    HHHHHHHHHH-TTEEEEEEEEEE-TTSBTTS-SEEEEEEEESSS---HHSHHHHHHHHHHHHT-HHHHHHHHTTT- CS
                AdoMet_Synthase 321 neiakeiveevegvkevyvrllsqiGkpidePlvasvqvilekgvsleevekeveeiideelekieeiteeliegk 396
                                    n iakei+eev+gv+evyv++lsqiGkpi++P++asvq++l++gv+l++ +++++ei+d++le+i ++++++ +g+
  gi|116754038|ref|YP_843156.1| 320 NLIAKEIAEEVDGVEEVYVKILSQIGKPISQPHIASVQLVLKEGVRLSSAHARAREITDRWLEDIPRVQQMIFHGE 395
                                    ************************************************************************9885 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 ?   -0.3   0.0      0.13   1.2e+03      51      66 ..      35      50 ..      33      61 .. 0.80
   2 ?   11.0   0.5     4e-05      0.36      12      75 ..     326     393 ..     320     395 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.13
                                   HHHHHHHHHHHHHHH- CS
                       ZT_dimer 51 aHeiadevekrikeef 66
                                   a  ia+e+ +++ +e+
  gi|116754038|ref|YP_843156.1| 35 ADGIAEEISRALCKEY 50
                                   6789999999999987 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 4e-05
                                    HHTT-SS-EEEEEEEEE-S-....---EEEEEEEE-TTS-HHHHHHHHHHHHHHHHHH-TT--EEEEE CS
                       ZT_dimer  12 iiksvpgvkgvhdlrtrksG....skifvdlhievdgdlsvkeaHeiadevekrikeefpgvadvliH 75 
                                    i+++v+gv++v      ++G    +  ++++++++++   ++ aH+ a e+ +r  e +p+v++++ H
  gi|116754038|ref|YP_843156.1| 326 IAEEVDGVEEVYVKILSQIGkpisQPHIASVQLVLKEGVRLSSAHARAREITDRWLEDIPRVQQMIFH 393
                                    55566666666555555666322224578999********************************9999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); expected 358.6 (0.02)
Passed bias filter:                      602  (0.0335769); expected 358.6 (0.02)
Passed Vit filter:                        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 0.25s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 3106.57
//
Query:       gi|116754039|ref|YP_843157.1|  [L=567]
Description: NAD+ synthetase [Methanosaeta thermophila PT]
Scores for complete 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  272.6   0.0    2.8e-81  272.2   0.0    1.2  1  NAD_synthase   NAD synthase
    3.8e-21   75.6   0.0      9e-21   74.4   0.0    1.6  1  CN_hydrolase   Carbon-nitrogen hydrolase
     0.0059   15.4   0.0     0.0086   14.9   0.0    1.2  1  tRNA_Me_trans  tRNA methyl transferase
     0.0068   16.1   0.0     0.0094   15.6   0.0    1.3  1  Asn_synthase   Asparagine synthase
  ------ inclusion threshold ------
        0.1   12.1   0.0       0.16   11.4   0.0    1.2  1  QueC           Queuosine biosynthesis protein QueC


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 !  272.2   0.0   7.9e-85   2.8e-81       2     242 .]     296     544 ..     295     544 .. 0.97

  Alignments for each domain:
  == domain 1  score: 272.2 bits;  conditional E-value: 7.9e-85
                                    HHHHHHHHHHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE--- CS
                   NAD_synthase   2 ieelvdflkeyvkkagakgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktidi 81 
                                    +++lv   ++yv+k+g++++v+GlSGGvDSsl+aa+a +alg+env+++l+Ps ++s+e++edal+la nl+i++ ti+i
  gi|116754039|ref|YP_843157.1| 296 WRALVLGTRDYVRKCGFRSAVIGLSGGVDSSLTAAIAAEALGPENVIGVLMPSPYTSRESMEDALELARNLSIQTITIPI 375
                                    78899999************************************************************************ PP

                                    HHHHHHHHHHHHHHH....-HHHHHHHHHHHHHHHHHHHHHHHTEEEB---BHHHHTTT-S-TTTTT--SBETTTTS-HH CS
                   NAD_synthase  82 kpivrafeqelkeak....edlakgNlkaRiRmailyaianklnllvlgTgnksElvvGyfTkyGDgaadlapiaellKt 157
                                    ++i++a+e +l++      +d++++N++aRiR ++l+a +nk++++vl+TgnksEl+vGy+T+yGD+++++a + ++ Kt
  gi|116754039|ref|YP_843157.1| 376 SEIMAAYERTLEPIFrgveKDVTEENIQARIRGNLLMALSNKFGHIVLSTGNKSELAVGYCTIYGDMSGGFAVLSDVPKT 455
                                    *********87776556669************************************************************ PP

                                    HHHHHHHHTT.....--HHHHCS--B--SSTT-BHHHHHSS-HHHHHHHHT.HSSSS...HHHHHTTT--HHHHHHHHHH CS
                   NAD_synthase 158 evkeLakeln.....vPervlkkpPsAdLkpgqtDeeeLgikYdelDeiLk.lvekkkspeeiikekelpaevvekiekl 231
                                     v+++a+++n     +P++vl+k+PsA+L+pgq D++ L+ +Y++lDeiL+  +e+++s+eei++ +++++++v+++ k+
  gi|116754039|ref|YP_843157.1| 456 MVYRMARWINmrgpvIPQSVLEKAPSAELRPGQRDQDTLP-PYETLDEILHrHIEQRQSEEEIVS-AGFDQKMVRYVLKM 533
                                    ****************************************.**********9***********99.************** PP

                                    HHHTGGGGSSS CS
                   NAD_synthase 232 vkksehKrklp 242
                                    vk  e+Krk++
  gi|116754039|ref|YP_843157.1| 534 VKTAEFKRKQA 544
                                    ********986 PP

>> CN_hydrolase  Carbon-nitrogen hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.4   0.0   2.5e-24     9e-21       1     252 [.      30     278 ..      30     285 .. 0.81

  Alignments for each domain:
  == domain 1  score: 74.4 bits;  conditional E-value: 2.5e-24
                                    EEEEEEBB-STTHHHHHHHHHHHHHHHHHHTTESEEEEETTTTTBSSSHHHHHHHHB.....HSSSHHHHHHHHHHHHHT CS
                   CN_hydrolase   1 rvAvvQlpqkaadleanlqklleliaeAarkgadLivlPElfitgykeeahfleaAe.....aglgetlallaalarkng 75 
                                    rvA+ Q++++  dle+n +++ +++++    +adL v PE++++gy  +++ l   +     +    +l +la  +++  
  gi|116754039|ref|YP_843157.1|  30 RVALLQINTTVGDLEGNASLIRKAVES---LDADLAVTPEMALVGY-PPRDLLLMPGfvknaW---DVLTRLALDLEDSP 102
                                    79*******99***************9...9***************.6666666666774444...89999998888888 PP

                                    EEEEEEEEEEEC.CTTEEEEEEEEEEEETTSEEEEEEE-SS--EECTTSCECCGHHTSCS-SSS-EEEETTEEEEEEEGG CS
                   CN_hydrolase  76 iavviglierel.tngklqayntavlldldgklvgkyrKlhLfpgeprpptaverelfepgdgipvfdtpvgkiGaaiCy 154
                                    +++v+   +++  t+  l  +n+a ll +dg++ ++ rK+ L    p+   + e  +fep  g +++ +++  +G++iC+
  gi|116754039|ref|YP_843157.1| 103 PMLVGIPEPNRSeTGRPL--FNSAALL-ADGSVKQIFRKTLL----PTYDVFDEDRYFEPASGPQMLNLKGRTFGISICE 175
                                    877765555544455555..******9.78899********8....68889999999999666688899999******** PP

                                    GGGSHHHHHHHH.........HTT-SEEEEBH.GCCCTCHHHHHHHHHHHHHHHHHHTSEEEEEEBEEEHCETTEEEE-- CS
                   CN_hydrolase 155 eigfpellrala.........lkgaeilvnlserapvpksmgppqwellgraralengcfviaanqvggyeqlilwpvgh 225
                                    +i+ ++ +   +         l+ga+  +n ++ +p++  +    +e++  + a   g+++i++nqvgg  +++l++ g 
  gi|116754039|ref|YP_843157.1| 176 DIWNDRDIFRRRryhrdpledLRGADCFIN-MSASPFTAGKH-LKREMMLSSIARKYGVPLIYVNQVGG--NDDLVFDGR 251
                                    *****9876433111111112567777777.33444444443.4569999*******************..********* PP

                                    EEEE-TTS-EEEECCSSSTEEEEEEEE CS
                   CN_hydrolase 226 SaiidpdGrilaglgeeeegvliaeid 252
                                    S++++p G+++a++  +ee+vli++id
  gi|116754039|ref|YP_843157.1| 252 SCAFSPSGELIARAAAFEEDVLIVDID 278
                                    **************************9 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.4e-06    0.0086       4      35 ..     316     349 ..     313     384 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.4e-06
                  tRNA_Me_trans   4 vvalSgGVDSsvaaallkeqg..yevigvflklw 35 
                                    v++lSgGVDSs++aa+ +e+    +vigv +   
  gi|116754039|ref|YP_843157.1| 316 VIGLSGGVDSSLTAAIAAEALgpENVIGVLMPSP 349
                                    799*************9998656899**999654 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   2.6e-06    0.0094      24      79 ..     319     373 ..     309     530 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.6e-06
                   Asn_synthase  24 LSGGlDSSliaalaarqsksplktFsigf.ee.kgsdeakyakevaehlgtehtelvl 79 
                                    LSGG+DSSl aa+aa+ +  p +   + + ++  + + ++ a e+a+ l ++ +   +
  gi|116754039|ref|YP_843157.1| 319 LSGGVDSSLTAAIAAEALG-PENVIGVLMpSPyTSRESMEDALELARNLSIQTI--TI 373
                                    9***************986.6666666663233444445666677777766643..33 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   4.5e-05      0.16       2      66 ..     315     380 ..     314     410 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.5e-05
                                    EEEE--SSHHHHHHHHHHHHH-..SEEEEEEE..ESS-TTSHHHHHHHHHHHHT--.-EEEEE-GGGGG CS
                           QueC   2 avvllSGGlDSttvlalakkeg..kevealtf..dYgqrhkkeleaakkiakelgveehkildldllke 66 
                                    av+ lSGG+DS+  +a+a ++   ++v+ + +   Y +r++  +e a ++a++l + ++ ++ ++ + +
  gi|116754039|ref|YP_843157.1| 315 AVIGLSGGVDSSLTAAIAAEALgpENVIGVLMpsPYTSRES--MEDALELARNLSI-QTITIPISEIMA 380
                                    899*********99999998875667766555114666655..5567788999988.666666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (567 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.39
# Mc/sec: 4404.39
//
Query:       gi|116754040|ref|YP_843158.1|  [L=172]
Description: CRISPR-associated Cas4 family protein [Methanosaeta thermophila PT]
Scores for 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   52.0   0.0    9.7e-14   51.8   0.0    1.1  1  Cas_Cas4  Domain of unknown function DUF83
    9.1e-07   29.0   0.0    1.1e-06   28.8   0.0    1.1  1  PDDEXK_1  PD-(D/E)XK nuclease superfamily
  ------ inclusion threshold ------
      0.047   13.0   0.0      0.062   12.6   0.0    1.2  1  Csa1      CRISPR-associated exonuclease Csa1


Domain annotation for each model (and alignments):
>> Cas_Cas4  Domain of unknown function DUF83
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.8   0.0   1.6e-17   9.7e-14      54     160 ..      60     168 ..      39     170 .. 0.85

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 1.6e-17
                       Cas_Cas4  54 sikiDvvekekeklvvvEvKkskkk..eeaaklQllyYlllLe.kkgveikeGvleypkekkreevelteelreelekai 130
                                    s+k D + ke+++l++vEvK+s      ++++lQl +Y l++e     ++  G++ y +   r ++el+ +lr+e+ +a+
  gi|116754040|ref|YP_843158.1|  60 SGKPDSIIKEGRHLIPVEVKSSLTEkpYRSHQLQLAAYGLIMEeLYRTDVPYGYIVYGNR--RHRIELDGDLRDEVLSAL 137
                                    899******************9655115688************888999********975..56799************* PP

                       Cas_Cas4 131 keieeiisse.kppkvkkkkiCkkCayaelC 160
                                    +e+++ +++  + ++ +++ +C kC++++ C
  gi|116754040|ref|YP_843158.1| 138 DEMRHALRNGhAQRNHNHRARCAKCSFRKGC 168
                                    ****9999993555566677*********99 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 !   28.8   0.0   1.8e-10   1.1e-06     118     255 .]      53     169 ..      18     169 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 1.8e-10
                       PDDEXK_1 118 alelefggekvrLkGriDrvddkegelriiDyKtgsappkskelaelkeglQlllYllalaegeelkeegepagalylrl 197
                                    ++      e++ L G+ D + +++++l  ++ K++ ++ k+ +    +++lQl++Y l+++e   +     ++   y+ +
  gi|116754040|ref|YP_843158.1|  53 RS------ERYGLSGKPDSIIKEGRHLIPVEVKSSLTE-KPYR----SHQLQLAAYGLIMEEL--YRT---DVPYGYIVY 116
                                    33......4445*********88889*******88844.4444....7999************..442...455555555 PP

                       PDDEXK_1 198 eepkvkdeevvkkmalteeeleallqeleelaeeilagefparpskk..CeyCpyksvCr 255
                                            ++ ++++l+ + ++++l+ l e   ++++g+ + +++++  C+ C++++ C+
  gi|116754040|ref|YP_843158.1| 117 -------GNRRHRIELDGDLRDEVLSALDEMRHALRNGHAQRNHNHRarCAKCSFRKGCK 169
                                    .......455666667777778888888888888999999999998889********996 PP

>> Csa1  CRISPR-associated exonuclease Csa1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0     1e-05     0.062     202     270 ..      86     147 ..      62     171 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1e-05
                           Csa1 202 ykeehelalaGYalalEsqleiPvDfGvlisvtvngevklkaelvaisdslRkefleeRdraidiveke 270
                                      ++h+l la Y+l +E  +   v +G++++        ++ + + ++ +lR e l + d++ +++ ++
  gi|116754040|ref|YP_843158.1|  86 PYRSHQLQLAAYGLIMEELYRTDVPYGYIVYG-------NRRHRIELDGDLRDEVLSALDEMRHALRNG 147
                                    45789************************983.......334445677778888877777777766654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); 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: 0.38u 0.21s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 1419.44
//
Query:       gi|116754041|ref|YP_843159.1|  [L=88]
Description: hypothetical protein Mthe_0729 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); 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: 0.33u 0.21s 00:00:00.54 Elapsed: 00:00:00.35
# Mc/sec: 745.01
//
Query:       gi|116754042|ref|YP_843160.1|  [L=386]
Description: chaperone protein DnaJ [Methanosaeta thermophila PT]
Scores for complete 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  145.2   0.0      2e-42  144.8   0.0    1.2  1  DnaJ_C          DnaJ C terminal domain
    2.6e-29  101.1   3.1    3.9e-29  100.6   3.1    1.3  1  DnaJ            DnaJ domain
    1.1e-13   51.3  17.7      2e-13   50.5  17.7    1.4  1  DnaJ_CXXCXGXG   DnaJ central domain
     0.0027   17.6  13.5      0.055   13.4   1.7    3.6  3  Anti-TRAP       Tryptophan RNA-binding attenuator protein inh
  ------ inclusion threshold ------
      0.049   13.5   2.2       0.18   11.6   2.4    1.9  2  zf-ZPR1         ZPR1 zinc-finger domain
       0.17   11.8   1.3       0.47   10.4   1.3    1.8  1  zinc_ribbon_4   zinc-ribbon domain
       0.89   10.1   3.8        2.2    8.8   3.8    1.7  1  Cytochrom_c3_2  Cytochrome c3
        1.7    8.7   8.7          4    7.5   0.9    2.3  2  HypA            Hydrogenase/urease nickel incorporation, meta


Domain annotation for each model (and alignments):
>> DnaJ_C  DnaJ C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.8   0.0   8.9e-46     2e-42       2     148 .]     121     341 ..     120     341 .. 0.96

  Alignments for each domain:
  == domain 1  score: 144.8 bits;  conditional E-value: 8.9e-46
                                    EEEEEE-HHHHHH-.EEE.EEEE......................................................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx...................................................... RF
                         DnaJ_C   2 eveleisleelykGktkkikikrnvi...................................................... 27 
                                    +++lei+le++++G +++i++ r++                                                       
  gi|116754042|ref|YP_843160.1| 121 RYDLEITLEQAASGLETTIEVPRTEVcrtcsgtgakpgtspvrcqschgtgqitrtqvtpfgqivtsttcskcggrgqvi 200
                                    79*********************999****************************************************** PP

                                    ................TEEEEEE-TT--TT-EEEETT-SS.....SS....S---EEEEEEE---SS-EEETTEEEEEEE CS
                                    ............xxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         DnaJ_C  28 ............kkekktlevkipaGikdgqkirlegeGd.....eeg..gepGDlivtikvkphpvFkrkgndlyveve 88 
                                                +++ ++++v+ip+G+++g++++l+g+G+     + g  +epGDl++ i+ +php F+r+g++l++e++
  gi|116754042|ref|YP_843160.1| 201 qtpcddcdgtgrVRRYRKINVRIPPGVDTGHHLKLRGQGEappfsP-GapAEPGDLYIFINIRPHPLFSRDGDNLIHEMN 279
                                    **********96444458**********************887642.267****************************** PP

                                    EEHHHHHHTEEEEEE-SS-EEEEEE...--TT-EEEETT-S-EET...TEE--EEEEEEEE-- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         DnaJ_C  89 islaeallGgklevptldgkvklki...tqpgevlrikgkGmpklkkpgkrGdlyvevkvefP 148
                                    is+++a+lG++l+vptldg+++lki   tq+g+ +rikgkGmp+l+ +++ Gdl+v+ +v +P
  gi|116754042|ref|YP_843160.1| 280 ISMTQAALGTELDVPTLDGRARLKIppgTQSGSLFRIKGKGMPRLH-GTGTGDLLVRTNVRIP 341
                                    *********************************************7.**************99 PP

>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.6   3.1   1.7e-32   3.9e-29       1      63 []       6      67 ..       6      67 .. 0.99

  Alignments for each domain:
  == domain 1  score: 100.6 bits;  conditional E-value: 1.7e-32
                                   HHHHHHTSSTTG-HHHHHHHHHHHHHHHSTTTSCCHHHHHHHHHHHHHHHHHHTSHHHHHHHH CS
                           DnaJ  1 dyYeiLgvskdasedeIkkaYrklalkyHPDknpkdpeaeekFkeineAyevLsdpekRkqYD 63
                                   dyYeiLgv+++a+e+eIk+aYrkla+kyHPD++ + p+aee+Fkei+eAy vLsdpekR+qYD
  gi|116754042|ref|YP_843160.1|  6 DYYEILGVDRNATEKEIKSAYRKLAMKYHPDRS-DAPDAEERFKEISEAYAVLSDPEKRRQYD 67
                                   8********************************.****************************9 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.5  17.7   8.7e-17     2e-13       1      67 []     147     211 ..     147     211 .. 0.90

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 8.7e-17
                  DnaJ_CXXCXGXG   1 CkkCkGsgakkgk.kktCktCkGsGvvreeqkt.lgpfvqqsqstCpeCeGtGkvikekdkCkkCkGkg 67 
                                    C++C+G+gak+g+ + +C++C+G+G+++++q+t +g++v  +++tC++C+G+G+vi  +++C++C+G+g
  gi|116754042|ref|YP_843160.1| 147 CRTCSGTGAKPGTsPVRCQSCHGTGQITRTQVTpFGQIV--TSTTCSKCGGRGQVI--QTPCDDCDGTG 211
                                    **********9776999********99888877788877..679************..779******86 PP

>> Anti-TRAP  Tryptophan RNA-binding attenuator protein inhibitory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   3.6   0.00017      0.38      11      42 ..     145     173 ..     137     177 .. 0.86
   2 !   13.4   1.7   2.4e-05     0.055      12      42 ..     163     199 ..     161     202 .. 0.86
   3 !    6.8   0.2    0.0029       6.5      10      22 ..     201     213 ..     198     224 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00017
                                    EE-TTTTTTSEETTE......E-TTTTTSSEE CS
                      Anti-TRAP  11 tkCdaCngsGkiepeeprasleCPkCsGkgli 42 
                                    + C +C g+G  +++   + + C  C G g i
  gi|116754042|ref|YP_843160.1| 145 EVCRTCSGTGAKPGT---SPVRCQSCHGTGQI 173
                                    46*************...889*******9987 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 2.4e-05
                                    E-TTTTTTSEETTE............E-TTTTTSSEE CS
                      Anti-TRAP  12 kCdaCngsGkiepe......eprasleCPkCsGkgli 42 
                                     C+ C+g+G+i  +      +  +s  C kC+G+g +
  gi|116754042|ref|YP_843160.1| 163 RCQSCHGTGQITRTqvtpfgQIVTSTTCSKCGGRGQV 199
                                    7**********99988887777899********9964 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0029
                                    EEE-TTTTTTSEE CS
                      Anti-TRAP  10 EtkCdaCngsGki 22 
                                     t+Cd C+g+G++
  gi|116754042|ref|YP_843160.1| 201 QTPCDDCDGTGRV 213
                                    689********97 PP

>> zf-ZPR1  ZPR1 zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   2.4   8.1e-05      0.18       2      44 ..     163     201 ..     162     213 .. 0.87
   2 ?   -3.1   0.0       2.7   6.1e+03      84     100 ..     301     317 ..     290     318 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.1e-05
                        zf-ZPR1   2 lCpsCgkengetrllltkiPyfkeviimsfeCehCgyknnevk 44 
                                     C sC+   g+ ++++t++  f++++ +s++C++Cg + + ++
  gi|116754042|ref|YP_843160.1| 163 RCQSCH---GTGQITRTQVTPFGQIV-TSTTCSKCGGRGQVIQ 201
                                    599996...899***********976.7899*****9988776 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.7
                        zf-ZPR1  84 eleippgtlegrlttvE 100
                                     l+ippgt++g+l  + 
  gi|116754042|ref|YP_843160.1| 301 RLKIPPGTQSGSLFRIK 317
                                    4899*****99987665 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.3   0.00021      0.47       3      32 ..     162     194 ..     161     196 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00021
                  zinc_ribbon_4   3 itCpsCkakyeiddeklpakgvkv...rCskCg 32 
                                    ++C+sC+ + +i   ++++ g+ v   +CskCg
  gi|116754042|ref|YP_843160.1| 162 VRCQSCHGTGQITRTQVTPFGQIVtstTCSKCG 194
                                    79**************998887552227****8 PP

>> Cytochrom_c3_2  Cytochrome c3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   3.8   0.00097       2.2       9      78 ..     147     207 ..     140     209 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00097
                                    GGGTSSSST-SSTTHHHHHHHHHHH--HHHCHTTSST.TSSBTTSSCTSSS-GGGTS-TTTSBT-GGGGT CS
                 Cytochrom_c3_2   9 CadCHtkekpkkdkaveeekClsCHgkleelakktkeakeanphkshekeleCteCHkeHkksekvCaeC 78 
                                    C++C ++  +     ++  +C+sCHg+ + ++++      ++p  ++ ++++C++C    +  ++ C++C
  gi|116754042|ref|YP_843160.1| 147 CRTCSGTGAK---PGTSPVRCQSCHGTGQITRTQ------VTPFGQIVTSTTCSKCGGRGQVIQTPCDDC 207
                                    6666665554...344556788888887765554......346777777888888877777777777777 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 ?    7.5   0.9    0.0018         4      60      96 ..     135     171 ..     110     179 .. 0.71
   2 ?    5.1   1.7    0.0099        22      69      95 ..     186     210 ..     177     222 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0018
                                    -EEEEEEE--EEEETTTS-EEECHHH.HHS-TTTSSS- CS
                           HypA  60 aeLeieevpvkvrCreCgkefeleek.alrCpkCgsad 96 
                                     e +i evp +  Cr+C+ ++ +  +  +rC++C++++
  gi|116754042|ref|YP_843160.1| 135 LETTI-EVPRTEVCRTCSGTGAKPGTsPVRCQSCHGTG 171
                                    33333.5677778*****999966644789****9864 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0099
                                    -EEEETTTS-EEECHHHHHS-TTTSSS CS
                           HypA  69 vkvrCreCgkefeleekalrCpkCgsa 95 
                                     +++C++Cg ++++ +  + C +C+++
  gi|116754042|ref|YP_843160.1| 186 TSTTCSKCGGRGQVIQ--TPCDDCDGT 210
                                    6789********9774..48****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); 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: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2717.19
//
Query:       gi|116754043|ref|YP_843161.1|  [L=615]
Description: molecular chaperone DnaK [Methanosaeta thermophila PT]
Scores for complete 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-232  770.7  13.1   9.1e-212  704.5   9.8    2.0  2  HSP70          Hsp70 protein
    6.6e-21   74.5   6.0    5.3e-20   71.5   6.0    2.4  1  MreB_Mbl       MreB/Mbl protein
    8.1e-06   25.7   0.1    1.5e-05   24.8   0.1    1.5  1  FGGY_C         FGGY family of carbohydrate kinases, C-termina
  ------ inclusion threshold ------
      0.047   13.6   0.4      0.087   12.8   0.4    1.4  1  Serglycin      Serglycin
       0.14   12.9   2.4       0.53   11.0   2.4    2.0  1  FliD_N         Flagellar hook-associated protein 2 N-terminus
       0.19   10.9   3.1        1.2    8.3   0.1    2.6  3  StbA           StbA protein
        0.2   11.2  10.7       0.49   10.0  10.7    1.6  1  PI3K_P85_iSH2  Phosphatidylinositol 3-kinase regulatory subun
       0.63   10.2  12.2        1.4    9.0  12.2    1.6  1  DUF1090        Protein of unknown function (DUF1090)
        1.3    9.1   5.2        2.3    8.2   4.1    1.9  2  DUF45          Protein of unknown function DUF45
        1.6    8.9   9.3        3.2    7.9   9.3    1.5  1  MRP-L28        Mitochondrial ribosomal protein L28
        1.7    9.0   8.5        2.7    8.3   8.5    1.2  1  Vfa1           AAA-ATPase Vps4-associated protein 1
        2.4    8.3   6.8        4.4    7.4   6.8    1.4  1  DUF3347        Protein of unknown function (DUF3347)


Domain annotation for each model (and alignments):
>> HSP70  Hsp70 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.4   0.1   1.2e-22   1.8e-19       1      75 [.       4      83 ..       4      86 .. 0.92
   2 !  704.5   9.8  6.1e-215  9.1e-212     100     599 .]      82     579 ..      81     579 .. 0.99

  Alignments for each domain:
  == domain 1  score: 69.4 bits;  conditional E-value: 1.2e-22
                                   EEEEEEXSSEEEEEEEETTEEEEEXXTTSX....SSEESEEEEXTT.SEEETHHHHHCTTTTGGGEEEXGGGTTTXBTTS CS
                          HSP70  1 viGiDLGttnsvvavmeggkievianeegn....rttPsvvaFtkk.erlvGeaAkrqavtnpkntvfsvKrliGrkfsd 75
                                   +iGiDLGt ns+ av+ gg++++i  +eg+    ++ Ps+vaFtk+ + lvGe+A+rqa+tnp+ t++ +Kr +G++++ 
  gi|116754043|ref|YP_843161.1|  4 IIGIDLGTSNSAAAVLIGGRPTIIPSAEGTslggKAFPSYVAFTKDgQVLVGEPARRQAITNPEGTITGIKRKMGTDYKV 83
                                   69***********************999763333789*********99****************************9985 PP

  == domain 2  score: 704.5 bits;  conditional E-value: 6.1e-215
                                    EEEETTEEEEHHHHHHHHHHHHHHHHHHHHTSBEEEEEEEEXTTXXHHHHHHHHHHHHHTTXEEEEEEEHHHHHHHHHHT CS
                          HSP70 100 eveaagekftpeqisamvLkklketaeaylgkkvtdavitvPaYfndaqRqatkdAgkiAGLnvlRivNepTAaalaYGl 179
                                    +v++ g+++tpe+isa +L+k+k++aea+lg+kv++avitvPaYfnd+qRqatkdAg+iAGL+v+Ri+NepTAaalaYGl
  gi|116754043|ref|YP_843161.1|  82 KVKVFGKEYTPEEISAHILRKIKQDAEAFLGEKVEKAVITVPAYFNDNQRQATKDAGTIAGLDVVRIINEPTAAALAYGL 161
                                    57888*************************************************************************** PP

                                    CCSSSCEEEEEEEEXSSXEEEEEEEEETTEEEEEEEEEETTXSHHHHHHHHHHHHHHHHHHHHSXXGGGSHHHHHHHHHH CS
                          HSP70 180 dkkdkernvlvyDlGggtfdvSilelekGvfevkaTagDthlGGedfDealvehlveefkkkegidlskdkkalqrlkea 259
                                    dk   e++++v+DlGggt dv i+e+++Gvfevk+T+gDt+lGG+d+De+l++++ve+f++++gi+l++d +a+qrl+ea
  gi|116754043|ref|YP_843161.1| 162 DKGG-EQKIMVFDLGGGTLDVTIMEMGEGVFEVKSTSGDTQLGGRDMDERLLDYIVEKFRQETGINLRNDVMAMQRLREA 240
                                    ***9.*************************************************************************** PP

                                    HHHHHHHTTTSSCSEEEEEEEEEETTT.EEEEEEEEHHHHHHHHHHHHHHTHHHHHHHHHHCTEEGGGCSEEEEESGGGG CS
                          HSP70 260 aekaKkeLSsskqteinleietvdedg.kdlseklsRakfeelvedllertlepvekalkdaklkkeeidevvlvGGstR 338
                                    ae aK+eLSs+ qt+inl+++t+d++g k+l+++++Rak+eel++d+ler+  p+e+al+dakl+k++id+++lvGG tR
  gi|116754043|ref|YP_843161.1| 241 AEVAKIELSSMLQTTINLPYITADASGpKHLNMTITRAKLEELIQDVLERCRGPMEQALSDAKLSKSDIDKIILVGGPTR 320
                                    ******************************************************************************** PP

                                    SHHHHHHHHHHTTCHHBSSSHTTTHHHHHHHHHHHHHCTCGCSHCCEEEEBESS-EEEEETTTEEEEEESTTCBSSEEEE CS
                          HSP70 339 iPkvqelvkelfgkepsktvnpDeavaiGAAvqagvlsgeeevkdllllDvtpLslgietlggvmtkliernttiptkks 418
                                    +P+vqe vk ++gk+ +++v+p e+va+GAA+qagvl+g  evkd+lllDvtpLslg+etlgg+mt+liernttipt+ks
  gi|116754043|ref|YP_843161.1| 321 MPAVQEFVKRVMGKDVERGVDPMECVAMGAAIQAGVLAG--EVKDILLLDVTPLSLGVETLGGIMTRLIERNTTIPTRKS 398
                                    ***************************************..*************************************** PP

                                    EEEEESSTTSSSEEEEEEESSSSBGGGSEEEEEEEEECESSCSTTCSEEEEEEEEETTSCEEEEEEETTTCCEEEEEEEC CS
                          HSP70 419 qvfstaadnqtaveievlqgerelvkdnkllgsfeldgippaprGvpqieVtfdidanGiltvsakdketgkeeeitiea 498
                                    q+f+taadnqt+vei+vlqger l+kdn +lg+f+l gippaprG pqieVtfdidanGil+vsakd +t+ke++iti+a
  gi|116754043|ref|YP_843161.1| 399 QIFTTAADNQTSVEIHVLQGERPLAKDNISLGRFTLVGIPPAPRGIPQIEVTFDIDANGILHVSAKDLATKKEQRITITA 478
                                    ******************************************************************************** PP

                                    CSSSBHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGSTHHHHHHHHHHHHHHHCHTTSSCHHH CS
                          HSP70 499 seglseeeiekmvkdaeesaeedkkkkeaieakneaeelvyslekkleeeaekvseaekekvesaieeLkeeleeeekee 578
                                     ++ls+eeie+ vk+ae++a+ed++++e+ie++n+a++l+y++ek l+e+++ ++++++e++e+ai+eL+++l++++++e
  gi|116754043|ref|YP_843161.1| 479 PHRLSKEEIEQKVKEAERYAQEDARRREEIETRNQADNLIYTTEKMLKEAGDVATSEQRERIEKAISELRDALSGKDVQE 558
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHHH CS
                          HSP70 579 ieakteelkkvvekiaeklye 599
                                    i++k+e+l+++v+++ +++y+
  gi|116754043|ref|YP_843161.1| 559 IKSKMEKLQNAVYELSAAMYQ 579
                                    ***************999986 PP

>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.5   6.0   3.5e-23   5.3e-20      74     317 ..      92     352 ..       2     358 .. 0.65

  Alignments for each domain:
  == domain 1  score: 71.5 bits;  conditional E-value: 3.5e-23
                                    HHHHHHHHHHHHHT.SS-S...S--EEEEEE-SS--HHHHHHHHHHHHHTT-SEEEEEEHHHHHHHHTT--TTSSS-EEE CS
                       MreB_Mbl  74 aeellkyfikkvkk.kksl...skprvvicvPsgiteverrAvkeaakkaGarevllieeplaAAiGaglpveepsgnmv 149
                                     ee+  ++++k+k+ ++++   + ++ vi+vP   ++ +r+A k+a + aG + v +i+ep aAA+  gl+    +  mv
  gi|116754043|ref|YP_843161.1|  92 PEEISAHILRKIKQdAEAFlgeKVEKAVITVPAYFNDNQRQATKDAGTIAGLDVVRIINEPTAAALAYGLDKGGEQKIMV 171
                                    455556677777664222323367889***************************************************** PP

                                    EEE-SS-EEEEEEETTEEE.EEEE....ES-SHHHHHHHHHHHHHHHHSEE--HHHHHHHHHHH-BSS--HHHH...... CS
                       MreB_Mbl 150 vdiGggttevavislggiv.tsks....vrvaGdeldeaiikyirkkynlliGertaekikieigsavkeeeee...... 218
                                     d+Gggt +v+++ +g+ v + ks     +++G ++de +++yi +k++   G +  +++   +  + + +e        
  gi|116754043|ref|YP_843161.1| 172 FDLGGGTLDVTIMEMGEGVfEVKStsgdTQLGGRDMDERLLDYIVEKFRQETGINLRNDVMA-MQRLREAAEVAkielss 250
                                    ***************9765233332233789*****************99999877666532.22222222222000222 PP

                                    ..EEEEEEEETTTTCEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHTS..-HHHHHHHHHH-EEEESGGGGSBTHHHHHH CS
                       MreB_Mbl 219 ..kmeikGrdlvtglpkevevsseevrealkepvsaiveavkevLekt..ppeLaadivdrgivltGGgallkgldklls 294
                                      +++i+   ++       +++ +  r  l+e ++ ++e  +  +e++   + L++  +d+ i+l+GG + +  ++++++
  gi|116754043|ref|YP_843161.1| 251 mlQTTINLPYITADASGPKHLNMTITRAKLEELIQDVLERCRGPMEQAlsDAKLSKSDIDK-IILVGGPTRMPAVQEFVK 329
                                    3444444444444443334444444444555555555555555555531145688776776.7788************** PP

                                    HHHSS-EEE-SSTTTHHHHHHHH CS
                       MreB_Mbl 295 eetglpvkvaedpltcvakGtgk 317
                                    + +g  v+ + dp++cva G+++
  gi|116754043|ref|YP_843161.1| 330 RVMGKDVERGVDPMECVAMGAAI 352
                                    ********************976 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 !   24.8   0.1   9.9e-09   1.5e-05     139     196 ..     280     356 ..     216     358 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 9.9e-09
                         FGGY_C 139 lealekd..................sgkpldrlavdGGgskndllmqllAdilgvpVerpkt.aeatalGaAilAav 196
                                    le+l +d                  s++++d+++++GG ++ ++++++   ++g++Ver  +  e++a+GaAi A+v
  gi|116754043|ref|YP_843161.1| 280 LEELIQDvlercrgpmeqalsdaklSKSDIDKIILVGGPTRMPAVQEFVKRVMGKDVERGVDpMECVAMGAAIQAGV 356
                                    44444444444444444455556668999******************************8888************98 PP

>> Serglycin  Serglycin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.4   5.8e-05     0.087      75     124 ..     563     613 ..     547     615 .] 0.65

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.8e-05
                      Serglycin  75 meksqnlndvfplsedy....sgsgsGsGsGsGsgsgsgflteieqeYqpvden 124
                                    mek q  n v+ ls  +    ++s+sGs  Gs sgs sg  + +e +Y  v+++
  gi|116754043|ref|YP_843161.1| 563 MEKLQ--NAVYELSAAMyqraAQSQSGSATGSASGSTSGG-KTVEADYEVVNDD 613
                                    33333..578888887778885555555555555555553.3578899888765 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 ?   11.0   2.4   0.00035      0.53      19      85 ..     536     601 ..     519     610 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00035
                                    XXXXXXXXXXXXXXXHH..HHHHHHHHHHHHHHHHHHHXXGGGGGXEEEEECSTTTEEEEEETTS-SEE CS
                         FliD_N  19 kldkleqkktklewkqs..ayrelnsklsnlksalsalsksstfsakkatssdesvvtatassgaaags 85 
                                    + +++e++ ++l    s  +++e++sk+++l++a+ +l  s+++ +++a+s++ s+ t +as++++ g+
  gi|116754043|ref|YP_843161.1| 536 QRERIEKAISELRDALSgkDVQEIKSKMEKLQNAVYEL--SAAMYQRAAQSQSGSA-TGSASGSTSGGK 601
                                    566677777776665542289************88766..5666666666665554.777666555544 PP

>> StbA  StbA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1   0.00081       1.2     160     209 ..     164     215 ..     130     246 .. 0.67
   2 ?    2.2   0.0     0.056        84     229     292 ..     266     331 ..     236     340 .. 0.80
   3 ?   -2.4   0.3       1.5   2.2e+03     237     267 ..     530     560 ..     502     575 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00081
                           StbA 160 deleslLiiDlGGttLDvakvr..gklegiskvkgdskiGvslitdavkeal 209
                                       ++ ++ DlGG tLDv+ ++    + ++  + gd ++G   + + + +++
  gi|116754043|ref|YP_843161.1| 164 GGEQKIMVFDLGGGTLDVTIMEmgEGVFEVKSTSGDTQLGGRDMDERLLDYI 215
                                    45678899*********98553112344556667888888877777776665 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.056
                           StbA 229 kdeeyLkrrindedkresvlevinekvkkLkerviravsefsgythvmvvGGGael..iaeaikka 292
                                       ++L+ +i+ ++  e + +v+++    +++ + +a  + s++ ++++vGG + +  ++e +k+ 
  gi|116754043|ref|YP_843161.1| 266 SGPKHLNMTITRAKLEELIQDVLERCRGPMEQALSDAKLSKSDIDKIILVGGPTRMpaVQEFVKRV 331
                                    556788999999999999999**99999********99999***********98764455666655 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.5
                           StbA 237 rindedkresvlevinekvkkLkerviravs 267
                                     +  +++re + ++i+e   +L+ + +++++
  gi|116754043|ref|YP_843161.1| 530 DVATSEQRERIEKAISELRDALSGKDVQEIK 560
                                    4667777788888887777777766555443 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 ?   10.0  10.7   0.00033      0.49      23     111 ..     484     570 ..     466     586 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00033
                  PI3K_P85_iSH2  23 skqlqekskeydqlkeeynkiseeiqlkrqaleaFneaikmFeeqiklqekfskeaqehEieklqenleqlksrlkelhs 102
                                    ++++++k ke +++ +e  + +eei+++ qa +    ++km++e   +  + ++e  e+ i++l + l+   + ++e++s
  gi|116754043|ref|YP_843161.1| 484 KEEIEQKVKEAERYAQEDARRREEIETRNQADNLIYTTEKMLKEAGDVATSEQRERIEKAISELRDALS--GKDVQEIKS 561
                                    57899**********************************************999998888888877664..456666666 PP

                  PI3K_P85_iSH2 103 skekLeedl 111
                                    ++ekL++++
  gi|116754043|ref|YP_843161.1| 562 KMEKLQNAV 570
                                    666666654 PP

>> DUF1090  Protein of unknown function (DUF1090)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0  12.2   0.00095       1.4      22     109 ..     484     574 ..     481     575 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00095
                        DUF1090  22 kqaIekqieaAk..ahgnqkrvagLekaLkevka.nCtdeklkaerqekveekeeeVaereaeLaeakekgdkdkiakrq 98 
                                    k++Ie+++++A+  a+++++r ++ e+  ++ +  + t++ lk+    + +e++e +++   eL++a   +d ++i+ + 
  gi|116754043|ref|YP_843161.1| 484 KEEIEQKVKEAEryAQEDARRREEIETRNQADNLiYTTEKMLKEAGDVATSEQRERIEKAISELRDALSGKDVQEIKSKM 563
                                    578999999998445788889999987766555414566666666677779***************************** PP

                        DUF1090  99 ekLaeakeeLk 109
                                    ekL++a  eL+
  gi|116754043|ref|YP_843161.1| 564 EKLQNAVYELS 574
                                    ******99996 PP

>> DUF45  Protein of unknown function DUF45
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.8   2.7e+03      82     122 ..      77     117 ..      51     128 .. 0.75
   2 ?    8.2   4.1    0.0016       2.3       6      76 ..     467     537 ..     464     590 .. 0.60

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.8
                          DUF45  82 lkreelelavkkeeeeeklrkaleewlrkeakeeleerlak 122
                                      ++++  +  ke ++e++ +++ + +++ a++ l e ++k
  gi|116754043|ref|YP_843161.1|  77 MGTDYKVKVFGKEYTPEEISAHILRKIKQDAEAFLGEKVEK 117
                                    44555666677788888888888888888888888888776 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0016
                          DUF45   6 rvepdgsvevsaPkgvseeeiedfvkkkakwiekklakleer.akeaekelesgesfpllGkkyrlkvekgk 76 
                                      +++++++++aP+++s+eeie+ vk+ ++  ++  ++ ee   +++ ++l  + + + l +   + + +++
  gi|116754043|ref|YP_843161.1| 467 ATKKEQRITITAPHRLSKEEIEQKVKEAERYAQEDARRREEIeTRNQADNLIYTTEKM-LKEAGDVATSEQR 537
                                    5677799*************************99999999974333333333333333.3333333333333 PP

>> MRP-L28  Mitochondrial ribosomal protein L28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   9.3    0.0021       3.2       9     129 ..     469     587 ..     461     596 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0021
                                    XXXXXX....XXXXXXXXXXXXXXXXXXXXXXXXXXXXSXSXXTTSSTTX..XSXXXXXX-..HHHHHHHHHHHHHHHHH CS
                        MRP-L28   9 kkkvdpqvvkrreerakkrlekqirkleksakelkPveelivplksvdsakrrqrkllels..keelerrallekqwary 86 
                                    kk      +       k+++e++++  e+ a+e     e i + + +d+    + k l+ +   + +e+r+ +ek+ ++ 
  gi|116754043|ref|YP_843161.1| 469 KKEQRI-TITAPHRLSKEEIEQKVKEAERYAQEDARRREEIETRNQADNLIYTTEKMLKEAgdVATSEQRERIEKAISEL 547
                                    333333.44556677899999999999999988888777777777777776666666666512357899*********** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TTTCTTCS-XXTT CS
                        MRP-L28  87 rqqekekdeqlirqqleaqeealeeLkkvseeLYeaAvkrdeg 129
                                    r +   kd q+i+  +e +++a+ eL   s  +Y++A ++++g
  gi|116754043|ref|YP_843161.1| 548 RDALSGKDVQEIKSKMEKLQNAVYEL---SAAMYQRAAQSQSG 587
                                    ************************99...7889***9999876 PP

>> Vfa1  AAA-ATPase Vps4-associated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   8.5    0.0018       2.7      66     155 ..     481     583 ..     458     596 .. 0.46

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0018
                           Vfa1  66 keleeeiekvkkeyeekqkkkkekekkk...kekd....kkdkdkkkekekdkkkekekeeekkkelkkaeeelee.... 134
                                    + ++eeie+  ke e+  +++++++++    +++d    +++k  k+  +  +++++e+ e++++el++a + ++     
  gi|116754043|ref|YP_843161.1| 481 RLSKEEIEQKVKEAERYAQEDARRREEIetrNQADnliyTTEKMLKEAGDVATSEQRERIEKAISELRDALSGKDVqeik 560
                                    22444554444444444444433333332222333566644444444444444444444333333333333333223344 PP

                           Vfa1 135 ..keeprvkkykLhkefyqsRle 155
                                       e+ +++ y+L+  +yq   +
  gi|116754043|ref|YP_843161.1| 561 skMEKLQNAVYELSAAMYQRAAQ 583
                                    4444455556*******996544 PP

>> DUF3347  Protein of unknown function (DUF3347)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   6.8     0.003       4.4      22     101 ..     498     588 ..     461     602 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.003
                        DUF3347  22 eeeeeeeeeeekekkkekse.......eeee..........kdeklkevlesYlklkdALvaddakeakkaakkleeklk 84 
                                    ++e+++++e e e+++   +       +  e          ++e+ +++ ++  +l+dAL  +d +e+k++ +kl++++ 
  gi|116754043|ref|YP_843161.1| 498 AQEDARRRE-EIETRN---QadnliytT--EkmlkeagdvaTSEQRERIEKAISELRDALSGKDVQEIKSKMEKLQNAVY 571
                                    111111111.111111...122344431..034555666667777777999999************************** PP

                        DUF3347  85 avdtsklkekekkelke 101
                                    +++++ +++ ++++  +
  gi|116754043|ref|YP_843161.1| 572 ELSAAMYQRAAQSQSGS 588
                                    **999998888876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (615 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1729  (0.0964359); expected 358.6 (0.02)
Passed bias filter:                      814  (0.0454013); 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):              12  [number of targets reported over threshold]
# CPU time: 0.76u 0.28s 00:00:01.04 Elapsed: 00:00:00.47
# Mc/sec: 3934.09
//
Query:       gi|116754044|ref|YP_843162.1|  [L=178]
Description: GrpE protein [Methanosaeta thermophila PT]
Scores for complete 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  135.0   5.5    3.3e-39  134.2   5.5    1.3  1  GrpE         GrpE
  ------ inclusion threshold ------
      0.073   13.0   1.1       0.15   11.9   1.0    1.6  1  GyrB_insert  DNA gyrase B subunit insert domain
      0.087   13.5   3.7       0.18   12.5   3.2    1.8  1  DUF4404      Domain of unknown function (DUF4404)
        0.1   12.7   2.2       0.22   11.6   2.2    1.6  1  Ada3         Histone acetyltransferases subunit 3
       0.18   11.8   1.5          3    7.9   0.5    2.1  2  TnpV         Transposon-encoded protein TnpV


Domain annotation for each model (and alignments):
>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.2   5.5   9.1e-43   3.3e-39      11     166 .]      31     176 ..      22     176 .. 0.97

  Alignments for each domain:
  == domain 1  score: 134.2 bits;  conditional E-value: 9.1e-43
                                    HHHHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC..HHH-HHH CS
                           GrpE  11 edeeeeleeeleelekevkelkekllrllaefenlrkrtekekeeakkfaiekfakdLLpvlDnleralksakeneeeks 90 
                                     de ++l++ele+ ++ ++e  e+llr +ae++n+ kr  +e+ee+++fa e ++k+LL  lD+le a k+         
  gi|116754044|ref|YP_843162.1|  31 VDEVAKLRQELEDVKRIADERLEQLLRCRAELDNVIKRNSREREELARFASEAIIKKLLVFLDSLEQAAKH--------- 101
                                    68999*****************************************************************8......... PP

                                    HHHHHHHHHHHHHHHHHHTT-EE---TTSB--TTTEEEEEEECSSC...TBEEEEEE--EEETTEEEE-EEEEEEE CS
                           GrpE  91 lleGvemtlkqllkiLekhgvekiepkgepFDpnlheavstveddekeegtvvevvqkGYklkdrvlRpAmVkVsk 166
                                      eG +  ++qll+i+ ++g+e+i+++g++FDp +hea+++ve++e+e+g vv+++qkGY+l++rv+R+++V V+k
  gi|116754044|ref|YP_843162.1| 102 -DEGAKALYDQLLDIMRSEGLEPIDAVGKKFDPFVHEAMMQVESQEAEDGIVVQEFQKGYTLHSRVIRTSKVAVAK 176
                                    .4899*********************************************************************97 PP

>> GyrB_insert  DNA gyrase B subunit insert domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.0   4.3e-05      0.15       7      74 ..      42     112 ..      35     127 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.3e-05
                    GyrB_insert   7 edappisgeaLeeLvrqyrkaeaiIkRlsrrydee...vLeallelpeldeedledeaaaeawakalearl 74 
                                    ed + i++e Le+L+r  ++ +++IkR+sr  +e    + ea+++   +  ++le++a+ ++ akal ++l
  gi|116754044|ref|YP_843162.1|  42 EDVKRIADERLEQLLRCRAELDNVIKRNSREREELarfASEAIIKKLLVFLDSLEQAAKHDEGAKALYDQL 112
                                    57789**********************98764432111344444433333334445555444444444444 PP

>> DUF4404  Domain of unknown function (DUF4404)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   3.2   4.9e-05      0.18       4      51 ..      33      78 ..      31     104 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.9e-05
                        DUF4404  4 lLekLheeLeqnesldeetralLeslaedieellaeedaaaeeeelae 51
                                   +++kL++eLe+++++ +e  ++L   + ++ +++++++ + ee  la 
  gi|116754044|ref|YP_843162.1| 33 EVAKLRQELEDVKRIADERLEQLLRCRAELDNVIKRNSREREE--LAR 78
                                   789*********************************9999888..444 PP

>> Ada3  Histone acetyltransferases subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   2.2   6.2e-05      0.22      31      71 ..      45      85 ..      31     101 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.2e-05
                           Ada3 31 gredDevaaeLrrlqaeLrevsliNgarkarLlelvkerma 71
                                   +r  De +++L r++aeL +v ++N++++++L++ ++e + 
  gi|116754044|ref|YP_843162.1| 45 KRIADERLEQLLRCRAELDNVIKRNSREREELARFASEAII 85
                                   56679999***************************999875 PP

>> TnpV  Transposon-encoded protein TnpV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.5   0.00084         3      51      88 ..      36      74 ..      34      89 .. 0.77
   2 ?    3.1   0.0     0.025        90      54     109 ..      96     154 ..      81     156 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00084
                           TnpV 51 kLnehlaeideqaeerlerlvkqlaekegvte.elkakd 88
                                   kL+++l+++ + a erle+l++  ae ++v + + ++++
  gi|116754044|ref|YP_843162.1| 36 KLRQELEDVKRIADERLEQLLRCRAELDNVIKrNSRERE 74
                                   89*******************999998776540445544 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.025
                           TnpV  54 ehlaeideqaeerlerlvkqlaek..egvteelkakdqmewvqrmnnirnraeE.ivlk 109
                                    e+ a+ de a+ ++++l++ + ++  e ++   k+ d+      m+   ++ae+ iv++
  gi|116754044|ref|YP_843162.1|  96 EQAAKHDEGAKALYDQLLDIMRSEglEPIDAVGKKFDPFVHEAMMQVESQEAEDgIVVQ 154
                                    5678999***********99998877888888899998877777766666666535555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       985  (0.0549389); expected 358.6 (0.02)
Passed bias filter:                      576  (0.0321267); 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: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1235.78
//
Query:       gi|116754045|ref|YP_843163.1|  [L=541]
Description: thermosome [Methanosaeta thermophila PT]
Scores for complete 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-174  581.4  17.8   1.5e-174  581.2  17.8    1.0  1  Cpn60_TCP1     TCP-1/cpn60 chaperonin family
  ------ inclusion threshold ------
       0.01   15.6   1.5      0.019   14.8   1.5    1.4  1  KDGP_aldolase  KDGP aldolase
      0.082   13.0   2.1       0.13   12.4   1.2    1.7  2  EIF_2_alpha    Eukaryotic translation initiation factor 2 alp
       0.11   12.5   0.2       0.96    9.4   0.0    2.5  3  AAA_5          AAA domain (dynein-related subfamily)
       0.12   11.7   0.0       0.22   10.8   0.0    1.4  1  tRNA-synt_1b   tRNA synthetases class I (W and Y)


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 !  581.2  17.8  4.2e-178  1.5e-174       1     490 [.      35     523 ..      35     524 .. 0.98

  Alignments for each domain:
  == domain 1  score: 581.2 bits;  conditional E-value: 4.2e-178
                                    HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHHHHH CS
                     Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleeaekl 80 
                                    +a++v+ttlGP+GmdKmlv+++g+vvvTnDGat+l el+iehP+ak++ve+a++qd+evGDGTtt+v+LageLl++ae+l
  gi|116754045|ref|YP_843163.1|  35 VAEAVRTTLGPRGMDKMLVDSNGDVVVTNDGATVLWELDIEHPVAKMIVEVARAQDDEVGDGTTTAVVLAGELLKKAEEL 114
                                    689***************************************************************************** PP

                                    HHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHHHCHCCCSEEC CS
                     Cpn60_TCP1  81 iaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAvklieenekel 160
                                    +++gvhptti++gy++a +ka e+L+++  +++++ ++re L+k+a t++++k +++ +e+l+++vvdA ++ie+n +++
  gi|116754045|ref|YP_843163.1| 115 LDKGVHPTTIVQGYKTAEAKASEILESM--SVEVTRDNREVLRKIAMTAMTGKGIEAMKEKLADIVVDAALAIEDN-GKV 191
                                    ****************************..8888888*********************************999888.799 PP

                                    SCCC.EECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCCHHHHHHHHHHH CS
                     Cpn60_TCP1 161 dlgr.ikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdaeeleklekaeek 239
                                    d+++ +k+vki+ggsl d+elv+G+vl+ + l+p+mp+++ena+++lld +Le +k  t++++++s++e l ++ + e+k
  gi|116754045|ref|YP_843163.1| 192 DVENrVKIVKITGGSLADTELVHGIVLELERLNPEMPRRVENARIALLDATLELKKLGTDAKITISEVEGLRNFKEGEKK 271
                                    99999*************************************************************************** PP

                                    HHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGGCGC-EEEEEEEECC CS
                     Cpn60_TCP1 240 qleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledltpeelGtakkveeek 319
                                     le ++e+++k+g+nvv+cqkgi   a hflak+++la+rrvk +d++ la atGa+++ ++++ ++++lG+a+ ve++k
  gi|116754045|ref|YP_843163.1| 272 VLEAQVEALAKAGANVVLCQKGIGVAASHFLAKHNMLAARRVKDEDMKMLALATGARIIGDPMQASSQDLGHARVVEDRK 351
                                    ******************************************************************************** PP

                                    ETT.CCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHHHHHHHHCCCCTSXCCH CS
                     Cpn60_TCP1 320 igs.ekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatelelakklkeyaksvsgee 398
                                    i++ +++++ie+++++k++ti++ g ++++lde+era++dAl vv  ++  +k+vpGGGa e+e+a++ +eya ++sg+e
  gi|116754045|ref|YP_843163.1| 352 IKKdKHMIFIEGCRDPKAVTIVVHGGSEVFLDEMERALNDALMVVGDVLSYRKIVPGGGAPEVEVAERMREYAATLSGRE 431
                                    *98345666*********************************************************************** PP

                                    HHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEECCCCTXEEEHHHHHHHHHHHHHHHH CS
                     Cpn60_TCP1 399 qlaieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiidlveagvvDplkvkrqalksAteaas 478
                                    qla++afa+A evip+tLaeNaGldpi+ +  lra+h +g+k +g++v +g + d+++ gvv+plkvk qa+ksA+e+a+
  gi|116754045|ref|YP_843163.1| 432 QLAVKAFADAVEVIPRTLAENAGLDPIDAIVALRAKHGEGHKAYGVNVLNGGTADMLDGGVVEPLKVKLQAVKSAAEVAT 511
                                    ******************************************************************************** PP

                                    HHHCEEEEEXXX CS
                     Cpn60_TCP1 479 tiLrideiikak 490
                                    +iLr+d++i ak
  gi|116754045|ref|YP_843163.1| 512 MILRVDDVIAAK 523
                                    *********998 PP

>> KDGP_aldolase  KDGP aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   1.5   5.3e-06     0.019      70     198 ..      79     203 ..      75     214 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.3e-06
                                    HHHHHHHCCCH--SEE--BGGGHHHHHHHCTTS-SEEEEEEBE-SSTTEEE---SCCHHHSS--EEEHHHHHHHHHHCT. CS
                  KDGP_aldolase  70 skmvaeiskklqpqhinqvftgvgltrallgqeetlinaLvsPtGkvGlvkistGpessqkekaivsvetaiallkdmg. 148
                                    +km+ e+++   ++  + + t+v l+  ll+++e l++  v+Pt       i  G ++++++++++    ++++++d   
  gi|116754045|ref|YP_843163.1|  79 AKMIVEVARAQDDEVGDGTTTAVVLAGELLKKAEELLDKGVHPTT------IVQGYKTAEAKASEILESMSVEVTRDNRe 152
                                    578888888877777777778888888888999999999999995......55677777777777877888888887651 PP

                                    .--EEEE---TTTTTHHHHHHHHHHHHHCT-EEEEBSS--TTTHHHHHHHH CS
                  KDGP_aldolase 149 .gssvkffpmeGlkrleelaavakaaakkgltlePtGGidldnfeeivqia 198
                                      + +   +m G+  +   + +a + +++ l++e  G +d++n  +iv+i+
  gi|116754045|ref|YP_843163.1| 153 vLRKIAMTAMTGKGIEAMKEKLADIVVDAALAIEDNGKVDVENRVKIVKIT 203
                                    14677788999999999999****************************996 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 ?   -3.8   0.0       3.7   1.3e+04      27      48 ..      66      87 ..      60      89 .. 0.77
   2 ?   12.4   1.2   3.6e-05      0.13      23      98 ..     118     198 ..      98     203 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 3.7
                                   THHHHHTTS-TTTHHHHHHCTH CS
                    EIF_2_alpha 27 eevldkleipeeveeaLveiik 48
                                    +vl +l+i+  v++++ve ++
  gi|116754045|ref|YP_843163.1| 66 ATVLWELDIEHPVAKMIVEVAR 87
                                   4488899999999999999887 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 3.6e-05
                                    HHSTTHHHHHTTS-TTTHHHHHHCTHHHHHHT-EEEEEEEEEEE-STTHHHHHHHHHH.....HHST.S..TTSSSEEEE CS
                    EIF_2_alpha  23 aitdeevldkleipeeveeaLveiikkklkpqkvkiradieltcftkdGveaIkeaLk.....ageeasneeeveeeeev 97 
                                     ++ +++++ ++  e+ +++++e ++ +++  + ++  +i +t +t +G+ea ke L      a+ + +++ +v++e++v
  gi|116754045|ref|YP_843163.1| 118 GVHPTTIVQGYKTAEAKASEILESMSVEVTRDNREVLRKIAMTAMTGKGIEAMKEKLAdivvdAALAIEDNGKVDVENRV 197
                                    444455666699999999***************************************95555433333333334444444 PP

                                    E CS
                    EIF_2_alpha  98 k 98 
                                    k
  gi|116754045|ref|YP_843163.1| 198 K 198
                                    4 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 ?   -0.6   0.0      0.35   1.2e+03      25      66 ..     120     165 ..     106     191 .. 0.69
   2 ?   -2.8   0.0       1.6   5.6e+03      34      64 ..     252     282 ..     245     316 .. 0.63
   3 ?    9.4   0.0   0.00027      0.96      63     107 ..     374     418 ..     334     446 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.35
                                    --EEEEE--T..T--HHHHH--B--...........--------G- CS
                          AAA_5  25 reveyvqltr..dtteedlkgrreik..ngttslvdsplvraareg 66 
                                     ++++vq+++    ++++++ +++++   ++++   +++++a++ +
  gi|116754045|ref|YP_843163.1| 120 HPTTIVQGYKtaEAKASEILESMSVEvtRDNREVLRKIAMTAMTGK 165
                                    5566666654114556888888888888777777777777788743 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.6
                                    TT--HHHHH--B--.........-------- CS
                          AAA_5  34 rdtteedlkgrreikngttslvdsplvraar 64 
                                    +++t +++ g r++k+g+++  +  +   a+
  gi|116754045|ref|YP_843163.1| 252 AKITISEVEGLRNFKEGEKKVLEAQVEALAK 282
                                    5678888888888875555544444333333 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.00027
                                    --G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE--- CS
                          AAA_5  63 aregeilvlDEveraesevlnsLlslleerrllleeggelvkakn 107
                                    +  g+ ++lDE era  ++l+++  +l+ r++ +  g  +v +++
  gi|116754045|ref|YP_843163.1| 374 VHGGSEVFLDEMERALNDALMVVGDVLSYRKIVPGGGAPEVEVAE 418
                                    3378889**************************888888888876 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 ?   10.8   0.0   6.2e-05      0.22     160     274 ..      25     132 ..      16     147 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6.2e-05
                                    GHHHHHHHHHHHHHHHHHSTTSS-EEEEET-BBSTTSSSBTTCETTCGC-BTTCCHHHHHHHHHHCHCSTTCSHHHHHHH CS
                   tRNA-synt_1b 160 QkqnielgrdlarrfnkkevfkkpegltvplltgldGekKmSKSagnsaIfLddekesvkkkiqkavtdsdeevekllkl 239
                                    Q++ni+++r +a++++ +         + ++l++++G       +g ++++ +d +  v k+i  + + +d+ev+    +
  gi|116754045|ref|YP_843163.1|  25 QHKNITAARAVAEAVRTT----LGPRGMDKMLVDSNGD-VVVTNDGATVLWELDIEHPVAKMIVEVARAQDDEVGDGTTT 99 
                                    99*************999....55555789********.888888889******************************** PP

                                    HHTHHHCHHHHHHHHCCSEEESSHHHHHHHHHCCC CS
                   tRNA-synt_1b 240 ktelsnelierleavsgkkpkreaeellaeevtkl 274
                                     ++l  el+++ e++++k+      ++++ ++t +
  gi|116754045|ref|YP_843163.1| 100 AVVLAGELLKKAEELLDKGV--HPTTIVQGYKTAE 132
                                    ***************99998..4455555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (541 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); 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: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 3738.31
//
Query:       gi|116754046|ref|YP_843164.1|  [L=55]
Description: hypothetical protein Mthe_0734 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00026   20.9   1.3    0.00066   19.7   1.4    1.6  2  zinc_ribbon_6  Zinc-ribbon
  ------ inclusion threshold ------
      0.018   15.3   1.4      0.024   14.9   1.4    1.2  1  LIM            LIM domain
      0.044   13.7   2.1        2.9    7.9   0.2    2.2  2  zf-dskA_traR   Prokaryotic dksA/traR C4-type zinc finger


Domain annotation for each model (and alignments):
>> zinc_ribbon_6  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   1.4   1.1e-07   0.00066      26      53 ..      15      45 ..      10      48 .. 0.82
   2 ?    2.1   0.1     0.033     2e+02      30      38 ..      40      48 ..      35      52 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.1e-07
                  zinc_ribbon_6 26 kkvkilCnDCekksevkfhvlglk...CkeC 53
                                   ++ +++C DC+k+++v+f+  g +   CkeC
  gi|116754046|ref|YP_843164.1| 15 EMHDVICSDCGKQTQVPFKPDGSRpvyCKEC 45
                                   6789***************999763336666 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.033
                  zinc_ribbon_6 30 ilCnDCekk 38
                                   ++C+ C +k
  gi|116754046|ref|YP_843164.1| 40 VYCKECYQK 48
                                   899999887 PP

>> LIM  LIM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   1.4   3.9e-06     0.024      28      57 ..      20      49 ..      16      50 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.9e-06
                                   B-TTT-SB-CTT.CEEETT.E.EEEHHHHHHH CS
                            LIM 28 tCsdCqkeLkegsfyekdg.k.lyCkkdylkk 57
                                   +CsdC+k+ +   ++  dg + +yCk++y+k 
  gi|116754046|ref|YP_843164.1| 20 ICSDCGKQTQV--PFKPDGsRpVYCKECYQKH 49
                                   7******8655..5999995369******985 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 ?    5.8   0.1    0.0022        13       5      11 ..      20      26 ..      17      29 .. 0.85
   2 ?    7.9   0.2   0.00049       2.9      25      34 ..      40      49 ..      37      55 .] 0.85

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0022
                   zf-dskA_traR  5 sCeeCGE 11
                                   +C++CG+
  gi|116754046|ref|YP_843164.1| 20 ICSDCGK 26
                                   4*****7 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00049
                   zf-dskA_traR 25 rlCveCqeka 34
                                   ++C+eC +k+
  gi|116754046|ref|YP_843164.1| 40 VYCKECYQKH 49
                                   5899999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); 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: 0.33u 0.23s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 437.26
//
Query:       gi|116754047|ref|YP_843165.1|  [L=417]
Description: hypothetical protein Mthe_0735 [Methanosaeta thermophila PT]
Scores for complete sequence (score 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   12.5   0.3       0.36   10.8   0.3    1.9  1  DUF4366   Domain of unknown function (DUF4366)


Domain annotation for each model (and alignments):
>> DUF4366  Domain of unknown function (DUF4366)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.3     2e-05      0.36      79     137 ..     214     272 ..     136     278 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 2e-05
                        DUF4366  79 ctekcaagkvntdcpveepepekeaepeepeeepekksn.nglllvvlavali.gg.gaayy 137
                                    ++++  ag+v++  p + pe+   a+   +e e e ++  ++ + ++la +li +g ga+++
  gi|116754047|ref|YP_843165.1| 214 EEKEDRAGEVQQPEPSAAPETRGGAK---EEIEAERRGYtRIQIGIILAALLIvAGiGAFFM 272
                                    23334455555555444444444433...233333332243333333333333033355554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       728  (0.0406046); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); 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: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3078.33
//
Query:       gi|116754048|ref|YP_843166.1|  [L=341]
Description: protein of unknown function Met10 [Methanosaeta thermophila PT]
Scores for 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-60  202.0   0.0    1.1e-59  201.5   0.0    1.2  1  Met_10           Met-10+ like-protein
    3.4e-09   36.4   0.1    9.2e-09   35.1   0.1    1.7  1  Trm5_N           tRNA methyltransferase 5 N-terminal domain
    0.00033   20.3   0.0    0.00057   19.5   0.0    1.4  1  MTS              Methyltransferase small domain
     0.0038   17.9   0.0     0.0062   17.2   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
  ------ inclusion threshold ------
      0.022   14.3   0.0      0.033   13.8   0.0    1.2  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
       0.07   13.1   0.0       0.13   12.2   0.0    1.4  1  Methyltransf_18  Methyltransferase domain
       0.15   11.2   0.0       0.21   10.7   0.0    1.1  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera


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 !  201.5   0.0   4.4e-63   1.1e-59       2     199 .]      93     288 ..      92     288 .. 0.97

  Alignments for each domain:
  == domain 1  score: 201.5 bits;  conditional E-value: 4.4e-63
                                    EEEEETTEEEEEB-TTSSHHHHHHHHHHHHHS.S-SCEEEE-S-SBTTTTB--EEEEEES-.SEEEEEETTEEEEEETTT CS
                         Met_10   2 kfeiiGdvvilnlreelkeykkvigevildkt.kvktvlrkvsevegefRtfelevlaGsdstetihkEngcrfklDvsk 80 
                                    ++ i Gd++i++++  l+e+k++ig+++l    ++++vl +++ v+g+fR++  ev+aG    etih+Eng+ fklD  k
  gi|116754048|ref|YP_843166.1|  93 GWFILGDTIIVRIHPALSEHKQIIGNALLRLYpRCRCVLADHG-VRGQFREPCREVIAGTP-GETIHRENGVLFKLDPMK 170
                                    68899***************************9******9876.5**************88.8***************** PP

                                    S---GGGHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-G CS
                         Met_10  81 vyfsskleaErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDg 160
                                    ++fs+++ +Er+r+a+l  ++evVvd+fAGiG+f++p+a++s++ r+ ai++nP + +yl eni+lN+ve++v+p+l+D+
  gi|116754048|ref|YP_843166.1| 171 IMFSQGNLKERMRMASLG-KDEVVVDMFAGIGYFSLPMAVHSRPYRITAIEINPVAHRYLVENIRLNRVEEIVEPVLGDC 249
                                    **************9975.679********************************************************** PP

                                    GG---TT-EEEEEE--TTTGGGGHHHHHHHEEEEEEEEE CS
                         Met_10 161 revireqladrvvmnlpksaieFldkvlaalkdggvihy 199
                                    + +++e  adrv+m+++  +  +l k ++al++gg+ hy
  gi|116754048|ref|YP_843166.1| 250 ALLTPEGEADRVIMGMVGITDRYLRKGIEALRHGGILHY 288
                                    **************************************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 !   35.1   0.1   3.6e-12   9.2e-09       1      43 [.      12      54 ..      12      58 .. 0.93

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 3.6e-12
                                   EEEEEGGGHHHHHHHHHHTT-B-TTS--EEETTEEEEEB-S-- CS
                         Trm5_N  1 cikVpkkegEkvRkkLlekglLdrnyKIksdddylyIPvkeep 43
                                   ++ V ++e+ +v+  Lle glLd+++KI + ++ ++IPv +e 
  gi|116754048|ref|YP_843166.1| 12 AVVVRRSEAANVIGMLLEGGLLDKRRKIVRRGGMVEIPVLKER 54
                                   68899**********************************9985 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   2.2e-07   0.00057      31     103 ..     189     263 ..     172     294 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.2e-07
                                    TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTSTTS-EEEEEE CS
                            MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvleeveekkfdlivs 103
                                    +++ v+D+ +G+G+ ++ +a +s   ++t+++++  A +   en++ n++e  ve v  d+   ++e++ d +++
  gi|116754048|ref|YP_843166.1| 189 KDEVVVDMFAGIGYFSLPMAVHSRPYRITAIEINPVAHRYLVENIRLNRVEeiVEPVLGDCALLTPEGEADRVIM 263
                                    45679**********************************************99999999*999999999999986 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.4e-06    0.0062       1      97 []     193     284 ..     193     284 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.4e-06
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEESTGGGSS CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssgalhhls 78 
                                    v+d+ +G G ++l +a +   +++t+++i++ + ++  e+++ +++   ve v gd+  l  ++g+ D v++ g++ + +
  gi|116754048|ref|YP_843166.1| 193 VVDMFAGIGYFSLPMAVHSRPYRITAIEINPVAHRYLVENIRLNRVeeIVEPVLGDCALLT-PEGEADRVIM-GMVGI-T 269
                                    899*************99768********************99988989999999998776.778******9.55443.3 PP

                                    HHHHHHHHHHHHHHEEEEE CS
                Methyltransf_25  79 dedlekalkeiarvLkpgG 97 
                                    d    ++l++  ++L+ gG
  gi|116754048|ref|YP_843166.1| 270 D----RYLRKGIEALRHGG 284
                                    2....55666666666665 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   1.3e-05     0.033       2      63 ..     191     254 ..     190     270 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.3e-05
                Methyltransf_15   2 rvilDlfsGaGGnviqfalv...fekviaieinleklacaqhNaevYgvsdkitlvlgdvfella 63 
                                    +v++D+f+G G  +  +a +   + ++ aiein+       +N ++  v++ + +vlgd+  l+ 
  gi|116754048|ref|YP_843166.1| 191 EVVVDMFAGIGYFSLPMAVHsrpY-RITAIEINPVAHRYLVENIRLNRVEEIVEPVLGDCALLTP 254
                                    689***************987755.9**********************************86655 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.9e-05      0.13      13      94 ..     188     268 ..     178     281 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.9e-05
                Methyltransf_18  13 ekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklkeeevdtvviaGmG 92 
                                     k+++v+D  +  gy ++ ++ +++  +++a++in+ + +   eni+ +++e+ +e +l+d      e+e+d v i+Gm 
  gi|116754048|ref|YP_843166.1| 188 GKDEVVVDMFAGIGYFSLPMAVHSRPYRITAIEINPVAHRYLVENIRLNRVEEIVEPVLGDCALLTPEGEADRV-IMGMV 266
                                    4578999999999*******99***************************************9877777888875.67887 PP

                Methyltransf_18  93 ge 94 
                                    g 
  gi|116754048|ref|YP_843166.1| 267 GI 268
                                    65 PP

>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0     8e-05      0.21      52     149 ..     192     286 ..     169     288 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 8e-05
                                    EEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHHHHTT--GGEEEE-S-HHHHHC--SS-EEEEEE--SS- CS
                            TRM  52 kvldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeNvklneveeivvineddAnvllaekkkrfdviDlDPfGs 131
                                     v+d +++ G  ++  a+  +   ++ a +i++ A   + eN++ln veeiv++  +d ++l    + + d + +   G 
  gi|116754048|ref|YP_843166.1| 192 VVVDMFAGIGYFSLPMAVH-SRPYRITAIEINPVAHRYLVENIRLNRVEEIVEPVLGDCALLT--PEGEADRVIMGMVGI 268
                                    5788888999999999988.77789999****************************9987665..444445555666666 PP

                                    -GGGHHHHHHHEEEEEEE CS
                            TRM 132 papfldsavqsvkekglL 149
                                    +  +l + +++++++g+L
  gi|116754048|ref|YP_843166.1| 269 TDRYLRKGIEALRHGGIL 286
                                    666666666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       225  (0.0125495); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 2516.42
//
Query:       gi|116754049|ref|YP_843167.1|  [L=244]
Description: hypothetical protein Mthe_0737 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-08   34.4   0.0    3.9e-08   33.6   0.0    1.4  1  Cas_Cas4  Domain of unknown function DUF83
    1.5e-05   25.1   0.0    0.00071   19.6   0.0    2.2  2  PDDEXK_1  PD-(D/E)XK nuclease superfamily
    0.00072   19.0   0.0     0.0021   17.5   0.1    1.6  2  Csa1      CRISPR-associated exonuclease Csa1


Domain annotation for each model (and alignments):
>> Cas_Cas4  Domain of unknown function DUF83
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.0   6.5e-12   3.9e-08      81     160 ..     155     233 ..     134     235 .. 0.90

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 6.5e-12
                       Cas_Cas4  81 aaklQllyYlllLe.kkgveikeGvleypkekkreevelteelreelekaikeieeiissekppkvkkkkiCkkCayael 159
                                     +++Ql  Y++lLe + gve+++G +ey+   +++++++   +r+++  + ++++ei + e +p v + ++C++C++a +
  gi|116754049|ref|YP_843167.1| 155 RDRIQLAGYAMLLEeRFGVEVSTGQVEYVRDGEMRRIRIRSLDRSRALWVRDRVREIRDGE-MPDV-RGERCDSCEMAGI 232
                                    569***********999****************************************9995.5554.5678*******99 PP

                       Cas_Cas4 160 C 160
                                    C
  gi|116754049|ref|YP_843167.1| 233 C 233
                                    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 ?    3.3   0.1     0.011        65      97     141 ..      75     120 ..      33     127 .. 0.77
   2 !   19.6   0.0   1.2e-07   0.00071     163     254 ..     153     233 ..     143     234 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.011
                       PDDEXK_1  97 leklverlaeeleakrg.frpvalelefggekvrLkGriDrvddke 141
                                    +  + + +++    +r  ++p  +e+e  +e++ L G++Dr+ ++e
  gi|116754049|ref|YP_843167.1|  75 IDGMRDSISRIASVPRDlIKPCDIEVELRSERLGLSGILDRLVRPE 120
                                    5555556666666677788888888877777888*******98443 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 1.2e-07
                       PDDEXK_1 163 elkeglQlllYllalaegeelkeegepagalylrleepkvkdeevvkkmalteeeleallqeleelaeeilagefparps 242
                                    + ++++Ql+ Y+++l+e    + e + +++ y+r         ++++++   + + ++ + +++++++ei++ge+p   +
  gi|116754049|ref|YP_843167.1| 153 WRRDRIQLAGYAMLLEER--FGVEVSTGQVEYVRD--------GEMRRIRIRSLD-RSRALWVRDRVREIRDGEMPDVRG 221
                                    456788***********9..555555999999887........344444222222.3445699999************** PP

                       PDDEXK_1 243 kkCeyCpyksvC 254
                                    ++C++C+++ +C
  gi|116754049|ref|YP_843167.1| 222 ERCDSCEMAGIC 233
                                    ************ PP

>> Csa1  CRISPR-associated exonuclease Csa1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.19   1.1e+03     113     179 ..      38     110 ..      23     115 .. 0.61
   2 !   17.5   0.1   3.6e-07    0.0021     204     289 ..     154     233 ..     135     236 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.19
                           Csa1 113 vadeivalledviekakelykylasrvs.aelsevrskfekatedsvaarv.....iPvlvefkvdGsllGls 179
                                    +  ++++++ d++ +  ++ + la+  +  e + vrs   ++++ s +a v      P   e+++    lGls
  gi|116754049|ref|YP_843167.1|  38 RHLALYSAPDDLRGDMSKVVRDLATVHRiPEEDVVRSIDGMRDSISRIASVprdliKPCDIEVELRSERLGLS 110
                                    4456777788888776666666665544145566677766666666555544444446666666666666666 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 3.6e-07
                           Csa1 204 eehelalaGYalalEsqleiPvDfGvlisvtvngevklkaelvaisdslRkefleeRdraidivekesDPGlakkCsskC 283
                                    ++ ++ laGYa+ lE   ++ v  G + +v+  + ++     ++i    R++ l +Rdr+ +i  +++ P +  +  ++C
  gi|116754049|ref|YP_843167.1| 154 RRDRIQLAGYAMLLEERFGVEVSTGQVEYVRDGEMRR-----IRIRSLDRSRALWVRDRVREI-RDGEMPDVRGERCDSC 227
                                    45599********************999987554445.....455555688888889999886.5566677765544578 PP

                           Csa1 284 lflevC 289
                                     +  +C
  gi|116754049|ref|YP_843167.1| 228 EMAGIC 233
                                    888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); 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 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1835.97
//
Query:       gi|116754050|ref|YP_843168.1|  [L=408]
Description: hypothetical protein Mthe_0738 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); 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):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2900.65
//
Query:       gi|116754051|ref|YP_843169.1|  [L=133]
Description: hypothetical protein Mthe_0739 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); 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: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 992.68
//
Query:       gi|116754052|ref|YP_843170.1|  [L=136]
Description: hypothetical protein Mthe_0740 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1044.86
//
Query:       gi|116754053|ref|YP_843171.1|  [L=129]
Description: NifU domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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  163.6   0.1    2.5e-48  163.5   0.1    1.0  1  NifU_N    NifU-like N terminal domain


Domain annotation for each model (and alignments):
>> NifU_N  NifU-like N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.5   0.1   1.4e-52   2.5e-48       2     128 ..       7     128 ..       6     129 .] 0.98

  Alignments for each domain:
  == domain 1  score: 163.5 bits;  conditional E-value: 1.4e-52
                                    SCHHHHHHHHSSSSBSS-TTSSS--EEEEEEETTTTEEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHHHHHTTSB CS
                         NifU_N   2 ysdkvldhyknPrnvGvleeedakvgvgevgapacGDavrLqikvdeetdriedakFktfGCgsaiAssslltelvkgkt 81 
                                    ys+kv++h+ nPrnvGv+++ d   g g+vg+p+cGD + + ikv +  ++ied+kF+tfGCg+aiA+ss++te+  gk+
  gi|116754053|ref|YP_843171.1|   7 YSKKVMEHFMNPRNVGVIDDPD---GYGKVGNPVCGDLMEIFIKVGD--EKIEDIKFRTFGCGAAIATSSMITEMARGKS 81 
                                    9*********************...8********************9..5****************************** PP

                                    HHHHCCCCHHHHHHHHTCSCSSSCHCSCHHHHHHHHHHHHHHHHCTH CS
                         NifU_N  82 leealkitnkeiaeelgglpkeklhcsvlaedalkaavkkYkakkke 128
                                    leea++it++++a++l glp++k+hcs+la+dal+aa+++Y +kk++
  gi|116754053|ref|YP_843171.1|  82 LEEAMRITRNDVADALDGLPPQKMHCSNLAADALHAAINDYLSKKQK 128
                                    ******************************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1009.94
//
Query:       gi|116754054|ref|YP_843172.1|  [L=94]
Description: non-histone chromosomal MC1 [Methanosaeta thermophila PT]
Scores for complete 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-39  133.0   0.3    4.8e-39  132.5   0.3    1.1  1  MC1       Non-histone chromosomal protein MC1


Domain annotation for each model (and alignments):
>> MC1  Non-histone chromosomal protein MC1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.5   0.3   2.7e-43   4.8e-39       1      96 []       7      92 ..       7      92 .. 0.99

  Alignments for each domain:
  == domain 1  score: 132.5 bits;  conditional E-value: 2.7e-43
                            MC1  1 dkrnfalrdedGeeisvfsGkqPrqaaLkaarrletadseeeakeeeirLrekGtkkvhiyegkaeeeeaPddkpdWledki 82
                                   +krnfalrd++G+ei+vfsGkqPrqaaLkaa+r+ t+          irLre+Gtkkvhi++g+++++ +P ++p+W++d i
  gi|116754054|ref|YP_843172.1|  7 EKRNFALRDAEGNEIGVFSGKQPRQAALKAANRGFTD----------IRLRERGTKKVHIFKGWRTQVPKPPNAPAWMPDMI 78
                                   79**********************************9..........*********************************** PP

                            MC1 83 tkanvskqgiekle 96
                                   +k+nv+k giekl+
  gi|116754054|ref|YP_843172.1| 79 WKPNVKKIGIEKLD 92
                                   ************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); 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: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 689.36
//
Query:       gi|116754055|ref|YP_843173.1|  [L=165]
Description: rubrerythrin [Methanosaeta thermophila PT]
Scores for 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-25   88.5  13.6      5e-24   85.2  13.6    2.0  1  Rubrerythrin     Rubrerythrin
     0.0041   17.1   6.1     0.0073   16.2   6.1    1.5  1  Ferritin         Ferritin-like domain
  ------ inclusion threshold ------
      0.045   13.4   2.8       0.95    9.2   0.2    2.3  2  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
      0.053   13.5   0.5      0.084   12.9   0.5    1.6  1  HypA             Hydrogenase/urease nickel incorporation, met
      0.075   13.1   0.4       0.11   12.5   0.4    1.3  1  DZR              Double zinc ribbon
       0.15   12.2   0.8        0.3   11.3   0.7    1.6  1  Acetone_carb_G   Acetone carboxylase gamma subunit
       0.22   11.6   7.5        2.6    8.1   2.1    2.6  2  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger doma
       0.37   10.3   4.1        2.7    7.5   0.5    2.2  2  zf-ribbon_3      zinc-ribbon domain
       0.42   11.2   1.4         18    6.0   0.1    2.8  2  zf-C2H2          Zinc finger, C2H2 type
       0.54   10.6   3.0        3.6    8.0   0.2    2.4  2  zf-Di19          Drought induced 19 protein (Di19), zinc-bind
       0.87    9.9   5.6       0.66   10.3   1.1    2.2  2  DUF2524          Protein of unknown function (DUF2524)
        1.9    8.9   5.3         16    6.0   0.2    2.8  3  Lar_restr_allev  Restriction alleviation protein Lar
        2.6    9.0   8.4        1.3   10.0   2.7    2.3  2  ERp29            Endoplasmic reticulum protein ERp29, C-termi
        5.7    6.9  12.0       0.76    9.7   1.0    3.4  3  Rad50_zn_hook    Rad50 zinc hook motif


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 !   85.2  13.6   3.9e-27     5e-24       1     136 [.       6     120 ..       6     121 .. 0.98

  Alignments for each domain:
  == domain 1  score: 85.2 bits;  conditional E-value: 3.9e-27
                                    HHHHHHHHHHHHHHHHHHHHHHCHH.TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS-------TTG CS
                   Rubrerythrin   1 eiLekAiagEssarrlYkelaekak.egypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakpkfl 79 
                                    e L++A+agEs+a r+Y ++aeka+ +gypq+a+lF++ Ae+E  Ha ++ ++l++++ ++e                  
  gi|116754055|ref|YP_843173.1|   6 EYLKEAFAGESQANRRYLAFAEKAEkDGYPQVARLFRAAAEAETVHAMNHLRALNAIRSTKE------------------ 67 
                                    78******************************************************999999.................. PP

                                    GHHHHHHHHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Rubrerythrin  80 ttaknLeeaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerlrkl 136
                                        nLeea++g+++e ++my+++ + a++eg++ a+ +f+++ e Ek H+e+++++
  gi|116754055|ref|YP_843173.1|  68 ----NLEEAVAGETHEFKDMYPEMLKTARDEGKKAAEISFRYANEVEKVHAELYKEA 120
                                    ....**************************************************986 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   6.1   5.7e-06    0.0073       2     107 ..       6     110 ..       5     131 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.7e-06
                                    HHHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHH.C-SSSS.CS CS
                       Ferritin   2 kaLneqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalGgtpvltraelee.ieapke.fg 79 
                                    + L e++a e +a   yla+a  ++  g++++a +f+  ae e+ ha+  +  ++a+      t+  lee ++++ + f+
  gi|116754055|ref|YP_843173.1|   6 EYLKEAFAGESQANRRYLAFAEKAEKDGYPQVARLFRAAAEAETVHAMNHLRALNAIRS----TKENLEEaVAGETHeFK 81 
                                    6799*******************************************998888888876....45555555544445666 PP

                                    .SHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Ferritin  80 .sveevleaalehekkvteslrelielae 107
                                       +e+l+ a +  kk+ e   + ++ +e
  gi|116754055|ref|YP_843173.1|  82 dMYPEMLKTARDEGKKAAEISFRYANEVE 110
                                    67788888888887777765544444444 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 ?    4.4   0.3     0.023        30       5      11 ..     134     140 ..     134     142 .. 0.90
   2 ?    9.2   0.2   0.00074      0.95       4      18 ..     148     164 ..     145     165 .] 0.77

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.023
                        zf-RRN7   5 ppCgvCg 11 
                                    ++C+vCg
  gi|116754055|ref|YP_843173.1| 134 FVCPVCG 140
                                    59****9 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00074
                        zf-RRN7   4 gppCgvCgc..rsftld 18 
                                     ++C++Cg+   sf+ +
  gi|116754055|ref|YP_843173.1| 148 PERCPICGAkgSSFRRI 164
                                    589******77788774 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 ?   12.9   0.5   6.6e-05     0.084      60      96 ..     122     158 ..      45     163 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.6e-05
                                    -EEE.EEEE--EEEETTTS-EEECHHHHHS-TTTSSS- CS
                           HypA  60 aeLe.ieevpvkvrCreCgkefeleekalrCpkCgsad 96 
                                    a+Le  +e+   + C +Cg ++  e   +rCp Cg+++
  gi|116754055|ref|YP_843173.1| 122 AKLEeSKEEYPYFVCPVCGMTVGREPP-ERCPICGAKG 158
                                    3444355667789******99997753.69*****986 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.4     9e-05      0.11      14      39 ..     135     159 ..     126     164 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9e-05
                            DZR  14 fCseCgtklkavaaedrCpsCgekvd 39 
                                    +C+ Cg ++   + ++rCp Cg+k +
  gi|116754055|ref|YP_843173.1| 135 VCPVCGMTVG-REPPERCPICGAKGS 159
                                    7********6.5669*******9855 PP

>> Acetone_carb_G  Acetone carboxylase gamma subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.7   0.00023       0.3      36      90 ..      88     146 ..      69     155 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00023
                                    EEETTS-GGGGSEEEEE-CHH...CCCTTSSTTTS-.-TTT-EEEEEE-TTT--EEEEE CS
                 Acetone_carb_G  36 fgdarenyKlkalvyvRdtee...kleeiyekllap.dpewqrirEyycPecgtllevE 90 
                                    +  ar++ K+ a +  R ++e    ++e+y++ la  +++  ++  ++cP cg  +  E
  gi|116754055|ref|YP_843173.1|  88 LKTARDEGKKAAEISFRYANEvekVHAELYKEALAKlEESKEEYPYFVCPVCGMTVGRE 146
                                    56788888999999888665422279999*988876266677888899*****988776 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   2.1     0.002       2.6       2      13 ..     136     147 ..     135     149 .. 0.89
   2 ?    5.9   0.3      0.01        13       1       7 [.     150     156 ..     150     157 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.002
                 DNA_ligase_ZBD   2 CPvCGsavvRee 13 
                                    CPvCG  v Re+
  gi|116754055|ref|YP_843173.1| 136 CPVCGMTVGREP 147
                                    ******999985 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.01
                 DNA_ligase_ZBD   1 hCPvCGs 7  
                                    +CP+CG+
  gi|116754055|ref|YP_843173.1| 150 RCPICGA 156
                                    5*****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 ?    3.9   0.2     0.029        38       4       9 ..     135     140 ..     132     143 .. 0.72
   2 ?    7.5   0.5    0.0021       2.7       4      11 ..     150     157 ..     149     160 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.029
                    zf-ribbon_3   4 rCPnCG 9  
                                     CP CG
  gi|116754055|ref|YP_843173.1| 135 VCPVCG 140
                                    477777 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0021
                    zf-ribbon_3   4 rCPnCGap 11 
                                    rCP CGa+
  gi|116754055|ref|YP_843173.1| 150 RCPICGAK 157
                                    89999985 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1     0.014        18       1       9 [.     134     142 ..     134     146 .. 0.86
   2 ?    3.3   0.1       0.1   1.3e+02       2       8 ..     150     156 ..     150     164 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.014
                                    EEETTTTEE CS
                        zf-C2H2   1 ykCpdCgks 9  
                                    ++Cp+Cg++
  gi|116754055|ref|YP_843173.1| 134 FVCPVCGMT 142
                                    89*****87 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.1
                                    EETTTTE CS
                        zf-C2H2   2 kCpdCgk 8  
                                    +Cp+Cg 
  gi|116754055|ref|YP_843173.1| 150 RCPICGA 156
                                    7****94 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 ?    8.0   0.2    0.0028       3.6      30      43 ..     132     145 ..     124     149 .. 0.78
   2 ?    2.8   0.2      0.11   1.4e+02      34      40 ..     151     157 ..     145     163 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0028
                        zf-Di19  30 kevvCPvCaekvtk 43 
                                     + vCPvC  +v++
  gi|116754055|ref|YP_843173.1| 132 PYFVCPVCGMTVGR 145
                                    5789****988875 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.11
                        zf-Di19  34 CPvCaek 40 
                                    CP+C +k
  gi|116754055|ref|YP_843173.1| 151 CPICGAK 157
                                    7777654 PP

>> DUF2524  Protein of unknown function (DUF2524)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.2      0.23     3e+02      20      56 ..      36      72 ..      16      84 .. 0.60
   2 ?   10.3   1.1   0.00052      0.66      19      52 ..      97     130 ..      80     135 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.23
                        DUF2524 20 eaeeqfeeakrqehyndeeYteAqlkLEeavneLekl 56
                                   ++   f+ a   e   ++++  A++ +  + ++Le+ 
  gi|116754055|ref|YP_843173.1| 36 QVARLFRAAAEAETVHAMNHLRALNAIRSTKENLEEA 72
                                   5555566666666666666666666666655555554 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00052
                        DUF2524  19 eeaeeqfeeakrqehyndeeYteAqlkLEeavne 52 
                                    + ae  f+ a+ +e+  +e Y+eA+ kLEe  +e
  gi|116754055|ref|YP_843173.1|  97 KAAEISFRYANEVEKVHAELYKEALAKLEESKEE 130
                                    456668***********************98776 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       8.3   1.1e+04      48      59 ..      43      54 ..      40      55 .. 0.72
   2 ?    6.0   0.2     0.012        16      15      36 ..     124     141 ..      90     150 .. 0.72
   3 ?    5.3   0.2     0.019        25       5      17 ..     150     162 ..     146     165 .] 0.82

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 8.3
                Lar_restr_allev 48 aeaekeaieaWN 59
                                   a+ae+e+++a N
  gi|116754055|ref|YP_843173.1| 43 AAAEAETVHAMN 54
                                   678888887766 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.012
                Lar_restr_allev  15 lersqrvvaeigqcvyCadCga 36 
                                    le+s+  +     ++ C  Cg+
  gi|116754055|ref|YP_843173.1| 124 LEESKEEYP----YFVCPVCGM 141
                                    333333333....999999999 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.019
                Lar_restr_allev   5 pCPfCggravler 17 
                                     CP Cg ++  +r
  gi|116754055|ref|YP_843173.1| 150 RCPICGAKGSSFR 162
                                    6*****9988776 PP

>> ERp29  Endoplasmic reticulum protein ERp29, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.4      0.27   3.4e+02      30      59 ..       6      34 ..       1      74 [. 0.65
   2 ?   10.0   2.7     0.001       1.3       1      61 [.      75     131 ..      67     133 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.27
                          ERp29 30 kaaeklksekekkaaeyYvkvmekiaekge 59
                                   +++++   + e++a + Y+  +ek+ ++g+
  gi|116754055|ref|YP_843173.1|  6 EYLKEAF-AGESQANRRYLAFAEKAEKDGY 34
                                   4444444.4556666677777777777663 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.001
                          ERp29   1 GrieeldelaaefvaaakaereelleeakkaaeklksekekkaaeyYvkvmekiaekgeey 61 
                                    G ++e+ ++  e++++a++e ++++e   ++a++++    k +ae Y +++ k+ e++eey
  gi|116754055|ref|YP_843173.1|  75 GETHEFKDMYPEMLKTARDEGKKAAEISFRYANEVE----KVHAELYKEALAKLEESKEEY 131
                                    556788888888888888888888888888888888....******************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 ?   -3.6   0.1       8.2   1.1e+04       4      11 ..       3      10 ..       2      11 .. 0.65
   2 ?    9.7   1.0   0.00059      0.76       5      26 ..     114     140 ..     111     146 .. 0.87
   3 ?    3.6   0.6     0.046        59      20      27 ..     149     156 ..     145     157 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 8.2
                                   HHHHHHHH CS
                  Rad50_zn_hook  4 eteelnkk 11
                                   +tee+ k 
  gi|116754055|ref|YP_843173.1|  3 KTEEYLKE 10
                                   77888765 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00059
                                    HHHHHHHHHHHTT-SE.....E-TTT- CS
                  Rad50_zn_hook   5 teelnkkieelkeakg.....cCPlCg 26 
                                    +e++++++ +l+e+k+      CP+Cg
  gi|116754055|ref|YP_843173.1| 114 AELYKEALAKLEESKEeypyfVCPVCG 140
                                    68999*******9999888889****8 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.046
                                    EE-TTT-- CS
                  Rad50_zn_hook  20 gcCPlCgR 27 
                                    ++CP Cg 
  gi|116754055|ref|YP_843173.1| 149 ERCPICGA 156
                                    69****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1468  (0.0818785); expected 358.6 (0.02)
Passed bias filter:                     1008  (0.0562218); expected 358.6 (0.02)
Passed Vit filter:                       149  (0.00831056); 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: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 1255.61
//
Query:       gi|116754056|ref|YP_843174.1|  [L=220]
Description: nitrite and sulphite reductase 4Fe-4S region [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-29  103.0   0.1    5.6e-29  100.7   0.1    1.8  2  NIR_SIR       Nitrite and sulphite reductase 4Fe-4S domain
    1.1e-15   57.3   0.0    1.8e-15   56.5   0.0    1.4  1  NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half 


Domain annotation for each model (and alignments):
>> NIR_SIR  Nitrite and sulphite reductase 4Fe-4S domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.05   4.5e+02      20      70 ..      28      78 ..      14      82 .. 0.77
   2 !  100.7   0.1   6.2e-33   5.6e-29       2     151 ..      84     217 ..      83     220 .] 0.96

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.05
                                   -SS-THHHHHHHHHHHCTCCCCTSSSS-BEEEEESSTCSTSSGGGSSEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        NIR_SIR 20 allDttelakaiedelepeygetylPrKfKiavsgcpnncvaveanDiglv 70
                                    ++D   l + ++ + + + +  +l    +ia+ g +  +++   +D+g+ 
  gi|116754056|ref|YP_843174.1| 28 GIIDPATLRRIADVAEKYNAKVLKLTSAQRIAIVGIRPEDIDNAWKDLGMS 78
                                   56666666666666777777777777778999***9999999999999986 PP

  == domain 2  score: 100.7 bits;  conditional E-value: 6.2e-33
                                    SSSCCCCCCSTCCCTBSS-SS-THHHHHHHHHHHCTCCCCTSSSS-BEEEEESSTCSTSSGGGSSEEEEEEEETTCEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        NIR_SIR   2 ganlrnvtlcpgaglceeallDttelakaiedelepeygetylPrKfKiavsgcpnncvaveanDiglvgvkkdekeigf 81 
                                    g ++r+v++cpg+++c+    D+  +  +++    ++y+ ++lP KfK+ vsgc n c++  ++D+gl+g+ k     g+
  gi|116754056|ref|YP_843174.1|  84 GMCVRSVKICPGTTFCKRGQQDSVGVGLKLD----ERYHGYQLPWKFKMGVSGCVNSCAEPWIKDVGLIGTSK-----GW 154
                                    569****************************....**************************************.....** PP

                                    EEEE--B-SSSTC-TCEEEEEEEEEGGGHHHHHHHHHHHHHHHS-CSSGGG-SHHHHHHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        NIR_SIR  82 nilvGGglgrthgakktsarlgfvpeeevlevveaivevyrdhgdrknrkkeRlkylverlGvekFrekv 151
                                    +++vGG++g++++ ++ +a    +++ee +++v+ i+++y+        +k+Rl++++e++G+ekF+++v
  gi|116754056|ref|YP_843174.1| 155 RVVVGGCAGAKPRIAQVLA--ENLNDEEAIDLVDRIINYYK-----AHARKQRLGEFIEEIGFEKFKAEV 217
                                    *******************..6799999*************.....666678****************99 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 !   56.5   0.0     2e-19   1.8e-15       2      66 ..      12      75 ..      11      78 .. 0.95

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 2e-19
                   NIR_SIR_ferr  2 kqkdgkgyymvrlrvpnGritaeqlraladiaekygsgeirlTtrQnlqlhgvpeedleeileeL 66
                                    q+d+++y ++  ++p+G+i++++lr++ad+aeky    ++lT+ Q + + g+++ed+++ +++L
  gi|116754056|ref|YP_843174.1| 12 VQRDKETY-AIAPHIPGGIIDPATLRRIADVAEKYNAKVLKLTSAQRIAIVGIRPEDIDNAWKDL 75
                                   69998887.*****************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); 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: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1555.92
//
Query:       gi|116754057|ref|YP_843175.1|  [L=440]
Description: diaminopimelate decarboxylase [Methanosaeta thermophila PT]
Scores for complete 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-60  204.3   0.0      4e-60  203.2   0.0    1.5  2  Orn_Arg_deC_N    Pyridoxal-dependent decarboxylase, pyridoxal
    3.9e-24   84.7   0.0    4.7e-24   84.5   0.0    1.3  1  Orn_DAP_Arg_deC  Pyridoxal-dependent decarboxylase, C-termina
    3.2e-12   46.6   0.0    7.2e-12   45.4   0.0    1.5  1  Ala_racemase_N   Alanine racemase, N-terminal domain
  ------ inclusion threshold ------
      0.034   13.7   0.0      0.061   12.8   0.0    1.3  1  S6PP             Sucrose-6F-phosphate phosphohydrolase
       0.05   13.4   0.0       0.21   11.5   0.0    2.0  3  Biotin_lipoyl_2  Biotin-lipoyl like


Domain annotation for each model (and alignments):
>> Orn_Arg_deC_N  Pyridoxal-dependent decarboxylase, pyridoxal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.2      0.98   3.5e+03     148     162 ..      17      31 ..       7      37 .. 0.81
   2 !  203.2   0.0   1.1e-63     4e-60       3     247 .]      53     302 ..      51     302 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.98
                                    HHTTEEEEEEE---B CS
                  Orn_Arg_deC_N 148 keenlqlvGvsfHvG 162
                                     ++++q+v  ++H++
  gi|116754057|ref|YP_843175.1|  17 GKDHIQVVNGHLHIS 31 
                                    5799****99***96 PP

  == domain 2  score: 203.2 bits;  conditional E-value: 1.1e-63
                                    HHHHHHHHHHHHCTCCEEEEEGGG---HHHHHHHHHTTEEEEESSHHHHHHHHHCTTTGGGEEEEESS--HHHHHHHHHC CS
                  Orn_Arg_deC_N   3 sierklkrwkkalprikvfYavKansdlavlellaelGlgldcaSkaElelvlaagvsperiifanpckqreelryalek 82 
                                    +++++++r+++a+p++  ++avKan ++ ++++la++G+g d+ S +El+l+  agv+ eri f ++ k  eelr+a+ +
  gi|116754057|ref|YP_843175.1|  53 RLRENIRRYHRAFPDADKYFAVKANGNISIIRILAQEGAGADVFSAGELYLARLAGVPRERILFNGNSKRDEELRMAVTS 132
                                    68999*************************************************************************** PP

                                    THTEEEESSHHHHHHHHHHHCC....EEEEEEEE-SCCSSSSTCCCSSSTTSSSSEEHCHHHHHHHHHHHHTTEEEEEEE CS
                  Orn_Arg_deC_N  83 gvkvvtvdnveeleklaklape....akvllRiktdvsaatcelistggessKFGaaleeavealleaakeenlqlvGvs 158
                                    gv+ v +d++eele l+++a e     ++l R+++d+s +t++ i+tg +ssKFG+ +++     ++a++ ++++ +G++
  gi|116754057|ref|YP_843175.1| 133 GVR-VSIDSEEELESLSRIASEesknVEILFRVNPDISVNTHPKIATGLKSSKFGIPAQSVRSICEKAMHMDGIKPIGLH 211
                                    ***.9**************999898899******************************88888889999*********** PP

                                    ---BSSC-SCHHHHHHHHHHHHHHHHHHHHT---SEEE--S-BS-HCSTTSSSST.HHHHHHHHHHHHHHHHH.TSSS-E CS
                  Orn_Arg_deC_N 159 fHvGSgvsdleafvkavekalklfdelaelGvklkiLdvGGGfgveyeeeeeplk.leeiaekirealeeafp.gdkevt 236
                                    +H+GS++ d+++f +a+ +++ l+ e++ +G ++++Ld+GGG+g++y  + +p +  e+ a+++ + +e+  +  + +++
  gi|116754057|ref|YP_843175.1| 212 CHIGSQILDVSSFSEAAARMMDLVGEIVDIGGDMELLDLGGGLGIQYDPAAPPAPsPEDLANAVLPVIERRSEeLGVRLK 291
                                    ************************************************99988764799************9987788** PP

                                    EEE--SHHHHG CS
                  Orn_Arg_deC_N 237 iiaEpGRalva 247
                                    +i+EpGR++va
  gi|116754057|ref|YP_843175.1| 292 LILEPGRSIVA 302
                                    *********98 PP

>> Orn_DAP_Arg_deC  Pyridoxal-dependent decarboxylase, C-terminal sheet domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.5   0.0   1.3e-27   4.7e-24       5      98 .]     259     391 ..      46     391 .. 0.71

  Alignments for each domain:
  == domain 1  score: 84.5 bits;  conditional E-value: 1.3e-27
                                    E...........................................GGEEEEEEEEEEEEETCEEEEEES--TTTS-HHHHC CS
                                    x...........................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                Orn_DAP_Arg_deC   5 d...........................................eagvLvtrViavkesekkkfvivdaGmndllrpaly 41 
                                    d                                           ++ +L+t V+ vk+ +  +fv vdaG+n l+rp ly
  gi|116754057|ref|YP_843175.1| 259 DpaappapspedlanavlpvierrseelgvrlklilepgrsivaDTTILLTGVNVVKRAHV-TFVGVDAGFNVLARPMLY 337
                                    055555555555555555555555555555555555566666667899*********9987.8***************** PP

                                    TT-S-EESBTT-SCEEC.EEEEEEEE-SSSSTT-EEEEEEEEEE--TT-EEEESS-S CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                Orn_DAP_Arg_deC  42 gsfheipvkeeeaekeeeeeeevdvvGptCesgDvlakdrelpelevGdllafedaG 98 
                                    +++h i+v +   ++++e +e+++vvGp+CesgDvla++r+lp ++ Gd+laf daG
  gi|116754057|ref|YP_843175.1| 338 DAYHYIVVAN---RADAEISERYTVVGPICESGDVLARNRALPVVKKGDILAFLDAG 391
                                    ******4432...233445678*********************************99 PP

>> Ala_racemase_N  Alanine racemase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   0.0     2e-15   7.2e-12       2     159 ..      50     217 ..      49     241 .. 0.83

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 2e-15
                                    EHHHHHHHHHHHHHHSCTTSEEEEE-HHHHHTTHHHHHHHHHHHTTESEEEESSHHHHHHHHHTTSCSEEEEESC..STG CS
                 Ala_racemase_N   2 dldalrhNlrrlralagpgaklmavvKanayghgavevaralaeggadgfgvatleEalelreagitapilvleg..fsp 79 
                                    + d+lr+N+rr  +++ p+a  +  vKan+ +  +++++  ++ +gad   v++  E+   r ag+ ++ ++++g   + 
  gi|116754057|ref|YP_843175.1|  50 SEDRLRENIRRYHRAF-PDADKYFAVKANG-NISIIRILA-QEGAGAD---VFSAGELYLARLAGVPRERILFNGnsKRD 123
                                    579*************.777789999**65.455556665.3334455...88899999999999966666787777799 PP

                                    GGHHHHHHTTEEEEESSHHHHHHHHHHHHH............TTS-EEEEEEBESSSS..SSSBSCHHHHHHHHHHHHTT CS
                 Ala_racemase_N  80 eelaalaeydltvtvdsleqlealaaaare............agkplrvhlkidtgmg..RlGftpeeleellealaalp 145
                                    eel+ ++  ++ v +ds+e+le l+++a+e             +  ++ h ki tg+   + G++++ +++++e++ +++
  gi|116754057|ref|YP_843175.1| 124 EELRMAVTSGVRVSIDSEEELESLSRIASEesknveilfrvnPDISVNTHPKIATGLKssKFGIPAQSVRSICEKAMHMD 203
                                    99****************************9999999999888889999999999999********************** PP

                                    TEEEEEEE-S-SST CS
                 Ala_racemase_N 146 glrleglmtHfasa 159
                                    g++++gl  H +s 
  gi|116754057|ref|YP_843175.1| 204 GIKPIGLHCHIGSQ 217
                                    **********9886 PP

>> S6PP  Sucrose-6F-phosphate phosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.7e-05     0.061     172     219 ..     102     149 ..      92     163 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.7e-05
                                    HHHHHHT--GGGEEEEE-SGGGHHHHTSSSEEEE-TT--HHHHHHHHH CS
                           S6PP 172 yLakkleleleqilvcGdsgnDeellignvlgVvVgnaqeellqwlle 219
                                    yLa+  ++++e+il+ G+s+ Deel ++ + gV V+  +ee l+ l+ 
  gi|116754057|ref|YP_843175.1| 102 YLARLAGVPRERILFNGNSKRDEELRMAVTSGVRVSIDSEEELESLSR 149
                                    8999999****************************9888876665544 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       3.3   1.2e+04      27      32 ..     367     372 ..     365     372 .. 0.81
   2 ?   11.5   0.0   5.8e-05      0.21      23      38 ..     378     393 ..     378     399 .. 0.92
   3 ?   -3.6   0.0         3   1.1e+04      14      21 ..     408     415 ..     408     416 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 3.3
                Biotin_lipoyl_2  27 GdvLae 32 
                                    GdvLa+
  gi|116754057|ref|YP_843175.1| 367 GDVLAR 372
                                    9***95 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 5.8e-05
                Biotin_lipoyl_2  23 rVkaGdvLaelDsral 38 
                                    +Vk+Gd+La lD  a+
  gi|116754057|ref|YP_843175.1| 378 VVKKGDILAFLDAGAY 393
                                    5***********9887 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 3
                Biotin_lipoyl_2  14 aqlnVkdG 21 
                                    a+++V+dG
  gi|116754057|ref|YP_843175.1| 408 AEVLVRDG 415
                                    689****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); 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: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 3079.46
//
Query:       gi|116754058|ref|YP_843176.1|  [L=313]
Description: HEAT repeat-containing PBS lyase [Methanosaeta thermophila PT]
Scores for complete 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-75  248.0  30.3    1.1e-19   70.6   4.7    4.9  5  HEAT_2     HEAT repeats
    1.4e-33  112.0  15.0    2.7e-05   24.0   0.0    9.2  9  HEAT       HEAT repeat
    6.5e-30  100.7  38.9    8.3e-07   29.1   0.1    9.3  9  HEAT_PBS   PBS lyase HEAT-like repeat
    9.3e-23   80.3  23.6    7.5e-06   26.3   0.0    8.4  8  HEAT_EZ    HEAT-like repeat
    3.6e-14   52.2   7.1       0.05   13.7   0.0    7.5  9  Arm        Armadillo/beta-catenin-like repeat
    1.5e-12   47.8   0.0      0.073   13.1   0.1    4.9  4  Cnd1       non-SMC mitotic condensation complex subunit 1
    1.3e-06   27.3   0.0      0.035   12.7   0.0    3.8  3  Adaptin_N  Adaptin N terminal region
     0.0012   18.4   0.2          4    6.9   0.2    3.6  3  CLASP_N    CLASP N terminal
  ------ inclusion threshold ------
      0.016   15.3   0.0        1.7    8.8   0.0    3.5  2  RTP1_C1    Required for nuclear transport of RNA pol II C-ter
      0.047   13.4   0.3        1.8    8.2   0.5    2.7  3  UTP15_C    UTP15 C terminal
      0.058   13.1   1.6         39    3.9   0.2    4.3  6  DUF4042    Domain of unknown function (DUF4042)
       0.11   12.6   2.1       0.28   11.4   2.1    1.6  1  Flot       Flotillin
       0.21   10.4   0.4        4.9    5.9   0.0    2.1  2  API5       Apoptosis inhibitory protein 5 (API5)


Domain annotation for each model (and alignments):
>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.4   0.2   2.1e-18   2.9e-15      10      87 ..      11      87 ..       5      88 .. 0.93
   2 !   70.6   4.7   7.7e-23   1.1e-19       1      88 []      33     120 ..      33     120 .. 0.97
   3 !   48.6   1.5   5.6e-16   7.8e-13       2      73 ..     126     196 ..     125     198 .. 0.95
   4 !   60.5   0.7   1.1e-19   1.5e-16       3      85 ..     189     270 ..     186     270 .. 0.94
   5 !   56.5   0.1   1.9e-18   2.6e-15       8      87 ..     225     305 ..     224     306 .. 0.93

  Alignments for each domain:
  == domain 1  score: 56.4 bits;  conditional E-value: 2.1e-18
                         HEAT_2 10 ndpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkellddddddvvReaAaeaL 87
                                   +++++   ++a+++L  +g+ +a+p L+++l+d+ p+vR+ aa+aLg+igd +a+ aL ++l+ ddd+ vRe++a aL
  gi|116754058|ref|YP_843176.1| 11 RSENYFESQKAAWELVGMGE-SAVPGLIKALDDPTPHVRYRAAWALGKIGDTRAVGALSRCLLGDDDRAVREWSAAAL 87
                                   6788888899*********9.6*****************************************************998 PP

  == domain 2  score: 70.6 bits;  conditional E-value: 7.7e-23
                         HEAT_2   1 ldaLlqalendpdpevrraairaLgrignpealpaLvell.ededpavRraaaeaLgaigdpealpaLkellddddddvv 79 
                                    ++ L++al +dp p vr++a++aLg+ig+++a+ aL ++l  d+d+avR+  a aL aigdp+a+paL ++ ++d+  +v
  gi|116754058|ref|YP_843176.1|  33 VPGLIKAL-DDPTPHVRYRAAWALGKIGDTRAVGALSRCLlGDDDRAVREWSAAALEAIGDPSAVPALVQAIRSDSAKDV 111
                                    578*****.*****************************777*************************************** PP

                         HEAT_2  80 ReaAaeaLa 88 
                                    R +Aa aL+
  gi|116754058|ref|YP_843176.1| 112 RLRAAAALR 120
                                    ******995 PP

  == domain 3  score: 48.6 bits;  conditional E-value: 5.6e-16
                         HEAT_2   2 daLlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkelldd 73 
                                    +aL+ +l nd dp vr +ai aL+r++++ealpa + ll+dedp+vRr  a  +g+++ ++ +++L+ ll d
  gi|116754058|ref|YP_843176.1| 126 AALIDLL-NDTDPMVRSMAITALARLKSREALPAATALLRDEDPEVRRRTAGFMGELAIDDIADLLAPLLGD 196
                                    5899*99.**************************************************99999999999876 PP

  == domain 4  score: 60.5 bits;  conditional E-value: 1.1e-19
                         HEAT_2   3 aLlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkellddddddvvRea 82 
                                    +L  +l  d+  +vr +a++aLgri++++a +++v++l de+p++R  a+++Lg++++p+al  L   ++ +d +++R++
  gi|116754058|ref|YP_843176.1| 189 LLAPLL-GDEYLDVRVEAVKALGRIRTDRACDLVVSALGDENPEIRLCAVTTLGEMANPKALTPLIGVMLGEDLEEIRAW 267
                                    455556.9************************************************************************ PP

                         HEAT_2  83 Aae 85 
                                    Aa+
  gi|116754058|ref|YP_843176.1| 268 AAW 270
                                    985 PP

  == domain 5  score: 56.5 bits;  conditional E-value: 1.9e-18
                         HEAT_2   8 lendpdpevrraairaLgrignpealpaLvelleded.pavRraaaeaLgaigdpealpaLkelldddd.ddvvReaAae 85 
                                    l  d++pe+r  a+ +Lg+++np+al  L+ ++  ed +++R+ aa++Lg+i dp+a++ Lk+++ +d+  ++vRe+A  
  gi|116754058|ref|YP_843176.1| 225 L-GDENPEIRLCAVTTLGEMANPKALTPLIGVMLGEDlEEIRAWAAWSLGEINDPRAIEPLKRACSSDQcPEIVREKARA 303
                                    5.8****************************99666659*****************************977*******99 PP

                         HEAT_2  86 aL 87 
                                    +L
  gi|116754058|ref|YP_843176.1| 304 SL 305
                                    98 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0     2e-08   2.7e-05       2      28 ..      33      59 ..      32      61 .. 0.93
   2 !    8.7   0.1    0.0016       2.2       8      27 ..      70      90 ..      64      92 .. 0.84
   3 !    9.9   0.2   0.00068      0.94       2      25 ..      96     120 ..      95     122 .. 0.90
   4 !   18.5   0.1   1.2e-06    0.0016       5      27 ..     128     150 ..     126     152 .. 0.92
   5 !   12.1   0.0   0.00013      0.18       2      28 ..     156     182 ..     155     183 .. 0.88
   6 !   12.7   0.0   8.6e-05      0.12       3      27 ..     188     212 ..     186     212 .. 0.92
   7 !   17.9   0.0   1.8e-06    0.0025       4      28 ..     220     244 ..     218     245 .. 0.92
   8 !    6.5   0.0    0.0085        12      14      27 ..     262     275 ..     249     277 .. 0.78
   9 ?    3.0   0.0      0.11   1.5e+02       5      24 ..     284     305 ..     281     309 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2e-08
                                   HHHHHHHHT-SSHHHHHHHHHHHHHHH CS
                           HEAT  2 lPlllkllsDpspeVReaAakaLgala 28
                                   +P l+k+l Dp p+VR+ Aa+aLg++ 
  gi|116754058|ref|YP_843176.1| 33 VPGLIKALDDPTPHVRYRAAWALGKIG 59
                                   699*********************996 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0016
                                   HH.T-SSHHHHHHHHHHHHHH CS
                           HEAT  8 ll.sDpspeVReaAakaLgal 27
                                   +l  D++  VRe +a aL a+
  gi|116754058|ref|YP_843176.1| 70 CLlGDDDRAVREWSAAALEAI 90
                                   544***************998 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00068
                                    HHHHHHHH.T-SSHHHHHHHHHHHH CS
                           HEAT   2 lPlllkll.sDpspeVReaAakaLg 25 
                                    +P+l++++ sD++ +VR  Aa aL 
  gi|116754058|ref|YP_843176.1|  96 VPALVQAIrSDSAKDVRLRAAAALR 120
                                    799****98999999********96 PP

  == domain 4  score: 18.5 bits;  conditional E-value: 1.2e-06
                                    HHHHHT-SSHHHHHHHHHHHHHH CS
                           HEAT   5 llkllsDpspeVReaAakaLgal 27 
                                    l+ ll+D++p VR++A+ aL++l
  gi|116754058|ref|YP_843176.1| 128 LIDLLNDTDPMVRSMAITALARL 150
                                    899*****************987 PP

  == domain 5  score: 12.1 bits;  conditional E-value: 0.00013
                                    HHHHHHHHT-SSHHHHHHHHHHHHHHH CS
                           HEAT   2 lPlllkllsDpspeVReaAakaLgala 28 
                                    lP+   ll+D++peVR+ +a  +g+la
  gi|116754058|ref|YP_843176.1| 156 LPAATALLRDEDPEVRRRTAGFMGELA 182
                                    67778899*********9999999886 PP

  == domain 6  score: 12.7 bits;  conditional E-value: 8.6e-05
                                    HHHHHHHT-SSHHHHHHHHHHHHHH CS
                           HEAT   3 PlllkllsDpspeVReaAakaLgal 27 
                                    +ll  ll D+  +VR  A+kaLg++
  gi|116754058|ref|YP_843176.1| 188 DLLAPLLGDEYLDVRVEAVKALGRI 212
                                    58999******************97 PP

  == domain 7  score: 17.9 bits;  conditional E-value: 1.8e-06
                                    HHHHHHT-SSHHHHHHHHHHHHHHH CS
                           HEAT   4 lllkllsDpspeVReaAakaLgala 28 
                                    l++++l D++pe+R  A+ +Lg++a
  gi|116754058|ref|YP_843176.1| 220 LVVSALGDENPEIRLCAVTTLGEMA 244
                                    78899******************98 PP

  == domain 8  score: 6.5 bits;  conditional E-value: 0.0085
                                    HHHHHHHHHHHHHH CS
                           HEAT  14 peVReaAakaLgal 27 
                                     e+R+ Aa++Lg++
  gi|116754058|ref|YP_843176.1| 262 EEIRAWAAWSLGEI 275
                                    78**********98 PP

  == domain 9  score: 3.0 bits;  conditional E-value: 0.11
                                    HHHHH.T-SSHH.HHHHHHHHH CS
                           HEAT   5 llkll.sDpspe.VReaAakaL 24 
                                    l +++ sD++pe VRe A  +L
  gi|116754058|ref|YP_843176.1| 284 LKRACsSDQCPEiVREKARASL 305
                                    5566669*****77*9986555 PP

>> HEAT_PBS  PBS lyase HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0     0.004       5.5       5      27 .]      21      42 ..      19      42 .. 0.93
   2 !   26.1   0.6   5.4e-09   7.5e-06       1      25 [.      47      71 ..      47      73 .. 0.96
   3 !   19.5   0.3   7.7e-07    0.0011       1      25 [.      79     103 ..      79     105 .. 0.95
   4 !    6.8   2.8    0.0095        13       1      22 [.     111     132 ..     111     133 .. 0.90
   5 !    9.0   0.7    0.0019       2.6       1      20 [.     139     158 ..     139     165 .. 0.90
   6 ?    2.3   0.1      0.27   3.8e+02       1      26 [.     170     195 ..     170     196 .. 0.90
   7 !   17.6   0.1   3.1e-06    0.0042       1      27 []     201     227 ..     201     227 .. 0.93
   8 ?    4.0   0.0     0.078   1.1e+02       5      22 ..     236     253 ..     233     256 .. 0.92
   9 !   29.1   0.1     6e-10   8.3e-07       1      26 [.     264     289 ..     264     290 .. 0.94

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.004
                                   HHHHHHHCTSGGGHHHHHHHCTC CS
                       HEAT_PBS  5 AakaLgqlgdeeaipaLleaLqd 27
                                   Aa+ L  +g   a+p L++aL+d
  gi|116754058|ref|YP_843176.1| 21 AAWELVGMGE-SAVPGLIKALDD 42
                                   8999999999.**********98 PP

  == domain 2  score: 26.1 bits;  conditional E-value: 5.4e-09
                                   HHHHHHHHHHHCTSGGGHHHHHHHC CS
                       HEAT_PBS  1 vRraAakaLgqlgdeeaipaLleaL 25
                                   vR++Aa+aLg++gd++a+ aL ++L
  gi|116754058|ref|YP_843176.1| 47 VRYRAAWALGKIGDTRAVGALSRCL 71
                                   9********************9998 PP

  == domain 3  score: 19.5 bits;  conditional E-value: 7.7e-07
                                    HHHHHHHHHHHCTSGGGHHHHHHHC CS
                       HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaL 25 
                                    vR + a aL ++gd+ a+paL++a 
  gi|116754058|ref|YP_843176.1|  79 VREWSAAALEAIGDPSAVPALVQAI 103
                                    9*********************996 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.0095
                                    HHHHHHHHHHHCTSGGGHHHHH CS
                       HEAT_PBS   1 vRraAakaLgqlgdeeaipaLl 22 
                                    vR +Aa aL  +++e+a+  Ll
  gi|116754058|ref|YP_843176.1| 111 VRLRAAAALRGMRAEAALIDLL 132
                                    8*************99997776 PP

  == domain 5  score: 9.0 bits;  conditional E-value: 0.0019
                                    HHHHHHHHHHHCTSGGGHHH CS
                       HEAT_PBS   1 vRraAakaLgqlgdeeaipa 20 
                                    vR  A+ aL++l++ ea+pa
  gi|116754058|ref|YP_843176.1| 139 VRSMAITALARLKSREALPA 158
                                    899***********999987 PP

  == domain 6  score: 2.3 bits;  conditional E-value: 0.27
                                    HHHHHHHHHHHCTSGGGHHHHHHHCT CS
                       HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLq 26 
                                    vRr+ a  +g+l  ++++++L  +L 
  gi|116754058|ref|YP_843176.1| 170 VRRRTAGFMGELAIDDIADLLAPLLG 195
                                    89999999************998886 PP

  == domain 7  score: 17.6 bits;  conditional E-value: 3.1e-06
                                    HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                       HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLqd 27 
                                    vR +A+kaLg++++++a ++ + aL d
  gi|116754058|ref|YP_843176.1| 201 VRVEAVKALGRIRTDRACDLVVSALGD 227
                                    9******************99999865 PP

  == domain 8  score: 4.0 bits;  conditional E-value: 0.078
                                    HHHHHHHCTSGGGHHHHH CS
                       HEAT_PBS   5 AakaLgqlgdeeaipaLl 22 
                                    A+  Lg++  + a+ +L+
  gi|116754058|ref|YP_843176.1| 236 AVTTLGEMANPKALTPLI 253
                                    7889************98 PP

  == domain 9  score: 29.1 bits;  conditional E-value: 6e-10
                                    HHHHHHHHHHHCTSGGGHHHHHHHCT CS
                       HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLq 26 
                                    +R++Aa++Lg+++d++ai++L++a+ 
  gi|116754058|ref|YP_843176.1| 264 IRAWAAWSLGEINDPRAIEPLKRACS 289
                                    69*********************985 PP

>> HEAT_EZ  HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   5.4e-09   7.5e-06      28      55 .]      31      58 ..      30      58 .. 0.94
   2 !    8.7   0.3    0.0018       2.5      30      55 .]      64      90 ..      61      90 .. 0.75
   3 !   11.0   0.5   0.00034      0.47      27      52 ..      93     119 ..      93     120 .. 0.91
   4 !   12.1   0.3   0.00016      0.22      31      55 .]     126     150 ..     123     150 .. 0.93
   5 !    8.5   0.1    0.0021       2.9      28      53 ..     154     179 ..     152     181 .. 0.80
   6 !   10.4   0.1   0.00052      0.72      23      55 .]     180     212 ..     178     212 .. 0.92
   7 !    7.2   0.0    0.0053       7.4      34      55 .]     222     243 ..     217     243 .. 0.87
   8 !    7.2   0.0    0.0052       7.2      30      55 .]     250     275 ..     245     275 .. 0.68

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 5.4e-09
                        HEAT_EZ 28 eilpaLlalLnddsdeVRaaAagaLgnl 55
                                    ++p L+++L d+ ++VR+ Aa+aLg++
  gi|116754058|ref|YP_843176.1| 31 SAVPGLIKALDDPTPHVRYRAAWALGKI 58
                                   589***********************97 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0018
                        HEAT_EZ 30 lpaLl.alLnddsdeVRaaAagaLgnl 55
                                   + aL   lL dd+ +VR+ +a aL+++
  gi|116754058|ref|YP_843176.1| 64 VGALSrCLLGDDDRAVREWSAAALEAI 90
                                   55566245588888**********986 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00034
                        HEAT_EZ  27 peilpaLlalLnddsd.eVRaaAagaL 52 
                                    p ++paL+++ ++ds+ +VR  Aa aL
  gi|116754058|ref|YP_843176.1|  93 PSAVPALVQAIRSDSAkDVRLRAAAAL 119
                                    679********999999**99999999 PP

  == domain 4  score: 12.1 bits;  conditional E-value: 0.00016
                        HEAT_EZ  31 paLlalLnddsdeVRaaAagaLgnl 55 
                                    +aL+ lLnd +++VR  A+ aL++l
  gi|116754058|ref|YP_843176.1| 126 AALIDLLNDTDPMVRSMAITALARL 150
                                    689*******************997 PP

  == domain 5  score: 8.5 bits;  conditional E-value: 0.0021
                        HEAT_EZ  28 eilpaLlalLnddsdeVRaaAagaLg 53 
                                    e+lpa  alL+d+++eVR  +ag  g
  gi|116754058|ref|YP_843176.1| 154 EALPAATALLRDEDPEVRRRTAGFMG 179
                                    567777899999999**999998655 PP

  == domain 6  score: 10.4 bits;  conditional E-value: 0.00052
                        HEAT_EZ  23 qplvpeilpaLlalLnddsdeVRaaAagaLgnl 55 
                                    ++++++i ++L++lL d+  +VR  A+ aLg++
  gi|116754058|ref|YP_843176.1| 180 ELAIDDIADLLAPLLGDEYLDVRVEAVKALGRI 212
                                    578999*********99999***********97 PP

  == domain 7  score: 7.2 bits;  conditional E-value: 0.0053
                        HEAT_EZ  34 lalLnddsdeVRaaAagaLgnl 55 
                                    +++L d+++e+R  A+ +Lg +
  gi|116754058|ref|YP_843176.1| 222 VSALGDENPEIRLCAVTTLGEM 243
                                    678899999***********86 PP

  == domain 8  score: 7.2 bits;  conditional E-value: 0.0052
                        HEAT_EZ  30 lpaLlalLnddsd..eVRaaAagaLgnl 55 
                                     p+ + +L   +d  e+Ra Aa+ Lg +
  gi|116754058|ref|YP_843176.1| 250 TPLIGVML--GEDleEIRAWAAWSLGEI 275
                                    34444555..5555699*********86 PP

>> Arm  Armadillo/beta-catenin-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   3.6e-05      0.05      13      39 ..      32      58 ..      28      60 .. 0.91
   2 ?    0.1   0.0      0.67   9.2e+02      13      30 ..      63      81 ..      57      88 .. 0.68
   3 !   13.1   0.1   5.5e-05     0.076       6      37 ..      88     120 ..      83     122 .. 0.92
   4 !   11.5   0.1   0.00018      0.25      16      38 ..     127     149 ..     126     150 .. 0.93
   5 ?    5.9   0.0      0.01        14      13      40 ..     155     182 ..     154     183 .. 0.87
   6 ?    2.4   0.0      0.12   1.7e+02      16      39 ..     189     212 ..     186     214 .. 0.88
   7 ?    0.3   0.0      0.57   7.9e+02      15      40 ..     219     244 ..     216     245 .. 0.83
   8 ?   -1.5   0.0       2.1   2.9e+03      14      38 ..     249     274 ..     242     275 .. 0.61
   9 ?   -1.5   0.0       2.2     3e+03      10      30 ..     277     298 ..     273     299 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.6e-05
                                   HHHHHHHHTTTSSHHHHHHHHHHHHHH CS
                            Arm 13 avppLvrLLssedeevqeeAawALsNL 39
                                   avp L++ L+++ + v+  AawAL+ +
  gi|116754058|ref|YP_843176.1| 32 AVPGLIKALDDPTPHVRYRAAWALGKI 58
                                   9***********************965 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.67
                                   HHHHHHHHTT.TSSHHHHH CS
                            Arm 13 avppLvrLLs.sedeevqe 30
                                   av +L r+L  ++d  v+e
  gi|116754058|ref|YP_843176.1| 63 AVGALSRCLLgDDDRAVRE 81
                                   7889999999555555555 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 5.5e-05
                                    HHHHHTTHHHHHHHHTT.TSSHHHHHHHHHHHH CS
                            Arm   6 davieaGavppLvrLLs.sedeevqeeAawALs 37 
                                    +a+ +  avp+Lv+ ++ +   +v+  Aa+AL+
  gi|116754058|ref|YP_843176.1|  88 EAIGDPSAVPALVQAIRsDSAKDVRLRAAAALR 120
                                    5788999************************98 PP

  == domain 4  score: 11.5 bits;  conditional E-value: 0.00018
                                    HHHHHTTTSSHHHHHHHHHHHHH CS
                            Arm  16 pLvrLLssedeevqeeAawALsN 38 
                                    +L++LL+++d++v+  A +AL+ 
  gi|116754058|ref|YP_843176.1| 127 ALIDLLNDTDPMVRSMAITALAR 149
                                    7********************85 PP

  == domain 5  score: 5.9 bits;  conditional E-value: 0.01
                                    HHHHHHHHTTTSSHHHHHHHHHHHHHHT CS
                            Arm  13 avppLvrLLssedeevqeeAawALsNLa 40 
                                    a+p+  +LL++ed+ev++  a+ ++ La
  gi|116754058|ref|YP_843176.1| 155 ALPAATALLRDEDPEVRRRTAGFMGELA 182
                                    5788889*************99888887 PP

  == domain 6  score: 2.4 bits;  conditional E-value: 0.12
                                    HHHHHTTTSSHHHHHHHHHHHHHH CS
                            Arm  16 pLvrLLssedeevqeeAawALsNL 39 
                                     L  LL +e  +v+ eA+ AL+ +
  gi|116754058|ref|YP_843176.1| 189 LLAPLLGDEYLDVRVEAVKALGRI 212
                                    5778999**************966 PP

  == domain 7  score: 0.3 bits;  conditional E-value: 0.57
                                    HHHHHHTTTSSHHHHHHHHHHHHHHT CS
                            Arm  15 ppLvrLLssedeevqeeAawALsNLa 40 
                                    +  v+ L +e++e++  A+++L+ +a
  gi|116754058|ref|YP_843176.1| 219 DLVVSALGDENPEIRLCAVTTLGEMA 244
                                    5668889999****999999999775 PP

  == domain 8  score: -1.5 bits;  conditional E-value: 2.1
                                    HHHHHHHTT.TSSHHHHHHHHHHHHH CS
                            Arm  14 vppLvrLLs.sedeevqeeAawALsN 38 
                                    + pL+  +   + ee++  Aaw L+ 
  gi|116754058|ref|YP_843176.1| 249 LTPLIGVMLgEDLEEIRAWAAWSLGE 274
                                    55555555545556666668888876 PP

  == domain 9  score: -1.5 bits;  conditional E-value: 2.2
                                    HTTHHHHHHHHTT.TSSHHHHH CS
                            Arm  10 eaGavppLvrLLs.sedeevqe 30 
                                    +  a++pL r  s ++ +e+++
  gi|116754058|ref|YP_843176.1| 277 DPRAIEPLKRACSsDQCPEIVR 298
                                    6678999999888777777776 PP

>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0    0.0001      0.14      20      89 ..      30      94 ..      24     111 .. 0.82
   2 !   13.1   0.1   5.3e-05     0.073      62      89 ..     127     154 ..     113     160 .. 0.84
   3 !    6.3   0.0    0.0066       9.1      28      49 ..     161     182 ..     154     213 .. 0.77
   4 !   10.6   0.0   0.00032      0.44       2      87 ..     201     277 ..     200     297 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0001
                           Cnd1 20 eylvepLrkrLkDedpyVRktaaivvakLilndmvkekgflselakll.eDenprVvanalaalteiseks 89
                                   e  v+ L k+L D+ p+VR  aa ++ k+ +         +  l ++l  D+++ V++ + aal+ i + s
  gi|116754058|ref|YP_843176.1| 30 ESAVPGLIKALDDPTPHVRYRAAWALGKIGDT------RAVGALSRCLlGDDDRAVREWSAAALEAIGDPS 94
                                   66788899******************997555......456677787779**************9997765 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 5.3e-05
                           Cnd1  62 elaklleDenprVvanalaalteiseks 89 
                                     l +ll+D++p+V+++a++al  +++++
  gi|116754058|ref|YP_843176.1| 127 ALIDLLNDTDPMVRSMAITALARLKSRE 154
                                    5788999999999999999999988875 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0066
                           Cnd1  28 krLkDedpyVRktaaivvakLi 49 
                                    + L+Dedp VR+ +a  + +L 
  gi|116754058|ref|YP_843176.1| 161 ALLRDEDPEVRRRTAGFMGELA 182
                                    679*********9998888873 PP

  == domain 4  score: 10.6 bits;  conditional E-value: 0.00032
                           Cnd1   2 iRalairtlgcirvpnlveylvepLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaa 81 
                                    +R  a+++lg ir +   + +v    ++L De+p +R +a+ ++ ++ +++      +   +  +l ++ ++++a a  +
  gi|116754058|ref|YP_843176.1| 201 VRVEAVKALGRIRTDRACDLVV----SALGDENPEIRLCAVTTLGEMANPK-----ALTPLIGVMLGEDLEEIRAWAAWS 271
                                    7888999999999877776666....5789************998776665.....455667777777777888888888 PP

                           Cnd1  82 lteise 87 
                                    l ei++
  gi|116754058|ref|YP_843176.1| 272 LGEIND 277
                                    877776 PP

>> Adaptin_N  Adaptin N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.0    0.0021         3     268     344 ..      32     103 ..      28     120 .. 0.82
   2 !   12.7   0.0   2.5e-05     0.035     117     189 ..     126     190 ..     122     217 .. 0.78
   3 ?    3.3   0.0     0.018        25     157     187 ..     221     250 ..     208     277 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0021
                                    CHHCHHHHHHSSCCTCHHHHHCHHHHHHHHXXTTTTTTTCCCCSXXTTSXHHHHHHHHHHHCCCXXTTTHHHHHHHH CS
                      Adaptin_N 268 avnaLvrllsskdenlryvaLrtllkivkkepkavqhldlkifllktdddvsirlkaldlllklvdesNvkeivkeL 344
                                    av  L++ l+++ + +ry a  +l ki  ++  av      +++l  ddd+ +r +    l +++d s v ++v+ +
  gi|116754058|ref|YP_843176.1|  32 AVPGLIKALDDPTPHVRYRAAWALGKIGDTR--AVGA---LSRCLLGDDDRAVREWSAAALEAIGDPSAVPALVQAI 103
                                    5667888888888888888888888888888..5554...4789999999999999999999999999999999976 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 2.5e-05
                                    HHHHHHHT-SSHHHHHHHHHHHHHCCCCCHHCCCCCHHHHHHHCTT-SSHHHHHHHHHHHHHHHCCCCCCCHH CS
                      Adaptin_N 117 paikkllkdrspyvrkkAalailklykkdpdllrkqlveeikellsdkdpgvvlaAvalleeikkndrlllkl 189
                                     a+ +ll+d++p+vr+ A++a+++l   + ++     ++  + ll d+dp v + +   + e+   d+++  l
  gi|116754058|ref|YP_843176.1| 126 AALIDLLNDTDPMVRSMAITALARLK--SREA-----LPAATALLRDEDPEVRRRTAGFMGEL-AIDDIADLL 190
                                    67889999999999999999999984..4444.....56678999999999888888888888.777664444 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.018
                                    HHHCTT-SSHHHHHHHHHHHHHHHCCCCCCC CS
                      Adaptin_N 157 ikellsdkdpgvvlaAvalleeikkndrlll 187
                                    ++++l d++p + l+Av++l e+  n+++l+
  gi|116754058|ref|YP_843176.1| 221 VVSALGDENPEIRLCAVTTLGEM-ANPKALT 250
                                    44555555555555555555555.5555433 PP

>> CLASP_N  CLASP N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.0    0.0039       5.4     162     195 ..      14      50 ..       6      81 .. 0.84
   2 !    6.9   0.2    0.0029         4     176     224 ..     123     172 ..      99     175 .. 0.78
   3 ?    0.6   0.0      0.25   3.4e+02     135     157 ..     221     243 ..     203     310 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0039
                        CLASP_N 162 e...shkskleasllldliekslkkgleDanptVRet 195
                                    +   s+k++ e  ++ +++++ l+k+l D+ p VR  
  gi|116754058|ref|YP_843176.1|  14 NyfeSQKAAWELVGMGESAVPGLIKALDDPTPHVRYR 50 
                                    34446777888888889******************65 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0029
                        CLASP_N 176 liekslkkgleDanptVRetaRstfwef.fkvwPsrAksllssldpkvrk 224
                                     +e +l+ +l+D +p VR+ a +++ ++ ++ +   A +ll + dp+vr+
  gi|116754058|ref|YP_843176.1| 123 RAEAALIDLLNDTDPMVRSMAITALARLkSREALPAATALLRDEDPEVRR 172
                                    47899***************999999884233444567777888888887 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.25
                        CLASP_N 135 lsvalqdKnvqpReysaiwLkil 157
                                    + +al d n+++R+++++ L  +
  gi|116754058|ref|YP_843176.1| 221 VVSALGDENPEIRLCAVTTLGEM 243
                                    44444444444444444444433 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 ?    4.5   0.0     0.027        37       5      26 ..     129     150 ..      35     155 .. 0.75
   2 ?    8.8   0.0    0.0013       1.7       5      69 ..     129     245 ..     124     262 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.027
                        RTP1_C1   5 lkdlqdpllpvrahglvlLrkl 26 
                                    ++ l+d+ + vr+ +++ L++l
  gi|116754058|ref|YP_843176.1| 129 IDLLNDTDPMVRSMAITALARL 150
                                    4455666666666666665555 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0013
                        RTP1_C1   5 lkdlqdpllpvrahglvlLrkliekkske................................................... 33 
                                    ++ l+d+ + vr+ +++ L++l +++                                                      
  gi|116754058|ref|YP_843176.1| 129 IDLLNDTDPMVRSMAITALARLKSREALPaatallrdedpevrrrtagfmgelaiddiadllapllgdeyldvrveavka 208
                                    67899999999999999999997777654888999999999999999999888888888888888888888888888877 PP

                        RTP1_C1  34 .avldiekilkllleaLkdedsYvYLnaikgLvaLad 69 
                                      ++  ++  +l+++aL de++ + L a+ +L ++a+
  gi|116754058|ref|YP_843176.1| 209 lGRIRTDRACDLVVSALGDENPEIRLCAVTTLGEMAN 245
                                    7778888888888888888888888888888888876 PP

>> UTP15_C  UTP15 C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.14   1.9e+02      61      99 ..      65     103 ..      54     105 .. 0.91
   2 ?    8.2   0.5    0.0013       1.8      24      68 ..     117     161 ..     101     168 .. 0.87
   3 ?   -2.4   0.0       2.5   3.5e+03      32      57 ..     215     240 ..     207     287 .. 0.48

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.14
                        UTP15_C  61 galraALagrdeeslepiLkfllkhitdpryvsllvdva 99 
                                    gal ++L g d++ +       l+ i+dp+ v+ lv+++
  gi|116754058|ref|YP_843176.1|  65 GALSRCLLGDDDRAVREWSAAALEAIGDPSAVPALVQAI 103
                                    89*******************************999986 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0013
                        UTP15_C  24 klLrkfryskALdavlekkvekspevvvtlleeLrhRgalraALa 68 
                                     +Lr +r ++AL   l+ ++   +++++t l  L++R+al aA a
  gi|116754058|ref|YP_843176.1| 117 AALRGMRAEAALIDLLNDTDPMVRSMAITALARLKSREALPAATA 161
                                    579***************889999****************99865 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2.5
                        UTP15_C  32 skALdavlekkvekspevvvtlleeL 57 
                                     +A d v++   +++pe+ +  +++L
  gi|116754058|ref|YP_843176.1| 215 DRACDLVVSALGDENPEIRLCAVTTL 240
                                    55556666553355555543333333 PP

>> DUF4042  Domain of unknown function (DUF4042)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.43   5.9e+02      48      67 ..      39      58 ..      30      64 .. 0.86
   2 ?   -1.2   0.0         1   1.4e+03      43      78 ..      66     102 ..      57     111 .. 0.74
   3 ?   -1.4   0.0       1.2   1.7e+03      41      65 ..      96     120 ..      79     129 .. 0.79
   4 ?    3.9   0.2     0.028        39      48      67 ..     131     150 ..     114     165 .. 0.79
   5 ?   -0.5   0.0      0.63   8.7e+02      43      66 ..     188     211 ..     184     215 .. 0.86
   6 ?    3.1   0.0     0.049        68      40      68 ..     216     244 ..     211     250 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.43
                        DUF4042 48 llkDpspkvRaaalqvlaal 67
                                   +l Dp p vR  a+ +l ++
  gi|116754058|ref|YP_843176.1| 39 ALDDPTPHVRYRAAWALGKI 58
                                   689**********9998876 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1
                        DUF4042  43 tLltillkDpspkvRaaalqvlaalLdgsk.sfLsqa 78 
                                     L  +ll D    vR  ++ +l a+ d s+ + L qa
  gi|116754058|ref|YP_843176.1|  66 ALSRCLLGDDDRAVREWSAAALEAIGDPSAvPALVQA 102
                                    6889999999999999999998887666542455555 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.2
                        DUF4042  41 eatLltillkDpspkvRaaalqvla 65 
                                       L++ + +D+   vR+ a+ +l 
  gi|116754058|ref|YP_843176.1|  96 VPALVQAIRSDSAKDVRLRAAAALR 120
                                    5678888999999999999888775 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.028
                        DUF4042  48 llkDpspkvRaaalqvlaal 67 
                                    ll+D+ p vR +a+ +la l
  gi|116754058|ref|YP_843176.1| 131 LLNDTDPMVRSMAITALARL 150
                                    689***************98 PP

  == domain 5  score: -0.5 bits;  conditional E-value: 0.63
                        DUF4042  43 tLltillkDpspkvRaaalqvlaa 66 
                                     Ll  ll D ++ vR+ a+++l  
  gi|116754058|ref|YP_843176.1| 188 DLLAPLLGDEYLDVRVEAVKALGR 211
                                    68888999***********99876 PP

  == domain 6  score: 3.1 bits;  conditional E-value: 0.049
                        DUF4042  40 seatLltillkDpspkvRaaalqvlaalL 68 
                                    ++  L+  +l D +p +R++a+ +l ++ 
  gi|116754058|ref|YP_843176.1| 216 RACDLVVSALGDENPEIRLCAVTTLGEMA 244
                                    5667888999***************9985 PP

>> Flot  Flotillin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   2.1   0.00021      0.28       5      57 ..     107     159 ..     105     163 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00021
                           Flot   5 eAeaakleAeAkrakaeaeAegiralnEAenalseeqialqvklallealPei 57 
                                    +A+  +l+A A+   ++aeA+ i +ln+ + ++ + +i++ ++l+  ealP  
  gi|116754058|ref|YP_843176.1| 107 SAKDVRLRAAAALRGMRAEAALIDLLNDTDPMVRSMAITALARLKSREALPAA 159
                                    68999**********************************99999999****75 PP

>> API5  Apoptosis inhibitory protein 5 (API5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0    0.0035       4.9      63      86 ..     127     150 ..     121     160 .. 0.89
   2 ?    2.5   0.1     0.036        50      62      91 ..     188     217 ..     178     227 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0035
                           API5  63 aqlDLiedddlgirkqAikdLpsl 86 
                                    a++DL++d d ++r  Ai +L++l
  gi|116754058|ref|YP_843176.1| 127 ALIDLLNDTDPMVRSMAITALARL 150
                                    799******************987 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.036
                           API5  62 daqlDLiedddlgirkqAikdLpslckdtk 91 
                                    d +  L+ d+ l +r+ A+k+L ++ +d  
  gi|116754058|ref|YP_843176.1| 188 DLLAPLLGDEYLDVRVEAVKALGRIRTDRA 217
                                    444457789**************9988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); 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 0.30s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 2115.14
//
Query:       gi|116754059|ref|YP_843177.1|  [L=146]
Description: large conductance mechanosensitive channel protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-38  132.3   0.7    1.3e-38  132.0   0.7    1.0  1  MscL             Large-conductance mechanosensitive channel, 
    5.4e-06   26.4   3.8    8.7e-06   25.7   3.8    1.3  1  UPF0547          Uncharacterised protein family UPF0547
     0.0049   17.2   3.3      0.072   13.5   0.0    2.4  2  FeoB_associated  FeoB-associated Cys-rich membrane protein
     0.0064   16.5   1.3     0.0087   16.1   1.3    1.2  1  DZR              Double zinc ribbon
  ------ inclusion threshold ------
      0.025   14.3   2.7      0.071   12.9   2.4    1.8  2  zinc_ribbon_2    zinc-ribbon domain
        0.1   12.5   2.2        3.8    7.5   0.3    2.2  2  Cys_rich_CPXG    Cysteine-rich CPXCG
        0.8    9.6   4.8       0.89    9.5   0.5    2.1  2  zf-C3HC4_3       Zinc finger, C3HC4 type (RING finger)
        1.3    9.3   6.6        7.8    6.9   0.5    2.2  2  zf-Di19          Drought induced 19 protein (Di19), zinc-bind
        2.3    8.4   6.2         15    5.7   0.5    2.6  3  zf-CHCC          Zinc-finger domain
        6.8    6.2   7.4         44    3.7   7.4    2.0  1  zf-ribbon_3      zinc-ribbon domain


Domain annotation for each model (and alignments):
>> MscL  Large-conductance mechanosensitive channel, MscL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.0   0.7   7.2e-42   1.3e-38       1     113 [.       3     126 ..       3     133 .. 0.89

  Alignments for each domain:
  == domain 1  score: 132.0 bits;  conditional E-value: 7.2e-42
                           MscL   1 llkeFkefilrGnvidLAvgviiGaaftkiVtslvkdiimpliglllggvdfselkikl............kaeaavlky 68 
                                    +++eFkef+++Gn +d+Avg+iiG af++iV+slv+diimp++gl+lg v+f++l+i+l            +a+a +++y
  gi|116754059|ref|YP_843177.1|   3 FIDEFKEFAVKGNAVDMAVGIIIGVAFGAIVNSLVRDIIMPPLGLILGRVNFTDLFIALdgkvypslaaaqAAGAPTINY 82 
                                    689********************************************99********************998899***** PP

                           MscL  69 gafiqavinFliiafviFlivkainkkkkeeeeeeeaeekeeell 113
                                    g fi+++inF+i+a++iF++++ in+ kk+ +   e+++ke+ ++
  gi|116754059|ref|YP_843177.1|  83 GLFINTIINFIIVALAIFIVIRRINAMKKAPAPP-EPNTKECPYC 126
                                    *************************965554444.3444444443 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   3.8   4.8e-09   8.7e-06       1      20 [.     121     140 ..     121     141 .. 0.99

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 4.8e-09
                        UPF0547   1 KvCPeCeakvPvaaqfCphC 20 
                                    K+CP C++ +P+aa++Cp+C
  gi|116754059|ref|YP_843177.1| 121 KECPYCRESIPLAAVRCPYC 140
                                    99****************** 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 ?    3.6   1.0      0.05        90       4      23 ..      20      39 ..      17      40 .. 0.82
   2 !   13.5   0.0     4e-05     0.072       2      27 ..      87     112 ..      86     129 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.05
                FeoB_associated  4 IVgliiaaavafvirrlikk 23
                                    Vg+ii +a ++++ +l+++
  gi|116754059|ref|YP_843177.1| 20 AVGIIIGVAFGAIVNSLVRD 39
                                   58999999999999998886 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 4e-05
                FeoB_associated   2 tiIVgliiaaavafvirrlikkkkkG 27 
                                    + I+  ii+a+++f+++r i + kk 
  gi|116754059|ref|YP_843177.1|  87 NTIINFIIVALAIFIVIRRINAMKKA 112
                                    77999999999999999999996664 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   1.3   4.9e-06    0.0087      28      49 .]     120     141 ..     107     146 .] 0.57

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.9e-06
                            DZR  28 edrCpsCgekvdpearfCpeCG 49 
                                     + Cp C e++++ a  Cp+C+
  gi|116754059|ref|YP_843177.1| 120 TKECPYCRESIPLAAVRCPYCT 141
                                    4555555555555555555553 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.3   0.00077       1.4      11      22 ..     118     129 ..     117     130 .. 0.83
   2 ?   12.9   2.4   3.9e-05     0.071       2      21 ..     123     142 ..     122     144 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00077
                  zinc_ribbon_2  11 dnakFCpyCGtp 22 
                                    +n k CpyC++ 
  gi|116754059|ref|YP_843177.1| 118 PNTKECPYCRES 129
                                    79999****985 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 3.9e-05
                  zinc_ribbon_2   2 CpnCGaelqdnakFCpyCGt 21 
                                    Cp C + ++  a+ CpyC +
  gi|116754059|ref|YP_843177.1| 123 CPYCRESIPLAAVRCPYCTS 142
                                    ******************65 PP

>> Cys_rich_CPXG  Cysteine-rich CPXCG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.3    0.0021       3.8       2      10 ..     122     130 ..     122     134 .. 0.84
   2 ?    4.8   0.1     0.014        25       1       9 [.     135     143 ..     135     146 .] 0.78

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0021
                  Cys_rich_CPXG   2 qCPyCgeei 10 
                                    +CPyC e+i
  gi|116754059|ref|YP_843177.1| 122 ECPYCRESI 130
                                    5******98 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.014
                  Cys_rich_CPXG   1 iqCPyCgee 9  
                                    + CPyC   
  gi|116754059|ref|YP_843177.1| 135 VRCPYCTSD 143
                                    58****865 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 ?    9.5   0.5    0.0005      0.89      36      47 ..     119     130 ..     109     133 .. 0.85
   2 ?    2.2   0.3     0.094   1.7e+02      39      46 ..     136     143 ..     132     146 .] 0.77

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0005
                                    TT-B-TTT--B- CS
                     zf-C3HC4_3  36 rkkkCpiCrrpi 47 
                                    ++k+Cp+Cr++i
  gi|116754059|ref|YP_843177.1| 119 NTKECPYCRESI 130
                                    679*******99 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.094
                                    B-TTT--B CS
                     zf-C3HC4_3  39 kCpiCrrp 46 
                                    +Cp+C ++
  gi|116754059|ref|YP_843177.1| 136 RCPYCTSD 143
                                    79999876 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 ?    6.2   0.6     0.007        13       4      12 ..     122     130 ..     119     135 .. 0.79
   2 ?    6.9   0.5    0.0044       7.8       3      12 ..     135     144 ..     133     146 .] 0.79

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.007
                        zf-Di19   4 tCPyCgkel 12 
                                     CPyC++++
  gi|116754059|ref|YP_843177.1| 122 ECPYCRESI 130
                                    7****9865 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0044
                        zf-Di19   3 ftCPyCgkel 12 
                                    + CPyC+ +l
  gi|116754059|ref|YP_843177.1| 135 VRCPYCTSDL 144
                                    78****9876 PP

>> zf-CHCC  Zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       4.8   8.6e+03      10      17 ..      72      79 ..      62      80 .. 0.63
   2 ?    5.7   0.5    0.0083        15      24      33 ..     117     126 ..     115     128 .. 0.86
   3 ?    5.0   0.4     0.015        26      28      33 ..     135     140 ..     133     142 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.8
                                   STTSEEEE CS
                        zf-CHCC 10 ggalGHPr 17
                                    +a G+P 
  gi|116754059|ref|YP_843177.1| 72 AQAAGAPT 79
                                   56778885 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0083
                                    TTSEEEETTT CS
                        zf-CHCC  24 kkgpvdCgYC 33 
                                    ++ + +C+YC
  gi|116754059|ref|YP_843177.1| 117 EPNTKECPYC 126
                                    57789***** PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.015
                                    EEETTT CS
                        zf-CHCC  28 vdCgYC 33 
                                    v+C+YC
  gi|116754059|ref|YP_843177.1| 135 VRCPYC 140
                                    89**** PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   7.4     0.025        44       2      22 ..     120     140 ..     119     144 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.025
                    zf-ribbon_3   2 tvrCPnCGaplssddnvCpyC 22 
                                    t++CP+C + +   ++ CpyC
  gi|116754059|ref|YP_843177.1| 120 TKECPYCRESIPLAAVRCPYC 140
                                    899******77999999***9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       967  (0.053935); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); 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 0.27s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1067.55
//
Query:       gi|116754060|ref|YP_843178.1|  [L=259]
Description: hypothetical protein Mthe_0748 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-13   51.5   0.5    2.7e-07   30.5   0.0    2.1  2  Phosphodiest   Type I phosphodiesterase / nucleotide pyrophos
      2e-12   47.2   0.0    3.1e-09   36.7   0.0    2.9  3  Sulfatase      Sulfatase
    0.00015   21.2   0.0    0.00061   19.2   0.0    1.8  2  Metalloenzyme  Metalloenzyme superfamily


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 !   30.5   0.0   4.5e-11   2.7e-07       2      66 ..      52     114 ..      51     121 .. 0.89
   2 !   19.5   0.1   9.7e-08   0.00058     169     234 ..     177     238 ..     136     253 .. 0.85

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 4.5e-11
                                    EEEEETT-BTTHHHHHGSTSHHHHHHHHHSEEESEEE-SSS-SHHHHHHHHHHSS-HHHHS--SS CS
                   Phosphodiest   2 lvislDGlradlldrlaellpnlaaLakegvsapnlrpvfPtlTfpnhaslvTGlyPgeHGivgN 66 
                                    ++i++D+l  +l + +  +l +++++a  g+ ++    ++  +T p+ as+++Gl+P++HGi++ 
  gi|116754060|ref|YP_843178.1|  52 ILIIVDSLGYELYRSFLPHLRHMREIAASGFLFR--ALHVADHTSPAIASILSGLTPEHHGIYDT 114
                                    89***********996569999999999***999..567889*********************85 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 9.7e-08
                                    CT..SSESEEEEEECCCHHHHHHH-TTSHHHHHHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES--- CS
                   Phosphodiest 169 el..ekpdlllvyleetDtvgHkfGpdspevedalrrvDkaigdLlealderglsaetniilvSDHGm 234
                                    e    +p+l++ y+ ++D++ H+ G +   +  a  ++D+ +g++++ + ++     t +++v+DH +
  gi|116754060|ref|YP_843178.1| 177 EAlsTDPNLVVSYFIGLDKAAHN-GLHLDGFVRAAVSIDAQVGKIFNRAGPE-----TMMVIVGDHPV 238
                                    235699****************6.59*9999999******************.....*********55 PP

>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.029   1.7e+02     286     308 ..       7      29 ..       3      30 .. 0.83
   2 !   36.7   0.0   5.1e-13   3.1e-09       3      99 ..      51     139 ..      49     186 .. 0.89
   3 !    5.5   0.0    0.0016       9.6     213     254 ..     205     241 ..     193     255 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.029
                                    HCEEECSEEEGGGHHHHHHHHTT CS
                      Sulfatase 286 aprvseelvshiDlfptildlag 308
                                    ++++    vs+iD++p+i++++g
  gi|116754060|ref|YP_843178.1|   7 SNQNIMRTVSQIDIAPSIAKVLG 29 
                                    556777899**********9998 PP

  == domain 2  score: 36.7 bits;  conditional E-value: 5.1e-13
                                    EEEEEESSE-TTGSGGGTTTSCSSHHHHHHHHTSEEESSEE-SSSSHHHHHHHHHHSS-HHHHTHSSCCSTTTHHCTTTS CS
                      Sulfatase   3 vvliladdlgagdlglyggktattpnldrlaeeglrftnfysaaplcspsraalltgryphnsgvasntevgggglpqte 82 
                                     +li++d+lg+    ++  + +   ++ ++a++g++f+  ++a  ++sp+ a++l+g+ p+++g+++++    + +    
  gi|116754060|ref|YP_843178.1|  51 AILIIVDSLGYELYRSFLPHLR---HMREIAASGFLFRALHVAD-HTSPAIASILSGLTPEHHGIYDTE----SAKRSPI 122
                                    599******8876666666666...566668************8.*********************999....999**** PP

                                    -HHHHHHHHTT-EEEEE CS
                      Sulfatase  83 atLpellkeaGYntaai 99 
                                     ++pe+  +aG ++a+i
  gi|116754060|ref|YP_843178.1| 123 LSIPEMASSAGLRSAVI 139
                                    ***********999877 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.0016
                                    HHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEEEESSSSCCC CS
                      Sulfatase 213 aylnsveyvDdligrvlaaLeenglldntlvvftSDhgasle 254
                                     + ++  ++D ++g++++++       +t++v+++Dh  + +
  gi|116754060|ref|YP_843178.1| 205 GFVRAAVSIDAQVGKIFNRA-----GPETMMVIVGDHPVHAG 241
                                    56788899************.....9***********87774 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0     0.096   5.7e+02       2      16 ..      50      64 ..      49     119 .. 0.65
   2 !   19.2   0.0     1e-07   0.00061     113     196 ..     165     247 ..     126     253 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.096
                                   EEEEEEETTBB---- CS
                                   xxxxxxxxxxxxxxx RF
                  Metalloenzyme  2 kvvlvvlDGlGeapa 16
                                   +++l+++D+lG+   
  gi|116754060|ref|YP_843178.1| 50 RAILIIVDSLGYELY 64
                                   788999999998655 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 1e-07
                                    T--HHHHHHHHHHHH.CC.-SEEEEEE-HHHHHHHTT.-HHHHHHHHHHHHHHHHHHHTTS-TTTEEEEEE-SSB--TTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Metalloenzyme 113 emkavevaekaldailsgkfdlvvvniknaDmvGHtg.dleatiaaieaaDeavkeildaieqvdgilvvtADHgnaedm 191
                                    +    ++++ +l+a+ s++ +lvv  +   D ++H+g  l + ++a   +D++v++i+++   +  ++v+++DH+    +
  gi|116754060|ref|YP_843178.1| 165 DEFDHHICRLTLEAL-STDPNLVVSYFIGLDKAAHNGlHLDGFVRAAVSIDAQVGKIFNRAGPET-MMVIVGDHPVHAGH 242
                                    555667889999999.77699***************96799*******************88877.********988776 PP

                                    SS... CS
                                    xxxxx RF
                  Metalloenzyme 192 vkrdk 196
                                    +k+d+
  gi|116754060|ref|YP_843178.1| 243 MKNDD 247
                                    66554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1835.71
//
Query:       gi|116754061|ref|YP_843179.1|  [L=194]
Description: hypothetical protein Mthe_0749 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.8e-16   58.7   2.9    1.1e-15   58.1   2.9    1.3  1  CxxCxxCC  Putative zinc- or iron-chelating domain


Domain annotation for each model (and alignments):
>> CxxCxxCC  Putative zinc- or iron-chelating domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.1   2.9   5.9e-20   1.1e-15       2      84 ..      47     147 ..      46     148 .. 0.91

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 5.9e-20
                       CxxCxxCC   2 CkeCgaCCk.elkvklteedlerlkaaevaeeeeeskkiak..............adgrCvfldeetklCkiYeeRpkic 66 
                                    Ck+Cg+CC+    +kl+e+d++r++++ +++ ++  k++a               ++ +C+f+d+ tk C+iYe Rp  c
  gi|116754061|ref|YP_843179.1|  47 CKRCGTCCTtGDPIKLREDDVRRIARHLRITPSRAMKRYAArrvsetgksflamkHTRPCRFYDQSTKGCRIYEARPWSC 126
                                    *********77899***************9999999999989*************9************************ PP

                       CxxCxxCC  67 rlfpas...ekeellaraetC 84 
                                    r+fp+      e+  +++++C
  gi|116754061|ref|YP_843179.1| 127 RIFPFLgiyGSEDAVKVHTSC 147
                                    *****9887666666777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1430.63
//
Query:       gi|116754062|ref|YP_843180.1|  [L=220]
Description: phosphoribosyltransferase [Methanosaeta thermophila PT]
Scores for 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-20   70.8   0.0    1.3e-19   70.3   0.0    1.2  1  Pribosyltran  Phosphoribosyl transferase domain
  ------ inclusion threshold ------
      0.017   14.6   0.0      0.023   14.2   0.0    1.1  1  UPRTase       Uracil phosphoribosyltransferase
       0.16   11.8   0.0       0.32   10.8   0.0    1.4  1  RD3           RD3 protein


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 !   70.3   0.0   2.1e-23   1.3e-19      14     153 ..      19     154 ..       9     158 .. 0.85

  Alignments for each domain:
  == domain 1  score: 70.3 bits;  conditional E-value: 2.1e-23
                                    EEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHS.TT-EE-EEEEEE-TTT--EE........EE----TTSEEEE CS
                   Pribosyltran  14 avarlaaeileeyngkpdvvvgiargGvpfakiladeL.evplayvrkvkyrpdgseeaargssdesrlledpagkkVli 92 
                                      ++la++i ++ +++pd+vv+i rgG+++a  + d+L   +l+ +r+++     +     ++  +  l+ ++ +++Vl+
  gi|116754062|ref|YP_843180.1|  19 LERELASRIKSS-GYRPDLVVAIGRGGFVPARVVCDRLlHTQLTSIRIERWGVAANKLERATIRFP--LSVSISNMSVLV 95 
                                    557888888888.*************************9889*******98888888777777776..9*********** PP

                                    E-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHHHHHHH-TTS.....EEEEEEE- CS
                   Pribosyltran  93 VDDildtGgTllaalelLkekgpeevriavlvdkpateeevdknakrvfslspdnfvavvg 153
                                    VDD+ dtG Tl aal+ L + gp+ev++ vl+ k +++ e+d++   v      ++v ++ 
  gi|116754062|ref|YP_843180.1|  96 VDDVTDTGDTLSAALDYLWSLGPAEVKTGVLHHKVSSKVEPDYCSEIVHRW--RWIVYPWA 154
                                    **********************************99999998865544433..35555555 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   3.8e-06     0.023      71     149 ..      37     118 ..      21     133 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.8e-06
                        UPRTase  71 lVpilRaGegmeealrellpearvghlglqreeet...lepveyynkLPkkiaertvlllDpviaTGgsaaaaiqlLker 147
                                    +V+i R+G   ++ + + l + ++  + ++r       le   +   L  +i++ +vl++D v  TG ++ aa++ L + 
  gi|116754062|ref|YP_843180.1|  37 VVAIGRGGFVPARVVCDRLLHTQLTSIRIERWGVAankLERATIRFPLSVSISNMSVLVVDDVTDTGDTLSAALDYLWSL 116
                                    7888899988888888888888888888888554410144444444555556999*********************9887 PP

                        UPRTase 148 gv 149
                                    g 
  gi|116754062|ref|YP_843180.1| 117 GP 118
                                    64 PP

>> RD3  RD3 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   5.4e-05      0.32      82     103 ..     130     151 ..     127     170 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.4e-05
                            RD3  82 lCakikPsecgkvisrfrevla 103
                                    + +k++P++c++++ r+r ++ 
  gi|116754062|ref|YP_843180.1| 130 VSSKVEPDYCSEIVHRWRWIVY 151
                                    679***************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1580.74
//
Query:       gi|116754063|ref|YP_843181.1|  [L=91]
Description: hypothetical protein Mthe_0751 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); 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: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 699.12
//
Query:       gi|116754064|ref|YP_843182.1|  [L=400]
Description: hypothetical protein Mthe_0752 [Methanosaeta thermophila PT]
Scores for complete 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-56  190.5   0.0    3.1e-56  189.8   0.0    1.3  1  Lar_N       Lactate racemase N-terminal domain
     0.0087   16.4   0.0       0.02   15.2   0.0    1.7  2  GRASP55_65  GRASP55/65 PDZ-like domain
  ------ inclusion threshold ------
      0.016   15.4   0.0      0.026   14.8   0.0    1.3  1  DUF362      Domain of unknown function (DUF362)


Domain annotation for each model (and alignments):
>> Lar_N  Lactate racemase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.8   0.0   5.2e-60   3.1e-56       1     204 []       5     193 ..       5     193 .. 0.94

  Alignments for each domain:
  == domain 1  score: 189.8 bits;  conditional E-value: 5.2e-60
                          Lar_N   1 ygkkkleleipeenllgvlepkevkeekdeeeaieeaLenpigsekleelvkekekvvivvsDiTRptpskiilplllee 80 
                                    yg++++++++++ +  +vl+p+e+++ +d e  ie+aL++pig+  le+l    ++ +++vsDiTRp ps++ilp l+++
  gi|116754064|ref|YP_843182.1|   5 YGNSSVRIKLQDGW--EVLRPNELPPAHDGE--IERALDSPIGA-GLEDLSG--RSAAVIVSDITRPSPSHRILPPLVRR 77 
                                    9************9..*********999998..**********8.9***987..7999********************** PP

                          Lar_N  81 lkeagvkdeditilvAtGlHrkqteeelkkilGeevvkrikvvnhdaedksslvklGttskGtpveinklvaeadlvilt 160
                                    lk +gv  +d+++++A+G+Hr++te+e++++l   v  r   + h ++d+s++v+lG+tskGtpvei+ lv ++dl+i t
  gi|116754064|ref|YP_843182.1|  78 LKGVGV--KDLRVVFALGTHRRMTEDEVRHLLRGCV--R---LPHFQHDASRCVHLGETSKGTPVEIFDLVESSDLIIGT 150
                                    **9999..67**********************9887..4...55555678****************************** PP

                          Lar_N 161 GfiepHyfaGfsGGrKsilpGvasretimanHkavlaepraalg 204
                                    G+ie+Hy+aG+sGG+K++lpGv+s+++i++nH+++  epra++g
  gi|116754064|ref|YP_843182.1| 151 GNIEYHYYAGYSGGAKALLPGVSSERSIHHNHMMMR-EPRARSG 193
                                    *********************************988.9998865 PP

>> GRASP55_65  GRASP55/65 PDZ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.3   7.9e+03      41      71 ..      14      44 ..       8      54 .. 0.78
   2 !   15.2   0.0   3.3e-06      0.02      28      73 ..     107     152 ..      79     230 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.3
                                   TTS-EEEEEEBTTSHHHHHT--TTTEEEEEE CS
                     GRASP55_65 41 aeevwhvldvlegsPaakagLvpksDYiiGl 71
                                   +++ w vl  +e  Pa+  ++    D  iG+
  gi|116754064|ref|YP_843182.1| 14 LQDGWEVLRPNELPPAHDGEIERALDSPIGA 44
                                   5678999999999999999988888777665 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 3.3e-06
                                    SSEEEEEEE-TTTTTS-EEEEEEBTTSHHHHHT--TTTEEEEEEE. CS
                     GRASP55_65  28 lGlslrlaslekaaeevwhvldvlegsPaakagLvpksDYiiGldk 73 
                                    l   +rl ++++ a++++h+ ++ +g P++  +Lv+ sD iiG+ +
  gi|116754064|ref|YP_843182.1| 107 LRGCVRLPHFQHDASRCVHLGETSKGTPVEIFDLVESSDLIIGTGN 152
                                    555689999**********************************976 PP

>> DUF362  Domain of unknown function (DUF362)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   4.3e-06     0.026      58     174 ..      98     280 ..      62     296 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.3e-06
                                    xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                         DUF362  58 aeeagydelaega.diadglegedevvvpvkgkhlkke.lkiakavleaDviInlpklKgHalagvtgalKn.lfGcisg 134
                                    + e  +++l++g+ ++   ++ + +++v + g+++k + ++i   v+  D iI       H +ag++g+ K  l G+ s+
  gi|116754064|ref|YP_843182.1|  98 MTEDEVRHLLRGCvRLPHFQH-DASRCVHL-GETSKGTpVEIFDLVESSDLIIGTGNIEYHYYAGYSGGAKAlLPGVSSE 175
                                    455556666677754444444.44455545.55555556999999***************************88888888 PP

                                    xxxxxxxx...................................................................xxxxx RF
                         DUF362 135 sgkaeiHs...................................................................krdse 147
                                    ++ ++ H+                                                                   +   e
  gi|116754064|ref|YP_843182.1| 176 RSIHHNHMmmreprarsgfldspvrqdmeeaagiagldlilnvvlnsrkeivsavagdyikahragasvvdrmylR---E 252
                                    8766666688889988888888888888888888888888888877777777777776666666665555332221...1 PP

                                    xxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                         DUF362 148 kfaekiadlaka.lkpdlnvvdgikame 174
                                    +    i+  +++  ++d+n+  ++ka+e
  gi|116754064|ref|YP_843182.1| 253 VKPAEIVITCAGgRPKDINLYQAVKALE 280
                                    1122333333331234477777776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2976.10
//
Query:       gi|116754065|ref|YP_843183.1|  [L=81]
Description: hypothetical protein Mthe_0753 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.23   11.2   8.4        3.6    7.4   8.4    2.0  1  DUF2157   Predicted membrane protein (DUF2157)


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 ?    7.4   8.4    0.0002       3.6      73     123 ..      32      80 ..       2      81 .] 0.69

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0002
                        DUF2157  73 llllslllgavlwrdrrvpprlgeallllaalllgaaialvgqifqlsgda 123
                                    + l+s+ +g+vl+   +vp+ +  ++l + +++++a++++++  f+  gd 
  gi|116754065|ref|YP_843183.1|  32 IGLGSATMGVVLLS--NVPQGWEMVALGFFGIAVLAGLWMISVGFKQAGDN 80 
                                    33455555566666..899***********************999998885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 642.17
//
Query:       gi|116754066|ref|YP_843184.1|  [L=203]
Description: hypothetical protein Mthe_0754 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-05   24.3   0.5    8.5e-05   22.0   0.0    2.4  3  HTH_24         Winged helix-turn-helix DNA-binding
      8e-05   22.4   0.4    0.00069   19.4   0.0    2.5  3  HTH_AsnC-type  AsnC-type helix-turn-helix domain
     0.0012   18.8   0.0     0.0053   16.8   0.0    2.1  1  HTH_29         Winged helix-turn helix
      0.002   18.0   0.0      0.005   16.7   0.0    1.7  1  HTH_11         HTH domain
     0.0089   15.8   0.0      0.019   14.7   0.0    1.6  1  HTH_38         Helix-turn-helix domain
      0.009   15.8   0.0      0.027   14.3   0.0    1.9  1  HTH_23         Homeodomain-like domain
     0.0097   15.6   0.0      0.017   14.9   0.0    1.4  1  HTH_DeoR       DeoR-like helix-turn-helix domain
  ------ inclusion threshold ------
      0.022   14.9   0.0       0.21   11.7   0.0    2.5  3  HTH_28         Helix-turn-helix domain
      0.039   13.9   0.4       0.15   12.1   0.0    2.2  2  HTH_Crp_2      Crp-like helix-turn-helix domain
      0.042   13.5   0.9       0.58    9.9   0.0    2.8  3  GntR           Bacterial regulatory proteins, gntR family
      0.043   14.0   0.0       0.17   12.1   0.0    2.1  1  HTH_17         Helix-turn-helix domain
      0.082   12.8   0.0       0.22   11.5   0.0    1.7  1  MarR_2         MarR family
      0.091   12.5   0.1       0.27   11.0   0.1    1.8  1  Sigma70_r4_2   Sigma-70, region 4
      0.096   12.6   0.0       0.23   11.4   0.0    1.6  1  MarR           MarR family
       0.11   12.1   0.1       0.24   11.0   0.1    1.5  1  GerE           Bacterial regulatory proteins, luxR family
       0.15   12.0   0.3       0.76    9.8   0.0    2.1  2  HTH_36         Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       8.6   9.6e+03       5      11 ..      55      61 ..      53      62 .. 0.77
   2 ?   -1.3   0.0       1.5   1.7e+03      30      39 ..     142     151 ..     141     154 .. 0.72
   3 !   22.0   0.0   7.6e-08   8.5e-05      15      45 ..     169     199 ..     162     199 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 8.6
                         HTH_24  5 drkILel 11
                                   ++kIL++
  gi|116754066|ref|YP_843184.1| 55 TKKILSI 61
                                   6899987 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.5
                         HTH_24  30 Spstvnrrlk 39 
                                    S + ++rr++
  gi|116754066|ref|YP_843184.1| 142 SEGKISRRVR 151
                                    6777777776 PP

  == domain 3  score: 22.0 bits;  conditional E-value: 7.6e-08
                         HTH_24  15 nprisqreLAerlglSpstvnrrlkrLeeeG 45 
                                    +pr s +e+A  ++ S++tv+ ++kr++++G
  gi|116754066|ref|YP_843184.1| 169 DPRPSVQEIASLVNYSQTTVRNQIKRMQNSG 199
                                    9***************************998 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 ?   -2.6   0.0       4.5   5.1e+03      17      21 ..     108     112 ..      99     118 .. 0.52
   2 ?   -0.1   0.0      0.73   8.2e+02      23      30 ..     146     153 ..     141     156 .. 0.57
   3 !   19.4   0.0   6.1e-07   0.00069      13      42 .]     167     196 ..     160     196 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 4.5
                  HTH_AsnC-type  17 Risya 21 
                                    R + +
  gi|116754066|ref|YP_843184.1| 108 RKTLK 112
                                    44444 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.73
                  HTH_AsnC-type  23 LAervGlS 30 
                                    +++rv lS
  gi|116754066|ref|YP_843184.1| 146 ISRRVRLS 153
                                    55566555 PP

  == domain 3  score: 19.4 bits;  conditional E-value: 6.1e-07
                  HTH_AsnC-type  13 qedaRisyaeLAervGlSestvlrRvrrLe 42 
                                      d+R s++e+A  v+ S++tv++ ++r++
  gi|116754066|ref|YP_843184.1| 167 ALDPRPSVQEIASLVNYSQTTVRNQIKRMQ 196
                                    569*************************96 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   4.7e-06    0.0053       9      40 ..     163     199 ..     156     202 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.7e-06
                         HTH_29   9 aeGvs.....tvsqiAkllglsrrtvyrwlkrfeegG 40 
                                    ++ +      +v++iA l+++s +tv++ +kr+++ G
  gi|116754066|ref|YP_843184.1| 163 KQLWAldprpSVQEIASLVNYSQTTVRNQIKRMQNSG 199
                                    55544555557***********************999 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   4.5e-06     0.005       5      43 ..     161     199 ..     157     202 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.5e-06
                         HTH_11   5 ilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg 43 
                                     +++L + ++  s +e+A   n S +tvr+ Ik+++ +g
  gi|116754066|ref|YP_843184.1| 161 KIKQLWALDPRPSVQEIASLVNYSQTTVRNQIKRMQNSG 199
                                    567777788888***********************9988 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.7e-05     0.019      22      43 ..     173     194 ..     160     195 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.7e-05
                         HTH_38  22 slreIArrLgrspsTIsRElkR 43 
                                    s+ eIA ++++s +T+ + +kR
  gi|116754066|ref|YP_843184.1| 173 SVQEIASLVNYSQTTVRNQIKR 194
                                    899******************9 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   0.0   2.4e-05     0.027      13      45 ..     167     199 ..     155     203 .] 0.77

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.4e-05
                         HTH_23  13 llaeGlsvreIAreLgvsrrTvyrwlkryreeG 45 
                                    +l+ + sv+eIA + + s+ Tv++ +kr +++G
  gi|116754066|ref|YP_843184.1| 167 ALDPRPSVQEIASLVNYSQTTVRNQIKRMQNSG 199
                                    55545699********************87787 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 !   14.9   0.0   1.5e-05     0.017      16      42 ..     173     199 ..     159     202 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.5e-05
                       HTH_DeoR  16 sveelvellgvSeaTiRRDLneLeeqg 42 
                                    sv+e++ l ++S++T+R+ ++ ++++g
  gi|116754066|ref|YP_843184.1| 173 SVQEIASLVNYSQTTVRNQIKRMQNSG 199
                                    89********************99998 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       1.2   1.3e+03      30      49 ..      14      34 ..       9      36 .. 0.82
   2 ?   -2.8   0.0       6.5   7.3e+03      12      25 ..     138     153 ..     136     155 .. 0.68
   3 ?   11.7   0.0   0.00019      0.21      10      41 ..     168     200 ..     159     203 .] 0.83

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.2
                         HTH_28 30 yrWikryee.gGiagLvprrr 49
                                   +++ kry +  G+ +  +r+r
  gi|116754066|ref|YP_843184.1| 14 SDLQKRYVQiSGFGSYPDRSR 34
                                   678899999899999999987 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6.5
                         HTH_28  12 Ghsvre..aArelgis 25 
                                    G++v+e  ++r++ +s
  gi|116754066|ref|YP_843184.1| 138 GNPVSEgkISRRVRLS 153
                                    6677777777877777 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00019
                         HTH_28  10 aaGh.svreaArelgisrrtvyrWikryeegGi 41 
                                    ++ + sv e+A +++ s++tv+  ikr +  G+
  gi|116754066|ref|YP_843184.1| 168 LDPRpSVQEIASLVNYSQTTVRNQIKRMQNSGE 200
                                    4556799********************998885 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       2.4   2.7e+03      34      49 ..     107     122 ..     105     124 .. 0.71
   2 ?   12.1   0.0   0.00013      0.15      18      49 ..     168     199 ..     144     201 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.4
                                    SHHHHHHHHHHHHHTT CS
                      HTH_Crp_2  34 tretvsrilseLkreg 49 
                                     r t+ r+ seL  +g
  gi|116754066|ref|YP_843184.1| 107 QRKTLKRLASELILKG 122
                                    5778888888876666 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00013
                                    EEEEHHHHHHHHHTTSSHHHHHHHHHHHHHTT CS
                      HTH_Crp_2  18 ielpltqeelAsmlGltretvsrilseLkreg 49 
                                    ++ + + +e+As+++ ++ tv   ++++++ g
  gi|116754066|ref|YP_843184.1| 168 LDPRPSVQEIASLVNYSQTTVRNQIKRMQNSG 199
                                    5668899**********************987 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       3.7   4.1e+03      38      46 ..      32      40 ..      31      43 .. 0.80
   2 ?    0.9   0.1      0.32   3.5e+02      43      58 ..      95     110 ..      94     120 .. 0.79
   3 ?    9.9   0.0   0.00052      0.58      25      50 ..     172     197 ..     161     201 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 3.7
                                   HHHHHHHHH CS
                           GntR 38 rttvReALr 46
                                   r+ +ReA+r
  gi|116754066|ref|YP_843184.1| 32 RSRLREAMR 40
                                   778999997 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.32
                                    HHHHHHHHTTSEEEET CS
                           GntR  43 eALrrLeaeglverrq 58 
                                    eA+  Leae +++r+ 
  gi|116754066|ref|YP_843184.1|  95 EAYMGLEAEAILQRKT 110
                                    6777888888888875 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00052
                                    --HHHHHHHHTS-HHHHHHHHHHHHH CS
                           GntR  25 PsereLaaefgVsrttvReALrrLea 50 
                                    Ps++e+a+  + s ttvR  ++r + 
  gi|116754066|ref|YP_843184.1| 172 PSVQEIASLVNYSQTTVRNQIKRMQN 197
                                    9*****************99888765 PP

>> HTH_17  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   0.00015      0.17       3      29 ..     173     203 .]     173     203 .] 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00015
                         HTH_17   3 tveEaAelLgvsrstvyrlir....rgelpa 29 
                                    +v+E+A l + s++tv++ i+    +gelp+
  gi|116754066|ref|YP_843184.1| 173 SVQEIASLVNYSQTTVRNQIKrmqnSGELPP 203
                                    69******************54444999986 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00019      0.22      19      49 ..     170     199 ..     163     201 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00019
                                    TSEEEHHHHHHHHTSSHHHHHHHHHHHHHTT CS
                         MarR_2  19 grdltvgelarrlglsksavsrilkrLvaaG 49 
                                    +r  +v+e+a   ++s+ +v + +kr++  G
  gi|116754066|ref|YP_843184.1| 170 PR-PSVQEIASLVNYSQTTVRNQIKRMQNSG 199
                                    33.5***********************9877 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 ?   11.0   0.1   0.00024      0.27      28      49 ..     173     194 ..     173     195 .. 0.96

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00024
                                    -HHHHHHHHT--HHHHHHHHHH CS
                   Sigma70_r4_2  28 sykEIAellgisegtVksrlsR 49 
                                    s +EIA+l + s +tV+++++R
  gi|116754066|ref|YP_843184.1| 173 SVQEIASLVNYSQTTVRNQIKR 194
                                    789*****************98 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0002      0.23      13      45 ..     166     199 ..     158     200 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0002
                                    HHSTT.EEHHHHHHHHTS-HHHHHHHHHHHHHTT CS
                           MarR  13 yeqgp.lsvseLakklgvskstvtrvldrLekkG 45 
                                    +  +p +sv+e+a+ ++ s++tv ++++r+   G
  gi|116754066|ref|YP_843184.1| 166 WALDPrPSVQEIASLVNYSQTTVRNQIKRMQNSG 199
                                    55555599*********************98765 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00021      0.24      19      42 ..     173     196 ..     172     197 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00021
                                    -HHHHHHHHTS-HHHHHHHHHHHH CS
                           GerE  19 snkeIAeelniSekTVkvhksnim 42 
                                    s++eIA+  n S++TV++++++++
  gi|116754066|ref|YP_843184.1| 173 SVQEIASLVNYSQTTVRNQIKRMQ 196
                                    689*******************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 ?   -0.9   0.1       1.5   1.6e+03      39      54 ..     108     123 ..     102     123 .. 0.85
   2 ?    9.8   0.0   0.00068      0.76      26      48 ..     172     194 ..     164     199 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.5
                         HTH_36  39 knTvsraikeLeqlGy 54 
                                    ++T  r   eL+ +G+
  gi|116754066|ref|YP_843184.1| 108 RKTLKRLASELILKGI 123
                                    8999999999999985 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00068
                         HTH_36  26 psqetlakrlglsknTvsraike 48 
                                    ps++ +a++ + s  Tv++ ik 
  gi|116754066|ref|YP_843184.1| 172 PSVQEIASLVNYSQTTVRNQIKR 194
                                    8********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1566.84
//
Query:       gi|116754067|ref|YP_843185.1|  [L=213]
Description: NADPH-dependent FMN reductase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.8e-33  114.1   0.0    6.3e-33  113.7   0.0    1.1  1  FMN_red       NADPH-dependent FMN reductase
    4.7e-07   29.7   0.0    6.4e-07   29.3   0.0    1.2  1  Flavodoxin_2  Flavodoxin-like fold


Domain annotation for each model (and alignments):
>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.7   0.0     7e-37   6.3e-33       3     150 ..      12     163 ..      10     167 .. 0.92

  Alignments for each domain:
  == domain 1  score: 113.7 bits;  conditional E-value: 7e-37
                                    EEEEES--STT-HHHHHHHHHHCCT-T.T-CEEEEETTTS..--.....---HCHGHTCGGSHHHHHHHHHHHH-SCEEE CS
                        FMN_red   3 ilvisGSlrkgsntrklaewaaealkeagaevelidladl.ilpc...alcdkdlesegqtsddvaellekiaaadalii 78 
                                    il+isGS+r ++ t+ ++ +a+e+l+e+g+e+el++++++ i  c   ++c+k ++  +  +dd+ el+  +++a +li+
  gi|116754067|ref|YP_843185.1|  12 ILGISGSPR-NRATEHVLSRALEMLRESGFETELFTVRGKnIGFCrhcDYCLKNKT--CAIKDDMYELYPLLKNARGLIF 88 
                                    9*******7.******************************9999988777776664..68******************** PP

                                    EEEECTTCE-HHHHHHHHCHT-...SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHH.HTT-EEEECSEEEE CS
                        FMN_red  79 vtPeYngsysgllKnalDrlsr..trgkkelrgKpvalvavgggrrgglraeeqlrqvla.elgaivvpraavav 150
                                    +tP+Yng++s++ K+++Dr+++   ++ + +rgK+++++avgg+r gg++a+      +   +g+i+v+++ + +
  gi|116754067|ref|YP_843185.1|  89 ATPVYNGGVSAQTKAVMDRCRAlvAADFDFFRGKVGMAIAVGGDRIGGQEAAIYQIITFYiLNGVIPVGGGSFGA 163
                                    ********************99**9***************************99999999668888888887765 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0   7.2e-11   6.4e-07       3     103 ..      12     108 ..      11     146 .. 0.77

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 7.2e-11
                                    EEEEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCCT-----CCCCHCCHHHHTT....CHHHHHHHHHHHHCS CS
                   Flavodoxin_2   3 iLiinahprpeksfssalaqafvealekagphevtvrdLyadflpvlttrdlaaklayeek....padveseqiekllaa 78 
                                    iL i ++pr     + +++ +++e l+++g  e + + +    + ++++ d+      ++k    + d ++     l++a
  gi|116754067|ref|YP_843185.1|  12 ILGISGSPRN--RATEHVLSRALEMLRESG-FETELFTVRGKNIGFCRHCDYC----LKNKtcaiKDDMYELY-PLLKNA 83 
                                    78899****9..888***************.8888888877655555443332....2222322235555555.****** PP

                                    SEEEEEEE-BTTB--HHHHHHHHHH CS
                   Flavodoxin_2  79 daivlqfPlwwfgvPailKgwiDrv 103
                                      +++++P+++ gv+a+ K+ +Dr 
  gi|116754067|ref|YP_843185.1|  84 RGLIFATPVYNGGVSAQTKAVMDRC 108
                                    ***********************94 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1551.01
//
Query:       gi|116754068|ref|YP_843186.1|  [L=235]
Description: hypothetical protein Mthe_0756 [Methanosaeta thermophila PT]
Scores for complete 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  194.6  15.3    1.2e-57  194.6  15.3    1.6  2  DUF1614   Protein of unknown function (DUF1614)


Domain annotation for each model (and alignments):
>> DUF1614  Protein of unknown function (DUF1614)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.7      0.21   3.7e+03     105     121 ..      13      29 ..       5      40 .. 0.42
   2 !  194.6  15.3   6.8e-62   1.2e-57       1     170 []      56     234 ..      56     234 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.21
                        DUF1614 105 aalaalllaeeeaaava 121
                                     ++a l+l     ++v 
  gi|116754068|ref|YP_843186.1|  13 LFMAVLALLAFLVVSVL 29 
                                    22222333333333333 PP

  == domain 2  score: 194.6 bits;  conditional E-value: 6.8e-62
                        DUF1614   1 llgslinipvaelkskeelve...vkvlgisykvpvleeeekktvvavNvGGaviPlllslylllrlavsllaallavli 77 
                                    l+gs+inip  e+ks+ +l++   v+v+g++y++p++e+  ++t+va+NvGGa+iP+l+s+yll++++ +l+ a++a++i
  gi|116754068|ref|YP_843186.1|  56 LVGSSINIPFREMKSEMPLTRtayVRVFGVNYRIPIYETVYNSTTVALNVGGALIPILVSAYLLMMFSHALAYAVAATVI 135
                                    79*************887744479********************************************99********** PP

                        DUF1614  78 vaavvyllarpvpgvGivvpllipplvaalaalllaeeea......aavaYisgvlGtLiGadllnlkkieklgapvvsI 151
                                    v+++v+++arpvpg+Giv+p+l+ppl+aal++l++           ++vaY+sg+lGtLiGad+lnl++i+ lgapvvsI
  gi|116754068|ref|YP_843186.1| 136 VTIAVHRIARPVPGLGIVTPALLPPLIAALSSLAVIIIAGgpreleFVVAYVSGTLGTLIGADILNLNRIQGLGAPVVSI 215
                                    ******************************9955544333456889********************************** PP

                        DUF1614 152 GGaGtFdGifltgilavll 170
                                    GGaGtFdG+fltg++avll
  gi|116754068|ref|YP_843186.1| 216 GGAGTFDGVFLTGLIAVLL 234
                                    *****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       917  (0.0511462); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1789.18
//
Query:       gi|116754069|ref|YP_843187.1|  [L=218]
Description: phosphoglycerate mutase 1 family protein [Methanosaeta thermophila PT]
Scores for 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  110.2   0.0    1.4e-22   80.3   0.0    2.0  2  His_Phos_1  Histidine phosphatase superfamily (branch 1)


Domain annotation for each model (and alignments):
>> His_Phos_1  Histidine phosphatase superfamily (branch 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.3   0.0   7.8e-27   1.4e-22       1     105 [.       4     113 ..       4     122 .. 0.87
   2 !   28.6   0.0   5.6e-11     1e-06      94     164 ..     120     192 ..     112     197 .. 0.82

  Alignments for each domain:
  == domain 1  score: 80.3 bits;  conditional E-value: 7.8e-27
                                    EEEEE---BTTB--....TT----B-HHHHHHHHHHHHHHTT..S---EEEE-SSHHHHHHHHHHHHCTT...--EEE-G CS
                     His_Phos_1   1 lyLvRHGetewnaegrlqgrtdvpLteeGreqAealaerlag..epidaiysSplkRarqTaeliaealg...lpvelde 75 
                                    l+L+RHG++ +nae+r+ g++d++Lt++G+ +A+++++ l++    +d +++S l+Ra++T   ++++++   +pv++  
  gi|116754069|ref|YP_843187.1|   4 LVLLRHGQSSYNAERRFTGWSDPDLTAQGMIEAREAGRILRRsgYTLDIAFVSMLRRAIKTLCGVLDEMDllwIPVRKSW 83 
                                    79***************************************977777888****************************** PP

                                    GGS----GGGTT-B.HHHHHH..HSHHHHH CS
                     His_Phos_1  76 gLrEidfGdweglttaeiaeeypeeleawl 105
                                     L+E+++G++eg+  +++ +e + + + ++
  gi|116754069|ref|YP_843187.1|  84 MLNERHYGELEGQIIDDVPDELKMYRHSFD 113
                                    *************66666655444444333 PP

  == domain 2  score: 28.6 bits;  conditional E-value: 5.6e-11
                                    HHH..HSHHHHHHHHH-GGG-BS-BHHHHHHHHHHHHH.HHHHHTTTSE.EEEEE-HHHHHHHHHHHHT--GG CS
                     His_Phos_1  94 aeeypeeleawlrdpadvrppggEsledvaaRvaaale.elaarheget.vlvVsHggvirallarllglple 164
                                     e+ p+ ++  +r ++ ++pp gEs++dv++R+   +  e+a +  +++ v+v +H+ vira++++l g+p e
  gi|116754069|ref|YP_843187.1| 120 SEDDPRHPRFDRRYSDLESPPAGESIRDVQERLLILWTyEIAPEILSGRgVIVTTHANVIRAFMNYLEGVPTE 192
                                    5666777777777777778888***********99888777777666666*******************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       198  (0.0110436); expected 358.6 (0.02)
Passed bias filter:                      193  (0.0107647); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1668.20
//
Query:       gi|116754070|ref|YP_843188.1|  [L=161]
Description: hypothetical protein Mthe_0758 [Methanosaeta thermophila PT]
Scores for complete sequence (score 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   13.8   0.1       0.18   12.5   0.1    1.7  1  NADH-u_ox-rdase  NADH-ubiquinone oxidoreductase complex I, 21


Domain annotation for each model (and alignments):
>> NADH-u_ox-rdase  NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1     1e-05      0.18       3      38 ..      89     124 ..      87     136 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1e-05
                NADH-u_ox-rdase   3 aYpvIdsdPsfsrvlrnfrpsDYvkaaaitaafpla 38 
                                     YpvI ++P   +v++++  ++Y+++  + ++ pl 
  gi|116754070|ref|YP_843188.1|  89 SYPVIAEQPGYYDVVSSISYTEYGAMRELQMVSPLV 124
                                    6***********************998777666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); 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: 00:00:00.40
# Mc/sec: 1212.33
//
Query:       gi|116754071|ref|YP_843189.1|  [L=359]
Description: hypothetical protein Mthe_0759 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-09   37.6   0.0      6e-05   22.5   0.0    2.2  2  Glyco_trans_1_3  Glycosyl transferase family 1
    4.7e-05   23.4   0.0    7.1e-05   22.8   0.0    1.2  1  Glyco_tran_28_C  Glycosyltransferase family 28 C-terminal dom
    0.00013   22.0   0.0     0.0004   20.4   0.0    1.7  2  Glyco_transf_4   Glycosyltransferase Family 4
    0.00061   20.3   0.0     0.0011   19.5   0.0    1.3  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain


Domain annotation for each model (and alignments):
>> Glyco_trans_1_3  Glycosyl transferase family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   1.3e-08     6e-05      11      48 ..       9      48 ..       2     107 .. 0.83
   2 !   13.2   0.0   8.8e-06     0.039     248     299 ..     260     312 ..     217     329 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.3e-08
                Glyco_trans_1_3 11 GaGhasRsrvvlehL.arghevkvvvsgraldvLekef.d 48
                                   G GhasR   +++ L argh+v v++sg al+ L+kef +
  gi|116754071|ref|YP_843189.1|  9 GLGHASRDIPIIRELlARGHDVTVASSGNALELLRKEFpE 48
                                   89**********9998********************9944 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 8.8e-06
                Glyco_trans_1_3 248 leDLataraviagagftLmtealyLkk.PlLavPvarqFeqvlnalyLerlgy 299
                                    +e + +ar vi+ +g+t m e   L+k   L +P  +q eq    ++  + g+
  gi|116754071|ref|YP_843189.1| 260 VELMNRARFVISRSGYTTMMEIAELGKkHGLFIPTPGQTEQEYLSRFYRKRGW 312
                                    677889***************999976156***********999999888775 PP

>> Glyco_tran_28_C  Glycosyltransferase family 28 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   1.6e-08   7.1e-05      58     108 ..     249     300 ..     203     306 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.6e-08
                                    EEEESS..SSHHHHHHHH-EEEECS-CHHHHHHHHTT--E.EEE--TT....S- CS
                Glyco_tran_28_C  58 evfefi..dkmaeaikaadLvIsRAGagtiaEllalgkpl.Ilvplpeaaenhq 108
                                    +v++++  d  +e++ +a  vIsR+G +t +E++ lgk++ +++p p ++e  q
  gi|116754071|ref|YP_843189.1| 249 RVYSYVptDVKVELMNRARFVISRSGYTTMMEIAELGKKHgLFIPTPGQTE--Q 300
                                    44444411336799***********************975499***99884..4 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   8.9e-08    0.0004      12     139 ..      20     154 ..      19     158 .. 0.62
   2 ?   -1.9   0.0      0.66     3e+03      21      60 ..     287     323 ..     272     334 .. 0.58

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 8.9e-08
                 Glyco_transf_4  12 araLarrGheVtvvtpgddgpleeev............elvvrvprvplpllkrllrslafl........rrlrrllkre 71 
                                    +r+L +rGh+Vtv ++g   +l +++            +    + +  +++l+++  +l+ +        r l+++l r 
  gi|116754071|ref|YP_843189.1|  20 IRELLARGHDVTVASSGNALELLRKEfpecrfivfedyP---VPYSSTRFFLPKFTAYLPIMmkaladerRNLAHILSRD 96 
                                    699***********9999999999999998887775332...22222222222222222111222233336889999999 PP

                 Glyco_transf_4  72 kpDvvHahspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrvia 139
                                    ++D++ + + + + ++       ++ip  +  H l     ++++ +p +    ++  +++++   vi+
  gi|116754071|ref|YP_843189.1|  97 RYDLIISDNRMGV-YS-------KDIPSFFITHQLR--FSVPFFMWPVELTTLYVNGYFHKKFTGVIV 154
                                    *****98886665.22.......4888888888887..355555555555555555555555555555 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.66
                 Glyco_transf_4  21 eVtvvtpgddgpleeevelvvrvprvplpllkrllrslaf 60 
                                    +  ++ p++++ ++e    + r+ r++ ++l r +++l  
  gi|116754071|ref|YP_843189.1| 287 KHGLFIPTPGQTEQEY---LSRFYRKRGWFLSRSQYRLDL 323
                                    5555555555555555...555555555555555555544 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 !   19.5   0.0   2.4e-07    0.0011      10      83 ..      19     107 ..      14     143 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.4e-07
                Glyco_trans_4_4  10 laraLaarGheVtvltpapapgapeleedgvrvhrl...pvprrpspladlaal..............ralrrllrqrre 72 
                                    ++r+L arGh+Vtv  ++ a +  + e + +r + +   pvp+++ ++  ++++              r l+ +l   r 
  gi|116754071|ref|YP_843189.1|  19 IIRELLARGHDVTVASSGNALELLRKEFPECRFIVFedyPVPYSSTRFFLPKFTaylpimmkaladerRNLAHIL--SRD 96 
                                    689*******************9999999***99664448****9888887877555666666666666677788..9** PP

                Glyco_trans_4_4  73 rpdvvhahspt 83 
                                    r+d++++ + +
  gi|116754071|ref|YP_843189.1|  97 RYDLIISDNRM 107
                                    *****976654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); 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 0.23s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2678.66
//
Query:       gi|116754072|ref|YP_843190.1|  [L=100]
Description: hypothetical protein Mthe_0760 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); 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: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 729.26
//
Query:       gi|116754073|ref|YP_843191.1|  [L=265]
Description: coenzyme M methyltransferase subunit X [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 1926.45
//
Query:       gi|116754074|ref|YP_843192.1|  [L=321]
Description: AIR synthase-like protein [Methanosaeta thermophila PT]
Scores for 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-17   62.1   0.6    1.1e-16   61.3   0.6    1.4  1  AIRS      AIR synthase related protein, N-terminal domain
    6.6e-17   62.1   0.0    1.3e-16   61.1   0.0    1.5  1  AIRS_C    AIR synthase related protein, C-terminal domain
  ------ inclusion threshold ------
      0.092   12.4   0.0       0.17   11.5   0.0    1.4  1  PP2C      Protein phosphatase 2C


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 !   61.3   0.6   1.8e-20   1.1e-16       1      92 [.      45     148 ..      45     150 .. 0.84

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 1.8e-20
                                    SSSEE........EEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC...HHHHHHHHHHHHHHHT CS
                           AIRS   1 dDaav........vvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp...wleevvrglaeaaeel 69 
                                    +Daav        ++++d+  + ++ ++ + +G+ av vn+ D+aamG++P+a++++l+++     ++v+rg+++++e++
  gi|116754074|ref|YP_843192.1|  45 EDAAVidngdevlLLAADGIWSVLMDADPEWAGYCAVLVNVHDIAAMGGTPIAMVDVLSVNspeVTDAVLRGVKRGIEKF 124
                                    58884444444448889988888888777889*******************************999************** PP

                                    T-EEEEEEEEEESS.EEEEEEEEE CS
                           AIRS  70 gvplvgGdtsfsne.ptisvtavG 92 
                                    gvp+vgG+++ ++    + v+++G
  gi|116754074|ref|YP_843192.1| 125 GVPIVGGHLHPDTPySALDVAILG 148
                                    *********998654566777766 PP

>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.1   0.0   2.2e-20   1.3e-16      38     154 ..     190     301 ..     162     303 .. 0.86

  Alignments for each domain:
  == domain 1  score: 61.1 bits;  conditional E-value: 2.2e-20
                                    HHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHHHHHHHTTTEEEEEECGTHHHHHHHHHHHHHHHCSTTTEEEE CS
                         AIRS_C  38 lgdvlleptliyvkralaalkglvkaahDvTgGGLlgalaemapasgvgaeidldkvpifdelesplemllsensGrllv 117
                                      d + + ++i  +ral ++ +lv+a +D+++ G lg+l ++++ sgvga++dld++p+ + l   l  +   + G ++v
  gi|116754074|ref|YP_843192.1| 190 HKDRETLARQISSMRALGER-KLVTAGKDISNPGMLGTLGMLLETSGVGAVVDLDAIPVPESL--NLVDWMKMYPGMGFV 266
                                    57888888999********8.****************************************98..678888999999999 PP

                                    EEEHGGHHHHHHHHHHTTCCCEEEEEEEEESSSEEEE CS
                         AIRS_C 118 avppeeadavlaileeeglpeaavIGevtakeelsvi 154
                                    +  ++ + +v+++++++gl  aa+IG+v+++++l+v+
  gi|116754074|ref|YP_843192.1| 267 VTTRDPS-EVVDVFGKHGL-SAARIGRVIEERRLEVV 301
                                    9999999.9**********.7***********99875 PP

>> PP2C  Protein phosphatase 2C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   2.8e-05      0.17     198     222 ..      47      71 ..      14      73 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.8e-05
                                    EEEE-TTEEEEEEE-HHHHTTSHHH CS
                           PP2C 198 svklteedefliLacdGlwdvlsdq 222
                                     + +++ de l+La dG+w vl d 
  gi|116754074|ref|YP_843192.1|  47 AAVIDNGDEVLLLAADGIWSVLMDA 71 
                                    5668899**************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 2469.67
//
Query:       gi|116754075|ref|YP_843193.1|  [L=190]
Description: hypothetical protein Mthe_0763 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); 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: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 1604.37
//
Query:       gi|116754076|ref|YP_843194.1|  [L=401]
Description: phosphotransferase domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score 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      0.017   15.4   0.0    1.4  1  PHP       PHP domain
      0.024   14.4   0.0      0.083   12.7   0.0    1.9  2  PHP_C     PHP-associated
      0.092   11.1   0.1       0.13   10.5   0.1    1.1  1  DUF530    Protein of unknown function (DUF530)


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 ?   15.4   0.0   2.9e-06     0.017       1      36 [.       6      42 ..       6     179 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.9e-06
                                   EEEE--CCC.--.S-H..HHHHHHHHHCT-SEEEEEE CS
                                   xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            PHP  1 dlHvHteys.lldgalsieelvkkakelglkaiaiTD 36
                                   dlH+H++ys +++ ++ ++ ++++a+++g++ ++  D
  gi|116754076|ref|YP_843194.1|  6 DLHIHSKYSaATSKMMDLDTIAAEARRKGIHIVGTGD 42
                                   89********8889****************9998766 PP

>> PHP_C  PHP-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.4e-05     0.083       7      52 ..     178     225 ..     174     228 .. 0.87
   2 ?   -3.2   0.0       1.3   7.5e+03      12      22 ..     264     274 ..     260     274 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.4e-05
                          PHP_C   7 ArrfAeklglpgtgGSDAHrle..eVGrayTefeepiatpdelleair 52 
                                    A+r+ e +++ ++ +SD H+++  ++Gr +++f+ +  +++e+  ai 
  gi|116754076|ref|YP_843194.1| 178 ADRISELRDKTFLSNSDGHSPWsnKLGREFNQFDIRDISFQEIRLAIE 225
                                    999*****************98556********999989999988876 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.3
                          PHP_C  12 eklglpgtgGS 22 
                                    e+lg +++gGS
  gi|116754076|ref|YP_843194.1| 264 ERLGRCACGGS 274
                                    78999999999 PP

>> DUF530  Protein of unknown function (DUF530)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   2.2e-05      0.13     123     172 ..     245     289 ..     241     292 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 2.2e-05
                         DUF530 123 yaelkCksCekkyklseleleskkCecgseefklkvnkegiyRleiipyL 172
                                    y    C++C+k+y ++e+ ++  +C cg   +kl v      R+ei++ L
  gi|116754076|ref|YP_843194.1| 245 YNRTACTRCYKQYTMREMDERLGRCACGG-SIKLGV----RDRVEILADL 289
                                    77789***********************8.444443....3466666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); 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:                         3  (0.000167327); expected 0.2 (1e-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 0.23s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 3241.51
//
Query:       gi|116754077|ref|YP_843195.1|  [L=1624]
Description: hypothetical protein Mthe_0765 [Methanosaeta thermophila PT]
Scores for complete 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  136.9   1.4    4.6e-11   42.9   0.4    9.2 10  DUF11        Domain of unknown function DUF11
      1e-10   41.9   0.8       0.17   12.1   0.0    7.3  8  bMG10        Bacterial Alpha-2-macroglobulin MG10 domain
    2.4e-09   37.4   0.0       0.49   10.7   0.0    6.0  7  Chlam_OMP6   Chlamydia cysteine-rich outer membrane protein 6
    5.3e-08   33.1   5.9       0.01   16.0   0.7    5.3  5  CARDB        CARDB
    7.3e-05   22.9   1.3      0.099   12.9   0.1    5.1  5  NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosi
  ------ inclusion threshold ------
        1.2    8.4   3.0        1.8    7.9   3.0    1.2  1  GpcrRhopsn4  Rhodopsin-like GPCR transmembrane domain


Domain annotation for each model (and alignments):
>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.1   3.2e+03      52      79 ..      56      89 ..      46      95 .. 0.67
   2 ?    1.2   0.0      0.15   4.5e+02      11      46 ..      93     126 ..      82     130 .. 0.79
   3 !   27.0   1.1   1.4e-09   4.2e-06       5      86 ..     212     295 ..     206     299 .. 0.85
   4 !   13.3   0.0   2.6e-05     0.077       7      51 ..     348     392 ..     342     438 .. 0.76
   5 !   23.4   0.0   1.9e-08   5.5e-05      12      83 ..     492     571 ..     482     577 .. 0.90
   6 ?    4.1   0.0     0.019        57      29      83 ..     766     829 ..     736     836 .. 0.69
   7 ?    2.7   0.0     0.051   1.5e+02      15      74 ..     874     955 ..     864     971 .. 0.65
   8 !   42.9   0.4   1.6e-14   4.6e-11       4      79 ..     982    1061 ..     979    1068 .. 0.86
   9 !    7.2   0.0     0.002       6.1       3      39 ..    1101    1137 ..    1099    1181 .. 0.79
  10 ?   -2.2   0.0       1.8   5.2e+03      24      79 ..    1534    1591 ..    1531    1597 .. 0.65

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.1
                          DUF11 52 qgtasaltsv....gsL..eagesatlsftvrvt 79
                                   +g+ s  ++v    ++L  + g+ a l++tv++ 
  gi|116754077|ref|YP_843195.1| 56 SGNTSSVYTVdgipRDLyePLGNDAELTITVEPD 89
                                   4566666666666766688889999999999875 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.15
                          DUF11  11 rpGdtvtytltvtNtgpasangvvvtDtlPaglayv 46 
                                    + Gd v++t+ +      +  +++++ tlP+gl y 
  gi|116754077|ref|YP_843195.1|  93 TIGDVVVFTVRLE--LSEDVHELQIKNTLPSGLDYL 126
                                    6788888888775..6666779**********9986 PP

  == domain 3  score: 27.0 bits;  conditional E-value: 1.4e-09
                          DUF11   5 vdksevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsas....qgtasaltsvgsLeagesatlsftvrvtr 80 
                                    ++ ++v +Gd v+ ++t++N+g ++a++v +t t   gl+  sv +     +g++  ++  ++++ g+  tl++ +rv++
  gi|116754077|ref|YP_843195.1| 212 SNITKVEAGDIVEQVVTLSNRGSSDAYDVNLTVTIADGLEVLSVESDhvadRGSIASTY--TRIPRGAAETLKLVLRVRN 289
                                    445699****************************************9775544443333..69***************** PP

                          DUF11  81 taasga 86 
                                    t  sg 
  gi|116754077|ref|YP_843195.1| 290 TVVSGE 295
                                    *98875 PP

  == domain 4  score: 13.3 bits;  conditional E-value: 2.6e-05
                          DUF11   7 ks.evrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsas 51 
                                    +    + Gd vty + + N   a + +v +tD+lP+g++y ++s  
  gi|116754077|ref|YP_843195.1| 348 TNkSCAIGDSVTYKIHL-NLPRAILREVIITDILPSGTTYNPSSLM 392
                                    4447899********98.77777779****************9987 PP

  == domain 5  score: 23.4 bits;  conditional E-value: 1.9e-08
                          DUF11  12 pGdtvtytltvtNtgpasa..ngvvvtDtlPaglayvsvsas......qgtasaltsvgsLeagesatlsftvrvtrtaa 83 
                                     Gd+vt+tl +   g++ +  +++ + D  P+g ++++  as      q+  +  +s ++L  ges t+++t+ v++t++
  gi|116754077|ref|YP_843195.1| 492 VGDEVTFTLSFHHDGTSRSdaYDLLLVDSIPEGARLMEINASrpmgfeQAGRDLVWSLQRLDRGESVTITYTILVNTTGS 571
                                    7**********98887654449********************9999998888999999*******************987 PP

  == domain 6  score: 4.1 bits;  conditional E-value: 0.019
                          DUF11  29 sangvvvtDtlPaglayvsvsas....qgtasaltsv.........gsLeagesatlsftvrvtrtaa 83 
                                    +a +vv++   P+++ + + s +    +g ++    +         ++L +gesa l++ + +   ++
  gi|116754077|ref|YP_843195.1| 766 DAWNVVLRESIPSNTGILPESVKtspeRGDIE----IcdglliwriKRLGPGESALLEYDIVALSDGR 829
                                    4589***********99999988566633333....2333356666999********99888776665 PP

  == domain 7  score: 2.7 bits;  conditional E-value: 0.051
                          DUF11  15 tvtytltvtNtgpasangvvvtDtlPaglayvsvsas......................qgtasaltsvgsLeagesatl 72 
                                     v+yt+  +N g +   g+v++    + la++s+s                        +g+++  t++g+ ++g     
  gi|116754077|ref|YP_843195.1| 874 FVNYTIHYRNIGEREIRGAVIEARYDPLLAFISSSPMpcspdgsiwsgcalpevlhpgdEGVIRIITRAGRAANGTDVDT 953
                                    589******************99998888888888876666444444444444444444444444444444455555555 PP

                          DUF11  73 sf 74 
                                    +f
  gi|116754077|ref|YP_843195.1| 954 TF 955
                                    55 PP

  == domain 8  score: 42.9 bits;  conditional E-value: 1.6e-14
                          DUF11    4 tvdksevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsv....gsLeagesatlsftvr 77  
                                     t ++++v  G+tvtyt+  +Ntg+++a++v+++ + P+++++vs+s+  g+ + +  v     +L +g  +t+s+++ 
  gi|116754077|ref|YP_843195.1|  982 TGSPERVERGGTVTYTVSYRNTGTTKATNVTLRALFPSNVRIVSASHMPGISNSEDIVwsksSELMPGDMRTVSIRAL 1059
                                     5677899*****************************************55555554444559**************98 PP

                          DUF11   78 vt 79  
                                     v 
  gi|116754077|ref|YP_843195.1| 1060 VD 1061
                                     86 PP

  == domain 9  score: 7.2 bits;  conditional E-value: 0.002
                          DUF11    3 KtvdksevrpGdtvtytltvtNtgpasangvvvtDtl 39  
                                     K+ + +e r G+t++y + v N++ +++ +++v+ ++
  gi|116754077|ref|YP_843195.1| 1101 KQPSCTECRRGETIDYEIRVCNPSDTDLRNITVKEIP 1137
                                     5666678999***********************9977 PP

  == domain 10  score: -2.2 bits;  conditional E-value: 1.8
                          DUF11   24 NtgpasangvvvtDtlPaglayvsvsasqgtasaltsv..gsLeagesatlsftvrvt 79  
                                     N g ++++ v +t ++P g +   v     + + l++     L ag s+ +++++ v+
  gi|116754077|ref|YP_843195.1| 1534 NDGIRDLSPVYITAMVPNGSKVLGVYPEPEIEEDLMNWivDLLRAGDSLVITLRMDVR 1591
                                     6677777777777777777766666555333333333344888999999999998886 PP

>> bMG10  Bacterial Alpha-2-macroglobulin MG10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   0.00018      0.54      22      56 ..      91     125 ..      68     129 .. 0.84
   2 !    5.2   0.1    0.0075        22      21      67 ..     213     263 ..     196     280 .. 0.81
   3 !   12.1   0.0   5.8e-05      0.17      17      57 ..     348     387 ..     334     425 .. 0.82
   4 ?    1.1   0.0      0.14   4.2e+02      25      60 ..     492     531 ..     474     571 .. 0.69
   5 ?    1.5   0.0      0.11   3.2e+02      22      67 ..     744     793 ..     721     811 .. 0.80
   6 ?   -0.6   0.0      0.49   1.5e+03      22      60 ..     987    1027 ..     973    1053 .. 0.78
   7 ?   -3.4   0.0       3.4     1e+04      21      46 ..    1102    1133 ..    1089    1135 .. 0.64
   8 ?   -1.9   0.0       1.2   3.7e+03      23      46 ..    1576    1600 ..    1562    1603 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00018
                          bMG10  22 klkvGdkvrvrltvttprdleyvaledplPAGlep 56 
                                    + + Gd+v  +++++ ++d+++ +++  lP+Gl  
  gi|116754077|ref|YP_843195.1|  91 NRTIGDVVVFTVRLELSEDVHELQIKNTLPSGLDY 125
                                    6789****************************975 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0075
                          bMG10  21 a..klkvGdkvrvrltvt..tprdleyvaledplPAGlepvnpslgteses 67 
                                    +  k+++Gd v+ ++t++   ++d ++v l   ++ Gle++ +++    ++
  gi|116754077|ref|YP_843195.1| 213 NitKVEAGDIVEQVVTLSnrGSSDAYDVNLTVTIADGLEVLSVESDHVADR 263
                                    13489*******9999995456699****************9988766655 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 5.8e-05
                          bMG10  17 sksdaklkvGdkvrvrltvttprdl.eyvaledplPAGlepv 57 
                                    ++  ++ + Gd v+ +++++ pr++ ++v++ d lP+G++  
  gi|116754077|ref|YP_843195.1| 348 TN--KSCAIGDSVTYKIHLNLPRAIlREVIITDILPSGTTYN 387
                                    22..2799***************877************9855 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.14
                          bMG10  25 vGdkvrvrltvt....tprdleyvaledplPAGlepvnps 60 
                                    vGd+v+ +l+      + +d ++ +l+d++P G+ + + +
  gi|116754077|ref|YP_843195.1| 492 VGDEVTFTLSFHhdgtSRSDAYDLLLVDSIPEGARLMEIN 531
                                    7888888777642221556888888888888887766544 PP

  == domain 5  score: 1.5 bits;  conditional E-value: 0.11
                          bMG10  22 klkvGdkvrvrltvt.tpr...dleyvaledplPAGlepvnpslgteses 67 
                                     +++Gd+ r +l+++ +++   d  +v+l++++P+ + ++ +s +t+ e+
  gi|116754077|ref|YP_843195.1| 744 GMARGDTSRLTLRINhSQEsrcDAWNVVLRESIPSNTGILPESVKTSPER 793
                                    48899999999999953332234469*********999999888887765 PP

  == domain 6  score: -0.6 bits;  conditional E-value: 0.49
                          bMG10   22 klkvGdkvrvrltvt.tpr.dleyvaledplPAGlepvnps 60  
                                     ++++G +v+ +++ + t + + ++v l+  +P+ + +v  s
  gi|116754077|ref|YP_843195.1|  987 RVERGGTVTYTVSYRnTGTtKATNVTLRALFPSNVRIVSAS 1027
                                     78899999988888854443669999999999999998765 PP

  == domain 7  score: -3.4 bits;  conditional E-value: 3.4
                          bMG10   21 a....klkvGdkvrvrltvttpr..dleyval 46  
                                     +    + ++G+++  +++v  p+  dl+++ +
  gi|116754077|ref|YP_843195.1| 1102 QpsctECRRGETIDYEIRVCNPSdtDLRNITV 1133
                                     23454789999999999998655115566655 PP

  == domain 8  score: -1.9 bits;  conditional E-value: 1.2
                          bMG10   23 lkvGdkvrvrltvttprdl.eyval 46  
                                     l++Gd + ++l++ + ++l +++++
  gi|116754077|ref|YP_843195.1| 1576 LRAGDSLVITLRMDVRDALcREILV 1600
                                     899*********9998877566665 PP

>> Chlam_OMP6  Chlamydia cysteine-rich outer membrane protein 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.4   4.1e+03      36      81 ..     106     154 ..      77     160 .. 0.66
   2 !    9.7   0.0   0.00034         1      16      87 ..     484     562 ..     476     566 .. 0.75
   3 !   10.7   0.0   0.00017      0.49      37      83 ..     764     816 ..     752     821 .. 0.71
   4 ?    0.5   0.0      0.26   7.8e+02      18      69 ..     867     917 ..     860     924 .. 0.83
   5 ?   -2.2   0.0       1.7   5.1e+03      27      72 ..     995    1040 ..     983    1049 .. 0.81
   6 !    6.6   0.0    0.0033       9.8      52      86 ..    1138    1170 ..    1109    1173 .. 0.73
   7 ?   -1.9   0.0       1.4   4.2e+03      31      86 ..    1531    1585 ..    1525    1588 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.4
                     Chlam_OMP6  36 gkkdcvdvvitqqlpcevefvrsd...pastptadgklvwkidrlgqge 81 
                                      +d+ ++ i + lp   ++++ +   pa +      l+w i   g+ e
  gi|116754077|ref|YP_843195.1| 106 LSEDVHELQIKNTLPSGLDYLKWEgdlPAPACPEGNTLLWSIGDAGRTE 154
                                    5567778888889999999987542234544444456999998888766 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00034
                     Chlam_OMP6  16 qavpeyatvgspypieit....avgkkdcvdvvitqqlpcevefv...rsdpastptadgklvwkidrlgqgekskitv 87 
                                    +  p ya vg      +      + + d+ d+++ + +p  + ++    s p     a   lvw ++rl +ge   it 
  gi|116754077|ref|YP_843195.1| 484 KNAPLYAIVGDEVTFTLSfhhdGTSRSDAYDLLLVDSIPEGARLMeinASRPMGFEQAGRDLVWSLQRLDRGESVTITY 562
                                    667888888876554432112257789999********98875541116888899999999*************99985 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00017
                     Chlam_OMP6  37 kkdcvdvvitqqlpcev....efvrsdpas..tptadgklvwkidrlgqgeks 83 
                                    + d+ +vv+ + +p ++    e v++ p        dg l+w+i rlg ge +
  gi|116754077|ref|YP_843195.1| 764 RCDAWNVVLRESIPSNTgilpESVKTSPERgdIEICDGLLIWRIKRLGPGESA 816
                                    557778888888888872222444555543114568**************976 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.26
                     Chlam_OMP6  18 vpeyatvgspypieitavgkkdcvdvvitqqlpcevefvrsdpastptadgk 69 
                                     p+ a     y i    +g ++    vi  +      f++s p    ++dg 
  gi|116754077|ref|YP_843195.1| 867 APDVACGFVNYTIHYRNIGEREIRGAVIEARYDPLLAFISSSPMPC-SPDGS 917
                                    57777777899********************9999******99753.46664 PP

  == domain 5  score: -2.2 bits;  conditional E-value: 1.7
                     Chlam_OMP6   27 pypieitavgkkdcvdvvitqqlpcevefvrsdpastptadgklvw 72  
                                      y +    +g   + +v +   +p +v +v++      ++   +vw
  gi|116754077|ref|YP_843195.1|  995 TYTVSYRNTGTTKATNVTLRALFPSNVRIVSASHMPGISNSEDIVW 1040
                                     578888899999999****99******9999887766666666777 PP

  == domain 6  score: 6.6 bits;  conditional E-value: 0.0033
                     Chlam_OMP6   52 evefvrsdpastptadgklvwkidrlgqgekskit 86  
                                     +  fv  +   +p +dg  +w+idrl  ge s i 
  gi|116754077|ref|YP_843195.1| 1138 DPRFVIQNADPAPGPDG--LWHIDRLRAGECSVIR 1170
                                     45677666666788999..8**********98875 PP

  == domain 7  score: -1.9 bits;  conditional E-value: 1.4
                     Chlam_OMP6   31 eitavgkkdcvdvvitqqlpcevefvrsdpastptadgklvwkidrlgqgekskit 86  
                                     +i   g +d   v it  +p   + +   p      +  + w +d l  g+   it
  gi|116754077|ref|YP_843195.1| 1531 KIQNDGIRDLSPVYITAMVPNGSKVLGVYPEPEIE-EDLMNWIVDLLRAGDSLVIT 1585
                                     56677888888888888888888888777754333.33456888888888777666 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.1         5   1.5e+04      60      93 ..      79     113 ..      57     117 .. 0.63
   2 !   16.0   0.7   3.5e-06      0.01       2      86 ..     204     287 ..     203     295 .. 0.75
   3 ?    0.2   0.0      0.29   8.8e+02      52      77 ..     547     571 ..     539     576 .. 0.83
   4 !   11.5   0.1   9.4e-05      0.28       2      85 ..     975    1061 ..     974    1076 .. 0.74
   5 ?    2.4   0.0     0.062   1.9e+02      13      50 ..    1518    1569 ..    1509    1594 .. 0.71

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 5
                                    TEEEEEEEEEE-S..-S-CEEE.EEEEESTT-SS--S CS
                          CARDB  60 gesttvsftwtte..ategevt.ltvvvDpdnevaEs 93 
                                    +++   ++t+ ++  +t g+v  +tv  + + +v E 
  gi|116754077|ref|YP_843195.1|  79 DAE--LTITVEPDsnRTIGDVVvFTVRLELSEDVHEL 113
                                    333..34444444447777777777777777777775 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 3.5e-06
                                    --EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEE..SEE-CTEEEEEEEEEE-S-S-CEEE CS
                          CARDB   2 pDLtvtntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtv..psLaagesttvsftwtteategevt 79 
                                    pD ++t+++n +++++g+ ++  vt++N G+ +++++++++++ + l +  +v    +a  +s+  ++t  ++      t
  gi|116754077|ref|YP_843195.1| 204 PDIVITVSSNITKVEAGDIVEQVVTLSNRGSSDAYDVNLTVTIADGL-EVLSVesDHVADRGSIASTYTRIPR--GAAET 280
                                    9****************************************986655.3333433777777777777777776..22223 PP

                                    EEEEEST CS
                          CARDB  80 ltvvvDp 86 
                                    l++v   
  gi|116754077|ref|YP_843195.1| 281 LKLVLRV 287
                                    5555544 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.29
                                    EEESEE-CTEEEEEEEEEE-S-S-CE CS
                          CARDB  52 vtvpsLaagesttvsftwtteatege 77 
                                    ++++ L+ ges+t+++t+ ++ t+g+
  gi|116754077|ref|YP_843195.1| 547 WSLQRLDRGESVTITYTILVN-TTGS 571
                                    677899999999999999998.7776 PP

  == domain 4  score: 11.5 bits;  conditional E-value: 9.4e-05
                                     --EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE..EEEEESEE-CTEEEEEEEEEE-S.-S-C CS
                          CARDB    2 pDLtvtntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelv..gtvtvpsLaagesttvsftwtte.ateg 76  
                                     p L ++ t +p+ ++ g ++t tv+ +N+Gt ++++++++     ++   + +  p+++++e +  s +   +     
  gi|116754077|ref|YP_843195.1|  975 PELSINATGSPERVERGGTVTYTVSYRNTGTTKATNVTLRALFPSNVRivSASHMPGISNSEDIVWSKSSELMpGDMR 1052
                                     899**9999*****************************9987766664456667766666665554444444434445 PP

                                     EEEEEEEES CS
                          CARDB   77 evtltvvvD 85  
                                     +v +++ vD
  gi|116754077|ref|YP_843195.1| 1053 TVSIRALVD 1061
                                     555555555 PP

  == domain 5  score: 2.4 bits;  conditional E-value: 0.062
                                     SEEETTSEEEEEEEEEE-SSS-.EEEEEEEEEETTEEE.............E CS
                          CARDB   13 seafvgeentitvtvkNqGtaa.sgatkvalyldgelv.............g 50  
                                     + ++  e ++i+++++N G  + s+   +a++ +g++v              
  gi|116754077|ref|YP_843195.1| 1518 TYMEGSEIMSIRMKIQNDGIRDlSPVYITAMVPNGSKVlgvypepeieedlM 1569
                                     5566677889************999999999999988865555444444444 PP

>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       2.2   6.7e+03      50      77 ..      77     103 ..      75     105 .. 0.77
   2 ?    2.8   0.1     0.047   1.4e+02       1      44 [.     217     260 ..     217     303 .. 0.88
   3 ?    0.7   0.0      0.22   6.5e+02       4      20 ..     493     509 ..     490     574 .. 0.74
   4 !   12.9   0.1   3.3e-05     0.099       1      36 [.     988    1023 ..     988    1030 .. 0.88
   5 ?   -1.5   0.0         1   3.1e+03       9      35 ..    1528    1554 ..    1524    1561 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.2
                    NPCBM_assoc  50 GetveatvkVtppagaaaGdyevtakar 77 
                                    G  +e t++V p ++   Gd  v++++r
  gi|116754077|ref|YP_843195.1|  77 GNDAELTITVEPDSNRTIGD-VVVFTVR 103
                                    77789999999999988899.6666665 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.047
                    NPCBM_assoc   1 vepGetvtltltvtndgtaaatnvslslslPeGWtvvevspasa 44 
                                    ve+G+ v+  +t++n g++ a +v+l+++  +G +v +v+ + +
  gi|116754077|ref|YP_843195.1| 217 VEAGDIVEQVVTLSNRGSSDAYDVNLTVTIADGLEVLSVESDHV 260
                                    57999999********************9888877766666655 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.22
                    NPCBM_assoc   4 Getvtltltvtndgtaa 20 
                                    G++vt+tl++  dgt+ 
  gi|116754077|ref|YP_843195.1| 493 GDEVTFTLSFHHDGTSR 509
                                    78888888888888653 PP

  == domain 4  score: 12.9 bits;  conditional E-value: 3.3e-05
                    NPCBM_assoc    1 vepGetvtltltvtndgtaaatnvslslslPeGWtv 36  
                                     ve+G tvt+t++  n+gt+ atnv l++ +P++ ++
  gi|116754077|ref|YP_843195.1|  988 VERGGTVTYTVSYRNTGTTKATNVTLRALFPSNVRI 1023
                                     589****************************97665 PP

  == domain 5  score: -1.5 bits;  conditional E-value: 1
                    NPCBM_assoc    9 ltltvtndgtaaatnvslslslPeGWt 35  
                                     +++ + ndg + ++ v++++ +P G +
  gi|116754077|ref|YP_843195.1| 1528 IRMKIQNDGIRDLSPVYITAMVPNGSK 1554
                                     789999*****************9955 PP

>> GpcrRhopsn4  Rhodopsin-like GPCR transmembrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   3.0    0.0006       1.8     192     230 ..       2      40 ..       1      45 [. 0.90

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0006
                    GpcrRhopsn4 192 glrntikkekskkkkqFllkfgivgllwflsfPvlviia 230
                                    +++ ++ +++++ kk F++ f  +   wf + P+++ii 
  gi|116754077|ref|YP_843195.1|   2 CMYISVSENNTPFKKLFFYSFCSYLHAWFKAIPIIIIIV 40 
                                    678889999999***********************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1624 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); 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: 0.89u 0.30s 00:00:01.19 Elapsed: 00:00:00.46
# Mc/sec: 10501.91
//
Query:       gi|116754078|ref|YP_843196.1|  [L=317]
Description: hypothetical protein Mthe_0766 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2312.09
//
Query:       gi|116754079|ref|YP_843197.1|  [L=288]
Description: triphosphoribosyl-dephospho-CoA protein [Methanosaeta thermophila PT]
Scores for complete 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-68  231.3   0.1      2e-68  231.1   0.1    1.0  1  CitG      ATP:dephospho-CoA triphosphoribosyl transferase


Domain annotation for each model (and alignments):
>> CitG  ATP:dephospho-CoA triphosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  231.1   0.1   1.1e-72     2e-68       1     281 []      14     281 ..      14     281 .. 0.92

  Alignments for each domain:
  == domain 1  score: 231.1 bits;  conditional E-value: 1.1e-72
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXHHHHHHHHHTTHHHHHHHH...........HH--HHHHHHHHHHHH. CS
                           CitG   1 aelavlAlllEvsatpKPGlVdrrdsgahdDmdfetFlaSaealapyfeeaaaaGleakalfeelrsiGelaekamlaa. 79 
                                    a++a++A+llE+s +pKPG+Vdr++++  +Dm+f +F+aSa+ ++p f++aa          ++  ++G+l+ +++  + 
  gi|116754079|ref|YP_843197.1|  14 AQMAQMAMLLELSSSPKPGNVDRCHDY--EDMSFSHFVASAVLSYPSFRRAA----------SGASNMGRLILDTVSTWr 81 
                                    799************************..***********************..........7889***********999 PP

                                    ..------HHHHHHHHHHHHTTTTS-.......SHHHHHHHHHHHHHT--HHHHHHH.HHHHHH--.....---.....H CS
                           CitG  80 ..tggvNThkGaifllgllaaaagrraaeeeeasleelveeaaevlaeltvedavaf.rairlakv.....eel.....k 146
                                         +NTh+G i ll++la aa+r          + l++e+ +vl+++tved++ f ra++la +     + +     +
  gi|116754079|ref|YP_843197.1|  82 ewGLRGNTHFGEIALLIPLASAASRP---------GPLRSEIYRVLESTTVEDSICFyRAFELAGAraadvK-EmslkdP 151
                                    976789******************66.........79*****************************876652.0567774 PP

                                    HHHHH...TT--HHHHHHTS-TT-HHHHHHHHTSHHHHHHHH........HH-SSHHHHHHHHHHHHHHS--HHHHHHHH CS
                           CitG 147 delve..kksltlgevlelsygvdgirgeaasgFpsvfeialpalrealasgadlndalvqallallaelpDtnilrrgG 224
                                    ++l e  ++s+ l + +++s+g+d i++e+a+gF ++fe+a  al e++  +++ln+ +v ++l+ l+  pD+++++++G
  gi|116754079|ref|YP_843197.1| 152 KALEEieARSMRLIDLMRISQGHDLIAREWATGFSRSFELAD-ALCEMV-PRHGLNRGVVITYLTALSGEPDSLVASKFG 229
                                    444556679******************************777.788876.4589************************** PP

                                    HHHHHHHHHHHH..........H-SHHHHHHHHHHHHHHT---HHHHHHHHHHHHHH CS
                           CitG 225 aegaeevqeeArallaaggvaaeaglealeeldrelvernisPGgsADllaatlfla 281
                                     ++a ev+++A   l++     ++   ++ e+dr+l++r+i+PG++ADl+a++lf+a
  gi|116754079|ref|YP_843197.1| 230 IDVALEVSRMASVALRS-----HDVISSAMEMDRALISRDINPGSTADLIASSLFIA 281
                                    ************99998.....6789999**************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       249  (0.0138881); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 2089.65
//
Query:       gi|116754080|ref|YP_843198.1|  [L=193]
Description: hypothetical protein Mthe_0768 [Methanosaeta thermophila PT]
Scores for complete 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-52  178.0   0.1    1.7e-52  177.8   0.1    1.0  1  DUF447    Protein of unknown function (DUF447)


Domain annotation for each model (and alignments):
>> DUF447  Protein of unknown function (DUF447)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.8   0.1   9.2e-57   1.7e-52       1     176 []      17     186 ..      17     186 .. 0.97

  Alignments for each domain:
  == domain 1  score: 177.8 bits;  conditional E-value: 9.2e-57
                                    EEEEEEEE-TT-EEEEEEEEEESSSEEEEEEETTSHHHHHHHHHSEEEEEE---HHHHHHHHHS---GGGEEEETTTCTT CS
                         DUF447   1 yEvivtTksekrpnaaPiGvivkgdkvvlrlfkgsrTleNllengelvinvtdDpllfakaalgdleesdfdsetkpaki 80 
                                    +EvivtT+++ +pnaaPiG+i+ +++v++rlf g++T+eN+l++g+lv+nvt+Dp++f++aa++dl e++f +++    +
  gi|116754080|ref|YP_843198.1|  17 NEVIVTTERDGVPNAAPIGIIR-DENVTVRLFLGTHTYENVLATGQLVANVTHDPMIFVEAAMSDLGEECFLRRDG---V 92 
                                    7********88**********7.999*********************************************99995...6 PP

                                    .EETT-SEEEEEEEEEECTCECCEEEEEEEEEEEEETTB---B-HHHHHHHHHHHHHHCCCCSHHHHHHHHHHHHHHHHH CS
                         DUF447  81 avlksaeawveveveevegdsealelelepvkeeileervkpfnRgdaaviEaaVlatRldiedkeklleeieylssvik 160
                                     +lk+ae+w+ +++  +  +++ ++ ele v+ e+++++++++nRg ++viEaa++atR++ ++ + +leei++l+++++
  gi|116754080|ref|YP_843198.1|  93 LTLKDAESWALFRCSPY--RTDIIMPELEFVRGEVIRREFRAINRGVSCVIEAAIAATRYNALRVDSYLEEIRRLKRIVQ 170
                                    7**************98..8899********************************************************* PP

                                    HH--HHHHHHHHHHHH CS
                         DUF447 161 ktggerekealellke 176
                                    ++gg+re++a+++l+e
  gi|116754080|ref|YP_843198.1| 171 RCGGPREIAAMKRLEE 186
                                    *************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); 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: 1392.07
//
Query:       gi|116754081|ref|YP_843199.1|  [L=543]
Description: thermosome [Methanosaeta thermophila PT]
Scores for complete 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-188  626.8  21.0   2.7e-188  626.6  21.0    1.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family
  ------ inclusion threshold ------
       0.01   15.4   0.0       0.02   14.4   0.0    1.5  1  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 !  626.6  21.0    3e-192  2.7e-188       1     490 [.      35     522 ..      35     523 .. 0.99

  Alignments for each domain:
  == domain 1  score: 626.6 bits;  conditional E-value: 3e-192
                                    HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHHHHH CS
                     Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleeaekl 80 
                                    +a++v+ttlGPkGmdKmlv+  g+vv+TnDG+tilke++iehPaak++ve+a++qdeevGDGTtt+v+LageLl++ae l
  gi|116754081|ref|YP_843199.1|  35 VASAVRTTLGPKGMDKMLVDTLGDVVITNDGVTILKEMDIEHPAAKMMVEIAKTQDEEVGDGTTTAVVLAGELLKQAELL 114
                                    5899**************************************************************************** PP

                                    HHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHHHCHCCCSEEC CS
                     Cpn60_TCP1  81 iaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAvklieenekel 160
                                    +++++hpt+i  gy+ a+ ka+e+Lk    +++++ +d+e L+k+a t++++k + + + el++l+v+Avk+i ++++++
  gi|116754081|ref|YP_843199.1| 115 LEQEIHPTVIATGYRDAATKAIEILKDL--AVKVSPDDEELLKKIAITAMTGKGSGNARGELAELAVKAVKAIVDEDGSV 192
                                    ****************************..66666779********************************9999999*** PP

                                    SCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCCHHHHHHHHHHHH CS
                     Cpn60_TCP1 161 dlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdaeeleklekaeekq 240
                                    d+++i v+k+ ggs++ds+l++G+v+dk+ l+p+mpkk++nak++ll+ ++eiekte++++++++++++l++++++ee++
  gi|116754081|ref|YP_843199.1| 193 DIDNITVEKKVGGSITDSQLIHGMVIDKERLHPNMPKKVKNAKIALLNAPIEIEKTEVDAKIEITSPDQLQAFLDQEEAM 272
                                    ******************************************************************************** PP

                                    HHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGGCGC-EEEEEEEECCE CS
                     Cpn60_TCP1 241 leellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledltpeelGtakkveeeki 320
                                    l+e++ ki+++g+nvv+cqkgiddla+hflak+gi +lrrvkk+d+e+la+atGa++v+sl +ltp++lG+a+ vee+ki
  gi|116754081|ref|YP_843199.1| 273 LKEMVNKIVSTGANVVFCQKGIDDLAQHFLAKAGIYTLRRVKKSDMEKLARATGARIVTSLHELTPNDLGKAGLVEERKI 352
                                    ******************************************************************************** PP

                                    TTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHHHHHHHHCCCCTSXCCHHH CS
                     Cpn60_TCP1 321 gsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatelelakklkeyaksvsgeeql 400
                                      +++t++ee++++k+++i+lrg t++v+de++ra edAl+vv  ++ed+ +vpGGGa e+ela +l+eya +v g+eql
  gi|116754081|ref|YP_843199.1| 353 AGDDMTFVEECENPKSVSIILRGGTEHVVDELNRAMEDALRVVGVVVEDGMLVPGGGAPEVELALRLREYAATVGGREQL 432
                                    ******************************************************************************** PP

                                    HHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEECCCCTXEEEHHHHHHHHHHHHHHHHHH CS
                     Cpn60_TCP1 401 aieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiidlveagvvDplkvkrqalksAteaasti 480
                                    aieafa+A+e+ipktLaeNaGld+i++l  lr++h+kg k +g+d+e+ge++d++e+gvv+pl+vk+qa++sA+eaa +i
  gi|116754081|ref|YP_843199.1| 433 AIEAFAEAMEIIPKTLAENAGLDQIDTLVALRSKHEKGMKAAGLDMETGEAVDMLERGVVEPLRVKTQAINSAAEAAVMI 512
                                    ******************************************************************************** PP

                                    HCEEEEEXXX CS
                     Cpn60_TCP1 481 Lrideiikak 490
                                    Lrid++i  k
  gi|116754081|ref|YP_843199.1| 513 LRIDDVIASK 522
                                    *******976 PP

>> TrwC  TrwC relaxase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.2e-06      0.02      43     116 ..     312     394 ..     255     405 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.2e-06
                           TrwC  43 evteeqfeallegrhpd........tgerlgrakesaererkavagfDltf....saPKSvSllalvgdderraaieaah 110
                                    +v++ ++e+l + + ++        t + lg+a      e++++ag D+tf      PKSvS++   g++++  ++ +a+
  gi|116754081|ref|YP_843199.1| 312 RVKKSDMEKLARATGARivtslhelTPNDLGKAGLV---EERKIAGDDMTFveecENPKSVSIILRGGTEHVVDELNRAM 388
                                    566667777766555554444444466666664443...469********9444457******97766666655555555 PP

                           TrwC 111 daAvka 116
                                    ++A + 
  gi|116754081|ref|YP_843199.1| 389 EDALRV 394
                                    555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (543 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 3787.01
//
Query:       gi|116754082|ref|YP_843200.1|  [L=579]
Description: hypothetical protein Mthe_0770 [Methanosaeta thermophila PT]
Scores for complete 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   62.6   5.9    3.3e-17   62.6   5.9    1.8  2  BatA      Aerotolerance regulator N-terminal
     0.0016   19.1   0.2     0.0045   17.6   0.3    1.8  2  VWA_2     von Willebrand factor type A domain
     0.0038   17.2   0.1     0.0079   16.1   0.1    1.5  1  VWA_3     von Willebrand factor type A domain
  ------ inclusion threshold ------
      0.062   12.2   0.5       0.11   11.4   0.5    1.3  1  MFS_1     Major Facilitator Superfamily


Domain annotation for each model (and alignments):
>> BatA  Aerotolerance regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.6   5.9   7.4e-21   3.3e-17       1      77 []       1      76 [.       1      76 [. 0.98
   2 ?   -2.2   0.4       1.3   5.6e+03      11      26 ..     561     576 ..     553     578 .. 0.56

  Alignments for each domain:
  == domain 1  score: 62.6 bits;  conditional E-value: 7.4e-21
                           BatA  1 MlpFlnPllLlallllplpiillyllkrrpqevvfsslrlleevekdeea.lqrlkknllllLrllalallvlalArP 77
                                   M pF nP++Ll+ll + + +i+lyl+k++p+ v f+s+r+le+ + +++a l+r+ k+ l++L+l +l+ l +a A+P
  gi|116754082|ref|YP_843200.1|  1 M-PFRNPYALLGLLSVLP-LIILYLIKPKPRDVLFPSIRFLEAGKARRSAaLSRMIKDPLFWLQLFILIILSIAAAGP 76
                                   9.9***********9999.9**********************999999999**************************9 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.3
                           BatA  11 lallllplpiillyll 26 
                                    +al+ll + +++++++
  gi|116754082|ref|YP_843200.1| 561 VALMLLMAELWIIRWR 576
                                    4455555555665555 PP

>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.3     1e-06    0.0045       1     105 [.      88     179 ..      88     181 .. 0.77
   2 ?   -3.4   0.0       3.3   1.5e+04      38      48 ..     505     515 ..     503     527 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1e-06
                          VWA_2   1 lvfvlDtSgSmrngdygptrleaakdaveallkslpgdrvglvtfsdgpevlipltkdkakilnalrnleakgggtnlaa 80 
                                    lv+vlD+S+Sm+++      ++ a +++++ l+    drv++v  ++ p v +  + + ++ +++l +++  +   ++ +
  gi|116754082|ref|YP_843200.1|  88 LVIVLDVSASMEST------FQNALSIASSELSG--YDRVSVVLAESIPVVALR-EGSADEARSILGKIDVLDLPADISS 158
                                    79***********9......88888877776666..699999988886665554.344566666666666666789**** PP

                          VWA_2  81 aLqlarkalkkrrkgekrvivlitD 105
                                    a++la  +  ++       i++i+D
  gi|116754082|ref|YP_843200.1| 159 AMNLAYTLTGAE----GGDILVISD 179
                                    ******999977....599999998 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3.3
                          VWA_2  38 drvglvtfsdg 48 
                                    drvgl tf+++
  gi|116754082|ref|YP_843200.1| 505 DRVGLYTFDGK 515
                                    79******985 PP

>> VWA_3  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   1.8e-06    0.0079       2      73 ..      87     152 ..      86     177 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.8e-06
                          VWA_3   2 evvivvDvsssmsaenklvkdaLsvalrqLptndkiavllfgtkprplfpgsravsaaelqealqkikelel 73 
                                     +viv+Dvs+sm++   + ++aLs a  +L+  d+++v+l+ + p+      r+ sa+e + +l ki+ l+l
  gi|116754082|ref|YP_843200.1|  87 HLVIVLDVSASMES---TFQNALSIASSELSGYDRVSVVLAESIPV---VALREGSADEARSILGKIDVLDL 152
                                    58***********8...79*********************999876...34444455556666666666544 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.5   2.4e-05      0.11     150     226 ..       3      79 ..       2     115 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.4e-05
                          MFS_1 150 Wravfyilaivsllafvlfllllpeepperkrkspkeee.kgtgpaplvpawkallkdpvlw...illialllfffgfsg 225
                                    +r ++ +l+++s+l +++  l+l  ++p+   +++++ + +g++++++  a++ + kdp +w   ++li+l ++++g ++
  gi|116754082|ref|YP_843200.1|   3 FRNPYALLGLLSVLPLII--LYLIKPKPRDVLFPSIRFLeAGKARRSA--ALSRMIKDPLFWlqlFILIILSIAAAGPYT 78 
                                    577888888888888665..*************999996444444444..46*********9876444444444444444 PP

                          MFS_1 226 l 226
                                    l
  gi|116754082|ref|YP_843200.1|  79 L 79 
                                    3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (579 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); 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: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 4296.37
//
Query:       gi|116754083|ref|YP_843201.1|  [L=789]
Description: von Willebrand factor, type A [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-14   53.4   0.0      1e-13   51.8   0.0    1.9  1  VWA_2            von Willebrand factor type A domain
    6.4e-10   39.6   0.0    3.6e-05   24.1   0.0    2.4  2  VWA              von Willebrand factor type A domain
    2.3e-09   37.0   0.1    1.7e-05   24.4   0.0    2.2  2  GATase1_like     Putative glutamine amidotransferase
     0.0031   17.1   0.0       0.18   11.3   0.0    2.2  2  LBP_M            Lacto-N-biose phosphorylase central domain
     0.0041   17.3   0.0     0.0066   16.7   0.0    1.3  1  ThuA             Trehalose utilisation
  ------ inclusion threshold ------
      0.039   13.5   0.2        7.4    6.0   0.0    2.3  2  Glyco_hydro_42M  Beta-galactosidase trimerisation domain
      0.086   11.5   0.0       0.43    9.2   0.0    1.9  2  Fibrillarin_2    Fibrillarin-like archaeal protein


Domain annotation for each model (and alignments):
>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.8   0.0     4e-17     1e-13       1     106 [.     359     471 ..     359     472 .. 0.92

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 4e-17
                          VWA_2   1 lvfvlDtSgSmrngdy...gptrleaakdaveallk..slpgdrvglvtfsdgpevliplt..kdkakilnalrnleak. 72 
                                    l++v+D SgS  ++     ++t+l++ k+++++ll+  +l++ rvg+v+f+++p+v++++   +++a i++ +++l++  
  gi|116754083|ref|YP_843201.1| 359 LIMVIDISGSTMAPMRigeSTTYLDYEKSLAIELLQspELRDARVGIVVFGTKPYVVSQPVpiRNRAVIEESIKSLQTPl 438
                                    689*******9888446768****************6666888***************99778**************99* PP

                          VWA_2  73 .gggtnlaaaLqlarkalkkrrkgekrvivlitDg 106
                                     +++tnl+++L+la k++++ +  +++ +v+i+Dg
  gi|116754083|ref|YP_843201.1| 439 gRDETNLDEGLRLAWKIINESK--AEADLVIISDG 471
                                    *******************875..**********9 PP

>> VWA  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   3.9e-05     0.099     106     146 ..     125     166 ..     115     184 .. 0.85
   2 !   24.1   0.0   1.4e-08   3.6e-05       3     116 ..     360     474 ..     359     527 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.9e-05
                                    EEEEEESS--CSS.HTHHHHHHHHGCTEEEEEEEESSSHHHH CS
                            VWA 106 viilltdGksndg.dpkeaaneakeqgikvfavGvgnadeke 146
                                     i+l++dG+sn+g  +++a+  a++++++vfa+ ++ + +++
  gi|116754083|ref|YP_843201.1| 125 SILLVSDGYSNSGrPLRDALLLARSSNVSVFAIEMSPVAKEA 166
                                    689*********87899999999999*******998888777 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 1.4e-08
                                    EEEEE-STTS........CHHHHHHHHHHHHHHHHHHTBTTTTEEEEEEEESSSEEEEEETTSHCHHHHHHHHHHTG.SG CS
                            VWA   3 vfvlDgSgsm........geenfekvkefikklveklevgpegtrvglvqfssevktefslndysskeellsalnnl.ky 73 
                                    + v+D Sgs         +   +++ k+ +++l+++ e   +++rvg+v f+++++++ +    ++++ + +++++l + 
  gi|116754083|ref|YP_843201.1| 360 IMVIDISGSTmapmrigeSTTYLDYEKSLAIELLQSPE--LRDARVGIVVFGTKPYVVSQPVPIRNRAVIEESIKSLqTP 437
                                    789******99999998888888899999999999999..99***********************************999 PP

                                    GGGSSC-HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--C CS
                            VWA  74 sgggttntgkalkyaleklfkssagaRenakkviilltdGksn 116
                                     g ++tn++++l  a + + +s+a+        +++++dG+ +
  gi|116754083|ref|YP_843201.1| 438 LGRDETNLDEGLRLAWKIINESKAE------ADLVIISDGRIE 474
                                    9999999**********77777777......667888888763 PP

>> GATase1_like  Putative glutamine amidotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00013      0.34      89     118 ..     301     329 ..     291     349 .. 0.78
   2 !   24.4   0.0   6.7e-09   1.7e-05     139     243 ..     535     638 ..     487     641 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00013
                   GATase1_like  89 esksvPnrlkllkdyvaeGggllmvGGyls 118
                                    ++k +P+ l  lkdyva Gggl++vGG  +
  gi|116754083|ref|YP_843201.1| 301 NIKYNPD-LDRLKDYVASGGGLVVVGGADA 329
                                    5666776.7778**************9655 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 6.7e-09
                   GATase1_like 139 vtcldvddrvevP...eGlaaevvasehpvlkglssewPkllGyneveakdnaevlatvsedshPllvvGeygkGrtaaf 215
                                    v   +++  +ev     G++ +v++ +h +++ +     ++ G+n+v++k++a+ l  +++ ++P++ + +yg Gr++  
  gi|116754083|ref|YP_843201.1| 535 VRTPEIERGIEVAknvSGYTLVVTDENHYITSDIEI-NATISGFNDVTPKPGAQRLVALTD-GKPIVTAMRYGLGRSVSL 612
                                    55555555555541125899999***********95.5789***************99976.5***************** PP

                   GATase1_like 216 tsdisphwlspefldwegyarlwknvld 243
                                    ++d ++ w    +++  + + l   +++
  gi|116754083|ref|YP_843201.1| 613 ATDDGNAWAQSIYAE--ENSMLISSMVN 638
                                    ********9876654..33445555555 PP

>> LBP_M  Lacto-N-biose phosphorylase central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.02        51      88     114 ..     309     335 ..     300     341 .. 0.86
   2 !   11.3   0.0     7e-05      0.18     140     198 ..     557     614 ..     540     644 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.02
                          LBP_M  88 aalrkfvaeGggfiGvgePsavekqgr 114
                                    ++l+ +va+Ggg++ vg   a+e  g 
  gi|116754083|ref|YP_843201.1| 309 DRLKDYVASGGGLVVVGGADAYELGGY 335
                                    5799*************9999887665 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 7e-05
                          LBP_M 140 eaeekhfitedveeeldfgeevkniyalegevevlaekdgevklavneyGkGrsvYlsg 198
                                     ++e+h+it+d+e +  + ++ +++ ++ g+ +++a +dg+  +++ +yG Grsv l++
  gi|116754083|ref|YP_843201.1| 557 VTDENHYITSDIEINATI-SGFNDVTPKPGAQRLVALTDGKPIVTAMRYGLGRSVSLAT 614
                                    34567*******666655.5779********************************9975 PP

>> ThuA  Trehalose utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   2.6e-06    0.0066      46     182 ..     289     609 ..     274     640 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.6e-06
                                    HHHHT-SEEEEE-G..GS-HHHHHH.HHHHHHTT-EEEEEGGG.GS.....HHHH.HH-SEEEEET.............. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx............. RF
                           ThuA  46 enLaqydvvvflstegevldaaqeaalqryveaGgGfvglhsA.adaeerskwfsgLiGarfvghpp............. 111
                                    ++L+ y++vv  +      +++ ++ l++yv +GgG+v++ +A a  e       g  G++f+++ p             
  gi|116754083|ref|YP_843201.1| 289 QSLSGYKAVVLDNI---KYNPDLDR-LKDYVASGGGLVVVGGAdAY-ELG-----GYYGTEFEKALPvisspslfeggkv 358
                                    67999999998775...48999999.**************999443.222.....35689***9944577889******* PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                           ThuA 112 ................................................................................ 111
                                                                                                                    
  gi|116754083|ref|YP_843201.1| 359 limvidisgstmapmrigesttyldyekslaiellqspelrdarvgivvfgtkpyvvsqpvpirnravieesikslqtpl 438
                                    ******************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                           ThuA 112 ................................................................................ 111
                                                                                                                    
  gi|116754083|ref|YP_843201.1| 439 grdetnldeglrlawkiineskaeadlviisdgriepdkvkgdqvflnsvdilremnatvtliqvqsyagsagrfeelaa 518
                                    ******************************************************************************** PP

                                    ..........................................TSGGGTT--.SEEEEEEEEE.-S---SE..EEEEE... CS
                                    ...............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                           ThuA 112 ...............................vqeatvkvedrshpateglpeewertdewYn.fkpnprgvhvlatvdes 159
                                                                   v   t+ v+d++h +t+ ++  ++ t   +n ++p+p + +++a +d  
  gi|116754083|ref|YP_843201.1| 519 ltgatfrpavypssltvrtpeiergievaknVSGYTLVVTDENHYITSDIE--INATISGFNdVTPKPGAQRLVALTD-- 594
                                    ************************999888776789999*********996..6777555555666555566666662.. PP

                                    ............ETE...TTEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxx RF
                           ThuA 160 tydpngadhPiaWcreydgkGrv 182
                                             Pi+   +y g Gr+
  gi|116754083|ref|YP_843201.1| 595 -------GKPIVTAMRY-GLGRS 609
                                    .......3466665556.55666 PP

>> Glyco_hydro_42M  Beta-galactosidase trimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0    0.0029       7.4      53      89 ..     289     323 ..     275     330 .. 0.85
   2 ?    5.1   0.0    0.0055        14     129     198 ..     560     626 ..     543     631 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0029
                Glyco_hydro_42M  53 adlsgYklvvaPtlylvseelvkkleafvenGGtlvl 89 
                                    ++lsgYk+vv+  + +  +   ++l+++v++GG lv+
  gi|116754083|ref|YP_843201.1| 289 QSLSGYKAVVLDNIKYNPD--LDRLKDYVASGGGLVV 323
                                    67999****9988887554..47*********99986 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0055
                Glyco_hydro_42M 129 eevevs.aegktyearlwseilepetaevlatyatdfyagtpAvtrnnygkGkaiYvgsrleddlldaLlk 198
                                    e++ ++   + +++++ + ++    +a+ l     + + g+p vt+ +yg G+ + ++++ +++ ++ +++
  gi|116754083|ref|YP_843201.1| 560 ENHYITsDIEINATISGFNDVTPKPGAQRLV----ALTDGKPIVTAMRYGLGRSVSLATDDGNAWAQSIYA 626
                                    5555552223333344444444444444444....44559*******************999999888876 PP

>> Fibrillarin_2  Fibrillarin-like archaeal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.16     4e+02     214     254 ..     119     163 ..     108     178 .. 0.76
   2 ?    9.2   0.0   0.00017      0.43     360     441 ..     391     472 ..     380     506 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.16
                  Fibrillarin_2 214 ygkgleailfvgdGyddlikgleaai....elgvdvfvveGgPfn 254
                                    y    ++il v+dGy +  + l+ a+      +v vf++e +P  
  gi|116754083|ref|YP_843201.1| 119 YMPQADSILLVSDGYSNSGRPLRDALllarSSNVSVFAIEMSPVA 163
                                    5556789********98666666555222267899****999975 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00017
                  Fibrillarin_2 360 kvvgkeniyPkkigalavGdahWaalkesklakklkvkktvediakeveadkvallGgrfvsWviakeldkkvdeilisd 439
                                     ++++ ++   ++g ++ G   +++ +  ++ ++  +++++++++  +  d+  l  g  ++W i++e + ++d ++isd
  gi|116754083|ref|YP_843201.1| 391 ELLQSPELRDARVGIVVFGTKPYVVSQPVPIRNRAVIEESIKSLQTPLGRDETNLDEGLRLAWKIINESKAEADLVIISD 470
                                    5566666777889999999999*********************************************************9 PP

                  Fibrillarin_2 440 ad 441
                                      
  gi|116754083|ref|YP_843201.1| 471 GR 472
                                    64 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (789 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.65u 0.24s 00:00:00.89 Elapsed: 00:00:00.41
# Mc/sec: 5708.13
//
Query:       gi|116754084|ref|YP_843202.1|  [L=77]
Description: hypothetical protein Mthe_0772 [Methanosaeta thermophila PT]
Scores for complete sequence (score 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   11.7   0.0      0.089   11.6   0.0    1.0  1  Mgr1      Mgr1-like, i-AAA protease complex subunit


Domain annotation for each model (and alignments):
>> 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 ?   11.6   0.0     5e-06     0.089     247     305 ..      15      73 ..       2      76 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5e-06
                           Mgr1 247 npiikWfGPleykPmsfseyLdrleyhLdmlellqekrkskeaskellekikhteeele 305
                                    +++ik + P  y+P+s+s+ +  +e  +  le +  ++   +  +elle i+  ++ele
  gi|116754084|ref|YP_843202.1|  15 DIFIKSYNPFTYNPISWSDRMSGIEEAIRRLEEIAGRHICAARREELLEIIEILRRELE 73 
                                    689*********************************99999999999999998888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); 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: 0.34u 0.27s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 581.14
//
Query:       gi|116754085|ref|YP_843203.1|  [L=497]
Description: lysyl-tRNA synthetase [Methanosaeta thermophila PT]
Scores for 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-123  412.8   0.0   1.3e-123  412.5   0.0    1.1  1  tRNA-synt_1f  tRNA synthetases class I (K)
    2.4e-07   29.9   0.0     0.0019   17.1   0.0    2.1  2  tRNA-synt_1g  tRNA synthetases class I (M)
    0.00032   20.1   0.0       0.62    9.3   0.0    2.3  2  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
  ------ inclusion threshold ------
       0.28   10.5   0.0       0.43    9.8   0.0    1.2  1  tRNA-synt_1b  tRNA synthetases class I (W and Y)


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 !  412.5   0.0  2.9e-127  1.3e-123       2     339 ..       4     331 ..       3     345 .. 0.97

  Alignments for each domain:
  == domain 1  score: 412.5 bits;  conditional E-value: 2.9e-127
                   tRNA-synt_1f   2 aWadklaeklieerkkkkaekdevvvesGispSGliHiGnlrevltadlvaralrkrgeevrlilisDdmDglRkvpenl 81 
                                    +Wad++ae+l     +    ++ +++++Gi+pSG++HiGnlrev+tad+v+ral +rg e+rli+i+D++D+lR+++++l
  gi|116754085|ref|YP_843203.1|   4 HWADVIAERLK----D----HGPHTLATGITPSGPVHIGNLREVMTADAVYRALVDRGVEARLIYIADTYDRLRRLYPFL 75 
                                    78888888888....2....3789******************************************************** PP

                   tRNA-synt_1f  82 pekllekylgkpltsiPdpkgkhesyaehfnaelvesLdelgievefisatelYksglydeaikealenrekikeileky 161
                                    +e+ +++++gkpl++iP+p+g+++sy+ehf +++++++d l+i+ e+++a +lYk+g+y +aik+al++r++i++il+++
  gi|116754085|ref|YP_843203.1|  76 DES-FREHVGKPLSEIPCPEGCCSSYSEHFLQPFLRAMDLLDIKPEVYRADQLYKEGVYLDAIKTALKKRDEIARILKEV 154
                                    ***.**************************************************************************** PP

                   tRNA-synt_1f 162 rgeereetyspylpvcekcgrvdttevvevdaeeeeieYkceecGeeeevdiregngKLqWkvdwamrWaalgVdfEpaG 241
                                     g++ +  +sp+ p+c +cgr++tt+v+ +d ++e++ Y+c ecG +++v++r+g gKL W+vdw++rW +l V++Ep+G
  gi|116754085|ref|YP_843203.1| 155 SGRDVSPGWSPFDPICRDCGRMNTTRVTGFDLDSERVDYVC-ECGSTGSVSMRGG-GKLVWRVDWPARWHILRVTVEPFG 232
                                    *****************************************.***********97.************************ PP

                   tRNA-synt_1f 242 kDhaaaGgSvdvsskia.eilggeaPekvvYelillkggekmssSkGnvltledwlevaepevlrflilrrkPkkakkld 320
                                    kDha+aGgS+d++++i+ ++++++aP+++vYe+i+lkg+++m+sS+G v+t++++l+v++pevlr+li+r+kP+k++++d
  gi|116754085|ref|YP_843203.1| 233 KDHATAGGSYDTGKRISeDVYNYPAPYPIVYEWIHLKGKGAMHSSTGLVVTVQEMLDVVPPEVLRYLIIRTKPEKHIEFD 312
                                    ******************************************************************************** PP

                   tRNA-synt_1f 321 ldleilrlvdeYdklerky 339
                                    ++l +l lvde+d+ + ++
  gi|116754085|ref|YP_843203.1| 313 PGLPLLTLVDEFDQRRGDA 331
                                    *************987665 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   3.9e-05      0.18      11      48 ..      28      65 ..      22      67 .. 0.88
   2 !   17.1   0.0   4.1e-07    0.0019     317     361 ..     262     307 ..     248     312 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 3.9e-05
                                   SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE--- CS
                   tRNA-synt_1g 11 ngklHlGhllevisaDifaRykrlrgeevlfvcgtDeh 48
                                   +g++H+G+l+ev+ aD+++R    rg e   +   D++
  gi|116754085|ref|YP_843203.1| 28 SGPVHIGNLREVMTADAVYRALVDRGVEARLIYIADTY 65
                                   799*******************9999998887777765 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 4.1e-07
                                    EE--EEE---.-----------HHHHHHHH-HHHHHHHHHHHS-TT CS
                   tRNA-synt_1g 317 aheyltvegk.KlSkSrgvvvkakealerldadllRYylaaeapek 361
                                    + e++ ++gk  + +S g vv+++e+l+ +++++lRY +++++pek
  gi|116754085|ref|YP_843203.1| 262 VYEWIHLKGKgAMHSSTGLVVTVQEMLDVVPPEVLRYLIIRTKPEK 307
                                    679999999735999**************************99987 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0   0.00026       1.2      14      94 ..      22     119 ..      10     141 .. 0.74
   2 !    9.3   0.0   0.00014      0.62     244     292 ..     263     312 ..     251     315 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00026
                                    EEEEBTTS--BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-..................HHHH CS
                   tRNA-synt_1e  14 vCGptvydashlGhaRslvafDilrrilqalgYdvqfvqnvtDidDkiikrareeeks..................vkel 75 
                                      G+t    +h+G+ R++++ D + r l ++g + +++  + D  D++ +     ++s                  +++ 
  gi|116754085|ref|YP_843203.1|  22 ATGITPSGPVHIGNLREVMTADAVYRALVDRGVEARLIY-IADTYDRLRRLYPFLDESfrehvgkplseipcpegcCSSY 100
                                    579999999**********************99988874.7777776644333322224556666666666666666666 PP

                                    HHHHHHHHHHHHHHTT--- CS
                   tRNA-synt_1e  76 aekfieefkkdleaLnvlk 94 
                                    +e+f + f ++++ L++++
  gi|116754085|ref|YP_843203.1| 101 SEHFLQPFLRAMDLLDIKP 119
                                    6666666666666666665 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00014
                                    E--EEETTB.E--TTTT---BHHHHHTTS-HHHHHHHHHSS-TTS-EEE- CS
                   tRNA-synt_1e 244 nghlkiege.kmsksLknfitikdvlkkfdprqlRllllsahyrsqldfk 292
                                     ++++++g+  m  s + ++t++++l  + p++lR+l++ ++ +++++f+
  gi|116754085|ref|YP_843203.1| 263 YEWIHLKGKgAMHSSTGLVVTVQEMLDVVPPEVLRYLIIRTKPEKHIEFD 312
                                    567888775369999*************************9999999985 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 ?    9.8   0.0   9.6e-05      0.43       3      29 ..      16      42 ..      14      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 9.6e-05
                                   HS--EEEEEEETSSS-BGGGHHHHHHH CS
                   tRNA-synt_1b  3 erplrvysGidPTgklHlGylvplkkl 29
                                   ++p ++ +Gi P+g++H+G+l  +++ 
  gi|116754085|ref|YP_843203.1| 16 HGPHTLATGITPSGPVHIGNLREVMTA 42
                                   6788999************99877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (497 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 3749.88
//
Query:       gi|116754086|ref|YP_843204.1|  [L=141]
Description: formylmethanofuran dehydrogenase subunit E-like [Methanosaeta thermophila PT]
Scores for complete 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-23   81.4   0.0    6.8e-23   81.2   0.0    1.1  1  FmdE      FmdE, Molybdenum formylmethanofuran dehydrogenase o


Domain annotation for each model (and alignments):
>> FmdE  FmdE, Molybdenum formylmethanofuran dehydrogenase operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.2   0.0   3.8e-27   6.8e-23       1     101 [.      21     118 ..      21     138 .. 0.84

  Alignments for each domain:
  == domain 1  score: 81.2 bits;  conditional E-value: 3.8e-27
                                    HHSS--CHHHHHHHHHHHHHHCC....-TTSSSEEEEES-S.....TCHHHHHHHHCS--TTTTSEEE--SS-SEEEEEE CS
                           FmdE   1 fHGHlCpglvlGyrmakaalkelgpkeeegdeelvaivetd.....sCldDAiqvltgctlGkgnlivmdygkkaltfkk 75 
                                    fHGHl+p+lvlG+rm+ aal elg    +g +++ a+v+       sCl+D+iq+ tgctlGkgn+ v + g  ++tf +
  gi|116754086|ref|YP_843204.1|  21 FHGHLGPFLVLGIRMGLAALSELGS---RGHKDISAVVRSGsrppvSCLADGIQISTGCTLGKGNISVLQDGVPEATFSS 97 
                                    9**********************95...45799*********************************************95 PP

                                    TTT-EEEEEEE-CCTHHHHHHHCCT- CS
                           FmdE  76 rktgkavrlklkeelpelreklakgk 101
                                      +g++v  +++     + ek+ k +
  gi|116754086|ref|YP_843204.1|  98 --NGRTVSFRVR---GSIAEKISKLS 118
                                    ..6788888877...44555555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       228  (0.0127168); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.37
# Mc/sec: 1157.00
//
Query:       gi|116754087|ref|YP_843205.1|  [L=243]
Description: ABC transporter related [Methanosaeta thermophila PT]
Scores for complete 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-27   94.6   0.0    8.7e-27   94.3   0.0    1.1  1  ABC_tran         ABC transporter
    6.7e-09   36.0   0.1    0.00073   19.4   0.0    2.1  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    7.5e-06   26.6   0.0      1e-05   26.2   0.0    1.1  1  AAA_23           AAA domain
    1.9e-05   24.2   0.1      0.059   12.8   0.1    2.1  2  SMC_N            RecF/RecN/SMC N terminal domain
    0.00048   20.5   0.0    0.00092   19.6   0.0    1.5  1  AAA_16           AAA ATPase domain
    0.00057   19.6   0.1     0.0018   17.9   0.1    1.9  2  AAA_29           P-loop containing region of AAA domain
      0.003   17.8   0.0      0.083   13.1   0.0    2.2  1  SbcCD_C          Putative exonuclease SbcCD, C subunit
     0.0049   16.3   0.0     0.0074   15.7   0.0    1.2  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0053   17.2   0.1       0.71   10.3   0.0    2.1  2  AAA              ATPase family associated with various cellul
     0.0074   16.0   0.0      0.012   15.3   0.0    1.3  1  AAA_30           AAA domain
  ------ inclusion threshold ------
      0.017   14.9   0.0      0.031   14.0   0.0    1.4  1  AAA_24           AAA domain
      0.017   15.0   0.0      0.028   14.3   0.0    1.3  1  RsgA_GTPase      RsgA GTPase
      0.023   14.3   0.0      0.037   13.6   0.0    1.2  1  AAA_27           AAA domain
      0.039   13.0   0.1      0.071   12.2   0.1    1.4  1  T2SSE            Type II/IV secretion system protein
       0.04   14.2   0.2      0.098   12.9   0.1    1.6  2  AAA_22           AAA domain
      0.044   13.7   0.0      0.098   12.6   0.0    1.6  1  NACHT            NACHT domain
      0.059   10.9   0.9      0.079   10.5   0.9    1.0  1  DUF3584          Protein of unknown function (DUF3584)
      0.075   12.8   0.0       0.12   12.2   0.0    1.3  1  ATP_bind_1       Conserved hypothetical ATP binding protein
        0.1   12.2   0.5       0.15   11.6   0.1    1.5  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
       0.11   12.8   0.0       0.22   11.7   0.0    1.6  1  AAA_28           AAA domain
       0.11   12.6   0.0       0.23   11.6   0.0    1.7  2  AAA_33           AAA domain
       0.11   12.2   0.0       0.16   11.7   0.0    1.2  1  AAA_15           AAA ATPase domain
       0.13   11.0   0.4        2.6    6.7   0.4    2.1  2  ABC_ATPase       Predicted ATPase of the ABC class
       0.18   12.1   0.3       0.25   11.7   0.2    1.5  1  AAA_19           AAA domain
       0.18   11.4   0.0       0.33   10.6   0.0    1.4  1  Thymidylate_kin  Thymidylate kinase
       0.19   11.6   0.1        0.4   10.6   0.0    1.6  2  NTPase_1         NTPase
       0.24   10.2   0.1       0.35    9.7   0.1    1.1  1  DLIC             Dynein light intermediate chain (DLIC)


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 !   94.3   0.0   1.3e-29   8.7e-27       1     136 [.      22     170 ..      22     171 .. 0.92

  Alignments for each domain:
  == domain 1  score: 94.3 bits;  conditional E-value: 1.3e-29
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSB..HHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpelt..vre 78 
                                    lk ++l++ +ge+v ++G+nGaGK+tLl+++ g l p  G++++ g+d ++   ++ rk ig++ q +++ +++   vr+
  gi|116754087|ref|YP_843205.1|  22 LKGITLSIGAGEMVCVMGPNGAGKTTLLETINGIL-PSTGRVEVFGRDARR-HGPEIRKDIGYMLQAKTFPEDTPylVRD 99 
                                    789*******************************8.79************9.999************6655555443555 PP

                                    H.................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    x.................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  79 n.................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                      ++ + + +a++ ++ ++l d+++     +LSgGq qrv lar+l+k+p++lllDEp 
  gi|116754087|ref|YP_843205.1| 100 VvlmgrfgkigmlrrpgrNDWNAARDAARFMEVDHLWDRPI----GKLSGGQTQRVLLARLLAKNPRILLLDEPY 170
                                    5*************99988888899999999**********....*****************************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 !   19.4   0.0   1.1e-06   0.00073       3      25 ..      36      58 ..      34      95 .. 0.72
   2 !   15.2   0.0   2.1e-05     0.014     220     279 ..     126     182 ..      68     200 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.1e-06
                         AAA_21  3 vliGpNgsGKSnLLdaldllarl 25
                                   ++ GpNg+GK++LL+++ ++   
  gi|116754087|ref|YP_843205.1| 36 CVMGPNGAGKTTLLETINGILPS 58
                                   677**************999654 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 2.1e-05
                         AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrll 279
                                      +f+e ++  ++p+ +lS G+ +   ll+ ll+ ++  ++ll+DEp ++L+ ++++ + 
  gi|116754087|ref|YP_843205.1| 126 AARFMEVDHLWDRPIGKLSGGQTQR-VLLARLLAKNP--RILLLDEPYSNLDCRAVEDVS 182
                                    6778888888899********7666.47777777776..*************98887655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   1.5e-08     1e-05       2      62 ..       5      73 ..       5      99 .. 0.70

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 1.5e-08
                         AAA_23  2 Lkienfrsf....rdqe...idF...skgltlItGpNGaGKTTildAiklaL..ygetprlsrksgrgfeksd 62
                                   +++en++ f    ++ +   i +      ++++ GpNGaGKTT+l+ i  +L  +g+++      gr++ ++ 
  gi|116754087|ref|YP_843205.1|  5 IRLENVHTFydgeKNSTlkgITLsigAGEMVCVMGPNGAGKTTLLETINGILpsTGRVE----VFGRDARRHG 73
                                   7899999998765333333455566544699*****************99994444433....2344445555 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   8.9e-05     0.059      25      45 ..      33      53 ..      17      63 .. 0.85
   2 !    9.6   0.0   0.00082      0.54     136     190 ..     142     192 ..      75     218 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.9e-05
                                   SEEEEEESTTSSHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 25 sftaivGpNGSGKsnlldAil 45
                                   ++ +++GpNG+GK+ ll+ i 
  gi|116754087|ref|YP_843205.1| 33 EMVCVMGPNGAGKTTLLETIN 53
                                   5789**************996 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00082
                                    CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskna 190
                                     LSgG+ + v la l+A    k   + llDe  ++LD + v+ v++ + + +++ 
  gi|116754087|ref|YP_843205.1| 142 KLSGGQTQRVLLARLLA----KNPRILLLDEPYSNLDCRAVEDVSRKICTLHTRN 192
                                    79****99888888776....4455889*****************9998655443 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.4e-06   0.00092      19      62 ..      27      70 ..      19     169 .. 0.52

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.4e-06
                         AAA_16 19 vrsgrpelvllsGesGvGKsslvrellralekdggif.lrgkcdq 62
                                   ++ g +e+v + G+ G GK++l++++   l  +g  + + g+  +
  gi|116754087|ref|YP_843205.1| 27 LSIGAGEMVCVMGPNGAGKTTLLETINGILPSTG-RVeVFGRDAR 70
                                   567888********************97666662.2223333222 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 !   17.9   0.1   2.8e-06    0.0018      13      47 ..      23      57 ..       7      64 .. 0.83
   2 ?   -2.1   0.0         5   3.3e+03      40      50 ..     224     234 ..     222     242 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.8e-06
                         AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqalLv 47
                                   +g t++i   +++ ++Gp+G+GK+Tll  i+ +L 
  gi|116754087|ref|YP_843205.1| 23 KGITLSIGAGEMVCVMGPNGAGKTTLLETINGILP 57
                                   5566777755699**************99988875 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5
                         AAA_29  40 DAiqalLvpak 50 
                                    DA+  +++p++
  gi|116754087|ref|YP_843205.1| 224 DAHPDVMLPSR 234
                                    99999999998 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   0.00013     0.083      26      84 ..     136     181 ..     121     185 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00013
                        SbcCD_C  26 lsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatl 84 
                                    ++r +g+lSGG++q ++   l+        +      ++r+++LDE +s+lD + ++ +
  gi|116754087|ref|YP_843205.1| 136 WDRPIGKLSGGQTQRVLLARLL-------AK------NPRILLLDEPYSNLDCRAVEDV 181
                                    7899999999999766544444.......44......69*************9988765 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.1e-05    0.0074      15      54 ..      25      64 ..      15      72 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-05
                   Mg_chelatase 15 leiaaaGgHnlllvGppGsGKtmlakrlpsllpplseeea 54
                                   +++++  g  + ++Gp G+GKt l + ++++lp+  + e+
  gi|116754087|ref|YP_843205.1| 25 ITLSIGAGEMVCVMGPNGAGKTTLLETINGILPSTGRVEV 64
                                   55566566678899*******************9887765 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0    0.0011      0.71       1      21 [.      35      55 ..      35     108 .. 0.85
   2 ?    5.2   0.0     0.041        27      48     120 ..     151     215 ..     118     222 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0011
                                   EEEESSTTSSHHHHHHHHHHH CS
                            AAA  1 vllyGppGtGKTllakavake 21
                                   v+++Gp G GKT+l + +   
  gi|116754087|ref|YP_843205.1| 35 VCVMGPNGAGKTTLLETINGI 55
                                   689***********9988665 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.041
                                    HHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS.GGGSTHHHH CS
                            AAA  48 elfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnr.pdkldpall 120
                                     l++++ +k +p il++DE ++    r        e+v  ++ t   + k    +v+vi  t + pd  d+ ll
  gi|116754087|ref|YP_843205.1| 151 VLLARLLAK-NPRILLLDEPYSNLDCR------AVEDVSRKICTLHTRNKL--TTVMVIHDTAHvPDICDRILL 215
                                    344444444.49**********99999......777788888877777777..468888877775666666555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.9e-05     0.012      19      53 ..      33      66 ..      24      90 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.9e-05
                         AAA_30 19 rvavltGpAGtGKttalkalreaweaaggrviglA 53
                                    ++++ Gp G+GKtt+l++++ ++ + g rv ++ 
  gi|116754087|ref|YP_843205.1| 33 EMVCVMGPNGAGKTTLLETINGILPSTG-RVEVFG 66
                                   4899******************999987.555554 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   4.6e-05     0.031       4      22 ..      34      52 ..      31      79 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.6e-05
                         AAA_24  4 kiliyGpsgiGKTtlakel 22
                                   +++++Gp+g+GKTtl+ ++
  gi|116754087|ref|YP_843205.1| 34 MVCVMGPNGAGKTTLLETI 52
                                   79**************998 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   4.2e-05     0.028      87     121 ..      19      54 ..       4      71 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.2e-05
                                    HTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase  87 kegleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                    +++l+ ++  +   ++++++G+ G+GK+tL++++++
  gi|116754087|ref|YP_843205.1|  19 NSTLKGITLSIGAgEMVCVMGPNGAGKTTLLETING 54 
                                    5556666656655599***************99876 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   5.5e-05     0.037      20      50 ..      26      56 ..      20      61 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.5e-05
                         AAA_27 20 dfsaeeadlhliyGpNEAGKstalrAisdll 50
                                   ++s ++ ++  ++GpN AGK+t+l+ i+ +l
  gi|116754087|ref|YP_843205.1| 26 TLSIGAGEMVCVMGPNGAGKTTLLETINGIL 56
                                   55556778899**************998765 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 ?   12.2   0.1   0.00011     0.071     120     156 ..      23      59 ..       5      68 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                          T2SSE 120 evlrkavrerglilvsGgTgsGKttllyallkeinks 156
                                    + +  ++ +  ++ v G+ g GKttll ++  +++++
  gi|116754087|ref|YP_843205.1|  23 KGITLSIGAGEMVCVMGPNGAGKTTLLETINGILPST 59 
                                    556677788899*****************99998877 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   0.00015     0.098       6      26 ..      33      53 ..      29      72 .. 0.87
   2 ?   -2.4   0.0         8   5.3e+03      92      99 ..     161     168 ..     143     203 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00015
                         AAA_22  6 gilvvtGesGtGKTtllrrll 26
                                    +++v+G+ G+GKTtll+++ 
  gi|116754087|ref|YP_843205.1| 33 EMVCVMGPNGAGKTTLLETIN 53
                                   5889*************9875 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 8
                         AAA_22  92 ielliiDE 99 
                                    +++l++DE
  gi|116754087|ref|YP_843205.1| 161 PRILLLDE 168
                                    35666666 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00015     0.098       2      20 ..      34      52 ..      33      59 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00015
                                   CEEEEC-TTTCHHHHHHHH CS
                          NACHT  2 lvilqGeaGsGKTtLlqkl 20
                                   +v++ G++G GKTtLl+ +
  gi|116754087|ref|YP_843205.1| 34 MVCVMGPNGAGKTTLLETI 52
                                   699*************988 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.9   0.00012     0.079       4      37 ..      19      52 ..      18      54 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00012
                        DUF3584  4 dsflkGrvaeldldghtnieGtNaaGKTtLlrLi 37
                                   +s lkG +  +   + + + G N+aGKTtLl +i
  gi|116754087|ref|YP_843205.1| 19 NSTLKGITLSIGAGEMVCVMGPNGAGKTTLLETI 52
                                   89999*9999999*****************9886 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 ?   12.2   0.0   0.00017      0.12       1      25 [.      37      61 ..      37      65 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00017
                     ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgr 25
                                   v+Gp G+GKtt+ ++++ il+++gr
  gi|116754087|ref|YP_843205.1| 37 VMGPNGAGKTTLLETINGILPSTGR 61
                                   89******************99976 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00023      0.15       3      20 ..      35      52 ..      33      64 .. 0.88
   2 ?   -3.3   0.0       8.5   5.6e+03      74      87 ..     186     199 ..     175     221 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00023
                                   EEEEESTTCCHHHHHHHH CS
                           cobW  3 tvltGflGsGKTtLlnhl 20
                                   + + G+ G+GKTtLl+++
  gi|116754087|ref|YP_843205.1| 35 VCVMGPNGAGKTTLLETI 52
                                   6799***********987 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 8.5
                                    HHHHHHHTT-SEEE CS
                           cobW  74 ealeereerldvil 87 
                                      l +r++   v++
  gi|116754087|ref|YP_843205.1| 186 CTLHTRNKLTTVMV 199
                                    44444442222222 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00034      0.22       2      20 ..      35      53 ..      34      90 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00034
                         AAA_28  2 ivitGgestGKTtlleaLa 20
                                   ++++G+ ++GKTtlle ++
  gi|116754087|ref|YP_843205.1| 35 VCVMGPNGAGKTTLLETIN 53
                                   89*************9887 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00035      0.23       1      19 [.      34      52 ..      34     137 .. 0.91
   2 ?   -1.9   0.0         5   3.3e+03      17      32 ..     154     170 ..     144     212 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00035
                         AAA_33  1 lvllvGlpGsGKstlaerl 19
                                   +v + G++G+GK+tl+e +
  gi|116754087|ref|YP_843205.1| 34 MVCVMGPNGAGKTTLLETI 52
                                   68899**********9975 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5
                         AAA_33  17 erllkklg.avllssdt 32 
                                     rll+k++   ll++++
  gi|116754087|ref|YP_843205.1| 154 ARLLAKNPrILLLDEPY 170
                                    45555555466666665 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00024      0.16      23      44 ..      33      53 ..      21      85 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00024
                         AAA_15 23 eeltvliGkNnsGKSsileald 44
                                   e + ++ G+N++GK+++le ++
  gi|116754087|ref|YP_843205.1| 33 E-MVCVMGPNGAGKTTLLETIN 53
                                   4.899**************997 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   0.4     0.004       2.6     235     265 ..      20      53 ..      10      59 .. 0.78
   2 ?    2.2   0.0     0.091        60     371     413 ..     176     218 ..     144     222 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.004
                                    EEEEEEE..E-SS.EEEEEE-TTSSHHHHHHHHH CS
                     ABC_ATPase 235 kkvsGmg..ipkG.vtlIvGggfhGKsTLLeAle 265
                                     +++G+   i  G ++ ++G++  GK+TLLe ++
  gi|116754087|ref|YP_843205.1|  20 STLKGITlsIGAGeMVCVMGPNGAGKTTLLETIN 53 
                                    56666541145568899**************996 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.091
                                    --B--HHHCHHHHHHHH--EEEEEESS-GCCTTT-SEEEEEET CS
                     ABC_ATPase 371 epitplvdrvrelykklgvstilvvggsgdyldvAdtvilmee 413
                                    ++++ ++ ++  l++++ ++t++v+    +  d+ d+++l+++
  gi|116754087|ref|YP_843205.1| 176 RAVEDVSRKICTLHTRNKLTTVMVIHDTAHVPDICDRILLLKD 218
                                    56777788999999*************************9986 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   0.00037      0.25      11      41 ..      33      63 ..      27     204 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00037
                         AAA_19 11 kvllvtaGpGtGKTrvlkhivallvelggvk 41
                                   ++++v+++ G GKT++l++i  +l ++g+v+
  gi|116754087|ref|YP_843205.1| 33 EMVCVMGPNGAGKTTLLETINGILPSTGRVE 63
                                   7899***************999998888775 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00049      0.33       3      34 ..      39      70 ..      37      94 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00049
                                   ESTTSSHHHHHHHHHHHHHHTTE.EEEESSST CS
                Thymidylate_kin  3 GlDGaGKttqaellkerlkeegikvvltrepg 34
                                   G +GaGKtt +e++   l++ g+  v+ r  +
  gi|116754087|ref|YP_843205.1| 39 GPNGAGKTTLLETINGILPSTGRVEVFGRDAR 70
                                   89********************8777776654 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0    0.0006       0.4       2      27 ..      35      60 ..      34      85 .. 0.82
   2 ?   -2.4   0.0       5.9   3.9e+03     124     144 ..     192     213 ..     177     222 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0006
                                   EEEE--TTSSHHHHHHHHHHHH...G CS
                       NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssg 27
                                   v++ Gp G GKtTl++ +   l s g
  gi|116754087|ref|YP_843205.1| 35 VCVMGPNGAGKTTLLETINGILPSTG 60
                                   6789**************99998775 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.9
                                    TTSEEEEE--SS-.-SHHHHHH CS
                       NTPase_1 124 sekpvlavihrrk.dlalveei 144
                                    ++   ++vih +   +++ ++i
  gi|116754087|ref|YP_843205.1| 192 NKLTTVMVIHDTAhVPDICDRI 213
                                    3444566666665555555555 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   0.00052      0.35      23      48 ..      30      55 ..      23      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00052
                           DLIC 23 PsgksvlvlGedgsGkttliaklqGv 48
                                    +g  v v+G +g+Gkttl+  + G+
  gi|116754087|ref|YP_843205.1| 30 GAGEMVCVMGPNGAGKTTLLETINGI 55
                                   57889******************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); 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: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 1732.59
//
Query:       gi|116754088|ref|YP_843206.1|  [L=271]
Description: ABC-3 protein [Methanosaeta thermophila PT]
Scores for complete 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  165.6  37.8    1.7e-48  165.4  37.8    1.0  1  ABC-3     ABC 3 transport family
    5.4e-07   28.9  40.0    1.8e-06   27.2  40.0    1.7  1  FecCD     FecCD transport family
  ------ inclusion threshold ------
       0.29   10.5   2.4       0.43    9.9   2.4    1.2  1  DUF3482   Domain of unknown function (DUF3482)
        1.1    9.5   7.0        0.3   11.3   3.7    1.8  2  DUF4213   Putative heavy-metal chelation


Domain annotation for each model (and alignments):
>> ABC-3  ABC 3 transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.4  37.8   3.9e-52   1.7e-48       4     257 ..       6     261 ..       4     262 .. 0.98

  Alignments for each domain:
  == domain 1  score: 165.4 bits;  conditional E-value: 3.9e-52
                          ABC-3   4 flqrallasilvslacallgsfvvlrrqsllgdalsHaalpGvalayllgvnlllgailvgliaavalellkrktklked 83 
                                    ++++ ++++ l +++c+++g+f+v    s +g  +sHaa++G al+++++  +++ a+ +++++a++l+ ++ k++l+ d
  gi|116754088|ref|YP_843206.1|   6 IVMNTIVGASLAAVVCSMIGVFIVRMNLSSMGFCMSHAAFAGAALGLAISKDPFALALGMATAVALILGPVSDKARLQAD 85 
                                    578999************************************************************************** PP

                          ABC-3  84 taigivlsvflalglvlvslikk..skvdldsyLfGniltisqedliliaiieavvllllllfwkelllitfdeelAkve 161
                                    +++g ++s ++al+l+++s++++  +++   s L+G++l+i+  d+i ++++ + +ll+++lf+ke+ +i++d++lA+ +
  gi|116754088|ref|YP_843206.1|  86 VVLGTMFSLTMALALLFLSIAPGsvVSSTALSVLWGSVLGITTADIIRLLVLMLTLLLVIFLFYKEFFAIMLDRKLAEES 165
                                    ***********************98899999************************************************* PP

                          ABC-3 162 glsvkllkllllalialavvvalqavGviLvialliiPaatArrltrslesllivAillglvsvvaGlllSyyldlatGa 241
                                    g+++k +++ +l l +++v+v+l+++G +L++al++ P + A++++++++ +++++ l+gl ++v+Gl+ S  ld++ G+
  gi|116754088|ref|YP_843206.1| 166 GINTKPFYYAILFLCGVTVSVSLKLIGGLLIFALMVNPVSSAYQFSHDMRWIMLISPLIGLAASVSGLAASLCLDIPVGS 245
                                    ******************************************************************************** PP

                          ABC-3 242 vivlvatllfllallv 257
                                    +i+++++++fl+++++
  gi|116754088|ref|YP_843206.1| 246 SIAIMSVAIFLVSVAL 261
                                    ************9975 PP

>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2  40.0     4e-10   1.8e-06      50     308 ..      10     257 ..       3     260 .. 0.70

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 4e-10
                          FecCD  50 llvGaaLavaGallQtvtrNpLadPsi.lGissgaalgavlalllllgslslfalplaaflgallalllvlllarkrkga 128
                                     +vGa+La+  +++ +v+  ++  +s+   +s++a +ga+l+l+       +   p+a  lg ++a++l+l     + +a
  gi|116754088|ref|YP_843206.1|  10 TIVGASLAAVVCSMIGVFIVRMNLSSMgFCMSHAAFAGAALGLA-------ISKDPFALALGMATAVALILGP--VSDKA 80 
                                    44444444444444443332222222111222333333333222.......2334444444444444444443..46666 PP

                          FecCD 129 splkliLaGiavsallsaltsllllllneealesilfwllGslsgaswskvllllvllllllllllllarkldllalgde 208
                                    +    ++ G ++s+ ++ +  +l +   +  ++++l  l Gs+ g++  +++ llvl+l lll+++l+++++ +++l+++
  gi|116754088|ref|YP_843206.1|  81 RLQADVVLGTMFSLTMALALLFLSIAPGSVVSSTALSVLWGSVLGITTADIIRLLVLMLTLLLVIFLFYKEFFAIMLDRK 160
                                    6666677788888777666666665558889999********************************************** PP

                          FecCD 209 tAkslGvnvervrllllllvalltavavalvGpigFvGLiv.PhiarllvgadhrkllplsallGallllladllarlll 287
                                    +A+  G+n++ + +++l+l+ + ++v+  l+G +   +L+v P    + +++d+r+++++s l+G +  +    ++ +l 
  gi|116754088|ref|YP_843206.1| 161 LAEESGINTKPFYYAILFLCGVTVSVSLKLIGGLLIFALMVnPVSSAYQFSHDMRWIMLISPLIGLAASVSGLAASLCL- 239
                                    ***************************988876665555552777788899**************98877766666555. PP

                          FecCD 288 sptelpvgivtaliGapffiy 308
                                       ++pvg  +a++ + +f++
  gi|116754088|ref|YP_843206.1| 240 ---DIPVGSSIAIMSVAIFLV 257
                                    ...799999999999999986 PP

>> DUF3482  Domain of unknown function (DUF3482)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   2.4   9.6e-05      0.43     142     190 ..      32      80 ..      29      91 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 9.6e-05
                        DUF3482 142 tlkelGlslgaGaaaGAaaGagiDlavgGltLGaaaaiGalaGglaatl 190
                                    +l ++G  +  +a aGAa+G++i      l LG+a+a+  ++G ++  +
  gi|116754088|ref|YP_843206.1|  32 NLSSMGFCMSHAAFAGAALGLAISKDPFALALGMATAVALILGPVSDKA 80 
                                    78899999******************************99999877655 PP

>> DUF4213  Putative heavy-metal chelation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   3.7   6.8e-05       0.3      14      73 ..      19      71 ..       6      72 .. 0.85
   2 ?   -3.2   0.1       2.4   1.1e+04      52      64 ..     224     236 ..     216     239 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.8e-05
                        DUF4213 14 VedvviGlnwtlVelsdggaGlAyteagklvgkparelaelllswnplersvGlAaiNAl 73
                                   V   +iG++ +   ls  ++G++++     +   a +++ l+ s++p++ ++G+A++ Al
  gi|116754088|ref|YP_843206.1| 19 VVCSMIGVFIVRMNLS--SMGFCMS-----HAAFAGAALGLAISKDPFALALGMATAVAL 71
                                   4555788888888888..9******.....8899999999999*************9988 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.4
                        DUF4213  52 aelllswnplers 64 
                                    + l+ s + l++s
  gi|116754088|ref|YP_843206.1| 224 IGLAASVSGLAAS 236
                                    3444444455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       904  (0.0504211); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1983.45
//
Query:       gi|116754089|ref|YP_843207.1|  [L=77]
Description: hypothetical protein Mthe_0777 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       211  (0.0117686); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.27s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 576.36
//
Query:       gi|116754090|ref|YP_843208.1|  [L=333]
Description: alcohol dehydrogenase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.1e-33  113.9   0.0    4.7e-33  113.3   0.0    1.3  1  ADH_N         Alcohol dehydrogenase GroES-like domain
    0.00033   20.6   0.0    0.00066   19.7   0.0    1.5  1  ADH_zinc_N    Zinc-binding dehydrogenase
     0.0021   19.1   0.0     0.0031   18.6   0.0    1.2  1  ADH_zinc_N_2  Zinc-binding dehydrogenase


Domain annotation for each model (and alignments):
>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.3   0.0   7.8e-37   4.7e-33       2     109 .]      29     136 ..      28     136 .. 0.96

  Alignments for each domain:
  == domain 1  score: 113.3 bits;  conditional E-value: 7.8e-37
                                    TEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE.-SSSHHHHTT-GGG CS
                          ADH_N   2 gevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvveplis.cgeCaaCkegeenl 80 
                                     evli v+a+g+C++Dlhil+g +  e klpli+GHEivG v++ g++ ++++ Gdr+ v++l   +++C++C +geenl
  gi|116754090|ref|YP_843208.1|  29 REVLISVSACGVCRTDLHILDG-ELAEPKLPLIPGHEIVGRVVAKGENAERFSTGDRIGVPWLGYtDESCRYCLRGEENL 107
                                    69********************.8************************************998775899*********** PP

                                    -TTBEETTTSS-SSSBSEEEECGGGEEEE CS
                          ADH_N  81 CeeakllgvsldGgfaeyvvvpekklvkl 109
                                    C++a+++g+++dGg+aey+v++e++++++
  gi|116754090|ref|YP_843208.1| 108 CDNARFTGYTIDGGYAEYTVADERYCLPI 136
                                    *************************9985 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.1e-07   0.00066      56     110 ..     225     281 ..     179     299 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.1e-07
                                    TSSEEEEEESSCSHHHHHHHHHCEEEEEEEEECSC.TSSEEEEEHHHHH.HTT-EEE CS
                     ADH_zinc_N  56 gegvdvvfecvGsgatleaalkllkpgGrlvvvGg.gkgeeefdlrnll.lkeksil 110
                                    ++ +d+++ ++ +g+ ++aal+++ +gG++v+ G+ +++  +f+ ++l+  ++++ +
  gi|116754090|ref|YP_843208.1| 225 PQELDAAIIFAPVGSLVPAALRAVSKGGTVVCGGIhMSDIPSFPYSMLWeERSIRSV 281
                                    44555555555556********************98777777999988844444433 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 !   18.6   0.0   5.2e-07    0.0031      24     132 ..     229     330 ..     205     331 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 5.2e-07
                                    EEEEES-HHHHH.HHHHHHEEEEEEEEE----.S-EEE-CHHHCTTT-EEEE--GGG...-.-HHHHHHHHHHHHHHH-- CS
                   ADH_zinc_N_2  24 DvvldtvggealleaslkvlpggGrlvsiggpplsaallkpakkrkgrsvkyeflfsmkasaqadileelaalieeGklr 103
                                    D+++  +   +l+ a+l+++++gG++v+ g ++      + +  +++rs++ +  ++     ++d  ee   l  + ++r
  gi|116754090|ref|YP_843208.1| 229 DAAIIFAPVGSLVPAALRAVSKGGTVVCGGIHMSDIPSFPYSMLWEERSIRSVANLT-----RRD-GEEFISLARDLHIR 302
                                    55555555345668999999777***9977544222222222223334444444443.....556.78999999****** PP

                                    --EEEEEEGGGHHHHHHHHHSS--SSEEE CS
                   ADH_zinc_N_2 104 pvvdrvfpleeaaeAhrylesgrarGKiV 132
                                    + ++ +f+l+ea+ A+++l++gr  G  V
  gi|116754090|ref|YP_843208.1| 303 TEIQ-EFGLDEANVALDLLRAGRLQGAAV 330
                                    ***8.7*****************999666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 2343.03
//
Query:       gi|116754091|ref|YP_843209.1|  [L=932]
Description: DEAD/DEAH box helicase domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.5e-33  115.3   0.0    1.7e-32  112.6   0.0    2.1  2  DEAD        DEAD/DEAH box helicase
      3e-30  105.4   0.0    5.7e-30  104.5   0.0    1.5  1  DEAD_assoc  DEAD/H associated
    4.2e-21   75.4   0.0    4.7e-19   68.8   0.0    3.1  3  Helicase_C  Helicase conserved C-terminal domain
    1.6e-07   31.5   0.0    2.7e-07   30.7   0.0    1.3  1  ResIII      Type III restriction enzyme, res subunit
    0.00037   20.8   0.0      0.038   14.3   0.0    2.5  2  AAA_19      AAA domain
     0.0024   16.6   0.0     0.0046   15.7   0.0    1.4  1  SNF2_N      SNF2 family N-terminal domain
  ------ inclusion threshold ------
      0.045   13.5   0.7       0.11   12.2   0.7    1.6  1  YdjO        Cold-inducible protein YdjO
       0.12   12.6   0.8        1.2    9.4   0.2    2.7  2  AAA_22      AAA domain
       0.14   12.7   0.1        8.4    7.0   0.0    3.3  3  FliG_N      FliG 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 !  112.6   0.0   8.5e-36   1.7e-32       4     170 ..      27     190 ..      24     198 .. 0.90
   2 ?   -0.2   0.0      0.38   7.5e+02      49      79 ..     654     683 ..     581     697 .. 0.81

  Alignments for each domain:
  == domain 1  score: 112.6 bits;  conditional E-value: 8.5e-36
                                    HHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEET CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD   4 QaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliig 83 
                                    Q+ aip+il g++vl+ a+TGsGKT+a+++pvl+++++  + +g k+l+++P+r+L +++l++l+++ + +++++ +  g
  gi|116754091|ref|YP_843209.1|  27 QRMAIPEILAGNNVLLIAPTGSGKTEAAVLPVLHNIMD-IDGPGIKTLYITPLRALNRDMLRRLEEWSDALGVKIAVRHG 105
                                    99**********************************98.89999**************************9999998899 PP

                                    TSSHHHHHHHHHTTCSEEEEEHHHHHHHH..HCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  84 gvaardqlskldngvdivvgtpgrlddll..stgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrq 161
                                    ++++ +  s+ ++ +d++++tp+ l+ +l  ++ + nl++vr++++DE+++l +++++ ++  +l++l +    g+   q
  gi|116754091|ref|YP_843209.1| 106 DTTKGERASQSRSPPDLLITTPETLQVMLtgKRLRSNLKSVRTVIVDEIHELASSKRGSQLAVLLERLVEV--AGE--IQ 181
                                    99999999999777*************9955455567*******************************444..333..56 PP

                                    EEEEESSBS CS
                                    xxxxxxxxx RF
                           DEAD 162 vivlSATlp 170
                                     i lSAT+ 
  gi|116754091|ref|YP_843209.1| 182 RIGLSATVG 190
                                    *******96 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.38
                                    EEEEEESSHHHHHHHHHHHHHHTTTSTSEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  49 kalivePtreLaeqtlnnlkkfkkyidlrvl 79 
                                    ++ +  P r Lae+ ln ++ + +  +++v 
  gi|116754091|ref|YP_843209.1| 654 RIQLTLPKRMLAEELLNVISDLSSA-QMKVI 683
                                    5667889***********9999884.34444 PP

>> DEAD_assoc  DEAD/H associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.5   0.0   2.9e-33   5.7e-30       1     183 [.     601     767 ..     601     772 .. 0.92

  Alignments for each domain:
  == domain 1  score: 104.5 bits;  conditional E-value: 2.9e-33
                     DEAD_assoc   1 lPtdrtllvErfrdelgdwrlvvhspfGrrvnealalllaarlsrrfgidvqvaanDdgivlllpleerlpllldellel 80 
                                    +P+d+t+ +E+          v++s+ G+r+n+a++++++a ls rfg++v++ +++++i l+lp++  + ++l ++++ 
  gi|116754091|ref|YP_843209.1| 601 VPDDKTVTIESDGS-----FAVINSCIGHRANDAFGRAITAILSTRFGSSVGMEIDPYRIQLTLPKRMLA-EELLNVISD 674
                                    8*********9765.....78*****************************************99765555.456679*** PP

                     DEAD_assoc  81 lspdeleedleaalnaselfkrrFrevAaralllprrypgkrkplwqqrlraaqLldvareypdfpllleavrevledql 160
                                    ls+++++ +le +l+++ lf++++ +vA++++ l+++ +        +r++  + l v++   ++p+++ea+re+ ++ l
  gi|116754091|ref|YP_843209.1| 675 LSSAQMKVILELSLKNTTLFRWKMIHVARKFGSLSKDIDY-------ERVSLVRVLGVFE---NTPMYREAIREIYQERL 744
                                    *************************************999.......8999888999988...***************** PP

                     DEAD_assoc 161 Dlerlaellrriaageirvveve 183
                                    D++ + ++l+r+ +gei+v + +
  gi|116754091|ref|YP_843209.1| 745 DVDTAGNILDRMVSGEIQVITCD 767
                                    *******************9854 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 ?    2.2   0.0      0.11   2.3e+02      28      58 ..      85     115 ..      57     135 .. 0.72
   2 !   68.8   0.0   2.4e-22   4.7e-19      14     108 ..     254     348 ..     244     350 .. 0.88
   3 ?   -1.2   0.0       1.3   2.5e+03       4      29 ..     790     815 ..     788     842 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.11
                                    HHHHHHHHHHHT...TSTEEEESTTSTHHHHHHH CS
                     Helicase_C  28 rlekvklllekk...gikvavlhgelpqnereei 58 
                                    +l   + l+e +   g+k+av hg++++ er   
  gi|116754091|ref|YP_843209.1|  85 ML---RRLEEWSdalGVKIAVRHGDTTKGERASQ 115
                                    33...44433335679*************99865 PP

  == domain 2  score: 68.8 bits;  conditional E-value: 2.4e-22
                                    TTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEESSS CS
                     Helicase_C  14 eeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVinfdl 93 
                                    ++ +k+lifvnt++ +e + + l+  g  + v+hg+l+ + r ++ ++f++g+ + Li+t+ +e Gidi +v++Vi+++ 
  gi|116754091|ref|YP_843209.1| 254 VRLKKSLIFVNTRQAAEVLGFRLKMLGEPIEVHHGSLSREARVDAEDAFKRGDLRGLICTSSMELGIDIGDVEHVIQYSS 333
                                    4779**********99653333445599**************************************************** PP

                                    SSSHHHHHHHHTTSS CS
                     Helicase_C  94 prnvtsyiqriGRtg 108
                                    pr+v+++iqr+GR g
  gi|116754091|ref|YP_843209.1| 334 PREVSRLIQRVGRSG 348
                                    *************87 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.3
                                    HHHHHHHHHTTTTSEEEEEESSHHHH CS
                     Helicase_C   4 eallellkleeeggkilifvntidrl 29 
                                    +a++ellk++  ++++++f+ ++++ 
  gi|116754091|ref|YP_843209.1| 790 AAVIELLKNRILHDRVILFCVSCKKW 815
                                    578899999999********999865 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.0   1.4e-10   2.7e-07      25     169 ..      38     189 ..      20     191 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 1.4e-10
                                    SEEEEEESTTSTHHHHH.HHHHHHH-S.......-EEEEESSHHHHHHHHHHGGGGTGG........GEEEESSS-B--. CS
                         ResIII  25 krglikmaTGtGKTlva.aklierllkkgkee..kflflvprkslleqtleefkkflseayke....igkkvsgdkkkak 97 
                                    +++l+ ++TG+GKT  a + +  +++   +    k+l + p ++l   +l++++++++    +    +g  ++g++ ++ 
  gi|116754091|ref|YP_843209.1|  38 NNVLLIAPTGSGKTEAAvLPVLHNIMDIDG-PgiKTLYITPLRALNRDMLRRLEEWSDALGVKiavrHGDTTKGERASQ- 115
                                    57899**********996666666666433.258****************88888877664444456666666666666. PP

                                    ......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T.......TTHHHHHT---SEEEEEESS- CS
                         ResIII  98 ekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk.......swreilekfkeavllglTATp 169
                                      +++  ++l+tt ++l+  +   + ++ +   ++   +i+DE H l+++k         ++++e   e  ++gl+AT 
  gi|116754091|ref|YP_843209.1| 116 --SRSPPDLLITTPETLQVML---TGKRLRSNLKSVRTVIVDEIHELASSKrgsqlavLLERLVEVAGEIQRIGLSATV 189
                                    ..88999**************...8889999999999************8655555555566677778899*******6 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   1.9e-05     0.038       1     115 [.      27     158 ..      27     182 .. 0.68
   2 ?    3.8   0.0     0.033        66      41      83 ..     255     295 ..     243     398 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.9e-05
                         AAA_19   1 qreave.alkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaf....tgrAakelrerlaalgaeatTiHrl 75 
                                    qr a+   l+ +++l++a+ G+GKT+  +  v + +   + +  + l +++    ++   ++l+e  +alg+++   H+ 
  gi|116754091|ref|YP_843209.1|  27 QRMAIPeILAGNNVLLIAPTGSGKTEAAVLPVLHNIMDIDGPGIKTLYITPlralNRDMLRRLEEWSDALGVKIAVRHGD 106
                                    788885589999*************9887776666655556667777777622215556667777777788887777765 PP

                         AAA_19  76 al...............ldfddlltealelleeaeeekklqeeellivDEfqdvd 115
                                    ++               +  ++ +t ++ +l  ++ +++l++  ++ivDE+ ++ 
  gi|116754091|ref|YP_843209.1| 107 TTkgerasqsrsppdllI--TTPETLQV-MLTGKRLRSNLKSVRTVIVDEIHELA 158
                                    556777778877777532..22222233.334556778886777******98876 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.033
                         AAA_19  41 kpeeillvaftgrAakelrerlaalgaeatTiHrlalldfddl 83 
                                     +++ l+   t++Aa+ l  rl++lg++++  H+   l  + +
  gi|116754091|ref|YP_843209.1| 255 RLKKSLIFVNTRQAAEVLGFRLKMLGEPIEVHHGS--LSREAR 295
                                    4578899999********************99976..444433 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 !   15.7   0.0   2.3e-06    0.0046      99     201 ..      72     169 ..      17     199 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.3e-06
                                    EEEE--H.HHHHHHHHHHHHH-TTS-EEE--SSHHHH-----------------EEEE-HHHHHHHT......TTS-S-S CS
                                    xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SNF2_N  99 tLivvPa.slldqWeneierhvsssalrvlvyggqkkmkkkntkvapklladydvvittYdvlsreaelqkkrsvlkqve 177
                                    tL + P  +l +   + +e++     +++ v +g++     + + a +     d +itt ++l+     +  rs lk+v+
  gi|116754091|ref|YP_843209.1|  72 TLYITPLrALNRDMLRRLEEWSDALGVKIAVRHGDT----TKGERASQSRSPPDLLITTPETLQVMLTGKRLRSNLKSVR 147
                                    77777877777777889999*9************86....4455688889999***********9998889999999876 PP

                                    -SEEEES-GGGT--TTSHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxx RF
                         SNF2_N 178 wkrvvlDEghtlknstskaaeavs 201
                                       v++DE h l +s++  + av+
  gi|116754091|ref|YP_843209.1| 148 --TVIVDEIHELASSKRGSQLAVL 169
                                    ..7************755555544 PP

>> YdjO  Cold-inducible protein YdjO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.7   5.5e-05      0.11      26      52 ..     812     840 ..     808     843 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.5e-05
                           YdjO  26 CngW..mRdnFsfeeePtCplCkseMvke 52 
                                    C+ W  +R+  ++ ++P CplC+s+M+  
  gi|116754091|ref|YP_843209.1| 812 CKKWrsLREVGRVPDRPECPLCGSRMIAA 840
                                    777766688888899***********976 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.2   0.00061       1.2       8     114 ..      40     175 ..      36     199 .. 0.60
   2 ?   -3.1   0.0       4.3   8.5e+03      56      86 ..     553     595 ..     548     599 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00061
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka................. 70 
                                    +++++++G+GKT  +   +  +    +++ ++ +++++t+      +d+lr+l +  +    a                 
  gi|116754091|ref|YP_843209.1|  40 VLLIAPTGSGKTEAAVLPVLHN--IMDIDGPGIKTLYITPLRAL-NRDMLRRLEEWSD----Algvkiavrhgdttkger 112
                                    6889999999999887777765..22333366666666554433.3444444444444....344447889999999999 PP

                         AAA_22  71 .............erlsseell..ealeqalraravielliiDEaqhlr.s......eealeeLrs 114
                                                  + +++ +l  ++l+ +l++ ++   +i+DE++ l  s      + +le L++
  gi|116754091|ref|YP_843209.1| 113 asqsrsppdllitTPETLQVMLtgKRLRSNLKSVRT---VIVDEIHELAsSkrgsqlAVLLERLVE 175
                                    999998777777744444444423555555555555...********9872454455555555543 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4.3
                         AAA_22  56 llrellralglelka............erlsseellealeqal 86 
                                    ++++l+r+l++ +++             r   e+l++++ +++
  gi|116754091|ref|YP_843209.1| 553 IRSHLARELEEHGEEdairwllarypvDREAAEQLVDQIKHQI 595
                                    5556666666555555666666555555555777777777766 PP

>> FliG_N  FliG N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.7   5.5e+03      69      97 ..     564     593 ..     551     597 .. 0.71
   2 ?    1.0   0.0       0.3     6e+02      73      98 ..     734     759 ..     729     767 .. 0.83
   3 ?    7.0   0.0    0.0042       8.4       8      33 ..     884     911 ..     878     916 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.7
                                    CHHHHHHHHHHHHH.HSHHHHHHHCHHHHX CS
                         FliG_N  69 eggeeyarelLeka.lgeekaeellerlta 97 
                                    +g e+++r lL +  ++ e ae+l++++++
  gi|116754091|ref|YP_843209.1| 564 HGEEDAIRWLLARYpVDREAAEQLVDQIKH 593
                                    566777777777643677888888888875 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.3
                                    HHHHHHHHHHHSHHHHHHHCHHHHXX CS
                         FliG_N  73 eyarelLekalgeekaeellerltae 98 
                                    e++re+ ++ l+ ++a ++l+r++++
  gi|116754091|ref|YP_843209.1| 734 EAIREIYQERLDVDTAGNILDRMVSG 759
                                    77899999999999999999999875 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0042
                                    HHHHHHH..CXHHHHHHHHTTSXHHHHH CS
                         FliG_N   8 aAillla..LgeeeaaevlkhLdeeeie 33 
                                    aAi l++  Lg+e+aa+v+k+++ +e+e
  gi|116754091|ref|YP_843209.1| 884 AAIALASrgLGPETAARVIKKMHSDELE 911
                                    555555455***************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (932 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); 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: 0.71u 0.31s 00:00:01.02 Elapsed: 00:00:00.45
# Mc/sec: 6202.34
//
Query:       gi|116754092|ref|YP_843210.1|  [L=211]
Description: ribonuclease HII [Methanosaeta thermophila PT]
Scores for 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-45  152.9   0.1    1.1e-44  152.7   0.1    1.0  1  RNase_HII  Ribonuclease HII


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 !  152.7   0.1   5.9e-49   1.1e-44       1     197 [.       5     202 ..       5     203 .. 0.91

  Alignments for each domain:
  == domain 1  score: 152.7 bits;  conditional E-value: 5.9e-49
                                    EEEEEE-TT-SBS-EEEEEEEECGHHHHHHHCTTGTTGTTS-HHHHHHHHHHHH...SEEEEEEE-HHHHH.HHTTTS-H CS
                      RNase_HII   1 iGiDEaGrGpvlGplvvaavavekereeelkklgvkDSKkLskqkreeLaklik...kkiekrklvaeeikyaseneinl 77 
                                    +G+DEaG+Gpv+G+++va+v+ ++e++  l + gvkDSK Ls+ +re ++++i     +    ++ a++i+      ++ 
  gi|116754092|ref|YP_843210.1|   5 LGVDEAGKGPVIGSMFVAGVVFSEEDIFDLAACGVKDSKLLSPTRRESMERKILsiaRESFVLEVTAQQID-DLRMVMSM 83 
                                    6****************************************************944433344555555555.5566899* PP

                                    HHHHHHHHHHHHHHHHHTCEECCECCCE--SSHHHHHHHHHHHHC..CEEEEETTGGGT-HHHHHHHHHHHHHHHHHHHH CS
                      RNase_HII  78 neikaaltlaviklleklgvkvdeilvdgvttpeslkkkleqiik..ikvtvekkadekyllvaaASiiAkverdeelel 155
                                    nei + ++++v  +l+++++ +d+ +v+    +e++++ ++++ +  i + +e+ ad+k+++vaaASiiAkv rd  ++ 
  gi|116754092|ref|YP_843210.1|  84 NEIMVRAHSRVVSRLQADRAILDAADVN----AERFAQRVREVSGkpIDILAEHNADRKHIVVAAASIIAKVARDRSIRD 159
                                    ****************************....77778888888877888******************************* PP

                                    HHHHCSH.--TTSSTTSHHHHHHHHHHHHH..S--TTB-TTSHH CS
                      RNase_HII 156 lkrkpgtldkgsGyasdektrallkkgats..klpdivrlsfkt 197
                                    l+++ g  + gsGy+sd++t  +lk+++ +   lp++vr s+ t
  gi|116754092|ref|YP_843210.1| 160 LEAALG-RPLGSGYPSDPATVRFLKEWIEEngDLPSFVRKSWST 202
                                    ****96.9**********************999*********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); 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: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1557.94
//
Query:       gi|116754093|ref|YP_843211.1|  [L=381]
Description: aminotransferase, class V [Methanosaeta thermophila PT]
Scores for complete 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-46  156.7   0.0    9.2e-46  156.5   0.0    1.0  1  Aminotran_5      Aminotransferase class-V
  ------ inclusion threshold ------
       0.12   11.7   0.0       0.19   11.0   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 !  156.5   0.0     1e-49   9.2e-46       2     342 ..       7     330 ..       6     349 .. 0.91

  Alignments for each domain:
  == domain 1  score: 156.5 bits;  conditional E-value: 1e-49
                                    EEBTTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHH.HHHHHHHH CS
                    Aminotran_5   2 yldsaAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtte.ainlvals 80 
                                    +l+ +++ ++ ++Vl+a+++           +++h++ e+ ++++++re ++e++++++  ei+++sG+++ ++ +++ +
  gi|116754093|ref|YP_843211.1|   7 LLMIPGPVKVAPRVLRAMSKP----------MISHRSPEFGRIYDDCRELLQEFFETKN--EIVVMSGSGTcGMDAAVGG 74 
                                    578899999999999999998..........99*************************7..9****998777******** PP

                                    CCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHH CS
                    Aminotran_5  81 larslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGtiqpvee 160
                                    l   +  +d+i++ ++++ +++    e+ +r g  +  + ++++   dl+++e++l+e +k+va+ h++++ G+i+p  e
  gi|116754093|ref|YP_843211.1|  75 L---IGSDDRILTITNGKFGER--FTEIGNRYGRAI-SVDFEWGMPFDLERVEAALEEGVKAVAMVHNETSVGIINPARE 148
                                    *...9*****************..************.78***************************************** PP

                                    HHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTT.TTSSTT-EEEEEEHHHHHTS..SS.STTSEEEEETTEE CS
                    Aminotran_5 161 igklakkkgalvlvDaaqavghipidvkklgvDflafsghK.llgPtGiGvlyvrkellekleplllggemveevsleet 239
                                    ig+la+k++a+++vD+ +++g  +++++++g+D++  +++K l  P+G+ +++v++++ e+l   + +g++ ++ + + +
  gi|116754093|ref|YP_843211.1| 149 IGRLARKHDAIFIVDGISSIGGNEFKTDEWGIDIAITGSQKcLAVPPGLAIVSVSERAEEAL--NESSGGYYADLRAHLK 226
                                    *****************************************8889*****************..6666777788888888 PP

                                    EEHCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES..-B-CTCBSEEEEEE.T CS
                    Aminotran_5 240 tfaeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyllerlkslpgvrlyg.pdkaerrasivsfnf.k 317
                                    +++++p++    Tp v+ +++l++al + ee g+ea +++ ++lae+++++ ++l+   + +  +  + +++++++++ +
  gi|116754093|ref|YP_843211.1| 227 SVRKKPTQTPF-TPAVPLFYALQEALHMAEEEGFEARRARIARLAEAVRAAASALGIELFPVlNEYSRYSNTVTAMKIpP 305
                                    88899998886.9**************************************99976666633134566677788888889 PP

                                    TCSHHHHHHHHHHTTEEEEEE-TTT CS
                    Aminotran_5 318 gvhaedvatlLdeegIavrsGhhca 342
                                    +++ e+++  ++++g+ v++G++ +
  gi|116754093|ref|YP_843211.1| 306 EIDDEKLRGGMKKQGVVVSGGQERL 330
                                    9********************9877 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   2.1e-05      0.19      98     150 ..     114     169 ..      39     179 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 2.1e-05
                                    SB-GGGCGGG--TTEEEEEEB-...GGGB---HHHHHHHHHHCT-EEEEE-TT-TT CS
                DegT_DnrJ_EryC1  98 nidpaaieaaitertkaIlpVh...lyGqvadmdalkaiaakhglkvieDaAhAlG 150
                                      d +++eaa++e  ka+ +Vh    +G ++   ++ ++a+kh+ ++i D   ++G
  gi|116754093|ref|YP_843211.1| 114 PFDLERVEAALEEGVKAVAMVHnetSVGIINPAREIGRLARKHDAIFIVDGISSIG 169
                                    56999*****************444478888999****************888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); 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: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2540.13
//
Query:       gi|116754094|ref|YP_843212.1|  [L=107]
Description: alkylhydroperoxidase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-14   54.3   3.7    1.3e-14   54.0   3.7    1.2  1  CMD       Carboxymuconolactone decarboxylase family


Domain annotation for each model (and alignments):
>> CMD  Carboxymuconolactone decarboxylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.0   3.7     7e-19   1.3e-14       4      84 ..      18      97 ..      15      98 .. 0.90

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 7e-19
                                   HHHHHHHHHHHCCGSSTS-HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHSHHHHHHHHHHHH CS
                            CMD  4 lraltalreallareggLdpkereLialavsaangceyCvdaHtraAleaGvteeeiaevlaqaaayagwpaaraAlaaae 84
                                    ra+  l+  +l  +g+L+++e+ Liala s+a +ce+C + H+++A+  G+t+ee  e++a+a     +  ++ A+ ++e
  gi|116754094|ref|YP_843212.1| 18 SRAFRSLASMILG-DGALSAREKALIALACSVAIRCEDCTRRHMEQARALGATREEMIEAAAVASLIRMGSGLNTAAVILE 97
                                   5889999999998.9*************************************************99988888887766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); 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 0.27s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 782.02
//
Query:       gi|116754095|ref|YP_843213.1|  [L=151]
Description: pyridoxamine 5'-phosphate oxidase-related, FMN-binding [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      4e-15   55.8   0.0    8.1e-15   54.8   0.0    1.5  2  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
     0.0025   17.6   0.1     0.0036   17.1   0.1    1.3  1  DUF447          Protein of unknown function (DUF447)
     0.0026   17.7   0.0     0.0035   17.3   0.0    1.2  1  Pyridox_ox_2    Pyridoxamine 5'-phosphate oxidase
     0.0032   17.1   0.2       0.71    9.6   0.0    2.5  2  SSXT            SSXT protein (N-terminal region)
  ------ inclusion threshold ------
      0.026   14.1   0.2      0.035   13.7   0.2    1.3  1  Pyrid_ox_like   Pyridoxamine 5'-phosphate oxidase like
      0.034   12.8   0.1      0.039   12.6   0.1    1.1  1  MMS1_N          Mono-functional DNA-alkylating methyl methane


Domain annotation for each model (and alignments):
>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.8   0.0   2.7e-18   8.1e-15       1      88 []       3      89 ..       3      89 .. 0.94
   2 ?   -2.7   0.0       2.4     7e+03      60      68 ..     133     141 ..     122     146 .. 0.75

  Alignments for each domain:
  == domain 1  score: 54.8 bits;  conditional E-value: 2.7e-18
                                   HHHHHHHHHHHSSEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETTGSEEEEEEEEEE CS
                 Putative_PNPOx  1 ldeelreflaeskavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallflddelgrgvrieGtae 82
                                   l+ee++++l e ++v lAT ++dG+Pnv+p++ ++   ++ i+++     ++ +nle+np+va++f d    ++++++Gta+
  gi|116754095|ref|YP_843213.1|  3 LSEEIKQMLDE-NIVYLATSTRDGKPNVVPIGSAYAISDNEILIHDMMFVKTRANLEANPQVAISFTDTRRWESYQLKGTAK 83
                                   57899999996.********************999888888****99999******************************** PP

                                   EESCHH CS
                 Putative_PNPOx 83 lvsdge 88
                                   + ++ge
  gi|116754095|ref|YP_843213.1| 84 IFTEGE 89
                                   **9987 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.4
                                    -EEEEEEEE CS
                 Putative_PNPOx  60 prvallfld 68 
                                    p++a+l++ 
  gi|116754095|ref|YP_843213.1| 133 PKAAVLIIV 141
                                    888888875 PP

>> DUF447  Protein of unknown function (DUF447)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   1.2e-06    0.0036       5      58 ..      19      73 ..      14     132 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.2e-06
                                   EEEE-TT.-EEEEEEEEEE..SSSEEEEEEETTSHHHHHHHHHSEEEEEE---HHHH CS
                         DUF447  5 vtTksek.rpnaaPiGviv..kgdkvvlrlfkgsrTleNllengelvinvtdDpllf 58
                                   +t+++ + +pn+ PiG  +  ++++++++     +T +Nl++n++++i++td ++  
  gi|116754095|ref|YP_843213.1| 19 ATSTR-DgKPNVVPIGSAYaiSDNEILIHDMMFVKTRANLEANPQVAISFTD-TRRW 73
                                   45555.559*******9999877776665444448***************98.5555 PP

>> Pyridox_ox_2  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.2e-06    0.0035       3     112 ..       5     104 ..       4     132 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.2e-06
                                    HHHHHHHHC-SEEEEEEEE.TTEEEEEEEEEEEE..TTEEEEEEETTSHCCHCCCT--.ECEEEEEEEEEEE-SEGGEEE CS
                   Pyridox_ox_2   3 eeilalLdegevgrlafvd.dgepvilPvnyvvd..gdslyfhgakgsrlaaalrgap.vcvvvtevdglvlarsfnsln 78 
                                    eei ++Lde+ v  la+++ dg+p ++P+  ++   ++++++h     +  a l+++p v+++ t++      r+     
  gi|116754095|ref|YP_843213.1|   5 EEIKQMLDENIVY-LATSTrDGKPNVVPIGSAYAisDNEILIHDMMFVKTRANLEANPqVAISFTDT------RR----- 72 
                                    6778888887665.666654999*****97666665999****777666667777556688888884......55..... PP

                                    EEEEEEEEEEEEE--HHHHHHHCCCHHHHHSTTT CS
                   Pyridox_ox_2  79 yrSVvvrGraeevtdeeekaealellvekivpgr 112
                                    + S +++G+a+  t+ e  +++le +  ki  +r
  gi|116754095|ref|YP_843213.1|  73 WESYQLKGTAKIFTEGEMFEKVLEIM--KIKAER 104
                                    **************999999999987..444444 PP

>> SSXT  SSXT protein (N-terminal region)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0   0.00024      0.71       8      51 ..       6      20 ..       2      28 .. 0.68
   2 !    5.1   0.1    0.0058        17      31      46 ..     116     131 ..      97     136 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00024
                           SSXT  8 qIqklLDENsqLIqtIielqnkGraeecdqyqqiLhrNLvyLAt 51
                                   +                              +q+L +N+vyLAt
  gi|116754095|ref|YP_843213.1|  6 E-----------------------------IKQMLDENIVYLAT 20
                                   3.............................45666666666665 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0058
                           SSXT  31 raeecdqyqqiLhrNL 46 
                                    r++e +q    Lh+NL
  gi|116754095|ref|YP_843213.1| 116 RTKERMQRMMELHKNL 131
                                    7889999999999998 PP

>> Pyrid_ox_like  Pyridoxamine 5'-phosphate oxidase like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   1.2e-05     0.035       6      93 ..       7      93 ..       2     118 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.2e-05
                  Pyrid_ox_like  6 lkelvkdiktamLttteadgklksrPMatqkveedgdlwfltkkdsdkvkeirkdsqvnlafsdeskkkyvsvsGtaevved 87
                                   +k++++  ++  L+t+++dgk ++ P   + +  d+++        +  +++++++qv + f d+   +  +++Gta++ ++
  gi|116754095|ref|YP_843213.1|  7 IKQMLD-ENIVYLATSTRDGKPNVVPIGSAYAISDNEILIHDMMFVKTRANLEANPQVAISFTDTRRWESYQLKGTAKIFTE 87
                                   444444.49999****************************************************9999999********998 PP

                  Pyrid_ox_like 88 rakiee 93
                                    +  e+
  gi|116754095|ref|YP_843213.1| 88 GEMFEK 93
                                   776665 PP

>> MMS1_N  Mono-functional DNA-alkylating methyl methanesulfonate N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   1.3e-05     0.039      85     163 ..      34     142 ..       4     148 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.3e-05
                         MMS1_N  85 splearksegvilsmvFldpgykeednpiialleqdrrg.....................kteltlyewdlglnlvrkis 143
                                    s+  +  +e +i++m F++++++ e np +a+ ++d+r+                       e++ ++ + +++++++is
  gi|116754095|ref|YP_843213.1|  34 SAYAISDNEILIHDMMFVKTRANLEANPQVAISFTDTRRwesyqlkgtakiftegemfekVLEIMKIKAERQKDHMESIS 113
                                    4455578999************9888*************99999998888888888774433444444444444444443 PP

                         MMS1_N 144 ktsepkk.............nldsganlLiplp 163
                                          +             nl+++a  Li + 
  gi|116754095|ref|YP_843213.1| 114 DQ----RtkermqrmmelhkNLKPKAAVLIIVE 142
                                    32....123356666666666666666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1443  (0.0804841); expected 358.6 (0.02)
Passed bias filter:                      657  (0.0366445); 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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1122.21
//
Query:       gi|116754096|ref|YP_843214.1|  [L=512]
Description: extracellular solute-binding protein [Methanosaeta thermophila PT]
Scores for 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-81  272.9   0.6    5.3e-81  272.5   0.6    1.1  1  SBP_bac_5  Bacterial extracellular solute-binding proteins, f
  ------ inclusion threshold ------
      0.052   13.9   0.0       0.36   11.2   0.0    2.3  2  Rap1a      Rap1a immunity proteins


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 !  272.5   0.6   5.9e-85   5.3e-81       2     363 ..      70     416 ..      69     426 .. 0.89

  Alignments for each domain:
  == domain 1  score: 272.5 bits;  conditional E-value: 5.9e-85
                                    EEESSEEEEEEEETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHCTCTEEEEEEEETTEEEEE CS
                      SBP_bac_5   2 vvpaLAeswwevsdDgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyaslleedqdikkveavddytvrft 81 
                                    +vpaLAes we  +    y f+L+++vk++DG+p+tA Dvvf++++++d+++++  +s        +++e++dd+tv+++
  gi|116754096|ref|YP_843214.1|  70 FVPALAES-WEYLEGENAYLFNLNPNVKWHDGEPFTANDVVFTINYIKDHPYQWVDSSIV------DRAEKIDDHTVKIY 142
                                    79******.799******************************************998875......8************* PP

                                    ESSETTTTTTHCHHHHHHHGCCHTCTCTTT.TTGTTTSE-BSSSEEEEEEETTT.EEEEEE-TTSTTTSCSSSSEEEEEE CS
                      SBP_bac_5  82 lkkpnalfltllaavpasiakkaaekeddk.dkdtnekpvgtGPYklkefkpgq.kivlernpdYwgggkpkldriefkv 159
                                    l+kp+a+fl  +a + + ++++ +++ +++ d + ++++ gtGP+kl+++++ q +  +e+n+dY+ +g+pk+++++f  
  gi|116754096|ref|YP_843214.1| 143 LAKPYAPFLDQVAGTLPILPEHIYSDVTNPeDFQDPKALTGTGPFKLVDYDKAQgTYLYEANEDYY-QGAPKVKQLKFVK 221
                                    ******99999999999999966655555505666777788***********995666*******9.************* PP

                                    -.SHHHHHHHHHTTSSSEEESTTCCTHCHHHHHTTEEEEEEEEEEEEEEEEETTTSTGGGSHHHHHHHHHHS-HHHHHHH CS
                      SBP_bac_5 160 ipdsdaraaalqsGeiddvaepppsdieqlkeakglkvlyespgggvtylafNtkkppfddkrvRqAlsyAiDreeivka 239
                                      +s+    al+ Ge+ d++ +pp+ +++l+   +  v  e++  +   l++N+kk+pf+d+r+RqAl+yAiDre++v++
  gi|116754096|ref|YP_843214.1| 222 L-SSEMSGPALKRGEV-DATAVPPEVADELRG--SFVV-LEGAHDWLAKLMINHKKEPFSDVRFRQALAYAIDREKLVEI 296
                                    9.999999999*****.888999999999855..4555.56*************************************** PP

                                    CTTTSSEEESSS.STTTSTTCCSCHCCCSHHSHHHHHHHHHHHTT-BCSSTSCEETC..EEEEEEEEETTSHHHHHHHHH CS
                      SBP_bac_5 240 vlegyatpansl.lppsspgadeeykpaykaydpekAkklLkeaGykdgdggglrek..klkltlllasgspaekaiael 316
                                    + +gy++pa    ++p s + +++ +++  ++dpekA  lLke Gy +++ + ++++  +l++ ll++s    ++++ e+
  gi|116754096|ref|YP_843214.1| 297 AQRGYGVPASPGlFAPDSEWCNPDVEQY--EHDPEKAGDLLKEMGYVKKG-DFFEKDgnTLEVELLVTS---SNERAGEI 370
                                    *********9999********9999987..67***************996.567777555554554444...45689*** PP

                                    HHHHHHHTTEEEEEEEECHHHHHHHHHHCTTESEEEEEEECTTSTTH CS
                      SBP_bac_5 317 iqqqlkkiGikvevktvdwaatylervkdgdfdmillgwgadypdpd 363
                                    i+++l+++Gikv++++vd+ +t +++v++++fd++l+g g+  +dp+
  gi|116754096|ref|YP_843214.1| 371 IKNDLEEAGIKVNMRSVDS-KTLDNAVNEWNFDLALSGHGGMGGDPE 416
                                    *******************.*********************999997 PP

>> Rap1a  Rap1a immunity proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       0.3   2.7e+03      48      61 ..     364     377 ..     359     378 .. 0.86
   2 ?   11.2   0.0     4e-05      0.36      16      49 ..     424     457 ..     422     462 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.3
                          Rap1a  48 kerAaslvveaLae 61 
                                    +erA +++++ L+e
  gi|116754096|ref|YP_843214.1| 364 NERAGEIIKNDLEE 377
                                    79*********998 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 4e-05
                          Rap1a  16 egteWCsarrvkpselreivyeylkklpaerlke 49 
                                    eg+++Cs+r + +++l++ + ++++++ ++r+k+
  gi|116754096|ref|YP_843214.1| 424 EGYTFCSDRYIVNQTLNDLLDQEVAEMNPDRRKQ 457
                                    8**************************9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (512 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); 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: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 3667.62
//
Query:       gi|116754097|ref|YP_843215.1|  [L=84]
Description: hypothetical protein Mthe_0786 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 590.48
//
Query:       gi|116754098|ref|YP_843216.1|  [L=647]
Description: nitrous oxidase accessory protein-like [Methanosaeta thermophila PT]
Scores for complete 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-67  227.1  93.1    7.6e-32  110.5  32.3    4.0  5  NosD             Periplasmic copper-binding protein (NosD)
    4.2e-49  166.4  76.4    9.6e-21   74.3  25.4    4.4  4  Beta_helix       Right handed beta helix region
     0.0087   14.8   0.0      0.017   13.9   0.0    1.5  1  Pectinesterase   Pectinesterase
  ------ inclusion threshold ------
       0.15   11.9  40.0      0.031   14.1   4.0    4.8  4  Pectate_lyase_3  Pectate lyase superfamily protein


Domain annotation for each model (and alignments):
>> NosD  Periplasmic copper-binding protein (NosD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.2       1.2   5.3e+03     203     223 ..      21      40 ..      14      49 .. 0.66
   2 !   66.4  12.5   5.1e-22   2.3e-18      15     154 ..      86     223 ..      74     224 .. 0.91
   3 !   54.8  13.8   1.7e-18   7.8e-15      16     145 ..     197     330 ..     197     350 .. 0.87
   4 !   38.9  10.4   1.3e-13   5.7e-10      28     155 ..     323     444 ..     318     448 .. 0.80
   5 !  110.5  32.3   1.7e-35   7.6e-32      16     212 ..     371     556 ..     361     578 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.2
                           NosD 203 gGNyWsdydgeDadgDGigDt 223
                                    + Ny  d dg  ad D igD 
  gi|116754098|ref|YP_843216.1|  21 SRNYIVDDDGF-ADSDSIGDA 40 
                                    56666666666.788888886 PP

  == domain 2  score: 66.4 bits;  conditional E-value: 5.1e-22
                           NosD  15 rgngiqlensegseisnneisnsrdgilldnssnntitgntienlryGihlensesntiedntlssnesGialmsssnn. 93 
                                    r  gi++  +eg+++++  i+ ++++  l +ss+n+i+gnt++++r+G+ +e+  sn+ie+n ++s++ Gi+l++  ++ 
  gi|116754098|ref|YP_843216.1|  86 RSVGIRI-AAEGCTVEGLIITGYSEAGILLTSSGNSIKGNTLSENRAGVLIEGGGSNRIEKNMVYSSTGGIVLYRGARDn 164
                                    5567776.679*********99999999**********************************************998555 PP

                           NosD  94 tlenNtisnnenyGillsdssnntisnNtisnnnkGiflensssntitgNriesnqkiGil 154
                                     + +N+i+++++ +i+ +++ +n i++N+is+ ++G++l ns+++++  N+i +    Gi+
  gi|116754098|ref|YP_843216.1| 165 SVIDNEIRSCNY-SIISKEAYYNIIEKNNISSAGEGVHLINSTDTVVATNTIFDA-LSGIV 223
                                    999*******88.***************************************888.77775 PP

  == domain 3  score: 54.8 bits;  conditional E-value: 1.7e-18
                           NosD  16 gngiqlensegseisnneisnsrdgilldnssnntitgntienlryGihlensesntiedntlssnesGialmsssnntl 95 
                                    g+g++l ns++ ++  n+i +  +gi ++ ss ++++g+t++n  ++i l  ++s+t++dn +ss+++Gi l  +s + l
  gi|116754098|ref|YP_843216.1| 197 GEGVHLINSTDTVVATNTIFDALSGIVIEGSSRIKLSGCTVNNTGTAIALGATSSSTVTDNSISSSNDGIDLVGTSSCLL 276
                                    579*************************************************************************99** PP

                           NosD  96 enNtisnnenyGillsdssnntisnNtisnnnkGiflens....ssntit.gNri 145
                                    e N i n ++ G ++ ds nnti++N+i + + G+f+++s     sn i+  N i
  gi|116754098|ref|YP_843216.1| 277 ERNSIENVTT-GLMIVDSFNNTIRDNEIRDVELGLFVDGStreaYSNIISdTNLI 330
                                    ********99.****************************9555444555533333 PP

  == domain 4  score: 38.9 bits;  conditional E-value: 1.3e-13
                           NosD  28 eisnneisnsrdgilldnssnntitgntienlryGihlensesntiedntlssnesGialmsssnntlenNtisnnenyG 107
                                     is++++++++  +++ n+sn++itg     +++ +++ +++++ i+ n++ +  ++++l+  +n+t+e Nt+++  + G
  gi|116754098|ref|YP_843216.1| 323 IISDTNLIDGMPVVYVFNQSNANITGH----EAAHMTVAYCDRCDISRNIIAH--DALFLYGITNSTVEENTLKGTYG-G 395
                                    567777777777788888888888885....4556788899999999999988..67888888888999999999888.9 PP

                           NosD 108 illsdssnntisnNtis.nnnkGiflensssntitgNriesnqkiGill 155
                                    i l ds+nnt+++Nt+s  +++G fl+++ +n +++N++++n++ G+ l
  gi|116754098|ref|YP_843216.1| 396 IRLLDSTNNTLKENTASgTKYTGMFLRGTAYNLVQNNSLNKNGNNGLAL 444
                                    9999999999999999999999999999999999999999998888764 PP

  == domain 5  score: 110.5 bits;  conditional E-value: 1.7e-35
                           NosD  16 gngiqlensegseisnneisnsrdgilldnssnntitgntienl.ryGihlensesntiedntlssne.sGialmsssnn 93 
                                     + + l+++++s++++n+++ ++ gi l +s+nnt+++nt +   ++G++l ++  n +++n l++n+ +G+al  s +n
  gi|116754098|ref|YP_843216.1| 371 HDALFLYGITNSTVEENTLKGTYGGIRLLDSTNNTLKENTASGTkYTGMFLRGTAYNLVQNNSLNKNGnNGLALILSYRN 450
                                    46788999*********************************999899********************************* PP

                           NosD  94 tlenNtisnnenyGillsdssnntisnNtis.nnnkGiflensssntitgNriesnqkiGilllsssegntiynNyFinn 172
                                     +++N + +n++yGi  ++s++n+i+ Ntis n+++Gi+++ns+++ i gN++++n  +Gil +++s +n++y N++i+n
  gi|116754098|ref|YP_843216.1| 451 SISGNLMMENSEYGIRSNYSEENEIASNTISgNKKAGIWFDNSNRSSIYGNNVTNN-VMGIL-MTNSYENRVYHNNLIDN 528
                                    ********************************************************.*****.99999************ PP

                           NosD 173 senvkydgsnnneWnttktsgtniiggpylgGNyWsdydg 212
                                    +e++++d   +n+W+           gp  gGNyWsd ++
  gi|116754098|ref|YP_843216.1| 529 EEQASDDF--GNSWDM----------GPDEGGNYWSDHRC 556
                                    ******99..8***44..........6689*******876 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 !   46.3  15.5   8.8e-16   3.9e-12      11     136 ..      97     217 ..      88     219 .. 0.65
   2 !   54.6  16.7   2.4e-18   1.1e-14       2     138 ..     199     333 ..     199     353 .. 0.86
   3 !   74.3  25.4   2.1e-24   9.6e-21      14     158 .]     360     503 ..     336     503 .. 0.91
   4 !   32.3  14.7   1.7e-11   7.8e-08      48     116 ..     464     531 ..     464     538 .. 0.93

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 8.8e-16
                                    .EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT.--S--EEES-EEES CS
                     Beta_helix  11 vtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialf.gasnnlienneitd 89 
                                    +t+++ +i++ + +Gi l +s+n  i++n+++  +  G+ i+g+  n i++n ++ ++ ggi l+ ga  n + +nei+ 
  gi|116754098|ref|YP_843216.1|  97 CTVEGLIITGYSEAGILLTSSGN-SIKGNTLSE-NRAGVLIEGGGSNRIEKNMVYSST-GGIVLYrGARDNSVIDNEIRS 173
                                    47777777777777777777777.777777777.777777777777777777777777.555555577777777777777 PP

                                    -SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES CS
                     Beta_helix  90 nggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitn 136
                                    ++   i  + ++ n+ie+N+i++ +  G+++ +s  +++v  Nti++
  gi|116754098|ref|YP_843216.1| 174 CNY-SIISKEAYYNIIEKNNISSAG-EGVHLINST-DTVVATNTIFD 217
                                    754.565556777777777777777.777777777.66667776665 PP

  == domain 2  score: 54.6 bits;  conditional E-value: 2.4e-18
                                    SEEE-SS-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--E CS
                     Beta_helix   2 gisingssnvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasnnl 81 
                                    g+++ +s+++ +  nti +   +Gi ++gss++ +++++++n +g+ i++  +s +t+++n+is +n +gi l g+s  l
  gi|116754098|ref|YP_843216.1| 199 GVHLINSTDTVVATNTIFD-ALSGIVIEGSSRIKLSGCTVNN-TGTAIALGATSSSTVTDNSISSSN-DGIDLVGTSSCL 275
                                    676667777799*******.6*********************.************************.************ PP

                                    EES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT...---EEES-EEES-S CS
                     Beta_helix  82 ienneitdnggsGiylnyssnntienNiidnnagsGividdss...snvtvtnNtitnnk 138
                                    +e+n i++  + G+++ +s nnti++N i++++  G+++d s    +++ +++ ++ + +
  gi|116754098|ref|YP_843216.1| 276 LERNSIENVTT-GLMIVDSFNNTIRDNEIRDVE-LGLFVDGSTreaYSNIISDTNLIDGM 333
                                    *********98.*********************.*********88844445555555444 PP

  == domain 3  score: 74.3 bits;  conditional E-value: 2.1e-24
                                    ESEEEES-..SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES-EEES-S CS
                     Beta_helix  14 knntisns..ggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasnnlienneitdng 91 
                                    + ++is++   +++++l+g +n ++e+n++ + ++ Gi++l s+nnt+++nt s+ +++g+ l+g+ +nl++nn  ++ng
  gi|116754098|ref|YP_843216.1| 360 DRCDISRNiiAHDALFLYGITNSTVEENTLKG-TYGGIRLLDSTNNTLKENTASGTKYTGMFLRGTAYNLVQNNSLNKNG 438
                                    455555558888********************.*********************************************** PP

                                    S-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS--EEES-E. CS
                     Beta_helix  92 gsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsssnvtvrnNti 158
                                    ++G+ l  s++n+i++N + +n+++Gi  ++s+ ++++  Nti++nk+aGi++ +s++   +++N++
  gi|116754098|ref|YP_843216.1| 439 NNGLALILSYRNSISGNLMMENSEYGIRSNYSE-ENEIASNTISGNKKAGIWFDNSNR-SSIYGNNV 503
                                    *********************************.************************.99999975 PP

  == domain 4  score: 32.3 bits;  conditional E-value: 1.7e-11
                                    SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES-EEES-SS-SEE-TT-S--EEES-EEESTT-- CS
                     Beta_helix  48 GiyilgssnntisnntisdnngggialfgasnnlienneitdnggsGiylnyssnntienNiidnnags 116
                                    Gi+ ++s++n i  ntis+n+  gi++++++++ i++n++t+n   Gi +++s+ n++ +N++ +n+++
  gi|116754098|ref|YP_843216.1| 464 GIRSNYSEENEIASNTISGNKKAGIWFDNSNRSSIYGNNVTNNVM-GILMTNSYENRVYHNNLIDNEEQ 531
                                    89999**************************************98.************99999999854 PP

>> Pectinesterase  Pectinesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   3.7e-06     0.017       3      57 ..      25      75 ..      23     100 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.7e-06
                                   EE-TTS-SSBSSHHHHHHHS-SS-SS-EEEEE-SEEEE--EEE-TTS-SEEEEES CS
                 Pectinesterase  3 vvakdgsgkfktiseavaavpeksekrfviyvkaGvYeenvevekkktnvvlvGd 57
                                   +v +dg ++  +i +av+a+++      +iyvk G Y+e+v+v+k+ t   l+G+
  gi|116754098|ref|YP_843216.1| 25 IVDDDGFADSDSIGDAVKAASDG----DIIYVKPGEYSEEVQVDKTLTIKPLLGE 75
                                   78999************999854....59***************98776666665 PP

>> Pectate_lyase_3  Pectate lyase superfamily protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4  12.4   0.00039       1.8      16     214 ..      32     266 ..      21     266 .. 0.55
   2 ?   14.1   4.0   6.9e-06     0.031     118     213 ..     220     309 ..     206     311 .. 0.80
   3 ?    6.7   7.3    0.0013       5.7      92     214 ..     368     488 ..     330     488 .. 0.78
   4 ?    1.3   9.8     0.059   2.6e+02     114     189 ..     459     530 ..     422     544 .. 0.54

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00039
                                    E-HHHHHHHH......HTSS-EEE-SEEEEESS-E..........EE-SSEEEEES-TTTEEEEE-TT-SS--SEEES-T CS
                Pectate_lyase_3  16 DdtaaiqkaiscasatttgavVYfPaGtYlvsspi..........ilksgvqLvGdgngrpvlkaaaafvgaglidgdpy 85 
                                     d+  i +a+   +a ++g+++Y+ +G Y  +  +            + +++L Gd + + +  aa + + +gli  + y
  gi|116754098|ref|YP_843216.1|  32 ADSDSIGDAV---KAASDGDIIYVKPGEYSEEVQVdktltikpllGERGECVLKGDDRSVGIRIAAEGCTVEGLI-ITGY 107
                                    3566788888...89999999999999998777777777888888667777777777666665555555333333.1222 PP

                                    TT-.............................-EEEEEEEEEEEGGGG-SS---S.....SEEEES-EEEEEEEEEEES- CS
                Pectate_lyase_3  86 vsggs...........................ealiatnnfyrqirnlkiditav.....apgatgihwqtaqatslenv 133
                                     ++g+                            + i++n +y++   +++   a      +++ + +++   ++   +n+
  gi|116754098|ref|YP_843216.1| 108 SEAGIlltssgnsikgntlsenragvliegggSNRIEKNMVYSSTGGIVLYRGARdnsviDNEIRSCNYSIISKEAYYNI 187
                                    21111112220011111111111111111111444445555555444444433332121122224444444444444444 PP

                                    SSEEE-SSS---TT---SS--EEEE.ES-EEES-SS-SEEES-EEEEEES-EEE-S--SEEE-TT-EEEEEEEEEESSSE CS
                Pectate_lyase_3 134 efemseasgtkhqgifiengsggfl.ndlvfsglgdigiavgnqqftvrnitfnnattgievlwgwgwtlknvkinnceg 212
                                     +e ++ s   ++g+ + n+   ++ ++ +f+ l++i i+  +  + ++ +t+nn++t+i ++ +++ t+ +++i+++++
  gi|116754098|ref|YP_843216.1| 188 -IEKNNIS-SAGEGVHLINSTDTVVaTNTIFDALSGIVIEG-SSRIKLSGCTVNNTGTAIALGATSSSTVTDNSISSSND 264
                                    .2222222.23455555554444447899999966666665.999******************999999999*9999999 PP

                                    EE CS
                Pectate_lyase_3 213 Gi 214
                                    Gi
  gi|116754098|ref|YP_843216.1| 265 GI 266
                                    97 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 6.9e-06
                                    ES-EEEEEEEEEEES-SSEEE-SSS---TT---SS--EEEEES-EEES-SS-SEEE.S-EEEEEES-EEE-S--SEEE-T CS
                Pectate_lyase_3 118 tgihwqtaqatslenvefemseasgtkhqgifiengsggflndlvfsglgdigiav.gnqqftvrnitfnnattgievlw 196
                                    +gi  + +++ +l+ ++++++         i +  +s+++++d  +s  +++gi + g+    ++++ ++n ttg  + +
  gi|116754098|ref|YP_843216.1| 220 SGIVIEGSSRIKLSGCTVNNTGT------AIALGATSSSTVTDNSISS-SNDGIDLvGTSSCLLERNSIENVTTGLMIVD 292
                                    56666666666666666666544......5889999999999999999.9****9999999999**************99 PP

                                    T-EEEEEEEEEESSSEE CS
                Pectate_lyase_3 197 gwgwtlknvkinncegG 213
                                    + + t+++++i + e G
  gi|116754098|ref|YP_843216.1| 293 SFNNTIRDNEIRDVELG 309
                                    99999999999988776 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0013
                                    EEEEEEEEEEEGGGG-SS---SSEEEES-EEEEEEEEEEES-SSEEE-SSS---TT---SS--EEEEES-EEES-SS-SE CS
                Pectate_lyase_3  92 aliatnnfyrqirnlkiditavapgatgihwqtaqatslenvefemseasgtkhqgifiengsggflndlvfsglgdigi 171
                                     + +++ f+ +i+n ++  + ++ ++ gi+   +++ +l+++     +asgtk +g f++ ++ + +++   +++g+ g+
  gi|116754098|ref|YP_843216.1| 368 IIAHDALFLYGITNSTVEENTLKGTYGGIRLLDSTNNTLKEN-----TASGTKYTGMFLRGTAYNLVQNNSLNKNGNNGL 442
                                    455566677778888888887777778888777777777776.....555566669***********88888888***** PP

                                    EE..S-EEEEEES-EEE-S--SEEE-TT-EEEEEEEEEESSSE.EE CS
                Pectate_lyase_3 172 av..gnqqftvrnitfnnattgievlwgwgwtlknvkinnceg.Gi 214
                                    a+  +  +++  n+ ++n++ gi+ +++++  +++++i++ ++ Gi
  gi|116754098|ref|YP_843216.1| 443 ALilSYRNSISGNLMMENSEYGIRSNYSEENEIASNTISGNKKaGI 488
                                    *96558889999***************9999999999988877675 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.059
                                    SEEEES-EEEEEEEEEEES-SSEEE-SSS---TT---SS--EEEE.ES-EEES-SS-SEEES.-EEEEEES-EEE-S- CS
                Pectate_lyase_3 114 apgatgihwqtaqatslenvefemseasgtkhqgifiengsggfl.ndlvfsglgdigiavg.nqqftvrnitfnnat 189
                                    +++ +gi+ ++++  ++ ++++  ++++     gi  +n++++ +  + v +++ +i ++ + ++ ++++n+ + n +
  gi|116754098|ref|YP_843216.1| 459 ENSEYGIRSNYSEENEIASNTISGNKKA-----GIWFDNSNRSSIyGNNVTNNVMGILMTNSyENRVYHNNL-IDNEE 530
                                    3344555555555555555544444444.....788888777444477777777777777752444444444.44433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (647 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); 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: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.45
# Mc/sec: 4293.82
//
Query:       gi|116754099|ref|YP_843217.1|  [L=382]
Description: 3-isopropylmalate dehydratase [Methanosaeta thermophila PT]
Scores for complete 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-95  319.2   0.2    6.3e-93  312.3   0.2    2.2  1  Aconitase  Aconitase family (aconitate hydratase)
  ------ inclusion threshold ------
      0.045   12.5   0.0      0.089   11.5   0.0    1.4  1  DUF521     Protein of unknown function (DUF521)


Domain annotation for each model (and alignments):
>> Aconitase  Aconitase family (aconitate hydratase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  312.3   0.2   7.1e-97   6.3e-93      22     461 .]       1     374 [.       1     374 [. 0.92

  Alignments for each domain:
  == domain 1  score: 312.3 bits;  conditional E-value: 7.1e-97
                      Aconitase  22 llqdvtgvqalvdlaaareav.rrlggtlatidhlvpvdlvidhsvgaeealeknledefernkeryefLksaakafgi. 99 
                                    +++d t+v a++ ++++++++ ++ ++ +   dh vp++          ++ ++ l+ e++r         +a +a gi 
  gi|116754099|ref|YP_843217.1|   1 MSHDGTSVLAIKAFREMGSEKvWDKSRIVIPFDHIVPAN----------NETAATLQAEVRR---------WA-RAQGIe 60 
                                    58************9998776599999999999999999..........2223344444444.........44.455664 PP

                      Aconitase 100 rvvppgqGIvHqvnlEyglalpgktvvgtDSHTtmigglGvlaiGvGgieaeavllgqplelkipkvvgvkltGklkegv 179
                                    ++++ g+GI+Hqv  E+g+alpg++vvg DSH++++g+lG++++GvG ++++++     l++++p+++ ++l+G+l+++v
  gi|116754099|ref|YP_843217.1|  61 NFYDCGHGICHQVFCEMGFALPGALVVGADSHSCTYGALGAFGTGVGATDMAEIYSRGRLWFRVPETICMRLEGTLGDMV 140
                                    79****************************************************************************** PP

                      Aconitase 180 takDlvlavigklrkkgvvgkvvEffGegvesLsledraTiaNMaaEvGAttglfpvdektleYLkatgreeaavlveay 259
                                    +akDl+l v+++++++g++   vEf+G +ve+Ls+ +r+T++NM++E+GA+++++p+de++ +YL+  +r+  +      
  gi|116754099|ref|YP_843217.1| 141 SAKDLALFVVKEMGADGANYMSVEFVGGAVERLSISGRMTLCNMGVEMGAKAAIVPPDESVDAYLA--RRARRP------ 212
                                    ******************************************************************..665555...... PP

                      Aconitase 260 dkaqalfelaadedaeydkvleldlstlepsvagpkrPqdavplselvkkefkeelekeaaekaleyklkegtklkdgkv 339
                                         + ++++d++ +y +++e d+s++ p++a p+r++++ p+++                            l  ++v
  gi|116754099|ref|YP_843217.1| 213 -----YTHIHSDPG-SYYREIEYDVSDIPPMIAAPYRVDNVHPVRD----------------------------LAGIEV 258
                                    .....335778998.78889************************33............................23567* PP

                      Aconitase 340 diaaigSCTNssnedvraaagllakavekglkvkpgvktsvaPGSevvkayleaeGlleiLekaGfevvgagCstCig.n 418
                                    d+++ig CTN+++ed+++aa++++     g++vk   +t+v P+S+++   + ++G+ e+L +aG+ +  +gC++C+g  
  gi|116754099|ref|YP_843217.1| 259 DQVFIGTCTNGRLEDLEMAARIVK-----GKRVKI--RTLVIPASREIYLGALRSGVIETLVEAGAMIGPPGCGPCLGaH 331
                                    ************************.....*99998..*****************************************99 PP

                      Aconitase 419 sdrleegeaivsssNRNFegRqgpntrayLaSPelvvaaAlaG 461
                                     + l +ge+++s+sNRNF gR+g+n++ yLaSP+ ++a+A++G
  gi|116754099|ref|YP_843217.1| 332 MGVLGDGEVCLSTSNRNFPGRMGRNGKVYLASPATAAATAITG 374
                                    9****************************************98 PP

>> DUF521  Protein of unknown function (DUF521)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   9.9e-06     0.089     290     357 ..     257     324 ..     244     340 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.9e-06
                         DUF521 290 kvdlvalG.cPhlsleElrelaellkgkkkkvkvelwvttsrevkeeaerlglveklekaGvkvlsdtC 357
                                    +vd v++G c    le+l+  a+++kgk++k  ++l++ +sre++  a r+g++e+l +aG+ +    C
  gi|116754099|ref|YP_843217.1| 257 EVDQVFIGtCTNGRLEDLEMAARIVKGKRVK-IRTLVIPASREIYLGALRSGVIETLVEAGAMIGPPGC 324
                                    78888888677788999********666654.4567889***********************9977666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.49
# Mc/sec: 2363.48
//
Query:       gi|116754100|ref|YP_843218.1|  [L=216]
Description: phosphotransferase domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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   56.5   2.1    2.7e-15   55.9   0.1    2.3  3  PHP_C     PHP-associated
    1.1e-12   48.6   0.0    1.3e-12   48.3   0.0    1.3  1  PHP       PHP domain
  ------ inclusion threshold ------
       0.76   10.3   3.0         17    5.9   0.0    3.5  4  CBS       CBS 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 ?   -0.5   0.0      0.18     1e+03       7      20 ..      21      34 ..      15      37 .. 0.78
   2 !   55.9   0.1   4.5e-19   2.7e-15       2      56 .]     135     187 ..     134     187 .. 0.93
   3 ?   -3.5   0.1       1.5   8.9e+03       4      14 ..     201     211 ..     199     215 .. 0.63

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.18
                          PHP_C  7 ArrfAeklglpgtg 20
                                     r+A++ gl g++
  gi|116754100|ref|YP_843218.1| 21 IVRVARRKGLGGIA 34
                                   56899999999987 PP

  == domain 2  score: 55.9 bits;  conditional E-value: 4.5e-19
                          PHP_C   2 eaNrrArrfAeklglpgtgGSDAHrleeVGrayTefeepiatpdelleairegrt 56 
                                     +N rA   A+++ +p+++GSDAH++e+VG ++T + + ++  d++l++ir+ rt
  gi|116754100|ref|YP_843218.1| 135 LSNLRAMLEARRRRIPMVAGSDAHVAETVGLGVTILNAASE--DDVLDEIRKNRT 187
                                    5899********************************77766..*********998 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 1.5
                          PHP_C   4 NrrArrfAekl 14 
                                     r A+++ +kl
  gi|116754100|ref|YP_843218.1| 201 KRLAKKIYRKL 211
                                    46666666665 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.0   2.2e-16   1.3e-12       1      74 [.       4      80 ..       4     213 .. 0.71

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 2.2e-16
                                   EEEE--CCC--.S-H..HHHHHHHHHCT-SEEEEEEEEBTTHHHHHHHHHHHHTTTTSEEEEEEE............... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......x RF
                            PHP  1 dlHvHteyslldgalsieelvkkakelglkaiaiTDhgnlfgyvefykaakkkykagikpiiGleayvaddse......k 74
                                   dlH+H++ys   ++  +ee+v+ a+++gl  ia+TDh+ l+g + + + ++ +yk ++ +i G+e++  +++       +
  gi|116754100|ref|YP_843218.1|  4 DLHIHSKYSDGGAS--VEEIVRVARRKGLGGIAVTDHNTLDGSMAALRICRSRYK-EMIIIRGAEIDTSEGHLivlgvdE 80
                                   89*******66244..6***********************************996.666******655554434444440 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0    0.0029        17      16      43 ..      16      42 ..      12      45 .. 0.85
   2 ?    1.4   0.1     0.073   4.4e+02      12      23 ..      86      97 ..      85     123 .. 0.69
   3 ?    0.3   0.0      0.16   9.6e+02      23      39 ..     139     156 ..     135     165 .. 0.67
   4 ?   -3.0   0.0       1.7     1e+04      20      29 ..     177     186 ..     173     189 .. 0.61

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0029
                                   SBHHHHHHHHHHHTSSEEEEEETTTBEE CS
                            CBS 16 ttleealelmrekgvsrlPVVdedgklv 43
                                   +++ee+++  r+kg++++ V+d +  l 
  gi|116754100|ref|YP_843218.1| 16 ASVEEIVRVARRKGLGGIAVTDHNT-LD 42
                                   79******************97654.65 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.073
                                   EETTSBHHHHHH CS
                            CBS 12 vppdttleeale 23
                                   ++p++t+eea +
  gi|116754100|ref|YP_843218.1| 86 LTPEETIEEAHD 97
                                   579999999984 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.16
                                    HHHHHHTSSEEEEE.ETT CS
                            CBS  23 elmrekgvsrlPVV.ded 39 
                                    + m e++ +r+P V  +d
  gi|116754100|ref|YP_843218.1| 139 RAMLEARRRRIPMVaGSD 156
                                    556677789**9985333 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 1.7
                                    HHHHHHHHHT CS
                            CBS  20 ealelmrekg 29 
                                    ++l+++r+++
  gi|116754100|ref|YP_843218.1| 177 DVLDEIRKNR 186
                                    7777785444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); 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:                         3  (0.000167327); expected 0.2 (1e-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 0.23s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1542.29
//
Query:       gi|116754101|ref|YP_843219.1|  [L=174]
Description: phosphopantetheine adenylyltransferase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-18   67.2   0.0      2e-18   67.0   0.0    1.0  1  CTP_transf_like  Cytidylyltransferase-like
    5.3e-06   26.4   0.0      9e-06   25.7   0.0    1.4  1  FAD_syn          FAD synthetase
     0.0072   17.0   0.0      0.016   15.9   0.0    1.5  1  PTS_IIB          PTS system, Lactose/Cellobiose specific IIB 
  ------ inclusion threshold ------
       0.17   11.1   0.0       0.23   10.6   0.0    1.2  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 !   67.0   0.0   4.4e-22     2e-18       2     141 ..      26     162 ..      25     164 .. 0.89

  Alignments for each domain:
  == domain 1  score: 67.0 bits;  conditional E-value: 4.4e-22
                                    EEE--TT--HHHHHHHHHHHHHSSES..EEEEEESSTHCSST.-SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHH.... CS
                CTP_transf_like   2 agGtFDpiHlGHlrlleqakklleed..livgvpsdeppkkk.kkplasaeeRlemlelakevdevisvdpweltr.... 74 
                                    +gGtFDpiH GHl+ll++a++  +e   ++++++sde ++++ k+p+ + ++Rl++l++    +e + vd +e+++    
  gi|116754101|ref|YP_843219.1|  26 VGGTFDPIHDGHLALLKKAFEVAGENgtVVIALTSDEMARSQrKRPVRDFDTRLKNLRRV--LKEKLGVDSFEVEKisdv 103
                                    69****************************************77****************..444468999999988887 PP

                                    ..HHHHHTTTTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHH CS
                CTP_transf_like  75 ..evlkklkpdklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkir 141
                                      + ++k   d  y+v++ ++  ++ + +e+++  g ++l +v+++       +k + +   iSst+i 
  gi|116754101|ref|YP_843219.1| 104 fgSAIEKD-YD--YIVVSPETAPTACRINEIRRENGLRPLKIVQIE-------YKMADDNMRISSTRIA 162
                                    76333333.59..************9999**************999.......99************96 PP

>> FAD_syn  FAD synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0     2e-09     9e-06       9      84 ..      24      99 ..      17     116 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 2e-09
                        FAD_syn  9 vvtlGnFDGvHlGHqallkkaveaakekglpsvvvtFephPrevlakekaparLttleeklelleelgvdavlvvd 84
                                   v + G FD +H GH allkka e a e+g+ ++ +t ++  r+  ++   +++    + +  l e+lgvd + v +
  gi|116754101|ref|YP_843219.1| 24 VAVGGTFDPIHDGHLALLKKAFEVAGENGTVVIALTSDEMARSQRKRPVRDFDTRLKNLRRVLKEKLGVDSFEVEK 99
                                   444589******************************9999888877655555544444555556788898876655 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 !   15.9   0.0   3.7e-06     0.016      19      82 ..      81     152 ..      79     156 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.7e-06
                                    HHHHHHHHCT....EEEEETTEEGGGHHHHHHT-SEEEEEESSGG.....CTHHHHTT.SEEEEECTTHHHCCH CS
                        PTS_IIB  19 klekaakelg....ieaegeagveleaeeiaddaDlvllapqvrv.....kdlarfag.kpvavinikdalgim 82 
                                    +l++++ke+     +e+e  + v    ++i++d+D+++++p+++      +++ r +g  p+++++i+  +  +
  gi|116754101|ref|YP_843219.1|  81 NLRRVLKEKLgvdsFEVEKISDV--FGSAIEKDYDYIVVSPETAPtacriNEIRRENGlRPLKIVQIEYKMADD 152
                                    67777777666666666666666..99**************999777888999999997699999999866555 PP

>> HIGH_NTase1  HIGH Nucleotidyl Transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   5.1e-05      0.23      10      36 ..      30      56 ..      21      65 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5.1e-05
                    HIGH_NTase1 10 YNPfHnGHlyhlekakeltgadvviav 36
                                   + P H GHl +l+ka e +g++ ++++
  gi|116754101|ref|YP_843219.1| 30 FDPIHDGHLALLKKAFEVAGENGTVVI 56
                                   89******************9977776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); 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: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 1255.57
//
Query:       gi|116754102|ref|YP_843220.1|  [L=143]
Description: cytidyltransferase-like protein [Methanosaeta thermophila PT]
Scores for complete 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   72.2   0.0    5.5e-20   72.0   0.0    1.0  1  CTP_transf_like  Cytidylyltransferase-like


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.0   0.0   3.1e-24   5.5e-20       2     142 ..      10     136 ..       9     137 .. 0.96

  Alignments for each domain:
  == domain 1  score: 72.0 bits;  conditional E-value: 3.1e-24
                                    EEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHHHHHHHTT CS
                CTP_transf_like   2 agGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkkkplasaeeRlemlelakevdevisvdpweltrevlkklk 81 
                                    a GtFD++H GHl +le+ ++l++e l+v v+ d ++k+k +p++++++Rl+m+ ++k vd ++  +  ++  e ++ l+
  gi|116754102|ref|YP_843220.1|  10 ATGTFDILHPGHLLYLERSRALGDE-LVVVVARDINVKHKPRPVVPEDQRLRMVSALKMVDMAVLGSVTDIF-EPVRALR 87 
                                    78***********************.***********9999*******************************.699**** PP

                                    TTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHHH CS
                CTP_transf_like  82 pdklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkire 142
                                    pd  ++ +g d+++d   ++ le  l++++l+ ++++       + + ++++ +Ss +i e
  gi|116754102|ref|YP_843220.1|  88 PD--IITLGYDQYMD---ENWLEGELRKRGLMARVVR-------ISEREPCELCSSRQIVE 136
                                    **..***********...9***************999.......99999999***999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); 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: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 1019.79
//
Query:       gi|116754103|ref|YP_843221.1|  [L=124]
Description: Mov34 family protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-08   34.5   0.3    3.1e-08   33.4   0.3    1.6  1  Prok-JAB  Prokaryotic homologs of the JAB domain
  ------ inclusion threshold ------
       0.18   11.8   0.1       0.29   11.1   0.1    1.3  1  RadC      RadC-like JAB domain


Domain annotation for each model (and alignments):
>> Prok-JAB  Prokaryotic homologs of the JAB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.3   3.5e-12   3.1e-08       3     117 ..      10     109 ..       8     110 .. 0.79

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 3.5e-12
                       Prok-JAB   3 svlsalvaharrahpeEtcGlllgkeseseevivvplvnewsnrfeipdpedslarlkfearerglevvgiwHSHpggsa 82 
                                    ++l+ +++  r++ p+E +Gll  +     ++i++            + + +++a +    +     +vg  HSHp + +
  gi|116754103|ref|YP_843221.1|  10 DALAFILETSRSCMPREFAGLLQASD-GVISEILILPG---------TESSEWMAWVP-MYMLPSVPIVGSCHSHPVPNP 78 
                                    56666778888889999999998887.67777777666.........47888888887.78889999************* PP

                       Prok-JAB  83 rPSetDrrdaaalarvkalliivgdkaeelrawrl 117
                                     PS++D++ +++++  ++++i  +    + r+wr+
  gi|116754103|ref|YP_843221.1|  79 APSREDLAFFSHTG--SYHIIAFPP--FDERSWRC 109
                                    ************87..677777775..44559998 PP

>> RadC  RadC-like JAB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   3.2e-05      0.29      70      87 ..      70      87 ..      64      93 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.2e-05
                                   EEE-TTS--S--HHHHHH CS
                           RadC 70 aHnhPsgdlepSeeDiel 87
                                   +H hP  ++ pS+eD+++
  gi|116754103|ref|YP_843221.1| 70 CHSHPVPNPAPSREDLAF 87
                                   8**************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 960.30
//
Query:       gi|116754104|ref|YP_843222.1|  [L=336]
Description: biotin--acetyl-CoA-carboxylase ligase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-19   70.7   0.0    1.6e-19   70.1   0.0    1.3  1  BPL_LplA_LipB    Biotin/lipoate A/B protein ligase family
      7e-13   48.3   0.0    1.7e-12   47.1   0.0    1.6  1  HTH_11           HTH domain
      3e-08   33.4   0.3    6.6e-08   32.3   0.3    1.6  1  BPL_C            Biotin protein ligase C terminal domain
    4.2e-06   26.4   0.0    6.4e-06   25.8   0.0    1.3  1  BPL_LplA_LipB_2  Biotin/lipoate A/B protein ligase family
  ------ inclusion threshold ------
      0.015   14.9   0.0      0.038   13.6   0.0    1.7  1  HTH_24           Winged helix-turn-helix DNA-binding


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 !   70.1   0.0   4.5e-23   1.6e-19      18     131 .]      99     208 ..      85     208 .. 0.88

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 4.5e-23
                                    GGG--TT-EEEEEEESS-B....-B--B-TTSEEEEEEEEESS...-CCGTHHHHHHHHHHHHHHH......HHTT-TTE CS
                  BPL_LplA_LipB  18 sselesgglvvvrrqtgGr....nvwhspkgeltyslllspeqktfqnrvlelyvsllvlavlealgyrdskpgiegipv 93 
                                     +e e+ ++v+++ qt+Gr    + w+sp g++++s++l+p+    +++++ +y+   ++av++al      +   g  +
  gi|116754104|ref|YP_843222.1|  99 ANEAENWTVVIAEVQTAGRgrlgRKWFSPSGGVWMSIILKPRV---TPSEAFRYTMAGSVAVCRAL------RDLYGLDA 169
                                    4567999*********************************775...********************......799***** PP

                                    EEETTTEEEETTEEEEEEEEEEEE.TTS-EEEEEEEEEE CS
                  BPL_LplA_LipB  94 fikwpnDlyvngrKlaGiavtstr.gktlhhivigvgvn 131
                                    + kwpnD++vngrK+ G++++       + +++ig+g+n
  gi|116754104|ref|YP_843222.1| 170 RTKWPNDVLVNGRKICGVLTEISAeLDVINYMIIGIGIN 208
                                    *********************999667778899999998 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.0   4.7e-16   1.7e-12       5      55 .]      12      63 ..      11      63 .. 0.98

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 4.7e-16
                         HTH_11  5 ilelLleargp.isgeeLAeeLnvSrrtvrrdIkaLeelgvpIesepgrGYr 55
                                   i++ L++a g  +sg+ + + L+vSr++v+++I+ L+++g++Ie++ + GYr
  gi|116754104|ref|YP_843222.1| 12 IIRKLRAASGGwVSGKAMGDGLGVSRAAVWKHIRHLRSMGYRIEASTRLGYR 63
                                   999************************************************8 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 !   32.3   0.3   1.8e-11   6.6e-08       1      47 [.     265     310 ..     265     311 .. 0.96

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 1.8e-11
                                    STTSEEEEEETSCEEEEEEEEE-TTSEEEEEETTE.EEEESSCCEEE CS
                          BPL_C   1 hsGqeVtlededgkveGiavGIdddGaLllktddglqpdinsGdisl 47 
                                    +++++V+++   ++v+Gia+ +d dGaL+++ ddg ++ i +Gd+++
  gi|116754104|ref|YP_843222.1| 265 TLNRRVRVKG-FDEVTGIAESLDPDGALVVRKDDGGIVRILAGDCIH 310
                                    69********.88********************************98 PP

>> BPL_LplA_LipB_2  Biotin/lipoate A/B protein ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   1.8e-09   6.4e-06      42     157 ..     131     242 ..      99     252 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 1.8e-09
                BPL_LplA_LipB_2  42 leaAlvlaPevplakAaamlpvlmvalqdAlgalaPPevavhlewpgtilvngarvGgvrlaaseadeeevPdwlvvgle 121
                                    + ++++l+P v+ ++A +  +++ va++ Al+ l    +  + +wp+++lvng ++ gv  ++s  +e +v +++++g+ 
  gi|116754104|ref|YP_843222.1| 131 VWMSIILKPRVTPSEAFRYTMAGSVAVCRALRDLYG--LDARTKWPNDVLVNGRKICGVLTEIS--AELDVINYMIIGIG 206
                                    5689******************************98..88899**********98877766665..578899******** PP

                BPL_LplA_LipB_2 122 lalekeseepGetpdetaLeeEGcaeveavallesl 157
                                    ++++ ++++  e+ ++t+++eE   ev + +l++ +
  gi|116754104|ref|YP_843222.1| 207 INANMSASSLPEEWNATTIYEELHREVPRGELVAKV 242
                                    ****999988888999*******9999999998765 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   0.0   1.1e-05     0.038      25      46 ..      31      52 ..      24      52 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.1e-05
                         HTH_24 25 erlglSpstvnrrlkrLeeeGl 46
                                   + lg+S+++v+++++ L ++G+
  gi|116754104|ref|YP_843222.1| 31 DGLGVSRAAVWKHIRHLRSMGY 52
                                   679******************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); 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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 2700.59
//
Query:       gi|116754105|ref|YP_843223.1|  [L=499]
Description: pyruvate carboxylase subunit A [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-76  257.1   0.0    1.5e-76  256.6   0.0    1.2  1  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    3.4e-48  162.8   0.2    6.3e-47  158.7   0.1    2.5  2  Biotin_carb_N    Biotin carboxylase, N-terminal domain
      1e-43  147.8   0.0      2e-43  146.9   0.0    1.5  1  Biotin_carb_C    Biotin carboxylase C-terminal domain
    2.5e-12   46.8   0.0    5.2e-12   45.7   0.0    1.5  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    4.5e-06   26.3   0.0    1.2e-05   25.0   0.0    1.6  2  ATP-grasp        ATP-grasp domain
      6e-06   26.4   0.0    1.8e-05   24.8   0.0    1.9  1  ATP-grasp_3      ATP-grasp domain
  ------ inclusion threshold ------
      0.014   15.0   0.0      0.035   13.7   0.0    1.7  1  ATP-grasp_4      ATP-grasp domain
      0.021   15.1   0.0       0.81   10.0   0.0    3.0  3  DUF1611_N        Domain of unknown function (DUF1611_N) Rossm
      0.047   13.4   0.0      0.092   12.5   0.0    1.4  1  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T
      0.082   12.3   0.0       0.16   11.4   0.0    1.4  1  ATP-grasp_5      ATP-grasp domain
       0.16   11.1   0.0        0.4    9.9   0.0    1.5  2  ATPgrasp_ST      Sugar-transfer associated ATP-grasp


Domain annotation for each model (and alignments):
>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  256.6   0.0   9.4e-80   1.5e-76       2     209 ..     116     321 ..     115     323 .. 0.99

  Alignments for each domain:
  == domain 1  score: 256.6 bits;  conditional E-value: 9.4e-80
                                    HHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHSTS CS
                    CPSase_L_D2   2 kesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgnk 81 
                                    k +a++++k+++vp+vp++++ +++ ee  ++a++igyP+iik+a+g+GG Gm++++  e+la +v +a++ a++afg+ 
  gi|116754105|ref|YP_843223.1| 116 KITARQMMKDAGVPIVPGTERGISDPEEIADVAERIGYPIIIKPAAGGGGIGMKIVDRPEDLAPAVVSAQSIATSAFGDG 195
                                    7899**************************************************************************** PP

                                    -EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCECTCCCCEEEES-SS--HHHHHHHHHHHHHHHHHHT-EEEEEEE CS
                    CPSase_L_D2  82 qvlvekslkgpkeiEvevlrDakgnvitvcerenslqlrtqkvievAPsqtLtdeerqalreaavkvvrevgvvgagtve 161
                                    +v++ek+l++p++iE+++++D++g +++v ere+s+q+r+qk+ie+APs+++t+e r++++e avk+++++ +++agtve
  gi|116754105|ref|YP_843223.1| 196 TVYLEKYLSEPRHIEFQIMADNRGRTVYVSERECSIQRRHQKLIEEAPSPVMTPELRKRMGEIAVKAAKAIRYRSAGTVE 275
                                    ******************************************************************************** PP

                                    EEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT--GC CS
                    CPSase_L_D2 162 flldpkskeyyviEvNtRlsvesalaekaTGldlvkeaakialgekLe 209
                                    f++++  +++y++E+NtRl+ve++++e++TG+dl+ke++ +a+ge+L+
  gi|116754105|ref|YP_843223.1| 276 FMYSH--GDFYFLEMNTRLQVEHPITEMVTGIDLAKEQISVAAGEDLS 321
                                    ****5..**************************************996 PP

>> Biotin_carb_N  Biotin carboxylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.7   0.1   3.9e-50   6.3e-47       1     110 []       1     110 [.       1     110 [. 0.98
   2 ?    1.2   0.0      0.32   5.2e+02      11      33 ..     256     279 ..     253     292 .. 0.80

  Alignments for each domain:
  == domain 1  score: 158.7 bits;  conditional E-value: 3.9e-50
                                    ---EEEE---HHHHHHHHHHHHHTT-EEEEEEEGGGTTSHHHHHSSEEEEEESSTTCCGGG-HHHHHHHHHHTT-SEEE- CS
                  Biotin_carb_N   1 kikkvlianrGeiAvriiravrelgietvavyseedanslhvreadeavelgpasasesYlniekivkaakesgadavhp 80 
                                    ++kk+l+anrGeiA+ri+ra+relgi +vavys++d+++l++++adeav +gp+++sesYln+ekivkaa ++ga+a+hp
  gi|116754105|ref|YP_843223.1|   1 MFKKILVANRGEIAIRIMRACRELGILSVAVYSDADRHALFAKYADEAVYIGPSPSSESYLNMEKIVKAALQTGAEAIHP 80 
                                    79****************************************************************************** PP

                                    -SSTTTT-HHHHHHHHHTT-EESSS-HHHH CS
                  Biotin_carb_N  81 GyGflsEnaefaeaveeagivfiGPsaeal 110
                                    GyGfl+En++fa+++ee+g+vfiGPs++++
  gi|116754105|ref|YP_843223.1|  81 GYGFLAENPAFAKLCEENGVVFIGPSSSSI 110
                                    **************************9875 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.32
                                    HHHHHHHHHHHHHTT-EEEE.EEE CS
                  Biotin_carb_N  11 GeiAvriiravrelgietva.vys 33 
                                    GeiAv+ ++a+r  +  tv  +ys
  gi|116754105|ref|YP_843223.1| 256 GEIAVKAAKAIRYRSAGTVEfMYS 279
                                    9***********999888851444 PP

>> Biotin_carb_C  Biotin carboxylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.9   0.0   1.2e-46     2e-43       1     107 [.     335     441 ..     335     442 .. 0.99

  Alignments for each domain:
  == domain 1  score: 146.9 bits;  conditional E-value: 1.2e-46
                                    EEEEESEETTTTTEE--CE-SEEE---STTEEEEE---TT-EE-TTS-SEEEEEEEEESSHHHHHHHHHHHHHT-EEESS CS
                  Biotin_carb_C   1 eaRinaEdpeknflpssGkvtelelpegpgvRvdsgveegsevspyyDsllaKlivhgetreealarlrraLaelrieGv 80 
                                    e+RinaEdp ++f+ps+G++++++ p+gpg+Rvdsgv++g+ ++pyyDsl++Kl++hg++r+ea+ar++raL e+ i Gv
  gi|116754105|ref|YP_843223.1| 335 ECRINAEDPMNDFAPSPGRLRRYRSPGGPGIRVDSGVYTGYVIPPYYDSLISKLVAHGRDRSEAIARMERALYEYIIVGV 414
                                    8******************************************************************************* PP

                                    -BSHHHHHHHHH-HHHHHT---TTTCC CS
                  Biotin_carb_C  81 ktnieflrailedeefakgeldtkfle 107
                                    +tni+f++a+l++e+f++g+++t+f++
  gi|116754105|ref|YP_843223.1| 415 ATNIPFHKAVLRNERFRRGDINTHFIK 441
                                    *************************98 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   0.0   3.2e-15   5.2e-12      26     174 ..     142     290 ..     122     292 .. 0.83

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 3.2e-15
                                    HHHHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT......-SCEEEEE--.ESEEEEEEEEETSSCEE CS
                Dala_Dala_lig_C  26 ellekveeelgypvfVKpareGSSvGvskveseeelkeaieeafky......dekvlvEeai.egreievavlgneklev 98 
                                    e +++v e++gyp+++Kpa  G  +G++ v   e+l+ a+ +a +       d +v  E+++ e r ie  ++ +++ ++
  gi|116754105|ref|YP_843223.1| 142 EEIADVAERIGYPIIIKPAAGGGGIGMKIVDRPEDLAPAVVSAQSIatsafgDGTVYLEKYLsEPRHIEFQIMADNRGRT 221
                                    56889********************************99988766433444499********99**********999998 PP

                                    EEEEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEES CS
                Dala_Dala_lig_C  99 sevgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEvNt 174
                                      v e+  +  + + ++k ++++ +      +++e ++++ e+a+ka ka+  r  + v f+++ +g++++ E+Nt
  gi|116754105|ref|YP_843223.1| 222 VYVSERECS--IQRRHQKLIEEAPS----PVMTPELRKRMGEIAVKAAKAIRYRSAGTVEFMYS-HGDFYFLEMNT 290
                                    888887664..56778888743322....23578999*************************98.9*********9 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       2.9   4.7e+03     124     148 ..      12      36 ..       7      42 .. 0.78
   2 !   25.0   0.0   7.2e-09   1.2e-05      14     159 ..     138     291 ..     124     293 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.9
                                    HHHHHHHHHHTSSEEEEEEEEEETT CS
                      ATP-grasp 124 eiakkiveeLggvGvfavElFvled 148
                                    eia +i+++   +G+++v ++  +d
  gi|116754105|ref|YP_843223.1|  12 EIAIRIMRACRELGILSVAVYSDAD 36 
                                    6888999999999999998887655 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 7.2e-09
                                    ECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC........GTTCEEEEE----SEEEEEEEEEE CS
                      ATP-grasp  14 veskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal........keekvivEefvpfekElsvlvvrs 85 
                                    +++ ee+ ++ae++g+p+++K +  g  G G ++v  +edl  a+  +        ++++v++E++ +  + +   ++ +
  gi|116754105|ref|YP_843223.1| 138 ISDPEEIADVAERIGYPIIIK-PAAGGGGIGMKIVDRPEDLAPAVVSAqsiatsafGDGTVYLEKYLSEPRHIEFQIMAD 216
                                    67889****************.99999*************99888777789999999*********************** PP

                                    TTC-EEE--EEE.EEEETTEEEEEEECEE.-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCTEEEEEEESS CS
                      ATP-grasp  86 aeGetafypvve.tvqedgilrlsvapae.vsekaqkkaeeiakkiveeLggvGvfavElFvledgellvnElapR 159
                                     +G+t+ +   e  +q++    +  ap++ ++ +  k+  eia k+++++ +    +vE+ +  +g+ ++ E+  R
  gi|116754105|ref|YP_843223.1| 217 NRGRTVYVSEREcSIQRRHQKLIEEAPSPvMTPELRKRMGEIAVKAAKAIRYRSAGTVEFMYS-HGDFYFLEMNTR 291
                                    ***97666544425666655555556655156779999*********************8777.899888888766 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   1.1e-08   1.8e-05       6     159 ..     118     293 ..     113     295 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.1e-08
                                    HHHHHHTTT.S-.--............-EESS--SSSEEEEESS-------B--SS--TTE................... CS
                    ATP-grasp_3   6 ktykkLkeagvk.vP........tkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve............ 64 
                                       + +k+agv+ vP         +  a+ +e+  +++++Kp+ G+gg ++ +v+  e++  a+ + +            
  gi|116754105|ref|YP_843223.1| 118 TARQMMKDAGVPiVPgtergisdPEEIADVAERIGYPIIIKPAAGGGGIGMKIVDRPEDLAPAVVSAQsiatsafgdgtv 197
                                    55555666665523464443332233334455669**********************99998888888999999999998 PP

                                    .EEEE---SEEEEEEEEE.SSSEEEEEEEEEEEET....TEEEEEEES----H.HHHHHHHHHHHHTTSTT--EEEEEEE CS
                    ATP-grasp_3  65 .lvqefieGkplSvsllsdgekvlvlavnrqliekaekefvyaGnvtpietel.keevvelaeevvekleglaGyvGvDl 142
                                     l +   e +++  ++++d+    v +  r+   +++++       +p+ t + ++++ e+a ++ +++   ++   v++
  gi|116754105|ref|YP_843223.1| 198 yLEKYLSEPRHIEFQIMADNRGRTVYVSERECSIQRRHQKLIEEAPSPVMTPElRKRMGEIAVKAAKAI-RYRSAGTVEF 276
                                    666666688999999999886666666666665566666777778888888766***************.9999999*** PP

                                    EESS.SEEEEEEESS-- CS
                    ATP-grasp_3 143 vlkdeepyviEvNPRlt 159
                                    +++ ++ y++E N Rl+
  gi|116754105|ref|YP_843223.1| 277 MYSHGDFYFLEMNTRLQ 293
                                    ***************97 PP

>> ATP-grasp_4  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.2e-05     0.035       1      37 [.     151     187 ..     151     210 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.2e-05
                    ATP-grasp_4   1 islPvviKPsvgffSlGVykinneeewkaavaaieee 37 
                                    i +P++iKP+ g + +G+ +++++e++  av + ++ 
  gi|116754105|ref|YP_843223.1| 151 IGYPIIIKPAAGGGGIGMKIVDRPEDLAPAVVSAQSI 187
                                    579**************************99877754 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 ?   10.0   0.0    0.0005      0.81      17      87 ..      29     101 ..      18     104 .. 0.81
   2 ?    0.6   0.0      0.41   6.7e+02      58      88 ..     125     155 ..     118     156 .. 0.89
   3 ?   -1.1   0.0       1.4   2.2e+03      26      40 ..     402     416 ..     387     422 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0005
                      DUF1611_N  17 ipvvssleea...laagaevlviGiapeggklpeswreavkeAleaGldvvsGlHerLsddpelaalakkkgvk 87 
                                    + v+s+ +     ++   e+++iG  p+ +    ++ + vk+Al+ G + +     +L+++p++a+l +++gv 
  gi|116754105|ref|YP_843223.1|  29 VAVYSDADRHalfAKYADEAVYIGPSPSSESY-LNMEKIVKAALQTGAEAIHPGYGFLAENPAFAKLCEENGVV 101
                                    55666665555666666788889999888777.7999*********************************9985 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.41
                      DUF1611_N  58 eaGldvvsGlHerLsddpelaalakkkgvki 88 
                                    +aG+ +v G    +sd +e+a++a++ g  i
  gi|116754105|ref|YP_843223.1| 125 DAGVPIVPGTERGISDPEEIADVAERIGYPI 155
                                    58999*******************9988766 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.4
                      DUF1611_N  26 alaagaevlviGiap 40 
                                     ++a +e++++G+a+
  gi|116754105|ref|YP_843223.1| 402 MERALYEYIIVGVAT 416
                                    3678899******97 PP

>> ATPgrasp_Ter  ATP-grasp in the biosynthetic pathway with Ter operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.7e-05     0.092      44     112 ..     250     319 ..     217     336 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.7e-05
                   ATPgrasp_Ter  44 ekdeelielaerlaeefgldglvnvQvrededgpkLLEiNpRasGGlgys.alaGvnlpylalklllgle 112
                                    e ++++ e+a + a++++      v + + ++  + LE+N+R +    ++ +++G++l++  +  + g++
  gi|116754105|ref|YP_843223.1| 250 ELRKRMGEIAVKAAKAIRYRSAGTVEFMYSHGDFYFLEMNTRLQVEHPITeMVTGIDLAKEQISVAAGED 319
                                    56778889*************************************999883567******9999999953 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   9.5e-05      0.16      13      52 ..     117     158 ..     108     163 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.5e-05
                    ATP-grasp_5  13 aeakelleaygipvvetrl..assaeeaveaaeeigypvvlK 52 
                                      a++++++ g+p+v+     +s++ee +++ae+igyp+ +K
  gi|116754105|ref|YP_843223.1| 117 ITARQMMKDAGVPIVPGTErgISDPEEIADVAERIGYPIIIK 158
                                    67999**********976656*******************99 PP

>> ATPgrasp_ST  Sugar-transfer associated ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00024       0.4      18      91 ..     112     183 ..     106     201 .. 0.70
   2 ?   -3.0   0.0         2   3.3e+03     230     269 ..     257     295 ..     253     310 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00024
                    ATPgrasp_ST  18 lvddKlkfkelalraglkv.pkllgvikeqaeiseleafvkeleegvviKpakgsgGkGilviteredqdylkss 91 
                                     + +K+  ++++++ag+++ p +   i+     +e++++ +++   ++iKpa g gG G+ ++ + ed      s
  gi|116754105|ref|YP_843223.1| 112 AMGSKITARQMMKDAGVPIvPGTERGISD---PEEIADVAERIGYPIIIKPAAGGGGIGMKIVDRPEDLAPAVVS 183
                                    56789999999999999962555555555...55555555555333***************99887665555555 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2
                    ATPgrasp_ST 230 elaakaaeklpglgylGwDivldeekgplllElNarpgla 269
                                    e+a+kaa+     +  G+   +  +++ + lE+N+r  ++
  gi|116754105|ref|YP_843223.1| 257 EIAVKAAK-AIRYRSAGTVEFMYSHGDFYFLEMNTRLQVE 295
                                    56666666.5555555555556666778899999995544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (499 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.54u 0.22s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 3763.34
//
Query:       gi|116754106|ref|YP_843224.1|  [L=165]
Description: hypothetical protein Mthe_0795 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       774  (0.0431703); expected 358.6 (0.02)
Passed bias filter:                      648  (0.0361426); 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: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.50
# Mc/sec: 997.50
//
Query:       gi|116754107|ref|YP_843225.1|  [L=71]
Description: trehalose-6-phosphate synthase [Methanosaeta thermophila PT]
Scores for complete sequence (score 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   13.5   0.0      0.023   13.4   0.0    1.0  1  Glyco_transf_20  Glycosyltransferase family 20
        1.6    8.8   3.8        2.6    8.1   3.8    1.3  1  Ibs_toxin        Toxin Ibs, type I toxin-antitoxin system


Domain annotation for each model (and alignments):
>> Glyco_transf_20  Glycosyltransferase family 20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.6e-06     0.023       2      61 ..       3      66 ..       2      70 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.6e-06
                                   -EEEEEEE-SECEEE-S.SCG..EEECCGSSHHHHHCCCHHCC........C-EEEEEEECCES-CCC CS
                Glyco_transf_20  2 klvvvsnrlplklereseeekeeyelkkssgglvsalkglkee........tevvwvgwlgvevdese 61
                                   +lv++snrlp+++  e+  +   +++ +s ggl + + ++ ++        ++ +wvgw+gv+++ ++
  gi|116754107|ref|YP_843225.1|  3 RLVIISNRLPVTVVEEK--GA--IRFMDSVGGLSTGIRSFIASdkaraemiQDCLWVGWPGVDIKRRN 66
                                   689*******9977775..44..7888999999888888877777777777777*********99887 PP

>> Ibs_toxin  Toxin Ibs, type I toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   3.8   0.00029       2.6       1       7 [.       1       7 [.       1       7 [. 0.99

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00029
                      Ibs_toxin 1 MMKLVII 7
                                  MM+LVII
  gi|116754107|ref|YP_843225.1| 1 MMRLVII 7
                                  ******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       205  (0.011434); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 561.48
//
Query:       gi|116754108|ref|YP_843226.1|  [L=408]
Description: glycosyl transferase, group 1 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-22   79.8   0.0    3.7e-22   78.7   0.0    1.6  2  Glycos_transf_1  Glycosyl transferases group 1
    2.2e-10   41.1   0.0    3.9e-10   40.3   0.0    1.4  1  Glyco_trans_1_4  Glycosyl transferases group 1
    6.4e-06   26.5   0.0    1.2e-05   25.6   0.0    1.5  1  Glyco_trans_1_2  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0      0.85   5.1e+03      52      72 ..      13      32 ..      12      38 .. 0.77
   2 !   78.7   0.0   6.2e-26   3.7e-22       8     171 ..     213     377 ..     207     378 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.85
                                   EES.STTHHHHHHHHHHHCTT CS
                Glycos_transf_1 52 iaGngeeekelkklaeelels 72
                                   i+G  ee +el  la +le +
  gi|116754108|ref|YP_843226.1| 13 IVG-DEEVDELYLLANKLEGK 32
                                   788.68889999999998864 PP

  == domain 2  score: 78.7 bits;  conditional E-value: 6.2e-26
                                    HTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES......STTHHHHHHHHHHHCTTCGGGEEECCH CS
                Glycos_transf_1   8 klgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaG.....ngeeekelkklaeelelsdnviflgevs 82 
                                    ++g++ +++++  v+r+++ K++  +i++++++k+  + +++lv+aG     + e  + l++  +++e   +++++ + +
  gi|116754108|ref|YP_843226.1| 213 RYGIDRERPVVTQVSRFDRLKDPFGVIEVYRKVKE--HIDCQLVLAGggaadDPEGPAILEQIRAAAETDPDIHVIYNPP 290
                                    5788999**************************84..9*************9999999********************** PP

                                    SSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHH CS
                Glycos_transf_1  83 redleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelr 162
                                    + ++ +l + + +++++s  EgfG++++EA+  g+pvias++gg++ ++++ +tG+l ++   e  + ++r ll+++  +
  gi|116754108|ref|YP_843226.1| 291 DIEINALQRGSTVILQKSLGEGFGLTVTEALWKGKPVIASAVGGIPLQIRHRQTGILTHSI--EGTVHYLRILLNQPRYA 368
                                    *********************************************************8876..99999999999999999 PP

                                    HHHHHHHHH CS
                Glycos_transf_1 163 erlgenark 171
                                     +lge +r+
  gi|116754108|ref|YP_843226.1| 369 SKLGECGRE 377
                                    999998876 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 !   40.3   0.0   6.5e-14   3.9e-10       1     122 [.     220     352 ..     220     364 .. 0.80

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 6.5e-14
                                    SEEEEEES---GG.GTHHHHHHHHHHHH.H.HEEEEEES---..........HHHHHHHTT-T.TEEEE---TH..HHHH CS
                Glyco_trans_1_4   1 rpvilfvGrleenvkgvdllleavpllrkk.dvrlvivGdgp.rp.......eeleelaagleerveftGfved..lael 69 
                                    rpv+  v+r+ ++ k    ++e   +++++ d++lv++G+g  ++       e++++ a + ++++++    +d  +++l
  gi|116754108|ref|YP_843226.1| 220 RPVVTQVSRF-DRLKDPFGVIEVYRKVKEHiDCQLVLAGGGAaDDpegpailEQIRAAA-ETDPDIHVIYNPPDieINAL 297
                                    5889999999.7889999**********8878*******88653246754444444333.66788999888866669999 PP

                                    HHH-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HH CS
                Glyco_trans_1_4  70 laaadvfvaPs..egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpe 122
                                     + ++v +  s  egfgl++ Ea+  g+pv+a++vggi+  +   ++g+l    + e
  gi|116754108|ref|YP_843226.1| 298 QRGSTVILQKSlgEGFGLTVTEALWKGKPVIASAVGGIPLQIrhRQTGILTH--SIE 352
                                    99999999999**************************999888779999986..455 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 !   25.6   0.0   2.1e-09   1.2e-05       6      91 ..     308     393 ..     294     394 .. 0.92

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 2.1e-09
                Glyco_trans_1_2   6 srsespnlrlfEaaacGafaltddaegleelftpgkevilfedleelaekiryllanpeerraiaeaarervlaehtydh 85 
                                    s  e++ l + Ea+  G ++++++  g++  ++  +++il ++ e  +  +r ll++p  +++++e +re+v++++  ++
  gi|116754108|ref|YP_843226.1| 308 SLGEGFGLTVTEALWKGKPVIASAVGGIPLQIRHRQTGILTHSIEGTVHYLRILLNQPRYASKLGECGREHVRNNFLITR 387
                                    44589999***************99***************************************************9999 PP

                Glyco_trans_1_2  86 raeqll 91 
                                     ++++l
  gi|116754108|ref|YP_843226.1| 388 HIKDYL 393
                                    988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 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:                        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 0.27s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2807.23
//
Query:       gi|116754109|ref|YP_843227.1|  [L=214]
Description: hypothetical protein Mthe_0798 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1563.08
//
Query:       gi|116754110|ref|YP_843228.1|  [L=733]
Description: putative bifunctional trehalose-6-phosphate synthase/HAD hydrolase subfamily IIB [Methanosaeta thermophila PT]
Scores for complete 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-149  498.7   0.0     2e-149  498.3   0.0    1.1  1  Glyco_transf_20  Glycosyltransferase family 20
    1.4e-52  178.1   0.0    3.5e-52  176.9   0.0    1.6  1  Trehalose_PPase  Trehalose-phosphatase
    1.3e-05   24.8   0.1    0.00029   20.4   0.1    2.4  1  Glycos_transf_1  Glycosyl transferases group 1
    2.5e-05   24.1   0.0     0.0043   16.8   0.0    2.4  2  Hydrolase_3      haloacid dehalogenase-like hydrolase
     0.0018   17.9   0.0      0.011   15.3   0.0    2.1  1  S6PP             Sucrose-6F-phosphate phosphohydrolase
  ------ inclusion threshold ------
      0.015   15.7   0.0       0.04   14.3   0.0    1.8  1  Glyco_trans_1_4  Glycosyl transferases group 1
      0.069   12.6   1.0       0.13   11.7   1.0    1.4  1  TryThrA_C        Tryptophan-Threonine-rich plasmodium antigen
       0.13   11.9   0.2       0.24   11.1   0.2    1.4  1  Glyco_transf_5   Starch synthase catalytic domain
       0.17   11.4   0.0        0.3   10.6   0.0    1.3  1  UMPH-1           Pyrimidine 5'-nucleotidase (UMPH-1)


Domain annotation for each model (and alignments):
>> Glyco_transf_20  Glycosyltransferase family 20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  498.3   0.0  9.8e-153    2e-149       2     472 ..       2     467 ..       1     469 [. 0.95

  Alignments for each domain:
  == domain 1  score: 498.3 bits;  conditional E-value: 9.8e-153
                                    -EEEEEEE-SECEEE-S.SCG..EEECCGSSHHHHHCCCHHCC........C-EEEEEEECCES-CCC..HCCCCHHHCC CS
                Glyco_transf_20   2 klvvvsnrlplklereseeekeeyelkkssgglvsalkglkee........tevvwvgwlgvevdeseeakekvskelee 73 
                                    +lv++snrlp+++  e+  +   +++ +s ggl + + ++ ++        ++ +wvgw+gv+ + ++   ++++ +l+ 
  gi|116754110|ref|YP_843228.1|   2 RLVIISNRLPVTVVEEK--GA--IRFMDSVGGLSTGIRSFIASdkaraemiQDCLWVGWPGVDLKRRN--IQDITSQLK- 74 
                                    689*******9977775..44..7888899999888888877777777777777************99..888887766. PP

                                    CCCEEEEEE-HHHHHHHCCCHHHHCHHHHHTT-GG....G----HHHHHHHHHHHHHHHHHHHCC--TT-EEEEESGGGT CS
                Glyco_transf_20  74 kfsvvpvflsdekveeyyngfsksvLWpllHYklpdsseekefersawdaYvkvnklFAdkiveeikdgdliwvhDYhLm 153
                                    ++++ pvf s++ ++++y+gf+++++Wpl+HY +      + +++ +w+ Y ++n++FA++i +++ +gdl+w+hDYhLm
  gi|116754110|ref|YP_843228.1|  75 DMNCWPVFFSNRVIDKFYHGFCNRTIWPLFHYFPS----LTSYNKDHWNTYIHANRVFAEEISRILMPGDLVWIHDYHLM 150
                                    578****************************9988....999************************************** PP

                                    THHHHHHHCCTTSEEEEEE-S----HHHHTTST..THHHHHHHHTTSSEEEESSHHHHHHHHHHHHHHSSEEEECTTEEE CS
                Glyco_transf_20 154 llPellRkkledakigfflHiPFPsseifriLp..vreeilegllgadliGFhtedyarhFlsccsrllgleveskrggv 231
                                    llP++lR++++d+ igfflHiPFPs e+f+iLp  ++++i++gllg++liGFht+dyar+Fl ++ r++g+e +     +
  gi|116754110|ref|YP_843228.1| 151 LLPQMLRERFHDLPIGFFLHIPFPSYEVFQILPkdWQRAIVDGLLGSNLIGFHTYDYARNFLRAALRIVGAESHLG--NI 228
                                    *********************************999*********************************8887766..79 PP

                                    EETTEEEEEEE------HHHHHHHCCSCHHHHHHHHHHHHT.TTSEEEEEEEEC-GGG-HHHHHHHHHHHHHH-GGGTTT CS
                Glyco_transf_20 232 eykgrkvsvkalpigidverlesalkkesvsekvkelkerfenkkklilgvDrlDyikGvkqkllaferfLeeypelrgk 311
                                     ykg+ v+v+++p gid ++++s+ ++++v+  ++  k  f+++ k +l+ DrlDy+kG+ ++l+ +e fL+++p+++g+
  gi|116754110|ref|YP_843228.1| 229 LYKGHLVRVDVFPMGIDFDKFHSSRQNPAVQVEMEAFKAAFRDR-KTVLSIDRLDYTKGIVKRLEGYEAFLKKNPSWHGR 307
                                    *****************************************885.*********************************** PP

                                    EEEEEEEEB-STTSHHHHHHHHHHHHHHHHHHHHH-BTTB-SEEEEES---HHHHHHHHHH-SEEEE--SSBSS-CHHHH CS
                Glyco_transf_20 312 vvlvqiavpsredveeyqelekeveelvgrINgefgtldytPvvylersldfeeliallaaadvllvtslRdGmnlvake 391
                                    v+lv ++vpsr +ve+yq++++++ e vg INg+fg++d+tP+ y +r l+  +l al++  d +l+t+lRdGmnlvake
  gi|116754110|ref|YP_843228.1| 308 VILVLVVVPSRVRVEHYQQMKRQIDEKVGDINGKFGKVDWTPILYTYRYLPEPQLQALYNLCDTALITPLRDGMNLVAKE 387
                                    ******************************************************************************** PP

                                    HHHCSTTT--EEEEETTBGGGGT-TTTSEEE-TT-HHHHHHHHHHHHC--HHHHHHHHHHHHHHHHHT-HHHHHHHHHHH CS
                Glyco_transf_20 392 yvvcqqekkgvLiLSeFaGaaqsLkdaailvNPwdieevaeaikeaLkmseeerkkrekkllkqvskhdvqsWaesflse 471
                                    y++ + +  gvLiLSe aGa+++  + ail+NP++iee+a+ai +aL+m+e+e+  r +   ++++++d+ +Wa+sf+++
  gi|116754110|ref|YP_843228.1| 388 YIASKVDCRGVLILSEMAGASKEAVE-AILINPYNIEEIADAILKALEMPEDEQIWRCRMIQSRLKRNDIFKWASSFVRS 466
                                    ************************96.5**************************************************99 PP

                                    H CS
                Glyco_transf_20 472 l 472
                                    l
  gi|116754110|ref|YP_843228.1| 467 L 467
                                    8 PP

>> Trehalose_PPase  Trehalose-phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.9   0.0   1.8e-55   3.5e-52       3     219 ..     505     713 ..     503     722 .. 0.92

  Alignments for each domain:
  == domain 1  score: 176.9 bits;  conditional E-value: 1.8e-55
                                    ETBTTTB---SSGGG--B-TTHHHHHHHHHTTS-..EEEE-SS-HHHHHHHH---SSEEEEGGGTEEE-TT--EEE-HHH CS
                Trehalose_PPase   3 DydGTlspivedpdaavpssellslLkkLasdpknvvaivSGrslkeeellvkvpelglaaeHGaeirspsgedwenqae 82 
                                    DydGTl+p +e p  a+p+++++slL+++ +dpk+ + ++SGr++k+ e+ ++  +++l+aeHG+ ++ ++++ w +   
  gi|116754110|ref|YP_843228.1| 505 DYDGTLVPFAEYPGLARPDKRVRSLLRRIVDDPKTDILLISGRDKKTLEEWFGEFDMYLVAEHGFWLKLKENS-WMKIHK 583
                                    ***********************************************66666999*****************5.555699 PP

                                    HTTHHHHHHHHHHHHHHHTTSTT-EEEEETTEEEEE-TT--TT....THHHHHHHHHHHHHHH.--EEEE-SSEEEEE-S CS
                Trehalose_PPase  83 vedlewlkevkeileektertpGsyiEekkfalsvHyrnadde..elqakelaehlesvltdkpdlevtqgkkvvevrpq 160
                                    + d++w+ ++++ile++++r+pGs+iE+k+f++++H+r ad+e  + + +el + l s +t++ d+++  g++v+e+rp+
  gi|116754110|ref|YP_843228.1| 584 NVDTSWIPSIQAILERYVDRVPGSFIETKDFSVVWHFRMADPElaSQKFSELIDDLMS-YTANIDVQILPGNRVIEIRPS 662
                                    *******************************************988888999999999.77777**************** PP

                                    ---HHHHHHHHHHTS--------EEEEEE-SSTTHHHHTTS-TT...-EEEEE--TTS- CS
                Trehalose_PPase 161 gvsKGkaverlleslgsadseddfvlciGDdrtDedmFsvlrktkesgvsievsavevg 219
                                    gv+KG+a++ +l++  +     df+l+ GDd+tDedmF++l +     + i+v+  e++
  gi|116754110|ref|YP_843228.1| 663 GVNKGNALRYFLSRETY-----DFILAMGDDVTDEDMFRALPDS---ACTIKVGMIESV 713
                                    **************997.....5****************99886...777777777644 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 !   20.4   0.1   1.5e-07   0.00029       7     165 ..     265     442 ..     259     446 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.5e-07
                                    HHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES..........STTHHHHHHHHHHHCTTCG... CS
                Glycos_transf_1   7 kklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaG.........ngeeekelkklaeelelsdn... 74 
                                    +k ++  ++k++ls+ rl+++Kg+   ++ ++ + k+ np ++  ++           +e+ +++k++++e     n   
  gi|116754110|ref|YP_843228.1| 265 FKAAF-RDRKTVLSIDRLDYTKGIVKRLEGYEAFLKK-NPSWHGRVILvlvvvpsrvRVEHYQQMKRQIDEKVGDINgkf 342
                                    55555.6999***********************9999.5555443333344478***99999999999998754433111 PP

                                    ..GGE......EECCHSSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEET.TTTHCHHCHTTTSEEEE-TT-H CS
                Glycos_transf_1  75 ..vif......lgevsredleellknadifvlpsisEgfGivllEAmaaglpviasn.aggpaevvkdgetGllvkpnna 145
                                      v +      + ++++ +l +l++ +d ++++  ++g+ +v+ E++a+++ +  +   + +a   k+++  +l+ p+n+
  gi|116754110|ref|YP_843228.1| 343 gkVDWtpilytYRYLPEPQLQALYNLCDTALITPLRDGMNLVAKEYIASKVDCRGVLiLSEMAGASKEAVEAILINPYNI 422
                                    114443333336789999*****************************97765544444444444556666778******* PP

                                    HHHHHHHHHHHHSHHHHHHH CS
                Glycos_transf_1 146 ealaeairklledeelrerl 165
                                    e++a+ai k+le +e+ + +
  gi|116754110|ref|YP_843228.1| 423 EEIADAILKALEMPEDEQIW 442
                                    **************987765 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.012        23       1      87 [.     502     593 ..     502     614 .. 0.78
   2 !   16.8   0.0   2.2e-06    0.0043     153     222 ..     631     698 ..     609     708 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.012
                                    EEEEIIIIIS-.....TTS---HHHHHHHHHHHH.TTSEEEEE-SS-HHHHHHHHHHCCCCSEEEEGGGTEE.ECTTTEE CS
                    Hydrolase_3   1 ialDlDGTLln.....sdkkisektkeaikklke.kgikvviATGRslravlpvleelgldlpvialNGali.ddekgki 73 
                                    +++D DGTL+         + +++ ++ ++++ +     + + +GR  +++++ + e++  ++++a +G +   +e+  +
  gi|116754110|ref|YP_843228.1| 502 VVSDYDGTLVPfaeypGLARPDKRVRSLLRRIVDdPKTDILLISGRDKKTLEEWFGEFD--MYLVAEHGFWLkLKENSWM 579
                                    689******998887655568899999999988757899*****************776..99*******9954444444 PP

                                    EEE--B-HHHHHHH CS
                    Hydrolase_3  74 lykstiskedvkei 87 
                                      +++++ + + +i
  gi|116754110|ref|YP_843228.1| 580 KIHKNVDTSWIPSI 593
                                    45666666655555 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 2.2e-06
                                    HHHHHHHHHHHHCTTTEEEEEESTTEEEEEETT-SHHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHS CS
                    Hydrolase_3 153 kldelekelksklnklltitssskgyleimpkgvsKgtalkklakelnisleeviafGDgeNDieMLeaa 222
                                    k++el+++l s +++    +  ++ ++ei p gv+Kg+al++++++  ++   ++a+GD+  D  M+ a 
  gi|116754110|ref|YP_843228.1| 631 KFSELIDDLMSYTANIDVQILPGNRVIEIRPSGVNKGNALRYFLSRETYD--FILAMGDDVTDEDMFRAL 698
                                    44555555555544432334457889******************877665..69*************875 PP

>> S6PP  Sucrose-6F-phosphate phosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   5.6e-06     0.011       2     199 ..     499     697 ..     498     708 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.6e-06
                                    SEEEEE-TBTTTB..........S-HHHHHHHHHHHH.GGGGGEEEEEE-SS-HHHHHHHHHHHT----SEEEETTTTEE CS
                           S6PP   2 klllvsdLDntlv.........dgdnealarlnelleaeerkdvllvfaTGRsldsakellkeknllkPdvlitsvGtei 72 
                                    ++l+vsd D+tlv          +d++    l+++++   ++++ + +++GR  +  +e   e+ +    +l+++ G  +
  gi|116754110|ref|YP_843228.1| 499 RRLVVSDYDGTLVpfaeypglaRPDKRVRSLLRRIVD---DPKTDILLISGRDKKTLEEWFGEFDM----YLVAEHGFWL 571
                                    5788888888888888886664444444444444444...77777777888888888888888886....7888888888 PP

                                    EE..TTEE-HHHHHHHHTT--HHHHHHHHHT-TTEEE--GGG-BTTBEEEEE-TTS...-THHHHHHHHHHHTTTS-EEE CS
                           S6PP  73 yygeelvpdkaweeildekwdrqavvealaklpeLtlQpeeeqrehKvSyfvdkek...aaevlkeleqlLekreldvkv 149
                                      +e+  +  + ++ +d+ w +  ++++l+++ +  + +  e + + v ++ ++++   a +  +el + L +   +++v
  gi|116754110|ref|YP_843228.1| 572 KLKEN--SWMKIHKNVDTSWIP-SIQAILERYVDRVPGSFIETKDFSVVWHFRMADpelASQKFSELIDDLMSYTANIDV 648
                                    87333..333445667777765.355666666666666666777777777665544111333355565666655555554 PP

                                    .EEETTTEEEEEETT-SHHHHHHHHHHHHT--GGGEEEEE-SGGGHHHHTS CS
                           S6PP 150 .iyssgkdlDvlPkraskgeAlryLakkleleleqilvcGdsgnDeellig 199
                                     i+  ++ + + P + +kg+Alry++++  ++   il  Gd   De+++++
  gi|116754110|ref|YP_843228.1| 649 qILPGNRVIEIRPSGVNKGNALRYFLSRETYD--FILAMGDDVTDEDMFRA 697
                                    25788999******************998765..69*************75 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0     2e-05      0.04      63     133 ..     355     434 ..     273     435 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2e-05
                                    -....THHHHHHHH-SEEEE.--.---SHHHHHHHHTT-....EEEE-TGGGT.TT--TTSSEE--TT-HHHHHHHHHHH CS
                Glyco_trans_1_4  63 v....edlaellaaadvfva.Ps.egfglkllEamaagl....pvVatdvggi.aevvgengllvppgdpealaeailrL 131
                                    +    ++l++l++ +d +++ P+  g++l++ E+ a+++      + ++++g+ +e   ++++l++p + e++a+ail+ 
  gi|116754110|ref|YP_843228.1| 355 RylpePQLQALYNLCDTALItPLrDGMNLVAKEYIASKVdcrgVLILSEMAGAsKE--AVEAILINPYNIEEIADAILKA 432
                                    14554569*******9996516677***********87633335688887664277..6789****************99 PP

                                    HH CS
                Glyco_trans_1_4 132 le 133
                                    le
  gi|116754110|ref|YP_843228.1| 433 LE 434
                                    86 PP

>> TryThrA_C  Tryptophan-Threonine-rich plasmodium antigen C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.0   6.7e-05      0.13       6      57 ..     549     600 ..     548     642 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.7e-05
                      TryThrA_C   6 lkkleeeWekFneslenekkkwlekkekeweewlkeienKWlhynekldeey 57 
                                    +k+lee + +F  +l  e   wl+ ke+ w +  k++   W    + + e y
  gi|116754110|ref|YP_843228.1| 549 KKTLEEWFGEFDMYLVAEHGFWLKLKENSWMKIHKNVDTSWIPSIQAILERY 600
                                    58899999*********************************98777777766 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 ?   11.1   0.2   0.00012      0.24     107     169 ..     113     169 ..      63     216 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00012
                 Glyco_transf_5 107 dyednaerfalfsraalelleklgwkpdvihahDWhtalvpallkelykerglfkkiktvfti 169
                                      +d+ + ++  +r+ +e + ++ +  d++ +hD+h +l+p +l+e  +      + ++ f +
  gi|116754110|ref|YP_843228.1| 113 YNKDHWNTYIHANRVFAEEISRILMPGDLVWIHDYHLMLLPQMLRERFH------DLPIGFFL 169
                                    35688889999999*9*****987889******************9753......35555554 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 ?   10.6   0.0   0.00015       0.3     171     215 ..     671     715 ..     639     727 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00015
                         UMPH-1 171 eyfdqlkkrtnvillGDslGDlsmadGvpevetilkiGflndkve 215
                                     yf   ++++ ++ +GD + D +m   +p++  ++k+G +   + 
  gi|116754110|ref|YP_843228.1| 671 RYFLSRETYDFILAMGDDVTDEDMFRALPDSACTIKVGMIESVAK 715
                                    57777789999***************************9976655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (733 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.67u 0.26s 00:00:00.93 Elapsed: 00:00:00.43
# Mc/sec: 5077.03
//
Query:       gi|116754111|ref|YP_843229.1|  [L=693]
Description: ski2-like helicase [Methanosaeta thermophila PT]
Scores for 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-26   90.9   0.0    2.6e-24   86.0   0.0    2.3  2  DEAD             DEAD/DEAH box helicase
    1.8e-12   47.7   1.1    6.7e-12   45.8   0.8    2.2  2  HHH_5            Helix-hairpin-helix domain
    3.7e-09   36.8   0.0    6.3e-09   36.1   0.0    1.4  1  ResIII           Type III restriction enzyme, res subunit
    6.9e-08   32.8   0.0    4.2e-07   30.3   0.0    2.3  2  Helicase_C       Helicase conserved C-terminal domain
    2.1e-07   30.6   0.0    8.2e-07   28.8   0.0    2.0  1  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
     0.0006   19.9   0.0     0.0032   17.5   0.0    2.3  2  HHH_2            Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.024   14.0   0.0       0.15   11.4   0.0    2.2  2  ATPase           KaiC
      0.032   13.5   0.0      0.092   12.0   0.0    1.7  2  SecA_DEAD        SecA DEAD-like domain
      0.044   14.0   0.0       0.11   12.8   0.0    1.6  1  Cdd1             Pathogenicity locus
       0.11   12.4   0.8       0.87    9.6   0.0    2.9  3  HHH              Helix-hairpin-helix motif


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.0   0.0   1.4e-27   2.6e-24       2     170 ..      29     185 ..      28     191 .. 0.89
   2 ?    2.3   0.0     0.071   1.3e+02      34      89 ..     234     292 ..     233     305 .. 0.70

  Alignments for each domain:
  == domain 1  score: 86.0 bits;  conditional E-value: 1.4e-27
                                    HHHHHHHHHHH.TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEE CS
                                    xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD   2 diQaeaiplil.gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvll 80 
                                    + Qaeai+  l +g++++++ +T++GKTl + +++l+        +g++ l+++P+r+La + ++ +++f k ++lrv  
  gi|116754111|ref|YP_843229.1|  29 PPQAEAIERGLlDGRNMIISVPTAAGKTLLAELAMLRGA-----LSGKRSLYIVPLRALASEKFESFSRFSK-LGLRVGI 102
                                    67******98889***********************777.....568999**********************.7999984 PP

                                    EETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  81 iiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqr 160
                                      +  + ++  ++l  + di+++t ++ d+l+++g   ++++ +lV+DE++ l + +++++++  +++l +     + + 
  gi|116754111|ref|YP_843229.1| 103 --STGDFEKRDERL-GRNDIIIATSEKADSLIRNGASWVRRIGVLVVDEIHLLDSANRGPTLEMTMTKLMHL----NPEM 175
                                    ..444566667788.789**************999999*******************************444....4455 PP

                                    EEEEEESSBS CS
                                    xxxxxxxxxx RF
                           DEAD 161 qvivlSATlp 170
                                    qvi lSAT+ 
  gi|116754111|ref|YP_843229.1| 176 QVIGLSATIA 185
                                    6*******96 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.071
                                    HHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTT....TSTSEEEEEETTSSHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxx RF
                           DEAD  34 pvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkk....yidlrvlliiggvaard 89 
                                    pvl+ v++ + ++g ++li e tr  ae ++++++  ++    +i+l + l  +g++a++
  gi|116754111|ref|YP_843229.1| 234 PVLNLVLD-TVDQGGQMLIFESTRRNAESMAKKVSGALQesgeTIELAERLSGEGKTAKK 292
                                    66777776.667888****************99987777222134466655544555544 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       7.7   1.4e+04       5      21 ..     502     518 ..     500     524 .. 0.80
   2 !   45.8   0.8   3.7e-15   6.7e-12       3      57 .]     636     688 ..     634     688 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 7.7
                                    HTSTT--HHHHHHHHTT CS
                          HHH_5   5 lsvsGiGpktAlallsa 21 
                                    +++ Gi + t+l+ll  
  gi|116754111|ref|YP_843229.1| 502 QEIRGIRRPTVLTLLHV 518
                                    78999999999999976 PP

  == domain 2  score: 45.8 bits;  conditional E-value: 3.7e-15
                                    HHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHHHH CS
                          HHH_5   3 eLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilelkd 57 
                                    +Ll+++GiG+++A++l+ aG++s+edl+aad+ +L++i  +G+k Ae +i +lk+
  gi|116754111|ref|YP_843229.1| 636 QLLELKGIGRVRARKLYQAGYRSLEDLKAADKSTLSEI--LGPKIAEGVISQLKE 688
                                    69************************************..*************96 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 !   36.1   0.0   3.5e-12   6.3e-09       3     169 ..      26     184 ..      24     186 .. 0.89

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 3.5e-12
                                    EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG.. CS
                         ResIII   3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseay 82 
                                    el++ Q+eaie+ l      + ++++i  +T +GKTl+a  ++ r + +gk  + l +vp ++l +   e f++f++   
  gi|116754111|ref|YP_843229.1|  26 ELYPPQAEAIERGL-----LDGRNMIISVPTAAGKTLLAELAMLRGALSGK--RSLYIVPLRALASEKFESFSRFSKLGL 98 
                                    68899999999998.....467899**************999999998877..9*********************99987 PP

                                    ..GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T.......TTHHHHH CS
                         ResIII  83 keigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk.......swreile 155
                                        ++ +gd +k+  ++   ++i+++t +++d+ +      +      r+ v+++DE H l +++       ++++++ 
  gi|116754111|ref|YP_843229.1|  99 --RVGISTGDFEKR-DERLGRNDIIIATSEKADSLI-----RNGASWVRRIGVLVVDEIHLLDSANrgptlemTMTKLMH 170
                                    ..789999999999.88999****************.....66777788899***********98466677789999999 PP

                                    T---SEEEEEESS- CS
                         ResIII 156 kfkeavllglTATp 169
                                     ++e  ++gl+AT+
  gi|116754111|ref|YP_843229.1| 171 LNPEMQVIGLSATI 184
                                    9999*********8 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 ?   -1.8   0.0       2.1   3.9e+03      65      74 ..     115     124 ..      57     138 .. 0.56
   2 !   30.3   0.0   2.4e-10   4.2e-07       7     111 .]     236     378 ..     231     378 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.1
                                    TSSSEEEESG CS
                     Helicase_C  65 gesdvLiatd 74 
                                    g+ d++iat+
  gi|116754111|ref|YP_843229.1| 115 GRNDIIIATS 124
                                    5556666666 PP

  == domain 2  score: 30.3 bits;  conditional E-value: 2.4e-10
                                    HHH.HHHTTTTSEEEEEESSHHHHHH..HHHH......................HHHT.......TSTEEEESTTSTHHH CS
                     Helicase_C   7 lel.lkleeeggkilifvntidrlek..vkll......................lekk.......gikvavlhgelpqne 54 
                                    l+l l++  +gg++lif  t++++e+     +                      +             +a +h+ l  ++
  gi|116754111|ref|YP_843229.1| 236 LNLvLDTVDQGGQMLIFESTRRNAESmaK-KVsgalqesgetielaerlsgegkT--AkklamclRHGAAFHHAGLLPEQ 312
                                    55534778899999999999995544421.2223334444444444554555531..034566777888999999***** PP

                                    HHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEESSSSSSH.........HHHHHHHTTSSSTT CS
                     Helicase_C  55 reeileqfnkgesdvLiatdvaerGidipkvnlVinfdlprnv.........tsyiqriGRtgRag 111
                                    r+ i   f+++ ++v+ +t  ++ G+++p  +++i+    ++           +y q++GR+gR g
  gi|116754111|ref|YP_843229.1| 313 RRLIELGFRQNVVKVIACTPTLAAGLNLPARRVLIRSYKRYEAglgtrpipvMEYRQMAGRAGRPG 378
                                    *****************************99999977777553444455666************75 PP

>> DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   4.5e-10   8.2e-07       7      36 ..     641     671 ..     636     674 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 4.5e-10
                DNA_pol_lambd_f   7 yGVGpktAkkwyakGirtledlra.krakLt 36 
                                     G+G+++A+k+y++G+r+ledl+a ++++L+
  gi|116754111|ref|YP_843229.1| 641 KGIGRVRARKLYQAGYRSLEDLKAaDKSTLS 671
                                    69**********************7557776 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.4   4.4e+03      14      33 ..     427     446 ..     423     472 .. 0.66
   2 !   17.5   0.0   1.8e-06    0.0032       6      60 ..     638     691 ..     633     693 .] 0.88

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.4
                          HHH_2  14 ktAklLakrFksldaLkkas 33 
                                    + A   a + +sl +L++ +
  gi|116754111|ref|YP_843229.1| 427 TIASRFADSVDSLSRLMAST 446
                                    45555566666666666554 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 1.8e-06
                          HHH_2   6 LGIrhVGektAklLakr.FksldaLkkasleeLlevddiGeeiAqsivefFenekn 60 
                                    L ++ +G   A++L ++ ++sl+ Lk+a+  +L+e+   G++iA+ +++ ++++ +
  gi|116754111|ref|YP_843229.1| 638 LELKGIGRVRARKLYQAgYRSLEDLKAADKSTLSEI--LGPKIAEGVISQLKEPGV 691
                                    66789*********9866******************..79********99998865 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   8.5e-05      0.15      11     131 ..      34     152 ..      22     188 .. 0.63
   2 ?   -1.0   0.0       0.5     9e+02     121     163 ..     488     532 ..     483     549 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.5e-05
                         ATPase  11 ilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfv....tveepaedlrenakslGwdlekleeegklaii 86 
                                     +++G+ +gr + i+  + +GKt++a+  +++ga + g++ +++    ++ +++ +   ++++lG  +    ++g +   
  gi|116754111|ref|YP_843229.1|  34 AIERGLLDGRNMIISVPTAAGKTLLAELAMLRGALS-GKRSLYIvplrALASEKFESFSRFSKLGLRVG--ISTGDFEKR 110
                                    4569********************************.******93333333333333333333333222..233333333 PP

                         ATPase  87 dasesaeesaeekdkedleelieelaeaikeikakrvviDsitgl 131
                                    d    +++++   ++e++++li++ a+ +++i++  +v+D i  l
  gi|116754111|ref|YP_843229.1| 111 DERLGRNDIII-ATSEKADSLIRNGASWVRRIGV--LVVDEIHLL 152
                                    33333333222.5556666666666666666654..566666665 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.5
                         ATPase 121 krvviDsitgl.ayeekeavaReilrqlvrvl.kklgvTailvse 163
                                    +r+ iD+++++ + +e     R ++ +l++v+    ++  ++v++
  gi|116754111|ref|YP_843229.1| 488 SRLYIDPLSAMvMIQEIRGIRRPTVLTLLHVItMTPDMELLFVQQ 532
                                    7999*******8888888889999*****9994444555555555 PP

>> SecA_DEAD  SecA DEAD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   5.2e-05     0.092      93     174 ..      45     124 ..      35     156 .. 0.84
   2 ?   -2.6   0.1       1.5   2.7e+03      93     105 ..     278     290 ..     267     298 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.2e-05
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      SecA_DEAD  93 kiaemkTGEGKtlvatlpaylnaltgkgvhvvtvndYLakrdaewmgpvyeflGlsvgvieseleseerreaYeaditYg 172
                                    +i  + T  GKtl a l+++  al+gk    +     La+  +e +++ ++ lGl+vg+ + ++e+++ r   + di+ +
  gi|116754111|ref|YP_843229.1|  45 MIISVPTAAGKTLLAELAMLRGALSGKRSLYIVPLRALASEKFESFSR-FSKLGLRVGISTGDFEKRDERL-GRNDIIIA 122
                                    6888999********************9988888899*******9998.6789******999988776654.35566666 PP

                                    xx RF
                      SecA_DEAD 173 tn 174
                                    t+
  gi|116754111|ref|YP_843229.1| 123 TS 124
                                    65 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.5
                                    xxxxxxxxxxxxx RF
                      SecA_DEAD  93 kiaemkTGEGKtl 105
                                    ++ae   GEGKt 
  gi|116754111|ref|YP_843229.1| 278 ELAERLSGEGKTA 290
                                    5788899****96 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     6e-05      0.11       4      42 ..     633     671 ..     631     680 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6e-05
                           Cdd1   4 alkelqdiPniGkalaedlvelGirsveelkgedpeely 42 
                                    +l +l ++ +iG+  a++l++ G+rs+e+lk  d   l 
  gi|116754111|ref|YP_843229.1| 633 ELLQLLELKGIGRVRARKLYQAGYRSLEDLKAADKSTLS 671
                                    5778999************************99987776 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.3   2.4e+03       5      16 ..     387     398 ..     385     399 .. 0.87
   2 ?    9.6   0.0   0.00048      0.87      12      28 ..     636     652 ..     636     654 .. 0.89
   3 ?   -3.4   0.1       6.4   1.2e+04       1      14 [.     658     671 ..     658     673 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.3
                                    HHTSSHHHHHTS CS
                            HHH   5 lipasreeLlal 16 
                                    ++++s+ eL++l
  gi|116754111|ref|YP_843229.1| 387 IMARSESELQKL 398
                                    6789******98 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00048
                                    HHHTSTT-SHHHHHHHH CS
                            HHH  12 eLlalPGVGpktAeaIl 28 
                                    +Ll+l+G+G+ +A++ +
  gi|116754111|ref|YP_843229.1| 636 QLLELKGIGRVRARKLY 652
                                    79***********9976 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 6.4
                                    SHHHHHTSSHHHHH CS
                            HHH   1 sleglipasreeLl 14 
                                    sle l++a+   L 
  gi|116754111|ref|YP_843229.1| 658 SLEDLKAADKSTLS 671
                                    57778888777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (693 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        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 0.23s 00:00:00.86 Elapsed: 00:00:00.42
# Mc/sec: 4969.74
//
Query:       gi|116754112|ref|YP_843230.1|  [L=384]
Description: aminotransferase, class I and II [Methanosaeta thermophila PT]
Scores for 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-58  199.3   0.0    1.2e-58  199.1   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
  ------ inclusion threshold ------
      0.061   12.6   0.0      0.099   11.9   0.0    1.3  1  Beta_elim_lyase  Beta-eliminating lyase


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.1   0.0   1.3e-62   1.2e-58       2     363 .]      30     381 ..      29     381 .. 0.96

  Alignments for each domain:
  == domain 1  score: 199.1 bits;  conditional E-value: 1.3e-62
                                    EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHH CS
                  Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagali 81 
                                    dvi+L++++++      t+++++k++ e a + + +++y+ ++g  e++ea+a+++++  +++l+++++++++ G+++++
  gi|116754112|ref|YP_843230.1|  30 DVIDLSVGDPDIP----TPEHIVKEMCE-AVKRPANHQYPSYEGKIEFREAVAEWYRDLFGVDLDPSTEILTLIGSKEGL 104
                                    89**********9....***********.****************************999******************** PP

                                    HHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT CS
                  Aminotran_1_2  82 ealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPt 161
                                    + ++ ++ +npg+ +lvpdp y+ y++++  +gg   r+pl ++++f  dl ++ + l+++p  ++  ++i+++ p+NPt
  gi|116754112|ref|YP_843230.1| 105 AHAPLAF-VNPGEIVLVPDPAYTVYSTAVMFAGGIPERMPLLKKNSFLPDLGSIRARLEQDPDWRP--RLIFLNYPNNPT 181
                                    *******.9***************************************************997777..************ PP

                                    --B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTT.EEEEEESSSTTSSGGG-EEEEEEEHHHH CS
                  Aminotran_1_2 162 GtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepn.llivgslsKafGlaGeRvGyilgnaavv 240
                                    G+va  +  ++l+dla++y++l++ D  Y++ +f+   + + +++v  + +  +   slsK ++++G+R+G+++g+++++
  gi|116754112|ref|YP_843230.1| 182 GAVAGIDFFRELVDLAREYGILVMHDNPYSEIYFDGR-PPS-ILQVPGARDvAVEFHSLSKTYNMTGWRIGMVSGSSRII 259
                                    **********************************954.445.7777666665799************************* PP

                                    HHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEEEEETHHCHH CS
                  Aminotran_1_2 241 sqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmflltdlsaetak 318
                                    + + k+++++ s    ++q a  aal+ ++++   ++  r+ + +r + l+++L ++gl+  +++++++l+  +      
  gi|116754112|ref|YP_843230.1| 260 EGIGKVKSNIDSgnFGAVQDAGIAALRSPPEV---VDGLRAVYRERIEILHSALCDIGLELSKPKATFYLWAWTGGD-SR 335
                                    ******************************96...***********************************9888887.88 PP

                                    HHHHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHHHH CS
                  Aminotran_1_2 319 elskkLleevgvyvtpgtsftv..pgrlRitvAglteeeleelveal 363
                                    e +k+Lle+ g++vtpg  f+   +g +R++v + ++e +e ++e+l
  gi|116754112|ref|YP_843230.1| 336 EYAKMLLEKTGIVVTPGVGFGEhgEGYIRLSV-TQPTERIEMAAERL 381
                                    ********************************.************97 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.1e-05     0.099     109     167 ..     152     207 ..     106     208 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.1e-05
                                    E-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEE CS
                Beta_elim_lyase 109 mdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlD 167
                                     dl +++a ++++ +   +++li l   nn   G v  ++  re+ ++a++ygi ++ D
  gi|116754112|ref|YP_843230.1| 152 PDLGSIRARLEQDPD--WRPRLIFLNYPNNP-TGAVAGIDFFRELVDLAREYGILVMHD 207
                                    578899999999888..999**********5.9************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); 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: 2743.33
//
Query:       gi|116754113|ref|YP_843231.1|  [L=950]
Description: leucyl-tRNA synthetase [Methanosaeta thermophila PT]
Scores for complete 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-59  199.7   0.0    2.4e-42  145.0   0.0    3.0  3  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    6.9e-23   81.0   0.0    1.4e-10   40.5   0.0    3.2  3  tRNA-synt_1g   tRNA synthetases class I (M)
    3.9e-21   75.6   0.1    7.8e-21   74.6   0.1    1.5  1  Anticodon_1    Anticodon-binding domain of tRNA
    1.9e-07   30.8   0.0    3.9e-07   29.8   0.0    1.4  1  tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
    1.4e-06   27.9   0.0      8e-05   22.1   0.0    2.3  2  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain
  ------ inclusion threshold ------
      0.024   13.6   0.0      0.044   12.7   0.0    1.4  1  tRNA-synt_1d   tRNA synthetases class I (R)
      0.062   13.3   0.0       0.18   11.8   0.0    1.8  1  HTH_29         Winged helix-turn helix
      0.091   13.1   0.2       0.28   11.5   0.2    1.9  1  CPSase_L_D3    Carbamoyl-phosphate synthetase large chain, ol
       0.14   11.0   0.0       0.32    9.9   0.0    1.6  1  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 !  145.0   0.0   1.2e-45   2.4e-42       2     304 ..      15     323 ..      14     331 .. 0.86
   2 !   19.7   0.0     1e-07    0.0002     319     433 ..     391     507 ..     369     535 .. 0.92
   3 !   31.3   0.0   3.3e-11   6.6e-08     508     601 ..     574     668 ..     559     669 .. 0.91

  Alignments for each domain:
  == domain 1  score: 145.0 bits;  conditional E-value: 1.2e-45
                    tRNA-synt_1   2 lyekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlai....e 77 
                                    ++  Weee+vf++e    +++k+f l+++ Py +G+lH Gh  + t+ d + ry+rm G++vl+ + +   G +i    e
  gi|116754113|ref|YP_843231.1|  15 WQRIWEEEGVFHAE---PDSRKKFFLTIPYPYLNGNLHAGHTRTFTIGDAIARYHRMLGENVLFPMAFHATGTPIvglsE 91 
                                    7889*********9...778999******************************************999999999833323 PP

                    tRNA-synt_1  78 akvekk.lgakekkerkklgreefrekv..rewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkg 154
                                       ++  l  +  +  + + +ee  + +   ++++++ ++ + +++ +G s+D+ re  T d+ ++  +++ f+ l +kg
  gi|116754113|ref|YP_843231.1|  92 LIANRDpLIWDVYTRLHGIPEEELEKLTtpEAIVDYFRKQAKLAMRSIGYSIDWRREFTTTDPAYNRFIEWQFGILREKG 171
                                    33333323333334556677777766552257999999999*************************************** PP

                    tRNA-synt_1 155 liyrgkklvnwstklktalselEveykdkkda..lihvafpladkeevklviaTTtPeTllgdtavavnpel.dyv..it 229
                                     + +g+++v w+++ + ++ + ++   +      ++ ++f l+dk    l  aT +PeT++g t + vnp++ +y+  ++
  gi|116754113|ref|YP_843231.1| 172 YVTKGSHPVRWCPNDQNPVEDHDILRGEDATIldFTLIKFRLDDK---VLPCATLRPETVFGVTNLWVNPNVvHYIarVN 248
                                    ************************665555441156788888765...479********************635669999 PP

                    tRNA-synt_1 230 keklilaeallkslvkkesekkiledergkeLegkevelplvnrkipiiaddyvdkeaGtGvVkiaPahdedDye 304
                                    +e +i+  +  ++l+  + + k   ++ g+eL+gk++++p+++ +i i+   +vd ++G+G+V   Pah + Dy 
  gi|116754113|ref|YP_843231.1| 249 DEVWIVSPQAYHKLTFTDRSVKKIGEIPGEELIGKKARNPVTGDEIIILPATFVDPDSGSGIVMSVPAHAPLDYL 323
                                    *********99999999977777789***********************************************96 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 1e-07
                    tRNA-synt_1 319 edgtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrateqWfvrvke..ladaalkave 396
                                    ++g+l+e ++ ++g  v   +++++++l ++g+     +++ +  +c  +   ++ ++ +qWf + ++   +  +l+ + 
  gi|116754113|ref|YP_843231.1| 391 HNGVLKEITGRYAGTPVHRIKDILLQDLINQGVAEIFYEFSETPVICRCGARCVVKMVRDQWFLEYSDpvWKSRVLECLA 470
                                    589999***********************************9999999999**************998777889999999 PP

                    tRNA-synt_1 397 kvqfvpkskekryaswleniqdWciSRqrwWGhripl 433
                                     +q++p+  ++++ + +   +d +  R +  G+r+p 
  gi|116754113|ref|YP_843231.1| 471 GMQIIPEEMRAEFINKIDWLKDKACARRKGLGTRLPW 507
                                    **********************************994 PP

  == domain 3  score: 31.3 bits;  conditional E-value: 3.3e-11
                    tRNA-synt_1 508 teelkkffpadmlleGlDiirgWvarlillslaltgsePf.kevlvhglvrdeeGrKmSKslgNvidpldvikkygadal 586
                                    +e+++  +p d+ ++G D +   +   +   +a++ ++ + + + v+g+v   eG+KmSKs g ++  ++ + + gad+ 
  gi|116754113|ref|YP_843231.1| 574 REDFEYWYPVDLRTSGKDLVANHLLFFLYHHVAIFPESLWpRAIAVNGFVS-LEGQKMSKSRGPILTLKQAVAENGADVT 652
                                    789******************************9999965378999**996.68************************** PP

                    tRNA-synt_1 587 Rltli.lsdvgrdinl 601
                                    Rl+++ ++++++d ++
  gi|116754113|ref|YP_843231.1| 653 RLYILaNAEYTQDADW 668
                                    ***999******9987 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 !   32.1   0.1   2.6e-11   5.2e-08       2      53 ..      36      87 ..      35      93 .. 0.95
   2 !    4.5   0.0     0.006        12      58     133 ..     116     193 ..     105     198 .. 0.82
   3 !   40.5   0.0   7.2e-14   1.4e-10     286     372 ..     586     674 ..     565     679 .. 0.87

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 2.6e-11
                                   EEEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHH CS
                   tRNA-synt_1g  2 lvttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpie 53
                                   ++t + pY ng+lH Gh ++  ++D++aRy+r+ ge+vlf  +  + Gtpi 
  gi|116754113|ref|YP_843231.1| 36 FLTIPYPYLNGNLHAGHTRTFTIGDAIARYHRMLGENVLFPMAFHATGTPIV 87
                                   6899*********************************************995 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.006
                                    HTTS-HHHHHHHHHHHHHHHHHHTT---S..EEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GG CS
                   tRNA-synt_1g  58 kegvtpeelvekvheeikelfkklnisfd..kygrttseehkelvqeifkklkekgliyekeieqlycpkderflpdr 133
                                    ++ +tpe++v+ ++++ k  +++++ s d     +tt+ + +++ +  f  l ekg++++++  + +cp+d++   d 
  gi|116754113|ref|YP_843231.1| 116 EKLTTPEAIVDYFRKQAKLAMRSIGYSIDwrREFTTTDPAYNRFIEWQFGILREKGYVTKGSHPVRWCPNDQNPVEDH 193
                                    5567999999999999999999988887733333577788889999999*********************99877776 PP

  == domain 3  score: 40.5 bits;  conditional E-value: 7.2e-14
                                    EEEEGGGHHHHHTHHHHHHHH..TT----S-EEEE--EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS- CS
                   tRNA-synt_1g 286 hfigkdiikFHtifwPaillg..aelklpkkvvaheyltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkD 363
                                       gkd +  H +f+     +   e   p+++++++++ +eg+K+SkSrg + + k+a+ +  ad+ R y++a+a+ ++D
  gi|116754113|ref|YP_843231.1| 586 RTSGKDLVANHLLFFLYHHVAifPESLWPRAIAVNGFVSLEGQKMSKSRGPILTLKQAVAENGADVTRLYILANAEYTQD 665
                                    4469***********9999998777889**************************************************** PP

                                    EEE-HHHHH CS
                   tRNA-synt_1g 364 ldfswedfv 372
                                    +d++ + ++
  gi|116754113|ref|YP_843231.1| 666 ADWRNDGAQ 674
                                    **9988766 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 !   74.6   0.1   3.9e-24   7.8e-21       1     136 [.     706     821 ..     706     834 .. 0.79

  Alignments for each domain:
  == domain 1  score: 74.6 bits;  conditional E-value: 3.9e-24
                    Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrllaPf 80 
                                    drw+ls+l++ + e+t+a+++ + ++a++++++ ++ndl +wy +    r             + l+ +l+ ++rl+aPf
  gi|116754113|ref|YP_843231.1| 706 DRWMLSRLQRRIIETTDALNNIQTRRALQSAFYHMLNDL-RWYERR-GGR-------------NQLRRILNVWVRLMAPF 770
                                    9**************************************.9**555.333.............349************** PP

                    Anticodon_1  81 mPfitEelwqr.eeeelgkkesimlaewpe.kaeelekeleeeevellkeivkairkl 136
                                    +P+i+Ee+wq+  e        +++a+wp  +a+  ++++ e++ ++l+++ k i+++
  gi|116754113|ref|YP_843231.1| 771 TPHICEEIWQNiGE------GYVSRAPWPVpDASLIDEQA-ERAEAYLEQTQKDIEEI 821
                                    *********87533......47*******96665556666.55666655555544442 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 !   29.8   0.0     2e-10   3.9e-07      12     126 ..     209     322 ..     206     334 .. 0.77

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 2e-10
                  tRNA-synt_1_2  12 iefkveeseeklevfttrpdtlfGvtfvalapehplveklaekkkelaafieevkkksesereletk..ekeGv.ftglk 88 
                                    i+f+++++   l   t rp+t+fGvt + + p+  +v+ +a+ ++e+     ++ +k + + ++ +k  e  G    g k
  gi|116754113|ref|YP_843231.1| 209 IKFRLDDK--VLPCATLRPETVFGVTNLWVNPN--VVHYIARVNDEVWIVSPQAYHKLTFTDRSVKKigEIPGEeLIGKK 284
                                    66777664..4888899**********999886..78888888888866655544444433332222114566667899* PP

                  tRNA-synt_1_2  89 aihPitgekipiwvanyvlmeygtgavmavPahdqrDf 126
                                    a +P+tg++i i  a +v  + g+g vm+vPah   D+
  gi|116754113|ref|YP_843231.1| 285 ARNPVTGDEIIILPATFVDPDSGSGIVMSVPAHAPLDY 322
                                    *********************************88776 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 ?    3.2   0.0     0.023        46      21      50 ..      46      75 ..      33      81 .. 0.90
   2 !   22.1   0.0     4e-08     8e-05     208     294 ..     583     671 ..     573     677 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.023
                                   S--BHHHHHHHHHHHHHHHHHHHTT-EEEE CS
                   tRNA-synt_1e 21 dashlGhaRslvafDilrrilqalgYdvqf 50
                                    + h Gh+R++ + D ++r+ ++lg +v f
  gi|116754113|ref|YP_843231.1| 46 GNLHAGHTRTFTIGDAIARYHRMLGENVLF 75
                                   578*********************999987 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 4e-08
                                    EEEEEEEGGGTTTHHHHHHHHHHHHSS.S--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHH.HSS-T CS
                   tRNA-synt_1e 208 idihsGGiDLafPhhenelaqseaafd.kqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRlll.lsahy 285
                                    +d+ + G+DL+  h    l  + a f  + + +    ng++++eg+kmsks + ++t+k+++ +  + + Rl++ ++a+y
  gi|116754113|ref|YP_843231.1| 583 VDLRTSGKDLVANHLLFFLYHHVAIFPeSLWPRAIAVNGFVSLEGQKMSKSRGPILTLKQAVAENGADVTRLYIlANAEY 662
                                    7899999999999999999999999986778899999**********************************875157899 PP

                                    TS-EEE-HH CS
                   tRNA-synt_1e 286 rsqldfkee 294
                                     +  d++++
  gi|116754113|ref|YP_843231.1| 663 TQDADWRND 671
                                    998888765 PP

>> tRNA-synt_1d  tRNA synthetases class I (R)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.2e-05     0.044      19      61 ..      32      74 ..      16      80 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.2e-05
                                   T-EEEEE----BTTS--BHHHHHHHHHHHHHHHHHHHCT-EEE CS
                   tRNA-synt_1d 19 kkkvvvdfssPniakemhvGhLrstiiGdavsrlleflGydvi 61
                                   +kk  +    P +  ++h+Gh r+  iGda++r + +lG +v+
  gi|116754113|ref|YP_843231.1| 32 RKKFFLTIPYPYLNGNLHAGHTRTFTIGDAIARYHRMLGENVL 74
                                   5666666677888999***********************9996 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0     9e-05      0.18      11      37 ..     552     578 ..     551     580 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9e-05
                         HTH_29  11 GvstvsqiAkllglsrrtvyrwlkrfe 37 
                                    G +t+ ++  l+g++ +tv+r++++fe
  gi|116754113|ref|YP_843231.1| 552 GKGTPEEVSSLTGVDVDTVRRIREDFE 578
                                    556999*******************97 PP

>> CPSase_L_D3  Carbamoyl-phosphate synthetase large chain, oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   0.00014      0.28       7      56 ..     679     729 ..     673     748 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00014
                    CPSase_L_D3   7 tdeRifaiaealrrglsveeiheltkidpwFLekle.elvelekelkkkkk 56 
                                    + eR++++a+ + +  +++e +elt id+w L++l+ +++e+ ++l++ ++
  gi|116754113|ref|YP_843231.1| 679 QVERFYTLAREIIERNDIDESAELTLIDRWMLSRLQrRIIETTDALNNIQT 729
                                    6789999*99998899******************97369999999887764 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 ?    9.9   0.0   0.00016      0.32     236     311 ..     584     659 ..     579     704 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00016
                   tRNA-synt_1f 236 dfEpaGkDhaaaGgSvdvsskiaeilggeaPekvvYelillkggekmssSkGnvltledwlevaepevlrflilrr 311
                                    d+  +GkD++a+   + +++++a + +   P  +  + +   +g+kms+S+G +ltl++++     +v r++il +
  gi|116754113|ref|YP_843231.1| 584 DLRTSGKDLVANHLLFFLYHHVAIFPESLWPRAIAVNGFVSLEGQKMSKSRGPILTLKQAVAENGADVTRLYILAN 659
                                    555666666666666666666666666666766666655555666******************99***99998873 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (950 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.73u 0.29s 00:00:01.02 Elapsed: 00:00:00.47
# Mc/sec: 6034.60
//
Query:       gi|116754114|ref|YP_843232.1|  [L=182]
Description: DJ-1 family protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.8e-52  176.1   0.4    5.5e-52  175.9   0.4    1.0  1  DJ-1_PfpI       DJ-1/PfpI family
     0.0002   21.0   0.0    0.00026   20.6   0.0    1.2  1  GATase_3        CobB/CobQ-like glutamine amidotransferase dom
  ------ inclusion threshold ------
       0.22   11.4   0.0       0.25   11.2   0.0    1.1  1  PS_pyruv_trans  Polysaccharide pyruvyl transferase


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 !  175.9   0.4   9.2e-56   5.5e-52       1     164 [.       1     163 [.       1     164 [. 0.99

  Alignments for each domain:
  == domain 1  score: 175.9 bits;  conditional E-value: 9.2e-56
                                    EEEEEEEETTBEHHHHHHHHHHHHHTTEEEEEEESSTSEEEETTSEEEE-SEEGGGCTCCG-SEEEE--BHHHHHHHHTS CS
                      DJ-1_PfpI   1 kkvlvlladgvedvElivpvdvlkragikvdvvsvdkeevkgsrGlkvtvdaslddvkaaeyDalvlpGGragperlren 80 
                                    +kv+v la+g+e++E+++ vd+l+ragi+v+++++ +++v+gs+G++v +d+++d+v+ ++ Da+vlpGG+ g  +l ++
  gi|116754114|ref|YP_843232.1|   1 MKVVVPLAEGFEEIEFVTVVDILRRAGIDVEIAGLRDGPVQGSHGVRVIPDTTFDKVDLNSADAIVLPGGNPGFINLGKD 80 
                                    69****************************************************************************** PP

                                    HHHHHHHHHHHHTT-EEEEETTTHHHHHHTTTTTTSEE--SGGGHHHHHHTTSEE-SSSEEEETTEEEESSGGGHHHHHH CS
                      DJ-1_PfpI  81 ekvvelvkefaekgklvaaICagpqlLaaagvlkgrrvTsypavkdklekagakyvdkrvvvdgnlvTsrgpgaaiefal 160
                                    e+v++ v+++  +gk vaaIC +p +L++agvl+gr +T +pa k+++ +a a+y+d+rvvvdg++vTs+gpg+a++fal
  gi|116754114|ref|YP_843232.1|  81 ERVLDAVRKMSAAGKYVAAICGAPSVLVKAGVLSGRMATVHPAGKEEV-AACARYMDERVVVDGKMVTSQGPGTAMDFAL 159
                                    ************************************************.******************************* PP

                                    HHHH CS
                      DJ-1_PfpI 161 elle 164
                                    +l+e
  gi|116754114|ref|YP_843232.1| 160 KLVE 163
                                    **98 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   4.4e-08   0.00026      30      88 ..      52     107 ..      39     135 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 4.4e-08
                       GATase_3  30 vplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmL 88 
                                     ++ + +l++ ad+++lpGg++    ++l +++++ +a++++++ag+ v +iCG   +L
  gi|116754114|ref|YP_843232.1|  52 TTFDKVDLNS-ADAIVLPGGNPGF--INLGKDERVLDAVRKMSAAGKYVAAICGAPSVL 107
                                    5667788865.**********976..66677778********************76555 PP

>> PS_pyruv_trans  Polysaccharide pyruvyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   4.2e-05      0.25      11      85 ..      19      83 ..      17     133 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.2e-05
                                   HHHHHHHTT-EEEEEESSTTT--HHHHHHHHHTS-GGGEE................EEE--E....EEEETT-HH CS
                 PS_pyruv_trans 11 lvklLrelgpdaeiivltpdpsetkkllkvktpilkklskvllkrlrkkdiddaddviivGgdgtlgndgdlsrl 85
                                   +v++Lr++g+d+ei  l++ p++ ++  +v+   ++++++ +           ad +++ Gg+ +  n+g ++r 
  gi|116754114|ref|YP_843232.1| 19 VVDILRRAGIDVEIAGLRDGPVQGSHGVRVIPDTTFDKVDLNS----------ADAIVLPGGNPGFINLGKDERV 83
                                   6899********************************9999987..........6679999997555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 1300.35
//
Query:       gi|116754115|ref|YP_843233.1|  [L=119]
Description: hypothetical protein Mthe_0804 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-07   31.8   0.2    1.6e-07   31.3   0.2    1.2  1  HTH_20    Helix-turn-helix domain
     0.0014   19.0   0.1     0.0032   17.8   0.0    1.7  2  FaeA      FaeA-like protein
  ------ inclusion threshold ------
      0.029   14.3   0.3      0.042   13.8   0.3    1.3  1  HTH_12    Ribonuclease R winged-helix domain
      0.049   13.6   0.0      0.071   13.1   0.0    1.2  1  HTH_45    Winged helix-turn-helix


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.2   3.6e-11   1.6e-07       6      60 ..      47     100 ..      43     101 .. 0.90

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 3.6e-11
                                    HHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                         HTH_20   6 ALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60 
                                    +L  P Rr++lr + + ++++  e+ ++++ls  +++yHL+ Le+   ve v+e+
  gi|116754115|ref|YP_843233.1|  47 VLQLPLRRKMLRFI-GLKARSRDEIEREFGLSEEQARYHLAMLEKGLVVEKVGES 100
                                    5555**********.****************************888889999986 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   7.2e-07    0.0032      17      48 ..      67      97 ..      52     100 .. 0.79
   2 ?   -3.1   0.0       2.3   1.1e+04      33      40 ..     108     115 ..     107     117 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 7.2e-07
                                   -HHHHHHHHTS-HHHHHHHHHHHHHHSSEEEE CS
                           FaeA 17 kTreiAdalglsaYQaRyYLeqLekegkikrs 48
                                   +  ei   +gls  QaRy L +Lek   ++++
  gi|116754115|ref|YP_843233.1| 67 R-DEIEREFGLSEEQARYHLAMLEKGLVVEKV 97
                                   3.58999******************9888886 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.3
                                    HHHHHHHH CS
                           FaeA  33 RyYLeqLe 40 
                                    R YLe+ +
  gi|116754115|ref|YP_843233.1| 108 RLYLEKVD 115
                                    78888776 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 ?   13.8   0.3   9.3e-06     0.042      25      59 ..      71     106 ..      55     112 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.3e-06
                         HTH_12  25 krgydigeravRyrLrkleergltrrvgya.grelt 59 
                                    +r+  ++e+  Ry+L +le+   +++vg +   ++t
  gi|116754115|ref|YP_843233.1|  71 EREFGLSEEQARYHLAMLEKGLVVEKVGESyRPTIT 106
                                    57788999999*******99999****998333555 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.6e-05     0.071      11      70 ..      56     115 ..      52     118 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.6e-05
                         HTH_45  11 ILeaisegeakkTkimykanLsykllnkYLdmLvekglikkskekYvlTekGlelleklk 70 
                                    +L+ i  +  +  +i  +  Ls ++++  L mL +  +++k +e+Y+ T  G+ +lek++
  gi|116754115|ref|YP_843233.1|  56 MLRFIGLKARSRDEIEREFGLSEEQARYHLAMLEKGLVVEKVGESYRPTITGRLYLEKVD 115
                                    677777777777788888999999999899888655556999**************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 913.51
//
Query:       gi|116754116|ref|YP_843234.1|  [L=195]
Description: heat shock protein Hsp20 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.5e-11   44.3   2.0    4.7e-10   39.5   2.0    2.2  1  HSP20       Hsp20/alpha crystallin family
    2.7e-06   26.8   0.1      4e-06   26.3   0.1    1.3  1  ArsA_HSP20  HSP20-like domain found in ArsA
    0.00039   20.8   0.1     0.0006   20.2   0.1    1.3  1  PIH1_CS     PIH1 CS-like domain
     0.0047   17.0   0.4      0.015   15.4   0.2    1.9  2  FKBP26_C    FKBP26_C-terminal
     0.0053   17.7   0.3     0.0091   17.0   0.3    1.4  1  CS          CS domain


Domain annotation for each model (and alignments):
>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   2.0   1.3e-13   4.7e-10       1     101 [.     112     194 ..     112     195 .] 0.92

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 1.3e-13
                                    E--SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--..---TT----SS---EEEEEE--STTB-TTT-EEEEETTE CS
                          HSP20   1 dikeeeeefevkldvpglkkeelkvkvednrvlvkgeheeeeedekglikerssrkFsrkftLPenvdadkvkaslkdGv 80 
                                    di+ee++++++ +++pg++k+++k++v +++v ++   e               +kF ++++L   vd+d+ ka +++Gv
  gi|116754116|ref|YP_843234.1| 112 DIMEEKDSYKIFVELPGVDKSNIKLDVAEDSVEIRTDDE---------------KKFYKMIQLERPVDPDSAKAIYNNGV 176
                                    799********************************9999...............689999***9**************** PP

                                    EEEEEEBSS--..-------- CS
                          HSP20  81 Ltvtvpkkepekkkkerkiqi 101
                                    Lt+t++kke+    k ++++i
  gi|116754116|ref|YP_843234.1| 177 LTLTLEKKEKR---KGKEVKI 194
                                    *******9998...5555555 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 !   26.3   0.1   1.1e-09     4e-06       2      63 .]     118     181 ..     117     181 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.1e-09
                     ArsA_HSP20   2 deyvlkldLPfvdkeeidlsrsgdeLtIkig...nfrRqitLPsvlarkevtsAkfedgvLeIrF 63 
                                    d y++ ++LP+vdk++i+l  ++d   I+ +   +f + i L + ++ + + +A +++gvL+ ++
  gi|116754116|ref|YP_843234.1| 118 DSYKIFVELPGVDKSNIKLDVAEDSVEIRTDdekKFYKMIQLERPVDPDSA-KAIYNNGVLTLTL 181
                                    8899***************************66666677**********77.*********9875 PP

>> PIH1_CS  PIH1 CS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.1   1.7e-07    0.0006      32      94 ..     119     181 ..     111     184 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.7e-07
                        PIH1_CS  32 elaieielPllksikevklrvgerrleleskk.akyfLslkLpYpvdedkveAkFvkktklLkv 94 
                                    +++i +elP++    ++kl+v e+++e+ ++  +k+   ++L+ pvd d+++A +++   +L++
  gi|116754116|ref|YP_843234.1| 119 SYKIFVELPGV-DKSNIKLDVAEDSVEIRTDDeKKFYKMIQLERPVDPDSAKAIYNNGVLTLTL 181
                                    78999******.6678************877754555559****************98777776 PP

>> FKBP26_C  FKBP26_C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.2   4.2e-06     0.015       9      48 ..     122     161 ..     114     163 .. 0.86
   2 ?   -1.8   0.0      0.94   3.4e+03      17      37 ..     164     184 ..     161     186 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4.2e-06
                                    HHHH-TT--..--EEEEETTEEEEE--TTGGGSTTHHHHH CS
                       FKBP26_C   9 IkryiPnidlekfkieiedktvtIelpeeakFieniqlak 48 
                                    I + +P +d+ ++k+ +++ +v+I  ++e kF++ iql +
  gi|116754116|ref|YP_843234.1| 122 IFVELPGVDKSNIKLDVAEDSVEIRTDDEKKFYKMIQLER 161
                                    55567********************************865 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.94
                                    -..--EEEEETTEEEEE--TT CS
                       FKBP26_C  17 dlekfkieiedktvtIelpee 37 
                                    d + +k  ++++++t +l ++
  gi|116754116|ref|YP_843234.1| 164 DPDSAKAIYNNGVLTLTLEKK 184
                                    667888899999999999886 PP

>> CS  CS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.3   2.5e-06    0.0091       8      76 .]     116     183 ..     111     183 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.5e-06
                                    ETTEEEEEEE-TTCTTTTTCEEEEEETTEEEEEE.TSCEEEEECEBSS-BETTTEEEEEETTEEEEEEEB CS
                             CS   8 tldeVvvtiyvkkvnikkkdvkvefkerslkvki.gkeklliegeLfgpIdpeesswtieskkveitLkK 76 
                                    ++d+ ++ +++++v  +k+++k++  e+s+++   +++k+++  +L  p+dp++++    +  + +tL+K
  gi|116754116|ref|YP_843234.1| 116 EKDSYKIFVELPGV--DKSNIKLDVAEDSVEIRTdDEKKFYKMIQLERPVDPDSAKAIYNNGVLTLTLEK 183
                                    56777999*****9..*************8888853356666667***********99999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1290.00
//
Query:       gi|116754117|ref|YP_843235.1|  [L=162]
Description: hypothetical protein Mthe_0806 [Methanosaeta thermophila PT]
Scores for complete 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-46  155.2   0.0    7.8e-46  154.9   0.0    1.1  1  Ribo_biogen_C  Ribosome biogenesis protein, C-terminal
    9.9e-15   54.1   0.1    1.5e-14   53.5   0.1    1.3  1  RLI            Possible Fer4-like domain in RNase L inhibitor


Domain annotation for each model (and alignments):
>> Ribo_biogen_C  Ribosome biogenesis protein, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.9   0.0   8.7e-50   7.8e-46       1     127 []      40     162 .]      40     162 .] 0.95

  Alignments for each domain:
  == domain 1  score: 154.9 bits;  conditional E-value: 8.7e-50
                                    EEE-TT-SSB--GGGHHHHHHT-EEEE---TTT--GGGTTT-E....EB--S-B--STTTTT-BS---HHHHHHHHHHHT CS
                  Ribo_biogen_C   1 ivlspkakkvlspaDreiveksgiavvdcsWarleevkfkklkakeerlLPyLvAaNpvnYgkplkLscvEAlaaalyil 80 
                                    ++lsp+++++lspaDr  ++ +g+a++dcsWa++e+v  +++ + ++r+LP+L+AaNpvn+g+p++Ls++EAlaaal+il
  gi|116754117|ref|YP_843235.1|  40 LILSPFSERALSPADR--YSCRGLAALDCSWAEAERVF-ERI-HANTRALPFLLAANPVNFGRPFRLSTAEALAAALFIL 115
                                    69*************5..5689***********98886.887.579********************************** PP

                                    T-HHHHHHHHTSSTTHHHHHHHCHHHHHHH.TT--HHHHHHHHHHHH CS
                  Ribo_biogen_C  81 glkeeaeellskfkwgeeFlelnkelleeYakckdseevvevqkeyl 127
                                    g++e+a+ +lskf+wg++F+eln+e+leeYa++kds+evv++q+ey+
  gi|116754117|ref|YP_843235.1| 116 GEREQASLVLSKFSWGHTFFELNREPLEEYAAAKDSAEVVRIQSEYI 162
                                    ********************************************996 PP

>> RLI  Possible Fer4-like domain in RNase L inhibitor, RLI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.5   0.1   1.7e-18   1.5e-14       1      33 [.       1      34 [.       1      36 [. 0.92

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 1.7e-18
                                   --EEEES---------TTHHHHHTTSEEE.ESS- CS
                            RLI  1 mrlAivdadqCdPKKCtgkkcarfcpvrl.vrtg 33
                                   m l i++a+qCdPKKCtg+k+arf+++rl +r+ 
  gi|116754117|ref|YP_843235.1|  1 MDLLIYHANQCDPKKCTGRKLARFGIARLtHRIS 34
                                   7899************************988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 1120.02
//
Query:       gi|116754118|ref|YP_843236.1|  [L=855]
Description: valyl-tRNA synthetase [Methanosaeta thermophila PT]
Scores for complete 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-135  450.8   0.5   2.2e-133  445.7   0.5    2.1  1  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    1.7e-37  128.7   0.0    3.2e-37  127.8   0.0    1.4  1  Anticodon_1    Anticodon-binding domain of tRNA
    2.6e-23   82.4   0.3      2e-14   53.2   0.0    3.1  3  tRNA-synt_1g   tRNA synthetases class I (M)
      9e-07   28.5   0.0     0.0058   16.0   0.0    2.3  2  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain
    0.00054   19.5   0.0     0.0017   17.9   0.0    1.8  1  tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  445.7   0.5  6.2e-137  2.2e-133       2     600 ..      17     560 ..      16     562 .. 0.94

  Alignments for each domain:
  == domain 1  score: 445.7 bits;  conditional E-value: 6.2e-137
                    tRNA-synt_1   2 lyekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakve 81 
                                    + e+W+ + ++        ek+++i+  +PPy tG+ HiG+al+    d+v rykrm+G++v +  GwD++Gl++e kve
  gi|116754118|ref|YP_843236.1|  17 WIERWDPSVYYFDW---GSEKPQYIIDTPPPYPTGNFHIGNALNWCYIDFVARYKRMRGYNVMFPQGWDCHGLPTEVKVE 93 
                                    78899999888776...789************************************************************ PP

                    tRNA-synt_1  82 kklgakekkerkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgliyrgkk 161
                                    +++ ++++    ++ reefr  + e+ a+ +e++r++++rlG+s+D+++ey+T+++e+   +++ fv++++kg+iyr  +
  gi|116754118|ref|YP_843236.1|  94 ETYHITKN----QVPREEFRRLCEEMTAQAIERMRRTITRLGISTDWSNEYITMKPEYYVKTQRSFVQMYEKGMIYREDH 169
                                    ***88886....99****************************************************************** PP

                    tRNA-synt_1 162 lvnwstklktalselEveykdkkdalihvafpladkeevklviaTTtPeTllgdtavavnpeldyvitkeklilaeallk 241
                                    +vnw+++++ta++ +Evey   + +l +++f+ +++    l+iaTT+Pe l++ +avavnp+                  
  gi|116754118|ref|YP_843236.1| 170 PVNWCPRCATAIAFAEVEYDTRTTTLNYMRFESDHG---CLEIATTRPELLPACVAVAVNPN------------------ 228
                                    ******************************986544...58*********************.................. PP

                    tRNA-synt_1 242 slvkkesekkiledergkeLegkevelplvnrkipiiaddyvdkeaGtGvVkiaPahdedDyevgkkynlevinildedg 321
                                                 der   ++gk v+ pl + ++p+++d  vd  +GtGvV i    d++D +   +++l++ +++d +g
  gi|116754118|ref|YP_843236.1| 229 -------------DERHIGFVGKSVKVPLFDYEVPVLSDPAVDPSFGTGVVMICTFGDKQDVRWWVEHKLPLRQAIDREG 295
                                    .............9999*************************************************************** PP

                    tRNA-synt_1 322 tlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrateqWfvrvkeladaalkavekvqfv 401
                                    +lte a++f g+++ +a+k++v+e+  +g + ++e+ e +v++c+r k+pi+  +  qWfvr+ +  d ++k+ +++++v
  gi|116754118|ref|YP_843236.1| 296 RLTEIAGKFGGMSITEAKKAIVDEMLSRGIIYRQEPLEQNVGLCWRCKTPIEILSERQWFVRIYP--DVIIKTADEIEWV 373
                                    **************************************************************986..99*********** PP

                    tRNA-synt_1 402 pkskekryaswleniq.dWciSRqrwWGhriplfvsketeevvvreelkelvagreeeeaekkalekeakdklkkekgel 480
                                    p+  + r ++w   ++ dWciSRqr+  ++ip+++ k+ +ev+v   ++e+       ++++         +  ++ +e+
  gi|116754118|ref|YP_843236.1| 374 PEHMKLRLKNWTGTMEwDWCISRQRVFATPIPAWYCKRCGEVMV--AKEEWLP--LDPTKTQPP------VSCSCGSNEF 443
                                    ************99866***************************..4445544..222222222......23457899** PP

                    tRNA-synt_1 481 ekdedvlDvWFsSgswpfstlgypeedteelkkffpadmlleGlDiirgWvarlillslaltgsePfkevlvhglvrdee 560
                                    e +edvlD+W +S+ +   + g+ ++  e+ +  +pa++  +G Diir W    il s+al+g +P++++l++g+v+ e+
  gi|116754118|ref|YP_843236.1| 444 EPEEDVLDTWMDSSISALHVTGWLSR--EDPR--YPAQLRPQGHDIIRTWAFYTILRSMALVGVKPWETILINGMVLGED 519
                                    **********************9887..6666..********************************************** PP

                    tRNA-synt_1 561 GrKmSKslgNvidpldvikkygadalRltli.lsdvgrdin 600
                                    GrKmSKsl N + p++v +k gadalR + +   + g+d+ 
  gi|116754118|ref|YP_843236.1| 520 GRKMSKSLNNFVIPEEVFEKNGADALRQWAAlGGSPGSDVM 560
                                    ****************************9987777777775 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   0.0     9e-41   3.2e-37       1     148 [.     598     735 ..     598     741 .. 0.90

  Alignments for each domain:
  == domain 1  score: 127.8 bits;  conditional E-value: 9e-41
                    Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrllaPf 80 
                                    drw+l el  lv++vt+a+e ++f++a++a+  f+w+ l+d y+e+vk+rly+ +++++raaq++l+ vl+ l+rl+aPf
  gi|116754118|ref|YP_843236.1| 598 DRWLLGELGMLVSKVTDAMEAFQFDEAFRAIRAFTWEVLADDYIEIVKSRLYGPDSDERRAAQATLYRVLDVLCRLMAPF 677
                                    9***************************************************988766666******************* PP

                    Anticodon_1  81 mPfitEelwqreeeelgkkesimlaewpe.kaeelekeleeeevellkeivkairklrselkikpssel 148
                                    +PfitEe++    ++    +s++ ++wp+ +    ++     e +l++ei  air+++se +++ +++l
  gi|116754118|ref|YP_843236.1| 678 IPFITEEIY----TS-LTGKSVHTQSWPSlET---YTSP---EGALIREIAAAIRRYKSERGMALNAPL 735
                                    *********....66.35568*******6444...5555...679999****************99985 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 !   53.2   0.0   5.6e-18     2e-14       2     131 ..      38     182 ..      37     194 .. 0.78
   2 ?   -0.3   0.1     0.099   3.5e+02     206     238 ..     373     405 ..     327     415 .. 0.82
   3 !   25.2   0.0   1.8e-09   6.4e-06     291     373 ..     484     568 ..     453     576 .. 0.82

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 5.6e-18
                                    EEEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHT......TS-H.......HHHHH CS
                   tRNA-synt_1g   2 lvttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAeke......gvtp.......eelve 68 
                                    ++ t+ pY++g+ H+G++l+    D +aRykr+rg++v+f  g D hG p+e+k e+       +v         ee+++
  gi|116754118|ref|YP_843236.1|  38 IIDTPPPYPTGNFHIGNALNWCYIDFVARYKRMRGYNVMFPQGWDCHGLPTEVKVEETyhitknQVPReefrrlcEEMTA 117
                                    789999***********************************************998742111112322112111134455 PP

                                    HHHHHHHHHHHHTT---S..EEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE- CS
                   tRNA-synt_1g  69 kvheeikelfkklnisfd..kygrttseehkelvqeifkklkekgliyekeieqlycpkderflp 131
                                    ++ e+++++ ++l+is d  + + t + e +  +q+ f +++ekg+iy+++  + +cp++ + ++
  gi|116754118|ref|YP_843236.1| 118 QAIERMRRTITRLGISTDwsNEYITMKPEYYVKTQRSFVQMYEKGMIYREDHPVNWCPRCATAIA 182
                                    56677899999*****98432234777888888999999********************998766 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.099
                                    SHHHHHHHH.HHHHT----EE-ESS-SSS-EET CS
                   tRNA-synt_1g 206 leenvkkivkewlkegLkdlaisrdldwGipvP 238
                                     +e++k  +k+w  +   d++isr+  ++ p+P
  gi|116754118|ref|YP_843236.1| 373 VPEHMKLRLKNWTGTMEWDWCISRQRVFATPIP 405
                                    567778888999988788*************99 PP

  == domain 3  score: 25.2 bits;  conditional E-value: 1.8e-09
                                    GGHHHHHTHHHHHHHH.TT----S-EEEE--EE.E--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-H CS
                   tRNA-synt_1g 291 diikFHtifwPaillg.aelklpkkvvaheylt.vegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfsw 368
                                    dii+  + +     ++  ++k  +++  ++++   +g+K+SkS +++v ++e+ e+  ad+lR + a  ++  +D+ f+w
  gi|116754118|ref|YP_843236.1| 484 DIIRTWAFYTILRSMAlVGVKPWETILINGMVLgEDGRKMSKSLNNFVIPEEVFEKNGADALRQWAALGGSPGSDVMFQW 563
                                    55554443333333334566677788888876515789****************************************** PP

                                    HHHHH CS
                   tRNA-synt_1g 369 edfve 373
                                    +++v+
  gi|116754118|ref|YP_843236.1| 564 KEIVA 568
                                    **986 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 !   10.0   0.0   0.00011      0.39      22      52 ..      49      79 ..      45     176 .. 0.81
   2 !   16.0   0.0   1.6e-06    0.0058     228     278 ..     496     547 ..     481     554 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00011
                                   --BHHHHHHHHHHHHHHHHHHHTT-EEEEEE CS
                   tRNA-synt_1e 22 ashlGhaRslvafDilrrilqalgYdvqfvq 52
                                   + h+G+a +   +D ++r+ +++gY+v+f q
  gi|116754118|ref|YP_843236.1| 49 NFHIGNALNWCYIDFVARYKRMRGYNVMFPQ 79
                                   57**************************976 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.6e-06
                                    HHHHHSSS--EEEEEEE--EE.ETTBE--TTTT---BHHHHHTTS-HHHHHH CS
                   tRNA-synt_1e 228 qseaafdkqlvkyflhnghlk.iegekmsksLknfitikdvlkkfdprqlRl 278
                                    +s+a+++ +  +  l ng++   +g+kmsksL+nf+  ++v++k  + +lR 
  gi|116754118|ref|YP_843236.1| 496 RSMALVGVKPWETILINGMVLgEDGRKMSKSLNNFVIPEEVFEKNGADALRQ 547
                                    6889999666666777777651689*******************99999996 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 !   17.9   0.0   4.8e-07    0.0017      84     146 ..     235     297 ..     222     321 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 4.8e-07
                  tRNA-synt_1_2  84 ftglkaihPitgekipiwvanyvlmeygtgavmavPahdqrDfeFakkynlpikqvikpedee 146
                                    f g  +  P+ + ++p+     v  ++gtg+vm +   d++D +++ +++lp++q i  e++ 
  gi|116754118|ref|YP_843236.1| 235 FVGKSVKVPLFDYEVPVLSDPAVDPSFGTGVVMICTFGDKQDVRWWVEHKLPLRQAIDREGRL 297
                                    56778899*************************************************987654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (855 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      647  (0.0360868); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.76u 0.29s 00:00:01.05 Elapsed: 00:00:00.49
# Mc/sec: 5241.12
//
Query:       gi|116754119|ref|YP_843237.1|  [L=193]
Description: putative adenylyl cyclase CyaB [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-31  109.1   0.5    2.9e-31  108.8   0.5    1.1  1  CYTH      CYTH domain
  ------ inclusion threshold ------
       0.15   11.5   1.4       0.33   10.4   1.4    1.5  1  DUF963    Schizosaccharomyces pombe repeat of unknown functio


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 !  108.8   0.5   3.2e-35   2.9e-31       1     148 [.       1     136 [.       1     152 [. 0.93

  Alignments for each domain:
  == domain 1  score: 108.8 bits;  conditional E-value: 3.2e-35
                                    EEEEEEEEEE-HHHHHHHHHHHHHCTCEEEEEEEEEEEEEE-TTTHHHHTTEEEEEEEETTTEEEEEEEEECSSST...E CS
                           CYTH   1 miEvEvKflvsaaeyedlelrlaelrakeettveqrdtYydtpdrdlartdeaLRiRraegdgeeltlKgpgvdge...r 77 
                                    miEvE K++      ed e+r+   ++  e+ +  +d+Y+ +p rd+a+tdeaLRiR++ +dg  lt+Kgp++d+e   r
  gi|116754119|ref|YP_843237.1|   1 MIEVEAKARAL----EDAEERILRMGGVLEGVESHTDIYFRSPVRDFASTDEALRIRIK-DDGVHLTYKGPKLDSEtktR 75 
                                    89*******95....555566889*********************************77.77777************999 PP

                                    EEEEEEECCCEEECCCCHHHHHHHHHHHTT-EEEEEEEEEEEEEEETTEEEEEEEETTTTEEEEEEEEEES CS
                           CYTH  78 eevegevsreEyeeplsdaaeaaelldglglepvasvkklRrkyklegvevalDaveflegeevEiEleve 148
                                     e+++ v+         daa+a +ll++lg+  +a+v+k+R+ky+l+++ valD v++l g +vE+E+ ++
  gi|116754119|ref|YP_843237.1|  76 LELSIRVD---------DAAAAEKLLESLGFSRFAVVRKRRAKYRLGDAIVALDDVDGL-GRFVEVEISAD 136
                                    99999999.........******************************************.*******9765 PP

>> DUF963  Schizosaccharomyces pombe repeat of unknown function (DUF963)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.4   3.7e-05      0.33       7      26 ..     170     190 ..     169     191 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 3.7e-05
                         DUF963   7 lnsSTPvtsS.TpVnsSTPIt 26 
                                    ++sSTP+t S ++ ++STP +
  gi|116754119|ref|YP_843237.1| 170 ARSSTPITASgSADEKSTPAR 190
                                    689999986647788999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1417.29
//
Query:       gi|116754120|ref|YP_843238.1|  [L=275]
Description: F420-dependent methylenetetrahydromethanopterin dehydrogenase [Methanosaeta thermophila PT]
Scores for complete 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-122  407.9   1.1   2.1e-122  407.7   1.1    1.0  1  MTD             methylene-5,6,7,8-tetrahydromethanopterin deh
  ------ inclusion threshold ------
       0.17   11.9   0.0        4.5    7.2   0.0    2.1  2  Glyco_transf_4  Glycosyltransferase Family 4
        5.9    7.2   6.4        1.1    9.5   2.2    2.1  2  Se-cys_synth_N  Selenocysteine synthase N terminal


Domain annotation for each model (and alignments):
>> MTD  methylene-5,6,7,8-tetrahydromethanopterin dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  407.7   1.1  3.5e-126  2.1e-122       1     273 [.       2     272 ..       2     273 .. 0.99

  Alignments for each domain:
  == domain 1  score: 407.7 bits;  conditional E-value: 3.5e-126
                                    EEEEEEEES--HHHHHTTGGGSTTS--SSEEEEEEEEET--SHHHHHHHHHHHHHH--SEEEEE-S-TTSHHHHHHHHHH CS
                            MTD   1 vkigiiklGnigtslvidlllDeradRedievrvvgsgaklkkeeveevveklkefdpdlvivisPnaaapgptkarell 80 
                                    +kig+iklGni++slv+dl+lDe+a+R++ie +vv++g+k+++ e e+ +e+++++ p++v+v+sPnaa+pgpt+ar++l
  gi|116754120|ref|YP_843238.1|   2 FKIGFIKLGNIASSLVVDLALDEIAERTEIESKVVSHGPKMSRGEGERLAEEMRAWGPQMVVVVSPNAATPGPTAARSML 81 
                                    59****************************************************************************** PP

                                    HHSSS-EEEEEEGGGGGGH.HHHHHTT-EEEEETTS------TTT--HHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHH CS
                            MTD  81 sekdvpaivisDapgkkek.deleeeglGYiivkaDpliGarrefLDptemalfnadvlkvLaatGavRlvqeeldkvie 159
                                      k++p ivisD+p+kke+ d++e+eg+GYii+++DpliGa+refLDp+ema+fnad+lkvL+++GavRlvqee+d++i+
  gi|116754120|ref|YP_843238.1|  82 --KGIPLIVISDGPTKKEArDAMETEGFGYIILPMDPLIGAKREFLDPAEMAIFNADALKVLSICGAVRLVQEEIDRAIA 159
                                    ..9**************999************************************************************ PP

                                    HHTTT-GGGS-EEEESGGGGGGSS--SSHHHHHHHHHHHHHHHHHHHHHHHHHHT---HHHHHHHHHHHHHHHHHHHHHH CS
                            MTD 160 kvkagkeielPkividaekaveaaefsnPYakakalaayeiaekvadidvkaCfmekelekyilivasahellraaakLa 239
                                    +v+ag+ ++lP+i++++e + e+++f+nPYa+aka+aa+++a++ a+id++aCf+ kele ++l +a++he++raaa+La
  gi|116754120|ref|YP_843238.1| 160 SVAAGS-PQLPHILATPELCAERMDFANPYARAKAIAALYMAQTAASIDAQACFRLKELEAIALAAAAGHEVIRAAARLA 238
                                    *****9.9************************************************************************ PP

                                    HHHHHHHHHTT---B--B-TTSSB--BSSTTS-- CS
                            MTD 240 deaReieksndtvlRkphakdGkvlsktkllekP 273
                                    deaRe+eks dtv+Rkpha++G++l k+kllekP
  gi|116754120|ref|YP_843238.1| 239 DEARELEKSGDTVSRKPHARSGDLLVKRKLLEKP 272
                                    *********************************9 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0   0.00076       4.5      54     101 ..      40      88 ..      21     108 .. 0.84
   2 ?    2.5   0.0     0.022   1.3e+02      16      55 ..     224     263 ..     218     275 .] 0.73

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00076
                 Glyco_transf_4  54 llrslaflrrlrrllkrekpDvvHahspaalgaallalrr.rlgiplVl 101
                                    ++ s     rl++ +++++p  v + sp a+  +  a+r   +gipl++
  gi|116754120|ref|YP_843238.1|  40 PKMSRGEGERLAEEMRAWGPQMVVVVSPNAATPGPTAARSmLKGIPLIV 88 
                                    5555666789*************9999999999988888899*****97 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.022
                 Glyco_transf_4  16 arrGheVtvvtpgddgpleeevelvvrvprvplpllkrll 55 
                                    a++GheV   + +  ++++e ++ +  v r+p+  +++ll
  gi|116754120|ref|YP_843238.1| 224 AAAGHEVIRAAARLADEARELEKSGDTVSRKPHARSGDLL 263
                                    559*******999888888887777788777777666655 PP

>> Se-cys_synth_N  Selenocysteine synthase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1       2.3   1.4e+04      30      39 ..     148     157 ..     147     157 .. 0.78
   2 ?    9.5   2.2   0.00019       1.1      11      33 ..     214     236 ..     214     242 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.3
                 Se-cys_synth_N  30 davrafLdrc 39 
                                     +v +++dr+
  gi|116754120|ref|YP_843238.1| 148 RLVQEEIDRA 157
                                    6899999986 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00019
                 Se-cys_synth_N  11 LtalearallaalpRalvrdavr 33 
                                    L++lea al+aa +++++r+a r
  gi|116754120|ref|YP_843238.1| 214 LKELEAIALAAAAGHEVIRAAAR 236
                                    899******************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 2128.52
//
Query:       gi|116754121|ref|YP_843239.1|  [L=210]
Description: hypothetical protein Mthe_0810 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-11   42.9   0.0    8.3e-11   42.2   0.0    1.2  1  LTD       Lamin Tail Domain


Domain annotation for each model (and alignments):
>> LTD  Lamin Tail Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.0   4.6e-15   8.3e-11       5     107 ..      74     164 ..      72     167 .. 0.86

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 4.6e-15
                            LTD   5 agdvvIsevmedgagnnanefvelyNtsskavdLsgwkledasge....ytfpngtgtlaageyvvvwsgsgttsasngs 80 
                                    a+dvv++ev  +++++++ ++velyN+++++v ++gw ++   +     + +p+g+  +++++ +v   ++       + 
  gi|116754121|ref|YP_843239.1|  74 AADVVLNEVELGPPEGSS-DWVELYNSGNESVMIGGWCVRIIDESwigeIHIPDGV-LIEPHGFYVAMGSK-------E- 143
                                    78***********88776.******************9988887788********9.************94.......3. PP

                            LTD  81 kasssavwnn.ggdavaLydasgevvds 107
                                           w   ++  v+L+d +g++vd+
  gi|116754121|ref|YP_843239.1| 144 -------WMHnNSGVVQLIDGAGNIVDE 164
                                    .......4441444566*******9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1567.39
//
Query:       gi|116754122|ref|YP_843240.1|  [L=192]
Description: HEAT repeat-containing PBS lyase [Methanosaeta thermophila PT]
Scores for complete 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-43  146.2   5.4    1.1e-17   64.1   0.0    3.1  3  HEAT_2         HEAT repeats
    2.1e-38  127.0   7.4    1.3e-07   31.6   0.1    5.3  5  HEAT_PBS       PBS lyase HEAT-like repeat
    7.8e-26   87.9   2.2    0.00051   20.1   0.0    6.1  6  HEAT           HEAT repeat
    2.6e-18   66.1   8.0     0.0038   17.7   0.2    5.5  6  HEAT_EZ        HEAT-like repeat
    3.6e-16   58.6   4.3     0.0024   17.9   0.1    5.3  5  Arm            Armadillo/beta-catenin-like repeat
    1.1e-07   32.1   0.0     0.0039   17.3   0.0    4.2  3  Cnd1           non-SMC mitotic condensation complex subunit 1
    3.1e-05   24.5   0.0        2.9    8.6   0.0    4.6  5  Vac14_Fab1_bd  Vacuolar 14 Fab1-binding region
    7.8e-05   22.4   0.0      0.039   13.5   0.0    2.1  2  ERAP1_C        ERAP1-like C-terminal domain
    0.00028   19.6   0.0      0.019   13.5   0.0    2.2  2  Adaptin_N      Adaptin N terminal region
     0.0061   16.6   0.1       0.17   12.0   0.1    2.5  2  Aconitase_B_N  Aconitate B N-terminal domain
  ------ inclusion threshold ------
      0.011   16.2   0.2          3    8.3   0.0    3.4  4  RasGEF_N_2     Rapamycin-insensitive companion of mTOR RasGEF
      0.018   14.9   0.0          3    7.7   0.0    2.9  3  DUF3385        Domain of unknown function (DUF3385)


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 !   36.9   0.1   2.4e-12   3.6e-09      28      80 ..       5      56 ..       3      57 .. 0.89
   2 !   59.6   1.8   1.9e-19   2.9e-16       3      73 ..      43     112 ..      42     114 .. 0.96
   3 !   64.1   0.0   7.5e-21   1.1e-17       1      83 [.     103     182 ..     103     189 .. 0.91

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 2.4e-12
                         HEAT_2 28 gnpealpaLvellededpavRraaaeaLgaigdpealpaLkellddddddvvR 80
                                   ++pe +++ ++ l+d++++vR++aaeaLg+igdp+a+  L ++l+d  d+ vR
  gi|116754122|ref|YP_843240.1|  5 ADPEKVEMYIKNLKDDSSNVRAQAAEALGKIGDPKAVGPLIDALLD-VDASVR 56
                                   6788899999*********************************996.566666 PP

  == domain 2  score: 59.6 bits;  conditional E-value: 1.9e-19
                         HEAT_2   3 aLlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkelldd 73 
                                    +L+ al  d d  vr +a++aLg+i++ +a++ L ++l+d+++ vR++aa+aLg igdp+a++aL   l+d
  gi|116754122|ref|YP_843240.1|  43 PLIDAL-LDVDASVRSEAAEALGKIKDARAVEPLSRALNDANAIVRWNAAWALGSIGDPRAVEALIGVLND 112
                                    699999.8**********************************************************99987 PP

  == domain 3  score: 64.1 bits;  conditional E-value: 7.5e-21
                         HEAT_2   1 ldaLlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkellddddddvvR 80 
                                    ++aL+ +l nd +++vr +a+ aLg+ig+p+a++ L+++l+d+++ vR+++ +aLg igdp+ +++L+ +  +d++++v+
  gi|116754122|ref|YP_843240.1| 103 VEALIGVL-NDMSQDVRLNAACALGSIGDPRAVDPLLPMLKDTSWKVRYHVTRALGLIGDPRIIDHLESI--SDESPIVQ 179
                                    57999999.***********************************************************95..46677777 PP

                         HEAT_2  81 eaA 83 
                                     a+
  gi|116754122|ref|YP_843240.1| 180 KAV 182
                                    664 PP

>> HEAT_PBS  PBS lyase HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.2   1.4e-08   2.1e-05       1      27 []      24      50 ..      24      50 .. 0.97
   2 !   26.9   0.2   2.9e-09   4.3e-06       1      27 []      55      81 ..      55      81 .. 0.98
   3 !   31.6   0.1   8.5e-11   1.3e-07       1      27 []      86     112 ..      86     112 .. 0.96
   4 !   26.7   0.0   3.3e-09   4.9e-06       1      27 []     117     143 ..     117     143 .. 0.97
   5 !   17.5   0.0     3e-06    0.0045       1      23 [.     148     170 ..     148     174 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.4e-08
                                   HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                       HEAT_PBS  1 vRraAakaLgqlgdeeaipaLleaLqd 27
                                   vR+ Aa+aLg++gd+ a+ +L+ aL d
  gi|116754122|ref|YP_843240.1| 24 VRAQAAEALGKIGDPKAVGPLIDALLD 50
                                   9************************87 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 2.9e-09
                                   HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                       HEAT_PBS  1 vRraAakaLgqlgdeeaipaLleaLqd 27
                                   vR +Aa+aLg+++d +a+++L +aL+d
  gi|116754122|ref|YP_843240.1| 55 VRSEAAEALGKIKDARAVEPLSRALND 81
                                   9************************98 PP

  == domain 3  score: 31.6 bits;  conditional E-value: 8.5e-11
                                    HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                       HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLqd 27 
                                    vR++Aa+aLg +gd++a++aL+ +L+d
  gi|116754122|ref|YP_843240.1|  86 VRWNAAWALGSIGDPRAVEALIGVLND 112
                                    9*********************99987 PP

  == domain 4  score: 26.7 bits;  conditional E-value: 3.3e-09
                                    HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                       HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLqd 27 
                                    vR +Aa aLg +gd++a+++Ll  L+d
  gi|116754122|ref|YP_843240.1| 117 VRLNAACALGSIGDPRAVDPLLPMLKD 143
                                    8*********************99997 PP

  == domain 5  score: 17.5 bits;  conditional E-value: 3e-06
                                    HHHHHHHHHHHCTSGGGHHHHHH CS
                       HEAT_PBS   1 vRraAakaLgqlgdeeaipaLle 23 
                                    vR+  ++aLg +gd+++i++L  
  gi|116754122|ref|YP_843240.1| 148 VRYHVTRALGLIGDPRIIDHLES 170
                                    9*******************975 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   3.4e-07   0.00051       5      27 ..      13      35 ..      10      37 .. 0.90
   2 !   13.7   0.0     4e-05     0.059       5      27 ..      44      66 ..      41      68 .. 0.86
   3 !   17.5   0.1   2.2e-06    0.0033       4      27 ..      74      97 ..      71      99 .. 0.89
   4 !    9.0   0.1    0.0012       1.8       3      27 ..     104     128 ..     102     130 .. 0.88
   5 !   18.6   0.0     1e-06    0.0015       3      27 ..     135     159 ..     133     161 .. 0.91
   6 ?    3.4   0.0     0.077   1.1e+02       3      23 ..     166     185 ..     164     189 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3.4e-07
                                   HHHHHT-SSHHHHHHHHHHHHHH CS
                           HEAT  5 llkllsDpspeVReaAakaLgal 27
                                    +k+l+D+s++VR+ Aa+aLg++
  gi|116754122|ref|YP_843240.1| 13 YIKNLKDDSSNVRAQAAEALGKI 35
                                   689******************99 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 4e-05
                                   HHHHHT-SSHHHHHHHHHHHHHH CS
                           HEAT  5 llkllsDpspeVReaAakaLgal 27
                                   l+ +l D +++VR+ Aa+aLg++
  gi|116754122|ref|YP_843240.1| 44 LIDALLDVDASVRSEAAEALGKI 66
                                   566778***************98 PP

  == domain 3  score: 17.5 bits;  conditional E-value: 2.2e-06
                                   HHHHHHT-SSHHHHHHHHHHHHHH CS
                           HEAT  4 lllkllsDpspeVReaAakaLgal 27
                                   +l ++l+D ++ VR +Aa+aLg +
  gi|116754122|ref|YP_843240.1| 74 PLSRALNDANAIVRWNAAWALGSI 97
                                   67889*****************98 PP

  == domain 4  score: 9.0 bits;  conditional E-value: 0.0012
                                    HHHHHHHT-SSHHHHHHHHHHHHHH CS
                           HEAT   3 PlllkllsDpspeVReaAakaLgal 27 
                                     +l+  l+D s +VR +Aa aLg +
  gi|116754122|ref|YP_843240.1| 104 EALIGVLNDMSQDVRLNAACALGSI 128
                                    578899*************999987 PP

  == domain 5  score: 18.6 bits;  conditional E-value: 1e-06
                                    HHHHHHHT-SSHHHHHHHHHHHHHH CS
                           HEAT   3 PlllkllsDpspeVReaAakaLgal 27 
                                    ++ll +l+D+s++VR+ + +aLg +
  gi|116754122|ref|YP_843240.1| 135 DPLLPMLKDTSWKVRYHVTRALGLI 159
                                    689*******************977 PP

  == domain 6  score: 3.4 bits;  conditional E-value: 0.077
                                    HHHHHHHT-SSHHHHHHHHHH CS
                           HEAT   3 PlllkllsDpspeVReaAaka 23 
                                    ++l + +sD+sp V +a+ ++
  gi|116754122|ref|YP_843240.1| 166 DHLES-ISDESPIVQKAVKET 185
                                    55444.8*******9998655 PP

>> HEAT_EZ  HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.1e-05     0.017      34      55 .]      14      35 ..      10      35 .. 0.92
   2 !    9.9   0.1   0.00072       1.1      29      55 .]      40      66 ..      37      66 .. 0.71
   3 !   17.7   0.2   2.6e-06    0.0038      29      55 .]      71      97 ..      69      97 .. 0.92
   4 !   13.1   0.1   6.9e-05       0.1      27      55 .]     100     128 ..      99     128 .. 0.95
   5 !   10.3   0.0   0.00051      0.77      27      55 .]     131     159 ..     130     159 .. 0.91
   6 ?   -2.0   0.0       3.8   5.7e+03      28      47 ..     163     181 ..     162     189 .. 0.54

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-05
                        HEAT_EZ 34 lalLnddsdeVRaaAagaLgnl 55
                                   ++ L+dds++VRa+Aa aLg++
  gi|116754122|ref|YP_843240.1| 14 IKNLKDDSSNVRAQAAEALGKI 35
                                   5789****************97 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00072
                        HEAT_EZ 29 ilpaLlalLnddsd.eVRaaAagaLgnl 55
                                   ++ +L+ +L  d d +VR  Aa aLg++
  gi|116754122|ref|YP_843240.1| 40 AVGPLIDALL-DVDaSVRSEAAEALGKI 66
                                   4555554444.6666***********97 PP

  == domain 3  score: 17.7 bits;  conditional E-value: 2.6e-06
                        HEAT_EZ 29 ilpaLlalLnddsdeVRaaAagaLgnl 55
                                   ++ +L ++Lnd ++ VR++Aa+aLg +
  gi|116754122|ref|YP_843240.1| 71 AVEPLSRALNDANAIVRWNAAWALGSI 97
                                   788999*******************86 PP

  == domain 4  score: 13.1 bits;  conditional E-value: 6.9e-05
                        HEAT_EZ  27 peilpaLlalLnddsdeVRaaAagaLgnl 55 
                                    p+++ aL+  Lnd s++VR +Aa aLg +
  gi|116754122|ref|YP_843240.1| 100 PRAVEALIGVLNDMSQDVRLNAACALGSI 128
                                    7899***********************86 PP

  == domain 5  score: 10.3 bits;  conditional E-value: 0.00051
                        HEAT_EZ  27 peilpaLlalLnddsdeVRaaAagaLgnl 55 
                                    p+++++Ll++L+d s +VR+ + +aLg +
  gi|116754122|ref|YP_843240.1| 131 PRAVDPLLPMLKDTSWKVRYHVTRALGLI 159
                                    7899********9888**********965 PP

  == domain 6  score: -2.0 bits;  conditional E-value: 3.8
                        HEAT_EZ  28 eilpaLlalLnddsdeVRaa 47 
                                    +i++ L +  +d+s+ V++a
  gi|116754122|ref|YP_843240.1| 163 RIIDHLESI-SDESPIVQKA 181
                                    566666633.3344444444 PP

>> Arm  Armadillo/beta-catenin-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.0    0.0071        11      14      38 ..      10      34 ..      10      36 .. 0.89
   2 !   14.4   0.0     2e-05      0.03       9      37 ..      36      64 ..      33      66 .. 0.91
   3 !   13.7   0.1   3.3e-05     0.049       8      39 ..      66      97 ..      65      99 .. 0.92
   4 !   17.9   0.1   1.6e-06    0.0024       9      39 ..      98     128 ..      96     130 .. 0.91
   5 !    5.9   0.0    0.0091        14       9      37 ..     129     157 ..     127     160 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0071
                                   HHHHHHHTTTSSHHHHHHHHHHHHH CS
                            Arm 14 vppLvrLLssedeevqeeAawALsN 38
                                   v+  ++ L++++ +v+ +Aa AL+ 
  gi|116754122|ref|YP_843240.1| 10 VEMYIKNLKDDSSNVRAQAAEALGK 34
                                   5678899****************85 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 2e-05
                                   HHTTHHHHHHHHTTTSSHHHHHHHHHHHH CS
                            Arm  9 ieaGavppLvrLLssedeevqeeAawALs 37
                                    +  av pL++ L + d +v+ eAa AL+
  gi|116754122|ref|YP_843240.1| 36 GDPKAVGPLIDALLDVDASVRSEAAEALG 64
                                   67889***********************8 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 3.3e-05
                                   HHHTTHHHHHHHHTTTSSHHHHHHHHHHHHHH CS
                            Arm  8 vieaGavppLvrLLssedeevqeeAawALsNL 39
                                   + +a av+pL r L++ +  v+ +AawAL+ +
  gi|116754122|ref|YP_843240.1| 66 IKDARAVEPLSRALNDANAIVRWNAAWALGSI 97
                                   56899************************976 PP

  == domain 4  score: 17.9 bits;  conditional E-value: 1.6e-06
                                    HHTTHHHHHHHHTTTSSHHHHHHHHHHHHHH CS
                            Arm   9 ieaGavppLvrLLssedeevqeeAawALsNL 39 
                                     +  av++L+  L++++++v+ +Aa+AL+ +
  gi|116754122|ref|YP_843240.1|  98 GDPRAVEALIGVLNDMSQDVRLNAACALGSI 128
                                    57789***********************976 PP

  == domain 5  score: 5.9 bits;  conditional E-value: 0.0091
                                    HHTTHHHHHHHHTTTSSHHHHHHHHHHHH CS
                            Arm   9 ieaGavppLvrLLssedeevqeeAawALs 37 
                                     +  av+pL+ +L++++ +v+  +++AL+
  gi|116754122|ref|YP_843240.1| 129 GDPRAVDPLLPMLKDTSWKVRYHVTRALG 157
                                    57789*********998888888888886 PP

>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0012       1.9      28      87 ..      15      68 ..       8      71 .. 0.80
   2 !   11.8   0.0   0.00012      0.18      25      83 ..      43      95 ..      38      98 .. 0.59
   3 !   17.3   0.0   2.6e-06    0.0039      22      88 ..      71     131 ..      68     192 .] 0.79

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0012
                           Cnd1 28 krLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaalteise 87
                                   k LkD+++ VR +aa ++ k+ +++ v        l ++l D +++V++ a  al +i++
  gi|116754122|ref|YP_843240.1| 15 KNLKDDSSNVRAQAAEALGKIGDPKAV------GPLIDALLDVDASVRSEAAEALGKIKD 68
                                   679999999999999999998887765......467788888888888888888887765 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00012
                           Cnd1 25 pLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaalt 83
                                   pL  +L D d+ VR  aa ++ k      +k+   ++ l ++l+D n+ V+ na  al 
  gi|116754122|ref|YP_843240.1| 43 PLIDALLDVDASVRSEAAEALGK------IKDARAVEPLSRALNDANAIVRWNAAWALG 95
                                   56666666666666666666655......455555556666666666666666666655 PP

  == domain 3  score: 17.3 bits;  conditional E-value: 2.6e-06
                           Cnd1  22 lvepLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaalteisek 88 
                                     vepL ++L+D ++ VR +aa ++  + ++  v      + l   l+D ++ V+ na +al  i + 
  gi|116754122|ref|YP_843240.1|  71 AVEPLSRALNDANAIVRWNAAWALGSIGDPRAV------EALIGVLNDMSQDVRLNAACALGSIGDP 131
                                    589*********************998888766......579999999999********99999776 PP

>> Vac14_Fab1_bd  Vacuolar 14 Fab1-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.076   1.1e+02      29      52 ..      10      33 ..       7      39 .. 0.85
   2 ?    4.3   0.0     0.042        63      29      54 ..      41      66 ..      37      71 .. 0.84
   3 ?    1.5   0.0       0.3   4.5e+02      29      51 ..      72      94 ..      65     115 .. 0.83
   4 ?    0.0   0.0      0.88   1.3e+03      29      49 ..     103     123 ..      93     131 .. 0.73
   5 !    8.6   0.0    0.0019       2.9      29      51 ..     134     156 ..     129     189 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.076
                  Vac14_Fab1_bd 29 vkpvlkcfsDkdsrvRyyacEsly 52
                                   v++ +k ++D++s vR  a+E+l 
  gi|116754122|ref|YP_843240.1| 10 VEMYIKNLKDDSSNVRAQAAEALG 33
                                   56678899*************995 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.042
                  Vac14_Fab1_bd 29 vkpvlkcfsDkdsrvRyyacEslyni 54
                                   v p+++++ D d+ vR  a+E+l  i
  gi|116754122|ref|YP_843240.1| 41 VGPLIDALLDVDASVRSEAAEALGKI 66
                                   77899999999999*99999999665 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.3
                  Vac14_Fab1_bd 29 vkpvlkcfsDkdsrvRyyacEsl 51
                                   v+p+ ++++D+++ vR+ a+ +l
  gi|116754122|ref|YP_843240.1| 72 VEPLSRALNDANAIVRWNAAWAL 94
                                   7899999**********998777 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 0.88
                  Vac14_Fab1_bd  29 vkpvlkcfsDkdsrvRyyacE 49 
                                    v+ ++ +++D ++ vR  a+ 
  gi|116754122|ref|YP_843240.1| 103 VEALIGVLNDMSQDVRLNAAC 123
                                    556666777777777776655 PP

  == domain 5  score: 8.6 bits;  conditional E-value: 0.0019
                  Vac14_Fab1_bd  29 vkpvlkcfsDkdsrvRyyacEsl 51 
                                    v+p+l +++D++ +vRy+++ +l
  gi|116754122|ref|YP_843240.1| 134 VDPLLPMLKDTSWKVRYHVTRAL 156
                                    899***************99988 PP

>> ERAP1_C  ERAP1-like C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0025       3.8     182     235 ..      10      63 ..       3      66 .. 0.80
   2 !   13.5   0.0   2.6e-05     0.039     107     222 ..      72     172 ..      59     186 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0025
                                    HHHHHHHHHC-SSHHHHHHHHHHHCC-S-HHHHHHHHHHCTT.T..S-GGGHHHH CS
                        ERAP1_C 182 wdallerykdtsapsekeaalralaatpdpellerllnfvle.sdevrnqdlral 235
                                    ++  ++  kd s+ + + +a++al+ + dp+++  l++ +l+ + +vr++ ++al
  gi|116754122|ref|YP_843240.1|  10 VEMYIKNLKDDSS-NVRAQAAEALGKIGDPKAVGPLIDALLDvDASVRSEAAEAL 63 
                                    5555666667777.99************************955888999887765 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 2.6e-05
                                    HHHHHHHHHHT.TTS-HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHCSTT-S-HHHHHHHHHHHHHHS-HHHHHHHH CS
                        ERAP1_C 107 leplaeklgwepgeshldaqlrslllsaacaagdpevveearklfkawlegddlippdlrwavycalaanggeaewdall 186
                                    +epl ++l+ +      +a +r ++  a+++ gdp++ve++   +++        ++d+r  + cal + g++  +d ll
  gi|116754122|ref|YP_843240.1|  72 VEPLSRALN-D-----ANAIVRWNAAWALGSIGDPRAVEALIGVLNDM-------SQDVRLNAACALGSIGDPRAVDPLL 138
                                    555555554.2.....5678888888889999***9999999888877.......58**********888********** PP

                                    HHHHC-SSHHHHHHHHHHHCC-S-HHHHHHHHHHCT CS
                        ERAP1_C 187 erykdtsapsekeaalralaatpdpellerllnfvl 222
                                     + kdts    + ++ ral+ + dp ++   l+ ++
  gi|116754122|ref|YP_843240.1| 139 PMLKDTSW-KVRYHVTRALGLIGDPRIIDH-LESIS 172
                                    *9999999.99****************999.77774 PP

>> Adaptin_N  Adaptin N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   1.3e-05     0.019      82     182 ..      11      99 ..       9     107 .. 0.83
   2 !    8.6   0.0   0.00041      0.62      84     179 ..      75     159 ..      70     190 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.3e-05
                                    HHHHHHCCSSSHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHT-SSHHHHHHHHHHHHHCCCCCHHCCCCCHHHHHHHCT CS
                      Adaptin_N  82 nslqkDlkdpnqlirglALrvLssirvpelaedlapaikkllkdrspyvrkkAalailklykkdpdllrkqlveeikell 161
                                     ++ k lkd ++++r+ A  +L++i++p+ +  l +    +l d +++vr++Aa a+ k+    +d+  +  ve +  +l
  gi|116754122|ref|YP_843240.1|  11 EMYIKNLKDDSSNVRAQAAEALGKIGDPKAVGPLID----ALLDVDASVRSEAAEALGKI----KDA--RA-VEPLSRAL 79 
                                    68899***********************98877665....56788***********9998....344..33.7779999* PP

                                    T-SSHHHHHHHHHHHHHHHCC CS
                      Adaptin_N 162 sdkdpgvvlaAvalleeikkn 182
                                    +d + +v  +A  +l +i   
  gi|116754122|ref|YP_843240.1|  80 NDANAIVRWNAAWALGSI-GD 99 
                                    *******99999999888.43 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00041
                                    HHHHCCSSSHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHT-SSHHHHHHHHHHHHHCCCCCHHCCCCCHHHHHHHCTT- CS
                      Adaptin_N  84 lqkDlkdpnqlirglALrvLssirvpelaedlapaikkllkdrspyvrkkAalailklykkdpdllrkqlveeikellsd 163
                                    l ++l+d n ++r +A  +L+si++p+ +e+l      +l+d+s  vr +Aa+a+  +   dp +     v+ +   l+d
  gi|116754122|ref|YP_843240.1|  75 LSRALNDANAIVRWNAAWALGSIGDPRAVEAL----IGVLNDMSQDVRLNAACALGSIG--DPRA-----VDPLLPMLKD 143
                                    7899*********************9987765....56889999999999999987663..3333.....4445556666 PP

                                    SSHHHHHHHHHHHHHH CS
                      Adaptin_N 164 kdpgvvlaAvalleei 179
                                    ++ +v ++++ +l  i
  gi|116754122|ref|YP_843240.1| 144 TSWKVRYHVTRALGLI 159
                                    6666666666666555 PP

>> Aconitase_B_N  Aconitate B N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.1   0.00011      0.17      80     120 ..      25      65 ..      11      86 .. 0.89
   2 ?    2.3   0.0       0.1   1.6e+02      76     118 ..      83     125 ..      66     128 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                  Aconitase_B_N  80 peeAvelLgtMlGGynvksLidllkekdeelaeeaaeaLkk 120
                                    +++A e Lg++    +v +Lid+l + d+++++eaaeaL k
  gi|116754122|ref|YP_843240.1|  25 RAQAAEALGKIGDPKAVGPLIDALLDVDASVRSEAAEALGK 65 
                                    56899*********************************976 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.1
                  Aconitase_B_N  76 plispeeAvelLgtMlGGynvksLidllkekdeelaeeaaeaL 118
                                    ++i + +A   Lg +    +v++Li +l++ +++++ +aa aL
  gi|116754122|ref|YP_843240.1|  83 NAIVRWNAAWALGSIGDPRAVEALIGVLNDMSQDVRLNAACAL 125
                                    56777778888888888899*********99999999999888 PP

>> RasGEF_N_2  Rapamycin-insensitive companion of mTOR RasGEF_N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0     0.002         3       7      32 ..      10      35 ..       9      41 .. 0.89
   2 ?    1.6   0.0      0.25   3.7e+02       9      36 ..      43      70 ..      40     100 .. 0.75
   3 ?    2.1   0.0      0.16   2.4e+02       7      31 ..     103     127 ..     101     156 .. 0.83
   4 ?   -2.2   0.0       3.5   5.3e+03       7      29 ..     134     156 ..     133     173 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.002
                     RasGEF_N_2  7 iellvnqLydqsrevvaaaleiLeea 32
                                   +e+++++L+d+s++v+a+a+e+L ++
  gi|116754122|ref|YP_843240.1| 10 VEMYIKNLKDDSSNVRAQAAEALGKI 35
                                   79*******************99765 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.25
                     RasGEF_N_2  9 llvnqLydqsrevvaaaleiLeeacddk 36
                                    l++ L d + +v++ a+e+L ++ d +
  gi|116754122|ref|YP_843240.1| 43 PLIDALLDVDASVRSEAAEALGKIKDAR 70
                                   6889999999999999999998885554 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.16
                     RasGEF_N_2   7 iellvnqLydqsrevvaaaleiLee 31 
                                    +e l+  L+d s++v+  a+ +L +
  gi|116754122|ref|YP_843240.1| 103 VEALIGVLNDMSQDVRLNAACALGS 127
                                    678999999******9999998865 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 3.5
                     RasGEF_N_2   7 iellvnqLydqsrevvaaaleiL 29 
                                    ++ l+  L+d s +v+ +  ++L
  gi|116754122|ref|YP_843240.1| 134 VDPLLPMLKDTSWKVRYHVTRAL 156
                                    56778888888888888877776 PP

>> DUF3385  Domain of unknown function (DUF3385)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.42   6.3e+02      20      39 ..      18      36 ..       2      79 .. 0.77
   2 ?    4.0   0.0     0.029        43      12      43 ..     103     136 ..      99     139 .. 0.84
   3 ?    7.7   0.0     0.002         3      15      47 ..     137     166 ..     131     191 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.42
                        DUF3385 20 kteqsqsirrevikllGilG 39
                                   k ++s ++r +++  lG +G
  gi|116754122|ref|YP_843240.1| 18 K-DDSSNVRAQAAEALGKIG 36
                                   4.347888888888888888 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.029
                        DUF3385  12 LelLlnilkteqsqsirrevikllGilG...ALDP 43 
                                    +e L+++l+ ++sq++r++++  lG +G   A+DP
  gi|116754122|ref|YP_843240.1| 103 VEALIGVLN-DMSQDVRLNAACALGSIGdprAVDP 136
                                    567888886.78****************8888887 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.002
                        DUF3385  15 LlnilkteqsqsirrevikllGilGALDPykhk 47 
                                    Ll +lk ++s+++r  v + lG++G  DP    
  gi|116754122|ref|YP_843240.1| 137 LLPMLK-DTSWKVRYHVTRALGLIG--DPRIID 166
                                    566666.77****************..665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 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:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 1394.29
//
Query:       gi|116754123|ref|YP_843241.1|  [L=219]
Description: phosphotransferase domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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-11   43.0   0.1    9.3e-11   42.3   0.1    1.4  1  PHP          PHP domain
    9.6e-06   25.2   0.0    1.8e-05   24.3   0.0    1.7  1  RNase_P_p30  RNase P subunit p30
  ------ inclusion threshold ------
        0.2   11.4   0.0       0.39   10.4   0.0    1.4  1  Pox_VLTF3    Poxvirus Late Transcription Factor VLTF3 like


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 !   42.3   0.1   1.6e-14   9.3e-11       1      82 [.       3      83 ..       3     177 .. 0.77

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 1.6e-14
                                   EEEE--CCC--.S-H..HHHHHHHHHCT-SEEEEEEEEBTT......HHHHHHHHHHHHTTTTSEEEEEEE........... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            PHP  1 dlHvHteyslldgalsieelvkkakelglkaiaiTDhgnlf......gyvefykaakkkykagikpiiGleayvaddseker 76
                                   dlH+Ht +s     l + el+++a++ g+ aiaiTDh+++       g +  +k++++ y   +k+iiG+e++ ++ ++   
  gi|116754123|ref|YP_843241.1|  3 DLHTHTVFSDG--ELIPAELLRRAEASGYTAIAITDHVDFTnvehvvGSMLKVKEMEDAY--SLKVIIGVEITHVPPEK--- 77
                                   799**999944..3336************************9998887777777775556..8********88887765... PP

                                   ...... CS
                                   xxxxxx RF
                            PHP 77 pshltl 82
                                     +l+l
  gi|116754123|ref|YP_843241.1| 78 IERLVL 83
                                   333333 PP

>> RNase_P_p30  RNase P subunit p30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0     3e-09   1.8e-05      11     145 ..      13     144 ..       2     206 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 3e-09
                                    .......HHHHHHHHH-SEEEEEEEEEESS---HHHHH.......HHHHHHHH..HHSSEEEEEEES-H.HHHHHHHHH- CS
                    RNase_P_p30  11 dskkksrtiktlaelgytgvainftveaekekkpnasepikeelkelkkelsglkllsRvtlvvsdpsklqrlskvrqkf 90 
                                    ++  +++++++++++gyt++ai+ +v+  +++    s     ++ +++++ ++lk+  +v+++   p+k++rl  ++++ 
  gi|116754123|ref|YP_843241.1|  13 GELIPAELLRRAEASGYTAIAITDHVDFTNVEHVVGSM----LKVKEMEDAYSLKVIIGVEITHVPPEKIERLVLLSRAL 88 
                                    444566899******************99999999888....55666777799***************997766666654 PP

                                    -..EEEEE--S......HHHHHHHHHT.T-SEEE-TTTTSSS-S--HHHHHHHHHHT-EEEEE CS
                    RNase_P_p30  91 d..llavrPtt......ekalraacenldvDiisidltsrlpfglkhktiraAvergvafEin 145
                                       +++v++ t         +raa+e   vDi+ ++       ++  +++++A+e+ v +Ei+
  gi|116754123|ref|YP_843241.1|  89 GaeIVVVHGETpvepvaPGTNRAAIEA-GVDILAHPG------FIALEEAELARENDVVLEIT 144
                                    333998875552211116789999977.9******99......68999*************96 PP

>> Pox_VLTF3  Poxvirus Late Transcription Factor VLTF3 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   6.5e-05      0.39      54      90 ..      45      81 ..      31      88 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 6.5e-05
                      Pox_VLTF3 54 akvlkiLKelglkklyedvklIleiltgkrpdklssl 90
                                   + v ++LK +++++ y   + I   +t+++p+k+++l
  gi|116754123|ref|YP_843241.1| 45 HVVGSMLKVKEMEDAYSLKVIIGVEITHVPPEKIERL 81
                                   56899*****************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1745.86
//
Query:       gi|116754124|ref|YP_843242.1|  [L=426]
Description: hypothetical protein Mthe_0813 [Methanosaeta thermophila PT]
Scores for 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-59  199.5  24.2      5e-59  199.5  24.2    3.3  4  DUF4010   Domain of unknown function (DUF4010)
    3.8e-15   56.3  14.5    3.8e-15   56.3  14.5    3.5  3  MgtC      MgtC family


Domain annotation for each model (and alignments):
>> DUF4010  Domain of unknown function (DUF4010)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   5.4      0.73   6.5e+03     126     149 ..      39      62 ..       4     106 .. 0.44
   2 ?   -6.3  11.7         2   1.8e+04      75     139 ..      94     158 ..      33     161 .. 0.55
   3 !  199.5  24.2   5.5e-63     5e-59       1     210 []     182     388 ..     182     388 .. 0.94
   4 ?   -3.3   0.3      0.65   5.8e+03      87     104 ..     400     413 ..     394     420 .. 0.44

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 0.73
                        DUF4010 126 ksAlkfallfalilllakaaqeyf 149
                                    ++ + +all al + l+++  ++f
  gi|116754124|ref|YP_843242.1|  39 RTFVLIALLGALAASLSEIFGHLF 62 
                                    333333333333333333322222 PP

  == domain 2  score: -6.3 bits;  conditional E-value: 2
                        DUF4010  75 vavvnpallvalalp...llalallallvaalllrrrekeeeeeelelenPlelksAlkfallfalil 139
                                    va+  + ll al +    +l++++l++lv++ l+ r+ ++     +e  +  el   lk+al+ ++il
  gi|116754124|ref|YP_843242.1|  94 VAAAITFLLGALCYFedsMLLAVALSILVTWTLATRKITHR---YVEAISDTELLDTLKMALVALVIL 158
                                    33222222222222133345545455555555444444444...366778888888899988888886 PP

  == domain 3  score: 199.5 bits;  conditional E-value: 5.5e-63
                        DUF4010   1 VlisaisfagYvalrllgarrGllltgllGGlvSStAvtlslarrskeepelarllaagillAnavmllrvllivavvnp 80 
                                    Vl+s is++gY+++r+lg  rGl ltg+lGG++SStAvt+s+a++++e++++ ++++++++lA+++m++r+lliv+vvn+
  gi|116754124|ref|YP_843242.1| 182 VLVSLISYVGYILIRVLGDDRGLTLTGILGGIISSTAVTMSMASEVRERRQSLASAVFATTLASCTMFPRILLIVMVVNM 261
                                    8******************************************************************************* PP

                        DUF4010  81 allvalalpllalallallvaalllrrrekeeeeeelelenPlelksAlkfallfalilllakaaqeyfGdaglyalaal 160
                                    +l+  l + l+a  ++++ va+++++r++ +  + ++e++ P++l +Alkf++lfa il+++k+a+  +Gdag ya+ ++
  gi|116754124|ref|YP_843242.1| 262 ELVLPLSVQLAA--MAGVGVALAYIHRNNLAPIKGSVEHKDPFRLIPALKFGALFAFILFVTKLASVSLGDAGSYAAGVI 339
                                    ***988666665..4566666666677666666667******************************************** PP

                        DUF4010 161 sGladvdAitlslarlaaegtlsaataalaillavlsntlvKavlalviG 210
                                    sGladvdA++l++a+laa gt++ +ta++ai+la+++nt +K+v+a+++G
  gi|116754124|ref|YP_843242.1| 340 SGLADVDAVVLTMATLAA-GTITGETAVIAITLAAITNTGLKLVIAFLMG 388
                                    *****************8.****************************987 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 0.65
                        DUF4010  87 alpllalallallvaall 104
                                    ++p++a+++++l    ++
  gi|116754124|ref|YP_843242.1| 400 FIPMMAAGIMML----FW 413
                                    344444333333....33 PP

>> MgtC  MgtC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3  14.5   4.2e-19   3.8e-15       2     120 ..      10     134 ..       9     135 .. 0.76
   2 ?   -2.0   4.8       0.5   4.5e+03      28      88 ..     182     245 ..     179     289 .. 0.52
   3 ?   -2.7   7.0      0.79   7.1e+03      52      83 ..     341     375 ..     307     420 .. 0.48

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 4.2e-19
                           MgtC   2 llAlllGlliGleRel...rek...aaGlRTfaLvalgaalfvllslelaesrvaaq...vvsgigflg..agvilkeke 70 
                                    ++++++G+liG+eR++   ++k   +aGlRTf+L+al++al++ l      s ++     v++  gfl   +    + ++
  gi|116754124|ref|YP_843242.1|  10 VMSMIIGALIGIERQRrivENKtrgVAGLRTFVLIALLGALAASL------SEIFGHlfiVIAYAGFLIlvGIGYATASR 83 
                                    79**************555233567********************......44444433345555555532222222333 PP

                           MgtC  71 gakvkglTTaaslwvtaaiGllvglgl.yllavvatvlvllllallreler 120
                                     +   ++T+a+++ +t+++G+l++++  +llav++++lv+ +la  +  +r
  gi|116754124|ref|YP_843242.1|  84 ITGWLDFTSAVAAAITFLLGALCYFEDsMLLAVALSILVTWTLATRKITHR 134
                                    348999*******************85499*************99887776 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.5
                           MgtC  28 aLvalgaalfvllslelae...srvaaqvvsgigflgagvilkekega.kvkglTTaaslwvtaa 88 
                                    +Lv+l++++  +l   l        + +++ gi+  +a ++ + +e + + ++l +a+ + + a 
  gi|116754124|ref|YP_843242.1| 182 VLVSLISYVGYILIRVL-GddrGLTLTGILGGIISSTAVTMSMASEVReRRQSLASAVFATTLAS 245
                                    57777777777772222.22332222334444444444444333332234455555444333332 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 0.79
                           MgtC  52 q......vvsgigflgagvilkekegakvkglTTaasl 83 
                                    +      vv+ ++ l+ag+i  e+   +v  +T aa  
  gi|116754124|ref|YP_843242.1| 341 GladvdaVVLTMATLAAGTITGET---AVIAITLAAIT 375
                                    233333356666666666666222...23333322222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1106  (0.0616878); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); 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):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 3010.42
//
Query:       gi|116754125|ref|YP_843243.1|  [L=294]
Description: hypothetical protein Mthe_0814 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00013   22.1   7.1    0.00013   22.1   7.1    2.6  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 !   22.1   7.1   7.5e-09   0.00013       2     136 ..       6     138 ..       5     139 .. 0.83
   2 !    4.1   7.4    0.0027        48      13     107 ..     158     254 ..     153     262 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 7.5e-09
                           EamA   2 lgillallaalfwaiyfvlskillrkv..spltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlaf 79 
                                    +++llal +++++ ++++l k +l ++  +p  ++  +  +a  +++++a+ + ++   +   d ll + +g    vl  
  gi|116754125|ref|YP_843243.1|   6 SWLLLALFGTVSFTLAGLLDKLILDRYlqEPKVYLLCQV-LAQQVFSLTAFAFIRPE--FVFPDALLAMGIGS-IQVLPT 81 
                                    5889***********************887888888886.56666666666666666..55555555444443.356666 PP

                           EamA  80 llffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                    + f+ a+k+ + s+++ + ++  v++l+ls+ ll e+l  + ++g++lill+ +++ 
  gi|116754125|ref|YP_843243.1|  82 VYFLRAIKEDELSRVTSLEYFYIVLVLFLSASLLDESLPARNYAGAALILLSSIIVA 138
                                    8999***********************************************999875 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0027
                           EamA  13 fwaiyfvlskillrkvspltltfvrfliagillliiallkegkl...aklslkdwllllllgllgtvlafllffyalkkt 89 
                                    + aiy++++k+ll+++  + +  ++++   i++++++   +++       s   + ++l+      +l+++lf+ a  ++
  gi|116754125|ref|YP_843243.1| 158 MNAIYYIAMKYLLCSMGEWDMYIWSSFGNLIAVVPFLRSGGISGlcmMASSAHTICSILVEE-AFQFLGMILFIFAYASG 236
                                    669************************99999999988888888774444444444444444.45566778999999999 PP

                           EamA  90 sasnaslitslePvftli 107
                                    + + +  + +l+P++t i
  gi|116754125|ref|YP_843243.1| 237 PLALVNGVGALQPMMTFI 254
                                    999999999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 2132.70
//
Query:       gi|116754126|ref|YP_843244.1|  [L=1124]
Description: hypothetical protein Mthe_0815 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-23   83.5   3.9    4.5e-23   82.1   3.9    1.6  1  DUF1616          Protein of unknown function (DUF1616)
    5.7e-10   39.8  29.2       0.25   12.2   0.1    8.5  9  Big_7            Bacterial Ig domain
    1.1e-08   35.0   8.2        2.7    8.1   0.0    7.2  7  BiPBP_C          Penicillin-Binding Protein C-terminus Family
    4.3e-08   33.1   0.0        2.8    8.0   0.0    5.9  6  CE2_N            Carbohydrate esterase 2 N-terminal
      1e-05   25.8   1.2          3    8.3   0.0    6.0  7  DUF4399          Domain of unknown function (DUF4399)
    3.1e-05   23.9   0.0      0.089   12.6   0.0    3.5  3  Bac_rhamnosid_N  Alpha-L-rhamnosidase N-terminal domain
    0.00023   21.0   0.0        0.3   11.1   0.0    3.8  4  Y_Y_Y            Y_Y_Y domain
     0.0032   17.7   2.0      0.008   16.4   2.0    1.6  1  DUF755           Domain of unknown function (DUF755)
  ------ inclusion threshold ------
      0.067   12.7   0.0         13    5.4   0.0    3.6  3  TcfC             E-set like domain


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 !   82.1   3.9   2.3e-26   4.5e-23      37     273 ..      20     220 ..       8     236 .. 0.81

  Alignments for each domain:
  == domain 1  score: 82.1 bits;  conditional E-value: 2.3e-26
                        DUF1616  37 YaliaaLFPekrdidgi.eRlaLSfglSiaivpliglvlnvtpwgirlepilvslslftlllalvAivrRsrlpeeerfs 115
                                    Yali+a+FPek+ +  i  R++LS+g+ +++   + +     ++g+   p l ++++++l+l+++A +rR ++p+ +rfs
  gi|116754126|ref|YP_843244.1|  20 YALISAVFPEKEPLGSIfHRIILSIGVTLVVSL-AEV-----ALGMGEFPAL-IVAILVLILVVLAHIRRGAVPRRRRFS 92 
                                    **************77659*******9887653.333.....4466667755.5799999******************** PP

                        DUF1616 116 vplral.ieslkeeleeksesrldkalnvlLvvsivlavaalgyavvaPkegekfTelyllgedgdelvaenypteltag 194
                                    v+  ++ ++s +++l++       k++  +++v +++a+ ++gy+ v+  ++e+fTe+y++g              ++++
  gi|116754126|ref|YP_843244.1|  93 VHTYRYaLRSNRRSLPQ-------KIV-PAIIVLLIVAAISFGYVTVKSDRQEGFTEFYVTGLS------------INSN 152
                                    *5433325555555444.......444.4556667788889********************977............4677 PP

                        DUF1616 195 esqevivgieNhEheevnYtvvvllqevtdeeevevlerteldrrevtladnetweqelevepea.tgenlrleflLYkd 273
                                     + + +vg+ NhE+ e nYt+ v ++              +  +r ++lad+ + e++le  +++ tge   l +lLY++
  gi|116754126|ref|YP_843244.1| 153 GNATATVGVINHEGVEANYTIDVEMNG------------VRAAQRYAHLADGGAYEETLEWGIPMhTGELCTLRILLYRN 220
                                    88999********************96............5678999*******************9************97 PP

>> Big_7  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.4       2.3   4.5e+03      35      70 .]     141     175 ..     140     175 .. 0.76
   2 ?   -3.7   0.6         9   1.8e+04       1      26 [.     241     265 ..     241     271 .. 0.66
   3 !    8.9   0.1    0.0012       2.5      16      70 .]     444     496 ..     428     496 .. 0.76
   4 ?    1.5   0.0      0.26   5.2e+02      36      70 .]     560     592 ..     529     592 .. 0.71
   5 !    8.4   0.2    0.0018       3.6      16      70 .]     636     689 ..     620     689 .. 0.78
   6 !    9.7   0.0   0.00071       1.4      14      70 .]     728     784 ..     721     784 .. 0.86
   7 !   11.9   0.2   0.00015      0.29      17      70 .]     828     880 ..     818     880 .. 0.80
   8 ?    2.9   0.0     0.095   1.9e+02      35      70 .]     946     977 ..     921     977 .. 0.72
   9 !   12.2   0.1   0.00012      0.25      35      70 .]    1042    1075 ..    1022    1075 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.3
                                    EEEETTEE.EEEE-SSSEEEEEE--...SEEEEEEE CS
                          Big_7  35 efyvdgtlglgtdtsapysltwtttaltagthtltV 70 
                                    efyv g + ++++ +a+ ++ +    + + ++t+ V
  gi|116754126|ref|YP_843244.1| 141 EFYVTGLS-INSNGNATATVGVINHEGVEANYTIDV 175
                                    79999999.999988888887777766677777765 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 9
                                    XEEEEEE--TT--EBTSEEEEEEEEE CS
                          Big_7   1 PtvtitsPangatvsggtvtisasAs 26 
                                    P+ +++   + ++v+ +t +++a A 
  gi|116754126|ref|YP_843244.1| 241 PVANMSESGDAQQVN-TTSNVTAVAK 265
                                    566666667777888.6666666664 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0012
                                    TSEEEEEEEEE-S.S-EEEEEEEETTEE.EEEE-SSSEEEEEE--...SEEEEEEE CS
                          Big_7  16 ggtvtisasAsdd.ggvskVefyvdgtlglgtdtsapysltwtttaltagthtltV 70 
                                    g+tv  s+ As + +g  +  f+++g + +++ +s+p s+tw t+  +ag++++++
  gi|116754126|ref|YP_843244.1| 444 GTTVVWSVRASTHaDGL-SYRFFLNGRP-ITSWSSSP-SWTWYTSGIPAGEYNVSA 496
                                    56777777777774444.4589******.*9997766.9**************986 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.26
                                    EEETTEE.EEEE-SSSEEEEEE--...SEEEEEEE CS
                          Big_7  36 fyvdgtlglgtdtsapysltwtttaltagthtltV 70 
                                    f+vdg + +  d s    ++ +t+al+ g+ht++V
  gi|116754126|ref|YP_843244.1| 560 FSVDGLT-V-RDWSRSGIFEMNTSALAPGNHTVRV 592
                                    5555555.4.333444557788999********98 PP

  == domain 5  score: 8.4 bits;  conditional E-value: 0.0018
                                    TSEEEEEEEEE-S.S-EEEEEEEETTEE.EEEE-SSSEEEEEE--...SEEEEEEE CS
                          Big_7  16 ggtvtisasAsdd.ggvskVefyvdgtlglgtdtsapysltwtttaltagthtltV 70 
                                    g+ +t +asA d+ +      f+vd++  ++  +++  ++ w+t+ +++g+h ++V
  gi|116754126|ref|YP_843244.1| 636 GSVITWTASADDPdNDTLLYRFFVDDVA-VSGWSTN-PQFVWNTSGYSDGEHRVSV 689
                                    6677888888888666666799*****9.9888665.589*************998 PP

  == domain 6  score: 9.7 bits;  conditional E-value: 0.00071
                                    EB.TSEEEEEEEEE-S.S-EEEEEEEETTEE.EEEE-SSSEEEEEE--...SEEEEEEE CS
                          Big_7  14 vs.ggtvtisasAsdd.ggvskVefyvdgtlglgtdtsapysltwtttaltagthtltV 70 
                                     + g+ +t sa A+d+ +   +  f+vdg+  + +d s+   ++++t+ l+ g+htl+V
  gi|116754126|ref|YP_843244.1| 728 QPvGSRITWSALAEDPdNDPIQYRFFVDGVA-V-SDWSSSAVFELDTSGLSPGNHTLSV 784
                                    55578899999999999999999********.8.67789999***************98 PP

  == domain 7  score: 11.9 bits;  conditional E-value: 0.00015
                                    SEEEEEEEEE-S.S-EEEEEEEETTEE.EEEE-SSSEEEEEE--...SEEEEEEE CS
                          Big_7  17 gtvtisasAsdd.ggvskVefyvdgtlglgtdtsapysltwtttaltagthtltV 70 
                                    + +t +asA d+ +      f+++g   + td s   s++w+t+ l+ag+ht+ V
  gi|116754126|ref|YP_843244.1| 828 SVITWTASADDPdNDTLLYRFSLNGRA-V-TDWSPSGSWSWNTSGLSAGEHTVGV 880
                                    556677777777655556689999999.7.78899*****************965 PP

  == domain 8  score: 2.9 bits;  conditional E-value: 0.095
                                    EEEETTEE.EEEE-SSSEEEEEE--...SEEEEEEE CS
                          Big_7  35 efyvdgtlglgtdtsapysltwtttaltagthtltV 70 
                                     f+vdg   + +d s++ ++t++t+  ++g h++t+
  gi|116754126|ref|YP_843244.1| 946 RFFVDGAA-V-SDWSGTERWTLSTS--EEGRHSITA 977
                                    68899998.7.55566667777776..9******97 PP

  == domain 9  score: 12.2 bits;  conditional E-value: 0.00012
                                     EEEETTEE.EEEE-SSSEEEEEE--...SEEEEEEE CS
                          Big_7   35 efyvdgtlglgtdtsapysltwtttaltagthtltV 70  
                                      f vdg++  +td s+   +tw+t  ++ag h++t+
  gi|116754126|ref|YP_843244.1| 1042 RFLVDGSP--ATDWSSSSKFTWNTVGVAAGDHNITA 1075
                                     699*****..799999******************97 PP

>> BiPBP_C  Penicillin-Binding Protein C-terminus Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0    0.0033       6.6      33      68 ..     445     484 ..     413     497 .. 0.68
   2 ?    1.4   0.0      0.16   3.2e+02      17      77 ..     522     592 ..     517     598 .. 0.66
   3 ?    1.0   0.0      0.21   4.3e+02      45      77 ..     654     689 ..     615     694 .. 0.81
   4 !    8.1   0.0    0.0014       2.7      35      82 ..     734     789 ..     714     794 .. 0.78
   5 ?    3.2   0.1     0.047        94      45      85 ..     845     888 ..     809     893 .. 0.80
   6 !    5.6   0.0    0.0083        17      45      77 ..     944     977 ..     906     982 .. 0.81
   7 !    5.5   0.0    0.0086        17      44      81 ..    1036    1079 ..    1013    1083 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0033
                        BiPBP_C  33 qrlqlkargg.ea...plrWlldgeplaetkrgrelawqp 68 
                                      ++ ++r++ +a   ++r++l+g+p+++ +++ +++w  
  gi|116754126|ref|YP_843244.1| 445 TTVVWSVRAStHAdglSYRFFLNGRPITSWSSSPSWTWYT 484
                                    3445555666333789***********9999998888865 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.16
                        BiPBP_C  17 PadGailaldpdipkrq..rlqlkarggea......plrWlldgeplaetkrgrelawqp...epGrhrLtv 77 
                                    P+d + +  dp+ p++q  ++  +a+++ +       +r+ +dg  ++  +r+  +++      pG+h+++v
  gi|116754126|ref|YP_843244.1| 522 PPDLTAVISDPEGPQPQgtQIRWSAAAS-DeendtlLYRFSVDGLTVRDWSRSGIFEMNTsalAPGNHTVRV 592
                                    6666777777777755501444555555.23588777888889999966666555555447799*****998 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.21
                        BiPBP_C  45 plrWlldgeplaetkrgrelawqp...epGrhrLtv 77 
                                     +r+++d++ +   +++ ++ w     + G+hr++v
  gi|116754126|ref|YP_843244.1| 654 LYRFFVDDVAVSGWSTNPQFVWNTsgySDGEHRVSV 689
                                    578999*****99999999999999999******99 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.0014
                        BiPBP_C  35 lqlkarggea.....plrWlldgeplaetkrgrelawqp...epGrhrLtvvDaaG 82 
                                    ++ +a + ++     ++r+++dg+ +   ++++ ++++    +pG+h+L+v+  +G
  gi|116754126|ref|YP_843244.1| 734 ITWSALAEDPdndpiQYRFFVDGVAVSDWSSSAVFELDTsglSPGNHTLSVHVRDG 789
                                    55555555334667899*********8888888888988999*********87666 PP

  == domain 5  score: 3.2 bits;  conditional E-value: 0.047
                        BiPBP_C  45 plrWlldgeplaetkrgrelawqp...epGrhrLtvvDaaGrvd 85 
                                     +r+ l+g+ ++  +++ +++w     + G+h++ v   +Gr +
  gi|116754126|ref|YP_843244.1| 845 LYRFSLNGRAVTDWSPSGSWSWNTsglSAGEHTVGVWVRDGRHA 888
                                    467789*****************9999*******9988888866 PP

  == domain 6  score: 5.6 bits;  conditional E-value: 0.0083
                        BiPBP_C  45 plrWlldgeplaetkrgrelawqp.epGrhrLtv 77 
                                     +r+++dg+ +   +  ++++++  e+Grh++t+
  gi|116754126|ref|YP_843244.1| 944 LYRFFVDGAAVSDWSGTERWTLSTsEEGRHSITA 977
                                    67999******88888888888889*******96 PP

  == domain 7  score: 5.5 bits;  conditional E-value: 0.0086
                        BiPBP_C   44 a...plrWlldgeplaetkrgrelawqp...epGrhrLtvvDaa 81  
                                     +    +r+l+dg+p +  +++++++w       G h +t++  +
  gi|116754126|ref|YP_843244.1| 1036 NdplMYRFLVDGSPATDWSSSSKFTWNTvgvAAGDHNITAQVMD 1079
                                     15567899********************9999******985444 PP

>> CE2_N  Carbohydrate esterase 2 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.0    0.0061        12      28      85 ..     539     595 ..     536     602 .. 0.77
   2 ?    0.5   0.0      0.29   5.8e+02      40      83 ..     649     690 ..     640     710 .. 0.78
   3 !    5.9   0.0    0.0062        12      39      85 ..     743     787 ..     733     794 .. 0.83
   4 !    8.0   0.0    0.0014       2.8      40      98 ..     840     896 ..     830     905 .. 0.83
   5 ?    3.6   0.0     0.033        65      46     110 .]     945    1006 ..     932    1006 .. 0.77
   6 ?   -2.1   0.0       1.8   3.6e+03      45      80 ..    1040    1073 ..    1028    1079 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0061
                                    EEEEEEEEEE...SSS-EEEEEEETTS--EEEEE-SS-EEEEEEEEEEEEEEEEEEEE- CS
                          CE2_N  28 Gtslsvrlkd.kedkgknrlaviiDgkrvkdlkldgeektytlaeglepgehtvrlvkr 85 
                                    Gt+++ +++   e++++  +++++Dg +v+d++ +g  + ++  ++l+pg+htvr+  r
  gi|116754126|ref|YP_843244.1| 539 GTQIRWSAAAsDEENDTLLYRFSVDGLTVRDWSRSGIFE-MN-TSALAPGNHTVRVDVR 595
                                    555555544434778888899***********8888888.44.479*********9655 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.29
                                    SSS-EEEEEEETTS--EEEEE-SS-EEEEEEEEEEEEEEEEEEE CS
                          CE2_N  40 dkgknrlaviiDgkrvkdlkldgeektytlaeglepgehtvrlv 83 
                                    d+++  +++++D+ +v+ +  +++ + ++  +g ++geh+v ++
  gi|116754126|ref|YP_843244.1| 649 DNDTLLYRFFVDDVAVSGW--STNPQFVWNTSGYSDGEHRVSVL 690
                                    5566668899999998887..45555689999********9874 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.0062
                                    .SSS-EEEEEEETTS--EEEEE-SS-EEEEEEEEEEEEEEEEEEEE- CS
                          CE2_N  39 edkgknrlaviiDgkrvkdlkldgeektytlaeglepgehtvrlvkr 85 
                                     d++  ++++++Dg +v+d++ ++  + +++ +gl+pg+ht+ +  r
  gi|116754126|ref|YP_843244.1| 743 PDNDPIQYRFFVDGVAVSDWSSSAVFE-LDT-SGLSPGNHTLSVHVR 787
                                    5788899*************8877777.666.9*********99876 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.0014
                                    SSS-EEEEEEETTS--EEEEE-SS-EEEEEEEEEEEEEEEEEEEE-S-GGG--EEEEEE CS
                          CE2_N  40 dkgknrlaviiDgkrvkdlkldgeektytlaeglepgehtvrlvkrtEaeagkteflgf 98 
                                    d+++  ++++++g++v+d++ +g+ +  +  +gl++gehtv +  r    ag+++f   
  gi|116754126|ref|YP_843244.1| 840 DNDTLLYRFSLNGRAVTDWSPSGSWS--WNTSGLSAGEHTVGVWVRDGRHAGAVGFDSA 896
                                    56666788999*******99888888..7779*****************9999999854 PP

  == domain 5  score: 3.6 bits;  conditional E-value: 0.033
                                     EEEEETTS--EEEEE-SS-EEEEEEEEEEEEEEEEEE.EE-S-GGG--EEEEEEEEE.EEEE-S-- CS
                          CE2_N   46 laviiDgkrvkdlkldgeektytlaeglepgehtvrl.vkrtEaeagkteflgfvldeggkllppP 110 
                                     +++++Dg++v+d+  +g+e+  ++++ +e+g+h+++  v+ t  e+ +    +f+++++ ++ +pP
  gi|116754126|ref|YP_843244.1|  945 YRFFVDGAAVSDW--SGTER--WTLSTSEEGRHSITAaVRDTSHETVQSITSEFAVESKMTVNQPP 1006
                                     6789*****9998..67777..7779999******9834445556666667778888777777776 PP

  == domain 6  score: -2.1 bits;  conditional E-value: 1.8
                                     EEEEEETTS--EEEEE-SS-EEEEEEEEEEEEEEEE CS
                          CE2_N   45 rlaviiDgkrvkdlkldgeektytlaeglepgehtv 80  
                                      +++++Dg++++d++ +++ +  t   g ++g h++
  gi|116754126|ref|YP_843244.1| 1040 MYRFLVDGSPATDWSSSSKFTWNT--VGVAAGDHNI 1073
                                     578899999999997766655333..3556666655 PP

>> DUF4399  Domain of unknown function (DUF4399)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       5.3   1.1e+04       3      50 ..     142     192 ..     141     202 .. 0.53
   2 ?    4.5   0.0     0.023        46      57      87 ..     582     612 ..     574     615 .. 0.79
   3 ?    1.5   0.0       0.2     4e+02      60      79 ..     682     701 ..     677     708 .. 0.88
   4 !    8.3   0.0    0.0015         3      58      80 ..     775     797 ..     769     806 .. 0.87
   5 ?   -0.6   0.0      0.88   1.7e+03      58      76 ..     871     889 ..     867     899 .. 0.88
   6 ?    1.7   0.0      0.17   3.4e+02      58      83 ..     968     992 ..     958     999 .. 0.81
   7 ?    0.4   0.0      0.44   8.7e+02      55      73 ..    1063    1081 ..    1059    1092 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 5.3
                        DUF4399   3 fglegmgvapageetentG...hhhllvdeeapeagepipaddqvlHfgkg 50 
                                    f ++g+ ++  g++t++ G   h  +  + +   + + + a +++ H+ +g
  gi|116754126|ref|YP_843244.1| 142 FYVTGLSINSNGNATATVGvinHEGVEANYTIDVEMNGVRAAQRYAHLADG 192
                                    667777777777777777722122222223333334445555777777665 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.023
                        DUF4399  57 elppGkhtLqlqlgdaahvplkpsvlskkit 87 
                                     l pG+ht+++ + d+ h +   + + + ++
  gi|116754126|ref|YP_843244.1| 582 ALAPGNHTVRVDVRDGLHSAEYDDAIEQVVE 612
                                    699***************9866555666555 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.2
                        DUF4399  60 pGkhtLqlqlgdaahvplkp 79 
                                     G+h++ +++ d++h+ ++ 
  gi|116754126|ref|YP_843244.1| 682 DGEHRVSVLVKDKHHEDHDR 701
                                    7***************9985 PP

  == domain 4  score: 8.3 bits;  conditional E-value: 0.0015
                        DUF4399  58 lppGkhtLqlqlgdaahvplkps 80 
                                    l+pG+htL + + d++h  ++ +
  gi|116754126|ref|YP_843244.1| 775 LSPGNHTLSVHVRDGMHADHDDE 797
                                    89****************99865 PP

  == domain 5  score: -0.6 bits;  conditional E-value: 0.88
                        DUF4399  58 lppGkhtLqlqlgdaahvp 76 
                                    l++G+ht+ + + d++h  
  gi|116754126|ref|YP_843244.1| 871 LSAGEHTVGVWVRDGRHAG 889
                                    899************9975 PP

  == domain 6  score: 1.7 bits;  conditional E-value: 0.17
                        DUF4399  58 lppGkhtLqlqlgdaahvplkpsvls 83 
                                     + G+h ++  + d++h+ ++ s++s
  gi|116754126|ref|YP_843244.1| 968 SEEGRHSITAAVRDTSHETVQ-SITS 992
                                    578***************998.6555 PP

  == domain 7  score: 0.4 bits;  conditional E-value: 0.44
                        DUF4399   55 elelppGkhtLqlqlgdaa 73  
                                     ++   +G+h+++ q++d++
  gi|116754126|ref|YP_843244.1| 1063 TVGVAAGDHNITAQVMDGS 1081
                                     677889***********86 PP

>> Bac_rhamnosid_N  Alpha-L-rhamnosidase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   4.5e-05     0.089       6      54 ..     453     500 ..     450     505 .. 0.86
   2 ?   -4.0   0.0       5.5   1.1e+04      49      72 ..     772     795 ..     772     810 .. 0.78
   3 !    6.7   0.0    0.0029       5.8      49      82 ..     868     901 ..     844     913 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.5e-05
                                    EEEEEEEESEEEEEETTEE-SSBSSBT----TTTEEEEEEEE-TTT--S CS
                Bac_rhamnosid_N   6 arlyitaLGvyelelNGkrvgdevLaPgwtdyrkrvqyqtyDvtsllre 54 
                                    a  ++ +L  y+++lNG++++  + +P wt y + +    y+v+  +r 
  gi|116754126|ref|YP_843244.1| 453 ASTHADGL-SYRFFLNGRPITSWSSSPSWTWYTSGIPAGEYNVSACVRG 500
                                    55566666.49*********************************99875 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 5.5
                                    TTT--SEEEEEEEEEE-HHHHS-- CS
                Bac_rhamnosid_N  49 tsllregeNaigvlvgeGwyagrv 72 
                                    ts l+ g+ ++ v+v +G+ a + 
  gi|116754126|ref|YP_843244.1| 772 TSGLSPGNHTLSVHVRDGMHADHD 795
                                    567888999999999999988654 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0029
                                    TTT--SEEEEEEEEEE-HHHHS--TTS...S-SS CS
                Bac_rhamnosid_N  49 tsllregeNaigvlvgeGwyagrvgfgekrrsty 82 
                                    ts l+ ge ++gv+v +G  ag vgf++ ++s++
  gi|116754126|ref|YP_843244.1| 868 TSGLSAGEHTVGVWVRDGRHAGAVGFDSAQTSKF 901
                                    778999********************97776655 PP

>> Y_Y_Y  Y_Y_Y domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00015       0.3       4      61 ..     552     608 ..     549     613 .. 0.89
   2 ?    5.2   0.0     0.011        21       8      60 ..     748     799 ..     743     804 .. 0.83
   3 ?   -2.7   0.0         3   5.9e+03       6      46 ..     842     881 ..     840     885 .. 0.52
   4 ?   -3.2   0.0       4.3   8.5e+03      20      52 ..    1052    1082 ..    1039    1092 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00015
                                    CCTTEEEEEEEETTE.SSEEEESSTS.EEEEES--SEEEEEEEEEEETTS-B-SS-EEE CS
                          Y_Y_Y   4 nperllYrYrlegid.keWveasdysqeasytnlppGdYtlkVkakdndgqwnyditsl 61 
                                     ++ llYr+ ++g+   +W+ ++ +  e + + l pG+ t++V ++d + + +yd++  
  gi|116754126|ref|YP_843244.1| 552 ENDTLLYRFSVDGLTvRDWSRSGIF--EMNTSALAPGNHTVRVDVRDGLHSAEYDDAIE 608
                                    567899********999********..9***************************9654 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.011
                                    EEEEEEEETTE.SSEEEESSTS.EEEEES--SEEEEEEEEEEETTS-B-SS-EE CS
                          Y_Y_Y   8 llYrYrlegid.keWveasdysqeasytnlppGdYtlkVkakdndgqwnydits 60 
                                    ++Yr+ ++g+   +W+++  +  e+  + l+pG+ tl V ++d      +d+++
  gi|116754126|ref|YP_843244.1| 748 IQYRFFVDGVAvSDWSSSAVF--ELDTSGLSPGNHTLSVHVRDGMHADHDDEKE 799
                                    789998888888888888888..9*******************88877777654 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 3
                                    TTEEEEEEEETTE.SSEEEESSTS.EEEEES--SEEEEEEEE CS
                          Y_Y_Y   6 erllYrYrlegid.keWveasdysqeasytnlppGdYtlkVk 46 
                                    + llYr+ l g    +W+ +++   + + + l++G+ t+ V 
  gi|116754126|ref|YP_843244.1| 842 DTLLYRFSLNGRAvTDWSPSGSW--SWNTSGLSAGEHTVGVW 881
                                    66788887766543334333332..44445555555555555 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 4.3
                                     SEEEESSTS.EEEEES--SEEEEEEEEEEETTS CS
                          Y_Y_Y   20 eWveasdysqeasytnlppGdYtlkVkakdndg 52  
                                     +W+++s++  + +     +Gd  ++++++d ++
  gi|116754126|ref|YP_843244.1| 1052 DWSSSSKF--TWNTVGVAAGDHNITAQVMDGSS 1082
                                     34443333..23333345666666666666655 PP

>> DUF755  Domain of unknown function (DUF755)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   2.0     4e-06     0.008      43     119 ..     222     303 ..     218     308 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4e-06
                         DUF755  43 qLlkEcqktsqLiqlsqqlqqkk...qkkrkeqkkssqthkkkkkksrnvssrsakkksakkr....kksssSSssssss 115
                                    ++lk++qkt ++   + ++  ++   ++  ++ +++s+ +   k+ s+++s rs+   sa +r    +    S sssss 
  gi|116754126|ref|YP_843244.1| 222 EMLKDYQKTLRISDYITEAPVANmseSGDAQQVNTTSNVTAVAKNISQDTSLRSTPVASATRRvssgS--GGSGSSSSSG 299
                                    78*************99996666666777888888999999999999999999999999999954321..1122222222 PP

                         DUF755 116 ssss 119
                                    ssss
  gi|116754126|ref|YP_843244.1| 300 SSSS 303
                                    2222 PP

>> TcfC  E-set like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0       0.2     4e+02      38      56 ..     484     502 ..     483     508 .. 0.85
   2 ?    5.4   0.0    0.0065        13      31      54 ..     573     596 ..     564     601 .. 0.89
   3 ?    1.0   0.0      0.15   3.1e+02      35      55 ..     769     789 ..     767     801 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.2
                           TcfC  38 tssLPsGiYeveirvyeng 56 
                                    ts  P G Y+v   v++++
  gi|116754126|ref|YP_843244.1| 484 TSGIPAGEYNVSACVRGSN 502
                                    8999*******98888754 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0065
                           TcfC  31 aGnqeidtssLPsGiYeveirvye 54 
                                     G+ e++ts+L+ G+ +v++ v++
  gi|116754126|ref|YP_843244.1| 573 SGIFEMNTSALAPGNHTVRVDVRD 596
                                    68999***************9987 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.15
                           TcfC  35 eidtssLPsGiYeveirvyen 55 
                                    e+dts L  G+ ++ + v+++
  gi|116754126|ref|YP_843244.1| 769 ELDTSGLSPGNHTLSVHVRDG 789
                                    79**************99874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       769  (0.0428914); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.82u 0.30s 00:00:01.11 Elapsed: 00:00:00.45
# Mc/sec: 7464.88
//
Query:       gi|116754127|ref|YP_843245.1|  [L=304]
Description: hypothetical protein Mthe_0816 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0014   18.5   0.0      0.039   13.9   0.0    2.2  2  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 !   13.9   0.0   2.2e-06     0.039      47      99 ..      62     113 ..      42     128 .. 0.81
   2 !    2.2   0.0    0.0095   1.7e+02      24      60 ..     142     181 ..     131     207 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.2e-06
                        DUF5643  47 sldfevvDdkGnelegisgggsgtgkkefeyeitfepldenpksLtikPylik 99 
                                    ++ fevvD++ n +    + + + + ++f+  + + p+++++ +Lt++P   +
  gi|116754127|ref|YP_843245.1|  62 NVTFEVVDQNNNTYPVDINHSRALQPGRFSLVFML-PMSSDAAYLTVIPEGSN 113
                                    678************97776666666888888887.*************8765 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.0095
                        DUF5643  24 itPlstrisysgdvenskeikek...sldfevvDdkGnel 60 
                                    ++ +s +is+ ++ +n+ ++ e+     +f +vD+ G ++
  gi|116754127|ref|YP_843245.1| 142 LSNTSQTISVDISLSNNATEGEIvmsPENFTLVDQWGWRY 181
                                    677888888866666665555555544559****999776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); 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 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2271.21
//
Query:       gi|116754128|ref|YP_843246.1|  [L=404]
Description: phosphoglycerate kinase [Methanosaeta thermophila PT]
Scores for complete 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-110  369.6   0.1   1.9e-110  369.4   0.1    1.0  1  PGK       Phosphoglycerate kinase


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 !  369.4   0.1  1.1e-114  1.9e-110       1     377 [.       7     385 ..       7     386 .. 0.92

  Alignments for each domain:
  == domain 1  score: 369.4 bits;  conditional E-value: 1.1e-114
                                    GGGS--TT-EEEEEE-----EECTTEES--HHHHHHHHHHHHHHHTT-EEEEEE--S--TTS-GGG-SHHHHHHHHHHHT CS
                            PGK   1 vkdldlkgkrvlvRvDfNvplkkegkitddtriraalpTikyllekgakvvllsHlgrpkgekeklslkpvaerLsellg 80 
                                    ++dl l++krvlvRvD+N+p++ +g+i dd+r+r++l+T+k+l  ++ kvvl++H++rp g+k+  +++p+a++Ls+ll 
  gi|116754128|ref|YP_843246.1|   7 MDDLILEDKRVLVRVDINSPMDPTGRILDDKRFRSHLETLKAL--DNSKVVLMAHQSRP-GKKDFSTMEPHARQLSRLLR 83 
                                    68999*************************************9..8899**********.7999999************* PP

                                    T-EEEESSTTSHHHHHHHHT-TTT-EEEES-GGGSTTTTTT-H.......HHHHHHHHT-SEEEE--GGGTTS--TTTTH CS
                            PGK  81 keVkfvedvvgeeveeaiaelkegevllLeNvrfykeEeknde.......elakklasladvyVnDAFgtahrahaStvg 153
                                    k+V++v+d++g+++++ai++l++ge+llLeN+rfy+eE+ +++       ++++kla l+d+++nDAF+++hr+h S+vg
  gi|116754128|ref|YP_843246.1|  84 KDVTYVDDIFGSTARNAIRSLESGEMLLLENTRFYAEESLSRSpadhaksHMVQKLAPLFDAFINDAFAVSHRSHLSVVG 163
                                    **************************************7432224444447***************************** PP

                                    HHHCSEEEE-HHHHHHHHHHHHHHHS--SSEEEEEEES-HHHCHHHHHHHTTT-.SEEEEETCHHHHHHHHTT-B-TTSS CS
                            PGK 154 iakvlsaaaGllmekElealskvlenperplvailGGakvsdkikvienLlekv.dkliigGgmantFlkaqgleigksl 232
                                    +++vl++aaG+lm+kE++al+k l+  e+p+v+ lGGakv+d ikv +n+l++  d+++  G++ ++Fl a+g+++g+  
  gi|116754128|ref|YP_843246.1| 164 FTEVLPSAAGILMDKEIQALDKGLKASEHPCVFALGGAKVDDSIKVAQNVLRRGaDSVLALGLVSVVFLMAAGVNVGETN 243
                                    *****99********************************************9988**********************665 PP

                                    -...-G....GGHHHHHHHHHHHHHHT-EEE--SEEEEESSSSTTS.EEEECCG--TT-EEEEE-HHHHHHHHHHHCC-S CS
                            PGK 233 v...ee....dklelakellekakkkgvkillpvDvvvakeeaekeakvveveaipedemalDigpktielfaeaikeak 305
                                        e+    d++e+a+++l+++     k++lp D++v k+    e+  v+v++i  d+ + Dig +ti +f++++++a+
  gi|116754128|ref|YP_843246.1| 244 RrfvESqgymDQVEIAQKILNEHP---GKVILPRDIAVDKDG---ERLEVSVDSI-PDYPISDIGLETIVEFSKILRSAR 316
                                    533355666678********9987...89**********832...2345688888.5789******************** PP

                                    EEEEES-SS-TTSGCCCHHHHHHHHHHHHHCHTSEEEEESHHHHHHHHHTT-GGGSSEEESSSHHHHHHHCT CS
                            PGK 306 tvvwnGpmGvfeiekfakGTkaiakalaeatkgalsivGGgdsaaaveklgladkvshvStGGgAsLelLeg 377
                                    + v+nGp+G++e e+f  GT +i+ka+++a    +si+GGg+++aa+eklgl++++shvS GGgAs+++L+g
  gi|116754128|ref|YP_843246.1| 317 VAVLNGPAGITEKERFILGTAEILKAATDA---GYSIAGGGHTVAAIEKLGLESRFSHVSMGGGASITYLSG 385
                                    ***************************996...49***********************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3009.05
//
Query:       gi|116754129|ref|YP_843247.1|  [L=315]
Description: phosphoesterase domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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-11   42.6   0.1    8.1e-11   42.1   0.1    1.3  1  DHH       DHH family
    4.6e-07   30.3   3.1    5.9e-07   30.0   1.8    1.8  2  DHHA1     DHHA1 domain


Domain annotation for each model (and alignments):
>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   0.1     9e-15   8.1e-11       1     101 []      17     151 ..      17     151 .. 0.83

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 9e-15
                                    EEEEE-ECSSSHHHHHHHHHHHH.......................................CECS--TCGGCGCCHHCC CS
                                    xxxxxxxxxxxxxxxxxxxxxxx.......................................xxxxxxxxxxxxxxxxxx RF
                            DHH   1 kilivghknpDtDsigSaialan.......................................llvDhneksqavegeake 41 
                                    ki++ +hkn D D+igSa+al+                                        +l+D++ +sq   +    
  gi|116754129|ref|YP_843247.1|  17 KIYL-CHKNADPDAIGSAFALSWlfggdigavgdlskaasqladsigikpiidpdlqsydlvVLIDTSVSSQIGGA---- 91 
                                    5777.9*****************7777777777777777777777766666666666666666*********9976.... PP

                                    CSEEEEEEE-S---SS---SS--EEEE-SSS-HHHHHHHHHHH..TT----HHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxx RF
                            DHH  42 eaedviiiDHHrlgeefetlapilflnepvgstaeivaellee..kkeeiskeiaellllgi 101
                                       +  +iDHH   + +e+    ++++ +v sta+iv+++++     +++++e+a +ll+gi
  gi|116754129|ref|YP_843247.1|  92 MLRRYGVIDHHLDTDLLEDA--EFYIQREVDSTAQIVWDIIKSsgMADRVPREVALALLAGI 151
                                    788999*******9656665..48889****************99899999*********98 PP

>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0         1   9.3e+03      74     101 ..     147     185 ..     115     189 .. 0.57
   2 !   30.0   1.8   6.6e-11   5.9e-07      70     122 ..     238     294 ..     223     313 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1
                                    EEEEEECTEEEEEEEESSH...........SS-HHHHHH CS
                          DHHA1  74 fvakeegdkvkvsarskkd...........gvdagelak 101
                                    ++a+   d+ ++  +s+++           +vd ge+++
  gi|116754129|ref|YP_843247.1| 147 LLAGIVSDTGRFRHASSEAfrcvheileagDVDYGEVME 185
                                    333333334455555554444444455555666666666 PP

  == domain 2  score: 30.0 bits;  conditional E-value: 6.6e-11
                                    TCEEEEEEEECTEEEEEEEESSH....SS-HHHHHHHHHHHTTCCEEEETCEEEEEE CS
                          DHHA1  70 pvivfvakeegdkvkvsarskkd....gvdagelakeaaaklgggGGGHdlAaGagi 122
                                    + i+f+a+  g   +vs+r++ +    g+d+++l+k +a+  gg+GGGH+ Aa++  
  gi|116754129|ref|YP_843247.1| 238 ADIAFAASSHGGVFRVSGRASFRaiqaGIDLADLMKSIARSHGGSGGGHRGAAAMEA 294
                                    568888888888999999988888999**********************99998755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 2584.72
//
Query:       gi|116754130|ref|YP_843248.1|  [L=437]
Description: potassium transporter peripheral membrane component [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-49  165.8   1.8    1.1e-23   83.6   0.0    2.3  2  TrkA_N           TrkA-N domain
    4.5e-24   84.1   2.5    3.4e-14   52.4   0.1    3.0  3  TrkA_C           TrkA-C domain
    2.2e-09   37.7   0.9    8.1e-05   23.0   0.2    2.6  2  NAD_binding_7    Putative NAD(P)-binding
    1.9e-05   24.1   0.3     0.0018   17.6   0.0    2.5  2  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
    5.3e-05   23.7   1.5     0.0095   16.5   0.1    2.9  2  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
    8.9e-05   21.9   1.2       0.21   10.9   0.0    2.2  2  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
    0.00011   21.6   0.4       0.01   15.1   0.0    2.2  2  FAD_binding_3    FAD binding domain
    0.00038   20.4   0.6       0.83    9.5   0.0    2.4  2  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
    0.00053   19.6   0.9      0.034   13.7   0.1    2.2  2  DUF1188          Protein of unknown function (DUF1188)
    0.00067   19.7   1.0       0.13   12.3   0.3    2.4  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    0.00076   20.0   0.2       0.69   10.5   0.0    2.8  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
     0.0011   19.2   0.1      0.021   15.1   0.0    2.5  2  NAD_binding_8    NAD(P)-binding Rossmann-like domain
     0.0023   18.0   1.0       0.66   10.1   0.2    2.5  2  Ldh_1_N          lactate/malate dehydrogenase, NAD binding do
     0.0036   17.6   1.7      0.011   16.0   0.4    2.1  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0043   17.5   0.2        4.1    7.9   0.1    2.6  2  XdhC_C           XdhC Rossmann domain
     0.0095   15.5   0.7        2.9    7.4   0.0    2.6  3  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
  ------ inclusion threshold ------
      0.011   15.2   0.4       0.58    9.6   0.0    2.3  2  Epimerase        NAD dependent epimerase/dehydratase family
      0.013   15.1   0.2        5.6    6.6   0.0    2.5  2  ApbA             Ketopantoate reductase PanE/ApbA
      0.025   14.5   0.3       0.77    9.6   0.2    2.4  2  NAD_binding_10   NAD(P)H-binding
       0.08   12.3   0.0        3.5    6.9   0.0    2.3  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
       0.12   12.2   0.3          2    8.3   0.3    2.4  2  Rossmann-like    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 !   81.4   0.4   6.5e-26   5.5e-23       1     116 []       3     120 ..       3     120 .. 0.95
   2 !   83.6   0.0   1.3e-26   1.1e-23       2     116 .]     226     341 ..     225     341 .. 0.96

  Alignments for each domain:
  == domain 1  score: 81.4 bits;  conditional E-value: 6.5e-26
                                    EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHHHHH CS
                         TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeanilav 80 
                                    ++i G+G+vG +lae + +++ dv+vidkd +++ +++   l+  vg+a++  +Lee+g+e++d+v+a+tg+de ni+++
  gi|116754130|ref|YP_843248.1|   3 VLITGAGEVGHRLAEAMVADH-DVTVIDKDIAALSRFEGMDLKPRVGNAANARLLEEIGVEDMDLVLAVTGSDEINIITC 81 
                                    689******************.7***************999*************************************** PP

                                    HHHHHHTSSSEEEEEESSGGG....HHHHHHHTTSEEEEH CS
                         TrkA_N  81 llakelnpkkkiiaraqdpeh....aellkklgadvvisp 116
                                     +a  +    ++iar+++pe+    ++ l++lg++++i p
  gi|116754130|ref|YP_843248.1|  82 IIASRMGV-NHTIARVRNPEYidrpVKPLRELGIEYMICP 120
                                    ***97666.79**********9999999999***999987 PP

  == domain 2  score: 83.6 bits;  conditional E-value: 1.3e-26
                                    EEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTT..SEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHHHH CS
                         TrkA_N   2 iiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeg..levvvgdatdeevLeeagiekadaviaatgddeanila 79 
                                    +i+G G vG  la++L++ g+d  +i+ d +r++e++     +++++gd+td ++L e g+ +ad+v a+tg de+n+l 
  gi|116754130|ref|YP_843248.1| 226 VIVGGGLVGFYLAQRLENMGIDLKLIEIDNQRCREISMYLsdTMILNGDGTDISLLTEEGVGDADVVFAVTGIDEKNLLS 305
                                    8*****************8879**************98886788************************************ PP

                                    HHHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEEEEH CS
                         TrkA_N  80 vllakelnpkkkiiaraqdpehaellkklgadvvisp 116
                                    +ll ++l   kkii+r++++ +++l++++g+d+++sp
  gi|116754130|ref|YP_843248.1| 306 SLLSRQLGA-KKIISRVNRSYYVKLFERVGIDRAVSP 341
                                    *****9887.79***********************98 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       9.8   8.4e+03      13      30 ..      11      28 ..       9      29 .. 0.79
   2 !   30.7   0.2   2.4e-10     2e-07       1      68 [.     150     215 ..     150     217 .. 0.95
   3 !   52.4   0.1   3.9e-17   3.4e-14       1      69 [.     369     435 ..     369     436 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 9.8
                                   TTSBHHHHTHHHHS-EEE CS
                         TrkA_C 13 vGktlkelnlrargvlvv 30
                                   vG++l+e+ + +++v+v+
  gi|116754130|ref|YP_843248.1| 11 VGHRLAEAMVADHDVTVI 28
                                   799999977777788876 PP

  == domain 2  score: 30.7 bits;  conditional E-value: 2.4e-10
                                    CEEEEEE--GGGTTSBHHHHTHHHHS-EEEEEE-T-EEES--TT-B--TT-EEEEEEEHHHHHHHHHH CS
                         TrkA_C   1 lvevtvpagsplvGktlkelnlrargvlvvairRggeliipsgdtvLeeGDvllvvgspsdlaelrel 68 
                                    l+e++v++g plvG+ +++l++++ g  +va++ +g++ + +++ +++++D+++ + +p+++ +lr  
  gi|116754130|ref|YP_843248.1| 150 LIELKVREGMPLVGQ-VRDLRIPR-GSKIVAVKSNGKVRLGDPNITIKPNDHVTMLIDPKAITDLRQS 215
                                    689***********6.********.********99***************************999876 PP

  == domain 3  score: 52.4 bits;  conditional E-value: 3.9e-17
                                    CEEEEEE--GGGTT.SBHHHHTHHHHS-EEEEEE-T-EEES--TT-B--TT-EEEEEEEHHHHHHHHHHH CS
                         TrkA_C   1 lvevtvpagsplvG.ktlkelnlrargvlvvairRggeliipsgdtvLeeGDvllvvgspsdlaelrell 69 
                                    l+ ++v+a+s+l+G + +ke  l+a g++   i R+g++++p+++t+Le GD+++vv+ +s+++++++++
  gi|116754130|ref|YP_843248.1| 369 LMDFVVKANSRLAGrHIMKE--LPA-GAIAGMILRNGHPLVPDEHTILEVGDRVFVVAYQSSISRIKRIF 435
                                    5789**********666678..***.*****************************************998 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 !   23.0   0.2   9.5e-08   8.1e-05       9      78 ..       2      80 ..       1     103 [. 0.70
   2 !   12.8   0.0   0.00014      0.12       5      75 ..     220     302 ..     216     318 .. 0.72

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 9.5e-08
                  NAD_binding_7  9 kvlvvGgGevAarkvrklleagakvtvvapevkeele........elvklaeeel.ekd..legadlviaatddrelneri 78
                                   +vl+ G+Gev+ r ++ +++   +vtv+++++++ +         +  ++a+  l e +  +e++dlv+a+t  +e+n   
  gi|116754130|ref|YP_843248.1|  2 RVLITGAGEVGHRLAEAMVAD-HDVTVIDKDIAALSRfegmdlkpRVGNAANARLlE-EigVEDMDLVLAVTGSDEINIIT 80
                                   89**********999999877.*********74443363443332222233333433.14699***********9998655 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00014
                  NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtvvapevkeele.......elvklaeee....l..ekdlegadlviaatdd 71 
                                     ++++ ++vGgG v+   +++l + g +++++  + ++ +        +++ l+ +     l  e+ + +ad+v+a+t  
  gi|116754130|ref|YP_843248.1| 220 TRDENAVIVGGGLVGFYLAQRLENMGIDLKLIEID-NQRCReismylsDTMILNGDGtdisLltEEGVGDADVVFAVTGI 298
                                    68999**************************9999.44444222333332223322233331335669999999999987 PP

                  NAD_binding_7  72 reln 75 
                                    +e n
  gi|116754130|ref|YP_843248.1| 299 DEKN 302
                                    6655 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 ?    4.3   0.2     0.024        20     144     199 ..       2      62 ..       1      81 [. 0.71
   2 !   17.6   0.0   2.1e-06    0.0018     133     189 ..     213     269 ..     190     333 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.024
                                    EEEEES-SHHHHHHHHHHHHHT-EEEEEE....SSSSSS.TTS-HHHHHHHHHHHHHT.TEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxx.xxxxxxxxxxxxxxxxxx.xxx RF
                    Pyr_redox_2 144 rivvvGgGyiGvElAaalaklgkevtlve....ardrll.raldkelsaaleealeke.Gve 199
                                    r+++ G+G +G  lA a + + ++vt+++    a++r+    l++++++a++++l +e Gve
  gi|116754130|ref|YP_843248.1|   2 RVLITGAGEVGHRLAEA-MVADHDVTVIDkdiaALSRFEgMDLKPRVGNAANARLLEEiGVE 62 
                                    68899999999999988.44445788766222255555566666888888888887776775 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 2.1e-06
                                    HHHHCCSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 133 aealklkllpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaal 189
                                     + l+++ +++++v+vGgG++G  lA+ l ++g +  l+e  ++ +r+    ls+++
  gi|116754130|ref|YP_843248.1| 213 RQSLHEETRDENAVIVGGGLVGFYLAQRLENMGIDLKLIEIDNQRCREISMYLSDTM 269
                                    4567777777*****************************999888865555555544 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.2     0.034        29       1      39 [.       2      40 ..       2      62 .. 0.80
   2 !   16.5   0.1   1.1e-05    0.0095       2      51 ..     225     270 ..     224     291 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.034
                                   EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS.TTSS CS
                      Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkll.rllD 39
                                   +v++ G+G +g  lA+a+ +  ++Vtv++     l r ++
  gi|116754130|ref|YP_843248.1|  2 RVLITGAGEVGHRLAEAMVA-DHDVTVIDKDIAALsRFEG 40
                                   799**************976.4589999988877755554 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.1e-05
                                    EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHH CS
                      Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqekle 51 
                                    +v+vGgG++g  lA+ l ++g + +++e  ++ +    +e+s +l + + 
  gi|116754130|ref|YP_843248.1| 225 AVIVGGGLVGFYLAQRLENMGIDLKLIEIDNQRC----REISMYLSDTMI 270
                                    79**************************999988....677777666655 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 !    9.5   0.5   0.00063      0.54      30      96 ..       2      68 ..       1      87 [. 0.79
   2 !   10.9   0.0   0.00024      0.21      30      73 ..     224     268 ..     216     307 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00063
                                   EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHHH.HHH-SEEE CS
                    AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeellaea.vkeadvvi 96
                                   +vl+ G+G +G    a a+  + +Vtv+D+++a+l ++e +  k     +++++ll+e  v+++d+v 
  gi|116754130|ref|YP_843248.1|  2 RVLITGAGEVGHRL-AEAMVADHDVTVIDKDIAALSRFEGMDLKPRVGNAANARLLEEIgVEDMDLVL 68
                                   79*********985.56888899****************98888444456666666664477788775 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00024
                                    EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TTTC CS
                    AlaDh_PNT_C  30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqles.lgak 73 
                                    + +++GgG +G   ++   ++g + ++++++ +r ++++  l  +
  gi|116754130|ref|YP_843248.1| 224 NAVIVGGGLVGFYLAQRLENMGIDLKLIEIDNQRCREISMyLSDT 268
                                    689**********************************99844333 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.2     0.019        16       3      60 ..       2      63 ..       1     102 [. 0.82
   2 !   15.1   0.0   1.2e-05      0.01       4      35 ..     225     256 ..     222     262 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.019
                                   EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSS.....S--EEEHHHHHHHHHTT-HH CS
                  FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlp.....radglnqrtmellrqlGled 60
                                    VlI GaG +G  la  +     +v++++k   +   +     + ++ n    +ll+++G+ed
  gi|116754130|ref|YP_843248.1|  2 RVLITGAGEVGHRLAEAMVAD-HDVTVIDKDIAALSRFegmdlKPRVGNAANARLLEEIGVED 63
                                   69*************999888.8*******988888774455555666666778888888877 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.2e-05
                                    EEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                  FAD_binding_3   4 VlIVGaGpaGlmlallLseaGvrvvlvekrst 35 
                                     +IVG+G++G+ la+ L + G++  l+e  ++
  gi|116754130|ref|YP_843248.1| 225 AVIVGGGLVGFYLAQRLENMGIDLKLIEIDNQ 256
                                    68***********************9997665 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 !    9.0   0.1    0.0014       1.2       2      40 ..       3      40 ..       2      80 .. 0.81
   2 !    9.5   0.0   0.00097      0.83       3      43 ..     226     266 ..     224     275 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0014
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHH CS
                        3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealekale 40
                                   v + GaG +G+ +a++++ a+++V+++d + +al + + 
  gi|116754130|ref|YP_843248.1|  3 VLITGAGEVGHRLAEAMV-ADHDVTVIDKDIAALSRFEG 40
                                   6789***********986.789*******9999988665 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00097
                                    EEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHH CS
                        3HCDH_N   3 aviGaGtmGagiaavfasagleVvlvdiseealekalekie 43 
                                     ++G G++G  +a+ + + g++ +l++i++++ ++    ++
  gi|116754130|ref|YP_843248.1| 226 VIVGGGLVGFYLAQRLENMGIDLKLIEIDNQRCREISMYLS 266
                                    69****************************99888766665 PP

>> DUF1188  Protein of unknown function (DUF1188)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1     0.025        22      45      75 ..       2      32 ..       1      78 [. 0.68
   2 !   13.7   0.1     4e-05     0.034      30     107 ..     210     298 ..     192     311 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.025
                                   EEEEES-CCCHHHHHHHHCCCEEEEEEESSG CS
                        DUF1188 45 nvlviGaYltGaaiakkLskkeevtlvDiep 75
                                   +vl+ Ga  +G  +a+++ ++++vt++D + 
  gi|116754130|ref|YP_843248.1|  2 RVLITGAGEVGHRLAEAMVADHDVTVIDKDI 32
                                   699*************************763 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 4e-05
                                    HHHHHHHTT--E..EEEEEES-CCCHHHHHHHHCCC.EEEEEEESSGGGGGGSSST...........HHHHHHHHTTS-- CS
                        DUF1188  30 eavleyleeeeleeknvlviGaYltGaaiakkLskk.eevtlvDiephlkellekd...........vefklsleevern 97 
                                      +++ l+e e +++n++++G  l+G ++a++L++   ++ l++i+++  + ++              +++l  ee   +
  gi|116754130|ref|YP_843248.1| 210 TDLRQSLHE-ETRDENAVIVGGGLVGFYLAQRLENMgIDLKLIEIDNQRCREISMYlsdtmilngdgTDISLLTEEGVGD 288
                                    445566664.5569********************9999999999987633222222233466667777777777888888 PP

                                    -SEEEE---T CS
                        DUF1188  98 adlviDltGl 107
                                    ad+v  +tG+
  gi|116754130|ref|YP_843248.1| 289 ADVVFAVTGI 298
                                    8888888887 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.3   0.00016      0.13      14      88 ..       2      76 ..       1     100 [. 0.77
   2 ?    5.8   0.0     0.015        13       4      86 ..     214     299 ..     211     319 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00016
                                   EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHH.....HHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS- CS
                   Shikimate_DH 14 kvlliGaGemaelvakhLlakgvkkvvvaNRtle.....rakelaeelkgeeiealkleelkellaeadvvisataseep 88
                                   +vl+ GaGe+++++a++++a +  +v+v+  +++        +l  ++ g+ ++a+ lee+   ++++d+v++ t+s e+
  gi|116754130|ref|YP_843248.1|  2 RVLITGAGEVGHRLAEAMVADH--DVTVIDKDIAalsrfEGMDLKPRV-GNAANARLLEEIG--VEDMDLVLAVTGSDEI 76
                                   79*****************875..567777766511111455666777.5559999999998..99******99999886 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.015
                                    HHHHS..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGH....HHHHHT-SEE CS
                   Shikimate_DH   4 kkkleslkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleel....kellaeadvv 79 
                                    ++  e+ ++++++++G G ++  +a+ L + g++ +  +  + +r +e+   l+++ i   + +++    +e + +advv
  gi|116754130|ref|YP_843248.1| 214 QSLHEETRDENAVIVGGGLVGFYLAQRLENMGID-LKLIEIDNQRCREISMYLSDTMILNGDGTDIslltEEGVGDADVV 292
                                    667789999*********************9987.555555556666665555555444333333311113456778888 PP

                                    EE-SSSS CS
                   Shikimate_DH  80 isatase 86 
                                    ++ t+  
  gi|116754130|ref|YP_843248.1| 293 FAVTGID 299
                                    8777655 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 ?    6.7   0.0     0.012        11       4      38 ..       5      34 ..       2      75 .. 0.78
   2 !   10.5   0.0   0.00081      0.69       4      96 ..     227     322 ..     223     323 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.012
                                   EETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCC CS
                  F420_oxidored  4 iiGaGnmgealasgllaagaqpheivvansrnpek 38
                                   i GaG++g+ la+ ++a     h+++v+ +++   
  gi|116754130|ref|YP_843248.1|  5 ITGAGEVGHRLAEAMVAD----HDVTVI-DKDIAA 34
                                   45***********99988....899988.665554 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00081
                                    EETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.....-EEECECHHHHHHH-SEEEE-S-HHHHHHHH CS
                  F420_oxidored   4 iiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.....vkvtavdneeaaeeadvvvlavkpedveevl 78 
                                    i+G+G +g+ la++l + g + + i + n+r  e   +l +++       +++   +ee + +advv+ av   d +++l
  gi|116754130|ref|YP_843248.1| 227 IVGGGLVGFYLAQRLENMGIDLKLIEIDNQRCREISMYLSDTMIlngdgTDISL-LTEEGVGDADVVF-AVTGIDEKNLL 304
                                    55*****************55555554455555555555555548888655555.5577777899887.89999999999 PP

                                    HHCGHHHHTTSEEEEESS CS
                  F420_oxidored  79 selakdalkgklvisvla 96 
                                    s+l +++l  k +is ++
  gi|116754130|ref|YP_843248.1| 305 SSLLSRQLGAKKIISRVN 322
                                    999999999999999776 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 ?    1.1   0.0      0.57   4.8e+02      13      27 ..      13      30 ..       5      33 .. 0.70
   2 !   15.1   0.0   2.4e-05     0.021       1      29 [.     227     255 ..     227     261 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.57
                                   HHHHCC...TEEEEEE-S CS
                  NAD_binding_8 13 ylLaka...gfdvlllek 27
                                   ++La+a   ++dv++++k
  gi|116754130|ref|YP_843248.1| 13 HRLAEAmvaDHDVTVIDK 30
                                   55665444489******9 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 2.4e-05
                                    EE--SHHHHHHHHHHHCCTEEEEEE-SSS CS
                  NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrd 29 
                                    IvG+Gl G ++A++L + g+d  l+e  +
  gi|116754130|ref|YP_843248.1| 227 IVGGGLVGFYLAQRLENMGIDLKLIEIDN 255
                                    9************************9876 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 ?    6.3   0.0     0.011       9.7       1      23 [.       1      22 [.       1      74 [. 0.81
   2 !   10.1   0.2   0.00077      0.66       4      82 ..     226     301 ..     224     303 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.011
                                   EEEEEETTTSHHHHHHHHHHHHT CS
                        Ldh_1_N  1 vkvavvGaaGgiGqslalllank 23
                                   ++v ++Ga G++G+ la ++++ 
  gi|116754130|ref|YP_843248.1|  1 MRVLITGA-GEVGHRLAEAMVAD 22
                                   689*****.********999876 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00077
                                    EEETTTSHHHHHHHHHHHHTTSSSEEEEE-SSHHHHHHHHHHHHHCHCCSTS-EEEEESSGGGGTTESEEEE--S-SS- CS
                        Ldh_1_N   4 avvGaaGgiGqslalllankkladelaLlDiakekleGvaldlshistflsvkvkvsekeeealkdadvvvitagvprk 82 
                                    ++vG  G +G  la  l n +   +l+L++i++++ +   + ls++ +     + +s  +ee + dadvv  + g+  k
  gi|116754130|ref|YP_843248.1| 226 VIVGG-GLVGFYLAQRLENMG--IDLKLIEIDNQRCREISMYLSDTMILNGDGTDISLLTEEGVGDADVVFAVTGIDEK 301
                                    68999.******999998765..578**********************9999999999************999998765 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 !   16.0   0.4   1.3e-05     0.011       1      77 [.       3      71 ..       3      89 .. 0.88
   2 ?    0.3   0.0      0.92   7.9e+02       2      21 ..     226     245 ..     225     292 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.3e-05
                                   EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHH.HTTSSEEEE-S CS
                Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaal.lkegdlvvnls 77
                                   vli GaG vG+ +ae +++ +dv    tv+d++ + l +      g +++++  +a+n +  L+++ +++ dlv+ ++
  gi|116754130|ref|YP_843248.1|  3 VLITGAGEVGHRLAEAMVADHDV----TVIDKDIAALSRF----EGMDLKPRVGNAANARL-LEEIgVEDMDLVLAVT 71
                                   7999***************9986....*********8888....79999***99****998.9999888889998665 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.92
                                    EEE--SHHHHHHHHHHHCTC CS
                Sacchrp_dh_NADP   2 liiGaGsvGqavaellarhf 21 
                                    +i+G+G vG  +a+ l++ +
  gi|116754130|ref|YP_843248.1| 226 VIVGGGLVGFYLAQRLENMG 245
                                    79*******99999998765 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.1    0.0048       4.1       1      51 [.       3      71 ..       3      97 .. 0.67
   2 !    6.9   0.0    0.0097       8.3       2      64 ..     226     295 ..     225     362 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0048
                                   EEEE--STTHHHHHHHHHHHTEEEEEEES-GGGG-GGG-TT-SE.....................-EEEE-- CS
                         XdhC_C  1 lvifGaghvaqalarlaaalgfrvtvvdpreefatkerfpeade.....................tavvvlt 51
                                   ++i Gag+v++ la+ +  ++ +vtv+d++ +  + +rf++ d                      + v+++t
  gi|116754130|ref|YP_843248.1|  3 VLITGAGEVGHRLAEAM-VADHDVTVIDKDIA--ALSRFEGMDLkprvgnaanarlleeigvedmDLVLAVT 71
                                   689***********976.579*******9985..45566554434455555444445555555444444444 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0097
                                    EEE--STTHHHHHHHHHHHTEEEEEEES-GGGG-GGG-TT-SE.......-EEEE--S-HHHHHHHHHHH CS
                         XdhC_C   2 vifGaghvaqalarlaaalgfrvtvvdpreefatkerfpeade.......tavvvlthdhklDaealeaa 64 
                                    vi+G+g v+  la+ ++++g+++ +++ +++  ++ ++   d+       t + +lt++   Da+++ a+
  gi|116754130|ref|YP_843248.1| 226 VIVGGGLVGFYLAQRLENMGIDLKLIEIDNQRCREISMYLSDTmilngdgTDISLLTEEGVGDADVVFAV 295
                                    79************************99997554444443333566666655555555555555544444 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 !    6.0   0.0    0.0094         8       1      36 [.       1      35 [.       1      44 [. 0.84
   2 ?   -3.8   0.0       9.7   8.3e+03     131     156 ..      78     102 ..      74     108 .. 0.72
   3 !    7.4   0.0    0.0034       2.9       4      39 ..     226     261 ..     223     270 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0094
                                   SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHH CS
                 UDPG_MGDP_dh_N  1 mkisviGlGYvGlvtaavlaeighevigvDideekv 36
                                   m++ + G+G vG   a ++ +  h+v+++D+d ++ 
  gi|116754130|ref|YP_843248.1|  1 MRVLITGAGEVGHRLAEAMVA-DHDVTVIDKDIAAL 35
                                   8999*********99988864.599*****997665 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 9.7
                                    CHHHHHHHHCSS-TTCEEEEE----- CS
                 UDPG_MGDP_dh_N 131 lvkkileeaskkkgvdfdvvsnPEfl 156
                                    ++ +i++++    ++ +  v nPE++
  gi|116754130|ref|YP_843248.1|  78 IITCIIASRMGV-NHTIARVRNPEYI 102
                                    566677766664.4788888999987 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0034
                                    EEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHH CS
                 UDPG_MGDP_dh_N   4 sviGlGYvGlvtaavlaeighevigvDideekvdkl 39 
                                    +++G G vG   a  l ++g+++ ++ id+++ +++
  gi|116754130|ref|YP_843248.1| 226 VIVGGGLVGFYLAQRLENMGIDLKLIEIDNQRCREI 261
                                    79****************************998877 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.043        37       1      44 [.       3      44 ..       3      84 .. 0.72
   2 ?    9.6   0.0   0.00067      0.58       2      69 ..     226     293 ..     225     307 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.043
                                   EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCE CS
                      Epimerase  1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledle 44
                                   +l+tGa G +G  l++a+ + +++v+++d++  a  + +  dl+
  gi|116754130|ref|YP_843248.1|  3 VLITGA-GEVGHRLAEAMVA-DHDVTVIDKDIAALSRFEGMDLK 44
                                   699998.*********9986.79******996555554444444 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00067
                                    EEETTTSHHHHHHHHHHHHCT..SEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEE CS
                      Epimerase   2 lVtGatGfiGsalvkallekg..yevigldrlssasntarledlelveldltdrsalerlfkeeqpdavi 69 
                                    +++G+ G++G +l+++l++ g   ++i +d+++ ++ +  l d+ + ++d td s l++     ++d+v+
  gi|116754130|ref|YP_843248.1| 226 VIVGG-GLVGFYLAQRLENMGidLKLIEIDNQRCREISMYLSDTMILNGDGTDISLLTEEGVG-DADVVF 293
                                    57777.***************55559******9999888889889999999999988775543.666666 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0065       5.6       1      44 [.       3      44 ..       3      70 .. 0.79
   2 ?    6.4   0.0    0.0075       6.4       2      36 ..     226     261 ..     225     295 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0065
                                   EEEES-SHHHHHHHHHHHHHTHCEEEE-SCHHHHHHHHHCEEEE CS
                           ApbA  1 iailGaGaiGsllaakLakagadvtlilrsrrlealkknGlrlt 44
                                   ++i GaG +G  la  +  a +dvt+i+++  ++  + +G++l+
  gi|116754130|ref|YP_843248.1|  3 VLITGAGEVGHRLAEAM-VADHDVTVIDKDI-AALSRFEGMDLK 44
                                   689***********999.67*******9977.333455555555 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0075
                                    EEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHH CS
                           ApbA   2 ailGaGaiGsllaakLakagadvtlilrsr.rleal 36 
                                    +i+G G +G +la +L + g d  li  ++ r+ ++
  gi|116754130|ref|YP_843248.1| 226 VIVGGGLVGFYLAQRLENMGIDLKLIEIDNqRCREI 261
                                    69********************99998888777665 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 ?    9.6   0.2   0.00091      0.77       3      72 ..       8      75 ..       7     104 .. 0.85
   2 ?    2.6   0.0      0.13   1.1e+02       6      85 ..     233     321 ..     229     360 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00091
                                   TSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHH.HTT-SEEEES---TC CS
                 NAD_binding_10  3 tGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaea.lkgadaVvsalgggg 72
                                    G vG++l++  +a+  h+vt++  + + l+++e    l+  +g++ ++  l+e  +++ d V++ +g+++
  gi|116754130|ref|YP_843248.1|  8 AGEVGHRLAEAMVAD--HDVTVIDKDIAALSRFE-GMDLKPRVGNAANARLLEEIgVEDMDLVLAVTGSDE 75
                                   79********99998..8***************8.69************9999975799999999998765 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.13
                                    HHHHHHHHHHHC-T-EEEEEETTHHHCHHHH.CTTTCEEEE--TT-CCHH.HHHHTT-SEEEES---TCC........HH CS
                 NAD_binding_10   6 vGrllvkellargghevtalvRnpeklaele.aeeglevvegdvtdvedl.aealkgadaVvsalggggk........de 75 
                                    vG +l+++l +  g++++++  + ++  e++   + + ++ gd td + l +e + +ad+V++ +g ++k        + 
  gi|116754130|ref|YP_843248.1| 233 VGFYLAQRLENM-GIDLKLIEIDNQRCREISmYLSDTMILNGDGTDISLLtEEGVGDADVVFAVTGIDEKnllssllsR- 310
                                    555566666555.366666655555555555222566677788888766415668899****99999888776666433. PP

                                    HH..HHHHHHHH CS
                 NAD_binding_10  76 eg..aknivdaa 85 
                                     +  ak+i+  +
  gi|116754130|ref|YP_843248.1| 311 -QlgAKKIISRV 321
                                    .24588886544 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     0.073        63      38      56 ..       2      20 ..       1      42 [. 0.78
   2 ?    6.9   0.0    0.0041       3.5      29      69 ..     215     255 ..     205     270 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.073
                                   EEEEES-SHHHHHHHHHHH CS
                   2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlk 56
                                   +v i G+G++G+++a+ + 
  gi|116754130|ref|YP_843248.1|  2 RVLITGAGEVGHRLAEAMV 20
                                   799************9765 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0041
                                    GSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSH CS
                   2-Hacid_dh_C  29 llgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrsk 69 
                                     l +e +++   i+G G +G  +a+rl+ +g+++  ++  +
  gi|116754130|ref|YP_843248.1| 215 SLHEETRDENAVIVGGGLVGFYLAQRLENMGIDLKLIEIDN 255
                                    556789999*******************9999776665554 PP

>> Rossmann-like  Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.3    0.0024         2      13      47 ..       3      37 ..       1      94 [. 0.63
   2 ?    1.3   0.0      0.34   2.9e+02      14      82 ..     226     292 ..     215     305 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0024
                  Rossmann-like 13 vGiisaGrvGtalgaaleraghvvvgis.aisaasr 47
                                   v i +aG+vG  l++a+  a+h v+ i   i+a sr
  gi|116754130|ref|YP_843248.1|  3 VLITGAGEVGHRLAEAMV-ADHDVTVIDkDIAALSR 37
                                   7799************95.89999877413444444 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.34
                  Rossmann-like  14 GiisaGrvGtalgaaleraghvvvgisaisaasreraerrlPdvpvlevedvaaraellllavPdaelp 82 
                                     i++ G vG  l++ le  g  +  i    +  re  +  l d+ +l+  d ++ + l    v da++ 
  gi|116754130|ref|YP_843248.1| 226 VIVGGGLVGFYLAQRLENMGIDLKLIEIDNQRCREI-SMYLSDTMILNG-DGTDISLLTEEGVGDADVV 292
                                    59999************9998888887766666664.456777777776.5566665555566666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); 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 0.23s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3303.91
//
Query:       gi|116754131|ref|YP_843249.1|  [L=730]
Description: elongation factor EF-2 [Methanosaeta thermophila PT]
Scores for complete 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-63  213.6   0.0    3.2e-63  212.8   0.0    1.3  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    8.9e-28   96.5   0.4    7.7e-27   93.5   0.2    2.8  3  EFG_IV       Elongation factor G, domain IV
    7.5e-25   86.8   0.6    2.1e-24   85.4   0.1    2.1  2  EFG_C        Elongation factor G C-terminus
    1.2e-24   86.2   1.9    1.8e-24   85.6   0.6    2.1  2  EFG_II       Elongation Factor G, domain II
    2.1e-14   53.6   0.8    5.6e-14   52.3   0.8    1.8  1  GTP_EFTU_D2  Elongation factor Tu domain 2
      0.001   19.1   0.0     0.0024   17.9   0.0    1.6  1  MMR_HSR1     50S ribosome-binding GTPase
  ------ inclusion threshold ------
       0.02   14.9   0.0      0.069   13.1   0.0    1.9  2  DUF3748      Protein of unknown function (DUF3748)
      0.028   14.2   0.0      0.067   13.0   0.0    1.6  1  RF3_C        Class II release factor RF3, C-terminal domain
       0.11   12.4   0.0       0.23   11.4   0.0    1.4  1  DUF2888      Protein of unknown function (DUF2888)
       0.14   11.7   0.0        0.4   10.2   0.0    1.7  2  Ras          Ras family
        2.8    8.0   4.3        8.7    6.4   0.2    3.0  3  FliH         Flagellar assembly protein FliH


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 !  212.8   0.0   1.9e-66   3.2e-63       2     193 ..      20     257 ..      19     258 .. 0.88

  Alignments for each domain:
  == domain 1  score: 212.8 bits;  conditional E-value: 1.9e-66
                                    CEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE.T.TCSSEEEEEEEESS CS
                       GTP_EFTU   2 rirnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle.k.etkkylinliDtPG 79 
                                    rirnigi++h+DhGKtTL+d+Ll+ +g+is+  e a+++ ++D+ + E++rgiTi++a++s+  + e+k+ylin+iDtPG
  gi|116754131|ref|YP_843249.1|  20 RIRNIGIVAHIDHGKTTLSDNLLAGAGMISM--ELAGKQLFMDFDPLEQARGITIDAANVSMVhEyEGKEYLINMIDTPG 97 
                                    89*****************************..889999************************626************** PP

                                    SGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHHHHHHHH CS
                       GTP_EFTU  80 HvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrlkaelkeiveevkqklsrkeeklek 159
                                    HvdF  +v+r++r++Dgav+vvdaveG +pqte+vlr+al+egv++++f+NK+Dr+++elk  ++e+  +l r+ ++++k
  gi|116754131|ref|YP_843249.1|  98 HVDFGGDVTRAMRAVDGAVVVVDAVEGAMPQTETVLRQALREGVRPVLFVNKVDRMINELKVEKKEMAIRLGRVIDNINK 177
                                    ***********************************************************************999666666 PP

                                    HHHTTT............TTEEEEEEBTTTTBTHH..................................HHHHHHHHHSH CS
                       GTP_EFTU 160 ygekge............kevpvvfgSalkgegvk..................................tllealvellp 193
                                       + +             + +v+fgSal +++++                                  ++ ++++++lp
  gi|116754131|ref|YP_843249.1| 178 LIRSMDeehykagwrldaANGSVAFGSALYNWAISvpqmkrtgigfdqvydycrsdrmkelsqkcplyvAVNDMIIRFLP 257
                                    544444456677777777899***********888777777777777777777777777777777777777777777666 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 ?   -3.5   0.0       5.3   8.6e+03      69      89 ..     283     302 ..     278     308 .. 0.74
   2 !   93.5   0.2   4.7e-30   7.7e-27       6     120 ..     511     617 ..     506     618 .. 0.91
   3 ?   -1.5   0.0       1.3   2.1e+03      20      62 ..     679     718 ..     673     721 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 5.3
                                    CCCCTTS-TTTS--EESEEEE CS
                         EFG_IV  69 fqealkeGplagepvtdvkvt 89 
                                    ++    +Gp+a + vt +kv 
  gi|116754131|ref|YP_843249.1| 283 MTACDPNGPVA-FMVTKIKVD 302
                                    55555689999.999999996 PP

  == domain 2  score: 93.5 bits;  conditional E-value: 4.7e-30
                                    CEE.SS-CCHCCCCCCCHTSSSHCCCCCEEEECCTTTTSSEEEEE--STCCCHCCCCHHHHCCCCCCTTS-TTTS--EES CS
                         EFG_IV   6 rEtirkpvkereeklkkqsggdgqyakvileiePleegsgnefvdetkggqvpkeyieavekGfqealkeGplagepvtd 85 
                                    +    +++ er+++l++ +g+d+++a+ ++++       +n+f ++tkg+q+++e++e++ +Gf+ea   Gp+++epv++
  gi|116754131|ref|YP_843249.1| 511 K----MEEVERRKILIE-AGMDKEEARNMVNFVG-----TNMFLNMTKGIQYLRETMELILEGFEEAITAGPICREPVQG 580
                                    4....344446767777.9**************9.....8**************************************** PP

                                    EEEEEEEEE--T..TTC-HHHHHHHHCHHHHHHHHCC CS
                         EFG_IV  86 vkvtLldgslhe..vdsseaafkpaarralkeallkA 120
                                    +k++L+d++lhe  v++++a+++pa+r+a+++++l+A
  gi|116754131|ref|YP_843249.1| 581 IKAKLVDVKLHEdaVHRGPAQVIPAVRQAVQAGILMA 617
                                    *********************************9998 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.3
                                    CCCHTSSSHCCCCCEEEECCTTTTSSEEEEE--STCCCHCCCC CS
                         EFG_IV  20 lkkqsggdgqyakvileiePleegsgnefvdetkggqvpkeyi 62 
                                    +   ++g+  +++    +eP +    n++ d++++++  k  +
  gi|116754131|ref|YP_843249.1| 679 IRSATEGRALWSTEFAGFEPIP---ANMMLDTVRQIRTRKGLK 718
                                    56667889999999999***99...999999999988777666 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 ?   -2.3   0.1       2.8   4.6e+03       3      14 ..     388     399 ..     386     401 .. 0.83
   2 !   85.4   0.1   1.3e-27   2.1e-24       2      85 ..     621     703 ..     620     707 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.8
                                    EEEEEEEEEEEE CS
                          EFG_C   3 lEPivkveievp 14 
                                     EP+++v +e+ 
  gi|116754131|ref|YP_843249.1| 388 SEPVMTVAVEAK 399
                                    6******99976 PP

  == domain 2  score: 85.4 bits;  conditional E-value: 1.3e-27
                                    EEEEEEEEEEEEECCCCCCHHHHHHHCT-EEEEEEEE.TTEEEEEEEEEGGG-TTHHHCHHHCTTTS-EEEEEEEEEEE- CS
                          EFG_C   2 llEPivkveievpeeyvgkvisdlssrrGeiedmeqdasgrviieaeiPlaeligfateLrslTkGegsfsmefsgYeev 81 
                                    llEP++ v i+vp++ +g ++s+++ rrG i++me++ +++++i+a++P+ae++gfa ++rs+T+G++ +s+ef+g+e++
  gi|116754131|ref|YP_843249.1| 621 LLEPMQYVFIQVPQDQMGGAMSEIQGRRGVILSMETE-GDMITIKAKMPVAEMFGFAGAIRSATEGRALWSTEFAGFEPI 699
                                    8************************************.****************************************** PP

                                    -HHH CS
                          EFG_C  82 pgdk 85 
                                    p ++
  gi|116754131|ref|YP_843249.1| 700 PANM 703
                                    9986 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 !   85.6   0.6   1.1e-27   1.8e-24       1      74 [.     387     460 ..     387     461 .. 0.98
   2 ?   -2.6   0.0       3.7     6e+03      40      51 ..     553     564 ..     528     567 .. 0.84

  Alignments for each domain:
  == domain 1  score: 85.6 bits;  conditional E-value: 1.1e-27
                         EFG_II   1 fPePvislaiepkskadedklskaLarlleEDptlrverdeeTketilsGmGelHleivverlkreykvevelg 74 
                                    ++ePv+++a+e+k+ +d  kl ++L++ ++EDptl+++ +eeT+e +++GmGelHleiv++r++r+ +ve++++
  gi|116754131|ref|YP_843249.1| 387 VSEPVMTVAVEAKNMRDLPKLIEVLRQTAKEDPTLQITINEETGEHLMAGMGELHLEIVATRIQRDKGVEIKTS 460
                                    689*******************************************************************9986 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.7
                         EFG_II  40 deeTketilsGm 51 
                                     +eT e+il+G 
  gi|116754131|ref|YP_843249.1| 553 LRETMELILEGF 564
                                    5799*****997 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 !   52.3   0.8   3.4e-17   5.6e-14       1      73 [.     306     372 ..     306     373 .. 0.94

  Alignments for each domain:
  == domain 1  score: 52.3 bits;  conditional E-value: 3.4e-17
                                    EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
                    GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtl 73 
                                    G+va+gr++sGtl +G+e++i  ++++ +    ri+++  +++ e+++v+  +aG+i+a+ gl da ivG+t+
  gi|116754131|ref|YP_843249.1| 306 GEVATGRLFSGTLVRGMELHI--SGVPHT---NRIQQTGIMMGAERIEVERIPAGNIAAVTGLRDA-IVGSTV 372
                                    89*******************..777444...*********************************8.*****8 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.5e-06    0.0024       2     112 ..      24     147 ..      23     150 .. 0.56

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.5e-06
                                    EEEEESTTSSHHHHHHHHHT................STEEESSSTTSSSSEEEEEEE....ETTEEEEEEECGGCSSHHH CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltg................ekaivsdkpgtTrdinegrvk....lkgkeielvDtpGliegas 61 
                                    ++iv +   GK+tL   l+                 +    ++  g T+d     +      k+  i+++DtpG ++   
  gi|116754131|ref|YP_843249.1|  24 IGIVAHIDHGKTTLSDNLLAgagmismelagkqlfmDFDPLEQARGITIDAANVSMVheyeGKEYLINMIDTPGHVD--- 100
                                    7788888889999999888534444444444333322345566667777774444432432222559*******665... PP

                                    HHHHHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHH.HHHHHHTTSEEEEEE CS
                       MMR_HSR1  62 eekglgkaflaleeadlillvvdaseeklkpldeel.eelleeakkplilvl 112
                                     + ++++a++    +d +++vvda e+   p+ e++  + l+e  +p +l +
  gi|116754131|ref|YP_843249.1| 101 FGGDVTRAMR---AVDGAVVVVDAVEG-AMPQTETVlRQALREGVRP-VLFV 147
                                    2223444444...58********9955.5555555404555444444.4444 PP

>> DUF3748  Protein of unknown function (DUF3748)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       4.3     7e+03      45      66 ..     113     134 ..     108     137 .. 0.84
   2 ?   13.1   0.0   4.2e-05     0.069       3      69 ..     613     683 ..     611     693 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.3
                        DUF3748  45 pekastldalditpPytpGaLr 66 
                                    +++++ +da++ + P t+ +Lr
  gi|116754131|ref|YP_843249.1| 113 DGAVVVVDAVEGAMPQTETVLR 134
                                    5678899********9999998 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 4.2e-05
                        DUF3748   3 GvvtvsPv..eperlvfihGpenpdeqWkydfsrrrGviveeaepekastldald.itpPy.tpGaLrGGs 69 
                                    G+  ++P+  ep ++vfi+ p+++      +++ rrGvi++ ++++ ++t+ a   +++ +  +Ga+r  +
  gi|116754131|ref|YP_843249.1| 613 GILMANPTllEPMQYVFIQVPQDQMGGAMSEIQGRRGVILSMETEGDMITIKAKMpVAEMFgFAGAIRSAT 683
                                    5666666533799**************************************99651444553467777655 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 ?   13.0   0.0   4.1e-05     0.067      14      80 ..     395     461 ..     387     487 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.1e-05
                                    EEEESSGGGHHHHHHHHHHHHHCT.SSEEEEET.TSS-EEEEESSTHHHHHHHHHHHHHH---EEEEE CS
                          RF3_C  14 rvrlkdplkrkqlrkgleqLaeEG.avqvfkeeeageelilgaVGqLQfeVveeRlknEYgvevrles 80 
                                     v++k+     +l + l+q a+E  + q+  +e ++ e +++ +G+L +e+v++R+++  gve+++++
  gi|116754131|ref|YP_843249.1| 395 AVEAKNMRDLPKLIEVLRQTAKEDpTLQITINE-ETGEHLMAGMGELHLEIVATRIQRDKGVEIKTSP 461
                                    577777777888888999999887245665555.788899999********************99876 PP

>> DUF2888  Protein of unknown function (DUF2888)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00014      0.23      16      98 ..      67     148 ..      59     167 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00014
                        DUF2888  16 nrnftidlvnlsvstefqvkitmtphhdlgtfvvepknvfsikravkgdaafkveraagwlpdtpqvltlfvyerlnpve 95 
                                     r +tid  n+s+  e++ k  +    d    v    +v    rav g a + v+   g +p+t  vl   + e + pv 
  gi|116754131|ref|YP_843249.1|  67 ARGITIDAANVSMVHEYEGKEYLINMIDTPGHVDFGGDVTRAMRAVDG-AVVVVDAVEGAMPQTETVLRQALREGVRPVL 145
                                    6899*************************99**99***********99.567899*******************999997 PP

                        DUF2888  96 whs 98 
                                    + +
  gi|116754131|ref|YP_843249.1| 146 FVN 148
                                    754 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00025       0.4      29     116 ..      69     152 ..      58     172 .. 0.75
   2 ?   -3.6   0.0       4.7   7.6e+03     112     143 ..     415     446 ..     382     449 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00025
                                    TTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEEEEEETTBHHHHHTHHHHHHHHHHHSTTTSEEE CS
                            Ras  29 esTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegillvyditsresfenvkkwveeikrvaeenvpiv 108
                                      Ti +++ +   e++gke+ +++ DT G  +f    +  +r ++g+++v d  + +   + ++ ++   +  +e v  v
  gi|116754131|ref|YP_843249.1|  69 GITIDAANVSMVHEYEGKEYLINMIDTPGHVDFGGDVTRAMRAVDGAVVVVDAVEGA-MPQTETVLR---QALREGVRPV 144
                                    5799999999999*************************************9976543.333333333...3333556677 PP

                                    EEEETTTG CS
                            Ras 109 LvGnKvDl 116
                                    L  nKvD 
  gi|116754131|ref|YP_843249.1| 145 LFVNKVDR 152
                                    77888884 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 4.7
                                    ETTTGGGG-SS-HHHHHHHHHHHTSEEEEEBT CS
                            Ras 112 nKvDleekravsteegeelakelglkfletSA 143
                                     K D + + ++++e+ge+l   +g  +le+ A
  gi|116754131|ref|YP_843249.1| 415 AKEDPTLQITINEETGEHLMAGMGELHLEIVA 446
                                    34444447777777888777777777777666 PP

>> FliH  Flagellar assembly protein FliH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1       0.4   6.6e+02      34      75 ..     126     169 ..     118     200 .. 0.69
   2 ?    6.4   0.2    0.0053       8.7      30     103 ..     381     455 ..     371     457 .. 0.88
   3 ?    0.2   0.1      0.44   7.2e+02      42      64 ..     592     614 ..     581     623 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.4
                                    HHHHHHHHHHS--S..-HHHHHHHHHHHHTTSCHHHS-EEEEE- CS
                           FliH  34 ldiarkvikkelsv..dpekilalvrealaklpvdekkitlrvn 75 
                                    +  ++ v++++l++  +p ++++ v  ++++l v +k++ +r+ 
  gi|116754131|ref|YP_843249.1| 126 MPQTETVLRQALREgvRPVLFVNKVDRMINELKVEKKEMAIRLG 169
                                    55677888888886225777789999999999999999998885 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0053
                                    HHHHHHHHHHHHHHS--S-HHHHHHHHHHHHTTSCHHHS-EEEEE-HHHHHHHHHHHH.HHHHHCT-EEEE-TTS CS
                           FliH  30 vqlaldiarkvikkelsvdpekilalvrealaklpvdekkitlrvnpdDlelvrehlg.eelsargwrlvaDssl 103
                                     +++ ++++ v+ ++++ +++  l+ + e+l++ +  ++ +++ +n++  e++ + +g  +l+    r++ D+++
  gi|116754131|ref|YP_843249.1| 381 FEIIKHVSEPVMTVAVEAKNMRDLPKLIEVLRQTAKEDPTLQITINEETGEHLMAGMGeLHLEIVATRIQRDKGV 455
                                    57888999****************************************999999998877777777788888766 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.44
                                    HHS--S-HHHHHHHHHHHHTTSC CS
                           FliH  42 kkelsvdpekilalvrealaklp 64 
                                    + ++   p++++++vr+a+++ +
  gi|116754131|ref|YP_843249.1| 592 EDAVHRGPAQVIPAVRQAVQAGI 614
                                    5788899***********96544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (730 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.40
# Mc/sec: 5476.81
//
Query:       gi|116754132|ref|YP_843250.1|  [L=424]
Description: elongation factor 1-alpha [Methanosaeta thermophila PT]
Scores for complete 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  194.8   0.0    1.7e-57  194.1   0.0    1.3  1  GTP_EFTU      Elongation factor Tu GTP binding domain
    1.5e-39  134.8   0.6    4.8e-39  133.1   0.2    2.0  2  GTP_EFTU_D3   Elongation factor Tu C-terminal domain
    1.1e-15   57.7   1.7    2.9e-15   56.4   0.4    2.4  3  GTP_EFTU_D2   Elongation factor Tu domain 2
    8.8e-07   29.0   0.0    1.9e-05   24.7   0.0    2.3  1  MMR_HSR1      50S ribosome-binding GTPase
     0.0012   18.7   0.6     0.0034   17.3   0.6    1.7  1  GTP_EFTU_D4   Elongation factor Tu domain 4
     0.0026   17.2   0.0      0.034   13.5   0.0    2.1  1  Gtr1_RagA     Gtr1/RagA G protein conserved region
  ------ inclusion threshold ------
      0.052   13.1   0.1       0.42   10.1   0.1    2.3  2  FeoB_N        Ferrous iron transport protein B
      0.066   13.6   0.0       0.12   12.8   0.0    1.4  1  NTP_transf_3  MobA-like NTP transferase domain
       0.11   12.6   0.0        9.5    6.2   0.0    2.5  2  Dynamin_N     Dynamin family
       0.15   12.3   0.1         23    5.3   0.0    2.4  2  Roc           Ras of Complex, Roc, domain of DAPkinase


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 !  194.1   0.0   9.6e-61   1.7e-57       1     183 [.       5     208 ..       5     232 .. 0.89

  Alignments for each domain:
  == domain 1  score: 194.1 bits;  conditional E-value: 9.6e-61
                                    TCEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHH..HHHST.............HCHSHHHHHHTSCSSCEEEEEET CS
                       GTP_EFTU   1 krirnigiighvDhGKtTLtdrLlyktgaiskkgeka..eeerv.............lDtlkeErergiTiksaaislek 65 
                                    k+++n+++ighvDhGK+TL++r++y+ gai+++  ++  + e +             +D+lkeErerg+Ti++a+  ++ 
  gi|116754132|ref|YP_843250.1|   5 KPHLNLAFIGHVDHGKSTLVGRMMYEMGAIDEHIIEQyrK-E-AaakgkatfefawvMDSLKEERERGVTIDIAHQRFD- 81 
                                    579*****************************88888642.2.235788999***************************. PP

                                    TCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTE.EEEEEESCGST.....HHHH CS
                       GTP_EFTU  66 etkkylinliDtPGHvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvp.iivfiNKmDrl.....kael 139
                                     t+ky ++++D+PGH+dF+k++i+g++++D avlvv+a +Gv++qt+e++ la+++gv+ +iv+iNKmD +     ++++
  gi|116754132|ref|YP_843250.1|  82 -TDKYYFTVVDCPGHRDFVKNMITGASQADAAVLVVAAPDGVMAQTKEHVFLARTLGVNqLIVAINKMDATeppydEKRY 160
                                    .**********************************************************************999999999 PP

                                    HHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHH............H CS
                       GTP_EFTU 140 keiveevkqklsrkeeklekygekgekevpvvfgSalkgegvk............t 183
                                    +e++eev  kl      l+ +g+k + evp++++Sa++g++v             t
  gi|116754132|ref|YP_843250.1| 161 NEVKEEVG-KL------LRMVGYKID-EVPFIPVSAYNGDNVVkhsdrtkwytgpT 208
                                    99999999.55......588888885.9************9875555555555554 PP

>> GTP_EFTU_D3  Elongation factor Tu C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0         2   3.6e+03       7      53 ..     108     152 ..     103     167 .. 0.65
   2 !  133.1   0.2   2.7e-42   4.8e-39       3     111 ..     315     421 ..     313     422 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2
                                    CEEEEEEESSS..SS-BSTT-EEEEESSS-EEEEEEEEEEECCSSTT CS
                    GTP_EFTU_D3   7 kfeAqvyilekerhtpitagYrpvlyirtadvtgkvveLlskldkkt 53 
                                    + +A v+++     + + +  + v+ +rt  v+  +v++ +k+d  +
  gi|116754132|ref|YP_843250.1| 108 QADAAVLVVAA-PDGVMAQTKEHVFLARTLGVNQLIVAI-NKMDATE 152
                                    55666666666.445555666778999999999888888.6666544 PP

  == domain 2  score: 133.1 bits;  conditional E-value: 2.7e-42
                                    EEECCEEEEEEESSS..SS-BSTT-EEEEESSS-EEEEEEEEEEECCSSTTSB-BSS-SSCCSTT-CEEEEEEECCEEEE CS
                    GTP_EFTU_D3   3 kphtkfeAqvyilekerhtpitagYrpvlyirtadvtgkvveLlskldkktekvsekkpefvkpGdnvivevelikpial 82 
                                    + +++f+Aq+++l++  +++i agY+pv++++ta+v+++++e+++kld++t++v+e++p f+k+Gd++i++v+++kp+++
  gi|116754132|ref|YP_843250.1| 315 TVAKEFTAQIVVLQH--PSAISAGYTPVFHCHTAQVACTITEIKAKLDPRTGSVKEQNPAFIKTGDAAIISVRPTKPMVI 392
                                    6789***********..*************************************************************** PP

                                    --TTTHCCCCEEEEECTTCEEEEEEEEEE CS
                    GTP_EFTU_D3  83 ekgseypqlGrFaiReggrTvaaGvvtei 111
                                    ek++e+pqlGrFaiR++g T+aaG+ +++
  gi|116754132|ref|YP_843250.1| 393 EKVKEIPQLGRFAIRDMGMTIAAGMCQNV 421
                                    ************************99887 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       5.3   9.6e+03      23      51 ..      14      40 ..      10      48 .. 0.75
   2 ?   -2.1   0.0       2.9   5.2e+03      46      63 ..     159     176 ..     141     181 .. 0.60
   3 !   56.4   0.4   1.6e-18   2.9e-15       1      73 [.     241     307 ..     241     308 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 5.3
                                   C.TCTTSEEEEEEEEEEEEETEEESEEETT CS
                    GTP_EFTU_D2 23 g.ndtskkeivtrissletfhededeavag 51
                                   g +d +k+   t ++++  +++  de + +
  gi|116754132|ref|YP_843250.1| 14 GhVDHGKS---TLVGRMMYEMGAIDEHIIE 40
                                   44667788...8899999999999988655 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.9
                                    SEEETTSEEEEEEEESSC CS
                    GTP_EFTU_D2  46 deavaganaGvivaikgl 63 
                                    +  ++ + +G +++++g+
  gi|116754132|ref|YP_843250.1| 159 RYNEVKEEVGKLLRMVGY 176
                                    333555556655555554 PP

  == domain 3  score: 56.4 bits;  conditional E-value: 1.6e-18
                                    EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
                    GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtl 73 
                                    Gtv  grv++G+lkkGd+v + +     +   ++++s+e +h++  ea++g+n+G +v+++g +d i++Gd+ 
  gi|116754132|ref|YP_843250.1| 241 GTVPVGRVETGVLKKGDKVIFEP--AHVS---GEVKSIEIHHQEIPEAYPGDNIGWNVRGIGKND-IRRGDVC 307
                                    99*******************66..4357...99*******************************.*****95 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0     1e-08   1.9e-05       2      96 ..      10     128 ..       9     174 .. 0.71

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1e-08
                                    EEEEESTTSSHHHHHHHHH................T...............STEEESSSTTSSSSEEEEEEEETTEEEEE CS
                       MMR_HSR1   2 vaivGrpNvGKStLinalt................g...............ekaivsdkpgtTrdinegrvklkgkeiel 50 
                                     a++G+   GKStL+ +++                +               +  + +++ g+T+di + r+++++  +++
  gi|116754132|ref|YP_843250.1|  10 LAFIGHVDHGKSTLVGRMMyemgaidehiieqyrkEaaakgkatfefawvmDSLKEERERGVTIDIAHQRFDTDKYYFTV 89 
                                    689***************977766666666665550555566666665554567899999************9999**** PP

                                    EECGGCSSHHHHHHHHHHHHHHHHCTSEEEEEEETTTTCSHHHHHH CS
                       MMR_HSR1  51 vDtpGliegaseekglgkaflaleeadlillvvdaseeklkpldee 96 
                                    vD+pG  +    +  +++ +    +ad+++lvv a  +++ ++ +e
  gi|116754132|ref|YP_843250.1|  90 VDCPG--H----RDFVKNMITGASQADAAVLVVAAP-DGVMAQTKE 128
                                    *****..3....223555556666789999999766.333333333 PP

>> GTP_EFTU_D4  Elongation factor Tu domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.6   1.9e-06    0.0034      21      83 ..     245     305 ..     234     307 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.9e-06
                                    EEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEESS-TTT.S--TT- CS
                    GTP_EFTU_D4  21 vGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisiegkivGr.qikegd 83 
                                    vG +v +Gv+k g k+i e  +  Ge+++i+ +++++ ea  G++++  ++g  +G+ +i  gd
  gi|116754132|ref|YP_843250.1| 245 VG-RVETGVLKKGDKVIFEPAHVSGEVKSIEIHHQEIPEAYPGDNIGWNVRG--IGKnDIRRGD 305
                                    88.9******************************************999998..3441466666 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 !   13.5   0.0   1.9e-05     0.034      29     144 ..      67     171 ..      60     192 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.9e-05
                      Gtr1_RagA  29 lrlgatidveksevrflgnltlnlwDcgGqeafveeylssqkeeifrnvgvliyVfDvesreleedletlkeilealrqy 108
                                    ++ g+tid+ ++++  +++ ++ ++Dc+G ++fv+++++  ++      ++ + V+ +     +  +++ ke +  +r+ 
  gi|116754132|ref|YP_843250.1|  67 RERGVTIDIAHQRF-DTDKYYFTVVDCPGHRDFVKNMITGASQ-----ADAAVLVVAAP----DGVMAQTKEHVFLARTL 136
                                    56689*******99.58999****************8654332.....33333333333....23333334444333333 PP

                      Gtr1_RagA 109 speakvfvlihKmDliqedereeifeerkeeireei 144
                                      + ++ v i+KmD  +    e+ ++e kee+ + +
  gi|116754132|ref|YP_843250.1| 137 GVN-QLIVAINKMDATEPPYDEKRYNEVKEEVGKLL 171
                                    332.34455666666666666666666666665555 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.46   8.3e+02       2      20 ..       9      27 ..       8      34 .. 0.85
   2 ?   10.1   0.1   0.00023      0.42      32     117 ..      70     150 ..      69     196 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.46
                                   EEEEEESTTSSHHHHHHHH CS
                         FeoB_N  2 tvalvGnpnvGkttlfnal 20
                                   ++a++G  + Gk+tl+ ++
  gi|116754132|ref|YP_843250.1|  9 NLAFIGHVDHGKSTLVGRM 27
                                   5799***********8765 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00023
                                    TSSSEEEEEEEEETTEEEEEEE----SSS..SSSSHHHHHHHHHHHCTSSSEEEE.EEEGGGHHHHHHHHHHHHHTTSSE CS
                         FeoB_N  32 GvtvekkegklklkgkeveivDlPGiYsl..sayseeekvardflleeepdvvvn.vvdatnlernLyLtlqllelgvpv 108
                                    Gvt++ ++ +++++++ +++vD PG  ++  + ++   +    +l+   pd v+    +   l r+L +         ++
  gi|116754132|ref|YP_843250.1|  70 GVTIDIAHQRFDTDKYYFTVVDCPGHRDFvkNMITGASQADAAVLVVAAPDGVMAqTKEHVFLARTLGV--------NQL 141
                                    9************************97764355666666666667667777665302222223333322........345 PP

                                    EEEEETHHH CS
                         FeoB_N 109 vlalnmide 117
                                    ++a+n++d+
  gi|116754132|ref|YP_843250.1| 142 IVAINKMDA 150
                                    555555555 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 ?   12.8   0.0   6.5e-05      0.12      58     127 ..      54     122 ..      16     172 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.5e-05
                                    CTS-EEE-TTS.S-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSEE CS
                   NTP_transf_3  58 lgvrvvededp.gkgplaslaaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvptyeger 127
                                    ++  +v d+ + ++  + ++  a ++  d+d ++++ +D+P   +++v+ ++  a +++a+v+v+++ ++ 
  gi|116754132|ref|YP_843250.1|  54 FEFAWVMDSLKeERERGVTIDIAHQRF-DTDKYYFTVVDCPG-HRDFVKNMITGASQADAAVLVVAAPDGV 122
                                    456677776552477778888888888.9*************.99**********9999999888777665 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.027        49       1      17 [.      10      26 ..      10      31 .. 0.85
   2 ?    6.2   0.0    0.0053       9.5      64     158 ..      55     140 ..      26     147 .. 0.64

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.027
                                   EEEEEBTTTTHHHHHHH CS
                      Dynamin_N  1 iavvGsqSsGKSSvlna 17
                                   +a++G++ +GKS+++  
  gi|116754132|ref|YP_843250.1| 10 LAFIGHVDHGKSTLVGR 26
                                   589**********9865 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0053
                                    -CHHHHHHHHHHHHHHHTSSSS--SS-EEEEEEETTS-SEEEEE---B-SSSGTTSHHHHHHHSTTEEEEEEEETTS-CC CS
                      Dynamin_N  64 dfsevreeieketekiagankgiskkvillkilsllvkgltlvDlPGldsvnkrdqelvkeyikkadiilavtsanhdls 143
                                    +f  v + +++e+e+         ++ i ++ ++ ++   t+vD PG  +  k   ++++ + +  +++l+v + +  ++
  gi|116754132|ref|YP_843250.1|  55 EFAWVMDSLKEERERGV-------TIDIAHQRFDTDKYYFTVVDCPGHRDFVK---NMITGASQADAAVLVVAAPDGVMA 124
                                    33333333333333333.......3378899999999**********988433...578888877777777776666777 PP

                                    C-.CHHHHHHHHSTTB CS
                      Dynamin_N 144 ns.ealflarevdpkg 158
                                    ++ e  flar + +++
  gi|116754132|ref|YP_843250.1| 125 QTkEHVFLARTLGVNQ 140
                                    6658888888776665 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.019        34       2      22 ..      10      30 ..       9      42 .. 0.87
   2 ?    5.3   0.0     0.013        23      10     119 ..      49     149 ..      46     150 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.019
                                   EEEESSTTSSHHHHHHCHCT- CS
                            Roc  2 vvlvGdsgvGKtsllkrfved 22
                                   + ++G    GK++l+ r++ +
  gi|116754132|ref|YP_843250.1| 10 LAFIGHVDHGKSTLVGRMMYE 30
                                   5789*************9976 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.013
                                    SSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHHHCTSCEEEEEEE. CS
                            Roc  10 vGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhplylreaalailvyd. 88 
                                     GK ++   +v d+ +e+++  + +d++++++           ++k+ + + D  G+ +f + +    ++a++a+lv+  
  gi|116754132|ref|YP_843250.1|  49 KGKATFEFAWVMDSLKEERERGVTIDIAHQRFD----------TDKYYFTVVDCPGHRDFVKNMITGASQADAAVLVVAa 118
                                    699999999999999999999999999988762..........23578************99888888888888888773 PP

                                    .GHHHHCHHHHHHHHHHHCSSS-EEEEEE-TT CS
                            Roc  89 .srssenlkeWlkelkkvagkspvilvgnkiD 119
                                     +   ++ ke +  l +  g +++i+ +nk+D
  gi|116754132|ref|YP_843250.1| 119 pDGVMAQTKEHVF-LARTLGVNQLIVAINKMD 149
                                    2223344444444.455566677888888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); 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:                        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 0.27s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 3215.09
//
Query:       gi|116754133|ref|YP_843251.1|  [L=102]
Description: 30S ribosomal protein S10P [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.2e-26   90.7   0.0    5.8e-26   90.6   0.0    1.0  1  Ribosomal_S10  Ribosomal protein S10p/S20e
  ------ inclusion threshold ------
      0.016   16.0   0.0      0.035   14.9   0.0    1.5  2  PriA_C         Primosomal protein N C-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_S10  Ribosomal protein S10p/S20e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.6   0.0   6.5e-30   5.8e-26       1      97 [.       5      98 ..       5      99 .. 0.99

  Alignments for each domain:
  == domain 1  score: 90.6 bits;  conditional E-value: 6.5e-30
                                   EEEEEESSHHHHHHHHHHHHHHTTSSS-EE---EEEEEEEEEEEEE--SS--.S--EEEEEEEEEEEEEEEE.E-HHHHHHH CS
                  Ribosomal_S10  1 rirlkSydsklLekavkkivraakelgikvkgpvplPtkrkrvtvlksphvd.kksreqfeirthkRlidisdatketidtl 81
                                   rirl++++++ L+++++++  +a+++g+ + gp+plPtkr+ v+ +ksp ++ + +++++e+r+hkRlid+ da+++ +++l
  gi|116754133|ref|YP_843251.1|  5 RIRLSGTNPATLDEICNQVRGIAQRTGVHMAGPIPLPTKRLVVPCRKSPDGEgSATWDHWEMRVHKRLIDL-DADERALRQL 85
                                   8**********************************************************************.8********* PP

                                   S-...S---SS-EEEE CS
                  Ribosomal_S10 82 lkllqlnlpegVsvev 97
                                   ++   +++p+ V++e+
  gi|116754133|ref|YP_843251.1| 86 MR---IQVPKNVNIEI 98
                                   **...*********97 PP

>> PriA_C  Primosomal protein N C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   3.9e-06     0.035       6      51 ..       4      45 ..       1      47 [. 0.93
   2 ?   -2.3   0.0      0.94   8.4e+03      68      74 ..      81      87 ..      70      98 .. 0.54

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.9e-06
                         PriA_C  6 alirvsgkdeekveeaaeelaellkealkleeveilgpapapiaki 51
                                   a+ir+sg++ +++ e +++++ + ++    ++v++ gp+p p +++
  gi|116754133|ref|YP_843251.1|  4 ARIRLSGTNPATLDEICNQVRGIAQR----TGVHMAGPIPLPTKRL 45
                                   89*********************999....6799********9986 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.94
                         PriA_C 68 alqkllk 74
                                   al++l++
  gi|116754133|ref|YP_843251.1| 81 ALRQLMR 87
                                   3333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); 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: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 784.40
//
Query:       gi|116754134|ref|YP_843252.1|  [L=190]
Description: GTP-binding protein [Methanosaeta thermophila PT]
Scores for complete 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-16   58.9   0.0    5.9e-16   58.6   0.0    1.2  1  MMR_HSR1     50S ribosome-binding GTPase
    1.8e-11   43.8   0.0    1.8e-10   40.5   0.0    2.0  1  FeoB_N       Ferrous iron transport protein B
    3.2e-05   24.0   0.0     0.0064   16.6   0.0    2.1  2  Dynamin_N    Dynamin family
    0.00049   20.0   0.0      0.049   13.5   0.0    2.3  2  RsgA_GTPase  RsgA GTPase
    0.00053   19.6   0.0      0.034   13.7   0.0    2.2  2  GTP_EFTU     Elongation factor Tu GTP binding domain
     0.0033   17.1   0.0       0.84    9.2   0.0    2.1  2  Ras          Ras family
     0.0085   16.6   0.0     0.0098   16.4   0.0    1.5  1  ABC_tran     ABC transporter
  ------ inclusion threshold ------
      0.013   15.7   0.0      0.023   14.9   0.0    1.7  1  Roc          Ras of Complex, Roc, domain of DAPkinase
      0.016   15.0   0.0      0.021   14.6   0.0    1.4  1  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
      0.033   13.6   0.0      0.048   13.1   0.0    1.3  1  SRPRB        Signal recognition particle receptor beta subuni
      0.044   13.5   0.0      0.079   12.7   0.0    1.5  1  PduV-EutP    Ethanolamine utilisation - propanediol utilisati
      0.063   13.8   0.0       0.48   11.0   0.0    2.1  2  AAA_18       AAA domain
       0.15   11.8   0.0       0.28   11.0   0.0    1.4  1  AAA_29       P-loop containing region of AAA domain
       0.18   11.2   0.0       0.34   10.3   0.0    1.5  2  Arf          ADP-ribosylation factor family
       0.19   11.0   0.0        2.9    7.1   0.0    2.0  2  Septin       Septin


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 !   58.6   0.0   4.9e-19   5.9e-16       1      87 [.       3      99 ..       3     131 .. 0.67

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 4.9e-19
                                   EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSS........HHHHHH.HHHHHHHHH CS
                       MMR_HSR1  1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGlie........gaseek.glgkaflal 73
                                   e+++vGr+NvGKStL++altge++ ++++pg+T  +   r+     +++ vD+pG +         ++++   +l  ++l+ 
  gi|116754134|ref|YP_843252.1|  3 EIVLVGRSNVGKSTLFRALTGERVPIGRRPGVTFRPYSVRIG----NLTYVDMPG-YGfmkyrswrDQER-VkDLIVRYLE- 77
                                   699************************************997....6********.74322333312222.2355555554. PP

                                   HCTSEEEEEEETT........T CS
                       MMR_HSR1 74 eeadlillvvdas........e 87
                                   + ad i+  v+++         
  gi|116754134|ref|YP_843252.1| 78 DHADRIITAVQVTdaasfleiA 99
                                   3378888888755333333331 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 !   40.5   0.0   1.5e-13   1.8e-10       2      91 ..       3      92 ..       2     152 .. 0.73

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 1.5e-13
                                   EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSS.HHHHHHHHHHH...CTSS CS
                         FeoB_N  2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsays.eeekvardfll...eeep 79
                                   +++lvG  nvGk+tlf altg +  +g  pGvt    ++++     +++ vD+PG   ++  s ++++ ++d+++   e+++
  gi|116754134|ref|YP_843252.1|  3 EIVLVGRSNVGKSTLFRALTGERVPIGRRPGVTFRPYSVRIG----NLTYVDMPGYGFMKYRSwRDQERVKDLIVrylEDHA 80
                                   699*********************************999999....999******755554443466666666654556777 PP

                                   SEEEEEEEGGGH CS
                         FeoB_N 80 dvvvnvvdatnl 91
                                   d +++ v+ t  
  gi|116754134|ref|YP_843252.1| 81 DRIITAVQVTDA 92
                                   777654444333 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   5.3e-06    0.0064       1      40 [.       4      43 ..       4      45 .. 0.82
   2 !    7.9   0.0    0.0024       2.9      92     139 ..      35      90 ..      33     108 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.3e-06
                                   EEEEEBTTTTHHHHHHHHHTS--S---SS.S---S-EEEEE CS
                      Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilprgpn.ptTrrplelql 40
                                   i++vG  + GKS++  aL+ge++ p+g    +T rp  ++ 
  gi|116754134|ref|YP_843252.1|  4 IVLVGRSNVGKSTLFRALTGERV-PIGRRpGVTFRPYSVRI 43
                                   89********************6.55555268988888876 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0024
                                    EEEEEETTS-SEEEEE---B-SSSGTTS.......HHHHHHH.STTEEEEEEEETT CS
                      Dynamin_N  92 llkilsllvkgltlvDlPGldsvnkrdq.......elvkeyi.kkadiilavtsan 139
                                    +++++s    +lt vD+PG+  ++ r         +l+ +y+ ++ad i+  ++  
  gi|116754134|ref|YP_843252.1|  35 TFRPYSVRIGNLTYVDMPGYGFMKYRSWrdqervkDLIVRYLeDHADRIITAVQVT 90 
                                    5788999999*********87655544444589999******99999988655544 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   4.1e-05     0.049     102     122 ..       4      24 ..       2      43 .. 0.92
   2 ?    4.3   0.0     0.027        33      45      71 ..     121     147 ..     115     186 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.1e-05
                                    EEEECSTTSSHHHHHHHHCTT CS
                    RsgA_GTPase 102 svlvGqSGvGKStLinallpe 122
                                    +vlvG S vGKStL  al++e
  gi|116754134|ref|YP_843252.1|   4 IVLVGRSNVGKSTLFRALTGE 24 
                                    69****************987 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.027
                                    TT-EEEEEEE-GGG--HHHHHHHHHHH CS
                    RsgA_GTPase  45 kgiepvivlnKiDlleeeeeleelkee 71 
                                     +++p+++ nKiD + ++e++ ++ +e
  gi|116754134|ref|YP_843252.1| 121 LKLNPILAANKIDRIANREQVLDWIAE 147
                                    5789***********999955555443 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.025        29       5      27 ..       3      25 ..       1      54 [. 0.85
   2 !   13.7   0.0   2.8e-05     0.034      85     144 ..      81     147 ..      77     183 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.025
                                   EEEEEESTTSSHHHHHHHHHHHT CS
                       GTP_EFTU  5 nigiighvDhGKtTLtdrLlykt 27
                                    i+++g  + GK+TL  +L+ + 
  gi|116754134|ref|YP_843252.1|  3 EIVLVGRSNVGKSTLFRALTGER 25
                                   5889999*********9998665 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 2.8e-05
                                    HHHHHHHHT-SEEEEEEETT....TBSTHHHHHHHHHHHHTTTEEEEEEESCGST...HHHHHHHHH CS
                       GTP_EFTU  85 kevirglrvlDgavlvvdav....eGvepqteevlrlalkegvpiivfiNKmDrl...kaelkeive 144
                                    + +i++++v+D a ++  a+    +G  p   e+++ + ++++++i++ NK+Dr+   ++ l++i+e
  gi|116754134|ref|YP_843252.1|  81 DRIITAVQVTDAASFLEIAErwesRGEVPVEIEMWEFLCDLKLNPILAANKIDRIanrEQVLDWIAE 147
                                    566777777777766665555666788888899*********************9554444444444 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0    0.0007      0.84       2      22 ..       4      24 ..       3      51 .. 0.82
   2 !    6.1   0.0    0.0064       7.6      58     117 ..      65     135 ..      57     158 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0007
                                   EEEEESTTSSHHHHHHHHHHS CS
                            Ras  2 lvlvGdsavGKtslllrfvkd 22
                                   +vlvG s+vGK++l    + +
  gi|116754134|ref|YP_843252.1|  4 IVLVGRSNVGKSTLFRALTGE 24
                                   89************8877665 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0064
                                    SGGGHHHHHHHHTT.ESEEEEEEETTBHHHHHTHH.HHHHHHHHHST.........TTSEEEEEEETTTGG CS
                            Ras  58 qeefkslrelyyrd.aegillvyditsresfenvk.kwveeikrvae.........envpivLvGnKvDle 117
                                    qe+ k l   y++d a+ i+   ++t+++sf +++ +w +  +  +e          +++ +L +nK+D  
  gi|116754134|ref|YP_843252.1|  65 QERVKDLIVRYLEDhADRIITAVQVTDAASFLEIAeRWESRGEVPVEiemweflcdLKLNPILAANKIDRI 135
                                    8999999999998637889999***********99677653332222335556655457777888887754 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   8.2e-06    0.0098      14      37 ..       4      27 ..       3     162 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 8.2e-06
                                   EEEEESTTSSHHHHHHHHTTSS-- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran 14 vaivGenGaGKStLlkllagllkp 37
                                   +++vG++  GKStL+++l+g+  p
  gi|116754134|ref|YP_843252.1|  4 IVLVGRSNVGKSTLFRALTGERVP 27
                                   689*****************9776 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 ?   14.9   0.0   1.9e-05     0.023       2      32 ..       4      34 ..       3     134 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.9e-05
                                   EEEESSTTSSHHHHHHCHCT-CCC-EEETTT CS
                            Roc  2 vvlvGdsgvGKtsllkrfvedkfsekeksti 32
                                   +vlvG s+vGK++l++ ++ +++   +++ +
  gi|116754134|ref|YP_843252.1|  4 IVLVGRSNVGKSTLFRALTGERVPIGRRPGV 34
                                   89****************9988866665544 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.8e-05     0.021       3      21 ..       5      23 ..       4      86 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.8e-05
                         AAA_21  3 vliGpNgsGKSnLLdaldl 21
                                   vl+G+ ++GKS+L++al +
  gi|116754134|ref|YP_843252.1|  5 VLVGRSNVGKSTLFRALTG 23
                                   9****************54 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 ?   13.1   0.0     4e-05     0.048       5      99 ..       3      96 ..       1     112 [. 0.70

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4e-05
                                   EEEEE-STTSSHHHHHHHHHHSS---B---SS-EEETTG...GGTT-SEEEETT-GCCSHHHHHHHHHHGGEEEEE.....E CS
                          SRPRB  5 avllvGlsdsGKTslftrLttdsvkktvtSqessaalkvksekgskltliDfPGheklrqklleklkaksslkglv.....f 81
                                    ++lvG s+ GK +lf  Lt + v    +   + ++ +  s +  +lt +D+PG   ++++       ++++k l+      
  gi|116754134|ref|YP_843252.1|  3 EIVLVGRSNVGKSTLFRALTGERVP---IGRRPGVTFRPYSVRIGNLTYVDMPGYGFMKYRSWRD---QERVKDLIvryleD 78
                                   589****************988764...566788888877889999*******998888775544...33333333120003 PP

                                   EEETTS-HHHHHHHHHHH CS
                          SRPRB 82 vvDStidpkevkevAEll 99
                                     D  i   +v++ A +l
  gi|116754134|ref|YP_843252.1| 79 HADRIITAVQVTDAASFL 96
                                   445556666666666665 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   6.7e-05     0.079       1      26 [.       1      26 [.       1      65 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.7e-05
                      PduV-EutP  1 mkkilliGkvgsGKttLtqalkgeel 26
                                   m +i+l+G++++GK tL +al+ge++
  gi|116754134|ref|YP_843252.1|  1 MCEIVLVGRSNVGKSTLFRALTGERV 26
                                   6689******************9976 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0004      0.48       1      45 [.       4      61 ..       4      86 .. 0.67
   2 ?    0.7   0.0      0.61   7.3e+02     101     123 ..      93     114 ..      62     120 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0004
                         AAA_18  1 IlltGtpGvGKttlakeLskrl.gf...........gvnlrdvakenglllevdpe.a 45
                                   I+l G + vGK+tl ++L  +   +           +v+++ + + +++ +++ ++  
  gi|116754134|ref|YP_843252.1|  4 IVLVGRSNVGKSTLFRALTGERvPIgrrpgvtfrpySVRIGNLTYVDMPGYGFMKYrS 61
                                   899***************4442233556655666666666666666666666666653 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.61
                         AAA_18 101 aspeelleRlekRgyeeakiken 123
                                    as  e +eR e Rg+ + +i e+
  gi|116754134|ref|YP_843252.1|  93 ASFLEIAERWESRGEVPVEI-EM 114
                                    56678999999999999988.54 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00023      0.28      26      42 ..       5      21 ..       2      27 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00023
                         AAA_29 26 lltGpsGsGKSTllDAi 42
                                   +l+G+s +GKSTl+ A+
  gi|116754134|ref|YP_843252.1|  5 VLVGRSNVGKSTLFRAL 21
                                   799**********9886 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00028      0.34      16      69 ..       3      55 ..       1     101 [. 0.76
   2 ?   -2.8   0.0       3.1   3.7e+03     120     129 ..     127     136 ..     122     160 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00028
                                   EEEEEESTTSSHHHHHHHHHHSSCEE.CSSSSSEEEEEEEETTEEEEEEEE-SSG CS
                            Arf 16 rilllGLDnaGKtTilkklkleelvt.tvPTigfnveeleiknlkftvwDvGGqe 69
                                    i+l+G  n GK+T+   l+ e++     P + f   +++i nl++   D+ G  
  gi|116754134|ref|YP_843252.1|  3 EIVLVGRSNVGKSTLFRALTGERVPIgRRPGVTFRPYSVRIGNLTY--VDMPGYG 55
                                   699*******************9976589*********99999875..4555544 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.1
                                    EEEE-TTSTT CS
                            Arf 120 vlaNKqDlpe 129
                                    + aNK+D   
  gi|116754134|ref|YP_843252.1| 127 LAANKIDRIA 136
                                    5577777543 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0    0.0025       2.9       6      27 ..       3      24 ..       1      31 [. 0.87
   2 ?    1.9   0.0     0.096   1.1e+02      63      99 ..      45      86 ..      36      96 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0025
                                   EEEEEEBTTSSCCCCCCTTSSS CS
                         Septin  6 tlmvvGesglGkttlintlfet 27
                                    +++vG+s +Gk+tl+++l  +
  gi|116754134|ref|YP_843252.1|  3 EIVLVGRSNVGKSTLFRALTGE 24
                                   5899************999765 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.096
                                   EEEEEE---BS.....SSSSHHCCCHHHHHHHHHHHHHHHHH CS
                         Septin 63 nltviDtpgfG.....davdnskswepiveyideqfeeylre 99
                                   nlt +D pg+G        d ++  + iv+y++++ ++++++
  gi|116754134|ref|YP_843252.1| 45 NLTYVDMPGYGfmkyrSWRDQERVKDLIVRYLEDHADRIITA 86
                                   8999******94333223467777788888988888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1407.29
//
Query:       gi|116754135|ref|YP_843253.1|  [L=148]
Description: hypothetical protein Mthe_0824 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.028   14.2   0.0      0.059   13.2   0.0    1.5  1  WIYLD     Ubiquitin-binding WIYLD domain


Domain annotation for each model (and alignments):
>> WIYLD  Ubiquitin-binding WIYLD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.3e-06     0.059      31      46 ..      60      75 ..      57      79 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.3e-06
                          WIYLD 31 kLLkvYgknWeliEed 46
                                    LL vYg++W+ iE++
  gi|116754135|ref|YP_843253.1| 60 ALLMVYGEDWSWIEDQ 75
                                   79************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); 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: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1178.36
//
Query:       gi|116754136|ref|YP_843254.1|  [L=257]
Description: dihydrodipicolinate reductase [Methanosaeta thermophila PT]
Scores for complete 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-44  148.7   0.1    9.7e-44  148.3   0.1    1.2  1  DapB_C           Dihydrodipicolinate reductase, C-terminus
    2.7e-28   98.6   0.1    5.1e-28   97.7   0.1    1.4  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
  ------ inclusion threshold ------
      0.037   14.3   0.5        0.2   11.9   0.0    2.2  3  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma


Domain annotation for each model (and alignments):
>> DapB_C  Dihydrodipicolinate reductase, C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.3   0.1   1.6e-47   9.7e-44       1     121 []     124     254 ..     124     254 .. 0.92

  Alignments for each domain:
  == domain 1  score: 148.3 bits;  conditional E-value: 1.6e-47
                                    HHHHHHHHHHHHCCCSTTT-EEEEEEEESTT--SSS-HHHHHHHHHHH.................-S-ETTCCCEEEETT CS
                         DapB_C   1 GvnlllklveeaakllkeaydveiiEkHhnkKaDaPSGTAlalaeaia.........egke....arkkkeigihsvRgg 67 
                                    Gvn++ klve+aa+ l++ ydve+iE+Hh+kK+DaPSGTA++++e ++         +        ++ +eig+h+vR+g
  gi|116754136|ref|YP_843254.1| 124 GVNVFWKLVEMAARSLSD-YDVEVIEAHHRKKKDAPSGTAMRTVEILSrslgiedvrH--GregmCERGREIGVHAVRAG 200
                                    9***************99.*****************************8888776652..0446534457********** PP

                                    T--CCCCEEEECTTEEEEEEEEEESCHHHHHHHHHHHHHH.HCTSSEESHHHHH CS
                         DapB_C  68 gvvgehevlfagegevieikhealsreiFaeGallaaewlakkkkglysmedvL 121
                                    ++vg+h+vlfag ge+ieikh+a+sr+ Fa+Gal+aa+w++k+++g+ sme+vL
  gi|116754136|ref|YP_843254.1| 201 DIVGDHTVLFAGPGERIEIKHQAHSRSAFARGALRAARWVVKAPPGIHSMEEVL 254
                                    ****************************************999*********98 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.7   0.1   8.5e-32   5.1e-28       2     124 .]       3     121 ..       2     121 .. 0.90

  Alignments for each domain:
  == domain 1  score: 97.7 bits;  conditional E-value: 8.5e-32
                                    EEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEB..SSHHHHHHH..-SEEEE-S-H CS
                         DapB_N   2 kvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavt..ddleevlek..advliDFTtp 77 
                                     va++Ga+GrmG+ +++ +++++dl+lvaa+d  +  + ++ +g        +v v+   d+++vl++   dvliDFT+p
  gi|116754136|ref|YP_843254.1|   3 DVALTGAKGRMGSLIIDEIRSSPDLKLVAAIDIIG--IGDRVLG--------DVCVSdaRDVQRVLREsrPDVLIDFTVP 72 
                                    699******************************98..3444444........344443389999999999********** PP

                                    HHHHHHHHHHHHTT-EEEE--SS--HHHHHHHHHHTTT..SEEEE-S-- CS
                         DapB_N  78 eavlenlklalekgvklViGTTGlseeelaeleelakk..igvviapNf 124
                                    +a+len+++a+++gv+lV+GTTG+see+l+ +ee+ k+  i++vi+pNf
  gi|116754136|ref|YP_843254.1|  73 SAALENIHAAADTGVALVVGTTGFSEEQLSIIEEMIKSagIAAVISPNF 121
                                    **********************************999999********8 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   0.1      0.22   1.3e+03       3      24 ..       6      28 ..       4      39 .. 0.80
   2 ?   11.9   0.0   3.4e-05       0.2      56     113 ..      48      99 ..      44     116 .. 0.77
   3 ?   -2.5   0.0      0.94   5.6e+03      26      61 ..     143     180 ..     131     197 .. 0.51

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.22
                                   EE--.SHHHHHHHHHHHCTCCT- CS
                Sacchrp_dh_NADP  3 iiGa.GsvGqavaellarhfdvd 24
                                   + Ga G++G+ +++++  + d++
  gi|116754136|ref|YP_843254.1|  6 LTGAkGRMGSLIIDEIRSSPDLK 28
                                   66999*********999988873 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 3.4e-05
                                    TTTHHHHHHHHHTTS..SEEEE-SSGGGHHHHHHHHHHHT-EEEE..SS-BCGCCSCHCCSH CS
                Sacchrp_dh_NADP  56 aenyeavLaallkeg..dlvvnlsppissldvlkaCietgvhyvd..tsiskeertnyalre 113
                                    +++ ++ ++++l+e   d++++ ++p  +l+ + a+++tgv+ v   t +          +e
  gi|116754136|ref|YP_843254.1|  48 VSDARD-VQRVLRESrpDVLIDFTVPSAALENIHAAADTGVALVVgtTGF---------SEE 99 
                                    678899.999999999*************************999765666.........222 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.94
                                    EEEEEESSHHHHHHHHCHH..TTTCEEEEE--TTTHHH CS
                Sacchrp_dh_NADP  26 eitvadrskeklealaaka..lgvrfeaialdaenyea 61 
                                    ++ v++ +++k + + + +  + v++ +++l +e++++
  gi|116754136|ref|YP_843254.1| 143 DVEVIEAHHRKKKDAPSGTamRTVEILSRSLGIEDVRH 180
                                    44444444444333332223355555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); 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 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1917.62
//
Query:       gi|116754137|ref|YP_843255.1|  [L=295]
Description: dihydrodipicolinate synthase [Methanosaeta thermophila PT]
Scores for complete 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-98  327.1   0.0      7e-98  326.9   0.0    1.0  1  DHDPS            Dihydrodipicolinate synthetase family
  ------ inclusion threshold ------
      0.093   12.9   0.1       0.27   11.4   0.0    1.8  2  YjgF_endoribonc  YjgF/chorismate_mutase-like, putative endori


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 !  326.9   0.0  7.8e-102     7e-98       2     288 ..       2     286 ..       1     287 [. 0.98

  Alignments for each domain:
  == domain 1  score: 326.9 bits;  conditional E-value: 7.8e-102
                                    -SEEEEE----B-TTSSB-HHHHHHHHHHHHHCT-SEEEESSCCCTGGGS-HHHHHHHHHHHHHHHTTSSEEEEE---SS CS
                          DHDPS   2 fsgiitalvtpfdedgkldkealrklieflinkgvdglvvaGttGEsatlsteekeqlveiaveaakgripviagvGsns 81 
                                    f+g+++a++tpf+ dg ld+  lr+++e l + g++g+v +GttGEsatls+ee++++vei+v++ +  +pv+ag+Gsn+
  gi|116754137|ref|YP_843255.1|   2 FRGVFPAIITPFKDDGSLDEDGLRRNVEVLSKTGISGVVPCGTTGESATLSHEEHKKVVEIVVDCSD--VPVVAGTGSNN 79 
                                    89***************************************************************76..*********** PP

                                    HHHHHHHHHCCCCCT-SEEEEE---SS---HHHHHHHHHHHHHCHSS-EEEEE-HHHHSHHHHHHHHHHHHTSTTEEEEE CS
                          DHDPS  82 tseaiklakkaeeaGadgvlavtPYYnkpsqeglyqhfkaiieatdlpvilYnvpsrtgadlspetvkrLaelenivgvK 161
                                    tseai+l+++a++aGad++l++tPYYn+p+ +gl +hf++++e+ d p++lYnvp+rtg++l p++v+rL+e++niv++K
  gi|116754137|ref|YP_843255.1|  80 TSEAIELTRHAADAGADAALLITPYYNRPNERGLFEHFRKVAESSDIPIVLYNVPKRTGVELRPDVVARLSEISNIVAIK 159
                                    ******************************************************************************** PP

                                    E-SS-CTHHHHHHC.CCSTTSEEEES-GGGHHHHHHTT-SEEEESCHHCHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                          DHDPS 162 eavgdleevikikk.evgkdlviysGddelllsalslGadGvisvtsniagermrqlikalkeGdlaeaaelnekllpli 240
                                    ea+g+l++v +i++ +++k+++++sGdd+l+l++l lGa+Gv+sv +n+a++   ++++a  +G++  a+el+ +l pl+
  gi|116754137|ref|YP_843255.1| 160 EASGSLTQVSRIIElTADKNFAVLSGDDDLTLPMLALGATGVVSVVANVAPRATVEMVNAFLDGNITRAQELHYRLAPLV 239
                                    ***********998246789************************************************************ PP

                                    HHCCCCSCCHHHHHHHHCTTSSSBB.--TTS--S-HHHHHHHHHHHHH CS
                          DHDPS 241 kilfaepnvilvktalellGlvveatlrkPltpleeeekeeleallka 288
                                     ++f e+n+i+vkta ++lG+ +++ lr Pl+p+++e++ +l+++l++
  gi|116754137|ref|YP_843255.1| 240 RAMFLETNPIPVKTAYRMLGMAAGP-LRLPLAPMSDENEAKLRDVLTK 286
                                    *************************.****************999875 PP

>> YjgF_endoribonc  YjgF/chorismate_mutase-like, putative endoribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.46   4.1e+03      93     124 ..      59      89 ..      49      96 .. 0.75
   2 ?   11.4   0.0     3e-05      0.27      62      93 ..     146     177 ..     142     207 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.46
                                    EE-B-TT---HHHHHHHHHHHHHHHHGGGG-- CS
                YjgF_endoribonc  93 vlnvtqdyiempkvldaasdlllevlGeaGrh 124
                                    v+++  d+ + p v  + s+   e + e  rh
  gi|116754137|ref|YP_843255.1|  59 VVEIVVDCSDVPVVAGTGSNNTSEAI-ELTRH 89 
                                    67888899999999888887666654.45555 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 3e-05
                                    HHHHHHHHHHHHHHHHHSSGGG-SEEEEEEEE CS
                YjgF_endoribonc  62 aarlaalnalaqlkeaaGelarvkrlirleGv 93 
                                     arl+ +  +  +kea+G+l++v r+i l   
  gi|116754137|ref|YP_843255.1| 146 VARLSEISNIVAIKEASGSLTQVSRIIELTAD 177
                                    58*************************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); 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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2183.20
//
Query:       gi|116754138|ref|YP_843256.1|  [L=86]
Description: ribosomal protein S17E-like [Methanosaeta thermophila PT]
Scores for complete 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   46.0   0.2      5e-12   45.8   0.2    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 !   45.8   0.2   2.8e-16     5e-12       1      60 [.      15      74 ..      15      82 .. 0.96

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 2.8e-16
                                   XX----HHHHHHHHHHHHS-TTT--S-HHHHHHHHHHHS----SHHHHHHHHHHHHHHHH CS
                 Ribosomal_S17e  1 mgrvrtktvKkaarviiekyyskltndFhtnkkvceevaiipskklrnkiaGyvthlmkr 60
                                   mg+v+   +K  a++++ +y  ++t+dF++nk+ ++  + +++k +rn+iaGy+t+++++
  gi|116754138|ref|YP_843256.1| 15 MGCVKPSYIKNFAKKLLSTYEGEFTTDFEMNKEKVSAYTNVRNKAIRNRIAGYITRILEQ 74
                                   9*******************************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.27s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 630.42
//
Query:       gi|116754139|ref|YP_843257.1|  [L=452]
Description: phosphomethylpyrimidine kinase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-83  280.0   0.4    1.9e-83  279.7   0.4    1.1  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase
    5.4e-65  218.0   0.3    8.8e-65  217.3   0.3    1.4  1  ThiP_synth    Thiamine-phosphate synthase
    9.8e-12   44.8   0.3    2.2e-11   43.6   0.3    1.4  1  PfkB          pfkB family carbohydrate kinase


Domain annotation for each model (and alignments):
>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  279.7   0.4   3.1e-87   1.9e-83       1     246 []      12     261 ..      12     261 .. 0.99

  Alignments for each domain:
  == domain 1  score: 279.7 bits;  conditional E-value: 3.1e-87
                                    ETTSSSHHHHHHHHHHHTTEEEEEEEEEEEEEETTCEEEEEE--HHHHHHHHHHHHHTS--SEEEE-S--SHHHHHHHHH CS
                   Phos_pyr_kin   1 DssGGAGiqADlktfsalgvygmsvitaltaqntkgvkevhplpaelveaqleavledvkvdavKiGmlasaeiievvae 80 
                                    Ds+GGAGiqADlktf+algv+g+svita+taqnt gv+ev+p+pae++++ql+a++ed++++ +K+Gml+s ++i++vae
  gi|116754139|ref|YP_843257.1|  12 DSGGGAGIQADLKTFAALGVHGLSVITAVTAQNTLGVREVFPIPAEMIASQLDALVEDFDISWAKTGMLFSPDAISLVAE 91 
                                    9******************************************************************************* PP

                                    HHHHTTSSEEEE---SSCTSSSBSSHHHHHHHHHHTGGG-SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHHTT-SEEE CS
                   Phos_pyr_kin  81 klkkykvpvVlDPVmvaksgselleeeavealkeeLlplatvitPNlpEaeaLlgekikteedmkeaakkllklgakaVl 160
                                     l++ ++ vV+DPV++a+ g +l++e a+ +l++eL+p a+vitPN++Eaea++g k+ ++e+++eaa ++l++ga+aV+
  gi|116754139|ref|YP_843257.1|  92 RLRELRCSVVVDPVIAAEAGGSLIAEGAILTLRDELIPVASVITPNIFEAEAITGVKVVDLESAREAAMRILDMGARAVV 171
                                    ******************************************************************************** PP

                                    EEEGGS-S.....SSEEEEEEEETSSEEEEEEEE----S--BTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHHHHCG CS
                   Phos_pyr_kin 161 ikGghleg.....eeavvtdvlydgeeveeleaerietknthGtGCtlssaiaaelakgesleeAvkkAkeyvteaikea 235
                                    i+Gghl+        ++++d+l++++ v  ++++r e   +hG GCt+s+a++a l+ g+sl +Av++A+++  ++i+ +
  gi|116754139|ref|YP_843257.1| 172 ITGGHLDCraagmPADECVDLLVTKDAVACVSGKRRE-GGNHGVGCTYSAALTALLSMGMSLDDAVRQAHNFAARSIEGS 250
                                    ******8889999888999******************.99**************************************** PP

                                    -BSTSSS-B-- CS
                   Phos_pyr_kin 236 lelgkgagpvn 246
                                      +g+ga pv+
  gi|116754139|ref|YP_843257.1| 251 RPVGHGAAPVD 261
                                    ********996 PP

>> ThiP_synth  Thiamine-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  217.3   0.3   1.5e-68   8.8e-65       2     163 ..     279     440 ..     278     442 .. 0.98

  Alignments for each domain:
  == domain 1  score: 217.3 bits;  conditional E-value: 1.5e-68
                                    HHHHHHHHHCC--.GCC--TT-B-EEEE-ST--SGGGEEEETT-EEE-TSSEEE-S-EEETS-CHHHHHHHHHHCC-TT- CS
                     ThiP_synth   2 leralelleeeeefakliPevgsNiayalpdAksieDvaavpGRIvrvkgrvkvvgepefgasshvarvllaamkfdpev 81 
                                    l+ a+++l +ee fa+liPevgsNi++a+p+A+s +Dvaav+GRIvr+++r +v g+++fgas+h+ar++laam+fd  +
  gi|116754139|ref|YP_843257.1| 279 LDHAVSMLRDEETFAELIPEVGSNIGMAIPGARSRADVAAVEGRIVRAGRRSHVSGCIRFGASRHIARIILAAMRFDMGI 358
                                    889***************************************************************************** PP

                                    -EEEEEE--HHHHHHHCCTTSEEEE--CCCS-CCCT-HHHHHHHHHHHCC.S-ECEEEE--BCTB--EEEEEESSHHHHH CS
                     ThiP_synth  82 raainirydekilealeelglkvvefdreeepeevgstmewgvaeaieel.evpdviydeGgvGkEpmiyvlgkdaeevv 160
                                    raa+nir+de++l+ ++++gl++++fdreeep++ +stm+wg+a+aie+l +vpd+i+d Gg+GkEpmi++lg+da++v+
  gi|116754139|ref|YP_843257.1| 359 RAAMNIRLDENLLSEASRMGLRISSFDREEEPPG-ESTMSWGTARAIERLgAVPDIIWDGGGMGKEPMIRILGRDAVSVA 437
                                    **********************************.8**************99***************************9 PP

                                    HHH CS
                     ThiP_synth 161 ekv 163
                                    + +
  gi|116754139|ref|YP_843257.1| 438 TVA 440
                                    866 PP

>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   0.3   3.7e-15   2.2e-11     176     291 ..     123     248 ..      78     253 .. 0.84

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 3.7e-15
                                    HHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEEGGGEEEEEE............TTEEEEE CS
                           PfkB 176 allellaladllkpneeElealtgekledieealaalhklkakgaktvvvtlGkeGalvve............kdgelkv 243
                                      +el++ a++++pn  E+ea+tg k +d e+a +a+  ++  ga+ vv+t G   + ++             kd++ +v
  gi|116754139|ref|YP_843257.1| 123 LRDELIPVASVITPNIFEAEAITGVKVVDLESAREAAMRILDMGARAVVITGGHLDCRAAGmpadecvdllvtKDAVACV 202
                                    446889***********************************************************999998866666666 PP

                                    EE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHT CS
                           PfkB 244 pavpkvkvvDttGAGDsfvggflaallegksleealrfanavAalvvq 291
                                    +   k+      G G ++ ++++a l+ g+sl +a+r a+++Aa +++
  gi|116754139|ref|YP_843257.1| 203 SG--KRREGGNHGVGCTYSAALTALLSMGMSLDDAVRQAHNFAARSIE 248
                                    66..56667779*******************************98886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); 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: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 3097.23
//
Query:       gi|116754140|ref|YP_843258.1|  [L=181]
Description: hypothetical protein Mthe_0829 [Methanosaeta thermophila PT]
Scores for complete 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-08   32.5  10.2      0.088   12.7   0.6    4.9  5  Clathrin_H_link  Clathrin-H-link
     0.0074   16.5   1.2        4.2    7.6   0.1    3.6  4  LPD22            Large polyvalent protein associated domain 2
     0.0082   15.8   4.9       0.27   11.0   0.1    3.3  3  Ribosomal_S21    Ribosomal protein S21
  ------ inclusion threshold ------
      0.011   15.8   1.0       0.33   11.0   0.1    3.4  4  TFIIB            Transcription factor TFIIB repeat
      0.024   14.2   0.0        8.4    5.9   0.0    2.5  2  E3_UFM1_ligase   E3 UFM1-protein ligase 1
      0.034   14.2   0.7         29    5.0   0.0    3.6  3  TPR_7            Tetratricopeptide repeat
      0.045   13.5   0.1         18    5.2   0.0    3.3  3  PHF12_MRG_bd     PHD finger protein 12 MRG binding domain
       0.05   13.3   0.0          6    6.7   0.0    3.0  3  DnaB_2           Replication initiation and membrane attachme
      0.054   13.8   0.4        8.9    6.7   0.0    2.3  2  DUF5024          Domain of unknown function (DUF5024)
       0.11   12.4   0.1        2.7    7.9   0.0    2.4  3  Utp13            Utp13 specific WD40 associated domain
       0.15   12.4   1.1         24    5.5   0.0    2.7  2  PPR              PPR repeat


Domain annotation for each model (and alignments):
>> Clathrin_H_link  Clathrin-H-link
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0013       2.2      10      28 ..       9      27 ..       2      38 .. 0.89
   2 ?    0.6   0.0      0.33   5.3e+02       7      28 ..      40      61 ..      35      64 .. 0.84
   3 !   12.7   0.6   5.4e-05     0.088       8      31 ..      75      98 ..      71     105 .. 0.87
   4 ?    5.3   0.1     0.011        19       5      31 ..     106     132 ..     100     143 .. 0.88
   5 !    8.6   0.0     0.001       1.7       9      31 ..     144     166 ..     139     178 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0013
                Clathrin_H_link 10 vqqFeqllaqgnykeAakv 28
                                   ++ F++ +a+g ykeAa++
  gi|116754140|ref|YP_843258.1|  9 IRLFKESMARGGYKEAARI 27
                                   678**************98 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.33
                Clathrin_H_link  7 dlyvqqFeqllaqgnykeAakv 28
                                   d +   F + ++ g+y+ Aa++
  gi|116754140|ref|YP_843258.1| 40 DAVEAAFRKNIEIGEYSVAAEL 61
                                   5677889999999****99986 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 5.4e-05
                Clathrin_H_link  8 lyvqqFeqllaqgnykeAakvAae 31
                                      ++F++ + +++yk+Aak+A e
  gi|116754140|ref|YP_843258.1| 75 AAARSFQRKMDSEQYKAAAKCAKE 98
                                   56799****************976 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.011
                Clathrin_H_link   5 addlyvqqFeqllaqgnykeAakvAae 31 
                                     +d  ++ F + +  g  k+Aak+A e
  gi|116754140|ref|YP_843258.1| 106 VQDAATKAFRKSMDFGLLKNAAKIAEE 132
                                    56888999****************976 PP

  == domain 5  score: 8.6 bits;  conditional E-value: 0.001
                Clathrin_H_link   9 yvqqFeqllaqgnykeAakvAae 31 
                                     +  F+ ++++g y++A+k+A +
  gi|116754140|ref|YP_843258.1| 144 AQAAFDMYVSSGMYSKAIKLARK 166
                                    5789****************965 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 ?   -2.1   0.0       2.8   4.5e+03      21      42 ..      24      46 ..      23      57 .. 0.66
   2 !    7.6   0.1    0.0026       4.2      18      55 ..      55      93 ..      38      96 .. 0.83
   3 ?    4.4   0.6     0.026        43      12      44 ..      83     116 ..      75     152 .. 0.80
   4 ?    4.1   0.0     0.032        52      19      37 ..     158     176 ..     142     180 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.8
                          LPD22 21 alrlaeelGlppdvvern.leaf 42
                                   a r+ e++ lp d+ ++   +af
  gi|116754140|ref|YP_843258.1| 24 AARIKEQYSLPNDLLQDAvEAAF 46
                                   56777777777777777633444 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0026
                          LPD22 18 aAralrlaeelGlppdvvern.leaferaaeaedwdall 55
                                   +  a +l + +Gl+p++v++    +f+r+ ++e+++a++
  gi|116754140|ref|YP_843258.1| 55 YSVAAELGKTYGLDPTIVKEAaARSFQRKMDSEQYKAAA 93
                                   5568899**************778999999999999876 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.026
                          LPD22  12 nenPDeaAralrlaeelGlppdvvern.leafer 44 
                                    + + +++  a + a+e+ lp+ +v++   +af++
  gi|116754140|ref|YP_843258.1|  83 KMDSEQYKAAAKCAKEFDLPKNMVQDAaTKAFRK 116
                                    556778888999************9985566654 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.032
                          LPD22  19 AralrlaeelGlppdvver 37 
                                     +a +la+++Glp dv+++
  gi|116754140|ref|YP_843258.1| 158 SKAIKLARKYGLPEDVIRA 176
                                    57899**********9975 PP

>> Ribosomal_S21  Ribosomal protein S21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.1   0.00017      0.27       8      37 ..       3      32 ..       2      49 .. 0.86
   2 ?    4.5   0.3     0.017        28      11      29 ..      74      92 ..      73      99 .. 0.80
   3 ?    0.3   0.0      0.35   5.7e+02       7      21 ..     104     118 ..     100     119 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00017
                  Ribosomal_S21  8 enierALkrfkrkveragvirevrrrryye 37
                                   e++e+A++ fk  ++r g +  +r ++ y 
  gi|116754140|ref|YP_843258.1|  3 ESFEEAIRLFKESMARGGYKEAARIKEQYS 32
                                   89********************99998886 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.017
                  Ribosomal_S21 11 erALkrfkrkveragvire 29
                                   e+A + f+rk++++  ++ 
  gi|116754140|ref|YP_843258.1| 74 EAAARSFQRKMDSEQYKAA 92
                                   7899*********987665 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.35
                  Ribosomal_S21   7 genierALkrfkrkv 21 
                                    +  +++A k f++ +
  gi|116754140|ref|YP_843258.1| 104 NMVQDAATKAFRKSM 118
                                    55699*******988 PP

>> TFIIB  Transcription factor TFIIB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       1.1   1.8e+03      11      27 ..      69      85 ..      56      90 .. 0.73
   2 ?   11.0   0.1   0.00021      0.33       4      31 ..      95     123 ..      93     125 .. 0.87
   3 ?    0.2   0.0       0.5   8.1e+02       3      25 ..     128     150 ..     126     158 .. 0.73
   4 ?   -1.5   0.0       1.7   2.8e+03       4      17 ..     163     176 ..     161     179 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.1
                                   -HHHHHHHHHHHHHHTT CS
                          TFIIB 11 pekVadaAkelaklale 27
                                   p +V++aA   +++ ++
  gi|116754140|ref|YP_843258.1| 69 PTIVKEAAARSFQRKMD 85
                                   45899999888887666 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00021
                                    HHHHTT--H.HHHHHHHHHHHHHTTSTTT CS
                          TFIIB   4 fadaleLpe.kVadaAkelaklaleekvl 31 
                                     a++ +Lp+ +V+daA+++++++++ ++l
  gi|116754140|ref|YP_843258.1|  95 CAKEFDLPKnMVQDAATKAFRKSMDFGLL 123
                                    58899***99************9987666 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.5
                                    HHHHHTT--HHHHHHHHHHHHHH CS
                          TFIIB   3 rfadaleLpekVadaAkelakla 25 
                                    ++a++ +Lp + + +A ++a  +
  gi|116754140|ref|YP_843258.1| 128 KIAEEFDLPITLRMEAAQAAFDM 150
                                    68999999999887777765444 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 1.7
                                    HHHHTT--HHHHHH CS
                          TFIIB   4 fadaleLpekVada 17 
                                    +a + +Lpe V +a
  gi|116754140|ref|YP_843258.1| 163 LARKYGLPEDVIRA 176
                                    788999***99987 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 ?    5.9   0.0    0.0051       8.4     123     160 ..      14      51 ..       5      65 .. 0.83
   2 ?    5.7   0.0     0.006       9.8     119     182 ..      78     142 ..      73     175 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0051
                 E3_UFM1_ligase 123 eklqeagqvsiaelakqydlpvdflkellekrlgkiik 160
                                    e +   g  + a + +qy+lp d+l++++e+   k i+
  gi|116754140|ref|YP_843258.1|  14 ESMARGGYKEAARIKEQYSLPNDLLQDAVEAAFRKNIE 51 
                                    55666677788999***************988876665 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.006
                 E3_UFM1_ligase 119 eeineklqeagqvsiaelakqydlpvdflkellekrlgkiik.grldgevlyTeafvarqkakvr 182
                                     + + k+ +++  + a+ ak++dlp ++++++ +k   k ++ g l++   + e+f   ++ ++ 
  gi|116754140|ref|YP_843258.1|  78 RSFQRKMDSEQYKAAAKCAKEFDLPKNMVQDAATKAFRKSMDfGLLKNAAKIAEEFDLPITLRME 142
                                    5667788888899999***************9998885544413334555555555555555555 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.025        41      15      29 ..       5      17 ..       5      29 .. 0.81
   2 ?   -0.0   0.1      0.73   1.2e+03      17      35 ..      75      91 ..      74      95 .. 0.77
   3 ?    5.0   0.0     0.018        29       8      21 ..     150     163 ..     149     172 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.025
                          TPR_7 15 yeeAielyeqsLalt 29
                                   +eeAi+l+++   ++
  gi|116754140|ref|YP_843258.1|  5 FEEAIRLFKE--SMA 17
                                   79********..544 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.73
                          TPR_7 17 eAielyeqsLaltkdpeda 35
                                    A++ +++   +++++++a
  gi|116754140|ref|YP_843258.1| 75 AAARSFQR--KMDSEQYKA 91
                                   68888888..888888765 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.018
                          TPR_7   8 lysrlGdyeeAiel 21 
                                    +y++ G y++Ai+l
  gi|116754140|ref|YP_843258.1| 150 MYVSSGMYSKAIKL 163
                                    79**********98 PP

>> PHF12_MRG_bd  PHD finger protein 12 MRG binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.037        60      22      30 ..      29      37 ..      23      41 .. 0.86
   2 ?    5.2   0.0     0.011        18      21      30 ..      96     105 ..      90     108 .. 0.83
   3 ?    0.3   0.0      0.35   5.7e+02      22      30 ..     131     139 ..     118     144 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.037
                   PHF12_MRG_bd 22 kQFeLPkEl 30
                                    Q++LP++l
  gi|116754140|ref|YP_843258.1| 29 EQYSLPNDL 37
                                   6******98 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.011
                   PHF12_MRG_bd  21 PkQFeLPkEl 30 
                                    +k+F+LPk +
  gi|116754140|ref|YP_843258.1|  96 AKEFDLPKNM 105
                                    79******98 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.35
                   PHF12_MRG_bd  22 kQFeLPkEl 30 
                                     +F+LP  l
  gi|116754140|ref|YP_843258.1| 131 EEFDLPITL 139
                                    79***9666 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 ?    1.0   0.0      0.23   3.7e+02      22      45 ..      26      49 ..       5      59 .. 0.75
   2 ?    2.3   0.0     0.086   1.4e+02      17      45 ..      55      85 ..      41     100 .. 0.70
   3 ?    6.7   0.0    0.0037         6       2      36 ..     142     176 ..     141     180 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.23
                                   HHHHHHHHHHHHHHHHHHHHHHHT CS
                         DnaB_2 22 ywlddlglspevilllleyavekg 45
                                    + +++ l++++++ ++e a++k+
  gi|116754140|ref|YP_843258.1| 26 RIKEQYSLPNDLLQDAVEAAFRKN 49
                                   566889999999999999998554 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.086
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHH..T CS
                         DnaB_2 17 letilywlddlglspevilllleyavek..g 45
                                   +    ++ +++gl+p +++++  +++++   
  gi|116754140|ref|YP_843258.1| 55 YSVAAELGKTYGLDPTIVKEAAARSFQRkmD 85
                                   55556666899**********9999844243 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0037
                                    .HHHTTS-.S--HHHHHHHHHHHHHHHHHHHHHHH CS
                         DnaB_2   2 eeiekefgrplspseletilywlddlglspevill 36 
                                    e ++  f   +s+  + +  ++ +++gl+++vi +
  gi|116754140|ref|YP_843258.1| 142 EAAQAAFDMYVSSGMYSKAIKLARKYGLPEDVIRA 176
                                    6688889999***********************75 PP

>> DUF5024  Domain of unknown function (DUF5024)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0055       8.9      34      65 ..      26      57 ..      21      88 .. 0.85
   2 ?    5.6   0.1     0.012        20      32      61 ..      92     121 ..      74     163 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0055
                        DUF5024 34 kvVksfsvkdeglgkelkeAFerdeeeaekai 65
                                   ++ +++s++++ l++ +  AF+++ e +e  +
  gi|116754140|ref|YP_843258.1| 26 RIKEQYSLPNDLLQDAVEAAFRKNIEIGEYSV 57
                                   67789*******************99988665 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.012
                        DUF5024  32 VvkvVksfsvkdeglgkelkeAFerdeeea 61 
                                      k  k+f ++++ +++   +AF++    +
  gi|116754140|ref|YP_843258.1|  92 AAKCAKEFDLPKNMVQDAATKAFRKSMDFG 121
                                    57899*******************987665 PP

>> Utp13  Utp13 specific WD40 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       3.2   5.3e+03       6      31 ..      14      39 ..      10      55 .. 0.67
   2 ?    2.0   0.0      0.11   1.7e+02       3      31 ..      79     107 ..      77     134 .. 0.85
   3 ?    7.9   0.0    0.0017       2.7       3      34 ..     147     178 ..     145     181 .] 0.85

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.2
                                   HHHHCCHHHHHHHHHHHSSSTHHHHH CS
                          Utp13  6 nllrkkdyreAiaLAlkldqpkrllk 31
                                     ++++ y+eA ++  +   p+ ll+
  gi|116754140|ref|YP_843258.1| 14 ESMARGGYKEAARIKEQYSLPNDLLQ 39
                                   55666677777776666666665554 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.11
                                    HHHHHHHCCHHHHHHHHHHHSSSTHHHHH CS
                          Utp13   3 elqnllrkkdyreAiaLAlkldqpkrllk 31 
                                    ++q  + +++y+ A + A ++d pk++++
  gi|116754140|ref|YP_843258.1|  79 SFQRKMDSEQYKAAAKCAKEFDLPKNMVQ 107
                                    68888999**************9998865 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0017
                                    HHHHHHHCCHHHHHHHHHHHSSSTHHHHHHHH CS
                          Utp13   3 elqnllrkkdyreAiaLAlkldqpkrllkllk 34 
                                     ++ +++++ y++Ai+LA k   p+ +++ ++
  gi|116754140|ref|YP_843258.1| 147 AFDMYVSSGMYSKAIKLARKYGLPEDVIRAVE 178
                                    6899**************99998888877665 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.2      0.02        33      15      30 ..       4      19 ..       1      20 [. 0.81
   2 ?    5.5   0.0     0.015        24       8      22 ..     149     163 ..     146     166 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.02
                            PPR 15 kleeAlelfkeMkekG 30
                                    +eeA++lfke   +G
  gi|116754140|ref|YP_843258.1|  4 SFEEAIRLFKESMARG 19
                                   58********976665 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.015
                            PPR   8 sgycknGkleeAlel 22 
                                    + y+++G++++A++l
  gi|116754140|ref|YP_843258.1| 149 DMYVSSGMYSKAIKL 163
                                    78***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); 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: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1304.19
//
Query:       gi|116754141|ref|YP_843259.1|  [L=144]
Description: hypothetical protein Mthe_0830 [Methanosaeta thermophila PT]
Scores for 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-45  151.7   0.4    1.1e-44  151.5   0.4    1.0  1  DUF61     Protein of unknown function DUF61


Domain annotation for each model (and alignments):
>> DUF61  Protein of unknown function DUF61
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.5   0.4   6.2e-49   1.1e-44       2     127 .]       8     135 ..       7     135 .. 0.97

  Alignments for each domain:
  == domain 1  score: 151.5 bits;  conditional E-value: 6.2e-49
                                    S---SHHHHHGGGSBSS-EEHHHHHHT--EEEB.TTS-EEE--HHHHHHHHTTS-GGGGGT-EESEEEEE-SSSSE..EE CS
                          DUF61   2 rilakeiksinkhlPaerktLkelLeeekptivtkdgsehrfdkeeleklkeilpeelwdklkLPIllemdpelgesvyl 81 
                                    +il k+i+++n+hlP +rktL+elLeee+p i++kd++++++dk ele +++ +p+ +w++++LPIl+em+pelg++ ++
  gi|116754141|ref|YP_843259.1|   8 KILIKTIQTMNQHLPPKRKTLAELLEEERPGIKGKDNTFYVMDKPELELISKSIPRFMWSRIRLPILIEMSPELGSGSAR 87 
                                    89****************************************************************************** PP

                                    EES-HHHHHHHHHHT--.....-SSEEEHH.HHHHHHHH-ST...TEE CS
                          DUF61  82 vrgkaevkvvskilgke..reeedelviykpevrelrrklptatqliF 127
                                    ++g+ae ++vskil+++     + ++viy p+vrelrrklpt+tq++F
  gi|116754141|ref|YP_843259.1|  88 IQGEAEIEAVSKILNLKrgDIGRRSMVIYLPDVRELRRKLPTTTQYAF 135
                                    *****************66567889**********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.29s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 1010.84
//
Query:       gi|116754142|ref|YP_843260.1|  [L=285]
Description: Pre-mRNA processing ribonucleoprotein, binding region [Methanosaeta thermophila PT]
Scores for complete 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-43  148.8   0.1    2.6e-43  148.1   0.1    1.2  1  Nop       snoRNA binding domain, fibrillarin


Domain annotation for each model (and alignments):
>> Nop  snoRNA binding domain, fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.1   0.1   1.4e-47   2.6e-43      91     223 ..     136     269 ..     128     275 .. 0.88

  Alignments for each domain:
  == domain 1  score: 148.1 bits;  conditional E-value: 1.4e-47
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHCHHHHHHHHHHHHSSHHHHHCS-HHHHTTTT-HHHHCCCHH.T---S CS
                            Nop  91 lcdrvleleelrkelleYlesrmsaiAPNlsaLvGeevaarLishaGgLtnLakmPastiqilGaekalfralk.kkntp 169
                                    +++++lel+++r++l+e le+r +++APNlsa++G+ +aarLis aGgL++La +Pastiq++Gae++lfr+l+ k  +p
  gi|116754142|ref|YP_843260.1| 136 VARSLLELTRAREDLEELLETRARELAPNLSAILGPVLAARLISRAGGLEKLAMLPASTIQVIGAERSLFRHLRgKAPSP 215
                                    678899********************************************************************5559** PP

                                    SSCHHHCSHHHHHTS-CCCHHHHHHHHHHHHHHHHHHH.HTT----SHHHHHHHH CS
                            Nop 170 kyGliyhselvqkatppklkkkiaRllaaKvalaaRiD.afsekdgslGkklree 223
                                    k+G+i+ ++l+q++ p++l+++iaR+laaK+a+aaRiD  ++  d  + ++l e 
  gi|116754142|ref|YP_843260.1| 216 KHGIIFRHPLIQSS-PKRLRGRIARALAAKLAIAARIDlYSGTLDPGIAQALNER 269
                                    ************66.***********************54433334455555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); 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: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 2177.58
//
Query:       gi|116754143|ref|YP_843261.1|  [L=141]
Description: histidine triad (HIT) protein [Methanosaeta thermophila PT]
Scores for complete 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   53.9   0.0    3.3e-14   53.4   0.0    1.3  1  HIT       HIT domain
    6.8e-11   42.7   0.0    9.1e-11   42.2   0.0    1.2  1  DcpS_C    Scavenger mRNA decapping enzyme C-term binding
    2.6e-05   24.1   0.0    3.4e-05   23.7   0.0    1.2  1  CwfJ_C_1  Protein similar to CwfJ C-terminus 1


Domain annotation for each model (and alignments):
>> HIT  HIT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   0.0   5.5e-18   3.3e-14       2      97 ..      13     103 ..      12     104 .. 0.94

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 5.5e-18
                                    GCC-CCEEEE-SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEESGGG CS
                            HIT   2 keipstvvyeddlvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqkkfknkglrvvinngaha 81 
                                    + +p++++ ed+l++a+ldi+p a+gh+Lvipk+h++ +hdl+e e++ l++++  v   +++ f+ +++ ++       
  gi|116754143|ref|YP_843261.1|  13 GDEPAHIIDEDELSMAILDINPLARGHCLVIPKRHVPWWHDLNEREVSSLFRLAWSVSGRIKRAFEPDFVAMYA-----R 87 
                                    56899**********************************************************99988888887.....8 PP

                                    T-SSSS-EEEEEEC-T CS
                            HIT  82 gqsvahlHiHviprre 97 
                                    g  ++h Hi ++p+++
  gi|116754143|ref|YP_843261.1|  88 GRRIPHTHIFLVPTYK 103
                                    999******9999886 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 !   42.2   0.0   1.5e-14   9.1e-11       1      74 [.       4      77 ..       4     101 .. 0.87

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 1.5e-14
                                   T-HHHHHHTTSS-B-EEEE-SSEEEEE-SS-SSSEEEEEEESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT CS
                         DcpS_C  1 kwvfnilakgkepervvyedekfvvlkDikpkaklhllvipkrdikslrdLtkehlpllkemrekakkvieeky 74
                                   ++vf+++++g ep+ ++ ede  +++ Di+p a+ h+lvipkr+++  +dL++ +++ l ++   +   i++ +
  gi|116754143|ref|YP_843261.1|  4 SCVFCRIVRGDEPAHIIDEDELSMAILDINPLARGHCLVIPKRHVPWWHDLNEREVSSLFRLAWSVSGRIKRAF 77
                                   69*****************************************************9999888877777776665 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 !   23.7   0.0   5.8e-09   3.4e-05      12     109 ..       3     101 ..       1     107 [. 0.83

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 5.8e-09
                                    HH-S----SS---SS--S-B-SSEEEE---S-SSTT-EEEEESS--SSTTSS-HHHHHHHHHHHHHHH.HHHHHTT--EE CS
                       CwfJ_C_1  12 dsClfClsnpklekhlivsignkvYlalpkgpLssgHvliipieHisallsldeevldeirkfrkalv.kmykkqdkdav 90 
                                    +sC fC      e + i+   +   + l  +pL+ gH+l+ip  H++    l+e + +++ +   ++  ++  +++ d v
  gi|116754143|ref|YP_843261.1|   3 ESCVFCRIVRGDEPAHIIDEDELSMAILDINPLARGHCLVIPKRHVPWWHDLNEREVSSLFRLAWSVSgRIKRAFEPDFV 82 
                                    789999888888888888866665555556************************99999999998887245778999999 PP

                                    EEEE-SSS-----EEEEE- CS
                       CwfJ_C_1  91 vfEissersvHlaiqvipv 109
                                          +r +H++i ++p 
  gi|116754143|ref|YP_843261.1|  83 AMYARGRRIPHTHIFLVPT 101
                                    8888899999999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       244  (0.0136092); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1051.45
//
Query:       gi|116754144|ref|YP_843262.1|  [L=420]
Description: phosphopyruvate hydratase [Methanosaeta thermophila PT]
Scores for complete 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-109  364.2   0.0   5.7e-109  363.9   0.0    1.1  1  Enolase_C  Enolase, C-terminal TIM barrel domain
    7.5e-62  207.3   0.0    2.4e-61  205.6   0.0    1.8  2  Enolase_N  Enolase, N-terminal domain
    2.9e-05   23.7   0.0    7.9e-05   22.3   0.0    1.8  3  MR_MLE_C   Enolase C-terminal domain-like
  ------ inclusion threshold ------
      0.011   15.0   0.0      0.048   12.8   0.0    1.8  2  MAAL_C     Methylaspartate ammonia-lyase C-terminus


Domain annotation for each model (and alignments):
>> Enolase_C  Enolase, C-terminal TIM barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  363.9   0.0  1.3e-112  5.7e-109       3     291 ..     140     417 ..     138     420 .] 0.97

  Alignments for each domain:
  == domain 1  score: 363.9 bits;  conditional E-value: 1.3e-112
                                    EE-EE-EEEEE-GGGSSSS--SSEEEEE-TT-SSHHHHHHHHHHHHHHHHHHHHHCC.GGGG-B-TTS-B----SSHHHH CS
                      Enolase_C   3 vlPvPalnvinGGshagnklalqefmilPvgassfkealrlGaevyhklksvlkkkygksatnvGdeGGfaPnlqsnkea 82 
                                     lPvP+lnv+nGG+hagn+l++qefmi P ga+sf+ealr+ ae+yh l ++l+ kyg+ atnvG eGG+aP ++++++a
  gi|116754144|ref|YP_843262.1| 140 RLPVPSLNVLNGGKHAGNDLSIQEFMIEPWGADSFSEALRMAAETYHALGRILRGKYGNVATNVGFEGGYAPPISKTRDA 219
                                    69****************************************************************************** PP

                                    HHHHHHHHHHCT-TCTBEEEEE--GGGCEETCTTEEECTTTTTT..GGCEEEHHHHHHHHHHHHHHS-EEEEES-S-TT- CS
                      Enolase_C  83 ldliveaiekaGykgkvkialdvassefykekdkkydldfkeeesdkskkltseqladlykelvkkyPivsiedpldedd 162
                                    ld i++a++ +Gy++++k++ld a+s fy   d+ y +d +         l+  +l d+y+elvk yPiv iedp++e+ 
  gi|116754144|ref|YP_843262.1| 220 LDAIMAALDVTGYTEEIKLGLDSAASSFY--LDGGYSVDDN--------RLSPGELIDFYVELVKTYPIVLIEDPFEENA 289
                                    *****************************..6678887754........59***************************** PP

                                    HHHHHHHHHHHTTTSEEEESTTTTT-HHHHHHHHHCT--SEEEE-HHHH-SHHHHHHHHHHHHHTT-EEEEE--SC--S- CS
                      Enolase_C 163 weawkklteelgdkvqivGddltvtnpkrlkeaiekkaanalllkvnqiGsltesleavklakeagygvvvshrsGeted 242
                                    +e +++lt++l d + ivGddl+vtn  r++++i  +++nalllk+nqiG+++e+++a+ la+++++ v+vshrs eted
  gi|116754144|ref|YP_843262.1| 290 FEEFAELTKKLPDTI-IVGDDLYVTNMARIEKGIRMRSTNALLLKLNQIGTVSEAFDAATLAYRNSFKVMVSHRSAETED 368
                                    ***********9765.9*************************************************************** PP

                                    -HHHHHHHHCT-SEEE---S-SHHHHHHHHHHHHHHHHHGCC-EE-GGG CS
                      Enolase_C 243 ttiadlavglsaGqiktGaparserlakynqllrieeelgekakyaGkk 291
                                    + +ad++v++ a  iktGaparser akynqllri+e+lg++a yaG++
  gi|116754144|ref|YP_843262.1| 369 SALADVSVAIGAELIKTGAPARSERNAKYNQLLRIQEALGSSASYAGRR 417
                                    ***********************************************96 PP

>> Enolase_N  Enolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.6   0.0   5.5e-65   2.4e-61       1     131 []       5     133 ..       5     133 .. 0.99
   2 ?   -1.8   0.0      0.75   3.3e+03      84      99 ..     217     232 ..     214     240 .. 0.78

  Alignments for each domain:
  == domain 1  score: 205.6 bits;  conditional E-value: 5.5e-65
                                    EEEEEEEEEE-TTS-EEEEEEEEETTC-EEEEE--B-BSSSSSS-B----SSTTSGGGT--HHHHHHHHHTHHHHHTTSB CS
                      Enolase_N   1 IkkvkareildSrGnpTvevevttedgalgraavpsGaStgekealelrDgdkkrylgkgvekavenvnekiapaligld 80 
                                    I+k++areildSrGnpTvev+v+t  g +graavpsGaStg++ealelrDg  +ry gkgv+kav+nvne+i p+lig+d
  gi|116754144|ref|YP_843262.1|   5 IEKIHAREILDSRGNPTVEVDVWTCCG-FGRAAVPSGASTGTYEALELRDG-GDRYDGKGVLKAVRNVNEVIGPKLIGMD 82 
                                    89**********************877.8*********************9.89************************** PP

                                    TT-HHHHHHHHHHHH-STT-TTT-HHHHHHHHHHHHHHHHHHHTS-HHHHH CS
                      Enolase_N  81 vtdqeeiDkllielDgtenksklGaNailavSlAvakaaAkakelplyryl 131
                                    v dq+ +D+++ie+Dgt+nks+lGaNail+vSlAvakaaA+++++plyryl
  gi|116754144|ref|YP_843262.1|  83 VIDQRGVDQIMIEMDGTPNKSNLGANAILGVSLAVAKAAASSLGMPLYRYL 133
                                    **************************************************8 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.75
                                    HHHHHHHHHHHH-STT CS
                      Enolase_N  84 qeeiDkllielDgten 99 
                                      ++D+++ +lD t  
  gi|116754144|ref|YP_843262.1| 217 RDALDAIMAALDVTGY 232
                                    5689********8865 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 ?   -3.7   0.0       1.6   7.2e+03      25      44 ..      56      77 ..      41      83 .. 0.66
   2 ?   -2.9   0.0      0.89     4e+03      48      70 ..     163     185 ..     161     192 .. 0.80
   3 !   22.3   0.0   1.8e-08   7.9e-05      26     157 ..     215     362 ..     176     400 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 1.6
                                   S..HHHHHHHHHHHHHHHHTTT CS
                       MR_MLE_C 25 d..dvaedvervravreavgpg 44
                                   d  d +  ++ vr v e++gp+
  gi|116754144|ref|YP_843262.1| 56 DryDGKGVLKAVRNVNEVIGPK 77
                                   4556666788899999999774 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.89
                                    EEEEE-TTTSBHHHHHHHHHHHG CS
                       MR_MLE_C  48 dlmvDanqawdlatAirvarele 70 
                                    ++m++  +a + ++A+r+a e++
  gi|116754144|ref|YP_843262.1| 163 EFMIEPWGADSFSEALRMAAETY 185
                                    57888888889999999999874 PP

  == domain 3  score: 22.3 bits;  conditional E-value: 1.8e-08
                                    HHHHHHHHHHHHHHHHTTTSTSEEEEE-TTT.S.............BHHHHHHHHHHHGG.GTESEEESSSSTTTHHHHH CS
                       MR_MLE_C  26 dvaedvervravreavgpgddvdlmvDanqa.w.............dlatAirvarelee.ldllwlEEPvppeddlegl 90 
                                    + ++ ++ + a+ +++g  ++++l +D  ++ +             ++ + i +  el + + + ++E+P+   +  e+ 
  gi|116754144|ref|YP_843262.1| 215 KTRDALDAIMAALDVTGYTEEIKLGLDSAASsFyldggysvddnrlSPGELIDFYVELVKtYPIVLIEDPFEE-NAFEEF 293
                                    5667778888888888888888888886665335777777788777999*****999977699*********9.78**** PP

                                    HHHHHHH..SSEEEEST.TSSSHHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHHHHHHTT-EEEEBSC CS
                       MR_MLE_C  91 aelrara..sipiaagE.slysradfrelleagavdivqpdvsrvgGitearkvaalaeafgvpvapHsg 157
                                    ael++ +  ++ i+++  +++++a++++ ++ +   ++ ++++++g ++ea + a la  +  +v++ + 
  gi|116754144|ref|YP_843262.1| 294 AELTK-KlpDTIIVGDDlYVTNMARIEKGIRMRSTNALLLKLNQIGTVSEAFDAATLAYRNSFKVMVSHR 362
                                    ****5.5554444444324567************************************987777666552 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 ?   -0.8   0.0      0.15   6.8e+02     193     218 ..      94     119 ..      83     128 .. 0.77
   2 ?   12.8   0.0   1.1e-05     0.048     109     216 ..     280     380 ..     255     387 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.15
                         MAAL_C 193 aylGGscnetdvsarvsvhvalatrp 218
                                    + + G+ n  + +a+++  v+la+  
  gi|116754144|ref|YP_843262.1|  94 IEMDGTPNKSNLGANAILGVSLAVAK 119
                                    55789**********99999998754 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 1.1e-05
                         MAAL_C 109 liegPldagskeeqierlaelreklkekgikvelvaDe.WcntledirefvdaeaadlvqiktPDlGginntieavlyck 187
                                    lie+P +    e++ e++ael++kl     +  +v D+ +  ++  i++ +  ++++++ +k   +G+++++ +a   + 
  gi|116754144|ref|YP_843262.1| 280 LIEDPFE----ENAFEEFAELTKKL----PDTIIVGDDlYVTNMARIEKGIRMRSTNALLLKLNQIGTVSEAFDAATLAY 351
                                    4566654....34556666666665....4556777663788899*********************************** PP

                         MAAL_C 188 ekgvgaylGGscnetdvsarvsvhvalat 216
                                    ++  ++++   + et+ sa + v va+ +
  gi|116754144|ref|YP_843262.1| 352 RNSFKVMVSHRSAETEDSALADVSVAIGA 380
                                    *******************9999998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2899.22
//
Query:       gi|116754145|ref|YP_843263.1|  [L=1202]
Description: periplasmic component of the Tol biopolymer transport system-like [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-11   42.4  11.6     0.0033   16.7   1.1    5.5  6  DUF5050          Domain of unknown function (DUF5050)
    5.4e-10   39.0  74.4       0.62   10.1   0.4   19.5 22  PD40             WD40-like Beta Propeller Repeat
    6.2e-06   25.2  22.9      0.063   12.0   0.1    8.7 10  DPPIV_N          Dipeptidyl peptidase IV (DPP IV) N-terminal 
    4.3e-05   22.4   4.3       0.35    9.5   0.1    5.5  6  Pectate_lyase22  Oligogalacturonate lyase
    0.00039   20.8   4.3     0.0087   16.5   0.0    5.5  6  PQQ_3            PQQ-like domain
     0.0092   15.9  12.4        5.4    7.1   0.0    8.8  8  PQQ              PQQ enzyme repeat
  ------ inclusion threshold ------
          8    6.2  23.7       0.35   10.6   0.1    7.2  8  DUF2606          Protein of unknown function (DUF2606)
        9.4    6.2  18.0        1.3    9.0   0.1    5.5  7  phage_tail_N     Prophage tail fibre N-terminal


Domain annotation for each model (and alignments):
>> DUF5050  Domain of unknown function (DUF5050)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0   0.00036      0.82     119     212 ..     140     239 ..      80     281 .. 0.50
   2 !   16.7   1.1   1.5e-06    0.0033     146     256 ..     334     451 ..     325     454 .. 0.80
   3 !    8.3   0.1   0.00053       1.2     146     251 ..     418     536 ..     400     549 .. 0.66
   4 !    9.0   0.3   0.00033      0.75     150     253 ..     693     800 ..     678     838 .. 0.74
   5 ?   -4.0   0.0         3   6.8e+03     180     206 ..     846     870 ..     841     877 .. 0.66
   6 !    7.6   0.0   0.00091         2     148     245 ..    1058    1158 ..    1025    1195 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00036
                                    EEEEEEETTS---EEE...ESS----SEEETTEEEEE-T.TT--EEEEETTTTEEEEEE-..S-EEEEEEEETTEEEEEG CS
                        DUF5050 119 lklykikidgkektkl...sdeaieplsvkdgwiYytgesedhslykldtdgksiskvse..enlyllvvegdyiYyidl 193
                                     ++y  +i  ++++++   ++++i p   ++ ++   + s +  +y +d++g+s++ ++   ++ +l+ ++g+ i + d 
  gi|116754145|ref|YP_843263.1| 140 WNIYLKDISTNQQKRVtsaQNDQITPKVSEGRVVWADDRSGNFDIYMYDLKGGSEKAICTasGDQTLPAIDGEIIAWADN 219
                                    23333333333333332212222322222222222222222335555555554444444322333445555555544443 PP

                                    .GGTT-EEEE-SSS---EE- CS
                        DUF5050 194 .sknyaLyrvklsgsekevl 212
                                     s ++  + ++ls+++++vl
  gi|116754145|ref|YP_843263.1| 220 rSGEMDVAFYDLSSGKETVL 239
                                    23444444455555555554 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 1.5e-06
                                    TTEEEEE-T.TT-.-EEEEETTTTEEEEEE-S-EEE..EEEEETTEEEEEG.GGTT-EEEE-SSS---EE-S-S-EEE.E CS
                        DUF5050 146 dgwiYytgesedh.slykldtdgksiskvseenlyl..lvvegdyiYyidl.sknyaLyrvklsgsekevltedkvdn.y 220
                                    ++ + +t+  ++h ++y +++ ++++ +++++++ +  + ++gdy+ y+d+ + n     ++l  +++  l++d  d  y
  gi|116754145|ref|YP_843263.1| 334 NDRVVWTDDRTGHyQVYMMNLTTGEEIRITNDDIDHssPDISGDYVIYTDMrNGNLDVFLYDLRAGNERQLSKDPFDQrY 413
                                    444445566666769****************9998777*************666889******************97766 PP

                                    E.EETTEEEEEE-SSS-E.EEEEE.TTS---EEEEES- CS
                        DUF5050 221 N.vtgnwiYyqkesdeekalyrik.ldGsekeklaegn 256
                                      ++g+++  + + + + ++y ++ l+Gse+++ ++++
  gi|116754145|ref|YP_843263.1| 414 PmIDGRYVVWMDNRTGSDQIYVYDvLQGSERQITTQQQ 451
                                    6369999999999888888**99835788877776655 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.00053
                                    TTEEEEE-T.TT-.-EEEEETTTTEEEEEE-...S-EEEEEEEETTEEEEEG.GGTT-EEEE-SSS---EE-S-S-EEEE CS
                        DUF5050 146 dgwiYytgesedh.slykldtdgksiskvse...enlyllvvegdyiYyidl.sknyaLyrvklsgsekevltedkvdny 220
                                    + ++ + ++ +++ ++y +d+ ++s+++++     +l ++v++gd i + d  s +  +y+++l++++++ ++++ ++ +
  gi|116754145|ref|YP_843263.1| 418 GRYVVWMDNRTGSdQIYVYDVLQGSERQITTqqqAQLLSPVISGDRIVWADRrSGKWDIYMYNLTTGKETPICTNPANQV 497
                                    5554444444443499999998877777765211456669*******99998677889**************99988776 PP

                                    E..EETTEEEEEE-SSS-E.......EEEEETTS---EE CS
                        DUF5050 221 N..vtgnwiYyqkesdeeka......lyrikldGsekek 251
                                       ++gn+i  +   +  +a      +y+++l + +++ 
  gi|116754145|ref|YP_843263.1| 498 QpwIHGNTIVWADGRNALNAsirnwdIYSYNLTTGKETP 536
                                    544566666554444333333555556666666555555 PP

  == domain 4  score: 9.0 bits;  conditional E-value: 0.00033
                                    EEE-T.TT--EEEEETTTTEEEEEE-S-EEE..EEEEETTEEEEEG.GGTT-EEEE-SSS---EE-S-S-EEEEE.EETT CS
                        DUF5050 150 Yytgesedhslykldtdgksiskvseenlyl..lvvegdyiYyidl.sknyaLyrvklsgsekevltedkvdnyN.vtgn 225
                                       + s ++ +y +++ ++++++v  +      + +++d i ++d  s n   + +++s +++e l ++  ++y  ++g+
  gi|116754145|ref|YP_843263.1| 693 WSDYRSGSSDVYMINLTTGEVTDVATGPGDQvwADISEDRIVWMDNsSGNWDVVLYNISDGSTESLRKQGNQMYPkISGS 772
                                    44555666788888888888888887544432367778888777764668889999999999999988888887548899 PP

                                    EEEEEE-SSS-E.EEEEETTS---EEEE CS
                        DUF5050 226 wiYyqkesdeekalyrikldGsekekla 253
                                     i  q + + + ++y ++l++ +++kl+
  gi|116754145|ref|YP_843263.1| 773 LIAWQDDRSGNWDIYVYDLKTGNETKLT 800
                                    9999999988888999999988888886 PP

  == domain 5  score: -4.0 bits;  conditional E-value: 3
                                    EEEEEETTEEEEEGGGTT-EEEE-SSS CS
                        DUF5050 180 llvvegdyiYyidlsknyaLyrvklsg 206
                                    ++ v+g+yi y+d  ++ +L r+++++
  gi|116754145|ref|YP_843263.1| 846 SPAVSGKYIAYVD--DDGSLRRLDITT 870
                                    5677777777744..777777777665 PP

  == domain 6  score: 7.6 bits;  conditional E-value: 0.00091
                                     EEEEE-T.TT--EEEEETTTTEEEEEE-S-EEEEEEEETTEEEEEG.GGTT-EEEE-SSS---EE-S-S-EEEEE..E CS
                        DUF5050  148 wiYytgesedhslykldtdgksiskvseenlyllvvegdyiYyidl.sknyaLyrvklsgsekevltedkvdnyN..v 222 
                                      +Y  +++ + ++y  + ++k+  ++   +   +  +g  + y d  + n  +y  ++++s++  +t+d++d  N  +
  gi|116754145|ref|YP_843263.1| 1058 AVYQDNKDGNWNVYIWKGQQKNPVTLDPADQINPATDGYIVVYQDNrNGNWDIYAFDTNNSKEIRITSDTTDQTNpdI 1135
                                     445555555557777777777777777777666666666665555535566777777777777777777777666333 PP

                                     ETTEEEEEE-SSS-E.EEEEETT CS
                        DUF5050  223 tgnwiYyqkesdeekalyrikld 245 
                                     +  +i  q   + + ++y  +l 
  gi|116754145|ref|YP_843263.1| 1136 ESGVIVWQDRRNGDWDIYAFDLS 1158
                                     34444444443333336666655 PP

>> PD40  WD40-like Beta Propeller Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1      0.13   2.9e+02      19      38 .]      42      60 ..      42      60 .. 0.84
   2 ?    1.7   0.0      0.11   2.6e+02      20      37 ..      85     101 ..      75     102 .. 0.89
   3 !    6.9   0.7    0.0028       6.3      19      37 ..     126     143 ..     126     144 .. 0.96
   4 !    5.5   0.1    0.0075        17      22      38 .]     171     186 ..     170     186 .. 0.90
   5 ?    1.4   0.0      0.15   3.3e+02      19      35 ..     210     225 ..     210     226 .. 0.91
   6 ?   -0.6   0.0      0.62   1.4e+03      24      38 .]     294     309 ..     293     309 .. 0.90
   7 ?    3.1   0.0     0.043        95       9      38 .]     325     351 ..     319     351 .. 0.85
   8 ?   -1.4   0.1       1.1   2.4e+03      20      37 ..     376     392 ..     361     394 .. 0.78
   9 !    8.0   0.3    0.0013       2.9      19      38 .]     417     435 ..     417     435 .. 0.98
  10 !   10.1   0.4   0.00028      0.62      20      38 .]     461     478 ..     460     478 .. 0.95
  11 ?   -1.7   0.0       1.4   3.1e+03      20      37 ..     503     525 ..     503     526 .. 0.85
  12 ?    0.3   0.0      0.33   7.4e+02      20      37 ..     551     567 ..     551     568 .. 0.94
  13 ?   -3.7   0.0       5.8   1.3e+04      21      36 ..     610     624 ..     610     624 .. 0.82
  14 !    6.7   0.4    0.0031       6.9      19      37 ..     645     662 ..     641     662 .. 0.92
  15 ?    2.9   0.1     0.051   1.1e+02      20      38 .]     688     705 ..     686     705 .. 0.93
  16 !    9.9   0.1   0.00031       0.7      20      38 .]     771     788 ..     767     788 .. 0.96
  17 ?   -1.6   0.0       1.3     3e+03      14      28 ..     847     859 ..     840     867 .. 0.70
  18 ?    5.0   0.0     0.011        24      20      38 .]     927     944 ..     925     944 .. 0.89
  19 ?   -1.1   0.1      0.89     2e+03      21      38 .]    1056    1072 ..    1055    1073 .. 0.77
  20 ?    4.9   0.3     0.011        25      19      37 ..    1094    1111 ..    1093    1112 .. 0.94
  21 ?    2.9   0.1      0.05   1.1e+02      23      37 ..    1140    1153 ..    1138    1154 .. 0.92
  22 !    6.9   0.1    0.0028       6.3      21      38 .]    1180    1196 ..    1179    1196 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.13
                                   TSSEEEEEEECT.TCEEEEE CS
                           PD40 19 DGkrlaFsSdRgsGkpdIyv 38
                                   DG   +++  R+ G++dI++
  gi|116754145|ref|YP_843263.1| 42 DGHIVVWADGRS-GNFDIFM 60
                                   677778999999.*****96 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.11
                                    SSEEEEEEECT.TCEEEE CS
                           PD40  20 GkrlaFsSdRgsGkpdIy 37 
                                    G r+++   R+ G+ dIy
  gi|116754145|ref|YP_843263.1|  85 GYRIVWQDMRS-GNADIY 101
                                    789********.*****9 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0028
                                    TSSEEEEEEECT.TCEEEE CS
                           PD40  19 DGkrlaFsSdRgsGkpdIy 37 
                                    DG   ++s dR+ G+++Iy
  gi|116754145|ref|YP_843263.1| 126 DGDVVVWSDDRD-GDWNIY 143
                                    99**********.*****9 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.0075
                                    EEEEEEECT.TCEEEEE CS
                           PD40  22 rlaFsSdRgsGkpdIyv 38 
                                    r +++ dR+ G++dIy+
  gi|116754145|ref|YP_843263.1| 171 RVVWADDRS-GNFDIYM 186
                                    578999***.******7 PP

  == domain 5  score: 1.4 bits;  conditional E-value: 0.15
                                    TSSEEEEEEECT.TCEE CS
                           PD40  19 DGkrlaFsSdRgsGkpd 35 
                                    DG  +a++ +R+ G  d
  gi|116754145|ref|YP_843263.1| 210 DGEIIAWADNRS-GEMD 225
                                    9**********9.9887 PP

  == domain 6  score: -0.6 bits;  conditional E-value: 0.62
                                    EEEEECT..TCEEEEE CS
                           PD40  24 aFsSdRg.sGkpdIyv 38 
                                    +++ +R+ + +pdIy+
  gi|116754145|ref|YP_843263.1| 294 VWTDYRQgLQDPDIYM 309
                                    78999999*******7 PP

  == domain 7  score: 3.1 bits;  conditional E-value: 0.043
                                    S.EEEEEE-TTSSEEEEEEECT.TCEEEEE CS
                           PD40   9 gnegaPsfSPDGkrlaFsSdRgsGkpdIyv 38 
                                    +n ++Ps+ +D    +++ dR+ G +++y+
  gi|116754145|ref|YP_843263.1| 325 FNHTNPSIFNDR--VVWTDDRT-GHYQVYM 351
                                    488999999998..********.***9996 PP

  == domain 8  score: -1.4 bits;  conditional E-value: 1.1
                                    SSEEEEEEECT.TCEEEE CS
                           PD40  20 GkrlaFsSdRgsGkpdIy 37 
                                    G + +++  R+ G+ d++
  gi|116754145|ref|YP_843263.1| 376 GDYVIYTDMRN-GNLDVF 392
                                    77888999999.999865 PP

  == domain 9  score: 8.0 bits;  conditional E-value: 0.0013
                                    TSSEEEEEEECT.TCEEEEE CS
                           PD40  19 DGkrlaFsSdRgsGkpdIyv 38 
                                    DG++ ++  +R+ G+ +Iyv
  gi|116754145|ref|YP_843263.1| 417 DGRYVVWMDNRT-GSDQIYV 435
                                    9***********.******8 PP

  == domain 10  score: 10.1 bits;  conditional E-value: 0.00028
                                    SSEEEEEEECT.TCEEEEE CS
                           PD40  20 GkrlaFsSdRgsGkpdIyv 38 
                                    G r++++ +R+ Gk+dIy+
  gi|116754145|ref|YP_843263.1| 461 GDRIVWADRRS-GKWDIYM 478
                                    89*********.******7 PP

  == domain 11  score: -1.7 bits;  conditional E-value: 1.4
                                    SSEEEEEEECT......TCEEEE CS
                           PD40  20 GkrlaFsSdRg.....sGkpdIy 37 
                                    G++++++  R+       ++dIy
  gi|116754145|ref|YP_843263.1| 503 GNTIVWADGRNalnasIRNWDIY 525
                                    89999999999888888889998 PP

  == domain 12  score: 0.3 bits;  conditional E-value: 0.33
                                    SSEEEEEEECT.TCEEEE CS
                           PD40  20 GkrlaFsSdRgsGkpdIy 37 
                                    G++ a+  +Rg G  dIy
  gi|116754145|ref|YP_843263.1| 551 GSYVAWLDERG-GAADIY 567
                                    8999*******.*****9 PP

  == domain 13  score: -3.7 bits;  conditional E-value: 5.8
                                    SEEEEEEECT.TCEEE CS
                           PD40  21 krlaFsSdRgsGkpdI 36 
                                    k++++  d + G+p+I
  gi|116754145|ref|YP_843263.1| 610 KYIVWMDDSS-GRPQI 624
                                    6888888877.99998 PP

  == domain 14  score: 6.7 bits;  conditional E-value: 0.0031
                                    TSSEEEEEEECT.TCEEEE CS
                           PD40  19 DGkrlaFsSdRgsGkpdIy 37 
                                    +G+ +++s +R  G++dIy
  gi|116754145|ref|YP_843263.1| 645 NGSLMVWSDNRR-GDWDIY 662
                                    89*********9.*****9 PP

  == domain 15  score: 2.9 bits;  conditional E-value: 0.051
                                    SSEEEEEEECT.TCEEEEE CS
                           PD40  20 GkrlaFsSdRgsGkpdIyv 38 
                                    G+  ++s +R+ G++d+y+
  gi|116754145|ref|YP_843263.1| 688 GQNVVWSDYRS-GSSDVYM 705
                                    9999*******.*****96 PP

  == domain 16  score: 9.9 bits;  conditional E-value: 0.00031
                                    SSEEEEEEECT.TCEEEEE CS
                           PD40  20 GkrlaFsSdRgsGkpdIyv 38 
                                    G+ +a+  dR+ G++dIyv
  gi|116754145|ref|YP_843263.1| 771 GSLIAWQDDRS-GNWDIYV 788
                                    899********.******8 PP

  == domain 17  score: -1.6 bits;  conditional E-value: 1.3
                                    EEE-TTSSEEEEEEE CS
                           PD40  14 PsfSPDGkrlaFsSd 28 
                                    P++S  Gk++a++ d
  gi|116754145|ref|YP_843263.1| 847 PAVS--GKYIAYVDD 859
                                    5555..899999866 PP

  == domain 18  score: 5.0 bits;  conditional E-value: 0.011
                                    SSEEEEEEECT.TCEEEEE CS
                           PD40  20 GkrlaFsSdRgsGkpdIyv 38 
                                    G+  ++  +R+ G+pdIyv
  gi|116754145|ref|YP_843263.1| 927 GNFVVWMDNRT-GNPDIYV 944
                                    66778999***.******8 PP

  == domain 19  score: -1.1 bits;  conditional E-value: 0.89
                                     SEEEEEEECT.TCEEEEE CS
                           PD40   21 krlaFsSdRgsGkpdIyv 38  
                                        ++  +++ G++++y+
  gi|116754145|ref|YP_843263.1| 1056 DIAVYQDNKD-GNWNVYI 1072
                                     5667888888.****885 PP

  == domain 20  score: 4.9 bits;  conditional E-value: 0.011
                                     TSSEEEEEEECT.TCEEEE CS
                           PD40   19 DGkrlaFsSdRgsGkpdIy 37  
                                     DG   ++  +R+ G++dIy
  gi|116754145|ref|YP_843263.1| 1094 DGYIVVYQDNRN-GNWDIY 1111
                                     899999******.*****9 PP

  == domain 21  score: 2.9 bits;  conditional E-value: 0.05
                                     EEEEEECT.TCEEEE CS
                           PD40   23 laFsSdRgsGkpdIy 37  
                                     +++  +R+ G++dIy
  gi|116754145|ref|YP_843263.1| 1140 IVWQDRRN-GDWDIY 1153
                                     89999***.*****9 PP

  == domain 22  score: 6.9 bits;  conditional E-value: 0.0028
                                     SEEEEEEECT.TCEEEEE CS
                           PD40   21 krlaFsSdRgsGkpdIyv 38  
                                     ++++++ +R+ G+ dIy+
  gi|116754145|ref|YP_843263.1| 1180 RKIVWTDNRS-GDKDIYI 1196
                                     79********.******7 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 !    7.4   0.6   0.00072       1.6      20      86 ..      95     163 ..      86     175 .. 0.72
   2 ?   -0.9   0.0      0.23   5.2e+02     245     277 ..     167     199 ..     159     225 .. 0.77
   3 ?    1.7   0.1      0.04        90     247     282 ..     334     368 ..     321     406 .. 0.70
   4 ?    1.8   0.0     0.035        79     246     278 ..     417     448 ..     407     452 .. 0.82
   5 !    5.9   0.3     0.002       4.5      18      83 ..     469     543 ..     464     554 .. 0.78
   6 ?   -0.8   0.0      0.22   4.9e+02     289     340 ..     675     732 ..     655     743 .. 0.63
   7 !   12.0   0.1   2.8e-05     0.063      21      87 ..     741     807 ..     735     819 .. 0.81
   8 ?   -1.2   0.0       0.3   6.8e+02     139     162 ..     829     853 ..     813     874 .. 0.73
   9 ?    2.2   0.5     0.027        61      62      85 ..    1107    1130 ..    1088    1145 .. 0.81
  10 ?   -1.2   0.0       0.3   6.8e+02     199     226 ..    1139    1166 ..    1130    1189 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00072
                                    EETTEEEEEETTTEECEEEETT.TT.BSEEEEESSTTEEEEEE....TTEEEEESTTTSEEEECES-STTTE CS
                        DPPIV_N  20 sytaeyyiydletneveelspg.eeklqlakwSPagdklafvr....nnnLyvrelatgkeiqlTsdgsagi 86 
                                    s+ a+ y+yd+++ +ve++  g ++ ++++++  +gd +++      ++n+y+++++t++++++Ts  +++i
  gi|116754145|ref|YP_843263.1|  95 SGNADIYLYDVKN-RVEQIVCGdNGNQTDPDI--DGDVVVWSDdrdgDWNIYLKDISTNQQKRVTSAQNDQI 163
                                    7788899999998.666655554666666655..566666654222279****************9776665 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.23
                                    TTSSEEEEEEETTSSEEEEEEESSS-C.EEESS CS
                        DPPIV_N 245 rdesgflwisekdGfkHLylfdldgkseikqlT 277
                                     +e +++w+ +++G   +y++dl+g+se++  T
  gi|116754145|ref|YP_843263.1| 167 VSEGRVVWADDRSGNFDIYMYDLKGGSEKAICT 199
                                    56789999999***99*********99555333 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.04
                                    SSEEEEEEETTSSEEEEEEESSS-C.EEESS-SSS- CS
                        DPPIV_N 247 esgflwisekdGfkHLylfdldgkseikqlTsGewe 282
                                    +++++w+ +++G  ++y+++l++++ ++ +T+ + +
  gi|116754145|ref|YP_843263.1| 334 NDRVVWTDDRTGHYQVYMMNLTTGE-EIRITNDDID 368
                                    5667777777777777777777777.6666655544 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.035
                                    TSSEEEEEEETTSSEEEEEEESSS-C.EEESS- CS
                        DPPIV_N 246 desgflwisekdGfkHLylfdldgkseikqlTs 278
                                    d+ +++w+ +++G +++y++d+ ++s ++q+T 
  gi|116754145|ref|YP_843263.1| 417 DGRYVVWMDNRTGSDQIYVYDVLQGS-ERQITT 448
                                    6677888888************9999.888885 PP

  == domain 5  score: 5.9 bits;  conditional E-value: 0.002
                                    SSEETTEEEEEETTTEECEEEETT.......TT.BSEEEEESSTTEE.EEEETTEEEEESTTTSEEEECES-S.T CS
                        DPPIV_N  18 Rhsytaeyyiydletneveelspg.......eeklqlakwSPagdkl.afvrnnnLyvrelatgkeiqlTsdg.s 83 
                                    R s++ + y+y+l t++ ++++ +           +++ w+   ++l a +rn+++y  +l tgke+ + ++g +
  gi|116754145|ref|YP_843263.1| 469 RRSGKWDIYMYNLTTGKETPICTNpanqvqpWIHGNTIVWADGRNALnASIRNWDIYSYNLTTGKETPICTNGyN 543
                                    788899999999999999999988776665423345667777755543889******************999943 PP

  == domain 6  score: -0.8 bits;  conditional E-value: 0.22
                                    EETTTTEEEEEESSSE.......TTEBEEEEEESSCTTEEEESSTTTSEEEEEEE-TTS CS
                        DPPIV_N 289 vdekrdlvyFtatkds.......PlerhlYsvslesggeltrltdeegdhysasfspsg 340
                                    v ++ d++y  a++++       ++ + +Y ++l+ +ge+t + +  gd+  a +s++ 
  gi|116754145|ref|YP_843263.1| 675 VRAEGDQLYPRASGQNvvwsdyrSGSSDVYMINLT-TGEVTDVATGPGDQVWADISEDR 732
                                    55555555555555555555555777888888888.88888888777777555555554 PP

  == domain 7  score: 12.0 bits;  conditional E-value: 2.8e-05
                                    ETTEEEEEETTTEECEEEETTTT.BSEEEEESSTTEEEE....EETTEEEEESTTTSEEEECES-STTTEE CS
                        DPPIV_N  21 ytaeyyiydletneveelspgeeklqlakwSPagdklaf....vrnnnLyvrelatgkeiqlTsdgsagif 87 
                                    +  ++++y+++++++e+l ++ + ++++k+S     +a+      n+++yv +l+tg+e++lT dg +++f
  gi|116754145|ref|YP_843263.1| 741 GNWDVVLYNISDGSTESLRKQ-GNQMYPKISGS--LIAWqddrSGNWDIYVYDLKTGNETKLTGDG-DQVF 807
                                    5668899***********999.********965..555511114689*******************.5566 PP

  == domain 8  score: -1.2 bits;  conditional E-value: 0.3
                                    SS-EEEEEE--BTTS--.-EEEEEE CS
                        DPPIV_N 139 qypevksikYPkaGskn.pkVelkv 162
                                     y ++ s +YP++G++  p V+ k 
  gi|116754145|ref|YP_843263.1| 829 IYDKKWSKRYPRPGMQTsPAVSGKY 853
                                    4677778889999987767776554 PP

  == domain 9  score: 2.2 bits;  conditional E-value: 0.027
                                     TTEEEEESTTTSEEEECES-STTT CS
                        DPPIV_N   62 nnnLyvrelatgkeiqlTsdgsag 85  
                                     n+++y  ++ ++kei++Tsd +++
  gi|116754145|ref|YP_843263.1| 1107 NWDIYAFDTNNSKEIRITSDTTDQ 1130
                                     79*******999*******98443 PP

  == domain 10  score: -1.2 bits;  conditional E-value: 0.3
                                     EEEEEETTSTEEEEEEEETTTCCEEEEE CS
                        DPPIV_N  199 lvqwlnRsqnrlkvvlvdaetgravvkl 226 
                                     +++w++R +   +++++d++tg+  +++
  gi|116754145|ref|YP_843263.1| 1139 VIVWQDRRNGDWDIYAFDLSTGKEIPIC 1166
                                     789999************9999987766 PP

>> Pectate_lyase22  Oligogalacturonate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.1   0.00016      0.35      45      82 ..     125     162 ..     105     182 .. 0.88
   2 ?   -0.8   0.0      0.21   4.8e+02      50      85 ..     172     207 ..     167     269 .. 0.69
   3 ?   -1.6   0.0      0.37   8.2e+02      46      80 ..     687     721 ..     642     724 .. 0.52
   4 ?   -0.8   0.0       0.2   4.5e+02      46      85 ..     687     726 ..     681     740 .. 0.85
   5 !    5.7   0.1    0.0022       4.9      47      85 ..     771     808 ..     758     834 .. 0.82
   6 ?    2.5   0.0     0.021        47      45      84 ..    1093    1132 ..    1087    1166 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00016
                Pectate_lyase22  45 rdgskllfggafdgprnyylldlntqqavqltegkgdn 82 
                                     dg+ ++++ + dg++n yl d+ t+q  ++t  + d+
  gi|116754145|ref|YP_843263.1| 125 IDGDVVVWSDDRDGDWNIYLKDISTNQQKRVTSAQNDQ 162
                                    59999***************************999886 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.21
                Pectate_lyase22  50 llfggafdgprnyylldlntqqavqltegkgdntfg 85 
                                    ++++ +  g+++ y+ dl+      +    gd+t+ 
  gi|116754145|ref|YP_843263.1| 172 VVWADDRSGNFDIYMYDLKGGSEKAICTASGDQTLP 207
                                    567778889999999999988888888888888875 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.37
                Pectate_lyase22  46 dgskllfggafdgprnyylldlntqqavqltegkg 80 
                                     g++++++    g+ + y+++l t + ++++ g g
  gi|116754145|ref|YP_843263.1| 687 SGQNVVWSDYRSGSSDVYMINLTTGEVTDVATGPG 721
                                    34444444444555555555555555555555555 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 0.2
                Pectate_lyase22  46 dgskllfggafdgprnyylldlntqqavqltegkgdntfg 85 
                                     g++++++    g+ + y+++l t + ++++ g gd+ + 
  gi|116754145|ref|YP_843263.1| 687 SGQNVVWSDYRSGSSDVYMINLTTGEVTDVATGPGDQVWA 726
                                    578888888889999*********************9876 PP

  == domain 5  score: 5.7 bits;  conditional E-value: 0.0022
                Pectate_lyase22  47 gskllfggafdgprnyylldlntqqavqltegkgdntfg 85 
                                    gs + +  +  g+++ y+ dl+t + ++lt g gd+ f 
  gi|116754145|ref|YP_843263.1| 771 GSLIAWQDDRSGNWDIYVYDLKTGNETKLT-GDGDQVFP 808
                                    66677788899******************9.89999984 PP

  == domain 6  score: 2.5 bits;  conditional E-value: 0.021
                Pectate_lyase22   45 rdgskllfggafdgprnyylldlntqqavqltegkgdntf 84  
                                      dg  +++  + +g+++ y +d n  + +++t  + d+t 
  gi|116754145|ref|YP_843263.1| 1093 TDGYIVVYQDNRNGNWDIYAFDTNNSKEIRITSDTTDQTN 1132
                                     6999999999***********************9999985 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   0.0       4.4   9.8e+03      24      34 ..      30      46 ..      25      48 .. 0.86
   2 ?   -0.2   0.1      0.72   1.6e+03      15      33 ..     370     389 ..     363     391 .. 0.86
   3 !   16.5   0.0   3.9e-06    0.0087       3      40 .]     832     870 ..     831     870 .. 0.88
   4 ?   -2.8   0.0       4.7   1.1e+04      14      24 ..     920     930 ..     916     931 .. 0.78
   5 ?   -2.0   0.0       2.5   5.7e+03      26      39 ..    1097    1116 ..    1085    1117 .. 0.67
   6 ?   -2.6   0.0         4     9e+03      32      40 .]    1151    1159 ..    1148    1159 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4.4
                          PQQ_3 24 vyvgtg......dGtly 34
                                   vy+g++      dG+++
  gi|116754145|ref|YP_843263.1| 30 VYTGSEqeqpdiDGHIV 46
                                   89999999999999987 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.72
                          PQQ_3  15 sspavdgglvyvgtg.dGtl 33 
                                    ssp ++g++v  +++ +G+l
  gi|116754145|ref|YP_843263.1| 370 SSPDISGDYVIYTDMrNGNL 389
                                    8999********99988886 PP

  == domain 3  score: 16.5 bits;  conditional E-value: 3.9e-06
                          PQQ_3   3 vlWsvqlpgpvn.sspavdgglvyvgtgdGtlyAlDaet 40 
                                     +Ws++ p p+  +spav+g ++  +++dG+l+ lD +t
  gi|116754145|ref|YP_843263.1| 832 KKWSKRYPRPGMqTSPAVSGKYIAYVDDDGSLRRLDITT 870
                                    68***88875555***********************987 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 4.7
                          PQQ_3  14 nsspavdgglv 24 
                                    +s pav+g+ v
  gi|116754145|ref|YP_843263.1| 920 QSRPAVSGNFV 930
                                    488*****987 PP

  == domain 5  score: -2.0 bits;  conditional E-value: 2.5
                          PQQ_3   26 vgtg......dGtlyAlDae 39  
                                     ++ +      +  +yA+D++
  gi|116754145|ref|YP_843263.1| 1097 IVVYqdnrngNWDIYAFDTN 1116
                                     44444456556779999975 PP

  == domain 6  score: -2.6 bits;  conditional E-value: 4
                          PQQ_3   32 tlyAlDaet 40  
                                      +yA+D  t
  gi|116754145|ref|YP_843263.1| 1151 DIYAFDLST 1159
                                     69****977 PP

>> PQQ  PQQ enzyme repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.23   5.1e+02      10      23 ..     262     275 ..     253     276 .. 0.82
   2 ?    1.8   0.0      0.11   2.6e+02       8      23 ..     345     360 ..     343     360 .. 0.88
   3 ?   -0.3   0.0      0.55   1.2e+03      12      22 ..     476     486 ..     475     486 .. 0.90
   4 ?    0.0   0.0      0.43   9.7e+02      12      22 ..     524     534 ..     523     534 .. 0.91
   5 ?   -1.1   0.0      0.98   2.2e+03      12      22 ..     703     713 ..     699     713 .. 0.88
   6 ?    2.5   0.0     0.069   1.5e+02      12      22 ..     786     796 ..     783     796 .. 0.92
   7 ?   -3.3   0.2       4.9   1.1e+04       7      19 ..     858     870 ..     853     870 .. 0.79
   8 !    7.1   0.0    0.0024       5.4      12      23 ..    1152    1163 ..    1148    1163 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.23
                                    SEEEEEETTTCCEE CS
                            PQQ  10 GylyAlDadTGkvl 23 
                                    + ++ +++dTG+++
  gi|116754145|ref|YP_843263.1| 262 TEIVLYNVDTGEER 275
                                    568889******97 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.11
                                    TTSEEEEEETTTCCEE CS
                            PQQ   8 adGylyAlDadTGkvl 23 
                                     ++++y  +++TG+++
  gi|116754145|ref|YP_843263.1| 345 GHYQVYMMNLTTGEEI 360
                                    5789**********96 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.55
                                    EEEEETTTCCE CS
                            PQQ  12 lyAlDadTGkv 22 
                                    +y ++++TGk+
  gi|116754145|ref|YP_843263.1| 476 IYMYNLTTGKE 486
                                    799******97 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 0.43
                                    EEEEETTTCCE CS
                            PQQ  12 lyAlDadTGkv 22 
                                    +y ++++TGk+
  gi|116754145|ref|YP_843263.1| 524 IYSYNLTTGKE 534
                                    899******97 PP

  == domain 5  score: -1.1 bits;  conditional E-value: 0.98
                                    EEEEETTTCCE CS
                            PQQ  12 lyAlDadTGkv 22 
                                    +y ++++TG+v
  gi|116754145|ref|YP_843263.1| 703 VYMINLTTGEV 713
                                    899******97 PP

  == domain 6  score: 2.5 bits;  conditional E-value: 0.069
                                    EEEEETTTCCE CS
                            PQQ  12 lyAlDadTGkv 22 
                                    +y +D++TG++
  gi|116754145|ref|YP_843263.1| 786 IYVYDLKTGNE 796
                                    8********96 PP

  == domain 7  score: -3.3 bits;  conditional E-value: 4.9
                                    ETTSEEEEEETTT CS
                            PQQ   7 sadGylyAlDadT 19 
                                    ++dG l+ lD++T
  gi|116754145|ref|YP_843263.1| 858 DDDGSLRRLDITT 870
                                    7899999999988 PP

  == domain 8  score: 7.1 bits;  conditional E-value: 0.0024
                                     EEEEETTTCCEE CS
                            PQQ   12 lyAlDadTGkvl 23  
                                     +yA+D++TGk++
  gi|116754145|ref|YP_843263.1| 1152 IYAFDLSTGKEI 1163
                                     9*********96 PP

>> DUF2606  Protein of unknown function (DUF2606)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.17   3.9e+02      85     108 ..      40      64 ..      13      73 .. 0.82
   2 ?    3.6   0.4     0.024        54      85     124 ..     124     162 ..     112     168 .. 0.72
   3 ?   -0.4   0.0      0.39   8.8e+02      86     104 ..     168     186 ..     162     197 .. 0.86
   4 ?   10.6   0.1   0.00016      0.35      88     129 ..     335     374 ..     330     375 .. 0.91
   5 ?   -2.5   0.1       1.8   4.1e+03      89     109 ..     463     483 ..     460     489 .. 0.79
   6 ?   -2.3   0.0       1.5   3.4e+03      89     109 ..     690     713 ..     686     717 .. 0.70
   7 ?   -4.1   0.0       5.6   1.3e+04      90     107 ..     774     791 ..     771     801 .. 0.68
   8 ?    1.9   0.8     0.081   1.8e+02      70     103 ..    1114    1153 ..    1076    1167 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.17
                        DUF2606  85 dkeGd.vkwdtvrkGdyivaltkne 108
                                    d +G+ v+w ++r G++ +++ + e
  gi|116754145|ref|YP_843263.1|  40 DIDGHiVVWADGRSGNFDIFMYDLE 64 
                                    66776257**********9987766 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.024
                        DUF2606  85 dkeGdv.kwdtvrkGdyivaltknetsvthqivliedkddt 124
                                    d +Gdv +w + r Gd+ ++l +  t+   q  ++  ++d+
  gi|116754145|ref|YP_843263.1| 124 DIDGDVvVWSDDRDGDWNIYLKDISTNQ--QKRVTSAQNDQ 162
                                    56788537*************9998844..44444444444 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.39
                        DUF2606  86 keGdvkwdtvrkGdyival 104
                                     eG v+w + r G++ +++
  gi|116754145|ref|YP_843263.1| 168 SEGRVVWADDRSGNFDIYM 186
                                    58************98875 PP

  == domain 4  score: 10.6 bits;  conditional E-value: 0.00016
                        DUF2606  88 GdvkwdtvrkGdyivaltknetsvthqivliedkddtkkilv 129
                                      v+w + r+G+y v++ +  t    +i +++d  d+  + +
  gi|116754145|ref|YP_843263.1| 335 DRVVWTDDRTGHYQVYMMNLTT--GEEIRITNDDIDHSSPDI 374
                                    679***************9999..999*********999887 PP

  == domain 5  score: -2.5 bits;  conditional E-value: 1.8
                        DUF2606  89 dvkwdtvrkGdyivaltknet 109
                                     ++w + r G++ +++ +  t
  gi|116754145|ref|YP_843263.1| 463 RIVWADRRSGKWDIYMYNLTT 483
                                    599********9988766544 PP

  == domain 6  score: -2.3 bits;  conditional E-value: 1.5
                        DUF2606  89 dvkwdtvrkGd...yivaltknet 109
                                    +v+w + r G    y++ lt +e 
  gi|116754145|ref|YP_843263.1| 690 NVVWSDYRSGSsdvYMINLTTGEV 713
                                    699999999973346666666664 PP

  == domain 7  score: -4.1 bits;  conditional E-value: 5.6
                        DUF2606  90 vkwdtvrkGdyivaltkn 107
                                    + w++ r G++ +++ + 
  gi|116754145|ref|YP_843263.1| 774 IAWQDDRSGNWDIYVYDL 791
                                    789999*99988766443 PP

  == domain 8  score: 1.9 bits;  conditional E-value: 0.081
                        DUF2606   70 deePskeiGiilGktd......keGdvkwdtvrkGdyiva 103 
                                     d + skei i+   td      + G ++w++ r+Gd+ ++
  gi|116754145|ref|YP_843263.1| 1114 DTNNSKEIRITSDTTDqtnpdiESGVIVWQDRRNGDWDIY 1153
                                     5677888888888888333333468999*******98765 PP

>> phage_tail_N  Prophage tail fibre N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       4.4   9.9e+03      68      90 ..      38      60 ..      29      64 .. 0.76
   2 ?   -1.4   0.1      0.94   2.1e+03      43      92 ..      95     146 ..      87     155 .. 0.66
   3 ?    4.3   0.2     0.017        38      40      93 ..     341     396 ..     328     407 .. 0.77
   4 ?   -3.4   0.0         4   8.9e+03      41      88 ..     426     476 ..     423     487 .. 0.67
   5 ?   -3.6   0.2       4.7   1.1e+04      44      85 ..     782     824 ..     777     829 .. 0.67
   6 ?    9.0   0.1   0.00057       1.3      66      90 ..    1048    1072 ..    1043    1079 .. 0.88
   7 ?    2.3   0.1     0.068   1.5e+02      60      85 ..    1081    1107 ..    1074    1119 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 4.4
                   phage_tail_N 68 peshaGditvyedskPGtlndfl 90
                                   ++   G+i v+ d + G ++ f+
  gi|116754145|ref|YP_843263.1| 38 QPDIDGHIVVWADGRSGNFDIFM 60
                                   566679999**999999988776 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.94
                   phage_tail_N  43 pdeaGrysldvetGkysvilkvdg..fpeshaGditvyedskPGtlndflia 92 
                                    +++a  y +dv++    ++   +g   ++   Gd+ v+ d + G  n +l  
  gi|116754145|ref|YP_843263.1|  95 SGNADIYLYDVKNRVEQIVCGDNGnqTDPDIDGDVVVWSDDRDGDWNIYLKD 146
                                    5566666666665544444443331145667799999999999999988865 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.017
                   phage_tail_N  40 senpdeaGrysldvetGkysvilk..vdgfpeshaGditvyedskPGtlndfliam 93 
                                    ++ +++   y ++  tG+   i +  +d  ++   Gd  +y d + G l+ fl   
  gi|116754145|ref|YP_843263.1| 341 DDRTGHYQVYMMNLTTGEEIRITNddIDHSSPDISGDYVIYTDMRNGNLDVFLYDL 396
                                    55666666788999999866555411567788899*****************9765 PP

  == domain 4  score: -3.4 bits;  conditional E-value: 4
                   phage_tail_N  41 enpdeaGrysldvetG...kysvilkvdgfpeshaGditvyedskPGtlnd 88 
                                    + ++ +  y +dv +G   + +   +    ++   Gd  v+ d + G  + 
  gi|116754145|ref|YP_843263.1| 426 NRTGSDQIYVYDVLQGserQITTQQQAQLLSPVISGDRIVWADRRSGKWDI 476
                                    567778888888888832233444444556788888888888888886655 PP

  == domain 5  score: -3.6 bits;  conditional E-value: 4.7
                   phage_tail_N  44 deaGrysldvetGkys.vilkvdgfpeshaGditvyedskPGt 85 
                                    ++   y +d +tG+ + ++   d   +   G+  v+ed   G 
  gi|116754145|ref|YP_843263.1| 782 GNWDIYVYDLKTGNETkLTGDGDQVFPDVSGNTIVWEDRATGD 824
                                    5555688888888765133445666677888889999987775 PP

  == domain 6  score: 9.0 bits;  conditional E-value: 0.00057
                   phage_tail_N   66 gfpeshaGditvyedskPGtlndfl 90  
                                     g ++  aGdi+vy+d k G  n ++
  gi|116754145|ref|YP_843263.1| 1048 GTNPRTAGDIAVYQDNKDGNWNVYI 1072
                                     78999**************999775 PP

  == domain 7  score: 2.3 bits;  conditional E-value: 0.068
                   phage_tail_N   60 vilk.vdgfpeshaGditvyedskPGt 85  
                                     v+l   d  ++   G i vy+d + G 
  gi|116754145|ref|YP_843263.1| 1081 VTLDpADQINPATDGYIVVYQDNRNGN 1107
                                     555436999**************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); 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):               8  [number of targets reported over threshold]
# CPU time: 0.75u 0.32s 00:00:01.07 Elapsed: 00:00:00.44
# Mc/sec: 8271.28
//
Query:       gi|116754146|ref|YP_843264.1|  [L=1242]
Description: cobaltochelatase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
          0 1062.2   0.0          0 1062.0   0.0    1.0  1  CobN-Mg_chel  CobN/Magnesium Chelatase
  ------ inclusion threshold ------
       0.15   12.7   0.0       0.54   11.0   0.0    1.9  2  DUF2281       Protein of unknown function (DUF2281)


Domain annotation for each model (and alignments):
>> CobN-Mg_chel  CobN/Magnesium Chelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1062.0   0.0         0         0       2    1088 ..     156    1220 ..     155    1221 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1062.0 bits;  conditional E-value: 0
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel    2 aYlkeggveNlknllryladkllgkkeeeveppvelpeegiyhpdakelfesleeylewykkakkekaptvgilfyra 79  
                                     +Y+++gg+eNl+nll++l +++lg + +++++p ++pe giyh     +++sl++ l++     + ++ t+g+lfy +
  gi|116754146|ref|YP_843264.1|  156 RYWRYGGTENLQNLLTLLLREYLGCDLPRPPDPLPFPEYGIYH--RGGFLDSLDALLPH----LDAERATIGVLFYGN 227 
                                     8***********************999999*************..66799999999987....6899*********** PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel   80 hllagntavidaliraleerglnvlpvfvssldseaqealeelftkegeekvdalinttsfalvkgpaeeeeeeaeee 157 
                                      ++++ + v++al ++l +  +nv+pvf+++   ++ +a++++f k++ + +da+in+t f++++gp +++ +  +++
  gi|116754146|ref|YP_843264.1|  228 MHFDQCLPVLKALDDRLGD--MNVIPVFSDG--IHNLRAIRSFFLKDK-PVIDAMINLTWFRINGGPLGGDPD-LTKN 299 
                                     *****************97..69********..9999*******8777.******************887776.6677 PP

                                     xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  158 alkelnvPvlqa.ilssqsreeWeessqGlspldlamsvalpEldGriepvvisfkeeee.eetevekyepiperver 233 
                                      l+ l+vPv+++  ++++s+++We+s++Glsp++  m v++pEldG+ ep+++ + ++ + ++ ev+++ +i++r++r
  gi|116754146|ref|YP_843264.1|  300 LLNDLDVPVFAPvSMYQSSIDDWERSDAGLSPTESIMAVIWPELDGCAEPIPCCGVRSFKiDDMEVREVAAIDDRISR 377 
                                     78**********9999**************************************987555699*************** PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  234 vadlaarwarLrrkpnaekkvaiilanyppgegrlgnavgLdvpaSlvnlLkalkeeGYdveelpesgdeLiellleg 311 
                                     +a+++++w++Lrr +na k++a+i++nyppge++lg a++Ldv+aSl +lL ++k++GY+++  p+   eL +l+ + 
  gi|116754146|ref|YP_843264.1|  378 IASRIRSWVHLRREENARKRIALIIYNYPPGEENLGRASYLDVFASLKRLLYTMKDAGYSLSI-PD--MELDHLFYKM 452 
                                     *************************************************************55.74..4555555555 PP

                                     xx.xxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  312 gt.ndpew..eelkvgaaallpaeeYeewfeeLpeelreeveerWgeppgemveeeksgekklvipglqlGnvfvgvQ 386 
                                     ++ n  +w  +++  +++ +++ eeY + f++Lpeel++e+ + Wgeppg    e + +++ ++ipgl+lGnvf+gvQ
  gi|116754146|ref|YP_843264.1|  453 AAvNTGKWlqTDITLRECPSMSREEYMQAFKSLPEELQNEILDFWGEPPG----EVMVSGGGILIPGLDLGNVFIGVQ 526 
                                     5544577755555669**********************************....555669****************** PP

                                     xxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  387 Parg..yeedpsklyhdpdlpPthqYlAfYlWlreefgadavvHvGkHGtlEwlPGKqvglseecyPdillgdlPhlY 462 
                                     Par    + d +++ hd++ pP+hqY+AfY+Wl+++++adavvH+G+HG  E++ GK+++ls++cyPd l+gd+P+lY
  gi|116754146|ref|YP_843264.1|  527 PARPplEGIDLNEISHDKTKPPHHQYIAFYHWLQRVWRADAVVHIGTHGLAEFMKGKELALSSRCYPDFLIGDMPNLY 604 
                                     ***966677889****************************************************************** PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  463 pYivnnpgEGtqAKRRsyAviidHltPpmtraelygelaeLeelideYeeaesldperlkalreqilelveelnldkd 540 
                                      Y v n +E ++AKRR yA++i+++ Pp+t+a+ly+ ++eLeelide+ +a + d++r+++lre+i + + eln+++ 
  gi|116754146|ref|YP_843264.1|  605 FYHVVNTSEVIIAKRRLYAMTISYNSPPYTNADLYEGYMELEELIDEHSQAVTYDHSRADRLRERIFKRAGELNITA- 681 
                                     ***************************************************************************43. PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  541 lgleeakeeeeeefeellekldgyleelkeaqirdglhilGeapegeqlvdlvvailrleneegesltealaealgld 618 
                                                    + +++++++l e+k++ i++glh+lGe++++e+l++++  +lr++++  +sl++ +aea+gld
  gi|116754146|ref|YP_843264.1|  682 ---------------KSIDEIQDMLYEMKRRIIPKGLHVLGESYRKEDLESFMRMLLRYDRDGVRSLNSIVAEAMGLD 744 
                                     ...............34999********************************************************** PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                   CobN-Mg_chel  619 ldeleeksekelrtagdalealeeeaee........lveelleeeaeeeeaeaeeleeeeeeeee.eteeEitallra 687 
                                     ++el ++++++l++  +++++++  a +         ++ +l++e +++ +       e+ ++   + + Ei++++r+
  gi|116754146|ref|YP_843264.1|  745 YRELLKNRSRKLDEVDKICSEITGIAVDgsdrsyplEIKGYLSDELKKTLS----YGLEAVRR-YsDNSIEIKNFIRG 817 
                                     *****9999999999999999988888777777776677777664433222....11111112.124458******** PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  688 LdGeyippgpsGdptrgraevLPTGrNfysvDpraiPteaAwevGkklaeellerylqehgeyPekvglslwgtetmr 765 
                                     LdG++i+p+ +Gd++r++  +LPTG+N+ ++Dp +iPt  A+++G+++ae++++ y +++g+yP  vg++lwg et++
  gi|116754146|ref|YP_843264.1|  818 LDGRFIEPSVGGDIIRSPH-ALPTGKNLVQFDPTRIPTSDAIKRGEEIAENTIRAYIERTGSYPSMVGVVLWGFETTK 894 
                                     ****************955.********************************************************** PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  766 teGediAqiLallGvrPvwdaagrvvdlelipleeLgRPRiDVtvriSGffRDafpnlielldkavelvaeldEpeed 843 
                                     t+Ge+i+qiL +lGvr  +d     v++  + leeLgRPR+D +v+i+GffRD+fpn+++lld+a++lv++l+Ep ++
  gi|116754146|ref|YP_843264.1|  895 TGGETIGQILRYLGVRLERDPGSLAVRIIPLTLEELGRPRVDCLVNICGFFRDMFPNVVQLLDRAFALVSSLEEPLDM 972 
                                     **********************9999999999********************************************** PP

                                     xxxxxxxxxxxxxxxx...xxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  844 Nfvrkhvleeeaelee...keeae..eratyRvFgskpGaYgagvqeliessnWedeedLaeaYlnwssyaYgkgaeg 916 
                                     N+vrkh+l+++++l +   + e++    a+ R+Fg+++G+Yg+ +  l+e+s W++e++Lae+Y ++++++Y++g ++
  gi|116754146|ref|YP_843264.1|  973 NYVRKHTLDNMKSLLQngmE-EKQagVLAKGRIFGPRAGEYGTRMLPLVEDSVWRTEDELAEVYASSMGHIYTEGIHA 1049
                                     ***************95532.333579*************************************************** PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  917 eeaeeafearLkrvdvvvqnqdsrehdlldsddyyqflGGltaavrslsgkkpeayfgdssnpenpkvrtlkeeiare 994 
                                     +++ ++++++++rvd+v q +ds+ ++++d+d+y++f+GGl+ avrs++g++p ++++d+ + e +++++++ +++  
  gi|116754146|ref|YP_843264.1| 1050 AQQLDLYRSNISRVDLVSQIRDSHDWEFIDLDHYFEFFGGLSSAVRSARGSDPVMLVSDT-TGEVIRTEDIRSAVEIG 1126
                                     ************************************************************.7899************* PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  995 lrsrvlNPkWiegmmrhGykGafelaatvdnlfgwdatadvvddwvyeevaetYvlDeevrefleekNpwAlreiaer 1072
                                     +r+r+lNP+Wi+gm  h ++Ga+++a++++n++g  at++ v++wv+ ++ae+Y++De++r+ l e+N +A  +i e 
  gi|116754146|ref|YP_843264.1| 1127 VRTRLLNPRWIDGMLAHRFHGAQQIADRIENMLGLAATTHSVESWVWSSIAERYMFDETTRQKLLENNHYAAVKIGEW 1204
                                     ****************************************************************************** PP

                                     xxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel 1073 LlEaarrglWeaseet 1088
                                     L+Ea+rrg+W+a++++
  gi|116754146|ref|YP_843264.1| 1205 LMEAHRRGYWKAEDDE 1220
                                     ************9987 PP

>> DUF2281  Protein of unknown function (DUF2281)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   6.1e-05      0.54       4      20 ..     480     496 ..     478     497 .. 0.94
   2 ?   -3.1   0.0       1.5   1.3e+04      18      59 ..     743     781 ..     743     782 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.1e-05
                        DUF2281   4 ekiqeLPedlkqEvldF 20 
                                    ++++ LPe+l++E+ldF
  gi|116754146|ref|YP_843264.1| 480 QAFKSLPEELQNEILDF 496
                                    789*************9 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.5
                        DUF2281  18 ldFaefLleKyaakkkktlkl..rlaGilkglltmsdDfdepLE 59 
                                    ld+ e L++++++   +  k   ++ Gi+ +     +D   pLE
  gi|116754146|ref|YP_843264.1| 743 LDYRELLKNRSRK-LDEVDKIcsEITGIAVDG----SDRSYPLE 781
                                    7999999999943.333333335777777666....56556665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.34s 00:00:01.15 Elapsed: 00:00:00.47
# Mc/sec: 7922.38
//
Query:       gi|116754147|ref|YP_843265.1|  [L=397]
Description: periplasmic binding protein [Methanosaeta thermophila PT]
Scores for complete 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   67.5   0.0    1.7e-18   67.1   0.0    1.1  1  Peripla_BP_2  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.1   0.0   9.4e-23   1.7e-18       1     234 [.      88     332 ..      88     335 .. 0.87

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 9.4e-23
                                    EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT....TS-BSBESSSB-HHHHHHH--SEEEE-GGG......... CS
                   Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadklee..aivevgadgeidvEklaalkPDlvilskgl......glt 72 
                                    ia++ + + e+l  +G+++ +v   + +sd +++    e  + + +g+  e+d+E+++  +PDl+++ +g        l+
  gi|116754147|ref|YP_843265.1|  88 IACTVSHQLETLRSIGIPRAMV--VAVPSDIEKYSIFQEyhDLPQIGHFYEPDLEQIIRIHPDLLLVHPGPgptgqnYLQ 165
                                    89999999***********665..455666666665666679***************************99677666666 PP

                                    GGGHHHHHHHS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT.-EEEEEEEETTE..EE CS
                   Peripla_BP_2  73 dedeellksgiptvivessntgeslkeqiralgellgledeaeklvaeidsklaaaksaidsekpkpvlvfggadeggyv 152
                                    +  ++l   gi ++    s   +s+ e+i+ lg +l++ +e   + a++++ l ++  +++ + +++ + ++  ++  ++
  gi|116754147|ref|YP_843265.1| 166 TVLDRLNGTGITVFCLACSRP-DSYSEEIEKLGRILERGNESASFRAFYEGVLGSVIGRTEGIPDEERPKVYVEYG--PY 242
                                    666777777888888877777.*****************************************7777777776565..77 PP

                                    EE-TTSTTTHHHHT.S--EESTTT--STT-EEE-HHHHHHH--SEEEEEEH..........HHHT-S--HHHHT-SHHHH CS
                   Peripla_BP_2 153 vagsnsyigdllda.lgieniaaeskkseyeeisaEqilasdpdvifvsgr..........aeadnktgleflkenplla 221
                                      ++n+   ++  + +g+++i+       ++e+s+E++  +dpdvi+              + ++ k   ++++e+p+l+
  gi|116754147|ref|YP_843265.1| 243 RVSNNPILDAMPVEmAGGRSIITG---RTGGEVSPETVIVEDPDVIIRLVYdedydakdakDISKLKFARDEILERPELQ 319
                                    888888888886667******877...5999***************************99999999999*********** PP

                                    TSHHHHTT-EEEE CS
                   Peripla_BP_2 222 elpAvkngrVyal 234
                                    +++Av+ngrV+ +
  gi|116754147|ref|YP_843265.1| 320 NVTAVRNGRVFVM 332
                                    ***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); 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 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2878.92
//
Query:       gi|116754148|ref|YP_843266.1|  [L=89]
Description: translation elongation factor aEF-1 beta [Methanosaeta thermophila PT]
Scores for complete 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   70.0   0.5    1.5e-19   69.9   0.5    1.0  1  EF1_GNE   EF-1 guanine nucleotide exchange domain
  ------ inclusion threshold ------
      0.052   14.0   1.5       0.33   11.4   0.2    2.1  2  HMA       Heavy-metal-associated 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 !   69.9   0.5   1.7e-23   1.5e-19       3      88 ..       7      87 ..       5      89 .] 0.93

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 1.7e-23
                                   EEEEEESSS---HHHHHHHHHH.HS-T.SEE--.--EEE-SSS-EEEEEEEEESSS-G.GGGHHHHHHTTS-S.....SEEE CS
                        EF1_GNE  3 vlevkPeddetdleelekkvksikleg.lvwgeasklepiafGlkkLqiscvieddkv.stdeleekieeiegeledlVqsv 82
                                    ++v+Pe+++ d+e+l++++ks +++  ++++ a+++ piafGlk+L   +  +d+ + +t+e+ee++++++g     V+sv
  gi|116754148|ref|YP_843266.1|  7 KIRVMPESTDIDMESLKESIKS-AVPAsAKLH-AMDVRPIAFGLKALIAVVLLDDKAGgGTEEVEEAFSKVKG-----VESV 81
                                   799*******************.77776****.7********************999889*************.....**** PP

                                   EEEEEE CS
                        EF1_GNE 83 eivsfn 88
                                   e++++ 
  gi|116754148|ref|YP_843266.1| 82 EVEEVG 87
                                   **9986 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1     0.048   4.3e+02      40      59 ..      10      29 ..       3      31 .. 0.65
   2 ?   11.4   0.2   3.7e-05      0.33      15      32 ..      67      84 ..      64      87 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.048
                            HMA 40 Vegdaestklrkiieaieka 59
                                   V+ + ++++ + ++e+i++a
  gi|116754148|ref|YP_843266.1| 10 VMPESTDIDMESLKESIKSA 29
                                   44444444449999999875 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 3.7e-05
                            HMA 15 kvekvLselpgVesvkvd 32
                                    ve+++s+++gVesv+v 
  gi|116754148|ref|YP_843266.1| 67 EVEEAFSKVKGVESVEVE 84
                                   69*************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.33u 0.27s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 660.38
//
Query:       gi|116754149|ref|YP_843267.1|  [L=79]
Description: hypothetical protein Mthe_0838 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-06   28.5   5.7    1.1e-06   28.5   5.7    2.2  2  DUF1610          Domain of unknown function (DUF1610)
     0.0032   17.5   6.2      0.005   16.9   6.2    1.3  1  Zn_Tnp_IS91      Transposase zinc-binding domain
  ------ inclusion threshold ------
      0.024   15.0   9.2       0.38   11.1   4.8    2.2  2  C1_2             C1 domain
        0.1   13.0   8.5      0.086   13.2   7.7    1.4  1  Rhodanese_C      Rhodanase C-terminal
       0.11   12.8   4.5       0.13   12.5   4.5    1.1  1  FYVE_2           FYVE-type zinc finger
       0.17   12.0  14.8       0.67   10.1   0.1    4.0  3  zf-ACC           Acetyl-coA carboxylase zinc finger domain
       0.17   12.0  10.1        8.7    6.5   1.9    3.1  3  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
       0.19   11.6   8.3        1.1    9.2   0.1    2.3  2  C1_1             Phorbol esters/diacylglycerol binding domain
       0.27    9.0   3.6       0.29    8.9   3.6    1.0  1  PolC_DP2         DNA polymerase II large subunit DP2
       0.28   11.7  10.1        1.1    9.8   7.5    2.1  2  zf-CHY           CHY zinc finger
       0.34   10.8   0.2       0.34   10.8   0.2    3.6  4  Fer4             4Fe-4S binding domain
       0.38   10.6   2.4       0.79    9.6   2.4    1.5  1  Pput2613-deam    Pput_2613-like deaminase
       0.61   10.1  10.9       0.62   10.1   4.8    2.3  2  zf-C2HC5         Putative zinc finger motif, C2HC5-type
        1.1    9.5   0.1        1.1    9.5   0.1    3.6  1  Fer4_2           4Fe-4S binding domain
        1.6    7.5   5.5        1.8    7.3   5.5    1.0  1  NMDAR2_C         N-methyl D-aspartate receptor 2B3 C-terminus
        1.8    8.3   9.2        7.8    6.3   0.0    3.4  3  zinc_ribbon_10   Predicted integral membrane zinc-ribbon meta
        2.2    8.5   9.5        9.1    6.5   9.5    2.1  2  Prok-RING_2      Prokaryotic RING finger family 2
        2.8    8.0   9.1         13    5.8   0.2    2.1  2  HypA             Hydrogenase/urease nickel incorporation, met
        4.4    7.3  10.6        2.3    8.2   6.5    2.1  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
        4.8    7.5  11.7         11    6.4   0.1    3.2  2  zf-LITAF-like    LITAF-like zinc ribbon domain
        6.5    6.3  17.9       0.45   10.0   0.4    3.8  3  zf-ribbon_3      zinc-ribbon domain
        8.8    6.0  11.8        3.3    7.4   0.2    3.3  3  zf_UBZ           Ubiquitin-Binding Zinc Finger
        9.7    6.0  17.8       0.67    9.7   0.4    4.0  4  Rubredoxin_2     Rubredoxin metal binding domain


Domain annotation for each model (and alignments):
>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   5.7   1.4e-09   1.1e-06       1      24 []      32      54 ..      32      54 .. 0.99
   2 ?    0.3   0.8      0.89   6.9e+02       1       5 [.      71      75 ..      71      77 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.4e-09
                        DUF1610  1 CtSCGaelaprEravvFpCPNCGE 24
                                   C+SCG+ l + + +v FpCP CGE
  gi|116754149|ref|YP_843267.1| 32 CISCGVTLLGIG-GVRFPCPSCGE 54
                                   ************.**********9 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.89
                        DUF1610  1 CtSCG 5 
                                   C SCG
  gi|116754149|ref|YP_843267.1| 71 CKSCG 75
                                   99**9 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   6.2   6.4e-06     0.005      12      64 ..      16      75 ..       6      77 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.4e-06
                    Zn_Tnp_IS91 12 k.kkklrpsqrkavekilrCrtaal..GfaryeCeeCghekivyfsCksrh....CpsCq 64
                                   + +++ r+s++++ ek ++C+   l  G+ r+ C++Cg+    +++Ck+++    C+sC+
  gi|116754149|ref|YP_843267.1| 16 TsRRSERRSMKDVPEKCISCGVTLLgiGGVRFPCPSCGEVIARCNRCKKQSniytCKSCG 75
                                   34456688999999*******988633788889***************975545588886 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1     0.013       9.9      18      39 ..      29      53 ..      17      57 .. 0.81
   2 ?   11.1   4.8   0.00049      0.38      20      41 ..      58      77 ..      53      77 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.013
                           C1_2 18 sfnCsaCgrk...idgffYsCseCd 39
                                     +C  Cg +   i g ++ C+ C 
  gi|116754149|ref|YP_843267.1| 29 PEKCISCGVTllgIGGVRFPCPSCG 53
                                   579*******98888888***9994 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00049
                           C1_2 20 nCsaCgrkidgffYsCseCdfs 41
                                   +C+ C++++  + Y+C+ C f+
  gi|116754149|ref|YP_843267.1| 58 RCNRCKKQS--NIYTCKSCGFT 77
                                   8******96..56***99*995 PP

>> Rhodanese_C  Rhodanase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   7.7   0.00011     0.086      10      63 ..      22      74 ..       9      75 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00011
                    Rhodanese_C 10 RlalksevvgkCieCgkpvdelrkrnCanedCnelvlvCeeCaeklkgvcseeC 63
                                   R ++ ++v  kCi Cg     +  ++  +++C e +  C++C+++ + + +++C
  gi|116754149|ref|YP_843267.1| 22 RRSM-KDVPEKCISCGVTLLGIGGVRFPCPSCGEVIARCNRCKKQSNIYTCKSC 74
                                   3344.56899*********988866666689**************999977799 PP

>> FYVE_2  FYVE-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   4.5   0.00016      0.13      53     100 ..      28      74 ..       9      77 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00016
                         FYVE_2  53 gethCilCleefkllvnskrqCldCklnvCkkCsvenkkekvwlCkiC 100
                                      ++Ci C  ++  +   +  C  C   v  +C + +k+ +++ Ck C
  gi|116754149|ref|YP_843267.1|  28 VPEKCISCGVTLLGIGGVRFPCPSCGE-VIARCNRCKKQSNIYTCKSC 74 
                                    3579*****9999999999******86.56789999************ PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1     0.014        11       3      12 ..      31      40 ..      31      42 .. 0.88
   2 ?   10.1   0.1   0.00086      0.67       4      12 ..      49      57 ..      47      58 .. 0.88
   3 ?   -2.1   6.1       5.5   4.3e+03      19      26 .]      67      74 ..      57      74 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.014
                         zf-ACC  3 KCpsCgemly 12
                                   KC sCg +l+
  gi|116754149|ref|YP_843267.1| 31 KCISCGVTLL 40
                                   9*****9885 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00086
                         zf-ACC  4 CpsCgemly 12
                                   CpsCge++ 
  gi|116754149|ref|YP_843267.1| 49 CPSCGEVIA 57
                                   ******996 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 5.5
                         zf-ACC 19 nlyVCPkC 26
                                   n y+C +C
  gi|116754149|ref|YP_843267.1| 67 NIYTCKSC 74
                                   55666666 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 ?    3.0   0.0      0.14   1.1e+02      11      25 ..      24      38 ..      11      40 .. 0.80
   2 ?    6.3   1.5     0.013        10      15      26 ..      45      56 ..      42      60 .. 0.81
   3 ?    6.5   1.9     0.011       8.7       2      24 ..      59      76 ..      58      78 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.14
                       zf-Mss51 11 apkhvdfeCpdCGip 25
                                   + k+v  +C  CG+ 
  gi|116754149|ref|YP_843267.1| 24 SMKDVPEKCISCGVT 38
                                   56888999*****96 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.013
                       zf-Mss51 15 vdfeCpdCGipt 26
                                   v+f Cp CG ++
  gi|116754149|ref|YP_843267.1| 45 VRFPCPSCGEVI 56
                                   89*******665 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.011
                       zf-Mss51  2 CPvpkhkqtapkhvdfeCpdCGi 24
                                   C+ +k     +++  ++C+ CG+
  gi|116754149|ref|YP_843267.1| 59 CNRCK-----KQSNIYTCKSCGF 76
                                   88885.....67799*******8 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 ?    9.2   0.1    0.0014       1.1       9      37 ..      27      55 ..      20      57 .. 0.87
   2 ?    4.4   4.2     0.043        34      12      36 ..      57      76 ..      56      77 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0014
                                   SS--B-TTT-SB--SSSS-EEEETTT--E CS
                           C1_1  9 kqptfCkhCgeflwgkekqglkCswCkll 37
                                   + p +C  Cg  l g + + + C  C+++
  gi|116754149|ref|YP_843267.1| 27 DVPEKCISCGVTLLGIGGVRFPCPSCGEV 55
                                   5689*********99***********986 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.043
                                   -B-TTT-SB--SSSS-EEEETTT-- CS
                           C1_1 12 tfCkhCgeflwgkekqglkCswCkl 36
                                   ++C+ C+++       +++C+ C++
  gi|116754149|ref|YP_843267.1| 57 ARCNRCKKQS-----NIYTCKSCGF 76
                                   5899999988.....9*******87 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 ?    8.9   3.6   0.00037      0.29     615     662 ..      26      75 ..       7      78 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00037
                       PolC_DP2 615 eiarrkCkkCgke.....tlearCeeCgekteeklvCkkceeeveeekcekce 662
                                    +   +kC +Cg +     ++++ C++Cge +     C++c+++++  +c+ c+
  gi|116754149|ref|YP_843267.1|  26 KDVPEKCISCGVTllgigGVRFPCPSCGEVIAR---CNRCKKQSNIYTCKSCG 75 
                                    444567888875433232677888888888777...88888888888888886 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.2     0.035        27      50      73 ..      25      53 ..       5      55 .. 0.65
   2 ?    9.8   7.5    0.0014       1.1      44      74 ..      49      76 ..      44      77 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.035
                         zf-CHY 50 eqekavlCkkCkk.....efaeyfCpiCk 73
                                    +++ ++C +C+         ++ Cp C 
  gi|116754149|ref|YP_843267.1| 25 MKDVPEKCISCGVtllgiGGVRFPCPSCG 53
                                   34667889999995554434455799985 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0014
                         zf-CHY 44 cllCeteqekavlCkkCkkefaeyfCpiCkl 74
                                   c  C +   +   C++Ckk+ + y+C+ C +
  gi|116754149|ref|YP_843267.1| 49 CPSCGE---VIARCNRCKKQSNIYTCKSCGF 76
                                   555655...6899****************75 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   0.00044      0.34       4      12 ..      28      36 ..      25      37 .. 0.86
   2 ?   -2.1   0.6       5.1     4e+03       8      12 ..      49      53 ..      49      54 .. 0.69
   3 ?    0.9   0.3      0.58   4.5e+02       7      12 ..      58      63 ..      57      64 .. 0.63
   4 ?    0.3   0.3      0.88   6.8e+02       8      12 ..      71      75 ..      69      76 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00044
                                   ETTTSSS-T CS
                           Fer4  4 deekCigCG 12
                                    +ekCi CG
  gi|116754149|ref|YP_843267.1| 28 VPEKCISCG 36
                                   69******9 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5.1
                                   SSS-T CS
                           Fer4  8 CigCG 12
                                   C  CG
  gi|116754149|ref|YP_843267.1| 49 CPSCG 53
                                   66788 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.58
                                   TSSS-T CS
                           Fer4  7 kCigCG 12
                                   +C +C+
  gi|116754149|ref|YP_843267.1| 58 RCNRCK 63
                                   576664 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 0.88
                                   SSS-T CS
                           Fer4  8 CigCG 12
                                   C  CG
  gi|116754149|ref|YP_843267.1| 71 CKSCG 75
                                   88998 PP

>> Pput2613-deam  Pput_2613-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   2.4     0.001      0.79      50      90 ..      19      61 ..       4      76 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.001
                  Pput2613-deam 50 htearivrelslqqll.Gdvlv.idGqyaPCssCkGkmrvase 90
                                     e r +++++++ +  G +l+ i G   PC+sC   + + ++
  gi|116754149|ref|YP_843267.1| 19 RSERRSMKDVPEKCIScGVTLLgIGGVRFPCPSCGEVIARCNR 61
                                   348899999*99999887665449**********776655444 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 ?   10.1   4.8   0.00079      0.62      18      44 ..      30      56 ..      20      64 .. 0.84
   2 ?    3.5   7.9     0.088        69      20      41 ..      49      75 ..      48      77 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00079
                       zf-C2HC5 18 pnClnCGkiiCakeglskpCsfCgspl 44
                                     C++CG  +    g+  pC++Cg+ +
  gi|116754149|ref|YP_843267.1| 30 EKCISCGVTLLGIGGVRFPCPSCGEVI 56
                                   57*********************9866 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.088
                       zf-C2HC5 20 ClnCGkii.....CakeglskpCsfCg 41
                                   C +CG +i     C+k+    +C +Cg
  gi|116754149|ref|YP_843267.1| 49 CPSCGEVIarcnrCKKQSNIYTCKSCG 75
                                   99*****977555555555599****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 ?    9.5   0.1    0.0015       1.1       4      14 ..      26      36 ..      23      39 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0015
                         Fer4_2  4 vvdtdrCigCg 14
                                   + ++++Ci+Cg
  gi|116754149|ref|YP_843267.1| 26 KDVPEKCISCG 36
                                   5679******9 PP

>> NMDAR2_C  N-methyl D-aspartate receptor 2B3 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   5.5    0.0023       1.8     371     422 ..      16      70 ..       6      73 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0023
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXX.XXXXXXXXXXXXX CS
                       NMDAR2_C 371 aspsesndrlkeksthCRsClsklsayg...agsssvrspykrCdaCkklgnLYd 422
                                    +s   +  ++k+ + +C sC   l + g       s +  ++rC+ Ckk +n+Y 
  gi|116754149|ref|YP_843267.1|  16 TSRRSERRSMKDVPEKCISCGVTLLGIGgvrFPCPSCGEVIARCNRCKKQSNIYT 70 
                                    45555556667777789999986655530003344566899*************6 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 ?    1.6   0.0      0.31   2.4e+02      46      52 ..      31      37 ..      19      39 .. 0.74
   2 ?    6.3   0.0      0.01       7.8      43      53 ..      45      55 ..      42      56 .. 0.87
   3 ?    1.2   4.2       0.4   3.1e+02      41      51 ..      65      75 ..      58      77 .. 0.59

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.31
                 zinc_ribbon_10 46 rCpkCga 52
                                   +C +Cg+
  gi|116754149|ref|YP_843267.1| 31 KCISCGV 37
                                   8****97 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.01
                 zinc_ribbon_10 43 vkyrCpkCgal 53
                                   v++ Cp+Cg++
  gi|116754149|ref|YP_843267.1| 45 VRFPCPSCGEV 55
                                   799******86 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.4
                 zinc_ribbon_10 41 eevkyrCpkCg 51
                                   +   y C +Cg
  gi|116754149|ref|YP_843267.1| 65 QSNIYTCKSCG 75
                                   44567777777 PP

>> Prok-RING_2  Prokaryotic RING finger family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1       2.1   1.6e+03      43      48 ..      31      36 ..      23      42 .. 0.68
   2 ?    6.5   9.5     0.012       9.1      20      48 ..      43      75 ..      29      77 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2.1
                    Prok-RING_2 43 tcksca 48
                                    c sc+
  gi|116754149|ref|YP_843267.1| 31 KCISCG 36
                                   455554 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.012
                    Prok-RING_2 20 aglr.qcvlcGrW..acdacWkd.eyytcksca 48
                                    g+r  c  cG     c+ c k  + ytcksc+
  gi|116754149|ref|YP_843267.1| 43 GGVRfPCPSCGEViaRCNRCKKQsNIYTCKSCG 75
                                   5555337788875326****875379******7 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.2     0.017        13      70      94 ..      29      54 ..      17      55 .. 0.76
   2 ?    5.5   4.4     0.022        17      69      93 ..      55      75 ..      54      78 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.017
                                   EEEETTTS-EEECHHH.HHS-TTTSS CS
                           HypA 70 kvrCreCgkefeleek.alrCpkCgs 94
                                     +C +Cg +       ++ Cp+Cg+
  gi|116754149|ref|YP_843267.1| 29 PEKCISCGVTLLGIGGvRFPCPSCGE 54
                                   55899999887744334789****96 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.022
                                   -EEEETTTS-EEECHHHHHS-TTTS CS
                           HypA 69 vkvrCreCgkefeleekalrCpkCg 93
                                   v +rC++C+k+ ++     +C++Cg
  gi|116754149|ref|YP_843267.1| 55 VIARCNRCKKQSNIY----TCKSCG 75
                                   6789*****998865....8****8 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.6    0.0037       2.9      30      58 ..      31      58 ..      13      58 .. 0.90
   2 ?    8.2   6.5     0.003       2.3      31      55 ..      49      77 ..      47      78 .. 0.94

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0037
                 OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgfeadr 58
                                   +C  Cg ++     g +f Cp+Cg ++ r
  gi|116754149|ref|YP_843267.1| 31 KCISCGVTLLG-IGGVRFPCPSCGEVIAR 58
                                   79999999999.9999********98765 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.003
                 OrfB_Zn_ribbon 31 CseCgsknke....alsgrtfkCpnCgfe 55
                                   C+ Cg++  +    +++++ ++C++Cgf+
  gi|116754149|ref|YP_843267.1| 49 CPSCGEVIARcnrcKKQSNIYTCKSCGFT 77
                                   ***********999999**********96 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 ?    6.4   0.1     0.014        11      50      66 ..      23      39 ..       3      43 .. 0.90
   2 ?   -0.3  11.8       1.6   1.3e+03      32      67 ..      35      67 ..      32      77 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.014
                  zf-LITAF-like 50 dslkdvehyCpnCgall 66
                                   +s+kdv  +C +Cg +l
  gi|116754149|ref|YP_843267.1| 23 RSMKDVPEKCISCGVTL 39
                                   589**********9765 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.6
                  zf-LITAF-like 32 lllclfgcllccliPfcvdslkdvehyCpnCgallg 67
                                   + + l+g+ +++   f + s+ +v+ +C +C+++  
  gi|116754149|ref|YP_843267.1| 35 CGVTLLGI-GGVR--FPCPSCGEVIARCNRCKKQSN 67
                                   44445553.4444..558999999999999999755 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1       0.5   3.9e+02      18      23 ..      31      36 ..      30      39 .. 0.70
   2 ?   10.0   0.4   0.00058      0.45       5      12 ..      49      56 ..      47      58 .. 0.72
   3 ?    0.9   6.5      0.42   3.2e+02       4      23 ..      58      75 ..      56      77 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.5
                    zf-ribbon_3 18 vCpyCG 23
                                   +C +CG
  gi|116754149|ref|YP_843267.1| 31 KCISCG 36
                                   577787 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00058
                    zf-ribbon_3  5 CPnCGapl 12
                                   CP+CG+++
  gi|116754149|ref|YP_843267.1| 49 CPSCGEVI 56
                                   88888854 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.42
                    zf-ribbon_3  4 rCPnCGaplssddnvCpyCG 23
                                   rC++C+++  s   +C++CG
  gi|116754149|ref|YP_843267.1| 58 RCNRCKKQ--SNIYTCKSCG 75
                                   89999997..6666899998 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.2    0.0042       3.3       3      13 ..      47      57 ..      45      58 .. 0.88
   2 ?    2.9   0.8      0.11        83       5      11 ..      59      65 ..      57      68 .. 0.85
   3 ?    2.7   0.5      0.12        97       3       9 ..      69      75 ..      67      77 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0042
                         zf_UBZ  3 ylCerCgkeip 13
                                   ++C+ Cg+ i 
  gi|116754149|ref|YP_843267.1| 47 FPCPSCGEVIA 57
                                   89******995 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.11
                         zf_UBZ  5 CerCgke 11
                                   C rC+k+
  gi|116754149|ref|YP_843267.1| 59 CNRCKKQ 65
                                   *****97 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.12
                         zf_UBZ  3 ylCerCg 9 
                                   y+C+ Cg
  gi|116754149|ref|YP_843267.1| 69 YTCKSCG 75
                                   9*****9 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      0.49   3.9e+02       3       7 ..      32      36 ..      31      41 .. 0.67
   2 ?    3.9   0.8     0.058        45      17      22 ..      49      54 ..      47      54 .. 0.88
   3 ?    1.7   1.0      0.28   2.1e+02       2       7 ..      58      63 ..      58      67 .. 0.58
   4 ?    9.7   0.4   0.00086      0.67       1      10 [.      69      78 ..      69      79 .] 0.89

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.49
                   Rubredoxin_2  3 CsqCG 7 
                                   C +CG
  gi|116754149|ref|YP_843267.1| 32 CISCG 36
                                   66666 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.058
                   Rubredoxin_2 17 CpsCgs 22
                                   CpsCg+
  gi|116754149|ref|YP_843267.1| 49 CPSCGE 54
                                   9***96 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.28
                   Rubredoxin_2  2 vCsqCG 7 
                                   +C++C 
  gi|116754149|ref|YP_843267.1| 58 RCNRCK 63
                                   566664 PP

  == domain 4  score: 9.7 bits;  conditional E-value: 0.00086
                   Rubredoxin_2  1 YvCsqCGfes 10
                                   Y C++CGf+ 
  gi|116754149|ref|YP_843267.1| 69 YTCKSCGFTG 78
                                   99******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       976  (0.0544369); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        39  (0.00217525); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.51
# Mc/sec: 468.49
//
Query:       gi|116754150|ref|YP_843268.1|  [L=206]
Description: aspartate/glutamate/uridylate kinase [Methanosaeta thermophila PT]
Scores for complete 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-14   52.0   0.0    7.9e-07   28.9   0.0    2.1  2  AA_kinase        Amino acid kinase family
  ------ inclusion threshold ------
       0.16   12.0   0.0       0.48   10.5   0.0    1.7  2  Ribonuc_red_lgN  Ribonucleotide reductase, all-alpha 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 !   28.9   0.0   8.9e-11   7.9e-07       3      97 ..       4      78 ..       2      93 .. 0.89
   2 !   21.3   0.0   1.9e-08   0.00017     154     209 ..     111     158 ..     101     173 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 8.9e-11
                                   EEEEE-TTCCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHH.TCCCCCHHHC....E..HHHHHHHHHHHHH CS
                      AA_kinase  3 vVvKlGGssltdkeeaslrrlaeqiaalkesgnklvvVhGggsftdgllal.ksglssgelaaglrstleeagevatrdala 83
                                    VvK+GGs+++       +++++ +  l+e+g+   +V Ggg+++d   +l ksgl s+e+a                +++a
  gi|116754150|ref|YP_843268.1|  4 YVVKIGGSLIGC-----AKDIVRRLFLLSENGYGFLLVPGGGPMADLVRSLyKSGLVSDEAA----------------HWMA 64
                                   6**********5.....566****************************************99................8888 PP

                                   HHHHHHHHHHHHTT CS
                      AA_kinase 84 slgerlvaallaag 97
                                    l+ +  a+lla g
  gi|116754150|ref|YP_843268.1| 65 VLAMEEYAYLLADG 78
                                   88888888887766 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 1.9e-08
                                    EEEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHH CS
                      AA_kinase 154 elgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaee 209
                                    +++  +sD iaal+A  lg   +i +tdVdGV+ +        rl++ei+++e++ 
  gi|116754150|ref|YP_843268.1| 111 HSWDYTSDAIAALVACRLGS-DMIKVTDVDGVMISG-------RLVSEIRASELMG 158
                                    388899**************.88999*******775.......9999999999986 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 ?   -1.8   0.0      0.35   3.2e+03      12      28 ..      70      87 ..      63      88 .. 0.73
   2 ?   10.5   0.0   5.3e-05      0.48      11      41 ..      96     126 ..      91     155 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.35
                Ribonuc_red_lgN 12 edrYllkdeng.eivEsp 28
                                   e  Yll d  g e+v +p
  gi|116754150|ref|YP_843268.1| 70 EYAYLLADGTGaELVDDP 87
                                   567999999887777665 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 5.3e-05
                Ribonuc_red_lgN  11 l.edrYllkdengeivEspqqmfmRvAlalai 41 
                                    l + rYllk++ g ++ s+++    +A+++a+
  gi|116754150|ref|YP_843268.1|  96 LrPYRYLLKNDSG-LEHSWDYTSDAIAALVAC 126
                                    5578*******99.*****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1430.84
//
Query:       gi|116754151|ref|YP_843269.1|  [L=271]
Description: NAD(+) kinase [Methanosaeta thermophila PT]
Scores for complete 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-52  179.0   0.1    1.6e-52  178.6   0.1    1.1  1  NAD_kinase  ATP-NAD kinase
  ------ inclusion threshold ------
      0.016   14.8   0.0      0.027   14.1   0.0    1.4  1  DAGK_cat    Diacylglycerol kinase catalytic domain


Domain annotation for each model (and alignments):
>> NAD_kinase  ATP-NAD kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.6   0.1   1.7e-56   1.6e-52      74     291 ..      50     256 ..      45     257 .. 0.96

  Alignments for each domain:
  == domain 1  score: 178.6 bits;  conditional E-value: 1.7e-56
                                    TTTTSSSEEEEEE-HHHHHHHHHHHHHCT-EEEEEESSS--SS-SEEGGGHHHHHHHHHHT-SEEEEEEEEEEEEEETTE CS
                     NAD_kinase  74 fadagvdliivvGGDGTaldvarllqkaeiPvlgvnaGvkgfltefepeaaaellekllegeirvekrevldavimrskg 153
                                    + +++vd+i+ +GGDGT+l+  + +++   P+lg+n+G++gfl ++ep++a +++e+ll  +++v++r+++++ ++ +  
  gi|116754151|ref|YP_843269.1|  50 VEEMDVDFIVSIGGDGTILRTIHKMED-PRPILGINMGTVGFLVDVEPKDAVRTIEHLLL-GFEVDERTRIETLLRGERL 127
                                    56899*********************7.99*****************************9.9**********66655554 PP

                                    ......EEEEEEESSEEEEEESSSSS-EEEEEEETTEEEEEEEESEEEEE-TGGGGTHHHHTT--EE-TT---EEEEEES CS
                     NAD_kinase 154 eediadiviensvlnevviirgpgstlielelyvdtelleadqldglivstPtGstayslsaGgplisPgvlailivpic 233
                                              + + nev +i+ ++++++++e++v++++le +++dg+i +t tGstay++saGgp+++P ++ai++vp+ 
  gi|116754151|ref|YP_843269.1| 128 ----------PPATNEVALITSSPAKMLDFEIKVNGSPLERLRADGMIFATSTGSTAYAMSAGGPIVDPHLDAIVLVPVA 197
                                    ..........568******************************************************************* PP

                                    ESSS----EEE-TT-EEEEEE-.SS--EEEEETTTEEEEE-TT-EEEEEEESSEEEEEE CS
                     NAD_kinase 234 PhslssrpiVvssssklrirva.srseallaldGseelelspgdevrvtasdkkfklir 291
                                    P++ls+rp V+  +s +++ ++  ++eal+++dG+    +++gde+  +++++++++++
  gi|116754151|ref|YP_843269.1| 198 PFKLSARPWVIRGDSMIEVDLKlPGKEALVVVDGQTMATVTHGDEIIMRKAERPARFVK 256
                                    *********************************************************97 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0     3e-06     0.027      52      87 ..      51      83 ..      16     109 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3e-06
                                   HHCC-SEEEEEESHHHHHHHHHHHCTHHCTTSEEEE CS
                       DAGK_cat 52 keegvdlivvaGGDGtvsevlnglleelatkpplgi 87
                                   +e +vd+iv +GGDGt+   ++ + +    +p lgi
  gi|116754151|ref|YP_843269.1| 51 EEMDVDFIVSIGGDGTILRTIHKMED---PRPILGI 83
                                   344679************99999999...5555553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       242  (0.0134977); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        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 0.26s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 2014.28
//
Query:       gi|116754152|ref|YP_843270.1|  [L=272]
Description: bifunctional inositol-1 monophosphatase/fructose-1,6-bisphosphatase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.8e-29  102.5   0.0    3.4e-29  102.2   0.0    1.0  1  Inositol_P  Inositol monophosphatase family
     0.0087   15.6   0.0      0.012   15.1   0.0    1.2  1  FBPase      Fructose-1-6-bisphosphatase, N-terminal domain


Domain annotation for each model (and alignments):
>> Inositol_P  Inositol monophosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.2   0.0   3.8e-33   3.4e-29      39     266 ..      43     266 ..       4     270 .. 0.84

  Alignments for each domain:
  == domain 1  score: 102.2 bits;  conditional E-value: 3.8e-33
                                    HHHHHHHHHHHHHHHHHHHHHHHSTTSEEEHHCHHHHCCCT.SSSSSEEEEEEEEETHHHHHHT-SG-EEEEEEEETTEE CS
                     Inositol_P  39 eedlvtaadeaveelilealaekfpshkilgeetlakgekseltedgltwivDPiDGTknFvrgipqvaVsigllvegkp 118
                                    +  + +a+d+ +ee+ l+ l+   ++ ++l+ee +++     +++  +++ +DP+DGT n ++gip +a+si ++ +g  
  gi|116754152|ref|YP_843270.1|  43 DGTPTKAIDQIAEEAALAPLRNYGSGFRVLSEEMGESVI---GEDPVYFIHLDPLDGTFNAIHGIPFYAISI-FISDGST 118
                                    3458999***************************99988...677779999*********************.999**** PP

                                    EEEEEEETTTTEEECEETTTEEEETC...EEEEECTTSEGGGTEEEEEESSSSSSHHHHCHHHHHHHCCCCCHEEEBESS CS
                     Inositol_P 119 vlGviaqPllgqlysaakgkGaflng...eklplsrappiseallvtlfavssrkdtseasllekvesavsaegvrsvgs 195
                                    +l+ + + + g+ y a  g Ga+ ++    ++ +s+++   + + ++ +a+  r++ts+   + +v   v++   r++g+
  gi|116754152|ref|YP_843270.1| 119 HLAYVRDLVRGTKYYAEPGYGAYREDssvDRINVSGTS---NLMDFSISAYTMRPRTSR---IVGVGDVVRRM--RNLGA 190
                                    **********************9999777777777777...444555567788888888...99998888888..***** PP

                                    HHHHHHHHHHTSTSEEEEEC..EBHHHHHHHHHHHHHTTEEEEESSSC.....SSSTTSSEEEEESCHHHHHHHHHH CS
                     Inositol_P 196 salklaavaeGkadaylefg.rekkWDhAAGeaileeaGGvvtdakge.....grlllargiiaanqkelaellaaa 266
                                    + l+l++va+G++da+++ + ++   D+ AG++ +eeaGGv tda ge     +++++ +++ia+n + l+  ++++
  gi|116754152|ref|YP_843270.1| 191 ASLELCYVADGRLDAFIDLRgSLRVVDVIAGILMVEEAGGVATDALGEklhlrRNMWERTDLIASN-GLLHREILEL 266
                                    *******************999**************************999988888999999999.6666666554 PP

>> FBPase  Fructose-1-6-bisphosphatase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.3e-06     0.012      30     116 ..      12      99 ..       2     141 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.3e-06
                         FBPase  30 lalkiisskvrkaelvnllGlaga.....eNvtGdeqkklDvladeiliealkaseevkvlvSEEeeelivlerekegky 104
                                      +  +s++v  a    + G+a+a        +G   k++D +a+e   + l++ +    + SEE+ e ++    ++  y
  gi|116754152|ref|YP_843270.1|  12 SLCDLMSDNVASAV-RGIAGTASAgshikIGADGTPTKAIDQIAEEAALAPLRNYGSGFRVLSEEMGESVIG---EDPVY 87 
                                    44444555554443.455554443111115678999********************************8877...6778* PP

                         FBPase 105 vvafDPlDGSSn 116
                                     + +DPlDG  n
  gi|116754152|ref|YP_843270.1|  88 FIHLDPLDGTFN 99 
                                    *********877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       220  (0.0122706); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1949.87
//
Query:       gi|116754153|ref|YP_843271.1|  [L=159]
Description: riboflavin synthase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-17   63.5   0.4    2.2e-17   63.2   0.4    1.1  1  DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase
  ------ inclusion threshold ------
      0.016   15.5   0.1      0.071   13.4   0.1    2.0  1  SpoU_sub_bind  RNA 2'-O ribose methyltransferase substrate bi


Domain annotation for each model (and alignments):
>> DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.2   0.4   2.5e-21   2.2e-17       3     137 ..       3     128 ..       1     131 [. 0.83

  Alignments for each domain:
  == domain 1  score: 63.2 bits;  conditional E-value: 2.5e-21
                                    EEEEEEESTTHHHHHHHHHHHHHHHHHCTTSSCCEEEEEESSCCCHHHHHHHHCTSTT-.SEEEEEEEEE--SSCHHHHH CS
                  DMRL_synthase   3 riaiVvarfneeitdkllegaldelkeagvaeenidvvtVPGafElplaakklaesskyldavialGvvirGetphfeyv 82 
                                    ri+i  ++f      ++ ++a++e+k++     +i+++tVPG+ +lp+aak+l+e++k +d vialG  + G+ p ++++
  gi|116754153|ref|YP_843271.1|   3 RIGIADTTF---ARYDMARAAIREIKKHAS--VEIVRYTVPGVKDLPVAAKRLIEEHK-CDIVIALG--MPGAAPIDKVC 74 
                                    788888888...78899**********995..59*********************654.5*******..9********** PP

                                    HHHHHHHHHHHHHHCTS-EEEEEEEESSHHCCHHCCTSTC..CCHHHHHHHHHHHHH CS
                  DMRL_synthase  83 aeavskglmrvsldtgvPvifgvltvdteeqaleraggka..gnkGeeaaeaalema 137
                                    a+++s gl+ ++l t+  +i   +  d  e   er  + +  +++++e+a +a++++
  gi|116754153|ref|YP_843271.1|  75 AHEASTGLIMAQLMTNRHIIEVFVHED--EAGDERTLA-RlaEKRAAEHALNAVRLL 128
                                    ****************87776544443..334444422.23499*********9985 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 ?   13.4   0.1   7.9e-06     0.071       8      66 ..      83     146 ..      80     146 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.9e-06
                  SpoU_sub_bind   8 VleaLksgrriekllvteg.radkrleellklakkr......gikvelvdkekLdklsgtanHQGv 66 
                                    +++ L  +r i +++v+e+ + d+r  +l +la+kr      +    l  +e+L +++gt++ QG+
  gi|116754153|ref|YP_843271.1|  83 IMAQLMTNRHIIEVFVHEDeAGDER--TLARLAEKRaaehalNAVRLLFRPEELTRMAGTGQRQGF 146
                                    7788999999*********555555..788887777433344445567789999999999999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1164.55
//
Query:       gi|116754154|ref|YP_843272.1|  [L=426]
Description: histidinol dehydrogenase [Methanosaeta thermophila PT]
Scores for complete 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-172  573.3   2.1   3.4e-172  573.1   2.1    1.0  1  Histidinol_dh  Histidinol dehydrogenase


Domain annotation for each model (and alignments):
>> Histidinol_dh  Histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  573.1   2.1  1.9e-176  3.4e-172       7     409 .]      23     424 ..      18     424 .. 0.99

  Alignments for each domain:
  == domain 1  score: 573.1 bits;  conditional E-value: 1.9e-176
                                    --HHHHHHHHHHHHHHHHHCHHHHHHHHHHCCSSSSGGCCEE-HHHHHHHHHCS-HHHHHHHHHHHHHHHHHHHCC---- CS
                  Histidinol_dh   7 dseeveetvkeiledvreeGdealleytekFDkvkkleslrvseeeieealekldeelkealeeaaenirkfheaqkese 86 
                                      ++v ++v++i+ dv e+Gdeal++yte+FD+v+ les+rvs++eieea++++de+l ++le aa+ni +fh ++++++
  gi|116754154|ref|YP_843272.1|  23 GIQDVLQRVNDIVMDVAENGDEALRRYTEQFDGVR-LESFRVSDDEIEEAYDAVDESLLRSLELAAQNIYAFHDEERTKD 101
                                    568999**************************774.789***************************************99 PP

                                    EEEEEECTTEEEEEEEEE-SEEEEE---STT--CHHHHHHHHHHHHHT-SEEEEEE-SS.GG.--HHHHHHHHHCT-SEE CS
                  Histidinol_dh  87 eevketepgvvlgqkvrpiervGlYvPgGkaaypStvlmnavpAkvAgvkeivvvtPpq.dgkvnpavlaaaklagvdei 165
                                     ++++ +pgvv+gqkv+p+e+vG YvPgG+aaypS++lm ++pAkvAgv+++vv+tPp+ +g+++p +laaa++ag+dei
  gi|116754154|ref|YP_843272.1| 102 LWLYQVAPGVVAGQKVVPLESVGAYVPGGRAAYPSSALMCVIPAKVAGVERMVVCTPPDrSGRISPLTLAAADIAGADEI 181
                                    ******************************************************************************** PP

                                    EE--HHHHHHHHHH--SSS---SEEE---SHHHHHHHHHHCTTBEES----S-EEEEEE-TTS-HHHHHHHHHHHHTT-T CS
                  Histidinol_dh 166 ykvGGaqAiaalAyGtesipkvdkivGPGniyVaaAKrlvsgevgiDmiaGPsEvlviaDetadpefvAaDLlsqaEHde 245
                                    yk+GGaqAiaa+A Gtesi++v+kivGPGniyV+aAK+lv+g+v+iD++aGPsEvl+iaD++adpefvAaD+++qaEHd+
  gi|116754154|ref|YP_843272.1| 182 YKLGGAQAIAAMALGTESIERVEKIVGPGNIYVTAAKMLVRGSVEIDFPAGPSEVLIIADSSADPEFVAADMIAQAEHDP 261
                                    ******************************************************************************** PP

                                    T-EEEEEES-HHHHHHHHHHHHHHHCC-TTHHHHHHHHCCH-EEEE-SSHHHHHHHHHHH--SEEEEESTTHHHHGGG-- CS
                  Histidinol_dh 246 daqavlvttseelaeaveeevekqleelprkeiaekslekqsaiilvedleeaielaneyApEHlelqvedpeellekik 325
                                    ++ av+vttse la+a+e+e+ +q+e+++r++i+++sle+  ai+l+e+l++a++++n++ApEHlel+v+dp+++l+ ++
  gi|116754154|ref|YP_843272.1| 262 SSIAVVVTTSEPLAKAIETEIPSQIEKAERRDIVQASLER-CAILLAESLDDALAFSNAFAPEHLELMVRDPMDALNLVR 340
                                    ****************************************.9************************************** PP

                                    S-SEEEESTT--HHHHHHTSSS------TTGGGT---S-GGGGEEEEEEEEE-HHHHHHHHHHHHHHHHHTT-HHHHHHH CS
                  Histidinol_dh 326 naGaiflGeyspeslgDYaaGtnhvLPTsgtArfssglsvedFlkkisvqelskealkelaeavetlAeaEgLeaHaeav 405
                                    +aG++flG+y+p+++gDYa+GtnhvLPT+g+Ar++sgl+++ F+kkis+q++++++l++la+a++++Ae EgL+aHae+v
  gi|116754154|ref|YP_843272.1| 341 SAGSVFLGHYTPVAAGDYATGTNHVLPTAGYARIFSGLNIDAFTKKISIQSMTADGLESLADAIIKMAESEGLRAHAESV 420
                                    ******************************************************************************** PP

                                    HHHH CS
                  Histidinol_dh 406 kvRl 409
                                    ++R+
  gi|116754154|ref|YP_843272.1| 421 RIRM 424
                                    **96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); 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 0.27s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3066.76
//
Query:       gi|116754155|ref|YP_843273.1|  [L=552]
Description: DNA ligase I, ATP-dependent Dnl1 [Methanosaeta thermophila PT]
Scores for complete 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  190.5   0.0      4e-56  189.9   0.0    1.3  1  DNA_ligase_A_M  ATP dependent DNA ligase domain
    1.6e-39  136.0   0.0    3.8e-36  125.0   0.0    2.4  2  DNA_ligase_A_N  DNA ligase N terminus
    3.9e-17   62.7   0.0    8.3e-17   61.6   0.0    1.6  1  DNA_ligase_A_C  ATP dependent DNA ligase C terminal region
    4.1e-06   27.2   0.0    7.6e-06   26.3   0.0    1.4  1  RNA_ligase      RNA ligase


Domain annotation for each model (and alignments):
>> DNA_ligase_A_M  ATP dependent DNA ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.9   0.0     9e-60     4e-56       2     204 .]     224     416 ..     223     416 .. 0.95

  Alignments for each domain:
  == domain 1  score: 189.9 bits;  conditional E-value: 9e-60
                                    EEEEEESCHHHHHHHTTTSEEEEEEEESSEEEEEEEETTEEEEEETTS-B-GGGCHHHHHHHHHHBSTTESEEEEEEEEE CS
                 DNA_ligase_A_M   2 mLAeslksiekalkkleekafivEiKyDGeRaqvhkegdkvklfSRrlkditaakpelvkalkeafkkdeksvilDGElv 81 
                                    mLA+  +sie  l +  ++++ vE+K+DG+R+q+hk++++v++fSRrl+d+t+++pe+ + ++  + ++   +ilDGE+v
  gi|116754155|ref|YP_843273.1| 224 MLAQIGESIEASLAE--GATA-VEWKFDGARVQIHKDKGNVRIFSRRLEDVTSSLPEIREIVRGHVRAR--TAILDGEAV 298
                                    9********999998..4555.9***************************************9999987..7******** PP

                                    EEETTTTCBEHHHHHCHHHHCHCCTHHHHHHSEEEEEEEEEEEETTEEHTTSCHHHHHHHHHHHB--BTTTEEE--EEEE CS
                 DNA_ligase_A_M  82 avdketgeilpfqklasrkkkkkkveeklkeaelclfvFDiLyldgesltdeplkeRrklLeeilkesedrvelaeslev 161
                                    a   e+g++lpfq++ +r+++k+ v++++k+++l l +FDi+y+dg sl+depl+eRr++L ++   +++   +ae+ ++
  gi|116754155|ref|YP_843273.1| 299 AT-GEDGRPLPFQEILRRFRRKYGVARTAKTIPLKLHLFDIIYMDGASLLDEPLEERRRVLVSVA--DPE--IIAEQVVT 373
                                    *5.777*********************************************************99..333..479***** PP

                                    SSHHHHHHHHHHHHHTTECEEEEEETT-CC-TTCEEEEEEEEE CS
                 DNA_ligase_A_M 162 kdveeleelleeaiseglEGlvvKnpdskYepgkrsknwlKvK 204
                                    +dv  +ee+++ea+++g+EG+++Knp+s+Y+pgkr+knwlK+K
  gi|116754155|ref|YP_843273.1| 374 SDVHRVEEIYREALAAGHEGVMLKNPSSTYTPGKRGKNWLKIK 416
                                    ******************************************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 !  125.0   0.0   8.5e-40   3.8e-36       2     173 .]       4     178 ..       3     178 .. 0.96
   2 !   14.2   0.0   9.5e-06     0.042      64     111 ..     173     225 ..     172     294 .. 0.76

  Alignments for each domain:
  == domain 1  score: 125.0 bits;  conditional E-value: 8.5e-40
                                    CHHHHHHHHHHCC.---HHHHHHHHHHHHHTS-..SHHHHHHHHHHSS-CCC.S------HHHHHHHHHHHHT--HHHHH CS
                 DNA_ligase_A_N   2 FaelaelfekieestkkrlekrailanffrkvesagpedlypalrLllPdyd.greygigesllakalaealglskkkik 80 
                                    Fa++ael+e+i++ t+  lek++ila+f++++e   ++dl +++ ++++    g+e+g+g+sll++ +++a+gls++ ++
  gi|116754155|ref|YP_843273.1|   4 FARFAELCERISQ-TSGSLEKTDILASFLSDLE---SDDLRIVAGFVMGVVIpGTELGVGPSLLYESISRATGLSSDAVN 79 
                                    99***********.8889***********8876...679*******8888888889************************ PP

                                    HHHHHHS-HHHHHHHHHCCHHHH.....------BHHHHHHHHHHHHH-.STTHHHHHHHHHHHHHHHS-HHHHHHHHHH CS
                 DNA_ligase_A_N  81 dalakvgDlgevaeevlskrstl.....akkspltieevnelLdklaaa.gkgsedekkkilkkllkraspeEakyliri 154
                                    + l+ +gD g va++++++r++l       ++ l +++v++ +  +a+a g+gs++ ++k l+ ++++asp+Eaky++r+
  gi|116754155|ref|YP_843273.1|  80 ELLRATGDPGLVAYRAVERRKPLtlaafSGSEGLEVQDVYQRFLSIAKAsGRGSQEIRVKNLQYMFSEASPLEAKYIARL 159
                                    **999****************999**9999999**************999****************************** PP

                                    HCT---SS--HHHHHHHHH CS
                 DNA_ligase_A_N 155 ilkdlriglsektvldala 173
                                      +d+rig++e++v+da+a
  gi|116754155|ref|YP_843273.1| 160 AMEDMRIGVGEGLVRDAIA 178
                                    *****************97 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 9.5e-06
                                    HHHHHHHHHT--HHHHHHHHHHHS-HHHHHHHHHCCHHHH.....------BH CS
                 DNA_ligase_A_N  64 lakalaealglskkkikdalakvgDlgevaeevlskrstl.....akksplti 111
                                    ++ a+a+a+g+sk++++ a++ ++Dlg vae ++  r +      + + ++ +
  gi|116754155|ref|YP_843273.1| 173 VRDAIAKAFGVSKEDVERAYNLTNDLGLVAEYAKLGRLNElgisiNRPIKMML 225
                                    6789****************99**********998887755554444444444 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 !   61.6   0.0   1.9e-20   8.3e-17       2      99 .]     437     528 ..     436     528 .. 0.94

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 1.9e-20
                                    GGSEEEEEEEEEE..TTEEEEEEEE-SS--HHHHHHHHHHHGGGEECTTCESS---HHHHTTEEE-TT-EEEEEESEEEC CS
                 DNA_ligase_A_C   2 gglvgslllgvyd..dgkleyvgkvgtGfsdaeleelrkklkelerkkppfaekvpeeekrdvWvePelvveVkfaeita 79 
                                    ++l+gs+ l++ d  +g+l+ vg v+tG++d++l+el++ ++el  k++ +    + e      v+Pe+v+eV ++ei++
  gi|116754155|ref|YP_843273.1| 437 ANLLGSYRLACIDtdTGELKDVGWVATGITDEMLAELTELFRELIVKENGM----EVE------VHPEIVFEVGYEEIQR 506
                                    6789*********99999******************************999....333......89************** PP

                                    TSSSTT..EECT-EEEEE-TTS CS
                 DNA_ligase_A_C  80 sgkyka..slRfPrfkrlReDk 99 
                                    s++y++  +lRfPr++ +R+Dk
  gi|116754155|ref|YP_843273.1| 507 SPNYSSgyALRFPRLIAVRDDK 528
                                    *********************8 PP

>> RNA_ligase  RNA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   1.7e-09   7.6e-06       5     161 .]     243     416 ..     240     416 .. 0.66

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.7e-09
                                    EEEE-SSEEEEEEEETT.EEEEETTCEBCTTTHHHHHHTHHHHHHHHHHHHH..ECCEEEEEEEES...........SS. CS
                     RNA_ligase   5 vtEKlDGtnfriylvke.vgvasRsqilpfgeekfkefkrwaaalrkklkeklaneelilyGElig..........hsi. 72 
                                    v+ K DG++++i+++k+ v+++sR+ +           +    + r+ ++ + + ++ il GE +           + i 
  gi|116754155|ref|YP_843273.1| 243 VEWKFDGARVQIHKDKGnVRIFSRRLED---------VTSSLPEIREIVRGHVRARTAILDGEAVAtgedgrplpfQEIl 313
                                    778************667*******888.........222333444444445556689********87776655554445 PP

                                    .......TTSS.........EEEEEEEEEEE.CTT........BECE--HHHHHHHHHCCTB..EEEEE.SS.HHHHHCC CS
                     RNA_ligase  73 .....kygglpk........efyvFdifdir.dke........eqrylspdevealakglgtvpvlyegkfl.aaeelle 129
                                         kyg   +        ++ +Fdi+ ++             +  +s ++ e++a+           +++ + + ++e
  gi|116754155|ref|YP_843273.1| 314 rrfrrKYGV--ArtaktiplKLHLFDIIYMDgASLldepleerRRVLVSVADPEIIAE----------QVVTsDVHRVEE 381
                                    555555555..04568999999******999633333334433444444444444444..........333345555555 PP

                                    C..HHHHTC--EEEEEESSSSBE.TTE.BSEEEEE CS
                     RNA_ligase 130 ll.lskgnkrEGlVikpeselyk.nkg.raifKvk 161
                                    ++ +      EG+ +k++s++y+  k+ ++++K+k
  gi|116754155|ref|YP_843273.1| 382 IYrEALAAGHEGVMLKNPSSTYTpGKRgKNWLKIK 416
                                    533333459***************9999*****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (552 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); 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: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 3890.56
//
Query:       gi|116754156|ref|YP_843274.1|  [L=335]
Description: homoserine dehydrogenase [Methanosaeta thermophila PT]
Scores for complete 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-57  194.1   0.3    4.3e-57  192.8   0.1    1.6  2  Homoserine_dh    Homoserine dehydrogenase
    4.2e-12   46.7   0.2    7.2e-12   46.0   0.2    1.4  1  NAD_binding_3    Homoserine dehydrogenase, NAD binding domain
      0.004   16.9   0.1     0.0077   16.0   0.1    1.4  1  ELFV_dehydrog    Glutamate/Leucine/Phenylalanine/Valine dehyd
  ------ inclusion threshold ------
       0.12   12.6   0.4       0.28   11.4   0.2    1.8  2  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 ?   -1.3   0.0      0.41   1.8e+03      98     128 ..      66      97 ..      29     124 .. 0.61
   2 !  192.8   0.1   9.6e-61   4.3e-57       1     173 []     152     323 ..     152     323 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.41
                                    HHHHHHH.CTTEEEEEEEEECEEEEEEEEEET CS
                  Homoserine_dh  98 edikeak.eegkvlklvasavearVkpelvpk 128
                                    +++++ + ++ ++++ v+s + ++V p+ + +
  gi|116754156|ref|YP_843274.1|  66 HEVANSEmSAKETIRSVNSELVVEVTPTNIVH 97 
                                    23333332455667777776667777776655 PP

  == domain 2  score: 192.8 bits;  conditional E-value: 9.6e-61
                                    --HHHHHHTCTTSEEEEEEEE--HHHHHHHHHHHCHTT-HHHHHHHHHHTTSS-SSTHHHHTTHHHHHHHHHHHHHHCTT CS
                  Homoserine_dh   1 PiiktlkeilsgdritrieGilngtlnyiltemeeegasfsevlkeaqelGyaeaDptdDveGlDaarKlailarlafgl 80 
                                    P+i+ ++++l g++i  i+Gi+ngt+nyilt+m+ee+  fs++l+eaqelGyaeaDpt D+eG+D+a+K++ila+ +f++
  gi|116754156|ref|YP_843274.1| 152 PLINLIERTLVGNTILGIRGIFNGTCNYILTRMAEEQYPFSRALAEAQELGYAEADPTYDIEGVDTAAKIVILANAIFNM 231
                                    99*********************************9999***************************************** PP

                                    T--GGGSEE--STTS-HHHHHHHHCTTEEEEEEEEECEEEEEEEEEETTSGGGHSSST-EEEEEEESSSEEEEEEES-SS CS
                  Homoserine_dh  81 eveledvevegiskltaedikeakeegkvlklvasavearVkpelvpkshplasvkgsenavlvetdrlgelviqGpgaG 160
                                    +v+++dv+v+gi+++t+e ++ ak++g+v+kl++++  ++V+p+lvp  +pla v  + na +++td  g+++++G gaG
  gi|116754156|ref|YP_843274.1| 232 NVKYNDVQVRGITEITPESLALAKKHGYVIKLIGEVPALTVRPMLVPIRSPLA-VGSTLNAAAIYTDLSGTITVTGLGAG 310
                                    ***********************************769***************.9************************* PP

                                    HHHHHHHHHHHHH CS
                  Homoserine_dh 161 aepTAsavlsDll 173
                                    + +TA+a+lsD++
  gi|116754156|ref|YP_843274.1| 311 GLETAAAILSDIV 323
                                    ***********96 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 !   46.0   0.2   1.6e-15   7.2e-12       1     116 [.      10     143 ..      10     144 .. 0.93

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 1.6e-15
                                    --SHHHHHHHHHHHH---S.....SEEEEEEEEESS.EEE-TT.........HHHHHT--CB---HHHHHHHHS-EEEEE CS
                  NAD_binding_3   1 GlGaiGsavleqlkrqqse.....ielelvavadrd.sllskd.........rkallasealtldlddliahldpdvvVE 65 
                                    G+G++G +v++ + r+++      ++l++v ++d+  +l+++d          k l + +   ++ ++ i+ ++  +vVE
  gi|116754156|ref|YP_843274.1|  10 GYGVVGHGVVDVISRKRKMlrglgLDLKIVSITDHTgTLVNEDgisgesvlsHKTLHEVANSEMSAKETIRSVNSELVVE 89 
                                    99***************99*******************************9988899999999999999**99******* PP

                                    -S--HHHHT.....THHHHHHTTEEEE-S--CGGG-HHHHHHHTSSSTTS--.EE- CS
                  NAD_binding_3  66 casseavae.....lvlkaLkagkdvvtankgaladealyeeLreaaeangakiyv 116
                                    +++ + v++     ++++aL++gk+vvt nkg l+  + y++L  +a  ng+ + +
  gi|116754156|ref|YP_843274.1|  90 VTPTNIVHGqpglgHMEEALSNGKHVVTSNKGPLV--VAYDKLKRLADDNGVMLKF 143
                                    ********6444448********************..*************997766 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 !   16.0   0.1   1.7e-06    0.0077      54     105 ..      34      84 ..       3      97 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.7e-06
                                    CT-EEEEEEESSEEEEETTEE-HHHHHHHHHCSSSSTTHSHHSTSTSEEESH CS
                  ELFV_dehydrog  54 lgakvvavsDssGviydpeGldieellelkeerksvkeykkssekkaeyien 105
                                    l  k+v++ D++G++++++G++ e++l++k+ ++ v+++++s +++++ +++
  gi|116754156|ref|YP_843274.1|  34 LDLKIVSITDHTGTLVNEDGISGESVLSHKTLHE-VANSEMSAKETIRSVNS 84 
                                    4569*****************9999999988765.44444444545555555 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 ?   11.4   0.2   6.2e-05      0.28       2      98 ..       7     117 ..       6     141 .. 0.67
   2 ?   -2.9   0.0       1.8   7.8e+03      60      78 ..     249     265 ..     224     272 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.2e-05
                                    EEE--SHHHHHHHHHHHCTCCT-G....EEEEEESSHHHHHHHHCHH...TTTCEEEEE--TTTHHHHHHHHHTTS..SE CS
                Sacchrp_dh_NADP   2 liiGaGsvGqavaellarhfdvda....eitvadrskeklealaaka...lgvrfeaialdaenyeavLaallkeg..dl 72 
                                     +iG+G vG++v+++++r+ ++ +    ++ +++ +++    + ++     +v  +++   ++n e   ++ +++   +l
  gi|116754156|ref|YP_843274.1|   7 SLIGYGVVGHGVVDVISRKRKMLRglglDLKIVSITDHTGTLVNEDGisgESVLSHKTLHEVANSEMSAKETIRSVnsEL 86 
                                    68******************999888898888888877766665554654333333333456666666777777777788 PP

                                    EEE-SSGG.....GHHHHHHHHHHHT-EEEE CS
                Sacchrp_dh_NADP  73 vvnlsppi.....ssldvlkaCietgvhyvd 98 
                                    vv ++p        +l  ++ ++++g h+v+
  gi|116754156|ref|YP_843274.1|  87 VVEVTPTNivhgqPGLGHMEEALSNGKHVVT 117
                                    8888776665554455677777777777777 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.8
                                    HHHHHHHHTTSSEEEE-SS CS
                Sacchrp_dh_NADP  60 eavLaallkegdlvvnlsp 78 
                                    e+   al k+++ v+ l++
  gi|116754156|ref|YP_843274.1| 249 ES--LALAKKHGYVIKLIG 265
                                    33..234455566665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); 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: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2571.02
//
Query:       gi|116754157|ref|YP_843275.1|  [L=167]
Description: amino acid-binding ACT domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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   0.0     0.0078   16.0   0.0    1.8  2  ACT             ACT domain
     0.0025   18.2   0.2     0.0069   16.8   0.1    1.7  2  Saccharop_dh_N  LOR/SDH bifunctional enzyme conserved region


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 !   16.0   0.0   8.7e-07    0.0078       5      64 ..       7      68 ..       4      70 .. 0.94
   2 ?   -2.3   0.0      0.45     4e+03      50      65 ..     136     151 ..     126     153 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 8.7e-07
                                   EEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTT..ECEEEEEEEEEEHHHHHHHHHHHHT CS
                            ACT  5 vgvpDrPGlLarvfgaladrgiNidsieqrssedk..vagivfvvivvdeedleevlealkk 64
                                   ++++D+PG L   ++ + ++  Ni+s+ +++++ +  +   v ++++ d + le v+++l++
  gi|116754157|ref|YP_843275.1|  7 LELQDVPGQLLLALQPIKNARGNIISVVHHRDRKTprGTVPVRLIVEMDRSKLEGVKKELER 68
                                   6899********************************99999999***************986 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.45
                                    EEHHHHHHHHHHHHTT CS
                            ACT  50 vdeedleevlealkkl 65 
                                    ++ ++ + +le l+++
  gi|116754157|ref|YP_843275.1| 136 TGKKEMQRALEILREV 151
                                    5667778888888876 PP

>> Saccharop_dh_N  LOR/SDH bifunctional enzyme conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.52   4.6e+03      55      75 ..      55      75 ..      45      86 .. 0.67
   2 !   16.8   0.1   7.7e-07    0.0069       3      74 ..      86     156 ..      83     165 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.52
                                   SHHHHHHHHHHHHHHHHHSCC CS
                 Saccharop_dh_N 55 deevLeeileeltelgaelve 75
                                   d+++Le + +el++ g  +v+
  gi|116754157|ref|YP_843275.1| 55 DRSKLEGVKKELERSGIVVVR 75
                                   567788888888887776664 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 7.7e-07
                                    EEEEEEXXTTSSHHHHHHHHHHHTTXEEEEEEEEXXSS.TTSXEEEEEEEEESSHHHHHHHHHHHHHHHHHSC CS
                 Saccharop_dh_N   3 eveleGhliDsgilnkvldlileaggsfevlefevGkk.kkdtSyaelevsaedeevLeeileeltelgaelv 74 
                                    +v l Gh++Ds +   ++ +i +  g  ev ++++     +++S+a ++++a+ ++++++ le l e+ga+++
  gi|116754157|ref|YP_843275.1|  86 SVILVGHVLDSDLGD-TVSRI-DSTGYAEVMDLSLSMPgVDEPSSAYMKIRATGKKEMQRALEILREVGAQKK 156
                                    57799*****99654.55565.667899******997626789**************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        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: 00:00:00.41
# Mc/sec: 1213.68
//
Query:       gi|116754158|ref|YP_843276.1|  [L=172]
Description: cell surface protein [Methanosaeta thermophila PT]
Scores for complete 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   27.8   4.3    1.9e-06   27.3   3.8    1.4  1  NosD            Periplasmic copper-binding protein (NosD)
    0.00011   21.7   2.0    0.00061   19.2   2.0    1.9  1  DUF1565         Protein of unknown function (DUF1565)
  ------ inclusion threshold ------
      0.033   12.9   0.2      0.036   12.8   0.2    1.2  1  Pectinesterase  Pectinesterase


Domain annotation for each model (and alignments):
>> NosD  Periplasmic copper-binding protein (NosD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   3.8   3.2e-10   1.9e-06     126     189 ..     111     169 ..      77     171 .. 0.77

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 3.2e-10
                           NosD 126 nnkGiflensssntitgNriesnqkiGilllsssegntiynNyFinnsenvkydgsnnneWntt 189
                                     n+Gi++ + ++nti +N  ++n k+Gi+ +++s +n++++N+  +n ++++++g+ +n W+  
  gi|116754158|ref|YP_843276.1| 111 GNAGIKVLS-DNNTIADNVAQGN-KYGIH-CTGS-RNSFMRNDIHDNDISMYDEGK-DNVWDVR 169
                                    578999988.8************.*****.7766.9************99999996.9***865 PP

>> DUF1565  Protein of unknown function (DUF1565)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   2.0     1e-07   0.00061      17     156 ..      34     155 ..      26     165 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1e-07
                        DUF1565  17 tiTkAlllakageviqlapGtYseatgEtFPlvipegvnlvGneagKGlskslyagkkvgplisgggddlsgvqnvtivl 96 
                                    ++  A+ +a ag++i++  G Y e+      +++ +  +lvG  +g G+           p+i+ +g        +  + 
  gi|116754158|ref|YP_843276.1|  34 SVQEAINAASAGDTIEVHSGIYFEH------VYVSKSLTLVGVDTGGGM-----------PVIDAEGIG-----SAITIS 91 
                                    5666777777777777777777665......466777777777777777...........555555544.....233356 PP

                        DUF1565  97 aneatiaGvtitNpni..lkgtgvliesasakianNtitgniadGiev...siyeaktgaggnii 156
                                    a+++t++G+++tN       + g+ + s + +ia+N  +gn + Gi+    ++ ++++++ +n i
  gi|116754158|ref|YP_843276.1|  92 ADNVTLRGFRVTNSGScgCGNAGIKVLSDNNTIADNVAQGN-KYGIHCtgsRNSFMRNDIHDNDI 155
                                    889***********665678899***************997.99999844422224555555444 PP

>> Pectinesterase  Pectinesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2     6e-06     0.036       2      53 ..      23      69 ..      22     151 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6e-06
                                   EEE-TTS-SSBSSHHHHHHHS-SS-SS-EEEEE-SEEEE--EEE-TTS-SEE CS
                 Pectinesterase  2 vvvakdgsgkfktiseavaavpeksekrfviyvkaGvYeenvevekkktnvv 53
                                   v+v+ +g ++f++++ea++a+++       i v++G+Y e+v v+k+ t v 
  gi|116754158|ref|YP_843276.1| 23 VTVCGEG-CDFSSVQEAINAASAGD----TIEVHSGIYFEHVYVSKSLTLVG 69
                                   5666665.79*********998665....599************99755443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1335.80
//
Query:       gi|116754159|ref|YP_843277.1|  [L=151]
Description: hypothetical protein Mthe_0848 [Methanosaeta thermophila PT]
Scores for complete 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-54  182.6   0.1    3.9e-54  182.4   0.1    1.0  1  DUF2124   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2124  Uncharacterized protein conserved in archaea (DUF2124)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.4   0.1   2.2e-58   3.9e-54       1     141 []       8     145 ..       8     145 .. 0.99

  Alignments for each domain:
  == domain 1  score: 182.4 bits;  conditional E-value: 2.2e-58
                                    EHHHHHHHHHHHHTTT-SEEEEEE-TTTTHHHHHHHHHHTTT..SEEEEEETT-GGG-EEEEEETTEEEEEEE-.-S-EE CS
                        DUF2124   1 kglsgllrefkelvkesekivfvGspgvCtpfaellayaiRdlekelvfvpdldlekarklevtdvGmqleeeaeeekad 80 
                                    kgl+g+l+ f+++vk+ e+i+f+Gspg+Ctpfa +l+y +R+  k+l+fvp ++ ek+r++++t++Gm+l+e + + +ad
  gi|116754159|ref|YP_843277.1|   8 KGLGGMLNGFRDMVKDFESITFIGSPGFCTPFALFLGYPVRE--KRLAFVPGVSPEKTRRVIATEYGMELGEMC-SPDAD 84 
                                    8*****************************************..9*****************************.***** PP

                                    EEEEEGGGGSTTTS--HHHHHHHHHHHEEEEEEEEEETTHHHHTTHHHHS--SEEEEEEEE CS
                        DUF2124  81 vvvllGGlampkikveaedvkeliekiekkkviGvcfmsifekagWldkidFdliidakle 141
                                    v+v+lGG+ampki+v++ed+++l+ ki++k+v+Gvcfm ifekagW+d+i+Fd+++++ +e
  gi|116754159|ref|YP_843277.1|  85 VLVVLGGMAMPKIGVSIEDMRQLLGKIPHKSVMGVCFMGIFEKAGWCDSIEFDYVMNTIIE 145
                                    *********************************************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 1252.39
//
Query:       gi|116754160|ref|YP_843278.1|  [L=230]
Description: phage shock protein A, PspA [Methanosaeta thermophila PT]
Scores for complete 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-31  108.9  26.9    2.9e-31  108.8  26.9    1.0  1  PspA_IM30     PspA/IM30 family
     0.0044   16.7  11.9     0.0044   16.7  11.9    2.4  3  Snf7          Snf7
  ------ inclusion threshold ------
      0.015   15.3  11.6       0.24   11.4   4.8    2.8  2  DUF1664       Protein of unknown function (DUF1664)
      0.041   13.7   0.6       0.15   11.8   0.0    2.2  3  NOG1          Nucleolar GTP-binding protein 1 (NOG1)
      0.052   13.8  14.0       0.27   11.5   6.1    2.9  2  DUF5082       Domain of unknown function (DUF5082)
      0.052   13.9  12.1        0.6   10.5   0.1    3.5  3  Flagellin_C   Bacterial flagellin C-terminal helical region
      0.088   10.8   3.6       0.11   10.5   3.6    1.2  1  Prominin      Prominin
        0.1   10.1  19.5      0.044   11.3  10.8    2.0  2  DUF3584       Protein of unknown function (DUF3584)
       0.18   10.7  21.6       0.33    9.8  17.6    2.1  2  Spc7          Spc7 kinetochore protein
       0.19   12.4  13.4       0.31   11.7   3.0    2.7  3  YabA          Initiation control protein YabA
       0.31   11.1  14.0       0.55   10.2  11.8    2.4  2  FlxA          FlxA-like protein
       0.37   10.8   9.5       0.67   10.0   3.8    2.6  3  Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C
       0.52   10.8   7.7          5    7.7   1.9    3.2  3  NPV_P10       Nucleopolyhedrovirus P10 protein
        1.3    9.4  15.8       0.43   10.9   6.8    2.7  2  YlqD          YlqD protein
        1.3    9.3  24.8       0.11   12.7   4.2    4.4  4  ABC_tran_CTD  ABC transporter C-terminal domain
        2.2    8.1  15.7       0.31   10.9   5.5    2.5  3  DUF724        Protein of unknown function (DUF724)
        2.2    8.8  13.1        1.5    9.3   3.1    2.7  2  UPF0449       Uncharacterised protein family UPF0449
        2.6    8.8  17.3       0.21   12.3   6.4    2.9  3  DUF4472       Domain of unknown function (DUF4472)
        2.9    8.4  27.4        4.5    7.8  20.0    3.2  2  APG6_N        Apg6 coiled-coil region
        3.3    7.6  25.0        0.1   12.4   5.5    3.6  4  DivIC         Septum formation initiator
        3.6    7.7  18.5       0.19   11.7   8.9    3.1  2  TMF_DNA_bd    TATA element modulatory factor 1 DNA binding
        7.4    5.8  21.7         21    4.3  20.9    2.0  1  DUF4407       Domain of unknown function (DUF4407)
        7.8    5.0  13.3        2.9    6.4   7.9    1.9  2  FapA          Flagellar Assembly Protein A


Domain annotation for each model (and alignments):
>> PspA_IM30  PspA/IM30 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.8  26.9   3.7e-34   2.9e-31       1     218 [.       2     228 ..       2     230 .] 0.95

  Alignments for each domain:
  == domain 1  score: 108.8 bits;  conditional E-value: 3.7e-34
                      PspA_IM30   1 gifkrllrllraniselldkaeDPekileqairdmqselakarqalaqviarqkqlerkleeqkeqakklekkAkaALtk 80 
                                    g+++r+++++r+++s  +dk+eDP  +l+   +   + l+++++ +a+v +++k+le + ++ ++ a++le kA++AL+ 
  gi|116754160|ref|YP_843278.1|   2 GLLDRMGTIVRSKMSRIMDKMEDPREVLDYSYEKQLELLQNVKRGIAEVATSKKRLELQRARLAQNAEQLEGKAREALNS 81 
                                    689****************************9999999****************************************** PP

                      PspA_IM30  81 geeeLArealaeikslekqaealetqlaqqrsaveqlrkqlealetkieelkakkellkarekaakaqeavqkslgkls. 159
                                    g+e+LAr al++++sl++q+e l++q a++   +++l +  ++l tkie l+a ke++ka+ +aa aq +v++s+ ++s 
  gi|116754160|ref|YP_843278.1|  82 GREDLARQALERKVSLQNQIETLDAQIAELDREEQKLIAVETRLSTKIETLRARKEAIKAQYSAAEAQVKVSESVTGISe 161
                                    *******************************************************************************7 PP

                      PspA_IM30 160 .tesatdslerieeKieerearadaaaelae....saqd....ldakleaagiqkevseqvlarlkae 218
                                      ++   + +r eeK e ++ara a   l e    ++ +    ld +l  a+   +v +++larl++e
  gi|116754160|ref|YP_843278.1| 162 eLADVGLAIQRAEEKTEGMKARAAALDDLLEkgvlEDYTggdaLDRELSKAKTSSAV-DAELARLRGE 228
                                    777777899*******************998777733336778**************.*******986 PP

>> Snf7  Snf7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       2.1   1.7e+03     107     126 ..      16      28 ..      11      43 .. 0.56
   2 !   16.7  11.9   5.6e-06    0.0044       4     100 ..      48     145 ..      45     165 .. 0.88
   3 ?    2.0   2.5      0.18   1.4e+02       3      48 ..     108     151 ..     106     194 .. 0.58

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.1
                                    HHHHHHHHHHHHHHTCHHHH CS
                           Snf7 107 dklmdeiedqmekaeeisEa 126
                                     ++md +ed         E+
  gi|116754160|ref|YP_843278.1|  16 SRIMDKMED-------PREV 28 
                                    344444444.......3333 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 5.6e-06
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           Snf7   4 rsLrkaerkldkkqeslekkikkleaelkklakkgnkdralllLKqkkryekqldqldnqlanleqvslaienlksnkev 83 
                                     ++ +++++l+ ++ +l +  ++le ++++   +g++d a+++L +k+ + +q++ ld+q a+l+    ++   ++  ++
  gi|116754160|ref|YP_843278.1|  48 AEVATSKKRLELQRARLAQNAEQLEGKAREALNSGREDLARQALERKVSLQNQIETLDAQIAELDREEQKLIAVETRLST 127
                                    566788999*******************************************************9988888777777766 PP

                                    .HHHHHHHHHHHHHHHHC CS
                           Snf7  84 .lnamkqgakamkamnkk 100
                                     +++++   +a+ka+++ 
  gi|116754160|ref|YP_843278.1| 128 kIETLRARKEAIKAQYSA 145
                                    578888888888888765 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.18
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTT-HHHHHHHHH CS
                           Snf7   3 irsLrkaerkldkkqeslekkikkleaelkklakkgnkdralllLK 48 
                                    i +L ++e+kl   + +l +ki+ l+a     +++ +  +a    K
  gi|116754160|ref|YP_843278.1| 108 IAELDREEQKLIAVETRLSTKIETLRARKEAIKAQYS--AAEAQVK 151
                                    6778888888888888888888886554444444433..3333334 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.5    0.0076       5.9      62     117 ..      20      75 ..       4      81 .. 0.84
   2 ?   11.4   4.8   0.00031      0.24      37     121 ..      95     181 ..      91     189 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0076
                        DUF1664  62 rhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskl 117
                                    +++++  + +d + ++q e+ +++k+ ++ev    ++++ +   + +  e+le+k 
  gi|116754160|ref|YP_843278.1|  20 DKMEDPREVLDYSYEKQLELLQNVKRGIAEVATSKKRLELQRARLAQNAEQLEGKA 75 
                                    5555555679999****************************************996 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00031
                        DUF1664  37 rslsdavesvskqleqvs...eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegl 113
                                     sl++ +e++  q+ ++    ++l a+  +Ls +i+++ ++ ++ k+  ++ +++v +v+e ++ i+e++  v  a++  
  gi|116754160|ref|YP_843278.1|  95 VSLQNQIETLDAQIAELDreeQKLIAVETRLSTKIETLRARKEAIKAQYSAAEAQV-KVSESVTGISEELADVGLAIQRA 173
                                    578888888888876665444899999************99999999888888888.58899999999999999999999 PP

                        DUF1664 114 esklerie 121
                                    e+k e ++
  gi|116754160|ref|YP_843278.1| 174 EEKTEGMK 181
                                    98877665 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 ?   11.8   0.0    0.0002      0.15      22      47 ..      24      49 ..      22      54 .. 0.88
   2 ?   -1.9   0.1       3.9     3e+03      29      39 ..      95     105 ..      91     121 .. 0.70
   3 ?   -2.9   0.0       7.6   5.9e+03      30      42 ..     145     157 ..     140     161 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0002
                           NOG1 22 DpseecgysleeQlsLleeikelfan 47
                                   Dp e   ys e+Ql+Ll+++k  +a+
  gi|116754160|ref|YP_843278.1| 24 DPREVLDYSYEKQLELLQNVKRGIAE 49
                                   999999***************98875 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.9
                           NOG1  29 ysleeQlsLle 39 
                                    +sl++Q++ l+
  gi|116754160|ref|YP_843278.1|  95 VSLQNQIETLD 105
                                    67888887665 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 7.6
                           NOG1  30 sleeQlsLleeik 42 
                                      e Q+++ e++ 
  gi|116754160|ref|YP_843278.1| 145 AAEAQVKVSESVT 157
                                    4688999988875 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   1.2     0.014        11      21      77 ..      32      88 ..      12      91 .. 0.86
   2 ?   11.5   6.1   0.00035      0.27      12      90 ..      94     181 ..      87     186 .. 0.53

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.014
                        DUF5082 21 aleekIerLkeaktklsdekeslkqkkkklekplnssesWkGkeennydgirsnles 77
                                   ++e+++e L+ +k+ + ++  s k  + + +  + + e + Gk+++  ++ r++l  
  gi|116754160|ref|YP_843278.1| 32 SYEKQLELLQNVKRGIAEVATSKKRLELQRARLAQNAEQLEGKAREALNSGREDLAR 88
                                   689****************9999999999999999999*****99999999888765 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00035
                        DUF5082  12 iaelrseiaaleekIerLk.......eaktklsdekeslkqkkkklekplnssesWkGkeennydgirs...nlessyqt 81 
                                    + +l+++i++l+ +I++L        ++ t+ls++ e+l + k++++ +     + + k ++++ gi +   ++  ++q+
  gi|116754160|ref|YP_843278.1|  94 KVSLQNQIETLDAQIAELDreeqkliAVETRLSTKIETLRARKEAIKAQYSAA-EAQVKVSESVTGISEelaDVGLAIQR 172
                                    44677777777777777772222222555555555555555555554444333.33334444444444444666666666 PP

                        DUF5082  82 yvdkldeli 90 
                                     ++k++ ++
  gi|116754160|ref|YP_843278.1| 173 AEEKTEGMK 181
                                    666666655 PP

>> Flagellin_C  Bacterial flagellin C-terminal helical region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.3      0.53   4.1e+02       8      42 ..      40      74 ..      34      82 .. 0.77
   2 ?    8.2   1.1    0.0041       3.2       2      44 ..     102     144 ..      98     148 .. 0.91
   3 ?   10.5   0.1   0.00077       0.6       3      39 ..     151     187 ..     149     193 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.53
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHH CS
                    Flagellin_C  8 itdldkvrselGavqnRlesaitnlkaqsenlkaa 42
                                   +++++   +e+ ++++Rle + ++l +  e l+ +
  gi|116754160|ref|YP_843278.1| 40 LQNVKRGIAEVATSKKRLELQRARLAQNAEQLEGK 74
                                   66777777888888889999888888887777655 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0041
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHC CS
                    Flagellin_C   2 divdeaitdldkvrselGavqnRlesaitnlkaqsenlkaaes 44 
                                    +++d +i +ld +  +l av++Rl+  i+ l a +e +ka+ s
  gi|116754160|ref|YP_843278.1| 102 ETLDAQIAELDREEQKLIAVETRLSTKIETLRARKEAIKAQYS 144
                                    6789999********************************9977 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.00077
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHH CS
                    Flagellin_C   3 ivdeaitdldkvrselGavqnRlesaitnlkaqsenl 39 
                                    +v+e +t+++++ +++G++ +R e+ ++ +ka    l
  gi|116754160|ref|YP_843278.1| 151 KVSESVTGISEELADVGLAIQRAEEKTEGMKARAAAL 187
                                    68999*************************9987665 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   3.6   0.00014      0.11     615     700 ..      41     135 ..       8     172 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00014
                       Prominin 615 eqlckkltkvnletlaekle..elanelsngkknlkqslkneaqdlraiqqelvlplessvkklkksvkkldeensd... 689
                                    +++++ +++v  ++   +l+   la++ ++ + +++++l++  +dl +   e+ + l++++++l  ++ +ld+e+++   
  gi|116754160|ref|YP_843278.1|  41 QNVKRGIAEVATSKKRLELQraRLAQNAEQLEGKAREALNSGREDLARQALERKVSLQNQIETLDAQIAELDREEQKlia 120
                                    44444444444433333332113344444444667777777777777777777777777777777777777775555222 PP

                       Prominin 690 ....lqesikkllaa 700
                                        l+++i+ l a+
  gi|116754160|ref|YP_843278.1| 121 vetrLSTKIETLRAR 135
                                    111155555555443 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3  10.8   5.6e-05     0.044     673     742 ..      48     117 ..      11     122 .. 0.77
   2 ?    3.7   2.8     0.011       8.6     832     908 ..     119     192 ..     114     214 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.6e-05
                        DUF3584 673 kaiaerkqqaeeqlqkldaqlkqleeqqkaaleelkedlseerlekkakwqevvgeldeqlaelkkaiea 742
                                    + +a  k+  e q+  l+++++qle + ++al+  +edl  + le+k  +q+ +++ld+q+ael+ + ++
  gi|116754160|ref|YP_843278.1|  48 AEVATSKKRLELQRARLAQNAEQLEGKAREALNSGREDLARQALERKVSLQNQIETLDAQIAELDREEQK 117
                                    234557788899999*************************************************988665 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.011
                        DUF3584 832 eeleqeltrliedtklerkklekerkalekqldqldenlrklrdllsklaelkldadaeqaegelaerlaaleelkr 908
                                      +e +l+++ie ++++ ++++ + +a+e+ +++++e+++++  +l  ++ l++++  e+ e  ++ r aal++l++
  gi|116754160|ref|YP_843278.1| 119 IAVETRLSTKIETLRARKEAIKAQYSAAEA-QVKVSESVTGISEELADVG-LAIQRAEEKTE-GMKARAAALDDLLE 192
                                    444555666666666666666555555544.3456666665555544442.22222222222.34555555555554 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8  17.6   0.00042      0.33     139     259 ..      38     152 ..       9     158 .. 0.50
   2 ?    8.9  10.9   0.00077       0.6     145     234 ..      91     189 ..      84     197 .. 0.54

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00042
                           Spc7 139 gLkegleenlegleedkelLekqeeeldellpeleeeka.eleeeleklqeaaeelesidkeeLeelreelaelkaeiee 217
                                    +L +++++ ++++ + k++Le q++ l +  ++le +   +l++  e+l ++a e + +       l++++++l+a+i+e
  gi|116754160|ref|YP_843278.1|  38 ELLQNVKRGIAEVATSKKRLELQRARLAQNAEQLEGKAReALNSGREDLARQALERKVS-------LQNQIETLDAQIAE 110
                                    34444444444444444444444444444444444332214444444444444443333.......44455555555555 PP

                           Spc7 218 kkkelaelqeqleeleekieelkeqkseleeeiaeaervlee 259
                                    + +e ++l +  ++l++kie+l+++k+ ++++ ++ae  ++ 
  gi|116754160|ref|YP_843278.1| 111 LDREEQKLIAVETRLSTKIETLRARKEAIKAQYSAAEAQVKV 152
                                    555555555555555555555555555555555555554443 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00077
                           Spc7 145 eenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeeles........id.keeLeelreelaelkaei 215
                                     e+  +l+++ e+L++q +eld+  ++l + +++l+ ++e+l++++e +++        ++ +e++  + eela++   i
  gi|116754160|ref|YP_843278.1|  91 LERKVSLQNQIETLDAQIAELDREEQKLIAVETRLSTKIETLRARKEAIKAqysaaeaqVKvSESVTGISEELADVGLAI 170
                                    55555566666666666666666666666666666666666666555555443222223444566666666666666666 PP

                           Spc7 216 eekkkelaelqeqleelee 234
                                    ++ +++++ ++++ ++l++
  gi|116754160|ref|YP_843278.1| 171 QRAEEKTEGMKARAAALDD 189
                                    6555555555555555444 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   2.2     0.025        19      13      75 ..      29      88 ..      15      93 .. 0.76
   2 ?   11.7   3.0   0.00039      0.31       9      66 ..      93     150 ..      86     162 .. 0.75
   3 ?    0.3   0.0       1.4   1.1e+03      14      52 ..     153     191 ..     148     225 .. 0.63

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.025
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXXXXX CS
                           YabA 13 leeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkelsegkenLar 75
                                   l+ + e+ le l+++k+ +ae+    ++Lel+  +l ++ e   + e + +++l++g+e Lar
  gi|116754160|ref|YP_843278.1| 29 LDYSYEKQLELLQNVKRGIAEVATSKKRLELQRARLAQNAE---QLEGKAREALNSGREDLAR 88
                                   55667788889999*****************9999998883...4445555566666666664 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00039
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXX CS
                           YabA   9 kleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkel 66 
                                    +  +l++q+e+l ++++el +e ++l+  +++L++  e+lr r e  +++ ++ ++++
  gi|116754160|ref|YP_843278.1|  93 RKVSLQNQIETLDAQIAELDREEQKLIAVETRLSTKIETLRARKEAIKAQYSAAEAQV 150
                                    455799***********************************99854444433333333 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 1.4
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           YabA  14 eeqleelleeleelkeelaelleenaeLeleneklrerl 52 
                                    +e+++ ++eel+++  ++++  e+ + +++    l ++l
  gi|116754160|ref|YP_843278.1| 153 SESVTGISEELADVGLAIQRAEEKTEGMKARAAALDDLL 191
                                    566666777777777777777777777777777766666 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2  11.8   0.00071      0.55       9      74 ..      51     117 ..      45     142 .. 0.79
   2 ?    0.2   1.2      0.95   7.4e+02      47      65 ..     132     150 ..     113     185 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00071
                           FlxA   9 sssssgsasqiasLqkQiknlqkqLkelses.deltkeekkkqqqliqaQIqqlqaQIaqlqqqqae 74 
                                    ++s++  + q a+L +  ++l+ + +e  +s  e  + +  +++  +q+QI+ l aQIa l +++++
  gi|116754160|ref|YP_843278.1|  51 ATSKKRLELQRARLAQNAEQLEGKAREALNSgREDLARQALERKVSLQNQIETLDAQIAELDREEQK 117
                                    56777788899999999*****9999988887777777899********************998775 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.95
                           FlxA  47 kkkqqqliqaQIqqlqaQI 65 
                                     +++++ i+aQ ++ +aQ+
  gi|116754160|ref|YP_843278.1| 132 LRARKEAIKAQYSAAEAQV 150
                                    2333333444433333333 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 ?    3.0   0.4      0.13        99      46      94 ..      36      86 ..      27      90 .. 0.75
   2 ?   10.0   3.8   0.00086      0.67      42     115 ..      96     170 ..      86     192 .. 0.78
   3 ?    4.2   0.0     0.052        41      24      77 ..     138     192 ..     134     214 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.13
                   Baculo_PEP_C 46 qLnalsedlksllaeldt...rldtlltnLtdalnalqdtlrneLtnlnsil 94
                                   qL+   +++k+ +ae++t   rl+ + ++L +   +l+ + r++L++   +l
  gi|116754160|ref|YP_843278.1| 36 QLEL-LQNVKRGIAEVATskkRLELQRARLAQNAEQLEGKAREALNSGREDL 86
                                   4543.45578888888777778999999999999999999999888766555 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00086
                   Baculo_PEP_C  42 aietqLnalsedlksllaeldtrldtlltnLtdalnalq...dtlrneLtnlnsiltnLlssvtNinstLnnllqal 115
                                    ++++q+++l++++ + l   +++l ++ t+L++++ +l    ++++ +  + ++++     svt+i + L+ +  a+
  gi|116754160|ref|YP_843278.1|  96 SLQNQIETLDAQIAE-LDREEQKLIAVETRLSTKIETLRarkEAIKAQYSAAEAQVK-VSESVTGISEELADVGLAI 170
                                    488999999999988.55567789999999999999999999999999999999985.6779999998888766655 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.052
                   Baculo_PEP_C  24 airlqnvqilaql..atlldaietqLnalsedlksllaeldtrldtlltnLtdaln 77 
                                    ai++q +   aq+  ++ ++ i ++L ++  ++++  +e ++ +++ +++L+d l 
  gi|116754160|ref|YP_843278.1| 138 AIKAQYSAAEAQVkvSESVTGISEELADVGLAIQR-AEEKTEGMKARAAALDDLLE 192
                                    7888888887775226899**************99.66677788888888888765 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1       1.4   1.1e+03      28      53 ..      41      66 ..      11      81 .. 0.68
   2 ?    7.7   1.9    0.0065         5      14      52 ..      89     126 ..      79     149 .. 0.74
   3 ?    4.7   0.0     0.052        41      15      55 ..     151     191 ..     138     198 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.4
                        NPV_P10 28 ddvqenlpdvtelnekLdaqsaqLae 53
                                   ++v+  + +v   +++L+ q a La+
  gi|116754160|ref|YP_843278.1| 41 QNVKRGIAEVATSKKRLELQRARLAQ 66
                                   44444555555555566666665554 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0065
                        NPV_P10  14 kavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLa 52 
                                    +a++ kV +lq+q++ +++++ +++  ++kL a  + L 
  gi|116754160|ref|YP_843278.1|  89 QALERKV-SLQNQIETLDAQIAELDREEQKLIAVETRLS 126
                                    5788999.9999999999999995555555555544443 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.052
                        NPV_P10  15 avddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaele 55 
                                    +v++ V+ ++++++dv   ++  +e +e + a +a+L++l 
  gi|116754160|ref|YP_843278.1| 151 KVSESVTGISEELADVGLAIQRAEEKTEGMKARAAALDDLL 191
                                    58888999999999999999999999999999999998875 PP

>> YlqD  YlqD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   2.7      0.25   1.9e+02      21      62 ..      39      80 ..      30      96 .. 0.52
   2 ?   10.9   6.8   0.00056      0.43      23      72 ..      95     150 ..      87     193 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.25
                           YlqD 21 lqqqlqaqieqldkelqqLefqakrlikeikkqsaqqieeiq 62
                                   l+q++++ i ++ +  ++Le+q  rl +++++ + ++ e+++
  gi|116754160|ref|YP_843278.1| 39 LLQNVKRGIAEVATSKKRLELQRARLAQNAEQLEGKAREALN 80
                                   555555555555555556666666555555554444333333 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00056
                           YlqD  23 qqlqaqieqldkelqqLefqakrlikeikkqsaq......qieeiqeqvekekser 72 
                                     +lq+qie+ld ++++L+ ++++li+   + s++      ++e+i++q+++ ++++
  gi|116754160|ref|YP_843278.1|  95 VSLQNQIETLDAQIAELDREEQKLIAVETRLSTKietlraRKEAIKAQYSAAEAQV 150
                                    579**********************9998877655666665555555554444333 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 ?   -0.4   2.7       1.8   1.4e+03       3      28 ..      32      58 ..      12      81 .. 0.58
   2 ?    0.9   8.6       0.7   5.5e+02      13      30 ..      97     114 ..      51     127 .. 0.80
   3 ?   12.7   4.2   0.00014      0.11      12      63 ..     124     176 ..     113     178 .. 0.86
   4 ?    1.0   0.4      0.64     5e+02      14      54 ..     174     213 ..     169     228 .. 0.66

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.8
                   ABC_tran_CTD  3 sykeqre.leeleaeIeaLEeeiaele 28
                                   sy +q e l+++ + I++  + ++ le
  gi|116754160|ref|YP_843278.1| 32 SYEKQLElLQNVKRGIAEVATSKKRLE 58
                                   444444433444444555555555554 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.7
                   ABC_tran_CTD  13 leaeIeaLEeeiaeleae 30 
                                    l ++Ie L+++iael+ e
  gi|116754160|ref|YP_843278.1|  97 LQNQIETLDAQIAELDRE 114
                                    666666666666666543 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 0.00014
                   ABC_tran_CTD  12 eleaeIeaLEeeiaeleaeladpelysdp.eklaelsaeleeleaeLeelyer 63 
                                    +l  +Ie L ++++++ a+ +++e   +  e ++ +s+el+++  ++++++e+
  gi|116754160|ref|YP_843278.1| 124 RLSTKIETLRARKEAIKAQYSAAEAQVKVsESVTGISEELADVGLAIQRAEEK 176
                                    5889********************88555699***********9999999985 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.64
                   ABC_tran_CTD  14 eaeIeaLEeeiaeleaeladpelysdpeklaelsaeleele 54 
                                    e++ e + ++ a+l++ l++  + +d++   +l +el +++
  gi|116754160|ref|YP_843278.1| 174 EEKTEGMKARAAALDDLLEKG-VLEDYTGGDALDRELSKAK 213
                                    555566667777777777654.5577776666666666554 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   1.5     0.065        51     103     146 ..      32      75 ..      11      86 .. 0.81
   2 ?   10.9   5.5   0.00039      0.31     110     182 ..      82     151 ..      73     157 .. 0.80
   3 ?   -1.5   0.0       2.4   1.8e+03     130     151 ..     161     182 ..     150     222 .. 0.59

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.065
                         DUF724 103 eqtklleerkklekkieeeesekrkleeeidelekkilelerql 146
                                    +++k le ++++++ i+e +++k++le + + l ++  +le ++
  gi|116754160|ref|YP_843278.1|  32 SYEKQLELLQNVKRGIAEVATSKKRLELQRARLAQNAEQLEGKA 75 
                                    67788888899999999999999999999999999988888765 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00039
                         DUF724 110 erkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleeeledveqeFe 182
                                     r++l ++  e +    +l+++i+ l+ +i+el r+++ l + + + + +i +l++ +e+++ +++++e +++
  gi|116754160|ref|YP_843278.1|  82 GREDLARQALERK---VSLQNQIETLDAQIAELDREEQKLIAVETRLSTKIETLRARKEAIKAQYSAAEAQVK 151
                                    4455555555444...46779*****************99999999********************9999986 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 2.4
                         DUF724 130 eeidelekkilelerqlallke 151
                                    ee++++  +i++ e++ + +k+
  gi|116754160|ref|YP_843278.1| 161 EELADVGLAIQRAEEKTEGMKA 182
                                    4444444444444444433332 PP

>> UPF0449  Uncharacterised protein family UPF0449
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   3.2       0.1        81      65      93 ..      48      76 ..       9      90 .. 0.70
   2 ?    9.3   3.1    0.0019       1.5      36      96 ..      92     147 ..      78     152 .. 0.64

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.1
                        UPF0449 65 rtylelnerLeeakeeLkqkceeLktage 93
                                    +    ++rLe ++ +L q+ e+L+  ++
  gi|116754160|ref|YP_843278.1| 48 AEVATSKKRLELQRARLAQNAEQLEGKAR 76
                                   44556678888888888888888886554 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0019
                        UPF0449  36 sdsveedkkassseeedleaeveelYeqvrtylelnerLeeakeeLkqkceeLktageeLe 96 
                                    ++     k + +++ e l+a++ el ++ ++++++++rL+ + e+L+ + e +k++ +  e
  gi|116754160|ref|YP_843278.1|  92 ER-----KVSLQNQIETLDAQIAELDREEQKLIAVETRLSTKIETLRARKEAIKAQYSAAE 147
                                    33.....333333344555777778888888888888888888888888888877766555 PP

>> DUF4472  Domain of unknown function (DUF4472)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   1.6      0.47   3.7e+02      36      74 ..      38      77 ..      27      85 .. 0.53
   2 ?   12.3   6.4   0.00028      0.21      22      88 ..      86     152 ..      82     162 .. 0.91
   3 ?    0.0   0.0       1.8   1.4e+03       8      33 ..     159     184 ..     153     225 .. 0.66

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.47
                        DUF4472 36 kvlalenr.vlelelerekaaeeiqslrerlaeleeekke 74
                                   ++l+  +r + e+   +++++ +++ l+++ ++le +++e
  gi|116754160|ref|YP_843278.1| 38 ELLQNVKRgIAEVATSKKRLELQRARLAQNAEQLEGKARE 77
                                   4443333325555555555555555555555555555444 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00028
                        DUF4472  22 lreqheaekfelknkvlalenrvlelelerekaaeeiqslrerlaeleeekkeleeeyvvlkknyqa 88 
                                    l +q+ + k  l+n++ +l+ ++ el+ e++k+   ++ l+++ ++l++ k++++++y++ + ++++
  gi|116754160|ref|YP_843278.1|  86 LARQALERKVSLQNQIETLDAQIAELDREEQKLIAVETRLSTKIETLRARKEAIKAQYSAAEAQVKV 152
                                    67888899999*************************************************9988775 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 1.8
                        DUF4472   8 isKeLVdlqietnklreqheaekfel 33 
                                    is eL d+ +  ++  e+ e +k   
  gi|116754160|ref|YP_843278.1| 159 ISEELADVGLAIQRAEEKTEGMKARA 184
                                    67777777777777777777665544 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  20.0    0.0058       4.5      44     132 ..      49     149 ..      11     150 .. 0.69
   2 ?    0.0   1.5       1.5   1.2e+03      48      85 ..     155     192 ..     146     229 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0058
                         APG6_N  44 k.......qdeeleeleeeleklekeeeellee....L.kelekereeleaelaaleeelealeeeeerfwreynelqle 111
                                    +        + ++++l +  e+le + +e+l+     L +++ + + +l++++++l ++ ++l++ee++ +     l+++
  gi|116754160|ref|YP_843278.1|  49 EvatskkrLELQRARLAQNAEQLEGKAREALNSgredLaRQALERKVSLQNQIETLDAQIAELDREEQKLIAVETRLSTK 128
                                    133333343334445555555555555555543211131455566789******************************** PP

                         APG6_N 112 lleleeeldsleaqyehaqnq 132
                                     + l  ++++++aqy  a++q
  gi|116754160|ref|YP_843278.1| 129 IETLRARKEAIKAQYSAAEAQ 149
                                    ****************99887 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.5
                         APG6_N  48 eleeleeeleklekeeeelleeLkelekereeleaela 85 
                                    ++  + eel+++  + ++++e+ + +++  ++l++ l+
  gi|116754160|ref|YP_843278.1| 155 SVTGISEELADVGLAIQRAEEKTEGMKARAAALDDLLE 192
                                    55566677777777777777777777777777766555 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   4.5     0.026        20      20      66 ..      34      80 ..      30      85 .. 0.81
   2 ?   12.4   5.5   0.00013       0.1      16      60 ..      98     142 ..      88     143 .. 0.92
   3 ?   -0.0   0.1      0.98   7.6e+02      24      53 ..     161     189 ..     154     196 .. 0.71
   4 ?   -2.9   0.1       7.7     6e+03      43      62 ..     205     224 ..     203     227 .. 0.45

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.026
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXXXXXXXXX CS
                          DivIC 20 kqlkqeiaalqaelaklkaeneeLeaevkdLksdedyieerARselg 66
                                    ++ + ++  ++ +a++   +++Le + ++L ++ + +e +AR+ l+
  gi|116754160|ref|YP_843278.1| 34 EKQLELLQNVKRGIAEVATSKKRLELQRARLAQNAEQLEGKAREALN 80
                                   55555567778889999999999999999999999999999998886 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00013
                                    XXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXXX CS
                          DivIC  16 llaykqlkqeiaalqaelaklkaeneeLeaevkdLksdedyieer 60 
                                    ++++  l+++ia+l +e +kl a + +L  +++ L+  +++i+++
  gi|116754160|ref|YP_843278.1|  98 QNQIETLDAQIAELDREEQKLIAVETRLSTKIETLRARKEAIKAQ 142
                                    6788999****************************99****9876 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.98
                                    HHHHHHHHHHHHHHHHHHHHHHHHCC-XXX CS
                          DivIC  24 qeiaalqaelaklkaeneeLeaevkdLksd 53 
                                    +e+a+    +++  ++ e ++a+ + L +d
  gi|116754160|ref|YP_843278.1| 161 EELADVGLAIQRAEEKTEGMKARAAAL-DD 189
                                    566666667777777777777777777.33 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 7.7
                                    HHHHHCC-XXXXXXXXXXXX CS
                          DivIC  43 LeaevkdLksdedyieerAR 62 
                                    L++e+++ k + +  +e AR
  gi|116754160|ref|YP_843278.1| 205 LDRELSKAKTSSAVDAELAR 224
                                    55555555433333334444 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 ?   -0.2   2.0       1.3   9.9e+02      36      71 ..      41      76 ..      27      80 .. 0.58
   2 ?   11.7   8.9   0.00025      0.19       2      59 ..      96     155 ..      95     188 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.3
                     TMF_DNA_bd 36 kkLrkknkelekeikelkkkleklekeleeleerlk 71
                                    + +  ++e  ++ k+l+ + ++l ++ e+le +++
  gi|116754160|ref|YP_843278.1| 41 QNVKRGIAEVATSKKRLELQRARLAQNAEQLEGKAR 76
                                   444444555555666666666666666666666555 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00025
                     TMF_DNA_bd   2 slekklkeKDeqIaqLmeEGekLskkelklnntikkLrkknkele..keikelkkklekl 59 
                                    sl+++++  D+qIa+L  E +kL + e +l+++i  Lr+  +     ++ +e + k++++
  gi|116754160|ref|YP_843278.1|  96 SLQNQIETLDAQIAELDREEQKLIAVETRLSTKIETLRARKEAIKaqYSAAEAQVKVSES 155
                                    789999999****************************98655444114444444554444 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3  20.9     0.027        21     139     244 ..      41     160 ..      10     198 .. 0.47

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.027
                        DUF4407 139 eaqiaalqaeidaaearldalraeaqkeldgtk.gtgttgvaGkgpaakekkaqldaaqaelaelkakld.......... 207
                                    ++  +   ae+++ ++rl+ +ra +++++++   ++++    G+++ a+++ +    +q+++++l+a++           
  gi|116754160|ref|YP_843278.1|  41 QNVKR-GIAEVATSKKRLELQRARLAQNAEQLEgKAREALNSGREDLARQALERKVSLQNQIETLDAQIAeldreeqkli 119
                                    22222.22233333333333333333222222212222233455555555444444444444444444434444444788 PP

                        DUF4407 208 .....atarlaalraelaeleaerakeraasqaaaaaddGll 244
                                          ++++++lra+++ ++a++++++a+ +  +++ +G+ 
  gi|116754160|ref|YP_843278.1| 120 avetrLSTKIETLRARKEAIKAQYSAAEAQVKV-SESVTGIS 160
                                    888885555555555555555555555555544.22333333 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   7.9    0.0037       2.9     331     411 ..      40     118 ..      28     130 .. 0.86
   2 ?    1.9   1.1     0.085        66     340     409 ..     123     192 ..     115     207 .. 0.56

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0037
                           FapA 331 depelkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeeles 410
                                      +++k+ ++e+ +  ++le +  +l ++ ++l+  ka+++l+s +++   ++le k +l++++e l+++++el+ e ++
  gi|116754160|ref|YP_843278.1|  40 L-QNVKRGIAEVATSKKRLELQRARLAQNAEQLEG-KAREALNSGREDLARQALERKVSLQNQIETLDAQIAELDREEQK 117
                                    4.788999999999999999999999999999999.99************************************999887 PP

                           FapA 411 k 411
                                     
  gi|116754160|ref|YP_843278.1| 118 L 118
                                    7 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.085
                           FapA 340 keleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeele 409
                                    ++l +++e l+++ e +k++++  ++  + ++    ++e+l+ +  + ++ +e+ e ++++ ++l++ le
  gi|116754160|ref|YP_843278.1| 123 TRLSTKIETLRARKEAIKAQYSAAEAQVKVSESVTGISEELADVGLAIQRAEEKTEGMKARAAALDDLLE 192
                                    4555555555555555555555555433344444555555555555556666666666665555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1631  (0.0909699); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        38  (0.00211947); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.73u 0.29s 00:00:01.02 Elapsed: 00:00:00.45
# Mc/sec: 1542.41
//
Query:       gi|116754161|ref|YP_843279.1|  [L=92]
Description: hypothetical protein Mthe_0850 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 679.59
//
Query:       gi|116754162|ref|YP_843280.1|  [L=190]
Description: hypothetical protein Mthe_0851 [Methanosaeta thermophila PT]
Scores for complete sequence (score 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   12.0   0.0       0.41   10.8   0.0    1.5  1  NigD_N    NigD-like N-terminal OB domain


Domain annotation for each model (and alignments):
>> NigD_N  NigD-like N-terminal OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   2.3e-05      0.41       8      37 ..      72     101 ..      69     102 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 2.3e-05
                                    TTSSS-EEEETTS-EEEEEEESS--TT--T CS
                         NigD_N   8 tdgdgfylqlDdggtlyptnpavsgytpdd 37 
                                    ++g+++ l++D++g+l+++ +++++++ ++
  gi|116754162|ref|YP_843280.1|  72 ETGTAYRLESDSYGYLWVVLTDQDFEDLVS 101
                                    6899***************88888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1414.15
//
Query:       gi|116754163|ref|YP_843281.1|  [L=287]
Description: heat shock protein HtpX [Methanosaeta thermophila PT]
Scores for complete 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-41  140.1   0.0    7.3e-41  140.1   0.0    1.4  2  Peptidase_M48  Peptidase family M48
    1.5e-06   27.6   4.1    1.9e-05   24.0   0.5    2.6  2  Peptidase_M56  BlaR1 peptidase M56
  ------ inclusion threshold ------
      0.049   13.2   0.0      0.072   12.7   0.0    1.2  1  DUF2268        Predicted Zn-dependent protease (DUF2268)
       0.25   11.6   0.8       0.88    9.9   0.5    2.0  2  DUF4157        Domain of unknown function (DUF4157)
        6.8    5.3   7.9        1.2    7.8   0.1    2.0  2  DUF2207        Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> Peptidase_M48  Peptidase family M48
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.8         2   7.1e+03     111     111 ..      34      34 ..      10      59 .. 0.34
   2 !  140.1   0.0     2e-44   7.3e-41       2     195 ..      73     282 ..      72     283 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2
                                    T CS
                                    x RF
                  Peptidase_M48 111 g 111
                                    +
  gi|116754163|ref|YP_843281.1|  34 A 34 
                                    1 PP

  == domain 2  score: 140.1 bits;  conditional E-value: 2e-44
                                    --SSHHHHHHHHHHHHTT-..-EEEEEEE-GGGT-EEEEESSS-E.EEEEEHHHH-SSB-HHHHHHHHHHHHHHHHTTHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M48   2 lreaelkevveelakeaglpkpltkvyvvnspkrNAFalgggknk.rivltdgLlkqllseeelaaVlGHElGHikhrhs 80 
                                    ++++el+e v +l + agl  p++++++v+ +  NAFa+g+++++  +++t+gLl + l+++el+aVl+HEl+Hik+r++
  gi|116754163|ref|YP_843281.1|  73 SEAPELHELVGRLCAIAGL--PKPRIAIVRTDIPNAFATGRSQSSsVVAVTTGLL-RRLDKSELEAVLAHELSHIKNRDV 149
                                    6899***************..999999****999**********999********.************************ PP

                                    HHHHHHHHHHHHHHHHHHHHHTT-SHHHHHTT--S---HHHHHHHHHHTT...HHHHHHHHHHHHHHHHTTT.HHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M48  81 vvslivsllasillllglallisraeedaagafldalavliglliillfl...alSRkrEyqADeagvellkrakdlvra 157
                                    +v++i s l++++  ++  +++   ++d+ ++ l a   + +++ i++f+    lSR+rE++AD+ ++ ++ r+ +lv+a
  gi|116754163|ref|YP_843281.1| 150 AVMTIASFLSTVASVIVQNIFFLGDRRDRESGNLFAVWLVSLIVWIVSFIlirTLSRYREFSADRGSAIITGRPSALVSA 229
                                    ****************9999999888888888888888887888888888889*************************** PP

                                    HHHHHHHTT--S---HHHH...............HHS-SS--HHHHHHHHHH- CS
                                    xxxxxxxxxxxxxxxxxxx...............xxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M48 158 liklakdlerqdvsaslrs...............ellstHPplleRiqalkel 195
                                    l+k++ +++r ++++  +                +llstHPp++ Ri+al++l
  gi|116754163|ref|YP_843281.1| 230 LMKISGTMARIPREDLRKVegmnaffiiptgaiaNLLSTHPPIEARIAALERL 282
                                    **********999999877999****************************976 PP

>> Peptidase_M56  BlaR1 peptidase M56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.5   5.4e-09   1.9e-05     179     224 ..     116     161 ..      21     166 .. 0.81
   2 !    5.0   0.3    0.0033        12      26      62 ..     176     212 ..     158     257 .. 0.71

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 5.4e-09
                  Peptidase_M56 179 prIvlPadflkklsdeeleyillHElaHlkrkDllvnllvavlqcl 224
                                    +++ + + +l++l++ ele +l+HEl+H+k++D+ v  ++ +l+ +
  gi|116754163|ref|YP_843281.1| 116 SVVAVTTGLLRRLDKSELEAVLAHELSHIKNRDVAVMTIASFLSTV 161
                                    46677788999************************99999988765 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0033
                  Peptidase_M56  26 rllsaiaaYalWlivllallipfipesavslpvkfet 62 
                                    r  +  + +a+Wl+ l+  ++ fi+ +++s   +f++
  gi|116754163|ref|YP_843281.1| 176 RDRESGNLFAVWLVSLIVWIVSFILIRTLSRYREFSA 212
                                    4456677899999999999999999999984444433 PP

>> DUF2268  Predicted Zn-dependent protease (DUF2268)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0     2e-05     0.072      34      76 ..     101     144 ..      81     162 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2e-05
                        DUF2268  34 klieekgykgglaipdkiflfl.leneyskerlaallaHEyhHv 76 
                                    ++i++   +g+  +++ + ++  l +  +k++l+a+laHE+ H 
  gi|116754163|ref|YP_843281.1| 101 TDIPNAFATGRSQSSSVVAVTTgLLRRLDKSELEAVLAHELSHI 144
                                    56677777899999999999999********************6 PP

>> DUF4157  Domain of unknown function (DUF4157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.5   0.00024      0.88      55      74 ..     127     146 ..      98     151 .. 0.68
   2 ?   -1.1   0.0      0.65   2.3e+03      31      57 ..     153     179 ..     146     183 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00024
                        DUF4157  55 qpesaagrellaHELtHvvq 74 
                                    + ++++ +++laHEL+H+  
  gi|116754163|ref|YP_843281.1| 127 RLDKSELEAVLAHELSHIKN 146
                                    346777899********965 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.65
                        DUF4157  31 raaralgAqAfTlgndivfaageyqpe 57 
                                    + a+ l++ A  + ++i+f  ++ + e
  gi|116754163|ref|YP_843281.1| 153 TIASFLSTVASVIVQNIFFLGDRRDRE 179
                                    556667888889999***966665554 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   4.7      0.18   6.3e+02     388     430 ..      17      53 ..       6      72 .. 0.50
   2 ?    7.8   0.1   0.00035       1.2     152     235 ..     116     209 ..      93     245 .. 0.55

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.18
                        DUF2207 388 lgliilglilillallllvlllvfllilllillliaiivlllf 430
                                    +++++++++li++      + ++ +++ + +++li+ ++l++ 
  gi|116754163|ref|YP_843281.1|  17 TMFLLAAVYLIFIN-----V-IMAMGVGIQGVVLIMGLFLFIQ 53 
                                    22222222222221.....1.3444444444444444444443 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00035
                        DUF2207 152 gsvtftarnlppgeglevrvlf..ptn..narktsgnkldeilkeeqk..........ntreraarlslallillillli 217
                                    + v +t++ l+  +  e+++++  + +  ++r+   ++ +++l++ +            +r+r+  + +a++++++++ i
  gi|116754163|ref|YP_843281.1| 116 SVVAVTTGLLRRLDKSELEAVLahELShiKNRDVAVMTIASFLSTVASvivqnifflgDRRDRESGNLFAVWLVSLIVWI 195
                                    45566666666666667777774311235666666666666666666677776665544444444443333333333333 PP

                        DUF2207 218 lllllllllliklllwkk 235
                                    +     ++l+++l +++ 
  gi|116754163|ref|YP_843281.1| 196 V----SFILIRTLSRYRE 209
                                    3....3333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       895  (0.0499191); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); 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):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2019.18
//
Query:       gi|116754164|ref|YP_843282.1|  [L=161]
Description: 3-isopropylmalate dehydratase, small subunit [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-20   74.3   0.0    1.7e-20   73.7   0.0    1.4  1  Aconitase_C  Aconitase C-terminal domain


Domain annotation for each model (and alignments):
>> Aconitase_C  Aconitase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.7   0.0   9.5e-25   1.7e-20      60     123 ..      37      99 ..       9     105 .. 0.83

  Alignments for each domain:
  == domain 1  score: 73.7 bits;  conditional E-value: 9.5e-25
                                    EEHHHHHHHHHHTT--EEEE--SSBTBS---THHHHHHHHTTEEEEEES-B-HHHHHHHHHTT- CS
                    Aconitase_C  60 edvvdaaerykkegaklvviagknfGeGSSRehAAkalrllGikaviaeSFerIfennlikngl 123
                                    ++  d  +  k+++ +++v++ knfG+GSSRe+A++al+l Gi  ++a SF+rIf++n+i+ gl
  gi|116754164|ref|YP_843282.1|  37 MEGLDPSFSSKVQPGDVIVAG-KNFGCGSSREQAPLALKLAGISCIVARSFARIFYRNAINIGL 99 
                                    466677778888899988887.****************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); 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: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1234.75
//
Query:       gi|116754165|ref|YP_843283.1|  [L=276]
Description: hypothetical protein Mthe_0854 [Methanosaeta thermophila PT]
Scores for complete sequence (score 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   13.5   0.0      0.061   12.6   0.0    1.4  2  T4_neck-protein  Virus neck protein


Domain annotation for each model (and alignments):
>> T4_neck-protein  Virus neck protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   3.4e-06     0.061     121     192 ..       2      72 ..       1      86 [. 0.81
   2 ?   -3.9   0.0      0.37   6.6e+03     136     146 ..     161     171 ..     151     173 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.4e-06
                T4_neck-protein 121 inpklfkqqvdGkepkeGdliyfplanslfeiswveredpfyq...lGvlairkikatkfvysGeeinlekpeav 192
                                    i p+ +kq +  +ep+ Gd +yf  +   + is+  +e   y+    G   +r+ k   ++ sGeei  e pe v
  gi|116754165|ref|YP_843283.1|   2 IFPEDYKQIGVSREPRHGDPVYFATK---YLISYDGNEISIYRiesEGEGFMRRAKHVELLSSGEEI-AEYPEIV 72 
                                    679999*****************865...5566666666666522279999****************.8999944 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 0.37
                T4_neck-protein 136 keGdliyfpla 146
                                     +Gd +yfp  
  gi|116754165|ref|YP_843283.1| 161 FKGDDVYFPCR 171
                                    57999999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       228  (0.0127168); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 2005.13
//
Query:       gi|116754166|ref|YP_843284.1|  [L=323]
Description: isopropylmalate/isohomocitrate dehydrogenases [Methanosaeta thermophila PT]
Scores for complete 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-93  313.4   0.0    4.5e-93  312.2   0.0    1.5  1  Iso_dh    Isocitrate/isopropylmalate dehydrogenase


Domain annotation for each model (and alignments):
>> Iso_dh  Isocitrate/isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  312.2   0.0   2.5e-97   4.5e-93       1     348 []       3     313 ..       3     313 .. 0.97

  Alignments for each domain:
  == domain 1  score: 312.2 bits;  conditional E-value: 2.5e-97
                                    EEEEEEESTTHHHHHHHHHHHHHHHHHHHT-EEEEEE---THHHHHHHSSSS-HHHHHHHHHSSEEEEEE---CSSSSSS CS
                         Iso_dh   1 kiallegdgiGpevveaalkvlkaakekaglelefeevdvGgaaidetgeplpeetleaikeadvvllgavgtpkekevr 80 
                                    kial++gdgiGpev+++al+vl+aa      + e+ e+d+G    ++ g++++++ +e +k+ d +l+ga++tp + + r
  gi|116754166|ref|YP_843284.1|   3 KIALVPGDGIGPEVISSALRVLNAAG----FDGELVEFDIGYGRWRRDGKAITDDDIERMKDCDCILFGAITTPPDPGYR 78 
                                    79**********************99....456899***************************************99999 PP

                                    HHHHHHHHHHHTTEEEEEEEEE-BCCTTCCSSBTHHHHCT-EEEEEEE-SSCGGCSSEEEEETTG.GGGEEEEEEEEEHH CS
                         Iso_dh  81 pengLlaLrkeldlfanlrpvkvfeklkvksplkrevveevdlvivReltggiYfgeekekkgsifteevavdtklysee 160
                                    +    +++rkeldl+an+rp ++           r     +d++ivRe+t+g+Y+g e   ++      +a ++ +++++
  gi|116754166|ref|YP_843284.1|  79 SVL--IRIRKELDLYANIRPLRSS----------R-----IDVIIVRENTEGLYSGLEMLGDE------EARTVRVITRK 135
                                    976..9**************9998..........3.....8***************9987766......599******** PP

                                    HHHHHHHHHHHHHHHTTTSEEEEEESTTTTHHHHHHHHHHHHHHCCTTTTSEEEEEEHHHHHHHHHHSGGGGSEEEE-HH CS
                         Iso_dh 161 eieriaraafelAlkrgkkkvtlvdKanvlksselwrkiveevaeeeypdielehqlvDsaamqlvkspkqfdVivtkNl 240
                                    +++ria++a+ +A +r  k++t+++Kanvlks  l+ k++ evae    +i+++++lvD+aa+++v +p++fdV+vt+Nl
  gi|116754166|ref|YP_843284.1| 136 GSQRIAEVACRIASER--KHLTIIHKANVLKSDVLFLKTCREVAE--RYGIRYDDMLVDAAAYNMVIRPEMFDVMVTTNL 211
                                    **************99..9*************************9..668****************************** PP

                                    HHHHHHHHHHHHTTSGCC-EEEEEETSS-EEEEESS---CCCTTSS-S-THHHHHHHHHHHHHTTT-HHHHHHHHHHHHH CS
                         Iso_dh 241 fGDilSDeaaalvGslGllpSaslgekkvaifEavHGsapdiagkdkaNpiavilSaalmLryslgleeaAdkiekAvek 320
                                    fGDilSDe a +vGslGl +Sa+lg ++ a+fE++HGsapdiag ++aNp+++i Saa+mL+  +g+ e A+ i++Av++
  gi|116754166|ref|YP_843284.1| 212 FGDILSDEGAGIVGSLGLCASANLG-DRWALFEPIHGSAPDIAGNGIANPVGAIRSAAMMLEW-FGEMERAQSIHQAVDR 289
                                    *************************.79***********************************.**************** PP

                                    HHHHTSCCHHHCTTSTCCCHHHHHHHHH CS
                         Iso_dh 321 vleagivTkDlageaakevstsefgdav 348
                                    +l +g++T Dl+g      +tsef+dav
  gi|116754166|ref|YP_843284.1| 290 TLSKGVKTPDLGGLC----TTSEFTDAV 313
                                    *************99....*******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2301.68
//
Query:       gi|116754167|ref|YP_843285.1|  [L=558]
Description: oligopeptide/dipeptide ABC transporter, ATPase subunit [Methanosaeta thermophila PT]
Scores for 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  205.5   0.0    1.2e-30  106.8   0.0    2.2  2  ABC_tran         ABC transporter
    2.7e-23   82.3   0.1      1e-16   61.1   0.0    2.6  2  oligo_HPY        Oligopeptide/dipeptide transporter, C-termin
    1.3e-14   54.7   6.5    2.1e-05   24.5   0.1    4.1  4  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    2.7e-11   43.3   0.0      2e-05   24.1   0.0    2.7  2  SMC_N            RecF/RecN/SMC N terminal domain
      3e-09   37.2   7.0    0.00082   19.7   0.5    3.9  2  AAA_22           AAA domain
    1.1e-07   32.4   3.2     0.0032   17.9   0.1    2.7  2  AAA_16           AAA ATPase domain
    6.8e-06   26.1   2.3      0.032   14.2   0.1    2.8  2  NACHT            NACHT domain
      9e-06   25.4   4.4      0.016   14.8   0.9    3.4  2  AAA_25           AAA domain
    9.7e-06   25.2   1.0      0.072   12.8   0.1    2.4  2  AAA_29           P-loop containing region of AAA domain
    2.3e-05   24.3   0.2      0.068   13.1   0.0    2.5  2  RsgA_GTPase      RsgA GTPase
    2.6e-05   24.7   0.0      0.085   13.3   0.0    2.8  2  AAA              ATPase family associated with various cellul
    5.8e-05   22.2   0.1       0.08   11.8   0.0    2.2  2  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
    8.6e-05   22.3   0.0       0.32   10.7   0.0    2.3  2  AAA_24           AAA domain
    8.8e-05   21.8   0.1       0.38    9.9   0.2    2.6  2  NB-ARC           NB-ARC domain
    0.00012   21.9   2.7        1.1    8.9   0.0    3.9  4  IstB_IS21        IstB-like ATP binding protein
    0.00015   21.2   0.4      0.023   14.1   0.0    3.2  3  Mg_chelatase     Magnesium chelatase, subunit ChlI
    0.00043   20.3   0.4       0.26   11.3   0.0    2.3  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    0.00094   18.9   2.2       0.49   10.1   0.0    3.1  2  AAA_30           AAA domain
     0.0011   19.1   1.5        1.5    8.9   0.1    2.5  2  DUF87            Helicase HerA, central domain
     0.0011   18.3   0.0        1.4    8.2   0.0    2.3  2  ATPase           KaiC
     0.0014   18.0   0.2       0.78    9.0   0.0    2.5  2  Zeta_toxin       Zeta toxin
      0.002   17.3   0.0      0.018   14.2   0.0    2.0  2  G-alpha          G-protein alpha subunit
     0.0021   18.3   0.2        2.1    8.6   0.1    2.4  2  Roc              Ras of Complex, Roc, domain of DAPkinase
      0.003   17.4   0.7        1.3    8.9   0.1    2.8  2  MobB             Molybdopterin guanine dinucleotide synthesis
     0.0035   17.5   2.2        4.7    7.5   0.3    4.5  2  SbcCD_C          Putative exonuclease SbcCD, C subunit
     0.0037   17.3   0.1       0.55   10.2   0.0    2.8  2  AAA_5            AAA domain (dynein-related subfamily)
     0.0039   17.7   0.0        4.5    7.8   0.0    2.6  2  AAA_18           AAA domain
     0.0046   16.5   0.6        2.4    7.6   0.1    2.4  2  Pox_A32          Poxvirus A32 protein
     0.0065   17.0   1.1        1.2    9.6   0.2    2.3  2  AAA_23           AAA domain
     0.0084   15.6   0.2        1.9    8.0   0.0    2.3  2  AAA_7            P-loop containing dynein motor region
     0.0085   15.8   0.4          2    8.1   0.1    2.7  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
     0.0085   14.4   0.2        1.5    7.0   0.0    2.1  2  Myosin_head      Myosin head (motor domain)
     0.0088   16.1   2.4        5.8    7.1   0.1    4.5  4  HTH_20           Helix-turn-helix domain
  ------ inclusion threshold ------
      0.011   15.2   0.1         35    3.7   0.0    3.6  3  TniB             Bacterial TniB protein
      0.011   16.2   0.0        1.9    8.9   0.0    2.5  2  RNA_helicase     RNA helicase
      0.012   15.3   0.0        4.6    6.9   0.0    2.3  2  PRK              Phosphoribulokinase / Uridine kinase family
      0.015   15.0   0.0        3.4    7.3   0.0    2.4  2  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
      0.015   15.4   0.8        1.4    9.0   0.1    2.6  2  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
      0.015   15.0   1.3          2    8.1   0.0    3.1  3  Sigma54_activat  Sigma-54 interaction domain
      0.018   14.9   0.2        6.6    6.6   0.0    2.4  2  APS_kinase       Adenylylsulphate kinase
      0.027   13.9   0.1        5.3    6.4   0.0    2.4  2  PhoH             PhoH-like protein
      0.031   13.5   0.1        5.5    6.2   0.0    2.2  2  Septin           Septin
      0.042   14.0   7.0          2    8.6   0.2    3.5  3  AAA_33           AAA domain
      0.053   13.4   0.1        8.9    6.2   0.1    2.5  2  NTPase_1         NTPase
      0.058   12.2   0.2        2.2    7.0   0.0    2.2  2  DLIC             Dynein light intermediate chain (DLIC)
      0.061   13.4   0.1         15    5.7   0.0    2.5  2  MMR_HSR1         50S ribosome-binding GTPase
      0.069   12.9   0.6        4.3    7.1   0.1    2.8  2  DEAD             DEAD/DEAH box helicase
      0.084   12.7   0.0        1.1    9.1   0.0    2.6  2  TrkA_C           TrkA-C domain
      0.093   12.4   0.4          6    6.5   0.1    2.3  2  DUF188           Uncharacterized BCR, YaiI/YqxD family COG167
       0.12   12.7   0.2         22    5.4   0.0    3.1  3  AAA_19           AAA domain
       0.19   11.3   0.9         15    5.1   0.1    2.4  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
        0.3   10.8   0.0        1.5    8.5   0.0    2.1  2  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 !   96.8   0.0   4.2e-30   1.4e-27       1     137 []      17     171 ..      17     171 .. 0.88
   2 !  106.8   0.0   3.6e-33   1.2e-30       2     137 .]     322     470 ..     321     470 .. 0.85

  Alignments for each domain:
  == domain 1  score: 96.8 bits;  conditional E-value: 4.2e-30
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--.SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS..--S-TT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx....xxxxxxxxxxxxxxxx..xxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp.teGeilldgkdlke....qeleslrkeigvlpqe..pqlfpe 73 
                                    lk ++l l++g  +a+vGe+GaGK+tL   +++l     eGei +dg++l e    + ++    ++++++q+  + l+p 
  gi|116754167|ref|YP_843285.1|  17 LKGIDLRLERGDSLAVVGESGAGKTTLGLSIMRLAAAkLEGEIVFDGTNLLElsedEMRRLRGDRMAMVFQNveDALDPV 96 
                                    7899***********************999999987758***********999997777777889*******999***** PP

                                    SBHHHH...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    xxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  74 ltvren...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                    +t++e+           ++++  e+a++ l  ++l+ t+ +  p++LSgG++qrv +a+al+++p+ll+lDEpta
  gi|116754167|ref|YP_843285.1|  97 YTAEEQvceaiaahnrwNKSRIRERARALLTAVGLDGTRYRLYPHQLSGGERQRVLIAMALANDPELLILDEPTA 171
                                    ****99******9999744444566666666666666777777******************************97 PP

  == domain 2  score: 106.8 bits;  conditional E-value: 3.6e-33
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS..--S-TTSBHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxx RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe..pqlfpeltvren 79 
                                    ++vsl+l+ege++a+vGe+G+GK+tL+k+++g  +p++Geill+ +  +      + +++++++q+  +++  +l+v + 
  gi|116754167|ref|YP_843285.1| 322 SHVSLTLYEGETLALVGESGSGKTTLAKIIMGIIEPDSGEILLERERARW--DAGFYRRVQMIFQNpkESISHRLNVLQA 399
                                    689**************************************988665555..5677789*******65555666656666 PP

                                    ...........HHHTCHHHHHHHSTTGG..TTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    ...........xxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ...........esdeeiekalsklglke..lkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                                ++e+i+ a++ l++ e  ++ + +++ p++LSgG+ qrva+aral+ +pkll++DEpt+
  gi|116754167|ref|YP_843285.1| 400 vrepldvqrigSEEERIASAMKALENAElsTDPEFLRRYPHQLSGGEAQRVAIARALVMHPKLLIADEPTS 470
                                    9999*****9988888888888888888333556788999*****************************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 !   61.1   0.0     3e-19     1e-16       1      65 []     220     280 ..     220     280 .. 0.89
   2 !   18.6   0.0   5.8e-06     0.002       1      25 [.     521     545 ..     521     555 .. 0.93

  Alignments for each domain:
  == domain 1  score: 61.1 bits;  conditional E-value: 3e-19
                      oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                                    +E g++++l+++p+HPYT++Llrs+p+++  kd l++i+g+   +    +GCpF+pRC+++ e C
  gi|116754167|ref|YP_843285.1| 220 LEVGRTADLIRNPRHPYTRGLLRSFPSMNTTKD-LQGIPGR---TIPGISGCPFHPRCTQKIEVC 280
                                    699******************************.6666666...455666************999 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 5.8e-06
                      oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsv 25 
                                    vE+gps ++++ep+H+YT+ L+r++
  gi|116754167|ref|YP_843285.1| 521 VEEGPSGEVIREPAHRYTASLVRCA 545
                                    8*********************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 ?    2.3   0.0      0.35   1.2e+02       3      19 ..      31      47 ..      29      76 .. 0.79
   2 !   24.5   0.1   6.1e-08   2.1e-05     226     299 ..     132     201 ..      89     205 .. 0.82
   3 !    8.6   0.1    0.0042       1.4       3      28 ..     335     354 ..     334     381 .. 0.80
   4 !   20.2   0.3   1.2e-06   0.00042     235     301 ..     440     504 ..     402     506 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.35
                         AAA_21  3 vliGpNgsGKSnLLdal 19
                                   +++G  g+GK++L   +
  gi|116754167|ref|YP_843285.1| 31 AVVGESGAGKTTLGLSI 47
                                   68**********96555 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 6.1e-08
                         AAA_21 226 ngdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSp 299
                                    +g ++ l +++lS G ++   ++ al+ ++    ll++DEp ++L+    + ++ell+++++ ++  ++ TH+ 
  gi|116754167|ref|YP_843285.1| 132 DGTRYRLYPHQLSGGERQRVLIAMALANDP---ELLILDEPTASLDALTKADIVELLRSATSDRIS-LIITHDI 201
                                    6788999***********977777777777...9***********************999995555.5556665 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0042
                         AAA_21   3 vliGpNgsGKSnLLdaldllarldrd 28 
                                    +l+G  gsGK++L +++       + 
  gi|116754167|ref|YP_843285.1| 335 ALVGESGSGKTTLAKIIM------GI 354
                                    79**************93......33 PP

  == domain 4  score: 20.2 bits;  conditional E-value: 1.2e-06
                         AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHSpll 301
                                    ++lS G  +  a++ al   +   +ll+ DEp + L+P++++++l+ll ++ +r g  +++ TH+  l
  gi|116754167|ref|YP_843285.1| 440 HQLSGGEAQRVAIARALVMHP---KLLIADEPTSALDPSVQAKILRLLmDLQERMGLSILFITHDIAL 504
                                    555555555545555555444...79999****************9996666669*********9766 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 !   24.1   0.0   5.8e-08     2e-05      28     211 ..      31     213 ..      19     219 .. 0.73
   2 !   16.1   0.0   1.7e-05    0.0059      24     211 ..     331     514 ..     312     521 .. 0.73

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 5.8e-08
                                    EEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCC...CCCC--.BTTCSSTTEEEEEEEEEETTEE.SSSSSSCEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxx.xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx RF
                          SMC_N  28 aivGpNGSGKsnlldAilFvLGersakklrsekl...sdlihk.skekasvkkaeveitfdnedkk.lkiekeevsisrr 102
                                    a+vG+ G+GK+ l  +i   L    a kl  e +   ++l+   ++e +++   +++++f+n +++  ++ + e ++   
  gi|116754167|ref|YP_843285.1|  31 AVVGESGAGKTTLGLSI-MRLAA--A-KLEGEIVfdgTNLLELsEDEMRRLRGDRMAMVFQNVEDAlDPVYTAEEQVCEA 106
                                    799***********999.44443..2.44444331115566554677788888899999*99887753444444444444 PP

                                    EETTSE.EEEEETTEEE-H.HHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHH CS
                                    xxxxxx.xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 103 vkrkge.seykingkevtk.kevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkva 180
                                    +  +++ ++ +i ++     + v     + ++++++LSgGe++ v +a+ +A    +   l +lDe  a LD+   + ++
  gi|116754167|ref|YP_843285.1| 107 IAAHNRwNKSRIRERARALlTAVGLDGTRYRLYPHQLSGGERQRVLIAMALA----NDPELLILDEPTASLDALTKADIV 182
                                    44444437777766554444888888889999999*******9888887766....445699****************** PP

                                    HHHHHHCTTSEEEEE-SSHHHCCC-SCEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 181 ellkeksknaQfivislreemlekadklvgv 211
                                    ell++++++   ++i+++  + +  +k + v
  gi|116754167|ref|YP_843285.1| 183 ELLRSATSDRISLIITHDISLASALSKKIAV 213
                                    *********9999**9998887777666655 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.7e-05
                                    SSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTC.SSTTEEEEEEEEEETTEESSSSSSCEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  24 ksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskek.asvkkaeveitfdnedkklkiekeevsisrr 102
                                     +  a+vG+ GSGK+ l   i   +G      +  ++ + l+ +++++ ++    +v+++f+n++++    ++++++ + 
  gi|116754167|ref|YP_843285.1| 331 GETLALVGESGSGKTTLAKII---MGI-----IEPDSGEILLERERARwDAGFYRRVQMIFQNPKES---ISHRLNVLQA 399
                                    456789***********9998...894.....566778888887333303334568********999...3444444444 PP

                                    EETTSEEEEEETTEEE-HHHHHHHHHCTT-STT.........CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-H CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 103 vkrkgeseykingkevtkkevsellesagiske.........lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDe 173
                                    v +  +   +i  +e + +  ++ le+a++s +         +LSgGe + va+a  + ++      l + De  +aLD 
  gi|116754167|ref|YP_843285.1| 400 VREPLD-VQRIGSEEERIASAMKALENAELSTDpeflrryphQLSGGEAQRVAIARALVMHP----KLLIADEPTSALDP 474
                                    433333.55677777777888888888888888888888888*******9999987765553....48899********* PP

                                    HHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC-SCEEEE CS
                                    xxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 174 knvkkvaellkekskn..aQfivislreemlekadklvgv 211
                                    +  +k+ +ll   +++    ++ i+++  + +k++  + v
  gi|116754167|ref|YP_843285.1| 475 SVQAKILRLLMDLQERmgLSILFITHDIALARKVSDRIAV 514
                                    **********988777335677788877777776655555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   1.1   4.7e-05     0.016       5     115 ..      27     188 ..      23     212 .. 0.64
   2 !   19.7   0.5   2.4e-06   0.00082       8     129 ..     334     499 ..     329     506 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.7e-05
                         AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee............................................erp 40 
                                      +l+v+GesG+GKTtl   +++ +   ak e                                             +  
  gi|116754167|ref|YP_843285.1|  27 GDSLAVVGESGAGKTTLGLSIMRLAA--AKLEGeivfdgtnllelsedemrrlrgdrmamvfqnvedaldpvytaeeQVC 104
                                    6789**************99999984..3444456888888888888888888887777777777777777776433222 PP

                         AAA_22  41 evv.fvtlpsstsskdllrellralglelkaerlsseell.ealeqalrarav....ielliiDEaqh.lr...seeale 110
                                    e +   +  +++  ++ +r+ll a+gl++ ++rl  ++l     ++ l a  +    +elli+DE    l+   +++++e
  gi|116754167|ref|YP_843285.1| 105 EAIaAHNRWNKSRIRERARALLTAVGLDGTRYRLYPHQLSgGERQRVLIAM-AlandPELLILDEPTAsLDaltKADIVE 183
                                    222344444444666666666666666666655555555533333333333.2477789999999777676654477777 PP

                         AAA_22 111 eLrsl 115
                                     Lrs 
  gi|116754167|ref|YP_843285.1| 184 LLRSA 188
                                    77554 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 2.4e-06
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee...............erpevvfvtlpsst.sskdllrellralglelka. 70 
                                    l+++GesG+GKTtl++ ++   + +    e               +r++ +f ++++s   + ++l+++ + l++++ + 
  gi|116754167|ref|YP_843285.1| 334 LALVGESGSGKTTLAKIIMGIIEPD--SGEillererarwdagfyRRVQMIFQNPKESIsHRLNVLQAVREPLDVQRIGs 411
                                    799**************99987432..22244566777766666444444444444443444444555555555555559 PP

                         AAA_22  71 .............................erlsseellealeqalraravielliiDEaqh.lr...seealeeLrslln 117
                                                                 +    e+ + a+++al  + +  lli DE    l+   ++++l+ L +l++
  gi|116754167|ref|YP_843285.1| 412 eeeriasamkalenaelstdpeflrryphQLSGGEAQRVAIARALVMHPK--LLIADEPTSaLDpsvQAKILRLLMDLQE 489
                                    9999********99998888888776554444444444555666666655..********99987444888888888888 PP

                         AAA_22 118 lsrkgvqliLvG 129
                                      r g++++++ 
  gi|116754167|ref|YP_843285.1| 490 --RMGLSILFIT 499
                                    ..****997764 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.8   0.00015     0.052      23     107 ..      26     139 ..      15     214 .. 0.51
   2 !   17.9   0.1   9.2e-06    0.0032      24     164 ..     331     490 ..     321     498 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00015
                         AAA_16  23 rpelvllsGesGvGKsslvrellralekd..........................ggiflrgkcdqlesaipy....... 69 
                                    r+ ++ ++GesG GK++l  +++r + ++                          ++               +       
  gi|116754167|ref|YP_843285.1|  26 RGDSLAVVGESGAGKTTLGLSIMRLAAAKlegeivfdgtnllelsedemrrlrgdRMA--------------Mvfqnved 91 
                                    446899*************999987777766544444333333333333333332111..............11122222 PP

                         AAA_16  70 ..salaqalareellrqllde...aesaeleawrekleeala...........a 107
                                      +++ +a   e+++++++++         ++ re+ ++ l+            
  gi|116754167|ref|YP_843285.1|  92 alDPVYTAE--EQVCEAIAAHnrwN----KSRIRERARALLTavgldgtryrlY 139
                                    114444444..36666666663222....3333333333333333555555551 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 9.2e-06
                         AAA_16  24 pelvllsGesGvGKsslvrellralekd...................ggiflrgkcdqlesaipysalaqalareellrq 84 
                                    +e + l+GesG+GK++l++ ++  +e d                   ++  + ++ +++    +++ ++qa  re l  q
  gi|116754167|ref|YP_843285.1| 331 GETLALVGESGSGKTTLAKIIMGIIEPDsgeillererarwdagfyrRVQMIFQNPKES--ISHRLNVLQAV-REPLDVQ 407
                                    47899******************999998888888887777655543333355555554..23334477777.4455555 PP

                         AAA_16  85 lldeaesaeleawrekleeala........avpelagaeasrllellkrllallsrderplvlvlDdlqwadeaslql.. 154
                                        +e++ ++a ++   ++l+           +l+g ea+r++ + ++l+       +p +l+ D+   a + s q+  
  gi|116754167|ref|YP_843285.1| 408 RIGSEEERIASAMKALENAELStdpeflrrYPHQLSGGEAQRVAIA-RALV------MHPKLLIADEPTSALDPSVQAki 480
                                    4444444455544444444444444444442224444444443333.1111......23444444444433332222223 PP

                         AAA_16 155 laaLlrlles 164
                                    l++L++l+e+
  gi|116754167|ref|YP_843285.1| 481 LRLLMDLQER 490
                                    5555555555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.4    0.0009      0.31       3      27 ..      30      54 ..      28     199 .. 0.86
   2 !   14.2   0.1   9.2e-05     0.032       2      21 ..     333     352 ..     332     361 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0009
                                   EEEEC-TTTCHHHHHHHHHHHHCTS CS
                          NACHT  3 vilqGeaGsGKTtLlqklalawaeg 27
                                   +++ Ge+G GKTtL  ++++++a++
  gi|116754167|ref|YP_843285.1| 30 LAVVGESGAGKTTLGLSIMRLAAAK 54
                                   689***************9988765 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 9.2e-05
                                    CEEEEC-TTTCHHHHHHHHH CS
                          NACHT   2 lvilqGeaGsGKTtLlqkla 21 
                                    +++l Ge+GsGKTtL++ ++
  gi|116754167|ref|YP_843285.1| 333 TLALVGESGSGKTTLAKIIM 352
                                    789************99887 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.9   4.6e-05     0.016      29     117 ..      23     139 ..      13     197 .. 0.60
   2 !    8.9   0.1    0.0029      0.99      30      50 ..     328     348 ..     323     352 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.6e-05
                         AAA_25  29 llpagelallaGapgtGKttlaldlalava...tGkpwlgpvapeqgkVlyvsaEdsedelr.rRlravgeal....... 97 
                                     l +g+  +++G +g+GKttl l+++   a   +G+ +++       + l +s Ed   +lr  R++ v++++       
  gi|116754167|ref|YP_843285.1|  23 RLERGDSLAVVGESGAGKTTLGLSIMRLAAaklEGEIVFD-----GTNLLELS-EDEMRRLRgDRMAMVFQNVedaldpv 96 
                                    688999*****************99887774545555555.....44555555.44433555566666666663333333 PP

                         AAA_25  98 ........................rddarllvldlagveslpLf 117
                                                            r++a l+++ l+g ++ +L+
  gi|116754167|ref|YP_843285.1|  97 ytaeeqvceaiaahnrwnksrireRARALLTAVGLDG-TRYRLY 139
                                    3322222222255555555555444344444444444.355554 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0029
                         AAA_25  30 lpagelallaGapgtGKttla 50 
                                    l +ge+ +l+G +g+GKttla
  gi|116754167|ref|YP_843285.1| 328 LYEGETLALVGESGSGKTTLA 348
                                    56899**************98 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.1     0.001      0.35      16      38 ..      21      43 ..      15      54 .. 0.82
   2 !   12.8   0.1   0.00021     0.072      20      38 ..     329     347 ..     316     359 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.001
                         AAA_29 16 tieidlkgatlltGpsGsGKSTl 38
                                   ++++++ ++  ++G+sG+GK+Tl
  gi|116754167|ref|YP_843285.1| 21 DLRLERGDSLAVVGESGAGKTTL 43
                                   56677666999***********8 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00021
                         AAA_29  20 dlkg.atlltGpsGsGKSTl 38 
                                      +g +  l+G+sGsGK+Tl
  gi|116754167|ref|YP_843285.1| 329 Y-EGeTLALVGESGSGKTTL 347
                                    3.344889***********9 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0048       1.7      91     116 ..      18      44 ..       3      59 .. 0.77
   2 !   13.1   0.0    0.0002     0.068      97     130 ..     329     362 ..     311     371 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0048
                                    HHHHHHCTT.SEEEEECSTTSSHHHHH CS
                    RsgA_GTPase  91 eelkellkd.ktsvlvGqSGvGKStLi 116
                                    + +  +l+  +  ++vG+SG+GK+tL 
  gi|116754167|ref|YP_843285.1|  18 KGIDLRLERgDSLAVVGESGAGKTTLG 44 
                                    55556666558899***********95 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.0002
                                    CTTSEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                    RsgA_GTPase  97 lkdktsvlvGqSGvGKStLinallpelelktgev 130
                                     +++t +lvG+SG GK+tL + +++  e   ge+
  gi|116754167|ref|YP_843285.1| 329 YEGETLALVGESGSGKTTLAKIIMGIIEPDSGEI 362
                                    4569****************99988766666665 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 !    8.5   0.0    0.0075       2.6       3      54 ..      32      90 ..      30     168 .. 0.80
   2 !   13.3   0.0   0.00025     0.085       2      55 ..     335     388 ..     334     399 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0075
                                   EESSTTSSHHHHHHHHHHHH...........THEEEEEETTTCSSSSTTHHHHHHHHHHHHHH CS
                            AAA  3 lyGppGtGKTllakavakel...........gvefleisgsellskyvgesekkirelfkeak 54
                                   ++G  G GKT+l  ++++ +           g+++le+s  e++      + ++++++f++++
  gi|116754167|ref|YP_843285.1| 32 VVGESGAGKTTLGLSIMRLAaaklegeivfdGTNLLELSEDEMR----RLRGDRMAMVFQNVE 90
                                   79**************9997554454444444667777776666....566666667776654 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00025
                                    EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHH CS
                            AAA   2 llyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeake 55 
                                     l+G  G GKT+lak ++  ++ +  ei + + +  +     ++++++f++ ke
  gi|116754167|ref|YP_843285.1| 335 ALVGESGSGKTTLAKIIMGIIEPDSGEILLERERARWDAGFYRRVQMIFQNPKE 388
                                    599***************999888777777777777888888888888887655 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 !    7.9   0.1    0.0036       1.2      18      52 ..      30      64 ..      17      67 .. 0.88
   2 !   11.8   0.0   0.00023      0.08      15      94 ..     331     410 ..     321     416 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0036
                  TrwB_AAD_bind 18 ilivGttGsGKtqalekllrairargdraivlDlt 52
                                   +++vG  G+GKt+   +++r + a+ +  iv+D t
  gi|116754167|ref|YP_843285.1| 30 LAVVGESGAGKTTLGLSIMRLAAAKLEGEIVFDGT 64
                                   5789*****************************65 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00023
                  TrwB_AAD_bind  15 tqhilivGttGsGKtqalekllrairargdraivlDltGafvsrfydegkdillnPlDaRsaaWsvfaeikeksdfaeiA 94 
                                     + +++vG  GsGKt+ ++ ++  i+     ++         + fy+  + i  nP ++ s++ +v++ ++e+ d+++i 
  gi|116754167|ref|YP_843285.1| 331 GETLALVGESGSGKTTLAKIIMGIIEPDSGEILLERERARWDAGFYRRVQMIFQNPKESISHRLNVLQAVREPLDVQRIG 410
                                    566789*********98888887777777777777777888899*****99***********************999985 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0    0.0022      0.77       4      23 ..      29      55 ..      26     110 .. 0.69
   2 !   10.7   0.0   0.00092      0.32       4      22 ..     333     351 ..     330     372 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0022
                         AAA_24  4 kiliyGpsgiGKTtlakel.......g 23
                                   +++++G+sg+GKTtl +++        
  gi|116754167|ref|YP_843285.1| 29 SLAVVGESGAGKTTLGLSImrlaaakL 55
                                   689************998844444441 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00092
                         AAA_24   4 kiliyGpsgiGKTtlakel 22 
                                     ++++G+sg+GKTtlak +
  gi|116754167|ref|YP_843285.1| 333 TLALVGESGSGKTTLAKII 351
                                    5799************966 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    0.0022      0.74      21      84 ..      28      94 ..      14     113 .. 0.70
   2 !    9.9   0.2    0.0011      0.38      22      40 ..     333     351 ..     321     356 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0022
                                   EEEEEEESTTSSHHHHHHHHCCSH.CCCCC..CBTEEEEEEEESXXHHHHHHHXXHHHHHCCCTTSS CS
                         NB-ARC 21 lvvalvGmgGvGKttlakqilnks.deveg..rFdsvawvvvsktdkseeiletilkeLslseddle 84
                                   + +a+vG  G GKttl  +i++   +++eg   Fd+   + +s+  + +   ++++ ++++ ed l+
  gi|116754167|ref|YP_843285.1| 28 DSLAVVGESGAGKTTLGLSIMRLAaAKLEGeiVFDGTNLLELSEDEMRRLRGDRMAMVFQNVEDALD 94
                                   4689************999998531556665578888888888777776666666666666655554 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0011
                                    EEEEEESTTSSHHHHHHHH CS
                         NB-ARC  22 vvalvGmgGvGKttlakqi 40 
                                     +alvG  G+GKttlak i
  gi|116754167|ref|YP_843285.1| 333 TLALVGESGSGKTTLAKII 351
                                    689*************977 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0    0.0033       1.1      44      80 ..      24      61 ..      16      90 .. 0.77
   2 ?    3.1   0.1      0.21        72     106     152 ..     158     204 ..     142     212 .. 0.79
   3 ?    6.8   0.1     0.015       5.2      46      65 ..     330     349 ..     321     355 .. 0.88
   4 ?   -0.8   0.0       3.1   1.1e+03     103     141 ..     454     491 ..     442     506 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0033
                      IstB_IS21 44 iekkenivllGpsGvGKshlaialgvea.vraglsvlf 80
                                   +e+ ++++++G sG+GK+ l  ++ + a ++ + +++f
  gi|116754167|ref|YP_843285.1| 24 LERGDSLAVVGESGAGKTTLGLSIMRLAaAKLEGEIVF 61
                                   578899**************999876440445555555 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.21
                      IstB_IS21 106 llkvdllilDdlgllpldqaeaellfeviek.ryerrsiiitsnlpfa 152
                                       ++llilD+  +  ld   ++++ e++ +   +r s+iit ++++a
  gi|116754167|ref|YP_843285.1| 158 ANDPELLILDEP-TASLDALTKADIVELLRSaTSDRISLIITHDISLA 204
                                    45679******6.568999999999999965157899*****998876 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.015
                      IstB_IS21  46 kkenivllGpsGvGKshlai 65 
                                    + e ++l+G sG GK+ la 
  gi|116754167|ref|YP_843285.1| 330 EGETLALVGESGSGKTTLAK 349
                                    56899*************96 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 3.1
                      IstB_IS21 103 lkrllkvdllilDdlgllpldqaeaellfeviekryerr 141
                                     + +++++lli D+  +  ld   ++++++++ +  er 
  gi|116754167|ref|YP_843285.1| 454 RALVMHPKLLIADEP-TSALDPSVQAKILRLLMDLQERM 491
                                    344567799999996.46677777777777777666664 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.19        66      22      49 ..      27      54 ..       9      75 .. 0.79
   2 !   14.1   0.0   6.7e-05     0.023      22      65 ..     331     374 ..     317     394 .. 0.75
   3 ?   -0.3   0.0       1.7     6e+02     119     135 ..     393     409 ..     387     423 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.19
                   Mg_chelatase 22 gHnlllvGppGsGKtmlakrlpsllppl 49
                                   g +l +vG +G+GKt l   ++ l ++ 
  gi|116754167|ref|YP_843285.1| 27 GDSLAVVGESGAGKTTLGLSIMRLAAAK 54
                                   567899***********98888876654 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 6.7e-05
                   Mg_chelatase  22 gHnlllvGppGsGKtmlakrlpsllpplseeealevakiasvag 65 
                                    g  l lvG +GsGKt lak +++++ p s e  le ++ +  ag
  gi|116754167|ref|YP_843285.1| 331 GETLALVGESGSGKTTLAKIIMGIIEPDSGEILLERERARWDAG 374
                                    56789********************9999998888877665555 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.7
                   Mg_chelatase 119 krkvlevLRePledgev 135
                                    + +vl+++RePl+ +++
  gi|116754167|ref|YP_843285.1| 393 RLNVLQAVREPLDVQRI 409
                                    5689********99887 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1      0.02         7      19      41 ..      27      49 ..      13      59 .. 0.77
   2 !   11.3   0.0   0.00076      0.26      18      40 ..     328     352 ..     312     359 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.02
                                   TEEEEEEESTTSSHHHHHHHHHH CS
                           TsaE 19 gdvilLeGdLGaGKTtlvrglak 41
                                   gd ++  G+ GaGKTtl  ++++
  gi|116754167|ref|YP_843285.1| 27 GDSLAVVGESGAGKTTLGLSIMR 49
                                   778999**********9877776 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00076
                                    H..TEEEEEEESTTSSHHHHHHHHH CS
                           TsaE  18 l..gdvilLeGdLGaGKTtlvrgla 40 
                                    l  g++++L G+ G+GKTtl++ ++
  gi|116754167|ref|YP_843285.1| 328 LyeGETLALVGESGSGKTTLAKIIM 352
                                    134788***************9886 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   1.2     0.022       7.5      20      50 ..      29      60 ..      20     201 .. 0.76
   2 !   10.1   0.0    0.0014      0.49      19      96 ..     332     467 ..     322     498 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.022
                         AAA_30 20 vavltGpAGtGKttalkalreaweaa.ggrvi 50
                                     +++G  G+GKtt+  ++ ++++a+ +g+++
  gi|116754167|ref|YP_843285.1| 29 SLAVVGESGAGKTTLGLSIMRLAAAKlEGEIV 60
                                   46799*********988886666666555554 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0014
                         AAA_30  19 rvavltGpAGtGKttalkalreaweaa.g..................grviglAptgkaAkvLa...........eelgi 68 
                                     + +l+G  G+GKtt+ k +  ++e + g                   ++i   p++  +++L+           + +g 
  gi|116754167|ref|YP_843285.1| 332 ETLALVGESGSGKTTLAKIIMGIIEPDsGeillererarwdagfyrrVQMIFQNPKESISHRLNvlqavrepldvQRIGS 411
                                    37789***************999998855666666666666666655555555666666666665555555555545555 PP

                         AAA_30  69 eastiakllkrlk............................grarlepgtllivDE 96 
                                    e ++ia+ +k+l+                            +ra + + +lli DE
  gi|116754167|ref|YP_843285.1| 412 EEERIASAMKALEnaelstdpeflrryphqlsggeaqrvaiARALVMHPKLLIADE 467
                                    55555555555555555555555555555555655555555434444445555555 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   0.1    0.0048       1.7      25      56 ..      29      60 ..      19      65 .. 0.85
   2 !    8.9   0.1    0.0043       1.5      26      44 ..     334     352 ..     327     364 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0048
                          DUF87 25 HlAilgsTGsGKSntvavLleellekkgatil 56
                                   +lA++g++G+GK+++  ++++ +++k  ++i+
  gi|116754167|ref|YP_843285.1| 29 SLAVVGESGAGKTTLGLSIMRLAAAKLEGEIV 60
                                   68**************9999999977766654 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0043
                          DUF87  26 lAilgsTGsGKSntvavLl 44 
                                    lA +g++GsGK++++++++
  gi|116754167|ref|YP_843285.1| 334 LALVGESGSGKTTLAKIIM 352
                                    799*********9999875 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0052       1.8      16      38 ..      24      46 ..      15      61 .. 0.83
   2 !    8.2   0.0    0.0041       1.4      16      37 ..     328     349 ..     316     425 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0052
                         ATPase 16 ipegrvvlitGepGtGKtifalq 38
                                   + +g +  ++Ge+G+GKt+++l 
  gi|116754167|ref|YP_843285.1| 24 LERGDSLAVVGESGAGKTTLGLS 46
                                   6789999*************986 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0041
                         ATPase  16 ipegrvvlitGepGtGKtifal 37 
                                    ++eg++  ++Ge+G+GKt++a+
  gi|116754167|ref|YP_843285.1| 328 LYEGETLALVGESGSGKTTLAK 349
                                    68999**************996 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0023      0.78      15      58 ..      26      78 ..      14     115 .. 0.74
   2 ?    6.3   0.1     0.015       5.1      20      47 ..     335     362 ..     332     392 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0023
                     Zeta_toxin 15 rPklillgGqpGAGKsel....aellkdele.....rqgnvvrldpDdlRelh 58
                                   r +++ ++G +GAGK++l    ++l++++le      + n ++l++D++R+l 
  gi|116754167|ref|YP_843285.1| 26 RGDSLAVVGESGAGKTTLglsiMRLAAAKLEgeivfDGTNLLELSEDEMRRLR 78
                                   55677899********9644435666666666677899999999999999986 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.015
                     Zeta_toxin  20 llgGqpGAGKselaellkdelerqgnvv 47 
                                     l+G +G+GK++la+ +   +e++++ +
  gi|116754167|ref|YP_843285.1| 335 ALVGESGSGKTTLAKIIMGIIEPDSGEI 362
                                    589***********99877666555555 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0       0.6   2.1e+02      25      50 ..      29      54 ..      14     180 .. 0.74
   2 !   14.2   0.0   5.3e-05     0.018      25      96 ..     333     415 ..     321     489 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.6
                                   EEEEEESTTSSHHHHHHHHHHHCS-- CS
                        G-alpha 25 kllllGqseSGKsTilkqlkllykkg 50
                                   +l ++G+s+ GK+T+  ++ +l   +
  gi|116754167|ref|YP_843285.1| 29 SLAVVGESGAGKTTLGLSIMRLAAAK 54
                                   57789999999*99966655555444 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 5.3e-05
                                    EEEEEESTTSSHHHHHHHHH.HHCS--....--HHHHHCCHH.......HHHHHHHHHHHHHHHHHHHTT.......... CS
                        G-alpha  25 kllllGqseSGKsTilkqlk.llykkg....fseeelatwra.......viqlnivrsiktilealesleselsesf... 89 
                                    +l l+G+s+SGK+T+ k +  +++ +       e+e+a w a       +i++n  +si++ l+ l+   ++l+ +    
  gi|116754167|ref|YP_843285.1| 333 TLALVGESGSGKTTLAKIIMgIIE-PDsgeiLLERERARWDAgfyrrvqMIFQNPKESISHRLNVLQAVREPLDVQRigs 411
                                    588***************995555.54488867777888999999999999***99999999999999777774444333 PP

                                    HHHC-SS CS
                        G-alpha  90 elqelke 96 
                                    e    ++
  gi|116754167|ref|YP_843285.1| 412 E---EER 415
                                    1...222 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 ?    7.4   0.0     0.014       4.8       2      21 ..      30      49 ..      29      77 .. 0.85
   2 !    8.6   0.1     0.006       2.1       2      20 ..     334     352 ..     333     359 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.014
                                   EEEESSTTSSHHHHHHCHCT CS
                            Roc  2 vvlvGdsgvGKtsllkrfve 21
                                   + +vG+sg+GKt+l  ++++
  gi|116754167|ref|YP_843285.1| 30 LAVVGESGAGKTTLGLSIMR 49
                                   579***********888876 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.006
                                    EEEESSTTSSHHHHHHCHC CS
                            Roc   2 vvlvGdsgvGKtsllkrfv 20 
                                    + lvG+sg+GKt+l+k ++
  gi|116754167|ref|YP_843285.1| 334 LALVGESGSGKTTLAKIIM 352
                                    679***********98665 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1      0.03        10       2      19 ..      30      47 ..      29      56 .. 0.80
   2 !    8.9   0.1    0.0038       1.3       2      20 ..     334     352 ..     333     361 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.03
                           MobB  2 lgivgksgsGKTtLlekl 19
                                   l++vg sg+GKTtL   +
  gi|116754167|ref|YP_843285.1| 30 LAVVGESGAGKTTLGLSI 47
                                   789**********96554 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0038
                           MobB   2 lgivgksgsGKTtLlekli 20 
                                    l++vg sgsGKTtL + ++
  gi|116754167|ref|YP_843285.1| 334 LALVGESGSGKTTLAKIIM 352
                                    789***********87665 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.3     0.014       4.7      33      89 ..     143     186 ..     132     187 .. 0.73
   2 ?    4.5   0.0      0.12        41      26      86 ..     435     482 ..     413     486 .. 0.60

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.014
                        SbcCD_C  33 lSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                    lSGGe+q +    +a+al           ++++l++LDE  ++lD+ + a ++ell+
  gi|116754167|ref|YP_843285.1| 143 LSGGERQRV---LIAMAL----------ANDPELLILDEPTASLDALTKADIVELLR 186
                                    666666322...222222..........24689*************99999999987 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.12
                        SbcCD_C  26 lsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatlle 86 
                                    l+r   +lSGGe+q    +a+a al++          +++l++ DE  s lD+  +a++l+
  gi|116754167|ref|YP_843285.1| 435 LRRYPHQLSGGEAQR---VAIARALVM----------HPKLLIADEPTSALDPSVQAKILR 482
                                    566667888888854...333333322..........244556666666666666666655 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 ?    4.0   0.1      0.13        46       3      23 ..      31      51 ..      29      62 .. 0.80
   2 !   10.2   0.0    0.0016      0.55       3      23 ..     335     355 ..     333     379 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.13
                                   EEE--SSSSHHHHHHHGGGGB CS
                          AAA_5  3 lLvGppGtgKselaerlaaal 23
                                    +vG++G gK++l  ++ ++ 
  gi|116754167|ref|YP_843285.1| 31 AVVGESGAGKTTLGLSIMRLA 51
                                   579**********88877765 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0016
                                    EEE--SSSSHHHHHHHGGGGB CS
                          AAA_5   3 lLvGppGtgKselaerlaaal 23 
                                     LvG++G+gK++la+ +   +
  gi|116754167|ref|YP_843285.1| 335 ALVGESGSGKTTLAKIIMGII 355
                                    69************9988777 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0      0.02       6.8       3      66 ..      32      91 ..      30     130 .. 0.58
   2 ?    7.8   0.0     0.013       4.5       3      18 ..     336     351 ..     334     388 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.02
                         AAA_18  3 ltGtpGvGKttlakeLskrlgf...gvnlrdvakenglllevdpealdeskrldedkldklldalee 66
                                   + G +G+GKttl+  + ++ +    g    ++++++  lle  ++   e +rl+ d+++ +++++e 
  gi|116754167|ref|YP_843285.1| 32 VVGESGAGKTTLGLSIMRLAAAkleG----EIVFDGTNLLELSED---EMRRLRGDRMAMVFQNVED 91
                                   7899*********9997774222332....333332222222222...4555555555555555544 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.013
                         AAA_18   3 ltGtpGvGKttlakeL 18 
                                    l G +G+GKttlak +
  gi|116754167|ref|YP_843285.1| 336 LVGESGSGKTTLAKII 351
                                    7899*********987 PP

>> Pox_A32  Poxvirus A32 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.013       4.6      15      36 ..      29      50 ..      22      61 .. 0.86
   2 !    7.6   0.1     0.007       2.4      16      31 ..     334     349 ..     326     357 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.013
                        Pox_A32 15 rlalvGgsGsGktvyLlsLlrt 36
                                    la+vG+sG+Gkt+  ls++r 
  gi|116754167|ref|YP_843285.1| 29 SLAVVGESGAGKTTLGLSIMRL 50
                                   589***********99999875 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.007
                        Pox_A32  16 lalvGgsGsGktvyLl 31 
                                    lalvG+sGsGkt+  +
  gi|116754167|ref|YP_843285.1| 334 LALVGESGSGKTTLAK 349
                                    89**********9654 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.055        19      23      35 ..      31      43 ..      14      47 .. 0.87
   2 !    9.6   0.2    0.0034       1.2      11      39 ..     322     351 ..     312     355 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.055
                         AAA_23 23 lItGpNGaGKTTi 35
                                   +++G+ GaGKTT+
  gi|116754167|ref|YP_843285.1| 31 AVVGESGAGKTTL 43
                                   679*********8 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0034
                         AAA_23  11 rdqeidF.skgltlItGpNGaGKTTildAi 39 
                                    +++++ + +    +++G+ G+GKTT+   i
  gi|116754167|ref|YP_843285.1| 322 SHVSLTLyEGETLALVGESGSGKTTLAKII 351
                                    556666644445589**********98766 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 ?    5.3   0.0     0.036        12      28      54 ..      22      48 ..      18      58 .. 0.82
   2 !    8.0   0.0    0.0055       1.9      28      55 ..     326     353 ..     319     363 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.036
                          AAA_7 28 lllknkkpvllvGptGtGKtviikdll 54
                                   l l+++ ++ +vG++G GKt++  +++
  gi|116754167|ref|YP_843285.1| 22 LRLERGDSLAVVGESGAGKTTLGLSIM 48
                                   6678889999**********9877665 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0055
                          AAA_7  28 lllknkkpvllvGptGtGKtviikdllk 55 
                                    l l ++  + lvG++G+GKt+++k ++ 
  gi|116754167|ref|YP_843285.1| 326 LTLYEGETLALVGESGSGKTTLAKIIMG 353
                                    5667788899***********9987765 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.062        21       5      21 ..      31      47 ..      28      73 .. 0.77
   2 !    8.1   0.1    0.0058         2       5      22 ..     335     352 ..     332     356 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.062
                      PduV-EutP  5 lliGkvgsGKttLtqal 21
                                    ++G++g+GKttL  ++
  gi|116754167|ref|YP_843285.1| 31 AVVGESGAGKTTLGLSI 47
                                   589**********7665 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0058
                      PduV-EutP   5 lliGkvgsGKttLtqalk 22 
                                     l+G++gsGKttL++ + 
  gi|116754167|ref|YP_843285.1| 335 ALVGESGSGKTTLAKIIM 352
                                    69***********99875 PP

>> Myosin_head  Myosin head (motor domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0042       1.5      85     111 ..      27      53 ..      21      66 .. 0.84
   2 ?    5.3   0.1     0.014       4.9      87     107 ..     333     353 ..     326     360 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0042
                                    EEEEEEESSTTSSHHHHHHHHHHHHHH CS
                    Myosin_head  85 nqsilisGEsGAGKteatKkvlqylas 111
                                      s+ + GEsGAGKt     +++  a+
  gi|116754167|ref|YP_843285.1|  27 GDSLAVVGESGAGKTTLGLSIMRLAAA 53 
                                    568999**********99999987665 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.014
                                    EEEEESSTTSSHHHHHHHHHH CS
                    Myosin_head  87 silisGEsGAGKteatKkvlq 107
                                    ++ + GEsG GKt  +K ++ 
  gi|116754167|ref|YP_843285.1| 333 TLALVGESGSGKTTLAKIIMG 353
                                    56678**************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 ?    3.7   0.0      0.19        64      14      50 ..      88     127 ..      83     131 .. 0.86
   2 ?   -0.1   0.0         3     1e+03      45      58 ..     173     186 ..     170     189 .. 0.86
   3 ?   -0.6   0.0       4.1   1.4e+03      37      50 ..     386     399 ..     382     410 .. 0.77
   4 ?    7.1   0.1     0.017       5.8       3      58 ..     468     525 ..     466     528 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.19
                                    HHHHHH...STCTTB-HHHHHHHHTS-HHHHHHHHHHHHH CS
                         HTH_20  14 rilraL...araegltaselaerldlskntlsyHLrvLee 50 
                                     +++aL    +ae++ ++++a+  ++ k+ ++ + r+L  
  gi|116754167|ref|YP_843285.1|  88 NVEDALdpvYTAEEQVCEAIAAHNRWNKSRIRERARALLT 127
                                    67888888899***********************999976 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 3
                                    HHHHHHCTTEEEEC CS
                         HTH_20  45 LrvLeeagLvevvr 58 
                                    L++L +a++ve+ r
  gi|116754167|ref|YP_843285.1| 173 LDALTKADIVELLR 186
                                    789*******9876 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 4.1
                                    -HHHHHHHHHHHHH CS
                         HTH_20  37 skntlsyHLrvLee 50 
                                    +k ++s++L+vL+ 
  gi|116754167|ref|YP_843285.1| 386 PKESISHRLNVLQA 399
                                    56678899998865 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.017
                                    HHHHHS-HHHHHHHHHH...STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                         HTH_20   3 iaeALahPvRrrilraL...araegltaselaerldlskntlsyHLrvLeeagLvevvr 58 
                                     ++AL+  v+++ilr+L    +++gl+   + + +      +s++++v+ +  +ve   
  gi|116754167|ref|YP_843285.1| 468 PTSALDPSVQAKILRLLmdlQERMGLSILFITHDI-ALARKVSDRIAVMLRGSIVEEGP 525
                                    5789999**********999999999999999987.55556999999999999998755 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0      0.12        41      33      51 ..      25      43 ..      20      56 .. 0.85
   2 ?    3.4   0.0      0.13        45      37      53 ..     333     349 ..     329     425 .. 0.87
   3 ?    3.7   0.0       0.1        35     113     160 ..     453     498 ..     433     510 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.12
                           TniB 33 krmpnlllvGdsnnGKtmi 51
                                   +r  +l +vG+s  GKt++
  gi|116754167|ref|YP_843285.1| 25 ERGDSLAVVGESGAGKTTL 43
                                   567899***********97 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.13
                           TniB  37 nlllvGdsnnGKtmive 53 
                                     l lvG+s  GKt++++
  gi|116754167|ref|YP_843285.1| 333 TLALVGESGSGKTTLAK 349
                                    6899**********987 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.1
                           TniB 113 rllrelkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlv 160
                                    +    +++++Li DE  ++l    + q ++l +l  L++++ ++i  +
  gi|116754167|ref|YP_843285.1| 453 ARALVMHPKLLIADEPTSAL--DPSVQAKILRLLMDLQERMGLSILFI 498
                                    44446899************..6777899**********999999765 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0      0.11        37       3      25 ..      32      54 ..      30      78 .. 0.82
   2 ?    8.9   0.0    0.0056       1.9       3      23 ..     336     356 ..     334     389 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.11
                   RNA_helicase  3 lyGpsgeGKStlakeLakallkk 25
                                   ++G+sg GK+tl  ++++  + k
  gi|116754167|ref|YP_843285.1| 32 VVGESGAGKTTLGLSIMRLAAAK 54
                                   89**********98877766555 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0056
                   RNA_helicase   3 lyGpsgeGKStlakeLakall 23 
                                    l+G+sg GK+tlak ++  ++
  gi|116754167|ref|YP_843285.1| 336 LVGESGSGKTTLAKIIMGIIE 356
                                    89************9776655 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.027       9.2       3      24 ..      31      52 ..      30      97 .. 0.73
   2 ?    6.9   0.0     0.013       4.6       3      24 ..     335     356 ..     333     368 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.027
                            PRK  3 gvagsSGaGkttvarklekifg 24
                                   +v g+SGaGktt+   +  + +
  gi|116754167|ref|YP_843285.1| 31 AVVGESGAGKTTLGLSIMRLAA 52
                                   799*********9888776554 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.013
                            PRK   3 gvagsSGaGkttvarklekifg 24 
                                    ++ g+SG+Gktt+a+ +  i++
  gi|116754167|ref|YP_843285.1| 335 ALVGESGSGKTTLAKIIMGIIE 356
                                    789***********99988775 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 ?    5.4   0.0     0.036        12      12      48 ..      25      63 ..      20     239 .. 0.71
   2 ?    7.3   0.0    0.0099       3.4       9      36 ..     326     353 ..     319     427 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.036
                                   BTT-EEEEEESTTSSHHHHHHHHHHHSSTS.S.EEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x.xxxxxx RF
                    ATP-synt_ab 12 vqGqrtlipgafgvGktvisqslskqsnsd.d.aiiyvg 48
                                    +G  ++++g++g Gkt++  s+++ + ++ +  i++ g
  gi|116754167|ref|YP_843285.1| 25 ERGDSLAVVGESGAGKTTLGLSIMRLAAAKlEgEIVFDG 63
                                   58999***************9999987666434566555 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0099
                                    S-EBTT-EEEEEESTTSSHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab   9 fpivqGqrtlipgafgvGktvisqslsk 36 
                                    +++ +G++++++g++g Gkt++++ ++ 
  gi|116754167|ref|YP_843285.1| 326 LTLYEGETLALVGESGSGKTTLAKIIMG 353
                                    68899*****************988865 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 ?    9.0   0.1    0.0039       1.4       5      26 ..      33      54 ..      30     220 .. 0.85
   2 ?    4.5   0.1       0.1        35       6      19 ..     338     351 ..     334     361 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0039
                                   ESSTTSSHHHHHHHHHHHHHHT CS
                                   xxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA  5 stkGGvGKTtlaanLaralarr 26
                                    + +G+GKTtl ++++r+ a +
  gi|116754167|ref|YP_843285.1| 33 VGESGAGKTTLGLSIMRLAAAK 54
                                   578**************99985 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.1
                                    SSTTSSHHHHHHHH CS
                                    xxxxxxxxxxxxxx RF
                           CbiA   6 tkGGvGKTtlaanL 19 
                                    + +G+GKTtla  +
  gi|116754167|ref|YP_843285.1| 338 GESGSGKTTLAKII 351
                                    78*******99665 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0      0.12        43      24      46 ..      29      51 ..      13      69 .. 0.76
   2 ?    8.1   0.0    0.0058         2      23      44 ..     332     353 ..     316     365 .. 0.78
   3 ?   -0.8   0.1         3     1e+03     103     119 ..     470     486 ..     461     497 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.12
                                   -EEEECSTTSSHHHHHHHHHHHS CS
                Sigma54_activat 24 svlitGesGtGKellaraiheas 46
                                   s+ ++GesG+GK++l  +i +  
  gi|116754167|ref|YP_843285.1| 29 SLAVVGESGAGKTTLGLSIMRLA 51
                                   67799********9988877655 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0058
                                    S-EEEECSTTSSHHHHHHHHHH CS
                Sigma54_activat  23 lsvlitGesGtGKellaraihe 44 
                                     ++ ++GesG+GK++la+ i  
  gi|116754167|ref|YP_843285.1| 332 ETLALVGESGSGKTTLAKIIMG 353
                                    567799************9865 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 3
                                    GGS-HHHHHHHHHHHHH CS
                Sigma54_activat 103 gelplelQekLlrvlqe 119
                                    + l++++Q+k+lr+l +
  gi|116754167|ref|YP_843285.1| 470 SALDPSVQAKILRLLMD 486
                                    568999*******9865 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.028       9.7       5      44 ..      30      69 ..      26     127 .. 0.78
   2 ?    6.6   0.0     0.019       6.6       2      22 ..     331     351 ..     330     363 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.028
                                   EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTT CS
                     APS_kinase  5 vwltGlsgsGKstianalekkLvekgisvylLdGdnvRhg 44
                                   + + G sg+GK+t+   + +   +k    ++ dG n+ + 
  gi|116754167|ref|YP_843285.1| 30 LAVVGESGAGKTTLGLSIMRLAAAKLEGEIVFDGTNLLEL 69
                                   55789************99877777788899999998544 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.019
                                    -EEEEEESSTTSSHHHHHHHH CS
                     APS_kinase   2 gvvvwltGlsgsGKstianal 22 
                                    g ++ l G sgsGK+t+a+ +
  gi|116754167|ref|YP_843285.1| 331 GETLALVGESGSGKTTLAKII 351
                                    678999************976 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.016       5.3      18      94 ..      26     100 ..      15     119 .. 0.71
   2 ?    4.9   0.0     0.045        16      19      37 ..     331     349 ..     321     362 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.016
                                    H-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-S.EEEEEE-S-.-T.T----SS---------TTTHHHHHHHTTTS-TT CS
                           PhoH  18 kndivfaiGpaGtGKtylavalavealkkkkvk.riiltrpav.ea.geelGflpgdleekvdpylrplydaLkdllgae 94 
                                    + d + ++G++G+GKt l +++    l + k++ +i++   ++ e  ++e+  l gd   ++++ ++ + daL+ ++ ae
  gi|116754167|ref|YP_843285.1|  26 RGDSLAVVGESGAGKTTLGLSI--MRLAAAKLEgEIVFDGTNLlELsEDEMRRLRGD---RMAMVFQNVEDALDPVYTAE 100
                                    55677899********999875..344444444156665444326667788888885...88888888888888877654 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.045
                                    -SEEEEE--TTSSTTHHHH CS
                           PhoH  19 ndivfaiGpaGtGKtylav 37 
                                     + +  +G++G+GKt la 
  gi|116754167|ref|YP_843285.1| 331 GETLALVGESGSGKTTLAK 349
                                    5667889**********95 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.034        12       7      25 ..      30      48 ..      26      69 .. 0.85
   2 ?    6.2   0.0     0.016       5.5       6      25 ..     333     352 ..     331     397 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.034
                                   EEEEEBTTSSCCCCCCTTS CS
                         Septin  7 lmvvGesglGkttlintlf 25
                                   l vvGesg Gkttl  +++
  gi|116754167|ref|YP_843285.1| 30 LAVVGESGAGKTTLGLSIM 48
                                   779**********966655 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.016
                                    EEEEEEBTTSSCCCCCCTTS CS
                         Septin   6 tlmvvGesglGkttlintlf 25 
                                    tl +vGesg Gkttl + ++
  gi|116754167|ref|YP_843285.1| 333 TLALVGESGSGKTTLAKIIM 352
                                    7889***********88765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.6     0.029       9.9       4      22 ..      32      49 ..      30     134 .. 0.69
   2 ?    8.6   0.2    0.0057         2       4      17 ..     336     349 ..     334     353 .. 0.87
   3 ?   -0.9   0.0       4.8   1.7e+03      82     117 ..     365     396 ..     354     416 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.029
                         AAA_33  4 lvGlpGsGKstlaerllkk 22
                                   +vG +G+GK+tl  +++ +
  gi|116754167|ref|YP_843285.1| 32 VVGESGAGKTTLGLSIM-R 49
                                   79*********987776.3 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0057
                         AAA_33   4 lvGlpGsGKstlae 17 
                                    lvG +GsGK+tla+
  gi|116754167|ref|YP_843285.1| 336 LVGESGSGKTTLAK 349
                                    89**********98 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 4.8
                         AAA_33  82 rrerarflklarrlgvpvrivvvetdeetlkeRlak 117
                                    +rerar+++ +     ++  ++++ + e + +Rl +
  gi|116754167|ref|YP_843285.1| 365 ERERARWDAGFY----RRVQMIFQNPKESISHRLNV 396
                                    689999999985....66678888888888888765 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.075        26       2      23 ..      30      51 ..      29      83 .. 0.82
   2 ?    6.2   0.1     0.026       8.9       2      23 ..     334     355 ..     333     361 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.075
                                   EEEE--TTSSHHHHHHHHHHHH CS
                       NTPase_1  2 vfiTGppGvGKtTlvkkvlell 23
                                   +++ G++G GKtTl   +++l 
  gi|116754167|ref|YP_843285.1| 30 LAVVGESGAGKTTLGLSIMRLA 51
                                   5789**********88887765 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.026
                                    EEEE--TTSSHHHHHHHHHHHH CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvlell 23 
                                    +++ G++G+GKtTl k ++  +
  gi|116754167|ref|YP_843285.1| 334 LALVGESGSGKTTLAKIIMGII 355
                                    5788**********99887765 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.11        37      21      41 ..      23      43 ..      14      61 .. 0.83
   2 ?    7.0   0.0    0.0063       2.2      22      55 ..     328     361 ..     318     365 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.11
                           DLIC 21 klPsgksvlvlGedgsGkttl 41
                                   +l  g s+ v+Ge+g+Gkttl
  gi|116754167|ref|YP_843285.1| 23 RLERGDSLAVVGESGAGKTTL 43
                                   67789999************9 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0063
                           DLIC  22 lPsgksvlvlGedgsGkttliaklqGveeekkGr 55 
                                    l  g ++ ++Ge+gsGkttl   + G+ e+  G 
  gi|116754167|ref|YP_843285.1| 328 LYEGETLALVGESGSGKTTLAKIIMGIIEPDSGE 361
                                    667788999***********99999*99988775 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.064        22       2      19 ..      30      47 ..      29      59 .. 0.81
   2 ?    5.7   0.0     0.043        15       2      21 ..     334     353 ..     333     369 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.064
                                   EEEEESTTSSHHHHHHHH CS
                       MMR_HSR1  2 vaivGrpNvGKStLinal 19
                                    a+vG + +GK+tL  ++
  gi|116754167|ref|YP_843285.1| 30 LAVVGESGAGKTTLGLSI 47
                                   59***********96555 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.043
                                    EEEEESTTSSHHHHHHHHHT CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltg 21 
                                     a+vG + +GK+tL + ++g
  gi|116754167|ref|YP_843285.1| 334 LALVGESGSGKTTLAKIIMG 353
                                    699***********988776 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1      0.19        65      13      31 ..      26      44 ..      16     229 .. 0.73
   2 ?    7.1   0.1     0.012       4.3      11      35 ..     328     352 ..     321     499 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.19
                                   TTCEEEEEESTTSSHHHHH CS
                                   xxxxxxxxxxxxxxxxxxx RF
                           DEAD 13 gggdvlvaaeTGsGKTlaf 31
                                   +g+++ v +e G+GKT+  
  gi|116754167|ref|YP_843285.1| 26 RGDSLAVVGESGAGKTTLG 44
                                   456777999999**99873 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.012
                                    HHTTCEEEEEESTTSSHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  11 ilgggdvlvaaeTGsGKTlaflipv 35 
                                    +++g+ + + +e GsGKT+ + i +
  gi|116754167|ref|YP_843285.1| 328 LYEGETLALVGESGSGKTTLAKIIM 352
                                    55899999**********9988766 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0    0.0032       1.1      29      60 ..       4      37 ..       2      42 .. 0.86
   2 ?   -0.3   0.0       2.7   9.4e+02      44      61 ..     325     342 ..     313     350 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0032
                                   EEEEE-T.-EEES--T.T-B--TT-EEEEEEEHH CS
                         TrkA_C 29 vvairRg.geliipsg.dtvLeeGDvllvvgsps 60
                                   v+++r + ge ++  g d++Le GD l vvg++ 
  gi|116754167|ref|YP_843285.1|  4 VIGLRARyGENEVLKGiDLRLERGDSLAVVGESG 37
                                   78887555999999999**************986 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 2.7
                                    T-B--TT-EEEEEEEHHH CS
                         TrkA_C  44 dtvLeeGDvllvvgspsd 61 
                                    +++L+eG +l +vg++ +
  gi|116754167|ref|YP_843285.1| 325 SLTLYEGETLALVGESGS 342
                                    789***********9876 PP

>> DUF188  Uncharacterized BCR, YaiI/YqxD family COG1671
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1     0.017         6      51      73 ..     192     213 ..     174     217 .. 0.77
   2 ?    3.6   0.0      0.14        50      54      74 ..     496     516 ..     485     523 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.017
                         DUF188  51 agDlvvTqDipLAarvlekgaaa 73 
                                    +  l++T+Di LA+  l+k++a+
  gi|116754167|ref|YP_843285.1| 192 RISLIITHDISLASA-LSKKIAV 213
                                    4579*********96.5555555 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.14
                         DUF188  54 lvvTqDipLAarvlekgaaal 74 
                                    l +T+Di LA +v ++ a+ l
  gi|116754167|ref|YP_843285.1| 496 LFITHDIALARKVSDRIAVML 516
                                    88*********9988766655 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0       0.4   1.4e+02      12      36 ..      29      53 ..      23     134 .. 0.88
   2 ?    5.4   0.0     0.064        22       9      33 ..     330     354 ..     324     367 .. 0.83
   3 ?    0.3   0.0       2.4   8.3e+02      98     129 ..     455     488 ..     387     499 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.4
                         AAA_19 12 vllvtaGpGtGKTrvlkhivallve 36
                                    l+v++  G GKT++   i++l+ +
  gi|116754167|ref|YP_843285.1| 29 SLAVVGESGAGKTTLGLSIMRLAAA 53
                                   67899********998887776655 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.064
                         AAA_19   9 kekvllvtaGpGtGKTrvlkhival 33 
                                    + ++l++++  G+GKT++ k i+ +
  gi|116754167|ref|YP_843285.1| 330 EGETLALVGESGSGKTTLAKIIMGI 354
                                    567899**********998887765 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 2.4
                         AAA_19  98 kklqeeellivDE.fqdvd.elqyrLlkallgek 129
                                      + + +lli DE ++ +d  +q ++l+ l++ +
  gi|116754167|ref|YP_843285.1| 455 ALVMHPKLLIADEpTSALDpSVQAKILRLLMDLQ 488
                                    34446669999*9778999999999999888554 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 ?    4.4   0.1     0.072        25       4      22 ..      31      49 ..      29      72 .. 0.82
   2 ?    5.1   0.1     0.044        15       3      19 ..     334     350 ..     332     364 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.072
                                   EEEESTTCCHHHHHHHHHC CS
                           cobW  4 vltGflGsGKTtLlnhlle 22
                                    ++G  G+GKTtL  ++++
  gi|116754167|ref|YP_843285.1| 31 AVVGESGAGKTTLGLSIMR 49
                                   589999*******777764 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.044
                                    EEEEESTTCCHHHHHHH CS
                           cobW   3 tvltGflGsGKTtLlnh 19 
                                    + l+G  GsGKTtL + 
  gi|116754167|ref|YP_843285.1| 334 LALVGESGSGKTTLAKI 350
                                    57999********9765 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       4.7   1.6e+03      26      43 ..      30      47 ..      19      77 .. 0.78
   2 ?    8.5   0.0    0.0043       1.5      13      44 ..     320     352 ..     314     413 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 4.7
                         AAA_15 26 tvliGkNnsGKSsileal 43
                                     ++G+ ++GK+++   +
  gi|116754167|ref|YP_843285.1| 30 LAVVGESGAGKTTLGLSI 47
                                   578*********985555 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0043
                         AAA_15  13 slkdveidlsee.ltvliGkNnsGKSsileald 44 
                                    + ++v++ l e  +  l+G+ +sGK+++++++ 
  gi|116754167|ref|YP_843285.1| 320 AVSHVSLTLYEGeTLALVGESGSGKTTLAKIIM 352
                                    5666677776665779**************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (558 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                       108  (0.00602376); expected 17.9 (0.001)
Passed Fwd filter:                        52  (0.00290033); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              52  [number of targets reported over threshold]
# CPU time: 0.73u 0.29s 00:00:01.02 Elapsed: 00:00:00.43
# Mc/sec: 3859.65
//
Query:       gi|116754168|ref|YP_843286.1|  [L=277]
Description: binding-protein-dependent transport systems inner membrane component [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-19   70.3  11.7    1.7e-19   70.3  11.7    2.0  2  BPD_transp_1  Binding-protein-dependent transport system inne
     0.0013   18.6   0.2     0.0013   18.6   0.2    3.5  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 ?   -0.9   0.4      0.13   1.2e+03     156     167 ..      18      29 ..       5      40 .. 0.51
   2 !   70.3  11.7   1.9e-23   1.7e-19       2     184 ..      91     274 ..      90     275 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.13
                   BPD_transp_1 156 ggvlalviavll 167
                                    g+++++vi++l+
  gi|116754168|ref|YP_843286.1|  18 GMLIMAVILILA 29 
                                    223333333322 PP

  == domain 2  score: 70.3 bits;  conditional E-value: 1.9e-23
                   BPD_transp_1   2 illGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilg.hlilpviillllsaapyvrlirraalrslp 80 
                                    +++G  aa   +++ d++ ++ ++++ +lPs++++il+       s+l  +l l +i+++l+s+++ +r++r++ l+ ++
  gi|116754168|ref|YP_843286.1|  91 VVIGGSAA-ILGGTYDRICMRAVDAVIALPSMIVMILVA------SYLRpNLGLLIILISLFSWPGGARIVRSQTLSLRE 163
                                    78999999.9***********************999999......9999788888************************* PP

                   BPD_transp_1  81 kdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis...... 154
                                    + +v aar+ Gasr+ +++++++P + p +++ +i  + +++   + l flg    ++++ + +++g+++ +++      
  gi|116754168|ref|YP_843286.1| 164 RLHVLAARTFGASRRYLLFRHIVPDLSPILVAIMIQDARRAVLMEAGLAFLG----VSDP-MIVSWGRMMKQAMsftyld 238
                                    ****************************************************....6655.55678888887778***** PP

                   BPD_transp_1 155 ......nggvlalviavlllnlvadilqrlldprvr 184
                                          + + + l + ++ l+l+a  l r+ dpr+r
  gi|116754168|ref|YP_843286.1| 239 vwkwwlIPTGVLLSLTLVGLSLIAASLERAMDPRLR 274
                                    ******9999************************98 PP

>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.2   1.5e-07    0.0013       5      39 ..       4      38 ..       3      50 .. 0.86
   2 ?   -3.2   1.7      0.97   8.7e+03      19      28 ..      81      90 ..      75     102 .. 0.54
   3 ?   -4.6   4.9         2   1.8e+04      24      24 ..     137     137 ..     114     153 .. 0.62
   4 ?   -3.9   0.5       1.6   1.5e+04      25      33 ..     254     262 ..     249     265 .. 0.51

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.5e-07
                         OppC_N  5 dawrrFkrNklAvvglvilllllliaifaPliaPy 39
                                   d+w+  ++  +  +g+ i +++l++a+ aPliaP 
  gi|116754168|ref|YP_843286.1|  4 DIWKEMRSSLAGTFGMLIMAVILILAASAPLIAPS 38
                                   799999***************************94 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.97
                         OppC_N 19 glvillllll 28
                                   g +il +l+ 
  gi|116754168|ref|YP_843286.1| 81 GVAILSALIS 90
                                   3333333332 PP

  == domain 3  score: -4.6 bits;  conditional E-value: 2
                         OppC_N  24 l 24 
                                    l
  gi|116754168|ref|YP_843286.1| 137 L 137
                                    2 PP

  == domain 4  score: -3.9 bits;  conditional E-value: 1.6
                         OppC_N  25 lllliaifa 33 
                                    +l+ ++++a
  gi|116754168|ref|YP_843286.1| 254 TLVGLSLIA 262
                                    344444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 2011.40
//
Query:       gi|116754169|ref|YP_843287.1|  [L=339]
Description: binding-protein-dependent transport systems inner membrane component [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-34  118.7  11.9    2.4e-34  118.7  11.9    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 ?    0.8   0.8     0.019   3.5e+02      26      44 ..      23      73 ..       9     126 .. 0.57
   2 !  118.7  11.9   1.4e-38   2.4e-34       1     185 []     131     337 ..     127     337 .. 0.98

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.019
                   BPD_transp_1 26 vllslPsfvlaillvlvf................................v 44
                                   +  ++ sf+++++l +v+                                +
  gi|116754169|ref|YP_843287.1| 23 LSNYIISFLIILILNFVLprmvpgdplhaiygeealiamtpemeaeiikrF 73
                                   333333444444444444555555555555555555555555555555552 PP

  == domain 2  score: 118.7 bits;  conditional E-value: 1.4e-38
                   BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf.......................vilsilghlilpvi 57 
                                    g++lGi ++++r++kld +++  + +l ++P f ++i+l+l+f                        +l+i++hlilp+i
  gi|116754169|ref|YP_843287.1| 131 GFILGIESGYRRGSKLDGCMLSSMMFLGGMPDFFIGIVLLLLFgvalgwaplggamspyaghtgidLLLDIVHHLILPLI 210
                                    556777777*********************************************************************** PP

                   BPD_transp_1  58 illllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGl 137
                                     l+l+++ap+ +l+r+a+l +l   ++ +a+a G+++  i ++++ +n+l p++t ++++++++++ga++le+++s+pG+
  gi|116754169|ref|YP_843287.1| 211 SLVLVQLAPTYLLTRNAMLTTLRARFIMTAKATGLKEGAIRYRHAGRNSLLPVVTAMGMRVPHMITGALFLEIVFSYPGV 290
                                    ******************************************************************************** PP

                   BPD_transp_1 138 gtllleailgydyseisnggvlalviavlllnlvadilqrlldprvrk 185
                                    gtll +a++++dy++i+ g++l++++ vl+ n+++d  +  ldprvr+
  gi|116754169|ref|YP_843287.1| 291 GTLLNTALSARDYPLIQ-GVLLIVTVTVLITNFLVDMTYIRLDPRVRY 337
                                    *****************.****************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       776  (0.0432818); 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):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2517.79
//
Query:       gi|116754170|ref|YP_843288.1|  [L=289]
Description: transposase, IS4 family protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.2e-33  113.1   0.0    3.2e-31  107.9   0.0    2.2  2  DDE_Tnp_1_5  Transposase DDE domain
      9e-21   74.5   0.1    1.6e-20   73.7   0.1    1.4  1  DDE_Tnp_1    Transposase DDE domain


Domain annotation for each model (and alignments):
>> DDE_Tnp_1_5  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.9   0.0   3.6e-35   3.2e-31       2     111 ..      18     125 ..      17     126 .. 0.95
   2 ?    2.8   0.0     0.016   1.4e+02      40      67 ..     252     281 ..     246     287 .. 0.82

  Alignments for each domain:
  == domain 1  score: 107.9 bits;  conditional E-value: 3.6e-35
                    DDE_Tnp_1_5   2 kRGsltiwldeeaiaawkek...kkngkrgrpqvysdaaiqtcltvkvlfklplRqlqGfvqsllklaglellvpdystl 78 
                                    +RG  +++l+++++++w+e+    +++k+grp++y++++iq+c +++++++lp+Rql+Gf+q+l+ ++   ll++dystl
  gi|116754170|ref|YP_843288.1|  18 RRG--WFYLSTDFVNNWDEEllkMNKNKNGRPYRYPETFIQFCGLAYAFLHLPYRQLEGFIQALSGFVPG-LLAADYSTL 94 
                                    799..************9987745569******************************************9.99******* PP

                    DDE_Tnp_1_5  79 srraktlevkipvkrkskglhlvvdstGlkvlg 111
                                    ++r ++le++ip+ +++  l+++vdstG+kv++
  gi|116754170|ref|YP_843288.1|  95 WQRITNLELNIPIPDND--LVVAVDSTGMKVTN 125
                                    **************999..99**********97 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.016
                    DDE_Tnp_1_5  40 tcltvkvlfklplRql..qGfvqsllklag 67 
                                    ++  +k++f+ ++R++  +G+++ + ++ +
  gi|116754170|ref|YP_843288.1| 252 VFSAIKRIFGETVRATskEGMIREVRRMFT 281
                                    56789*********9855699999988876 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.7   0.1   1.8e-24   1.6e-20       5     200 ..     112     271 ..     108     285 .. 0.83

  Alignments for each domain:
  == domain 1  score: 73.7 bits;  conditional E-value: 1.8e-24
                      DDE_Tnp_1   5 evlivDattvrvpgtkedarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrprkgklvlaDa 84 
                                     v++vD+t ++v+  + ++r++++  + + ++k+hiavd +++ ++ ++it+  v d++ +k+ll+ +   k    l+D+
  gi|116754170|ref|YP_843288.1| 112 LVVAVDSTGMKVTNRGDWMRESHGVER-RGWIKVHIAVDVETRKPVTFEITDETVTDHEMVKPLLEDV---KLEDSLMDG 187
                                    699******************888666.79************************************99...89******* PP

                      DDE_Tnp_1  85 GYasaelldtleekgvd.yiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgdvyyvtntnsells 163
                                    +Y++++++d+++ekgvd + i+++kn+ ++        r +    +++  +  +++ +++                    
  gi|116754170|ref|YP_843288.1| 188 AYDKEGVFDFMKEKGVDmPGIKIRKNAIVKAG----SSRAEPVLEFMKYGYHSWKIVHGY-------------------- 243
                                    ****************9568899999988866....344445555555555555555555.................... PP

                      DDE_Tnp_1 164 aeevaelyrlRwqiErvFkwlkrkfgldrlryrglnr 200
                                             +Rw  E+vF+ +kr fg + +r+ ++++
  gi|116754170|ref|YP_843288.1| 244 --------GRRWAAESVFSAIKRIFG-ETVRATSKEG 271
                                    ........***************998.6666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); 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:                         2  (0.000111551); expected 0.2 (1e-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: 2047.84
//
Query:       gi|116754171|ref|YP_843289.1|  [L=231]
Description: Ion transport protein [Methanosaeta thermophila PT]
Scores for complete 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   98.2   6.3    5.3e-28   97.9   6.3    1.0  1  Ion_trans      Ion transport protein
    7.2e-14   51.5   0.9    7.2e-14   51.5   0.9    1.8  2  Ion_trans_2    Ion channel
  ------ inclusion threshold ------
      0.059   13.4   0.0      0.096   12.7   0.0    1.3  1  V4R            V4R domain
      0.061   12.8   0.1      0.098   12.1   0.1    1.3  1  zf-ribbon_3    zinc-ribbon domain
      0.067   13.3   0.5       0.11   12.6   0.5    1.3  1  Zn-ribbon_8    Zinc ribbon domain
      0.077   12.7   0.1       0.12   12.2   0.1    1.3  1  zinc_ribbon_2  zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Ion_trans  Ion transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.9   6.3   1.8e-31   5.3e-28      33     244 ..      14     209 ..       5     210 .. 0.93

  Alignments for each domain:
  == domain 1  score: 97.9 bits;  conditional E-value: 1.8e-31
                                    HHHHHHHHHHHHHHHHHHHHHHHHHTH........HHHHHHCHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGG CS
                      Ion_trans  33 tileilelvftaiftlemllkilalgl........likkrYlrdpwnilDflvvlpsllslvlseesllllsvlrlfrvl 104
                                    +++ ++e++ +a+ft+e +l+++++ +         +++r++ +p  ++D+l+ lp++l +vl +    +l+v+rlfr++
  gi|116754171|ref|YP_843289.1|  14 SLFRAFEIFSVAVFTIEYILRVWSCTVdprfrepiRGRLRFMVTPLAVIDLLAFLPFYLPFVLPD--TRVLRVVRLFRLF 91 
                                    57889*******************99999******************************997754..9************ PP

                                    GGGHHHCHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCCCCCCSCCSTSSSTTTSSSSSSHHHHHH CS
                      Ion_trans 105 rllklisrleglrtlvtalirsvkdllnvlllllvvlfifaligvqlfkgklreknecaktwenpnngntnFdnfftall 184
                                    r++kl +++e++  ++  l+    +ll+v++ ++++l++ + +++++                 ++ +  +F++++ a++
  gi|116754171|ref|YP_843289.1|  92 RVMKLARYSESVDLFIDVLKLKKDELLLVFVSIMILLLVSSTLMYEVE----------------HDAQPDKFSSIPAAMW 155
                                    **************9999999999999999999999999999999999................3444578********* PP

                                    HHHHHHTTSSHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Ion_trans 185 wlfrlmttegwgdilyatldekskvaliyfvifiilgsflllNlliaviadnfqeltere 244
                                    w ++++ t+g+gd+++ t  +k      + ++++++ ++ l++l+ ++ia+ f+e+ +r+
  gi|116754171|ref|YP_843289.1| 156 WGLVTLATVGYGDMFPITPAGK------LIGSMVVMLGIGLFALPAGIIASGFSEVLQRR 209
                                    **********************......***************************98875 PP

>> Ion_trans_2  Ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.3       1.7     5e+03       8      16 ..      21      29 ..       4      38 .. 0.56
   2 !   51.5   0.9   2.4e-17   7.2e-14       2      75 ..     124     200 ..     123     204 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.7
                                   HHHHHHHHT CS
                    Ion_trans_2  8 ifgaviysl 16
                                   if+++++++
  gi|116754171|ref|YP_843289.1| 21 IFSVAVFTI 29
                                   333333333 PP

  == domain 2  score: 51.5 bits;  conditional E-value: 2.4e-17
                                    HHHHTCHHHHHHHHT..........T---HHHHHHHHHHHHTTS----SSTT-----HHHHHHHHHHHHHHHHHHHHHHH CS
                    Ion_trans_2   2 vlllvlifgaviysl......eegwekwsfldalYfsfvtltTiGYGdivpetdagrlftivyillGlalfalflavlgk 75 
                                    +++l+l++++++y +      ++++   s+  a+++ +vtl T+GYGd+ p+t+ag+l+  ++++lG++lfal   ++++
  gi|116754171|ref|YP_843289.1| 124 IMILLLVSSTLMYEVehdaqpDKFS---SIPAAMWWGLVTLATVGYGDMFPITPAGKLIGSMVVMLGIGLFALPAGIIAS 200
                                    67999**********9875544444...8999****************************************99988876 PP

>> V4R  V4R domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.2e-05     0.096      26      52 ..     195     221 ..     192     224 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.2e-05
                                    HHHHHHHHHHHHSSEEEEEEEE-GGGT CS
                            V4R  26 aGllagalsellgkrveveEveCaaeG 52 
                                    aG++a  +se l++r e++E+ C ++G
  gi|116754171|ref|YP_843289.1| 195 AGIIASGFSEVLQRRRECREIICPHCG 221
                                    9************************99 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   3.3e-05     0.098       2      16 ..     214     228 ..     213     229 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.3e-05
                    zf-ribbon_3   2 tvrCPnCGaplssdd 16 
                                    ++ CP+CG p+++++
  gi|116754171|ref|YP_843289.1| 214 EIICPHCGRPIKEEM 228
                                    567888887777765 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.5   3.8e-05      0.11      16      37 ..     204     225 ..     200     228 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.8e-05
                    Zn-ribbon_8  16 evlqsisdapltaCPeCgsevr 37 
                                    evlq+  +  ++ CP+Cg + +
  gi|116754171|ref|YP_843289.1| 204 EVLQRRRECREIICPHCGRPIK 225
                                    89**999***********8765 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   3.9e-05      0.12       2      12 ..     217     227 ..     216     230 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.9e-05
                  zinc_ribbon_2   2 CpnCGaelqdn 12 
                                    Cp+CG++++++
  gi|116754171|ref|YP_843289.1| 217 CPHCGRPIKEE 227
                                    *******9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); 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: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1613.67
//
Query:       gi|116754172|ref|YP_843290.1|  [L=546]
Description: CTP synthetase [Methanosaeta thermophila PT]
Scores for complete 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-124  412.8   0.3   6.9e-124  412.4   0.3    1.2  1  CTP_synth_N    CTP synthase N-terminus
    3.3e-57  193.3   0.0    5.5e-57  192.6   0.0    1.4  1  GATase         Glutamine amidotransferase class-I
    5.8e-07   29.5   0.0    1.4e-05   25.0   0.0    2.7  1  Peptidase_C26  Peptidase C26
    0.00017   21.7   0.0    0.00025   21.1   0.0    1.6  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
  ------ inclusion threshold ------
      0.038   13.8   0.0       0.31   10.8   0.0    2.2  2  DJ-1_PfpI      DJ-1/PfpI family
      0.097   11.8   0.0       0.95    8.6   0.0    2.2  2  ArsA_ATPase    Anion-transporting ATPase
       0.12   11.9   0.0       0.24   11.0   0.0    1.4  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
       0.16   12.1   0.0       0.45   10.7   0.0    1.7  1  Tubulin_C      Tubulin C-terminal domain


Domain annotation for each model (and alignments):
>> CTP_synth_N  CTP synthase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  412.4   0.3  3.1e-127  6.9e-124       1     265 []       2     264 ..       2     264 .. 0.99

  Alignments for each domain:
  == domain 1  score: 412.4 bits;  conditional E-value: 3.1e-127
                                    EEEEEEE--STTTTHHHHHHHHHHHHHCTT--EEEEEEE-SSSSSSTT--CCCC--EEE-TT--EEETHHHHHHHHHT-- CS
                    CTP_synth_N   1 kyilvtGGvvSglGkGiiaaslgallksrglkvtlikiDPYlnvdagtlsplehGEvfvlddGaetDlDlGnYeRfldik 80 
                                    +yi+vtGGv+SglGkGi+aas+g+ll ++g++vt+ikiDPY+n+dag +sp++hGEv+vl+dG+e+DlDlGnYeRfldi+
  gi|116754172|ref|YP_843290.1|   2 RYIVVTGGVMSGLGKGITAASIGRLLMNKGYRVTAIKIDPYINIDAGLMSPFQHGEVYVLKDGGEVDLDLGNYERFLDIE 81 
                                    7******************************************************************************* PP

                                    --GGGEEEHHHHHHHHHHHHHTTTTTT----CCCHHHHHHHHHHHHHH.HCT-SEEEEEE-S-TTSGGGHHHHHHHHHHH CS
                    CTP_synth_N  81 ltkennittGkiyksviekerrGdylGktvqviphvtdeikeriekvakkveadvviveigGtvgdieslpfleairqlk 160
                                    lt+++nittGk+y++viekerrG+ylGktvq+iph+tdeik+ri++v+++  ++++++e+gGtvgdies+pflea+rqlk
  gi|116754172|ref|YP_843290.1|  82 LTRDHNITTGKVYSTVIEKERRGEYLGKTVQIIPHITDEIKRRIRQVSRTGGSEICLIEVGGTVGDIESMPFLEAMRQLK 161
                                    ************************************************9989**************************** PP

                                    HHH-TTTEEEEEEEE--B-TTTSSB-HHHHHHHHHHHHHHT---SEEEEEESS---HHHHHHHHHHCT--GGGEEEEE-- CS
                    CTP_synth_N 161 lelgkenvllihvtlvpvlkaagelktkptqhsvkelrslGiqpdiivcrsekeleeevkekialfcnvekeavisvkdv 240
                                    +e  + n++++hvtl p+  + ge+ktkptqhsvke+r+lG+qpd+iv+r++k+l  e+k+kia+fc+v+ eavis +d 
  gi|116754172|ref|YP_843290.1| 162 YEE-SGNIFFVHVTLAPMT-SDGEQKTKPTQHSVKEMRELGLQPDMIVVRCKKPLLPETKAKIAHFCDVPIEAVISGHDS 239
                                    996.89***********98.69********************************************************** PP

                                    S-GGGHHHHHHHCTHHHHHHHHTT- CS
                    CTP_synth_N 241 esiyevpllleeqglaelileklkl 265
                                    ++iy+vpl le +gl+++i++ ++l
  gi|116754172|ref|YP_843290.1| 240 DDIYRVPLQLEAEGLTKYIMKAMRL 264
                                    ********************99876 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.6   0.0   2.4e-60   5.5e-57       2     189 ..     305     526 ..     304     527 .. 0.95

  Alignments for each domain:
  == domain 1  score: 192.6 bits;  conditional E-value: 2.4e-60
                                    EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHH..T.HHSTSEEEEEEESSCTTTTTHHHHHHHHCTSTS-EEEET CS
                         GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeile..l.lknpdgilvsgGpgspgvegkieaikearenkiPiLGIC 78 
                                    ++D+y s+ e+l+ha++e+gv  e+ +ida+++e ++  + l ++dgilv+gG+g++g+egk++ai++are++iP+LGIC
  gi|116754172|ref|YP_843290.1| 305 MKDAYLSIREALKHAGIEAGVMPEISWIDAEDLERIQpeKvLRDFDGILVPGGFGARGTEGKMNAIRYAREKGIPYLGIC 384
                                    58*********************************998636*************************************** PP

                                    HHHHHHHHHTTTEEE......................EEECEEEEEEEEEEEETTT........CGGTTTTSEEEEEEEE CS
                         GATase  79 LGmQllaiefgrkvv......................kekekehhggtmrlgddet........allyglknevierhrH 128
                                    +GmQl++ief+r+v                       ++++  ++g+tmrlg++++        +++yg+  e+ erhrH
  gi|116754172|ref|YP_843290.1| 385 FGMQLAVIEFARNVCglegasstefgetphpviallpEQEKVRQMGATMRLGNYPAhliegtlaHRIYGT-TEIVERHRH 463
                                    ************999999999999999999999****77779****************************.9******** PP

                                    EEEEESG...CHHHTTEEEEEEEETTEEEEEEEEETT.T.EEEESSBTTSTTSTTHHHHHHHHHHH CS
                         GATase 129 ryevnpk...elepaglevtakseddeelmeiiekkn.p.fvgvQFHPEststpegpellfnflik 189
                                    ryevnp+    le++gl +++++  +  lmei+e +  p f+++QFHPE++s+p++p+++f  +++
  gi|116754172|ref|YP_843290.1| 464 RYEVNPAyieVLEKNGLLFSGRN--G-DLMEIMEIPGhPfFFACQFHPEMRSRPGRPSPPFLAFVE 526
                                    *********8899999***9999..3.499****999999**********************9997 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   6.2e-09   1.4e-05      95     216 .]     367     509 ..     292     509 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 6.2e-09
                  Peptidase_C26  95 laLiraalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhrehe..............q.....saashavkvek 155
                                    +  ir a e+g+P lgiC G+ql  + +  ++     +  + t++ e+               q        +   ++ +
  gi|116754172|ref|YP_843290.1| 367 MNAIRYAREKGIPYLGICFGMQLAVIEFARNVCGLEGA--SSTEFGETPhpviallpeqekvrQmgatmRLGNYPAHLIE 444
                                    66789999***************988766554432221..222222222234555555444431333344445555666* PP

                  Peptidase_C26 156 gsllaellgseeievnslHhqaike.....laeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                    g+l ++++g++ei     H+  ++      l+++    +  + +++E +e++ ++ f+++ Q+HPE
  gi|116754172|ref|YP_843290.1| 445 GTLAHRIYGTTEIVERHRHRYEVNPayievLEKNGLLFSGRNGDLMEIMEIPGHP-FFFACQFHPE 509
                                    *********9999999****999888888888888888888899*********88.*********9 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   1.1e-07   0.00025       6      47 ..      10      48 ..       4     382 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.1e-07
                                   SSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA  6 tkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileg 47
                                     +G GK  +aa+++r+l ++g+rV +++ Dp  n +a   g
  gi|116754172|ref|YP_843290.1| 10 VMSGLGKGITAASIGRLLMNKGYRVTAIKIDPYINIDA---G 48
                                   479*****************************998877...3 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 ?   -0.3   0.0      0.37   8.2e+02      86     154 ..      23      96 ..       3      99 .. 0.59
   2 ?   10.8   0.0   0.00014      0.31      55     106 ..     347     389 ..     309     395 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.37
                                    HHHHHHHTT-EEEEETTTHHHHHHTTTTTTSEE--SGGGH....HHH.HHTTSEE-SSSEEEETTEEEESSGGG CS
                      DJ-1_PfpI  86 lvkefaekgklvaaICagpqlLaaagvlkgrrvTsypavk....dkl.ekagakyvdkrvvvdgnlvTsrgpga 154
                                    + +  ++kg +v aI   p + ++ag+++  ++  +  +k     +l   + ++++d +  +d n++T +   +
  gi|116754172|ref|YP_843290.1|  23 IGRLLMNKGYRVTAIKIDPYINIDAGLMSPFQHGEVYVLKdggeVDLdLGNYERFLDIELTRDHNITTGKVYST 96 
                                    55555666666666666666666666666666666666664433333223445688888888998888876655 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00014
                                    GGCTCCG-SEEEE--BHHHHHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHH CS
                      DJ-1_PfpI  55 ddvkaaeyDalvlpGGragperlrenekvvelvkefaekgklvaaICagpql 106
                                          ++D +++pGG       r +e  ++ ++ + ekg ++  IC g ql
  gi|116754172|ref|YP_843290.1| 347 R-----DFDGILVPGGFG----ARGTEGKMNAIRYAREKGIPYLGICFGMQL 389
                                    3.....7***********....67777889******************9875 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0   0.00043      0.95       1      61 [.       1      63 [.       1     130 [. 0.70
   2 ?    0.8   0.0     0.099   2.2e+02     221     257 ..     187     226 ..     145     231 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00043
                                   -EEEEEEE..STTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS--BSS-EEETSS CS
                    ArsA_ATPase  1 lkvilvgG..KGGVGKttvsaatavklsekgkkvllistDPAhslsDsfdqklgkeptkvkeN 61
                                   +++i+v+G    G GK   +a+++  l +kg++v  i  DP  ++   +   +++ +  v + 
  gi|116754172|ref|YP_843290.1|  1 MRYIVVTGgvMSGLGKGITAASIGRLLMNKGYRVTAIKIDPYINIDAGLMSPFQHGEVYVLKD 63
                                   789999883447*****************************9999888888888877777654 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.099
                                    HHHHHHHHHHHHTT-EEEEEEEE..E.E-TTCSSSTSHHH CS
                    ArsA_ATPase 221 kEteRaikeLkkygikvdavivN..k.llpeeeqenCefl 257
                                    k t+ ++ke+ ++g++ d+++v   k llpe++++  +f+
  gi|116754172|ref|YP_843290.1| 187 KPTQHSVKEMRELGLQPDMIVVRckKpLLPETKAKIAHFC 226
                                    56888999*************9532489999998866666 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 ?   11.0   0.0   0.00011      0.24      30      87 ..     340     389 ..     330     412 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00011
                       GATase_3  30 vplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqm 87 
                                    ++ +++ l +d d +++pGg+  +        +g  +ai+ a e+g+p lgiC G+q+
  gi|116754172|ref|YP_843290.1| 340 IQ-PEKVL-RDFDGILVPGGFGARG------TEGKMNAIRYAREKGIPYLGICFGMQL 389
                                    44.45555.6699999999987655......4688999*******************7 PP

>> Tubulin_C  Tubulin C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0    0.0002      0.45       3      44 ..     168     211 ..     167     220 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0002
                                    C-EEEEEEESSSCTT..TTTCS-HHHHHHHHHTCSGGGBSSSTS CS
                      Tubulin_C   3 lhFlltsyaPlvsae..kaavektsvqdvtrallepknimvkvd 44 
                                    + F+ +++aP++s+   k++  ++sv+++ +  l+p+ i v+++
  gi|116754172|ref|YP_843290.1| 168 IFFVHVTLAPMTSDGeqKTKPTQHSVKEMRELGLQPDMIVVRCK 211
                                    689***********95455556789****************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (546 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); 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: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 3799.76
//
Query:       gi|116754173|ref|YP_843291.1|  [L=262]
Description: hypothetical protein Mthe_0863 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); 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:                         0  (0); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 1841.52
//
Query:       gi|116754174|ref|YP_843292.1|  [L=62]
Description: hypothetical protein Mthe_0864 [Methanosaeta thermophila PT]
Scores for complete 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-13   48.8   0.3    1.3e-12   48.1   0.3    1.4  1  Trm112p          Trm112p-like protein
     0.0041   17.0   0.1        1.8    8.5   0.0    2.3  2  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
     0.0047   16.9   0.8      0.033   14.2   0.0    2.1  2  ADK_lid          Adenylate kinase, active site lid
     0.0052   16.5   1.0        1.5    8.6   0.1    2.2  2  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
     0.0075   16.3   0.0     0.0081   16.2   0.0    1.1  1  Elf1             Transcription elongation factor Elf1 like
     0.0088   15.9   1.5      0.021   14.7   1.5    1.7  1  Nudix_N_2        Nudix N-terminal
  ------ inclusion threshold ------
      0.019   14.5   4.4      0.046   13.3   4.4    1.7  1  TF_Zn_Ribbon     TFIIB zinc-binding
      0.019   15.3   0.2      0.022   15.2   0.2    1.1  1  Lar_restr_allev  Restriction alleviation protein Lar
       0.02   14.8   1.3      0.055   13.3   1.3    1.9  1  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
      0.053   13.5   0.8       0.12   12.4   0.9    1.6  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.071   13.2   0.2      0.082   13.0   0.2    1.1  1  DUF1644          Protein of unknown function (DUF1644)
      0.072   13.1   0.1        5.4    7.1   0.0    2.1  2  Rubredoxin       Rubredoxin


Domain annotation for each model (and alignments):
>> Trm112p  Trm112p-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   0.3   8.8e-16   1.3e-12       2      68 .]       3      49 ..       2      49 .. 0.94

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 8.8e-16
                                   TGGCCC-B-TTTHHC--HHHHHHHHHTT---S-SS----SCHHTTEECCCCEEEETTTTEEEEEETT CS
                        Trm112p  2 llllniLaCpackgpLdwealvevaalglnelpkekpedyellleldieegeLvCpncgraYpIkdG 68
                                   ++l++iL+Cp+c+g L++e++ e+++                    +i++g L+C++cg +YpI++G
  gi|116754174|ref|YP_843292.1|  3 RDLMEILVCPVCRGDLELEVFEENER--------------------EILTGRLTCRSCGEVYPIEEG 49
                                   78**************9999999997....................9******************98 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 !    6.5   0.0    0.0052       7.8      27      36 ..      10      20 ..       8      21 .. 0.76
   2 !    8.5   0.0    0.0012       1.8      14      26 ..      37      48 ..      35      54 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0052
                        DUF35_N 27 vCphCgsd.dl 36
                                   vCp C++d +l
  gi|116754174|ref|YP_843292.1| 10 VCPVCRGDlEL 20
                                   8****887565 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0012
                        DUF35_N 14 CpdCGtvqfPPra 26
                                   C++CG v +P + 
  gi|116754174|ref|YP_843292.1| 37 CRSCGEV-YPIEE 48
                                   *******.68665 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 ?    1.3   0.2      0.23   3.5e+02       3      28 ..      10      15 ..       8      19 .. 0.60
   2 !   14.2   0.0   2.2e-05     0.033       1      17 [.      34      55 ..      34      60 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.23
                                   E-TTT--EEETTTB--SSTTB-TTT- CS
                        ADK_lid  3 vCpkCGrsYhvvfnpPkveglCDkCG 28
                                   v                    C +C 
  gi|116754174|ref|YP_843292.1| 10 V--------------------CPVCR 15
                                   4....................55555 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 2.2e-05
                                   EEE-TTT--EEETT.....TB- CS
                        ADK_lid  1 RrvCpkCGrsYhvv.....fnp 17
                                   R++C++CG++Y ++     + p
  gi|116754174|ref|YP_843292.1| 34 RLTCRSCGEVYPIEegipnMLP 55
                                   99*********76644443345 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.1    0.0029       4.4       6      13 ..      10      17 ..       7      27 .. 0.76
   2 !    8.6   0.1   0.00098       1.5      20      30 ..      33      43 ..      28      45 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0029
                        zf-RRN7  6 pCgvCgcr 13
                                   +C+vC+++
  gi|116754174|ref|YP_843292.1| 10 VCPVCRGD 17
                                   9****983 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00098
                        zf-RRN7 20 GfyyCrrChtq 30
                                   G+  Cr+C+ +
  gi|116754174|ref|YP_843292.1| 33 GRLTCRSCGEV 43
                                   99*******76 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   5.4e-06    0.0081      18      57 ..       5      46 ..       1      54 [. 0.79

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.4e-06
                           Elf1 18 lptkFdCpfCnheksvevkldkkek..iaevsCkvCgesfet 57
                                   l +   Cp+C  +  +ev  +++++  +++++C++Cge + +
  gi|116754174|ref|YP_843292.1|  5 LMEILVCPVCRGDLELEVFEENEREilTGRLTCRSCGEVYPI 46
                                   566778*******777776665555899*********98865 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   1.5   1.4e-05     0.021       3      31 ..      11      43 ..      10      44 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.4e-05
                                   -TTT--B-EEE--TT-SS-....EEEETTTTEE CS
                      Nudix_N_2  3 CsqCGtpvelripdgDnre....RlvCpaCgti 31
                                   C+ C + +el++ ++ +re    Rl+C +Cg +
  gi|116754174|ref|YP_843292.1| 11 CPVCRGDLELEVFEENEREiltgRLTCRSCGEV 43
                                   ******************99999********87 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   4.4     3e-05     0.046       2      28 ..      10      43 ..       9      51 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3e-05
                                   EETTTTCEE.C......HEETSTTCEEESSSSBE CS
                   TF_Zn_Ribbon  2 kCPnCgstn.l......veDpergelvCtdCGlV 28
                                   +CP+C ++  l      +++  +g l+C +CG+V
  gi|116754174|ref|YP_843292.1| 10 VCPVCRGDLeLevfeenEREILTGRLTCRSCGEV 43
                                   8******9777*99888888999**********9 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 ?   15.2   0.2   1.4e-05     0.022       2      36 ..       7      42 ..       6      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.4e-05
                Lar_restr_allev  2 eLkpCPfCggravlersqrvvaeigq.cvyCadCga 36
                                   e++ CP C g+ +le  + +  ei +   +C  Cg 
  gi|116754174|ref|YP_843292.1|  7 EILVCPVCRGDLELEVFEENEREILTgRLTCRSCGE 42
                                   7889******************99999*******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 ?   13.3   1.3   3.7e-05     0.055      16      35 ..      33      48 ..      10      49 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.7e-05
                                   CSCCCEEEESSSS-EEESSC CS
                 RNA_POL_M_15KD 16 dkegknfeCrqCgYeepadq 35
                                   ++    + Cr+Cg ++p+++
  gi|116754174|ref|YP_843292.1| 33 GR----LTCRSCGEVYPIEE 48
                                   22....66**********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 ?   12.4   0.9     8e-05      0.12      20      45 ..      10      42 ..       5      43 .. 0.87
   2 ?    6.4   0.1    0.0057       8.6      17      30 ..      33      44 ..      23      51 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8e-05
                  Zn_Tnp_IS1595 20 vCPhCgsr.kayrikt......rglfqCkeCrk 45
                                   vCP C ++ ++  ++        g++ C++C++
  gi|116754174|ref|YP_843292.1| 10 VCPVCRGDlELEVFEEnereilTGRLTCRSCGE 42
                                   8*******977777777899999********85 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0057
                  Zn_Tnp_IS1595 17 ngfvCPhCgsrkay 30
                                   ++ +C  Cg  ++y
  gi|116754174|ref|YP_843292.1| 33 GRLTCRSCG--EVY 44
                                   345666666..555 PP

>> DUF1644  Protein of unknown function (DUF1644)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   5.5e-05     0.082      86     116 ..       8      40 ..       2      45 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.5e-05
                        DUF1644  86 elkCPlCrGevkgwkvveearkylnekk..rsC 116
                                     l+CP+CrG+++  +  e+ r++l  +   rsC
  gi|116754174|ref|YP_843292.1|   8 ILVCPVCRGDLELEVFEENEREILTGRLtcRSC 40 
                                    589*******99888888999999876422666 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.024        36      35      41 ..       9      15 ..       3      23 .. 0.75
   2 ?    7.1   0.0    0.0036       5.4       2      18 ..      35      51 ..      34      56 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.024
                                   -BBTTTB CS
                     Rubredoxin 35 WvCPdCg 41
                                    vCP+C 
  gi|116754174|ref|YP_843292.1|  9 LVCPVCR 15
                                   68****6 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0036
                                   EEETTT-BEEETTTBBG CS
                     Rubredoxin  2 yeCkvCgyvYdpakGdp 18
                                   + C+ Cg vY  ++G p
  gi|116754174|ref|YP_843292.1| 35 LTCRSCGEVYPIEEGIP 51
                                   68********9999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 451.46
//
Query:       gi|116754175|ref|YP_843293.1|  [L=114]
Description: peptidyl-tRNA hydrolase [Methanosaeta thermophila PT]
Scores for complete 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   0.0    3.7e-38  130.4   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 !  130.4   0.0     2e-42   3.7e-38       1     117 []       3     114 .]       3     114 .] 0.97

  Alignments for each domain:
  == domain 1  score: 130.4 bits;  conditional E-value: 2e-42
                                    EEEEEEEESSSSS-HHHHHHHHHHHHHHHHHHHHHH.CHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHHHTT-SEEE CS
                           PTH2   1 lkmvlvvrkDLkmskGkiaaqcahAavalvkkllkesnekellkeWeeegqkkivlkveseeeLlelaakakalglpaal 80 
                                    lk+++vvr+DL +s+Gk+a+q+ahA++++++ ++ke     +++eW++eg++kivl+ ++ee+L +l+++a++lg+paa+
  gi|116754175|ref|YP_843293.1|   3 LKQCIVVREDLRLSTGKLAVQVAHASIMAMELARKE-----IVEEWMQEGMRKIVLRGRDEEHLFQLRSEAESLGIPAAI 77 
                                    59*****************************88874.....89************************************* PP

                                    EEETSSSSSSTTCEEEEEEEEEEHHHHHHHHTTSEB- CS
                           PTH2  81 irDagrtqiepgtkTvlaigPapksivdkvtgkLkll 117
                                    +rDag t+i+pgt+T+l++gPap++i+d+vtg+L ll
  gi|116754175|ref|YP_843293.1|  78 VRDAGLTEIPPGTVTALGLGPAPDDIMDRVTGRLSLL 114
                                    **********************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 886.11
//
Query:       gi|116754176|ref|YP_843294.1|  [L=344]
Description: hypothetical protein Mthe_0866 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00039   20.6   0.0        1.2    9.4   0.0    2.6  2  NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosi


Domain annotation for each model (and alignments):
>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0   6.9e-05       1.2      46      78 ..     124     158 ..     112     159 .. 0.78
   2 !    8.7   0.0   0.00012       2.1      40      79 .]     254     293 ..     219     293 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 6.9e-05
                    NPCBM_assoc  46 slapGetve..atvkVtppagaaaGdyevtakarl 78 
                                    sl+ G++++   +++V++ + a aG y++++++++
  gi|116754176|ref|YP_843294.1| 124 SLKSGDKTRnpLKFTVKIAKHAPAGVYPLKLNLEY 158
                                    7777776663369*****************99876 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00012
                    NPCBM_assoc  40 spasaaslapGetveatvkVtppagaaaGdyevtakarlt 79 
                                    + a + +l pGe++++ +++ + ++a + +y +  ++++t
  gi|116754176|ref|YP_843294.1| 254 DQAYIGDLGPGEEATVVFRLDVDSDATPKEYGINSEIKYT 293
                                    5566779**************************9999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); 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 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 2425.78
//
Query:       gi|116754177|ref|YP_843295.1|  [L=778]
Description: HAE1 family efflux transporter [Methanosaeta thermophila PT]
Scores for complete 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-54  183.2  19.5    5.6e-29  101.1   2.9    2.1  2  MMPL            MMPL family
    8.2e-12   45.2  17.3    2.5e-06   27.4   4.1    2.7  2  Sterol-sensing  Sterol-sensing domain of SREBP cleavage-activ
    9.5e-08   31.6   9.0    9.5e-08   31.6   9.0    2.5  2  SecD_SecF       Protein export membrane protein
    1.6e-07   29.8  22.2     0.0001   20.6  13.5    2.7  3  Patched         Patched family
    2.3e-07   29.0  25.7    0.00018   19.4   5.7    2.9  3  ACR_tran        AcrB/AcrD/AcrF family
  ------ inclusion threshold ------
        0.2   11.7   0.0       0.38   10.8   0.0    1.3  1  RTX_C           RTX C-terminal domain
        0.6   10.3   2.5        2.1    8.6   0.5    2.6  2  DUF211          Uncharacterized ArCR, COG1888


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 !  101.1   2.9   2.2e-32   5.6e-29      39     295 ..      81     358 ..      57     407 .. 0.79
   2 !   87.7   8.8   2.7e-28   6.8e-25      87     304 ..     540     755 ..     535     765 .. 0.88

  Alignments for each domain:
  == domain 1  score: 101.1 bits;  conditional E-value: 2.2e-32
                           MMPL  39 ealgsaaaeaavdelvdelkkdtkhvgevsdf.............................lsdpdvaaafvSkDgkaar 89 
                                    +  ++ +  +a+d+l+ ++ +  ++v +v                                 +dp + ++++ +D k ++
  gi|116754177|ref|YP_843295.1|  81 DVTTP-EVLKAMDRLAVHM-ESVPDVISVEGIsqivktsaenelgrgcipdeqelidalllKGDPRLLQNIL-PDRKHTI 157
                                    44444.5555555555555.2333344444445555555555555555555555444444333666666655.999999* PP

                           MMPL  90 alvtlegdpgsteadesvaairaaveearpleglkvevtGpaatladlrdasdrdlklievvtlvvilviLlivyrSlva 169
                                    + ++l +   ++e +e +++ ++av+ a+ + g+ v vtG aa+   +++  +++ + +  ++ v+ ++ Ll+v+r +  
  gi|116754177|ref|YP_843295.1| 158 LSIELPLTLTDEEREEVLHETEKAVAMAEFPLGVGVIVTGDAALGVAIKKEMSENFGSLLGASGVLMILALLLVFRHVNW 237
                                    *******************************************************9999999999999999********* PP

                           MMPL 170 allplltvvvsllaalglvlilalllglelstfvlgl.lvvlliavGtDYallLvsRyreelaagedreeaviravastg 248
                                    +llpl +v ++++ ++g+      +  l++ ++++++ ++ +li++G+DYa+ +  R+ ee  +g + ++av ++va t+
  gi|116754177|ref|YP_843295.1| 238 PLLPLPVVFLGIIWTFGI------MGLLKIPMTMISMsAFPILIGIGIDYAIQFHNRIEEEFSKGGSIKKAVVETVAHTA 311
                                    ******************......344444455555548899************************************** PP

                           MMPL 249 kvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTll 295
                                    ++v++a ++ a+ +++L ++++p+++++Gv + +G+++  l +l + 
  gi|116754177|ref|YP_843295.1| 312 PAVLIALAITAAGFFSLFTSSVPMIRTFGVLCLIGLIMCYLSALFVG 358
                                    **************************************999987655 PP

  == domain 2  score: 87.7 bits;  conditional E-value: 2.7e-28
                           MMPL  87 aaralvtlegdpgsteadesvaairaaveear....pleglkvevtGpaatladlrdasdrdlklievvtlvvilviLli 162
                                    +a + +++  ++  ++++e v+++ +   + +     + g+ v +tG  ++++ + +a +  ++ +++ +lvvi+ iLl+
  gi|116754177|ref|YP_843295.1| 540 TAVMDINIG-NALRDLGEEGVDRLIKEMYKDVewfgVPPGTSVVITGNLVVMTTVIEALTTGRTEMTLFGLVVIFFILLL 618
                                    566677776.8888888888888655555555599999****************************************** PP

                           MMPL 163 vyrSlvaallplltvvvsllaalglvlilalllglelstfvlgllvvlliavGtDYallLvsRyreelaagedreeavir 242
                                    +yr l+ a++p+l  +v ++   g+     ++ g++ +  +++l  +l+++vG+ Y +l++ R+ eel++  d ++a+ +
  gi|116754177|ref|YP_843295.1| 619 IYRDLIKATMPVLPMLVVIGWMGGV----MYITGMKYTPLTATL-GALILGVGSEYSILMMERFYEELKRCNDIDQAISK 693
                                    ***********99887777666666....778888887777776.57889****************************** PP

                           MMPL 243 avastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTllPAllvllGr 304
                                    a  s+g++ +a+Glt ++ + +L ++ + + +++G++  l+v++++  ++T+ P ll  l r
  gi|116754177|ref|YP_843295.1| 694 ASSSIGSALVASGLTTVFGFGALITSPFVITNNFGTVTVLAVIFALITTFTVFPVLLIQLER 755
                                    ******************************************************99976655 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 !   27.4   4.1   9.8e-10   2.5e-06      15     133 ..     244     362 ..     239     375 .. 0.87
   2 !   25.0   2.9   5.2e-09   1.3e-05      23     148 ..     640     766 ..     623     770 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 9.8e-10
                                    HHHCCHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCHHCCHHCHHHHHHHHTTTCH.HHHHHHHHHHHCCCCHHCCCHHH CS
                 Sterol-sensing  15 ivllsvasslgllaylgltltliilevlPflvlavgvdnifvlvkavqrtsrslde.seriaealgevgpsilltsltel 93 
                                    +v l ++ ++g++ +l++++t+i++  +P  ++ +g+d    + + +++  ++    ++ + e++ +++p++l+ ++  +
  gi|116754177|ref|YP_843295.1| 244 VVFLGIIWTFGIMGLLKIPMTMISMSAFPI-LIGIGIDYAIQFHNRIEEEFSKGGSiKKAVVETVAHTAPAVLIALAITA 322
                                    57899************************5.57*****9999998887765555546*****************999999 PP

                                    HHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHH CS
                 Sterol-sensing  94 lalllgaltdvpavqeFclfaavavlvdFllqitfFvavL 133
                                    + ++  + ++vp +++F + + +++++ +l  +++ ++vL
  gi|116754177|ref|YP_843295.1| 323 AGFFSLFTSSVPMIRTFGVLCLIGLIMCYLSALFVGITVL 362
                                    999866799*******************998887777766 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 5.2e-09
                                    HCCHHHHHHHHHHHHHHHHHHHHHHHHCHHCCHHCH.HHHHHHHTTTCHHHHHHHHHHHHCCCCHHCCCHHHHHHHHHHH CS
                 Sterol-sensing  23 slgllaylgltltliilevlPflvlavgvdnifvlv.kavqrtsrsldeseriaealgevgpsilltsltellalllgal 101
                                      g++++ g+++t++++  l  l+l vg + + +++ + +++++r +d ++ i +a +++g +++++ lt   ++ +gal
  gi|116754177|ref|YP_843295.1| 640 MGGVMYITGMKYTPLTA-TLGALILGVGSEYSILMMeRFYEELKRCNDIDQAISKASSSIGSALVASGLTT--VFGFGAL 716
                                    558999**********9.9999********7666661556788888888***************9999986..5677777 PP

                                    CCHHHH..HHHHHHHHHHHHHHHHHHHTHHHHHHH.HHHHHHHCTXXTTT CS
                 Sterol-sensing 102 tdvpav..qeFclfaavavlvdFllqitfFvavLs.ldirreeserldvl 148
                                    ++ p v  ++F + +++av++  +   t+F  +L  l+ +re+ +rl+v+
  gi|116754177|ref|YP_843295.1| 717 ITSPFVitNNFGTVTVLAVIFALITTFTVFPVLLIqLERERERIQRLNVM 766
                                    7777764489********************87764134444466777665 PP

>> SecD_SecF  Protein export membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   9.0   3.7e-11   9.5e-08      22     185 ..     202     364 ..     193     368 .. 0.92
   2 ?   -3.4  14.7       2.1   5.5e+03      24     185 ..     592     752 ..     579     756 .. 0.78

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 3.7e-11
                                    -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-H.HHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHHTTSSSHH CS
                      SecD_SecF  22 gpsvskelaekavlallialvliliyvalrFew.rvalaaiialvhDviitvgvlsllgievdlatvaalLtiiGYSvnd 100
                                    g  + ke+ e+    l+++ vl+++ + l F+  +++l  +  ++  +i t g++ ll+i++++ +++a   +iG  ++ 
  gi|116754177|ref|YP_843295.1| 202 GVAIKKEMSENFGSLLGASGVLMILALLLVFRHvNWPLLPLPVVFLGIIWTFGIMGLLKIPMTMISMSAFPILIGIGIDY 281
                                    5566678888888889999999999******96379******************************************** PP

                                    HHHHHHHHHHHHHH--SS-HHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHTTTTHHHHHHHHHHTSTTTTTHHHHHH CS
                      SecD_SecF 101 tvvvfdrvrenlrkkkratlkeiinlslnqtLtrtiltslttllvvvallllggdslkdfalallvGlivgtyssifias 180
                                     +   +r++e++ k    ++k+++ + + +t    +++ ++t+   ++l+     +++ f +  l+Gli+  +s++f+  
  gi|116754177|ref|YP_843295.1| 282 AIQFHNRIEEEFSK--GGSIKKAVVETVAHTAPAVLIALAITAAGFFSLFTSSVPMIRTFGVLCLIGLIMCYLSALFVGI 359
                                    ***********998..899**************99*******************************************99 PP

                                    HHHHH CS
                      SecD_SecF 181 pllll 185
                                    ++l++
  gi|116754177|ref|YP_843295.1| 360 TVLYA 364
                                    98875 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.1
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHT-HHH.HHHHHHHHHHHHHHHHHHHHHTT----H..HHHHHHHHHTTSSSHH CS
                      SecD_SecF  24 svskelaekavlallialvliliyvalrFewrv.alaaiialvhDviitvgvlsllgievdl..atvaalLtiiGYSvnd 100
                                    +v + l++      l+ lv+i++ + l++++ + a+  ++ ++  +  + gv+ ++g++ ++  at++al  i+G   + 
  gi|116754177|ref|YP_843295.1| 592 TVIEALTTGRTEMTLFGLVVIFFILLLIYRDLIkATMPVLPMLVVIGWMGGVMYITGMKYTPltATLGAL--ILGVGSEY 669
                                    55566666666677889999999999999998736667777999999999*******9999722456666..78888899 PP

                                    HHHHHHHHHHHHHH--SS-HHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHTTTTHHHHHHHHHHTSTTTTTHHHHHH CS
                      SecD_SecF 101 tvvvfdrvrenlrkkkratlkeiinlslnqtLtrtiltslttllvvvallllggdslkdfalallvGlivgtyssifias 180
                                    ++++++r  e+l++   ++++++i ++ ++  +  ++  ltt++   al+  +  + ++f ++ ++++i+  +++  +  
  gi|116754177|ref|YP_843295.1| 670 SILMMERFYEELKR--CNDIDQAISKASSSIGSALVASGLTTVFGFGALITSPFVITNNFGTVTVLAVIFALITTFTVFP 747
                                    9**********888..6778888888777777777788888888888888888899999999999999999888876666 PP

                                    HHHHH CS
                      SecD_SecF 181 pllll 185
                                     ll++
  gi|116754177|ref|YP_843295.1| 748 VLLIQ 752
                                    55555 PP

>> Patched  Patched family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.15   3.7e+02     478     535 ..      50     105 ..      11     112 .. 0.72
   2 !   13.8   0.7   4.5e-06     0.012     265     391 ..     246     372 ..     237     511 .. 0.71
   3 !   20.6  13.5   3.9e-08    0.0001     222     396 ..     597     767 ..     579     775 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.15
                        Patched 478 vledsplvevlkliekeiwkeglqvevvv.nNppdltikesrdrleelveefentpyal 535
                                    v e s l ++++++   + ++ ++v++ v     d+t++e  + +++l+ ++e++p ++
  gi|116754177|ref|YP_843295.1|  50 VDEGSMLYQTYEHL---FKERFATVSITVvIEGDDVTTPEVLKAMDRLAVHMESVPDVI 105
                                    55555566666544...4445566666441456799*****************999876 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 4.5e-06
                        Patched 265 vlAivsslGlllwlGfrfnsivtvtPFLvLaiGvDdmflmvaawkr.teaklsvkkrigealseagvaitiTslTdvlsF 343
                                    +l i+  +G++ +l ++   i + +  + ++iG+D +    +++++  ++  s+kk + e+++++++a++i     ++ F
  gi|116754177|ref|YP_843295.1| 246 FLGIIWTFGIMGLLKIPMTMISMSAFPILIGIGIDYAIQFHNRIEEeFSKGGSIKKAVVETVAHTAPAVLIALAITAAGF 325
                                    677888999999999999988776555678*****887666666541566667*******************99999999 PP

                        Patched 344 giGaittlpaiqlFciytavailfdfiYqitffaavlaiaakaeaegr 391
                                       +++ +p i  F +   + ++++++  + f +  + +aa++  ++r
  gi|116754177|ref|YP_843295.1| 326 FSLFTSSVPMIRTFGVLCLIGLIMCYLSAL-FVGITVLYAAETSGNNR 372
                                    999***********************9655.44444444444444443 PP

  == domain 3  score: 20.6 bits;  conditional E-value: 3.9e-08
                        Patched 222 lvvtiaiLlvfsiivsvvlssdalkidwvrskpilailgvlspvlAivsslGlllwlGfrfnsivtvtPFLvLaiGvDdm 301
                                    l+ + + +++f ++v++          ++    i a + vl  ++ i    G++++ G+++   +     L+L++G   +
  gi|116754177|ref|YP_843295.1| 597 LTTGRTEMTLFGLVVIFFILL------LIYRDLIKATMPVLPMLVVIGWMGGVMYITGMKYTPLTATLGALILGVGSEYS 670
                                    555555566666666665555......566777888899998888899999***************************** PP

                        Patched 302 flmvaaw.krteaklsvkkrigealseagvaitiTslTdvlsFgiGaittlpaiqlFciytavailfdfiYqitffaavl 380
                                     lm++++ +++++ +++ + i++a s  g+a++   lT v+ Fg+ ++++    + F  +t +a++f+ i ++t+f  +l
  gi|116754177|ref|YP_843295.1| 671 ILMMERFyEELKRCNDIDQAISKASSSIGSALVASGLTTVFGFGALITSPFVITNNFGTVTVLAVIFALITTFTVFPVLL 750
                                    9999986267888899************************************************************6655 PP

                        Patched 381 a.iaakaeaegrhslll 396
                                      +  ++e+ +r  ++l
  gi|116754177|ref|YP_843295.1| 751 IqLERERERIQRLNVML 767
                                    41333445555555554 PP

>> ACR_tran  AcrB/AcrD/AcrF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   5.7     7e-08   0.00018     308     447 ..     185     326 ..     160     377 .. 0.75
   2 ?    1.6   0.0     0.016        40       2      34 ..     401     433 ..     400     448 .. 0.92
   3 !   14.0  10.1     3e-06    0.0077     334     488 ..     602     752 ..     536     771 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 7e-08
                                    GGSSTTEEEEEEEESH..HHHHHHHHHHHHHHHHH.HHHHHHHHHHHHSSHHHHHHHHHHHHHHHHHHHHHHHHTT--BC CS
                       ACR_tran 308 eslPegveivvvydrt..efvrasieeVvktLlea.ivLvvlvvflFLqnlratlipaiavPlsllgtfavlkalgfslN 384
                                    +++P gv + v+ d +    +++ ++e   +Ll a  vL +l ++l  + +   l p+ +v l ++ tf ++ +l++ + 
  gi|116754177|ref|YP_843295.1| 185 AEFPLGVGVIVTGDAAlgVAIKKEMSENFGSLLGAsGVLMILALLLVFRHVNWPLLPLPVVFLGIIWTFGIMGLLKIPMT 264
                                    34788888888888762246778888888787765269****************************************** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHHHHHHHHHHHHHHHHHHHCT CS
                       ACR_tran 385 lltLfgLvlAiGlvvDdAiVvvEnierkleeegekpleaalksmkeiqgalvaialvllavfl 447
                                    ++++ +  + iG+ +D Ai     ie++ ++ g + ++a+ +++   + a++   ++  a f 
  gi|116754177|ref|YP_843295.1| 265 MISMSAFPILIGIGIDYAIQFHNRIEEEFSK-GGSIKKAVVETVAHTAPAVLIALAITAAGFF 326
                                    ******************************9.6677777777777666665544444444443 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.016
                                    HHHHHTSHHHHHHHHHHHHHHHHHHHCTSSBES CS
                       ACR_tran   2 ikffikrpifalvlaliilllGilsilslPvda 34 
                                    ++f+++r  ++l+lal++ l+G++s   +Pvd 
  gi|116754177|ref|YP_843295.1| 401 VRFSLRRGPMILLLALLLSLAGVYSDTLVPVDT 433
                                    689***************************985 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 3e-06
                                    HHHHHHHHHHHHHHHHHHHSSHHHHHHHH..HHHHHHHHHHHHHHHHTT--BCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       ACR_tran 334 vktLleaivLvvlvvflFLqnlratlipa..iavPlsllgtfavlkalgfslNlltLfgLvlAiGlvvDdAiVvvEnier 411
                                     +  l ++v+++ +++l  ++l  + +p+  + v +  +g+++ +  ++++  + tL++L l++G     +i ++E  ++
  gi|116754177|ref|YP_843295.1| 602 TEMTLFGLVVIFFILLLIYRDLIKATMPVlpMLVVIGWMGGVMYITGMKYTPLTATLGALILGVGS--EYSILMMERFYE 679
                                    334466888888888888888777666661245667779***********************9998..89********** PP

                                    HHHHHTS-HHHHHHHHHHHHHHHHHHHHHHHHHHCTGGGGSBHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHH CS
                       ACR_tran 412 kleeegekpleaalksmkeiqgalvaialvllavflPilflgGveGklfrqfaltivlaillsvlvaltltPalcal 488
                                    +l+    +  +a+ k+++ i++alva+ l+ +  f    +l  +   + ++f+   vla++ +++   t+ P+l   
  gi|116754177|ref|YP_843295.1| 680 ELKR-CNDIDQAISKASSSIGSALVASGLTTVFGF---GALITSPFVITNNFGTVTVLAVIFALITTFTVFPVLLIQ 752
                                    ***9.788899***************998776555...5555677788899999999***************98544 PP

>> RTX_C  RTX C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00015      0.38      96     159 ..     660     731 ..     653     738 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00015
                          RTX_C  96 kvinnknkleeklsssesynllkqkknlsndieklisstsa.ftsssk........alsaspldirnnlssya 159
                                     +i   +   + l   + y+ lk  +++ + i+k  ss+++ + +s +        al +sp  i nn++++ 
  gi|116754177|ref|YP_843295.1| 660 ALILGVGSEYSILMMERFYEELKRCNDIDQAISKASSSIGSaLVAS-GlttvfgfgALITSPFVITNNFGTVT 731
                                    566666667788999999******7777777777777775414444.3599999***************9875 PP

>> DUF211  Uncharacterized ArCR, COG1888
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.5   0.00082       2.1      44      82 ..      70     108 ..      67     115 .. 0.89
   2 ?   -0.2   0.1      0.44   1.1e+03      45      71 ..     460     486 ..     451     500 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00082
                                    EEEEEEEEEESSE-HHHHHHHHHCTT-EEEEEEEEEEES CS
                         DUF211  44 tenlkitieGenidyeeieeaieelggvihSiDevvaGk 82 
                                    t +++++ieG+++   e+ +a++ l   + S+ +v+  +
  gi|116754177|ref|YP_843295.1|  70 TVSITVVIEGDDVTTPEVLKAMDRLAVHMESVPDVISVE 108
                                    889*****************************9998755 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.44
                                    EEEEEEEEESSE-HHHHHHHHHCTT-E CS
                         DUF211  45 enlkitieGenidyeeieeaieelggv 71 
                                      l+i+++G++i   ++ e ++e+g  
  gi|116754177|ref|YP_843295.1| 460 DELNIIVQGDDITDPKMLEWMNEFGEY 486
                                    5789********999999999998864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (778 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1008  (0.0562218); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.80u 0.31s 00:00:01.11 Elapsed: 00:00:00.49
# Mc/sec: 4795.36
//
Query:       gi|116754178|ref|YP_843296.1|  [L=192]
Description: hypothetical protein Mthe_0868 [Methanosaeta thermophila PT]
Scores for complete 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-05   23.2   0.0    0.00013   21.7   0.0    1.8  1  HTH_5            Bacterial regulatory protein, arsR family
     0.0021   18.4   0.0     0.0071   16.7   0.0    1.9  2  Penicillinase_R  Penicillinase repressor
     0.0064   16.3   0.1       0.02   14.8   0.1    1.8  2  TrmB             Sugar-specific transcriptional regulator Trm
     0.0094   16.0   0.0      0.028   14.5   0.0    1.7  1  DprA_WH          DprA winged helix domain
  ------ inclusion threshold ------
      0.033   14.6   2.1       0.33   11.5   0.7    2.3  2  PhoU             PhoU domain
      0.035   14.1   0.1       0.11   12.5   0.0    1.8  2  HTH_11           HTH domain
      0.048   13.5   0.2       0.15   11.9   0.0    1.9  2  HTH_IclR         IclR helix-turn-helix domain
       0.08   12.5   0.0       0.12   11.9   0.0    1.2  1  PET10            Petite colonies protein 10
       0.12   12.9   0.2       0.26   11.8   0.1    1.5  2  DUF2115          Uncharacterized protein conserved in archaea
       0.17   11.0   0.0       0.23   10.6   0.0    1.3  1  PLU-1            PLU-1-like protein


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 !   21.7   0.0   7.3e-08   0.00013       8      44 ..      59      95 ..      55      98 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 7.3e-08
                                   HHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                          HTH_5  8 LklLaegelcvcelaeelglsqstvShHLkkLreaGL 44
                                   + +L+e +l+  +l+e++g s+stvS   ++L+  G+
  gi|116754178|ref|YP_843296.1| 59 ILMLSETPLSLDDLVEITGYSKSTVSTNMSILEGIGV 95
                                   579*****************************98776 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.8   3.3e+03     101     114 ..      24      37 ..      17      38 .. 0.82
   2 !   16.7   0.0   3.9e-06    0.0071      32      85 ..      77     132 ..      64     160 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.8
                                    XXXXXXXXXXXXXX CS
                Penicillinase_R 101 lseddleeLrelle 114
                                    ++ +++e++r++++
  gi|116754178|ref|YP_843296.1|  24 MNREEIEAIRRYIT 37 
                                    78999****99986 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 3.9e-06
                                    ---HHHHHHHHHHHHHTTS-EEEEE..TTEEEEE----XXXXXXXXXXXXXXXXXX CS
                Penicillinase_R  32 elaysTVktllrrLvkKgllsreke..grafiYsplvseeeavasavkqlldklfe 85 
                                      ++sTV t ++ L+  g+ +r  +  +++++Y p+++ e +++ +++++ +++ +
  gi|116754178|ref|YP_843296.1|  77 GYSKSTVSTNMSILEGIGVAKRVVTpgEKRYRYIPVTDTEMLRNAMMNHVSKEIST 132
                                    5789************9999998887789***********9999999999888763 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   1.1e-05      0.02      17      67 ..      61     112 ..      59     113 .. 0.91
   2 ?   -2.5   0.0       2.7   4.9e+03       6      21 ..     176     191 ..     176     192 .] 0.80

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.1e-05
                                    HHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.TTEEEE--H CS
                           TrmB  17 LlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.pklYravdp 67 
                                    +l++ p++ d++ e++g ++s+v   ++ Le  G+ +r+     k+Yr++++
  gi|116754178|ref|YP_843296.1|  61 MLSETPLSLDDLVEITGYSKSTVSTNMSILEGIGVAKRVVTPgEKRYRYIPV 112
                                    67999**********************************8778889999885 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.7
                                    HHHHCCCHCHHHHHHC CS
                           TrmB   6 LseyEakvYlaLlklg 21 
                                    +++y+++  + +l++g
  gi|116754178|ref|YP_843296.1| 176 IQKYDVDSLIEILERG 191
                                    5789999999999887 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   1.6e-05     0.028      21      50 ..      62      91 ..      56      98 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.6e-05
                        DprA_WH 21 LgpePvhvDqLvrrtglpaaevsaaLleLE 50
                                   L+ +P+++D+Lv+ tg + ++vs+  + LE
  gi|116754178|ref|YP_843296.1| 62 LSETPLSLDDLVEITGYSKSTVSTNMSILE 91
                                   899*********************999998 PP

>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.12   2.2e+02      33      57 ..      25      50 ..      19      78 .. 0.75
   2 ?   11.5   0.7   0.00018      0.33       7      54 ..     132     178 ..     126     190 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.12
                                   HHHHHHHHHHHHHHHHHHHH.HHHGG CS
                           PhoU 33 rddeidrlekeierslleal.akrqp 57
                                   +++ei+++++ i++++++++ +++ +
  gi|116754178|ref|YP_843296.1| 25 NREEIEAIRRYITEACVQIArMRGYS 50
                                   56899999999999999999555333 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00018
                                    HHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           PhoU   7 iveemlddalealeekdtelarevierddeidrlekeiersllealak 54 
                                    ++  +ld+a +al++ +t  a++++er + i +++ + +r  l+++ k
  gi|116754178|ref|YP_843296.1| 132 TIMAALDRAERALSDSETPEADKIRERINGIRNFYSKTDRL-LKLIQK 178
                                    56679*******************************99888.655533 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       5.2   9.3e+03      31      37 ..      31      37 ..      30      38 .. 0.81
   2 ?   12.5   0.0   5.9e-05      0.11       8      44 ..      59      95 ..      56     103 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 5.2
                         HTH_11 31 tvrrdIk 37
                                   ++rr+I 
  gi|116754178|ref|YP_843296.1| 31 AIRRYIT 37
                                   7999995 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 5.9e-05
                         HTH_11  8 lLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                   +L+ ++ p+s ++L e ++ S++tv   + +Le +gv
  gi|116754178|ref|YP_843296.1| 59 ILMLSETPLSLDDLVEITGYSKSTVSTNMSILEGIGV 95
                                   57788899*************************9994 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   8.3e-05      0.15      16      42 ..      64      90 ..      52      99 .. 0.78
   2 ?   -1.9   0.0       1.7     3e+03       8      20 ..     133     145 ..     132     148 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.3e-05
                                   BSS-BHHHHHHHHTS-HHHHHHHHHHH CS
                       HTH_IclR 16 pqeltlselArrtglpkStvhRlLqtL 42
                                     +l+l +l + tg +kStv+  ++ L
  gi|116754178|ref|YP_843296.1| 64 ETPLSLDDLVEITGYSKSTVSTNMSIL 90
                                   5689****************8655555 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.7
                                    HHCT-CTTBSS-B CS
                       HTH_IclR   8 iLdalaeapqelt 20 
                                    i+ al +a ++l+
  gi|116754178|ref|YP_843296.1| 133 IMAALDRAERALS 145
                                    8889999988865 PP

>> PET10  Petite colonies protein 10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   6.5e-05      0.12      15      87 ..     114     186 ..     104     190 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.5e-05
                          PET10  15 skllkkvlslplvskvlsvvlsvaaklkealvdskkaPa..lvkkvynavlklllklDelvnlLvlreGidalle 87 
                                    +  + +   ++ vsk +s+++++++++++al ds++ P+   +++ +n + ++  k D l++l + +  +d+l+e
  gi|116754178|ref|YP_843296.1| 114 DTEMLRNAMMNHVSKEISTIMAALDRAERALSDSET-PEadKIRERINGIRNFYSKTDRLLKL-IQKYDVDSLIE 186
                                    445666677899*********************975.54126999***************985.67778888876 PP

>> DUF2115  Uncharacterized protein conserved in archaea (DUF2115)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       4.7   8.5e+03      75      89 ..      25      39 ..      12      48 .. 0.49
   2 ?   11.8   0.1   0.00014      0.26      29      95 ..     104     171 ..      95     185 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.7
                        DUF2115 75 deeelkeflemleeq 89
                                   ++ee++++ + ++e+
  gi|116754178|ref|YP_843296.1| 25 NREEIEAIRRYITEA 39
                                   233333333333333 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00014
                        DUF2115  29 ekeikklpekyrkelseslteylfeaykelkn.krsgdkseykeevideeelkeflemleeqceeeke 95 
                                    ek+ +++p    + l++++++++ +++ +++    + + +  ++e+ + ++++e ++ +++ ++++++
  gi|116754178|ref|YP_843296.1| 104 EKRYRYIPVTDTEMLRNAMMNHVSKEISTIMAaLDRAERALSDSETPEADKIRERINGIRNFYSKTDR 171
                                    78899***************************866666666777999999999999999999888765 PP

>> PLU-1  PLU-1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00013      0.23     100     144 ..     148     191 ..     122     192 .] 0.94

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00013
                          PLU-1 100 dlpeieqLkelleeieefqkkarellseesedssieeleklieeG 144
                                    ++pe+++++e+ + i +f +k+++ll+   ++++++ l +++e G
  gi|116754178|ref|YP_843296.1| 148 ETPEADKIRERINGIRNFYSKTDRLLKL-IQKYDVDSLIEILERG 191
                                    68*************************9.8999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       881  (0.0491383); expected 358.6 (0.02)
Passed bias filter:                      738  (0.0411624); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); 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 0.29s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1332.38
//
Query:       gi|116754179|ref|YP_843297.1|  [L=95]
Description: hypothetical protein Mthe_0869 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 718.96
//
Query:       gi|116754180|ref|YP_843298.1|  [L=203]
Description: hypothetical protein Mthe_0870 [Methanosaeta thermophila PT]
Scores for complete sequence (score 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   1.1        4.5    7.2   0.1    2.4  2  DUF502    Protein of unknown function (DUF502)
        5.4    6.6   7.4    3.3e+02    0.8   7.4    2.2  1  DUF4131   Domain of unknown function (DUF4131)


Domain annotation for each model (and alignments):
>> DUF502  Protein of unknown function (DUF502)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1   0.00051       4.5       8      72 ..      79     141 ..      74     147 .. 0.84
   2 ?    3.6   0.1    0.0068        61       3      20 ..     178     195 ..     176     203 .] 0.75

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00051
                         DUF502   8 llvGllasnligrkllklgerllkriPlvksiYsalkqvvetfsseekksfrevvlveyprkglw 72 
                                    +l G++a+ ++g  ++++ +  +  +Pl +s +  l + ++++ +  ++  re ++v+y  k +w
  gi|116754180|ref|YP_843298.1|  79 VLYGVIAALIFGALIYGYSDIRILGVPLWSSFFAGLGSSAQILTGVVDDLRREGMVVRY--KRIW 141
                                    789******************************98888888888777777777778888..4455 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.0068
                         DUF502   3 vlllillvGllasnligr 20 
                                    ++l+++l+G+++++li r
  gi|116754180|ref|YP_843298.1| 178 TMLVCFLTGFMTNWLINR 195
                                    78999****998776654 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   7.4     0.037   3.3e+02       5      59 ..      76     128 ..      73     202 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.037
                        DUF4131   5 lalvllalllllllllllllrrrprrrvllllllllllallgfalrapqpnandl 59 
                                    l++vl +++++l++ +l++ +     r+l++ l   ++a+lg  ++ ++  ++dl
  gi|116754180|ref|YP_843298.1|  76 LYAVLYGVIAALIFGALIYGY--SDIRILGVPLWSSFFAGLGSSAQILTGVVDDL 128
                                    677888888888888888874..44444444444455555555554444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       907  (0.0505884); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); 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: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1457.95
//
Query:       gi|116754181|ref|YP_843299.1|  [L=130]
Description: hypothetical protein Mthe_0871 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); 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: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1000.07
//
Query:       gi|116754182|ref|YP_843300.1|  [L=382]
Description: aminotransferase, class V [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-90  303.5   0.0    2.2e-90  303.3   0.0    1.0  1  Aminotran_5      Aminotransferase class-V
    5.8e-08   32.4   0.0    7.6e-08   32.0   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase
    7.6e-08   32.0   0.0    1.7e-07   30.9   0.1    1.4  2  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    6.1e-06   25.0   0.0    8.6e-06   24.5   0.0    1.1  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
  ------ inclusion threshold ------
      0.086   11.5   0.0       0.12   11.0   0.0    1.3  1  Pyridoxal_deC    Pyridoxal-dependent decarboxylase conserved 


Domain annotation for each model (and alignments):
>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  303.3   0.0   6.2e-94   2.2e-90       1     371 []       4     364 ..       4     364 .. 0.96

  Alignments for each domain:
  == domain 1  score: 303.3 bits;  conditional E-value: 6.2e-94
                                    EEEBTTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHH CS
                    Aminotran_5   1 iyldsaAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlvals 80 
                                    iy+d +Att++ +eVlda+  y+++ ++n+ +s+h++g ea +ave are++a li+a+  eei+ftsG+te+ nl++++
  gi|116754182|ref|YP_843300.1|   4 IYMDHSATTPVAPEVLDAMLPYFREKYGNA-SSLHEFGREARDAVESAREELASLIGASP-EEIYFTSGGTESDNLALKG 81 
                                    8*****************************.****************************7.******************* PP

                                    CCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHH CS
                    Aminotran_5  81 larslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGtiqpvee 160
                                    +a   ++g++i++t++eh a l  ++ l+ r g++v+ +p+d++g +++ e+e +++++t l++++h++n++Gtiqp++e
  gi|116754182|ref|YP_843300.1|  82 VAL-SSKGKHIITTSIEHPAVLEVCRSLE-RMGFDVTCVPVDDQGIVNPGEIERAIRDDTVLISVMHANNEIGTIQPIKE 159
                                    *65.89**********************8.99************************************************ PP

                                    HHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTTTTSSTT-EEEEEEHHHHHTS..SS.STTSEEEEETTEEE CS
                    Aminotran_5 161 igklakkkgalvlvDaaqavghipidvkklgvDflafsghKllgPtGiGvlyvrkellekleplllggemveevsleett 240
                                    i+++a ++++l+++Da+q+vg+ip++v++lgvD+l++s+hK++gP+G+G+lyvrk    ++e +  gg+       +e++
  gi|116754182|ref|YP_843300.1| 160 IAEIASERDILLHTDAVQTVGKIPVNVDQLGVDLLSISAHKFYGPKGVGALYVRK--GTRIESIIQGGG-------HERG 230
                                    *******************************************************..999999999999.......8999 PP

                                    EHCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH.HHCTSTTEEEES.-B-CTCBSEEEEEETTC CS
                    Aminotran_5 241 faeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeylle.rlkslpgvrlygpdkaerrasivsfnfkgv 319
                                           +++GT+nv+gi+g+g a+e+ +e  +++ +++ ++l+e+l++  l+++++  l+g ++++r +  ++f f +v
  gi|116754182|ref|YP_843300.1| 231 -------LRSGTENVPGIVGMGRAAELASE-MMDREAERLTALRERLKSfVLSNIDDSWLNG-HPTKRLPINLNFGFGRV 301
                                    .......9*******************955.5777777888888888773688899999999.799************** PP

                                    SHHHHHHHHHHTTEEEEEE-TTT....HHHHHHTT.S.......-EEEEE--TTS-HHHHHHH CS
                    Aminotran_5 320 haedvatlLdeegIavrsGhhca....qplmkrlale.......gtvRaSlyiynteeevdrl 371
                                    + e +  +Ld++gIav++G++c+    +p+++++a+        g++R+ l++ nt+e+vd++
  gi|116754182|ref|YP_843300.1| 302 EGESLLLYLDSKGIAVSTGSACSskklEPSHVLRAIGldpvrchGSLRITLGRDNTQEDVDYV 364
                                    *************************99999999999999*********************975 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.0   2.1e-11   7.6e-08      26     169 ..      28     176 ..       9     276 .. 0.70

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 2.1e-11
                                    CCCT--HHHHHHHHHHHH...........HTT-..SEEEEES-HHHHHHHHHHHH-..-TTEEEEEETT-HHHHSSTTHH CS
                Beta_elim_lyase  26 esYgedktvnrLedavae...........lfgk..eaalfvpqGtaAnsillkill..qrgeevivtepahihfdetgai 90 
                                    e Yg++++ +++  ++++           l+g+  e + f+  Gt +++++lk ++   +g+ +i t+  h    e    
  gi|116754182|ref|YP_843300.1|  28 EKYGNASSLHEFGREARDavesareelasLIGAspEEIYFTSGGTESDNLALKGVAlsSKGKHIITTSIEHPAVLEVCRS 107
                                    5677777777777777776666666666666662246668889*********54444489999999999**999999555 PP

                                    HHCC--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEET CS
                Beta_elim_lyase  91 aelagvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgA 169
                                     e  g  ++ ++ +++G +++ ++e+ai++      ++ lis+  +nn     + +++ ++e+a+ia +++i lh D+ 
  gi|116754182|ref|YP_843300.1| 108 LERMGFDVTCVPVDDQGIVNPGEIERAIRD------DTVLISVMHANNE----IGTIQPIKEIAEIASERDILLHTDAV 176
                                    5666788999999999*************9......488*********5....6688889999**************74 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 !   30.9   0.1   4.7e-11   1.7e-07      31     150 ..      53     180 ..      42     204 .. 0.84
   2 ?   -3.3   0.0       1.2   4.2e+03     238     304 ..     252     317 ..     242     321 .. 0.69

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 4.7e-11
                                    HHHHHHT.-SEEE.EESSHHHHHHHHHHHTTTT.TT-EEEEESSS-THHHHHHH...HTT-EEEEE-B-TTTSSB-GGGC CS
                DegT_DnrJ_EryC1  31 afaaylg.vkhai.avssGtaAlhlaLralgvg.pgdeVIvpsltFvatanavl...elgakpvfvDvdpdtynidpaai 104
                                    ++a  +g +   i  +s Gt++  laL+ + ++ +g+ +I++s+   a  ++ +   ++g ++  v vd d+  ++p +i
  gi|116754182|ref|YP_843300.1|  53 ELASLIGaSPEEIyFTSGGTESDNLALKGVALSsKGKHIITTSIEHPAVLEVCRsleRMGFDVTCVPVD-DQGIVNPGEI 131
                                    5666666433444045678*********9888889*************998754222789*********.999******* PP

                                    GGG--TTEEEEEEB-G...GGB---HHHHHHHHHHCT-EEEEE-TT-TT CS
                DegT_DnrJ_EryC1 105 eaaitertkaIlpVhl...yGqvadmdalkaiaakhglkvieDaAhAlG 150
                                    e+ai   t  I + h+    G +  ++++ +ia++ ++ +  Da + +G
  gi|116754182|ref|YP_843300.1| 132 ERAIRDDTVLISVMHAnneIGTIQPIKEIAEIASERDILLHTDAVQTVG 180
                                    ********99999998333588889999999***************998 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.2
                                    HHHHHHHHHHHHHHHHHHHTCCCCEESCGGTTSSSEEESCEEEEEHCCHH.HCHHHHHHHHHHCCEE- CS
                DegT_DnrJ_EryC1 238 delvarRreiaelykeeLaelegtaelttpketkkhawhlyavlveeeae.vkrdelvealkeegigt 304
                                    +e+++r  e ++ ++e+L++         + + + h   ++++ ++ ++  v+ + l+  l+++gi++
  gi|116754182|ref|YP_843300.1| 252 SEMMDREAERLTALRERLKSFVL--SNIDDSWLNGHPTKRLPINLNFGFGrVEGESLLLYLDSKGIAV 317
                                    57777888888888888888764..3344444445777788888887777777777777777777765 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 !   24.5   0.0   2.4e-09   8.6e-06      41     200 ..      34     202 ..      17     213 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 2.4e-09
                                    SSS-SBTTT--HHHHHHHHHHHHHHT-..SEEEEESSHHHHHHHHH..HTTS-TTEEEEEESTSSHHHHHHHHHTHHHTT CS
                Cys_Met_Meta_PP  41 ekgyeYsRsgnptrsvleeriaaLegg..eaalavssGmaAiaaai..lallkaGdeivvsddlYggtqrllkkvlkklg 116
                                    ++ +e++R     ++   e++a L g+  e+ + +s G+ + ++a+  +al ++G++i++++  +    +++++ l+++g
  gi|116754182|ref|YP_843300.1|  34 SSLHEFGREARDAVESAREELASLIGAspEEIYFTSGGTESDNLALkgVALSSKGKHIITTSIEHPAVLEVCRS-LERMG 112
                                    444888888888888999999999999755566666666666566622457788*******9999999998876.67777 PP

                                    CEEEEEST.....TSHHHHHHHCCTTEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGTTTHT.TTS-GGGGT-S CS
                Cys_Met_Meta_PP 117 ievkfvdt.....sdleelekaikentklvylEtptnpllkvvDiekiaklakkagvlvvvDntfasp.llqrplklgaD 190
                                     +v+ v +      ++ e+e+ai++ t l+ +    n    +  i++ia++a ++++l+  D++ + + + ++  +lg+D
  gi|116754182|ref|YP_843300.1| 113 FDVTCVPVddqgiVNPGEIERAIRDDTVLISVMHANNEIGTIQPIKEIAEIASERDILLHTDAVQTVGkIPVNVDQLGVD 192
                                    77776666224445689***********************************************999977788889**** PP

                                    EEEEETTTTT CS
                Cys_Met_Meta_PP 191 ivvhSaTKyl 200
                                    +   Sa K+ 
  gi|116754182|ref|YP_843300.1| 193 LLSISAHKFY 202
                                    ********96 PP

>> Pyridoxal_deC  Pyridoxal-dependent decarboxylase conserved domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   3.4e-05      0.12     165     236 ..     111     176 ..      75     221 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.4e-05
                                    HT-EEEEE--BTTTBB-HHHHHHHHHHHHCTT.EEEEEEEEBS-TTT-BB--HHHHHHHHHHCT-EEEEE-T CS
                  Pyridoxal_deC 165 lgvklrvipldengklrgaalekaieedkekGlipffvvatlGttvlgaFddlkelgdicekydlwlHvDAA 236
                                    +g+ +  +p+d++g++ + + e+ai +d     i     +       g    +ke+++i ++ d+ lH DA 
  gi|116754182|ref|YP_843300.1| 111 MGFDVTCVPVDDQGIVNPGEIERAIRDDTVL--IS----VMHANNEIGTIQPIKEIAEIASERDILLHTDAV 176
                                    5677999******************988766..32....3333455666789******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2711.74
//
Query:       gi|116754183|ref|YP_843301.1|  [L=324]
Description: hypothetical protein Mthe_0873 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); 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: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 2280.89
//
Query:       gi|116754184|ref|YP_843302.1|  [L=390]
Description: hypothetical protein Mthe_0874 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2777.95
//
Query:       gi|116754185|ref|YP_843303.1|  [L=235]
Description: hypothetical protein Mthe_0875 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-20   72.0   0.0    7.3e-20   71.3   0.0    1.3  1  Thg1      tRNAHis guanylyltransferase
    2.5e-06   27.6   0.0    3.7e-06   27.1   0.0    1.2  1  Thg1C     Thg1 C terminal domain
  ------ inclusion threshold ------
        0.1   11.8   0.0       0.52    9.5   0.0    2.0  2  MRF_C1    Myelin gene regulatory factor -C-terminal domain 1


Domain annotation for each model (and alignments):
>> Thg1  tRNAHis guanylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.3   0.0   1.2e-23   7.3e-20      11     123 ..      20     125 ..      11     127 .. 0.92

  Alignments for each domain:
  == domain 1  score: 71.3 bits;  conditional E-value: 1.2e-23
                           Thg1  11 dkllpntlivvRiDGrgFhkfskkhkfekPnDeralklmneaakelvkefe.divlaYgqSDEislvlsketklynrraq 89 
                                    ++l  ++++ vR+DGrgF ++ +  +f+kP+D  +++ +++aa++++++    ++laY++SDEi+l++ +e   +++r +
  gi|116754185|ref|YP_843303.1|  20 SELRVRSPFFVRVDGRGFGRMLR--DFSKPYDLGFARSIVSAARAFMESSGlAPILAYTFSDEINLLFLDEP--FRGRLE 95 
                                    567778899**************..9**********************99669*****************99..****** PP

                           Thg1  90 klvslvaslftaafvkllskafeelpsFDarvvl 123
                                    kl s++as+++++   +l +++    s Darv++
  gi|116754185|ref|YP_843303.1|  96 KLDSITASYISSSLSISLGRVV----SMDARVIP 125
                                    ***************9999996....58999886 PP

>> Thg1C  Thg1 C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   6.2e-10   3.7e-06       2      78 ..     130     204 ..     129     216 .. 0.93

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 6.2e-10
                          Thg1C   2 nlrDYlsWRqvDchinnlYNttFWalvqkgglteqeaeeeLkgtlskdkneiLfsefginYnnepeifrkGsvlvre 78 
                                    ++  Yl+  q+++  n ++   F+al+  +g+++++a e L++   +d +e+Lf++ g+n ++ p+  r+G +++r+
  gi|116754185|ref|YP_843303.1| 130 EILSYLQESQAEAWRNHVFSYGFYALL-GEGKSHADAMESLRNMKESDIHEMLFQR-GVNLAKTPAWERRGVMVYRS 204
                                    56789999******************9.799***********************76.9***************9996 PP

>> MRF_C1  Myelin gene regulatory factor -C-terminal domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.13   7.6e+02       6      12 ..      60      66 ..      56      68 .. 0.76
   2 ?    9.5   0.0   8.7e-05      0.52       3      14 ..     219     230 ..     217     234 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.13
                         MRF_C1  6 dRiFmEn 12
                                    R FmE+
  gi|116754185|ref|YP_843303.1| 60 ARAFMES 66
                                   699***7 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 8.7e-05
                         MRF_C1   3 VdkdRiFmEnVg 14 
                                     d++RiFmE ++
  gi|116754185|ref|YP_843303.1| 219 TDDGRIFMEEIL 230
                                    59*******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 1786.25
//
Query:       gi|116754186|ref|YP_843304.1|  [L=88]
Description: PRC-barrel domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-14   53.3   0.8    2.3e-14   53.2   0.8    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 !   53.2   0.8   1.3e-18   2.3e-14       5      76 ..       4      76 ..       1      79 [. 0.92

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 1.3e-18
                                   CS---TT-EEEETTSSEEEEEEEEEEETTTTEEEEEEEEETTT.......-EEEEEGG.CEECCCTEEEETTS- CS
                            PRC  5 rasdliGkeVytedGeklGkVkDvvidekegrvralvvsvggflgi..gekevliPfdlavkigkdriivdapk 76
                                   ++s++ G+eVyt+ G  +GkV+D v+d ++g + ++ v+  ++  +  +++ +++Pf+ ++ +++d+ii++ +k
  gi|116754186|ref|YP_843304.1|  4 EISSILGLEVYTDRGVFVGKVEDAVLDADSGTLSGIAVGSLNKELFdlKGRGIIVPFR-WITAVGDIIIMRHTK 76
                                   589************************************999854499**********.**********98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       211  (0.0117686); expected 358.6 (0.02)
Passed bias filter:                      197  (0.0109878); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 656.35
//
Query:       gi|116754187|ref|YP_843305.1|  [L=797]
Description: Pyrrolo-quinoline quinone [Methanosaeta thermophila PT]
Scores for 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-65  213.9  39.4      9e-06   26.0   0.9   16.2 16  PQQ_3     PQQ-like domain
      4e-61  206.6   0.7    1.6e-17   63.9   0.0    7.3  6  PQQ_2     PQQ-like domain
    2.4e-39  131.4  22.4    7.3e-05   22.5   0.0   14.0 15  PQQ       PQQ enzyme repeat
     0.0015   18.3   0.1         10    6.1   0.0    4.8  6  DUF4905   Domain of unknown function (DUF4905)


Domain annotation for each model (and alignments):
>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.9     2e-09     9e-06       3      40 .]      68     104 ..      68     104 .. 0.93
   2 !   16.5   0.2     2e-06     0.009       1      38 [.     105     144 ..     105     146 .. 0.85
   3 !    4.9   0.0    0.0086        38       4      27 ..     150     174 ..     149     187 .. 0.79
   4 ?    3.9   0.1     0.019        83       1      37 [.     193     231 ..     193     233 .. 0.89
   5 ?    1.4   0.0      0.11   4.9e+02      10      29 ..     256     275 ..     252     287 .. 0.82
   6 !    7.7   0.1    0.0012       5.3       5      37 ..     300     335 ..     297     338 .. 0.88
   7 !   15.3   0.0   4.7e-06     0.021       1      37 [.     339     381 ..     339     383 .. 0.87
   8 !   20.1   0.3   1.5e-07   0.00067       1      36 [.     387     428 ..     387     431 .. 0.88
   9 ?    1.7   0.0     0.086   3.8e+02      14      37 ..     468     490 ..     457     491 .. 0.84
  10 !   16.1   0.0   2.7e-06     0.012       1      39 [.     494     534 ..     494     535 .. 0.79
  11 !   22.1   0.0   3.4e-08   0.00015       1      39 [.     536     578 ..     536     579 .. 0.86
  12 !   20.9   0.0   8.1e-08   0.00036       1      38 [.     580     621 ..     580     623 .. 0.96
  13 !   18.5   0.0   4.6e-07    0.0021       1      36 [.     624     663 ..     624     665 .. 0.95
  14 !   17.7   0.0   8.6e-07    0.0038       1      40 []     668     711 ..     668     711 .. 0.86
  15 !   19.5   0.0   2.2e-07   0.00099       1      39 [.     712     757 ..     712     758 .. 0.79
  16 !   14.7   0.3   7.2e-06     0.032       1      36 [.     759     790 ..     759     793 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 2e-09
                          PQQ_3   3 vlWsvqlpgpvnsspavdgglvyvgtgdGtlyAlDaet 40 
                                    +lWs ++  +v  +p++ +g vyv +g+GtlyA+Da t
  gi|116754187|ref|YP_843305.1|  68 ILWSADIQ-RVDVTPVICDGAVYVIAGNGTLYAFDAGT 104
                                    58999999.88889**********************87 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 2e-06
                          PQQ_3   1 GevlWsvqlpgpvn..sspavdgglvyvgtgdGtlyAlDa 38 
                                    Ge +W+  l+g v   s+pa +g +v+++t+ G+l A+D 
  gi|116754187|ref|YP_843305.1| 105 GEAIWASHLDGWVFqtSTPACGGKKVFAATDSGNLAAVDR 144
                                    7778999999944444999********************6 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.0086
                          PQQ_3   4 lWsvqlpgpvnsspavdggl.vyvg 27 
                                    lW+++l ++   +p++++gl +y+g
  gi|116754187|ref|YP_843305.1| 150 LWNYSLTDKRFEAPLTYDGLrLYIG 174
                                    8******955667766666549998 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.019
                          PQQ_3   1 GevlWsv..qlpgpvnsspavdgglvyvgtgdGtlyAlD 37 
                                    G+++W++  ++ g+ +++    g++v+vg  dG + +l+
  gi|116754187|ref|YP_843305.1| 193 GTECWNYtsETKGYQWCGSCSIGNYVVVGQNDGIILSLN 231
                                    99*****99999999999999999999999999887776 PP

  == domain 5  score: 1.4 bits;  conditional E-value: 0.11
                          PQQ_3  10 pgpvnsspavdgglvyvgtg 29 
                                    pg++ ++++  +g +y++++
  gi|116754187|ref|YP_843305.1| 256 PGRIRAPVTCKDGWIYTTSE 275
                                    8999999999*******997 PP

  == domain 6  score: 7.7 bits;  conditional E-value: 0.0012
                          PQQ_3   5 Wsvqlpgpvnsspavdgglvyvgtg....dGtlyAlD 37 
                                    Wsv+++  + s+pa+  ++vy g g     G l++++
  gi|116754187|ref|YP_843305.1| 300 WSVPIGFST-STPAIFADRVYLGVGehghPGALVCIN 335
                                    9*****655.9**************999999999987 PP

  == domain 7  score: 15.3 bits;  conditional E-value: 4.7e-06
                          PQQ_3   1 GevlWsvqlpgpvnssp....avdgglvyvgtg..dGtlyAlD 37 
                                    G+ +W++++ + v++sp    a+d  ++ + t   dG++y+++
  gi|116754187|ref|YP_843305.1| 339 GDMIWTYPVEAGVKASPaistAYDKPRIIFNTAqiDGSVYCIE 381
                                    899**************77777777788888888*******96 PP

  == domain 8  score: 20.1 bits;  conditional E-value: 1.5e-07
                          PQQ_3   1 GevlWsvqlpg..pvnsspavdgglvyvgtg....dGtlyAl 36 
                                    Ge+lW+++ p+  ++ +++av+ g++y+gt+     G+ly+l
  gi|116754187|ref|YP_843305.1| 387 GELLWKFDPPDngYILGGVAVYKGRLYFGTEgdqhYGKLYCL 428
                                    9******655444999***************99999999998 PP

  == domain 9  score: 1.7 bits;  conditional E-value: 0.086
                          PQQ_3  14 nsspavdgglvyvgtgdGtlyAlD 37 
                                    +ss+ v+ g v+v +   +l++lD
  gi|116754187|ref|YP_843305.1| 468 GSSVSVASGMVFVNCV-DRLVCLD 490
                                    4889*********996.9999998 PP

  == domain 10  score: 16.1 bits;  conditional E-value: 2.7e-06
                          PQQ_3   1 GevlWsvql...pg.pvnsspavdgglvyvgtgdGtlyAlDae 39 
                                    G+vlWs+++   ++ + +++p++ +g+v++++   + y+l+a 
  gi|116754187|ref|YP_843305.1| 494 GRVLWSHPFksaGDyAFGFTPVYHDGKVFFTS--DRTYCLNAS 534
                                    99*****77432334666888*********99..599999986 PP

  == domain 11  score: 22.1 bits;  conditional E-value: 3.4e-08
                          PQQ_3   1 GevlWsv..qlpg.pvnsspavdgglvyvgtg.dGtlyAlDae 39 
                                    Ge++Ws+  +++  ++ +spa+++g+++v+++  ++ y+l+ e
  gi|116754187|ref|YP_843305.1| 536 GEEVWSYtpPTGRfAIDGSPAIAEGKIFVSDWdGHHYYCLEEE 578
                                    9******8877779999***************77777777655 PP

  == domain 12  score: 20.9 bits;  conditional E-value: 8.1e-08
                          PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtg....dGtlyAlDa 38 
                                    G+++W++++ g ++s+pa+d +++++g++     G++y+++ 
  gi|116754187|ref|YP_843305.1| 580 GKEIWNFTVEGNAQSTPAIDLNRLVFGSWewglGGRIYCVHL 621
                                    9**************************************986 PP

  == domain 13  score: 18.5 bits;  conditional E-value: 4.6e-07
                          PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtg....dGtlyAl 36 
                                    G+++W+ ++     +s+++ +g+vy+ t+    dG l Al
  gi|116754187|ref|YP_843305.1| 624 GTEIWNLSTENSPCGSATINDGVVYMPTYnfdgDGDLLAL 663
                                    99*******99889***********************999 PP

  == domain 14  score: 17.7 bits;  conditional E-value: 8.6e-07
                          PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtg.....dGtlyAlDaet 40 
                                    G +lW+ ++  p+ s+pa+++++vyv +g       + y++Da+t
  gi|116754187|ref|YP_843305.1| 668 GSILWRAEIS-PTDSTPAFADDRVYVCGGcegfsKLHTYCFDAKT 711
                                    889******9.899**************97777777777777766 PP

  == domain 15  score: 19.5 bits;  conditional E-value: 2.2e-07
                          PQQ_3   1 GevlWsv....qlpgpvnsspavdgglvyvgtg....dGtlyAlDae 39 
                                    Ge++W++    +++ +  +spa+++glv+vg +      +++Al+a+
  gi|116754187|ref|YP_843305.1| 712 GELIWKTpselEIG-DWRCSPAYADGLVFVGRPdfmeYDGIFALNAT 757
                                    9******8877777.677*************8866666666666665 PP

  == domain 16  score: 14.7 bits;  conditional E-value: 7.2e-06
                          PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtgdGtlyAl 36 
                                    Ge++Ws++ +g   sspav+ g v++ +  G++yA+
  gi|116754187|ref|YP_843305.1| 759 GEIVWSYPAGG---SSPAVACGMVFTIGN-GRVYAF 790
                                    9*******996...58**********995.****98 PP

>> PQQ_2  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.7   0.2   2.4e-18   1.1e-14      59     233 ..      69     237 ..      67     238 .. 0.74
   2 !   20.4   0.0   6.9e-08   0.00031      82     237 .]     181     345 ..     157     345 .. 0.73
   3 !    8.0   0.0   0.00043       1.9       2      51 ..     374     428 ..     373     435 .. 0.74
   4 !   31.0   0.0     4e-11   1.8e-07      10     101 ..     451     541 ..     447     543 .. 0.81
   5 !   63.9   0.0   3.5e-21   1.6e-17       7     183 ..     530     697 ..     529     704 .. 0.87
   6 !   32.0   0.0   1.9e-11   8.6e-08       6      90 ..     705     789 ..     700     797 .] 0.71

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 2.4e-18
                          PQQ_2  59 lWettlegpvvgaplvaegrvvvvasdgqlialdaedGkrlWstqqrseepaelrssaspavagdtvvvgessgklvald 138
                                    lW+++ +  v  +p + +g v+v a++g+l+a+da +G+  W  ++++     + ++++pa +g++v++++ sg+l+a+d
  gi|116754187|ref|YP_843305.1|  69 LWSADIQR-VDVTPVICDGAVYVIAGNGTLYAFDAGTGEAIWASHLDG----WVFQTSTPACGGKKVFAATDSGNLAAVD 143
                                    67777655.445579****************************88888....799************************* PP

                          PQQ_2 139 pkdGkvlWerelaaprgtselsrvgdisgrpvvaegtVyassgqgrllal.dlatgrrlwske..issingl.pildgdl 214
                                      +G +lW+++l++ r ++    ++    r+ + eg+ y  s ++ + ++ d +t    w+ +   ++++ + ++  g++
  gi|116754187|ref|YP_843305.1| 144 RLTGIKLWNYSLTDKRFEAP---LTYDGLRLYIGEGSAYGTSEKK-FFCIfDNGTEC--WNYTseTKGYQWCgSCSIGNY 217
                                    ************88773332...2333334444455555555444.78887888888..633312444443315667777 PP

                          PQQ_2 215 lyvvsa.gelialdratGav 233
                                    ++v+ + g ++ l+r +G+v
  gi|116754187|ref|YP_843305.1| 218 VVVGQNdGIILSLNRVNGEV 237
                                    77777469999999999987 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 6.9e-08
                          PQQ_2  82 vasdgqlialdaedGkrlWstqqrseepaelrssaspavagdtvvvgessgklvaldpkdGkvlWerel.aaprgtsels 160
                                     ++++ ++ +d  +G++ W+ + ++++       +s+++ g++vvvg+ +g +  l+  +G+v +  +l  ++r + +  
  gi|116754187|ref|YP_843305.1| 181 TSEKKFFCIFD--NGTECWN-YTSETKGYQW--CGSCSI-GNYVVVGQNDGIILSLNRVNGEVADALSLnDSTRLSFSQN 254
                                    45555666666..7888888.5555433332..344444.69**********************9999955555444444 PP

                          PQQ_2 161 rvgdisgrpvvaeg...tVyassgqgr.l..laldlatgr...rlwskeissinglpildgdllyvvs.a....gelial 226
                                      g+i + ++ ++g   t+  ++ +++ +  +a+d +tgr   r ws +i+  +++p+  +d +y++  +    g l+++
  gi|116754187|ref|YP_843305.1| 255 NPGRIRAPVTCKDGwiyTTSEITANEGyVwkIAFDKETGRfedRGWSVPIGFSTSTPAIFADRVYLGVgEhghpGALVCI 334
                                    9999999999999966633333333333244***********666*9998888888888888888887667********* PP

                          PQQ_2 227 dratGavlWkt 237
                                    +  +G  +W++
  gi|116754187|ref|YP_843305.1| 335 NDTSGDMIWTY 345
                                    *********96 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.00043
                          PQQ_2   2 egvvsalda..atGaelWrvdlarp....lgggvsravlsggtlfva....tgggrlval 51 
                                    +g+v++++   + G++lW++d+  p    + ggv  av  +g+l+ +    + +g+l++l
  gi|116754187|ref|YP_843305.1| 374 DGSVYCIEDsgDRGELLWKFDP--PdngyILGGV--AV-YKGRLYFGtegdQHYGKLYCL 428
                                    5788888875559*******98..2344799999..99.99****993443355556555 PP

  == domain 4  score: 31.0 bits;  conditional E-value: 4e-11
                          PQQ_2  10 aatGaelWrv.dlarplgggvsravlsggtlfvatgggrlvaldaatGkvlWettlegpvvga....plvaegrvvvvas 84 
                                    +++ ++ W + d+  + g+ v   v + g +fv    +rlv+ld  +G+vlW+  +++    a    p   +g+v++ + 
  gi|116754187|ref|YP_843305.1| 451 PRDNRTAWISeDIRAQPGSSV--SV-ASGMVFVN-CVDRLVCLDQISGRVLWSHPFKSAGDYAfgftPVYHDGKVFFTS- 525
                                    678889999977766677777..77.99*****5.*********************55533335555********9985. PP

                          PQQ_2  85 dgqlialdaedGkrlWs 101
                                    d++++ l+a dG+++Ws
  gi|116754187|ref|YP_843305.1| 526 DRTYC-LNASDGEEVWS 541
                                    66655.999*******9 PP

  == domain 5  score: 63.9 bits;  conditional E-value: 3.5e-21
                          PQQ_2   7 aldaatGaelWrvdlarp...lgggvsravlsggtlfvat.gggrlvaldaatGkvlWettlegpvvgaplvaegrvvvv 82 
                                    +l+a +G+e+W+ ++ ++   ++g +  a  ++g++fv + +g   ++l+ +tGk++W++t+eg ++++p ++ +r+v+ 
  gi|116754187|ref|YP_843305.1| 530 CLNASDGEEVWSYTPPTGrfaIDGSP--AI-AEGKIFVSDwDGHHYYCLEEETGKEIWNFTVEGNAQSTPAIDLNRLVFG 606
                                    78999********8733245599999..99.8888888854999************************************ PP

                          PQQ_2  83 a....sdgqlialdaedGkrlWstqqrseepaelrssaspavagdtvvvges....sgklvaldpkdGkvlWerelaapr 154
                                    +     +g+++ +  ++G++ W+   ++ +     + +s ++ +++v++++     +g+l al++ +G+ lW +e++ + 
  gi|116754187|ref|YP_843305.1| 607 SwewgLGGRIYCVHLNNGTEIWNLSTEN-S-----PCGSATINDGVVYMPTYnfdgDGDLLALSLVNGSILWRAEISPTD 680
                                    *99988889999***********44444.3.....344788999999999999999******************997766 PP

                          PQQ_2 155 gtselsrvgdisgrpvvaegtVyassgqg 183
                                                ++p +a+++Vy+++g +
  gi|116754187|ref|YP_843305.1| 681 ------------STPAFADDRVYVCGGCE 697
                                    ............8*****99*****9876 PP

  == domain 6  score: 32.0 bits;  conditional E-value: 1.9e-11
                          PQQ_2   6 saldaatGaelWrv..dlar..plgggvsravlsggtlfva....tgggrlvaldaatGkvlWettlegpvvgaplvaeg 77 
                                    +++da+tG+++W++  +l +  ++++ +  a+ ++g +fv+     +++ + al+a+tG+++W++ + g    +p va g
  gi|116754187|ref|YP_843305.1| 705 YCFDAKTGELIWKTpsEL-EigDWRCSP--AY-ADGLVFVGrpdfMEYDGIFALNATTGEIVWSYPAGGS---SPAVACG 777
                                    578999999999995422.122356666..88.9999999866555999999999999999999998776...7788888 PP

                          PQQ_2  78 rvvvvasdgqlia 90 
                                    +v+   +++++ a
  gi|116754187|ref|YP_843305.1| 778 MVFTIGNGRVY-A 789
                                    88877544433.3 PP

>> PQQ  PQQ enzyme repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.3   8.4e-07    0.0038       5      32 ..      90     117 ..      86     121 .. 0.83
   2 !   13.5   0.0   1.1e-05     0.051       2      30 ..     129     157 ..     128     164 .. 0.90
   3 ?   -1.9   0.1      0.87   3.9e+03      18      26 ..     191     199 ..     191     203 .. 0.84
   4 ?    0.9   0.1      0.11   5.1e+02       3      22 ..     218     237 ..     215     238 .. 0.87
   5 ?   -2.4   0.0       1.2   5.5e+03      14      21 ..     287     294 ..     286     295 .. 0.88
   6 !   12.0   0.0   3.3e-05      0.15      10      37 ..     329     356 ..     321     357 .. 0.84
   7 ?    3.9   0.0     0.012        56      20      31 ..     387     398 ..     370     402 .. 0.79
   8 !    5.5   0.0    0.0039        18       1      27 [.     476     501 ..     476     505 .. 0.89
   9 !   16.0   0.0   1.8e-06    0.0083      11      30 ..     527     546 ..     519     550 .. 0.84
  10 !   12.8   0.0   1.9e-05     0.085      13      37 ..     573     597 ..     571     598 .. 0.91
  11 ?    3.8   0.0     0.014        62       9      24 ..     613     628 ..     610     636 .. 0.88
  12 !   10.4   0.0   0.00011       0.5       8      33 ..     656     681 ..     645     685 .. 0.88
  13 !   12.7   0.0     2e-05     0.091      12      27 ..     704     719 ..     701     726 .. 0.88
  14 !   22.5   0.0   1.6e-08   7.3e-05      12      31 ..     751     770 ..     748     774 .. 0.90
  15 ?   -2.1   0.1      0.97   4.3e+03       9      15 ..     784     790 ..     782     791 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 8.4e-07
                                    EEETTSEEEEEETTTCCEEEEEESSSCG CS
                            PQQ   5 lgsadGylyAlDadTGkvlWrfktggpv 32 
                                    +   +G+lyA+Da TG+ +W   ++g+v
  gi|116754187|ref|YP_843305.1|  90 VIAGNGTLYAFDAGTGEAIWASHLDGWV 117
                                    4456****************98888765 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 1.1e-05
                                    EEEEEETTSEEEEEETTTCCEEEEEESSS CS
                            PQQ   2 vvylgsadGylyAlDadTGkvlWrfktgg 30 
                                    +v+++++ G+l A+D+ TG +lW + + +
  gi|116754187|ref|YP_843305.1| 129 KVFAATDSGNLAAVDRLTGIKLWNYSLTD 157
                                    699********************998765 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.87
                                    TTCCEEEEE CS
                            PQQ  18 dTGkvlWrf 26 
                                    d+G+++W +
  gi|116754187|ref|YP_843305.1| 191 DNGTECWNY 199
                                    68*****77 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.11
                                    EEEEETTSEEEEEETTTCCE CS
                            PQQ   3 vylgsadGylyAlDadTGkv 22 
                                    v++g++dG ++ l++ +G+v
  gi|116754187|ref|YP_843305.1| 218 VVVGQNDGIILSLNRVNGEV 237
                                    5677**************97 PP

  == domain 5  score: -2.4 bits;  conditional E-value: 1.2
                                    EEETTTCC CS
                            PQQ  14 AlDadTGk 21 
                                    A+D +TG+
  gi|116754187|ref|YP_843305.1| 287 AFDKETGR 294
                                    9******6 PP

  == domain 6  score: 12.0 bits;  conditional E-value: 3.3e-05
                                    SEEEEEETTTCCEEEEEESSSCGSSESE CS
                            PQQ  10 GylyAlDadTGkvlWrfktggpvlslpi 37 
                                    G l+ ++ ++G+++W++++++ v ++p+
  gi|116754187|ref|YP_843305.1| 329 GALVCINDTSGDMIWTYPVEAGVKASPA 356
                                    7788888455**************9996 PP

  == domain 7  score: 3.9 bits;  conditional E-value: 0.012
                                    CCEEEEEESSSC CS
                            PQQ  20 GkvlWrfktggp 31 
                                    G++lW+f+++++
  gi|116754187|ref|YP_843305.1| 387 GELLWKFDPPDN 398
                                    9*******9875 PP

  == domain 8  score: 5.5 bits;  conditional E-value: 0.0039
                                    TEEEEEETTSEEEEEETTTCCEEEEEE CS
                            PQQ   1 gvvylgsadGylyAlDadTGkvlWrfk 27 
                                    g v++ + d +l+ lD  +G+vlW+++
  gi|116754187|ref|YP_843305.1| 476 GMVFVNCVD-RLVCLDQISGRVLWSHP 501
                                    568999999.**************986 PP

  == domain 9  score: 16.0 bits;  conditional E-value: 1.8e-06
                                    EEEEEETTTCCEEEEEESSS CS
                            PQQ  11 ylyAlDadTGkvlWrfktgg 30 
                                    + y l+a++G+++W++ ++ 
  gi|116754187|ref|YP_843305.1| 527 RTYCLNASDGEEVWSYTPPT 546
                                    79**************9875 PP

  == domain 10  score: 12.8 bits;  conditional E-value: 1.9e-05
                                    EEEETTTCCEEEEEESSSCGSSESE CS
                            PQQ  13 yAlDadTGkvlWrfktggpvlslpi 37 
                                    y l  +TGk++W f ++g+ +s+p+
  gi|116754187|ref|YP_843305.1| 573 YCLEEETGKEIWNFTVEGNAQSTPA 597
                                    678889****************996 PP

  == domain 11  score: 3.8 bits;  conditional E-value: 0.014
                                    TSEEEEEETTTCCEEE CS
                            PQQ   9 dGylyAlDadTGkvlW 24 
                                    +G++y + +++G+++W
  gi|116754187|ref|YP_843305.1| 613 GGRIYCVHLNNGTEIW 628
                                    79************** PP

  == domain 12  score: 10.4 bits;  conditional E-value: 0.00011
                                    TTSEEEEEETTTCCEEEEEESSSCGS CS
                            PQQ   8 adGylyAlDadTGkvlWrfktggpvl 33 
                                     dG l+Al + +G +lWr ++++ + 
  gi|116754187|ref|YP_843305.1| 656 GDGDLLALSLVNGSILWRAEISPTDS 681
                                    59******************998775 PP

  == domain 13  score: 12.7 bits;  conditional E-value: 2e-05
                                    EEEEETTTCCEEEEEE CS
                            PQQ  12 lyAlDadTGkvlWrfk 27 
                                     y +Da+TG+++W+++
  gi|116754187|ref|YP_843305.1| 704 TYCFDAKTGELIWKTP 719
                                    799**********987 PP

  == domain 14  score: 22.5 bits;  conditional E-value: 1.6e-08
                                    EEEEETTTCCEEEEEESSSC CS
                            PQQ  12 lyAlDadTGkvlWrfktggp 31 
                                    ++Al+a+TG+++W++++gg 
  gi|116754187|ref|YP_843305.1| 751 IFALNATTGEIVWSYPAGGS 770
                                    8****************996 PP

  == domain 15  score: -2.1 bits;  conditional E-value: 0.97
                                    TSEEEEE CS
                            PQQ   9 dGylyAl 15 
                                    +G++yA+
  gi|116754187|ref|YP_843305.1| 784 NGRVYAF 790
                                    8*****7 PP

>> DUF4905  Domain of unknown function (DUF4905)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.64   2.9e+03      71      83 .]      97     109 ..      94     109 .. 0.89
   2 ?   -3.3   0.0         2   8.7e+03      69      83 .]     137     151 ..     135     151 .. 0.88
   3 ?   -1.4   0.0       0.5   2.2e+03      49      83 .]     312     343 ..     286     343 .. 0.71
   4 ?   -1.9   0.0      0.73   3.3e+03      30      57 ..     387     414 ..     383     416 .. 0.81
   5 !    6.1   0.0    0.0023        10      24      83 .]     618     672 ..     615     672 .. 0.80
   6 !    5.4   0.0    0.0039        17      23      83 .]     705     763 ..     700     763 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.64
                        DUF4905  71 liaiDiktgkllW 83 
                                    l a+D+ tg+ +W
  gi|116754187|ref|YP_843305.1|  97 LYAFDAGTGEAIW 109
                                    78**********9 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2
                        DUF4905  69 kgliaiDiktgkllW 83 
                                     +l+a+D  tg  lW
  gi|116754187|ref|YP_843305.1| 137 GNLAAVDRLTGIKLW 151
                                    5799*******9999 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.5
                        DUF4905  49 aiykgvlllhkyekpdsPehkgliaiDiktgkllW 83 
                                    ai+++ ++l     ++ + +  l+ i+  +g ++W
  gi|116754187|ref|YP_843305.1| 312 AIFADRVYLG---VGEHGHPGALVCINDTSGDMIW 343
                                    5555555553...3566778889999999999999 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 0.73
                        DUF4905  30 gkllfedlvleekwwtgleaiykgvlll 57 
                                    g+ll++    ++ +  g  a+ykg l++
  gi|116754187|ref|YP_843305.1| 387 GELLWKFDPPDNGYILGGVAVYKGRLYF 414
                                    56677777778889999999******98 PP

  == domain 5  score: 6.1 bits;  conditional E-value: 0.0023
                        DUF4905  24 aldletgkllfedlvleekwwtgleaiykgvlllhkyekpdsPehkgliaiDiktgkllW 83 
                                    +++l++g+ +++     e+  +g ++i++gv+++  y+ +      +l+a+ +++g +lW
  gi|116754187|ref|YP_843305.1| 618 CVHLNNGTEIWNLS--TENSPCGSATINDGVVYMPTYNFDG---DGDLLALSLVNGSILW 672
                                    77777777777643..344468999************9776...568************9 PP

  == domain 6  score: 5.4 bits;  conditional E-value: 0.0039
                        DUF4905  23 saldletgkllfedlvlee..kwwtgleaiykgvlllhkyekpdsPehkgliaiDiktgkllW 83 
                                    +++d +tg+l+++  +  e  +w +  + +y++ l ++   +pd  e  g+ a+++ tg+++W
  gi|116754187|ref|YP_843305.1| 705 YCFDAKTGELIWKTPSELEigDWRC--SPAYADGLVFVG--RPDFMEYDGIFALNATTGEIVW 763
                                    6899999999999887776446777..667777777764..89999***************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (797 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); 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):               4  [number of targets reported over threshold]
# CPU time: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.42
# Mc/sec: 5648.53
//
Query:       gi|116754188|ref|YP_843306.1|  [L=1812]
Description: cobaltochelatase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
          0 1120.7   0.0          0 1120.5   0.0    1.0  1  CobN-Mg_chel  CobN/Magnesium Chelatase
    4.6e-65  219.5  12.3    4.2e-25   88.7   0.4    3.7  4  PQQ_2         PQQ-like domain
    2.8e-53  177.1  25.5    2.1e-07   31.2   0.0    9.0  9  PQQ_3         PQQ-like domain
    5.4e-27   92.4  10.9    8.7e-07   28.6   0.0    8.5  8  PQQ           PQQ enzyme repeat
     0.0043   16.9   0.0        3.5    7.6   0.0    3.4  3  DUF4905       Domain of unknown function (DUF4905)
  ------ inclusion threshold ------
      0.023   15.3   0.5       0.45   11.1   0.0    3.3  4  DUF4430       Domain of unknown function (DUF4430)


Domain annotation for each model (and alignments):
>> CobN-Mg_chel  CobN/Magnesium Chelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1120.5   0.0         0         0       3    1086 ..     610    1681 ..     608    1684 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1120.5 bits;  conditional E-value: 0
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel    3 YlkeggveNlknllryladkllgkkeeeveppvelpeegiyhpdakelfesleeylewykkakkekaptvgilfyrah 80  
                                     Y+++ggveN+++l++yla++++g  +  v++p++ p+e iyhpda++lfe++++y+ewy  +++++aptvgi  y+ +
  gi|116754188|ref|YP_843306.1|  610 YWEYGGVENMRRLIAYLAAHFCG-VDVMVDAPMPAPKEYIYHPDAPDLFENITSYMEWY--RYNTSAPTVGIASYYGD 684 
                                     **********************8.77789*****************************9..6**************** PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel   81 llagntavidaliraleerglnvlpvfvssldseaqealeelftkegeekvdalinttsfalvkgpaeeeeeeaeeea 158 
                                     + + +     +lira+e+rg+nv+++ +s+     ++ le++f  ++++ vd+ i t sf+l+ g  ++       e 
  gi|116754188|ref|YP_843306.1|  685 MGQPD---RIDLIRAFERRGANVICIGFSN-----ASSLERFFVLNNTSLVDLAIVTKSFRLSYGDPDRG-----VEI 749 
                                     95555...457***************7777.....6789999999999**************97775444.....456 PP

                                     xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  159 lkelnvPvlqa.ilssqsreeWeessqGlspldlamsvalpEldGriepvvisfkeeeeeetevekyepiperverva 235 
                                     l++lnvPvl +  l++qs  eW++s   ++p++l ++valpE+dG  +p++is+k       + ++y  i+  ver+a
  gi|116754188|ref|YP_843306.1|  750 LESLNVPVLRGmRLYYQSPMEWTNS--SINPMELYFQVALPEMDGIFDPIAISGK-------NDTVYSSIEPEVERIA 818 
                                     8***********************9..9**************************5.......3579************ PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  236 dlaarwarLrrkpnaekkvaiilanyppgegrlgnavgLdvpaSlvnlLkalkeeGYdveelpesgdeLiellleggt 313 
                                     d+a++++rL+ kpn+ek+vaii++n+  g++++  + +L+vp+Sl n+L+++k+ GY++e++  +++ L++ll ++gt
  gi|116754188|ref|YP_843306.1|  819 DRAMAQIRLQ-KPNSEKRVAIIYYNHGGGKDNIE-GCYLNVPRSLRNILEHMKRLGYRIESDVPDEKVLVDLLAHQGT 894 
                                     *********7.89********************9.77**********************877559************* PP

                                     xxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  314 ndpew......eelkvgaaallpaeeYeewfeeLpeelreeveerWgeppgemveeeksgekklvipglqlGnvfvgv 385 
                                     n  +w      +++k g+a+l+paeeY +wfeeLpe+ + e +++Wg+ppg+++  ++s+++++vip+l++Gnv++++
  gi|116754188|ref|YP_843306.1|  895 NVGTWapgeldAMVKGGNATLIPAEEYIQWFEELPEDRQMEAVNHWGPPPGDIMVFRNSSGSYMVIPKLSFGNVILLP 972 
                                     *999998777555566************************************666678889***************** PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  386 QPargyeedpsklyhdpdlpPthqYlAfYlWlreefgadavvHvGkHGtlEwlPGKqvglseecyPdillgdlPhlYp 463 
                                     QP+rg+ e+ + lyh++d+pP+hqY+AfYlWl++efgada++H+GkHGt+EwlPG++  + ++++P++l++d+P++Yp
  gi|116754188|ref|YP_843306.1|  973 QPSRGWLENGTVLYHSTDVPPHHQYIAFYLWLKHEFGADAIIHLGKHGTQEWLPGREGVVGGDDWPALLVQDVPVVYP 1050
                                     ****************************************************************************** PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  464 YivnnpgEGtqAKRRsyAviidHltPpmtraelygelaeLeelideYeeaesldperlkalreqilelveelnldkdl 541 
                                     Yiv+n++EGtqAKRR+ Av+i+HltPp++ a+lyg+l++L+e +deY+++ ++  + +++ r +ile++++l+ld+dl
  gi|116754188|ref|YP_843306.1| 1051 YIVDNIAEGTQAKRRGDAVMISHLTPPIVAAGLYGNLSDLKESVDEYRNVLNE--SVKDEYRMKILETCRDLHLDEDL 1126
                                     *************************************************8554..66777888*************** PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  542 gleeakeeeeeefeellekldgyleelkeaqirdglhilGeapegeqlvdlvvailrleneegesltealaealgldl 619 
                                     g++ ++ +e+++fee+l +l++yleelk++ +++glh++G+++e+++lv++v ++l      g+s+ +++  al    
  gi|116754188|ref|YP_843306.1| 1127 GANLSALQEPAAFEEFLPELEDYLEELKSSFMPYGLHTFGQPYENDSLVAMVRSML------GDSYIKEIEGAL---- 1194
                                     *9999999************************************************......999999999995.... PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............xxxxxxxxx RF
                   CobN-Mg_chel  620 deleeksekelrtagdalealeeeaeelveelleeeaeeeeaeaeeleeeeeeeee.............eteeEital 684 
                                                  +++ ++++e+ +++l+ e++ +++++e+a+++ l e+ ++ +e             ++e+E+t++
  gi|116754188|ref|YP_843306.1| 1195 -------------NSSDVDRIENVSSSLLYEVVINGSSPETAQENLLGETGSNLTEilnlsriyadglrSCENELTNM 1259
                                     .............34568999*********************99999999999988************9999****** PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                   CobN-Mg_chel  685 lraLdGeyippgpsGdptrgraevLPTGrNfysvDpraiPteaAwevGkklaeellerylqeh.geyPekvglslwgt 761 
                                      +aL+++yipp+p++dp+r+++ vLPTGrNf svDpr++Pt+aAwevG+klaeell++y+ +h g+yP+k++++lw+ 
  gi|116754188|ref|YP_843306.1| 1260 TNALSAGYIPPSPADDPIRDPQ-VLPTGRNFRSVDPRRVPTPAAWEVGRKLAEELLDEYRLKHnGTYPRKMAIVLWAW 1336
                                     ********************77.*************************************9999*************9 PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  762 etmrteGediAqiLallGvrPvwdaagrvvdlelipleeLgRPRiDVtvriSGffRDafpnlielldkavelvaeldE 839 
                                     + m  +G   ++iL+l+G+rPv+da g v+d+ l+pl+eLgRPRiDV+v  SG++RD+fp+ ++l+dka++l+a+  +
  gi|116754188|ref|YP_843306.1| 1337 A-MTDHGVVDSEILQLIGARPVYDAYGGVSDVALVPLSELGRPRIDVVVVPSGLYRDLFPEKLRLIDKAIRLAANDTD 1413
                                     6.7788************************************************************************ PP

                                     xxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  840 peedNfvrkhvleeeaelee.....keeaeeratyRvFgskpGaYgagvqelies.snWedeedLaeaYlnwssyaYg 911 
                                      ++ N++r++++  ++ l +     +e+ae  ++ R+F +++G+Yg ++++ +++ ++We++++L  ++++++sy+Yg
  gi|116754188|ref|YP_843306.1| 1414 ATYPNYIRENSEILKDMLLQtgnytAEDAEFLSRSRIFLEAAGTYGPNLDAPVSAsDRWENDSELGSLFISRMSYIYG 1491
                                     ******************9966654446679************************9*********************9 PP

                                     xx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  912 kg...........aegeeaeeafearLkrvdvvvqnqdsrehdlldsddyyqflGGltaavrslsgkkpeayfgdssn 978 
                                      g            + e++ e+++a+L++vd++v++++s+ ++++d dd++q+lGG+++avr+++g++pe+y++d ++
  gi|116754188|ref|YP_843306.1| 1492 DGiwggrfdsgrsLSLEQQMEVYTANLRDVDAAVHHTNSNLYGFIDNDDVFQYLGGIALAVRTVTGSTPEMYVTDVRD 1569
                                     777777777777799999999********************************************************* PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx.. RF
                   CobN-Mg_chel  979 penpkvrtlkeeiarelrsrvlNPkWiegmmrhGykGafelaatvdnlfgwdata.dvvddwvyeevaetYvlDee.. 1053
                                     p++ +v++l e+++relr+r+ NPkWi+gmm++Gy+Ga+e++++v++l+gw+ t  ++v++++++ev++ Yv+D++  
  gi|116754188|ref|YP_843306.1| 1570 PRKERVHELGEFFSRELRTRYYNPKWIQGMMEQGYSGAREMDRFVEYLWGWETTVpELVSENTWNEVHDIYVEDRYnl 1647
                                     ****************************************************************************** PP

                                     .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel 1054 .vrefleekNpwAlreiaerLlEaarrglWease 1086
                                      ++ef++e+NpwA + + +rLlE+ar++ W++s+
  gi|116754188|ref|YP_843306.1| 1648 gLQEFFRENNPWAAQVMDARLLETARKDRWHPSA 1681
                                     ******************************9986 PP

>> PQQ_2  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.61   1.8e+03       4      42 ..      43      80 ..      40      85 .. 0.64
   2 !   88.7   0.4   1.4e-28   4.2e-25       6     207 ..      94     281 ..      88     283 .. 0.88
   3 !   74.0   0.5   4.3e-24   1.3e-20      12     157 ..     186     320 ..     186     322 .. 0.92
   4 !   83.4   0.6     6e-27   1.8e-23       3     206 ..     257     444 ..     255     463 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.61
                          PQQ_2  4 vvsaldaatGaelWrvdl.arplgggvsravlsggtlfva 42
                                    vs   +++ ++lW+++l + +  gg+  a+ s g++fv 
  gi|116754188|ref|YP_843306.1| 43 NVSGSGPDSPELLWSTSLtGHGYIGGS--ASISSGRVFVS 80
                                   555556667777888877444555555..66677777775 PP

  == domain 2  score: 88.7 bits;  conditional E-value: 1.4e-28
                          PQQ_2   6 saldaatGaelWrvdlarplgggvsravlsggtlfvatgggrlvaldaatGkvlWettlegp.....vvgaplvaegrvv 80 
                                    +++d+++G++lW   +  +  gg s++ + g+++f+++ +g+++++d  tGk lW++t e       v ++pl+++g ++
  gi|116754188|ref|YP_843306.1|  94 ACIDERNGTVLWINPV--GGKGGASTPAVFGNKVFTGSLTGEIYCVDVLTGKTLWNRTIERDpkywgVASSPLIENGTLY 171
                                    689***********88..66788888999*****************************9654111124455********* PP

                          PQQ_2  81 vva.sdgqlialdaedGkrlWstqqrseepaelrssaspavagdtvvvgessgklvaldpkdGkvlWerelaaprgtsel 159
                                    v++ sdg+l al+  dG++lW++   s     +++ aspa +g+++++++ +  l+++++++ k +W+++  a       
  gi|116754188|ref|YP_843306.1| 172 VMSfSDGALHALS-LDGDELWNVSTGS-----VSPFASPAASGERIYFPGGDPALYCINATTQKIVWKTPADA------- 238
                                    *************.********55555.....99999********************************9855....... PP

                          PQQ_2 160 srvgdisgrpvvaegtVyassgqgrllaldlatgrrlwskeissingl 207
                                         i+++p +++ tV++++    + al+++tg++lw+++i++  ++
  gi|116754188|ref|YP_843306.1| 239 ----VITSSPAIWNSTVFFVTERS-ISALNATTGSTLWQRSINGTEST 281
                                    ....388******99******888.7888*************998775 PP

  == domain 3  score: 74.0 bits;  conditional E-value: 4.3e-24
                          PQQ_2  12 tGaelWrvdlarplgggvsravlsggtlfvatgggrlvaldaatGkvlWettlegpvvgaplvaegrvvvvasdgqlial 91 
                                    +G elW v+   ++ + ++ +  sg +++  +g + l++++a+t k++W+t +++ + ++p + +  v++v+ +++++al
  gi|116754188|ref|YP_843306.1| 186 DGDELWNVST--GSVSPFASPAASGERIYFPGGDPALYCINATTQKIVWKTPADAVITSSPAIWNSTVFFVT-ERSISAL 262
                                    699*****87..78899999999************************************************7.99***** PP

                          PQQ_2  92 daedGkrlWstqqrseepaelrssaspavagdtvvvgessgklvaldpkdGkvlWerelaaprgts 157
                                    +a++G +lW++  ++       + ++pa+a ++v+vg+++g +v+ld ++G+++We+e+  p ++s
  gi|116754188|ref|YP_843306.1| 263 NATTGSTLWQRSING-------TESTPAIAFGRVYVGTADGHVVCLD-TNGSQIWETEVNGPVRSS 320
                                    **********44444.......77999999*****************.99*********8887766 PP

  == domain 4  score: 83.4 bits;  conditional E-value: 6e-27
                          PQQ_2   3 gvvsaldaatGaelWrvdlarplgggvsravlsggtlfvatgggrlvaldaatGkvlWettlegpvvgaplvaegrvvvv 82 
                                     ++sal+a+tG++lW+ ++    +g  s++  + g+++v+t  g +v+ld ++G+++Wet+++gpv+++pl+ +gr+++ 
  gi|116754188|ref|YP_843306.1| 257 RSISALNATTGSTLWQRSI----NGTESTPAIAFGRVYVGTADGHVVCLD-TNGSQIWETEVNGPVRSSPLFLDGRIYFG 331
                                    689**************87....33333466688****************.99*************************** PP

                          PQQ_2  83 a..sdg.qlialdaedGkrlWstqqrseepaelrssaspavagdtvvvgessgklvaldpkdGkvlWerel.aaprgtse 158
                                    +  + g +++al+a dG ++W  +  +    e    +sp+ +++ +++g  +g+l+a++    ++lW+ e+  +++    
  gi|116754188|ref|YP_843306.1| 332 TntD-GgAVYALNASDGSVVWM-YTVN----E-YIMSSPSASDGILFIGADDGRLYAFSSLQKDLLWSGEVvLENK---- 400
                                    9744.46***************.8888....2.222455555788888888********************88888.... PP

                          PQQ_2 159 lsrvgdisgrpvvaegtVyassgqgrllal.dlatgr..rl.wskeissing 206
                                            + +v+++g+Vy +s +  l+al   a+ +  ++  ++++ si g
  gi|116754188|ref|YP_843306.1| 401 --------SLNVSVKGDVYTISMKSALGALiSFASSNgiNVsVNDSLISIYG 444
                                    ........78888989******999988887777776543324555555554 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.1   0.00051       1.5       2      28 ..      53      81 ..      53      91 .. 0.87
   2 !   25.0   0.6   6.2e-09   1.9e-05       1      38 [.     101     139 ..     101     141 .. 0.92
   3 !   14.7   0.0   1.1e-05     0.033       1      37 [.     142     184 ..     142     186 .. 0.84
   4 !   29.4   0.1   2.6e-10   7.6e-07       1      40 []     187     227 ..     187     227 .. 0.94
   5 !   20.3   0.1   1.9e-07   0.00057       2      40 .]     229     266 ..     229     266 .. 0.97
   6 !   28.1   0.1   6.4e-10   1.9e-06       1      38 [.     267     303 ..     267     304 .. 0.93
   7 !   31.2   0.1   7.3e-11   2.2e-07       1      39 [.     305     345 ..     305     346 .. 0.97
   8 !   31.2   0.0     7e-11   2.1e-07       1      36 [.     347     382 ..     347     384 .. 0.97
   9 ?   -3.7   0.0         6   1.8e+04       3      23 ..     459     487 ..     458     490 .. 0.46

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00051
                          PQQ_3  2 evlWsvqlpg..pvnsspavdgglvyvgt 28
                                   e+lWs++l g  ++++s+ ++ g+v+v+ 
  gi|116754188|ref|YP_843306.1| 53 ELLWSTSLTGhgYIGGSASISSGRVFVSN 81
                                   68****996555**************975 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 6.2e-09
                          PQQ_3   1 GevlWsvqlpg.pvnsspavdgglvyvgtgdGtlyAlDa 38 
                                    G+vlW  +++g  + s+pav g++v++g+  G +y++D 
  gi|116754188|ref|YP_843306.1| 101 GTVLWINPVGGkGGASTPAVFGNKVFTGSLTGEIYCVDV 139
                                    9**********6666999********************6 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 1.1e-05
                          PQQ_3   1 GevlWsvql...pg..pvnsspavdgglvyvgtg.dGtlyAlD 37 
                                    G++lW++++   p    v ssp++ +g++yv +  dG l+Al 
  gi|116754188|ref|YP_843306.1| 142 GKTLWNRTIerdPKywGVASSPLIENGTLYVMSFsDGALHALS 184
                                    99*****663334368888**********************96 PP

  == domain 4  score: 29.4 bits;  conditional E-value: 2.6e-10
                          PQQ_3   1 GevlWsvqlpg..pvnsspavdgglvyvgtgdGtlyAlDaet 40 
                                    G++lW+v++++  p  +spa++g ++y+ +gd  ly+++a+t
  gi|116754188|ref|YP_843306.1| 187 GDELWNVSTGSvsPF-ASPAASGERIYFPGGDPALYCINATT 227
                                    99********99555.9***********************98 PP

  == domain 5  score: 20.3 bits;  conditional E-value: 1.9e-07
                          PQQ_3   2 evlWsvqlpgpvnsspavdgglvyvgtgdGtlyAlDaet 40 
                                    +++W+++ ++ ++sspa+++ +v+++t+  ++ Al+a+t
  gi|116754188|ref|YP_843306.1| 229 KIVWKTPADAVITSSPAIWNSTVFFVTE-RSISALNATT 266
                                    689************************9.********98 PP

  == domain 6  score: 28.1 bits;  conditional E-value: 6.4e-10
                          PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtgdGtlyAlDa 38 
                                    G +lW++++ g + s+pa++ g+vyvgt dG++++lD+
  gi|116754188|ref|YP_843306.1| 267 GSTLWQRSING-TESTPAIAFGRVYVGTADGHVVCLDT 303
                                    889*******8.459**********************6 PP

  == domain 7  score: 31.2 bits;  conditional E-value: 7.3e-11
                          PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtg..dGtlyAlDae 39 
                                    G ++W++++ gpv ssp++ +g++y+gt    G +yAl+a 
  gi|116754188|ref|YP_843306.1| 305 GSQIWETEVNGPVRSSPLFLDGRIYFGTNtdGGAVYALNAS 345
                                    889************************************96 PP

  == domain 8  score: 31.2 bits;  conditional E-value: 7e-11
                          PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtgdGtlyAl 36 
                                    G v+W +++ +++ ssp +++g++++g++dG+lyA+
  gi|116754188|ref|YP_843306.1| 347 GSVVWMYTVNEYIMSSPSASDGILFIGADDGRLYAF 382
                                    889********************************9 PP

  == domain 9  score: -3.7 bits;  conditional E-value: 6
                          PQQ_3   3 vlWsv.........qlpgpvnsspavdggl 23 
                                    + W++         +l gp  s+++ dg++
  gi|116754188|ref|YP_843306.1| 459 RAWRYwvnypdepvPLTGPE-SAMLNDGDR 487
                                    67999554443333333333.333445544 PP

>> PQQ  PQQ enzyme repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.074   2.2e+02      14      32 ..      95     113 ..      92     119 .. 0.78
   2 !   14.6   0.1     8e-06     0.024       1      24 [.     123     146 ..     123     151 .. 0.95
   3 ?    2.8   0.0     0.043   1.3e+02       4      32 ..     171     199 ..     168     205 .. 0.79
   4 !    8.3   0.0   0.00076       2.3       3      37 ..     211     245 ..     210     246 .. 0.90
   5 !   11.1   0.0    0.0001       0.3      12      30 ..     259     277 ..     253     280 .. 0.88
   6 !   28.6   0.0   2.9e-10   8.7e-07       1      37 [.     287     322 ..     287     323 .. 0.96
   7 !   19.8   0.1   1.8e-07   0.00054       1      32 [.     326     359 ..     326     365 .. 0.85
   8 ?    3.7   0.0     0.022        67       1      15 [.     368     382 ..     368     385 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.074
                                    EEETTTCCEEEEEESSSCG CS
                            PQQ  14 AlDadTGkvlWrfktggpv 32 
                                     +D ++G+vlW  ++gg+ 
  gi|116754188|ref|YP_843306.1|  95 CIDERNGTVLWINPVGGKG 113
                                    69*********88887765 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 8e-06
                                    TEEEEEETTSEEEEEETTTCCEEE CS
                            PQQ   1 gvvylgsadGylyAlDadTGkvlW 24 
                                    ++v+ gs  G +y +D+ TGk lW
  gi|116754188|ref|YP_843306.1| 123 NKVFTGSLTGEIYCVDVLTGKTLW 146
                                    789********************* PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.043
                                    EEE.ETTSEEEEEETTTCCEEEEEESSSCG CS
                            PQQ   4 ylg.sadGylyAlDadTGkvlWrfktggpv 32 
                                    y+    dG l Al   +G++lW + tg++ 
  gi|116754188|ref|YP_843306.1| 171 YVMsFSDGALHALS-LDGDELWNVSTGSVS 199
                                    55556799999999.9******99999876 PP

  == domain 4  score: 8.3 bits;  conditional E-value: 0.00076
                                    EEEEETTSEEEEEETTTCCEEEEEESSSCGSSESE CS
                            PQQ   3 vylgsadGylyAlDadTGkvlWrfktggpvlslpi 37 
                                    +y +  d  ly ++a+T k++W++++++++ s+p+
  gi|116754188|ref|YP_843306.1| 211 IYFPGGDPALYCINATTQKIVWKTPADAVITSSPA 245
                                    788888999*******************9998885 PP

  == domain 5  score: 11.1 bits;  conditional E-value: 0.0001
                                    EEEEETTTCCEEEEEESSS CS
                            PQQ  12 lyAlDadTGkvlWrfktgg 30 
                                    + Al+a+TG  lW+  ++g
  gi|116754188|ref|YP_843306.1| 259 ISALNATTGSTLWQRSING 277
                                    89***********987765 PP

  == domain 6  score: 28.6 bits;  conditional E-value: 2.9e-10
                                    TEEEEEETTSEEEEEETTTCCEEEEEESSSCGSSESE CS
                            PQQ   1 gvvylgsadGylyAlDadTGkvlWrfktggpvlslpi 37 
                                    g+vy+g+adG+++ lD ++G  +W+++++gpv+s+p+
  gi|116754188|ref|YP_843306.1| 287 GRVYVGTADGHVVCLD-TNGSQIWETEVNGPVRSSPL 322
                                    78**************.******************96 PP

  == domain 7  score: 19.8 bits;  conditional E-value: 1.8e-07
                                    TEEEEE..ETTSEEEEEETTTCCEEEEEESSSCG CS
                            PQQ   1 gvvylg..sadGylyAlDadTGkvlWrfktggpv 32 
                                    g++y g  +++G +yAl+a++G v+W + ++  +
  gi|116754188|ref|YP_843306.1| 326 GRIYFGtnTDGGAVYALNASDGSVVWMYTVNEYI 359
                                    67899999******************99887655 PP

  == domain 8  score: 3.7 bits;  conditional E-value: 0.022
                                    TEEEEEETTSEEEEE CS
                            PQQ   1 gvvylgsadGylyAl 15 
                                    g +++g +dG+lyA+
  gi|116754188|ref|YP_843306.1| 368 GILFIGADDGRLYAF 382
                                    5789**********8 PP

>> DUF4905  Domain of unknown function (DUF4905)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0012       3.5      31      83 .]      53     105 ..      48     105 .. 0.94
   2 !    5.1   0.0    0.0069        21      23      63 ..     135     178 ..     132     182 .. 0.79
   3 ?   -4.0   0.0       4.8   1.4e+04      53      68 ..    1708    1723 ..    1698    1724 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0012
                        DUF4905  31 kllfedlvleekwwtgleaiykgvlllhkyekpdsPehkgliaiDiktgkllW 83 
                                    +ll++    +  +  g ++i++g +++ ++++     + gl+ iD ++g++lW
  gi|116754188|ref|YP_843306.1|  53 ELLWSTSLTGHGYIGGSASISSGRVFVSNWPDMTFKGELGLACIDERNGTVLW 105
                                    6789999999999999************************************* PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0069
                        DUF4905  23 saldletgkllfedlvlee.kwwtglea..iykgvlllhkyekp 63 
                                    +++d+ tgk+l+++++  + k+w  +++  i +g+l++  + ++
  gi|116754188|ref|YP_843306.1| 135 YCVDVLTGKTLWNRTIERDpKYWGVASSplIENGTLYVMSFSDG 178
                                    699**********99887637775443344999*****999875 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 4.8
                        DUF4905   53 gvlllhkyekpdsPeh 68  
                                     g++ll++y ++ +P +
  gi|116754188|ref|YP_843306.1| 1708 GNILLKEYMSGMLPST 1723
                                     789*****99999975 PP

>> DUF4430  Domain of unknown function (DUF4430)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       2.3   6.9e+03      31      54 ..     259     281 ..     249     292 .. 0.76
   2 ?   -1.1   0.0         1     3e+03      43      50 ..     350     357 ..     341     367 .. 0.81
   3 ?   11.1   0.0   0.00015      0.45       8      73 ..     422     493 ..     416     494 .. 0.75
   4 ?   -2.4   0.0       2.5   7.4e+03      25      35 ..    1173    1196 ..    1150    1226 .. 0.58

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.3
                        DUF4430  31 IngleqdtakksyWmyevNGepsd 54 
                                    I  l + t+ ++ W+ ++NG+ s+
  gi|116754188|ref|YP_843306.1| 259 ISAL-NATTGSTLWQRSINGTEST 281
                                    5555.44555699******98766 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1
                        DUF4430  43 yWmyevNG 50 
                                     Wmy+vN 
  gi|116754188|ref|YP_843306.1| 350 VWMYTVNE 357
                                    6******7 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00015
                        DUF4430   8 leaaakkkedkteaqsge......hyitsIngl.eqdtakksyWmyevNGepsdvGagsyklkdgdkivfryt 73 
                                    l ++a+ +++  + +  +      + ++sI+ l +  + + +yW+ + +   +  G  s  l+dgd++vf+y 
  gi|116754188|ref|YP_843306.1| 422 LISFASSNGINVSVND-SlisiygLTVESIGDLvSTKERAWRYWVNYPDEPVPLTGPESAMLNDGDRLVFYYG 493
                                    5555555555554433.246666789*******66666666999999999999*******************6 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 2.5
                        DUF4430   25 e...........hyitsIngl..e 35  
                                     +            yi+ I+g   +
  gi|116754188|ref|YP_843306.1| 1173 SlvamvrsmlgdSYIKEIEGAlnS 1196
                                     155455555555699999997541 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1812 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); 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: 0.96u 0.30s 00:00:01.26 Elapsed: 00:00:00.44
# Mc/sec: 12492.73
//
Query:       gi|116754189|ref|YP_843307.1|  [L=159]
Description: AsnC family transcriptional regulator [Methanosaeta thermophila PT]
Scores for complete 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-15   55.1   0.4    8.7e-15   54.5   0.1    1.5  2  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    5.8e-08   32.2   0.5    1.1e-07   31.3   0.5    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
    1.4e-07   31.4   0.1    7.3e-07   29.1   0.1    2.0  2  HTH_Crp_2       Crp-like helix-turn-helix domain
    1.5e-06   27.9   1.2      4e-06   26.5   0.7    1.9  2  HTH_AsnC-type   AsnC-type helix-turn-helix domain
      3e-05   24.0   0.1    5.8e-05   23.1   0.1    1.4  1  HTH_20          Helix-turn-helix domain
     0.0014   18.6   0.3     0.0029   17.5   0.3    1.6  1  HTH_11          HTH domain
     0.0015   18.4   0.1     0.0027   17.6   0.1    1.3  1  MarR            MarR family
  ------ inclusion threshold ------
      0.013   15.4   0.1      0.032   14.1   0.1    1.6  1  MarR_2          MarR family
      0.027   14.2   0.3       0.08   12.7   0.3    1.8  1  HTH_38          Helix-turn-helix domain
       0.04   13.6   0.1      0.063   13.0   0.1    1.3  1  DUF4423         Domain of unknown function (DUF4423)
       0.06   13.2   0.1        0.2   11.5   0.0    1.9  2  HTH_23          Homeodomain-like domain
      0.065   13.4   0.0       0.13   12.5   0.0    1.5  1  HTH_34          Winged helix DNA-binding domain
      0.073   13.0   0.2       0.18   11.7   0.2    1.8  1  TrmB            Sugar-specific transcriptional regulator TrmB
      0.074   13.2   0.3       0.16   12.1   0.3    1.5  1  Sigma70_r3      Sigma-70 region 3
      0.088   12.5   0.1       0.11   12.1   0.1    1.2  1  Stk19           Serine-threonine protein kinase 19
      0.093   13.2   0.3       0.14   12.6   0.3    1.4  1  YflT            Heat induced stress protein YflT
       0.11   12.2   0.1        0.2   11.4   0.1    1.4  1  HTH_DeoR        DeoR-like helix-turn-helix domain
       0.14   11.9   0.1       0.28   10.9   0.1    1.5  1  Crp             Bacterial regulatory proteins, crp family
       0.15   11.7   0.2       0.97    9.0   0.1    1.9  2  ATP-synt_ab     ATP synthase alpha/beta family, nucleotide-bi
       0.15   12.0   0.0       0.26   11.3   0.0    1.4  1  HTH_36          Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       8.2   7.3e+03      14      23 ..      28      37 ..      24      39 .. 0.66
   2 !   54.5   0.1   9.7e-18   8.7e-15       4      74 ..      67     137 ..      64     138 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 8.2
                                   HHHHHHHHTS CS
                 AsnC_trans_reg 14 eefeealael 23
                                   ee++++++el
  gi|116754189|ref|YP_843307.1| 28 EEVAREIKEL 37
                                   6677777765 PP

  == domain 2  score: 54.5 bits;  conditional E-value: 9.7e-18
                                    EE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
                 AsnC_trans_reg   4 slepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74 
                                    ++  +++  +++++e++a++ eV+++  ++Gd+d+ + v+ r++++   f+ ek+a l+gv++t t+++l+
  gi|116754189|ref|YP_843307.1|  67 KVALQRSTGYDSVAERIARFSEVQSVRLISGDHDLSVTVRGRSMKDVAFFVAEKIAPLEGVQSTCTHFILK 137
                                    4553336689***********************************************************98 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   0.5   1.2e-10   1.1e-07       7      48 .]       3      44 ..       2      44 .. 0.98

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 1.2e-10
                         HTH_24  7 kILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                   +IL++L +n+r + +e+A  lg +   v r +k+Le++G+I+
  gi|116754189|ref|YP_843307.1|  3 EILQILSENARATPAEIAALLGRTEEEVAREIKELEDSGVIR 44
                                   6****************************************7 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 !   29.1   0.1   8.2e-10   7.3e-07      21      64 ..      13      54 ..       4      54 .. 0.90
   2 ?   -0.7   0.0       1.6   1.4e+03      41      53 ..     135     147 ..     119     158 .. 0.70

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 8.2e-10
                                   EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETEEEEES-HHH CS
                      HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglisrgrririldlea 64
                                   + t +e+A++lG t e v r+++eL++ g+i++ + i+i d+e+
  gi|116754189|ref|YP_843307.1| 13 RATPAEIAALLGRTEEEVAREIKELEDSGVIRK-Y-ITIIDWEK 54
                                   56889**************************95.4.*****986 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.6
                                    HHHHHHHTTSEEE CS
                      HTH_Crp_2  41 ilseLkreglisr 53 
                                    il+  k++g+i +
  gi|116754189|ref|YP_843307.1| 135 ILKSYKEHGVILT 147
                                    6888888999873 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 !   26.5   0.7   4.5e-09     4e-06       7      42 .]       3      38 ..       2      38 .. 0.96
   2 ?   -1.2   0.0       2.1   1.9e+03      33      40 ..      78      85 ..      76      86 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 4.5e-09
                  HTH_AsnC-type  7 kILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                    IL++L e+aR++ ae+A+ +G +e++v+r ++ Le
  gi|116754189|ref|YP_843307.1|  3 EILQILSENARATPAEIAALLGRTEEEVAREIKELE 38
                                   59****************************999997 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.1
                  HTH_AsnC-type 33 tvlrRvrr 40
                                    v++R++r
  gi|116754189|ref|YP_843307.1| 78 SVAERIAR 85
                                   69999998 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.1   6.5e-08   5.8e-05      15      55 ..       4      44 ..       3      46 .. 0.96

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 6.5e-08
                                   HHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                         HTH_20 15 ilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                   il+ L++++ +t++e+a++l+ +  ++ + +++Le+ g ++
  gi|116754189|ref|YP_843307.1|  4 ILQILSENARATPAEIAALLGRTEEEVAREIKELEDSGVIR 44
                                   9*************************************997 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.3   3.3e-06    0.0029       3      44 ..       2      42 ..       1      51 [. 0.87

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.3e-06
                         HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                   + il++L e+    + +e+A  L++++  v r Ik+Le++gv
  gi|116754189|ref|YP_843307.1|  2 NEILQILSENAR-ATPAEIAALLGRTEEEVAREIKELEDSGV 42
                                   68*****66665.9**************************94 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1     3e-06    0.0027       8      50 ..       4      46 ..       3      48 .. 0.96

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3e-06
                                   HHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                           MarR  8 iLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                   iL il+e+  ++ +e+a  lg +   v r +++Le+ G i+++
  gi|116754189|ref|YP_843307.1|  4 ILQILSENARATPAEIAALLGRTEEEVAREIKELEDSGVIRKY 46
                                   9***************************************987 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   3.6e-05     0.032      13      53 ..       7      45 ..       3      48 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.6e-05
                                   HHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                         MarR_2 13 aLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                    L  + +   t++e+a+ lg +   v r +k+L++ G +++
  gi|116754189|ref|YP_843307.1|  7 ILSENAR--ATPAEIAALLGRTEEEVAREIKELEDSGVIRK 45
                                   5666665..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 ?   12.7   0.3   8.9e-05      0.08      12      42 ..       3      35 ..       2      36 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.9e-05
                         HTH_38 12 eIerllaeG..lslreIArrLgrspsTIsRElk 42
                                   eI + l+e+   + +eIA +Lgr    ++RE+k
  gi|116754189|ref|YP_843307.1|  3 EILQILSENarATPAEIAALLGRTEEEVAREIK 35
                                   455555444348999****************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 ?   13.0   0.1     7e-05     0.063      34      73 ..      11      48 ..       2      74 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7e-05
                        DUF4423 34 dfkadpeelakrlrpkisaeevekalefLlklgllkkded 73
                                   +++a+p+e+a  l+   ++eev++ ++ L+++g+++k   
  gi|116754189|ref|YP_843307.1| 11 NARATPAEIAALLG--RTEEEVAREIKELEDSGVIRKYIT 48
                                   4579**********..*******************99655 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00023       0.2       9      46 ..       6      42 ..       3      45 .. 0.80
   2 ?   -2.9   0.0       7.7   6.9e+03      37      46 ..     135     144 ..     135     145 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00023
                         HTH_23  9 rillllaeGlsvreIAreLgvsrrTvyrwlkryreeGl 46
                                   +il   a +++++eIA++Lg+++  v r +k  + +G+
  gi|116754189|ref|YP_843307.1|  6 QILSENA-RATPAEIAALLGRTEEEVAREIKELEDSGV 42
                                   5555555.8**************999999999855775 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 7.7
                         HTH_23  37 wlkryreeGl 46 
                                    +lk y+e+G+
  gi|116754189|ref|YP_843307.1| 135 ILKSYKEHGV 144
                                    6889999885 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 ?   12.5   0.0   0.00014      0.13       4      45 ..       3      44 ..       2      55 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                         HTH_34  4 avlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYie 45
                                   ++l++L+++ +a+++e+ + l+ t+ + + ++k Le+ g i 
  gi|116754189|ref|YP_843307.1|  3 EILQILSENARATPAEIAALLGRTEEEVAREIKELEDSGVIR 44
                                   699**********************************99775 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   0.2   0.00021      0.18      15      54 ..       6      45 ..       3      67 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00021
                                   HHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
                           TrmB 15 laLlklgpatadeiaeelgvprskvYevLrsLedkGlVer 54
                                   + L ++ +at  eia  lg+ +  v + +++Led G++++
  gi|116754189|ref|YP_843307.1|  6 QILSENARATPAEIAALLGRTEEEVAREIKELEDSGVIRK 45
                                   4566999*****************************9986 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.3   0.00018      0.16      20      39 ..      13      32 ..       4      41 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00018
                                   XXXHHHHHHHHTXXHHHHHH CS
                     Sigma70_r3 20 ePtpeEiAeeLglseekVre 39
                                    +tp+EiA+ Lg +ee+V +
  gi|116754189|ref|YP_843307.1| 13 RATPAEIAALLGRTEEEVAR 32
                                   69****************65 PP

>> Stk19  Serine-threonine protein kinase 19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00013      0.11      35     105 ..      16      84 ..       3     103 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                          Stk19  35 vahlhsllaqsptkvereleelirkgklrklvingrgkdisklgevlvltedyeklikesseleeeekvle 105
                                     a + +ll +++ +v re++el ++g++rk +     +++s  ++ +  + +++  +++s++ ++ ++ + 
  gi|116754189|ref|YP_843307.1|  16 PAEIAALLGRTEEEVAREIKELEDSGVIRKYITIIDWEKAS--ESYVYAVIELKVALQRSTGYDSVAERIA 84 
                                    57789999889*******************76544444433..3555555556666666666555555555 PP

>> YflT  Heat induced stress protein YflT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.3   0.00016      0.14       5      38 ..      25      58 ..      23     100 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00016
                           YflT  5 eneeellsaieelkaeGyneddiyvvakdkdrle 38
                                   ++eee+ ++i+el+++G+ ++ i ++ ++k+  +
  gi|116754189|ref|YP_843307.1| 25 RTEEEVAREIKELEDSGVIRKYITIIDWEKASES 58
                                   589***********************99998544 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   0.1   0.00022       0.2       3      46 ..       2      45 ..       1      47 [. 0.95

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00022
                       HTH_DeoR  3 eqilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltR 46
                                   ++il+ l +    +  e+++llg +e+ + R ++eLe +g++++
  gi|116754189|ref|YP_843307.1|  2 NEILQILSENARATPAEIAALLGRTEEEVAREIKELEDSGVIRK 45
                                   68***************************************987 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   0.00031      0.28       6      32 .]      17      43 ..      15      43 .. 0.96

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00031
                                   HHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                            Crp  6 qdIAdylGlTrETVSRlLtrLrekGLI 32
                                    +IA +lG T E V R  + L+ +G+I
  gi|116754189|ref|YP_843307.1| 17 AEIAALLGRTEEEVAREIKELEDSGVI 43
                                   59************************9 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1    0.0011      0.97      29      76 ..       3      50 ..       1      71 [. 0.78
   2 ?    0.9   0.0      0.34     3e+02     158     198 ..      82     122 ..      61     125 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0011
                                   HHHHHHHHHSSTSSEEEEEEESEEHHHHHHHHHHCHHSSGGGGEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab 29 visqslskqsnsddaiiyvgiGergnevaevleefpegtimkrtvlva 76
                                   +i+q ls++++++ a i ++ G  ++eva+ ++e+++++++++ + ++
  gi|116754189|ref|YP_843307.1|  3 EILQILSENARATPAEIAALLGRTEEEVAREIKELEDSGVIRKYITII 50
                                   68899999987777***********************99555555444 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.34
                                    SEEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEEEEB-HHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab 158 rtGsvtivaavspaggDfsdpvttatlgitdgfivLdkkla 198
                                    r    + v+ v   +gD +  vt   +++ d+ +++ +k+a
  gi|116754189|ref|YP_843307.1|  82 RIARFSEVQSVRLISGDHDLSVTVRGRSMKDVAFFVAEKIA 122
                                    44455788999999999999999999999999998888876 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00029      0.26      29      55 .]      17      43 ..       9      43 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00029
                         HTH_36 29 etlakrlglsknTvsraikeLeqlGyi 55
                                   + +a++lg  ++ v r ikeLe+ G i
  gi|116754189|ref|YP_843307.1| 17 AEIAALLGRTEEEVAREIKELEDSGVI 43
                                   689*******************99965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); expected 358.6 (0.02)
Passed bias filter:                      652  (0.0363657); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1256.33
//
Query:       gi|116754190|ref|YP_843308.1|  [L=396]
Description: aminotransferase, class I and II [Methanosaeta thermophila PT]
Scores for complete 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-70  236.7   0.0    5.1e-70  236.5   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    1.8e-09   37.4   0.0    3.2e-09   36.6   0.0    1.4  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    1.8e-05   23.9   0.0    3.3e-05   23.0   0.0    1.3  1  Aminotran_5      Aminotransferase class-V
    0.00047   18.8   0.0    0.00098   17.8   0.0    1.5  2  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
  ------ inclusion threshold ------
      0.013   14.8   0.0      0.023   14.0   0.0    1.3  1  Beta_elim_lyase  Beta-eliminating lyase
       0.02   15.5   0.3      0.034   14.8   0.3    1.3  1  Forkhead_N       Forkhead N-terminal region


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 !  236.5   0.0   1.7e-73   5.1e-70       3     363 .]      41     389 ..      39     389 .. 0.95

  Alignments for each domain:
  == domain 1  score: 236.5 bits;  conditional E-value: 1.7e-73
                                    EEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHH CS
                  Aminotran_1_2   3 vinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagalie 82 
                                     i Lg++e+++     t+ +v++a +   +  +++++y+ ++g pel+ea+a+f +++ +l++++ ++++v++G +++ +
  gi|116754190|ref|YP_843308.1|  41 AISLGVGEPDFV----TPWHVREACIY--SLESGYTSYTSNKGMPELREAIADFTKEQLGLDYDPTDQILVTTGVSEAVD 114
                                    689*********....*********99..9999***********************999********************* PP

                                    HHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT- CS
                  Aminotran_1_2  83 alifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtG 162
                                    ++++++ lnpgde++vp+p y  y +++ l+gg  +++p++  ++f+++ e++  a++e      ktk +++  p+NPtG
  gi|116754190|ref|YP_843308.1| 115 LAFRAT-LNPGDEVIVPEPCYVAYVPDIILAGGVPRQIPTRIDDEFRVTPESIVPAITE------KTKALVLSYPNNPTG 187
                                    ******.****************************************************......*************** PP

                                    -B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTT.EEEEEESSSTTSSGGG-EEEEEEEHHHHH CS
                  Aminotran_1_2 163 tvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepn.llivgslsKafGlaGeRvGyilgnaavvs 241
                                    +++t+ +le ++dl+ ++ ll+++De+Y+ + +  + a +  a+++   + ++i+++lsK+ +++G+R+Gy+lg++ ++ 
  gi|116754190|ref|YP_843308.1| 188 AIMTRSDLESIADLVVEHDLLVISDEVYGMLTYSGTHA-S-FAQLDGMYErTIILNGLSKSHAMTGWRIGYALGDPMLIG 265
                                    ********************************996532.3.56666655569**************************** PP

                                    HHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEEEEETHH..CH CS
                  Aminotran_1_2 242 qlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmflltdlsae..ta 317
                                    +++k+++      +   q a+ +al + ++   e+ +m+ +++ rr+ ++++L+++gl ++++q++++ +  + +   + 
  gi|116754190|ref|YP_843308.1| 266 AMTKIHQYTMLcaPIMSQMAAIEALLHGEE---EMLKMKHEYNLRRRLFVAGLNRIGLRCIEPQGAFYAFPSIAETglSS 342
                                    ******988887899999999999999997...9****************************************99*999 PP

                                    HHHHHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHHHH CS
                  Aminotran_1_2 318 kelskkLleevgvyvtpgtsftv..pgrlRitvAglteeeleelveal 363
                                    +++++ Ll e+ v+v+pg+ f+   +g+lR ++ ++++eel e+++++
  gi|116754190|ref|YP_843308.1| 343 EAFAERLLREQRVAVVPGNVFGQsgEGFLRCSY-ATSREELIEALDRI 389
                                    ******99999**********************.99999999999997 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 !   36.6   0.0   1.1e-12   3.2e-09      42     144 ..     104     212 ..      58     223 .. 0.81

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 1.1e-12
                                    EEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-T.TTSSB-GGGCGGG--TTEEEEE...E CS
                DegT_DnrJ_EryC1  42 iavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdp.dtynidpaaieaaitertkaIl...p 117
                                    + ++  ++A+ la ra  ++pgdeVIvp   +va +  ++ +g +p  +   + d + ++p++i  aite+tka +   p
  gi|116754190|ref|YP_843308.1| 104 LVTTGVSEAVDLAFRA-TLNPGDEVIVPEPCYVAYVPDIILAGGVPRQIPTRIdDEFRVTPESIVPAITEKTKALVlsyP 182
                                    4444557899999999.4899*************************9887776267******************984444 PP

                                    B-GGGB--...-HHHHHHHHHHCT-EEEEE CS
                DegT_DnrJ_EryC1 118 VhlyGqva...dmdalkaiaakhglkvieD 144
                                     +  G+++   d++++ ++  +h+l vi+D
  gi|116754190|ref|YP_843308.1| 183 NNPTGAIMtrsDLESIADLVVEHDLLVISD 212
                                    56777765455*****************99 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   1.1e-08   3.3e-05      43     179 ..      76     216 ..      65     222 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.1e-08
                                    HHHHHHHHHHHHH......HT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEE CS
                    Aminotran_5  43 kaveearekvael......inaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakv 116
                                    k + e re +a++      +  + +++i++t G +ea+ l+ ++    l+pgde++v e  + a + p   la   g+  
  gi|116754190|ref|YP_843308.1|  76 KGMPELREAIADFtkeqlgLDYDPTDQILVTTGVSEAVDLAFRAT---LNPGDEVIVPEPCYVAYV-PDIILA--GGVPR 149
                                    56777777777772222222345689*****************99...***********9999998.555555..66655 PP

                                    EEE.EBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB...--HHHHHHHHHHTT-EEEEE-TTT CS
                    Aminotran_5 117 kvi.pldeegeldldelekllnektklvaithvsnvtGti...qpveeigklakkkgalvlvDaaqa 179
                                    ++  ++d+e +++++ +  +++ektk++ ++  +n tG i    ++e+i++l+ +++ lv+ D + +
  gi|116754190|ref|YP_843308.1| 150 QIPtRIDDEFRVTPESIVPAITEKTKALVLSYPNNPTGAImtrSDLESIADLVVEHDLLVISDEVYG 216
                                    554389********************************8622269999*************998865 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 !   17.8   0.0   3.3e-07   0.00098      71     176 ..     103     215 ..      81     220 .. 0.79
   2 ?   -3.8   0.0       1.2   3.5e+03      80     117 ..     283     320 ..     269     322 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.3e-07
                                    EEESSHHH.HHHHHHHTTS-TTEEEEEESTSSHHHH..HHHHHTHHHTTCEEEEEST..TSHHHHHHHCCTTEEEEEEES CS
                Cys_Met_Meta_PP  71 lavssGma.AiaaailallkaGdeivvsddlYggtq..rllkkvlkklgievkfvdt..sdleelekaikentklvylEt 145
                                    ++v++G++ A+++a++a l+ Gde++v + +Y       +l   ++  +i +++ d     +e++  ai+e+tk++ l  
  gi|116754190|ref|YP_843308.1| 103 ILVTTGVSeAVDLAFRATLNPGDEVIVPEPCYVAYVpdIILAGGVP-RQIPTRIDDEfrVTPESIVPAITEKTKALVLSY 181
                                    4556665549999*******************86431133333333.456666666544789*****************9 PP

                                    S-TTTT---...-HHHHHHHHHHTT-EEEEEGTT CS
                Cys_Met_Meta_PP 146 ptnpllkvv...DiekiaklakkagvlvvvDntf 176
                                    p np+  ++   D+e+ia+l+ ++++lv+ D ++
  gi|116754190|ref|YP_843308.1| 182 PNNPTGAIMtrsDLESIADLVVEHDLLVISDEVY 215
                                    999986553333*****************99865 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 1.2
                                    HHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTC CS
                Cys_Met_Meta_PP  80 iaaailallkaGdeivvsddlYggtqrllkkvlkklgi 117
                                    ++aai all+  +e++ +++ Y+  +rl+   l+++g+
  gi|116754190|ref|YP_843308.1| 283 QMAAIEALLHGEEEMLKMKHEYNLRRRLFVAGLNRIGL 320
                                    34667888888888999999998888888888888776 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   7.6e-06     0.023      15     167 ..      58     212 ..      53     213 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.6e-06
                                    HHHH.HCS----CCCT--HHHHHHHHHHHHHTT-SEEEE........ES-H.HHHHHHHHHHH--TTEEEEEETT-HHHH CS
                Beta_elim_lyase  15 sdaq.aaamlGdesYgedktvnrLedavaelfgkeaalf........vpqG.taAnsillkillqrgeevivtepahihf 84 
                                    ++a  + ++ G  sY  +k++ +L +a+a+ +  + +l         v++G   A  +++++ l++g+eviv ep+ +  
  gi|116754190|ref|YP_843308.1|  58 REACiYSLESGYTSYTSNKGMPELREAIADFTKEQLGLDydptdqilVTTGvSEAVDLAFRATLNPGDEVIVPEPCYVAY 137
                                    6777788999********************877777773366777777777367999******************98765 PP

                                    SSTTHHHHCC--EEEEE-EBTT..TBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT- CS
                Beta_elim_lyase  85 detgaiaelagvklrdlknkea..GkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygi 162
                                         i   +gv +r+++++ +    +++e++  ai+e      k+k+++l   nn   G +++   l+ +a+++ ++++
  gi|116754190|ref|YP_843308.1| 138 V--PDIILAGGV-PRQIPTRIDdeFRVTPESIVPAITE------KTKALVLSYPNNP-TGAIMTRSDLESIADLVVEHDL 207
                                    4..445455555.9999977763366788999999998......6899999999995.9********************* PP

                                    EEEEE CS
                Beta_elim_lyase 163 plhlD 167
                                     ++ D
  gi|116754190|ref|YP_843308.1| 208 LVISD 212
                                    99887 PP

>> Forkhead_N  Forkhead N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.3   1.1e-05     0.034      38     110 ..     231     305 ..     211     317 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.1e-05
                                    XXXXXXXX....XXXXX..XXXXXXXXX.XXXXXX...XXXXXXXXXX.XXXXX..XXXXXXXXXXX..XXXXXXXXX CS
                     Forkhead_N  38 anmngyagaaamngmss.ssmtgmssgyasagspl...gmmgmssmss.slspsgtmgamgsapagsremgslspnsa 110
                                     +m  y  +  +ng+s   +mtg   gy + g p+    m +++++++  + ++++m+a+ +  +g++em +++++ +
  gi|116754190|ref|YP_843308.1| 231 DGM--YERTIILNGLSKsHAMTGWRIGY-ALGDPMligAMTKIHQYTMlCAPIMSQMAAIEALLHGEEEMLKMKHEYN 305
                                    333..4456689****9899********.7888888*99999******999*******************99998744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.23s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 3141.78
//
Query:       gi|116754191|ref|YP_843309.1|  [L=206]
Description: CDP-alcohol phosphatidyltransferase [Methanosaeta thermophila PT]
Scores for complete 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-06   28.4   1.6    2.1e-06   28.4   1.6    2.6  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 !   28.4   1.6   1.2e-10   2.1e-06       5      66 .]      28      88 ..      24      88 .. 0.80
   2 ?   -1.2   2.9       0.2   3.6e+03      29      29 ..     173     173 ..      92     200 .. 0.58

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 1.2e-10
                                   HHHHHHHHHHHHHHHGGGS-H..HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
                CDP-OH_P_transf  5 aiTllrlllsvlailllltyyplvlailllliasltDalDGklARrlnqvstlGkllDslaD 66
                                   a +ll+l ++++ +lll     l+ ++l++l+++ +D +DG +AR + +v+ lG++ D ++D
  gi|116754191|ref|YP_843309.1| 28 AWSLLSLPFAFAGMLLL-GRGELIPGLLMFLASGAMDVIDGAVARATSTVTLLGAYVDGVLD 88
                                   56788888888888644.333378888888999**************99888******9988 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.2
                                    H CS
                CDP-OH_P_transf  29 l 29 
                                    l
  gi|116754191|ref|YP_843309.1| 173 L 173
                                    2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); 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 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1515.80
//
Query:       gi|116754192|ref|YP_843310.1|  [L=137]
Description: hypothetical protein Mthe_0882 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.9e-06   26.7   2.2    7.5e-06   26.1   1.4    1.7  2  LIM            LIM domain
      0.006   16.4   0.0     0.0083   16.0   0.0    1.2  1  TFIIE_alpha    TFIIE alpha subunit
     0.0099   15.9   0.1      0.015   15.3   0.1    1.4  1  HTH_20         Helix-turn-helix domain
  ------ inclusion threshold ------
      0.049   13.6   0.2      0.084   12.8   0.2    1.5  1  DUF4428        Domain of unknown function (DUF4428)
      0.079   13.0   0.6       0.16   12.0   0.6    1.5  1  DZR            Double zinc ribbon
      0.099   12.6   0.0       0.28   11.2   0.0    1.8  2  HTH_Crp_2      Crp-like helix-turn-helix domain
       0.11   12.3   0.3        1.2    8.9   0.3    2.3  1  zinc_ribbon_2  zinc-ribbon domain
       0.11   12.0   2.7       0.31   10.6   2.4    2.0  2  zf-FLZ         zinc-finger of the FCS-type, C2-C2


Domain annotation for each model (and alignments):
>> LIM  LIM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   1.4   3.3e-09   7.5e-06      28      57 ..       2      31 ..       1      32 [. 0.94
   2 ?   -2.1   0.0       2.1   4.8e+03      49      52 ..      72      75 ..      57      83 .. 0.61

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 3.3e-09
                                   B-TTT-SB-CTT.CEEETTEEEEHHHHHHH CS
                            LIM 28 tCsdCqkeLkegsfyekdgklyCkkdylkk 57
                                   +C+ C++ L+e+++y++dg+ +C+++y+++
  gi|116754192|ref|YP_843310.1|  2 RCQMCGRDLEEDDVYIHDGETLCEDCYIEA 31
                                   8**************************975 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.1
                                   EEHH CS
                            LIM 49 yCkk 52
                                   +C++
  gi|116754192|ref|YP_843310.1| 72 VCSR 75
                                   4433 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   3.7e-06    0.0083      16      64 ..      65     113 ..      54     123 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.7e-06
                                    HHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEE CS
                    TFIIE_alpha  16 vlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrd 64 
                                     + l  L+   +vt edl+ el++ ++el + ++ L+  +lvk +r+ d
  gi|116754192|ref|YP_843310.1|  65 QKRLYNLVCSRKVTREDLQAELGLSPQELENEIAILRHCQLVKGRREGD 113
                                    55677788899********************************999876 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   6.9e-06     0.015      23      60 ..      75     112 ..      62     113 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.9e-06
                                    TTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                         HTH_20  23 egltaselaerldlskntlsyHLrvLeeagLvevvreg 60 
                                    + +t ++l ++l+ls+++l + +++L+   Lv+++reg
  gi|116754192|ref|YP_843310.1|  75 RKVTREDLQAELGLSPQELENEIAILRHCQLVKGRREG 112
                                    56899********************************8 PP

>> DUF4428  Domain of unknown function (DUF4428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   3.7e-05     0.084       2      31 ..       3      32 ..       2      56 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.7e-05
                        DUF4428  2 CaiCgkKigllkrlkleDg.yvCkdClkKls 31
                                   C  Cg  +     + + Dg ++C dC+ ++s
  gi|116754192|ref|YP_843310.1|  3 CQMCGRDLEEDD-VYIHDGeTLCEDCYIEAS 32
                                   788888888777.889***99******9983 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.6   7.1e-05      0.16      15      46 ..       3      39 ..       1      41 [. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.1e-05
                            DZR 15 CseCgtklkavaa......edrCpsCgekvdpearfCp 46
                                   C+ Cg +l++  +      e+ C  C  +++ + r+C+
  gi|116754192|ref|YP_843310.1|  3 CQMCGRDLEED-DvyihdgETLCEDCYIEASHRIRVCD 39
                                   ********844.36999************999999997 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.2   2.6e+03      48      62 ..      26      40 ..      21      41 .. 0.69
   2 ?   11.2   0.0   0.00012      0.28      19      59 ..      74     117 ..      49     122 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.2
                                   TTSEE.ETEEEEES-H CS
                      HTH_Crp_2 48 eglis.rgrririldl 62
                                   + +i+  +r ir+ d+
  gi|116754192|ref|YP_843310.1| 26 DCYIEaSHR-IRVCDP 40
                                   556884445.999997 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00012
                                    EEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ET.EE.EEE CS
                      HTH_Crp_2  19 elpltqeelAsmlGltretvsrilseLkreglis.rg.rr.iri 59 
                                      ++t+e+l + lGl+++ +  +++ L+  +l++ r+ ++ + i
  gi|116754192|ref|YP_843310.1|  74 SRKVTREDLQAELGLSPQELENEIAILRHCQLVKgRReGDkVYI 117
                                    4579******************************6542224555 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.3   0.00055       1.2       1      15 [.       2      16 ..       2      27 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00055
                  zinc_ribbon_2  1 fCpnCGaelqdnakF 15
                                   +C  CG+ l++++++
  gi|116754192|ref|YP_843310.1|  2 RCQMCGRDLEEDDVY 16
                                   6*********99988 PP

>> zf-FLZ  zinc-finger of the FCS-type, C2-C2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   2.4   0.00014      0.31      15      36 ..       2      22 ..       1      27 [. 0.90
   2 ?   -2.2   0.0       1.3     3e+03      11      20 ..      98     107 ..      92     117 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00014
                         zf-FLZ 15 aCflCkkkLgegkDiymYrGdk 36
                                    C +C ++L e++D+y+  G++
  gi|116754192|ref|YP_843310.1|  2 RCQMCGRDL-EEDDVYIHDGET 22
                                   6********.899******986 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.3
                         zf-FLZ  11 hfLsaCflCk 20 
                                    + L++C l k
  gi|116754192|ref|YP_843310.1|  98 AILRHCQLVK 107
                                    5688887754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1067.53
//
Query:       gi|116754193|ref|YP_843311.1|  [L=133]
Description: hypothetical protein Mthe_0883 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      5e-14   52.7   1.6    6.7e-14   52.3   1.6    1.1  1  CxxCxxCC  Putative zinc- or iron-chelating domain
  ------ inclusion threshold ------
      0.046   14.3   0.0      0.074   13.6   0.0    1.2  1  DUF2385   Protein of unknown function (DUF2385)
      0.093   12.5   2.9        4.5    7.0   0.1    2.2  2  DUF3109   Protein of unknown function (DUF3109)


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 !   52.3   1.6   1.1e-17   6.7e-14       1      84 [.       9     103 ..       9     104 .. 0.83

  Alignments for each domain:
  == domain 1  score: 52.3 bits;  conditional E-value: 1.1e-17
                       CxxCxxCC   1 eCkeCgaCCk..elkvklteedlerlkaaevaeeeeeskkiak........adgrCvfldeetklCkiYeeRpkicrlfp 70 
                                    +C++Cg CC+   ++  l+  d++r++++    +++ ++   +         +++C+f+d+ +  C+iYe Rp++crl+p
  gi|116754193|ref|YP_843311.1|   9 KCRRCGRCCYtpGAGLVLERGDIKRISEFLG-SKKRLRSMC-RkgedgtwiLKQPCPFYDSSE-GCRIYEVRPLTCRLYP 85 
                                    6*********88889999**********999.333334444.34899***99*********96.**************** PP

                       CxxCxxCC  71 as....ekeellaraetC 84 
                                     +    +  ++la++++C
  gi|116754193|ref|YP_843311.1|  86 LHpplkDMPFNLAVDSFC 103
                                    998886666777777777 PP

>> DUF2385  Protein of unknown function (DUF2385)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.2e-05     0.074       5      31 ..      30      56 ..      28      60 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.2e-05
                        DUF2385  5 qllrLaeiLGalhyLrelCgaeedqew 31
                                   ++ r++e LG+ + Lr++C + ed +w
  gi|116754193|ref|YP_843311.1| 30 DIKRISEFLGSKKRLRSMCRKGEDGTW 56
                                   789******************999999 PP

>> DUF3109  Protein of unknown function (DUF3109)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.3    0.0015       9.1      23      52 ..       8      39 ..       2      52 .. 0.79
   2 ?    7.0   0.1   0.00076       4.5     105     128 ..      64      87 ..      52     114 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0015
                        DUF3109 23 eaCk..GaCCvegdaGapleeeElekleeile 52
                                    +C+  G CC    aG  le+ ++++++e l 
  gi|116754193|ref|YP_843311.1|  8 FKCRrcGRCCYTPGAGLVLERGDIKRISEFLG 39
                                   4454449******************9998765 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00076
                        DUF3109 105 iekayregkikfkKPisChlyPir 128
                                    + ++ +  +i   +P+ C+lyP++
  gi|116754193|ref|YP_843311.1|  64 FYDSSEGCRIYEVRPLTCRLYPLH 87 
                                    55566667788899********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      196  (0.010932); 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: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1066.45
//
Query:       gi|116754194|ref|YP_843312.1|  [L=222]
Description: SPP-like hydrolase [Methanosaeta thermophila PT]
Scores for 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  104.6   0.0      3e-19   69.8   0.0    2.1  2  Hydrolase_3  haloacid dehalogenase-like hydrolase
    2.5e-10   41.0   0.1    1.2e-08   35.6   0.1    2.7  1  Hydrolase    haloacid dehalogenase-like hydrolase
    5.4e-07   30.2   4.4     0.0033   17.8   0.0    3.4  4  HAD          haloacid dehalogenase-like hydrolase
    0.00058   19.5   0.0     0.0038   16.8   0.0    2.2  3  S6PP         Sucrose-6F-phosphate phosphohydrolase


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 !   33.2   0.0   9.4e-12   4.2e-08       1      93 [.       5      94 ..       5     111 .. 0.91
   2 !   69.8   0.0   6.7e-23     3e-19     176     255 .]     134     213 ..     113     213 .. 0.92

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 9.4e-12
                                   EEEEIIIIIS-TTS---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEEEGGGTEE.ECTTTEEEEE--B-H CS
                    Hydrolase_3  1 ialDlDGTLlnsdkkisektkeaikklkekgikvviATGRslravlpvleelgldlpvialNGali.ddekgkilykstisk 81
                                   +a+D+DGTL +    +s+ ++++i++l+   + v++ TG+ + +++  +  +g+  +++a NG++i  d + +++ ++++  
  gi|116754194|ref|YP_843312.1|  5 VAVDIDGTLTDASRVLSPVSVSVIRELE---VPVILVTGNTHCFTRAAAVLFGVR-HFVAENGGVIsSDDRIEVVGDRKLCD 82
                                   699***********************98...**********************99.9999******9999999999999999 PP

                                   HHHHHHHHHHHH CS
                    Hydrolase_3 82 edvkeiikllke 93
                                   e++k++ + ++ 
  gi|116754194|ref|YP_843312.1| 83 EAYKHLKEKFNI 94
                                   999999887765 PP

  == domain 2  score: 69.8 bits;  conditional E-value: 6.7e-23
                                    TTEEEEEETT-SHHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GGGTHHHHHH CS
                    Hydrolase_3 176 kgyleimpkgvsKgtalkklakelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnnedGVakal 255
                                    ++ + i ++g++Kgt+l+++ ++l+i+ ++++a+GD+  Di+M+e +g+  A+gna+++vk+aA+yv + +  +G a+++
  gi|116754194|ref|YP_843312.1| 134 GFAIHIKNRGITKGTGLRRISERLGIPTKRIAAIGDSPSDIPMMEISGFPAAVGNAHPSVKSAARYVADRAFGEGFAEII 213
                                    56799***************************************************************998888877765 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.1   2.6e-12   1.2e-08       1     207 [.       2     178 ..       2     181 .. 0.80

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 2.6e-12
                                    SSEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTE.HHHHTHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                      Hydrolase   1 iktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrg.ayaigkpewlta 79 
                                    i++v+ D+dGTLt+ ++++  v vs+                    +++ +   + +tg+++   r  a++ g + ++++
  gi|116754194|ref|YP_843312.1|   2 IEAVAVDIDGTLTDASRVLSPVSVSV--------------------IRELEVPVILVTGNTHCFTRAaAVLFGVRHFVAE 61 
                                    789*************9999999999....................77777777777888883333369999******** PP

                                    HHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHT.TE.EEEEEESSEHHHHHHHHHHTT. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.xxxxxxxxxxxxxxxxxxxxx. RF
                      Hydrolase  80 ldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaa.gi.evvlltgdnpetaeraanqlG. 156
                                    +          g   s++r++++  +r l + + ++    k++    ++++ ++  + ++vl+ g +   a r ++ l+ 
  gi|116754194|ref|YP_843312.1|  62 N---------GGVISSDDRIEVVG-DRKLCDEAYKHL---KEKF--NIKKFDSRyRLtDLVLIRGFDVDAASRYLESLNl 126
                                    *.........66667777777777.344444444322...3333..2333444445668********************* PP

                                    .GGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHH CS
                                    .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 157 .ddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvnDaaala 207
                                      d +d  +a+ i+  +  +  g++++ ++L+++ +++a++GD++ D+++++
  gi|116754194|ref|YP_843312.1| 127 pVDLVDTGFAIHIKNRGITKGTGLRRISERLGIPTKRIAAIGDSPSDIPMME 178
                                    88888*********************************************86 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.4     0.029   1.3e+02       2      13 ..       6      17 ..       5      21 .. 0.82
   2 !    9.9   0.0   0.00021      0.94      94     154 ..      28      86 ..      16     109 .. 0.76
   3 !   17.8   0.0   7.4e-07    0.0033     149     188 .]     145     178 ..     114     178 .. 0.79
   4 ?   -3.0   0.0       1.8   8.2e+03     116     130 ..     198     215 ..     191     220 .. 0.45

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.029
                            HAD  2 lfDfDgTLldgd 13
                                     D+DgTL+d +
  gi|116754194|ref|YP_843312.1|  6 AVDIDGTLTDAS 17
                                   57*******985 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00021
                            HAD  94 laahraaGdrvvvvSgglrplvepllaelgadevlat..elevdd.rltgelglegkpvrgegk 154
                                    ++   +  ++v++v+g+   ++++ + ++g+ +++a+   + + d r+     ++ k++ ++ k
  gi|116754194|ref|YP_843312.1|  28 IR---ELEVPVILVTGNTHCFTRAAAVLFGVRHFVAEngGVISSDdRIEVV--GDRKLCDEAYK 86 
                                    55...7889*********************999998844333333444444..66777766555 PP

  == domain 3  score: 17.8 bits;  conditional E-value: 7.4e-07
                            HAD 149 vrgegkvaalrewlaaegegidleevvayGDspsDlpllr 188
                                    ++g    + lr+    e  gi+ +++ a+GDspsD+p+++
  gi|116754194|ref|YP_843312.1| 145 TKG----TGLRR--ISERLGIPTKRIAAIGDSPSDIPMME 178
                                    444....66777..77789999999*************96 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 1.8
                            HAD 116 epll.aelg..adevlat 130
                                    + ++ +++g  + e++++
  gi|116754194|ref|YP_843312.1| 198 RYVAdRAFGegFAEIIDH 215
                                    334433444444444433 PP

>> S6PP  Sucrose-6F-phosphate phosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.26   1.2e+03       5      43 ..       5      40 ..       3      51 .. 0.64
   2 ?   -1.4   0.0      0.31   1.4e+03     150     180 ..      65      95 ..      62     103 .. 0.84
   3 !   16.8   0.0   8.5e-07    0.0038     156     216 ..     136     195 ..     113     217 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.26
                                   EEE-TBTTTB.S-HHHHHHHHHHHH.GGGGGEEEEEE-S CS
                           S6PP  5 lvsdLDntlvdgdnealarlnelleaeerkdvllvfaTG 43
                                   ++ d+D+tl+  d++ + +  ++    ++ +v ++++TG
  gi|116754194|ref|YP_843312.1|  5 VAVDIDGTLT--DASRVLSPVSVSV-IRELEVPVILVTG 40
                                   67899***99..4444444333333.4566666666666 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.31
                                    EEETTTEEEEEETT-SHHHHHHHHHHHHT-- CS
                           S6PP 150 iyssgkdlDvlPkraskgeAlryLakklele 180
                                    ++ss+  + v+  r   +eA ++L +k++++
  gi|116754194|ref|YP_843312.1|  65 VISSDDRIEVVGDRKLCDEAYKHLKEKFNIK 95 
                                    5788888888888888999999999999986 PP

  == domain 3  score: 16.8 bits;  conditional E-value: 8.5e-07
                                    EEEEEETT-SHHHHHHHHHHHHT--GGGEEEEE-SGGGHHHHTSSSEEEE-TT--HHHHHH CS
                           S6PP 156 dlDvlPkraskgeAlryLakkleleleqilvcGdsgnDeellignvlgVvVgnaqeellqw 216
                                    ++ +  ++  kg  lr ++++l+++ ++i   Gds  D+ +++ +     Vgna++  ++ 
  gi|116754194|ref|YP_843312.1| 136 AIHIKNRGITKGTGLRRISERLGIPTKRIAAIGDSPSDIPMMEISGFPAAVGNAHPS-VKS 195
                                    5556667778********************************88888999*****99.333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); 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: 0.42u 0.20s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1815.59
//
Query:       gi|116754195|ref|YP_843313.1|  [L=322]
Description: DNA repair and recombination protein RadA [Methanosaeta thermophila PT]
Scores for complete 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-83  279.1   0.0    3.3e-83  278.9   0.0    1.0  1  Rad51            Rad51
    3.2e-13   50.1   1.0      6e-13   49.2   1.0    1.5  1  HHH_5            Helix-hairpin-helix domain
    4.7e-13   49.2   0.0    2.3e-05   24.0   0.0    2.2  2  RecA             recA bacterial DNA recombination protein
      1e-07   31.7   0.0    1.9e-07   30.8   0.0    1.5  1  AAA_25           AAA domain
    5.4e-07   29.2   0.0      8e-07   28.6   0.0    1.3  1  ATPase           KaiC
    2.2e-06   27.2   4.1     0.0022   17.8   0.1    2.6  2  HHH              Helix-hairpin-helix motif
    2.1e-05   24.5   0.5    4.9e-05   23.4   0.5    1.6  1  HHH_2            Helix-hairpin-helix motif
    5.8e-05   22.8   0.1     0.0013   18.5   0.0    3.0  2  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
    6.4e-05   23.1   0.0    0.00012   22.3   0.0    1.4  1  Cdd1             Pathogenicity locus
     0.0026   17.5   0.0     0.0058   16.4   0.0    1.6  1  AAA_24           AAA domain
     0.0031   17.9   0.0     0.0079   16.6   0.0    1.7  1  AAA              ATPase family associated with various cellul
     0.0035   16.9   0.0      0.043   13.4   0.1    2.2  2  CobU             Cobinamide kinase / cobinamide phosphate gua
  ------ inclusion threshold ------
      0.018   15.3   0.0      0.057   13.8   0.0    1.9  1  IMS_HHH          IMS family HHH motif
       0.04   14.5   0.0       0.16   12.5   0.0    2.2  1  AAA_18           AAA domain
      0.046   13.4   0.0       0.12   12.0   0.0    1.7  1  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
      0.048   13.9   0.1         16    5.9   0.0    2.5  2  HHH_3            Helix-hairpin-helix motif
      0.052   13.9   0.2       0.96    9.9   0.0    2.5  2  HHH_8            Helix-hairpin-helix domain
       0.11   12.5   0.0       0.25   11.3   0.0    1.6  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.14   12.4   0.1       0.34   11.2   0.1    1.7  1  AAA_22           AAA domain
       0.16   12.4   0.0       0.38   11.2   0.0    1.6  1  BAF              Barrier to autointegration factor


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 !  278.9   0.0   3.6e-86   3.3e-83       2     254 ..      63     322 .]      62     322 .] 0.93

  Alignments for each domain:
  == domain 1  score: 278.9 bits;  conditional E-value: 3.6e-86
                                    S-EBHHHHHHHHHSS-EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEESSS CS
                          Rad51   2 gfvsavellekrsellqlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidteg 81 
                                    gf ++ ++le+r+ + ++ttGs+++DelLgGG+et++i e++Gef+sGktq++h+l+v vqlp elgG +g a+ idte 
  gi|116754195|ref|YP_843313.1|  63 GFETGDQVLERRKLVGKITTGSRNFDELLGGGMETQAIVELYGEFGSGKTQVAHQLAVNVQLPPELGGLNGSAIIIDTEN 142
                                    799999************************************************************************** PP

                                    ---GGGGHHHH......HHTT--HHHHGGGEEEEE--STTHHHHHHH...HTHHHH..HHS-EEEEEEETTTGGGCH--- CS
                          Rad51  82 tfrperlveia......erykldkeevlenvayaRaytiehqeellq...qaaall..aedkfallivDsvtalyRtdfs 150
                                    tfrper+ ++       +  +  +e+ l+n+ +aRay+++hq  l +   ++a+ l  +e+ ++llivDsvta++R+++ 
  gi|116754195|ref|YP_843313.1| 143 TFRPERISQMVmglraiDDREWRPEDFLKNIHVARAYNSNHQILLAEsamELAESLreTEHPVRLLIVDSVTAHFRAEYV 222
                                    *********9977777755678899*****************987763333455552235679***************** PP

                                    ----THHHHHHHHHHHHHHHHHHHHH--EEEEEEE-------.------------HHHHHHHH-SEEEEEEE-STTEEEE CS
                          Rad51 151 grgelakRqqklgkllrtLrkladefevavvitnqvvaqvdgqaalfsadpkkPigGlvlahasttRlalrkgkgeeRiv 230
                                    grg la+Rqqkl+k+l+ L ++ad  ++ +++tnqv+a++d+    f +dp+kP+gG+vl+h++t R++lrk kg++Ri+
  gi|116754195|ref|YP_843313.1| 223 GRGTLADRQQKLNKHLHDLMRFADLNNALILVTNQVMAKPDT----FFGDPTKPVGGHVLGHTATFRVYLRKSKGDKRIA 298
                                    *****************************************9....99******************************** PP

                                    EEES-SSS-S-EEEEEEETTEEE- CS
                          Rad51 231 kvvdsPnlpeleavfaigeeGied 254
                                    ++vdsP++p+ eavf+++ eG+ d
  gi|116754195|ref|YP_843313.1| 299 RLVDSPSMPDGEAVFSVTMEGLRD 322
                                    *********************876 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   1.0   6.7e-16     6e-13       2      57 .]       2      57 ..       1      57 [. 0.97

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 6.7e-16
                                   HHHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHHHH CS
                          HHH_5  2 eeLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilelkd 57
                                   ++L +++G+Gp+tA +l +aG++++e++a a++ eL ++  +G+ tA +ii ++++
  gi|116754195|ref|YP_843313.1|  2 KLLEDLPGVGPATAEKLREAGFTTIEAVAVASPGELVAAAEVGEATAAKIIAAARE 57
                                   57999************************************************996 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   2.5e-08   2.3e-05      29      97 ..      75     148 ..      64     159 .. 0.81
   2 !   23.0   0.0   5.1e-08   4.6e-05     116     224 ..     188     293 ..     178     303 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.5e-08
                                    ----EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHH......HTT--EEEEESS----HHH CS
                           RecA  29 lkvetissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaq......kkggvaafidaehaldpky 97 
                                    + v  i++Gs  +d  lG GG+    i+e+yG   sGkt +a ++ +++q        +g a  id+e ++ p+ 
  gi|116754195|ref|YP_843313.1|  75 KLVGKITTGSRNFDELLG-GGMETQAIVELYGEFGSGKTQVAHQLAVNVQlppelgGLNGSAIIIDTENTFRPER 148
                                    568899************.***********************999999994332222467789999999888765 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 5.1e-08
                                    HHHHHHHHHHHHTTT.--SEEEEE-TTT---STT--..---------HHHHHHHHHHHHHHHHHTTT--EEEEEEE---- CS
                           RecA 116 Geqaleiadalvrsg.aidlivvdsvaalvpkaeie..Gemgdskvglqarlmsqalrkltgaisksntvvifinqirek 192
                                     e+a+e+a++l ++   + l++vdsv+a   +ae    G ++d +     + + + l  l    + +n++++  nq+  k
  gi|116754195|ref|YP_843313.1| 188 AESAMELAESLRETEhPVRLLIVDSVTAHF-RAEYVgrGTLADRQ-----QKLNKHLHDLMRFADLNNALILVTNQVMAK 261
                                    699********987527**********976.66665014444443.....44578899999999999************* PP

                                    -------------HHHHHHH-SEEEEEEEES- CS
                           RecA 193 iGvmfgnpetttGGralkfyasvrldvrriee 224
                                        fg+p    GG+ l   a+ r+ +r+++ 
  gi|116754195|ref|YP_843313.1| 262 PDTFFGDPTKPVGGHVLGHTATFRVYLRKSKG 293
                                    ****************************9875 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0   2.2e-10   1.9e-07      14     157 ..      79     219 ..      66     255 .. 0.79

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 2.2e-10
                         AAA_25  14 dlaapppprrwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlrav 93 
                                    ++ +  +  + l++g +  ++++ l+G  g+GKt +a +la+ v +  p lg     +g  +++++E++    ++R++++
  gi|116754195|ref|YP_843313.1|  79 KITTGSRNFDELLGGGMETQAIVELYGEFGSGKTQVAHQLAVNVQL-PPELGG---LNGSAIIIDTENTF--RPERISQM 152
                                    5555666667788888899999**********************98.445553...69***********8..79999999 PP

                         AAA_25  94 geal...rddarllvldlagveslpLfak.drggtl.ltadvdaleaaieeveg.vrlvviDplsralgg 157
                                       l   +d+++ +   l   ++++++ +  +++++ l++   +l++ ++e+e  vrl+++D++++ +++
  gi|116754195|ref|YP_843313.1| 153 VMGLraiDDREWRPEDFL---KNIHVARAyNSNHQIlLAESAMELAESLRETEHpVRLLIVDSVTAHFRA 219
                                    966644465666655555...4566665523444446899999********9778*********987665 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   8.9e-10     8e-07       2     138 ..      81     221 ..      80     266 .. 0.72

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 8.9e-10
                         ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikga...ekygepgvfvtveepaedlrenakslGwdlekle 78 
                                     tg   +De+l gG+  +++v ++Ge G+GKt +a q +++     e  g +g  + ++ +++   e+++++ + l+++ 
  gi|116754195|ref|YP_843313.1|  81 TTGSRNFDELLGGGMETQAIVELYGEFGSGKTQVAHQLAVNVQlppELGGLNGSAIIIDTENTFRPERISQMVMGLRAID 160
                                    79999***********************************9752223457788788888777666677777777777777 PP

                         ATPase  79 eegklaiidasesaeesaee..kdkedleelieelaeaikeika..krvviDsitglayeekea 138
                                    ++ ++   d  ++ +   +   +++  l e + elae ++e++   + +++Ds+t++     e 
  gi|116754195|ref|YP_843313.1| 161 DR-EWRPEDFLKNIHVARAYnsNHQILLAESAMELAESLRETEHpvRLLIVDSVTAH--FRAEY 221
                                    76.5666666555443222233444445555555666666555444999******98..34444 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   2.5e-06    0.0022      12      29 ..       3      20 ..       1      21 [. 0.87
   2 !    9.8   1.3    0.0008      0.72       2      29 ..      26      53 ..      25      54 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.5e-06
                                   HHHTSTT-SHHHHHHHHH CS
                            HHH 12 eLlalPGVGpktAeaIls 29
                                    L++lPGVGp+tAe+ ++
  gi|116754195|ref|YP_843313.1|  3 LLEDLPGVGPATAEKLRE 20
                                   5999**********9875 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0008
                                   HHHHHTSSHHHHHTSTT-SHHHHHHHHH CS
                            HHH  2 leglipasreeLlalPGVGpktAeaIls 29
                                   +e++  as+ eL+a   VG++tA +I++
  gi|116754195|ref|YP_843313.1| 26 IEAVAVASPGELVAAAEVGEATAAKIIA 53
                                   688999********************86 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.5   5.4e-08   4.9e-05       9      53 ..       8      53 ..       6      60 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 5.4e-08
                          HHH_2  9 rhVGektAklLakr.FksldaLkkasleeLlevddiGeeiAqsive 53
                                   + VG +tA++L ++ F +++a + as  eL++  ++Ge +A++i+ 
  gi|116754195|ref|YP_843313.1|  8 PGVGPATAEKLREAgFTTIEAVAVASPGELVAAAEVGEATAAKIIA 53
                                   78*********9866****************************986 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 !   18.5   0.0   1.5e-06    0.0013       3      29 ..       4      30 ..       2      44 .. 0.84
   2 ?    0.8   0.1      0.51   4.6e+02       9      19 ..      43      53 ..      41      91 .. 0.55

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.5e-06
                DNA_pol_lambd_f  3 FtkvyGVGpktAkkwyakGirtledlr 29
                                   +    GVGp+tA+k+ ++G++t+e + 
  gi|116754195|ref|YP_843313.1|  4 LEDLPGVGPATAEKLREAGFTTIEAVA 30
                                   56667*******************885 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.51
                DNA_pol_lambd_f  9 VGpktAkkwya 19
                                   VG +tA k +a
  gi|116754195|ref|YP_843313.1| 43 VGEATAAKIIA 53
                                   66666666554 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   1.3e-07   0.00012       6      46 ..       2      42 ..       1      50 [. 0.90

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.3e-07
                           Cdd1  6 kelqdiPniGkalaedlvelGirsveelkgedpeelyekle 46
                                   k l+d+P++G+a+ae+l+e G++++e ++  +p el+++ e
  gi|116754195|ref|YP_843313.1|  2 KLLEDLPGVGPATAEKLREAGFTTIEAVAVASPGELVAAAE 42
                                   5699********************************98876 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   6.5e-06    0.0058       6      78 ..     102     217 ..      97     236 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.5e-06
                         AAA_24   6 liyGpsgiGKTtlakel.............gpkplfidtekGlksldadkfpdie...........swedfldevvel.. 59 
                                     +yG+ g+GKT +a +l               ++++idte+      + ++ ++              edfl+ +     
  gi|116754195|ref|YP_843313.1| 102 ELYGEFGSGKTQVAHQLavnvqlppelgglNGSAIIIDTEN---TFRPERISQMVmglraiddrewRPEDFLKNIHVAra 178
                                    59***************************99**********...457777776667778888887733455555555566 PP

                         AAA_24  60 ....................aaeladyktlviDtidele 78 
                                                        ++ +++ + l++D+++   
  gi|116754195|ref|YP_843313.1| 179 ynsnhqillaesamelaeslRETEHPVRLLIVDSVTAHF 217
                                    66666777777777777777999999********99765 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 !   16.6   0.0   8.8e-06    0.0079       3     114 ..     103     261 ..     101     267 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 8.8e-06
                                    EESSTTSSHHHHHHHHHHHHTHE..EEEEETTTCS.SS.......................................... CS
                            AAA   3 lyGppGtGKTllakavakelgve..fleisgsell.sk.......................................... 37 
                                    lyG  G GKT +a+++a +++ +  +  ++gs ++ +                                           
  gi|116754195|ref|YP_843313.1| 103 LYGEFGSGKTQVAHQLAVNVQLPpeLGGLNGSAIIiDTentfrperisqmvmglraiddrewrpedflknihvaraynsn 182
                                    9******************8644443444444444222444444566666666666666777777777777777777779 PP

                                    ...STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH..TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS. CS
                            AAA  38 ...yvgesekkirelfkeakekakpsilfiDEidalaksr..sgseseeeervvnqLlteldgvkkkeskvivigatnr. 111
                                       ++ es+++++e ++e ++      l++D + a ++++   +++  ++++ +n+ l+ l ++ + ++   +i++tn+ 
  gi|116754195|ref|YP_843313.1| 183 hqiLLAESAMELAESLRETEHPV--RLLIVDSVTAHFRAEyvGRGTLADRQQKLNKHLHDLMRFADLNN--ALILVTNQv 258
                                    99999999999999998865543..9**************98444555555555555555555555555..788899985 PP

                                    GGG CS
                            AAA 112 pdk 114
                                    + k
  gi|116754195|ref|YP_843313.1| 259 MAK 261
                                    544 PP

>> CobU  Cobinamide kinase / cobinamide phosphate guanyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.37   3.3e+02       5      22 ..     105     122 ..     102     127 .. 0.83
   2 !   13.4   0.1   4.8e-05     0.043      56     127 ..     187     259 ..     163     262 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.37
                           CobU   5 GgarSGKSefAeklaees 22 
                                    G   SGK ++A +la + 
  gi|116754195|ref|YP_843313.1| 105 GEFGSGKTQVAHQLAVNV 122
                                    6778**********9765 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 4.8e-05
                           CobU  56 tveepldlaealkeeek.kevvLvDcltlwltnllleeeaek.veekleeeveellealkelkatvvlVsnEvg 127
                                    + e+  +lae l+e+e+  + ++vD++t       + + + +  ++kl++++++l++  ++l++ ++lV+n v 
  gi|116754195|ref|YP_843313.1| 187 LAESAMELAESLRETEHpVRLLIVDSVTAHFRAEYVGRGTLAdRQQKLNKHLHDLMRF-ADLNNALILVTNQVM 259
                                    5688899*****99988899********988777766543333888999999999876.567899******995 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   6.3e-05     0.057      13      31 ..       4      22 ..       4      23 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.3e-05
                        IMS_HHH 13 itkipGiGgklgekLeklG 31
                                   + ++pG+G+ ++ekL+  G
  gi|116754195|ref|YP_843313.1|  4 LEDLPGVGPATAEKLREAG 22
                                   679***********99877 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00018      0.16       1      91 [.     101     222 ..     101     309 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00018
                         AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....................gvnlrdvakenglllevdpe.............al 46 
                                    + l G  G+GKt++a+ L+   ++                      +++++++   +  +++++                
  gi|116754195|ref|YP_843313.1| 101 VELYGEFGSGKTQVAHQLAVNVQLppelgglngsaiiidtentfrPERISQMVMGLRAIDDREWRpedflknihvaraYN 180
                                    568999************76644466666667778888888888855555555554444444444445444444444333 PP

                         AAA_18  47 deskrldedkldklldaleenssaleegknlvidghlaeleseaa 91 
                                    +++++l  +  ++l + l+e    ++    l++d++ a+++ e+ 
  gi|116754195|ref|YP_843313.1| 181 SNHQILLAESAMELAESLRET---EHPVRLLIVDSVTAHFRAEYV 222
                                    445555555555555555554...45666669*****99998875 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00013      0.12      19     120 ..     103     219 ..      87     222 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                                    EEESTTSSHHHHHHHHHHHSSTS........S.EEEEEEESEEHHHHHHHHHHCHH........SSGGGGEEEEEEETTS CS
                                    xxxxxxxxxxxxxxxxxxxxxxx........x.xxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxx RF
                    ATP-synt_ab  19 ipgafgvGktvisqslskqsnsd........d.aiiyvgiGergnevaevleefpe........gtimkrtvlvantsne 81 
                                    + g+fg Gkt+++++l+ + +          + +ii      r + ++++++ ++         ++ +k+   va   n+
  gi|116754195|ref|YP_843313.1| 103 LYGEFGSGKTQVAHQLAVNVQLPpelgglngSaIIIDTENTFRPERISQMVMGLRAiddrewrpEDFLKNI-HVARAYNS 181
                                    689**************997665999***874477778888899999999999999888777644466654.55555554 PP

                                    -HHHHHHHHHHHHHHHHHHHHTTSEE.EEEEETHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx RF
                    ATP-synt_ab  82 pvaareasiytgitlAEyfrdqgknv.lliadslsrwaeA 120
                                        +++ +  ++ lAE +r++++ v lli+ds++ + +A
  gi|116754195|ref|YP_843313.1| 182 --NHQILLAESAMELAESLRETEHPVrLLIVDSVTAHFRA 219
                                    ..357889999**********9998857899***999877 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.017        16      14      30 ..       2      18 ..       1      22 [. 0.85
   2 ?    5.5   0.0     0.023        21      11      48 ..      32      72 ..      29      81 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.017
                          HHH_3 14 eeLqklpGlgpklAknI 30
                                   ++L+ lpG+gp++A+++
  gi|116754195|ref|YP_843313.1|  2 KLLEDLPGVGPATAEKL 18
                                   589999******99986 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.023
                          HHH_3 11 AsaeeLqklpGlgpklAknIva.yRekn..GpfksreeLlk 48
                                   As  eL   + +g+++A +I+a +Re+   G+f++ ++ l+
  gi|116754195|ref|YP_843313.1| 32 ASPGELVAAAEVGEATAAKIIAaAREAAdiGGFETGDQVLE 72
                                   88889999999**9999888862677655578888777766 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0    0.0011      0.96      49      65 ..       4      20 ..       1      21 [. 0.89
   2 ?    1.1   0.1      0.57   5.1e+02      49      64 ..      37      52 ..      26      56 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0011
                                   CTTSTT--HHHHHHHHH CS
                          HHH_8 49 ltklpgiGkkiaakiee 65
                                   l++lpg+G+++a+k++e
  gi|116754195|ref|YP_843313.1|  4 LEDLPGVGPATAEKLRE 20
                                   688************99 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.57
                                   CTTSTT--HHHHHHHH CS
                          HHH_8 49 ltklpgiGkkiaakie 64
                                   l +   +G+++aaki 
  gi|116754195|ref|YP_843313.1| 37 LVAAAEVGEATAAKII 52
                                   6666789*******96 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00028      0.25      18      43 ..      95     122 ..      78     128 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00028
                                    H..TEEEEEEESTTSSHHHHHHHHHHHT CS
                           TsaE  18 l..gdvilLeGdLGaGKTtlvrglakal 43 
                                    +  ++++ L+G+ G+GKT+ +++la ++
  gi|116754195|ref|YP_843313.1|  95 MetQAIVELYGEFGSGKTQVAHQLAVNV 122
                                    23356799*************9998776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00037      0.34       4      98 ..      97     211 ..      95     257 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00037
                         AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka............. 70 
                                    t+ i+ ++Ge G+GKT ++ +l+ + +  ++    + + + ++  +   ++ + +++      +  +             
  gi|116754195|ref|YP_843313.1|  97 TQAIVELYGEFGSGKTQVAHQLAVNVQLPPELGGLNGSAIIIDTENTFRPERISQMVMGLRAIDDREwrpedflknihva 176
                                    788999**************999887655555555555555555555555555444433333333333344444444444 PP

                         AAA_22  71 ..erlsseell.ealeqalrarav....ielliiD 98 
                                      ++ + + ll e   + +++ +     ++lli+D
  gi|116754195|ref|YP_843313.1| 177 raYNSNHQILLaESAMELAESLREtehpVRLLIVD 211
                                    44455555555444444444444455566666666 PP

>> BAF  Barrier to autointegration factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00043      0.38      18      44 ..       2      28 ..       1      31 [. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00043
                            BAF 18 KevtalaGigevlgkkLeekGfdkAyv 44
                                   K  ++l+G+g+  ++kL+e+Gf + + 
  gi|116754195|ref|YP_843313.1|  2 KLLEDLPGVGPATAEKLREAGFTTIEA 28
                                   67899*****************97655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 2227.49
//
Query:       gi|116754196|ref|YP_843314.1|  [L=371]
Description: replication factor A [Methanosaeta thermophila PT]
Scores for complete 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   89.9   7.6    3.9e-09   36.4   1.1    3.3  3  tRNA_anti-codon  OB-fold nucleic acid binding domain
    3.2e-13   49.9   0.1    0.00026   20.8   0.0    3.1  3  CDC24_OB3        Cell division control protein 24, OB domain 
    2.9e-09   36.7   0.0      0.008   16.1   0.0    3.2  3  REPA_OB_2        Replication protein A OB domain
  ------ inclusion threshold ------
      0.093   12.5   0.1         24    4.7   0.0    3.1  3  Rep_fac-A_C      Replication factor-A C terminal domain


Domain annotation for each model (and alignments):
>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   1.1   8.7e-13   3.9e-09       1      70 [.      68     145 ..      68     161 .. 0.91
   2 !   20.5   0.1   7.9e-08   0.00035       2      76 .]     178     257 ..     177     257 .. 0.83
   3 !   35.8   0.1   1.3e-12   5.7e-09       3      70 ..     284     359 ..     282     360 .. 0.90

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 8.7e-13
                                    EEEEEEEEEEE........EEEETTEEEEEEEETTEEEEEEEET.HHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEE CS
                tRNA_anti-codon   1 VtvaGrvtsis........drsggkvifidlrDgtgriqvvlfr.eeatklaenlkeGdvvrvtGrvkrrpggelelkv 70 
                                    Vt+ Grv+ is        d+s+g+v+++++ D+tg+i+v+l++ + +  +  +++++++++v+G ++  + g  e+++
  gi|116754196|ref|YP_843314.1|  68 VTFTGRVVHISevrefsrsDGSIGRVASLTVGDETGMIKVTLWDdATDLVVSGDIRVDQCLKVRGFPRLGRSG-TEISI 145
                                    89******************************************5555556677**************99999.77665 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 7.9e-08
                                    EEEEEEEEEE........EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEE.EEEEECTTSSEEEEEEE CS
                tRNA_anti-codon   2 tvaGrvtsis........drsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvt.Grvkrrpggelelkvee 72 
                                    ++ +rv++          d+s+g v ++ l D+tg+i+++l++   +  + +  eGdv++v  +  ++r+g  +el+ ++
  gi|116754196|ref|YP_843314.1| 178 SIIARVIDPGkakeftrkDGSKGFVRSMLLGDDTGSINITLWN---DHALIDASEGDVLEVInCSSRERYGF-IELQTSR 253
                                    56667776667777755567777777777**************...99999999****************99.9999988 PP

                                    EEEE CS
                tRNA_anti-codon  73 iell 76 
                                    ++++
  gi|116754196|ref|YP_843314.1| 254 YTVI 257
                                    8875 PP

  == domain 3  score: 35.8 bits;  conditional E-value: 1.3e-12
                                    EEEEEEEEE........EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEE.EEEEECTTSSEEEEE CS
                tRNA_anti-codon   3 vaGrvtsis........drsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvt.Grvkrrpggelelkv 70 
                                    +aG +t i         d+ +g v +i ++D+tgr++v+l+  + ++l+en + G+ v++  G+vk   +gele+++
  gi|116754196|ref|YP_843314.1| 284 IAGYLTGIGelrefqrdDGTKGYVTSINVTDETGRVRVSLWG-DLYRLLENADLGCRVEIMgGQVKNGWNGELEVSC 359
                                    66777777777777788999**********************.*************************8888*9976 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 !   20.8   0.0   5.8e-08   0.00026       1      63 [.      60     126 ..      60     146 .. 0.79
   2 !   15.0   0.0   3.4e-06     0.015       2      51 ..     170     222 ..     169     262 .. 0.77
   3 !   10.7   0.0   6.9e-05      0.31      12      65 ..     285     340 ..     278     350 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 5.8e-08
                      CDC24_OB3   1 DLrekmlnvtLlGrvvai.....freknsek.kkmdryslrieDttGaidatlweeagklhfk.rlrvGh 63 
                                    D+r++   vt  Grvv+i     f   + ++    ++ sl++ D+tG i++tlw+ a  l+ + ++rv +
  gi|116754196|ref|YP_843314.1|  60 DIRPESGAVTFTGRVVHIsevreF---SRSDgSIGRVASLTVGDETGMIKVTLWDDATDLVVSgDIRVDQ 126
                                    78888889**********885433...33333455556******************99988776555555 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 3.4e-06
                      CDC24_OB3   2 LrekmlnvtLlGrvvai.....freknsekkkmdryslrieDttGaidatlweea 51 
                                    +r+ m ++++++rv++      f  k++   k +++s+ + D+tG+i++tlw+  
  gi|116754196|ref|YP_843314.1| 170 IRPDMGEISIIARVIDPgkakeFTRKDG--SKGFVRSMLLGDDTGSINITLWNDH 222
                                    688999**********977554434444..568999****************873 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 6.9e-05
                      CDC24_OB3  12 lGrvvai.....freknsekkkmdryslrieDttGaidatlweeagklhfkrlrvGhlv 65 
                                     G +++i     f ++++++ k +++s++++D+tG +++ lw    +l ++   +G  v
  gi|116754196|ref|YP_843314.1| 285 AGYLTGIgelreF-QRDDGT-KGYVTSINVTDETGRVRVSLWGDLYRLLEN-ADLGCRV 340
                                    4666666775433.444444.67778*****************99999988.6665544 PP

>> REPA_OB_2  Replication protein A OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.0    0.0027        12      17      62 ..      72     115 ..      57     141 .. 0.76
   2 !   16.1   0.0   1.8e-06     0.008      13      73 ..     177     234 ..     167     257 .. 0.82
   3 !   11.0   0.0   6.8e-05       0.3       5      61 ..     274     328 ..     271     355 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0027
                      REPA_OB_2  17 gvvksveevseitskstekelkkreltlvDesgasvevtlWgkeae 62 
                                    g v +++ev+e+ + +++   +  +lt+ De+g +++vtlW++ ++
  gi|116754196|ref|YP_843314.1|  72 GRVVHISEVREFSRSDGS-IGRVASLTVGDETG-MIKVTLWDDATD 115
                                    556677777777776666.55567899999999.59*****99554 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.8e-06
                      REPA_OB_2  13 vDvigvvksveevseitskstekelkkreltlvDesgasvevtlWgkeaekfesseepvva 73 
                                    + +i+ v + ++++e+t+k+++ +   r++ l D++g s+++tlW+++a   ++se +v+ 
  gi|116754196|ref|YP_843314.1| 177 ISIIARVIDPGKAKEFTRKDGS-KGFVRSMLLGDDTG-SINITLWNDHALI-DASEGDVLE 234
                                    567888889999*********9.56678999****98.7********8753.666666665 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 6.8e-05
                      REPA_OB_2   5 envekdsivDvigvvksveevseitskstekelkkreltlvDesgasvevtlWgkea 61 
                                     ++  ++i+ + g ++ ++e++e+++ +++ +    +++++De+g+ v+v lWg+  
  gi|116754196|ref|YP_843314.1| 274 ADLRVGEICNIAGYLTGIGELREFQRDDGT-KGYVTSINVTDETGR-VRVSLWGDLY 328
                                    56677899*****************99999.566789*******96.9******944 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 ?    1.8   0.0     0.041   1.8e+02      57      78 ..      95     116 ..      92     125 .. 0.85
   2 ?    1.6   0.0     0.047   2.1e+02      57      76 ..     204     223 ..     199     269 .. 0.76
   3 ?    4.7   0.0    0.0053        24      53      74 ..     305     326 ..     298     332 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.041
                                    EEEEE-SS-EEEEEEEHHHHHH CS
                    Rep_fac-A_C  57 sikvsDstgqlwvtlFneaaek 78 
                                    s+ v D+tg + vtl+++a   
  gi|116754196|ref|YP_843314.1|  95 SLTVGDETGMIKVTLWDDATDL 116
                                    6889*************98765 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.047
                                    EEEEE-SS-EEEEEEEHHHH CS
                    Rep_fac-A_C  57 sikvsDstgqlwvtlFneaa 76 
                                    s+ + D tg++ +tl+n++a
  gi|116754196|ref|YP_843314.1| 204 SMLLGDDTGSINITLWNDHA 223
                                    56789*************87 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.0053
                                    EEEEEEEEE-SS-EEEEEEEHH CS
                    Rep_fac-A_C  53 ryilsikvsDstgqlwvtlFne 74 
                                     y+ si+v+D+tg+++v+l+ +
  gi|116754196|ref|YP_843314.1| 305 GYVTSINVTDETGRVRVSLWGD 326
                                    5999**************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2857.83
//
Query:       gi|116754197|ref|YP_843315.1|  [L=567]
Description: ABC transporter related [Methanosaeta thermophila PT]
Scores for 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-56  191.2   0.0      4e-27   95.4   0.0    2.3  2  ABC_tran       ABC transporter
    9.9e-14   51.8   0.0     0.0016   18.4   0.0    4.0  4  AAA_21         AAA domain, putative AbiEii toxin, Type IV TA 
      7e-08   32.6   0.1     0.0056   16.6   0.0    2.7  2  RsgA_GTPase    RsgA GTPase
    2.1e-07   30.5   1.2     0.0025   17.5   0.0    2.4  2  AAA_29         P-loop containing region of AAA domain
    7.7e-07   28.8   1.9       0.01   15.3   0.0    4.0  4  SMC_N          RecF/RecN/SMC N terminal domain
    7.5e-05   23.2   0.1      0.095   13.1   0.0    2.6  2  AAA_16         AAA ATPase domain
    0.00011   22.5   5.4       0.35   11.1   0.1    3.9  3  AAA_22         AAA domain
    0.00012   21.8   0.3          1    9.1   0.1    3.2  2  AAA_30         AAA domain
    0.00046   19.9   0.0       0.11   12.2   0.0    2.4  2  ATP-synt_ab    ATP synthase alpha/beta family, nucleotide-bin
    0.00049   20.7   4.2       0.17   12.3   0.6    2.3  2  AAA_23         AAA domain
    0.00061   20.0   0.9       0.11   12.7   0.1    3.8  2  SbcCD_C        Putative exonuclease SbcCD, C subunit
     0.0007   19.9   0.9        1.8    8.8   0.0    3.1  3  AAA_28         AAA domain
      0.001   18.7   4.6       0.51    9.9   0.3    4.3  4  AAA_25         AAA domain
     0.0015   18.6   0.0        1.1    9.3   0.0    2.8  2  MMR_HSR1       50S ribosome-binding GTPase
     0.0023   18.1   1.6       0.77    9.8   0.1    2.5  2  DUF87          Helicase HerA, central domain
     0.0023   17.7   0.5        6.7    6.4   0.0    3.7  4  IstB_IS21      IstB-like ATP binding protein
     0.0042   16.8   0.2       0.95    9.1   0.1    2.5  2  AAA_24         AAA domain
     0.0086   15.8   0.1        3.3    7.4   0.0    2.3  2  PRK            Phosphoribulokinase / Uridine kinase family
  ------ inclusion threshold ------
      0.018   13.9   0.1        3.5    6.4   0.0    2.2  2  DLIC           Dynein light intermediate chain (DLIC)
      0.018   14.9   0.8          4    7.4   0.1    2.5  2  MobB           Molybdopterin guanine dinucleotide synthesis p
       0.02   14.6   0.3        1.1    8.9   0.0    2.6  3  AAA_15         AAA ATPase domain
      0.023   13.9   0.9        2.1    7.4   0.1    2.4  2  NB-ARC         NB-ARC domain
      0.023   14.0   0.0        4.6    6.5   0.0    2.4  2  Zeta_toxin     Zeta toxin
      0.027   14.1   0.4       0.95    9.0   0.1    2.4  2  cobW           CobW/HypB/UreG, nucleotide-binding domain
      0.031   14.0   0.1        1.9    8.2   0.0    2.5  2  PduV-EutP      Ethanolamine utilisation - propanediol utilisa
      0.036   14.6   3.2        3.4    8.2   0.0    4.1  3  AAA_18         AAA domain
      0.072   12.0   0.7        2.8    6.8   0.0    2.3  2  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
      0.089   12.2   3.2        8.8    5.7   0.0    3.8  4  TniB           Bacterial TniB protein
       0.11   12.8   0.0       0.23   11.8   0.0    1.4  1  DUF4061        Domain of unknown function (DUF4061)
       0.12   12.8   0.1         19    5.7   0.1    2.4  2  RNA_helicase   RNA helicase
       0.12   12.3   5.5        2.1    8.2   0.4    3.2  3  NACHT          NACHT domain
       0.13   11.0   1.8        2.3    6.9   0.1    2.9  4  ABC_ATPase     Predicted ATPase of the ABC class
       0.15   12.3   0.1         16    5.8   0.0    2.4  2  Roc            Ras of Complex, Roc, domain of DAPkinase
       0.18   12.0   1.6        8.6    6.5   0.1    2.8  2  AAA_33         AAA domain
       0.25   10.9   0.1        3.2    7.2   0.0    2.2  2  AAA_7          P-loop containing dynein motor region
       0.28   10.2   2.7         29    3.6   0.0    3.1  3  T2SSE          Type II/IV secretion system protein
         10    5.4   8.2        6.9    5.9   0.1    3.8  6  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 !   95.4   0.0   8.2e-30     4e-27       1     136 [.      21     180 ..      21     181 .. 0.86
   2 !   93.8   0.0   2.6e-29   1.3e-26       2     136 ..     286     491 ..     285     492 .. 0.91

  Alignments for each domain:
  == domain 1  score: 95.4 bits;  conditional E-value: 8.2e-30
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG...B-HHHCCHCEEEE-SS..--S-TTSB CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx..xxxxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke...qeleslrkeigvlpqe..pqlfpelt 75 
                                    lk+vs++ +ege+++ivG++G GKStL+++l g ++ ++G+i +dg +++    ++ +  +++i  ++ +    l+ e+ 
  gi|116754197|ref|YP_843315.1|  21 LKDVSFSANEGEILGIVGKSGGGKSTLMRILRGIEDFDAGRIVIDGLEITPesgEDVRMQQRRITAIHLQreFGLWTESA 100
                                    79************************************************988855555555555544333466666665 PP

                                    HHHH.......................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEE CS
                                    xxxx.......................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  76 vren.......................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllll 132
                                    +++                        e+ ee++ +l+ +gl +++++ +    + LSgG+kqr+ +ar l+kkpkllll
  gi|116754197|ref|YP_843315.1| 101 IKNVvrrvysretgyealpipedarydEYYEEAKGFLELVGLGHKANHLA----TILSGGEKQRLLIARQLAKKPKLLLL 176
                                    5555888888899*******999998888888************999998....************************** PP

                                    ESTT CS
                                    xxxx RF
                       ABC_tran 133 DEpt 136
                                    DEp 
  gi|116754197|ref|YP_843315.1| 177 DEPA 180
                                    ***6 PP

  == domain 2  score: 93.8 bits;  conditional E-value: 2.6e-29
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCE.GGG.....B-HHHCCHCEEEE-SS--S-TTSB CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx.....xxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkd.lke.....qeleslrkeigvlpqepqlfpelt 75 
                                    +n+ l++++ge++ai+G++GaGK+tLl ++ gl  p+ G+i ++ +d + +      ++ + r+++g++ qe  l p+ t
  gi|116754197|ref|YP_843315.1| 286 SNLRLNINRGETTAIIGSSGAGKTTLLTMIEGLRMPDDGHIYYRHEDgWVDittysPTRMEIRRRLGIMYQEFALMPHET 365
                                    6999*************************************88844414446668889999******************* PP

                                    HHHH......................................HHHTCHHHHHHHSTTGG..................... CS
                                    xxxx......................................xxxxxxxxxxxxxxxxx..................... RF
                       ABC_tran  76 vren......................................esdeeiekalsklglke..................... 96 
                                    + e+                                       +++e++++l++lg+                       
  gi|116754197|ref|YP_843315.1| 366 ILEQiayklgvkgqhvieyarevaaeigisdrvldmlytltdMREDEAKAVLERLGIGRdvlselfpkfpdtearrfaep 445
                                    ****************************9999999999999877777888888888888899999999999999999999 PP

                                    ......TTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    ......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  97 ......lkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                          l+++++++ p++LSgG+ +r +la +l+ +p++l+lDEp+
  gi|116754197|ref|YP_843315.1| 446 vfrimdLDTSILDKYPEQLSGGESVRASLAILLAANPSILILDEPF 491
                                    999998999999999******************************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 !   18.4   0.0   3.2e-06    0.0016       2      92 ..      34     122 ..      33     155 .. 0.82
   2 ?    1.2   0.1      0.53   2.6e+02     246     266 ..     161     179 ..     146     215 .. 0.73
   3 !   12.2   0.0   0.00025      0.12       2      23 ..     298     319 ..     297     357 .. 0.73
   4 !   14.9   0.0   3.7e-05     0.018     248     301 ..     474     526 ..     432     528 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.2e-06
                         AAA_21   2 nvliGpNgsGKSnLLdaldllarl...drdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrl 78 
                                     +++G+ g GKS+L+++l+++ ++   +  ++gl +++ +g + r++ ++++ ++   +f + +e   ++ vr  y+ + 
  gi|116754197|ref|YP_843315.1|  34 LGIVGKSGGGKSTLMRILRGIEDFdagRIVIDGLEITPESGEDVRMQQRRITAIHLQREFGLWTESAIKNVVRRVYSRET 113
                                    579**********************9999999999999999999999999999999999999999999999999999988 PP

                         AAA_21  79 ersqveeklssvet 92 
                                    +++++       ++
  gi|116754197|ref|YP_843315.1| 114 GYEAL-----PIPE 122
                                    88888.....3333 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.53
                         AAA_21 246 alltallralkkgsllliDEp 266
                                     l++   +++kk++lll+DEp
  gi|116754197|ref|YP_843315.1| 161 LLIAR--QLAKKPKLLLLDEP 179
                                    44444..4456669******9 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 0.00025
                         AAA_21   2 nvliGpNgsGKSnLLdaldlla 23 
                                    +++iG  g+GK++LL  +++l+
  gi|116754197|ref|YP_843315.1| 298 TAIIGSSGAGKTTLLTMIEGLR 319
                                    89*****************996 PP

  == domain 4  score: 14.9 bits;  conditional E-value: 3.7e-05
                         AAA_21 248 ltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSpll 301
                                    l++ll+a++  s+l++DEp   ++P  lr ++  +k+ ++  g+ +i+++H   l
  gi|116754197|ref|YP_843315.1| 474 LAILLAANP--SILILDEPFGDIDPITLRDVANAMKRIQArYGTTIIIVSHHVDL 526
                                    344444444..************************555555**********8655 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   0.00016     0.078      97     128 ..      28      60 ..       7      68 .. 0.77
   2 !   16.6   0.0   1.2e-05    0.0056      90     121 ..     285     317 ..     271     339 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00016
                                    CTT.SEEEEECSTTSSHHHHHHHHCTT-----S CS
                    RsgA_GTPase  97 lkd.ktsvlvGqSGvGKStLinallpelelktg 128
                                     ++ ++  +vG+SG GKStL+  l++ ++   g
  gi|116754197|ref|YP_843315.1|  28 ANEgEILGIVGKSGGGKSTLMRILRGIEDFDAG 60 
                                    44448899***************9997666655 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1.2e-05
                                    HHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase  90 leelkellkd.ktsvlvGqSGvGKStLinallp 121
                                    +++l+ +++  +t++++G+SG+GK+tL+ ++ +
  gi|116754197|ref|YP_843315.1| 285 ISNLRLNINRgETTAIIGSSGAGKTTLLTMIEG 317
                                    566776776669****************99876 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 !   11.5   0.3    0.0004      0.19      19      39 ..      28      48 ..      20      51 .. 0.75
   2 !   17.5   0.0   5.2e-06    0.0025      16      46 ..     289     319 ..     284     328 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0004
                         AAA_29 19 idlkg.atlltGpsGsGKSTll 39
                                    ++ g +  ++G+sG GKSTl+
  gi|116754197|ref|YP_843315.1| 28 ANE-GeILGIVGKSGGGKSTLM 48
                                   343.34778***********97 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 5.2e-06
                         AAA_29  16 tieidlkgatlltGpsGsGKSTllDAiqalL 46 
                                    +++i++ ++t ++G sG+GK+Tll  i  l 
  gi|116754197|ref|YP_843315.1| 289 RLNINRGETTAIIGSSGAGKTTLLTMIEGLR 319
                                    56788666***************96665555 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 ?    2.3   0.1       0.2        99      25      42 ..      32      49 ..       9      54 .. 0.79
   2 ?    3.4   0.0     0.091        44     136     197 ..     152     211 ..      65     224 .. 0.77
   3 ?    4.1   0.1     0.055        27      25      43 ..     296     314 ..     286     316 .. 0.83
   4 !   15.3   0.0   2.1e-05      0.01     117     205 ..     407     530 ..     378     541 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.2
                                   SEEEEEESTTSSHHHHHH CS
                                   xxxxxxxxxxxxxxxxxx RF
                          SMC_N 25 sftaivGpNGSGKsnlld 42
                                   ++  ivG+ G GKs l+ 
  gi|116754197|ref|YP_843315.1| 32 EILGIVGKSGGGKSTLMR 49
                                   4678**********9985 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.091
                                    CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-S CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx RF
                          SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivisl 197
                                     LSgGek+     Ll+A q +k+  l llDe +     k  ++v + +k+ +++     +v+s+
  gi|116754197|ref|YP_843315.1| 152 ILSGGEKQ----RLLIARQLAKKPKLLLLDEPATMACPKTKQEVLDTIKRVNEElgLTTLVVSH 211
                                    8******8....78899999999999999*9988888888888888888777663345566666 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.055
                                    SEEEEEESTTSSHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxx RF
                          SMC_N  25 sftaivGpNGSGKsnlldA 43 
                                    + tai+G+ G+GK+ ll  
  gi|116754197|ref|YP_843315.1| 296 ETTAIIGSSGAGKTTLLTM 314
                                    579***********99865 PP

  == domain 4  score: 15.3 bits;  conditional E-value: 2.1e-05
                                    EE-HHHHHHHHHCTT-STT.....................................CS-HHHHHHHHHHHHHHHHCCS-- CS
                                    xxxxxxxxxxxxxxxxxxx.....................................xxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 117 evtkkevsellesagiske.....................................lLSgGektLvalaLlfAiqkvkpa 159
                                    ++++ e + +le+ gi ++                                     +LSgGe   ++la+l+A +     
  gi|116754197|ref|YP_843315.1| 407 DMREDEAKAVLERLGIGRDvlselfpkfpdtearrfaepvfrimdldtsildkypeQLSGGESVRASLAILLAAN----P 482
                                    56677777888888888888888888888888888888888888888888888888***************9964....4 PP

                                    SEEEECTTTTTS-HHHHHHHHHHHH..HHCTTSEEEEE-SSHHHCCC- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 160 plyllDeidaaLDeknvkkvaellk..eksknaQfivislreemleka 205
                                    ++ +lDe    +D    + va+ +k  +++  + +i++s++ ++++++
  gi|116754197|ref|YP_843315.1| 483 SILILDEPFGDIDPITLRDVANAMKriQARYGTTIIIVSHHVDLVKEV 530
                                    6899*********************4444555999*****99988876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0087       4.2      20      45 ..      27      52 ..      16     116 .. 0.86
   2 !   13.1   0.0    0.0002     0.095      19      46 ..     290     317 ..     281     489 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0087
                         AAA_16 20 rsgrpelvllsGesGvGKsslvrell 45
                                   +++++e++ ++G sG GKs+l+r l+
  gi|116754197|ref|YP_843315.1| 27 SANEGEILGIVGKSGGGKSTLMRILR 52
                                   4566799**************98776 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.0002
                         AAA_16  19 vrsgrpelvllsGesGvGKsslvrellr 46 
                                    ++ +r+e + ++G sG GK++l++++  
  gi|116754197|ref|YP_843315.1| 290 LNINRGETTAIIGSSGAGKTTLLTMIEG 317
                                    566777999**************99874 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   1.2    0.0056       2.7       6      29 ..      32      55 ..      28     219 .. 0.58
   2 !   11.1   0.1   0.00073      0.35       8      29 ..     298     319 ..     292     417 .. 0.74
   3 ?   -0.5   0.0       2.8   1.3e+03      51      99 ..     437     489 ..     402     528 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0056
                         AAA_22  6 gilvvtGesGtGKTtllrrlleql 29
                                    il ++G sG GK+tl+r l+   
  gi|116754197|ref|YP_843315.1| 32 EILGIVGKSGGGKSTLMRILRGIE 55
                                   57789************9887665 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00073
                         AAA_22   8 lvvtGesGtGKTtllrrlleql 29 
                                    ++++G sG+GKTtll ++    
  gi|116754197|ref|YP_843315.1| 298 TAIIGSSGAGKTTLLTMIEGLR 319
                                    79************99887655 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 2.8
                         AAA_22  51 tsskdllrellralglelka.....erlsseellealeqalraravielliiDE 99 
                                    t+ + +++ ++r+++l+++      e ls  e ++a    l a+   ++li+DE
  gi|116754197|ref|YP_843315.1| 437 TEARRFAEPVFRIMDLDTSIldkypEQLSGGESVRASLAILLAANP-SILILDE 489
                                    4667777777777777666676666555555555555556666666.7999998 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.1    0.0021         1      17      48 ..      30      61 ..      24     205 .. 0.74
   2 !    8.3   0.0    0.0036       1.7      19      39 ..     296     316 ..     288     342 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0021
                         AAA_30 17 gdrvavltGpAGtGKttalkalreaweaaggr 48
                                   +  +  ++G  G GK+t+++ lr + + + gr
  gi|116754197|ref|YP_843315.1| 30 EGEILGIVGKSGGGKSTLMRILRGIEDFDAGR 61
                                   4458889**************99887766333 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0036
                         AAA_30  19 rvavltGpAGtGKttalkalr 39 
                                     ++++ G  G+GKtt+l+ ++
  gi|116754197|ref|YP_843315.1| 296 ETTAIIGSSGAGKTTLLTMIE 316
                                    47899************9876 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 ?    5.5   0.0     0.024        12       6      48 ..      23      66 ..      19     223 .. 0.70
   2 !   12.2   0.0   0.00022      0.11      10      46 ..     291     327 ..     283     421 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.024
                                   HHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSS.EEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                    ATP-synt_ab  6 DalfpivqGqrtlipgafgvGktvisqslskqsnsdd.aiiyvg 48
                                   D+ f+  +G+ ++i+g++g Gk+++++ l    + d   i++ g
  gi|116754197|ref|YP_843315.1| 23 DVSFSANEGEILGIVGKSGGGKSTLMRILRGIEDFDAgRIVIDG 66
                                   77789999*****************9888777665655666666 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00022
                                    -EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab  10 pivqGqrtlipgafgvGktvisqslskqsnsddaiiy 46 
                                     i +G++t+i+g +g Gkt+++ ++      dd  iy
  gi|116754197|ref|YP_843315.1| 291 NINRGETTAIIGSSGAGKTTLLTMIEGLRMPDDGHIY 327
                                    6889******************999766555555555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.2    0.0032       1.5      19      40 ..      31      52 ..      14      54 .. 0.76
   2 !   12.3   0.6   0.00036      0.17      20      39 ..     296     315 ..     283     317 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0032
                         AAA_23 19 kgltlItGpNGaGKTTildAik 40
                                     +  I+G+ G GK+T+++ ++
  gi|116754197|ref|YP_843315.1| 31 GEILGIVGKSGGGKSTLMRILR 52
                                   35788*************9776 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00036
                         AAA_23  20 gltlItGpNGaGKTTildAi 39 
                                      t+I+G  GaGKTT+l  i
  gi|116754197|ref|YP_843315.1| 296 ETTAIIGSSGAGKTTLLTMI 315
                                    479*************9876 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0       0.5   2.4e+02      33      42 ..     153     162 ..     143     197 .. 0.63
   2 !   12.7   0.1   0.00024      0.11      31      89 ..     462     507 ..     449     508 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.5
                        SbcCD_C  33 lSGGekqfla 42 
                                    lSGGekq l+
  gi|116754197|ref|YP_843315.1| 153 LSGGEKQRLL 162
                                    5677776554 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00024
                        SbcCD_C  31 gtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                    ++lSGGe+       + a+la l+        ++++++LDE F+ +D+ +++ + ++++
  gi|116754197|ref|YP_843315.1| 462 EQLSGGES-------VRASLAILLAA------NPSILILDEPFGDIDPITLRDVANAMK 507
                                    67889998.......55556666666......4899****************9999886 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0059       2.8       4      48 ..      36      91 ..      34     115 .. 0.78
   2 !    8.8   0.0    0.0037       1.8       3      20 ..     299     316 ..     297     333 .. 0.84
   3 ?   -1.7   0.0       6.2     3e+03      15      40 ..     366     394 ..     365     419 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0059
                         AAA_28  4 itGgestGKTtlleaLa.....ar......gypvvpEaareileeklakgedalpw 48
                                   i+G +++GK+tl++ L      +       g ++ pE++ ++  ++ + +  +l+ 
  gi|116754197|ref|YP_843315.1| 36 IVGKSGGGKSTLMRILRgiedfDAgrividGLEITPESGEDVRMQQRRITAIHLQR 91
                                   78999***********9886661145778899999999999998888888777765 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0037
                         AAA_28   3 vitGgestGKTtlleaLa 20 
                                    +i+G +++GKTtll  ++
  gi|116754197|ref|YP_843315.1| 299 AIIGSSGAGKTTLLTMIE 316
                                    79***********98765 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 6.2
                         AAA_28  15 lleaLaar...gypvvpEaareileekla 40 
                                    +le++a +   + ++v E+are+  e + 
  gi|116754197|ref|YP_843315.1| 366 ILEQIAYKlgvKGQHVIEYAREVAAEIGI 394
                                    66666654533445889999999877654 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1       0.7   3.4e+02      32      49 ..      30      47 ..      28      51 .. 0.86
   2 ?    0.8   0.0      0.63   3.1e+02     166     189 ..     189     212 ..     172     214 .. 0.90
   3 !    9.9   0.3     0.001      0.51      30      51 ..     292     313 ..     286     421 .. 0.88
   4 ?    5.0   0.0     0.034        16     167     188 ..     501     522 ..     495     525 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.7
                         AAA_25 32 agelallaGapgtGKttl 49
                                   +ge+  ++G +g GK+tl
  gi|116754197|ref|YP_843315.1| 30 EGEILGIVGKSGGGKSTL 47
                                   67777899*********9 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.63
                         AAA_25 166 galvealeriarrtgaavllvhHv 189
                                    +++++ ++r+ +++g ++l+v H+
  gi|116754197|ref|YP_843315.1| 189 QEVLDTIKRVNEELGLTTLVVSHL 212
                                    6788999****************7 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.001
                         AAA_25  30 lpagelallaGapgtGKttlal 51 
                                    + +ge+++++G +g+GKttl++
  gi|116754197|ref|YP_843315.1| 292 INRGETTAIIGSSGAGKTTLLT 313
                                    679****************986 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.034
                         AAA_25 167 alvealeriarrtgaavllvhH 188
                                     + +a++ri++r+g ++++v H
  gi|116754197|ref|YP_843315.1| 501 DVANAMKRIQARYGTTIIIVSH 522
                                    6889************999988 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0024       1.1       3      21 ..      35      53 ..      33      88 .. 0.85
   2 ?    6.3   0.0     0.021        10       2      18 ..     298     314 ..     297     326 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0024
                                   EEEESTTSSHHHHHHHHHT CS
                       MMR_HSR1  3 aivGrpNvGKStLinaltg 21
                                   +ivG++  GKStL++ l g
  gi|116754197|ref|YP_843315.1| 35 GIVGKSGGGKSTLMRILRG 53
                                   8*************99865 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.021
                                    EEEEESTTSSHHHHHHH CS
                       MMR_HSR1   2 vaivGrpNvGKStLina 18 
                                     ai+G + +GK+tL+  
  gi|116754197|ref|YP_843315.1| 298 TAIIGSSGAGKTTLLTM 314
                                    59************975 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.1    0.0016      0.77      26      45 ..      34      52 ..      30      65 .. 0.76
   2 ?    6.9   0.2     0.012       5.9      25      43 ..     297     315 ..     279     318 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0016
                          DUF87 26 lAilgsTGsGKSntvavLle 45
                                   l+i+g++G GKS+++++L +
  gi|116754197|ref|YP_843315.1| 34 LGIVGKSGGGKSTLMRIL-R 52
                                   69*************965.4 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.012
                          DUF87  25 HlAilgsTGsGKSntvavL 43 
                                     +Ai+gs+G+GK+++   +
  gi|116754197|ref|YP_843315.1| 297 TTAIIGSSGAGKTTLLTMI 315
                                    58************98665 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.023        11      29      64 ..      12      48 ..       7      63 .. 0.81
   2 ?   -1.0   0.0       2.6   1.2e+03     103     130 ..     165     192 ..     145     219 .. 0.73
   3 ?    6.4   0.0     0.014       6.7      44      67 ..     292     315 ..     282     336 .. 0.81
   4 ?   -0.3   0.0       1.6   7.9e+02     108     148 ..     481     523 ..     466     530 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.023
                      IstB_IS21 29 sldkrkvkeLatlsfiekk.enivllGpsGvGKshla 64
                                   +++ rk+ +L   sf +++ e + ++G sG GKs l 
  gi|116754197|ref|YP_843315.1| 12 DVKGRKILALKDVSFSANEgEILGIVGKSGGGKSTLM 48
                                   567899999999***877615556**********885 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.6
                      IstB_IS21 103 lkrllkvdllilDdlgllpldqaeaell 130
                                     +   k++ll+lD+ ++    + ++e+l
  gi|116754197|ref|YP_843315.1| 165 RQLAKKPKLLLLDEPATMACPKTKQEVL 192
                                    34456789*****999888777666655 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.014
                      IstB_IS21  44 iekkenivllGpsGvGKshlaial 67 
                                    i++ e  +++G sG+GK+ l + +
  gi|116754197|ref|YP_843315.1| 292 INRGETTAIIGSSGAGKTTLLTMI 315
                                    789999************987655 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 1.6
                      IstB_IS21 108 kvdllilDd.lg.llpldqaeaellfeviekryerrsiiitsn 148
                                    ++++lilD+ +g + p+   + ++ ++ i++ry+++ ii++  
  gi|116754197|ref|YP_843315.1| 481 NPSILILDEpFGdIDPITLRDVANAMKRIQARYGTTIIIVSHH 523
                                    5678999985443677888888888899999**9999998865 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.033        16       6      38 ..      35      64 ..      31     105 .. 0.78
   2 !    9.1   0.1     0.002      0.95       5      22 ..     298     315 ..     294     326 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.033
                         AAA_24  6 liyGpsgiGKTtlakelgpkplfidtekGlksl 38
                                    i+G+sg GK+tl++ l     + d+++G   +
  gi|116754197|ref|YP_843315.1| 35 GIVGKSGGGKSTLMRIL---RGIEDFDAGRIVI 64
                                   699***********988...3344555555555 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.002
                         AAA_24   5 iliyGpsgiGKTtlakel 22 
                                     +i+G+sg+GKTtl++++
  gi|116754197|ref|YP_843315.1| 298 TAIIGSSGAGKTTLLTMI 315
                                    68************9887 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0069       3.3       1      21 [.      33      53 ..      33      84 .. 0.86
   2 ?    6.1   0.0     0.017       8.3       3      20 ..     299     316 ..     298     332 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0069
                            PRK  1 vIgvagsSGaGkttvarklek 21
                                   ++g+ g+SG Gk+t++r l+ 
  gi|116754197|ref|YP_843315.1| 33 ILGIVGKSGGGKSTLMRILRG 53
                                   789*************98875 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.017
                            PRK   3 gvagsSGaGkttvarkle 20 
                                    ++ gsSGaGktt+   +e
  gi|116754197|ref|YP_843315.1| 299 AIIGSSGAGKTTLLTMIE 316
                                    689*********988775 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0072       3.5      30      55 ..      36      61 ..      26      86 .. 0.86
   2 ?    5.3   0.0     0.015       7.2      25      54 ..     295     324 ..     281     339 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0072
                           DLIC 30 vlGedgsGkttliaklqGveeekkGr 55
                                   ++G++g Gk+tl+  l+G+e+   Gr
  gi|116754197|ref|YP_843315.1| 36 IVGKSGGGKSTLMRILRGIEDFDAGR 61
                                   78*******************99998 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.015
                           DLIC  25 gksvlvlGedgsGkttliaklqGveeekkG 54 
                                    g +  ++G +g+Gkttl++ + G+  +  G
  gi|116754197|ref|YP_843315.1| 295 GETTAIIGSSGAGKTTLLTMIEGLRMPDDG 324
                                    5667899****************9877666 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.029        14       1      18 [.      33      50 ..      33      59 .. 0.89
   2 ?    7.4   0.1    0.0082         4       3      18 ..     299     314 ..     297     321 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.029
                           MobB  1 vlgivgksgsGKTtLlek 18
                                   +lgivgksg GK tL+  
  gi|116754197|ref|YP_843315.1| 33 ILGIVGKSGGGKSTLMRI 50
                                   79*************975 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0082
                           MobB   3 givgksgsGKTtLlek 18 
                                    +i+g sg+GKTtLl+ 
  gi|116754197|ref|YP_843315.1| 299 AIIGSSGAGKTTLLTM 314
                                    699**********975 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.17        84      24      44 ..      31      52 ..      20      78 .. 0.77
   2 ?   -1.8   0.0       3.9   1.9e+03     320     354 ..     167     201 ..     146     215 .. 0.78
   3 ?    8.9   0.0    0.0023       1.1      16      44 ..     287     316 ..     284     331 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.17
                         AAA_15 24 e.ltvliGkNnsGKSsileald 44
                                     +  ++Gk + GKS+++++l 
  gi|116754197|ref|YP_843315.1| 31 GeILGIVGKSGGGKSTLMRILR 52
                                   257789*************995 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.9
                         AAA_15 320 keeknvilliEEPEahLHpqaqkvlikllkeland 354
                                      +k+++ll++EP +   p+ ++++ +++k++ ++
  gi|116754197|ref|YP_843315.1| 167 LAKKPKLLLLDEPATMACPKTKQEVLDTIKRVNEE 201
                                    46789999999999999999999999999887655 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0023
                         AAA_15  16 dveidlsee.ltvliGkNnsGKSsileald 44 
                                    +  ++++   +t +iG  ++GK+++l +++
  gi|116754197|ref|YP_843315.1| 287 NLRLNINRGeTTAIIGSSGAGKTTLLTMIE 316
                                    55555555569****************997 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1    0.0044       2.1      17      38 ..      30      49 ..      18      57 .. 0.84
   2 ?    4.4   0.1     0.036        18      23      40 ..     298     315 ..     285     321 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0044
                                   TSCSEEEEEEESTTSSHHHHHH CS
                         NB-ARC 17 elqslvvalvGmgGvGKttlak 38
                                   e +  ++++vG+ G GK+tl++
  gi|116754197|ref|YP_843315.1| 30 EGE--ILGIVGKSGGGKSTLMR 49
                                   444..9**************96 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.036
                                    EEEEESTTSSHHHHHHHH CS
                         NB-ARC  23 valvGmgGvGKttlakqi 40 
                                     a+ G  G GKttl++ i
  gi|116754197|ref|YP_843315.1| 298 TAIIGSSGAGKTTLLTMI 315
                                    5899**********9876 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.031        15      21      94 ..      36     107 ..      21     110 .. 0.76
   2 ?    6.5   0.0    0.0095       4.6      22      37 ..     301     316 ..     290     326 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.031
                     Zeta_toxin  21 lgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPeyeeilkadpkkaseltqkdaselvekllqeaien 94 
                                    ++G +G GKs+l++ l+   + + + +++d+ ++ +     e+++ ++ + ++++ q++ + ++e++++ ++ +
  gi|116754197|ref|YP_843315.1|  36 IVGKSGGGKSTLMRILRGIEDFDAGRIVIDGLEITPESG--EDVRMQQRRITAIHLQREFGLWTESAIKNVVRR 107
                                    7899***********998876677777777766655543..355556777788899999999999999888765 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0095
                     Zeta_toxin  22 gGqpGAGKselaellk 37 
                                     G++GAGK++l+++++
  gi|116754197|ref|YP_843315.1| 301 IGSSGAGKTTLLTMIE 316
                                    59***********987 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.17        83       3      19 ..      34      50 ..      32      81 .. 0.86
   2 ?    9.0   0.1     0.002      0.95       3      20 ..     298     315 ..     296     324 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.17
                                   EEEEESTTCCHHHHHHH CS
                           cobW  3 tvltGflGsGKTtLlnh 19
                                   ++++G  G GK+tL++ 
  gi|116754197|ref|YP_843315.1| 34 LGIVGKSGGGKSTLMRI 50
                                   7899**********975 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.002
                                    EEEEESTTCCHHHHHHHH CS
                           cobW   3 tvltGflGsGKTtLlnhl 20 
                                    t + G+ G+GKTtLl+ +
  gi|116754197|ref|YP_843315.1| 298 TAIIGSSGAGKTTLLTMI 315
                                    7899***********865 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1      0.16        78       6      23 ..      36      53 ..      32      57 .. 0.88
   2 ?    8.2   0.0    0.0039       1.9       6      26 ..     300     320 ..     296     337 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.16
                      PduV-EutP  6 liGkvgsGKttLtqalkg 23
                                   ++Gk+g GK tL++ l+g
  gi|116754197|ref|YP_843315.1| 36 IVGKSGGGKSTLMRILRG 53
                                   69************9987 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0039
                      PduV-EutP   6 liGkvgsGKttLtqalkgeel 26 
                                    +iG++g+GKttL   ++g ++
  gi|116754197|ref|YP_843315.1| 300 IIGSSGAGKTTLLTMIEGLRM 320
                                    89************9999776 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    0.0069       3.4       3      25 ..      36      60 ..      34      92 .. 0.82
   2 ?   -1.8   0.0       9.1   4.4e+03      27      86 ..     163     216 ..     148     226 .. 0.72
   3 ?    3.9   0.6      0.16        75       3      17 ..     300     314 ..     299     512 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0069
                         AAA_18  3 ltGtpGvGKttlakeLskrlgf..g 25
                                   + G++G GK+tl + L+  + f  g
  gi|116754197|ref|YP_843315.1| 36 IVGKSGGGKSTLMRILRGIEDFdaG 60
                                   89**************755544444 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 9.1
                         AAA_18  27 nlrdvakenglllevdpealdeskrldedkldklldaleenssaleegknlvidghlael 86 
                                    + r++ak+  lll ++p+ +  + + ++++ld + + +ee         +lv++ +++ +
  gi|116754197|ref|YP_843315.1| 163 IARQLAKKPKLLLLDEPA-TMACPKTKQEVLDTIKRVNEELGL-----TTLVVSHLPEIH 216
                                    567888888888888888.777777777777777777776655.....566666666555 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.16
                         AAA_18   3 ltGtpGvGKttlake 17 
                                    + G +G+GKttl   
  gi|116754197|ref|YP_843315.1| 300 IIGSSGAGKTTLLTM 314
                                    8899*******9765 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 ?    3.3   0.1     0.067        32      14      50 ..      30      65 ..      19      67 .. 0.81
   2 ?    6.8   0.0    0.0057       2.8      17      47 ..     297     326 ..     284     332 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.067
                  TrwB_AAD_bind 14 etqhilivGttGsGKtqalekllrairargdraivlD 50
                                   e + + ivG  G GK++ +  +lr+i+      iv+D
  gi|116754197|ref|YP_843315.1| 30 EGEILGIVGKSGGGKSTLM-RILRGIEDFDAGRIVID 65
                                   4555789*********877.58999999998888888 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0057
                  TrwB_AAD_bind  17 hilivGttGsGKtqalekllrairargdrai 47 
                                     ++i+G+ G+GKt+ l  +++++r   d +i
  gi|116754197|ref|YP_843315.1| 297 TTAIIGSSGAGKTTLL-TMIEGLRMPDDGHI 326
                                    589**********865.68888888777776 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1       1.7   8.1e+02      38      53 ..      34      49 ..      27      53 .. 0.86
   2 ?    5.7   0.0     0.018       8.8     117     158 ..     168     207 ..     146     216 .. 0.81
   3 ?    2.1   0.0      0.23   1.1e+02      34      53 ..     294     313 ..     287     325 .. 0.83
   4 ?    1.3   0.0       0.4   1.9e+02     108     160 ..     470     520 ..     452     527 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.7
                           TniB 38 lllvGdsnnGKtmive 53
                                   l +vG+s  GK+++++
  gi|116754197|ref|YP_843315.1| 34 LGIVGKSGGGKSTLMR 49
                                   569**********986 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.018
                           TniB 117 elkvrvLiiDEihnllagsarkqreflnalksLgnelkipiv 158
                                    + k+++L++DE   +     ++++e+l ++k+ ++el ++  
  gi|116754197|ref|YP_843315.1| 168 AKKPKLLLLDEPATMA--CPKTKQEVLDTIKRVNEELGLTTL 207
                                    4589*******99988..5667789***********998755 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.23
                           TniB  34 rmpnlllvGdsnnGKtmive 53 
                                    r +   ++G s  GKt+++ 
  gi|116754197|ref|YP_843315.1| 294 RGETTAIIGSSGAGKTTLLT 313
                                    667789***********986 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.4
                           TniB 108 eqqvlrllrelkvrvLiiDE.ihnllagsarkqreflnalksLgnelkipivlv 160
                                     ++ l++l + ++ +Li+DE + ++      + r + na+k+++ ++  +i++v
  gi|116754197|ref|YP_843315.1| 470 VRASLAILLAANPSILILDEpFGDI---DPITLRDVANAMKRIQARYGTTIIIV 520
                                    556788999999*******943444...46777888888888888888888776 PP

>> DUF4061  Domain of unknown function (DUF4061)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00047      0.23      11      50 ..      51      90 ..      44     103 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00047
                        DUF4061 11 lklledFhsGklkafGkdcsleqleeiReqQekLarlhfe 50
                                   l+ +edF++G++   G +++ e  e++R qQ +++  h++
  gi|116754197|ref|YP_843315.1| 51 LRGIEDFDAGRIVIDGLEITPESGEDVRMQQRRITAIHLQ 90
                                   44469*****************************999975 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.038        19       3      18 ..      36      51 ..      34      58 .. 0.88
   2 ?    4.7   0.0     0.081        39       3      37 ..     300     329 ..     298     340 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.038
                   RNA_helicase  3 lyGpsgeGKStlakeL 18
                                   ++G+sg GKStl++ L
  gi|116754197|ref|YP_843315.1| 36 IVGKSGGGKSTLMRIL 51
                                   78***********975 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.081
                   RNA_helicase   3 lyGpsgeGKStlakeLakallkklklkkkdsvysr 37 
                                    + G+sg GK+tl +       + l ++ ++++y+r
  gi|116754197|ref|YP_843315.1| 300 IIGSSGAGKTTLLTM-----IEGLRMPDDGHIYYR 329
                                    78**********998.....334446777777765 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.6     0.057        27       5      18 ..      36      49 ..      32      54 .. 0.86
   2 ?   -1.8   0.0       5.3   2.6e+03      43      66 ..     193     216 ..     190     225 .. 0.84
   3 ?    8.2   0.4    0.0044       2.1       2      20 ..     297     315 ..     296     318 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.057
                                   EEC-TTTCHHHHHH CS
                          NACHT  5 lqGeaGsGKTtLlq 18
                                   + G++G GK+tL++
  gi|116754197|ref|YP_843315.1| 36 IVGKSGGGKSTLMR 49
                                   89**********98 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 5.3
                                    TTTTTS-...-HCHHHCCCCTS-- CS
                          NACHT  43 relsrsgnarsladllfsqlpepa 66 
                                     +++r +++++l +l++s+lpe+ 
  gi|116754197|ref|YP_843315.1| 193 DTIKRVNEELGLTTLVVSHLPEIH 216
                                    5788888899*********99976 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0044
                                    CEEEEC-TTTCHHHHHHHH CS
                          NACHT   2 lvilqGeaGsGKTtLlqkl 20 
                                    + ++ G +G GKTtLl  +
  gi|116754197|ref|YP_843315.1| 297 TTAIIGSSGAGKTTLLTMI 315
                                    7899***********9765 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1      0.17        84     245     264 ..      31      51 ..      26      76 .. 0.84
   2 ?   -2.8   0.0       4.2     2e+03     335     349 ..     165     179 ..     154     227 .. 0.56
   3 ?    6.9   0.1    0.0048       2.3     241     266 ..     291     317 ..     289     331 .. 0.84
   4 ?   -2.6   0.0       3.6   1.7e+03     377     413 ..     503     539 ..     495     542 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.17
                                    S.EEEEEE-TTSSHHHHHHHH CS
                     ABC_ATPase 245 G.vtlIvGggfhGKsTLLeAl 264
                                    G +  IvG    GKsTL++ l
  gi|116754197|ref|YP_843315.1|  31 GeILGIVGKSGGGKSTLMRIL 51 
                                    55888************9866 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.2
                                    HHHHTT-SEEEEEGG CS
                     ABC_ATPase 335 ealeagakllLiDED 349
                                    ++l  + kllL+DE 
  gi|116754197|ref|YP_843315.1| 165 RQLAKKPKLLLLDEP 179
                                    555555555555553 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0048
                                    EE-SS.EEEEEE-TTSSHHHHHHHHHH CS
                     ABC_ATPase 241 gipkG.vtlIvGggfhGKsTLLeAlek 266
                                     i +G  t+I+G+   GK+TLL+ +e 
  gi|116754197|ref|YP_843315.1| 291 NINRGeTTAIIGSSGAGKTTLLTMIEG 317
                                    58889899**************99984 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 3.6
                                    HHCHHHHHHHH--EEEEEESS-GCCTTT-SEEEEEET CS
                     ABC_ATPase 377 vdrvrelykklgvstilvvggsgdyldvAdtvilmee 413
                                    ++ ++++ +++g ++i+v+  ++   +vA++ il ++
  gi|116754197|ref|YP_843315.1| 503 ANAMKRIQARYGTTIIIVSHHVDLVKEVAHRAILFDN 539
                                    5667778888999999999999999999999998875 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0      0.12        59       4      28 ..      36      61 ..      34      91 .. 0.69
   2 ?    5.8   0.0     0.032        16       4      18 ..     300     314 ..     298     323 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.12
                                   EESSTTSSHHHHHHCHCT.-CCC-EE CS
                            Roc  4 lvGdsgvGKtsllkrfve.dkfseke 28
                                   +vG+sg GK++l++ +   ++f+  +
  gi|116754197|ref|YP_843315.1| 36 IVGKSGGGKSTLMRILRGiEDFDAGR 61
                                   89**********98765445555555 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.032
                                    EESSTTSSHHHHHHC CS
                            Roc   4 lvGdsgvGKtsllkr 18 
                                    ++G sg+GKt+ll+ 
  gi|116754197|ref|YP_843315.1| 300 IIGSSGAGKTTLLTM 314
                                    8***********975 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1      0.15        71       4      17 ..      36      49 ..      33      57 .. 0.89
   2 ?    6.5   0.1     0.018       8.6       4      17 ..     300     313 ..     298     319 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.15
                         AAA_33  4 lvGlpGsGKstlae 17
                                   +vG +G GKstl +
  gi|116754197|ref|YP_843315.1| 36 IVGKSGGGKSTLMR 49
                                   69*********987 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.018
                         AAA_33   4 lvGlpGsGKstlae 17 
                                    ++G +G+GK+tl++
  gi|116754197|ref|YP_843315.1| 300 IIGSSGAGKTTLLT 313
                                    69*********975 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 ?    1.1   0.0      0.51   2.5e+02      38      51 ..      36      49 ..      24      60 .. 0.82
   2 ?    7.2   0.0    0.0066       3.2      11      51 ..     274     313 ..     269     327 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.51
                          AAA_7 38 lvGptGtGKtviik 51
                                   +vG++G GK+++++
  gi|116754197|ref|YP_843315.1| 36 IVGKSGGGKSTLMR 49
                                   89*********986 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0066
                          AAA_7  11 eilVptvdtvrysyllelllknkkpvllvGptGtGKtviik 51 
                                    + lV t + +r+s  l+l ++++  + ++G++G GKt++++
  gi|116754197|ref|YP_843315.1| 274 NYLVGTGEVLRISN-LRLNINRGETTAIIGSSGAGKTTLLT 313
                                    56888888888886.5788999***************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 ?    3.6   0.0      0.06        29     134     197 ..      36     106 ..      19     108 .. 0.75
   2 ?    1.1   0.9      0.34   1.6e+02     125     149 ..     291     315 ..     284     327 .. 0.77
   3 ?    3.2   0.0     0.079        38      11      65 ..     331     385 ..     326     403 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.06
                          T2SSE 134 vsGgTgsGKttllyallkeinksderivtvEDpvEiqleganqvqlnak.........kakvtfadllraaLR 197
                                    + G  g GK+tl+ +l  + + +  riv+  D  Ei +e  + v+++++         + ++ +++++++++R
  gi|116754197|ref|YP_843315.1|  36 IVGKSGGGKSTLMRILRGIEDFDAGRIVI--DGLEITPESGEDVRMQQRritaihlqrEFGLWTESAIKNVVR 106
                                    78999******998877777777788877..999**9999999999999666665555555555666666555 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.34
                          T2SSE 125 avrerglilvsGgTgsGKttllyal 149
                                     +++  +  + G  g GKttll ++
  gi|116754197|ref|YP_843315.1| 291 NINRGETTAIIGSSGAGKTTLLTMI 315
                                    55555666788**********9765 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.079
                          T2SSE  11 dekvsdihvekpervkvrervdgielreveelekaalerlisriaalakldisee 65 
                                    +++ +di    p r+ +r r++ ++++ + ++++  le++++++ +  ++ i+  
  gi|116754197|ref|YP_843315.1| 331 EDGWVDITTYSPTRMEIRRRLGIMYQEFALMPHETILEQIAYKLGVKGQHVIEYA 385
                                    56789******************99999999999*******99998877766655 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.6      0.64   3.1e+02      18      36 ..      30      48 ..      27      64 .. 0.84
   2 ?   -1.4   0.0       2.5   1.2e+03     110     131 ..      49      70 ..      43      87 .. 0.66
   3 ?   -1.6   0.0       2.8   1.4e+03     140     166 ..     188     214 ..     168     224 .. 0.73
   4 ?    5.9   0.1     0.014       6.9      16      35 ..     292     311 ..     287     321 .. 0.91
   5 ?   -1.2   0.0       2.1     1e+03     105     147 ..     379     420 ..     356     421 .. 0.81
   6 ?   -2.8   0.0       6.6   3.2e+03     141     163 ..     500     522 ..     495     534 .. 0.62

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.64
                         ATPase 18 egrvvlitGepGtGKtifa 36
                                   eg++  i+G++G GK+++ 
  gi|116754197|ref|YP_843315.1| 30 EGEILGIVGKSGGGKSTLM 48
                                   688999*********9975 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.5
                         ATPase 110 elaeaikeikakrvviDsitgl 131
                                    ++ + i+++ a r+viD ++  
  gi|116754197|ref|YP_843315.1|  49 RILRGIEDFDAGRIVIDGLEIT 70 
                                    45566899999******87655 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2.8
                         ATPase 140 aReilrqlvrvlkklgvTailvsekss 166
                                      e l++++rv ++lg+T++ vs  ++
  gi|116754197|ref|YP_843315.1| 188 KQEVLDTIKRVNEELGLTTLVVSHLPE 214
                                    445666777777999999999998665 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.014
                         ATPase  16 ipegrvvlitGepGtGKtif 35 
                                    i +g+++ i G++G+GKt++
  gi|116754197|ref|YP_843315.1| 292 INRGETTAIIGSSGAGKTTL 311
                                    6799**************97 PP

  == domain 5  score: -1.2 bits;  conditional E-value: 2.1
                         ATPase 105 eelieelaeaikeikakrvviDsitglayeekeavaReilrql 147
                                    +++ie  +e+ +ei+++  v+D + +l ++++e++a++ l +l
  gi|116754197|ref|YP_843315.1| 379 QHVIEYAREVAAEIGISDRVLDMLYTL-TDMREDEAKAVLERL 420
                                    56777888999999*************.888888888887776 PP

  == domain 6  score: -2.8 bits;  conditional E-value: 6.6
                         ATPase 141 ReilrqlvrvlkklgvTailvse 163
                                    R+    ++r+ + +g+T i+vs 
  gi|116754197|ref|YP_843315.1| 500 RDVANAMKRIQARYGTTIIIVSH 522
                                    44444444444666667677665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (567 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); 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: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.40
# Mc/sec: 4229.29
//
Query:       gi|116754198|ref|YP_843316.1|  [L=669]
Description: methionyl-tRNA synthetase [Methanosaeta thermophila PT]
Scores for 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-152  506.2   0.0   6.1e-152  505.9   0.0    1.1  1  tRNA-synt_1g   tRNA synthetases class I (M)
    1.8e-27   95.3   0.3    3.3e-27   94.4   0.3    1.4  1  tRNA_bind      Putative tRNA binding domain
    1.9e-16   59.4   0.1    7.5e-08   31.1   0.0    3.7  3  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    2.2e-13   50.3   0.0    5.1e-08   32.6   0.0    2.1  2  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain
    1.9e-09   37.7   0.0    3.2e-09   36.9   0.0    1.4  1  Anticodon_1    Anticodon-binding domain of tRNA
    0.00012   21.2   0.0      0.027   13.4   0.0    2.2  2  tRNA-synt_1f   tRNA synthetases class I (K)
  ------ inclusion threshold ------
      0.031   13.2   0.0       0.11   11.4   0.0    1.8  2  tRNA-synt_1d   tRNA synthetases class I (R)
       0.07   13.2   5.8       0.26   11.4   5.9    1.9  1  DZR            Double zinc ribbon
        4.5    7.1   8.6          2    8.2   2.2    2.7  2  zinc_ribbon_2  zinc-ribbon domain


Domain annotation for each model (and alignments):
>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  505.9   0.0  3.1e-155  6.1e-152       1     390 [.       8     393 ..       8     394 .. 0.97

  Alignments for each domain:
  == domain 1  score: 505.9 bits;  conditional E-value: 3.1e-155
                                    EEEEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHH CS
                   tRNA-synt_1g   1 vlvttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvheeikelfkk 80 
                                    +lvt++lpYang+ H+Ghl+++++aDif+R  r  g++vlf+cg+D+hGtpi ++Ae++g++p+elve +h++++++f++
  gi|116754198|ref|YP_843316.1|   8 ILVTCGLPYANGPAHIGHLRTYVPADIFVRALRRMGHDVLFICGSDAHGTPIVVNAESRGMSPRELVEFYHKHFEDVFRS 87 
                                    69****************************************************************************** PP

                                    TT---SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG-EE........-TTS-EE.-TTSSB- CS
                   tRNA-synt_1g  81 lnisfdkygrttseehkelvqeifkklkekgliyekeieqlycpkderflpdryvegtCPkckseeargdqc.eecgkkl 159
                                    +n+ fd++g t++ ++++ +qei+++l e+g++y keie +ycp++erflpdryveg CP+c+   argd+c + cg++l
  gi|116754198|ref|YP_843316.1|  88 INVRFDYFGCTDDPSNHHRTQEIVRALMERGHVYPKEIELAYCPRCERFLPDRYVEGICPYCG-VPARGDECdQGCGRHL 166
                                    ***************************************************************.56******889***** PP

                                    E................EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EETT CS
                   tRNA-synt_1g 160 eptelinpksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvPg 239
                                    ep e+++++++++g+++e+++++h+ff+ls+f+++l ++++  +   + +++++++ew++++Lkd++i+r+++wG+++Pg
  gi|116754198|ref|YP_843316.1| 167 EPGEIKDAVCKVCGTRAEYRKQTHYFFRLSAFREFLLDYLQ--RLGGTASARNYALEWVRQELKDWCITRNMSWGVKFPG 244
                                    ****************************************4..44599******************************** PP

                                    ECCEEE-HHHHHHHHHHHTTTTT-...TTSGGGG.G--S......EEEEEGGGHHHHHTHHHHHHHHTT----S-EEEE- CS
                   tRNA-synt_1g 240 aekkvlYVWldAligYisatkelakkkgeeekwkeyWakdkevelvhfigkdiikFHtifwPaillgaelklpkkvvahe 319
                                    +e+ v+YVW+dA+igYis+t+e++k++     w++yW    +++++hfig di+++H+ifwPa+l+ga+++lp+ vva++
  gi|116754198|ref|YP_843316.1| 245 SEDLVVYVWVDAPIGYISFTEEWCKAH--GVPWERYW--RGKSRIIHFIGGDIVYHHCIFWPAMLEGAGYTLPSDVVASG 320
                                    ************************666..679*****..579************************************** PP

                                    -EEE--------------H.HHHHHH.H-HHHHHHHHHHHS-TTS-EEE-HHHHHHHHHHHCCCHHHHHHHHH CS
                   tRNA-synt_1g 320 yltvegkKlSkSrgvvvka.kealer.ldadllRYylaaeapekkDldfswedfvervNseLadklgnlvnRv 390
                                    +l++++kK+SkSrg+vv++ +++l++ l++d+lRYyla+ ++++k+++fsw+ ++e+vN+eL++++gn++nR+
  gi|116754198|ref|YP_843316.1| 321 MLKIDDKKFSKSRGYVVWVkDDYLDQgLEPDYLRYYLASYTSHTKEVNFSWKILQEKVNTELVGAFGNFLNRA 393
                                    ******************956799999*********************************************7 PP

>> tRNA_bind  Putative tRNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.4   0.3   1.7e-30   3.3e-27       1      94 [.     576     665 ..     576     666 .. 0.98

  Alignments for each domain:
  == domain 1  score: 94.4 bits;  conditional E-value: 1.7e-30
                                    EEEEEEEEEEEETTSSTEEEEEEEESSSSEEEEEESCTTTSTHHHHTTEEEEEETTSESEEETTEEESSEE-EEECCESS CS
                      tRNA_bind   1 lrvGkvleaeehpnadkLlvlkvdvGeeeprqivsgaknvyepeelvakkvvvvanlkpkklrGveSeGMilsaeeldek 80 
                                    lrvG+vleae+++++dkLl+l+vd+Ge++  qiv+g++++y+peelv+++vvvvanl+p k+ GveS+GM+l+a+   ++
  gi|116754198|ref|YP_843316.1| 576 LRVGTVLEAERIKGSDKLLRLIVDIGEKR--QIVAGIAKMYKPEELVGRQVVVVANLEPVKIFGVESRGMLLAAD--ING 651
                                    79************************988..********************************************..799 PP

                                    CEEEEEESST--TT CS
                      tRNA_bind  81 evgilelpadveaG 94 
                                    +  +l+++++v+aG
  gi|116754198|ref|YP_843316.1| 652 DAVLLKPDKEVPAG 665
                                    9***********98 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 !   31.1   0.0   3.8e-11   7.5e-08      26     109 ..       9      90 ..       3     143 .. 0.80
   2 !   19.3   0.0   1.4e-07   0.00028     356     432 ..     167     243 ..     159     258 .. 0.84
   3 !    4.2   0.0    0.0053        11     558     602 .]     323     370 ..     311     370 .. 0.75

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 3.8e-11
                    tRNA-synt_1  26 ilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakvekklgakekkerkklgreefrekvr 105
                                     ++ g Py++G  HiGh  + +  di +r  r  G++vl+  G D +G +i  + e + g + + e  ++ +++f +  r
  gi|116754198|ref|YP_843316.1|   9 LVTCGLPYANGPAHIGHLRTYVPADIFVRALRRMGHDVLFICGSDAHGTPIVVNAESR-GMSPR-ELVEFYHKHFEDVFR 86 
                                    567789*********************************************8888877.33332.455666666666666 PP

                    tRNA-synt_1 106 ewka 109
                                    ++  
  gi|116754198|ref|YP_843316.1|  87 SINV 90 
                                    6554 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 1.4e-07
                    tRNA-synt_1 356 ekiehsvpfcerskkpiiyrateqWfvrvkeladaalkavekvqfvpkskekryaswl.eniqdWciSRqrwWGhrip 432
                                    e+ e +  +c+  ++  +yr ++ +f r++++++ +l+ +++   +   ++    +w+ ++ +dWci R+  WG++ p
  gi|116754198|ref|YP_843316.1| 167 EPGEIKDAVCKVCGTRAEYRKQTHYFFRLSAFREFLLDYLQRLGGTASARN-YALEWVrQELKDWCITRNMSWGVKFP 243
                                    5566667789999999*************************9987766555.4556762579*************987 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.0053
                    tRNA-synt_1 558 deeGrKmSKslgNvidpld..vikkygadalRltli.lsdvgrdinls 602
                                      + +K SKs g v+  +d  + + +  d lR++l+ +++ ++++n+s
  gi|116754198|ref|YP_843316.1| 323 KIDDKKFSKSRGYVVWVKDdyLDQGLEPDYLRYYLAsYTSHTKEVNFS 370
                                    44669*******99755441144556789*******9*******9986 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 !   32.6   0.0   2.6e-11   5.1e-08      14     125 ..      11     124 ..       3     132 .. 0.85
   2 !   15.5   0.0   4.2e-06    0.0084     241     298 ..     316     376 ..     281     379 .. 0.77

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 2.6e-11
                                    EEE.EBTTS--BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHTT- CS
                   tRNA-synt_1e  14 vCG.ptvydashlGhaRslvafDilrrilqalgYdvqfvqnvtDidDkiikrareeeksvkelaekfieefkkdleaLnv 92 
                                    +CG p +   +h+Gh R++v  Di+ r l+ +g+dv f+         i+ +a++++ s +el+e + ++f++ ++++nv
  gi|116754198|ref|YP_843316.1|  11 TCGlPYANGPAHIGHLRTYVPADIFVRALRRMGHDVLFICGSDAHGTPIVVNAESRGMSPRELVEFYHKHFEDVFRSINV 90 
                                    57733455679*****************************99888999******************************** PP

                                    ---SB-.-BGGGGHHHHHHHHHHHHHTTSEEE-T CS
                   tRNA-synt_1e  93 lkptle.prvsekvdeiielvekliekgyaYavs 125
                                    +   +  +    + +   e+v  l+e+g+ Y+ +
  gi|116754198|ref|YP_843316.1|  91 RFDYFGcTDDPSNHHRTQEIVRALMERGHVYPKE 124
                                    98765413344556678899999********876 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 4.2e-06
                                    EEEE--EEETTBE--TTTT---BHHH.HH.TTS-HHHHHHHHHSS.-TTS-EEE-HHHHHH CS
                   tRNA-synt_1e 241 flhnghlkiegekmsksLknfitikd.vl.kkfdprqlRllllsa.hyrsqldfkeellee 298
                                     + +g+lki+++k sks + ++ +kd  l +  +p  lR++l+s   + ++++f+ + l+e
  gi|116754198|ref|YP_843316.1| 316 VVASGMLKIDDKKFSKSRGYVVWVKDdYLdQGLEPDYLRYYLASYtSHTKEVNFSWKILQE 376
                                    5679********************974563568*********9852578899999888876 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 !   36.9   0.0   1.6e-12   3.2e-09       1      99 [.     411     504 ..     411     567 .. 0.80

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 1.6e-12
                    Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaq...evllevletllrll 77 
                                    d ++ ++++  v +v+ ++ ey+f++a +a+ ++   d++++y+++++p+   +s+  +  a    +++l +++++++l+
  gi|116754198|ref|YP_843316.1| 411 DPEVMKRIEMSVGDVSSSLMEYEFKRASDAVLSL--ADYANTYFQSHEPWKLIRSDRRA--AGsvlRNCLQMVKAMIILM 486
                                    5677889999999********************8..99*************99876333..552237777777999**** PP

                    Anticodon_1  78 aPfmPfitEelwqreeeelgkk 99 
                                    +PfmP  +  +w    ++lg +
  gi|116754198|ref|YP_843316.1| 487 EPFMPSRMAVAW----KQLGME 504
                                    ************....666655 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 !   13.4   0.0   1.4e-05     0.027      22      69 ..       5      53 ..       2      57 .. 0.88
   2 !    5.3   0.0    0.0038       7.6     275     326 ..     322     374 ..     306     380 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.4e-05
                   tRNA-synt_1f 22 kdevvvesGis.pSGliHiGnlrevltadlvaralrkrgeevrlilisD 69
                                   +d ++v  G+  + G+ HiG lr  + ad+ +ralr++g++v +i+ sD
  gi|116754198|ref|YP_843316.1|  5 NDPILVTCGLPyANGPAHIGHLRTYVPADIFVRALRRMGHDVLFICGSD 53
                                   57788888886357*******************************9998 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0038
                   tRNA-synt_1f 275 llkggekmssSkGnvltled.wl.evaepevlrflilrrkPkkakkldldleil 326
                                    l   ++k s+S+G v+ ++d  l + +ep+ lr+++++    + k+++++ +il
  gi|116754198|ref|YP_843316.1| 322 LKIDDKKFSKSRGYVVWVKDdYLdQGLEPDYLRYYLAS-YTSHTKEVNFSWKIL 374
                                    4445569*********99873443678*********99.777777888777776 PP

>> tRNA-synt_1d  tRNA synthetases class I (R)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   5.8e-05      0.11      22     108 ..       8      92 ..       2     115 .. 0.71
   2 ?   -1.5   0.0      0.47   9.4e+02     271     300 ..     320     349 ..     283     352 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.8e-05
                                    EEEE----BTTS--BHHHHHHHHHHHHHHHHHHHCT-EEEEEE--B-SSTCHHHHHHHHHHHTTTTTTS-----SCCCHH CS
                   tRNA-synt_1d  22 vvvdfssPniakemhvGhLrstiiGdavsrlleflGydvirlnhvGDWGtqfGlLiaylekkqdekllqeqelqdLeafy 101
                                    ++v    P    + h+GhLr+ +  d  +r l  +G+dv+ +      Gt    + a  + + + + l+e   +++e+++
  gi|116754198|ref|YP_843316.1|   8 ILVTCGLPYANGPAHIGHLRTYVPADIFVRALRRMGHDVLFICGSDAHGTPIV-VNAESRGMSP-RELVEFYHKHFEDVF 85 
                                    66666777778899*************************97765555555432.2222223333.334466666666666 PP

                                    HHHHHHC CS
                   tRNA-synt_1d 102 keakkdy 108
                                    + ++ ++
  gi|116754198|ref|YP_843316.1|  86 RSINVRF 92 
                                    6666665 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.47
                                    --EE-TTSSBSBCSSSTC-BH.HHHHHHHHH CS
                   tRNA-synt_1d 271 GmvlgkdkkkfktrkGetvkL.adlLdeale 300
                                    Gm+   d+kkf+  +G +v + +d Ld++le
  gi|116754198|ref|YP_843316.1| 320 GML-KIDDKKFSKSRGYVVWVkDDYLDQGLE 349
                                    655.778899999999999872568888876 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   5.9   0.00013      0.26       1      49 []     130     180 ..     130     190 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00013
                            DZR   1 CpqCgeelppdar..fCseCgtklkavaaedrCps.Cgekvdp...earfCpeCG 49 
                                    Cp+C++ lp++     C++Cg + +     d C++ Cg+ ++p   ++++C+ CG
  gi|116754198|ref|YP_843316.1| 130 CPRCERFLPDRYVegICPYCGVPAR----GDECDQgCGRHLEPgeiKDAVCKVCG 180
                                    ***********9888*********9....79998669999887222457799998 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   2.2     0.001         2       1      20 [.     129     150 ..     129     152 .. 0.94
   2 ?    1.8   0.5      0.11   2.2e+02       5      21 ..     162     181 ..     162     182 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.001
                  zinc_ribbon_2   1 fCpnCGaelqdnakF..CpyCG 20 
                                    +Cp+C + l+d+ +   CpyCG
  gi|116754198|ref|YP_843316.1| 129 YCPRCERFLPDRYVEgiCPYCG 150
                                    8********************* PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.11
                  zinc_ribbon_2   5 CGaelqdnakF...CpyCGt 21 
                                    CG+ l++++     C  CGt
  gi|116754198|ref|YP_843316.1| 162 CGRHLEPGEIKdavCKVCGT 181
                                    88888888888888999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (669 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); 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:                        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: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.44
# Mc/sec: 4530.11
//
Query:       gi|116754199|ref|YP_843317.1|  [L=130]
Description: transcriptional regulator, TrmB [Methanosaeta thermophila PT]
Scores for 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-06   25.8   0.0    1.2e-05   25.0   0.0    1.4  1  TrmB         Sugar-specific transcriptional regulator TrmB
     0.0021   17.9   0.1     0.0053   16.6   0.0    1.7  2  MarR_2       MarR family
     0.0041   17.3   0.0     0.0073   16.5   0.0    1.4  1  HTH_34       Winged helix DNA-binding domain
     0.0051   16.4   0.1       0.01   15.4   0.0    1.6  1  SMC_ScpB     Segregation and condensation complex subunit Scp
     0.0096   15.8   1.0      0.013   15.4   1.0    1.2  1  TFIIE_alpha  TFIIE alpha subunit
  ------ inclusion threshold ------
      0.024   14.5   0.8      0.049   13.5   0.6    1.5  1  DUF5100      Domain of unknown function (DUF5100)
      0.078   13.5   0.1       0.17   12.4   0.1    1.6  1  HTH_27       Winged helix DNA-binding domain


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   4.8e-09   1.2e-05       2      63 ..      21      89 ..      20      95 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 4.8e-09
                                   HHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.......TTEEE CS
                           TrmB  2 qklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.......pklYr 63
                                    ++GL+ + akv ++L   ++at ++i  ++++ ++ v  ++r+L + G++  ++++       +++Yr
  gi|116754199|ref|YP_843317.1| 21 MDIGLRRNVAKVLTYLAGVDEATSRDIETNSDLRQPEVSIAMRELRELGWISERDEKnpgkgrpYRIYR 89
                                   6799***********************************************999988888888555776 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   2.1e-06    0.0053       2      60 ..      24      82 ..      23      83 .. 0.87
   2 ?   -1.8   0.0       1.2     3e+03      39      39 ..     113     113 ..      96     127 .. 0.59

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.1e-06
                                   T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE..ESSSSS CS
                         MarR_2  2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr..pgpeDk 60
                                   gl +  a vL +L+  ++   t ++++   +l ++ vs + ++L + G++ +r  ++p+ +
  gi|116754199|ref|YP_843317.1| 24 GLRRNVAKVLTYLAGVDE--ATSRDIETNSDLRQPEVSIAMRELRELGWISERdeKNPGKG 82
                                   66677789*********9..9*****************************99955555555 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.2
                                    H CS
                         MarR_2  39 s 39 
                                     
  gi|116754199|ref|YP_843317.1| 113 M 113
                                    2 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 !   16.5   0.0   2.9e-06    0.0073       4      51 ..      31      78 ..      30      93 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.9e-06
                         HTH_34  4 avlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefk 51
                                   +vl+yLa vdea+ +++ +   + + + s+ ++ L + g+i+ + e++
  gi|116754199|ref|YP_843317.1| 31 KVLTYLAGVDEATSRDIETNSDLRQPEVSIAMRELRELGWISERDEKN 78
                                   69***************************************8765554 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 !   15.4   0.0   4.1e-06      0.01      81     140 ..      25      89 ..      10     109 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4.1e-06
                       SMC_ScpB  81 LsqaaletLaiIaykqpvtraeie...eiRGvnsdsvvrtLlerglieekgrkee.pgrpil.Yg 140
                                    L +   ++L + a  +  t+ +ie   ++R  +++ ++r+L e g+i+e+ +k+  +grp+  Y+
  gi|116754199|ref|YP_843317.1|  25 LRRNVAKVLTYLAGVDEATSRDIEtnsDLRQPEVSIAMRELRELGWISERDEKNPgKGRPYRiYR 89 
                                    7788899999999999*******744469999****************99877544888874355 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   1.0     5e-06     0.013      14     101 ..      28     114 ..      19     122 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5e-06
                                    HHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEECCCHCCCHHHHHHHHH CS
                    TFIIE_alpha  14 eavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywrinyeklvdvvkrkleevv 93 
                                    ++++vl  L+   e t  d++ +  + ++e+  ++ +L+e + ++ + +++++k+     +r+++ ++ +++ +  ++ +
  gi|116754199|ref|YP_843317.1|  28 NVAKVLTYLAGVDEATSRDIETNSDLRQPEVSIAMRELRELGWISERDEKNPGKGRPYRIYRLEK-NIDEIINYLEDQKL 106
                                    789************************************************99998888888764.34445544444444 PP

                                    HHHHHHHC CS
                    TFIIE_alpha  94 kkLeekle 101
                                    +++e  ++
  gi|116754199|ref|YP_843317.1| 107 QEIERTMR 114
                                    44443332 PP

>> DUF5100  Domain of unknown function (DUF5100)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.6   1.9e-05     0.049      80     108 ..      87     115 ..      76     127 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.9e-05
                        DUF5100  80 veewneaidevldiLeeieleevefeesk 108
                                    + + +++ide++++Le+ +l+e+e +  +
  gi|116754199|ref|YP_843317.1|  87 IYRLEKNIDEIINYLEDQKLQEIERTMRQ 115
                                    557789****************9988776 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 ?   12.4   0.1   6.5e-05      0.17       8      59 ..      32      82 ..      25      90 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.5e-05
                         HTH_27  8 vLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdea.drre 59
                                   vL  ++  +++++ +d+    ++ +  +s ++++L e G++ +++de+ +++ 
  gi|116754199|ref|YP_843317.1| 32 VLTYLA-GVDEATSRDIETNSDLRQPEVSIAMRELRELGWI-SERDEKnPGKG 82
                                   666677.8999******************************.44444404544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1332  (0.074293); expected 358.6 (0.02)
Passed bias filter:                      825  (0.0460148); 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: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 928.00
//
Query:       gi|116754200|ref|YP_843318.1|  [L=368]
Description: cell division protein FtsZ [Methanosaeta thermophila PT]
Scores for complete 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   0.1    9.9e-42  143.4   0.1    1.2  1  Tubulin         Tubulin/FtsZ family, GTPase domain
    7.8e-35  119.1   0.7      2e-34  117.7   0.7    1.8  1  FtsZ_C          FtsZ family, C-terminal domain
     0.0036   17.2   0.7       0.01   15.8   0.4    2.0  2  NAD_binding_10  NAD(P)H-binding
  ------ inclusion threshold ------
       0.64    9.1   7.3        0.3   10.2   1.7    2.2  2  Tubulin_2       Tubulin like


Domain annotation for each model (and alignments):
>> Tubulin  Tubulin/FtsZ family, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.4   0.1   2.2e-45   9.9e-42       2     196 ..      39     198 ..      38     199 .. 0.97

  Alignments for each domain:
  == domain 1  score: 143.4 bits;  conditional E-value: 2.2e-45
                                    EEEEEEHHHHHHHHHHHHH...HHHCH....HHHT.....TTEEEEE....EEESBHHHHHTS-GS......EEEE--CC CS
                        Tubulin   2 iivigvGqcGnqignelwellakehgiqsdgdslesfFsesgkveyiprsvaidtdpqvlneikagselfnpnklllgke 81 
                                    i vig+G++G++++++l e    + gi             +g +e++    ai+td+q+l +i+a+      +++l+g  
  gi|116754200|ref|YP_843318.1|  39 IRVIGCGGGGSNTIDRLSE----A-GI-------------QG-AELY----AINTDAQHLLHINAD------RRFLIGRR 89 
                                    789****************....5.**.............88.8999....9**************......******** PP

                                    CCTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE.SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTSEEEEEEEE--GG. CS
                        Tubulin  82 gagnngaggypevgkeaaeeileeirkevekcdslqgffitaslgGGTGSGlgpvilevlkeeypkalvvtvvvlPsefs 161
                                     ++++gag+ p +g+eaa+e  e+i+ +v+++d+   +fit +lgGGTG+G++pv++e+++e   +al++++v+lP++  
  gi|116754200|ref|YP_843318.1|  90 TTRGLGAGSLPAIGEEAAQEDIEQIKAAVQGADM---VFITCGLGGGTGTGASPVVAEAAREA--GALTIAIVTLPFSA- 163
                                    **********************************...**************************..************99. PP

                                    G-HHHHHHHHHHHHHHHHT-SEEEEEEHHHHHCCS CS
                        Tubulin 162 evvvepynailalkelieesdavividNdaLlkil 196
                                    e+ +++ na+ +lk+l+e++d+viv++Nd+Ll+++
  gi|116754200|ref|YP_843318.1| 164 EGSIRMANAEAGLKRLRESADTVIVVPNDKLLEVA 198
                                    *******************************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 !  117.7   0.7   4.5e-38     2e-34       1      94 [.     246     339 ..     246     340 .. 0.99

  Alignments for each domain:
  == domain 1  score: 117.7 bits;  conditional E-value: 4.5e-38
                                    EEEEEEEEEEESTTHHHHHHHHHHTSGGGT--GGG-SEEEEEEEE-TT--HHHHHHHHHHHHHHS-TTSEEEEEEEE-TT CS
                         FtsZ_C   1 GvAmmgvGeasgedraeeaaeaaisspLLdvdlsgAkgvlvnitggsdltlkEveevaetireevdeeanvivGavidee 80 
                                    GvAm+g+Gea+ge+ra++++ +a++spLLdvd+sgA+++lvn+ gg+d+t+ ++e v+e+++++++++a++i+Ga+id+e
  gi|116754200|ref|YP_843318.1| 246 GVAMIGLGEADGEERARDSVMRALRSPLLDVDVSGATSALVNVVGGPDMTIADAEMVVEEVYSRINPDARIIWGAQIDPE 325
                                    99****************************************************************************** PP

                                    --SEEEEEEEEES- CS
                         FtsZ_C  81 ledeirvtvvatgl 94 
                                    l+++ir++ v+tg+
  gi|116754200|ref|YP_843318.1| 326 LKGTIRTMLVVTGV 339
                                    *************8 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.61   2.7e+03      51      76 ..      25      50 ..      11      67 .. 0.67
   2 !   15.8   0.4   2.2e-06      0.01      48      97 ..     108     158 ..     103     269 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.61
                                   CCHHHHHHTT-SEEEES---TCCHHH CS
                 NAD_binding_10 51 vedlaealkgadaVvsalggggkdee 76
                                    edl + l+g  +V+  +g gg+ ++
  gi|116754200|ref|YP_843318.1| 25 DEDLVSILEGLTTVIRVIGCGGGGSN 50
                                   57888889999988877754444322 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 2.2e-06
                                    TT-CCHHHHHHTT-SEEEES---TCCHHHH.HHHHHHHHHHCT--EEEEEE CS
                 NAD_binding_10  48 vtdvedlaealkgadaVvsalggggkdeeg.aknivdaakeagvkRfvlvs 97 
                                     +d e++++a++gad V+++ g gg++ +g    +++aa+eag   + +v+
  gi|116754200|ref|YP_843318.1| 108 QEDIEQIKAAVQGADMVFITCGLGGGTGTGaSPVVAEAAREAGALTIAIVT 158
                                    5799*************9999888876677245556899999988888776 PP

>> Tubulin_2  Tubulin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.3     0.026   1.1e+02       2      19 ..      41      58 ..      41      86 .. 0.77
   2 ?   10.2   1.7   6.6e-05       0.3     134     181 ..     106     147 ..      79     184 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.026
                      Tubulin_2  2 viGLGGtGgkvlaelrrr 19
                                   viG+GG G++++++l + 
  gi|116754200|ref|YP_843318.1| 41 VIGCGGGGSNTIDRLSEA 58
                                   7************99875 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 6.6e-05
                      Tubulin_2 134 eirealrdaikrlrgsageeeglnvfVvgSLaGGTGSGiflDvayllr 181
                                     ++e +++  ++++g         vf+ ++L GGTG G    va   r
  gi|116754200|ref|YP_843318.1| 106 AAQEDIEQIKAAVQGA------DMVFITCGLGGGTGTGASPVVAEAAR 147
                                    4455566666666664......68**************8776655544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.28s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2584.29
//
Query:       gi|116754201|ref|YP_843319.1|  [L=104]
Description: hypothetical protein Mthe_0891 [Methanosaeta thermophila PT]
Scores for 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   25.0   0.0    4.1e-05   23.0   0.2    1.8  2  HTH_24    Winged helix-turn-helix DNA-binding
     0.0023   18.2   0.0     0.0034   17.7   0.0    1.2  1  Rrf2      Transcriptional regulator
     0.0026   17.6   0.0     0.0039   17.0   0.0    1.3  1  TrmB      Sugar-specific transcriptional regulator TrmB
     0.0028   17.5   0.2     0.0046   16.8   0.2    1.4  1  HTH_5     Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
      0.014   15.3   0.0      0.028   14.3   0.0    1.6  1  HTH_12    Ribonuclease R winged-helix domain
      0.032   14.3   0.0      0.051   13.7   0.0    1.4  1  HTH_20    Helix-turn-helix domain
      0.033   14.3   0.0      0.058   13.5   0.0    1.4  1  DUF2250   Uncharacterized protein conserved in archaea (DUF22
       0.11   12.3   0.0         16    5.3   0.0    2.2  2  MerR      MerR family regulatory protein
       0.11   12.4   0.0       0.17   11.8   0.0    1.3  1  MarR_2    MarR family


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.2   2.1e-08   4.1e-05       4      47 ..      15      58 ..      12      59 .. 0.94
   2 ?   -0.7   0.0      0.56   1.1e+03      32      44 ..      72      84 ..      70      84 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 2.1e-08
                         HTH_24  4 tdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                    ++ IL+++ +n  i +  LAe++ +++  v++ l+ Le+eGlI
  gi|116754201|ref|YP_843319.1| 15 RHLIILKCVVENEPIGILKLAEETKIPSHKVRYSLRVLEQEGLI 58
                                   5667***************************************9 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.56
                         HTH_24 32 stvnrrlkrLeee 44
                                   ++ ++rl+++++e
  gi|116754201|ref|YP_843319.1| 72 GPFLERLDEMIDE 84
                                   78999***99986 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.7e-06    0.0034       3      57 ..       6      60 ..       5      66 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.7e-06
                                   --HHHHHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                           Rrf2  3 lsskteyalhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvks 57
                                   ++s++++  + l++L+   e+ep+ + ++ae+++i+ + ++  l+ L+++gl+ +
  gi|116754201|ref|YP_843319.1|  6 VTSELDMLKRHLIILKCVVENEPIGILKLAEETKIPSHKVRYSLRVLEQEGLIAA 60
                                   67888888899******************************************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 !   17.0   0.0     2e-06    0.0039      16      54 ..      22      60 ..      10      67 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2e-06
                                   HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
                           TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVer 54
                                    +++++p  + ++aee+++p  kv  +Lr Le+ Gl+  
  gi|116754201|ref|YP_843319.1| 22 CVVENEPIGILKLAEETKIPSHKVRYSLRVLEQEGLIAA 60
                                   57899*******************************976 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.2   2.3e-06    0.0046       7      45 ..      19      58 ..      14      60 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.3e-06
                                   HHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_5  7 ILklLae.gelcvcelaeelglsqstvShHLkkLreaGLV 45
                                   ILk + e ++  +  laee++++  +v++ L++L+++GL+
  gi|116754201|ref|YP_843319.1| 19 ILKCVVEnEPIGILKLAEETKIPSHKVRYSLRVLEQEGLI 58
                                   666666745577778************************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 ?   14.3   0.0   1.4e-05     0.028      14      49 ..      29      59 ..      17      69 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.4e-05
                         HTH_12 14 igakeiaeeLkkrgydigeravRyrLrkleergltr 49
                                   ig  ++ae     + +i    vRy Lr+le++gl+ 
  gi|116754201|ref|YP_843319.1| 29 IGILKLAE-----ETKIPSHKVRYSLRVLEQEGLIA 59
                                   55555555.....467888889***********985 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.5e-05     0.051      23      55 ..      27      59 ..      10      64 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.5e-05
                                   TTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                         HTH_20 23 egltaselaerldlskntlsyHLrvLeeagLve 55
                                   e+     lae+  ++   ++y LrvLe+ gL+ 
  gi|116754201|ref|YP_843319.1| 27 EPIGILKLAEETKIPSHKVRYSLRVLEQEGLIA 59
                                   555566799999*******************97 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.9e-05     0.058       4      56 ..      10      62 ..       7      71 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.9e-05
                        DUF2250  4 leedelalkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlerve 56
                                   l   +++l +lk + + ++   + +a+e++ip ++vr  l+ Le+ GL+    
  gi|116754201|ref|YP_843319.1| 10 LDMLKRHLIILKCVVENEPIGILKLAEETKIPSHKVRYSLRVLEQEGLIAASA 62
                                   5666778888888888888888999***********************98765 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0    0.0081        16       4      18 ..      33      47 ..      29      47 .. 0.89
   2 ?    4.7   0.0     0.013        26      16      26 ..      49      59 ..      48      63 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0081
                                   HHHHHHTTTHHHHHH CS
                           MerR  4 evAeltGvsprtLRy 18
                                    +Ae t ++++++Ry
  gi|116754201|ref|YP_843319.1| 33 KLAEETKIPSHKVRY 47
                                   58************9 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.013
                                   HHHHHHTTSST CS
                           MerR 16 LRyYEreGLip 26
                                   LR +E+eGLi 
  gi|116754201|ref|YP_843319.1| 49 LRVLEQEGLIA 59
                                   899*******4 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   8.6e-05      0.17      27      54 ..      34      61 ..      25      71 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.6e-05
                                   HHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                         MarR_2 27 larrlglsksavsrilkrLvaaGLverr 54
                                   la++++++ + v + l+ L++ GL+  +
  gi|116754201|ref|YP_843319.1| 34 LAEETKIPSHKVRYSLRVLEQEGLIAAS 61
                                   8************************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); 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:                         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: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 812.23
//
Query:       gi|116754202|ref|YP_843320.1|  [L=335]
Description: thiamine biosynthesis protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-54  184.3   0.0    2.4e-54  183.9   0.0    1.1  1  ThiI           Thiamine biosynthesis protein (ThiI)
    2.6e-17   63.2   0.0    4.4e-17   62.5   0.0    1.3  1  THUMP          THUMP domain
    8.5e-05   22.2   0.0     0.0073   15.8   0.0    2.3  1  QueC           Queuosine biosynthesis protein QueC
  ------ inclusion threshold ------
      0.011   14.6   0.0      0.018   13.9   0.0    1.3  1  tRNA_Me_trans  tRNA methyl transferase


Domain annotation for each model (and alignments):
>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.9   0.0   5.3e-58   2.4e-54       1     195 [.     125     315 ..     125     317 .. 0.94

  Alignments for each domain:
  == domain 1  score: 183.9 bits;  conditional E-value: 5.3e-58
                           ThiI   1 gtqgkvlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlkeil 80 
                                    g+q + laL+SgGiDSpVaa+l+++RGc v l+hl+ +p+  ++ ie+v + ae+l ++ ++ ++ l +v   + ++ i+
  gi|116754202|ref|YP_843320.1| 125 GSQSRMLALISGGIDSPVAAWLIMRRGCPVALLHLDVSPY--ADSIEQVVRQAEVLQSWMSGRRLDLAIVRNARAIEMIS 202
                                    7899*******************************87776..56778888889***********************9999 PP

                           ThiI  81 ekvkekltivllkrkmlriAekvaeeegakalvtGesLgqVaSqtleNlrvisavvnllilrPLigldKeeiiklAkeig 160
                                    ++ +   t+vl++r m++i   v ++ +ak +vtG sLgqVaSqt eN+ + +  ++ ++  PLi++dK eii+lA++ig
  gi|116754202|ref|YP_843320.1| 203 SRYPR-ETCVLCRRLMYHISTLVMKRLRAKGIVTGYSLGQVASQTPENIMAEQVGIEAPVYHPLIAMDKTEIIELARRIG 281
                                    99875.69************************************************************************ PP

                           ThiI 161 tyeisiekedkCsvlakhPttkakleevekaeekl 195
                                    ty+isi   ++C + +k+P+t+a+lee+ ++e +l
  gi|116754202|ref|YP_843320.1| 282 TYDISIGS-QQCRAAPKKPVTRARLEEILRIEGEL 315
                                    *****986.689****************9999876 PP

>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.5   0.0   9.9e-21   4.4e-17      36     142 ..      13     113 ..       4     115 .. 0.92

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 9.9e-21
                                    THHHHHHHHHTSTTECEEEEEEEEEESSHHHHHHHHHHHHHHHHHHCT-EEEEEEEESSSTSSSHHHHHHHHHHHHHHCC CS
                          THUMP  36 deellkealekargiqrvipvcevceadledileaakeivkkkfeeeketFaVrvkrrgkhfeftsreinrevGkaivek 115
                                     +e++ ++++k++g+++v+p+ + +  ++ di ++a+ i   +  +   +Fa+r++r g   e+ s +i+ evG+a+ ++
  gi|116754202|ref|YP_843320.1|  13 SDERAPSTISKVFGVVSVSPA-YSVSPRMADISKLAVDIAMMRSPG---SFAIRARRAGG--EMPSGRIAVEVGAAVQRA 86 
                                    46889999*************.*******************88766...***********..8***************** PP

                                    TT-EE-SSS-SEEEEEEEETTEEEEEE CS
                          THUMP 116 tglkVdlenPdivvrveiikdkayisi 142
                                    tg+ Vdl+nPd+ +++e + d+a++++
  gi|116754202|ref|YP_843320.1|  87 TGADVDLDNPDLEIFIEARPDRALVFT 113
                                    ************************997 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.6e-06    0.0073       2     174 ..     130     281 ..     129     296 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.6e-06
                                    EEEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-GGGGGGSCGGG--------- CS
                           QueC   2 avvllSGGlDSttvlalakkegkevealtfdYgqrhkkeleaakkiakelgveehkildldllkelggsaLtdeeievpk 81 
                                     + l+SGG+DS ++++l +++g  v++l++d         ++ ++++++++v     l+  +  +  + a++++  +++ 
  gi|116754202|ref|YP_843320.1| 130 MLALISGGIDSPVAAWLIMRRGCPVALLHLDVSPY----ADSIEQVVRQAEV-----LQSWMSGRRLDLAIVRNARAIEM 200
                                    6789**************************97554....4556677777777.....33333455567788888888887 PP

                                    --...--------TTHHHHHHHHHHHHHHHHT-SEEEE---S-STT--GGGSHHHHHHHHHHHHHHHTS--EEE-TTTT- CS
                           QueC  82 eeleeeelpntfVpaRNliflslaasyaealgaeaiiiGvneedfsgYPDcrdefvkalnkalnlgedkkieieaPlidl 161
                                      ++++  ++t V  R  +++ + +   ++l a+ i++G +  +++     ++e + a ++ +      +  +  Pli++
  gi|116754202|ref|YP_843320.1| 201 --ISSRYPRETCVLCRR-LMYHISTLVMKRLRAKGIVTGYSLGQVAS---QTPENIMAEQVGI------EAPVYHPLIAM 268
                                    ..677888999999996.56788888999999999999999877543...3444454444333......34678999999 PP

                                    -HHHHHHHHHHTT CS
                           QueC 162 sKaeivklgkelg 174
                                    +K+ei++l+ ++g
  gi|116754202|ref|YP_843320.1| 269 DKTEIIELARRIG 281
                                    9999999999988 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0     4e-06     0.018       2      42 ..     129     169 ..     128     189 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4e-06
                  tRNA_Me_trans   2 kvvvalSgGVDSsvaaallkeqgyevigvflklweeedeeg 42 
                                    ++++++SgG+DS vaa l+ ++g  v  ++l ++  +d+ +
  gi|116754202|ref|YP_843320.1| 129 RMLALISGGIDSPVAAWLIMRRGCPVALLHLDVSPYADSIE 169
                                    56789*************************99998888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2277.76
//
Query:       gi|116754203|ref|YP_843321.1|  [L=141]
Description: hypothetical protein Mthe_0893 [Methanosaeta thermophila PT]
Scores for complete 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   39.5   0.2      6e-10   38.8   0.2    1.4  1  DUF1232   Protein of unknown function (DUF1232)


Domain annotation for each model (and alignments):
>> DUF1232  Protein of unknown function (DUF1232)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.2   3.3e-14     6e-10       4      36 ..      49      82 ..      46      83 .. 0.94

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 3.3e-14
                        DUF1232  4 liagalaYlisPiDlIPD.fiPvlGflDDlavlt 36
                                   l+++a+aY+i+P D+IP+   +  G++DD+++++
  gi|116754203|ref|YP_843321.1| 49 LVIAAIAYFILPSDIIPEeSHGAEGYVDDIFLCA 82
                                   89*****************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1105.86
//
Query:       gi|116754204|ref|YP_843322.1|  [L=320]
Description: radical SAM domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.3e-17   63.9   0.1      4e-17   63.1   0.1    1.4  1  Radical_SAM  Radical SAM superfamily
    3.8e-05   24.1   0.9    8.6e-05   23.0   0.2    2.0  2  SPASM        Iron-sulfur cluster-binding domain
  ------ inclusion threshold ------
      0.073   12.4   1.0       0.21   10.9   0.1    2.1  2  rpo132       Poxvirus DNA dependent RNA polymerase
       0.14   12.0   0.0       0.24   11.2   0.0    1.4  1  DUF3463      Domain of unknown function (DUF3463)


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.1   0.1   8.9e-21     4e-17       5     163 ..      31     171 ..      28     175 .. 0.89

  Alignments for each domain:
  == domain 1  score: 63.1 bits;  conditional E-value: 8.9e-21
                                    SEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   5 rgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritvet 84 
                                     +CnlrCsfC+ +     ++r r++s  ei   ++ + a+ g++       epll++d+ e+l++++ l   g+ ++++t
  gi|116754204|ref|YP_843322.1|  31 TACNLRCSFCPHW-----RKRRREMSFGEITGMLDDA-ARFGIGAYNAWATEPLLRDDIPEILRHARSL---GMITSLVT 101
                                    68********999.....79*****************.8******************************...******** PP

                                    CSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  85 ngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGendeeleel 163
                                    ng+l+ +e +e l    +++++++++ + +    + + rg ++ee+++++  +r++gi+ v  ++v+    n eel  l
  gi|116754204|ref|YP_843322.1| 102 NGILL-RERMEDLES--LNYLTVSVDGIESL---REI-RGIGIEEIMDGIVEARRRGIE-VLMNCVI-SAKNLEELTSL 171
                                    *****.888888888..77**********96...899.99*******************.6666554.33666666555 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.4   6.3e+03      18      35 ..      39      55 ..      23      59 .. 0.58
   2 !   23.0   0.2   1.9e-08   8.6e-05       1      67 [.     242     295 ..     242     296 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.4
                          SPASM 18 pCcvdkktyvee...lklGni 35
                                    C +   +++++   +++G i
  gi|116754204|ref|YP_843322.1| 39 FC-P---HWRKRrreMSFGEI 55
                                   33.2...22222334888877 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 1.9e-08
                          SPASM   1 CfapsrslfInsdGdVvpCcvdkktyveelklGnireesleeIwnseeyqefrkskkfplielCrnC 67 
                                    C+a    l ++sdG+V+ C  +    v+e+ +G++++  ++++w+++  +e+rk+  +     C+ C
  gi|116754204|ref|YP_843322.1| 242 CHAADLILHVSSDGYVYIC--R----VHEVPVGHVSQ-GISNVWRDS--REMRKRISDG----CSGC 295
                                    777788899**********..2....457******75.******998..5666222444....8888 PP

>> rpo132  Poxvirus DNA dependent RNA polymerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.29   1.3e+03      18      28 ..     155     164 ..     154     167 .. 0.77
   2 ?   10.9   0.1   4.7e-05      0.21       2      16 ..     300     314 ..     299     315 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.29
                         rpo132  18 LVNaiiEStKe 28 
                                    L N++i S+K+
  gi|116754204|ref|YP_843322.1| 155 LMNCVI-SAKN 164
                                    89***9.6665 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 4.7e-05
                         rpo132   2 FIrnsLsYDMPeEvi 16 
                                    +I nsL YDM +Evi
  gi|116754204|ref|YP_843322.1| 300 YIENSLLYDMVPEVI 314
                                    9*************9 PP

>> DUF3463  Domain of unknown function (DUF3463)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   5.3e-05      0.24       4     127 ..     185     312 ..     182     318 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.3e-05
                        DUF3463   4 spgysYekapdqdlfl.erektkelfrkilelkkkkyklnesplyldflagkq.eykCtpW.gnptrnvlGwqkPCYlle 80 
                                    +p +++++a+ +dl + + e+ ++++ ++++lk ++  +++s +yl+++++++  ++C +    + ++  G++  C +  
  gi|116754204|ref|YP_843322.1| 185 EPLHEFDEAEFEDLRIgDLERYRSAIGELIDLKSRGAPIINSITYLKMIQKREpGFRCHAAdLILHVSSDGYVYICRVH- 263
                                    6667788887777766245788999**************************8879***986145678999999999987. PP

                        DUF3463  81 egyaktfkelleetdwekyg..kgkdpkCanCmvhsgyEasavsdtvks 127
                                    e  + ++++ ++++  ++ +  k+ ++ C+ C    + E+s++ d+v +
  gi|116754204|ref|YP_843322.1| 264 EVPVGHVSQGISNVWRDSREmrKRISDGCSGCLFFGYIENSLLYDMVPE 312
                                    6555555555555544444421667788999999999999999887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); 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: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2526.44
//
Query:       gi|116754205|ref|YP_843323.1|  [L=558]
Description: preprotein translocase subunit SecD [Methanosaeta thermophila PT]
Scores for complete 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-15   55.4   7.7    9.2e-15   54.5   7.7    1.3  1  SecD_SecF       Protein export membrane protein
  ------ inclusion threshold ------
      0.024   14.1   0.1      0.059   12.9   0.1    1.7  1  Sec_GG          SecD/SecF GG Motif
      0.041   13.7   2.5      0.084   12.7   2.5    1.5  1  Sterol-sensing  Sterol-sensing domain of SREBP cleavage-activ
      0.099   10.7   1.4       0.17    9.9   1.4    1.3  1  Patched         Patched family
          1    6.9   5.8        1.5    6.4   5.8    1.1  1  ACR_tran        AcrB/AcrD/AcrF 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 !   54.5   7.7   2.6e-18   9.2e-15      12     172 ..     370     539 ..     362     541 .. 0.83

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 2.6e-18
                                    -EEEEEEEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-HH.HHHHHHHHHHHHHHHHHHHHHHTT----HHHHHHH CS
                      SecD_SecF  12 daekisvetvgpsvskelaekavlallialvliliyvalrFewr.valaaiialvhDviitvgvlsllgievdlatvaal 90 
                                    ++++i    v++ ++++++ +++la ++a++++ ++v+ r++ r + l ++++ ++ vi+++g+ s+ g ++dla++a++
  gi|116754205|ref|YP_843323.1| 370 NVKIIGSGQVDAALGSQFKFQVALAGILAILAVGLMVFYRYRERrIVLPIVCTSFSEVIMMLGIWSAAGWQLDLASIAGI 449
                                    567777889********************************875166677778*************************** PP

                                    HHHTTSSSHHHHHHHHHHH..HHHHH--SS-HHHHHHHH......HHHHHHHHHHTTHHHHHHHHHHHHHHTTTTHHHHH CS
                      SecD_SecF  91 LtiiGYSvndtvvvfdrvr..enlrkkkratlkeiinls......lnqtLtrtiltslttllvvvallllggdslkdfal 162
                                    +++iG  v+   +++d +   e++++ +++++k ++ ++      l+  +   + + +tt+ +++ ll +g ++l +fal
  gi|116754205|ref|YP_843323.1| 450 IMVIGTGVDHLFIITDELLhgERITERSEQEAKGVLLTGkiylarLSRAFYIILGAAVTTIAAMIPLLWMGFGALMGFAL 529
                                    ****************987334477777777666655442211115555555566888899999**************** PP

                                    HHHHHTSTTT CS
                      SecD_SecF 163 allvGlivgt 172
                                    + ++G+++g+
  gi|116754205|ref|YP_843323.1| 530 ITIIGVLIGV 539
                                    ********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 ?   12.9   0.1   1.7e-05     0.059       6      24 ..      39      57 ..      36      61 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.7e-05
                                   C--EE-TTTS-EEEEEEEE CS
                         Sec_GG  6 kGlNLGlDFtGGthielqf 24
                                    Gl++GlD+ GG+ ++l+ 
  gi|116754205|ref|YP_843323.1| 39 SGLKYGLDLEGGSWLQLEL 57
                                   59**********9777776 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 ?   12.7   2.5   2.3e-05     0.084      12     106 ..     419     511 ..     413     538 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.3e-05
                                    HHHHHHCCHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCHHCCHHCHHHHHHHHTTTCHHHHHHHHHHHHCCCCHHCCCH CS
                 Sterol-sensing  12 gviivllsvasslgllaylgltltliilevlPflvlavgvdnifvlvkavqrtsrsldeseriaealgevgpsilltslt 91 
                                    +v +  + v++ lg++++ g +l l ++     +v+  gvd  f+++ ++ + +r ++ se+ a+++  +g  i l  l+
  gi|116754205|ref|YP_843323.1| 419 IVCTSFSEVIMMLGIWSAAGWQLDLASI-AGIIMVIGTGVDHLFIITDELLHGERITERSEQEAKGVLLTGK-IYLARLS 496
                                    567777889****************999.666799***************9999999999999999988885.5666677 PP

                                    HHHHHHHHHHCCHHH CS
                 Sterol-sensing  92 ellalllgaltdvpa 106
                                     ++ ++lga+++  a
  gi|116754205|ref|YP_843323.1| 497 RAFYIILGAAVTTIA 511
                                    777777776665544 PP

>> Patched  Patched family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.4   4.8e-05      0.17     666     727 ..     395     459 ..     385     479 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 4.8e-05
                        Patched 666 allcmfvvallfip...elitvlvitlsivsidigviGflslWgvdLDpismitiimsiGfsvdl 727
                                     +l +++v l+  +   e  +vl i+++  s  i ++G+ s  g +LD  s++ iim iG  vd 
  gi|116754205|ref|YP_843323.1| 395 GILAILAVGLMVFYryrERRIVLPIVCTSFSEVIMMLGIWSAAGWQLDLASIAGIIMVIGTGVDH 459
                                    556666666666551224568899999999999999***************************95 PP

>> ACR_tran  AcrB/AcrD/AcrF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   5.8   0.00041       1.5     808     980 ..     333     516 ..     320     541 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.00041
                                    ETTCEEEEEEEEESTTS-HHHHHHHHHHHCTT..SSTTEEEEEEHHHHHHHHHHCHHHHHH..HHHHHHHHHHHHHHHTS CS
                       ACR_tran 808 engsrsvvisgnvaegdslseaeeavekiakkvklpegvtiewtgqaeqeqeasnsllilv..alalllvflvLaalyes 885
                                     ++ ++  + ++v +gd  s   ++     ++  lp  v+i  +gq +++  ++ ++++ +  +la+l+v l+ +  y  
  gi|116754205|ref|YP_843323.1| 333 LDKAPMRNLVAEVGTGDAGSRKAKELYIHLREGALPVNVKIIGSGQVDAALGSQFKFQVALagILAILAVGLMVFYRYRE 412
                                    5677888889999999999975555555555559***************9999988776542279*************** PP

                                    SSTCHHHHTTHHHHHHHHHHHHHHTT--BSHHHHHHHHHHHHHHHHHHHHHHHHH........HHHHHTTTTCHHHHHHH CS
                       ACR_tran 886 lsepllilltvPlalvGallalllrglelsviaqvGlilliGlavkNaillvefa........kelrekegksleeaile 957
                                     ++ l i+ t    ++  l   + +g +l+++++ G+i++iG  v    ++ +          ++++e +g  l   i+ 
  gi|116754205|ref|YP_843323.1| 413 RRIVLPIVCTSFSEVIMMLGIWSAAGWQLDLASIAGIIMVIGTGVDHLFIITDELlhgeriteRSEQEAKGVLLTGKIYL 492
                                    9999999988766666655555689*****************98887776665441111111112222233334444555 PP

                                    HHHHC.HHHHHHHHHHHHHHHHHH CS
                       ACR_tran 958 aakeR.LrPiLMTalaailGvlPL 980
                                    a + R +  iL  a+++i  ++PL
  gi|116754205|ref|YP_843323.1| 493 ARLSRaFYIILGAAVTTIAAMIPL 516
                                    555553344555666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (558 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); 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):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.40
# Mc/sec: 4226.74
//
Query:       gi|116754206|ref|YP_843324.1|  [L=296]
Description: preprotein translocase subunit SecF [Methanosaeta thermophila PT]
Scores for complete 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  104.9  13.0    3.2e-30  104.9  13.0    1.4  2  SecD_SecF  Protein export membrane protein
    4.1e-06   26.1   0.0    8.2e-06   25.1   0.0    1.6  1  Sec_GG     SecD/SecF GG Motif
     0.0028   15.8  14.5     0.0035   15.5  14.5    1.1  1  Patched    Patched family
  ------ inclusion threshold ------
        1.2    9.0   8.5      0.097   12.5   2.5    2.3  2  DUF1232    Protein of unknown function (DUF1232)
          5    5.9  20.6       0.27   10.1  15.5    1.4  2  MMPL       MMPL family


Domain annotation for each model (and alignments):
>> SecD_SecF  Protein export membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       1.1   3.8e+03      34      48 ..      15      29 ..       8      45 .. 0.55
   2 !  104.9  13.0   8.8e-34   3.2e-30       7     188 ..     100     285 ..      94     286 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.1
                                   HHHHHHHHHHHHHHH CS
                      SecD_SecF 34 vlallialvliliyv 48
                                   ++a+ +a++++ i +
  gi|116754206|ref|YP_843324.1| 15 MIAVPAAVLALSIII 29
                                   445544444444433 PP

  == domain 2  score: 104.9 bits;  conditional E-value: 8.8e-34
                                    --SSS-EEEEEEEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-HHHHHHHHHH.HHHHHHHHHHHHHHTT----HH CS
                      SecD_SecF   7 kevdkdaekisvetvgpsvskelaekavlallialvliliyvalrFewrvalaaiia.lvhDviitvgvlsllgievdla 85 
                                    ++v+++++  ++  +gp +sk+l+++a   ll++++l++++v++ F+++v ++++++ ++ D+ii++g++ ++g++++l 
  gi|116754206|ref|YP_843324.1| 100 RTVNEKFTDAEIRYIGPVYSKQLQRDAPRYLLMSFILMALVVFFVFRQPVISGIVVLcALADIIIAAGMMTAVGVKLSLG 179
                                    6677799999*******************************************9999899******************** PP

                                    HHHHHHHHTTSSSHHHHHHHHHHHHHHHH--SS-HHHHHHHHHHHHHHHHHHTTHH.HHHHHH..HHHHHHT......TT CS
                      SecD_SecF  86 tvaalLtiiGYSvndtvvvfdrvrenlrkkkratlkeiinlslnqtLtrtiltslt.tllvvv..allllgg......ds 156
                                    tvaalL++iGYSv+++++++ rv ++     r +++e +  ++ + L++t +t    ++l++v  +++l+ +      d+
  gi|116754206|ref|YP_843324.1| 180 TVAALLMLIGYSVDTDILLTVRVLKR-----RGPVNEKVLGAMRTGLMMTSTTLSAvVVLILVssIIYLV-SptftkiDV 253
                                    ***********************998.....678999999999999988877654423333331134443.2477778** PP

                                    THHHHHHHHHHTSTTTTTHHHHHHHHHHHHH- CS
                      SecD_SecF 157 lkdfalallvGlivgtyssifiasplllllke 188
                                    ++d++++l++Gl++++++++ ++ + l ++ +
  gi|116754206|ref|YP_843324.1| 254 ISDISVVLFFGLLADMMNTWITNVQALRWYLQ 285
                                    ***********************999999865 PP

>> Sec_GG  SecD/SecF GG Motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   2.3e-09   8.2e-06       4      27 ..      37      60 ..      34      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 2.3e-09
                                   HHC--EE-TTTS-EEEEEEEE-TT CS
                         Sec_GG  4 ftkGlNLGlDFtGGthielqfdqp 27
                                   ++ ++++G++FtGGt+i++ +d p
  gi|116754206|ref|YP_843324.1| 37 TGSPVRMGIEFTGGTLITVPADEP 60
                                   67899*****************98 PP

>> Patched  Patched family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5  14.5   9.9e-07    0.0035     664     786 ..     131     251 ..     120     270 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 9.9e-07
                        Patched 664 vlallcmfvval.lfipelitvlvitlsivsidigviGflslWgvdLDpismitiimsiGfsvdlsaHiayafvrsekdd 742
                                    ++++++m++v + +f + +i+ +v+ ++++ i i  +G+++  gv+L   ++++++m iG+svd     + +  + ++  
  gi|116754206|ref|YP_843324.1| 131 LMSFILMALVVFfVFRQPVISGIVVLCALADIII-AAGMMTAVGVKLSLGTVAALLMLIGYSVDTDILLTVRVLKRRG-P 208
                                    6789999977661566666778888999999866.58*****************************************.9 PP

                        Patched 743 akeRvvealealgwPvvqgalSTilgvlvLlfvdsymvqv...Ffkt 786
                                     +e+v  a+ + g+ +    lS   +v+vL++v s + +v   F k 
  gi|116754206|ref|YP_843324.1| 209 VNEKVLGAMRT-GLMMTSTTLS---AVVVLILVSSIIYLVsptFTKI 251
                                    9*******987.6666555554...6677777766554432226664 PP

>> DUF1232  Protein of unknown function (DUF1232)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.4      0.64   2.3e+03       4      12 ..      27      35 ..      24      37 .. 0.83
   2 ?   12.5   2.5   2.7e-05     0.097       2      29 ..     233     266 ..     232     269 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.64
                        DUF1232  4 liagalaYl 12
                                   +i++a  Y+
  gi|116754206|ref|YP_843324.1| 27 IIILAATYF 35
                                   8999*9999 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 2.7e-05
                        DUF1232   2 klliagalaYlisPi....DlIPD..fiPvlGfl 29 
                                     l++++ ++Yl+sP+    D+I D  ++ ++G+l
  gi|116754206|ref|YP_843324.1| 233 VLILVSSIIYLVSPTftkiDVISDisVVLFFGLL 266
                                    5899********************5446667776 PP

>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.2       1.3   4.5e+03     201     212 ..      20      31 ..      10      43 .. 0.51
   2 ?   10.1  15.5   7.6e-05      0.27     142     289 ..     123     270 ..     107     286 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 1.3
                           MMPL 201 tfvlgllvvlli 212
                                     +vl+l++++l 
  gi|116754206|ref|YP_843324.1|  20 AAVLALSIIILA 31 
                                    333333333332 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 7.6e-05
                           MMPL 142 drdlklievvtlvvilviLlivyrSlvaallplltvvvsllaalglvlilalllglelstfvlgllvvlliavGtDYall 221
                                    +rd+    ++++++ +++ + v+r +v+ ++++l ++ ++++a g+  ++a    l l t++   + ++li+ ++D  +l
  gi|116754206|ref|YP_843324.1| 123 QRDAPRYLLMSFILMALVVFFVFRQPVISGIVVLCALADIIIAAGM--MTAVGVKLSLGTVA---ALLMLIGYSVDTDIL 197
                                    6777788899************************************..66666556665544...3445677777888** PP

                           MMPL 222 LvsRyreelaagedreeavira.vastgkvvtaaGltvaiamlgLv......varlpvlaqvGvaialGvlvdvl 289
                                    L+ R   +++   ++  +++r+ +  +    t ++++v i + +        ++++ v++ + v++  G+l d++
  gi|116754206|ref|YP_843324.1| 198 LTVRVLKRRGPVNEKVLGAMRTgL--MMTSTTLSAVVVLILVSSIIylvsptFTKIDVISDISVVLFFGLLADMM 270
                                    ****98887777776344333312..2334566666666655554400022266666666677777777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1062  (0.0592336); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2140.17
//
Query:       gi|116754207|ref|YP_843325.1|  [L=192]
Description: nitroreductase [Methanosaeta thermophila PT]
Scores for complete 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  119.0   1.6    2.1e-17   63.7   0.1    2.0  2  Nitroreductase  Nitroreductase family
      9e-10   38.5   0.0     0.0076   15.8   0.0    3.2  3  TM1586_NiRdase  Putative TM nitroreductase
  ------ inclusion threshold ------
      0.077   12.9   1.2        1.6    8.6   0.1    2.9  3  3-alpha         3-alpha domain


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 !   55.9   0.1   8.7e-19   5.2e-15       2      57 ..      31      86 ..      30      90 .. 0.91
   2 !   63.7   0.1   3.5e-21   2.1e-17      82     170 .]      87     173 ..      83     173 .. 0.97

  Alignments for each domain:
  == domain 1  score: 55.9 bits;  conditional E-value: 8.7e-19
                                   HH--B---B-S----HHHHHHHHHHHHTS--GGG---EEEEEE.-CCCHHHHHHHH CS
                 Nitroreductase  2 rkRrSiRkFddepvpkeelekileaarraPsagnlqpwrfvvvqdkelryklaeaa 57
                                   ++RrSiR+++d+pv++e++ek+l+aa  aPsagnlq+ r+vvv  ++lr++la aa
  gi|116754207|ref|YP_843325.1| 31 EGRRSIRAYQDRPVSRETVEKLLQAAELAPSAGNLQSRRYVVVMCQDLRKALALAA 86
                                   78*****************************************7799998888776 PP

  == domain 2  score: 63.7 bits;  conditional E-value: 3.5e-21
                                    HHHHHHHHSSEEEEE---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGGGGHHHHHHHHT-S..SE CS
                 Nitroreductase  82 kaqkalagapvlivivatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfdeaaeevrkllglpdeee 161
                                    + q+++  apv iv+ a+  +s+r++++r+  ya++da aa++ +lLaA+a+Glg+c+ g+fde+   vr++l ++++  
  gi|116754207|ref|YP_843325.1|  87 YGQSHISSAPVDIVVCADVRRSSRRYGDRGSLYAIQDADAAVMCMLLAAHAMGLGACWNGAFDEEM--VRDILSIEEGVA 164
                                    6789999***********************************************************..************ PP

                                    EEEEEEEE- CS
                 Nitroreductase 162 ivvliavGy 170
                                    +v++i++G+
  gi|116754207|ref|YP_843325.1| 165 PVAIISLGW 173
                                    ********8 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.1   6.7e-06      0.04       2      31 ..      26      55 ..      25      56 .. 0.90
   2 !   10.6   0.1   5.2e-05      0.31     158     181 ..      47      70 ..      45      84 .. 0.85
   3 !   15.8   0.0   1.3e-06    0.0076      90     136 ..     130     177 ..     127     187 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.7e-06
                                   HHHHHHH--B---B--S---HHHHHHHHH- CS
                 TM1586_NiRdase  2 lyeaiekRhsvRkYkdealeeelleelkea 31
                                   +++a+e R+s+R+Y+d++++ e++e+l +a
  gi|116754207|ref|YP_843325.1| 26 VFDALEGRRSIRAYQDRPVSRETVEKLLQA 55
                                   6899********************999875 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 5.2e-05
                                    HHHHHHHHHHHTS--GGG----EE CS
                 TM1586_NiRdase 158 ewfkeileaarlAPsAlNqqpwrf 181
                                    e ++++l+aa+lAPsA N q  r 
  gi|116754207|ref|YP_843325.1|  47 ETVEKLLQAAELAPSAGNLQSRRY 70 
                                    7899**************998665 PP

  == domain 3  score: 15.8 bits;  conditional E-value: 1.3e-06
                                    HHHHHHHHTT-EEEEES--SST............T-S-EEEEE-BS-- CS
                 TM1586_NiRdase  90 qlvLkltalGlgtcWvggtykk.kkakvelkkgeklvivIalGyaktk 136
                                    +++L + a Glg cW g+  ++ ++  +++++g   v++I+lG ++++
  gi|116754207|ref|YP_843325.1| 130 CMLLAAHAMGLGACWNGAFDEEmVRDILSIEEGVAPVAIISLGWPAES 177
                                    689**************98777888889***************99875 PP

>> 3-alpha  3-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1   0.00027       1.6      12      33 ..      41      62 ..      33      69 .. 0.79
   2 ?   -0.7   0.1      0.22   1.3e+03      19      28 ..      77      86 ..      76      89 .. 0.87
   3 ?    1.4   0.0     0.048   2.9e+02      12      28 ..     145     161 ..     142     161 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00027
                                   TS---HHHHHHHHTSTT--HHH CS
                        3-alpha 12 hdkldrealrrllelpaLspsW 33
                                   +++  re+ ++ll++++L+ps 
  gi|116754207|ref|YP_843325.1| 41 DRPVSRETVEKLLQAAELAPSA 62
                                   566689**************95 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.22
                                   HHHHHHTSTT CS
                        3-alpha 19 alrrllelpa 28
                                   +lr++l+l+a
  gi|116754207|ref|YP_843325.1| 77 DLRKALALAA 86
                                   799****986 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.048
                                    TS---HHHHHHHHTSTT CS
                        3-alpha  12 hdkldrealrrllelpa 28 
                                    +  +d+e+ r +l++++
  gi|116754207|ref|YP_843325.1| 145 NGAFDEEMVRDILSIEE 161
                                    6679**********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1391.49
//
Query:       gi|116754208|ref|YP_843326.1|  [L=512]
Description: ELP3 family histone acetyltransferase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-26   92.7   0.2      2e-26   91.8   0.2    1.5  1  Radical_SAM_C    Radical_SAM C-terminal domain
    2.6e-20   73.5   0.1    2.9e-19   70.1   0.0    2.2  2  Radical_SAM      Radical SAM superfamily
    1.6e-07   31.6   0.2    3.3e-07   30.6   0.2    1.5  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    9.7e-07   28.8   0.0    2.4e-06   27.5   0.0    1.6  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.071   13.6   0.1       0.13   12.7   0.1    1.5  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
       0.18   12.1   0.1       0.18   12.1   0.1    2.7  2  PCP_red          Proto-chlorophyllide reductase 57 kD subunit


Domain annotation for each model (and alignments):
>> Radical_SAM_C  Radical_SAM C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.8   0.2   6.5e-30     2e-26       1      81 [.     297     377 ..     297     378 .. 0.98

  Alignments for each domain:
  == domain 1  score: 91.8 bits;  conditional E-value: 6.5e-30
                  Radical_SAM_C   1 pdgvKlypllvikgTeLaelyksgeykplsleeyvdlvadilellppdirvhRltgdipkelliagpwhknlreliekrl 80 
                                    pd +K+yp+lvi+gTeL++++ +g+y+pls +e+ +l+ +i+e+lp  +r++R+++dip +l+ ag+ ++nlr+l++krl
  gi|116754208|ref|YP_843326.1| 297 PDYLKIYPTLVIEGTELHRMWIRGDYEPLSDDEAAELISRIKEILPRYTRLQRVQRDIPAHLITAGVRKSNLRQLARKRL 376
                                    89*****************************************************************************9 PP

                  Radical_SAM_C  81 k 81 
                                    +
  gi|116754208|ref|YP_843326.1| 377 E 377
                                    7 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.1   0.0   9.6e-23   2.9e-19       5     158 ..      81     280 ..      77     290 .. 0.87
   2 ?    0.7   0.0       0.2     6e+02      56      93 ..     323     367 ..     315     380 .. 0.82

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 9.6e-23
                                    SEESS-.-TTTSCCTT...................HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHH CS
                                    xxxxxx.xxxxxxxxx...................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   5 rgCnlr.CsfCarpet...................vrregrgrslsveeileevkelkaekgvkevilgggepllypdfv 64 
                                      C+++ C+ C+ +                     v+ + +++     +++++ +++ +  ++ e+il+gg+ + +p  +
  gi|116754208|ref|YP_843326.1|  81 ARCPHGiCIPCPGGVLgercspqsytgrepaalraVQHNFDPYAQVAARLKQLSEIG-HPVDKAELILMGGTITSRPLGY 159
                                    568888899999999999999999*******99977777777777777777777777.7888**************9999 PP

                                    HHHHHHHHTC............................CCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHH CS
                                    xxxxxxxxxx............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  65 ellerlakla............................vpgiritvetngtlpdeeklerllelgvdrvslgleaaddek 116
                                    + ++ ++ l+                            v+++ it+et + + +e +++ +l lg + v+lg++++ d+ 
  gi|116754208|ref|YP_843326.1| 160 QCWFVRRCLEamndypdtrrstrwrsfrevadantsaaVRNVGITFETRPDWCRENHIKNMLLLGATKVELGVQSIYDD- 238
                                    999999999999999********************6666666666666666666*************************. PP

                                    HHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM 117 vlklmnrghtfeevlealeklreagikrvvdrivglpGende 158
                                    vl  ++rgh++ee+++a ++lreag+k+ +++++glpG   +
  gi|116754208|ref|YP_843326.1| 239 VLSAIRRGHSVEETIRANRLLREAGLKVGFHMMPGLPGSDPD 280
                                    **************************************8753 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.2
                                    TGGGSTTHHHHHHHHHHTC.........CCTEEEEEEECSSCHGHHH CS
                                    xxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  56 epllypdfvellerlakla.........vpgiritvetngtlpdeek 93 
                                    epl +++ +el+ r++++           ++i  +++t g++ +   
  gi|116754208|ref|YP_843326.1| 323 EPLSDDEAAELISRIKEILprytrlqrvQRDIPAHLITAGVRKS--N 367
                                    89999999999999999999999999999999999999999943..3 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.2   1.1e-10   3.3e-07      35     117 .]     417     501 ..     389     501 .. 0.85

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 1.1e-10
                                    EEE.EEETTEEEEEEEEEEEETTSTTEEEEEEEEE.........SGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETT CS
                 Acetyltransf_1  35 llv.aeedgeliGfisllkipdekggvayieslaV.........speyrgkGlGsaLlealeerareegikkivlaveed 104
                                    +++    d++l+Gf++l+   +     a i++l+V         +  ++++G+G +L+e +ee ar++g+++i +    +
  gi|116754208|ref|YP_843326.1| 417 FISfDTVDDTLVGFLRLRLGAE-----ARIRELHVygplvplgrRGGWQHRGIGARLIERAEEMARDQGYERISV---TS 488
                                    333455669*************.....9999999999999**99*****************************88...68 PP

                                    EHHHHHHHHHTTE CS
                 Acetyltransf_1 105 ndaairlYeklGF 117
                                      + +++Y  lG+
  gi|116754208|ref|YP_843326.1| 489 GIGVRGYYASLGY 501
                                    9999999977997 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   8.1e-10   2.4e-06      30     107 ..     415     502 ..     403     510 .. 0.77

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 8.1e-10
                Acetyltransf_10  30 ealllvaeeggkivGvielrdgs.......hisllfV....dpeyrgqGigkaLleaveeeaekdgikleltvnaspyav 98 
                                    e+++   ++++++vG+++lr g        h++   V    +  ++++Gig++L+e++ee a+++g++ +++v +    +
  gi|116754208|ref|YP_843326.1| 415 EHFISFDTVDDTLVGFLRLRLGAearirelHVYGPLVplgrRGGWQHRGIGARLIERAEEMARDQGYE-RISVTSGIGVR 493
                                    555555566677777776655555655555555555544445679***********************.*********** PP

                Acetyltransf_10  99 pfYeklGFk 107
                                    ++Y +lG++
  gi|116754208|ref|YP_843326.1| 494 GYYASLGYR 502
                                    ********8 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   4.5e-05      0.13      35      75 ..     458     502 ..     414     503 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.5e-05
                                    GGTTSSHHHHHHH.HTT....SEEEEEEEEETHH..HHHHHHHHTTEE CS
                 Acetyltransf_7  35 eyrgkGiGraLle.aae....kgiileqlelnae..kaikfYeklGFe 75 
                                     ++ +GiG +L+e a+e    +g++ +   ++ +    +++Y++lG++
  gi|116754208|ref|YP_843326.1| 458 GWQHRGIGARLIErAEEmardQGYERI--SVT-SgiGVRGYYASLGYR 502
                                    589*********965335567776433..222.1234567******97 PP

>> PCP_red  Proto-chlorophyllide reductase 57 kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   2.8       1.4   4.2e+03       2      23 ..     327     353 ..     327     381 .. 0.75
   2 ?   12.1   0.1     6e-05      0.18      22      38 ..     470     486 ..     456     487 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.4
                                    -HHHHHHHTTS....-HHHH.HHHHHH CS
                        PCP_red   2 tdeAealLkki....PffvR.kkaRra 23 
                                    +deA +l+ +i    P ++R  +++r 
  gi|116754208|ref|YP_843326.1| 327 DDEAAELISRIkeilPRYTRlQRVQRD 353
                                    688999998888889999998555554 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 6e-05
                                    HHHHHHHHHHT-SEE-H CS
                        PCP_red  22 raaEklArerGleeVtv 38 
                                     +aE++Ar++G+e+++v
  gi|116754208|ref|YP_843326.1| 470 ERAEEMARDQGYERISV 486
                                    79*************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (512 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 3747.08
//
Query:       gi|116754209|ref|YP_843327.1|  [L=152]
Description: 4Fe-4S ferredoxin iron-sulfur binding domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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   61.5  35.1    3.8e-06   26.5   3.1    4.9  5  Fer4         4Fe-4S binding domain
    8.5e-17   60.4  35.5    1.2e-07   31.5   3.0    4.2  4  Fer4_6       4Fe-4S binding domain
    2.5e-13   49.9  47.5      5e-06   26.6  12.5    3.0  4  Fer4_9       4Fe-4S dicluster domain
    2.5e-13   50.4  70.6    5.7e-06   26.8  12.0    3.8  5  Fer4_7       4Fe-4S dicluster domain
    1.8e-12   47.2  28.5    5.7e-07   29.6  10.9    2.7  2  Fer4_10      4Fe-4S dicluster domain
    2.6e-12   46.0  35.2    0.00013   21.8   3.9    4.3  4  Fer4_2       4Fe-4S binding domain
    1.5e-11   45.0  22.2     0.0056   17.6   0.4    4.2  4  Fer4_16      4Fe-4S double cluster binding domain
    2.4e-08   33.8  34.7     0.0012   19.2   2.7    4.6  4  Fer4_4       4Fe-4S binding domain
    2.3e-07   30.9  11.2    2.3e-07   30.9  11.2    2.2  2  Fer4_11      4Fe-4S dicluster domain
    5.8e-07   30.0  43.6      0.025   15.5   4.1    4.2  4  Fer4_3       4Fe-4S binding domain
    1.3e-05   25.2  28.3        0.2   11.8  10.0    3.4  3  Fer4_21      4Fe-4S dicluster domain
    5.8e-05   23.7   2.9    5.8e-05   23.7   2.9    4.1  3  Fer4_15      4Fe-4S single cluster domain
    0.00011   22.6  27.7      0.061   13.9   1.8    3.8  5  Fer4_17      4Fe-4S dicluster domain
    0.00015   22.1  27.9      0.038   14.4   7.5    3.5  3  Fer4_8       4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.051   13.8  26.4        1.2    9.3   0.8    3.2  3  Fer4_18      4Fe-4S dicluster domain
      0.071   13.5   0.2       0.33   11.4   0.0    2.0  2  DUF4258      Domain of unknown function (DUF4258)
      0.086   13.7   2.5      0.086   13.7   2.5    4.1  4  Fer4_22      4Fe-4S dicluster domain
       0.69    9.7   3.1       0.33   10.7   1.1    1.5  1  MafB19-deam  MafB19-like deaminase


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 !   17.6   1.8   2.4e-06    0.0024       4      18 ..      27      41 ..      25      42 .. 0.93
   2 ?   -0.1   0.3      0.97   9.7e+02      11      15 ..      73      77 ..      71      78 .. 0.73
   3 !   14.7   0.3   1.9e-05     0.019      13      23 ..      80      90 ..      80      91 .. 0.92
   4 !   26.5   3.1   3.8e-09   3.8e-06       1      23 [.      98     120 ..      98     121 .. 0.87
   5 !   22.4   3.2   7.6e-08   7.5e-05       7      23 ..     130     146 ..     128     147 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.4e-06
                                   ETTTSSS-THHHHHS CS
                           Fer4  4 deekCigCGaCvevC 18
                                   ++e+CigC  C+ +C
  gi|116754209|ref|YP_843327.1| 27 HPERCIGCLSCMFAC 41
                                   69************* PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.97
                                   -THHH CS
                           Fer4 11 CGaCv 15
                                   C aC+
  gi|116754209|ref|YP_843327.1| 73 CHACE 77
                                   88997 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 1.9e-05
                                   HHHHHSTTTEE CS
                           Fer4 13 aCvevCPvgAI 23
                                   aCv +CP+gA+
  gi|116754209|ref|YP_843327.1| 80 ACVRACPTGAL 90
                                   7*********8 PP

  == domain 4  score: 26.5 bits;  conditional E-value: 3.8e-09
                                    EEEETTTSSS-THHHHHSTTTEE CS
                           Fer4   1 vvideekCigCGaCvevCPvgAI 23 
                                    vv+d ++C gCG+Cv++C  gAI
  gi|116754209|ref|YP_843327.1|  98 VVFDRDLCDGCGRCVDACLIGAI 120
                                    689***************66665 PP

  == domain 5  score: 22.4 bits;  conditional E-value: 7.6e-08
                                    TSSS-THHHHHSTTTEE CS
                           Fer4   7 kCigCGaCvevCPvgAI 23 
                                    kC +CGaCv  CP++++
  gi|116754209|ref|YP_843327.1| 130 KCKHCGACVAFCPHDVL 146
                                    8**************97 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   1.3   1.1e-05     0.011       5      20 ..      27      42 ..      25      49 .. 0.89
   2 !   12.4   5.3   0.00013      0.13       9      24 .]      73      90 ..      72      90 .. 0.92
   3 !   31.5   3.0   1.2e-10   1.2e-07       2      24 .]      98     120 ..      97     120 .. 0.90
   4 !   18.7   3.1   1.3e-06    0.0013       8      24 .]     130     146 ..     127     146 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-05
                         Fer4_6  5 dpdkCigCgdCvrvCP 20
                                    p++CigC  C+ +C 
  gi|116754209|ref|YP_843327.1| 27 HPERCIGCLSCMFACS 42
                                   69*************6 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00013
                         Fer4_6  9 CigCgd..CvrvCPegai 24
                                   C  C+d  Cvr+CP+ga+
  gi|116754209|ref|YP_843327.1| 73 CHACEDpaCVRACPTGAL 90
                                   999*989*********97 PP

  == domain 3  score: 31.5 bits;  conditional E-value: 1.2e-10
                         Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                    v++d+d+C+gCg+Cv++C  gai
  gi|116754209|ref|YP_843327.1|  98 VVFDRDLCDGCGRCVDACLIGAI 120
                                    89****************77665 PP

  == domain 4  score: 18.7 bits;  conditional E-value: 1.3e-06
                         Fer4_6   8 kCigCgdCvrvCPegai 24 
                                    kC +Cg+Cv+ CP++++
  gi|116754209|ref|YP_843327.1| 130 KCKHCGACVAFCPHDVL 146
                                    8************9985 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   1.3    0.0001       0.1      25      48 ..      20      43 ..       4      46 .. 0.65
   2 !   22.3   8.9   1.1e-07   0.00011       1      50 [.      30      89 ..      30      90 .. 0.84
   3 !   25.9  10.1   8.3e-09   8.2e-06       2      50 ..      73     119 ..      72     120 .. 0.88
   4 !   26.6  12.5     5e-09     5e-06       2      50 ..     105     145 ..     104     146 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.0001
                         Fer4_9 25 karlraaseeaCigCgaCveaCpk 48
                                    +rl+ a  e+CigC +C+ aC +
  gi|116754209|ref|YP_843327.1| 20 RRRLKVAHPERCIGCLSCMFACSR 43
                                   223333333889999999999976 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 1.1e-07
                         Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase........eaCigCga..CveaCpkga 50
                                   +C+gC +C+ aC    + + + er a   +++           C+ C++  Cv aCp+ga
  gi|116754209|ref|YP_843327.1| 30 RCIGCLSCMFACSRINTGRASLERSAIRIKTQGgiegdpivVVCHACEDpaCVRACPTGA 89
                                   6***********99888887777776654444479999***88*****999*******97 PP

  == domain 3  score: 25.9 bits;  conditional E-value: 8.3e-09
                         Fer4_9   2 CtgCga..CveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                    C  C    Cv+aCp+g+ ++++ +  +  r      C gCg+Cv+aC  ga
  gi|116754209|ref|YP_843327.1|  73 CHACEDpaCVRACPTGALSRKEDGSVVFDRD----LCDGCGRCVDACLIGA 119
                                    999*8556******************99876....6***********7666 PP

  == domain 4  score: 26.6 bits;  conditional E-value: 5e-09
                         Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                    C gCg+Cv+aC  g+++ d+ ++ ++        C +CgaCv+ Cp+++
  gi|116754209|ref|YP_843327.1| 105 CDGCGRCVDACLIGAISLDSEGKAVK--------CKHCGACVAFCPHDV 145
                                    ********************999988........9***********985 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   1.5   9.5e-05     0.095      27      48 ..      19      41 ..       6      44 .. 0.69
   2 !   17.7  11.6     4e-06    0.0039       1      52 []      30      89 ..      30      89 .. 0.68
   3 !   22.8  11.8   1.1e-07    0.0001       2      51 ..      73     118 ..      71     119 .. 0.91
   4 !   26.8  12.0   5.7e-09   5.7e-06       2      52 .]     105     145 ..     104     145 .. 0.93
   5 !   18.5   2.6   2.3e-06    0.0023       1      19 [.     130     148 ..     130     152 .] 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.5e-05
                         Fer4_7 27 gtekvei.dpekClgCgaCvavC 48
                                   +++++++ +pe+C+gC +C+ +C
  gi|116754209|ref|YP_843327.1| 19 KRRRLKVaHPERCIGCLSCMFAC 41
                                   33444442799999999999999 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 4e-06
                         Fer4_7  1 rCigCgaCvaaCp...vkaieldee.enekgtekveidp..ekClgCga..CvavCPtga 52
                                   rCigC  C+ aC+   ++  +l+ +  + k++  +e+dp    C  C+   Cv++CPtga
  gi|116754209|ref|YP_843327.1| 30 RCIGCLSCMFACSrinTGRASLERSaIRIKTQGGIEGDPivVVCHACEDpaCVRACPTGA 89
                                   8***********7544444444332133344455666652257****9888*******98 PP

  == domain 3  score: 22.8 bits;  conditional E-value: 1.1e-07
                         Fer4_7   2 CigCg..aCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtg 51 
                                    C  C+  aCv+aCp++a++ +e+       +v++d + C gCg+Cv++C  g
  gi|116754209|ref|YP_843327.1|  73 CHACEdpACVRACPTGALSRKED------GSVVFDRDLCDGCGRCVDACLIG 118
                                    9999778*************887......59******************766 PP

  == domain 4  score: 26.8 bits;  conditional E-value: 5.7e-09
                         Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                    C gCg+Cv+aC  +ai+ld e          +++ kC +CgaCva CP+++
  gi|116754209|ref|YP_843327.1| 105 CDGCGRCVDACLIGAISLDSE----------GKAVKCKHCGACVAFCPHDV 145
                                    ******************986..........6889*************985 PP

  == domain 5  score: 18.5 bits;  conditional E-value: 2.3e-06
                         Fer4_7   1 rCigCgaCvaaCpvkaiel 19 
                                    +C +CgaCva Cp+++++l
  gi|116754209|ref|YP_843327.1| 130 KCKHCGACVAFCPHDVLKL 148
                                    799**********999886 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   9.6   7.3e-08   7.3e-05       3      56 .]      25      86 ..      23      86 .. 0.87
   2 !   29.6  10.9   5.7e-10   5.7e-07       2      56 .]      98     142 ..      97     142 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 7.3e-08
                        Fer4_10  3 vidddtCirCgkCvkaCPadl........tsvgakgeaseeeavrkkvekCtgcg..aCveaCP 56
                                   v  +++Ci+C  C+ aC +          +++  + ++ ++ + +  v  C++c+  aCv+aCP
  gi|116754209|ref|YP_843327.1| 25 VAHPERCIGCLSCMFAC-S-RintgraslERSAIRIKTQGGIEGDPIVVVCHACEdpACVRACP 86
                                   66899************.5.459*****9888888888888888889999****999******9 PP

  == domain 2  score: 29.6 bits;  conditional E-value: 5.7e-10
                        Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                    vv+d+d C +Cg+Cv+aC           +  ++   ++k  kC +cgaCv+ CP
  gi|116754209|ref|YP_843327.1|  98 VVFDRDLCDGCGRCVDAC----------LIGAISLDSEGKAVKCKHCGACVAFCP 142
                                    789***************..........56777777778889************9 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   1.5   2.8e-06    0.0027       5      20 ..      26      41 ..      22      43 .. 0.89
   2 ?    4.9   5.8     0.033        32      10      22 .]      73      87 ..      68      87 .. 0.87
   3 !   21.8   3.9   1.3e-07   0.00013       3      20 ..      98     115 ..      96     115 .. 0.95
   4 !   19.2   1.5   9.1e-07    0.0009       9      22 .]     130     143 ..     119     143 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.8e-06
                         Fer4_2  5 vdtdrCigCgaCvsaC 20
                                   + ++rCigC +C  aC
  gi|116754209|ref|YP_843327.1| 26 AHPERCIGCLSCMFAC 41
                                   679************* PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.033
                         Fer4_2 10 CigCg..aCvsaCPa 22
                                   C +C+  aCv aCP+
  gi|116754209|ref|YP_843327.1| 73 CHACEdpACVRACPT 87
                                   6689889*******7 PP

  == domain 3  score: 21.8 bits;  conditional E-value: 1.3e-07
                         Fer4_2   3 vvvdtdrCigCgaCvsaC 20 
                                    vv+d+d C gCg Cv+aC
  gi|116754209|ref|YP_843327.1|  98 VVFDRDLCDGCGRCVDAC 115
                                    79**************** PP

  == domain 4  score: 19.2 bits;  conditional E-value: 9.1e-07
                         Fer4_2   9 rCigCgaCvsaCPa 22 
                                    +C +CgaCv  CP+
  gi|116754209|ref|YP_843327.1| 130 KCKHCGACVAFCPH 143
                                    8************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 !    8.4   0.4    0.0042       4.2      51      64 ..      28      41 ..       8      45 .. 0.67
   2 !   16.2   0.9   1.6e-05     0.016       2      25 ..      73      98 ..      72     103 .. 0.84
   3 !   17.6   0.4   5.6e-06    0.0056       2      23 ..     105     126 ..     104     129 .. 0.88
   4 !   16.3   2.1   1.4e-05     0.014       1      18 [.     130     147 ..     130     151 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0042
                        Fer4_16 51 qeaitgCdiCqdvC 64
                                    e+++gC  C+ +C
  gi|116754209|ref|YP_843327.1| 28 PERCIGCLSCMFAC 41
                                   46677777777777 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.6e-05
                        Fer4_16  2 CgtCgk..CaevCPtnaikekkekei 25
                                   C+ C+   C+ +CPt+a++ k++ ++
  gi|116754209|ref|YP_843327.1| 73 CHACEDpaCVRACPTGALSRKEDGSV 98
                                   99999777***********9977665 PP

  == domain 3  score: 17.6 bits;  conditional E-value: 5.6e-06
                        Fer4_16   2 CgtCgkCaevCPtnaikekkek 23 
                                    C +Cg+C+++C  +ai+ ++e 
  gi|116754209|ref|YP_843327.1| 105 CDGCGRCVDACLIGAISLDSEG 126
                                    *****************99765 PP

  == domain 4  score: 16.3 bits;  conditional E-value: 1.4e-05
                        Fer4_16   1 rCgtCgkCaevCPtnaik 18 
                                    +C+ Cg+C+  CP++++k
  gi|116754209|ref|YP_843327.1| 130 KCKHCGACVAFCPHDVLK 147
                                    5*************9987 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   1.8   0.00056      0.56       1      15 [.      28      42 ..      28      50 .. 0.90
   2 !    7.4   3.8    0.0072       7.2       4      17 .]      73      88 ..      72      88 .. 0.80
   3 !   13.5   3.5   8.1e-05     0.081       2      14 ..     103     115 ..     101     116 .. 0.92
   4 !   19.2   2.7   1.2e-06    0.0012       3      15 ..     130     142 ..     128     147 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00056
                         Fer4_4  1 qerCigCgsCvaaCP 15
                                   +erCigC sC+ aC+
  gi|116754209|ref|YP_843327.1| 28 PERCIGCLSCMFACS 42
                                   69********98886 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0072
                         Fer4_4  4 CigCg..sCvaaCPqg 17
                                   C  C   +Cv+aCP+g
  gi|116754209|ref|YP_843327.1| 73 CHACEdpACVRACPTG 88
                                   66777668******86 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 8.1e-05
                         Fer4_4   2 erCigCgsCvaaC 14 
                                    + C gCg+Cv+aC
  gi|116754209|ref|YP_843327.1| 103 DLCDGCGRCVDAC 115
                                    67*********** PP

  == domain 4  score: 19.2 bits;  conditional E-value: 1.2e-06
                         Fer4_4   3 rCigCgsCvaaCP 15 
                                    +C +Cg+Cva+CP
  gi|116754209|ref|YP_843327.1| 130 KCKHCGACVAFCP 142
                                    7***********9 PP

>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.3       1.1   1.1e+03       7      22 ..      28      41 ..      21      59 .. 0.62
   2 !   30.9  11.2   2.3e-10   2.3e-07       9      77 ..      72     137 ..      68     150 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.1
                        Fer4_11  7 peqCrhCleppCvasa 22
                                   pe C  Cl+  C+ ++
  gi|116754209|ref|YP_843327.1| 28 PERCIGCLS--CMFAC 41
                                   666666653..33333 PP

  == domain 2  score: 30.9 bits;  conditional E-value: 2.3e-10
                        Fer4_11   9 qCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivrkneetgkvekCdmcldr 77 
                                     C+ C++p+Cv+++p++a+ ++e +G V++d++ ++ ++ ++v+ac   ++  ++e + + kC+ c + 
  gi|116754209|ref|YP_843327.1|  72 VCHACEDPACVRACPTGALSRKE-DGSVVFDRDLCD-GCGRCVDACLIGAISLDSEGK-AVKCKHCGAC 137
                                    6**************99987766.***********8.************999987755.999**99654 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   3.1     0.033        33       1      11 [.      31      41 ..      31      45 .. 0.90
   2 !   13.5   6.5   0.00011      0.11       1      15 []      73      89 ..      73      89 .. 0.94
   3 !   15.5   4.1   2.5e-05     0.025       1      15 []     105     119 ..     105     119 .. 0.94
   4 !   14.1   6.2     7e-05     0.069       1      14 [.     131     144 ..     131     145 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.033
                         Fer4_3  1 CtgCgaCvevC 11
                                   C+gC  C+ +C
  gi|116754209|ref|YP_843327.1| 31 CIGCLSCMFAC 41
                                   ****88**999 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00011
                         Fer4_3  1 CtgCg..aCvevCPvgA 15
                                   C+ C+  aCv++CP+gA
  gi|116754209|ref|YP_843327.1| 73 CHACEdpACVRACPTGA 89
                                   999*9999********9 PP

  == domain 3  score: 15.5 bits;  conditional E-value: 2.5e-05
                         Fer4_3   1 CtgCgaCvevCPvgA 15 
                                    C+gCg+Cv++C  gA
  gi|116754209|ref|YP_843327.1| 105 CDGCGRCVDACLIGA 119
                                    ***********9887 PP

  == domain 4  score: 14.1 bits;  conditional E-value: 7e-05
                         Fer4_3   1 CtgCgaCvevCPvg 14 
                                    C +CgaCv  CP +
  gi|116754209|ref|YP_843327.1| 131 CKHCGACVAFCPHD 144
                                    9***********75 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8  10.0    0.0002       0.2       4      56 ..      27      89 ..      24      92 .. 0.65
   2 !   11.1   9.8   0.00033      0.33       8      58 ..      73     121 ..      71     122 .. 0.82
   3 !    9.5   2.7    0.0011       1.1       7      27 ..     130     150 ..     127     152 .] 0.68

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0002
                        Fer4_21  4 dedkCigCgkCliaCed..tsh.....qaieidaktvl..kvvedeCvGCn..lCssvCPvedc 56
                                   ++++CigC +C+ aC+   t+       ai+i+++  +    +   C +C+   C+  CP+ ++
  gi|116754209|ref|YP_843327.1| 27 HPERCIGCLSCMFACSRinTGRaslerSAIRIKTQGGIegDPIVVVCHACEdpACVRACPT-GA 89
                                   789************962233311111455666665552233467899998557******6.55 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00033
                        Fer4_21   8 CigCg..kCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58 
                                    C  C+   C+ aC+   + a++ +++  +    d C GC  C++ C + ++i+
  gi|116754209|ref|YP_843327.1|  73 CHACEdpACVRACP---TGALSRKEDGSVVFDRDLCDGCGRCVDACLI-GAIS 121
                                    66665335999999...588999999999999**************87.8876 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0011
                        Fer4_21   7 kCigCgkCliaCedtshqaie 27 
                                    kC +Cg C+  C+    + ie
  gi|116754209|ref|YP_843327.1| 130 KCKHCGACVAFCPHDVLKLIE 150
                                    677888888888866666655 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 ?    0.6   7.6      0.99   9.9e+02       6      25 ..      29      48 ..      27      92 .. 0.53
   2 !   23.7   2.9   5.8e-08   5.8e-05       1      30 [.      98     128 ..      98     130 .. 0.93
   3 ?    3.2   3.3      0.15   1.5e+02       7      19 ..     130     142 ..     129     149 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.99
                        Fer4_15  6 daCigcglCvaeapevfeld 25
                                   ++Cigc  C+ +++++ +  
  gi|116754209|ref|YP_843327.1| 29 ERCIGCLSCMFACSRINTGR 48
                                   79********9997554443 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 5.8e-08
                        Fer4_15   1 VvvDrdaCigcglCvaea.pevfeldedgla 30 
                                    Vv+Drd+C+gcg+Cv+++    + ld++g+a
  gi|116754209|ref|YP_843327.1|  98 VVFDRDLCDGCGRCVDAClIGAISLDSEGKA 128
                                    89****************88899******99 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.15
                        Fer4_15   7 aCigcglCvaeap 19 
                                    +C  cg+Cva +p
  gi|116754209|ref|YP_843327.1| 130 KCKHCGACVAFCP 142
                                    6*********998 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   2.4    0.0081       8.1      45      56 ..      30      41 ..      14      45 .. 0.68
   2 !   10.5   8.9   0.00068      0.68       1      59 [.      30      88 ..      30      89 .. 0.74
   3 ?    6.6   1.4     0.011        11       2      20 ..      73      93 ..      72     103 .. 0.76
   4 !    9.5   1.4    0.0014       1.4       2      17 ..     105     120 ..     104     130 .. 0.78
   5 !   13.9   1.8   6.1e-05     0.061      42      60 ..     127     145 ..     118     146 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0081
                        Fer4_17 45 lCieCgeCerkC 56
                                   +Ci+C  C  +C
  gi|116754209|ref|YP_843327.1| 30 RCIGCLSCMFAC 41
                                   666666666666 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00068
                        Fer4_17  1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCg..eCerkCPqg 59
                                   rCi+C  C+ +C++ +  +   ++ +   +++  +++e ++ +  C+ C+   C+r+CP g
  gi|116754209|ref|YP_843327.1| 30 RCIGCLSCMFACSRINTGRASLERSAI--RIKTQGGIEGDPIVVVCHACEdpACVRACPTG 88
                                   7*********99998775543333333..334556778889999***998446******76 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.011
                        Fer4_17  2 CiqCgy..ClpeCpsyeaydn 20
                                   C+ C+   C+++Cp+++  ++
  gi|116754209|ref|YP_843327.1| 73 CHACEDpaCVRACPTGALSRK 93
                                   999995569999998877655 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.0014
                        Fer4_17   2 CiqCgyClpeCpsyea 17 
                                    C +Cg C+++C  +++
  gi|116754209|ref|YP_843327.1| 105 CDGCGRCVDACLIGAI 120
                                    9999999999988776 PP

  == domain 5  score: 13.9 bits;  conditional E-value: 6.1e-05
                        Fer4_17  42 kaslCieCgeCerkCPqgl 60 
                                    ka +C +Cg C++ CP+++
  gi|116754209|ref|YP_843327.1| 127 KAVKCKHCGACVAFCPHDV 145
                                    7889999999999999986 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   7.5   3.8e-05     0.038       3      64 ..      29      88 ..      28      89 .. 0.71
   2 !    8.2   1.9    0.0033       3.3       5      16 ..     105     116 ..     101     127 .. 0.72
   3 !   11.6   2.4   0.00028      0.28      48      64 ..     128     144 ..     118     145 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.8e-05
                         Fer4_8  3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcga..CtevCpvg 64
                                   e+Ci+C  C+ aC    +t++ +l+    +++   ++ + e++ ++  C++c+   C+++Cp+g
  gi|116754209|ref|YP_843327.1| 29 ERCIGCLSCMFACS-RINTGRASLERSAIRIK---TQGGIEGDPIVVVCHACEDpaCVRACPTG 88
                                   68***********5.44444555555555455...2223333788********888******87 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0033
                         Fer4_8   5 CieCgaCqsaCp 16 
                                    C +Cg+C +aC 
  gi|116754209|ref|YP_843327.1| 105 CDGCGRCVDACL 116
                                    667777777774 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00028
                         Fer4_8  48 lwsCttcgaCtevCpvg 64 
                                    + +C +cgaC+  Cp +
  gi|116754209|ref|YP_843327.1| 128 AVKCKHCGACVAFCPHD 144
                                    56799999999999976 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.8    0.0012       1.2      84     111 ..      30      58 ..      23      61 .. 0.80
   2 ?    7.9   8.7    0.0035       3.5      61      95 ..      73     115 ..      64     126 .. 0.77
   3 ?    7.8   2.4    0.0037       3.7      57      75 ..     127     145 ..     117     148 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0012
                        Fer4_18  84 eciscllcidacdkvm.eklgkpkgliry 111
                                     ci cl c+ ac+++  ++ +++++ ir 
  gi|116754209|ref|YP_843327.1|  30 RCIGCLSCMFACSRINtGRASLERSAIRI 58 
                                    6*************962567778877775 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0035
                        Fer4_18  61 cidce..scvkvcPtgidirk..Glql.e...ciscllcidac 95 
                                    c +ce  +cv+ cPtg   rk  G  + +   c  c++c+dac
  gi|116754209|ref|YP_843327.1|  73 CHACEdpACVRACPTGALSRKedGSVVfDrdlCDGCGRCVDAC 115
                                    88887557********999863354332233599********* PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0037
                        Fer4_18  57 gagdcidcescvkvcPtgi 75 
                                    +a +c +c++cv+ cP ++
  gi|116754209|ref|YP_843327.1| 127 KAVKCKHCGACVAFCPHDV 145
                                    566899**********865 PP

>> DUF4258  Domain of unknown function (DUF4258)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00033      0.33      37      56 ..      61      80 ..      42      83 .. 0.76
   2 ?   -0.4   0.0       1.5   1.5e+03      39      56 ..     121     138 ..      94     151 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00033
                        DUF4258 37 gktsegrplhvvvapdedpv 56
                                   + ++eg+p++vv++ +edp 
  gi|116754209|ref|YP_843327.1| 61 QGGIEGDPIVVVCHACEDPA 80
                                   456899************97 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.5
                        DUF4258  39 tsegrplhvvvapdedpv 56 
                                    + + +   v +++++ +v
  gi|116754209|ref|YP_843327.1| 121 SLDSEGKAVKCKHCGACV 138
                                    344455566666666654 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.4      0.01        10       1      13 [.      30      42 ..      12      54 .. 0.78
   2 ?    0.3   1.5       1.3   1.3e+03       2      16 ..      73      89 ..      71      97 .. 0.70
   3 ?   13.7   2.5   8.6e-05     0.086      76      93 ..      99     116 ..      90     119 .. 0.84
   4 ?    7.3   1.1    0.0083       8.3      81      94 ..     130     143 ..     121     145 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.01
                        Fer4_22  1 rClsCgaCtlvCp 13
                                   rC++C +C ++C+
  gi|116754209|ref|YP_843327.1| 30 RCIGCLSCMFACS 42
                                   4666666666664 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.3
                        Fer4_22  2 ClsCg..aCtlvCptCs 16
                                   C +C   aC  +Cpt  
  gi|116754209|ref|YP_843327.1| 73 CHACEdpACVRACPTGA 89
                                   77776336999999865 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 8.6e-05
                        Fer4_22  76 kfgesgCvGCgRCieacp 93 
                                     f++  C GCgRC++ac 
  gi|116754209|ref|YP_843327.1|  99 VFDRDLCDGCGRCVDACL 116
                                    57899************7 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.0083
                        Fer4_22  81 gCvGCgRCieacpv 94 
                                    +C  Cg C++ cp+
  gi|116754209|ref|YP_843327.1| 130 KCKHCGACVAFCPH 143
                                    56666666666665 PP

>> MafB19-deam  MafB19-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.1   0.00033      0.33      54      91 ..      77     113 ..      65     131 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00033
                    MafB19-deam  54 EiaalqqAakklkskrlddatlyvtlepCdmCagaivq 91 
                                    E  a  +A+  ++ +r++d  ++ ++++Cd C++  v 
  gi|116754209|ref|YP_843327.1|  77 EDPACVRACPTGALSRKEDGSVVFDRDLCDGCGRC-VD 113
                                    556888**************************654.44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); 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):              18  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1143.29
//
Query:       gi|116754210|ref|YP_843328.1|  [L=578]
Description: aldehyde ferredoxin oxidoreductase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-67  227.9   0.0    2.4e-67  227.6   0.0    1.1  1  AFOR_C    Aldehyde ferredoxin oxidoreductase, domains 2 & 3
    3.5e-66  222.9   0.1      5e-66  222.3   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 !  227.6   0.0   2.7e-71   2.4e-67       3     366 ..     217     577 ..     215     578 .] 0.91

  Alignments for each domain:
  == domain 1  score: 227.6 bits;  conditional E-value: 2.7e-71
                                    HHHHHHHHHHSH.HHHHHHHH-GGGHHHHHHHTT---BTTTTBS--TTGGGGSHHHHHHHTEEEE.E-TT-SS--EEEEE CS
                         AFOR_C   3 gkkiqkeiksspqvtaelrkyGTaelvnianetgalptknfqegtfekaekisgealeekylvknegCfsCpiaCgrevk 82 
                                     ++i++ + ++++ +++++++GT+  vn++n  + lpt+nfq ++f++ae+isge+l+e+yl ++ +C+ Cpi C ++ +
  gi|116754210|ref|YP_843328.1| 217 YNRIYRMVVQTDA-MEKYHDLGTPMNVNVLNLLKGLPTRNFQSTSFAEAENISGERLAEEYLFRRVSCAHCPIGCIHVAM 295
                                    6678888888884.55***************************99********************99************* PP

                                    .......ET.....EE---HHHHHHHTGGGT---HHHHHHHHHHHHHHTB-HHHHHHHHHHHHHHHHTTSS-HHHHTS-- CS
                         AFOR_C  83 veegkk.vk.....vegpeyetlaalGsnlgiddleailklnelcdelGlDtisaGntiafamelyekGllkkedtdgle 156
                                     ++  +  +        ++ye +++lGsnlg++  e +l l ++c++lGlD +s+G ++++a e+yek+l++ ++t g++
  gi|116754210|ref|YP_843328.1| 296 LKTAFTpHHefevrRVSYDYEPIYSLGSNLGVTTAEGVLVLIDTCERLGLDAMSTGVVLSWATEAYEKDLITPQETLGVP 375
                                    998887544999996678************************************************************** PP

                                    --TT-THHHHHHHHHHHTT-T.THHHHTT-HHHHHHCTT-GGG--EETTEE--SS-GGG-HHHHHHHHH-TTSS-SGGG- CS
                         AFOR_C 157 lefgdaeallellekiAkreg.igdllAeGvkrlaeklgaeelamhvkGlelpaydprgakgmalaYatsnrGacHlray 235
                                    l++++ +  ++++e i    + + + lA Gv+ +a ++g+ ++am+  G e++ y      +  ++  +  r  +Hl++ 
  gi|116754210|ref|YP_843328.1| 376 LQWNNVKGYIKAMENIVAAPNeFYAALARGVEFAASRYGGMDFAMTLGGNEVSGYHTGP--ASIVGQLVGVR-HSHLDNA 452
                                    ****************999999*********************************8764..55556666666.5688855 PP

                                    THHHH..S---TT--HHHHHHHHHHHHHHHHHHHHT--GGGG-HHH......HHHHHHHHHT----HHHHHHHHHHHHHH CS
                         AFOR_C 236 liale..ekvdpletegkaelvkwfqdltalvdslglCkftseaeerldlelyakllsavtGidvteeellkaGeRiynl 313
                                     ++++   ++++l+ +  +  ++   d +++++sl+ C+f++     +++e++ ++l + +Gi+ ++eel + G+Ri+  
  gi|116754210|ref|YP_843328.1| 453 GYSIDqtAAKKQLDLSSMVDQIIKEDDSRSVFNSLVGCLFAR---GVYTEENIIDALGS-VGITKSKEELTELGRRIFME 528
                                    555554477888888999999999******************...6799********99.9******************* PP

                                    HHHHHHHHT--HHHS---HHHHHS---SSTTTT---..-HHHHHHHHHHHHT- CS
                         AFOR_C 314 eRlfnlreGltrkddtlperlleeplkegpakgkvledeleemldeyYelrGW 366
                                    +  f +reG++ ++ ++p+r++e   + g  +     + +e+m+  y e+rGW
  gi|116754210|ref|YP_843328.1| 529 KYRFKTREGFDLSKARIPRRFFETVSTLGRIDP----ETVEKMIALYKERRGW 577
                                    **********************77777777773....448************* 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 !  222.3   0.1   5.6e-70     5e-66       2     198 .]       4     202 ..       3     202 .. 0.96

  Alignments for each domain:
  == domain 1  score: 222.3 bits;  conditional E-value: 5.6e-70
                                    EEEEEETTTTEEEEEE--HHHHHHH-SCHHHHHHHHHHHS-TTS-TTSTTS-EEEEE-TTTTSSSTTB-EEEEEEE-TTT CS
                         AFOR_N   2 kilrvdLstgkieveelpeelaekylGgrglaakllldevppgvdplspenplvfatGpltgtpapgsgrlvvvaksPlt 81 
                                    ++l++dL++g+ +vee   +l+e++lGg+g+a+++ll+e+p+gvdplsp+ p++f++Gpl+ + +p+++++v+ +ksPlt
  gi|116754210|ref|YP_843328.1|   4 RVLYIDLTRGESWVEEKH-DLFEEWLGGTGVATQILLKETPEGVDPLSPDAPIIFSIGPLSTM-FPAMTKTVAQFKSPLT 81 
                                    89**************98.79***************************************987.**************** PP

                                    SSEEEEEEETCHHHHHHHCT-SEEEEES--SS-EEEEEETTEEEEEE-TTTTTS-HHHHHHHHHH.HHTS....EEEEE- CS
                         AFOR_N  82 gtlgesnaGgrfgaelkraGydaivieGkaekpvylvieddkveiedaedlwgldtyettealke.elgd....kvaviG 156
                                    g+lge++aGgr+++++++aG + ivi+G+ae+p+y++ie+d v+i+da+++wg ++  +   l++ e +     +++ iG
  gi|116754210|ref|YP_843328.1|  82 GELGECYAGGRLAMAMRFAGHESIVIRGRAERPCYISIENDVVRIRDATSIWGIGAARVGVILRDvE-KGvgrrSIIRIG 160
                                    *********************************************************9999999952.334667999*** PP

                                    HHHHTT-TTB-E.EETTEEE-SSSHHHHHHHTTEEEEEEE-- CS
                         AFOR_N 157 paGenlvrfAsisvddgraagrgGlGavmgsKnlkaivvrgt 198
                                    paGe++vr+A+++vd++r++gr GlGav+gsKnlkaiv++gt
  gi|116754210|ref|YP_843328.1| 161 PAGERMVRYACVVVDTYRHFGRLGLGAVFGSKNLKAIVISGT 202
                                    ***************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (578 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 4259.25
//
Query:       gi|116754211|ref|YP_843329.1|  [L=403]
Description: nucleotidyl transferase [Methanosaeta thermophila PT]
Scores for complete 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  112.8   0.0    2.3e-32  112.5   0.0    1.1  1  NTP_transferase  Nucleotidyl transferase
    1.3e-14   53.3  21.8    3.8e-10   39.1   0.8    4.6  4  Hexapep          Bacterial transferase hexapeptide (six repea
    3.5e-13   50.2   0.0    4.8e-13   49.8   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
     0.0016   17.4   0.4       0.16   10.9   0.1    2.4  2  Fucokinase       L-fucokinase
     0.0049   16.6   3.3     0.0049   16.6   3.3    4.2  4  Hexapep_2        Hexapeptide repeat of succinyl-transferase
  ------ inclusion threshold ------
      0.018   14.8   0.0      0.029   14.1   0.0    1.3  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
       0.14   10.2   1.5       0.22    9.6   1.5    1.2  1  DUF4954          Domain of unknown function (DUF4954)


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 !  112.5   0.0     9e-36   2.3e-32       2     246 ..       6     231 ..       5     233 .. 0.94

  Alignments for each domain:
  == domain 1  score: 112.5 bits;  conditional E-value: 9e-36
                                    EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEES CS
                NTP_transferase   2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialep 81 
                                    a+ILa G+G+R++PLt +++k ++pv+g  +l++  + r+ ++gi++ ++v+  +++  v +++k+gs+f+v++++a+++
  gi|116754211|ref|YP_843329.1|   6 AIILAAGEGSRMRPLTASRPKVMLPVGGA-PLLEELVLRCREAGINRFVFVVG-YRRDVVTSYFKDGSDFDVDISYAVQE 83 
                                    8****************************.*****************777776.8999********************** PP

                                    S--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECTTSBEEE CS
                NTP_transferase  82 egkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvieadeegrver 161
                                    ++ gt +A++ a++l +d++     +v++gD+l +    +a+++ i+ +    +++++ +v ea++yGv    + g ve 
  gi|116754211|ref|YP_843329.1|  84 KQLGTGHALMTARDLSDDRF-----FVINGDVLPD---VQALRRMISMED---LSVATHRVVEASRYGVFLLRD-GLVEG 151
                                    ***************99887.....7*********...789999999988...9999*************9998.89*** PP

                                    EECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEEXSSHHHHHHH CS
                NTP_transferase 162 fvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsDvGtldsllea 241
                                     vEK   ++ s++a++GiY+ ++e+++   + +  + rge e+td ++++ ++g++  a+  +    W  vG + ++l+a
  gi|116754211|ref|YP_843329.1| 152 VVEKSPSPP-SDMANAGIYLLDREIFELM-EEVPVSIRGEYELTDGINALASAGRKIWAIELSE---WVEVGVPWDILTA 226
                                    ****99999.9****************99.7799999*****************9998866655...************9 PP

                                    HHHHH CS
                NTP_transferase 242 nekla 246
                                    +++++
  gi|116754211|ref|YP_843329.1| 227 SNAVL 231
                                    99876 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.8   1.5e-13   3.8e-10       1      35 [.     251     285 ..     251     286 .. 0.95
   2 !   19.8   2.6   1.8e-07   0.00047       4      30 ..     278     304 ..     277     307 .. 0.93
   3 !   16.1   0.6   2.7e-06    0.0069       1      35 [.     304     337 ..     304     338 .. 0.88
   4 ?    4.1   0.7     0.016        40       2      24 ..     364     386 ..     363     387 .. 0.81

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 1.5e-13
                                    TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                        Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                    ++ IGs++l++++a+i g+V IG+n+ Ig++++i+
  gi|116754211|ref|YP_843329.1| 251 NVSIGSGTLVRNGAYIEGPVWIGRNCDIGPNCYIR 285
                                    589******************************98 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 1.8e-07
                                    EETTEEE-TTEEEETTEEE-TTEEEET CS
                        Hexapep   4 IGsnvlIgpfaviggnVkIGdnvkIga 30 
                                    IG n++I++++ ig+ V +G+ v I +
  gi|116754211|ref|YP_843329.1| 278 IGPNCYIRAGSCIGNSVRVGNAVEIKN 304
                                    9**********************9987 PP

  == domain 3  score: 16.1 bits;  conditional E-value: 2.7e-06
                                    TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                        Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                    +++I ++++Ig+ +++ g+ +IG ++ +gag+ + 
  gi|116754211|ref|YP_843329.1| 304 NSTIMDDTKIGHLSYV-GDSVIGYGCNLGAGTIVS 337
                                    579*************.5555**********9986 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.016
                                    EEEETTEEE-TTEEEETTEEE-T CS
                        Hexapep   2 tvIGsnvlIgpfaviggnVkIGd 24 
                                    ++ G++v+ g  + i+++++I +
  gi|116754211|ref|YP_843329.1| 364 VIMGDGVKTGVHTCIYPGTVIEP 386
                                    67899999999999999999865 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 !   49.8   0.0   1.9e-16   4.8e-13       1     110 [.       6     123 ..       6     181 .. 0.78

  Alignments for each domain:
  == domain 1  score: 49.8 bits;  conditional E-value: 1.9e-16
                                    EEEEEESS-TTTT.....TTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHH...TTCTS-EEE-.TTSS CS
                   NTP_transf_3   1 aviLAGGrSsRmg.....gdKallplggkpllervldalraagvdevvvvggd..eevlaal...arlgvrvved.edpg 69 
                                    a+iLA+G++sRm      ++K +lp+gg plle ++ + r+ag+++ v v+g+  + v++++    +++v++ +  ++++
  gi|116754211|ref|YP_843329.1|   6 AIILAAGEGSRMRpltasRPKVMLPVGGAPLLEELVLRCREAGINRFVFVVGYrrDVVTSYFkdgSDFDVDISYAvQEKQ 85 
                                    79**********6444435*************************999999988533445444221344555433323347 PP

                                    -SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHC CS
                   NTP_transf_3  70 kgplaslaaalraaadadavlvlacDmPlltpelverllaa 110
                                     g++++l +a + + ++d+++v+ +D+ l + ++++r++  
  gi|116754211|ref|YP_843329.1|  86 LGTGHALMTARD-L-SDDRFFVINGDV-LPDVQALRRMISM 123
                                    888888888887.4.79*********9.7799999999874 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    0.0085        22     277     314 ..     227     264 ..     222     286 .. 0.82
   2 !   10.9   0.1   6.2e-05      0.16     272     319 ..     298     345 ..     285     371 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.0085
                     Fucokinase 277 inSvlessvsvgegsviehsslkgnvsigsnsivsgle 314
                                     n+vl+ +v v +g v    +lkgnvsigs+++v +  
  gi|116754211|ref|YP_843329.1| 227 SNAVLSRKVPVMDGDVESGATLKGNVSIGSGTLVRNGA 264
                                    68899999999999999999***********9998754 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 6.2e-05
                     Fucokinase 272 esavvinSvlessvsvgegsviehsslkgnvsigsnsivsglelesse 319
                                    + + + nS +  + ++g  s++ +s ++ +++ g+++ivs+l+ ++ +
  gi|116754211|ref|YP_843329.1| 298 NAVEIKNSTIMDDTKIGHLSYVGDSVIGYGCNLGAGTIVSNLRHDNRN 345
                                    567799************************************998763 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 ?    2.3   0.3     0.056   1.4e+02      17      32 ..     250     266 ..     242     268 .. 0.77
   2 !   16.6   3.3   1.9e-06    0.0049       1      28 [.     269     298 ..     269     304 .. 0.85
   3 !    4.7   0.7    0.0099        25      10      32 ..     313     336 ..     306     338 .. 0.67
   4 ?   -2.3   0.1       1.5   3.8e+03      17      25 ..     363     371 ..     362     375 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.056
                                    S.EEE-TT-EE-TT-EE CS
                      Hexapep_2  17 G.vslGdncvvgaGvvi 32 
                                    G vs+G +  v +G +i
  gi|116754211|ref|YP_843329.1| 250 GnVSIGSGTLVRNGAYI 266
                                    55999999999999998 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1.9e-06
                                    .EEE-TT-EE-TT-EE..SEEE-TT-EE-T CS
                      Hexapep_2   1 pviIGdnCliGanagi..GvslGdncvvga 28 
                                    pv IG nC iG+n++i  G  +G+ + vg+
  gi|116754211|ref|YP_843329.1| 269 PVWIGRNCDIGPNCYIraGSCIGNSVRVGN 298
                                    789************999988888888876 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.0099
                                    E-TT-EES.EEE-TT-EE-TT-EE CS
                      Hexapep_2  10 iGanagiG.vslGdncvvgaGvvi 32 
                                    iG  +++G   +G +c +gaG ++
  gi|116754211|ref|YP_843329.1| 313 IGHLSYVGdSVIGYGCNLGAGTIV 336
                                    666666644667778888888766 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 1.5
                                    SEEE-TT-E CS
                      Hexapep_2  17 GvslGdncv 25 
                                    Gv+ Gd+++
  gi|116754211|ref|YP_843329.1| 363 GVIMGDGVK 371
                                    899999985 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 ?   14.1   0.0   1.1e-05     0.029       1      40 [.       4      46 ..       4      67 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.1e-05
                                   EEEEEECTTSSCTT-...SSS-GGGSEETTEEHHHHHHHHHHC CS
                           IspD  1 vvvvipAAGsGkRmk...aglpKqflelkgqtllehtvdalla 40
                                   + ++i AAG+G+Rm+   a +pK  l + g +lle+ v    +
  gi|116754211|ref|YP_843329.1|  4 MQAIILAAGEGSRMRpltASRPKVMLPVGGAPLLEELVLRCRE 46
                                   579**********9644489***************98866655 PP

>> DUF4954  Domain of unknown function (DUF4954)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.5   8.5e-05      0.22     192     257 ..     271     333 ..     237     344 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 8.5e-05
                        DUF4954 192 kigdyatiegasklengtinSskeapveiGegViledfiissGskikdgavisrcfvGqavklkkq 257
                                     ig  + i     ++ g+ + +    v++G+ V+++++ i+  +ki + + + ++++G +++l+ +
  gi|116754211|ref|YP_843329.1| 271 WIGRNCDIGPNCYIRAGSCIGN---SVRVGNAVEIKNSTIMDDTKIGHLSYVGDSVIGYGCNLGAG 333
                                    4444444444444444443333...35555555555555555555555555555555555555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         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: 00:00:00.43
# Mc/sec: 2787.53
//
Query:       gi|116754212|ref|YP_843330.1|  [L=83]
Description: hypothetical protein Mthe_0902 [Methanosaeta thermophila PT]
Scores for complete 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   95.1   0.8    2.1e-27   94.9   0.8    1.0  1  HTH_45    Winged helix-turn-helix
     0.0013   18.5   0.1     0.0015   18.3   0.1    1.2  1  DUF4364   Domain of unknown function (DUF4364)


Domain annotation for each model (and alignments):
>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.9   0.8   2.4e-31   2.1e-27       1      73 [.       4      78 ..       4      81 .. 0.95

  Alignments for each domain:
  == domain 1  score: 94.9 bits;  conditional E-value: 2.4e-31
                         HTH_45  1 rRskleIiadILeaisegeakkTkimykanLsykllnkYLdmLvekgli...kkskekYvlTekGlelleklkele 73
                                   rRsk +I++dILe++  ++a+kTki+y+anL++k+ln+YLd+L++kgl+   ++++++Yv+Te+Gl++le++++++
  gi|116754212|ref|YP_843330.1|  4 RRSKAQIMSDILEIC-IDGANKTKIVYDANLNFKMLNSYLDTLTKKGLLhvrNDRSNEYVTTEEGLRILETCRCID 78
                                   8**************.********************************8777779*****************9985 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   1.7e-07    0.0015      27      73 ..      29      74 ..      10      76 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.7e-07
                        DUF4364 27 eneytnYfdlqqalseLvesglieeeekenktlykiTekGketlelf 73
                                    +  +n+  l+++l+ L+++gl+++++ + ++ y  Te+G ++le++
  gi|116754212|ref|YP_843330.1| 29 YDANLNFKMLNSYLDTLTKKGLLHVRN-DRSNEYVTTEEGLRILETC 74
                                   455689******************965.8899999********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); 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: 0.34u 0.27s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 614.94
//
Query:       gi|116754213|ref|YP_843331.1|  [L=462]
Description: dihydrolipoamide dehydrogenase [Methanosaeta thermophila PT]
Scores for complete 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  175.9   0.0      2e-51  175.0   0.0    1.4  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    3.5e-23   82.0   0.3    6.3e-23   81.1   0.3    1.4  1  Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase,
    2.3e-16   60.1   1.0    5.6e-16   58.9   0.0    2.2  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    9.7e-07   28.3   0.1    3.1e-06   26.7   0.0    1.8  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    7.4e-05   22.0   4.3      0.005   16.0   0.9    2.9  3  FAD_binding_2  FAD binding domain
     0.0052   15.5   0.2      0.011   14.4   0.2    1.6  1  HI0933_like    HI0933-like protein
  ------ inclusion threshold ------
      0.083   12.8   0.6       0.42   10.5   0.0    2.1  2  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
       0.13   11.3   1.5        0.3   10.1   0.5    2.0  3  Lycopene_cycl  Lycopene cyclase protein


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.0   0.0   8.8e-55     2e-51       1     291 [.       5     319 ..       5     322 .. 0.82

  Alignments for each domain:
  == domain 1  score: 175.0 bits;  conditional E-value: 8.8e-55
                                    CSEEEE--SHHHHHHHHHHHHHTS-EEEEE...TTHCHHHCSHHHHCHHHHHHHHHHHHH........HHHHCHHHH.CC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxx.xx RF
                    Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve...legtclnggcllskallgvaedaeias........evvkklnqg.ie 68 
                                    +dv+viG+G AGl +a+++   g++v+l+e   l+gtcln gc++sk l + a+  + ++         +v+++  + i+
  gi|116754213|ref|YP_843331.1|   5 YDVIVIGSG-AGLIVAQRALFEGLRVALIEhgpLGGTCLNTGCIPSKMLIHPADIVRMVEdgsrlgikAHVDSIDFEfIM 83 
                                    69*******.677777888888*******99******************999999998889*******667777766666 PP

                                    CCHC...............CT.CEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHH CS
                                    xxxx...............xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  69 lllg...............ee.vvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtlds 132
                                    ++++               ee  ++ ++  + ++  ++ +  ee+i++ ++v+A G+++  +++ G++e +     +ld+
  gi|116754213|ref|YP_843331.1|  84 KRMRdlieaergemekaigEEeQLRWYRSTGVFVGDHLIRVGEEEITAPWIVIAAGARTLVPPVAGLGEAG-----YLDN 158
                                    66662222222222222223335555555555555555558999***********************5555.....79** PP

                                    HHHHCCSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHT.TEEEEESCEEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                    Pyr_redox_2 133 aealklkllpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealeke.Gvevklgtsvkeidg 211
                                    +  ++l++ p+++++ GgGyi++E+  +++ +g++vt+v +++rll++ d+e+s+++ +al k+  +++ +++  ++++g
  gi|116754213|ref|YP_843331.1| 159 VSVFSLAKPPESLIILGGGYIACEFGHFFSAMGSDVTIVGRNPRLLKSEDHEISDMALKALSKHmRIHTNMEAIRVDLEG 238
                                    ***************************************************************97777777776667777 PP

                                    TTEEEEEEETTSCE...EEESEEEE-S-EEES-HHCS.HCCT-EEEETTEEE--TTSBESSTTEEE-GGGCTECCSS--H CS
                                    xxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 212 ngeklevvledgee...idadlvvvavGvrpstelle.eklglelderggivvdeflrtnvpgiyaiGDvaggkggpela 287
                                     ++ ++ ++ +  e   +  d +++a+G+rp+t+ l+ ek+g+e+d++g++ v+e+l+t+ pgi+a+GD++   g+ +  
  gi|116754213|ref|YP_843331.1| 239 GKKVVTAIDRSRGEtvsFVGDEILLAAGRRPNTDMLQpEKSGVEIDRAGWVRVNEHLETTAPGIWALGDIT---GKHMFR 315
                                    77766644333333466******************************************************...666666 PP

                                    HHHH CS
                                    xxxx RF
                    Pyr_redox_2 288 qaAv 291
                                    ++A 
  gi|116754213|ref|YP_843331.1| 316 HTAN 319
                                    6665 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 !   81.1   0.3   2.8e-26   6.3e-23       1     108 [.     347     454 ..     347     456 .. 0.91

  Alignments for each domain:
  == domain 1  score: 81.1 bits;  conditional E-value: 2.8e-26
                                    BEEEEESSSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTHTEEEEEEEEETTTTBEEEEEEECTTHHHHHHHHH CS
                  Pyr_redox_dim   1 iptvvftdpevasvGlteeeAkaagieikvgkfpfkangralayaetkgfvKlvadaktgkvlGahivGpgageliqela 80 
                                    +p ++ft p++a vG+tee+A+a+g++i vg++++k+++   a+ +++g++K ++da++g++lG+h++G +a el+q+++
  gi|116754213|ref|YP_843331.1| 347 VPHAIFTYPQIAGVGMTEEQARANGYDILVGRAYYKQTAMGYAM-DEDGMAKAIVDARSGRILGFHVIGSSAPELVQQVT 425
                                    799********************************876555444.49********************************* PP

                                    HHHHTTS.BHHHHHTSBSSSSSTGGGGHC CS
                  Pyr_redox_dim  81 vaikagl.tvedladtihihPtlsealke 108
                                     +++a+   v  +a+   ihP +se++  
  gi|116754213|ref|YP_843331.1| 426 YLMNAENqDVTPMARSQVIHPAISEVVAR 454
                                    ****99835668************99876 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.2       2.5   5.5e+03       2      29 ..       7      33 ..       6      36 .. 0.68
   2 !   58.9   0.0   2.5e-19   5.6e-16       2      77 ..     171     243 ..     170     250 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.5
                                   EEEECSSHHHHHHHHHHHHTTSEEEEEE CS
                      Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvve 29
                                   v+v+G+G  gl +A+ +   g +V ++e
  gi|116754213|ref|YP_843331.1|  7 VIVIGSGA-GLIVAQRALFEGLRVALIE 33
                                   78999995.6667766666666666666 PP

  == domain 2  score: 58.9 bits;  conditional E-value: 2.5e-19
                                    EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEE CS
                      Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedgvesvk 77 
                                    ++++GgGyi++E++ +++++g++Vt+v r+++ll+ +D+e+s++  + l+k+ +++++n ++ +++ ++ +  +v+
  gi|116754213|ref|YP_843331.1| 171 LIILGGGYIACEFGHFFSAMGSDVTIVGRNPRLLKSEDHEISDMALKALSKH-MRIHTNMEAIRVDLEGGK--KVV 243
                                    79*************************************************9.************976665..233 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.9      0.94   2.1e+03       1      34 [.       8      39 ..       8      43 .. 0.87
   2 !   26.7   0.0   1.4e-09   3.1e-06     119     305 .]     125     306 ..     118     306 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.94
                    Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgnign 34
                                   i+iG G aGl +a  +   gl ++  +E g +g 
  gi|116754213|ref|YP_843331.1|  8 IVIGSG-AGLIVAQRALFEGL-RVALIEHGPLGG 39
                                   89***9.69*****9999999.799999998875 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 1.4e-09
                    Pyr_redox_3 119 sketyeAkkviiAtGefdkPnklnipGeeklvkhyskvkefhkya.gqkvvViGgknSavDaAlelvrkgaeVtvvtrgs 197
                                     +e+++A+ ++iA+G   +  ++ + G  + +    +v+ f+  +  + +++ Gg+  a++    + ++g++Vt+v r+ 
  gi|116754213|ref|YP_843331.1| 125 GEEEITAPWIVIAAGA--RTLVPPVAGLGE-AGYLDNVSVFSLAKpPESLIILGGGYIACEFGHFFSAMGSDVTIVGRNP 201
                                    5689999999999999..777788888773.3333344444333326899999*************************** PP

                    Pyr_redox_3 198 eiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekeeeykvk...tedgkkvev.kddvvlatGykpdlsf 273
                                     + k+e   + +++ +  + l +     ++++++n e+ +++ +  +  v+    ++g++v+   d+++la G +p++++
  gi|116754213|ref|YP_843331.1| 202 RLLKSE---DHEISDMALKALSK-----HMRIHTNMEAIRVDLEGGKKVVTaidRSRGETVSFvGDEILLAAGRRPNTDM 273
                                    999886...45566666666654.....4678888888888865555444422267777776547888888********* PP

                    Pyr_redox_3 274 lkk..slfeldedgrpvlteeteetnvpglflaG 305
                                    l+   s++e+d+ g++ ++e+  et+ pg++  G
  gi|116754213|ref|YP_843331.1| 274 LQPekSGVEIDRAGWVRVNEHL-ETTAPGIWALG 306
                                    *99889************9876.56699998776 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.9   2.2e-06     0.005       1      33 [.       6      37 ..       6      46 .. 0.90
   2 !    5.0   0.0    0.0047        11     147     206 ..     215     273 ..     197     284 .. 0.80
   3 ?    0.3   0.0      0.13   2.8e+02     376     406 ..     289     313 ..     277     324 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.2e-06
                                   SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSG CS
                  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqe 33
                                   DviViGsG+ GL  A +a  +Gl+va++e ++ 
  gi|116754213|ref|YP_843331.1|  6 DVIVIGSGA-GLIVAQRALFEGLRVALIEHGPL 37
                                   9*******7.*******************9985 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0047
                                    HHHHHHTCTEEEEESEEEEEEEECTT.EEEEEEEEETTTTCEEEEEESEEEE-----GG... CS
                  FAD_binding_2 147 lvesarkagvdfqerteadeLivedg.rvtGavvenpesgrevrirakavvlatgGfgr.al 206
                                     ++++ + ++++++++ea ++  e+g +v++a+ +  + g++v ++ + ++la+g  ++ ++
  gi|116754213|ref|YP_843331.1| 215 ALKAL-SKHMRIHTNMEAIRVDLEGGkKVVTAIDR--SRGETVSFVGDEILLAAGRRPNtDM 273
                                    44444.55589999999999999988899999888..******************9998544 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.13
                                    EEBETTSBESTTEEESSBTEEE-STCEESSS CS
                  FAD_binding_2 376 vetdengrvldadgqpipGLYAaGevaaggv 406
                                    v+++e++      +++ pG +A G  ++ ++
  gi|116754213|ref|YP_843331.1| 289 VRVNEHL------ETTAPGIWALGDITGKHM 313
                                    4455555......55**********997665 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.2   5.1e-06     0.011       1      33 [.       5      36 ..       5      45 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.1e-06
                                   -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
                    HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekak 33
                                   +dviviG G AGl  A +a  +g rV+l+e+++
  gi|116754213|ref|YP_843331.1|  5 YDVIVIGSG-AGLIVAQRALFEGLRVALIEHGP 36
                                   59*******.6********************86 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 ?   -0.0   0.2      0.31     7e+02       2      29 ..       7      33 ..       6      37 .. 0.89
   2 ?   10.5   0.0   0.00019      0.42       4      62 ..     173     231 ..     170     249 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.31
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE- CS
                        3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvd 29
                                   v viG+G  G  +a+ ++ +gl+V l++
  gi|116754213|ref|YP_843331.1|  7 VIVIGSGA-GLIVAQRALFEGLRVALIE 33
                                   78999997.999*************997 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00019
                                    EE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHH.HHHCCTTTTSS-HHHHCC CS
                        3HCDH_N   4 viGaGtmGagiaavfasagleVvlvdiseealekalekiek.sleklvekgklkeeevea 62 
                                    ++G G +  +  + f + g +V++v ++++ l++  ++i++  l+ l ++ +++  ++ea
  gi|116754213|ref|YP_843331.1| 173 ILGGGYIACEFGHFFSAMGSDVTIVGRNPRLLKSEDHEISDmALKALSKHMRIH-TNMEA 231
                                    89**************************************95556665555555.44444 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.5   0.00013       0.3       1      34 [.       6      36 ..       6      43 .. 0.94
   2 ?   -3.9   0.0       2.3   5.2e+03     126     143 ..     125     142 ..     121     148 .. 0.79
   3 ?   -1.3   0.0      0.39   8.8e+02       2      45 ..     171     212 ..     170     247 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00013
                  Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieasp 34
                                   Dv+viG+G Agl +A+r      gl+v lie +p
  gi|116754213|ref|YP_843331.1|  6 DVIVIGSG-AGLIVAQRA--LFEGLRVALIEHGP 36
                                   9*******.8********..999********998 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 2.3
                  Lycopene_cycl 126 ggrkirarlvvdarglas 143
                                    g+++i a+++v a g+  
  gi|116754213|ref|YP_843331.1| 125 GEEEITAPWIVIAAGART 142
                                    67899*******999655 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.39
                  Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlieaspsllfpnnyvWs 45 
                                    +++ G+G   +   +    +++g  v+++   p ll + ++  s
  gi|116754213|ref|YP_843331.1| 171 LIILGGGYIACEFGHFF--SAMGSDVTIVGRNPRLLKSEDHEIS 212
                                    79999999999999999..9999999999999999888887333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (462 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3206.84
//
Query:       gi|116754214|ref|YP_843332.1|  [L=47]
Description: YHS domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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-21   74.5   1.9    5.6e-21   74.4   1.9    1.0  1  YHS              YHS domain
     0.0022   18.3   0.7     0.0023   18.2   0.4    1.3  1  Arc_trans_TRASH  Archaeal TRASH domain
  ------ inclusion threshold ------
      0.015   16.0   0.1      0.017   15.8   0.1    1.1  1  ATPase-cat_bd    Putative metal-binding domain of cation tran
      0.063   13.5   0.0      0.063   13.5   0.0    1.1  1  DUF2011          Fungal protein of unknown function (DUF2011)
       0.18   11.3   0.1        0.2   11.1   0.1    1.0  1  FAP206           Domain of unknown function


Domain annotation for each model (and alignments):
>> YHS  YHS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.4   1.9   1.6e-24   5.6e-21       2      45 ..       3      46 ..       2      47 .] 0.97

  Alignments for each domain:
  == domain 1  score: 74.4 bits;  conditional E-value: 1.6e-24
                            YHS  2 tdPvcgmkvdkekaeekseYkGkeYyFcSegCkdkFedePekYa 45
                                   +dPvc+m vd ++a++ seY G++YyFcS+gCk +F+++PekY+
  gi|116754214|ref|YP_843332.1|  3 IDPVCKMEVDEGTAKFVSEYRGRRYYFCSPGCKKAFDKDPEKYL 46
                                   8******************************************8 PP

>> Arc_trans_TRASH  Archaeal TRASH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.4   6.5e-07    0.0023      14      35 ..      19      40 ..      11      42 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 6.5e-07
                Arc_trans_TRASH 14 vyklknkvYyvCCktCkselkk 35
                                   v +++ + Yy+C + Ck+ + k
  gi|116754214|ref|YP_843332.1| 19 VSEYRGRRYYFCSPGCKKAFDK 40
                                   678999************9987 PP

>> ATPase-cat_bd  Putative metal-binding domain of cation transport ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   0.1   4.8e-06     0.017       5      35 ..       7      38 ..       6      44 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.8e-06
                  ATPase-cat_bd  5 Cglpveesa.klkaeiegeerefCCkGCqava 35
                                   C+ +v+e++ k+ +e++g++ +fC +GC+  +
  gi|116754214|ref|YP_843332.1|  7 CKMEVDEGTaKFVSEYRGRRYYFCSPGCKKAF 38
                                   999998876599****************9876 PP

>> DUF2011  Fungal protein of unknown function (DUF2011)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.8e-05     0.063      28      48 ..      12      32 ..       4      46 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.8e-05
                        DUF2011 28 eegeggfivpeRpksYYfaep 48
                                   +eg ++f+ + R+++YYf +p
  gi|116754214|ref|YP_843332.1| 12 DEGTAKFVSEYRGRRYYFCSP 32
                                   368899************997 PP

>> FAP206  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   5.6e-05       0.2     225     252 ..      19      46 ..      15      47 .] 0.93

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.6e-05
                         FAP206 225 vlkykdkyyaFsseeaareFaadpdrfi 252
                                    v +y+++ y F s+ + ++F +dp++++
  gi|116754214|ref|YP_843332.1|  19 VSEYRGRRYYFCSPGCKKAFDKDPEKYL 46 
                                    678************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 354.19
//
Query:       gi|116754215|ref|YP_843333.1|  [L=802]
Description: heavy metal translocating P-type ATPase [Methanosaeta thermophila PT]
Scores for complete 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-58  195.0   0.9    2.1e-57  193.6   0.1    2.2  2  E1-E2_ATPase  E1-E2 ATPase
    4.2e-48  164.4   2.2    6.9e-48  163.7   2.2    1.4  1  Hydrolase     haloacid dehalogenase-like hydrolase
    1.9e-33  114.7   1.8    4.4e-17   62.3   0.0    2.9  2  HMA           Heavy-metal-associated domain
    3.5e-07   30.2   0.4       0.01   15.6   0.1    2.3  2  Hydrolase_3   haloacid dehalogenase-like hydrolase
     0.0099   16.3   0.1      0.044   14.2   0.1    2.0  1  HAD           haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.013   15.6   0.1       0.07   13.3   0.0    2.1  2  Tox-PL-2      Papain fold toxin 2
       0.17   12.0   0.6         27    4.8   0.0    2.8  3  DUF1940       Domain of unknown function (DUF1940)
       0.68   10.3   2.9         15    6.0   0.2    3.4  3  Fer2_BFD      BFD-like [2Fe-2S] 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 ?   -1.5   0.1       0.7   1.6e+03     114     158 ..     151     193 ..     138     212 .. 0.57
   2 !  193.6   0.1   9.2e-61   2.1e-57       2     179 ..     283     467 ..     282     469 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.7
                                    HHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHHH CS
                   E1-E2_ATPase 114 kldklgkvlvpvvlliallvflialllgkslaeallralallvaa 158
                                     ++ l + + ++++ +++ ++l+al++  +   + + +++++ +a
  gi|116754215|ref|YP_843333.1| 151 RARDLRERMRKIIVGFGASALLMALMYLAPM--THTMSIVMMCVA 193
                                    4455555555556666666666666655554..222334444444 PP

  == domain 2  score: 193.6 bits;  conditional E-value: 9.2e-61
                                    SS--EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEEE-EE CS
                   E1-E2_ATPase   2 llpptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvvsgea 81 
                                    l+p+ta++i dg+e+ei+a+ ++pGDi+l+++g+rvpaDg+i+eg+  vdes++ GE +pv k+ g++v++Gt +++  +
  gi|116754215|ref|YP_843333.1| 283 LQPRTATLIVDGSEKEIPAEMVKPGDIILIRPGERVPADGEIIEGEGYVDESMISGEPVPVLKKPGSQVIGGTLNKNAAL 362
                                    89****************************************************************************** PP

                                    EEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTT.......HHHHHHHHH CS
                   E1-E2_ATPase  82 kavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgksla.......eallralal 154
                                    k+++ ++g++t+l++i++lv +a+ +++++q+ +d++++v++p+vl ia+l fl++++ g+s         +a+ +++++
  gi|116754215|ref|YP_843333.1| 363 KMRAMRVGRETFLAQIIDLVDKAQGSRPEIQRLADRVVGVFIPIVLSIAILSFLAWYFFGRSYLpedrilmFAISSMISV 442
                                    **************************************************************99**************** PP

                                    HHHHS-TTHHHHHHHHHHHHHHHHH CS
                   E1-E2_ATPase 155 lvaaiPcaLplavplalalgarrla 179
                                    lv+a+PcaL+la+p+a+++g++r a
  gi|116754215|ref|YP_843333.1| 443 LVVACPCALGLATPTAVTVGIGRGA 467
                                    **********************988 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.7   2.2   3.1e-51   6.9e-48       2     210 .]     486     698 ..     485     698 .. 0.95

  Alignments for each domain:
  == domain 1  score: 163.7 bits;  conditional E-value: 3.1e-51
                                    SEEEEESBTTTBCHHHHHHHHHHHH.CHHHHHHHHHHHHCHHHHHHHHHHHHH...HHHHHHHHHETTTE........HH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxx........xx RF
                      Hydrolase   2 ktvvfDkdGTLttgepsvedvivsa.alalaaaletgsehpigkalvaaakar...sgaltgfatfigrg........ay 69 
                                    +tv+fDk+GTLt g+p+v++++     l laa +e  sehp+g+a+v+ a       +++++f +f+g g        ++
  gi|116754215|ref|YP_843333.1| 486 TTVIFDKTGTLTVGRPEVTEIVGDErMLRLAAGIESRSEHPLGEAIVRMAISKgidIPETKDFYAFPGMGvvgvvdgvEV 565
                                    69******************99888789999999999*************9995544444******************** PP

                                    HHTHHHHHHHH..HCHHHHHHHHHHHHHHCHHHHHH..TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEH CS
                                    xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase  70 aigkpewltal..dippdlgaaigsaqsqgrtvall..qaralavftiadplkvkpeaaeavasLkaagievvlltgdnp 145
                                    a+g++ ++ +    ip+d+ ++ +++++ g+tv ++  ++ a + f+i+d   +k+ a+ av++Lk++g++vv++tgdn 
  gi|116754215|ref|YP_843333.1| 566 AVGNRSFISERgtRIPDDMLERASALEELGQTVLFVsvSGAAAGAFAISDA--IKDSAKAAVQKLKSMGLDVVMITGDNI 643
                                    ************************************9999***********..*************************** PP

                                    HHHHHHHHHTTGGGESEEEEHHCES.STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 146 etaeraanqlGddyfdaviasdiet.vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                    + a+++a+q+G           ie+ +a+++p++k   +r+Lq  ++ va+VGDg+nDa+ala+A+
  gi|116754215|ref|YP_843333.1| 644 RSARSVAEQIG-----------IEEvHAEVLPQDKASEVRKLQQAGRTVAFVGDGINDAPALAQAD 698
                                    ***********...........6666*****************99999*****************8 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.3   0.0     2e-20   4.4e-17       2      62 .]       7      66 ..       6      66 .. 0.97
   2 !   50.6   0.7     9e-17     2e-13       1      62 []      73     134 ..      73     134 .. 0.98

  Alignments for each domain:
  == domain 1  score: 62.3 bits;  conditional E-value: 2e-20
                            HMA  2 vrvsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaestklrkiieaiekagyk 62
                                   +r+sgm+Ca Ca+++e++L e +gVes++v+l++ t+ Ve+d++ +kl+++ +ai++agy+
  gi|116754215|ref|YP_843333.1|  7 IRISGMTCATCASTIESALRE-KGVESASVNLGSETAHVEYDPSRLKLSELERAIRDAGYD 66
                                   79*****************77.**************************************7 PP

  == domain 2  score: 50.6 bits;  conditional E-value: 9e-17
                            HMA   1 tvrvsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaestklrkiieaiekagyk 62 
                                    tv+v gm Ca C+++v +++ e++gV++v+v+l t ++ V++++  ++l +i++a+e+agy+
  gi|116754215|ref|YP_843333.1|  73 TVKVGGMVCATCESTVADAIREIDGVSDVTVNLSTEKAYVTYNPKVVSLDDIRRAVEDAGYQ 134
                                    799*********************************************************95 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   3.9e-05     0.087      16      55 ..     617     656 ..     613     663 .. 0.92
   2 !   15.6   0.1   4.6e-06      0.01     202     239 ..     677     714 ..     666     723 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.9e-05
                                    --HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCC CS
                    Hydrolase_3  16 isektkeaikklkekgikvviATGRslravlpvleelgld 55 
                                    i++++k+a++klk+ g  vv  TG ++r++++v+e++g++
  gi|116754215|ref|YP_843333.1| 617 IKDSAKAAVQKLKSMGLDVVMITGDNIRSARSVAEQIGIE 656
                                    8999**********************************98 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 4.6e-06
                                    -GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHS CS
                    Hydrolase_3 202 sleeviafGDgeNDieMLeaaglgvAmgnaseevkkaA 239
                                        v+ +GDg ND + L +a+lg+A+g++++ +++a 
  gi|116754215|ref|YP_843333.1| 677 AGRTVAFVGDGINDAPALAQADLGIAIGSGTDVAIEAG 714
                                    55678889***********************9998875 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.1   1.9e-05     0.044      87     187 ..     618     694 ..     604     695 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.9e-05
                            HAD  87 dpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrgegkvaalrewlaaeg 166
                                    +  a++++++ ++ G  vv+++g + + ++ ++++ g++ev a+                  v  ++k++++r+ l+++g
  gi|116754215|ref|YP_843333.1| 618 KDSAKAAVQKLKSMGLDVVMITGDNIRSARSVAEQIGIEEVHAE------------------VLPQDKASEVRK-LQQAG 678
                                    45799999*999*************************5555555..................233344455555.33333 PP

                            HAD 167 egidleevvayGDspsDlpll 187
                                          +v ++GD+++D p+l
  gi|116754215|ref|YP_843333.1| 679 -----RTVAFVGDGINDAPAL 694
                                    .....235566********98 PP

>> Tox-PL-2  Papain fold toxin 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.1e-05      0.07      12      47 ..       8      43 ..       3      67 .. 0.83
   2 ?   -0.8   0.0      0.76   1.7e+03      12      45 ..      75     109 ..      66     116 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.1e-05
                       Tox-PL-2 12 rfklleCveCAaalekyLkeqgisGkrlklktksae 47
                                   r++ + C +CA+++e++L+e+g++   ++l +++a+
  gi|116754215|ref|YP_843333.1|  8 RISGMTCATCASTIESALREKGVESASVNLGSETAH 43
                                   567899******************999998776655 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.76
                       Tox-PL-2  12 rfklleCveCAaalekyLke.qgisGkrlklktks 45 
                                    ++  + C +C ++++++++e  g+s  +++l+t++
  gi|116754215|ref|YP_843333.1|  75 KVGGMVCATCESTVADAIREiDGVSDVTVNLSTEK 109
                                    566788********999987457887788888776 PP

>> DUF1940  Domain of unknown function (DUF1940)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       3.7   8.4e+03      43      63 ..     476     496 ..     464     497 .. 0.69
   2 ?    4.8   0.0     0.012        27      19      44 ..     522     547 ..     512     551 .. 0.88
   3 ?    4.1   0.1     0.021        47      24      54 ..     694     725 ..     689     738 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.7
                                    HHHHHHHHHHHHTTT------ CS
                        DUF1940  43 relldilDtlyqslsDpeskL 63 
                                     e l+  D+l+  + D+  +L
  gi|116754215|ref|YP_843333.1| 476 GEALEASDKLTTVIFDKTGTL 496
                                    467778888888888876655 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.012
                                    HHHHHHHHHHHHHHHHT-SSHHHHHH CS
                        DUF1940  19 rseiklaeaslGlaiseGikvqatre 44 
                                    rse  l ea + +ais+Gi +++t++
  gi|116754215|ref|YP_843333.1| 522 RSEHPLGEAIVRMAISKGIDIPETKD 547
                                    567778999***************97 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.021
                                    HHHHHHHHHHHT-SSHH.HHHHHHHHHHHHHH CS
                        DUF1940  24 laeaslGlaiseGikvq.atrelldilDtlyq 54 
                                    la+a lG+ai +G  v  +  e++ i D l++
  gi|116754215|ref|YP_843333.1| 694 LAQADLGIAIGSGTDVAiEAGEIVLIRDDLMD 725
                                    89***********9997467899888888765 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 ?    1.9   0.1      0.13   2.9e+02      35      50 ..      11      26 ..       5      27 .. 0.85
   2 ?    6.0   0.2    0.0067        15      12      50 ..      55      93 ..      50      94 .. 0.77
   3 ?   -0.3   0.0      0.65   1.5e+03       8      22 ..     119     133 ..     117     143 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.13
                       Fer2_BFD 35 gtgCggCrpaieeiLa 50
                                   g+ C++C   ie  L+
  gi|116754215|ref|YP_843333.1| 11 GMTCATCASTIESALR 26
                                   788********99886 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0067
                       Fer2_BFD 12 eIrdairraglttveevkrrtkagtg.CggCrpaieeiLa 50
                                   e+++air ag   ++e ++ +k+g+  C++C+  +++ ++
  gi|116754215|ref|YP_843333.1| 55 ELERAIRDAGYDVINE-RATVKVGGMvCATCESTVADAIR 93
                                   7888996665555555.5889999999******9998775 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.65
                       Fer2_BFD   8 vtegeIrdairragl 22 
                                    v+ ++Ir+a++ ag 
  gi|116754215|ref|YP_843333.1| 119 VSLDDIRRAVEDAGY 133
                                    7889******77765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (802 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       912  (0.0508673); expected 358.6 (0.02)
Passed bias filter:                      615  (0.034302); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.71u 0.29s 00:00:01.00 Elapsed: 00:00:00.43
# Mc/sec: 5567.94
//
Query:       gi|116754216|ref|YP_843334.1|  [L=120]
Description: hypothetical protein Mthe_0906 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-08   33.7   1.7    2.9e-08   33.2   1.7    1.3  1  SHOCT           Short C-terminal domain
  ------ inclusion threshold ------
      0.011   16.2   3.4      0.013   15.9   3.4    1.2  1  DUF4199         Protein of unknown function (DUF4199)
      0.027   14.3   0.1      0.045   13.6   0.1    1.3  1  VbhA            Antitoxin VbhA
       0.04   13.5   4.7      0.049   13.2   4.7    1.0  1  Virul_fac_BrkB  Virulence factor BrkB
       0.12   12.3   0.4       0.14   12.1   0.4    1.1  1  Wzy_C_2         Virulence factor membrane-bound polymerase, C
        5.5    7.2   6.0         10    6.3   6.0    1.4  1  DUF3099         Protein of unknown function (DUF3099)


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 !   33.2   1.7   9.6e-12   2.9e-08       3      27 ..      91     115 ..      89     116 .. 0.93

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 9.6e-12
                          SHOCT   3 LekLkeLyarGeIteEEFeakKakL 27 
                                      +L+e+yarGe+t++E+ ++K++L
  gi|116754216|ref|YP_843334.1|  91 ESILDERYARGELTRDEYLRMKEDL 115
                                    679********************98 PP

>> DUF4199  Protein of unknown function (DUF4199)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.9   3.4   4.5e-06     0.013       6      65 ..      31      88 ..      22      94 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.5e-06
                        DUF4199  6 lglvwilifllilyllglh.qi.lstgpllgllallllllvpflvylalkkyrkknlgGfis 65
                                   +  +w+++ + i+yl+ ++ +   ++g l+++l++l ++   fl++++lk  r+++ gG+i+
  gi|116754216|ref|YP_843334.1| 31 MIGYWLVFLV-IAYLVYKDaEArGMNGLLWAVLVVLPWIGMLFLLIYLLK--REEI-GGSIR 88
                                   7789******.6777777777888999999999999999999********..9999.99775 PP

>> VbhA  Antitoxin VbhA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   1.5e-05     0.045      28      42 ..      96     110 ..      94     111 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.5e-05
                           VbhA  28 eayvrGeIdadElvr 42 
                                    e+y+rGe++ dE++r
  gi|116754216|ref|YP_843334.1|  96 ERYARGELTRDEYLR 110
                                    89***********97 PP

>> Virul_fac_BrkB  Virulence factor BrkB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   4.7   1.6e-05     0.049     147     215 ..      10      79 ..       2      88 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.6e-05
                 Virul_fac_BrkB 147 lglglelsell.llqllrwlvallllvlafallYrvlpnvkvrlraalpGallaallwllvkilfslyls 215
                                     ++ ++   ++ ++ ++++++ ++  ++++++ Y v  ++  r    l+ a+l++l w+++ +l+ ++l+
  gi|116754216|ref|YP_843334.1|  10 DHMMDWGPMWWgTWGIFPFIWMIGYWLVFLVIAYLVYKDAEARGMNGLLWAVLVVLPWIGMLFLLIYLLK 79 
                                    4555566677789999999766666677778888888889*************************98876 PP

>> Wzy_C_2  Virulence factor membrane-bound polymerase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.4   4.5e-05      0.14      18      72 ..      26      77 ..      26     108 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.5e-05
                        Wzy_C_2 18 YPlwYspfllaaflvlglldsksrsrrlrlrpklvlrvvalvlallglalllsil 72
                                   +P+  +   +++flv+++l     +    + + ++l++v +vl+ +g+++ll  l
  gi|116754216|ref|YP_843334.1| 26 FPFIWMIGYWLVFLVIAYLVY---KDAEARGMNGLLWAVLVVLPWIGMLFLLIYL 77
                                   8***************66666...1333334788999999999988888877654 PP

>> DUF3099  Protein of unknown function (DUF3099)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   6.0    0.0035        10      21      62 ..      29      71 ..      27      72 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0035
                        DUF3099 21 lilmgiRvvclilavvlvsv.engwlalvllvlavvLPwvAVv 62
                                   +++ g  +v+l++a ++++  e+  ++ +l ++ vvLPw+  +
  gi|116754216|ref|YP_843334.1| 29 IWMIGYWLVFLVIAYLVYKDaEARGMNGLLWAVLVVLPWIGML 71
                                   678888899********99875555666666666*****9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 932.87
//
Query:       gi|116754217|ref|YP_843335.1|  [L=163]
Description: rubredoxin-type Fe(Cys)4 protein [Methanosaeta thermophila PT]
Scores for complete 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   77.8   0.1    5.6e-22   77.8   0.1    1.4  2  FeThRed_B  Ferredoxin thioredoxin reductase catalytic beta ch
     0.0019   17.7   1.6     0.0049   16.4   1.6    1.7  1  RecR       RecR protein
  ------ inclusion threshold ------
       0.14   12.5   0.4       0.12   12.7   0.4    1.2  1  zf-C4H2    Zinc finger-containing protein
        2.1    8.4   4.9       0.33   11.0   0.9    1.7  2  HypA       Hydrogenase/urease nickel incorporation, metalloch


Domain annotation for each model (and alignments):
>> FeThRed_B  Ferredoxin thioredoxin reductase catalytic beta chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.8   0.1   1.2e-25   5.6e-22       5      93 ..      10      96 ..       6     106 .. 0.92
   2 ?   -3.8   0.9         3   1.3e+04      65      73 ..     149     158 ..     136     161 .. 0.63

  Alignments for each domain:
  == domain 1  score: 77.8 bits;  conditional E-value: 1.2e-25
                                   HHHHHHHHHHHTT-B-BSSHHHHHHHHHHHHHHHHHHSS-B-SSC--S-HHHHHHH-TTBSS-HHHHHH....---TTSSSB CS
                      FeThRed_B  5 trkflekvakklgtkfnpdeevtevvieglarnkeeyGkrlCPCrlvedkeeeekkavwnCPCvplreeldeekeChCglfv 86
                                   + + l+  a++ g+ +n+d++++ +v++gl+ n+e++G+  CPCrl  +k+ee+ +++  CPC++++++l e ++C+C l+v
  gi|116754217|ref|YP_843335.1| 10 LYQRLKDDAESAGYHLNSDRQFVMGVVRGLLTNEERFGYMACPCRLPSGKREEDLDII--CPCDYRDQDLAEFGACYCALYV 89
                                   55667778999***********************************************..********************** PP

                                   -TTSTTB CS
                      FeThRed_B 87 tkdnaee 93
                                   ++ +a  
  gi|116754217|ref|YP_843335.1| 90 SERVARG 96
                                   *988765 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 3
                                    SS.-HHHHHH CS
                      FeThRed_B  65 CP.Cvplree 73 
                                    CP C+  re+
  gi|116754217|ref|YP_843335.1| 149 CPiCKASRER 158
                                    5545555555 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   1.6   1.1e-06    0.0049      16      37 ..     130     155 ..     122     156 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.1e-06
                                    -EE-TTT--EESSS....S-CCCCST CS
                           RecR  16 vrhCsrCgnlteed....lCaICsdp 37 
                                    v +C++Cg l+ +d    +C+IC+ +
  gi|116754217|ref|YP_843335.1| 130 VWRCRVCGYLCARDeppeICPICKAS 155
                                    678*******999888888****866 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.4   2.7e-05      0.12     162     203 ..     114     156 ..       8     160 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.7e-05
                        zf-C4H2 162 sapstatasfrqqpPPMKsClsChqqIHRNAP..iCPlCKaKsR 203
                                    +a+ ta+++++  + P   C  C     R  P  iCP+CKa sR
  gi|116754217|ref|YP_843335.1| 114 PASETAEPHIEGLSKPVWRCRVCGYLCARDEPpeICPICKA-SR 156
                                    2235666777778899**************9999******9.44 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 ?   -1.4   0.2      0.53   2.4e+03      73      94 ..      51      72 ..       7      86 .. 0.66
   2 ?   11.0   0.9   7.3e-05      0.33      68      96 ..     128     156 ..     111     161 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.53
                                   ETTTS-EEE.CHHH.HHS-TTTSS CS
                           HypA 73 CreCgkefe.leek.alrCpkCgs 94
                                   C  C+      ee+ ++ Cp C+ 
  gi|116754217|ref|YP_843335.1| 51 CP-CRLPSGkREEDlDIICP-CDY 72
                                   43.43332212223455666.554 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 7.3e-05
                                    --EEEETTTS-EEECHHHHHS-TTTSSS- CS
                           HypA  68 pvkvrCreCgkefeleekalrCpkCgsad 96 
                                    + + rCr+Cg+    +e  + Cp C++++
  gi|116754217|ref|YP_843335.1| 128 KPVWRCRVCGYLCARDEPPEICPICKASR 156
                                    67889*******998875456****9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1223.02
//
Query:       gi|116754218|ref|YP_843336.1|  [L=93]
Description: glutaredoxin [Methanosaeta thermophila PT]
Scores for complete 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-13   48.5   0.0      1e-12   48.1   0.0    1.2  1  Glutaredoxin  Glutaredoxin
      2e-06   28.1   0.0    2.7e-06   27.7   0.0    1.1  1  GST_N_3       Glutathione S-transferase, N-terminal domain
    0.00022   21.4   0.0    0.00029   21.1   0.0    1.1  1  GST_N_2       Glutathione S-transferase, N-terminal domain
    0.00078   19.7   0.0    0.00098   19.4   0.0    1.1  1  GST_N         Glutathione S-transferase, N-terminal domain
  ------ inclusion threshold ------
      0.047   13.4   0.0      0.058   13.1   0.0    1.2  1  PI3K_p85B     PI3-kinase family, p85-binding domain


Domain annotation for each model (and alignments):
>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   0.0   2.9e-16     1e-12       1      60 []      14      78 ..      14      78 .. 0.90

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 2.9e-16
                                   EEEEESTSSHHHHHHHHHHHHTTGGEEEEEGCCSH.....HHHHHHHHHHTSSSSSEEEETTEEE CS
                   Glutaredoxin  1 vvlftkptCpyCkkakrlLkelgvkfeeidvdkde.....eireelkelsgvrtvPqvfidgkhv 60
                                   v+l+  +tC +Ckk+++lL +lgv+++++ vd  +     e+ +el+++++  t+P+++ +g+++
  gi|116754218|ref|YP_843336.1| 14 VTLYALSTCMWCKKTRDLLSKLGVSYDYVYVDLTSgaeraELIDELRKFNPDLTFPTLVANGRVI 78
                                   89******************************99886666777777777788**********997 PP

>> GST_N_3  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0   7.6e-10   2.7e-06       1      58 [.      16      79 ..      16      80 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 7.6e-10
                                   EES-TTSHHHHHHHHHHHHHT--EEEE---.....TTTT...HHHHHHH-TT--SSEEETTS-EEE CS
                        GST_N_3  1 LygfpaSpyarrvrlaLnekglpvevvevt.....pgeh...deellaknplgkvPvLeddgealt 58
                                   Ly   ++ ++++ r +L  +g+++ +v v+     +  +    +el++ np  ++P+L+ +g+++ 
  gi|116754218|ref|YP_843336.1| 16 LYALSTCMWCKKTRDLLSKLGVSYDYVYVDltsgaE--RaelIDELRKFNPDLTFPTLVANGRVII 79
                                   8999*******************9987776444331..2445999*****************9985 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 !   21.1   0.0     8e-08   0.00029       2      60 ..      22      81 ..      21      92 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 8e-08
                                   -HHHHHHHHHHHHCT--EEEEEE..H...-TTSHHHHHHHHCTTTSSSEEE-CTTEEEESH CS
                        GST_N_2  2 CPwahRvlialalkglediisvv..vlepkgfekseefprlnprgtVPvLwdkdgqvineS 60
                                   C w+ +++ +l  +g+ + +  v   ++ +  e  +e+ ++np +t P+L+  +g+vi  +
  gi|116754218|ref|YP_843336.1| 22 CMWCKKTRDLLSKLGVSYDYVYVdlTSGAERAELIDELRKFNPDLTFPTLVA-NGRVIIGF 81
                                   9******************9998444455555667788*************6.99999844 PP

>> GST_N  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   2.7e-07   0.00098       3      64 ..      14      78 ..      12      80 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.7e-07
                                   EEEESSSTSHTHHHHHHHHHHTT-EEEEEEECSTTTCGGC...HHHHHHCTTS-SSEEEETTEEE CS
                          GST_N  3 ltlysirgsprahrirlllaakgveyevvpldfeageeks...pellklnplgkvPaLedngkkl 64
                                   +tly   ++++  ++r ll  +gv+y +v +d++ g+e++   +el k np    P+L+ ng ++
  gi|116754218|ref|YP_843336.1| 14 VTLYALSTCMWCKKTRDLLSKLGVSYDYVYVDLTSGAERAeliDELRKFNPDLTFPTLVANGRVI 78
                                   89**************************9999988887653466788888889******999987 PP

>> PI3K_p85B  PI3-kinase family, p85-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.6e-05     0.058      25      58 ..      29      62 ..      14      71 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.6e-05
                      PI3K_p85B 25 yplfgllkdpsdYvFvginqtaekeelyDEtrrL 58
                                     l ++l+   dYv v +++ ae+ el+DE r++
  gi|116754218|ref|YP_843336.1| 29 RDLLSKLGVSYDYVYVDLTSGAERAELIDELRKF 62
                                   5688999***********************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); 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: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 714.43
//
Query:       gi|116754219|ref|YP_843337.1|  [L=260]
Description: acetolactate decarboxylase [Methanosaeta thermophila PT]
Scores for complete 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-82  274.2   0.0    6.8e-82  274.0   0.0    1.0  1  AAL_decarboxy  Alpha-acetolactate decarboxylase


Domain annotation for each model (and alignments):
>> AAL_decarboxy  Alpha-acetolactate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  274.0   0.0   3.8e-86   6.8e-82       1     218 [.      28     244 ..      28     245 .. 0.99

  Alignments for each domain:
  == domain 1  score: 274.0 bits;  conditional E-value: 3.8e-86
                  AAL_decarboxy   1 lyqvstlsaLmegvyegtltvsellkhGdfGlGTfeeldGEliildgkvYqlksdgsvrevddeektPFavvtkfepekt 80 
                                    l+qvst+saLm+g ++g++ +++l+khGdfGlGTf++ldGE++ ldg++Yq+++dgsv+ev+d+  tPFa vt+f+p+++
  gi|116754219|ref|YP_843337.1|  28 LFQVSTISALMDGAFDGSVAFGDLKKHGDFGLGTFDALDGEMVGLDGRFYQVRADGSVHEVNDSMLTPFADVTFFDPDDA 107
                                    79****************************************************************************** PP

                  AAL_decarboxy  81 vklkealskeeleealeellpskNlfyairidGtfksvkvRsvpkqekpyeplaevakkqsefefenveGtlvGfrtPey 160
                                    v+l++  +++e+e+ leellp++N+fyairidGtf++v++Rsvp+q +py++l+ ++ +qs+fe+ n +Gt vGf+tP+y
  gi|116754219|ref|YP_843337.1| 108 VALSS-SNMTEVERSLEELLPTRNIFYAIRIDGTFSHVRARSVPAQIRPYTNLTIAVTNQSIFELYNQSGTAVGFWTPSY 186
                                    *9997.69************************************************************************ PP

                  AAL_decarboxy 161 lqginvaGlHlHFisddrkfGGHvldfeleeveveiakisklelelpedeeFeeadlk 218
                                    ++g+nv+G+HlHFi+d+r++GGH+ldf+l++++++i+ ++ + + lp +e F++a+l+
  gi|116754219|ref|YP_843337.1| 187 ASGLNVPGYHLHFINDERTAGGHLLDFHLTNGSASIDYTDIFMMVLPANEGFRRAELE 244
                                    *******************************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1981.83
//
Query:       gi|116754220|ref|YP_843338.1|  [L=118]
Description: hypothetical protein Mthe_0910 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.12   11.8   0.3       0.27   10.6   0.0    1.6  2  ZYG-11_interact  Interactor of ZYG-11


Domain annotation for each model (and alignments):
>> ZYG-11_interact  Interactor of ZYG-11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.06   1.1e+03     100     127 ..       4      32 ..       2      37 .. 0.74
   2 ?   10.6   0.0   1.5e-05      0.27     188     229 ..      53      93 ..      42     107 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.06
                ZYG-11_interact 100 iveiFalssilLlvaslssli.GgYilaP 127
                                    i+ +F   ++ L+ a  +  + GgY+ +P
  gi|116754220|ref|YP_843338.1|   4 ISILFMALIVSLICADAADWLeGGYVGSP 32 
                                    56677777888888887776559999888 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 1.5e-05
                ZYG-11_interact 188 sePfsvltqivssFayPlvaiqtdtsrkkllgtvvgasilih 229
                                    s+P+s+  +    F+yPl a+q d  r+k+l+  +   + ++
  gi|116754220|ref|YP_843338.1|  53 SQPLSFYRPYTGGFSYPLTAVQSDF-RNKSLAAMIWEPFEVN 93 
                                    89**********************9.***9998876666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); 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: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 988.33
//
Query:       gi|116754221|ref|YP_843339.1|  [L=219]
Description: HhH-GPD family protein [Methanosaeta thermophila PT]
Scores for complete 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-15   56.3   0.0    5.9e-15   55.6   0.0    1.4  1  HhH-GPD         HhH-GPD superfamily base excision DNA repair 
    0.00013   22.5   0.1      0.075   13.6   0.0    2.5  2  HHH_5           Helix-hairpin-helix domain
    0.00016   21.4   0.2     0.0019   18.0   0.0    2.5  2  HHH             Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.029   14.4   0.0      0.073   13.1   0.0    1.6  2  DUF2400         Protein of unknown function (DUF2400)
      0.036   14.4   5.1      0.061   13.7   5.1    1.4  1  EndIII_4Fe-2S   Iron-sulfur binding domain of endonuclease II
      0.062   13.6   0.0       0.12   12.7   0.0    1.5  1  Transposase_20  Transposase IS116/IS110/IS902 family
      0.071   13.2   0.0         15    5.7   0.0    2.4  2  HHH_2           Helix-hairpin-helix motif
       0.12   12.8   0.0       0.25   11.8   0.0    1.5  1  IMS_HHH         IMS family HHH motif


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 !   55.6   0.0   2.6e-18   5.9e-15       2     107 ..      33     176 ..      32     177 .. 0.96

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 2.6e-18
                                    HHHHHTTS-HHHHHHHHHHHHHHHSHCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH............... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............... RF
                        HhH-GPD   2 sailsqqtsderanriierlferfgfptpedladadeekLrelirelGfyrrKakyikelArilv............... 66 
                                     +ilsq+tsd +  r++e+l++rfg  +  ++++a+ee+++++ir+ G+   Ka +ik + + l                
  gi|116754221|ref|YP_843339.1|  33 LTILSQNTSDINSSRAFEQLKRRFG--SYTEILNASEEEIADAIRPGGLADIKAARIKGALERLRddfgsvdlsplkrms 110
                                    58*********************98..***************************************************** PP

                                    .........................S-SSS--TTSHHHHHHHHHHTTSSSSTTHHHHHHHHHHHHH CS
                                    .........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        HhH-GPD  67 .........................gkpdvlivvDvhvrrilkrlrsikekktkkkvekkleelle 107
                                                             g+   +++vD+hv r+ +r++++ e+ + +++++ lee+ +
  gi|116754221|ref|YP_843339.1| 111 avearnylksipgigpktasvlmlfGFGMSAMPVDTHVYRVSRRMGLVPENASIEETQRILEEITP 176
                                    *************************6657899*****************************88765 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.1    0.0064        14       9      52 ..      42      88 ..      32      96 .. 0.77
   2 !   13.6   0.0   3.4e-05     0.075      35      50 ..     116     131 ..      98     135 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0064
                                   T--HHHHHHHHTTT--SHHHHHHS-HHHHHTS...TTS-HHHHHHHH CS
                          HHH_5  9 GiGpktAlallsaGiesvedlaaadveeLaki...pGiGkktAerii 52
                                    i+ ++A   l+  ++s+ ++++a++ee+a++    G+   +A ri+
  gi|116754221|ref|YP_843339.1| 42 DINSSRAFEQLKRRFGSYTEILNASEEEIADAirpGGLADIKAARIK 88
                                   577777766566669***************97685557888888875 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 3.4e-05
                                    HHHHTSTTS-HHHHHH CS
                          HHH_5  35 eeLakipGiGkktAer 50 
                                    + L +ipGiG+ktA  
  gi|116754221|ref|YP_843339.1| 116 NYLKSIPGIGPKTASV 131
                                    4477788888888765 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.34   7.6e+02       5      14 ..      62      71 ..      58      73 .. 0.82
   2 !   18.0   0.0   8.5e-07    0.0019      13      29 ..     118     134 ..     117     135 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.34
                                   HHTSSHHHHH CS
                            HHH  5 lipasreeLl 14
                                   + +as+ee++
  gi|116754221|ref|YP_843339.1| 62 ILNASEEEIA 71
                                   789*****97 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 8.5e-07
                                    HHTSTT-SHHHHHHHHH CS
                            HHH  13 LlalPGVGpktAeaIls 29 
                                    L+++PG+GpktA + + 
  gi|116754221|ref|YP_843339.1| 118 LKSIPGIGPKTASVLML 134
                                    899*********99876 PP

>> DUF2400  Protein of unknown function (DUF2400)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.6   3.5e+03      75      78 ..      60      63 ..      32     110 .. 0.55
   2 ?   13.1   0.0   3.2e-05     0.073     173     193 ..     142     162 ..     139     180 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.6
                        DUF2400 75 edll 78
                                   +++l
  gi|116754221|ref|YP_843339.1| 60 TEIL 63
                                   2222 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 3.2e-05
                        DUF2400 173 iPlDvHvarvarklgllkrkq 193
                                    +P+D+Hv rv+r++gl+ ++ 
  gi|116754221|ref|YP_843339.1| 142 MPVDTHVYRVSRRMGLVPENA 162
                                    8***************96543 PP

>> EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   5.1   2.7e-05     0.061       1      17 []     195     211 ..     195     211 .. 0.99

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.7e-05
                  EndIII_4Fe-2S   1 CTARkPkCeaCPLaDlC 17 
                                    C+AR+P C  C L  lC
  gi|116754221|ref|YP_843339.1| 195 CKARNPLCKKCELKGLC 211
                                    ****************9 PP

>> Transposase_20  Transposase IS116/IS110/IS902 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   5.4e-05      0.12       3      20 ..     117     134 ..     115     163 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.4e-05
                 Transposase_20   3 lLesipGiGpvtaaalla 20 
                                     L+sipGiGp ta++l+ 
  gi|116754221|ref|YP_843339.1| 117 YLKSIPGIGPKTASVLML 134
                                    79************9986 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0    0.0068        15      18      38 ..      51      71 ..      46      92 .. 0.89
   2 ?    5.2   0.0      0.01        23      37      49 ..     118     130 ..      92     135 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0068
                          HHH_2 18 lLakrFksldaLkkasleeLl 38
                                   +L +rF+s  ++ +as+ee++
  gi|116754221|ref|YP_843339.1| 51 QLKRRFGSYTEILNASEEEIA 71
                                   7999***************96 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.01
                          HHH_2  37 LlevddiGeeiAq 49 
                                    L ++++iG+++A+
  gi|116754221|ref|YP_843339.1| 118 LKSIPGIGPKTAS 130
                                    6667777777665 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00011      0.25      13      27 ..     118     132 ..     112     137 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                        IMS_HHH  13 itkipGiGgklgekL 27 
                                    +++ipGiG+k++  L
  gi|116754221|ref|YP_843339.1| 118 LKSIPGIGPKTASVL 132
                                    89*********9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); 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:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1749.58
//
Query:       gi|116754222|ref|YP_843340.1|  [L=329]
Description: 4Fe-4S ferredoxin, iron-sulfur binding [Methanosaeta thermophila PT]
Scores for complete 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   96.2   7.7    1.6e-27   96.2   7.7    2.0  2  Fer4_22   4Fe-4S dicluster domain
    1.9e-07   31.5   8.1    0.00051   20.5   0.6    2.5  2  Fer4_17   4Fe-4S dicluster domain
      2e-06   28.1   9.6    1.1e-05   25.8   9.6    2.1  1  Fer4_8    4Fe-4S dicluster domain
    0.00032   20.8   9.4      0.026   14.6   2.5    2.6  2  Fer4_21   4Fe-4S dicluster domain
     0.0022   18.5  13.4       0.16   12.6  14.4    2.6  2  Fer4_7    4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.017   15.2  16.4       0.11   12.6  16.4    2.3  1  Fer4_10   4Fe-4S dicluster domain
       0.04   14.1   4.3       0.98    9.6   1.6    2.3  2  Fer4_18   4Fe-4S dicluster domain
       0.14   12.4  18.0       0.26   11.5   3.1    2.8  4  Fer4_9    4Fe-4S dicluster domain
          1    9.3  24.5      0.065   13.1   4.1    2.8  3  Fer4      4Fe-4S binding domain
        1.9    9.6  19.4        2.8    9.1   4.7    3.5  3  Fer4_3    4Fe-4S binding domain
        6.5    7.1  22.8       0.11   12.7   3.0    3.0  3  Fer4_2    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 ?    0.0   0.1      0.96   1.6e+03       7      21 ..     127     141 ..     123     150 .. 0.80
   2 !   96.2   7.7   9.7e-31   1.6e-27       1      94 [.     230     320 ..     230     322 .. 0.96

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.96
                        Fer4_22   7 aCtlvCptCsCfdve 21 
                                    +Ct    +C+C ++ 
  gi|116754222|ref|YP_843340.1| 127 NCTEPSESCFCAQMG 141
                                    79999999***9986 PP

  == domain 2  score: 96.2 bits;  conditional E-value: 9.7e-31
                        Fer4_22   1 rClsCgaCtlvCptCsCfdvedetkeeskegervrvwdsClleeftkvaggenvrkekkerlrqrllhklsefkekfges 80 
                                    +C+sCg C++vCptC+Cf++ d       +ger+r+ dsC+l++f+++a+g+n+r++ +erl +++++kl+++  ++g+ 
  gi|116754222|ref|YP_843340.1| 230 ECISCGGCSFVCPTCHCFTIADLGL---PDGERIRCADSCILSGFHRMASGANPRARPEERLLSWYMEKLEHMPVRTGML 306
                                    6*********************994...579************************************************* PP

                        Fer4_22  81 gCvGCgRCieacpv 94 
                                    gCvGCgRC+++c +
  gi|116754222|ref|YP_843340.1| 307 GCVGCGRCDRVCFS 320
                                    ************86 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   1.6   2.7e-05     0.044      33      57 ..     218     242 ..     188     244 .. 0.75
   2 !   20.5   0.6   3.1e-07   0.00051       8      60 ..     262     322 ..     259     323 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.7e-05
                        Fer4_17  33 lleeaekeekaslCieCgeCerkCP 57 
                                    +l+e+  ++  ++Ci+Cg+C+ +CP
  gi|116754222|ref|YP_843340.1| 218 RLREIDWRSLSKECISCGGCSFVCP 242
                                    455666668899************9 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 3.1e-07
                        Fer4_17   8 ClpeCpsyeaydn.....epkkllraaklglleeaeke...ekaslCieCgeCerkCPqgl 60 
                                    C+++C     ++       ++++ +++ ++ +e+ e +   + +  C++Cg+C+r+C +gl
  gi|116754222|ref|YP_843340.1| 262 CADSCILSGFHRMasganPRARPEERLLSWYMEKLEHMpvrTGMLGCVGCGRCDRVCFSGL 322
                                    888888633322211222444555555555555555554438***************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 !   25.8   9.6   6.6e-09   1.1e-05       3      62 ..     229     319 ..     227     322 .. 0.74

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 6.6e-09
                         Fer4_8   3 ekCieCgaCqsaCpvlrrtk.khlldargeaae.......................dvqeeqvlee.............. 44 
                                    ++Ci Cg C   Cp+++++   +l  + ge++                        +        e              
  gi|116754222|ref|YP_843340.1| 229 KECISCGGCSFVCPTCHCFTiADLGLPDGERIRcadscilsgfhrmasganprarpE--------Erllswymeklehmp 300
                                    68****************998899999999888666666666655555555544441........044445555667777 PP

                         Fer4_8  45 .eealwsCttcgaCtevCp 62 
                                     ++++  C++cg+C++vC 
  gi|116754222|ref|YP_843340.1| 301 vRTGMLGCVGCGRCDRVCF 319
                                    8*****************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 !   14.6   2.5   1.6e-05     0.026      36      58 ..     226     248 ..     211     249 .. 0.85
   2 !    9.4   0.6   0.00067       1.1      40      51 ..     307     318 ..     292     323 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.6e-05
                        Fer4_21  36 vvedeCvGCnlCssvCPvedcie 58 
                                     +++eC+ C  Cs vCP+  c +
  gi|116754222|ref|YP_843340.1| 226 SLSKECISCGGCSFVCPTCHCFT 248
                                    56789************998876 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00067
                        Fer4_21  40 eCvGCnlCssvC 51 
                                     CvGC  C  vC
  gi|116754222|ref|YP_843340.1| 307 GCVGCGRCDRVC 318
                                    588888888888 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   4.0    0.0011       1.7      34      50 ..     227     243 ..     200     245 .. 0.77
   2 !   12.6  14.4   9.9e-05      0.16       2      51 ..     231     321 ..     230     322 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0011
                         Fer4_7  34 dpekClgCgaCvavCPt 50 
                                     + +C++Cg C  vCPt
  gi|116754222|ref|YP_843340.1| 227 LSKECISCGGCSFVCPT 243
                                    55678888888888886 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 9.9e-05
                         Fer4_7   2 CigCgaCvaaCp.vkaieldeeenek...................................gtekv........eidpek 37 
                                    Ci Cg C  +Cp  +++++ +   ++                                       +        +  +  
  gi|116754222|ref|YP_843340.1| 231 CISCGGCSFVCPtCHCFTIADLGLPDgerircadscilsgfhrmasganprarpeerllswY---MeklehmpvRTGMLG 307
                                    ***********977888877643333222334444444433333333333333333344441...033333344788889 PP

                         Fer4_7  38 ClgCgaCvavCPtg 51 
                                    C+gCg+C +vC +g
  gi|116754222|ref|YP_843340.1| 308 CVGCGRCDRVCFSG 321
                                    ***********765 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6  16.4   6.7e-05      0.11       6      55 ..     228     318 ..     223     319 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.7e-05
                        Fer4_10   6 ddtCirCgkCvkaCPadl.........................................tsvgakgeaseeeavrkkvek 44 
                                    ++ Ci Cg C  +CP+++                                         +  + + e+ e+ +vr+++  
  gi|116754222|ref|YP_843340.1| 228 SKECISCGGCSFVCPTCHcftiadlglpdgerircadscilsgfhrmasganprarpeeRLLSWYMEKLEHMPVRTGMLG 307
                                    678*************99***************************************998899999************** PP

                        Fer4_10  45 CtgcgaCveaC 55 
                                    C gcg C ++C
  gi|116754222|ref|YP_843340.1| 308 CVGCGRCDRVC 318
                                    *********99 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.6    0.0006      0.98      56      74 ..     226     244 ..     211     275 .. 0.74
   2 ?    4.7   0.0     0.021        34      56      74 ..     303     321 ..     283     327 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0006
                        Fer4_18  56 kgagdcidcescvkvcPtg 74 
                                    + + +ci+c+ c  vcPt 
  gi|116754222|ref|YP_843340.1| 226 SLSKECISCGGCSFVCPTC 244
                                    55789************84 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.021
                        Fer4_18  56 kgagdcidcescvkvcPtg 74 
                                    +g+  c+ c+ c +vc  g
  gi|116754222|ref|YP_843340.1| 303 TGMLGCVGCGRCDRVCFSG 321
                                    3445577777777777555 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.2       8.6   1.4e+04      33      37 ..     131     136 ..     116     139 .. 0.51
   2 ?   11.5   3.1   0.00016      0.26      33      48 ..     221     243 ..     188     247 .. 0.73
   3 ?   10.1   2.1   0.00044      0.72      33      47 ..     294     319 ..     260     323 .. 0.55
   4 ?    9.7   1.9   0.00059      0.96       2      19 ..     308     325 ..     307     328 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 8.6
                         Fer4_9  33 e.eaCi 37 
                                      e+C+
  gi|116754222|ref|YP_843340.1| 131 PsESCF 136
                                    223444 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00016
                         Fer4_9  33 e.......eaCigCgaCveaCpk 48 
                                    e       ++Ci+Cg C  +Cp+
  gi|116754222|ref|YP_843340.1| 221 EidwrslsKECISCGGCSFVCPT 243
                                    0333445668***********97 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00044
                         Fer4_9  33 e...........eaCigCgaCveaCp 47 
                                    e             C+gCg+C  +C 
  gi|116754222|ref|YP_843340.1| 294 EklehmpvrtgmLGCVGCGRCDRVCF 319
                                    25566666666656888888888885 PP

  == domain 4  score: 9.7 bits;  conditional E-value: 0.00059
                         Fer4_9   2 CtgCgaCveaCpagvvve 19 
                                    C+gCg+C ++C +g+++ 
  gi|116754222|ref|YP_843340.1| 308 CVGCGRCDRVCFSGLHKT 325
                                    999999999998777665 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   4.1     4e-05     0.065       7      20 ..     230     243 ..     228     243 .. 0.93
   2 ?   -2.9   0.4       4.5   7.4e+03      13      18 ..     261     266 ..     261     266 .. 0.86
   3 ?    7.5   6.1    0.0024       3.8       8      18 ..     308     318 ..     307     321 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4e-05
                                    TSSS-THHHHHSTT CS
                           Fer4   7 kCigCGaCvevCPv 20 
                                     Ci CG C  vCP+
  gi|116754222|ref|YP_843340.1| 230 ECISCGGCSFVCPT 243
                                    7************7 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.5
                                    HHHHHS CS
                           Fer4  13 aCvevC 18 
                                    +C++ C
  gi|116754222|ref|YP_843340.1| 261 RCADSC 266
                                    599999 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0024
                                    SSS-THHHHHS CS
                           Fer4   8 CigCGaCvevC 18 
                                    C+gCG+C  vC
  gi|116754222|ref|YP_843340.1| 308 CVGCGRCDRVC 318
                                    *********** PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   2.5    0.0053       8.7       1      13 [.     231     243 ..     231     245 .. 0.94
   2 ?    0.3   0.3       1.1   1.8e+03       1      11 [.     244     266 ..     244     267 .. 0.72
   3 ?    9.1   4.7    0.0017       2.8       1      14 [.     308     321 ..     308     321 .. 0.95

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0053
                         Fer4_3   1 CtgCgaCvevCPv 13 
                                    C+ Cg C  vCP+
  gi|116754222|ref|YP_843340.1| 231 CISCGGCSFVCPT 243
                                    ************6 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.1
                         Fer4_3   1 CtgCg.............aCvevC 11 
                                    C +C              +C ++C
  gi|116754222|ref|YP_843340.1| 244 C-HCFtiadlglpdgeriRCADSC 266
                                    6.8866667777777777799988 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0017
                         Fer4_3   1 CtgCgaCvevCPvg 14 
                                    C+gCg+C +vC++g
  gi|116754222|ref|YP_843340.1| 308 CVGCGRCDRVCFSG 321
                                    ***********987 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   3.0   6.6e-05      0.11      10      22 .]     231     243 ..     227     243 .. 0.92
   2 ?   -3.4   0.4       8.8   1.4e+04      16      20 ..     262     266 ..     261     267 .. 0.62
   3 ?    5.3   5.5     0.015        24      10      20 ..     308     318 ..     304     318 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.6e-05
                         Fer4_2  10 CigCgaCvsaCPa 22 
                                    Ci+Cg C  +CP+
  gi|116754222|ref|YP_843340.1| 231 CISCGGCSFVCPT 243
                                    ************7 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 8.8
                         Fer4_2  16 CvsaC 20 
                                    C ++C
  gi|116754222|ref|YP_843340.1| 262 CADSC 266
                                    66666 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.015
                         Fer4_2  10 CigCgaCvsaC 20 
                                    C+gCg C  +C
  gi|116754222|ref|YP_843340.1| 308 CVGCGRCDRVC 318
                                    *******9999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.44u 0.20s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 2590.35
//
Query:       gi|116754223|ref|YP_843341.1|  [L=668]
Description: formate dehydrogenase, alpha subunit [Methanosaeta thermophila PT]
Scores for complete 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-88  295.5   0.0    8.1e-88  295.2   0.0    1.1  1  Molybdopterin    Molybdopterin oxidoreductase
    6.4e-27   93.8   0.0    1.2e-26   92.9   0.0    1.4  1  Molydop_binding  Molydopterin dinucleotide binding domain
    2.4e-11   43.4   0.7      5e-11   42.4   0.7    1.6  1  Molybdop_Fe4S4   Molybdopterin oxidoreductase Fe4S4 domain
  ------ inclusion threshold ------
      0.038   13.9   0.1      0.075   12.9   0.1    1.4  1  SIS              SIS domain


Domain annotation for each model (and alignments):
>> Molybdopterin  Molybdopterin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  295.2   0.0   1.8e-91   8.1e-88       1     431 [.      57     476 ..      57     477 .. 0.94

  Alignments for each domain:
  == domain 1  score: 295.2 bits;  conditional E-value: 1.8e-91
                                    B--S-EEECTTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEEEEEBTSSCSHHHHHHHHHHHHHTT-EEE-BEECC CS
                  Molybdopterin   1 RlkyPmvRkqargeGkFvrvsWdeAleliaaslkytikkygpdrvagfssgplmsmeslaslkkllsllggknlsfydwy 80 
                                    Rl+ P++R   r  +++v+ sW eAl +ia+s+ +++ + gpd+ a+  s +++ +e+ ++l kl ++ +g  ++++d+ 
  gi|116754223|ref|YP_843341.1|  57 RLREPLIR---R-GDRYVQTSWSEALSYIAESFSEIKRDSGPDALAVLTSAKAT-NEENYLLMKLCRAAFG--TNNIDNV 129
                                    9*******...9.899*******************************9999999.999999**********..8****** PP

                                    GGGTTHHHHCHHCCCCCTTTS-SS-CCGGGG-SEEEEESS-HHHHSHHHHHHHHHHHHTTC-EEEEECSSB-HCGGGCSE CS
                  Molybdopterin  81 adlppasaqqtigsdsrsnyessnpledlensdliilwGsNvreerpilnarirkaalkkkakvivigpryaellkfade 160
                                    a+l++a +  ++gs++  + +++np+e+l +sd+i ++GsN  e +p +  +i+  a++++a++ivi+pr +++++ ad+
  gi|116754223|ref|YP_843341.1| 130 ARLCHAPTLFALGSSLG-SGSMTNPMESLLHSDAIMIIGSNTTEQHPAVAFHIME-ARRNGARIIVIDPRRTQIAEIADL 207
                                    *****998888888655.777778*************************777776.56657******************* PP

                                    EEEEHTTTHHHHHHHHHHHHHHCCCCTCHHHHHHEECHHHCCCCCCCEECCSHHHHHHCCHHHHHHHHHHHHHHTSSEEE CS
                  Molybdopterin 161 wlaikpgtdaalalamghvilqelkvdkeflrkytygkeetdmpllvtleeetgkkkevvariarelarnaaktagksmi 240
                                    +l ++pgtd al++a+ +v++qe++ d+ef+r++t g++  ++ + ++++e ++ +++v+a+ +   a  +  ++  ++i
  gi|116754223|ref|YP_843341.1| 208 HLQLRPGTDIALLNAILNVLVQEGMIDEEFIRSRTEGFDAARDRIAEYTPEVAERICGVPADLIHDAAVLYGGADN-AAI 286
                                    ***************************************************8888888888877777777777777.999 PP

                                    EECHHHHTSTTHHHHHHHHHHHHHHCTHCSSTTCEEEEESSCTTHHHCHHHHTCCTTCCCCCCCTT.HHHHHCCCTTTCS CS
                  Molybdopterin 241 ivGaglnhrqdgdaiyravinLallvgnvgqpgGgwahlnGqlilagaaekvgalpvllsvkslke.ekikfaaeqpgnl 319
                                    ++ +g++++++g+++++a++nLal++gn g++g+g   l+G  +++g a+++galp  ++ ++ ++  + kf + +  +l
  gi|116754223|ref|YP_843341.1| 287 VYAMGITQHTHGTDNVQAIVNLALATGNLGRDGSGIYPLRGHQNVQG-ACDMGALPDYYTGYQRVSeFRGKFEDAWDVKL 365
                                    9*********************************************9.***********9888777478899999999** PP

                                    TSS--ECGGCHHHHHHTTSSSEEEEESH.HHHHSTTSCCCHCHHHCSSEEEEEESCSSHHHHTSSEEEEBE-CCGSEEEE CS
                  Molybdopterin 320 gnfprnlfversnllkssgkkvlyllgnnpevdhadenevekalekldlvvvldgrltstalyaDiiLPaatwyEkedly 399
                                    +   +n++ve +  ++ s+++ +y+ g+np  + ++ +++ +ale+ldl+vv+d++ t+t ++aD++LP a++ Ek++++
  gi|116754223|ref|YP_843341.1| 366 PTSQGNTAVEIMGSAG-SDIRGMYISGENPLLSYPNSSRIRRALESLDLLVVSDIFPTETTRMADVVLPIASFAEKDGTV 444
                                    **********999999.7************************************************************** PP

                                    E-TTSEEEEEEESSS-STT-BEHHHHHHHHHH CS
                  Molybdopterin 400 tndegrfqhlkqavsppgeaksdwkIlkaLak 431
                                    t++e+++q +++a++ppg a ++w +  +L +
  gi|116754223|ref|YP_843341.1| 445 TSTERKVQLIRKAIDPPGSALPEWVVAAKLLE 476
                                    ************************99988876 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.9   0.0   2.7e-30   1.2e-26       1     110 [.     554     659 ..     554     660 .. 0.97

  Alignments for each domain:
  == domain 1  score: 92.9 bits;  conditional E-value: 2.7e-30
                                    EEEEEE-BTTBSTTTTTCGCCHHHHCSSS.-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEEEEESS CS
                Molydop_binding   1 lrLitgrsldqlhsqtrtrpvlrlakpep.evveinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvvfmpfg 79 
                                    ++Li grs++q+h++ +tr+v  l ++ p ++v inpedAaalGi++G  V +es+ G++++ra+++++v++G++f+pf+
  gi|116754223|ref|YP_843341.1| 554 FTLIIGRSQYQFHTGSMTRRVCILEREVPeAFVDINPEDAAALGIRNGTGVILESESGTIRARARLSDNVKRGTLFIPFH 633
                                    68999********************99999************************************************** PP

                                    HCC.....S-GHCTS--SCSTTT--CSTT-E CS
                Molydop_binding  80 wweagekggnaNaltddatdplsgtpefksv 110
                                    + e     ++aN+lt  ++dp s++p +k +
  gi|116754223|ref|YP_843341.1| 634 FRE-----SPANMLTGWQLDPHSRIPGLKIT 659
                                    *88.....******************99975 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   0.7   1.1e-14     5e-11       2      55 .]       2      54 ..       1      54 [. 0.92

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 1.1e-14
                                   EEEEEE-SSBTT--EEEEEEETTEEEEEEE-TTSTTTTT---HHHHTCHHCCCB CS
                 Molybdop_Fe4S4  2 kvvktaCpyCgvgCglevhvkdgkivkvegdpdhpvnegrlCvKGrtllervyn 55
                                     + t+C yCg+gCgl +hv++ k+ +v +  + p+ +grlC+KG  l+ +v++
  gi|116754223|ref|YP_843341.1|  2 DAIETTCVYCGCGCGLYLHVENSKVIAVTPSLKPPA-RGRLCAKGWLLHGFVNH 54
                                   5689**************************998885.6*********9999986 PP

>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   1.7e-05     0.075      49     118 ..     156     227 ..     144     233 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.7e-05
                                    GG-STTCEEEEEESSSHHHHHHHHHH.HHHHTTSEEEEEESSTTSHHHHHSSEEEEEEEECHC..SSSHCHHH CS
                            SIS  49 alideddlvilisfsgetkdlvaaae.lakergakiiaITdskgsplareadlalyinaepet..lvastksl 118
                                    +l+ +d ++i+ s + e+++ va    +a+++ga+ii+I     +++a+ adl+l+++ +  +  l+a++++l
  gi|116754223|ref|YP_843341.1| 156 SLLHSDAIMIIGSNTTEQHPAVAFHImEARRNGARIIVID-PRRTQIAEIADLHLQLRPGTDIalLNAILNVL 227
                                    566777777777888888888887777************8.88899*************99997666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (668 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 4682.53
//
Query:       gi|116754224|ref|YP_843342.1|  [L=293]
Description: ferredoxin-NADP(+) reductase subunit alpha [Methanosaeta thermophila PT]
Scores for 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-12   44.6   3.4      3e-11   42.9   3.4    1.9  1  DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydr
  ------ inclusion threshold ------
       0.16   12.0   0.4       0.28   11.2   0.4    1.3  1  Fer2_3           2Fe-2S iron-sulfur cluster binding domain


Domain annotation for each model (and alignments):
>> DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   3.4   3.3e-15     3e-11       3      41 ..     214     248 ..     212     249 .. 0.91

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 3.3e-15
                                    --SSSSSSS-TTEEEETTCTT.CEEETTTT-CEEECCCB CS
                DHODB_Fe-S_bind   3 rMaCGvGaClgCvvktkggdggeykrvCkdGPvFdadev 41 
                                     M++G+G+C++C+v++ g+    ++++C+dGP Fd++ v
  gi|116754224|ref|YP_843342.1| 214 LMVDGTGMCGACRVEVGGE----TRFACVDGPDFDGHLV 248
                                    6***************764....8************988 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 ?   11.2   0.4   3.2e-05      0.28      54      73 ..     219     238 ..     210     242 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.2e-05
                         Fer2_3  54 egiCGscavainGkptlaCt 73 
                                     g+CG+c v++ G+++ aC 
  gi|116754224|ref|YP_843342.1| 219 TGMCGACRVEVGGETRFACV 238
                                    79*****************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 2307.42
//
Query:       gi|116754225|ref|YP_843343.1|  [L=920]
Description: formate dehydrogenase, alpha subunit [Methanosaeta thermophila PT]
Scores for complete 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-90  303.0   0.0    4.6e-90  302.6   0.0    1.1  1  Molybdopterin    Molybdopterin oxidoreductase
      1e-31  109.2   0.1    3.5e-31  107.5   0.0    2.0  2  Molydop_binding  Molydopterin dinucleotide binding domain
    5.9e-18   64.7   1.4    7.4e-18   64.4   0.1    1.9  1  Fer2_4           2Fe-2S iron-sulfur cluster binding domain
      2e-14   53.3   0.7      2e-14   53.3   0.7    3.0  2  Molybdop_Fe4S4   Molybdopterin oxidoreductase Fe4S4 domain
    7.9e-09   35.0  19.0    3.9e-07   29.6   1.7    3.7  3  Fer4             4Fe-4S binding domain
      2e-08   33.6  10.1    0.00093   18.7   0.3    3.2  3  NADH-G_4Fe-4S_3  NADH-ubiquinone oxidoreductase-G iron-sulfur
    2.3e-07   30.6  15.6    0.00012   22.0   0.6    3.9  3  Fer4_6           4Fe-4S binding domain
    0.00019   21.5   9.9    0.00019   21.5   9.9    4.0  4  Fer4_9           4Fe-4S dicluster domain
    0.00032   20.8   5.2    0.00032   20.8   5.2    2.8  1  Fer4_21          4Fe-4S dicluster domain
    0.00038   20.4  10.9       0.15   12.2   2.5    3.7  2  Fer4_2           4Fe-4S binding domain
     0.0004   20.9  11.1     0.0004   20.9  11.1    4.2  3  Fer4_7           4Fe-4S dicluster domain
    0.00047   20.2   5.7    0.00047   20.2   5.7    3.4  2  Fer4_10          4Fe-4S dicluster domain
     0.0094   16.8  21.0      0.033   15.1   6.1    3.9  2  Fer4_3           4Fe-4S binding domain
  ------ inclusion threshold ------
      0.039   14.1   0.0       0.16   12.1   0.0    2.1  2  CDC48_N          Cell division protein 48 (CDC48), N-terminal
      0.046   13.2   0.0      0.098   12.2   0.0    1.6  1  DNA_gyraseA_C    DNA gyrase C-terminal domain, beta-propeller
       0.12   13.1   8.1        2.7    8.8   0.5    3.0  2  Fer4_15          4Fe-4S single cluster domain
        7.9    7.1  10.3         11    6.6   1.8    2.8  2  Fer4_13          4Fe-4S single cluster domain of Ferredoxin I


Domain annotation for each model (and alignments):
>> Molybdopterin  Molybdopterin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  302.6   0.0   4.4e-93   4.6e-90       1     430 [.     296     713 ..     296     715 .. 0.91

  Alignments for each domain:
  == domain 1  score: 302.6 bits;  conditional E-value: 4.4e-93
                                    B--S-EEECTTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEEEEEBTSSCSHHHHHHHHHHHHHTT-EEE-BEECC CS
                  Molybdopterin   1 RlkyPmvRkqargeGkFvrvsWdeAleliaaslkytikkygpdrvagfssgplmsmeslaslkkllsllggknlsfydwy 80 
                                    Rlk+Pm+R   r +G +v ++WdeAl+lia++l      y+ d+   ++++  + +e++++++k+++ ++g  ++++d++
  gi|116754225|ref|YP_843343.1| 296 RLKTPMIR---R-DGVLVSATWDEALDLIAERLSS----YKGDEFG-MVASAKCTNEEVYLAQKFARVVMG--TNNIDNC 364
                                    9*******...9.**********************....5555555.55556666****************..9****** PP

                                    GGGTTHHHH....CHHCCCCCTTTS-SS-CCGGGG-SEEEEESS-HHHHSHHHHHHHHHHHHTTC-EEEEECSSB-HCGG CS
                  Molybdopterin  81 adlppasaq....qtigsdsrsnyessnpledlensdliilwGsNvreerpilnarirkaalkkkakvivigpryaellk 156
                                    a+l++as+      +igs+     +++n++ dl n++ i+++GsN  e +p+   ri  a ++ +a++iv  pr  el  
  gi|116754225|ref|YP_843343.1| 365 ARLCHASTIsglsIAIGSG-----AMTNSIDDLRNAGCILVIGSNTTEQHPVIGLRIKEAKRR-GARIIVANPRRIELCG 438
                                    *******876665555554.....7899*************************8888888888.5************999 PP

                                    GCSEEEEEHTTTHHHHHHHHHHHHHHCCCCTCHHHHHHEECHHHCCCCCCCEECCSHHHHHHCCHHHHHHHHHHHHHHTS CS
                  Molybdopterin 157 fadewlaikpgtdaalalamghvilqelkvdkeflrkytygkeetdmpllvtleeetgkkkevvariarelarnaaktag 236
                                     ad w+ ++pgtd++l+l+m++ i + ++ d  f+r +t g+e ++  l++++ +     ++v    ++e a  +a+ ++
  gi|116754225|ref|YP_843343.1| 439 IADVWIRNRPGTDLPLILGMCKSIKDAGLADMGFIRDRTEGFEDFARSLDELQMDVICGLTGVDESLIKEAALLYANGNP 518
                                    *****************************************************997777777777777777777777788 PP

                                    SEEEEECHHHHTSTTHHHHHHHHHHHHHHCTHCSSTTCEEEEESSCTTHHHCHHHHTCCTTCCCCCCCTT.HHHHHCCC. CS
                  Molybdopterin 237 ksmiivGaglnhrqdgdaiyravinLallvgnvgqpgGgwahlnGqlilagaaekvgalpvllsvkslke.ekikfaae. 314
                                     s i++ +g+++++ g++++ a++nLa+++gn+g+pgGg + l+Gq++++g a+++galp +l+ ++ +   + ++++e 
  gi|116754225|ref|YP_843343.1| 519 -SSIVYSMGITQHACGTDNVLALANLAMMTGNIGVPGGGINPLRGQNNVQG-ACDMGALPNMLPGYQNVLsAEARAMIEg 596
                                    .77777*********************************************.*******988776655544666666662 PP

                                    .TTTCSTSS--ECGGCHHHHHHTTSSSEEEEESH.HHHHSTTSCCCHCHHHCSSEEEEEESCSSHHHHTSSEEEEBE-CC CS
                  Molybdopterin 315 .qpgnlgnfprnlfversnllkssgkkvlyllgnnpevdhadenevekalekldlvvvldgrltstalyaDiiLPaatwy 393
                                     +   ++  p+ ++ve+ ++++s+ ++++y++g+np+ + +d+++v++al++ld++vv d++lt+ta+ aD++LPaa+ +
  gi|116754225|ref|YP_843343.1| 597 iWGMRIPERPGLTLVEMFDAARSGRIRAMYIIGENPVLSEPDAGHVIEALGDLDFLVVQDIFLTETAQLADVVLPAACSL 676
                                    2567999************************************************************************* PP

                                    GSEEEEE-TTSEEEEEEESSS-STT-BEHHHHHHHHH CS
                  Molybdopterin 394 EkedlytndegrfqhlkqavsppgeaksdwkIlkaLa 430
                                    Ek++++t++e+r+q  +++  ppg+a++dw+Il+++a
  gi|116754225|ref|YP_843343.1| 677 EKDGTFTSTERRVQMVRRILAPPGDARPDWWILQEIA 713
                                    ***********************************98 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1       9.8     1e+04      42      57 ..     259     274 ..     258     282 .. 0.82
   2 !  107.5   0.0   3.4e-34   3.5e-31       2     111 .]     800     905 ..     799     905 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 9.8
                                    HT--TT-EEEEEETTE CS
                Molydop_binding  42 lGikdGdlVevesrrG 57 
                                     G +++ +V+v+ +rG
  gi|116754225|ref|YP_843343.1| 259 VGARNNHIVRVRGQRG 274
                                    57889999***99999 PP

  == domain 2  score: 107.5 bits;  conditional E-value: 3.4e-34
                                    EEEEE-BTTBSTTTTTCGCCHHHHCSSS.-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEEEEESSH CS
                Molydop_binding   2 rLitgrsldqlhsqtrtrpvlrlakpep.evveinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvvfmpfgw 80 
                                    +L tgr l+++h++t+tr+v  l   ++ evveinped a lG+++GdlVev+srrGsv++r+++t+r ++G+vfm+f++
  gi|116754225|ref|YP_843343.1| 800 VLLTGRILYHYHTGTMTRRVHDLEYLRGeEVVEINPEDGANLGLNEGDLVEVASRRGSVRARVRLTDRSPKGTVFMTFHF 879
                                    799*****************9999999999************************************************** PP

                                    CC.....S-GHCTS--SCSTTT--CSTT-EE CS
                Molydop_binding  81 weagekggnaNaltddatdplsgtpefksva 111
                                     e     +++N+lt++ +dp++++pe+k +a
  gi|116754225|ref|YP_843343.1| 880 SE-----TPTNVLTSRCLDPVAKIPELKFCA 905
                                    99.....********************9885 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 !   64.4   0.1     7e-21   7.4e-18       3      81 ..       3      78 ..       1      79 [. 0.95

  Alignments for each domain:
  == domain 1  score: 64.4 bits;  conditional E-value: 7e-21
                         Fer2_4  3 pvtltfDGkevtvpeGdtvasAllangvdvprsckygrprgelcaggeCrnClVevegepnv.racstpvedGlkvetqt 81
                                   ++ lt+DG ev+vp G+t+++A+ ++g+++p++c +      l+++g C+ C+Ve+ g +    +c+t +e+G++v+t+t
  gi|116754225|ref|YP_843343.1|  3 KICLTIDGVEVSVPRGTTILNAARKAGIYIPALCDH----PDLKPIGICKLCIVEIAGWETYpTSCTTYAENGMVVRTDT 78
                                   6789********************************....89****************88887***************98 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   1.1      0.97     1e+03       4      12 ..     211     219 ..     209     221 .. 0.85
   2 !   53.3   0.7   1.9e-17     2e-14       3      53 ..     243     291 ..     241     293 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.97
                                    EEEE-SSBT CS
                 Molybdop_Fe4S4   4 vktaCpyCg 12 
                                    + ++C++Cg
  gi|116754225|ref|YP_843343.1| 211 IESTCKFCG 219
                                    579*****9 PP

  == domain 2  score: 53.3 bits;  conditional E-value: 1.9e-17
                                    EEEEE-SSBTT--EEEEEEETTEEEEEEE-TTSTTTTT---HHHHTCHHCC CS
                 Molybdop_Fe4S4   3 vvktaCpyCgvgCglevhvkdgkivkvegdpdhpvnegrlCvKGrtllerv 53 
                                    ++ t+Cp+CgvgC++ev  +++ iv+v+g++ +p neg+lCvKGr++le+ 
  gi|116754225|ref|YP_843343.1| 243 SAVTTCPFCGVGCQIEVGARNNHIVRVRGQR-GP-NEGQLCVKGRFGLEFA 291
                                    678**************************99.77.99**********9986 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   1.0       8.5     9e+03       9      14 ..     125     130 ..     125     130 .. 0.88
   2 !   15.8   2.3   8.2e-06    0.0087       4      18 ..     170     184 ..     167     185 .. 0.94
   3 !   29.6   1.7   3.7e-10   3.9e-07       4      24 .]     211     231 ..     209     231 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 8.5
                                    SS-THH CS
                           Fer4   9 igCGaC 14 
                                    +gC++C
  gi|116754225|ref|YP_843343.1| 125 VGCKYC 130
                                    799999 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 8.2e-06
                                    ETTTSSS-THHHHHS CS
                           Fer4   4 deekCigCGaCvevC 18 
                                    d+++Ci CG+C+ +C
  gi|116754225|ref|YP_843343.1| 170 DYNLCIMCGRCARIC 184
                                    99************* PP

  == domain 3  score: 29.6 bits;  conditional E-value: 3.7e-10
                                    ETTTSSS-THHHHHSTTTEEE CS
                           Fer4   4 deekCigCGaCvevCPvgAIt 24 
                                    +e+ C +CGaCv++CP+gA++
  gi|116754225|ref|YP_843343.1| 211 IESTCKFCGACVDACPTGALY 231
                                    6899***************85 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 !   18.5   2.5   9.8e-07     0.001       1      25 [.      85     111 ..      85     121 .. 0.89
   2 !   18.7   0.3   8.8e-07   0.00093      16      40 .]     127     151 ..     124     151 .. 0.94
   3 ?   -2.5   0.0       3.6   3.8e+03      27      37 ..     709     719 ..     709     720 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 9.8e-07
                NADH-G_4Fe-4S_3   1 RktilellLa..nHpldCltCdknGnC 25 
                                    R+++lellLa  +Hp  Cl+C++  +C
  gi|116754225|ref|YP_843343.1|  85 RRNTLELLLAitSHPVSCLICERKRDC 111
                                    9*******97669************** PP

  == domain 2  score: 18.7 bits;  conditional E-value: 8.8e-07
                NADH-G_4Fe-4S_3  16 CltCdknGnCeLQdlayelgveesr 40 
                                    C +C+k G+Ce Q  a++lg e++r
  gi|116754225|ref|YP_843343.1| 127 CKYCPKDGECEIQRAAEYLGLERIR 151
                                    999*****************99876 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 3.6
                NADH-G_4Fe-4S_3  27 LQdlayelgve 37 
                                    LQ++a ++g +
  gi|116754225|ref|YP_843343.1| 709 LQEIALRMGYR 719
                                    9*******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 ?   -2.1   0.3       4.5   4.8e+03       6      16 ..      33      51 ..      31      53 .. 0.67
   2 !   22.0   0.6   1.2e-07   0.00012       5      21 ..     170     186 ..     166     193 .. 0.87
   3 !   15.9   2.7   9.5e-06      0.01       6      24 .]     212     230 ..     211     230 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 4.5
                         Fer4_6  6 pdkCig........CgdCv 16
                                   p +C++        C  C+
  gi|116754225|ref|YP_843343.1| 33 PALCDHpdlkpigiCKLCI 51
                                   7789855555666788886 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 1.2e-07
                         Fer4_6   5 dpdkCigCgdCvrvCPe 21 
                                    d+++Ci Cg+C+r+C e
  gi|116754225|ref|YP_843343.1| 170 DYNLCIMCGRCARICSE 186
                                    99*************96 PP

  == domain 3  score: 15.9 bits;  conditional E-value: 9.5e-06
                         Fer4_6   6 pdkCigCgdCvrvCPegai 24 
                                    ++ C  Cg+Cv++CP+ga+
  gi|116754225|ref|YP_843343.1| 212 ESTCKFCGACVDACPTGAL 230
                                    567888***********97 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   2.1       9.4     1e+04      33      43 ..      89     112 ..      47     121 .. 0.58
   2 !   12.6   2.6   0.00011      0.12       4      47 ..     126     185 ..     123     188 .. 0.75
   3 !   21.5   9.9   1.8e-07   0.00019       2      50 ..     174     229 ..     173     230 .. 0.77
   4 ?   -1.8   0.1       3.4   3.6e+03      34      42 ..     246     255 ..     231     269 .. 0.68

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 9.4
                         Fer4_9  33 e..........eaCigCga...Cv 43 
                                                +C+ C++   C 
  gi|116754225|ref|YP_843343.1|  89 LelllaitshpVSCLICERkrdCS 112
                                    255666666666677776655554 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00011
                         Fer4_9   4 gCgaCvea..Cpagvvvedaaerkarlraase...............eaCigCgaCveaCp 47 
                                    gC++C +   C+ + + e  + + +r+    +               + Ci+Cg+C+ +C 
  gi|116754225|ref|YP_843343.1| 126 GCKYCPKDgeCEIQRAAEYLGLERIRYPVS-YkglpvfrepffdrdyNLCIMCGRCARICS 185
                                    899995533487777777666666666444.247888999999999999***********7 PP

  == domain 3  score: 21.5 bits;  conditional E-value: 1.8e-07
                         Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase........eaCigCgaCveaCpkga 50 
                                    C+ Cg+C + C   +  e   + +a +++ s+        + C +CgaCv+aCp+ga
  gi|116754225|ref|YP_843343.1| 174 CIMCGRCARICSE-LRGEGVLQMIADYHRGSWigpdslieSTCKFCGACVDACPTGA 229
                                    ***********54.4555555555555555667778888889*************97 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 3.4
                         Fer4_9  34 eaCigCga.C 42 
                                    + C +Cg  C
  gi|116754225|ref|YP_843343.1| 246 TTCPFCGVgC 255
                                    5577776533 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   5.2     3e-07   0.00032       5      55 ..     171     228 ..     168     232 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3e-07
                        Fer4_21   5 edkCigCgkCliaCedtshqai.eidaktvl.......kvvedeCvGCnlCssvCPved 55 
                                     + Ci Cg+C+  C++   + + ++ a+ +         ++e++C  C  C++ CP+ +
  gi|116754225|ref|YP_843343.1| 171 YNLCIMCGRCARICSELRGEGVlQMIADYHRgswigpdSLIESTCKFCGACVDACPT-G 228
                                    578***********997666663444443336677887889***************6.5 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   1.4   0.00042      0.45       3      20 ..     165     184 ..     163     186 .. 0.80
   2 !   12.2   2.5   0.00014      0.15       8      22 .]     213     227 ..     205     227 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00042
                         Fer4_2   3 vvvdtd..rCigCgaCvsaC 20 
                                    +++d+d   Ci Cg C   C
  gi|116754225|ref|YP_843343.1| 165 PFFDRDynLCIMCGRCARIC 184
                                    56666666*********999 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00014
                         Fer4_2   8 drCigCgaCvsaCPa 22 
                                     +C  CgaCv+aCP+
  gi|116754225|ref|YP_843343.1| 213 STCKFCGACVDACPT 227
                                    57888*********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 !   20.9  11.1   3.7e-07    0.0004       2      52 .]     174     229 ..     173     229 .. 0.80
   2 !   14.7   8.9   3.2e-05     0.034       1      45 [.     214     256 ..     214     258 .. 0.80
   3 ?   -1.9   0.1         5   5.3e+03      42      48 ..     362     368 ..     330     376 .. 0.66

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 3.7e-07
                         Fer4_7   2 CigCgaCvaaCp....vkaieldeeenekgtekv....eidpekClgCgaCvavCPtga 52 
                                    Ci Cg+C++ C+     +++++  + +++g  ++     + +++C +CgaCv++CPtga
  gi|116754225|ref|YP_843343.1| 174 CIMCGRCARICSelrgEGVLQMIAD-YHRG--SWigpdSLIESTCKFCGACVDACPTGA 229
                                    ***********87776888888665.6776..443454667889*************98 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 3.2e-05
                         Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveid.pekClgCga.Cv 45 
                                    +C  CgaCv+aCp++a++ + e+     e++e++  ++C +Cg+ C+
  gi|116754225|ref|YP_843343.1| 214 TCKFCGACVDACPTGALYARIEK----WERAEHSaVTTCPFCGVgCQ 256
                                    5999**************98874....44455543789999999887 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 5
                         Fer4_7  42 gaCvavC 48 
                                    ++C++ C
  gi|116754225|ref|YP_843343.1| 362 DNCARLC 368
                                    4455555 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.3   0.00078      0.82       5      19 ..     170     184 ..     166     201 .. 0.80
   2 !   20.2   5.7   4.4e-07   0.00047       6      52 ..     212     256 ..     208     258 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00078
                        Fer4_10   5 dddtCirCgkCvkaC 19 
                                    d + Ci Cg+C + C
  gi|116754225|ref|YP_843343.1| 170 DYNLCIMCGRCARIC 184
                                    678899999999999 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 4.4e-07
                        Fer4_10   6 ddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcg.aCv 52 
                                    ++tC  Cg+Cv+aCP+   +  +  +++ e a++ +v  C++cg  C+
  gi|116754225|ref|YP_843343.1| 212 ESTCKFCGACVDACPT---GALYARIEKWERAEHSAVTTCPFCGvGCQ 256
                                    689*************...5555555555555666********97786 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   3.5     0.005       5.3       1      11 [.     174     184 ..     174     187 .. 0.94
   2 !   15.1   6.1   3.1e-05     0.033       1      15 []     215     229 ..     215     229 .. 0.97

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.005
                         Fer4_3   1 CtgCgaCvevC 11 
                                    C++Cg+C + C
  gi|116754225|ref|YP_843343.1| 174 CIMCGRCARIC 184
                                    *********** PP

  == domain 2  score: 15.1 bits;  conditional E-value: 3.1e-05
                         Fer4_3   1 CtgCgaCvevCPvgA 15 
                                    C  CgaCv++CP+gA
  gi|116754225|ref|YP_843343.1| 215 CKFCGACVDACPTGA 229
                                    99************9 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 ?   -2.9   0.0       7.6     8e+03      16      47 ..      73     104 ..      70     117 .. 0.61
   2 ?   12.1   0.0   0.00016      0.16      12      48 ..     826     863 ..     816     876 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 7.6
                                    EEEE-HHHHHHHTS-TTSEEEEECCCCEEEEE CS
                        CDC48_N  16 ivridpedmeelglepgdvveiegkrkTvaiv 47 
                                    +vr d++ ++e++ ++ + +    ++   +++
  gi|116754225|ref|YP_843343.1|  73 VVRTDTSEIQEMRRNTLELLLAITSHPVSCLI 104
                                    56666666666666666666666655555555 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00016
                                    SSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEE.EEEE CS
                        CDC48_N  12 vgrgivridpedmeelglepgdvveiegkrkTv.aivw 48 
                                     g  +v i+ped ++lgl++gd ve+  +r +v a v 
  gi|116754225|ref|YP_843343.1| 826 RGEEVVEINPEDGANLGLNEGDLVEVASRRGSVrARVR 863
                                    58899**********************98765525554 PP

>> DNA_gyraseA_C  DNA gyrase C-terminal domain, beta-propeller
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   9.3e-05     0.098       8      27 ..      69      88 ..      68      89 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.3e-05
                                   TTSEEEEEEGGGS-BT-TTS CS
                  DNA_gyraseA_C  8 snGyvkrfplselpeqgRga 27
                                   +nG+v+r++ se+ e++R++
  gi|116754225|ref|YP_843343.1| 69 ENGMVVRTDTSEIQEMRRNT 88
                                   79****************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 ?    8.8   0.5    0.0026       2.7       4      21 ..     170     187 ..     167     201 .. 0.83
   2 ?    6.5   1.8     0.014        14       6      20 ..     213     227 ..     212     232 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0026
                        Fer4_15   4 DrdaCigcglCvaeapev 21 
                                    D ++Ci+cg+C++ ++e+
  gi|116754225|ref|YP_843343.1| 170 DYNLCIMCGRCARICSEL 187
                                    7789***********865 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.014
                        Fer4_15   6 daCigcglCvaeape 20 
                                    ++C  cg+Cv+++p+
  gi|116754225|ref|YP_843343.1| 213 STCKFCGACVDACPT 227
                                    69***********96 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   1.6     0.058        61       4      18 ..     172     186 ..     170     187 .. 0.86
   2 ?    6.6   1.8      0.01        11       2      18 ..     212     227 ..     211     234 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.058
                        Fer4_13   4 dtCiacgaCvelaPd 18 
                                    + Ci cg C+ ++ +
  gi|116754225|ref|YP_843343.1| 172 NLCIMCGRCARICSE 186
                                    67***********86 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.01
                        Fer4_13   2 DrdtCiacgaCvelaPd 18 
                                    + +tC  cgaCv+++P 
  gi|116754225|ref|YP_843343.1| 212 E-STCKFCGACVDACPT 227
                                    5.89************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (920 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); 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):              17  [number of targets reported over threshold]
# CPU time: 0.67u 0.24s 00:00:00.91 Elapsed: 00:00:00.41
# Mc/sec: 6705.34
//
Query:       gi|116754226|ref|YP_843344.1|  [L=560]
Description: thermosome [Methanosaeta thermophila PT]
Scores for complete 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-173  577.5   9.3   2.6e-173  577.2   9.3    1.1  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family
  ------ inclusion threshold ------
      0.044   13.7   0.1      0.044   13.7   0.1    2.3  2  Dak2        DAK2 domain
      0.086   13.2   0.3         40    4.6   0.0    3.7  3  Antiterm    Antitermination protein
       0.17   11.5   2.4        1.3    8.6   0.0    3.2  4  PrpR_N      Propionate catabolism activator


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  577.2   9.3  5.8e-177  2.6e-173       1     491 []      35     526 ..      35     526 .. 0.98

  Alignments for each domain:
  == domain 1  score: 577.2 bits;  conditional E-value: 5.8e-177
                                    HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHHHHH CS
                     Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleeaekl 80 
                                    +a++vkttlGPkGmdK+lv++ g+v++TnDG+til+e+e++hPaak++veaa++qd+evGDGTttv+iL+geLl+ a +l
  gi|116754226|ref|YP_843344.1|  35 VANAVKTTLGPKGMDKLLVDALGDVTITNDGVTILREMEVQHPAAKMVVEAAKTQDKEVGDGTTTVAILIGELLKHAREL 114
                                    689***************************************************************************** PP

                                    HHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHH.HCHCCCS.. CS
                     Cpn60_TCP1  81 iaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAv.klieene.. 157
                                    +++g+hpt+i +gy +a+eka+e+L++ia+++s  ekdr  L kva t++++kl ++ + ++++ +vd v +++++ +  
  gi|116754226|ref|YP_843344.1| 115 MEKGLHPTVIARGYSMAAEKAVEYLNSIARDVS--EKDRALLEKVAITAMTGKLAETPSHKVARYAVDLVlSTVDKFDgk 192
                                    ****************************66665..679********************************8888877798 PP

                                    EECSCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCCHHHHHHHHH CS
                     Cpn60_TCP1 158 keldlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdaeeleklekae 237
                                    + +dl+++ v+k  gg +edsel++G+++dk+ ++++mp+++ena+++ll+v++e   tetk+++ +++ ++++ ++++e
  gi|116754226|ref|YP_843344.1| 193 TVVDLDNVMVEKRVGGGIEDSELIRGVIIDKERVHQNMPRRVENARIALLNVPIERRDTETKAEISITSGDQFQLFMDHE 272
                                    99****************************************************************************** PP

                                    HHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGGCGC-EEEEEEEE CS
                     Cpn60_TCP1 238 ekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledltpeelGtakkvee 317
                                    +++++++++k+i+sg+nvv+cqkgiddla+hflak+gi+a rr++k+dle+l++atG++++++l++++pe+lG+a  vee
  gi|116754226|ref|YP_843344.1| 273 KEEIKKVVDKVIRSGANVVFCQKGIDDLAQHFLAKAGIMAYRRIRKSDLEKLSRATGGRLITNLDEMKPEDLGEAALVEE 352
                                    ******************************************************************************** PP

                                    CCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHHHHHHHHCCCCTSXCC CS
                     Cpn60_TCP1 318 ekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatelelakklkeyaksvsge 397
                                    + +g   +t+++++k+++  +++lrg t++v+d +era++dAl++v+ aie++++++GGGa e+++  kl+eya s++g+
  gi|116754226|ref|YP_843344.1| 353 RIVGAGPMTFVTGCKNPGYLSLILRGGTQQVVDSLERALDDALHAVATAIESGRLLAGGGAPETAVGIKLREYAASLKGR 432
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEECCCCTXEEEHHHHHHHHHHHHHHH CS
                     Cpn60_TCP1 398 eqlaieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiidlveagvvDplkvkrqalksAteaa 477
                                    eqla+e+fa+A+ev+pktLaeNaG++pi+ +  lr++h+k   ++g+++ +gei+d+++ gvv+pl+vk qa+ sAt+aa
  gi|116754226|ref|YP_843344.1| 433 EQLAVEKFAEAIEVVPKTLAENAGFNPIDKMVALRSKHEKFGSTYGLNAYTGEIVDMWDIGVVEPLRVKVQAIYSATDAA 512
                                    ***************************************9999************************************* PP

                                    HHHHCEEEEEXXXX CS
                     Cpn60_TCP1 478 stiLrideiikakk 491
                                    s+iLrid++i akk
  gi|116754226|ref|YP_843344.1| 513 SLILRIDDVIAAKK 526
                                    ***********985 PP

>> Dak2  DAK2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.2      0.64   2.9e+03      91     138 ..      40      87 ..      13     100 .. 0.46
   2 ?   13.7   0.1   9.9e-06     0.044      13      97 ..     378     462 ..     375     471 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.64
                                    ---TTSSSTHHHHHHHHHHHHT...........T---HHHHHHHHHHC CS
                           Dak2  91 karpgdkTmlDvlrpavealekakdgedlkealekaakaaekgaeaTk 138
                                    k++ g k m   l+ a   +  ++dg ++ + +e    aa+  +ea k
  gi|116754226|ref|YP_843344.1|  40 KTTLGPKGMDKLLVDALGDVTITNDGVTILREMEVQHPAAKMVVEAAK 87 
                                    333444444333333333333333333444444444444444444444 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 9.9e-06
                                    HHHHHHHHHHHC---SSHHHHHHHHHHHHHHH--STHHHHHHHHHHHHHHHC.....TT---HHHHHHHHHHHHHHHH-- CS
                           Dak2  13 rgaeavlkaleeleeaslaevlkalakallsgagGtsGvlysqflralakalkekeeldaedlaaalkaaleaiqavgka 92 
                                     g ++v++ le++ ++ l +v++a+ ++ l + gG+  +  ++ lr+ a++lk++e+l +e++a+a++   +++ + ++ 
  gi|116754226|ref|YP_843344.1| 378 GGTQQVVDSLERALDDALHAVATAIESGRLLAGGGAPETAVGIKLREYAASLKGREQLAVEKFAEAIEVVPKTLAENAGF 457
                                    68999***************************************************************999999998888 PP

                                    -TTSS CS
                           Dak2  93 rpgdk 97 
                                    +p dk
  gi|116754226|ref|YP_843344.1| 458 NPIDK 462
                                    88887 PP

>> Antiterm  Antitermination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0    0.0089        40      24      59 ..       5      39 ..       1      56 [. 0.84
   2 ?    3.7   0.0     0.018        80      34      63 ..     126     153 ..     118     169 .. 0.79
   3 ?   -0.8   0.0      0.43   1.9e+03      47      77 ..     173     203 ..     166     205 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0089
                                   HXTSXXETTTXXBXSTTHHHHHHHHHCCCCCHGHHH CS
                       Antiterm 24 qlGvpvflakrGysrldsteaiealtklapaltekt 59
                                     Gvpv++ k+G +r    eaie   + a+a+++ +
  gi|116754226|ref|YP_843344.1|  5 G-GVPVIILKEGTQRESGREAIENNIMAARAVANAV 39
                                   5.9*******************99888888888876 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.018
                                    XXBXSTTHHHHHHHHHCCCCCHGHHHHHTS CS
                       Antiterm  34 rGysrldsteaiealtklapaltektlrkl 63 
                                    rGys + +++a+e+l+ +a++++ek  r+l
  gi|116754226|ref|YP_843344.1| 126 RGYS-MAAEKAVEYLNSIARDVSEKD-RAL 153
                                    7999.5556***************99.433 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.43
                                    HHHCCCCCHGHHHHHTSHHHHCHHHHHHHHH CS
                       Antiterm  47 altklapaltektlrklwerkvkpflelLvt 77 
                                     + ++a +l+ +t+ k ++++v ++ +++v+
  gi|116754226|ref|YP_843344.1| 173 KVARYAVDLVLSTVDKFDGKTVVDLDNVMVE 203
                                    5677888888888888899999999888887 PP

>> PrpR_N  Propionate catabolism activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1     0.078   3.5e+02     144     164 ..      19      39 ..      14      42 .. 0.89
   2 ?   -3.0   0.0         1   4.6e+03      16      37 ..     106     128 ..     100     132 .. 0.76
   3 ?    8.6   0.0   0.00029       1.3      90     135 ..     258     303 ..     232     314 .. 0.78
   4 ?   -1.9   0.0      0.48   2.1e+03     127     159 ..     360     392 ..     353     403 .. 0.55

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.078
                         PrpR_N 144 tsgkesvrqAieeAleiarat 164
                                    +sg+e++++ i  A+++a+a 
  gi|116754226|ref|YP_843344.1|  19 ESGREAIENNIMAARAVANAV 39 
                                    79***************9986 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1
                         PrpR_N  16 eavelakel.eaegvdviiSrGg 37 
                                    e +++a+el e+     +i+rG 
  gi|116754226|ref|YP_843344.1| 106 ELLKHARELmEKGLHPTVIARGY 128
                                    56889999956666779999996 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.00029
                         PrpR_N  90 selldldieiytinseeeaeaavkelkaegvevvvGdgvvadlAek 135
                                    s   + + +++  ++ ee++++v+++ ++g +vv + + + dlA++
  gi|116754226|ref|YP_843344.1| 258 SITSGDQFQLFMDHEKEEIKKVVDKVIRSGANVVFCQKGIDDLAQH 303
                                    4445666777777999****************************97 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 0.48
                         PrpR_N 127 gvvadlAekaGlksvlltsgkesvrqAieeAle 159
                                    ++ ++ +++ G+ s++l+ g + v  ++e+Al+
  gi|116754226|ref|YP_843344.1| 360 MTFVTGCKNPGYLSLILRGGTQQVVDSLERALD 392
                                    555555555555566666655555444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (560 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 4031.78
//
Query:       gi|116754227|ref|YP_843345.1|  [L=364]
Description: hypothetical protein Mthe_0917 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-13   51.7   0.1    1.4e-13   51.7   0.1    2.3  2  MacB_PCD         MacB-like periplasmic core domain
    3.5e-10   40.2   7.1    6.7e-10   39.3   1.1    2.8  3  FtsX             FtsX-like permease family
  ------ inclusion threshold ------
       0.13   11.4   3.7        0.2   10.7   3.7    1.3  1  ABC2_membrane_3  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> MacB_PCD  MacB-like periplasmic core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.7   0.1   2.3e-17   1.4e-13       5     193 ..       1     205 [.       1     207 [. 0.74
   2 ?   -1.7   4.3      0.53   3.2e+03       2      21 ..     237     256 ..     236     281 .. 0.88

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 2.3e-17
                       MacB_PCD   5 vLGiaiGvaaviaivslgeglqasvlsqisdlgnlvtvtpgkgsgeslsdpdveal.rr..evp.veavapvv.....tv 75 
                                    +L+i ++va+ ++ vsl +g+q+++l+ i    +l++v++++ +ge+    ++++l +r  +++ v+av+p++     + 
  gi|116754227|ref|YP_843345.1|   1 MLAIGLAVAVSVTSVSLQAGFQEYLLDIIV--KDLAHVSVSPKEGEE-YIYLYRTLmERiwQLEgVTAVSPRLstpasL- 76 
                                    9**************************776..668999998755555.22345444234576778******98776432. PP

                       MacB_PCD  76 rgggsgeeevtvvgvdpdyfk.vfglklaeGrffteadlr..ggpnvvvigeelaerlf.pvGdtirl.......kpftV 144
                                    +  + + e+v ++gv p++ + ++     + r+    +l+  +++n +v++++lae+l   + dt+          ++ V
  gi|116754227|ref|YP_843345.1|  77 SHKN-NVENVILIGVIPSEMErIYPS--ISERM-VYGELEsiQQENRIVMSKKLAEKLDvELDDTVDArfpdanpLNLMV 152
                                    2332.234599999776554424333..44564.5555553469999**********88*9*****9999**98888*** PP

                       MacB_PCD 145 vGvledppgsgsalgddavylplttlqrrs.........itvrlkdgadleaaaaele 193
                                    +G++++p +   ++ +   +++l+t++ ++         i ++l d   ++ +++e+ 
  gi|116754227|ref|YP_843345.1| 153 TGIFDPP-Q---GFPEEMTFVSLRTAR-NFlgegdvingIDIKLHDIYMADRISREIS 205
                                    ****544.2...3468899***99983.334677777779999999999999988886 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.53
                       MacB_PCD   2 lltvLGiaiGvaaviaivsl 21 
                                    ll ++  a+G+a+v+ +++l
  gi|116754227|ref|YP_843345.1| 237 LLIMIIAAFGIASVMYMLVL 256
                                    78999************997 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.35   2.1e+03      34      54 ..       3      19 ..       1      47 [. 0.55
   2 ?    3.3   0.1      0.02   1.2e+02      58      83 ..     230     255 ..     198     258 .. 0.67
   3 !   39.3   1.1   1.1e-13   6.7e-10       2      96 .]     260     358 ..     259     358 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.35
                           FtsX 34 viGlglgllaaqllsdvllss 54
                                   +iGl++++ ++ +     l+ 
  gi|116754227|ref|YP_843345.1|  3 AIGLAVAVSVTSV----SLQA 19
                                   3444443333333....3333 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.02
                           FtsX  58 selkisidlitvliiivlllllalla 83 
                                    +e  i + li+++++++++ ++++l+
  gi|116754227|ref|YP_843345.1| 230 FENRIIMLLIMIIAAFGIASVMYMLV 255
                                    45555555666666666666665555 PP

  == domain 3  score: 39.3 bits;  conditional E-value: 1.1e-13
                           FtsX   2 reigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfs.....selkisidlitvliiivll 76 
                                    +eig+l a G++ + ++ ++l+++ +++l++ + G + g+++  l  ++++ +v +     + l++ id+   lii+v +
  gi|116754227|ref|YP_843345.1| 260 SEIGMLMAEGATGAMIRNIFLIQSTVLGLIGGICGAAGGVAL-SLYLKGMEFEVEApgweeFVLPVVIDPWNTLIIVVAA 338
                                    7**********************************6666555.666788888877678888******************* PP

                           FtsX  77 lllallagllsiskilkkep 96 
                                    +ll l+ag++++ k++k +p
  gi|116754227|ref|YP_843345.1| 339 VLLSLAAGVYPAHKASKLDP 358
                                    *****************987 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   3.7   3.3e-05       0.2     157     206 ..     228     274 ..     196     349 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 3.3e-05
                ABC2_membrane_3 157 snvasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqyw 206
                                    +n+++ ++ l+++i++ ++++++++++v Ek+s i +l+      ++  +
  gi|116754227|ref|YP_843345.1| 228 ENFENRIIMLLIMIIAAFGIASVMYMLVLEKTSEIGMLMA---EGATGAM 274
                                    6777778999999999999999***********9997763...3444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       821  (0.0457917); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 2866.84
//
Query:       gi|116754228|ref|YP_843346.1|  [L=389]
Description: hypothetical protein Mthe_0918 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-19   70.5   0.5      3e-19   70.1   0.5    1.2  1  MacB_PCD  MacB-like periplasmic core domain
      5e-15   55.7   4.7      5e-15   55.7   4.7    2.9  3  FtsX      FtsX-like permease family


Domain annotation for each model (and alignments):
>> MacB_PCD  MacB-like periplasmic core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.1   0.5   3.4e-23     3e-19       2     194 ..      22     229 ..      21     230 .. 0.76

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 3.4e-23
                       MacB_PCD   2 lltvLGiaiGvaaviaivslgeglqasvlsq.isdlgnlvtvtpgkgsgeslsdpdvealrr..evp.veavapvv.... 73 
                                    ++tvL++a++va ++++++l+ g+++ + ++ i+++ + v++ p++g++e   ++ ++a       p veav+p++    
  gi|116754228|ref|YP_843346.1|  22 FFTVLSVALAVAIIVVMMGLMGGFREEIMRTtIENNPH-VVIEPKEGENEIHLYRTLSA--IvwTYPgVEAVSPRLkgka 98 
                                    89*************************99994444444.55777654333322333333..1345899******998887 PP

                       MacB_PCD  74 tvrgggsgeeevtvvg..vdpdyfkvfgl..klaeGrffteadlrggpnvvvigeelaerlf.pvGdtirl......kpf 142
                                    +v ++++ +++v v g  ++ d+  +  +  +l eG+f    dl+  +++ vig++lae++    Gd+i+l      +++
  gi|116754228|ref|YP_843346.1|  99 VVEYRDR-ARGVEVLGviPT-DEDPLMRVerDLIEGSF---MDLELSRYSTVIGSKLAEEIRaSTGDRIELirqnrsINL 173
                                    5566654.555889997655.88887788656699976...578888999**********8899*********999999* PP

                       MacB_PCD 143 tVvGvledppgsgsalgddavylplttl........qrrsitvrlkdgadleaaaaelek 194
                                    +++G++e+  g  +a + + vy+pl+t+         ++++ vrl d  d++ +a+e+++
  gi|116754228|ref|YP_843346.1| 174 EIAGIVET--G--TATDKTLVYIPLKTAqdilgegdVVSEVSVRLYDLYDASYLAEEINR 229
                                    *****944..5..4456889****8888444444433555*****999999999998875 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1     0.081   7.2e+02      70      83 ..      23      36 ..       3      52 .. 0.56
   2 ?    0.2   0.3      0.12   1.1e+03      26      37 ..     258     269 ..     235     281 .. 0.53
   3 !   55.7   4.7   5.6e-19     5e-15       2      96 .]     284     382 ..     283     382 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.081
                           FtsX 70 liiivlllllalla 83
                                   ++++ ++l +a+++
  gi|116754228|ref|YP_843346.1| 23 FTVLSVALAVAIIV 36
                                   22222222222222 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.12
                           FtsX  26 llitlvalviGl 37 
                                    ++++l+ +++G+
  gi|116754228|ref|YP_843346.1| 258 IFYILIFAIAGF 269
                                    112222222222 PP

  == domain 3  score: 55.7 bits;  conditional E-value: 5.6e-19
                           FtsX   2 reigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfs....selkisidlitvliiivlll 77 
                                    +eigil a+G+++ ++++++++e+l+++ ++++iG++l+++aa l++ +  +  +     s++++ ++++ ++ +++ ++
  gi|116754228|ref|YP_843346.1| 284 KEIGILMAMGATRLSIMKIFILESLILAPPSALIGCILAYIAARLIMMYPVELPSEiymvSRMTVVMKPEFFFWAVIYSM 363
                                    8********************************************887776664435556******************** PP

                           FtsX  78 llallagllsiskilkkep 96 
                                    ++ l+agl++++++++ +p
  gi|116754228|ref|YP_843346.1| 364 IVNLVAGLYPAYRASRLDP 382
                                    ****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       849  (0.0473534); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); 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 0.28s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2780.40
//
Query:       gi|116754229|ref|YP_843347.1|  [L=297]
Description: pyridoxal biosynthesis lyase PdxS [Methanosaeta thermophila PT]
Scores for complete 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-105  349.6  10.0   5.6e-105  349.6  10.0    1.5  2  SOR_SNZ       SOR/SNZ family
    3.4e-08   33.1  12.2    1.2e-07   31.4   0.8    2.6  2  ThiG          Thiazole biosynthesis protein ThiG
    3.6e-06   26.3   0.7       0.02   14.0   0.0    2.5  2  Dus           Dihydrouridine synthase (Dus)
    8.7e-05   21.8   0.1    0.00088   18.5   0.0    2.1  2  IGPS          Indole-3-glycerol phosphate synthase
    0.00017   21.1   5.4    0.00043   19.8   0.2    2.2  2  NMO           Nitronate monooxygenase
    0.00021   20.5   2.4       0.02   14.1   0.0    2.6  2  NanE          Putative N-acetylmannosamine-6-phosphate epimer
     0.0076   15.5   1.4       0.19   10.9   0.1    2.4  2  DUF561        Protein of unknown function (DUF561)
  ------ inclusion threshold ------
      0.023   14.2   0.2       0.15   11.5   0.0    2.1  2  His_biosynth  Histidine biosynthesis protein
      0.033   13.2   1.1      0.046   12.7   0.0    1.8  3  FMN_dh        FMN-dependent dehydrogenase
      0.042   13.2   1.7        1.6    8.0   0.1    2.3  2  TMP-TENI      Thiamine monophosphate synthase
      0.087   12.9   0.0       0.32   11.1   0.0    1.9  1  TetR_C_27     Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> SOR_SNZ  SOR/SNZ family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  349.6  10.0  3.4e-108  5.6e-105       3     207 .]      12     215 ..      10     215 .. 0.99
   2 ?   -2.8   0.0       2.7   4.4e+03     150     159 ..     252     261 ..     244     271 .. 0.58

  Alignments for each domain:
  == domain 1  score: 349.6 bits;  conditional E-value: 3.4e-108
                                    HHHHHHHHTTTSSEEEEESSHHHHHHHHHHT-SEEEE-SS-HHHHHHH-S------HHHHHHHHHH-SS-EEEEEETT-H CS
                        SOR_SNZ   3 kvkaglaemlkgGvimdvvnaeqakiaeeaGavavmalervpadirkeggvarmsdpklikeikeavsipvmakvriGhf 82 
                                     +k+g+a+m+kgGvimdv+++eqa iaeeaGavavmal+ vpadirk ggvarm+dpk+i+ei++av+ipvmakvriGhf
  gi|116754229|ref|YP_843347.1|  12 LLKRGFAKMQKGGVIMDVTTPEQAMIAEEAGAVAVMALHAVPADIRKMGGVARMADPKVIEEIIDAVTIPVMAKVRIGHF 91 
                                    589***************************************************************************** PP

                                    HHHHHHHHTT-SEEEEETTS--S-SS----GGG-SS-EEEEESSHHHHHHHHHHT-SEEEEES-TTS--THHHHHHHHHH CS
                        SOR_SNZ  83 veaqilealgvdyiDesevltpadeeahidkkkfkvpfvcGarnlgealrriaeGaamirtkGeagtGdvveavrhvrki 162
                                    veaqilea+gvd+iDesevltpade +hidk+kfkvpfvcGarnlgealrri+eGaamirtkGeagtGdv++avrh+++i
  gi|116754229|ref|YP_843347.1|  92 VEAQILEAIGVDMIDESEVLTPADE-FHIDKTKFKVPFVCGARNLGEALRRIKEGAAMIRTKGEAGTGDVSQAVRHMKMI 170
                                    ************************7.8***************************************************** PP

                                    HHHHHHHTTS-HHHHHHHHHHHHGGGHHHHHHHHHTTS-S---T. CS
                        SOR_SNZ 163 keeirklkslseeelvalakelkaplelvkevaelgrlpvvnfaa 207
                                    + +irklk +++eel+++a+e++a+ elv+e+a+ +rlpvvnfaa
  gi|116754229|ref|YP_843347.1| 171 MGDIRKLKGMNSEELMKFAREIEADPELVAECARIQRLPVVNFAA 215
                                    *******************************************98 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.7
                                    --THHHHHHH CS
                        SOR_SNZ 150 Gdvveavrhv 159
                                      +veav+h 
  gi|116754229|ref|YP_843347.1| 252 SAIVEAVHHY 261
                                    4555565554 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   3.8    0.0025         4     137     200 ..      35     104 ..       3     126 .. 0.74
   2 !   31.4   0.8   7.1e-11   1.2e-07     175     225 ..     207     259 ..     189     268 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0025
                                    HHHHHHTT-SEBEEBSSS......TTS----S-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SE CS
                           ThiG 137 arrleevGcaavmPlaap......iGsglGllnkealkiiieeakvPvivDAGigspsdaaqamelGada 200
                                    a   ee+G+ avm l a       +G    ++++++++ ii+ +++Pv+    ig+  +a     +G+d 
  gi|116754229|ref|YP_843347.1|  35 AMIAEEAGAVAVMALHAVpadirkMGGVARMADPKVIEEIIDAVTIPVMAKVRIGHFVEAQILEAIGVDM 104
                                    444589*******9976323322256666678899********************999998877788876 PP

  == domain 2  score: 31.4 bits;  conditional E-value: 7.1e-11
                                    SS-BEEES..---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHHHHHHHHHH CS
                           ThiG 175 kvPvivDA..GigspsdaaqamelGadavllntavaeakdpvamArafklave 225
                                    ++Pv+  A  Gi +p daa  m+lGad+v++ + + ++++p amA+a+  av+
  gi|116754229|ref|YP_843347.1| 207 RLPVVNFAagGIATPADAALMMQLGADGVFVGSGIFKSENPEAMASAIVEAVH 259
                                    67887544349**************************************9996 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.1   0.00019      0.31      95     133 ..      56      90 ..      52     106 .. 0.81
   2 !   14.0   0.0   1.2e-05      0.02     179     229 ..     205     257 ..     185     274 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00019
                                    TTEEEGGGGGGSHHHHHHHHHHHHCCSSS-EEEEEESES CS
                            Dus  95 trggaGaaLlrkpdlvaqivkavvkaveiPvtvkirigi 133
                                    +r+++G a +++p+++++i+    +av iPv +k+rig 
  gi|116754229|ref|YP_843347.1|  56 IRKMGGVARMADPKVIEEII----DAVTIPVMAKVRIGH 90 
                                    68999999999999988887....5789*********96 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 1.2e-05
                                    HHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHC..CSTTHHHH.HHHH CS
                            Dus 179 kqavsipviaNGdIkdaedaqaileetGadgvmigrgal..gnPwlfae.stav 229
                                     q+++++ +a G+I ++ da  +++  Gadgv +g g    +nP  +a+   ++
  gi|116754229|ref|YP_843347.1| 205 IQRLPVVNFAAGGIATPADAALMMQL-GADGVFVGSGIFksENPEAMASaIVEA 257
                                    477888889***********999998.*********975226888887543333 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.11   1.7e+02      61      88 ..      22      49 ..      18     105 .. 0.78
   2 !   18.5   0.0   5.4e-07   0.00088     180     251 ..     176     251 ..     162     254 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.11
                                   TEESBSS--HHHHHHHHTTT.-SEEEEE CS
                           IGPS 61 kgliredfdpaeiAkkyeeagAsaiSVL 88
                                   kg + +d+  +e+A   eeagA a+  L
  gi|116754229|ref|YP_843347.1| 22 KGGVIMDVTTPEQAMIAEEAGAVAVMAL 49
                                   7888999999999999999999988555 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 5.4e-07
                                    SEEEEESEETTTTEE-CHHHHHHCHCC-..TT..SEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC-TTHHHHH CS
                           IGPS 180 kiiGvNnRnLktlevdlntteeLaklvp..kd..vllvaeSGiktredveklkeegvnafLvGeslmrqedvekai 251
                                    k+ G+N+ +L ++  +++   eL+++    +   v+  a  Gi+t++d+  + + g++++ vG+ + ++e+ e++ 
  gi|116754229|ref|YP_843347.1| 176 KLKGMNSEELMKFAREIEADPELVAECAriQRlpVVNFAAGGIATPADAALMMQLGADGVFVGSGIFKSENPEAMA 251
                                    778********************99877552324777899*****************************9988765 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   1.3     0.028        45     180     198 ..      66      84 ..      18     100 .. 0.72
   2 !   19.8   0.2   2.6e-07   0.00043     181     268 ..     195     286 ..     176     295 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.028
                            NMO 180 glfaLvpqvldavdiPviA 198
                                       ++++++ dav iPv+A
  gi|116754229|ref|YP_843347.1|  66 ADPKVIEEIIDAVTIPVMA 84 
                                    456899************9 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 2.6e-07
                            NMO 181 lfaLvpqvldavdiPvi..AaGGiidrrgvaaaLalGAsgvqigtrfLltk..esdakdahkkklleaklddteltsavs 256
                                      +Lv++ +    +Pv+  AaGGi +  + a ++ lGA gv +g+     +  e+ a++++++     + + +  +s+  
  gi|116754229|ref|YP_843347.1| 195 DPELVAECARIQRLPVVnfAAGGIATPADAALMMQLGADGVFVGSGIFKSEnpEAMASAIVEAVHHYDEPEVLAKVSRGL 274
                                    55688888888889**877**************************98877622455555555554444444444445555 PP

                            NMO 257 GrpaRalatell 268
                                    Grp++++  + l
  gi|116754229|ref|YP_843347.1| 275 GRPMKGIDVGTL 286
                                    677766666555 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   0.6    0.0054       8.8      96     170 ..      26     105 ..      11     118 .. 0.73
   2 !   14.1   0.0   1.2e-05      0.02     145     180 ..     210     245 ..     177     260 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0054
                                    EEE-SSHHHHHHHHHTT-SEEE-TTTTSSTTS-......SS--HHHHHHHHHT.T--EEEES---SHHHHHHHHTT--SE CS
                           NanE  96 maDistleeglvakklGvdivGttlsGytkeeek.....aepDfalvkalsea.glkviaeGrintPekakkaieiGvda 169
                                    + D+ t e++++a+++G+  v  +l     + +k        D ++++++ +a  + v+a  ri    +a+    iGvd+
  gi|116754229|ref|YP_843347.1|  26 IMDVTTPEQAMIAEEAGAVAVM-ALHAVPADIRKmggvaRMADPKVIEEIIDAvTIPVMAKVRIGHFVEAQILEAIGVDM 104
                                    4599999999999999987664.455555555444556567888999998887356699999999999999999999988 PP

                                    E CS
                           NanE 170 v 170
                                    +
  gi|116754229|ref|YP_843347.1| 105 I 105
                                    7 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 1.2e-05
                                    --EEEES---SHHHHHHHHTT--SEEEE-HHHH-HH CS
                           NanE 145 lkviaeGrintPekakkaieiGvdavvvGsaitrle 180
                                    +   a G i tP+ a+ ++++G+d v vGs i + e
  gi|116754229|ref|YP_843347.1| 210 VVNFAAGGIATPADAALMMQLGADGVFVGSGIFKSE 245
                                    345689*************************98754 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.2     0.021        34      47      85 ..      65     105 ..      44     115 .. 0.72
   2 !   10.9   0.1   0.00012      0.19     182     232 ..     203     256 ..     134     265 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.021
                         DUF561  47 aadpklvkkvksvsniPiCvsaveakllleav...kaGadlv 85 
                                     adpk+++++ +++ iP+  + v + +++ea+   + G+d++
  gi|116754229|ref|YP_843347.1|  65 MADPKVIEEIIDAVTIPVM-AKVRIGHFVEAQileAIGVDMI 105
                                    6889999999999999984.5677777777762223455555 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00012
                         DUF561 182 skkvslPvi..casGlsd.vtvplalslgasGiGigsavsklndeeemvallse 232
                                    ++  +lPv+  +a G+++   + l ++lga G+ +gs + k ++ e+m +++ e
  gi|116754229|ref|YP_843347.1| 203 ARIQRLPVVnfAAGGIATpADAALMMQLGADGVFVGSGIFKSENPEAMASAIVE 256
                                    5667899975578999762568999***********************998876 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.26   4.2e+02      60      79 ..      66      85 ..      37     106 .. 0.71
   2 ?   11.5   0.0     9e-05      0.15      63     108 ..     197     244 ..     185     270 .. 0.63

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.26
                                   HHHHHHHHHHHH-SSEEEEE CS
                   His_biosynth 60 anldlveeiaeevfipvqvG 79
                                   a+ +++eei+++v+ipv+  
  gi|116754229|ref|YP_843347.1| 66 ADPKVIEEIIDAVTIPVMAK 85
                                   44467777777777777654 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 9e-05
                                    HHHHHHHHH-SSEE..EEESSSSSHHHHHHHHHCT-SEEEESHHHHH- CS
                   His_biosynth  63 dlveeiaeevfipv..qvGGGIrsledveelleagadkviigtaavkn 108
                                    +lv+e a+  ++pv     GGI +  d++ ++++gad v +g+  +k+
  gi|116754229|ref|YP_843347.1| 197 ELVAECARIQRLPVvnFAAGGIATPADAALMMQLGADGVFVGSGIFKS 244
                                    444444444444442235566666666666666666666666665543 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       1.3   2.2e+03     223     242 ..      28      47 ..      22      48 .. 0.85
   2 ?   -3.1   0.2       1.8   2.9e+03     204     240 ..      67     104 ..      31     106 .. 0.56
   3 ?   12.7   0.0   2.8e-05     0.046     194     243 ..     188     237 ..     121     242 .. 0.64

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.3
                                    EE-SHHHHHHHHHTTESEEE CS
                         FMN_dh 223 GvltaedakraveaGvdgiv 242
                                     v t+e a  a eaG+ +++
  gi|116754229|ref|YP_843347.1|  28 DVTTPEQAMIAEEAGAVAVM 47 
                                    589999********998885 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.8
                                    -HHHHHHHHHHHSSEEEEE.EE-SHHHHHHHHHTTESE CS
                         FMN_dh 204 twddikwlreqtklplvvK.GvltaedakraveaGvdg 240
                                    + + i+++ +++ +p++ K  + +  +a+ + ++Gvd 
  gi|116754229|ref|YP_843347.1|  67 DPKVIEEIIDAVTIPVMAKvRIGHFVEAQILEAIGVDM 104
                                    44456666666666666663355556666666666665 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 2.8e-05
                                    HCCCHB-TC--HH.HHHHHHHHHSSEEEEEEE-SHHHHHHHHHTTESEEEE CS
                         FMN_dh 194 fvgkqldpsltwd.dikwlreqtklplvvKGvltaedakraveaGvdgivv 243
                                    f+++ ++++ +   + +++++   +++   G+ t++da +++++G+dg+ v
  gi|116754229|ref|YP_843347.1| 188 FARE-IEADPELVaECARIQRLPVVNFAAGGIATPADAALMMQLGADGVFV 237
                                    3333.3333332225666666666667777888888888888888888877 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.013        21     104     155 ..      30      84 ..      24     105 .. 0.84
   2 ?    8.0   0.1   0.00099       1.6     140     181 .]     197     241 ..     186     241 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.013
                       TMP-TENI 104 hsleeaeeaealgadYigvGpifpTdtKkda...eplgleglkelaealeiPvva 155
                                     ++e+a+ ae++ga  +++ +  p d +k+    ++++ + ++e+ +a++iPv+a
  gi|116754229|ref|YP_843347.1|  30 TTPEQAMIAEEAGAVAVMALHAVPADIRKMGgvaRMADPKVIEEIIDAVTIPVMA 84 
                                    6889999*******999999999999999975557789999***********998 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00099
                       TMP-TENI 140 eglkelaealeiPvv..aiGGi.tlenvaevleagadgvavvsai 181
                                    e+++e+a+  ++Pvv  a GGi t++++a +++ gadgv v s+i
  gi|116754229|ref|YP_843347.1| 197 ELVAECARIQRLPVVnfAAGGIaTPADAALMMQLGADGVFVGSGI 241
                                    555666666667764449999967899**************9987 PP

>> TetR_C_27  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0    0.0002      0.32      61      94 ..     238     271 ..     231     276 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0002
                                    HCT-STT--HHHHHHHHHHHSGGGTSHHHHHHHG CS
                      TetR_C_27  61 aaGeFkaadpeaaaravfdatarfhhPalaaews 94 
                                     +G Fk+++pea+a+a+++a+ ++ +P ++a+ s
  gi|116754229|ref|YP_843347.1| 238 GSGIFKSENPEAMASAIVEAVHHYDEPEVLAKVS 271
                                    689************************9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); 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 0.25s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2251.02
//
Query:       gi|116754230|ref|YP_843348.1|  [L=186]
Description: SNO glutamine amidotransferase [Methanosaeta thermophila PT]
Scores for 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-51  172.3   0.0    1.1e-50  172.1   0.0    1.0  1  SNO            SNO glutamine amidotransferase family
    1.9e-09   37.4   0.0    2.2e-09   37.2   0.0    1.2  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
    0.00017   21.3   0.0    0.00023   20.9   0.0    1.1  1  Peptidase_S51  Peptidase family S51
    0.00073   19.4   0.1      0.053   13.3   0.1    2.1  2  GATase         Glutamine amidotransferase class-I
     0.0053   16.6   0.2     0.0088   15.9   0.2    1.3  1  DJ-1_PfpI      DJ-1/PfpI family
  ------ inclusion threshold ------
      0.013   14.6   0.0      0.028   13.5   0.0    1.4  2  BPL_N          Biotin-protein ligase, N terminal
      0.076   13.2   0.2       0.39   11.0   0.0    2.1  2  Peptidase_M23  Peptidase family M23


Domain annotation for each model (and alignments):
>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.1   0.0   4.2e-54   1.1e-50       1     184 [.       6     185 ..       6     186 .] 0.98

  Alignments for each domain:
  == domain 1  score: 172.1 bits;  conditional E-value: 4.2e-54
                                    EESSSSSHHHHHHHHHHTTSEEEEE-SGGGGCC-SEEEE-SS-HHHHHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHH CS
                            SNO   1 vlalqGaveehveaikkclaenktvkrkedlaevdaliiPGGestamskliertglyedllefvknsekvvlGtCaGlil 80 
                                    v+alqG+v eh+ ai++++ ++  v+r   +  + +++iPGGest++s+ +ertg+  ++++ ++n+  +vl tCaGl+l
  gi|116754230|ref|YP_843348.1|   6 VIALQGDVSEHISAIEAAGGQAVPVRRAGIIPTCSGIVIPGGESTTISRQLERTGIAAEIKQAAANG-TPVLATCAGLVL 84 
                                    89****************************************************************9.9*********** PP

                                    HCCEETTBSS-SS--CCEEEETTTT-SCCGEEEEEEEETTTCSEEEEEESS--EEEEE-.TTTCEEEEECTTEEEEEEET CS
                            SNO  81 lskelenelvktlellkvkvkrnafGrqvdsfekeldfknliekftavfiraPvieeilddeavkvlyeldgeivvakqk 160
                                     +ke++  +vk l+l++++v rnafG q +sfe+e+++++++ ++ avfiraPv+ + +  e v+ l    g+ v+++q+
  gi|116754230|ref|YP_843348.1|  85 AAKEIDAGDVKPLGLIDISVGRNAFGPQRESFEAEINVEGFDRPYRAVFIRAPVVLRCG--EGVEKLARFGGRTVAVRQG 162
                                    ***********************************************************..899999999********** PP

                                    TEEEESS-GGGSTTHCHHHHHHHH CS
                            SNO 161 kilatsfhPelaeddirvhdyfve 184
                                    ++++++fhPel+ d  r+h++++e
  gi|116754230|ref|YP_843348.1| 163 NVIGLAFHPELTGD-LRFHKMLLE 185
                                    ************99.****99876 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   0.0   8.6e-13   2.2e-09      27     115 ..      25     104 ..      14     171 .. 0.84

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 8.6e-13
                       GATase_3  27 vrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGeeiedpegvegeageve 106
                                    ++ vp+++  + + +  +++pGg++t+ + +l+r  g++ +ik+aa++g+pvl+ C+Gl +  +ei            v+
  gi|116754230|ref|YP_843348.1|  25 GQAVPVRRAGIIPTCSGIVIPGGESTTISRQLERT-GIAAEIKQAAANGTPVLATCAGLVLAAKEIDAG--------DVK 95 
                                    56677777777788******************999.***********************9988887653........578 PP

                       GATase_3 107 glglLdiet 115
                                     lgl+di++
  gi|116754230|ref|YP_843348.1|  96 PLGLIDISV 104
                                    888888876 PP

>> Peptidase_S51  Peptidase family S51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0     9e-08   0.00023      84     136 ..      40      92 ..      27     103 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 9e-08
                                    SEEEE--S-HHHHHHHHHHTTHHHHHHHHHHTT-EEEEETHHHHTTSSB-GGG CS
                  Peptidase_S51  84 dviyvgGGntfrLlkllketgldkllreavqqglvyiGvSAGaivagesiett 136
                                     +i++ GG+   + ++l++tg+++ +++a ++g+++  + AG + a+++i + 
  gi|116754230|ref|YP_843348.1|  40 SGIVIPGGESTTISRQLERTGIAAEIKQAAANGTPVLATCAGLVLAAKEIDAG 92 
                                    589*********************************************99875 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.1   2.1e-05     0.053      42      89 ..      38      90 ..      17     139 .. 0.83
   2 ?    4.5   0.0      0.01        27     162     182 ..     162     182 ..     144     185 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.1e-05
                                   STSEEEEEEESSCTT.....TTTHHHHHHHHCTSTS-EEEETHHHHHHHHHTT CS
                         GATase 42 npdgilvsgGpgspg.....vegkieaikearenkiPiLGICLGmQllaiefg 89
                                   ++ gi+++gG  +       ++g  + ik+a+ n++P+L  C G+ l+a+e+ 
  gi|116754230|ref|YP_843348.1| 38 TCSGIVIPGGESTTIsrqleRTGIAAEIKQAAANGTPVLATCAGLVLAAKEID 90
                                   5789******887666779977777788888888**************99874 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.01
                                    TTEEEESSBTTSTTSTTHHHH CS
                         GATase 162 npfvgvQFHPEststpegpel 182
                                     +++g+ FHPE t   + +++
  gi|116754230|ref|YP_843348.1| 162 GNVIGLAFHPELTGDLRFHKM 182
                                    2599********987776665 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 !   15.9   0.2   3.4e-06    0.0088      64     112 ..      41      89 ..      37      93 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.4e-06
                                    EEEE--BHHH..HHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHHHHTTT CS
                      DJ-1_PfpI  64 alvlpGGrag..perlrenekvvelvkefaekgklvaaICagpqlLaaagv 112
                                     +v+pGG++   + +l+  + + + +k++a +g++v a Cag ++Laa+++
  gi|116754230|ref|YP_843348.1|  41 GIVIPGGESTtiSRQLE-RTGIAAEIKQAAANGTPVLATCAG-LVLAAKEI 89 
                                    69*****9941123333.35788999****************.88888765 PP

>> BPL_N  Biotin-protein ligase, N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.1e-05     0.028      49     100 ..      38      90 ..      36      96 .. 0.90
   2 ?   -3.3   0.0       1.4   3.5e+03     206     222 ..     158     174 ..     155     179 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.1e-05
                          BPL_N  49 tcallVlPgGaDlpYvrelngegn.rkikeyVekGGkylGlCAGaYygskrve 100
                                    tc+ +V+PgG  +   r+l+++g+ ++ik+   +G   l+ CAG   ++k+++
  gi|116754230|ref|YP_843348.1|  38 TCSGIVIPGGESTTISRQLERTGIaAEIKQAAANGTPVLATCAGLVLAAKEID 90 
                                    89******************9987268*****************999988875 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.4
                          BPL_N 206 kvgeGkalLtgvhpEfa 222
                                     v +G+++  + hpE +
  gi|116754230|ref|YP_843348.1| 158 AVRQGNVIGLAFHPELT 174
                                    67899999999***976 PP

>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00015      0.39       8      29 ..      67      88 ..      60     101 .. 0.83
   2 ?   -1.0   0.0      0.83   2.1e+03      63      71 ..     159     167 ..     145     176 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00015
                                   EEETTT-EEEESSSEEEEEEEE CS
                  Peptidase_M23  8 iaapkgtpVlAaadGtVvfagk 29
                                    aa++gtpVlA+++G V+ a++
  gi|116754230|ref|YP_843348.1| 67 QAAANGTPVLATCAGLVLAAKE 88
                                   57889************99987 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.83
                                    E-TTCEEEE CS
                  Peptidase_M23  63 VkaGqvIGt 71 
                                    V++G+vIG 
  gi|116754230|ref|YP_843348.1| 159 VRQGNVIGL 167
                                    677777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1478.79
//
Query:       gi|116754231|ref|YP_843349.1|  [L=118]
Description: hypothetical protein Mthe_0921 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      0.006   17.2   6.4       0.55   10.9   1.3    2.1  2  YabA           Initiation control protein YabA
  ------ inclusion threshold ------
      0.014   15.3   6.7      0.017   15.0   6.7    1.1  1  KASH_CCD       Coiled-coil region of CCDC155 or KASH
       0.02   14.8   1.8       0.18   11.7   0.1    2.0  2  Sec34          Sec34-like family
      0.021   13.7   8.2      0.025   13.5   8.2    1.0  1  Spc7           Spc7 kinetochore protein
      0.046   12.9   8.2      0.057   12.6   8.2    1.0  1  HAP1_N         HAP1 N-terminal conserved region
      0.055   13.3   6.6         14    5.6   0.2    3.1  3  Synaptobrevin  Synaptobrevin
       0.74   10.0  11.3       0.14   12.4   1.5    2.4  3  Metal_resist   Heavy-metal resistance
       0.82    9.8   5.4         11    6.2   0.7    2.6  2  MIT            MIT (microtubule interacting and transport) do
          1    9.7  10.7        4.2    7.7   1.1    3.1  2  kleA_kleC      Uncharacterized KorC regulated protein A
        1.6    9.3   9.0        4.6    7.8   2.9    2.2  2  ZapB           Cell division protein ZapB
        2.2    8.7   5.5        4.5    7.7   2.8    2.2  2  DUF1771        Domain of unknown function (DUF1771)


Domain annotation for each model (and alignments):
>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   1.3   0.00034      0.55       8      51 ..      12      55 ..       6      62 .. 0.85
   2 !   10.1   0.7   0.00058      0.94      15      58 ..      58     101 ..      50     116 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00034
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           YabA  8 dkleeleeqleelleeleelkeelaelleenaeLeleneklrer 51
                                   ++ ee+ +++e+ll++ e+l++e a+ +ee ++L+     +r++
  gi|116754231|ref|YP_843349.1| 12 KSYEEMRREMEDLLKRSEQLRAESASAMEESDSLRRRSVDMRQL 55
                                   67789999**************************9998888876 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00058
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXX CS
                           YabA  15 eqleelleeleelkeelaelleenaeLeleneklrerleeeekk 58 
                                    eq e+l  e +el+++  el+ e  eL++    +++rl+ +e+ 
  gi|116754231|ref|YP_843349.1|  58 EQAESLWIESDELRTKARELMRESVELRIKAADIKHRLDIHEQI 101
                                    67788888999***************************544443 PP

>> KASH_CCD  Coiled-coil region of CCDC155 or KASH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   6.7     1e-05     0.017      69     146 ..      14      95 ..       8     111 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1e-05
                       KASH_CCD  69 leelkalvkeleEkrarlkaqnkqlekenqsLi...akiesLq.eenikllaekdelkkklkeLlkekaeLkkqlhelee 144
                                     ee+++ +++l  + ++l a++  +  e +sL+   + + +L+ e+ + l  e del++k +eL++e  eL+ ++  +++
  gi|116754231|ref|YP_843349.1|  14 YEEMRREMEDLLKRSEQLRAESASAMEESDSLRrrsVDMRQLDpEQAESLWIESDELRTKARELMRESVELRIKAADIKH 93 
                                    699********************9999*****73225689998455667889*********************9988776 PP

                       KASH_CCD 145 ll 146
                                     l
  gi|116754231|ref|YP_843349.1|  94 RL 95 
                                    55 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.2     0.047        76      32      66 ..      13      47 ..       9      61 .. 0.59
   2 ?   11.7   0.1   0.00011      0.18      39      79 ..      66     106 ..      50     114 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.047
                          Sec34 32 kfksvsektsslheaceqlleeqkrleelaeeiee 66
                                   +++++  ++++l +++eql +e  + +e +++++ 
  gi|116754231|ref|YP_843349.1| 13 SYEEMRREMEDLLKRSEQLRAESASAMEESDSLRR 47
                                   55555666666666666666665555555555544 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00011
                          Sec34  39 ktsslheaceqlleeqkrleelaeeieekLkyFeeldpitr 79 
                                    ++ +l++++ +l++e  +l+  a +i+++L++ e++++i  
  gi|116754231|ref|YP_843349.1|  66 ESDELRTKARELMRESVELRIKAADIKHRLDIHEQIESIPD 106
                                    6789*********************************9965 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   8.2   1.5e-05     0.025     155     246 ..      14     104 ..      10     115 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.5e-05
                           Spc7 155 kelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleelee 234
                                    +e++ +++e l +  ++l++e a+ +ee ++l++++ ++ ++d+e+ e+l  e +el ++ +e+++e  el+ + ++++ 
  gi|116754231|ref|YP_843349.1|  14 YEEMRREMEDLLKRSEQLRAESASAMEESDSLRRRSVDMRQLDPEQAESLWIESDELRTKARELMRESVELRIKAADIKH 93 
                                    56777888888888999999999999999999999999999999999999999999999999999999999999999999 PP

                           Spc7 235 kieelkeqksel 246
                                    ++ +++eq++++
  gi|116754231|ref|YP_843349.1|  94 RL-DIHEQIESI 104
                                    98.677777665 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 ?   12.6   8.2   3.5e-05     0.057     113     200 ..      14     102 ..      10     110 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.5e-05
                         HAP1_N 113 reeiaqlrhelslkddLLqlysds.eeeseeeseeseelreeesleslqklvqldlLqeklreLeeeNekLreeasqLkt 191
                                     ee+ +   +l ++ + L+  s s +ees++   +s  +r+ + ++ ++  ++ d L+ k reL  e  +Lr +a+++k+
  gi|116754231|ref|YP_843349.1|  14 YEEMRREMEDLLKRSEQLRAESASaMEESDSLRRRSVDMRQLDPEQAESLWIESDELRTKARELMRESVELRIKAADIKH 93 
                                    567777778899999999998876378888888888889***************************************99 PP

                         HAP1_N 192 etdtlEekE 200
                                      d  E+ E
  gi|116754231|ref|YP_843349.1|  94 RLDIHEQIE 102
                                    888777766 PP

>> Synaptobrevin  Synaptobrevin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   1.7     0.011        17      19      60 ..      17      48 ..      11      56 .. 0.53
   2 ?    5.6   0.2    0.0085        14      31      58 ..      58      85 ..      48      89 .. 0.65
   3 ?    4.2   0.0     0.024        38      22      47 ..      90     115 ..      85     117 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.011
                                   HCCHHHHCHCCCCCHHHHCCCCHHHHHHHHHHHHHHHHHHHH CS
                  Synaptobrevin 19 mkeNidkvlergekldeLvdktenLqssaqqFkkqarklkrk 60
                                   m++ +          ++L +++e+L++++ +  +++  l+r+
  gi|116754231|ref|YP_843349.1| 17 MRREM----------EDLLKRSEQLRAESASAMEESDSLRRR 48
                                   44445..........555555555555555555555555544 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0085
                                   CCHHHHCCCCHHHHHHHHHHHHHHHHHH CS
                  Synaptobrevin 31 ekldeLvdktenLqssaqqFkkqarklk 58
                                   e+ ++L  ++++L+++a++  +++ +l+
  gi|116754231|ref|YP_843349.1| 58 EQAESLWIESDELRTKARELMRESVELR 85
                                   4455555566666666666666666665 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.024
                                    HHHHCHCCCCCHHHHCCCCHHHHHHH CS
                  Synaptobrevin  22 NidkvlergekldeLvdktenLqssa 47 
                                    +i+  l+ +e+++++ dk+e+L  +a
  gi|116754231|ref|YP_843349.1|  90 DIKHRLDIHEQIESIPDKAEKLWRKA 115
                                    677788899************98776 PP

>> Metal_resist  Heavy-metal resistance
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   2.4      0.08   1.3e+02      57      81 ..      16      40 ..      10      48 .. 0.59
   2 ?   12.4   1.5   8.5e-05      0.14      36      77 ..      48      89 ..      41      91 .. 0.90
   3 ?   -2.4   0.0       3.1     5e+03      39      55 ..     100     116 ..      92     117 .. 0.57

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.08
                                   HHHHHHHHHHHHHHHHHHHHHHHHC CS
                   Metal_resist 57 dharelralrrelraarrelaalla 81
                                   + +re+++l +++++ r+e a+++ 
  gi|116754231|ref|YP_843349.1| 16 EMRREMEDLLKRSEQLRAESASAME 40
                                   4455666666666666666555554 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 8.5e-05
                                   HHHHHS-TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Metal_resist 36 llraalgLpaeqraelraalrdharelralrrelraarrela 77
                                   +   +++L++eq++ l+   ++ + ++r+l+re+ + r ++a
  gi|116754231|ref|YP_843349.1| 48 RSVDMRQLDPEQAESLWIESDELRTKARELMRESVELRIKAA 89
                                   56689*******************************998876 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 3.1
                                    HHS-TTHHHHHHHHHHH CS
                   Metal_resist  39 aalgLpaeqraelraal 55 
                                      + +p+++++ +r+a+
  gi|116754231|ref|YP_843349.1| 100 QIESIPDKAEKLWRKAV 116
                                    45555666666666655 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.7    0.0066        11      45      64 ..      13      32 ..       8      33 .. 0.89
   2 ?    5.4   0.3     0.012        20      22      63 ..      73     111 ..      65     113 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0066
                            MIT 45 rrellrekieeYleRaeeLk 64
                                   + e +r+++e  l+R e+L+
  gi|116754231|ref|YP_843349.1| 13 SYEEMRREMEDLLKRSEQLR 32
                                   67999*************97 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.012
                            MIT  22 eAlelYkealelLlqalkekneerrellrekieeYleRaeeL 63 
                                    +A el +e++el ++a    + ++r  ++e+ie+  ++ae+L
  gi|116754231|ref|YP_843349.1|  73 KARELMRESVELRIKAA---DIKHRLDIHEQIESIPDKAEKL 111
                                    45566666666666666...569999**************98 PP

>> kleA_kleC  Uncharacterized KorC regulated protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   1.9    0.0083        14      28      51 ..      16      37 ..      12      52 .. 0.73
   2 ?    7.7   1.1    0.0026       4.2      29      49 ..      70      90 ..      56     113 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0083
                      kleA_kleC 28 aklaeAeeLvrqaeeLRakvyees 51
                                   ++ +e e+L ++ e+LRa+    s
  gi|116754231|ref|YP_843349.1| 16 EMRREMEDLLKRSEQLRAESA--S 37
                                   677899***********9753..2 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0026
                      kleA_kleC 29 klaeAeeLvrqaeeLRakvye 49
                                   +  +A eL+r+  eLR+k+  
  gi|116754231|ref|YP_843349.1| 70 LRTKARELMRESVELRIKAAD 90
                                   456899999999999999865 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   2.9    0.0028       4.6      16      52 ..      10      46 ..       8      63 .. 0.83
   2 ?    5.2   0.8     0.017        28      21      46 ..      68      93 ..      58     114 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0028
                           ZapB 16 aidtitlLqmeieeLkeeneelkeenreleeeneqlk 52
                                   a+  +++++ e+e+L +++e+l  e +   ee + l+
  gi|116754231|ref|YP_843349.1| 10 AVKSYEEMRREMEDLLKRSEQLRAESASAMEESDSLR 46
                                   7889999***************999999999988887 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.017
                           ZapB 21 tlLqmeieeLkeeneelkeenrelee 46
                                   ++L+ + +eL++e+ el  +++ +++
  gi|116754231|ref|YP_843349.1| 68 DELRTKARELMRESVELRIKAADIKH 93
                                   45667777777777776666666663 PP

>> DUF1771  Domain of unknown function (DUF1771)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   2.8    0.0028       4.5       1      55 [.      14      81 ..      14      83 .. 0.88
   2 ?    5.1   0.3     0.019        31       3      30 ..      69      96 ..      68     117 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0028
                        DUF1771  1 YerlRaeAdeharkrnelfekAaeAyrrGd.............gaaAkelseqGkehgekmeeanreA 55
                                   Ye+ R+e  ++ ++  +l +++a A ++ d              ++A  l  +  e++ k++e+ re+
  gi|116754231|ref|YP_843349.1| 14 YEEMRREMEDLLKRSEQLRAESASAMEESDslrrrsvdmrqldPEQAESLWIESDELRTKARELMRES 81
                                   89999999999999999999999999999999888888888889999999999999999999998876 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.019
                        DUF1771  3 rlRaeAdeharkrnelfekAaeAyrrGd 30
                                   +lR +A+e++r+  el  kAa+  +r d
  gi|116754231|ref|YP_843349.1| 69 ELRTKARELMRESVELRIKAADIKHRLD 96
                                   79**********9999999998766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1373  (0.0765798); expected 358.6 (0.02)
Passed bias filter:                      591  (0.0329634); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); 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: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 905.38
//
Query:       gi|116754232|ref|YP_843350.1|  [L=333]
Description: radical SAM domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-20   74.6   0.0    2.5e-20   73.5   0.0    1.6  1  Radical_SAM    Radical SAM superfamily
     0.0032   17.8   0.4     0.0075   16.5   0.0    1.8  2  Fer4_12        4Fe-4S single cluster domain
  ------ inclusion threshold ------
       0.28   11.1   8.7         19    5.3   0.1    4.2  4  zinc_ribbon_4  zinc-ribbon domain
       0.41   10.5   7.7         16    5.4   0.5    3.4  3  ZZ             Zinc finger, ZZ type
          9    6.4   8.9        0.9    9.6   0.1    3.0  3  NCD3G          Nine Cysteines Domain of family 3 GPCR


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     166 ..      78     236 ..      76     237 .. 0.95

  Alignments for each domain:
  == domain 1  score: 73.5 bits;  conditional E-value: 6.9e-24
                                    EESEESS--TTTSCCTT.....HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCT CS
                                    xxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   3 vtrgCnlrCsfCarpet.....vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpg 77 
                                     t gCn+rC++C++         ++   g ++s+e+i++ + e+     v  +  +  ep+   +f+ +++  ak+   g
  gi|116754232|ref|YP_843350.1|  78 ATVGCNFRCIHCQNADIsqmpvDKNMIIGSERSPEDIVAAALEAG----VQSISYTYTEPTIFFEFALDTAVKAKE--FG 151
                                    689************99************************9998....**********************99999..7* PP

                                    EEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  78 iritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGend 157
                                    +++ +++ng++  e  +++++++  d ++++l+  d++ ++k++     +e v++++e++ ++g+  + ++++++pG+nd
  gi|116754232|ref|YP_843350.1| 152 LKNNFVSNGYMS-EAAARAIAPYL-DAINIDLKGDDEF-YKKIC-S-ARVEPVKRNIELFPKLGVW-TEVTTLVIPGYND 225
                                    ***********8.*********98.*************.*****.5.89*****************.************* PP

                                    ..HHHHHHHHH CS
                                    ..xxxxxxxxx RF
                    Radical_SAM 158 ..eeleellel 166
                                      e+l+e++e+
  gi|116754232|ref|YP_843350.1| 226 svEQLREIAEF 236
                                    77777777777 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 ?   -3.1   0.6       2.5   8.9e+03       7      20 ..      16      25 ..      10      27 .. 0.55
   2 !   16.5   0.0   2.1e-06    0.0075       5     121 ..      71     187 ..      69     199 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.5
                        Fer4_12  7 rlslfvsgCnlsCk 20
                                   r+ l    C+++C+
  gi|116754232|ref|YP_843350.1| 16 RCNL----CSHNCR 25
                                   4444....666664 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 2.1e-06
                        Fer4_12   5 Gvr.lslfvsgCnlsCkgCfnketwsfksgkef...tkelleeiiedlkkesiegltllGGEPllpenaeallelvkevk 80 
                                    G r +s+ + gCn++C  C n ++ ++   k++   ++   e i++ + +  ++ ++++  EP      e  l+ + + k
  gi|116754232|ref|YP_843350.1|  71 GSRsYSIATVGCNFRCIHCQNADISQMPVDKNMiigSERSPEDIVAAALEAGVQSISYTYTEPTI--FFEFALDTAVKAK 148
                                    6554688899***************998888886666999999999999****************..6777778888888 PP

                        Fer4_12  81 eekpekdiwlytgytleelskkekeellkeidvlvdGkfee 121
                                    e ++ k+ ++++gy+ e+  + +  + l+ i++ ++G  e+
  gi|116754232|ref|YP_843350.1| 149 EFGL-KNNFVSNGYMSEAAAR-AIAPYLDAINIDLKGDDEF 187
                                    8888.89*********99986.5889999988888776555 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1     0.013        47      22      33 ..      11      22 ..       9      23 .. 0.88
   2 ?    2.3   0.7     0.044   1.6e+02      25      33 ..      83      91 ..      76      92 .. 0.77
   3 ?    1.4   0.0     0.087   3.1e+02      19      32 ..     288     301 ..     283     304 .. 0.69
   4 ?    5.3   0.1    0.0053        19      27      34 ..     321     328 ..     310     330 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.013
                  zinc_ribbon_4 22 kgvkvrCskCgh 33
                                   +g+ vrC  C+h
  gi|116754232|ref|YP_843350.1| 11 EGSDVRCNLCSH 22
                                   5889******99 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.044
                  zinc_ribbon_4 25 kvrCskCgh 33
                                   + rC +C++
  gi|116754232|ref|YP_843350.1| 83 NFRCIHCQN 91
                                   679999997 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.087
                  zinc_ribbon_4  19 lpakgvkvrCskCg 32 
                                    +p++g +  C +C+
  gi|116754232|ref|YP_843350.1| 288 IPGEGENTHCHNCS 301
                                    66666666777776 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.0053
                  zinc_ribbon_4  27 rCskCghv 34 
                                    rC++C++ 
  gi|116754232|ref|YP_843350.1| 321 RCPRCRTQ 328
                                    77777776 PP

>> ZZ  Zinc finger, ZZ type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.5    0.0044        16       4      17 ..      14      27 ..      11      31 .. 0.84
   2 ?    3.1   0.2     0.023        82      14      30 ..      78      94 ..      76      97 .. 0.85
   3 ?    4.8   0.1    0.0068        24       3      20 ..     293     310 ..     291     314 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0044
                                   -EE-TTT-S..EES CS
                             ZZ  4 kytCdgCseaplig 17
                                    + C+ Cs+ + i+
  gi|116754232|ref|YP_843350.1| 14 DVRCNLCSHNCRIR 27
                                   689******98775 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.023
                                   .EESSEEEESSSSS-EE CS
                             ZZ 14 pligvRyhclrcsdYDL 30
                                   +++g  ++c  c++ D+
  gi|116754232|ref|YP_843350.1| 78 ATVGCNFRCIHCQNADI 94
                                   5788999******9997 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.0068
                                    S-EE-TTT-S..EESSEE CS
                             ZZ   3 kkytCdgCseapligvRy 20 
                                    ++ +C+ Cse  + ++ y
  gi|116754232|ref|YP_843350.1| 293 ENTHCHNCSELLVERFAY 310
                                    6789*****966656655 PP

>> NCD3G  Nine Cysteines Domain of family 3 GPCR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   1.0      0.59   2.1e+03       4      14 ..      19      31 ..      17      36 .. 0.76
   2 ?    9.6   0.1   0.00025       0.9      10      38 ..      69      96 ..      67     105 .. 0.79
   3 ?    0.7   0.2      0.14   5.2e+02      40      48 ..     294     302 ..     285     328 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.59
                          NCD3G  4 vCsesCp..pgfr 14
                                    Cs++C+  pg+r
  gi|116754232|ref|YP_843350.1| 19 LCSHNCRirPGHR 31
                                   5999997556665 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00025
                          NCD3G 10 ppgfrkkvqegepvCCwdCvpCpegeist 38
                                   +pg+r +   +   C + C+ C++  is+
  gi|116754232|ref|YP_843350.1| 69 QPGSRSYSIATVG-CNFRCIHCQNADISQ 96
                                   6888888777766.***********9993 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.14
                          NCD3G  40 seeCtkCpe 48 
                                    +++C++C+e
  gi|116754232|ref|YP_843350.1| 294 NTHCHNCSE 302
                                    556666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); 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):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 2586.58
//
Query:       gi|116754233|ref|YP_843351.1|  [L=285]
Description: UspA domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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  136.2   5.4    2.6e-21   76.6   1.2    2.0  2  Usp       Universal stress protein family
  ------ inclusion threshold ------
      0.022   14.6   2.4       0.43   10.4   0.2    2.4  2  DUF5612   Domain of unknown function (DUF5612)


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.6   1.2   2.9e-25   2.6e-21       1     135 [.       1     127 [.       1     133 [. 0.95
   2 !   61.9   0.2   9.7e-21   8.7e-17       3     141 .]     151     278 ..     150     278 .. 0.96

  Alignments for each domain:
  == domain 1  score: 76.6 bits;  conditional E-value: 2.9e-25
                                    S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTC CS
                            Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggv 80 
                                    m+++Il+++D+s++++k++e A +    ++  ++llhvi+ ++ + v d+  e +e+e+ le++++       ++   ++
  gi|116754233|ref|YP_843351.1|   1 MFEKILIPTDFSKHARKVIECAGQIPGVKD--VVLLHVISRDPLARVWDPVAEIREAEKRLEGEAAL------LHGMNVK 72 
                                    99**********************999985..9*******************************997......579**** PP

                                    EEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSS CS
                            Usp  81 kvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapc 135
                                    ++ v v+eg++a +i +va+ee+++l+ +G+rg+s ++ +llGSvs++vlr  + 
  gi|116754233|ref|YP_843351.1|  73 VRAVSVLEGEVASAIQKVADEENVSLVAMGARGKSLIESVLLGSVSRNVLRYGNT 127
                                    **************************************************97665 PP

  == domain 2  score: 61.9 bits;  conditional E-value: 9.7e-21
                                    SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCEE CS
                            Usp   3 krIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggvkv 82 
                                    +++l+++D+s+ +++Al +  +  +   +el+llhv++  + +++ d++ + ++e+l + +ael         ++gg +v
  gi|116754233|ref|YP_843351.1| 151 HKVLYPTDFSQPAEAALSFLKNISEI--GELMLLHVVSRGETKEEIDSAVQYGTERLNEIAAEL---------RKGGLNV 219
                                    69********************9887..68*******************************988.........689**** PP

                                    EEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                            Usp  83 evvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                     +++++g++ e i  va +ed++li + s g +++++  +GS++  v++ a+ pVl+ r
  gi|116754233|ref|YP_843351.1| 220 STKIVVGEACEQIRSVAAQEDVSLIAMSSQGATAIKKGRIGSTAYGVANTASRPVLILR 278
                                    ********************************************************987 PP

>> DUF5612  Domain of unknown function (DUF5612)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   4.7e-05      0.43      64     104 ..      65     105 ..      47     117 .. 0.87
   2 ?    3.9   0.1    0.0048        43      66     106 ..     212     252 ..     183     259 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 4.7e-05
                                    GSTTEEEEEEESSB--THHHHHHHHHHHT.T-EEEEES-BS CS
                        DUF5612  64 rlprvkvlvlaGslmGGkiteavkklkeekdiivislnmaG 104
                                     l+ ++v v a s++ G++++a++k+ +e+++ ++++   G
  gi|116754233|ref|YP_843351.1|  65 LLHGMNVKVRAVSVLEGEVASAIQKVADEENVSLVAMGARG 105
                                    47888999*************************99987776 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.0048
                                    TTEEEEEEESSB--THHHHHHHHHHHT.T-EEEEES-BSSH CS
                        DUF5612  66 prvkvlvlaGslmGGkiteavkklkeekdiivislnmaGsv 106
                                     r   l ++  ++ G+  e+++++  ++d+ +i+++ +G+ 
  gi|116754233|ref|YP_843351.1| 212 LRKGGLNVSTKIVVGEACEQIRSVAAQEDVSLIAMSSQGAT 252
                                    4555666777899999******************9998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2089.14
//
Query:       gi|116754234|ref|YP_843352.1|  [L=90]
Description: hypothetical protein Mthe_0924 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); 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: 0.33u 0.28s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 666.33
//
Query:       gi|116754235|ref|YP_843353.1|  [L=114]
Description: hypothetical protein Mthe_0925 [Methanosaeta thermophila PT]
Scores for complete 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  156.6   0.1      2e-46  156.4   0.1    1.0  1  DUF555    Protein of unknown function (DUF555)
  ------ inclusion threshold ------
      0.072   13.4   0.1       0.15   12.4   0.1    1.5  1  Dodecin   Dodecin


Domain annotation for each model (and alignments):
>> DUF555  Protein of unknown function (DUF555)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.4   0.1   2.3e-50     2e-46       1     101 []       3     104 ..       3     104 .. 0.99

  Alignments for each domain:
  == domain 1  score: 156.4 bits;  conditional E-value: 2.3e-50
                         DUF555   1 dyevvleaawivrdvksvddAigiAiseagkrlnpe.ldfveievgetecPkcgeelesalvvadtalvglllemkvfna 79 
                                    ++ v+le+awivrdvks+ddAig+Aiseagkrln++ +++ve+evg++ cP+c+e+le++l+va+talvgl++e+k+fna
  gi|116754235|ref|YP_843353.1|   3 NFLVALEGAWIVRDVKSADDAIGVAISEAGKRLNQSsMEYVEVEVGHSYCPSCEEPLEGVLLVAGTALVGLVFEIKIFNA 82 
                                    789********************************99******************************************* PP

                         DUF555  80 eseEhaeriakseigkaledvP 101
                                    eseEha riak++igkal +vP
  gi|116754235|ref|YP_843353.1|  83 ESEEHAGRIAKAMIGKALGSVP 104
                                    *********************9 PP

>> Dodecin  Dodecin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   1.6e-05      0.15      13      32 ..      18      37 ..      17      49 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.6e-05
                                   S-HHHHHHHHHHHHHHH-SS CS
                        Dodecin 13 kSwedAiqnAiaeAsktlrn 32
                                   kS +dAi  Ai+eA k l++
  gi|116754235|ref|YP_843353.1| 18 KSADDAIGVAISEAGKRLNQ 37
                                   799*************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); 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: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 854.68
//
Query:       gi|116754236|ref|YP_843354.1|  [L=221]
Description: DNA repair and recombination protein RadB [Methanosaeta thermophila PT]
Scores for 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-34  116.8   0.2    1.1e-33  116.6   0.2    1.1  1  Rad51          Rad51
    5.3e-11   42.5   0.3    6.2e-11   42.3   0.3    1.1  1  RecA           recA bacterial DNA recombination protein
    1.3e-10   41.0   4.2    1.2e-08   34.6   4.2    2.3  1  ATPase         KaiC
    1.9e-09   37.4   0.0    3.6e-09   36.5   0.0    1.4  1  AAA_25         AAA domain
    1.8e-07   31.1   0.0    2.6e-07   30.5   0.0    1.2  1  AAA_24         AAA domain
    1.4e-06   28.1   0.0    1.6e-06   27.9   0.0    1.1  1  Zot            Zonular occludens toxin (Zot)
    0.00018   21.3   0.0    0.00037   20.3   0.0    1.6  1  IstB_IS21      IstB-like ATP binding protein
    0.00019   21.5   0.0    0.00023   21.2   0.0    1.2  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
    0.00064   18.7   0.4     0.0052   15.7   0.0    2.0  2  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
     0.0014   18.0   2.9       0.35   10.2   0.4    2.3  3  DnaB_C         DnaB-like helicase C terminal domain
     0.0028   18.1   0.1      0.005   17.3   0.1    1.5  1  AAA            ATPase family associated with various cellular
     0.0039   17.4   0.0     0.0076   16.5   0.0    1.4  1  AAA_22         AAA domain
     0.0042   17.2   0.1     0.0075   16.4   0.1    1.4  1  DUF87          Helicase HerA, central domain
     0.0081   15.7   0.0      0.016   14.7   0.0    1.4  1  CobU           Cobinamide kinase / cobinamide phosphate guany
  ------ inclusion threshold ------
       0.02   14.8   0.0      0.026   14.4   0.0    1.2  1  ATPase_2       ATPase domain predominantly from Archaea
      0.031   14.7   0.2      0.065   13.6   0.2    1.7  1  AAA_16         AAA ATPase domain
      0.087   12.7   0.0       0.13   12.2   0.0    1.3  1  AAA_31         AAA domain
       0.09   12.6   0.0       0.21   11.4   0.0    1.5  2  Bac_DnaA       Bacterial dnaA  protein
       0.11   11.9   0.1        6.6    6.0   0.0    2.2  2  IPT            Isopentenyl transferase
       0.12   12.9   0.2       0.22   12.0   0.2    1.5  1  ABC_tran       ABC transporter
       0.18   10.9   0.3          2    7.4   0.2    2.0  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 !  116.6   0.2   1.3e-36   1.1e-33      18     251 ..       4     219 ..       1     221 [] 0.87

  Alignments for each domain:
  == domain 1  score: 116.6 bits;  conditional E-value: 1.3e-36
                                    EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEESSS---GGGGHHHHHHTT- CS
                          Rad51  18 qlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidtegtfrperlveiaerykl 97 
                                    ++  G++++D+lLgGG+e+g it i+Ge+++Gkt +  +l+v +          +++++idteg f p+r v+ia   + 
  gi|116754236|ref|YP_843354.1|   4 RIPSGCQSIDDLLGGGFEAGIITQIYGESGTGKTNIVIQLSVQA------VRLGSRVIFIDTEG-FSPDRFVQIA---GE 73 
                                    6889******************************9988877754......344589*******6.**********...56 PP

                                    -HHHHGGGEEEEE--STTHHHHHHHHTHHHHHHS-EEEEEEETTTGGGCH-------THHHHHHHHHHHHHHHHHHHHH- CS
                          Rad51  98 dkeevlenvayaRaytiehqeellqqaaallaedkfallivDsvtalyRtdfsgrgelakRqqklgkllrtLrkladefe 177
                                    + +e+ +++ +    + e+q+  ++ a+  ++ + f+l+++Ds+t+lyR+  +  ++    ++ l+  l++L+++a +++
  gi|116754236|ref|YP_843354.1|  74 NAKEIASKIVVFQPLSLEQQHMAIRDAS-RIVGQGFGLVVLDSATSLYRAALEANDNRQ-IKRSLTAQLSELQEIARRHS 151
                                    99****************9988887766.567889****************99999854.44679999************ PP

                                    -EEEEEEE-------.------------HHHHHHHH-SEEEEEEE-STTEEEEEEES-SSS-S-EE.EEEEETTE CS
                          Rad51 178 vavvitnqvvaqvdgqaalfsadpkkPigGlvlahasttRlalrkgkgeeRivkvvdsPnlpelea.vfaigeeG 251
                                    + vv+tnqv  +v++          +P+gG  + h  +  lal +    +R ++vv+  + pe e+  f i+ +G
  gi|116754236|ref|YP_843354.1| 152 IPVVVTNQVYMDVET-------GILRPVGGTSMEHLCKAILALERLDKGRRRMRVVKHRSQPEGETaDFLITPSG 219
                                    **********99998.......5679****************998887788889999999999875157887777 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.3   7.3e-14   6.2e-11      31     200 ..       2     171 ..       1     214 [. 0.78

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 7.3e-14
                                    --EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEESS----HHHHHHTT--GGG... CS
                           RecA  31 vetissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafidaehaldpkyakklGvdide... 107
                                    ++ i+sG  ++d  lG GG+  G i++iyG   +Gkt + +++ ++a + g  + fid+e     ++ +  G + +e   
  gi|116754236|ref|YP_843354.1|   2 IKRIPSGCQSIDDLLG-GGFEAGIITQIYGESGTGKTNIVIQLSVQAVRLGSRVIFIDTEGFSPDRFVQIAGENAKEias 80 
                                    6789************.*******************************************98888899999988765222 PP

                                    .-EEE--SSHHH.HHHHHHH.HHTTT--SEEEEE-TTT---STT-----------HHHHHHHHHHHHHHHHHTTT--EEE CS
                           RecA 108 .llvsqpdtGeq.aleiada.lvrsgaidlivvdsvaalvpkaeieGemgdskvglqarlmsqalrkltgaisksntvvi 184
                                     ++v qp + eq  + i da  +   +  l+v+ds ++l  +a +e + +  +     r ++  l  l+   ++  + v+
  gi|116754236|ref|YP_843354.1|  81 kIVVFQPLSLEQqHMAIRDAsRIVGQGFGLVVLDSATSLY-RAALEANDN--R--QIKRSLTAQLSELQEIARRHSIPVV 155
                                    27899**998862578887624677889*******99986.666765422..2..2245566678889999999999999 PP

                                    EEEE------------ CS
                           RecA 185 finqirekiGvmfgnp 200
                                      nq+ + +      p
  gi|116754236|ref|YP_843354.1| 156 VTNQVYMDVETGILRP 171
                                    9999999886555555 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   4.2   1.4e-11   1.2e-08       1     223 [.       5     219 ..       5     221 .] 0.69

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 1.4e-11
                         ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleee 80 
                                    +++g + +D++l gG+  g ++ i+Ge+GtGKt ++ q  ++ ++  g +++f+ +e  + d  + ++  G + +++ ++
  gi|116754236|ref|YP_843354.1|   5 IPSGCQSIDDLLGGGFEAGIITQIYGESGTGKTNIVIQLSVQAVRL-GSRVIFIDTEGFSPD--RFVQIAGENAKEIASK 81 
                                    6899**********************************99888655.*******99986654..4456678999999988 PP

                         ATPase  81 gklaiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitgl.ayeekeavaReilrqlvrvlkklgvTa. 158
                                      +++ +  + +++      +++++  +      i   +   vv+Ds t+l     +++  R+i r l+ +l++l+  a 
  gi|116754236|ref|YP_843354.1|  82 --IVVFQPLSLEQQ------HMAIRDAS-----RIVGQGFGLVVLDSATSLyRAALEANDNRQIKRSLTAQLSELQEIAr 148
                                    ..665555554433......33333332.....23334557899999999976677777788887777777766543322 PP

                         ATPase 159 ......ilvsekss.....seeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIteeg 223
                                          + ++++ +       + +gg   e+ +++ ++ L+     ++ +R +++vk R+ +   ++  f It++g
  gi|116754236|ref|YP_843354.1| 149 rhsipvVVTNQVYMdvetgILRPVGGTSMEH-LCKAILALE---RLDKGRRRMRVVKHRSQPEG-ETADFLITPSG 219
                                    2222226777766666555456778888888.666666665...33456778899999987644.45566666655 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.0   4.2e-12   3.6e-09      22     187 ..      12     158 ..       3     161 .. 0.77

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 4.2e-12
                         AAA_25  22 rrwlvkgllpagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsedelrrRlravg.ealrd 99 
                                     ++l++g   ag ++ ++G +gtGKt ++++l++  + +G+           +V+++++E+     + R+ ++  e++++
  gi|116754236|ref|YP_843354.1|  12 IDDLLGGGFEAGIITQIYGESGTGKTNIVIQLSVQAVrLGS-----------RVIFIDTEGFS---PDRFVQIAgENAKE 77 
                                    5678888889***************************4444...........8**********...99998876255555 PP

                         AAA_25 100 darllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralgg..densnsdv....galveale 173
                                     a   v+        pL  ++++++     +++  + + +  g +lvv+D+ ++++++  + n+n+++    +a ++ l+
  gi|116754236|ref|YP_843354.1|  78 IASKIVVF------QPLSLEQQHMA-----IRDASRIVGQ--GFGLVVLDSATSLYRAalEANDNRQIkrslTAQLSELQ 144
                                    55555554......34433444443.....4445667777..7***************9********6533466777788 PP

                         AAA_25 174 riarrtgaavllvh 187
                                    +iarr+ + v+++ 
  gi|116754236|ref|YP_843354.1| 145 EIARRHSIPVVVTN 158
                                    88899988888875 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0   3.1e-10   2.6e-07       5      86 ..      26     128 ..      22     140 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 3.1e-10
                         AAA_24   5 iliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdie..swedfldevvel................ 59 
                                     +iyG+sg+GKT ++ +l       g +++fidte+      +d+f++i   + +++ +++v +                
  gi|116754236|ref|YP_843354.1|  26 TQIYGESGTGKTNIVIQLsvqavrlGSRVIFIDTEG----FSPDRFVQIAgeNAKEIASKIVVFqplsleqqhmairdas 101
                                    68**********************************....6678888776664555555555556778888888888889 PP

                         AAA_24  60 aaeladyktlviDtideleelclaevi 86 
                                    +   +++  +v+D+++ l++ +l+  +
  gi|116754236|ref|YP_843354.1| 102 RIVGQGFGLVVLDSATSLYRAALEAND 128
                                    999****************98877654 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   1.8e-09   1.6e-06       5     104 ..      28     137 ..      24     191 .. 0.75

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1.8e-09
                            Zot   5 vtGapGsgKtsgavkkdllpalkegRkiitnidGlrlerieqvlgekvs..tarliridnpegaetlkef.akwatid.k 80 
                                     +G+ G+gKt  +++  ++      R+i+ + +G+  +r+ q+ ge+ +  + +++  + p++ e+++ + ++  +i  +
  gi|116754236|ref|YP_843354.1|  28 IYGESGTGKTNIVIQLSVQAVRLGSRVIFIDTEGFSPDRFVQIAGENAKeiASKIVVFQ-PLSLEQQHMAiRDASRIVgQ 106
                                    58**************999888899********************99998888888777.66666554430333334356 PP

                            Zot  81 g.allviDEcqeifpvrakegrkd......p 104
                                    g +l+v+D +  ++ +  + + ++       
  gi|116754236|ref|YP_843354.1| 107 GfGLVVLDSATSLYRAALEANDNRqikrslT 137
                                    6599**********99887533334444443 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   4.4e-07   0.00037      52      84 ..      28      60 ..      13      91 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 4.4e-07
                      IstB_IS21 52 llGpsGvGKshlaialgveavraglsvlfvrve 84
                                   + G sG+GK+ + i l+v+avr g +v+f+ +e
  gi|116754236|ref|YP_843354.1| 28 IYGESGTGKTNIVIQLSVQAVRLGSRVIFIDTE 60
                                   79***************************9886 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 !   21.2   0.0   2.6e-07   0.00023       4      68 ..      28     142 ..      25     210 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 2.6e-07
                                    EESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH.HTTEB-HHHH............................ CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx............................ RF
                           CbiA   4 astkGGvGKTtlaanLaralarrglrVllvDaDpqannlai.leglendiep............................ 54 
                                    + + +G+GKT +++ L +   r g rV+ +D+   ++  ++ +   en +e                             
  gi|116754236|ref|YP_843354.1|  28 IYGESGTGKTNIVIQLSVQAVRLGSRVIFIDTEGFSPDRFVqI-AGENAKEIaskivvfqplsleqqhmairdasrivgq 106
                                    5689****************************99999999752.333333334677888888888888888877777777 PP

                                    .....................CCHCCCHHH.HHHCH CS
                                    .....................xxxxxxxxx.xxxxx RF
                           CbiA  55 .....................dlkrllell.ealgk 68 
                                                         d  +++++l ++l++
  gi|116754236|ref|YP_843354.1| 107 gfglvvldsatslyraaleanDNRQIKRSLtAQLSE 142
                                    777777777777777777777333444443333333 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   6.1e-06    0.0052      19      61 ..      27      69 ..      24      90 .. 0.85
   2 ?    1.3   0.1      0.14   1.2e+02     120     161 ..     115     157 ..      73     170 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 6.1e-06
                  TrwB_AAD_bind 19 livGttGsGKtqalekllrairargdraivlDltGafvsrfyd 61
                                    i G  G+GKt+ + +l  ++ + g r+i +D++G   +rf +
  gi|116754236|ref|YP_843354.1| 27 QIYGESGTGKTNIVIQLSVQAVRLGSRVIFIDTEGFSPDRFVQ 69
                                   689********************************99999987 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.14
                  TrwB_AAD_bind 120 tlrelvrekkksn.aallralltadleeLkellagteaaalva 161
                                     + +l r   + n ++ +++ lta+l+eL+e+++++++  +v 
  gi|116754236|ref|YP_843354.1| 115 SATSLYRAALEANdNRQIKRSLTAQLSELQEIARRHSIPVVVT 157
                                    4455555555555467788888899999999888887765554 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0    0.0019       1.7       2      56 ..       5      59 ..       4      69 .. 0.82
   2 !   10.2   0.4    0.0004      0.35     114     184 ..      94     166 ..      64     172 .. 0.68
   3 ?   -3.5   0.0       6.1   5.2e+03     224     240 ..     192     208 ..     182     211 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0019
                                   BXSSTHHHHHHCT.SBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEES CS
                                   xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         DnaB_C  2 lstgfkdLDklts.GlqkgdliiiAarpsmGktalalniaenaavkeklpvavfsl 56
                                   +++g +++D+l++ G++ g ++ i + +++Gkt +++++  +a+     +v+++  
  gi|116754236|ref|YP_843354.1|  5 IPSGCQSIDDLLGgGFEAGIITQIYGESGTGKTNIVIQLSVQAVR-LGSRVIFIDT 59
                                   6899999999885279999999****************9987664.4456666655 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0004
                                    HHHHHHHHHHHHHH..TTEEEEEEEEGGGTBTS..CSSSCCCHH..HHHHHHHHHHHHHHCTSXEEEEEEXSGGGCC CS
                                    xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxx..xxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         DnaB_C 114 vseirskarrlkke..kglgliviDyLqlmegs..eekenreqe..vseisrsLkalakelnvpvialsqLsraves 184
                                     + ir   r       +g gl+v+D    +  +  e+++nr+ +  +++   +L+++a+  ++pv++  q+  +ve+
  gi|116754236|ref|YP_843354.1|  94 HMAIRDASR----IvgQGFGLVVLDSATSLYRAalEANDNRQIKrsLTAQLSELQEIARRHSIPVVVTNQVYMDVET 166
                                    333344333....34479*******98766644334477887652244455689****************9888875 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 6.1
                                    HCEEEEEEEEETTSXXE CS
                                    xxxxxxxxxxxxxxxxx RF
                         DnaB_C 224 kgkaeiiiaKhRnGptg 240
                                    kg   + + KhR+ p g
  gi|116754236|ref|YP_843354.1| 192 KGRRRMRVVKHRSQPEG 208
                                    56678889999987766 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   5.8e-06     0.005       3     111 ..      28     159 ..      26     192 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.8e-06
                                    EESSTTSSHHHHHHHHHHHH...THEEEEEETTTCSSS...................STTHHHHHHHHHHHHHHHTS..T CS
                            AAA   3 lyGppGtGKTllakavakel...gvefleisgsellsk...................yvgesekkirelfkeakeka..k 58 
                                    +yG  GtGKT ++ ++  ++   g++++ i+   +  +                   ++  s ++ ++ +++a++    +
  gi|116754236|ref|YP_843354.1|  28 IYGESGTGKTNIVIQLSVQAvrlGSRVIFIDTEGFSPDrfvqiagenakeiaskivvFQPLSLEQQHMAIRDASRIVgqG 107
                                    79*************99995555666555555555533344444444444555677744445555555555554444634 PP

                                    SEEEEEETGGGHHHHH.TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS CS
                            AAA  59 psilfiDEidalaksr.sgseseeeervvnqLlteldgvkkkeskvivigatnr 111
                                       +++D + +l ++  + +++++ +r + + l+el++  +++   i +++tn+
  gi|116754236|ref|YP_843354.1| 108 FGLVVLDSATSLYRAAlEANDNRQIKRSLTAQLSELQEIARRH--SIPVVVTNQ 159
                                    59**********9999655555555555555555555555543..355556665 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   8.9e-06    0.0076       8     127 ..      26     156 ..      21     160 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 8.9e-06
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka....erlsseelleale 83 
                                    + ++GesGtGKT  + +l  q+++       +++v+f++  + + ++ + +   ++ ++ +++    ++ls+e+   a++
  gi|116754236|ref|YP_843354.1|  26 TQIYGESGTGKTNIVIQLSVQAVRL------GSRVIFIDTEGFS-PDRFVQIAGENAKEIASKivvfQPLSLEQQHMAIR 98 
                                    569******************9876......********98888.88888888888888888899997777777777777 PP

                         AAA_22  84 qalrarav.ielliiDEaqhlr......s.........eealeeLrsllnlsrkgvqliL 127
                                    +a+r  +   +l+++D a  l       +          ++l+eL +++   r+++++++
  gi|116754236|ref|YP_843354.1|  99 DASRIVGQgFGLVVLDSATSLYraaleaNdnrqikrslTAQLSELQEIAR--RHSIPVVV 156
                                    77777777778*********976766551556677778888888888888..99998886 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   8.7e-06    0.0075      28     108 ..      28     106 ..      26     163 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 8.7e-06
                          DUF87  28 ilgsTGsGKSntvavLleellekkgatililDpHGEYgkal........ekllsekvkvitpspsakdkelkinpwsldp 99 
                                    i g++G+GK+n v  L  +++ + g++++ +D  G +++ +        +k++++k++v++p        l++  +++ +
  gi|116754236|ref|YP_843354.1|  28 IYGESGTGKTNIVIQLSVQAV-RLGSRVIFIDTEG-FSPDRfvqiagenAKEIASKIVVFQP--------LSLEQQHMAI 97 
                                    89*******************.************9.55544577779999999999999997........7888888877 PP

                          DUF87 100 eelldllee 108
                                    ++  ++++ 
  gi|116754236|ref|YP_843354.1|  98 RDASRIVGQ 106
                                    777777766 PP

>> CobU  Cobinamide kinase / cobinamide phosphate guanyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.9e-05     0.016      73     130 ..     108     164 ..      88     168 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.9e-05
                           CobU  73 kevvLvDcltlwltnllleeeaekveekleeeveellealkelkatvvlVsnEvglgv 130
                                       v++D+ t +   +l ++++++++++l+++++el e++++++ +v +V+n v ++v
  gi|116754236|ref|YP_843354.1| 108 FGLVVLDSATSLYRAALEANDNRQIKRSLTAQLSELQEIARRHSIPV-VVTNQVYMDV 164
                                    56899****************999************99999988775.69***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 ?   14.4   0.0   3.1e-05     0.026      22     127 ..      25     160 ..      17     189 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.1e-05
                       ATPase_2  22 iyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekal................... 82 
                                    i  iYG  g GKt ++ ++  +   ++ +vi+++  ++ s +++ +     e++k+++ ++                   
  gi|116754236|ref|YP_843354.1|  25 ITQIYGESGTGKTNIVIQLSVQAVRLGSRVIFID-TEGFSPDRFVQIA--GENAKEIASKIvvfqplsleqqhmairdas 101
                                    778***************99999999*9999975.6777777777763..333344444444688889999999999999 PP

                       ATPase_2  83 ..............giavpkaeleeilk.eksklvfkaielllekikkkgkk...iiiiiDel 127
                                                  ++ + +a+l    + + ++++++++++ l ++++ +++   ++++   +
  gi|116754236|ref|YP_843354.1| 102 rivgqgfglvvldsATSLYRAAL----EaNDNRQIKRSLTAQLSELQEIARRhsiPVVVTNQV 160
                                    99988888776655444444444....445777788888888877777777777677776555 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   0.2   7.6e-05     0.065      28      78 ..      27      72 ..      12     197 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.6e-05
                         AAA_16 28 llsGesGvGKsslvrellralekd..ggiflrgkcdqlesaipysalaqalar 78
                                    ++GesG+GK+ +v +l  ++ +   ++if+ ++  + ++      ++q++  
  gi|116754236|ref|YP_843354.1| 27 QIYGESGTGKTNIVIQLSVQAVRLgsRVIFIDTEGFSPDR------FVQIA-G 72
                                   59************88887777763335554444444422......33333.2 PP

>> AAA_31  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      0.13      10      45 ..      31      66 ..      23     146 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                         AAA_31 10 KGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanat 45
                                     G GKT  +++l++   +lg +v+ +D    +   
  gi|116754236|ref|YP_843354.1| 31 ESGTGKTNIVIQLSVQAVRLGSRVIFIDTEGFSPDR 66
                                   569*************************97654443 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       2.7   2.3e+03     139     163 ..       4      28 ..       3      28 .. 0.91
   2 ?   11.4   0.0   0.00024      0.21      39      87 ..      28      74 ..      25      86 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.7
                                    S-TTT-SS--HHHHHHHHSSEEEE- CS
                       Bac_DnaA 139 rsPkeleeledrlrsrfeaGlvvdi 163
                                    r P+  ++++d l   feaG++++i
  gi|116754236|ref|YP_843354.1|   4 RIPSGCQSIDDLLGGGFEAGIITQI 28 
                                    7899999**************9986 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00024
                                   EE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHH.HHHHHHTT- CS
                       Bac_DnaA 39 iygevGlGktHLlkaignevlenapelrvvYltaeeFlne.lvkalrdkk 87
                                   iyge+G Gkt ++  i+  v++     rv+++ +e F  + +v++   ++
  gi|116754236|ref|YP_843354.1| 28 IYGESGTGKTNIV--IQLSVQAVRLGSRVIFIDTEGFSPDrFVQIA-GEN 74
                                   9**********98..566666777899**********865155544.444 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0    0.0077       6.6       3      24 ..      25      46 ..      23      62 .. 0.76
   2 ?    3.9   0.0     0.036        31      20      49 ..     145     172 ..     136     194 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0077
                            IPT  3 vylifGatttGKtaeaiklake 24
                                   +  i+G  +tGKt+  i+l+ +
  gi|116754236|ref|YP_843354.1| 25 ITQIYGESGTGKTNIVIQLSVQ 46
                                   5679**************9765 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.036
                            IPT  20 klaketgapvivlDRvqcyselavgsGrpl 49 
                                    ++a+++++pv+v    q y ++ +g  rp+
  gi|116754236|ref|YP_843354.1| 145 EIARRHSIPVVVTN--QVYMDVETGILRPV 172
                                    79**********98..67999999988876 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   0.00026      0.22       8      61 ..      20      82 ..      15     159 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00026
                                   EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEE.EETTCEGGG........B-HHHCCHCE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx........xxxxxxxxxx RF
                       ABC_tran  8 lkegekvaivGenGaGKStLlkllagllkpteGei.lldgkdlke........qeleslrkei 61
                                   +++g +++i Ge+G+GK+ ++  l+ +      ++  +d + ++         ++ ++  ++i
  gi|116754236|ref|YP_843354.1| 20 FEAGIITQIYGESGTGKTNIVIQLSVQAVRLGSRViFIDTEGFSPdrfvqiagENAKEIASKI 82
                                   78999*************998777766554444432333333333444544444444444444 PP

>> PAXNEB  PAXNEB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.2    0.0024         2      21      42 ..       7      28 ..       4      41 .. 0.84
   2 ?    1.5   0.0      0.15   1.3e+02     214     288 ..     117     194 ..      93     208 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0024
                         PAXNEB 21 tGtpsLDklLgGGLplGsilli 42
                                   +G++s+D+lLgGG+  G i  i
  gi|116754236|ref|YP_843354.1|  7 SGCQSIDDLLGGGFEAGIITQI 28
                                   9*************99988776 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.15
                         PAXNEB 214 psLlspllydyppeeskpedllkFLhsLrallrssnlvalitlplslia....rssslvrkieqlvDtvieLesfagse 288
                                    +sL   +l++ +++ + +++l+  L  L+ ++r+ ++ +++t  + +       ++   + +e+l+ +++ Le +++ +
  gi|116754236|ref|YP_843354.1| 117 TSLYRAALEA-NDNRQIKRSLTAQLSELQEIARRHSIPVVVTNQVYMDVetgiLRPVGGTSMEHLCKAILALERLDKGR 194
                                    5777778865.67788899999999999999997777777664444332002233334457899999999999887744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 1516.25
//
Query:       gi|116754237|ref|YP_843355.1|  [L=305]
Description: ribonuclease Z [Methanosaeta thermophila PT]
Scores for 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-26   90.8   0.0    2.4e-12   46.8   0.0    2.1  2  Lactamase_B_2  Beta-lactamase superfamily domain
    1.1e-12   48.4   0.0    1.9e-10   41.1   0.0    2.6  2  Lactamase_B    Metallo-beta-lactamase superfamily
    8.5e-09   35.0   0.0    1.7e-08   34.0   0.0    1.4  1  Lactamase_B_4  tRNase Z endonuclease


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 !   46.8   0.0     4e-16   2.4e-12       3     128 ..      32     145 ..      31     161 .. 0.83
   2 !   42.1   0.0   1.1e-14   6.4e-11     132     201 .]     198     267 ..     176     267 .. 0.90

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 4e-16
                                    EEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC...C--EE..EEEEEEHHHHHHCCTTCGHH CS
                  Lactamase_B_2   3 iLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlre...lrpkk..lplyapkgvlavleanfvyl 77 
                                    +L+D+g ++  q++       +r  + ++  ++lth H+DH+ g++ l e   +++++  l + +p+++++ ++   +  
  gi|116754237|ref|YP_843355.1|  32 LLFDCGEGTQRQMMI------ARTGMMRLSHIFLTHLHADHILGIPGLLEtmaFQGREnpLVIAGPPRTARMVSILNSLG 105
                                    69******7666333......367899************************99877774344459999999988887777 PP

                                    HCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEE CS
                  Lactamase_B_2  78 aleeepavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGl 128
                                       ++++v++ e+ +g+ ++++  g ++ta++ +h+ +          lG+
  gi|116754237|ref|YP_843355.1| 106 CCTRDFEVRAMEMRPGDAVRMN--GYTVTAIATQHSVPS---------LGY 145
                                    7777788**************9..899*********998.........444 PP

  == domain 2  score: 42.1 bits;  conditional E-value: 1.1e-14
                                    CTTEEEEEESS-S---HHHHHHHCT-SEEEEE-S-SSTTHHHH...HHT---STSHHHHCTTSSSSEEEEESB CS
                  Lactamase_B_2 132 gggkrvyyigDtgyipeeigerlggadllllditayeddemir...hmgHltpeeaveaaadlgakrlvliHi 201
                                    ++g++++y+gDt  +  ei+e  ++adll++d+ + +d    +   +  H t +ea+++aa++g++rlvl+Hi
  gi|116754237|ref|YP_843355.1| 198 RPGRKIVYSGDTRPTA-EIEEASRNADLLIHDGALADDML--EwavETKHTTAGEAAALAARAGVRRLVLTHI 267
                                    689**********665.99*************99999944..4569**************************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 !   41.1   0.0   3.2e-14   1.9e-10       8      87 ..      22      96 ..      16     148 .. 0.86
   2 !    4.5   0.1    0.0051        30     141     162 ..     199     220 ..     198     266 .. 0.76

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 3.2e-14
                                   EEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHH CS
                    Lactamase_B  8 syliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeea 87
                                   ++l+  +g+++L+D+G +t+++++      ++ +  ++++++lTHlH+DHi g +gl e+  +  ++++++ + +++ ++
  gi|116754237|ref|YP_843355.1| 22 AILVNREGDLLLFDCGEGTQRQMMI-----ARTGMMRLSHIFLTHLHADHILGIPGLLETMAFQGRENPLVIAGPPRTAR 96
                                   68999*******************9.....8****************************999999988888877777666 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0051
                                    TTCCEEEECTTTSSHHCCCCCC CS
                    Lactamase_B 141 gggkvlftGDallagetgridl 162
                                    +g+k++++GD+ +++e+++ ++
  gi|116754237|ref|YP_843355.1| 199 PGRKIVYSGDTRPTAEIEEASR 220
                                    689*************999988 PP

>> Lactamase_B_4  tRNase Z endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.0   2.8e-12   1.7e-08       5      62 ..      13      68 ..      10      69 .. 0.92

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 2.8e-12
                  Lactamase_B_4  5 tptsDtsgPlllLqldskrYlfGkvgEgtQRavneqkvrlsklesiFLtgkvswssig 62
                                    pt+D s P +l++ + +  lf ++gEgtQR ++  ++ + +l++iFLt+ +  ++i 
  gi|116754237|ref|YP_843355.1| 13 LPTPDRSLPAILVNREGDLLLF-DCGEGTQRQMMIARTGMMRLSHIFLTHLH-ADHIL 68
                                   599*******************.***************************99.66665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2273.43
//
Query:       gi|116754238|ref|YP_843356.1|  [L=161]
Description: hypothetical protein Mthe_0928 [Methanosaeta thermophila PT]
Scores for complete 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-38  129.5   0.0    6.6e-38  129.3   0.0    1.1  1  DNase-RNase  Bifunctional nuclease


Domain annotation for each model (and alignments):
>> DNase-RNase  Bifunctional nuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.3   0.0   3.7e-42   6.6e-38       3     126 ..      20     145 ..      18     148 .. 0.90

  Alignments for each domain:
  == domain 1  score: 129.3 bits;  conditional E-value: 3.7e-42
                                    EEEEEETTTT...EEEEEEEETTSSEEEEEE--HHHHHHHHHHHCT---SS--HHHHHHHHHHHTTEEEEEEEEEEEETT CS
                    DNase-RNase   3 agialdassq...spvvlLreeegrrvlpIwigaaeaqaialalegeeppRPlthDLlasllealgakvervvItdledg 79 
                                    +g+ ++++ +   spvvlL++e++r ++pI++g +ea +i+ al+ge  pRP+thDL++s+le l+a+++ v I+dle g
  gi|116754238|ref|YP_843356.1|  20 KGVYIAETLGgspSPVVLLEDEKSR-IVPIFVGLSEAISIHNALSGEVSPRPMTHDLFISVLECLEATISDVLIDDLEGG 98 
                                    566655444223489*****99999.****************************************************** PP

                                    EEEEEEEEEET---EEEEE-HHHHHHHHHHHT--EEEEHHHHHHH-E CS
                    DNase-RNase  80 tfyAelvlrkeeeeleidaRpSDaiaLAlrtgapIyveeevleeasi 126
                                    ++yA+l l +++++ e+daRpSD++aLA+r++apI ++++++e +++
  gi|116754238|ref|YP_843356.1|  99 IYYARLSLVHGSKRSELDARPSDCLALAIRAKAPIHIQQRIIEISGM 145
                                    **********8666***************************998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       243  (0.0135535); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.20s 00:00:00.55 Elapsed: 00:00:00.35
# Mc/sec: 1388.81
//
Query:       gi|116754239|ref|YP_843357.1|  [L=1049]
Description: isoleucyl-tRNA synthetase [Methanosaeta thermophila PT]
Scores for complete 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-197  655.3   0.1   1.1e-196  654.7   0.1    1.2  1  tRNA-synt_1   tRNA synthetases class I (I, L, M and V)
      3e-34  118.2   0.0    6.8e-34  117.0   0.0    1.6  2  Anticodon_1   Anticodon-binding domain of tRNA
    1.2e-27   96.6   1.2    1.5e-12   47.0   0.4    4.0  3  tRNA-synt_1g  tRNA synthetases class I (M)
    1.8e-07   30.8   0.0    3.3e-05   23.4   0.0    2.3  2  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
    3.3e-05   23.0   0.0    0.00019   20.5   0.0    2.1  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 !  654.7   0.1    3e-200  1.1e-196       3     599 ..      19     633 ..      17     636 .. 0.95

  Alignments for each domain:
  == domain 1  score: 654.7 bits;  conditional E-value: 3e-200
                    tRNA-synt_1   3 yekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakvek 82 
                                     e+W+ ed+++k ++ +   ++f +vdgPPy tG++H+G a++k++kd + ry +m+G++ + + GwD++Gl+ie kve+
  gi|116754239|ref|YP_843357.1|  19 REFWHREDTYHKVRRLRSGGRRFFFVDGPPYTTGRIHLGTAWNKVIKDSILRYMSMRGYDLKDRAGWDMHGLPIEVKVEE 98 
                                    589***************************************************************************** PP

                    tRNA-synt_1  83 klgakekkerkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgliyrgkkl 162
                                    +lg + k++ +++g+++f+e++++++ ++++e+++q+k lGv++D+d++y+Tl++e+ ea +++++r +++gl+ rg ++
  gi|116754239|ref|YP_843357.1|  99 HLGFRSKRDIESYGVDRFIEQCKSFALRQKDEMTEQFKSLGVWLDWDNPYMTLKNEYIEAAWWTLKRAHERGLLERGLRV 178
                                    ******************************************************************************** PP

                    tRNA-synt_1 163 vnwstklktalselEveykdkkdalihvafpladkeevklviaTTtPeTllgdtavavnpeldyv........itkekli 234
                                    vnw+++++ta+++ Evey d++d++i+v+fp+++++++++vi+TTtP+T+++++avav++++ y+         t e li
  gi|116754239|ref|YP_843357.1| 179 VNWCPRCQTAIADSEVEYWDESDPSIYVKFPVEGEDNTYIVIWTTTPWTIPANVAVAVHKDFMYSkvrawrrdGTYEILI 258
                                    ****************************************************************999999877778999* PP

                    tRNA-synt_1 235 laeallkslvkke..sekkiledergkeLegkevelpl.......vnrkipiiaddyvdkeaGtGvVkiaPahdedDyev 305
                                    +a +l+++++k+   ++++ile +rg++L  +++++pl        +   ++   d+v++e+ tG+V+iaP+h+ +Dye+
  gi|116754239|ref|YP_843357.1| 259 MATDLIENVLKQGryVDYEILESMRGEDLLSLTYKNPLqdlvpaqRDIVHRVHLADFVTAEN-TGIVHIAPGHGLEDYEL 337
                                    **********99877899********************99988544444567788***9986.***************** PP

                    tRNA-synt_1 306 gkkynlevinildedgtlteea.aefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrateqWfvrv 384
                                    g +  l++ +++ edg++t ea +++eg +v da+  vve+l e+g+ll + +  h +++c+r k+pii+ at qWf+ +
  gi|116754239|ref|YP_843357.1| 338 GLEKRLPIFCPVGEDGRYTSEAgKKYEGKYVRDANPEVVEDLMERGALLASGELVHRYGHCWRCKTPIIFIATRQWFIGI 417
                                    *******************999789******************************************************* PP

                    tRNA-synt_1 385 keladaalkavekvqfvpks.kekryaswleniqdWciSRqrwWGhriplfvsketeevvvreelkelvagreeeeaekk 463
                                    +el+d++lk++e+v+++p++ + +r+++w+ n++dWciSRqr+WG ++p+++ ++ + + v     el+a      +  +
  gi|116754239|ref|YP_843357.1| 418 SELRDQMLKEIERVSWYPDWaGSARFKDWISNARDWCISRQRYWGIPLPIWICRSCGAMDVIGTAAELEA---RAGRPVE 494
                                    ********************99***********************************8888555555555...5566678 PP

                    tRNA-synt_1 464 alekeakdkl...kkekgelekdedvlDvWFsSgswpfstlgypeedteelkkffpadmlleGlDiirgWvarlillsla 540
                                    +l++ a+d++    +  g +e+++dv+DvWF+S+    +tl++p   +ee++  +pad+++eG D++rgW+++ +  s+ 
  gi|116754239|ref|YP_843357.1| 495 DLHRPAVDDVrlrCSCGGAMERVPDVFDVWFDSAVASWATLNFPRD-EEEFRVWWPADFITEGHDQTRGWFYSQLGASMV 573
                                    8899999998774455789*************************99.9******************************** PP

                    tRNA-synt_1 541 ltgsePfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltli.lsdvgrdi 599
                                     +g++P+k+vl+hg+++de+GrKmSKs+gNv+ p+dv+++ygad lR++++ ++   +d+
  gi|116754239|ref|YP_843357.1| 574 AFGRAPYKSVLMHGFTLDEQGRKMSKSIGNVVHPEDVVERYGADTLRFYVLsSNAPWEDL 633
                                    **************************************************9555555555 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 !  117.0   0.0   1.9e-37   6.8e-34       1     150 [.     682     834 ..     682     837 .. 0.89
   2 ?   -3.7   0.0       2.9   1.1e+04     124     149 ..     964     989 ..     940     991 .. 0.76

  Alignments for each domain:
  == domain 1  score: 117.0 bits;  conditional E-value: 1.9e-37
                    Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkra.aqevllevletllrllaP 79 
                                    drwi+s++n+l+ke++e++  y +++a ++l+ef+++dl++wy++lv+pr + e++++++  a+++l+ v++tl++l+aP
  gi|116754239|ref|YP_843357.1| 682 DRWIISRVNSLAKEIEENMSGYMLHRATRSLQEFVLEDLSRWYIQLVRPRTWIETEDPDKLaAYATLYNVMSTLVKLMAP 761
                                    9******************************************************999977799**************** PP

                    Anticodon_1  80 fmPfitEelwqr..eeeelgkkesimlaewpekaeel..ekeleeeevellkeivkairklrselkikpsselkv 150
                                    f+Pf++E ++q+  ++     +es+++++wp  + e   +k l ee++++++ei +a+ ++r++ + k +++++ 
  gi|116754239|ref|YP_843357.1| 762 FTPFLAESIYQNlvRGLDPSAPESVHMCDWPG-YREDliDKGL-EESMSYVREISEAAANARQKGGRKLRWPVSR 834
                                    ************87332225569********6.4333357777.9*******************99999998654 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2.9
                    Anticodon_1 124 ellkeivkairklrselkikpsselk 149
                                     +++ei++ i+++r++l++k ++ ++
  gi|116754239|ref|YP_843357.1| 964 GYAREIIRRIQDMRKDLDLKVDEMIR 989
                                    46678999999999999888777655 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 !   28.2   0.0   2.1e-10   7.7e-07       8     135 ..      48     194 ..      43     197 .. 0.70
   2 !   16.5   0.0   7.5e-07    0.0027     154     238 ..     381     466 ..     351     475 .. 0.78
   3 !   47.0   0.4   4.1e-16   1.5e-12     244     376 ..     520     644 ..     513     653 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 2.1e-10
                                    B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHT.......TS..........-HHHHHHHH CS
                   tRNA-synt_1g   8 pYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAeke.......gv..........tpeelvekv 70 
                                    pY++g++HlG + + ++ D + Ry  +rg++    +g D+hG pie+k e++       ++          + + ++ + 
  gi|116754239|ref|YP_843357.1|  48 PYTTGRIHLGTAWNKVIKDSILRYMSMRGYDLKDRAGWDMHGLPIEVKVEEHlgfrskrDIesygvdrfieQCKSFALRQ 127
                                    8***********************************************98753222211221111111111223344455 PP

                                    HHHHHHHHHHTT-..--SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG- CS
                   tRNA-synt_1g  71 heeikelfkklni..sfdkygrttseehkelvqeifkklkekgliyekeieqlycpkderflpdryv 135
                                    ++e++e+fk+l++   +d+ + t ++e  e++   +k+ +e+gl++++   + +cp++++ ++d++v
  gi|116754239|ref|YP_843357.1| 128 KDEMTEQFKSLGVwlDWDNPYMTLKNEYIEAAWWTLKRAHERGLLERGLRVVNWCPRCQTAIADSEV 194
                                    5666777777765225666677777777777777777777777777777777777777777777776 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 7.5e-07
                                    TTSSB-E..................EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS- CS
                   tRNA-synt_1g 154 ecgkkleptelin..pksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdl 231
                                    e g+ l + el+    ++  +++  ++  t+++f  +s++++++ + ie+ +       +   k+w+++  +d++isr+ 
  gi|116754239|ref|YP_843357.1| 381 ERGALLASGELVHryGHCWRCKTPIIFIATRQWFIGISELRDQMLKEIERVSWYPDWAGSARFKDWISN-ARDWCISRQR 459
                                    44566666666552268999999999**********************7777556666778899***99.9********* PP

                                    SSS-EET CS
                   tRNA-synt_1g 232 dwGipvP 238
                                     wGip+P
  gi|116754239|ref|YP_843357.1| 460 YWGIPLP 466
                                    *****99 PP

  == domain 3  score: 47.0 bits;  conditional E-value: 4.1e-16
                                    EE-HHHHHHHHHHHTTTTT-...TTSGGGG.G--S......EEEE..EGGGHH..HHHTHHHHHHHHTT----S-EEEE- CS
                   tRNA-synt_1g 244 vlYVWldAligYisatkelakkkgeeekwkeyWakdkevelvhfi..gkdiik..FHtifwPaillgaelklpkkvvahe 319
                                    v+ VW+d  +   ++++       +ee+++ +W +        fi  g d ++  F +  + a + + +    k+v  h+
  gi|116754239|ref|YP_843357.1| 520 VFDVWFDSAVASWATLNFPR----DEEEFRVWWPA-------DFIteGHDQTRgwFYSQ-LGASMVAFGRAPYKSVLMHG 587
                                    7889***9988776666554....789******44.......45522566654324444.45666677778889999999 PP

                                    -.EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHHHHHHHH CS
                   tRNA-synt_1g 320 y.ltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswedfvervN 376
                                    + l  +g+K+SkS g+vv +++++er+ ad+lR+y+++++   +Dl+fswe +++ vN
  gi|116754239|ref|YP_843357.1| 588 FtLDEQGRKMSKSIGNVVHPEDVVERYGADTLRFYVLSSNAPWEDLHFSWEGAMN-VN 644
                                    9456789********************************************9886.44 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 !    4.7   0.0    0.0044        16      21      49 ..      52      80 ..      42      82 .. 0.90
   2 !   23.4   0.0   9.3e-09   3.3e-05     228     284 ..     570     627 ..     554     643 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0044
                                   S--BHHHHHHHHHHHHHHHHHHHTT-EEE CS
                   tRNA-synt_1e 21 dashlGhaRslvafDilrrilqalgYdvq 49
                                     +hlG a + v+ D + r++ ++gYd++
  gi|116754239|ref|YP_843357.1| 52 GRIHLGTAWNKVIKDSILRYMSMRGYDLK 80
                                   578***********************985 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 9.3e-09
                                    HHHHHSS.S--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS- CS
                   tRNA-synt_1e 228 qseaafd.kqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRllllsah 284
                                     s+ af+  ++    +h   l  +g+kmsks++n++  +dv++++ + +lR+++ls +
  gi|116754239|ref|YP_843357.1| 570 ASMVAFGrAPYKSVLMHGFTLDEQGRKMSKSIGNVVHPEDVVERYGADTLRFYVLSSN 627
                                    577788867788889999999********************************98764 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 ?   -1.2   0.0      0.21   7.4e+02      34      64 ..      51      81 ..      45     149 .. 0.74
   2 !   20.5   0.0   5.2e-08   0.00019     269     312 ..     584     627 ..     552     645 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.21
                   tRNA-synt_1f 34 SGliHiGnlrevltadlvaralrkrgeevrl 64
                                    G+iH+G++ + +  d + r ++ rg + + 
  gi|116754239|ref|YP_843357.1| 51 TGRIHLGTAWNKVIKDSILRYMSMRGYDLKD 81
                                   5788888888777777777777777766554 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 5.2e-08
                   tRNA-synt_1f 269 vvYelillkggekmssSkGnvltledwlevaepevlrflilrrk 312
                                    ++  + l+++g+kms+S Gnv+ +ed++e +  ++lrf++l+++
  gi|116754239|ref|YP_843357.1| 584 LMHGFTLDEQGRKMSKSIGNVVHPEDVVERYGADTLRFYVLSSN 627
                                    567788899999***************************99854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1049 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); 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: 0.79u 0.25s 00:00:01.04 Elapsed: 00:00:00.46
# Mc/sec: 6868.51
//
Query:       gi|116754240|ref|YP_843358.1|  [L=846]
Description: magnesium-translocating P-type ATPase [Methanosaeta thermophila PT]
Scores for complete 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-52  177.0   0.0    2.6e-52  177.0   0.0    3.2  4  E1-E2_ATPase     E1-E2 ATPase
      9e-18   64.6  10.2      9e-18   64.6  10.2    2.0  2  Cation_ATPase_C  Cation transporting ATPase, C-terminus
    1.4e-17   63.2   0.0    3.4e-17   61.9   0.0    1.7  1  Cation_ATPase_N  Cation transporter/ATPase, N-terminus
    1.1e-16   61.8   0.2    2.1e-16   60.9   0.2    1.5  1  Hydrolase        haloacid dehalogenase-like hydrolase
    3.3e-05   23.9   0.0      7e-05   22.8   0.0    1.5  1  Cation_ATPase    Cation transport ATPase (P-type)
    0.00013   21.8   0.5    0.00022   21.1   0.5    1.3  1  Hydrolase_3      haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.2      0.83   2.5e+03     122     155 ..      67      99 ..      59     103 .. 0.51
   2 !  177.0   0.0   8.6e-56   2.6e-52       3     179 ..     122     310 ..     120     312 .. 0.98
   3 ?   -2.3   1.9       0.9   2.7e+03     120     157 ..     722     769 ..     714     771 .. 0.49
   4 ?   -3.6   1.6       2.3   6.7e+03     121     157 ..     783     825 ..     776     831 .. 0.56

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.83
                                    HHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHH CS
                   E1-E2_ATPase 122 lvpvvlliallvflialllgkslaeallralall 155
                                     +p+vll++++++l  ++l +++   ++ a++++
  gi|116754240|ref|YP_843358.1|  67 RSPIVLLLVFAALLS-VYLHQTIEAGIVLAIVFA 99 
                                    445555555444444.444444445555566554 PP

  == domain 2  score: 177.0 bits;  conditional E-value: 8.6e-56
                                    S--EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-S.EEE-TTTS---S-EE-............G-TTE CS
                   E1-E2_ATPase   3 lpptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsa.evdesaLTGEslpvek............ekgdm 69 
                                     + +a+v+r+ +e+ei+++++vpGDiv+lkagd++p D+ri+e+ +  v+e+aLTGE  pvek            e++++
  gi|116754240|ref|YP_843358.1| 122 VQVRATVLRASSEKEIPVENIVPGDIVILKAGDIIPGDCRIIESRDlFVNEAALTGETYPVEKidedlpadaplaERRNS 201
                                    56789*************************************************************************** PP

                                    E-TT-EEEE-EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHH CS
                   E1-E2_ATPase  70 vfsGtvvvsgeakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeall 149
                                    +f+Gt+vvsg+a+a+V++tg+dte+g+i +++e   + +t++++ l+++g +l+ + ll+++++f+i+++l++++ e++l
  gi|116754240|ref|YP_843358.1| 202 LFMGTNVVSGRATAIVVHTGRDTEFGRISHHLELR-RPETDFERGLRNFGYFLMELTLLLVVAIFAINVYLNRPVLESFL 280
                                    *********************************98.9******************************************* PP

                                    HHHHHHHHHS-TTHHHHHHHHHHHHHHHHH CS
                   E1-E2_ATPase 150 ralallvaaiPcaLplavplalalgarrla 179
                                    ++lal+v+ +P  Lp++v++ la gar++a
  gi|116754240|ref|YP_843358.1| 281 FSLALAVGLTPQLLPAIVSVNLAHGAREMA 310
                                    *****************************9 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.9
                                    HHHHHHHHHHHHHHHHS-STTTSSTT.........HHHHH.HHHHHHH CS
                   E1-E2_ATPase 120 kvlvpvvlliallvflialllgksla.........eallr.alallva 157
                                    +v+ +++ l+  l+f ++l+l + ++         e++++ ++++lv+
  gi|116754240|ref|YP_843358.1| 722 AVFGMLSSLFDYLTFGALLFLLHATTaqfrtgwfmESVISaSMVVLVI 769
                                    555555555555555555554444444444433334444436666665 PP

  == domain 4  score: -3.6 bits;  conditional E-value: 2.3
                                    HHHHHHHHHHHHHHHS-STTTSSTT......HHHHHHHHHHHH CS
                   E1-E2_ATPase 121 vlvpvvlliallvflialllgksla......eallralallva 157
                                    +l++  l++++++fl+ ++  ++l+       ++l a +++va
  gi|116754240|ref|YP_843358.1| 783 YLIISTLAVGAAAFLLPYTPLGGLFmftplpLSFLAATVVIVA 825
                                    4555555555555555555444444556665555555555554 PP

>> Cation_ATPase_C  Cation transporting ATPase, C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.2   3.4e+03     132     169 ..     252     286 ..     227     293 .. 0.53
   2 !   64.6  10.2     3e-21     9e-18       1     180 [.     674     835 ..     674     836 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.2
                Cation_ATPase_C 132 illslllqvlivyvpglnavfgtaplsleewliallla 169
                                    +l++l+l+++++ +  +n ++  +++ le++l +l+la
  gi|116754240|ref|YP_843358.1| 252 FLMELTLLLVVAIFA-INVYL--NRPVLESFLFSLALA 286
                                    444444444443332.33322..233345555555544 PP

  == domain 2  score: 64.6 bits;  conditional E-value: 3e-21
                Cation_ATPase_C   1 plplsaiqiLwinLvtDllpalaLaleppekdimkrpPrkkkepliskkmlrri.liqgllqalvtllvffltlllfgis 79 
                                    +lp+ ++q+L+ nL+tDl   +a+a +  +++ + rp r      +s++++r++ ++ g+l++l+ +l+f + l+l +++
  gi|116754240|ref|YP_843358.1| 674 FLPMLPVQVLLTNLLTDLP-EMAIASDSVDPEYLVRPRR------WSIRFIRNFmAVFGMLSSLFDYLTFGALLFLLHAT 746
                                    58***************87.*******************......*************************9999988877 PP

                Cation_ATPase_C  80 ekenklssnyaqtmaFitlvlsqifnalnlrsrreslfkfsglfsnkllllaillslllqvlivyvpglnavfgtaplsl 159
                                    + +       ++t +F+  v+s  + +l++r+ r+++f+  ++  +++l++++l+  + ++l+ y+p l+ +f ++pl+l
  gi|116754240|ref|YP_843358.1| 747 TAQ-------FRTGWFMESVISASMVVLVIRT-RRPFFR--SV-PSRYLIISTLAVGAAAFLLPYTP-LGGLFMFTPLPL 814
                                    766.......**********************.555555..44.688*******************9.************ PP

                Cation_ATPase_C 160 eewlialllalvvllvdelvK 180
                                    + ++ ++++++v++l +e+ K
  gi|116754240|ref|YP_843358.1| 815 SFLAATVVIVAVYVLTAEVAK 835
                                    ******************998 PP

>> Cation_ATPase_N  Cation transporter/ATPase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.9   0.0   1.1e-20   3.4e-17       2      69 .]      15      81 ..      14      81 .. 0.98

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 1.1e-20
                Cation_ATPase_N  2 halsleevlekLetdlenGLtqaeaaerlkkyGpNelkekkkkslwvkllkqftnplvilLlvaalvs 69
                                   +als+e v+e+L+ + ++GLt++eaaerl+kyG+N+  e +++  +++ll+qf++p+v+lL++aal+s
  gi|116754240|ref|YP_843358.1| 15 WALSAERVMEELG-TGPDGLTEDEAAERLRKYGSNIPREMRRPGDLFLLLSQFRSPIVLLLVFAALLS 81
                                   99**********9.9***************************************************98 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   0.2     7e-20   2.1e-16       1     210 []     328     605 ..     328     605 .. 0.73

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 7e-20
                                    SSEEEEESBTTTBCHHHHHHHHHHHH.........CHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTE.... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.... RF
                      Hydrolase   1 iktvvfDkdGTLttgepsvedvivsa.........alalaaaletgsehpigkalvaaakarsgaltgfatfigrg.... 67 
                                    +++++ Dk+GTLt+g    + +++               +a  etg + pi +a+  + +    +++gf+++ +      
  gi|116754240|ref|YP_843358.1| 328 MNVLCCDKTGTLTEGAAKMHAALDVDgkenqnvflLAYVNAFHETGFTSPIDQAILSYRQP---DVSGFEKLDEVPydfv 404
                                    799*************666665555533222222111223333444777777777544444...4555555333334445 PP

                                    .............HHHHTHHHHHHHHHCHHHHHHHHHHHHHHCHHHHHH............................... CS
                                    .............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................... RF
                      Hydrolase  68 .............ayaigkpewltaldippdlgaaigsaqsqgrtvall............................... 103
                                                          +       ++ +  +saq+ + +val+                               
  gi|116754240|ref|YP_843358.1| 405 rkrlsilvsrdeeN-------IMITKGALRNVLEVCSSAQTSDGIVALDsvkeniqqifsdysskgyrvlgiafrkisgr 477
                                    55565543333332.......222223344444667778888888888899999999999999999999999******** PP

                                    ........TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT....GGGE.SEEEEHHCES CS
                                    ........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxx.xxxxxxxxxx RF
                      Hydrolase 104 ........qaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG....ddyf.daviasdiet 170
                                            +   l+ + + dp  vk+++a++va L   g+ + ++tgdn+  a  + +q+G       +  +++ + ++ 
  gi|116754240|ref|YP_843358.1| 478 pvtkdderDMTFLGFLIFFDP--VKEGIAKTVADLAGLGVSLKMITGDNKLVASTVGEQVGlrkeI--VlTGSDLRRVSD 553
                                    ****999999***********..**************************************99541..333333333333 PP

                                    ............STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                    ............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 171 ............vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                                +a+++p++k+++i  ++ ++  v   GDg+nD++al a +
  gi|116754240|ref|YP_843358.1| 554 ealqrlvrdvdiFAEVEPNQKERIILAIRRNGDVVGYMGDGINDVSALHASD 605
                                    457777777999*****************99999**************9875 PP

>> Cation_ATPase  Cation transport ATPase (P-type)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   2.4e-08     7e-05      45      90 ..     372     435 ..     319     436 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 2.4e-08
                  Cation_ATPase  45 e....................tkkvqeipFnssrKrmsvvlklepekkvrlyvKGApeiilkrCth 90 
                                                         ++k+ e+p++ +rKr s++++   ++++++++KGA   +l+ C++
  gi|116754240|ref|YP_843358.1| 372 TgftspidqailsyrqpdvsgFEKLDEVPYDFVRKRLSILVSR--DEENIMITKGALRNVLEVCSS 435
                                    04444455555555555666699*******************5..6******************96 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.5   7.3e-08   0.00022     206     245 ..     588     627 ..     575     634 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 7.3e-08
                                    EEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE-- CS
                    Hydrolase_3 206 viafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtks 245
                                    v  +GDg ND++ L a+++++ ++na + +k aAd v   
  gi|116754240|ref|YP_843358.1| 588 VGYMGDGINDVSALHASDISISVENAVDVAKDAADIVLME 627
                                    5569*******************************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (846 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       824  (0.0459591); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); 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):               6  [number of targets reported over threshold]
# CPU time: 0.71u 0.29s 00:00:01.00 Elapsed: 00:00:00.45
# Mc/sec: 5683.62
//
Query:       gi|116754241|ref|YP_843359.1|  [L=82]
Description: hypothetical protein Mthe_0931 [Methanosaeta thermophila PT]
Scores for complete 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-20   71.1   0.4    4.5e-20   71.1   0.4    1.3  1  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 !   71.1   0.4   2.5e-24   4.5e-20       3      60 ..      13      74 ..      11      76 .. 0.93

  Alignments for each domain:
  == domain 1  score: 71.1 bits;  conditional E-value: 2.5e-24
                         DUF131  3 vvlkalekeee....eaekeesrvkgGGVvliGPIPIiFGsdkrlaktaiiLaIilmillli 60
                                    +++++++ee+    +  ++++++kgG+Vv+iGP+P+++Gsd+r+a ++++LaI lm+++++
  gi|116754241|ref|YP_843359.1| 13 SIMRERRYEEMeetvMPAERRTDIKGGAVVMIGPLPVVIGSDQRMAAVLMVLAITLMAIWMV 74
                                   6899999999988999999*****************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       981  (0.0547158); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 609.22
//
Query:       gi|116754242|ref|YP_843360.1|  [L=70]
Description: hypothetical protein Mthe_0932 [Methanosaeta thermophila PT]
Scores for 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-14   52.0   8.9      4e-14   52.0   8.9    2.0  2  DUF131         Protein of unknown function DUF131
  ------ inclusion threshold ------
        1.2    9.0  14.2        1.8    8.4   2.0    2.0  2  7TMR-DISM_7TM  7TM diverse intracellular signalling
        1.5    8.8   7.0        1.7    8.7   0.9    2.1  2  SHP            Small hydrophobic protein


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 ?    1.7   1.6     0.034     2e+02      47      60 ..       9      22 ..       3      24 .. 0.82
   2 !   52.0   8.9   6.7e-18     4e-14      20      61 ..      26      67 ..      25      68 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.034
                         DUF131 47 aiiLaIilmillli 60
                                   +i++++i+++++l+
  gi|116754242|ref|YP_843360.1|  9 LILIGVIITFVSLL 22
                                   68899***999997 PP

  == domain 2  score: 52.0 bits;  conditional E-value: 6.7e-18
                         DUF131 20 srvkgGGVvliGPIPIiFGsdkrlaktaiiLaIilmilllil 61
                                   s++ +GGV+liGPIPI+FGs + +a  a+iLaI +m+++++l
  gi|116754242|ref|YP_843360.1| 26 SSSGFGGVILIGPIPIVFGSTPYMALAAMILAIAIMLISIAL 67
                                   6789***********************************987 PP

>> 7TMR-DISM_7TM  7TM diverse intracellular signalling
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   2.0    0.0003       1.8     156     179 ..       4      27 ..       1      31 [. 0.83
   2 ?    7.1   4.7   0.00078       4.7     107     147 ..      30      70 .]      27      70 .] 0.89

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0003
                  7TMR-DISM_7TM 156 liawlllligvlidilsllgllps 179
                                    li+w+l+ligv+i+++sll+l +s
  gi|116754242|ref|YP_843360.1|   4 LIGWSLILIGVIITFVSLLSLPSS 27 
                                    8************99998876555 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.00078
                  7TMR-DISM_7TM 107 lsllllllpllpyteslslaqllallvillllligikawrk 147
                                    +++++l+ p+ ++  s++++ l a+++++ ++li+i++wr+
  gi|116754242|ref|YP_843360.1|  30 FGGVILIGPIPIVFGSTPYMALAAMILAIAIMLISIALWRR 70 
                                    567889999999999999999******************86 PP

>> SHP  Small hydrophobic protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.6    0.0096        57      19      31 ..      10      22 ..       3      26 .. 0.82
   2 ?    8.7   0.9   0.00028       1.7      12      35 ..      45      66 ..      37      68 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.0096
                            SHP 19 tlihmiltlisll 31
                                    li +i+t++sll
  gi|116754242|ref|YP_843360.1| 10 ILIGVIITFVSLL 22
                                   5889999999998 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00028
                            SHP 12 skfwpyftlihmiltlislliiit 35
                                   s   py++l  mil++  +li i+
  gi|116754242|ref|YP_843360.1| 45 S--TPYMALAAMILAIAIMLISIA 66
                                   4..4***********999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       938  (0.0523175); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); 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):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.44
# Mc/sec: 477.48
//
Query:       gi|116754243|ref|YP_843361.1|  [L=470]
Description: histidyl-tRNA synthetase [Methanosaeta thermophila PT]
Scores for complete 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  207.2   0.3    1.3e-59  202.1   0.3    2.0  1  tRNA-synt_His    Histidyl-tRNA synthetase
      2e-16   60.5   0.0    3.5e-16   59.7   0.0    1.4  1  tRNA-synt_2b     tRNA synthetase class II core domain (G, H, 
      5e-09   36.2   0.3    1.2e-08   34.9   0.3    1.6  1  HGTP_anticodon   Anticodon binding domain
    0.00096   18.3   0.7      0.036   13.1   0.1    2.8  2  tRNA-synt_2      tRNA synthetases class II (D, K and N)
  ------ inclusion threshold ------
       0.15   12.1   0.6        0.4   10.8   0.6    1.7  1  FANCI_S1-cap     FANCI solenoid 1 cap
       0.15   11.4   0.0          1    8.8   0.0    2.2  2  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
       0.16   11.5   0.0       0.69    9.3   0.0    2.0  2  tRNA-synt_2d     tRNA synthetases class II core domain (F)
       0.98   10.1   3.7       0.44   11.2   0.5    2.0  2  MgtE_N           MgtE intracellular N domain


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 !  202.1   0.3   5.6e-63   1.3e-59       1     310 []      21     360 ..      21     360 .. 0.93

  Alignments for each domain:
  == domain 1  score: 202.1 bits;  conditional E-value: 5.6e-63
                                    T---EETCHHHHHHHHHHHHHHHHHHTT-EEEE--SEEEHHHHCTTSTCC.HHHS-EEE-TTSSEEEE-SSSHHHHHHHH CS
                  tRNA-synt_His   1 glrdllpeeaekieelrrrlldlfeswGYelVspPllEyldslltgaged.ldqtfklvDqsgrllglRaDiTpqvaRia 79 
                                    g+rd+ peea +++++r++++d++e+wGY++V +P++E+l+ ++ ++ge   ++++ ++D+ gr ++lR+++T+ v R++
  gi|116754243|ref|YP_843361.1|  21 GTRDFPPEEAYRRRAVREKMIDVMERWGYREVATPTFEHLELFTLKSGEGvIEEIYSFKDKGGRDIALRPELTAPVMRMY 100
                                    789****************************************99999995679************************** PP

                                    HHHHH.TSS-EEEEEEEEEEESS-SSTT--CCEEEEEEEEESS-SHHHHHHHHHHHHHHHHHHCTSSSEEEEEEETCHHH CS
                  tRNA-synt_His  80 ahrln.rerplRlcYaGsvlrtrpdglgrsreplQvGaEliGaegleadlEvlslllealeaaagvkelrldlghvglvr 158
                                       l+  ++plRl+Y+++++r ++ + gr re+ Q+G+EliG   +++++Ev+ ++ e+l +a+g+ +  + +g  gl+r
  gi|116754243|ref|YP_843361.1| 101 VSELHsSPKPLRLYYFANCFRYERPQKGRFREFWQLGCELIGGRRPDSEAEVIAMADEVL-RAVGI-RGDIHIGYLGLIR 178
                                    ****99******************************************************.6****.889999******* PP

                                    HHHHHTT--HHHHHHHHHHHHCT-HHHHHHHHHCCTTH................................HHCCHCC... CS
                  tRNA-synt_His 159 alleaaglsesleeallaalarkdlaelkelaaeaglk................................ealrellkal 206
                                    ++l++++  e++++ +++++++k++ +l+el+++ g++                                 +++++++++
  gi|116754243|ref|YP_843361.1| 179 SMLKKVP--EAHRQSIMRLIDKKERDALRELLQSIGAEdlgiielislkgkdaleraeelsaalssieipGENASAAQSV 256
                                    ****876..99**********************988889*******************************5555555555 PP

                                    .HCCHCCCHHHHCHCCHCTHHHHHHHHHHHHHHHHHHHHHHHH-TTEEE-TT--TTTTT--SEEEEEEETT-SS..-SEE CS
                  tRNA-synt_His 207 .elygdaevleealealaaapalqaaldeleelaallealakpevrvtlDlaelrgyeYytGlvFaayaegvgq..aiar 283
                                       + + ++ ++a +++ ++p+ +  l+e++e+ +ll+a+   +v+ t+D+  +rg+eYytG+vF++ya+g g+  +i +
  gi|116754243|ref|YP_843361.1| 257 aAPGASGREGARASARAGRSPESEMDLSEFREMLELLDAY---DVEATIDFEIVRGLEYYTGTVFEIYASGLGAqnQICG 333
                                    55555556666666778999999999************98...5**************************988555**** PP

                                    EEEECTTTGGG.T---EEEEEEEEHHHH CS
                  tRNA-synt_His 284 GGrYdelgaaf.grarpAtGfsldleal 310
                                    GG Y el + f g++  +tGf l  +++
  gi|116754243|ref|YP_843361.1| 334 GGSY-ELASLFgGSETFSTGFGLGFDRI 360
                                    ****.9*****99********9988775 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 !   59.7   0.0   1.6e-19   3.5e-16       1     132 [.      76     332 ..      76     368 .. 0.82

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 1.6e-19
                                    EEEEETTSEEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2b   1 YkledrndreyiLkPtneetfvelirdevlrskrLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeaslddsl 80 
                                    Y ++d+ +r+ +L+P+ ++++++++  e l s   Pl+ly++  ++R+E++ ++G  R reF q +++ ++     +ds 
  gi|116754243|ref|YP_843361.1|  76 YSFKDKGGRDIALRPELTAPVMRMYVSE-LHSSPKPLRLYYFANCFRYERP-QKG--RFREFWQLGCELIGGRR--PDSE 149
                                    99**************************.766555****************.***..*************9887..9*** PP

                                    HHHHHHHHHHHHHTT.SCEEEEEEGTTSC................................................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................................... RF
                   tRNA-synt_2b  81 rdlikaisriferlglefraiielmsaks................................................... 109
                                    +++i  ++++++++g+     i+  + +                                                    
  gi|116754243|ref|YP_843361.1| 150 AEVIAMADEVLRAVGIRGDIHIGYLGLIRsmlkkvpeahrqsimrlidkkerdalrellqsigaedlgiielislkgkda 229
                                    ***************98844444433222344456777777788888888888888888888888888888888888888 PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                   tRNA-synt_2b 110 ................................................................................ 109
                                                                                                                    
  gi|116754243|ref|YP_843361.1| 230 leraeelsaalssieipgenasaaqsvaapgasgregarasaragrspesemdlsefremlelldaydveatidfeivrg 309
                                    88888888888888888888888888888888888888888888888888888888888888888888888888888888 PP

                                    BTTSEEEEEEEEETTTSEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2b 110 adykdkkefeavsesltkgieig 132
                                    ++y+  ++fe++   l+++ +i 
  gi|116754243|ref|YP_843361.1| 310 LEYYTGTVFEIYASGLGAQNQIC 332
                                    88888888888888888887764 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.3   5.5e-12   1.2e-08      17      91 ..     385     458 ..     374     460 .. 0.91

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 5.5e-12
                                    HHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEEEEEETTHHHHHH CS
                 HGTP_anticodon  17 yakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtreqervsldelvekl 91 
                                     a ++a++Lr+  + v++d  ++s+  +++ a  ++   ++++G +el++g++ +rd+ +++qe++s++e++e l
  gi|116754243|ref|YP_843361.1| 385 DAIRIAKRLRNI-VPVVMDVMGRSLSAQLKSASAINAEHVIIIGRRELDSGKLVLRDMVKGSQEELSIEEIEEQL 458
                                    578999****88.8999999***************************************************9977 PP

>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.1   1.6e-05     0.036      25     122 ..      33     140 ..      28     165 .. 0.71
   2 ?    1.9   0.0     0.044        98     284     298 ..     350     364 ..     336     371 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.6e-05
                                    HHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT...TEEE..............-E-S.-SHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxx..............xxxx.xxxxxxxxxx RF
                    tRNA-synt_2  25 rstvtkavrkyleengfieietPiLsksdteegarlFkvksrek..ekeff..............aLtq.spqlylelli 87 
                                    r  v + + +++e+ g+ e+ tP++ +       +lF++ks e   e e +               Lt   + +y   l 
  gi|116754243|ref|YP_843361.1|  33 RRAVREKMIDVMERWGYREVATPTFEHL------ELFTLKSGEGviE-EIYsfkdkggrdialrpELTApVMRMYVSELH 105
                                    5566677778888888888888888877......7777776666532.44445566677665666343314667776666 PP

                                    HCT.HSEEEEEEEEE--S--BTTB-S-CEEEEEEEE CS
                                    xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2  88 vag.idrvfqiaraFRaEdsrtdrhlaEFtqieaem 122
                                    ++    r + +a++FR E+ ++ r   EF+q+ +e+
  gi|116754243|ref|YP_843361.1| 106 SSPkPLRLYYFANCFRYERPQKGRFR-EFWQLGCEL 140
                                    6632679****************999.*****9997 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.044
                                    EEEEEEEHHHHHHHH CS
                                    xxxxxxxxxxxxxxx RF
                    tRNA-synt_2 284 hgGlglGldRlvmll 298
                                      G+glG+dR++ ++
  gi|116754243|ref|YP_843361.1| 350 STGFGLGFDRIMEVV 364
                                    57********98776 PP

>> FANCI_S1-cap  FANCI solenoid 1 cap
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.6   0.00018       0.4       3      42 ..     190     228 ..     188     230 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00018
                   FANCI_S1-cap   3 qkIlsLaaedsteeLqkfLqtLkedeLtelitnsAlKGke 42 
                                    q I+ L ++++ + L++ Lq+   ++L  +i   +lKGk+
  gi|116754243|ref|YP_843361.1| 190 QSIMRLIDKKERDALRELLQSIGAEDLG-IIELISLKGKD 228
                                    89************************95.89999999998 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 ?    8.8   0.0   0.00045         1      16     161 ..      31     168 ..      22     190 .. 0.79
   2 ?   -1.4   0.0      0.59   1.3e+03      18      51 ..     197     230 ..     180     245 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00045
                tRNA_synthFbeta  16 nkeqklrrklrdllagaGlnEvitysfvsekeldklleddderkavelanPlsedqsvlRtsLlpglLevlarNlargne 95 
                                     +++++r+k+ d++   G+ Ev t +f + + +     +   ++    +   + d  +lR+ L++ ++    + l+ + +
  gi|116754243|ref|YP_843361.1|  31 YRRRAVREKMIDVMERWGYREVATPTFEHLELFTLKSGEGVIEEIYSFKDKGGRD-IALRPELTAPVMRMYVSELHSSPK 109
                                    5677788888888888888888888887777765553333333444444433344.479*************99999999 PP

                tRNA_synthFbeta  96 dvrlFEigkvflkd.seeelpeeerhlaivltgkreeeswsekaravdfydlkgivealleslgi.ek 161
                                     +rl+ ++++f+ +  ++ +++e ++l++ l g r         r+ + +++ ++++++l+++gi ++
  gi|116754243|ref|YP_843361.1| 110 PLRLYYFANCFRYErPQKGRFREFWQLGCELIGGR---------RPDSEAEVIAMADEVLRAVGIrGD 168
                                    9*************999999***************.........888889999999999999999555 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.59
                tRNA_synthFbeta  18 eqklrrklrdllagaGlnEvitysfvsekeldkl 51 
                                     +k r++lr+ll+++G  +     ++s k  d+l
  gi|116754243|ref|YP_843361.1| 197 DKKERDALRELLQSIGAEDLGIIELISLKGKDAL 230
                                    5678899999999999988777777777666666 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 ?    9.3   0.0   0.00031      0.69      22     132 ..      36     141 ..      24     167 .. 0.72
   2 ?   -1.4   0.1      0.58   1.3e+03     211     223 ..     350     362 ..     341     368 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00031
                                    HHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-ECESEEE-SSTHHHHHHHH....TT CS
                   tRNA-synt_2d  22 vleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpekaveekllLRthttavqirtl....ek 97 
                                    v+e++ +++ + g++ev+ p  e      +   +++ ++   +++ + + k++    ++  LR   ta  +r+     ++
  gi|116754243|ref|YP_843361.1|  36 VREKMIDVMERWGYREVATPTFE----HLELFTLKSGEG--VIEEIYSF-KDKG--GRDIALRPELTAPVMRMYvselHS 106
                                    55666666666666666666542....222222222222..34555555.4444..578999999999888877677688 PP

                                    S-SSEEEEEEEEEEBSST-SSSB-SEEEEEEEEEE CS
                   tRNA-synt_2d  98 kkppikiisigrvfRrdavDathlaeFhqveglvv 132
                                    + +p+++  + ++fR +   + +  eF q+ + ++
  gi|116754243|ref|YP_843361.1| 107 SPKPLRLYYFANCFRYERPQKGRFREFWQLGCELI 141
                                    899**************************987555 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.58
                                    EEEEEEEHHHHHH CS
                   tRNA-synt_2d 211 gfafGlGveRlam 223
                                      +fGlG++R+  
  gi|116754243|ref|YP_843361.1| 350 STGFGLGFDRIME 362
                                    568*******965 PP

>> MgtE_N  MgtE intracellular N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.5    0.0002      0.44      69      98 ..     180     209 ..     177     209 .. 0.94
   2 ?   -2.2   0.2         3   6.6e+03      49      63 ..     281     295 ..     279     303 .. 0.39

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0002
                                    HHCCCHHHHHHHHHHCS-HHHHHHHHHHCT CS
                         MgtE_N  69 lleelpeekveellsaldeeereeieells 98 
                                    +l+ +pe +++++++++d++er++++ell+
  gi|116754243|ref|YP_843361.1| 180 MLKKVPEAHRQSIMRLIDKKERDALRELLQ 209
                                    68899***********************96 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3
                                    S-HHHHHHHHCCS-H CS
                         MgtE_N  49 lsdeelaelleelds 63 
                                    ++ +e +e+le ld+
  gi|116754243|ref|YP_843361.1| 281 MDLSEFREMLELLDA 295
                                    233333333333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (470 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); 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: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2988.38
//
Query:       gi|116754244|ref|YP_843362.1|  [L=349]
Description: peptidase M42 family protein [Methanosaeta thermophila PT]
Scores for complete 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-102  341.4   0.3   3.8e-102  341.2   0.3    1.0  1  Peptidase_M42  M42 glutamyl aminopeptidase
    3.6e-12   46.4   0.1      5e-12   46.0   0.1    1.2  1  Peptidase_M20  Peptidase family M20/M25/M40
     0.0068   16.1   0.1       0.58    9.8   0.0    2.4  2  Peptidase_M28  Peptidase family M28
  ------ inclusion threshold ------
      0.055   13.1   0.0        1.1    8.8   0.0    2.2  2  DUF2715        Domain of unknown function (DUF2715)
      0.093   13.0   0.2       0.57   10.5   0.1    2.4  2  FeoA           FeoA domain


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 !  341.2   0.3  1.1e-105  3.8e-102       1     292 []      42     333 ..      42     333 .. 0.98

  Alignments for each domain:
  == domain 1  score: 341.2 bits;  conditional E-value: 1.1e-105
                                    S-EEEEEESSTTSSEEEEEEE--B-EEEEEEEETTSEEEEEEESS--GGGTTTEEEEEEETTEEEEEEEEE--CGGCHHH CS
                  Peptidase_M42   1 GnliakkkgkekepkvmiaAHmDeiGfmVkeIkedGflrfekvGGvdpkvlegqrvkiltkkgkisGvigskppHllkee 80 
                                    Gnl+a+++g  k+p+vmiaAH DeiG+mVk ++e+Gf+ f k+GG+ +++l +qrv ++tk+g + GvigskppH++kee
  gi|116754244|ref|YP_843362.1|  42 GNLVATRRG--KSPSVMIAAHADEIGLMVKFVDEKGFVYFVKIGGWFDQTLLNQRVILHTKNGPVFGVIGSKPPHVMKEE 119
                                    9********..99******************************************************************* PP

                                    HHHCT--GCGEEEEGSGSSHHHHHHTTS-TT-EEEES---EEETTECEEETTHHHHHHHHHHHHHHHHHCTSS-SSEEEE CS
                  Peptidase_M42  81 erkkaleikelfiDigakskeeaeelGisvGdivvfdkefvelangkivskalDdragvavllellkelkeeeleatvyl 160
                                    +rkk+++  ++fiD+ga++++ea+e+Gi +G ++++d++fv l ++++++ka+D+ragva+++e++k+ ++e   +tvy+
  gi|116754244|ref|YP_843362.1| 120 DRKKPVDSRDMFIDVGARDQNEAREMGIVPGVPITIDRSFVPLRGDRVTGKAFDNRAGVAMMIEAMKRTRTE---CTVYA 196
                                    ********************************************************************9887...9**** PP

                                    EEESTCTTTSHHHHHHHHHH--SEEEEEEEEEE-CSTTSTTTTSS..TTS-CEEEEEETT...CCSHHHHHHHHHHHHHH CS
                  Peptidase_M42 161 vatvqEEvGlrGaktsaekikpdiaiavDvtaagdtpgskekeak..lgkGpvirvkDas...giyhpklrkkllelAkk 235
                                    v tv EEvGl+Gakt+a+ i+pd+ai+ D+t+ gd+pg ++k+++  +gkGpvi+v+Das   +i+++++ ++l+++A++
  gi|116754244|ref|YP_843362.1| 197 VSTVMEEVGLKGAKTCAFGIRPDLAIVTDTTIPGDHPGIEKKDSAleMGKGPVITVVDASgrgLIADEDVLDWLQKTAEQ 276
                                    *******************************************9899************99989**************** PP

                                    TT--EEEEEESSSSSTHHHHHTSTTTSEEEEEEEEEBSTTSTTEEEEHHHHHHHHHH CS
                  Peptidase_M42 236 nnipyqlevlsgggtDAgaihltgegvptalisiptryiHspvevahlddleatvkL 292
                                     +ip+ql+v  gg+tDA+ai+l++egv+t+++si+tryiHspvev++l+dl++ ++L
  gi|116754244|ref|YP_843362.1| 277 FSIPVQLDVSGGGTTDATAIQLSREGVKTGVVSIATRYIHSPVEVLSLEDLDKGAEL 333
                                    ***************************************************987765 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 !   46.0   0.1   1.4e-15     5e-12      19     206 ..     159     339 ..     147     340 .. 0.78

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 1.4e-15
                                    S.TTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTHHHHHHHHHHTTTCESEEEEE CS
                                    x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M20  19 t.pfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggrgGakallegleerekvdavfel 97 
                                    + p +++  +G      a d+ +gv++++ea+++ +      + t+  + ++ EE+g +Gak  +     + ++d    +
  gi|116754244|ref|YP_843362.1| 159 FvPLRGDRVTG-----KAFDNRAGVAMMIEAMKRTRT-----ECTVYAVSTVMEEVGLKGAKTCAF----GIRPDL---A 221
                                    45555555555.....599*************88555.....57***********98899999999....678888...5 PP

                                    EEESSSBTCHSTETEEEE............EEEEEEEEEESHEEECCHHHHHHHHHHHHHHHTSCEEEEEESSSBHTHHH CS
                                    xxxxxxxxxxxxxxxxxx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M20  98 hieepgileagklaigvv............kvevelleggapvtlndsplvkalaeaaeelfgekvelivsgpggtdarf 165
                                    ++ +++i+  +  ++g+              ++v    +g+   + d+++ ++l+++ae++    v+l vsg g+tda  
  gi|116754244|ref|YP_843362.1| 222 IVTDTTIPG-D--HPGIEkkdsalemgkgpVITVV-DASGRG-LIADEDVLDWLQKTAEQF-SIPVQLDVSGGGTTDATA 295
                                    699999999.4..4777788999999986435555.244454.4555************96.777888866669****** PP

                                    H....TTTEEEEEEESSGGCTTSTTTEEEHHHHHHHHHHHHHHHH CS
                                    x....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M20 166 f....agiptvmifgpgsglaHspnEyvdledlekgikvlarlle 206
                                    +    +g++t ++       +Hsp E ++ledl kg++++ar+le
  gi|116754244|ref|YP_843362.1| 296 IqlsrEGVKTGVVSIAT-RYIHSPVEVLSLEDLDKGAELIARALE 339
                                    *8766666666544433.89**********************987 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.1   0.0    0.0088        32       1      26 [.      43      66 ..      43      77 .. 0.85
   2 !    9.8   0.0   0.00016      0.58      35      82 ..     171     213 ..     155     318 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0088
                                   EEEEEESTTCESEEEEEEEE--B-TT CS
                  Peptidase_M28  1 NviatlegkatdevlllgAHyDsvgv 26
                                   N++at +gk+    ++++AH D +g 
  gi|116754244|ref|YP_843362.1| 43 NLVATRRGKS--PSVMIAAHADEIGL 66
                                   8999999999..58********9875 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00016
                                    TTTTHHHHHHHHHHHHHCHHGGCCSSEEEEEEEESSCSGSSHHHHHHH CS
                  Peptidase_M28  35 AdDnAsgvaalLelarvlaasgsrpkrgvrflffdaEEagllGSkafa 82 
                                    A Dn +gva+++e ++   +     + +v  + +  EE gl G+k  a
  gi|116754244|ref|YP_843362.1| 171 AFDNRAGVAMMIEAMKRTRT-----ECTVYAVSTVMEEVGLKGAKTCA 213
                                    89************998887.....78*****************9877 PP

>> DUF2715  Domain of unknown function (DUF2715)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00032       1.1      24      54 ..      46      82 ..      28     100 .. 0.73
   2 ?    1.8   0.0     0.046   1.7e+02      98     116 ..     269     286 ..     237     287 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00032
                        DUF2715 24 edkg......kyvdvepqvGltvgfvaqnGftfmina 54
                                   + +       +++++   +Gl v+fv ++Gf + ++ 
  gi|116754244|ref|YP_843362.1| 46 ATRRgkspsvMIAAHADEIGLMVKFVDEKGFVYFVKI 82
                                   3332344445999********************9875 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.046
                        DUF2715  98 ilakssfasfgvpiqldvq 116
                                     l+k   ++f++p+qldv+
  gi|116754244|ref|YP_843362.1| 269 WLQKTA-EQFSIPVQLDVS 286
                                    344444.55********95 PP

>> FeoA  FeoA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00016      0.57      24      44 ..     138     159 ..     127     184 .. 0.73
   2 ?   -1.6   0.0      0.91   3.3e+03      31      51 ..     242     261 ..     228     262 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00016
                                    HHHHHHHHT--TT-EEEEEE.E CS
                           FeoA  24 llrrLremGlvpGarievva.r 44 
                                     ++  remG+vpG  i++ +  
  gi|116754244|ref|YP_843362.1| 138 DQNEAREMGIVPGVPITIDRsF 159
                                    567889***********98533 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.91
                                    HT--TT-EEEEEEE-TTS-SE CS
                           FeoA  31 mGlvpGarievvarapfggpl 51 
                                    + + +G +i+vv +a ++g +
  gi|116754244|ref|YP_843362.1| 242 LEMGKGPVITVV-DASGRGLI 261
                                    455578899999.77777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); 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:                         5  (0.000278878); expected 0.2 (1e-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 0.28s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2359.29
//
Query:       gi|116754245|ref|YP_843363.1|  [L=509]
Description: beta-ribofuranosylaminobenzene 5'-phosphate synthase [Methanosaeta thermophila PT]
Scores for complete 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-31  107.5   0.0      1e-30  106.7   0.0    1.4  1  DUF98           p-hydroxybenzoic acid synthase
    1.3e-07   31.8   1.9    3.6e-07   30.3   1.9    1.9  1  GHMP_kinases_N  GHMP kinases N terminal domain
    2.5e-07   30.6   0.1    5.3e-07   29.6   0.1    1.6  1  UTRA            UTRA domain
    5.3e-07   29.9   0.4    0.00074   19.8   0.0    2.5  2  GHMP_kinases_C  GHMP kinases C terminal


Domain annotation for each model (and alignments):
>> DUF98  p-hydroxybenzoic acid synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.7   0.0   2.3e-34     1e-30       1     144 [.      29     181 ..      28     186 .. 0.96

  Alignments for each domain:
  == domain 1  score: 106.7 bits;  conditional E-value: 2.3e-34
                                    HH--S-HHHHHHHHHSS-EEEEEEEEEEEE--HHHHHHHTS-TT-EEEEEEEEEEE..TTEEEEEEEEEEEGGGS-HHHH CS
                          DUF98   1 LlgDGsvTrhlelltqekveveliemeaeeseeeeapkeveelkkpllrRqVwlra..ngqklayAeSwwneeelekylk 78 
                                    L +DGsvT  le++t+++v +e++e+++++++++ a +   ++++ +++R+V l++  +g++l++A+S+++ ++le  +k
  gi|116754245|ref|YP_843363.1|  29 LGTDGSVTSLLEVITGSPVGIETLEQRVVPATDDVARELDIDVGEDVNYRVVRLKNarTGETLIHAVSYTPLKRLEPGFK 108
                                    568*****************************************************999********************* PP

                                    H....SSS-HHHHHHHTT--BEEEEEEEEEEE--.HHHHHHT..SS-EEEEEEEEEEETTEEEEEEEEEEEG. CS
                          DUF98  79 e....kdqpiwksLtkerlelfReirglalgead.eLeeafg..ekgpfwsRhYrlfhkgkpltvirEvFspa 144
                                    +    +d+pi+++L+k+r+e++R+i + + ++ad ++++ f+   k  ++sR Y++++kg+pl+ irE+F+ +
  gi|116754245|ref|YP_843363.1| 109 NdlmrADIPIGQILHKHRIESRRDITQTECEQADdRMSQLFNifPKELMLSRRYKIIRKGEPLIAIRETFPYN 181
                                    999999***************************989*****9766899**********************985 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 !   30.3   1.9     8e-11   3.6e-07       1      66 []     261     322 ..     261     322 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 8e-11
                                    EEEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                 GHMP_kinases_N   1 divikseiPvgaGLGSSAAlavalvaAllallglsleeaklaleaerlaqggngsggDvaasvyGg 66 
                                    +i+++s   ++ GLGS++ lava+ +Al++l+g +   a +   a  ++ +g +sg+ vaa+ +Gg
  gi|116754245|ref|YP_843363.1| 261 RISVRSCYRTHVGLGSGTQLAVAVGKALCELYGEK---ASIREIAS-AVSRGGTSGIGVAAFEMGG 322
                                    589999999***********************932...33333333.456699*********9998 PP

>> UTRA  UTRA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.1   1.2e-10   5.3e-07       6     139 ..      47     182 ..      43     193 .. 0.87

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 1.2e-10
                                    EEEEEEEEEEEE--HHHHHHHTS-TTSEE.EEEEEEEEE.TTEEEEEEEEEEEGGGTTTCHHHHHH..CS-HHHHHHHHH CS
                           UTRA   6 pktevlsleevpasaeiaeaLglpagepv.lrieRlrla.dgepvaleesylpaslvpdlleedle..egslyayleerl 81 
                                    ++ e+l+ ++vpa++++a++L+++ ge+v +r++Rl  a  ge ++++ sy p++++++  + dl   + ++ ++l + +
  gi|116754245|ref|YP_843363.1|  47 VGIETLEQRVVPATDDVARELDIDVGEDVnYRVVRLKNArTGETLIHAVSYTPLKRLEPGFKNDLMraDIPIGQILHK-H 125
                                    67899***********************8799999999999**************8876666666447999*****99.* PP

                                    TTSEEEEEEEEEEEE--HHHHHHHTSTTT-EEEEEEEEEEETTSCEEEEEEEEEETTT CS
                           UTRA  82 gvpitraeetiearladaeeaelLgisagspvLviervtydadgrpveysrsyyrgdr 139
                                     ++ +r  ++ e + ad++ ++l++i + + +L+ +     + g+p+   r++++ + 
  gi|116754245|ref|YP_843363.1| 126 RIESRRDITQTECEQADDRMSQLFNIFPKELMLSRRYKIIRK-GEPLIAIRETFPYNM 182
                                    ****************************99988866555555.777777777776665 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 !    7.6   0.3    0.0011       4.8      30      83 ..     239     292 ..     228     294 .. 0.85
   2 !   19.8   0.0   1.7e-07   0.00074       1      69 [.     408     475 ..     408     487 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0011
                 GHMP_kinases_C  30 gilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvaralreef 83 
                                    + + ++le++++ +++ G  ga++s  +++ t ++l+   + a +v  al+e++
  gi|116754245|ref|YP_843363.1| 239 EQSERALEAAKRVAERFGLGGARISVRSCYRTHVGLGSGTQLAVAVGKALCELY 292
                                    567899*****************************9977777777777777766 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 1.7e-07
                 GHMP_kinases_C   1 llealergdlellgellnlsqrs.elkavvgilppeleellealselGalgaklsGaGgGptvfalfkdk 69 
                                    +++ + ++dl+++g ++n+ q++  ++ +v+  +p ++ l +++ ++G  +a+   +++Gptv+a++++ 
  gi|116754245|ref|YP_843363.1| 408 MMPSVVEEDLDAFGMAVNRIQQLgFKRVEVELQHPMIKMLMQEMVSAG--AACAGLSSFGPTVYAVTDTN 475
                                    67788999****************9999********************..****************9443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (509 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); 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: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3728.26
//
Query:       gi|116754246|ref|YP_843364.1|  [L=419]
Description: hydroxymethylglutaryl-CoA reductase, degradative [Methanosaeta thermophila PT]
Scores for complete 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-115  386.0   6.7     2e-115  385.7   6.7    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 !  385.7   6.7  1.1e-119    2e-115       7     367 .]      20     376 ..      14     376 .. 0.96

  Alignments for each domain:
  == domain 1  score: 385.7 bits;  conditional E-value: 1.1e-119
                                    HHHHHS-HHHHHHHTT----HHHHHHHSSS---------EEEEEEEETTEEEEEEE---STTHHHHHHHHHHHHHHTT-B CS
                    HMG-CoA_red   7 klleelteeeleelkeesldeevadkmiEnviGyvqlPlGvagpllingkeylvPmAteEgslvAsasrgakainesgGv 86 
                                    k++e+  ++e++e+ +++l+ ++adkm+EnviG +q+PlGva+++ i+g+e+lvPmAteE+s++A+as+ga++++++gG+
  gi|116754246|ref|YP_843364.1|  20 KIVEACGDAEIKEMIKSGLSLDQADKMVENVIGLFQVPLGVATNFIIDGREVLVPMATEEPSVIAAASNGARMARDGGGF 99 
                                    45566888999999999*************************************************************** PP

                                    .EEEE----EEEEEEEE.--S-HHHHHHHH.HTHHHHHHHHHHCSHH..CCT-EEEEEEE.EE-...SSEEEEEEEEE-T CS
                    HMG-CoA_red  87 kttvlkdgmtraqvvllesvedaaelkkwi.ekkeeleelanaaest..srggglkdiev.vla...grlvvlrlkvdtg 159
                                      t+++  ++raq++ + +++d++ +++ i e++ e++++an+++++  + ggg+  +ev v++   g++vv +l vd++
  gi|116754246|ref|YP_843364.1| 100 -FTSSTGPVMRAQIQAV-DLKDPYGARCRIlEHSSEITKIANEVDPMlvRLGGGAVGLEVhVIDsraGPMVVTHLLVDCR 177
                                    .7777777*********.******************************99**********888899999*********** PP

                                    TC--HHHHHHHHHHHHHHHHHHHTSEEEEEEE-S--GGGEEEEEEEEEHHHH..-SSTTHHHHHHHHHHHHHHHHHH-HH CS
                    HMG-CoA_red 160 DAmGaNmvnkateaaaelieeefgeeellsilsNlctdkkasainaiegrgksvvaeatigeevvekilkasaealvdln 239
                                    DAmGaN+vn+++ea+a+ ie+ +g++++l+i sNl++ ++a+a+++++ +++        g+evv+ i+k+ a a+vd++
  gi|116754246|ref|YP_843364.1| 178 DAMGANAVNTMAEAVAPEIERLTGGKVHLRIISNLADTRLARARAVFKADAI-------GGAEVVSAIFKTAALAEVDPY 250
                                    **********************************************998888.......9******************** PP

                                    HH..HHHHHHH.......HHHHHHHHHHTT--HHHHHHHHHHHTT.......SEEE...TTTEEEEEEEEE.----SBSH CS
                    HMG-CoA_red 240 ranigtankGiggfnahaaNgiaAvflAtGqDlaaveesshaiaa.......leev...edgdlygsvtlPsleVGtvGG 309
                                    ra  +t+nkGi       +Ng++A++lAtG+D++ave+++ha+aa       l+++   e+gdl+g+++lP ++VG vGG
  gi|116754246|ref|YP_843364.1| 251 RA--ATHNKGI-------MNGVTALVLATGNDTRAVEAGAHAYAArsgryasLSRYeidENGDLVGTIELP-MAVGLVGG 320
                                    **..*******.......**********************************88888889999********.******** PP

                                    HHHH-HHHHHH.HHTT---HH...HHHHHHHHHHHHHHHHHHHHHT-----HHHHHHHH CS
                    HMG-CoA_red 310 gtklppqaell.kllgvkgaknakeLaeiiaavgLAqelsalrALaaeglqkgHmklhr 367
                                    +t+++p a+++ ++lgv++a+   eL+++iaavgLAq+++alrALa+eg+q+gHm+lh+
  gi|116754246|ref|YP_843364.1| 321 ATRVHPVARAAvRMLGVRSAD---ELSRVIAAVGLAQNFAALRALATEGIQRGHMSLHA 376
                                    *********************...*********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 3339.15
//
Query:       gi|116754247|ref|YP_843365.1|  [L=272]
Description: prephenate dehydratase [Methanosaeta thermophila PT]
Scores for 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-61  204.8   0.0    1.3e-60  204.3   0.0    1.2  1  PDT        Prephenate dehydratase
    1.6e-12   47.0   0.0    3.1e-12   46.0   0.0    1.5  1  ACT        ACT domain
     0.0096   15.4   0.0      0.018   14.5   0.0    1.3  1  SBP_bac_3  Bacterial extracellular solute-binding proteins, f
  ------ inclusion threshold ------
      0.028   13.7   0.0      0.045   13.0   0.0    1.3  1  DUF3834    Protein of unknown function (DUF3834)
       0.12   12.7   0.0        1.1    9.5   0.0    2.4  3  DUF3135    Protein of unknown function (DUF3135)


Domain annotation for each model (and alignments):
>> PDT  Prephenate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.3   0.0   3.8e-64   1.3e-60       1     182 [.       3     177 ..       3     178 .. 0.98

  Alignments for each domain:
  == domain 1  score: 204.3 bits;  conditional E-value: 3.8e-64
                                    EEEES-TTSHHHHHHCCCS.....EEEEES-HHHHHHHHCTTS-SEEEEEEEESSS-B-HHHHHHHHH.SSEEEEEEEEE CS
                            PDT   1 vaylGpegtyshqAalkvfkaedvelipvasieevfeavekgeadyavvPiENsteGsVnetlDlLlkesdlkivgEvvl 80 
                                    +++lGp+g+ys++Aa++ f  +d+el+ ++ ie+vf+ave+++ad +vvP+ENs+eGsV  tlDlLl+ ++l i+gEvv+
  gi|116754247|ref|YP_843365.1|   3 IGVLGPRGSYSEMAASRRF--PDAELVYFDDIEDVFDAVESHKADAGVVPLENSLEGSVALTLDLLLS-RSLFICGEVVI 79 
                                    789****************..***********************************************.77********* PP

                                    E---EEEE-TT--TTT--EEEE-HHHHHHTHHHHHH-.TTSEEEE-S-HHHHHHHHHHCT-TTEEEEE-HHHHHHTT-EE CS
                            PDT  81 piehcLlakpktkleeikkvyShpqalgQcrkfLeehlpqvervavestaeAakkveassdkdaaaiasevaaelyglkv 160
                                    pi+hcLl++ +   ++++ ++Shpqal+Qcr+++++++p+ve++++ st++Aa+   a++  ++aaia+ +aa++ygl+v
  gi|116754247|ref|YP_843365.1|  80 PIRHCLLGRGDP--DSVRIILSHPQALAQCRQYIRRRYPGVEMRTTGSTSHAARL--AQEFPEMAAIANLEAAKTYGLRV 155
                                    *******99988..99***************************************..999******************** PP

                                    EECS-SS-S--EEEEEEEEETT CS
                            PDT 161 leeniedkknntTRFlvlakee 182
                                    l+++i+d+knn+TRF+vl++e+
  gi|116754247|ref|YP_843365.1| 156 LDRDIQDSKNNMTRFVVLSREM 177
                                    *******************985 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.0   0.0   8.7e-16   3.1e-12       2      63 ..     187     249 ..     186     253 .. 0.94

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 8.7e-16
                                    EEEEEEE.SSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHH CS
                            ACT   2 vlrvgvp.DrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealk 63 
                                    ++ v+++ DrPG+L+++++ +a r+iN+++ie+r+s+ ++++++f+++++++ ++++v eal 
  gi|116754247|ref|YP_843365.1| 187 SIVVYLEkDRPGALFAILREFAVRNINLTRIESRPSRKELGDYYFFIDLEGHVEDDAVREALD 249
                                    78899999*****************************************************97 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 !   14.5   0.0     5e-06     0.018     116     158 ..       8      49 ..       2      55 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5e-06
                                    ETTSHHHHHHHHHHHCTSEEEEESSHHHHHHHHHTTSSSEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      SBP_bac_3 116 qagstaeellkeelkkgaeivefdtleealqaLkngrvdavva 158
                                     +gs++e ++ + ++ +ae+v+fd++e+++ a+++ ++da v+
  gi|116754247|ref|YP_843365.1|   8 PRGSYSEMAASRRFP-DAELVYFDDIEDVFDAVESHKADAGVV 49 
                                    589999977777666.9***********************987 PP

>> DUF3834  Protein of unknown function (DUF3834)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.3e-05     0.045      95     149 ..      24      81 ..      13      85 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.3e-05
                        DUF3834  95 aevvyaddpeevlkllnegevdsavva..selkkgeaf.edllkklgvyvpGsCgaav 149
                                    ae+vy dd e+v++++++++ d+ vv+  + l+   a+  dll +  +++ G+ ++ +
  gi|116754247|ref|YP_843365.1|  24 AELVYFDDIEDVFDAVESHKADAGVVPleNSLEGSVALtLDLLLSRSLFICGEVVIPI 81 
                                    79************************97667777777767999999999999988866 PP

>> DUF3135  Protein of unknown function (DUF3135)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.64   2.3e+03      14      25 ..      99     110 ..      94     114 .. 0.81
   2 ?    9.5   0.0   0.00031       1.1      49      73 ..     156     180 ..     147     185 .. 0.92
   3 ?   -2.1   0.0       1.4   4.9e+03      11      28 ..     192     209 ..     189     228 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.64
                        DUF3135  14 edPealealrqe 25 
                                    ++P+al + rq 
  gi|116754247|ref|YP_843365.1|  99 SHPQALAQCRQY 110
                                    689***999985 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00031
                        DUF3135  49 iDmqlsraknPvaacvalsrmmqek 73 
                                    +D+ ++ +kn++ + v+lsr+m+++
  gi|116754247|ref|YP_843365.1| 156 LDRDIQDSKNNMTRFVVLSREMSKR 180
                                    699*******************987 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.4
                        DUF3135  11 LakedPealealrqelie 28 
                                    L k+ P al a+ +e   
  gi|116754247|ref|YP_843365.1| 192 LEKDRPGALFAILREFAV 209
                                    788999999988777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); 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:                         5  (0.000278878); expected 0.2 (1e-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 0.19s 00:00:00.60 Elapsed: 00:00:00.35
# Mc/sec: 2318.30
//
Query:       gi|116754248|ref|YP_843366.1|  [L=235]
Description: hypothetical protein Mthe_0938 [Methanosaeta thermophila PT]
Scores for complete 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-89  298.0   0.0    3.3e-89  297.8   0.0    1.0  1  PIN_5     PINc domain ribonuclease


Domain annotation for each model (and alignments):
>> PIN_5  PINc domain ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  297.8   0.0   1.8e-93   3.3e-89       1     205 [.       5     220 ..       5     221 .. 0.96

  Alignments for each domain:
  == domain 1  score: 297.8 bits;  conditional E-value: 1.8e-93
                          PIN_5   1 rfvlDTsaltdpevreklgeeeleeavkklldliaearlklgiscyip.psvykElkeflkreeveeeviakldtwlvkk 79 
                                    rfv DT+altd++++e+ g+++l+e+++++l+ +a+arl+lgiscy+p psvy+E+++f+++++++  ++ k+dtwlvkk
  gi|116754248|ref|YP_843366.1|   5 RFVFDTTALTDSQAWESEGCTTLCEGMSAILHRVAQARLHLGISCYVPyPSVYNEIRDFVRNNNCDIAILGKIDTWLVKK 84 
                                    8******************************************************************************* PP

                          PIN_5  80 spdryevkipaeilyeyveevrerinkGlrvaEeavreaaeesekl...ekee.........eeeevgelikklRekYre 147
                                    +pdry vkip++i+yeyv+++r+rinkG++v+Eea++ea++++ ++      e         e+e+vg++i+k+RekYr+
  gi|116754248|ref|YP_843366.1|  85 TPDRYRVKIPSKIFYEYVDYMRSRINKGMNVSEEAIWEAVSRCLSIsatG--EgreqmreeiEREVVGSIIRKFREKYRA 162
                                    *******************************************9995540..24556777889***************** PP

                          PIN_5 148 alRkGilDsaeDldvllLAkELdaavvssDeGikkwaeklGlrlveakkfpkvlkeyl 205
                                    alR+GilDsa+D+dvllLAk+Ldaavvs+D Gi++wae+lGlr++ea+ fp++++ey+
  gi|116754248|ref|YP_843366.1| 163 ALRYGILDSAPDIDVLLLAKDLDAAVVSQDLGIQRWAEQLGLRFMEARAFPQMVREYM 220
                                    *********************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.36
# Mc/sec: 1950.19
//
Query:       gi|116754249|ref|YP_843367.1|  [L=714]
Description: TPR repeat-containing protein [Methanosaeta thermophila PT]
Scores for complete 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  120.6  11.3    6.6e-13   48.8   0.0    5.4  5  TPR_12       Tetratricopeptide repeat
    1.4e-29  100.7   7.6    1.3e-06   27.9   0.1    7.6  7  TPR_1        Tetratricopeptide repeat
    1.5e-28   96.7   4.4    0.00018   21.3   0.0    8.1  7  TPR_7        Tetratricopeptide repeat
      7e-25   85.1  19.0    0.00013   21.8   0.0    8.0  8  TPR_2        Tetratricopeptide repeat
    8.9e-21   73.1  13.6      0.018   14.9   0.0    7.5  7  TPR_10       Tetratricopeptide repeat
    5.5e-20   69.9   8.0    0.00029   20.8   0.1    7.4  7  TPR_8        Tetratricopeptide repeat
    3.9e-15   55.3  17.2       0.14   13.1   0.0    9.0  9  TPR_14       Tetratricopeptide repeat
      2e-12   47.1   0.5    0.00091   18.7   0.0    4.2  4  SNAP         Soluble NSF attachment protein, SNAP
    2.1e-09   37.7   1.2       0.19   12.3   0.0    5.3  5  TPR_19       Tetratricopeptide repeat
    5.7e-09   35.8   0.8    2.8e-05   23.7   0.1    2.4  2  TPR_MalT     MalT-like TPR region
    8.6e-09   35.5   5.9        5.6    7.8   0.0    7.4  6  TPR_6        Tetratricopeptide repeat
    4.8e-08   32.8   0.4        1.9    9.0   0.1    5.5  5  TPR_17       Tetratricopeptide repeat
    1.3e-07   32.1  13.6      0.014   16.0   0.0    5.6  6  TPR_16       Tetratricopeptide repeat
    2.4e-06   27.1   2.9       0.13   11.9   0.2    6.0  6  TPR_11       TPR repeat
     0.0044   16.6   7.3       0.31   10.6   0.1    3.7  4  Foie-gras_1  Foie gras liver health family 1
     0.0072   16.0   2.2         13    5.5   0.0    4.4  3  RPN7         26S proteasome subunit RPN7
  ------ inclusion threshold ------
      0.012   16.2  11.8        2.1    9.2   0.0    6.1  5  TPR_4        Tetratricopeptide repeat
      0.085   13.1   0.0       0.26   11.6   0.0    1.8  1  Coat_F       Coat F domain
       0.27   10.9   6.7         13    5.4   0.1    4.8  6  TPR_21       Tetratricopeptide repeat-like domain
       0.28   10.9   1.1         18    5.0   0.0    2.3  2  APP_E2       E2 domain of amyloid precursor protein
        6.3    6.9  14.7        5.9    7.0   0.5    5.8  7  MIT          MIT (microtubule interacting and transport) doma


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 !   34.5   0.0   2.1e-11   1.8e-08       8      75 ..      69     131 ..      61     132 .. 0.90
   2 !   37.2   0.2     3e-12   2.6e-09       2      77 .]     140     213 ..     139     213 .. 0.96
   3 !   48.8   0.0   7.8e-16   6.6e-13       2      77 .]     220     293 ..     219     293 .. 0.96
   4 ?    1.4   1.5      0.46   3.9e+02       3      44 ..     307     346 ..     301     360 .. 0.54
   5 ?    0.2   0.0       1.1   9.4e+02      18      35 ..     372     389 ..     367     394 .. 0.80

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 2.1e-11
                         TPR_12   8 nlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                    +l++++rr+g  + A +++ kal +a+   +p+    +  l+nLg+++ + g++ +A+ ++++al+ +
  gi|116754249|ref|YP_843367.1|  69 RLGDICRRAGMPEIAMKCYSKALSQAQ---EPHV--RSVLLNNLGQVHAQKGDLSKAIVYYKKALEGF 131
                                    7*************************4...4755..9****************************976 PP

  == domain 2  score: 37.2 bits;  conditional E-value: 3e-12
                         TPR_12   2 vatalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiaek 77 
                                    +a ++ nla+++rr+ ++d A e++ k l  +++l   d+ ++a+    Lgr+y ++g+ e A+ ++e++l+++e+
  gi|116754249|ref|YP_843367.1| 140 AAHVMGNLASAYRRAYQWDRAVECYFKGLKGFEKL--NDSFGVAQMTGSLGRVYAEMGERELAVLYYEKSLRMFEQ 213
                                    577889*****************************..9999********************************986 PP

  == domain 3  score: 48.8 bits;  conditional E-value: 7.8e-16
                         TPR_12   2 vatalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiaek 77 
                                    +a++l++l+ v++++gr+d++ ++++++l i++ l  +++ ++ ++l nLgr y++ g+++ A+  le+al++++k
  gi|116754249|ref|YP_843367.1| 220 AAWLLSRLGRVYAEMGRWDDSKRCFDRSLSIFEDL--GQSQNAGIVLSNLGRFYLEKGDPDSARVSLERALKLLRK 293
                                    688999*****************************..9999*******************************9986 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.46
                         TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhplt 44 
                                    a+a++ la+ +++  +  ++ +l+  a + +++l    hp  
  gi|116754249|ref|YP_843367.1| 307 AAAYSLLASRYAAERNAKQSSQLYSNASDCFSEL--ALHPRI 346
                                    4455555555555555555555555555555555..444443 PP

  == domain 5  score: 0.2 bits;  conditional E-value: 1.1
                         TPR_12  18 rydeAlellekaleiarr 35 
                                    r deA +l+e+a+ + ++
  gi|116754249|ref|YP_843367.1| 372 RGDEAVALCERAISALES 389
                                    568999999999988765 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   6.9e-06    0.0059       3      30 ..      66      93 ..      64      96 .. 0.91
   2 !   27.9   0.1   1.5e-09   1.3e-06       3      29 ..     103     129 ..     101     129 .. 0.95
   3 !    7.8   0.2    0.0035         3       5      29 ..     145     169 ..     141     169 .. 0.92
   4 !   11.7   0.0   0.00021      0.18       7      30 ..     187     210 ..     185     213 .. 0.91
   5 !   16.8   0.0   5.2e-06    0.0044       1      32 [.     221     252 ..     221     254 .. 0.92
   6 !   15.2   0.0   1.7e-05     0.014       3      30 ..     263     290 ..     262     293 .. 0.94
   7 ?    0.9   0.0      0.53   4.5e+02      18      28 ..     374     384 ..     373     386 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.9e-06
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                          TPR_1  3 alynlGnayfklgkydeAleyyekALel 30
                                    l++lG ++++ g+++ A ++y+kAL+ 
  gi|116754249|ref|YP_843367.1| 66 ELKRLGDICRRAGMPEIAMKCYSKALSQ 93
                                   589***********************75 PP

  == domain 2  score: 27.9 bits;  conditional E-value: 1.5e-09
                                    HHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                          TPR_1   3 alynlGnayfklgkydeAleyyekALe 29 
                                     l+nlG+++ ++g++ +A+ yy+kALe
  gi|116754249|ref|YP_843367.1| 103 LLNNLGQVHAQKGDLSKAIVYYKKALE 129
                                    69************************8 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0035
                                    HHHHHHHHHTT-HHHHHHHHHHHHH CS
                          TPR_1   5 ynlGnayfklgkydeAleyyekALe 29 
                                     nl+ ay++  ++d A+e+y k L+
  gi|116754249|ref|YP_843367.1| 145 GNLASAYRRAYQWDRAVECYFKGLK 169
                                    69*******************9986 PP

  == domain 4  score: 11.7 bits;  conditional E-value: 0.00021
                                    HHHHHHHTT-HHHHHHHHHHHHHH CS
                          TPR_1   7 lGnayfklgkydeAleyyekALel 30 
                                    lG +y ++g+ + A+ yyek L+ 
  gi|116754249|ref|YP_843367.1| 187 LGRVYAEMGERELAVLYYEKSLRM 210
                                    99*******************985 PP

  == domain 5  score: 16.8 bits;  conditional E-value: 5.2e-06
                                    HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                          TPR_1   1 akalynlGnayfklgkydeAleyyekALelnP 32 
                                    a  l +lG +y ++g++d+   ++++ L++ +
  gi|116754249|ref|YP_843367.1| 221 AWLLSRLGRVYAEMGRWDDSKRCFDRSLSIFE 252
                                    67899***********************9976 PP

  == domain 6  score: 15.2 bits;  conditional E-value: 1.7e-05
                                    HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                          TPR_1   3 alynlGnayfklgkydeAleyyekALel 30 
                                    +l nlG  y+++g++d A    e+AL+l
  gi|116754249|ref|YP_843367.1| 263 VLSNLGRFYLEKGDPDSARVSLERALKL 290
                                    689************************9 PP

  == domain 7  score: 0.9 bits;  conditional E-value: 0.53
                                    HHHHHHHHHHH CS
                          TPR_1  18 deAleyyekAL 28 
                                    deA++ +e+A+
  gi|116754249|ref|YP_843367.1| 374 DEAVALCERAI 384
                                    89********9 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0    0.0089       7.6       2      32 ..      67      97 ..      66     101 .. 0.84
   2 !   21.3   0.0   2.1e-07   0.00018       2      29 ..     104     132 ..     103     139 .. 0.88
   3 !   14.1   0.0   4.1e-05     0.035       3      27 ..     145     167 ..     143     177 .. 0.89
   4 !   18.6   0.1   1.5e-06    0.0013       4      35 ..     186     217 ..     184     222 .. 0.91
   5 !   15.2   0.0   1.8e-05     0.016       2      32 ..     224     254 ..     223     257 .. 0.89
   6 !   10.9   0.0   0.00043      0.36       2      29 ..     264     292 ..     263     297 .. 0.86
   7 ?    2.3   0.0      0.24     2e+02      16      30 ..     374     389 ..     372     401 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0089
                          TPR_7  2 LlnLarlysrlGdyeeAielyeqsLaltkdp 32
                                   L +L+++++r G  e A ++y ++L  + +p
  gi|116754249|ref|YP_843367.1| 67 LKRLGDICRRAGMPEIAMKCYSKALSQAQEP 97
                                   679********************77666666 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 2.1e-07
                          TPR_7   2 LlnLarlysrlGdyeeAielyeqsL.alt 29 
                                    L+nL++++ + Gd ++Ai +y+++L +++
  gi|116754249|ref|YP_843367.1| 104 LNNLGQVHAQKGDLSKAIVYYKKALeGFE 132
                                    8**********************885555 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 4.1e-05
                          TPR_7   3 lnLarlysrlGdyeeAielyeqsLa 27 
                                     nLa++y+r  ++++A+e+y +  +
  gi|116754249|ref|YP_843367.1| 145 GNLASAYRRAYQWDRAVECYFK--G 167
                                    7*******************88..4 PP

  == domain 4  score: 18.6 bits;  conditional E-value: 1.5e-06
                          TPR_7   4 nLarlysrlGdyeeAielyeqsLaltkdpeda 35 
                                     L+r+y ++G++e A+ +ye+sL++ ++ +d+
  gi|116754249|ref|YP_843367.1| 186 SLGRVYAEMGERELAVLYYEKSLRMFEQLGDR 217
                                    69*********************998887776 PP

  == domain 5  score: 15.2 bits;  conditional E-value: 1.8e-05
                          TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdp 32 
                                    L++L+r+y ++G++++  +++ +sL + +d 
  gi|116754249|ref|YP_843367.1| 224 LSRLGRVYAEMGRWDDSKRCFDRSLSIFEDL 254
                                    899********************99887665 PP

  == domain 6  score: 10.9 bits;  conditional E-value: 0.00043
                          TPR_7   2 LlnLarlysrlGdyeeAielyeqsL.alt 29 
                                    L+nL+r y + Gd + A   +e++L  l+
  gi|116754249|ref|YP_843367.1| 264 LSNLGRFYLEKGDPDSARVSLERALkLLR 292
                                    99*********************994444 PP

  == domain 7  score: 2.3 bits;  conditional E-value: 0.24
                          TPR_7  16 eeAielyeqsL.altk 30 
                                    +eA+ l+e+++ al++
  gi|116754249|ref|YP_843367.1| 374 DEAVALCERAIsALES 389
                                    89*******8888875 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   4.2e-05     0.035       4      30 ..      67      93 ..      64      96 .. 0.91
   2 !   21.8   0.0   1.5e-07   0.00013       3      29 ..     103     129 ..     101     129 .. 0.95
   3 !    7.0   0.4    0.0084       7.2       4      24 ..     144     164 ..     141     169 .. 0.89
   4 !   11.5   0.1    0.0003      0.26       7      31 ..     187     211 ..     186     214 .. 0.92
   5 !   20.3   0.0   4.7e-07    0.0004       3      33 ..     223     253 ..     221     254 .. 0.91
   6 !   16.9   0.0   5.6e-06    0.0048       3      30 ..     263     290 ..     261     293 .. 0.93
   7 ?   -2.5   0.7       9.1   7.8e+03       1      26 [.     307     332 ..     307     335 .. 0.81
   8 ?   -0.5   0.1       2.2   1.9e+03      18      29 ..     374     385 ..     373     388 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.2e-05
                          TPR_2  4 lynlGlayyklgdyeeAleafekAlel 30
                                   l +lG++++++g +e A +++ kAl+ 
  gi|116754249|ref|YP_843367.1| 67 LKRLGDICRRAGMPEIAMKCYSKALSQ 93
                                   789**********************86 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 1.5e-07
                          TPR_2   3 alynlGlayyklgdyeeAleafekAle 29 
                                    +l+nlG++++++gd+ +A+ +++kAle
  gi|116754249|ref|YP_843367.1| 103 LLNNLGQVHAQKGDLSKAIVYYKKALE 129
                                    689**********************97 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0084
                          TPR_2   4 lynlGlayyklgdyeeAleaf 24 
                                      nl+ ay+++ ++++A+e++
  gi|116754249|ref|YP_843367.1| 144 MGNLASAYRRAYQWDRAVECY 164
                                    569*****************9 PP

  == domain 4  score: 11.5 bits;  conditional E-value: 0.0003
                          TPR_2   7 lGlayyklgdyeeAleafekAleld 31 
                                    lG++y+++g+ e A+ ++ek+l+  
  gi|116754249|ref|YP_843367.1| 187 LGRVYAEMGERELAVLYYEKSLRMF 211
                                    8*********************976 PP

  == domain 5  score: 20.3 bits;  conditional E-value: 4.7e-07
                          TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                    +l +lG++y+++g++++ +++f+++l++ ++
  gi|116754249|ref|YP_843367.1| 223 LLSRLGRVYAEMGRWDDSKRCFDRSLSIFED 253
                                    789***********************99865 PP

  == domain 6  score: 16.9 bits;  conditional E-value: 5.6e-06
                          TPR_2   3 alynlGlayyklgdyeeAleafekAlel 30 
                                    +l nlG+ y+++gd++ A+  +e+Al+l
  gi|116754249|ref|YP_843367.1| 263 VLSNLGRFYLEKGDPDSARVSLERALKL 290
                                    799************************9 PP

  == domain 7  score: -2.5 bits;  conditional E-value: 9.1
                          TPR_2   1 aealynlGlayyklgdyeeAleafek 26 
                                    a a+  l+  y++  + ++  +++  
  gi|116754249|ref|YP_843367.1| 307 AAAYSLLASRYAAERNAKQSSQLYSN 332
                                    67999999999999998888777765 PP

  == domain 8  score: -0.5 bits;  conditional E-value: 2.2
                          TPR_2  18 eeAleafekAle 29 
                                    +eA++++e+A++
  gi|116754249|ref|YP_843367.1| 374 DEAVALCERAIS 385
                                    79********96 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.1e-05     0.018       5      30 ..     104     129 ..     102     132 .. 0.95
   2 !   11.2   0.2   0.00032      0.27       2      24 ..     141     163 ..     140     165 .. 0.91
   3 !   14.1   0.1   3.6e-05     0.031       7      35 ..     186     214 ..     180     217 .. 0.91
   4 !   13.6   0.0   5.6e-05     0.047       3      33 ..     222     252 ..     221     256 .. 0.89
   5 !   14.5   0.0   2.9e-05     0.025       5      34 ..     264     293 ..     263     297 .. 0.92
   6 ?   -1.1   1.3       2.3   1.9e+03       1      21 [.     306     326 ..     306     332 .. 0.75
   7 ?    6.3   0.1     0.011       9.3      17      33 ..     372     388 ..     372     391 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.1e-05
                         TPR_10   5 lnNLanalrqrgrydeAealleeala 30 
                                    lnNL+ ++ q g++ +A  ++++al+
  gi|116754249|ref|YP_843367.1| 104 LNNLGQVHAQKGDLSKAIVYYKKALE 129
                                    8***********************97 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00032
                         TPR_10   2 AsslnNLanalrqrgrydeAeal 24 
                                    A  + NLa a+r+ +++d+A++ 
  gi|116754249|ref|YP_843367.1| 141 AHVMGNLASAYRRAYQWDRAVEC 163
                                    66899***************986 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 3.6e-05
                         TPR_10   7 NLanalrqrgrydeAealleealairrrl 35 
                                     L++++ ++g+++ A+ ++e++l++ ++l
  gi|116754249|ref|YP_843367.1| 186 SLGRVYAEMGERELAVLYYEKSLRMFEQL 214
                                    69**********************98876 PP

  == domain 4  score: 13.6 bits;  conditional E-value: 5.6e-05
                         TPR_10   3 sslnNLanalrqrgrydeAealleealairr 33 
                                      l+ L++++ ++gr+d++ + ++++l+i +
  gi|116754249|ref|YP_843367.1| 222 WLLSRLGRVYAEMGRWDDSKRCFDRSLSIFE 252
                                    56899**********************9865 PP

  == domain 5  score: 14.5 bits;  conditional E-value: 2.9e-05
                         TPR_10   5 lnNLanalrqrgrydeAealleealairrr 34 
                                    l+NL++ + + g+ d A+  le+al + r+
  gi|116754249|ref|YP_843367.1| 264 LSNLGRFYLEKGDPDSARVSLERALKLLRK 293
                                    89************************9766 PP

  == domain 6  score: -1.1 bits;  conditional E-value: 2.3
                         TPR_10   1 tAsslnNLanalrqrgrydeA 21 
                                    +A++++ La ++ + ++ +++
  gi|116754249|ref|YP_843367.1| 306 LAAAYSLLASRYAAERNAKQS 326
                                    5999999**999876666555 PP

  == domain 7  score: 6.3 bits;  conditional E-value: 0.011
                         TPR_10  17 rydeAealleealairr 33 
                                    r+deA+al+e+a+++ +
  gi|116754249|ref|YP_843367.1| 372 RGDEAVALCERAISALE 388
                                    79***********9765 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0028       2.4       6      31 ..      69      94 ..      69      97 .. 0.91
   2 !   20.8   0.1   3.5e-07   0.00029       4      29 ..     104     129 ..     102     129 .. 0.95
   3 ?    0.3   0.1       1.3   1.1e+03       2      24 ..     142     164 ..     141     169 .. 0.72
   4 !   14.5   0.1   3.6e-05     0.031       6      30 ..     186     210 ..     181     213 .. 0.91
   5 ?    6.5   0.0     0.013        11       6      31 ..     226     251 ..     223     258 .. 0.91
   6 !   15.8   0.0   1.4e-05     0.012       5      30 ..     265     290 ..     263     293 .. 0.93
   7 ?   -1.2   0.1       3.9   3.3e+03      18      29 ..     374     385 ..     374     386 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0028
                                   HHHHHHHHTT-HHHHHHHHHHHHHHH CS
                          TPR_8  6 nlgsiylklgdyeeAkeyyekaleld 31
                                   +lg+i++  g  e A+++y kal+ +
  gi|116754249|ref|YP_843367.1| 69 RLGDICRRAGMPEIAMKCYSKALSQA 94
                                   59*********************865 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 3.5e-07
                                    HHHHHHHHHHTT-HHHHHHHHHHHHH CS
                          TPR_8   4 yynlgsiylklgdyeeAkeyyekale 29 
                                    ++nlg+++ ++gd+ +A+ yy+kale
  gi|116754249|ref|YP_843367.1| 104 LNNLGQVHAQKGDLSKAIVYYKKALE 129
                                    79**********************97 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 1.3
                                    CHHHHHHHHHHHTT-HHHHHHHH CS
                          TPR_8   2 eayynlgsiylklgdyeeAkeyy 24 
                                    +++ nl+s+y+   + + A+e+y
  gi|116754249|ref|YP_843367.1| 142 HVMGNLASAYRRAYQWDRAVECY 164
                                    67788899988777777777777 PP

  == domain 4  score: 14.5 bits;  conditional E-value: 3.6e-05
                                    HHHHHHHHTT-HHHHHHHHHHHHHH CS
                          TPR_8   6 nlgsiylklgdyeeAkeyyekalel 30 
                                     lg++y ++g+ e A+ yyek l++
  gi|116754249|ref|YP_843367.1| 186 SLGRVYAEMGERELAVLYYEKSLRM 210
                                    59********************987 PP

  == domain 5  score: 6.5 bits;  conditional E-value: 0.013
                                    HHHHHHHHTT-HHHHHHHHHHHHHHH CS
                          TPR_8   6 nlgsiylklgdyeeAkeyyekaleld 31 
                                    +lg++y ++g+ + +k ++ + l++ 
  gi|116754249|ref|YP_843367.1| 226 RLGRVYAEMGRWDDSKRCFDRSLSIF 251
                                    79*********************985 PP

  == domain 6  score: 15.8 bits;  conditional E-value: 1.4e-05
                                    HHHHHHHHHTT-HHHHHHHHHHHHHH CS
                          TPR_8   5 ynlgsiylklgdyeeAkeyyekalel 30 
                                     nlg+ yl++gd ++A  ++e+al+l
  gi|116754249|ref|YP_843367.1| 265 SNLGRFYLEKGDPDSARVSLERALKL 290
                                    69**********************97 PP

  == domain 7  score: -1.2 bits;  conditional E-value: 3.9
                                    HHHHHHHHHHHH CS
                          TPR_8  18 eeAkeyyekale 29 
                                    +eA++ +e+a++
  gi|116754249|ref|YP_843367.1| 374 DEAVALCERAIS 385
                                    79********98 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00046      0.39       4      31 ..      67      94 ..      66     105 .. 0.85
   2 !    8.9   0.0    0.0034       2.9       7      29 ..     107     129 ..     102     145 .. 0.83
   3 ?    4.2   0.0      0.11        95       7      24 ..     147     164 ..     146     174 .. 0.88
   4 ?    3.7   0.2      0.17   1.5e+02       7      32 ..     187     212 ..     181     224 .. 0.76
   5 !   13.1   0.0   0.00016      0.14       2      33 ..     222     253 ..     219     256 .. 0.92
   6 !   12.7   0.0   0.00021      0.18       7      30 ..     267     290 ..     263     308 .. 0.88
   7 ?    0.8   0.3       1.4   1.2e+03       2      27 ..     308     333 ..     300     344 .. 0.81
   8 ?    3.7   0.1      0.16   1.4e+02      12      30 ..     368     386 ..     357     392 .. 0.84
   9 ?   -1.4   0.1       7.1   6.1e+03      16      27 ..     479     490 ..     474     507 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00046
                         TPR_14  4 llalaeallalGdpdeAiallrralala 31
                                   l++l+++++++G p+ A++++ +al++a
  gi|116754249|ref|YP_843367.1| 67 LKRLGDICRRAGMPEIAMKCYSKALSQA 94
                                   5789**********************76 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0034
                         TPR_14   7 laeallalGdpdeAiallrrala 29 
                                    l++++++ Gd+ +Ai ++++al+
  gi|116754249|ref|YP_843367.1| 107 LGQVHAQKGDLSKAIVYYKKALE 129
                                    89********************9 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.11
                         TPR_14   7 laeallalGdpdeAiall 24 
                                    la+a++++ ++d+A++++
  gi|116754249|ref|YP_843367.1| 147 LASAYRRAYQWDRAVECY 164
                                    89*************988 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.17
                         TPR_14   7 laeallalGdpdeAiallrralalaP 32 
                                    l++++++ G+ + A+ ++++ l+ + 
  gi|116754249|ref|YP_843367.1| 187 LGRVYAEMGERELAVLYYEKSLRMFE 212
                                    89******************999443 PP

  == domain 5  score: 13.1 bits;  conditional E-value: 0.00016
                         TPR_14   2 eallalaeallalGdpdeAiallrralalaPd 33 
                                    ++l +l++++++ G++d++ ++++r l+ + d
  gi|116754249|ref|YP_843367.1| 222 WLLSRLGRVYAEMGRWDDSKRCFDRSLSIFED 253
                                    67899**********************99876 PP

  == domain 6  score: 12.7 bits;  conditional E-value: 0.00021
                         TPR_14   7 laeallalGdpdeAiallrralal 30 
                                    l++++l+ Gdpd A+  l+ral+l
  gi|116754249|ref|YP_843367.1| 267 LGRFYLEKGDPDSARVSLERALKL 290
                                    89********************96 PP

  == domain 7  score: 0.8 bits;  conditional E-value: 1.4
                         TPR_14   2 eallalaeallalGdpdeAiallrra 27 
                                    +a+ +la+ ++a ++ +++ +l+  a
  gi|116754249|ref|YP_843367.1| 308 AAYSLLASRYAAERNAKQSSQLYSNA 333
                                    67888899999999988888888766 PP

  == domain 8  score: 3.7 bits;  conditional E-value: 0.16
                         TPR_14  12 lalGdpdeAiallrralal 30 
                                    +a  + deA+al++ra+++
  gi|116754249|ref|YP_843367.1| 368 RAEPRGDEAVALCERAISA 386
                                    566788**********996 PP

  == domain 9  score: -1.4 bits;  conditional E-value: 7.1
                         TPR_14  16 dpdeAiallrra 27 
                                    ++++A+++lr+ 
  gi|116754249|ref|YP_843367.1| 479 NLKRAAEHLRAS 490
                                    667777777765 PP

>> SNAP  Soluble NSF attachment protein, SNAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.1   0.00046      0.39      86     160 ..      76     146 ..      71     149 .. 0.78
   2 !   18.7   0.0   1.1e-06   0.00091      34     126 ..     140     233 ..     136     240 .. 0.91
   3 !   14.6   0.0     2e-05     0.017      91     172 ..     238     318 ..     233     323 .. 0.93
   4 ?    0.6   1.1      0.36   3.1e+02      42      67 ..     314     339 ..     307     407 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00046
                                    HHT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHH CS
                           SNAP  86 kkvspeeAvealekAieiytekgrfrraAklkkeiaelyekelgdlekAieaYekAaelyeqeeakalankcllk 160
                                    +   pe A+++++kA +    +   +  + l ++++++  ++ gdl+kAi +Y+kA e +e  +  ++a +++ +
  gi|116754249|ref|YP_843367.1|  76 RAGMPEIAMKCYSKALSQ---AQEPHVRSVLLNNLGQVHAQK-GDLSKAIVYYKKALEGFEYAGDPSSAAHVMGN 146
                                    555677888888888664...444555667899********9.****************9988887777776655 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 1.1e-06
                                    HHHHHHHHHHHHHHTT-THHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHT.-HHHHHHHHHHHHHHHHHTT-HHH CS
                           SNAP  34 AadlyeqAAnayklakkweeAgeaflkaAecqeklkekdeaanayveAakcykkv.speeAvealekAieiytekgrfrr 112
                                    Aa +  + A ay+ a +w++A e++ k  +  ekl+++   a++    + +y +  + e Av  +ek+  ++ + g  r 
  gi|116754249|ref|YP_843367.1| 140 AAHVMGNLASAYRRAYQWDRAVECYFKGLKGFEKLNDSFGVAQMTGSLGRVYAEMgERELAVLYYEKSLRMFEQLGDRRS 219
                                    6777777899******************************************99879999******************** PP

                                    HHHHHHHHHHHHHH CS
                           SNAP 113 aAklkkeiaelyek 126
                                    aA l   ++ +y +
  gi|116754249|ref|YP_843367.1| 220 AAWLLSRLGRVYAE 233
                                    *********99985 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 2e-05
                                    HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT- CS
                           SNAP  91 eeAvealekAieiytekgrfrraAklkkeiaelyekelgdlekAieaYekAaelyeqeeakalankcllkvAelsaelek 170
                                    +++ ++++++ +i+ + g+ ++a+    +++  y ++ gd ++A  + e+A +l ++e      n++   +A +s    +
  gi|116754249|ref|YP_843367.1| 238 DDSKRCFDRSLSIFEDLGQSQNAGIVLSNLGRFYLEK-GDPDSARVSLERALKLLRKEMLPVYPNTVAALAAAYSLLASR 316
                                    67889******************************99.*********************999999999999999988888 PP

                                    HH CS
                           SNAP 171 ye 172
                                    y+
  gi|116754249|ref|YP_843367.1| 317 YA 318
                                    85 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.36
                                    HHHHHHTT-THHHHHHHHHHHHHHHH CS
                           SNAP  42 AnayklakkweeAgeaflkaAecqek 67 
                                    A +y  +++ +++++ + +a++c ++
  gi|116754249|ref|YP_843367.1| 314 ASRYAAERNAKQSSQLYSNASDCFSE 339
                                    55555555555555555555555544 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.59   5.1e+02      30      65 ..      69     103 ..      62     107 .. 0.89
   2 !    8.2   0.1    0.0042       3.6       3      47 ..     113     163 ..     111     169 .. 0.83
   3 !   10.4   0.0   0.00083      0.71      11      55 ..     208     251 ..     191     258 .. 0.70
   4 !   12.3   0.0   0.00022      0.19      22      57 ..     257     293 ..     244     306 .. 0.78
   5 ?   -1.8   0.0       5.6   4.8e+03       8      19 ..     374     385 ..     367     409 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.59
                         TPR_19  30 lLAeallalgqldeAealLdalpeedpddaryasLl 65 
                                    +L +++  +g ++ A+++ ++++ +++  + ++s+l
  gi|116754249|ref|YP_843367.1|  69 RLGDICRRAGMPEIAMKCYSKALSQAQE-PHVRSVL 103
                                    48999999*******************9.9999875 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0042
                         TPR_19   3 aegdyaeAlalleqalqe.....dpk.naearllLAeallalgqldeAeal 47 
                                    + gd+  A+ ++++al+      dp   a +  +LA a+  + q+d A ++
  gi|116754249|ref|YP_843367.1| 113 QKGDLSKAIVYYKKALEGfeyagDPSsAAHVMGNLASAYRRAYQWDRAVEC 163
                                    679*************776655577656666669**************986 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00083
                         TPR_19  11 lalleqalqedpknaearllLAeallalgqldeAealLdalpeed 55 
                                    l+++eq l +    a+++ +L +++ ++g++d+ +++ d+ +  +
  gi|116754249|ref|YP_843367.1| 208 LRMFEQ-LGDRRSAAWLLSRLGRVYAEMGRWDDSKRCFDRSLSIF 251
                                    444555.2333335555669******************9987655 PP

  == domain 4  score: 12.3 bits;  conditional E-value: 0.00022
                         TPR_19  22 pknaearl.lLAeallalgqldeAealLdalpeedpd 57 
                                     +na + l +L + +l+ g++d A+  L+++++  ++
  gi|116754249|ref|YP_843367.1| 257 SQNAGIVLsNLGRFYLEKGDPDSARVSLERALKLLRK 293
                                    3566666669********************9987765 PP

  == domain 5  score: -1.8 bits;  conditional E-value: 5.6
                         TPR_19   8 aeAlalleqalq 19 
                                    +eA+al e+a++
  gi|116754249|ref|YP_843367.1| 374 DEAVALCERAIS 385
                                    677777777654 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0016       1.4      63     151 ..      84     170 ..      69     182 .. 0.71
   2 !   23.7   0.1   3.3e-08   2.8e-05      43     189 ..     184     335 ..     175     359 .. 0.51

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0016
                       TPR_MalT  63 lqeaeklarqadslhvallallqqaeilvaqGrLheAletyeqalqlateqglqqlplvgfllvlladllyEwndLeeAe 142
                                    ++  +k++ qa+ +hv  + l  +++++ ++G+L +A+  y++al+  + +g +      +++  la  ++   + ++A 
  gi|116754249|ref|YP_843367.1|  84 MKCYSKALSQAQEPHVRSVLLNNLGQVHAQKGDLSKAIVYYKKALEGFEYAGDPSSA--AHVMGNLASAYRRAYQWDRAV 161
                                    444556677888888888888888888888888888888888888877777766433..333356677777777777777 PP

                       TPR_MalT 143 qhlqeGiel 151
                                    ++  +G++ 
  gi|116754249|ref|YP_843367.1| 162 ECYFKGLKG 170
                                    776666665 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 3.3e-08
                       TPR_MalT  43 tavlGeasllqGdleaAlqalqeaeklarqadslhvallallqqaeilvaqGrLheAletyeqalqlateqglqqlplvg 122
                                    t +lG+++   G++e A+  +++  ++  q +  + a++ l +++ ++ + Gr +++ + + ++l   ++ g++q   +g
  gi|116754249|ref|YP_843367.1| 184 TGSLGRVYAEMGERELAVLYYEKSLRMFEQLGDRRSAAWLLSRLGRVYAEMGRWDDSKRCFDRSLSIFEDLGQSQ--NAG 261
                                    455555555555555555555555555555555555555555555555555555555555555555555444443..555 PP

                       TPR_MalT 123 fllvlladllyEwndLeeAeqhlqeGielleql......ep.eaaldayvllarialaqGdleeAetllekaee 189
                                    ++l  l++ ++E++d + A+  l+++++ll++       ++ +a ++ay lla  ++a  +++++ +l  +a  
  gi|116754249|ref|YP_843367.1| 262 IVLSNLGRFYLEKGDPDSARVSLERALKLLRKEmlpvypNTvAALAAAYSLLASRYAAERNAKQSSQLYSNASD 335
                                    55555555555555555555555555555555222222111112223555555555555555555555444443 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0       0.7     6e+02       5      28 ..      69      92 ..      69      94 .. 0.86
   2 ?    5.3   0.0      0.04        35       5      28 ..     106     129 ..     106     131 .. 0.89
   3 ?    5.6   0.1     0.033        28       5      23 ..     146     164 ..     146     166 .. 0.89
   4 ?    3.6   0.1      0.14   1.2e+02       6      25 ..     187     206 ..     186     214 .. 0.92
   5 !    7.8   0.0    0.0065       5.6       5      25 ..     226     246 ..     224     253 .. 0.89
   6 ?    6.3   0.0      0.02        17       5      28 ..     266     289 ..     263     290 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.7
                                   HHHHHHHHHHHHHHHHHHHHHHHH CS
                          TPR_6  5 klalsyrklgdtdkAlealerlik 28
                                   +l+   r++g ++ A++ + + ++
  gi|116754249|ref|YP_843367.1| 69 RLGDICRRAGMPEIAMKCYSKALS 92
                                   6888888988*********99876 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.04
                                    HHHHHHHHHHHHHHHHHHHHHHHH CS
                          TPR_6   5 klalsyrklgdtdkAlealerlik 28 
                                    +l++ + + gd +kA+ ++++ ++
  gi|116754249|ref|YP_843367.1| 106 NLGQVHAQKGDLSKAIVYYKKALE 129
                                    5899999988**********9886 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.033
                                    HHHHHHHHHHHHHHHHHHH CS
                          TPR_6   5 klalsyrklgdtdkAleal 23 
                                    +la +yr++ ++d+A+e +
  gi|116754249|ref|YP_843367.1| 146 NLASAYRRAYQWDRAVECY 164
                                    5899****88*******87 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.14
                                    HHHHHHHHHHHHHHHHHHHH CS
                          TPR_6   6 lalsyrklgdtdkAlealer 25 
                                    l++ y ++g+ + A+ ++e+
  gi|116754249|ref|YP_843367.1| 187 LGRVYAEMGERELAVLYYEK 206
                                    79****************98 PP

  == domain 5  score: 7.8 bits;  conditional E-value: 0.0065
                                    HHHHHHHHHHHHHHHHHHHHH CS
                          TPR_6   5 klalsyrklgdtdkAlealer 25 
                                    +l++ y ++g++d++++ ++r
  gi|116754249|ref|YP_843367.1| 226 RLGRVYAEMGRWDDSKRCFDR 246
                                    89****************998 PP

  == domain 6  score: 6.3 bits;  conditional E-value: 0.02
                                    HHHHHHHHHHHHHHHHHHHHHHHH CS
                          TPR_6   5 klalsyrklgdtdkAlealerlik 28 
                                    +l++ y++ gd+d A+  ler +k
  gi|116754249|ref|YP_843367.1| 266 NLGRFYLEKGDPDSARVSLERALK 289
                                    79******99***********987 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0083       7.1      13      33 ..     101     121 ..      86     121 .. 0.78
   2 !    9.0   0.1    0.0022       1.9       1      34 []     123     162 ..     123     162 .. 0.88
   3 ?    1.3   0.0      0.65   5.6e+02      13      31 ..     221     239 ..     203     242 .. 0.77
   4 !    7.8   0.0    0.0055       4.7      14      33 ..     262     281 ..     250     282 .. 0.90
   5 ?   -2.2   0.0       8.8   7.5e+03      14      30 ..     493     509 ..     481     510 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0083
                         TPR_17  13 adaynnLAelllknGdlmtAr 33 
                                    ++++nnL+++++++Gdl +A+
  gi|116754249|ref|YP_843367.1| 101 SVLLNNLGQVHAQKGDLSKAI 121
                                    789*************99885 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0022
                         TPR_17   1 lylkalel.....dPnn.adaynnLAelllknGdlmtArq 34 
                                    +y+kale      dP++ a ++ nLA +++++ ++++A++
  gi|116754249|ref|YP_843367.1| 123 YYKKALEGfeyagDPSSaAHVMGNLASAYRRAYQWDRAVE 162
                                    588999997766679999*******************975 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.65
                         TPR_17  13 adaynnLAelllknGdlmt 31 
                                    a+++  L++++++ G++++
  gi|116754249|ref|YP_843367.1| 221 AWLLSRLGRVYAEMGRWDD 239
                                    7888899*****9999886 PP

  == domain 4  score: 7.8 bits;  conditional E-value: 0.0055
                         TPR_17  14 daynnLAelllknGdlmtAr 33 
                                     ++ nL++++l++Gd++ Ar
  gi|116754249|ref|YP_843367.1| 262 IVLSNLGRFYLEKGDPDSAR 281
                                    6889*************997 PP

  == domain 5  score: -2.2 bits;  conditional E-value: 8.8
                         TPR_17  14 daynnLAelllknGdlm 30 
                                    +++   Ae+l+++G+++
  gi|116754249|ref|YP_843367.1| 493 ESFEKIAETLEMAGRSE 509
                                    56667899999999875 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.6e-05     0.014       8      62 ..      75     131 ..      69     140 .. 0.84
   2 ?    0.0   0.4       1.6   1.4e+03      30      53 ..     137     160 ..     130     164 .. 0.46
   3 ?    3.6   0.8      0.13   1.1e+02       3      63 ..     147     210 ..     146     213 .. 0.75
   4 ?    4.7   0.2     0.055        47       3      41 ..     187     225 ..     186     227 .. 0.88
   5 !   15.9   0.0   1.8e-05     0.016       3      61 ..     227     288 ..     225     294 .. 0.88
   6 ?   -1.4   0.3       4.4   3.8e+03      46      61 ..     369     384 ..     351     390 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.6e-05
                         TPR_16   8 lragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraal..r 62 
                                    +rag ++ A + +  al ++ ++ ++   l++lg++++++g+l +A+ +y++al   
  gi|116754249|ref|YP_843367.1|  75 RRAGMPEIAMKCYSKALSQAQEPHVRSVLLNNLGQVHAQKGDLSKAIVYYKKALegF 131
                                    678889999999999999998888899999***********************9443 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.6
                         TPR_16  30 sPdaaeAllllgdaalrqgrlaeA 53 
                                    ++ aa+ + +l+ a+ r+  +++A
  gi|116754249|ref|YP_843367.1| 137 PSSAAHVMGNLASAYRRAYQWDRA 160
                                    334444444444444444333333 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.13
                         TPR_16   3 laraalragdyddAaaaleaalkrdpssPd...aaeAllllgdaalrqgrlaeAaalyraalra 63 
                                    la a++ra ++d+A++ +   lk + +  d    a++   lg+++++ g+ ++A+ +y++ lr 
  gi|116754249|ref|YP_843367.1| 147 LASAYRRAYQWDRAVECYFKGLKGFEKLNDsfgVAQMTGSLGRVYAEMGERELAVLYYEKSLRM 210
                                    6777777777777777777777777544447778888899999999999999999999887765 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.055
                         TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllg 41 
                                    l+r +++ g+ + A+ ++e  l+++    d++ A++ll 
  gi|116754249|ref|YP_843367.1| 187 LGRVYAEMGERELAVLYYEKSLRMFEQLGDRRSAAWLLS 225
                                    7999*********************88888888888875 PP

  == domain 5  score: 15.9 bits;  conditional E-value: 1.8e-05
                         TPR_16   3 laraalragdyddAaaaleaalkrdpssPd...aaeAllllgdaalrqgrlaeAaalyraal 61 
                                    l+r +++ g++dd  + +++ l  + +  +   a   l +lg+ +l++g+ + A+  +++al
  gi|116754249|ref|YP_843367.1| 227 LGRVYAEMGRWDDSKRCFDRSLSIFEDLGQsqnAGIVLSNLGRFYLEKGDPDSARVSLERAL 288
                                    89***********************55555*************************6666655 PP

  == domain 6  score: -1.4 bits;  conditional E-value: 4.4
                         TPR_16  46 rqgrlaeAaalyraal 61 
                                    + +r +eA+al+++a+
  gi|116754249|ref|YP_843367.1| 369 AEPRGDEAVALCERAI 384
                                    4578899999999987 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.13   1.1e+02       1      22 [.      71      92 ..      71      95 .. 0.86
   2 !   11.9   0.2   0.00016      0.13       1      22 [.     108     129 ..     108     129 .. 0.95
   3 ?   -0.2   0.1      0.94     8e+02       4      21 ..     151     168 ..     148     169 .. 0.74
   4 ?    0.4   0.1      0.62   5.3e+02       1      21 [.     188     208 ..     188     213 .. 0.89
   5 ?    1.3   0.0      0.33   2.9e+02      28      42 .]     221     235 ..     214     250 .. 0.72
   6 ?    3.4   0.0     0.073        62       1      23 [.     268     290 ..     268     293 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.13
                         TPR_11  1 GdayyeqGkyeeAieaYkkAlk 22
                                   Gd+++  G  e A+++Y+kAl 
  gi|116754249|ref|YP_843367.1| 71 GDICRRAGMPEIAMKCYSKALS 92
                                   788888888889********96 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00016
                         TPR_11   1 GdayyeqGkyeeAieaYkkAlk 22 
                                    G++  ++G++ +Ai  YkkAl+
  gi|116754249|ref|YP_843367.1| 108 GQVHAQKGDLSKAIVYYKKALE 129
                                    88999***************97 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.94
                         TPR_11   4 yyeqGkyeeAieaYkkAl 21 
                                    y+   +++ A+e+Y k l
  gi|116754249|ref|YP_843367.1| 151 YRRAYQWDRAVECYFKGL 168
                                    5555699*******7665 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 0.62
                         TPR_11   1 GdayyeqGkyeeAieaYkkAl 21 
                                    G++y e G+ e A+  Y+k l
  gi|116754249|ref|YP_843367.1| 188 GRVYAEMGERELAVLYYEKSL 208
                                    899******999999999876 PP

  == domain 5  score: 1.3 bits;  conditional E-value: 0.33
                         TPR_11  28 aeayynLGlayykqG 42 
                                    a++++ LG +y+++G
  gi|116754249|ref|YP_843367.1| 221 AWLLSRLGRVYAEMG 235
                                    566666666666665 PP

  == domain 6  score: 3.4 bits;  conditional E-value: 0.073
                         TPR_11   1 GdayyeqGkyeeAieaYkkAlkl 23 
                                    G+ y e+G+ + A  ++++Alkl
  gi|116754249|ref|YP_843367.1| 268 GRFYLEKGDPDSARVSLERALKL 290
                                    66799****************98 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 !   10.6   0.1   0.00036      0.31     165     213 ..     116     164 ..      75     166 .. 0.83
   2 !    7.6   0.0     0.003       2.6     167     215 ..     198     246 ..     182     255 .. 0.88
   3 ?   -0.6   0.2      0.97   8.3e+02     101     192 ..     307     406 ..     290     423 .. 0.62
   4 ?   -1.4   0.1       1.6   1.4e+03     185     218 ..     471     504 ..     455     510 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00036
                    Foie-gras_1 165 hskliidlLekaleeFskrkqtRlaeelsleiAeeylrlgdwkkalell 213
                                    + +++i  ++kale F++ + +  a++++ ++A +y r+ +w+ a+e +
  gi|116754249|ref|YP_843367.1| 116 DLSKAIVYYKKALEGFEYAGDPSSAAHVMGNLASAYRRAYQWDRAVECY 164
                                    44566779*************************************9975 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.003
                    Foie-gras_1 167 kliidlLekaleeFskrkqtRlaeelsleiAeeylrlgdwkkalellqp 215
                                    +l++  +ek+l  F++ + +R a+ l  ++++ y ++g+w+++++ ++ 
  gi|116754249|ref|YP_843367.1| 198 ELAVLYYEKSLRMFEQLGDRRSAAWLLSRLGRVYAEMGRWDDSKRCFDR 246
                                    56666899***********************************998875 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.97
                    Foie-gras_1 101 agyyyqlaakhakerrelaeqiandpeqspassiassayvydty............lapepheeyplsgseekgvahskl 168
                                    a+ y+ la+++a er++  ++ +     s+as   s++ +   +            +++++  + +++ +  + va  + 
  gi|116754249|ref|YP_843367.1| 307 AAAYSLLASRYAAERNAKQSSQL----YSNASDCFSELALHPRIliselkaaagqaRSLSYLVKLRAEPRGDEAVALCER 382
                                    45566666666666554443332....23333333333333333344444444445555555555555555678888888 PP

                    Foie-gras_1 169 iidlLekaleeFskrkqtRlaeel 192
                                    +i +Le+ +++ ++++ +++a+ +
  gi|116754249|ref|YP_843367.1| 383 AISALESTIASTTSKDREKVASLV 406
                                    888888888888888888877766 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 1.6
                    Foie-gras_1 185 qtRlaeelsleiAeeylrlgdwkkalellqpltl 218
                                     +R +++  l+ A e+lr+ + ++  ++ ++l++
  gi|116754249|ref|YP_843367.1| 471 RQRRDSSANLKRAAEHLRASQTESFEKIAETLEM 504
                                    4788889999999999998775544444444433 PP

>> RPN7  26S proteasome subunit RPN7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.028        24      39      64 ..     104     129 ..      66     136 .. 0.87
   2 ?    5.5   0.0     0.015        13      22      69 ..     167     214 ..     152     341 .. 0.70
   3 ?   -2.4   0.1         4   3.4e+03      51      70 ..     379     398 ..     376     408 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.028
                                    HHHHHHHHHHCT-HHHHHHHHHTCCC CS
                           RPN7  39 kldlaehYlkigdleeAlkaysrire 64 
                                     ++l++ +++ gdl++A+ +y++++e
  gi|116754249|ref|YP_843367.1| 104 LNNLGQVHAQKGDLSKAIVYYKKALE 129
                                    57899999999999999999999876 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.015
                                    HHHHHHHTT-HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTCCCC--SH CS
                           RPN7  22 elkdakenlgkeeirrakldlaehYlkigdleeAlkaysrireyctsl 69 
                                     lk+ ++   +  +++    l++ Y+++g++e A+ +y++ +    +l
  gi|116754249|ref|YP_843367.1| 167 GLKGFEKLNDSFGVAQMTGSLGRVYAEMGERELAVLYYEKSLRMFEQL 214
                                    555556666666677777778888888888888888887755544444 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 4
                                    -HHHHHHHHHTCCCC--SHH CS
                           RPN7  51 dleeAlkaysrireyctslk 70 
                                     +e A+ a++ ++  +ts +
  gi|116754249|ref|YP_843367.1| 379 LCERAISALESTIASTTSKD 398
                                    69999999999999999875 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0       1.7   1.5e+03       4      17 ..     104     117 ..     101     120 .. 0.82
   2 ?    0.4   0.0       1.7   1.4e+03       6      20 ..     186     200 ..     184     201 .. 0.87
   3 ?    7.9   0.0    0.0068       5.8       1      25 [.     221     245 ..     221     246 .. 0.87
   4 ?    9.2   0.0    0.0025       2.1       4      26 .]     264     286 ..     262     286 .. 0.93
   5 ?   -1.4   0.2       6.4   5.5e+03      16      26 .]     372     382 ..     372     382 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.7
                          TPR_4   4 llaLArallalGdl 17 
                                    l +L++++++ Gdl
  gi|116754249|ref|YP_843367.1| 104 LNNLGQVHAQKGDL 117
                                    669*******9997 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.7
                          TPR_4   6 aLArallalGdldeA 20 
                                     L+r++++ G+ + A
  gi|116754249|ref|YP_843367.1| 186 SLGRVYAEMGERELA 200
                                    59*********9977 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0068
                          TPR_4   1 arallaLArallalGdldeAralle 25 
                                    a++l+ L+r++++ G++d+  + ++
  gi|116754249|ref|YP_843367.1| 221 AWLLSRLGRVYAEMGRWDDSKRCFD 245
                                    7999**************9877766 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.0025
                          TPR_4   4 llaLArallalGdldeAraller 26 
                                    l++L+r +l+ Gd+d Ar  ler
  gi|116754249|ref|YP_843367.1| 264 LSNLGRFYLEKGDPDSARVSLER 286
                                    89****************99997 PP

  == domain 5  score: -1.4 bits;  conditional E-value: 6.4
                          TPR_4  16 dldeAraller 26 
                                    + deA al er
  gi|116754249|ref|YP_843367.1| 372 RGDEAVALCER 382
                                    679*****997 PP

>> Coat_F  Coat F domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0003      0.26      18      52 ..      85     119 ..      83     123 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0003
                         Coat_F  18 rnyataitEasnpelRqtlkqilneeiemqeelfn 52 
                                    ++y+ a+ +a+ p++R++l + l + +++  +l++
  gi|116754249|ref|YP_843367.1|  85 KCYSKALSQAQEPHVRSVLLNNLGQVHAQKGDLSK 119
                                    79*************************99998886 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.027        23     152     183 ..      70     102 ..      62     109 .. 0.81
   2 ?    5.4   0.1     0.016        13     134     176 ..      89     131 ..      82     144 .. 0.81
   3 ?   -1.1   0.0       1.5   1.3e+03     146     177 ..     181     212 ..     164     223 .. 0.80
   4 ?    2.6   0.0      0.11        98     130     178 ..     245     293 ..     205     303 .. 0.73
   5 ?   -0.4   0.2      0.96   8.2e+02      16      48 ..     303     335 ..     297     405 .. 0.73
   6 ?   -3.7   0.2       9.4     8e+03      42      59 ..     479     496 ..     469     505 .. 0.43

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.027
                         TPR_21 152 rGDilvaqgkldeAraaYqaAlaaleeka.rel 183
                                     GDi  + g  + A + Y++Al++ +e + r++
  gi|116754249|ref|YP_843367.1|  70 LGDICRRAGMPEIAMKCYSKALSQAQEPHvRSV 102
                                    4**********************9999864444 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.016
                         TPR_21 134 ktLeakkeeafaalvaelrGDilvaqgkldeAraaYqaAlaal 176
                                    k+L++++e   ++   +  G +++++g+l +A   Y++Al+  
  gi|116754249|ref|YP_843367.1|  89 KALSQAQEPHVRSVLLNNLGQVHAQKGDLSKAIVYYKKALEGF 131
                                    456666677777777788899******************9875 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.5
                         TPR_21 146 alvaelrGDilvaqgkldeAraaYqaAlaale 177
                                    a++    G +++++g+++ A   Y+++l+  e
  gi|116754249|ref|YP_843367.1| 181 AQMTGSLGRVYAEMGERELAVLYYEKSLRMFE 212
                                    677788899************99999998665 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.11
                         TPR_21 130 deAlktLeakkeeafaalvaelrGDilvaqgkldeAraaYqaAlaalee 178
                                    d+ l+  e+  +++ a+ v    G  ++++g+ d Ar   ++Al+ l +
  gi|116754249|ref|YP_843367.1| 245 DRSLSIFEDLGQSQNAGIVLSNLGRFYLEKGDPDSARVSLERALKLLRK 293
                                    4455555666666667777777899999999999999999999987766 PP

  == domain 5  score: -0.4 bits;  conditional E-value: 0.96
                         TPR_21  16 vlalvglaGwqgwqdyqeeqaeeAsalYqqlqe 48 
                                    v+al++ +   + ++  e++a++ s+lY++  +
  gi|116754249|ref|YP_843367.1| 303 VAALAAAYSLLASRYAAERNAKQSSQLYSNASD 335
                                    666777777777778888888999999988765 PP

  == domain 6  score: -3.7 bits;  conditional E-value: 9.4
                         TPR_21  42 lYqqlqeaveakdaakak 59 
                                      +   e+++a+++++++
  gi|116754249|ref|YP_843367.1| 479 NLKRAAEHLRASQTESFE 496
                                    222223333333333333 PP

>> APP_E2  E2 domain of amyloid precursor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.021        18     114     159 ..      83     129 ..      79     153 .. 0.84
   2 ?    4.0   0.4     0.041        35      62      91 ..     480     509 ..     468     513 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.021
                         APP_E2 114 alekylqal.qeeppnaerilkaLkkllraeqkdrvhtlrhykhllk 159
                                    a+++y +al q+++p+ +++l      ++a++ d + ++ +yk++l+
  gi|116754249|ref|YP_843367.1|  83 AMKCYSKALsQAQEPHVRSVLLNNLGQVHAQKGDLSKAIVYYKKALE 129
                                    9********889999999998777777999************99876 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.041
                         APP_E2  62 dpkaaeklkkevtarFqetvealEeeaaae 91 
                                     ++aae+l++  t+ F+++ e+lE  + +e
  gi|116754249|ref|YP_843367.1| 480 LKRAAEHLRASQTESFEKIAETLEMAGRSE 509
                                    45799*******************987766 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 ?   -2.5   0.0       6.5   5.5e+03      21      31 ..      81      91 ..      77      93 .. 0.81
   2 ?    7.0   0.5    0.0069       5.9      16      37 ..     113     134 ..     106     154 .. 0.85
   3 ?    2.2   0.0      0.22   1.9e+02       4      36 ..     141     173 ..     138     177 .. 0.82
   4 ?    0.2   0.1      0.94     8e+02      18      37 ..     195     214 ..     190     221 .. 0.83
   5 ?    1.5   0.3      0.37   3.1e+02      11      37 ..     314     340 ..     306     352 .. 0.84
   6 ?   -0.8   0.0         2   1.7e+03      21      51 ..     374     404 ..     372     409 .. 0.79
   7 ?   -2.3   0.0       5.7   4.8e+03      30      40 ..     435     445 ..     433     450 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 6.5
                            MIT 21 eeAlelYkeal 31
                                   e A+++Y++al
  gi|116754249|ref|YP_843367.1| 81 EIAMKCYSKAL 91
                                   56999***998 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0069
                            MIT  16 nagnyeeAlelYkealelLlqa 37 
                                    ++g+ ++A+ +Yk+ale +  a
  gi|116754249|ref|YP_843367.1| 113 QKGDLSKAIVYYKKALEGFEYA 134
                                    899**************99766 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.22
                            MIT   4 AlelvkkAveeDnagnyeeAlelYkealelLlq 36 
                                    A+ + + A  + +a +++ A+e+Y ++l+ + +
  gi|116754249|ref|YP_843367.1| 141 AHVMGNLASAYRRAYQWDRAVECYFKGLKGFEK 173
                                    6666777888889999***********998876 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 0.94
                            MIT  18 gnyeeAlelYkealelLlqa 37 
                                    g+ e A+ +Y+++l+ + q+
  gi|116754249|ref|YP_843367.1| 195 GERELAVLYYEKSLRMFEQL 214
                                    677899**********9986 PP

  == domain 5  score: 1.5 bits;  conditional E-value: 0.37
                            MIT  11 AveeDnagnyeeAlelYkealelLlqa 37 
                                    A  +  + n +   +lY++a + ++++
  gi|116754249|ref|YP_843367.1| 314 ASRYAAERNAKQSSQLYSNASDCFSEL 340
                                    66777889999999*********9875 PP

  == domain 6  score: -0.8 bits;  conditional E-value: 2
                            MIT  21 eeAlelYkealelLlqalkekneerrellre 51 
                                    +eA+ l + a+  L   ++ +++++re++ +
  gi|116754249|ref|YP_843367.1| 374 DEAVALCERAISALESTIASTTSKDREKVAS 404
                                    5888888999999999999877788888765 PP

  == domain 7  score: -2.3 bits;  conditional E-value: 5.7
                            MIT  30 alelLlqalke 40 
                                    a+e+L+ +++e
  gi|116754249|ref|YP_843367.1| 435 ACEYLMGGIRE 445
                                    99****99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (714 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.68u 0.27s 00:00:00.95 Elapsed: 00:00:00.44
# Mc/sec: 4882.23
//
Query:       gi|116754250|ref|YP_843368.1|  [L=417]
Description: UbiD family decarboxylase [Methanosaeta thermophila PT]
Scores for complete 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-96  322.7   1.7    3.5e-96  322.5   1.7    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 !  322.5   1.7    2e-100   3.5e-96       1     406 []       7     380 ..       7     380 .. 0.93

  Alignments for each domain:
  == domain 1  score: 322.5 bits;  conditional E-value: 2e-100
                                    HHHCCCTTSEEEEESEB-TBTHHHHHHHHHHHHT--EEEEEEBTTB.TT-EEEE-TTS-HCHHHHHHTS-GHHHHHHHHH CS
                           UbiD   1 lealekagelvrikeevdpelEiaeiarrvleeggpallFenvkgkgskfpvltnlfgtrervalalglssleeilekla 80 
                                    le+l+++g l +++e v++e+E+a  a          +lF+n +    +  + +n++g+re +a+al ++  +++++ l+
  gi|116754250|ref|YP_843368.1|   7 LEDLRADGVLEETHEHVSTEYELAMRATGR-----GPMLFHNAD----GHVCCINILGSRELLARALRMD-ARNLARDLS 76 
                                    689*******************98655554.....499*****4....35899**************975.599****98 PP

                                    HHHHS..----EE--GCG-GGGSEEECCCCC--HHHS---BSSTTSSS-EEECEEEEEE-TTTT-EEEEEEEEEEEETTE CS
                           UbiD  81 ellepkppippkvvesekapcqeevvlegddvdLskLPvltlwpgDgGpyitlglvitrdpetgkrnlgiyRmqvldknk 160
                                    ++         ++v+s   ++qe++ le   +dL +LPvl++++gDgG+yit+g+v++r   +++ n+ ++R++vld+n+
  gi|116754250|ref|YP_843368.1|  77 AVGFD---GHVREVDS--SQFQENI-LE---PDLMRLPVLRHFRGDGGRYITSGIVVSRL--DDRINACVHRLMVLDRNR 145
                                    88665...67899966..679*888.45...9**************************96..4689************** PP

                                    EEE--TTTHCHHHHHHHHHHCCT--EEEEEEES--HHHHHHCTS--TTT-TCHHHHHHHHTS--EEEE-SSSSSEEETT- CS
                           UbiD 161 lglhwqihkggaehlrkakkkggeplpvavaiGvdPaltlaAvaplPeglsElefaGalrgepvelvkcetvdlevpadA 240
                                    l+ +++++++ ++ + +a + g ++lpva+aiGvdP++++aA++++P + +E+e+a+alrg  ve+v+ e ++++vp +A
  gi|116754250|ref|YP_843368.1| 146 LAARLVPGRHTHQMYSRAIETG-RRLPVAIAIGVDPVVLIAASTRVP-ENKEFEYASALRGDVVEVVTLE-NGVPVP-HA 221
                                    *************9********.8***********************.779****************995.59****.** PP

                                    SEEEEEEEECCEEEECTTTC-TTSCEEC--CCEEEEEEEEEEE-TT-EEEE-SSSCCSHHHHCHHHHHHHHHHHHHHCCS CS
                           UbiD 241 EivleGeidpgetapEGPfgdhtGyysevrdefpvfkVtaithRkdpiypttvvgkppeedallgkalealflpllkkqv 320
                                    EivleG+++ + +apEGPf+d+tG+++ vr+e pv+++t+i++R+d+iy+++++    e+ +l+g+++e+l+++  +k v
  gi|116754250|ref|YP_843368.1| 222 EIVLEGYLTEK-RAPEGPFVDITGTMDIVREE-PVIEITRIMMRDDAIYHALLPAGG-EHRMLMGVPYEPLIYREASKVV 298
                                    *********96.7*************999996.*****************9988888.******************8866 PP

                                    TTEEEEEE-GGGTTTCEEEEECHHHTCCHHHHHHHHHHCCTTGGC-SEEEEEEETTS-TTSHHHHHHHHHHC--CCCCEE CS
                           UbiD 321 pevkdvhlpeeggfhllavvsikkrypghakkvmealwalkqqlsltKlvivvDedvdvrdlkevlwaiatrvdpdrDlv 400
                                     +v++v l+e g+ +++avv+i+k+ +++  k+++a++a++   sl K+v+vvD d+d++d++e+++aiatrv+ d+D++
  gi|116754250|ref|YP_843368.1| 299 -RVRNVLLTEGGCTYFHAVVQIEKQEEEDGLKAIQAAMAAHG--SL-KHVLVVDTDIDIHDPRELEYAIATRVRGDQDIY 374
                                    .5**************************************99..99.********************************* PP

                                    EECCCE CS
                           UbiD 401 iiegtr 406
                                    +++++r
  gi|116754250|ref|YP_843368.1| 375 MYPNVR 380
                                    **9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 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:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2894.67
//
Query:       gi|116754251|ref|YP_843369.1|  [L=185]
Description: beta-lactamase domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-16   60.6   3.3    3.5e-12   46.8   0.9    2.1  2  Lactamase_B    Metallo-beta-lactamase superfamily
     0.0058   15.8   0.1     0.0084   15.3   0.1    1.2  1  Lar_N          Lactate racemase N-terminal domain
  ------ inclusion threshold ------
      0.016   14.7   0.1      0.021   14.3   0.1    1.3  1  Lactamase_B_2  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.9   5.8e-16   3.5e-12       6      67 ..      24      84 ..      21     102 .. 0.91
   2 !   14.5   0.1   4.5e-06     0.027     125     186 ..     105     160 ..      95     170 .. 0.78

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 5.8e-16
                                   SEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTH CS
                    Lactamase_B  6 vnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglvea 67
                                   ++++li   ++ +++DtG+  e++r ++ l+++g+  +d++ v++THlH+DH+G ++ +++a
  gi|116754251|ref|YP_843369.1| 24 SSVTLI-ISDRILVVDTGSADERERVFDGLKRAGVSTDDIEIVVNTHLHVDHTGCNDIFRNA 84
                                   678888.899***********************************************99987 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 4.5e-06
                                    HECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC.TTCEEE-SHCHHHHHHHHHHHHH CS
                    Lactamase_B 125 vtggpghghghgvveygggkvlftGDallagetgridltlrgaevrdpsdaekyldsllkla 186
                                     + +pgh+ ++++v +  ++v+++GDal+++++   dl     ++r ++d + +++s+ ++a
  gi|116754251|ref|YP_843369.1| 105 LMETPGHTLDSISVLCS-ENVVIAGDALPTADNYIKDL-----PPRIHVDRALAMRSMHRIA 160
                                    67899999999999996.6899****************.....7777777777776666655 PP

>> Lar_N  Lactate racemase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   1.4e-06    0.0084      50     104 ..      19      75 ..      11      83 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.4e-06
                          Lar_N  50 lvkekekvvivvsDiTRp..tpskiilpllleelkeagvkdeditilvAtGlHrkqt 104
                                    ++ ++++v++++sD      t s+   + +++ lk+agv+ +di+i+v t lH ++t
  gi|116754251|ref|YP_843369.1|  19 ILYASSSVTLIISDRILVvdTGSADERERVFDGLKRAGVSTDDIEIVVNTHLHVDHT 75 
                                    6667899*******98883456688899*************************9887 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 ?   14.3   0.1   3.5e-06     0.021      26      52 ..      57      82 ..      33     131 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.5e-06
                                   --..SEEEEE-SS--HHHHGGGGCCCC CS
                  Lactamase_B_2 26 delppidaVllthaHyDHlaglltlre 52
                                    + ++i+ V+ th H+DH+ g  ++ +
  gi|116754251|ref|YP_843369.1| 57 VSTDDIEIVVNTHLHVDHT-GCNDIFR 82
                                   33469**************.7777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1317.28
//
Query:       gi|116754252|ref|YP_843370.1|  [L=135]
Description: nucleic acid binding, OB-fold, tRNA/helicase-type [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-06   26.6   0.0    6.4e-06   26.1   0.0    1.3  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
    0.00048   20.3   0.0    0.00078   19.6   0.0    1.3  1  tRNA_anti_2      OB-fold nucleic acid binding domain


Domain annotation for each model (and alignments):
>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   7.1e-10   6.4e-06       1      70 [.      60     126 ..      60     132 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 7.1e-10
                                    EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEE CS
                tRNA_anti-codon   1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrrpggelelkv 70 
                                    V++ G+++si+++ +g+++ i+l+  +  +q++l +  a+++  +l  Gd+v+v+G ++++ g+  e+ v
  gi|116754252|ref|YP_843370.1|  60 VSLSGKIVSIRETRTGGHLIITLD--STPMQIFLPSRVAKEVRGSLSAGDHVQVRGHLTEYMGR-SEIEV 126
                                    899*******87777888888885..99*********************************999.55554 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 !   19.6   0.0   8.8e-08   0.00078      21      88 ..      59     125 ..      44     129 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 8.8e-08
                    tRNA_anti_2  21 avwvrGeisnlkr.kasghvYftLkDekakisavifrsraaklkftledGmkVlvkgrlsvYeprGsyq 88 
                                    +v + G i ++++ ++ gh+ +tL   +  +++ + ++ a++++ +l+ G++V v+g+l+ Y  r++++
  gi|116754252|ref|YP_843370.1|  59 DVSLSGKIVSIREtRTGGHLIITLD--STPMQIFLPSRVAKEVRGSLSAGDHVQVRGHLTEYMGRSEIE 125
                                    58999******8535589******9..5569999999999**9999*****************999775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1036.11
//
Query:       gi|116754253|ref|YP_843371.1|  [L=130]
Description: hypothetical protein Mthe_0943 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-34  117.9   0.0    2.8e-34  117.7   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 !  117.7   0.0   1.5e-38   2.8e-34       1     115 []      14     123 ..      14     123 .. 0.98

  Alignments for each domain:
  == domain 1  score: 117.7 bits;  conditional E-value: 1.5e-38
                                    E-HHHHHHHHHHHT.SEEEEEEEESSSSEEEEEEESSSHHHHHHHHHHHHHHSTTTT-GGGTTS..THHHHHHHHHH-SE CS
                        UPF0047   1 diteeveeavkesgvkeGlvlvfsrhttasltinEnadpdvqeDleealeklvpeeeYrhnaegpdnadaHlkssllgss 80 
                                    dit++v++av+ sgv +G++lv++ htt++l++nE+ ++++  D+ + ++++vp   Yrh   +  n++aHl++sllg+s
  gi|116754253|ref|YP_843371.1|  14 DITPQVQRAVRDSGVIDGICLVYTLHTTTALIVNEA-ESGLLIDIIDKIREIVPGVGYRHG--E--NGPAHLQASLLGNS 88 
                                    8**********************************9.*****************99****9..5..89************ PP

                                    EEEEEETTEE---TTEEEEEEESS-SSEEEEEEEE CS
                        UPF0047  81 ltipvedgklalGtwqsiylveldgpreRkvvvqv 115
                                    +++pve+g   lGtwq+i++veldgpr+R+v v+v
  gi|116754253|ref|YP_843371.1|  89 VVVPVEKGIPLLGTWQRILFVELDGPRRRRVGVKV 123
                                    *******************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.37
# Mc/sec: 1057.51
//
Query:       gi|116754254|ref|YP_843372.1|  [L=324]
Description: glycosyl transferase family protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.7e-33  113.9  17.6    6.7e-33  113.9  17.6    1.6  2  Glycos_transf_4  Glycosyl transferase family 4


Domain annotation for each model (and alignments):
>> Glycos_transf_4  Glycosyl transferase family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.3       0.7   1.2e+04     147     158 ..      51      62 ..      49      64 .. 0.72
   2 !  113.9  17.6   3.7e-37   6.7e-33       2     159 ..      78     237 ..      77     238 .. 0.95

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 0.7
                Glycos_transf_4 147 flGlvlavlail 158
                                    + G+vl+vl+++
  gi|116754254|ref|YP_843372.1|  51 VFGFVLGVLVYI 62 
                                    578888888776 PP

  == domain 2  score: 113.9 bits;  conditional E-value: 3.7e-37
                Glycos_transf_4   2 llllltillilllGflDDv....lglkarlKlilqilaalililtldlslttlgllltqvlielglilavlltllvivgv 77 
                                    l++l+t+l+++++G++DD+     gl++++K ++ ++aa++++++ +++ tt++l+l+ + ++ g+++ ++++ + +vg+
  gi|116754254|ref|YP_843372.1|  78 LAALCTVLMACIIGIMDDIlgwkAGLRQWQKPMFMLFAAMPMMVI-NAGHTTMSLPLI-GRVDWGILYPLVIIPIGVVGA 155
                                    578999************97776799***************9775.55**********.9******************** PP

                Glycos_transf_4  78 tNavNliDGldGlaagvsiiialalvvlaavdgrsellllalallgallGfllfNrypAkvFmGDsgslflGlvlavlai 157
                                    +Na+N+++G++Gl+ag+ +ii++al++  +v g+++ ++l++++lg+ll+fl+fNrypA+vF GD+ ++++G++ a++ai
  gi|116754254|ref|YP_843372.1| 156 SNAFNMVAGYNGLEAGMGVIIFAALGYAGLVMGKTSAAALSIIMLGSLLAFLYFNRYPARVFPGDTMTYSVGALAACVAI 235
                                    *******************************************************************************9 PP

                Glycos_transf_4 158 lg 159
                                    lg
  gi|116754254|ref|YP_843372.1| 236 LG 237
                                    87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2639.96
//
Query:       gi|116754255|ref|YP_843373.1|  [L=280]
Description: lipopolysaccharide biosynthesis [Methanosaeta thermophila PT]
Scores for 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-10   40.3   0.1      3e-10   40.3   0.1    2.5  3  Wzz       Chain length determinant protein
    1.4e-08   34.6   0.2    1.4e-08   34.6   0.2    1.7  2  GNVR      G-rich domain on putative tyrosine kinase


Domain annotation for each model (and alignments):
>> Wzz  Chain length determinant protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.1   3.3e-14     3e-10       1      85 [.       7      79 ..       7      86 .. 0.87
   2 ?   -2.4   0.1      0.71   6.3e+03      70      83 ..     154     167 ..     138     179 .. 0.55
   3 ?   -1.4   0.0      0.34   3.1e+03      15      35 ..     245     266 ..     240     268 .. 0.61

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 3.3e-14
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-EEEEEEEES--CHHHHHHHHHCCHHHHHHHHHHHHHHHHHSS CS
                            Wzz  1 eeiDLieLlsvLwkrkklIilvtllfallaviyaflatpkYtataqilvpekkqveassltaqdvqanlqlasteieilkSr 82
                                   +eiDL+++++vLw++++l++ + l+++++a++++++++ +Y a+ +++  +  +            ++++ +s  +eil+S+
  gi|116754255|ref|YP_843373.1|  7 DEIDLRDIIRVLWENRFLVVGIFLIAVVAAGAVSIMMPSVYRASCLVALGNFGD------------PVYTIQSGASEILTSD 76
                                   79*********************************************9988776............6677777777777777 PP

                                   SS- CS
                            Wzz 83 dvl 85
                                    + 
  gi|116754255|ref|YP_843373.1| 77 AFV 79
                                   665 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.71
                                    HHHHHHHHHHHSSS CS
                            Wzz  70 qlasteieilkSrd 83 
                                    + +s+ +++l+S +
  gi|116754255|ref|YP_843373.1| 154 EQLSATNQLLDSVE 167
                                    33444455555543 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.34
                                    XXXXXXXXX.XXXXXXXXXXXX CS
                            Wzz  15 rkklIilvt.llfallaviyaf 35 
                                    r++lI+ v+ +l+++l+v+ af
  gi|116754255|ref|YP_843373.1| 245 RRMLIVGVAgMLGLMLGVFAAF 266
                                    6677777662556666666556 PP

>> GNVR  G-rich domain on putative tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -5.3   1.7         2   1.8e+04      63      73 ..      30      40 ..      24      43 .. 0.50
   2 !   34.6   0.2   1.5e-12   1.4e-08      40      81 ..     228     269 ..     213     270 .. 0.86

  Alignments for each domain:
  == domain 1  score: -5.3 bits;  conditional E-value: 2
                           GNVR 63 vlalllGlllg 73
                                   ++a+++++ ++
  gi|116754255|ref|YP_843373.1| 30 LIAVVAAGAVS 40
                                   44444444444 PP

  == domain 2  score: 34.6 bits;  conditional E-value: 1.5e-12
                           GNVR  40 nVrivDeavvpekpvkPkkalivvlalllGlllgvalvllrr 81 
                                      +iv   +vp +pvkP+++liv +a +lGl+lgv +++lr 
  gi|116754255|ref|YP_843373.1| 228 SLEIVEAPAVPLQPVKPRRMLIVGVAGMLGLMLGVFAAFLRV 269
                                    4789************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       898  (0.0500865); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); 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: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2220.11
//
Query:       gi|116754256|ref|YP_843374.1|  [L=191]
Description: hypothetical protein Mthe_0946 [Methanosaeta thermophila PT]
Scores for complete 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-21   75.6   0.1    7.9e-21   74.3   0.0    1.7  2  Acylphosphatase  Acylphosphatase
     0.0079   16.0   3.0      0.014   15.2   3.0    1.5  1  CdvA             CdvA-like coiled-coil domain
  ------ inclusion threshold ------
       0.02   14.8   1.6      0.032   14.1   1.6    1.3  1  CK2S             Casein Kinase 2 substrate
       0.25   10.6   1.7       0.37   10.0   1.7    1.2  1  TMPIT            TMPIT-like protein
       0.78    9.2   4.0        3.7    7.0   0.6    2.0  2  DUF4238          Protein of unknown function (DUF4238)


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 !   74.3   0.0   2.2e-24   7.9e-21       1      85 []       7      98 ..       7      98 .. 0.97
   2 ?   -2.2   0.0       1.6   5.6e+03      64      64 ..     170     170 ..     143     186 .. 0.53

  Alignments for each domain:
  == domain 1  score: 74.3 bits;  conditional E-value: 2.2e-24
                Acylphosphatase  1 vrllvtG.rVQgvgFRkfvrrlAkelglkGy.vrNlsdg...sVeivaegeeekvekfleelksgppk.arvdeveveelee 76
                                   vr+l++G rV+gvg+R++++++A++l+++G+ +rNl+++    Ve+++eg++++v++f+++++s++pk a+v+e+++ee++ 
  gi|116754256|ref|YP_843374.1|  7 VRALIRGqRVHGVGYRNHLFSEADSLCMDGFsARNLRENglqLVEVLFEGDDRQVSSFMAFIRSSWPKaAEVSEISFEEYDG 88
                                   5789***9***********************9****9999999*************************************** PP

                Acylphosphatase 77 eeef.kdFei 85
                                   + e+ ++F+i
  gi|116754256|ref|YP_843374.1| 89 RVEKlTRFAI 98
                                   ***9999987 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.6
                Acylphosphatase  64 a 64 
                                    a
  gi|116754256|ref|YP_843374.1| 170 A 170
                                    2 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   3.0   3.9e-06     0.014       7      66 ..     127     186 ..     118     191 .] 0.90

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.9e-06
                           CdvA   7 eeLvsegdipkstyeeikekleealkklkekakelkeklkkrlkeledqikslekalanl 66 
                                    + +++++d +  + + + ek +e++++ +  +++lke ++kr + +e +i+++++++  l
  gi|116754256|ref|YP_843374.1| 127 DRMLEKQDQMLGKQDLMLEKQDETVEEFRGVRSDLKEHMEKRFARIEGEIAEIKRVIREL 186
                                    568899999999999***************************************998665 PP

>> CK2S  Casein Kinase 2 substrate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   1.6   8.9e-06     0.032      28     110 ..      91     180 ..      84     187 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.9e-06
                           CK2S  28 eslsnlaeqlqalqnvklygtp......lrdfpdlqerLrekqleal...eevlakLrekleelqkvrdsleklvrdalq 98 
                                    e+l+  a + qa+q +k  ++        +++ + q+r++ekq + l   + +l+k  e++ee+++vr++l+++ ++ + 
  gi|116754256|ref|YP_843374.1|  91 EKLTRFAIRFQAIQLSKGVESIlrieakQDQMLEKQDRMLEKQDQMLgkqDLMLEKQDETVEEFRGVRSDLKEHMEKRFA 170
                                    5566666666666666644444555544566777788999999876644489**************************** PP

                           CK2S  99 lyeekadklslk 110
                                     +e++ ++  +k
  gi|116754256|ref|YP_843374.1| 171 RIEGEIAE--IK 180
                                    99999884..44 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.7    0.0001      0.37      10      85 ..     111     186 ..     103     190 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0001
                          TMPIT  10 efkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlkev 85 
                                    ++ ++e++++++ +k +++ + q+++  + +   ++  e  ++++ +++++ke+ e+++++++ e++e+k+v++e+
  gi|116754256|ref|YP_843374.1| 111 SILRIEAKQDQMLEKQDRMLEKQDQMLGKQDLMLEKQDETVEEFRGVRSDLKEHMEKRFARIEGEIAEIKRVIREL 186
                                    566899999999*****************999999999*********************************99986 PP

>> DUF4238  Protein of unknown function (DUF4238)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.7      0.01        38      34     152 ..      14     139 ..       5     160 .. 0.73
   2 ?    7.0   0.6     0.001       3.7      54      80 ..     159     185 ..     134     189 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.01
                        DUF4238  34 rsvkricgekdmYtikned............sgedpnhiEktlaklEskaakiirkilk...egkstrtltreerkqlrk 98 
                                    ++v  +++++++++  ++d            + +  + +E ++   + ++++   +i++   ++ ++ +++ ee +   +
  gi|116754256|ref|YP_843374.1|  14 QRVHGVGYRNHLFS--EADslcmdgfsarnlRENGLQLVEVLFEGDDRQVSSFMAFIRSswpKAAEVSEISFEEYDGRVE 91 
                                    56677777777777..3335666666666666667778888888888888888888888888888899999999999999 PP

                        DUF4238  99 flfllkyRtprfreeydtedkeelesymrekkkfekpldelldelkvildtkvd 152
                                     l+ +++R  ++       +++ +es  r ++k++++l++  ++l+++ +   +
  gi|116754256|ref|YP_843374.1|  92 KLTRFAIRFQAIQ------LSKGVESILRIEAKQDQMLEKQDRMLEKQDQMLGK 139
                                    9999999987777......88888888888888888888777777776655444 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.001
                        DUF4238  54 gedpnhiEktlaklEskaakiirkilk 80 
                                     + ++h+Ek +a++E+++a+i r i++
  gi|116754256|ref|YP_843374.1| 159 SDLKEHMEKRFARIEGEIAEIKRVIRE 185
                                    56789***************9888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1140  (0.0635841); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); 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: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1487.08
//
Query:       gi|116754257|ref|YP_843375.1|  [L=79]
Description: hypothetical protein Mthe_0947 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.21s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 658.58
//
Query:       gi|116754258|ref|YP_843376.1|  [L=201]
Description: acylphosphatase [Methanosaeta thermophila PT]
Scores for complete 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   0.4    1.1e-21   77.0   0.4    1.6  1  Acylphosphatase  Acylphosphatase
    9.1e-05   22.3   4.2    0.00022   21.1   4.2    1.6  1  CdvA             CdvA-like coiled-coil domain
     0.0034   17.6   0.6     0.0063   16.7   0.5    1.4  2  CHDCT2           CHDCT2 (NUC038) domain
  ------ inclusion threshold ------
      0.011   15.5   0.0      0.022   14.5   0.0    1.5  1  T2SSM_b          Type II secretion system (T2SS), protein M s
      0.032   14.3   1.9      0.059   13.4   1.9    1.5  1  DUF1664          Protein of unknown function (DUF1664)
      0.048   13.8   1.1       0.13   12.4   0.9    1.8  1  DUF1115          Protein of unknown function (DUF1115)
       0.11   12.0   0.1         14    5.3   0.1    2.4  2  SHNi-TPR         SHNi-TPR
       0.12   12.5   0.2        7.3    7.0   0.0    2.5  2  TPR_2            Tetratricopeptide repeat
       0.16   11.3   2.7       0.22   10.9   2.7    1.1  1  FAM76            FAM76 protein
       0.22   11.8   4.7       0.36   11.1   4.1    1.6  1  KxDL             Uncharacterized conserved protein
       0.88    9.7   9.0        1.5    8.9   9.0    1.6  1  UPF0242          Uncharacterised protein family (UPF0242) N-t


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 !   77.0   0.4   6.6e-25   1.1e-21       2      85 .]       5      88 ..       4      88 .. 0.98

  Alignments for each domain:
  == domain 1  score: 77.0 bits;  conditional E-value: 6.6e-25
                Acylphosphatase  2 rllvtGrVQgvgFRkfvrrlAkelglkGyvrNlsdgsVeivaegeeekvekfleelksgppkarvdeveveeleeeeefkdF 83
                                   +++ +G VQ+vg+R  v+++A++lg++G v+N +  +V+ivaegee+++++fl++++ ++ ++rv+e+ev ++++++ef+ F
  gi|116754258|ref|YP_843376.1|  5 EIIAKGDVQRVGYRDAVQNIARRLGVSGIVQNVEPYDVRIVAEGEEDALKEFLRAINIQERPIRVEELEVRWADATGEFQYF 86
                                   7899****************************************************************************** PP

                Acylphosphatase 84 ei 85
                                   +i
  gi|116754258|ref|YP_843376.1| 87 RI 88
                                   98 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   4.2   1.3e-07   0.00022       7      66 ..     137     196 ..     135     201 .] 0.94

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.3e-07
                           CdvA   7 eeLvsegdipkstyeeikekleealkklkekakelkeklkkrlkeledqikslekalanl 66 
                                    +++++++d + ++ + + ek +e++++l+  +++l+e ++kr + +e++i+++++a+  l
  gi|116754258|ref|YP_843376.1| 137 DQMLEKQDQMLEKQDAMLEKQDETIEELRGVRSDLREHMDKRFARIENEIAEIKRAIREL 196
                                    68999**************************************************98766 PP

>> CHDCT2  CHDCT2 (NUC038) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       6.3     1e+04     141     163 ..      10      31 ..       9      32 .. 0.65
   2 !   16.7   0.5   3.9e-06    0.0063      24     146 ..      75     196 ..      71     200 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 6.3
                         CHDCT2 141 advsrlpatlsrlrpvaeRLqms 163
                                    +dv+r+      ++ +a RL +s
  gi|116754258|ref|YP_843376.1|  10 GDVQRVG-YRDAVQNIARRLGVS 31 
                                    6666653.345678888888876 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 3.9e-06
                         CHDCT2  24 RwqDiqndpr.faiinepFkseaekgnfleiknkflarrfklleqalvieeqlrraallnlqeekekvgslaqrfaelel 102
                                    Rw D + + + f i+   +++e  +    ++  ++l+r ++l eq l + ++      + l+++ +  ++ +q + + + 
  gi|116754258|ref|YP_843376.1|  75 RWADATGEFQyFRILRGDWQEELGE--RFDVAIRYLQRSIELGEQNLAVGRENLSIGRMMLEKQDQMLEKQDQMLEKQDA 152
                                    8899888866257888888888865..579*******************88877787888888888999999999***** PP

                         CHDCT2 103 laeshqkllkesaagnknanavlekvLnqleelLsdmkadvsrl 146
                                    + e + ++++e +   +  ++ + k   ++e+ ++++k  +  l
  gi|116754258|ref|YP_843376.1| 153 MLEKQDETIEELRGVRSDLREHMDKRFARIENEIAEIKRAIREL 196
                                    ***********99999999******************9988876 PP

>> T2SSM_b  Type II secretion system (T2SS), protein M subtype b
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.4e-05     0.022      46      88 ..      35      77 ..      13      87 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.4e-05
                        T2SSM_b 46 gkvrriavrvslegeleaLqklLasLeaqrPflfVDelsvqas 88
                                   ++v++  vr+ +ege++aL ++L++++ q++ + V+el+v+  
  gi|116754258|ref|YP_843376.1| 35 QNVEPYDVRIVAEGEEDALKEFLRAINIQERPIRVEELEVRWA 77
                                   56777789********************************953 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   1.9   3.6e-05     0.059      57     120 ..     132     196 ..     109     200 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.6e-05
                        DUF1664  57 laatkrhLssridrvdkkldeqkeiskeikeevtevredls.eigedvesvkeavegleskleri 120
                                    + + ++++ ++ d++ +k+d++ e + e+ ee+  vr+dl+ ++++ +  +++ + +++  ++++
  gi|116754258|ref|YP_843376.1| 132 MLEKQDQMLEKQDQMLEKQDAMLEKQDETIEELRGVRSDLReHMDKRFARIENEIAEIKRAIREL 196
                                    33444455555555556666666666666666666666553134555555555555555554444 PP

>> DUF1115  Protein of unknown function (DUF1115)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.9   7.9e-05      0.13      14      55 ..      18      60 ..      10     168 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.9e-05
                        DUF1115 14 rfkvdknAkqlsltGvvllg.pkfnlvvveGgekaikkYkklm 55
                                   r  v++ A  l+++G+v    p+   +v+eG+e a+k++ + +
  gi|116754258|ref|YP_843376.1| 18 RDAVQNIARRLGVSGIVQNVePYDVRIVAEGEEDALKEFLRAI 60
                                   7889***********99888644488*************9987 PP

>> SHNi-TPR  SHNi-TPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1    0.0084        14      18      32 ..      50      64 ..      50      65 .. 0.93
   2 ?    4.2   0.0     0.018        30      15      35 ..      99     119 ..      97     121 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0084
                       SHNi-TPR 18 pqAveDlrkaLeLre 32
                                   ++A++++ +a++++e
  gi|116754258|ref|YP_843376.1| 50 EDALKEFLRAINIQE 64
                                   69************9 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.018
                       SHNi-TPR  15 enFpqAveDlrkaLeLreqll 35 
                                    e+F+ A+  l++++eL eq+l
  gi|116754258|ref|YP_843376.1|  99 ERFDVAIRYLQRSIELGEQNL 119
                                    89**************99986 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1     0.079   1.3e+02      18      31 ..      50      63 ..      49      66 .. 0.87
   2 ?    7.0   0.0    0.0045       7.3      16      33 ..     100     117 ..      87     118 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.079
                          TPR_2 18 eeAleafekAleld 31
                                   e+Al+ f +A+ + 
  gi|116754258|ref|YP_843376.1| 50 EDALKEFLRAINIQ 63
                                   79*********986 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0045
                          TPR_2  16 dyeeAleafekAleldPn 33 
                                    +++ A++++++++el ++
  gi|116754258|ref|YP_843376.1| 100 RFDVAIRYLQRSIELGEQ 117
                                    55************9665 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   2.7   0.00013      0.22     225     276 ..     136     188 ..     114     197 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00013
                          FAM76 225 keei.aslkkqleqkdqellekdkkitelkaellekekelreklkelekeake 276
                                    ++++ ++  ++le++d +l ++d +i el++   + ++++ +++ ++e+e+ e
  gi|116754258|ref|YP_843376.1| 136 QDQMlEKQDQMLEKQDAMLEKQDETIEELRGVRSDLREHMDKRFARIENEIAE 188
                                    44440445566777777777889999999999988888888888887776654 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   4.1   0.00022      0.36      16      74 ..     134     196 ..     128     199 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00022
                           KxDL  16 alQaqtsgr...lnkknreLlelnalsqerlaklrarfkqgt.kllkevkkdLesifkkirsl 74 
                                     +Q q++ +   + +k+  +le ++++ e+l  +r+++++++ k   ++ +++  i++ ir l
  gi|116754258|ref|YP_843376.1| 134 EKQDQMLEKqdqMLEKQDAMLEKQDETIEELRGVRSDLREHMdKRFARIENEIAEIKRAIREL 196
                                    555555543111234666666778899999999999999999999999999999999999987 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   9.0   0.00091       1.5     121     174 ..     132     184 ..      50     194 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00091
                        UPF0242 121 qLqekleaiaedfeelkleleeqLaekqellqeyqetieeqrsvlekrqdqieq 174
                                     L+++ ++  e  ++++ + ++ L+++ e ++e++   +++r+ ++kr ++ie+
  gi|116754258|ref|YP_843376.1| 132 MLEKQDQM-LEKQDQMLEKQDAMLEKQDETIEELRGVRSDLREHMDKRFARIEN 184
                                    33433333.333344444556677777788888888888888888888777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1687  (0.0940934); expected 358.6 (0.02)
Passed bias filter:                      909  (0.0507); expected 358.6 (0.02)
Passed Vit filter:                       134  (0.00747392); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.36
# Mc/sec: 1667.67
//
Query:       gi|116754259|ref|YP_843377.1|  [L=229]
Description: acylphosphatases-like [Methanosaeta thermophila PT]
Scores for complete 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-21   76.5   0.3    4.2e-21   75.2   0.3    1.7  1  Acylphosphatase  Acylphosphatase
    0.00036   18.2  11.1    0.00047   17.8  11.1    1.1  1  DUF3584          Protein of unknown function (DUF3584)
    0.00049   19.9   6.8    0.00049   19.9   6.8    2.5  3  CdvA             CdvA-like coiled-coil domain
     0.0015   18.3   0.0     0.0031   17.3   0.0    1.5  1  T2SSM_b          Type II secretion system (T2SS), protein M s
     0.0037   16.7  14.7      0.006   16.0  14.7    1.5  1  DUF3552          Domain of unknown function (DUF3552)
  ------ inclusion threshold ------
      0.061   13.0   8.5        0.1   12.3   8.5    1.5  1  DUF745           Protein of unknown function (DUF745)
      0.064   12.1  14.2       0.11   11.3  13.2    1.8  2  Spc7             Spc7 kinetochore protein
       0.12   12.5  17.4       0.16   12.1  16.9    1.5  1  UPF0242          Uncharacterised protein family (UPF0242) N-t
       0.16   11.4  14.0       0.19   11.1  14.0    1.1  1  GBP_C            Guanylate-binding protein, C-terminal domain
       0.16   12.0   2.4        0.2   11.7   2.4    1.1  1  TERB2            Telomere-associated protein TERB2
       0.19   11.9   3.7       0.72    9.9   3.6    2.0  1  DUF1115          Protein of unknown function (DUF1115)
       0.26   11.5   7.4        2.6    8.3   2.2    2.4  2  DUF1283          Protein of unknown function (DUF1283)
        1.9    8.0  12.1        2.4    7.7  11.4    1.4  1  Exonuc_VII_L     Exonuclease VII, large subunit
        1.9    7.6   8.5        2.8    7.1   8.5    1.1  1  TMPIT            TMPIT-like protein
        2.4    7.9  10.8        3.4    7.4  10.8    1.4  1  AAA_11           AAA domain
        3.4    7.7  11.3        7.6    6.6  10.2    2.2  1  DUF1664          Protein of unknown function (DUF1664)
        3.5    8.0  17.7        2.4    8.6   7.8    2.7  2  TBCA             Tubulin binding cofactor A
        4.3    7.5  10.5         15    5.7  10.5    2.0  1  Fib_alpha        Fibrinogen alpha/beta chain family
        5.4    7.6  14.3         23    5.5  14.3    2.3  1  DUF16            Protein of unknown function DUF16


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 !   75.2   0.3   4.4e-24   4.2e-21       2      85 .]       5      88 ..       4      88 .. 0.98

  Alignments for each domain:
  == domain 1  score: 75.2 bits;  conditional E-value: 4.4e-24
                Acylphosphatase  2 rllvtGrVQgvgFRkfvrrlAkelglkGyvrNlsdgsVeivaegeeekvekfleelksgppkarvdeveveeleeeeefkdF 83
                                   +++ +G VQ+vg+R  v+++A++l l+G+v+N +  +V+ivaegee+++++fl++++ ++ ++rv+e++v ++++++ef+ F
  gi|116754259|ref|YP_843377.1|  5 EIIAKGDVQRVGYRDAVQNIARKLRLSGTVENVEPYDVRIVAEGEEDALKEFLRAINIQERPIRVEELQVRWADATGEFQYF 86
                                   7899****************************************************************************** PP

                Acylphosphatase 84 ei 85
                                   +i
  gi|116754259|ref|YP_843377.1| 87 RI 88
                                   98 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8  11.1     5e-07   0.00047     633     741 ..     111     222 ..      89     225 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5e-07
                        DUF3584 633 naeleeakravaeaatalknardtlerlqnekesekdklekaiaerkqqaeeqlqkldaqlkqleeqqkaaleelkedls 712
                                    + el+e++ av++   a+ ++++ ++r+  ek+ +  +++  + e++++  e+ +++ ++++q++e+q+a+le+++e+++
  gi|116754259|ref|YP_843377.1| 111 SIELGEQNLAVSKETLAVSKENLSIGRMMLEKQDQMLEKQDRMLEKQDAMLEKQDQMLEKQDQMLEKQDAMLEKQDETIE 190
                                    568899999*****************************************9999999999******************99 PP

                        DUF3584 713 eer...lekkakwqevvgeldeqlaelkkaie 741
                                    e r    + ++++ +  + +++++ae+k ai 
  gi|116754259|ref|YP_843377.1| 191 ELRgmrSDLREHMDKRFARIENEIAEIKRAIR 222
                                    98811134456677777888888888888775 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       8.1   7.6e+03       8      31 ..       5      28 ..       5      29 .. 0.66
   2 ?   -1.3   0.2       1.9   1.8e+03      95      95 ..     134     134 ..      99     160 .. 0.54
   3 !   19.9   6.8   5.2e-07   0.00049       7      66 ..     165     224 ..     162     229 .] 0.94

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 8.1
                           CdvA  8 eLvsegdipkstyeeikekleeal 31
                                   e++++gd+++  y++  +++ ++l
  gi|116754259|ref|YP_843377.1|  5 EIIAKGDVQRVGYRDAVQNIARKL 28
                                   577778887777777766666655 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.9
                           CdvA  95 l 95 
                                    +
  gi|116754259|ref|YP_843377.1| 134 S 134
                                    2 PP

  == domain 3  score: 19.9 bits;  conditional E-value: 5.2e-07
                           CdvA   7 eeLvsegdipkstyeeikekleealkklkekakelkeklkkrlkeledqikslekalanl 66 
                                    +++++++d + ++ + + ek +e++++l+  +++l+e ++kr + +e++i+++++a+  l
  gi|116754259|ref|YP_843377.1| 165 DQMLEKQDQMLEKQDAMLEKQDETIEELRGMRSDLREHMDKRFARIENEIAEIKRAIREL 224
                                    6899***************************************************98766 PP

>> T2SSM_b  Type II secretion system (T2SS), protein M subtype b
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   3.3e-06    0.0031      42      88 ..      31      77 ..      12      87 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.3e-06
                        T2SSM_b 42 ageegkvrriavrvslegeleaLqklLasLeaqrPflfVDelsvqas 88
                                   +g+ ++v++  vr+ +ege++aL ++L++++ q++ + V+el+v+  
  gi|116754259|ref|YP_843377.1| 31 SGTVENVEPYDVRIVAEGEEDALKEFLRAINIQERPIRVEELQVRWA 77
                                   67788999999*********************************953 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0  14.7   6.4e-06     0.006      79     136 ..     139     196 ..     112     223 .. 0.60

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6.4e-06
                        DUF3552  79 elqrlekRllqkeetLdrkeeslekkeesleekekelkqkeqsleekeeeleelveeq 136
                                     l+++++ l++++ +L+++++ lek+++ le++++ l+++ + le+++e++eel   +
  gi|116754259|ref|YP_843377.1| 139 MLEKQDQMLEKQDRMLEKQDAMLEKQDQMLEKQDQMLEKQDAMLEKQDETIEELRGMR 196
                                    4555555555555555555555555555555555555555555555555555554433 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   8.5   0.00011       0.1      67     160 ..     108     201 ..     102     221 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                         DUF745  67 leqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaAkk 146
                                    l ++++  e+ +   k+ l+ s++n+++ +++ ++  q le   ++l++  + le+ +q+ ++  q l+++ ++le+  +
  gi|116754259|ref|YP_843377.1| 108 LHRSIELGEQNLAVSKETLAVSKENLSIGRMMLEKQDQMLEKQDRMLEKQDAMLEKQDQMLEKQDQMLEKQDAMLEKQDE 187
                                    666677778888889999***********************************************************999 PP

                         DUF745 147 RveeLkkqlkeark 160
                                     +eeL+   ++ r+
  gi|116754259|ref|YP_843377.1| 188 TIEELRGMRSDLRE 201
                                    99999866666555 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.62   5.8e+02       5      18 ..      50      63 ..      46      63 .. 0.82
   2 ?   11.3  13.2   0.00012      0.11     150     229 ..     139     221 ..     106     227 .. 0.44

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.62
                           Spc7  5 pisLqdFLnmtgIr 18
                                   +  L++FL+ ++I+
  gi|116754259|ref|YP_843377.1| 50 EDALKEFLRAINIQ 63
                                   5579*********7 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00012
                           Spc7 150 gleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesid..keeLeelreelaelkae.ieekkkelaelq 226
                                     le+++++Lekq   l++    le++ + le++ ++l+++ + le+ d   eeL+ +r++l+e++ +  ++ ++e+ae +
  gi|116754259|ref|YP_843377.1| 139 MLEKQDQMLEKQDRMLEKQDAMLEKQDQMLEKQDQMLEKQDAMLEKQDetIEELRGMRSDLREHMDKrFARIENEIAEIK 218
                                    33344444444444444444444444444444444444433333333322344444444444443221334444444443 PP

                           Spc7 227 eql 229
                                    + +
  gi|116754259|ref|YP_843377.1| 219 RAI 221
                                    333 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1  16.9   0.00017      0.16      57     174 ..      93     212 ..      75     219 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00017
                        UPF0242  57 wekalkekl......ekskleekeaklteldeglktkeeal....eelqeeeeeLkeeldakeeelerlkeenqqLqekl 126
                                    w+++l e++            ++   l e++  l++ +e+l    e+l    + L+++ +  e++ + l+++++ L+++ 
  gi|116754259|ref|YP_843377.1|  93 WQEELGERFdvairyL-----HRSIELGEQN--LAVSKETLavskENLSIGRMMLEKQDQMLEKQDRMLEKQDAMLEKQD 165
                                    6666666665433331.....2222233333..44555544111133334445555555555666666777777888777 PP

                        UPF0242 127 eaiaedfeelkleleeqLaekqellqeyqetieeqrsvlekrqdqieq 174
                                    ++  ++ ++++ + ++ L+++ e ++e++ + +++r+ ++kr ++ie+
  gi|116754259|ref|YP_843377.1| 166 QMLEKQ-DQMLEKQDAMLEKQDETIEELRGMRSDLREHMDKRFARIEN 212
                                    775555.5555667999****************************987 PP

>> GBP_C  Guanylate-binding protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1  14.0    0.0002      0.19     185     295 ..      98     216 ..      49     218 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0002
                          GBP_C 185 keaveeailqtdkaltakekeieaeqakaeaaeaekelleekqkeeeqrmeakeksleehvkqLke..kleeerekllee 262
                                     e    ai  + ++++  e++ + ++++ +  +++  + + + +++ q++e++++ le++ ++L++  ++ e++ ++le+
  gi|116754259|ref|YP_843377.1|  98 GERFDVAIRYLHRSIELGEQNLAVSKETLAVSKENLSIGRMMLEKQDQMLEKQDRMLEKQDAMLEKqdQMLEKQDQMLEK 177
                                    4566779999999999**********9999999999************************99997622688888899999 PP

                          GBP_C 263 qerllekklkeqeel......lkegfkeeaeslekeike 295
                                    q+ +lek+    eel      l+e + ++ ++ e+ei e
  gi|116754259|ref|YP_843377.1| 178 QDAMLEKQDETIEELrgmrsdLREHMDKRFARIENEIAE 216
                                    999999987655554222222345555555556666665 PP

>> TERB2  Telomere-associated protein TERB2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   2.4   0.00022       0.2      80     168 ..     112     202 ..     103     224 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00022
                          TERB2  80 valgkyvLppakvqeeirk...kigrfiweqdnqslveqssevhsaeepeiakdslleekeeqasklaksaeksatstsk 156
                                    ++lg+  L   k++ ++ k    igr++ e+++  ++e+++++  ++   ++k++++ ek++q+ ++++   +++ +t +
  gi|116754259|ref|YP_843377.1| 112 IELGEQNLAVSKETLAVSKenlSIGRMMLEKQD-QMLEKQDRMLEKQDAMLEKQDQMLEKQDQMLEKQDAMLEKQDETIE 190
                                    555555555555444444311158999888877.67899999999999999999999999999999988888999***** PP

                          TERB2 157 sekqlcselkey 168
                                    + + ++s l+e+
  gi|116754259|ref|YP_843377.1| 191 ELRGMRSDLREH 202
                                    *99999999765 PP

>> DUF1115  Protein of unknown function (DUF1115)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   3.6   0.00076      0.72      14      55 ..      18      60 ..      10     196 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00076
                        DUF1115 14 rfkvdknAkqlsltGvvllg.pkfnlvvveGgekaikkYkklm 55
                                   r  v++ A +l l+G v    p+   +v+eG+e a+k++ + +
  gi|116754259|ref|YP_843377.1| 18 RDAVQNIARKLRLSGTVENVePYDVRIVAEGEEDALKEFLRAI 60
                                   7889***********88777555488*************9987 PP

>> DUF1283  Protein of unknown function (DUF1283)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.9     0.015        14       8      55 ..     115     167 ..     109     172 .. 0.77
   2 ?    8.3   2.2    0.0028       2.6       6      51 ..     169     216 ..     164     223 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.015
                        DUF1283   8 G..dsalskeaarqskeqWnetrsLRnkvnkrveke...fdkadkaidkrdkC 55 
                                    G  + a+ske+ + ske+    r++ +k ++  ek+   ++k d  ++k+d+ 
  gi|116754259|ref|YP_843377.1| 115 GeqNLAVSKETLAVSKENLSIGRMMLEKQDQMLEKQdrmLEKQDAMLEKQDQM 167
                                    53367899**********99999999999988777544478888888888875 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0028
                        DUF1283   6 enGdsalskeaarqsk..eqWnetrsLRnkvnkrvekefdkadkaidk 51 
                                    e+ d+ l+k+ a  +k  e  +e r +R+ + ++++k+f +++++i +
  gi|116754259|ref|YP_843377.1| 169 EKQDQMLEKQDAMLEKqdETIEELRGMRSDLREHMDKRFARIENEIAE 216
                                    6668899999997554227899*********************99865 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7  11.4    0.0025       2.4     162     237 ..     138     212 ..      92     226 .. 0.42

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0025
                   Exonuc_VII_L 162 rlleekkqrleklasrlkspeellerkrqrldeleerleralkkqlkkkrerleelkerl.kekleekkerlkklke 237
                                     +le++ q+lek ++ l++++++le++ q l++  + le+ ++  l+k+ e++eel+  + ++  e++++r++++++
  gi|116754259|ref|YP_843377.1| 138 MMLEKQDQMLEKQDRMLEKQDAMLEKQDQMLEKQDQMLEK-QDAMLEKQDETIEELR-GMrSDLREHMDKRFARIEN 212
                                    2234444444444444444444444444444443333333.3334444444444444.1111111122222222222 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   8.5     0.003       2.8       5      85 ..     144     224 ..     140     227 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.003
                          TMPIT   5 eelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlke 84 
                                    +++ ++++++ e+++ + +k +++ + q+++ ++ +   ++  e  ++l+ ++++++e+ +++++++++e++e+k+ ++e
  gi|116754259|ref|YP_843377.1| 144 DQMLEKQDRMLEKQDAMLEKQDQMLEKQDQMLEKQDAMLEKQDETIEELRGMRSDLREHMDKRFARIENEIAEIKRAIRE 223
                                    556666777777888999999999999***99999999999999999********99******************99987 PP

                          TMPIT  85 v 85 
                                    +
  gi|116754259|ref|YP_843377.1| 224 L 224
                                    5 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4  10.8    0.0036       3.4      89     194 ..     110     216 ..      19     222 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0036
                         AAA_11  89 kivRvgneeeriseavksvsleekvekrlekeekaqlakeiskeleklakelrafeeeeek.eklkkskekskskleqer 167
                                    + + +g ++ ++s+++ +vs e+    r+  e++ q+ ++ ++ lek++++l+++++  ek ++ +++++   +k+ ++ 
  gi|116754259|ref|YP_843377.1| 110 RSIELGEQNLAVSKETLAVSKENLSIGRMMLEKQDQMLEKQDRMLEKQDAMLEKQDQMLEKqDQMLEKQDAMLEKQDETI 189
                                    44445555566777777777777777777777789999999999999999999988887766788888889999999999 PP

                         AAA_11 168 rklkkerkelskeleeaeesleeevld 194
                                    ++l+  r++l++ ++++ +++e+e+ +
  gi|116754259|ref|YP_843377.1| 190 EELRGMRSDLREHMDKRFARIENEIAE 216
                                    999999999999999999999888765 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6  10.2     0.008       7.6      53     120 ..     156     224 ..     103     228 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.008
                        DUF1664  53 vseslaatkrhLssridrvdkkldeqkeiskeikeevtevredls.eigedvesvkeavegleskleri 120
                                     ++++ + ++++ ++ d++ +k+d++ e + e+ ee+  +r+dl+ ++++ +  +++ + +++  ++++
  gi|116754259|ref|YP_843377.1| 156 KQDAMLEKQDQMLEKQDQMLEKQDAMLEKQDETIEELRGMRSDLReHMDKRFARIENEIAEIKRAIREL 224
                                    235555556666666677777777777777777777777777774246666666666666666666655 PP

>> TBCA  Tubulin binding cofactor A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5  10.2      0.39   3.7e+02      23      72 ..     141     176 ..     113     179 .. 0.54
   2 ?    8.6   7.8    0.0025       2.4      23      77 ..     162     216 ..     161     224 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.39
                           TBCA  23 eeqearleklkadgdedeydlkkqeevleetkamipdlkkrlekavekLe 72 
                                    e+q              + +l+kq ++le+  am+++ ++ lek+ + Le
  gi|116754259|ref|YP_843377.1| 141 EKQ--------------DQMLEKQDRMLEKQDAMLEKQDQMLEKQDQMLE 176
                                    222..............344444444444444444444444444444444 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0025
                           TBCA  23 eeqearleklkadgdedeydlkkqeevleetkamipdlkkrlekavekLeellee 77 
                                    e+q + lek  +  ++ + +l+kq e +ee + m +dl++ ++k +++ e+ ++e
  gi|116754259|ref|YP_843377.1| 162 EKQDQMLEKQDQMLEKQDAMLEKQDETIEELRGMRSDLREHMDKRFARIENEIAE 216
                                    7888888888886656699***************************999988776 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 ?    5.7  10.5     0.016        15      30     120 ..     144     205 ..     104     228 .. 0.49

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.016
                                    CCCCCHH...HCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHH CS
                      Fib_alpha  30 ekdvkkd...lekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirv 106
                                    ++ ++k+   lek    le+  ++ ++ +++ ++ + +l                                 +q ++i++
  gi|116754259|ref|YP_843377.1| 144 DQMLEKQdrmLEKQDAMLEKQDQMLEKQDQMLEKQDAML--------------------------------EKQDETIEE 191
                                    222222200022222223333333333333333333333................................344455555 PP

                                    HHHHHHHHHHHHHH CS
                      Fib_alpha 107 Lqnvlesneqkiqk 120
                                    L+++ +++++++ k
  gi|116754259|ref|YP_843377.1| 192 LRGMRSDLREHMDK 205
                                    55555554444433 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5  14.3     0.024        23      32     103 ..     143     211 ..      49     225 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.024
                                    BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHHHHHHHC CS
                          DUF16  32 nkqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqkinkRlDsie 103
                                     +q L+k +  ++k++  ++k+ q  ekq++ ++++ +  ++q+e +++      +  +  ++++kR+ +ie
  gi|116754259|ref|YP_843377.1| 143 QDQMLEKQDRMLEKQDAMLEKQDQMLEKQDQMLEKQDAMLEKQDETIEE---LRGMRSDLREHMDKRFARIE 211
                                    3444555555555555555555555555555554444444555443331...11111222344555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1944  (0.108428); expected 358.6 (0.02)
Passed bias filter:                      649  (0.0361983); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); 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):              19  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 1566.85
//
Query:       gi|116754260|ref|YP_843378.1|  [L=215]
Description: acylphosphatases-like [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-21   75.2   0.6    9.6e-21   74.0   0.6    1.6  1  Acylphosphatase  Acylphosphatase
     0.0015   18.4   8.8     0.0017   18.2   7.2    2.0  2  CdvA             CdvA-like coiled-coil domain
     0.0038   16.7  11.9     0.0061   16.0  11.9    1.4  1  DUF3552          Domain of unknown function (DUF3552)
     0.0088   15.0   7.9      0.018   13.9   7.6    1.6  2  Spc7             Spc7 kinetochore protein
  ------ inclusion threshold ------
      0.048   13.8   3.0      0.081   13.1   3.0    1.4  1  CHDCT2           CHDCT2 (NUC038) domain
      0.065   13.3   6.7      0.065   13.3   5.4    1.6  2  DUF1664          Protein of unknown function (DUF1664)
       0.11   12.0   0.0         12    5.4   0.0    2.5  2  SHNi-TPR         SHNi-TPR
       0.11   12.5   2.9       0.57   10.3   2.8    2.0  1  DUF1115          Protein of unknown function (DUF1115)
       0.19   11.1   5.8       0.31   10.4   5.8    1.3  1  FAM76            FAM76 protein
       0.38    9.9   6.2       0.55    9.4   6.2    1.1  1  TMPIT            TMPIT-like protein
       0.73   10.1   9.8        3.1    8.1   9.3    2.2  1  KxDL             Uncharacterized conserved protein
          1    9.9  12.8        3.7    8.1  12.8    1.9  1  FadA             Adhesion protein FadA
        1.4    9.1   9.3        4.4    7.5   9.3    1.9  1  Fib_alpha        Fibrinogen alpha/beta chain family
        1.4    8.4   9.8        1.5    8.3   8.7    1.4  1  Exonuc_VII_L     Exonuclease VII, large subunit
        2.2    8.8  13.2        2.8    8.5  10.7    2.3  2  DUF16            Protein of unknown function DUF16
        2.4    8.2  16.3        4.6    7.3  15.8    1.7  1  UPF0242          Uncharacterised protein family (UPF0242) N-t
        2.9    8.2   5.2        3.4    7.9   2.2    2.3  2  DUF1283          Protein of unknown function (DUF1283)
        5.5    7.4  14.5        5.4    7.4   7.0    2.7  2  TBCA             Tubulin binding cofactor A


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 !   74.0   0.6   9.6e-24   9.6e-21       2      85 .]       5      88 ..       4      88 .. 0.98

  Alignments for each domain:
  == domain 1  score: 74.0 bits;  conditional E-value: 9.6e-24
                Acylphosphatase  2 rllvtGrVQgvgFRkfvrrlAkelglkGyvrNlsdgsVeivaegeeekvekfleelksgppkarvdeveveeleeeeefkdF 83
                                   +++ +G VQ+vg+R  v+++A++l l+G+v+N +  +V+ivaegee+++++f+++++ ++ ++rv+e++v ++++++ef+ F
  gi|116754260|ref|YP_843378.1|  5 EIIAKGDVQRVGYRDAVQNIARKLRLSGTVENVEPYDVRIVAEGEEAALKEFVNAVNIQERPIRVEELQVRWADATGEFQYF 86
                                   7899****************************************************************************** PP

                Acylphosphatase 84 ei 85
                                   +i
  gi|116754260|ref|YP_843378.1| 87 RI 88
                                   98 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0         7     7e+03       8      31 ..       5      28 ..       5      29 .. 0.66
   2 !   18.2   7.2   1.7e-06    0.0017       7      66 ..     151     210 ..     142     215 .] 0.93

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 7
                           CdvA  8 eLvsegdipkstyeeikekleeal 31
                                   e++++gd+++  y++  +++ ++l
  gi|116754260|ref|YP_843378.1|  5 EIIAKGDVQRVGYRDAVQNIARKL 28
                                   577778887777777766666655 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 1.7e-06
                           CdvA   7 eeLvsegdipkstyeeikekleealkklkekakelkeklkkrlkeledqikslekalanl 66 
                                    +++++++d + ++ + + ek +e++++l+  +++l+e ++kr + +e++i+++++a+  l
  gi|116754260|ref|YP_843378.1| 151 DQMLEKQDQMLEKQDAMLEKQDETIEELRGVRSDLREHMDKRFARIENEIAEIKRAIREL 210
                                    6899***************************************************98766 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0  11.9   6.1e-06    0.0061      78     130 ..     131     183 ..     113     207 .. 0.60

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6.1e-06
                        DUF3552  78 nelqrlekRllqkeetLdrkeeslekkeesleekekelkqkeqsleekeeele 130
                                      l+++++ l++++++L+++++ lek+++ le+++  l+++ +++ee +   +
  gi|116754260|ref|YP_843378.1| 131 MMLEKQDQMLEKQDQMLEKQDQMLEKQDQMLEKQDAMLEKQDETIEELRGVRS 183
                                    44556666666666666666666666666666666666666666666543333 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.1   1.1e+03       2      18 ..      47      63 ..      46      65 .. 0.85
   2 !   13.9   7.6   1.8e-05     0.018     150     223 ..     132     208 ..      91     213 .. 0.56

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.1
                           Spc7  2 evepisLqdFLnmtgIr 18
                                   e e+  L++F n ++I+
  gi|116754260|ref|YP_843378.1| 47 EGEEAALKEFVNAVNIQ 63
                                   56788899999999997 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1.8e-05
                           Spc7 150 gleedkelLekqeeeldellpeleeekaeleeeleklqeaaeeles...idkeeLeelreelaelkaeieekkkela 223
                                     le+++++Lekq + l++  + le++ + le++ ++l+++ e +e+   + ++  e + +++a++++ei+e k+ + 
  gi|116754260|ref|YP_843378.1| 132 MLEKQDQMLEKQDQMLEKQDQMLEKQDQMLEKQDAMLEKQDETIEElrgVRSDLREHMDKRFARIENEIAEIKRAIR 208
                                    34555555555555555555555555555555555555544433331112222223333444444444444444444 PP

>> CHDCT2  CHDCT2 (NUC038) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   3.0   8.2e-05     0.081      24     153 ..      75     203 ..      69     211 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.2e-05
                         CHDCT2  24 RwqDiqndpr.faiinepFkseaekgnfleiknkflarrfklleqalvieeqlrraallnlqeekekvgslaqrfaelel 102
                                    Rw D + + + f i+   +++e  +    ++  ++l+r ++l eq l + ++      + l+++ +  ++ +q + + ++
  gi|116754260|ref|YP_843378.1|  75 RWADATGEFQyFRILRGDWQEELGE--RFDVAIRYLQRSIELGEQNLAVGRENLSIGRMMLEKQDQMLEKQDQMLEKQDQ 152
                                    8999888866257888889888865..579*******************8877777777778888888888888888999 PP

                         CHDCT2 103 laeshqkllkesaagnknanavlekvLnqleelLsdmkadvsrlpatlsrl 153
                                    + e + ++l++  a  +++ +++e++    ++l + m +  +r+ + ++ +
  gi|116754260|ref|YP_843378.1| 153 MLEKQDQMLEKQDAMLEKQDETIEELRGVRSDLREHMDKRFARIENEIAEI 203
                                    999988888887776666666666555555555555555555555555554 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       8.6   8.6e+03      39      50 ..      17      28 ..      12      36 .. 0.66
   2 ?   13.3   5.4   6.5e-05     0.065      34     120 ..     121     210 ..     108     213 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 8.6
                        DUF1664 39 lsdavesvskql 50
                                    +dav++++++l
  gi|116754260|ref|YP_843378.1| 17 YRDAVQNIARKL 28
                                   566777776665 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 6.5e-05
                        DUF1664  34 vTkrslsdavesvskq..leqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredls.eigedvesvkeav 110
                                    v + +ls     + kq  + + ++++ + ++++ ++ d++ +k+d++ e + e+ ee+  vr+dl+ ++++ +  +++ +
  gi|116754260|ref|YP_843378.1| 121 VGRENLSIGRMMLEKQdqMLEKQDQMLEKQDQMLEKQDQMLEKQDAMLEKQDETIEELRGVRSDLReHMDKRFARIENEI 200
                                    56666666666665542255566788888888888999999999999999999999999999998526788888888888 PP

                        DUF1664 111 egleskleri 120
                                     +++  ++++
  gi|116754260|ref|YP_843378.1| 201 AEIKRAIREL 210
                                    8888887776 PP

>> SHNi-TPR  SHNi-TPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.012        12      19      32 ..      51      64 ..      50      65 .. 0.91
   2 ?    4.1   0.0     0.033        33      15      35 ..      99     119 ..      97     121 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.012
                       SHNi-TPR 19 qAveDlrkaLeLre 32
                                    A++++  a++++e
  gi|116754260|ref|YP_843378.1| 51 AALKEFVNAVNIQE 64
                                   7************9 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.033
                       SHNi-TPR  15 enFpqAveDlrkaLeLreqll 35 
                                    e+F+ A+  l++++eL eq+l
  gi|116754260|ref|YP_843378.1|  99 ERFDVAIRYLQRSIELGEQNL 119
                                    89**************99986 PP

>> DUF1115  Protein of unknown function (DUF1115)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   2.8   0.00057      0.57      14      55 ..      18      60 ..      10     180 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00057
                        DUF1115 14 rfkvdknAkqlsltGvvllg.pkfnlvvveGgekaikkYkklm 55
                                   r  v++ A +l l+G v    p+   +v+eG+e a+k++ + +
  gi|116754260|ref|YP_843378.1| 18 RDAVQNIARKLRLSGTVENVePYDVRIVAEGEEAALKEFVNAV 60
                                   7889***********88777555488*************9876 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   5.8   0.00031      0.31     213     275 ..     134     201 ..     102     211 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00031
                          FAM76 213 nssdhlva....vtqLkeeias.lkkqleqkdqellekdkkitelkaellekekelreklkelekeak 275
                                    +++d++++    + + ++++ +   ++le++d +l ++d +i el++   + ++++ +++ ++e+e+ 
  gi|116754260|ref|YP_843378.1| 134 EKQDQMLEkqdqMLEKQDQMLEkQDQMLEKQDAMLEKQDETIEELRGVRSDLREHMDKRFARIENEIA 201
                                    33444443111122223344330344555556666666777777777777766666666666665544 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   6.2   0.00055      0.55       9      85 ..     134     210 ..     129     213 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00055
                          TMPIT   9 kefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlkev 85 
                                    ++++++ e+++++ +k +++ + q+++ ++ +   ++  e  ++l+ ++++++e+ +++++++++e++e+k+ ++e+
  gi|116754260|ref|YP_843378.1| 134 EKQDQMLEKQDQMLEKQDQMLEKQDQMLEKQDAMLEKQDETIEELRGVRSDLREHMDKRFARIENEIAEIKRAIREL 210
                                    45566677777999999999999999999999999999999999999999999999**************9999875 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   9.3    0.0031       3.1      12      74 ..     144     210 ..     130     213 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0031
                           KxDL  12 deilalQaqtsgr...lnkknreLlelnalsqerlaklrarfkqgt.kllkevkkdLesifkkirsl 74 
                                    d++l +Q q++ +   + +k+  +le ++++ e+l  +r+++++++ k   ++ +++  i++ ir l
  gi|116754260|ref|YP_843378.1| 144 DQMLEKQDQMLEKqdqMLEKQDAMLEKQDETIEELRGVRSDLREHMdKRFARIENEIAEIKRAIREL 210
                                    6788888888864222445667777788999999***********9999999999999999999987 PP

>> FadA  Adhesion protein FadA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1  12.8    0.0037       3.7       5      62 ..     133     190 ..     131     210 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0037
                           FadA   5 LeaelqkLekkeeqrykkekakaeaaaaklakkkelkakieeklaklea.dsevrfykd 62 
                                    Le++ q+Le k++q ++k+ + +e++ + l+k+ ++ +k +e +++l    s+ r + d
  gi|116754260|ref|YP_843378.1| 133 LEKQDQMLE-KQDQMLEKQDQMLEKQDQMLEKQDAMLEKQDETIEELRGvRSDLREHMD 190
                                    677777765.5788999999999999999999999999999999998887777777755 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 ?    7.5   9.3    0.0044       4.4      67     120 ..     135     191 ..      95     214 .. 0.52

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0044
                                    HHHHHHHHHHHHHHHHHHHHHHCCCHHHH...HHHCCHHHHHHHHHHHHHHHHHHHH CS
                      Fib_alpha  67 ekqkskkdndnvikksskeleeeilrlke...tidaqesnirvLqnvlesneqkiqk 120
                                    ++ +  +++d++++k  ++le++ + l++    + +q ++i++L++v +++++++ k
  gi|116754260|ref|YP_843378.1| 135 KQDQMLEKQDQMLEKQDQMLEKQDQMLEKqdaMLEKQDETIEELRGVRSDLREHMDK 191
                                    222222333555555555555444433331113445556666666666666665543 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 ?    8.3   8.7    0.0015       1.5     168     254 ..     116     198 ..      88     212 .. 0.35

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0015
                   Exonuc_VII_L 168 kqrleklasrlkspeellerkrqrldeleerleralkkqlkkkrerleelkerl.k..ekleekkerlkklkerlellee 244
                                    +q+l   +++l+  +++le++ q l++  + le+ +++ l+k+ + le+  + l k  e    + e+l+ +++ l+  e+
  gi|116754260|ref|YP_843378.1| 116 EQNLAVGRENLSIGRMMLEKQDQMLEKQDQMLEK-QDQMLEKQDQMLEKQDAMLeKqdE----TIEELRGVRSDLR--EH 188
                                    4444433444433344444444444443333333.333344444444333322211111....1111111111111..11 PP

                   Exonuc_VII_L 245 kkerleelee 254
                                     ++r++++e+
  gi|116754260|ref|YP_843378.1| 189 MDKRFARIEN 198
                                    1111111111 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   0.0       1.4   1.3e+03      50      69 ..      53      74 ..      30     109 .. 0.66
   2 ?    8.5  10.7    0.0028       2.8      45     103 ..     135     197 ..     117     210 .. 0.56

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.4
                                   HHHHHHHHHHHHHHH..HHHHH CS
                          DUF16 50 inkleqkvekqgeki..kelkv 69
                                   +++  ++v+ q+  i  +el+v
  gi|116754260|ref|YP_843378.1| 53 LKEFVNAVNIQERPIrvEELQV 74
                                   3344444555544330033433 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0028
                                    ...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHH...HHHH.HHHHHHHHHHC CS
                          DUF16  45 klgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleli...letL.qkinkRlDsie 103
                                    k+++ ++k+ q  ekq++ ++++ +  ++q++ l+k+det+e +      L ++++kR+ +ie
  gi|116754260|ref|YP_843378.1| 135 KQDQMLEKQDQMLEKQDQMLEKQDQMLEKQDAMLEKQDETIEELrgvRSDLrEHMDKRFARIE 197
                                    445555555555555555555555555555555555555544331112222134555555544 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 ?    7.3  15.8    0.0047       4.6     109     174 ..     134     198 ..      94     204 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0047
                        UPF0242 109 eeelerlkeenqqLqekleaiaedfeelkleleeqLaekqellqeyqetieeqrsvlekrqdqieq 174
                                    e++ + l++++q L+++ ++  ++ ++++ + ++ L+++ e ++e++   +++r+ ++kr ++ie+
  gi|116754260|ref|YP_843378.1| 134 EKQDQMLEKQDQMLEKQDQMLEKQ-DQMLEKQDAMLEKQDETIEELRGVRSDLREHMDKRFARIEN 198
                                    444556777777888776665544.44455568889999999999999999999999999999986 PP

>> DUF1283  Protein of unknown function (DUF1283)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.7      0.25   2.5e+02      29      49 ..     141     161 ..     123     169 .. 0.48
   2 ?    7.9   2.2    0.0034       3.4       6      51 ..     155     202 ..     150     209 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.25
                        DUF1283  29 sLRnkvnkrvekefdkadkai 49 
                                    +  +++ +++++ ++k d+ +
  gi|116754260|ref|YP_843378.1| 141 EKQDQMLEKQDQMLEKQDQML 161
                                    222223333333344444444 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0034
                        DUF1283   6 enGdsalskeaarqsk..eqWnetrsLRnkvnkrvekefdkadkaidk 51 
                                    e+ d+ l+k+ a  +k  e  +e r +R+ + ++++k+f +++++i +
  gi|116754260|ref|YP_843378.1| 155 EKQDQMLEKQDAMLEKqdETIEELRGVRSDLREHMDKRFARIENEIAE 202
                                    6668899999997554227899*********************99865 PP

>> TBCA  Tubulin binding cofactor A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   8.1      0.17   1.7e+02      42      73 ..     132     163 ..     113     168 .. 0.64
   2 ?    7.4   7.0    0.0054       5.4      23      77 ..     148     202 ..     147     210 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.17
                           TBCA  42 dlkkqeevleetkamipdlkkrlekavekLee 73 
                                    +l+kq ++le+  +m+++ ++ lek+ + Le+
  gi|116754260|ref|YP_843378.1| 132 MLEKQDQMLEKQDQMLEKQDQMLEKQDQMLEK 163
                                    45555555555555555555555555555544 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0054
                           TBCA  23 eeqearleklkadgdedeydlkkqeevleetkamipdlkkrlekavekLeellee 77 
                                    e+q + lek  +  ++ + +l+kq e +ee + + +dl++ ++k +++ e+ ++e
  gi|116754260|ref|YP_843378.1| 148 EKQDQMLEKQDQMLEKQDAMLEKQDETIEELRGVRSDLREHMDKRFARIENEIAE 202
                                    7888888888886656699**************************9999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1752  (0.0977188); expected 358.6 (0.02)
Passed bias filter:                      668  (0.0372581); expected 358.6 (0.02)
Passed Vit filter:                       118  (0.00658152); 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):              18  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.61
# Mc/sec: 1068.88
//
Query:       gi|116754261|ref|YP_843379.1|  [L=208]
Description: acylphosphatases-like [Methanosaeta thermophila PT]
Scores for complete 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-20   72.7   0.4    5.2e-20   71.7   0.4    1.6  1  Acylphosphatase  Acylphosphatase
    0.00033   20.5   4.4    0.00033   20.5   4.4    1.9  3  CdvA             CdvA-like coiled-coil domain
  ------ inclusion threshold ------
      0.016   15.4   0.7      0.025   14.7   0.7    1.3  1  CHDCT2           CHDCT2 (NUC038) domain
      0.035   13.5   2.7      0.047   13.0   2.7    1.2  1  FAM76            FAM76 protein
      0.043   13.9   4.0      0.041   13.9   2.7    1.7  2  DUF1664          Protein of unknown function (DUF1664)
      0.046   13.8   0.3       0.18   11.9   0.0    1.8  2  DUF1115          Protein of unknown function (DUF1115)
      0.069   13.0   0.0       0.14   12.0   0.0    1.5  1  T2SSM_b          Type II secretion system (T2SS), protein M s
       0.15   12.0   0.9        0.3   11.0   0.9    1.4  1  UPF0227          Uncharacterised protein family (UPF0227)
       0.16   12.3   4.7       0.25   11.6   4.2    1.6  1  KxDL             Uncharacterized conserved protein
       0.33   11.2   3.3        2.7    8.2   1.8    2.3  2  DUF1283          Protein of unknown function (DUF1283)
       0.54   10.3   8.5          1    9.4   8.5    1.6  1  UPF0242          Uncharacterised protein family (UPF0242) N-t
       0.68   10.3   8.4       0.16   12.3   5.1    1.6  2  DUF737           Protein of unknown function (DUF737)
        1.5    9.0   5.1        4.1    7.6   5.1    1.8  1  Fib_alpha        Fibrinogen alpha/beta chain family
        2.4    7.9   6.0        3.9    7.2   6.0    1.5  1  AAA_11           AAA domain
        4.1    8.0   8.2        5.5    7.5   6.5    2.1  2  DUF16            Protein of unknown function DUF16
        8.8    6.4   8.9         49    4.1   9.2    2.0  1  ABC_tran_Xtn     ABC transporter


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 !   71.7   0.4   4.6e-23   5.2e-20       2      85 .]       5      88 ..       4      88 .. 0.98

  Alignments for each domain:
  == domain 1  score: 71.7 bits;  conditional E-value: 4.6e-23
                Acylphosphatase  2 rllvtGrVQgvgFRkfvrrlAkelglkGyvrNlsdgsVeivaegeeekvekfleelksgppkarvdeveveeleeeeefkdF 83
                                   +++ +G VQ+vg+R  v+++A++l l+G+v+N +  +V+ivaegee+++++f+++++ ++ ++ v+e+ev + ++++ef+ F
  gi|116754261|ref|YP_843379.1|  5 EIIAKGDVQRVGYRDAVQNIARKLRLSGTVENVEPYDVRIVAEGEEDALKEFVNAVNIQERPIMVEELEVRWGDATGEFQYF 86
                                   7899****************************************************************************** PP

                Acylphosphatase 84 ei 85
                                   +i
  gi|116754261|ref|YP_843379.1| 87 RI 88
                                   98 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0         6   6.7e+03       8      31 ..       5      28 ..       5      29 .. 0.67
   2 ?   -2.8   0.0       4.8   5.3e+03      69      92 ..     108     131 ..      99     134 .. 0.57
   3 !   20.5   4.4   2.9e-07   0.00033       7      66 ..     144     203 ..     140     208 .] 0.94

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 6
                           CdvA  8 eLvsegdipkstyeeikekleeal 31
                                   e++++gd+++  y++  +++ ++l
  gi|116754261|ref|YP_843379.1|  5 EIIAKGDVQRVGYRDAVQNIARKL 28
                                   577778888777777766666655 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.8
                           CdvA  69 syasGEidEeaYksaieairelle 92 
                                     + s E+ E++   ++e +  ++e
  gi|116754261|ref|YP_843379.1| 108 LHRSIELGEQNLAVSKETLAVSKE 131
                                    455556666666666665555554 PP

  == domain 3  score: 20.5 bits;  conditional E-value: 2.9e-07
                           CdvA   7 eeLvsegdipkstyeeikekleealkklkekakelkeklkkrlkeledqikslekalanl 66 
                                    +++++++d + ++ + + ek +e++++l+  +++l+e ++kr + +e++i+++++a+  l
  gi|116754261|ref|YP_843379.1| 144 DQMLEKQDRMLEKQDAMLEKQDETIEELRGVRSDLREHMDKRFSRIENEIAEIKRAIREL 203
                                    68999**************************************************98766 PP

>> CHDCT2  CHDCT2 (NUC038) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.7   2.3e-05     0.025      24     148 ..      75     198 ..      68     205 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.3e-05
                         CHDCT2  24 RwqDiqndpr.faiinepFkseaekgnfleiknkflarrfklleqalvieeqlrraallnlqeekekvgslaqrfaelel 102
                                    Rw D + + + f i+   +++e  +    ++  ++l r ++l eq l + +++  +++ nl+  +   ++ +q + + + 
  gi|116754261|ref|YP_843379.1|  75 RWGDATGEFQyFRILRGDWQEELGE--RFDVAIRYLHRSIELGEQNLAVSKETLAVSKENLSIGRMMLEKQDQMLEKQDR 152
                                    7888887765256888888888755..569****************************9998888888888888888888 PP

                         CHDCT2 103 laeshqkllkesaagnknanavlekvLnqleelLsdmkadvsrlpa 148
                                    + e +  +l++  +  ++ + v + + +++++  s + ++++ +  
  gi|116754261|ref|YP_843379.1| 153 MLEKQDAMLEKQDETIEELRGVRSDLREHMDKRFSRIENEIAEIKR 198
                                    8888888888888888888888888888888888888887776654 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   2.7   4.2e-05     0.047     224     276 ..     143     195 ..     101     204 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.2e-05
                          FAM76 224 Lkeeiaslkkqleqkdqellekdkkitelkaellekekelreklkelekeake 276
                                      + +++  ++le++d +l ++d +i el++   + ++++ ++++++e+e+ e
  gi|116754261|ref|YP_843379.1| 143 QDQMLEKQDRMLEKQDAMLEKQDETIEELRGVRSDLREHMDKRFSRIENEIAE 195
                                    3444567789999999999999********99999999999888888877654 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       6.7   7.5e+03      39      50 ..      17      28 ..      12      37 .. 0.64
   2 ?   13.9   2.7   3.6e-05     0.041      52     120 ..     134     203 ..     109     207 .. 0.63

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 6.7
                        DUF1664 39 lsdavesvskql 50
                                    +dav++++++l
  gi|116754261|ref|YP_843379.1| 17 YRDAVQNIARKL 28
                                   566666666665 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 3.6e-05
                        DUF1664  52 qvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredls.eigedvesvkeavegleskleri 120
                                    ++   + + ++++ ++ dr+ +k+d++ e + e+ ee+  vr+dl+ ++++ ++ +++ + +++  ++++
  gi|116754261|ref|YP_843379.1| 134 SIGRMMLEKQDQMLEKQDRMLEKQDAMLEKQDETIEELRGVRSDLReHMDKRFSRIENEIAEIKRAIREL 203
                                    3335556666666677777777777777777777777777777764245666666666666666666555 PP

>> DUF1115  Protein of unknown function (DUF1115)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00016      0.18      14      54 ..      18      59 ..      10      65 .. 0.85
   2 ?   -0.1   0.1      0.78   8.8e+02      71      91 ..     121     159 ..      74     202 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00016
                        DUF1115 14 rfkvdknAkqlsltGvvllg.pkfnlvvveGgekaikkYkkl 54
                                   r  v++ A +l l+G v    p+   +v+eG+e a+k++ + 
  gi|116754261|ref|YP_843379.1| 18 RDAVQNIARKLRLSGTVENVePYDVRIVAEGEEDALKEFVNA 59
                                   7889***********88777555488*************876 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.78
                        DUF1115  71 e..................eeekeaakekkeeeekdede 91 
                                                        e+++++ ek++++ +++d 
  gi|116754261|ref|YP_843379.1| 121 VsketlavskenlsigrmmLEKQDQMLEKQDRMLEKQDA 159
                                    044444555445555555522222233333333333332 PP

>> T2SSM_b  Type II secretion system (T2SS), protein M subtype b
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00012      0.14      42      87 ..      31      76 ..      12      85 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                        T2SSM_b 42 ageegkvrriavrvslegeleaLqklLasLeaqrPflfVDelsvqa 87
                                   +g+ ++v++  vr+ +ege++aL ++  +++ q++ ++V+el+v+ 
  gi|116754261|ref|YP_843379.1| 31 SGTVENVEPYDVRIVAEGEEDALKEFVNAVNIQERPIMVEELEVRW 76
                                   67788999999*********************************94 PP

>> UPF0227  Uncharacterised protein family (UPF0227)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.9   0.00027       0.3     100     183 ..     113     197 ..     104     200 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00027
                        UPF0227 100 klgeeavqstqetyvleeyhiielkalelsrlkrperilvllskqDevldy.rravaefraaaeiveddgdHafkdvseh 178
                                     lge+++  ++et  + ++++  ++++  ++ +  e+   +l+kqD +l+   ++++e+r ++    +  d  f+ ++++
  gi|116754261|ref|YP_843379.1| 113 ELGEQNLAVSKETLAVSKENLSIGRMMLEKQDQMLEKQDRMLEKQDAMLEKqDETIEELRGVRSDLREHMDKRFSRIENE 192
                                    689999999999999999999999999888888888888889********956899************************ PP

                        UPF0227 179 lqqii 183
                                    + +i+
  gi|116754261|ref|YP_843379.1| 193 IAEIK 197
                                    *9997 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   4.2   0.00022      0.25      14      74 ..     139     203 ..     125     206 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00022
                           KxDL  14 ilalQaqtsg...rlnkknreLlelnalsqerlaklrarfkqgt.kllkevkkdLesifkkirsl 74 
                                    +l +Q q++    r+ +k+  +le ++++ e+l  +r+++++++ k  +++ +++  i++ ir l
  gi|116754261|ref|YP_843379.1| 139 MLEKQDQMLEkqdRMLEKQDAMLEKQDETIEELRGVRSDLREHMdKRFSRIENEIAEIKRAIREL 203
                                    7888999986222456778888888999999*************999***************988 PP

>> DUF1283  Protein of unknown function (DUF1283)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.7     0.017        19       8      53 ..     115     165 ..     109     167 .. 0.75
   2 ?    8.2   1.8    0.0024       2.7       8      51 ..     150     195 ..     145     202 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.017
                        DUF1283   8 G..dsalskeaarqskeqWnetrsLRnkvnkrveke...fdkadkaidkrd 53 
                                    G  + a+ske+ + ske+    r++ +k ++  ek+   ++k d  ++k+d
  gi|116754261|ref|YP_843379.1| 115 GeqNLAVSKETLAVSKENLSIGRMMLEKQDQMLEKQdrmLEKQDAMLEKQD 165
                                    5336789999999****9999999999988877775333677777777776 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0024
                        DUF1283   8 Gdsalskeaarqsk..eqWnetrsLRnkvnkrvekefdkadkaidk 51 
                                     d  l+k+ a  +k  e  +e r +R+ + ++++k+f++++++i +
  gi|116754261|ref|YP_843379.1| 150 QDRMLEKQDAMLEKqdETIEELRGVRSDLREHMDKRFSRIENEIAE 195
                                    57778888886544227899*********************99865 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 ?    9.4   8.5   0.00092         1     115     174 ..     129     191 ..      50     197 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00092
                        UPF0242 115 lkeenq....qLqekleaiaedfeelkleleeqLaekqellqeyqetieeqrsvlekrqdqieq 174
                                     ke+       L+ k  ++ e  ++++ + ++ L+++ e ++e++   +++r+ ++kr  +ie+
  gi|116754261|ref|YP_843379.1| 129 SKENLSigrmMLE-KQDQMLEKQDRMLEKQDAMLEKQDETIEELRGVRSDLREHMDKRFSRIEN 191
                                    3333223332333.33333444555555666777777777777777777777777777777765 PP

>> DUF737  Protein of unknown function (DUF737)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       6.4   7.2e+03     108     131 ..      42      65 ..      20      73 .. 0.71
   2 ?   12.3   5.1   0.00014      0.16     124     176 ..     118     170 ..     106     173 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 6.4
                         DUF737 108 lakllerEreaaqeelteailrer 131
                                    ++ ++e E  a +e +++  ++er
  gi|116754261|ref|YP_843379.1|  42 VRIVAEGEEDALKEFVNAVNIQER 65 
                                    555677777777777777777777 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00014
                         DUF737 124 teailrerlstedErlkaqllelerkarqLeekekeLkkqdafYkeqlakLee 176
                                    + a+ +e l +++E l   ++ le++ + Le++++ L+kqda+  +q +++ee
  gi|116754261|ref|YP_843379.1| 118 NLAVSKETLAVSKENLSIGRMMLEKQDQMLEKQDRMLEKQDAMLEKQDETIEE 170
                                    56899***************************************999999987 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 ?    7.6   5.1    0.0036       4.1      61     120 ..     129     184 ..      95     207 .. 0.42

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0036
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHH CS
                      Fib_alpha  61 ikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvlesneqkiqk 120
                                     k+ l       +++d++++k  ++le++    ++ + +q ++i++L++v +++++++ k
  gi|116754261|ref|YP_843379.1| 129 SKENLSIGRMMLEKQDQMLEKQDRMLEKQ----DAMLEKQDETIEELRGVRSDLREHMDK 184
                                    33333333333333444444444444422....222333344444444444444444432 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   6.0    0.0035       3.9      89     182 ..     110     201 ..      19     207 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0035
                         AAA_11  89 kivRvgneeeriseavksvsleekvekrlekeekaqlakeiskeleklakelrafeeeeekeklkkskekskskleqerr 168
                                    + + +g ++ ++s+++ +vs e+    r+  e++ q+ ++ ++ lek++++l++++e++e  +l+  +++ ++++ ++ +
  gi|116754261|ref|YP_843379.1| 110 RSIELGEQNLAVSKETLAVSKENLSIGRMMLEKQDQMLEKQDRMLEKQDAMLEKQDETIE--ELRGVRSDLREHMDKRFS 187
                                    334445555566666666666666666666666888888888888888888888888875..455555555555555555 PP

                         AAA_11 169 klkkerkelskele 182
                                     +++e+ e+++ ++
  gi|116754261|ref|YP_843379.1| 188 RIENEIAEIKRAIR 201
                                    55555555555444 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       2.8   3.2e+03      50      64 ..      53      67 ..      24      84 .. 0.63
   2 ?    7.5   6.5    0.0049       5.5      35     103 ..     118     190 ..     107     203 .. 0.58

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.8
                                   HHHHHHHHHHHHHHH CS
                          DUF16 50 inkleqkvekqgeki 64
                                   +++  ++v+ q+  i
  gi|116754261|ref|YP_843379.1| 53 LKEFVNAVNIQERPI 67
                                   333344444444443 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0049
                                    HHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHH...HHHH.HHHHHHHHHHC CS
                          DUF16  35 rLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleli...letL.qkinkRlDsie 103
                                    +L  +++++++ +e+++      ekq++ ++++    ++q++ l+k+det+e +      L ++++kR+ +ie
  gi|116754261|ref|YP_843379.1| 118 NLAVSKETLAVSKENLSIGRMMLEKQDQMLEKQDRMLEKQDAMLEKQDETIEELrgvRSDLrEHMDKRFSRIE 190
                                    5555555566555555555556666666666666666666666666655554431112233134566665555 PP

>> ABC_tran_Xtn  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   9.2     0.044        49      19      72 ..     140     191 ..     138     203 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.044
                   ABC_tran_Xtn  19 leekeerleqqqkayekqqkeikkleefIerfrakakkakqaqsrekaLeklek 72 
                                    le+ ++ le+q +  ekq + ++k+ e Ie +r    ++   + + k++ ++e+
  gi|116754261|ref|YP_843379.1| 140 LEKQDQMLEKQDRMLEKQDAMLEKQDETIEELRG--VRSDLREHMDKRFSRIEN 191
                                    6889999*************************98..777777888888888854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1669  (0.0930894); expected 358.6 (0.02)
Passed bias filter:                      847  (0.0472419); expected 358.6 (0.02)
Passed Vit filter:                       114  (0.00635841); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 1463.88
//
Query:       gi|116754262|ref|YP_843380.1|  [L=404]
Description: UDP-glucose 6-dehydrogenase [Methanosaeta thermophila PT]
Scores for complete 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-56  189.6   0.0      5e-56  189.3   0.0    1.2  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
    2.8e-39  133.2   0.0      1e-38  131.4   0.0    2.0  2  UDPG_MGDP_dh    UDP-glucose/GDP-mannose dehydrogenase family,
    6.8e-16   58.6   0.0    7.4e-15   55.3   0.0    2.5  3  UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family,
      9e-05   23.0   0.2      9e-05   23.0   0.2    2.6  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    0.00011   21.9   0.0    0.00017   21.2   0.0    1.3  1  ApbA            Ketopantoate reductase PanE/ApbA
    0.00039   19.8   1.5     0.0015   17.9   1.4    1.9  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    0.00095   18.5   0.2     0.0023   17.2   0.2    1.7  1  FAD_binding_3   FAD binding domain
     0.0028   17.8   0.1     0.0028   17.8   0.1    3.0  3  NAD_binding_8   NAD(P)-binding Rossmann-like domain
     0.0055   16.6   0.3      0.017   15.0   0.3    1.9  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
     0.0064   16.3   0.0      0.021   14.7   0.1    1.8  2  Rossmann-like   Rossmann-like domain
  ------ inclusion threshold ------
      0.017   15.7   0.1       0.45   11.1   0.3    2.8  2  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
      0.017   14.7   4.8      0.023   14.3   3.8    2.1  2  DAO             FAD dependent oxidoreductase
      0.019   13.7   1.0       0.11   11.1   0.5    2.0  2  HI0933_like     HI0933-like protein
      0.028   13.5   0.8       0.18   10.8   0.3    2.1  2  FAD_binding_2   FAD binding domain
      0.052   13.5   0.0       0.15   12.1   0.0    1.8  1  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
      0.056   13.7   0.3       0.43   10.8   0.0    2.6  3  TrkA_N          TrkA-N 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 !  189.3   0.0   4.4e-59     5e-56       1     183 [.       4     185 ..       4     189 .. 0.91

  Alignments for each domain:
  == domain 1  score: 189.3 bits;  conditional E-value: 4.4e-59
                                    SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--TTHHHHHHHHCHTTTEEEES-HHHHHHC-SEE CS
                 UDPG_MGDP_dh_N   1 mkisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiyepgLeelvkkavesgrlsfttdvekaveeadvi 80 
                                    m+i++iG+GYvGl+t+a+la +gh+v++v +d +k ++l+ g++pi epg ee++++a   +rl ft+d+++a   ad+i
  gi|116754262|ref|YP_843380.1|   4 MRIAIIGAGYVGLTTGAALAYLGHHVTCVENDGRKLASLKGGRCPIREPGVEEIMRDAG--ERLLFTSDISEA-VGADAI 80 
                                    89********************************************************9..8**********5.579*** PP

                                    EE-----B-TTTTCB-THHHHHHHHHHHHHHHC..EEEEEE-S---TTHHHHCHHHHHHHHCSS-.TTCEEEEE------ CS
                 UDPG_MGDP_dh_N  81 fiaVgTPskkkgkaaDlkyvesaarsiaealkk..gkvvvvkSTvpvgtaeelvkkileeaskkk.gvdfdvvsnPEflr 157
                                    +iaVgTPs++ + +aDl+yve aar++aea+++  + +vv+kSTvpvgt++ + ++i e  s++  +++f+vvsnPEfl 
  gi|116754262|ref|YP_843380.1|  81 MIAVGTPSRE-DGSADLRYVEGAAREVAEAMRSgrRYTVVMKSTVPVGTNRRVRDMIREILSERDsTAEFQVVSNPEFLS 159
                                    **********.8888*****************97788*************976666666666555689************ PP

                                    TTSHHHHHHS-S-EEEEESSCHHHHH CS
                 UDPG_MGDP_dh_N 158 egsavkdllnpdrvviGveekkaeaa 183
                                    eg+a++d+l pdr+v+G++  +  ++
  gi|116754262|ref|YP_843380.1| 160 EGQALRDFLYPDRIVVGADGPEGLEV 185
                                    *****************987665555 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 ?   -2.6   0.0         6   6.8e+03      25      40 ..      69      84 ..      68      94 .. 0.74
   2 !  131.4   0.0   8.9e-42     1e-38       2      93 ..     222     313 ..     221     314 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 6
                   UDPG_MGDP_dh 25 anlcealgidveeVie 40
                                   +++ ea+g+d+  ++ 
  gi|116754262|ref|YP_843380.1| 69 SDISEAVGADAIMIAV 84
                                   5788999999877664 PP

  == domain 2  score: 131.4 bits;  conditional E-value: 8.9e-42
                   UDPG_MGDP_dh   2 tAEliKlaaNaflatkIsfiNelanlcealgidveeVieavgldprigpkflkpglGvGGsclpkDvkaLvalaeelgle 81 
                                    +AE+iK+aaNafla+k+sfiNe+a lce++g+dv+eV++++gldprigp+fl++g+G+GGsc+pkD++aL+al +++g+e
  gi|116754262|ref|YP_843380.1| 222 SAEMIKYAANAFLALKVSFINEMAGLCERVGADVREVARGIGLDPRIGPRFLQAGAGWGGSCFPKDTAALIALGRDNGYE 301
                                    8******************************************************************************* PP

                   UDPG_MGDP_dh  82 aelleavrevNe 93 
                                    +++++a+r vN+
  gi|116754262|ref|YP_843380.1| 302 MPIVSATRLVNQ 313
                                    ***********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 ?   -0.7   0.0       1.7   1.9e+03      36      75 ..      50      85 ..      39      92 .. 0.72
   2 ?   -2.2   0.0       5.1   5.8e+03      51      66 ..     314     329 ..     299     331 .. 0.69
   3 !   55.3   0.0   6.6e-18   7.4e-15       2      47 ..     337     382 ..     336     402 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.7
                                   E-SSTHHCCCCHHGGBTCCEEES-CHHHHTT-SEEEE-S- CS
                 UDPG_MGDP_dh_C 36 yDPkvkeeaveaeleekgvevvdsleealkgadaivilte 75
                                    +P v+e  + a    +++ ++++++ea+ gadai+i++ 
  gi|116754262|ref|YP_843380.1| 50 REPGVEEIMRDA---GERLLFTSDISEAV-GADAIMIAVG 85
                                   566666655555...45778888888877.8999999875 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.1
                                    BTCCEEES-CHHHHTT CS
                 UDPG_MGDP_dh_C  51 ekgvevvdsleealkg 66 
                                    +++v++vd+le+al+g
  gi|116754262|ref|YP_843380.1| 314 RQRVHIVDKLEDALDG 329
                                    4678888888888876 PP

  == domain 3  score: 55.3 bits;  conditional E-value: 6.6e-18
                                    EE-SSSSTT-S--TT-HHHHHHHHHHHCTSEEEEE-SSTHHCCCCH CS
                 UDPG_MGDP_dh_C   2 ilGlafKkdtdDlReSpaldiieeLleegaevkiyDPkvkeeavea 47 
                                    +lG+afK++tdD+R++p+ldi++ L+e+ga+v+++DP ++ +a++a
  gi|116754262|ref|YP_843380.1| 337 VLGIAFKPGTDDIRDAPSLDIMRLLRERGARVRAHDPAAMMNARAA 382
                                    9***************************************999877 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.2     8e-08     9e-05       1      35 [.       5      39 ..       5      47 .. 0.92
   2 ?   -2.7   0.0         8   8.9e+03      13      52 ..     105     142 ..     103     145 .. 0.62
   3 ?   -1.9   0.0       4.8   5.3e+03      15      35 ..     307     327 ..     305     336 .. 0.70

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 8e-08
                                   EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                      Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                   +++++G+Gy+gl  ++ala lg++Vt+ve+  + l
  gi|116754262|ref|YP_843380.1|  5 RIAIIGAGYVGLTTGAALAYLGHHVTCVENDGRKL 39
                                   79***************************987755 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 8
                                    HHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHH CS
                      Pyr_redox  13 ElAgalaelgkkVtvversdkllrllDeeaskilqeklek 52 
                                    E+A+a++  g + tvv  s  +  + ++ ++++++e l++
  gi|116754262|ref|YP_843380.1| 105 EVAEAMRS-GRRYTVVMKSTVPV-GTNRRVRDMIREILSE 142
                                    55555543.55677776666666.6677777777666655 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 4.8
                                    HHHHHHTTSEEEEEESSSSSS CS
                      Pyr_redox  15 AgalaelgkkVtvversdkll 35 
                                    A+ l + +++V++v+  +  l
  gi|116754262|ref|YP_843380.1| 307 ATRLVNQRQRVHIVDKLEDAL 327
                                    556677788999999887777 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   1.6e-07   0.00017       1      76 [.       6      84 ..       6     100 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.6e-07
                                   EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETTCEEEEEECEE.ECCH.SCCCCS-ESEEEE-S CS
                           ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseggeeilrppea.lsae.ekselepidlvivtv 76
                                   iai+GaG +G + +a La  g++vt++ ++  +l++lk   + ++++g eei+r+  + l ++ ++se+  +d ++++v
  gi|116754262|ref|YP_843380.1|  6 IAIIGAGYVGLTTGAALAYLGHHVTCVENDGrKLASLKGGRCPIREPGVEEIMRDAGErLLFTsDISEAVGADAIMIAV 84
                                   89*****************************999999999999999996666655443033335566666666666666 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   1.4   1.3e-06    0.0015     144     178 ..       5      39 ..       3      95 .. 0.82
   2 ?   -0.8   0.0      0.65   7.3e+02      95     110 ..      72      87 ..      40     116 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.3e-06
                                    EEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 144 rivvvGgGyiGvElAaalaklgkevtlveardrll 178
                                    ri+++G+Gy+G+ + aala lg++vt ve   r l
  gi|116754262|ref|YP_843380.1|   5 RIAIIGAGYVGLTTGAALAYLGHHVTCVENDGRKL 39 
                                    68999999999999999999999999998766554 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.65
                                    EEEEEESEEEE---EE CS
                                    xxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  95 eekiaydklvlAtGss 110
                                     e + +d++++A G  
  gi|116754262|ref|YP_843380.1|  72 SEAVGADAIMIAVGTP 87 
                                    3456666666666642 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.2   2.1e-06    0.0023       4      79 ..       6      87 ..       4     163 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.1e-06
                                   EEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSS...S--EEEHHHHHHHHHTT...-HHHHHHHSEECCCCEEEEEEE CS
                  FAD_binding_3  4 VlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlp...radglnqrtmellrqlG...ledrilaegapnelmgealyne 79
                                   ++I+GaG +Gl+++  L+  G  v++ve   ++       r  + ++   e++r++G   l  + ++e++  + + +a++++
  gi|116754262|ref|YP_843380.1|  6 IAIIGAGYVGLTTGAALAYLGHHVTCVENDGRKLASLkggRCPIREPGVEEIMRDAGerlLFTSDISEAVGADAIMIAVGTP 87
                                   78**************************999887665334778889999999999993333333444555555555555555 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   2.5e-06    0.0028       1      29 [.       8      36 ..       8      75 .. 0.84
   2 ?   -2.6   0.0       6.2   6.9e+03      49      67 ..     120     138 ..     106     139 .. 0.68
   3 ?    0.0   0.0      0.91     1e+03      10      29 ..     305     324 ..     304     334 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.5e-06
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSS CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrd 29
                                   I+GaG  Gl++ ++La  g++v+++e+  
  gi|116754262|ref|YP_843380.1|  8 IIGAGYVGLTTGAALAYLGHHVTCVENDG 36
                                   9*************************865 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6.2
                                    ---EEETTHHHHCHHHHCC CS
                  NAD_binding_8  49 ahifhgsgyypnvrrllre 67 
                                    +    ++g +++vr+++re
  gi|116754262|ref|YP_843380.1| 120 MKSTVPVGTNRRVRDMIRE 138
                                    4555566778999999987 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.91
                                    HHHHHHHCCTEEEEEE-SSS CS
                  NAD_binding_8  10 vaAylLakagfdvlllekrd 29 
                                    v A +L +++ +v++++k +
  gi|116754262|ref|YP_843380.1| 305 VSATRLVNQRQRVHIVDKLE 324
                                    679999999********976 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   0.3   1.6e-05     0.017       2      83 ..       6      81 ..       5      85 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.6e-05
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHHC-SEEE CS
                        3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisfttdleeavdadlvi 83
                                   +a+iGaG +G    a++a  g++V+ v+ + ++l++ +           e g   ee +++a +r+ ft+d++eav+ad ++
  gi|116754262|ref|YP_843380.1|  6 IAIIGAGYVGLTTGAALAYLGHHVTCVENDGRKLASLKGGRCP----IREPGV--EEIMRDAGERLLFTSDISEAVGADAIM 81
                                   8****************************99988877665544....222232..467777888888888888888888776 PP

>> Rossmann-like  Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   1.8e-05     0.021      12      40 ..       5      33 ..       2      57 .. 0.90
   2 ?   -3.0   0.0       5.6   6.3e+03      86     112 ..     160     186 ..     138     190 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.8e-05
                  Rossmann-like 12 svGiisaGrvGtalgaaleraghvvvgis 40
                                    + ii+aG vG + gaal+  gh+v+ + 
  gi|116754262|ref|YP_843380.1|  5 RIAIIGAGYVGLTTGAALAYLGHHVTCVE 33
                                   689**********************9986 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.6
                  Rossmann-like  86 kglaatgavraGtivahtsganGveil 112
                                    +g a  + + + +iv+ + g +G+e++
  gi|116754262|ref|YP_843380.1| 160 EGQALRDFLYPDRIVVGADGPEGLEVM 186
                                    555666667778899999999999887 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 ?   11.1   0.3    0.0004      0.45       1      70 [.       5      85 ..       5     101 .. 0.78
   2 ?    1.0   0.0      0.59   6.6e+02      33      78 ..     177     245 ..     157     253 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0004
                                   EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC................-EEECECHHHHHHH-SEEE CS
                  F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg................vkvtavdneeaaeeadvvv 66
                                   +i+iiGaG +g +    l+  g   h+++ + +++  k+++l+                    + ++++d +ea+  ad + 
  gi|116754262|ref|YP_843380.1|  5 RIAIIGAGYVGLTTGAALAYLG---HHVTCV-ENDGRKLASLKGGRCpirepgveeimrdageRLLFTSDISEAVG-ADAIM 81
                                   79********************...****77.88888888886432257777777777777776666667777774.77777 PP

                                   E-S- CS
                  F420_oxidored 67 lavk 70
                                   +av 
  gi|116754262|ref|YP_843380.1| 82 IAVG 85
                                   7775 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.59
                                    ESSCCCHHHHHHHHC........................-EEECECHHHHHHH-SEEEE-S-HHHHHHHH CS
                  F420_oxidored  33 srnpekaeelaeelg........................vkvtavdneeaaeeadvvvlavkpedveevl 78 
                                       pe +e +++ +                         v + + + +e+++ a   +la+k + + e++
  gi|116754262|ref|YP_843380.1| 177 ADGPEGLEVMRRMYLpvleqsfeppvwlprpanytrpslVATDP-ASAEMIKYAANAFLALKVSFINEMA 245
                                    55555555555555555555555555555555555554333344.7789999999999999998888776 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   3.8   2.1e-05     0.023       2      29 ..       6      35 ..       5     267 .. 0.88
   2 ?   -3.0   0.0       3.6     4e+03     152     163 ..     357     368 ..     296     389 .. 0.52

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.1e-05
                                   EEEECTSHHHHHHHHHHHHTT..EEEEESS CS
                            DAO  2 vviiGGGiiGlstAyeLarrg..Vtllekg 29
                                   ++iiG+G++Gl+t  +La  g  Vt +e +
  gi|116754262|ref|YP_843380.1|  6 IAIIGAGYVGLTTGAALAYLGhhVTCVEND 35
                                   9****************988889*****88 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.6
                                    HHHHHHHTT-EE CS
                            DAO 152 laraaealGvei 163
                                    ++r ++++G+++
  gi|116754262|ref|YP_843380.1| 357 IMRLLRERGARV 368
                                    223333333333 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.5    0.0001      0.11       2      48 ..       5      48 ..       4      52 .. 0.94
   2 ?    0.7   0.0      0.15   1.7e+02     132     166 ..      54      88 ..      48     102 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0001
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHHHCGGGT-E CS
                    HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrKilisGgGrcN 48
                                   ++++iG+G  Gl + +++a  g++V+ +e+    grK++   gGrc 
  gi|116754262|ref|YP_843380.1|  5 RIAIIGAGYVGLTTGAALAYLGHHVTCVEND---GRKLASLKGGRCP 48
                                   689***************************9...******99***96 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.15
                                    EEEEECETTE.EEEEE.TTEEEEESEEEE----SS CS
                    HI0933_like 132 vksvekeedgkfrvktkseeeleadklvlAtGGlS 166
                                    v+++ +++++++ ++ + +e++ ad++++A+G  S
  gi|116754262|ref|YP_843380.1|  54 VEEIMRDAGERLLFTSDISEAVGADAIMIAVGTPS 88 
                                    889999999999999999**************988 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.3   0.00016      0.18       2      33 ..       6      37 ..       5      55 .. 0.91
   2 ?    0.5   0.0      0.22   2.5e+02      14     104 ..     306     397 ..     304     402 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00016
                                   EEEE--SHHHHHHHHHHHHTTT-EEEEESSSG CS
                  FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqe 33
                                   + +iG+G  GL+ ++++a  G+ v++ve+ ++
  gi|116754262|ref|YP_843380.1|  6 IAIIGAGYVGLTTGAALAYLGHHVTCVENDGR 37
                                   67**************************9876 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.22
                                    HHHHHHHTTT-EEEEESSS.GGGSGGGG--S-EE-TT..SSGGSTC.CHHHHHHHHHHHHTTT-S..-HHHHHHHHHTHH CS
                  FAD_binding_2  14 AAleaaeaGlkvavvekeq.efggatawsqGgidavlspeqkkagikdspelhrtdtlkaldela..dqplveafveaap 90 
                                    +A+++ ++ ++v +v+k + +  g +    G + ++ +p    ++i+d p l ++ +l + + +   + p++ + ++aa 
  gi|116754262|ref|YP_843380.1| 306 SATRLVNQRQRVHIVDKLEdALDGFAGKTVGVLGIAFKPGT--DDIRDAPSLDIMRLLRERGARVraHDPAAMMNARAAL 383
                                    68888889999999999661445566666677777775555..6677777777777777665554425556666666888 PP

                                    HHHHHHHHTT---- CS
                  FAD_binding_2  91 eavdeLeelgvpfs 104
                                    + ++ + e+   ++
  gi|116754262|ref|YP_843380.1| 384 DGLRRFVEWMQSYN 397
                                    88888888866665 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 ?   12.1   0.0   0.00013      0.15       2     134 ..       6     156 ..       5     161 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                                    EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHSSBTTT..BTT--..--TTEEEES-HHHHHTT--EEEE-- CS
                 NAD_Gly3P_dh_N   2 iavlGaGswGtalAkvlaenghevrlwvreeelieeineehenvky..Lpgik..lpenlvattdlaealkgadiivlvv 77 
                                    ia++GaG  G +  ++la  gh+v+   ++   + +++  ++  +   +++i     e l +t+d+ ea+  ad i+++v
  gi|116754262|ref|YP_843380.1|   6 IAIIGAGYVGLTTGAALAYLGHHVTCVENDGRKLASLKGGRCPIREpgVEEIMrdAGERLLFTSDISEAVG-ADAIMIAV 84 
                                    9*************************************999987742255554125689*********995.88888888 PP

                                    -H..........HHHHHHHHHHCCC--TT-EEEE---SE.ET.TTEEHHHHHHHHH-S--....EEEEESS- CS
                 NAD_Gly3P_dh_N  78 Ps..........qalrevlkklkgllkkkailvsliKGi.eegtlkllsevieeelkeek....vavlsGps 134
                                     +           +++  ++++++ ++   +   ++K     gt++++ ++i+e+l+e        v+s p 
  gi|116754262|ref|YP_843380.1|  85 GTpsredgsadlRYVEGAAREVAEAMRSGRRYTVVMKSTvPVGTNRRVRDMIREILSERDstaeFQVVSNPE 156
                                    552233333332356677777777778887777788876588999999999999998876555566666665 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   0.00038      0.43       1      38 [.       6      43 ..       6      62 .. 0.89
   2 ?   -3.0   0.0       7.3   8.2e+03      11      30 ..     104     122 ..     102     131 .. 0.77
   3 ?   -1.4   0.0       2.4   2.6e+03      14      38 ..     307     331 ..     304     339 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00038
                                   EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHH CS
                         TrkA_N  1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelr 38
                                   i+iiG+G vG +    L   g+ +v+ +++d +++++l+
  gi|116754262|ref|YP_843380.1|  6 IAIIGAGYVGLTTGAALAYlGH-HVTCVENDGRKLASLK 43
                                   79*****************888.5*********999886 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 7.3
                                    HHHHHHHHHTTEEEEEEESS CS
                         TrkA_N  11 rslaeeLseggkdvvvidkd 30 
                                    r++ae +++g  +++v+ k+
  gi|116754262|ref|YP_843380.1| 104 REVAEAMRSGR-RYTVVMKS 122
                                    78999999988.48888765 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 2.4
                                    HHHHHH.TTEEEEEEESSHHHHHHHH CS
                         TrkA_N  14 aeeLse.ggkdvvvidkdeerveelr 38 
                                    a +L + ++ +v ++dk e++++ ++
  gi|116754262|ref|YP_843380.1| 307 ATRLVNqRQ-RVHIVDKLEDALDGFA 331
                                    556667356.6******999987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); 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 0.26s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 2959.46
//
Query:       gi|116754263|ref|YP_843381.1|  [L=281]
Description: dTDP-4-dehydrorhamnose reductase [Methanosaeta thermophila PT]
Scores for complete 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-97  324.6   0.0    5.4e-97  324.3   0.0    1.0  1  RmlD_sub_bind    RmlD substrate binding domain
    9.1e-21   74.4   0.0    1.6e-20   73.6   0.0    1.4  1  Epimerase        NAD dependent epimerase/dehydratase family
    2.2e-12   47.0   0.0    7.1e-12   45.4   0.0    1.8  2  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    3.1e-11   43.0   0.2    1.6e-09   37.3   0.0    2.7  2  Polysacc_synt_2  Polysaccharide biosynthesis protein
    3.6e-08   32.8   0.0    1.1e-07   31.2   0.0    1.8  2  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    5.2e-07   29.1   0.0    1.7e-06   27.4   0.0    1.8  1  NAD_binding_4    Male sterility protein


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 !  324.3   0.0  1.8e-100   5.4e-97       1     285 [.       1     277 [.       1     278 [. 0.98

  Alignments for each domain:
  == domain 1  score: 324.3 bits;  conditional E-value: 1.8e-100
                                    EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TTT--TTSHHHHHHHHHHH--SEEEE------HHHHHHSHHHHHHHHTH CS
                  RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeglevlaltreeldltdaeavaellkeakpdvvvnaAAytavDkaEseeeaayavnae 80 
                                    m+il++Ga+GqlG+eL + l +++  + +++  e+d++d  av +  + ++pdv++n AAyt+vD +Es +++a  vna 
  gi|116754263|ref|YP_843381.1|   1 MRILIFGAEGQLGTELCRVLGHHD--LAPFSHIEADVADLGAVLRQTERIRPDVIINSAAYTDVDGCESARDKAVLVNAI 78 
                                    99******************9665..8888999*********************************************** PP

                                    HHHHHHHHHHHCT-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHHH-SSEEEEEE-SEESSSSS-HH CS
                  RmlD_sub_bind  81 avealAeaaaavgalLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavlaagkkalivRtswvygekgknfv 160
                                    ++++ A aa+++ga+++h+StDyVFdG+k+ pY e d+++PlnvYG +Kl+GE++vl+++++  i+R++w+yg  g+nfv
  gi|116754263|ref|YP_843381.1|  79 GARNAAIAARRAGAKFVHISTDYVFDGKKDGPYVEYDPPNPLNVYGWSKLLGERMVLEQNPDSFILRVAWLYGPAGRNFV 158
                                    ******************************************************************************** PP

                                    HHHHHHHHH-SEEEEESS-EE--EEHHHHHHHHHHHHHHCHH.GGG-EEEE---BS-EEHHHHHHHHHHHHCHTTSEEEE CS
                  RmlD_sub_bind 161 ktmlrlakereelkvvaDqlgsPTsardlAevllqllekaaeekelagvyHlanegetswlefArailkeagadseevkp 240
                                    ktml+la+ r+el+vv+Dq g+PT a d+A+ +  l+e++      +g+yH++++ge++w+efA +i++ +g+d  +v p
  gi|116754263|ref|YP_843381.1| 159 KTMLSLARARDELRVVNDQRGTPTFAGDVANQIDLLIETES-----YGLYHCTSQGECTWYEFAVEIFRLLGMDL-RVVP 232
                                    *********************************99999998.....6**************************77.**** PP

                                    E-CCCS--SS---SBE-B--HHHHHCCT----BHHHHHHHHHHHH CS
                  RmlD_sub_bind 241 istaeyptpAkRPanSvLdtekleatfgiklrewrealkevlkel 285
                                    +st+e+p+pA+RPanSvLd+  l+ +++  +++wr++l++ + e+
  gi|116754263|ref|YP_843381.1| 233 VSTSEFPRPARRPANSVLDNLLLRVQGMDIMPHWRDSLRDHISEV 277
                                    ***************************************998875 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.6   0.0   5.3e-24   1.6e-20       1     227 [.       3     196 ..       3     203 .. 0.86

  Alignments for each domain:
  == domain 1  score: 73.6 bits;  conditional E-value: 5.3e-24
                                    EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHH CS
                      Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggvaas 80 
                                    il+ Ga G++G+ l++ l    +++  +++                e+d+ d  a+ r  ++ +pd++i+ Aa+ +v+  
  gi|116754263|ref|YP_843381.1|   3 ILIFGAEGQLGTELCRVLGH--HDLAPFSHI---------------EADVADLGAVLRQTERIRPDVIINSAAYTDVDGC 65 
                                    89****************96..679999999...............********************************** PP

                                    HHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHHHHHH CS
                      Epimerase  81 sedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklveayaaqy 160
                                     + + + +  n++g++n + aar+ag+ +++++s++ v+  +++ p  e+    p +p + Y+ +Kl+ge++v + + + 
  gi|116754263|ref|YP_843381.1|  66 ESARDKAVLVNAIGARNAAIAARRAGA-KFVHISTDYVFDGKKDGPYVEYD---PPNPLNVYGWSKLLGERMVLEQNPDS 141
                                    ***************************.***********988888999999...********************876666 PP

                                    T-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHH CS
                      Epimerase 161 glnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvle 227
                                         ilr+  lyGp  g ++v+     +++ + ++  e+ +++  +++    ++ Dva+ i l++e
  gi|116754263|ref|YP_843381.1| 142 ----FILRVAWLYGPA-GRNFVKT----MLSLARARD-ELRVVN--DQRGTPTFAGDVANQIDLLIE 196
                                    ....9**********9.5555555....555555555.666666..333344566666666666665 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 ?   -0.6   0.0      0.23   6.9e+02       1      17 [.       4      20 ..       4      26 .. 0.90
   2 !   45.4   0.0   2.4e-15   7.1e-12      53     267 ..      27     225 ..      14     249 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.23
                                   EEETTTSHHHHHHHHHH CS
                  GDP_Man_Dehyd  1 LiTGiaGfiGsylaelL 17
                                   Li G  G+ G  l++ L
  gi|116754263|ref|YP_843381.1|  4 LIFGAEGQLGTELCRVL 20
                                   89***********9988 PP

  == domain 2  score: 45.4 bits;  conditional E-value: 2.4e-15
                                    CEEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGG CS
                  GDP_Man_Dehyd  53 nlklhkgDltDssslerllaevqpdevynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEv 132
                                     ++ +++D+ D  ++ r  ++++pd ++n AA   Vd   +  ++ + vn++G+ +   a+r++g    ++f+++St+ v
  gi|116754263|ref|YP_843381.1|  27 PFSHIEADVADLGAVLRQTERIRPDVIINSAAYTDVDGCESARDKAVLVNAIGARNAAIAARRAG----AKFVHISTDYV 102
                                    577899*******************************9999999*******************98....69********* PP

                                    G-S-SSSSB-TTS-----SHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-E CS
                  GDP_Man_Dehyd 133 YGkvqevpqtEttpfyPrsPYaaaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevl 212
                                    +   ++ p+ E  p +P + Y+ +Kl  + +v + +        + ++   ++p  g++fv+  +++  ar+  ++    
  gi|116754263|ref|YP_843381.1| 103 FDGKKDGPYVEYDPPNPLNVYGWSKLLGERMVLEQN----PDSFILRVAWLYGPA-GRNFVKTMLSL--ARARDEL---- 171
                                    *999*************************9996533....333344556667777.66677444443..3333322.... PP

                                    ECTTTT-EEEEEEHHHHHHHHHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCC CS
                  GDP_Man_Dehyd 213 ylGnldakRdwghvkDyveamwlmlqqdkpedyviatgethsvrefvelaflelg 267
                                    ++ n d++   +++ D+++ ++l+++ ++   y + ++ + +  ef+   f  lg
  gi|116754263|ref|YP_843381.1| 172 RVVN-DQRGTPTFAGDVANQIDLLIETESYGLYHCTSQGECTWYEFAVEIFRLLG 225
                                    2222.34445566777777777777777766666666666666666665555555 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.028        85       1      18 [.       3      20 ..       3      28 .. 0.87
   2 !   37.3   0.0   5.5e-13   1.6e-09      60     153 ..      32     138 ..      22     146 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.028
                                   EEEETTTSHHHHHHHHHH CS
                Polysacc_synt_2  1 vlvtGagGsiGselvrqi 18
                                   +l+ Ga G +G el+r +
  gi|116754263|ref|YP_843381.1|  3 ILIFGAEGQLGTELCRVL 20
                                   89*************976 PP

  == domain 2  score: 37.3 bits;  conditional E-value: 5.5e-13
                                    E--TT-HHHHHHHTT..T-SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGGGS....... CS
                Polysacc_synt_2  60 igdvrdkerlekaleelkvdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStDKAv....... 132
                                     +dv+d   + +  e++++dv++++AA+  V  +e+   +a+  N +g++n + aa +ag  k+v iStD          
  gi|116754263|ref|YP_843381.1|  32 EADVADLGAVLRQTERIRPDVIINSAAYTDVDGCESARDKAVLVNAIGARNAAIAARRAGA-KFVHISTDYVFdgkkdgp 110
                                    589**************************************************99999986.7*******7643333333 PP

                                    .......S--SHHHHHHHHHHHHHHHGG CS
                Polysacc_synt_2 133 .......nPtnvmGatKrlaekllqala 153
                                           nP nv+G +K+l e ++ + +
  gi|116754263|ref|YP_843381.1| 111 yveydppNPLNVYGWSKLLGERMVLEQN 138
                                    3344444799**********99998776 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 ?   -2.0   0.0      0.47   1.4e+03       1      17 [.       4      20 ..       4      26 .. 0.87
   2 !   31.2   0.0   3.6e-11   1.1e-07      49     225 ..      30     191 ..      22     233 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.47
                      3Beta_HSD  1 vvtGgaGFlGralvkeL 17
                                   ++ G+ G lG +l++ L
  gi|116754263|ref|YP_843381.1|  4 LIFGAEGQLGTELCRVL 20
                                   589***********987 PP

  == domain 2  score: 31.2 bits;  conditional E-value: 3.6e-11
                      3Beta_HSD  49 viegDvtdkdkleealegv..dvvihlaslvdvag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnsl 125
                                     ie+Dv d   + + +e +  dv+i  a+++dv g +  +d+   vn  G rn   a+++ag + +v+ S+ + v++ ++
  gi|116754263|ref|YP_843381.1|  30 HIEADVADLGAVLRQTERIrpDVIINSAAYTDVDGcESARDKAVLVNAIGARNAAIAARRAGAK-FVHIST-DYVFDGKK 107
                                    5789999999999999987558*************9999***********************75.788886.78898444 PP

                      3Beta_HSD 126 geeilngdEeleyeslhqdaypesKalaEklvlkaNgrtlknggrlyTcaLRpagiyGegdkllvpllkqlaklglalfk 205
                                         +g   ++ ++++ ++y  sK l E++vl+ N     +        LR a +yG+  + +v+++  la+ +   ++
  gi|116754263|ref|YP_843381.1| 108 -----DGPYVEYDPPNPLNVYGWSKLLGERMVLEQNP----DS-----FILRVAWLYGPAGRNFVKTMLSLARARD-ELR 172
                                    .....45555788999********************9....44.....68*************************5.556 PP

                      3Beta_HSD 206 igdeevlsdrvYvgNvawah 225
                                    +++++    ++++g va  +
  gi|116754263|ref|YP_843381.1| 173 VVNDQR-GTPTFAGDVANQI 191
                                    666555.6899999999764 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   5.6e-10   1.7e-06      88     203 ..      50     146 ..      31     194 .. 0.77

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 5.6e-10
                                    --EEEE--SS-S.ST...TSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H......HHH-- CS
                  NAD_binding_4  88 vdviihsaAtvnfde...pykellrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegekeeklded 164
                                     dvii+saA +++d+     ++++ vN  G+r+    a++  ++  ++h+ST yv + +++                   
  gi|116754263|ref|YP_843381.1|  50 PDVIINSAAYTDVDGcesARDKAVLVNAIGARNAAIAARRAGAK--FVHISTDYVFDGKKDGP----------------Y 111
                                    59**********9975546678***********98777766555..******66655555332................2 PP

                                    EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE CS
                  NAD_binding_4 165 eraklkglpntYeqsKalaEklvrearrrsglpvvivRp 203
                                     + +  +  n Y +sK l+E++v e++        i+R+
  gi|116754263|ref|YP_843381.1| 112 VEYDPPNPLNVYGWSKLLGERMVLEQNPD----SFILRV 146
                                    3456778899*************998833....346665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); 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: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2002.86
//
Query:       gi|116754264|ref|YP_843382.1|  [L=354]
Description: glucose-1-phosphate thymidyltransferase [Methanosaeta thermophila PT]
Scores for complete 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-54  183.5   0.0    5.9e-54  183.3   0.0    1.1  1  NTP_transferase  Nucleotidyl transferase
    4.1e-11   43.5   0.0    5.9e-11   43.0   0.0    1.3  1  NTP_transf_3     MobA-like NTP transferase domain
     0.0005   19.7   9.5     0.0016   18.0   1.1    3.8  3  Hexapep          Bacterial transferase hexapeptide (six repea
    0.00059   18.9   0.0    0.00079   18.5   0.0    1.2  1  Fucokinase       L-fucokinase
  ------ inclusion threshold ------
       0.15   12.4   2.7          1    9.7   0.2    2.3  2  Bactofilin       Polymer-forming cytoskeletal


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 !  183.3   0.0   1.6e-57   5.9e-54       1     246 [.       2     235 ..       2     237 .. 0.95

  Alignments for each domain:
  == domain 1  score: 183.3 bits;  conditional E-value: 1.6e-57
                                    EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEE CS
                NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevliale 80 
                                    ka++L+GG+GtRL+PLt t+ k+lvpv++  +++ + + ++ ++gie++ v++ +e+ + v+e l+++  ++ +++++ +
  gi|116754264|ref|YP_843382.1|   2 KALVLSGGKGTRLRPLTYTMTKQLVPVANR-PILHYAMDQIRSAGIEDVGVIIAPETGEQVKESLASNP-WNFNLEFIPQ 79 
                                    699***************************.***********************************998.99******** PP

                                    SS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECTTSBEE CS
                NTP_transferase  81 pegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvieadeegrve 160
                                    + ++g+A+Av++a+++led+     +++L gD li++ +  +v+++++ ++  ++++++++ve+++ +Gv+e+d +g+v+
  gi|116754264|ref|YP_843382.1|  80 DAPRGLAHAVKVAQDFLEDDPF---LMYL-GDNLIGESIVPFVRDFESGGS--DAMILLKEVEDPRMFGVAEVDASGNVR 153
                                    ******************9995...5555.6667888************99..9************************** PP

                                    EEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEEXSSHHHHHH CS
                NTP_transferase 161 rfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsDvGtldslle 240
                                    r+vEKPk ++ s+la  G+Y+f + +++   + +++++rge eitd+++++l++g +  +++ + +  W D+G+ d+lle
  gi|116754264|ref|YP_843382.1| 154 RLVEKPKDPP-SNLALVGVYLFSPAIHDAV-SEIKPSWRGELEITDAIQRLLDKGLRVKSYILRRW--WLDTGKKDDLLE 229
                                    **********.*****************99.56********************************6..************ PP

                                    HHHHHH CS
                NTP_transferase 241 anekla 246
                                    an+ ++
  gi|116754264|ref|YP_843382.1| 230 ANRVVL 235
                                    *98765 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   0.0   1.7e-14   5.9e-11       1     126 [.       3     136 ..       3     206 .. 0.80

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 1.7e-14
                                    EEEEEESS-TTTT..T...THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH...CHHHHHHTTCTS-E....EE-TTS CS
                   NTP_transf_3   1 aviLAGGrSsRmg..g...dKallplggkpllervldalraagvdevvvvggd...eevlaalarlgvrv....vededp 68 
                                    a++L GG+++R+   +    K+l+p++++p+l++++d++r+ag+++v v+  +   e+v++ la+ ++ +    ++++ +
  gi|116754264|ref|YP_843382.1|   3 ALVLSGGKGTRLRplTytmTKQLVPVANRPILHYAMDQIRSAGIEDVGVIIAPetgEQVKESLASNPWNFnlefIPQD-A 81 
                                    79**********85415579***************************9998774556888888888655522215555.5 PP

                                    S-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSE CS
                   NTP_transf_3  69 gkgplaslaaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvptyege 126
                                     +g +++++ a + + ++d++l+ ++D      e +  +++ +++ g+d++++  e e
  gi|116754264|ref|YP_843382.1|  82 PRGLAHAVKVAQDFL-EDDPFLMYLGDNLI--GESIVPFVRDFESGGSDAMILLKEVE 136
                                    79**********999.9**********943..56666677777877777777666655 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   1.1   4.6e-07    0.0016       2      31 ..     274     302 ..     273     304 .. 0.92
   2 !    5.5   3.9    0.0041        15       2      12 ..     291     301 ..     284     334 .. 0.56
   3 ?   -3.1   0.0       2.2     8e+03      22      27 ..     346     351 ..     345     353 .. 0.59

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.6e-07
                                    EEEETTEEE-TTEEEETTEEE-TTEEEETT CS
                        Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgag 31 
                                    +vIG++++I+ ++ ig+ + IG+++++++ 
  gi|116754264|ref|YP_843382.1| 274 AVIGEGAVIR-GSFIGPYTSIGRGCVVESS 302
                                    89********.****************985 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0041
                                    EEEETTEEE-T CS
                        Hexapep   2 tvIGsnvlIgp 12 
                                    t IG ++++ +
  gi|116754264|ref|YP_843382.1| 291 TSIGRGCVVES 301
                                    22333333333 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 2.2
                                    E-TTEE CS
                        Hexapep  22 IGdnvk 27 
                                    IGd++ 
  gi|116754264|ref|YP_843382.1| 346 IGDDAE 351
                                    666665 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   2.2e-07   0.00079     270     318 ..     254     307 ..     221     346 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.2e-07
                     Fucokinase 270 k.....kesavvinSvlessvsvgegsviehsslkgnvsigsnsivsgleless 318
                                          +++a vi+S + + + +geg+vi  s +++ +sig +++v +  +e+s
  gi|116754264|ref|YP_843382.1| 254 VgrvslARGARVIESTVRGPAVIGEGAVIRGSFIGPYTSIGRGCVVESSAIEHS 307
                                    255556899*************************************98888876 PP

>> Bactofilin  Polymer-forming cytoskeletal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.2   0.00029         1      53      96 ..     242     285 ..     237     286 .. 0.93
   2 ?    2.5   0.2     0.049   1.8e+02       2      44 ..     292     333 ..     291     345 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00029
                     Bactofilin  53 vvaGtvkGnveaeekvelkktakveGdikaksleieegavfeGk 96 
                                    +++G+++G  ++ ++v+l+  a+v  +   +  +i egav++G+
  gi|116754264|ref|YP_843382.1| 242 DIQGEIDGRSRVVGRVSLARGARVIESTVRGPAVIGEGAVIRGS 285
                                    699**********************999999999*******997 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.049
                     Bactofilin   2 ligegtkikGelevegdlridGkveGdieakgklvvgeggkve 44 
                                     ig+g++++ +  +e+++++dG v  +i+  ++ v+g++++v+
  gi|116754264|ref|YP_843382.1| 292 SIGRGCVVESS-AIEHSVVLDGVVIRNIDRLEDSVIGRNTVVS 333
                                    58888888886.7899999999999999888888999998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); 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: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2717.88
//
Query:       gi|116754265|ref|YP_843383.1|  [L=187]
Description: dTDP-4-dehydrorhamnose 3,5-epimerase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-76  254.3   0.0    4.7e-76  254.2   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 !  254.2   0.0   2.6e-80   4.7e-76       2     168 ..       8     176 ..       7     177 .. 0.98

  Alignments for each domain:
  == domain 1  score: 254.2 bits;  conditional E-value: 2.6e-80
                                    -SSTTCEEEEE-EEEETTEEEEEEEEHHHHHHHTS-----EEEEEEEETTBEEEEEEESSCS---EEEEEEESEEEEEEE CS
                dTDP_sugar_isom   2 teiegvlliepkvfgDeRGfflesfneeefaeagleaefvqdnlsvskkgvlRGlHfqkepkaqaklvrvvrGevldvaV 81 
                                    ++i +v+liep+vf+DeRGff+es++++efa+ g++++fvqdn+s+s++gvlRGlH+q++p+aq+klvr v+Ge++dvaV
  gi|116754265|ref|YP_843383.1|   8 LDIYDVILIEPRVFRDERGFFMESYKHSEFAAFGIKERFVQDNHSRSRRGVLRGLHYQNPPRAQGKLVRAVSGEIFDVAV 87 
                                    5799**************************************************************************** PP

                                    E-BTTSTTTT-EEEEEEETTT--EEEE-TTEEEEEEE-SSEEEEEEEESS---GGGEEEE-TT-TTTT---..SS.B--H CS
                dTDP_sugar_isom  82 DlRkgSptfgkwvgveLsaenkrqlyipegfahGflvlsdeaevlYkvteyyapesergirwnDpelgidw..eelilSe 159
                                    D+R+gSpt+g+wvgv+Ls+en r+lyip+gfahGf++lsd a+v+Yk+t+ y+pe+e+gi wnDp +gi+w  ++++lS 
  gi|116754265|ref|YP_843383.1|  88 DIRRGSPTYGRWVGVNLSEENMRMLYIPPGFAHGFMTLSDVADVMYKTTDEYSPEHEAGIIWNDPGIGIEWpaSRPVLSP 167
                                    *************************************************************************99***** PP

                                    HHHT-B-HH CS
                dTDP_sugar_isom 160 kDkaapsla 168
                                    +D+++p l+
  gi|116754265|ref|YP_843383.1| 168 RDAKWPGLR 176
                                    ******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       239  (0.0133304); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1520.96
//
Query:       gi|116754266|ref|YP_843384.1|  [L=344]
Description: dTDP-glucose 4,6-dehydratase [Methanosaeta thermophila PT]
Scores for 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-83  278.3   0.0    1.1e-82  278.1   0.0    1.0  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    1.8e-70  237.2   0.0    2.3e-70  236.8   0.0    1.2  1  Epimerase        NAD dependent epimerase/dehydratase family
      2e-20   73.0   0.0    2.5e-20   72.6   0.0    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    7.9e-19   67.8   0.0      1e-18   67.4   0.0    1.2  1  RmlD_sub_bind    RmlD substrate binding domain
    8.7e-16   57.9   0.0    5.6e-15   55.2   0.0    1.9  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    1.3e-14   54.0   0.0    2.9e-13   49.6   0.0    2.5  1  NAD_binding_4    Male sterility protein
    9.8e-10   38.6   0.0    1.5e-09   38.1   0.0    1.2  1  NAD_binding_10   NAD(P)H-binding
  ------ inclusion threshold ------
       0.07   13.4   0.0       0.14   12.5   0.0    1.5  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
       0.08   12.4   0.0        0.8    9.1   0.0    2.2  1  adh_short        short chain dehydrogenase


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 !  278.1   0.0   5.5e-86   1.1e-82       1     331 [.       5     313 ..       5     314 .. 0.92

  Alignments for each domain:
  == domain 1  score: 278.1 bits;  conditional E-value: 5.5e-86
                                    EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEE CS
                  GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevy 80 
                                    L+TG+ GfiGs+++++ l+++   + +v+++ ++++g+ ++l +    e +e++++++gD+ D++ ++ l+++   d+v+
  gi|116754266|ref|YP_843384.1|   5 LVTGGCGFIGSNFIHYALREHD-DWEVVNLDRLTYAGNPANLSDI---EGDERYRFVRGDIADRDLVDGLFRDG-LDAVV 79 
                                    9*****************9955.5577888889999999998764...45789*******************98.9**** PP

                                    E--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHHHHHHHH CS
                  GDP_Man_Dehyd  81 nLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYaaaKlya 160
                                    n+AA+ hVd+s+ +P  ++++nv Gt+ LLea+r++ +    rf+++St+EvYG+v+e  +tE+ p++P+sPYaa+K++a
  gi|116754266|ref|YP_843384.1|  80 NFAAETHVDRSILDPSPFIDTNVRGTQVLLEAARNHDV---GRFVHISTDEVYGSVTEGRFTEDSPLRPNSPYAASKAAA 156
                                    ***********************************987...5************************************** PP

                                    HHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHHCS CS
                  GDP_Man_Dehyd 161 dwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyveamwlmlqqd 240
                                    d ++++y+ +yg+++++++ +n+++p++   f++++i++++ ++++g  + +++G++ ++Rdw++v+D ++a+  +l ++
  gi|116754266|ref|YP_843384.1| 157 DLLCRAYHISYGVPVMVTRSSNNYGPYQ---FPEKLIPLMIRNALAGM-DLPVYGEGAQVRDWLYVEDNCRAIGVVLMKG 232
                                    ***************************6...****************8.8999*************************** PP

                                    S---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB--B-THHHHHHH--- CS
                  GDP_Man_Dehyd 241 kpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlllgdaskakeeLgWk 320
                                    +p       ge +++++  e+ ++e+++ i+    g e  +r+ e  k +++  + ++  +++ +++ ++sk++  LgW 
  gi|116754266|ref|YP_843384.1| 233 RP-------GEIYNIGGGSERRNIEVVEMICRVL-G-ERLNRDPEDFKRLIKHIRDPRGAAHDFRYALECSKMR-GLGWM 302
                                    98.......9999999999999999999888654.2.34566777888889888899999*************9.9**** PP

                                    -SS-HHHHHHH CS
                  GDP_Man_Dehyd 321 pkvsfeelvre 331
                                    p+v+fe+++++
  gi|116754266|ref|YP_843384.1| 303 PQVTFEDGLAR 313
                                    *******9987 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  236.8   0.0   1.2e-73   2.3e-70       2     241 .]       5     241 ..       4     241 .. 0.97

  Alignments for each domain:
  == domain 1  score: 236.8 bits;  conditional E-value: 1.2e-73
                                    EEETTTSHHHHHHHHHHHHCT..SEEEEEES-STTTTCHHCHHC......EEEE--TT-HHHHHHHHHHHT-SEEEE--S CS
                      Epimerase   2 lVtGatGfiGsalvkallekg..yevigldrlssasntarledl......elveldltdrsalerlfkeeqpdavihlAa 73 
                                    lVtG+ GfiGs+++++ l+++  +ev++ldrl++a+n a+l d+      ++v++d+ dr+ ++ lf++ + dav+++Aa
  gi|116754266|ref|YP_843384.1|   5 LVTGGCGFIGSNFIHYALREHddWEVVNLDRLTYAGNPANLSDIegderyRFVRGDIADRDLVDGLFRD-GLDAVVNFAA 83 
                                    9****************99998999*******************************************8.********** PP

                                    ---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHH CS
                      Epimerase  74 vggvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklv 153
                                    + +v++s+ dp+ fi++n++gt+ lleaar ++v r++++s++evYG ++e   +e++   pl+pnspYaa+K+a++ l+
  gi|116754266|ref|YP_843384.1|  84 ETHVDRSILDPSPFIDTNVRGTQVLLEAARNHDVGRFVHISTDEVYGSVTEGRFTEDS---PLRPNSPYAASKAAADLLC 160
                                    ***************************************************4356666...******************* PP

                                    HHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT-S CS
                      Epimerase 154 eayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvdagd 233
                                    +ay+ +yg++++++r +n+yGp+   ++++++ip +ir++l+g  ++ ++g+g ++Rd+lyveD ++ai  vl +   g+
  gi|116754266|ref|YP_843384.1| 161 RAYHISYGVPVMVTRSSNNYGPY---QFPEKLIPLMIRNALAGM-DLPVYGEGAQVRDWLYVEDNCRAIGVVLMK---GR 233
                                    ***********************...9*****************.******************************...99 PP

                                    TTEEEEES CS
                      Epimerase 234 kgeiyniG 241
                                    +geiyniG
  gi|116754266|ref|YP_843384.1| 234 PGEIYNIG 241
                                    *******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 !   72.6   0.0   1.3e-23   2.5e-20       1     221 [.       5     221 ..       5     231 .. 0.88

  Alignments for each domain:
  == domain 1  score: 72.6 bits;  conditional E-value: 1.3e-23
                      3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlD...lrespelleelskvnvkkviegDvtdkdkleeal.egvdvvihlasl 76 
                                    +vtGg+GF+G++ ++  +r+++ +ev  lD    + +p  l++++  ++  ++ gD+ d d ++    +g d+v+  a+ 
  gi|116754266|ref|YP_843384.1|   5 LVTGGCGFIGSNFIHYALREHDDWEVVNLDrltYAGNPANLSDIEGDERYRFVRGDIADRDLVDGLFrDGLDAVVNFAAE 84 
                                    69****************************766666777778888878888*************9873689********* PP

                      3Beta_HSD  77 vdvag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKalaEk 155
                                    + v    l    + + nv+GT+ +lea+++++v ++v+ S+ ev g       +++g  ++  +  ++++y+ sKa a+ 
  gi|116754266|ref|YP_843384.1|  85 THVDRsILDPSPFIDTNVRGTQVLLEAARNHDVGRFVHISTDEVYGS------VTEGRFTEDSPLRPNSPYAASKAAAD- 157
                                    **98846788889*********************************9......888999999999**********9885. PP

                      3Beta_HSD 156 lvlkaNgrtlkngg.rlyTcaLRpagiyGegd..kllvpllkqlaklglalfkigdeevlsdrvYvgNv 221
                                    l+ +a    ++ g   ++T   R++  yG+++  ++l pl+ + a  g+ l  +g+  ++ d+ Yv+  
  gi|116754266|ref|YP_843384.1| 158 LLCRAYH--ISYGVpVMVT---RSSNNYGPYQfpEKLIPLMIRNALAGMDLPVYGEGAQVRDWLYVEDN 221
                                    6677777..7888556665...********9765799999999999********************964 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 !   67.4   0.0   5.2e-22     1e-18       1     282 [.       2     315 ..       2     319 .. 0.79

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 5.2e-22
                                    EEEEEESTTSHHHHHHHHHCTT..TSEEEEEE-TT.....................T--TTSHHHHHHHHHHH--SEEEE CS
                  RmlD_sub_bind   1 mkilvtGanGqlGseLakqlae..eglevlaltre.....................eldltdaeavaellkeakpdvvvn 57 
                                    m++lvtG+ G +Gs+ ++ + +  +++ev+ l+r                      + d++d++ v+ l+++   d+vvn
  gi|116754266|ref|YP_843384.1|   2 MRLLVTGGCGFIGSNFIHYALRehDDWEVVNLDRLtyagnpanlsdiegderyrfvRGDIADRDLVDGLFRD-GLDAVVN 80 
                                    89**************98775534789*****9999************************************.899**** PP

                                    ------HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-.EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHH CS
                  RmlD_sub_bind  58 aAAytavDkaEseeeaayavnaeavealAeaaaavga.lLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqav 136
                                     AA t vD+   ++      n+++++ l eaa+++++  ++h+StD V+   ++  ++ed++  P + Y+++K+a     
  gi|116754266|ref|YP_843384.1|  81 FAAETHVDRSILDPSPFIDTNVRGTQVLLEAARNHDVgRFVHISTDEVYGSVTEGRFTEDSPLRPNSPYAASKAAADLLC 160
                                    ************************************867***************************************99 PP

                                    HH....H-SSEEEEEE-SEESS..SSS-HHHHHHHHHHH-SEEEEESS..-EE--EEHHHHHHHHHHHHHHCHH.GGG-E CS
                  RmlD_sub_bind 137 la....agkkalivRtswvyge..kgknfvktmlrlakereelkvvaD..qlgsPTsardlAevllqllekaaeekelag 208
                                    +a    +g  +++ R s  yg     + ++  m+r a     l v     q++   +++d  +++  +l k        +
  gi|116754266|ref|YP_843384.1| 161 RAyhisYGVPVMVTRSSNNYGPyqFPEKLIPLMIRNALAGMDLPVYGEgaQVRDWLYVEDNCRAIGVVLMKGRP----GE 236
                                    99665566678999999999973345778888888887777777764322666666666666666666666654....66 PP

                                    EEE---BS-EEHHHHHHHHHHHHCHTT.....SEEEEE-CCCS--SS---SBE-B--HHHHHCCT----BHHHHHHHHH CS
                  RmlD_sub_bind 209 vyHlanegetswlefArailkeagads.....eevkpistaeyptpAkRPanSvLdtekleatfgiklrewrealkevl 282
                                    +y +++  e    e+ + i + +g++         + i++   p+ A    + +L+++k++  + ++  +++++l++++
  gi|116754266|ref|YP_843384.1| 237 IYNIGGGSERRNIEVVEMICRVLGERLnrdpeDFKRLIKHIRDPRGAAHDFRYALECSKMRGLGWMPQVTFEDGLARTV 315
                                    6666666666666666666666555444444322233555566666666666666666666666666666666666665 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.2   0.0   2.8e-18   5.6e-15       1     253 [.       4     265 ..       4     279 .. 0.80

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 2.8e-18
                                    EEEETTTSHHHHHHHHHHHHH.B-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-S CS
                Polysacc_synt_2   1 vlvtGagGsiGselvrqilkk.kpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvd 79 
                                    +lvtG+ G iGs++++  l++ +  +++ l+r  ++    + +  +   ++++++      gd++d++ ++ +++  + d
  gi|116754266|ref|YP_843384.1|   4 LLVTGGCGFIGSNFIHYALREhDDWEVVNLDRLTYAGNPANLS--DIEGDERYRFV----RGDIADRDLVDGLFR-DGLD 76 
                                    59**************999985677888888877766655544..34455566555....8**************.9*** PP

                                    EEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGGG..............SS--SHHHHHHHHH CS
                Polysacc_synt_2  80 vvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStDKA..............vnPtnvmGatKrla 145
                                    +v++ AA  hV      p   i+tNv gt+ ++eaa +++v ++v iStD                 +P + + a+K++a
  gi|116754266|ref|YP_843384.1|  77 AVVNFAAETHVDRSILDPSPFIDTNVRGTQVLLEAARNHDVGRFVHISTDEVygsvtegrftedspLRPNSPYAASKAAA 156
                                    *************************************************9863332233332332357899999999999 PP

                                    HHHHHHGGG--SSS--EEEEEEE-EETTGT...TSSHHHHHHHHHTTSSEEES-T.T-EEEEE-HHHHHHHHHHHHHH-- CS
                Polysacc_synt_2 146 ekllqalakeseekktkfvvvRfGNVlgSr...GSviplFkkqikeggpvtvTdp.emtRyfmtieeavqLvlqalalak 221
                                    ++l+ a++ +       ++v+R  N  g       +ipl  +   +g +++v  +   +R ++ +e+ ++ +   l +++
  gi|116754266|ref|YP_843384.1| 157 DLLCRAYHISY---GVPVMVTRSSNNYGPYqfpEKLIPLMIRNALAGMDLPVYGEgAQVRDWLYVEDNCRAIGVVLMKGR 233
                                    99999998887...788999998888886522257999999999999999996541668999999999999999999999 PP

                                    SS-EEEE--.-EEEHHHHHHHH.......... CS
                Polysacc_synt_2 222 ggeifvldmGepvkivdlakalielsgleekk 253
                                     gei+    G   + +++++ ++++ g + ++
  gi|116754266|ref|YP_843384.1| 234 PGEIYNIGGGSERRNIEVVEMICRVLGERLNR 265
                                    99999988888888888888888888766554 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   0.0   1.4e-16   2.9e-13       1     205 [.       6     178 ..       6     188 .. 0.82

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 1.4e-16
                                    EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHHHHHHHHHHT-SS-HHHHHHHHHTTTEEEEE--TTSGGGG--HHH CS
                  NAD_binding_4   1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksgesaeeRleeelekkelfsallkelaerikvveGDlseprlGLseed 80 
                                    +TG+ GF+G+ +++  Lr++++ +++           ++Rl+ +    +l + +     er ++v GD+++ +l   +  
  gi|116754266|ref|YP_843384.1|   6 VTGGCGFIGSNFIHYALREHDDWEVVN----------LDRLTYAGNPANLSDIE---GDERYRFVRGDIADRDL--VDGL 70 
                                    7*******************9866665..........46775555555555555...599***********995..5555 PP

                                    HHHHHHH--EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H.... CS
                  NAD_binding_4  81 lqelaeevdviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegek 157
                                    ++   + +d++++ aA +++d+++ +   ++++Nv+Gt+ +le a++      ++h+ST  v+g  +             
  gi|116754266|ref|YP_843384.1|  71 FR---DGLDAVVNFAAETHVDRSILDpspFIDTNVRGTQVLLEAARNHDVG-RFVHISTDEVYGSVT------------- 133
                                    55...669**************87665559****************99999.*******55555554............. PP

                                    ..HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-E CS
                  NAD_binding_4 158 eekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsi 205
                                       +   ++++    +  Y  sKa+a+ l+r+++ + g+pv++ R s+
  gi|116754266|ref|YP_843384.1| 134 ---EGRFTEDSPLRPNSPYAASKAAADLLCRAYHISYGVPVMVTRSSN 178
                                    ...223456677777789***************************986 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.0   7.3e-13   1.5e-09       1     137 [.       8     166 ..       8     171 .. 0.79

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 7.3e-13
                                    TTTSHHHHHHHHHHHHC-.T-EEEEEET.....THHHCHHHHCTTTCEEEE--TT-CCHHHHHHT.T-SEEEES---TCC CS
                 NAD_binding_10   1 GAtGkvGrllvkellarg.ghevtalvR.....npeklaeleaeeglevvegdvtdvedlaealk.gadaVvsalggggk 73 
                                    G+ G +G+  ++ +l+++ ++ev+ l R     np+ l+++e +e+ + v gd+ d + +   ++ g daVv  ++ ++ 
  gi|116754266|ref|YP_843384.1|   8 GGCGFIGSNFIHYALREHdDWEVVNLDRltyagNPANLSDIEGDERYRFVRGDIADRDLVDGLFRdGLDAVVNFAAETHV 87 
                                    889**************99999988766555558******************************6589**9988877777 PP

                                    HHHH.............HHHHHHHHHHCT--EEEEEEETTTTSGCGCH.HHHHHH.HCCHHHHHHHHHHHHHHHHSSSE CS
                 NAD_binding_10  74 deeg.............aknivdaakeagvkRfvlvsaigvgdevpge.fgewnk.ellkaylaakraaeellrasgld 137
                                    d+ +             ++ +++aa++++v Rfv +s+  v+ +v +  f e    +  ++y+a k+aa+ l ra ++ 
  gi|116754266|ref|YP_843384.1|  88 DRSIldpspfidtnvrgTQVLLEAARNHDVGRFVHISTDEVYGSVTEGrFTEDSPlRPNSPYAASKAAADLLCRAYHIS 166
                                    54555556666666688************************99776541444333123367777788888777776655 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 ?   12.5   0.0   6.8e-05      0.14       5      80 ..       9      85 ..       4      93 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.8e-05
                                   --SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH....TTTCEEEEE--TTTHHHHHHHHHTTS.SEEEE-SSGG CS
                Sacchrp_dh_NADP  5 GaGsvGqavaellarhfdvdaeitvadrskeklealaaka....lgvrfeaialdaenyeavLaallkeg.dlvvnlsppi 80
                                   G+G++G+ ++++ +r++d   e++  dr     +   a++      +r  ++  d+++++  ++ l ++g d+vvn +  +
  gi|116754266|ref|YP_843384.1|  9 GCGFIGSNFIHYALREHDDW-EVVNLDR--LTYAGNPANLsdieGDERYRFVRGDIADRDL-VDGLFRDGlDAVVNFAAET 85
                                   67*************99962.5555555..444444444445579999**********998.**************98766 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0    0.0004       0.8       4     163 ..       5     163 ..       3     174 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0004
                                    EEESTTSHHHHHHHHHHHHT..T-EEEEEESCHHHHHHHHHHHHHT..TSEEEEEE-TTTSHHHHHHHHHHHHHHHSSES CS
                      adh_short   4 lvtGassGIGraiakelake..Gakvvvvdrseekleevakelkee..gakalaiqvDvtdreevealvekavkklgkld 79 
                                    lvtG+++ IG ++ +  ++e  +++vv +dr     +   ++l +    +++ ++++D++dr+ v+ l+++      +ld
  gi|116754266|ref|YP_843384.1|   5 LVTGGCGFIGSNFIHYALREhdDWEVVNLDRLTY--AGNPANLSDIegDERYRFVRGDIADRDLVDGLFRD------GLD 76 
                                    7999999999998888887622455555666544..44555555555467899999999999999888886......599 PP

                                    EEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEE......EG.GG....TSB-TTBHH CS
                      adh_short  80 vLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvs......Sv.ag....kvpvagvaa 148
                                    ++vn A+ t      + s  +    i++N+ g+  l +a+ ++      Gr v +s      Sv  g      p+   ++
  gi|116754266|ref|YP_843384.1|  77 AVVNFAAET----HVDRSILDPSPFIDTNVRGTQVLLEAARNH----DVGRFVHIStdevygSVtEGrfteDSPLRPNSP 148
                                    999988883....223333344556889988888877777666....677777776222222221222111345666789 PP

                                    HHHHHHHHHHHHHHH CS
                      adh_short 149 YsAsKaavagltrsl 163
                                    Y+AsKaa + l r+ 
  gi|116754266|ref|YP_843384.1| 149 YAASKAAADLLCRAY 163
                                    999999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       264  (0.0147247); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 2737.63
//
Query:       gi|116754267|ref|YP_843385.1|  [L=72]
Description: hypothetical protein Mthe_0957 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 536.26
//
Query:       gi|116754268|ref|YP_843386.1|  [L=517]
Description: polysaccharide biosynthesis protein [Methanosaeta thermophila PT]
Scores for 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-14   51.5  24.5    9.1e-14   51.5  24.5    3.0  3  Polysacc_synt    Polysaccharide biosynthesis protein
    8.4e-06   25.2  13.6    8.4e-06   25.2  13.6    3.3  3  Polysacc_synt_3  Polysaccharide biosynthesis protein


Domain annotation for each model (and alignments):
>> Polysacc_synt  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.5  24.5     1e-17   9.1e-14       9     270 ..      25     299 ..      17     303 .. 0.81
   2 ?   -0.9   5.2     0.094   8.4e+02      70     202 ..     310     448 ..     296     451 .. 0.66
   3 ?   -3.1   7.8      0.44     4e+03     115     192 ..     417     496 ..     410     515 .. 0.65

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 1e-17
                  Polysacc_synt   9 llsqlitkllafvtlvylarilgpegfGlvalalaivtllviltdlGlnaalvreiakyrek..kelvslillnvllvll 86 
                                    ++  l++  ++++ ++y+  +lg   +Gl  la++i+++  i++++ ln+a++r+   + ++  +   +++++ +l++l+
  gi|116754268|ref|YP_843386.1|  25 IVYFLANIVIGILLVPYFIKTLGVGAYGLIPLATSITGYVAIIVQS-LNTAVSRFLTINLQQedYVAANKTFNTALFGLT 103
                                    44455555679*********************************96.*********999998889999************ PP

                  Polysacc_synt  87 vlvllfllllliaa..........flglpelavlylilalmllllvgvasfrrglf..qglermkyaavsqvveqlsrvi 154
                                    v++ll++   li a            +++ +++l+l   +++l+     sf ++lf  ++l  ++ + ++++v q++ + 
  gi|116754268|ref|YP_843386.1| 104 VVILLMIPVILIIAyfapllfhvpAGQETGAVLLLLGVLAAFLIRSWSGSFTVQLFayNRLDLQNLVNITNLVVQTGLI- 182
                                    ******9999998889999766655555556666666666666666666666666633455555555555555555555. PP

                  Polysacc_synt 155 lvliavflfld.ivaavlgavlaalvggivslavlrkkf.r..prfvilslklvrellsfsapltisslaillytyidsi 230
                                      +i++ l ++ +  ++++++++alv++ vs+++ r    +  ++   ++++ +r+l  ++++++++ ++ ll+ +id i
  gi|116754268|ref|YP_843386.1| 183 --IILFKLLGPdLGLVGGAYLVGALVASGVSIILARQVCpHlrVSIRYFDRRAIRDLCEMGWWVVVNNIGALLFLQIDLI 260
                                    ..444444444599999999999999999999999977774458888888****************************** PP

                  Polysacc_synt 231 llglllgaeavGiYnaayqllvaisgllapivtaalfPvf 270
                                    +  ll ga+++G+Y  a q ++ +   + +  + +l P +
  gi|116754268|ref|YP_843386.1| 261 VVNLLFGATSAGEYAIALQWSSFLRAMAGMLSG-VLAPSI 299
                                    *******************99999888888888.888865 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.094
                  Polysacc_synt  70 k..kelvslillnvllvllvlvllfllllliaaflglpelavlylilalmllllvgvasfrrglfq..glerm...kyaa 142
                                    +  + + s  +l+ l + l   l++ +++ + ++  + e+a+l++++ l  + l+++ ++   ++    ++r      ++
  gi|116754268|ref|YP_843386.1| 310 TliRATKSAVKLMGLAMALPIGLVCGFAPELLTIWVGDEFAFLWPLIVLLTVHLTINLAVLPIFLIniSHNRVrvpGIVT 389
                                    255678888999999999999999999999999************99999994444444443333301233321114556 PP

                  Polysacc_synt 143 vsqvveqlsrvilvliavflfldivaavlgavlaalvggivslavlrkkfrprfvilslk 202
                                    + + + + + ++ + +++ +++ + +a++ga + +l ++++  ++ ++ +r+  +++s++
  gi|116754268|ref|YP_843386.1| 390 LFMGIGNFGLAVSLPLLTGMGY-YGVAAAGAIVLTLKNAFFIPWYATRVLRVASHTFSRS 448
                                    6666666666554444444444.7788888888888888888888887777777777665 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 0.44
                  Polysacc_synt 115 almllllvgvasfrrglfqglermky.aavsqvveqlsrvilvliavflfld.ivaavlgavlaalvggivslavlrkkf 192
                                    a +++l + +a f+ ++ +++ r  + +++++++  ++ ++l++i   l +  i+  v  a ++a +++i++ a+  +++
  gi|116754268|ref|YP_843386.1| 417 AGAIVLTLKNAFFIPWYATRVLRVAShTFSRSMIPGITATVLIAISAALLGEvITFPVTLAIASAAITSIYFVAIWIFAL 496
                                    55566677777777777777777654155666778899999999999999996555555566666667777777766444 PP

>> Polysacc_synt_3  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   4.1     0.024   2.1e+02     131     280 ..      55     124 ..      18     132 .. 0.52
   2 !   25.2  13.6   9.4e-10   8.4e-06      10     288 ..      50     349 ..      46     353 .. 0.62
   3 ?   -1.4   1.4      0.12   1.1e+03      48      90 ..     442     484 ..     435     510 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.024
                Polysacc_synt_3 131 vlAllglgvwALvigtllssllslvllwlaskwrprlkfslkslkelfsfglklllsnllnylarnldnlliGkvlssaa 210
                                     lA  + g                                                                        
  gi|116754268|ref|YP_843386.1|  55 PLATSITG------------------------------------------------------------------------ 62 
                                    22222233........................................................................ PP

                Polysacc_synt_3 211 LGlYsvakrlaslpvaeitsviakVlfPalSrlqddkkklrelylkvl...rlialivlPiavglavvaellv 280
                                             ++ ++v+ +++++++ l  ++   q+d  + +++++++l    ++ l+++P++ ++a++a ll 
  gi|116754268|ref|YP_843386.1|  63 ---------YVAIIVQSLNTAVSRFL--TINLQQEDYVAANKTFNTALfglTVVILLMIPVILIIAYFAPLLF 124
                                    .........33444555555555544..445566666666666666542224555666777777777777665 PP

  == domain 2  score: 25.2 bits;  conditional E-value: 9.4e-10
                Polysacc_synt_3  10 dFGvvaialvvislanlfvdm...Glssal...iqkedltee...dlstvftfnlvlgll..ialvlfllapliasfynq 78 
                                    ++G++ +a+ +++ + ++v++    +s++l   +q+ed  ++     + +f +++v+ l+  + l+++++apl+  +   
  gi|116754268|ref|YP_843386.1|  50 AYGLIPLATSITGYVAIIVQSlntAVSRFLtinLQQEDYVAAnktFNTALFGLTVVILLMipVILIIAYFAPLLFHVPAG 129
                                    67888888888877777776522233333332245554433323133445655554444411466777888888888888 PP

                Polysacc_synt_3  79 pelvtvlrvlal..vlilsglssvqeallrrelkFkklfkitlvssvvg.....vivaivlAllglgvwALvigtllssl 151
                                    +e   vl +l++   +++++ s   + +l    + + +  ++++  vv+     +++ ++   lgl   A ++g l++s 
  gi|116754268|ref|YP_843386.1| 130 QETGAVLLLLGVlaAFLIRSWSGSFTVQLFAYNRLDLQNLVNITNLVVQtgliiILFKLLGPDLGLVGGAYLVGALVASG 209
                                    88888888877622355555443333333333333333333344444441000022222222333334577888888888 PP

                Polysacc_synt_3 152 lslvllwlaskwr.prl.kfslkslkelfsfglklllsnllnylarnldnlliGkvlssaaLGlYsvakrlaslpva... 226
                                    +s++l   ++++  +++  f+++++++l + g++++++n+   l+ ++d +++  ++++++ G Y++a +++s++ a   
  gi|116754268|ref|YP_843386.1| 210 VSIILARQVCPHLrVSIrYFDRRAIRDLCEMGWWVVVNNIGALLFLQIDLIVVNLLFGATSAGEYAIALQWSSFLRAmag 289
                                    88888888877633433149**************************************************9887654111 PP

                Polysacc_synt_3 227 eitsviakVlfPalSrlqddkkklrelylkvlrlial.ivlPiavglavvaellvkvllGsqW 288
                                    +++ v+a+ +++ ++r q +   l ++++ +++l++l ++lPi  +++ +a +l+++  G+++
  gi|116754268|ref|YP_843386.1| 290 MLSGVLAPSIISCYARRQTE--TLIRATKSAVKLMGLaMALPIG-LVCGFAPELLTIWVGDEF 349
                                    45566666666666666655..8999999999999872467876.467788888888888876 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.12
                Polysacc_synt_3  48 stvftfnlvlgllialvlfllapliasfynqpelvtvlrvlal 90 
                                    s  f  +++ g+ ++++++++a l+ +++  p    + + +  
  gi|116754268|ref|YP_843386.1| 442 SHTFSRSMIPGITATVLIAISAALLGEVITFPVTLAIASAAIT 484
                                    5567777788888888888888887777766665555544443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (517 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       983  (0.0548274); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.44
# Mc/sec: 3557.46
//
Query:       gi|116754269|ref|YP_843387.1|  [L=453]
Description: 4Fe-4S ferredoxin iron-sulfur binding domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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-30  105.4   0.0    3.9e-30  104.7   0.0    1.2  1  FrhB_FdhB_C  Coenzyme F420 hydrogenase/dehydrogenase, beta su
    1.1e-13   51.1   0.0    1.9e-13   50.4   0.0    1.4  1  FrhB_FdhB_N  Coenzyme F420 hydrogenase/dehydrogenase, beta su
    8.1e-08   31.8  14.5    3.8e-06   26.5   1.8    2.9  3  Fer4         4Fe-4S binding domain
    4.7e-06   27.1   7.2    4.7e-06   27.1   7.2    2.8  3  Fer4_7       4Fe-4S dicluster domain
    1.2e-05   25.4   6.6    1.2e-05   25.4   6.6    2.2  2  Fer4_9       4Fe-4S dicluster domain
    5.7e-05   23.0   8.7    0.00025   21.0   0.6    2.9  2  Fer4_6       4Fe-4S binding domain
    6.8e-05   22.9  14.8      0.011   15.8   1.3    3.0  3  Fer4_10      4Fe-4S dicluster domain
     0.0001   22.3   9.6     0.0001   22.3   9.6    2.5  2  Fer4_21      4Fe-4S dicluster domain
    0.00093   19.7  12.1     0.0071   16.9   0.6    3.0  3  Fer4_17      4Fe-4S dicluster domain
     0.0064   16.9  12.0       0.29   11.6   1.3    3.0  3  Fer4_8       4Fe-4S dicluster domain
     0.0067   16.5   2.3     0.0067   16.5   2.3    3.2  3  Fer4_2       4Fe-4S binding domain
  ------ inclusion threshold ------
      0.016   15.7   1.4      0.016   15.7   1.4    2.9  2  Fer4_4       4Fe-4S binding domain
      0.022   15.6   0.5      0.022   15.6   0.5    2.9  3  Fer4_22      4Fe-4S dicluster domain
      0.058   14.3   0.8      0.058   14.3   0.8    2.9  2  Fer4_16      4Fe-4S double cluster binding domain
      0.086   13.6   0.9      0.086   13.6   0.9    2.4  2  Fer4_15      4Fe-4S single cluster domain
       0.53   10.9   8.5       0.19   12.3   1.7    2.5  2  Fer4_13      4Fe-4S single cluster domain of Ferredoxin I
       0.98   10.5  25.1       0.28   12.2   4.1    3.1  2  Fer4_3       4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> FrhB_FdhB_C  Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.7   0.0   3.7e-33   3.9e-30       3     140 ..     178     332 ..     177     342 .. 0.85

  Alignments for each domain:
  == domain 1  score: 104.7 bits;  conditional E-value: 3.7e-33
                    FrhB_FdhB_C   3 kvavvGtPCqiaalrklqk..kklkekilltiglfCggnfspealrklleelgvdpedvkklefr.........gkgkfr 71 
                                    ++a++G+PC i+a+r +q+  kkl+e+i++tigl+Cg+ +s+++++ ++   gv+  +v ++++r         + ++++
  gi|116754269|ref|YP_843387.1| 178 RYAITGLPCFIKAIRLAQRqnKKLQERIVVTIGLVCGQLKSRHFTDYVAAIAGVQG-SVMRVRYRgkspdqpasN-YHYT 255
                                    89****************99*9*******************************996.9*******9999888643.4444 PP

                    FrhB_FdhB_C  72 velkd........ekeislk.eleefirpsCkvCkdktaelADisvGdvwgpekkgdddegvstvlvrtekgeellek 140
                                     + +d        + +is +   ++f++++C++C+d +ae+AD++++d+w+pe++ +d++g+s+vlvr+   +e+le+
  gi|116754269|ref|YP_843387.1| 256 FTISDggerkifwSDGISEAwINRWFTPKACNYCDDIFAECADVTCMDAWLPEYS-QDSRGTSLVLVRSPVVREVLER 332
                                    4445566654444334444444444******************************.7*****************9985 PP

>> FrhB_FdhB_N  Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   0.0   1.8e-16   1.9e-13       2      76 ..      95     168 ..      94     170 .. 0.95

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 1.8e-16
                    FrhB_FdhB_N   2 vaArstdkeirkkaqsGGivtallkylLeegiidgvivvapskdpwr.pkpviattkeellaaaGskYtlspnlkl 76 
                                    ++++s+++  r+ ++sGG++t+ll+ lL eg  d+vi+v p+ dp r +  ++   + e+ a aGs Y++++++ +
  gi|116754269|ref|YP_843387.1|  95 YVGYSKKH--RPISASGGVATWLLETLLSEGVADYVICVVPTGDPDRlFAFRVFDAPGEVHAGAGSAYYPVEMSRA 168
                                    899**999..********************************889998************************9987 PP

>> Fer4  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   3.6e-09   3.8e-06       3      23 ..      10      30 ..       9      31 .. 0.89
   2 !   13.0   1.6   6.4e-05     0.067      11      20 ..      52      61 ..      50      62 .. 0.91
   3 ?   -2.1   0.1       3.7   3.9e+03       6      11 ..     284     289 ..     281     290 .. 0.69

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 3.6e-09
                                   EETTTSSS-THHHHHSTTTEE CS
                           Fer4  3 ideekCigCGaCvevCPvgAI 23
                                   + +++CigCG+C+  CP + +
  gi|116754269|ref|YP_843387.1| 10 VKTDLCIGCGLCAALCPQNIL 30
                                   5689*************9976 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 6.4e-05
                                   -THHHHHSTT CS
                           Fer4 11 CGaCvevCPv 20
                                   CG+C++vCP+
  gi|116754269|ref|YP_843387.1| 52 CGLCMKVCPF 61
                                   *********7 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 3.7
                                    TTSSS- CS
                           Fer4   6 ekCigC 11 
                                      C +C
  gi|116754269|ref|YP_843387.1| 284 KACNYC 289
                                    567777 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   7.2   4.5e-09   4.7e-06       2      50 ..      15      61 ..      14      62 .. 0.81
   2 ?   -0.6   0.0       2.1   2.2e+03      12      32 ..     186     206 ..     185     220 .. 0.81
   3 ?   -1.0   0.3       2.6   2.7e+03      37      43 ..     285     291 ..     276     315 .. 0.70

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 4.5e-09
                         Fer4_7  2 CigCgaCvaaCpvkaieldeeenekgtekveidpekCl.gCgaCvavCPt 50
                                   CigCg C+a Cp++ + ++     +  ++  ++ + Cl  Cg C++vCP+
  gi|116754269|ref|YP_843387.1| 15 CIGCGLCAALCPQNILVMQWN---RYGMYNPVEVSPCLkECGLCMKVCPF 61
                                   **************9999875...333445577899*736*********7 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.1
                         Fer4_7  12 Cpvkaieldeeenekgtekve 32 
                                    C  kai+l +++n+k +e+++
  gi|116754269|ref|YP_843387.1| 186 CFIKAIRLAQRQNKKLQERIV 206
                                    8899*******9999766654 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 2.6
                         Fer4_7  37 kClgCga 43 
                                     C +C+ 
  gi|116754269|ref|YP_843387.1| 285 ACNYCDD 291
                                    5555553 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   6.6   1.1e-08   1.2e-05       2      47 ..      15      60 ..      14      63 .. 0.88
   2 ?   -0.4   0.2       1.2   1.3e+03      34      42 ..     284     296 ..     260     311 .. 0.66

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1.1e-08
                         Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraaseeaC.igCgaCveaCp 47
                                   C+gCg C + Cp+++ v++++++ + +  +  + C  +Cg C+++Cp
  gi|116754269|ref|YP_843387.1| 15 CIGCGLCAALCPQNILVMQWNRYGMYNPVE-VSPClKECGLCMKVCP 60
                                   ********************9999997654.458*667********9 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.2
                         Fer4_9  34 eaCigCga....C 42 
                                    +aC  C +    C
  gi|116754269|ref|YP_843387.1| 284 KACNYCDDifaeC 296
                                    4555555533333 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   0.6   2.4e-07   0.00025       3      23 ..       9      29 ..       7      30 .. 0.89
   2 !   14.1   2.1   3.6e-05     0.038       7      21 ..      46      61 ..      43      66 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.4e-07
                         Fer4_6  3 eidpdkCigCgdCvrvCPega 23
                                   +++ d+CigCg C++ CP ++
  gi|116754269|ref|YP_843387.1|  9 TVKTDLCIGCGLCAALCPQNI 29
                                   8999**************765 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 3.6e-05
                         Fer4_6  7 dkCi.gCgdCvrvCPe 21
                                   ++C+  Cg C++vCP+
  gi|116754269|ref|YP_843387.1| 46 SPCLkECGLCMKVCPF 61
                                   789846*********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 !   15.8   1.3     1e-05     0.011       5      23 ..      11      29 ..       8      46 .. 0.76
   2 !   15.6   1.2   1.2e-05     0.013       7      36 ..      46      73 ..      41      81 .. 0.71
   3 ?   -1.0   0.3       1.9     2e+03       8      51 ..     285     296 ..     274     315 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1e-05
                        Fer4_10  5 dddtCirCgkCvkaCPadl 23
                                    +d Ci+Cg C + CP+++
  gi|116754269|ref|YP_843387.1| 11 KTDLCIGCGLCAALCPQNI 29
                                   5789************976 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1.2e-05
                        Fer4_10  7 dtCi.rCgkCvkaCPadltsvgakgeaseee 36
                                   + C+ +Cg C+k+CP+   +++ ++e+++++
  gi|116754269|ref|YP_843387.1| 46 SPCLkECGLCMKVCPF---ADSEENEDTIGK 73
                                   568549**********...555555555554 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.9
                        Fer4_10   8 tCirCg....kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaC 51 
                                     C  C     +                                    C
  gi|116754269|ref|YP_843387.1| 285 ACNYCDdifaE------------------------------------C 296
                                    33333322222....................................3 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   9.6   9.8e-08    0.0001       3      55 ..      10      63 ..       8      65 .. 0.74
   2 ?   -1.5   0.6       2.8   2.9e+03       7      20 ..     285     298 ..     281     312 .. 0.69

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 9.8e-08
                        Fer4_21  3 idedkCigCgkCliaCedtshqaieidakt...vlkvvedeCv.GCnlCssvCPved 55
                                   ++ d CigCg+C+  C++   + + ++ ++   + +v  + C   C lC++vCP  d
  gi|116754269|ref|YP_843387.1| 10 VKTDLCIGCGLCAALCPQ---NILVMQWNRygmYNPVEVSPCLkECGLCMKVCPFAD 63
                                   7899*************4...333444443222557778999637*********865 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.8
                        Fer4_21   7 kCigCgkCliaCed 20 
                                     C  C   +  C d
  gi|116754269|ref|YP_843387.1| 285 ACNYCDDIFAECAD 298
                                    56667777777776 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.6   6.8e-06    0.0071      42      60 ..      11      29 ..       4      30 .. 0.88
   2 !   10.1   0.2   0.00088      0.93       4      21 ..      51      68 ..      48      94 .. 0.75
   3 ?   -2.0   0.8       5.2   5.4e+03       5      13 ..     286     297 ..     284     313 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.8e-06
                        Fer4_17 42 kaslCieCgeCerkCPqgl 60
                                   k +lCi+Cg+C++ CPq++
  gi|116754269|ref|YP_843387.1| 11 KTDLCIGCGLCAALCPQNI 29
                                   6789************997 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00088
                        Fer4_17  4 qCgyClpeCpsyeaydne 21
                                   +Cg C+++Cp+    +ne
  gi|116754269|ref|YP_843387.1| 51 ECGLCMKVCPFADSEENE 68
                                   7*********98876664 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 5.2
                        Fer4_17   5 CgyClp...eCp 13 
                                    C yC +   eC 
  gi|116754269|ref|YP_843387.1| 286 CNYCDDifaECA 297
                                    777776555554 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   0.00028      0.29       4      17 ..      14      30 ..      11      46 .. 0.70
   2 !   11.0   1.0   0.00044      0.46       7      23 ..      51      67 ..      44      97 .. 0.81
   3 ?   -0.9   0.1       2.2   2.3e+03       5      16 ..     286     297 ..     283     346 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00028
                         Fer4_8  4 kCieCgaCqsaCp...v 17
                                    Ci+Cg+C + Cp   +
  gi|116754269|ref|YP_843387.1| 14 LCIGCGLCAALCPqniL 30
                                   58888888888875443 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00044
                         Fer4_8  7 eCgaCqsaCpvlrrtkk 23
                                   eCg+C++ Cp++ ++ +
  gi|116754269|ref|YP_843387.1| 51 ECGLCMKVCPFADSEEN 67
                                   8*********9887664 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 2.2
                         Fer4_8   5 CieCgaCqsaCp 16 
                                    C+ C   +++C 
  gi|116754269|ref|YP_843387.1| 286 CNYCDDIFAECA 297
                                    555544446664 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   2.3   6.4e-06    0.0067       5      22 .]      10      27 ..       9      27 .. 0.89
   2 !   10.3   2.6   0.00059      0.62       9      21 ..      47      60 ..      42      61 .. 0.82
   3 ?   -1.6   1.6       3.6   3.8e+03       4      20 ..     280     301 ..     277     302 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.4e-06
                         Fer4_2  5 vdtdrCigCgaCvsaCPa 22
                                   v td CigCg C   CP+
  gi|116754269|ref|YP_843387.1| 10 VKTDLCIGCGLCAALCPQ 27
                                   679*********999**6 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00059
                         Fer4_2  9 rCi.gCgaCvsaCP 21
                                    C+ +Cg C ++CP
  gi|116754269|ref|YP_843387.1| 47 PCLkECGLCMKVCP 60
                                   59659********* PP

  == domain 3  score: -1.6 bits;  conditional E-value: 3.6
                         Fer4_2   4 vvdtdrCigCg....aCvsa.C 20 
                                    ++ + +C+ C      C ++ C
  gi|116754269|ref|YP_843387.1| 280 WFTPKACNYCDdifaECADVtC 301
                                    6667788888555556766655 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   1.4   1.5e-05     0.016       2      17 .]      13      28 ..      12      28 .. 0.92
   2 ?    7.7   2.2    0.0055       5.8       4      16 ..      48      61 ..      45      66 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.5e-05
                         Fer4_4  2 erCigCgsCvaaCPqg 17
                                   + CigCg C a CPq+
  gi|116754269|ref|YP_843387.1| 13 DLCIGCGLCAALCPQN 28
                                   78************86 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0055
                         Fer4_4  4 Ci.gCgsCvaaCPq 16
                                   C+ +Cg C+ +CP+
  gi|116754269|ref|YP_843387.1| 48 CLkECGLCMKVCPF 61
                                   6559*********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 ?   15.6   0.5   2.1e-05     0.022      69      96 .]       2      29 ..       1      29 [. 0.90
   2 ?    4.3   0.1     0.069        73       2      24 ..      48      71 ..      47      95 .. 0.80
   3 ?   -2.2   0.4       7.4   7.8e+03       2      19 ..     286     303 ..     285     322 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.1e-05
                        Fer4_22 69 klsefkekfgesgCvGCgRCieacpvki 96
                                   kls + +++++  C+GCg C + cp++i
  gi|116754269|ref|YP_843387.1|  2 KLSVVSSTVKTDLCIGCGLCAALCPQNI 29
                                   7778888999***************987 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.069
                        Fer4_22  2 Cl.sCgaCtlvCptCsCfdvedet 24
                                   Cl +Cg C  vCp     + ed++
  gi|116754269|ref|YP_843387.1| 48 CLkECGLCMKVCPFADSEENEDTI 71
                                   553699******987766666665 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 7.4
                        Fer4_22   2 ClsCgaCtlvCptCsCfd 19 
                                    C  C    + C+  +C+d
  gi|116754269|ref|YP_843387.1| 286 CNYCDDIFAECADVTCMD 303
                                    445555555566556655 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   0.8   5.5e-05     0.058       2      20 ..      15      33 ..      14      42 .. 0.87
   2 ?    8.0   2.5    0.0051       5.3      55      66 ..      50      61 ..      39      62 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.5e-05
                        Fer4_16  2 CgtCgkCaevCPtnaikek 20
                                   C++Cg Ca  CP+n + ++
  gi|116754269|ref|YP_843387.1| 15 CIGCGLCAALCPQNILVMQ 33
                                   **************99876 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0051
                        Fer4_16 55 tgCdiCqdvCPa 66
                                   + C+ C++vCP+
  gi|116754269|ref|YP_843387.1| 50 KECGLCMKVCPF 61
                                   678888888887 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 ?   13.6   0.9   8.2e-05     0.086       5      21 ..      12      28 ..       9      32 .. 0.86
   2 ?   -1.0   0.4         3   3.2e+03      11      22 ..      52      61 ..      48      74 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.2e-05
                        Fer4_15  5 rdaCigcglCvaeapev 21
                                    d+CigcglC+a++p+ 
  gi|116754269|ref|YP_843387.1| 12 TDLCIGCGLCAALCPQN 28
                                   79************975 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3
                        Fer4_15 11 cglCvaeapevf 22
                                   cglC++++p  f
  gi|116754269|ref|YP_843387.1| 52 CGLCMKVCP--F 61
                                   999999998..3 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.7   0.00018      0.19       4      18 ..      13      27 ..      10      28 .. 0.88
   2 ?    1.9   0.7      0.33   3.4e+02       8      17 ..      51      60 ..      43      71 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00018
                        Fer4_13  4 dtCiacgaCvelaPd 18
                                   d Ci+cg+C++l+P+
  gi|116754269|ref|YP_843387.1| 13 DLCIGCGLCAALCPQ 27
                                   78************7 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.33
                        Fer4_13  8 acgaCvelaP 17
                                   +cg+C +++P
  gi|116754269|ref|YP_843387.1| 51 ECGLCMKVCP 60
                                   6********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 ?   12.2   4.1   0.00026      0.28       1      14 [.      15      28 ..      15      29 .. 0.94
   2 ?   12.0   3.5   0.00032      0.33       1      12 [.      48      60 ..      48      63 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00026
                         Fer4_3  1 CtgCgaCvevCPvg 14
                                   C+gCg+C   CP +
  gi|116754269|ref|YP_843387.1| 15 CIGCGLCAALCPQN 28
                                   ************87 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00032
                         Fer4_3  1 Ct.gCgaCvevCP 12
                                   C+  Cg+C++vCP
  gi|116754269|ref|YP_843387.1| 48 CLkECGLCMKVCP 60
                                   6537********* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); 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: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 3248.12
//
Query:       gi|116754270|ref|YP_843388.1|  [L=418]
Description: polysaccharide pyruvyl transferase [Methanosaeta thermophila PT]
Scores for 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-45  154.4   0.2      7e-45  154.1   0.2    1.0  1  PS_pyruv_trans  Polysaccharide pyruvyl transferase


Domain annotation for each model (and alignments):
>> PS_pyruv_trans  Polysaccharide pyruvyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.1   0.2   3.9e-49     7e-45       1     285 [.      18     347 ..      18     348 .. 0.91

  Alignments for each domain:
  == domain 1  score: 154.1 bits;  conditional E-value: 3.9e-49
                                    -HHHHHHHHHHHHHHHHTT-EEEEEESSTTT--HHHHHHHHHTS-GGGEE.............................. CS
                 PS_pyruv_trans   1 NyGDelilealvklLrelgpdaeiivltpdpsetkkllkvktpilkklskvllkrlrkkdi................... 61 
                                    N G e+i+ ++vk+Lre++ d+ +i l++  ++ +++   ++   +++ + + ++l kk+                    
  gi|116754270|ref|YP_843388.1|  18 NRGCEAIVRGTVKILREHFKDPQFICLSHFQNDEQFRKQCLEESDPSITHLRSYILSKKKAiknfwkpgtwsyvyrhffn 97 
                                    89****************************************************************************** PP

                                    .....................EEE--E....EEEETT-HHH.HHHHHHHHHHS-SSEEEE-SEEE...-S-HHHHHHHHH CS
                 PS_pyruv_trans  62 ................ddaddviivGgdgtlgndgdlsrlp.dalrllflakkagkpviilgqgiGp.flnealrkllkk 123
                                                    dda+ v+ vGg     n+  ++  p  + +l+ +++ ++kp++++g+++Gp    ++++++++ 
  gi|116754270|ref|YP_843388.1|  98 rpalkyhiyrdmlshlDDAAAVLSVGG----DNYSLDYGVPqFFTDLDDIVLEKKKPLFLWGASVGPfSAIPEYERYMRH 173
                                    ***************************....8888888899999***********************999********** PP

                                    HHHHTTEEEESSHHHHH.HHHHHHTT-EEE---GGGGG---HHHHHHS-.........------------SS--EE---S CS
                 PS_pyruv_trans 124 ilakadlisvRdelSaelleslglkrnveltpDpaflleqlapseilet.........dkrkylrvakssekdledleel 194
                                     l+ ++ i++R+ l+ ++l+s g+++nv+ ++Dpafl+e+ +p++i+++         ++   l ++    +dle + + 
  gi|116754270|ref|YP_843388.1| 174 HLKEVTGIFARESLTINYLKSIGVTENVYSVADPAFLMEPVKPQGIDAKlpingeaigINLSPLMAKYVTNGDLEVWSSM 253
                                    ************************99*************************99999775555555666666888888888 PP

                                    SS---HH...................................HH-TTS-HHHHHHHHHHHHHHHHHTSSEEEE--HHHHH CS
                 PS_pyruv_trans 195 lakvydllle.kgarllllpivkkdglelddlyllllra...aakkekvtildrfaspeellsliaradfvitsRlHgli 270
                                    +a ++  +++  g  ++l+p+v  ++    ++y++ +r    ++ k +++i+++ ++++e +++i+r+ ++ + R+H++i
  gi|116754270|ref|YP_843388.1| 254 AASIIESVAQkTGLLIYLIPHVTQPNQ-FSNDYAFMQRVlsqIKDKYNIIIVPPVYNAAETKWIISRMTLFAGARMHSTI 332
                                    888888888855555555555555555.6666666666679999************************************ PP

                                    HHHHHT--EEEE--S CS
                 PS_pyruv_trans 271 falsfgvPvigisyd 285
                                    +a+s+gvP++ ++y+
  gi|116754270|ref|YP_843388.1| 333 AAISSGVPTLSFAYS 347
                                    *************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      580  (0.0323498); 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: 3061.08
//
Query:       gi|116754271|ref|YP_843389.1|  [L=302]
Description: glycosyl transferase family protein [Methanosaeta thermophila PT]
Scores for complete 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-40  136.7   0.1    8.6e-40  136.3   0.1    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
    5.1e-24   85.2   0.1    7.3e-24   84.7   0.1    1.1  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
    3.9e-22   79.3   0.0    5.8e-22   78.7   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    0.00051   20.5   0.1    0.00095   19.6   0.1    1.4  1  Glyco_tranf_2_4  Glycosyl transferase family 2
     0.0054   15.6   0.0     0.0073   15.1   0.0    1.2  1  GNT-I            GNT-I family
  ------ inclusion threshold ------
        0.1   12.5   0.1       0.19   11.7   0.1    1.4  1  Jacalin          Jacalin-like lectin domain


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.3   0.1   2.9e-43   8.6e-40       1     164 [.       5     162 ..       5     168 .. 0.77

  Alignments for each domain:
  == domain 1  score: 136.3 bits;  conditional E-value: 2.9e-43
                                    EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--S CS
                Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatg 80 
                                    sv+ ptyN+++ + ++++s+l+q +y+dfe+ivvDDgStD+t+e+++++   d r+r+ir+++n+G ++a+n+g++ a+g
  gi|116754271|ref|YP_843389.1|   5 SVILPTYNRAHVVGRAIRSVLEQ-TYEDFELIVVDDGSTDSTEEVVRSF--DDRRIRYIRHKQNKGRSAARNTGIKIAKG 81 
                                    8**********************.*************************..59*************************** PP

                                    SEEEEEESSEEE-TTHHHHHHHHHHH...TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTCSTCC CS
                Glycos_transf_2  81 dyilflDaDdepdpdwleklvealekd..gadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfeigsa 158
                                    +yi+f D+Dde+ p++le+ +e ++    +++ v+++ ++ f+++++i  ++     +   +  +   +  +  f+  +a
  gi|116754271|ref|YP_843389.1|  82 EYIAFQDSDDEWLPEKLEEQMEVFKTSspQVG-VVYTGFYLFYDDKKIYIPSA----NVKTKDGNIYDELLKGNFVGTPA 156
                                    ************************99832333.44444444444444443332....33333333333333444444455 PP

                                    CEEEEH CS
                Glycos_transf_2 159 allrre 164
                                    a++r e
  gi|116754271|ref|YP_843389.1| 157 AVVRAE 162
                                    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 !   84.7   0.1   2.4e-27   7.3e-24       1     205 [.       5     192 ..       5     204 .. 0.84

  Alignments for each domain:
  == domain 1  score: 84.7 bits;  conditional E-value: 2.4e-27
                Glyco_tranf_2_2   1 svviplraseerhyieervlqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGaska 80 
                                    sv++p ++  +   +   ++    +  e++elivvddgS++ + e+v+s+ d + + y++++++k  + +aarN G++ a
  gi|116754271|ref|YP_843389.1|   5 SVILPTYNRAH--VVGRAIRSVLEQTYEDFELIVVDDGSTDSTEEVVRSFDDRRIR-YIRHKQNK--GRSAARNTGIKIA 79 
                                    67777777654..488888777777779*********************9887765.66888555..8999********* PP

                Glyco_tranf_2_2  81 esdlvlFlDaDcfissDkfekilklitikklrenidaavvlpvvdlnkedsevl.kdvedltassrvledllaakstlvk 159
                                    +++++ F D+D+ + ++k+e ++++ +       ++  vv++  +l  +d++++    + +t ++++ ++ll        
  gi|116754271|ref|YP_843389.1|  80 KGEYIAFQDSDDEWLPEKLEEQMEVFK----TSSPQVGVVYTGFYLFYDDKKIYiPSANVKTKDGNIYDELLK------G 149
                                    ************************544....35799*****99999888877651678899*******88888......3 PP

                Glyco_tranf_2_2 160 ffapssssilinrraflevGGyDErfrGhgaEDfdlllRlakaiks 205
                                     f+  +  ++++ + + +vG +DE++  h  ED++l++R+ k + +
  gi|116754271|ref|YP_843389.1| 150 NFVG-TPAAVVRAECLKKVGMFDESL--HCLEDWELFIRISKEYIF 192
                                    3443.46789****************..*************99865 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 !   78.7   0.0   1.9e-25   5.8e-22       4     196 ..       4     188 ..       2     203 .. 0.88

  Alignments for each domain:
  == domain 1  score: 78.7 bits;  conditional E-value: 1.9e-25
                Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralneal 83 
                                    ++v+ pt+n++ v+g+ ++s+l q+y ++e++vv+d+s+++t ev++     ++d r+r+++ ++n g ++++r  n ++
  gi|116754271|ref|YP_843389.1|   4 VSVILPTYNRAHVVGRAIRSVLEQTYEDFELIVVDDGSTDSTEEVVRS----FDDRRIRYIRHKQNKG-RSAAR--NTGI 76 
                                    89********************************************97....9********9988767.45555..9*** PP

                Glyco_tranf_2_3  84 ravksdlvllvDdDtvvePdtlkrllqff..ltpkvgavgtpv.fllnrstlvsalgalefaerhlrflaarralgvltl 160
                                    +++k++++++ D+D+ + P+ l+ +  +f   +p+vg+v+t   +++ +++   ++ ++++++ ++     ++ l+  ++
  gi|116754271|ref|YP_843389.1|  77 KIAKGEYIAFQDSDDEWLPEKLEEQMEVFktSSPQVGVVYTGFyLFYDDKKIYIPSANVKTKDGNI----YDELLKGNFV 152
                                    *****************************98899******99845577888888889989888888....4555555555 PP

                Glyco_tranf_2_3 161 nGsgslirrevlkelegldplflltdDyelglrlrr 196
                                    ++   ++r+e+lk  + +d++ +  +D+el  r+ +
  gi|116754271|ref|YP_843389.1| 153 GTPAAVVRAECLKKVGMFDESLHCLEDWELFIRISK 188
                                    55579***************99999****9888765 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   3.2e-07   0.00095       2      81 ..      12      90 ..      11     101 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.2e-07
                Glyco_tranf_2_4  2 neadiLpeflahhlalgfdr..ilvydndstDgtrailkelpevkllhvdksyederrqvellkallaryaeadwvlvvDaD 81
                                   n a++ ++ ++  l+  +++  ++v+d++stD t +++++ ++ ++ +++++ ++   ++++ +++  ++a+++++++ D+D
  gi|116754271|ref|YP_843389.1| 12 NRAHVVGRAIRSVLEQTYEDfeLIVVDDGSTDSTEEVVRSFDDRRIRYIRHKQNK---GRSAARNTGIKIAKGEYIAFQDSD 90
                                   88899999999988888864449******************99999988887654...444333344456788999999998 PP

>> GNT-I  GNT-I family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.4e-06    0.0073      95     156 ..       4      64 ..       1      77 [. 0.88

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.4e-06
                          GNT-I  95 iavlvlacsradavrrtvekllkyrpsaekfPlivsqdcsneevkkevlsygd.kvtyikhld 156
                                    ++v++ + +ra++v r++ ++l+   + e f liv  d+s + +++ v+s+ d ++ yi+h  
  gi|116754271|ref|YP_843389.1|   4 VSVILPTYNRAHVVGRAIRSVLE--QTYEDFELIVVDDGSTDSTEEVVRSFDDrRIRYIRHKQ 64 
                                    67888899*************97..57899*********************87459****975 PP

>> Jacalin  Jacalin-like lectin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   6.3e-05      0.19       4      48 ..      37      79 ..      35      96 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.3e-05
                                   CS-SS-CEECEEEEEEESSSEEEEEEEEEETTSEE-EEEEEEEET CS
                        Jacalin  4 wDdgeydgvrkvyvgqgedgiayikfeYvkaggkvegdehGkkgl 48
                                    Ddg++d    v+  +++ +i+yi+ +++k++    +++ G k+ 
  gi|116754271|ref|YP_843389.1| 37 VDDGSTDSTEEVVRSFDDRRIRYIRHKQNKGR--SAARNTGIKIA 79
                                   6*****************************54..59999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2328.70
//
Query:       gi|116754272|ref|YP_843390.1|  [L=101]
Description: hypothetical protein Mthe_0962 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.029   13.7   0.1        4.6    6.7   0.0    2.4  2  Enolase_like_N  Enolase N-terminal domain-like
      0.039   14.2   0.6      0.044   14.0   0.6    1.3  1  Ribosomal_L2_C  Ribosomal Proteins L2, C-terminal domain


Domain annotation for each model (and alignments):
>> Enolase_like_N  Enolase N-terminal domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0   0.00052       4.6      20      49 ..      12      40 ..       2      42 .. 0.83
   2 ?    4.8   0.1    0.0021        19      17      29 ..      80      92 ..      68      95 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.00052
                 Enolase_like_N 20 lleGpaGwgEfspFleYddaeaarWlaaai 49
                                   +++Gp+G      F + +   +arW++aa 
  gi|116754272|ref|YP_843390.1| 12 MIRGPQGVQAL-GFHQLTTVRSARWMHAAS 40
                                   68899997655.599999*********995 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0021
                 Enolase_like_N 17 eavlleGpaGwgE 29
                                   e+v++ G +Gw E
  gi|116754272|ref|YP_843390.1| 80 EVVMVAGRRGWRE 92
                                   89*********88 PP

>> 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 ?   14.0   0.6   4.9e-06     0.044      90     115 ..      44      88 ..       1      97 [. 0.68

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.9e-06
                                    T.............TBS----SSSS-TTTSSS--SS......SS- CS
                 Ribosomal_L2_C  90 l.............grrpkvrGvamnpvdHphGGGe......Gkt 115
                                    +             g+r + +G+a ++++H  GGGe      G+ 
  gi|116754272|ref|YP_843390.1|  44 RrdsslphgsparaGVRMRLQGLAFQAIEHARGGGEevvmvaGRR 88 
                                    234444444444449999*****************9766666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); 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: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 746.82
//
Query:       gi|116754273|ref|YP_843391.1|  [L=387]
Description: putative transmembrane protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1205  (0.0672095); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); 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):               0  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.46
# Mc/sec: 2539.00
//
Query:       gi|116754274|ref|YP_843392.1|  [L=297]
Description: glycosyl transferase family protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.6e-16   58.8   0.1    7.4e-16   58.4   0.1    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
     0.0054   16.7   0.0     0.0087   16.0   0.0    1.3  1  Glyco_trans_2_3  Glycosyl transferase family group 2
  ------ inclusion threshold ------
       0.14   11.6   0.0       0.64    9.5   0.0    2.0  2  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 !   58.4   0.1   1.2e-19   7.4e-16       3     169 ..       7     173 ..       5     174 .. 0.86

  Alignments for each domain:
  == domain 1  score: 58.4 bits;  conditional E-value: 1.2e-19
                                    EEEESS-.TTTHHHHHHHHHHHGGCCEEEEEEEEES-.SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--S CS
                Glycos_transf_2   3 viptyNe.ektlletlesllaqdpypdfeiivvDDgS.tDetveileelakedprvrvirreenvGkagalnaglraatg 80 
                                    +i+ty      l +t+ sl++q     ++ii+vD+ +   + ++il +    + ++++i++ +n G ++a n g++ a  
  gi|116754274|ref|YP_843392.1|   7 IIVTYKPnVRVLIKTIYSLKDQ----VYKIIIVDNTEdGFNFQQILTAN---NYKIKIIKLWNNYGIGKAQNIGIKIAID 79 
                                    899999999*************....**********9444556666666...8*************************** PP

                                    S...EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SS..EEEECCHCCCCHCCCCCCSTTCS CS
                Glycos_transf_2  81 d...yilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrv..generlyfkerkrslkgnlsfei 155
                                    +   yi++ D+D+e++p+++e +++a+ +  +     +    ++e+ ++  ++++   +n+ + ++++ ++    +s   
  gi|116754274|ref|YP_843392.1|  80 EgaeYIMLSDQDTEYPPNYIENMIKAIGDLSYNNSQIAAIGPSYEDLNKDGRRGYfvIFNSFFIKRIYAKEGCLPVSQLL 159
                                    *****************************988888888888888888888777777788888888888888888888888 PP

                                    TCCCEEEEHHHHHC CS
                Glycos_transf_2 156 gsaallrrealeel 169
                                     + +++ +++l+++
  gi|116754274|ref|YP_843392.1| 160 ATGMIIPVKILKSV 173
                                    88888877777665 PP

>> Glyco_trans_2_3  Glycosyl transferase family group 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.5e-06    0.0087       1     174 [.      84     268 ..      84     291 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.5e-06
                Glyco_trans_2_3   1 iilllDaDtvlppdclreiaaelaspevaivq....gpvlvm....nvanwleelaalffaedhgkdilvrealgrvvps 72 
                                    +i+l D+Dt  pp++++  +  + +  +   q    gp++ +    +++ +++      f+  ++k i   e++  v  +
  gi|116754274|ref|YP_843392.1|  84 YIMLSDQDTEYPPNYIENMIKAIGDLSYNNSQiaaiGPSYEDlnkdGRRGYFVI-----FNSFFIKRIYAKEGCLPVSQL 158
                                    79999************9999888644444441112333322433344445544.....555556667777888888889 PP

                Glyco_trans_2_3  73 vGsgaflrrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkeksplt......lraalrQrkRwayGc.. 144
                                       g++++++ l++vg+ + d +    D++++ ++++ Gy+++  + ++vk +  +        +  lr  +R++y++  
  gi|116754274|ref|YP_843392.1| 159 LATGMIIPVKILKSVGYMREDLFIDWVDMEWCWKARSMGYQIFGNANVVVKHVLGDKsvkvgpKYFNLRSPSRHYYMIrn 238
                                    9******************9999*******************776666555554443455555777899999*****753 PP

                Glyco_trans_2_3 145 ..eleklillvrllgylgsl.lwsalplhlall 174
                                          l l  + + + ++l l+ +++++++++
  gi|116754274|ref|YP_843392.1| 239 glY---LALNSSYINWQMKLrLLISMFCRVLFY 268
                                    320...222223333333331334444444333 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 ?    9.5   0.0   0.00011      0.64      31      57 ..      82     108 ..      67     176 .. 0.90
   2 ?   -0.4   0.0      0.12     7e+02       5      24 ..     209     228 ..     205     238 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00011
                Glyco_transf_21  31 ydllvisDsdvrvkpdyLeellaaled 57 
                                    ++++++sD d+  +p+y+e++ +a+ d
  gi|116754274|ref|YP_843392.1|  82 AEYIMLSDQDTEYPPNYIENMIKAIGD 108
                                    689*******************99876 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.12
                Glyco_transf_21   5 rllvsgdpvgvnpKvnnllq 24 
                                    ++++++++v+v pK +nl  
  gi|116754274|ref|YP_843392.1| 209 KHVLGDKSVKVGPKYFNLRS 228
                                    689999**********9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); 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):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 2080.87
//
Query:       gi|116754275|ref|YP_843393.1|  [L=275]
Description: glycosyl transferase family protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-11   44.2   0.0    3.9e-11   43.0   0.0    1.6  1  Glycos_transf_2  Glycosyl transferase family 2
    6.2e-09   36.1   0.0    8.8e-09   35.6   0.0    1.1  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    1.3e-06   28.4   0.1    7.9e-06   25.9   0.1    2.0  1  Glyco_trans_2_3  Glycosyl transferase family group 2
  ------ inclusion threshold ------
       0.03   14.0   0.1      0.079   12.6   0.1    1.7  1  Glyco_transf_7C  N-terminal domain of galactosyltransferase


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   0.0   8.7e-15   3.9e-11       4     169 ..       7     188 ..       5     189 .. 0.77

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 8.7e-15
                                    EEESS-.TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SS. CS
                Glycos_transf_2   4 iptyNe.ektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatgd. 81 
                                    i+ty    ++++++++  l+    + ++++++D++      + l+el + d r+++i +++n G+++a n ++ ++  + 
  gi|116754275|ref|YP_843393.1|   7 IVTYKSsLDLVRRVVTCSLKS--NLVKKLYILDNSP----TAELQELTALDYRIKYIFNNKNLGFGRAHNIAMLRSIKEn 80 
                                    889999899999999866665..7777777777777....566667777799***********************99999 PP

                                    ..EEEEEESSEEE-TTHHHHHHHHHHH.TT.CEEEEEEEEEECCCCCCCHC-SS.................EEEECCHCC CS
                Glycos_transf_2  82 ..yilflDaDdepdpdwleklvealekdga.dvvlgqrprifgetdeiernkrv.................generlyfk 141
                                      y l+l+ D  ++++ + +l++++e++++ ++v++++ + +ge     + + +                 ++n+++  +
  gi|116754275|ref|YP_843393.1|  81 vkYHLVLNPDISFHENVIDELYDYMEANPDvGLVMPKVLYPSGEIQYLCKLLPTpfdlffrrfmpfkklneKRNNIYELR 160
                                    ***************************865044555555555555555555555*****999999998884444444444 PP

                                    CCHCCCCCCSTTCSTCCCEEEEHHHHHC CS
                Glycos_transf_2 142 erkrslkgnlsfeigsaallrrealeel 169
                                     +  ++  n+++ +g+++ lr +ale++
  gi|116754275|ref|YP_843393.1| 161 FTGYNKIMNVPYLSGCFMFLRTKALEDV 188
                                    4444445588888888999998888887 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 !   35.6   0.0     2e-12   8.8e-09      17     215 ..      17     228 ..       3     237 .. 0.76

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 2e-12
                Glyco_tranf_2_3  17 lgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnealravk..sdlvllv 94 
                                    +++v++  l++ +   ++++ ++  +ae l+++ +l     d r+++++n +nlg+ g++++++ +lr +k   ++ l++
  gi|116754275|ref|YP_843393.1|  17 VRRVVTCSLKS-NLVKKLYILDNSPTAE-LQELTAL-----DYRIKYIFNNKNLGF-GRAHNIA-MLRSIKenVKYHLVL 87 
                                    33455555552.3334444444444444.5556663.....56************9.8888776.66666645779999* PP

                Glyco_tranf_2_3  95 DdDtvvePdtlkrllqff.ltpkvgavgtpvfllnrs..tl..............vsalgalefaerhlrflaar...ra 154
                                    + D   + ++++ l  ++ + p+vg v  +v+   ++  +l              + +  +l  +++++++l+++   + 
  gi|116754275|ref|YP_843393.1|  88 NPDISFHENVIDELYDYMeANPDVGLVMPKVLYPSGEiqYLckllptpfdlffrrFMPFKKLNEKRNNIYELRFTgynKI 167
                                    ******************99999999988777766555433777888899998886667899999999999999966566 PP

                Glyco_tranf_2_3 155 lgvltlnGsgslirrevlkelegldplfllt.dDyelglrlrragfrtayvpgaavrevfps 215
                                     +v++l+G +++ r++ l++ +++d++f +  +D +l++r+ + +++t+++p + ++++f +
  gi|116754275|ref|YP_843393.1| 168 MNVPYLSGCFMFLRTKALEDVGLFDERFFMYlEDTDLCRRIYS-KYKTVFYPNVSIYHEFAR 228
                                    68************************666666********986.79************9875 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 !   25.9   0.1   1.8e-09   7.9e-06      11     128 ..      93     228 ..      83     256 .. 0.65

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 1.8e-09
                Glyco_trans_2_3  11 lppdclreiaaela.spevaivqgpvlvm.nvanwleelaalffaedhgkdilvrealgrvvp................. 71 
                                     +++++ e+++ ++ +p+v++v  +vl+  +   +l +l  + f++ + +++++ + + +                    
  gi|116754275|ref|YP_843393.1|  93 FHENVIDELYDYMEaNPDVGLVMPKVLYPsGEIQYLCKLLPTPFDLFFRRFMPFKKLNEKRNNiyelrftgynkimnvpy 172
                                    56666666666666446666666666665433344444444445555555555555444444444555555555555555 PP

                Glyco_trans_2_3  72 svGsgaflrrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkekspl 128
                                    + G  +flr +al++vg +d +++   ED+d++ r+++k y+++f+p + ++ ++ +
  gi|116754275|ref|YP_843393.1| 173 LSGCFMFLRTKALEDVGLFDERFFMYLEDTDLCRRIYSK-YKTVFYPNVSIYHEFAR 228
                                    66999**********************************.66666666646555444 PP

>> Glyco_transf_7C  N-terminal domain of galactosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   1.8e-05     0.079      18      68 ..     171     221 ..     160     236 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.8e-05
                Glyco_transf_7C  18 kyfgG.vlalrkedfekiNGfsntfwgWGgEDdelyaRlakkgleierpekg 68 
                                     y +G  + lr++  e+++ f+++f+ +  ED++l++R+ +k  ++  p+ +
  gi|116754275|ref|YP_843393.1| 171 PYLSGcFMFLRTKALEDVGLFDERFFMY-LEDTDLCRRIYSKYKTVFYPNVS 221
                                    455550555688999*************.**********9988777766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); 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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1925.12
//
Query:       gi|116754276|ref|YP_843394.1|  [L=159]
Description: transposase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.5e-17   61.5   0.1      5e-16   59.1   0.0    2.0  2  HTH_32    Homeodomain-like domain
    5.6e-15   55.1   0.3    3.3e-14   52.6   0.2    2.2  2  HTH_29    Winged helix-turn helix
    6.5e-13   48.1   0.4    2.2e-10   40.0   0.1    2.5  2  HTH_23    Homeodomain-like domain
    6.6e-06   26.2   0.0    1.5e-05   25.0   0.0    1.6  1  HTH_28    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.27   1.2e+03      28      54 ..      10      35 ..       2      55 .. 0.64
   2 !   59.1   0.0   1.1e-19     5e-16       1      73 []      61     140 ..      61     140 .. 0.96

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.27
                         HTH_32 28 klsdevrariiallreeprWsprqlaa 54
                                    l + +r+++   +r+  + s+r l +
  gi|116754276|ref|YP_843394.1| 10 SLKEGERDELESFIRKG-KASARSLTR 35
                                   57778888888888444.555555543 PP

  == domain 2  score: 59.1 bits;  conditional E-value: 1.1e-19
                         HTH_32   1 TvsrwlkRyneeGle.gLkdrprrgrprklsdevrariiallreep.....rWsprqlaarlaere.gvkvShstvyriL 73 
                                    Tv++++ Ry ++Gl+ +L ++pr+g+p+k++ +v+a++  l++++p     rW+  +l+++l+e +  +++Sh tvyr L
  gi|116754276|ref|YP_843394.1|  61 TVRNTRDRYWKGGLDcALNEKPRSGAPSKIDGRVEAELTLLACSDPpdgrsRWTVMLLRDKLVEMGvVDSISHMTVYRTL 140
                                    9******************************************9988***************99995555********97 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   0.2   7.4e-18   3.3e-14       1      63 []      35      96 ..      35      96 .. 0.98
   2 ?   -0.5   0.0      0.29   1.3e+03      28      35 ..     135     142 ..     129     151 .. 0.83

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 7.4e-18
                         HTH_29  1 RaqallllaeGvstvsqiAkllglsrrtvyrwlkrfeegGlaalld.rrrsgrprnrlseeqea 63
                                   Ra++lll+++G s  ++i+ +l ++r tv+++++r+ +gGl+++l+ ++rsg+p++ +++++ea
  gi|116754276|ref|YP_843394.1| 35 RARILLLADDGRS-DKEIVDVLKVCRGTVRNTRDRYWKGGLDCALNeKPRSGAPSK-IDGRVEA 96
                                   99**********8.****************************************96.9***997 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.29
                         HTH_29  28 tvyrwlkr 35 
                                    tvyr+lk 
  gi|116754276|ref|YP_843394.1| 135 TVYRTLKK 142
                                    9***9985 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.1   4.9e-14   2.2e-10       2      48 ..      30      76 ..      29      78 .. 0.93
   2 !    5.9   0.0    0.0025        11      29      40 ..     131     142 ..     130     151 .. 0.89

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 4.9e-14
                         HTH_23  2 asereRlrillllaeGlsvreIAreLgvsrrTvyrwlkryreeGleg 48
                                   a+ + R+rilll+++G s +eI + L v r Tv++ + ry ++Gl+ 
  gi|116754276|ref|YP_843394.1| 30 ARSLTRARILLLADDGRSDKEIVDVLKVCRGTVRNTRDRYWKGGLDC 76
                                   66789***********************************99**986 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0025
                         HTH_23  29 vsrrTvyrwlkr 40 
                                    +s++Tvyr lk+
  gi|116754276|ref|YP_843394.1| 131 ISHMTVYRTLKK 142
                                    89*******997 PP

>> HTH_28  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   3.4e-09   1.5e-05       2      51 ..      35      85 ..      34      87 .. 0.95

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 3.4e-09
                         HTH_28  2 RleiikllaaGhsvreaArelgisrrtvyrWikryeegGia.gLvprrrrp 51
                                   R++i++l+ +G+s +e+   l ++r tv+  + ry +gG++ +L+ ++r++
  gi|116754276|ref|YP_843394.1| 35 RARILLLADDGRSDKEIVDVLKVCRGTVRNTRDRYWKGGLDcALNEKPRSG 85
                                   9****************************************9999998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       796  (0.0443973); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1144.60
//
Query:       gi|116754277|ref|YP_843395.1|  [L=207]
Description: transposase [Methanosaeta thermophila PT]
Scores for complete 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   92.1   0.0    3.4e-26   91.8   0.0    1.2  1  DDE_3            DDE superfamily endonuclease
  ------ inclusion threshold ------
      0.014   15.2   0.3      0.025   14.4   0.2    1.4  1  Sulfotransfer_4  Sulfotransferase domain


Domain annotation for each model (and alignments):
>> DDE_3  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.8   0.0   3.8e-30   3.4e-26       2     146 .]      18     168 ..      17     168 .. 0.97

  Alignments for each domain:
  == domain 1  score: 91.8 bits;  conditional E-value: 3.8e-30
                          DDE_3   2 vvfiDEsgfqlgt.vrrrawakkGkrer.leeygrrgrvnligaldekgglafvtfeetlnaedfaeflerlletalqak 79 
                                    v+++DE ++ql   +    ++k+G+  +  +ey+r+g++ +++a+++  g+ +v + e++++ d aef+ +l+ ++++a+
  gi|116754277|ref|YP_843395.1|  18 VICFDERTCQLLGdTIVPIPMKPGSPRKeHYEYERNGTCCVFMAFEPLAGRGIVSVRERRTKIDYAEFMVDLANQYPDAE 97 
                                    89****99998888************777*************************************************** PP

                          DDE_3  80 kivlilDnasiHkseslrelveee.....adrlellylPpySPelNpiEivwsklkrellkrrsfksldeLk 146
                                    ki+++ Dn+++H+  s+++++        a+++e+ y+P++ ++lN+ Ei  s l +++l+ r+++++ +L+
  gi|116754277|ref|YP_843395.1|  98 KIIVVQDNLNTHTMGSFYDAMPPDdafklAKQFEFNYTPKKGSWLNMAEIELSALSKQCLD-RRIPDINKLR 168
                                    ***********************9*************************************.****999885 PP

>> Sulfotransfer_4  Sulfotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.2   2.8e-06     0.025      79     172 ..      84     206 ..      75     207 .] 0.87

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.8e-06
                Sulfotransfer_4  79 lfaeelleayPdakvIlteRdp.................................ekWlksmkktllalrsetlsrllal 125
                                     f+ +l+++yPda  I+++ d                                   +Wl+  +  l al++++l r +  
  gi|116754277|ref|YP_843395.1|  84 EFMVDLANQYPDAEKIIVVQDNlnthtmgsfydamppddafklakqfefnytpkkGSWLNMAEIELSALSKQCLDRRIPD 163
                                    58899*******99999999888******************************9999******************99999 PP

                Sulfotransfer_4 126 ldpllellaklvellralvrrlfgagsdaedeeaakeayeehnervr 172
                                    +++l++   ++++  r+++r+ ++ +    ++++a++ +++h+++v+
  gi|116754277|ref|YP_843395.1| 164 INKLRDE-INIWQQERNAIRATVQWK---FSKDNARAKLKRHYNTVK 206
                                    9997654.455555556667777775...889999999*****9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); 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: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1623.77
//
Query:       gi|116754278|ref|YP_843396.1|  [L=180]
Description: methyltransferase type 12 [Methanosaeta thermophila PT]
Scores for complete 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-09   35.7   0.0    9.8e-09   35.2   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    6.7e-08   33.1   0.0      1e-07   32.5   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    2.1e-05   25.2   0.1    7.2e-05   23.5   0.1    1.9  1  Methyltransf_12  Methyltransferase domain
    3.8e-05   23.5   0.1    0.00012   21.9   0.1    1.7  1  Methyltransf_31  Methyltransferase domain
    0.00021   22.0   0.0     0.0004   21.0   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
     0.0051   16.3   0.0     0.0065   16.0   0.0    1.4  1  CheR             CheR methyltransferase, SAM binding domain


Domain annotation for each model (and alignments):
>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.0   3.3e-12   9.8e-09       9     124 ..      35     152 ..      27     169 .. 0.73

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 3.3e-12
                Methyltransf_23   9 lsdklerllpk.lraggrvLdiGcGtG.illevl.rengfsvtgvDlspeaveiae.....kakkaqkdqfdeqeaaepq 80 
                                    ++d l+ + pk  r +  v diG G+  +++  + ++   +++gvD++++  + a+     k++ a        ++++ +
  gi|116754278|ref|YP_843396.1|  35 YQDVLHSVIPKyVRDDWVVYDIGGGKNpYVTIDMkSKLNLHIIGVDINENELNTAPlgvydKKIVA--------DITKYE 106
                                    555565555552366667889*****97777778444577********997777655543322222........444556 PP

                Methyltransf_23  81 g..kfdlIvlrevlehvpdppellrqiatllkpgGylllseplasl 124
                                    g    dl+v+  vlehv++++++lr i+++lk gG++++ +p +++
  gi|116754278|ref|YP_843396.1| 107 GtcDGDLAVCLAVLEHVQNVEAALRGINSCLKRGGLCVIFVPSKNA 152
                                    622568********************************99987765 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.0   3.4e-11     1e-07       2      96 .]      55     145 ..      54     145 .. 0.82

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 3.4e-11
                                    EET-T.TSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCT.SS-TT-EEEEEEES-CCC-CCHH CS
                Methyltransf_11   2 dvGcG.tGrlaealakrg.arvvgvDlskemlklakekaseeglkvefvvadaekl.pfednsfDlvvssevlhhvedpe 78 
                                    d+G G + +++ +++++   +++gvD++++ l++a   + +++     +vad++k         Dl v+  vl+hv+++e
  gi|116754278|ref|YP_843396.1|  55 DIGGGkNPYVTIDMKSKLnLHIIGVDINENELNTAPLGVYDKK-----IVADITKYeGTC--DGDLAVCLAVLEHVQNVE 127
                                    667773344555555444599***********99988888887.....9*****952333..58**************** PP

                                    HHHHHHHHHEEEEEEEEE CS
                Methyltransf_11  79 kalkeiaRvLkpgGllvi 96 
                                    +al+ i  +Lk gGl+vi
  gi|116754278|ref|YP_843396.1| 128 AALRGINSCLKRGGLCVI 145
                                    ****************97 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.1   2.4e-08   7.2e-05      18      98 ..      71     142 ..      54     143 .. 0.67

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2.4e-08
                Methyltransf_12  18 lpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlkdirevldnirklLkpgG 97 
                                      +++++gvDi+++ ++ a   l  ++++ ++ ++  +            Dl v++ vl+h+++++++l+ i ++Lk gG
  gi|116754278|ref|YP_843396.1|  71 KLNLHIIGVDINENELNTAP--LGVYDKKIVADITKYEGT-------CDGDLAVCLAVLEHVQNVEAALRGINSCLKRGG 141
                                    36889999999999993333..333333233333322222.......367****************************** PP

                Methyltransf_12  98 r 98 
                                     
  gi|116754278|ref|YP_843396.1| 142 L 142
                                    7 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.1     4e-08   0.00012       6     113 ..      52     149 ..      48     170 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 4e-08
                Methyltransf_31   6 rvlDlGCGtG.eltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevl 84 
                                    +v+D+G G+  + t+ + ++l  + +++G+Di+e+ ++ A     ++++      ++di++ e + +d   Dl ++ +vl
  gi|116754278|ref|YP_843396.1|  52 VVYDIGGGKNpYVTIDMKSKL--NLHIIGVDINENELNTAPLGVYDKKI------VADITKYEGT-CD--GDLAVCLAVL 120
                                    688888886425666666666..689**************997776666......7*****7754.44..8********* PP

                Methyltransf_31  85 naladpdkileeiervlkpggilliedpr 113
                                     ++ + +++l++i + lk gg ++i  p+
  gi|116754278|ref|YP_843396.1| 121 EHVQNVEAALRGINSCLKRGGLCVIFVPS 149
                                    ************************98887 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.3e-07    0.0004       1      97 []      53     141 ..      53     141 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.3e-07
                                    EEEET-TTS.HHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSH CS
                Methyltransf_25   1 vLdlGcGtG.rltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsd 79 
                                    v d+G G+   +t+++  +l + +++gvDi+e+ l++a   +       + +++d+++++      Dl v+  +l+h++ 
  gi|116754278|ref|YP_843396.1|  53 VYDIGGGKNpYVTIDMKSKL-NLHIIGVDINENELNTAPLGVY-----DKKIVADITKYEGT-CDGDLAVCLAVLEHVQ- 124
                                    67888888635889999998.6***************998774.....45699*****9854.36799999766***87. PP

                                    HHHHHHHHHHHHHEEEEE CS
                Methyltransf_25  80 edlekalkeiarvLkpgG 97 
                                     ++e+al+ i ++Lk gG
  gi|116754278|ref|YP_843396.1| 125 -NVEAALRGINSCLKRGG 141
                                    .789*************9 PP

>> CheR  CheR methyltransferase, SAM binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   2.2e-06    0.0065      60      95 ..      69     104 ..      39     145 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.2e-06
                                    TSSS-EEEEEEESSCHHHHHHHHTEEECCHHTTS-H CS
                           CheR  60 aaklkvkilAtDidlkvlekAkagvykeeeleglse 95 
                                    + kl+++i+++Di+++ l++A+ gvy+++ ++++++
  gi|116754278|ref|YP_843396.1|  69 KSKLNLHIIGVDINENELNTAPLGVYDKKIVADITK 104
                                    4566799************************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); 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:                         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 0.22s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1342.63
//
Query:       gi|116754279|ref|YP_843397.1|  [L=289]
Description: transposase, IS4 family protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.2e-33  113.1   0.0    3.2e-31  107.9   0.0    2.2  2  DDE_Tnp_1_5  Transposase DDE domain
      9e-21   74.5   0.1    1.6e-20   73.7   0.1    1.4  1  DDE_Tnp_1    Transposase DDE domain


Domain annotation for each model (and alignments):
>> DDE_Tnp_1_5  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.9   0.0   3.6e-35   3.2e-31       2     111 ..      18     125 ..      17     126 .. 0.95
   2 ?    2.8   0.0     0.016   1.4e+02      40      67 ..     252     281 ..     246     287 .. 0.82

  Alignments for each domain:
  == domain 1  score: 107.9 bits;  conditional E-value: 3.6e-35
                    DDE_Tnp_1_5   2 kRGsltiwldeeaiaawkek...kkngkrgrpqvysdaaiqtcltvkvlfklplRqlqGfvqsllklaglellvpdystl 78 
                                    +RG  +++l+++++++w+e+    +++k+grp++y++++iq+c +++++++lp+Rql+Gf+q+l+ ++   ll++dystl
  gi|116754279|ref|YP_843397.1|  18 RRG--WFYLSTDFVNNWDEEllkMNKNKNGRPYRYPETFIQFCGLAYAFLHLPYRQLEGFIQALSGFVPG-LLAADYSTL 94 
                                    799..************9987745569******************************************9.99******* PP

                    DDE_Tnp_1_5  79 srraktlevkipvkrkskglhlvvdstGlkvlg 111
                                    ++r ++le++ip+ +++  l+++vdstG+kv++
  gi|116754279|ref|YP_843397.1|  95 WQRITNLELNIPIPDND--LVVAVDSTGMKVTN 125
                                    **************999..99**********97 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.016
                    DDE_Tnp_1_5  40 tcltvkvlfklplRql..qGfvqsllklag 67 
                                    ++  +k++f+ ++R++  +G+++ + ++ +
  gi|116754279|ref|YP_843397.1| 252 VFSAIKRIFGETVRATskEGMIREVRRMFT 281
                                    56789*********9855699999988876 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.7   0.1   1.8e-24   1.6e-20       5     200 ..     112     271 ..     108     285 .. 0.83

  Alignments for each domain:
  == domain 1  score: 73.7 bits;  conditional E-value: 1.8e-24
                      DDE_Tnp_1   5 evlivDattvrvpgtkedarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrprkgklvlaDa 84 
                                     v++vD+t ++v+  + ++r++++  + + ++k+hiavd +++ ++ ++it+  v d++ +k+ll+ +   k    l+D+
  gi|116754279|ref|YP_843397.1| 112 LVVAVDSTGMKVTNRGDWMRESHGVER-RGWIKVHIAVDVETRKPVTFEITDETVTDHEMVKPLLEDV---KLEDSLMDG 187
                                    699******************888666.79************************************99...89******* PP

                      DDE_Tnp_1  85 GYasaelldtleekgvd.yiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgdvyyvtntnsells 163
                                    +Y++++++d+++ekgvd + i+++kn+ ++        r +    +++  +  +++ +++                    
  gi|116754279|ref|YP_843397.1| 188 AYDKEGVFDFMKEKGVDmPGIKIRKNAIVKAG----SSRAEPVLEFMKYGYHSWKIVHGY-------------------- 243
                                    ****************9568899999988866....344445555555555555555555.................... PP

                      DDE_Tnp_1 164 aeevaelyrlRwqiErvFkwlkrkfgldrlryrglnr 200
                                             +Rw  E+vF+ +kr fg + +r+ ++++
  gi|116754279|ref|YP_843397.1| 244 --------GRRWAAESVFSAIKRIFG-ETVRATSKEG 271
                                    ........***************998.6666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2315.98
//
Query:       gi|116754280|ref|YP_843398.1|  [L=429]
Description: periplasmic binding protein [Methanosaeta thermophila PT]
Scores for complete 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-29  101.3   0.0    7.6e-29  100.9   0.0    1.1  1  Peripla_BP_2    Periplasmic binding protein
  ------ inclusion threshold ------
      0.011   15.9   0.9      0.027   14.7   0.9    1.7  1  Dockerin_1      Dockerin type I domain
       0.11   12.0   0.1        4.4    6.8   0.0    2.6  2  Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.9   0.0   1.3e-32   7.6e-29       2     237 ..     109     370 ..     108     371 .. 0.92

  Alignments for each domain:
  == domain 1  score: 100.9 bits;  conditional E-value: 1.3e-32
                                    EE-SHHHHHHHHHTT-GGGEEEB.-GGG--GGGGGGT..TS-BSBESSSB-HHHHHHH--SEEEE-GGG...GGGHHHHH CS
                   Peripla_BP_2   2 aslspsvteillalGatdkvvgv.dtttsdpldadkleeaivevgadgeidvEklaalkPDlvilskglgltdedeellk 80 
                                    + ++   +e+l+++G+ d+vvgv dt+++  +  ++l  +++++g++ge+++E+++++kP +v++ +++ + d+ + +l 
  gi|116754280|ref|YP_843398.1| 109 VIYNHQCAEVLQLMGVDDRVVGVrDTFAEQRNRFPRLS-QVTSIGSGGEPNIEAILKVKPQVVLAYTFYPVEDALDAKLP 187
                                    67888899*************97478888888888877.***************************************** PP

                                    HHS-EEE----TTS...HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT..-EEEEEEEETTE........ CS
                   Peripla_BP_2  81 sgiptvivessntg...eslkeqiralgellgledeaeklvaeidsklaaaksaidse.kpkpvlvfggade......gg 150
                                    ++++++  +  + g   +   e i++ g ++g++d+aek+ +++d  + +++++++++  +k v v+ ++ +       +
  gi|116754280|ref|YP_843398.1| 188 PDVKVLRLDCECSGigpDAMREKITMMGYIFGTQDRAEKYLKWHDAIVSQVEERVKTIpEDKRVRVYLESTPegsnpqTS 267
                                    **********9999********************************************9666666666666669999889 PP

                                    EEEE-TTSTTTHHHHTS--EESTTT--......STT-EEE-HHHHHHH--SEEEEEEH..........HHHT-S--HHHH CS
                   Peripla_BP_2 151 yvvagsnsyigdlldalgieniaaesk......kseyeeisaEqilasdpdvifvsgr..........aeadnktglefl 214
                                     + +gs++  ++l++ +g+ nia  +         ey+ei  E++ +++pdvi+ + +           ++  +  + ++
  gi|116754280|ref|YP_843398.1| 268 RTAIGSGHAANKLIEMAGGVNIAVGHLpkyldtPTEYGEIETEWVISQNPDVIVGRAMgkgirpyenvNSSLLQSYDREI 347
                                    9*********************888889*****9******************************9998888888888899 PP

                                    T-SHHHHTSHHHHTT-EEEE-HH CS
                   Peripla_BP_2 215 kenpllaelpAvkngrVyaldss 237
                                     + p++ +++Av+ grVy + ++
  gi|116754280|ref|YP_843398.1| 348 RNLPGFDRVKAVQDGRVYIITND 370
                                    999***************99876 PP

>> Dockerin_1  Dockerin type I domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.9   4.5e-06     0.027       5      58 .]      35      83 ..      32      90 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.5e-06
                                   TSSSC-SHHHHHHHHHHCTSSEBTTSCCCHGGGSTT-SSCESHHHHHHHHHHHT CS
                     Dockerin_1  5 NgDgkVnalDalliinylnqregqssssngkaaDvNgDGrvnalDallvinyLl 58
                                   N D +++  D+  i+  ++     + +s ++ +D + +G v+a D+++v + ++
  gi|116754280|ref|YP_843398.1| 35 NMDDRIDENDLEFIRMVIQ-----GEKSATELCDADHNGVVDASDITQVERIIN 83
                                   8899*******99999999.....9999999******************99876 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 ?    6.8   0.0   0.00074       4.4       9      40 ..      98     129 ..      94     137 .. 0.81
   2 ?    2.1   0.1     0.021   1.3e+02      13      37 ..     264     288 ..     248     292 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.00074
                                    EEEEE--TT--EES-HHHHHHHHHHT--SEE- CS
                 Ribosomal_S5_C   9 vllkpaprGtGiiaggavravlelaGikDvla 40 
                                    v   p+p    +i ++   +vl+l+G++D ++
  gi|116754280|ref|YP_843398.1|  98 VVTLPQPLERLVIYNHQCAEVLQLMGVDDRVV 129
                                    55567777777999***************776 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.021
                                    E--TT--EES-HHHHHHHHHHT--S CS
                 Ribosomal_S5_C  13 paprGtGiiaggavravlelaGikD 37 
                                    p+   t i +g+a+ ++ e+aG  +
  gi|116754280|ref|YP_843398.1| 264 PQTSRTAIGSGHAANKLIEMAGGVN 288
                                    445557888999********99666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); 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: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 3310.89
//
Query:       gi|116754281|ref|YP_843399.1|  [L=82]
Description: hypothetical protein Mthe_0973 [Methanosaeta thermophila PT]
Scores for complete 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   43.7   0.3    2.7e-11   43.4   0.3    1.0  1  DUF3387   Domain of unknown function (DUF3387)


Domain annotation for each model (and alignments):
>> DUF3387  Domain of unknown function (DUF3387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   0.3   1.5e-15   2.7e-11     292     330 ..      29      67 ..      27      68 .. 0.94

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 1.5e-15
                        DUF3387 292 vrAklrvavkrlLrkygYPpdkqeeaveeVleQaellak 330
                                    + A++rv+vkr+Lr++gYP d q+eav +VleQae++a+
  gi|116754281|ref|YP_843399.1|  29 ATAQIRVKVKRILRRHGYPVDRQDEAVLTVLEQAEAVAA 67 
                                    679********************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 684.78
//
Query:       gi|116754282|ref|YP_843400.1|  [L=312]
Description: ornithine carbamoyltransferase [Methanosaeta thermophila PT]
Scores for complete 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  180.1   0.0      4e-53  179.7   0.0    1.2  1  OTCace    Aspartate/ornithine carbamoyltransferase, Asp/Orn b
    5.4e-51  172.5   0.0    8.7e-51  171.8   0.0    1.3  1  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 !  179.7   0.0   4.5e-57     4e-53       1     156 [.     155     305 ..     155     306 .. 0.98

  Alignments for each domain:
  == domain 1  score: 179.7 bits;  conditional E-value: 4.5e-57
                                    CC.EEEEESSTTSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEEE--S CS
                         OTCace   1 kglkiafvGdkknnvanslikllarlgmdvvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvytdvw 80 
                                    +gl+ia++Gd+ nnv+nsli + a+l+m + +++P g+ep+ ++le+a++     gg  +it +++ea+ +aDv++td+w
  gi|116754282|ref|YP_843400.1| 155 EGLRIAWIGDG-NNVCNSLILASAMLNMRMIVASPRGYEPKGQILERAREL----GGVPEITAEPSEAAHDADVLVTDTW 229
                                    599********.*********************************999998....9************************ PP

                                    SETTCCGGHHHHHHHHCCCSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHHHHHHHHHH CS
                         OTCace  81 vsmgeekereerlkklkdyqvteellklakkdaivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlhtikAllvl 156
                                    +smg+e+e+ erl+++ +yq+++ +l+ a  daiv+HcLPa+rg+E+tdeV+d+p+svv e+aeNrlht kA+l +
  gi|116754282|ref|YP_843400.1| 230 ISMGDEAEEAERLRSFSGYQINQRILEIAGRDAIVMHCLPAHRGQEITDEVMDGPQSVVLEEAENRLHTSKAVLEW 305
                                    *************************************************************************976 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 !  171.8   0.0   9.7e-55   8.7e-51       1     148 []       4     149 ..       4     149 .. 0.94

  Alignments for each domain:
  == domain 1  score: 171.8 bits;  conditional E-value: 9.7e-55
                                    S-BSSGGGS-HHHHHHHHHHHHHHHHHHHT.....TT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTT CS
                       OTCace_N   1 rhllsledlskeeieelldlaaelkekvkk.....ekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseae 75 
                                    r+l+s++dls+eei +lld+a++lk++++         +  l+gk++a++Fe+pStRTrvS evAa++lGg++l+ls a+
  gi|116754282|ref|YP_843400.1|   4 RSLISIADLSPEEIVALLDRAEDLKAERSGrggcaFGDRLPLAGKSVAMIFEKPSTRTRVSLEVAATELGGHPLYLS-AN 82 
                                    79***********************998877777644444589**********************************.88 PP

                                    TSCTTTGGSTTSSCHHHHHHHHHHHTSEEEEEESSHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHHHH CS
                       OTCace_N  76 diqlssvskgrkEsleDtarvlsryvdaiviRhpgaeeleelakyasvpviNagdgdgeHPtQaLaDlltire 148
                                    ++ql+     r+E++ Dtarvlsryv++i +R+++++++eela+++svpviNa+ +d+eHP+Q+LaD++tire
  gi|116754282|ref|YP_843400.1|  83 ELQLG-----RGETIGDTARVLSRYVHGITARVFSHRTVEELAAHSSVPVINAL-SDQEHPLQILADMMTIRE 149
                                    9***9.....78******************************************.****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); 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: 00:00:00.42
# Mc/sec: 2227.10
//
Query:       gi|116754283|ref|YP_843401.1|  [L=125]
Description: molydopterin dinucleotide-binding region [Methanosaeta thermophila PT]
Scores for complete 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-19   67.8   0.0    9.2e-19   67.5   0.0    1.1  1  Molydop_binding  Molydopterin dinucleotide binding domain


Domain annotation for each model (and alignments):
>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.5   0.0   5.1e-23   9.2e-19       3     109 ..       5     101 ..       3     103 .. 0.90

  Alignments for each domain:
  == domain 1  score: 67.5 bits;  conditional E-value: 5.1e-23
                                    EEEE-BTTBSTTTTTCGCCHHHHCSSS-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEEEEESSHCC CS
                Molydop_binding   3 LitgrsldqlhsqtrtrpvlrlakpepevveinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvvfmpfgwwe 82 
                                     +t r   q   q   r  + +++ +  vv +   dAa+ GikdG +V ves++G+v+v a+++++ +pG +fmp   w+
  gi|116754283|ref|YP_843401.1|   5 IVTFRDIFQSEVQEVDRFGEDYRRMSA-VVFLDKSDAAKAGIKDGSNVLVESDNGRVVVVARISDDAHPGLAFMPNSPWS 83 
                                    578888888888888888888888888.**************************************************** PP

                                    .....S-GHCTS--SCSTTT--CSTT- CS
                Molydop_binding  83 agekggnaNaltddatdplsgtpefks 109
                                            N+l++++td+ +++p++ks
  gi|116754283|ref|YP_843401.1|  84 --------NRLVPAETDD-TRIPSYKS 101
                                    ........****777765.68898887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); 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: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 938.06
//
Query:       gi|116754284|ref|YP_843402.1|  [L=406]
Description: tungsten formylmethanofuran dehydrogenase subunit B [Methanosaeta thermophila PT]
Scores for complete 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   24.1   0.0       0.38   10.5   0.0    3.2  3  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
  ------ inclusion threshold ------
      0.097   12.4   0.1       0.24   11.2   0.0    1.6  2  CO_dh         CO dehydrogenase beta subunit/acetyl-CoA syntha


Domain annotation for each model (and alignments):
>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   4.2e-05      0.38       1      41 [.      60      99 ..      60     106 .. 0.89
   2 ?    2.7   0.0     0.011        99       5      39 ..     226     262 ..     224     280 .. 0.92
   3 !    7.0   0.0   0.00051       4.6      68      87 ..     306     325 ..     285     354 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 4.2e-05
                                   HHHHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-E CS
                   TPP_enzyme_M  1 iekaaellkaakrpvilvGggvarsgaseelrelaeklgiP 41
                                   i++aae+l+ akrp++ +G  +++ +a+++  ela+k+++ 
  gi|116754284|ref|YP_843402.1| 60 ISRAAEMLRDAKRPLL-FGWSCSTLEAQRKGIELARKTRAI 99
                                   689***********86.69****9***********999876 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.011
                                    HHHHHH-SSEEEEE-CHHCHT..TGHHHHHHHHHHHT CS
                   TPP_enzyme_M   5 aellkaakrpvilvGggvars..gaseelrelaeklg 39 
                                    +  lk+a   vi+ G g a+s  g  + l++l+ +l+
  gi|116754284|ref|YP_843402.1| 226 ITTLKKADMGVIFPGLGLAYSlkGRMDRLKALVSRLN 262
                                    5679****************998999******99987 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.00051
                                    CHHHHHHHHH-SEEEEES-S CS
                   TPP_enzyme_M  68 skaanealeeaDlvlalGar 87 
                                     +++ eal+++Dl l++G++
  gi|116754284|ref|YP_843402.1| 306 MYSVVEALKSCDLALVVGTD 325
                                    67899*************76 PP

>> CO_dh  CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   2.7e-05      0.24      16      41 ..      51      76 ..      45      96 .. 0.91
   2 ?   -3.4   0.0      0.79     7e+03      25      45 ..     222     242 ..     214     273 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.7e-05
                                   XX--EEE--SHHHHHHHHHSSSEEEE CS
                          CO_dh 16 skkatleealkvvakmikkakrPlli 41
                                   +k++ + ea+  +a+m++ akrPll+
  gi|116754284|ref|YP_843402.1| 51 GKQVGIDEAISRAAEMLRDAKRPLLF 76
                                   6899999*****************97 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.79
                                    SHHHHHHHHHSSSEEEEE-S- CS
                          CO_dh  25 lkvvakmikkakrPllivGpq 45 
                                    +      +kka+  ++++G  
  gi|116754284|ref|YP_843402.1| 222 MISMITTLKKADMGVIFPGLG 242
                                    444445567777777776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2964.75
//
Query:       gi|116754285|ref|YP_843403.1|  [L=152]
Description: Fe-S cluster domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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   52.5   1.8    2.8e-14   52.5   1.8    2.4  1  FeS       Putative Fe-S cluster
    2.7e-08   33.3  18.6    6.7e-07   28.9   4.6    3.3  3  Fer4      4Fe-4S binding domain
      7e-06   26.1  18.8    2.3e-05   24.4  12.6    3.3  2  Fer4_10   4Fe-4S dicluster domain
    1.1e-05   26.0  20.1     0.0019   18.8   9.6    3.1  2  Fer4_7    4Fe-4S dicluster domain
      5e-05   23.4   8.6      5e-05   23.4   8.6    3.1  3  Fer4_9    4Fe-4S dicluster domain
    0.00013   22.0  16.0     0.0017   18.5   2.8    3.4  4  Fer4_21   4Fe-4S dicluster domain
    0.00023   21.0   2.6    0.00023   21.0   2.6    3.6  3  Fer4_2    4Fe-4S binding domain
    0.00045   20.2   4.3    0.00045   20.2   4.3    3.4  3  Fer4_6    4Fe-4S binding domain
     0.0011   19.6   5.2     0.0021   18.8   0.8    2.4  2  Fer4_15   4Fe-4S single cluster domain
     0.0012   19.3  15.6      0.012   16.0   6.0    3.2  2  Fer4_8    4Fe-4S dicluster domain
     0.0054   17.6  22.9      0.089   13.8   7.5    3.5  3  Fer4_3    4Fe-4S binding domain
     0.0082   17.1  12.7     0.0082   17.1  12.7    3.0  3  Fer4_16   4Fe-4S double cluster binding domain
  ------ inclusion threshold ------
      0.018   15.6   5.5      0.018   15.6   5.5    3.1  2  Fer4_17   4Fe-4S dicluster domain
      0.025   15.0   3.2      0.025   15.0   3.2    3.9  3  Fer4_4    4Fe-4S binding domain
       0.11   13.0  14.0       0.89   10.1   9.4    3.0  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I


Domain annotation for each model (and alignments):
>> FeS  Putative Fe-S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.5   1.8   2.3e-17   2.8e-14       2      33 .]      12      43 ..      12      43 .. 0.99

  Alignments for each domain:
  == domain 1  score: 52.5 bits;  conditional E-value: 2.3e-17
                            FeS  2 PgtNCgaCGypgCmafAealvegeaqledCpp 33
                                   P++NC++CG p+CmafA al++ e+q+edC+p
  gi|116754285|ref|YP_843403.1| 12 PKLNCKKCGLPTCMAFAVALLAREKQIEDCTP 43
                                   9*****************************98 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.6      0.63   7.6e+02       8      12 ..      16      20 ..      14      21 .. 0.77
   2 !   28.9   4.6   5.6e-10   6.7e-07       2      22 ..      72      92 ..      71      93 .. 0.93
   3 !   12.9   0.7   6.3e-05     0.075       9      24 .]     135     150 ..     135     150 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.63
                                   SSS-T CS
                           Fer4  8 CigCG 12
                                   C +CG
  gi|116754285|ref|YP_843403.1| 16 CKKCG 20
                                   89998 PP

  == domain 2  score: 28.9 bits;  conditional E-value: 5.6e-10
                                   EEETTTSSS-THHHHHSTTTE CS
                           Fer4  2 videekCigCGaCvevCPvgA 22
                                   +i+e++C gCG+Cv +CPv++
  gi|116754285|ref|YP_843403.1| 72 IIHEDRCYGCGNCVVACPVNV 92
                                   799****************96 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 6.3e-05
                                    SS-THHHHHSTTTEEE CS
                           Fer4   9 igCGaCvevCPvgAIt 24 
                                    i C++C   CP  AI+
  gi|116754285|ref|YP_843403.1| 135 ILCNLCTATCPSKAIE 150
                                    78************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 ?    1.9   0.5      0.21   2.5e+02       8      16 ..      15      25 ..       9      43 .. 0.72
   2 !   24.4  12.6     2e-08   2.3e-05       3      56 .]      72     145 ..      70     145 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.21
                        Fer4_10  8 tCirCg..kCv 16
                                    C +Cg  +C+
  gi|116754285|ref|YP_843403.1| 15 NCKKCGlpTCM 25
                                   35555544444 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 2e-08
                        Fer4_10   3 vidddtCirCgkCvkaCPadl.......tsvgakgeaseeeavrkkvekCtg.............cgaCveaCP 56 
                                    +i +d+C +Cg+Cv aCP+++           + + ++ + +v+++v kC +             c  C++ CP
  gi|116754285|ref|YP_843403.1|  72 IIHEDRCYGCGNCVVACPVNVandpkgsAIGLGPKSDKVILVVEDGVVKCLNpkecrrfgpnrilCNLCTATCP 145
                                    7899***************99******96667777777777777788888888887779999999********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 !   18.8   9.6   1.6e-06    0.0019       4      52 .]      15      92 ..      14      92 .. 0.59
   2 !   13.2   0.7   8.7e-05       0.1       3      19 ..     135     151 ..     133     152 .] 0.90

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.6e-06
                         Fer4_7  4 gCgaCv.aaCpvkaieldeeenek...................gtekv............eidpekClgCgaCvavCPtga 52
                                   +C++C  ++C++ a+ l  +e++                    +   v             i++++C+gCg+Cv +CP+++
  gi|116754285|ref|YP_843403.1| 15 NCKKCGlPTCMAFAVALLAREKQIedctpllepkyeeklkklrE---VmapvagatetglIIHEDRCYGCGNCVVACPVNV 92
                                   57777558888777666544222223444444444434444430...1444445555555889***************986 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 8.7e-05
                         Fer4_7   3 igCgaCvaaCpvkaiel 19 
                                    i C+ C+a+Cp+kaie+
  gi|116754285|ref|YP_843403.1| 135 ILCNLCTATCPSKAIEF 151
                                    67************997 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   1.7      0.41   4.9e+02       4      14 ..      15      26 ..       5      44 .. 0.67
   2 !   12.8  10.1   8.7e-05       0.1       4      49 ..      15      91 ..      14      93 .. 0.63
   3 !   23.4   8.6   4.2e-08     5e-05       1      51 []      77     149 ..      77     149 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.41
                         Fer4_9  4 gCgaC.veaCpa 14
                                   +C++C  + C a
  gi|116754285|ref|YP_843403.1| 15 NCKKCgLPTCMA 26
                                   344444444544 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 8.7e-05
                         Fer4_9  4 gCgaC.veaCpagvvvedaaerkarlraase...............................eaCigCgaCveaCpkg 49
                                   +C++C  + C a +v   a e+ ++  ++                                 ++C+gCg Cv aCp +
  gi|116754285|ref|YP_843403.1| 15 NCKKCgLPTCMAFAVALLAREKQIED-CTPLlepkyeeklkklrevmapvagatetgliiheDRCYGCGNCVVACPVN 91
                                   46666566674444433333333222.2222335556677777777778888888889999899***********986 PP

  == domain 3  score: 23.4 bits;  conditional E-value: 4.2e-08
                         Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase......................eaCigCgaCveaCpkgai 51 
                                    +C+gCg+Cv aCp +v+++ ++  +    + ++                       + i C+ C++ Cp++ai
  gi|116754285|ref|YP_843403.1|  77 RCYGCGNCVVACPVNVANDPKGSAIGLGPKSDKvilvvedgvvkclnpkecrrfgPNRILCNLCTATCPSKAI 149
                                    6*******************9999999988777*********888877777776644466777*******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 ?    0.2   0.4      0.69   8.2e+02      10      19 ..      15      25 ..      12      43 .. 0.66
   2 !   18.5   2.8   1.4e-06    0.0017      33      53 ..      70      90 ..      59      95 .. 0.70
   3 !   15.7   5.5     1e-05     0.012       3      21 ..      73      91 ..      71     135 .. 0.69
   4 !    9.6   0.9    0.0008      0.95      44      58 ..     137     150 ..     131     151 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.69
                        Fer4_21 10 gCgkCli.aCe 19
                                   +C+kC + +C 
  gi|116754285|ref|YP_843403.1| 15 NCKKCGLpTCM 25
                                   78888432555 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 1.4e-06
                        Fer4_21 33 vlkvvedeCvGCnlCssvCPv 53
                                    l + ed+C GC  C+  CPv
  gi|116754285|ref|YP_843403.1| 70 GLIIHEDRCYGCGNCVVACPV 90
                                   555667788888888888887 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 1e-05
                        Fer4_21  3 idedkCigCgkCliaCedt 21
                                   i+ed+C gCg+C++aC+ +
  gi|116754285|ref|YP_843403.1| 73 IHEDRCYGCGNCVVACPVN 91
                                   7777777777777777644 PP

  == domain 4  score: 9.6 bits;  conditional E-value: 0.0008
                        Fer4_21  44 CnlCssvCPvedcie 58 
                                    CnlC++ CP +++ie
  gi|116754285|ref|YP_843403.1| 137 CNLCTATCP-SKAIE 150
                                    889999998.47765 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.4      0.18   2.1e+02       9      16 ..      15      24 ..      10      27 .. 0.70
   2 !   21.0   2.6     2e-07   0.00023       5      21 ..      73      89 ..      71      90 .. 0.90
   3 ?    2.5   6.2      0.15   1.8e+02      12      21 ..     136     145 ..     110     146 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.18
                         Fer4_2  9 rCigCg..aC 16
                                   +C  Cg  +C
  gi|116754285|ref|YP_843403.1| 15 NCKKCGlpTC 24
                                   5777776666 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 2e-07
                         Fer4_2  5 vdtdrCigCgaCvsaCP 21
                                   + +drC gCg Cv aCP
  gi|116754285|ref|YP_843403.1| 73 IHEDRCYGCGNCVVACP 89
                                   568************** PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.15
                         Fer4_2  12 gCgaCvsaCP 21 
                                     C+ C+  CP
  gi|116754285|ref|YP_843403.1| 136 LCNLCTATCP 145
                                    3****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 ?    0.3   1.3      0.71   8.5e+02       8      16 ..      15      25 ..      14      26 .. 0.74
   2 !   20.2   4.3   3.8e-07   0.00045       4      23 ..      73      92 ..      72      94 .. 0.90
   3 !   10.2   2.3   0.00052      0.62      10      24 .]     135     149 ..     120     149 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.71
                         Fer4_6  8 kCigCgd..Cv 16
                                   +C  Cg   C+
  gi|116754285|ref|YP_843403.1| 15 NCKKCGLptCM 25
                                   69999876675 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 3.8e-07
                         Fer4_6  4 idpdkCigCgdCvrvCPega 23
                                   i +d+C gCg+Cv++CP ++
  gi|116754285|ref|YP_843403.1| 73 IHEDRCYGCGNCVVACPVNV 92
                                   679**************875 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00052
                         Fer4_6  10 igCgdCvrvCPegai 24 
                                    i C+ C++ CP +ai
  gi|116754285|ref|YP_843403.1| 135 ILCNLCTATCPSKAI 149
                                    58**********998 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.8   1.7e-06    0.0021       4      30 ..      74     100 ..      72     127 .. 0.85
   2 ?    2.6   0.3       0.2   2.4e+02      57      65 ..     142     150 ..     133     151 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.7e-06
                        Fer4_15   4 DrdaCigcglCvaeapevfeldedgla 30 
                                     +d+C gcg+Cv ++p  + +d +g a
  gi|116754285|ref|YP_843403.1|  74 HEDRCYGCGNCVVACPVNVANDPKGSA 100
                                    589*******************99998 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.2
                        Fer4_15  57 raCPvdAIr 65 
                                    ++CP +AI+
  gi|116754285|ref|YP_843403.1| 142 ATCPSKAIE 150
                                    678888886 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   6.0     1e-05     0.012       4      65 .]      15      92 ..      13      92 .. 0.73
   2 !   11.9  10.8    0.0002      0.24       3      63 ..      76     146 ..      74     148 .. 0.54

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1e-05
                         Fer4_8  4 kCieCg..aCq.............saC.pvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvgi 65
                                   +C +Cg   C+             + C p+l+ + +++l++  e+++ v    ++      ++C +cg+C+++Cpv++
  gi|116754285|ref|YP_843403.1| 15 NCKKCGlpTCMafavallarekqiEDCtPLLEPKYEEKLKKLREVMAPVAGATETGLIIHEDRCYGCGNCVVACPVNV 92
                                   788898777888888888888877778555555558888888888884444444333677899************986 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.0002
                         Fer4_8   3 ekCieCgaCqsaCpvlrrtk.khlldargeaaedvqeeqvleeeealwsC.............ttcgaCtevCpv 63 
                                    ++C +Cg C  aCpv  + + k +    g +++ ++   v   e+++ +C               c+ Ct  Cp 
  gi|116754285|ref|YP_843403.1|  76 DRCYGCGNCVVACPVNVANDpKGSAIGLGPKSD-KVILVV---EDGVVKClnpkecrrfgpnrILCNLCTATCPS 146
                                    58************8777763433333333333.444444...45566662221113333333555556666665 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   1.0      0.74   8.8e+02       1       8 [.      16      25 ..      16      27 .. 0.79
   2 !   13.8   7.5   7.4e-05     0.089       1      14 [.      78      91 ..      78      92 .. 0.95
   3 !   12.0   0.7   0.00028      0.33       3      15 .]     136     148 ..     135     148 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.74
                         Fer4_3  1 CtgCg..aCv 8 
                                   C  Cg  +C+
  gi|116754285|ref|YP_843403.1| 16 CKKCGlpTCM 25
                                   999*966698 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 7.4e-05
                         Fer4_3  1 CtgCgaCvevCPvg 14
                                   C gCg Cv++CPv+
  gi|116754285|ref|YP_843403.1| 78 CYGCGNCVVACPVN 91
                                   99**********98 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.00028
                         Fer4_3   3 gCgaCvevCPvgA 15 
                                     C++C   CP++A
  gi|116754285|ref|YP_843403.1| 136 LCNLCTATCPSKA 148
                                    7**********98 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5  11.8    0.0068       8.1      51      67 .]      75      91 ..      14      91 .. 0.61
   2 !   17.1  12.7   6.9e-06    0.0082       1      66 [.      77     146 ..      77     147 .. 0.79
   3 !   11.4   1.4   0.00041      0.49       5      18 ..     137     150 ..     133     152 .] 0.90

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0068
                        Fer4_16 51 qeaitgCdiCqdvCPan 67
                                   + +++gC++C+ +CP+n
  gi|116754285|ref|YP_843403.1| 75 EDRCYGCGNCVVACPVN 91
                                   37789999999999998 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 6.9e-06
                        Fer4_16   1 rCgtCgkCaevCPtnaikekkekeiearecisy.....ntaekkdlaedeekckkqeaitgCdiCqdvCPa 66 
                                    rC +Cg+C+ +CP+n+ + +k   i    + ++     ++   k l+++e ++  +++ + C+ C+++CP 
  gi|116754285|ref|YP_843403.1|  77 RCYGCGNCVVACPVNVANDPKGSAIGLGPKSDKvilvvEDGVVKCLNPKECRRF-GPNRILCNLCTATCPS 146
                                    6*******************7777776666666786655555677777777666.8889***********5 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00041
                        Fer4_16   5 CgkCaevCPtnaik 18 
                                    C+ C+ +CP++ai+
  gi|116754285|ref|YP_843403.1| 137 CNLCTATCPSKAIE 150
                                    *************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 ?   15.6   5.5   1.5e-05     0.018       1      60 [.      15      92 ..      15      93 .. 0.62
   2 ?    3.0   4.6      0.13   1.5e+02      48      58 ..     136     146 ..     112     149 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.5e-05
                        Fer4_17  1 rCiqCgy..Clp.............eCpsyea..ydnepkkllraaklglleeaeke..ekaslCieCgeCerkCPqgl 60
                                   +C +Cg   C++              C  + +  y+++ kkl++ +++   +++e+      ++C +Cg+C+ +CP ++
  gi|116754285|ref|YP_843403.1| 15 NCKKCGLptCMAfavallarekqieDCTPLLEpkYEEKLKKLREVMAP-VAGATETGliIHEDRCYGCGNCVVACPVNV 92
                                   588898666888666666666666666655554455555555544333.33444444444669*************886 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.13
                        Fer4_17  48 eCgeCerkCPq 58 
                                     C++C++ CP+
  gi|116754285|ref|YP_843403.1| 136 LCNLCTATCPS 146
                                    68888888887 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.6      0.31   3.7e+02       3      12 ..      15      26 ..      13      27 .. 0.56
   2 ?   15.0   3.2   2.1e-05     0.025       2      17 .]      76      91 ..      75      93 .. 0.93
   3 ?    6.8   3.6    0.0093        11       5      16 ..     135     146 ..     120     147 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.31
                         Fer4_4  3 rCigCg..sCva 12
                                   +C  Cg   C+a
  gi|116754285|ref|YP_843403.1| 15 NCKKCGlpTCMA 26
                                   466666444665 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 2.1e-05
                         Fer4_4  2 erCigCgsCvaaCPqg 17
                                   +rC gCg Cv aCP++
  gi|116754285|ref|YP_843403.1| 76 DRCYGCGNCVVACPVN 91
                                   8*************75 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0093
                         Fer4_4   5 igCgsCvaaCPq 16 
                                    i C  C+a+CP+
  gi|116754285|ref|YP_843403.1| 135 ILCNLCTATCPS 146
                                    57999******7 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1       1.2   1.4e+03       6      45 ..      16      57 ..      14      61 .. 0.57
   2 ?   10.1   9.4   0.00075      0.89       3      51 ..      75     121 ..      73     150 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.2
                        Fer4_13  6 Ciacg..aCvelaPdvFeeddeggasvvaeqptseeekadae 45
                                   C  cg  +C ++a  + +++++ + +    +p+ ee+ ++++
  gi|116754285|ref|YP_843403.1| 16 CKKCGlpTCMAFAVALLAREKQIEDCTPLLEPKYEEKLKKLR 57
                                   555553357777777766666665555555565555555555 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00075
                        Fer4_13   3 rdtCiacgaCvelaPdvFeeddeggasvvaeqptseeekadaeeAadaC 51 
                                    +d+C +cg+Cv ++P   + d++g+a  +  +p+s++ +  +e+ +  C
  gi|116754285|ref|YP_843403.1|  75 EDRCYGCGNCVVACPVNVANDPKGSA--IGLGPKSDKVILVVEDGVVKC 121
                                    69********************9765..556777755544444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); 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: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1158.83
//
Query:       gi|116754286|ref|YP_843404.1|  [L=155]
Description: hypothetical protein Mthe_0979 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 1315.82
//
Query:       gi|116754287|ref|YP_843405.1|  [L=440]
Description: CoB--CoM heterodisulfide reductase [Methanosaeta thermophila PT]
Scores for 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-30  102.8  11.1    7.5e-16   58.1   0.0    2.8  3  CCG       Cysteine-rich domain
    6.8e-09   36.1   3.5    6.8e-09   36.1   3.5    3.4  4  Fer4_8    4Fe-4S dicluster domain
      3e-06   28.1   4.9      3e-06   28.1   4.9    3.2  3  Fer4_16   4Fe-4S double cluster binding domain
    3.1e-06   27.3   6.0    3.1e-06   27.3   6.0    3.9  4  Fer4_9    4Fe-4S dicluster domain
    3.1e-06   27.6   4.5    3.1e-06   27.6   4.5    3.3  5  Fer4_17   4Fe-4S dicluster domain
    3.4e-06   27.6   7.7    3.4e-06   27.6   7.7    3.5  4  Fer4_7    4Fe-4S dicluster domain
    7.5e-05   22.8   9.0    7.5e-05   22.8   9.0    3.7  5  Fer4_10   4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.13   13.2  15.0        6.2    7.7   0.3    4.3  4  Fer4_22   4Fe-4S dicluster domain
       0.16   12.2   5.0        4.3    7.6   0.6    2.8  2  Fer4_18   4Fe-4S dicluster domain
       0.66   10.2  17.5       0.23   11.7   2.2    3.5  3  Fer4_2    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   1.0       5.5   9.9e+03      68      82 ..      71      85 ..      65      87 .. 0.74
   2 !   51.2   1.5   6.1e-17   1.1e-13       1      81 [.     152     232 ..     152     235 .. 0.98
   3 !   58.1   0.0   4.2e-19   7.5e-16       1      83 [.     277     370 ..     277     372 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 5.5
                            CCG 68 tgadaivtacpgCll 82
                                   t++ + +t+c+ C +
  gi|116754287|ref|YP_843405.1| 71 TEDTYYCTTCGVCGT 85
                                   467788899999975 PP

  == domain 2  score: 51.2 bits;  conditional E-value: 6.1e-17
                            CCG   1 vayfdgChllraaypevrkalkkllealgveleel.ekesCCGagggrsgkeelaealakrnvetaeetgadaivtacpg 79 
                                    +ayf gC  + +++++++ a+ ++l+algv++  l ++e+CC ++ +r+g+ +++++ a +n++++++ g++ ++ ac+g
  gi|116754287|ref|YP_843405.1| 152 IAYFAGC-TAAYRQQALGVATVRVLNALGVDFCMLgKDEWCCASALVRTGQRDVMKEHAVHNIDALKDRGVETVLYACAG 230
                                    69*****.9*********************************************************************** PP

                            CCG  80 Cl 81 
                                    C 
  gi|116754287|ref|YP_843405.1| 231 CM 232
                                    *7 PP

  == domain 3  score: 58.1 bits;  conditional E-value: 4.2e-19
                            CCG   1 vayfdgChllraa.........ypevrkalkkllealgveleel.ekesCCGagggrsgkee.laealakrnvetaeetg 69 
                                    v+++d+Ch +r+           +++r +l+ +++ +++++e+  e + CCGaggg++   + la++ a ++++ ae++g
  gi|116754287|ref|YP_843405.1| 277 VTFHDPCHSGRHLmhiqgrdwaFEAPRDVLQSIPGLKFIDMERSrEFQRCCGAGGGVKAGIPdLALDCAVNRLRDAEQVG 356
                                    89******************************************************9999777***************** PP

                            CCG  70 adaivtacpgCllq 83 
                                    ad+i+++cp+C  +
  gi|116754287|ref|YP_843405.1| 357 ADIIASTCPFCRRN 370
                                    ***********876 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   3.5   3.8e-12   6.8e-09       1      63 [.       7      89 ..       7      91 .. 0.67
   2 ?    2.2   0.4      0.14   2.6e+02      44      56 ..     212     233 ..     179     235 .. 0.62
   3 ?   -1.8   0.0       2.5   4.4e+03      13      23 ..     362     372 ..     356     398 .. 0.77
   4 ?   -3.2   0.1       6.7   1.2e+04      57      62 ..     417     422 ..     414     431 .. 0.66

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 3.8e-12
                         Fer4_8  1 elekCieCgaCqsaCpvlrrtk.khlldargeaae......dvqeeqvlee.....................eealwsCttc 54
                                   el++C++C  C++ Cp++  +  +   ++ ++ a+               +                      e  ++Cttc
  gi|116754287|ref|YP_843405.1|  7 ELNACTRCKECMNWCPTYAVRPdRPEITPMYKIAKfrelldS--------QyglraklfgpkplheddinkyTEDTYYCTTC 80
                                   5799************99998844444444444444443330........23344555555555556666669999****** PP

                         Fer4_8 55 gaCtevCpv 63
                                   g C +vC  
  gi|116754287|ref|YP_843405.1| 81 GVCGTVCES 89
                                   *******86 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.14
                         Fer4_8  44 e.........eealwsCttcga 56 
                                    +         e+ l++C +c++
  gi|116754287|ref|YP_843405.1| 212 NidalkdrgvETVLYACAGCMR 233
                                    12233335558899******96 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 2.5
                         Fer4_8  13 saCpvlrrtkk 23 
                                    s+Cp++rr  +
  gi|116754287|ref|YP_843405.1| 362 STCPFCRRNIM 372
                                    68999988654 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 6.7
                         Fer4_8  57 CtevCp 62 
                                    C++vC+
  gi|116754287|ref|YP_843405.1| 417 CKDVCK 422
                                    555554 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 !   28.1   4.9   1.7e-09     3e-06       2      64 ..      11      87 ..      10      90 .. 0.85
   2 ?   -1.5   0.2       2.9   5.2e+03      52      61 ..     223     232 ..     191     234 .. 0.55
   3 ?   -1.6   0.1         3   5.5e+03      59      64 ..     416     421 ..     399     428 .. 0.73

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 1.7e-09
                        Fer4_16  2 CgtCgkCaevCPtnaikekkekeiearecisy.............ntaekkdlaedeekckkq..eaitgCdiCqdvC 64
                                   C++C++C++ CPt a++ + ++ei +  +i++             +  + k l+ed  +++ +  + +t C++C +vC
  gi|116754287|ref|YP_843405.1| 11 CTRCKECMNWCPTYAVRPD-RPEITPMYKIAKfrelldsqyglraKLFGPKPLHEDDINKYTEdtYYCTTCGVCGTVC 87
                                   *****************99.788887777777788888899999999999999999988884433778********** PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.9
                        Fer4_16  52 eaitgCdiCq 61 
                                    + ++ C+ C+
  gi|116754287|ref|YP_843405.1| 223 TVLYACAGCM 232
                                    2236666665 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 3
                        Fer4_16  59 iCqdvC 64 
                                    +C+dvC
  gi|116754287|ref|YP_843405.1| 416 VCKDVC 421
                                    467777 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   6.0   1.7e-09   3.1e-06       1      49 [.      10      90 ..      10      92 .. 0.95
   2 ?    0.4   0.8      0.41   7.3e+02      15      40 ..     203     232 ..     183     234 .. 0.69
   3 ?   -2.8   0.1       4.2   7.5e+03      34      40 ..     362     368 ..     344     375 .. 0.64
   4 ?   -0.3   0.0      0.68   1.2e+03       8      26 ..     417     435 ..     414     439 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1.7e-09
                         Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase................................eaCigCgaCveaCpkg 49
                                   +Ct+C++C++ Cp+ +v++d+ e +  +++a+                                   C++Cg C  +C++ 
  gi|116754287|ref|YP_843405.1| 10 ACTRCKECMNWCPTYAVRPDRPEITPMYKIAKFrelldsqyglraklfgpkplheddinkytedtYYCTTCGVCGTVCESA 90
                                   6************************9999988899*****************************988***********986 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.41
                         Fer4_9  15 gvvvedaaerkarlraase....eaCigCg 40 
                                    +v++e+a++++++l+ ++      aC gC+
  gi|116754287|ref|YP_843405.1| 203 DVMKEHAVHNIDALKDRGVetvlYACAGCM 232
                                    555566666666665555577777899998 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 4.2
                         Fer4_9  34 eaCigCg 40 
                                    + C +C+
  gi|116754287|ref|YP_843405.1| 362 STCPFCR 368
                                    4566664 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 0.68
                         Fer4_9   8 CveaCpagvvvedaaerka 26 
                                    C ++C+ ++v++++a++ +
  gi|116754287|ref|YP_843405.1| 417 CKDVCKLETVTGKEAGKDI 435
                                    9999999999988887765 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   4.5   1.8e-09   3.1e-06       1      58 [.      10      89 ..      10      91 .. 0.80
   2 ?   -0.5   0.4       1.1   1.9e+03      22      50 ..     201     232 ..     182     235 .. 0.65
   3 ?   -2.3   0.0       3.8   6.9e+03      35      49 ..     315     329 ..     293     331 .. 0.73
   4 ?   -3.4   0.1       8.3   1.5e+04      12      17 ..     364     369 ..     361     378 .. 0.67
   5 ?   -3.8   0.1        10   1.8e+04       8      15 ..     417     424 ..     416     431 .. 0.67

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 1.8e-09
                        Fer4_17  1 rCiqCgyClpeCpsyeaydnepk.kllraakl...................glleeaeke..ekaslCieCgeCerkCPq 58
                                   +C++C+ C++ Cp+y+ ++++p+ +++++++                     l+e+ +++  e    C++Cg C ++C +
  gi|116754287|ref|YP_843405.1| 10 ACTRCKECMNWCPTYAVRPDRPEiTPMYKIAKfrelldsqyglraklfgpkPLHEDDINKytEDTYYCTTCGVCGTVCES 89
                                   6******************9998679999966787788888777777777534444444356799*************87 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.1
                        Fer4_17  22 pkkllraaklglleeaeke...ekaslCieCg 50 
                                    ++ ++++ +++ +++ +++   ++   C++C 
  gi|116754287|ref|YP_843405.1| 201 QRDVMKEHAVHNIDALKDRgveTVLYACAGCM 232
                                    45566666666666665555656888899986 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 3.8
                        Fer4_17  35 eeaekeekaslCieC 49 
                                     ++e+++++++C++ 
  gi|116754287|ref|YP_843405.1| 315 IDMERSREFQRCCGA 329
                                    456778899999976 PP

  == domain 4  score: -3.4 bits;  conditional E-value: 8.3
                        Fer4_17  12 Cpsyea 17 
                                    Cp++++
  gi|116754287|ref|YP_843405.1| 364 CPFCRR 369
                                    666655 PP

  == domain 5  score: -3.8 bits;  conditional E-value: 10
                        Fer4_17   8 ClpeCpsy 15 
                                    C ++C   
  gi|116754287|ref|YP_843405.1| 417 CKDVCKLE 424
                                    77777655 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   7.7   1.9e-09   3.4e-06       1      50 [.      10      89 ..      10      91 .. 0.68
   2 ?   -1.3   0.2       1.9   3.5e+03      32      42 ..     222     232 ..     190     240 .. 0.57
   3 ?   -3.3   0.0         8   1.4e+04      36      41 ..     362     367 ..     349     374 .. 0.69
   4 ?    0.1   0.0      0.71   1.3e+03       8      22 ..     417     431 ..     413     437 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 1.9e-09
                         Fer4_7  1 rCigCgaCvaaCpvkaieldeeenek..............................gtekveidpekClgCgaCvavCPt 50
                                   +C+ C+ C++ Cp++a++ d  e  +                               + k++ d  +C++Cg+C +vC +
  gi|116754287|ref|YP_843405.1| 10 ACTRCKECMNWCPTYAVRPDRPEITPmykiakfrelldsqyglraklfgpkplhedDINKYTEDTYYCTTCGVCGTVCES 89
                                   5*****************9864333344444444444444554444444444433355888999**************76 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.9
                         Fer4_7  32 eidpekClgCg 42 
                                    e +   C gC 
  gi|116754287|ref|YP_843405.1| 222 ETVLYACAGCM 232
                                    44444566665 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 8
                         Fer4_7  36 ekClgC 41 
                                    ++C +C
  gi|116754287|ref|YP_843405.1| 362 STCPFC 367
                                    455555 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.71
                         Fer4_7   8 CvaaCpvkaieldee 22 
                                    C ++C+ ++++ +e+
  gi|116754287|ref|YP_843405.1| 417 CKDVCKLETVTGKEA 431
                                    999999998888775 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   9.0   4.2e-08   7.5e-05       6      55 ..       8      87 ..       4      88 .. 0.91
   2 !    7.3   2.0    0.0029       5.1       5      19 ..      73      87 ..      69     115 .. 0.77
   3 ?   -0.8   0.2      0.97   1.7e+03      37      49 ..     220     232 ..     189     236 .. 0.74
   4 ?   -1.5   0.1       1.6   2.8e+03      39      49 ..     358     368 ..     342     375 .. 0.68
   5 ?   -3.0   0.1       4.6   8.3e+03      15      28 ..     417     428 ..     416     435 .. 0.64

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 4.2e-08
                        Fer4_10  6 ddtCirCgkCvkaCPadl.............................tsvgakgeaseeeavrk.kvekCtgcgaCveaC 55
                                    + C+rC++C++ CP+++                             +  g k+  +++  + + + + Ct+cg C  +C
  gi|116754287|ref|YP_843405.1|  8 LNACTRCKECMNWCPTYAvrpdrpeitpmykiakfrelldsqyglraKLFGPKPLHEDDINKYTeDTYYCTTCGVCGTVC 87
                                   689******************************************9988888877777777777799************* PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0029
                        Fer4_10  5 dddtCirCgkCvkaC 19
                                   d+  C+ Cg C ++C
  gi|116754287|ref|YP_843405.1| 73 DTYYCTTCGVCGTVC 87
                                   455677777777777 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.97
                        Fer4_10  37 avrkkvekCtgcg 49 
                                     v++++++C gc 
  gi|116754287|ref|YP_843405.1| 220 GVETVLYACAGCM 232
                                    4555777777775 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 1.6
                        Fer4_10  39 rkkvekCtgcg 49 
                                    ++  + C++c 
  gi|116754287|ref|YP_843405.1| 358 DIIASTCPFCR 368
                                    44677777775 PP

  == domain 5  score: -3.0 bits;  conditional E-value: 4.6
                        Fer4_10  15 CvkaCPadltsvga 28 
                                    C+++C  +l++v +
  gi|116754287|ref|YP_843405.1| 417 CKDVC--KLETVTG 428
                                    89999..5655544 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   1.1     0.017        30      81      94 ..      10      23 ..       2      28 .. 0.64
   2 ?    7.7   0.3    0.0034       6.2      77      95 ..      72      90 ..      54      91 .. 0.77
   3 ?    6.7   0.5    0.0074        13      37      89 ..     180     235 ..     156     239 .. 0.82
   4 ?   -0.1   0.0      0.98   1.8e+03      34      86 ..     277     330 ..     261     336 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.017
                        Fer4_22 81 gCvGCgRCieacpv 94
                                   +C+ C  C+++cp+
  gi|116754287|ref|YP_843405.1| 10 ACTRCKECMNWCPT 23
                                   55555555555553 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0034
                        Fer4_22 77 fgesgCvGCgRCieacpvk 95
                                    +++ C+ Cg C ++c + 
  gi|116754287|ref|YP_843405.1| 72 EDTYYCTTCGVCGTVCESA 90
                                   4788899999999999876 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0074
                        Fer4_22  37 wdsClleeftkvaggenvrkekkerlrqrllhklsefkekf...gesgCvGCgRCi 89 
                                    +d C+l + +   +++ vr+ +++ ++++ +h +  +k++      ++C GC R  
  gi|116754287|ref|YP_843405.1| 180 VDFCMLGKDEWCCASALVRTGQRDVMKEHAVHNIDALKDRGvetVLYACAGCMRTA 235
                                    577998888888888899*****************999987444567899999965 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 0.98
                        Fer4_22  34 vrvwdsClleeftkvaggenvr.kekkerlrqrllhklsefkekfgesgCvGCg 86 
                                    v  +d C++ ++ ++ +g++   +  ++ l++    k+ +++++ + + C+G g
  gi|116754287|ref|YP_843405.1| 277 VTFHDPCHSGRHLMHIQGRDWAfEAPRDVLQSIPGLKFIDMERSREFQRCCGAG 330
                                    556777888777766666554414445555566678999999999999999988 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.6    0.0024       4.3      57      73 ..       7      23 ..       2      27 .. 0.84
   2 ?    5.4   0.3     0.011        20      54      75 ..      70      91 ..      57      95 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0024
                        Fer4_18 57 gagdcidcescvkvcPt 73
                                   + + c+ c+ c++ cPt
  gi|116754287|ref|YP_843405.1|  7 ELNACTRCKECMNWCPT 23
                                   5678************9 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.011
                        Fer4_18 54 kekgagdcidcescvkvcPtgi 75
                                    ++++  c++c++c +vc   i
  gi|116754287|ref|YP_843405.1| 70 YTEDTYYCTTCGVCGTVCESAI 91
                                   4566678***********8765 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   2.2   0.00013      0.23       7      22 .]       8      23 ..       5      23 .. 0.89
   2 ?    6.2   3.3    0.0071        13       6      20 ..      73      87 ..      69      89 .. 0.84
   3 ?   -2.0   0.1       2.7   4.9e+03       9      13 ..     227     231 ..     222     233 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                         Fer4_2  7 tdrCigCgaCvsaCPa 22
                                    ++C++C+ C + CP+
  gi|116754287|ref|YP_843405.1|  8 LNACTRCKECMNWCPT 23
                                   579************7 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0071
                         Fer4_2  6 dtdrCigCgaCvsaC 20
                                   dt  C+ Cg C ++C
  gi|116754287|ref|YP_843405.1| 73 DTYYCTTCGVCGTVC 87
                                   5556*********** PP

  == domain 3  score: -2.0 bits;  conditional E-value: 2.7
                         Fer4_2   9 rCigC 13 
                                    +C gC
  gi|116754287|ref|YP_843405.1| 227 ACAGC 231
                                    69999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.37
# Mc/sec: 3584.11
//
Query:       gi|116754288|ref|YP_843406.1|  [L=250]
Description: heterodisulfide reductase, subunit E [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00024   20.7  19.3     0.0082   15.7   5.4    3.1  3  Nitrate_red_gam  Nitrate reductase gamma subunit


Domain annotation for each model (and alignments):
>> Nitrate_red_gam  Nitrate reductase gamma subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    1.6   0.9    0.0094   1.7e+02      98     149 ..      72     124 ..      49     140 .. 0.73
   2 !   15.7   5.4   4.6e-07    0.0082      75     143 ..     122     192 ..      78     208 .. 0.71
   3 !   12.2   3.7   5.5e-06     0.098     158     210 ..     191     245 ..     188     248 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.0094
                Nitrate_red_gam  98 alvGlllLllRRltnkrvraatsasDkvvlllLllqillGllttlvsaldy.g 149
                                    +l+  +lLl R l ++ vr + +++ ++ ++ L++   lGl++ +++++++ g
  gi|116754288|ref|YP_843406.1|  72 TLILDVLLLRRTLRRSPVRWVMHMAIFYGFVTLAALSGLGLFMDIIEHFNIlG 124
                                    45544566666678889999999999999999999999999999998886543 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 4.6e-07
                Nitrate_red_gam  75 algvseelyqll.al.vaGliagvlalvGlllLllRRltnkrvraatsasDkvvlllLllqillGllttlv 143
                                    +lg+ +++  +  a+ +   i+g l+l+G ++ +lRR+  k+vr at+  D+v++  ++l +++G+++ ++
  gi|116754288|ref|YP_843406.1| 122 ILGMAHQAEMVKkAMeLPFDIFGYLLLFGSTISILRRILLKEVRDATTGYDVVLIGGVFLITITGFYAEWM 192
                                    3344433333321221233589*******************************************998776 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 5.5e-06
                Nitrate_red_gam 158 wlrslltlqpd.aellaevplifklHvllglllfa.lfPFtrLvHvlsapleYll 210
                                    w+r+  +l  d  +  + +p +  +H++l+l+lfa ++P++r +Hv++ap++ l+
  gi|116754288|ref|YP_843406.1| 191 WMRGNAFLVGDvFANPVYAPHFALIHTILALCLFAfILPWSRYLHVIAAPMTILA 245
                                    5555555555544455567788889********97478************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       878  (0.0489709); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); 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):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1795.26
//
Query:       gi|116754289|ref|YP_843407.1|  [L=138]
Description: hypothetical protein Mthe_0982 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0008   19.5   0.0     0.0017   18.5   0.0    1.5  2  HTH_34    Winged helix DNA-binding domain
     0.0033   17.3   0.7      0.061   13.2   0.2    2.3  2  TrmB      Sugar-specific transcriptional regulator TrmB
     0.0049   16.8   0.2      0.013   15.5   0.0    1.7  2  PadR      Transcriptional regulator PadR-like family
  ------ inclusion threshold ------
      0.018   14.6   0.2      0.036   13.7   0.1    1.6  2  SMC_ScpB  Segregation and condensation complex subunit ScpB


Domain annotation for each model (and alignments):
>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   3.7e-07    0.0017       4      62 ..      31      91 ..      30     107 .. 0.86
   2 ?   -2.5   0.0       1.4   6.1e+03      46      61 ..      97     112 ..      95     114 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 3.7e-07
                         HTH_34  4 avlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYie...vdkefkgkkprtllriT 62
                                   a+++yL+ v+ea+ +e+    ++ + + sv +++L +++++e    +k+ kg+ p+ ++r+T
  gi|116754289|ref|YP_843407.1| 31 AMITYLSNVEEATSREIEIGSNLRQPEVSVAMRTLRANNWVEereLKKDGKGR-PMKVYRLT 91
                                   5789*************************************732245555555.*******9 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.4
                         HTH_34  46 vdkefkgkkprtllri 61 
                                    + k f++ k+r+  +i
  gi|116754289|ref|YP_843407.1|  97 IIKHFEEEKKREAAKI 112
                                    6688888888877766 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.2   1.4e-05     0.061      19      63 ..      38      89 ..      20      93 .. 0.84
   2 ?    2.3   0.0     0.034   1.5e+02      30      50 ..     103     123 ..      98     124 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.4e-05
                                   HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.......TTEEE CS
                           TrmB 19 klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.......pklYr 63
                                   + ++at +ei   +++ ++ v  ++r L    +Ve ++ +        k+Yr
  gi|116754289|ref|YP_843407.1| 38 NVEEATSREIEIGSNLRQPEVSVAMRTLRANNWVEERELKkdgkgrpMKVYR 89
                                   6689*******************************99966577777444666 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.034
                                    CCTTSSCHCHHHHHHHHHHCT CS
                           TrmB  30 eelgvprskvYevLrsLedkG 50 
                                    ee +++ +k+ e++++L + G
  gi|116754289|ref|YP_843407.1| 103 EEKKREAAKIMESIQRLRELG 123
                                    6778999**********9987 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.8e-06     0.013      37      66 ..      61      91 ..      49      93 .. 0.92
   2 ?   -1.9   0.0      0.77   3.4e+03      15      22 ..      97     104 ..      94     123 .. 0.54

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.8e-06
                                   HHHHHHHTTSEEEEEE-S.TSSS-EEEEEES CS
                           PadR 37 aLkrLekeglvesewees.gegpprkyYrlT 66
                                   a+++L+++++ve+++ ++ g+g+p k+YrlT
  gi|116754289|ref|YP_843407.1| 61 AMRTLRANNWVEERELKKdGKGRPMKVYRLT 91
                                   6789**********99999***********9 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.77
                                    HHHHHHCC CS
                           PadR  15 iikeleel 22 
                                    iik++ee 
  gi|116754289|ref|YP_843407.1|  97 IIKHFEEE 104
                                    45555444 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 ?   13.7   0.1     8e-06     0.036      99     145 ..      43      94 ..      14     109 .. 0.75
   2 ?   -0.2   0.0      0.15   6.8e+02      14      39 ..      92     118 ..      88     126 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8e-06
                       SMC_ScpB  99 traeie...eiRGvnsdsvvrtLlerglieekg.rkeepgrpil.YgtTekF 145
                                    t+ eie   ++R  +++ ++rtL + +++ee++ +k+ +grp+  Y++T  +
  gi|116754289|ref|YP_843407.1|  43 TSREIEigsNLRQPEVSVAMRTLRANNWVEERElKKDGKGRPMKvYRLTVSL 94 
                                    445554333789999***************99835566****8769999654 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.15
                       SMC_ScpB  14 lsleeLakilels.keeveealeeLke 39 
                                    +sl+e+ k +e + k+e+++++e++++
  gi|116754289|ref|YP_843407.1|  92 VSLDEIIKHFEEEkKREAAKIMESIQR 118
                                    677777777764457777777777664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1030  (0.0574488); expected 358.6 (0.02)
Passed bias filter:                      641  (0.0357521); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1052.81
//
Query:       gi|116754290|ref|YP_843408.1|  [L=69]
Description: hypothetical protein Mthe_0983 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0015   19.1   0.1     0.0017   19.0   0.1    1.1  1  ThiS      ThiS family


Domain annotation for each model (and alignments):
>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   9.4e-08    0.0017       8      75 ..       7      67 ..       2      69 .] 0.87

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 9.4e-08
                                   HHHHT...CEEEEESSTSBHHHHHHHHHHHTCHHGTTTTEEEEETTEEEGCCTTTSB--TTCEEEEEESTT CS
                           ThiS  8 relag...eeelelaegstvaelleaLgerypelalerrvavavNgeivprlwldtelkdgDevailppVa 75
                                   r +ag   e++l+l+eg++  e+l+ Lg +       + va+ ++g  vp+   +  + +g e++i+ +V+
  gi|116754290|ref|YP_843408.1|  7 RIFAGvesERQLVLPEGTSYYEILDLLGINP------ETVAITRDGVPVPF---NDLVLPG-EIEIIRVVS 67
                                   55666668999********************......**************...7777777.899999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       174  (0.00970495); expected 358.6 (0.02)
Passed bias filter:                      165  (0.00920297); 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 0.21s 00:00:00.55 Elapsed: 00:00:00.38
# Mc/sec: 541.99
//
Query:       gi|116754291|ref|YP_843409.1|  [L=49]
Description: hypothetical protein Mthe_0984 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); 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: 0.31u 0.25s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 395.68
//
Query:       gi|116754292|ref|YP_843410.1|  [L=283]
Description: hypothetical protein Mthe_0985 [Methanosaeta thermophila PT]
Scores for complete 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-73  247.8  22.7    1.7e-73  247.6  22.7    1.0  1  SPP             Signal-peptide peptidase, presenilin aspartyl
    2.3e-09   37.2   8.7    5.3e-09   36.0   8.7    1.6  1  Peptidase_A22B  Signal peptide peptidase


Domain annotation for each model (and alignments):
>> SPP  Signal-peptide peptidase, presenilin aspartyl protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  247.6  22.7   1.9e-77   1.7e-73       3     283 .]      15     280 ..      12     280 .. 0.94

  Alignments for each domain:
  == domain 1  score: 247.6 bits;  conditional E-value: 1.9e-77
                            SPP   3 lfvvvqvlalllavplesaelqatedPtqvlnsvvyivlllvftlfvlivikkdkkliiskviyvivvavifyvflvlls 82 
                                    +++ vqvl+l +  +l ++e++ +edP  ++n ++yivl+l+ft+f+l++ +    + +s+ + +   + +fyv+ v l+
  gi|116754292|ref|YP_843410.1|  15 VIISVQVLSLGMMPALSASEVRVFEDPSATSNAILYIVLVLIFTGFLLLATRLGWGWLVSGTVQLCLFLSVFYVLGVYLP 94 
                                    45568999999999***************************************************************999 PP

                            SPP  83 ivlvvaglvnlaslvvaialvvllyaypeWyvidlaGvilavGvsalfGislgvlpavvllialavydaisvyktkhmia 162
                                     vl  a       + +++al+ ++  ypeWyv+dl+G++++ Gvs lfG+s+  lp+vvll +lavydaisvyktkhm++
  gi|116754292|ref|YP_843410.1|  95 WVL--A-------FSISLALMLAMVYYPEWYVVDLLGILVSAGVSVLFGLSMETLPVVVLLAILAVYDAISVYKTKHMVT 165
                                    993..3.......3557788888889****************************************************** PP

                            SPP 163 laegvvdlklPillvvPetlaysfveeafeeaeeaearnvlfiGlGdavlPsilvvsaavfles.hilaglelavllala 241
                                    lae v++++ P+l+v+P++ +ysf++ +++ +e       +f+GlGda++Ps+lvvsa+  l + h + g+ l++++a++
  gi|116754292|ref|YP_843410.1| 166 LAESVINIRAPLLFVIPKSRSYSFRGRGADRREA------YFLGLGDAIMPSVLVVSANWSLPAgHEIFGVALPAIGAML 239
                                    ***************************9987654......*******************9885437889*********** PP

                            SPP 242 GtlvGllvlsilvlrgrpaaGlPllnsGaiaGfligvlaagv 283
                                    Gt +G+++l      ++p+aGlP+ln+Ga++Gfl g + +gv
  gi|116754292|ref|YP_843410.1| 240 GTYMGFMFLAT-TSGEKPQAGLPFLNGGAVIGFLAGCMLSGV 280
                                    **********9.999*********************999886 PP

>> Peptidase_A22B  Signal peptide peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   8.7   5.9e-13   5.3e-09      88     201 ..      93     215 ..       8     218 .. 0.73

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 5.9e-13
                                    XXXXXXXXX------S--XXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX... CS
                 Peptidase_A22B  88 aaeivalllsiviavlwllkrhwilndilglala..ilviellrlpslkvgalLLvglflYDifwVFgtdvmvevAk... 162
                                       ++a+ +s+++++  +  ++w + d+lg+ ++  + v+  l +++l v ++LL+ l +YD   V+ t+ mv++A+   
  gi|116754292|ref|YP_843410.1|  93 LPWVLAFSISLALMLAMVYYPEWYVVDLLGILVSagVSVLFGLSMETLPV-VVLLAILAVYDAISVYKTKHMVTLAEsvi 171
                                    4456788888888888899999********86653367788888888876.57889999******************999 PP

                                    XXXXXXXXXXXX.....XXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                 Peptidase_A22B 163 eldiPillklPq.....lsneieeaskfsiLGlGDivlPGllia 201
                                    ++ +P+l+++P+      +      ++   LGlGD ++P +l+ 
  gi|116754292|ref|YP_843410.1| 172 NIRAPLLFVIPKsrsysFRGRGADRREAYFLGLGDAIMPSVLVV 215
                                    9***********877544445667778889**********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       824  (0.0459591); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); 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: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2049.21
//
Query:       gi|116754293|ref|YP_843411.1|  [L=385]
Description: DNA ligase domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.2e-14   52.9   0.0    3.7e-10   40.4   0.0    2.6  3  DNA_ligase_A_N  DNA ligase N terminus
      1e-05   25.3   0.1    2.3e-05   24.1   0.1    1.5  1  DNA_ligase_A_M  ATP dependent DNA ligase domain


Domain annotation for each model (and alignments):
>> DNA_ligase_A_N  DNA ligase N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.0   4.1e-14   3.7e-10      18     152 ..      15     141 ..       3     146 .. 0.83
   2 !    9.5   0.0   0.00013       1.2      56      97 ..     148     189 ..     142     209 .. 0.85
   3 ?   -2.5   0.0      0.63   5.6e+03      36      62 ..     277     303 ..     245     306 .. 0.59

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 4.1e-14
                                    -HHHHHHHHHHHHHTS-..SHHHHHHHHHH....SS-CCCS------HHHHHHHHHHHHT--HHHHHHHHHHHS-HHHHH CS
                 DNA_ligase_A_N  18 krlekrailanffrkvesagpedlypalrL....llPdydgreygigesllakalaealglskkkikdalakvgDlgeva 93 
                                    kr  ++ +la+++r++    +e++ pa+rL    + P++   e+  g  +l+ a+  ++ + +          gD+ge a
  gi|116754293|ref|YP_843411.1|  15 KR-DRIGALASLLRSIS---KEEICPAVRLltggIRPSWSPGELT-GRDILMDAILSISDRIE---------GGDMGEMA 80 
                                    23.4788999***9965...678*******999999999976765.77788888887776442.........3******* PP

                                    HHHHCCHHHH.------BHHHHHHHHHHHHH-.STTHHHHHHHHHHHHHHHS-HHHHHHHH CS
                 DNA_ligase_A_N  94 eevlskrstl.akkspltieevnelLdklaaa.gkgsedekkkilkkllkraspeEakyli 152
                                    e +++ ++++   +++lti  v++ L k+ ++ g+gse +++ +l++ll ++ p+E +y++
  gi|116754293|ref|YP_843411.1|  81 EHAIRHKRQRgIGEPSLTICYVHSVLNKIMKSkGRGSEGRRRSMLTGLLLSSPPLEGRYIA 141
                                    *9998887777******************9889**************************96 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00013
                                    -----HHHHHHHHHHHHT--HHHHHHHHHHHS-HHHHHHHHH CS
                 DNA_ligase_A_N  56 eygigesllakalaealglskkkikdalakvgDlgevaeevl 97 
                                    + gig++++a a+++a+g++ +k+ +a+ ++ ++g vae++ 
  gi|116754293|ref|YP_843411.1| 148 RSGIGPRTIAAAISRAYGVDVEKVWAAYSRLPEMGHVAEAAS 189
                                    569*****************9989999999888888877765 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.63
                                    .SHHHHHHHHHHSS-CCCS------HH CS
                 DNA_ligase_A_N  36 agpedlypalrLllPdydgreygiges 62 
                                    ++ edl +++rL+  ++  r+  i++s
  gi|116754293|ref|YP_843411.1| 277 HTGEDLSQITRLINRRRSARRSSIRPS 303
                                    344467777777666666666666555 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 !   24.1   0.1   2.6e-09   2.3e-05      30     196 ..     233     375 ..     221     378 .. 0.67

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 2.6e-09
                                    SEEEEEEEETTEEEEEETTS-B-GGGCHHHHHHHHHHBSTTESEEEEEEEEEEEETTTTCBEHHHHHCHHHHCHCCTHHH CS
                 DNA_ligase_A_M  30 GeRaqvhkegdkvklfSRrlkditaakpelvkalkeafkkdeksvilDGElvavdketgeilpfqklasrkkkkkkveek 109
                                    G R+q+h ++++  lf+ r +di++ +  l        ++  +s++l+GE+ +     +   + + l +r +++   ++ 
  gi|116754293|ref|YP_843411.1| 233 GIRVQLHVSEERSWLFTNRRRDISHVLSGL-------KTEASRSAMLEGEMHT----GEDLSQITRLINR-RRSA--RR- 297
                                    889999988888888888888888744443.......33344579******99....2233333333333.3333..22. PP

                                    HHHSEEEEEEEEEEEETTEEHTTSCHHHHHHHHHHHB--BTTTEEE--EEEESSHHHHHHHHHHHHHTTECEEEEEETT- CS
                 DNA_ligase_A_M 110 lkeaelclfvFDiLyldgesltdeplkeRrklLeeilkesedrvelaeslevkdveeleelleeaiseglEGlvvKnpds 189
                                     ++++++++++D  ++dg++++d++++eR +l ++++++++++       +v+ ve le   ee +++gl  ++v+ +++
  gi|116754293|ref|YP_843411.1| 298 -SSIRPSIIIWDAVCIDGKEIVDLEYSERLQLASDVVQNINGETI-----NVSVVEPLEH--EELLQSGLP-VMVRAQSA 368
                                    .479*********************************77777653.....3333333322..344444443.56666666 PP

                                    CC-TTCE CS
                 DNA_ligase_A_M 190 kYepgkr 196
                                    +Y  gkr
  gi|116754293|ref|YP_843411.1| 369 PYLLGKR 375
                                    6666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 2799.57
//
Query:       gi|116754294|ref|YP_843412.1|  [L=428]
Description: metalloenzyme domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-11   44.4   0.0    2.8e-11   43.2   0.0    1.6  2  Metalloenzyme    Metalloenzyme superfamily
    4.5e-11   42.9   0.2    8.9e-08   32.1   0.0    2.5  2  Phosphodiest     Type I phosphodiesterase / nucleotide pyroph
    2.3e-10   40.4   0.0    3.6e-10   39.7   0.0    1.3  1  Sulfatase        Sulfatase
    0.00044   19.3   0.0     0.0013   17.7   0.0    1.7  2  Alk_phosphatase  Alkaline phosphatase
     0.0012   18.3   0.1     0.0024   17.3   0.1    1.4  1  TcfC             E-set like domain


Domain annotation for each model (and alignments):
>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1         1   3.7e+03       3      13 ..      34      44 ..      32      47 .. 0.84
   2 !   43.2   0.0   7.9e-15   2.8e-11     134     247 ..     206     316 ..     188     317 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1
                                   EEEEEETTBB- CS
                                   xxxxxxxxxxx RF
                  Metalloenzyme  3 vvlvvlDGlGe 13
                                   +vl+++DGlG 
  gi|116754294|ref|YP_843412.1| 34 AVLLIVDGLGS 44
                                   689******97 PP

  == domain 2  score: 43.2 bits;  conditional E-value: 7.9e-15
                                    EEEEEE-HHHHHHHTT-HHHHHHHHHHHHHHHHHHHTTS-TTTEEEEEE-SSB--TTTSS...........-----EEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxx RF
                  Metalloenzyme 134 lvvvniknaDmvGHtgdleatiaaieaaDeavkeildaieqvdgilvvtADHgnaedmvkrdk...qplTsHtlepVPil 210
                                    l++vn+   D++GH + + ++i+a+ a+D  ++e++ ++++ d +l+vtADHg   +     +   +         +P++
  gi|116754294|ref|YP_843412.1| 206 LLIVNLGGIDSAGHYRGFDEYIRAVRALDVGLGELVRTCRERDVLLIVTADHGMSFKGSRGGHageNYSDRLESLRIPLI 285
                                    689**************************************************987776633355333333344579999 PP

                                    EESTT----S--SSHHHHTT-TTEEEEGGGHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Metalloenzyme 211 ivgkglapdkvkegakfrekggLanvaatllnllgle 247
                                     +g+g++       + +  k + a++a+tll llg+e
  gi|116754294|ref|YP_843412.1| 286 AIGPGVDD------VIVGGKWSQADIAPTLLALLGIE 316
                                    99999885......33334778889999999888876 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.2   0.00044       1.6       2      55 ..      35      95 ..      34     106 .. 0.71
   2 !   32.1   0.0   2.5e-11   8.9e-08     159     235 ..     193     260 ..     143     282 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00044
                                   EEEEETT-BTTHHHHHGSTSHHHHHHHH.............HSEEESEEE-SSS-SHHHHHHHHHHS CS
                   Phosphodiest  2 lvislDGlradlldrlaellpnlaaLak.............egvsapnlrpvfPtlTfpnhaslvTG 55
                                   +++++DGl  +++++  e+ p      +              g ++  +r+ +P+ T+p+h+++vTG
  gi|116754294|ref|YP_843412.1| 35 VLLIVDGLGSSYIYP--EHIPYS---VEgrplkqavlfnisDGARVLDIRAPVPS-TVPGHSTIVTG 95
                                   788899999999988..544432...22222444555656677777777777776.9*********9 PP

  == domain 2  score: 32.1 bits;  conditional E-value: 2.5e-11
                                    CHTHSHHHHHCTSSESEEEEEECCCHHHHHHH-TTSHHHHHHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES---E CS
                   Phosphodiest 159 aafakvvlekelekpdlllvyleetDtvgHkfGpdspevedalrrvDkaigdLlealderglsaetniilvSDHGma 235
                                    aa+    + ++l+ p ll+v+l ++D++gH+ G d  e   a+r +D  +g+L++  +er    ++ +i+++DHGm+
  gi|116754294|ref|YP_843412.1| 193 AATD---IVRRLDLPFLLIVNLGGIDSAGHYRGFD--EYIRAVRALDVGLGELVRTCRER----DVLLIVTADHGMS 260
                                    3332...2234499****************99966..599********************....************8 PP

>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.0     1e-13   3.6e-10     208     309 .]     195     315 ..     160     315 .. 0.83

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 1e-13
                                    H.........................HHHHHHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEEEESSSSCCCGHHTTSSS CS
                      Sulfatase 208 r.........................qlleaylnsveyvDdligrvlaaLeenglldntlvvftSDhgasleesngplrg 262
                                    +                         +  ++y ++v+  D ++g+++ +       +++l+++t+Dhg s ++s+g + g
  gi|116754294|ref|YP_843412.1| 195 TdivrrldlpfllivnlggidsaghyRGFDEYIRAVRALDVGLGELVRTC----RERDVLLIVTADHGMSFKGSRGGHAG 270
                                    144456777777777777777777778899********************....*******************9999999 PP

                                    CTTCSSSHHHHBEEEEEEETTTSHCEEECSEEEGGGHHHHHHHHTTE CS
                      Sulfatase 263 gkganayeggtrvPllvwwpgekaprvseelvshiDlfptildlagi 309
                                    +++ +   +++r+Pl+  +pg     ++ +  s+ D++pt+l+l+gi
  gi|116754294|ref|YP_843412.1| 271 ENY-SDRLESLRIPLIAIGPGVDDV-IVGGKWSQADIAPTLLALLGI 315
                                    999.*********************.*******************97 PP

>> Alk_phosphatase  Alkaline phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.37   1.3e+03       4      17 ..      34      47 ..      32      52 .. 0.86
   2 !   17.7   0.0   3.8e-07    0.0013     241     314 ..     193     263 ..     183     279 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.37
                                   EEEEEETT-SHHHH CS
                Alk_phosphatase  4 villigDGmgvstv 17
                                    +lli DG+g s++
  gi|116754294|ref|YP_843412.1| 34 AVLLIVDGLGSSYI 47
                                   699*********98 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 3.8e-07
                                    HHHHHHTTSTT-EEEEEEETCHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHCHHCTTEEEEEEESSEESEEEES CS
                Alk_phosphatase 241 vAiklLsknekGFFLlVEGsrIDhaaHendavgalsEvvefdeAvkaalefakkeketlvvvTaDHshvfsfgg 314
                                    +A ++ ++ +  F L+V  + ID a+H     + ++ v ++d  + + +   + e++ l++vTaDH    sf g
  gi|116754294|ref|YP_843412.1| 193 AATDIVRRLDLPFLLIVNLGGIDSAGHYRGFDEYIRAVRALDVGLGELVRTCR-ERDVLLIVTADHGM--SFKG 263
                                    5667777777789**********************************999998.************98..6665 PP

>> TcfC  E-set like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   6.7e-07    0.0024       6      49 ..     336     376 ..     332     378 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 6.7e-07
                           TcfC   6 vvflpragrveiyRdgqLlstqnvnaGnqeidtssLPsGiYeve 49 
                                     v lpr+g+v+iyR+g L+  +    G  +  ++ L  G+Y++ 
  gi|116754294|ref|YP_843412.1| 336 RVELPRPGDVDIYRNGSLIAED---SGSSSYTFRGLERGVYDLH 376
                                    5779***************986...5888888888888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3162.67
//
Query:       gi|116754295|ref|YP_843413.1|  [L=392]
Description: bifunctional formaldehyde-activating enzyme/3-hexulose-6-phosphate synthase [Methanosaeta thermophila PT]
Scores for complete 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-72  243.2   0.3      2e-72  242.3   0.3    1.5  1  Fae             Formaldehyde-activating enzyme (Fae)
    4.3e-19   69.0   1.0    1.5e-18   67.2   1.0    1.9  1  OMPdecase       Orotidine 5'-phosphate decarboxylase / HUMPS 
    6.9e-05   22.3   1.7    0.00046   19.6   1.7    2.3  1  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
    0.00024   20.9   0.2    0.00056   19.7   0.1    1.6  1  QRPTase_C       Quinolinate phosphoribosyl transferase, C-ter
     0.0033   16.9   0.5       0.19   11.2   0.1    2.3  2  PcrB            PcrB family
      0.008   15.7   0.1      0.015   14.7   0.1    1.5  1  His_biosynth    Histidine biosynthesis protein
  ------ inclusion threshold ------
      0.023   13.8   0.8      0.054   12.5   0.8    1.6  1  FMN_dh          FMN-dependent dehydrogenase
      0.034   13.3   0.1      0.064   12.4   0.1    1.6  1  NanE            Putative N-acetylmannosamine-6-phosphate epim
      0.064   12.4   0.6       0.15   11.2   0.2    1.9  2  IGPS            Indole-3-glycerol phosphate synthase
      0.067   12.5   0.7       0.12   11.7   0.2    1.6  2  TMP-TENI        Thiamine monophosphate synthase
       0.22   11.2   1.2        1.6    8.5   0.1    2.5  3  PRAI            N-(5'phosphoribosyl)anthranilate (PRA) isomer


Domain annotation for each model (and alignments):
>> Fae  Formaldehyde-activating enzyme (Fae)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  242.3   0.3   1.2e-75     2e-72       1     159 []       4     162 ..       4     162 .. 0.99

  Alignments for each domain:
  == domain 1  score: 242.3 bits;  conditional E-value: 1.2e-75
                            Fae   1 vGEalvgegeevAhidliiGekdgpvgtAfanalanqskghtpllavlrpnllvkPatlmvnkvtiknekqaellfGpaQ 80 
                                    vGEal+g+++evAhidl+iG+k+gpvg Afan l++ s+ghtpll+v+rpnll+kP+tl+v+kvt+kn++qa+++fGpaQ
  gi|116754295|ref|YP_843413.1|   4 VGEALIGKEPEVAHIDLLIGDKNGPVGIAFANGLTQLSAGHTPLLSVIRPNLLAKPSTLIVPKVTVKNMEQAAIIFGPAQ 83 
                                    8******************************************************************************* PP

                            Fae  81 aavakavadaveegiipkeeaddlviivsvfidpeakdkkkiyeynyeAtklAikrAlkeePsidevleekdkakhpfv 159
                                    +avakavadaveeg+ipke+a++lviivsvfi+p+akd+++iy+yny AtklAi+rA++++P++d+vl ek+++ hp++
  gi|116754295|ref|YP_843413.1|  84 TAVAKAVADAVEEGVIPKERAEELVIIVSVFIHPDAKDYDAIYRYNYGATKLAIQRAMEGFPDVDKVLYEKERSVHPVM 162
                                    ****************************************************************************986 PP

>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.2   1.0   9.5e-22   1.5e-18       2     224 ..     174     373 ..     173     374 .. 0.88

  Alignments for each domain:
  == domain 1  score: 67.2 bits;  conditional E-value: 9.5e-22
                                    EEEEEE-SSSHHHHHHHHHHHGG.GSSEEEEEHHHHHHHTHH.HHTHHHHHHHHHT..SEEEEEEEE-S-HHHHHHHHHS CS
                      OMPdecase   2 nLclalDvatarelleladkvgp.sivvlKthydlvegwgfegtgaklaalarkhg..flifeDrKfaDIGntvekqata 78 
                                     L++a D+ +  e+ +++ ++ +  ++ ++++++lv+ +g     +++++++r+      +++D+K+ D Gn + + a  
  gi|116754295|ref|YP_843413.1| 174 YLQIAFDIVDLAEVKRVLSEIPEsDHLLIEMGTPLVKMHG-----VQVVREVRRARpgSFVVLDLKTLDTGNLEVRLA-- 246
                                    69*********************99***************.....*********9888********************.. PP

                                    TCHHHHTTESEEEEEGTGHHHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHHH.SHHHHHHHHHHHHHHHTTESEEEC CS
                      OMPdecase  79 gsarikewadivtvhavaGkasvkalaeaaekwgnrgllilaqmsskgnlmlqek.gytqacveaarehkaedfvmGfva 157
                                        +++ ad+v ++++a  ++++ ++++a+k+g     i+++++  +  ++ ++ ++  ++ve  r+   e        
  gi|116754295|ref|YP_843413.1| 247 ----ADASADAVVISGLAPRKTIELAIKEAKKTG--IYSIVDMLNVRDPVEVLRSlSVLPDVVELHRAIDME-------- 312
                                    ....6999*************************9..9*****************557777788777777743........ PP

                                    CCHTHHHHHHTTCSCEEEHHHTTEEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSHHHHHHH CS
                      OMPdecase 158 qetlnateedaddfihltpgigleqggdgkgqqyntpekligiagadiiivGRgIlkagdpveeaer 224
                                        n +e +++ ++ ++   g    ++++g++ +++ ++ + agadii+vGR+I++++d +  +e+
  gi|116754295|ref|YP_843413.1| 313 ----N-SEHAWQSIPEIKSLGGKILVAVAGGIRVDNVRDALR-AGADIIVVGRAITRSKDVRDMTEQ 373
                                    ....2.11224566666665555789********99999988.99***************9877665 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 !   19.6   1.7   2.8e-07   0.00046     162     197 ..     326     361 ..     212     362 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.8e-07
                                    HHT---EEEEESS--TTTCHHHHHHT--EEEESHHH CS
                 Ribul_P_3_epim 162 ekeldlkievDGGvkldnieqiaeagadvlVagsav 197
                                    + + ++ + v GG+++dn++ + +agad++V+g+a+
  gi|116754295|ref|YP_843413.1| 326 SLGGKILVAVAGGIRVDNVRDALRAGADIIVVGRAI 361
                                    33456999**************************98 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 !   19.7   0.1   3.5e-07   0.00056      89     163 ..     285     366 ..     262     371 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3.5e-07
                                    SHHHHHHHHH...HT-SEEEEES-....-HHHHHHHHHHHHHHSTTSEEEEESS--TTTHHHHHCTT-SEEEECHHCHTB CS
                      QRPTase_C  89 sleeleevle...aeadiimLDnf....sveelkkaveelkeknkrvlievSGgvtlenveeyaksgvdvisvgalthsv 161
                                    ++ +  evl    + +d++ L       ++e+  + + e+k+  +++l+ v+Gg+  +nv++  + g d+i vg +++++
  gi|116754295|ref|YP_843413.1| 285 NVRDPVEVLRslsVLPDVVELHRAidmeNSEHAWQSIPEIKSLGGKILVAVAGGIRVDNVRDALRAGADIIVVGRAITRS 364
                                    4444444444222668999887654333556666666678899999****************************988877 PP

                                    -- CS
                      QRPTase_C 162 ka 163
                                    k 
  gi|116754295|ref|YP_843413.1| 365 KD 366
                                    64 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.024        40      23      68 ..     243     289 ..     226     299 .. 0.76
   2 !   11.2   0.1   0.00011      0.19     175     216 ..     325     366 ..     311     378 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.024
                                    HHHHHCTT-SEEEEECST.CHHHHHHHHHHHHHCTSSS-EEEEESSG CS
                           PcrB  23 veiviesgtDavmigGsq.svtldntvrllkkvsriklPivlepsnv 68 
                                    v+ +++  +Dav+i+G     t + +++  kk   +++  +l + ++
  gi|116754295|ref|YP_843413.1| 243 VRLAADASADAVVISGLApRKTIELAIKEAKKTGIYSIVDMLNVRDP 289
                                    66678999********9988888888888888766666555555555 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00011
                                    HHHHSSSEEEEESS--SHHHHHHHHCC.SSEEEE-CHHHHHHH CS
                           PcrB 175 kkklekarlivGGGirsaEkAkevvea.ADvivvGnvveekde 216
                                    k    k+ + v GGir   + ++ ++a AD+ivvG ++  +++
  gi|116754295|ref|YP_843413.1| 325 KSLGGKILVAVAGGIRVD-NVRDALRAgADIIVVGRAITRSKD 366
                                    444445666799***975.678888888**********98883 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   9.5e-06     0.015      70     122 ..     329     377 ..     282     389 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 9.5e-06
                                    HH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGG CS
                   His_biosynth  70 eevfipvqvGGGIrsledveelleagadkviigtaavknpelikelaekfgsq 122
                                     +  i v v GGIr  + v+++l+agad +++g a  + ++ ++++ e+f sq
  gi|116754295|ref|YP_843413.1| 329 GK--ILVAVAGGIRVDN-VRDALRAGADIIVVGRAITR-SKDVRDMTEQFLSQ 377
                                    33..8899*****9766.**********9999976555.55678888888765 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.8   3.3e-05     0.054     233     303 ..     246     361 ..     214     381 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.3e-05
                                    HHHTTESEEEE--GGG.........................TSSTT---HHHCHHHHHHHH................... CS
                         FMN_dh 233 aveaGvdgivvSNHGG.........................RqldgapatidvLpeiveav................... 268
                                    a++a +d++v+S                             R    +  +++vLp++ve                     
  gi|116754295|ref|YP_843413.1| 246 AADASADAVVISGLAPrktielaikeakktgiysivdmlnvRDPVEVLRSLSVLPDVVELHraidmensehawqsipeik 325
                                    55555555555554445555555555555555555555555333333344444444433333334444444444444444 PP

                                    ....SS-EEEESS--SHHHHHHHHHTT-SEEEESHHH CS
                         FMN_dh 269 ..ggrievlvDgGirrGsDvlkAlalGAdavllGRpf 303
                                      gg+i v v gGir    v  Al  GAd++++GR++
  gi|116754295|ref|YP_843413.1| 326 slGGKILVAVAGGIRV-DNVRDALRAGADIIVVGRAI 361
                                    4488999999999986.67999999999999999987 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 ?   12.4   0.1   3.9e-05     0.064     157     188 ..     342     376 ..     246     380 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.9e-05
                                    HHHHHHHTT--SEEEE-HHHH-HHHH...HHHHHH CS
                           NanE 157 ekakkaieiGvdavvvGsaitrleei...akkfve 188
                                    ++ ++a++ G+d +vvG aitr +++   +++f +
  gi|116754295|ref|YP_843413.1| 342 DNVRDALRAGADIIVVGRAITRSKDVrdmTEQFLS 376
                                    4568899***************9876222555655 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0         2   3.2e+03     235     245 ..       2      12 ..       1      18 [. 0.79
   2 ?   11.2   0.2   8.9e-05      0.15     168     253 ..     289     373 ..     213     374 .. 0.69

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2
                                    EEESHHHHC-T CS
                           IGPS 235 fLvGeslmrqe 245
                                    fLvGe+l+ +e
  gi|116754295|ref|YP_843413.1|   2 FLVGEALIGKE 12 
                                    9******9775 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 8.9e-05
                                    HHHHHHHHHTT-SEEEEESEETTTTEE-CHHHHHHCHCC-.....TTSEEEEESSS-SHHHHHHHCCTT-SEEEESHHHH CS
                           IGPS 168 eeeleralklgakiiGvNnRnLktlevdlntteeLaklvp.....kdvllvaeSGiktredveklkeegvnafLvGeslm 242
                                      e+ r l++  +++     +L+   +d++++e+  +++p        +lva  G    ++v++  ++g++ + vG +++
  gi|116754295|ref|YP_843413.1| 289 PVEVLRSLSVLPDVV-----ELHR-AIDMENSEHAWQSIPeikslGGKILVAVAGGIRVDNVRDALRAGADIIVVGRAIT 362
                                    445555555555555.....3433.5788888877777775533223899**999999********************** PP

                                    C-TTHHHHHHH CS
                           IGPS 243 rqedvekaire 253
                                    r++dv+ ++++
  gi|116754295|ref|YP_843413.1| 363 RSKDVRDMTEQ 373
                                    *****998876 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.6   4.2e+03     112     130 ..     246     264 ..     239     286 .. 0.51
   2 ?   11.7   0.2   7.3e-05      0.12     140     181 .]     319     361 ..     310     361 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.6
                       TMP-TENI 112 aealgadYigvGpifpTdt 130
                                    a+++ ad ++++ + p +t
  gi|116754295|ref|YP_843413.1| 246 AADASADAVVISGLAPRKT 264
                                    4444444444444444333 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 7.3e-05
                       TMP-TENI 140 eglkelaeale.iPvvaiGGitlenvaevleagadgvavvsai 181
                                    + + e+++    i v + GGi+ +nv ++l+agad + v +ai
  gi|116754295|ref|YP_843413.1| 319 QSIPEIKSLGGkILVAVAGGIRVDNVRDALRAGADIIVVGRAI 361
                                    556666666555778889*********************9998 PP

>> PRAI  N-(5'phosphoribosyl)anthranilate (PRA) isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       3.8   6.2e+03      31      56 ..      82     115 ..      65     126 .. 0.49
   2 ?    2.9   0.0     0.049        79      40     100 ..     269     327 ..     242     330 .. 0.68
   3 ?    8.5   0.1   0.00097       1.6     136     164 ..     318     349 ..     314     358 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.8
                                    BTTB--HHHHHHHCCCS--E........EEEEES CS
                           PRAI  31 skrevseeqaqellekvpak........lVGVfv 56 
                                    ++++v++  a ++ e v +k        +V Vf 
  gi|116754295|ref|YP_843413.1|  82 AQTAVAKAVADAVEEGVIPKeraeelviIVSVFI 115
                                    3555555555554444432222334455566665 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.049
                                    HHHHCCCS--EEEEEESSS-HHHHHHHHHHCTECEEEE-CGG.-HHHHHHHHHHS-TTSEE CS
                           PRAI  40 aqellekvpaklVGVfvNqpieevlriaqelgldvvQLHGdedeqeyeellktelpvikal 100
                                    ++e ++ +   +V      +  evlr +++l  dvv LH+   ++e +e + +++p ik l
  gi|116754295|ref|YP_843413.1| 269 IKEAKKTGIYSIVDMLNVRDPVEVLRSLSVL-PDVVELHRAI-DMENSEHAWQSIPEIKSL 327
                                    5555555555566666666667899999999.9********9.555555555588887765 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.00097
                                    GGGGTTSXX....TTEEEESSXXTTTHHHHHT CS
                           PRAI 136 wsliskllks...lkviLAGGLtpeNvaeaik 164
                                    w++i++++     + v +AGG+  +Nv++a++
  gi|116754295|ref|YP_843413.1| 318 WQSIPEIKSLggkILVAVAGGIRVDNVRDALR 349
                                    888888884476688999************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 2775.54
//
Query:       gi|116754296|ref|YP_843414.1|  [L=267]
Description: tRNA pseudouridine synthase A [Methanosaeta thermophila PT]
Scores for complete 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-30  103.7   0.0    3.6e-24   85.3   0.0    2.3  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 !   16.3   0.0   5.8e-07      0.01       4     106 ..       8     101 ..       6     103 .. 0.90
   2 !   85.3   0.0     2e-28   3.6e-24       1     107 [.     126     223 ..     126     224 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.8e-07
                PseudoU_synth_1   4 elvGthdfgsfckqkqekkntvrtileaaieevsgeekellvvtvkgsgFldhqVRamvgvlfavgqgklspedvkelln 83 
                                    +++G +++g f  q+q++ +tv ++++ a+ ++          +++ +g++d++V a+++v+    +++++   +++++n
  gi|116754296|ref|YP_843414.1|   8 AYLGDRYYG-F--QRQPGLRTVESVMRDALLRIGVA-----NGDFCYAGRTDRGVSALGQVIDFWIEEDRAYLAFPRVIN 79 
                                    699******.9..99****************88888.....89*******************666677999999****** PP

                PseudoU_synth_1  84 akkrkkiavetapavglvlfhvr 106
                                    + ++++    +a av  v f++r
  gi|116754296|ref|YP_843414.1|  80 SLLPSD-VWAWARAVAPVGFSAR 101
                                    ***999.8888888888887776 PP

  == domain 2  score: 85.3 bits;  conditional E-value: 2e-28
                PseudoU_synth_1   1 AakelvGthdfgsfckqkqekkntvrtileaaieevsgeekellvvtvkgsgFldhqVRamvgvlfavgqgklspedvke 80 
                                    Aa +lvGthdf++f     +k +tvr+i+++++      + + +v++v+++gF +++VR++vg+l ++g g+++++++ e
  gi|116754296|ref|YP_843414.1| 126 AAGHLVGTHDFRNF---SMSKVDTVRRIISIDVN----AHCGIVVFDVRAEGFIWNMVRRIVGALELIGIGEKPVDWILE 198
                                    799***********...789999***********....667789************************************ PP

                PseudoU_synth_1  81 llnakkrkkiavetapavglvlfhvrY 107
                                    ll+  +++   ++tap++gl+l++v Y
  gi|116754296|ref|YP_843414.1| 199 LLDPSTPHG--APTAPPEGLMLMDVGY 223
                                    ******977..9*************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); 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 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 2038.26
//
Query:       gi|116754297|ref|YP_843415.1|  [L=423]
Description: 3-isopropylmalate dehydratase large subunit [Methanosaeta thermophila PT]
Scores for complete 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-95  318.6   1.4    1.3e-92  311.2   1.4    2.4  1  Aconitase  Aconitase family (aconitate hydratase)


Domain annotation for each model (and alignments):
>> Aconitase  Aconitase family (aconitate hydratase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  311.2   1.4   7.2e-97   1.3e-92       1     461 []      15     415 ..      15     415 .. 0.91

  Alignments for each domain:
  == domain 1  score: 311.2 bits;  conditional E-value: 7.2e-97
                      Aconitase   1 ekiwdahlvee..egiayv...pdrvllqdvtgvqalvdl...aaareavrrlggtlatidhlvpvdlvidhsvgaeeal 72 
                                    eki+++ +++e   g ++v    d  +++d+tg+ a+ ++   a  + +v+++++ +   dh+vp+d     s+      
  gi|116754297|ref|YP_843415.1|  15 EKIFSRAANKEarAG-EFVmasIDCAMIHDITGPLAVRGFyeiAGKGARVWNPSRIVILFDHQVPAD-----SI------ 82 
                                    678776655443333.3333457*************99985334458889*****************.....66...... PP

                      Aconitase  73 eknledefernkeryefLksaakafgirvvppgqGIvHqvnlEyglalpgktvvgtDSHTtmigglGvlaiGvGgieaea 152
                                        +      +e+ ++L+ +ak+ gi  +++ +GI+Hqv++E+g +lpg+++vgtDSHT+++g+lG++a+G+G++++++
  gi|116754297|ref|YP_843415.1|  83 ----K-----AAENHQMLRAFAKEQGIINYDVFSGICHQVMPENGHVLPGQLIVGTDSHTCTYGALGAFATGIGSTDMAS 153
                                    ....2.....235678999************************************************************* PP

                      Aconitase 153 vllgqplelkipkvvgvkltGklkegvtakDlvlavigklrkkgvvgkvvEffGegvesLsledraTiaNMaaEvGAttg 232
                                    v+++ +l++ +p++++  ++G+l+  vt+kD++l +ig ++++g++  + Ef+G++ve++s+++r+T++NM++E+GA++g
  gi|116754297|ref|YP_843415.1| 154 VFATGKLWFMVPQTLRLVIDGRLRRRVTSKDVILRIIGDIGADGANYLACEFAGSAVERMSIAERMTMTNMSIEMGAKAG 233
                                    ******************************************************************************** PP

                      Aconitase 233 lfpvdektleYLkatgreeaavlveaydkaqalfelaadedaeydkvleldlstlepsvagpkrPqdavplselvkkefk 312
                                    l+++d+ t++YLk            ++ +++    ++ deda +++  + d+++lep+va+p+r++++vp+ ++      
  gi|116754297|ref|YP_843415.1| 234 LVEPDRVTMTYLK------------EWLTEEP---IRGDEDAIFEE-KHWDVNDLEPQVAMPHRVDNVVPV-SRL----- 291
                                    *************............3555555...67899998876.589*********************.444..... PP

                      Aconitase 313 eelekeaaekaleyklkegtklkdgkvdiaaigSCTNssnedvraaagllakavekglkvkpgvktsvaPGSevvkayle 392
                                                           ++k+d+ ++gSCTN++ ed+++aa+++      +  v++gv+++v P+S++   ++ 
  gi|116754297|ref|YP_843415.1| 292 ----------------------PHVKIDQIFLGSCTNGRFEDLKLAAEVMG-----DEPVARGVRMIVIPASRKEYMRAL 344
                                    ......................4678*************************.....899********************* PP

                      Aconitase 393 aeGlleiLekaGfevvgagCstCig.nsdrleegeaivsssNRNFegRqg.pntrayLaSPelvvaaAlaG 461
                                    ++Gl e++++aG+ v ++ C++C+g   + + +ge+++s+sNRNF gRqg p+++ yL+SP+++ a+A++G
  gi|116754297|ref|YP_843415.1| 345 RAGLIEKFMEAGAIVESPCCGPCMGgSFGLIGPGEVSLSTSNRNFVGRQGsPKGEVYLCSPAVAGASAITG 415
                                    *************************7788889*****************8799999*************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); 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: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2934.39
//
Query:       gi|116754298|ref|YP_843416.1|  [L=413]
Description: amidohydrolase [Methanosaeta thermophila PT]
Scores for complete 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-63  214.3   0.0    3.3e-63  214.1   0.0    1.0  1  Amidohydro_1  Amidohydrolase family
    3.7e-17   63.0   0.3      1e-10   41.7   0.0    2.2  2  Amidohydro_3  Amidohydrolase family
    6.3e-05   22.5   0.0    0.00011   21.7   0.0    1.3  1  A_deaminase   Adenosine/AMP deaminase


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.1   0.0   5.6e-67   3.3e-63       2     343 ..      49     385 ..      48     386 .. 0.92

  Alignments for each domain:
  == domain 1  score: 214.1 bits;  conditional E-value: 5.6e-67
                                    EEE-EEEEEEECETTECSSS....GHHHHH..........STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHHHHHH CS
                   Amidohydro_1   2 vlPGlIDaHvHleqsllrga....tledwl..........vppetaaealesgiktalksGtttvadmgattstgieall 67 
                                     +PGl+++H+Hl ++llrg      l  wl          ++p++++++++ g+ ++++ G+t  +dm++     ++  +
  gi|116754298|ref|YP_843416.1|  49 AVPGLVNSHTHLAMTLLRGYaddmELIPWLqekiwplearLKPSDVRAGVKLGCLELIRFGVTCYNDMYY----FMDETA 124
                                    68*******************9998888889***************************************....9***** PP

                                    HHHHTSSSEEEEEEESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHHHHHHHHHTTE CS
                   Amidohydro_1  68 eaaeelplglrilggkvsldrgsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealkeakkrdlp 147
                                     a++e+  g+r ++++v +d   +e +++ +e +++ +      + d+++k+a++ph+ +++s+e+l  a + a+++d++
  gi|116754298|ref|YP_843416.1| 125 AATREM--GIRGVLSGVLFD-MRPE-FINDVEPFIKKW------RDDDLIKPAVGPHAVYTCSEETLLRAKDIAERYDVK 194
                                    *****8..***********9.5545.889999998888......6889999***************************** PP

                                    EEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHHHHHHHCEEHHHHHHHHSEH CS
                   Amidohydro_1 148 vaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpteaellkerlkeagvahcpfsnsilrs 227
                                    ++iH++et+ ev    + f+    h++++e++e lg+l e ++++ah+v+ltp ++++l+er   ++vahcp sn++l+s
  gi|116754298|ref|YP_843416.1| 195 IHIHLSETRDEV----DTFV-NQRHMSPVEYLENLGFLSE-RVVAAHCVWLTPRDIRILAER--HVNVAHCPISNLKLAS 266
                                    ***********8....6777.678899*************.*********************..**************** PP

                                    HHHHHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS- CS
                   Amidohydro_1 228 grealrkaldeGvkvglgtDgaasgnslnlleelrlalklqrgllyedeegglslkealrmaTingAkalglddkvGsie 307
                                    g+++++ +++ Gv+v lgtDga+s+n+l+++ee+++a+ +q+ +   +  + l++  + rmaT n+ ka++l  + G i 
  gi|116754298|ref|YP_843416.1| 267 GIAPVATLIEHGVNVCLGTDGASSNNNLDIFEEMKVAAVVQKCSVG-R-SAILPADAVWRMATENAYKAFSL--DMG-IR 341
                                    **************************************88883333.3.4447777799*************..8**.** PP

                                    TTSB--EEEECC.CT........CGGGTTTCTSEEEEEEEETTEE CS
                   Amidohydro_1 308 vGkdADlvvvdl.di........laafvglkkdgnvkkvivkGkl 343
                                     G  ADl++++   +        ++++v++ + g+   +i++G++
  gi|116754298|ref|YP_843416.1| 342 RGALADLALINMrRPwfipvtsmISHLVYSMS-GEASYTICNGRV 385
                                    **********8884466677788999999988.899999999987 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1   9.4e-08   0.00056       1      25 [.      40      64 ..      40      76 .. 0.86
   2 !   41.7   0.0   1.7e-14     1e-10     265     472 ..     181     386 ..     154     387 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 9.4e-08
                   Amidohydro_3  1 eviDakGrlvlPGFvDsHtHlaggg 25
                                   e+iDa+++l +PG+v sHtHla + 
  gi|116754298|ref|YP_843416.1| 40 EIIDARNMLAVPGLVNSHTHLAMTL 64
                                   68******************88765 PP

  == domain 2  score: 41.7 bits;  conditional E-value: 1.7e-14
                   Amidohydro_3 265 laelvaaadergldvaihaigdaavd.dvldafeaa....aekngnqdrr.rlehaegvtesqiervaalqvaagvqpvf 338
                                    l +  + a  +++ ++ih  ++ +    ++++  +      e++g+   r  ++h+ ++t+++i+ +a+  v  + +p++
  gi|116754298|ref|YP_843416.1| 181 LLRAKDIAERYDVKIHIHLSETRDEVdTFVNQRHMSpveyLENLGFLSERvVAAHCVWLTPRDIRILAERHVNVAHCPIS 260
                                    555555566666666666555544443555554444777778888888888***************************** PP

                   Amidohydro_3 339 nfedelldsrlgperargstpvkellnagvkvalgsD..apvgpfdpwprigaavmrktrrggevlrpdeelsleealal 416
                                    n            + a+g++pv++l+++gv+v+lg+D  +  + +d + ++  a   ++      ++++  l+  ++ ++
  gi|116754298|ref|YP_843416.1| 261 NL-----------KLASGIAPVATLIEHGVNVCLGTDgaSSNNNLDIFEEMKVAAVVQK----CSVGRSAILPADAVWRM 325
                                    **...........899*********************9877788888888888777777....5788999********** PP

                   Amidohydro_3 417 yTrgpAkalgledrkGtLevGadADlvvld.adpldvdppelaear.......vrltvvdGrvv 472
                                     T+++ ka++l+    +++ Ga ADl++++ + p  ++ + + + +       +++t+++Grv+
  gi|116754298|ref|YP_843416.1| 326 ATENAYKAFSLDM---GIRRGALADLALINmRRPWFIPVTSMISHLvysmsgeASYTICNGRVL 386
                                    ************9...5**************88888887776666688999***********96 PP

>> A_deaminase  Adenosine/AMP deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   1.8e-08   0.00011     234     300 ..     247     310 ..     242     333 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.8e-08
                                    HHHCT-EEEE-HHHHCCCSST-TTTT-CHHHHHHTT-EEEE--BSCCCC.T-SHHHHHHHHHHHHT-- CS
                    A_deaminase 234 lalaqiplevcPlSNvalgafleyaenPlkeflerglnvslntDDPlqf.gttLieeYaiaaqvfkls 300
                                    la++ + ++ cP+SN +l    +    P+ +++e+g+nv l+tD      ++++ ee+++aa v k s
  gi|116754298|ref|YP_843416.1| 247 LAERHVNVAHCPISNLKL----ASGIAPVATLIEHGVNVCLGTDGASSNnNLDIFEEMKVAAVVQKCS 310
                                    78999*************....77789*****************987651566********9887755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 2902.51
//
Query:       gi|116754299|ref|YP_843417.1|  [L=452]
Description: putative pseudouridylate synthase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-10   40.7   0.0    4.2e-09   36.6   0.0    2.6  2  THUMP     THUMP domain
  ------ inclusion threshold ------
      0.049   14.0   0.0        0.6   10.5   0.0    2.3  1  TruB_N    TruB family pseudouridylate synthase (N terminal do


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 !   36.6   0.0   4.7e-13   4.2e-09      67     143 ..     108     199 ..      34     200 .. 0.82
   2 ?    1.3   0.1     0.038   3.4e+02      55      82 ..     323     349 ..     279     401 .. 0.69

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 4.7e-13
                                    HHHHHHHHHHHHHHHCT-EEEEEEEESSSTS...............SSHHHHHHHHHHHHHHCCTT-EE-SSS-SEEEEE CS
                          THUMP  67 ileaakeivkkkfeeeketFaVrvkrrgkhf...............eftsreinrevGkaivektglkVdlenPdivvrv 131
                                    ++e+a  +v + +  e  +F V+++  g  +               e  + einrevGk+i  k g+  dl+nP++vv++
  gi|116754299|ref|YP_843417.1| 108 LEELADRAVDELKGIECSRFLVGTFMSGLLAeneellladgcsrhaEPMKSEINREVGKLIALKSGKQPDLNNPEVVVHL 187
                                    44444444444443333378888887777777777888888888889********************************* PP

                                    EEETTEEEEEEE CS
                          THUMP 132 eiikdkayisid 143
                                    ++ + +++i+i 
  gi|116754299|ref|YP_843417.1| 188 HLSDGHVEIQIQ 199
                                    **********96 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.038
                                    EEEEEEESSHHHHHHHHHHHHHHHHHHC CS
                          THUMP  55 pvcevceadledileaakeivkkkfeee 82 
                                    + ++v+++++e+ +ea  e+  +  ee+
  gi|116754299|ref|YP_843417.1| 323 V-EMVKNERFEKTYEALIEFSVPVEEEK 349
                                    3.35555555555555555554444443 PP

>> TruB_N  TruB family pseudouridylate synthase (N terminal domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   6.7e-05       0.6     116     149 .]     374     407 ..     322     407 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 6.7e-05
                                    ------EEEEEEEEEEEEEEEEEEEEEESTTTTH CS
                         TruB_N 116 erkkrkvtiyelelleveepevelevecskGtYi 149
                                      k r+  +++ el e++ ++++++v+c +G Y+
  gi|116754299|ref|YP_843417.1| 374 ADKVRRRAVHSAELEEFSGRTARITVRCDSGLYV 407
                                    45779999*************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 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:                        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: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 3183.53
//
Query:       gi|116754300|ref|YP_843418.1|  [L=96]
Description: 50S ribosomal protein L21e [Methanosaeta thermophila PT]
Scores for complete 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  116.6   0.9    4.2e-34  116.4   0.9    1.0  1  Ribosomal_L21e  Ribosomal protein L21e


Domain annotation for each model (and alignments):
>> Ribosomal_L21e  Ribosomal protein L21e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.4   0.9   2.3e-38   4.2e-34       1     100 [.       1      96 []       1      96 [] 0.98

  Alignments for each domain:
  == domain 1  score: 116.4 bits;  conditional E-value: 2.3e-38
                                    X--S-STTTT-TTTTS--GGG-SS--SHHHH----TT-EEEE---TT--SS---GGGTT-EEEE..EEEETTEEEEEEEE CS
                 Ribosomal_L21e   1 mknskglrrgtrklfskkfrkkgvpplstylreykkGdkVdikidpsvqkgmphkryhGktgrvynvtkravgvivnkkv 80 
                                    m++s+g+r++tr++++k++r++g++p+ ++++++ +G+kV+i idps++kgmph+ +hG+tg+v  v++r++++++++ +
  gi|116754300|ref|YP_843418.1|   1 MPKSHGFRKNTRDKLKKSVRERGISPVVRAIQDFAVGEKVHIIIDPSIHKGMPHPKFHGRTGTV--VGRRGRAYVLEVPD 78 
                                    89**************************************************************..************** PP

                                    TTE..EEEEEE-GGGEEE-- CS
                 Ribosomal_L21e  81 ggkileKriivriehlkksk 100
                                    ++   +K +i+ +ehl  +k
  gi|116754300|ref|YP_843418.1|  79 QSA--KKLVIALPEHLVAQK 96 
                                    ***..***********8876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.27s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 754.27
//
Query:       gi|116754301|ref|YP_843419.1|  [L=115]
Description: RNA polymerase Rpb4 [Methanosaeta thermophila PT]
Scores for 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-10   42.0   0.9    1.7e-10   41.3   0.9    1.3  1  RNA_pol_Rpb4     RNA polymerase Rpb4
  ------ inclusion threshold ------
      0.012   15.5   0.2      0.046   13.6   0.0    2.0  3  EF-hand_8        EF-hand domain pair
      0.021   15.0   0.5        8.8    6.6   0.1    2.5  2  SelB-wing_2      Elongation factor SelB, winged helix
      0.042   14.2   0.2      0.074   13.4   0.2    1.4  1  DNA_ligase_A_N   DNA ligase N terminus
      0.086   12.8   1.1         11    6.1   0.4    2.7  2  HRDC             HRDC domain
       0.11   12.5   0.1       0.13   12.1   0.1    1.2  1  NleF_casp_inhib  NleF caspase inhibitor
       0.16   12.4   5.6       0.35   11.3   0.3    3.0  3  FumaraseC_C      Fumarase C C-terminus


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 !   41.3   0.9   6.8e-14   1.7e-10       1     120 [.      11     113 ..      11     114 .. 0.85

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 6.8e-14
                                    EE-HHHHHHHHHHHHHHHHCHHHHHTCCCCCHHSHCHTCHHCHHHHHHHHHHHCTHHTTSSHHHHHHHHHHHTTST.STH CS
                   RNA_pol_Rpb4   1 lLsnsEvllvlkeeleerknkdkkeseddkisekeevkgnlnkilkktleyltnkfsrlkneekfnelvellksfe.Ltk 79 
                                    lL+  Ev  +lk e+ er +                  ++l ++l++++ + +  fs+ + +e+ ++lve l   e  t+
  gi|116754301|ref|YP_843419.1|  11 LLTIAEVNALLK-EIRER-RS--------------GEAEELGYELRRAMRHAEL-FSHST-PEESRQLVEALLALEkVTP 72 
                                    589999999999.55555.22..............3468999***********8.99988.7777777777776666*** PP

                                    HHHHHHHHCSTSSHHHHHHHSTTGTTTSTSHHHHHHHHHHH CS
                   RNA_pol_Rpb4  80 aEklqlvnlkPesavelktlieeleerfedeqleeiLdelk 120
                                      ++++ +l+P +++el+++ ++++  +++e+l++iLd+++
  gi|116754301|ref|YP_843419.1|  73 EIAVKIADLRPMTRDELRAIYAKEKFSLTEEELDAILDIVR 113
                                    **************************************997 PP

>> EF-hand_8  EF-hand domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.8   4.7e+03      26      34 ..      15      23 ..       6      30 .. 0.65
   2 ?   -2.1   0.0       1.4   3.7e+03       9      15 ..      38      44 ..      38      62 .. 0.66
   3 ?   13.6   0.0   1.8e-05     0.046       5      33 ..      84     110 ..      83     112 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.8
                      EF-hand_8 26 eevdilfre 34
                                    ev +l++e
  gi|116754301|ref|YP_843419.1| 15 AEVNALLKE 23
                                   466666666 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.4
                      EF-hand_8  9 elrrilr 15
                                   elrr++r
  gi|116754301|ref|YP_843419.1| 38 ELRRAMR 44
                                   6888875 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 1.8e-05
                      EF-hand_8   5 Itreelrrilrilglkk.glseeevdilfr 33 
                                    +tr+elr i+    ++k +l+eee+d++++
  gi|116754301|ref|YP_843419.1|  84 MTRDELRAIY---AKEKfSLTEEELDAILD 110
                                    7*********...455789*********97 PP

>> SelB-wing_2  Elongation factor SelB, winged helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1    0.0034       8.8      11      40 ..      37      66 ..      36      77 .. 0.89
   2 ?    6.3   0.1    0.0044        11      17      40 ..      84     110 ..      80     113 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0034
                                   -TTS--EEHHHHHHHCSSSS-HCCHHHHHH CS
                    SelB-wing_2 11 nPlrpGmskeeLrsrlaprlpaklfqalle 40
                                   + lr+ m  +eL s   p+ +  l++all+
  gi|116754301|ref|YP_843419.1| 37 YELRRAMRHAELFSHSTPEESRQLVEALLA 66
                                   67999***********9**********997 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0044
                                    EEHHHHHHHCSS...SS-HCCHHHHHH CS
                    SelB-wing_2  17 mskeeLrsrlap...rlpaklfqalle 40 
                                    m ++eLr + a+    l ++ ++a+l+
  gi|116754301|ref|YP_843419.1|  84 MTRDELRAIYAKekfSLTEEELDAILD 110
                                    99*******663344677999999997 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 ?   13.4   0.2   2.9e-05     0.074     105     156 ..       8      65 ..       2      71 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.9e-05
                                    -----BHHHHHHHHHHHHH-......STTHHHHHHHHHHHHHHHS-HHHHHHHHHHHC CS
                 DNA_ligase_A_N 105 kkspltieevnelLdklaaa......gkgsedekkkilkkllkraspeEakyliriil 156
                                    k + lti+evn+lL+++ +       + g e +++   ++l+++++peE + l+  +l
  gi|116754301|ref|YP_843419.1|   8 KDELLTIAEVNALLKEIRERrsgeaeELGYELRRAMRHAELFSHSTPEESRQLVEALL 65 
                                    55679************8554433333333466677777777777****999998776 PP

>> HRDC  HRDC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.4    0.0043        11       2      33 ..      18      49 ..      17      75 .. 0.88
   2 ?    5.0   0.0    0.0093        24      34      50 ..      77      93 ..      76     112 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0043
                                   HHHHHHHHHHHHHHHHHHTS-HHHHS-HHHHH CS
                           HRDC  2 lallkaLrewReelAreedvppyvvfpdktLl 33
                                   +allk+ re R  +A+e++   ++ ++ + L 
  gi|116754301|ref|YP_843419.1| 18 NALLKEIRERRSGEAEELGYELRRAMRHAELF 49
                                   689***************99888888877775 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0093
                                   HHHHH---SHHHHHTST CS
                           HRDC 34 eiAeklPttleeLlqie 50
                                   +iA  +P t++eL++i 
  gi|116754301|ref|YP_843419.1| 77 KIADLRPMTRDELRAIY 93
                                   7999**********994 PP

>> NleF_casp_inhib  NleF caspase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   5.2e-05      0.13      43     117 ..      16      91 ..       4     105 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.2e-05
                NleF_casp_inhib  43 kltklknsvlseredlYevedykleggqk.veLkegitaedRdnylkdlvalyqiknavkekidnakiktikdsvk 117
                                    ++++l +++ ++r+   e + y+l + ++  eL ++ t e+  ++++ l+al ++   +  ki + +  t +++  
  gi|116754301|ref|YP_843419.1|  16 EVNALLKEIRERRSGEAEELGYELRRAMRhAELFSHSTPEESRQLVEALLALEKVTPEIAVKIADLRPMTRDELRA 91 
                                    588999999*****99999******9987369***************************99998766666666555 PP

>> FumaraseC_C  Fumarase C C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1      0.45   1.2e+03      32      47 ..       6      21 ..       2      24 .. 0.81
   2 ?    4.6   0.2     0.018        45      23      54 .]      55      86 ..      32      86 .. 0.92
   3 ?   11.3   0.3   0.00014      0.35      14      49 ..      75     111 ..      73     113 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.45
                                   HHHTT-.-HHHHHHHT CS
                    FumaraseC_C 32 vlelgllteeeldell 47
                                   vl+ +llt +e+++ll
  gi|116754301|ref|YP_843419.1|  6 VLKDELLTIAEVNALL 21
                                   7889999999999887 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.018
                                   HHT--HHHHHHHTT-.-HHHHHHHT-HHHHH. CS
                    FumaraseC_C 23 kegktlreavlelgllteeeldelldpekMtg 54
                                   +e ++l ea l+l+ +t e   ++ d + Mt+
  gi|116754301|ref|YP_843419.1| 55 EESRQLVEALLALEKVTPEIAVKIADLRPMTR 86
                                   5789999*****************99999995 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00014
                                    HHHHHHHHHHHT--HHHHHHHTT-..-HHHHHHHT-H CS
                    FumaraseC_C  14 AakIAkeAlkegktlreavlelgl.lteeeldelldp 49 
                                    A kIA     ++  lr +  ++++ lteeeld++ld+
  gi|116754301|ref|YP_843419.1|  75 AVKIADLRPMTRDELRAIYAKEKFsLTEEELDAILDI 111
                                    6677777777888999999999998**********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       813  (0.0453455); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 901.97
//
Query:       gi|116754302|ref|YP_843420.1|  [L=201]
Description: hypothetical protein Mthe_0995 [Methanosaeta thermophila PT]
Scores for complete 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-62  210.0   0.1      3e-62  209.8   0.1    1.0  1  DUF655         Protein of unknown function (DUF655)
      3e-06   27.4   0.0    5.9e-06   26.4   0.0    1.5  1  HHH_6          Helix-hairpin-helix motif
    9.9e-05   22.5   0.0    0.00022   21.4   0.0    1.6  1  HHH_3          Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.024   14.7   0.1      0.047   13.8   0.0    1.5  2  RC-P840_PscD   Photosystem P840 reaction centre protein PscD
      0.064   13.1   0.0        1.8    8.4   0.1    2.5  2  HTH_AsnC-type  AsnC-type helix-turn-helix domain


Domain annotation for each model (and alignments):
>> DUF655  Protein of unknown function (DUF655)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  209.8   0.1   8.4e-66     3e-62       2     180 ..      10     186 ..       9     187 .. 0.98

  Alignments for each domain:
  == domain 1  score: 209.8 bits;  conditional E-value: 8.4e-66
                                    --EEEEEEEETT--TT--S-GGG---EEEEEETTT--EEEEEE-TT----TT-EEE-SSS--SSEEEEEEE--GGGS-HH CS
                         DUF655   2 eeeaivLDylpeGypddkhrehrdkpvvqalgereltLlelvplkevdilkldevaigkgksdkivkikreisyedLtdv 81 
                                    e++a +LDylp+G+ ++    ++++p+vqa+ge ++ L+e++p++ v   + ++v++    +d i++++r+i y dLt++
  gi|116754302|ref|YP_843420.1|  10 ETVARILDYLPYGHVSEAITSYQKRPLVQAVGEGNFVLMEMTPKEGVVPTVGQRVNLT--ARDVIERVNRRITYGDLTNS 87 
                                    67899**************************************************986..69****************** PP

                                    HHHHHHHHHHHHHHTTHHHHHHHH-----B-SSSBGGGGSTT--HHHHHHHHHHHHHS---SHHHHHHHSTT---HHHHH CS
                         DUF655  82 araeLpdvvekivkekEdrfveffneaepitiRlHaLelLpgvgkklarkileeRerrrFesFedvkkrvkglkdpaeil 161
                                    a+ eL + ++kiv ++Edrf+++fnea pit+R+H LelLpg+gkkl+++il+eR++ +F sF+d+++rvkgl++p++++
  gi|116754302|ref|YP_843420.1|  88 AKLELGYEIQKIVLDNEDRFIRYFNEAGPITTRMHGLELLPGIGKKLMWAILNERKKGPFRSFKDLSERVKGLHNPEKLI 167
                                    ******************************************************************************** PP

                                    HHHHHHHHH-TTSS--SS- CS
                         DUF655 162 verileEiedktekYylFv 180
                                    ++ri eE+ d++ kY++F+
  gi|116754302|ref|YP_843420.1| 168 AKRIEEELMDDRIKYRVFT 186
                                    ******************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 !   26.4   0.0   1.7e-09   5.9e-06      27      66 ..     122     161 ..     106     178 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 1.7e-09
                          HHH_6  27 lGLaaikglgeaaaerivaeRekegpfksledlarrvds.l 66 
                                     GL+ + g+g++ + +i++eR+ +gpf+s++dl++rv+   
  gi|116754302|ref|YP_843420.1| 122 HGLELLPGIGKKLMWAILNERK-KGPFRSFKDLSERVKGlH 161
                                    59999****************9.8*************9642 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   6.2e-08   0.00022      15      52 ..     123     160 ..     115     165 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 6.2e-08
                          HHH_3  15 eLqklpGlgpklAknIvayReknGpfksreeLl.kvkgl 52 
                                     L+ lpG+g+kl  +I++ R k+Gpf+s+++L  +vkgl
  gi|116754302|ref|YP_843420.1| 123 GLELLPGIGKKLMWAILNER-KKGPFRSFKDLSeRVKGL 160
                                    6899****************.99*********9678887 PP

>> RC-P840_PscD  Photosystem P840 reaction centre protein PscD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.3e-05     0.047      51     109 ..      56     115 ..      49     127 .. 0.82
   2 ?   -3.4   0.0       2.6   9.3e+03      64      84 ..     169     189 ..     164     190 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.3e-05
                   RC-P840_PscD  51 ispasgrrklsptkeliekliegeielfvlt..tqpdiaidlkkkvldnenryvidfdkrg 109
                                    ++p+ g+r  ++++++ie++   +i    lt  ++ +++ +++k vldne+r++  f++ g
  gi|116754302|ref|YP_843420.1|  56 VVPTVGQRVNLTARDVIERVNR-RITYGDLTnsAKLELGYEIQKIVLDNEDRFIRYFNEAG 115
                                    7899**************9965.67666665115678899**************9999887 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.6
                   RC-P840_PscD  64 keliekliegeielfvlttqp 84 
                                    k + e+l++ +i+  v+t++p
  gi|116754302|ref|YP_843420.1| 169 KRIEEELMDDRIKYRVFTAEP 189
                                    556667777777777777766 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 ?    8.4   0.1   0.00051       1.8      23      40 ..      60      77 ..      57      77 .. 0.93
   2 ?    1.8   0.0     0.059   2.1e+02      14      27 ..     144     157 ..     136     158 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00051
                  HTH_AsnC-type 23 LAervGlSestvlrRvrr 40
                                   +++rv+l++  v++Rv+r
  gi|116754302|ref|YP_843420.1| 60 VGQRVNLTARDVIERVNR 77
                                   79**************98 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.059
                  HTH_AsnC-type  14 edaRisyaeLAerv 27 
                                    + + +s+++L+erv
  gi|116754302|ref|YP_843420.1| 144 KGPFRSFKDLSERV 157
                                    55669*******99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); 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: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1532.42
//
Query:       gi|116754303|ref|YP_843421.1|  [L=249]
Description: dimethyladenosine transferase [Methanosaeta thermophila PT]
Scores for complete 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-53  179.8   0.0      6e-53  179.6   0.0    1.0  1  RrnaAD           Ribosomal RNA adenine dimethylase
    8.7e-08   32.8   0.0    1.8e-07   31.8   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
    6.7e-05   23.5   0.0    0.00013   22.5   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
     0.0095   15.7   0.0      0.031   14.0   0.0    1.7  2  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
  ------ inclusion threshold ------
       0.01   15.6   0.0      0.015   15.1   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
      0.019   15.2   0.0      0.036   14.3   0.0    1.4  1  TrkA_N           TrkA-N domain
      0.036   13.9   0.0      0.053   13.3   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
      0.053   13.5   0.0      0.082   12.9   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
       0.11   12.0   0.0       0.19   11.2   0.0    1.3  1  MTS              Methyltransferase small domain
       0.12   11.9   0.0       0.18   11.4   0.0    1.3  1  MetW             Methionine biosynthesis protein MetW
       0.23    9.8   0.0       0.32    9.3   0.0    1.1  1  Rod_C            Rough deal protein C-terminal region


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 !  179.6   0.0   3.7e-56     6e-53       7     234 ..       2     212 ..       1     240 [. 0.93

  Alignments for each domain:
  == domain 1  score: 179.6 bits;  conditional E-value: 3.7e-56
                                    GCG--EE--HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTTTCCCEEEE-S-CC CS
                         RrnaAD   7 sygqnflknkkvineIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkklskdeklkvvhqDfl 86 
                                    + gq+fl+++ ++++I   +++++++ +leigpGkG lTe La ra  v ++E d++La  +++   + ++++v++ D+l
  gi|116754303|ref|YP_843421.1|   2 KSGQHFLTDRGIAERIAGYAEISPSDRILEIGPGKGSLTEFLAARAGRVYAIEADPELARYVEE---SFPNVEVIQGDAL 78 
                                    569*************************************************************...467********** PP

                                    GHHHHHHHCTTTCCCCEEEEEEE--TTTHHHHHHHHHHGGGGCEEEEEEEEEHHHHHHHH--TTSTT-SHHHHHHHHHEE CS
                         RrnaAD  87 kfetpeevtekdsihqeflvvanlPyeistqlvkqlleesrfglvkmllwlqkefarrllarpgskkrsrlsvlreaftd 166
                                      ++pe            +vv+nlPy+ist++  +ll     ++  m+l+ q+ef++r+la+pgs++++rlsv++ +++d
  gi|116754303|ref|YP_843421.1|  79 RVDLPE----------YNKVVSNLPYHISTKITLRLLR---NPFDLMVLMYQREFVERMLASPGSREYGRLSVNVSYYAD 145
                                    ******..........349******************6...44579********************************** PP

                                    EEEEEEC-GGCECS--SSSEEEEEEEE-SS-S--S-HHHHHHHHHHHHCTTTSBCCCHCCCTSTCHHH CS
                         RrnaAD 167 vklvakveksifsPppkvdsalvelerkdedlpqkdlkkyesvvrkllnrkrktlstslksllpggel 234
                                    v+++++v++s+f+P p v s++v+l+++  + + +d   ++s+ r l++++rk+++++l s++  + +
  gi|116754303|ref|YP_843421.1| 146 VEVLETVPRSAFRPMPHVSSSVVRLRPRRDR-ELVDELIFSSISRDLFTKRRKKVKNALASIGVADDV 212
                                    ******************************9.99***************************9988765 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.0   1.1e-10   1.8e-07       1      88 [.      29     107 ..      29     116 .. 0.87

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 1.1e-10
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHH CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsde 80 
                                    +L++G G+G lt+ la+r   ++v++++ ++e+ ++++e +    +nve++qgda ++++++  ++ vvs+    h+s +
  gi|116754303|ref|YP_843421.1|  29 ILEIGPGKGSLTEFLAARA--GRVYAIEADPELARYVEESF----PNVEVIQGDALRVDLPE--YNKVVSN-LPYHISTK 99 
                                    8*****************6..9*******************....9**********999997..9999995.53446666 PP

                                    HHHHHHHH CS
                Methyltransf_25  81 dlekalke 88 
                                     + ++l++
  gi|116754303|ref|YP_843421.1| 100 ITLRLLRN 107
                                    66666665 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   8.1e-08   0.00013       1      59 [.      30      84 ..      30     115 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 8.1e-08
                                   EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-T CS
                Methyltransf_11  1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfed 59
                                   L++G G+G+l+e la r++rv++++ ++e+ ++++e  ++    ve++++da ++ +++
  gi|116754303|ref|YP_843421.1| 30 LEIGPGKGSLTEFLAARAGRVYAIEADPELARYVEESFPN----VEVIQGDALRVDLPE 84
                                   89*************9999************888777766....668*****9998887 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 !   14.0   0.0   1.9e-05     0.031      66     116 ..      18      65 ..       9      84 .. 0.79
   2 ?   -2.0   0.0       1.6   2.6e+03      23      36 ..     147     160 ..     143     167 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.9e-05
                                    HHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHH CS
                           PCMT  66 lellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakr 116
                                      + e+++ +r+Le+G G G lt  la    + grv +ie  +el++  ++
  gi|116754303|ref|YP_843421.1|  18 AGYAEISPSDRILEIGPGKGSLTEFLAA---RAGRVYAIEADPELARYVEE 65 
                                    568899*****************99986...56677799999999765444 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.6
                                    HHHHHS-GGGGSSC CS
                           PCMT  23 ealeevdReefvpe 36 
                                    e+le+v+R+ f p 
  gi|116754303|ref|YP_843421.1| 147 EVLETVPRSAFRPM 160
                                    899********886 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   9.4e-06     0.015      16      62 ..      17      75 ..       7     129 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 9.4e-06
                Methyltransf_23 16 llpk..lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae..........k 62
                                   ++++    ++ r+L+iG+G+G+l+e l+++   v++++++pe+   +e          +
  gi|116754303|ref|YP_843421.1| 17 IAGYaeISPSDRILEIGPGKGSLTEFLAARAGRVYAIEADPELARYVEesfpnveviqG 75
                                   44443257788****************99999*******99876655455554443331 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   2.2e-05     0.036      12      53 ..      38      81 ..      35      84 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.2e-05
                                   HHHHHHHH.TTEEEEEEESSHHHHHHHHHTT..SEEEES-TTSHH CS
                         TrkA_N 12 slaeeLse.ggkdvvvidkdeerveelreeg..levvvgdatdee 53
                                   sl+e L + +g +v++i+ d+e ++ ++e +  +ev++gda + +
  gi|116754303|ref|YP_843421.1| 38 SLTEFLAArAG-RVYAIEADPELARYVEESFpnVEVIQGDALRVD 81
                                   57788888566.6******************7777******8765 PP

>> Methyltransf_31  Methyltransferase 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     0.053       4      83 ..      26      93 ..      23     128 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.3e-05
                Methyltransf_31  4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnev 83
                                     r+l++G G+G lt  la ++   ++v+ i+ ++e  ++ +e      + nve+ qgd+   +  l    ++ ++sn +
  gi|116754303|ref|YP_843421.1| 26 SDRILEIGPGKGSLTEFLAARA---GRVYAIEADPELARYVEES-----FPNVEVIQGDALRVD--LP--EYNKVVSNLP 93
                                   5789***************775...56*********99999995.....99*********9977..44..3777777643 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     5e-05     0.082      21      66 ..      21      62 ..      11      77 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5e-05
                Methyltransf_32 21 akesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvek 66
                                   a+ s++ +++++G Gkg L+  la    +   +v++i+a  el++ 
  gi|116754303|ref|YP_843421.1| 21 AEISPSDRILEIGPGKGSLTEFLAA---R-AGRVYAIEADPELARY 62
                                   45578999*****************...4.99********999865 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00012      0.19      32     117 ..      26     104 ..      16     110 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00012
                                    CSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEEE---STTTC CS
                            MTS  32 sgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdlivsNPPfhagk 111
                                    s+++l +G G G l+  la++  +  v ++++d +  +      e++  +vev++ d+l      +++ +vsN P+h ++
  gi|116754303|ref|YP_843421.1|  26 SDRILEIGPGKGSLTEFLAARAGR--VYAIEADPELARYV----EESFPNVEVIQGDALRVDL-PEYNKVVSNLPYHIST 98 
                                    6789****************9999..89999998755554....4455668899999997655.79***********999 PP

                                    HCHHHH CS
                            MTS 112 atelav 117
                                    +++l++
  gi|116754303|ref|YP_843421.1|  99 KITLRL 104
                                    976655 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00011      0.18      11      72 ..      23      86 ..      15     116 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                           MetW 11 ikpgsrvldlGcGdGellellkeekqvdgrGleldeeg..vaecvakGlsviqgdl.dkdlenfe 72
                                   i p  r+l++G G+G+l e+l+  +  + + +e d e    +e     ++viqgd+   dl +++
  gi|116754303|ref|YP_843421.1| 23 ISPSDRILEIGPGKGSLTEFLAA-RAGRVYAIEADPELarYVEESFPNVEVIQGDAlRVDLPEYN 86
                                   78999****************76.78899999999753112233335689999996255777765 PP

>> Rod_C  Rough deal protein C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00019      0.32     174     227 ..      94     147 ..      87     152 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00019
                          Rod_C 174 yklndeellklvgkPaeLIvsLYehssiekrikepagrdyPdihalvkeiaeln 227
                                    y+++++  l+l+++P  L+v +Y+ + +e+ + +p +r+y  +   v+  a+++
  gi|116754303|ref|YP_843421.1|  94 YHISTKITLRLLRNPFDLMVLMYQREFVERMLASPGSREYGRLSVNVSYYADVE 147
                                    78899999********************************99888888777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1848.15
//
Query:       gi|116754304|ref|YP_843422.1|  [L=415]
Description: cytochrome c biogenesis protein, transmembrane region [Methanosaeta thermophila PT]
Scores for complete 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-20   72.4  16.0    6.4e-20   72.0  16.0    1.2  1  DsbD      Cytochrome C biogenesis protein transmembrane regio
    2.9e-12   47.0  17.9    5.5e-09   36.2  13.1    2.2  2  DsbD_2    Cytochrome C biogenesis protein transmembrane regio


Domain annotation for each model (and alignments):
>> DsbD  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.0  16.0   7.1e-24   6.4e-20       2     211 ..     185     405 ..     184     407 .. 0.79

  Alignments for each domain:
  == domain 1  score: 72.0 bits;  conditional E-value: 7.1e-24
                           DsbD   2 flaGllsflsPCilpliPaylsyisgvsvedvktekkkvkvllkallFvlGlslvfvslglsaaflgqllkdvkevirrv 81 
                                    f  G++++lsPC ++l+ a +syi +    d  ++    + l   + F +G++ vf  +gl +++lg  +  +++    +
  gi|116754304|ref|YP_843422.1| 185 FALGMMTSLSPCSVALLAALFSYIISRRRRDTADG--YREGLAIGIAFTIGMAAVFFVIGLFVSQLGIFM-RSSRLFDLA 261
                                    677*********************98888888887..4468999**********************9777.788999*** PP

                           DsbD  82 aglivillGlhflgvfk......ievleklkll...........lkikkkaelsvlgalllGltFalgwsPCigP.vlas 143
                                    agl+ ++lG++ +  ++      +    + ++            lki +++  s+lga+ lG  F+lgw+PC+   v+  
  gi|116754304|ref|YP_843422.1| 262 AGLLLVVLGVNSIIPLSefvgpiF---SFRRSEksylerlinvsLKIFERS--STLGAFFLGAFFSLGWAPCAISlVFPV 336
                                    **********99854446665552...333333444666666444444444..45*****************76515555 PP

                           DsbD 144 vlalaaskeslakgallllvyvlGlaipfllvglllellk.kklkslkkyskaveiaggvllvllGvll 211
                                    ++ l +++ s + g ++l+v+ lG ++p++ ++ l+ ++  + +    +  ++++++ g+l+++lGvl+
  gi|116754304|ref|YP_843422.1| 337 IIWLISQDISPLGGGIMLFVFGLGHGVPVIPMAALSRSAAaRIADRYISAGSYITKIFGILVITLGVLF 405
                                    5666777778889999*************977766665550455556667789**************97 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 !   20.8   7.1   3.4e-08   0.00031     103     198 ..     167     271 ..     134     272 .. 0.77
   2 !   36.2  13.1   6.2e-13   5.5e-09      38     198 ..     230     403 ..     228     404 .. 0.65

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.4e-08
                         DsbD_2 103 llsrllkklakklkslasalllGllnGllpCgl.vysalllalas.......gsaleGalvmlaFgLGTlpalllfglll 174
                                    + s +l++  +   s  ++++lG++++l pC + +++al+  + s       + + eG ++ +aF +G   +++++gl++
  gi|116754304|ref|YP_843422.1| 167 RSSGWLSSSRAG-TSAIGMFALGMMTSLSPCSVaLLAALFSYIISrrrrdtaDGYREGLAIGIAFTIGMAAVFFVIGLFV 245
                                    445555555554.68899*************98455555555543333333367899*********************** PP

                         DsbD_2 175 gllskklr.kkllr.lagvllillgl 198
                                    ++l+  +r  +l+  +ag+ll++lg+
  gi|116754304|ref|YP_843422.1| 246 SQLGIFMRsSRLFDlAAGLLLVVLGV 271
                                    *****888678888677888888886 PP

  == domain 2  score: 36.2 bits;  conditional E-value: 6.2e-13
                         DsbD_2  38 ynlGRilsYallGalvgllgsvlqlageleglrallgvllgllllllglkll.l....kkkllklerlgkllsrllkkla 112
                                    +++G  + + ++G++v  lg ++ +       ++l+ +++glll++lg++ +       + + +++r +k + ++l +++
  gi|116754304|ref|YP_843422.1| 230 FTIGMAAVFFVIGLFVSQLGIFMRS-------SRLFDLAAGLLLVVLGVNSIiPlsefVGPIFSFRRSEKSYLERLINVS 302
                                    5555555666666666666655544.......455555555555555555542211112223446666666555555555 PP

                         DsbD_2 113 kkl...kslasalllGlln..GllpCgl..vysalllalas.gsaleGalvmlaFgLGTlpalllfglllgllskklr.. 182
                                     k+    s+ +a++lG+++  G++pC++  v++++++ +++  s+l+G++++++FgLG  ++++ +++l++ + +++   
  gi|116754304|ref|YP_843422.1| 303 LKIferSSTLGAFFLGAFFslGWAPCAIslVFPVIIWLISQdISPLGGGIMLFVFGLGHGVPVIPMAALSRSAAARIAdr 382
                                    445687899*******8854499***76558899999887647****************999999999999998877744 PP

                         DsbD_2 183 .....kkllrlagvllillgl 198
                                           ++++ g+l+i lg+
  gi|116754304|ref|YP_843422.1| 383 yisagSYITKIFGILVITLGV 403
                                    444546667777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       820  (0.045736); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 3110.67
//
Query:       gi|116754305|ref|YP_843423.1|  [L=171]
Description: hypothetical protein Mthe_0998 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.21   11.4   0.0       0.25   11.2   0.0    1.1  1  TraF      F plasmid transfer operon protein


Domain annotation for each model (and alignments):
>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   1.4e-05      0.25     124     179 ..      54     108 ..      45     145 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.4e-05
                           TraF 124 lkklakeygLlfFyrgkcpyceaqapilqafadkyglevraVsvdgrplpelpnar 179
                                    l++l+++   l+F+  +c yc++q + ++++ ++y  +v + ++ g  + + ++  
  gi|116754305|ref|YP_843423.1|  54 LNALKDKPV-LIFVHLNCDYCAPQKEAVDSVMQDYAGDVTFFDLSGDSDARAADVL 108
                                    555555555.5678899*******************99999999998887766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1374.96
//
Query:       gi|116754306|ref|YP_843424.1|  [L=206]
Description: hypothetical protein Mthe_0999 [Methanosaeta thermophila PT]
Scores for complete sequence (score 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   12.7   0.0       0.44   11.0   0.0    1.8  2  DUF2340   Uncharacterized conserved protein (DUF2340)


Domain annotation for each model (and alignments):
>> DUF2340  Uncharacterized conserved protein (DUF2340)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   2.5e-05      0.44      49     113 ..      38     100 ..      29     109 .. 0.79
   2 ?   -1.1   0.0      0.14   2.5e+03      91     110 ..     138     157 ..     118     180 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 2.5e-05
                        DUF2340  49 frnvkydtlKiytkahgsKttnlvinlddddelilkdeektLaelgvenEtelslfnredYeefk 113
                                    f n  +d  Kiy   +g K ++lv+ +     ++ ++++   ++ + ++E+e+ + n+  Y e++
  gi|116754306|ref|YP_843424.1|  38 FVNGYMDETKIYETDYGFKGQKLVVGTRGSG-TVSRRQTIDFWSSNTSDESEMYF-NEWGYFEYH 100
                                    66667899*******************9998.89999999************965.544444443 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.14
                        DUF2340  91 aelgvenEtelslfnredYe 110
                                    +++ + +  ++sl++ + Y 
  gi|116754306|ref|YP_843424.1| 138 KDTTIYQSENVSLYQINSYL 157
                                    44455555566666666664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); 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: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1517.97
//
Query:       gi|116754307|ref|YP_843425.1|  [L=252]
Description: histone deacetylase superfamily protein [Methanosaeta thermophila PT]
Scores for complete 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  113.3   2.3    3.8e-24   85.7   0.4    3.0  3  Hist_deacetyl  Histone deacetylase domain


Domain annotation for each model (and alignments):
>> Hist_deacetyl  Histone deacetylase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.0   0.00044       7.8       3      52 ..      19      60 ..      16      62 .. 0.78
   2 !   85.7   0.4   2.1e-28   3.8e-24      86     182 ..      63     154 ..      60     161 .. 0.93
   3 !   20.3   0.1   1.7e-08   0.00031     229     294 ..     174     239 ..     169     250 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.00044
                                   CGTHHHHHHHHHHHHT.THHHHCCE.EE-----HHHHTTTS-HHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Hist_deacetyl  3 enpkRlsaileslaesvglldelelliqpseatkeellkvHskeYlelle 52
                                   enp+R++   ++l    +       +++p +a++ee++ vH++ ++e+++
  gi|116754307|ref|YP_843425.1| 19 ENPDRVRLTAQELSGY-E-------FFEPAPASQEEIASVHTSGHIERVR 60
                                   6777777666666653.4.......4689*****************9986 PP

  == domain 2  score: 85.7 bits;  conditional E-value: 2.1e-28
                                    TCCHHHHHHHHHHHHHHHHHHTTSSSEEEETTSS--TT-BTTB-BTTBSS-HHHHHHHHHHHCC-SS-EEEEE-SSS--H CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Hist_deacetyl  86 ktlkaallavgavleavdavlsgsvkaafvlvrPpgHHakaseasGFClvNnvaiaikylqakhelkrvailDvDvHhGn 165
                                    +++ aa la+g++++a++  l++    af l+rPpgHHa +++  G C++Nn+a+a+k ++   +++rv+ilD+D+H+G+
  gi|116754307|ref|YP_843425.1|  63 GLYGAAALAAGGAVAAARIALRE---PAFGLIRPPGHHASSDHSWGMCFFNNIAVAVKAIRP--HVRRVLILDIDLHFGD 137
                                    578899************99966...9*******************************9999..689************* PP

                                    HHHHHCTT-TTEEEEEE CS
                                    xxxxxxxxxxxxxxxxx RF
                  Hist_deacetyl 166 GteeafysdpdvltlSi 182
                                    Gt ++f+ dpdv ++ i
  gi|116754307|ref|YP_843425.1| 138 GTVSIFRWDPDVSVVNI 154
                                    ************98866 PP

  == domain 3  score: 20.3 bits;  conditional E-value: 1.7e-08
                                    CHHHHHCCH--SEEEEEE-STTBTTSTT-S-BB-HHHHHHHHHHHCCCHGS-.G..EEEEE-S---HH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x.xxxxxxxxxxxxx RF
                  Hist_deacetyl 229 ilrpvleefkPdlilvsaGfDalkgdplgelnlsvegykeltkklaeladkv.k.kvvllleGGYnle 294
                                     ++++le ++ d+i vsaGfD+++ d  g l  ++++y ++ + +++ +++  + +  ++leGGY+++
  gi|116754307|ref|YP_843425.1| 174 QVKNALEFHEYDIIGVSAGFDTYRLDWGGML--DIDDYRKIGSLIRDASEERcGgRRFAVLEGGYHQD 239
                                    56788999999***************99976..6678**********99999988**********874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); 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 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1960.38
//
Query:       gi|116754308|ref|YP_843426.1|  [L=467]
Description: cobyrinic acid a,c-diamide synthase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-40  138.6   0.0    2.6e-40  138.2   0.0    1.2  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
      5e-19   68.9   0.2    7.3e-11   42.3   0.0    2.2  2  AAA_26         AAA domain
    2.1e-18   66.6   0.0    3.4e-18   65.9   0.0    1.3  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
     0.0075   15.9   0.0      0.012   15.3   0.0    1.2  1  Peptidase_S51  Peptidase family S51
  ------ inclusion threshold ------
       0.01   15.1   0.0      0.021   14.1   0.0    1.4  1  DUF1611        Domain of unknown function (DUF1611_C) P-loop 
      0.029   13.9   0.0      0.064   12.8   0.0    1.5  1  AAA_25         AAA domain
      0.059   13.2   0.0       0.12   12.2   0.0    1.4  1  SNO            SNO glutamine amidotransferase family
       0.11   13.0   0.0       0.26   11.7   0.0    1.6  1  GlpM           GlpM protein
       0.12   10.6   0.1       0.17   10.0   0.1    1.1  1  FTHFS          Formate--tetrahydrofolate ligase
       0.14   12.1   0.0       0.25   11.3   0.0    1.5  1  MobB           Molybdopterin guanine dinucleotide synthesis p
       0.17   11.8   0.2       0.56   10.1   0.2    1.8  2  NTPase_1       NTPase


Domain annotation for each model (and alignments):
>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.2   0.0   1.6e-43   2.6e-40       1     193 [.     264     451 ..     264     454 .. 0.92

  Alignments for each domain:
  == domain 1  score: 138.2 bits;  conditional E-value: 1.6e-43
                       GATase_3   1 kiavirlpaisnyt..dldpLeaepevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpv 78 
                                    +ia++ ++a+ +y+  ++d L+ ++++ + f+p  +++l +d+d ++++Gg++++++ al++  +   +i+eaa++g+p+
  gi|116754308|ref|YP_843426.1| 264 RIAIALDEAFCFYYqdNIDRLRSTGAEIIPFSP-IRDAL-PDVDGIYIGGGYPELHATALEAG-RCIPQIREAASDGMPI 340
                                    69*******************************.78889.56*****************9998.8999************ PP

                       GATase_3  79 lgiCGGlqmLGeeiedpegvegeageveglglLdietefekekltgqvegevel........aaegeevkGyEiHsGrti 150
                                    +g+CGGl++LGe+++ +++      +++++g+L+++t ++k +l+    g+ve+        +++g+ ++G+E+H++r  
  gi|116754308|ref|YP_843426.1| 341 YGECGGLMYLGEHLVVEDR------SYKMTGVLPASTMMTK-RLQ--ALGYVEAevvrdnpfSQKGSVIRGHEFHYSRME 411
                                    **************98875......7***************.877..66666666689**998899************** PP

                       GATase_3 151 lkekakpllkvkvggnng.ekdGavkksedgnvlGtYlHglfdn 193
                                     +++ak ++++++g +++ + dG++++     +lG YlH +f++
  gi|116754308|ref|YP_843426.1| 412 CDRDAKFAYRLRRGRGIEnGMDGLIEH----MTLGGYLHAHFAS 451
                                    ***********88666666******88....***********87 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.1   1.2e-08   1.9e-05       3      36 ..      31      64 ..      30      68 .. 0.93
   2 !   42.3   0.0   4.5e-14   7.3e-11      99     195 ..     107     206 ..      90     209 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.2e-08
                         AAA_26  3 ifvtgtdtgvGKTvvslgLvralkrkgvkvgyfK 36
                                   ++++gt  gvGKT+v+lgL++al+r+g+ v+ fK
  gi|116754308|ref|YP_843426.1| 31 FIIAGTHSGVGKTTVTLGLMAALRRRGMTVQPFK 64
                                   689*************************998776 PP

  == domain 2  score: 42.3 bits;  conditional E-value: 4.5e-14
                         AAA_26  99 adivvVEGagglgvpi..teellnadiaknlgapvilVarggl..gtinqllltiealrqknvrvlGvilNkvrnpenve 174
                                    ad+ vVEG+ gl ++i   ee+++a +ak l +pv+lV++++   ++ ++l+    ++    v+++GvilN+v +++ +e
  gi|116754308|ref|YP_843426.1| 107 ADVAVVEGVMGLYDGIggGEEASTAHVAKVLSIPVVLVVNVHGmsRSAAALIHGFRSFDP-SVNIIGVILNQVGSERHLE 185
                                    6999*********99722577*******************96621455556666666655.8****************** PP

                         AAA_26 175 tlekksgipvlGvvPylpdle 195
                                    +l+++++ +++G++P  ++++
  gi|116754308|ref|YP_843426.1| 186 ALRESINFRIFGALPRRRSIS 206
                                    ***************998875 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 !   65.9   0.0   2.1e-21   3.4e-18       2     125 ..      32     211 ..      31     214 .. 0.87

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 2.1e-21
                                    EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH....HTTEB-HHHH....................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxx....................... RF
                           CbiA   2 aiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai....leglendiep....................... 54 
                                    +ia+t +GvGKTt++++L++al rrg  V++++++p+    ++         +++ +                       
  gi|116754308|ref|YP_843426.1|  32 IIAGTHSGVGKTTVTLGLMAALRRRGMTVQPFKVGPDFIDPTHhtaiC----GRHSRnldtfmmgedgvrrsflsairga 107
                                    89***********************************77777644431....22222556788888888899******** PP

                                    ......................................CCHCCCHHHHHHCHCHHHH.....EEEEEEEEESS...-TTC CS
                                    ......................................xxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxx RF
                           CbiA  55 ......................................dlkrllellealgkkkall...lkiagvvlnrvdgeneetll 93 
                                                                          ++  ++++++al ++++ +   ++i+gv+ln v++e++ ++l
  gi|116754308|ref|YP_843426.1| 108 dvavvegvmglydgigggeeastahvakvlsipvvlvvNVHGMSRSAAALIHGFRSFdpsVNIIGVILNQVGSERHLEAL 187
                                    *************************************************************************9777777 PP

                                    HHHHHHHHHHCTS-EEEEEE--CCHCCCCHHT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA  94 kealeelkqrygvpvlgviprdeavaeaparg 125
                                    +e++       + +++g +pr+ ++  +p+r+
  gi|116754308|ref|YP_843426.1| 188 RESI-------NFRIFGALPRRRSI-SLPSRH 211
                                    6666.......77899999998877.566665 PP

>> Peptidase_S51  Peptidase family S51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   7.2e-06     0.012      76     157 ..     297     385 ..     280     396 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 7.2e-06
                                    HHHHHHHSSEEEE--S-HHHHHHHHHHTTHHHHHHHHHHTT-EEEEETHHHHTTSSB-GGGTT.TS-GGG-S......-- CS
                  Peptidase_S51  76 ieeklleadviyvgGGntfrLlkllketgldkllreavqqglvyiGvSAGaivagesiettsy.sdspikap......es 148
                                    i++ l + d+iy+gGG     +++l+  +    +rea ++g+++ G   G +  ge +  ++    ++ + p      + 
  gi|116754308|ref|YP_843426.1| 297 IRDALPDVDGIYIGGGYPELHATALEAGRCIPQIREAASDGMPIYGECGGLMYLGEHLVVEDRsYKMTGVLPastmmtKR 376
                                    7889999*********9999999*****************************9999876544202333333333456666 PP

                                    -B----SSS CS
                  Peptidase_S51 149 feaLgLvkf 157
                                    ++aLg v+ 
  gi|116754308|ref|YP_843426.1| 377 LQALGYVEA 385
                                    666666665 PP

>> DUF1611  Domain of unknown function (DUF1611_C) P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.3e-05     0.021      13      50 ..      29      66 ..      20      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.3e-05
                        DUF1611 13 krvlvvGTdcavGKrttaleleealeerGlkaafvaTg 50
                                   +  ++ GT + vGK t +l l +al++rG++++ +  g
  gi|116754308|ref|YP_843426.1| 29 PAFIIAGTHSGVGKTTVTLGLMAALRRRGMTVQPFKVG 66
                                   666899************************99876665 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     4e-05     0.064      23      59 ..      20      56 ..      11      67 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4e-05
                         AAA_25 23 rwlvkgllpagelallaGapgtGKttlaldlalava.t 59
                                   rw +++++ + ++++   ++g+GKtt++l l++a+  +
  gi|116754308|ref|YP_843426.1| 20 RWCIQEFM-MPAFIIAGTHSGVGKTTVTLGLMAALRrR 56
                                   89****97.899********************998644 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   7.2e-05      0.12      29      89 ..     299     358 ..     278     374 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.2e-05
                                    GGGCC-SEEEE-SS-HHHHHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHCCEETTBS CS
                            SNO  29 edlaevdaliiPGGestamskliertglyedllefvknsekvvlGtCaGlillskelenel 89 
                                    + l +vd++ i GG     +  +e    +++++e + ++  +++G C Gl++l ++l  e+
  gi|116754308|ref|YP_843426.1| 299 DALPDVDGIYIGGGYPELHATALEAGRCIPQIREAASDG-MPIYGECGGLMYLGEHLVVED 358
                                    57899*********998888889999999*******999.9*************9998774 PP

>> GlpM  GlpM protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00016      0.26       7      64 ..     141     200 ..     134     207 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00016
                           GlpM   7 aavvlliallsksknyyiaGlvplfptfaliahyi..vgserslealrttilfglwsiip 64 
                                     ++v+ +  +s+s    i G+  + p+  +i   +  vgser lealr++i f ++  +p
  gi|116754308|ref|YP_843426.1| 141 VVLVVNVHGMSRSAAALIHGFRSFDPSVNIIGVILnqVGSERHLEALRESINFRIFGALP 200
                                    33444455588999999*****999**99998765559******************9998 PP

>> FTHFS  Formate--tetrahydrofolate ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00011      0.17      62      87 ..      33      58 ..      28      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00011
                                   SS--TT--SHHHHHHHHHHHHHHTT- CS
                          FTHFS 62 itPtplGeGKttttigLaqalnklgk 87
                                   i+ t  G GKtt+t+gL+ al++ g 
  gi|116754308|ref|YP_843426.1| 33 IAGTHSGVGKTTVTLGLMAALRRRGM 58
                                   67899****************99886 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00015      0.25       4      34 ..      33      64 ..      30     114 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00015
                           MobB  4 ivgk.sgsGKTtLleklipelkarglrvgtiK 34
                                   i+g+ sg GKTt    l+++l++rg++v   K
  gi|116754308|ref|YP_843426.1| 33 IAGThSGVGKTTVTLGLMAALRRRGMTVQPFK 64
                                   555449*********************98776 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.2   0.00034      0.56       3      33 ..      32      63 ..      30      66 .. 0.84
   2 ?   -1.4   0.0       1.2     2e+03     117     147 ..     132     164 ..      80     197 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00034
                                   EEE-.-TTSSHHHHHHHHHHHH...GGGEEEE CS
                       NTPase_1  3 fiTG.ppGvGKtTlvkkvlellkssgvkvgGf 33
                                   +i G ++GvGKtT+   ++ +l+++g++v+ f
  gi|116754308|ref|YP_843426.1| 32 IIAGtHSGVGKTTVTLGLMAALRRRGMTVQPF 63
                                   4555258**********************976 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.2
                                    HHHHHHTTTSEEEEE--SS-..-SHHHHHHHT- CS
                       NTPase_1 117 aveevLksekpvlavihrrk..dlalveeirer 147
                                     v +vL+  +++++ +h  +    al++ +r+ 
  gi|116754308|ref|YP_843426.1| 132 HVAKVLSIPVVLVVNVHGMSrsAAALIHGFRSF 164
                                    566667766666666665554445555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (467 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3531.16
//
Query:       gi|116754309|ref|YP_843427.1|  [L=410]
Description: glutamyl-tRNA(Gln) amidotransferase subunit D [Methanosaeta thermophila PT]
Scores for complete 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-63  212.7   0.5    5.6e-63  212.0   0.4    1.4  2  Asparaginase    Asparaginase, N-terminal
    7.4e-31  106.7   0.0    3.5e-30  104.6   0.0    2.0  2  Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
    2.7e-16   58.6   0.3    6.1e-16   57.5   0.3    1.6  1  GatD_N          GatD N-terminal domain
  ------ inclusion threshold ------
      0.016   13.6   0.0      0.028   12.8   0.0    1.3  1  Gly_reductase   Glycine/sarcosine/betaine reductase component
      0.026   14.1   0.0       0.13   11.8   0.0    1.9  2  Peripla_BP_4    Periplasmic binding protein domain


Domain annotation for each model (and alignments):
>> Asparaginase  Asparaginase, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  212.0   0.4   1.6e-66   5.6e-63       2     185 ..      70     260 ..      69     266 .. 0.95
   2 ?   -3.4   0.0       1.7   6.1e+03     139     166 ..     330     357 ..     326     364 .. 0.74

  Alignments for each domain:
  == domain 1  score: 212.0 bits;  conditional E-value: 1.6e-66
                                    EEEEEEESGGGEEECTTS--CCEES-HHHHHCCTTTCCCCSEEEEEEEEEE-GGG--HHHHHHHHHHHHHHCCT.-SEEE CS
                   Asparaginase   2 vlvlatGGTiasekdesggalapalsaeellealpelekiaeleseqlanidSsnmtpadwlklaeaieealee.ydgfV 80 
                                    v +++tGGTias++d+++ga++ ++saee+++a+pel +ia++++++l  i S+nm  + w +la+a++e++++ ++g+V
  gi|116754309|ref|YP_843427.1|  70 VTIISTGGTIASKVDYRTGAVTSQFSAEEIISAIPELGDIARYHARVLYTILSENMRAEYWIELARAVAEEIQNgAEGVV 149
                                    89**********************************************************************666***** PP

                                    EE--STTHHHHHHHHHHHEES.SSEEEEE--SS-TTSTT-SHHHHHHHHHHHHHCGGTTSECEEEETTE.......EEET CS
                   Asparaginase  81 vlhGTDTlaytAsaLslmlknldkpvvltGsqrplselrsDgpeNlldAllvaasseriagvlvvfngk.......llra 153
                                    ++hGTDT+ ytA+aLs+ml++ ++pvvl+Gsqr++++++sD+++N + A +va s+  ia+v+vv++g+       ++r+
  gi|116754309|ref|YP_843427.1| 150 ITHGTDTMTYTAAALSFMLRT-PVPVVLVGSQRSSDRPSSDAAMNAICASTVAVSD--IAEVCVVMHGStsddyclIHRG 226
                                    *********************.********************************87..********************** PP

                                    TTEEE-BSSSSS-EEETTT--SEEE..ETTEEEE CS
                   Asparaginase 154 nrvtKvhtssldaFespnlgplaev..egskvkv 185
                                    +rv+K+hts++daF+s+n++p+++v  +++++++
  gi|116754309|ref|YP_843427.1| 227 TRVRKMHTSRRDAFQSINHPPIGRVdyTTRRIEI 260
                                    ************************9555555555 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.7
                                    TSECEEEETTEEEETTTEEE-BSSSSS- CS
                   Asparaginase 139 iagvlvvfngkllranrvtKvhtsslda 166
                                     +g+ vv++ ++lr++ + +v  + +d 
  gi|116754309|ref|YP_843427.1| 330 DNGIPVVVASQCLRGRICDRVYDTGRDM 357
                                    5688888899999998888877666665 PP

>> Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.47   1.7e+03      21      35 ..     142     156 ..     113     205 .. 0.66
   2 !  104.6   0.0   9.7e-34   3.5e-30       3     113 ..     283     393 ..     281     394 .. 0.98

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.47
                                    HTT--EEEEEEBTTT CS
                 Asparaginase_C  21 kkgakGvvlegtGvG 35 
                                    ++ga+Gvv+  +  +
  gi|116754309|ref|YP_843427.1| 142 QNGAEGVVITHGTDT 156
                                    567777777654333 PP

  == domain 2  score: 104.6 bits;  conditional E-value: 9.7e-34
                                    EEEE--TT--HHHHHHHHHTT--EEEEEEBTTTB--HHHHHHHHHHHTTT-EEEEEESSSBS-----H.....HHHHHTE CS
                 Asparaginase_C   3 vvlklhpgmdtkvlkallkkgakGvvlegtGvGnlpsallealkeakargivvvatsqcpsgsvsnseyeagkelerlgv 82 
                                    +++k +pg+d++++++l++ g++G+v+egtG G++ +++++ +k+a+++gi+vv++sqc++g++ + +y++g+++ ++g+
  gi|116754309|ref|YP_843427.1| 283 ALIKYFPGADPEIFNHLIELGYRGIVIEGTGLGHVATDWIPFIKKATDNGIPVVVASQCLRGRICDRVYDTGRDMLAAGA 362
                                    799***************************************************************************** PP

                                    EE-TT--HHHHHHHHHHHCTT---HHHHHHH CS
                 Asparaginase_C  83 isaddmtpeaarikLmlllgkgldpaevrkl 113
                                    i+a+dm pe a +kLm+ll++  + +e r++
  gi|116754309|ref|YP_843427.1| 363 IEAEDMLPEVALVKLMWLLANASSLDEARDM 393
                                    **************************99986 PP

>> GatD_N  GatD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.5   0.3   1.7e-19   6.1e-16       1      50 [.       1      46 [.       1      49 [. 0.94

  Alignments for each domain:
  == domain 1  score: 57.5 bits;  conditional E-value: 1.7e-19
                                   --TT-EEEEE-SS-EEEEEE----TTS-SSEEEEEETTS-EEEEE-TT-. CS
                         GatD_N  1 ievGDlikvekkgreyeGilmPrselsdddiivlKLdnGYNiGikieeie 50
                                   +e GD++ v k+g +yeGilmP+     +d++v+KL+nGYNiG+  ++ie
  gi|116754309|ref|YP_843427.1|  1 MELGDRVAVIKGGMRYEGILMPSR----SDHVVIKLSNGYNIGLVPDSIE 46
                                   799*********************....****************999984 PP

>> Gly_reductase  Glycine/sarcosine/betaine reductase component B subunits
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   7.9e-06     0.028     301     345 ..     301     345 ..     295     350 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.9e-06
                  Gly_reductase 301 lLgadgvivseeGyGnpdtdlimnikklekaGiktvlitdelaGr 345
                                    +Lg  g+++   G G+  td i  ikk++++Gi +v+ ++ l Gr
  gi|116754309|ref|YP_843427.1| 301 ELGYRGIVIEGTGLGHVATDWIPFIKKATDNGIPVVVASQCLRGR 345
                                    6999********************************999988886 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 ?   -0.6   0.0      0.22   7.8e+02      49      99 ..     138     193 ..     126     264 .. 0.55
   2 ?   11.8   0.0   3.6e-05      0.13      47     115 ..     295     368 ..     293     374 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.22
                                    HHHHHTT-SEEEE--SSH.HHHH.HHHHHHHHTT-EEEEESTT...GCTTT-CEEE CS
                   Peripla_BP_4  49 edaiakgvdgiivapvds.tala.palkkakaaGIpVvafdsd...dapsgerlay 99 
                                       i++g+ g++++      + + +al       +pVv + s+   d ps++ + +
  gi|116754309|ref|YP_843427.1| 138 AEEIQNGAEGVVITHGTDtMTYTaAALSFMLRTPVPVVLVGSQrssDRPSSDAAMN 193
                                    45567777755544433313333355555666666666666665554444444444 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 3.6e-05
                                    HHHHHHHTT-SEEEE--SSH....HHHHHHHHHHHHTT-EEEEESTT.GCTTT-CEEEEEC-HHHHHHHHHHHH CS
                   Peripla_BP_4  47 qiedaiakgvdgiivapvds....talapalkkakaaGIpVvafdsd.dapsgerlayvgfdneaaGelqaeyl 115
                                    +++ +i+ g+ gi++  +      t   p++kka+++GIpVv+  +       +r++  g d  aaG++ ae +
  gi|116754309|ref|YP_843427.1| 295 IFNHLIELGYRGIVIEGTGLghvaTDWIPFIKKATDNGIPVVVASQClRGRICDRVYDTGRDMLAAGAIEAEDM 368
                                    67888888999999887776555577889***********9996665666667777777777777777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 3120.20
//
Query:       gi|116754310|ref|YP_843428.1|  [L=242]
Description: phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase [Methanosaeta thermophila PT]
Scores for complete 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-72  242.3   0.2    4.8e-72  242.1   0.2    1.0  1  His_biosynth    Histidine biosynthesis protein
    8.6e-09   35.2   1.3    8.8e-07   28.6   0.2    2.1  2  NMO             Nitronate monooxygenase
    9.4e-08   31.5   0.1     0.0095   15.1   0.0    2.1  2  Dus             Dihydrouridine synthase (Dus)
    2.6e-06   26.9   0.6    0.00055   19.3   0.1    2.2  2  TMP-TENI        Thiamine monophosphate synthase
    3.4e-06   26.6   1.4     0.0038   16.6   0.1    2.1  2  ThiG            Thiazole biosynthesis protein ThiG
      4e-06   26.2   0.1     0.0024   17.2   0.1    2.1  2  DHO_dh          Dihydroorotate dehydrogenase
    0.00023   20.7   0.2       0.24   10.8   0.0    2.2  2  G3P_antiterm    Glycerol-3-phosphate responsive antiterminato
    0.00059   18.9   1.0       0.26   10.2   0.1    2.1  2  IMPDH           IMP dehydrogenase / GMP reductase domain
      0.001   18.3   0.0      0.079   12.1   0.0    2.2  2  IGPS            Indole-3-glycerol phosphate synthase
  ------ inclusion threshold ------
       0.02   14.1   0.2        2.3    7.3   0.1    2.2  2  NanE            Putative N-acetylmannosamine-6-phosphate epim
      0.033   13.7   0.6       0.18   11.2   0.1    2.0  2  PcrB            PcrB family
      0.036   13.2   0.1      0.057   12.6   0.1    1.2  1  DUF561          Protein of unknown function (DUF561)
      0.059   12.8   0.1       0.81    9.1   0.0    2.1  2  PEP_mutase      Phosphoenolpyruvate phosphomutase
      0.068   12.6   0.7        7.4    5.9   0.1    2.3  2  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
      0.085   12.5   0.2       0.31   10.6   0.0    1.8  2  DeoC            DeoC/LacD family aldolase
       0.14   11.2   4.6       0.74    8.8   0.8    2.1  2  FMN_dh          FMN-dependent dehydrogenase


Domain annotation for each model (and alignments):
>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  242.1   0.2   4.3e-75   4.8e-72       2     228 ..       5     230 ..       4     231 .. 0.99

  Alignments for each domain:
  == domain 1  score: 242.1 bits;  conditional E-value: 4.3e-75
                                    EEEEEEEETTEEEEECTTCSTCEEEETTSHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEEEESS CS
                   His_biosynth   2 iipalDlkdGkvVrlvkGdrfqelryagdpvelakryeeegadelhvvDldaakegreanldlveeiaeevfipvqvGGG 81 
                                    i+pa+Dl+ G++V+lv+G+  +e +  +dp+ +a r+++ gad lh++Dld+a eg++ n  ++++i+ e+++ vqvGGG
  gi|116754310|ref|YP_843428.1|   5 IFPAVDLRGGRCVQLVQGVPGSEVVSLDDPLVQAVRWADMGADHLHIIDLDGAIEGTRLNAPILRRIVGELEVFVQVGGG 84 
                                    99****************************************************************************** PP

                                    SSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEECEEEEETTTTEEEEEEHHHHHHHHHHTT- CS
                   His_biosynth  82 IrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarrgykvaikgwreetgldavelakkleelga 161
                                    Irs +dv+e+l+ g+d+vi+gt+a+++p ++kelae++g ++i+va+D+r+g +v+ +gw+++ ++da+el   +e+ ga
  gi|116754310|ref|YP_843428.1|  85 IRSRSDVAEVLDTGVDRVILGTMALRDPPVVKELAEEYGPDRIMVALDVRDG-RVTSEGWQRTLEFDAIELGIVFESFGA 163
                                    ****************************************************.*************************** PP

                                    SEEEEEETTTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHHHHTTCSEEEESHHHHTTSS CS
                   His_biosynth 162 geilltdidrdGtlsGpdleltkelaeavkipviasGGvgsledlkelksegvdavivgsalyegel 228
                                    g+il+t+id++G + G+d e t+el eav+ipvia+GGv+sl+d+k l ++g++++++g+a+y+g+l
  gi|116754310|ref|YP_843428.1| 164 GSILFTNIDTEGQQRGVDPEPTRELVEAVSIPVIAAGGVSSLDDIKLLSDAGAAGAVIGTAIYTGTL 230
                                    ****************************************************************986 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8   0.0     0.007       7.9     188     225 ..      71     108 ..      55     148 .. 0.85
   2 !   28.6   0.2   7.9e-10   8.8e-07     188     225 ..     188     225 ..     176     234 .. 0.94

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.007
                            NMO 188 vldavdiPviAaGGiidrrgvaaaLalGAsgvqigtrf 225
                                    ++  +++ v   GGi  r +va +L  G   v +gt  
  gi|116754310|ref|YP_843428.1|  71 IVGELEVFVQVGGGIRSRSDVAEVLDTGVDRVILGTMA 108
                                    555566777788***********************965 PP

  == domain 2  score: 28.6 bits;  conditional E-value: 7.9e-10
                            NMO 188 vldavdiPviAaGGiidrrgvaaaLalGAsgvqigtrf 225
                                     ++av+iPviAaGG+    +++    +GA+g+ igt+ 
  gi|116754310|ref|YP_843428.1| 188 LVEAVSIPVIAAGGVSSLDDIKLLSDAGAAGAVIGTAI 225
                                    689*********************************96 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   8.5e-06    0.0095     175     226 ..      68     119 ..      57     135 .. 0.84
   2 !   14.4   0.0   1.3e-05     0.015     176     217 ..     186     226 ..     173     232 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 8.5e-06
                                    HHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHHH.H CS
                            Dus 175 IkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlfae.s 226
                                     + +  ++++ v + G+I++++d+ ++l+  G+d v+ g  al++P +++e  
  gi|116754310|ref|YP_843428.1|  68 LRRIVGELEVFVQVGGGIRSRSDVAEVLDT-GVDRVILGTMALRDPPVVKElA 119
                                    56677788999*****************98.****************998533 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 1.3e-05
                                    HHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHC CS
                            Dus 176 kevkqavsipviaNGdIkdaedaqaileetGadgvmigrgal 217
                                    +e+ +avsipvia G++ +++d++   +  Ga g +ig + +
  gi|116754310|ref|YP_843428.1| 186 RELVEAVSIPVIAAGGVSSLDDIKLL-SDAGAAGAVIGTAIY 226
                                    7899*******************865.555*******98765 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   0.0    0.0061       6.8     138     176 ..      64     103 ..      42     107 .. 0.86
   2 !   19.3   0.1   4.9e-07   0.00055     119     181 .]     160     225 ..     148     225 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0061
                       TMP-TENI 138 gleglkelaealeiPvvaiGGitl.envaevleagadgva 176
                                    +   l++++ +le+ v + GGi+  ++vaevl++g+d+v 
  gi|116754310|ref|YP_843428.1|  64 NAPILRRIVGELEVFVQVGGGIRSrSDVAEVLDTGVDRVI 103
                                    5567888999999999999***75278*********9985 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 4.9e-07
                       TMP-TENI 119 YigvGpifpTdtKkdaeplgl..eglkelaealeiPvvaiGGit.lenvaevleagadgvavvsai 181
                                     +g+G+i  T+  ++ + +g+  e  +el+ea++iPv+a GG++ l++++ + +aga+g  + +ai
  gi|116754310|ref|YP_843428.1| 160 SFGAGSILFTNIDTEGQQRGVdpEPTRELVEAVSIPVIAAGGVSsLDDIKLLSDAGAAGAVIGTAI 225
                                    579999*9999999886655421789****************963799**********98877765 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   3.4e-06    0.0038     135     206 ..      36     107 ..      25     121 .. 0.75
   2 !    9.3   0.1   0.00056      0.63     164     209 ..     182     227 ..     161     241 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.4e-06
                                    HHHHHHHHTT-SEBEEBSSSTTS----.S-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHH CS
                           ThiG 135 vlarrleevGcaavmPlaapiGsglGl.lnkealkiiieeakvPvivDAGigspsdaaqamelGadavllnta 206
                                    v a r  ++G+  +  +    G+ +G  ln+  l+ i+ e++v v v  Gi+s sd+a++++ G+d v+l t 
  gi|116754310|ref|YP_843428.1|  36 VQAVRWADMGADHLH-IIDLDGAIEGTrLNAPILRRIVGELEVFVQVGGGIRSRSDVAEVLDTGVDRVILGTM 107
                                    556666666665432.222224444441578899***********************************9884 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00056
                                    HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHT CS
                           ThiG 164 kealkiiieeakvPvivDAGigspsdaaqamelGadavllntavae 209
                                    +e  + ++e +++Pvi   G+ s  d+    + Ga + ++ ta+ +
  gi|116754310|ref|YP_843428.1| 182 PEPTRELVEAVSIPVIAAGGVSSLDDIKLLSDAGAAGAVIGTAIYT 227
                                    55668899***********************************976 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0026         3     249     290 ..      81     121 ..      62     123 .. 0.84
   2 !   17.2   0.1   2.1e-06    0.0024     235     281 ..     186     229 ..     182     239 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0026
                                    EESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHHHHHH CS
                         DHO_dh 249 gvGGiesgeDalekieaGAslvqvytalvfegpkiakkikke 290
                                      GGi s  D+ e +  G   v ++t    ++p ++k++ +e
  gi|116754310|ref|YP_843428.1|  81 VGGGIRSRSDVAEVLDTGVDRVILGTMA-LRDPPVVKELAEE 121
                                    459***********************98.8999999988776 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 2.1e-06
                                    HHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGT CS
                         DHO_dh 235 relykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegp 281
                                    rel + ++  ip+I+ GG++s +D      aGA+   ++ta+ ++g 
  gi|116754310|ref|YP_843428.1| 186 RELVEAVS--IPVIAAGGVSSLDDIKLLSDAGAAGAVIGTAI-YTGT 229
                                    67777888..****************9**************9.8776 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 !    7.8   0.0    0.0018         2     130     168 ..      67     105 ..      62     109 .. 0.87
   2 !   10.8   0.0   0.00022      0.24     128     165 ..     182     219 ..     179     224 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0018
                                    HHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE- CS
                   G3P_antiterm 130 vikeikkelkipiiaGGLietkedveealkaGaiavsts 168
                                    ++++i  el++ +  GG i++++dv e+l+ G++ v  +
  gi|116754310|ref|YP_843428.1|  67 ILRRIVGELEVFVQVGGGIRSRSDVAEVLDTGVDRVILG 105
                                    678899999999*********************998765 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00022
                                    HHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEE CS
                   G3P_antiterm 128 pkvikeikkelkipiiaGGLietkedveealkaGaiav 165
                                    p+ ++e+ ++++ip+ia+G +++ +d++ + +aGa + 
  gi|116754310|ref|YP_843428.1| 182 PEPTRELVEAVSIPVIAAGGVSSLDDIKLLSDAGAAGA 219
                                    667789999*************************9865 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.1    0.0014       1.6     205     238 ..      74     107 ..      67     111 .. 0.89
   2 !   10.2   0.1   0.00024      0.26     168     238 ..     150     224 ..     114     231 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0014
                                    TCT-EEEEES---SHHHHHHHHHTT-SEEEESCC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 205 kagvpviaDGGikysgdivkAlaaGadavmlGsl 238
                                    + +v v   GGi++  d++  l  G d v+lG +
  gi|116754310|ref|YP_843428.1|  74 ELEVFVQVGGGIRSRSDVAEVLDTGVDRVILGTM 107
                                    667888999***********************87 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00024
                                    SEEEE-S.....S-STTBHHHHHCSB---HHHHHHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCC CS
                                    xxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 168 davkvGi.....GpGsiCttrvvagvGvpqltAvaevaeaakkagvpviaDGGikysgdivkAlaaGadavmlGsl 238
                                    da+  Gi     G+Gsi  t +    G  +      + e ++   +pvia GG+++  di     aGa   ++G  
  gi|116754310|ref|YP_843428.1| 150 DAIELGIvfesfGAGSILFTNID-TEGQQRGVDPEPTRELVEAVSIPVIAAGGVSSLDDIKLLSDAGAAGAVIGTA 224
                                    55555544455588888888764.45666666666778899999****************9999999999999975 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.021        23     214     247 ..      81     114 ..      65     120 .. 0.80
   2 !   12.1   0.0     7e-05     0.079     194     243 ..     180     227 ..     176     237 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.021
                                    EESSS-SHHHHHHHCCTT-SEEEESHHHHC-TTH CS
                           IGPS 214 aeSGiktredveklkeegvnafLvGeslmrqedv 247
                                       Gi++r dv ++ ++gv+ ++ G+  +r++ v
  gi|116754310|ref|YP_843428.1|  81 VGGGIRSRSDVAEVLDTGVDRVILGTMALRDPPV 114
                                    4579*********************987777655 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 7e-05
                                    E-CHHHHHHCHCC-TTSEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC CS
                           IGPS 194 vdlntteeLaklvpkdvllvaeSGiktredveklkeegvnafLvGeslmr 243
                                    vd + t+eL++ v   + ++a  G+++ +d++ l+++g+ +  +G+++  
  gi|116754310|ref|YP_843428.1| 180 VDPEPTRELVEAVS--IPVIAAGGVSSLDDIKLLSDAGAAGAVIGTAIYT 227
                                    67788999999887..99****************************9865 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 ?    4.9   0.0     0.011        13     142     186 ..      74     118 ..      54     123 .. 0.83
   2 ?    7.3   0.1    0.0021       2.3     132     176 ..     180     225 ..     151     232 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.011
                                    HTT--EEEES---SHHHHHHHHTT--SEEEE-HHHH-HHHHHHHH CS
                           NanE 142 eaglkviaeGrintPekakkaieiGvdavvvGsaitrleeiakkf 186
                                    e +++v + G i +    ++++++Gvd v++G+   r   ++k  
  gi|116754310|ref|YP_843428.1|  74 ELEVFVQVGGGIRSRSDVAEVLDTGVDRVILGTMALRDPPVVKEL 118
                                    5578899999**********************9888877777665 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0021
                                    --HHHHHHHHHT.T--EEEES---SHHHHHHHHTT--SEEEE-HHH CS
                           NanE 132 pDfalvkalsea.glkviaeGrintPekakkaieiGvdavvvGsai 176
                                     D +  ++l+ea  + via G + + +  k   + G++  v+G+ai
  gi|116754310|ref|YP_843428.1| 180 VDPEPTRELVEAvSIPVIAAGGVSSLDDIKLLSDAGAAGAVIGTAI 225
                                    4555556676663688*****************************9 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00016      0.18     183     214 ..      79     111 ..      37     122 .. 0.82
   2 ?    0.8   0.1      0.25   2.8e+02     181     214 ..     194     228 ..     171     239 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00016
                                    EEEESS--SHHHHHHHHCC.SSEEEE-CHHHHH CS
                           PcrB 183 livGGGirsaEkAkevvea.ADvivvGnvveek 214
                                    + vGGGirs+ + +ev+    D ++ G++   +
  gi|116754310|ref|YP_843428.1|  79 VQVGGGIRSRSDVAEVLDTgVDRVILGTMALRD 111
                                    558****************9*******986655 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.25
                                    SEEEEESS--SHHHHHHHHCC.SSEEEE-CHHHHH CS
                           PcrB 181 arlivGGGirsaEkAkevvea.ADvivvGnvveek 214
                                    + +i  GG+ s ++ k    a A   v+G++++  
  gi|116754310|ref|YP_843428.1| 194 IPVIAAGGVSSLDDIKLLSDAgAAGAVIGTAIYTG 228
                                    56788999999999999999999999999999975 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1     5e-05     0.057     178     218 ..     185     226 ..     183     239 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5e-05
                         DUF561 178 tyeiskkvslPvicasGlsdvt.vplalslgasGiGigsavs 218
                                    t e++++vs+Pvi+a G+s++  ++l   +ga+G  ig a+ 
  gi|116754310|ref|YP_843428.1| 185 TRELVEAVSIPVIAAGGVSSLDdIKLLSDAGAAGAVIGTAIY 226
                                    567999*************99538899999*******99985 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0   0.00073      0.81     159     225 ..      35     110 ..      18     121 .. 0.81
   2 ?    1.8   0.0      0.13   1.4e+02      60     104 ..     184     221 ..     145     237 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00073
                     PEP_mutase 159 ieRaraYaeAGAdgvfvpgl........qkdaeiaelvaavdvplnvvpl.kgtlsvaelaelGvarislgnhllr 225
                                    +  a ++a+ GAd + ++ l         +++ ++++v +++v + v  + +++ +vae+ + Gv r++lg+ +lr
  gi|116754310|ref|YP_843428.1|  35 LVQAVRWADMGADHLHIIDLdgaiegtrLNAPILRRIVGELEVFVQVGGGiRSRSDVAEVLDTGVDRVILGTMALR 110
                                    555778889999999999887777775455555788888888888888855778*****************99887 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.13
                     PEP_mutase  60 avraiaevvslPlivDledGygespeevaetvrrliaaGvvgvni 104
                                     +r+++e+vs+P+i+    G      +  + ++ l +aG++g +i
  gi|116754310|ref|YP_843428.1| 184 PTRELVEAVSIPVIAA--GGV-----SSLDDIKLLSDAGAAGAVI 221
                                    4677777777777763..221.....1234566666777776666 PP

>> Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.013        14     161     195 ..      73     106 ..      63     109 .. 0.81
   2 ?    5.9   0.1    0.0066       7.4     165     198 .]     192     226 ..     183     226 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.013
                                    HHHT---EEEEESS--T.TTCHHHHHHT--EEEESH CS
                 Ribul_P_3_epim 161 dekeldlkievDGGvkl.dnieqiaeagadvlVags 195
                                       el++ ++v GG++    ++++ + g+d ++ g+
  gi|116754310|ref|YP_843428.1|  73 G--ELEVFVQVGGGIRSrSDVAEVLDTGVDRVILGT 106
                                    4..488999******862679***********9997 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0066
                                    ---EEEEESS--.TTTCHHHHHHT--EEEESHHHH CS
                 Ribul_P_3_epim 165 ldlkievDGGvk.ldnieqiaeagadvlVagsavf 198
                                    +++ + + GGv+ ld i+ + +aga   V+g+a++
  gi|116754310|ref|YP_843428.1| 192 VSIPVIAAGGVSsLDDIKLLSDAGAAGAVIGTAIY 226
                                    567788899996379******************98 PP

>> DeoC  DeoC/LacD family aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       0.8   8.9e+02     184     230 ..      65     110 ..      42     111 .. 0.76
   2 ?   10.6   0.0   0.00028      0.31     185     233 ..     183     226 ..     173     236 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.8
                                    HHHHHHHHHCHSSTEEEEETTS.SHHHHHHHHHHHHHHHTHCEEEESH CS
                           DeoC 184 aevfkdvikaapvpgvvlsGGv.seedfletvedAvkeagasGvlsGR 230
                                    a + ++ +++ +v  v + GG+ s  d++e++++ v + +  G +++R
  gi|116754310|ref|YP_843428.1|  65 APILRRIVGELEVF-VQVGGGIrSRSDVAEVLDTGV-DRVILGTMALR 110
                                    55666677766666.889999999999999999998.77777777776 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00028
                                    HHHHHHHHCHSSTEEEEETTSSHHHHHHHHHHHHH..HHTHCEEEESHHHH CS
                           DeoC 185 evfkdvikaapvpgvvlsGGvseedfletvedAvk..eagasGvlsGRaif 233
                                    e  +++++a+ +p v+ +GGv      + ++d     +aga+G+++G ai+
  gi|116754310|ref|YP_843428.1| 183 EPTRELVEAVSIP-VIAAGGV------SSLDDIKLlsDAGAAGAVIGTAIY 226
                                    5568999******.*******......555554444577788888887776 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.8   0.00066      0.74     263     302 ..      66     107 ..      37     111 .. 0.73
   2 ?    4.1   0.2     0.018        20     263     306 ..     187     228 ..     175     236 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00066
                                    HHHHHH....SS-EEEESS--SHHHHHHHHHTT-SEEEESHH CS
                         FMN_dh 263 eiveavgg..rievlvDgGirrGsDvlkAlalGAdavllGRp 302
                                     i +++ g  ++ v v gGir+ sDv+  l  G d v+lG  
  gi|116754310|ref|YP_843428.1|  66 PILRRIVGelEVFVQVGGGIRSRSDVAEVLDTGVDRVILGTM 107
                                    44444444023556678**********************975 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.018
                                    HHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHHHH CS
                         FMN_dh 263 eiveavggrievlvDgGirrGsDvlkAlalGAdavllGRpflyg 306
                                    e+veav   i+v++ gG+++  D+      GA + ++G ++  g
  gi|116754310|ref|YP_843428.1| 187 ELVEAVS--IPVIAAGGVSSLDDIKLLSDAGAAGAVIGTAIYTG 228
                                    5566665..88888888888888877777888888888777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1895.80
//
Query:       gi|116754311|ref|YP_843429.1|  [L=418]
Description: adenosylhomocysteinase [Methanosaeta thermophila PT]
Scores for complete 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-66  223.2   0.0    9.6e-39  133.3   0.0    2.0  2  AdoHcyase       S-adenosyl-L-homocysteine hydrolase
      7e-51  172.5   0.2    1.7e-50  171.2   0.0    1.8  3  AdoHcyase_NAD   S-adenosyl-L-homocysteine hydrolase, NAD bind
      4e-09   36.1   0.6    1.1e-08   34.7   0.1    2.0  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    1.7e-07   30.9   0.0    2.9e-07   30.2   0.0    1.4  1  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
  ------ inclusion threshold ------
      0.011   16.0   0.0       0.04   14.2   0.0    2.0  1  TrkA_N          TrkA-N domain
      0.041   12.6   0.1       0.33    9.6   0.0    2.0  2  Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
      0.073   12.3   0.1       0.25   10.5   0.1    1.8  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
      0.084   12.1   0.1       0.14   11.5   0.1    1.3  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain


Domain annotation for each model (and alignments):
>> AdoHcyase  S-adenosyl-L-homocysteine hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.3   0.0   4.3e-42   9.6e-39       3     141 ..       5     138 ..       3     142 .. 0.97
   2 !   89.7   0.0   8.2e-29   1.8e-25     173     286 ..     137     412 ..     135     418 .] 0.98

  Alignments for each domain:
  == domain 1  score: 133.3 bits;  conditional E-value: 4.3e-42
                                    B-S-GGGHHHHHHHHHHHHCC-HHHHHHHHHCTTT-TTTT-EEEEES--SHHHHHHHHHHHHTT-EEEEE-SSTTT--HH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      AdoHcyase   3 kvkdislaefGrkeielaekempglmalreeyaeekplkgariaGslhmtiqtavLietLvalGaevrWasCnifstqde 82 
                                     vkdi+la++G ++ie a + mp l  ++ee+++e+pl+g ri+ +lh+t++ta Lie+L a Gae+  +  n  stqd+
  gi|116754311|ref|YP_843429.1|   5 IVKDITLADAGARRIEWARRHMPVLQLIKEEFERERPLEGIRIVACLHVTVETANLIEALRAGGAEIALTGSNPLSTQDD 84 
                                    69****************************************************************************** PP

                                    HHHHHCCTTEEEE--TT--HHHHHHHHHHCHS-SSTS-S-SEEEESSSHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      AdoHcyase  83 aaaaiaeagvpvfawkgetleeywwcieqalkwaedekepnlilDdGGDltllvhkgvk 141
                                    +aaa+a++g+ v+a++ge+++ey +cie+al+      +pn+ lDdG D  ++vhk  +
  gi|116754311|ref|YP_843429.1|  85 VAAALASRGIHVYAFRGENESEYYECIERALEL-----RPNVTLDDGADTIAVVHKSHR 138
                                    *******************************66.....7****************9654 PP

  == domain 2  score: 89.7 bits;  conditional E-value: 8.2e-29
                                    HCCCHCC--EEEE-SHHHHHHHHHHHHTT---SEEEESTTSHHHCTTH................................ CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................ RF
                      AdoHcyase 173 ytellkkikGvseetttGvhrLyelakkgkLlvpainvndsvtkskfD................................ 220
                                    ++el+ +i G  eetttGv+rL  +a++g L  p i vnd+ tk  fD                                
  gi|116754311|ref|YP_843429.1| 137 HRELIPEILGGCEETTTGVMRLRAMADDGALAYPVIAVNDAETKMMFDnrygtgqstlhgimnatnflfagktvvvagyg 216
                                    67889999************************************************************************ PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                      AdoHcyase 221 ................................................................................ 220
                                                                                                                    
  gi|116754311|ref|YP_843429.1| 217 wcgrgfamrakglganvivveteprkaleaamdgyrvmsmrsaaplgdlfvtltgdinvirnehfelmkdqvilansghf 296
                                    ******************************************************************************** PP

                                    ..................................................S-HHHHHHHHHHHHHHHHHHHHTTSSS-SS CS
                                    ..................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      AdoHcyase 221 ..................................................hpsfvmsasftnqvlaqielfkkekkyekk 250
                                                                                      hp  vm++sf+nq+l+   + ++ ++ e+k
  gi|116754311|ref|YP_843429.1| 297 nveidipglesmavstdeiqpnvkeyvmpdgrriyllaegrlinlaaaygHPPEVMDMSFANQALSVRYIVENGRRLERK 376
                                    *************************************************************************9****** PP

                                    EEE--CHHHHHHHHHCCCCCT-------HHHHHCCT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      AdoHcyase 251 vyvlpkklDekvarlhleklgaklteltkeqaeyig 286
                                    vy +p ++D +va+l+l+++g+++++lt eq +y++
  gi|116754311|ref|YP_843429.1| 377 VYPVPVEIDRRVAELKLKAMGIEIERLTPEQDRYLH 412
                                    **********************************97 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       3.4   7.7e+03      40      58 ..      62      80 ..      53      86 .. 0.83
   2 !  171.2   0.0   7.7e-54   1.7e-50       1     161 [.     185     345 ..     185     346 .. 0.99
   3 ?   -4.2   0.0       6.9   1.5e+04     120     138 ..     392     410 ..     384     412 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.4
                                   HHHHHCT-EEEEE-S-HHH CS
                  AdoHcyase_NAD 40 aslkglGarvivtevdPic 58
                                   ++l++ Ga + +t  +P++
  gi|116754311|ref|YP_843429.1| 62 EALRAGGAEIALTGSNPLS 80
                                   6899999999999888875 PP

  == domain 2  score: 171.2 bits;  conditional E-value: 7.7e-54
                                    HHHHHCCCCCHHHHHHH-S--TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HHHCTTT-S CS
                  AdoHcyase_NAD   1 nlygcreslvdgikratdvllaGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevvtleevvkkad 80 
                                    n yg+ +s + gi+ at++l+aGk++vvaGyG  G+G a   kglGa viv e +P  al aam+G++v+ +  ++  +d
  gi|116754311|ref|YP_843429.1| 185 NRYGTGQSTLHGIMNATNFLFAGKTVVVAGYGWCGRGFAMRAKGLGANVIVVETEPRKALEAAMDGYRVMSMRSAAPLGD 264
                                    78****************************************************************************** PP

                                    EEEE-SSSSSSB-HHHHCCS-TTEEEEE-SSTTTTBTHHHHHTTT-EEEEEETTEEEEE-TTS-EEEEEGGGSBCHHHTS CS
                  AdoHcyase_NAD  81 ivvtttGnkdiitlehlkkmkddaivcniGhfdseidvaaleanalkkeevkpqvdrvtlkdgkkiillaeGrllnlgca 160
                                    ++vt tG  ++i++eh++ mkd++i++n Ghf+ eid+ +le++a++++e++p+v++++++dg++i llaeGrl+nl++a
  gi|116754311|ref|YP_843429.1| 265 LFVTLTGDINVIRNEHFELMKDQVILANSGHFNVEIDIPGLESMAVSTDEIQPNVKEYVMPDGRRIYLLAEGRLINLAAA 344
                                    *****************************************************************************998 PP

                                    - CS
                  AdoHcyase_NAD 161 t 161
                                     
  gi|116754311|ref|YP_843429.1| 345 Y 345
                                    6 PP

  == domain 3  score: -4.2 bits;  conditional E-value: 6.9
                                    HHHTTT-EEEEEETTEEEE CS
                  AdoHcyase_NAD 120 aleanalkkeevkpqvdrv 138
                                    +l+a+++++e++ p+ dr+
  gi|116754311|ref|YP_843429.1| 392 KLKAMGIEIERLTPEQDRY 410
                                    5778889999999999987 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 ?   -2.3   0.0       1.1   2.5e+03     132     149 ..      55      72 ..      52      88 .. 0.82
   2 !   34.7   0.1   4.9e-12   1.1e-08      34     127 ..     205     294 ..     181     299 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.1
                                    B-HHHHHHHHHTTSCCEE CS
                   2-Hacid_dh_C 132 vdeeaLleaLksgkiaga 149
                                    v+++ L+eaL++g  + a
  gi|116754311|ref|YP_843429.1|  55 VETANLIEALRAGGAEIA 72 
                                    889999999999876655 PP

  == domain 2  score: 34.7 bits;  conditional E-value: 4.9e-12
                                    GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S--STTTTTSBSHHH CS
                   2-Hacid_dh_C  34 lsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleellaesDivslhlpltpetrhlinaee 113
                                     +gktv + G+G  G+ +a r+k++g++vi++++ ++k  e++  g++++s+  +    D  +     t    ++i +e+
  gi|116754311|ref|YP_843429.1| 205 FAGKTVVVAGYGWCGRGFAMRAKGLGANVIVVETEPRKALEAAMDGYRVMSMRSAAPLGDLFVTL---TG-DINVIRNEH 280
                                    689**********************************9999999999********9999977654...44.4689***** PP

                                    HHCSTTTEEEEESS CS
                   2-Hacid_dh_C 114 lakmkkgailiNta 127
                                    +++mk+++il N +
  gi|116754311|ref|YP_843429.1| 281 FELMKDQVILANSG 294
                                    **********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 !   30.2   0.0   1.3e-10   2.9e-07       3     101 ..     206     300 ..     204     317 .. 0.90

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 1.3e-10
                                    HTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHHHHHHHHTG CS
                           IlvN   3 kgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelqkevyeeeie 82 
                                     gk+++v GyG  G+  a+  +  g +v+v   e +k + +A  +g++v++++ a+   d+ ++l+ D    +v+++e  
  gi|116754311|ref|YP_843429.1| 206 AGKTVVVAGYGWCGRGFAMRAKGLGANVIVVETEPRK-ALEAAMDGYRVMSMRSAAPLGDLFVTLTGDI---NVIRNEHF 281
                                    79***************************99888885.5567789*********************996...79999999 PP

                                    GG--TT-EEEESSSHHHHT CS
                           IlvN  83 pnlkegkalafahGfnihf 101
                                    + +k++ +la +  fn+  
  gi|116754311|ref|YP_843429.1| 282 ELMKDQVILANSGHFNVEI 300
                                    9999999999999999976 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   1.8e-05      0.04       1      45 [.     210     254 ..     210     261 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.8e-05
                                    EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEEE CS
                         TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeglevv 45 
                                    ++++G+G  Gr  a + +  g  +v+v++++++++ e++ +g++v+
  gi|116754311|ref|YP_843429.1| 210 VVVAGYGWCGRGFAMRAKGlGA-NVIVVETEPRKALEAAMDGYRVM 254
                                    79*****************777.6***************9999986 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 ?    0.8   0.0     0.073   1.6e+02     330     383 ..      56     110 ..      32     122 .. 0.80
   2 ?    9.6   0.0   0.00015      0.33     249     311 ..     184     245 ..     134     296 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.073
                                    CHHHHHHHHHHHT-SEEEE-CCHHHHHHHTT--EEE-TS-ECCTTTCS.S---SH CS
                 Oxidored_nitro 330 dleeleelikelkpdlllggskeryiaeklgiplvrvgfPildrhgya.rgpyvG 383
                                    +   l e++++ ++++ l+gs+    +++  ++l+  g+ ++   g+  +  y +
  gi|116754311|ref|YP_843429.1|  56 ETANLIEALRAGGAEIALTGSNPLSTQDDVAAALASRGIHVYAFRGENeSEYYEC 110
                                    4567889999999999999999999999999999999999988888775555555 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00015
                                    HHHHHHHHHHHHHHHHHHHHHHTT-EEEEECSSHHHHHHHHHHHHHT-EEEEEEESSS-HHHH CS
                 Oxidored_nitro 249 periaeerarlldaladyheylagkrvaiygdpdrvvalarllkelGmevvaagtetahrdde 311
                                    ++r+   +++l   + ++ + +agk+v+++g++    ++a+  k lG++v+++ te +++ +e
  gi|116754311|ref|YP_843429.1| 184 DNRYGTGQSTLHGIMNATNFLFAGKTVVVAGYGWCGRGFAMRAKGLGANVIVVETEPRKA-LE 245
                                    5556666667777788999***********************************999844.34 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 ?   10.5   0.1   0.00011      0.25     143     177 ..     208     242 ..     157     260 .. 0.80
   2 ?   -1.8   0.0      0.65   1.5e+03      93     122 ..     278     308 ..     264     321 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00011
                                    SEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 143 krivvvGgGyiGvElAaalaklgkevtlveardrl 177
                                    k +vv G G +G  +A+ ++ lg++v +ve  +r 
  gi|116754311|ref|YP_843429.1| 208 KTVVVAGYGWCGRGFAMRAKGLGANVIVVETEPRK 242
                                    67999999999999999999999999999999985 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.65
                                    TCEEEEEESEEEE-.--EEE-BCTCTTC.TT CS
                                    xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  93 gdeekiaydklvlA.tGssprdlgipGvaen 122
                                    ++++++  d+++lA +G  +  ++ipG++  
  gi|116754311|ref|YP_843429.1| 278 NEHFELMKDQVILAnSGHFNVEIDIPGLESM 308
                                    6778888999999955778888899998544 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 ?   11.5   0.1   6.1e-05      0.14      28      67 ..     207     246 ..     182     291 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.1e-05
                                    --EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHH CS
                    AlaDh_PNT_C  28 pakvlviGgGvaGlqAiatakglgakVtvlDvrparleql 67 
                                      +v+v G G  G   +  akglga+V v++++p+++ + 
  gi|116754311|ref|YP_843429.1| 207 GKTVVVAGYGWCGRGFAMRAKGLGANVIVVETEPRKALEA 246
                                    3468899*************************99876554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); 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: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 2960.99
//
Query:       gi|116754312|ref|YP_843430.1|  [L=361]
Description: hypothetical protein Mthe_1005 [Methanosaeta thermophila PT]
Scores for complete 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   44.8   0.2    1.8e-11   44.4   0.2    1.2  1  APH       Phosphotransferase enzyme family
  ------ inclusion threshold ------
       0.17   11.5   0.0       0.54    9.8   0.0    1.8  2  RIO1      RIO1 family


Domain annotation for each model (and alignments):
>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   0.2     2e-15   1.8e-11      63     225 ..     113     286 ..      93     313 .. 0.76

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 2e-15
                                    -EEETTEEEEEEE----EE-SS.......HHHHHHHHHHHHHHHHHHCCHHCH.-STTTB-SHHC..HTCCHHHHHHCHH CS
                            APH  63 ddeeigllfalieyvpgrsllr.......klsaaqlpellealgeflaalhqvdpaalpladfla..qdlellrqlesat 133
                                    +++++   f+++e+++gr +             + +++ ++al+e+la++h+v + ++p+ ++++  +++ + + ++   
  gi|116754312|ref|YP_843430.1| 113 SCGDAQEFFLVMERIEGREYFFdlervkeSGATELDRARAAALAEYLAEIHSV-KHSCPPLYRRRirDTIGHGEGIMGIL 191
                                    55666668999999999998777778987555677889999************.88899998885337788999999999 PP

                                    H.CCCGCCTCC..HHHHHHHHHHHHHHHH--SSS-EEEE-SS-SGGGEEEC..TTEEEEE---TT-EEEECCHHHHCCH. CS
                            APH 134 a.rllaselld..lleeleeqvlaalaallpgelptvllHgDlhpgNllvdpddgrvtGviDfedaglgpplyDlavll. 209
                                        +a+e+l+  +l e+e++  +++++l+    + + +HgD+hp+N++++++ +    v+D  +  +g ++ Dl  +  
  gi|116754312|ref|YP_843430.1| 192 DdYPDAPEFLErgELCEIEKRCVEWRWKLRSMTHRLCQVHGDFHPWNVMFREGSDF--SVLDRSRGEWGEAADDLSAMSm 269
                                    855566777779988999999999999888888999999************55444..59**999999999999965553 PP

                                    HH.CSCHCCCHCHHHHH CS
                            APH 210 rs.wtseldpeflaall 225
                                    ++ ++s + +  la++l
  gi|116754312|ref|YP_843430.1| 270 NYiFYSVQKEMRLAGGL 286
                                    44444444444444443 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.34   3.1e+03      82     102 ..     121     143 ..     116     174 .. 0.50
   2 ?    9.8   0.0   6.1e-05      0.54     111     149 ..     210     252 ..     186     255 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.34
                                    EEEEE--EETT..EEGGBHHHCG CS
                           RIO1  82 vlvmefigedg..vaapklkdve 102
                                     lvme i+ ++  + + ++k+  
  gi|116754312|ref|YP_843430.1| 121 FLVMERIEGREyfFDLERVKESG 143
                                    57777777333112344444444 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 6.1e-05
                                    HHHHHH...HHHHHHHTSTEEESS-STTSEEEETT.EEEE--G CS
                           RIO1 111 yeevle...emrklykeaglvHaDLSeyNvlvded.kvviIDv 149
                                     + ++e   ++r + ++   vH+D+  +Nv++ e+ ++ ++D 
  gi|116754312|ref|YP_843430.1| 210 EKRCVEwrwKLRSMTHRLCQVHGDFHPWNVMFREGsDFSVLDR 252
                                    44445444467888888889**************989988886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); 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: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2710.28
//
Query:       gi|116754313|ref|YP_843431.1|  [L=346]
Description: putative RNA methylase [Methanosaeta thermophila PT]
Scores for complete 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   87.0   0.0    6.9e-24   84.6   0.0    1.9  1  UPF0020          Putative RNA methylase family UPF0020
    1.1e-08   35.6   0.0    6.7e-08   33.1   0.0    2.1  2  Methyltransf_25  Methyltransferase domain
    6.8e-07   29.9   0.0      2e-06   28.4   0.0    1.9  2  Methyltransf_11  Methyltransferase domain
    1.7e-05   25.0   0.0    2.9e-05   24.2   0.0    1.4  1  THUMP            THUMP domain
    0.00075   19.3   0.0      0.048   13.4   0.0    2.2  2  N6_N4_Mtase      DNA methylase
     0.0053   16.4   0.0      0.027   14.1   0.0    2.0  2  Cons_hypoth95    Conserved hypothetical protein 95
  ------ inclusion threshold ------
      0.031   13.8   0.0      0.051   13.0   0.0    1.3  1  AviRa            RRNA methyltransferase AviRa


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 !   84.6   0.0   2.7e-27   6.9e-24       2     196 ..     171     336 ..     170     337 .. 0.84

  Alignments for each domain:
  == domain 1  score: 84.6 bits;  conditional E-value: 2.7e-27
                                    SSS-SS---SS-HHHHHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEE CS
                        UPF0020   2 gyRefngpapLketLAaalvrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklyg 81 
                                    + ++f++p+ L +++A+alv+++ ++pge llDP++G+G+il+Ea+l+g + a                          g
  gi|116754313|ref|YP_843431.1| 171 HLKPFFYPGVLMPRMARALVNITMVRPGELLLDPFSGTGGILVEACLIGVRGA--------------------------G 224
                                    6789*************************************************..........................* PP

                                    EES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE---------.-HHHHHHHHHHHHHHHHHH-TT.. CS
                        UPF0020  82 sDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGerlg.skkalekLYseflrelkrvlrggg 160
                                    +D ++++ +gar N+e    +    +   da+ L+ k+++vd+iv++ PYG++   ++++++++ s   +e+ rvl+  g
  gi|116754313|ref|YP_843431.1| 225 VDVQEKLNRGARANLEGLDAD----LILGDARCLPFKDASVDAIVSDTPYGRSAViKARSKDEILSRSFEEMFRVLKA-G 299
                                    ***************976654....45578889998889*************97615556688888888999999**9.5 PP

                                    -EEEEEESSHHHHHCC---..ESEEEEEEETTEEEEEE CS
                        UPF0020 161 rlvlltsenkalekaleer..alrkvkeknvklglllk 196
                                    r +++++++   e++l+++  ++ + ++ +v+ +l+++
  gi|116754313|ref|YP_843431.1| 300 RRAVIVTDR-PAEELLRSKefRIVELHSDRVHRSLTRY 336
                                    555555444.4566666654688889999999999875 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.87   2.2e+03      26      42 ..      79      95 ..      62     110 .. 0.75
   2 !   33.1   0.0   2.6e-11   6.7e-08       2      96 ..     202     299 ..     201     299 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.87
                                   EEESSHHHHHHHHHHHH CS
                Methyltransf_25 26 gvDiseemleaarerae 42
                                    +D s+e +e+a + ++
  gi|116754313|ref|YP_843431.1| 79 VCDASPENIEKALRSLD 95
                                   68999999999988774 PP

  == domain 2  score: 33.1 bits;  conditional E-value: 2.6e-11
                                    EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEE......EST.G CS
                Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvs......sga.l 74 
                                    Ld   GtG ++ ++    g  +  gvD++e++ + ar+++  egl+++++ gda+ lpf+d+s+D++vs      s a +
  gi|116754313|ref|YP_843431.1| 202 LDPFSGTGGILVEACLI-G-VRGAGVDVQEKLNRGARANL--EGLDADLILGDARCLPFKDASVDAIVSdtpygrS-AvI 276
                                    66678999999998865.5.999*****************..799************************8888743.447 PP

                                    GG.SSHHHHHHHHHHHHHHEEEE CS
                Methyltransf_25  75 hh.lsdedlekalkeiarvLkpg 96 
                                        +de l + ++e++rvLk g
  gi|116754313|ref|YP_843431.1| 277 KArSKDEILSRSFEEMFRVLKAG 299
                                    77345556799*********986 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       6.8   1.7e+04      24      38 ..      80      94 ..      69     108 .. 0.65
   2 !   28.4   0.0   7.7e-10     2e-06       5      92 ..     206     300 ..     202     304 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 6.8
                                   EES-HHHHHHHHHHC CS
                Methyltransf_11 24 vDlskemlklakeka 38
                                   +D s+e ++ a +  
  gi|116754313|ref|YP_843431.1| 80 CDASPENIEKALRSL 94
                                   577777776665444 PP

  == domain 2  score: 28.4 bits;  conditional E-value: 7.7e-10
                                    -TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES......-CCC-...C CS
                Methyltransf_11   5 cGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvsse......vlhhv...e 75 
                                    +GtG ++ +    g r  gvD+ +++ + a+++ ++ +   +++ +da+ lpf+d+s+D++vs        v+      e
  gi|116754313|ref|YP_843431.1| 206 SGTGGILVEACLIGVRGAGVDVQEKLNRGARANLEGLD--ADLILGDARCLPFKDASVDAIVSDTpygrsaVIKARskdE 283
                                    788888888887999*******************9999..899********************99777775555547767 PP

                                    CHHHHHHHHHHHEEEEE CS
                Methyltransf_11  76 dpekalkeiaRvLkpgG 92 
                                     +++ ++e+ RvLk g 
  gi|116754313|ref|YP_843431.1| 284 ILSRSFEEMFRVLKAGR 300
                                    899***********985 PP

>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   1.1e-08   2.9e-05      15     139 ..      42     152 ..      28     156 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.1e-08
                                    SEEEEETTEEEEECTEEEEEETHHHHHHHHHTSTTECEEEEEEEEEESSHHHHHHHHHHHHHHHHHHCT-EEEEEEEESS CS
                          THUMP  15 erveagkgrivvelkgekpeedeellkealekargiqrvipvcevceadledileaakeivkkkfeeeketFaVrvkrrg 94 
                                    ++v +++++++ve        d+  l  + ++++  +r++ v+ vc a+ e i++a ++++ +++     +++ r+ r g
  gi|116754313|ref|YP_843431.1|  42 REVAEVDRCLLVEA-------DDLDLRILEQRLAMTHRILEVLKVCDASPENIEKALRSLDLPRL-----RYRMRASRLG 109
                                    45555555555554.......4444444555666788***************************9.....89******** PP

                                    STSSSHHHHHHHHHHHHHHCCTT-EE-SSS-SEEEEEEEETTEEE CS
                          THUMP  95 khfeftsreinrevGkaivektglkVdlenPdivvrveiikdkay 139
                                    +   + s +++r+ G+ +++ +  + dlenP+  +r+ i ++k+ 
  gi|116754313|ref|YP_843431.1| 110 EG-FVKSHDLERMAGRVLHSMGY-RADLENPEMDIRAIISRSKVV 152
                                    **.9****************777.************999998876 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   1.9e-05     0.048     179     224 ..     184     230 ..     162     236 .. 0.83
   2 ?    3.8   0.0     0.016        41       1      57 [.     261     307 ..     261     328 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.9e-05
                                    HHHHHHHHHH.S-TT-EEEETT-TTTHHHHHHHHTT-EEEEEESSHH CS
                    N6_N4_Mtase 179 allerlIkls.tkkgdivlDpFaGSGtTavaakelgrkfiGieieee 224
                                     +++ l++++  ++g++ lDpF G+G ++v+a   g +  G++++e+
  gi|116754313|ref|YP_843431.1| 184 RMARALVNITmVRPGELLLDPFSGTGGILVEACLIGVRGAGVDVQEK 230
                                    57777776652578****************************99987 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.016
                                    EEEEEE--SSSSSCS.....GCCGCCHHHHHHHHHHHHHHHHHHHEEEEEEEEEEE- CS
                    N6_N4_Mtase   1 vdlivtdpPYntgkdyendeqyeeedsyeeyleflekvlkevrrvLkddgsifinid 57 
                                    vd iv d PY+ +        +++ ++     e l + ++e+ rvLk +  ++i  d
  gi|116754313|ref|YP_843431.1| 261 VDAIVSDTPYGRSAV------IKARSK----DEILSRSFEEMFRVLKAGRRAVIVTD 307
                                    688999999999988......443333....578889999********999999765 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.34   8.8e+02      64      90 ..      47      73 ..      44      93 .. 0.79
   2 !   14.1   0.0     1e-05     0.027      41     131 ..     197     278 ..     182     327 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.34
                                   -SEEEEEES-HHHHHHHHHHHCCCT-- CS
                  Cons_hypoth95 64 akkavlvekdkeavkilkenleelkle 90
                                   +++++lve d+  ++il++ l++++  
  gi|116754313|ref|YP_843431.1| 47 VDRCLLVEADDLDLRILEQRLAMTHRI 73
                                   6799***************99998844 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 1e-05
                                    CC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEEE- CS
                  Cons_hypoth95  41 egarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdivflD 120
                                     g+ +LD f+G+G++ +EA   g++    v+ +++  +  ++nle l+++     l+  +++ l+ +   ++++d +  D
  gi|116754313|ref|YP_843431.1| 197 PGELLLDPFSGTGGILVEACLIGVR-GAGVDVQEKLNRGARANLEGLDAD-----LILGDARCLPFK---DASVDAIVSD 267
                                    45568***************99965.5679******************44.....455555555444...6789****** PP

                                    -SSSTTCH.HH CS
                  Cons_hypoth95 121 PPyakelliee 131
                                     Py ++++i++
  gi|116754313|ref|YP_843431.1| 268 TPYGRSAVIKA 278
                                    ****9987543 PP

>> AviRa  RRNA methyltransferase AviRa
   #    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     163     225 ..     257     321 ..     223     326 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2e-05
                          AviRa 163 aekevdivitDlPYGelvswqge.seepvkqlleslaavldpeesvvaviadkkkk.ieherfrr 225
                                    +  +vd ++ D PYG  +  +   ++e +++ +e++ +vl++ +  v+v+++  ++ ++ ++fr 
  gi|116754313|ref|YP_843431.1| 257 KDASVDAIVSDTPYGRSAVIKARsKDEILSRSFEEMFRVLKAGRRAVIVTDRPAEElLRSKEFRI 321
                                    33459*************9999956778899*********9988888888775554055555655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 2475.92
//
Query:       gi|116754314|ref|YP_843432.1|  [L=269]
Description: hypothetical protein Mthe_1007 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-16   60.8   0.0    2.1e-16   59.8   0.0    1.5  1  DUF1724   Domain of unknown function (DUF1724)
     0.0025   17.7   0.1     0.0057   16.5   0.1    1.6  1  HTH_5     Bacterial regulatory protein, arsR family
      0.003   17.4   0.1     0.0057   16.5   0.1    1.4  1  MarR_2    MarR family
  ------ inclusion threshold ------
       0.05   13.7   0.2       0.11   12.6   0.2    1.5  1  HTH_20    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> DUF1724  Domain of unknown function (DUF1724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.8   0.0   4.6e-20   2.1e-16       1      61 [.     204     264 ..     204     265 .. 0.97

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 4.6e-20
                        DUF1724   1 tklyvydeeikplsltvtDkflslslfdkdgkydhk.dlisfdesAlkWGeeLFeyYlkrSe 61 
                                    ++ly +d e+  +++tv D+ lsl+lf+ dg yd   dli++++ A +WG +LF + +kr+e
  gi|116754314|ref|YP_843432.1| 204 FELYRLDAEV-RAAFTVIDSSLSLGLFRLDGGYDIGhDLICTGPGAREWGMRLFLHHKKRAE 264
                                    689*******.*************************************************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 !   16.5   0.1   1.3e-06    0.0057       4      43 ..      23      62 ..      20      64 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.3e-06
                                   HHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTT CS
                          HTH_5  4 RlkILklLaegelcvcelaeelglsqstvShHLkkLreaG 43
                                   R k+L +L +gel++++l + lg   st+ h  k + e+G
  gi|116754314|ref|YP_843432.1| 23 RTKVLLSLKDGELTAGDLERLLGTRASTILHAVKDMIESG 62
                                   899**************************99777777776 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   1.3e-06    0.0057       8      53 ..      24      66 ..      15      72 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.3e-06
                                   HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                         MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                     vL+ L +++   lt+g+l+r lg   s++  ++k++ + G v+r
  gi|116754314|ref|YP_843432.1| 24 TKVLLSLKDGE---LTAGDLERLLGTRASTILHAVKDMIESGTVVR 66
                                   55888888888...9***************************9987 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   2.4e-05      0.11      12      52 ..      23      62 ..      18      69 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.4e-05
                                   HHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCT CS
                         HTH_20 12 RrrilraLaraegltaselaerldlskntlsyHLrvLeeag 52
                                   R ++l  L  +++lta++l ++l+++ +t+ + ++ + e g
  gi|116754314|ref|YP_843432.1| 23 RTKVLLSL-KDGELTAGDLERLLGTRASTILHAVKDMIESG 62
                                   77899999.9**********************999988877 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:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1910.49
//
Query:       gi|116754315|ref|YP_843433.1|  [L=286]
Description: putative phosphoserine phosphatase [Methanosaeta thermophila PT]
Scores for complete sequence (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    8.7   5.6        7.2    6.9   0.5    3.0  2  DUF948    Bacterial protein of unknown function (DUF948)


Domain annotation for each model (and alignments):
>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.5    0.0004       7.2      38      72 ..      50      84 ..      25      94 .. 0.65
   2 ?    3.2   0.5    0.0057     1e+02      40      72 ..     150     175 ..      95     203 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0004
                         DUF948 38 lekqvdpilkevedllakvnelledvneklekvdp 72
                                     ++++++ +e ++ +a++++l +++nek++++ +
  gi|116754315|ref|YP_843433.1| 50 KAQELKKLRDEYNTKVAESKRLRDELNEKTNQIYA 84
                                   23567777777777777777777777777766544 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.0057
                         DUF948  40 kqvdpilkevedllakvnelledvneklekvdp 72 
                                    ++++++l+e+++l +++ +       + e+v +
  gi|116754315|ref|YP_843433.1| 150 EELKKLLEEAQALREQASK-------HHEDVTR 175
                                    3344444444444444444.......4444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3189  (0.177868); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                       102  (0.00568911); expected 17.9 (0.001)
Passed Fwd filter:                        52  (0.00290033); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 1.14u 0.35s 00:00:01.48 Elapsed: 00:00:00.51
# Mc/sec: 1673.43
//
Query:       gi|116754316|ref|YP_843434.1|  [L=831]
Description: ATPase, P-type (transporting), HAD superfamily, subfamily IC [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-53  179.8   3.0    3.6e-53  179.8   3.0    2.0  2  E1-E2_ATPase     E1-E2 ATPase
    1.2e-37  129.4   1.9    1.2e-37  129.4   1.9    1.9  2  Cation_ATPase_C  Cation transporting ATPase, C-terminus
    9.6e-19   68.5   5.8    1.2e-17   65.0   5.8    2.6  1  Hydrolase        haloacid dehalogenase-like hydrolase
    1.5e-17   63.4   0.0    3.7e-17   62.2   0.0    1.7  2  Cation_ATPase    Cation transport ATPase (P-type)
    3.9e-07   30.1   1.1     0.0011   18.7   0.7    2.4  2  Hydrolase_3      haloacid dehalogenase-like hydrolase
    3.2e-06   27.7   0.2      1e-05   26.0   0.1    1.9  1  HAD              haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.027   14.6   0.2        1.7    8.8   0.0    2.6  2  Isochorismatase  Isochorismatase family


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 !  179.8   3.0   1.4e-56   3.6e-53       2     181 .]      49     242 ..      48     242 .. 0.98
   2 ?   -1.7   0.1      0.71   1.8e+03      91     136 ..     605     650 ..     586     664 .. 0.65

  Alignments for each domain:
  == domain 1  score: 179.8 bits;  conditional E-value: 1.4e-56
                                    SS--EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-S.EEE-TTTS---S-EE-.............G-T CS
                   E1-E2_ATPase   2 llpptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsa.evdesaLTGEslpvek.............ekg 67 
                                    l  + a+v+r+g+  e+da+e vpGDivll++g++vpaD r++e +a +vdes+LTGEs pv+k             ++ 
  gi|116754316|ref|YP_843434.1|  49 LVRTYARVVREGESFEVDAEECVPGDIVLLEEGMKVPADLRLIETHAlNVDESLLTGESAPVSKdasavlkwnaalgDRV 128
                                    56789************************************************************************9** PP

                                    TEE-TT-EEEE-EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHH CS
                   E1-E2_ATPase  68 dmvfsGtvvvsgeakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaea 147
                                    +m+f+Gt+v++g+ k+vV+atg +telg++a+ + + +s+k+pl++ ++ +++ ++++vl+++ll+++i + +g ++a+ 
  gi|116754316|ref|YP_843434.1| 129 NMAFAGTIVTRGRGKGVVVATGIETELGRLAETLTDVESAKPPLTRRMEVFSGNIAKAVLIAVLLIIAIEVRRGMDPAQV 208
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHS-TTHHHHHHHHHHHHHHHHHHT CS
                   E1-E2_ATPase 148 llralallvaaiPcaLplavplalalgarrlakk 181
                                    +++++al+v+aiP++Lp+a++++la++++r+a++
  gi|116754316|ref|YP_843434.1| 209 FVQSVALAVSAIPEGLPVALTVVLAVAVNRMARR 242
                                    ********************************96 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.71
                                    TSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS CS
                   E1-E2_ATPase  91 dtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvfli 136
                                    d  ++ i++ vee + + +++ k +  l+++ ++ ++l++l +f++
  gi|116754316|ref|YP_843434.1| 605 DDNFASIVAGVEEGRVAYSNVRKVIFLLVSTGAAEIVLFFLSLFAA 650
                                    4456667777777777777777777777777666666666666654 PP

>> Cation_ATPase_C  Cation transporting ATPase, C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1         2   5.2e+03      53      63 ..     186     196 ..     169     233 .. 0.61
   2 !  129.4   1.9   4.6e-41   1.2e-37       1     181 [.     652     823 ..     652     824 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2
                Cation_ATPase_C  53 riliqgllqal 63 
                                     +li  ll+++
  gi|116754316|ref|YP_843434.1| 186 AVLIAVLLIIA 196
                                    33332222222 PP

  == domain 2  score: 129.4 bits;  conditional E-value: 4.6e-41
                Cation_ATPase_C   1 plplsaiqiLwinLvtDllpalaLaleppekdimkrpPrkkkepliskkmlrriliqgllqalvtllvffltlllfgise 80 
                                    plpl a+q+Lw+nLvt ++  + Lalep+e d m+rpPr++ e ++++ m+ ril+ +++++ +t++++ + l+  g+s 
  gi|116754316|ref|YP_843434.1| 652 PLPLLAVQLLWLNLVTNGIQHIGLALEPAEGDEMRRPPRPHGEGIFNRIMVERILLSSIVMGGITFMLYRYLLS-TGSSM 730
                                    89*******************************************************************76666.66666 PP

                Cation_ATPase_C  81 kenklssnyaqtmaFitlvlsqifnalnlrsrreslfkfsglfsnkllllaillslllqvlivyvpglnavfgtaplsle 160
                                    +e       a+ ++ + +vl++ ++++n+rs+ +s+f+  +  +n++l++++l++ l++++ +y+p+l  v+++ p+sle
  gi|116754316|ref|YP_843434.1| 731 DE-------ARNSTMLLMVLFENLQVFNSRSELRSAFS-LSPMRNPILVIGTLGAQLVHITAMYTPWLSGVLNIGPVSLE 802
                                    66.......9****************************.66668************************************ PP

                Cation_ATPase_C 161 ewlialllalvvllvdelvKl 181
                                    +w+ +l+lal +l+ +e++K+
  gi|116754316|ref|YP_843434.1| 803 HWARLLALALTILVAMEAYKM 823
                                    *******************97 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.0   5.8   4.6e-21   1.2e-17       4     209 ..     261     581 ..     258     582 .. 0.57

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 4.6e-21
                                    EEEESBTTTBCHHHHHHHHHHHH....................CHHHHHHHHHH......HHCHHHHHHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxx....................xxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase   4 vvfDkdGTLttgepsvedvivsa....................alalaaaletg......sehpigkalvaaakarsgal 57 
                                    ++ Dk+GTLt       +  +++                    +      ++t+       e ++ k++v aa    +a 
  gi|116754316|ref|YP_843434.1| 261 IASDKTGTLTMNV---LT--ARLvaipghgymevtgdgispegE------IRTAhgrpteREEHLIKRVVTAATLCNEAF 329
                                    6667777777333...11..111112323333333332322221......222223333333333333333333332222 PP

                                    HHHHHETTTE.......................................................HHHHTHHHHHHHHHC CS
                                    xxxxxxxxxx.......................................................xxxxxxxxxxxxxxx RF
                      Hydrolase  58 tgfatfigrg.......................................................ayaigkpewltaldi 82 
                                     g++   gr                                                        ++ +g pe l ++  
  gi|116754316|ref|YP_843434.1| 330 FGMRN--GRWvhhgdtvdvallvmahkvgvmqadvtakhpmvaqipfaserkfaatlnrvgerhqVFVKGAPEILIEM-- 405
                                    22222..22222224444444222222222222222222222222222222222333333333346666666666666.. PP

                                    HHHHHHHHHHHHHHCHHHHHH...................................................TTHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxx...................................................xxxxxxxx RF
                      Hydrolase  83 ppdlgaaigsaqsqgrtvall...................................................qaralavf 111
                                                        +                                                       la++
  gi|116754316|ref|YP_843434.1| 406 --------------------CdrmvtidgdaplerdaiercaadmanngyrvlaiadgvvesdeefsdkqlrGLTFLALI 465
                                    ....................04444444444444444444677777779999*********9999997766555888888 PP

                                    HHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT................GGGESEEEEHHCES..... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................xxxxxxxxxxxxxx..... RF
                      Hydrolase 112 tiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG................ddyfdaviasdiet..... 170
                                     + dp  ++pea++ava+ ++agi+v+++tgd+p ta ++a++lG                +            +     
  gi|116754316|ref|YP_843434.1| 466 GMIDP--LRPEAEHAVARCRKAGIQVAMVTGDHPITALAIARELGlaqsmeevvtgpelkkA------------Ehigde 531
                                    888**..***************************************6666666665554443............034444 PP

                                    ...........STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHT CS
                                    ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 171 ...........vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaA 209
                                               +a ++p++k+ +++ L   ++ va+ GDg+nDa+a++aA
  gi|116754316|ref|YP_843434.1| 532 afddlirqarvFARVEPRQKLDIVQSLIRLGHTVAVTGDGANDAPAMRAA 581
                                    444555669999999************655999****************9 PP

>> Cation_ATPase  Cation transport ATPase (P-type)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.2   0.0   1.4e-20   3.7e-17       1      90 [.     323     408 ..     323     409 .. 0.97
   2 ?   -3.4   0.0       4.2   1.1e+04      73      85 ..     630     642 ..     620     642 .. 0.75

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 1.4e-20
                  Cation_ATPase   1 ilcNsaafsensekdevkllGnktEsALlvlaeklgldteelreetkkvqeipFnssrKrmsvvlklepekkvrlyvKGA 80 
                                    +lcN+a f   + ++++  +G+  ++ALlv+a+k+g  + ++ ++++ v++ipF s+rK+++++ +    +++ ++vKGA
  gi|116754316|ref|YP_843434.1| 323 TLCNEAFF--GMRNGRWVHHGDTVDVALLVMAHKVGVMQADVTAKHPMVAQIPFASERKFAATLNRV--GERHQVFVKGA 398
                                    59******..********************************************************6..5********** PP

                  Cation_ATPase  81 peiilkrCth 90 
                                    pei+++ C++
  gi|116754316|ref|YP_843434.1| 399 PEILIEMCDR 408
                                    ********86 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 4.2
                  Cation_ATPase  73 vrlyvKGApeiil 85 
                                    ++l+  GA+ei+l
  gi|116754316|ref|YP_843434.1| 630 FLLVSTGAAEIVL 642
                                    6778889999997 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0   0.00041         1      18      56 ..     473     511 ..     466     518 .. 0.90
   2 !   18.7   0.7   4.5e-07    0.0011     205     250 ..     564     610 ..     553     614 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00041
                                    HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCS CS
                    Hydrolase_3  18 ektkeaikklkekgikvviATGRslravlpvleelgldl 56 
                                    +++ +a+++++++gi+v+  TG ++ ++l +++elgl +
  gi|116754316|ref|YP_843434.1| 473 PEAEHAVARCRKAGIQVAMVTGDHPITALAIARELGLAQ 511
                                    68899******************************9875 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 4.5e-07
                                    GEEEEESSGGGHHHHHHSSEEEEET.TS-HHHHHHSSEEE--GGGTH CS
                    Hydrolase_3 205 eviafGDgeNDieMLeaaglgvAmg.naseevkkaAdyvtksnnedG 250
                                     v++ GDg ND + + aa +gvAmg ++++ +k+ A  v+++ n  +
  gi|116754316|ref|YP_843434.1| 564 TVAVTGDGANDAPAMRAAHVGVAMGmSGTDIAKESAELVITDDNFAS 610
                                    57788*******************96789*********999888655 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.1     4e-09     1e-05      86     188 .]     471     579 ..     446     579 .. 0.75

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 4e-09
                            HAD  86 ldpgalellaahraaGdrvvvvSgglrplvepllaelg....adevlat.elevddrltgelglegkpvrgegkvaalre 160
                                    l+p+a  ++a++r+aG++v++v+g + + + ++++elg     +ev+   el++ +++  e   +++++r++   a+++ 
  gi|116754316|ref|YP_843434.1| 471 LRPEAEHAVARCRKAGIQVAMVTGDHPITALAIARELGlaqsMEEVVTGpELKKAEHIGDE--AFDDLIRQARVFARVEP 548
                                    4699999999999*************************55553333333244444466666..77777777444455555 PP

                            HAD 161 ..wlaaegegidleevvay.GDspsDlpllr 188
                                      +l+     i+l ++va+ GD+ +D p++r
  gi|116754316|ref|YP_843434.1| 549 rqKLDIVQSLIRLGHTVAVtGDGANDAPAMR 579
                                    77777777777777899999*********98 PP

>> Isochorismatase  Isochorismatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00065       1.7     128     164 ..     424     460 ..     422     469 .. 0.87
   2 ?    3.2   0.0     0.034        86      23      52 ..     468     497 ..     460     537 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00065
                Isochorismatase 128 eatardaldlGyevvvvsDAvaalspelhdaalkrlk 164
                                    e  a d++++Gy+v  ++D+v  +++e  d+ l+ l 
  gi|116754316|ref|YP_843434.1| 424 ERCAADMANNGYRVLAIADGVVESDEEFSDKQLRGLT 460
                                    566899************************9999886 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.034
                Isochorismatase  23 isavveninkllkaarkagipviftrdvhe 52 
                                    i+ + ++++++++++rkagi v +++  h+
  gi|116754316|ref|YP_843434.1| 468 IDPLRPEAEHAVARCRKAGIQVAMVTGDHP 497
                                    56678999*****************99999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (831 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); 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: 0.67u 0.28s 00:00:00.95 Elapsed: 00:00:00.43
# Mc/sec: 5780.53
//
Query:       gi|116754317|ref|YP_843435.1|  [L=308]
Description: MscS mechanosensitive ion channel [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-38  132.8   0.2    1.7e-38  132.3   0.2    1.2  1  MS_channel  Mechanosensitive ion channel


Domain annotation for each model (and alignments):
>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.3   0.2   9.3e-43   1.7e-38       4     206 .]      62     259 ..      59     259 .. 0.94

  Alignments for each domain:
  == domain 1  score: 132.3 bits;  conditional E-value: 9.3e-43
                                    HHHHHHHHHHHHHHHTTT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEEEE-SSE CS
                     MS_channel   4 lkiliivvgilivlsllgvnvsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtVediglrt 83 
                                     +i+++++++ ++ + +g+  ++l++++G++++++gla+++++sn+vaGi++++++pf+iGD v + d   +Ved+ l  
  gi|116754317|ref|YP_843435.1|  62 ALIGAMATVTTVFPQAIGMI-TSLFVAAGFASIVVGLAAQSSLSNVVAGILISISQPFRIGDAVMFRDEYCYVEDMRLVH 140
                                    56677777777777777776.899999***************************************************** PP

                                    EEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-T.TS-EEEEEEE CS
                     MS_channel  84 tkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlk.dkellvvlde 162
                                    t +rt+d+r ++iPns l ++  +N+s  ++ + + v ++v y+sd   l+k+++++ ++++++p++l+    +++v+ +
  gi|116754317|ref|YP_843435.1| 141 TVLRTWDNRRLVIPNSVLQSEVLTNYSIVDPSVLVPVYVQVSYDSD---LKKAMDIMVDVARRHPDCLPtGSLPNAVVMA 217
                                    **********************************************...******************985678899**** PP

                                    E-SSSEEEEEEEEEET...TTHHHHHHHHHHHHHHHHHHHT--- CS
                     MS_channel 163 fgdsslnfevrvfvktvvpeeylsvqseinlrikkileeegiei 206
                                    f+ds++++++   +k+   +  +++ +++  +ikk+++++gi i
  gi|116754317|ref|YP_843435.1| 218 FEDSGISLRLLTRAKD--QSTAFDMTRDLLFEIKKEFDRNGIVI 259
                                    ****************..8**********************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       843  (0.0470188); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); 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):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2374.44
//
Query:       gi|116754318|ref|YP_843436.1|  [L=247]
Description: anaerobic ribonucleoside-triphosphate reductase activating protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.8e-20   73.3   1.5    1.2e-19   71.3   0.9    2.1  2  Radical_SAM  Radical SAM superfamily
      6e-11   42.8   0.0    9.1e-11   42.2   0.0    1.3  1  Fer4_12      4Fe-4S single cluster domain
    2.6e-08   34.0   0.0    1.1e-07   32.0   0.0    1.9  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 !   71.3   0.9     2e-23   1.2e-19       1     163 [.      23     191 ..      23     195 .. 0.78
   2 ?   -2.7   0.0       1.1   6.5e+03      23      47 ..     215     239 ..     210     243 .. 0.70

  Alignments for each domain:
  == domain 1  score: 71.3 bits;  conditional E-value: 2e-23
                                    EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHH........HHHHH......HTTSEEEEEESSTGGGSTTHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxx......xxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileev........kelka......ekgvkevilgggepllypdfvel 66 
                                    vv++rgC++rC+fC++ e       +  + + e+++++                   +  ++ v+l+ggepl+++d v++
  gi|116754318|ref|YP_843436.1|  23 VVFLRGCPFRCPFCQNAEL---QSGWTPVEISELINHLfprrgagqS---IlhefsgSVCIDSVVLSGGEPLAQSDAVVA 96 
                                    689**************94...4444444444444444332222221...02222222336677777************* PP

                                    HHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT.-SEEEEEEBSSSHH.HHHHHHTCTSHHHHHHHHHHHHHHTTSET CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  67 lerlaklavpgiritvetngtlpdeeklerllelg.vdrvslgleaadde.kvlklmnrghtfeevlealeklreagikr 144
                                    ++r++    +g+ + +etng+   +e le l   + +d v l+++aa  e ++++ ++ ++ + +vl++l+ + e+gi+ 
  gi|116754318|ref|YP_843436.1|  97 IAREVDV--RGLDLGIETNGYY--PESLEVLISEEyLDMVFLDIKAAPREdMYQRATGIRDALPRVLRSLDVIVEHGIP- 171
                                    ******9..8************..6********99***************9*******77*******************. PP

                                    EEEEEEEBTTTSH.HHHHHH CS
                                    xxxxxxxxxxxxx.xxxxxx RF
                    Radical_SAM 145 vvdrivglpGend.eeleel 163
                                      +ri+++pG    +el+e+
  gi|116754318|ref|YP_843436.1| 172 FEIRITVFPGMPSeDELKEV 191
                                    **********9861455554 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.1
                                    HHHHHHHHHHHHHHHHHHHHHHTTS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  23 egrgrslsveeileevkelkaekgv 47 
                                    +g  + +s e+++++++ lk++ ++
  gi|116754318|ref|YP_843436.1| 215 RGEFEPVSEEDLIRLAQLLKFNIRI 239
                                    5666677888888888888766554 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 !   42.2   0.0   1.5e-14   9.1e-11       6     100 ..      20     121 ..      14     152 .. 0.81

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 1.5e-14
                        Fer4_12   6 vrlslfvsgCnlsCkgCfnketwsfk........sgkeft.kelleeiiedlkk.esiegltllGGEPllpenaeallel 75 
                                    + +++f+ gC+++C++C n e++s           ++ f+ + + + i+++++    i+ ++l+GGEPl+  + +a++ +
  gi|116754318|ref|YP_843436.1|  20 LSAVVFLRGCPFRCPFCQNAELQSGWtpveiselINHLFPrRGAGQSILHEFSGsVCIDSVVLSGGEPLA--QSDAVVAI 97 
                                    5579******************95554445445578888779999*******9725569***********..******** PP

                        Fer4_12  76 vkevkeekpekdiwlytgytleels 100
                                    ++ev  ++++   ++++gy  e l+
  gi|116754318|ref|YP_843436.1|  98 AREVDVRGLD-LGIETNGYYPESLE 121
                                    *********6.89******888775 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 !   32.0   0.0   1.9e-11   1.1e-07       2      97 ..      25     122 ..      23     138 .. 0.71

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 1.9e-11
                        Fer4_14   2 fvrlsgCnlsCkgCdnketwkselgkpqteelleqilk..........dlkkseikiqglvltGGePLhyenkkellklv 71 
                                    f  l gC++ C++C n e  +s +++++ +el+++ +           +++ s + i+ +vl+GGePL  ++ ++++ + 
  gi|116754318|ref|YP_843436.1|  25 F--LRGCPFRCPFCQNAE-LQSGWTPVEISELINHLFPrrgagqsilhEFSGSVC-IDSVVLSGGEPL--AQSDAVVAIA 98 
                                    3..58**********998.677666666666665444322222221115555544.999*********..8899****** PP

                        Fer4_14  72 krlkeeypekkiwletngtleielek 97 
                                    +++  ++  ++  +etng +  +le+
  gi|116754318|ref|YP_843436.1|  99 REVDVRG--LDLGIETNGYYPESLEV 122
                                    *******..99999***999877773 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1934.99
//
Query:       gi|116754319|ref|YP_843437.1|  [L=182]
Description: hypothetical protein Mthe_1012 [Methanosaeta thermophila PT]
Scores for 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-17   61.6   0.1    1.5e-16   61.1   0.1    1.2  1  AAA_17    AAA domain
    1.8e-14   54.4   0.1    2.6e-14   53.9   0.1    1.3  1  AAA_18    AAA domain
    6.7e-08   32.8   0.0    9.2e-08   32.4   0.0    1.2  1  AAA_33    AAA domain
  ------ inclusion threshold ------
       0.03   14.0   0.1       0.15   11.7   0.0    1.9  2  CoaE      Dephospho-CoA kinase
      0.033   14.3   0.0      0.038   14.1   0.0    1.3  1  ADK       Adenylate kinase


Domain annotation for each model (and alignments):
>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.1   0.1   4.1e-20   1.5e-16       1     131 [.       7     127 ..       7     129 .. 0.73

  Alignments for each domain:
  == domain 1  score: 61.1 bits;  conditional E-value: 4.1e-20
                                    EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSH.HHHCTSHHHHHHHHHHHHHHHHHHHH.HSSEEEEEE CS
                         AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrgglakar.demrklpleekkelqkeaaekiaeea.kkkgvlvdg 78 
                                    +G+PGsGK+ +++ +++++g+ ++ +Gd++r+ea+r+gl++++ ++ + +++ ++ e  + +a+++ e   ++++++vdg
  gi|116754319|ref|YP_843437.1|   7 VGMPGSGKS-VASDVAREMGIRVVVMGDVVRAEARRRGLEPTDaNHGMVGDELRRSEGEDAIARRCLEGLsRDETIVVDG 85 
                                    7********.555**************************66541566666777777777766666666533777789999 PP

                                    -SEEEETTEEEESSHHHHHHHH...SEEEEEE--HHHHHHHHHHHTTST-TS-S CS
                         AAA_17  79 hprikeqagfldglpkevleelkp.daiilleadpeeilerrlkdrtrgrdddn 131
                                      +           ++e ++++    ++i + ++pe+ l+r +    rgr+ddn
  gi|116754319|ref|YP_843437.1|  86 IRSG---------AEVEYFRSVADrFHLIEIFTPPEQRLRRIA---ARGRSDDN 127
                                    8864.........33444444433138888*****97776665...59999998 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   0.1   7.2e-18   2.6e-14       1     120 [.       4     128 ..       4     144 .. 0.91

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 7.2e-18
                         AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpe.aldeskrldedkldklldaleenssaleeg 74 
                                    I+  G+pG+GK+  ++  +++ g+     g+++r  a+ +gl+ ++ ++ ++ +++r  e+ ++ + ++le+ s+     
  gi|116754319|ref|YP_843437.1|   4 IGFVGMPGSGKSVASDVAREM-GIrvvvmGDVVRAEARRRGLEPTDANHgMVGDELRRSEGEDAIARRCLEGLSR----D 78 
                                    7899*********99999998.5667**********************************************987....8 PP

                         AAA_18  75 knlvidghlaeleseaakdikk....vvLtaspeelleRlekRgyeeaki 120
                                    +++v+dg+++  e e+++        + + ++pe++l+R+++Rg++++  
  gi|116754319|ref|YP_843437.1|  79 ETIVVDGIRSGAEVEYFRSVADrfhlIEIFTPPEQRLRRIAARGRSDDNN 128
                                    9****************99888*9********************988664 PP

>> AAA_33  AAA 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   9.2e-08       3     125 ..       5     128 ..       3     143 .. 0.69

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 2.6e-11
                         AAA_33   3 llvGlpGsGKstlaerllkklg.avllssdtlrrrlfg.....tdqqskt..dytrvldrlyqilnelarkalsagrnvi 74 
                                     +vG+pGsGKs  ++ ++++ g  v++  d++r   +      td ++    d  r ++     +++++ + ls+   +i
  gi|116754319|ref|YP_843437.1|   5 GFVGMPGSGKSVASD-VAREMGiRVVVMGDVVRAEARRrglepTDANHGMvgDELRRSEGED-AIARRCLEGLSRDE-TI 81 
                                    59*********8777.8999999777777776664443222225555554433333333333.44455556666555.66 PP

                         AAA_33  75 ldatnlsrrerarflklarrlgvpvrivvvetdeetlkeRlakRaangddr 125
                                    +  + +s +e + f+++a     +++++ + t++e+  +R+a+R ++ d+ 
  gi|116754319|ref|YP_843437.1|  82 VVDGIRSGAEVEYFRSVAD----RFHLIEIFTPPEQRLRRIAARGRSDDNN 128
                                    6669**************9....77799******************86654 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   4.1e-05      0.15       2      43 ..       3      45 ..       2      74 .. 0.77
   2 ?    0.0   0.0      0.16   5.8e+02     126     147 ..     105     126 ..      95     143 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.1e-05
                                   EEEEEESTTSSHHHHHHHHHHTT-EEE.EHHHHHHHTTCCTHH CS
                           CoaE  2 ivgltGgiasGKstvanlfadlgvpiv.DaDlvArqvvepgse 43
                                   i+g  G  +sGKs+++++ +++g+ +v   D+v  +++  g e
  gi|116754319|ref|YP_843437.1|  3 IIGFVGMPGSGKSVASDVAREMGIRVVvMGDVVRAEARRRGLE 45
                                   89**********************9751678887777776655 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.16
                                    EEEE--HHHHHHHHHHCCTSTH CS
                           CoaE 126 lvvdvelelqveRlvardgvse 147
                                    + +  ++e++++R+ ar   + 
  gi|116754319|ref|YP_843437.1| 105 IEIFTPPEQRLRRIAARGRSDD 126
                                    55678999*****999965544 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.1e-05     0.038       2      81 ..       7      85 ..       6     142 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.1e-05
                                   EESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHHCT-HHHHHHHHHHHTTSS--HHHHHHHHHHHHHCHGTTTEEEEES CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            ADK  2 lGaPgaGKGtqaeklvkkyglahlstGdllRaevksgtelGkeakevmdkgelvpdevvvklvkeelekedkkkgfllDG 81
                                   +G Pg+GK  +a+ +++++g+  +  Gd++Rae ++     + a++ m   el  +e   ++ +  le  ++++  ++DG
  gi|116754319|ref|YP_843437.1|  7 VGMPGSGKS-VASDVAREMGIRVVVMGDVVRAEARRRGLEPTDANHGMVGDELRRSEGEDAIARRCLEGLSRDETIVVDG 85
                                   8*******6.7889*******************99877766666666666666666666666666666555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1417.28
//
Query:       gi|116754320|ref|YP_843438.1|  [L=52]
Description: hypothetical protein Mthe_1013 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-05   24.0   0.5    4.7e-05   23.4   0.5    1.3  1  Zn-ribbon_8     Zinc ribbon domain
    0.00031   20.7   0.3    0.00035   20.5   0.3    1.1  1  DZR             Double zinc ribbon
     0.0013   18.7   0.3     0.0014   18.6   0.3    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
     0.0071   16.2   2.0       0.73    9.7   0.1    2.1  2  TFIIS_C         Transcription factor S-II (TFIIS)
  ------ inclusion threshold ------
      0.014   16.1   0.4      0.015   16.0   0.4    1.1  1  FYDLN_acid      Protein of unknown function (FYDLN_acid)
      0.019   15.2   0.4        6.9    7.0   0.1    2.2  2  zinc_ribbon_9   zinc-ribbon
       0.02   14.8   0.1      0.032   14.2   0.1    1.3  1  zf-LYAR         LYAR-type C2HC zinc finger
      0.027   14.1   0.0      0.035   13.8   0.0    1.2  1  TackOD1         Thaumarchaeal output domain 1
       0.03   13.8   4.1        1.9    8.1   0.4    2.2  2  TF_Zn_Ribbon    TFIIB zinc-binding
      0.034   14.0   1.1      0.043   13.7   1.1    1.2  1  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)
      0.046   13.6   0.7        2.4    8.1   0.0    2.1  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
       0.25   11.2   1.9        2.9    7.9   0.2    2.1  2  zf-trcl         Probable zinc-ribbon domain
       0.37   10.6   2.8        6.7    6.5   2.8    2.1  1  Rubredoxin_2    Rubredoxin metal binding domain


Domain annotation for each model (and alignments):
>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.5   3.4e-08   4.7e-05       5      36 ..      21      48 ..      20      50 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 3.4e-08
                    Zn-ribbon_8  5 eYrCeeCghefevlqsisdapltaCPeCgs.ev 36
                                   +Y C +Cg++f  + +      + CP+C+s +v
  gi|116754320|ref|YP_843438.1| 21 DYICLDCGNKFKGMGK-----RPMCPSCKSrNV 48
                                   8***********8875.....667******776 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.3   2.6e-07   0.00035       9      38 ..      18      48 ..      13      52 .] 0.85

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.6e-07
                            DZR  9 ppdarfCseCgtklkavaaedrCpsCgek.v 38
                                   ++++  C +Cg+k k + +  +CpsC++  v
  gi|116754320|ref|YP_843438.1| 18 SAKDYICLDCGNKFKGMGKRPMCPSCKSRnV 48
                                   567889*********************9844 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 !   18.6   0.3     1e-06    0.0014      71      99 ..      22      50 ..      13      52 .] 0.84

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1e-06
                                   EEETTTS-EEECHHHHHS-TTTSSS-EEE CS
                           HypA 71 vrCreCgkefeleekalrCpkCgsadvei 99
                                   + C +Cg++f+   k+  Cp+C+s++v++
  gi|116754320|ref|YP_843438.1| 22 YICLDCGNKFKGMGKRPMCPSCKSRNVKL 50
                                   68*********6655578********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 !    9.7   0.1   0.00053      0.73      29      39 .]      22      32 ..      18      32 .. 0.92
   2 !    6.3   0.2    0.0064       8.8       3      11 ..      40      48 ..      39      50 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00053
                        TFIIS_C 29 ykCtkCghrWr 39
                                   y C++Cg++++
  gi|116754320|ref|YP_843438.1| 22 YICLDCGNKFK 32
                                   99*******97 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0064
                        TFIIS_C  3 CpkCgsrea 11
                                   Cp+C+sr++
  gi|116754320|ref|YP_843438.1| 40 CPSCKSRNV 48
                                   ******986 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 ?   16.0   0.4   1.1e-05     0.015      11      34 ..      23      45 ..      14      51 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.1e-05
                     FYDLN_acid 11 iCpscgakFYDLnkdPivcpkcge 34
                                   iC +cg+kF  ++k+P+ cp+c++
  gi|116754320|ref|YP_843438.1| 23 ICLDCGNKFKGMGKRPM-CPSCKS 45
                                   8***************6.****86 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0061       8.4      20      31 ..      20      31 ..      12      31 .. 0.76
   2 ?    7.0   0.1     0.005       6.9      22      30 ..      38      46 ..      34      49 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0061
                  zinc_ribbon_9 20 sdvlCPhCgggF 31
                                    d +C +Cg+ F
  gi|116754320|ref|YP_843438.1| 20 KDYICLDCGNKF 31
                                   3446******99 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.005
                  zinc_ribbon_9 22 vlCPhCggg 30
                                   ++CP+C++ 
  gi|116754320|ref|YP_843438.1| 38 PMCPSCKSR 46
                                   58****985 PP

>> zf-LYAR  LYAR-type C2HC zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   2.3e-05     0.032       1      13 [.      22      34 ..      22      37 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.3e-05
                        zf-LYAR  1 fsCiDCsktFdgd 13
                                   + C+DC+++F+g 
  gi|116754320|ref|YP_843438.1| 22 YICLDCGNKFKGM 34
                                   79********985 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.6e-05     0.035      63     100 ..      11      50 ..       6      52 .] 0.75

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.6e-05
                        TackOD1  63 glleeelvdrirlCpsCksgh..lnvrevCpkCkSidiee 100
                                    g++ee l  +  +C  C  +   +  r +Cp+CkS +++ 
  gi|116754320|ref|YP_843438.1|  11 GAIEEGLSAKDYICLDCGNKFkgMGKRPMCPSCKSRNVKL 50 
                                    6777888888889999976542267788999999999876 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.3    0.0016       2.2      18      28 ..      20      30 ..       1      32 [. 0.82
   2 ?    8.1   0.4    0.0013       1.9       2      11 ..      39      48 ..      38      52 .] 0.84

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0016
                                   TCEEESSSSBE CS
                   TF_Zn_Ribbon 18 gelvCtdCGlV 28
                                    +++C dCG+ 
  gi|116754320|ref|YP_843438.1| 20 KDYICLDCGNK 30
                                   58999999975 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0013
                                   EETTTTCEEC CS
                   TF_Zn_Ribbon  2 kCPnCgstnl 11
                                   +CP C+s+n+
  gi|116754320|ref|YP_843438.1| 39 MCPSCKSRNV 48
                                   8******984 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 ?   13.7   1.1   3.1e-05     0.043      25      45 ..      23      45 ..      20      50 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.1e-05
                                   E-HHHHHHHHH..TT-B-TTT-- CS
                     zf-C3HC4_3 25 lCeeCaekllk..rkkkCpiCrr 45
                                   +C +C +k++   +++ Cp C++
  gi|116754320|ref|YP_843438.1| 23 ICLDCGNKFKGmgKRPMCPSCKS 45
                                   8********8799********97 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0018       2.4       5      15 ..      22      32 ..      21      33 .. 0.87
   2 ?    4.3   0.1     0.028        38       7      16 ..      40      46 ..      39      52 .] 0.68

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0018
                 Zn_ribbon_SprT  5 YrCtgCgreyt 15
                                   Y C +Cg++++
  gi|116754320|ref|YP_843438.1| 22 YICLDCGNKFK 32
                                   9******9875 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.028
                 Zn_ribbon_SprT  7 CtgCgreyth 16
                                   C++C+    +
  gi|116754320|ref|YP_843438.1| 40 CPSCK---SR 46
                                   89998...44 PP

>> zf-trcl  Probable zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.2    0.0021       2.9       3      14 ..      20      31 ..      18      32 .. 0.90
   2 ?    3.3   0.1     0.055        76      36      42 ..      40      46 ..      33      50 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0021
                        zf-trcl  3 ktltCkdCgaef 14
                                   k ++C dCg++f
  gi|116754320|ref|YP_843438.1| 20 KDYICLDCGNKF 31
                                   7799******98 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.055
                        zf-trcl 36 CkaCRka 42
                                   C++C+++
  gi|116754320|ref|YP_843438.1| 40 CPSCKSR 46
                                   8888875 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   2.8    0.0048       6.7       1      22 [.      22      45 ..      22      47 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0048
                   Rubredoxin_2  1 YvCsqCGfesakwfGr...CpsCgs 22
                                   Y+C +CG+++   +G+   CpsC+s
  gi|116754320|ref|YP_843438.1| 22 YICLDCGNKFK-GMGKrpmCPSCKS 45
                                   88999998875.4666666999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); 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: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.39
# Mc/sec: 399.23
//
Query:       gi|116754321|ref|YP_843439.1|  [L=150]
Description: hypothetical protein Mthe_1014 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       207  (0.0115455); expected 358.6 (0.02)
Passed bias filter:                      200  (0.0111551); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 1177.46
//
Query:       gi|116754322|ref|YP_843440.1|  [L=183]
Description: histidinol-phosphatase and imidazoleglycerol-phosphate dehydratase HisB [Methanosaeta thermophila PT]
Scores for 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   0.4    3.7e-28   98.7   0.1    1.5  2  IGPD      Imidazoleglycerol-phosphate dehydratase
  ------ inclusion threshold ------
       0.12   12.3   0.0       0.98    9.4   0.0    2.0  2  DUF4265   Domain of unknown function (DUF4265)


Domain annotation for each model (and alignments):
>> IGPD  Imidazoleglycerol-phosphate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.52   4.7e+03      70      83 ..      16      29 ..       8      33 .. 0.75
   2 !   98.7   0.1   4.1e-32   3.7e-28       1     144 []      35     169 ..      35     169 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.52
                                   TEEEEEEEE--SS- CS
                           IGPD 70 ealaevaldlsgrp 83
                                   e+ + v +dl gr 
  gi|116754322|ref|YP_843440.1| 16 ETDVDVCIDLHGRG 29
                                   66677888888885 PP

  == domain 2  score: 98.7 bits;  conditional E-value: 4.1e-32
                                    ....HHHHHHHHHHHHHT--EEEEEEESSH...HHHHHHHHHHHHHHHHHHS..-SSB--EEEEEEEETTEEEEEEEE-- CS
                           IGPD   1 TgigfldhmLdqlakhggfdlkvkvkgdlevddHhtvedvgialGqalkealgdkrgikRfgsallpmDealaevaldls 80 
                                    Tgi++ld mL+ +a+ g+fd+++k++gd +  dHh+vedvgi+lG +l+     k+g   +gsa++p  e+ a +a+ + 
  gi|116754322|ref|YP_843440.1|  35 TGIELLDDMLRIIASSGQFDIRIKARGDET-GDHHLVEDVGITLGMCLSAV---KSG---TGSAIVPYGECTALAAVSFG 107
                                    9***************************76.899**************865...567...79****************95 PP

                                    SS-EEE--..-SB--TT.--HHHHHHHHHHHHHHHT-EEEEEEEE--BHHHHHHHHHHHHHHHH CS
                           IGPD  81 grpylvleaelkrekigeldtelveeffeslaeaagitlhvkvlrgenahhivealfKafaraL 144
                                     +p +  + +l+ ekig +++e++ +f++s+a +  +tlhv +  g ++ +++ +++Ka++ aL
  gi|116754322|ref|YP_843440.1| 108 -APGFRGDLKLSFEKIGGMAMENLVHFMRSMAYSGSFTLHVITD-GGDDREKIVSAMKALGAAL 169
                                    .788888999*******************************988.99999999*********98 PP

>> DUF4265  Domain of unknown function (DUF4265)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0     0.067     6e+02      44      63 ..      45      64 ..      40      80 .. 0.75
   2 ?    9.4   0.0   0.00011      0.98      42      80 ..     133     169 ..     125     174 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.067
                        DUF4265 44 rvvkesGnstirvlvdekae 63
                                   r++ +sG++ ir+ ++ ++ 
  gi|116754322|ref|YP_843440.1| 45 RIIASSGQFDIRIKARGDET 64
                                   78999*******98766554 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00011
                        DUF4265  42 fervvkesGnstirvlvdekaelgesevreeLealgcev 80 
                                    f r +  sG +t++v+ d ++++  ++++++++alg+ +
  gi|116754322|ref|YP_843440.1| 133 FMRSMAYSGSFTLHVITDGGDDR--EKIVSAMKALGAAL 169
                                    6667789*********9999886..9*********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); 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: 0.37u 0.20s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 1566.99
//
Query:       gi|116754323|ref|YP_843441.1|  [L=152]
Description: hypothetical protein Mthe_1016 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-09   37.0   0.0    5.4e-09   36.2   0.0    1.4  1  PgpA      Phosphatidylglycerophosphatase A


Domain annotation for each model (and alignments):
>> PgpA  Phosphatidylglycerophosphatase A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.0     3e-13   5.4e-09      18     141 ..      13     145 ..       3     147 .. 0.87

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 3e-13
                                    --HHHHHHHHHHHTT.............HHHHH.HHH...HHHHHHHHHHHHHHHHHHT-S-........HHT-TT--HH CS
                           PgpA  18 gtvgslaalllallll............lleslslll...llilllflvGiwackktekelg........ekDpgeiviD 74 
                                    +tv++++a++l+l++             +++   +++   ++++ll+++Gi ++++ + ++         e+D + ++ D
  gi|116754323|ref|YP_843441.1|  13 ITVDDIVATALELYVPhpgvetrekadaVFRRELNIAlsdPNLALLIYAGILLEERGRMKMLpnlrgedyERDLTYLIAD 92 
                                    8999*******9999889999888888744444444468999**************9998777999************** PP

                                    HHTTHHHHH........TTHHHHHHHHHHHHS--THHHHTSSS.-S---TTHHHHHHHHHHHHHHHH CS
                           PgpA  75 EvvgqwiallllpatllalllafilFrlfDivKpgpigwldrklkgglgvmlDDllAgiaaalvlal 141
                                    Ev+g++ia       +++   +++ +  +D++Kpg++++l          ++DD+++g+++++ + +
  gi|116754323|ref|YP_843441.1|  93 EVLGMSIAK------YIGGYKGTFEYVRYDKAKPGILSRLGP--------FMDDVIGGLIGGVSSNM 145
                                    *********......456799******************977........9**********998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.21s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 1280.61
//
Query:       gi|116754324|ref|YP_843442.1|  [L=246]
Description: cobalamin 5'-phosphate synthase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.8e-38  132.8  14.9    2.1e-38  132.6  14.9    1.0  1  CobS       Cobalamin-5-phosphate synthase
  ------ inclusion threshold ------
      0.072   12.7   0.5      0.072   12.7   0.5    2.7  3  CbiQ       Cobalt transport protein
        8.6    6.3  13.7        1.7    8.6   1.7    3.2  3  RseC_MucC  Positive regulator of sigma(E), RseC/MucC


Domain annotation for each model (and alignments):
>> CobS  Cobalamin-5-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.6  14.9   3.5e-42   2.1e-38       2     204 .]       5     233 ..       4     233 .. 0.82

  Alignments for each domain:
  == domain 1  score: 132.6 bits;  conditional E-value: 3.5e-42
                           CobS   2 lsflTrlPvp.......elaralaffPlvGlllGlll.llallllllll.llaallavaalvlltgglHlDGlaDtaDgl 72 
                                    ++fl+++Pv        +l r +++fP++G+ lGl++ ++a+ll l+l+  ++a+++++a++++ g++H+DGlaD++Dg+
  gi|116754324|ref|YP_843442.1|   5 FGFLSTIPVGitmegieALMRHVYIFPIIGMALGLIFaAVAYLLDLFLPqDITAVCIMIAIYWVCGINHIDGLADFGDGV 84 
                                    79*******8766655455779999***********98888888888779788888888999****************** PP

                           CobS  73 gsgrdrerrleImkDsrvGafGvlalvlvlllkvaalaala.......lllapvlsRlaallaiallpyaeeglgalfae 145
                                     ++++ e+++++mkD ++G++G++++++vll  ++a+ ++        l+++++ ++ ++l+++a++++ ++glg+++++
  gi|116754324|ref|YP_843442.1|  85 TAHGSIEKKIKAMKDVNLGSGGAVFVMMVLLSLYSAIRSMDhyilpaaLIVSEISAKQSMLAFAAFTEPFHSGLGQIMID 164
                                    9999********************************7444344567888999****************9999*******9 PP

                           CobS 146 aqkk......lvllal.......avllllla...lllaallvalllrrlarrklggvtGDvlGavieltellvll 204
                                    ++ k      l    +       ++l +  +   +++a ++ al+l r+++r++gg +GD +Ga++e++++++l+
  gi|116754324|ref|YP_843442.1| 165 RTGKrefliaL----IitsiasaLLLNT--TgliMVIASVISALYLVRVSKRNFGGGSGDGIGASNEIGRAVALC 233
                                    54444764321....1234443211221..1223567777789999*************************9985 PP

>> CbiQ  Cobalt transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.7     0.062   3.7e+02      16      40 ..      42      66 ..       8      76 .. 0.68
   2 ?   -1.3   0.2      0.22   1.3e+03      17      50 ..     108     138 ..     101     154 .. 0.57
   3 ?   12.7   0.5   1.2e-05     0.072       7      52 ..     165     210 ..     160     214 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.062
                                   HHHHHHHHHHS-HHHHHHHHHHHHH CS
                           CbiQ 16 wlfllllalvlapnlvtlliiiall 40
                                   +  ++ll l+l++ + ++ i+ia++
  gi|116754324|ref|YP_843442.1| 42 AAVAYLLDLFLPQDITAVCIMIAIY 66
                                   3345555566666666666666655 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.22
                                    HHHHHHHHHS-HHHHHHHHHHHHHHHHHTTS--- CS
                           CbiQ  17 lfllllalvlapnlvtlliiiallllllllvilp 50 
                                    +f ++++l+l++++ ++     ++l ++l+v + 
  gi|116754324|ref|YP_843442.1| 108 VFVMMVLLSLYSAIRSM---DHYILPAALIVSEI 138
                                    66677777777766666...33344444444433 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 1.2e-05
                                    S-HHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHTTS---HH CS
                           CbiQ   7 rldprvkliwlfllllalvlapnlvtlliiiallllllllvilprv 52 
                                    r   r +li+l+++++a+ l+ n+ +l+++ia ++ +l lv ++++
  gi|116754324|ref|YP_843442.1| 165 RTGKREFLIALIITSIASALLLNTTGLIMVIASVISALYLVRVSKR 210
                                    5567899**********************99999999999988765 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 ?    8.6   1.7   0.00028       1.7      66     107 ..      23      65 ..      10      76 .. 0.65
   2 ?    2.3   0.1     0.025   1.5e+02      33      89 ..      87     145 ..      82     164 .. 0.75
   3 ?    2.1   1.3     0.029   1.8e+02      75     113 ..     172     207 ..     171     218 .. 0.57

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00028
                      RseC_MucC  66 aallvYllPllllilgallgsall.....gssellaalgallglvlg 107
                                     +  vY++P++++ lg++++ ++      + ++++a++++++     
  gi|116754324|ref|YP_843442.1|  23 LMRHVYIFPIIGMALGLIFAAVAYlldlfLPQDITAVCIMIA----I 65 
                                    55679***********99998887655544444444443333....3 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.025
                      RseC_MucC  33 leskekrleveneigakvGdkVevgieeksllkaallv..YllPllllilgallgsall 89 
                                     +s ek++++ +++++  G  V v +   sl++a+  +  Y+lP +l++  + + +++l
  gi|116754324|ref|YP_843442.1|  87 HGSIEKKIKAMKDVNLGSGGAVFVMMVLLSLYSAIRSMdhYILPAALIVSEISAKQSML 145
                                    56678889999999999999999999999999986544449999999888777777665 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.029
                      RseC_MucC  75 llllilgallgsallgssellaalgallglvlgflivrl 113
                                    l++li++ ++  +l +++++l +++a ++ +l+++  r+
  gi|116754324|ref|YP_843442.1| 172 LIALIITSIASALL-LNTTGLIMVIASVISALYLV--RV 207
                                    56666666666666.45555555555555555544..33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       888  (0.0495287); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.37
# Mc/sec: 1971.90
//
Query:       gi|116754325|ref|YP_843443.1|  [L=200]
Description: putative nucleotidyltransferase [Methanosaeta thermophila PT]
Scores for complete 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   67.8   0.0    1.7e-18   67.5   0.0    1.1  1  NTP_transf_3     MobA-like NTP transferase domain
    1.4e-05   25.2   0.0    3.1e-05   24.0   0.0    1.5  1  CTP_transf_3     Cytidylyltransferase
     0.0026   17.0   0.0     0.0051   16.0   0.0    1.5  2  CofC             Guanylyl transferase CofC like
     0.0054   16.3   0.0     0.0069   16.0   0.0    1.3  1  NTP_transferase  Nucleotidyl transferase
  ------ inclusion threshold ------
       0.01   15.6   0.0      0.045   13.5   0.0    1.8  2  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
      0.041   13.7   0.0      0.062   13.1   0.0    1.2  1  DUF2064          Uncharacterized protein conserved in bacteri


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 !   67.5   0.0   5.8e-22   1.7e-18       4     119 ..       1     116 [.       1     127 [. 0.93

  Alignments for each domain:
  == domain 1  score: 67.5 bits;  conditional E-value: 5.8e-22
                                    EEESS-TTTT.TTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHHTTCTS-EEE-TTSS-SHHHHHHHHH CS
                   NTP_transf_3   4 LAGGrSsRmg.gdKallplggkpllervldalraagvdevvvvggd..eevlaalarlgvrvvededpgkgplaslaaal 80 
                                    +AGG++sR+g g+K++++l +kpl+++v+ alr++  ++++v++ +  +e ++   +++++vv  +  g g +  +  a+
  gi|116754325|ref|YP_843443.1|   1 MAGGKGSRLGmGEKPMVRLYKKPLIDYVVSALRPS-TERIIVATTRatPETRRWSLGKNLEVVDTS--GSGYIPDMVEAV 77 
                                    59********66***********************.7******877678999999999*****998..99********** PP

                                    HHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEE CS
                   NTP_transf_3  81 raaadadavlvlacDmPlltpelverllaaaaasgadvv 119
                                    ++a+ + +v+v+++D+Pl+t+e+v+++++a++++++ ++
  gi|116754325|ref|YP_843443.1|  78 ERAGISGPVMVIMADLPLITEEIVREVIDAYKSRPEPAL 116
                                    ******************************998887664 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0     1e-08   3.1e-05      14     122 ..      12     115 ..       7     148 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1e-08
                                    TTGGGSEETTEEHHHHHHHHHHHTTTTSEEEEEES-HHHHHHHHHTTSEEEE--TTCSSHHHHHHHHHHHHTTT.TTSEE CS
                   CTP_transf_3  14 pgKnlldlggkpliayvleaalkskafekvivaTDseeiknvakefgasvlvtrsslesdterflevvkaflmseneeii 93 
                                     +K++ +l  kpli+yv+ a++ s   e++ivaT+    +    ++g    v ++s +     ++e+v++  +s     +
  gi|116754325|ref|YP_843443.1|  12 GEKPMVRLYKKPLIDYVVSALRPS--TERIIVATTRATPETRRWSLGKNLEVVDTSGSGYIPDMVEAVERAGIS---GPV 86 
                                    58********************95..56*******999888888888666666666667777899999999999...778 PP

                                    EEE-TT-TT--HHHHHHHHHHHHHSTTSS CS
                   CTP_transf_3  94 vnlqGdnPllqeevikkaietlkenqedy 122
                                    + + +d Pl+ ee ++++i+++k ++e+ 
  gi|116754325|ref|YP_843443.1|  87 MVIMADLPLITEEIVREVIDAYKSRPEPA 115
                                    88899*****************9998873 PP

>> CofC  Guanylyl transferase CofC like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.7e-06    0.0051      37     113 ..      28     108 ..      12     112 .. 0.63
   2 ?   -2.8   0.0      0.97   2.9e+03     168     179 ..     171     182 ..     149     188 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.7e-06
                           CofC  37 vidalkr.ldvlvvsedeevleyaldelg..vevvkek....ekdlntavekafeeieekeviiipsdiPlikkedvkdl 109
                                    v+ al +  + ++v+  +   e  + +lg  +evv         d+ +ave+a       +v++i++d+Pli++e v+++
  gi|116754325|ref|YP_843443.1|  28 VVSALRPsTERIIVATTRATPETRRWSLGknLEVVDTSgsgyIPDMVEAVERA---GISGPVMVIMADLPLITEEIVREV 104
                                    55566554445555555555555544443225555554211123555666666...34789******************9 PP

                           CofC 110 lele 113
                                    ++  
  gi|116754325|ref|YP_843443.1| 105 IDAY 108
                                    9875 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.97
                           CofC 168 ylsvdinteedl 179
                                     l+++int++dl
  gi|116754325|ref|YP_843443.1| 171 ELAININTPDDL 182
                                    567888888887 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   2.3e-06    0.0069       5      59 ..       1      49 [.       1     109 [. 0.86

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.3e-06
                                   E--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHH CS
                NTP_transferase  5 LaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsf 59
                                   +aGG+G+RL        k++v  ++k +li++++s+l   ++e+iiv +t+ + +
  gi|116754325|ref|YP_843443.1|  1 MAGGKGSRLG----MGEKPMVRLYKK-PLIDYVVSALR-PSTERIIVATTRATPE 49
                                   8********5....799*********.**********9.5888977777765554 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 ?   13.5   0.0   1.5e-05     0.045       7     118 ..       2     109 ..       1     122 [. 0.76
   2 ?   -0.3   0.0      0.24   7.2e+02     201     220 ..     171     190 ..     163     191 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.5e-05
                                    CTTSSCTT-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGGCCEEEEE.--SSHHHHHHHHH CS
                           IspD   7 AAGsGkRmkaglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllldksiqlva.GGdeRaesVlngl 85 
                                    A G+G+R++ g  K  + l  ++l+   v+al    + ++i+v+ ++   +e++  +l k++++v+  G+      ++++
  gi|116754325|ref|YP_843443.1|   2 AGGKGSRLGMGE-KPMVRLYKKPLIDYVVSALRP--STERIIVATTRAT-PETRRWSLGKNLEVVDtSGSGYIPDMVEAV 77 
                                    88********95.8999**************976..899****999887.999999999999999723555555555555 PP

                                    HTTSSTTSEEEE--TT-TT--HHHHHHHHHHHH CS
                           IspD  86 kalegeakfVLvHDaARpllkaadiaellaaae 118
                                    +  +g    V+v  a  pl++++ + e++ a +
  gi|116754325|ref|YP_843443.1|  78 ER-AGISGPVMVIMADLPLITEEIVREVIDAYK 109
                                    54.344466777777777777777777777665 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.24
                                    TTG----SHHHHHHHHHHHH CS
                           IspD 201 ednlKittpeDlalAeailr 220
                                    e ++ i tp+Dl + e i++
  gi|116754325|ref|YP_843443.1| 171 ELAININTPDDLRICERIIK 190
                                    57899**********99987 PP

>> DUF2064  Uncharacterized protein conserved in bacteria (DUF2064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.1e-05     0.062      12      86 ..      37     108 ..      28     117 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.1e-05
                                    EEEEEE----TTHHHHHHHH-TTSEEEE--SSSHHHHHHHHHHHHHHTT-S.EEEEE-SS-TT--HHHHHHHHHHT CS
                        DUF2064  12 evvlaldgaldkalaeqlalakglevlpQqggdlgeRlarafdrafeagee.pvlliGsDcpqltaalleqAfeaL 86 
                                    e+ ++ +    ++ +++  l+k+lev+  +g+     + +a++ra   g + pv++i +D+p +t++++++ ++a 
  gi|116754325|ref|YP_843443.1|  37 ERIIVATTRATPETRRW-SLGKNLEVVDTSGSGYIPDMVEAVERA---GISgPVMVIMADLPLITEEIVREVIDAY 108
                                    44444444444555555.8999999999999999999********...7777******************998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1530.45
//
Query:       gi|116754326|ref|YP_843444.1|  [L=120]
Description: hypothetical protein Mthe_1019 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.018   14.6   0.0       0.02   14.4   0.0    1.1  1  DUF2031   Protein of unknown function (DUF2031)


Domain annotation for each model (and alignments):
>> DUF2031  Protein of unknown function (DUF2031)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.1e-06      0.02      23      99 ..      10      89 ..       6     116 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.1e-06
                        DUF2031 23 eLylvnereiyl.erniinfrnnR.iLada.dnqfdlndfYqstlsLanqfndyndddeeiiklrniidshikkhkennt 99
                                   e+y + e e+   ern +n r+   +La++ +n + l +       L n +++ + ++  ++ lr  ids++++h++   
  gi|116754326|ref|YP_843444.1| 10 EVYRISELELLTgERNPKNTRDYIlLLAKVlQNPMRLPELLREFCTLRNTLSEPEKEELRMALLRVQIDSELRMHEDILR 89
                                   67777777654339999999986515788889*******************************************98655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.37
# Mc/sec: 978.81
//
Query:       gi|116754327|ref|YP_843445.1|  [L=255]
Description: hypothetical protein Mthe_1020 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1871.95
//
Query:       gi|116754328|ref|YP_843446.1|  [L=243]
Description: metallophosphoesterase [Methanosaeta thermophila PT]
Scores for complete 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   37.6   0.0    4.2e-09   37.2   0.0    1.3  1  Metallophos    Calcineurin-like phosphoesterase
    2.3e-06   27.9   0.0    3.4e-06   27.4   0.0    1.2  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
  ------ inclusion threshold ------
      0.096   11.5   0.0       0.16   10.8   0.0    1.3  1  Epimerase_2    UDP-N-acetylglucosamine 2-epimerase


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 !   37.2   0.0     7e-13   4.2e-09       1      76 [.      18     115 ..      18     193 .. 0.71

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 7e-13
                                    EEEEEEESBTB..........TTCCTHHHHHHHHHHHH...HHHTTESEEEEEST...SSSSSHHHHHHHHH.HHHHHHH CS
                    Metallophos   1 lrilvigDlHl..........algggqlddllkllddl...lreekpdlvllaGD...lvdrgdlekellel.laalvky 63 
                                    +r++v++DlHl          a  + q   + +lld++   ++ ++p  ++++GD   +v r++++++++   +  +++ 
  gi|116754328|ref|YP_843446.1|  18 HRVMVVADLHLgieyelwlggANLPSQ---TGRLLDRIlgvIEAHDPERLVVLGDlkhNVPRTSWQERVEVPeFISKLSK 94 
                                    69***************7555433444...44444555444677899999999**5555555599998887765555555 PP

                                    TSEEEEEC-TTS........C CS
                    Metallophos  64 pipvylllGNHe........g 76 
                                     ++v+l++GNH+        g
  gi|116754328|ref|YP_843446.1|  95 VVKVVLVPGNHDtglrdlapG 115
                                    999*********766666553 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 !   27.4   0.0   5.6e-10   3.4e-06       2     100 ..      19     135 ..      19     166 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 5.6e-10
                  Metallophos_2   2 klaiiSDlH................snldaleavlealkevgvdaiihaGD.............leeeepevleellela 52 
                                    ++++++DlH                + +++l+++l  ++++++++++++GD             +  e pe++ +l ++ 
  gi|116754328|ref|YP_843446.1|  19 RVMVVADLHlgieyelwlgganlpsQTGRLLDRILGVIEAHDPERLVVLGDlkhnvprtswqerV--EVPEFISKLSKVV 96 
                                    5899********************999************************55555555533332..4448999999999 PP

                  Metallophos_2  53 pvlaVrGNnDeevveedvlreaaelgtdlpeeaelelagek...vlliHgd 100
                                    +v+ V+GN+D            ++l++  p ++++e +g+    v+ +Hg+
  gi|116754328|ref|YP_843446.1|  97 KVVLVPGNHD------------TGLRDLAPGAEVCEPEGVVidgVGYFHGH 135
                                    **********............55555555666666555555556666666 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 ?   10.8   0.0   2.7e-05      0.16      13      77 ..      12      70 ..       7      77 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 2.7e-05
                                   EEEE-S--SGGGTHHHHHHTT----SEEE---S--HHHHHHHHHHHHHHHHHHH--SEEEEESSS CS
                    Epimerase_2 13 lvvtGqHldremgdtvfeeleiekpdydlnsdsqslakstgrvligleevleeekpDlvlvlGDt 77
                                   l++ G+H       +v ++l++  ++y+l  ++ +l  +tgr+l ++  v+e+ +p+ ++vlGD 
  gi|116754328|ref|YP_843446.1| 12 LIAEGEH-----RVMVVADLHL-GIEYELWLGGANLPSQTGRLLDRILGVIEAHDPERLVVLGDL 70
                                   5555556.....3445667777.889**************************************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       236  (0.013163); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1769.45
//
Query:       gi|116754329|ref|YP_843447.1|  [L=382]
Description: hypothetical protein Mthe_1022 [Methanosaeta thermophila PT]
Scores for complete 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-53  179.5 133.0    8.4e-18   64.7  31.9    3.2  4  Beta_helix    Right handed beta helix region
    5.5e-34  117.5  55.8      3e-22   79.1  27.9    2.3  2  NosD          Periplasmic copper-binding protein (NosD)
  ------ inclusion threshold ------
       0.24   10.0   2.0       0.35    9.5   2.0    1.2  1  RdRP_3        Viral RNA dependent RNA polymerase


Domain annotation for each model (and alignments):
>> Beta_helix  Right handed beta helix region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.9  21.4   5.1e-17     3e-13       2     120 ..      33     146 ..      32     148 .. 0.84
   2 !   63.3  34.1   3.9e-21   2.3e-17       5     157 ..      80     228 ..      80     229 .. 0.92
   3 !   64.7  31.9   1.4e-21   8.4e-18       2     145 ..     121     262 ..     120     264 .. 0.94
   4 !   42.8  21.6     8e-15   4.8e-11      13     124 ..     200     313 ..     200     330 .. 0.84

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 5.1e-17
                                    SEEE-SS-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--E CS
                     Beta_helix   2 gisingssnvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasnnl 81 
                                    gi+i+++++  i+++++s++ g+G+ +r+s+n  i n+ i+ ns  G+ i g snnt++ n+i+ n + gi ++ +++n+
  gi|116754329|ref|YP_843447.1|  33 GIVIESNGS-RIEGCNVSECAGSGVVIRSSGN-SIINCSITRNSLVGMKIWG-SNNTVQWNRINANDDCGIIVY-GDGNV 108
                                    899999999.**********************.6666999999********9.9**********9996666665.67799 PP

                                    EES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE- CS
                     Beta_helix  82 ienneitdnggsGiylnyssnntienNiidnnagsGivi 120
                                    ie ne  +n  +G+++++ssn++ +nN+  + + +Gi+i
  gi|116754329|ref|YP_843447.1| 109 IESNELLENIHDGMEIEGSSNMISRNNVSMSHG-AGIEI 146
                                    *********999****97555555555555554.99987 PP

  == domain 2  score: 63.3 bits;  conditional E-value: 3.9e-21
                                    E-SS-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT.--S--EEE CS
                     Beta_helix   5 ingssnvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialf.gasnnlie 83 
                                    i+gs+n t++ n i+ + ++Gi ++g++n vie+ne+  n ++G++i+g s n is+n++s ++g gi +   +s+n+ie
  gi|116754329|ref|YP_843447.1|  80 IWGSNN-TVQWNRINANDDCGIIVYGDGN-VIESNELLENIHDGMEIEG-SSNMISRNNVSMSHGAGIEILnMSSGNVIE 156
                                    577888.9999999999************.******************9.666777777777777***9999******** PP

                                    S-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS--EEES-E CS
                     Beta_helix  84 nneitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsssnvtvrnNt 157
                                     n+i+ ng++Gi++  s+ n i++N +++n+  Gi  +    n+ ++ Nt+ ++ + Gi + + s+ + v++N+
  gi|116754329|ref|YP_843447.1| 157 SNDIYGNGECGIEVIESYENNISGNSLNGNG-FGIKTERAT-NNLISSNTVISSIKDGILISDESRCNIVHRNN 228
                                    *******************************.*********.999*********************77777776 PP

  == domain 3  score: 64.7 bits;  conditional E-value: 1.4e-21
                                    SEEE-SS-E.EEESEEEES-SS-SEEE-SSS-..EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S-- CS
                     Beta_helix   2 gisingssnvtiknntisnsggyGiylrgssn.vvienneiannsgsGiyilgssnntisnntisdnngggialfgasnn 80 
                                    g +i+gssn  i+ n++s s+g+Gi + + s+ +vie+n+i++n++ Gi++ +s +n+is+n+ ++n+ +gi+++ a nn
  gi|116754329|ref|YP_843447.1| 121 GMEIEGSSN-MISRNNVSMSHGAGIEILNMSSgNVIESNDIYGNGECGIEVIESYENNISGNSLNGNG-FGIKTERATNN 198
                                    668999***.*****************9988779**********************************.*********** PP

                                    EEES-EEES-SS-SEE-TT-S-.-EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-T CS
                     Beta_helix  81 lienneitdnggsGiylnyssn.ntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavv 145
                                    li+ n+++   ++Gi +++ s+ n++++N++++n  +Gi i+ s+ ++ v +N++++n+  Gi++ 
  gi|116754329|ref|YP_843447.1| 199 LISSNTVISSIKDGILISDESRcNIVHRNNASSNHDAGIRIEGSK-DNMVIGNSVHSNA-IGIDIS 262
                                    ******************86665899*******************.8889********8.888876 PP

  == domain 4  score: 42.8 bits;  conditional E-value: 8e-15
                                    EESEEEES-SS-SEEE-SSS-.EEE.S-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES-EEES-S CS
                     Beta_helix  13 iknntisnsggyGiylrgssnvvie.nneiannsgsGiyilgssnntisnntisdnngggialfgasnnlienneitdng 91 
                                    i+ nt+ +s ++Gi + + s++ i  +n+ ++n + Gi+i+gs++n + +n+++ n   gi ++ + nn+i++n+  +ng
  gi|116754329|ref|YP_843447.1| 200 ISSNTVISSIKDGILISDESRCNIVhRNNASSNHDAGIRIEGSKDNMVIGNSVHSNA-IGIDISRSENNTIRGNRAMMNG 278
                                    678999999************555559999999*********************999.*********************8 PP

                                    S-SEE-T.T-S--EEES-EEESTT..--SEE---TT CS
                     Beta_helix  92 gsGiyln.yssnntienNiidnna..gsGividdss 124
                                      Gi+l+ ys+ nt+ +N + +n+  +   +++++ 
  gi|116754329|ref|YP_843447.1| 279 V-GIRLDiYSTANTLYHNAMIDNRqsALDSSVYYGR 313
                                    7.**********************442233344444 PP

>> NosD  Periplasmic copper-binding protein (NosD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1  26.8   3.4e-17     2e-13      15     172 ..      30     186 ..       8     188 .. 0.89
   2 !   79.1  27.9     5e-26     3e-22      40     212 ..     167     330 ..     167     356 .. 0.89

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 3.4e-17
                           NosD  15 rgngiqlensegseisnneisnsrdgilldnssnntitgntienl.ryGihlensesntiedntlssne.sGialmsssn 92 
                                    +g gi + +s+gs+i++ ++s+   +  +  ss+n+i ++ i+ +   G+ +++s++ t++ n ++ n+ +Gi+++    
  gi|116754329|ref|YP_843447.1|  30 IGGGI-VIESNGSRIEGCNVSECAGSGVVIRSSGNSIINCSITRNsLVGMKIWGSNN-TVQWNRINANDdCGIIVYGDG- 106
                                    34344.4578**************9999************88877699******998.**********99*******99. PP

                           NosD  93 ntlenNtisnnenyGillsdssnntisnNtis.nnnkGiflens.ssntitgNriesnqkiGilllsssegntiynNyFi 170
                                    n++e N++ +n   G+ +++ss n is+N++s + ++Gi + n  s+n+i++N i++n+++Gi  + +s +n+i +N++ 
  gi|116754329|ref|YP_843447.1| 107 NVIESNELLENIHDGMEIEGSS-NMISRNNVSmSHGAGIEILNMsSGNVIESNDIYGNGECGIE-VIESYENNISGNSLN 184
                                    *************9*9999999.57*******9*******999889******************.99999********95 PP

                           NosD 171 nn 172
                                    +n
  gi|116754329|ref|YP_843447.1| 185 GN 186
                                    55 PP

  == domain 2  score: 79.1 bits;  conditional E-value: 5e-26
                           NosD  40 gilldnssnntitgntienlryGihlensesntiedntlssne.sGialmsssnn.tlenNtisnnenyGillsdssnnt 117
                                    gi + +s +n+i+gn ++ +  Gi  e + +n i++nt+ s+  +Gi+++++s++ +++ N++s+n ++Gi +++s++n 
  gi|116754329|ref|YP_843447.1| 167 GIEVIESYENNISGNSLNGNGFGIKTERATNNLISSNTVISSIkDGILISDESRCnIVHRNNASSNHDAGIRIEGSKDNM 246
                                    5778899******************************9877666******999988************************ PP

                           NosD 118 isnNtisnnnkGiflensssntitgNriesnqkiGilllsssegntiynNyFinnsenvkydgsn..nneWnttktsgtn 195
                                    + +N + +n+ Gi +++s++nti+gNr   n ++Gi l  +s+ nt+y N +i+n++++ +++     n W++ +     
  gi|116754329|ref|YP_843447.1| 247 VIGNSVHSNAIGIDISRSENNTIRGNRAMMN-GVGIRLDIYSTANTLYHNAMIDNRQSALDSSVYygRNIWDNGS----- 320
                                    *******************************.*****9999999**************999987799********..... PP

                           NosD 196 iiggpylgGNyWsdydg 212
                                           +GNy+sd  +
  gi|116754329|ref|YP_843447.1| 321 -------EGNYYSDHIC 330
                                    .......******9644 PP

>> RdRP_3  Viral RNA dependent RNA polymerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   2.0   5.8e-05      0.35     251     310 ..      34     102 ..      28     119 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 5.8e-05
                                    EEE-TTS-..E.EEEE-S--TTSTTHHHHHHHHHHHHHHHHHHHH......T.SSEEEEEETTEEEEEE CS
                         RdRP_3 251 tavasdGq.ik.ykvrgcRmSGdlnTSlGNcllmclivkalckal......g.idaeLlnnGDDcvvic 310
                                    + + s+G  i+ ++v  c  SG++  S+GN+++ c i+++ +  +      + ++ + +n+ DDc +i+
  gi|116754329|ref|YP_843447.1|  34 IVIESNGSrIEgCNVSECAGSGVVIRSSGNSIINCSITRNSLVGMkiwgsnNtVQWNRINANDDCGIIV 102
                                    5555666543238999**********************9977654111111234555567777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 2882.00
//
Query:       gi|116754330|ref|YP_843448.1|  [L=289]
Description: transposase, IS4 family protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.2e-33  113.1   0.0    3.2e-31  107.9   0.0    2.2  2  DDE_Tnp_1_5  Transposase DDE domain
      9e-21   74.5   0.1    1.6e-20   73.7   0.1    1.4  1  DDE_Tnp_1    Transposase DDE domain


Domain annotation for each model (and alignments):
>> DDE_Tnp_1_5  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.9   0.0   3.6e-35   3.2e-31       2     111 ..      18     125 ..      17     126 .. 0.95
   2 ?    2.8   0.0     0.016   1.4e+02      40      67 ..     252     281 ..     246     287 .. 0.82

  Alignments for each domain:
  == domain 1  score: 107.9 bits;  conditional E-value: 3.6e-35
                    DDE_Tnp_1_5   2 kRGsltiwldeeaiaawkek...kkngkrgrpqvysdaaiqtcltvkvlfklplRqlqGfvqsllklaglellvpdystl 78 
                                    +RG  +++l+++++++w+e+    +++k+grp++y++++iq+c +++++++lp+Rql+Gf+q+l+ ++   ll++dystl
  gi|116754330|ref|YP_843448.1|  18 RRG--WFYLSTDFVNNWDEEllkMNKNKNGRPYRYPETFIQFCGLAYAFLHLPYRQLEGFIQALSGFVPG-LLAADYSTL 94 
                                    799..************9987745569******************************************9.99******* PP

                    DDE_Tnp_1_5  79 srraktlevkipvkrkskglhlvvdstGlkvlg 111
                                    ++r ++le++ip+ +++  l+++vdstG+kv++
  gi|116754330|ref|YP_843448.1|  95 WQRITNLELNIPIPDND--LVVAVDSTGMKVTN 125
                                    **************999..99**********97 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.016
                    DDE_Tnp_1_5  40 tcltvkvlfklplRql..qGfvqsllklag 67 
                                    ++  +k++f+ ++R++  +G+++ + ++ +
  gi|116754330|ref|YP_843448.1| 252 VFSAIKRIFGETVRATskEGMIREVRRMFT 281
                                    56789*********9855699999988876 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.7   0.1   1.8e-24   1.6e-20       5     200 ..     112     271 ..     108     285 .. 0.83

  Alignments for each domain:
  == domain 1  score: 73.7 bits;  conditional E-value: 1.8e-24
                      DDE_Tnp_1   5 evlivDattvrvpgtkedarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrprkgklvlaDa 84 
                                     v++vD+t ++v+  + ++r++++  + + ++k+hiavd +++ ++ ++it+  v d++ +k+ll+ +   k    l+D+
  gi|116754330|ref|YP_843448.1| 112 LVVAVDSTGMKVTNRGDWMRESHGVER-RGWIKVHIAVDVETRKPVTFEITDETVTDHEMVKPLLEDV---KLEDSLMDG 187
                                    699******************888666.79************************************99...89******* PP

                      DDE_Tnp_1  85 GYasaelldtleekgvd.yiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgdvyyvtntnsells 163
                                    +Y++++++d+++ekgvd + i+++kn+ ++        r +    +++  +  +++ +++                    
  gi|116754330|ref|YP_843448.1| 188 AYDKEGVFDFMKEKGVDmPGIKIRKNAIVKAG----SSRAEPVLEFMKYGYHSWKIVHGY-------------------- 243
                                    ****************9568899999988866....344445555555555555555555.................... PP

                      DDE_Tnp_1 164 aeevaelyrlRwqiErvFkwlkrkfgldrlryrglnr 200
                                             +Rw  E+vF+ +kr fg + +r+ ++++
  gi|116754330|ref|YP_843448.1| 244 --------GRRWAAESVFSAIKRIFG-ETVRATSKEG 271
                                    ........***************998.6666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.36
# Mc/sec: 2382.67
//
Query:       gi|116754331|ref|YP_843449.1|  [L=389]
Description: pentapeptide repeat-containing protein [Methanosaeta thermophila PT]
Scores for complete 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-106  345.7  83.3    4.3e-13   48.6   3.4   10.2 15  Pentapeptide     Pentapeptide repeats (8 copies)
    6.9e-46  154.3   0.0    1.7e-09   37.7   0.0    5.6  6  Pentapeptide_4   Pentapeptide repeats (9 copies)
    2.9e-32  110.6   4.3    7.6e-06   26.0   0.3    8.3  7  Pentapeptide_3   Pentapeptide repeats (9 copies)
    4.1e-05   23.6   0.0         19    5.2   0.0    4.5  6  CfAFP            Choristoneura fumiferana antifreeze protein 
     0.0024   17.8   0.3        6.8    6.7   0.0    5.2  5  DNA_ligase_OB    NAD-dependent DNA ligase OB-fold domain
     0.0079   16.8   0.4        4.2    8.1   0.0    4.0  5  Methyltransf_11  Methyltransferase domain
  ------ inclusion threshold ------
        0.1   12.6   0.0        8.3    6.4   0.0    2.7  2  ADH_zinc_N       Zinc-binding dehydrogenase


Domain annotation for each model (and alignments):
>> Pentapeptide  Pentapeptide repeats (8 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   2.2   3.2e-13   8.2e-10       1      39 [.      44      82 ..      44      82 .. 0.96
   2 !   48.6   3.4   1.7e-16   4.3e-13       1      40 []      74     113 ..      74     113 .. 0.99
   3 !   45.7   2.9   1.4e-15   3.6e-12       3      40 .]      86     123 ..      84     123 .. 0.96
   4 !   41.2   3.0   3.5e-14   8.8e-11       6      39 ..     104     137 ..     104     137 .. 0.88
   5 !   27.0   0.7   9.6e-10   2.5e-06       1      38 [.     124     161 ..     124     163 .. 0.97
   6 !   26.7   0.4   1.2e-09   3.1e-06       1      40 []     134     173 ..     134     173 .. 0.97
   7 !   39.0   0.1   1.8e-13   4.5e-10       1      39 [.     154     192 ..     154     193 .. 0.96
   8 !   32.3   0.1   2.1e-11   5.4e-08       1      37 [.     169     205 ..     169     206 .. 0.95
   9 !   40.0   0.1   8.6e-14   2.2e-10       1      40 []     184     223 ..     184     223 .. 0.93
  10 !   40.5   0.2   5.8e-14   1.5e-10       1      38 [.     204     241 ..     204     242 .. 0.97
  11 !   39.9   0.4   9.3e-14   2.4e-10       1      38 [.     239     276 ..     239     277 .. 0.96
  12 !   32.1   0.1   2.5e-11   6.3e-08       1      31 [.     249     279 ..     249     285 .. 0.90
  13 !   18.9   0.0   3.3e-07   0.00084       1      40 []     274     313 ..     274     313 .. 0.95
  14 !   19.6   0.2     2e-07    0.0005       3      35 ..     326     358 ..     325     359 .. 0.58
  15 ?    3.4   0.0     0.024        62      13      22 ..     369     378 ..     368     381 .. 0.30

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 3.2e-13
                                   -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEEC CS
                   Pentapeptide  1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLs 39
                                   ++L+  +L+g +Lsga+l++++LtgA+l+gA+L+ga L+
  gi|116754331|ref|YP_843449.1| 44 SDLRFSDLRGRDLSGASLNQSDLTGADLRGANLNGAYLR 82
                                   68999*******************************997 PP

  == domain 2  score: 48.6 bits;  conditional E-value: 1.7e-16
                                    -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
                   Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                                    AnL+gA+L+ a L +anl+gA+L gA+ls AdLsganLsg
  gi|116754331|ref|YP_843449.1|  74 ANLNGAYLRSAWLVNANLEGASLAGADLSMADLSGANLSG 113
                                    9**************************************8 PP

  == domain 3  score: 45.7 bits;  conditional E-value: 1.4e-15
                                    -TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
                   Pentapeptide   3 LsgAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                                    L +AnL+ga+L ga+ls A+L+gAnlsg+dLs+a+L++
  gi|116754331|ref|YP_843449.1|  86 LVNANLEGASLAGADLSMADLSGANLSGTDLSRAKLRN 123
                                    789*********************************97 PP

  == domain 4  score: 41.2 bits;  conditional E-value: 3.5e-14
                                    -B-CCSCCEECCCESEEECT-B-TT-EECCEEEC CS
                   Pentapeptide   6 AnLsganLsganlsgAnLtgAnlsgAdLsganLs 39 
                                    A+LsganLsg++ls+A+L++A lsgA L +anL+
  gi|116754331|ref|YP_843449.1| 104 ADLSGANLSGTDLSRAKLRNARLSGASLVNANLT 137
                                    8999999999999999999999999999999997 PP

  == domain 5  score: 27.0 bits;  conditional E-value: 9.6e-10
                                    -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEE CS
                   Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganL 38 
                                    A+LsgA L +anL+ a++++A +++++l++A ++g+++
  gi|116754331|ref|YP_843449.1| 124 ARLSGASLVNANLTMADCTEALMDDVSLEDAEMTGTRF 161
                                    89**********************************98 PP

  == domain 6  score: 26.7 bits;  conditional E-value: 1.2e-09
                                    -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
                   Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                                    AnL+ A++++a +++++l++A +tg+ + ++dL+ga +sg
  gi|116754331|ref|YP_843449.1| 134 ANLTMADCTEALMDDVSLEDAEMTGTRFFRTDLTGAVFSG 173
                                    89999*********************************98 PP

  == domain 7  score: 39.0 bits;  conditional E-value: 1.8e-13
                                    -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEEC CS
                   Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLs 39 
                                    A+++g+++  ++L+ga +sgA+L++An+ gA Ls a++s
  gi|116754331|ref|YP_843449.1| 154 AEMTGTRFFRTDLTGAVFSGASLSHANFVGAHLSWADMS 192
                                    789**********************************98 PP

  == domain 8  score: 32.3 bits;  conditional E-value: 2.1e-11
                                    -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEE CS
                   Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsgan 37 
                                    A +sgA Ls+an+ ga+ls A+++++ ++ +++s+a 
  gi|116754331|ref|YP_843449.1| 169 AVFSGASLSHANFVGAHLSWADMSRSRFRESQFSRAE 205
                                    779*******************************995 PP

  == domain 9  score: 40.0 bits;  conditional E-value: 8.6e-14
                                    -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
                   Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                                    A Ls+A+ s + ++++ +s+A L+gAnl+g+dLsg+++++
  gi|116754331|ref|YP_843449.1| 184 AHLSWADMSRSRFRESQFSRAELYGANLTGTDLSGSDFTR 223
                                    67999********************************985 PP

  == domain 10  score: 40.5 bits;  conditional E-value: 5.8e-14
                                    -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEE CS
                   Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganL 38 
                                    A+L+gAnL+g++Lsg++++++ + +A ++gAdLs+a L
  gi|116754331|ref|YP_843449.1| 204 AELYGANLTGTDLSGSDFTRSYMMRARMTGADLSDASL 241
                                    89**********************************98 PP

  == domain 11  score: 39.9 bits;  conditional E-value: 9.3e-14
                                    -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEE CS
                   Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganL 38 
                                    A+L  A+L++a L++++lsg+++++A+lsgA+L ga+ 
  gi|116754331|ref|YP_843449.1| 239 ASLDYADLTEAELRDTDLSGCKMRYADLSGANLAGADI 276
                                    899*********************************96 PP

  == domain 12  score: 32.1 bits;  conditional E-value: 2.5e-11
                                    -B-TT-B-CCSCCEECCCESEEECT-B-TT- CS
                   Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgA 31 
                                    A+L++++Lsg++++ a+lsgAnL gA++s  
  gi|116754331|ref|YP_843449.1| 249 AELRDTDLSGCKMRYADLSGANLAGADISEV 279
                                    89*************************9976 PP

  == domain 13  score: 18.9 bits;  conditional E-value: 3.3e-07
                                    -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
                   Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                                    A+ s++ L   + +g+nlsgA L++++l + dL++ ++ g
  gi|116754331|ref|YP_843449.1| 274 ADISEVVLDSVKTTGVNLSGAILYKTSLFNLDLRDIDMHG 313
                                    7889999*****************************9987 PP

  == domain 14  score: 19.6 bits;  conditional E-value: 2e-07
                                    -TT-B-CCSCCEECCCESEEECT-B-TT-EECC CS
                   Pentapeptide   3 LsgAnLsganLsganlsgAnLtgAnlsgAdLsg 35 
                                    L++ nL ga L+++ +    +t+++lsgA L++
  gi|116754331|ref|YP_843449.1| 326 LTNSNLAGAVLNDVTMHMVEMTNVDLSGASLRN 358
                                    555666666666666666666666666666655 PP

  == domain 15  score: 3.4 bits;  conditional E-value: 0.024
                                    CEECCCESEE CS
                   Pentapeptide  13 LsganlsgAn 22 
                                    L++anl gA+
  gi|116754331|ref|YP_843449.1| 369 LEKANLDGAS 378
                                    2222222222 PP

>> Pentapeptide_4  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   7.2e-11   1.8e-07       5      75 ..      58     129 ..      44     136 .. 0.70
   2 !   36.4   0.1   1.7e-12   4.3e-09       2      77 .]     105     181 ..     104     181 .. 0.91
   3 !   29.7   0.0     2e-10   5.2e-07      11      73 ..     164     227 ..     163     235 .. 0.62
   4 !   37.7   0.0   6.6e-13   1.7e-09       2      75 ..     200     274 ..     189     285 .. 0.61
   5 !   27.3   0.0   1.1e-09   2.9e-06       3      74 ..     231     308 ..     229     324 .. 0.62
   6 !   20.5   0.0   1.6e-07    0.0004       5      74 ..     308     368 ..     305     382 .. 0.57

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 7.2e-11
                 Pentapeptide_4   5 rcsfnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnfsd.klkdi 75 
                                     +s+n+++l++++++ a+l+++ ++++ l+n+n++ ++l  +d++++dl  a++sg +l+ +++++  l ++
  gi|116754331|ref|YP_843449.1|  58 GASLNQSDLTGADLRGANLNGAYLRSAWLVNANLEGASLAGADLSMADLSGANLSGTDLSRAKLRNaRLSGA 129
                                    567777777777777777777777777777777777777777777777777777777777777744355544 PP

  == domain 2  score: 36.4 bits;  conditional E-value: 1.7e-12
                 Pentapeptide_4   2 eftrcsfnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnfsd.klkdidF 77 
                                    +++ + + +++ls++ +++arl ++++++++l+ +  +e++ +dv++++++++ ++F + +l++++fs+ +l +++F
  gi|116754331|ref|YP_843449.1| 105 DLSGANLSGTDLSRAKLRNARLSGASLVNANLTMADCTEALMDDVSLEDAEMTGTRFFRTDLTGAVFSGaSLSHANF 181
                                    667778889999999999999999999999999999*******************************9879*99998 PP

  == domain 3  score: 29.7 bits;  conditional E-value: 2e-10
                 Pentapeptide_4  11 cklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnfsd.klk 73 
                                    ++l+++ Fs a l  +nF++++ls + ++++ +++++f+ ++l  a+++g +l+++ f +  ++
  gi|116754331|ref|YP_843449.1| 164 TDLTGAVFSGASLSHANFVGAHLSWADMSRSRFRESQFSRAELYGANLTGTDLSGSDFTRsYMM 227
                                    6777777888888888888888866666666666666666666666666666666666441333 PP

  == domain 4  score: 37.7 bits;  conditional E-value: 6.6e-13
                 Pentapeptide_4   2 eftrcsfnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnfsd.klkdi 75 
                                    +f+r+ + +++l+++++s +++ ++ ++ +r++ + +++++l+ +d++e++l+++ +sgc  + + +s+  l ++
  gi|116754331|ref|YP_843449.1| 200 QFSRAELYGANLTGTDLSGSDFTRSYMMRARMTGADLSDASLDYADLTEAELRDTDLSGCKMRYADLSGaNLAGA 274
                                    455555555555666666666666666666666666666666666677777777777777666666665455544 PP

  == domain 5  score: 27.3 bits;  conditional E-value: 1.1e-09
                 Pentapeptide_4   3 ftrcsfnncklsnvnFsearlrdcnFtecrl.....snvnFdecnlsdvdfaevdlkrasFsgcnlknvnf.sdklkd 74 
                                    +t + + ++ l++++++ea+lrd+++++c++     s +n++ +++s+v +  v+ + +++sg  l ++ + +  l+d
  gi|116754331|ref|YP_843449.1| 231 MTGADLSDASLDYADLTEAELRDTDLSGCKMryadlSGANLAGADISEVVLDSVKTTGVNLSGAILYKTSLfNLDLRD 308
                                    555666666677777777777777777777733333666666666666666666666666666666544442445555 PP

  == domain 6  score: 20.5 bits;  conditional E-value: 1.6e-07
                 Pentapeptide_4   5 rcsfnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnfsdklkd 74 
                                    +  +++++ +++ + ++ l ++n+ ++ l++v+++     +vd+++++l+++++ +++l+         +
  gi|116754331|ref|YP_843449.1| 308 DIDMHGVQIKKAKMDTVFLTNSNLAGAVLNDVTMHMVEMTNVDLSGASLRNIEYDEFTLR---------S 368
                                    444556666666666666666666666666666666666666666666666644443333.........2 PP

>> Pentapeptide_3  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00014      0.35      11      45 ..      50      82 ..      40      85 .. 0.67
   2 !   17.5   0.0   1.3e-06    0.0033       2      47 ..      77     119 ..      76     120 .. 0.92
   3 !   20.4   0.0   1.7e-07   0.00042       2      47 ..     112     154 ..     111     155 .. 0.95
   4 !   25.1   3.3   5.6e-09   1.4e-05       2      47 ..     167     209 ..     153     210 .. 0.83
   5 !   26.0   0.3     3e-09   7.6e-06       1      48 []     196     240 ..     195     255 .. 0.97
   6 !   11.6   0.0   9.3e-05      0.24       3      47 ..     253     294 ..     246     302 .. 0.70
   7 ?    4.9   0.0     0.011        29       8      36 ..     328     354 ..     306     381 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00014
                 Pentapeptide_3 11 dFrgatFsgaasFsnadFgsadFsgarFtgdvdFs 45
                                   d+rg   sga s +++d+++ad++ga+ + ++ ++
  gi|116754331|ref|YP_843449.1| 50 DLRGRDLSGA-SLNQSDLTGADLRGANLN-GAYLR 82
                                   4555556667.788888888888888887.66665 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 1.3e-06
                 Pentapeptide_3   2 sganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFsga 47 
                                    +ga ++ a  + +a+ +ga s  +ad++ ad+sga+ + ++d+s+a
  gi|116754331|ref|YP_843449.1|  77 NGAYLRSA-WLVNANLEGA-SLAGADLSMADLSGANLS-GTDLSRA 119
                                    67778888.9*********.*****************9.****998 PP

  == domain 3  score: 20.4 bits;  conditional E-value: 1.7e-07
                 Pentapeptide_3   2 sganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFsga 47 
                                    sg+ +s+a  +r+a+ sga s  na+++ ad  +a ++ dv++++a
  gi|116754331|ref|YP_843449.1| 112 SGTDLSRA-KLRNARLSGA-SLVNANLTMADCTEALMD-DVSLEDA 154
                                    799999**.**********.******************.*****98 PP

  == domain 4  score: 25.1 bits;  conditional E-value: 5.6e-09
                 Pentapeptide_3   2 sganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFsga 47 
                                    +ga+Fsga ++++a+F ga   s ad+++++F++++F+ +++++ga
  gi|116754331|ref|YP_843449.1| 167 TGAVFSGA-SLSHANFVGA-HLSWADMSRSRFRESQFS-RAELYGA 209
                                    68888888.8888888888.788888888888888888.8888887 PP

  == domain 5  score: 26.0 bits;  conditional E-value: 3e-09
                 Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFsgat 48 
                                    F++++Fs+a  + ga+ +g+ + s++dF+++   +ar+t ++d+s+a+
  gi|116754331|ref|YP_843449.1| 196 FRESQFSRA-ELYGANLTGT-DLSGSDFTRSYMMRARMT-GADLSDAS 240
                                    999******.**********.******************.*****985 PP

  == domain 6  score: 11.6 bits;  conditional E-value: 9.3e-05
                 Pentapeptide_3   3 ganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFsga 47 
                                    ++ +sg+  +r a  sga +  +ad++++ ++ +  t +v++sga
  gi|116754331|ref|YP_843449.1| 253 DTDLSGC-KMRYADLSGA-NLAGADISEVVLDSVKTT-GVNLSGA 294
                                    4556677.7777777777.677777777777777777.7777766 PP

  == domain 7  score: 4.9 bits;  conditional E-value: 0.011
                 Pentapeptide_3   8 gaadFrgatFsgaasFsnadFgsadFsga 36 
                                    ++ ++ ga+ ++ + +    ++++d+sga
  gi|116754331|ref|YP_843449.1| 328 NS-NLAGAVLNDVT-MHMVEMTNVDLSGA 354
                                    22.33333333332.44444444444443 PP

>> CfAFP  Choristoneura fumiferana antifreeze protein (CfAFP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.037        95      52     107 ..      39      94 ..      27     106 .. 0.85
   2 ?    4.8   0.0      0.01        26      52     104 ..     109     161 ..      83     166 .. 0.84
   3 ?    4.0   0.0     0.018        45      59     133 ..     186     260 ..     166     264 .. 0.77
   4 ?    3.3   0.0      0.03        76      59     107 ..     246     294 ..     235     301 .. 0.84
   5 !    5.2   0.0    0.0075        19      45     102 ..     275     334 ..     259     347 .. 0.84
   6 ?    2.3   0.0     0.061   1.6e+02      43      96 ..     315     368 ..     310     375 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.037
                          CfAFP  52 sictrsqysdayvkksvttdcnidksqlygttctgsrydGvyitsstttgtrisGp 107
                                     ic rs+   + ++    + + +++s+l g+   g++ +G y++s+   ++++ G 
  gi|116754331|ref|YP_843449.1|  39 DICDRSDLRFSDLRGRDLSGASLNQSDLTGADLRGANLNGAYLRSAWLVNANLEGA 94 
                                    6899999999999999999999999*******************998888887775 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.01
                          CfAFP  52 sictrsqysdayvkksvttdcnidksqlygttctgsrydGvyitsstttgtri 104
                                    +  + ++ s a++++++ + + + +++l ++ ct++  d v +  +  tgtr 
  gi|116754331|ref|YP_843449.1| 109 ANLSGTDLSRAKLRNARLSGASLVNANLTMADCTEALMDDVSLEDAEMTGTRF 161
                                    455566778899999999999999*************************9985 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.018
                          CfAFP  59 ysdayvkksvttdcnidksqlygttctgsrydGvyitsstttgtrisGpgcsissctitrGvaapsaackisGct 133
                                     s a + +s+  + + ++++lyg+  tg+   G   t s    +r++G   s +s   +    a      +sGc 
  gi|116754331|ref|YP_843449.1| 186 LSWADMSRSRFRESQFSRAELYGANLTGTDLSGSDFTRSYMMRARMTGADLSDASLDYADLTEAELRDTDLSGCK 260
                                    566788899999999999999*99999999999999999999999999877666665555555555666666665 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.03
                          CfAFP  59 ysdayvkksvttdcnidksqlygttctgsrydGvyitsstttgtrisGp 107
                                     ++a+++++  + c+++ ++l g+  +g+    v + s  ttg ++sG 
  gi|116754331|ref|YP_843449.1| 246 LTEAELRDTDLSGCKMRYADLSGANLAGADISEVVLDSVKTTGVNLSGA 294
                                    5677788888889999999999999999999999999999999999985 PP

  == domain 5  score: 5.2 bits;  conditional E-value: 0.0075
                          CfAFP  45 dnsel..essictrsqysdayvkksvttdcnidksqlygttctgsrydGvyitsstttgt 102
                                    d se+  +s  +t  + s+a + k+   + ++++ +++g     ++ d v++t s  +g+
  gi|116754331|ref|YP_843449.1| 275 DISEVvlDSVKTTGVNLSGAILYKTSLFNLDLRDIDMHGVQIKKAKMDTVFLTNSNLAGA 334
                                    445544489999999999******99**************************99987776 PP

  == domain 6  score: 2.3 bits;  conditional E-value: 0.061
                          CfAFP  43 yidnselessictrsqysdayvkksvttdcnidksqlygttctgsrydGvyits 96 
                                    +i ++++++   t s+ ++a +++ +   +++ + +l g++  + +yd  +++s
  gi|116754331|ref|YP_843449.1| 315 QIKKAKMDTVFLTNSNLAGAVLNDVTMHMVEMTNVDLSGASLRNIEYDEFTLRS 368
                                    688999999999999999999999999999999999999999999999998887 PP

>> DNA_ligase_OB  NAD-dependent DNA ligase OB-fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.59   1.5e+03      21      42 ..      69      90 ..      57      95 .. 0.84
   2 !    6.7   0.0    0.0027       6.8      20      42 ..     103     125 ..      95     154 .. 0.88
   3 ?   -1.1   0.0      0.69   1.8e+03      21      41 ..     249     269 ..     242     276 .. 0.82
   4 ?    2.0   0.0     0.073   1.9e+02      24      42 ..     287     305 ..     257     330 .. 0.59
   5 ?    0.7   0.0       0.2   5.1e+02      16      41 ..     334     359 ..     318     365 .. 0.64

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.59
                                   XXXXXXXXXXXXXXXXXXXXXX CS
                  DNA_ligase_OB 21 AeLepvelaGttVsratLhned 42
                                   A+L+  +l+G   + a L n++
  gi|116754331|ref|YP_843449.1| 69 ADLRGANLNGAYLRSAWLVNAN 90
                                   7788888999999999888876 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0027
                                    XXXXXXXXXXXXXXXXXXXXXXX CS
                  DNA_ligase_OB  20 vAeLepvelaGttVsratLhned 42 
                                    +A+L+  +l+Gt  sra L n++
  gi|116754331|ref|YP_843449.1| 103 MADLSGANLSGTDLSRAKLRNAR 125
                                    79999**************9986 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.69
                                    XXXXXXXXXXXXXXXXXXXXX CS
                  DNA_ligase_OB  21 AeLepvelaGttVsratLhne 41 
                                    AeL+  +l+G +++ a L  +
  gi|116754331|ref|YP_843449.1| 249 AELRDTDLSGCKMRYADLSGA 269
                                    889999999999999988765 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.073
                                    XXXXXXXXXXXXXXXXXXX CS
                  DNA_ligase_OB  24 epvelaGttVsratLhned 42 
                                    + v+l+G +  + +L n d
  gi|116754331|ref|YP_843449.1| 287 TGVNLSGAILYKTSLFNLD 305
                                    3455555555555555544 PP

  == domain 5  score: 0.7 bits;  conditional E-value: 0.2
                                    XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                  DNA_ligase_OB  16 altpvAeLepvelaGttVsratLhne 41 
                                    a+     ++ ve+  +  s a+L n 
  gi|116754331|ref|YP_843449.1| 334 AVLNDVTMHMVEMTNVDLSGASLRNI 359
                                    33333445566666666666666665 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.078     2e+02      14      59 ..     104     153 ..      91     183 .. 0.73
   2 ?    0.1   0.0       0.5   1.3e+03      18      34 ..     225     244 ..     199     246 .. 0.66
   3 ?    0.8   0.0       0.3   7.6e+02      18      35 ..     225     245 ..     212     257 .. 0.71
   4 !    8.1   0.0    0.0016       4.2      11      69 ..     261     328 ..     255     356 .. 0.84
   5 ?   -1.5   0.0       1.6   4.2e+03       8      33 ..     333     358 ..     330     378 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.078
                                    HHHTTSEEEEEES-HHHHHHHHHHCCHHT-....EEEETTEECCCTSS-T CS
                Methyltransf_11  14 lakrgarvvgvDlskemlklakekaseegl....kvefvvadaeklpfed 59 
                                        ga++ g+Dls + l+ a+  +    +      ++ +a + ++ +ed
  gi|116754331|ref|YP_843449.1| 104 ADLSGANLSGTDLSRAKLRNARLSGASLVNanltMADCTEALMDDVSLED 153
                                    33447999999****99999988887776664454455555555555555 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.5
                                    T...SEEEEEES-HHHHHHH CS
                Methyltransf_11  18 g...arvvgvDlskemlkla 34 
                                    +   ar +g Dls++ l++a
  gi|116754331|ref|YP_843449.1| 225 YmmrARMTGADLSDASLDYA 244
                                    22336778888887777665 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.3
                                    T...SEEEEEES-HHHHHHHH CS
                Methyltransf_11  18 g...arvvgvDlskemlklak 35 
                                    +   ar +g Dls++ l++a 
  gi|116754331|ref|YP_843449.1| 225 YmmrARMTGADLSDASLDYAD 245
                                    3334899******99998885 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.0016
                                    HHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-.........EEEETTEECCCTSS-TT-EEEEEEES CS
                Methyltransf_11  11 aealakrgarvvgvDlskemlklakekaseegl.........kvefvvadaeklpfednsfDlvvsse 69 
                                    +++    ga++ g D+s+ +l+ +k+ +++            +++++  d++ ++++++++D v++++
  gi|116754331|ref|YP_843449.1| 261 MRYADLSGANLAGADISEVVLDSVKTTGVNLSGailyktslfNLDLRDIDMHGVQIKKAKMDTVFLTN 328
                                    556666789************9999999888778889999999999******************9986 PP

  == domain 5  score: -1.5 bits;  conditional E-value: 1.6
                                    SHHHHHHHHTTSEEEEEES-HHHHHH CS
                Methyltransf_11   8 GrlaealakrgarvvgvDlskemlkl 33 
                                    G+++++++ +  + ++vDls + l+ 
  gi|116754331|ref|YP_843449.1| 333 GAVLNDVTMHMVEMTNVDLSGASLRN 358
                                    66677777666788999998887754 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0032       8.3       8      50 ..     102     145 ..      99     162 .. 0.84
   2 ?    3.0   0.0     0.037        94       7      36 ..     261     290 ..     257     329 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0032
                                    HHHHHTT-EEEEEESSHHHHHHHHHTTESEEEETTTC.HHHHHH CS
                     ADH_zinc_N   8 qlAkalGaeviavdsseeklelakklGadevinykea.dlveri 50 
                                     +A  +Ga+  ++d s+ kl+ a+  Ga  v  + ++ d  e++
  gi|116754331|ref|YP_843449.1| 102 SMADLSGANLSGTDLSRAKLRNARLSGASLVNANLTMaDCTEAL 145
                                    58999***********************9998876666666665 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.037
                                    HHHHHHTT-EEEEEESSHHHHHHHHHTTES CS
                     ADH_zinc_N   7 vqlAkalGaeviavdsseeklelakklGad 36 
                                    + +A  +Ga+  ++d+se  l+ +k  G++
  gi|116754331|ref|YP_843449.1| 261 MRYADLSGANLAGADISEVVLDSVKTTGVN 290
                                    679999*******************99964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.38
# Mc/sec: 3063.24
//
Query:       gi|116754332|ref|YP_843450.1|  [L=223]
Description: hypothetical protein Mthe_1025 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); 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:                         0  (0); expected 0.2 (1e-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 0.20s 00:00:00.60 Elapsed: 00:00:00.35
# Mc/sec: 1892.20
//
Query:       gi|116754333|ref|YP_843451.1|  [L=85]
Description: transcription factor TFIIS [Methanosaeta thermophila PT]
Scores for complete 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   65.5   8.0    2.9e-18   65.4   3.4    2.1  2  TFIIS_C          Transcription factor S-II (TFIIS)
    6.9e-05   22.7   4.4    0.00037   20.4   0.8    2.3  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
    0.00013   21.4   3.6     0.0018   17.8   0.8    2.7  2  TF_Zn_Ribbon     TFIIB zinc-binding
      0.002   18.0   8.1      0.089   12.7   0.7    3.1  3  zinc_ribbon_4    zinc-ribbon domain
     0.0029   17.5   0.5      0.055   13.4   0.0    2.4  2  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
     0.0059   16.5   3.6       0.19   11.7   0.6    2.9  2  Nudix_N_2        Nudix N-terminal
      0.006   16.6   3.8       0.25   11.4   3.8    2.3  1  DZR              Double zinc ribbon
     0.0085   15.8  10.8        2.5    7.9   0.3    3.2  3  zinc_ribbon_2    zinc-ribbon domain
     0.0087   15.4   6.6        1.1    8.7   0.3    3.2  3  zf-ribbon_3      zinc-ribbon domain
     0.0091   16.0   1.8       0.26   11.3   0.1    2.1  2  HypA             Hydrogenase/urease nickel incorporation, met
     0.0098   15.8   1.8       0.18   11.7   0.0    2.6  3  DUF3797          Domain of unknown function (DUF3797)
  ------ inclusion threshold ------
      0.011   15.6   5.2        6.2    6.8   0.1    3.1  3  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
      0.017   15.2   7.3        1.2    9.3   0.2    3.2  3  Zn-ribbon_8      Zinc ribbon domain
      0.024   14.8   3.0        8.3    6.7   0.1    3.1  3  zf-RING_7        C4-type zinc ribbon domain
      0.029   14.2   0.1       0.13   12.1   0.0    1.9  2  zf-ZPR1          ZPR1 zinc-finger domain
      0.045   13.5  10.2        5.4    6.8   0.7    3.2  3  Rubredoxin_2     Rubredoxin metal binding domain
       0.05   13.6   5.3        5.1    7.1   0.2    3.3  3  YhfH             YhfH-like protein
      0.054   13.4   6.0       0.04   13.9   1.2    2.4  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.061   13.6   1.1        0.5   10.7   0.3    2.0  2  DUF3268          zinc-finger-containing domain
      0.072   12.8   8.8          3    7.6   0.6    3.2  3  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
       0.13   12.4   3.0         14    5.9   0.1    3.0  3  DiS_P_DiS        Bacterial Peptidase A24 N-terminal domain
       0.15   12.9   4.4        4.3    8.1   4.4    2.3  1  zinc_ribbon_15   zinc-ribbon family
       0.15   11.8   2.7         11    5.8   0.1    3.0  3  zinc_ribbon_10   Predicted integral membrane zinc-ribbon meta
       0.16   12.7   7.1        2.8    8.7   1.8    2.9  3  zf-3CxxC_2       Zinc-binding domain
       0.16   11.7   0.2       0.16   11.7   0.2    2.6  2  Baculo_LEF5_C    Baculoviridae late expression factor 5 C-ter
       0.16   11.9   0.5       0.16   11.9   0.5    2.0  2  Ogr_Delta        Ogr/Delta-like zinc finger
       0.19   11.7   9.1         11    6.0   0.0    3.2  3  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
       0.29   11.0   6.8         13    5.7   0.2    3.1  3  zf-C2H2_3        zinc-finger of acetyl-transferase ESCO
       0.33   10.7   3.7        3.5    7.4   0.1    2.8  3  Ribosomal_S27e   Ribosomal protein S27
       0.34   11.6   7.5        2.6    8.8   0.2    3.1  3  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
       0.34   10.6   7.5         11    5.8   0.3    3.1  3  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
       0.39   10.3   7.3        5.6    6.6   0.1    3.2  3  zf_UBZ           Ubiquitin-Binding Zinc Finger
       0.57   10.7   6.4        6.8    7.2   0.8    2.3  2  zf-3CxxC         Zinc-binding domain
       0.66   10.5   6.8         23    5.7   0.1    3.2  3  zf-C2H2          Zinc finger, C2H2 type
       0.86   10.1   2.0         24    5.4   0.0    2.9  3  DUF983           Protein of unknown function (DUF983)
        1.2    8.6   8.4       0.16   11.3   2.8    2.3  2  zf-TFIIB         Transcription factor zinc-finger
        1.5    8.5   0.1        1.5    8.5   0.1    3.1  3  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
        2.4    8.3  14.1        9.2    6.4   1.0    3.3  3  zf-ACC           Acetyl-coA carboxylase zinc finger domain
        2.4    8.3   4.6        1.1    9.4   0.2    2.4  3  Nop10p           Nucleolar RNA-binding protein, Nop10p family
        2.4    8.0   7.5         30    4.5   0.2    3.1  3  A2L_zn_ribbon    A2L zinc ribbon domain
        4.2    7.5   6.8         59    3.9   3.7    3.0  2  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
        6.1    7.1   6.5         68    3.7   0.5    3.0  3  zinc_ribbon_13   Nucleic-acid-binding protein containing Zn-r
        6.4    7.9   7.1         27    6.0   0.4    3.1  3  zf-C2H2_4        C2H2-type zinc finger
        6.5    6.8   8.2         48    4.0   0.3    3.1  3  ADK_lid          Adenylate kinase, active site lid
        6.5    6.6   6.9         28    4.6   0.1    3.0  3  zf-C2H2_11       zinc-finger C2H2-type
        7.7    6.6   7.5         26    4.9   2.1    2.8  2  CpXC             CpXC protein
        8.1    6.4   9.9         13    5.8   0.1    3.2  3  zf-FPG_IleRS     Zinc finger found in FPG and IleRS


Domain annotation for each model (and alignments):
>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1       0.3   1.2e+02      30      35 ..       2       7 ..       1      10 [. 0.57
   2 !   65.4   3.4   7.6e-21   2.9e-18       1      39 []      44      82 ..      44      82 .. 0.98

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.3
                        TFIIS_C 30 kCtkCg 35
                                   +C kCg
  gi|116754333|ref|YP_843451.1|  2 VCRKCG 7 
                                   466665 PP

  == domain 2  score: 65.4 bits;  conditional E-value: 7.6e-21
                        TFIIS_C  1 akCpkCgsreayffqlQtRsaDEpmtvfykCtkCghrWr 39
                                   akCp+Cg++ ay++ +Q+R+aDE++++f++CtkCg++Wr
  gi|116754333|ref|YP_843451.1| 44 AKCPECGNDTAYWWLRQLRAADESEVRFFRCTKCGNTWR 82
                                   59************************************8 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1      0.15        57      20      28 ..       2      10 ..       1      18 [. 0.78
   2 !   20.4   0.8   9.8e-07   0.00037      18      45 ..      43      79 ..      35      80 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.15
                  Zn_Tnp_IS1595 20 vCPhCgsrk 28
                                   vC +Cg r 
  gi|116754333|ref|YP_843451.1|  2 VCRKCGMRV 10
                                   8*****884 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 9.8e-07
                  Zn_Tnp_IS1595 18 gfvCPhCgsr.kayrikt........rglfqCkeCrk 45
                                   +  CP Cg++  ++ +++         + f+C +C+ 
  gi|116754333|ref|YP_843451.1| 43 KAKCPECGNDtAYWWLRQlraadeseVRFFRCTKCGN 79
                                   377*******66666666999**************86 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1      0.12        44      20      26 ..       1       7 [.       1      20 [. 0.73
   2 !   17.8   0.8   4.6e-06    0.0018       2      28 ..      45      80 ..      44      85 .] 0.84

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.12
                                   EEESSSS CS
                   TF_Zn_Ribbon 20 lvCtdCG 26
                                   +vC +CG
  gi|116754333|ref|YP_843451.1|  1 MVCRKCG 7 
                                   4788887 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 4.6e-06
                                   EETTTTCEE.C.......HEETSTTCE.EESSSSBE CS
                   TF_Zn_Ribbon  2 kCPnCgstn.l.......veDpergel.vCtdCGlV 28
                                   kCP+Cg+++ +         D+++  + +Ct+CG+ 
  gi|116754333|ref|YP_843451.1| 45 KCPECGNDTaYwwlrqlrAADESEVRFfRCTKCGNT 80
                                   8******9967*****998887777777******85 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.2         1   3.9e+02      28      32 ..       3       7 ..       1       9 [. 0.68
   2 !    7.7   0.1    0.0086       3.3      24      33 ..      42      51 ..      36      52 .. 0.88
   3 !   12.7   0.7   0.00023     0.089      26      36 .]      72      82 ..      66      82 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 1
                  zinc_ribbon_4 28 CskCg 32
                                   C kCg
  gi|116754333|ref|YP_843451.1|  3 CRKCG 7 
                                   77776 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0086
                  zinc_ribbon_4 24 vkvrCskCgh 33
                                   +k++C+ Cg+
  gi|116754333|ref|YP_843451.1| 42 TKAKCPECGN 51
                                   699*****97 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 0.00023
                  zinc_ribbon_4 26 vrCskCghvFr 36
                                    rC+kCg+++r
  gi|116754333|ref|YP_843451.1| 72 FRCTKCGNTWR 82
                                   69********7 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.2      0.63   2.4e+02      20      26 ..       1       7 [.       1       8 [. 0.86
   2 !   13.4   0.0   0.00014     0.055       4      29 ..      45      81 ..      38      82 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.63
                 PhnA_Zn_Ribbon 20 lvCpeCa 26
                                   +vC +C+
  gi|116754333|ref|YP_843451.1|  1 MVCRKCG 7 
                                   8999997 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00014
                 PhnA_Zn_Ribbon  4 kCplCaSeytY...........edgallvCpeCahEw 29
                                   kCp+C+ +++Y            +   + C +C++ w
  gi|116754333|ref|YP_843451.1| 45 KCPECGNDTAYwwlrqlraadeSEVRFFRCTKCGNTW 81
                                   9**********99999999877667788899998877 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.093        35       3       8 ..       3       8 ..       1      14 [. 0.67
   2 !   11.7   0.6   0.00051      0.19       3      30 ..      46      79 ..      46      81 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.093
                                  -TTT-- CS
                      Nudix_N_2 3 CsqCGt 8
                                  C++CG 
  gi|116754333|ref|YP_843451.1| 3 CRKCGM 8
                                  666665 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00051
                                   -TTT--B-E.....EE--TT-SS-EE.EETTTTE CS
                      Nudix_N_2  3 CsqCGtpve.....lripdgDnreRl.vCpaCgt 30
                                   C++CG+ ++     +   +++++ R+ +C++Cg 
  gi|116754333|ref|YP_843451.1| 46 CPECGNDTAywwlrQLRAADESEVRFfRCTKCGN 79
                                   *******998887444457888899648****95 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   3.8   0.00065      0.25      14      37 ..       2      52 ..       1      85 [] 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00065
                            DZR 14 fCseCgtklkavaa...........................edrCpsCgek 37
                                   +C +Cg ++++ ++                           + +Cp+Cg +
  gi|116754333|ref|YP_843451.1|  2 VCRKCGMRVPKSSNnpivsvtnklertvpvleqesaglpttKAKCPECGND 52
                                   699999999877779999999999999999999999999999999999976 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.033        12       2      12 ..       3      13 ..       2      15 .. 0.72
   2 !    7.7   1.1     0.008       3.1       1       7 [.      45      51 ..      45      52 .. 0.84
   3 !    7.9   0.3    0.0066       2.5       1       7 [.      73      79 ..      68      80 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.033
                  zinc_ribbon_2  2 CpnCGaelqdn 12
                                   C +CG  +++ 
  gi|116754333|ref|YP_843451.1|  3 CRKCGMRVPKS 13
                                   99999877765 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.008
                  zinc_ribbon_2  1 fCpnCGa 7 
                                   +Cp+CG+
  gi|116754333|ref|YP_843451.1| 45 KCPECGN 51
                                   7999998 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0066
                  zinc_ribbon_2  1 fCpnCGa 7 
                                   +C++CG+
  gi|116754333|ref|YP_843451.1| 73 RCTKCGN 79
                                   5999987 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1     0.024         9      18      25 ..       2       9 ..       1      10 [. 0.86
   2 !    8.7   0.3    0.0029       1.1       4      10 ..      45      51 ..      41      53 .. 0.69
   3 ?    3.2   0.2      0.16        62      19      23 ..      74      78 ..      71      80 .. 0.63

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.024
                    zf-ribbon_3 18 vCpyCGtk 25
                                   vC +CG++
  gi|116754333|ref|YP_843451.1|  2 VCRKCGMR 9 
                                   8*****86 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0029
                    zf-ribbon_3  4 rCPnCGa 10
                                   +CP+CG+
  gi|116754333|ref|YP_843451.1| 45 KCPECGN 51
                                   6777775 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.16
                    zf-ribbon_3 19 CpyCG 23
                                   C++CG
  gi|116754333|ref|YP_843451.1| 74 CTKCG 78
                                   55565 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 !   11.3   0.1   0.00068      0.26      72      95 ..       2      52 ..       1      57 [. 0.85
   2 ?    4.4   0.2     0.094        36      70      81 ..      71      82 ..      58      85 .] 0.72

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00068
                                   EETTTS-EEECHHHHH...........................S-TTTSSS CS
                           HypA 72 rCreCgkefeleekal...........................rCpkCgsa 95
                                    Cr+Cg ++ +++++                            +Cp+Cg+ 
  gi|116754333|ref|YP_843451.1|  2 VCRKCGMRVPKSSNNPivsvtnklertvpvleqesaglpttkaKCPECGND 52
                                   7********97764224678999*************************986 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.094
                                   EEEETTTS-EEE CS
                           HypA 70 kvrCreCgkefe 81
                                    +rC++Cg++++
  gi|116754333|ref|YP_843451.1| 71 FFRCTKCGNTWR 82
                                   468999988886 PP

>> DUF3797  Domain of unknown function (DUF3797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.2       9.1   3.5e+03      18      20 ..       5       7 ..       2      20 .. 0.59
   2 !   11.7   0.0   0.00048      0.18      13      22 ..      43      52 ..      23      55 .. 0.75
   3 ?    3.1   0.0      0.23        87      13      21 ..      71      79 ..      60      81 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 9.1
                        DUF3797 18 eCg 20
                                   +Cg
  gi|116754333|ref|YP_843451.1|  5 KCG 7 
                                   443 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00048
                        DUF3797 13 YvqCPeCgNn 22
                                    ++CPeCgN+
  gi|116754333|ref|YP_843451.1| 43 KAKCPECGND 52
                                   589******8 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.23
                        DUF3797 13 YvqCPeCgN 21
                                   +  C +CgN
  gi|116754333|ref|YP_843451.1| 71 FFRCTKCGN 79
                                   778999999 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 ?    3.7   0.1      0.16        60      13      20 ..       2       9 ..       1      13 [. 0.76
   2 ?    6.7   0.1     0.018       6.7      23      34 ..      40      52 ..      39      54 .. 0.75
   3 ?    6.8   0.1     0.016       6.2       3      18 ..      63      78 ..      61      80 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.16
                        DUF35_N 13 rCpdCGtv 20
                                    C++CG  
  gi|116754333|ref|YP_843451.1|  2 VCRKCGMR 9 
                                   69999965 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.018
                        DUF35_N 23 PPr.avCphCgsd 34
                                   P + a Cp Cg d
  gi|116754333|ref|YP_843451.1| 40 PTTkAKCPECGND 52
                                   5566899999976 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.016
                        DUF35_N  3 aaaegrLvgqrCpdCG 18
                                   aa+e ++++ rC++CG
  gi|116754333|ref|YP_843451.1| 63 AADESEVRFFRCTKCG 78
                                   7888889999*****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 ?    2.6   0.1      0.39   1.5e+02      29      35 ..       3       9 ..       1      15 [. 0.61
   2 ?    9.3   0.2    0.0031       1.2      26      35 ..      42      52 ..      31      54 .. 0.70
   3 ?    6.4   0.3     0.025       9.5       6      14 ..      72      80 ..      71      83 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.39
                    Zn-ribbon_8 29 CPeCgse 35
                                   C +Cg +
  gi|116754333|ref|YP_843451.1|  3 CRKCGMR 9 
                                   5555544 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0031
                    Zn-ribbon_8 26 lta.CPeCgse 35
                                    +a CPeCg +
  gi|116754333|ref|YP_843451.1| 42 TKAkCPECGND 52
                                   4556****985 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.025
                    Zn-ribbon_8  6 YrCeeCghe 14
                                   +rC++Cg++
  gi|116754333|ref|YP_843451.1| 72 FRCTKCGNT 80
                                   8******86 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 ?    2.8   0.1      0.35   1.3e+02       1      12 [.       2      13 ..       2      17 .. 0.82
   2 ?    6.7   0.1     0.022       8.3      24      30 ..      44      50 ..      30      50 .. 0.78
   3 ?    4.6   0.0     0.096        37      14      30 ..      58      78 ..      57      78 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.35
                                   EETTT--B--CC CS
                      zf-RING_7  1 tCgGChmelppq 12
                                   +C  C+m++p +
  gi|116754333|ref|YP_843451.1|  2 VCRKCGMRVPKS 13
                                   5888*****965 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.022
                                   EE-TTT- CS
                      zf-RING_7 24 vtCpeCG 30
                                   ++CpeCG
  gi|116754333|ref|YP_843451.1| 44 AKCPECG 50
                                   79****9 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.096
                                   HHHHCCSTB....-EE-TTT- CS
                      zf-RING_7 14 lselragde....vvtCpeCG 30
                                   l++lra+de     ++C  CG
  gi|116754333|ref|YP_843451.1| 58 LRQLRAADEsevrFFRCTKCG 78
                                   56889998877666***9998 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       1.5   5.7e+02      32      39 ..       2       9 ..       1      37 [. 0.77
   2 ?   12.1   0.0   0.00033      0.13       2      42 ..      45      83 ..      44      85 .] 0.88

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.5
                        zf-ZPR1 32 eCehCgyk 39
                                   +C++Cg++
  gi|116754333|ref|YP_843451.1|  2 VCRKCGMR 9 
                                   68888876 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00033
                        zf-ZPR1  2 lCpsCgkengetrllltkiPyfkeviimsfeCehCgyknne 42
                                   +Cp+Cg  n + + +l ++    e  +  f+C +Cg + +e
  gi|116754333|ref|YP_843451.1| 45 KCPECG--NDTAYWWLRQLRAADESEVRFFRCTKCGNTWRE 83
                                   8****8..458999999*******************88665 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   0.1     0.038        15       2      11 ..       2      11 ..       2      13 .. 0.82
   2 ?    6.7   0.6     0.016         6       3      13 ..      46      56 ..      45      57 .. 0.68
   3 ?    6.8   0.7     0.014       5.4       1       9 [.      72      80 ..      72      84 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.038
                   Rubredoxin_2  2 vCsqCGfesa 11
                                   vC++CG + +
  gi|116754333|ref|YP_843451.1|  2 VCRKCGMRVP 11
                                   7*****8876 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.016
                   Rubredoxin_2  3 CsqCGfesakw 13
                                   C +CG+++a w
  gi|116754333|ref|YP_843451.1| 46 CPECGNDTAYW 56
                                   77777777777 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.014
                   Rubredoxin_2  1 YvCsqCGfe 9 
                                   ++C +CG++
  gi|116754333|ref|YP_843451.1| 72 FRCTKCGNT 80
                                   8******97 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1      0.64   2.5e+02      16      21 ..       3       8 ..       2      12 .. 0.82
   2 ?    7.1   0.2     0.013       5.1      15      22 ..      45      52 ..      39      54 .. 0.84
   3 ?    5.9   0.0     0.034        13      16      25 ..      74      83 ..      66      85 .] 0.83

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.64
                           YhfH 16 CteCGk 21
                                   C +CG 
  gi|116754333|ref|YP_843451.1|  3 CRKCGM 8 
                                   99**95 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.013
                           YhfH 15 kCteCGke 22
                                   kC+eCG++
  gi|116754333|ref|YP_843451.1| 45 KCPECGND 52
                                   8*****86 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.034
                           YhfH 16 CteCGkeieE 25
                                   Ct+CG+   E
  gi|116754333|ref|YP_843451.1| 74 CTKCGNTWRE 83
                                   *****97655 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   2.7      0.29   1.1e+02      45      53 ..      42      50 ..       1      55 [. 0.65
   2 ?   13.9   1.2    0.0001      0.04      29      56 ..      44      81 ..      20      83 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.29
                 OrfB_Zn_ribbon 45 rtfkCpnCg 53
                                    + kCp+Cg
  gi|116754333|ref|YP_843451.1| 42 TKAKCPECG 50
                                   334444444 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 0.0001
                 OrfB_Zn_ribbon 29 ktCseCgsknke..........alsgrtfkCpnCgfea 56
                                    +C+eCg    +          + + r f+C++Cg ++
  gi|116754333|ref|YP_843451.1| 44 AKCPECGNDTAYwwlrqlraadESEVRFFRCTKCGNTW 81
                                   58*******99999999*9999999**********986 PP

>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0       0.7   2.7e+02      32      50 ..       2      18 ..       1      31 [. 0.52
   2 ?   10.7   0.3    0.0013       0.5       3      38 ..      44      79 ..      42      83 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.7
                        DUF3268 32 lCpkCdayvgvhkgtkipl 50
                                   +C+kC+  v   k ++ p+
  gi|116754333|ref|YP_843451.1|  2 VCRKCGMRV--PKSSNNPI 18
                                   566666443..33333333 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0013
                        DUF3268  3 trCpyCGekvilvsaseiYkerskgkllylCpkCda 38
                                    +Cp CG+ +++   +++  + + +  ++ C+kC+ 
  gi|116754333|ref|YP_843451.1| 44 AKCPECGNDTAYWWLRQLRAADESEVRFFRCTKCGN 79
                                   68*****************9999999********86 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 ?    7.6   0.6    0.0078         3      20      27 ..       3      10 ..       2      11 .. 0.94
   2 ?    4.1   0.1     0.097        37      19      24 ..      45      50 ..      40      54 .. 0.79
   3 ?    5.1   0.2     0.046        18      19      24 ..      73      78 ..      67      80 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0078
                                   -SSS---- CS
                 DNA_RNApol_7kD 20 CkeCGhRi 27
                                   C++CG+R+
  gi|116754333|ref|YP_843451.1|  3 CRKCGMRV 10
                                   *******8 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.097
                                   --SSS- CS
                 DNA_RNApol_7kD 19 RCkeCG 24
                                   +C eCG
  gi|116754333|ref|YP_843451.1| 45 KCPECG 50
                                   688887 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.046
                                   --SSS- CS
                 DNA_RNApol_7kD 19 RCkeCG 24
                                   RC++CG
  gi|116754333|ref|YP_843451.1| 73 RCTKCG 78
                                   9****9 PP

>> DiS_P_DiS  Bacterial Peptidase A24 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1     0.036        14      29      47 ..       2      20 ..       1      28 [. 0.91
   2 ?    4.9   0.1     0.073        28      23      39 ..      39      55 ..      21      59 .. 0.74
   3 ?    1.4   0.0      0.93   3.6e+02      29      38 ..      73      82 ..      63      85 .] 0.76

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.036
                      DiS_P_DiS 29 rCpkCghklkwleliPvlS 47
                                    C kCg ++    + P++S
  gi|116754333|ref|YP_843451.1|  2 VCRKCGMRVPKSSNNPIVS 20
                                   5*****************9 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.073
                      DiS_P_DiS 23 lvkprSrCpkCghklkw 39
                                   l + +++Cp+Cg+  + 
  gi|116754333|ref|YP_843451.1| 39 LPTTKAKCPECGNDTAY 55
                                   55678899999987655 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.93
                      DiS_P_DiS 29 rCpkCghklk 38
                                   rC+kCg++ +
  gi|116754333|ref|YP_843451.1| 73 RCTKCGNTWR 82
                                   6888887655 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   4.4     0.011       4.3      38      75 ..       1      53 [.       1      84 [. 0.78

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.011
                 zinc_ribbon_15 38 lacskCkslleaskelgkeiekkesse................kkeCknCgkev 75
                                   ++c+kC++++++s+++    + +++ e                k +C++Cg+ +
  gi|116754333|ref|YP_843451.1|  1 MVCRKCGMRVPKSSNNPIV-SVTNKLErtvpvleqesaglpttKAKCPECGNDT 53
                                   5799999999998744333.3233333468999999999999999999999876 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 ?    3.3   0.1      0.18        67      23      30 ..       1       8 [.       1      18 [. 0.84
   2 ?    1.8   0.0      0.54     2e+02      46      51 ..      45      50 ..      35      53 .. 0.82
   3 ?    5.8   0.1     0.029        11      41      52 ..      67      79 ..      60      81 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.18
                 zinc_ribbon_10 23 lICskChs 30
                                   ++C+kC +
  gi|116754333|ref|YP_843451.1|  1 MVCRKCGM 8 
                                   78999976 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.54
                 zinc_ribbon_10 46 rCpkCg 51
                                   +Cp+Cg
  gi|116754333|ref|YP_843451.1| 45 KCPECG 50
                                   799998 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.029
                 zinc_ribbon_10 41 eev.kyrCpkCga 52
                                   +ev  +rC kCg 
  gi|116754333|ref|YP_843451.1| 67 SEVrFFRCTKCGN 79
                                   445369*****96 PP

>> zf-3CxxC_2  Zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0       2.4   9.2e+02      30      39 ..       3      12 ..       2      37 .. 0.71
   2 ?    5.3   0.0     0.089        34      28      50 ..      44      66 ..      39      71 .. 0.78
   3 ?    8.7   1.8    0.0073       2.8       8      17 ..      72      81 ..      70      83 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 2.4
                     zf-3CxxC_2 30 CkkCkekvep 39
                                   C kC+ +v  
  gi|116754333|ref|YP_843451.1|  3 CRKCGMRVPK 12
                                   7788777654 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.089
                     zf-3CxxC_2 28 QeCkkCkekvepyklrekdkkkg 50
                                    +C +C++++  + lr+++  ++
  gi|116754333|ref|YP_843451.1| 44 AKCPECGNDTAYWWLRQLRAADE 66
                                   58999999999999999766554 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0073
                     zf-3CxxC_2  8 fkCekCgkeW 17
                                   f+C+kCg++W
  gi|116754333|ref|YP_843451.1| 72 FRCTKCGNTW 81
                                   9********* 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 ?    4.1   1.0       0.1        38      36      42 .]       2       8 ..       1       8 [. 0.89
   2 ?   11.7   0.2   0.00042      0.16      22      41 ..      59      78 ..      58      79 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.1
                  Baculo_LEF5_C 36 yCskCge 42
                                   +C+kCg+
  gi|116754333|ref|YP_843451.1|  2 VCRKCGM 8 
                                   6*****8 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00042
                  Baculo_LEF5_C 22 iQnRagDEi.vsfvryCskCg 41
                                   +Q+Ra DE  v f r C kCg
  gi|116754333|ref|YP_843451.1| 59 RQLRAADESeVRFFR-CTKCG 78
                                   7*******7477776.****9 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1         5   1.9e+03       2      10 ..       3      11 ..       2      25 .. 0.65
   2 ?   11.9   0.5   0.00043      0.16       1      35 [.      45      79 ..      45      83 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 5
                      Ogr_Delta  2 CPhCgapaa 10
                                   C +Cg +  
  gi|116754333|ref|YP_843451.1|  3 CRKCGMRVP 11
                                   666776654 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00043
                      Ogr_Delta  1 rCPhCgapaaartsrnlskdvre..ryyqCsnfeCga 35
                                   +CP+Cg+  a +  r+l +      r++ C+   Cg 
  gi|116754333|ref|YP_843451.1| 45 KCPECGNDTAYWWLRQLRAADESevRFFRCTK--CGN 79
                                   6***********99999874444689999998..775 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 ?    6.0   0.0     0.029        11      24      35 ..       3      14 ..       1      15 [. 0.84
   2 ?    3.1   2.7      0.23        89       4       9 ..      46      51 ..      46      51 .. 0.98
   3 ?    5.4   0.1     0.045        17      20      28 ..      69      78 ..      61      80 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.029
                                   ESSSS-EEESSC CS
                 RNA_POL_M_15KD 24 CrqCgYeepadq 35
                                   Cr+Cg   p+++
  gi|116754333|ref|YP_843451.1|  3 CRKCGMRVPKSS 14
                                   ****99999887 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.23
                                   ESTTTS CS
                 RNA_POL_M_15KD  4 CpkCgN 9 
                                   Cp+CgN
  gi|116754333|ref|YP_843451.1| 46 CPECGN 51
                                   *****9 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.045
                                   CE.EEESSSS CS
                 RNA_POL_M_15KD 20 kn.feCrqCg 28
                                   ++ f C +Cg
  gi|116754333|ref|YP_843451.1| 69 VRfFRCTKCG 78
                                   4457777775 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 ?    4.2   0.7       0.1        40      16      21 ..       3       8 ..       1      13 [. 0.90
   2 ?    5.7   0.2     0.035        13      15      20 ..      42      50 ..      32      50 .. 0.64
   3 ?    3.5   0.0      0.16        62      14      20 ..      72      78 ..      60      84 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.1
                      zf-C2H2_3 16 CkeCgM 21
                                   C +CgM
  gi|116754333|ref|YP_843451.1|  3 CRKCGM 8 
                                   ****** PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.035
                      zf-C2H2_3 15 q...CkeCg 20
                                   +   C+eCg
  gi|116754333|ref|YP_843451.1| 42 TkakCPECG 50
                                   2456****8 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.16
                      zf-C2H2_3 14 sqCkeCg 20
                                    +C++Cg
  gi|116754333|ref|YP_843451.1| 72 FRCTKCG 78
                                   45****9 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.2       2.1   8.2e+02      29      34 ..       3       8 ..       1      12 [. 0.71
   2 ?    7.4   0.1    0.0091       3.5       8      17 ..      44      53 ..      42      56 .. 0.85
   3 ?    3.0   0.0      0.22        86      28      35 ..      73      80 ..      66      83 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 2.1
                                   ESSSTC CS
                 Ribosomal_S27e 29 CisCgk 34
                                   C +Cg 
  gi|116754333|ref|YP_843451.1|  3 CRKCGM 8 
                                   888885 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0091
                                   EE-TTTS-EE CS
                 Ribosomal_S27e  8 vkCpdCenet 17
                                    kCp+C+n t
  gi|116754333|ref|YP_843451.1| 44 AKCPECGNDT 53
                                   69******88 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.22
                                   EESSSTCE CS
                 Ribosomal_S27e 28 kCisCgkv 35
                                    C +Cg++
  gi|116754333|ref|YP_843451.1| 73 RCTKCGNT 80
                                   57777665 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 ?    3.7   0.1      0.26     1e+02       4      13 ..       2      12 ..       1      31 [. 0.81
   2 ?    8.8   0.2    0.0068       2.6       3      14 ..      44      55 ..      42      73 .. 0.78
   3 ?    3.2   0.4      0.38   1.5e+02       4      12 ..      73      82 ..      70      85 .] 0.76

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.26
                        zf-ISL3  4 rCPnCgsk.tv 13
                                   +C++Cg + ++
  gi|116754333|ref|YP_843451.1|  2 VCRKCGMRvPK 12
                                   7****988554 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0068
                        zf-ISL3  3 hrCPnCgsktvv 14
                                    +CP+Cg+ t++
  gi|116754333|ref|YP_843451.1| 44 AKCPECGNDTAY 55
                                   68******9884 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.38
                        zf-ISL3  4 rCPnCgsk.t 12
                                   rC +Cg++  
  gi|116754333|ref|YP_843451.1| 73 RCTKCGNTwR 82
                                   8*****9855 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.2      0.31   1.2e+02      23      28 ..       2       7 ..       1       9 [. 0.83
   2 ?    5.7   0.1     0.031        12       6      13 ..      45      52 ..      42      56 .. 0.80
   3 ?    5.8   0.3     0.028        11       5      17 ..      72      83 ..      70      85 .] 0.74

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.31
                        zf-RRN7 23 yCrrCh 28
                                   +Cr C+
  gi|116754333|ref|YP_843451.1|  2 VCRKCG 7 
                                   899998 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.031
                        zf-RRN7  6 pCgvCgcr 13
                                    C++Cg++
  gi|116754333|ref|YP_843451.1| 45 KCPECGND 52
                                   5*****94 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.028
                        zf-RRN7  5 ppCgvCgcrsftl 17
                                   ++C  Cg+ ++++
  gi|116754333|ref|YP_843451.1| 72 FRCTKCGN-TWRE 83
                                   58*****9.5554 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     0.015       5.6       4      15 ..       2      13 ..       1      15 [. 0.88
   2 ?    3.7   0.2      0.13        48       4       9 ..      45      50 ..      42      54 .. 0.86
   3 ?    3.2   0.2      0.17        66       3      10 ..      72      79 ..      70      83 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.015
                         zf_UBZ  4 lCerCgkeipes 15
                                   +C +Cg ++p s
  gi|116754333|ref|YP_843451.1|  2 VCRKCGMRVPKS 13
                                   7********976 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.13
                         zf_UBZ  4 lCerCg 9 
                                    C++Cg
  gi|116754333|ref|YP_843451.1| 45 KCPECG 50
                                   6****9 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.17
                         zf_UBZ  3 ylCerCgk 10
                                   + C +Cg 
  gi|116754333|ref|YP_843451.1| 72 FRCTKCGN 79
                                   78****96 PP

>> zf-3CxxC  Zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.5     0.034        13      46      98 ..       3      50 ..       2      52 .. 0.73
   2 ?    7.2   0.8     0.018       6.8       5      16 ..      71      82 ..      67      84 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.034
                       zf-3CxxC 46 CkkCkkleepkldeeevekvlrnlvkkiekkfykekr.kkPykvHerelCeaCk 98
                                   C+kC  +  pk +++ +  v ++l +++   + ++++ + P     + +C +C 
  gi|116754333|ref|YP_843451.1|  3 CRKC-GMRVPKSSNNPIVSVTNKLERTVP--VLEQESaGLP---TTKAKCPECG 50
                                   9***.899999999999999999988764..3333444777...6777777775 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.018
                       zf-3CxxC  5 rfeCskCskkWt 16
                                    f+C+kC+++W+
  gi|116754333|ref|YP_843451.1| 71 FFRCTKCGNTWR 82
                                   69*********6 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1      0.06        23       2      15 ..       2      15 ..       1      16 [. 0.88
   2 ?    3.3   0.1      0.34   1.3e+02       2       7 ..      45      50 ..      45      58 .. 0.83
   3 ?    4.4   0.3      0.16        60       1       7 [.      72      78 ..      72      84 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.06
                                   EETTTTEEESSHHH CS
                        zf-C2H2  2 kCpdCgksFkrksn 15
                                   +C +Cg++ + +sn
  gi|116754333|ref|YP_843451.1|  2 VCRKCGMRVPKSSN 15
                                   7*****99998887 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.34
                                   EETTTT CS
                        zf-C2H2  2 kCpdCg 7 
                                   kCp+Cg
  gi|116754333|ref|YP_843451.1| 45 KCPECG 50
                                   7****9 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.16
                                   EEETTTT CS
                        zf-C2H2  1 ykCpdCg 7 
                                   ++C++Cg
  gi|116754333|ref|YP_843451.1| 72 FRCTKCG 78
                                   8999998 PP

>> DUF983  Protein of unknown function (DUF983)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1       2.2   8.5e+02      11      18 ..       3      10 ..       1      16 [. 0.82
   2 ?    5.4   0.0     0.064        24       6      18 ..      41      53 ..      37      65 .. 0.86
   3 ?    2.5   0.1       0.5   1.9e+02      10      21 ..      73      84 ..      71      85 .] 0.85

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 2.2
                         DUF983 11 CeaCgldl 18
                                   C++Cg++ 
  gi|116754333|ref|YP_843451.1|  3 CRKCGMRV 10
                                   *****876 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.064
                         DUF983  6 kvadaCeaCgldl 18
                                   +++ +C++Cg d 
  gi|116754333|ref|YP_843451.1| 41 TTKAKCPECGNDT 53
                                   56889*****985 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.5
                         DUF983 10 aCeaCgldlsha 21
                                   +C +Cg  ++ +
  gi|116754333|ref|YP_843451.1| 73 RCTKCGNTWREY 84
                                   7*****999876 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.3       2.6     1e+03      21      26 ..       2       7 ..       1       7 [. 0.82
   2 ?   11.3   2.8   0.00043      0.16       1      26 [.      45      78 ..      45      81 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 2.6
                       zf-TFIIB 21 yCpqCr 26
                                   +C +C+
  gi|116754333|ref|YP_843451.1|  2 VCRKCG 7 
                                   799997 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00043
                       zf-TFIIB  1 kCPkCqdele.....eser...ggveidyCpqCr 26
                                   kCP C+++       +++    ++v +++C++C+
  gi|116754333|ref|YP_843451.1| 45 KCPECGNDTAywwlrQLRAadeSEVRFFRCTKCG 78
                                   8****98666688874444666***********8 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.3         4   1.5e+03       9      14 ..       3       8 ..       2      11 .. 0.76
   2 ?    3.2   0.1      0.18        68       8      14 ..      45      51 ..      41      53 .. 0.89
   3 ?    8.5   0.1    0.0038       1.5       6      14 ..      71      79 ..      66      81 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 4
                                   -TTT-- CS
                Desulfoferrod_N  9 CevCGn 14
                                   C  CG 
  gi|116754333|ref|YP_843451.1|  3 CRKCGM 8 
                                   888995 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.18
                                   E-TTT-- CS
                Desulfoferrod_N  8 kCevCGn 14
                                   kC  CGn
  gi|116754333|ref|YP_843451.1| 45 KCPECGN 51
                                   9*****9 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0038
                                   EEE-TTT-- CS
                Desulfoferrod_N  6 vYkCevCGn 14
                                    ++C+ CGn
  gi|116754333|ref|YP_843451.1| 71 FFRCTKCGN 79
                                   69******9 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   1.4      0.21        79      21      26 .]       1       6 [.       1       6 [. 0.95
   2 ?    6.4   1.0     0.024       9.2       3       9 ..      45      51 ..      44      52 .. 0.91
   3 ?    6.2   0.2     0.029        11       1       9 [.      71      79 ..      71      80 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.21
                         zf-ACC 21 yVCPkC 26
                                   +VC+kC
  gi|116754333|ref|YP_843451.1|  1 MVCRKC 6 
                                   8***** PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.024
                         zf-ACC  3 KCpsCge 9 
                                   KCp+Cg+
  gi|116754333|ref|YP_843451.1| 45 KCPECGN 51
                                   9****96 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.029
                         zf-ACC  1 WtKCpsCge 9 
                                   +++C++Cg+
  gi|116754333|ref|YP_843451.1| 71 FFRCTKCGN 79
                                   689*****8 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 ?   -1.2   0.1       5.7   2.2e+03      19      25 ..       2       8 ..       1      17 [. 0.70
   2 ?    9.4   0.2    0.0028       1.1      15      27 ..      41      53 ..      32      55 .. 0.85
   3 ?   -0.6   0.1       3.6   1.4e+03      20      25 ..      74      79 ..      71      84 .. 0.64

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 5.7
                                   B-TTT-S CS
                         Nop10p 19 vcpecgg 25
                                   vc +cg 
  gi|116754333|ref|YP_843451.1|  2 VCRKCGM 8 
                                   5666664 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0028
                                   ESSSB-TTT-SB- CS
                         Nop10p 15 TLkkvcpecggpt 27
                                   T k +cpecg++t
  gi|116754333|ref|YP_843451.1| 41 TTKAKCPECGNDT 53
                                   8899*******99 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 3.6
                                   -TTT-S CS
                         Nop10p 20 cpecgg 25
                                   c +cg+
  gi|116754333|ref|YP_843451.1| 74 CTKCGN 79
                                   666765 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 ?    4.3   0.1     0.087        33      22      29 ..       1       8 [.       1      12 [. 0.84
   2 ?    4.5   0.2     0.079        30      24      29 ..      46      51 ..      44      55 .. 0.80
   3 ?    2.1   0.7      0.43   1.6e+02       6      11 ..      74      79 ..      73      80 .. 0.59

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.087
                  A2L_zn_ribbon 22 lvCieCga 29
                                   +vC +Cg 
  gi|116754333|ref|YP_843451.1|  1 MVCRKCGM 8 
                                   79999995 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.079
                  A2L_zn_ribbon 24 CieCga 29
                                   C+eCg+
  gi|116754333|ref|YP_843451.1| 46 CPECGN 51
                                   9***98 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.43
                  A2L_zn_ribbon  6 CsvCgg 11
                                   C++Cg+
  gi|116754333|ref|YP_843451.1| 74 CTKCGN 79
                                   666654 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 ?    2.5   0.1      0.42   1.6e+02      18      29 ..       2      13 ..       1      16 [. 0.76
   2 ?    3.9   3.7      0.15        59       1      23 [.      45      78 ..      30      82 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.42
                       zf-Mss51 18 eCpdCGiptycs 29
                                    C +CG+ +  s
  gi|116754333|ref|YP_843451.1|  2 VCRKCGMRVPKS 13
                                   6*****977555 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.15
                       zf-Mss51  1 lCPvpkhkqt...........apkhvdfeCpdCG 23
                                   +CP + ++ +           +++   f C +CG
  gi|116754333|ref|YP_843451.1| 45 KCPECGNDTAywwlrqlraadESEVRFFRCTKCG 78
                                   4777766666777777777733333446788887 PP

>> zinc_ribbon_13  Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1      0.31   1.2e+02       1       8 [.       2       9 ..       2      23 .. 0.82
   2 ?    3.0   0.1       0.3   1.2e+02       1      10 [.      45      54 ..      45      72 .. 0.87
   3 ?    3.7   0.5      0.18        68       1       8 [.      73      80 ..      73      85 .] 0.76

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.31
                 zinc_ribbon_13 1 kCpKCgnt 8
                                  +C+KCg +
  gi|116754333|ref|YP_843451.1| 2 VCRKCGMR 9
                                  59999976 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.3
                 zinc_ribbon_13  1 kCpKCgntea 10
                                   kCp Cgn++a
  gi|116754333|ref|YP_843451.1| 45 KCPECGNDTA 54
                                   6*****9986 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.18
                 zinc_ribbon_13  1 kCpKCgnt 8 
                                   +C KCgnt
  gi|116754333|ref|YP_843451.1| 73 RCTKCGNT 80
                                   59999997 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 ?    1.5   0.1       1.9   7.2e+02       3      11 ..       3      11 ..       2      16 .. 0.76
   2 ?    3.2   0.1      0.53     2e+02       2       7 ..      45      50 ..      44      56 .. 0.85
   3 ?    6.0   0.4      0.07        27       1      12 [.      72      83 ..      72      85 .] 0.83

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 1.9
                      zf-C2H2_4  3 CpiCgksFs 11
                                   C+ Cg + +
  gi|116754333|ref|YP_843451.1|  3 CRKCGMRVP 11
                                   9***98765 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.53
                      zf-C2H2_4  2 kCpiCg 7 
                                   kCp Cg
  gi|116754333|ref|YP_843451.1| 45 KCPECG 50
                                   7****7 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.07
                      zf-C2H2_4  1 fkCpiCgksFss 12
                                   f+C+ Cg +++ 
  gi|116754333|ref|YP_843451.1| 72 FRCTKCGNTWRE 83
                                   89****999865 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.2      0.14        54       3       8 ..       2       7 ..       1      10 [. 0.74
   2 ?    4.0   0.3      0.13        48      18      29 ..      40      51 ..      33      53 .. 0.81
   3 ?    2.9   0.1      0.29   1.1e+02       4      11 ..      74      81 ..      72      84 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.14
                                  E-TTT- CS
                        ADK_lid 3 vCpkCG 8
                                  vC+kCG
  gi|116754333|ref|YP_843451.1| 2 VCRKCG 7
                                  788887 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.13
                                   -SSTTB-TTT-- CS
                        ADK_lid 18 PkveglCDkCGe 29
                                   P ++ +C +CG 
  gi|116754333|ref|YP_843451.1| 40 PTTKAKCPECGN 51
                                   777889999986 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.29
                                   -TTT--EE CS
                        ADK_lid  4 CpkCGrsY 11
                                   C kCG ++
  gi|116754333|ref|YP_843451.1| 74 CTKCGNTW 81
                                   88999875 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 ?    2.5   0.4      0.32   1.2e+02       7      12 ..       3       8 ..       1       9 [. 0.88
   2 ?    2.2   0.1       0.4   1.5e+02       5      11 ..      44      50 ..      41      52 .. 0.85
   3 ?    4.6   0.1     0.074        28       5      11 ..      72      78 ..      71      81 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.32
                     zf-C2H2_11  7 CleCGl 12
                                   C++CG+
  gi|116754333|ref|YP_843451.1|  3 CRKCGM 8 
                                   *****6 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.4
                     zf-C2H2_11  5 cqCleCG 11
                                    +C eCG
  gi|116754333|ref|YP_843451.1| 44 AKCPECG 50
                                   59****9 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.074
                     zf-C2H2_11  5 cqCleCG 11
                                   ++C++CG
  gi|116754333|ref|YP_843451.1| 72 FRCTKCG 78
                                   69****9 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   2.1     0.069        26      36      47 ..      42      53 ..       1      58 [. 0.66
   2 ?    3.6   0.3      0.17        66      34      46 ..      68      80 ..      60      83 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.069
                           CpXC 36 featCpkCgata 47
                                   ++a+Cp+Cg+++
  gi|116754333|ref|YP_843451.1| 42 TKAKCPECGNDT 53
                                   678999999876 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.17
                           CpXC 34 slfeatCpkCgat 46
                                   +++ ++C kCg+t
  gi|116754333|ref|YP_843451.1| 68 EVRFFRCTKCGNT 80
                                   677899*****87 PP

>> zf-FPG_IleRS  Zinc finger found in FPG and IleRS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.3     0.065        25       3      14 ..       2      13 ..       2      17 .. 0.81
   2 ?    5.8   0.1     0.033        13       3       9 ..      45      51 ..      43      54 .. 0.88
   3 ?    1.0   0.7         1   3.9e+02       3      10 ..      73      80 ..      71      83 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.065
                                   B-TTT--BBEEE CS
                   zf-FPG_IleRS  3 pCpRCwryierv 14
                                   +C+ C++ +++ 
  gi|116754333|ref|YP_843451.1|  2 VCRKCGMRVPKS 13
                                   6******99885 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.033
                                   B-TTT-- CS
                   zf-FPG_IleRS  3 pCpRCwr 9 
                                   +Cp C++
  gi|116754333|ref|YP_843451.1| 45 KCPECGN 51
                                   9*****8 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 1
                                   B-TTT--B CS
                   zf-FPG_IleRS  3 pCpRCwry 10
                                   +C  C+++
  gi|116754333|ref|YP_843451.1| 73 RCTKCGNT 80
                                   6999**97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                        51  (0.00284455); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              47  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 590.85
//
Query:       gi|116754334|ref|YP_843452.1|  [L=244]
Description: DNA polymerase sliding clamp [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-13   49.6   0.0    4.3e-11   43.1   0.0    3.2  3  PCNA_C    Proliferating cell nuclear antigen, C-terminal doma
    4.6e-12   45.7   0.3    1.8e-11   43.8   0.1    1.9  2  PCNA_N    Proliferating cell nuclear antigen, N-terminal doma
    0.00096   18.7   0.0     0.0031   17.0   0.0    1.7  2  Rad9      Rad9


Domain annotation for each model (and alignments):
>> PCNA_C  Proliferating cell nuclear antigen, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.24   1.4e+03      24      46 ..      17      39 ..       7      57 .. 0.77
   2 ?    1.5   0.0     0.053   3.1e+02      44      74 ..      61      91 ..      44      97 .. 0.84
   3 !   43.1   0.0   7.2e-15   4.3e-11       2     127 ..     122     239 ..     121     240 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.24
                                   HHTTT-SEEEEEEETTEEEEEEE CS
                         PCNA_C 24 dlsqlsdsvvisvtkegvkfsas 46
                                    +s+l d+v  ++t +g+  +a 
  gi|116754334|ref|YP_843452.1| 17 AVSSLVDEVKFTITEKGLELKAV 39
                                   56888999999999999988774 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.053
                                   EEEETTEEEEEEE--BEESSSGGGCBEEEES CS
                         PCNA_C 44 sasGdiGsasivlkqvkdvdkeeeavklelk 74
                                    + G+iG   + l++  ++++  e v lel 
  gi|116754334|ref|YP_843452.1| 61 ATPGEIGVDLVRLSDLLSMADRGERVRLELL 91
                                   4679*****************9999999975 PP

  == domain 3  score: 43.1 bits;  conditional E-value: 7.2e-15
                                    ---SS-SEEEEEEHHHHHHHHHHHTTT-SEEEEEEETTEEEEEEEETTEEEEEEE--BEESSSGGGCBEEEESS-EEEEE CS
                         PCNA_C   2 ipdseydavvklpssefaricrdlsqlsdsvvisvtkegvkfsasGdiGsasivlkqvkdvdkeeeavklelkepvtltf 81 
                                    ip+++  a v +p +ef r ++   ++sd vv+ v  +     a+Gdi + +++++  + +        ++  e+    f
  gi|116754334|ref|YP_843452.1| 122 IPELDLPAHVAIPGAEFRRAIKAAEKVSDHVVLGVKDDIFYMEAKGDIDALKLTMRSSELL-------DMKPGEAR-SLF 193
                                    9**********************************99999********9886666554444.......34444444.45* PP

                                    EHHHHHHHGGGGGC-SEEEEEEETTSEEEEEEEETTCEEEEEEE-B CS
                         PCNA_C  82 alkYlaeftkatsLservtlslssevPlvveykikdvgllayllak 127
                                    +l+Yl ++ k+   +++v+l++  + Pl + + +kd  ++ ylla+
  gi|116754334|ref|YP_843452.1| 194 SLDYLSDMSKSIGKAPEVKLEIGIDYPLRISFMLKDNVHVSYLLAP 239
                                    ********************************************98 PP

>> 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 !   43.8   0.1     3e-15   1.8e-11       8      94 ..       7      92 ..       1     102 [. 0.88
   2 ?   -0.7   0.0      0.18   1.1e+03      82     106 ..     155     179 ..     144     186 .. 0.80

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 3e-15
                                   SHHHHHHHHHHHTTTCSEEEEEEETTEEEEEEE-TTSSEEEEEEEEGGGSSEEEESS-EEEEEEHHHHHHHHTTSTTTSEEE CS
                         PCNA_N  8 qasllkklleaikdlvneanfdcddsGislqalDsshvaLvslelrsegfekyrCDrnlalgvnlnslskilkcannedsvt 89
                                   +a  l+  +ea+  lv+e+ f + ++G++l+a+D + va+vsl++ +++fe y+   +  +gv+l  ls +l +a+  + v 
  gi|116754334|ref|YP_843452.1|  7 DAETLRDAIEAVSSLVDEVKFTITEKGLELKAVDPANVAMVSLKIDASAFEFYQA-TPGEIGVDLVRLSDLLSMADRGERVR 87
                                   56778999*********************************************97.5789****************999998 PP

                                   EEEET CS
                         PCNA_N 90 lkaed 94
                                   l+  +
  gi|116754334|ref|YP_843452.1| 88 LELLE 92
                                   87554 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.18
                                    STTTSEEEEEEETTSSEEEEEEEEC CS
                         PCNA_N  82 annedsvtlkaedeadtlalvfese 106
                                    + ++d+  ++a+ + d+l+l+++s+
  gi|116754334|ref|YP_843452.1| 155 GVKDDIFYMEAKGDIDALKLTMRSS 179
                                    5678899999999999999988765 PP

>> Rad9  Rad9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   5.1e-07    0.0031       4      53 ..      14      62 ..      11      81 .. 0.89
   2 ?   -1.3   0.0       0.2   1.2e+03       1      27 [.     138     164 ..     138     166 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.1e-07
                           Rad9  4 alqclsrigdelyleisedglelrtvnssrSayalvtlkksfFdkyekev 53
                                   a++++s + de+ + i+e+glel++v+ ++ a +++++  s F+ y+  +
  gi|116754334|ref|YP_843452.1| 14 AIEAVSSLVDEVKFTITEKGLELKAVDPANVAMVSLKIDASAFEFYQ-AT 62
                                   78999***************************************994.33 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.2
                           Rad9   1 laralqclsrigdelyleisedglelr 27 
                                    + ra++++ +++d ++l  ++d + ++
  gi|116754334|ref|YP_843452.1| 138 FRRAIKAAEKVSDHVVLGVKDDIFYME 164
                                    6799************99999887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1773.32
//
Query:       gi|116754335|ref|YP_843453.1|  [L=330]
Description: DNA primase large subunit [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-33  116.2   0.0    6.2e-33  114.3   0.0    1.7  1  DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large s


Domain annotation for each model (and alignments):
>> DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.3   0.0   3.4e-37   6.2e-33       2     206 ..     125     305 ..     124     321 .. 0.84

  Alignments for each domain:
  == domain 1  score: 114.3 bits;  conditional E-value: 3.4e-37
                                    EEEEEHHHHHHHTT-G.........GS-EETTEEEE-HHHHHHHHHHHHHHHHHH..........HHGGGSSS---HHHH CS
                DNA_primase_lrg   2 fykvpfedvldlvkrr.........rvllkkGyaylpkeeleslllekfrkrlekalestkeslpeleeeikederekle 72 
                                    +++++f+d++  + +r         ++ +++Gy+ +++eel++l+ e++r+r++++l   + s   +     e   + l+
  gi|116754335|ref|YP_843453.1| 125 NFRIHFTDFVISA-ARfrsqkwkliNRTIDHGYLKVTREELLRLMQERIRDRIQEGLPLDAGS---I----CEGLSDHLR 196
                                    6999****99333.3334689*************************************93333...3....333333466 PP

                                    HHHCT--.............TTSSTTGGSHHHHTT--HHHHCCHHHHCCCSS--CHHHHHHHHHHHHCT--CHHHHCCCH CS
                DNA_primase_lrg  73 ellealsesyvaedvqeeedskisaknidklakesfPpCmrelleglkknghlkhegrlqltlFlkdiglsldeilelwk 152
                                    ++ ++l            ++++ s  ++++ +++++PpCmr+lle+l ++ +l+h++r++lt+Fl +i l +++i+ ++ 
  gi|116754335|ref|YP_843453.1| 197 SIRDELA-----------SSKRSSMVDLGEFSRDALPPCMRSLLEQLAAGRNLAHTARFALTSFLLNINLGVEDIIGIFN 265
                                    6666666...........5555677789**************************************************** PP

                                    CHST..HHHHHH.HTHCHCHHHCC-STT--------HHHHHHS....TT---S.-H CS
                DNA_primase_lrg 153 eaftrteekFdk.eyrynirhnyGkegkrtnyspysCekiltkpppgkgdahg.Cp 206
                                    +      ++Fd+  +ry+i+h++G    +t+y+p+sC+++          ++g Cp
  gi|116754335|ref|YP_843453.1| 266 NT-----PDFDEeMTRYQIEHIAG--STGTRYTPPSCSTM---------LTYGnCP 305
                                    *8.....*****9999********..88899*********.........8888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); 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 0.22s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2486.22
//
Query:       gi|116754336|ref|YP_843454.1|  [L=421]
Description: 3-phosphoshikimate 1-carboxyvinyltransferase [Methanosaeta thermophila PT]
Scores for complete 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-109  364.4   0.0   7.8e-109  364.1   0.0    1.0  1  EPSP_synthase    EPSP synthase (3-phosphoshikimate 1-carboxyv
     0.0029   17.7   2.6        1.8    8.7   0.1    4.1  4  Leucyl-specific  Leucine-tRNA synthetase-specific domain
  ------ inclusion threshold ------
       0.14   11.0   0.1       0.21   10.5   0.1    1.2  1  DUF4621          Protein of unknown function (DUF4621)


Domain annotation for each model (and alignments):
>> EPSP_synthase  EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  364.1   0.0  1.3e-112  7.8e-109       5     417 .]       8     410 ..       5     410 .. 0.94

  Alignments for each domain:
  == domain 1  score: 364.1 bits;  conditional E-value: 1.3e-112
                                    S--EEEEE--B-HHHHHHHHHHHGGGBSSEEEES---SHHHHHHHHHHHHTT.EEEEEECTSEEEEEGTT..--EE-HHH CS
                  EPSP_synthase   5 krlegevkvpGsksisnralllAaLaegestitnlLdseDvrsmlealreLgaeiikldeekevviveglggsfeapeel 84 
                                    + ++g+v +p+sks+++ra+l+ aL+++ + +  +L s+D+r+++ a+ ++ga++ kl   ++ + ++g  g+  +p e+
  gi|116754336|ref|YP_843454.1|   8 SSISGTVCAPPSKSYTHRAVLITALSDSGC-VHRPLISADTRATISACDAFGADV-KL--RGDSLEIQGVSGAPRTP-EN 82 
                                    689***********************9998.799******************766.77..57888899988999999.6* PP

                                    HTT-GGGGGGHHHHHHHHSEESSEEEEE-SBTTCGS--HHHHHHHHHTT-EEEEETTEEEEEESEET.SS-BEEEEETSS CS
                  EPSP_synthase  85 vldlgnsgtalrlLtallalasgevvLtGdesirkRPidrlldaLrqlGaeieveegenkaplkvkg.lklkgveikaev 163
                                    v+d+ nsgt+lr++ a++al     vLtGd sir+RP  +ll+aL++lGae  + +g+  apl ++g l++++++++++v
  gi|116754336|ref|YP_843454.1|  83 VIDVLNSGTTLRFMSAVAALT-DGAVLTGDSSIRSRPNGPLLKALNELGAEAFSIRGNDRAPLVIRGrLRGGSTSLDGSV 161
                                    *******************97.6799****************************************************** PP

                                    TTHHHHHHHHHHHTTSBS.EEEEES.-TTHHHHHHHHHHHHHTT-EEEETTSSEEEEEE--SSB--EEEE--B-HHHHHH CS
                  EPSP_synthase 164 sSqqvtsllllaallaeg.ttelee.lasepsiddtlkmlkkfgikietsgteesitvkGkeklpgteyvvegDassAay 241
                                    sSq++++ll++ +l + + t+ +++ l+s+p+ ++tl++l+k+g++i t  +++ ++++G+++   +ey+v+gD ssA+y
  gi|116754336|ref|YP_843454.1| 162 SSQFLSALLIACPLSSGEtTISIKGeLKSRPYAEMTLDILRKAGAEICT--DGDIFRMRGGQSYRLAEYTVPGDFSSASY 239
                                    *************888888899999************************..8889********77679************ PP

                                    HHHHHHHTT-EEEEES--GGGGHHH..HHHHHHHHTTEEEEEESTSE.EEEEETTS--BEEEEEBGSTTSBHGGGHHHHH CS
                  EPSP_synthase 242 flvaAaitggevtvenvginslqGdiealdeilekmgaeitqeedas.ivvgpsglklkdvdietlpdeaptlavlaafa 320
                                    +l+aAa++g   tve++++ s qGd +++d il++mgae+++  ++   +v+   l+++++d ++ pd++ptlavl a+a
  gi|116754336|ref|YP_843454.1| 240 PLAAAALAG-SATVEGLFP-SRQGDSAIVD-ILREMGAEVSWDMESGeVRVSGADLRGREIDASQTPDLVPTLAVLGAVA 316
                                    ********9.899***987.6789*88888.**********8765540444455************************** PP

                                    HHHHTSBSEEEEEGSSSTTCCHHHHHHHTTT-EEEEETTEEEEEEEEE.EB-EEEE-TTSTTTTHHHHHHHHHSBSEEEE CS
                  EPSP_synthase 321 egttviegiaelrvketdrlaamateLrklGaeveeeedgliiipaekqlkgaevesydDhRiamalalaglvaegevei 400
                                    eg+tvi++++++r ketdr++ama eL+k+Ga+++e++dgl+i +++  l+ga ++ y+DhRi mal+lag +++g+++i
  gi|116754336|ref|YP_843454.1| 317 EGRTVIKNAEHVRHKETDRIHAMAVELKKMGANIRERPDGLEIDGGD--LHGADLHGYHDHRIVMALTLAG-IVAGDTRI 393
                                    ******************************************99986..8*********************.88888*** PP

                                    ETTHHHHHHSSSHHHHH CS
                  EPSP_synthase 401 ddiectdksfpefeekL 417
                                    d +e +d+s+p+f+e++
  gi|116754336|ref|YP_843454.1| 394 DTAESVDVSYPGFFEDM 410
                                    **************976 PP

>> Leucyl-specific  Leucine-tRNA synthetase-specific domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0      0.01        60      29      50 ..     194     213 ..     183     216 .. 0.80
   2 ?    1.9   0.1     0.041   2.5e+02      34      47 ..     283     296 ..     274     299 .. 0.79
   3 !    8.7   0.1    0.0003       1.8      33      49 ..     340     356 ..     313     359 .. 0.72
   4 ?   -2.5   0.0      0.96   5.7e+03      34      45 ..     408     419 ..     407     420 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.01
                Leucyl-specific  29 seLsleevkKmGAELRehedGk 50 
                                    +e++l+ ++K GAE+ +  dG 
  gi|116754336|ref|YP_843454.1| 194 AEMTLDILRKAGAEICT--DGD 213
                                    67999*********984..444 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.041
                Leucyl-specific  34 eevkKmGAELRehe 47 
                                     ev+ +GA+LR  e
  gi|116754336|ref|YP_843454.1| 283 GEVRVSGADLRGRE 296
                                    49999*****9665 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0003
                Leucyl-specific  33 leevkKmGAELRehedG 49 
                                      e+kKmGA +Re  dG
  gi|116754336|ref|YP_843454.1| 340 AVELKKMGANIRERPDG 356
                                    5699*********9999 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 0.96
                Leucyl-specific  34 eevkKmGAELRe 45 
                                    e++++ GA  R+
  gi|116754336|ref|YP_843454.1| 408 EDMRRLGANVRA 419
                                    79999***9996 PP

>> DUF4621  Protein of unknown function (DUF4621)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   3.5e-05      0.21      40      99 ..     328     387 ..     298     405 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 3.5e-05
                                    EEEETTEEEEEEEEE-EE------------EEEEEEEE-GGGGGGSSS--B--BS--EEE CS
                        DUF4621  40 irevdgayvmiydgemkikgkslraasdkveiasedittgdidglfdgdfvlaltnphit 99 
                                    +r  +   +     e+k  g  +r   d +ei   d+   d+ g  d  +v+alt   i 
  gi|116754336|ref|YP_843454.1| 328 VRHKETDRIHAMAVELKKMGANIRERPDGLEIDGGDLHGADLHGYHDHRIVMALTLAGIV 387
                                    4444444444456799***************************************87765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2888.70
//
Query:       gi|116754337|ref|YP_843455.1|  [L=516]
Description: hypothetical protein Mthe_1030 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0029   17.9   0.0         21    5.5   0.0    3.5  3  DUF11     Domain of unknown function DUF11
     0.0033   17.7   0.0        1.2    9.4   0.0    2.9  3  CARDB     CARDB
  ------ inclusion threshold ------
      0.017   15.6   0.0       0.26   11.8   0.0    2.9  4  MG2       MG2 domain
        0.1   12.9   0.1       0.23   11.8   0.1    1.6  1  Flu_NS2   Influenza non-structural protein (NS2)


Domain annotation for each model (and alignments):
>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.0    0.0047        21      10      33 ..     150     173 ..     141     178 .. 0.85
   2 ?    2.8   0.0     0.033   1.5e+02      13      82 ..     269     328 ..     258     333 .. 0.77
   3 !    5.1   0.0    0.0061        27      14      77 ..     376     430 ..     365     436 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0047
                          DUF11  10 vrpGdtvtytltvtNtgpasangv 33 
                                     r+Gd++++ + v N+g  +a+ +
  gi|116754337|ref|YP_843455.1| 150 YRSGDQIRVEVFVENRGDGNAESI 173
                                    689***************999765 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.033
                          DUF11  13 GdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsv..gsLeagesatlsftvrvtrta 82 
                                    G t  ++   +Ntg + + g+  tD   ag +++s   +         v   +L +ges+ +s++v+++  +
  gi|116754337|ref|YP_843455.1| 269 GRTYYVINSIRNTGKVRL-GLSFTD--SAGNEFQSEGVA---------VkeFELIPGESKIISYAVKARHPG 328
                                    555555557899999999.999999..999999988888.........334589999999999999988765 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.0061
                          DUF11  14 dtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsftvr 77 
                                    d+ +++  v+Ntg++ a gv+   + P+++++  ++          s   L+ag+s+t+  +vr
  gi|116754337|ref|YP_843455.1| 376 DEFQVCMEVKNTGNRYA-GVRAYRIFPESVEISDGKND-------LS-FALAAGSSRTICWSVR 430
                                    5899*************.***99999999997777766.......22.3688888888776666 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0   0.00027       1.2      16      72 ..     151     218 ..     136     241 .. 0.71
   2 ?   -2.8   0.0       1.8     8e+03      26      67 ..     277     320 ..     267     329 .. 0.55
   3 !    5.2   0.0    0.0056        25      17      65 ..     374     425 ..     362     452 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00027
                                    ETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE.....EEEEE.........SEE-CTEEEEEEEEEE-S CS
                          CARDB  16 fvgeentitvtvkNqGtaasgatkvalyldgelv.....gtvtv.........psLaagesttvsftwtte 72 
                                      g++++++v v+N G+++++++++ l l++        +             + L +ge   +++ ++t+
  gi|116754337|ref|YP_843455.1| 151 RSGDQIRVEVFVENRGDGNAESIRLLLNLSEPHSdvlngT---MkeigkkmrrSLLRPGEVWRERICFQTP 218
                                    578999*****************99999988775333322...0444777777777777777777777666 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.8
                                    EEEE-SSS-EEEEEEEEEETTEEEEEEEE..SEE-CTEEEEEEE CS
                          CARDB  26 tvkNqGtaasgatkvalyldgelvgtvtv..psLaagesttvsf 67 
                                    +++N+G+   g + ++   ++ + + v v   +L +ges+ +s+
  gi|116754337|ref|YP_843455.1| 277 SIRNTGKVRLGLSFTDSAGNEFQSEGVAVkeFELIPGESKIISY 320
                                    57777776655555554444444444555333455555555555 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.0056
                                    TTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE..EEEEE.SEE-CTEEEEE CS
                          CARDB  17 vgeentitvtvkNqGtaasgatkvalyldgelv..gtvtv.psLaagesttv 65 
                                    + +e+++ ++vkN+G+ ++g    +++ +  +   g+ ++  +Laag+s+t+
  gi|116754337|ref|YP_843455.1| 374 DPDEFQVCMEVKNTGNRYAGVRAYRIFPESVEIsdGKNDLsFALAAGSSRTI 425
                                    567889999**********988888887777776655555346777777665 PP

>> MG2  MG2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.3   5.7e+03      12      37 ..      50      76 ..      49      93 .. 0.75
   2 ?   11.8   0.0   5.7e-05      0.26       6      45 ..     145     184 ..     140     191 .. 0.77
   3 ?   -0.8   0.0      0.47   2.1e+03       8      28 ..     200     220 ..     199     305 .. 0.68
   4 ?   -2.4   0.0       1.5   6.9e+03      32      60 ..     282     310 ..     264     319 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.3
                                   -TT-EEEEEEEEES.TTCSB---EEEE CS
                            MG2 12 rPgetVslkallrd.etlqglaklplk 37
                                   +Pge V++ +++ + ++ + +++ p+ 
  gi|116754337|ref|YP_843455.1| 50 QPGEMVEVDGYSVElSDISVVPESPAA 76
                                   799999999998777777777776655 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 5.7e-05
                                    ES-SEE-TT-EEEEEEEEESTTCSB---EEEEEEEE-TTS CS
                            MG2   6 tDRglYrPgetVslkallrdetlqglaklplkltirdpdg 45 
                                     DR++Yr g+++++++++ ++    +++ +l l+++ p++
  gi|116754337|ref|YP_843455.1| 145 PDRDIYRSGDQIRVEVFVENRGDGNAESIRLLLNLSEPHS 184
                                    5*****************8866555666677777776666 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.47
                                    -SEE-TT-EEEEEEEEESTTC CS
                            MG2   8 RglYrPgetVslkallrdetl 28 
                                    R l+rPge  + ++  ++++l
  gi|116754337|ref|YP_843455.1| 200 RSLLRPGEVWRERICFQTPSL 220
                                    788888887666666555444 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 1.5
                                    --EEEEEEEE-TTSSEEEEEEEEE-CTTE CS
                            MG2  32 aklplkltirdpdgkevkelplatdetgg 60 
                                     k +l l+++d+ g+e++++ +a +e+ +
  gi|116754337|ref|YP_843455.1| 282 GKVRLGLSFTDSAGNEFQSEGVAVKEFEL 310
                                    44566778888888888887777766655 PP

>> Flu_NS2  Influenza non-structural protein (NS2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   5.1e-05      0.23      17      88 ..      85     158 ..      78     164 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.1e-05
                                    XXXXXXXXXXXXXXXXXXX-CHHHHHHHHHHHHH...HHHHHHHHC----TTSH.HHHHHHHHHHHHHHHHHHHHH CS
                        Flu_NS2  17 slgelvmkstdlhslqnrnekwreqlgqkreeir...llieelrhklkiaessi.eqivslsllelllevkdvvev 88 
                                    s++  vm+++++  l++   + re+lg k eeir   +l +e r  l i   s  e  +s+s  + ++   d+++v
  gi|116754337|ref|YP_843455.1|  85 SISSTVMRAGEFFVLKD--MHNREKLGVKLEEIRregYLSNESRAILEIRMRSRpEISISMSPDRDIYRSGDQIRV 158
                                    88899********7765..5679**********9666678888888888777775666777777777766666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (516 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3715.84
//
Query:       gi|116754338|ref|YP_843456.1|  [L=130]
Description: hypothetical protein Mthe_1032 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.032   13.3   0.1      0.032   13.3   0.1    1.1  1  DUF973    Protein of unknown function (DUF973)
       0.15   12.3   0.7       0.35   11.1   0.0    1.8  2  DUF3522   Protein of unknown function (DUF3522)
       0.33   11.3   4.1       0.93    9.9   1.5    2.5  2  BatA      Aerotolerance regulator N-terminal
        1.1    9.7   4.6        1.4    9.4   3.3    1.7  2  MerC      MerC mercury resistance protein


Domain annotation for each model (and alignments):
>> DUF973  Protein of unknown function (DUF973)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1     7e-06     0.032     100     152 ..      53     105 ..      10     125 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7e-06
                         DUF973 100 gltliligaiiiiigvilaivsll.slilslillgviilligiilaliGqillg 152
                                    gl+l+l ga ++ + ++ +i+++   ++l ++l+g++i+  g   ++iG il++
  gi|116754338|ref|YP_843456.1|  53 GLFLLLTGAFVLSVPALAKIFGIEvRATLEQVLAGFLIASAGL-ALIIGTILII 105
                                    899*****************99976888888888888877665.5578998876 PP

>> DUF3522  Protein of unknown function (DUF3522)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   7.9e-05      0.35     118     171 ..       8      65 ..       1      75 [. 0.85
   2 ?   -0.6   0.1      0.31   1.4e+03     152     169 ..      80      98 ..      75     103 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 7.9e-05
                        DUF3522 118 ilvgllillvswliecvkkrklypsllr.....rrlkrlnlqqllpgllllalAlfllg 171
                                    +lv+  i+l++ ++ + ++r++y    +     + ++r+  ++l+ gl+ll++++f+l+
  gi|116754338|ref|YP_843456.1|   8 LLVAEGIPLLALVYYLEHRRRMYLLE-KgcmivESPERRAERRLCNGLFLLLTGAFVLS 65 
                                    677788999999999999***99863.258888999*******************9976 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.31
                        DUF3522 152 nlqqllpgllllalAl.fl 169
                                     l q+l+g+l++ ++l ++
  gi|116754338|ref|YP_843456.1|  80 TLEQVLAGFLIASAGLaLI 98 
                                    5679999999999998533 PP

>> BatA  Aerotolerance regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.5   0.00021      0.93       7      75 ..       5      70 ..       1      71 [. 0.68
   2 ?    1.0   0.0      0.13   5.7e+02      11      25 ..      93     107 ..      82     118 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00021
                           BatA  7 PllLlallllplpiillyllkrrpqevvfsslrlleevekdeealqrlkknllllLrllalallvlalA 75
                                    l Ll++  +pl ++l+y+l  r++   +    ++ e+++++    r++ n l+lL + a++l v alA
  gi|116754338|ref|YP_843456.1|  5 ILGLLVAEGIPL-LALVYYLEHRRRMYLLEKGCMIVESPERRAE--RRLCNGLFLLLTGAFVLSVPALA 70
                                   455566668999.8888888888887755554444444444433..59999999999999999998888 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.13
                           BatA  11 lallllplpiillyl 25 
                                    ++l+l++  i+++++
  gi|116754338|ref|YP_843456.1|  93 AGLALIIGTILIIRM 107
                                    334444433444444 PP

>> MerC  MerC mercury resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.65   2.9e+03      48      63 ..      13      27 ..       2      35 .. 0.47
   2 ?    9.4   3.3   0.00031       1.4      16      58 ..      57     101 ..      54     107 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.65
                           MerC 48 aigllalvvgyrrhrk 63
                                    i llalv+   +hr+
  gi|116754338|ref|YP_843456.1| 13 GIPLLALVYY-LEHRR 27
                                   3334444443.44444 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00031
                           MerC  16 lllPvllallpllglsf.la.sellhqvllilvvaigllalvvgy 58 
                                    ll+ ++++++p+l+ +f ++    l+qvl+ + +a ++lal++g+
  gi|116754338|ref|YP_843456.1|  57 LLTGAFVLSVPALAKIFgIEvRATLEQVLAGFLIASAGLALIIGT 101
                                    5688999*********99998999******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); 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: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 969.02
//
Query:       gi|116754339|ref|YP_843457.1|  [L=248]
Description: ABC transporter related [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-32  112.5   0.0    2.8e-32  112.1   0.0    1.2  1  ABC_tran         ABC transporter
    3.5e-12   46.8   0.8    1.8e-06   28.0   0.0    3.0  3  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    5.4e-05   23.6   0.0     0.0011   19.4   0.0    2.1  2  AAA              ATPase family associated with various cellul
    0.00012   22.4   0.2     0.0012   19.1   0.2    2.0  1  AAA_22           AAA domain
    0.00012   22.6   0.0     0.0035   17.9   0.0    2.2  2  AAA_18           AAA domain
    0.00034   20.1   0.0    0.00057   19.3   0.0    1.4  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
    0.00043   19.1   0.0       0.11   11.2   0.0    2.0  2  AAA_13           AAA domain
    0.00065   19.2   0.0      0.011   15.1   0.0    2.1  1  SMC_N            RecF/RecN/SMC N terminal domain
     0.0014   18.0   0.0       0.05   13.0   0.0    2.2  2  TniB             Bacterial TniB protein
     0.0036   17.5   0.0     0.0064   16.7   0.0    1.7  1  AAA_33           AAA domain
  ------ inclusion threshold ------
      0.013   15.5   0.1       0.29   11.1   0.0    2.2  2  AAA_5            AAA domain (dynein-related subfamily)
       0.02   14.6   0.1      0.034   13.9   0.1    1.4  1  AAA_29           P-loop containing region of AAA domain
      0.027   14.9   0.9      0.062   13.7   0.9    1.8  1  AAA_16           AAA ATPase domain
       0.03   14.0   0.0      0.044   13.5   0.0    1.3  1  AAA_24           AAA domain
      0.045   14.0   0.0       0.31   11.3   0.0    2.1  1  SbcCD_C          Putative exonuclease SbcCD, C subunit
       0.06   13.8   0.0       0.11   13.0   0.0    1.3  1  AAA_23           AAA domain
      0.064   12.9   0.0      0.086   12.5   0.0    1.2  1  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
      0.082   12.8   0.0       0.13   12.2   0.0    1.3  1  RsgA_GTPase      RsgA GTPase
      0.084   12.6   0.1       0.88    9.3   0.0    2.1  2  IstB_IS21        IstB-like ATP binding protein
      0.089   12.7   0.0       0.13   12.2   0.0    1.3  1  ATPase_2         ATPase domain predominantly from Archaea
       0.12   12.0   0.1        6.5    6.4   0.0    2.2  2  Sigma54_activat  Sigma-54 interaction domain
       0.13   12.5   0.0       0.25   11.6   0.0    1.5  1  AAA_28           AAA domain
       0.15   11.8   0.0       0.25   11.1   0.0    1.3  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
       0.21   11.3   0.1       0.34   10.6   0.1    1.3  1  Cytidylate_kin   Cytidylate kinase
       0.22   10.6   0.0       0.23   10.6   0.0    1.1  1  G-alpha          G-protein alpha subunit


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.1   0.0   3.9e-35   2.8e-32       1     137 []      25     176 ..      25     176 .. 0.93

  Alignments for each domain:
  == domain 1  score: 112.1 bits;  conditional E-value: 3.9e-35
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG...B-HHHCCHCEEEE-SS..--S-TTSB CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx..xxxxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke...qeleslrkeigvlpqe..pqlfpelt 75 
                                    l++v+++++eg++++++G++G+GK+tL+++lagl +p +G + +++k+l+    +e +++r+++++++q+  ++l+p +t
  gi|116754339|ref|YP_843457.1|  25 LRDVTVEIEEGHTLGLFGPSGSGKTTLARILAGLDHPSSGVVIFNSKELRGmrgHEFTEFRRSVQMVFQDpeSSLNPMKT 104
                                    689**********************************************9999999**************9999****** PP

                                    HHHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    xxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  76 vren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                    ++++             e +  i++al+ +gl+e   +v+ + p++LSgGq qr+alarall +p++l+lDEpta
  gi|116754339|ref|YP_843457.1| 105 IGRSlrevldllrvpdgEHEGIIKEALEVVGLSE---EVLCRFPRQLSGGQNQRIALARALLLNPRILILDEPTA 176
                                    99999*****999876666666888888888777...7887889*****************************97 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   5.9e-05     0.042       3      22 ..      39      58 ..      38      87 .. 0.82
   2 ?    2.2   0.0      0.18   1.3e+02     262     283 ..      91     117 ..      90     127 .. 0.79
   3 !   28.0   0.0   2.5e-09   1.8e-06     235     302 ..     146     211 ..     145     212 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.9e-05
                         AAA_21  3 vliGpNgsGKSnLLdaldll 22
                                   +l Gp gsGK++L ++l +l
  gi|116754339|ref|YP_843457.1| 39 GLFGPSGSGKTTLARILAGL 58
                                   599**************998 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.18
                         AAA_21 262 liDEpEngLHP.....kllrrllellk 283
                                    ++ +pE++L+P     + lr++l+ll+
  gi|116754339|ref|YP_843457.1|  91 VFQDPESSLNPmktigRSLREVLDLLR 117
                                    6889*******8777777777777774 PP

  == domain 3  score: 28.0 bits;  conditional E-value: 2.5e-09
                         AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSplll 302
                                    r+lS G+ + +al+ all  +   ++l++DEp ++L+ ++++ +l llke +r +g+  +  +H p ++
  gi|116754339|ref|YP_843457.1| 146 RQLSGGQNQRIALARALLLNP---RILILDEPTASLDVSVQAQILNLLKEIQRtRGIGYLYISHHPAVM 211
                                    688999988889999999999...************************999999************997 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   1.5e-06    0.0011       3      54 ..      40      96 ..      38     105 .. 0.75
   2 ?    2.0   0.0      0.35   2.5e+02      47      98 ..     153     195 ..     128     212 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.5e-06
                                   EESSTTSSHHHHHHHHHHH..HTHEEEEEETTTCSSS...STTHHHHHHHHHHHHHH CS
                            AAA  3 lyGppGtGKTllakavake..lgvefleisgsellsk...yvgesekkirelfkeak 54
                                   l+Gp G GKT+la+ +a     ++ ++ ++ +el+ +    + e  ++++++f++ +
  gi|116754339|ref|YP_843457.1| 40 LFGPSGSGKTTLARILAGLdhPSSGVVIFNSKELRGMrghEFTEFRRSVQMVFQDPE 96
                                   89***************9843246667777777775555578899999999999854 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.35
                                    HHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTT CS
                            AAA  47 relfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkk 98 
                                    ++ ++ a++   +p il++DE  a    +          v++q+l+ l++ ++
  gi|116754339|ref|YP_843457.1| 153 NQRIALARALLlNPRILILDEPTASLDVS----------VQAQILNLLKEIQR 195
                                    444445555556799*****987776666..........56666666655555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.2   1.7e-06    0.0012      10     125 ..      40     201 ..      32     210 .. 0.63

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.7e-06
                         AAA_22  10 vtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.....sskdllrellralglelka.............. 70 
                                    ++G+sG+GKTtl+r l+  ++        +++vv ++ +++      + ++++r +   ++++ ++              
  gi|116754339|ref|YP_843457.1|  40 LFGPSGSGKTTLARILAGLDHP-------SSGVVIFNSKELRgmrghEFTEFRRSVQMVFQDPESSlnpmktigrslrev 112
                                    89***************99963.......555553333333333344556666666666665555555566666666666 PP

                         AAA_22  71 ...............................erlsseellealeqalrarav...........ielliiDEaqh.lr... 104
                                                                       ++    +                     +++li+DE    l+   
  gi|116754339|ref|YP_843457.1| 113 ldllrvpdgehegiikealevvglseevlcrF--PRQLSGGQN--------QrialaralllnPRILILDEPTAsLDvsv 182
                                    66666666668888888888866655554221..222222333........13333333467788999999888888855 PP

                         AAA_22 105 seealeeLrsllnlsrkgvql 125
                                    ++++l+ L++++   + g+  
  gi|116754339|ref|YP_843457.1| 183 QAQILNLLKEIQR--TRGIGY 201
                                    5999999988888..776665 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   4.9e-06    0.0035       3      55 ..      40      93 ..      38     140 .. 0.72
   2 ?    2.8   0.0      0.23   1.7e+02      51      89 ..     177     214 ..     156     219 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 4.9e-06
                         AAA_18  3 ltGtpGvGKttlakeLskrl.gf.gvnlrdvakenglllevdpealdeskrlded 55
                                   l G++G+GKttla+ L+ +   + gv++      +g++  ++ e +++s +++ +
  gi|116754339|ref|YP_843457.1| 40 LFGPSGSGKTTLARILAGLDhPSsGVVIFNSKELRGMRGHEFTE-FRRSVQMVFQ 93
                                   89**************7764333677777777777777766666.6666555555 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.23
                         AAA_18  51 rldedkldklldaleenssaleegknlvidghlaelese 89 
                                     ld  +++++l++l+e+ +  +  + l+i+ h+a ++++
  gi|116754339|ref|YP_843457.1| 177 SLDVSVQAQILNLLKEIQR-TRGIGYLYISHHPAVMRFM 214
                                    5666778889999999987.5556677******999876 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0     8e-07   0.00057      16      92 ..      29     106 ..      21     128 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 8e-07
                   Mg_chelatase  16 eiaaaGgHnlllvGppGsGKtmlakrlpsllpplseeealevakiasvag.kkeeekllkrrpfraphhsaskaalvG 92 
                                    ++ +  gH l l+Gp+GsGKt la+ l++l  p s   ++++++++ + g + +e +   +  f++p  s   +  +G
  gi|116754339|ref|YP_843457.1|  29 TVEIEEGHTLGLFGPSGSGKTTLARILAGLDHPSSGVVIFNSKELRGMRGhEFTEFRRSVQMVFQDPESSLNPMKTIG 106
                                    5666779***********************999999999999999999994445556677788888888887777666 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   0.00015      0.11      21      42 ..      40      61 ..      39     117 .. 0.67
   2 !    6.1   0.0    0.0051       3.6     525     569 ..     164     207 ..     154     215 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00015
                         AAA_13 21 iYGwNGaGKTtLSrllrslelg 42
                                   ++G  G+GKTtL+r+l+ l + 
  gi|116754339|ref|YP_843457.1| 40 LFGPSGSGKTTLARILAGLDHP 61
                                   5899**************9542 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0051
                         AAA_13 525 gkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTH 569
                                     + +i ++D P  SLD  ++  + +l+k+   +   +  l+i+ H
  gi|116754339|ref|YP_843457.1| 164 LNPRILILDEPTASLDVSVQAQILNLLKEIQ-RTRGIGYLYISHH 207
                                    5789************************986.7888888888876 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 !   15.1   0.0   1.6e-05     0.011     121     206 ..     125     215 ..      21     225 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.6e-05
                                    HHHHHHHHCTT-STT.......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SE CS
                                    xxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xx RF
                          SMC_N 121 kevsellesagiske.......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQ 191
                                      ++e le +g+s+e       +LSgG+ + +ala  +     +p+ + +lDe  a LD +  +++ +llke + +    
  gi|116754339|ref|YP_843457.1| 125 GIIKEALEVVGLSEEvlcrfprQLSGGQNQRIALARALL---LNPR-ILILDEPTASLDVSVQAQILNLLKEIQRTrgIG 200
                                    34566666666666688888889******9988876543...3454.789*********************655443388 PP

                                    EEEE-SSHHHCCC-S CS
                                    xxxxxxxxxxxxxxx RF
                          SMC_N 192 fivislreemlekad 206
                                    ++ is++  +++ ++
  gi|116754339|ref|YP_843457.1| 201 YLYISHHPAVMRFMS 215
                                    999999998888774 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       0.1        72      36      54 ..      36      54 ..      28      64 .. 0.81
   2 !   13.0   0.0   6.9e-05      0.05     118     172 ..     164     216 ..     136     220 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.1
                           TniB 36 pnlllvGdsnnGKtmivek 54
                                   + l l+G+s  GKt++++ 
  gi|116754339|ref|YP_843457.1| 36 HTLGLFGPSGSGKTTLARI 54
                                   567799*********9875 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 6.9e-05
                           TniB 118 lkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlvGteealralrtD 172
                                    l++r+Li+DE    l   ++ q ++ln+lk ++++  i   ++  + a++ + +D
  gi|116754339|ref|YP_843457.1| 164 LNPRILILDEPTASL--DVSVQAQILNLLKEIQRTRGIGYLYISHHPAVMRFMSD 216
                                    689********9999..6777889**************99999999999888887 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   8.9e-06    0.0064       5      44 ..      41      83 ..      38     207 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 8.9e-06
                         AAA_33  5 vGlpGsGKstlaerllkklg...avllssdtlrrrlfgtdqqs 44
                                    G++GsGK+tla+ l+   +   +v++   +++r ++g + + 
  gi|116754339|ref|YP_843457.1| 41 FGPSGSGKTTLARILAGLDHpssGVVIFNSKELRGMRGHEFTE 83
                                   7************997544467888888888888888855444 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 ?   11.1   0.0    0.0004      0.29       4      22 ..      40      58 ..      37      75 .. 0.83
   2 ?    2.2   0.0      0.22   1.6e+02      59      95 ..     158     196 ..     137     215 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0004
                                   EE--SSSSHHHHHHHGGGG CS
                          AAA_5  4 LvGppGtgKselaerlaaa 22
                                   L Gp+G+gK++la+ la +
  gi|116754339|ref|YP_843457.1| 40 LFGPSGSGKTTLARILAGL 58
                                   89************99876 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.22
                                    ------.G-SEEEEESGGG--.HHHHHHHHHHHHSSEEE CS
                          AAA_5  59 lvraar.egeilvlDEverae.sevlnsLlslleerrll 95 
                                    l ra   +++il+lDE +     +v++  l+ll e ++ 
  gi|116754339|ref|YP_843457.1| 158 LARALLlNPRILILDEPTASLdVSVQAQILNLLKEIQRT 196
                                    455555799*******98666689999999999998776 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 ?   13.9   0.1   4.8e-05     0.034      15      38 ..      28      51 ..      24      70 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.8e-05
                         AAA_29 15 htieidlkgatlltGpsGsGKSTl 38
                                    t+ei++  +  l GpsGsGK+Tl
  gi|116754339|ref|YP_843457.1| 28 VTVEIEEGHTLGLFGPSGSGKTTL 51
                                   677887444677***********9 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.9   8.7e-05     0.062      23      51 ..      34      61 ..      17     204 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.7e-05
                         AAA_16 23 rpelvllsGesGvGKsslvrellralekd 51
                                   +++ + l G+sG+GK++l+r l+  l   
  gi|116754339|ref|YP_843457.1| 34 EGHTLGLFGPSGSGKTTLARILAG-LDHP 61
                                   44677899***********98884.3333 PP

>> AAA_24  AAA 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     0.044       5      23 ..      38      62 ..      34     111 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.1e-05
                         AAA_24  5 iliyGpsgiGKTtlakel......g 23
                                   + ++Gpsg+GKTtla+ l       
  gi|116754339|ref|YP_843457.1| 38 LGLFGPSGSGKTTLARILagldhpS 62
                                   679************9998877532 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 ?   11.3   0.0   0.00044      0.31      63      89 ..     165     191 ..     137     192 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00044
                        SbcCD_C  63 alrlvfLDEAFsklDeesiatllelle 89 
                                    ++r+++LDE  ++lD   +a++l+ll+
  gi|116754339|ref|YP_843457.1| 165 NPRILILDEPTASLDVSVQAQILNLLK 191
                                    489*********************997 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00015      0.11      11      38 ..      26      54 ..      18      58 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00015
                         AAA_23 11 rdqeidFskgltl.ItGpNGaGKTTildA 38
                                   rd++++ + g tl ++Gp G+GKTT+ + 
  gi|116754339|ref|YP_843457.1| 26 RDVTVEIEEGHTLgLFGPSGSGKTTLARI 54
                                   78888887776644***********9865 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00012     0.086       6      62 ..      27      87 ..      24     141 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                                   HHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSS.EEEEEE...ESEEHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx...xxxxxxxxxxxxxx RF
                    ATP-synt_ab  6 DalfpivqGqrtlipgafgvGktvisqslskqsnsdd.aiiyvg...iGergnevaevlee 62
                                   D+ + i +G +++++g +g Gkt++++ l+   + ++ ++i+      G rg+e +e+ ++
  gi|116754339|ref|YP_843457.1| 27 DVTVEIEEGHTLGLFGPSGSGKTTLARILAGLDHPSSgVVIFNSkelRGMRGHEFTEFRRS 87
                                   66778899******************99998866665588886522246666666655544 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00018      0.13      91     122 ..      26      58 ..       6      84 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00018
                                    HHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                    RsgA_GTPase  91 eelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                    ++++ ++++ +t  l G+SG GK+tL   l++ 
  gi|116754339|ref|YP_843457.1|  26 RDVTVEIEEgHTLGLFGPSGSGKTTLARILAGL 58 
                                    55666666669999*************999875 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0    0.0012      0.88      44      68 ..      32      56 ..      20      70 .. 0.87
   2 ?    1.0   0.0      0.44   3.1e+02      97     135 ..     154     191 ..     145     200 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0012
                      IstB_IS21 44 iekkenivllGpsGvGKshlaialg 68
                                   ie+ + + l+GpsG GK+ la  l+
  gi|116754339|ref|YP_843457.1| 32 IEEGHTLGLFGPSGSGKTTLARILA 56
                                   56777889*************8775 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.44
                      IstB_IS21  97 gklaralkrllkvdllilDdlgllpldqaeaellfevie 135
                                    +++a a + ll++++lilD+     ld   +++++++++
  gi|116754339|ref|YP_843457.1| 154 QRIALARALLLNPRILILDEPT-ASLDVSVQAQILNLLK 191
                                    5566666778999******954.3455555555555554 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00018      0.13      20      68 ..      35      84 ..      25     136 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00018
                       ATPase_2 20 neiyfiYGpegsGKtaLlkeiienledkdkyviyyi.alreesiskldef 68
                                    + + ++Gp gsGKt+L + ++   + ++  vi+ + +lr+ + ++++ef
  gi|116754339|ref|YP_843457.1| 35 GHTLGLFGPSGSGKTTLARILAGLDHPSSGVVIFNSkELRGMRGHEFTEF 84
                                   556668************98888887777788886526888888888888 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0091       6.5      22      47 ..      35      60 ..      20      74 .. 0.73
   2 ?    3.5   0.0      0.07        50      96     123 ..     168     196 ..     152     226 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0091
                                   SS-EEEECSTTSSHHHHHHHHHHHST CS
                Sigma54_activat 22 dlsvlitGesGtGKellaraiheask 47
                                     ++ + G sG+GK++lar +    +
  gi|116754339|ref|YP_843457.1| 35 GHTLGLFGPSGSGKTTLARILAGLDH 60
                                   4566689************9876555 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.07
                                    EEEEET.GGGS-HHHHHHHHHHHHHSEEE CS
                Sigma54_activat  96 tlfLDe.igelplelQekLlrvlqegeve 123
                                    +l LDe  ++l++++Q+++l++l+e + +
  gi|116754339|ref|YP_843457.1| 168 ILILDEpTASLDVSVQAQILNLLKEIQRT 196
                                    7899995679*************986544 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00034      0.25       4      21 ..      40      59 ..      38      86 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00034
                         AAA_28  4 itGgestGKTtlleaLa..a 21
                                   ++G++++GKTtl++ La  +
  gi|116754339|ref|YP_843457.1| 40 LFGPSGSGKTTLARILAglD 59
                                   68**************9442 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00034      0.25      35      54 ..      36      56 ..      26      76 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00034
                         RuvB_N 35 hvl.lyGpPGlGkttlakiia 54
                                   h+l l+Gp G Gkttla+i+a
  gi|116754339|ref|YP_843457.1| 36 HTLgLFGPSGSGKTTLARILA 56
                                   555599*************98 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00048      0.34       5      19 ..      42      56 ..      38      65 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00048
                                   -STTSSHHHHHHHHH CS
                 Cytidylate_kin  5 GPagsGKssvarala 19
                                   GP+gsGK ++ar+la
  gi|116754339|ref|YP_843457.1| 42 GPSGSGKTTLARILA 56
                                   **************9 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00032      0.23      24      85 ..      36     102 ..      20     203 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00032
                                    EEEEEEESTTSSHHHHHHHHHHHCS--.....--HHHHHCCHHHHHHHHHHHHHHHHHHHHHTT... CS
                        G-alpha  24 vkllllGqseSGKsTilkqlkllykkg.....fseeelatwraviqlnivrsiktilealeslesel 85 
                                     +l l G s+SGK+T+ + l  l  ++     f+ +el+ +r   ++ + rs++++++  es+ +++
  gi|116754339|ref|YP_843457.1|  36 HTLGLFGPSGSGKTTLARILAGLDHPSsgvviFNSKELRGMRGHEFTEFRRSVQMVFQDPESSLNPM 102
                                    567899***************99888889*****9*9**************9999999888865555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); 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: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1605.88
//
Query:       gi|116754340|ref|YP_843458.1|  [L=309]
Description: oligopeptide/dipeptide ABC transporter, ATPase subunit [Methanosaeta thermophila PT]
Scores for complete 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   74.3   0.0    1.7e-20   73.9   0.0    1.2  1  ABC_tran         ABC transporter
      3e-16   59.7   0.5    6.7e-16   58.6   0.5    1.6  1  oligo_HPY        Oligopeptide/dipeptide transporter, C-termin
    0.00013   21.5   0.1     0.0005   19.6   0.1    1.8  1  SMC_N            RecF/RecN/SMC N terminal domain
    0.00014   21.8   0.4     0.0091   15.8   0.0    2.1  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    0.00037   20.8   0.0     0.0012   19.1   0.0    1.8  1  AAA_22           AAA domain
     0.0016   18.8   0.0     0.0021   18.5   0.0    1.3  1  AAA_16           AAA ATPase domain
     0.0043   16.6   0.0     0.0066   16.0   0.0    1.2  1  AAA_7            P-loop containing dynein motor region
     0.0088   15.4   0.0      0.017   14.5   0.0    1.4  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
  ------ inclusion threshold ------
      0.013   15.3   0.0      0.025   14.3   0.0    1.4  1  AAA_29           P-loop containing region of AAA domain
      0.013   14.6   0.0      0.026   13.6   0.0    1.4  1  T2SSE            Type II/IV secretion system protein
      0.013   15.6   0.0      0.025   14.7   0.0    1.4  1  DUF87            Helicase HerA, central domain
      0.016   14.9   0.0       0.03   14.0   0.0    1.4  1  Sigma54_activat  Sigma-54 interaction domain
      0.019   14.7   0.0       0.05   13.3   0.0    1.6  2  IstB_IS21        IstB-like ATP binding protein
       0.02   15.4   0.0      0.028   14.9   0.0    1.2  1  AAA_23           AAA domain
      0.022   14.0   0.0      0.028   13.7   0.0    1.1  1  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.025   14.2   0.0      0.025   14.2   0.0    1.2  1  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
      0.027   13.7   0.0      0.043   13.0   0.0    1.3  1  NB-ARC           NB-ARC domain
      0.041   13.9   0.0      0.082   12.9   0.0    1.5  1  AAA_5            AAA domain (dynein-related subfamily)
      0.057   13.3   0.0      0.094   12.6   0.0    1.3  1  RsgA_GTPase      RsgA GTPase
      0.086   11.7   0.0        1.3    7.9   0.0    2.0  2  AAA_10           AAA-like domain
       0.13   11.6   0.0       0.18   11.1   0.0    1.2  1  AIG1             AIG1 family
       0.15   11.7   0.0       0.21   11.3   0.0    1.2  1  AAA_15           AAA ATPase domain
       0.16   11.9   0.0       0.23   11.3   0.0    1.4  1  NACHT            NACHT domain
       0.19   12.1   0.1        2.9    8.3   0.0    2.2  2  YqaH             Uncharacterized YqaH-like
       0.19   12.2   0.0       0.32   11.4   0.0    1.4  1  RNA_helicase     RNA helicase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.9   0.0   2.4e-23   1.7e-20       3     136 ..      25     177 ..      23     178 .. 0.91

  Alignments for each domain:
  == domain 1  score: 73.9 bits;  conditional E-value: 2.4e-23
                                    EEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--...SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS..--S-TT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxx....xxxxxxxxxxxxxxxx..xxxxxx RF
                       ABC_tran   3 nvslklkegekvaivGenGaGKStLlkllagllkp...teGeilldgkdlke....qeleslrkeigvlpqe..pqlfpe 73 
                                    +v l l e e++aivGe+G+GKS +++++++ll       G++ ++g dl +    +  ++  +ei++++q+  + l+p 
  gi|116754340|ref|YP_843458.1|  25 DVFLALDEHETLAIVGETGCGKSVIANAILRLLPEnasVTGSVIYRGMDLLKmserEISRIRGREIAIIFQNpsAALNPV 104
                                    6778999*************************98877788999999999888887667777889********98999*** PP

                                    SBHHHH..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    xxxxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  74 ltvren..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                    +++ ++              ++  e++++l  lgl++ + +     p +LSgG+ qr ++a++ + +pk+l++DEpt
  gi|116754340|ref|YP_843458.1| 105 HRILDQvsepllihlnlprhKALHEADRLLIALGLNG-AGRLY---PFQLSGGMNQRAMIACSSVLRPKILMADEPT 177
                                    *999999*********999988899************.55554...8*****************************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 !   58.6   0.5   9.4e-19   6.7e-16       1      65 []     229     288 ..     229     288 .. 0.95

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 9.4e-19
                      oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                                    vE+g++++++ +p HPYTkaL +s+p+        + i+g+ ps  + +eGC+F+pRCpf++++C
  gi|116754340|ref|YP_843458.1| 229 VEMGRTENVLCDPEHPYTKALRESMPDRG-----FKPIPGNTPSMIDPPEGCRFHPRCPFKMDIC 288
                                    8*************************984.....4467*************************** PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1     7e-07    0.0005      25     207 ..      34     218 ..      23     228 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 7e-07
                                    SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTC..HCCCCCC--.BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrs..eklsdlihk.skekasvkkaeveitfdnedkklkiekeevsisr 101
                                    +  aivG+ G+GKs + +Ail +L e+++    s   +  dl++  ++e +++   e++i+f+n++++    ++   i  
  gi|116754340|ref|YP_843458.1|  34 ETLAIVGETGCGKSVIANAILRLLPENAS-VTGSviYRGMDLLKMsEREISRIRGREIAIIFQNPSAA---LNPVHRILD 109
                                    5679********************98655.222211345677777456667788889*********99...444455555 PP

                                    EEETTSEEEEEETTEEE-H.HHHHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HH CS
                                    xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 102 rvkrkgeseykingkevtk.kevsellesagiske......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDek 174
                                    +v++     +++n  + +  +e  +ll   g++        +LSgG  + +++    A  +v +  + + De    LD++
  gi|116754340|ref|YP_843458.1| 110 QVSEPLL--IHLNLPRHKAlHEADRLLIALGLNGAgrlypfQLSGGMNQRAMI----ACSSVLRPKILMADEPTKGLDQS 183
                                    5554444..55554444434888899998888877888888*****6554443....3334444557788********** PP

                                    HHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC-SC CS
                                    xxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxx RF
                          SMC_N 175 nvkkvaellkekskn..aQfivislreemlekadk 207
                                     v++  el+ + +++  a +i+i+++ ++    ++
  gi|116754340|ref|YP_843458.1| 184 MVENALELIGSVRDEssASLIMITHDLDVALSISE 218
                                    *********96665534889999998776655554 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 ?    4.6   0.1     0.035        25       3      35 ..      37      62 ..      36      85 .. 0.77
   2 !   15.8   0.0   1.3e-05    0.0091     219     300 ..     114     211 ..      67     215 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.035
                         AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltde 35
                                   +++G  g+GKS +  a+  l        +++ +
  gi|116754340|ref|YP_843458.1| 37 AIVGETGCGKSVIANAILRLL-------PENAS 62
                                   79***************9984.......44444 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1.3e-05
                         AAA_21 219 r..................gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrlle 280
                                                        ++ l  ++ + l +++lS G+ +  a++ a+ + l + ++l  DEp  gL+ ++++  le
  gi|116754340|ref|YP_843458.1| 114 PllihlnlprhkalheadrLLIALGLNGAGRLYPFQLSGGMNQR-AMI-ACSSVLRP-KILMADEPTKGLDQSMVENALE 190
                                    1333333333456666666777788889999**********998.555.45555555.8********************* PP

                         AAA_21 281 ll...kelsrngaQviltTHSpl 300
                                    l+   +++s+  a +i+ TH+  
  gi|116754340|ref|YP_843458.1| 191 LIgsvRDESS--ASLIMITHDLD 211
                                    **99888888..********965 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.7e-06    0.0012       7      38 ..      35      86 ..      30     213 .. 0.58

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.7e-06
                         AAA_22  7 ilvvtGesGtGKTtllrrlleqldeeakaee....................e 38
                                    l+++Ge+G+GK++ ++ +l+ l+e a+ +                     +
  gi|116754340|ref|YP_843458.1| 35 TLAIVGETGCGKSVIANAILRLLPENASVTGsviyrgmdllkmsereisriR 86
                                   589********************99888877777755555555554444441 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   2.9e-06    0.0021      25     106 ..      34     113 ..      22     219 .. 0.64

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.9e-06
                         AAA_16  25 elvllsGesGvGKsslvrellralekd...ggiflrgkcdqlesaipysa.laqalareellrqlldeaesaeleawrek 100
                                    e + ++Ge G+GKs +++++lr l ++    g +++   d l+++       ++ + r + ++ + +++++ +l++ ++ 
  gi|116754340|ref|YP_843458.1|  34 ETLAIVGETGCGKSVIANAILRLLPENasvTGSVIYRGMDLLKMS----ErEISRI-RGREIAIIFQNPSA-ALNPVHRI 107
                                    7899*****************988888444333455555555333....2233334.22444444444333.55555554 PP

                         AAA_16 101 leeala 106
                                    l+++ +
  gi|116754340|ref|YP_843458.1| 108 LDQVSE 113
                                    444444 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 !   16.0   0.0   9.2e-06    0.0066      30      62 ..      30      62 ..      19      74 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 9.2e-06
                          AAA_7 30 lknkkpvllvGptGtGKtviikdllkkldkeky 62
                                   l+++  + +vG+tG+GK+vi++ +l+ l+++  
  gi|116754340|ref|YP_843458.1| 30 LDEHETLAIVGETGCGKSVIANAILRLLPENAS 62
                                   67788899******************9996554 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   2.4e-05     0.017      18      49 ..      29      60 ..      14      82 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.4e-05
                   Mg_chelatase 18 aaaGgHnlllvGppGsGKtmlakrlpsllppl 49
                                   a   +  l +vG  G+GK+++a+++  llp+ 
  gi|116754340|ref|YP_843458.1| 29 ALDEHETLAIVGETGCGKSVIANAILRLLPEN 60
                                   44444467899*******************86 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.5e-05     0.025      18      46 ..      29      57 ..      22      64 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.5e-05
                         AAA_29 18 eidlkgatlltGpsGsGKSTllDAiqalL 46
                                    +d++++  ++G++G GKS +  Ai  lL
  gi|116754340|ref|YP_843458.1| 29 ALDEHETLAIVGETGCGKSVIANAILRLL 57
                                   567777899****************9998 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.6e-05     0.026     121     156 ..      27      60 ..      10      66 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.6e-05
                          T2SSE 121 vlrkavrerglilvsGgTgsGKttllyallkeinks 156
                                    +l+  + e+ ++ + G Tg GK+++++a+l  ++++
  gi|116754340|ref|YP_843458.1|  27 FLA--LDEHETLAIVGETGCGKSVIANAILRLLPEN 60 
                                    444..459999********************99987 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   3.5e-05     0.025      24      48 ..      34      58 ..      16      68 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.5e-05
                          DUF87 24 rHlAilgsTGsGKSntvavLleell 48
                                   + lAi+g+TG GKS  +  +l+ l 
  gi|116754340|ref|YP_843458.1| 34 ETLAIVGETGCGKSVIANAILRLLP 58
                                   559******************9886 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   4.2e-05      0.03      18      47 ..      29      58 ..      14      67 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.2e-05
                                   HCTSSS-EEEECSTTSSHHHHHHHHHHHST CS
                Sigma54_activat 18 vaktdlsvlitGesGtGKellaraiheask 47
                                   + + + ++ i+Ge+G+GK+++a+ai +  +
  gi|116754340|ref|YP_843458.1| 29 ALDEHETLAIVGETGCGKSVIANAILRLLP 58
                                   455667888***************987655 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   6.9e-05      0.05      44      68 ..      30      54 ..      19      86 .. 0.83
   2 ?   -2.4   0.0       4.7   3.4e+03     103     148 ..     162     209 ..     155     213 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.9e-05
                      IstB_IS21 44 iekkenivllGpsGvGKshlaialg 68
                                   ++++e ++++G +G GKs +a a+ 
  gi|116754340|ref|YP_843458.1| 30 LDEHETLAIVGETGCGKSVIANAIL 54
                                   589*******************984 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.7
                      IstB_IS21 103 lkrllkvdllilDdlgllpldqaeaellfeviekryerrs...iiitsn 148
                                     +++l++++l+ D+  ++ ldq   e+ +e+i +  + +s   i+it +
  gi|116754340|ref|YP_843458.1| 162 CSSVLRPKILMADEP-TKGLDQSMVENALELIGSVRDESSaslIMITHD 209
                                    567778888888885.567777777777777765444433233556655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0     4e-05     0.028      21      43 ..      35      57 ..      21      96 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4e-05
                         AAA_23 21 ltlItGpNGaGKTTildAiklaL 43
                                     +I+G++G+GK+ i +Ai   L
  gi|116754340|ref|YP_843458.1| 35 TLAIVGETGCGKSVIANAILRLL 57
                                   568****************7666 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   3.9e-05     0.028       4      77 ..      36     107 ..      33     119 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.9e-05
                        DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakkeekkkkkeafeklssfinnlsef 77 
                                    + + G++G GK+v+++++l  l  ++   t  ++++  +l++  ++++++ + ++++   f+++s+  n++++ 
  gi|116754340|ref|YP_843458.1|  36 LAIVGETGCGKSVIANAILRLL-PENASVTGSVIYRGMDLLKMSEREISRIR-GREIAIIFQNPSAALNPVHRI 107
                                    5688***************999.78888899999**************9999.****************99954 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   3.5e-05     0.025       6      53 ..      25      71 ..      21     252 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.5e-05
                                   HHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEEESEEH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab  6 DalfpivqGqrtlipgafgvGktvisqslskqsnsddaiiyvgiGerg 53
                                   D+++ + + ++++i+g+ g+Gk+vi++++++   ++ a++   +  rg
  gi|116754340|ref|YP_843458.1| 25 DVFLALDEHETLAIVGETGCGKSVIANAILRLLPEN-ASVTGSVIYRG 71
                                   77778888899*****************99987655.55555444443 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   6.1e-05     0.043      16      42 ..      31      55 ..      18      68 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.1e-05
                                   TTSCSEEEEEEESTTSSHHHHHHHHCC CS
                         NB-ARC 16 delqslvvalvGmgGvGKttlakqiln 42
                                   de +   +a+vG  G+GK+++a+ il+
  gi|116754340|ref|YP_843458.1| 31 DEHE--TLAIVGETGCGKSVIANAILR 55
                                   5666..89***************9987 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   0.00011     0.082       3      36 ..      37      72 ..      35      83 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                                   EEE--SSSSHHHHHHHGGGGB..S--EEEEE--TT- CS
                          AAA_5  3 lLvGppGtgKselaerlaaal..nreveyvqltrdt 36
                                    +vG++G+gKs +a  ++++l  n++v+   ++r++
  gi|116754340|ref|YP_843458.1| 37 AIVGETGCGKSVIANAILRLLpeNASVTGSVIYRGM 72
                                   589******************988888776666665 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00013     0.094      91     121 ..      24      55 ..       6      87 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00013
                                    HHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase  91 eelkellkd.ktsvlvGqSGvGKStLinallp 121
                                    +++  +l++ +t ++vG++G GKS + na+l 
  gi|116754340|ref|YP_843458.1|  24 SDVFLALDEhETLAIVGETGCGKSVIANAILR 55 
                                    555556666699****************9764 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0018       1.3      24      42 ..      36      54 ..      29      63 .. 0.86
   2 ?    1.6   0.0      0.15   1.1e+02     153     195 ..     181     223 ..     155     229 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0018
                         AAA_10 24 sliiGdlGnGKSvlakllv 42
                                    +i+G++G GKSv+a+ + 
  gi|116754340|ref|YP_843458.1| 36 LAIVGETGCGKSVIANAIL 54
                                   59************99885 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.15
                         AAA_10 153 dekvareiarhlesvvkkslaklvfsdgsveeaislekkvtvl 195
                                    d+++++++ +++ sv+++s a l++   + ++a+s+ +++ v+
  gi|116754340|ref|YP_843458.1| 181 DQSMVENALELIGSVRDESSASLIMITHDLDVALSISERIAVM 223
                                    7889999999*********99999877778999**99999997 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00025      0.18       2      22 ..      35      55 ..      34      94 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00025
                                   EEEEESSTTSSHHHHHHHHHT CS
                           AIG1  2 tivlvGktgnGkSaTgNsilg 22
                                   t+ +vG tg+GkS  +N+il+
  gi|116754340|ref|YP_843458.1| 35 TLAIVGETGCGKSVIANAILR 55
                                   6889***************86 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   0.0   0.00029      0.21      17      50 ..      26      60 ..      21     104 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00029
                         AAA_15 17 veidlsee.ltvliGkNnsGKSsilealdlFlnnk 50
                                   v + l+e  +  ++G+ ++GKS i++a+  +l ++
  gi|116754340|ref|YP_843458.1| 26 VFLALDEHeTLAIVGETGCGKSVIANAILRLLPEN 60
                                   556677775779****************9998765 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00033      0.23       2      27 ..      35      60 ..      34     117 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00033
                                   CEEEEC-TTTCHHHHHHHHHHHHCTS CS
                          NACHT  2 lvilqGeaGsGKTtLlqklalawaeg 27
                                   ++++ Ge G+GK++ +  + +++ e+
  gi|116754340|ref|YP_843458.1| 35 TLAIVGETGCGKSVIANAILRLLPEN 60
                                   789****************9988766 PP

>> YqaH  Uncharacterized YqaH-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0     0.004       2.9      42      86 ..      61     106 ..      50     108 .. 0.86
   2 ?    1.3   0.0      0.59   4.3e+02      11      64 ..     185     237 ..     178     242 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.004
                           YqaH  42 ielagsivvlskDlkrlehke.kvvrLyeiaskfakrGlnvsvvkr 86 
                                     ++ gs++ +  Dl ++ ++e   +r  eia  f++    + +v+r
  gi|116754340|ref|YP_843458.1|  61 ASVTGSVIYRGMDLLKMSEREiSRIRGREIAIIFQNPSAALNPVHR 106
                                    5899***************992346778********9999999887 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.59
                           YqaH  11 rekaerliksaeeLvselLaealkegDfegaielagsivv.lskDlkrlehkekv 64 
                                    +e a  li s+++  s   +  +  +D + a++++  i v  + ++  + + e+v
  gi|116754340|ref|YP_843458.1| 185 VENALELIGSVRDESSA--SLIMITHDLDVALSISERIAVmYCGEIVEMGRTENV 237
                                    56666677777777444..556678899999999988854268888888777766 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00045      0.32       2      25 ..      37      60 ..      36      79 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00045
                   RNA_helicase  2 wlyGpsgeGKStlakeLakallkk 25
                                    ++G++g+GKS++a+ + + l ++
  gi|116754340|ref|YP_843458.1| 37 AIVGETGCGKSVIANAILRLLPEN 60
                                   589*************77766544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2218.74
//
Query:       gi|116754341|ref|YP_843459.1|  [L=276]
Description: binding-protein-dependent transport systems inner membrane component [Methanosaeta thermophila PT]
Scores for 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-23   80.9  14.2    9.4e-23   80.9  14.2    1.7  2  BPD_transp_1  Binding-protein-dependent transport system inne
      4e-05   23.5   2.1    5.3e-05   23.1   0.1    2.2  2  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 ?   -3.1   0.3      0.59   5.3e+03     162     169 ..      20      27 ..      11      35 .. 0.44
   2 !   80.9  14.2   1.1e-26   9.4e-23       1     174 [.      89     264 ..      89     269 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.59
                   BPD_transp_1 162 viavllln 169
                                     +a+ll+ 
  gi|116754341|ref|YP_843459.1|  20 FLAFLLIA 27 
                                    11111111 PP

  == domain 2  score: 80.9 bits;  conditional E-value: 1.1e-26
                   BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilg.hlilpviillllsaapyvrlirraalrsl 79 
                                    g+++G+ a+ ++++++d++l+++++++l++P + l+i++         l+ ++i+  +i+++l ++ ++r++r+++l+++
  gi|116754341|ref|YP_843459.1|  89 GTIIGASAG-YFRGWVDEVLMGITDIFLMIPQIPLVIVVA------AFLKpSSITITLIMGILWWTSLARIVRSRVLQVR 161
                                    7899*****.************************999999......7777567777************************ PP

                   BPD_transp_1  80 pkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis..... 154
                                    ++ +veaar+ G s+++i+ + vlPn++ +i++ ++l++++++ + + l+flg    lg++    ++g+ ++++      
  gi|116754341|ref|YP_843459.1| 162 EMAFVEAARVVGFSDRHIILTDVLPNTIHVIMPKFMLTVASAMIAEASLSFLG----LGDPN-AKSWGMIINFAFsrggf 236
                                    *****************************************************....99653.34566666666688999 PP

                   BPD_transp_1 155 ........nggvlalviavlllnlvadi 174
                                              + + +++++l l+ ++++
  gi|116754341|ref|YP_843459.1| 237 lngcwwwyLPPGICITLSILSLVSISML 264
                                    9999666655566666666555555554 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 !   23.1   0.1     6e-09   5.3e-05       8      43 ..       9      43 ..       4      52 .. 0.74
   2 ?   -2.6   0.2      0.61   5.5e+03      24      34 ..     122     132 ..     120     136 .. 0.72

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 6e-09
                         OppC_N  8 rrFkrNklAvvglvilllllliaifaPliaPydp...qd 43
                                   r++++N+ A++ l++ll    iai+ P++aP+dp    +
  gi|116754341|ref|YP_843459.1|  9 RSLLSNPGALIFLAFLL----IAILSPYLAPHDPwkrYE 43
                                   67777777776666665....99**********986533 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.61
                         OppC_N  24 llllliaifaP 34 
                                    l+++++a++ P
  gi|116754341|ref|YP_843459.1| 122 LVIVVAAFLKP 132
                                    56778787755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 2035.10
//
Query:       gi|116754342|ref|YP_843460.1|  [L=308]
Description: binding-protein-dependent transport systems inner membrane component [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.8e-37  126.8  14.3    1.3e-36  126.0  14.3    1.4  1  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
        0.2   12.1   4.8       0.65   10.4   0.1    3.0  3  GlpM          GlpM 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 !  126.0  14.3   1.5e-40   1.3e-36       1     184 [.     109     306 ..     109     307 .. 0.99

  Alignments for each domain:
  == domain 1  score: 126.0 bits;  conditional E-value: 1.5e-40
                   BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf................vilsilghlilpviillllsa 64 
                                    g+llG+la+  r ++ ++l ++++ +++s+P++ la+l +++f                +  +i++h ilpvi+++l+sa
  gi|116754342|ref|YP_843460.1| 109 GTLLGALAG-WRESPSSRLQTFIFLTIYSTPPYFLALLSLYIFgfhlswvpmkgfystgSPENIIHHIILPVILMSLFSA 187
                                    789******.*************************************************99999**************** PP

                   BPD_transp_1  65 apyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtlllea 144
                                        +++r ++++++ + +  +ara+G+ + qi+++++++na+ piit+++l fg+++ ga+++e+++s  G+g+l+ +a
  gi|116754342|ref|YP_843460.1| 188 SRNYMIMRGSVIQERRTLYALYARAKGLYDSQILFRHLFRNAILPIITLIALDFGFIFSGALFIEMVFSMRGMGNLIYSA 267
                                    ******************************************************************************** PP

                   BPD_transp_1 145 ilgydyseisnggvlalviavlllnlvadilqrlldprvr 184
                                    ++++dy+  + g++l+++ +v+  n +ad+l+ +ldprvr
  gi|116754342|ref|YP_843460.1| 268 LMYRDYPVLQ-GSFLVITMMVVTANMIADVLYGILDPRVR 306
                                    **********.****************************8 PP

>> GlpM  GlpM protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   7.3e-05      0.65      49      79 ..     124     154 ..     110     161 .. 0.86
   2 ?    2.1   0.1     0.028   2.5e+02      10      25 ..     179     194 ..     175     205 .. 0.89
   3 ?   -1.8   0.1      0.45   4.1e+03      65      65 ..     270     270 ..     222     300 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 7.3e-05
                           GlpM  49 ealrttilfglwsiipyavylaalyyfserl 79 
                                    + l+t i ++++s  py++ l++ly+f  +l
  gi|116754342|ref|YP_843460.1| 124 SRLQTFIFLTIYSTPPYFLALLSLYIFGFHL 154
                                    678999999*****************98776 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.028
                           GlpM  10 vlliallsksknyyia 25 
                                    v+l++l+s s+ny+i 
  gi|116754342|ref|YP_843460.1| 179 VILMSLFSASRNYMIM 194
                                    899**********984 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.45
                           GlpM  65 y 65 
                                    y
  gi|116754342|ref|YP_843460.1| 270 Y 270
                                    2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); 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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2392.26
//
Query:       gi|116754343|ref|YP_843461.1|  [L=256]
Description: methyltransferase type 12 [Methanosaeta thermophila PT]
Scores for 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-09   36.1   0.0    1.5e-08   35.3   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
      2e-05   25.1   0.0    3.3e-05   24.4   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    4.9e-05   24.0   0.0    0.00012   22.8   0.0    1.6  1  Methyltransf_12  Methyltransferase domain
     0.0002   21.2   0.0    0.00031   20.6   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    0.00058   19.7   0.0      0.001   19.0   0.0    1.5  1  Methyltransf_23  Methyltransferase domain
    0.00084   19.1   0.0     0.0019   18.0   0.0    1.5  2  Met_10           Met-10+ like-protein
     0.0056   16.8   0.0     0.0074   16.4   0.0    1.2  1  FtsJ             FtsJ-like methyltransferase
  ------ inclusion threshold ------
      0.028   14.0   0.0      0.051   13.2   0.0    1.4  1  MetW             Methionine biosynthesis protein MetW
      0.036   14.0   0.0      0.064   13.2   0.0    1.3  1  Methyltransf_18  Methyltransferase domain
      0.055   12.8   0.0      0.078   12.3   0.0    1.2  1  GidB             rRNA small subunit methyltransferase G
      0.061   12.7   0.0      0.089   12.2   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
      0.063   12.9   0.0       0.18   11.4   0.0    1.6  2  Cons_hypoth95    Conserved hypothetical protein 95
      0.064   12.3   0.0      0.089   11.8   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
       0.12   11.7   0.0       0.18   11.1   0.0    1.4  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
       0.18   11.5   0.0        0.3   10.8   0.0    1.3  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 !   35.3   0.0   1.2e-11   1.5e-08       1      92 [.      65     149 ..      65     153 .. 0.88

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 1.2e-11
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEESTGGGSSH CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssgalhhlsd 79 
                                    vLd+G+GtG +++ l++    ++++++D+se +l++  ++a  +g+ n++ ++    d +  d  +D+ +++++l h   
  gi|116754343|ref|YP_843461.1|  65 VLDIGAGTGAFSIPLSRIA--GRIIALDPSEHQLQILMRKA--RGIdNIKAICDRWPDAEIGD-DIDYTLAAYSLFH--- 136
                                    9***************996..9*******************..57779999999888888776.99****9988655... PP

                                    HHHHHHHHHHHHH CS
                Methyltransf_25  80 edlekalkeiarv 92 
                                    ed+e++l+++ +v
  gi|116754343|ref|YP_843461.1| 137 EDIEAFLRRMIDV 149
                                    799******9887 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   2.8e-08   3.3e-05       1      95 [.      66     157 ..      66     158 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 2.8e-08
                                    EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHH CS
                Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpeka 80 
                                    Ld+G+GtG+++ +l + ++r++++D+s+ +l++  +ka++ ++ ++ ++ +  +  + d  +D  ++  +l+h  d e++
  gi|116754343|ref|YP_843461.1|  66 LDIGAGTGAFSIPLSRIAGRIIALDPSEHQLQILMRKARGIDN-IKAICDRWPDAEIGD-DIDYTLAAYSLFHE-DIEAF 142
                                    8**************999**************99888888874.888999999999999.9************9.799** PP

                                    HHHHHHHEEEEEEEE CS
                Methyltransf_11  81 lkeiaRvLkpgGllv 95 
                                    l+ +  v   g ++v
  gi|116754343|ref|YP_843461.1| 143 LRRMIDVSHSGVFIV 157
                                    999998877766555 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   9.9e-08   0.00012       1      91 [.      66     148 ..      66     155 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 9.9e-08
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlk 80 
                                    L+iG+GtG+++ +l +     +++++D+s+++++   +k + ++n ++ + ++ + +++     +  D+ +a+  l h +
  gi|116754343|ref|YP_843461.1|  66 LDIGAGTGAFSIPLSRI--AGRIIALDPSEHQLQILMRKARGIDNIKAICDRWPDAEIG-----DDIDYTLAAYSLFH-E 137
                                    8*************999..**************66666666666666666666666655.....59*******99999.8 PP

                Methyltransf_12  81 direvldnirk 91 
                                    di+++l+++ +
  gi|116754343|ref|YP_843461.1| 138 DIEAFLRRMID 148
                                    ******99865 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   2.6e-07   0.00031       2     108 ..      60     157 ..      59     174 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.6e-07
                Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsn 81 
                                    + g +vlD+G+GtG++++ l +     ++++ +D se+ ++    +a+  g+dn++     + ++e  +  + +D+ l+ 
  gi|116754343|ref|YP_843461.1|  60 HPGSTVLDIGAGTGAFSIPLSRI---AGRIIALDPSEHQLQILMRKAR--GIDNIKAICDRWPDAE--IG-DDIDYTLAA 131
                                    67899****************44...578************9888655..**************99..88.799999998 PP

                Methyltransf_31  82 evlnaladpdkileeiervlkpggill 108
                                      l    d +++l+++++v ++g  ++
  gi|116754343|ref|YP_843461.1| 132 YSL-FHEDIEAFLRRMIDVSHSGVFIV 157
                                    888.44688888888888888665544 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   8.4e-07     0.001      11      61 ..      50     100 ..      31     172 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 8.4e-07
                Methyltransf_23  11 dklerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae 61 
                                    + l+r++    +g+ vLdiG+GtG ++  l++    +++ D+s+++ +i+ 
  gi|116754343|ref|YP_843461.1|  50 RILDRISSLIHPGSTVLDIGAGTGAFSIPLSRIAGRIIALDPSEHQLQILM 100
                                    56667776678899*******************99*********9988764 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.6e-06    0.0019      93     137 ..      54      96 ..      51     114 .. 0.84
   2 ?   -3.1   0.0       4.7   5.6e+03      65      78 ..     184     197 ..     181     198 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.6e-06
                                    HHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHH CS
                         Met_10  93 rlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesv 137
                                    r+ +l+++g +V+d+ AG G f+ip+++   a r++a d   +  
  gi|116754343|ref|YP_843461.1|  54 RISSLIHPGSTVLDIGAGTGAFSIPLSR--IAGRIIALDPSEHQL 96 
                                    8999***********************9..778899988655555 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4.7
                                    EEEEETTEEEEEET CS
                         Met_10  65 tihkEngcrfklDv 78 
                                     i +E g+ f++Dv
  gi|116754343|ref|YP_843461.1| 184 SILREMGYDFEVDV 197
                                    67899*******97 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   6.2e-06    0.0074      16      57 ..      56      94 ..      50     149 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.2e-06
                                   HT-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS CS
                           FtsJ 16 fklfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm 57
                                    +l++pg tv+D+ga++G++s  l++   a g+++a+D  + 
  gi|116754343|ref|YP_843461.1| 56 SSLIHPGSTVLDIGAGTGAFSIPLSRI--A-GRIIALDPSEH 94
                                   45889****************999888..4.89****99776 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.3e-05     0.051       6      31 ..      54      79 ..      51     134 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.3e-05
                           MetW  6 liaelikpgsrvldlGcGdGellell 31
                                    i  li+pgs+vld+G+G G +   l
  gi|116754343|ref|YP_843461.1| 54 RISSLIHPGSTVLDIGAGTGAFSIPL 79
                                   6899****************876555 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   5.3e-05     0.064       5      58 ..      52     103 ..      50     115 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.3e-05
                Methyltransf_18   5 LkaiaslvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeni 58 
                                    L +i sl+++gs+v+DiG+  g  +i l   ++a ++ia D +e+ l+   +++
  gi|116754343|ref|YP_843461.1|  52 LDRISSLIHPGSTVLDIGAGTGAFSIPLS--RIAGRIIALDPSEHQLQILMRKA 103
                                    7899***********************97..7999*******999998776655 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.5e-05     0.078      43     114 ..      57     123 ..      50     160 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.5e-05
                                    GCS-CCC-.EEEETSTTTTTHHHHHHH-TTSEEEEEES-HHHHHHHHHHHHHCT-SSEEEEES-CCCTTTTT CS
                           GidB  43 ellkekrdkviDvGsGaGlPGipLaiarpelkltLleslekkiaFLeevkeelklenveivearaeekqeee 114
                                    +l++    +v+D+G+G G  +ipL+ +     ++ l+++e + + L    ++ +++n++++++r  + +  +
  gi|116754343|ref|YP_843461.1|  57 SLIHPGS-TVLDIGAGTGAFSIPLSRIAGR--IIALDPSEHQLQILM--RKARGIDNIKAICDRWPDAEIGD 123
                                    5566666.7***************866544..457999999999884..56678889999999876655555 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   7.5e-05     0.089     154     194 ..      54      93 ..      50     105 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.5e-05
                           PrmA 154 aleklvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDe 194
                                     + +l+++g++vlD+G+G+G  +i  +++ a +++a+D  e
  gi|116754343|ref|YP_843461.1|  54 RISSLIHPGSTVLDIGAGTGAFSIPLSRI-AGRIIALDPSE 93 
                                    5677899*****************99998.56788888665 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00015      0.18      41      87 ..      61     106 ..      51     116 .. 0.86
   2 ?   -2.0   0.0         2   2.4e+03     130     152 ..     221     243 ..     215     250 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00015
                                    CC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCC CS
                  Cons_hypoth95  41 egarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleel 87 
                                     g++vLD+ aG+Ga ++  lSR a ++++++ +++ ++il ++ + +
  gi|116754343|ref|YP_843461.1|  61 PGSTVLDIGAGTGAFSI-PLSRIAGRIIALDPSEHQLQILMRKARGI 106
                                    4689*************.6*******************998877665 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2
                                    HHHHHHHHHTT-EEEEEEEEEEE CS
                  Cons_hypoth95 130 eevlelleekkllkenalvvvet 152
                                    ee++++l++   l e+ +v + +
  gi|116754343|ref|YP_843461.1| 221 EEIIDYLRNTDRLDEDMMVSFHS 243
                                    88999999999999999998876 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   7.5e-05     0.089      28      72 ..      59     103 ..      48     124 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.5e-05
                                    GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHT CS
                         RrnaAD  28 leekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkl 72 
                                    + +  tvl+ig+G+G+++ +L  +a    +l   e+ +++l  k 
  gi|116754343|ref|YP_843461.1|  59 IHPGSTVLDIGAGTGAFSIPLSRIAGRIIALDPSEHQLQILMRKA 103
                                    45999****************999987777776666666665555 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00015      0.18      46     142 ..      60     149 ..      35     172 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00015
                                    --TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES- CS
                Ubie_methyltran  46 krgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtvsfG 125
                                    ++g++vlD+ +Gtg +++ ls+ +   g+++ lD +e+ L++  +k++  g  ni+ ++    + +  dd  D+   ++ 
  gi|116754343|ref|YP_843461.1|  60 HPGSTVLDIGAGTGAFSIPLSRIA---GRIIALDPSEHQLQILMRKAR--GIDNIKAICDRWPDAEIGDD-IDYTLAAYS 133
                                    5799****************9876...68999********99998876..55666666655544444433.455555555 PP

                                    GGG-S-HHHHHHHHHHH CS
                Ubie_methyltran 126 lrnvtDklkaLkeayrv 142
                                    l    D++  L+ +  v
  gi|116754343|ref|YP_843461.1| 134 LF-HEDIEAFLRRMIDV 149
                                    53.35556666655555 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 ?   10.8   0.0   0.00025       0.3      70     111 ..      56      99 ..      47     114 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00025
                                    T..--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHH CS
                           PCMT  70 e..lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelv 111
                                    +  +++g+ vL++G+G+G  +  l+r+ g+   +   e++ ++ 
  gi|116754343|ref|YP_843461.1|  56 SslIHPGSTVLDIGAGTGAFSIPLSRIAGRIIALDPSEHQLQIL 99 
                                    445899*************9999999988766555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 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:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2029.86
//
Query:       gi|116754344|ref|YP_843462.1|  [L=524]
Description: extracellular solute-binding protein [Methanosaeta thermophila PT]
Scores for complete 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-73  248.3   3.7    1.7e-73  247.8   3.7    1.2  1  SBP_bac_5        Bacterial extracellular solute-binding prote
  ------ inclusion threshold ------
        0.4   10.8   1.3       0.84    9.8   1.3    1.5  1  Myco_arth_vir_N  Mycoplasma virulence signal region (Myco_art


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 !  247.8   3.7   1.9e-77   1.7e-73       2     368 ..      70     430 ..      69     439 .. 0.86

  Alignments for each domain:
  == domain 1  score: 247.8 bits;  conditional E-value: 1.9e-77
                                    EEESSEEEEEEEETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHCTCTEEEEEEEETTEEEEE CS
                      SBP_bac_5   2 vvpaLAeswwevsdDgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyaslleedqdikkveavddytvrft 81 
                                    + ++ A+s ++vs+Dg t++f + +++++sDGt+lt eDv+f+fe++ ++ +++g+ ++       ++   vd + v+f+
  gi|116754344|ref|YP_843462.1|  70 LSGQTAKS-YSVSEDGMTWRFEIDDNLYWSDGTKLTPEDVKFTFEYISEKYPPAGWIKNT------VDEISVDGNAVVFK 142
                                    56789***.8********************************************996665......778889******** PP

                                    ESSETT..TTTTHCHHHHHHHGCCHTCTCTTTTTGTTTS.E-BSSSEEEEEEETTTEEE.EEE-TTSTTTSCSSSSEEEE CS
                      SBP_bac_5  82 lkkpna..lfltllaavpasiakkaaekeddkdkdtnek.pvgtGPYklkefkpgqkiv.lernpdYwgggkpkldrief 157
                                    l+kp++  ++ ++++++ ++ +   +e+ ++++++tne  ++g GP+++++ + g  ++ ++rnp+ w+g++pk+d+ie+
  gi|116754344|ref|YP_843462.1| 143 LNKPYSrlNLEFTTYNILPKHV---WENIEKPTEYTNEGpMIGCGPFVIEKTDLGAGVIyFKRNPY-WKGKEPKIDSIEL 218
                                    ****997667777777777777...677777777777651688*************7775888888.679********** PP

                                    EE-.SHHHHHHHHHTTSSSEE....ESTTCCTHCHHHHHTTEEEEEEEEEEEEEEEEETTTSTGGGSHHHHHHHHHHS-H CS
                      SBP_bac_5 158 kvipdsdaraaalqsGeiddv....aepppsdieqlkeakglkvlyespgggvtylafNtkkppfddkrvRqAlsyAiDr 233
                                     +++++d+   al++G++d +       p + i++lk++ + +  +e+ + g  +l+fN +k+p++d  +R+A++yAi++
  gi|116754344|ref|YP_843462.1| 219 HMYENADVLSMALEKGDVDAYykyaGTYPYTGIQKLKDTGNFDF-VEKDNVGLVFLGFNLNKEPMSDLQFREAMAYAINY 297
                                    ***9999999999*****76655545666777888888888888.*********************************** PP

                                    HHHHHHCTTTSS.EEESSSSTTTSTTCCSCHCCCSHHSHHHHHHHHHHHTT-BCSSTSCEETC.EEEEEEEEETTSHHHH CS
                      SBP_bac_5 234 eeivkavlegya.tpansllppsspgadeeykpaykaydpekAkklLkeaGykdgdggglrek.klkltlllasgspaek 311
                                    +ei+k+   gy+ +p  +++pps++++++++     +ydp+kA++ L+eaGy dg+g g+ e+   + + ll    +  +
  gi|116754344|ref|YP_843462.1| 298 TEILKIDALGYGsVPNRGFVPPSMAYFKDTPAL---KYDPKKARESLEEAGYRDGNGNGILEDpSGNDVKLLLLARSKFQ 374
                                    *****99999885777788********999887...89**************************555556666678899* PP

                                    HHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHCTTESEEEEEEECTTSTTHHHHHH CS
                      SBP_bac_5 312 aiaeliqqqlkkiGikvevktvdwaatylervkdgdfdmillgwgadypdpdnflnp 368
                                    ++ael++++  ++Gi+ve+k+vd  at+ + +++ ++d+ +++ +++    ++   +
  gi|116754344|ref|YP_843462.1| 375 RVAELVKEYISAVGIDVELKVVDD-ATWIKLKDEYQYDLTITRTTPWGMMMHANWGT 430
                                    **********************99.88889999999999999888887666555544 PP

>> Myco_arth_vir_N  Mycoplasma virulence signal region (Myco_arth_vir_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   1.3   9.4e-05      0.84       7      19 ..       6      18 ..       5      25 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 9.4e-05
                Myco_arth_vir_N  7 KKikIltlalvaa 19
                                   KKi+Il+l l+++
  gi|116754344|ref|YP_843462.1|  6 KKIAILVLILATT 18
                                   9*********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (524 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 3682.58
//
Query:       gi|116754345|ref|YP_843463.1|  [L=534]
Description: transposase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.4e-44  148.6   0.0    1.7e-43  147.4   0.0    1.7  1  DUF4277    Domain of unknown function (DUF4277)
    3.3e-12   46.5   0.4    3.9e-11   43.0   0.4    2.1  1  DDE_Tnp_1  Transposase DDE domain


Domain annotation for each model (and alignments):
>> DUF4277  Domain of unknown function (DUF4277)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.4   0.0   1.9e-47   1.7e-43       2     109 .]       4     111 ..       3     111 .. 0.98

  Alignments for each domain:
  == domain 1  score: 147.4 bits;  conditional E-value: 1.9e-47
                        DUF4277   2 evksldhlglvaglidelglaelidelipkksqekvsagevvkalilngLgfvsrpLylfpeffedkplerLlgegveae 81 
                                    +++sldhlg+va+++d+lg+a++id+++pk +q+k++++ +vka++lngLgfv ++Lylfpef+e++p+erLlg+gv+a+
  gi|116754345|ref|YP_843463.1|   4 DTRSLDHLGIVAAVFDRLGIADVIDSRMPKLRQHKLEHSVIVKAMVLNGLGFVGQRLYLFPEFYERLPVERLLGDGVNAS 83 
                                    6899**************************************************************************** PP

                        DUF4277  82 hlnddrlgrtLDklyeagvtklfteial 109
                                    +lndd++grtLD++ye+g+t+lf+eial
  gi|116754345|ref|YP_843463.1|  84 DLNDDAIGRTLDAIYEQGATDLFNEIAL 111
                                    **************************96 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   0.4   4.4e-15   3.9e-11      35     213 ..     162     450 ..     124     451 .. 0.86

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 4.4e-15
                      DDE_Tnp_1  35 gyklhiavdtrsglilsvvitpgnvhdskglkq.lldelrpr....kgklvlaDaGYasaelldtleekgvdyiirlkkn 109
                                     + l +++++  g++l ++ ++gn +d++++++ +l  ++      +  +++aD++  ++++++ l  + +++i r++  
  gi|116754345|ref|YP_843463.1| 162 QFVLSLVTNQD-GIPLFAKAHSGNASDRNTIIEsFL-KIKSGlnleDCAYYIADSAVYTEPNIRMLG-REMKWITRVPAT 238
                                    44566777777.9********************644.4555577889999******888***99999.9********777 PP

                      DDE_Tnp_1 110 tklyrkgaeskrrgrlrkhdrnkiltksqkrrnk.............................................. 143
                                     k+ +   +s  ++ ++++ r+++++++    +                                               
  gi|116754345|ref|YP_843463.1| 239 IKECEMLLDSDVEMVECRDARYRCFSTTSDYGGVqqkwvlyqsepmrdlkaerfenhlekdgtkarrslaklkrreface 318
                                    7777777777788888888888888888887777888888888888888999999999999999999999999999**** PP

                      DDE_Tnp_1 144 .............................................................skkekgdvyyvtntnsell 162
                                                                                                 +k+    + ++  tn+   
  gi|116754345|ref|YP_843463.1| 319 adalketelwardhplyrfshislkkvckradkkrgrpkngeklieiyfidadieldqekvEKTKSRLGRFIIATNDLNI 398
                                    ************************************************************999999999*********** PP

                      DDE_Tnp_1 163 saeevaelyrlRwqiErvFkwlkrk.fgldrlryrglnrveaqllllllaln 213
                                    ++ ++  +y+ + ++Er F++lk+k f+   +++++ +r+ea ++++ l+l+
  gi|116754345|ref|YP_843463.1| 399 DPDTLLSYYKGQQEVERGFRFLKDKsFRVAEVYLKKEERIEALAMIMVLSLM 450
                                    ***********************************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (534 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); 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: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 3597.39
//
Query:       gi|116754346|ref|YP_843464.1|  [L=333]
Description: dienelactone hydrolase [Methanosaeta thermophila PT]
Scores for complete 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-16   60.4   0.0    8.1e-08   32.0   0.0    2.3  2  Peptidase_S9   Prolyl oligopeptidase family
    6.8e-11   41.9   0.0      2e-07   30.5   0.0    2.2  2  Hydrolase_4    Serine aminopeptidase, S33
    1.2e-08   35.9   0.0    1.5e-08   35.6   0.0    1.1  1  Abhydrolase_6  Alpha/beta hydrolase family
    6.7e-08   32.5   0.0      4e-07   29.9   0.0    1.9  1  Abhydrolase_1  alpha/beta hydrolase fold
    4.2e-05   23.2   0.0    0.00092   18.8   0.0    2.5  2  DLH            Dienelactone hydrolase family
    4.5e-05   23.5   0.0       0.17   11.8   0.0    2.1  2  BAAT_C         BAAT / Acyl-CoA thioester hydrolase C terminal
    0.00043   19.1   0.0     0.0024   16.6   0.1    2.2  2  AXE1           Acetyl xylan esterase (AXE1)
     0.0013   18.7   0.0      0.083   12.7   0.0    2.1  2  Abhydrolase_3  alpha/beta hydrolase fold
     0.0034   17.0   0.0      0.024   14.3   0.0    1.9  1  Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
  ------ inclusion threshold ------
      0.088   12.6   0.0       0.23   11.2   0.0    1.6  2  Abhydrolase_2  Phospholipase/Carboxylesterase


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 !   26.0   0.0   3.1e-09   5.5e-06      10     119 ..      75     177 ..      66     195 .. 0.78
   2 !   32.0   0.0   4.5e-11   8.1e-08     141     191 ..     243     296 ..     213     307 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 3.1e-09
                                    HHCCT-EEEEE--TTSSTTHCHHHHTTSGGGGHHHHHHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHHHHHHH-GGG- CS
                   Peptidase_S9  10 ladrGyvvvvanirGsggyGeafhdagkrklgqnefdDfiaaaealakegyvdserlaitGgSyGGyltgaalnqrpdlF 89 
                                    l+++G++ +  + rG g+   + +d g+ + g     D +aa +al + ++vd+er+a+ G S+G y++  +++ + ++ 
  gi|116754346|ref|YP_843464.1|  75 LSAEGFATFSWDRRGFGESESSIRDGGYLQDGI----DAMAAYQALSSLDLVDPERVAVLGQSAGVYTACLLAE-KESRP 149
                                    6789*********************99999885....99**************************999988888.77777 PP

                                    SEEEEESE---CCCHHCSTTSTHH.HCCCC- CS
                   Peptidase_S9  90 kaavaevpvvdvlrydsdtdllte.eymewg 119
                                    ka + + + +     +     ++  ++ ++ 
  gi|116754346|ref|YP_843464.1| 150 KAYILQGGLYRDYEEMMI---FNYlRVVDYA 177
                                    888888777755555544...4555555555 PP

  == domain 2  score: 32.0 bits;  conditional E-value: 4.5e-11
                                    -..---EEEEEEETT-SSS-THHHHHHHHHHH--S-S.EEEEEETTS-SSTTSS CS
                   Peptidase_S9 141 k..aypplLlihGlaDdrvppaealklvaaLqkkgkn.vlllifpdegHgvgkp 191
                                    +  +++p+L+ihG  D +vp++ a+++ + L+k+g++ v+l i pd++H++++ 
  gi|116754346|ref|YP_843464.1| 243 FkyIQKPTLVIHGACDLNVPVEDAFMIERDLKKHGNEnVELAIIPDADHSFQQI 296
                                    34789********************************************99864 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0   1.1e-10     2e-07      19     118 ..      67     166 ..      64     194 .. 0.74
   2 !    9.2   0.0   0.00036      0.65     189     233 ..     245     292 ..     224     295 .. 0.89

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 1.1e-10
                    Hydrolase_4  19 ryaelaeaLaaqGfavyalDhrGhGrse...gkrghvpsfddyvdDlaafvekvkeehpelplfllGhSmGGliallyll 95 
                                     + e+ ++L a+Gfa++ +D rG+G+se      g++++  d ++  +a+ + +    pe ++ +lG+S G ++a+l+++
  gi|116754346|ref|YP_843464.1|  67 FFLEISKRLSAEGFATFSWDRRGFGESEssiRDGGYLQDGIDAMAAYQAL-SSLDLVDPE-RVAVLGQSAGVYTACLLAE 144
                                    577899*********************95544444444444444433333.444444454.59****************8 PP

                    Hydrolase_4  96 rypdkvaglilsaPalkikaklk 118
                                    ++++  ++ il + +++  +++ 
  gi|116754346|ref|YP_843464.1| 145 KESR-PKAYILQGGLYRDYEEMM 166
                                    8888.89****999998877764 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00036
                    Hydrolase_4 189 kitlPllllhGeaDkvvdpeas...relyerlgskdktlklypglyHe 233
                                     i+ P+l++hG+ D  v+ e++   ++ +++ g ++++l+++p + H+
  gi|116754346|ref|YP_843464.1| 245 YIQKPTLVIHGACDLNVPVEDAfmiERDLKKHGNENVELAIIPDADHS 292
                                    5789******************9997778888889**********997 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.0   8.2e-12   1.5e-08       1     211 [.      38     295 ..      38     306 .. 0.59

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 8.2e-12
                                    EEEE--............GC.....G...CHHHH.HHHHCCTCEEEEE--TTSTS-..GGCS--HHHCHHHHHHHCCTT. CS
                  Abhydrolase_6   1 vlllHG............agssassW...lvapL.aallaagvhvlapDlpGhGrs..dpppldledladlaalldelaa 62 
                                    vll+HG             + ++ ++   ++ ++  +l+a+g+++++ D++G+G+s  + ++ ++  l+d  ++ ++  a
  gi|116754346|ref|YP_843464.1|  38 VLLIHGsleqdrdgnllnRPDGRPIFkknFFLEIsKRLSAEGFATFSWDRRGFGESesSIRDGGY--LQDGIDAMAAYQA 115
                                    789999666666666555445566675433335577777777************55113344444..5555444444444 PP

                                    ........TTSEEEEEETCHHHHHHHHHHCC......EE.EEES-..----TTTS----TTHH...HHHHTT-CCCCHCC CS
                  Abhydrolase_6  63 .......gggpvvlvGHSlGGalalaaapla....lvvg.vlldppptalpagllaaalelll...allallrllawlsr 127
                                           ++ +v ++G S G + a++   la    +  + +l  +    +++ +  +++++l+    + ++   l+w+ +
  gi|116754346|ref|YP_843464.1| 116 lssldlvDPERVAVLGQSAGVYTACL---LAekesRPKAyILQGG---LYRDYEEMMIFNYLRvvdYASKSPENLRWVEE 189
                                    45566677888*********888888...5544454444688888...77777755555554422144445555888877 PP

                                    H.............S-HSCCCCHHHC............CCCHCHCCCGHHHHCCHHCHTTCCHHTT-TTGCEEE.CTT-C CS
                  Abhydrolase_6 128 e.............plprlfladeda............daawrarlarlaallaglgllpaaawadlpvpllvl.ggeDp 181
                                    +             ++ r       a             ++wr ++++ + l  +     +  ++ +  p+lv+ g+ D 
  gi|116754346|ref|YP_843464.1| 190 NdplglviglnlytLMER-------ArmgevehqfsykGRTWRIWHDPICYLPEHAP---RNLFKYIQKPTLVIhGACDL 259
                                    654444443333331111.......01222233344457888888877776666555...44555555555666555555 PP

                                    ........HHHHCHHCCCHSTTEEETCE...SSS-HHH CS
                  Abhydrolase_6 182 ........lvprllerllaqagarlpvvlpgaGHlphl 211
                                            ++ r l++++  + ++l  ++p+a+H++++
  gi|116754346|ref|YP_843464.1| 260 nvpvedafMIERDLKKHGN-ENVEL-AIIPDADHSFQQ 295
                                    3333222666677777777.99999.********8766 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0   2.2e-10     4e-07       1     227 [.      36     263 ..      36     295 .. 0.69

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 2.2e-10
                                    SEEEEE-STTT.................CGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHH...SHHHHH CS
                  Abhydrolase_1   1 pvlvilhGlpg.................ssdvwaerglapaLakdgfdvillDlrGvgySspapacinddy...gtasva 60 
                                    p+++++hG ++                   + + e  + + L+ +gf ++  D rG+g+S+ +++     y   g++++a
  gi|116754346|ref|YP_843464.1|  36 PAVLLIHGSLEqdrdgnllnrpdgrpifKKNFFLE--ISKRLSAEGFATFSWDRRGFGESESSIRD--GGYlqdGIDAMA 111
                                    67888888888877665555555333322333555..66667777********************9..778555555555 PP

                                    HHHHHH.HHHCTTSSEEEEEETHHHHHHHHHHHHHGGGEEEEEEESE..CSSCCHHHHHHHHHHHHHHCHHCHHHHHHHH CS
                  Abhydrolase_1  61 ddldri.ldalgddkltlvGhSmGGmialayaaeyperVkalvllga..idpaaslieaqrqqaksfpdffdgyaadcar 137
                                    ++     ld  + ++++++G+S G  +a+ +a++  +r ka +l g+   d+  ++i   ++ +    +  ++ + ++++
  gi|116754346|ref|YP_843464.1| 112 AYQALSsLDLVDPERVAVLGQSAGVYTACLLAEK-ESRPKAYILQGGlyRDYEEMMIFNYLRVVDYASKSPENLRWVEEN 190
                                    5555336**************************8.88899*******999999999998888888888888888888888 PP

                                    HHHHHHHHCCSCHHHHHHHHHHHHHHHCHHHCCHHHHHHHCHHHHHHHHHHHHHHHHCCHHHHHHHHHCTHHHHSEEEEE CS
                  Abhydrolase_1 138 npagplladelaaleqrhrlvdalkfpdkskrfpssgsdnasslatgalksieqwpttdsaklllrlrelknvlaptlvi 217
                                     p+g+ ++  l +l  r r           +  + ++s+   ++  ++   i + p+++ ++l+  +++      ptlvi
  gi|116754346|ref|YP_843464.1| 191 DPLGLVIGLNLYTLMERARM----------GEVEHQFSYKGRTWRIWH-DPICYLPEHAPRNLFKYIQK------PTLVI 253
                                    88888888888888777553..........333333334444444444.55667777777777777777......77777 PP

                                    EETTCSSSCH CS
                  Abhydrolase_1 218 sgtsDplvpp 227
                                    +g+ D  vp 
  gi|116754346|ref|YP_843464.1| 254 HGACDLNVPV 263
                                    7766666655 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.094   1.7e+02      82     121 ..     109     148 ..      64     159 .. 0.73
   2 !   18.8   0.0   5.1e-07   0.00092     136     215 ..     239     331 ..     212     333 .] 0.83

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.094
                            DLH  82 lkaavaylksvpevstkkvgvvGfCmGGalalllaaevpe 121
                                    + aa ++l s   v++++v+v G   G   a lla ++ +
  gi|116754346|ref|YP_843464.1| 109 AMAAYQALSSLDLVDPERVAVLGQSAGVYTACLLAEKESR 148
                                    2367777777788888888888888888888888887755 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 5.1e-07
                            DLH 136 eleeaakikapilalfgeeDefipadevekleealkaa.nvdlelkvYpgagHaFandsre............syneeaa 202
                                    + +  + i++p l+++g  D  +p +++  +e  lk++ n ++el + p+a+H+F +  ++            s++    
  gi|116754346|ref|YP_843464.1| 239 PRNLFKYIQKPTLVIHGACDLNVPVEDAFMIERDLKKHgNENVELAIIPDADHSFQQIAESydltlrermsleSFRRPYR 318
                                    55667789***************************99835789************9877777777777777777777777 PP

                            DLH 203 edawervlelfkq 215
                                    ed + +v++++k+
  gi|116754346|ref|YP_843464.1| 319 EDYFMAVISFLKR 331
                                    7777777777776 PP

>> BAAT_C  BAAT / Acyl-CoA thioester hydrolase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   9.3e-05      0.17       9      84 ..     112     186 ..     110     220 .. 0.83
   2 !    9.6   0.0   0.00043      0.77     114     163 ..     246     293 ..     230     295 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.3e-05
                                    HHHHHHCSTTB--SSEEEEEETHHHHHHHHHHHHSSSEEEEEEES--SB--SSEEEETTE..EE----B-GGG-EE CS
                         BAAT_C   9 ainyllrhpkvkkdkigllGiSkGgelalllasflkkisavvlingsavvvegklvykdeskvlpelklsmeklkv 84 
                                    a++ l++   v  +++++lG+S G  +a lla + + ++a +l  g    +e+  ++++  +v+ + ++s e+l +
  gi|116754346|ref|YP_843464.1| 112 AYQALSSLDLVDPERVAVLGQSAGVYTACLLAEKESRPKAYILQGGLYRDYEEMMIFNYL-RVVDYASKSPENLRW 186
                                    7788999999*******************************9998887777777777766.888888888887777 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00043
                                    --SEEEEEEETT-SSS-HHHHHHHHHHHHHCTT--.--EEEEETTB-S-- CS
                         BAAT_C 114 akgpillvvgedDknwpSkesaekaserLkkagkkvevqlltYpkaGHli 163
                                    ++ p l++ g  D n+p ++   ++++ Lkk+g++ +v+l + p+a H +
  gi|116754346|ref|YP_843464.1| 246 IQKPTLVIHGACDLNVPVEDAF-MIERDLKKHGNE-NVELAIIPDADHSF 293
                                    67899************88877.************.****999**99976 PP

>> AXE1  Acetyl xylan esterase (AXE1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.38   6.8e+02      65      95 ..      17      47 ..      11      54 .. 0.82
   2 !   16.6   0.1   1.3e-06    0.0024     156     203 ..     107     154 ..      74     181 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.38
                                   GGEEEEEEEEEES.SSSSEEEEEEEE-TT-- CS
                           AXE1 65 rgarikaklvlPkekeeklPavvefhGYegs 95
                                   + +r+ + l  P+  +++ Pav+  hG  ++
  gi|116754346|ref|YP_843464.1| 17 GSSRLAGVLRYPSVIKDPAPAVLLIHGSLEQ 47
                                   5689999999**************9997665 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1.3e-06
                                    HHHHHHHHHHHTSTTEEEEEEEEEEETHHHHHHHHHHHH-SS-SEEEE CS
                           AXE1 156 lDavrlveivaslpevDeeRvavlGasqGGalalavaalekrikavva 203
                                    +Da+ + ++++sl+ vD+eRvavlG+s G   a   a  e+r+ka + 
  gi|116754346|ref|YP_843464.1| 107 IDAMAAYQALSSLDLVDPERVAVLGQSAGVYTACLLAEKESRPKAYIL 154
                                    6999*************************9888888888888887665 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   4.6e-05     0.083      51      92 ..     108     143 ..     102     194 .. 0.76
   2 ?    4.1   0.0     0.021        37     166     210 ..     247     294 ..     197     295 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.6e-05
                                    HHHHHHHHHHHTHHHHTETTCEEEEEEETHHHHHHHHHHHHH CS
                  Abhydrolase_3  51 dalaalrwlaeqawelgadpsrivlaGdSaGGnlaaavalra 92 
                                    da+aa++ l +      +dp+r++++G+SaG   a   +l a
  gi|116754346|ref|YP_843464.1| 108 DAMAAYQALSSL---DLVDPERVAVLGQSAGVYTA---CLLA 143
                                    677777777776...57**************4433...3333 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.021
                                    ---EEEEEETT-TTH..HHHHHHHHHHHHTT-.-EEEEEETTEETTGG CS
                  Abhydrolase_3 166 lpptlvvvaefDplr..degeayaerlraagv.evelieyegmvHgfa 210
                                     +ptlv+ + +D+    +++ +  + l+++g+ +vel  ++++ H+f+
  gi|116754346|ref|YP_843464.1| 247 QKPTLVIHGACDLNVpvEDAFMIERDLKKHGNeNVELAIIPDADHSFQ 294
                                    579******9998752166777789999976527************96 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 !   14.3   0.0   1.3e-05     0.024      53     258 ..      75     278 ..      32     292 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.3e-05
                                    HHHTT-EEEEEE-TTSTTS-S---TT.TTTHHHHHHHHHHHHHHC.TTEEEEEEEEEECHHHHHHHHHCTT--TTEEEEE CS
                  Peptidase_S15  53 fvarGYavVvqdvrGtggSeGeftvg.dsdeaedgadvidWlakq.pwsnGkVgmtGiSYlGttqllaaatgvpalkaiv 130
                                    + a+G+a    d rG+g+Se  +  g   ++  d+ ++ + l         +V+++G S + +t+ l+a+ +  + ka +
  gi|116754346|ref|YP_843464.1|  75 LSAEGFATFSWDRRGFGESESSIRDGgYLQDGIDAMAAYQALSSLdLVDPERVAVLGQSAGVYTACLLAE-KESRPKAYI 153
                                    6799****************9998886889999***********989999*****************999.888999999 PP

                                    EECE-S-TCCC.CSECTTEEBCCHHHHHHHHHCCCCHHTSSS-STTHHHHHHHHHHCHCCCCCCTTHHH....THHHHCC CS
                  Peptidase_S15 131 peaaisdlydd.yyregGlvrapgglswedldllaealtsrradegdalkaaaryeaasdellaeldrq....tpvesel 205
                                     + ++   y++ +++++  v+  +  s      l   + + +++ g  +     y+ +++  ++e++ q       ++ +
  gi|116754346|ref|YP_843464.1| 154 LQGGLYRDYEEmMIFNYLRVVDYASKSP---ENLR--WVEENDPLGLVIG-LNLYTLMERARMGEVEHQfsykGRTWRIW 227
                                    9999888888855554433333222222...2222..2222222222222.22244444445555555522223333333 PP

                                    CC--SSSHHHHTT-HHHHHCT--S-EEEEEECCSSTTC.CHHHHHHHHHCCTT- CS
                  Peptidase_S15 206 letgdydafWkdrnlsedadkvkapvllvgGwnDwnvk.ngaiklyealkapgv 258
                                    ++   y +    rn    ++ ++ p+l+++G  D nv  + a+ + + lk++g 
  gi|116754346|ref|YP_843464.1| 228 HDPICYLPEHAPRN---LFKYIQKPTLVIHGACDLNVPvEDAFMIERDLKKHGN 278
                                    33333333333333...3378888888888888888777777666666666655 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       3.2   5.8e+03     101     119 ..     117     139 ..      94     153 .. 0.70
   2 ?   11.2   0.0   0.00013      0.23     143     202 ..     235     294 ..     227     298 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.2
                                    T....--GGGEEEEEETHHHHHH CS
                  Abhydrolase_2 101 g....ipssriiigGFSqGaala 119
                                    +    ++ +r+++ G S G   a
  gi|116754346|ref|YP_843464.1| 117 SsldlVDPERVAVLGQSAGVYTA 139
                                    14555888999999999886655 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00013
                                    GGGTTTTS-GGGGG-EEEEEEETT-SSS-HHHHHHHHHHHHTTS-.GEEEEEETT--SS-- CS
                  Abhydrolase_2 143 sqklessatavtkklpilqiHgeeDpvvplalgkaakevlkkllk.kvelksyeglaHsid 202
                                    ++  + + ++   + p l iHg +D  vp+  + + +  lkk  + +vel ++++  Hs  
  gi|116754346|ref|YP_843464.1| 235 PEHAPRNLFKYI-QKPTLVIHGACDLNVPVEDAFMIERDLKKHGNeNVELAIIPDADHSFQ 294
                                    555566666666.67999*************************999************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2406.88
//
Query:       gi|116754347|ref|YP_843465.1|  [L=301]
Description: transport system permease protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-90  303.1  33.3    2.2e-90  302.8  33.3    1.0  1  FecCD     FecCD transport family
  ------ inclusion threshold ------
        3.2    7.9  16.1        0.3   11.3   5.8    2.7  4  IspA      Intracellular septation protein A


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 !  302.8  33.3   2.5e-94   2.2e-90      31     311 ..      12     294 ..       3     295 .. 0.98

  Alignments for each domain:
  == domain 1  score: 302.8 bits;  conditional E-value: 2.5e-94
                          FecCD  31 dsleaeivlelrlprvlaallvGaaLavaGallQtvtrNpLadPsilGissgaalgavlallll..lgslslfalplaaf 108
                                    d++ +++v+ lrlpr+l+++++Ga+L+v+Ga++Q+vtrNpL++P ++Giss+aa+ga +a++++  +++++++ ++l af
  gi|116754347|ref|YP_843465.1|  12 DPFVESVVWHLRLPRILMGIVAGAGLGVSGAVMQGVTRNPLVSPFTVGISSAAAFGASMAIMFGvgYTAAGTYVIILSAF 91 
                                    677889************************************************************************** PP

                          FecCD 109 lgallalllvlllarkrkgasplkliLaGiavsallsaltsllllllneealesilfwllGslsgaswskvllllvllll 188
                                    ++a+   +lv++++ + k++sp++++LaGia+++++++lt++l++++ne++l+++++w++G+lsga+w+++ +++++ ll
  gi|116754347|ref|YP_843465.1|  92 ISAIGCGFLVFFIS-RLKRSSPETMVLAGIALTYFFGSLTAILQFFANEQQLNAMVNWTFGTLSGADWHRLTIVAAAYLL 170
                                    **************.***************************************************************** PP

                          FecCD 189 llllllllarkldllal.gdetAkslGvnvervrllllllvalltavavalvGpigFvGLivPhiarllvgadhrkllpl 267
                                    ++++l+ ++ +l+++ + gde AkslG+nv+rvr + lll++++ta++v+++G+igFvGL++Ph+ar+++g+dhr ll++
  gi|116754347|ref|YP_843465.1| 171 VMPVLVRFSWDLNIMFTgGDEAAKSLGINVARVRNVSLLLSSFITAAIVCFTGIIGFVGLVAPHVARMVLGSDHRFLLLA 250
                                    **************987369999********************************************************* PP

                          FecCD 268 sallGallllladllarlllsptelpvgivtaliGapffiylll 311
                                    s+++Ga+l++ adl++r++l+p+ +p+giv++++G+p+f+yl++
  gi|116754347|ref|YP_843465.1| 251 SCIVGAILVIGADLVGRTILAPIIIPIGIVISFVGVPMFLYLMM 294
                                    ******************************************97 PP

>> IspA  Intracellular septation protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   5.8   3.3e-05       0.3      10      69 ..      71     134 ..      64     151 .. 0.88
   2 ?    4.4   0.5    0.0043        39      94     133 ..     135     175 ..     132     187 .. 0.84
   3 ?   -3.0   0.1      0.78     7e+03      49      64 ..     210     225 ..     192     235 .. 0.59
   4 ?   -3.5   0.0       1.1     1e+04      83     102 ..     252     271 ..     243     275 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.3e-05
                           IspA  10 lilFfvayklag....illAtavlivatvlqiailklrtrkvekmqlislvlvvvfGgltlllh 69 
                                     i+F v y+ ag    il A + +i   +l ++i++l+    e+m l  ++l+ +fG+lt +l+
  gi|116754347|ref|YP_843465.1|  71 AIMFGVGYTAAGtyviILSAFISAIGCGFLVFFISRLKRSSPETMVLAGIALTYFFGSLTAILQ 134
                                    5899999*96666666899999**************************************9986 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0043
                           IspA  94 lilkknllkrllgkele.LpdevWrkLnlawalfflvlavl 133
                                    ++ + + l+++++ ++  L+ + W++L++  a++ lv+ vl
  gi|116754347|ref|YP_843465.1| 135 FFANEQQLNAMVNWTFGtLSGADWHRLTIVAAAYLLVMPVL 175
                                    56677888888888885599****************99876 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 0.78
                           IspA  49 kmqlislvlvvvfGgl 64 
                                       +i++++v++ G +
  gi|116754347|ref|YP_843465.1| 210 LSSFITAAIVCFTGII 225
                                    3456666666666655 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 1.1
                           IspA  83 vlfalvLllsllilkknllk 102
                                    ++++++L++++ ++++++l 
  gi|116754347|ref|YP_843465.1| 252 CIVGAILVIGADLVGRTILA 271
                                    45667777777666777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       861  (0.0480228); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); 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):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 2233.30
//
Query:       gi|116754348|ref|YP_843466.1|  [L=354]
Description: periplasmic binding protein [Methanosaeta thermophila PT]
Scores for complete 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  159.2   0.0    1.4e-46  159.0   0.0    1.1  1  Peripla_BP_2  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.0   0.0   8.1e-51   1.4e-46       5     235 ..      57     299 ..      53     302 .. 0.92

  Alignments for each domain:
  == domain 1  score: 159.0 bits;  conditional E-value: 8.1e-51
                                    SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT....TS-BSBESSSB-HHHHHHH--SEEEE-GGG......GGGHHHH CS
                   Peripla_BP_2   5 spsvteillalGatdkvvgvdtttsdpldadklee..aivevgadgeidvEklaalkPDlvilskgl...gltdedeell 79 
                                     +  ++   alGa d++vg d +t+d+ d+  l+e  ++++vg+  e+++Ek+a+lkPD+vi  + +   ++ + +e+l+
  gi|116754348|ref|YP_843466.1|  57 WSNAAKEMRALGAVDRIVGMDQSTKDEVDKGTLPEltNVPVVGTQEEPNYEKIAELKPDVVICLSAGyppEPDEVQEKLD 136
                                    4555555679**************************************************99655555999999999999 PP

                                    HHHS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT...-EEEEEEEETTE...EEEE-T CS
                   Peripla_BP_2  80 ksgiptvivessntgeslkeqiralgellgledeaeklvaeidsklaaaksaidse..kpkpvlvfggade.ggyvvags 156
                                      gi++v  ++  t e + ++ir+lg++lg+e+eae++++++ s ++++++ ++++   ++++++f ga +  +y  ag 
  gi|116754348|ref|YP_843466.1| 137 PFGIKVVGLDFYRT-EVWFDEIRTLGKMLGKEAEAEEYMSFFRSYYDRINQTLATIpdPDRKTVYFEGAKKyLTYGGAGY 215
                                    99************.******************************************99999999999999445556788 PP

                                    TSTTTHHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEH......HHHT-S--HHHHT-SHHHHTSHHHHTT- CS
                   Peripla_BP_2 157 nsyigdlldalgieniaaeskkseyeeisaEqilasdpdvifvsgr......aeadnktgleflkenpllaelpAvkngr 230
                                    +s+i  +++a+g++++++e  ++ + e+++E ++ ++pdvif  ++       e++ k++ ++++++p+la+++Avkng+
  gi|116754348|ref|YP_843466.1| 216 GSGIPNMIRAAGGKDLYPER-SELAFEVDPEDVARRNPDVIFKGTTlgwdaeSEEEFKAIRDEIMSRPELANTNAVKNGQ 294
                                    9999****************.*****************************9999999*********************** PP

                                    EEEE- CS
                   Peripla_BP_2 231 Vyald 235
                                    Vy + 
  gi|116754348|ref|YP_843466.1| 295 VYVIS 299
                                    **985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); 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 0.22s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2730.41
//
Query:       gi|116754349|ref|YP_843467.1|  [L=178]
Description: adenylylsulfate kinase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-32  111.9   0.0    3.2e-32  111.6   0.0    1.1  1  APS_kinase       Adenylylsulphate kinase
    2.8e-15   56.7   0.0    4.4e-15   56.1   0.0    1.2  1  AAA_33           AAA domain
    8.5e-09   35.2   0.0      1e-08   35.0   0.0    1.0  1  KTI12            Chromatin associated protein KTI12
    2.9e-08   34.3   0.0    3.9e-08   33.9   0.0    1.1  1  AAA_18           AAA domain
    3.1e-06   27.1   0.1    1.8e-05   24.7   0.1    2.1  1  CPT              Chloramphenicol phosphotransferase-like prot
      5e-05   23.7   1.4      0.014   15.8   0.3    2.2  2  AAA              ATPase family associated with various cellul
    0.00011   21.5   0.1     0.0022   17.3   0.0    2.5  3  Zeta_toxin       Zeta toxin
    0.00023   20.3   0.0    0.00038   19.5   0.0    1.3  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
    0.00029   20.2   0.3     0.0021   17.4   0.3    1.9  1  6PF2K            6-phosphofructo-2-kinase
    0.00039   20.4   0.0    0.00067   19.6   0.0    1.5  1  NTPase_1         NTPase
     0.0007   20.0   0.0     0.0011   19.4   0.0    1.3  1  AAA_16           AAA ATPase domain
     0.0008   19.2   0.0     0.0015   18.3   0.0    1.4  1  PRK              Phosphoribulokinase / Uridine kinase family
    0.00091   19.7   0.3     0.0059   17.0   0.3    2.0  1  AAA_17           AAA domain
     0.0094   16.3   0.0      0.028   14.8   0.0    1.8  1  RNA_helicase     RNA helicase
  ------ inclusion threshold ------
      0.011   15.2   0.0      0.016   14.6   0.0    1.2  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.013   15.3   0.0      0.022   14.5   0.0    1.3  1  ATP_bind_1       Conserved hypothetical ATP binding protein
      0.019   15.2   1.5       0.14   12.4   0.2    2.2  2  AAA_28           AAA domain
      0.022   15.1   0.1      0.038   14.2   0.1    1.7  1  AAA_22           AAA domain
      0.027   14.5   0.0      0.055   13.5   0.0    1.5  1  AAA_14           AAA domain
      0.031   14.3   0.2        0.1   12.6   0.1    2.0  2  AAA_5            AAA domain (dynein-related subfamily)
      0.037   13.7   0.2       0.11   12.2   0.0    1.8  2  Thymidylate_kin  Thymidylate kinase
      0.041   14.0   0.0        5.8    7.0   0.0    2.2  2  SKI              Shikimate kinase
      0.052   13.3   0.0      0.075   12.8   0.0    1.3  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.056   13.1   0.0       0.15   11.7   0.0    1.6  2  SRP54            SRP54-type protein, GTPase domain
      0.057   13.1   0.1       0.12   12.1   0.1    1.4  1  AAA_30           AAA domain


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 !  111.6   0.0   4.4e-35   3.2e-32       3     155 ..       3     158 ..       1     161 [. 0.95

  Alignments for each domain:
  == domain 1  score: 111.6 bits;  conditional E-value: 4.4e-35
                                    EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT--SSHHHHHHHHHHHHHHHHHHHHTT-EEEEE-- CS
                     APS_kinase   3 vvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLgfseedRkenirrvaevaklladaglivlvafi 82 
                                      vw+tGl g GK+tia++ +++L ++g++v++L+ d++R+ ++ +  +++e+R+     +a +akll dag+ v++ + 
  gi|116754349|ref|YP_843467.1|   3 WAVWFTGLPGCGKTTIARRTKEHLSRMGVKVKILELDEIRRVVTPNPRYTDEERDIVYASLAYMAKLLCDAGVNVIIDAT 82 
                                    579***************************************************************************** PP

                                    --SHHHHHHHHHHHHCHTEEEEEEEE--HHHHHHHT........TTSHHHHHHTTSSSSHTTTSS-----SS-SEEEETT CS
                     APS_kinase  83 sPyreeReaarelleealkfievfvdtplevceerD........pkglYkkareGeikeftGidspYeaPenpelvvdtd 154
                                    +  r+ R+ ar+l+e   +f ev++++pl+vc+er+        pk +Ykka +G   +++G++ +Ye+P +pe+vvdt+
  gi|116754349|ref|YP_843467.1|  83 ANRRRYRDLARKLVE---RFAEVYIKAPLDVCMEREalrkaefaPKEIYKKAASGA--KVPGVSVAYEEPVSPEIVVDTT 157
                                    ***************...6***************97555556668*********96..99******************98 PP

                                    T CS
                     APS_kinase 155 k 155
                                    +
  gi|116754349|ref|YP_843467.1| 158 T 158
                                    6 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.1   0.0   6.2e-18   4.4e-15       2     121 ..       5     121 ..       5     137 .. 0.86

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 6.2e-18
                         AAA_33   2 vllvGlpGsGKstlaerllkklg.....avllssdtlrrrlfgtdqqsktdytrvldrlyqilnelarkalsagrnvild 76 
                                    v++ GlpG+GK+t a+r  ++l      + +l+ d++rr ++++ +    +  + +d +y+ l+ +a+  + ag nvi+d
  gi|116754349|ref|YP_843467.1|   5 VWFTGLPGCGKTTIARRTKEHLSrmgvkVKILELDEIRRVVTPNPR----YTDEERDIVYASLAYMAKLLCDAGVNVIID 80 
                                    7899*************87777777798899999999999987644....444567889****99**999********** PP

                         AAA_33  77 atnlsrrerarflklarrlgvpvrivvvetdeetlkeRlakRaan 121
                                    at  +rr r+  +kl++    +++ v+++++ +++ eR a R+a+
  gi|116754349|ref|YP_843467.1|  81 ATANRRRYRDLARKLVE----RFAEVYIKAPLDVCMEREALRKAE 121
                                    *****************....5667*****************996 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.0   1.4e-11     1e-08       4     150 ..       5     148 ..       2     175 .. 0.75

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 1.4e-11
                                    EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH...TTSS.S--GGGHHHHHHHHHHHHHHHH.TT.SEEEE-S- CS
                          KTI12   4 vvltGlPssGKstrakeLakaleeekrsvvviddeslg..iekds.ykdsakekalRsslrsavkrdL.skekvVIvDsl 79 
                                    v +tGlP  GK+t+a++ +++l+  + +v +++ + ++  ++ ++ y+   +e+++  +  + +++ L      VI+D++
  gi|116754349|ref|YP_843467.1|   5 VWFTGLPGCGKTTIARRTKEHLSRMGVKVKILELDEIRrvVTPNPrYT--DEERDIVYASLAYMAKLLcDAGVNVIIDAT 82 
                                    679******************************888886544444355..556666555555555555166677****** PP

                                    --SHHHHHHHHHHHHHTT-EEEEEEEE--HHHHHHHHHHTT-S..S-HHHHHHHHHH---TTSS-GGGS-S CS
                          KTI12  80 nyikgfRYeLyciakaakttlcvvyvvapldvlvkwneereekeeyekelldaLiqRyeePdsknrWDsPl 150
                                    +  + +R     +a++   +++ vy++apldv+++++  r+ +   +ke++++ ++    P  ++ +++P+
  gi|116754349|ref|YP_843467.1|  83 ANRRRYR----DLARKLVERFAEVYIKAPLDVCMEREALRKAE-FAPKEIYKKAASGAKVPGVSVAYEEPV 148
                                    9888887....58************************888766.456777777777666666666666665 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0   5.4e-11   3.9e-08       1     116 [.       5     121 ..       5     132 .. 0.83

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 5.4e-11
                         AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpe..aldeskrldedkldklldaleenssaleegknlv 78 
                                    ++ tG pG+GKtt+a++ +++l    +  +++  ++++  v+p+   +de++ ++   l++  ++l  +      g n++
  gi|116754349|ref|YP_843467.1|   5 VWFTGLPGCGKTTIARRTKEHLSRMGVKVKILELDEIRRVVTPNprYTDEERDIVYASLAYMAKLLCDA------GVNVI 78 
                                    689******************944555557888889999999997888999999999988888888886......89*** PP

                         AAA_18  79 idghlaeleseaakdikk.....vvLtaspeelleRlekRgye 116
                                    id   +  ++ ++ ++       v+++a+ ++++eR + R+ e
  gi|116754349|ref|YP_843467.1|  79 IDATANRRRYRDLARKLVerfaeVYIKAPLDVCMEREALRKAE 121
                                    ***9999986666554447*****************9999854 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.1   2.5e-08   1.8e-05      62     172 ..      53     171 ..       3     173 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 2.5e-08
                                    -HHHHHHHHHHHHHHHHHHHTT-EEEEEE--TTTHHHHHHHHHHHTTS-EEEEEEE--HHHHHHHHHHHTS......... CS
                            CPT  62 gpeldlllaalyeavaamaraGnnvivDdvilekewlvdllrrllsgldvllVGvrcplevlerRelergd......... 132
                                    + e+d ++a+l+   +   +aG nvi+D +  +++   dl+r+l+   ++  V +++pl+v  +Re+ r           
  gi|116754349|ref|YP_843467.1|  53 DEERDIVYASLAYMAKLLCDAGVNVIID-ATANRRRYRDLARKLV--ERFAEVYIKAPLDVCMEREALRKAefapkeiyk 129
                                    778899999999999999**********.66666668*******9..7888999***********998876577777776 PP

                                    ......SSTTHHHHHTTGGGTT---SEEEETTSS-HHHHHHHHHTT CS
                            CPT 133 ......RepGlaalqaeavHagaeyDlevDtsaktpeecArairer 172
                                          ++pG++        ++++  + vDt++ +pe  A+ i ++
  gi|116754349|ref|YP_843467.1| 130 kaasgaKVPGVSVAYE----EPVSPEIVVDTTTLDPEGAAELISKK 171
                                    6544444444444333....35666788999999999999888775 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   0.3   1.9e-05     0.014       2      30 ..       6      34 ..       5      38 .. 0.76
   2 !    9.2   0.1    0.0022       1.6      58     127 ..      32     102 ..      21     106 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.9e-05
                                   EEESSTTSSHHHHHHHHHHHHTHEEEEEE CS
                            AAA  2 llyGppGtGKTllakavakelgvefleis 30
                                    ++G pG+GKT++a+   ++l++  ++++
  gi|116754349|ref|YP_843467.1|  6 WFTGLPGCGKTTIARRTKEHLSRMGVKVK 34
                                   689************99998865555554 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0022
                                    TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS.SSTEEEEEEESS..GGGSTHHHHSTTSSEE CS
                            AAA  58 kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk.eskvivigatnr..pdkldpallrgRfdrk 127
                                    k +il +DEi ++++ +  + ++ee+++v + l+ + ++  +   +vi+ +++nr  +++l ++l+ +Rf ++
  gi|116754349|ref|YP_843467.1|  32 KVKILELDEIRRVVTPN-PRYTDEERDIVYASLAYMAKLLCDaGVNVIIDATANRrrYRDLARKLV-ERFAEV 102
                                    55899********9999.666667777766666666666555244677788999988889999999.999876 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0     3e-06    0.0022      20     103 ..       6      82 ..       3     104 .. 0.62
   2 ?    1.9   0.1      0.16   1.1e+02      78     136 ..      90     149 ..      77     160 .. 0.77
   3 ?   -2.2   0.0       2.9   2.1e+03      97     114 ..     151     168 ..     143     172 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3e-06
                     Zeta_toxin  20 llgGqpGAGKselaellkdelerqgnvv.rldpDdlRelh...Peyeeilkadpkkaseltqkdaselvekllqeaieng 95 
                                       G pG+GK+++a+ +k+ l r g  v  l+ D++R+     P+y +  ++++          ++   + + + + ++g
  gi|116754349|ref|YP_843467.1|   6 WFTGLPGCGKTTIARRTKEHLSRMGVKVkILELDEIRRVVtpnPRYTD--EERDI---------VYASLAYMAKLLCDAG 74 
                                    56799****************965555515789****97521144444..22222.........2222222333445556 PP

                     Zeta_toxin  96 yniivegt 103
                                    +n+i++ t
  gi|116754349|ref|YP_843467.1|  75 VNVIIDAT 82 
                                    66666666 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.16
                     Zeta_toxin  78 kdaselvekllqeaiengyniiveg.tlrspdvvkk.laealkkaGYevevvvvavkkelS 136
                                    + a++lve+  +  i++  ++ +e+ +lr+ + + k + +++ + G +v  v va ++ +S
  gi|116754349|ref|YP_843467.1|  90 DLARKLVERFAEVYIKAPLDVCMEReALRKAEFAPKeIYKKA-ASGAKVPGVSVAYEEPVS 149
                                    557899999999999999999999769999999999455555.448888777777776666 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2.9
                     Zeta_toxin  97 niivegtlrspdvvkkla 114
                                    +i+v++t  +p+ +++l+
  gi|116754349|ref|YP_843467.1| 151 EIVVDTTTLDPEGAAELI 168
                                    599999999999988754 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   5.3e-07   0.00038      31      66 ..       4      39 ..       1      44 [. 0.92

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 5.3e-07
                                   EEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE- CS
                           MeaB 31 vvGltGvPGaGkstlvealglelrrrGkrvavlavD 66
                                    v +tG+PG Gk t+  +  ++l r G +v +l +D
  gi|116754349|ref|YP_843467.1|  4 AVWFTGLPGCGKTTIARRTKEHLSRMGVKVKILELD 39
                                   6789****************************9988 PP

>> 6PF2K  6-phosphofructo-2-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.3   2.9e-06    0.0021      18      61 ..       7      50 ..       2     119 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.9e-06
                                   EESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHHHHHHSS-- CS
                          6PF2K 18 lvGLpargKtyiskkltrylkwlgvrtkvFnvgkyrreaskals 61
                                   + GLp  gKt+i+++    l+ +gv+ k+ ++ ++rr ++ +++
  gi|116754349|ref|YP_843467.1|  7 FTGLPGCGKTTIARRTKEHLSRMGVKVKILELDEIRRVVTPNPR 50
                                   67***********************************8876643 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   9.3e-07   0.00067       2      39 ..       5      42 ..       4      56 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 9.3e-07
                                   EEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE- CS
                       NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkvgGfyteevr 39
                                   v  TG pG GKtT+ ++  e l++ gvkv+ +   e+r
  gi|116754349|ref|YP_843467.1|  5 VWFTGLPGCGKTTIARRTKEHLSRMGVKVKILELDEIR 42
                                   668**************************866666666 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   1.5e-06    0.0011      27      69 ..       5      60 ..       4     143 .. 0.62

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.5e-06
                         AAA_16 27 vllsGesGvGKsslvrellralekd.............ggiflrgkcdqlesaipy 69
                                   v ++G +G+GK++++r+ +++l++              ++++ + ++++ e++i y
  gi|116754349|ref|YP_843467.1|  5 VWFTGLPGCGKTTIARRTKEHLSRMgvkvkileldeirRVVTPNPRYTDEERDIVY 60
                                   7799********************94444444444443233333333333344333 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   2.1e-06    0.0015       5      53 ..       8      56 ..       5      67 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.1e-06
                            PRK  5 agsSGaGkttvarklekifgrekvkaaeiegdsflrldraekdleleer 53
                                   +g  G+Gktt+ar+ ++ + r +vk +  e+d++ r++  + +++ eer
  gi|116754349|ref|YP_843467.1|  8 TGLPGCGKTTIARRTKEHLSRMGVKVKILELDEIRRVVTPNPRYTDEER 56
                                   7888*********************8888*****999999999888776 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.3   8.2e-06    0.0059       1     122 [.       8     118 ..       8     127 .. 0.58

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 8.2e-06
                                    EE-TTSSHHHHHHHHHHHH.....TEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHH.HHHHHHHHHSSEE CS
                         AAA_17   1 lGgPGsGKgtqceklveky.....gfthlsaGdllreeakrgglakardemrklpleekkelqkea.aekiaeeakkkgv 74 
                                    +G+PG+GK+t++++ +e++     ++++l+  d +r +++++       +    ++e++  +  +a ++k+   ++  +v
  gi|116754349|ref|YP_843467.1|   8 TGLPGCGKTTIARRTKEHLsrmgvKVKILE-LDEIRRVVTPNPR-----YT---DEERDIVYASLAyMAKLLC-DAGVNV 77 
                                    7****************9866655566666.4666666654433.....22...2222222222221222222.244567 PP

                                    EEEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHH CS
                         AAA_17  75 lvdghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkd 122
                                    ++d  +    +++ + +l ++ +e +   a ++++a+ ++++er + +
  gi|116754349|ref|YP_843467.1|  78 IIDATAN---RRR-YRDLARKLVERF---AEVYIKAPLDVCMEREALR 118
                                    7777763...223.344555566666...6667777777777776655 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   3.9e-05     0.028       1      27 [.       5      52 ..       5     131 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.9e-05
                   RNA_helicase  1 iwlyGpsgeGKStlakeLakallkkl......................k 27
                                   +w++G +g+GK+t+a++ +k+ l+++                       
  gi|116754349|ref|YP_843467.1|  5 VWFTGLPGCGKTTIARR-TKEHLSRMgvkvkileldeirrvvtpnpryT 52
                                   7****************.5655556556666666555555555555443 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   2.2e-05     0.016      25      65 ..       5      46 ..       2      59 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.2e-05
                   Mg_chelatase 25 lllvGppGsGKtmlakrlpsllpplsee.ealevakiasvag 65
                                   + ++G pG+GKt +a+r ++ l+++  + ++le  +i+ v++
  gi|116754349|ref|YP_843467.1|  5 VWFTGLPGCGKTTIARRTKEHLSRMGVKvKILELDEIRRVVT 46
                                   6799******************99975427788888877765 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 ?   14.5   0.0   3.1e-05     0.022       2      33 ..       8      39 ..       7      51 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.1e-05
                     ATP_bind_1  2 vGpaGsGKttfvgalseilelrgrsvavvNLD 33
                                   +G +G GKtt+ ++  e+l+  g +v+++ LD
  gi|116754349|ref|YP_843467.1|  8 TGLPGCGKTTIARRTKEHLSRMGVKVKILELD 39
                                   799****************************9 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2    0.0002      0.14       2      25 ..       5      32 ..       4      54 .. 0.75
   2 ?    2.0   0.1      0.32   2.3e+02     106     152 ..      62     110 ..      41     118 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0002
                         AAA_28  2 ivitGgestGKTtlleaLaar....gyp 25
                                   + +tG +++GKTt++++ +++    g++
  gi|116754349|ref|YP_843467.1|  5 VWFTGLPGCGKTTIARRTKEHlsrmGVK 32
                                   779************7666554444555 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.32
                         AAA_28 106 ekrydlvfllppapei..dddgeRredleereaiderlrealrelgipv 152
                                    +  y + +l++    +  d +++Rr   + ++++ er+ e++ +++ +v
  gi|116754349|ref|YP_843467.1|  62 SLAYMAKLLCDAGVNViiDATANRRRYRDLARKLVERFAEVYIKAPLDV 110
                                    4557777777774433358888888888889999999999888877666 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   5.4e-05     0.038      11      31 ..       8      28 ..       4     142 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.4e-05
                         AAA_22 11 tGesGtGKTtllrrlleqlde 31
                                   tG +G+GKTt +rr +e l +
  gi|116754349|ref|YP_843467.1|  8 TGLPGCGKTTIARRTKEHLSR 28
                                   8***************99853 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   7.7e-05     0.055       5      95 ..       5     102 ..       3     116 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.7e-05
                         AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderd.........kkladpe....kllelilek.lkeekktylfl 70 
                                    +  tG+  +GKTt++++  ++l     ++  ++ld+ r          ++    e        ++++k l +     +++
  gi|116754349|ref|YP_843467.1|   5 VWFTGLPGCGKTTIARRTKEHLSRMGVKVKILELDEIRRvvtpnprytDE----ErdivYASLAYMAKlLCD-AGVNVII 79 
                                    6779999*******999865555444566666666666644444332211....122222223334432555.6777999 PP

                         AAA_14  71 DEiqevpewekalkslvdegknldv 95 
                                    D   + ++ ++  ++lv++    +v
  gi|116754349|ref|YP_843467.1|  80 DATANRRRYRDLARKLVERFA--EV 102
                                    999999999999999999873..34 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 ?   12.6   0.1   0.00014       0.1       4      24 ..       7      30 ..       4      80 .. 0.85
   2 ?   -0.4   0.0       1.4     1e+03     113     138 .]      61      99 ..      31      99 .. 0.48

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                                   EE--SSSSHHHHHHHGGGGB...S CS
                          AAA_5  4 LvGppGtgKselaerlaaal...n 24
                                     G pG+gK+++a+r ++ l   +
  gi|116754349|ref|YP_843467.1|  7 FTGLPGCGKTTIARRTKEHLsrmG 30
                                   689**************9995333 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.4
                                    ..............-EEEEEESS--.-TT-TTHHHHTT- CS
                          AAA_5 113 r.............frviatanpldrslnelspalrsRf 138
                                    +             ++vi  a  ++r+  +l  +l+ Rf
  gi|116754349|ref|YP_843467.1|  61 AslaymakllcdagVNVIIDATANRRRYRDLARKLVERF 99 
                                    133444556666666666544444444555556666666 PP

>> Thymidylate_kin  Thymidylate kinase
   #    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       3      27 ..       9      33 ..       7      44 .. 0.89
   2 ?   -1.8   0.0         3   2.1e+03     123     140 ..     103     120 ..      88     135 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                                   ESTTSSHHHHHHHHHHHHHHTTE.E CS
                Thymidylate_kin  3 GlDGaGKttqaellkerlkeegikv 27
                                   Gl G GKtt+a+  ke+l+++g kv
  gi|116754349|ref|YP_843467.1|  9 GLPGCGKTTIARRTKEHLSRMGVKV 33
                                   999******************9885 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3
                                    EEESSHHHHHTSCCTTSS CS
                Thymidylate_kin 123 lldvdpevalkRlakrde 140
                                    +++ + +v+++R a r+ 
  gi|116754349|ref|YP_843467.1| 103 YIKAPLDVCMEREALRKA 120
                                    455555566666555555 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0081       5.8       1      18 [.      11      28 ..      11      43 .. 0.88
   2 ?    5.5   0.0     0.023        17      73     107 ..      83     120 ..      48     172 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0081
                                   TTSSHHHHHHHHHHHHTS CS
                            SKI  1 mGaGKstvGkllAkklgl 18
                                   +G+GK+t++++  ++l++
  gi|116754349|ref|YP_843467.1| 11 PGCGKTTIARRTKEHLSR 28
                                   6*********99888875 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.023
                                    GGSHHHHHHHH...HHSEEEEEE--HHHHHHHHHHTTS CS
                            SKI  73 vlseenrellk...ekgiviyLdvsleellerlkadke 107
                                    + ++++r+l +   e+   +y++++l++ +er + +k 
  gi|116754349|ref|YP_843467.1|  83 ANRRRYRDLARklvERFAEVYIKAPLDVCMEREALRKA 120
                                    5566777777777779999************9876665 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 ?   12.8   0.0    0.0001     0.075       4      46 ..       8      48 ..       5      60 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.0001
                Viral_helicase1  4 hGvpGcGKStlirkllrtsliltvnrptaelltegkpklpnls 46
                                    G pGcGK+t+ r+  ++    +++++  +l  +   ++ +++
  gi|116754349|ref|YP_843467.1|  8 TGLPGCGKTTIARRTKEH--LSRMGVKVKILELDEIRRVVTPN 48
                                   699*******77766655..66677775555555555555555 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00021      0.15       4      41 ..       5      42 ..       3      47 .. 0.93
   2 ?   -1.7   0.0       2.6   1.9e+03      87      94 ..      77      85 ..      49     122 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00021
                                   EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSS CS
                          SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvllvaaDtfR 41
                                   + + Gl G GKTt + +  ++l+++g kv +  +D  R
  gi|116754349|ref|YP_843467.1|  5 VWFTGLPGCGKTTIARRTKEHLSRMGVKVKILELDEIR 42
                                   5689*****************************99988 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.6
                                   EEEE.E--S CS
                          SRP54 87 vlvD.TaGr 94
                                   v++D Ta r
  gi|116754349|ref|YP_843467.1| 77 VIIDaTANR 85
                                   222212222 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   0.00017      0.12      22      52 ..       6      36 ..       2      40 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00017
                         AAA_30 22 vltGpAGtGKttalkalreaweaaggrvigl 52
                                     tG +G GKtt+ +  +e++ + g +v +l
  gi|116754349|ref|YP_843467.1|  6 WFTGLPGCGKTTIARRTKEHLSRMGVKVKIL 36
                                   679*******************999999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1189.13
//
Query:       gi|116754350|ref|YP_843468.1|  [L=198]
Description: response regulator receiver domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-08   33.8   0.0     0.0005   19.8   0.0    3.1  3  HTH_23           Homeodomain-like domain
    3.1e-08   33.2   0.1     0.0077   15.9   0.1    2.6  2  Sigma70_r4_2     Sigma-70, region 4
    6.8e-08   31.9   0.0     0.0027   17.2   0.0    2.6  2  GerE             Bacterial regulatory proteins, luxR family
    1.4e-05   24.7   0.0      0.002   17.9   0.0    2.5  2  HTH_38           Helix-turn-helix domain
    6.2e-05   22.4   0.1        0.1   12.2   0.0    3.3  3  Sigma70_r4       Sigma-70, region 4
     0.0018   18.4   0.0      0.017   15.2   0.0    2.6  4  HTH_28           Helix-turn-helix domain
     0.0018   17.8   0.0       0.05   13.2   0.0    2.3  2  CENP-B_N         CENP-B N-terminal DNA-binding domain
     0.0044   17.1   0.2        0.4   10.8   0.0    3.2  3  HTH_3            Helix-turn-helix
     0.0045   17.4   0.1       0.17   12.4   0.0    2.8  3  HTH_40           Helix-turn-helix domain
     0.0064   16.7   0.2       0.15   12.3   0.0    3.0  3  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
  ------ inclusion threshold ------
       0.03   14.2   0.0        3.3    7.7   0.0    2.3  2  Terminase_5      Putative ATPase subunit of terminase (gpP-li
      0.032   14.1   0.1       0.65    9.9   0.0    2.2  2  Sigma70_ECF      ECF sigma factor
      0.035   14.1   0.1       0.18   11.9   0.0    2.1  2  ROS_MUCR         ROS/MUCR transcriptional regulator protein
      0.054   13.9   0.0       0.49   10.8   0.0    2.2  2  GcrA             GcrA cell cycle regulator
      0.062   13.4   0.0         15    5.7   0.0    2.4  2  HTH_7            Helix-turn-helix domain of resolvase
      0.068   13.2   0.0        1.4    9.0   0.0    2.5  2  HTH_29           Winged helix-turn helix
      0.098   12.6   0.0       0.14   12.1   0.0    1.1  1  Glyco_hydro_92N  Glycosyl hydrolase family 92 N-terminal doma


Domain annotation for each model (and alignments):
>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   0.00043      0.46       8      28 ..      65      85 ..      59      88 .. 0.92
   2 !   19.8   0.0   4.7e-07    0.0005       7      44 ..     114     150 ..     112     165 .. 0.88
   3 ?   -1.2   0.0       1.9     2e+03      23      37 ..     166     180 ..     152     183 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00043
                         HTH_23  8 lrillllaeGlsvreIAreLg 28
                                   + +++l+ +Gls +eIA++Lg
  gi|116754350|ref|YP_843468.1| 65 AAVVRLFYKGLSDTEIAEQLG 85
                                   6799****************8 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 4.7e-07
                         HTH_23   7 RlrillllaeGlsvreIAreLgvsrrTvyrwlkryree 44 
                                    R + ++l  eG+sv+e ++ L+v ++Tv+ +++ ++ +
  gi|116754350|ref|YP_843468.1| 114 RELFIKLWEEGKSVKEMSEVLHVAPSTVSEYKNIFE-S 150
                                    56789**************************99994.3 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.9
                         HTH_23  23 IAreLgvsrrTvyrw 37 
                                    I    +vs+r v+++
  gi|116754350|ref|YP_843468.1| 166 ILSDQDVSERMVSHI 180
                                    444446777777665 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   7.3e-06    0.0077      10      54 .]      58     100 ..      57     101 .. 0.92
   2 !   14.4   0.0   2.1e-05     0.022      14      43 ..     112     141 ..     110     144 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7.3e-06
                                    TS-HHHHHHHHHHHTS---HHHHHHHHT--HHHHHHHHHHHHHHH CS
                   Sigma70_r4_2  10 eLperqreifllryleglsykEIAellgisegtVksrlsRArkkL 54 
                                    +L+++q ++++  +++gls  EIAe+lg  +++ ++ +sRAr kL
  gi|116754350|ref|YP_843468.1|  58 KLTPKQLAAVVRLFYKGLSDTEIAEQLG--DRALNKTVSRARIKL 100
                                    7999999999999**************6..999999999999887 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 2.1e-05
                                    HHHHHHHHHHTS---HHHHHHHHT--HHHH CS
                   Sigma70_r4_2  14 rqreifllryleglsykEIAellgisegtV 43 
                                     +re f+   +eg+s kE +e+l++ ++tV
  gi|116754350|ref|YP_843468.1| 112 FDRELFIKLWEEGKSVKEMSEVLHVAPSTV 141
                                    58999999999******************9 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   9.7e-05       0.1       3      28 ..      59      85 ..      57      99 .. 0.83
   2 !   17.2   0.0   2.6e-06    0.0027      12      38 ..     119     145 ..     114     149 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.7e-05
                                   S-HHHH.HHHHHHCTTS-HHHHHHHHT CS
                           GerE  3 LskREr.evLrllaeGksnkeIAeeln 28
                                   L+++++  v rl+++G+s +eIAe+l+
  gi|116754350|ref|YP_843468.1| 59 LTPKQLaAVVRLFYKGLSDTEIAEQLG 85
                                   788885269****************97 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 2.6e-06
                                    HHHCTTS-HHHHHHHHTS-HHHHHHHH CS
                           GerE  12 rllaeGksnkeIAeelniSekTVkvhk 38 
                                    +l+ eGks+ke +e l++++ TV+ +k
  gi|116754350|ref|YP_843468.1| 119 KLWEEGKSVKEMSEVLHVAPSTVSEYK 145
                                    7899*******************9887 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.032        34       4      31 ..      58      85 ..      56      88 .. 0.81
   2 !   17.9   0.0   1.9e-06     0.002       9      38 ..     113     142 ..     111     143 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.032
                         HTH_38  4 hLsleeReeIerllaeGlslreIArrLg 31
                                   +L++ +     rl  +Gls  eIA +Lg
  gi|116754350|ref|YP_843468.1| 58 KLTPKQLAAVVRLFYKGLSDTEIAEQLG 85
                                   566666666668999***********98 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 1.9e-06
                         HTH_38   9 eReeIerllaeGlslreIArrLgrspsTIs 38 
                                    +Re   +l++eG+s++e+   L+++psT+s
  gi|116754350|ref|YP_843468.1| 113 DRELFIKLWEEGKSVKEMSEVLHVAPSTVS 142
                                    6777779**********************8 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   9.5e-05       0.1       4      31 ..      58      85 ..      57     104 .. 0.88
   2 ?    5.7   0.0      0.01        11       9      38 ..     113     142 ..     110     145 .. 0.88
   3 ?   -0.0   0.0      0.61   6.4e+02      31      46 ..     171     186 ..     161     187 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.5e-05
                                   HS-HHHHHHHHHHHTTT--HHHHHHHHT CS
                     Sigma70_r4  4 sLpererevlelrfgeglTleEIgerlg 31
                                   +L++++   ++  f++gl+  EI+e+lg
  gi|116754350|ref|YP_843468.1| 58 KLTPKQLAAVVRLFYKGLSDTEIAEQLG 85
                                   7**************************8 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.01
                                    HHHHHHHHHTTT--HHHHHHHHTS-HHHHH CS
                     Sigma70_r4   9 erevlelrfgeglTleEIgerlgiSrerVr 38 
                                    +re +   ++eg + +E +e+l++  ++V+
  gi|116754350|ref|YP_843468.1| 113 DRELFIKLWEEGKSVKEMSEVLHVAPSTVS 142
                                    688888889******************998 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.61
                                    TS-HHHHHHHHHHHHH CS
                     Sigma70_r4  31 giSrerVrqiekrAlr 46 
                                    ++S+  V+ i k++l+
  gi|116754350|ref|YP_843468.1| 171 DVSERMVSHISKDGLQ 186
                                    6899999999998886 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       9.6     1e+04       7      20 ..      24      37 ..      21      38 .. 0.71
   2 ?   -2.4   0.0       5.1   5.4e+03      24      38 ..      59      73 ..      51      80 .. 0.77
   3 ?   -1.1   0.0         2   2.1e+03      11      23 ..      73      85 ..      62      85 .. 0.70
   4 !   15.2   0.0   1.6e-05     0.017       5      41 ..     117     153 ..     113     166 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 9.6
                         HTH_28  7 kllaaGhsvreaAr 20
                                   k+++++++ r +++
  gi|116754350|ref|YP_843468.1| 24 KPAKKHGTLRSTSE 37
                                   56777778877766 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.1
                         HTH_28 24 isrrtvyrWikryee 38
                                   +++ ++   ++ + +
  gi|116754350|ref|YP_843468.1| 59 LTPKQLAAVVRLFYK 73
                                   577888888887765 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 2
                         HTH_28 11 aGhsvreaArelg 23
                                   +G s +e+A++lg
  gi|116754350|ref|YP_843468.1| 73 KGLSDTEIAEQLG 85
                                   6778899999997 PP

  == domain 4  score: 15.2 bits;  conditional E-value: 1.6e-05
                         HTH_28   5 iikllaaGhsvreaArelgisrrtvyrWikryeegGi 41 
                                     ikl+ +G+sv+e ++ l++ ++tv+   + +e++  
  gi|116754350|ref|YP_843468.1| 117 FIKLWEEGKSVKEMSEVLHVAPSTVSEYKNIFESQRA 153
                                    699999*********************9999999875 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 ?    2.1   0.0      0.14   1.5e+02       5      33 ..      57      85 ..      54      95 .. 0.89
   2 !   13.2   0.0   4.8e-05      0.05      16      43 ..     118     145 ..     116     149 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.14
                                   SS--HHHHHHHHHHHHCTT-HHHHHHHHT CS
                       CENP-B_N  5 rsLTlreKievIqrleegeSkaelarrfn 33
                                   + LT+++  +v+++   g S  e+a +++
  gi|116754350|ref|YP_843468.1| 57 TKLTPKQLAAVVRLFYKGLSDTEIAEQLG 85
                                   78*************99999999997765 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 4.8e-05
                                    HHHHHCTT-HHHHHHHHT--CCHHHHHH CS
                       CENP-B_N  16 IqrleegeSkaelarrfnvpestlsdil 43 
                                    I++ eeg+S++e    ++v +st+s+ +
  gi|116754350|ref|YP_843468.1| 118 IKLWEEGKSVKEMSEVLHVAPSTVSEYK 145
                                    999*********************9865 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.39   4.1e+02       1      19 [.      50      68 ..      50      70 .. 0.86
   2 ?    0.6   0.0      0.59   6.2e+02       8      20 ..      73      85 ..      73      98 .. 0.77
   3 !   10.8   0.0   0.00038       0.4       7      30 ..     122     145 ..     118     146 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.39
                                   HHHHHHHTTHHHHHHHHHH CS
                          HTH_3  1 lkelRkqlglsqeeLAekl 19
                                   +k++  q +l+ ++LA+++
  gi|116754350|ref|YP_843468.1| 50 IKAYNIQTKLTPKQLAAVV 68
                                   78888999********986 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.59
                                   TTHHHHHHHHHHT CS
                          HTH_3  8 lglsqeeLAeklG 20
                                   +gls +e+Ae lG
  gi|116754350|ref|YP_843468.1| 73 KGLSDTEIAEQLG 85
                                   699999***9999 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00038
                                    HTTHHHHHHHHHHTSSHHHHHHHH CS
                          HTH_3   7 qlglsqeeLAeklGvsrstisriE 30 
                                    + g s +e++e+l v +st+s + 
  gi|116754350|ref|YP_843468.1| 122 EEGKSVKEMSEVLHVAPSTVSEYK 145
                                    6799*****************996 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       4.7     5e+03      54      61 ..      35      42 ..       6      62 .. 0.55
   2 ?    2.0   0.0      0.27   2.8e+02       6      22 ..      68      87 ..      63     105 .. 0.80
   3 !   12.4   0.0   0.00016      0.17       6      32 ..     118     144 ..     114     182 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 4.7
                         HTH_40 54 ekeIeeai 61
                                    +eIe+a+
  gi|116754350|ref|YP_843468.1| 35 TSEIEQAL 42
                                   33333333 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.27
                         HTH_40  6 lelleeglsieeIAke...r 22
                                    +l+ +gls  eIA++   r
  gi|116754350|ref|YP_843468.1| 68 VRLFYKGLSDTEIAEQlgdR 87
                                   68999*********995554 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.00016
                         HTH_40   6 lelleeglsieeIAkerglkesTIegH 32 
                                    ++l+eeg+s++e ++  ++++sT+ ++
  gi|116754350|ref|YP_843468.1| 118 IKLWEEGKSVKEMSEVLHVAPSTVSEY 144
                                    68**********************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 ?   -2.6   0.0       6.4   6.7e+03      25      33 ..      77      85 ..      75      95 .. 0.80
   2 !   12.3   0.0   0.00014      0.15      24      41 ..     126     143 ..     120     151 .. 0.91
   3 ?    0.3   0.0      0.78   8.3e+02      41      53 ..     175     187 ..     168     190 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 6.4
                                   HHHHHHHHT CS
                 Fe_dep_repress 25 tkdlaerLn 33
                                    +++ae L+
  gi|116754350|ref|YP_843468.1| 77 DTEIAEQLG 85
                                   688999986 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00014
                                    -HHHHHHHHTS-HHHHHH CS
                 Fe_dep_repress  24 ktkdlaerLnvspssVse 41 
                                    ++k+++e+L v+ps+Vse
  gi|116754350|ref|YP_843468.1| 126 SVKEMSEVLHVAPSTVSE 143
                                    6799*************8 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.78
                                    HHHHHHHHTTSEE CS
                 Fe_dep_repress  41 emlkkLekdGyve 53 
                                     m++  +kdG+ +
  gi|116754350|ref|YP_843468.1| 175 RMVSHISKDGLQD 187
                                    5999999999865 PP

>> Terminase_5  Putative ATPase subunit of terminase (gpP-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0031       3.3       7      26 ..      68      87 ..      61      95 .. 0.79
   2 ?    4.3   0.0     0.036        38      13      41 ..     124     152 ..     114     159 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0031
                    Terminase_5  7 rlLYwqGyrvaeIAeelglk 26
                                   + L+++G + +eIAe lg  
  gi|116754350|ref|YP_843468.1| 68 VRLFYKGLSDTEIAEQLGDR 87
                                   469**************965 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.036
                    Terminase_5  13 GyrvaeIAeelglkeatVysWkkrdewdd 41 
                                    G +v+e +e l + + tV  +k+ +e ++
  gi|116754350|ref|YP_843468.1| 124 GKSVKEMSEVLHVAPSTVSEYKNIFESQR 152
                                    5589******************9887665 PP

>> Sigma70_ECF  ECF sigma factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00062      0.65     134     180 ..      57     101 ..      34     106 .. 0.83
   2 ?    2.3   0.0      0.13   1.3e+02     150     169 ..     123     142 ..     101     157 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00062
                    Sigma70_ECF 134 lsldpeqarlvelrkleGlsveEiAeklgvskrtverrlalaRawle 180
                                    ++l p+q+  v   + +Gls +EiAe+lg   r+ ++    aR +l+
  gi|116754350|ref|YP_843468.1|  57 TKLTPKQLAAVVRLFYKGLSDTEIAEQLG--DRALNKTVSRARIKLH 101
                                    56899999999999************996..7888888877777765 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.13
                    Sigma70_ECF 150 eGlsveEiAeklgvskrtve 169
                                    eG sv+E++e+l v+ +tv 
  gi|116754350|ref|YP_843468.1| 123 EGKSVKEMSEVLHVAPSTVS 142
                                    6999**************96 PP

>> ROS_MUCR  ROS/MUCR transcriptional regulator protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0         6   6.4e+03      22      44 ..       6      28 ..       4      39 .. 0.67
   2 ?   11.9   0.0   0.00017      0.18       4      96 ..      44     146 ..      41     154 .. 0.62

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 6
                       ROS_MUCR 22 eelpslikevhaalkalseaeee 44
                                   ++l++l+ +++ + k +++++++
  gi|116754350|ref|YP_843468.1|  6 DHLRELVLKIAPTTKVVEKPAKK 28
                                   67777887777777776665554 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00017
                       ROS_MUCR   4 eltadiVsAyvsnnkveaeelpslikevhaalkalseaeeeeaaeeeekepavpikksvtpda...........iicled 72 
                                     ++ ++++Ay  ++k+++++l+++++  ++ l++++ ae+ + ++ +++++ ++ik  +++d+           i   e 
  gi|116754350|ref|YP_843468.1|  44 GVVSEMIKAYNIQTKLTPKQLAAVVRLFYKGLSDTEIAEQLGDRALNKTVSRARIKLHLFRDSdlkppfdrelfIKLWEE 123
                                    56789***************************999777777666444444444444333333211111111111334466 PP

                       ROS_MUCR  73 GkklksLkrhLasahgltpeeYra 96 
                                    Gk++k +   L +    t++eY++
  gi|116754350|ref|YP_843468.1| 124 GKSVKEMSEVL-HVAPSTVSEYKN 146
                                    66666666666.555666666665 PP

>> GcrA  GcrA cell cycle regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00047      0.49      10      33 ..      66      95 ..      57     108 .. 0.75
   2 ?    0.5   0.0       0.7   7.4e+02      10      28 ..     116     134 ..     113     143 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00047
                           GcrA 10 lLkklwleGlSasqiaaqlg......gvsR 33
                                   +  +l+ +GlS ++ia+qlg      +vsR
  gi|116754350|ref|YP_843468.1| 66 AVVRLFYKGLSDTEIAEQLGdralnkTVSR 95
                                   56689***************4444444444 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.7
                           GcrA  10 lLkklwleGlSasqiaaql 28 
                                    l  klw+eG S++++++ l
  gi|116754350|ref|YP_843468.1| 116 LFIKLWEEGKSVKEMSEVL 134
                                    5669********9988766 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 ?    5.4   0.0     0.019        20       5      32 ..      58      85 ..      56      85 .. 0.92
   2 ?    5.7   0.0     0.015        15      13      38 ..     116     141 ..     104     146 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.019
                                   SS-HHHHGGGGSSTTTT--STTTSSSS- CS
                          HTH_7  5 klskndinrvvkLleeGisiskIAkevn 32
                                   kl++++++ vv+L  +G s ++IA++++
  gi|116754350|ref|YP_843468.1| 58 KLTPKQLAAVVRLFYKGLSDTEIAEQLG 85
                                   7889999******************975 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.015
                                    GGGSSTTTT--STTTSSSS---SSSS CS
                          HTH_7  13 rvvkLleeGisiskIAkevnisRsTv 38 
                                      +kL eeG s+++  + + +++sTv
  gi|116754350|ref|YP_843468.1| 116 LFIKLWEEGKSVKEMSEVLHVAPSTV 141
                                    6689*********************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 ?    1.2   0.0      0.35   3.7e+02       2      23 ..      65      85 ..      65      85 .. 0.91
   2 ?    9.0   0.0    0.0013       1.4       5      42 ..     118     154 ..     114     165 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.35
                         HTH_29  2 aqallllaeGvstvsqiAkllg 23
                                   a++++l ++G+s   +iA++lg
  gi|116754350|ref|YP_843468.1| 65 AAVVRLFYKGLS-DTEIAEQLG 85
                                   67999******8.******998 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0013
                         HTH_29   5 llllaeGvstvsqiAkllglsrrtvyrwlkrfeegGla 42 
                                    + l +eG s v+++ ++l + ++tv  +++ fe  ++a
  gi|116754350|ref|YP_843468.1| 118 IKLWEEGKS-VKEMSEVLHVAPSTVSEYKNIFESQRAA 154
                                    667789*98.*******************999988754 PP

>> Glyco_hydro_92N  Glycosyl hydrolase family 92 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00013      0.14      68     160 ..      14     100 ..       9     107 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                Glyco_hydro_92N  68 slmPttgevkldpgkkkkdkeeyrsrfskedetaspgyYsvtlddygikaelTateragllrftFpkgkeanilvdlsds 147
                                    ++ Ptt+ v+      k++k++ + r + e e+a  g+ s  +++y+i+++lT+++ a++ r  ++  ++++i  +l+d+
  gi|116754350|ref|YP_843468.1|  14 KIAPTTKVVE------KPAKKHGTLRSTSEIEQALLGVVSEMIKAYNIQTKLTPKQLAAVVRLFYKGLSDTEIAEQLGDR 87 
                                    5667776665......3444455555566889***********************************9999**9999999 PP

                Glyco_hydro_92N 148 lssdkvsngsikv 160
                                    + +++vs ++ik+
  gi|116754350|ref|YP_843468.1|  88 ALNKTVSRARIKL 100
                                    9667788888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       757  (0.0422221); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 1516.09
//
Query:       gi|116754351|ref|YP_843469.1|  [L=134]
Description: pyridoxamine 5'-phosphate oxidase-related, FMN-binding [Methanosaeta thermophila PT]
Scores for complete 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   53.1   0.0    3.5e-14   52.7   0.0    1.1  1  Putative_PNPOx   Pyridoxamine 5'-phosphate oxidase
  ------ inclusion threshold ------
       0.07   13.7   0.0        0.1   13.2   0.0    1.3  1  Pyridox_oxase_2  Pyridoxamine 5'-phosphate oxidase


Domain annotation for each model (and alignments):
>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.7   0.0   3.9e-18   3.5e-14       1      87 [.       4      90 ..       4      91 .. 0.95

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 3.9e-18
                                   HHHHHHHHHHHSSEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETTGSEEEEEEEEEE CS
                 Putative_PNPOx  1 ldeelreflaeskavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallflddelgrgvrieGtae 82
                                   ++e +++ l+++k v +AT++++G Pnv+ ++l +  +++++++a n   ++++nl enp+ +++ ++ e+ ++++i+G +e
  gi|116754351|ref|YP_843469.1|  4 MPEDVKQTLEKQKPVPIATASKNGVPNVVFIGLLKILDDERLLIADNFFNKTAANLHENPKMSIVCYNSETKKSFQIKGSVE 85
                                   5688999*************************88888888****************************************** PP

                                   EESCH CS
                 Putative_PNPOx 83 lvsdg 87
                                   +++ g
  gi|116754351|ref|YP_843469.1| 86 VHKSG 90
                                   *9875 PP

>> Pyridox_oxase_2  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.1e-05       0.1      18      99 ..      13      87 ..       3      88 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.1e-05
                                   GGGGEEEEEEE-T.TS-EEEEEEE---B-TT...SS-.EEEEEETTSHHHHHHH.H--EEEEEEEETTTTEEEEEEEEEEEE CS
                Pyridox_oxase_2 18 kkstefqlaTvdeeegkPrvRtvvfRgfleekkeesdvltfttDvrseKvkqlessnaaveavfylketreQfRisGkafvi 99
                                   +k++ + +aT + ++g P+   vvf g l+  +  ++   +++D   +K++   ++n+++ +v y +et++ f i+G++ v+
  gi|116754351|ref|YP_843469.1| 13 EKQKPVPIATAS-KNGVPN---VVFIGLLKILD-DER--LLIADNFFNKTAANLHENPKMSIVCYNSETKKSFQIKGSVEVH 87
                                   566666677766.456565...57777777654.334..46789999998877779**********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1011.17
//
Query:       gi|116754352|ref|YP_843470.1|  [L=678]
Description: DNA mismatch repair protein MutS domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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   41.7   0.0      3e-10   40.5   0.0    1.6  1  MutS_V    MutS domain V
  ------ inclusion threshold ------
      0.014   15.8   0.3      0.062   13.7   0.1    2.3  2  AAA       ATPase family associated with various cellular acti
      0.081   12.0   0.0       0.16   11.0   0.0    1.4  1  Exo70     Exo70 exocyst complex subunit
       0.33   10.6   3.2        0.4   10.3   0.1    2.2  2  DUF885    Bacterial protein of unknown function (DUF885)


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 !   40.5   0.0   6.6e-14     3e-10       2     146 ..     474     614 ..     473     629 .. 0.82

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 6.6e-14
                                    EEE-STTSSHHHHHHHHHHHHHHHHHT--BSSSEEEEE--SEEEEEE--------SS-HHHHHHHHHHHHHTT--TTSEE CS
                         MutS_V   2 litGpnmaGkstylrqvalivllaqiGsfvpaekaeisivdkiftRvgasDdlakgkstFmvEmlEtasilknatekslv 81 
                                    ++ G n +Gk ++l  +a i++la++G  vpa++++isi+d+++    +s +l+ g  +F   m  ++++   + ++ lv
  gi|116754352|ref|YP_843470.1| 474 ILSGVNSGGKTSLLELMAQIAILAHMGLPVPASECRISIFDELYFFAKSSGTLSAG--AFESTMRKLSALA--TEKRKLV 549
                                    899*****************************************998888888776..6999999998874..45789** PP

                                    EEESTS-SS-HHHHHHHHHHHHHHHHHTT--EEEEEES-G.GGGGHHHHSTTEEEEEEEEEEETTE CS
                         MutS_V  82 ilDElGRGtstydGlaialavaeyllekikaktlfatHyh.eltklaekleevknlhlavkeeeed 146
                                    + DEl   t       i  ++++++ e + + +lf  H   e+ + +++  +v  ++ +  +e+++
  gi|116754352|ref|YP_843470.1| 550 LADELEAITEPGASARIIASILDMVQE-NGSVALFVSHLAdEIRRFSRTAVRVDGIEAEGLDERNN 614
                                    *****9888888888888888877665.99********8626777777777776666665555555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   1.4e-05     0.062       2     115 ..     474     591 ..     473     606 .. 0.66
   2 ?   -3.1   0.0       2.2     1e+04      68     100 ..     636     664 ..     635     668 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.4e-05
                                    EEESSTTSSHHHHHHHHHHHH..........THE...........EEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSE CS
                            AAA   2 llyGppGtGKTllakavakel..........gve...........fleisgsellskyvgesekkirelfkeakekakps 60 
                                    +l+G    GKT+l + +a+ +            +           f+  s  +l     g+ e+ +r+l + a ek+  +
  gi|116754352|ref|YP_843470.1| 474 ILSGVNSGGKTSLLELMAQIAilahmglpvpA-SecrisifdelyFFAKSSGTLS---AGAFESTMRKLSALATEKR--K 547
                                    68999999************654444443330.0333344444426666666665...8999999999999999887..9 PP

                                    EEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGS CS
                            AAA  61 ilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkl 115
                                     ++ DE++a+++         + r+++ +l ++++  +     + + +++  d++
  gi|116754352|ref|YP_843470.1| 548 LVLADELEAITEPG------ASARIIASILDMVQENGS-----VALFVSHLADEI 591
                                    **********8777......555555555555444333.....455555555554 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.2
                                    GGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSS CS
                            AAA  68 dalaksrsgseseeeervvnqLlteldgvkkke 100
                                    d+l+++     +++e++  ++Llt + + ++++
  gi|116754352|ref|YP_843470.1| 636 DRLVRTT----EGKERTFYEALLTRFRNTQSRS 664
                                    5555555....6778888888888888877765 PP

>> Exo70  Exo70 exocyst complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   3.6e-05      0.16      75     135 ..     241     300 ..     209     306 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.6e-05
                          Exo70  75 dmyealsdllpeleslfsgeaksevkaeleellkklsetakslleefeesikkdsskspvp 135
                                    + +e ls+l+  l++lf++e++ +  +++++llk+l  ++ s l++ + +++k+  +s+v 
  gi|116754352|ref|YP_843470.1| 241 EHFEDLSKLRNALRRLFDDEDQ-SDISRIDDLLKRLPAAVDSALAQANTELRKRIETSSVT 300
                                    45899************98555.8899*************************996667773 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 ?    0.1   0.5      0.11   4.8e+02      13     112 ..      25     131 ..      16     155 .. 0.64
   2 ?   10.3   0.1   8.9e-05       0.4      56     131 ..     224     298 ..     209     344 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.11
                                    TT-----SHHHHHHHHHHHHHHHHHHCT.S-CCHH.HH...HHHHHHHHHHHHHHHHHHHHHSHHHHTT-CCCCH..HHH CS
                         DUF885  13 ddrlpdlspaaeaaraarlraalaeldaaidrdkl.se...erldldllrerleleletaeagypleqlralagp..vqq 86 
                                    d+ ++dl +a  +++a ++ +a   l+  +++++  +    er+ + +l++ ++  ++ta+a + +++l +  +p    +
  gi|116754352|ref|YP_843470.1|  25 DEDMNDLRAAIGERHAIATVRAARGLRYGVSPESFlATdeaERIYRTILNR-IAEHANTAYAIMRISTLFPSGSPelIKE 103
                                    677778887777777777777777886666666655445656666666655.7777767777788888877777766444 PP

                                    HHH..HHCGTTSSCHHHHHHHHHHCCCH CS
                         DUF885  87 lps..llseepfateedleaylarlaav 112
                                    ++s  l +++  +   d++++l+r++ +
  gi|116754352|ref|YP_843470.1| 104 MRSvsLRAMDLRRRLGDVRDLLRRIKPL 131
                                    4443233333345566666666666544 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 8.9e-05
                                    HHHHHHHHHHHHHHHSHHHHTT-CCCCHHHHHHHHHCGTTSSCHHHHHHHHHHC.CCHHHHHHHHHHHHHHHHHTT. CS
                         DUF885  56 llrerleleletaeagypleqlralagpvqqlpsllseepfateedleaylarl.aavpaaldqaranlregaaagl 131
                                    +l+  +e  l++  ++  +e+++ l++  ++l++l++ e + +  +++++l+rl aav++al+qa + lr+++++  
  gi|116754352|ref|YP_843470.1| 224 ALEAAME--LAAVLEERGIEHFEDLSKLRNALRRLFDDEDQSDISRIDDLLKRLpAAVDSALAQANTELRKRIETSS 298
                                    4444222..3333333445555555888999***********************6689************9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (678 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.46
# Mc/sec: 4442.02
//
Query:       gi|116754353|ref|YP_843471.1|  [L=291]
Description: tubulin/FtsZ domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-12   47.0   0.1    6.8e-12   45.5   0.1    1.8  1  FtsZ_C    FtsZ family, C-terminal domain
  ------ inclusion threshold ------
      0.025   13.8   0.0      0.038   13.3   0.0    1.3  1  DUF3834   Protein of unknown function (DUF3834)


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 !   45.5   0.1   7.6e-16   6.8e-12      18      93 ..     196     270 ..     177     272 .. 0.88

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 7.6e-16
                                    HHHHHHHTSGGGT--GGG-SEEEEEEEE-TT--HHHHHHHHHHHHHHS-TTSEEEEEEEE-TT--SEEEEEEEEES CS
                         FtsZ_C  18 eaaeaaisspLLdvdlsgAkgvlvnitggsdltlkEveevaetireevdeeanvivGavideeledeirvtvvatg 93 
                                     a ++a+ + L  +  s  +g l++itgg +ltl++++ +ae ++ ++d++an+i+G ++ +el d+i +t+v+tg
  gi|116754353|ref|YP_843471.1| 196 LALQDALDKSLSLMAPSRVRGCLLHITGGLNLTLRDANLIAESMTGALDQHANIIWGMRVRDEL-DVIEITAVLTG 270
                                    4667788888777888899********************************************9.79********9 PP

>> DUF3834  Protein of unknown function (DUF3834)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.2e-06     0.038      67     116 ..       5      54 ..       1      90 [. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.2e-06
                        DUF3834  67 gkekIavwrkGsaaDvllrilldlkkikaevvyaddpeevlkllnegevd 116
                                    g+++I v   G+ aD++ r+++   +i ++v+y+d  + v+ + + + vd
  gi|116754353|ref|YP_843471.1|   5 GRPEIFVAGFGTGADLVRRLAVSRDGIAGDVIYTDRRSCVISIDDGQSVD 54 
                                    6778999999************************8888877776666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); 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 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 2093.94
//
Query:       gi|116754354|ref|YP_843472.1|  [L=325]
Description: tyrosyl-tRNA synthetase [Methanosaeta thermophila PT]
Scores for complete 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-51  173.9   0.0    5.4e-51  173.6   0.0    1.0  1  tRNA-synt_1b  tRNA synthetases class I (W and Y)
     0.0015   17.5   0.0      0.056   12.4   0.0    2.1  2  tRNA-synt_1f  tRNA synthetases class I (K)
  ------ inclusion threshold ------
       0.14   10.4   0.0       0.34    9.1   0.0    1.6  2  tRNA-synt_1   tRNA synthetases class I (I, L, M and V)


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 !  173.6   0.0   9.1e-55   5.4e-51       3     292 ..      27     309 ..      25     310 .. 0.91

  Alignments for each domain:
  == domain 1  score: 173.6 bits;  conditional E-value: 9.1e-55
                                    HS--EEEEEEETSSS-BGGGHHHHHHHHHHHHTTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHHHHHHHHHHHHTCHT CS
                   tRNA-synt_1b   3 erplrvysGidPTgklHlGylvplkklvelqkaghevffliaDlhAiigdpskaeerklrkreevlenaikaqlakgldp 82 
                                    +++ r+y+G +++g++HlG+++  +kl+++q+ag +v++l+aDlhA+++++   +++++r  +++  +     +a gldp
  gi|116754354|ref|YP_843472.1|  27 REHPRAYVGYETSGNIHLGHMLTANKLLDMQRAGFDVVVLLADLHAFLNEKG--SLEEVRRIADYNREC---FIALGLDP 101
                                    5789**********************************************99..899999999999999...******** PP

                                    TTEEEEETHHHHTTHHHHHHHHHHHTTCBHHHHHHHHHCCHHCSSSC--BHHHHHHHHHHHHHHHHTCHSEEEEEGGGHH CS
                   tRNA-synt_1b  83 ekaevvlqsewlehlelaellrdlgklgslnrmlqfksvkkrleegegislgeftYplLqaaDilllkadlvpgGsDQkq 162
                                    e++e+v+++e++   e+   + ++++ ++lnr  +  + ++r +e++   +++++Ypl+qa Di+ lk d+ +gG+DQ++
  gi|116754354|ref|YP_843472.1| 102 ERTEFVYGTEYQLRPEYVIKVLQMARNTTLNRARRSMDEVSRSAENP--MVSQMIYPLMQAVDIADLKIDVAVGGMDQRK 179
                                    ***************997666666677******98777555555535..8****************************** PP

                                    HHHHHHHHHHHHHHHSTTSS-EEEEET-BBSTTSSSBTTCETTCGC-BTTCCHHHHHHHHHHCHCSTTC......SHHHH CS
                   tRNA-synt_1b 163 nielgrdlarrfnkkevfkkpegltvplltgldGekKmSKSagnsaIfLddekesvkkkiqkavtdsde......evekl 236
                                    +  l+r+ ++++     f+ p+++ +pl++gldG+ KmS+S+gn  I  d+  e+++ ki  a++  +          + 
  gi|116754354|ref|YP_843472.1| 180 IHMLAREELPKL----GFPAPVCIHTPLIPGLDGK-KMSSSKGN-NIAVDEPAEEIERKILAAYCPAKItennpiTEIFK 253
                                    **********99....578****************.********.********************877665445555677 PP

                                    HHHHHTHHHCHHHHHHHHCCSEEESSHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH CS
                   tRNA-synt_1b 237 lklktelsnelierleavsgkkpkreaeellaeevtklvhggdlkkalaealnell 292
                                    +++++ ++  ++ r  +++g  + +++  l++++v++ +h+ dlkka ae ++++l
  gi|116754354|ref|YP_843472.1| 254 YHIFPRVDSVTVRRPAKFGGDATFESYRALEESFVNGSLHPLDLKKACAEYMIKIL 309
                                    788888888**************99***************************9998 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.0   0.0    0.0064        38      21      42 ..      26      47 ..      10      58 .. 0.75
   2 !   12.4   0.0   9.3e-06     0.056     261     308 ..     191     238 ..     167     261 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.0064
                   tRNA-synt_1f 21 ekdevvvesGispSGliHiGnl 42
                                    +++     G+ +SG iH+G +
  gi|116754354|ref|YP_843472.1| 26 AREHPRAYVGYETSGNIHLGHM 47
                                   445556667***********86 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 9.3e-06
                   tRNA-synt_1f 261 lggeaPekvvYelillkggekmssSkGnvltledwlevaepevlrfli 308
                                    lg++aP+ +   li    g+kmssSkGn +++++  e +e+++l+ ++
  gi|116754354|ref|YP_843472.1| 191 LGFPAPVCIHTPLIPGLDGKKMSSSKGNNIAVDEPAEEIERKILAAYC 238
                                    67788888888888777788*****************99999998665 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 ?   -2.2   0.1      0.15   9.3e+02      35      45 ..      39      49 ..      37      56 .. 0.82
   2 ?    9.1   0.0   5.7e-05      0.34     478     575 ..     129     223 ..     104     250 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.15
                    tRNA-synt_1 35 tGslHiGhala 45
                                    G++H+Gh+l+
  gi|116754354|ref|YP_843472.1| 39 SGNIHLGHMLT 49
                                   69******996 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 5.7e-05
                    tRNA-synt_1 478 gelekdedvlDvWFsSgswpf.stlgypeedteelkkffpadmlleGlDiirgWv.arlillslaltgsePfkevlvhgl 555
                                     +l++    +D    S+  p+ s++ yp  ++ +++     d+ + G+D+ +  + ar  l  l      P    + + l
  gi|116754354|ref|YP_843472.1| 129 TTLNRARRSMDEVSRSAENPMvSQMIYPLMQAVDIA-DLKIDVAVGGMDQRKIHMlAREELPKLG----FPAPVCIHTPL 203
                                    566666666666666666553367777777777777.5677777777777654320222222222....24445666778 PP

                    tRNA-synt_1 556 vrdeeGrKmSKslgNvidpl 575
                                    +   +G+KmS s+gN i+ +
  gi|116754354|ref|YP_843472.1| 204 IPGLDGKKMSSSKGNNIAVD 223
                                    9999***********98754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2487.21
//
Query:       gi|116754355|ref|YP_843473.1|  [L=95]
Description: hypothetical protein Mthe_1049 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.23s 00:00:00.55 Elapsed: 00:00:00.35
# Mc/sec: 806.17
//
Query:       gi|116754356|ref|YP_843474.1|  [L=134]
Description: NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 [Methanosaeta thermophila PT]
Scores for complete 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   4.6    1.5e-30  105.3   4.6    2.1  2  Oxidored_q4  NADH-ubiquinone/plastoquinone oxidoreductase, ch


Domain annotation for each model (and alignments):
>> Oxidored_q4  NADH-ubiquinone/plastoquinone oxidoreductase, chain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.9   0.3    0.0067   1.2e+02      37      52 ..       5      20 ..       2      24 .. 0.86
   2 !  105.3   4.6   8.4e-35   1.5e-30       3      99 .]      27     133 ..      25     133 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.0067
                                   -HHCHHHHHHHHHHHH CS
                    Oxidored_q4 37 rfsvkfylvallFliF 52
                                   ++ v +y+  +lFl++
  gi|116754356|ref|YP_843474.1|  5 PLAVDYYIPIILFLVM 20
                                   6789**********96 PP

  == domain 2  score: 105.3 bits;  conditional E-value: 8.4e-35
                                    HHHHHHCHSS-----HHHHS-SSSS--SS---.--HHCHHHHHHHHHHHHHHHHHHHHHHHHSST.......HHHH.... CS
                    Oxidored_q4   3 lllllsallgpkkpnkeklspYEcGfepvgearlrfsvkfylvallFliFDvevvflfpwavslkel.....glfg.... 73 
                                    ++l++ ++++p +pn++k s YE G++pv++ ++rf+v++yl+a++F+iFDvev+fl+pw+ ++ ++      +fg    
  gi|116754356|ref|YP_843474.1|  27 VALAAVKIISPLRPNRRKASVYEGGLKPVRDPKIRFNVQYYLFAIVFVIFDVEVLFLYPWIYVYASEfmkrfVIFGfinm 106
                                    678889999*****************************************************998776655523333334 PP

                                    .HHHHHHHHHHHHHHHHHHHHH-S-XX CS
                    Oxidored_q4  74 .liemllFllillvglvYewkkgaLeW 99 
                                     +iem+lF+++l+vgl+Y++kk+aL+W
  gi|116754356|ref|YP_843474.1| 107 aVIEMVLFIAVLVVGLLYAIKKEALRW 133
                                    48************************* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       806  (0.0449551); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); 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: 0.35u 0.21s 00:00:00.55 Elapsed: 00:00:00.35
# Mc/sec: 1144.81
//
Query:       gi|116754357|ref|YP_843475.1|  [L=190]
Description: NADH-quinone oxidoreductase, B subunit [Methanosaeta thermophila PT]
Scores for 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-21   73.9   0.0    1.9e-20   73.0   0.0    1.5  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 !   73.0   0.0     1e-24   1.9e-20      43     130 ..      94     176 ..      67     177 .. 0.85

  Alignments for each domain:
  == domain 1  score: 73.0 bits;  conditional E-value: 1e-24
                                    TTTSEEEEEESBE...EEEHHHHHHHHGGGSSEEEEESHHHHH-TGGGSTT-TEE-HHHHHHHC.S-E.EEE-SSS--HH CS
                    Oxidored_q6  43 ekeadvlvveGavtrkpkealellkelaekakaviavGtCAafGGipaaannpsvgeevgellevvpvdinipGCPphpe 122
                                     ++adv++++G +trk  +a+++l+e++ ++k++iavG+CA++GG +  +++++    +++ ++  p+d+++pGCPp+pe
  gi|116754357|ref|YP_843475.1|  94 PRQADVMIISGYITRKYLPAIKNLWEQMLEPKWCIAVGECAISGGPF--YDSYNI---IQNTSDFFPIDVYVPGCPPRPE 168
                                    349********************************************..663444...4589999*************** PP

                                    HHHHHHHH CS
                    Oxidored_q6 123 ailetlla 130
                                    ++++++++
  gi|116754357|ref|YP_843475.1| 169 QFIKGFVE 176
                                    ***99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 1588.88
//
Query:       gi|116754358|ref|YP_843476.1|  [L=390]
Description: NADH dehydrogenase (ubiquinone) [Methanosaeta thermophila PT]
Scores for complete 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-81  273.9   0.1    3.6e-54  183.7   0.0    2.2  2  Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd s
    1.1e-07   31.2   0.0    2.9e-07   29.8   0.0    1.7  2  NiFeSe_Hases    Nickel-dependent hydrogenase


Domain annotation for each model (and alignments):
>> Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.7   0.0     4e-58   3.6e-54       5     174 ..     149     318 ..     144     320 .. 0.96
   2 !   90.1   0.0   1.3e-29   1.2e-25     195     271 .]     314     390 .]     310     390 .] 0.97

  Alignments for each domain:
  == domain 1  score: 183.7 bits;  conditional E-value: 4e-58
                                    HHHHHHHHHHHHHHHHHHHHHHSSSSS-TTBESSBBSS---TTHHHHHHHHHHHHHHHHHHHHHHHHSSSSHHHHHSSSS CS
                 Complex1_49kDa   5 ltvflyafreRekildlleevtGaRltasyiriGGvarDlpegllekikeflkelekkldeleklltknrifkkRtkgvg 84 
                                     ++f y++ +Re i+ l+e++tGaR+t++++r+GGv++Dlp+g+ +k + +lk+++++ +e+ +ll +++i+++R++g+g
  gi|116754358|ref|YP_843476.1| 149 YSPFQYMIIDREDIVYLMESITGARITHTFVRFGGVRNDLPDGFADKARPILKRMRERTEEYMDLLHSDPIYTRRMRGIG 228
                                    579***************************************************************************** PP

                                    -BSHHHHHHHTT-SSSSGGGT-TTTHHHHSS-SSGGGS-------SSBSHHHHHHHHHHHHHHHHHHHHHHHHT--.S-S CS
                 Complex1_49kDa  85 vlskeealelgltGpvlRasGvkyDlRkaepYeaYdeldfdvpvgeegDvydRylvrveEmrqSlkIieqaleklpegpv 164
                                    vls  +a +lg++Gp lRas  +yD+R+++p  +Y +ldf+v+++++gD+ +R+ vr+eE+ +S++Iieq+l+++p+gp+
  gi|116754358|ref|YP_843476.1| 229 VLSPGDARRLGVSGPPLRASDTPYDMRREDPILVYPDLDFKVVTRKAGDAEARVEVRLEEILESIHIIEQCLDQIPDGPI 308
                                    *******************************************************************************9 PP

                                    B---TTTS-- CS
                 Complex1_49kDa 165 laedkkvalp 174
                                    + + +k + p
  gi|116754358|ref|YP_843476.1| 309 QEKLPKKIKP 318
                                    9987776655 PP

  == domain 2  score: 90.1 bits;  conditional E-value: 1.3e-29
                                    S-----SEEEEEEEEETTEEEEEEEEEESSSS-SEEEEE-HHHHTTTTHHHHTTTS-SGGGTHHHHTT---HHHHH- CS
                 Complex1_49kDa 195 egfkvpkgevyaavEapkGelgvylvsdgsskpyrlkirapsfvnlqaleellkgellaDvvailgsldivlgevDR 271
                                    +++k  +ge+y +vE p+Ge+g+y+vsdgs+kpyr+k+r p ++++qal+ ll+g+++aDvvai gs+d +++evDR
  gi|116754358|ref|YP_843476.1| 314 KKIKPEPGEAYYRVEDPRGEMGFYVVSDGSEKPYRVKVRGPVYAYMQALPPLLEGAYVADVVAIAGSMDACTSEVDR 390
                                    5678899*********************************************************************9 PP

>> NiFeSe_Hases  Nickel-dependent hydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   3.2e-11   2.9e-07       1      68 [.      68     135 ..      68     143 .. 0.97
   2 ?   -3.4   0.0      0.36   3.2e+03     415     440 ..     314     339 ..     288     349 .. 0.72

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 3.2e-11
                                    --HHHHTTTS-GGGHHHHHHTT-SSSTTHHHHHHHHHHHHHHT----HHHHHHHHHHHHHHHHHHHHH CS
                   NiFeSe_Hases   1 RGlElilkgrdprdawalvqRiCGVCttvHalasvravedAlgikipknarlirnliaaalllhdhiv 68 
                                    +G+E+i+++r+  +  ++++R+C     +   a   ave+ lgi++p+ a++ir ++a    +++h++
  gi|116754358|ref|YP_843476.1|  68 KGIEKIMENRTYLQGIVYTDRMCYLASITNNEAYCGAVEKLLGITPPERAQYIRVILAELSRIQSHLL 135
                                    59****************************************************************86 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.36
                                    GGGS-SEEEEEEEEEETTEEEEEEEE CS
                   NiFeSe_Hases 415 kkevpkeakGvglveapRGaLsHwik 440
                                    kk  p+  + +  ve pRG ++ +++
  gi|116754358|ref|YP_843476.1| 314 KKIKPEPGEAYYRVEDPRGEMGFYVV 339
                                    33345567888899999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.22s 00:00:00.65 Elapsed: 00:00:00.35
# Mc/sec: 3305.50
//
Query:       gi|116754359|ref|YP_843477.1|  [L=350]
Description: respiratory-chain NADH dehydrogenase, subunit 1 [Methanosaeta thermophila PT]
Scores for complete 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-107  358.2  18.2     4e-107  358.0  18.2    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 !  358.0  18.2  2.2e-111    4e-107       4     298 ..      31     342 ..      28     343 .. 0.96

  Alignments for each domain:
  == domain 1  score: 358.0 bits;  conditional E-value: 2.2e-111
                                    HHHHHHHHHHHHHHHHHHHHHHHHHTTS--S-SST.TTTTTHHHHHHHHHCCS-----TTS-HHHHHHHHHHHHHHHHCT CS
                         NADHdh   4 llllvvlllvvalltlleRkvlAriqdRlGPnrvG.plGllqplaDalKlllKediipkkadkllfllapvlalilalla 82 
                                    +++ +v+ + ++ +++leRk+l+ iq R GPnrvG  +Gllq+ aDa+Kl++Ked ip++adk ++++ap++a i+++l+
  gi|116754359|ref|YP_843477.1|  31 AIISAVINIGAMAVVWLERKFLGDIQARFGPNRVGsRWGLLQLGADAIKLFTKEDSIPRGADKPVYVWAPIIASITTMLV 110
                                    455666777888***********************779****************************************** PP

                                    TTTS-SSS..........SSS--TTHHHHHHHHHHHCHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         NADHdh  83 faviPfge..........vladlnvglllilalsslgvygillaGwasnskYallGalRsaaqmisyEvalglsllavvl 152
                                     a+iPfg+          v+a+++++ +++ a +s++++++++aG++sn+kY++lGa+R +a mi+yEv++g++++av+l
  gi|116754359|ref|YP_843477.1| 111 AAAIPFGAlridgkdyplVVANMDISAFYVEAALSIMTIAVFMAGFSSNNKYSMLGAFRGIARMIAYEVPMGVCVIAVAL 190
                                    *******5556678899*************************************************************** PP

                                    HH-SS-HHHHHHCCCTT-CCCCHHHHHHHHHHHHHHCCTCTTBTTTTSTTSSSSCCCTT-HCHHHHHHHHHHHHHHHHHH CS
                         NADHdh 153 lagslslseiveaqeeiwfillqllafiifliallaetnraPFDlpeaesELvaGfhtEYsgmkfalfflaeyanmvlvs 232
                                    +a+sl+l eive+q+  w++++q+l+fi+f ial+  ++r+PFD  eae+E++aG++tEY+g++++l++++ey+nm+l s
  gi|116754359|ref|YP_843477.1| 191 MAHSLNLVEIVESQT-LWYAFAQPLGFIVFTIALVTDLGRIPFDQSEAEEEIIAGYTTEYGGIRWGLLYFQEYINMLLGS 269
                                    **************6.9*************************************************************** PP

                                    HHHHHHCT.SS-HCCS.......HHHHHHHHHHHHHHHHHHHHHC----TCHHHHHHHCCTCHHHHHHHHHHH CS
                         NADHdh 233 alavllFlgGwllpfs.......gllwfllKvllllflfiwiratlpRlRydqlmklgwkvllplalanlllt 298
                                    +l+vllFlgGw++p +       +++wfl+Kvl++l+++iw+r +l R+R+dq+++lgwk++lpl+l+nl ++
  gi|116754359|ref|YP_843477.1| 270 ILLVLLFLGGWNGPSIpvitvlsPMVWFLMKVLIVLIFLIWVRGSLVRFRIDQVTDLGWKWMLPLSLVNLAWA 342
                                    *************988999**************************************************9885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2574.83
//
Query:       gi|116754360|ref|YP_843478.1|  [L=180]
Description: 4Fe-4S ferredoxin iron-sulfur binding domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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-14   50.8  18.0    3.7e-07   29.7   4.6    2.2  2  Fer4      4Fe-4S binding domain
    3.5e-11   43.0  21.0    7.4e-09   35.6  11.6    1.8  2  Fer4_10   4Fe-4S dicluster domain
    6.2e-11   42.7  14.6    1.5e-10   41.5  14.6    1.7  1  Fer4_7    4Fe-4S dicluster domain
    3.8e-10   39.8  26.4    9.2e-08   32.1  13.5    1.8  2  Fer4_21   4Fe-4S dicluster domain
      2e-08   34.2  25.4      7e-07   29.3  13.3    2.0  2  Fer4_9    4Fe-4S dicluster domain
    2.9e-07   30.2  13.2    0.00033   20.6   3.2    2.5  2  Fer4_2    4Fe-4S binding domain
    5.5e-07   30.4  17.9     0.0014   19.5   2.4    3.0  2  Fer4_16   4Fe-4S double cluster binding domain
    3.9e-06   26.7  17.9     0.0042   17.1   5.9    2.3  2  Fer4_6    4Fe-4S binding domain
    8.8e-06   26.2  12.5     0.0012   19.3   0.9    2.8  3  Fer4_17   4Fe-4S dicluster domain
    0.00023   21.4  16.8     0.0072   16.8   4.6    2.4  2  Fer4_4    4Fe-4S binding domain
    0.00056   20.3  18.0     0.0033   17.8  15.8    2.5  3  Fer4_8    4Fe-4S dicluster domain
     0.0044   17.7  20.8      0.071   13.9   3.1    2.9  2  Fer4_15   4Fe-4S single cluster domain
  ------ inclusion threshold ------
       0.03   14.9   2.9       0.03   14.9   2.9    3.4  3  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
      0.063   14.1   3.0      0.063   14.1   3.0    2.8  3  Fer4_22   4Fe-4S dicluster domain
      0.081   13.9  25.6          1   10.5   9.0    2.4  2  Fer4_3    4Fe-4S binding domain
       0.82    9.9  16.6          1    9.6   2.6    3.0  3  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 !   27.2   5.4     2e-09   2.3e-06       3      24 .]      40      61 ..      38      61 .. 0.91
   2 !   29.7   4.6   3.3e-10   3.7e-07       1      23 [.      79     101 ..      79     102 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 2e-09
                                   EETTTSSS-THHHHHSTTTEEE CS
                           Fer4  3 ideekCigCGaCvevCPvgAIt 24
                                    d   CigCG C+ vCP+ +I+
  gi|116754360|ref|YP_843478.1| 40 LDATTCIGCGSCARVCPNSCIE 61
                                   68899*************9996 PP

  == domain 2  score: 29.7 bits;  conditional E-value: 3.3e-10
                                    EEEETTTSSS-THHHHHSTTTEE CS
                           Fer4   1 vvideekCigCGaCvevCPvgAI 23 
                                    ++id+ +C++CG+Cv+ CPv ++
  gi|116754360|ref|YP_843478.1|  79 PQIDYGRCTFCGLCVDECPVSCL 101
                                    68******************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 !   35.6  11.6   6.6e-12   7.4e-09       4      56 .]      40      97 ..      37      97 .. 0.96
   2 !   19.6   1.9   6.4e-07   0.00072       3      24 ..      80     118 ..      78     172 .. 0.70

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 6.6e-12
                        Fer4_10  4 idddtCirCgkCvkaCPadl.....tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                   +d+ tCi+Cg C ++CP +       ++g+  ++ + +  ++++++Ct+cg Cv++CP
  gi|116754360|ref|YP_843478.1| 40 LDATTCIGCGSCARVCPNSCiemvpYKYGNPLKNRKMQFPQIDYGRCTFCGLCVDECP 97
                                   7999**************889****9*******************************9 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 6.4e-07
                        Fer4_10   3 vidddtCirCgkCvkaCPadl.................t 24 
                                    +id  +C+ Cg Cv+ CP++                   
  gi|116754360|ref|YP_843478.1|  80 QIDYGRCTFCGLCVDECPVSClkmgkrteiagwdrkdiV 118
                                    689999999999999999977555555555555444440 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5  14.6   1.3e-13   1.5e-10       1      51 [.      44      99 ..      44     100 .. 0.83

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 1.3e-13
                         Fer4_7  1 rCigCgaCvaaCpvkaieldeeenek.....gtekveidpekClgCgaCvavCPtg 51
                                   +CigCg C+++Cp+++ie+ ++++ +     +++ ++id+ +C++Cg Cv++CP+ 
  gi|116754360|ref|YP_843478.1| 44 TCIGCGSCARVCPNSCIEMVPYKYGNplknrKMQFPQIDYGRCTFCGLCVDECPVS 99
                                   6*****************9976444433332667789*****************85 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   5.0   4.1e-07   0.00046      33      59 .]      37      62 ..      30      62 .. 0.85
   2 !   32.1  13.5   8.2e-11   9.2e-08       3      59 .]      40     103 ..      38     103 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 4.1e-07
                        Fer4_21 33 vlkvvedeCvGCnlCssvCPvedciem 59
                                   ++++ + +C+GC  C+ vCP + ciem
  gi|116754360|ref|YP_843478.1| 37 IHELDATTCIGCGSCARVCP-NSCIEM 62
                                   56777899************.7***99 PP

  == domain 2  score: 32.1 bits;  conditional E-value: 8.2e-11
                        Fer4_21   3 idedkCigCgkCliaCedtshqai.......eidaktvl.kvvedeCvGCnlCssvCPvedciem 59 
                                    +d  +CigCg+C+ +C++++++ +        ++ k ++ ++   +C+ C lC++ CPv  c++m
  gi|116754360|ref|YP_843478.1|  40 LDATTCIGCGSCARVCPNSCIEMVpykygnpLKNRKMQFpQIDYGRCTFCGLCVDECPV-SCLKM 103
                                    6889**************999999776665422223333255578*************9.9*998 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   4.2   3.1e-06    0.0035      29      51 .]      38      60 ..      22      60 .. 0.70
   2 !   29.3  13.3   6.2e-10     7e-07       2      49 ..      45      99 ..      44     101 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.1e-06
                         Fer4_9 29 raaseeaCigCgaCveaCpkgai 51
                                   ++ +++ CigCg+C+ +Cp+ +i
  gi|116754360|ref|YP_843478.1| 38 HELDATTCIGCGSCARVCPNSCI 60
                                   2333368************9876 PP

  == domain 2  score: 29.3 bits;  conditional E-value: 6.2e-10
                         Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraase.......eaCigCgaCveaCpkg 49
                                   C+gCg+C ++Cp+  +++   ++ + l+++++        +C++Cg Cv+ Cp  
  gi|116754360|ref|YP_843478.1| 45 CIGCGSCARVCPNSCIEMVPYKYGNPLKNRKMqfpqidyGRCTFCGLCVDECPVS 99
                                   *****************99999999999998899*****99************86 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   3.2     3e-07   0.00033       5      22 .]      40      57 ..      37      57 .. 0.89
   2 !   14.6   2.4   2.3e-05     0.025       3      21 ..      79      97 ..      78      98 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3e-07
                         Fer4_2  5 vdtdrCigCgaCvsaCPa 22
                                    d+ +CigCg+C  +CP+
  gi|116754360|ref|YP_843478.1| 40 LDATTCIGCGSCARVCPN 57
                                   57889************5 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 2.3e-05
                         Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                   +++d  rC+ Cg Cv+ CP
  gi|116754360|ref|YP_843478.1| 79 PQIDYGRCTFCGLCVDECP 97
                                   789**************** PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   2.4   1.2e-06    0.0014       1      22 [.      44      65 ..      44      81 .. 0.81
   2 !   14.5   7.8   4.6e-05     0.051       1      39 [.      85     132 ..      85     176 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.2e-06
                        Fer4_16  1 rCgtCgkCaevCPtnaikekke 22
                                   +C++Cg Ca vCP ++i++  +
  gi|116754360|ref|YP_843478.1| 44 TCIGCGSCARVCPNSCIEMVPY 65
                                   5****************98744 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 4.6e-05
                        Fer4_16   1 rCgtCgkCaevCPtnaikekkekeieare..cisy..........ntaekk 39 
                                    rC+ Cg C++ CP++++k+ k++ei+  +  +i y          +   +k
  gi|116754360|ref|YP_843478.1|  85 RCTFCGLCVDECPVSCLKMGKRTEIAGWDrkDIVYgpdriavkkfS---DK 132
                                    6*****************9977776533311334456444443221...22 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   5.9   3.8e-06    0.0042       5      21 ..      41      57 ..      40      62 .. 0.87
   2 !   15.2   4.2   1.5e-05     0.017       1      22 [.      78      99 ..      78     101 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.8e-06
                         Fer4_6  5 dpdkCigCgdCvrvCPe 21
                                   d+  CigCg C+rvCP 
  gi|116754360|ref|YP_843478.1| 41 DATTCIGCGSCARVCPN 57
                                   6778************5 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.5e-05
                         Fer4_6  1 vveidpdkCigCgdCvrvCPeg 22
                                   +++id+ +C+ Cg Cv+ CP  
  gi|116754360|ref|YP_843478.1| 78 FPQIDYGRCTFCGLCVDECPVS 99
                                   689*****************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 !   19.3   0.9   1.1e-06    0.0012      37      59 ..      36      58 ..      11      60 .. 0.74
   2 !   11.4   3.1   0.00032      0.36      42      57 ..      82      97 ..      63     100 .. 0.72
   3 !    9.6   5.4    0.0012       1.3       1      15 [.      85     100 ..      85     172 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.1e-06
                        Fer4_17 37 aekeekaslCieCgeCerkCPqg 59
                                    + e  a +Ci+Cg C+r+CP++
  gi|116754360|ref|YP_843478.1| 36 GIHELDATTCIGCGSCARVCPNS 58
                                   34456899*************85 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00032
                        Fer4_17 42 kaslCieCgeCerkCP 57
                                     ++C+ Cg+C+ +CP
  gi|116754360|ref|YP_843478.1| 82 DYGRCTFCGLCVDECP 97
                                   5678888888888888 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0012
                        Fer4_17   1 rCiqCgyClpeCps.y 15 
                                    rC+ Cg C++eCp  +
  gi|116754360|ref|YP_843478.1|  85 RCTFCGLCVDECPVsC 100
                                    6999999999999523 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   4.6   6.4e-06    0.0072       3      15 ..      44      56 ..      42      68 .. 0.89
   2 !   10.0   4.3   0.00092         1       3      16 ..      85      98 ..      83     108 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6.4e-06
                         Fer4_4  3 rCigCgsCvaaCP 15
                                   +CigCgsC ++CP
  gi|116754360|ref|YP_843478.1| 44 TCIGCGSCARVCP 56
                                   7************ PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00092
                         Fer4_4  3 rCigCgsCvaaCPq 16
                                   rC+ Cg Cv+ CP+
  gi|116754360|ref|YP_843478.1| 85 RCTFCGLCVDECPV 98
                                   9************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 !   12.5   4.9   0.00014      0.15      48      64 ..      42      58 ..      13      59 .. 0.77
   2 !   17.8  15.8     3e-06    0.0033       2      64 ..      42      99 ..      41     100 .. 0.70
   3 !   12.0   5.7   0.00019      0.22       4      34 ..      85     116 ..      82     174 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                         Fer4_8 48 lwsCttcgaCtevCpvg 64
                                   + +C +cg+C++vCp++
  gi|116754360|ref|YP_843478.1| 42 ATTCIGCGSCARVCPNS 58
                                   56788888888888875 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 3e-06
                         Fer4_8  2 lekCieCgaCqsaCp.vlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                                   +  Ci+Cg C   Cp ++ ++   ++ ++ ++ + +q  q        ++Ct cg C+++Cpv+
  gi|116754360|ref|YP_843478.1| 42 ATTCIGCGSCARVCPnSCIEMVPYKYGNPLKNRK-MQFPQI-----DYGRCTFCGLCVDECPVS 99
                                   678***********95455544333333333333.455555.....589*************96 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.00019
                         Fer4_8   4 kCieCgaCqsaCp.vlrrtkkhlldargeaae 34 
                                    +C+ Cg+C ++Cp ++ +++k+   a  ++++
  gi|116754360|ref|YP_843478.1|  85 RCTFCGLCVDECPvSCLKMGKRTEIAGWDRKD 116
                                    79999999999994333333444444444444 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 !   13.9   3.1   6.3e-05     0.071       3      20 ..      40      57 ..      39      62 .. 0.91
   2 !    8.5   9.9     0.003       3.4       3      34 ..      81     134 ..      80     163 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.3e-05
                        Fer4_15  3 vDrdaCigcglCvaeape 20
                                   +D ++Cigcg C++++p+
  gi|116754360|ref|YP_843478.1| 40 LDATTCIGCGSCARVCPN 57
                                   89**************97 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.003
                        Fer4_15   3 vDrdaCigcglCvaea.......pevfeldedglasvl...............l 34 
                                    +D  +C+ cglCv+e+        ++ e+++ + ++++               +
  gi|116754360|ref|YP_843478.1|  81 IDYGRCTFCGLCVDECpvsclkmGKRTEIAGWDRKDIVygpdriavkkfsdkeV 134
                                    8999************66666665555555544444445666555544332221 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   2.9   2.7e-05      0.03       2      18 ..      41      57 ..      40      67 .. 0.93
   2 ?    7.1   2.7     0.007       7.9       1      17 [.      81      97 ..      81     103 .. 0.92
   3 ?    0.4   0.8      0.89   9.9e+02      34      48 ..     141     155 ..     119     163 .. 0.56

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.7e-05
                        Fer4_13  2 DrdtCiacgaCvelaPd 18
                                   D  tCi+cg+C+ ++P+
  gi|116754360|ref|YP_843478.1| 41 DATTCIGCGSCARVCPN 57
                                   788*************7 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.007
                        Fer4_13  1 VDrdtCiacgaCvelaP 17
                                   +D  +C+ cg+Cv+ +P
  gi|116754360|ref|YP_843478.1| 81 IDYGRCTFCGLCVDECP 97
                                   68889***********9 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.89
                        Fer4_13  34 qptseeekadaeeAa 48 
                                     +++ eek++a +Aa
  gi|116754360|ref|YP_843478.1| 141 AKRQAEEKKKAAAAA 155
                                    333344444444443 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   3.0   5.6e-05     0.063      75      94 ..      38      57 ..       7      59 .. 0.78
   2 ?    6.3   2.7     0.016        18      74      95 ..      78      99 ..      65     100 .. 0.79
   3 ?   -0.1   0.1       1.6   1.8e+03      27      53 ..     142     168 ..     124     176 .. 0.48

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.6e-05
                        Fer4_22 75 ekfgesgCvGCgRCieacpv 94
                                   ++ ++++C+GCg C ++cp+
  gi|116754360|ref|YP_843478.1| 38 HELDATTCIGCGSCARVCPN 57
                                   5668999***********97 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.016
                        Fer4_22 74 kekfgesgCvGCgRCieacpvk 95
                                     +++   C+ Cg C++ cpv+
  gi|116754360|ref|YP_843478.1| 78 FPQIDYGRCTFCGLCVDECPVS 99
                                   45678889***********985 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 1.6
                        Fer4_22  27 eskegervrvwdsClleeftkvaggen 53 
                                    ++++ e+ +  ++   e+ +k +g+en
  gi|116754360|ref|YP_843478.1| 142 KRQAEEKKKAAAAAAKEKAAKAKGKEN 168
                                    233333344444444444444444433 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   9.0   0.00089         1       1      13 [.      45      57 ..      45      59 .. 0.94
   2 ?    9.2   8.7    0.0023       2.6       1      13 [.      86      98 ..      86     100 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00089
                         Fer4_3  1 CtgCgaCvevCPv 13
                                   C+gCg C +vCP+
  gi|116754360|ref|YP_843478.1| 45 CIGCGSCARVCPN 57
                                   ************6 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0023
                         Fer4_3  1 CtgCgaCvevCPv 13
                                   Ct Cg+Cv+ CPv
  gi|116754360|ref|YP_843478.1| 86 CTFCGLCVDECPV 98
                                   ************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 ?    9.6   2.6   0.00092         1      54      73 ..      38      57 ..      25      63 .. 0.81
   2 ?    8.3   1.7    0.0022       2.5      55      74 ..      80      99 ..      65     110 .. 0.78
   3 ?   -0.2   0.2         1   1.1e+03      36      42 ..     146     152 ..     117     175 .. 0.51

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00092
                        Fer4_18 54 kekgagdcidcescvkvcPt 73
                                   +e +a+ ci c+sc +vcP 
  gi|116754360|ref|YP_843478.1| 38 HELDATTCIGCGSCARVCPN 57
                                   4556789************7 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0022
                        Fer4_18 55 ekgagdcidcescvkvcPtg 74
                                   + + g c+ c+ cv+ cP+ 
  gi|116754360|ref|YP_843478.1| 80 QIDYGRCTFCGLCVDECPVS 99
                                   45678999999999999985 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 1
                        Fer4_18  36 kiagrkk 42 
                                    + +++++
  gi|116754360|ref|YP_843478.1| 146 EEKKKAA 152
                                    1111111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2078  (0.115902); expected 358.6 (0.02)
Passed bias filter:                      907  (0.0505884); expected 358.6 (0.02)
Passed Vit filter:                       125  (0.00697194); 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: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 1335.38
//
Query:       gi|116754361|ref|YP_843479.1|  [L=96]
Description: NADH dehydrogenase subunit J [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-22   79.8   7.3    2.4e-22   79.2   7.3    1.3  1  Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase cha
    0.00031   20.8  11.2    0.00042   20.4  11.2    1.2  1  DUF4040      Domain of unknown function (DUF4040)
  ------ inclusion threshold ------
       0.15   11.6   0.3       0.16   11.5   0.3    1.1  1  DUF676       Putative serine esterase (DUF676)


Domain annotation for each model (and alignments):
>> Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase chain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.2   7.3     4e-26   2.4e-22       2      66 ..      28      92 ..      27      96 .] 0.92

  Alignments for each domain:
  == domain 1  score: 79.2 bits;  conditional E-value: 4e-26
                                   HHHHHH-SBHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHIIIIIHHHHHHHHHHHSSTTS-- CS
                    Oxidored_q3  2 allvitsknpvysalfLilsfvgvaglfillgaeFlallqilvYvGAilvlflFvimllesaeee 66
                                   a+l+++s+n+v+sal+Li sf gva+l+i l+a+Fl+++q+lvY+GA+ vl+lF++ml+++  +e
  gi|116754361|ref|YP_843479.1| 28 AVLTVYSRNIVHSALYLIGSFAGVAALYISLNAPFLGVAQVLVYIGAVGVLILFAVMLTRRTIME 92
                                   899*******************************************************8665554 PP

>> DUF4040  Domain of unknown function (DUF4040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4  11.2   7.1e-08   0.00042       1      66 [.      22      87 ..      22      88 .. 0.95

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 7.1e-08
                        DUF4040  1 lllvlaalaavlardrlaavillgvvGllvallfvllgAPDvAlTqaavveglttvllllalrrlp 66
                                   +l++ +a+++v +r+ ++++++l+    +va+l++ l+AP +  +q++v  g ++vl+l+a+  ++
  gi|116754361|ref|YP_843479.1| 22 VLILGLAVLTVYSRNIVHSALYLIGSFAGVAALYISLNAPFLGVAQVLVYIGAVGVLILFAVMLTR 87
                                   6899********************************************************998776 PP

>> DUF676  Putative serine esterase (DUF676)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.3   2.7e-05      0.16      92     132 ..      24      68 ..      18      90 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.7e-05
                         DUF676  92 iaraaiaklkekem.....tlkeaikglepvtfitlasPhLGvlys 132
                                    i   a+  +++++      +l + ++g+    +i+l+ P+LGv+  
  gi|116754361|ref|YP_843479.1|  24 ILGLAVLTVYSRNIvhsalYLIGSFAGVA-ALYISLNAPFLGVAQV 68 
                                    55566666665555555444556788885.57**********9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       826  (0.0460706); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 716.68
//
Query:       gi|116754362|ref|YP_843480.1|  [L=89]
Description: F(420)H(2) dehydrogenase, subunit FpoJ [Methanosaeta thermophila PT]
Scores for complete 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-10   39.0   0.7    7.5e-10   38.7   0.7    1.1  1  Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase cha
  ------ inclusion threshold ------
       0.26   11.4   0.3       0.26   11.4   0.3    2.1  2  DUF3309      Protein of unknown function (DUF3309)


Domain annotation for each model (and alignments):
>> Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase chain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   0.7   8.3e-14   7.5e-10      76     144 .]       7      83 ..       2      83 .. 0.69

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 8.3e-14
                                    HHHHHHHHHHHHHHHTT--..................--------TT-HHHHHHHHTTTTHHHHHHHHHHHHHHHHHHHH CS
                    Oxidored_q3  76 alaalligllllallllllles............sssavdaqvadvsnieaigsllftkyllpfelasllLLvaligaiv 143
                                    +++ ++  ++l+a + +    +             ++a +     +s i  +g  lft y++pfel+sl+LL+aligai+
  gi|116754362|ref|YP_843480.1|   7 TILLVIFLAALIASISV----TpweygevkkqysFQPAKEGVRMPESGIGDVGAELFTIYMFPFELLSLVLLAALIGAIY 82 
                                    33333333333333333....2455799999887334444555567799999***************************9 PP

                                    C CS
                    Oxidored_q3 144 l 144
                                    +
  gi|116754362|ref|YP_843480.1|  83 I 83 
                                    7 PP

>> DUF3309  Protein of unknown function (DUF3309)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3   2.9e-05      0.26       2      23 ..       7      28 ..       6      30 .. 0.90
   2 ?    1.2   0.5     0.045     4e+02       5      16 ..      70      81 ..      64      84 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.9e-05
                        DUF3309  2 tiLliiLillLiGalptwpysr 23
                                   tiLl+i + +Li+++++ p+ +
  gi|116754362|ref|YP_843480.1|  7 TILLVIFLAALIASISVTPWEY 28
                                   9***************999866 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.045
                        DUF3309  5 liiLillLiGal 16
                                    ++L+ +LiGa+
  gi|116754362|ref|YP_843480.1| 70 SLVLLAALIGAI 81
                                   356666677765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 673.37
//
Query:       gi|116754363|ref|YP_843481.1|  [L=92]
Description: NADH-ubiquinone oxidoreductase, chain 4L [Methanosaeta thermophila PT]
Scores for complete 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-24   83.9   5.1    5.5e-24   83.8   5.1    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 !   83.8   5.1   3.1e-28   5.5e-24       5     103 ..       2      87 ..       1      92 [] 0.97

  Alignments for each domain:
  == domain 1  score: 83.8 bits;  conditional E-value: 3.1e-28
                                    HHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHHHHHHHC.............TTSCGGHHHHHHHHHHHHHHHHH CS
                    Oxidored_q2   5 liallfliGlygvllrrnllkvliglelisnavnlllvlagvftegtlvitnpatefadplpqalvLtaivigaaetavg 84 
                                    l+a++f iGlyg+ ++rn +k ++++el++n++n++lv++++++              ++ +q+++L+ i+++aae+ +g
  gi|116754363|ref|YP_843481.1|   2 LAAVMFSIGLYGLATQRNGVKLMMCVELMLNSANINLVAFSAYQ-------------PNVSGQVFALFSIALAAAEAGIG 68 
                                    799*****************************************.............9********************** PP

                                    HHHHHHHHHHSSS-BCCG- CS
                    Oxidored_q2  85 Lallvrlyreygtddvqel 103
                                    La+l++lyr ygt+d++++
  gi|116754363|ref|YP_843481.1|  69 LAILITLYRLYGTIDLDNI 87 
                                    *****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 674.96
//
Query:       gi|116754364|ref|YP_843482.1|  [L=652]
Description: proton-translocating NADH-quinone oxidoreductase, chain L [Methanosaeta thermophila PT]
Scores for complete 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-78  263.1  18.2    2.8e-78  263.1  18.2    2.3  2  Proton_antipo_M  Proton-conducting membrane transporter
      2e-17   63.0   2.0      8e-17   61.1   0.5    2.9  2  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 
    0.00024   20.8   0.1     0.0006   19.5   0.1    1.6  1  Proton_antipo_C  NADH-dehyrogenase subunit F, TMs, (complex I
     0.0098   15.5   0.0     0.0098   15.5   0.0    4.9  4  NADH5_C          NADH dehydrogenase subunit 5 C-terminus


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   1.4      0.25   1.1e+03     237     276 ..      79     121 ..       6     126 .. 0.75
   2 !  263.1  18.2   6.3e-82   2.8e-78       1     282 [.     127     417 ..     127     432 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.25
                Proton_antipo_M 237 gLakkmPilalvllvlllsla...GlPptagFlskfliLeaav 276
                                    +L++   +++++ l+ + +l+   G P++a +++++ +++aa+
  gi|116754364|ref|YP_843482.1|  79 ALVMLLMVTFVCTLIHTYALGymnGDPGMARYFAEAGLFTAAM 121
                                    4555555666666666666655578888899999888888877 PP

  == domain 2  score: 263.1 bits;  conditional E-value: 6.3e-82
                Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskal........ 72 
                                    +++Ll+l++++Elv+l++ylLig+w++kp++++A+ k+fl+t++g++++L gi+llyn++ +l ++e    l        
  gi|116754364|ref|YP_843482.1| 127 SDNLLQLFIFWELVGLCSYLLIGFWYRKPSAASAAKKAFLTTRVGDVMFLAGIILLYNNMAKLGLPEGTYLLqfpviyen 206
                                    79***********************************************************9988876666667788875 PP

                Proton_antipo_M  73 elglnslelllllllllvgllvKsaqvplhlWlpdayveaPtpvsall.Aatlvkagvlllirlllllavssneisqlll 151
                                     + ++  +l+l++llll g++ Ks+q+pl  Wlpda +e+Pt vsa++ Aat+v+agv+l++r+++l+  +++     ++
  gi|116754364|ref|YP_843482.1| 207 LTRIDPTQLTLVSLLLLGGAAGKSGQFPLDIWLPDA-MEGPTTVSAMIhAATMVTAGVYLVARMFPLFY-AAPYGLLAVA 284
                                    5667778889999***********************.********************************.999999**** PP

                Proton_antipo_M 152 ilaiismllgslvalaqtdiKrllAySsishlGymlialav...atqygveaaiihllthalfkallFllagsviyerek 228
                                     ++  ++l++++++la +diKr+lA+S++s+lGym++al+v    ++ +v  +++hl+ h++fkallFl+agsvi++   
  gi|116754364|ref|YP_843482.1| 285 YVGGFTALYAATMGLAAFDIKRVLAFSTVSQLGYMMLALGVgsvVGAAAVGVSMFHLIGHSFFKALLFLCAGSVIHAV-A 363
                                    ****************************************9333344555668*********************9997.9 PP

                Proton_antipo_M 229 trdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslil 282
                                    t+d+r++gg   +m+ +a +++++ l+laG P+t+gF+sk++iL  a+++++++
  gi|116754364|ref|YP_843482.1| 364 TNDLREMGGVGRYMRWTAGTMAIGGLALAGFPGTTGFFSKDEILVTAWEYGAMT 417
                                    ************************************************998765 PP

>> Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.1   0.5   1.8e-20     8e-17      11      55 ..      68     112 ..      62     114 .. 0.94
   2 ?   -1.9   0.0      0.82   3.7e+03      30      37 ..     247     254 ..     246     255 .. 0.91

  Alignments for each domain:
  == domain 1  score: 61.1 bits;  conditional E-value: 1.8e-20
                Proton_antipo_N  11 sieigfllDklsalmllvvtfvsllvhlYSigYMaddegyqRFfa 55 
                                    ++++g+l+D+l ++mll+vtfv +l+h Y++gYM +d+g++R+fa
  gi|116754364|ref|YP_843482.1|  68 TLNVGILIDPLALVMLLMVTFVCTLIHTYALGYMNGDPGMARYFA 112
                                    679*****************************************8 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.82
                Proton_antipo_N  30 tfvsllvh 37 
                                    t+vs+++h
  gi|116754364|ref|YP_843482.1| 247 TTVSAMIH 254
                                    89*****9 PP

>> Proton_antipo_C  NADH-dehyrogenase subunit F, TMs, (complex I) C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1   1.3e-07    0.0006      93     189 ..     455     555 ..     437     594 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.3e-07
                Proton_antipo_C  93 PhEsdntmlfpllvLvlftlfvGl.........iGipfnqegidldilskwLtpsinllhknsnesvdwyefltnaifSv 163
                                     hEs++ ml pl++L+lf lf G+         +G +f++ g+d     + L+p    + ++  e + + e ++  i+ +
  gi|116754364|ref|YP_843482.1| 455 KHESPWIMLGPLVILALFALFFGMpaqegfyetVGNNFAHYGVD----FEELAPIGGHVVEHGGEEAAVHEPFIIKILPI 530
                                    59********************9733322233355555554444....5678898887777777778888988889999* PP

                Proton_antipo_C 164 sialfGifiAsllYkpvysslqnldl 189
                                     + + Gi++A+l+Y p +++l+  ++
  gi|116754364|ref|YP_843482.1| 531 LVGVGGIILALLFYSP-WKKLDIRKF 555
                                    **************99.555444443 PP

>> NADH5_C  NADH dehydrogenase subunit 5 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   1.4      0.08   3.6e+02      35      69 ..      33      68 ..      24     102 .. 0.71
   2 ?   -1.0   2.0      0.26   1.2e+03      41     109 ..     259     320 ..     242     351 .. 0.71
   3 !   15.5   0.0   2.2e-06    0.0098       1      45 [.     436     478 ..     436     482 .. 0.93
   4 !    7.0   1.6   0.00089         4      61     180 ..     522     643 ..     517     644 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.08
                        NADH5_C 35 rLalgsiiaGsllswlifp.ktpvitlplllKllal 69
                                   +L +++ +aG+++s  if    p  ++   + + a 
  gi|116754364|ref|YP_843482.1| 33 FLTVLATFAGFIISAGIFTeIFPEKVVHQSMHWFAT 68
                                   688999999***999999875555555555555443 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.26
                        NADH5_C  41 iiaGsllswlifpktpvitlplllKllallvtilGlllglelsklslkllkkslklnlssfssslwFlp 109
                                    ++aG++l   +fp   +   p       l v  +G +++l  +++ l  +  +     +s +s+l+++ 
  gi|116754364|ref|YP_843482.1| 259 VTAGVYLVARMFP--LFYAAP----YGLLAVAYVGGFTALYAATMGLAAFDIKRV-LAFSTVSQLGYMM 320
                                    5677777777776..222222....344778889999999999999888887754.6777777888875 PP

  == domain 3  score: 15.5 bits;  conditional E-value: 2.2e-06
                        NADH5_C   1 YSlRliyyvllgsprfsslspineenptllnpilrLalgsiiaGs 45 
                                    Y++R+ +++++g+pr    ++ +e+ +++l p+++Lal++++ G+
  gi|116754364|ref|YP_843482.1| 436 YTFRMWFLTFTGEPRS--DYHKHESPWIMLGPLVILALFALFFGM 478
                                    9*************98..57789******************9996 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.00089
                        NADH5_C  61 plllKllallvtilGlllglelsklslkl..lkkslkl.nlssfssslwFlpslshrllsklsLklgqklakqlDqgWlE 137
                                    p+++K+l++lv + G++l+l + +   kl   k   ++  l + +    +  ++++  +  +  +  +++a+ +D   ++
  gi|116754364|ref|YP_843482.1| 522 PFIIKILPILVGVGGIILALLFYSPWKKLdiRKFVGEKdLLRTILVKRYYQHEIFTAWFAETVVYGISLIANIFDIRIVD 601
                                    89999999999999999999998765555103334444677777778888888999999999999888888889999998 PP

                        NADH5_C 138 klgpkglaklllklskliqnlqkglikiyLlsflltlllllll 180
                                     +   +++++ l ++++i  +q+g i+ y++ +++ +++l+++
  gi|116754364|ref|YP_843482.1| 602 GVLN-KISETTLGFANSIRRAQTGVIQNYITALVFGIVVLVIV 643
                                    8875.5889999999999*************999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (652 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       883  (0.0492498); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.42
# Mc/sec: 4613.60
//
Query:       gi|116754365|ref|YP_843483.1|  [L=502]
Description: proton-translocating NADH-quinone oxidoreductase, chain M [Methanosaeta thermophila PT]
Scores for complete 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-74  248.5  25.7    1.3e-73  247.8  25.7    1.4  1  Proton_antipo_M  Proton-conducting membrane transporter
  ------ inclusion threshold ------
      0.026   14.6   0.2      0.026   14.6   0.2    4.2  5  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 
       0.03   14.4   0.5       0.03   14.4   0.5    3.9  5  Oxidored_q5_N    NADH-ubiquinone oxidoreductase chain 4, amin


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  247.8  25.7   2.2e-77   1.3e-73       1     291 [.     127     424 ..     127     427 .. 0.93

  Alignments for each domain:
  == domain 1  score: 247.8 bits;  conditional E-value: 2.2e-77
                Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltg....tlefeelskal.... 72 
                                    a d +l+y+++E+vl+p+++Lig+w+   ++ ++++k+f++t ++sl++Ll+i+++y        +  f+ l +      
  gi|116754365|ref|YP_843483.1| 127 ALDFFLFYIFWEIVLIPMFFLIGIWGGP-RKDYSAIKFFIYTHVASLVMLLAIFAMYFTYRlpdgSRTFDMLTLLQatsd 205
                                    57899********************766.999999*******************99976433333888887777766788 PP

                Proton_antipo_M  73 elglnslelllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla.vssneisqlll 151
                                    ++++    +++++  ll+g+lvK++++p+h+Wlpda+veaPt++s+ lAa+l+k+g+++++r++l++  +++++   +++
  gi|116754365|ref|YP_843483.1| 206 KTVFPPGLINAIFAGLLFGFLVKMPAFPFHTWLPDAHVEAPTAGSVVLAALLLKMGGYGIFRVILPMLpHVDKAFVTVIA 285
                                    7888888999**********************************************************9*********** PP

                Proton_antipo_M 152 ilaiismllgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFllagsviyerektrd 231
                                    +++++s+++g+++alaq diK+l+AySsish+G++++++++ t  ++++a+++ ++h++++ +lF+ ag + ++ + tr 
  gi|116754365|ref|YP_843483.1| 286 VIGVLSIIYGAFLALAQKDIKKLVAYSSISHMGFVTLGAVAFTWLSIQGAMFQQFSHGIITCALFMSAGTI-QHSVGTRI 364
                                    ********************************************************************777.5566**** PP

                Proton_antipo_M 232 irayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvlavvasv 291
                                    i ++ggLa +mP +a ++l ++l+  GlP+++gF+++f++L++++   ++  +l+v++sv
  gi|116754365|ref|YP_843483.1| 365 ISELGGLADRMPKFASLMLAAFLASLGLPGMSGFVAEFMVLTGSYPTFPVYTMLVVFTSV 424
                                    *********************************************998888888877764 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 ?   14.6   0.2   4.4e-06     0.026       2      57 ..      64     114 ..      63     115 .. 0.80
   2 ?   -0.7   0.9      0.26   1.5e+03      21      41 ..     158     178 ..     156     183 .. 0.78
   3 ?   -1.4   0.4      0.43   2.5e+03      25      39 ..     280     294 ..     275     296 .. 0.73
   4 ?   -2.4   0.1      0.88   5.3e+03       2      10 ..     327     336 ..     326     346 .. 0.69
   5 ?   -2.4   0.9       0.9   5.4e+03      24      34 ..     416     426 ..     414     429 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.4e-06
                Proton_antipo_N   2 ftWlsvgglsieigfllDklsalmllvvtfvsllvhlYSigYMaddegyqRFfayl 57 
                                    ++W+++    +  ++ +D +s   +l+  +vs+lv +Y++g   +  + ++Ffa+l
  gi|116754365|ref|YP_843483.1|  64 YDWVPSI--GVRYTVGVDCISFPLVLLTAIVSVLVVIYAWG---ENHRPNQFFALL 114
                                    6788833..4888889***********************99...344667777765 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.26
                Proton_antipo_N  21 lsalmllvvtfvsllvhlYSi 41 
                                    +sa+  ++ t v++lv+l +i
  gi|116754365|ref|YP_843483.1| 158 YSAIKFFIYTHVASLVMLLAI 178
                                    578888888999999988665 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.43
                Proton_antipo_N  25 mllvvtfvsllvhlY 39 
                                    +++v+ ++++l ++Y
  gi|116754365|ref|YP_843483.1| 280 FVTVIAVIGVLSIIY 294
                                    567788888887777 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 0.88
                Proton_antipo_N   2 ftWlsvgg.l 10 
                                    ftWls++g +
  gi|116754365|ref|YP_843483.1| 327 FTWLSIQGaM 336
                                    89*9987633 PP

  == domain 5  score: -2.4 bits;  conditional E-value: 0.9
                Proton_antipo_N  24 lmllvvtfvsl 34 
                                    +ml+v t v++
  gi|116754365|ref|YP_843483.1| 416 TMLVVFTSVGV 426
                                    89999999986 PP

>> Oxidored_q5_N  NADH-ubiquinone oxidoreductase chain 4, amino terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.5   5.1e-06      0.03      44      79 ..      63      98 ..      31     117 .. 0.78
   2 ?    0.0   1.9      0.15   8.7e+02       5      45 ..     141     182 ..     131     199 .. 0.61
   3 ?   -2.9   0.2       1.2   7.3e+03      45      45 ..     303     303 ..     269     333 .. 0.53
   4 ?   -2.5   0.6      0.87   5.2e+03      34      42 ..     322     330 ..     283     356 .. 0.55
   5 ?   -3.2   0.2       1.5   8.7e+03      95     108 ..     465     478 ..     457     485 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.1e-06
                  Oxidored_q5_N 44 lsssfslsnlsyllglDslSapLilLSlWllpLmil 79
                                   +++      + y++g+D +S+pL+lL++ +++L+++
  gi|116754365|ref|YP_843483.1| 63 SYDWVPSIGVRYTVGVDCISFPLVLLTAIVSVLVVI 98
                                   444445557899*********************987 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.15
                  Oxidored_q5_N   5 llptlmliplvllskkkllwststlvslllallsll.llnls 45 
                                    l+p+++li ++   +k +  + +++++ + +l++ll ++ ++
  gi|116754365|ref|YP_843483.1| 141 LIPMFFLIGIWGGPRKDYSAIKFFIYTHVASLVMLLaIFAMY 182
                                    556666665555555556666666666666666666443333 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.2
                  Oxidored_q5_N  45 s 45 
                                    +
  gi|116754365|ref|YP_843483.1| 303 K 303
                                    1 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 0.87
                  Oxidored_q5_N  34 lallsllll 42 
                                    l ++ +++l
  gi|116754365|ref|YP_843483.1| 322 LGAVAFTWL 330
                                    222222222 PP

  == domain 5  score: -3.2 bits;  conditional E-value: 1.5
                  Oxidored_q5_N  95 lFllllilLlllLi 108
                                    +Fl+ll+ L+ +Li
  gi|116754365|ref|YP_843483.1| 465 VFLTLLFGLQPALI 478
                                    45555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (502 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       885  (0.0493614); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 3527.86
//
Query:       gi|116754366|ref|YP_843484.1|  [L=490]
Description: proton-translocating NADH-quinone oxidoreductase, chain N [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-65  220.6  29.1    2.4e-65  220.6  29.1    2.8  2  Proton_antipo_M  Proton-conducting membrane transporter
  ------ inclusion threshold ------
       0.55   10.2   5.3         11    6.0   0.4    3.6  2  DUF3285          Protein of unknown function (DUF3285)


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   1.7      0.12   1.1e+03      44      93 ..      39      84 ..      12     115 .. 0.67
   2 !  220.6  29.1   2.7e-69   2.4e-65       1     292 [.     119     428 ..     119     429 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.12
                Proton_antipo_M 44 lgsliLLlgilllynltgtlefeelskalelglnslelllllllllvgll 93
                                   l+  +L++++ ++++++ ++ f + s+     ++   +++ ++++lv+ll
  gi|116754366|ref|YP_843484.1| 39 LSLAALVVAMWMVLTAETNTVFFYDSLR----VDGFSQFFKAVFVLVSLL 84
                                   5556677777766666655555555544....333333344444444333 PP

  == domain 2  score: 220.6 bits;  conditional E-value: 2.7e-69
                Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskalelglnsle 80 
                                    a dL++l++g+El +l++y ++g+ ++k k+leA++k+fl+++++s ++L+g+++ly++tg++++ +++ a +l++ +++
  gi|116754366|ref|YP_843484.1| 119 AIDLVSLFIGFELASLSTYAMAGFDRTK-KNLEAAMKYFLYGAASSAFMLFGFSMLYGMTGSTKIADIAAA-SLAAFNPA 196
                                    569**********************888.9****************************************9.999999** PP

                Proton_antipo_M  81 lllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla.vssneisqlllilaiisml 159
                                    +l++l++++vg+++K+a+vp+h+W pd y++aP+ vsallAa   k+g  + +r++l+     + e++  ++ila+++m 
  gi|116754366|ref|YP_843484.1| 197 ILIALIFVVVGFAFKMALVPFHMWAPDTYEGAPALVSALLAAGSKKMGFAAAFRVILIALlALKLEWYMAFAILAAVTMT 276
                                    ****************************************999***********99998888999*************** PP

                Proton_antipo_M 160 lgslvalaqtdiKrllAySsishlGymlialav.....at..........qygveaaiihllthalfkallFl...lags 221
                                    +g+lva  q++++r+lAySsi++ Gy+ ia++v     ++          qy++++ ++++l ha++k + F+   ++ s
  gi|116754366|ref|YP_843484.1| 277 VGNLVACWQNNVRRILAYSSIAQAGYISIAFVVlgvasEGmtgpnnlpldQYALAGGLLLVLGHAIMKTGAFIstaQVAS 356
                                    **************************999988754433222233333333577888999*************73335667 PP

                Proton_antipo_M 222 viyerektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvla.vvasvl 292
                                    + ++ e+ +di +y+gL  + Pi+a +++v++++laG+Pptag+++kf ++ +a+  +l++l+++ ++ s+l
  gi|116754366|ref|YP_843484.1| 357 IAKNSEDPDDISNYAGLGRRAPITAFCMTVFMFALAGIPPTAGYFGKFVVFGSAIYGGLVWLAVLaILNSAL 428
                                    777788999**************************************************9999996777766 PP

>> DUF3285  Protein of unknown function (DUF3285)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.6    0.0048        43      27      39 ..      15      27 ..      12      32 .. 0.90
   2 ?    6.0   0.4    0.0013        11      24      44 .]      72      92 ..      66      92 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0048
                        DUF3285 27 LTtvgllgllvgl 39
                                   LT+v ll +lvgl
  gi|116754366|ref|YP_843484.1| 15 LTAVSLLVVLVGL 27
                                   9***********8 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0013
                        DUF3285 24 HFfLTtvgllgllvglayLtr 44
                                    Ff  ++ l++llv +a Ltr
  gi|116754366|ref|YP_843484.1| 72 QFFKAVFVLVSLLVVIASLTR 92
                                   68889999************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (490 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       958  (0.053433); 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:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 3534.83
//
Query:       gi|116754367|ref|YP_843485.1|  [L=107]
Description: HesB/YadR/YfhF-family protein [Methanosaeta thermophila PT]
Scores for 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   24.8   0.0    2.7e-05   24.3   0.0    1.2  1  Fe-S_biosyn  Iron-sulphur cluster biosynthesis


Domain annotation for each model (and alignments):
>> Fe-S_biosyn  Iron-sulphur cluster biosynthesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   1.5e-09   2.7e-05       3      89 ..       2      76 ..       1      81 [. 0.89

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1.5e-09
                                   EEE-HHHHHHHHHHHHCTTEC.EEEEEECCTSCCGGS.TT.EEEEEEEEESSTSTTTEEEEEETTEEEEEEGGGHHHS.TTE CS
                    Fe-S_biosyn  3 itlteaAaeklkkllaedkke.lrLdvddgggpyskggCsiggkyslvlvdeedeeydevlesnggkvyvksyslvfldegl 83
                                   i++t+aAa   k++l ++k   + L+  d+           g++y l ++d + +e d+ +esng+++++++++++ l  ++
  gi|116754367|ref|YP_843485.1|  2 IEITDAAAMVMKEHLVPGKVVrMFLAAIDET----------GANYGLAVTD-P-AENDVLFESNGITIHMSPEDAEIL-SET 70
                                   99***************99866777777775..........******9988.5.7***********************.899 PP

                                   EEEEEE CS
                    Fe-S_biosyn 84 vldfve 89
                                    +df +
  gi|116754367|ref|YP_843485.1| 71 IIDFID 76
                                   999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.37
# Mc/sec: 858.51
//
Query:       gi|116754368|ref|YP_843486.1|  [L=303]
Description: NAD-dependent epimerase/dehydratase [Methanosaeta thermophila PT]
Scores for complete 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-39  134.8   0.0    4.1e-39  134.5   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    1.1e-35  123.6   0.0    5.8e-35  121.3   0.0    2.0  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    1.1e-09   37.7   0.0    5.7e-09   35.4   0.0    1.9  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    2.5e-06   26.9   0.0     0.0056   15.9   0.1    2.5  2  NAD_binding_4    Male sterility protein
    2.4e-05   23.6   0.1       0.15   11.2   0.0    2.0  2  RmlD_sub_bind    RmlD substrate binding domain
      0.007   16.3   0.0      0.022   14.7   0.0    1.8  2  KR               KR domain
     0.0087   15.5   0.1      0.013   14.9   0.1    1.3  1  adh_short        short chain dehydrogenase
  ------ inclusion threshold ------
      0.065   12.8   0.0       0.96    9.0   0.0    2.1  2  NmrA             NmrA-like family
       0.11   11.6   0.2       0.22   10.6   0.1    1.5  2  Polysacc_synt_2  Polysaccharide biosynthesis protein


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 !  134.5   0.0   2.1e-42   4.1e-39       1     241 []       3     229 ..       3     229 .. 0.87

  Alignments for each domain:
  == domain 1  score: 134.5 bits;  conditional E-value: 2.1e-42
                                    EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHH CS
                      Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggvaas 80 
                                    +lVtG++GfiGs+lv++l + g +vi+ld+l+++s ++    le  ++++   s+ +    ++++d ++hl+  ++ + +
  gi|116754368|ref|YP_843486.1|   3 ALVTGGAGFIGSNLVEELVRSGEDVIVLDNLQTGSLRN----LEGLDVEIVTMSCNDIPRLDVNADRIFHLGIPSSSPMY 78 
                                    59*****************************6655544....4445566665555555455679*******997777777 PP

                                    HHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHHHHHH CS
                      Epimerase  81 sedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklveayaaqy 160
                                     ++p  +  + l+g + ++e ar++++ r++++s+s++Y   ++ p  e++   ++k +  Y  a  a+e+++e y++ +
  gi|116754368|ref|YP_843486.1|  79 RDNPFLVG-EALNGFVAVMELARRCDA-RVVYASTSSLYNGLEP-PHREDM---EIKVTDYYTEARFAMERIAELYRKLF 152
                                    77777755.69****************.************9999.999999...99************************ PP

                                    T-EEEEEEESEEESTT.S-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT-STTEEEE CS
                      Epimerase 161 glnaiilrlfnlyGpr.ngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvdagdkgeiyn 239
                                    g++ + +r f++yGp  + +g+ ++++++++  + +++   +++gdg++ Rdf+yv+Dv++a++l+++     d ++++n
  gi|116754368|ref|YP_843486.1| 153 GVSSLGMRFFSVYGPKeESKGRYANMVTQFLWGMMRKE-TPVIYGDGSQTRDFIYVRDVVRALILAMDS----DYNGVLN 227
                                    ****************6666667777777777777777.*****************************9....6677999 PP

                                    ES CS
                      Epimerase 240 iG 241
                                    iG
  gi|116754368|ref|YP_843486.1| 228 IG 229
                                    98 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 !  121.3   0.0   2.9e-38   5.8e-35       1     331 [.       4     292 ..       4     293 .. 0.87

  Alignments for each domain:
  == domain 1  score: 121.3 bits;  conditional E-value: 2.9e-38
                                    EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEE CS
                  GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevy 80 
                                    L+TG+aGfiGs+l+e L++ g +v++++++    +tg++++l+         +++++ +  +D  +l     +v+ d+++
  gi|116754368|ref|YP_843486.1|   4 LVTGGAGFIGSNLVEELVRSGEDVIVLDNL----QTGSLRNLEGL-------DVEIVTMSCNDIPRL-----DVNADRIF 67 
                                    9***********************998765....45666666532.......467999999996655.....6899**** PP

                                    E--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHHHHHHHH CS
                  GDP_Man_Dehyd  81 nLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYaaaKlya 160
                                    +L+  s  +   ++P  + e+ + G + ++e++r++     +r++ aSts +Y  + e p +E+  ++ +  Y  a+ + 
  gi|116754368|ref|YP_843486.1|  68 HLGIPSSSPMYRDNPFLVGEA-LNGFVAVMELARRCD----ARVVYASTSSLYNGL-EPPHREDMEIKVTDYYTEARFAM 141
                                    *******************99.9************96....79**********777.69********************* PP

                                    HHHHHHHHHHH---EEEEEE-EEESTTS-TT.SCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHHC CS
                  GDP_Man_Dehyd 161 dwivvnyreayglfavngilfnhesprrget.fvtrkitravarialgkqevlylGnldakRdwghvkDyveamwlmlqq 239
                                    + i++ yr+ +g+  +  ++f  ++p+ + +    + +t+++  + +++ + +++G+++++Rd+ +v+D+v+a+ l++ +
  gi|116754368|ref|YP_843486.1| 142 ERIAELYRKLFGVSSLGMRFFSVYGPKEESKgRYANMVTQFLWGMMRKETP-VIYGDGSQTRDFIYVRDVVRALILAMDS 220
                                    ***************************987734667888888888777655.569************************* PP

                                    SS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB--B-THHHHHHH-- CS
                  GDP_Man_Dehyd 240 dkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlllgdaskakeeLgW 319
                                    d +   +i+tg+ hs ++++++   +lg ++  +                   + +++ +   v+ +l+d+ska+  Lg+
  gi|116754368|ref|YP_843486.1| 221 DYNGVLNIGTGRAHSFNDVIHILGRRLGVEVRPR-------------------YVENPIK-NYVQHTLADISKAEICLGF 280
                                    *********************9999999865443...................2222332.2367889************ PP

                                    --SS-HHHHHHH CS
                  GDP_Man_Dehyd 320 kpkvsfeelvre 331
                                    ++ +s+e++++e
  gi|116754368|ref|YP_843486.1| 281 RAAYSLEDGINE 292
                                    *********987 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.0   2.8e-12   5.7e-09       1     229 [.       4     218 ..       4     222 .. 0.74

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 2.8e-12
                      3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslvdva 80 
                                    +vtGgaGF+G++lv+eLvr +e  +v vlD  +  +l  +l+ ++v+ +++   +d ++l+    ++d ++hl ++  + 
  gi|116754368|ref|YP_843486.1|   4 LVTGGAGFIGSNLVEELVRSGE--DVIVLDNLQTGSL-RNLEGLDVE-IVTMSCNDIPRLDV---NADRIFHL-GIPSSS 75 
                                    69*******************6..******8887777.567777777.77777777777775...67889**9.887777 PP

                      3Beta_HSD  81 gkltedeim.kvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKalaEklvlk 159
                                     +++++ +     ++G   v+e +++++ r +vY S+ +   +    e+ +    ++ +e + +d y+e +   E++   
  gi|116754368|ref|YP_843486.1|  76 PMYRDNPFLvGEALNGFVAVMELARRCDAR-VVYASTSSLYNG---LEPPH----REDMEIKVTDYYTEARFAMERIAEL 147
                                    77777754414579**************76.79****998777...55555....4455666777777776666655433 PP

                      3Beta_HSD 160 aNgrtlknggrlyTcaLRpagiyGegdkllvpllkqlak......lglalfkigdeevlsdrvYvgNvawahilAa 229
                                         l +   +    +R   +yG++++   + ++ +++       +++ + +gd +++ d++Yv  v+ a ilA+
  gi|116754368|ref|YP_843486.1| 148 YRK--LFG---VSSLGMRFFSVYGPKEESKGRYANMVTQflwgmmRKETPVIYGDGSQTRDFIYVRDVVRALILAM 218
                                    333..443...466789********9987766666665522121123456789*********************97 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   2.8e-06    0.0056       1      27 [.       5      29 ..       5      36 .. 0.88
   2 !    8.6   0.0   0.00048      0.96      79     150 ..      54     125 ..      44     214 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.8e-06
                                   EE-TTSHHHHHHHHHHHHHS-.TEEEE CS
                  NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpevkiyl 27
                                   +TG+ GF+G+ L+e+L+r+ ++  +++
  gi|116754368|ref|YP_843486.1|  5 VTGGAGFIGSNLVEELVRSGED--VIV 29
                                   7******************996..443 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00048
                                    HHHHHHHHH--EEEE--..SS-S.STTSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEE.GGGTTS-TTT--SS CS
                  NAD_binding_4  79 edlqelaeevdviihsa..AtvnfdepykellrvNveGtrevlelakklkklkvllhvST.ayvngeregeveek 150
                                    +d+ +l  + d i+h +   +  + ++ + l+   ++G + v+ela+++ +   +++ ST +  ng +  + +e+
  gi|116754368|ref|YP_843486.1|  54 NDIPRLDVNADRIFHLGipSSSPMYRDNPFLVGEALNGFVAVMELARRCDAR--VVYASTsSLYNGLEPPH-RED 125
                                    5666777777888887744455566666668888999************888..99****66666665533.333 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 !   11.2   0.0   7.3e-05      0.15       1      33 [.       1      33 [.       1      65 [. 0.81
   2 !   10.8   0.0   9.5e-05      0.19      84     154 ..      94     167 ..      84     222 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.3e-05
                                   EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT CS
                  RmlD_sub_bind  1 mkilvtGanGqlGseLakqlaeeglevlaltre 33
                                   m+ lvtG+ G +Gs+L+++l ++g +v+ l++ 
  gi|116754368|ref|YP_843486.1|  1 MTALVTGGAGFIGSNLVEELVRSGEDVIVLDNL 33
                                   789*************************99654 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 9.5e-05
                                    HHHHHHHHCT-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHHH-S....SEEEEEE-SEESS CS
                  RmlD_sub_bind  84 alAeaaaavgalLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavlaagk....kalivRtswvyge 154
                                    a+ e+a++++a +++ St   ++G  + p +ed e +   +Y +++ a+E+  + + k      l +R+  vyg 
  gi|116754368|ref|YP_843486.1|  94 AVMELARRCDARVVYASTSSLYNGL-EPPHREDMEIKVTDYYTEARFAMERIAELYRKlfgvSSLGMRFFSVYGP 167
                                    677899999***************9.567*********************9876543311114444666666665 PP

>> KR  KR 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     0.022       2      60 ..       2      53 ..       1      61 [. 0.77
   2 ?   -2.0   0.0       1.5   2.9e+03      17      35 ..      95     113 ..      90     138 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.1e-05
                                   EEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE--- CS
                             KR  2 tylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaa 60
                                   t l+tGG+G +G  l++ l+++g+  +vl   +       +  +++le l++e+ ++++
  gi|116754368|ref|YP_843486.1|  2 TALVTGGAGFIGSNLVEELVRSGEDVIVLDNLQ-------TGSLRNLEGLDVEIVTMSC 53
                                   579*********************999985444.......3345666666666665555 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.5
                                    HHHHHHHHS-EEEEE-SS. CS
                             KR  17 arwlaekgarhlvllsRsa 35 
                                    +  la+++ +++v+ s s+
  gi|116754368|ref|YP_843486.1|  95 VMELARRCDARVVYASTSS 113
                                    5566777777777766664 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   6.7e-06     0.013       2      35 ..       2      35 ..       1      56 [. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6.7e-06
                                   EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHH CS
                      adh_short  2 vvlvtGassGIGraiakelakeGakvvvvdrsee 35
                                   ++lvtG+++ IG ++++el+++G +v+v+d+ + 
  gi|116754368|ref|YP_843486.1|  2 TALVTGGAGFIGSNLVEELVRSGEDVIVLDNLQT 35
                                   69**************************998765 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00048      0.96       2      54 ..       4      55 ..       3      68 .. 0.88
   2 ?    1.6   0.0     0.086   1.7e+02     163     230 ..     188     252 ..     172     257 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00048
                                   EESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT- CS
                           NmrA  2 lviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdldd 54
                                   lv+G++G +G+ +v+ l+++g +v +l  ++++  +++l+   ve+v  + +d
  gi|116754368|ref|YP_843486.1|  4 LVTGGAGFIGSNLVEELVRSGEDVIVL-DNLQTGSLRNLEGLDVEIVTMSCND 55
                                   79*********************9765.7899999999999999999888887 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.086
                                    TS.-EEEEESS-TTS-EE-HHHHHHHHHHHHHHHHHHHTTEEEEE-SEEE-HHHHHHHHHHHHTS-EE CS
                           NmrA 163 pedkvtllgpgnpkavlldaeeDiGafvikilkdprklkgkriklagntlsgneivelfekkigktvk 230
                                     +++ ++ g+g+    ++  ++D+ ++ i +++  ++++g+    +g   s+n++++++ +++g +v+
  gi|116754368|ref|YP_843486.1| 188 RKETPVIYGDGSQTRDFI-YVRDVVRALILAMD--SDYNGVLNIGTGRAHSFNDVIHILGRRLGVEVR 252
                                    344788999999888888.99999999988887..57889999999999***********99998885 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00011      0.22       2      29 ..       4      31 ..       3      55 .. 0.82
   2 ?   -3.5   0.0       2.2   4.4e+03     187     223 ..     188     224 ..     178     251 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00011
                                   EEETTTSHHHHHHHHHHHHHB-SEEEEE CS
                Polysacc_synt_2  2 lvtGagGsiGselvrqilkkkpkkiill 29
                                   lvtG++G iGs+lv++++++    i+l 
  gi|116754368|ref|YP_843486.1|  4 LVTGGAGFIGSNLVEELVRSGEDVIVLD 31
                                   8****************99887666654 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.2
                                    HTTSSEEES-TT-EEEEE-HHHHHHHHHHHHHH--SS CS
                Polysacc_synt_2 187 keggpvtvTdpemtRyfmtieeavqLvlqalalakgg 223
                                    ++++pv   d + tR f+ +++ v+ ++ a+    +g
  gi|116754368|ref|YP_843486.1| 188 RKETPVIYGDGSQTRDFIYVRDVVRALILAMDSDYNG 224
                                    5566777777777888888888887777776655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); 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: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2296.49
//
Query:       gi|116754369|ref|YP_843487.1|  [L=409]
Description: NAD-dependent epimerase/dehydratase [Methanosaeta thermophila PT]
Scores for 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-70  235.8   0.0    7.6e-66  222.8   0.0    3.0  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    3.8e-52  177.1   0.0      7e-52  176.3   0.0    1.4  1  Epimerase        NAD dependent epimerase/dehydratase family
    2.5e-09   36.7   0.0    3.8e-09   36.1   0.0    1.2  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    2.7e-09   36.5   0.0    4.8e-09   35.6   0.0    1.4  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    5.3e-07   29.1   0.0    1.6e-06   27.5   0.0    1.7  1  NAD_binding_4    Male sterility protein
    1.9e-06   27.2   0.0    1.1e-05   24.7   0.0    1.9  2  RmlD_sub_bind    RmlD substrate binding domain
    3.6e-05   23.7   0.0    5.9e-05   23.0   0.0    1.4  1  NAD_binding_10   NAD(P)H-binding
    0.00037   20.5   0.0    0.00085   19.3   0.0    1.6  1  KR               KR domain
    0.00086   18.8   0.0     0.0018   17.8   0.0    1.5  1  adh_short        short chain dehydrogenase
     0.0047   16.5   0.0     0.0096   15.5   0.0    1.5  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 !  222.8   0.0   4.3e-69   7.6e-66       1     331 [.       9     397 ..       9     398 .. 0.83

  Alignments for each domain:
  == domain 1  score: 222.8 bits;  conditional E-value: 4.3e-69
                                    EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TT.HHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEE CS
                  GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfnt.griehlakdpkeeleenlklhkgDltDssslerllaevqpdev 79 
                                    LiTG++Gf+Gs +a++L++ g  v+g+vrr s  ++  ++e+l       ++++++l++gDl++ ss+ +++   +pd +
  gi|116754369|ref|YP_843487.1|   9 LITGVSGFVGSRMARRLVDAGASVYGLVRRRSDGRMpVNLERLG------IKKDVRLIEGDLENISSIGNAITASDPDII 82 
                                    9*****************************99987524666664......67899************************* PP

                                    EE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-....................... CS
                  GDP_Man_Dehyd  80 ynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkv....................... 136
                                    ++LAAqs+V++sf +P +t+ +n  Gt +LLea+r   ++  + +++a++sE YG v                       
  gi|116754369|ref|YP_843487.1|  83 FHLAAQSFVPRSFVDPNETMLCNCWGTSNLLEAVRLKDVD--ATVVFAGSSEEYGLVisseeqykralekygavfpeper 160
                                    ***********************************98774..67778999999998866555444444444333443322 PP

                                    .SSSSB-TTS-----SHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECT CS
                  GDP_Man_Dehyd 137 .qevpqtEttpfyPrsPYaaaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylG 215
                                      e p++Et+p++P sPYa++K+y d++++ny+++yg+++v+++ fnhe+  rg  fvt  it +v++ +lg+ + +++G
  gi|116754369|ref|YP_843487.1| 161 iPELPISETNPLRPMSPYAVSKVYGDYLMRNYWHSYGIPTVVSRAFNHEGAGRGIMFVTSVITSQVMKLKLGEIDGITIG 240
                                    224677789*********************************************************************** PP

                                    TTT-EEEEEEHHHHHHHHHHHH.HCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH..................... CS
                  GDP_Man_Dehyd 216 nldakRdwghvkDyveamwlml.qqdkpedyviatgethsvrefvelaflelgktiewegkgeeevg............. 281
                                    n +a Rdw hv+D+++++ l+  ++++ + y+ ++ +t sv + + ++++e+g  +   ++   e+              
  gi|116754369|ref|YP_843487.1| 241 NVNAFRDWSHVDDIIDGYILLAvKAKRGDVYNQGSMRTNSVLSYILMSLEEAGYPVSRIETFHGEKIvddptepdsspif 320
                                    *****************877651667778899999*****************9765544333322223466677788888 PP

                                    ................................TTGGCCCEECGG--SS--SB--B-THHHHHHH----SS-HHHHHHH CS
                  GDP_Man_Dehyd 282 ............................rakesgkvvvevdpkyfrpgevdlllgdaskakeeLgWkpkvsfeelvre 331
                                                                +++ + ++++ +++++frp+ev  ll d++k++  +g+  + ++++++r+
  gi|116754369|ref|YP_843487.1| 321 glnfdkttvdgmmlrgelefvqedggiiAHSGERRIRIVFERERFRPAEVPILLSDTRKIE-SIGFMVRHTVRDIIRD 397
                                    8888888777777777777766666643334566677778999*****************9.89*9999999999986 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.3   0.0   3.9e-55     7e-52       1     239 [.       8     272 ..       8     274 .. 0.93

  Alignments for each domain:
  == domain 1  score: 176.3 bits;  conditional E-value: 3.9e-55
                                    EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.......EEEE--TT-HHHHHHHHHHHT-SEEEE--S CS
                      Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl.......elveldltdrsalerlfkeeqpdavihlAa 73 
                                    il+tG++Gf+Gs ++++l ++g  v gl r++s+++   + +        +l+e+dl + s++ +++   +pd+++hlAa
  gi|116754369|ref|YP_843487.1|   8 ILITGVSGFVGSRMARRLVDAGASVYGLVRRRSDGRMPVNLERlgikkdvRLIEGDLENISSIGNAITASDPDIIFHLAA 87 
                                    8***************************9998888776655557999********************************* PP

                                    ---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCT.EEEEEEEGGGGT.....................SCSSSSBSTCS CS
                      Epimerase  74 vggvaassedpadfieknlqgtlnlleaarkagvk.rllflsSsevYG.....................kdaeqpkeett 131
                                    ++ v++s+ dp++++  n+ gt nllea+r ++v+  ++f++Sse YG                     +++++p+   +
  gi|116754369|ref|YP_843487.1|  88 QSFVPRSFVDPNETMLCNCWGTSNLLEAVRLKDVDaTVVFAGSSEEYGlvisseeqykralekygavfpEPERIPELPIS 167
                                    **********************************99*****************************999644446866666 PP

                                    TTS----SSHHHHHHHHHHHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEE CS
                      Epimerase 132 ltgplkpnspYaaaKlageklveayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRd 211
                                    +t pl+p spYa++K++g+ l+++y+++yg+++++ r fn++G+++g  +v++vi+  + k+++g+ + + +g+ +a Rd
  gi|116754369|ref|YP_843487.1| 168 ETNPLRPMSPYAVSKVYGDYLMRNYWHSYGIPTVVSRAFNHEGAGRGIMFVTSVITSQVMKLKLGEIDGITIGNVNAFRD 247
                                    667***************************************************************666666******** PP

                                    EEEHHHHHHHHHHHHHHHTT-STTEEEE CS
                      Epimerase 212 flyveDvaeaillvlehvdagdkgeiyn 239
                                    + +v+D++++++l++ +    + g++yn
  gi|116754369|ref|YP_843487.1| 248 WSHVDDIIDGYILLAVKA---KRGDVYN 272
                                    *************99994...5566777 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.0   2.1e-12   3.8e-09       1     125 [.       8     126 ..       8     131 .. 0.90

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 2.1e-12
                                    EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SE CS
                Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdv 80 
                                    +l+tG +G +Gs++ r++++  ++   l+ r     + ++ e    +k+      +  + gd+++ +++ +a+++ ++d+
  gi|116754369|ref|YP_843487.1|   8 ILITGVSGFVGSRMARRLVDAGASVYGLVRRRSDGRMPVNLERLGIKKD------VRLIEGDLENISSIGNAITASDPDI 81 
                                    89***********************999999999988888885433333......33456******************** PP

                                    EEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEE CS
                Polysacc_synt_2  81 vfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvl 125
                                    +fh AA   VP     p e++  N  gt+n++ea   ++v++ v+
  gi|116754369|ref|YP_843487.1|  82 IFHLAAQSFVPRSFVDPNETMLCNCWGTSNLLEAVRLKDVDATVV 126
                                    ****************************************99887 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.0   2.7e-12   4.8e-09       1     119 [.       9     133 ..       9     176 .. 0.74

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 2.7e-12
                      3Beta_HSD   1 vvtGgaGFlGralvkeLvrlee.lkevrvlDlrespelleelskvnvkk...viegDvtdkdkleealegv..dvvihla 74 
                                    ++tG +GF+G+++ ++Lv+++  +     +  r + ++  +l+++++kk   +iegD+ + +++ +a+  +  d+++hla
  gi|116754369|ref|YP_843487.1|   9 LITGVSGFVGSRMARRLVDAGAsV--YGLVRRRSDGRMPVNLERLGIKKdvrLIEGDLENISSIGNAITASdpDIIFHLA 86 
                                    69*******************732..22222333334444555666655556***************98663379***** PP

                      3Beta_HSD  75 slvdvag.kltedeimkvnvkGTrnvleacvkagvrv.lvYtSsaev 119
                                    + + v    +  +e m  n  GT n+lea + ++v + +v+  s e 
  gi|116754369|ref|YP_843487.1|  87 AQSFVPRsFVDPNETMLCNCWGTSNLLEAVRLKDVDAtVVFAGSSEE 133
                                    *9999764778999*********************752677777664 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   0.0   8.7e-10   1.6e-06       1     202 [.      10     204 ..      10     207 .. 0.74

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 8.7e-10
                                    EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHHHHHHHHHHT-SS-HHHHHHHHHTTTEEEEE--TTSGGGG--HHH CS
                  NAD_binding_4   1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksgesaeeRleeelekkelfsallkelaerikvveGDlseprlGLseed 80 
                                    +TG++GF+G+++ ++L++  +   +y lvR +s+     R+  +le+ ++++++        + +eGDl++    +s+  
  gi|116754369|ref|YP_843487.1|  10 ITGVSGFVGSRMARRLVDAGA--SVYGLVRRRSD----GRMPVNLERLGIKKDV--------RLIEGDLEN----ISSIG 71 
                                    8******************98..8******9977....6776688888887666........7******97....66777 PP

                                    HHHHHHH--EEEE--SS-S.ST...TSSEEHHHHHHHHHHHHHHHT..SSS--.-EEEEEE.GGGTTS-TTT--SSS-H. CS
                  NAD_binding_4  81 lqelaeevdviihsaAtvnfde...pykellrvNveGtrevlelak..klkklkvllhvST.ayvngeregeveekvyee 154
                                        a+  d+i+h aA+  + +   + +e +  N  Gt ++le  +   + ++ v+   S+  y    +++e  ++++  
  gi|116754369|ref|YP_843487.1|  72 NAITASDPDIIFHLAAQSFVPRsfvDPNETMLCNCWGTSNLLEAVRlkDVDAT-VVFAGSSeEYGLVISSEEQYKRAL-- 148
                                    7778999*********97555522245678999**********9884334444.555556674433333322222222.. PP

                                    ..............HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEE CS
                  NAD_binding_4 155 ge.........keekldederaklkglpntYeqsKalaEklvrearrrsglpvvivR 202
                                     e         +   +   ++++       Y  sK+ +++l+r++ ++ g+p+v+ R
  gi|116754369|ref|YP_843487.1| 149 -EkygavfpepERIPELPISETNPLRPMSPYAVSKVYGDYLMRNYWHSYGIPTVVSR 204
                                    .1333577755555555666666666677*****************9********99 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 !   24.7   0.0   6.2e-09   1.1e-05       2      92 ..       7     119 ..       6     144 .. 0.92
   2 ?   -0.1   0.0      0.22     4e+02     112     139 ..     165     192 ..     153     204 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 6.2e-09
                                    EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT......................T--TTSHHHHHHHHHHH--SEEEE-- CS
                  RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre......................eldltdaeavaellkeakpdvvvnaA 59 
                                    +il+tG +G +Gs +a++l  +g++v++l r+                      e dl++ +++ +++ + +pd++ ++A
  gi|116754369|ref|YP_843487.1|   7 NILITGVSGFVGSRMARRLVDAGASVYGLVRRrsdgrmpvnlerlgikkdvrliEGDLENISSIGNAITASDPDIIFHLA 86 
                                    69***************************87789********************************************** PP

                                    ----HHHHHHSHHHHHHHHTHHHHHHHHHHHHC CS
                  RmlD_sub_bind  60 AytavDkaEseeeaayavnaeavealAeaaaav 92 
                                    A   v +   ++++ +  n  ++ +l ea +  
  gi|116754369|ref|YP_843487.1|  87 AQSFVPRSFVDPNETMLCNCWGTSNLLEAVRLK 119
                                    *********************999998887543 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.22
                                    -B-TTS----SSHHHHHHHHHHHHHHHH CS
                  RmlD_sub_bind 112 pYeeddetsPlnvYGrtKlaGEqavlaa 139
                                    p +e+++  P++ Y+ +K+ G    +++
  gi|116754369|ref|YP_843487.1| 165 PISETNPLRPMSPYAVSKVYGDYLMRNY 192
                                    678999**************99888775 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   3.3e-08   5.9e-05       1      95 [.      12     126 ..      12     153 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 3.3e-08
                                    TTTSHHHHHHHHHHHHC-T-EEEEEETT......HHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-S.EEEES---TCC CS
                 NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRn......peklaeleaeeglevvegdvtdvedlaealkgad.aVvsalggggk 73 
                                    G +G vG++ +++l+++g  +v  lvR+      p  l++l  ++ ++++egd+++ +++ +a++  d  +++ l++++ 
  gi|116754369|ref|YP_843487.1|  12 GVSGFVGSRMARRLVDAG-ASVYGLVRRrsdgrmPVNLERLGIKKDVRLIEGDLENISSIGNAITASDpDIIFHLAAQSF 90 
                                    779**************5.9******9944444444556777789********************999558999977776 PP

                                    ........HHHH........HHHHHHHHHHCT--EEEE CS
                 NAD_binding_10  74 ........deeg........aknivdaakeagvkRfvl 95 
                                            +           + n+++a++ ++v   v+
  gi|116754369|ref|YP_843487.1|  91 vprsfvdpN--EtmlcncwgTSNLLEAVRLKDVDATVV 126
                                    455555433..156999999999999999988876555 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   4.8e-07   0.00085       4     139 ..       9     132 ..       7     147 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 4.8e-07
                                    EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-..EEEE----TT-HHHHHHHHHHHHHHSS- CS
                             KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealga..evevvaaDvsdkdavealleeikaeepp 81 
                                    litG  G +G  +ar l++ ga+   l+ R+  +d ++     +le+lg+  +v++++ D+ + +++ +++++ +   p 
  gi|116754369|ref|YP_843487.1|   9 LITGVSGFVGSRMARRLVDAGASVYGLVRRR--SDGRMP---VNLERLGIkkDVRLIEGDLENISSIGNAITASD---PD 80 
                                    9**********************99999999..344433...46777776558**********999999999998...44 PP

                                    --EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEEEEHHH CS
                             KR  82 ikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelledesldffvlfSSiag 139
                                    i  ++h A     + +   +  d ++ +   + G+ nL e+++ +++d  v+f+  + 
  gi|116754369|ref|YP_843487.1|  81 I--IFHLAA----QSFVPRSFVDPNETMLCNCWGTSNLLEAVRLKDVDATVVFAGSSE 132
                                    4..999885....678888888899999999*******************99987765 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0     1e-06    0.0018       1      69 [.       6      75 ..       6      80 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1e-06
                                   SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT..TSEEEEEE-TTTSHHHHHHHHH CS
                      adh_short  1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee..gakalaiqvDvtdreevealve 69
                                   k +l+tG s+ +G  +a++l+ +Ga+v+ + r+ ++  ++  +l+++  ++++  i++D+++ +++ +++ 
  gi|116754369|ref|YP_843487.1|  6 KNILITGVSGFVGSRMARRLVDAGASVYGLVRRRSDG-RMPVNLERLgiKKDVRLIEGDLENISSIGNAIT 75
                                   789*************************955555555.46666677766899********99999888765 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   5.3e-06    0.0096       1      66 [.       8      78 ..       8      89 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.3e-06
                                   EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S.-SHHHHHHHHST....TEEEES-TT-HHHHHHHHTT-S CS
                           NmrA  1 IlviGaTGrqGksvvrallkaghkvralvRdt.kselakslkeaG....velvkgdlddkeslvealkgvd 66
                                   Il++G +G  G+ ++r l++ag +v  lvR   ++    +l+  G    v l++gdl++ +s+ +a+  +d
  gi|116754369|ref|YP_843487.1|  8 ILITGVSGFVGSRMARRLVDAGASVYGLVRRRsDGRMPVNLERLGikkdVRLIEGDLENISSIGNAITASD 78
                                   89***************************9986555555666655333489****************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); 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: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 2821.01
//
Query:       gi|116754370|ref|YP_843488.1|  [L=363]
Description: glycosyl transferase, group 1 [Methanosaeta thermophila PT]
Scores for complete 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-30  105.2   0.0    4.4e-30  104.5   0.0    1.2  1  Glycos_transf_1  Glycosyl transferases group 1
    1.5e-19   70.7   0.0    3.2e-19   69.7   0.0    1.5  1  Glyco_trans_1_4  Glycosyl transferases group 1
      3e-09   37.1   0.1    5.4e-09   36.3   0.1    1.4  1  Glyco_transf_4   Glycosyltransferase Family 4
      7e-05   23.2   0.6    0.00016   22.0   0.0    1.8  2  Glyco_trans_1_2  Glycosyl transferases group 1
    0.00038   19.4   0.0    0.00057   18.8   0.0    1.2  1  Epimerase_2      UDP-N-acetylglucosamine 2-epimerase


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.5   0.0   1.2e-33   4.4e-30      16     164 ..     194     338 ..     185     346 .. 0.89

  Alignments for each domain:
  == domain 1  score: 104.5 bits;  conditional E-value: 1.2e-33
                                    EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES...STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHHCE CS
                Glycos_transf_1  16 kiilsvgrlekeKgvdllikafallkkqlnpnvklviaG..ngeeekelkklaeelelsdnviflgevsredleellkna 93 
                                     + lsv+r+ +eK++dl  ++f++l++      +lv++G   + + +e  ++    ++ dnv++lg vs+++l  l+ ++
  gi|116754370|ref|YP_843488.1| 194 DFWLSVNRIYPEKRIDLQFDVFRKLPD-----ERLVVVGgyAKGDHAESYYRRLVKKIPDNVKMLGTVSEDELVDLYARC 268
                                    5789*******************9965.....599999999455555555566888999********************* PP

                                    SEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHH CS
                Glycos_transf_1  94 difvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelrer 164
                                    + +v++++ E fG++++EAma+g+pv+a+  gg+ e+v+dg+tG lv++   ++l++ai+ + +++e++++
  gi|116754370|ref|YP_843488.1| 269 KGLVCTAMDEDFGLTPVEAMASGKPVVAVREGGYVETVVDGVTGELVAAD-RDELIAAIKNISSNPERYRD 338
                                    *************************************************9.99*************76654 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 !   69.7   0.0     9e-23   3.2e-19       6     133 ..     198     331 ..     195     332 .. 0.84

  Alignments for each domain:
  == domain 1  score: 69.7 bits;  conditional E-value: 9e-23
                                    EES---GG.GTHHHHHHHHHHHH.HHEEEEEES...---...HHHHHHHTT-T.TEEEE---..THHHHHHHH-SEEEE- CS
                Glyco_trans_1_4   6 fvGrleenvkgvdllleavpllrkkdvrlvivG...dgp.rpeeleelaagleerveftGfv..edlaellaaadvfvaP 79 
                                     v r++++ k++dl  + + +l ++  rlv+vG   +g+  ++ +++l++++ ++v+++G v  ++l +l+a+++ +v++
  gi|116754370|ref|YP_843488.1| 198 SVNRIYPE-KRIDLQFDVFRKLPDE--RLVVVGgyaKGDhAESYYRRLVKKIPDNVKMLGTVseDELVDLYARCKGLVCT 274
                                    56788655.**************89..******33323333356666667999*********9555*************9 PP

                                    -..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH CS
                Glyco_trans_1_4  80 s..egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLle 133
                                       e fgl+ +Eama+g+pvVa + gg  e+v  g++g lv+  d ++l++ai ++ +
  gi|116754370|ref|YP_843488.1| 275 AmdEDFGLTPVEAMASGKPVVAVREGGYVETVvdGVTGELVA-ADRDELIAAIKNISS 331
                                    9999*********************99888777*****8886.59********98765 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.1   1.5e-12   5.4e-09       1     170 []      16     186 ..      16     186 .. 0.75

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 1.5e-12
                 Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvvtpgddgpleeev..elvvrvprvplpllkrllr...slaflrrlrrllkrekpDv 75 
                                    +GG er++l L raL ++     ++t + +++l ++         +++     k +++   s + l+ +  + +  ++D 
  gi|116754370|ref|YP_843488.1|  16 IGGGERVALMLGRALGAD-----IITTDLNPELVDRLgyG--DVTIKRLGDTIKLPPLkqiSASLLFGMCDVSD--GYDF 86 
                                    79***************9.....99999999999997542..33333333333333330003333333333333..9999 PP

                 Glyco_transf_4  76 vHahspaalgaallalrrrlgiplVltvHglye..............krllkarlkplsrllralerrllrradrviavS 141
                                        + ++++aa    r  ++ p  +++ ++                 ++ +   + + r   ++ +r +r+ dr++a+S
  gi|116754370|ref|YP_843488.1|  87 FIFSGNWSHYAA----R--KHHPNMWYCYTPVRafydlresmisrqpGYFRRLVTSSWIRCHSWFDQRSVRNLDRIVAIS 160
                                    977776666444....6..58899********99*********98887777777778888888889999*********** PP

                 Glyco_transf_4 142 eatadelrerygvppekitVipnGvDler 170
                                    e++++++++ y+  ++   Vi+++vD+ r
  gi|116754370|ref|YP_843488.1| 161 ETVRQRIEK-YH--KRSADVIYPPVDTGR 186
                                    *********.66..3558********965 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 ?   -2.1   0.1       1.4   5.1e+03      64      81 ..     154     171 ..     147     174 .. 0.68
   2 !   22.0   0.0   4.5e-08   0.00016       9      73 ..     278     344 ..     261     349 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.4
                Glyco_trans_1_2  64 eerraiaeaarervlaeh 81 
                                    +++ ai+e  r+r+++ h
  gi|116754370|ref|YP_843488.1| 154 DRIVAISETVRQRIEKYH 171
                                    566677777777777766 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 4.5e-08
                Glyco_trans_1_2   9 espnlrlfEaaacGafaltddaegleelftpgkevilfe.dleelaekiryllanpeerr.aiaeaa 73 
                                    e++ l  +Ea+a+G ++++ +  g+ e + +g ++ l++ d +el+++i+   +npe++r a  ++a
  gi|116754370|ref|YP_843488.1| 278 EDFGLTPVEAMASGKPVVAVREGGYVETVVDGVTGELVAaDRDELIAAIKNISSNPERYRdACLARA 344
                                    7788999**************************************************9872444444 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 !   18.8   0.0   1.6e-07   0.00057     204     324 ..     212     337 ..     202     356 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.6e-07
                                    HHHHHHHHHHH--EEEEE--..HHHHHHHHHHHHH-.TTEEEE----HHHHHHHHHC-SEEEE.....S-H.HHHHHHHH CS
                    Epimerase_2 204 lealkalakekdvevvvpvhnnprtrkrlleeleel.envtlieplgyldflsllknaklvlt.....dSg.GiqeEaps 276
                                    ++++++l +e ++ vv  +++ ++ ++  ++ ++++ +nv+++  +   +++ l +++k ++      d g +   Ea++
  gi|116754370|ref|YP_843488.1| 212 FDVFRKLPDE-RLVVVGGYAKGDHAESYYRRLVKKIpDNVKMLGTVSEDELVDLYARCKGLVCtamdeDFGlTPV-EAMA 289
                                    5677778776.67788889999999999999999*988********************96664366334454445.**** PP

                                    CT--EEESSSS-S-THHHHTTSEEE-TT-HHHHHHHHHHHCT-..--. CS
                    Epimerase_2 277 lgvpvvnlReeteRpegveagtnvlvgtdkeeIvaaleklledkkele 324
                                     g+pvv +Re +   + v+  t  lv +d++e++aa++++ ++ ++++
  gi|116754370|ref|YP_843488.1| 290 SGKPVVAVREGGYVETVVDGVTGELVAADRDELIAAIKNISSNPERYR 337
                                    ********99999888888999999***************98855554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2640.53
//
Query:       gi|116754371|ref|YP_843489.1|  [L=261]
Description: ABC-2 type transporter [Methanosaeta thermophila PT]
Scores for complete 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   86.3  32.5    2.5e-24   85.9  32.5    1.2  1  ABC2_membrane    ABC-2 type transporter


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.9  32.5   1.4e-28   2.5e-24       3     207 ..      18     219 ..      16     222 .. 0.89

  Alignments for each domain:
  == domain 1  score: 85.9 bits;  conditional E-value: 1.4e-28
                  ABC2_membrane   3 ikallkreflqrwrdpslgllwrliqplllalvfgtvfgnlgnsedglnrpgllffsvlflafsaltsvapvferergvl 82 
                                    i  l + +f++r+++++lg++w+l++p+l++lv+ +vf nl   + +   + ll +++l++++   ts+++  ++++++l
  gi|116754371|ref|YP_843489.1|  18 IIRLAWSDFKLRYKSSALGFFWSLLEPMLMLLVLYVVFTNLMRIQVEHYQLFLLLGIILWNFLDRGTSMSIWGIVGKPSL 97 
                                    77899**********************************87633333334****************************** PP

                  ABC2_membrane  83 erelvsplyslsayvlakvlvelpvsllqalifllivyflvgldlsrfflflllllltalaasslgllisalapsfedas 162
                                    +++ ++p           +l++ ++ +++ ++f+li+ ++  ++    ++f+lll+l ++++++l++++sa++++f+d++
  gi|116754371|ref|YP_843489.1|  98 VQKVYFPRDIIVISTCITALMMTALEFIVFVVFMLIFRVMPAWTA---VYFPLLLMLELMIITGLSMALSAMNVYFRDVQ 174
                                    ********6666666667777777777777777777777777777...******************************** PP

                  ABC2_membrane 163 qlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrs 207
                                    +++ +vl++ ++ +++++pi+  p+ ++w+  lnP++ ++ ++r 
  gi|116754371|ref|YP_843489.1| 175 FIWRVVLQVGFFATPVIYPITIFPEGVRWMVMLNPMAQIITMMRD 219
                                    ***********************99*****************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1016  (0.056668); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1800.28
//
Query:       gi|116754372|ref|YP_843490.1|  [L=399]
Description: ABC transporter related [Methanosaeta thermophila PT]
Scores for 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-24   84.1   0.1    1.9e-23   83.1   0.1    1.5  1  Wzt_C     Wzt C-terminal domain
    8.4e-23   81.4   0.1    3.4e-22   79.4   0.0    2.0  1  ABC_tran  ABC transporter
    1.1e-08   35.2   1.3    4.9e-05   23.3   0.6    2.3  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    0.00012   21.8   0.0    0.00027   20.6   0.0    1.5  1  AAA_29    P-loop containing region of AAA domain
    0.00015   21.6   0.0    0.00023   21.0   0.0    1.3  1  AAA_15    AAA ATPase domain
     0.0015   18.5   0.3        2.1    8.3   0.1    2.5  2  NTPase_1  NTPase
     0.0027   18.1   0.0     0.0039   17.6   0.0    1.3  1  AAA_16    AAA ATPase domain
     0.0036   17.8   1.9     0.0072   16.9   1.7    1.9  1  AAA_23    AAA domain
  ------ inclusion threshold ------
       0.02   15.3   0.1       0.15   12.5   0.1    2.1  1  AAA       ATPase family associated with various cellular acti
      0.053   12.5   0.0      0.081   11.9   0.0    1.2  1  MeaB      Methylmalonyl Co-A mutase-associated GTPase MeaB
      0.061   13.2   0.1      0.099   12.6   0.1    1.3  1  NACHT     NACHT domain
      0.073   12.5   0.2       0.15   11.5   0.0    1.5  2  SMC_N     RecF/RecN/SMC N terminal domain
      0.086   13.1   0.1       0.21   11.9   0.1    1.7  1  AAA_22    AAA domain
       0.09   13.3   0.1       0.17   12.4   0.1    1.5  1  AAA_18    AAA domain
       0.24   11.1   0.1        1.4    8.5   0.0    1.9  2  AAA_30    AAA domain


Domain annotation for each model (and alignments):
>> Wzt_C  Wzt C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.1   0.1   1.6e-26   1.9e-23       3     132 ..     257     380 ..     255     389 .. 0.88

  Alignments for each domain:
  == domain 1  score: 83.1 bits;  conditional E-value: 1.6e-26
                          Wzt_C   3 eryGsgeaeIedvelldaegeetstfesgeevtlrikvkahedvedpvfgfaikdrngqevfgtntelekksfeleelka 82 
                                    + ++ +e+eI+dv+++d+ g ++++f+ g+++++ri ++ah +v +pvfg+ +++ + ++++gt te+++++  +     
  gi|116754372|ref|YP_843490.1| 257 RASTRKEIEIVDVKFVDKYGCPNENFVAGDPLRVRIFFDAHGTVRSPVFGIIFYHGD-TYCYGTTTEFKGSD--T--GII 331
                                    567889************************************************766.59******999955..3..377 PP

                          Wzt_C  83 gervevefef.klpLapGeYlltvaledrdgeeneiydwlddalsfeVvss 132
                                    +++++v+f +  lp+ +G++ +tva++++d+++  +ydw+d+ + f+V++ 
  gi|116754372|ref|YP_843490.1| 332 NGKGYVDFIIpSLPFLQGRFEVTVAVASHDYST--QYDWHDRRYAFNVHNP 380
                                    77799*****989**************999998..*************843 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.4   0.0   2.8e-25   3.4e-22       1     135 [.      44     175 ..      44     177 .. 0.92

  Alignments for each domain:
  == domain 1  score: 79.4 bits;  conditional E-value: 2.8e-25
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                    lk+++l++++ge+++i+G+nG+GKStLlk++a+ l+pt+G +            +++ k   +l+    ++pel+vren 
  gi|116754372|ref|YP_843490.1|  44 LKDINLEVERGECIGIIGDNGSGKSTLLKIIAKILRPTSGFV------------KVFGKLTPFLELGVGFQPELSVRENi 111
                                    79****************************************............67777777777778888888888888 PP

                                    ............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEEST CS
                                    ............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEp 135
                                                  d++i+++++  gl+ ++d ++    ++LS G+++r+a   a+ ++p++ll+DE 
  gi|116754372|ref|YP_843490.1| 112 riyatimglpkkVIDDRIDDVIRFAGLERFEDAKL----KNLSSGMQVRLAFSTAIQTDPDILLVDEV 175
                                    888889999888899********************....****************************6 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.6   4.1e-08   4.9e-05       3      55 ..      58     104 ..      56     114 .. 0.80
   2 !   10.5   0.0   0.00033      0.39     234     299 ..     146     208 ..     113     212 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 4.1e-08
                         AAA_21   3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpe 55 
                                    ++iG+NgsGKS+LL+++      ++ ++++  +   +g+++    l  + +pe
  gi|116754372|ref|YP_843490.1|  58 GIIGDNGSGKSTLLKII------AKILRPTSGFVKVFGKLTPFLELGVGFQPE 104
                                    79***************......777888888887777777776666666665 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00033
                         AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSp 299
                                    + +lS+G++  la+ ta+  ++   ++ll+DE+ +  + +++ + ++++++ ++ g+ +++++H+ 
  gi|116754372|ref|YP_843490.1| 146 LKNLSSGMQVRLAFSTAIQTDP---DILLVDEVLAVGDMEFQQKCFRVFEDYRDSGVTILFVSHDL 208
                                    4578****************99...9*******999999999999999999999999999999986 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 !   20.6   0.0   2.2e-07   0.00027      17      50 ..      49      82 ..      38      86 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.2e-07
                         AAA_29 17 ieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                   +e+++ + + ++G++GsGKSTll  i+ +L p++
  gi|116754372|ref|YP_843490.1| 49 LEVERGECIGIIGDNGSGKSTLLKIIAKILRPTS 82
                                   4444444888*************99999998875 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0     2e-07   0.00023      14      84 ..      44     178 ..      40     277 .. 0.57

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2e-07
                         AAA_15  14 lkdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekkn....................................kk 56 
                                    lkd+ ++++      +iG N+sGKS++l+++ ++l  ++ +                                     kk
  gi|116754372|ref|YP_843490.1|  44 LKDINLEVERGeCIGIIGDNGSGKSTLLKIIAKILRPTSGFVkvfgkltpflelgvgfqpelsvreniriyatimglpKK 123
                                    566555555556778********************988444377777777777777777777777777777666666655 PP

                         AAA_15  57 vikiekedleifeniseskdikIdvef...........................a 84 
                                    vi++  +d+  f   +++ d k++                               
  gi|116754372|ref|YP_843490.1| 124 VIDDRIDDVIRFAGLERFEDAKLKNLSsgmqvrlafstaiqtdpdillvdevlaV 178
                                    5555555555555555555555544445555555555566666666666555551 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.1    0.0017       2.1       2      26 ..      57      81 ..      56      97 .. 0.77
   2 !    7.7   0.0    0.0025         3      92     134 ..     162     207 ..     146     228 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0017
                                   EEEE--TTSSHHHHHHHHHHHH... CS
                       NTPase_1  2 vfiTGppGvGKtTlvkkvlellkss 26
                                   + i G  G+GK+Tl+k +++ l+  
  gi|116754372|ref|YP_843490.1| 57 IGIIGDNGSGKSTLLKIIAKILRPT 81
                                   6788**************9999643 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0025
                                    HH.HHH-EEEE--...-STTGGG-HHHHHHHHHHHTTTSEEEEE--S CS
                       NTPase_1  92 al.seadviviDE...iGkmElkskkfkeaveevLksekpvlavihr 134
                                    a+ +++d++++DE   +G mE++ k f+   e+  +s++ +l+v h 
  gi|116754372|ref|YP_843490.1| 162 AIqTDPDILLVDEvlaVGDMEFQQKCFR-VFEDYRDSGVTILFVSHD 207
                                    333789*******5555*****998886.556666777777777665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   3.3e-06    0.0039      23      63 ..      53      94 ..      42     193 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.3e-06
                         AAA_16 23 rpelvllsGesGvGKsslvrellralekdggif.lrgkcdql 63
                                   r+e++ ++G+ G+GKs+l++ +++ l+ + g++ + gk + +
  gi|116754372|ref|YP_843490.1| 53 RGECIGIIGDNGSGKSTLLKIIAKILRPTSGFVkVFGKLTPF 94
                                   448999*****************9999997777899998888 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   1.7     6e-06    0.0072      20      40 ..      55      75 ..      36     267 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6e-06
                         AAA_23 20 gltlItGpNGaGKTTildAik 40
                                       I+G+NG+GK+T+l  i 
  gi|116754372|ref|YP_843490.1| 55 ECIGIIGDNGSGKSTLLKIIA 75
                                   5789*************9886 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   0.1   0.00013      0.15       3      74 ..      59     182 ..      57     214 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                                    EESSTTSSHHHHHHHHHHHHTHE..................................................EEEEETT CS
                            AAA   3 lyGppGtGKTllakavakelgve..................................................fleisgs 32 
                                    ++G  G GK++l k +ak l  +                                                  ++++ g 
  gi|116754372|ref|YP_843490.1|  59 IIGDNGSGKSTLLKIIAKILRPTsgfvkvfgkltpflelgvgfqpelsvreniriyatimglpkkviddriddVIRFAGL 138
                                    6899***************8533333445555666666666666777777777777777777777777777776666666 PP

                                    TCSSS...STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH CS
                            AAA  33 ellsk...yvgesekkirelfkeakekakpsilfiDEidalaksr 74 
                                    e +++       s +++r  f++a +   p il++DE+ a++  +
  gi|116754372|ref|YP_843490.1| 139 ERFEDaklKNLSSGMQVRLAFSTAIQTD-PDILLVDEVLAVGDME 182
                                    5553355555668899999999998887.99*****998876555 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 ?   11.9   0.0   6.8e-05     0.081      14      54 ..      39      79 ..      21      88 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.8e-05
                                   HHHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHH CS
                           MeaB 14 eakellerllakaGraqvvGltGvPGaGkstlvealglelr 54
                                   e+ ++l+ +  +  r + +G+ G  G+Gkstl++ ++  lr
  gi|116754372|ref|YP_843490.1| 39 ETFTVLKDINLEVERGECIGIIGDNGSGKSTLLKIIAKILR 79
                                   66789999999*********************998887776 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   8.3e-05     0.099       4      24 ..      58      78 ..      55      88 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.3e-05
                                   EEEC-TTTCHHHHHHHHHHHH CS
                          NACHT  4 ilqGeaGsGKTtLlqklalaw 24
                                    + G++GsGK+tLl+ +a  +
  gi|116754372|ref|YP_843490.1| 58 GIIGDNGSGKSTLLKIIAKIL 78
                                   589************999876 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 ?   11.5   0.0   0.00012      0.15      26      44 ..      56      74 ..      37      82 .. 0.78
   2 ?   -3.2   0.1       3.9   4.7e+03     149     188 ..     157     196 ..     146     213 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                                   EEEEEESTTSSHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxx RF
                          SMC_N 26 ftaivGpNGSGKsnlldAi 44
                                      i+G NGSGKs ll  i
  gi|116754372|ref|YP_843490.1| 56 CIGIIGDNGSGKSTLLKII 74
                                   5679**********99866 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.9
                                    HHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 149 LlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksk 188
                                    L f++       + l+De+ a  D +  +k  ++++  ++
  gi|116754372|ref|YP_843490.1| 157 LAFSTAIQTDPDILLVDEVLAVGDMEFQQKCFRVFEDYRD 196
                                    4444443344446778888888777777777766665554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00018      0.21       4      29 ..      53      78 ..      50     211 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00018
                         AAA_22  4 tagilvvtGesGtGKTtllrrlleql 29
                                   +  ++ ++G  G+GK+tll+ +++ l
  gi|116754372|ref|YP_843490.1| 53 RGECIGIIGDNGSGKSTLLKIIAKIL 78
                                   567899**************998877 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00014      0.17       1      22 [.      57      78 ..      57     182 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                         AAA_18  1 IlltGtpGvGKttlakeLskrl 22
                                   I++ G  G+GK+tl k ++k l
  gi|116754372|ref|YP_843490.1| 57 IGIIGDNGSGKSTLLKIIAKIL 78
                                   89****************9986 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0012       1.4      21      45 ..      57      81 ..      49      95 .. 0.81
   2 ?   -0.0   0.0      0.52   6.2e+02      85     122 ..     162     204 ..     122     208 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0012
                         AAA_30 21 avltGpAGtGKttalkalreaweaa 45
                                     + G  G+GK+t+lk ++++++  
  gi|116754372|ref|YP_843490.1| 57 IGIIGDNGSGKSTLLKIIAKILRPT 81
                                   56899**************998866 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.52
                         AAA_30  85 rlepg.tllivDEagmv....dtkqlaallkaaekagakvilv 122
                                    +++++ ++l+vDE+  v     +++  ++++  +++g+++++v
  gi|116754372|ref|YP_843490.1| 162 AIQTDpDILLVDEVLAVgdmeFQQKCFRVFEDYRDSGVTILFV 204
                                    4556669999999988732222344456666666667777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                       108  (0.00602376); 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: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 2786.67
//
Query:       gi|116754373|ref|YP_843491.1|  [L=234]
Description: methyltransferase type 11 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-07   32.0   0.0    3.4e-07   30.8   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
    9.5e-05   22.3   0.0    0.00022   21.1   0.0    1.4  1  Methyltransf_23  Methyltransferase domain
    0.00013   22.5   0.0    0.00066   20.3   0.0    2.1  1  Methyltransf_25  Methyltransferase domain
  ------ inclusion threshold ------
      0.012   15.4   0.0      0.019   14.7   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
      0.097   12.5   0.0       0.19   11.6   0.0    1.4  2  DUF268           Caenorhabditis protein of unknown function, 


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 !   30.8   0.0   9.4e-11   3.4e-07      45      96 .]      92     159 ..      71     159 .. 0.84

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 9.4e-11
                                    EEETTEECCCTSS-TT-EEEEEEES-CCC-..C..............CHHHHHHHHHHHEEEEEEEEE CS
                Methyltransf_11  45 vefvvadaeklpfednsfDlvvssevlhhv..e..............dpekalkeiaRvLkpgGllvi 96 
                                    ++ vv+da+++pf+d+ fD++++ ++l+h+  +                 +a++e+aR+ + +G++vi
  gi|116754373|ref|YP_843491.1|  92 IRPVVGDARSMPFRDGAFDMILCISTLEHIgrDntiyfngpipqdpeGDLSAIREMARITRRNGKIVI 159
                                    4559**************************8725788888888866544589*************986 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   6.1e-08   0.00022      20     123 ..      49     165 ..      36     196 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 6.1e-08
                Methyltransf_23  20 lraggrvLdiGcGtGi..llevl.rengfsvtgvDlspeaveiaekakkaqkdqfdeqeaaepqgkfdlIvlrevlehvp 96 
                                     r   rvLdiG++  +    +++ + n  +++g Dl  + ++ +      +++  d+ + ++ +g fd I ++ +leh+ 
  gi|116754373|ref|YP_843491.1|  49 YRGERRVLDIGYANAEdrYIDSInALNIPELYGLDLVGRSIPGI------RPVVGDARSMPFRDGAFDMILCISTLEHIG 122
                                    56678*******99953378888666677*******98877765......888888888889*****************9 PP

                Methyltransf_23  97 .dpp...............ellrqiatllkpgGylllseplas 123
                                     d +               +++r +a++++ +G +++++p  +
  gi|116754373|ref|YP_843491.1| 123 rDNTiyfngpipqdpegdlSAIREMARITRRNGKIVITVPYGR 165
                                    76567999******************************98333 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   1.8e-07   0.00066      47      81 ..      91     125 ..      82     155 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.8e-07
                                    TEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHH CS
                Methyltransf_25  47 nvefvqgdaedlpfedgsfDlvvssgalhhlsded 81 
                                     ++ v+gda+++pf dg fD+++++ +l+h+ +++
  gi|116754373|ref|YP_843491.1|  91 GIRPVVGDARSMPFRDGAFDMILCISTLEHIGRDN 125
                                    68999*******************988**987654 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   5.4e-06     0.019      60     113 ..      96     163 ..      91     214 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.4e-06
                Methyltransf_31  60 qgdieeleklledekfDlilsnevlnaladpdkile................eiervlkpggilliedpr 113
                                    +gd+ +++  + d  fD+il+ ++l ++   + i+                 e+ r  + +g ++i+ p 
  gi|116754373|ref|YP_843491.1|  96 VGDARSMP--FRDGAFDMILCISTLEHIGRDNTIYFngpipqdpegdlsairEMARITRRNGKIVITVPY 163
                                    79999***..***************666666666555666668888999999*************99877 PP

>> DUF268  Caenorhabditis protein of unknown function, DUF268
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       1.9   6.9e+03      21      46 ..      50      73 ..      35      79 .. 0.67
   2 ?   11.6   0.0   5.3e-05      0.19      61     114 ..     107     165 ..      92     184 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.9
                         DUF268 21 nGakkiltveynkleieeefkdrlss 46
                                   +G +++l + y++   e+++ d +++
  gi|116754373|ref|YP_843491.1| 50 RGERRVLDIGYAN--AEDRYIDSINA 73
                                   6777888887765..55666666655 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 5.3e-05
                         DUF268  61 ekfdfaasfssieksglg...rygdpl..dpiGdlrellkikCvlkkGgllflglPlGt 114
                                     +fd++ + s++e++g      +  p+  dp Gdl  +  +  + ++ g + + +P+G+
  gi|116754373|ref|YP_843491.1| 107 GAFDMILCISTLEHIGRDntiYFNGPIpqDPEGDLSAIREMARITRRNGKIVITVPYGR 165
                                    579************987443456665559****************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       278  (0.0155056); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1792.62
//
Query:       gi|116754374|ref|YP_843492.1|  [L=417]
Description: methyltransferase type 11 [Methanosaeta thermophila PT]
Scores for 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   74.2   0.0      2e-20   73.3   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    5.5e-20   71.8   0.0    9.1e-20   71.1   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    7.7e-16   58.4   0.0    1.2e-15   57.8   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    4.2e-12   46.7   0.0      7e-12   46.0   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
    2.2e-11   43.7   0.0    3.2e-11   43.2   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    4.6e-09   35.9   0.0    7.1e-09   35.3   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    5.7e-09   35.7   0.0    8.8e-09   35.1   0.0    1.2  1  MTS              Methyltransferase small domain
    2.1e-08   33.8   0.0      3e-08   33.3   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
    3.7e-06   26.5   0.0    4.9e-06   26.2   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    4.7e-06   26.1   0.0    7.2e-06   25.5   0.0    1.2  1  TehB             Tellurite resistance protein TehB
    0.00054   19.3   0.0      0.001   18.4   0.0    1.4  1  Methyltransf_2   O-methyltransferase domain
      0.006   15.6   0.0     0.0085   15.0   0.0    1.1  1  Methyltransf_9   Protein of unknown function (DUF1698)
     0.0068   16.1   0.0       0.01   15.4   0.0    1.2  1  NodS             Nodulation protein S (NodS)
     0.0069   16.0   0.0      0.012   15.2   0.0    1.3  1  MetW             Methionine biosynthesis protein MetW
  ------ inclusion threshold ------
      0.022   14.5   0.0      0.035   13.9   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
       0.14   11.3   0.0       0.19   10.8   0.0    1.2  1  DREV             DREV methyltransferase
       0.15   11.2   0.0       0.22   10.7   0.0    1.2  1  DUF3419          Protein of unknown function (DUF3419)
       0.18   11.0   0.0       0.78    8.9   0.0    1.8  2  NNMT_PNMT_TEMT   NNMT/PNMT/TEMT family


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 !   73.3   0.0     2e-23     2e-20       1      97 []      80     174 ..      80     174 .. 0.98

  Alignments for each domain:
  == domain 1  score: 73.3 bits;  conditional E-value: 2e-23
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHH CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsde 80 
                                    vLdlGcG+G ++l+++   g a+v++vD+s ++l + ++ra+++g+++e+ + d ++lpf+d+sfD v+++ + +h++d 
  gi|116754374|ref|YP_843492.1|  80 VLDLGCGPGVVALRCSLL-G-AEVYAVDPSRAALMISAKRARDAGARIELFEFDGRSLPFKDSSFDTVIMADVAEHIDDG 157
                                    9**************988.5.*************************************************988******* PP

                                    HHHHHHHHHHHHEEEEE CS
                Methyltransf_25  81 dlekalkeiarvLkpgG 97 
                                     l ++l+e++r L+pgG
  gi|116754374|ref|YP_843492.1| 158 TLSTLLSECFRTLTPGG 174
                                    ****************9 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.1   0.0   9.1e-23   9.1e-20       1      96 []      81     178 ..      81     178 .. 0.96

  Alignments for each domain:
  == domain 1  score: 71.1 bits;  conditional E-value: 9.1e-23
                                    EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-..CCHH CS
                Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhv..edpe 78 
                                    Ld+GcG G +a  +   ga+v++vD+s ++l ++ ++a+++g ++e+ + d ++lpf+d+sfD v++  v +h+    ++
  gi|116754374|ref|YP_843492.1|  81 LDLGCGPGVVALRCSLLGAEVYAVDPSRAALMISAKRARDAGARIELFEFDGRSLPFKDSSFDTVIMADVAEHIddGTLS 160
                                    8*************************************************************************65589* PP

                                    HHHHHHHHHEEEEEEEEE CS
                Methyltransf_11  79 kalkeiaRvLkpgGllvi 96 
                                     +l+e+ R L pgG+lv+
  gi|116754374|ref|YP_843492.1| 161 TLLSECFRTLTPGGRLVL 178
                                    ***************985 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.8   0.0   1.2e-18   1.2e-15      19     161 ..      73     235 ..      51     238 .. 0.74

  Alignments for each domain:
  == domain 1  score: 57.8 bits;  conditional E-value: 1.2e-18
                Methyltransf_23  19 klraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdqfdeq.......eaaepqgkfdlIvlrev 91 
                                    +  +g rvLd+GcG G ++  ++  g++v++vD+s++a  i  +ak a++  ++ +       + ++++ +fd++++ +v
  gi|116754374|ref|YP_843492.1|  73 RILPGERVLDLGCGPGVVALRCSLLGAEVYAVDPSRAALMI--SAKRARDAGARIElfefdgrSLPFKDSSFDTVIMADV 150
                                    456789*****************************988887..466666666655522222224444666********** PP

                Methyltransf_23  92 lehvpd..ppellrqiatllkpgGylllse.plasl............kedrllldwlylvpagrhisffsarslkelle 156
                                     eh++d  +  ll+  ++ l pgG+l+l++ p+ ++              + l ++   +  ++ hi+++s+ s++  ++
  gi|116754374|ref|YP_843492.1| 151 AEHIDDgtLSTLLSECFRTLTPGGRLVLHTaPALEAmraacllraislGTADLQKHLVTPEYEHLHIRYHSRGSIRGFMR 230
                                    *****98899********************5333335566666555432222222333346666778************* PP

                Methyltransf_23 157 eaGle 161
                                    +aGl+
  gi|116754374|ref|YP_843492.1| 231 AAGLS 235
                                    ***97 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.0   0.0     7e-15     7e-12       1      99 []      81     176 ..      81     176 .. 0.85

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 7e-15
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhl. 79 
                                    L++GcG G ++ ++     ++e+++vD+s++a+   +++ ++ ++ + + +e++ ++l  +d  ssfD+v++++v +h+ 
  gi|116754374|ref|YP_843492.1|  81 LDLGCGPGVVALRCSLL--GAEVYAVDPSRAALMISAKRARDAGA-RIELFEFDGRSLPFKD--SSFDTVIMADVAEHId 155
                                    8*************999..**************666666666664.5566666666665555..6**************9 PP

                Methyltransf_12  80 .kdirevldnirklLkpgGrl 99 
                                      ++  +l+++ + L+pgGrl
  gi|116754374|ref|YP_843492.1| 156 dGTLSTLLSECFRTLTPGGRL 176
                                    88899**************97 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   0.0   3.3e-14   3.2e-11       4     114 ..      77     183 ..      74     215 .. 0.86

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 3.3e-14
                Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnev 83 
                                    g rvlDlGCG G  +++   +l  +aev+ +D s  a+  + ++a++ g  ++e+ + d  +l+  ++d++fD ++  +v
  gi|116754374|ref|YP_843492.1|  77 GERVLDLGCGPGVVALRCS-LL--GAEVYAVDPSRAALMISAKRARDAGA-RIELFEFDGRSLP--FKDSSFDTVIMADV 150
                                    679***************9.76..58***********************9.6************..************** PP

                Methyltransf_31  84 l..naladpdkileeiervlkpggilliedprl 114
                                        +   +   l e +r l+pgg+l++ ++ +
  gi|116754374|ref|YP_843492.1| 151 AehIDDGTLSTLLSECFRTLTPGGRLVLHTAPA 183
                                    *5555556788999*************988773 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.0   7.1e-12   7.1e-09      38     151 ..      67     178 ..      57     197 .. 0.85

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 7.1e-12
                                    HHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-E CS
                Ubie_methyltran  38 fveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsf 117
                                    +v  l   ++g++vlD+ +G g +a++ s       +v  +D +   L ++ k++++ g  +ie+   ++  Lpf+d sf
  gi|116754374|ref|YP_843492.1|  67 KVVSLARILPGERVLDLGCGPGVVALRCSLL---GAEVYAVDPSRAALMISAKRARDAGA-RIELFEFDGRSLPFKDSSF 142
                                    5566677789***************998754...347999***************99985.8****************** PP

                                    EEEEEES-GGG-S-..HHHHHHHHHHHEEEEEEEEE CS
                Ubie_methyltran 118 DvvtvsfGlrnvtD..klkaLkeayrvlkpGGrlvv 151
                                    D+v ++     + D   ++ L e +r l pGGrlv 
  gi|116754374|ref|YP_843492.1| 143 DTVIMADVAEHIDDgtLSTLLSECFRTLTPGGRLVL 178
                                    ***99998888888434689*************974 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.0   8.8e-12   8.8e-09      32     141 ..      77     182 ..      66     197 .. 0.87

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 8.8e-12
                                    CSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTT.TSTTS-EEEEEE---STTT CS
                            MTS  32 sgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvle.eveekkfdlivsNPPfhag 110
                                     ++vlDlGcG Gv+++ +     e  v +vd + +Al ++ + +++ ++++e+++ d+ +  +++ +fd++++       
  gi|116754374|ref|YP_843492.1|  77 GERVLDLGCGPGVVALRCSLLGAE--VYAVDPSRAALMISAKRARDAGARIELFEFDGRSlPFKDSSFDTVIMA---DVA 151
                                    578***************998877..9*******************************9845779*******96...677 PP

                                    CHCHHHHHHHHHHHHHHHEEEEEEEEEEEET CS
                            MTS 111 katelavaeeliaeAkeaLkegGeLliVanr 141
                                    +++++ +  +l+ e  + L++gG+L++ +  
  gi|116754374|ref|YP_843492.1| 152 EHIDDGTLSTLLSECFRTLTPGGRLVLHTAP 182
                                    788899******************9976555 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.0     3e-11     3e-08      29     170 ..      46     184 ..      37     195 .. 0.82

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 3e-11
                                    ---S----SSTT--HHHHHHHHHHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS CS
                           CMAS  29 mtYsCAyferddmtLeeAqlaKldlileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdel 108
                                    + Ys  y+++   +L e  ++K+   +  +++ pG+++Ld+GcG G ++ r     +++v ++  S+     + kr  ++
  gi|116754374|ref|YP_843492.1|  46 TEYSEEYYRSSLYDLSEDRISKV---VSLARILPGERVLDLGCGPGVVALRCSLL-GAEVYAVDPSRAALMISAKRARDA 121
                                    67888888888887777666665...5667888***************9998776.***********9999999998888 PP

                                    -SSS-EEEEES-GGG---...--SEEEEES-GGGTSGGGHHHHHHHHHHHS-TT-EEEEEEEEE- CS
                           CMAS 109 dlerkvevklldyedlde...kvdrvvsvgafehvgkenydtffkklkkllkedGllllhtitsl 170
                                    +   + e+   d + l+     +d v+  ++ eh+    + t  ++++++l ++G+l+lht  +l
  gi|116754374|ref|YP_843492.1| 122 G--ARIELFEFDGRSLPFkdsSFDTVIMADVAEHIDDGTLSTLLSECFRTLTPGGRLVLHTAPAL 184
                                    8..3444444444554323379**************************************97665 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   4.9e-09   4.9e-06     159     257 ..      74     177 ..      40     179 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 4.9e-09
                           PrmA 159 vkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseell.keekadvivaNILae 237
                                    + +ge+vlD+G+G G+ a+  ++Lga +v+avD    A+ ++++ a+  + + +l  +  ++l+ k++++d ++   +ae
  gi|116754374|ref|YP_843492.1|  74 ILPGERVLDLGCGPGVVALRCSLLGA-EVYAVDPSRAALMISAKRARDAGARIELFEFDGRSLPfKDSSFDTVIMADVAE 152
                                    67899********************9.69************999888776665442222333335578898776655555 PP

                           PrmA 238 v.....lielaedikklvkegglli 257
                                          l  l+++  +++ +gg+l+
  gi|116754374|ref|YP_843492.1| 153 HiddgtLSTLLSECFRTLTPGGRLV 177
                                    4122225678888888888888776 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   7.2e-09   7.2e-06       6     131 ..      50     177 ..      47     198 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 7.2e-09
                                    CCHH.HHHHT----.-HHHHHHCCCS-S-EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEE CS
                           TehB   6 edyf.skkynltat.hsevveavkivkpgkvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknista 83 
                                    e+y+ s  y+l++   s+vv+ ++i+   +vldlgcg g  +l  sllg +v a+d    ++  +   + +++   i+  
  gi|116754374|ref|YP_843492.1|  50 EEYYrSSLYDLSEDrISKVVSLARILPGERVLDLGCGPGVVALRCSLLGAEVYAVDPSRAALM-ISAKRARDAGARIELF 128
                                    555515679998651699********999***************************9887765.4445556666667777 PP

                                    E--GGG---.-S-EEEEEEESSGGGS-GGGHHHHHHHHHHTEEEEEEEE CS
                           TehB  84 lydineakl.derydfilstvvlmfleaeripsiienmqectkvggynl 131
                                     +d  ++ + d  +d ++ + v   ++  ++++++++  ++  +gg  +
  gi|116754374|ref|YP_843492.1| 129 EFDGRSLPFkDSSFDTVIMADVAEHIDDGTLSTLLSECFRTLTPGGRLV 177
                                    7777777773457888888888888888888888888888888887644 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0     1e-06     0.001      40     166 ..      54     180 ..      37     198 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1e-06
                                    HHHHHTTHHHHHHHHHHSS-GGG-SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-HHHHHHHHHHS-----TTEEEEES- CS
                 Methyltransf_2  40 nkglqessslvakkvleafdleglkslvDvGGGtGalakaivsayPtikvivfDlpeVveaAkehlsageeervefvgGd 119
                                     + l + s+   +kv+    + + ++++D+G G G++a  ++ +  ++ ++    +  + +Ak+    ++  r+e  + d
  gi|116754374|ref|YP_843492.1|  54 RSSLYDLSEDRISKVVSLARILPGERVLDLGCGPGVVALRCSLLGAEVYAVDPSRAALMISAKRA--RDAGARIELFEFD 131
                                    4555555555666777777777778999*************999777777777777788888888..4555566666655 PP

                                    TTTS---....--SEEEEESSGGGS-HHHHHHHHHHHHHH--TT-EEEEEE CS
                 Methyltransf_2 120 ffkdslP....eaDaillkrvlhDwsdekcvklLkrvkkalpagGkvivve 166
                                     +  slP    + D ++++ v    +d++ ++lL ++ ++l +gG++++  
  gi|116754374|ref|YP_843492.1| 132 GR--SLPfkdsSFDTVIMADVAEHIDDGTLSTLLSECFRTLTPGGRLVLHT 180
                                    55..56643336799*******************************99865 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   8.6e-06    0.0085     112     220 ..      73     181 ..      53     194 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8.6e-06
                                    .--TT-EEEEET-TTSHHHHHHHHCT-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---GGGS-T.---EEEEEEES CS
                 Methyltransf_9 112 sdlkgrtildvGcgnGyhlwrmvgegaklvvGidPselfliqfeavrkllgedqrahllplgieqlpe.leafdtvfsmG 190
                                      l g ++ld+Gcg G    r    ga+ v  +dPs+  l+   + ++  +   r  l+ +    lp   ++fdtv    
  gi|116754374|ref|YP_843492.1|  73 RILPGERVLDLGCGPGVVALRCSLLGAE-VYAVDPSRAALMI--SAKRARDAGARIELFEFDGRSLPFkDSSFDTVIMAD 149
                                    357899***************9888886.689****998875..45677778889999999******85789******** PP

                                    -GGG-S.-HHHHH.HHHHCTEEEEEEEEEEEE CS
                 Methyltransf_9 191 vlyhrr.sPldhl.lqlkdqlvkgGelvletl 220
                                    v  h     l +l ++   +l+ gG lvl t 
  gi|116754374|ref|YP_843492.1| 150 VAEHIDdGTLSTLlSECFRTLTPGGRLVLHTA 181
                                    ***97525787761567899*********985 PP

>> NodS  Nodulation protein S (NodS)
   #    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      45     147 ..      78     181 ..      50     194 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1e-05
                           NodS  45 adalevGcaaGalterlapyckrltvvdvveeaiararervkes.shiswivsdvqqfs.tdekfdlivvaevlyyiedv 122
                                      +l++Gc  G ++ r + +   +  vd    a+  + +r +++ + i   + d + +  +d  fd++++a+v  +i+d 
  gi|116754374|ref|YP_843492.1|  78 ERVLDLGCGPGVVALRCSLLGAEVYAVDPSRAALMISAKRARDAgARIELFEFDGRSLPfKDSSFDTVIMADVAEHIDDG 157
                                    469******************************99999999876378*********99735779*************885 PP

                           NodS 123 aelraavrnlvsllapdgqlvfGsa 147
                                      l + + +  + l+p+g+lv+ +a
  gi|116754374|ref|YP_843492.1| 158 -TLSTLLSECFRTLTPGGRLVLHTA 181
                                    .7999**************998765 PP

>> MetW  Methionine biosynthesis protein MetW
   #    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      10      89 ..      73     155 ..      64     171 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.2e-05
                           MetW  10 likpgsrvldlGcGdGellellkeekqvdgrGleldeegvaecvak....Glsviqgdldkdlenfedksfdyvvlsqtl 85 
                                     i pg rvldlGcG G +  l     + + + ++ ++++++ + ++    G  +   + d     f+d+sfd v+++   
  gi|116754374|ref|YP_843492.1|  73 RILPGERVLDLGCGPGVVA-LRCSLLGAEVYAVDPSRAALMISAKRardaGARIELFEFDGRSLPFKDSSFDTVIMADVA 151
                                    47799***********863.334557788888888888765444332233889999999*9999************9876 PP

                           MetW  86 qatr 89 
                                      + 
  gi|116754374|ref|YP_843492.1| 152 EHID 155
                                    6655 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 ?   13.9   0.0   3.5e-05     0.035      64     171 ..      67     178 ..      57     189 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.5e-05
                                    HHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTGGG-SE CS
                           PCMT  64 lalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGyeekaPY 143
                                    +++ l ++ +g+rvL++G+G G  + +   l+g++    +++ ++     + ++ +    +++ + + DGr    + + +
  gi|116754374|ref|YP_843492.1|  67 KVVSLARILPGERVLDLGCGPGVVA-LRCSLLGAEV--YAVDPSRAALMISAKRARDA-GARIELFEFDGRSLPFKDSSF 142
                                    566777899*************875.5566777776..57787777777777776655.568999999***99999999* PP

                                    EEEEESSBBSS--H........HHHHTEEEEEEEEE CS
                           PCMT 144 daihvgaaapeiPe........alidQLkeGGrlvv 171
                                    d+++++  a++i +        + ++ L +GGrlv+
  gi|116754374|ref|YP_843492.1| 143 DTVIMADVAEHIDDgtlstllsECFRTLTPGGRLVL 178
                                    *99999999988752222111134567888888886 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00019      0.19      67     127 ..      54     109 ..      46     180 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00019
                           DREV  67 rGsmfvlseeqfrkllaiekespasdqedkklldlGaGdGeitkrvaptfeevyatelset 127
                                    r s++ lse++  k++ + +  p      +++ldlG G G ++ r +    evya + s  
  gi|116754374|ref|YP_843492.1|  54 RSSLYDLSEDRISKVVSLARILPG-----ERVLDLGCGPGVVALRCSLLGAEVYAVDPSRA 109
                                    567888899999998888855554.....59************************998865 PP

>> DUF3419  Protein of unknown function (DUF3419)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00022      0.22     293     337 ..     138     182 ..     114     202 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00022
                        DUF3419 293 kkksltravllDhmDWledeeleeeiqelnralkpggrvllRsaa 337
                                    k++s++ +++ D  + ++d +l+++++e  r+l+pggr++l +a 
  gi|116754374|ref|YP_843492.1| 138 KDSSFDTVIMADVAEHIDDGTLSTLLSECFRTLTPGGRLVLHTAP 182
                                    7899************************************99985 PP

>> NNMT_PNMT_TEMT  NNMT/PNMT/TEMT family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00079      0.78      19      74 ..      46      94 ..      43     102 .. 0.83
   2 ?   -1.1   0.0      0.85   8.5e+02     182     199 ..     163     180 ..     155     192 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00079
                                   HHHHHHHCSTTTTSTCCCCHHHHHHHHHHHHHHTSSS-ECEEEEET-TT--GGGTT CS
                 NNMT_PNMT_TEMT 19 raYLekyykkasedaaeeqvvlfaLknllqtlatgekkgdtllDiGaGPTvyqlls 74
                                   ++Y e+yy  +  d+ e+ +++     l+++l+     g+ +lD+G GP v  l +
  gi|116754374|ref|YP_843492.1| 46 TEYSEEYYRSSLYDLSEDRISKVV--SLARILP-----GERVLDLGCGPGVVALRC 94
                                   6899******99********9864..6777777.....556********9977655 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.85
                                    HHHHHTTEEEEEEEEEEE CS
                 NNMT_PNMT_TEMT 182 lrnlasllkpGGhlvlgg 199
                                    l +  + l pGG+lvl +
  gi|116754374|ref|YP_843492.1| 163 LSECFRTLTPGGRLVLHT 180
                                    5667889********875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); 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 0.25s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 3110.66
//
Query:       gi|116754375|ref|YP_843493.1|  [L=575]
Description: hypothetical protein Mthe_1069 [Methanosaeta thermophila PT]
Scores for complete sequence (score 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   12.8   1.1       0.23   11.8   1.1    1.5  1  ET        ET module


Domain annotation for each model (and alignments):
>> ET  ET module
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.1   1.3e-05      0.23       9      64 ..     250     313 ..     243     326 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.3e-05
                             ET   9 ekaistgaevaCdGeCasvsltttvngqn.......vtlytCdpts.vckslnlsnecasleed 64 
                                    e  i++g+ + C+G  +s+ +++t +g++       +++y Cdp++  c++ + +++ ++ +ed
  gi|116754375|ref|YP_843493.1| 250 EISIAAGQINLCNGATGSAAVSATASGKSsatggnmTSTYRCDPNTgYCDYSEYYTSATTSKED 313
                                    455689999*********99999999888777888889*****975489999999998888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (575 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 4104.32
//
Query:       gi|116754376|ref|YP_843494.1|  [L=506]
Description: hypothetical protein Mthe_1070 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (506 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.23s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 3694.77
//
Query:       gi|116754377|ref|YP_843495.1|  [L=231]
Description: rhodanese domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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   83.1   0.0    2.6e-10   40.7   0.0    2.1  2  Rhodanese  Rhodanese-like domain


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   0.0   1.5e-14   2.6e-10      16     106 ..       2      98 ..       1      99 [. 0.79
   2 !   40.4   0.0   1.9e-14   3.4e-10      10      92 ..     131     212 ..     127     219 .. 0.87

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 1.5e-14
                      Rhodanese  16 llDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellel....gidnkktvvvycdgggraaaaaallk.... 87 
                                    llDv++++e   +hIpgAv++     ++    e++ l+ pe+l++     gi++ + vv+y++ + +  +  ++ +    
  gi|116754377|ref|YP_843495.1|   2 LLDVSEEAE---SHIPGAVHI----NYTDLCGEDEILKPPEDLARIfgkaGISDSDSVVIYGECRPCGGSGVTIHPstlt 74 
                                    799999988...9********....5666666666667777777777779***************997777665554555 PP

                      Rhodanese  88 .....klGyknvsvldGGfkawke 106
                                         +lG+ nv++ld G+++w +
  gi|116754377|ref|YP_843495.1|  75 yfallYLGHRNVWLLDRGITGWTN 98 
                                    666656**777***********87 PP

  == domain 2  score: 40.4 bits;  conditional E-value: 1.9e-14
                      Rhodanese  10 ekgkvallDvRppeeYekghIpgAvnv.skdtlsrakkseapllelpeellelgidnkktvvvycdgggraaaaaallkk 88 
                                    ++ +v+l+D+R+ +e+e++ I g++n+ + +  s+++++e++ le++ +++ l  +++k+vvv+ ++g +a+ ++ +lk+
  gi|116754377|ref|YP_843495.1| 131 KNSDVQLVDARTVQEFEASTILGSINIpADTVVSGGWFREDSELENLFRAKGL--TKEKPVVVFTSTGVKATVVWFALKR 208
                                    456778*********************77778889999999999988888888..***************8888****** PP

                      Rhodanese  89 lGyk 92 
                                    +Gy 
  gi|116754377|ref|YP_843495.1| 209 MGYD 212
                                    **73 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); 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 0.28s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1631.67
//
Query:       gi|116754378|ref|YP_843496.1|  [L=302]
Description: hypothetical protein Mthe_1072 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 2035.87
//
Query:       gi|116754379|ref|YP_843497.1|  [L=1261]
Description: glycosyl transferase, group 1 [Methanosaeta thermophila PT]
Scores for complete 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-76  255.8   0.0    2.1e-31  108.8   0.0    3.3  3  Glycos_transf_1  Glycosyl transferases group 1
    6.4e-55  185.2   0.0    4.7e-22   78.9   0.0    3.4  3  Glyco_trans_1_4  Glycosyl transferases group 1
    3.6e-20   72.2   0.0    4.9e-09   36.5   0.0    4.3  4  Glyco_trans_1_2  Glycosyl transferases group 1
    2.9e-12   46.9   3.8    1.5e-09   38.1   0.1    4.6  4  Glyco_transf_4   Glycosyltransferase Family 4
  ------ inclusion threshold ------
       0.13   12.5   0.0         21    5.5   0.0    2.5  2  DUF1884          Domain of unknown function (DUF1884)


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 !  108.8   0.0   5.9e-35   2.1e-31       9     169 ..     222     382 ..     214     385 .. 0.92
   2 !   64.7   0.0     2e-21   7.3e-18       3     171 ..     617     789 ..     615     790 .. 0.96
   3 !   78.6   0.0   1.1e-25   3.8e-22      18     164 ..    1065    1219 ..    1051    1227 .. 0.93

  Alignments for each domain:
  == domain 1  score: 108.8 bits;  conditional E-value: 5.9e-35
                                    TTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES...STTHHHHHHHHHHHCTT.CGGGEEECCHSSS CS
                Glycos_transf_1   9 lgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaG..ngeeekelkklaeelels.dnviflgevsred 85 
                                    + + +++ +++  g  +++K++d+li+afa+l+++l+ + +lvi+   + e++k+l++ a  ++l+ d++ ++g+v +ed
  gi|116754379|ref|YP_843497.1| 222 YSI-SRPFVMCAPGGTDPRKNLDRLIRAFARLPDDLRRDHQLVIVStiDPEDKKRLEDIARDAHLEkDKLVITGYVTDED 300
                                    545.5677777788889*******************************************9999963789999******* PP

                                    HHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHHH CS
                Glycos_transf_1  86 leellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelrerl 165
                                    l +l++ + +fv+ps  EgfG+++lEAma+g pvias ++ ++ev+  ++  +l++p ++e+++ +++ +l +e+lr++l
  gi|116754379|ref|YP_843497.1| 301 LLKLYNLCRLFVFPSWHEGFGLPPLEAMACGAPVIASSTSSLPEVIGRED--ALFDPFSVESISSKMAVVLLNEDLRQDL 378
                                    **************************************************..9*************************** PP

                                    HHHH CS
                Glycos_transf_1 166 gena 169
                                    ++ +
  gi|116754379|ref|YP_843497.1| 379 IRHG 382
                                    9987 PP

  == domain 2  score: 64.7 bits;  conditional E-value: 2e-21
                                    HHHHHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES....STTHHHHHHHHHHHCTTCGGGEEE CS
                Glycos_transf_1   3 ekkrkklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaG...ngeeekelkklaeelelsdnviflg 79 
                                       rkklg +++  +++s g + ++K+ ++l+ a+ ++   ++  ++lv++G   +ge+ ++l k ++e +++d+v+++g
  gi|116754379|ref|YP_843497.1| 617 IAARKKLGVPQDAFLVCSFGLIAPTKNNHRLLNAWIKSSLSRDRHCQLVFVGenhGGEYGQSLLKTIKESGVQDRVHITG 696
                                    56799*******************************999999************************************** PP

                                    CCHSSSHHHHHHCESEEEEEESS...BSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT.-HHHHHHHHHHH CS
                Glycos_transf_1  80 evsredleellknadifvlpsis...EgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpn.naealaeairkl 155
                                     v+re   ++l++ad++v+  ++   E  G ++l  m++glp i+ ++g  ae+  d++  +  +    +e+l+ea++ l
  gi|116754379|ref|YP_843497.1| 697 WVDRETFRSYLEAADVAVQLRTRsrgETSG-TILDCMSYGLPLIVNAHGSSAELPDDAV--YMLPDDfRDEELVEALELL 773
                                    ********************9999*77777.799*************************..9999999************ PP

                                    HHSHHHHHHHHHHHHH CS
                Glycos_transf_1 156 ledeelrerlgenark 171
                                     +d e+re lg++ar+
  gi|116754379|ref|YP_843497.1| 774 WRDAERRESLGRRARE 789
                                    **************97 PP

  == domain 3  score: 78.6 bits;  conditional E-value: 1.1e-25
                                     EEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES............STTHHHHHHHHHHHCTTCGGGEEECCHSS CS
                Glycos_transf_1   18 ilsvgrlekeKgvdllikafallkkqlnpnvklviaG...........ngeeekelkklaeelelsdnviflgevsre 84  
                                     +l+vg +e++Kg+ ++i af+ l+ +   +v+lvi+G             +  +++ +l ++ el+ ++++l  +s+e
  gi|116754379|ref|YP_843497.1| 1065 FLMVGTIEPRKGYPQAIGAFEMLWMD-GADVNLVIVGregwthlsddmRRNIPETVNRLRHHPELGRRLFWLDGISDE 1141
                                     89***********************8.*******************997777789999999***************** PP

                                     SHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHH CS
                Glycos_transf_1   85 dleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelr 162 
                                      le ++++++++v+ s  EgfG++l+EA + ++p+ia +++ ++ev  d+   + +k  ++ +la ai+++le   + 
  gi|116754379|ref|YP_843497.1| 1142 YLERVYESCKCLVAASLGEGFGLPLIEAAQHKMPIIARDIPVFREVAGDHA--FYFKGDEPSDLASAIKEWLELYREK 1217
                                     ***************************************************..********************99555 PP

                                     HH CS
                Glycos_transf_1  163 er 164 
                                     ++
  gi|116754379|ref|YP_843497.1| 1218 RH 1219
                                     54 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 !   78.9   0.0   1.3e-25   4.7e-22       6     129 ..     232     366 ..     227     371 .. 0.83
   2 !   47.9   0.0   4.6e-16   1.7e-12       6     134 .]     634     776 ..     629     776 .. 0.78
   3 !   54.3   0.0   4.9e-18   1.8e-14       3     132 ..    1064    1211 ..    1062    1212 .. 0.80

  Alignments for each domain:
  == domain 1  score: 78.9 bits;  conditional E-value: 1.3e-25
                                    EES---GG.GTHHHHHHHHHHHH.H.H..EEEEEES---....HHHHHHHT..T-T..TEEEE---..THHHHHHHH-SE CS
                Glyco_trans_1_4   6 fvGrleenvkgvdllleavpllrkk.d..vrlvivGdgp..rpeeleelaa..gle.erveftGfv..edlaellaaadv 75 
                                      G   +++k++d l++a+++l ++ +   +lviv   +  ++++le+ a+  +le ++ ++tG+v  edl +l++ +++
  gi|116754379|ref|YP_843497.1| 232 APGGT-DPRKNLDRLIRAFARLPDDlRrdHQLVIVSTIDpeDKKRLEDIARdaHLEkDKLVITGYVtdEDLLKLYNLCRL 310
                                    45555.577**************6652459******65444447888766567676366*******9888********** PP

                                    EEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--TTSSEE--TT-HHHHHHHHH CS
                Glyco_trans_1_4  76 fvaPs..egfglkllEamaaglpvVatdvggiaevvgengllvppgdpealaeail 129
                                    fv+Ps  egfgl  lEama+g pv+a++++ ++ev+g++  l++p ++e++  +++
  gi|116754379|ref|YP_843497.1| 311 FVFPSwhEGFGLPPLEAMACGAPVIASSTSSLPEVIGREDALFDPFSVESISSKMA 366
                                    *****************************99***9999999**9999998887776 PP

  == domain 2  score: 47.9 bits;  conditional E-value: 4.6e-16
                                    EES---GG.GTHHHHHHHH.HHHH.HH..EEEEEES---.....HHHHHHHT..T-T.TEEEE---..THHHHHHHH-SE CS
                Glyco_trans_1_4   6 fvGrleenvkgvdllleav.pllrkkd..vrlvivGdgp.rp..eeleelaa..gleerveftGfv..edlaellaaadv 75 
                                     +G + ++ k+ + ll+a+ +  +++d  ++lv+vG++   +  ++l + ++  g+++rv++tG+v  e  +++l+aadv
  gi|116754379|ref|YP_843497.1| 634 SFGLI-APTKNNHRLLNAWiKSSLSRDrhCQLVFVGENHgGEygQSLLKTIKesGVQDRVHITGWVdrETFRSYLEAADV 712
                                    44544.5679999******9888877457*******764422455666666568************8666********** PP

                                    EEE--...-.--SHHHHHHHHTT-EEEE-TGGGTTT--TTSSEE--TT-..HHHHHHHHHHHHH- CS
                Glyco_trans_1_4  76 fvaPs...e.gfglkllEamaaglpvVatdvggiaevvgengllvppgd..pealaeailrLled 134
                                    +v      +  ++ ++l+ m++glp ++ + g  ae+  ++ +++p +d   e+l+ea++ L +d
  gi|116754379|ref|YP_843497.1| 713 AVQLRtrsRgETSGTILDCMSYGLPLIVNAHGSSAELPDDAVYMLP-DDfrDEELVEALELLWRD 776
                                    **9888664459*******************877896666667776.455799999999888765 PP

  == domain 3  score: 54.3 bits;  conditional E-value: 4.9e-18
                                     EEEEES---GG.GTHHHHHHHHHHHH.H..HEEEEEES---.............HHHHHHHT...T-T.TEEEE---T CS
                Glyco_trans_1_4    3 vilfvGrleenvkgvdllleavpllrkk..dvrlvivGdgprp...........eeleelaa...gleerveftGfve 64  
                                      +l+vG + e++kg    + a++ l+ +  dv+lvivG++ +            e ++ +++   +l  r  ++  ++
  gi|116754379|ref|YP_843497.1| 1064 SFLMVGTI-EPRKGYPQAIGAFEMLWMDgaDVNLVIVGREGWThlsddmrrnipETVN-RLRhhpELGRRLFWLDGIS 1139
                                     5799****.677**********999966545*******54221233333334442333.2223466778899999995 PP

                                     H..HHHHHHH-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--TTSSEE--TT-HHHHHHHHHHHH CS
                Glyco_trans_1_4   65 d..laellaaadvfvaPs..egfglkllEamaaglpvVatdvggiaevvgengllvppgdpealaeailrLl 132 
                                     d  l++++++++++va s  egfgl l+Ea+ +++p++a d++ ++ev g++++ ++ ++p++la ai + l
  gi|116754379|ref|YP_843497.1| 1140 DeyLERVYESCKCLVAASlgEGFGLPLIEAAQHKMPIIARDIPVFREVAGDHAFYFKGDEPSDLASAIKEWL 1211
                                     458****************************************99**88*******9777********9977 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.0   1.4e-12   4.9e-09       3      90 ..     312     398 ..     308     400 .. 0.91
   2 !   21.8   0.0   5.2e-08   0.00019      11      91 ..     724     805 ..     714     806 .. 0.82
   3 ?   -2.6   0.0       2.1   7.6e+03       9      19 ..     911     921 ..     903     922 .. 0.83
   4 !    8.2   0.0   0.00092       3.3       8      66 ..    1159    1218 ..    1143    1239 .. 0.83

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 1.4e-12
                Glyco_trans_1_2   3 LnpsrsespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarervlae 80 
                                    ++ps +e++ l  +Ea+acGa+++++++++l+e +  g+e  lf+  ++e++  k++ +l n+++r+ + +++ ++  ++
  gi|116754379|ref|YP_843497.1| 312 VFPSWHEGFGLPPLEAMACGAPVIASSTSSLPEVI--GREDALFDpfSVESISSKMAVVLLNEDLRQDLIRHGLQQ-AKR 388
                                    6788899***************************9..6666666668*****************************.89* PP

                Glyco_trans_1_2  81 htydhraeql 90 
                                    ++++  a+++
  gi|116754379|ref|YP_843497.1| 389 FSWNECARKV 398
                                    ****999986 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 5.2e-08
                Glyco_trans_1_2  11 pnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarervlaehtydhrae 88 
                                     ++ +++++  G +++++ a+g    + ++   +l +    eel+e+++ l ++ e+r++++++are + a+h   + a+
  gi|116754379|ref|YP_843497.1| 724 TSGTILDCMSYGLPLIVN-AHGSSAELPDDAVYMLPDdfRDEELVEALELLWRDAERRESLGRRAREVISANHAPSRCAK 802
                                    677889999999999999.6566666555545555557877*************************************** PP

                Glyco_trans_1_2  89 qll 91 
                                    q++
  gi|116754379|ref|YP_843497.1| 803 QYC 805
                                    997 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 2.1
                Glyco_trans_1_2   9 espnlrlfEaa 19 
                                     s+++r++E++
  gi|116754379|ref|YP_843497.1| 911 RSFTMRFLECP 921
                                    679******98 PP

  == domain 4  score: 8.2 bits;  conditional E-value: 0.00092
                Glyco_trans_1_2    8 sespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekirylla.npeer 66  
                                      e++ l l Eaa    ++++ d++ ++e    g+++++f+  ++ +la +i+++l+  +e+r
  gi|116754379|ref|YP_843497.1| 1159 GEGFGLPLIEAAQHKMPIIARDIPVFREVA--GDHAFYFKgdEPSDLASAIKEWLElYREKR 1218
                                     4889999*********************96..999******9*************9444444 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.1   4.2e-13   1.5e-09       2     165 ..      17     200 ..      16     205 .. 0.71
   2 ?    2.6   0.4     0.033   1.2e+02      53     164 ..     465     606 ..     427     607 .. 0.62
   3 ?    1.2   0.0      0.09   3.2e+02      89     148 ..     729     805 ..     708     814 .. 0.75
   4 ?    1.5   0.0     0.071   2.5e+02     122     152 ..     987    1017 ..     949    1040 .. 0.78

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 4.2e-13
                 Glyco_transf_4   2 GGverhvleLaraLar..rGheVtvv....tpgddgpleeev.....elvvrvprvplpllkrll...rslaflrrlrrl 67 
                                     G++r+ l +a+a ar    he+ +      p++ +p++ +      +  +rv + p p ++  +   ++ a++ r+r++
  gi|116754379|ref|YP_843497.1|  17 RGIGRYSLSIAQAIARnrEDHEILIAlngmFPETIEPIRAAFvgllpPENIRVWYAPGPVRESQPgndLRRAAAERIREA 96 
                                    599*************4444666666655544444444444488888555555555555444443000344445555554 PP

                 Glyco_transf_4  68 lkre....kpDvvHahspaalgaallalrr.....rlgiplVltvHglyekrllkarlkplsrllralerrl..lrradr 136
                                       +    +pDv+ + s + +++  +          l+ p+V+ +H+l +      +l+   ++ ++++r++  l+ra++
  gi|116754379|ref|YP_843497.1|  97 ---FlaslEPDVILVTSLFEGFVDDAV--TsigifDLRTPTVVALHDLIPLLNPDHYLRDNPAYKQYYLRKIyhLKRAHA 171
                                    ...24447*****99999998874222..2235699**************66677788888888888888888899**** PP

                 Glyco_transf_4 137 viavSeatadelrerygvppekitVipnG 165
                                     +avS++ a++ ++ +g+pp+++ + + +
  gi|116754379|ref|YP_843497.1| 172 WLAVSDSSARDAITALGIPPDRVFTTYEA 200
                                    **********************9877755 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.033
                 Glyco_transf_4  53 rllrslaflrrlrrllkre..kpDvv..HahspaalgaallalrrrlgiplVltvHglye.................... 108
                                    +++++   + r    +k++  ++D v  H+ +++++   ++  +     p V+ +H+ y                     
  gi|116754379|ref|YP_843497.1| 465 DPWIRACLPIRSVDYFKKNayRYDRVlyHIGNSPFH-HHMFEML--DEYPGVTVLHDFYLgnfkanmefngiypgawths 541
                                    455555555555555555556777774433333222.3455555..4777777777777777777777777777766665 PP

                 Glyco_transf_4 109 .krllkarlkplsrllralerrl.........lrradrviavSeatadelrerygvppekitVipn 164
                                     +  ++++  +++  ++ le+ +         ++++  +i+ S +  +  +++yg   ++ +Vip+
  gi|116754379|ref|YP_843497.1| 542 lYESHGYKAVFERFHEEDLEKTIftypcnfdaISKSLGIIVHSSYSSKLALKWYGAG-KDWAVIPH 606
                                    422333333333333334444446677777779999999999999999999999955.89999995 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.09
                 Glyco_transf_4  89 lalrrrlgiplVltvHglye..................krllkarlkplsrllralerrllrradrviavSeatadel 148
                                    l ++  +g+pl++ +Hg+ +                         l++   +++ l rr+     +  a+S+ ++++ 
  gi|116754379|ref|YP_843497.1| 729 LDCMS-YGLPLIVNAHGSSAelpddavymlpddfrdeeLVEALELLWRDAERRESLGRRAREVISANHAPSRCAKQYC 805
                                    56666.9***********999999999999988888663333445566666666677777667777777887777765 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.071
                 Glyco_transf_4  122 llralerrllrradrviavSeatadelrery 152 
                                     l  +++  ++r +d v+++S+++ad ++e++
  gi|116754379|ref|YP_843497.1|  987 LHSKWLSCVCRVSDGVLCISKSVADGVAEWL 1017
                                     555666667999***********99888855 PP

>> DUF1884  Domain of unknown function (DUF1884)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.015        55      13      43 ..      91     121 ..      84     131 .. 0.86
   2 ?    5.5   0.0    0.0058        21      17      48 ..    1086    1117 ..    1081    1127 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.015
                                    HHHHHHHHTT----EEEE-HHHHHHHHHHHH CS
                        DUF1884  13 ekineLkleGfePdiiLvGkeaieflkealk 43 
                                    e+i+e  l  +ePd+iLv   +  f+ +a+ 
  gi|116754379|ref|YP_843497.1|  91 ERIREAFLASLEPDVILVTSLFEGFVDDAVT 121
                                    56778888899***************99986 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0058
                                     HHHHTT----EEEE-HHHHHHHHHHHHHHHT- CS
                        DUF1884   17 eLkleGfePdiiLvGkeaieflkealkkelee 48  
                                      L ++G + ++++vG+e + +l++++++++ e
  gi|116754379|ref|YP_843497.1| 1086 MLWMDGADVNLVIVGREGWTHLSDDMRRNIPE 1117
                                     5789***********************97755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); 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: 0.79u 0.28s 00:00:01.07 Elapsed: 00:00:00.45
# Mc/sec: 8458.08
//
Query:       gi|116754380|ref|YP_843498.1|  [L=436]
Description: methyltransferase type 11 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.7e-16   58.6   0.0    1.3e-15   57.6   0.0    1.5  1  Methyltransf_23  Methyltransferase domain
    2.7e-14   53.6   0.0    5.3e-14   52.6   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
    1.2e-13   51.6   0.0    2.5e-13   50.5   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
    1.1e-10   41.4   0.0    2.6e-10   40.2   0.0    1.6  1  MetW             Methionine biosynthesis protein MetW
    1.9e-07   31.0   0.0    3.7e-07   30.0   0.0    1.5  1  Methyltransf_31  Methyltransferase domain
    1.7e-06   28.7   0.0    3.8e-06   27.6   0.0    1.6  1  Methyltransf_12  Methyltransferase domain
      7e-05   22.3   0.0    0.00015   21.1   0.0    1.5  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
     0.0033   16.8   0.0     0.0058   16.0   0.0    1.3  1  CMAS             Mycolic acid cyclopropane synthetase
  ------ inclusion threshold ------
      0.015   14.8   0.0      0.036   13.6   0.0    1.6  1  MTS              Methyltransferase small domain
      0.098   12.8   0.0       0.23   11.6   0.0    1.6  1  FtsJ             FtsJ-like methyltransferase


Domain annotation for each model (and alignments):
>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.6   0.0   7.4e-19   1.3e-15      25     123 ..      51     152 ..      16     183 .. 0.83

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 7.4e-19
                Methyltransf_23  25 rvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdqfd.eqeaaepqgkfdlIvlrevlehvp..dppel 101
                                    r +d+GcG G++le+l+engf+ +gvDl++++v+  +++  ++ +    e+ ++ ++++  +++ ++ +eh+p  ++ +l
  gi|116754380|ref|YP_843498.1|  51 RAVDLGCGRGEWLELLKENGFQAEGVDLDDAMVNTCRSKGLSVEKADAiEHLERLDDESAVIVSGFHIIEHIPfeSVKKL 130
                                    789*******************************9994444443333303344557779999999********888**** PP

                Methyltransf_23 102 lrqiatllkpgGylllseplas 123
                                    ++ +++ lkpgG+l+l++p+ +
  gi|116754380|ref|YP_843498.1| 131 VKDAYRVLKPGGLLILETPNPE 152
                                    *******************976 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   0.0     3e-17   5.3e-14       1      96 []      53     146 ..      53     146 .. 0.93

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 3e-17
                                    EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCT.SS-TT-EEEEEEES-CCC-..CCH CS
                Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaekl.pfednsfDlvvssevlhhv..edp 77 
                                    +d+GcG+G  +e l+++g +  gvDl+++m++++++k+   +         +e+l  + d+s  +v  ++ ++h+  e +
  gi|116754380|ref|YP_843498.1|  53 VDLGCGRGEWLELLKENGFQAEGVDLDDAMVNTCRSKGLSVE-----KADAIEHLeRLDDESAVIVSGFHIIEHIpfESV 127
                                    59********************************99998877.....5666778977******************999** PP

                                    HHHHHHHHHHEEEEEEEEE CS
                Methyltransf_11  78 ekalkeiaRvLkpgGllvi 96 
                                    +k++k ++RvLkpgGll++
  gi|116754380|ref|YP_843498.1| 128 KKLVKDAYRVLKPGGLLIL 146
                                    ****************985 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.5   0.0   1.4e-16   2.5e-13       2      97 .]      53     142 ..      52     142 .. 0.94

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 1.4e-16
                                    EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBC.CGBSSSTTTEEEEEEEST.GGGSSH CS
                Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgda.edlpfedgsfDlvvssga.lhhlsd 79 
                                    +dlGcG+G++++ l +++   +  gvD++++m++++r++       ++++++da e+l+  d++  ++vs ++ ++h++ 
  gi|116754380|ref|YP_843498.1|  53 VDLGCGRGEWLELLKENG--FQAEGVDLDDAMVNTCRSKG------LSVEKADAiEHLERLDDESAVIVSGFHiIEHIPF 124
                                    7**************995..*******************9......89999999899**999999999998999****** PP

                                    HHHHHHHHHHHHHEEEEE CS
                Methyltransf_25  80 edlekalkeiarvLkpgG 97 
                                    e ++k++k ++rvLkpgG
  gi|116754380|ref|YP_843498.1| 125 ESVKKLVKDAYRVLKPGG 142
                                    *****************9 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.0   1.4e-13   2.6e-10      13      76 ..      48     110 ..      39     141 .. 0.89

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 1.4e-13
                           MetW  13 pgsrvldlGcGdGellellkeekqvdgrGleldeegvaecvakGlsviqgdldkdlenfedksf 76 
                                     + r +dlGcG Ge lellke ++ +++G++ld++ v+ c +kGlsv + d+ + le  +d+s 
  gi|116754380|ref|YP_843498.1|  48 GELRAVDLGCGRGEWLELLKE-NGFQAEGVDLDDAMVNTCRSKGLSVEKADAIEHLERLDDESA 110
                                    566899*************87.9***********************************999984 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   2.1e-10   3.7e-07       4     113 ..      49     150 ..      46     184 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 2.1e-10
                Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDlilsne 82 
                                    +lr +DlGCG Ge +  l  e g++ae  G+D +  +++ +r+       + +++e++d+ e le l  de+  ++  + 
  gi|116754380|ref|YP_843498.1|  49 ELRAVDLGCGRGEWLELLK-ENGFQAE--GVDLDDAMVNTCRS-------KGLSVEKADAIEhLERL-DDESAVIVSGFH 117
                                    57889********999999.8899999..**************.......5788*****99999985.655555555566 PP

                Methyltransf_31  83 vl..naladpdkileeiervlkpggilliedpr 113
                                    ++    + + +k  + + rvlkpgg l++e+p+
  gi|116754380|ref|YP_843498.1| 118 IIehIPFESVKKLVKDAYRVLKPGGLLILETPN 150
                                    6676777788999*******************9 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   2.1e-09   3.8e-06       1      99 []      53     144 ..      53     144 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 2.1e-09
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhl. 79 
                                    +++GcG G+ l+ l e+  + +  gvD++ ++++  + k  + e  +++ +e  ++   d+   +s  +v  ++ ++h+ 
  gi|116754380|ref|YP_843498.1|  53 VDLGCGRGEWLELLKEN--GFQAEGVDLDDAMVNTCRSKGLSVE--KADAIEHLERL--DD---ESAVIVSGFHIIEHIp 123
                                    59***************..**************44444433333..33333333332..22...255566667******* PP

                Methyltransf_12  80 .kdirevldnirklLkpgGrl 99 
                                     + ++++++ ++++LkpgG l
  gi|116754380|ref|YP_843498.1| 124 fESVKKLVKDAYRVLKPGGLL 144
                                    *******************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 !   21.1   0.0   8.6e-08   0.00015      50     163 ..      51     157 ..      37     164 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 8.6e-08
                                    EEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS.TEEEEE--TTT-TTS-T-EEEEEEES-GGG CS
                Ubie_methyltran  50 kvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki.nieflqanaeeLpfeddsfDvvtvsfGlrn 128
                                    +++D+ +G g++  +l++  ++ ++ +++D+++ m+++ + k     k   i       e+L+  dd   v+  +f +  
  gi|116754380|ref|YP_843498.1|  51 RAVDLGCGRGEWL-ELLK--ENGFQAEGVDLDDAMVNTCRSKGLSVEKAdAI-------EHLERLDDESAVIVSGFHIIE 120
                                    689********95.4443..4567999**********999886554444234.......567777888888888888765 PP

                                    ...-S-HHHHHHHHHHHEEEEEEEEEEEE----SHHHH CS
                Ubie_methyltran 129 ...vtDklkaLkeayrvlkpGGrlvvlefskvelplls 163
                                       +   +k +k+ayrvlkpGG  ++le+ ++e  ++s
  gi|116754380|ref|YP_843498.1| 121 hipFESVKKLVKDAYRVLKPGGL-LILETPNPESLIVS 157
                                    3336788999************5.68999999877765 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   3.2e-06    0.0058      67     166 ..      53     148 ..      47     156 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.2e-06
                                    EEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-----SEEEE.ES-GGGTSGGGH CS
                           CMAS  67 LdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedldekvdrvvs.vgafehvgkeny 145
                                    +d+GcG G+ +    e+ + +  g+ l +   ++++ +  ++    ++   + + e ld++   +vs + ++eh+ +e+ 
  gi|116754380|ref|YP_843498.1|  53 VDLGCGRGEWLELLKEN-GFQAEGVDLDDAMVNTCRSKGLSV----EKADAIEHLERLDDESAVIVSgFHIIEHIPFESV 127
                                    799******99887777.*********998888877654444....455567788999999999988699********** PP

                                    HHHHHHHHHHS-TT-EEEEEE CS
                           CMAS 146 dtffkklkkllkedGllllht 166
                                    ++ +k ++++lk++Gll+l+t
  gi|116754380|ref|YP_843498.1| 128 KKLVKDAYRVLKPGGLLILET 148
                                    *****************9987 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0     2e-05     0.036      34     136 ..      51     145 ..      40     150 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2e-05
                                    EEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEEE---STTTCHC CS
                            MTS  34 kvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdlivsNPPfhagkat 113
                                    +++DlGcG G     l+ke+   + + vd d + ++ ++    + +   ++ a + le ++ ++  +ivs   fh  +++
  gi|116754380|ref|YP_843498.1|  51 RAVDLGCGRGEWLE-LLKENGF-QAEGVDLDDAMVNTCRSKGLSVE---KADAIEHLERLD-DESAVIVSG--FHIIEHI 122
                                    589*******9754.4444443.57888888887776664332222...233334455555.677899985..******* PP

                                    HHHHHHHHHHHHHHHEEEEEEEE CS
                            MTS 114 elavaeeliaeAkeaLkegGeLl 136
                                      + +++l+++A ++Lk+gG L+
  gi|116754380|ref|YP_843498.1| 123 PFESVKKLVKDAYRVLKPGGLLI 145
                                    ********************987 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00013      0.23      23      69 ..      50      97 ..      16     154 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00013
                                   -EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS...HHH.TTEEEECS- CS
                           FtsJ 23 ktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm...apl.pgvttiqgd 69
                                    ++vDlg++ G w + l ++ g   +  +vDl      +++ +g+++ ++d
  gi|116754380|ref|YP_843498.1| 50 LRAVDLGCGRGEWLELLKEN-G--FQAEGVDLDDAmvnTCRsKGLSVEKAD 97
                                   469**************999.5..688899995532332223444333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); 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: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 3180.68
//
Query:       gi|116754381|ref|YP_843499.1|  [L=744]
Description: hypothetical protein Mthe_1075 [Methanosaeta thermophila PT]
Scores for complete 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   20.0   8.1    0.00061   20.0   8.1    2.9  3  PMT_2     Dolichyl-phosphate-mannose-protein mannosyltransfer


Domain annotation for each model (and alignments):
>> PMT_2  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.11   1.9e+03      31      56 ..      26      51 ..      11      67 .. 0.76
   2 !   20.0   8.1   3.4e-08   0.00061      28     131 ..     138     242 ..     128     264 .. 0.80
   3 ?   -5.7   5.7         1   1.8e+04      65      65 ..     354     354 ..     293     416 .. 0.54

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.11
                          PMT_2 31 agvltilllyllarrlfgkraallaa 56
                                   +++l+++++y + +r +g+   + a+
  gi|116754381|ref|YP_843499.1| 26 LVLLSVYFIYNINCRTLGSGDTIPAS 51
                                   56788888998888888865555555 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 3.4e-08
                          PMT_2  28 salagvltilllyllarrlfgkraallaalllav.vplfvalsalftpdaplvllwalalylllraleknklkywllagv 106
                                    + l+++++++++yl +++l ++r+a++ a+l a+ +  ++++s+ +    +  l +a+++yl+l   + ++ k  + +gv
  gi|116754381|ref|YP_843499.1| 138 ASLIASTSVVFVYLSIKELINRRVAFIVAVLFAFgTNTWAISSQALWQHGLIELILAMFIYLVLINEKIKSNKIVISLGV 217
                                    5689999******************99999999945555555555555666666777777777766666667899***** PP

                          PMT_2 107 lfGlgflsKytaallliaallylli 131
                                    l Gl +++++   +ll ++l+y++ 
  gi|116754381|ref|YP_843499.1| 218 LSGLFVFNRPIDSVLLAPVLYYIFD 242
                                    ***********99999999999864 PP

  == domain 3  score: -5.7 bits;  conditional E-value: 1
                          PMT_2  65 f 65 
                                    +
  gi|116754381|ref|YP_843499.1| 354 W 354
                                    1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (744 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); 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: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 5092.74
//
Query:       gi|116754382|ref|YP_843500.1|  [L=298]
Description: glycosyl transferase family protein [Methanosaeta thermophila PT]
Scores for complete 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  118.0   0.1    4.8e-34  117.6   0.1    1.1  1  Glycos_transf_2  Glycosyl transferase family 2
    6.2e-08   32.8   0.1    8.8e-08   32.3   0.1    1.3  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    1.1e-06   29.1   0.0    1.7e-06   28.4   0.0    1.3  1  Glyco_tranf_2_4  Glycosyl transferase family 2
    1.8e-05   24.3   0.0    3.2e-05   23.6   0.0    1.3  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
    5.6e-05   22.7   0.0    9.1e-05   22.0   0.0    1.3  1  Glyco_transf_21  Glycosyl transferase family 21
  ------ inclusion threshold ------
       0.09   12.6   0.0       0.12   12.2   0.0    1.3  1  Glyco_transf_43  Glycosyltransferase family 43


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 !  117.6   0.1   1.6e-37   4.8e-34       1     169 [.       4     160 ..       4     161 .. 0.98

  Alignments for each domain:
  == domain 1  score: 117.6 bits;  conditional E-value: 1.6e-37
                                    EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--S CS
                Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatg 80 
                                    s v+p++Ne k l+ +++  l+      +eiivvDDgS+D+t e+++++a  +++v+++r++ n+Gk +al++g+++a+g
  gi|116754382|ref|YP_843500.1|   4 SLVVPAFNEVKGLPLVIAEYLEW----VDEIIVVDDGSNDGTYEVAKRFA--GEKVKIFRHDINRGKVAALRTGVKHASG 77 
                                    78*********************....**********************9..6*************************** PP

                                    SEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTCSTCCCE CS
                Glycos_transf_2  81 dyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfeigsaal 160
                                    d+i+f DaD +++  ++++lv+++ek gad+vlg+r  ++ +   ++r       ++++ +        n+++   ++++
  gi|116754382|ref|YP_843500.1|  78 DVIVFTDADYTYPARYVPELVREIEK-GADLVLGARLQNRTNIPAFNRL-----GNNIFSFLATYISCMNIQDSQTGMRA 151
                                    **************************.*********************8.....58999********************* PP

                                    EEEHHHHHC CS
                Glycos_transf_2 161 lrrealeel 169
                                    ++re++e+l
  gi|116754382|ref|YP_843500.1| 152 FKREMFEKL 160
                                    ******986 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.1     3e-11   8.8e-08       3     126 ..       2     114 ..       1     188 [. 0.71

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 3e-11
                Glyco_tranf_2_3   3 dlavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnea 82 
                                    +++++Vp+fne + l  v+++ l      +e++vv+d+s ++t eva+    ++ +++v++ ++ +    +gk+ al  +
  gi|116754382|ref|YP_843500.1|   2 RVSLVVPAFNEVKGLPLVIAEYLE---WVDEIIVVDDGSNDGTYEVAK----RFAGEKVKI-FRHD-IN-RGKVAALRTG 71 
                                    499********************9...69****************997....689999996.4544.34.69******** PP

                Glyco_tranf_2_3  83 lravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfl 126
                                    ++++++d++++ D+D     ++++ l++ +  ++++ v + ++ 
  gi|116754382|ref|YP_843500.1|  72 VKHASGDVIVFTDADYTYPARYVPELVREI-EKGADLVLGARLQ 114
                                    ***************998888888888887.7777777665543 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 !   28.4   0.0   5.8e-10   1.7e-06       2      81 ..      11      86 ..      10      94 .. 0.81

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 5.8e-10
                Glyco_tranf_2_4  2 neadiLpeflahhlalgfdrilvydndstDgtrailkelpevkllhvdksyederrqvellkallaryaeadwvlvvDaD 81
                                   ne + Lp ++a +l++ +d+i+v+d++s Dgt+++ k+ +  k+  ++++++  r +v++l++  ++ a +d +++ DaD
  gi|116754382|ref|YP_843500.1| 11 NEVKGLPLVIAEYLEW-VDEIIVVDDGSNDGTYEVAKRFAGEKVKIFRHDIN--RGKVAALRTGVKH-ASGDVIVFTDAD 86
                                   889999**********.*********************86655555555554..5567777766644.578888888888 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   1.1e-08   3.2e-05      23      92 ..      21      87 ..      11      97 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.1e-08
                Glyco_tranf_2_2 23 akyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGaskaesdlvlFlDaDc 92
                                   a y +   e+ivvddgS + + e+ + +   + +++ +d      ++ aa   G+++a +d+++F DaD 
  gi|116754382|ref|YP_843500.1| 21 AEYLEWVDEIIVVDDGSNDGTYEVAKRFAGEKVKIFRHD---INRGKVAALRTGVKHASGDVIVFTDADY 87
                                   566666779**************************9444...4779999999****************95 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 !   22.0   0.0   3.1e-08   9.1e-05      15     113 ..      60     157 ..      52     164 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 3.1e-08
                Glyco_transf_21  15 vnp.KvnnllqaleaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgsdak.glaaaleaaflntlagvlq 92 
                                    +n+ Kv +l ++++ a  d++v+ D+d + ++ y+ el++++e+ ++ lV ++ +  +++  + ++l + ++++la +++
  gi|116754382|ref|YP_843500.1|  60 INRgKVAALRTGVKHASGDVIVFTDADYTYPARYVPELVREIEK-GADLVLGARLQNRTNiPAFNRLGNNIFSFLATYIS 138
                                    5655***************************************6.9******9998887745777777777777777776 PP

                Glyco_transf_21  93 aklsglgfavGksmalrreaL 113
                                      +   +  +G+  a++re +
  gi|116754382|ref|YP_843500.1| 139 C-MNIQDSQTGMR-AFKREMF 157
                                    6.54445555553.5555555 PP

>> Glyco_transf_43  Glycosyltransferase family 43
   #    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      56     150 ..      57     171 ..      28     228 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4e-05
                Glyco_transf_43  56 kkrgvrqRnaALrhireerldGvVyFadddnvYsleLFde.lrkvkkvgvwpVglvggllvegPvcnss.gkvvgwhv.. 131
                                    +++  r + aALr   ++    v++F d+d +Y  +   e +r+++k + +  g   +++ + P++n+  +++  + +  
  gi|116754382|ref|YP_843500.1|  57 RHDINRGKVAALRTGVKHASGDVIVFTDADYTYPARYVPElVREIEKGADLVLGARLQNRTNIPAFNRLgNNIFSFLAty 136
                                    5566677888999988888888**************999978**********************9998867999998855 PP

                Glyco_transf_43 132 ...ewkkerk..................fpidmaGfavns 150
                                             +                  + ++  G+ +++
  gi|116754382|ref|YP_843500.1| 137 iscM-----NiqdsqtgmrafkremfekLDVNAKGLEFET 171
                                    4441.....1122223444555555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); 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: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2199.90
//
Query:       gi|116754383|ref|YP_843501.1|  [L=273]
Description: xylose isomerase domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-18   66.5   0.0    2.8e-18   66.2   0.0    1.1  1  AP_endonuc_2  Xylose isomerase-like TIM barrel


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.2   0.0   1.5e-22   2.8e-18       6     207 ..      25     233 ..      20     236 .. 0.84

  Alignments for each domain:
  == domain 1  score: 66.2 bits;  conditional E-value: 1.5e-22
                                    HCT-SEEEEECCTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCS....HHHHHHHHHHHHHHHHH CS
                   AP_endonuc_2   6 eaGfdgvElfgrdlvpvselsdeelrelrkaldelglriaslslftrfgypdederear....reesvdalkraielaaa 81 
                                    +aG++++El     +        +++el k+  +  + i+   +++r++              r++s++  +raiel++ 
  gi|116754383|ref|YP_843501.1|  25 NAGIRHIELGSCHSYIE------DIDELLKRYPDVEFVIHNYFPPPRDSFMMNLAA--QdkiiRQQSLNICRRAIELCSY 96 
                                    56666666654444444......478888888888888777777777777665434..3359****************** PP

                                    HTBSEEEEEBCC..........GBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTC.....HHHHH CS
                   AP_endonuc_2  82 LGapllvlhpGt..........agagpkgseeeawerlaeslneladyaekegvklalEtlagsgvelgd.....eelar 146
                                    +Ga++  +hpG             +g   ++eea++++ +sl+e++ ya+++ +k+alE+l  ++  + +     +e+  
  gi|116754383|ref|YP_843501.1|  97 IGAEFYSFHPGFriagalgrdfSLSGKTIPYEEAFRNFTRSLDEILSYAREHKIKVALENLEHKN--DAYmmtrpSEFTS 174
                                    *******************9986688888899********************************9..666779******* PP

                                    HHHHHTTTTEEEEEEHHHHHHH....TTTHHHHHHHHHGGEEEEEE.EESSTTTTSSTTEESTTS CS
                   AP_endonuc_2 147 lldavdspnvgvclDtgHllia....eedvddalraladrikhvHikDakgdlgagrdrhvpige 207
                                    +l+  +   + + lD gHl ia     + +++++  +  r+  vH++ ++     + d h+ + +
  gi|116754383|ref|YP_843501.1| 175 VLEMFPE--LFLLLDLGHLKIAsrrlCFTMEEFISCVHGRVIGVHVHENDS----RSDLHLDPSK 233
                                    ******7..*******************************99999988887....7777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1978.36
//
Query:       gi|116754384|ref|YP_843502.1|  [L=343]
Description: NAD-dependent epimerase/dehydratase [Methanosaeta thermophila PT]
Scores for complete 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-51  175.6   0.0    2.9e-51  174.8   0.0    1.4  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    1.2e-49  169.0   0.0    1.4e-49  168.7   0.0    1.0  1  Epimerase        NAD dependent epimerase/dehydratase family
    1.1e-13   50.8   0.0    2.2e-13   49.9   0.0    1.4  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    2.4e-12   46.5   0.0    3.4e-12   46.0   0.0    1.2  1  RmlD_sub_bind    RmlD substrate binding domain
    1.9e-08   33.8   0.0      4e-06   26.2   0.0    2.1  2  Polysacc_synt_2  Polysaccharide biosynthesis protein
      7e-07   28.7   0.0    0.00081   18.6   0.0    2.3  2  NAD_binding_4    Male sterility protein
    1.2e-06   28.1   0.0    2.3e-06   27.2   0.0    1.5  1  adh_short        short chain dehydrogenase
  ------ inclusion threshold ------
      0.023   14.6   0.2      0.095   12.6   0.3    2.0  2  KR               KR domain
      0.056   13.4   0.0        8.8    6.3   0.0    2.4  2  ADH_zinc_N       Zinc-binding dehydrogenase
        0.1   12.9   0.1         18    5.7   0.1    2.4  2  TrkA_N           TrkA-N domain
       0.17   11.6   0.0       0.26   10.9   0.0    1.3  1  ELFV_dehydrog    Glutamate/Leucine/Phenylalanine/Valine dehyd


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 !  174.8   0.0   1.8e-54   2.9e-51       1     332 []      27     331 ..      27     331 .. 0.87

  Alignments for each domain:
  == domain 1  score: 174.8 bits;  conditional E-value: 1.8e-54
                                    EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEE CS
                  GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevy 80 
                                    L+TG+aGf Gs++++ L+++g +v+ ++++ss   +++i+hl +       ++++++++D++D s+  ++ +  + d v+
  gi|116754384|ref|YP_843502.1|  27 LVTGGAGFLGSWICDALIAQGANVVCVDNLSSG-LISNISHLLD------ADRFEFIQHDVSDLSRPLKIDQ--KLDLVI 97 
                                    9*************************9998876.679*****96......3589*********887777655..569*** PP

                                    E--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TT.....S-----SHHHH CS
                  GDP_Man_Dehyd  81 nLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEt.....tpfyPrsPYaa 155
                                    ++A      +  + P + +++n +G +  L+++r++    ++r++ +StsEvYG+++ vp  E+     +p+ Pr +Y  
  gi|116754384|ref|YP_843502.1|  98 HMASRASPFEFEHYPIEILKANTIGLMASLDIARNH----DARLLYTSTSEVYGNPTVVPTPESyngnvNPIGPRGCYDE 173
                                    **********99**********************97....57******************9997777789********** PP

                                    HHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TT.SCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHH CS
                  GDP_Man_Dehyd 156 aKlyadwivvnyreayglfavngilfnhesprrget.fvtrkitravarialgkqevlylGnldakRdwghvkDyveamw 234
                                    aK   +  v++yr++ygl + ++++fn+++pr   + +  r ++r++a++ +g+ +++++G++ ++R++++v D +e++ 
  gi|116754384|ref|YP_843502.1| 174 AKRCGEAYVMAYRNQYGLDVRIARIFNTYGPRIRWDcIYARAVPRFIAQAIRGE-PITIFGDGTQTRSFTYVTDQIEGLL 252
                                    ********************************776647899************8.8999********************* PP

                                    HHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB--B-THHHH CS
                  GDP_Man_Dehyd 235 lmlqqdkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlllgdaskak 314
                                    ++   d+ +  v++ g+    re + +++++++ +i+ +           +sg     + +++  + +  +++ d++ka+
  gi|116754384|ref|YP_843502.1| 253 RLASIDEVKGAVVNIGND---RETMIIELAKIVLKITGS-----------DSG-----IVYQPLPEDDPLRRCPDITKAR 313
                                    ****9*987777666664...555556666666665543...........222.....33445545667788******** PP

                                    HHH----SS-HHHHHHHH CS
                  GDP_Man_Dehyd 315 eeLgWkpkvsfeelvrem 332
                                    e LgW pkv +e+++r++
  gi|116754384|ref|YP_843502.1| 314 ELLGWAPKVALEDGLRRT 331
                                    **************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 !  168.7   0.0   8.6e-53   1.4e-49       1     241 []      26     268 ..      26     268 .. 0.92

  Alignments for each domain:
  == domain 1  score: 168.7 bits;  conditional E-value: 8.6e-53
                                    EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC......EEEE--TT-HHHHHHHHHHHT-SEEEE--S- CS
                      Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl......elveldltdrsalerlfkeeqpdavihlAav 74 
                                    ilVtG++Gf+Gs +++al ++g +v+++d+lss+   +++ +l      e+++ d+ d s+  ++   ++ d vih+A  
  gi|116754384|ref|YP_843502.1|  26 ILVTGGAGFLGSWICDALIAQGANVVCVDNLSSGL-ISNISHLldadrfEFIQHDVSDLSRPLKID--QKLDLVIHMASR 102
                                    8******************************5554.45555556999999*******999888864..49********** PP

                                    --HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSS..BSTCSTTS----SSHHHHHHHHHHHH CS
                      Epimerase  75 ggvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqp..keettltgplkpnspYaaaKlagekl 152
                                    +++ +   +p +++++n++g +  l+ ar +++ rll+ s+sevYG+++ +p  ++ + +  p+ p+  Y  aK++ge +
  gi|116754384|ref|YP_843502.1| 103 ASPFEFEHYPIEILKANTIGLMASLDIARNHDA-RLLYTSTSEVYGNPTVVPtpESYNGNVNPIGPRGCYDEAKRCGEAY 181
                                    *********************************.*************99976535555556788**************** PP

                                    HHHHHHHHT-EEEEEEESEEESTT.S-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT CS
                      Epimerase 153 veayaaqyglnaiilrlfnlyGpr.ngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvda 231
                                    v ay++qygl++ i r+fn yGpr + +   +r +p++i+++ +g+ ++t++gdgt+ R f yv D +e++l+++   d+
  gi|116754384|ref|YP_843502.1| 182 VMAYRNQYGLDVRIARIFNTYGPRiRWDCIYARAVPRFIAQAIRGE-PITIFGDGTQTRSFTYVTDQIEGLLRLASI-DE 259
                                    **********************************************.*************************99887.55 PP

                                    -STTEEEEES CS
                      Epimerase 232 gdkgeiyniG 241
                                      kg ++niG
  gi|116754384|ref|YP_843502.1| 260 -VKGAVVNIG 268
                                    .678899998 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 !   49.9   0.0   1.3e-16   2.2e-13       1     162 [.      27     187 ..      27     246 .. 0.75

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 1.3e-16
                      3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkk..viegDvtdkdkleealegvdvvihlaslvd 78 
                                    +vtGgaGFlG+ ++ +L+  +   +v  +D   s  +++ ++ ++ +   +i+ Dv d ++  +  ++ d+vih+as   
  gi|116754384|ref|YP_843502.1|  27 LVTGGAGFLGSWICDALIAQGA--NVVCVDNLSSGLISNISHLLDADRfeFIQHDVSDLSRPLKIDQKLDLVIHMASRAS 104
                                    69******************95..88899977777666655555555566***************************888 PP

                      3Beta_HSD  79 vag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyesl...hqdaypesKalaE 154
                                     +  + +  ei k+n  G    l+ +++++ r l+YtS+ ev g+      ++   E+ + + +   +  +y e K+  E
  gi|116754384|ref|YP_843502.1| 105 PFEfEHYPIEILKANTIGLMASLDIARNHDAR-LLYTSTSEVYGN----PTVVPTPESYNGNVNpigPRGCYDEAKRCGE 179
                                    7776888889********************76.78*******999....44444555554444433499*********** PP

                      3Beta_HSD 155 klvlkaNg 162
                                    ++v++  +
  gi|116754384|ref|YP_843502.1| 180 AYVMAYRN 187
                                    ***98655 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 !   46.0   0.0   2.1e-15   3.4e-12       2     235 ..      25     290 ..      24     307 .. 0.80

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 2.1e-15
                                    EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT....................T--TTSHHHHHHHHHHH--SEEEE---- CS
                  RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre....................eldltdaeavaellkeakpdvvvnaAAy 61 
                                    +ilvtG+ G lGs + ++l ++g++v+ +++                     + d++d ++  +   ++k d+v+++A  
  gi|116754384|ref|YP_843502.1|  25 NILVTGGAGFLGSWICDALIAQGANVVCVDNLssglisnishlldadrfefiQHDVSDLSRPLK--IDQKLDLVIHMASR 102
                                    69**************************9776799******98888888766666666665444..46789********* PP

                                    --HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-EEEEEEEGGGS-S-....TTS-B-TT.S----SSHHHHHHHHHHHHH CS
                  RmlD_sub_bind  62 tavDkaEseeeaayavnaeavealAeaaaavgalLihvStDyVFdGe....kkrpYeed.detsPlnvYGrtKlaGEqav 136
                                       ++ E+ + +  ++n  + +a  + a++++a L++ St  V+       +++ Y+ + ++ +P++ Y ++K  GE  v
  gi|116754384|ref|YP_843502.1| 103 ASPFEFEHYPIEILKANTIGLMASLDIARNHDARLLYTSTSEVYGNPtvvpTPESYNGNvNPIGPRGCYDEAKRCGEAYV 182
                                    ********************************************8778888788898542788***************** PP

                                    HHH-SSE.EEEEE-SEESS.........SSS-HHHHHHHHHHH-SEEEEESS..-EE--EEHHHHHHHHHHHHHHCHH.G CS
                  RmlD_sub_bind 137 laagkka.livRtswvyge.........kgknfvktmlrlakereelkvvaD..qlgsPTsardlAevllqllekaaeek 204
                                     a+ +++ l vR++ ++                v +++  a + e+++++ D  q++s T++ d  e ll l++      
  gi|116754384|ref|YP_843502.1| 183 MAYRNQYgLDVRIARIFNTygprirwdcIYARAVPRFIAQAIRGEPITIFGDgtQTRSFTYVTDQIEGLLRLASIDEV-- 260
                                    **7766625599999998822233333322456777888888888899988877788888888888888888765543.. PP

                                    GG-EEEE---BS-EEHHHHHHHHHHHHCHTT CS
                  RmlD_sub_bind 205 elagvyHlanegetswlefArailkeagads 235
                                     +  v  ++n++et   e+A+ +lk +g+ds
  gi|116754384|ref|YP_843502.1| 261 -KGAVVNIGNDRETMIIELAKIVLKITGSDS 290
                                    .467788888888888888888888887776 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   2.5e-09     4e-06       1     124 [.      26     138 ..      26     152 .. 0.86
   2 !    5.7   0.0    0.0041       6.7     178     249 ..     215     288 ..     161     295 .. 0.70

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 2.5e-09
                                    EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SE CS
                Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdv 80 
                                    +lvtG++G +Gs +++ ++++ ++ + + + +   + +i++ l+    ++++++    +  dv d +r  k+ +  k d+
  gi|116754384|ref|YP_843502.1|  26 ILVTGGAGFLGSWICDALIAQGANVVCVDNLSSGLISNISHLLD----ADRFEF----IQHDVSDLSRPLKIDQ--KLDL 95 
                                    89*********************999999999999999999873....444533....4689999999999988..99** PP

                                    EEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEE CS
                Polysacc_synt_2  81 vfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvv 124
                                    v+h A        e++p+e +k N +g +  +++a +++ + ++
  gi|116754384|ref|YP_843502.1|  96 VIHMASRASPFEFEHYPIEILKANTIGLMASLDIARNHDAR-LL 138
                                    ****998887789**********************998864.44 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0041
                                    SHHHHHHHHHTTSSEEE.S-TT-EEEEE-HHHHHHHHHH.HHHH--SS-EEEE--.-EEEHHHHHHHH...... CS
                Polysacc_synt_2 178 viplFkkqikeggpvtv.TdpemtRyfmtieeavqLvlq.alalakggeifvldmGepvkivdlakalielsgl 249
                                     +p F +q  +g+p+t+  d + tR f  +++ ++ +l  a     +g +        + i++lak +++++g 
  gi|116754384|ref|YP_843502.1| 215 AVPRFIAQAIRGEPITIfGDGTQTRSFTYVTDQIEGLLRlASIDEVKGAVVNIGNDRETMIIELAKIVLKITGS 288
                                    59**************9558899**9999999998554413333444444444444789999****99999885 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0     0.001       1.7       1      26 [.      28      51 ..      28      56 .. 0.86
   2 !   18.6   0.0     5e-07   0.00081      84     205 ..      89     200 ..      83     263 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.001
                                   EE-TTSHHHHHHHHHHHHHS-.TEEE CS
                  NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpevkiy 26
                                   +TG+ GFLG+ +   L+ + ++v  +
  gi|116754384|ref|YP_843502.1| 28 VTGGAGFLGSWICDALIAQGANV--V 51
                                   7****************998854..3 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 5e-07
                                    HHHH--EEEE--SS-S....STTSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H......H CS
                  NAD_binding_4  84 laeevdviihsaAtvn...fdepykellrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegekeek 160
                                    + +++d++ih+a + +   f++   e+l++N+ G    l++a++  +   ll+ ST+ v+g+ +                
  gi|116754384|ref|YP_843502.1|  89 IDQKLDLVIHMASRASpfeFEHYPIEILKANTIGLMASLDIARNHDAR--LLYTSTSEVYGNPTVVP-----------TP 155
                                    56899*****9987652115555557*****************87666..******99999999433...........22 PP

                                    HH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-E CS
                  NAD_binding_4 161 ldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsi 205
                                    ++     +  g    Y   K ++E  v ++r++ gl v i R+ +
  gi|116754384|ref|YP_843502.1| 156 ESYNGNVNPIGPRGCYDEAKRCGEAYVMAYRNQYGLDVRIARIFN 200
                                    555666677788889**************************9755 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.0   1.4e-09   2.3e-06       1      62 [.      24      84 ..      24     105 .. 0.93

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 1.4e-09
                                   SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHH CS
                      adh_short  1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdre 62
                                   k +lvtG+++ +G  i+++l+++Ga+vv+vd+ ++ l   +++l + ++++ +iq Dv+d +
  gi|116754384|ref|YP_843502.1| 24 KNILVTGGAGFLGSWICDALIAQGANVVCVDNLSSGLISNISHLLD-ADRFEFIQHDVSDLS 84
                                   789**********************************999999998.599********9976 PP

>> KR  KR 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     0.095       4      29 ..      27      52 ..      25     101 .. 0.87
   2 ?   -1.3   0.0       1.1   1.8e+03     126     144 ..     131     149 ..     118     153 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.8e-05
                                   EEETTTSHHHHHHHHHHHHHHS-EEE CS
                             KR  4 litGGlGgLGlelarwlaekgarhlv 29
                                   l+tGG+G LG  +++ l+++ga+ + 
  gi|116754384|ref|YP_843502.1| 27 LVTGGAGFLGSWICDALIAQGANVVC 52
                                   9********************98765 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.1
                                    S--SEEEEEEEHHHHH--T CS
                             KR 126 esldffvlfSSiagllgsa 144
                                    ++ d  +l++S + ++g++
  gi|116754384|ref|YP_843502.1| 131 RNHDARLLYTSTSEVYGNP 149
                                    4566667777777777776 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.016        26       2      22 ..      35      55 ..      35      83 .. 0.92
   2 ?    6.3   0.0    0.0054       8.8      28      94 ..     172     238 ..     168     284 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.016
                                   HHHHHHHHHHHTT-EEEEEES CS
                     ADH_zinc_N  2 vGlaavqlAkalGaeviavds 22
                                   +G++ + ++ a Ga+v++vd 
  gi|116754384|ref|YP_843502.1| 35 LGSWICDALIAQGANVVCVDN 55
                                   799****************97 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0054
                                    HHHHHTTESEEEETTTC.HHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCEEEEEEEEECSCTSSE CS
                     ADH_zinc_N  28 elakklGadevinykea.dlverikeltggegvdvvfecvGsgatleaalkllkpgGrlvvvGggkge 94 
                                    + ak+ G  +v  y++   l+ ri++++++ g+ +  +c+   +++++ ++ + +g  ++++G g++ 
  gi|116754384|ref|YP_843502.1| 172 DEAKRCGEAYVMAYRNQyGLDVRIARIFNTYGPRIRWDCIY-ARAVPRFIAQAIRGEPITIFGDGTQT 238
                                    6799**********9999***********************.99999999999999999999954444 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0      0.02        33       5      51 ..      31      82 ..      26      93 .. 0.75
   2 ?    5.7   0.1     0.011        18      53      79 ..     250     276 ..     241     287 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.02
                                   S-SHHHHHHHHHHHHTTEEEEEEESSH....HHHHHHHHTT.SEEEES-TTS CS
                         TrkA_N  5 GlGrvGrslaeeLseggkdvvvidkde....erveelreeg.levvvgdatd 51
                                   G+G +G+ +++ L ++g +vv +d+      +++ +l +   +e++++d++d
  gi|116754384|ref|YP_843502.1| 31 GAGFLGSWICDALIAQGANVVCVDNLSsgliSNISHLLDADrFEFIQHDVSD 82
                                   7999***********6657*****9883333334444444457788888887 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.011
                                    HHHHHTTGGGESEEEE-SSSHHHHHHH CS
                         TrkA_N  53 evLeeagiekadaviaatgddeanila 79 
                                     +L+ a i+++++ ++ +g+d +++++
  gi|116754384|ref|YP_843502.1| 250 GLLRLASIDEVKGAVVNIGNDRETMII 276
                                    67999****************998887 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 ?   10.9   0.0   0.00016      0.26      18      69 ..       9      61 ..       2      86 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00016
                                   HHHHHHHTTTS-STTEEEEEE--.SHHHHHHHHHHHHCT-EEEEEEESSEEEE CS
                  ELFV_dehydrog 18 veemlkklkldslegkrvaisGs.GnvgsyaallltelgakvvavsDssGviy 69
                                   +e + ++l+ + +++k++ + G  G +gs+ +  l+ +ga+vv v + s  ++
  gi|116754384|ref|YP_843502.1|  9 IESINRELGEQYFQEKNILVTGGaGFLGSWICDALIAQGANVVCVDNLSSGLI 61
                                   566777778887887777665555********************988655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2359.84
//
Query:       gi|116754385|ref|YP_843503.1|  [L=304]
Description: UTP-glucose-1-phosphate uridylyltransferase GalU [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.9e-28   97.5   0.0    2.5e-27   96.0   0.0    1.6  1  NTP_transferase  Nucleotidyl transferase
    4.1e-11   43.5   0.0    6.3e-11   42.9   0.0    1.3  1  NTP_transf_3     MobA-like NTP transferase domain
     0.0022   17.7   0.0     0.0041   16.9   0.0    1.4  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
     0.0087   15.9   0.0      0.017   15.0   0.0    1.5  1  Glycos_transf_2  Glycosyl transferase family 2
  ------ inclusion threshold ------
      0.037   14.4   0.0       0.18   12.2   0.0    2.1  2  Smr              Smr domain
      0.065   13.2   0.0        0.1   12.5   0.0    1.3  1  CTP_transf_3     Cytidylyltransferase


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.0   0.0   8.4e-31   2.5e-27       1     211 [.      21     255 ..      21     277 .. 0.90

  Alignments for each domain:
  == domain 1  score: 96.0 bits;  conditional E-value: 8.4e-31
                                    EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGT........ CS
                NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfg........ 72 
                                    kavI a G+GtR+ P+tr+++k ++pv++k ++iq++++++++sgie+ i+++t + +  +e+++    +++        
  gi|116754385|ref|YP_843503.1|  21 KAVIPAAGQGTRFLPITRAQPKEMLPVVDK-PVIQYVVEEAISSGIED-ILIITGRGKRAIEDHFDVSCELEktllqknd 98 
                                    799***************************.*****************.77777788888999999998888999999** PP

                                    .............SEEEEEEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEEST......THHHHHHHHHTHSSTT CS
                NTP_transferase  73 .............vevlialepegkgtAdAvalaaelledeksdelvlvLggDhlikd......ayeeavkkaiekaakg 133
                                                  ++ ++ ++e++g+ dA++ a++  + e     + vL gD ++          ++++k+ +++ +  
  gi|116754385|ref|YP_843503.1|  99 aklydqyrrisdlADIHYIRQKEPRGLGDAILHAERHCDGEP----FAVLLGDTITVPyngsepCTSQMIKFYKKYHS-T 173
                                    ***************************************999....68888888876557777677899999999999.7 PP

                                    SEEEEEEESS-CTTSEEEEEC..TTS..BEEEEECS-SSHSH.CSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHH CS
                NTP_transferase 134 tvtfgivpveeateyGviead..eeg..rverfvEKPkeaka.selassGiYvfnsevllflakdleelkrgedeitdil 208
                                    +v++  vp+++ ++yG+i     e+g  +++++vEKP+ + a s+l + G Y+  +e++++l + +++ + ge ++td+l
  gi|116754385|ref|YP_843503.1| 174 IVAVERVPKNKIQDYGIIDGTllEDGvyKITDIVEKPSPEVApSDLGAIGRYILMPEIFDIL-RTIKPGHGGEIQLTDAL 252
                                    9999**************9989855567***********999899****************9.78***999999999998 PP

                                    HHH CS
                NTP_transferase 209 pka 211
                                    +  
  gi|116754385|ref|YP_843503.1| 253 KCC 255
                                    765 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 !   42.9   0.0   2.1e-14   6.3e-11       1     100 [.      22     152 ..      22     178 .. 0.86

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 2.1e-14
                                    EEEEEESS-TTT.....TTTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHH.................... CS
                   NTP_transf_3   1 aviLAGGrSsRm.....ggdKallplggkpllervldalraagvdevvvvggd..eevla.................... 53 
                                    avi A+G+++R+      ++K +lp+ +kp++++v++ + ++g++++++++g+  +++++                    
  gi|116754385|ref|YP_843503.1|  22 AVIPAAGQGTRFlpitrAQPKEMLPVVDKPVIQYVVEEAISSGIEDILIITGRgkRAIEDhfdvscelektllqkndakl 101
                                    7899********8887668*******************************999656676678888888888888887776 PP

                                    ......HHTTCTS-EEE-TTSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT-- CS
                   NTP_transf_3  54 ......alarlgvrvvededpgkgplaslaaalraaadadavlvlacDmPllt 100
                                            +  +++++++++  +g + ++++a r++ d ++++vl++D++ ++
  gi|116754385|ref|YP_843503.1| 102 ydqyrrISDLADIHYIRQKE-PRGLGDAILHAERHC-DGEPFAVLLGDTITVP 152
                                    665554223338999**986.59*************.9**********98765 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 !   16.9   0.0   1.4e-06    0.0041       3      52 ..      22      73 ..      21      93 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.4e-06
                                   EEEECTTSSCT...T-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE- CS
                           IspD  3 vvipAAGsGkR...mkaglpKqflelkgqtllehtvdallaskavdkivvvvs 52
                                   +vipAAG+G+R   +   +pK  l + ++++++  v+ + +s  ++ i+++  
  gi|116754385|ref|YP_843503.1| 22 AVIPAAGQGTRflpITRAQPKEMLPVVDKPVIQYVVEEAISS-GIEDILIITG 73
                                   79*********5555789*******************99995.5677776654 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 !   15.0   0.0   5.6e-06     0.017      52      86 ..     110     144 ..      96     186 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.6e-06
                                    C-TTEEEEEESSS-HHHHHHHHHHHH--SSEEEEE CS
                Glycos_transf_2  52 edprvrvirreenvGkagalnaglraatgdyilfl 86 
                                       ++++ir++e +G++ a+ ++ r+++g+ +++l
  gi|116754385|ref|YP_843503.1| 110 DLADIHYIRQKEPRGLGDAILHAERHCDGEPFAVL 144
                                    4458**************************44443 PP

>> Smr  Smr domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   5.9e-05      0.18      14      40 ..      52      78 ..      47     107 .. 0.82
   2 ?   -1.4   0.0         1     3e+03       2      24 ..     113     135 ..     112     190 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.9e-05
                                   HHHHHHHHHHHTT-SEEEEE--STTST CS
                            Smr 14 vletfldaasakglrsvevihGkGaha 40
                                   v++ ++++a+++g++ +++i+G+G++a
  gi|116754385|ref|YP_843503.1| 52 VIQYVVEEAISSGIEDILIITGRGKRA 78
                                   67789999****************964 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1
                                    E-TT--HHHHHHHHHHHHHHHHH CS
                            Smr   2 DLhglrraealnvletfldaasa 24 
                                    D+h  r++e +   +  l+a ++
  gi|116754385|ref|YP_843503.1| 113 DIHYIRQKEPRGLGDAILHAERH 135
                                    88888988888888888887433 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.3e-05       0.1      12      45 ..      38      71 ..      37     117 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.3e-05
                                   SSTTGGGSEETTEEHHHHHHHHHHHTTTTSEEEE CS
                   CTP_transf_3 12 RlpgKnlldlggkpliayvleaalkskafekviv 45
                                   R   K +l+  +kp i+yv+e+a++s+  + +i+
  gi|116754385|ref|YP_843503.1| 38 RAQPKEMLPVVDKPVIQYVVEEAISSGIEDILII 71
                                   667799*********************9555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2304.21
//
Query:       gi|116754386|ref|YP_843504.1|  [L=425]
Description: UDP-glucose 6-dehydrogenase [Methanosaeta thermophila PT]
Scores for complete 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-53  180.3   0.0    4.8e-53  179.5   0.0    1.4  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
    1.6e-38  130.8   0.1    2.9e-38  130.0   0.1    1.4  1  UDPG_MGDP_dh    UDP-glucose/GDP-mannose dehydrogenase family,
    2.2e-28   98.7   0.0    4.6e-28   97.7   0.0    1.5  1  UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family,
    0.00034   21.1   0.3     0.0012   19.3   0.3    1.9  1  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
     0.0034   16.7   0.1     0.0055   16.0   0.1    1.3  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
      0.009   15.9   0.1      0.028   14.3   0.0    1.9  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
  ------ inclusion threshold ------
      0.011   15.8   0.9       0.11   12.6   0.0    2.7  3  DpaA_N          Dipicolinate synthase subunit A N-terminal do
      0.029   14.6   0.5       0.09   13.0   0.5    1.8  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
      0.049   13.2   0.2      0.098   12.2   0.1    1.6  2  DAO             FAD dependent oxidoreductase
      0.074   13.2   0.0        5.8    7.1   0.0    2.4  2  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
      0.076   12.7   0.0       0.13   11.9   0.0    1.4  1  ApbA            Ketopantoate reductase PanE/ApbA
      0.088   12.1   0.0       0.17   11.1   0.0    1.5  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
       0.14   11.2   0.3       0.22   10.6   0.3    1.2  1  GIDA            Glucose inhibited division protein A
       0.17   11.9   0.0       0.47   10.4   0.0    1.8  2  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen


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 !  179.5   0.0   3.8e-56   4.8e-53       1     184 [.       1     186 [.       1     189 [. 0.93

  Alignments for each domain:
  == domain 1  score: 179.5 bits;  conditional E-value: 3.8e-56
                                    SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--TTHHHHHHHHCHTTTEEEES-HHHHHHC-SEE CS
                 UDPG_MGDP_dh_N   1 mkisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiyepgLeelvkkavesgrlsfttdvekaveeadvi 80 
                                    mkisv+G GYvGlv+a+++ae+gh v ++ id++k d++n+g+ piye gLee + +++  ++l++  ++++ ++ +d+i
  gi|116754386|ref|YP_843504.1|   1 MKISVVGGGYVGLVSAVCFAELGHSVDLIEIDRAKCDAINAGQPPIYEVGLEERLSAHA-GRNLHAYVEYDH-IKYSDII 78 
                                    8********************************************************99.8*********99.******* PP

                                    EE-----B-TTTTCB-THHHHHHHHHHHHHHHC.....EEEEEE-S---TTHHHHCHHHHHHHHCSS-TTCEEEEE---- CS
                 UDPG_MGDP_dh_N  81 fiaVgTPskkkgkaaDlkyvesaarsiaealkk.....gkvvvvkSTvpvgtaeelvkkileeaskkkgvdfdvvsnPEf 155
                                    fi+VgTP+   + ++D++ + sa++si++al++     ++vvvvkSTvp+gt+e  v + + ++  k++ +++ ++nPEf
  gi|116754386|ref|YP_843504.1|  79 FICVGTPQGP-DGHPDISNIISASESIGRALRDkdgtrYHVVVVKSTVPPGTTERQVIPSVLRQFGKNNDQIGFAVNPEF 157
                                    **********.8888****************99899999**************97666655555555679********** PP

                                    --TTSHHHHHHS-S-EEEEESSCHHHHHH CS
                 UDPG_MGDP_dh_N 156 lregsavkdllnpdrvviGveekkaeaal 184
                                    lreg av d+lnpdr+viG ++k  ++++
  gi|116754386|ref|YP_843504.1| 158 LREGMAVWDFLNPDRIVIGCRKKMDGDLV 186
                                    ********************999877655 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 !  130.0   0.1   2.3e-41   2.9e-38       2      93 ..     204     295 ..     203     296 .. 0.99

  Alignments for each domain:
  == domain 1  score: 130.0 bits;  conditional E-value: 2.3e-41
                   UDPG_MGDP_dh   2 tAEliKlaaNaflatkIsfiNelanlcealgidveeVieavgldprigpkflkpglGvGGsclpkDvkaLvalaeelgle 81 
                                    +AE+iK+a+NaflatkIs++Ne++n+c++lgidv eV++avgld+rigp+fl++g+G+GGsclpkDv+aL+alae+ g +
  gi|116754386|ref|YP_843504.1| 204 AAEMIKYASNAFLATKISYANEIGNICKKLGIDVYEVMRAVGLDRRIGPAFLNAGIGFGGSCLPKDVSALIALAEDMGED 283
                                    69****************************************************************************** PP

                   UDPG_MGDP_dh  82 aelleavrevNe 93 
                                    + ll++v+++N+
  gi|116754386|ref|YP_843504.1| 284 PILLKSVMQINK 295
                                    ***********6 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 !   97.7   0.0   3.6e-31   4.6e-28       1     103 [.     318     415 ..     318     417 .. 0.96

  Alignments for each domain:
  == domain 1  score: 97.7 bits;  conditional E-value: 3.6e-31
                                    EEE-SSSSTT-S--TT-HHHHHHHHHHHCTSEEEEE-SSTHHCCCCHHGGBTCCEEES-CHHHHTT-SEEEE-S--GGGG CS
                 UDPG_MGDP_dh_C   1 ailGlafKkdtdDlReSpaldiieeLleegaevkiyDPkvkeeaveaeleekgvevvdsleealkgadaiviltehdefk 80 
                                    a+lGl+fK++tdD+ReS+++ +i+eL ++ga+v +yDPk++++ ++    ++++ +++s++eal+gada++++te++ef 
  gi|116754386|ref|YP_843504.1| 318 AVLGLSFKENTDDVRESRSIVVIKELIRRGARVAAYDPKANQSMKRF---LTEIDYCSSASEALTGADACLVMTEWPEFA 394
                                    89****************************************99999...679*************************** PP

                                    GS-HHHHHHCCSS-EEEESSS-C CS
                 UDPG_MGDP_dh_C  81 eldlaklkelmkpavvfDgrnvl 103
                                    +l  +k  +lmk ++v+ gr++l
  gi|116754386|ref|YP_843504.1| 395 HL--DKEFDLMKSRIVIEGRRIL 415
                                    *7..67889***********997 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.3   9.5e-07    0.0012       1      30 [.       2      31 ..       2      38 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 9.5e-07
                                   EEEEECSSHHHHHHHHHHHHTTSEEEEEES CS
                      Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvver 30
                                   k+ vvGgGy+gl  A  +aelg++V ++e 
  gi|116754386|ref|YP_843504.1|  2 KISVVGGGYVGLVSAVCFAELGHSVDLIEI 31
                                   578************************995 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   4.3e-06    0.0055     144     173 ..       2      31 ..       1      54 [. 0.91

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.3e-06
                                    EEEEES-SHHHHHHHHHHHHHT-EEEEEES CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 144 rivvvGgGyiGvElAaalaklgkevtlvea 173
                                    +i vvGgGy+G++ A  +a+lg+ v l+e 
  gi|116754386|ref|YP_843504.1|   2 KISVVGGGYVGLVSAVCFAELGHSVDLIEI 31 
                                    688************************996 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 !   14.3   0.0   2.2e-05     0.028       1      37 [.       2      38 ..       2      63 .. 0.91
   2 ?   -3.1   0.0       4.7     6e+03      19      35 ..     344     360 ..     339     383 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.2e-05
                                   EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHH CS
                        3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdiseealek 37
                                   k+ v+G G +G   a  fa+ g++V l++i++++ ++
  gi|116754386|ref|YP_843504.1|  2 KISVVGGGYVGLVSAVCFAELGHSVDLIEIDRAKCDA 38
                                   689***************************9988765 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4.7
                                    HHTT-EEEEE-S-HHHH CS
                        3HCDH_N  19 asagleVvlvdiseeal 35 
                                    +++g +V  +d ++++ 
  gi|116754386|ref|YP_843504.1| 344 IRRGARVAAYDPKANQS 360
                                    56677777777654432 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 ?    0.0   0.1      0.68   8.7e+02       1      30 [.       2      31 ..       2      43 .. 0.83
   2 ?   -1.5   0.0         2   2.5e+03      99     116 .]     224     241 ..     193     241 .. 0.71
   3 ?   12.6   0.0   8.8e-05      0.11       9      56 ..     334     385 ..     333     389 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.68
                                   EEEEESB-HHHHHHHHHHHHTT-EEEEES- CS
                         DpaA_N  1 kiaviGGDaRqlylarkLaekgakvslygl 30
                                   ki v+GG    l+ a  +ae g++v l+ +
  gi|116754386|ref|YP_843504.1|  2 KISVVGGGYVGLVSAVCFAELGHSVDLIEI 31
                                   68999999999999999********99988 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2
                                    HHHHHHHHHCT-EEEEGG CS
                         DpaA_N  99 pelkelaeekgielvdlm 116
                                    +e+ +++++ gi ++++m
  gi|116754386|ref|YP_843504.1| 224 NEIGNICKKLGIDVYEVM 241
                                    566788899999998877 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 8.8e-05
                                    HHHHHHHHHHHHTT-EEEEES-....TSSS-BTTEEEE-GGGS-GGG-SEEE CS
                         DpaA_N   9 aRqlylarkLaekgakvslygl....eleekiegvekaesleealedadvii 56 
                                     R ++++++L+++ga+v +y      ++++  +++  ++s +eal  ad+++
  gi|116754386|ref|YP_843504.1| 334 SRSIVVIKELIRRGARVAAYDPkanqSMKRFLTEIDYCSSASEALTGADACL 385
                                    599*****************6666678899999***************9976 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.5     7e-05      0.09       1      27 [.       5      31 ..       5      35 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7e-05
                                   EE--SHHHHHHHHHHHCCTEEEEEE-S CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllek 27
                                   +vG+G  Glv A   a+ g++v+l+e 
  gi|116754386|ref|YP_843504.1|  5 VVGGGYVGLVSAVCFAELGHSVDLIEI 31
                                   8************************96 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   7.6e-05     0.098       2      31 ..       3      33 ..       2      91 .. 0.83
   2 ?   -3.2   0.0       3.6   4.6e+03     148     174 ..     222     248 ..     190     259 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.6e-05
                                   EEEECTSHHHHHHHHHHHHTT..EEEEESSSS CS
                            DAO  2 vviiGGGiiGlstAyeLarrg..Vtllekgdi 31
                                   + ++GGG++Gl  A   a+ g  V l+e + +
  gi|116754386|ref|YP_843504.1|  3 ISVVGGGYVGLVSAVCFAELGhsVDLIEID-R 33
                                   67****************99999****977.4 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.6
                                    HHHHHHHHHHHTT-EEEESECEEEEEE CS
                            DAO 148 ltaalaraaealGveilegtevtglee 174
                                    +++ + + +++lG++++e  +++gl++
  gi|116754386|ref|YP_843504.1| 222 YANEIGNICKKLGIDVYEVMRAVGLDR 248
                                    556666778888888888888888865 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 ?    3.6   0.0     0.054        69       1      65 [.       2      84 ..       2     100 .. 0.75
   2 ?    7.1   0.0    0.0045       5.8      16      62 ..     341     387 ..     338     399 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.054
                                   EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT.................EEE-SSHHHHHHHC.....SEEE CS
                  NAD_binding_2  1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg.................akaaesieelvasl.....dvvi 60
                                   ki ++G G  G   a  +++ g++v +++ +++k++++ a +                      ++ + v+       d+++
  gi|116754386|ref|YP_843504.1|  2 KISVVGGGYVGLVSAVCFAELGHSVDLIEIDRAKCDAINAGQppiyevgleerlsahagR----NLHAYVEYDhikysDIIF 79
                                   6999********************************999887787777777666633331....222222221334447777 PP

                                   E-SSS CS
                  NAD_binding_2 61 tmvka 65
                                   ++v  
  gi|116754386|ref|YP_843504.1| 80 ICVGT 84
                                   77765 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0045
                                    HHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE- CS
                  NAD_binding_2  16 lnllkagykvavynrtkekveelvaegakaaesieelvasldvvitm 62 
                                    ++l+++g +va+y+ ++++  +   ++++ ++s++e+++++d+ ++m
  gi|116754386|ref|YP_843504.1| 341 KELIRRGARVAAYDPKANQSMKRFLTEIDYCSSASEALTGADACLVM 387
                                    6899**********7776666666688**************999888 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0    0.0001      0.13       1      80 [.       3      86 ..       3     104 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0001
                                   EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETT.CEEEEEECEEECCH...SCCCCS-ESEEEE-SS CS
                           ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseg.geeilrppealsae...ekselepidlvivtvK 77
                                   i ++G G +G + a++ a+ g+ v li  +r +++a++     ++++g +e+              e  +++  d+++++v 
  gi|116754386|ref|YP_843504.1|  3 ISVVGGGYVGLVSAVCFAELGHSVDLIEIDRaKCDAINAGQPPIYEVGlEERLSAHAGRNL-HayvEYDHIKYSDIIFICVG 83
                                   789************************999999*****99999999995333332222222.23687788888899999886 PP

                                   GGG CS
                           ApbA 78 ayq 80
                                   + q
  gi|116754386|ref|YP_843504.1| 84 TPQ 86
                                   665 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 ?   11.1   0.0   0.00013      0.17      30      69 ..       2      41 ..       1      87 [. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00013
                                   EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH CS
                    AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqles 69
                                   k+ v+GgG +Gl ++   ++lg +V +++++ a+   +++
  gi|116754386|ref|YP_843504.1|  2 KISVVGGGYVGLVSAVCFAELGHSVDLIEIDRAKCDAINA 41
                                   789***************************9999887765 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.3   0.00017      0.22       2      33 ..       3      34 ..       2      43 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00017
                                   EEEE-SSHHHHHHHHHHHHTT--EEEEES-GG CS
                           GIDA  2 viViGgGhAGceAAlaaarlGakvlLithkld 33
                                   + V+GgG  G+  A+  a+lG++v Li  +  
  gi|116754386|ref|YP_843504.1|  3 ISVVGGGYVGLVSAVCFAELGHSVDLIEIDRA 34
                                   88************************954443 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00037      0.47       1      40 [.       2      41 ..       2      84 .. 0.93
   2 ?   -3.1   0.0       5.2   6.6e+03      67     104 ..     143     179 ..     137     188 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00037
                                   -EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHH CS
                 NAD_Gly3P_dh_N  1 kiavlGaGswGtalAkvlaenghevrlwvreeelieeine 40
                                   ki+v+G+G  G   A  +ae gh+v l+  +++ +++in+
  gi|116754386|ref|YP_843504.1|  2 KISVVGGGYVGLVSAVCFAELGHSVDLIEIDRAKCDAINA 41
                                   79************************************97 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.2
                                    HTT--EEEE---HHHHHHHHHHHCCC--TT-EEEE--- CS
                 NAD_Gly3P_dh_N  67 lkgadiivlvvPsqalrevlkklkgllkkkailvsliK 104
                                     k+ d i ++v  ++lre ++ ++ +l+++ i++ + K
  gi|116754386|ref|YP_843504.1| 143 GKNNDQIGFAVNPEFLREGMAVWD-FLNPDRIVIGCRK 179
                                    567788889999999999888765.5778888888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 3385.88
//
Query:       gi|116754387|ref|YP_843505.1|  [L=304]
Description: hypothetical protein Mthe_1082 [Methanosaeta thermophila PT]
Scores for complete 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-53  181.7  30.0    2.9e-53  181.4  30.0    1.0  1  LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
  ------ inclusion threshold ------
        1.1    8.4   6.2        1.1    8.4   0.8    2.1  2  7tm_7            7tm Chemosensory receptor
        2.7    8.2   9.7      0.096   12.9   1.4    2.3  2  DPM3             Dolichol-phosphate mannosyltransferase subun


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 !  181.4  30.0   4.8e-57   2.9e-53       3     301 .]      14     296 ..      13     296 .. 0.94

  Alignments for each domain:
  == domain 1  score: 181.4 bits;  conditional E-value: 4.8e-57
                LPG_synthase_TM   3 lglalsalllalllrgvdlaalaaalrsldpwwlllalllallsvllralrWrlllrslgarislrrllrayliglfvnn 82 
                                    l+la+++ll+a+ll++++++++a++++s++p ++l+a  +++l++l+ + rWr +l+ +g++i+l ++++a++ g+ ++ 
  gi|116754387|ref|YP_843505.1|  14 LRLAFGLLLVAVLLHRLGPSEVAQTIISARPVYVLMAASVYALTFLILSTRWRMILHDMGGNIPLVSAYQAFAGGMILSD 93 
                                    68999*************************************************************************** PP

                LPG_synthase_TM  83 vtPgalgGevvrayllkrkegvslskalasvvverlldllalvllgllallllggllaegaavllllalallllavlall 162
                                    +tP+++ Ge+ r +l++    ++ s+alasvv++rl+d+l++++lg+++l+l++g+ +      + + l+l+++a++ + 
  gi|116754387|ref|YP_843505.1|  94 ITPARI-GELSRPLLVRD--RIEMSRALASVVLDRLSDILTMFILGACGLGLFFGEEM------IEIPLVLAIVALTSV- 163
                                    ******.*******9999..***********************************954......444444444444443. PP

                LPG_synthase_TM 163 lllllrrrlarlarvlkrlarllarfarklasakrklvlasprrlllafllslliwllealtlylllralgvdvslalll 242
                                    +++++r   a ++r   rla+l+++f + +a  +   ++     +++++ll++++w+++al++y+l+ +++ ++sl  l+
  gi|116754387|ref|YP_843505.1| 164 VIWRRRTEIADRLRGSDRLAPLARSFDALSAIND---IRL---VMIRSVLLTTIAWITHALRVYILASSVDQTPSLQMLF 237
                                    579************************9999865...344...699********************************** PP

                LPG_synthase_TM 243 lillaltlvgalpplPgGlGvrEaalalllallGvsaaealaaallyrlitlylllllG 301
                                    l+l+++++++++p++++G+G++E+++a+lla+ G++a+++l++a+l+r +t+ + +++G
  gi|116754387|ref|YP_843505.1| 238 LLLPLVSALSLIPVSISGIGLVEGGMAALLASQGIPASTGLSIAFLDRMVTVAFHIIAG 296
                                    *******************************************************9998 PP

>> 7tm_7  7tm Chemosensory receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.5    0.0092        55     127     191 ..      11      72 ..       5      88 .. 0.74
   2 ?    8.4   0.8   0.00019       1.1      71     166 ..     148     246 ..     147     259 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.0092
                          7tm_7 127 lllvliillllvtllgylllsqyftlvlllllyllpylvlqlllllyfllllliyellrllnerL 191
                                     +++ +++ ll++++  ll+  +++ v  +++   p +   ++ + y l +l++++++r++++ +
  gi|116754387|ref|YP_843505.1|  11 RKTLRLAFGLLLVAV--LLHRLGPSEVAQTIISARPVY-VLMAASVYALTFLILSTRWRMILHDM 72 
                                    455556666666666..556666666667777777777.78899999999999999999999877 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00019
                          7tm_7  71 nlqlvlglltvlvillsllfqrrrlarllnellkldrrlkrlgnrrnkrrfnrllllllvliillllvtll..gylllsq 148
                                    ++++ l l++v ++ +  +++r ++a+ l+   +l  + ++    +  + ++++++  ++l+ +++ +++l  ++l +s 
  gi|116754387|ref|YP_843505.1| 148 MIEIPLVLAIVALTSVVIWRRRTEIADRLRGSDRLAPLARSFDALSAINDIRLVMIRSVLLTTIAWITHALrvYILASSV 227
                                    8999*************************998666555555555555566666666666666666767666666688888 PP

                          7tm_7 149 yftlvlllllyllpyl.vl 166
                                     +t  l +l++llp +  l
  gi|116754387|ref|YP_843505.1| 228 DQTPSLQMLFLLLPLVsAL 246
                                    8888888888888887433 PP

>> DPM3  Dolichol-phosphate mannosyltransferase subunit 3 (DPM3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.4   1.6e-05     0.096      18      59 ..      18      61 ..       1      65 [. 0.73
   2 ?   -0.7   1.6      0.28   1.7e+03      10      45 ..     205     244 ..     200     258 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.6e-05
                           DPM3 18 wlalllrlvslpl..skvqdevvpvlPlwalvlfGayslatlgy 59
                                   + +ll+ ++ ++l  s+v+++++ + P+++l++  +y+l+ l++
  gi|116754387|ref|YP_843505.1| 18 FGLLLVAVLLHRLgpSEVAQTIISARPVYVLMAASVYALTFLIL 61
                                   33344444433345699**********************98765 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.28
                           DPM3  10 lallllalwlalllrlvslpl....skvqdevvpvlPlwa 45 
                                     +ll +++w++  lr+  l      ++  + + ++lPl+ 
  gi|116754387|ref|YP_843505.1| 205 SVLLTTIAWITHALRVYILASsvdqTPSLQMLFLLLPLVS 244
                                    4677788888888887744411221223333334444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 2361.77
//
Query:       gi|116754388|ref|YP_843506.1|  [L=252]
Description: hypothetical protein Mthe_1083 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-18   67.6  12.0      1e-16   61.2  12.0    2.4  1  DUF1616   Protein of unknown function (DUF1616)


Domain annotation for each model (and alignments):
>> DUF1616  Protein of unknown function (DUF1616)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.2  12.0   5.7e-21     1e-16      17     106 ..      33     122 ..      19     250 .. 0.91

  Alignments for each domain:
  == domain 1  score: 61.2 bits;  conditional E-value: 5.7e-21
                        DUF1616  17 lnetplRivlglplvLflPGYaliaaLFPekrdidgieRlaLSfglSiaivpliglvlnvtpwgirlepilvslslftll 96 
                                        +   ++++p++L+lPGYal  aLFP+++d++ ieRl++S+gl + +v ++++++ +  + +  +p+lv+l++ t +
  gi|116754388|ref|YP_843506.1|  33 AGAYLGVPLIAFPVILLLPGYALSVALFPHRDDLNPIERLVMSIGLNVSLVCMLAVGIDFLGMRLWYAPLLVALTAATAA 112
                                    44444445789********************************************************************* PP

                        DUF1616  97 lalvAivrRs 106
                                    +++v+i++R+
  gi|116754388|ref|YP_843506.1| 113 FVIVSILQRR 122
                                    *******997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); 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 0.23s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2004.54
//
Query:       gi|116754389|ref|YP_843507.1|  [L=606]
Description: hypothetical protein Mthe_1084 [Methanosaeta thermophila PT]
Scores for complete 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-07   31.4  15.3    1.9e-07   31.4  15.3    4.0  4  PMT_2     Dolichyl-phosphate-mannose-protein mannosyltransfer


Domain annotation for each model (and alignments):
>> PMT_2  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.4      0.02   3.5e+02     106     139 ..      25      57 ..       8      81 .. 0.50
   2 !   31.4  15.3   1.1e-11   1.9e-07       3     158 ..     111     267 ..     109     268 .. 0.69
   3 ?   -2.7   2.3      0.34   6.1e+03      56      56 ..     350     350 ..     296     408 .. 0.56
   4 ?    0.1   1.9     0.048   8.5e+02      24      66 ..     418     462 ..     399     469 .. 0.59

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.02
                          PMT_2 106 vlfGlgflsKytaallliaallyllisarrilke 139
                                     l+Gl++      a++l+aa + +li  r +l e
  gi|116754389|ref|YP_843507.1|  25 GLLGLALSRIDILAVILFAACYSILIY-RTWLTE 57 
                                    444444332233333334444444444.344433 PP

  == domain 2  score: 31.4 bits;  conditional E-value: 1.1e-11
                          PMT_2   3 PPliawllalftklfgfselairlvsalagvltilllyllarrlfgkraallaalllavvplfvalsalftpdaplvllw 82 
                                    P l+a ++a++t    + +    ++   +++ +i+ lyllar++f+ r+a+++ lll+v + ++ +  +  ++++ ++  
  gi|116754389|ref|YP_843507.1| 111 PALHALIAAASTYMHTEAMPLQKFLVPSFSAAGIISLYLLARDFFDDRIAITSGLLLSVGTAYIHWISQAATESLGIPIA 190
                                    66666666666666555555555666668999***************************999****************** PP

                          PMT_2  83 alalylllraleknklkywllagvlfGlgflsK.ytaallliaall.....yllisarrilkekkpylalllal.llfsp 155
                                    ++a y+++ral + +  y+ +a + +    l++  ta+++++  +      yll+  +   k+     al+l l +l++p
  gi|116754389|ref|YP_843507.1| 191 LIAFYISYRALGSTR--YLPVALITISSLALTHhLTAMIFVVW-INsftiaYLLFV-SENHKDALR--ALILSLfALAVP 264
                                    ***********9987..99777776665555550555555542.223333788888.333333322..333333033334 PP

                          PMT_2 156 vli 158
                                     ++
  gi|116754389|ref|YP_843507.1| 265 LMW 267
                                    455 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 0.34
                          PMT_2  56 a 56 
                                     
  gi|116754389|ref|YP_843507.1| 350 L 350
                                    1 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.048
                          PMT_2  24 irlvsalagvltilllyllarrlf..gkraallaalllavvplfv 66 
                                    +r+++++  +l++++ y  +  +   +++a+++a++l+ ++ l+v
  gi|116754389|ref|YP_843507.1| 418 LRFIEFIYPSLAVIGAYGFVYLIQrsNAKAGATAMALMCLFSLVV 462
                                    566666666666666665555443004555555555554444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (606 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.42
# Mc/sec: 4296.68
//
Query:       gi|116754390|ref|YP_843508.1|  [L=153]
Description: bacitracin resistance protein BacA [Methanosaeta thermophila PT]
Scores for complete 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-20   72.1   5.8    6.8e-20   71.8   5.8    1.0  1  BacA      Bacitracin resistance protein BacA


Domain annotation for each model (and alignments):
>> BacA  Bacitracin resistance protein BacA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.8   5.8   3.8e-24   6.8e-20     117     256 .]      12     148 ..       2     148 .. 0.82

  Alignments for each domain:
  == domain 1  score: 71.8 bits;  conditional E-value: 3.8e-24
                           BacA 117 alivtglllllae...klrkkkkksledltlkdalliGlaQalAllPGvSRSGaTivaglllglsreaaaefSFllaiPa 193
                                      ++ g+ l++++   +lr +++ + e + +k++++ GlaQ++++lPGv R G+T+++ l++g++  +a+  SF++++ a
  gi|116754390|ref|YP_843508.1|  12 G-LLIGCPLIITRpmlRLRGSSTGDREAIITKEMAILGLAQSFSILPGVTRFGTTLTVHLMRGVNLYDALLISFIISVSA 90 
                                    3.34455555555466555556666679**************************************************** PP

                           BacA 194 ilgagllkllksaealtaselll.lvgfvvafvvallaikfllkllkkkklkvFaiYrivlGll 256
                                    +lga +l++++   +++ + l   ++ ++ +f+++++++++l ++++  +   F++ +i++G++
  gi|116754390|ref|YP_843508.1|  91 VLGAIALDCFTG--SVSIQPL-PgAAIMISSFITGYATVDVLTRFARDVS---FSWLCIAIGMI 148
                                    ********7733..3333433.35899**********************9...99*****9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1197.50
//
Query:       gi|116754391|ref|YP_843509.1|  [L=366]
Description: hypothetical protein Mthe_1086 [Methanosaeta thermophila PT]
Scores for complete 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-66  223.3   0.0    3.3e-66  222.8   0.0    1.2  1  DUF2117     Uncharacterized protein conserved in archaea (DUF
  ------ inclusion threshold ------
      0.013   14.7   0.1      0.021   14.0   0.1    1.2  1  NAD_kinase  ATP-NAD kinase


Domain annotation for each model (and alignments):
>> DUF2117  Uncharacterized protein conserved in archaea (DUF2117)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  222.8   0.0   3.7e-70   3.3e-66       1     212 []      77     283 ..      77     283 .. 0.98

  Alignments for each domain:
  == domain 1  score: 222.8 bits;  conditional E-value: 3.7e-70
                        DUF2117   1 DivfLlnygksketGhvFgkiVverskekkpliqierpgekdgeiilwnekaeklakklseelglkivkpeevekeives 80 
                                    D+ +Lln++ks+etG vFg+iV++r++  +pl+q+++ g+  ++++ ++ek++ +ak l++++g++i+++ + ++++  +
  gi|116754391|ref|YP_843509.1|  77 DLTVLLNHAKSRETGLVFGAIVAARARPANPLVQVDSGGRFVAALANLSEKSDAIAKGLASHFGFDILDACMPYDNLR-Q 155
                                    899************************************************************************999.8 PP

                        DUF2117  81 kgkrvvrkiagvspgenilvnGiviGkaeseevtivaedgkivdikggeiKehGvekLgkvdlekaivktgllRrskvke 160
                                    +g+++vr+++gv pge+i vnG+viG+a++++v+i+a+dg+iv  +g+++K+hG+ekL  vdl++ai+++g++Rr    +
  gi|116754391|ref|YP_843509.1| 156 EGDVIVRRMSGVLPGERISVNGTVIGTATDAHVEIMARDGRIVGGRGINLKRHGLEKLPYVDLRSAILRSGSVRR----T 231
                                    9**************************************************************************....5 PP

                        DUF2117 161 kllkkkklkkkkekkvgkvvlidHaaedvlelakkadlvvtvGDDTTavagd 212
                                    + + k +++++k++++g++++idHaae+++e+a++a++v+t+GDDTTa+agd
  gi|116754391|ref|YP_843509.1| 232 AGMLKPRISSVKTSRNGRFAIIDHAAEESFEHASDASFVITIGDDTTAIAGD 283
                                    667777789999***************************************8 PP

>> NAD_kinase  ATP-NAD kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   2.3e-06     0.021      73     111 ..     261     298 ..     224     301 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.3e-06
                                    TTTTTSSSEEEEEE-HHHHHHHHHHHHHCT-EEEEEESS CS
                     NAD_kinase  73 afadagvdliivvGGDGTaldvarllqkaeiPvlgvnaG 111
                                     ++ +++ ++i++G+D Ta +   +l++  iPvlg+  G
  gi|116754391|ref|YP_843509.1| 261 FEHASDASFVITIGDDTTAIA-GDVLSRLGIPVLGIVDG 298
                                    345678999*********985.56666689*****9766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2536.27
//
Query:       gi|116754392|ref|YP_843510.1|  [L=91]
Description: hypothetical protein Mthe_1087 [Methanosaeta thermophila PT]
Scores for complete 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   92.8   0.4    1.4e-26   92.7   0.4    1.0  1  DUF2098   Uncharacterized protein conserved in archaea (DUF20
  ------ inclusion threshold ------
      0.075   13.5   0.0       0.14   12.6   0.0    1.4  1  YdfZ      YdfZ protein


Domain annotation for each model (and alignments):
>> DUF2098  Uncharacterized protein conserved in archaea (DUF2098)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.7   0.4   1.5e-30   1.4e-26       1      94 []       2      91 .]       2      91 .] 0.97

  Alignments for each domain:
  == domain 1  score: 92.7 bits;  conditional E-value: 1.5e-30
                        DUF2098  1 eievGsvVrYinTgTvGkVvdikkeedgevwvkLdstdLyYrvdtLevidekekkkekeekekedleelekkekeleeevde 82
                                   ei+ Gs+VrY +TgTvG V+ ik eedge+w++LdstdLyY +++Le+i+   k  e++e + ++le+l++++ke++e ++ 
  gi|116754392|ref|YP_843510.1|  2 EIKEGSLVRYNGTGTVGVVKLIK-EEDGETWALLDSTDLYYLTSYLEPIE---KVPERKELSGMSLEDLTERMKEEKELMER 79
                                   69*********************.9*************************...89**********************99999 PP

                        DUF2098 83 eketdesceGGG 94
                                   ++ +de++e+GG
  gi|116754392|ref|YP_843510.1| 80 ARLHDENLECGG 91
                                   9999******99 PP

>> YdfZ  YdfZ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.6e-05      0.14      10      33 ..       3      26 ..       2      36 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.6e-05
                           YdfZ 10 ittGsrVMiagtgevgvikaihtd 33
                                   i+ Gs V  +gtg+vgv+k i+ +
  gi|116754392|ref|YP_843510.1|  3 IKEGSLVRYNGTGTVGVVKLIKEE 26
                                   889****************99866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 720.72
//
Query:       gi|116754393|ref|YP_843511.1|  [L=318]
Description: ATPase [Methanosaeta thermophila PT]
Scores for complete 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-62  209.1   0.1    2.8e-62  208.3   0.1    1.4  1  AAA_3            ATPase family associated with various cellul
    1.1e-16   60.4   0.2    2.6e-16   59.2   0.0    1.7  2  AAA_lid_2        AAA lid domain
      4e-11   43.1   0.0    6.6e-11   42.4   0.0    1.4  1  AAA_5            AAA domain (dynein-related subfamily)
    2.7e-06   27.8   0.0    4.5e-06   27.1   0.0    1.4  1  AAA              ATPase family associated with various cellul
    0.00012   21.2   0.0    0.00027   20.1   0.0    1.5  2  MCM              MCM P-loop domain
     0.0069   16.1   0.1      0.045   13.5   0.1    2.1  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
  ------ inclusion threshold ------
      0.012   15.3   0.0      0.056   13.2   0.0    1.8  2  Sigma54_activat  Sigma-54 interaction domain
      0.029   13.7   0.3       0.27   10.6   0.1    2.1  2  Mg_chelatase     Magnesium chelatase, subunit ChlI


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 !  208.3   0.1   1.3e-65   2.8e-62       1     131 []      46     178 ..      46     178 .. 0.98

  Alignments for each domain:
  == domain 1  score: 208.3 bits;  conditional E-value: 1.3e-65
                          AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeeke..kefefkkGpvfanllladeinrappkt 78 
                                    h lle+ PGl+ktll+k+ ak+++l+f+riq+tpdl+P+di+Gt+++ee +  k+f+f++Gp+fan++ladeinra+pkt
  gi|116754393|ref|YP_843511.1|  46 HALLESNPGLGKTLLIKTTAKTMSLSFSRIQCTPDLMPADITGTTIIEEVDgeKRFRFEPGPIFANIVLADEINRASPKT 125
                                    99*********************************************99776699************************* PP

                          AAA_3  79 qsalleameerqvtvegethklpepflvlatqnPieqeGtyplpeaqldrfll 131
                                    qsa+le+m+e+qvtv+++t++l++pf+vlatqnPie+eGt+plpeaqldrfl+
  gi|116754393|ref|YP_843511.1| 126 QSAMLESMQEKQVTVGNRTYRLDDPFFVLATQNPIEMEGTFPLPEAQLDRFLM 178
                                    ***************************************************98 PP

>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       5.6   1.3e+04      39      47 ..     226     234 ..     222     237 .. 0.77
   2 !   59.2   0.0   1.1e-19   2.6e-16       3      73 .]     241     312 ..     239     312 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 5.6
                      AAA_lid_2  39 tpeDvkeaa 47 
                                    + eD+++aa
  gi|116754393|ref|YP_843511.1| 226 ISEDLRKAA 234
                                    679999998 PP

  == domain 2  score: 59.2 bits;  conditional E-value: 1.1e-19
                      AAA_lid_2   3 trahlaielgvsgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlr..repeaegetteeiveei 73 
                                    tr+   +++g+s+r a++ l+ aA+ +A+l+gr+yV+ eD+  +a ++L+HRl+   e+e+ g t+++++++i
  gi|116754393|ref|YP_843511.1| 241 TRNWNGVRYGASPR-ASIGLVLAAKSRALLDGRNYVSREDLHVMAYPILRHRLIltFEAERRGLTQDQVITDI 312
                                    7888899*******.***************************************9999999999999999875 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 !   42.4   0.0     3e-14   6.6e-11       3     138 .]      48     176 ..      46     176 .. 0.92

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 3e-14
                                    EEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.............--------G-SEEEEESGGG-- CS
                          AAA_5   3 lLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik....ngttslvdsplvraaregeilvlDEverae 78 
                                    lL  +pG gK+ l++  a+ +  ++  +q+t d+ ++d++g + i+    +++ +++++p+      + i++ DE++ra+
  gi|116754393|ref|YP_843511.1|  48 LLESNPGLGKTLLIKTTAKTMSLSFSRIQCTPDLMPADITGTTIIEevdgEKRFRFEPGPIF-----ANIVLADEINRAS 122
                                    66668*******************************************9999999*******.....9************ PP

                                    HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--..-TT-TTHHHHTT- CS
                          AAA_5  79 sevlnsLlslleerrllleeggelvkaknddllerfrviatanpld.rslnelspalrsRf 138
                                    +++++++l  + e+++ + +++ + +  +      f v+at np +  +  +l +a ++Rf
  gi|116754393|ref|YP_843511.1| 123 PKTQSAMLESMQEKQVTVGNRTYRLDD-P------FFVLATQNPIEmEGTFPLPEAQLDRF 176
                                    *****************7777776654.3......99*********999999999999998 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0     2e-09   4.5e-06       2     130 ..      48     182 ..      47     184 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 2e-09
                                    EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS.......STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH CS
                            AAA   2 llyGppGtGKTllakavakelgvefleisgsellsk.......yvgesekkirelfkeakekakpsilfiDEidalaksr 74 
                                    ll  +pG GKTll+k  ak+++ +f +i+++  l         +++e   + r  f+     a   i++ DEi +  ++ 
  gi|116754393|ref|YP_843511.1|  48 LLESNPGLGKTLLIKTTAKTMSLSFSRIQCTPDLMPaditgttIIEEVDGEKRFRFEPGPIFA--NIVLADEINRASPKT 125
                                    78889***********************99655522478888888888888888888876666..9***********999 PP

                                    TTCCCHHHHHHHHHHHHHHHHTTTS........SSTEEEEEEESS.....GGGSTHHHHSTTSSEEEET CS
                            AAA  75 sgseseeeervvnqLlteldgvkkk........eskvivigatnr.....pdkldpallrgRfdrkiei 130
                                               ++++l+ +++ +          +++++v+++ n         l++a l +Rf +ki++
  gi|116754393|ref|YP_843511.1| 126 -----------QSAMLESMQEKQVTvgnrtyrlDDPFFVLATQNPiemegTFPLPEAQL-DRFLMKIKL 182
                                    ...........999999999999988889999766677777777644333334666666.888887776 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   1.2e-07   0.00027      53     174 ..      40     160 ..      15     179 .. 0.80
   2 ?   -3.1   0.0       1.5   3.4e+03      20      43 ..     218     241 ..     205     262 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.2e-07
                                    BBCSS-EEEEEESSTSTHHHHHHHHHHHSSSE..EEEESSSSSSSHSSSEEEEESSSSS..EEEEETHHHHTTTSEEEEE CS
                            MCM  53 klrgdinvllvgdpgtaKsqlLkyveklapra..vytsgkgssaagLtaavvrdeetge..fvleaGalvladkGvcciD 128
                                    ++++  + ll ++pg++K+ l+k+++k+++ +     +      a++t +   +e  ge  f +e G +      +++ D
  gi|116754393|ref|YP_843511.1|  40 SIIAGGHALLESNPGLGKTLLIKTTAKTMSLSfsRIQCTPDLMPADITGTTIIEEVDGEkrFRFEPGPIFAN---IVLAD 116
                                    56677799*****************998876511455666778899987777666665556******98764...9**** PP

                                    SGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--S CS
                            MCM 129 efdkmkeedrsalhEamEqqtisiaKaGivatLnartsvlaAanpk 174
                                    e+++ + +++sa++E m ++++++      + L+    vla  np+
  gi|116754393|ref|YP_843511.1| 117 EINRASPKTQSAMLESMQEKQVTVGNRT--YRLDDPFFVLATQNPI 160
                                    **********************997655..7888888888888887 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.5
                                    HHSSTTSSS-HHHHHHHHHHHH-- CS
                            MCM  20 ksiapsiyghedvkkaillqlfgg 43 
                                    ++ia+++  +ed +ka + +++++
  gi|116754393|ref|YP_843511.1| 218 QQIAREVPISEDLRKAAVQLVVST 241
                                    677888888888888765444443 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.1     2e-05     0.045      32      76 ..      43      87 ..      19     156 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2e-05
                         RuvB_N 32 aldhvllyGpPGlGkttlakiiakelgvkl.kitsgPvlekagdla 76
                                   a  h ll   PGlGkt l k  ak +  ++ +i ++P l  ++d++
  gi|116754393|ref|YP_843511.1| 43 AGGHALLESNPGLGKTLLIKTTAKTMSLSFsRIQCTPDLM-PADIT 87
                                   5579**********************99873566777664.44554 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       0.5   1.1e+03      16      44 ..      38      66 ..      27      88 .. 0.71
   2 ?   13.2   0.0   2.5e-05     0.056      97     146 ..     113     161 ..     109     166 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.5
                                   HHHCTSSS-EEEECSTTSSHHHHHHHHHH CS
                Sigma54_activat 16 kkvaktdlsvlitGesGtGKellaraihe 44
                                    + +    + l++ + G GK+ll ++  +
  gi|116754393|ref|YP_843511.1| 38 LASIIAGGHALLESNPGLGKTLLIKTTAK 66
                                   44455556789999999999998776544 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 2.5e-05
                                    EEEETGGGS-HHHHHHHHHHHHHSEEESBTSSSEEE--EEEEEEESS-HH CS
                Sigma54_activat  97 lfLDeigelplelQekLlrvlqegevervGsskeikvdvriiaatnedle 146
                                    ++ Dei++ ++++Q+ +l+ +qe++v+ vG+++ +  d  ++ at++ +e
  gi|116754393|ref|YP_843511.1| 113 VLADEINRASPKTQSAMLESMQEKQVT-VGNRTYRLDDPFFVLATQNPIE 161
                                    667*********************996.9*99999999999999998776 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00012      0.27       6      44 ..      28      66 ..      23      78 .. 0.76
   2 ?    0.8   0.0      0.12   2.6e+02     109     158 ..     112     159 ..      95     166 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00012
                   Mg_chelatase  6 kGqeeakraleia.aaGgHnlllvGppGsGKtmlakrlps 44
                                   +Gq+ a + l  + +aGgH  ll  +pG GKt+l+k  ++
  gi|116754393|ref|YP_843511.1| 28 VGQRVAIEQLLASiIAGGHA-LLESNPGLGKTLLIKTTAK 66
                                   68888877666551577776.5789*********997655 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.12
                   Mg_chelatase 109 vLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNp 158
                                    +++ DE+   + k+  ++ e +++++vt+   +++++ p  f ++a+ Np
  gi|116754393|ref|YP_843511.1| 112 IVLADEINRASPKTQSAMLESMQEKQVTVGNRTYRLDDP--FFVLATQNP 159
                                    66789***********************98877766544..666666676 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2452.55
//
Query:       gi|116754394|ref|YP_843512.1|  [L=284]
Description: hypothetical protein Mthe_1089 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.9e-19   69.1   0.3    9.1e-19   67.5   0.0    1.9  2  DUF58        Protein of unknown function DUF58
    1.3e-05   25.8   0.1    2.7e-05   24.8   0.1    1.5  1  VWA_2        von Willebrand factor type A domain
    5.9e-05   22.6   0.5    0.00022   20.7   0.5    2.0  1  VWA_CoxE     VWA domain containing CoxE-like protein
  ------ inclusion threshold ------
      0.017   15.3   0.1      0.026   14.8   0.1    1.3  1  VWA          von Willebrand factor type A domain
      0.074   13.1   0.1       0.34   11.0   0.0    2.1  2  Lambda_CIII  Lambda Phage CIII


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 !   67.5   0.0   2.5e-22   9.1e-19       1      85 [.      36     116 ..      36     117 .. 0.95
   2 ?   -1.4   0.0       0.8   2.9e+03      61      72 ..     182     193 ..     156     242 .. 0.66

  Alignments for each domain:
  == domain 1  score: 67.5 bits;  conditional E-value: 2.5e-22
                          DUF58   1 gldfaglReYvpgDplrrIdWkatARtgelyvrefeaerartvllvldlspemslgstgdekletavsaaaslarqllde 80 
                                    g+++ g ReY+ gD+++ +dWk++ARt +lyvre e+er+  v ++ld s +m+++     k+e a ++aa  a  +++e
  gi|116754394|ref|YP_843512.1|  36 GISPVGYREYRKGDDFKLVDWKVYARTERLYVREHEEERSLLVHILLDSSGSMRFN----RKFELASEIAAGFAFIAAQE 111
                                    57899*************************************************96....89************999999 PP

                          DUF58  81 gdrvg 85 
                                    + +++
  gi|116754394|ref|YP_843512.1| 112 NEKFS 116
                                    98876 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.8
                          DUF58  61 ekletavsaaas 72 
                                    +k+eta++ ++ 
  gi|116754394|ref|YP_843512.1| 182 DKVETAIYRLSR 193
                                    445555544443 PP

>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.1   7.5e-09   2.7e-05       3     105 ..      80     176 ..      78     179 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 7.5e-09
                          VWA_2   3 fvlDtSgSmrngdygptrleaakdav..eallkslpgdrvglvtfsdgpevliplt..kdkakilnalrnleakgggtnl 78 
                                    ++lD+SgSmr +    +++e a +++   a+++++ + ++++ tf+++ +   p+    +  k+ + l+++++ +ggt++
  gi|116754394|ref|YP_843512.1|  80 ILLDSSGSMRFN----RKFELASEIAagFAFIAAQENEKFSVSTFAEELRAGEPVRgvGNLLKVIDLLDGTKP-SGGTDI 154
                                    89*********9....3666666555116777888899*********98877777544888888888888888.5***** PP

                          VWA_2  79 aaaLqlarkalkkrrkgekrvivlitD 105
                                     +a ++   +++ +     + +vli+D
  gi|116754394|ref|YP_843512.1| 155 LKASDQFDRMISTT-----SLVVLISD 176
                                    **999999999955.....69999999 PP

>> VWA_CoxE  VWA domain containing CoxE-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.5   6.2e-08   0.00022      44     189 ..      62     204 ..      28     220 .. 0.65

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 6.2e-08
                       VWA_CoxE  44 lvelvrrkprerkprelvllvDvSgSmaaysaiflallhAllqqlp........rtevfaFdtrlvdlTralrerDpaea 115
                                    +++l  r+  e+++  + +l+D SgSm    +  + l+  + +++         + +v +F  +l +  + +r     ++
  gi|116754394|ref|YP_843512.1|  62 TERLYVREHEEERSLLVHILLDSSGSMRFNRK--FELASEIAAGFAfiaaqeneKFSVSTFAEEL-RAGEPVR--GVGNL 136
                                    556666664555554444799******86332..2333333333332232201144444444443.3344444..33344 PP

                       VWA_CoxE 116 Larv.saavedlgGgTrigaalaeflelvtrpaLsrravvvlvsDglergdreellaelarlvrrarrlvwlnpl 189
                                    L+ +     ++ +GgT+i +a  +f ++++       ++vvl+sD+   +d +++++++ rl+r    +v + + 
  gi|116754394|ref|YP_843512.1| 137 LKVIdLLDGTKPSGGTDILKASDQFDRMIST-----TSLVVLISDM--LDDLDKVETAIYRLSRHDLIVVQILSH 204
                                    44442223344799***************93.....479*******..678999999999999977666666655 PP

>> VWA  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   7.3e-06     0.026       3     152 ..      79     212 ..      78     231 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 7.3e-06
                                    EEEEE-STTSCHHHHHHHHHHHHHHHHHHT..BTTTTEEEEEEEESSSEEEEEETTSHCHHHHHHHHHHTGSGGGGSSC- CS
                            VWA   3 vfvlDgSgsmgeenfekvkefikklvekle..vgpegtrvglvqfssevktefslndysskeellsalnnlkysgggttn 80 
                                     ++lD+Sgsm   +f++  e +++++  +     +e+ ++++ +f++e +   +++   +  ++++ l+ +   +     
  gi|116754394|ref|YP_843512.1|  79 HILLDSSGSM---RFNRKFELASEIAAGFAfiAAQENEKFSVSTFAEELRAGEPVRGVGNLLKVIDLLDGT-KPS----- 149
                                    69********...899889999999999986449*****************99999999877888888774.333..... PP

                                    HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CS.SHTHHHHHHHHGCTEEEEEEEESSSHHHHHHHHHS CS
                            VWA  81 tgkalkyaleklfkssagaRenakkviilltdGksnd.gdpkeaaneakeqgikvfavGvgnadekelLnkia 152
                                     g+ + +a +++ ++ +      +++++l++d  + d +++++a+ ++   + ++++v + ++ e++ L  ia
  gi|116754394|ref|YP_843512.1| 150 GGTDILKASDQFDRMIST-----TSLVVLISDMLD-DlDKVETAIYRLS--RHDLIVVQILSHEERD-L-GIA 212
                                    444588888877777777.....899999998655.3246777766666..5588888887777777.5.455 PP

>> Lambda_CIII  Lambda Phage CIII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.82   2.9e+03       5      13 ..     126     134 ..     125     143 .. 0.75
   2 ?   11.0   0.0   9.5e-05      0.34       4      30 ..     211     239 ..     209     246 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.82
                    Lambda_CIII   5 AGwpvaGvp 13 
                                    AG pv Gv 
  gi|116754394|ref|YP_843512.1| 126 AGEPVRGVG 134
                                    888999986 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 9.5e-05
                    Lambda_CIII   4 iAGwpva.Gvpq.ESlLdRitrklRegwk 30 
                                    iAG ++   + + ESl+ R++++lR+ ++
  gi|116754394|ref|YP_843512.1| 211 IAGDARFiDMESgESLITRVSQRLRDDYR 239
                                    6666663134446************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 2089.28
//
Query:       gi|116754395|ref|YP_843513.1|  [L=91]
Description: hypothetical protein Mthe_1090 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); 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: 0.31u 0.25s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 726.26
//
Query:       gi|116754396|ref|YP_843514.1|  [L=462]
Description: carbohydrate kinase, YjeF related protein [Methanosaeta thermophila PT]
Scores for complete 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-53  179.6   0.1      1e-52  179.1   0.1    1.2  1  Carb_kinase   Carbohydrate kinase
    4.3e-37  127.6   0.3    2.1e-36  125.4   0.0    2.0  2  YjeF_N        YjeF-related protein N-terminus
    3.5e-10   39.7   0.0    6.5e-10   38.8   0.0    1.3  1  HK            Hydroxyethylthiazole kinase family
  ------ inclusion threshold ------
       0.04   13.3   0.0      0.074   12.4   0.0    1.4  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase


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 !  179.1   0.1   2.2e-56     1e-52       2     243 ..     222     457 ..     221     458 .. 0.92

  Alignments for each domain:
  == domain 1  score: 179.1 bits;  conditional E-value: 2.2e-56
                                    EEEE-BTTCHHHHHHHHHHHHCTT-SEEEEEESSTTTCCCCTTTTTCEECCTT.....HTTTS...--SSS-SEEEE-TT CS
                    Carb_kinase   2 lvigGsedytGAallaalaalrlgaglvsvateseaiavlksylpevivhpll.....edeqakileklerldavviGpG 76 
                                    lvigG   ytGA+ l+a aalr+ga++v+va+ + a+  + s +p++iv pl+     +++      +  r d+vviG+G
  gi|116754396|ref|YP_843514.1| 222 LVIGG-GPYTGAPALSAMAALRAGADIVTVAAPKSAADTISSFSPNMIVRPLTsdrlcMADIDILKGLIPRHDVVVIGMG 300
                                    78999.9**********************************************6666543333334455799******** PP

                                    -SSSHCHHHHCHHHCCCCS-EEEEGGGGGSGGGG...TTTTSSEEEE--HHHHHHHCTTTCHHCCSHHHHHHHHHHHHTT CS
                    Carb_kinase  77 LgrdekikklleevlekdeplviDAdgLnllaqknelserkaeviLTPhkkEfkrLlkaivkkeddrlelarelaqklna 156
                                    Lgrde++ k++ ++l   + +viDAd+L+        ++   + i TPh++Ef r++++ + k+++r e+++++a++++ 
  gi|116754396|ref|YP_843514.1| 301 LGRDEETLKAVSQILPLCDRVVIDADALQ--------PDMPLKGIVTPHAGEFRRISGLDLPKGKERIEIVKRFAREMGL 372
                                    ****************************6........5556689***************999****************** PP

                                    EEEEESTTSEEEECTTEEEEE----GGG-STTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHHHHHHCCCT-TS-HCH CS
                    Carb_kinase 157 vvllkgekdvivspegevlinstgssalakGGsGDvLaGligalLaqneasyeaaiaaawlhgaasdeaaekkgvgmlat 236
                                    vvllkg  d+i + ++ v  n tg++++++GG+GDvLaG+ ga+ a +  ++ aa+aaa+++g+a+d++  ++  gm at
  gi|116754396|ref|YP_843514.1| 373 VVLLKGRMDIITD-GEIVRGNTTGNPGMTVGGTGDVLAGITGAFYARAD-ALRAAAAAAFVNGRAGDLVYRERDFGMVAT 450
                                    *********9998.899999***********************988776.999*************************** PP

                                    HHHHHHC CS
                    Carb_kinase 237 elskiip 243
                                    +l+++ip
  gi|116754396|ref|YP_843514.1| 451 DLIDKIP 457
                                    *****98 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 !  125.4   0.0   4.7e-40   2.1e-36       3     171 .]      25     178 ..      23     178 .. 0.91
   2 ?   -0.2   0.0      0.18   8.1e+02      28      58 ..     220     250 ..     204     263 .. 0.76

  Alignments for each domain:
  == domain 1  score: 125.4 bits;  conditional E-value: 4.7e-40
                         YjeF_N   3 eLmenagravaevlrallgnspaekkvlvlvGsgnnGgdglaaArhLaqegakVtvllleeee.kldedaeralellkka 81 
                                    +Lmenag+a+a+ +ra+      ++++ +++G+gnnGgd+++aArhL   +++Vtv+l+ + +   +e+a+r+++ l+++
  gi|116754396|ref|YP_843514.1|  25 QLMENAGAALANEIRAIG-----GRRIAIIAGRGNNGGDAFVAARHL--DDLDVTVFLIGRARdISTEEARRNWDVLRRL 97 
                                    8*****************.....9***********************..888888855555443999************* PP

                         YjeF_N  82 ggkvveekpeedleeklsapvdlviDAllGiglrgelreelaeliewlnsseapvlavDiPSGldadtGavsgtavkadv 161
                                    + ++ e k++++ +    + +d+v+DAl+G+g+rg++++   ++i+ +ns ++ +++vD+PSG+ +   +    +v++d+
  gi|116754396|ref|YP_843514.1|  98 EFDLREIKDVSEIDL---SGYDVVVDALFGTGVRGPIKGLEGDIIDLINSCGKHIVSVDVPSGMGTG--K----EVSPDI 168
                                    *****9999998763...68*******************************************9443..3....5689** PP

                         YjeF_N 162 tvtfgapkrg 171
                                    tvtf+ pk g
  gi|116754396|ref|YP_843514.1| 169 TVTFHRPKIG 178
                                    *******976 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.18
                         YjeF_N  28 kvlvlvGsgnnGgdglaaArhLaqegak.Vtv 58 
                                    ++lv+ G+  +G+ +l a + L ++ga+ Vtv
  gi|116754396|ref|YP_843514.1| 220 RILVIGGGPYTGAPALSAMAAL-RAGADiVTV 250
                                    67777777799******99999.677774666 PP

>> HK  Hydroxyethylthiazole kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.0   1.5e-13   6.5e-10     124     240 ..     344     456 ..     336     460 .. 0.91

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 1.5e-13
                                    SSCCSCSSSSSS-SHHHHHHHHHHHHHHTSEEEEESSSEEEEESSEEEEEE-S-GGGGGSTTHHHHHHHHHHHHHTTBSS CS
                             HK 124 lelkvkGvDskeaataavaavqkvAqklrvvvvvtGevDvvsdgkkvyklknGtellgkitasGCllgsvvaaflavkkd 203
                                    +  ++ G+D  ++++  +++v++ A+++++vv++ G++D+++dg+ v   + G++ ++ + ++G +l+ + +af a   d
  gi|116754396|ref|YP_843514.1| 344 EFRRISGLDLPKGKER-IEIVKRFAREMGLVVLLKGRMDIITDGEIVRGNTTGNPGMT-VGGTGDVLAGITGAFYAR-AD 420
                                    5567889999999995.****************************************7.9***************95.67 PP

                                    HHHHHHHHHHHHHHHH.HHHHHHHTTHHHHHHHHHHH CS
                             HK 204 kllaaveavllykvAgkeaaarsegsgsFqvelldal 240
                                    +l aa++a  +   Ag   + r+++ g   + l+d++
  gi|116754396|ref|YP_843514.1| 421 ALRAAAAAAFVNGRAG-DLVYRERDFGMVATDLIDKI 456
                                    8888999999999999.889999999*********98 PP

>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.7e-05     0.074     117     224 ..     332     429 ..     321     437 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.7e-05
                                    GGG-SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHHTT-SEEEEEEGGS-SSSEEEEEEEETSSEEEEEEEE----S-- CS
                   Phos_pyr_kin 117 lplatvitPNlpEaeaLlgekikteedmkeaakkllklgakaVlikGghlegeeavvtdvlydgeeveeleaerietknt 196
                                    +pl  ++tP   E ++++g ++ + ++  e  k++++     Vl+kG           d++ +++e+++ ++   +  + 
  gi|116754396|ref|YP_843514.1| 332 MPLKGIVTPHAGEFRRISGLDLPKGKERIEIVKRFAREMGLVVLLKGRM---------DII-TDGEIVRGNTTGNPGMTV 401
                                    57889********************************88899*****86.........555.555667777777777899 PP

                                    BTHHHHHHHHHHHHHHCTSSHHHHHHHH CS
                   Phos_pyr_kin 197 hGtGCtlssaiaaelakgesleeAvkkA 224
                                     GtG++l+    a  a+ + l+ A + A
  gi|116754396|ref|YP_843514.1| 402 GGTGDVLAGITGAFYARADALRAAAAAA 429
                                    9********************9997665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (462 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.20s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 3793.36
//
Query:       gi|116754397|ref|YP_843515.1|  [L=149]
Description: putative molybdenum cofactor biosynthesis protein MoaC [Methanosaeta thermophila PT]
Scores for complete 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  164.4   1.0    1.6e-48  164.3   1.0    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 !  164.3   1.0   8.7e-53   1.6e-48       1     134 [.       8     146 ..       8     148 .. 0.98

  Alignments for each domain:
  == domain 1  score: 164.3 bits;  conditional E-value: 8.7e-53
                                    E---TTS--EEEEEEEEEEEEE-HHHHHHHHTTSSTTB-HHHHHHHHHHHHHHHHHHHSTT-----EEEEEEEEEEETTT CS
                           MoaC   1 mvdvsekeetkrtAvAegrvklseetlelikekklkkGdvlavariagimaaKktseliplcHplpltkveveleleeee 80 
                                    mvd+++k+ ++rtA+A+g +kl+++t+e+i +++++kGdvl++ari++i a+K+t++lip+cH++p+t v++e++le  +
  gi|116754397|ref|YP_843515.1|   8 MVDITDKPPVRRTATASGLIKLRRSTIEAIVSGRVSKGDVLTTARISAINAVKETPRLIPMCHNIPITGVDTEVSLE--D 85 
                                    9*************************************************************************987..7 PP

                                    TEEEEEEEEEEEESS--HHHHHHHHHHHHHHHHHHHTTTHTT.......-EEEEEEEEEEE CS
                           MoaC  81 esveieatvktegktGvemEALtavsvaaltvyDmvKavdke.......mvieevrlveKs 134
                                    ++v+++++v+  g+tGvemEALt++sva+lt++DmvK+++k+       + ie +r+ eK 
  gi|116754397|ref|YP_843515.1|  86 SAVRVKVKVTSVGRTGVEMEALTGASVALLTIWDMVKSLEKDehgcypdTSIEYIRVEEKV 146
                                    9****************************************999**************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); 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: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1114.99
//
Query:       gi|116754398|ref|YP_843516.1|  [L=325]
Description: thiamine-monophosphate kinase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-23   81.1   0.3    1.5e-22   80.0   0.1    1.7  2  AIRS      AIR synthase related protein, N-terminal domain
    2.3e-09   37.6   1.2      4e-09   36.8   1.2    1.3  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 !   80.0   0.1   1.7e-26   1.5e-22       1      94 []      42     152 ..      42     152 .. 0.94
   2 ?   -3.3   0.0       1.7   1.5e+04      29      44 ..     225     240 ..     222     266 .. 0.67

  Alignments for each domain:
  == domain 1  score: 80.0 bits;  conditional E-value: 1.7e-26
                                    SSSEE........EEEEEEEE.EECCTCCCC........HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HHHHH CS
                           AIRS   1 dDaav........vvttdshnrpvlvepvhf........iGakavavnlsDlaamGArPlalllslalp......wleev 58 
                                    dD+av        vvttd     +l  +++f        iG+ ++avnlsD+aamGA+Pl++l +  +p       +ee+
  gi|116754398|ref|YP_843516.1|  42 DDCAVveldgdylVVTTD-----MLHRETDFpdqatpwqIGWMSAAVNLSDIAAMGAEPLGVLIASGIPpetdleFVEEI 116
                                    8***555555666*****.....999999999*****************************9****************** PP

                                    HHHHHHHHHHTT-EEEEEEEEEESSEEEEEEEEEEE CS
                           AIRS  59 vrglaeaaeelgvplvgGdtsfsneptisvtavGlv 94 
                                    ++g++++++++g++++gGdt  + e+ti+ ta+G v
  gi|116754398|ref|YP_843516.1| 117 FEGIRDCVKAHGTEVLGGDTDAHRELTICGTALGRV 152
                                    **********************************86 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.7
                                    HHHHHHHHHTTTEEEE CS
                           AIRS  29 vavnlsDlaamGArPl 44 
                                    +a  l Dla  G++  
  gi|116754398|ref|YP_843516.1| 225 LALSLHDLAEAGGTGF 240
                                    5666778887777655 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 !   36.8   1.2   4.4e-13     4e-09       1     148 [.     164     303 ..     164     306 .. 0.80

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 4.4e-13
                                    STTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHH.HTTECEEEE--TTHHHHHHHHH CS
                         AIRS_C   1 kpGdvliltgslGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaal.kglvkaahDvTgGGLlgalaem 79 
                                    +pGd+l  tgslG  gag +++ ki++ +        l+  lle  + +v + +a++ +g v+a+ D ++ GL+ +l+ +
  gi|116754398|ref|YP_843516.1| 164 RPGDLLCTTGSLGGAGAG-LKALKIGRID--------LARRLLE-PCPRVREGIALAgTGAVTAMMDNSD-GLALSLHDL 232
                                    79*********9999999.7777666655........3444555.44444444444457***********.8******** PP

                                    HHTTTEEEEEECGTHHHHHHHH.......HHHHHHHCSTTTEEEEEEEHGGH.HHHHHHHHHTTCCCEEEEEEEEES CS
                         AIRS_C  80 apasgvgaeidldkvpifdele.......splemllsensGrllvavppeea.davlaileeeglpeaavIGevtak 148
                                    a+a+g g+ ++ +++pi +e++       ++lem l +     l++ ++e+  d +++++e       +vIG++++ 
  gi|116754398|ref|YP_843516.1| 233 AEAGGTGFLVECERIPIAEEVRaiaesddEALEMVLRAGGDFELLLTVREDMiDDARKACE------LTVIGRAVET 303
                                    **************************99988888888888877777777777577777776......6899999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); 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 0.22s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2517.17
//
Query:       gi|116754399|ref|YP_843517.1|  [L=70]
Description: hypothetical protein Mthe_1094 [Methanosaeta thermophila PT]
Scores for complete 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   23.2   1.1    8.2e-05   22.5   1.1    1.4  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
    0.00039   20.7   0.2    0.00048   20.5   0.2    1.2  1  Lar_restr_allev  Restriction alleviation protein Lar
    0.00049   19.6   1.3     0.0013   18.2   1.3    1.8  1  TF_Zn_Ribbon     TFIIB zinc-binding
     0.0037   17.4   0.3        1.5    9.0   0.1    2.2  2  Zn-ribbon_8      Zinc ribbon domain
     0.0043   16.7   0.7        0.9    9.3   0.0    2.2  2  A2L_zn_ribbon    A2L zinc ribbon domain
     0.0079   15.9   0.1     0.0099   15.6   0.1    1.2  1  TackOD1          Thaumarchaeal output domain 1
  ------ inclusion threshold ------
      0.013   15.2   7.3       0.17   11.6   7.3    2.2  1  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
      0.023   14.6   0.2      0.032   14.2   0.2    1.3  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.026   14.3   2.2       0.77    9.6   3.2    2.0  2  PADR1            PADR1 (NUC008) domain
      0.049   13.4   3.6       0.98    9.2   0.4    2.2  2  Rubredoxin_2     Rubredoxin metal binding domain
      0.087   12.7   1.5          3    7.8   0.1    2.2  2  TFIIS_C          Transcription factor S-II (TFIIS)
        0.1   12.2   0.9        4.2    7.0   0.1    2.4  2  RecR             RecR protein
        1.1    9.2   7.2        2.7    7.9   0.0    2.4  2  zf-CCHC_2        Zinc knuckle


Domain annotation for each model (and alignments):
>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   1.1     6e-08   8.2e-05      20      45 ..      10      38 ..       4      39 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 6e-08
                  Zn_Tnp_IS1595 20 vCPhCgsr....kayriktrglfqCkeCrk 45
                                   vCP Cgs+    +a  +++ +l++Ck+C++
  gi|116754399|ref|YP_843517.1| 10 VCPVCGSSdiyyEAGGYAG-KLYHCKRCGY 38
                                   8*******76666666666.********97 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 !   20.5   0.2   3.5e-07   0.00048       5      37 ..      10      45 ..       7      65 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 3.5e-07
                Lar_restr_allev  5 pCPfCggravlersqrvvaeigqcvyCadCga......s 37
                                    CP Cg+ +++ ++++ + +     +C+ Cg+       
  gi|116754399|ref|YP_843517.1| 10 VCPVCGSSDIYYEAGGYAGK---LYHCKRCGYigalvvE 45
                                   6*************999988...9********6555442 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   1.3   9.6e-07    0.0013       2      27 ..      10      38 ..       9      54 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 9.6e-07
                                   EETTTTCEECHEE...TSTTCEEESSSSB CS
                   TF_Zn_Ribbon  2 kCPnCgstnlveD...pergelvCtdCGl 27
                                   +CP+Cgs++++++   ++   + C++CG+
  gi|116754399|ref|YP_843517.1| 10 VCPVCGSSDIYYEaggYAGKLYHCKRCGY 38
                                   8*********999888887778******6 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   0.1    0.0011       1.5      25      34 ..       6      16 ..       1      19 [. 0.71
   2 !    6.7   0.0    0.0056       7.7       6      13 ..      31      38 ..      30      51 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0011
                    Zn-ribbon_8 25 plta.CPeCgs 34
                                    l++ CP Cgs
  gi|116754399|ref|YP_843517.1|  6 HLIEvCPVCGS 16
                                   46667*****9 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0056
                    Zn-ribbon_8  6 YrCeeCgh 13
                                   Y+C++Cg 
  gi|116754399|ref|YP_843517.1| 31 YHCKRCGY 38
                                   9*****96 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0   0.00065       0.9      18      30 ..       5      17 ..       1      20 [. 0.83
   2 !    6.1   0.1    0.0066       9.2       3      29 ..      30      38 ..      28      42 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00065
                  A2L_zn_ribbon 18 eqgylvCieCgas 30
                                   e+ ++vC+ Cg+s
  gi|116754399|ref|YP_843517.1|  5 EHLIEVCPVCGSS 17
                                   6679*******98 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0066
                  A2L_zn_ribbon  3 lkvCsvCggngilnseqgylvCieCga 29
                                   l++C+ C                  g+
  gi|116754399|ref|YP_843517.1| 30 LYHCKRC------------------GY 38
                                   4555555..................55 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   7.2e-06    0.0099      86     114 ..       7      41 ..       3      52 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 7.2e-06
                        TackOD1  86 vrevCpkCkSidieeq......elihhftCgnvgp 114
                                    ++evCp C+S+di  +      +l h+ +Cg++g 
  gi|116754399|ref|YP_843517.1|   7 LIEVCPVCGSSDIYYEaggyagKLYHCKRCGYIGA 41 
                                    689**********86533333379********986 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 ?   11.6   7.3   0.00012      0.17       5      28 ..       9      37 ..       5      38 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
                        zf-RRN7  5 ppCgvCgc.rsftlddGf....yyCrrCh 28
                                   ++C+vCg+ + ++++ G+    y C+rC+
  gi|116754399|ref|YP_843517.1|  9 EVCPVCGSsDIYYEAGGYagklYHCKRCG 37
                                   89************999533336677776 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 ?   14.2   0.2   2.3e-05     0.032      30      54 ..      10      38 ..       9      47 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.3e-05
                 OrfB_Zn_ribbon 30 tCseCgsknke....alsgrtfkCpnCgf 54
                                    C++Cgs + +      +g++++C++Cg+
  gi|116754399|ref|YP_843517.1| 10 VCPVCGSSDIYyeagGYAGKLYHCKRCGY 38
                                   6*******99999999************8 PP

>> PADR1  PADR1 (NUC008) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   3.2   0.00056      0.77      13      32 ..       8      27 ..       7      38 .. 0.77
   2 ?    3.7   0.2     0.038        53      11      21 ..      28      38 ..      27      60 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00056
                          PADR1 13 lekCpeCkegqlvfdssgYk 32
                                   +e Cp C+++ ++++ +gY 
  gi|116754399|ref|YP_843517.1|  8 IEVCPVCGSSDIYYEAGGYA 27
                                   678************99774 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.038
                          PADR1 11 GalekCpeCke 21
                                   G+l +C+ C+ 
  gi|116754399|ref|YP_843517.1| 28 GKLYHCKRCGY 38
                                   89999****85 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.2     0.013        18      17      23 ..      11      17 ..      10      18 .. 0.80
   2 ?    9.2   0.4   0.00071      0.98       1       9 [.      31      39 ..      31      43 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.013
                   Rubredoxin_2 17 CpsCgsW 23
                                   Cp Cgs 
  gi|116754399|ref|YP_843517.1| 11 CPVCGSS 17
                                   9999986 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00071
                   Rubredoxin_2  1 YvCsqCGfe 9 
                                   Y+C++CG+ 
  gi|116754399|ref|YP_843517.1| 31 YHCKRCGYI 39
                                   9******96 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1    0.0022         3       3      13 ..      11      21 ..       9      23 .. 0.90
   2 ?    4.2   0.2     0.029        40      29      36 ..      31      38 ..      28      41 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0022
                        TFIIS_C  3 CpkCgsreayf 13
                                   Cp Cgs ++y+
  gi|116754399|ref|YP_843517.1| 11 CPVCGSSDIYY 21
                                   *********98 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.029
                        TFIIS_C 29 ykCtkCgh 36
                                   y C+ Cg+
  gi|116754399|ref|YP_843517.1| 31 YHCKRCGY 38
                                   88999986 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.033        46      29      35 ..       9      15 ..       4      18 .. 0.64
   2 ?    7.0   0.1    0.0031       4.2      16      25 ..      30      39 ..      27      42 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.033
                                   SS-CCCC CS
                           RecR 29 dlCaICs 35
                                   ++C++C 
  gi|116754399|ref|YP_843517.1|  9 EVCPVCG 15
                                   4555554 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0031
                                   -EE-TTT--E CS
                           RecR 16 vrhCsrCgnl 25
                                   + hC+rCg +
  gi|116754399|ref|YP_843517.1| 30 LYHCKRCGYI 39
                                   679****987 PP

>> zf-CCHC_2  Zinc knuckle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0     0.002       2.7      11      20 ..       3      12 ..       2      13 .. 0.90
   2 ?    1.7   4.5      0.17   2.3e+02       4      10 ..      31      37 ..      31      38 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.002
                      zf-CCHC_2 11 kkGHyIqdCP 20
                                    k+H I  CP
  gi|116754399|ref|YP_843517.1|  3 RKEHLIEVCP 12
                                   589******* PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.17
                      zf-CCHC_2  4 YvChiCg 10
                                   Y C++Cg
  gi|116754399|ref|YP_843517.1| 31 YHCKRCG 37
                                   88****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 525.28
//
Query:       gi|116754400|ref|YP_843518.1|  [L=123]
Description: molydopterin dinucleotide-binding region [Methanosaeta thermophila PT]
Scores for complete 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-16   59.3   0.0    4.2e-16   59.0   0.0    1.1  1  Molydop_binding  Molydopterin dinucleotide binding domain


Domain annotation for each model (and alignments):
>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.0   0.0   2.3e-20   4.2e-16       3     110 ..       5     101 ..       3     102 .. 0.91

  Alignments for each domain:
  == domain 1  score: 59.0 bits;  conditional E-value: 2.3e-20
                                    EEEE-BTTBSTTTTTCGCCHHHHCSSS-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEEEEESSHCC CS
                Molydop_binding   3 LitgrsldqlhsqtrtrpvlrlakpepevveinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvvfmpfgwwe 82 
                                    +i+gr+l q     ++++ l+ ++++  ++++++ed +alG++dG +  ++s++Gs+++ra v+ ++++G+vf+p+g w+
  gi|116754400|ref|YP_843518.1|   5 MISGRTLAQGAGCEDKMSPLYINEVS--CCYLSEEDYRALGLSDGMNLLLTSPHGSAVLRAGVDRGLPQGMVFIPMGPWA 82 
                                    79999999999999999999999988..7*************************************************** PP

                                    .....S-GHCTS--SCSTTT--CSTT-E CS
                Molydop_binding  83 agekggnaNaltddatdplsgtpefksv 110
                                            N+lt  + ++ +g+p fk+v
  gi|116754400|ref|YP_843518.1|  83 --------NMLTGTD-TKGCGMPGFKGV 101
                                    ........****444.556788888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       202  (0.0112667); expected 358.6 (0.02)
Passed bias filter:                      181  (0.0100954); 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: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 912.25
//
Query:       gi|116754401|ref|YP_843519.1|  [L=430]
Description: molybdopterin oxidoreductase [Methanosaeta thermophila PT]
Scores for complete 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-14   51.8   0.0    2.3e-13   49.9   0.0    1.9  1  Molybdopterin   Molybdopterin oxidoreductase
  ------ inclusion threshold ------
      0.067   13.2   1.5       0.16   11.9   1.5    1.7  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 !   49.9   0.0   2.5e-17   2.3e-13       1     414 [.      46     406 ..      46     420 .. 0.77

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 2.5e-17
                                    B--S-EEECTTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEEE.EEBTSSCSHHHHHHHHHHHHHTT-EEE-BEEC CS
                  Molybdopterin   1 RlkyPmvRkqargeGkFvrvsWdeAleliaaslkytikkygpdrvag.fssgplmsmeslaslkkllsllggknlsfydw 79 
                                    R+k Pm+R     +G+++++s +eA+   a+ l +     +p    + ++    + +e+l  +  l++ +gg    ++d+
  gi|116754401|ref|YP_843519.1|  46 RIKSPMIR---V-NGELKEISYEEAYRRAAEILIN---ARHP----LlYGW-ASTTCEALKKGILLAEEIGG----VVDT 109
                                    9*******...6.9*****************9999...8888....52444.445599***99999**9*99....8999 PP

                                    CGGGTTHHHHCHHCCCCCTTTS-SS-CCGGGG.-SEEEEESS-HHHHSHHH......HHHHHHHHHTTC........-EE CS
                  Molybdopterin  80 yadlppasaqqtigsdsrsnyessnpledlen.sdliilwGsNvreerpil......narirkaalkkk........akv 144
                                     a ++++     ig +++   + +++l+++ n +dli+ wG N+ e +p        n      a             kv
  gi|116754401|ref|YP_843519.1| 110 TATVCHGPS--IIGIEEK--GAVGSTLGQIKNrADLIVFWGCNPSEAHPRHtlryssN------ACG-RftpdgrkgRKV 178
                                    999999986..7788765..55555699998779***************993344332......222.245566667*** PP

                                    EEECSSB-HCGGGCSEEEEEHTTTHHHHHHHHHHHHHHCCCCTCHHHHHHEECHHHCCCCCCCEECCSHHHHHHCCHHHH CS
                  Molybdopterin 145 ivigpryaellkfadewlaikpgtdaalalamghvilqelkvdkeflrkytygkeetdmpllvtleeetgkkkevvaria 224
                                     v++ r + +++ ad  l i+pgtd +++ a++  ++  +k d                     l+e      +v ++  
  gi|116754401|ref|YP_843519.1| 179 LVVDVRETRTARNADRFLRIQPGTDYEIISALR--MIIGGKADS--------------------LPE---DVAGVSKKEL 233
                                    ****************************99988..999999999....................444...3445556677 PP

                                    HHHHHHHHHHTSSEEEEECHHHHTSTTHHHHHHHHHHHHHHCTHCSSTTCEEEEESSCTTHHHCHHHHTCCTTCCCCCCC CS
                  Molybdopterin 225 relarnaaktagksmiivGaglnhrqdgdaiyravinLallvgnvgqpgGgwahlnGqlilagaaekvgalpvllsvksl 304
                                    +e a+ + +++   +i++G gl+h++    ++  +++L+  ++   +      +++G ++++g a +v a    + +++ 
  gi|116754401|ref|YP_843519.1| 234 IEIAEMMKSAKF-GAIFFGLGLTHSRGRYKNVDNALSLVSELNSHTK--FVIMAMRGHYNVTG-AGQVLAW--SSGYPMA 307
                                    788888888877.88888*******8777777777777776665554..24455566666777.4444444..5555555 PP

                                    TTHHHHHCCCTTTCSTSS--ECGGCHHHHHHTTSSSEEEEESH.HHHHSTTSCCCHCHHHCSSEEEEEESCSSHHHHTSS CS
                  Molybdopterin 305 keekikfaaeqpgnlgnfprnlfversnllkssgkkvlyllgnnpevdhadenevekalekldlvvvldgrltstalyaD 384
                                    +       +  +g   ++p+++++   +ll++ ++++  ++ ++p  + +    +  al     v+ +d + + t l+aD
  gi|116754401|ref|YP_843519.1| 308 V-------DYARGAPYYNPGETSC--CDLLSRRDVDAALIIASDPASNLPRGCVE--AL-AEMPVIQIDPFENPTTLFAD 375
                                    5.......5556666666666666..68999999999999997777777777666..55.66789999************ PP

                                    EEEEBE-C.CGSEEEEE-TTSEEEEEEESSS CS
                  Molybdopterin 385 iiLPaatw.yEkedlytndegrfqhlkqavs 414
                                    ++ P+a   +E e++   ++g   +l+++v+
  gi|116754401|ref|YP_843519.1| 376 VVIPSAIAgIEVEGTAYRMDGLSLRLRKLVD 406
                                    ****995437999999999988888888876 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.5   1.8e-05      0.16       7      32 ..       7      33 ..       1      43 [. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.8e-05
                                   E-SSBTT--E.EEEEEETTEEEEEEE- CS
                 Molybdop_Fe4S4  7 aCpyCgvgCg.levhvkdgkivkvegd 32
                                   +C++Cg+ C  ++v+v  g+i kv+g 
  gi|116754401|ref|YP_843519.1|  7 LCTFCGCLCDdIKVEVDEGRIEKVRGA 33
                                   7********55**************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        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: 2834.49
//
Query:       gi|116754402|ref|YP_843520.1|  [L=566]
Description: amidohydrolase 3 [Methanosaeta thermophila PT]
Scores for complete 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-88  298.6   0.7    1.5e-88  298.4   0.7    1.0  1  Amidohydro_3  Amidohydrolase family
    3.9e-06   26.4   0.0      0.022   14.1   0.0    2.6  3  Amidohydro_1  Amidohydrolase family
  ------ inclusion threshold ------
      0.013   15.2   0.0      0.032   13.9   0.0    1.6  1  YwhD          YwhD family


Domain annotation for each model (and alignments):
>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  298.4   0.7   2.5e-92   1.5e-88       1     473 []      36     495 ..      36     495 .. 0.97

  Alignments for each domain:
  == domain 1  score: 298.4 bits;  conditional E-value: 2.5e-92
                   Amidohydro_3   1 eviDakGrlvlPGFvDsHtHlagggvnl.rllrlpdarvtslegvltavrdqagttpkgrwi.vgeGwdeaqfaeerfpy 78 
                                    eviDa+G+lv+PG+vD+H+H+ag ++n  r +r++d+r+              gt+p +r+     G+++++ ++ +++y
  gi|116754402|ref|YP_843520.1|  36 EVIDARGLLVMPGGVDAHSHIAGPKLNTgRIMRPDDSRM--------------GTEPRTRVCrPSTGYTVPNCYAIGYRY 101
                                    79**********************************555..............4555566666679************** PP

                   Amidohydro_3  79 alaeldevledapvllaaldtHaavrnsaaldlagiteatpdpaggeilrdangegatgllregafhlvldlaplareae 158
                                    a+ ++++++e+a+++++a++tH+++  +++ d+            g++  ++ ++ +++ +re+           + + +
  gi|116754402|ref|YP_843520.1| 102 ARLGYTTAFEAATPIIEARHTHEELEEIPIVDK------------GALTLFGSNWTVMECVREN-----------DMDML 158
                                    *********************************............*******************...........***** PP

                   Amidohydro_3 159 aaavaaalaalasyGitsv.......eagggnvsslddleplfeltaeeklplrviikelldaaerlglpls........ 223
                                    aa+va++l+a+++yG+++v       ++ g nv s  d++p+f++t+++      ii  l++++erl+lp+s        
  gi|116754402|ref|YP_843520.1| 159 AAYVAWGLRAARGYGVKIVnpgggeaWGFGSNVKSVHDPVPHFDVTPAQ------IIRALAEVNERLRLPHSihlhfnnl 232
                                    ************************99999********************......999********************** PP

                   Amidohydro_3 224 ..pgseeltigavklfadgvl..gsrtalltepyf.....tgwpdfedea..laelvaaadergldvaihaigdaavd.. 290
                                      pg++ + i++++l++d+ +   ++++++++ +f     tgw+dfe++a  +ae++++ +++++d+++ ++g a+++  
  gi|116754402|ref|YP_843520.1| 233 grPGNYTTAIETLELLKDIKPsrMRQVVHVAHMQFsayggTGWKDFESKAsaIAEYFNQTNHATMDLGQIIFGPATTMta 312
                                    ******************8775589******************************************************* PP

                   Amidohydro_3 291 dvldafeaa...aekngnqdrrrlehaegv...tesqiervaalqvaagvqpvfnfedelldsrlgperargstpvkell 364
                                    d++ ++++a   ++k++n+d  +le ++gv    +  + +v a+q+a+g++                        +++l+
  gi|116754402|ref|YP_843520.1| 313 DAPLEYANArigHQKWSNHDI-ELEESSGVvpwVYTRKMPVNAVQWAIGLE------------------------LALLT 367
                                    *********************.*****************************........................***** PP

                   Amidohydro_3 365 nagvkvalgsD.apvgpfdpwprigaavmrktrrgg.............evlrpdeelsleealalyTrgpAkalgledr 430
                                    ++++kv++++D +++gpf ++p+i++++m++  r++             +++ +++e+++ e++ ++++ pA++lgled+
  gi|116754402|ref|YP_843520.1| 368 KDPWKVVMTTDhPNGGPFVNYPEIISLLMSREKREEemktlhevvrsrsTLPSIEREMDWSEIVIMTRAAPARILGLEDK 447
                                    ********************************99999******************************************8 PP

                   Amidohydro_3 431 kGtLevGadADlvvldadpldvdppelaear......vrltvvdGrvvy 473
                                     G+L++Gad+D+ ++++ p+++dp++++ ++      +++t+++G vv+
  gi|116754402|ref|YP_843520.1| 448 -GHLGIGADGDVSIYNIRPDEIDPSKDHAVVkagmsrAKYTIKGGAVVV 495
                                    .**********************************************97 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0   9.5e-05      0.57       1      17 [.      44      60 ..      44     118 .. 0.84
   2 ?   -2.4   0.0      0.38   2.3e+03     122     153 ..     196     228 ..     186     240 .. 0.78
   3 !   14.1   0.0   3.7e-06     0.022     241     320 ..     372     469 ..     362     494 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 9.5e-05
                                   EEEE-EEEEEEECETTE CS
                   Amidohydro_1  1 ivlPGlIDaHvHleqsl 17
                                   +v+PG++DaH H+ +  
  gi|116754402|ref|YP_843520.1| 44 LVMPGGVDAHSHIAGPK 60
                                   59***********8664 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.38
                                    EECGTCCSHHHHHHHHHHHHHHH.TTEEEEEET CS
                   Amidohydro_1 122 apheapafsdeelkealkeakkr.dlpvaiHal 153
                                    +p +++ ++++++  al e+ +r  lp +iH++
  gi|116754402|ref|YP_843520.1| 196 DPVPHFDVTPAQIIRALAEVNERlRLPHSIHLH 228
                                    566778889999988888888888999999985 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 3.7e-06
                                    CEEEEEECT.............TSSCCGGHHHH.........HHHHHHHHHHCCTT.TTHCHCHHHHHHHHHTHHHHHHT CS
                   Amidohydro_1 241 kvglgtDga.............asgnslnllee.........lrlalklqrgllye.deegglslkealrmaTingAkal 297
                                    kv+++tD+                                  ++ + ++ r+       e  ++++e++ m+   +A++l
  gi|116754402|ref|YP_843520.1| 372 KVVMTTDHPnggpfvnypeiisL---------LmsrekreeeMKTLHEVVRSRSTLpSIEREMDWSEIVIMTRAAPARIL 442
                                    67888887755544444333221.........022335555555555544444444544566****************** PP

                                    T-TTTSSSS-TTSB--EEEECC.....C CS
                   Amidohydro_1 298 glddkvGsievGkdADlvvvdl.....d 320
                                    gl+ ++G +  G d D  + +      d
  gi|116754402|ref|YP_843520.1| 443 GLE-DKGHLGIGADGDVSIYNIrpdeiD 469
                                    **6.************999866544333 PP

>> YwhD  YwhD family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   5.3e-06     0.032      14      76 ..     446     511 ..     439     523 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.3e-06
                           YwhD  14 tdghkgfga.GslsLdnvspviidveegeavvdigalharskvekgikfltdkeev..pngkkyWl 76 
                                     +gh g ga G +s+ n+ p  id+ +++avv  g   a+ ++  g   + d e v  p+g++yW+
  gi|116754402|ref|YP_843520.1| 446 DKGHLGIGAdGDVSIYNIRPDEIDPSKDHAVVKAGMSRAKYTIKGGAVVVRDGEIVaaPQGRTYWV 511
                                    479***997699***************************************9996633789****7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (566 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); 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 0.27s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 3973.17
//
Query:       gi|116754403|ref|YP_843521.1|  [L=257]
Description: formylmethanofuran dehydrogenase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-07   30.4  19.4     0.0014   18.2   2.8    3.2  3  GXGXG     GXGXG motif


Domain annotation for each model (and alignments):
>> GXGXG  GXGXG motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   2.7   3.7e-05      0.67     121     159 ..      66     107 ..      62     110 .. 0.85
   2 !   15.9   2.0   4.1e-07    0.0074      34      78 ..     108     158 ..     107     159 .. 0.80
   3 !   18.2   2.8   7.9e-08    0.0014      33      81 ..     152     199 ..     144     217 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 3.7e-05
                                    -EEEESEB...-SSTTTT-EEEEEEE-S-B-SSBTTT--EEE CS
                          GXGXG 121 atavvegv...gdhgceYmtGGvvvvLgktgrnfaaGmsgGi 159
                                    + +vveg     + ++e m  Gv+ ++g+ g++ + +m gG+
  gi|116754403|ref|YP_843521.1|  66 TRVVVEGDlskVKRLGEGMSAGVMEIIGDAGMHAGNSMRGGV 107
                                    6789999754456789*************************8 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 4.1e-07
                                    EEEEEEE-TTTTTT--TTEEEEEEEEE-STTTT.......T-ESSEEEEE-- CS
                          GXGXG  34 iklkGsaGqslgaflakGltleleGdandyvGk.......glsgGkivikps 78 
                                    +++kG aG+ lg  + +G ++e+ G+a +y+G        g+ gG+i+ik++
  gi|116754403|ref|YP_843521.1| 108 LRIKGDAGDWLGREM-RGGRIEVDGNAGNYAGAgyrgercGMRGGEIIIKGN 158
                                    679999999999999.999999999999999973333344599999999876 PP

  == domain 3  score: 18.2 bits;  conditional E-value: 7.9e-08
                                    EEEEEEEE-TTTTTT--TTEEEEEEEEE-STTTTT-ESSEEEEE--TT- CS
                          GXGXG  33 kiklkGsaGqslgaflakGltleleGdandyvGkglsgGkivikpskes 81 
                                    +i +kG+aG  lg  l  G t+e+ Gda d+ G   +gG i i+++++ 
  gi|116754403|ref|YP_843521.1| 152 EIIIKGNAGAFLGEHL-CGGTIEVMGDAGDFPGCANQGGIIRIHGHANL 199
                                    4668899999999998.77789999999999999999999999988854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); 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: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1920.71
//
Query:       gi|116754404|ref|YP_843522.1|  [L=379]
Description: 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase-like protein [Methanosaeta thermophila PT]
Scores for complete 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-80  266.9   0.0    9.8e-80  266.5   0.0    1.1  1  DUF1297   Domain of unknown function (DUF1297)
      2e-44  150.5   0.0    2.9e-44  150.0   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 !  266.5   0.0   1.1e-83   9.8e-80       1     188 []     188     379 .]     188     379 .] 0.99

  Alignments for each domain:
  == domain 1  score: 266.5 bits;  conditional E-value: 1.1e-83
                                    HHHHHHHHHHCTTSSSHHHHCCEEEEE---SEEEEEEEEEETTTTEEEEEEEEEEEEEECCCHCCS-HHHHHCCT-...- CS
                        DUF1297   1 efeekleellekglieeedlkkasieeyvvGanfnlnyfysplkeevellgidrRyesnldglvrlpakeqlelev...e 77 
                                    e++ek+e ll++g+i+++ l+ a+ie+y++G  fnl++fyspl++++ellgid+R+e++ldg+vrlpa +ql+l++   +
  gi|116754404|ref|YP_843522.1| 188 EYYEKSELLLRQGVIDSDGLELARIERYIIGPVFNLDFFYSPLRDRIELLGIDWRFETSLDGHVRLPAPQQLRLNEkqiN 267
                                    79***********************************************************************9988889 PP

                                    --EEEEEEEEEEE-GGGHHHHHHHHHHHHHHHHHHSTT---EEEEEEEEE-TTS-EEEEEEESSB-GGGGGGTT.--CCH CS
                        DUF1297  78 peyvvvGnipvvlREsllekvfelgekfveaakklvppGiiGpFcLqsvvtkdlelvvfdvsaRivggtnvyme.gspys 156
                                    pey+v+G+++++lREsllek+f+l+ek+v a+k+++ppGiiGpFcLq++v+kdl+++++dv++Ri+ggtn++m+ g+py 
  gi|116754404|ref|YP_843522.1| 268 PEYTVCGHNSATLRESLLEKAFDLAEKYVAATKEYYPPGIIGPFCLQTCVDKDLNFYIYDVAPRIGGGTNIHMAvGHPYG 347
                                    ******************************************************************************** PP

                                    HHTTSS---HHHHHHHHHHHHHHCT-GGGCEE CS
                        DUF1297 157 kllfgeplsmGrrialEikeaiekdrleeivt 188
                                    + l+++++s+Grr+a E++ aie+d+l++ivt
  gi|116754404|ref|YP_843522.1| 348 NALWRTNMSTGRRLAKEVRLAIESDSLRKIVT 379
                                    *******************************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 !  150.0   0.0   3.2e-48   2.9e-44       1     122 []      21     156 ..      21     156 .. 0.98

  Alignments for each domain:
  == domain 1  score: 150.0 bits;  conditional E-value: 3.2e-48
                                    EEEESSTTHHHHHHHHHHTT--EEEEC-CCCHHHHHTT.............TT-SEEEE.S.S..TTSS--HHHHHHTTC CS
                        DUF1246   1 iatlaSHsalqilkgAkkegfrtlavcekgreklYekf.............kvidevivldkfkdilkeevqeklreena 67 
                                    i+++aSHsal++++gA +egfrtlavc++gre++Y k+             ++idev+vl++fkdil+++  + l ++n+
  gi|116754404|ref|YP_843522.1|  21 IGMIASHSALDVADGAVEEGFRTLAVCQEGRERTYVKYfraerapdgriitGMIDEVVVLKRFKDILDQQ--DMLLRKNV 98 
                                    89*****************************************************************775..******** PP

                                    EE--BTTHHHHC-HHHHH.C-SS-EES-TTHHHHHCSHHHHHHH..HHHTT-BB--BE CS
                        DUF1246  68 ilvPhgsfveYvgiekie.elkvpifGnrkllrwEerrekkrky..LekAgiriPkki 122
                                    ++vP++sf++Y+gi+++e e++vp++G+r+llr+Eer +k ++y  LekAg+++P++i
  gi|116754404|ref|YP_843522.1|  99 LFVPNRSFTSYCGIDSVEdEFEVPLVGSRNLLRSEERGDKMDYYwlLEKAGLPYPEQI 156
                                    ******************************************999**********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2882.46
//
Query:       gi|116754405|ref|YP_843523.1|  [L=140]
Description: hypothetical protein Mthe_1100 [Methanosaeta thermophila PT]
Scores for complete 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   18.2   0.0     0.0028   18.0   0.0    1.3  1  bPH_3     Bacterial PH domain
     0.0031   17.7   0.1     0.0046   17.1   0.1    1.4  1  bPH_2     Bacterial PH domain
  ------ inclusion threshold ------
       0.13   12.6   0.0          4    7.8   0.0    2.1  2  PFOR_II   Pyruvate:ferredoxin oxidoreductase core domain II


Domain annotation for each model (and alignments):
>> bPH_3  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   4.7e-07    0.0028      19      72 ..      51     104 ..      20     126 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.7e-07
                          bPH_3  19 ldkpglivvTnkRiifldpkmfggkdfeeipYksIksvdlkkgllgakitlet.s 72 
                                    ++ +++++vT+k + f++++ +    +++ip++ I+++++ ++   ++i+++  +
  gi|116754405|ref|YP_843523.1|  51 VRISSWVIVTDKNLHFVRAG-ILWDSVQSIPLDRITDIEYVDEFHTNTIKIRVgE 104
                                    5667899*************.667999**********************998744 PP

>> bPH_2  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   7.6e-07    0.0046       5      39 ..      56      91 ..      52     124 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 7.6e-07
                          bPH_2  5 tytitdrrvvvrs.GillrktldiplerIqavsleq 39
                                   +  +td+ +++ + Gil+ +   ipl+rI+++++++
  gi|116754405|ref|YP_843523.1| 56 WVIVTDKNLHFVRaGILWDSVQSIPLDRITDIEYVD 91
                                   56789999986666******************9966 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 ?    2.8   0.0     0.024   1.5e+02       8      33 ..       4      29 ..       2      34 .. 0.86
   2 ?    7.8   0.0   0.00067         4      53      98 ..      55      99 ..      43     102 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.024
                                   -STHHHHHHHHHHHHHHTT--EEEEE CS
                        PFOR_II  8 mGsvagtaksavdelReegikvGllr 33
                                    G +++++++  d+l +eg++v l+ 
  gi|116754405|ref|YP_843523.1|  4 SGEHSRKLRRTLDKLAKEGENVQLVY 29
                                   58899****************97765 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00067
                                   SEEEEEE-S--TT-G-HHHHHHHHHTGGGTSEEEEEE--GGG---- CS
                        PFOR_II 53 kkvvvldrnisfgseGqlveevkaalkkskvkvvnfvaglgGrdit 98
                                   + v+v d+n +f  +G+l++ v++   ++ ++ +++v     ++i+
  gi|116754405|ref|YP_843523.1| 55 SWVIVTDKNLHFVRAGILWDSVQSIPLDR-ITDIEYVDEFHTNTIK 99
                                   5699*******************998777.8999998877766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1014.21
//
Query:       gi|116754406|ref|YP_843524.1|  [L=149]
Description: hypothetical protein Mthe_1101 [Methanosaeta thermophila PT]
Scores for complete 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   37.5   0.0    3.2e-09   36.9   0.0    1.2  1  DUF523          Protein of unknown function (DUF523)
  ------ inclusion threshold ------
       0.14   11.6   0.0       0.17   11.3   0.0    1.2  1  Porphobil_deam  Porphobilinogen deaminase, dipyromethane cofa


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 !   36.9   0.0   3.6e-13   3.2e-09       2     130 ..       7     133 ..       6     139 .. 0.75

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 3.6e-13
                         DUF523   2 lvSaCLlgekvrydgkakksevleeelkelvke.elvpv.CPEvaggLptPRepaelakrvlkkegedvtealekgaeea 79 
                                    +vS+CLl+  vr  g  +++         l+++  ++++ CPEv   ++  R ++  + ++   e + + ++l+  + +a
  gi|116754406|ref|YP_843524.1|   7 VVSHCLLNPLVRVRGLRQPE---------LCHRgPFIQLpCPEVIY-MGLDRWAVTRN-QLDVPEYRRFCRELMLSSLDA 75 
                                    79**************9992.........22223677777****84.67789888886.566666677788888888888 PP

                         DUF523  80 leelkeeeikgailkekSPSCGveki...Y.....dgtfskklvegeGvfaallkeegi 130
                                    +e+l++    +++  ++SPSCGv ++   Y     + + ++++++g+G+f++ l++++ 
  gi|116754406|ref|YP_843524.1|  76 MEMLSRRYRIAIVGVAGSPSCGVFTTttgYqggrvR-ESEHEEIRGMGIFMEELRRAMS 133
                                    8888875444555789*******9998999654431.33556699*********99865 PP

>> Porphobil_deam  Porphobilinogen deaminase, dipyromethane cofactor binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   1.9e-05      0.17      36      72 ..     106     142 ..      75     146 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.9e-05
                 Porphobil_deam  36 kGDkildkpLakiggkglFtkeleeaLlegeidlaVh 72 
                                    +G ++++++ ++i g g+F++el++a+ e+ id+  h
  gi|116754406|ref|YP_843524.1| 106 QGGRVRESEHEEIRGMGIFMEELRRAMSERGIDVEWH 142
                                    67888999999**********************9766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1121.65
//
Query:       gi|116754407|ref|YP_843525.1|  [L=282]
Description: periplasmic solute binding protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-73  246.5   0.0    3.1e-73  246.3   0.0    1.0  1  ZnuA      Zinc-uptake complex component A periplasmic


Domain annotation for each model (and alignments):
>> ZnuA  Zinc-uptake complex component A periplasmic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  246.3   0.0   1.7e-77   3.1e-73       1     255 [.      35     278 ..      35     279 .. 0.93

  Alignments for each domain:
  == domain 1  score: 246.3 bits;  conditional E-value: 1.7e-77
                                    EEESSHHHHHHHHHHHGGGCEEEECS-TTSTTTT----HHHHHHHHHSSEEEESSTTTSGTHHHHHHHHTTCCCEEEEET CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ZnuA   1 VvattsplgdlvrqvaGdrvevtvLvppgadpHsyeptprdvrklaeAdllvynglelEtwldkllasssqatrvevidl 80 
                                    Vvat+splg++v++v+Gdrv+v vL+ppgadpH++eptp +++ ++++dl+v ng++lE wld++   s   + ++v+d 
  gi|116754407|ref|YP_843525.1|  35 VVATISPLGEFVKAVGGDRVDVMVLLPPGADPHTFEPTPVQMKHIENSDLYVKNGAGLELWLDRFS--S---EGLKVVDS 109
                                    9**************************************************************993..2...35699999 PP

                                    TTTCCSEBCSS..ESTGGGSHHHHHHHHHHHHHHHHHHTGGGHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSGTEGEEEE CS
                                    xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ZnuA  81 segveeeeeee..DpHiWlspknaiamveniadaLveadpanadtyeanaaayiekLeeldaeireelaeipeekrklvt 158
                                    seg+e    +   DpHiWlsp+ a+ +veni  aL+e+dp++ + ye n +ayi++L+ ld+++++ l+++  + r++v+
  gi|116754407|ref|YP_843525.1| 110 SEGIELIYLNGtpDPHIWLSPRCAMIQVENICRALIEVDPDGREIYESNRDAYINELKGLDEYLKNILSSA--KGRIFVV 187
                                    9988655444477********************************************************55..5889*** PP

                                    SSSTTHHHHHHTT-EEEEEESSSSS..HHHHHHHHHHHHHTT-SEEEEETTS-THHHHHHHHHHT-EEEEE-STSSSTST CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ZnuA 159 thdafgylarayglevagiagiste..aaqiaalieeikeagvkaifveplaspklaetlaeeagvkvatlysldslgde 236
                                    +h+a++ylar+ygl +++i + + e  +++ia +i++++++++kai+vep ++pk+ae +a+eag +v+++++l +    
  gi|116754407|ref|YP_843525.1| 188 DHPAWSYLARDYGLVQVAIEEGEREpgPRRIAYIIKTVRDNNIKAILVEPEFNPKMAEVIASEAGCEVVEIDPLAG---- 263
                                    *****************9986666679**********************************************555.... PP

                                    TSTTSHHHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxx RF
                           ZnuA 237 gsaetYidmmranleslke 255
                                        +Yi+ mra  ++++e
  gi|116754407|ref|YP_843525.1| 264 ----NYINNMRAVGDTIAE 278
                                    ....9*******9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); 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 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1967.05
//
Query:       gi|116754408|ref|YP_843526.1|  [L=250]
Description: ABC transporter related [Methanosaeta thermophila PT]
Scores for complete 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   96.5   0.0    2.9e-27   95.8   0.0    1.3  1  ABC_tran  ABC transporter
    1.6e-13   51.1   0.6    1.3e-05   25.1   0.2    2.1  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
      3e-06   26.8   0.1      0.016   14.7   0.0    2.1  2  SMC_N     RecF/RecN/SMC N terminal domain
    0.00038   20.2   0.0    0.00067   19.4   0.0    1.3  1  AAA_29    P-loop containing region of AAA domain
     0.0007   19.4   0.0      0.066   12.9   0.0    2.1  2  AAA_15    AAA ATPase domain
      0.008   16.4   0.1       0.33   11.2   0.1    2.3  1  SbcCD_C   Putative exonuclease SbcCD, C subunit
     0.0081   16.7   0.0      0.013   16.0   0.0    1.3  1  AAA_23    AAA domain
  ------ inclusion threshold ------
      0.013   14.5   0.1       0.02   13.9   0.1    1.2  1  MeaB      Methylmalonyl Co-A mutase-associated GTPase MeaB
       0.02   13.8   0.0      0.027   13.4   0.0    1.2  1  AAA_PrkA  PrkA AAA domain
      0.025   14.3   0.0      0.055   13.2   0.0    1.7  1  AAA_30    AAA domain
      0.032   13.8   0.0      0.053   13.1   0.0    1.3  1  AAA_27    AAA domain
       0.11   12.6   0.1       0.25   11.5   0.1    1.8  1  MMR_HSR1  50S ribosome-binding GTPase
       0.15   12.0   0.2          4    7.4   0.2    2.4  2  AAA_5     AAA domain (dynein-related subfamily)
       0.16   11.4   0.1       0.55    9.6   0.0    1.8  2  TniB      Bacterial TniB protein


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.8   0.0   2.3e-30   2.9e-27       1     137 []      19     165 ..      19     165 .. 0.91

  Alignments for each domain:
  == domain 1  score: 95.8 bits;  conditional E-value: 2.3e-30
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                    l++v l++ e   ++++G+nG GKStLlk+++gl+kpt+G++++ g+d        +r  ig+lpq++ ++++  vr   
  gi|116754408|ref|YP_843526.1|  19 LEDVWLEVGERDFLGLIGPNGGGKSTLLKAILGLVKPTSGRVRVFGRDPVA-----ARPLIGYLPQHSIFDQRFPVRVLd 93 
                                    5788899999999*****************************999888777.....9**********8888888777778 PP

                                    ..................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    ..................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ..................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                                      e+ e +++al+ +g+ +l+d+ +      LSgG++qrv +ara++++pkllllDEpta
  gi|116754408|ref|YP_843526.1|  94 ivlmgryprvgilkryrnEDIEAAKRALDAVGMLGLADREI----GALSGGEQQRVFVARAIVSDPKLLLLDEPTA 165
                                    8************9977555555999***************....*****************************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 !   25.1   0.2     1e-08   1.3e-05       2      54 ..      32      78 ..      31      86 .. 0.74
   2 !   24.7   0.0   1.4e-08   1.8e-05     232     300 ..     132     196 ..      95     199 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1e-08
                         AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydp 54
                                    +liGpNg GKS+LL+a+ +l      v+++    + +g  ++ ++ l +y p
  gi|116754408|ref|YP_843526.1| 32 LGLIGPNGGGKSTLLKAILGL------VKPTSGRVRVFGRDPVAARPLIGYLP 78
                                   68****************666......66766666666666666666666665 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 1.4e-08
                         AAA_21 232 lparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpl 300
                                    + +  lS G ++  +++ a+ +++   +lll+DEp +g +   +r++++llk+l++ +  +i+++H+ +
  gi|116754408|ref|YP_843526.1| 132 REIGALSGGEQQRVFVARAIVSDP---KLLLLDEPTAGVDITQQREFYDLLKDLNS-RMAIIMVSHDLS 196
                                    556677888888878888888888...9***********************99988.9********976 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.2e-05     0.016      24      48 ..      29      50 ..      21      63 .. 0.85
   2 !   10.4   0.0   0.00025      0.32     136     203 ..     136     199 ..      77     211 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.2e-05
                                   SSEEEEEESTTSSHHHHHHHHHHHC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 24 ksftaivGpNGSGKsnlldAilFvL 48
                                   + f  ++GpNG GKs ll Ai   L
  gi|116754408|ref|YP_843526.1| 29 RDFLGLIGPNGGGKSTLLKAI---L 50
                                   678899***************...4 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00025
                                    CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemle 203
                                    +LSgGe++ v +    A   v+   l llDe  a  D ++ +++ +llk  ++++ +i++s++   ++
  gi|116754408|ref|YP_843526.1| 136 ALSGGEQQRVFV----ARAIVSDPKLLLLDEPTAGVDITQQREFYDLLKDLNSRMAIIMVSHDLSAIS 199
                                    799999886544....44456667799**********************************9876665 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   5.2e-07   0.00067      22      50 ..      29      57 ..      19      62 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 5.2e-07
                         AAA_29 22 kgatlltGpsGsGKSTllDAiqalLvpak 50
                                   +++  l+Gp+G GKSTll Ai  l  p++
  gi|116754408|ref|YP_843526.1| 29 RDFLGLIGPNGGGKSTLLKAILGLVKPTS 57
                                   556669***************99998876 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   0.0   5.1e-05     0.066      25      46 ..      31      52 ..      19      77 .. 0.85
   2 ?    4.6   0.0     0.017        22     320     364 ..     151     193 ..     141     198 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.1e-05
                         AAA_15 25 ltvliGkNnsGKSsilealdlF 46
                                   +  liG+N+ GKS++l+a+  +
  gi|116754408|ref|YP_843526.1| 31 FLGLIGPNGGGKSTLLKAILGL 52
                                   6779**************9655 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.017
                         AAA_15 320 keeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                    + +++++ll++EP a   + +q+++++llk+l +     +i+ +H
  gi|116754408|ref|YP_843526.1| 151 IVSDPKLLLLDEPTAGVDITQQREFYDLLKDLNSRMA--IIMVSH 193
                                    456899*************************977774..777777 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 !   11.2   0.1   0.00026      0.33      26      89 ..     130     180 ..     107     181 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00026
                        SbcCD_C  26 lsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                     +r++g+lSGGe+q ++  a     +a +s+       ++l++LDE  +++D + +++  +ll+
  gi|116754408|ref|YP_843526.1| 130 ADREIGALSGGEQQRVFV-A-----RAIVSD-------PKLLLLDEPTAGVDITQQREFYDLLK 180
                                    679999999999966543.2.....333444.......78999999999999998888888876 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0     1e-05     0.013      23      39 ..      33      49 ..      17      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1e-05
                         AAA_23 23 lItGpNGaGKTTildAi 39
                                    ++GpNG GK+T+l Ai
  gi|116754408|ref|YP_843526.1| 33 GLIGPNGGGKSTLLKAI 49
                                   578*************9 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   1.5e-05      0.02      16      69 ..      16      69 ..       7      75 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.5e-05
                                   HHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE---- CS
                           MeaB 16 kellerllakaGraqvvGltGvPGaGkstlvealglelrrrGkrvavlavDPss 69
                                   + +le +  + G+   +Gl G  G Gkstl++a+   ++    rv v   DP +
  gi|116754408|ref|YP_843526.1| 16 RIVLEDVWLEVGERDFLGLIGPNGGGKSTLLKAILGLVKPTSGRVRVFGRDPVA 69
                                   56789999999***********************999999999****9999976 PP

>> AAA_PrkA  PrkA AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.1e-05     0.027      88     148 ..      29      90 ..      23     125 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.1e-05
                       AAA_PrkA  88 kqilyllGPvggGksslverlkklleaa..piyalegsPvfeePlhli.peelrkkleeeygir 148
                                    +  l l+GP ggGks+l +++  l++ +   + ++ + Pv   Pl  + p++   ++++++ +r
  gi|116754408|ref|YP_843526.1|  29 RDFLGLIGPNGGGKSTLLKAILGLVKPTsgRVRVFGRDPVAARPLIGYlPQHS--IFDQRFPVR 90 
                                    66799****************99999887889999*********976658874..555555554 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.3e-05     0.055      20      62 ..      31      73 ..      24     200 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.3e-05
                         AAA_30 20 vavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvL 62
                                   +  l Gp G GK+t+lka+  +++   grv ++     aA+ L
  gi|116754408|ref|YP_843526.1| 31 FLGLIGPNGGGKSTLLKAILGLVKPTSGRVRVFGRDPVAARPL 73
                                   67799*********************999*9999999998876 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.1e-05     0.053      18      49 ..      21      52 ..       6      54 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.1e-05
                         AAA_27 18 sldfsaeeadlhliyGpNEAGKstalrAisdl 49
                                    + ++ +e+d+  ++GpN  GKst+l+Ai  l
  gi|116754408|ref|YP_843526.1| 21 DVWLEVGERDFLGLIGPNGGGKSTLLKAILGL 52
                                   45566679999999**************9876 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   0.00019      0.25       3      22 ..      33      57 ..      31     212 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00019
                                   EEEESTTSSHHHHHHHHHT.....S CS
                       MMR_HSR1  3 aivGrpNvGKStLinaltg.....e 22
                                   +++G    GKStL++a++g     +
  gi|116754408|ref|YP_843526.1| 33 GLIGPNGGGKSTLLKAILGlvkptS 57
                                   799***************9433331 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 ?    7.4   0.2    0.0031         4       4      23 ..      34      53 ..      32      68 .. 0.84
   2 ?    2.1   0.0      0.14   1.8e+02      25      45 ..     209     229 ..     178     232 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0031
                                   EE--SSSSHHHHHHHGGGGB CS
                          AAA_5  4 LvGppGtgKselaerlaaal 23
                                   L+Gp G gKs+l + ++ ++
  gi|116754408|ref|YP_843526.1| 34 LIGPNGGGKSTLLKAILGLV 53
                                   9************9998877 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.14
                                    --EEEEE--TT--HHHHH--B CS
                          AAA_5  25 reveyvqltrdtteedlkgrr 45 
                                    ++ +y+ +++ +teedl++ +
  gi|116754408|ref|YP_843526.1| 209 NQRLYYHGSKELTEEDLVQAY 229
                                    45679999**********986 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.85   1.1e+03      39      54 ..      33      48 ..      27      58 .. 0.83
   2 ?    9.6   0.0   0.00043      0.55     119     160 ..     154     193 ..     136     218 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.85
                           TniB 39 llvGdsnnGKtmivek 54
                                    l+G+   GK+++++ 
  gi|116754408|ref|YP_843526.1| 33 GLIGPNGGGKSTLLKA 48
                                   58999******99875 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00043
                           TniB 119 kvrvLiiDEihnllagsarkqreflnalksLgnelkipivlv 160
                                    ++++L++DE    +    ++qref  +lk L+ ++ i +v  
  gi|116754408|ref|YP_843526.1| 154 DPKLLLLDEPTAGV--DITQQREFYDLLKDLNSRMAIIMVSH 193
                                    6899*****98877..899*****************999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); 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: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1756.87
//
Query:       gi|116754409|ref|YP_843527.1|  [L=264]
Description: ABC-3 protein [Methanosaeta thermophila PT]
Scores for complete 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-72  242.9  39.3    4.2e-72  242.8  39.3    1.0  1  ABC-3     ABC 3 transport family
    5.4e-09   35.5  39.3      1e-08   34.6  39.3    1.5  1  FecCD     FecCD transport family


Domain annotation for each model (and alignments):
>> ABC-3  ABC 3 transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  242.8  39.3   4.6e-76   4.2e-72       1     257 [.       2     257 ..       2     258 .. 0.99

  Alignments for each domain:
  == domain 1  score: 242.8 bits;  conditional E-value: 4.6e-76
                          ABC-3   1 qyeflqrallasilvslacallgsfvvlrrqsllgdalsHaalpGvalayllgvnlllgailvgliaavalellkrktkl 80 
                                    qyef+  al+a++++s+ c+++g++vvl+r++++gd+++Haa++G++l+yllg+ +++ a++++++aa ++++++r  k+
  gi|116754409|ref|YP_843527.1|   2 QYEFMKTALVAGLMLSILCGVVGVYVVLNRIVFIGDGVAHAAFGGIGLGYLLGIDPFFLALVAAVLAAAGIGAVSR-FKV 80 
                                    79************************************************************************86.79* PP

                          ABC-3  81 kedtaigivlsvflalglvlvslikkskvdldsyLfGniltisqedliliaiieavvllllllfwkelllitfdeelAkv 160
                                    +edtaig+ l++++alg++l+s++ +++ dl+ yLfGnil++s  d+ +++++++++ +l+l ++ke+l+++fd+++ ++
  gi|116754409|ref|YP_843527.1|  81 SEDTAIGVFLAMGMALGVLLMSMSTGYSRDLFDYLFGNILAVSWIDVKIMIVLTVIITVLALALYKEFLILSFDPHYGEA 160
                                    ******************************************************************************** PP

                          ABC-3 161 eglsvkllkllllalialavvvalqavGviLvialliiPaatArrltrslesllivAillglvsvvaGlllSyyldlatG 240
                                     gl+v +lk+lll+++a +vv+ +++vG+i+via+l+iPaa+ r+   +l+ +++++++lg+++++aGll+Sy +dl++G
  gi|116754409|ref|YP_843527.1| 161 LGLPVGRLKMLLLCMVAFTVVMLIKIVGIIMVIAMLTIPAAISRQHLCNLKLIIALSVILGMIFATAGLLVSYAFDLPSG 240
                                    ******************************************************************************** PP

                          ABC-3 241 avivlvatllfllallv 257
                                    a+++l+a+++f+++ +v
  gi|116754409|ref|YP_843527.1| 241 ATVILIAAAAFFASTAV 257
                                    ************99875 PP

>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6  39.3   1.2e-12     1e-08      82     307 ..      42     252 ..       6     256 .. 0.77

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 1.2e-12
                          FecCD  82 gaalgavlalllllgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsallsaltsllllllneeale 161
                                    +a  g+ l++ll   ++  f l+l+a + a+++++ v  +   ++ +    ++ +G+a+++ll ++++          ++
  gi|116754409|ref|YP_843527.1|  42 AAFGGIGLGYLL---GIDPFFLALVAAVLAAAGIGAVSRFK-VSEDTAIGVFLAMGMALGVLLMSMST--------GYSR 109
                                    444444444443...34555555555555555555555444.44555555555556666666555555........4568 PP

                          FecCD 162 silfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrllllllvalltavavalvGp 241
                                    ++  +l+G++  +sw +v +++vl++++++l+l+l++++ +l+++    ++lG++v r+++lll++va+ + + + +vG+
  gi|116754409|ref|YP_843527.1| 110 DLFDYLFGNILAVSWIDVKIMIVLTVIITVLALALYKEFLILSFDPHYGEALGLPVGRLKMLLLCMVAFTVVMLIKIVGI 189
                                    9******************************************************************************* PP

                          FecCD 242 igFvGLi.vPhiarllvgadhrkllplsallGallllladllarlllsptelpvgivtaliGapffi 307
                                    i  ++++ +P  +++    + + ++ ls++lG+++ ++  l++  +    +lp g+ + li a  f+
  gi|116754409|ref|YP_843527.1| 190 IMVIAMLtIPAAISRQHLCNLKLIIALSVILGMIFATAGLLVSYAF----DLPSGATVILIAAAAFF 252
                                    *****7636777776666799*************999888877665....79999888888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1502  (0.0837749); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); 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):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.39
# Mc/sec: 2040.21
//
Query:       gi|116754410|ref|YP_843528.1|  [L=323]
Description: hypothetical protein Mthe_1105 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); 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: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2333.26
//
Query:       gi|116754411|ref|YP_843529.1|  [L=366]
Description: cytochrome c biogenesis protein, transmembrane region [Methanosaeta thermophila PT]
Scores for complete 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   66.1  17.8    5.2e-18   65.7  17.8    1.1  1  DsbD           Cytochrome C biogenesis protein transmembrane 
    1.1e-05   25.4   0.0    1.8e-05   24.7   0.0    1.3  1  Thioredoxin_3  Thioredoxin domain
    0.00013   22.1   0.0    0.00022   21.4   0.0    1.4  1  Glutaredoxin   Glutaredoxin
  ------ inclusion threshold ------
      0.073   13.1   0.0       0.12   12.4   0.0    1.2  1  Thioredoxin    Thioredoxin
        6.5    6.0   6.8        1.3    8.4   0.6    2.6  3  SLATT_5        SMODS and SLOG-associating 2TM effector domain


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 !   65.7  17.8   1.4e-21   5.2e-18       2     210 ..     150     360 ..     149     363 .. 0.78

  Alignments for each domain:
  == domain 1  score: 65.7 bits;  conditional E-value: 1.4e-21
                           DsbD   2 flaGllsflsPCilpliPaylsyisgvsvedvktekkkvkvllkallFvlGlslvfvslglsaaflgqllkdvkevirrv 81 
                                    + aGll+ + PC+l+++    ++++++ +++         +l   ++F lG+  v++ +g++   ++q   d  +++r v
  gi|116754411|ref|YP_843529.1| 150 LIAGLLAGFNPCLLAIL----AFLATTVLSSTGRR---RDMLSMIIFFSLGILSVYLIVGMGLFRVMQNT-DTASMLRLV 221
                                    78************986....66666655554443...235778899****************9999998.********* PP

                           DsbD  82 aglivillGlhflgvfk......ievleklklllkikkkaelsvlga.lllGltFalgwsPCigPvlasvlalaaskesl 154
                                     +++ illG+ +l+  +       +++++   l   ++ a ++ l a +llG++F+++ +PC+g v  +++++  +k+ +
  gi|116754411|ref|YP_843529.1| 222 LSMLLILLGMLQLEDARrlgssgRSLFRTDWILSYFQAAAGAQSLAAyFLLGMLFSMVKAPCVGAVYVAIITMIYTKGYA 301
                                    ************995556666643333433444566666777777663799***************************** PP

                           DsbD 155 akgallllvyvlGlaipfllvg..lllellkkklkslkk.yskaveiaggvllvllGvl 210
                                    ++++ +l++y lG ++p++l+g  + l++  + ++ +++ +  a++i++g+ l+ l  l
  gi|116754411|ref|YP_843529.1| 302 SSAIAYLFLYNLGVVLPVMLLGgaIALGMQPESVERFRHeHRVAIRIITGLTLIALAPL 360
                                    *******************9973344455555566665415567899999988887655 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0     5e-09   1.8e-05       4      59 ..      38      98 ..      35     106 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 5e-09
                                   EE.ESSSSTTCHHHHHHHHHHCHCC.TCEC..EEECCTTHHHH.HHCT-SSSSEEECTTCE CS
                  Thioredoxin_3  4 kv.lgpgCakCpklekavkeaaaek.gika..evekvtdfeei.ekygVmsvPalvidgkv 59
                                    +   pgCakC ++ ++++ ++ +  ++++  + +  ++ ++i ++++V  +P+++idg v
  gi|116754411|ref|YP_843529.1| 38 LIlTAPGCAKCAAAHSVLEDVLSSYeDVHIqeHTYTSEEGRKIiKEFRVKDIPSIIIDGSV 98
                                   5634799***************9995488765666779999999***************98 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   6.2e-08   0.00022       1      60 []      37      99 ..      37      99 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 6.2e-08
                                   EEEEESTSSHHHHHHHHHHHHTTGGEEEEEGCCSH....HHHHHHHHHHTSSSSSEEEETTEEE CS
                   Glutaredoxin  1 vvlftkptCpyCkkakrlLkelgvkfeeidvdkde....eireelkelsgvrtvPqvfidgkhv 60
                                   v++ t p+C  C++a  +L++   ++e + + ++     e r+ +ke+  v+ +P + idg ++
  gi|116754411|ref|YP_843529.1| 37 VLILTAPGCAKCAAAHSVLEDVLSSYEDVHIQEHTytseEGRKIIKEF-RVKDIPSIIIDGSVI 99
                                   678899****************************87775555555555.99**********986 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.3e-05      0.12      25      92 ..      40     108 ..      32     118 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.3e-05
                                    EE-TTSHHHHCHHHHHHHHHHHCTT.TSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTEEEEEEESS- CS
                    Thioredoxin  25 FyApwCghCkalaPeleklaeelkd.kvklakvdvdenedlakkyevegiPtlklfkngkevkkyegar 92 
                                     +Ap C++C a  ++le++ + ++d +++      +e +++ k++ v+ iP +++  +    ++y+g++
  gi|116754411|ref|YP_843529.1|  40 LTAPGCAKCAAAHSVLEDVLSSYEDvHIQEHTYTSEEGRKIIKEFRVKDIPSIIIDGSVIGYRDYDGNE 108
                                    589*********************66666666667777899************7644444666676664 PP

>> SLATT_5  SMODS and SLOG-associating 2TM effector domain family 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.14     5e+02      53      83 ..     127     157 ..     115     159 .. 0.84
   2 ?    8.4   0.6   0.00035       1.3      25      81 ..     180     232 ..     177     243 .. 0.84
   3 ?   -2.9   0.1      0.97   3.5e+03     169     189 ..     342     362 ..     334     363 .. 0.59

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.14
                        SLATT_5  53 kssestinenlldflsiilSilvlvislles 83 
                                     sse   +++l++ ++++++  vl+++ll++
  gi|116754411|ref|YP_843529.1| 127 ASSEMPYPSELFESITLSTALTVLIAGLLAG 157
                                    56667778999****************9987 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00035
                        SLATT_5  25 RlrrknklstfslsllSvyliv.lsllsnkssestinenlldflsiilSilvlvisll 81 
                                    R    + ++ fsl +lSvyliv + l++        n +  ++l ++lS+l++++++l
  gi|116754411|ref|YP_843529.1| 180 RRDMLSMIIFFSLGILSVYLIVgMGLFR-----VMQNTDTASMLRLVLSMLLILLGML 232
                                    5566667788999******997689999.....88899999999999**999998876 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 0.97
                        SLATT_5 169 rrylivifllylliillpvil 189
                                     r +i+i+  ++li l p+i+
  gi|116754411|ref|YP_843529.1| 342 HRVAIRIITGLTLIALAPLIY 362
                                    455666666667777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       890  (0.0496402); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); 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):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:02.47
# Mc/sec: 449.37
//
Query:       gi|116754412|ref|YP_843530.1|  [L=350]
Description: permease [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-70  238.1  27.5    1.4e-70  237.8  27.5    1.1  1  ArsP_1    Predicted permease


Domain annotation for each model (and alignments):
>> ArsP_1  Predicted permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.8  27.5   7.8e-75   1.4e-70       5     293 ..      13     346 ..      10     347 .. 0.94

  Alignments for each domain:
  == domain 1  score: 237.8 bits;  conditional E-value: 7.8e-75
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         ArsP_1   5 altlfasilleallaLvlgflisgaiqvfvkeekiielLg.prnrlisllvaallGfllpvCscsavPlarrllkkGapl 83 
                                    + +l++++  ++l++L+++f+i+gai++ +k+e i +++g ++++ + ++vaa++G +l+vCsc+++P+++++ +kGa++
  gi|116754412|ref|YP_843530.1|  13 LESLLEYLSAHVLTCLIPAFFIAGAISALLKKEIILKYFGaDASKWVCYPVAAISGTVLAVCSCTILPMFAGIERKGAGI 92 
                                    56899*************************************************************************** PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......... RF
                         ArsP_1  84 gaavaFlvaaPainiiaiiltlillgwqllvarivlalivaiviglvleylfkeeelekaarevaeaglek......... 154
                                    g+a+aFl+++Pain +ai+lt+ +lg+++++ar+++a+++a++iglv++ +f+ e+ + ++  +++ g+ +         
  gi|116754412|ref|YP_843530.1|  93 GPAIAFLFSGPAINLMAIVLTARVLGLDIGIARAIAAVTMAVLIGLVMSFVFPGERRSSSRNPSPKDGSVSrttllfigv 172
                                    ******************************************************************999999******** PP

                                    .................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         ArsP_1 155 .................................ltlkpklealkafaknevkewlelgkyLiiGvaiagviqaflpesvl 201
                                                                         + le ++ f  +++    +++++L+ G++++gvi  flp + +
  gi|116754412|ref|YP_843530.1| 173 liaillvatssaivavpkiailsaliliaayimWRYYTPLE-RRTFLGETWWLAKRIFPLLLAGTFVVGVIGYFLPMDLI 251
                                    ***********************998887777544445555.4678888887778888********************** PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         ArsP_1 202 lsllggnsvsssllamligvvlyvcslgevpfiaalf..esglal.GsalAfLlagpllslpellillkvlkkklvavll 278
                                    + ++g+ns++s l a+lig+vly+ +l evp++ +lf  +sg+++ G+alA+Llagp+lslp+++++  v +++++ v++
  gi|116754412|ref|YP_843530.1| 252 KMIMGSNSFISCLTASLIGAVLYMPTLLEVPIVGTLFgySSGVTApGPALALLLAGPSLSLPNMIVIARVIGPRKAGVYI 331
                                    ************************************9445777655********************************** PP

                                    xxxxxxxxxxxxxxx RF
                         ArsP_1 279 glvvvsvvlaglvin 293
                                    +lvv++++l+g++++
  gi|116754412|ref|YP_843530.1| 332 ALVVMISTLIGMIYG 346
                                    *************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       914  (0.0509789); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); 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: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2418.17
//
Query:       gi|116754413|ref|YP_843531.1|  [L=127]
Description: ArsR family transcriptional regulator [Methanosaeta thermophila PT]
Scores for complete 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-18   64.1   1.0    2.9e-17   62.2   0.2    2.0  2  HTH_5     Bacterial regulatory protein, arsR family
    3.9e-10   39.6   0.2    7.6e-10   38.7   0.0    1.6  2  HTH_20    Helix-turn-helix domain
     0.0031   17.4   0.0     0.0056   16.5   0.0    1.4  1  TrmB      Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.059   13.0   0.1       0.11   12.2   0.1    1.4  1  RP-C      Replication protein C N-terminal domain
      0.079   12.9   0.0       0.18   11.7   0.0    1.6  1  MarR      MarR family


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 !   62.2   0.2   8.2e-21   2.9e-17       1      46 [.      41      86 ..      41      87 .. 0.97
   2 ?    0.2   0.0       0.2   7.1e+02      24      42 ..     106     124 ..     102     125 .. 0.75

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 8.2e-21
                                   SHHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_5  1 dptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                   dp R+kIL lL++ge+cvce+  +++ sqst+S HL++L++aGL++
  gi|116754413|ref|YP_843531.1| 41 DPIRIKILLLLSDGERCVCEILPAFERSQSTISKHLSILYNAGLLD 86
                                   8*******************************************85 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.2
                                    HHTS-HHHHHHHHHHHHHT CS
                          HTH_5  24 elglsqstvShHLkkLrea 42 
                                     l+   ++   HL+ L e+
  gi|116754413|ref|YP_843531.1| 106 LLETADAIAIAHLSSLVES 124
                                    5666777778899999885 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   0.0   2.1e-13   7.6e-10       2      60 ..      34      91 ..      33      92 .. 0.95
   2 ?   -2.3   0.1       1.3   4.8e+03      48      54 ..     107     113 ..     101     123 .. 0.60

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 2.1e-13
                                   HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                         HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                   +i+ ALa+P R +il +L +++++++ e+  +++ s++t+s+HL +L  agL++++ eg
  gi|116754413|ref|YP_843531.1| 34 RIFGALADPIRIKILLLL-SDGERCVCEILPAFERSQSTISKHLSILYNAGLLDRRIEG 91
                                   6999**************.***********************************98665 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.3
                                    HHHCTTE CS
                         HTH_20  48 LeeagLv 54 
                                    Le a+++
  gi|116754413|ref|YP_843531.1| 107 LETADAI 113
                                    3335555 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.6e-06    0.0056      16      65 ..      49      99 ..      47     102 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.6e-06
                                   HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE.SSTTTEEEE- CS
                           TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVere.kgrpklYrav 65
                                    Ll+ g+  + ei  + ++++s++ + L+ L ++Gl +r+ +g++++Y+  
  gi|116754413|ref|YP_843531.1| 49 LLLSDGERCVCEILPAFERSQSTISKHLSILYNAGLLDRRiEGNRTIYSIK 99
                                   5889*********************************87616889999876 PP

>> RP-C  Replication protein C N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   2.9e-05      0.11      80     118 ..      64     102 ..      60     110 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.9e-05
                           RP-C  80 alglsestlrrhlaaLveaGliirrDspngkRyarrdre 118
                                    a+ +s+st+++hl+ L +aGl+ rr   n   y  ++r+
  gi|116754413|ref|YP_843531.1|  64 AFERSQSTISKHLSILYNAGLLDRRIEGNRTIYSIKNRR 102
                                    6789*********************99999888888875 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   5.1e-05      0.18      22      50 ..      60      88 ..      44      92 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.1e-05
                                   HHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                           MarR 22 eLakklgvskstvtrvldrLekkGlieRs 50
                                   e+  +++ s+st+++ l  L+ +Gl++R+
  gi|116754413|ref|YP_843531.1| 60 EILPAFERSQSTISKHLSILYNAGLLDRR 88
                                   77889999********************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); 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: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 999.99
//
Query:       gi|116754414|ref|YP_843532.1|  [L=247]
Description: response regulator receiver protein [Methanosaeta thermophila PT]
Scores for complete 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   56.5   0.0    5.1e-15   55.6   0.0    1.4  1  Response_reg  Response regulator receiver domain
  ------ inclusion threshold ------
      0.041   13.2   1.1       0.06   12.7   1.1    1.4  1  CorA          CorA-like Mg2+ transporter protein
       0.11   12.8   0.1        0.2   11.9   0.1    1.4  1  HalOD1        Halobacterial output domain 1
       0.11   12.4   1.4       0.66    9.9   0.7    2.2  2  CheZ          Chemotaxis phosphatase, CheZ


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.6   0.0   1.1e-18   5.1e-15       1     103 [.       7     114 ..       7     123 .. 0.86

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 1.1e-18
                                    EEEESSSHHHHHHHHHHHHHTTE.EEEEEESSHHHHHHHHHHHH...ESEEEEESSCSSSEHHHHHHHHHHCT.TTSEEE CS
                   Response_reg   1 vlivdDdplvrellrqlleeegy.eevaeaedgkealellkeek...vdlillDinmpgmdGlellkeireed.pelpvi 75 
                                    vl+v+D+ + + l+++++ee+g   +v  +++ ++a++ l+e++   +d+++ D ++p+ +Gl+l++   + +    p i
  gi|116754414|ref|YP_843532.1|   7 VLLVEDNDAHAVLIQRIFEENGSaWSVSRVSTLADAMRFLDENQdslPDIVIADYRLPDGTGLDLTRGAATPEdVGFPLI 86 
                                    89*****************7665347888888888888887777788********************996655489**** PP

                                    EEESSTSHHHHHHHHHCTESEEEESSG- CS
                   Response_reg  76 iltahseeedavealkagaddflsKpfd 103
                                    ilt+ ++e  av+ +k ga+d+++K  +
  gi|116754414|ref|YP_843532.1|  87 ILTGVGSERLAVQTMKSGAMDYVVKSSE 114
                                    *************************963 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.1   1.3e-05      0.06     112     158 ..     157     203 ..     112     219 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.3e-05
                           CorA 112 lyrlldeivdrlfellekleeeldeledeledstkkeilrelaqlrr 158
                                    l +++d+i ++l+e++ +++e   ++ ++l+d++++eil++l++++ 
  gi|116754414|ref|YP_843532.1| 157 LDEFMDRISHELEEAITTIKETNTRIRKRLSDNIDEEILNDLYRVES 203
                                    778999999999999999999999*******************9885 PP

>> HalOD1  Halobacterial output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   4.5e-05       0.2       3      47 ..     162     206 ..     161     215 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.5e-05
                         HalOD1   3 espstaVveavaavegvdptelepLydaiDpdALdaLfasradge 47 
                                    +++s++  ea+ ++++++    + L d iD + L++L++ +++ e
  gi|116754414|ref|YP_843532.1| 162 DRISHELEEAITTIKETNTRIRKRLSDNIDEEILNDLYRVESAAE 206
                                    578899999********9999999***************944443 PP

>> CheZ  Chemotaxis phosphatase, CheZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.7   0.00015      0.66      56     123 ..     105     172 ..      97     196 .. 0.75
   2 ?    0.5   0.0      0.11   4.8e+02       5      41 ..     206     242 ..     202     244 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00015
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                           CheZ  56 tldavekalpladklkeeakeleeewerllerelekeefrelvkeveaflkeveektealkkqLleil 123
                                    ++d+v k+    ++l ++a+++ +ew++l+er+ ++ e+ + v+++ea   +++e  ++++++L e +
  gi|116754414|ref|YP_843532.1| 105 AMDYVVKSSEDLRQLPSTASRILNEWSTLMERRRTEMEIAKCVSDLEADKLNLDEFMDRISHELEEAI 172
                                    799999999999********************999999666666666555555555555555555533 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.11
                                    XXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXX CS
                           CheZ   5 eeiGkltReLhdalrelgldekllekaaeeipdardr 41 
                                    e+ G lt +L + l  l +d++l++  ++++++ ++r
  gi|116754414|ref|YP_843532.1| 206 ERAGMLTDKLFEYLLPLYFDSSLVRLYMQNLEELKSR 242
                                    7889****************99999999999887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1138  (0.0634726); expected 358.6 (0.02)
Passed bias filter:                      700  (0.0390429); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 1800.33
//
Query:       gi|116754415|ref|YP_843533.1|  [L=208]
Description: hypothetical protein Mthe_1110 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1567.72
//
Query:       gi|116754416|ref|YP_843534.1|  [L=190]
Description: adenine phosphoribosyltransferase [Methanosaeta thermophila PT]
Scores for 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-18   64.2   2.9    1.3e-17   63.8   2.9    1.1  1  Pribosyltran  Phosphoribosyl transferase domain
    0.00099   18.6   0.0     0.0016   18.0   0.0    1.3  1  UPRTase       Uracil phosphoribosyltransferase
     0.0016   18.0   0.0     0.0021   17.6   0.0    1.2  1  PRTase_2      Phosphoribosyl transferase


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.8   2.9   2.1e-21   1.3e-17      15     138 ..      43     165 ..      33     184 .. 0.83

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 2.1e-21
                                    EEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE...........EE----TTSEEE CS
                   Pribosyltran  15 varlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes...rlledpagkkVl 91 
                                    v+++++     ++   d +v+++  G+p++++l+   ++pl+++rk+ y  +g  e++++   +     l ++++g +V+
  gi|116754416|ref|YP_843534.1|  43 VCHIIRI----ADLDVDKIVTVEAMGIPIGGALSLVTDIPLVIIRKKMYGLPGEIEVSQVTGYSKskiYLNGIKKGDRVI 118
                                    3444444....444599****************************************9876655589999********** PP

                                    EE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHHHHHHH-T CS
                   Pribosyltran  92 iVDDildtGgTllaalelLkekgpeevriavlvdkpateeevdknak 138
                                     VDD+++tGgT +a++++L+++g+ +  ++v+++++a++e+v+   +
  gi|116754416|ref|YP_843534.1| 119 FVDDVVSTGGTAIAVMKALEAAGAVIRDAVVVIERGAGAERVRSAGY 165
                                    ************************766666777*****999987555 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.6e-07    0.0016     120     172 ..     113     163 ..      87     179 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.6e-07
                        UPRTase 120 aertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegvkrlaee 172
                                    + ++v+ +D v++TGg+a+a+++ L  +g+  ++   + v+   +g++r+ ++
  gi|116754416|ref|YP_843534.1| 113 KGDRVIFVDDVVSTGGTAIAVMKALEAAGAVIRDA--VVVIERGAGAERVRSA 163
                                    4678***********************99866654..3456666666666554 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   3.5e-07    0.0021     118     155 ..     111     150 ..     101     175 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.5e-07
                       PRTase_2 118 laaakelvLvDDEistGktalnliralqek..lprkryvv 155
                                    +++ +++++vDD +stG ta+++++al+++  + r+ +vv
  gi|116754416|ref|YP_843534.1| 111 IKKGDRVIFVDDVVSTGGTAIAVMKALEAAgaVIRDAVVV 150
                                    567789*********************9984344455554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); 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 0.26s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1430.59
//
Query:       gi|116754417|ref|YP_843535.1|  [L=105]
Description: hypothetical protein Mthe_1112 [Methanosaeta thermophila PT]
Scores for 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-14   51.3   0.1    1.1e-13   51.0   0.1    1.2  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 !   51.0   0.1   6.2e-18   1.1e-13      19      72 ..      22      75 ..       6      76 .. 0.85

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 6.2e-18
                                   .TS---HHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTST CS
                         DUF357 19 eesplgeaaeevlemaesYleDakyflekgdlvnAlasfsYaeGwLDagarlgl 72
                                   e+ +  +  e++l ++++Y++D++yflekgdl++A+ ++ +a++wL+ g  lg 
  gi|116754417|ref|YP_843535.1| 22 ERLSGCRGDESFLSNIKAYISDSRYFLEKGDLIRAFEAVIWAWAWLEIGEELGR 75
                                   55555566799**************************************99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       208  (0.0116013); expected 358.6 (0.02)
Passed bias filter:                      193  (0.0107647); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 766.46
//
Query:       gi|116754418|ref|YP_843536.1|  [L=432]
Description: dihydroorotase [Methanosaeta thermophila PT]
Scores for complete 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   90.3   0.0    2.1e-25   89.8   0.0    1.2  1  Amidohydro_1     Amidohydrolase family
    1.1e-16   61.4   0.1    2.8e-10   40.3   0.0    2.2  2  Amidohydro_3     Amidohydrolase family
  ------ inclusion threshold ------
      0.018   14.7   0.0      0.032   13.9   0.0    1.4  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F


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 !   89.8   0.0   3.5e-29   2.1e-25       1     330 [.      48     388 ..      48     404 .. 0.75

  Alignments for each domain:
  == domain 1  score: 89.8 bits;  conditional E-value: 3.5e-29
                                    EEEE-EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTH..HHHHHHHHHHTSSSEEE CS
                   Amidohydro_1   1 ivlPGlIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattst..giealleaaeelplglr 78 
                                    i++PG ID+HvH++             +p+ t +e  esg   a  +G+ttv d ++t+++   +e  +e +        
  gi|116754418|ref|YP_843536.1|  48 IIIPGVIDMHVHFR-------------DPGYTHKEDWESGSISAAAGGVTTVVDQPNTDPPvmDAESYKEKLNL------ 108
                                    79***********9.............******************************98665544444443333...... PP

                                    EEEESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHHHHHHHHHTTEEEEEETSSCHH CS
                   Amidohydro_1  79 ilggkvsldrgsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealkeakkrdlpvaiHaletkge 158
                                        + ++d ++ +  +  +e l+++              +a+++ + ++ s+e l+ +lke+++ d+  ++Ha + + +
  gi|116754418|ref|YP_843536.1| 109 -AKRRSIVD-FCLNGGPGDIESLLREG------------AAAIGEIFMYEMSEERLARILKEVERLDVLATVHAEDGEVI 174
                                    .23333444.88888888898888885............399********************************888888 PP

                                    HHHHHHHHTTTEEE.ETTTTSTCC.......HHTTTHCCEEEHCTCEEE.HHHHHHHHHHHHHHCEE.....HHHHHHHH CS
                   Amidohydro_1 159 vedaeaafgetieh.gthlevaes.......lglldeiklilahgvhlt.pteaellkerlkeagva.....hcpfsnsi 224
                                      ++e  +g   ++ +   ++a         ++ + ++  ++ h++h++ ++ +el+k+r ++ +v+     h       
  gi|116754418|ref|YP_843536.1| 175 RRYSEPLGG---ICdPDVHSRARPpiaevsaIDRALSVSRCRIHICHIStADGLELVKRR-RNRKVScevapH------H 244
                                    888888888...440224444444888854433333344459*******65589999999.666666677772......2 PP

                                    ......................SEHHHHHHHHHHHHTSCEEEEEECT................TSSCCGGHHHHHHHHHH CS
                   Amidohydro_1 225 ......................lrsgrealrkaldeGvkvglgtDga................asgnslnlleelrlalk 266
                                                           + +++al++ l++  + ++++D+a                +   + ++l  + +a+ 
  gi|116754418|ref|YP_843536.1| 245 lflsrrdyrrlgtflktnpplrNTADCDALWDGLRRRDIDVIASDHAphlpeekrddiwhappGVPGVETMLPLMLYAV- 323
                                    2333336788888888888888***********************9999999988888776552222225655566666. PP

                                    HHHHCCTTTTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECC....CT.......CGGGTTTCT CS
                   Amidohydro_1 267 lqrgllyedeegglslkealrmaTingAkalglddkvGsievGkdADlvvvdl....di.......laafvglkk 330
                                             +  +++l++++++ +  +A +lgl + +G+i+ GkdADlv++d+     i        a+++  ++
  gi|116754418|ref|YP_843536.1| 324 ---------KSNMITLERVVDALSARPASILGL-RSKGEIAIGKDADLVIFDPkrqeRIdvqrlhsRADWTPYER 388
                                    .........5677********************.6****************996544115555555555554444 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.2e-07   0.00071       3      54 ..      42      92 ..      40     111 .. 0.74
   2 !   40.3   0.0   4.6e-14   2.8e-10     406     473 .]     326     405 ..     258     405 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.2e-07
                   Amidohydro_3  3 iDakGrlvlPGFvDsHtHlagggvnlrllrlpdarvtslegvltavrdqagt 54
                                   iDa+G++ +PG +D+H H    g+   + + ++ + ++++g  t+v dq +t
  gi|116754418|ref|YP_843536.1| 42 IDASGMIIIPGVIDMHVHFRDPGYTHKEDWESG-SISAAAGGVTTVVDQPNT 92
                                   9*****************999996665544444.566666666666666555 PP

  == domain 2  score: 40.3 bits;  conditional E-value: 4.6e-14
                   Amidohydro_3 406 eelsleealalyTrgpAkalgledrkGtLevGadADlvvld.adpldvdppelaear............vrltvvdGrvv 472
                                    + ++le ++++++++pA +lgl+ + G +++G+dADlv++d +   ++d ++l++              +++t+v+G vv
  gi|116754418|ref|YP_843536.1| 326 NMITLERVVDALSARPASILGLRSK-GEIAIGKDADLVIFDpKRQERIDVQRLHSRAdwtpyerkkaifPVMTLVRGSVV 404
                                    5689********************8.***************644556666667776699********************9 PP

                   Amidohydro_3 473 y 473
                                    +
  gi|116754418|ref|YP_843536.1| 405 F 405
                                    7 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   5.4e-06     0.032       4      72 ..     106     175 ..     103     185 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.4e-06
                                    H---TT-EEEESS..-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCH CS
                Methyltr_RsmB-F   4 LapqeeetilDlc..aaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkid 72 
                                    L++ +   i+D c   +PG   +++ e  +  g+++  ++++eRl r+ + ++rL v  ++v   D+  i 
  gi|116754418|ref|YP_843536.1| 106 LNLAKRRSIVDFClnGGPGDIESLLREGAAAIGEIFMYEMSEERLARILKEVERLDVL-ATVHAEDGEVIR 175
                                    7777888999*995558****************************************9.888888886654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 3212.22
//
Query:       gi|116754419|ref|YP_843537.1|  [L=160]
Description: hypothetical protein Mthe_1114 [Methanosaeta thermophila PT]
Scores for complete 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-73  245.7   0.0    1.6e-73  245.6   0.0    1.0  1  Adenosine_kin  Adenosine specific kinase


Domain annotation for each model (and alignments):
>> Adenosine_kin  Adenosine specific kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  245.6   0.0   9.1e-78   1.6e-73       1     154 []       6     159 ..       6     159 .. 1.00

  Alignments for each domain:
  == domain 1  score: 245.6 bits;  conditional E-value: 9.1e-78
                                    EEE---TTEEEEEEEESSTTHHHHHHHHHHCCSTTSEEEEEEE--STT-EEEEEESSHHHHHHHHHHHHHH--TTEEEEE CS
                  Adenosine_kin   1 vkiekpeevnvilgqshfiktvedlyealvtsvpgikfglafcEasgkrLvrvegndeelvelavknalaigaghvfvil 80 
                                    v++e+p++ n+ilgqshfikt edlyea++ svpg++fg+af+Easg++Lvr+egnd++l+e+a++n la+g+gh+fvil
  gi|116754419|ref|YP_843537.1|   6 VRMEIPDGSNLILGQSHFIKTAEDLYEAIAGSVPGARFGIAFSEASGDCLVRLEGNDDALKEAAKRNSLALGCGHTFVIL 85 
                                    789***************************************************************************** PP

                                    EEST-HHHHHHHHHHCTTCEEEEEEESSSEEEEEEEETTEEEEEEEEES---SEE--HHHHHHHHHHHHHTTS- CS
                  Adenosine_kin  81 lknafPinvlnaiksvpevvkifaAtanplevivaeteqgrgvlgvvDGfspkgveeeedkkerkellrkigYk 154
                                    ++ afPinvlnaiksv+ev+ if+Atanp+ev+va+teqg g+lgv+DG+spkgve  e+++er++llr++gYk
  gi|116754419|ref|YP_843537.1|  86 IQGAFPINVLNAIKSVQEVCGIFCATANPVEVVVASTEQGSGILGVIDGSSPKGVEGPEKVAERRSLLRRFGYK 159
                                    *************************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); 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: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1215.78
//
Query:       gi|116754420|ref|YP_843538.1|  [L=82]
Description: hypothetical protein Mthe_1115 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.058   11.7   0.7      0.065   11.5   0.7    1.0  1  DUF2070    Predicted membrane protein (DUF2070)
       0.14   12.1   1.0       0.19   11.7   1.0    1.1  1  RseC_MucC  Positive regulator of sigma(E), RseC/MucC


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 ?   11.5   0.7   7.2e-06     0.065     129     178 ..      10      69 ..       6      78 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.2e-06
                        DUF2070 129 kavlpaliqpllailllvly..........fspesfllllllslifalavylfivvvdrp 178
                                    +a+++ + ++l++++++++y           + es++ +l++slif++a y+  v + ++
  gi|116754420|ref|YP_843538.1|  10 RAMALPFQTLLIGAVFFTIYdlftyfghglGAIESAIEALIASLIFMAAYYFTSVALRSK 69 
                                    56666787888888888888*********988899*************999988777665 PP

>> RseC_MucC  Positive regulator of sigma(E), RseC/MucC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.0   2.1e-05      0.19      70     120 ..      11      72 ..       5      77 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.1e-05
                      RseC_MucC  70 vYllPllllilgallgsall...........gssellaalgallglvlgflivrllskrlkk 120
                                    + +lP+ +l++ga+++++             ++s + a++++l++++++++    l+++ ++
  gi|116754420|ref|YP_843538.1|  11 AMALPFQTLLIGAVFFTIYDlftyfghglgaIESAIEALIASLIFMAAYYFTSVALRSKSTE 72 
                                    6789**********999988889999*99988888888999999999999888777777554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); 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: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 623.89
//
Query:       gi|116754421|ref|YP_843539.1|  [L=295]
Description: hypothetical protein Mthe_1116 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.032   14.1  40.3        0.2   11.5  16.3    2.7  3  DUF4013       Protein of unknown function (DUF4013)


Domain annotation for each model (and alignments):
>> DUF4013  Protein of unknown function (DUF4013)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5  16.3   1.1e-05       0.2      50     167 ..      30     147 ..       3     148 .. 0.63
   2 ?   10.3  19.8   2.7e-05      0.48      55     165 ..     134     244 ..     133     245 .. 0.64
   3 ?   -3.7   0.0      0.53   9.5e+03       3      12 ..     262     271 ..     256     284 .. 0.49

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.1e-05
                        DUF4013  50 afvvslvYlliplii.....alltllvalaslaagdsaagallvlallglllalllvllllllfglllpvalarfartgs 124
                                    +++v+l+++l+ + i        ++ +  + + ++++a+  +++++ ++++l+++   l+ll ++ +++++++ +ar+ +
  gi|116754421|ref|YP_843539.1|  30 VIAVGLLFILLFVSIlgtmpE-AFMNIEDVPPEEIMQAFDQNGITIGVYVVLFFV---LALL-VSAFFTAGATGMARSAN 104
                                    334444433333333444421.122233334444455555555555555555555...5555.78888899999999999 PP

                        DUF4013 125 lsaafnfkeilklikkkigkyiialilllvigivlsllaillv 167
                                       + +++e+++  k+ +++++ + +l+l+i+++  l++++l+
  gi|116754421|ref|YP_843539.1| 105 ATGFSSLGEMWEAGKRYCIRLFSVSLLSLIIYALCVLVVSALF 147
                                    9999999*****9988779999999999999999999998886 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 2.7e-05
                        DUF4013  55 lvYlliplii.alltllvalaslaagdsaagallvlallglllalllvllllllfglllpvalarfartgslsaafnfke 133
                                    ++Y+l  l++ al++ ++ l +l++++++   +  +++  +++ +l++ l+l++++++l + +      +slsa   +++
  gi|116754421|ref|YP_843539.1| 134 IIYALCVLVVsALFVPFISLEALSSIAQSPEQIDPGLVALVIAWVLAICLILIVISMAL-AVVSPAIVVDSLSAISGIRA 212
                                    56775555556455555555555555555544444444444444444444444344443.44444445567888888*** PP

                        DUF4013 134 ilklikkkigkyiialilllvigivlsllail 165
                                     +++ + +i ++++ +++ + +++++s++++l
  gi|116754421|ref|YP_843539.1| 213 SMRFFRENIFDVFLLWLVTVGLSMAFSIIGML 244
                                    *****************************987 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 0.53
                        DUF4013   3 sllliiaivl 12 
                                    s+l+i ++  
  gi|116754421|ref|YP_843539.1| 262 SVLVIAPLTT 271
                                    3333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1176  (0.0655921); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); 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):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.42
# Mc/sec: 2093.63
//
Query:       gi|116754422|ref|YP_843540.1|  [L=395]
Description: IS605 family transposase OrfB [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-25   89.1   0.5    5.2e-25   88.0   0.5    1.5  1  OrfB_IS605      Probable transposase
      7e-24   83.6   1.0    2.6e-23   81.7   0.4    2.2  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    1.6e-08   33.9   0.1    3.2e-08   32.9   0.1    1.6  1  HTH_OrfB_IS605  Helix-turn-helix domain
  ------ inclusion threshold ------
      0.055   13.5   0.1       0.11   12.5   0.1    1.5  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.098   12.6   0.7       0.22   11.4   0.7    1.5  1  C1_1            Phorbol esters/diacylglycerol binding domain 
       0.14   12.2   2.1       0.28   11.2   2.1    1.4  1  DZR             Double zinc ribbon
       0.31   10.6   1.9        2.1    7.9   0.0    2.4  2  TF_Zn_Ribbon    TFIIB zinc-binding
       0.36   10.3   5.9        8.3    6.0   5.9    2.3  1  zf-ribbon_3     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 !   88.0   0.5   2.3e-28   5.2e-25       6     117 ..     167     275 ..     162     277 .. 0.96

  Alignments for each domain:
  == domain 1  score: 88.0 bits;  conditional E-value: 2.3e-28
                     OrfB_IS605   6 vevelpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrs 85 
                                     +++++ p ++k +giD+G++ +a+  +++    + ++r++ +   ++++ +++l++ +k+s+n++k ++kl ++h++++
  gi|116754422|ref|YP_843540.1| 167 DQEPETLPATGKSVGIDVGLKSFAVDTDGN---SVENPRFAEKVATKVKNIQRRLSRAMKGSNNREKFKEKLNKVHERIN 243
                                    46678999**********************...*********************************************** PP

                     OrfB_IS605  86 rrrkhllhklathliktlkevgvetLnvgnmk 117
                                    ++r+++lhkl++h +++++ + ve+L+v+++k
  gi|116754422|ref|YP_843540.1| 244 NQRLDFLHKLSRHYVNNYDIICVEDLDVKGLK 275
                                    *****************************998 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.89     2e+03      10      23 ..      38      51 ..      30      54 .. 0.74
   2 !   81.7   0.4   1.2e-26   2.6e-23       1      67 [.     292     358 ..     292     359 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.89
                 OrfB_Zn_ribbon 10 ykakeyGikveevn 23
                                   + ake+Gik+++ +
  gi|116754422|ref|YP_843540.1| 38 NEAKEKGIKLTTYD 51
                                   46999****98876 PP

  == domain 2  score: 81.7 bits;  conditional E-value: 1.2e-26
                 OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNil 67 
                                    ++k++ +l+yka+ +G+k+++v+p++T ++Cs Cgs+++++ls+r ++Cp Cgf++drD+nA++Nil
  gi|116754422|ref|YP_843540.1| 292 WSKFIFMLSYKAESAGRKLIKVDPRNTTQRCSTCGSIVRKELSDRIHECPYCGFSCDRDYNASMNIL 358
                                    99****************************************************************7 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 !   32.9   0.1   1.4e-11   3.2e-08       1      45 [.       1      44 [.       1      46 [. 0.94

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 1.4e-11
                 HTH_OrfB_IS605  1 MvlkaykyrlyPTpeQeeklartfGcvRfVYNkaLaerkeayeee 45
                                   M   +yky + P++  ++kla++++++R+ YN+ L+e +ea e++
  gi|116754422|ref|YP_843540.1|  1 M-IISYKYPIFPDEATQQKLAEALDACRWLYNRLLQELNEAKEKG 44
                                   7.899**********************************998876 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1     5e-05      0.11      46      94 ..     295     345 ..     280     363 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5e-05
                                    HHHHHHHCC.TTTT-EEEEEEE--EEEETTTS-EEECHH.H.HHS-TTTSS CS
                           HypA  46 fafellaegtvlegaeLeieevpvkvrCreCgkefelee.k.alrCpkCgs 94 
                                    f+f l  + + + ++ ++++  + + rC++Cg+ +++e  +   +Cp Cg 
  gi|116754422|ref|YP_843540.1| 295 FIFMLSYKAESAGRKLIKVDPRNTTQRCSTCGSIVRKELsDrIHECPYCGF 345
                                    555555566666666778999999********9999665435668****95 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 ?   11.4   0.7   9.8e-05      0.22      10      40 ..     318     349 ..     313     354 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.8e-05
                                    S--B-TTT-SB--S.SSS-EEEETTT--EE-C CS
                           C1_1  10 qptfCkhCgeflwg.kekqglkCswCkllvHk 40 
                                     +++C++Cg+++++ ++ ++  C  C+++++ 
  gi|116754422|ref|YP_843540.1| 318 TTQRCSTCGSIVRKeLSDRIHECPYCGFSCDR 349
                                    6899********888*************9975 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   2.1   0.00013      0.28      11      41 ..     318     350 ..     312     355 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00013
                            DZR  11 darfCseCgtklkavaa..edrCpsCgekvdpe 41 
                                      + Cs+Cg+ ++++ +   + Cp Cg ++d +
  gi|116754422|ref|YP_843540.1| 318 TTQRCSTCGSIVRKELSdrIHECPYCGFSCDRD 350
                                    557899999999988779999999999999876 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0   0.00093       2.1      11      31 ..     311     331 ..     307     337 .. 0.81
   2 ?    1.0   0.9      0.13     3e+02       2       7 ..     339     344 ..     338     356 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00093
                                    CHEETSTTCEEESSSSBEEEE CS
                   TF_Zn_Ribbon  11 lveDpergelvCtdCGlVled 31 
                                    + +Dp +++ +C+ CG+++  
  gi|116754422|ref|YP_843540.1| 311 IKVDPRNTTQRCSTCGSIVRK 331
                                    678999999********9865 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.13
                                    EETTTT CS
                   TF_Zn_Ribbon   2 kCPnCg 7  
                                     CP+Cg
  gi|116754422|ref|YP_843540.1| 339 ECPYCG 344
                                    599999 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   5.9    0.0037       8.3       2      23 ..     319     344 ..     318     346 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0037
                    zf-ribbon_3   2 tvrCPnCGaplss..ddnv..CpyCG 23 
                                    t+rC+ CG+++++  +d++  CpyCG
  gi|116754422|ref|YP_843540.1| 319 TQRCSTCGSIVRKelSDRIheCPYCG 344
                                    789******66542234444599999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1468  (0.0818785); expected 358.6 (0.02)
Passed bias filter:                      919  (0.0512577); expected 358.6 (0.02)
Passed Vit filter:                       115  (0.00641419); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.42
# Mc/sec: 2794.53
//
Query:       gi|116754423|ref|YP_843541.1|  [L=292]
Description: alpha-L-glutamate ligase [Methanosaeta thermophila PT]
Scores for 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-34  116.6   0.0    2.3e-33  115.4   0.0    1.5  2  RimK            RimK-like ATP-grasp domain
    7.2e-16   58.1   0.0    1.2e-15   57.4   0.0    1.3  1  GSH-S_ATP       Prokaryotic glutathione synthetase, ATP-grasp
    9.4e-08   32.3   0.0    6.2e-07   29.6   0.0    2.0  1  ATP-grasp_3     ATP-grasp domain
    1.6e-06   27.6   0.0      0.036   13.3   0.0    3.0  2  ATPgrasp_YheCD  YheC/D like ATP-grasp
      8e-05   22.0   0.0    0.00011   21.5   0.0    1.2  1  GSP_synth       Glutathionylspermidine synthase preATP-grasp
    0.00024   20.5   0.0      0.061   12.6   0.0    2.1  2  ATPgrasp_ST     Sugar-transfer associated ATP-grasp
  ------ inclusion threshold ------
      0.022   15.2   0.0      0.036   14.5   0.0    1.4  1  Rimk_N          RimK PreATP-grasp domain
       0.11   12.4   0.1        3.6    7.5   0.0    2.4  2  NIL             NIL domain


Domain annotation for each model (and alignments):
>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.2   2.6e+03     131     155 ..      35      59 ..      28      63 .. 0.80
   2 !  115.4   0.0     1e-36   2.3e-33       1     184 [.     101     282 ..     101     285 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.2
                                    HHHHHHHHHHHCT-SEEEEEEEEET CS
                           RimK 131 ekelAikaakamelvvaGvDllrak 155
                                      elA+++   +     GvDl++ +
  gi|116754423|ref|YP_843541.1|  35 ISELAVEIGFDLSFRKGGVDLFDLD 59 
                                    568899999899999999**99876 PP

  == domain 2  score: 115.4 bits;  conditional E-value: 1e-36
                                    HH-HHHHHHHHHHTT-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHH..HHHHHHHGGG--EE CS
                           RimK   1 ardKlkslklLakakikvpntalardeedaekliekiklrfPvvvKsvegsqGikvvlakkeqk..lkqvlealkeailv 78 
                                    a +K+ +   L +a++++p+t ++ ++++a k++e+++     v K ++g  G  + l +  ++  +k++    + a+ +
  gi|116754423|ref|YP_843541.1| 101 AANKFATSMALRRAGVPTPRTVVTSSYDEALKTVERMG---RAVCKPLFGYKGKDIALLRPGDAdlIKDL-LIRRGALYL 176
                                    6799999999***************************7...689************99986543115555.34677899* PP

                                    EEE--SS-SEEEEEEEETTEEEEEEEEE--SSS----TTTT-EEEE----HHHHHHHHHHHHHCT-SEEEEEEEEETTEE CS
                           RimK  79 qeyieeaenediRvlvvddevvaalrrvskeGdFRsnlhrGgvaeklqlseeekelAikaakamelvvaGvDllrakrgl 158
                                    qe+ie+ e +diR +vv++ev +a+ rv+  G++ snl rGg ae+ ++s+e +++A+ a +a++ ++ GvD+l++++g+
  gi|116754423|ref|YP_843541.1| 177 QEFIETPEKRDIRAFVVGEEVAGAIYRVAPPGEWISNLARGGRAERCEISDEIERIAVDANRAVGTMYSGVDMLESEDGM 256
                                    ******************************************************************************** PP

                                    EEEEEESS--SHHHHHHHT--HHHHH CS
                           RimK 159 lvlEvnsspglekiektlgidiakkl 184
                                    +v+Evn  p  ++i   lg+++   +
  gi|116754423|ref|YP_843541.1| 257 MVIEVNGTPSGKGIYSALGVNVGRTI 282
                                    *********************98776 PP

>> GSH-S_ATP  Prokaryotic glutathione synthetase, ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.4   0.0   5.3e-19   1.2e-15      12     162 ..     118     264 ..     109     272 .. 0.88

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 5.3e-19
                                    S--EEEES-HHHHHHHHHHHSSEEEEESS--TTTT-EEE-TT-TTHHHHHHHHTTTTTS-EEEEE--GGGGG-EEEEEEE CS
                      GSH-S_ATP  12 ipktlvskdkeeirafleeqgdvilKPldgkgGegvfrvkksdpnlksilellteegkepviaqrylpeikeGDkRillv 91 
                                    +p+t+v+++ +e  + +e++g+++ KPl g+ G+ +  ++  d++l  i +ll+++g   + +q++++  ++ D R ++v
  gi|116754423|ref|YP_843541.1| 118 TPRTVVTSSYDEALKTVERMGRAVCKPLFGYKGKDIALLRPGDADL--IKDLLIRRGA--LYLQEFIETPEKRDIRAFVV 193
                                    699**************************************99886..8899999998..779***************99 PP

                                    TTEE-SEEEEEE--SS-S---GGGTSCEEEEE--HHHHHHHHHHHHHHHHTT--EEEEEEETT....EEEEEE-S CS
                      GSH-S_ATP  92 dGepigyalaRvpaegevRsnlaaggraeatelterdreiaeelapkLkekGllfvGlDvigd....kltEinvt 162
                                      e  g a+ Rv+  ge  snla ggrae  e++++ ++ia + +   ++ G ++ G+D++++    +++E+n t
  gi|116754423|ref|YP_843541.1| 194 GEEVAG-AIYRVAPPGEWISNLARGGRAERCEISDEIERIAVDAN---RAVGTMYSGVDMLESedgmMVIEVNGT 264
                                    888777.*********************************98765...678*********964222256777754 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   2.8e-10   6.2e-07       1     156 [.     101     263 ..     101     268 .. 0.71

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 2.8e-10
                                    HTSHHHHHHHHTTT.S---..........-EESS--SSSEEEEESS-------B--SS--TTE.............EEEE CS
                    ATP-grasp_3   1 asdKlktykkLkeagvkvP......tkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve......lvqe 68 
                                    a++K++t  +L++agv++P      ++ ea +  e   + v Kp  G  g+ + + + ++++   i+ +        +qe
  gi|116754423|ref|YP_843541.1| 101 AANKFATSMALRRAGVPTPrtvvtsSYDEALKTVERMGRAVCKPLFGYKGKDIALLRPGDADL--IKDLLirrgalYLQE 178
                                    69*****************888764444445555558899*******************8776..3333345677789** PP

                                    ---S.EEEEEEEEE.SSSE....EEEEEEEEEEET....TEEEEEEES----HHHHHHHHHHHHHTTSTT--EEEEEEEE CS
                    ATP-grasp_3  69 fieG.kplSvsllsdgekv....lvlavnrqliekaekefvyaGnvtpietelkeevvelaeevvekleglaGyvGvDlv 143
                                    fie  ++  + + + ge+v    + +a + + i      +  +G+ ++   e ++e++++a ++ +++ g++ y GvD++
  gi|116754423|ref|YP_843541.1| 179 FIETpEKRDIRAFVVGEEVagaiYRVAPPGEWIS-----NLARGGRAERC-EISDEIERIAVDANRAV-GTM-YSGVDML 250
                                    **98334455554445444111133444444444.....44555555433.57889999999999999.554.9****** PP

                                    ESS.SEEEEEEES CS
                    ATP-grasp_3 144 lkdeepyviEvNP 156
                                     ++++ +viEvN 
  gi|116754423|ref|YP_843541.1| 251 ESEDGMMVIEVNG 263
                                    ************6 PP

>> ATPgrasp_YheCD  YheC/D like ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   9.3e-05      0.21      30      69 ..     119     158 ..     101     171 .. 0.89
   2 !   13.3   0.0   1.6e-05     0.036     139     166 ..     196     223 ..     167     277 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9.3e-05
                 ATPgrasp_YheCD  30 PetellesledleemlekyksvylKpanGskGkgilriek 69 
                                    P+t+  +s+++  + +e+ ++ ++Kp  G kGk+i  ++ 
  gi|116754423|ref|YP_843541.1| 119 PRTVVTSSYDEALKTVERMGRAVCKPLFGYKGKDIALLRP 158
                                    99*********************************99887 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 1.6e-05
                 ATPgrasp_YheCD 139 evtgiaaRiagkgsittnlsrGGtalpl 166
                                    ev+g++ R+a++g+ ++nl+rGG+a + 
  gi|116754423|ref|YP_843541.1| 196 EVAGAIYRVAPPGEWISNLARGGRAERC 223
                                    5899********************9765 PP

>> GSP_synth  Glutathionylspermidine synthase preATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0     5e-08   0.00011     187     360 ..      25     203 ..       7     215 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 5e-08
                      GSP_synth 187 eagleteflpiediglde........eegrfvdadgrkiellfkLyPwEwlvedefgeelaeallevrllePawklllsn 258
                                    e g ++ +++i+++ ++             ++d+d   i+ + +  P +  ++ e  + la+    v++++P+ +++   
  gi|116754423|ref|YP_843541.1|  25 ELGASAVMMDISELAVEIgfdlsfrkGGVDLFDLDTLIIRDMGRGAPQDVAFRFEALRSLADLG--VTVINPPDAIVRAA 102
                                    5555666666655544433444443345567888888888888888888888888888888888..999****9999765 PP

                      GSP_synth 259 KalLallWelypghpn...LL.payfeedeeeekgkkyvkKplfgREGanveiveegsevaeekegeygeekviyQeyae 334
                                     ++ + +  +  g p     +  +y e+ ++ e++ + v Kplfg  G+ + ++++g+    + +  + + ++  Qe++e
  gi|116754423|ref|YP_843541.1| 103 NKFATSMALRRAGVPTprtVVtSSYDEALKTVERMGRAVCKPLFGYKGKDIALLRPGDADLIK-DLLIRRGALYLQEFIE 181
                                    444444444444444444455145555555889999********************9999999.77899999999***** PP

                      GSP_synth 335 lpkfdgsypvlgswlvgdeaaGlgiR 360
                                     p+  +    + +++vg+e aG   R
  gi|116754423|ref|YP_843541.1| 182 TPEKRD----IRAFVVGEEVAGAIYR 203
                                    **9655....7899999999997666 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 !   12.6   0.0   2.7e-05     0.061      10      86 ..      92     162 ..      87     175 .. 0.81
   2 !    5.7   0.0    0.0034       7.5     231     267 ..     232     266 ..     225     276 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.7e-05
                    ATPgrasp_ST  10 yNpraefplvddKlkfkelalraglkvpkllgvikeqaeiseleafvkeleegvviKpakgsgGkGilviteredqd 86 
                                    +Np  ++   ++K+ ++  + rag+++p+++++ ++ + ++++e + +      v Kp  g  Gk+i  + + +d+d
  gi|116754423|ref|YP_843541.1|  92 INPPDAIVRAANKFATSMALRRAGVPTPRTVVTSSYDEALKTVERMGR-----AVCKPLFGYKGKDIALL-RPGDAD 162
                                    7999999999*******************8888776666665555444.....569***********988.435555 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0034
                    ATPgrasp_ST 231 laakaaeklpglgylGwDivldeekgplllElNarpg 267
                                    +a+ a    +g  y G+D+   e++  +++E+N +p+
  gi|116754423|ref|YP_843541.1| 232 IAVDANR-AVGTMYSGVDMLESEDG-MMVIEVNGTPS 266
                                    5666666.888999****9655555.*******9976 PP

>> Rimk_N  RimK PreATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.6e-05     0.036       3      94 .]       4      98 ..       1      98 [. 0.91

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.6e-05
                         Rimk_N  3 iaiLsrnpelystrrLveaaekrghevevldplrcylkieaekpevyykgekleefdavipR.i..gasi.tfygtavlrqF 80
                                   ++i  +np+ ++ r +   + + g ++ ++d++++ ++i   + +    g +l ++d  i R +  ga   + ++ + lr +
  gi|116754423|ref|YP_843541.1|  4 LGIVVSNPDDWTARAISMGLAELGASAVMMDISELAVEIGF-DLSFRKGGVDLFDLDTLIIRdMgrGAPQdVAFRFEALRSL 84
                                   57888999*******************************99.88899999************9955444459********** PP

                         Rimk_N 81 emmgvfvlneseAi 94
                                     +gv v+n ++Ai
  gi|116754423|ref|YP_843541.1| 85 ADLGVTVINPPDAI 98
                                   ************98 PP

>> NIL  NIL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0016       3.6       9      36 ..      27      54 ..      23      59 .. 0.93
   2 ?    2.2   0.0     0.071   1.6e+02      32      54 ..     244     265 ..     229     274 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0016
                                   S-S-SS-HHHHHHHHHT-EEEEEEEEEE CS
                            NIL  9 gksavePllshlvrqlglevnIlqGsve 36
                                   g+sav  ++s+l+ + g + ++ +G+v+
  gi|116754423|ref|YP_843541.1| 27 GASAVMMDISELAVEIGFDLSFRKGGVD 54
                                   899************************8 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.071
                                    EEEEEEETTEEEEEEEEEEES-H CS
                            NIL  32 qGsveriqgtpfGqlvielsgsq 54 
                                    + +v+ + +   G +vie+ g++
  gi|116754423|ref|YP_843541.1| 244 YSGVDML-ESEDGMMVIEVNGTP 265
                                    5566655.6778*******9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2036.47
//
Query:       gi|116754424|ref|YP_843542.1|  [L=171]
Description: hypothetical protein Mthe_1119 [Methanosaeta thermophila PT]
Scores for complete 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   17.5   0.7     0.0064   16.5   0.3    1.6  1  CarS-like  CDP-archaeol synthase


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 !   16.5   0.3   3.6e-07    0.0064      40     115 ..      62     139 ..      54     156 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.6e-07
                      CarS-like  40 GrrliGdG..vtyrGtvaGvlvGvlvgliqglleklsilaldssgsvlefvilalllafGallGdavGsfikrrlkie 115
                                    Gr + G     ++ G+++G+++G  +++   +l +    ++++sg +   ++ + ++ + +      Gsfi rr+  e
  gi|116754424|ref|YP_843542.1|  62 GREITGRCrsDAWSGVISGMVSGDQMSIAIAALYDDVLISIYMSGKFAGEMVNGEFIRMDSSGFSESGSFIARRVSSE 139
                                    667777541157*************9999999999999*********************9999999********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 1170.57
//
Query:       gi|116754425|ref|YP_843543.1|  [L=265]
Description: diphthine synthase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.8e-17   62.6   0.0    6.7e-17   62.1   0.0    1.2  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.1   0.0   3.7e-21   6.7e-17       1     212 [.       1     223 [.       1     224 [. 0.76

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 3.7e-21
                   TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealragk 80 
                                    +l++VG+G+ d  +++v++l++++ ad+v+++  ++++++   +++  +l+ +  +    l +   e +    e++r+  
  gi|116754425|ref|YP_843543.1|   1 MLFFVGLGLYDERDISVKGLEIVRCADAVYAEF-YTSRLMGTSIERLEQLYGREIR---MLSRSEIEGEPEWLEHARDR- 75 
                                    689**************************8777.7888887777653233333333...33333444445556666664. PP

                   TP_methylase  81 dVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl....lpglakeeerelea 156
                                    +V+llv+GDP++++t+  l   lra e gi+++vi G  +++a++  +g+  + +g + +v      +g+   + + ++a
  gi|116754425|ref|YP_843543.1|  76 NVALLVGGDPMISTTHLDLR--LRAIEMGIDTRVIHGSNIASAVPGITGLQNYRFGRSATVPfphiVRGKRIVSSTPYNA 153
                                    7******************7..99989**************************************944545556666666 PP

                   TP_methylase 157 llan....gdtlvllkapr.k...laelaelLkea......lyddttpvavveragtedervvrgtleel 212
                                    + +n     +tl+ l+  + +   ++e+a+lL+e        +     ++ ++rag ed  v+ gtl el
  gi|116754425|ref|YP_843543.1| 154 VKDNlrrdLHTLLYLDIQDeRfmcINEAAALLIEVangsgdEDFASNLAVGIARAGSEDMCVRAGTLLEL 223
                                    6666666689999998888549999999999977654322212223357888999999999999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1973.72
//
Query:       gi|116754426|ref|YP_843544.1|  [L=286]
Description: ribulose-1,5-biphosphate synthetase [Methanosaeta thermophila PT]
Scores for complete 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-76  255.8   4.1    3.4e-76  255.6   4.1    1.1  1  Thi4           Thi4 family
    1.7e-06   28.2   0.6    5.4e-06   26.6   0.6    1.9  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    4.8e-05   22.7   0.1      7e-05   22.2   0.1    1.3  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    9.7e-05   21.9   2.5    0.00019   21.0   2.5    1.4  1  FAD_oxidored   FAD dependent oxidoreductase
    0.00062   18.6   0.8    0.00088   18.1   0.8    1.2  1  HI0933_like    HI0933-like protein
    0.00076   18.8   0.0     0.0011   18.3   0.0    1.2  1  FAD_binding_3  FAD binding domain
    0.00094   18.4   3.3     0.0033   16.6   0.4    2.1  2  FAD_binding_2  FAD binding domain
     0.0024   17.0   2.0     0.0056   15.8   0.4    2.0  2  Lycopene_cycl  Lycopene cyclase protein
     0.0043   16.2   0.0     0.0069   15.6   0.0    1.3  1  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
     0.0067   16.4   0.1      0.022   14.8   0.2    1.8  2  NAD_binding_9  FAD-NAD(P)-binding
  ------ inclusion threshold ------
      0.077   12.6   3.8        2.6    7.5   0.4    2.2  2  DAO            FAD dependent oxidoreductase


Domain annotation for each model (and alignments):
>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  255.6   4.1   2.1e-79   3.4e-76       1     235 []      33     263 ..      33     263 .. 0.98

  Alignments for each domain:
  == domain 1  score: 255.6 bits;  conditional E-value: 2.1e-79
                                    HHHHHHHHHHHHHHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTBSEEEEETTTHHHHHHT CS
                           Thi4   1 sraiveryfedllkyaesDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlfsaivvrkpakelLdel 80 
                                    +raive+y+e +lk  + Dv++vGaG++ L aa+ la++ d++v+++e+++s+GGG w+GG++f +ivv+k+a  +Lde 
  gi|116754426|ref|YP_843544.1|  33 TRAIVESYLESFLKCTDVDVALVGAGPANLVAAKRLAEA-DVRVVLFEKRLSVGGGLWGGGMMFPRIVVQKEACRILDEY 111
                                    79*************************************.**************************************** PP

                                    T---EEESSEEEESEHHHHHHHHHHHHHTSTTEEEEESEEEEEEEEETBTEEEEEEEEEHHHHTC..TTTSS.-B-EEEE CS
                           Thi4  81 gikyedegdyvvvkdaalftstllskvlqlanvkllnavaveDlivregegvaGvvinwtlvela..hdtqscvDPlvir 158
                                    +i y + +++++v+d+++++++l++ +++ a++ l+n v+veD+++reg+++ G+vinwt+ ++a  h     vDPl ir
  gi|116754426|ref|YP_843544.1| 112 DIWYREFEEGYYVADSIEVVAKLTAGAID-AGAELINLVSVEDVMIREGDRIVGLVINWTAADMAgiH-----VDPLAIR 185
                                    *****************************.***********************************888.....******* PP

                                    EEEEEE--GSSSTTTTHHHHHH.HHCTTTS-----ECB-HHHHHHHHHHHECEEETTEEE-THHHHHHHT-EB--SB- CS
                           Thi4 159 akvvvdatGhdgeivavvvkki.kleakiekvkgeksldaekaedaivkktrevvpnlyvaGmevaevdganRmGpif 235
                                    a+vv+d tGhd+ +  vv+kki   +  ++ v gek+++a  +e+ +v  trev+p+l+vaGm+++ v  ++RmGpif
  gi|116754426|ref|YP_843544.1| 186 ARVVIDGTGHDAAVCRVVQKKIpGAIVGESGVIGEKPMWAALGEKIVVDATREVYPGLIVAGMAATTVAAGPRMGPIF 263
                                    **********************545667889**********************************************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 !   26.6   0.6   3.3e-09   5.4e-06       2      33 ..      55      86 ..      54      94 .. 0.97

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 3.3e-09
                                   E--SHHHHHHHHHHHCCTEEEEEE-SSSSSSG CS
                  NAD_binding_8  2 vGaGlsGlvaAylLakagfdvlllekrdrlGG 33
                                   vGaG + lvaA +La+a+++v+l+ekr ++GG
  gi|116754426|ref|YP_843544.1| 55 VGAGPANLVAAKRLAEADVRVVLFEKRLSVGG 86
                                   9******************************9 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 !   22.2   0.1   4.3e-08     7e-05       2      65 ..      51     136 ..      50     164 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 4.3e-08
                                    SEEEE--SHHHHHHHHHHHHHTS-EEEEE.........TTHCHHHCSHHHHCHHHHHHHHHHHHH.............HH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxx.............xx RF
                    Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlve.........legtclnggcllskallgvaedaeias.............ev 59 
                                    dv+ +G+GpA l aa++la+a ++v+l+e          +g +++ +++++k+++++ ++++i               ev
  gi|116754426|ref|YP_843544.1|  51 DVALVGAGPANLVAAKRLAEADVRVVLFEkrlsvggglWGGGMMFPRIVVQKEACRILDEYDIWYrefeegyyvadsiEV 130
                                    89**************************8888876777777777777777888888888887766777666655444444 PP

                                    HHCHHH CS
                                    xxxxxx RF
                    Pyr_redox_2  60 vkklnq 65 
                                    v kl++
  gi|116754426|ref|YP_843544.1| 131 VAKLTA 136
                                    444433 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   2.5   1.1e-07   0.00019       1     144 [.      51     194 ..      51     201 .. 0.63

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.1e-07
                   FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaee.....qvvtgiareflerlrqrggarl 75 
                                    Dv  vG+gpa ++AA   a+a+ +v+L e+r  +GG l +g+++ +    ++e           +ref e     ++ + 
  gi|116754426|ref|YP_843544.1|  51 DVALVGAGPANLVAAKRLAEADVRVVLFEKRLSVGGGLWGGGMMFPRIVVQKEacrilDEYDIWYREFEEGYYVADSIEV 130
                                    9*********************************9999988876555533333332222222233333333322222211 PP

                   FAD_oxidored  76 kkrskwntfepevakavleemlaeagvtvllntrlveveke..gkriesvtveskegrktirAkvfiDATg 144
                                     ++   ++   ++ +++++ +  e +v +  + r+v+ + +    ++ ++ v       +irA+v+iD+Tg
  gi|116754426|ref|YP_843544.1| 131 VAKL--TAGAIDAGAELINLVSVE-DVMIREGDRIVGLVINwtAADMAGIHVD----PLAIRARVVIDGTG 194
                                    1222..245555555555544444.6666666666666665322346666663....89999999999998 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.8   5.4e-07   0.00088       2      37 ..      51      86 ..      50      94 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 5.4e-07
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-H CS
                    HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgr 37
                                   dv+ +G+G+A l aA ++a+++ rV+l+ek  ++g 
  gi|116754426|ref|YP_843544.1| 51 DVALVGAGPANLVAAKRLAEADVRVVLFEKRLSVGG 86
                                   899***************************988885 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   6.9e-07    0.0011       1      33 [.      49      81 ..      49      84 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 6.9e-07
                                   EEEEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                  FAD_binding_3  1 etdVlIVGaGpaGlmlallLseaGvrvvlvekr 33
                                   ++dV+ VGaGpa l++a+ L+ea vrvvl ekr
  gi|116754426|ref|YP_843544.1| 49 DVDVALVGAGPANLVAAKRLAEADVRVVLFEKR 81
                                   689***************************997 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   0.4     2e-06    0.0033       1      44 [.      51      93 ..      51     106 .. 0.86
   2 ?    2.6   0.1     0.035        58     142     203 ..     129     197 ..     120     240 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2e-06
                                   SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S- CS
                  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGg 44
                                   Dv  +G+G A L+AA ++aea  +v++ ek  ++gg + w +G+
  gi|116754426|ref|YP_843544.1| 51 DVALVGAGPANLVAAKRLAEADVRVVLFEKRLSVGGGL-WGGGM 93
                                   899***************************99988754.55444 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.035
                                    HHHHHHHHHHHTCTEEEEESEEEEEEEECTT.EEEEEEEEET......TTTCEE....EEEESEEEE-----G CS
                  FAD_binding_2 142 allarlvesarkagvdfqerteadeLivedg.rvtGavvenp......esgrev....rirakavvlatgGfg 203
                                    +++a l ++a +ag ++ +  +++++++++g r++G v++             +    +ira+ v++ tg   
  gi|116754426|ref|YP_843544.1| 129 EVVAKLTAGAIDAGAELINLVSVEDVMIREGdRIVGLVINWTaadmagI----HvdplAIRARVVIDGTGHDA 197
                                    68899999999**************9987666*****999667643333....34555888888888777655 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.4   3.4e-06    0.0056       1      31 [.      51      79 ..      51      87 .. 0.92
   2 ?    0.0   0.0      0.21   3.4e+02     129     141 ..     183     195 ..     168     212 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.4e-06
                  Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlie 31
                                   Dv+++GaGpA+l  A+rl  a+++++vvl e
  gi|116754426|ref|YP_843544.1| 51 DVALVGAGPANLVAAKRL--AEADVRVVLFE 79
                                   9*****************..99999999987 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.21
                  Lycopene_cycl 129 kirarlvvdargl 141
                                     irar+v+d++g 
  gi|116754426|ref|YP_843544.1| 183 AIRARVVIDGTGH 195
                                    69*********93 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 !   15.6   0.0   4.2e-06    0.0069       3      53 ..      50     101 ..      48     104 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.2e-06
                    K_oxygenase   3 lDligiGiGpsnLsLailleevkkelkalflerqpefa...Whpgmllegaelq 53 
                                    +D++ +G+Gp+nL  a +l+e++  ++++ +e++ +++   W  gm+++   +q
  gi|116754426|ref|YP_843544.1|  50 VDVALVGAGPANLVAAKRLAEAD--VRVVLFEKRLSVGgglWGGGMMFPRIVVQ 101
                                    69*****************9999..*********9875555******9998777 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       2.8   4.5e+03      90     104 ..      31      45 ..      18      46 .. 0.79
   2 !   14.8   0.2   1.3e-05     0.022       1      42 [.      53      89 ..      53      96 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.8
                  NAD_binding_9  90 fvpRalyGrYlrdlf 104
                                     ++Ra++  Yl++++
  gi|116754426|ref|YP_843544.1|  31 KITRAIVESYLESFL 45 
                                    578999999999887 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.3e-05
                  NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsep.gagrvw 42
                                   a+vGaGp+ l +++rL++      ++++ lf+++ + g g+ w
  gi|116754426|ref|YP_843544.1| 53 ALVGAGPANLVAAKRLAEA-----DVRVVLFEKRLSvG-GGLW 89
                                   79***************99.....6********76636.9999 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.4    0.0016       2.6       1      35 [.      51      86 ..      51     112 .. 0.89
   2 ?    6.4   0.2    0.0035       5.7     142     227 ..     124     218 ..      96     257 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0016
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSS CS
                            DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiagsg 35
                                   dv+ +G+G + l +A  La++   V+l+ek+  +g g
  gi|116754426|ref|YP_843544.1| 51 DVALVGAGPANLVAAKRLAEADvrVVLFEKRLSVG-G 86
                                   8999****************9899*******8888.4 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0035
                                    EEEHHHHHHHHHHHHHHTT-EEEESECEEEE.EEEETCEEEEE....EECT.EEEE...EEEE..EEE--GGGHHHHHTT CS
                            DAO 142 qvdpakltaalaraaealGveilegtevtgl.eeedgkvwgve....rttp.gend...aada..vVnaaGawsdllgll 210
                                    ++d  +++a l + a ++G+e+++   v+++  +e+++++g+      +   g+ +   a++a  v+  +G+ +   + +
  gi|116754426|ref|YP_843544.1| 124 VADSIEVVAKLTAGAIDAGAELINLVSVEDVmIREGDRIVGLVinwtAADMaGIHVdplAIRArvVIDGTGHDAAVCRVV 203
                                    458889999*********************84445578888888887444446552588444454999999998644333 PP

                                    .CTTTSEEEEEEEEEEEE CS
                            DAO 211 .keldlpispvrgqvlvl 227
                                     k++  p  ++ g++ v+
  gi|116754426|ref|YP_843544.1| 204 qKKI--P-GAIVGESGVI 218
                                    3333..3.5555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2112.91
//
Query:       gi|116754427|ref|YP_843545.1|  [L=145]
Description: hypothetical protein Mthe_1122 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.9e-27   93.4   0.0    1.2e-26   93.1   0.0    1.1  1  UPF0146   Uncharacterised protein family (UPF0146)
  ------ inclusion threshold ------
        0.2   10.4   0.0       0.25   10.1   0.0    1.1  1  Gp23      Major capsid protein Gp23


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 !   93.1   0.0   1.3e-30   1.2e-26       5     111 ..       7     108 ..       4     127 .. 0.86

  Alignments for each domain:
  == domain 1  score: 93.1 bits;  conditional E-value: 1.3e-30
                                    HHHHHHHS-SSEEEEET-TT--HHHHHHHHHS-EEEEE-SS-S....STTEE---SSS--HHHHTTEEEEEEES--TTSH CS
                        UPF0146   5 akkiaeenargkvvEvGiGrkldvaealakrgvdlvatDikekkakegvrivrDDvtdPnleiYkgadliYslRpPaelq 84 
                                    +  +++  ++g+++E+G+G+  dva+++     dl+atDi++ ++ +gv+ vrDD+++P  e+Y+ga+l+Ys+RpP e+q
  gi|116754427|ref|YP_843545.1|   7 IAEFIRSHYTGRIIEIGVGQCGDVARLIP----DLIATDIRPVHV-DGVKTVRDDIFNPSEELYRGASLLYSIRPPIEVQ 81 
                                    6678999*******************996....78*******955.79******************************** PP

                                    HHHHHHHHHHT-EEEEE-BTTB----- CS
                        UPF0146  85 saildvakkvgAaliikpLlgedvvve 111
                                     a+ d+a ++gA+++i+pL +e    e
  gi|116754427|ref|YP_843545.1|  82 IAMGDLALRIGADVLIRPLEDEIADLE 108
                                    ********************9986555 PP

>> Gp23  Major capsid protein Gp23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   2.8e-05      0.25      75     110 ..      11      46 ..       3      59 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 2.8e-05
                                    HCT--SSSB--S-----EEEE--------STTSB-- CS
                           Gp23  75 aagvtsgavtqigpavmgmvrraipqliafdiagvq 110
                                     +   +g + +ig    g v r ip+lia di  v 
  gi|116754427|ref|YP_843545.1|  11 IRSHYTGRIIEIGVGQCGDVARLIPDLIATDIRPVH 46 
                                    556779**************************8664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       200  (0.0111551); expected 358.6 (0.02)
Passed bias filter:                      198  (0.0110436); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1078.77
//
Query:       gi|116754428|ref|YP_843546.1|  [L=342]
Description: radical SAM domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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   80.9   0.0    2.7e-22   79.9   0.0    1.5  1  Radical_SAM   Radical SAM superfamily
    4.1e-10   40.0   0.8    8.2e-10   39.1   0.8    1.5  1  SPASM         Iron-sulfur cluster-binding domain
    0.00036   20.8   0.0    0.00056   20.2   0.0    1.4  1  Fer4_12       4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.016   15.4   0.2       0.47   10.6   0.4    2.3  2  Furin-like_2  Furin-like repeat, cysteine-rich
      0.017   15.2   0.0      0.032   14.4   0.0    1.4  1  Fer4_14       4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.9   0.0   7.5e-26   2.7e-22       9     164 ..       1     147 [.       1     150 [. 0.93

  Alignments for each domain:
  == domain 1  score: 79.9 bits;  conditional E-value: 7.5e-26
                                    S--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   9 lrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritvetngtl 88 
                                    +rC +C++     + +   +ls++e +++++el a+  +  +il+ggepl+ ++f  ++++++++   ++r++++tngtl
  gi|116754428|ref|YP_843546.1|   1 MRCDHCYIDA---NDEMTDELSLDEGIRLIDEL-ADLKIPMLILTGGEPLMSRNFWAYAFHAKEK---NLRCAISTNGTL 73 
                                    59*******8...8*******************.7888**************************9...************ PP

                                    HGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  89 pdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglpGendeeleell 164
                                    +++e++ +l+e+g+ +v ++l++ ++e v+++++  ++   + +++l ++r+ag+k +  r+++ +  n+ ++ +ll
  gi|116754428|ref|YP_843546.1|  74 ITPEVAMLLREAGIRYVGVSLDSSSPE-VHDRFRgVPGAHARAVQGLINARNAGLK-TGLRVTLTR-DNWYDIPALL 147
                                    ***************************.999999999999****************.888888876.6666666655 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.8   2.3e-13   8.2e-10       1      67 [.     239     302 ..     239     311 .. 0.84

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 2.3e-13
                          SPASM   1 CfapsrslfInsdGdVvpCcvdkktyveelklGnireesleeIwnseeyqe...frkskkfplielCrnC 67 
                                    C a+s+ + I++ GdV+pC     ++   ++ Gn+re s+++Iw +   qe   +r + k+ l   C +C
  gi|116754428|ref|YP_843546.1| 239 CSAGSKVANISPRGDVHPC-----QFMPHIIAGNVRERSFRDIWIDNPSQElilIR-NSKKHLKGACGSC 302
                                    99999**************.....35456***************888888866566.5666667779888 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   1.6e-07   0.00056      18      94 ..       2      72 ..       1     108 [. 0.65

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.6e-07
                        Fer4_12 18 sCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdiwlytgy 94
                                   +C+ C+  +  +    +e + +   ++i++l++ +i+ l+l+GGEPl+  n   +   + + ke+++    ++++g+
  gi|116754428|ref|YP_843546.1|  2 RCDHCYIDANDE--MTDELSLDEGIRLIDELADLKIPMLILTGGEPLMSRN---FWAYAFHAKEKNL-RCAISTNGT 72
                                   688888443333..334444556679**********************555...4444555566665.244555555 PP

>> Furin-like_2  Furin-like repeat, cysteine-rich
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.062   2.2e+02      10      40 ..      69      98 ..      59     111 .. 0.75
   2 ?   10.6   0.4   0.00013      0.47      60      93 ..     297     330 ..     286     338 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.062
                   Furin-like_2 10 enGclkckkklfllleregirqiGvclascp 40
                                   +nG l  ++ + +ll+  gir +Gv l+s  
  gi|116754428|ref|YP_843546.1| 69 TNGTL-ITPEVAMLLREAGIRYVGVSLDSSS 98
                                   44544.6788999************998754 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00013
                   Furin-like_2  60 eecescfskdfctkckegfylhkGkclescpegl 93 
                                      c sc   d+c  c+++ + ++G  le+ p  +
  gi|116754428|ref|YP_843546.1| 297 GACGSCSYADLCGGCRQKAFYYRGDILETDPTCM 330
                                    47***********************999988765 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   8.9e-06     0.032      11      89 ..       2      71 ..       1      81 [. 0.67

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8.9e-06
                        Fer4_14 11 sCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekkiwletng 89
                                    C  C+  +  ++e++ + + ++  + +++l + +i    l ltGGePL+    +++     + ke+   ++  + tng
  gi|116754428|ref|YP_843546.1|  2 RCDHCYIDA--NDEMTDELSLDEGIRLIDELADLKI--PMLILTGGEPLMS---RNFWAYAFHAKEKN--LRCAISTNG 71
                                   699999777..5556655566666688877777777..66*********77...45555555555554..555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2585.83
//
Query:       gi|116754429|ref|YP_843547.1|  [L=491]
Description: uroporphyrin-III C-methyltransferase [Methanosaeta thermophila PT]
Scores for complete 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-55  187.7   0.4    5.3e-54  183.4   0.3    2.2  2  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
    4.6e-52  176.7   0.0    7.3e-52  176.0   0.0    1.3  1  HEM4          Uroporphyrinogen-III synthase HemD
  ------ inclusion threshold ------
      0.081   13.3   0.0       0.22   11.9   0.0    1.8  1  Radical_SAM   Radical SAM superfamily
       0.13   12.2   0.0         40    4.2   0.0    3.2  4  DUF2073       Uncharacterized protein conserved in archaea (D


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 !  183.4   0.3   1.2e-57   5.3e-54       1     212 [.       7     216 ..       7     217 .. 0.94
   2 ?    2.1   0.0     0.035   1.6e+02     129     183 ..     332     383 ..     324     397 .. 0.63

  Alignments for each domain:
  == domain 1  score: 183.4 bits;  conditional E-value: 1.2e-57
                   TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealragk 80 
                                    k+ylVG+GpGdpel+Tv++lr+l++advvl d+ +  ++l+dl ae      + gk    +   +eei+e l+e++r+gk
  gi|116754429|ref|YP_843547.1|   7 KVYLVGAGPGDPELITVKGLRLLREADVVLHDRLLNEKLLRDLKAE----IIDVGKAPGKHKLSQEEINELLIEKAREGK 82 
                                    79*******************************7799999999988....57777777788889**************** PP

                   TP_methylase  81 dVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl......lpglakeeerel 154
                                     Vv+l++GDP+++g+g+e++ alr+  agi++ev+PGv+s+ aa+a +gip+t++g +++++      +pg  k++e ++
  gi|116754429|ref|YP_843547.1|  83 IVVRLKGGDPYLFGRGGEEALALRE--AGIPFEVVPGVTSAIAAPALAGIPVTHRGISTALTvvtgheEPG--KDKELDW 158
                                    ********************99999..***************************************65555..5699999 PP

                   TP_methylase 155 eallangdtlvllkaprklaelaelLkea.lyddttpvavveragtedervvrgtleel 212
                                    +al+  g+tlv+l+++ ++ e    L++  l + t p+a++er++++d+r vrgtl+++
  gi|116754429|ref|YP_843547.1| 159 HALARLGGTLVVLMGVGRIRENTSMLLDGgLSPQT-PAALIERGSWPDQRCVRGTLGDI 216
                                    999999*************************9966.*********************97 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.035
                   TP_methylase 129 giplteggevlsvllpglakeeereleallangdtlvllkaprklaelaelLkea 183
                                     + l+e+g++++v+ p+ +  + r l ++l  + +++ll + +  + l++ L+ +
  gi|116754429|ref|YP_843547.1| 332 AQALSERGVNVDVI-PAEY--SSRGLVNALGGFKSVLLLRSAQGSPALLQGLRSS 383
                                    45677778888888.6644..5555555566677777777766666666666555 PP

>> HEM4  Uroporphyrinogen-III synthase HemD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.0   0.0   1.6e-55   7.3e-52       5     232 .]     262     481 ..     258     481 .. 0.93

  Alignments for each domain:
  == domain 1  score: 176.0 bits;  conditional E-value: 1.6e-55
                                    HHHHHTTEEEEE---EECCECCHHHHHHHHHT.....--SEEEE--HHHHHHHHHHHHHTT---HHHHHCSEEESSHHHH CS
                           HEM4   5 ealearGaeplelPlieiepaedraelraalddleagkydwliftSanavealfealkreeedvkalaslkvaavGpaTa 84 
                                    ++ e++G++p+++P i  ++ e ++++++ ++     k ++++ftS+n+ve+++ + +    +v+ +++++vaa+Gp+Ta
  gi|116754429|ref|YP_843547.1| 262 RLAERYGFIPVAAPSISLRALELPHDIKERIE-----KTECVVFTSSNGVEIISRRSD----LVDLIQKKRVAAIGPKTA 332
                                    6789****************999999999998.....888************999998....****************** PP

                                    HHHHHTT---SEE-..SSSHHHHGGGS-.---E.EEEEE-SS.S--HHHHHHHHHTTEEEEEE-SEEEEE-HHHHHHHHH CS
                           HEM4  85 raLeelglrvdlvpseegtaegLaeelaeslag.krvlllrgeiarddlaegLeergaevdevevYetvpaeeepeelke 163
                                    +aL e+g++vd++p+ e++++gL++    +l+g k+vlllr+ ++++ l +gL++ g+ev++v+vYe     +e ++l +
  gi|116754429|ref|YP_843547.1| 333 QALSERGVNVDVIPA-EYSSRGLVN----ALGGfKSVLLLRSAQGSPALLQGLRSSGIEVEDVPVYEV--KGSEDSRLDD 405
                                    **************9.*********....8889999********************************..4556666677 PP

                                    HHHT.T--SEEEESSHHHHHHHHHH-S-HH......HHHCTSEEEEESHHHHHHHHHTT---SEEETS--HHHHHH CS
                           HEM4 164 alka.gevdavvftSpstvrnllellkdeg......delkevkvaaiGptTaealkklglkvdvvaeeptaeglva 232
                                    ++++ + +d+ +ftS stvr l++++++ g      + l+++ v+aiGp Tae l ++g++vd+++e++t eg+++
  gi|116754429|ref|YP_843547.1| 406 LIRRaELIDVFAFTSGSTVRYLMRRSEELGmedhlrRALDSALVVAIGPPTAEVLGEFGVRVDLIPERYTFEGMLE 481
                                    77663666*****************************************************************985 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   4.8e-05      0.22      23      75 ..      59     115 ..      41     179 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.8e-05
                                    HHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC.....C CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....x RF
                    Radical_SAM  23 egrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla.....v 75 
                                     +  + ls+eei e++ e  a+ g+ +v l gg+p l  +  e++++l++       v
  gi|116754429|ref|YP_843547.1|  59 APGKHKLSQEEINELLIEK-AREGKIVVRLKGGDPYLFGRGGEEALALREAGipfevV 115
                                    5677899************.8****************************985555552 PP

>> DUF2073  Uncharacterized protein conserved in archaea (DUF2073)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0    0.0089        40       4      29 ..      65      90 ..      62      94 .. 0.76
   2 ?    3.8   0.0     0.011        50      14      40 ..     174     200 ..     163     202 .. 0.86
   3 ?   -3.8   0.0       2.7   1.2e+04      52      72 ..     339     359 ..     338     363 .. 0.82
   4 ?   -2.3   0.0      0.88     4e+03      51      74 ..     383     409 ..     381     414 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0089
                        DUF2073  4 mtsmekirlildkvkegkivvlEkgL 29
                                   +++ e  +l+++k +egkivv  kg 
  gi|116754429|ref|YP_843547.1| 65 LSQEEINELLIEKAREGKIVVRLKGG 90
                                   455566689***********976665 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.011
                        DUF2073  14 ldkvkegkivvlEkgLtpeeeakliet 40 
                                    + +++e + ++l+ gL+p++ a lie 
  gi|116754429|ref|YP_843547.1| 174 VGRIRENTSMLLDGGLSPQTPAALIER 200
                                    5678899999***************95 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 2.7
                        DUF2073  52 Gieietypkkekdkgllekll 72 
                                    G++++++p++ +++gl++ l 
  gi|116754429|ref|YP_843547.1| 339 GVNVDVIPAEYSSRGLVNALG 359
                                    899999999999999998875 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 0.88
                        DUF2073  51 sGieietypkkek...dkgllekllgk 74 
                                    sGie+e +p  e    + + l+ l+++
  gi|116754429|ref|YP_843547.1| 383 SGIEVEDVPVYEVkgsEDSRLDDLIRR 409
                                    699998766544322367777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (491 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); 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: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 3573.96
//
Query:       gi|116754430|ref|YP_843548.1|  [L=270]
Description: porphobilinogen deaminase [Methanosaeta thermophila PT]
Scores for complete 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  196.1   0.0    6.2e-58  195.7   0.0    1.1  1  Porphobil_deam   Porphobilinogen deaminase, dipyromethane cof
      6e-09   36.2   0.1    1.2e-08   35.2   0.1    1.4  1  Porphobil_deamC  Porphobilinogen deaminase, C-terminal domain


Domain annotation for each model (and alignments):
>> Porphobil_deam  Porphobilinogen deaminase, dipyromethane cofactor binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.7   0.0   6.9e-62   6.2e-58      32     196 ..       2     167 ..       1     173 [. 0.94

  Alignments for each domain:
  == domain 1  score: 195.7 bits;  conditional E-value: 6.9e-62
                 Porphobil_deam  32 tiktkGDkildkpLakiggkglFtkeleeaLlegeidlaVhSlKDlptelpeglelaavlkredprDvlvvks..sleel 109
                                    t++t+GD  ld+pL+ i+g+glF++e++e++l+geidlaVhS+KDlp++ pe+l++aa++kr++p D+l++k+   l++l
  gi|116754430|ref|YP_843548.1|   2 TVRTSGDLFLDRPLHMISGQGLFVREIDERMLSGEIDLAVHSMKDLPSKRPERLRIAAIMKRDSPCDILLTKDgsGLDDL 81 
                                    689*******************************************************************855779**** PP

                 Porphobil_deam 110 pegavvgTsSlRRkaqlkklrpdlevkdlRGnvdtRlrkldegeydaiiLAaAGLkRlgleeri.sevlspeellpavgQ 188
                                    ++gav+gTsS+RR+aql+++rpdl v++lRGn++tRlrkl++geyd+i++A+AG++R+g+  ++  +vl+p  ++p++ Q
  gi|116754430|ref|YP_843548.1|  82 KSGAVIGTSSMRRAAQLRRARPDLVVRSLRGNLQTRLRKLHAGEYDGIVIAEAGVQRMGY--HLgYKVLDPGFFVPSPNQ 159
                                    ***********************************************************4..333557************ PP

                 Porphobil_deam 189 Galavevr 196
                                    G++av   
  gi|116754430|ref|YP_843548.1| 160 GTIAVVSV 167
                                    ****9865 PP

>> Porphobil_deamC  Porphobilinogen deaminase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.1   1.4e-12   1.2e-08       4      71 ..     188     255 ..     186     256 .. 0.84

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 1.4e-12
                                    HHHHHHHHHHTT--TTSSEEEEEEEETTE.EEEEEEEE-TTS..S-EEEEEEEE...-GGGHHHHHHHHHH CS
                Porphobil_deamC   4 vlaERallkeLeGGCsvPiGvyaeveaneelkLkglvlsldglksaveeaeakg...eleeaeelGkklae 71 
                                     ++ER +++  +GGC vP +v+a+  +++ +  ++ +ls+dg++  + + e +     le ae +G +l e
  gi|116754430|ref|YP_843548.1| 188 TMVERRIMEVVGGGCLVPMAVFARHLGDR-IHVTAEILSKDGER--FVRLEDTVprdGLESAERIGRRLLE 255
                                    689*********************99877.************88..5555555544668999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       218  (0.0121591); expected 358.6 (0.02)
Passed bias filter:                      192  (0.0107089); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1932.27
//
Query:       gi|116754431|ref|YP_843549.1|  [L=429]
Description: glutamate-1-semialdehyde aminotransferase [Methanosaeta thermophila PT]
Scores for 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-67  225.4   0.0    1.2e-66  225.0   0.0    1.0  1  Aminotran_3    Aminotransferase class-III
  ------ inclusion threshold ------
       0.11   11.7   0.0       0.13   11.5   0.0    1.3  1  Aminotran_1_2  Aminotransferase class I and II


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.0   0.0   1.4e-70   1.2e-66       9     375 ..      41     398 ..      35     423 .. 0.89

  Alignments for each domain:
  == domain 1  score: 225.0 bits;  conditional E-value: 1.4e-70
                                    SCEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT-..S CS
                    Aminotran_3   9 lllvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapkgld 88 
                                     ++ +++aeG yl+d+dg+ ++D   ++ +++lGh++P+v+  v+eq++  ++     + ++  ++lae ++++ p  ++
  gi|116754431|ref|YP_843549.1|  41 YPFYVKRAEGPYLWDEDGNSFIDYCLAYGPMILGHRNPEVMRKVEEQIERGWLYG---TPTALEVELAERIISHYPS-IE 116
                                    55899**********************************************9887...77788899**********9.** PP

                                    EEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-TTBGGGT CS
                    Aminotran_3  89 kvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlkypdeevl 168
                                    ++ ++ +G+eA+++Al++ar        t k ki++++g+fHG     l  +gs  +  t   p + +v+   ++ ++ +
  gi|116754431|ref|YP_843549.1| 117 MIRFVSTGTEATMAALRIARG------FTGKDKIVKIEGGFHGAHDSVLVKAGS--GATTIGVPDSKGVPADTAKNTVLV 188
                                    *********************......***************************..555555566777777777778999 PP

                                    B-HHHHHHHHHHHHHHHH.CHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTT..TTTSSSS CS
                    Aminotran_3 169 keneeeeaalleeleale.kkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEvqtGf..GrTGklf 245
                                    ++n+         ++a+e +  +d+vaAvi+Ep+ g+ G v + +++l+++r ++++hd+lli+DEv tGf  +  G   
  gi|116754431|ref|YP_843549.1| 189 PYND---------IQAMEaALREDDVAAVIMEPVLGNIGPVLPMDGYLEGVRRITEEHDALLIFDEVITGFrlALGG--- 256
                                    9999.........999998999*************************************************877788... PP

                                    GGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTS...B--TTTT-HHHHHHHHHHHHHHHHTTHHHHHHHHHH CS
                    Aminotran_3 246 AlehagvspDlmtlaKaltgGlplsavlataevmqalapgs...hgsTfgGnplacavalavleiieeekllenaqelga 322
                                    A  ++ v +D++tl+K ++gG+p+ av +++e+m+ +ap++   +++Tf G p+ +a+ la+l+i+e+  +l++++e+g+
  gi|116754431|ref|YP_843549.1| 257 AQSYYRVRADITTLGKIIGGGFPIGAVGGRREIMENVAPQGgiyQAGTFNGSPVSMAAGLATLDILERG-VLDRINEMGS 335
                                    99999**********************************999***********************9985.7899****** PP

                                    HHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTC...........HHHHHHHHHCTEE-E CS
                    Aminotran_3 323 alkegLeelqkkyevikevRgkGlmiaielkeeaevke...........keilkkakekGvlil 375
                                    +l++g +++ ++ +   +v g+  m+ + ++ +  ++             +++ +++e+G+ + 
  gi|116754431|ref|YP_843549.1| 336 YLRKGISDIVEDLKLDYSVSGVASMFKV-FFGPLPRNYsealrcdkegyLRFFWRMLEAGIFLT 398
                                    *********9988777788888888877.66666655555666666666666666666666655 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 ?   11.5   0.0   1.4e-05      0.13     129     237 ..     190     287 ..      76     404 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.4e-05
                                    EE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHH.HHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGS CS
                  Aminotran_1_2 129 hldlealeealkeapegnkktkvilvesphNPtGtvatlee.leklldlakkynlllfvDeaYagfvfgsldavatranv 207
                                     +d++a+e+al+e+      +  ++ e +  + G v++ +  le + ++++++ +ll++De+  gf +   +a++ +  v
  gi|116754431|ref|YP_843549.1| 190 YNDIQAMEAALRED-----DVAAVIMEPVLGNIGPVLPMDGyLEGVRRITEEHDALLIFDEVITGFRLALGGAQS-YYRV 263
                                    47**********95.....4589***************98636779999*************9988777334444.5555 PP

                                    TTSTTEEEEEESSSTTSSGGG-EEEEEEEH CS
                  Aminotran_1_2 208 eeepnllivgslsKafGlaGeRvGyilgna 237
                                     +++      +l+K  G  G+ +G++ g  
  gi|116754431|ref|YP_843549.1| 264 RADIT-----TLGKIIG-GGFPIGAVGGRR 287
                                    54444.....5555555.355555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       250  (0.0139439); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 3124.64
//
Query:       gi|116754432|ref|YP_843550.1|  [L=392]
Description: hypothetical protein Mthe_1127 [Methanosaeta thermophila PT]
Scores for complete 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-120  400.8   0.3   6.4e-120  400.7   0.3    1.0  1  DUF111    Protein of unknown function DUF111
  ------ inclusion threshold ------
      0.027   14.3   0.0      0.076   12.8   0.0    1.8  1  IF2_N     Translation initiation factor IF-2, N-terminal regi


Domain annotation for each model (and alignments):
>> DUF111  Protein of unknown function DUF111
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  400.7   0.3  7.1e-124  6.4e-120       1     372 [.       4     375 ..       4     376 .. 0.98

  Alignments for each domain:
  == domain 1  score: 400.7 bits;  conditional E-value: 7.1e-124
                         DUF111   1 lyldcssGisGDmllgALldlgadkeeleealeklgleeveleiekvkksgisatkvdveeeehehehrslaeieeiiea 80 
                                    l++d+++G+sGDm+lgAL+dlgad e++++a+e++g+   +le+++ +  +i+a++v+v++   +++ rsl    +i++a
  gi|116754432|ref|YP_843550.1|   4 LLFDPYCGASGDMILGALIDLGADLEYVRSAVESVGC---RLEVNERRFDHIRAIRVKVIS---DKSFRSLGGAIDILKA 77 
                                    689********************************96...9******************76...8999************ PP

                         DUF111  81 aslsekvkekalaiferlaeAeakvhgvpleevhfhEvGavDaivdivgaalaldeLgvekvvasplalGsGtvrcahGi 160
                                    ++l++++ e+al+i++++a+Ae+kvhgv+ e+  fhE+G++Da++di g ++a+++L+v+++++ + ++G+G   ++hG+
  gi|116754432|ref|YP_843550.1|  78 SALTSRALERALRILDIMASAESKVHGVDRENARFHEMGSLDALADIAGSCAAMESLDVKRILSIAPSVGGGITDTSHGM 157
                                    ******************************************************************************** PP

                         DUF111 161 lPvPaPAvlellkelklkl..gevegElvTPTGaAilaalaeefg.slpamkvekiGyGaGkrdleeipnvlRvlleeee 237
                                    lPvPaPA+le+l+++++    g+v++El+TPTGaAilaa +++f  + p++ +e++GyGaG+r++  +pn+lR++l+e  
  gi|116754432|ref|YP_843550.1| 158 LPVPAPATLEILRSHRIPWrgGPVAHELLTPTGAAILAASVDTFLdHHPEIVTERVGYGAGSREI-GMPNLLRAILGEIP 236
                                    **************99998999**********************98999****************.9**********9** PP

                         DUF111 238 eelekeevvvletniDDlspevlgyvlerLleaGAlDvfltpilmKKgRpavllsvlckeedaeeleellfretttlGvR 317
                                    +++++++vv++etn+DD+++e+lg++++ L+++GAlDv+++p++mKKgR + ++s++++e+da++l+++l+ret++lGvR
  gi|116754432|ref|YP_843550.1| 237 HHMQHDRVVQIETNVDDVTGEILGSLIDMLMKEGALDVTVVPAVMKKGRSGSVISIISRENDARKLSAVLMRETGSLGVR 316
                                    ******************************************************************************** PP

                         DUF111 318 ese.verlvlereietvetelgevrvKva...eevvkvkpEyedvkkiAeetglplkev 372
                                     ++  +rl++er+ie+ve+ +++v vK++   +e+++vkpE++ +++iAee ++p+k++
  gi|116754432|ref|YP_843550.1| 317 VFPaLHRLIAERRIESVEVMGRSVPVKIGsigGEIISVKPEHDVCRRIAEELNIPVKDI 375
                                    ***9*************************99666**********************998 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 ?   12.8   0.0   8.5e-06     0.076       9      29 ..     364     383 ..     362     387 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.5e-06
                          IF2_N   9 LAkeLgvkskevikkLfkelG 29 
                                    +A+eL++++k++i+ + +e+G
  gi|116754432|ref|YP_843550.1| 364 IAEELNIPVKDIIRIA-SEKG 383
                                    8**************9.7688 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); 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: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2982.39
//
Query:       gi|116754433|ref|YP_843551.1|  [L=170]
Description: hypothetical protein Mthe_1128 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1331.05
//
Query:       gi|116754434|ref|YP_843552.1|  [L=177]
Description: deoxyuridine 5'-triphosphate nucleotidohydrolase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-11   42.3   0.0    7.7e-11   41.8   0.0    1.2  1  dUTPase   dUTPase
  ------ inclusion threshold ------
      0.049   12.4   0.0      0.083   11.7   0.0    1.5  1  DCD       2'-deoxycytidine 5'-triphosphate deaminase (DCD)


Domain annotation for each model (and alignments):
>> dUTPase  dUTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   0.0   8.6e-15   7.7e-11      29     106 ..      85     162 ..      76     176 .. 0.89

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 8.6e-15
                                    TEEEEEEEEEEEE--TTEEEEEEE-HHHHHHHEEEEEEEEETTBTSEEEEEEEE-SSS-EEE-TT-EEEEEEEEEBEC CS
                        dUTPase  29 getvlvptdisiklpdglaalilpRSglaakglivvpgvidsdyrGevkvvlfnltkkdvkikkgdRiAqLifarilt 106
                                    ++ +lv+++  +k+p +++a+ lpRS+l + g + +  ++d  y+G  +  l++++   ++ikk++R+ qL+f+ ++ 
  gi|116754434|ref|YP_843552.1|  85 QGAYLVTFNEIVKVPLDMMAFALPRSSLLRCGATLESAIWDPGYNGRSQSLLVVHNPHGIRIKKNARLMQLVFITMKS 162
                                    78899********************************************99**********************98876 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 ?   11.7   0.0   9.3e-06     0.083      59     168 ..      64     165 ..      15     176 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.3e-06
                            DCD  59 aekleelklheldLtegavlekgcvYivplleslaLpadlsaaanpksstGRlDvftRvitdkgeefdeveagYkGpl.y 137
                                    +++++e +  ++   e + le+g+ Y+v ++e +++p d+ a a p+ss  R        t +++ +d    gY+G+   
  gi|116754434|ref|YP_843552.1|  64 ERRVAETEAVQFGGDEWVFLEQGA-YLVTFNEIVKVPLDMMAFALPRSSLLRCGA-----TLESAIWD---PGYNGRSqS 134
                                    566777777777778888999996.************************877653.....44555555...677776514 PP

                            DCD 138 leisprsFsilvrkGsrLsqirfrrgeakls 168
                                    l ++ +   i+++k  rL q+ f + +++++
  gi|116754434|ref|YP_843552.1| 135 LLVVHNPHGIRIKKNARLMQLVFITMKSAAE 165
                                    5677778888888888888888877666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1303.17
//
Query:       gi|116754435|ref|YP_843553.1|  [L=107]
Description: hypothetical protein Mthe_1130 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); 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: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 830.97
//
Query:       gi|116754436|ref|YP_843554.1|  [L=173]
Description: hypothetical protein Mthe_1131 [Methanosaeta thermophila PT]
Scores for complete 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-07   30.9   0.2      5e-07   30.6   0.2    1.1  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 !   30.6   0.2   2.8e-11     5e-07       5     145 .]      24     165 ..      20     165 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 2.8e-11
                  ATC_hydrolase   5 eaail.valyealkkeigkeeakeiirkalerlgkergkklaekakakkdkadvekflalyseifekenalkfevlee.d 82 
                                    + +++ + ++ ++++++g ++a ei  ++++ + k ++++l+  +   +  +++   + +  ++  +    +fe+ ++ d
  gi|116754436|ref|YP_843554.1|  24 SYRAVdGLWFMKVEERYGFDTALEIDDDVWRVMPKIQARALKSIMNESNGLESLARCFTA--KLSLE----EFEFASTcD 97 
                                    556777999*********************9999*******9999977777777777665..45555....69***9988 PP

                  ATC_hydrolase  83 kdeleidvtrCpyceawkkeGlpel....gkllC.eiDkavaeginpkvklertktlaeGgdcCdfrf 145
                                        ++ vtrCp++e++++ G +el    g  +C    +++a++++  +  +r   + +G++ C++ f
  gi|116754436|ref|YP_843554.1|  98 GRCARFVVTRCPWHEIMVRAGRAELnervGSRICwSELEVWASEFGDGIVPRRDRRICRGDESCEIEF 165
                                    88888****************98642222888997777899999999999999***********9866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 1440.05
//
Query:       gi|116754437|ref|YP_843555.1|  [L=328]
Description: hypothetical protein Mthe_1132 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00025   20.6   0.1     0.0023   17.5   0.0    2.1  2  Lactamase_B_2  Beta-lactamase superfamily domain
     0.0058   16.5   0.1      0.017   15.0   0.1    1.7  2  Lactamase_B_3  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.022   14.8   2.7       0.12   12.4   2.7    2.0  1  Lactamase_B    Metallo-beta-lactamase superfamily
      0.068   13.1   0.1      0.068   13.1   0.1    1.7  2  RMMBL          Zn-dependent metallo-hydrolase RNA specificity


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   5.1e-07    0.0023      27     166 ..      49     158 ..      33     180 .. 0.80
   2 ?    0.6   0.0     0.075   3.4e+02     178     200 ..     273     295 ..     242     296 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 5.1e-07
                                    -..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEECSTTEEEE CS
                  Lactamase_B_2  27 elppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeepavnvheldwgesfelgdggleit 106
                                    e  + da l+thaH DH  g   +r   p   + +a+++++  le +            +   +++g+ ++++  g+e++
  gi|116754437|ref|YP_843555.1|  49 E--QPDAYLITHAHSDHH-GSSAMRS--P---RAIASRETALALEIRHE-------RSYAGSIFEIGDVLDIN--GVELR 111
                                    4..789***********9.9999999..4...36899999999999933.......356677899*******8..799** PP

                                    EEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HHHHHHHCT-SEEEEE-S- CS
                  Lactamase_B_2 107 atparhksgrrldrnagdtlGlriegggkrvyyigDtgyipeeigerlggadlllldita 166
                                    + p rh+ g          + ++  + g rv+ +gD++ +       l ++dll+ ++++
  gi|116754437|ref|YP_843555.1| 112 TYPTRHTIGS--------SAFYWENSLGVRVLVTGDVKDYR-----SLPKCDLLVAEANY 158
                                    ******9999........56666667888888999988444.....67778888888775 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.075
                                    ---STSHHHHCTTSSSSEEEEES CS
                  Lactamase_B_2 178 HltpeeaveaaadlgakrlvliH 200
                                    Hl+ ++ ++++++++++ +++ H
  gi|116754437|ref|YP_843555.1| 273 HLDFRGIMRMLDHVSPEAVIFYH 295
                                    9999****************999 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 !   15.0   0.1   3.8e-06     0.017      31      99 ..      45     124 ..      24     152 .. 0.67
   2 ?    0.4   0.0      0.12   5.3e+02       5      22 ..     119     137 ..     117     162 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.8e-06
                  Lactamase_B_3  31 eppaeeaDlvlisqaledHahletlkqlaenvkvlee......................geslevggleiravatshdav 88 
                                     p +e++D+ li++a++dH    ++++    ++ +++                      g+ l+++g+e+r+ +t h+  
  gi|116754437|ref|YP_843555.1|  45 SPGREQPDAYLITHAHSDHHGSSAMRS----PRAIASretalaleirhersyagsifeiGDVLDINGVELRTYPTRHT-- 118
                                    34459***************9999999....77777755566666666666665555555567777777777777773.. PP

                  Lactamase_B_3  89 ggsergenngf 99 
                                          + ++f
  gi|116754437|ref|YP_843555.1| 119 -----IGSSAF 124
                                    .....233444 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.12
                  Lactamase_B_3   5 lghnsflleta.garilvD 22 
                                    +g+++f +e + g+r+lv 
  gi|116754437|ref|YP_843555.1| 119 IGSSAFYWENSlGVRVLVT 137
                                    699*******88****995 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   2.7   2.7e-05      0.12      42     162 ..      48     151 ..      42     176 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.7e-05
                                    GGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEE CS
                    Lactamase_B  42 pkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrr 121
                                     +++da ++TH+H+DH G  +    ++ +      + +  +++ +a                 ++++ + +  ++ g  +
  gi|116754437|ref|YP_843555.1|  48 REQPDAYLITHAHSDHHGSSAMRSPRAIASRETALALEIRHERSYA-----------------GSIFEIGDVLDINGVEL 110
                                    6899999*********999876666666666655555555555555.................45677788888888888 PP

                                    EEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC CS
                    Lactamase_B 122 alyvtggpghghghgvveygggkvlftGDallagetgridl 162
                                    ++y+t +   ++  +   + g +vl+tGD+   ++ ++ dl
  gi|116754437|ref|YP_843555.1| 111 RTYPTRHTIGSSAFYWENSLGVRVLVTGDVKDYRSLPKCDL 151
                                    88888888888888888889999999999876666666666 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 ?   -4.6   0.7         4   1.8e+04      14      19 ..      58      63 ..      54      65 .. 0.74
   2 ?   13.1   0.1   1.5e-05     0.068      10      38 ..     267     295 ..     261     311 .. 0.91

  Alignments for each domain:
  == domain 1  score: -4.6 bits;  conditional E-value: 4
                          RMMBL 14 SgHadk 19
                                    +H+d+
  gi|116754437|ref|YP_843555.1| 58 HAHSDH 63
                                   799997 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 1.5e-05
                          RMMBL  10 eidfSgHadknellelirklkprnvilvH 38 
                                     i +S H d++++++++ +++p+ vi+ H
  gi|116754437|ref|YP_843555.1| 267 RIRLSDHLDFRGIMRMLDHVSPEAVIFYH 295
                                    5789***********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 2675.39
//
Query:       gi|116754438|ref|YP_843556.1|  [L=98]
Description: thioredoxin [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-24   85.3   0.0    2.7e-24   85.1   0.0    1.0  1  Thioredoxin    Thioredoxin
    1.1e-08   35.3   0.0      8e-05   22.9   0.0    2.1  2  Thioredoxin_8  Thioredoxin-like
    4.1e-08   33.6   0.0    1.3e-06   28.8   0.0    2.0  1  Thioredoxin_2  Thioredoxin-like domain
    3.3e-06   27.1   0.0    3.7e-06   26.9   0.0    1.1  1  TraF           F plasmid transfer operon protein
    6.5e-05   22.9   0.0    8.6e-05   22.5   0.0    1.2  1  Thioredoxin_3  Thioredoxin domain
    0.00021   21.0   0.1    0.00026   20.8   0.1    1.1  1  Thioredoxin_9  Thioredoxin
    0.00032   20.4   0.0     0.0033   17.2   0.0    1.9  2  Redoxin        Redoxin
     0.0019   18.1   0.0     0.0025   17.7   0.0    1.4  1  AhpC-TSA       AhpC/TSA family
     0.0056   16.4   0.0      0.007   16.1   0.0    1.2  1  KaiB           KaiB domain
      0.006   17.0   0.0     0.0082   16.5   0.0    1.1  1  DUF836         Glutaredoxin-like domain (DUF836)
  ------ inclusion threshold ------
      0.019   14.8   0.0       0.15   11.8   0.0    1.9  2  DSBA           DSBA-like thioredoxin domain
      0.034   14.1   0.0      0.043   13.8   0.0    1.2  1  HyaE           Hydrogenase-1 expression protein HyaE
      0.052   14.0   0.1       0.06   13.8   0.1    1.1  1  DUF4174        Domain of unknown function (DUF4174)
      0.066   13.4   0.1       0.13   12.4   0.1    1.7  1  Thioredoxin_7  Thioredoxin-like
       0.15   12.1   0.0       0.18   11.8   0.0    1.1  1  DUF1198        Protein of unknown function (DUF1198)
       0.16   12.2   0.0       0.27   11.5   0.0    1.4  1  Glutaredoxin   Glutaredoxin
       0.18   12.0   0.1       0.87    9.7   0.0    1.7  2  Thioredoxin_4  Thioredoxin


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 !   85.1   0.0   2.5e-27   2.7e-24      12     102 ..       5      95 ..       3      96 .. 0.97

  Alignments for each domain:
  == domain 1  score: 85.1 bits;  conditional E-value: 2.5e-27
                                    HHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTEEEEEEESS CS
                    Thioredoxin  12 eevakekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkngkevkkyega 91 
                                    eev++ +k+vl++F+A+wCg+C++ +P +e+l +++ +++ + k+dvd n +la++y++  +Pt++l k+gkev++  g 
  gi|116754438|ref|YP_843556.1|   5 EEVEDLDKPVLMDFFAEWCGPCRMQTPIMEELDKKYGGRIEIKKIDVDRNIELANRYNIMVVPTIILEKDGKEVRRWLGV 84 
                                    5789999************************************************************************* PP

                                    -HHHHHHHHHH CS
                    Thioredoxin  92 rekeklaaflk 102
                                     +ke+l + ++
  gi|116754438|ref|YP_843556.1|  85 TSKEELSSAID 95 
                                    *******9987 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   7.6e-08     8e-05       2      46 ..      12      54 ..      11      56 .. 0.89
   2 !   12.5   0.1   0.00013      0.14      69      94 ..      52      76 ..      47      77 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 7.6e-08
                                   SEEEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SS- CS
                  Thioredoxin_8  2 kvvlLyfgaswcppckaftpklkelyeklkkkkkveivyvsldkk 46
                                   k vl+ f+a+wc pc+  tp + el +k+    ++ei  + +d++
  gi|116754438|ref|YP_843556.1| 12 KPVLMDFFAEWCGPCRMQTPIMEELDKKYG--GRIEIKKIDVDRN 54
                                   89***************************9..8888888877776 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00013
                                   T-HHHHTT-S--TT-SEEEEE-TT-B CS
                  Thioredoxin_8 69 kkrnklkkkynvkaiPtlvvldknge 94
                                   +++ +l+++yn++ +Pt ++l k+g+
  gi|116754438|ref|YP_843556.1| 52 DRNIELANRYNIMVVPT-IILEKDGK 76
                                   5788*************.88899886 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   1.2e-09   1.3e-06       5     108 ..      11      93 ..       7      94 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 1.2e-09
                  Thioredoxin_2   5 gkpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPti 84 
                                     kpvl++f +++C+ C+     ++el    ++     ++    +++ +i+            ++n ela++y++  +Pti
  gi|116754438|ref|YP_843556.1|  11 DKPVLMDFFAEWCGPCRMQTPIMEEL---DKK-----YGGR--IEIKKIDV-----------DRNIELANRYNIMVVPTI 69 
                                    59***************988888888...444.....5555..33333333...........456689***********9 PP

                  Thioredoxin_2  85 v.fldgkeivarlpGyvpaeeleal 108
                                    +   dgk +v r+ G +++eel+ +
  gi|116754438|ref|YP_843556.1|  70 IlEKDGK-EVRRWLGVTSKEELSSA 93 
                                    9345666.99***********9865 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   3.5e-09   3.7e-06     132     203 ..      14      76 ..      10      94 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 3.5e-09
                           TraF 132 gLlfFyrgkcpyceaqapilqafadkyg..levraVsvdgrplpelpnarvdkgqaarlgvkrtPalvlvdpks 203
                                     L+ F+++ c+ c++q pi++++ +kyg  +e++ ++vd+++   l+n         r+++  +P+++l +  +
  gi|116754438|ref|YP_843556.1|  14 VLMDFFAEWCGPCRMQTPIMEELDKKYGgrIEIKKIDVDRNIE--LAN---------RYNIMVVPTIILEKDGK 76 
                                    5888***********************555***********99..999.........***********987775 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   8.2e-08   8.6e-05      10      74 ..      23      93 ..      16      95 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 8.2e-08
                                   STTCHHHHHHHHHHCHCCTCECEEECC..TTHHHH.HHCT-SSSSEEECT....TCEEEESS---CCHHHHH CS
                  Thioredoxin_3 10 CakCpklekavkeaaaekgikaevekv..tdfeei.ekygVmsvPalvid....gkvvvsGkvpseeeirkl 74
                                   C  C+  + +++e+ ++ g  +e++k+    + e+ ++y++m vP+++++    ++ ++ G v s+ee+ + 
  gi|116754438|ref|YP_843556.1| 23 CGPCRMQTPIMEELDKKYGGRIEIKKIdvDRNIELaNRYNIMVVPTIILEkdgkEVRRWLG-VTSKEELSSA 93
                                   778886666677777777877766665437777889*************999777789***.*****99765 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   2.5e-07   0.00026      49     115 ..      19      82 ..       6      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.5e-07
                                    --TT-HHHHHHHHHHHHHH.HH-TTEEEEEE-HHHHHHHTTTTTT-SS--SSEEEEE-TT--EEEEEE CS
                  Thioredoxin_9  49 tedwCgDaavnvPvlakia.elnpnievkillrdenlelmdqyltngaraiPtliildeegeelgvwg 115
                                     ++wCg +++  P+++++  ++  +ie+k +  d+n el ++y       +Pt+i l+++g+e+  w 
  gi|116754438|ref|YP_843556.1|  19 FAEWCGPCRMQTPIMEELDkKYGGRIEIKKIDVDRNIELANRYNI---MVVPTII-LEKDGKEVRRWL 82 
                                    578***************8467899******************66...8899865.678889998995 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   3.1e-06    0.0033      28      59 ..      11      41 ..       6      43 .. 0.91
   2 ?    1.4   0.0      0.22   2.4e+02      92     143 ..      52      93 ..      47      98 .] 0.67

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.1e-06
                                   TSEEEEEEESTTT-HHHHHTHHHHHTHHHHHH CS
                        Redoxin 28 gkkvvvnfvpgafcPtCsaehpyleklaellk 59
                                   +k+v++ f++  +c++C+ ++p +e+l+++++
  gi|116754438|ref|YP_843556.1| 11 DKPVLMDFFAE-WCGPCRMQTPIMEELDKKYG 41
                                   58899999999.****************9986 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.22
                                    -TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEEESSSCHTSTTSH CS
                        Redoxin  92 DgsaaftkalGlrleedaseglrtpryavidedgkvvylevepepeteesna 143
                                    D++ +++  ++  +            ++++ +dgk v + +++ +++e s+a
  gi|116754438|ref|YP_843556.1|  52 DRNIELANRYN--I--------MVVPTIILEKDGKEVRRWLGVTSKEELSSA 93 
                                    66666666666..3........344578889999999888888875555544 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   2.4e-06    0.0025      19      69 ..       3      53 ..       1      92 [. 0.73

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.4e-06
                                   ECHHHTT..SEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSS CS
                       AhpC-TSA 19 slsdykg..kpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvds 69
                                   s++++++  kpv+  f+++ wc +C+ + p +++l +++    +e+  + vd 
  gi|116754438|ref|YP_843556.1|  3 SFEEVEDldKPVLMDFFAE-WCGPCRMQTPIMEELDKKYGG-RIEIKKIDVDR 53
                                   6667744449*********.**************9999873.45666555555 PP

>> KaiB  KaiB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   6.6e-06     0.007      22      56 ..      36      70 ..      27      94 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.6e-06
                                   CCCHCTTTEEEEEEETTTSHCHHCCTCEESCCCCC CS
                           KaiB 22 eeedlgfqyeLqvvdvleqPelaeedrlvatPaLi 56
                                   ++++ g+++e++ +dv  + ela  + ++++P+ i
  gi|116754438|ref|YP_843556.1| 36 LDKKYGGRIEIKKIDVDRNIELANRYNIMVVPTII 70
                                   4567999**************************87 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   7.7e-06    0.0082       8      71 ..      21      93 ..      18      96 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 7.7e-06
                                   TT-HHHHHHHHHHHHHCCCTT..EEEEEEETTT-CCCHCCCCTT.TTEEEECTTCGGB.......TCCECGCC CS
                         DUF836  8 pgChlCeqakekLkelkleeg..leleviDIakdeeleakYgle.ipvlalegvkktss......lleelswr 71
                                   + C+ C     +++el ++ g  +e+++iD++++ el ++Y+ + +p + le+  k+ +      ++eels+ 
  gi|116754438|ref|YP_843556.1| 21 EWCGPCRMQTPIMEELDKKYGgrIEIKKIDVDRNIELANRYNIMvVPTIILEKDGKEVRrwlgvtSKEELSSA 93
                                   56999999999999887777789*******************8735888888855555466666655555555 PP

>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.071        75       5      39 ..      18      51 ..      15      54 .. 0.75
   2 ?   11.8   0.0   0.00015      0.15     152     192 ..      50      94 ..      45      95 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.071
                                   EEBTTBHHHHHHHHHHHHHHHHCCTEEEEEEE-SS CS
                           DSBA  5 ffDvlCPyCylgkerleklaarspdvkvvlrpfel 39
                                   ff   C+ C +  + +e+l++++ + ++ ++ ++ 
  gi|116754438|ref|YP_843556.1| 18 FFAEWCGPCRMQTPIMEELDKKY-GGRIEIKKIDV 51
                                   45557******************.55555555544 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00015
                                    HHHHHHHHHHHTT-SSSSEEEE..TTC..EEEESSSSHHHHHHHH CS
                           DSBA 152 avrentaaaqslgvtGvPtvvv..dgk..rmvfGadrldtladal 192
                                    +v++n ++a+++++  vPt+++  dgk  r + G+++ + l +a+
  gi|116754438|ref|YP_843556.1|  50 DVDRNIELANRYNIMVVPTIILekDGKevRRWLGVTSKEELSSAI 94 
                                    6999******************88787899***********9998 PP

>> HyaE  Hydrogenase-1 expression protein HyaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0     4e-05     0.043      49      96 ..      32      78 ..      26      90 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4e-05
                                   HHHHHHCT-TTS-EEEEEETHHHHHHHHHCCT-TSSSEEEEEETTEEE CS
                           HyaE 49 vlpEllkaFpnalraavvadreqeealaerfgvlktPsllflrdgeyl 96
                                   ++ El k++  + ++  +   +++ +la+r++++++P++++ +dg+ +
  gi|116754438|ref|YP_843556.1| 32 IMEELDKKYGGRIEIKKID-VDRNIELANRYNIMVVPTIILEKDGKEV 78
                                   788999***9999999998.888999**************99999755 PP

>> DUF4174  Domain of unknown function (DUF4174)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   5.7e-05      0.06      54     113 ..      39      96 ..      28      98 .] 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.7e-05
                        DUF4174  54 ketgkieeeqlsaeliselrkelklsekd.fsmvLigkdggvkeryekpisleelfdlIDs 113
                                    k  g+ie ++++ +   el +++++        +++ kdg++ +r+ + +s eel + ID+
  gi|116754438|ref|YP_843556.1|  39 KYGGRIEIKKIDVDRNIELANRYNI---MvVPTIILEKDGKEVRRWLGVTSKEELSSAIDA 96 
                                    4567889999999999999999999...548899**************************8 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00012      0.13      16      34 ..      10      28 ..       3      71 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                                   HT--EEEEE--TT-HHHHH CS
                  Thioredoxin_7 16 rgkpvlvffgaswcftCqa 34
                                     kpvl +f a+wc++C+ 
  gi|116754438|ref|YP_843556.1| 10 LDKPVLMDFFAEWCGPCRM 28
                                   579**************85 PP

>> DUF1198  Protein of unknown function (DUF1198)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00018      0.18      49     107 ..      36      94 ..      27      97 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                                    S-HHHH.HHHHHHHHHS-HHHHHHHHHHHHHHHTTTT---HHHHHHHHHHHHHTT----- CS
                        DUF1198  49 mGktag.eefvrylsrgneehlqnaaqvlliyqvfivdeseenlerWrrllrkarlaael 107
                                    + k+ g +  ++ ++ + + +l+n  +++ +  ++i +++ ++++rW  + +k +l++ +
  gi|116754438|ref|YP_843556.1|  36 LDKKYGgRIEIKKIDVDRNIELANRYNIM-VVPTIILEKDGKEVRRWLGVTSKEELSSAI 94 
                                    55554404458899999999999987765.668999********************9987 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00025      0.27       7      55 ..      21      71 ..      14      78 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00025
                                   TSSHHHHHHHHHHHHTTGGE.EEEEGCCSH.HHHHHHHHHHTSSSSSEEEE CS
                   Glutaredoxin  7 ptCpyCkkakrlLkelgvkf.eeidvdkde.eireelkelsgvrtvPqvfi 55
                                    +C+ C++   +++el  k+   i++ k + +   el ++ +++ vP++  
  gi|116754438|ref|YP_843556.1| 21 EWCGPCRMQTPIMEELDKKYgGRIEIKKIDvDRNIELANRYNIMVVPTIIL 71
                                   79***********9999666556666666533335777888999***9986 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.47   4.9e+02      15      51 ..      13      47 ..       9      54 .. 0.78
   2 ?    9.7   0.0   0.00083      0.87     126     165 ..      51      95 ..      47      96 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.47
                                   EEEEEEE-TT-HHHHHHHHHHHHHHHHHHHTTSEEEE CS
                  Thioredoxin_4 15 vtvieyedlrCphCakfeeeveklleeyidtGkvkfi 51
                                    +++ +    C  C+     +e+l ++y   G++++ 
  gi|116754438|ref|YP_843556.1| 13 PVLMDFFAEWCGPCRMQTPIMEELDKKY--GGRIEIK 47
                                   4566677778999**9999999999999..8887765 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00083
                                    HHHHHHHHHHHT--SS-EEEE..TTEEE...-TT--HHHHHHHHT CS
                  Thioredoxin_4 126 veaeskeakkagiestPtfii..ngekv...eepqtyeelkalid 165
                                    v ++ + a++ +i  +Pt+i+  +g+ v    +  + eel+++id
  gi|116754438|ref|YP_843556.1|  51 VDRNIELANRYNIMVVPTIILekDGKEVrrwLGVTSKEELSSAID 95 
                                    66788999*************998888744446788899999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); 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: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 715.11
//
Query:       gi|116754439|ref|YP_843557.1|  [L=149]
Description: AsnC family transcriptional regulator [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-20   72.3   0.0    4.6e-20   71.6   0.0    1.4  1  AsnC_trans_reg2  AsnC-like ligand binding domain
    7.8e-11   41.6   0.6    1.5e-10   40.7   0.6    1.5  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
    0.00015   21.2   4.6     0.0023   17.5   4.6    2.3  1  HTH_24           Winged helix-turn-helix DNA-binding
      0.003   17.5   0.2     0.0058   16.6   0.2    1.5  1  HTH_Crp_2        Crp-like helix-turn-helix domain
  ------ inclusion threshold ------
       0.02   15.2   0.0      0.074   13.4   0.0    1.9  2  PqqD             Coenzyme PQQ synthesis protein D (PqqD)
      0.023   14.6   1.4      0.036   14.0   0.5    1.8  2  MarR_2           MarR family


Domain annotation for each model (and alignments):
>> AsnC_trans_reg2  AsnC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.6   0.0   1.5e-23   4.6e-20       2      82 .]      62     141 ..      61     141 .. 0.95

  Alignments for each domain:
  == domain 1  score: 71.6 bits;  conditional E-value: 1.5e-23
                AsnC_trans_reg2   2 lGfkanalvawkvpeerveevaevvaelpevtHcYeR..ewpynlyfmvharseeeveevlaeiaaatgledyevLpstr 79 
                                    lG+   +l+a++v  e+ +++ +vv+e++ev+H+Y+R  e  yn++f+v+a+ ee+v+e+++ei+++tg+e + vLp+++
  gi|116754439|ref|YP_843557.1|  62 LGMI-GVLIAMRVSPEDADQISTVVNEYDEVSHNYLRpnESGYNMWFTVSAP-EERVDEIISEIRRRTGCE-MLVLPTIK 138
                                    8999.99******************************76689*********9.679***************.******** PP

                AsnC_trans_reg2  80 efK 82 
                                     fK
  gi|116754439|ref|YP_843557.1| 139 IFK 141
                                    **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 !   40.7   0.6     5e-14   1.5e-10       1      42 []       1      45 [.       1      45 [. 0.98

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 5e-14
                  HTH_AsnC-type  1 LDeiDrkILeaLqed...aRisyaeLAervGlSestvlrRvrrLe 42
                                   +DeiD++IL+aLqe      ++++ LAe +G+ e++ +rRv rL+
  gi|116754439|ref|YP_843557.1|  1 MDEIDLRILAALQESfplVDRPFRVLAESLGIEEEELIRRVSRLK 45
                                   9******************************************95 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   4.6   7.7e-07    0.0023       1      48 []       1      51 [.       1      51 [. 0.95

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 7.7e-07
                         HTH_24  1 ldetdrkILelLqk...nprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                   +de+d++IL +Lq+     + + r LAe lg+    + rr+ rL+e GlI+
  gi|116754439|ref|YP_843557.1|  1 MDEIDLRILAALQEsfpLVDRPFRVLAESLGIEEEELIRRVSRLKEIGLIR 51
                                   8**************777779*****************************7 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.2   1.9e-06    0.0058      26      65 ..      25      62 ..      17      65 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.9e-06
                                   HHHHHTTSSHHHHHHHHHHHHHTTSEEE.TEEEEES-HHHH CS
                      HTH_Crp_2 26 elAsmlGltretvsrilseLkreglisr.grririldleaL 65
                                    lA+ lG+  e + r  s+Lk+ gli+r g    ildl +L
  gi|116754439|ref|YP_843557.1| 25 VLAESLGIEEEELIRRVSRLKEIGLIRRiGP---ILDLRRL 62
                                   79*************************5477...9999888 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 ?   -1.6   0.0       1.1   3.3e+03      40      56 ..      27      43 ..      24      48 .. 0.73
   2 ?   13.4   0.0   2.5e-05     0.074       9      43 ..      90     127 ..      67     135 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.1
                                   HHHCT--HHHHHHHHHH CS
                           PqqD 40 aeeydvdeeeaeadvla 56
                                   ae  +++eee+ ++v +
  gi|116754439|ref|YP_843557.1| 27 AESLGIEEEELIRRVSR 43
                                   45557888888888875 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 2.5e-05
                                    -....EEE--CHHHHHHHH-SSSS-.HHHHHHHHHHHC CS
                           PqqD   9 t..gkyisLnetgafiWklldgers.veeivaalaeey 43 
                                        +y++ ne+g+ +W  ++ +   v+ei+ ++++++
  gi|116754439|ref|YP_843557.1|  90 EvsHNYLRPNESGYNMWFTVSAPEErVDEIISEIRRRT 127
                                    24489***************887778*******99887 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.5   1.2e-05     0.036       7      61 ..       5      60 ..       1      61 [. 0.88
   2 ?   -2.1   0.0       1.2   3.6e+03      24      32 ..     120     128 ..     108     129 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.2e-05
                                   HHHHHHHHHCTTTS.EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSS CS
                         MarR_2  7 qarvLaaLgrrpgr.dltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkR 61
                                   ++r+LaaL  + +  d   + la+ lg++   + r++ rL + GL++r     D+R
  gi|116754439|ref|YP_843557.1|  5 DLRILAALQESFPLvDRPFRVLAESLGIEEEELIRRVSRLKEIGLIRRIGPILDLR 60
                                   5799*******984555******************************987666777 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.2
                                    HHHHHHHHT CS
                         MarR_2  24 vgelarrlg 32 
                                    ++e+ rr+g
  gi|116754439|ref|YP_843557.1| 120 ISEIRRRTG 128
                                    678888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1152.33
//
Query:       gi|116754440|ref|YP_843558.1|  [L=325]
Description: radical SAM domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.5e-21   74.9   0.0    1.4e-20   74.4   0.0    1.2  1  Radical_SAM  Radical SAM superfamily
    6.9e-09   36.1   0.9    1.4e-08   35.1   0.9    1.6  1  SPASM        Iron-sulfur cluster-binding domain
    4.2e-06   27.1   0.0    7.1e-06   26.3   0.0    1.3  1  Fer4_12      4Fe-4S single cluster domain
    0.00021   21.4   0.0    0.00039   20.5   0.0    1.4  1  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.4   0.0     3e-24   1.4e-20       3     166 ..       8     160 ..       6     161 .. 0.91

  Alignments for each domain:
  == domain 1  score: 74.4 bits;  conditional E-value: 3e-24
                                    EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritv 82 
                                     t +Cnl Cs+C  +    + + g +ls+ ei+ ++ke+ a + +  +i++ggepll+ d  ++++r+a+   +g+r+++
  gi|116754440|ref|YP_843558.1|   8 STGACNLSCSYCRASAG--PAPSGDELSTGEIKGLIKEI-APM-GAMLIISGGEPLLRQDV-FEVARYAAG--SGVRVSL 80 
                                    6889***********96..********************.899.*************8766.666666665..6****** PP

                                    EECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  83 etngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGendeelee 162
                                     +ngtl+++e+++r+l  g+ rvs++l+ a+ + + + +++ ++f+  l+++++l  + ++   +++++ p  n +el+ 
  gi|116754440|ref|YP_843558.1|  81 ASNGTLITPEIVDRILLSGISRVSISLDGASAK-TNDATRGEGSFDLALRGIRALSGR-VE-FQINMTITP-ANIDELDP 156
                                    *********************************.*********************999.99.899999988.66667887 PP

                                    HHHH CS
                                    xxxx RF
                    Radical_SAM 163 llel 166
                                    +l+l
  gi|116754440|ref|YP_843558.1| 157 ILDL 160
                                    7776 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.9   3.1e-12   1.4e-08       1      68 []     233     292 ..     233     301 .. 0.81

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 3.1e-12
                          SPASM   1 CfapsrslfInsdGdVvpCcvdkktyveelklGnireesleeIwnse.eyqefrkskkfplielCrnCp 68 
                                    C a+ r +fI+  GdV+pC     ++  +l+ G+ir+ s++eIw+s+  ++++r   +++l   C +C+
  gi|116754440|ref|YP_843558.1| 233 CIAGIRFVFISRTGDVFPC----GYF--PLSAGSIRDRSFSEIWSSSpLLNDLR---ERRLKGRCGSCN 292
                                    88889999***********....455..7***************87769999**...333334477774 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   1.6e-09   7.1e-06      12      96 ..       9      87 ..       2     123 .. 0.77

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.6e-09
                        Fer4_12 12 vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdiwlytg 93
                                   ++ CnlsC++C + +   +++ +  t e+ + +i+++  +    l+++GGEPll   ++++ e++++    ++  + ++++g
  gi|116754440|ref|YP_843558.1|  9 TGACNLSCSYCRASAGPAPSGDELSTGEI-KGLIKEI-APMGAMLIISGGEPLL---RQDVFEVARYAAGSGV-RVSLASNG 84
                                   567*********88888887777776665.6667777.7999************...8899999999998888.57888888 PP

                        Fer4_12 94 ytl 96
                                   + +
  gi|116754440|ref|YP_843558.1| 85 TLI 87
                                   765 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   8.7e-08   0.00039       5      92 ..       9      87 ..       6     109 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 8.7e-08
                        Fer4_14  5 lsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekkiwle 86
                                   ++ CnlsC  C  ++  + +  + +t e+ +  +k+          l ++GGePL+    ++++++ ++   ++  +++ l 
  gi|116754440|ref|YP_843558.1|  9 TGACNLSCSYCRASAGPAPSGDELSTGEI-KGLIKEIAPMGA---MLIISGGEPLLR---QDVFEVARYAAGSG--VRVSLA 81
                                   689*********99977777777766655.577755555444...6*********55...88999999999999..999999 PP

                        Fer4_14 87 tngtle 92
                                   +ngtl 
  gi|116754440|ref|YP_843558.1| 82 SNGTLI 87
                                   999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2320.83
//
Query:       gi|116754441|ref|YP_843559.1|  [L=342]
Description: aspartate-semialdehyde dehydrogenase [Methanosaeta thermophila PT]
Scores for complete 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  135.0   0.0    7.4e-39  133.7   0.0    1.6  2  Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation dom
    4.3e-32  111.1   0.0    7.3e-32  110.4   0.0    1.4  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
  ------ inclusion threshold ------
      0.013   16.3   0.0      0.022   15.6   0.0    1.3  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 ?   -2.3   0.0      0.65   3.9e+03     119     141 ..      85     106 ..      74     114 .. 0.73
   2 !  133.7   0.0   1.2e-42   7.4e-39       1     182 [.     158     321 ..     158     323 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.65
                                    HHHHHHHHHHHHCSTTEEEEESS CS
                Semialdhyde_dhC 119 dveveeveellaaapevkvvvne 141
                                     +e+++ve+++aaa + +v  n+
  gi|116754441|ref|YP_843559.1|  85 SDEAKKVEAEFAAA-GFVVASNT 106
                                    57899999999999.77776665 PP

  == domain 2  score: 133.7 bits;  conditional E-value: 1.2e-42
                                    HHHHHHCTT.EEEEEEEEEEEGGGCHHHHHHHHHHHHHHHHHSTTS.CTTTSSHHTTSEESTCSTBTTTTCHCBHHHHHH CS
                Semialdhyde_dhC   1 LkPLldalgelervivatyqavSGaGkkgvreLlkqvaelqrsdeakpgvfgvpiagNlipyidkeedkgepetreelka 80 
                                    LkPL++  +++e+v+va++qavSGaG+                    +gv++++i++N+ipyi +ee+k e+e +++l+ 
  gi|116754441|ref|YP_843559.1| 158 LKPLMQ--FGIESVHVASMQAVSGAGY--------------------EGVPSMAILDNIIPYIAGEEEKVETEAQKILGR 215
                                    8*****..56*****************....................6******************************** PP

                                    HHHHHHHCTESCSEEEEEEEESBSSEEEEEEEEEES..SSHHHHHHHHHHHHCS.......TTEEEEESSHCHHSSHHHH CS
                Semialdhyde_dhC  81 vaetkkileftekvsatcvrVPvlrGhseavtiklk..lkdveveeveellaaa.......pevkvvvneeedrPtpaav 151
                                     + ++   ++++ vsa+c+rVPv++Gh+eav++++k  ++++ev++++  +          p ++++v++e+drP+p+++
  gi|116754441|ref|YP_843559.1| 216 FDGERIVPADFT-VSASCHRVPVMDGHTEAVWVRMKddPTPAEVRQAFLDFNPGlddlptsPRKAIIVRDEPDRPQPRLD 294
                                    ***********8.***********************988999999999999988************************** PP

                                    TTC..SSSEEEEEEEEETTCTTEEEEEEEEETT CS
                Semialdhyde_dhC 152 agg..tnsvsVGRirkdemgdeglklvvvgDNl 182
                                    ++   ++svsVGRir          ++++g+N+
  gi|116754441|ref|YP_843559.1| 295 RNAgrGMSVSVGRIRPGI------RYICMGHNT 321
                                    *9999*********9654......566777776 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 !  110.4   0.0   1.2e-35   7.3e-32       1     119 [.       5     128 ..       5     130 .. 0.98

  Alignments for each domain:
  == domain 1  score: 110.4 bits;  conditional E-value: 1.2e-35
                                    EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSG......GGTTTECEBEEEGGGGGCTT-SEEEE-S CS
                 Semialdhyde_dh   1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavk......aleegkdlkvedvdeeelkevdivflal 74 
                                    k++++GatG+vGq++++ L+ hp++el+ l++s+rsaGkk++ea+k       ++e +d++v  vd++e+ ++divf+al
  gi|116754441|ref|YP_843559.1|   5 KAGVLGATGAVGQRFIEGLRGHPWFELTSLAASDRSAGKKYREAAKwrleseLPDEFADMTVVRVDPKEV-DADIVFSAL 83 
                                    689***********************************************9999****************.9******** PP

                                    CHHHHHHHHHHHHHTTSEEEESSSTTTTSTTSEBE-HHHHGGGGG CS
                 Semialdhyde_dh  75 pagvskelapklaeagvkviDlssdfRlkddavyvlpevnreaik 119
                                    p++ +k++++++a+ag++v +++++ R+ +d+++ +pe n+++i+
  gi|116754441|ref|YP_843559.1|  84 PSDEAKKVEAEFAAAGFVVASNTATNRMVPDVPLLIPECNPDHIE 128
                                    *******************************************97 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 ?   15.6   0.0   3.7e-06     0.022       1      87 [.       4     100 ..       4     104 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.7e-06
                                    EEEEEETT.SHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHH..HHHTTHE.....EESSHHHHHTCT...TESEEEE- CS
                   GFO_IDH_MocA   1 lrvaiiGa.Gkigskhlrplnesqrleevvalldpdaeraeav..aesfgve.....aysdleelladp...eidaviva 69 
                                    ++ ++ Ga G +g+++++ l+ + ++ e++ l  +d ++ ++   a+++++e      ++d+  +  dp   ++d+v+ a
  gi|116754441|ref|YP_843559.1|   4 IKAGVLGAtGAVGQRFIEGLRGH-PWFELTSLAASDRSAGKKYreAAKWRLEselpdEFADMTVVRVDPkevDADIVFSA 82 
                                    5789****8899*****888888.*******************5545555557666666665544444443789999999 PP

                                    S-GGGHHHHHHHHHHTT- CS
                   GFO_IDH_MocA  70 tpngtheelakaaleagk 87 
                                     p+++ ++++ ++++ag 
  gi|116754441|ref|YP_843559.1|  83 LPSDEAKKVEAEFAAAGF 100
                                    999999999999998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); 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: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2435.74
//
Query:       gi|116754442|ref|YP_843560.1|  [L=499]
Description: hypothetical protein Mthe_1137 [Methanosaeta thermophila PT]
Scores for complete 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-283  939.4   9.7     4e-283  939.3   9.7    1.0  1  DUF2193      Uncharacterized protein conserved in archaea (DU
  ------ inclusion threshold ------
       0.16   11.8   0.9        3.6    7.5   0.3    2.6  2  DAGK_prokar  Prokaryotic diacylglycerol kinase


Domain annotation for each model (and alignments):
>> DUF2193  Uncharacterized protein conserved in archaea (DUF2193)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  939.3   9.7  4.5e-287    4e-283       2     498 .]       3     499 .]       2     499 .] 1.00

  Alignments for each domain:
  == domain 1  score: 939.3 bits;  conditional E-value: 4.5e-287
                        DUF2193   2 elyekmidealaaqkadvevikkkrgkefkiedakayvdavkkmkaaegqskevidLhkesvkahyeilksltdtvrPed 81 
                                    +ly+km+dea++aq+adve++k+krg++f ++d+kayvd+v+kmkaa+gqsk+vi+Lh++sv+ahy+il+slt+t+rPed
  gi|116754442|ref|YP_843560.1|   3 DLYKKMVDEAMMAQRADVETVKRKRGQDFVVSDTKAYVDVVNKMKAADGQSKAVIKLHVDSVNAHYDILSSLTKTIRPED 82 
                                    79****************************************************************************** PP

                        DUF2193  82 dpfvehyqtPaileiLyeeDeefrksvekfieaieksealigkeavrrygGfyGptcvvDfalipGstsnvvnkilkkvd 161
                                    dpfvehyqtPai+eiLyeeDe+frksve+fi+a++k+ealig+e+vrrygGfyGptcvvDfalipGstsnvvn+ilk+vd
  gi|116754442|ref|YP_843560.1|  83 DPFVEHYQTPAIMEILYEEDEKFRKSVEAFIQAVGKAEALIGLEVVRRYGGFYGPTCVVDFALIPGSTSNVVNRILKTVD 162
                                    ******************************************************************************** PP

                        DUF2193 162 ipeehkkaiLaaksWglntsygiGdefakaieegktlaeavekevealksiyeePveaqaklmdeaglksfdvrkymeey 241
                                    ipe+hk+aiLaaksWg+ntsygiG++fa++ie+g+tl++a++ke+e+++++y++P+eaqaklmd+ag++sfdvrkym++y
  gi|116754442|ref|YP_843560.1| 163 IPEHHKQAILAAKSWGMNTSYGIGEVFAHEIEKGATLSDAIRKEIEMIQTVYRTPIEAQAKLMDAAGHTSFDVRKYMQSY 242
                                    ******************************************************************************** PP

                        DUF2193 242 kkkmepvvkaalddgvhyanivtvPaycvGDiahhisqstynmckddvvlaiieavtevlestlrkaleklkseydvlsl 321
                                    k++m+++vk+a+ddgvhy+nivtvPaycvGD+ahhi+qst+nmckddvv+a+iea+tev+e+tl++a++k+k+ey+ l+l
  gi|116754442|ref|YP_843560.1| 243 KSRMKSAVKEAIDDGVHYGNIVTVPAYCVGDVAHHIAQSTFNMCKDDVVMATIEATTEVMETTLNNAVDKFKNEYQPLAL 322
                                    ******************************************************************************** PP

                        DUF2193 322 atgasaaavekileldgfnaemvvdlltkrfhnyvqlyptrgaaaeLhnvDflDliyrGeklldkarrakagseeklvpk 401
                                    atgasa+ave+ileldgfna+m+vdlltkrfhnyvqlyptr+aaaeLhn+Df+D+i rG+k+ldka+r+++gs++k+vpk
  gi|116754442|ref|YP_843560.1| 323 ATGASACAVEHILELDGFNAIMIVDLLTKRFHNYVQLYPTRSAAAELHNCDFMDMILRGWKYLDKAMRMRNGSKTKIVPK 402
                                    ******************************************************************************** PP

                        DUF2193 402 vkglevdlspieenevlmnpqryayPacaitvrfsalmrlaDyPClLtsepvtatlltniialekekaaaParvCknCas 481
                                    v g++vdl+pi++nevlmnpqryayP cai+vrfsalmrlaDyPClLtsepvtat++tniial+kek+a+ParvCk+Ca+
  gi|116754442|ref|YP_843560.1| 403 VLGFDVDLEPIHKNEVLMNPQRYAYPGCAISVRFSALMRLADYPCLLTSEPVTATMMTNIIALHKEKPASPARVCKDCAA 482
                                    ******************************************************************************** PP

                        DUF2193 482 aslidarheyCqwkeav 498
                                    aslid+rh+yCqwkeav
  gi|116754442|ref|YP_843560.1| 483 ASLIDFRHQYCQWKEAV 499
                                    ***************98 PP

>> DAGK_prokar  Prokaryotic diacylglycerol kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.3    0.0004       3.6      49      78 ..     294     323 ..     286     346 .. 0.81
   2 ?    1.7   0.0     0.025   2.3e+02      59      86 ..     457     484 ..     445     487 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0004
                    DAGK_prokar  49 llvlvaEllNtaiEavvDlvspeyhelakr 78 
                                    ++  ++E++ t + ++vD +++ey++la +
  gi|116754442|ref|YP_843560.1| 294 TIEATTEVMETTLNNAVDKFKNEYQPLALA 323
                                    556689********************9854 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.025
                    DAGK_prokar  59 taiEavvDlvspeyhelakraKDiaaaa 86 
                                    t++ +++ l +++    a+  KD+aaa 
  gi|116754442|ref|YP_843560.1| 457 TMMTNIIALHKEKPASPARVCKDCAAAS 484
                                    666777778888888999********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (499 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       854  (0.0476323); expected 358.6 (0.02)
Passed bias filter:                      604  (0.0336884); 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: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 3686.15
//
Query:       gi|116754443|ref|YP_843561.1|  [L=69]
Description: zinc finger protein [Methanosaeta thermophila PT]
Scores for 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-36  124.7   4.2    1.1e-36  124.6   4.2    1.0  1  DUF2180          Uncharacterized protein conserved in archaea
     0.0016   19.2   2.7      0.018   15.8   0.4    2.1  2  Tnp_zf-ribbon_2  DDE_Tnp_1-like zinc-ribbon
       0.01   16.2   1.7      0.017   15.5   1.7    1.4  1  Transp_Tc5_C     Tc5 transposase C-terminal domain
  ------ inclusion threshold ------
      0.048   13.4   0.7      0.072   12.9   0.7    1.2  1  zf-UBP_var       Variant UBP zinc finger
       0.05   13.8   0.8      0.064   13.4   0.8    1.2  1  FYVE             FYVE zinc finger


Domain annotation for each model (and alignments):
>> DUF2180  Uncharacterized protein conserved in archaea (DUF2180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.6   4.2     3e-40   1.1e-36       1      67 [.       1      67 [.       1      68 [. 0.98

  Alignments for each domain:
  == domain 1  score: 124.6 bits;  conditional E-value: 3e-40
                        DUF2180  1 mkCYeCakegkdtdavaiCivCGkGvCkdHlvreeievweGgypfpakklkktlprilCkeClealk 67
                                   m+CY Ca egk+t+avaiCivCG+GvC+dHlvr+eievweGgypfp+kklk++lprilCk+C+++++
  gi|116754443|ref|YP_843561.1|  1 MRCYLCALEGKTTEAVAICIVCGMGVCMDHLVRDEIEVWEGGYPFPSKKLKRRLPRILCKPCYAVYH 67
                                   9**************************************************************9986 PP

>> Tnp_zf-ribbon_2  DDE_Tnp_1-like zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.4   5.1e-06     0.018       2      30 ..       2      30 ..       1      30 [. 0.97
   2 ?    3.9   0.1     0.028        99      13      25 ..      52      66 ..      46      67 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.1e-06
                Tnp_zf-ribbon_2  2 RCkvClkkkikkeTriiCqeCdvplCrnh 30
                                   RC+ C   +  +e+  iC  C+ + C+ h
  gi|116754443|ref|YP_843561.1|  2 RCYLCALEGKTTEAVAICIVCGMGVCMDH 30
                                   9**************************87 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.028
                Tnp_zf-ribbon_2 13 ke.TriiCqeC.dvp 25
                                   +   ri C+ C +v+
  gi|116754443|ref|YP_843561.1| 52 RRlPRILCKPCyAVY 66
                                   333789999994465 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 !   15.5   1.7   4.8e-06     0.017      30      56 ..       6      32 ..       2      38 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.8e-06
                   Transp_Tc5_C 30 CkiegCselafikCarCkellCFdHfv 56
                                   C++eg +  a+  C+ C + +C dH+v
  gi|116754443|ref|YP_843561.1|  6 CALEGKTTEAVAICIVCGMGVCMDHLV 32
                                   9999999*******************8 PP

>> zf-UBP_var  Variant UBP zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.7     2e-05     0.072      15      45 ..       3      33 ..       2      38 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2e-05
                     zf-UBP_var 15 CvycFdtpesedGlyvcLkcFlgfckkhaek 45
                                   C +c  + ++ + + +c+ c +g+c +h+ +
  gi|116754443|ref|YP_843561.1|  3 CYLCALEGKTTEAVAICIVCGMGVCMDHLVR 33
                                   999*************************976 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.8   1.8e-05     0.064      11      67 ..       2      67 ..       1      68 [. 0.76

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.8e-05
                                   B-TTT--B--SSS--EE-TTT--EE-STTS.-EEE.EE........GGGTEEEEEEE-HHHHHHHH CS
                           FYVE 11 kCeiCakkFsllrrrhhCrlCGkvvCekCs.sklvall........ekeaeeksvrvCkeClaels 67
                                   +C  Ca + ++++    C +CG  vC ++  +  ++++        +k + + +  +Ck C+a ++
  gi|116754443|ref|YP_843561.1|  2 RCYLCALEGKTTEAVAICIVCGMGVCMDHLvRDEIEVWeggypfpsKKLKRRLPRILCKPCYAVYH 67
                                   69999999999999999*********9887344444558888887556666666778****99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 535.59
//
Query:       gi|116754444|ref|YP_843562.1|  [L=245]
Description: MIP family channel protein [Methanosaeta thermophila PT]
Scores for 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-49  166.3  17.1    9.4e-49  166.2  17.1    1.0  1  MIP       Major intrinsic protein
  ------ inclusion threshold ------
        1.9    8.4   5.2       0.97    9.3   1.4    2.5  2  Beta-APP  Beta-amyloid peptide (beta-APP)


Domain annotation for each model (and alignments):
>> MIP  Major intrinsic protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.2  17.1   1.1e-52   9.4e-49       7     227 .]       3     239 ..       1     239 [. 0.90

  Alignments for each domain:
  == domain 1  score: 166.2 bits;  conditional E-value: 1.1e-52
                                    HHHHHHHHHHHHHHHHHHHHH.HHHCCCSSCS.....SSSTTSS..........HHHHHHHHHHHHHHHHHHHHHHHCHT CS
                            MIP   7 flravlAEflatlllvfigvg.salnvkkkvs.....slaslvs..........vtleavalafglalavlvylaagiSG 70 
                                    + +++lAE+++t +lv++g g +a+++  +                        +++ a+ +af++a+a  +y+++ +SG
  gi|116754444|ref|YP_843562.1|   3 LAKRCLAEVVGTAILVYFGAGaAAITLMISKGssppnP-----FnigigalgglGDWFAIGMAFAIAIAGVIYALGRVSG 77 
                                    6799*****************66666655555334440.....2555666677899************************ PP

                                    -S-SHHHHHHHHHTTSSSHHHHHHHHHHHHHHHHHHHHHHHHHCHHH.HHHTTTTSSSSSTTSSHHHHHHHHHHHHHHHH CS
                            MIP  71 aHlNPavTlallvarkisllrailYivaQllGaivaaallklltkgl.esraglfanslkpglsagqalvvEiiltfvLv 149
                                    aH+NPavT+al+ +r+++   +i YivaQl+Ga ++++l  +   +  +++ gl+a+++ pg+s+gqa+ +E i tf+L+
  gi|116754444|ref|YP_843562.1|  78 AHINPAVTIALWATRRFPSGEVIPYIVAQLIGASLGSLLFAASAGSDaVMVGGLGATAPFPGISFGQAVLAEAIGTFLLM 157
                                    *************************************999877655438899999************************* PP

                                    HHHHHHCSTTSSSSTCHGHHHHHHHHHHHHHHHHHHHHST-SSHHHHHHHHHHHTH......STTTTHHHHHHHHHHHHH CS
                            MIP 150 lvvfaltddkrkvslgelaplaigllvaliilvgipltGaamNpArslgpavvlnk......fedhwvylvGPliGailg 223
                                    lv+++++ d+r+ + g +a+l igl+v  +i  +++++G ++NpAr +gp +v +       ++++ +y++GP++Ga+++
  gi|116754444|ref|YP_843562.1| 158 LVIMGVAVDERAPQ-G-FAGLIIGLTVGGVITTTGNIAGSSLNPARTFGPYLVDHImggpvlWSHYPIYVIGPVLGALVA 235
                                    ***********999.5.6***********************************9999*********************** PP

                                    HHHH CS
                            MIP 224 alvY 227
                                    a++Y
  gi|116754444|ref|YP_843562.1| 236 AFLY 239
                                    **99 PP

>> Beta-APP  Beta-amyloid peptide (beta-APP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.21   1.9e+03      31      35 ..     126     130 ..     115     131 .. 0.71
   2 ?    9.3   1.4   0.00011      0.97      26      37 ..     175     186 ..     173     188 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.21
                       Beta-APP  31 LMVGG 35 
                                     MVGG
  gi|116754444|ref|YP_843562.1| 126 VMVGG 130
                                    58888 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00011
                       Beta-APP  26 GAIIGLMVGGVV 37 
                                    G IIGL VGGV+
  gi|116754444|ref|YP_843562.1| 175 GLIIGLTVGGVI 186
                                    78*********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1927.91
//
Query:       gi|116754445|ref|YP_843563.1|  [L=264]
Description: hypothetical protein Mthe_1140 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.094   12.2   1.3       0.12   11.8   1.3    1.2  1  BCD       Beta-carotene 15,15'-dioxygenase
       0.36   10.1   2.3        1.2    8.4   0.0    2.0  2  S_4TM     SMODS-associating 4TM effector domain


Domain annotation for each model (and alignments):
>> BCD  Beta-carotene 15,15'-dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.3   1.3e-05      0.12     161     245 ..      18     113 ..       1     128 [. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.3e-05
                            BCD 161 aaetalllalfavvppllafglYFclwHSlrhvarllavalrkgrlkaslkrflrkaaplt..............latil 226
                                     a ++lll++fa +p+l+ +  Y+  +  +r +++    +l++g ++a+l +++++a+ +               +++++
  gi|116754445|ref|YP_843563.1|  18 TALVILLLFVFASLPILWNIKGYYDHLRDVRNLLEK---KLSSGCNQAELVQLVKDALVVQssgmqgvaratmalTLSVI 94 
                                    45578999*****************98777777777...8999***************9999999999999987777777 PP

                            BCD 227 llallyvllpksasllesl 245
                                    l+a++++l+ + ++l++  
  gi|116754445|ref|YP_843563.1|  95 LGAAIFLLIANPFKLQDTT 113
                                    7777777777666666555 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 ?    8.4   0.0   0.00013       1.2     182     257 ..       2      76 ..       1      81 [. 0.89
   2 ?    1.5   0.5     0.017   1.5e+02     170     211 ..      87     128 ..      80     135 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00013
                          S_4TM 182 lvvgliknlslsdlllsvivpllpllllalkeyreqresakelerlkeeiesllndaasgkleeeelkeelrklQd 257
                                    ++++++++ls+s+ ll+++v ll +++  l   ++ +   + l+++++ +e++l++  ++++  + l +++  +Q 
  gi|116754445|ref|YP_843563.1|   2 VLTFVAARLSMSTPLLTALVILLLFVFASLPILWNIKGYYDHLRDVRNLLEKKLSSGCNQAELVQ-LVKDALVVQS 76 
                                    78999*************************************************99998776544.7888877775 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.017
                          S_4TM 170 llfalvlwillvlvvgliknlslsdlllsvivpllpllllal 211
                                    + ++l++++ + +++ +++ ++l+d+ l  i+p+l  +llal
  gi|116754445|ref|YP_843563.1|  87 MALTLSVILGAAIFLLIANPFKLQDTTLDKILPTLKDILLAL 128
                                    344555555566666669999************999888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       861  (0.0480228); expected 358.6 (0.02)
Passed bias filter:                      616  (0.0343577); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1874.50
//
Query:       gi|116754446|ref|YP_843564.1|  [L=267]
Description: UbiA prenyltransferase [Methanosaeta thermophila PT]
Scores for complete 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-42  143.5  16.0    8.3e-42  143.2  16.0    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 !  143.2  16.0   4.6e-46   8.3e-42       6     246 ..      20     250 ..      15     262 .. 0.88

  Alignments for each domain:
  == domain 1  score: 143.2 bits;  conditional E-value: 4.6e-46
                           UbiA   6 lvglalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilglllla 85 
                                    l g+++++    +l + +l++ ++ll+++++na+NdyfDreiDa   ++p+RP++sGrisp++ali++++l+i+g+l++ 
  gi|116754446|ref|YP_843564.1|  20 LTGMLVSGALLQSLHTPVLVFSAVLLITGGGNAINDYFDREIDAV--NRPDRPIPSGRISPRAALIWSVALFIAGCLIA- 96 
                                    78999999999999999****************************..********************************. PP

                           UbiA  86 lllnpltallgllalllyvvYtglrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavflltwaialandl 165
                                     l+n  +++l+ll+ +++++Y   rlK  ++ g++ ++   g+ +l+g  a++ s s++a+l  l  +l t++  +++d+
  gi|116754446|ref|YP_843564.1|  97 GLINQSCLALALLNSFVLIIYA-ARLKGLPVAGNIAISYLTGTTFLFGGLAASPS-SITAFLSILS-ALATLSREIVKDI 173
                                    **********************.6****************************998.6555555555.************* PP

                           UbiA 166 rdregDrkagiktlpvvlGrkaarillalllavlllallllllalllllylllalllaalallraarlvrrrdakkaakf 245
                                    +d+ gD++ g ktlp+ +G++++++l+ l+l+v++    ll ++  l++ + +a+ +a+la+l +++++   da+  +++
  gi|116754446|ref|YP_843564.1| 174 EDLPGDLAHGAKTLPAFIGKRKSFVLASLVLIVAM----LLSYLVPLGIDYQAAVSIANLAFLLSIKRMLCGDASGSQRW 249
                                    ************************97443444433....35688888888888888888888888888887777666665 PP

                           UbiA 246 f 246
                                     
  gi|116754446|ref|YP_843564.1| 250 I 250
                                    5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); 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:                         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: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2016.96
//
Query:       gi|116754447|ref|YP_843565.1|  [L=255]
Description: ribosomal RNA methyltransferase RrmJ/FtsJ [Methanosaeta thermophila PT]
Scores for complete 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  196.2   0.0    5.5e-58  196.0   0.0    1.1  1  FtsJ             FtsJ-like methyltransferase
      2e-09   37.3   0.1    3.7e-09   36.4   0.1    1.5  1  TRAM             TRAM domain
    1.2e-05   25.2   0.0    4.1e-05   23.5   0.0    1.8  1  Methyltransf_23  Methyltransferase domain
    8.4e-05   22.4   0.0     0.0029   17.4   0.0    2.1  1  Methyltransf_31  Methyltransferase domain
      0.007   17.1   0.3       0.71   10.6   0.1    2.8  2  Methyltransf_25  Methyltransferase domain
  ------ inclusion threshold ------
       0.05   12.8   0.0        7.3    5.7   0.0    2.2  2  NNMT_PNMT_TEMT   NNMT/PNMT/TEMT family
        0.1   12.9   0.1       0.27   11.5   0.1    1.7  1  TrkA_N           TrkA-N domain


Domain annotation for each model (and alignments):
>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.0   0.0   2.2e-61   5.5e-58       1     176 [.      18     190 ..      18     191 .. 0.98

  Alignments for each domain:
  == domain 1  score: 196.0 bits;  conditional E-value: 2.2e-61
                                    CCCCHHHHHHHHHHHHT-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSSHHHTTEEEECS-CCCSSHHHHHC CS
                           FtsJ   1 yrsRsayKLleidekfklfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpmaplpgvttiqgditdpetiekik 80 
                                    yr+RsayKL +i++kf+++++g +vvDlgaaPGgw qv+ +  g  g vv+vDl  ++pl+g+ tiqgdit++et e+i 
  gi|116754447|ref|YP_843565.1|  18 YRARSAYKLKQINDKFHIIRRGSRVVDLGAAPGGWLQVARELSG--GIVVGVDLERIEPLEGIVTIQGDITKEETLEQIA 95 
                                    9**************************************99964..9********************************* PP

                                    HCHHHSSEEEEEE--S-SS-CHHHHHHHHHCCCCHHHHCCHCCCCECCCEEEECCCHCCCHHHHHHHHHCCEEEEEEEE- CS
                           FtsJ  81 ealserkvdlvvsDgapdvsgvhdldeylqsqLllaalelalkllkpggtfvlkifrgeeteallkqlkkfFekvsvvkP 160
                                     al++ ++d+v+sD ap+ sg++d+d++++++L +aal++a +ll+pgg+f++k+f+g+ ++++l+++k+ F++v+ + P
  gi|116754447|ref|YP_843565.1|  96 AALGG-QADVVISDAAPNLSGIWDVDHARSIDLSRAALRIAKRLLRPGGSFLVKVFQGDMFNDYLEEVKREFSSVHAYTP 174
                                    99976.************************************************************************** PP

                                    SS--CCG-EEEEEEEE CS
                           FtsJ 161 kssrsesseeflvcrg 176
                                    ++sr+es+e++++ ++
  gi|116754447|ref|YP_843565.1| 175 PASRKESAEIYVIGKK 190
                                    ************9875 PP

>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.1   1.4e-12   3.7e-09       3      62 .]     197     252 ..     195     252 .. 0.96

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 1.4e-12
                                    XXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEEEE CS
                           TRAM   3 yvGstqeVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGell 62 
                                      G+ ++V+v  ++ + g+gi+ ++ g++v+v++++p  G+++ +kI  vk +++++++l
  gi|116754447|ref|YP_843565.1| 197 RSGEIYDVTVDSVG-RTGDGIAMIQ-GFAVIVKNASP--GERLRIKIGPVKQRFAFASIL 252
                                    569***********.**********.***********..******************986 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   1.6e-08   4.1e-05      18     123 ..      34     153 ..      14     181 .. 0.68

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.6e-08
                Methyltransf_23  18 pklraggrvLdiGcGtGillevlren.gfsvtgvDlspeaveiaekakkaqkdqfdeqeaae.............pqgkf 83 
                                       r+g+rv+d+G++ G +l+v+re  g  v+gvDl +  +e +e++ + q d + e+  ++             +++ +
  gi|116754447|ref|YP_843565.1|  34 HIIRRGSRVVDLGAAPGGWLQVARELsGGIVVGVDLER--IEPLEGIVTIQGDITKEETLEQiaaalggqadvviSDAAP 111
                                    3478999****************775377999****64..6777777777777776665555444544433334433344 PP

                Methyltransf_23  84 dlIvlrev..lehvpdppellrqiatllkpgGylllseplas 123
                                    +l   ++v    +++   ++lr +++ll+pgG +l+ ++  +
  gi|116754447|ref|YP_843565.1| 112 NLSGIWDVdhARSIDLSRAALRIAKRLLRPGGSFLVKVFQGD 153
                                    443334431144566678******************997544 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.1e-06    0.0029       4     126 ..      39     166 ..      36     198 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.1e-06
                Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklled......ekfDl 77 
                                    g rv+DlG++ G  + ++ e+  +++ vvG+D +   i           l+ +   qgdi++ e+ le+       + D+
  gi|116754447|ref|YP_843565.1|  39 GSRVVDLGAAPGGWLQVAREL--SGGIVVGVDLER--I---------EPLEGIVTIQGDITKEET-LEQiaaalgGQADV 104
                                    667777777777777777733..456777777532..2.........246778889******887.5667899******* PP

                Methyltransf_31  78 ilsnevl...........naladpdkileeiervlkpggilliedpr..llaelpakveees 126
                                    ++s+++              +  + ++l+ ++r+l+pgg +l+  ++  +  +++++v++e 
  gi|116754447|ref|YP_843565.1| 105 VISDAAPnlsgiwdvdhaRSIDLSRAALRIAKRLLRPGGSFLVKVFQgdMFNDYLEEVKREF 166
                                    ****888888888998888999999******************9999663334444444444 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.1   0.00028      0.71       1      97 []      42     143 ..      42     143 .. 0.57
   2 !    7.2   0.0    0.0031         8      26      70 ..     124     171 ..     118     184 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00028
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBS.SSTTTEEEEEE........E CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlp.fedgsfDlvvs........s 71 
                                    v+dlG+ +G +++ + +  g + v+gvD+      +    ++ +       +  +e++     g+ D+v+s        +
  gi|116754447|ref|YP_843565.1|  42 VVDLGAAPGGWLQVARELSG-GIVVGVDLERIEPLEGIVTIQGD----ITKEETLEQIAaALGGQADVVISdaapnlsgI 116
                                    89*******99988877766.99*****9763333322223111....12333334443134567788888433332221 PP

                                    STGGG.SSHHHHHHHHHHHHHHEEEEE CS
                Methyltransf_25  72 galhh.lsdedlekalkeiarvLkpgG 97 
                                      + h  s +  ++al+ ++r+L+pgG
  gi|116754447|ref|YP_843565.1| 117 WDVDHaRSIDLSRAALRIAKRLLRPGG 143
                                    122242333444779999999999999 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0031
                                    EEESSHHHHHHHHHHHHHTTT.TEEEEESBCCG..BSSSTTTEEEEEE CS
                Methyltransf_25  26 gvDiseemleaareraeeegl.nvefvqgdaed..lpfedgsfDlvvs 70 
                                     +D+s ++l++a++ ++  g   v++ qgd+ +  l++ +++f  v++
  gi|116754447|ref|YP_843565.1| 124 SIDLSRAALRIAKRLLRPGGSfLVKVFQGDMFNdyLEEVKREFSSVHA 171
                                    689999999999999987665799999999944347777777777766 PP

>> NNMT_PNMT_TEMT  NNMT/PNMT/TEMT family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0    0.0044        11      23      68 ..       7      50 ..       2      65 .. 0.84
   2 ?    5.7   0.0    0.0029       7.3     165     200 ..     116     149 ..      77     170 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0044
                                   HHHCSTTTTSTCCCCHHHHHHHHHHHHHHTSSS-ECEEEEET-TT- CS
                 NNMT_PNMT_TEMT 23 ekyykkasedaaeeqvvlfaLknllqtlatgekkgdtllDiGaGPT 68
                                   ++yy ka+e+   +  + ++Lk +  ++    + g  ++D+Ga P 
  gi|116754447|ref|YP_843565.1|  7 DHYYRKAKEEGY-RARSAYKLKQINDKFHIIRR-GSRVVDLGAAPG 50
                                   579988888888.67899***********7766.*********996 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0029
                                    ESSHHHH-SSHHHHHHHHHHHHTTEEEEEEEEEEEE CS
                 NNMT_PNMT_TEMT 165 ifcleaacedleeylralrnlasllkpGGhlvlggv 200
                                    i  ++  +++++  ++alr + +ll+pGG +++  v
  gi|116754447|ref|YP_843565.1| 116 IWDVDH-ARSIDLSRAALRIAKRLLRPGGSFLVK-V 149
                                    344443.467888899*************99764.3 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00011      0.27      13      60 ..      55      96 ..      53     115 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00011
                                   HHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTG CS
                         TrkA_N 13 laeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLeeagi 60
                                   +a+eLs g   vv++d   er+e l+  g+ +++gd t+ee+Le++ +
  gi|116754447|ref|YP_843565.1| 55 VARELSGGI--VVGVDL--ERIEPLE--GIVTIQGDITKEETLEQIAA 96
                                   788886644..888887..7899985..999*************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); 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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1804.01
//
Query:       gi|116754448|ref|YP_843566.1|  [L=371]
Description: hypothetical protein Mthe_1144 [Methanosaeta thermophila PT]
Scores for complete 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-129  430.7   0.0   3.4e-129  430.5   0.0    1.1  1  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 !  430.5   0.0  1.9e-133  3.4e-129       1     312 []      12     330 ..      12     330 .. 0.98

  Alignments for each domain:
  == domain 1  score: 430.5 bits;  conditional E-value: 1.9e-133
                         DUF763   1 GiadLpLhegkvPewllermkkLskaiveliveeygkeellerlsdPlwFqslgnvlGmdWdsSGsTtvvlgalkealks 80 
                                    G+adLpLh+g++P+wl++rm+ L+++i+++i+ eyg++ell+r+sdP+wFq++++vlG+dW+sSG+Tt+++gal+++l+ 
  gi|116754448|ref|YP_843566.1|  12 GTADLPLHDGRAPPWLFSRMRLLAGEIARVIIYEYGEQELLRRISDPFWFQAFSCVLGFDWHSSGTTTTTTGALRASLR- 90 
                                    89**************************************************************************995. PP

                         DUF763  81 eelgilvaGGkGkksrktpeeleklaeklgldeek...lvkasrlvakvdnaalqdgyqlYlhalivsekgkwaviqQGm 157
                                     e g++vaGGkG++s+ktp e+++++e ++l+e+k   l++asrl+akvdna++qdgy+lY+ha+i++++g+wav+qQGm
  gi|116754448|ref|YP_843566.1|  91 PEDGVVVAGGKGATSLKTPVEIMRYGEIFSLSERKiedLIRASRLSAKVDNALVQDGYRLYHHAFILTSNGEWAVVQQGM 170
                                    567*****************************999999****************************************** PP

                         DUF763 158 neeerlARRYhwlseelesfveephsgiagekkeeevlnlvskeseearkaildlvkekpekllkelkelkallkgekkl 237
                                    ne  r+ARRYhwls++l s++eeph++i++++ e++v++l+skes+e+r+a+ldlv+++p++++k++++  +l++ + +l
  gi|116754448|ref|YP_843566.1| 171 NE--RYARRYHWLSDKLYSMIEEPHAAICAQRLESRVMDLTSKESRENRQATLDLVRDGPSHIKKYTAQR-SLEDFSPAL 247
                                    97..8*********************************************************99988876.689999999 PP

                         DUF763 238 klpakhev........lekvlekayelqpedfeellllkgvGpktlraLalvaeliygekasfkDPvkysfavGgKdgvP 309
                                    ++pa+he+          ++l++ayelqp+++eel++l+g+Gpk +raL+l+aeli+g+++s++DP++ysfa+GgKdg+P
  gi|116754448|ref|YP_843566.1| 248 RMPARHEIlpvdigrdGLRILQAAYELQPSTYEELVMLRGMGPKRVRALTLIAELIFGAPPSWRDPARYSFAHGGKDGYP 327
                                    **************99899************************************************************* PP

                         DUF763 310 ypv 312
                                    ypv
  gi|116754448|ref|YP_843566.1| 328 YPV 330
                                    **8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 2828.74
//
Query:       gi|116754449|ref|YP_843567.1|  [L=296]
Description: UbiA prenyltransferase [Methanosaeta thermophila PT]
Scores for complete 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-40  138.4  21.5    3.1e-40  138.1  21.5    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 !  138.1  21.5   1.7e-44   3.1e-40       4     243 ..      25     269 ..      20     284 .. 0.87

  Alignments for each domain:
  == domain 1  score: 138.1 bits;  conditional E-value: 1.7e-44
                           UbiA   4 palvglalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilglll 83 
                                    +al+++ +++g+ p +  +l++++g+++a+++++++Ndy+D++ D+     p+RPl+s ++s++ a i+a+vll+l+++ 
  gi|116754449|ref|YP_843567.1|  25 SALLSAYATTGSLPGAEPFLIATIGAYFAITSSYVFNDYVDVDVDRV--AMPDRPLPSAKVSRRGAGIYALVLLMLAAAA 102
                                    4566667777777777*******************************..99***************************** PP

                           UbiA  84 lalllnpltallgllalllyvvYtglrlKrrtllgtvvggiafglppllgwaavtgsl........sllalllalavfll 155
                                    +  +lnp +++++++a ++ +vY+  + Krrt+l  +++g+a+g++p++ w a++           +++al+l+l++ + 
  gi|116754449|ref|YP_843567.1| 103 A-TYLNPESLVMLIAATAIITVYS-AWAKRRTPLSWMFVGLAYGMVPVGVWLAISPAGylmpgpgfHPAALILGLMICIT 180
                                    *.**********************.6***************************88777889******************* PP

                           UbiA 156 twaialandlrdregDrkagiktlpvvlGrkaaril.lalllavlllallllllalllllylllalllaalallraarlv 234
                                     w++  + + rd+ gDr+ gi+t+p+++G   +  l +a+++++++l+lll  l +l+ ly + a+l+++++l   a +v
  gi|116754449|ref|YP_843567.1| 181 DWGFTNCDASRDVPGDRAKGIPTTPATYGIPLTSKLvAAFWTIGVILSLLLGILSGLGALYHATAILSGIWMLMQCADFV 260
                                    **********************************9977778888887755555555555555555555555555556666 PP

                           UbiA 235 rrrdakkaa 243
                                    r+ ++++++
  gi|116754449|ref|YP_843567.1| 261 RNPTPSRGE 269
                                    666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); 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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2226.32
//
Query:       gi|116754450|ref|YP_843568.1|  [L=241]
Description: glucose-6-phosphate isomerase [Methanosaeta thermophila PT]
Scores for complete 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  139.8   0.1    6.7e-41  139.5   0.1    1.1  1  GPI       Glucose-6-phosphate isomerase (GPI)
    0.00052   19.6   0.0    0.00082   19.0   0.0    1.3  1  Cupin_1   Cupin
    0.00073   19.2   0.0     0.0038   16.9   0.0    2.0  2  Cupin_2   Cupin domain
  ------ inclusion threshold ------
      0.031   14.5   0.0      0.048   13.9   0.0    1.2  1  ARD       ARD/ARD' family


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 !  139.5   0.1   1.5e-44   6.7e-41       2     181 ..      16     190 ..      15     191 .. 0.93

  Alignments for each domain:
  == domain 1  score: 139.5 bits;  conditional E-value: 1.5e-44
                            GPI   2 rkardlaavladeealkaltetldddvaYevsdslktaeegerlaadqliydvtvilPgkiGeEriktrGHyHkevd.rr 80 
                                    r+ +d+  +l d e  +    + d d +Y+ +d   +  +++ l + +l+yd+t+i+P  +G E++kt GHyH++v    
  gi|116754450|ref|YP_843568.1|  16 RRLSDMRELLCDTEWASS---ADDIDLYYMYRDLYLSRADQNTLIEHDLRYDITIIPPRMLGREYVKTAGHYHPKVPgTD 92 
                                    677777777777643333...57889*************************************************98899 PP

                            GPI  81 strPEvYevlkGealmlLekPeglkvddvivvevkartvvivPPnygHvsinigeedLvmanlvpkdagqdYdviakarG 160
                                     t+PEvYevl+Geal+lL++ +      v+ ++  +++ +++PP ygH++in ++  L m+n+v++ ++++Y ++   rG
  gi|116754450|ref|YP_843568.1|  93 VTYPEVYEVLEGEALYLLQNEDA---SSVVCIVASEGDKIVIPPGYGHITINRSNRRLKMSNFVCRSFSSIYGPYRDLRG 169
                                    ********************999...899*************************************************** PP

                            GPI 161 maayiieegevlrkrknddap 181
                                     a+y+ +eg v+ +r  d+ap
  gi|116754450|ref|YP_843568.1| 170 GAYYYTKEGFVKNPRYRDPAP 190
                                    ***********9999988875 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.8e-07   0.00082      51     104 ..      92     144 ..      83     155 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.8e-07
                                    ESSS-EEEEEEESEEEEEEEETTSS.EEEEEEEETTEEEEE-TT-EEEEEEESS CS
                        Cupin_1  51 hpnateiayvlqGegrvgfvvpgngnrdfhkklreGdvfvvPaglvhfqynsgd 104
                                       ++e+  vl+Ge++  ++ +++++++   + +eGd +v+P+g+ h ++n  +
  gi|116754450|ref|YP_843568.1|  92 DVTYPEVYEVLEGEAL-YLLQNEDASSVVCIVASEGDKIVIPPGYGHITINRSN 144
                                    556789999*******.888888889999999*******************974 PP

>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   8.4e-07    0.0038      21      67 ..      97     149 ..      81     154 .. 0.86
   2 ?   -0.6   0.0      0.24   1.1e+03      41      69 ..     167     195 ..     162     197 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 8.4e-07
                                    EEEEEEESEEEEEECTE......EEEEETTEEEEE-TT-EEEEEE-SSS-EEE CS
                        Cupin_2  21 effyVleGegeltvdge......eveleaGdsvyfpagtpHrfrNtgdeparl 67 
                                    e++ VleGe+ + + +e       ++ ++Gd +++p+g  H  +N+++  +++
  gi|116754450|ref|YP_843568.1|  97 EVYEVLEGEALYLLQNEdassvvCIVASEGDKIVIPPGYGHITINRSNRRLKM 149
                                    7777999**888877666788877899*********************99987 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.24
                                    EETTEEEEE-TT-EEEEEE-SSS-EEEEE CS
                        Cupin_2  41 leaGdsvyfpagtpHrfrNtgdeparllv 69 
                                    l+ G ++y++ g   + r +  +p+r+l 
  gi|116754450|ref|YP_843568.1| 167 LRGGAYYYTKEGFVKNPRYRDPAPVRWLE 195
                                    67789999999999999999999999996 PP

>> ARD  ARD/ARD' family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.1e-05     0.048      94     134 ..      97     138 ..      92     153 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.1e-05
                            ARD  94 eirliveGtgyFdvrskdeawirvlv.ekGDLivlPagiyhr 134
                                    e+  ++eG++++ ++++d + + + v  +GD iv+P+g  h 
  gi|116754450|ref|YP_843568.1|  97 EVYEVLEGEALYLLQNEDASSVVCIVaSEGDKIVIPPGYGHI 138
                                    667799***********998776655268*********9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1770.11
//
Query:       gi|116754451|ref|YP_843569.1|  [L=231]
Description: hypothetical protein Mthe_1147 [Methanosaeta thermophila PT]
Scores for complete sequence (score 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   16.5   0.0      0.034   15.2   0.0    1.7  1  PPC       Bacterial pre-peptidase C-terminal domain


Domain annotation for each model (and alignments):
>> PPC  Bacterial pre-peptidase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   1.9e-06     0.034       1      68 [.      57     155 ..      57     156 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.9e-06
                                    -EEEEEEEE-TT-EEEEEES-TT........................SEEEEE-TT..-SS-EE-STT-TT......... CS
                            PPC   1 dvDvysfevpagdsltididggti......................dldLylldsngtsvaaydansapsg......... 49 
                                    dvD+ysf+++ g+++ ++i   +i                       + +y + ++gt+  +   ++++ +         
  gi|116754451|ref|YP_843569.1|  57 DVDYYSFNATRGQTILLSILIPQIeghenfkprmalmgrglaparpPVRVYKPEGFGTVMLN---PPENATtffepftrt 133
                                    8*************999973333333666788888888888877766668888888999999...775444577777777 PP

                                    .....S-TTS-EE-SSSEEEEEEE CS
                            PPC  50 .....sdeyieftapqaGtYyvaV 68 
                                          +e+++   p++G Y vaV
  gi|116754451|ref|YP_843569.1| 134 tywtrQKELVR--IPADGRYLVAV 155
                                    88876556665..56699999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1650.82
//
Query:       gi|116754452|ref|YP_843570.1|  [L=298]
Description: molybdenum cofactor biosynthesis protein A [Methanosaeta thermophila PT]
Scores for complete 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  110.3   0.1      3e-31  109.0   0.0    1.7  2  Radical_SAM  Radical SAM superfamily
    5.8e-16   58.6   0.0    1.1e-15   57.7   0.0    1.4  1  Mob_synth_C  Molybdenum Cofactor Synthesis C
    1.2e-08   35.1   0.0      2e-08   34.4   0.0    1.4  1  Fer4_14      4Fe-4S single cluster domain
    2.8e-07   30.9   0.0      5e-07   30.1   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 !  109.0   0.0   6.8e-35     3e-31       1     166 [.      16     174 ..      16     175 .. 0.98
   2 ?   -2.3   0.0       1.1     5e+03      27      40 ..     268     281 ..     237     288 .. 0.52

  Alignments for each domain:
  == domain 1  score: 109.0 bits;  conditional E-value: 6.8e-35
                                    EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiri 80 
                                    ++vt  CnlrC++C+       e++g ++s e+ ++ v ++  + g++ v ++ggepl+++d++e ++  ++ a pg++i
  gi|116754452|ref|YP_843570.1|  16 ISVTSRCNLRCIYCHHE----GEVTGGEISREMAVNVVNAA-SRLGIRSVKITGGEPLMRSDLEEMIAGFKEVA-PGVEI 89 
                                    689**************....6*******************.6******************************8.***** PP

                                    EEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  81 tvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglpGendee 159
                                    +++tng+ + ++ +e l+ +g+ rv+++l+++d+++++++++ +g+++e+vl+++e++  +g+++v+ ++v+l+ en++e
  gi|116754452|ref|YP_843570.1|  90 SITTNGVYL-KDRAEGLAAAGLSRVNISLDSLDPDMYRRITGaGGGDLERVLDGIEAAQLSGLRPVKLNMVVLR-ENERE 167
                                    *********.****************************************************************.***** PP

                                    HHHHHHH CS
                                    xxxxxxx RF
                    Radical_SAM 160 leellel 166
                                    + e++e+
  gi|116754452|ref|YP_843570.1| 168 IPEMIEF 174
                                    ***9997 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.1
                                    HHHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxx RF
                    Radical_SAM  27 rslsveeileevke 40 
                                    +s +++ei++++ e
  gi|116754452|ref|YP_843570.1| 268 KSTDPDEIERLILE 281
                                    34455555555555 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 !   57.7   0.0   2.4e-19   1.1e-15      37     123 ..     204     287 ..     191     291 .. 0.77

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 2.4e-19
                                    -EEEE-..-SST-SSEEEEETTT--EEEEE-TTTS-.-GGG--EEEE-TTSEEESSSS-SS-.EEHHHHHHTT--HHHHH CS
                    Mob_synth_C  37 alleak..ketkgpakrykikdgkgeiglIapvsep.FCasCnRlRltadGklktCLfaeee.idlrdllregaseeeLk 112
                                    +++++   +++++ +++y ++++   +++++p++++ FCa+CnRlR+t+dG+lk+CL ++++ +++++    + + +e++
  gi|116754452|ref|YP_843570.1| 204 ESEAEMvlTREMHRRRKYFLNGAV--VEIVRPMDNTeFCAHCNRLRVTSDGRLKPCLLRNDNlLEIKS----T-DPDEIE 276
                                    44433322566999999*998888..9********99***********************99555543....3.344689 PP

                                    HHHHHHHHT-- CS
                    Mob_synth_C 113 elikealarkk 123
                                    +li ea++r+ 
  gi|116754452|ref|YP_843570.1| 277 RLILEAVKRRA 287
                                    99999999886 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   4.5e-12     2e-08       5      94 ..      19     100 ..      16     119 .. 0.81

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 4.5e-12
                        Fer4_14   5 lsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekkiw 84 
                                    +s+Cnl C  C ++   + + g++ ++e+ ++++    +s+  i+ + +tGGePL+    ++l +++   ke  p ++i 
  gi|116754452|ref|YP_843570.1|  19 TSRCNLRCIYCHHEG--EVTGGEI-SREMAVNVV--NAASRLGIRSVKITGGEPLMR---SDLEEMIAGFKEVAPGVEIS 90 
                                    89**********998..5555555.667777999..7777888899*********66...89999999999999****** PP

                        Fer4_14  85 letngtleie 94 
                                    + tng++ ++
  gi|116754452|ref|YP_843570.1|  91 ITTNGVYLKD 100
                                    *****98755 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 !   30.1   0.0   1.1e-10     5e-07       5      99 ..      13     101 ..      10     119 .. 0.81

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 1.1e-10
                        Fer4_12   5 GvrlslfvsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekp 84 
                                    G+r+s+ +s+Cnl+C +C+ +      +g e+++e++ ++++ ++   i+ + ++GGEPl+   +++l e++  +ke +p
  gi|116754452|ref|YP_843570.1|  13 GLRISV-TSRCNLRCIYCHHE---GEVTGGEISREMAVNVVNAASRLGIRSVKITGGEPLM---RSDLEEMIAGFKEVAP 85 
                                    566665.799********944...44577889999999******99***************...999**********999 PP

                        Fer4_12  85 .ekdiwlytgytleel 99 
                                      +  + ++g+ l++ 
  gi|116754452|ref|YP_843570.1|  86 gVEISITTNGVYLKDR 101
                                    6556677788877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2181.87
//
Query:       gi|116754453|ref|YP_843571.1|  [L=130]
Description: hypothetical protein Mthe_1149 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.15   10.4  13.5       0.17   10.1  13.5    1.0  1  DUF2070         Predicted membrane protein (DUF2070)
        1.3    8.8   4.6       0.93    9.3   3.3    1.3  1  Phtf-FEM1B_bdg  Male germ-cell putative homeodomain transcrip


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 ?   10.1  13.5   1.9e-05      0.17      72     173 ..      11     121 ..       2     126 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 1.9e-05
                        DUF2070  72 lflalltelivviisllaillsall.qalvllalvlslalvfalrllvlvavsdesllkavlpaliqpllailllvly.. 148
                                    +fla + + i ++++ ++++ ++ +    ++++l+l    ++a++++++va++++    +v+ +l+ +ll+ +ll+ +  
  gi|116754453|ref|YP_843571.1|  11 AFLASTLLGITIVLLAFGLIQVF-MyGPTLPHSLILV---ITAISFVIFVALFERYQVGSVAASLLVSLLSTALLTTLsg 86 
                                    66666666666665555555443.3467777777655...8999999999999999999999999999999999999999 PP

                        DUF2070 149 ..........fspesfllllllslifalavylfiv 173
                                              +++e+++ +l+ls+++ +a++ +++
  gi|116754453|ref|YP_843571.1|  87 gvvylmemsdIRWEDAISALALSMMLSMALLSYLK 121
                                    999**************************999986 PP

>> Phtf-FEM1B_bdg  Male germ-cell putative homeodomain transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   3.3    0.0001      0.93      69     140 ..      45     117 ..      31     123 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0001
                 Phtf-FEM1B_bdg  69 virkailrvlllplyakwwikqtsaaifllllllYl.lqliavvlyvlasekekeeeavslsevlvpillmll 140
                                    ++  ai  v++++l+ ++ + ++ a++++ ll   l + l   v+y+++ ++ + e+a+s+ ++ + + + ll
  gi|116754453|ref|YP_843571.1|  45 LVITAISFVIFVALFERYQVGSVAASLLVSLLSTALlTTLSGGVVYLMEMSDIRWEDAISALALSMMLSMALL 117
                                    5678999****************99999999876551566778999999888766666666666555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1140  (0.0635841); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 962.23
//
Query:       gi|116754454|ref|YP_843572.1|  [L=299]
Description: thioredoxin-disulfide reductase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-40  139.5   0.7    1.6e-40  139.2   0.7    1.0  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    3.9e-22   78.9   0.0    5.8e-17   61.9   0.0    2.1  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    1.1e-07   30.9   1.9     0.0021   16.8   0.3    2.6  3  HI0933_like    HI0933-like protein
    2.2e-07   30.3   3.1    0.00038   19.7   0.3    3.1  3  GIDA           Glucose inhibited division protein A
    5.1e-07   29.1   4.6    2.4e-05   23.6   1.4    2.6  3  FAD_binding_2  FAD binding domain
    2.7e-05   23.5   0.2    4.5e-05   22.8   0.2    1.3  1  Thi4           Thi4 family
    5.3e-05   22.8   0.0    8.6e-05   22.1   0.0    1.5  1  FAD_oxidored   FAD dependent oxidoreductase
    0.00013   21.6   2.5       0.51    9.9   2.1    2.3  2  DAO            FAD dependent oxidoreductase
    0.00044   19.6   0.1    0.00066   19.0   0.1    1.4  1  FAD_binding_3  FAD binding domain
  ------ inclusion threshold ------
      0.038   13.0   0.3       0.97    8.4   0.2    2.2  2  Lycopene_cycl  Lycopene cyclase protein
      0.052   13.8   0.2      0.052   13.8   0.2    2.5  3  NAD_binding_8  NAD(P)-binding Rossmann-like domain
      0.064   13.8   4.1       0.41   11.2   0.0    2.8  3  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.2   0.7   1.1e-43   1.6e-40       1     294 []       2     287 ..       2     288 .. 0.90

  Alignments for each domain:
  == domain 1  score: 139.2 bits;  conditional E-value: 1.1e-43
                                    CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH.........HHHHCHHHHCCCCH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxx RF
                    Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias.........evvkklnqgielll 71 
                                    +dv+v+G+GpAGl+a ++ a+ g+k++++   g++ + + ++   +++++++++ ++          + +k++++++  +
  gi|116754454|ref|YP_843572.1|   2 YDVIVVGAGPAGLTAGMYCARGGMKTLIL---GNVYTSQQSMGGLYENYPGFPDGIQgielsermlSQAQKYGAEYRQEM 78 
                                    69***********************9999...888899999999999999999999999999888877777887777666 PP

                                    CCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-TSEEEEES-S CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  72 geevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllpkrivvvGgG 151
                                     e++v++d    ++ +++  e++  ++ + +l+lAtG+s r+lg+pG++++v+++++++  +++     +   ++vvG G
  gi|116754454|ref|YP_843572.1|  79 VEKIVHLD---DTFRIKT--ESW--EYVCRALILATGASHRKLGVPGEEKYVTRGLSYCVYCDGALFRDRT--TAVVGYG 149
                                    65666664...4566632..234..7999************************999999999998777776..9****** PP

                                    HHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHT.TEEEEESCEEEEEEETTE..EEE.EEETTSCEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx..xxx.xxxxxxxxxx RF
                    Pyr_redox_2 152 yiGvElAaalaklgkevtlveardrllraldkelsaaleealeke.Gvevklgtsvkeidgnge..kle.vvledgeeid 227
                                    + +     +l+++ ++v+l+  r+rl+      ++a + ++l+   +++  +g +v++i+g++    +e vv ++ ++++
  gi|116754454|ref|YP_843572.1| 150 NGAARALLYLSNICSRVHLLCPRERLV------AEAVYLDRLKGInNITQTFGVEVTRITGDEFvsGIEfVVGGTPRSLK 223
                                    **************************9......99*******9977*****************988888*********** PP

                                    ESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTS.BESSTTEEE-GGGCTECCSS--HHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 228 adlvvvavGvrpstelleeklglelderggivvdefl.rtnvpgiyaiGDvaggkggpelaqaAvqqG 294
                                    +d ++v  Gv+p+t+l+ e+lglel+e+g+++v++   +t++pg++a+GDv+   gg +++ +Av +G
  gi|116754454|ref|YP_843572.1| 224 VDGIFVEMGVSPNTKLA-EDLGLELTEGGFVKVNRLTqETSMPGVFAAGDVT---GGRMQVATAVGSG 287
                                    *****************.*****************984689***********...8888888888766 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 !   15.0   0.2   7.2e-06     0.011       1      27 [.       5      30 ..       5      48 .. 0.87
   2 !   61.9   0.0   3.9e-20   5.8e-17     101     305 .]      76     271 ..      62     271 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.2e-06
                    Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylil 27
                                   i++GaGPaGl+a++ + + g+ + lil
  gi|116754454|ref|YP_843572.1|  5 IVVGAGPAGLTAGMYCARGGM-KTLIL 30
                                   89*******************.57888 PP

  == domain 2  score: 61.9 bits;  conditional E-value: 3.9e-20
                    Pyr_redox_3 101 feeVesvkkedegfevetsketyeAkkviiAtGefdkPnklnipGeeklvk...hyskvkefhkyagqkvvViGgknSav 177
                                    +e+Ve++ + d++f+++t++ +y ++ +i+AtG     +kl++pGeek+v+    y  + + + ++++  +V+G +n a+
  gi|116754454|ref|YP_843572.1|  76 QEMVEKIVHLDDTFRIKTESWEYVCRALILATGA--SHRKLGVPGEEKYVTrglSYCVYCDGALFRDRTTAVVGYGNGAA 153
                                    799******************************9..88999******96553336777789999**************** PP

                    Pyr_redox_3 178 DaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekeeeykvktedgkkvev 257
                                     a l l +  ++V+++ +++ + +         ++++ +rl+ +    +i+  f  ev++i+ +e    +++  g + ++
  gi|116754454|ref|YP_843572.1| 154 RALLYLSNICSRVHLLCPRERLVA---------EAVYLDRLKGIN---NITQTFGVEVTRITGDEFVSGIEFVVGGTPRS 221
                                    *******************86555.........478899999864...499***********999888999877766555 PP

                    Pyr_redox_3 258 .kddvvla.tGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                     k d +++ +G +p++++ ++ ++el+e g+++++  t+et +pg+f aG
  gi|116754454|ref|YP_843572.1| 222 lKVDGIFVeMGVSPNTKLAEDLGLELTEGGFVKVNRLTQETSMPGVFAAG 271
                                    588888888***************************************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   0.3   1.4e-06    0.0021       1      30 [.       2      31 ..       2      38 .. 0.92
   2 !   12.6   0.0   2.7e-05      0.04     102     172 ..      50     116 ..      49     128 .. 0.80
   3 ?   -1.8   0.1      0.66   9.8e+02     356     384 ..     248     273 ..     245     282 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.4e-06
                                   -SEEEE--SHHHHHHHHHHHHTT--EEEE- CS
                    HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVllle 30
                                   +dviv+G+G+AGl a + +a+ g ++l+l 
  gi|116754454|ref|YP_843572.1|  2 YDVIVVGAGPAGLTAGMYCARGGMKTLILG 31
                                   59***********************99985 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 2.7e-05
                                    EETT.-CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----SS-GGGT- CS
                    HI0933_like 102 FpvsdkaedivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGlSiPklGs 172
                                    Fp+  +  ++ + +l+++++ g ++r  + v+++ + +d  fr+kt ++ e+ +++l+lAtG +S  klG 
  gi|116754454|ref|YP_843572.1|  50 FPDGIQGIELSERMLSQAQKYGAEYRQ-EMVEKIVHLDDT-FRIKT-ESWEYVCRALILATG-ASHRKLGV 116
                                    666777777788899999999999875.578999776666.*****.9************76.67777775 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.66
                                    EEEE.E-GGGB-TTT-BBTTSTTEEE-GGG CS
                    HI0933_like 356 TaGG.VdlkevssktmeskkvpgLffaGEv 384
                                    T GG V+++ + ++t    ++pg+f aG v
  gi|116754454|ref|YP_843572.1| 248 TEGGfVKVNRLTQET----SMPGVFAAGDV 273
                                    556645555555554....59*******87 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.3   2.5e-07   0.00038       1      28 [.       3      30 ..       3      46 .. 0.85
   2 ?    0.5   0.0      0.17   2.6e+02     114     153 ..      75     112 ..      58     128 .. 0.67
   3 !    8.8   0.1   0.00049      0.74     351     388 ..     261     298 ..     252     299 .] 0.79

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2.5e-07
                                   CEEEE-SSHHHHHHHHHHHHTT--EEEE CS
                           GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi 28
                                   dviV+G+G AG+ A + +ar G+k+l++
  gi|116754454|ref|YP_843572.1|  3 DVIVVGAGPAGLTAGMYCARGGMKTLIL 30
                                   8************************998 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.17
                                    EES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT-BT CS
                           GIDA 114 ieeeveeliveekkvkgvvtedgetikakavviatGtflk 153
                                    ++e+ve+++   + +  ++te+  ++ ++a ++atG+  +
  gi|116754454|ref|YP_843572.1|  75 RQEMVEKIVH-LDDTFRIKTES-WEYVCRALILATGASHR 112
                                    5677777744.44555555554.45668899999998444 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.00049
                                    BBSSSBTEEE-CGGGTB-SHHH.HHHHHHHHHHHHHHHH CS
                           GIDA 351 etkkvkgLflAGqinGteGYeE.aaaqGllAGinaarka 388
                                    et + +g+f+AG+++G   +++ a+++G  A+i a r++
  gi|116754454|ref|YP_843572.1| 261 ET-SMPGVFAAGDVTGGRMQVAtAVGSGASAAISAMRYI 298
                                    44.489***********877762566*********9986 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   1.4   1.6e-08   2.4e-05       1      32 [.       3      34 ..       3      44 .. 0.86
   2 ?   -1.2   0.0      0.54     8e+02     184     204 ..      92     112 ..      36     139 .. 0.59
   3 !    5.8   0.1     0.004         6     388     414 ..     260     286 ..     208     289 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.6e-08
                                   SEEEE--SHHHHHHHHHHHHTTT-EEEEESSS CS
                  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeq 32
                                   DviV+G+G AGL+A++ +a+ G k++++ ++ 
  gi|116754454|ref|YP_843572.1|  3 DVIVVGAGPAGLTAGMYCARGGMKTLILGNVY 34
                                   9**************************98776 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.54
                                    TTCEEEEEESEEEE-----GG CS
                  FAD_binding_2 184 sgrevrirakavvlatgGfgr 204
                                    + +  +++ +a++latg+ +r
  gi|116754454|ref|YP_843572.1|  92 KTESWEYVCRALILATGASHR 112
                                    233345666777777777666 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.004
                                    EEESSBTEEE-STCEESSSSTTS--TT CS
                  FAD_binding_2 388 dgqpipGLYAaGevaaggvhganrlgG 414
                                    +++  pG +AaG v++g ++ a + g+
  gi|116754454|ref|YP_843572.1| 260 QETSMPGVFAAGDVTGGRMQVATAVGS 286
                                    56789***********99998887765 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.2     3e-08   4.5e-05      19      49 ..       3      32 ..       1      44 [. 0.86

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 3e-08
                                   EEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                           Thi4 19 DvvivGaGssGLtaayylakkpdlkvailer 49
                                   Dv++vGaG++GLta+ y a+  ++k++il +
  gi|116754454|ref|YP_843572.1|  3 DVIVVGAGPAGLTAGMYCARG-GMKTLILGN 32
                                   9*******************9.****99864 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   5.8e-08   8.6e-05       1      37 [.       3      43 ..       3     101 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 5.8e-08
                   FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLve....ergvlGGl 37
                                   Dv+VvG+gpaG++A + +ar G k+l++      ++ +GGl
  gi|116754454|ref|YP_843572.1|  3 DVIVVGAGPAGLTAGMYCARGGMKTLILGnvytSQQSMGGL 43
                                   9*************************986333345566665 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   2.1   0.00034      0.51       1      25 [.       3      29 ..       3      42 .. 0.85
   2 !    9.8   0.0   0.00035      0.52     148     207 ..      59     114 ..      38     147 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00034
                                   EEEEECTSHHHHHHHHHHHHTT..EEE CS
                            DAO  1 dvviiGGGiiGlstAyeLarrg..Vtl 25
                                   dv+++G+G +Gl++ ++ ar g  +++
  gi|116754454|ref|YP_843572.1|  3 DVIVVGAGPAGLTAGMYCARGGmkTLI 29
                                   9*****************887786554 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00035
                                    HHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHHHH CS
                            DAO 148 ltaalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsdll 207
                                    l   ++++a++ G+e +++  v+++ + d +  ++ +t++ + +  ++a+++a+Ga  ++l
  gi|116754454|ref|YP_843572.1|  59 LSERMLSQAQKYGAEYRQE-MVEKIVHLD-DTFRI-KTESwEYV--CRALILATGASHRKL 114
                                    5567999***********9.888885533.34666.66666765..7********997744 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   4.4e-07   0.00066       2      32 ..       2      32 ..       1      85 [. 0.92

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 4.4e-07
                                   EEEEEE--SHHHHHHHHHHHHTTHHEEEEES CS
                  FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvek 32
                                   +dV++VGaGpaGl++++  ++ G +++++  
  gi|116754454|ref|YP_843572.1|  2 YDVIVVGAGPAGLTAGMYCARGGMKTLILGN 32
                                   69***********************999865 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.2   0.00065      0.97       1      17 [.       3      19 ..       3      38 .. 0.78
   2 ?    2.5   0.0      0.04        59      88     145 ..      58     113 ..      52     131 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00065
                  Lycopene_cycl  1 DvvviGaGpAglslAar 17
                                   Dv+v+GaGpAgl     
  gi|116754454|ref|YP_843572.1|  3 DVIVVGAGPAGLTAGMY 19
                                   9**********986555 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.04
                  Lycopene_cycl  88 rlkeellerlvengvklleakvesveeeeageslvvleggrkirarlvvdarglaslk 145
                                    +l e++l +  + g+++++  ve++++ ++   ++ +e   +  +r+ + a+g+ ++k
  gi|116754454|ref|YP_843572.1|  58 ELSERMLSQAQKYGAEYRQEMVEKIVHLDD-TFRIKTESW-EYVCRALILATGASHRK 113
                                    78999999999****************999.566666655.55699999999965544 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   3.5e-05     0.052       1      25 [.       6      30 ..       6      49 .. 0.92
   2 ?   -3.3   0.0       7.6   1.1e+04      25      35 ..     268     278 ..     267     281 .. 0.78
   3 ?   -0.2   0.4      0.78   1.2e+03       2      14 ..     284     296 ..     283     299 .] 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.5e-05
                                   EE--SHHHHHHHHHHHCCTEEEEEE CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlll 25
                                   +vGaG +Gl+a  ++a+ g + l+l
  gi|116754454|ref|YP_843572.1|  6 VVGAGPAGLTAGMYCARGGMKTLIL 30
                                   8****************99998886 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 7.6
                                    E-SSSSSSGGG CS
                  NAD_binding_8  25 lekrdrlGGra 35 
                                    + ++d +GGr+
  gi|116754454|ref|YP_843572.1| 268 FAAGDVTGGRM 278
                                    66789999998 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.78
                                    E--SHHHHHHHHH CS
                  NAD_binding_8   2 vGaGlsGlvaAyl 14 
                                    vG+G+s++  A +
  gi|116754454|ref|YP_843572.1| 284 VGSGASAAISAMR 296
                                    9*****9998876 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.5     0.098   1.5e+02       2      24 ..       4      26 ..       3      32 .. 0.81
   2 ?   -2.3   0.0       4.7     7e+03      29      49 ..      58      81 ..      54      93 .. 0.57
   3 ?   11.2   0.0   0.00028      0.41       2      77 ..     143     212 ..     142     219 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.098
                                   EEEECSSHHHHHHHHHHHHTTSE CS
                      Pyr_redox  2 vvvvGgGyiglElAgalaelgkk 24
                                   v+vvG+G  gl ++ + a+ g k
  gi|116754454|ref|YP_843572.1|  4 VIVVGAGPAGLTAGMYCARGGMK 26
                                   89*********998887776665 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.7
                                   ESSSSSS...TTSSHHHHHHHHHH CS
                      Pyr_redox 29 ersdkll...rllDeeaskilqek 49
                                   e s+++l   +++++e ++++ ek
  gi|116754454|ref|YP_843572.1| 58 ELSERMLsqaQKYGAEYRQEMVEK 81
                                   555566643344455555555444 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00028
                                    EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHT.TEEEECSEEEEEEEEETTSEEEEE CS
                      Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekn.gievllntkveeiegsedgvesvk 77 
                                     +vvG G+ +  +  +l+++ ++V+++  +++l       a+++  ++l+   +i+  ++ +v++i+g+e  v++++
  gi|116754454|ref|YP_843572.1| 143 TAVVGYGNGAARALLYLSNICSRVHLLCPRERLV------AEAVYLDRLKGInNITQTFGVEVTRITGDEF-VSGIE 212
                                    58********************************......*********9866999999999999998875.77766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2095.07
//
Query:       gi|116754455|ref|YP_843573.1|  [L=313]
Description: radical SAM domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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-05   23.2   0.0    0.00022   21.6   0.0    1.7  2  Radical_SAM    Radical SAM superfamily
     0.0025   17.8   0.0      0.019   15.0   0.0    2.3  2  Radical_SAM_C  Radical_SAM C-terminal domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   2.5e-08   0.00022       3     159 ..      30     186 ..      28     194 .. 0.81
   2 ?   -1.8   0.0      0.39   3.5e+03     123     143 ..     225     245 ..     201     251 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.5e-08
                                    EESEESS-.-TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHH.HHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC....CC CS
                                    xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xx RF
                    Radical_SAM   3 vtrgCnlr.CsfCarpetvrregrgrslsveeileevkelk.aekgvkevilgggepllypdfvellerlakla....vp 76 
                                     trgC+ + C+ C   +       g + s e+i+++++++  +  g++ v +     +l+p +v +++rl  l+     +
  gi|116754455|ref|YP_843573.1|  30 RTRGCRWNrCVMCGYAQ------EGVDASAEDIIAQFRSILdKVEGAELVKIYTSGSFLDPAEVPEAARLEILRslrdMD 103
                                    79***9999*******7......79999************8766666666666555777777777777777777788999 PP

                                    TEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  77 giritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGen 156
                                     +r+++e+ +  +d+  le +l      + +gle+ +d +   l+n+g tf ++  a ++++++g+++ ++ ++ +pG +
  gi|116754455|ref|YP_843573.1| 104 VRRLVIESRPEYIDRLALEQILSFLDAEIGIGLESSSDLVRTYLINKGFTFFDFTGASDMIHSLGGRVKTYLLLKPPGLS 183
                                    9999999999999966666666666677***********555566699*******************9999999999988 PP

                                    HHH CS
                                    xxx RF
                    Radical_SAM 157 dee 159
                                    + e
  gi|116754455|ref|YP_843573.1| 184 EME 186
                                    754 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.39
                                    CTSHHHHHHHHHHHHHHTTSE CS
                                    xxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM 123 rghtfeevlealeklreagik 143
                                    +g+ +  ++ a+e lrea +k
  gi|116754455|ref|YP_843573.1| 225 GGYRPPWLWSAVEVLREASLK 245
                                    778888889999999999888 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 ?   -0.2   0.0      0.12   1.1e+03      14      37 ..      69      93 ..      67     134 .. 0.51
   2 !   15.0   0.0   2.1e-06     0.019       6      39 ..     207     240 ..     202     247 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.12
                  Radical_SAM_C 14 gTeLaelyksgey.kplsleeyvdl 37
                                   g eL + y sg +  p ++ e+ +l
  gi|116754455|ref|YP_843573.1| 69 GAELVKIYTSGSFlDPAEVPEAARL 93
                                   5566666666654344444444333 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 2.1e-06
                  Radical_SAM_C   6 lypllvikgTeLaelyksgeykplsleeyvdlva 39 
                                    l ++ v ++T+L++++++g y+p  l  +v+++ 
  gi|116754455|ref|YP_843573.1| 207 LNLCNVQRNTPLERMWQRGGYRPPWLWSAVEVLR 240
                                    66799******************99988888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2220.03
//
Query:       gi|116754456|ref|YP_843574.1|  [L=223]
Description: uridylate kinase, putative [Methanosaeta thermophila PT]
Scores for complete 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-28   99.2   3.8    1.7e-26   93.3   3.8    2.0  1  AA_kinase  Amino acid kinase family


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.3   3.8   9.4e-31   1.7e-26       1     241 []       1     201 [.       1     201 [. 0.86

  Alignments for each domain:
  == domain 1  score: 93.3 bits;  conditional E-value: 9.4e-31
                                    TEEEEEE-TTCCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC....E..HHHHHHHHHH CS
                      AA_kinase   1 krvVvKlGGssltdkeeaslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaaglrstleeagevatrd 80 
                                    ++vV  lGGs+l+  + a l+r+ae ++++  ++n++ vV+Ggg+ +++++ +++++ ++e+                 d
  gi|116754456|ref|YP_843574.1|   1 MIVVYSLGGSVLAAQDSAGLKRYAEALRTI-ARDNQVYVVVGGGALAREYIGKARDVGASEALC---------------D 64 
                                    789*******999555567***********.999*******************99999999883...............* PP

                                    HHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETTTEEEEE-H CS
                      AA_kinase  81 alaslgerlvaallaaglpavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvltgfigldeegelgrgss 160
                                    ++++l++r++aallaa+l   g  ++ +  +                 +aie + +  + +v+ g++    +g+    ++
  gi|116754456|ref|YP_843574.1|  65 SIGILATRMNAALLAAAL--DGSAPFRVPESY---------------DDAIEAS-KT-YRMVVMGGV---SPGQ----TT 118
                                    ******************..333444443222...............3344444.44.445555544...3777....9* PP

                                    HHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHH..CSSS.TTTHHHHCHHHHHHHHHCTT-EEE CS
                      AA_kinase 161 DtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaee..saselatgGmkvkhpaalaaarrggipvv 238
                                    D +aallAe+ +A  l+i+t+V+GVy++dp k+p a+++p++ ++++    s+ el  g+  +++p a+++++r+ ip+v
  gi|116754456|ref|YP_843574.1| 119 DAVAALLAEYTRATLLVIATSVNGVYTSDPEKDPGAVKIPRMGAKDLSRmmSQIELKAGSKSPVDPLAAKIIERSHIPTV 198
                                    ******************************************************************************** PP

                                    EEE CS
                      AA_kinase 239 Itn 241
                                    +++
  gi|116754456|ref|YP_843574.1| 199 VVD 201
                                    985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); 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: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1584.42
//
Query:       gi|116754457|ref|YP_843575.1|  [L=288]
Description: signal transduction protein [Methanosaeta thermophila PT]
Scores for complete 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-35  119.4   0.0    6.9e-35  118.6   0.0    1.5  1  HrcA_DNA-bdg   Winged helix-turn-helix transcription represso
    1.4e-15   57.5   0.9    5.8e-07   29.9   0.1    2.9  2  CBS            CBS domain
    3.8e-08   33.6   0.0    1.1e-07   32.1   0.0    1.8  1  Rrf2           Transcriptional regulator
    2.9e-06   27.1   0.4    1.2e-05   25.2   0.0    2.1  2  HTH_11         HTH domain
    0.00012   22.1   0.1    0.00052   20.0   0.0    2.0  2  HTH_20         Helix-turn-helix domain
     0.0017   18.2   0.1     0.0084   16.0   0.0    2.2  2  MarR_2         MarR family
  ------ inclusion threshold ------
      0.058   13.0   0.1      0.077   12.6   0.1    1.3  1  Aconitase_2_N  Aconitate hydratase 2 N-terminus
      0.058   13.3   0.1       0.45   10.4   0.0    2.5  4  TrmB           Sugar-specific transcriptional regulator TrmB
       0.08   12.6   0.2          1    9.1   0.0    2.7  3  Sigma70_r4_2   Sigma-70, region 4
       0.19   11.5   1.0       0.44   10.3   0.1    2.1  2  HTH_38         Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.6   0.0   3.8e-38   6.9e-35       1      76 [.       2      77 ..       2      80 .. 0.97

  Alignments for each domain:
  == domain 1  score: 118.6 bits;  conditional E-value: 3.8e-38
                   HrcA_DNA-bdg  1 eLtsvqkeilqaLielyrkkkravKgeeiAevlkrneGtvRNqlqsLkalgLvegvpGPkGGYkPtlkayealkiq 76
                                   eLt+vq++il+aLi+++r+++ravKgeeiAe+++rn+Gt+RNq+qsLkal+LvegvpGPkGGYk t +ayeal ++
  gi|116754457|ref|YP_843575.1|  2 ELTPVQRDILTALINIHRREGRAVKGEEIAELIDRNPGTIRNQMQSLKALNLVEGVPGPKGGYKATGAAYEALCLD 77
                                   69**********************************************************************9765 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.1   8.7e-09   1.6e-05       6      56 ..     177     224 ..     162     225 .. 0.85
   2 !   29.9   0.1   3.2e-10   5.8e-07       1      55 [.     232     285 ..     232     286 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 8.7e-09
                                    BSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                            CBS   6 trdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                     r+ v ++p++++ +a+++m+++gvs    Vde+    G+v+l+Dl+ra++
  gi|116754457|ref|YP_843575.1| 177 ARRAVRISPSSSIQDAARTMIHNGVSEA-LVDESS--PGLVSLSDLVRAIA 224
                                    455679********************99.887555..5***********97 PP

  == domain 2  score: 29.9 bits;  conditional E-value: 3.2e-10
                                    HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                            CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                    V++imtr ++t++ d+ + ea+++m ++g  ++ VV e g + G+v   D++r l
  gi|116754457|ref|YP_843575.1| 232 VREIMTRGYLTIDSDDLIYEAIKIMGKTGAAQI-VVTEGGVPWGLVNPLDIIRSL 285
                                    89***********************77666677.8889999***********975 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0   6.1e-11   1.1e-07       2      66 ..       2      65 ..       1      73 [. 0.89

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 6.1e-11
                                   ---HHHHHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCEE CS
                           Rrf2  2 klsskteyalhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGkgGGyr 66
                                   +l+   +  l+al+ + ++e++  v+ eeiae  + +p  ++  ++ L+  +lv+ v G++GGy+
  gi|116754457|ref|YP_843575.1|  2 ELTPVQRDILTALINIHRREGRA-VKGEEIAELIDRNPGTIRNQMQSLKALNLVEGVPGPKGGYK 65
                                   55555666799**********98.****************************************8 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   6.5e-09   1.2e-05      11      55 .]      19      65 ..       7      65 .. 0.84
   2 ?   -1.1   0.0       1.1   1.9e+03      31      51 ..     248     269 ..     240     271 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 6.5e-09
                         HTH_11 11 eargp.isgeeLAeeLnvSrrtvrrdIkaLeelgvpIesepgr..GYr 55
                                   + +g  + gee+Ae +++   t+r+ +++L++l   +e++pg+  GY+
  gi|116754457|ref|YP_843575.1| 19 RREGRaVKGEEIAELIDRNPGTIRNQMQSLKALN-LVEGVPGPkgGYK 65
                                   344555***************************9.*********9996 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.1
                         HTH_11  31 tvrrdIkaLeelg.vpIesepg 51 
                                     ++  Ik++ ++g ++I+ + g
  gi|116754457|ref|YP_843575.1| 248 LIYEAIKIMGKTGaAQIVVTEG 269
                                    5899999999999888877766 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   2.9e-07   0.00052      10      58 ..       5      58 ..       3      61 .. 0.88
   2 ?   -1.5   0.0       1.5   2.7e+03      15      32 ..     219     234 ..     216     241 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.9e-07
                                   HHHHHHHHHH.....STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                         HTH_20 10 PvRrrilraL.....araegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                   Pv+r+il aL     ++++++  +e+ae++d  + t++++++ L    Lve+v 
  gi|116754457|ref|YP_843575.1|  5 PVQRDILTALinihrREGRAVKGEEIAELIDRNPGTIRNQMQSLKALNLVEGVP 58
                                   9************66666666668***************************986 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.5
                                    HHHHHSTCTTB-HHHHHH CS
                         HTH_20  15 ilraLaraegltaselae 32 
                                    + ra+  aeg+t+ ++ e
  gi|116754457|ref|YP_843575.1| 219 LVRAI--AEGRTCVDVRE 234
                                    56777..99999988776 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   4.7e-06    0.0084       7      58 ..      10      61 ..       2      63 .. 0.87
   2 ?   -1.7   0.0       1.5   2.7e+03      22      40 ..     171     191 ..     164     200 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.7e-06
                                   HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSS CS
                         MarR_2  7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpe 58
                                   ++ +L +++rr+gr +   e+a+  +  ++++ +  + L a  Lve +pgp 
  gi|116754457|ref|YP_843575.1| 10 ILTALINIHRREGRAVKGEEIAELIDRNPGTIRNQMQSLKALNLVEGVPGPK 61
                                   4556788999**99**********************************9985 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.5
                                    EEHHHHHH.HHTSSH.HHHHH CS
                         MarR_2  22 ltvgelar.rlglsk.savsr 40 
                                    + v+ +ar + ++s+ s+++ 
  gi|116754457|ref|YP_843575.1| 171 IPVKKIARrAVRISPsSSIQD 191
                                    667777774566666455555 PP

>> Aconitase_2_N  Aconitate hydratase 2 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   4.3e-05     0.077      81     136 ..      79     138 ..      14     181 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.3e-05
                                    SEEETTEEEEEE--EEEEEEE-HHHHHHHHH....TT-EEEE---TT--TT-EEEEETTT CS
                  Aconitase_2_N  81 gedipyvPnkraggvvlGgkiaPiFfntved....sGalpieadvskletGdvieikpke 136
                                      d+  vP  ++g  v G++ + i fn v +    sG + i+ +v++++ Gd iei p+ 
  gi|116754457|ref|YP_843575.1|  79 SGDVVDVPIIKNGVQVEGASASEIIFNKVMQhdscSGMVRITGNVRDFNIGDEIEIGPTP 138
                                    568889*****************9999863223448********************8764 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00025      0.45      23      65 ..      25      67 ..       3      70 .. 0.90
   2 ?   -2.5   0.0       2.8     5e+03      28      42 ..     162     176 ..     161     183 .. 0.78
   3 ?   -2.3   0.0       2.4   4.3e+03      35      52 ..     185     202 ..     172     208 .. 0.76
   4 ?   -2.7   0.0       3.2   5.7e+03      39      54 ..     249     264 ..     246     268 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00025
                                   CHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE- CS
                           TrmB 23 atadeiaeelgvprskvYevLrsLedkGlVerekgrpklYrav 65
                                    + +eiae +++   ++ + ++sL+   lVe ++g +  Y+a+
  gi|116754457|ref|YP_843575.1| 25 VKGEEIAELIDRNPGTIRNQMQSLKALNLVEGVPGPKGGYKAT 67
                                   5679*****************************9999888875 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.8
                                    HCCCTTSSCHCHHHH CS
                           TrmB  28 iaeelgvprskvYev 42 
                                    ++e++ vpr  v ++
  gi|116754457|ref|YP_843575.1| 162 VSEMISVPRIPVKKI 176
                                    899999999777666 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.4
                                    SCHCHHHHHHHHHHCTSE CS
                           TrmB  35 prskvYevLrsLedkGlV 52 
                                    p s+++++ r ++  G+ 
  gi|116754457|ref|YP_843575.1| 185 PSSSIQDAARTMIHNGVS 202
                                    778899998888888875 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 3.2
                                    HHHHHHHHHHCTSEEE CS
                           TrmB  39 vYevLrsLedkGlVer 54 
                                    +Ye+++ + + G  ++
  gi|116754457|ref|YP_843575.1| 249 IYEAIKIMGKTGAAQI 264
                                    7999999999988776 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.97   1.7e+03      10      20 ..       2      12 ..       1      13 [. 0.88
   2 ?    9.1   0.0   0.00058         1      30      48 ..      28      46 ..      25      50 .. 0.92
   3 ?   -0.7   0.0      0.66   1.2e+03      27      43 ..     187     206 ..     186     207 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.97
                                   TS-HHHHHHHH CS
                   Sigma70_r4_2 10 eLperqreifl 20
                                   eL++ qr i++
  gi|116754457|ref|YP_843575.1|  2 ELTPVQRDILT 12
                                   79*******97 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00058
                                   HHHHHHHT--HHHHHHHHH CS
                   Sigma70_r4_2 30 kEIAellgisegtVksrls 48
                                   +EIAel++ ++gt++++++
  gi|116754457|ref|YP_843575.1| 28 EEIAELIDRNPGTIRNQMQ 46
                                   8***************986 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.66
                                    --HHHHHHHH...T--HHHH CS
                   Sigma70_r4_2  27 lsykEIAell...gisegtV 43 
                                    +s++++A+ +   g+se+ V
  gi|116754457|ref|YP_843575.1| 187 SSIQDAARTMihnGVSEALV 206
                                    6999****999999999866 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00025      0.44      19      39 ..      21      43 ..      13      46 .. 0.79
   2 ?   -2.2   0.1       2.1   3.8e+03      23      29 ..     173     179 ..     172     182 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00025
                         HTH_38 19 eGlslr..eIArrLgrspsTIsR 39
                                   eG  ++  eIA +++r+p+TI +
  gi|116754457|ref|YP_843575.1| 21 EGRAVKgeEIAELIDRNPGTIRN 43
                                   555555559************87 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.1
                         HTH_38  23 lreIArr 29 
                                    +++IArr
  gi|116754457|ref|YP_843575.1| 173 VKKIARR 179
                                    689**98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); 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: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2039.54
//
Query:       gi|116754458|ref|YP_843576.1|  [L=377]
Description: radical SAM domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.7e-19   69.7   0.0    5.5e-19   69.1   0.0    1.3  1  Radical_SAM  Radical SAM superfamily
    3.2e-06   27.5   0.0    5.2e-06   26.8   0.0    1.2  1  Fer4_12      4Fe-4S single cluster domain
      9e-06   26.1   0.1      9e-06   26.1   0.1    1.8  2  SPASM        Iron-sulfur cluster-binding domain
  ------ inclusion threshold ------
      0.012   15.7   0.0       0.02   15.0   0.0    1.3  1  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.1   0.0   1.2e-22   5.5e-19       1     166 [.      99     253 ..      99     254 .. 0.91

  Alignments for each domain:
  == domain 1  score: 69.1 bits;  conditional E-value: 1.2e-22
                                    EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiri 80 
                                    ++vt+ C++rC++Ca p     +g + sl +e++ ++++++  + g   +i+ ggep +y+++ el+     +    +++
  gi|116754458|ref|YP_843576.1|  99 ISVTEECPNRCKHCALPD----TGEHLSLEPEDVQRIIDQA-LDLGSTLIIFDGGEPCMYRELPELVSYVDDR---AVTT 170
                                    68999************5....8******************.8********************9999999997...6777 PP

                                    EEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  81 tvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglpGendee 159
                                     +++ ++   +  ++ l+++g+  v+++l+++ +e  ++ ++ r++ + + ++a++ + +ag+   vd +v+l+  n  +
  gi|116754458|ref|YP_843576.1| 171 MFTSGAGFT-DGLAKQLRDAGLQAVNVSLDSPLEE-EHDAIRgRKGVYRDAMNAIKHALSAGLL--VDLYVVLRHDNIMH 246
                                    777777775.*************************.5555555******************999..9**********999 PP

                                    HHHHHHH CS
                                    xxxxxxx RF
                    Radical_SAM 160 leellel 166
                                    l+ + el
  gi|116754458|ref|YP_843576.1| 247 LQSFHEL 253
                                    9988765 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0   1.2e-09   5.2e-06      12     124 ..     102     207 ..      92     215 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 1.2e-09
                        Fer4_12  12 vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdiwly 91 
                                    ++ C+ +Ck C    + +  ++   + e  ++ii+++ +   + +++ GGEP +   +++l elv +v  +++  + + +
  gi|116754458|ref|YP_843576.1| 102 TEECPNRCKHCA---LPDTGEHLSLEPEDVQRIIDQALDLGSTLIIFDGGEPCM---YRELPELVSYVDDRAV--TTMFT 173
                                    578*******87...666677778889999************************...99**************..68889 PP

                        Fer4_12  92 tgytleelskk.ekeellkeidvlvdGkfeesle 124
                                    +g  + + ++k  ++  l+ ++v +d ++ee+  
  gi|116754458|ref|YP_843576.1| 174 SGAGFTDGLAKqLRDAGLQAVNVSLDSPLEEEHD 207
                                    9999998877746677799999999999998764 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.7         4   1.8e+04      60      67 ..     105     112 ..      96     113 .. 0.70
   2 !   26.1   0.1     2e-09     9e-06       1      46 [.     313     352 ..     313     366 .. 0.85

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 4
                          SPASM  60 lielCrnC 67 
                                    +++ C++C
  gi|116754458|ref|YP_843576.1| 105 CPNRCKHC 112
                                    45568888 PP

  == domain 2  score: 26.1 bits;  conditional E-value: 2e-09
                          SPASM   1 CfapsrslfInsdGdVvpCcvdkktyveelklGnireesleeIwns 46 
                                    Cfa+++ + +++ GdV+pC     +y  + + Gn  +esl+ Iw+ 
  gi|116754458|ref|YP_843576.1| 313 CFAGRSWMHVTPSGDVYPC----ACY--PKSYGNGLRESLSRIWKR 352
                                    9******************....344..69*****999******53 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 ?   15.0   0.0   4.4e-06      0.02       5      77 ..     102     166 ..      99     199 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.4e-06
                        Fer4_14   5 lsgCnlsCkgCdnket.wkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkee 77 
                                    +  C+  Ck C   +t  + +l++++++++++q l      +     + + GGeP +y + +el   v+++ ++
  gi|116754458|ref|YP_843576.1| 102 TEECPNRCKHCALPDTgEHLSLEPEDVQRIIDQAL------DLGSTLIIFDGGEPCMYRELPEL---VSYVDDR 166
                                    578********955530445666666666666666......4444557899*******665555...5555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); 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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2682.79
//
Query:       gi|116754459|ref|YP_843577.1|  [L=121]
Description: phosphoribosyl-AMP cyclohydrolase [Methanosaeta thermophila PT]
Scores for complete 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  118.0   0.1    1.4e-34  117.7   0.1    1.1  1  PRA-CH    Phosphoribosyl-AMP cyclohydrolase


Domain annotation for each model (and alignments):
>> PRA-CH  Phosphoribosyl-AMP cyclohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.7   0.1   8.1e-39   1.4e-34       1      74 []      27     100 ..      27     100 .. 0.99

  Alignments for each domain:
  == domain 1  score: 117.7 bits;  conditional E-value: 8.1e-39
                                    EEEEE-HHHHHHHHHHSB-EEEETTTTEEEETTTTTS--EEEEEEEE-TTSSEEEEEEEESS-SSTTSBSSS-- CS
                         PRA-CH   1 mlaymnkealektletgkavyySrsrkklWkKGetSgnvqkvkeirlDcDqDalllkveqkgaaCHtgkesCFy 74 
                                    mlay+n+ al+ktletg a+y+Srsr klW+KGe+Sgn q vkei +DcD+Da+llkveqkg aCHtg++sCFy
  gi|116754459|ref|YP_843577.1|  27 MLAYINSIALSKTLETGVAHYWSRSRGKLWRKGESSGNEQIVKEILVDCDEDAILLKVEQKGGACHTGYRSCFY 100
                                    9************************************************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 867.39
//
Query:       gi|116754460|ref|YP_843578.1|  [L=226]
Description: hypothetical protein Mthe_1156 [Methanosaeta thermophila PT]
Scores for 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-58  195.2  20.8    1.1e-57  195.0  20.8    1.0  1  DUF2162     Predicted transporter (DUF2162)
  ------ inclusion threshold ------
      0.047   12.6   6.3      0.033   13.1   0.8    2.1  2  MFS_1_like  MFS_1 like family
       0.26   12.0   0.0          3    8.5   0.0    2.1  1  RCR         Chitin synthesis regulation, resistance to Congo 
        3.6    8.0  12.2        0.2   12.1   3.8    2.8  2  DUF805      Protein of unknown function (DUF805)


Domain annotation for each model (and alignments):
>> DUF2162  Predicted transporter (DUF2162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.0  20.8   2.5e-61   1.1e-57       3     223 .]       6     221 ..       4     221 .. 0.97

  Alignments for each domain:
  == domain 1  score: 195.0 bits;  conditional E-value: 2.5e-61
                        DUF2162   3 vlGiLfailifgiKtGlglglsnlsrkklllilllYlllflllalllssldekllesllrygmvlhllmAlllialGlyt 82 
                                     lG+L+++lif++K+ +g+gl++ls+++++l++++Yll+++++++++++++++l+ ++ r g+ +h+++A++l+alG++t
  gi|116754460|ref|YP_843578.1|   6 ALGVLTGLLIFALKASMGCGLAHLSCREIVLVASGYLLVATAMGFVIDRMSIDLMAEMIRAGVAMHTVLAICLVALGMLT 85 
                                    69****************************************************************************** PP

                        DUF2162  83 lkkwkkskkdvssrtflalvlPCPvCltailfsiillasslglspvevglvlglvflilvlvtyllsrkivkltktnypi 162
                                    l++w++s++d+s++tf+al++PCP+C++a+++s+ +la+++++sp ++g+++gl++++++++++ll+r+i+       p 
  gi|116754460|ref|YP_843578.1|  86 LREWRRSGTDISRKTFWALSIPCPACMVATFLSCGVLADVIKISPARIGAAVGLMLFVTITSISLLLRRIRG-----GPD 160
                                    ********************************************************************9999.....*** PP

                        DUF2162 163 iLGnlmlfiGlyfLlsaliipniaqakaiylspltessieslllv.lvlllallllGfllrk 223
                                    i+G++m+++G +++ls++++p+++q+++++l  ++ + ++s+l++ +++ll+l+ +G+++r+
  gi|116754460|ref|YP_843578.1| 161 IIGRVMMLLGGFYILSIMLLPSYIQLQKTSLDCIAPE-MHSELVPsYLILLLLISIGYVIRR 221
                                    ***********************************97.6666665499999999*****986 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 ?   13.1   0.8   7.3e-06     0.033     149     234 ..      32     116 ..      27     128 .. 0.64
   2 ?    2.6   0.5     0.011        51     154     213 ..     135     193 ..     129     219 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.3e-06
                     MFS_1_like 149 rqrlfGsvGyaifafitGilidhysvnllp..ysallyvlaallvisllvvlilnetekesklkvtkslqvllnilknpe 226
                                    r+++  + Gy ++a+++G++id +s++l+   ++a +++ ++l ++ +++  +l+  e+ ++      ++ +++ l+ p 
  gi|116754460|ref|YP_843578.1|  32 REIVLVASGYLLVATAMGFVIDRMSIDLMAemIRAGVAMHTVLAICLVAL-GMLTLREWRRSGTDIS-RKTFWA-LSIPC 108
                                    56667788*******************99998666555555555544444.5566667766665552.344443.44444 PP

                     MFS_1_like 227 viifllva 234
                                     ++++++ 
  gi|116754460|ref|YP_843578.1| 109 PACMVATF 116
                                    44444444 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.011
                     MFS_1_like 154 GsvGyaifafitGilidhysvnllp..ysallyvlaallvisllvvlilnetekesklkvtk 213
                                     +vG ++f++it+i +   ++   p  +  ++++l +++++s+++   l+   + +k+ + +
  gi|116754460|ref|YP_843578.1| 135 AAVGLMLFVTITSISLLLRRIRGGPdiIGRVMMLLGGFYILSIML---LPSYIQLQKTSLDC 193
                                    699**********99999999776699778899999999999998...44444444444444 PP

>> RCR  Chitin synthesis regulation, resistance to Congo red
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0   0.00068         3       9      70 ..      72     206 ..      66     209 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00068
                            RCR   9 ivlillvllltlrvakrRrrrGlqplygtgWlvsa............................................. 43 
                                    +vl++ ++ l +++ +  rr+G++  + t W+ s                                              
  gi|116754460|ref|YP_843578.1|  72 TVLAICLVALGMLTLREWRRSGTDISRKTFWALSIpcpacmvatflscgvladvikisparigaavglmlfvtitsisll 151
                                    45555566666667788888888888888888773455677777778888888888888888888888888888888888 PP

                            RCR  44 ..........................pppPsYgqsqqqynqa.es.ltsatvpty 70 
                                                              +  PsY q q++      + ++s+ vp+y
  gi|116754460|ref|YP_843578.1| 152 lrrirggpdiigrvmmllggfyilsiMLLPSYIQLQKTSLDCiAPeMHSELVPSY 206
                                    8888888888888888888889999999999999877555447555888888887 PP

>> DUF805  Protein of unknown function (DUF805)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   1.4      0.31   1.4e+03      19      54 ..      44      79 ..       4      93 .. 0.55
   2 ?   12.1   3.8   4.5e-05       0.2       8      71 ..      96     167 ..      91     222 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.31
                         DUF805 19 fllllvivlallaavlaaaavasalsvvlallllvp 54
                                   + +++ +v+  +++ l+a ++ + +++  +l+++++
  gi|116754460|ref|YP_843578.1| 44 VATAMGFVIDRMSIDLMAEMIRAGVAMHTVLAICLV 79
                                   222222332222222222333333333333333333 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 4.5e-05
                         DUF805   8 asRsefwwfvlfllllvivlallaavlaa....aavasalsvvlallllvpslavtvRRlHD....tgrsgw 71 
                                    +sR+ fw   + + +++++ +l   vla+    + +    +v l+l+++++s++++ RR++     +gr  +
  gi|116754460|ref|YP_843578.1|  96 ISRKTFWALSIPCPACMVATFLSCGVLADvikiSPARIGAAVGLMLFVTITSISLLLRRIRGgpdiIGRVMM 167
                                    69*****888888777777777777776667667777888888999999999*******9854444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); 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):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1603.27
//
Query:       gi|116754461|ref|YP_843579.1|  [L=214]
Description: integral membrane protein [Methanosaeta thermophila PT]
Scores for complete 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   39.3   0.1    6.9e-10   38.8   0.1    1.3  1  MotA_ExbB     MotA/TolQ/ExbB proton channel family
  ------ inclusion threshold ------
       0.36   10.7   1.1       0.48   10.3   0.2    1.6  2  Myc_target_1  Myc target protein 1


Domain annotation for each model (and alignments):
>> MotA_ExbB  MotA/TolQ/ExbB proton channel family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.1   7.7e-14   6.9e-10      22     106 ..      95     177 ..      71     196 .. 0.88

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 7.7e-14
                                    HHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSSSGGCTHHHHHHHHHHHHHHH CS
                      MotA_ExbB  22 aepeelrraleealsreeerlekglsilatigslaPllGLlGTVlGlieafqaladagsadlakvapgiaeALiaTalGl 101
                                     e++ lr  le+ l+ +e  + ++l+ l++   + P lGL+GT++ +  a+ +l+     d++++a ++  A+ +T++Gl
  gi|116754461|ref|YP_843579.1|  95 LESNILRVRLEKILQDAELDMARRLEPLRIGMRVGPILGLMGTLIPMGPALVSLSR---GDVQSMAASLIIAFATTVIGL 171
                                    56667788899999*****************************************9...677****************** PP

                                    HHH.HH CS
                      MotA_ExbB 102 vvA.ip 106
                                    vv  i 
  gi|116754461|ref|YP_843579.1| 172 VVGgIC 177
                                    **9554 PP

>> Myc_target_1  Myc target protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.39   3.5e+03      29      62 ..      27      60 ..      22      81 .. 0.56
   2 ?   10.3   0.2   5.3e-05      0.48      16      45 ..     156     183 ..     148     190 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.39
                   Myc_target_1 29 mvvGLllgaliyvlltwlsrrrasaritrrssrr 62
                                   ++ G  l  +  v+  + srrr   ++ + + r 
  gi|116754461|ref|YP_843579.1| 27 VLFGWSLILVGSVIQEYTSRRRDVHELEEVTLRA 60
                                   5555555555556666777777766555444443 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 5.3e-05
                   Myc_target_1  16 fdledlilaFcvSmvvGLllgaliyvlltw 45 
                                    + +  li+aF+   v+GL++g++ y  l +
  gi|116754461|ref|YP_843579.1| 156 M-AASLIIAFAT-TVIGLVVGGICYCSLLI 183
                                    4.689*****86.689*********98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1537.91
//
Query:       gi|116754462|ref|YP_843580.1|  [L=111]
Description: hypothetical protein Mthe_1158 [Methanosaeta thermophila PT]
Scores for complete 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  113.0   0.4    6.8e-33  112.8   0.4    1.0  1  DUF2149   Uncharacterized conserved protein (DUF2149)


Domain annotation for each model (and alignments):
>> DUF2149  Uncharacterized conserved protein (DUF2149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.8   0.4   3.8e-37   6.8e-33       1      92 []      12     103 ..      12     103 .. 0.99

  Alignments for each domain:
  == domain 1  score: 112.8 bits;  conditional E-value: 3.8e-37
                        DUF2149   1 lsgvaNLfDvalVlavallvalvsslnlqellsseedvtvvkkpgkekmeiivkegeelkkakesaekasgkGerlGtay 80 
                                    ++gvaNLfD+a+V+avall+alv+++n++ell+++++vtvvk+pg+++m+ii+k+ ++++  ++++++++g+G+r+Gtay
  gi|116754462|ref|YP_843580.1|  12 MEGVANLFDIAMVFAVALLLALVTAYNISELLDPTSSVTVVKNPGDPDMQIIIKNMSSIQVLNMTEQVGGGQGTRIGTAY 91 
                                    89****************************************************************************** PP

                        DUF2149  81 rlkdGkliyVPe 92 
                                    rlk+G++iyVPe
  gi|116754462|ref|YP_843580.1|  92 RLKSGQVIYVPE 103
                                    ***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 802.34
//
Query:       gi|116754463|ref|YP_843581.1|  [L=255]
Description: beta-lactamase domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.7e-15   55.1   0.0      9e-15   54.7   0.0    1.1  1  Lactamase_B_2  Beta-lactamase superfamily domain
    5.6e-12   46.1   0.2    4.7e-11   43.1   0.1    2.0  2  Lactamase_B    Metallo-beta-lactamase superfamily


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.7   0.0     1e-18     9e-15       3     200 ..      39     216 ..      38     217 .. 0.81

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 1e-18
                                    EEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC.....C--EE..EEEEEEHHHHHHCCTTCG CS
                  Lactamase_B_2   3 iLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlre.....lrpkk..lplyapkgvlavleanfv 75 
                                    +LiD+g +     l          ++ +id Vllth H DH+a+ll l++     +   +  l++++p g+ + +++  +
  gi|116754463|ref|YP_843581.1|  39 LLIDCGAGAILR-LGE-----IGMSPLEIDTVLLTHLHLDHVADLLPLAKaryllG---EpwLNIWGPVGTEELMRSLQS 109
                                    689999994333.222.....3456668**********************777433...146******999887777766 PP

                                    HHHCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HHHHHHHC CS
                  Lactamase_B_2  76 ylaleeepavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipeeigerlg 155
                                         +  +++v+e+ +g +fe+   g+ +    a h+ +          l +rie g ++v  +gDt+    ++ e+  
  gi|116754463|ref|YP_843581.1| 110 LYPYLRSIKLDVTEISAGCRFEIC--GFGVSSASAIHSVPA---------LCYRIE-GSRTVTCSGDTEPAA-SVSELAS 176
                                    6666666688*************6..455999999***999.........******.99**********666.7788*** PP

                                    T-SEEEEE-S-SSTTHHHHHHT---STSHHHHCTTSSSSEEEEES CS
                  Lactamase_B_2 156 gadllllditayeddemirhmgHltpeeaveaaadlgakrlvliH 200
                                    g dll++++ + +  e      H tp    +++ d+g    +l+H
  gi|116754463|ref|YP_843581.1| 177 GSDLLVHECSFPDGFE---VTNHTTPAALGRIVSDVGE--IILTH 216
                                    ********99988888...6789999999999888874..45555 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   0.1   5.3e-15   4.7e-11       6      67 ..      28      83 ..      24      86 .. 0.90
   2 ?    0.8   0.0     0.047   4.2e+02      35      53 ..     199     217 ..     154     217 .. 0.84

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 5.3e-15
                                   SEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTH CS
                    Lactamase_B  6 vnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglvea 67
                                   ++s li  d++v+LiD+G ++   +       +g  p+++d+v+lTHlHlDH+++l  l++a
  gi|116754463|ref|YP_843581.1| 28 QSSLLI-RDEDVLLIDCGAGAILRLGE-----IGMSPLEIDTVLLTHLHLDHVADLLPLAKA 83
                                   456666.7*****************98.....9***********************999987 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.047
                                    HHHHTSGGGGEEEEE-SBS CS
                    Lactamase_B  35 laalglkpkdvdavilTHl 53 
                                    +aalg+   dv  +ilTH+
  gi|116754463|ref|YP_843581.1| 199 PAALGRIVSDVGEIILTHF 217
                                    5678999999999*****6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 1823.60
//
Query:       gi|116754464|ref|YP_843582.1|  [L=221]
Description: chromosome segregation and condensation protein ScpA [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-19   70.1   4.1    7.5e-11   42.4   0.1    2.5  2  SMC_ScpA  Segregation and condensation protein ScpA


Domain annotation for each model (and alignments):
>> SMC_ScpA  Segregation and condensation protein ScpA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   0.1   4.2e-15   7.5e-11       1      70 [.      24      92 ..      24     102 .. 0.90
   2 !   27.7   1.3   1.3e-10   2.3e-06     133     239 ..     122     215 ..     101     216 .. 0.75

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 4.2e-15
                                   HHHHHHHHHTSSSSXXXXHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHSXXXXXXXXXXXXXXX CS
                       SMC_ScpA  1 LiiakeldvtdvavakvtdqflayiktllnkleleesteylviastlvelKaasLlpleqveeeedeele 70
                                   L+ ++eld++dv+++  t++fl+y++ l ++ +l + +  l+ a+ l+++K++ + + e++ee e+  +e
  gi|116754464|ref|YP_843582.1| 24 LARRGELDPWDVDIVRTTERFLEYVESL-ERRDLRIPARTLLYAAILLRMKSDAMEEQEEEEEIEEAPVE 92
                                   67799***********************.**************************999988887766555 PP

  == domain 2  score: 27.7 bits;  conditional E-value: 1.3e-10
                                    XXXXXXXXXXXXXXXXXXXXXXX...HHHHHHHHHHHH...............HHHTS-EEGGGSSTT...--HHHHHHH CS
                       SMC_ScpA 133 klieafnkllkrakivalaekqiseleisieeqleellaqleqflqarlkevLldlrswvdlseLladnkledkkelvgv 212
                                    +l +a     kra  ++lae + ++l++s+ee++ee +     +l+     v+ d+    +++e+++    e   + +  
  gi|116754464|ref|YP_843582.1| 122 ELKKAEMIGRKRAIRQRLAEPEEEILDLSHEENVEERIK----MLS----PVIEDM---LSMKEMVEI--KEIEGDRIMN 188
                                    3333333444555555556656689***********994....554....455566...8999***99..66678999** PP

                                    HHHHHHHHHTT-EEEEESSTTS-EEEE CS
                       SMC_ScpA 213 FlAlLeLiknqavaleQeeflddLqvs 239
                                    +lAlL + + + + leQe+f++dL+++
  gi|116754464|ref|YP_843582.1| 189 YLALLFMAQRKQIWLEQEQFFGDLFIT 215
                                    ************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       784  (0.043728); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); 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: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1660.63
//
Query:       gi|116754465|ref|YP_843583.1|  [L=1171]
Description: chromosome segregation protein SMC [Methanosaeta thermophila PT]
Scores for complete 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-71  239.6   0.2    3.2e-71  239.3   0.2    1.1  1  SMC_N            RecF/RecN/SMC N terminal domain
    5.6e-30  104.0   0.0    1.2e-29  102.9   0.0    1.6  1  SMC_hinge        SMC proteins Flexible Hinge Domain
    1.1e-14   55.4   0.2    1.1e-14   55.4   0.2    5.9  1  AAA_23           AAA domain
    2.6e-12   47.2   0.1    8.5e-11   42.2   0.0    3.4  1  AAA_15           AAA ATPase domain
    2.5e-10   40.7   9.7    2.3e-05   24.3   0.0    4.5  5  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    5.1e-07   29.3   0.0    9.6e-07   28.5   0.0    1.4  1  AAA_29           P-loop containing region of AAA domain
    7.8e-06   26.2  96.7     0.0047   17.2   6.8    8.4  7  ATG16            Autophagy protein 16 (ATG16)
    2.2e-05   25.0 110.0     0.0023   18.4  14.8    8.8  8  APG6_N           Apg6 coiled-coil region
    0.00097   17.9  48.1     0.0011   17.7   9.6    4.3  4  AAA_13           AAA domain
      0.002   18.4   3.4         27    5.1   0.0    6.6  7  DUF948           Bacterial protein of unknown function (DUF94
     0.0032   17.5  45.3      0.095   12.7   2.5    8.3 10  DUF1664          Protein of unknown function (DUF1664)
     0.0037   16.2  15.4     0.0037   16.2  15.4    6.4  4  DUF812           Protein of unknown function (DUF812)
     0.0055   16.8  13.0        6.6    6.8   0.3    6.2  7  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
     0.0074   16.3  12.4     0.0074   16.3  12.4    7.4  6  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
  ------ inclusion threshold ------
      0.019   13.9  88.8       0.14   11.0   6.7    7.2  8  Spc7             Spc7 kinetochore protein
      0.021   15.2   0.0      0.021   15.2   0.0    9.5 10  Snapin_Pallidin  Snapin/Pallidin
      0.032   11.8  77.8     0.0022   15.6  11.4    4.3  4  DUF3584          Protein of unknown function (DUF3584)
      0.034   14.0   0.1       0.32   10.9   0.0    2.7  2  GP41             Retroviral envelope protein
      0.038   14.3   7.1       0.67   10.2   0.0    4.4  4  AAA_22           AAA domain
      0.054   13.8   0.0        2.6    8.4   0.0    3.0  2  AAA_19           AAA domain
      0.072   11.8   0.0      0.072   11.8   0.0    3.4  3  RNA12            RNA12 protein
       0.13   11.6   0.0       0.13   11.6   0.0    3.6  4  FtsK_SpoIIIE     FtsK/SpoIIIE family
       0.65    9.3  77.1       0.87    8.9  15.7    8.2  7  GAS              Growth-arrest specific micro-tubule binding
       0.74   10.3   0.0       0.74   10.3   0.0    5.2  4  ABC_tran         ABC transporter
        1.1    9.7   0.0        1.1    9.7   0.0    5.8  2  AAA_16           AAA ATPase domain
        1.3    9.3  71.9       0.36   11.1  12.0    7.5  8  FliJ             Flagellar FliJ protein
        1.9    8.6  70.3       0.17   11.9   2.9    7.6  7  ADIP             Afadin- and alpha -actinin-Binding
        2.1    8.7  45.7       0.34   11.2   0.3    9.4  8  BLOC1_2          Biogenesis of lysosome-related organelles co
        2.7    7.5  86.8        5.4    6.5   9.1    6.4  3  Filament         Intermediate filament protein
          4    7.8  88.1      0.031   14.7  11.4    6.4  6  Fez1             Fez1
        4.5    7.2  10.5         22    5.0   0.0    5.3  5  Flg_hook         Flagellar hook-length control protein FliK


Domain annotation for each model (and alignments):
>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  239.3   0.2   5.5e-74   3.2e-71       1     219 [.       2    1163 ..       2    1164 .. 1.00

  Alignments for each domain:
  == domain 1  score: 239.3 bits;  conditional E-value: 5.5e-74
                                     EEEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEE CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N    1 vlkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkae 78  
                                     ++k++e++nFks+ g+++ ++++k f +++GpNGSGKsn++dA+lF L  +s++++r+e+l dli++ +++++ ++ae
  gi|116754465|ref|YP_843583.1|    2 HIKEIELRNFKSF-GRRALVQLKKDFIVVTGPNGSGKSNIIDALLFSLCLTSSRAMRAERLPDLIYRGDDGRAPDFAE 78  
                                     599**********.5*************************************************************** PP

                                     EEEEEEETTEESSSSSSCEEEEEEEETTSE...EEEEETTEEE-HHHHHHHHHCTT-STT.................. CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx.................. RF
                          SMC_N   79 veitfdnedkklkiekeevsisrrvkrkge...seykingkevtkkevsellesagiske.................. 135 
                                     v++ +dn+ ++++++++ev+i+rr+k +ge    ++++ng+ +t++e++e l++agi++e                  
  gi|116754465|ref|YP_843583.1|   79 VTVRLDNSTRTMPVDSDEVVITRRIKVNGEryhAQHYLNGRACTQAELQEHLARAGITPEgynvvmqgdvtriiemgp 156 
                                     *****************************9888899****************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gi|116754465|ref|YP_843583.1|  157 terrriideiagvsefeekkqramaeldvvreriarvdvileevgqqlrrlqaerdralryracreerkkqeayllla 234 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gi|116754465|ref|YP_843583.1|  235 rfkeaeaeisalddeitsitseksqllqsleagreelrrleerlkavegeishkgedeqlrvrreieeirgkiareet 312 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gi|116754465|ref|YP_843583.1|  313 rieaadadieeadrslsqcfiemdrvraeiaaiseqlsdkamrragiqgelddqrsqlsslranisdadsrfakyree 390 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gi|116754465|ref|YP_843583.1|  391 laqlikeiedtrsqigerlrerdrlldairrasmekeeiateitealssisaasteserlerevesiaseamdldkrr 468 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gi|116754465|ref|YP_843583.1|  469 eelesrrlslrrelaeldrslqrlqseyarveaqvraaeersgysraveavrsamkrgilqglcgtiadlgevdrrya 546 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gi|116754465|ref|YP_843583.1|  547 aalevaagarlqsviaesdedaavaidylkrsqigratflplnkmevgslpevprvpgvidfalnlirfddrfypafw 624 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gi|116754465|ref|YP_843583.1|  625 yvfrdtlvvedldtarrmigryrmvtldgdliersgamtgghytsrlkfaaeesrrlvgiserisatearrgellekl 702 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gi|116754465|ref|YP_843583.1|  703 dsveeeissisrklesldkeisrrtflleekralrgrmeryieerksrlsemereseewrsrltvleqemqelesals 780 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gi|116754465|ref|YP_843583.1|  781 ekgdlreklerdmqgsripemmeraeqlegeirrlesrimdldseimrcrlkeenlrnrldelartkellelkkndai 858 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gi|116754465|ref|YP_843583.1|  859 qrrssalssmedlraaldelsrkekdldrelhglkgergslmesiigkereiggmersierldarltavsgareeisi 936 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gi|116754465|ref|YP_843583.1|  937 smqslrseiesagidpseappksetiaakiraleeemaslepvnmlaideyervdkrfrnlsdrrevlhreregiiek 1014
                                     ****************************************************************************** PP

                                     .................................................................CS-HHHHHHHHHH CS
                                     .................................................................xxxxxxxxxxxxx RF
                          SMC_N  136 .................................................................lLSgGektLvala 148 
                                                                                                      ++SgGek+L+al+
  gi|116754465|ref|YP_843583.1| 1015 lerydqlkkdafmscfaavnqnfreifhelsggdgelvlecpddplsggmtirarpagkvfhrleAMSGGEKSLTALS 1092
                                     ****************************************************************************** PP

                                     HHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEEEEETTEE CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  149 LlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklvgvtkvengvs 219 
                                     L+fAiq+++pap+y +Deid+ LD +nv++va+++++ s +aQfiv+slr+ m+++a+ ++gv+++e+++s
  gi|116754465|ref|YP_843583.1| 1093 LIFAIQRFRPAPFYAMDEIDMFLDGANVERVAKMIRRISRDAQFIVVSLRRPMIQQASYTIGVSMQEKNIS 1163
                                     *****************************************************************999886 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 !  102.9   0.0   2.2e-32   1.2e-29       2     116 ..     529     642 ..     528     643 .. 0.97

  Alignments for each domain:
  == domain 1  score: 102.9 bits;  conditional E-value: 2.2e-32
                      SMC_hinge   2 kgvlGrladlievdegyekAveaalgnrlqalvvedeetakkiieflkkknagratflpldrikqknkadgandknsgav 81 
                                    +g+ G++adl evd++y +A+e+a+g+rlq+++ e++e+a  +i++lk+ + gratflpl++++  + ++ ++  +  + 
  gi|116754465|ref|YP_843583.1| 529 QGLCGTIADLGEVDRRYAAALEVAAGARLQSVIAESDEDAAVAIDYLKRSQIGRATFLPLNKMEVGSLPEVPRVPG-VID 607
                                    6899********************************************************************9998.*** PP

                      SMC_hinge  82 plidlvevddelrkalryllgdtlvvdsldeAeel 116
                                    ++++l+++dd++++a+ y+++dtlvv++ld+A+++
  gi|116754465|ref|YP_843583.1| 608 FALNLIRFDDRFYPAFWYVFRDTLVVEDLDTARRM 642
                                    ********************************987 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.4   0.2     2e-17   1.1e-14       2     199 ..       6     285 ..       5     286 .. 0.63

  Alignments for each domain:
  == domain 1  score: 55.4 bits;  conditional E-value: 2e-17
                         AAA_23   2 Lkienfrsfrdqe.idFskgltlItGpNGaGKTTildAiklaLygetprlsrks.............grgfeksdveies 67 
                                    ++++nf+sf++   ++++k + ++tGpNG+GK+ i+dA+ + L   ++r  r +               +f +  v++ +
  gi|116754465|ref|YP_843583.1|   6 IELRNFKSFGRRAlVQLKKDFIVVTGPNGSGKSNIIDALLFSLCLTSSRAMRAErlpdliyrgddgrAPDFAEVTVRLDN 85 
                                    89*******666559*************************9998888888887779999999888532266666666666 PP

                         AAA_23  68 e......gkvkayveltfenkdgry................................................trsiere 93 
                                    +      ++++ +++++++ +++ry                                                 r+i +e
  gi|116754465|ref|YP_843583.1|  86 StrtmpvDSDEVVITRRIKVNGERYhaqhylngractqaelqehlaragitpegynvvmqgdvtriiemgpteRRRIIDE 165
                                    6888887777777999999999988****************999999999999998888888766666666664444444 PP

                         AAA_23  94 relskkkgkttkkaklellei...........deleqfisellgskkiilnlilflgqerfeefelkdkke.......rl 155
                                    +   ++ +++++ a  el  +           +e  q++++l + + ++  ++  + +er+        k+       r 
  gi|116754465|ref|YP_843583.1| 166 IAGVSEFEEKKQRAMAELDVVreriarvdvilEEVGQQLRRL-QAERDRALRYRACREERK--------KQeaylllaRF 236
                                    444444444443332222222112322333334444444432.222222333333333332........22233333344 PP

                         AAA_23 156 eelekeleeledekkllekl.....eqekekekeleeleeeleeilkel 199
                                    +e+e e+  l de+  +  +     + ++  ++el  lee+l+ ++ e+
  gi|116754465|ref|YP_843583.1| 237 KEAEAEISALDDEITSITSEksqllQSLEAGREELRRLEERLKAVEGEI 285
                                    4444444444443333333333343344457778888888888776655 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.0   1.5e-13   8.5e-11       1     277 [.       1     404 [.       1     492 [. 0.69

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 1.5e-13
                         AAA_15   1 MkIkkikikNFRslkd.veidlseeltvliGkNnsGKSsilealdlFlnnkekkn......................... 54 
                                    M Ik+i+++NF+s+   + ++l++++ v+ G+N+sGKS+i++al  +++     +                         
  gi|116754465|ref|YP_843583.1|   1 MHIKEIELRNFKSFGRrALVQLKKDFIVVTGPNGSGKSNIIDAL--LFSLCLTSSramraerlpdliyrgddgrapdfae 78 
                                    99************998***************************..444332333568999999************9998 PP

                         AAA_15  55 ................................................kkvikiekedleifeniseskdikIdvef... 83 
                                                                                    +                           +   
  gi|116754465|ref|YP_843583.1|  79 vtvrldnstrtmpvdsdevvitrrikvngeryhaqhylngractqaelQ---------------------------Ehla 131
                                    7777777777777777777664444444444433333333333333330...........................2666 PP

                         AAA_15  84 ..................................................................aek.ekakeyektl 96 
                                                                                                      + + +++  +++++
  gi|116754465|ref|YP_843583.1| 132 ragitpegynvvmqgdvtriiemgpterrriideiagvsefeekkqramaeldvvreriarvdvilE-EvGQQLRRLQAE 210
                                    6666666666666666666666666666666666677777777766666666666699998888643.258889999999 PP

                         AAA_15  97 kskekkkadlllkkkesdlkktikdkklklkknelsdekisvekkks.........kkelpkekeeklekekeelkidke 167
                                    ++++ +++ +  ++k+++ + ++  +k +  ++   d+ i+    ++          +e     ee l+  + e++++ e
  gi|116754465|ref|YP_843583.1| 211 RDRALRYRACREERKKQEAYLLLARFKEAEAEISALDDEITSITSEKsqllqsleaGREELRRLEERLKAVEGEISHKGE 290
                                    99999999999999999999988888888877776666655554444478888888555555557777777788888877 PP

                         AAA_15 168 dlkklikkleeslkkeeelknvlksaiiklllisakRnvsd..edsekkssllgklkekileealqekl.....eeelte 240
                                    d +   ++ +e + ++    +    ++ + ++ +a+R+ s+   + +  + + ++++++ l++++  ++      +++++
  gi|116754465|ref|YP_843583.1| 291 DEQLRVRREIEEIRGKI-AREETRIEAADADIEEADRSLSQcfIEMDRVR-AEIAAISEQLSDKAMRRAgiqgeLDDQRS 368
                                    77777766666666666.56667777777778888888887432222222.22222222222223333367777666666 PP

                         AAA_15 241 klkeiqeklkeidkklaeelkkilkkkidkikkfnyk 277
                                    +l+++  +++++d+ + +++ ++l + i++i+++  +
  gi|116754465|ref|YP_843583.1| 369 QLSSLRANISDADSRF-AKYREELAQLIKEIEDTRSQ 404
                                    7777777777777776.55556666666666555444 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0     4e-08   2.3e-05       1      21 [.      26      46 ..      26      79 .. 0.80
   2 ?    0.7   0.2      0.63   3.6e+02     115     215 ..     221     327 ..     203     351 .. 0.74
   3 ?   -1.9   0.2         4   2.3e+03     165     165 ..     427     427 ..     354     519 .. 0.47
   4 ?   -0.7   0.3       1.7   9.7e+02     124     206 ..     699     789 ..     684     881 .. 0.74
   5 !   18.2   0.0     3e-06    0.0017     235     296 ..    1079    1140 ..     944    1140 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 4e-08
                         AAA_21  1 lnvliGpNgsGKSnLLdaldl 21
                                   + v++GpNgsGKSn++dal +
  gi|116754465|ref|YP_843583.1| 26 FIVVTGPNGSGKSNIIDALLF 46
                                   689****************55 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.63
                         AAA_21 115 argirggvsvfslkelsvsepndlqfgkaltditsrawsllllldglrke......rigllnifadyfgfakekrllqrl 188
                                     ++ ++++ +  l+ +  +e+++    + +t+its++++ll++l+++r+e      r    +  +++ g+++ +r +++ 
  gi|116754465|ref|YP_843583.1| 221 REERKKQEAYLLLARFKEAEAEISALDDEITSITSEKSQLLQSLEAGREElrrleeRLKAVEGEISHKGEDEQLRVRREI 300
                                    55555566666666677777788888888999999999999999999999888877777777777777777777777777 PP

                         AAA_21 189 vrslklveielsdlgegeeliasvder 215
                                    +  + ++  e + +++++ +i+++d+ 
  gi|116754465|ref|YP_843583.1| 301 EEIRGKIAREETRIEAADADIEEADRS 327
                                    777777777777777666666666655 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 4
                         AAA_21 165 r 165
                                    +
  gi|116754465|ref|YP_843583.1| 427 E 427
                                    2 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 1.7
                         AAA_21 124 vfslkelsvsepndlqfgkaltditsrawsllllldglrke........rigllnifadyfgfakekrllqrlvrslklv 195
                                     ++l + + +++++  + + l++ +sr  +ll+++++lr +        +++l ++ ++   + ++++ l++ + +l  +
  gi|116754465|ref|YP_843583.1| 699 LEKLDSVEEEISSISRKLESLDKEISRRTFLLEEKRALRGRmeryieerKSRLSEMERESEEWRSRLTVLEQEMQELESA 778
                                    55555556666666666666666666666666666666666666666667777777777777777777777777777777 PP

                         AAA_21 196 eielsdlgege 206
                                     +e  dl+e+ 
  gi|116754465|ref|YP_843583.1| 779 LSEKGDLREKL 789
                                    76666666554 PP

  == domain 5  score: 18.2 bits;  conditional E-value: 3e-06
                         AAA_21  235 relSdGtkrl..lalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltT 296 
                                       +S G k+l  l l+ a+ r ++  ++++ DE++ +L+ + ++r+++++++ sr +aQ+i+++
  gi|116754465|ref|YP_843583.1| 1079 EAMSGGEKSLtaLSLIFAIQRFRPA-PFYAMDEIDMFLDGANVERVAKMIRRISR-DAQFIVVS 1140
                                     34799**999744999999999998.*****************************.*****986 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   1.7e-09   9.6e-07       2      47 ..       4      49 ..       3      56 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.7e-09
                         AAA_29  2 krlqlvNWgtfdg.htieidlkgatlltGpsGsGKSTllDAiqalLv 47
                                   k+++l N  +f +   ++++ k+++++tGp+GsGKS ++DA+ + L+
  gi|116754465|ref|YP_843583.1|  4 KEIELRNFKSFGRrALVQLK-KDFIVVTGPNGSGKSNIIDALLFSLC 49
                                   68999********7777776.669*****************987665 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   8.4     0.019        11      63     126 ..     223     286 ..     173     292 .. 0.78
   2 !   17.2   6.8   8.1e-06    0.0047      80     186 ..     290     396 ..     286     407 .. 0.96
   3 !   15.3  16.7     3e-05     0.018      87     174 ..     423     510 ..     399     515 .. 0.89
   4 !    7.1   2.9    0.0097       5.6     100     152 ..     684     736 ..     674     739 .. 0.88
   5 ?    5.7   6.8     0.026        15     107     161 ..     740     794 ..     738     798 .. 0.88
   6 ?    2.2  11.0      0.31   1.8e+02      27     162 ..     801     947 ..     800     955 .. 0.76
   7 ?    2.9   1.1      0.19   1.1e+02     111     186 ..     938    1013 ..     932    1020 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.019
                          ATG16  63 asasqsnskqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerla 126
                                    ++++q++    a+ ++ e+++++l +e +    ++++l q+l +  eel++lee+lk+ e ++ 
  gi|116754465|ref|YP_843583.1| 223 ERKKQEAYLLLARFKEAEAEISALDDEITSITSEKSQLLQSLEAGREELRRLEERLKAVEGEIS 286
                                    222234566789999*****************************************99998875 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 8.1e-06
                          ATG16  80 eqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDE 159
                                    e++ +++r e +e   + +  ++r+ ++ + +++ +++l++   ++++++ae+aa++++l+d++++ ++ +  ++d++  
  gi|116754465|ref|YP_843583.1| 290 EDEQLRVRREIEEIRGKIAREETRIEAADADIEEADRSLSQCFIEMDRVRAEIAAISEQLSDKAMRRAGIQGELDDQRSQ 369
                                    67788999************************************************************************ PP

                          ATG16 160 lsaLqlqlnqaEeklrklekENkeLve 186
                                    ls+L+   + a+++  k ++E ++L++
  gi|116754465|ref|YP_843583.1| 370 LSSLRANISDADSRFAKYREELAQLIK 396
                                    *************************96 PP

  == domain 3  score: 15.3 bits;  conditional E-value: 3e-05
                          ATG16  87 reelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlq 166
                                      e +e   + +e  +++ ++++e ++le++ ++ +++  +l ++r++le ++ +++ el+e+++ +q lq E++  + q
  gi|116754465|ref|YP_843583.1| 423 SMEKEEIATEITEALSSISAASTESERLEREVESIASEAMDLDKRREELESRRLSLRRELAELDRSLQRLQSEYARVEAQ 502
                                    556666666677888999************************************************************** PP

                          ATG16 167 lnqaEekl 174
                                    +  aEe++
  gi|116754465|ref|YP_843583.1| 503 VRAAEERS 510
                                    ******96 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.0097
                          ATG16 100 laqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekekl 152
                                     ++r+ ++++   +l ekl + ee++ +++++ ++l +++++r+  l+ek++l
  gi|116754465|ref|YP_843583.1| 684 ISERISATEARRGELLEKLDSVEEEISSISRKLESLDKEISRRTFLLEEKRAL 736
                                    5789999999999999*********************************9976 PP

  == domain 5  score: 5.7 bits;  conditional E-value: 0.026
                          ATG16 107 lneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDEls 161
                                    ++  +++++++l+e+e++ +e +++ ++le++++++e +l ek  l ++l  +++
  gi|116754465|ref|YP_843583.1| 740 MERYIEERKSRLSEMERESEEWRSRLTVLEQEMQELESALSEKGDLREKLERDMQ 794
                                    6667889999999*****************************9999998887776 PP

  == domain 6  score: 2.2 bits;  conditional E-value: 0.31
                          ATG16  27 Lldrtsaleaenaklekaaasaks.......sksskksakekeasasq....snskqsakiqsleqklaqlreelaelyk 95 
                                    +++r+++le e ++le+++ +  s       ++ + +++  ++a++++    ++++  ++ +s  + +  lr+ l el +
  gi|116754465|ref|YP_843583.1| 801 MMERAEQLEGEIRRLESRIMDLDSeimrcrlKEENLRNRLDELARTKEllelKKNDAIQRRSSALSSMEDLRAALDELSR 880
                                    67888888888888888888888766665554444455555555555587775555556666666667778888999999 PP

                          ATG16  96 srgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsa 162
                                    +  +l   l  l+ e   l e++  +e+++  +e+++++l  +l     + +e    +q l+ E+++
  gi|116754465|ref|YP_843583.1| 881 KEKDLDRELHGLKGERGSLMESIIGKEREIGGMERSIERLDARLTAVSGAREEISISMQSLRSEIES 947
                                    9999999999999999999999999999999999999999999999999999988888888888876 PP

  == domain 7  score: 2.9 bits;  conditional E-value: 0.19
                          ATG16  111 lqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnqaEeklrklekENkeLve 186 
                                     +q l++++++      e+  + +++  k++ +eee++ +e ++    DE++    ++  + ++++ l++E +  +e
  gi|116754465|ref|YP_843583.1|  938 MQSLRSEIESAGIDPSEAPPKSETIAAKIRALEEEMASLEPVNMLAIDEYERVDKRFRNLSDRREVLHREREGIIE 1013
                                     5666666777777777777777777888888888888888888888888888888888888888877777666665 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4  14.8   4.1e-06    0.0023       8     103 ..     194     297 ..     191     304 .. 0.90
   2 ?    4.4   6.3     0.091        52      40     128 ..     299     386 ..     291     391 .. 0.80
   3 !   12.4  23.7    0.0003      0.17      15     129 ..     374     506 ..     360     509 .. 0.72
   4 ?    5.7   3.8     0.034        19      50      94 ..     682     726 ..     666     741 .. 0.82
   5 ?   -0.0  17.3       2.1   1.2e+03      14      96 ..     698     791 ..     695     797 .. 0.77
   6 ?   -2.0  22.6       8.3   4.8e+03      11     121 ..     744     863 ..     740     869 .. 0.66
   7 ?    5.6   3.4     0.038        22      46     101 ..     865     920 ..     852     948 .. 0.67
   8 ?    6.9   1.1     0.015       8.4      11     110 ..     917    1021 ..     913    1039 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 4.1e-06
                         APG6_N   8 dlLleeldkqleqaekerdaYeeflkklkkekkeeek.........qdeeleeleeeleklekeeeelleeLkelekere 78 
                                    d++lee+ +ql+++++erd  +++ +  +++kk+e +          + e+ +l++e+  + +e+++ll+ L++  +e +
  gi|116754465|ref|YP_843583.1| 194 DVILEEVGQQLRRLQAERDRALRYRACREERKKQE-AylllarfkeAEAEISALDDEITSITSEKSQLLQSLEAGREELR 272
                                    789****************9888888777776665.35999****99********************************* PP

                         APG6_N  79 eleaelaaleeelealeeeeerfwr 103
                                    +le+ l+a e e +++ e+e+  +r
  gi|116754465|ref|YP_843583.1| 273 RLEERLKAVEGEISHKGEDEQLRVR 297
                                    ***************9999986655 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.091
                         APG6_N  40 keeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlelleleeel 119
                                    + ee  + ++++ e ++e+ +++ ee+ + L +   e ++++ae+aa++e+l+++    +    e  +++ +l++l    
  gi|116754465|ref|YP_843583.1| 299 EIEE-IRGKIAREETRIEAADADIEEADRSLSQCFIEMDRVRAEIAAISEQLSDKAMRRAGIQGELDDQRSQLSSLRANI 377
                                    4444.467888888999999999999999999999999999999999999999999999999999999999999988877 PP

                         APG6_N 120 dsleaqyeh 128
                                       +++++ 
  gi|116754465|ref|YP_843583.1| 378 SDADSRFAK 386
                                    777777665 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.0003
                         APG6_N  15 dkqleqaekerdaYeeflkklkkekkeeek..................qdeeleeleeeleklekeeeelleeLkeleke 76 
                                       +++a++   +Y+e l++l ke +++++                     e ee+  e+ +  +  +++ +e ++le+e
  gi|116754465|ref|YP_843583.1| 374 RANISDADSRFAKYREELAQLIKEIEDTRSqigerlrerdrlldairrASMEKEEIATEITEALSSISAASTESERLERE 453
                                    55566666666666666666666655544466777777777666677767777778888888888888888888888888 PP

                         APG6_N  77 reeleaelaaleeelealeeeeerfwreynelqlelleleeeldsleaqyeha 129
                                     e++++e  +l +  e+le       re  el++ l++l+ e + +eaq++ a
  gi|116754465|ref|YP_843583.1| 454 VESIASEAMDLDKRREELESRRLSLRRELAELDRSLQRLQSEYARVEAQVRAA 506
                                    88888888888888888888888888888888888888888888888887766 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.034
                         APG6_N  50 eeleeeleklekeeeelleeLkelekereeleaelaaleeeleal 94 
                                      + e+++++e+ + elle+L+ +e+e +++ ++l++l +e +++
  gi|116754465|ref|YP_843583.1| 682 VGISERISATEARRGELLEKLDSVEEEISSISRKLESLDKEISRR 726
                                    5567889999*****************************999876 PP

  == domain 5  score: -0.0 bits;  conditional E-value: 2.1
                         APG6_N  14 ldkqleqaekerdaYeeflkklkkekkeeek............qdeeleeleeeleklekeeeelleeLkelekereele 81 
                                    l ++l+++e+e+ + ++ l+ l+ke +   +             +  +ee + +l+++e+e ee  + L  le+e +ele
  gi|116754465|ref|YP_843583.1| 698 LLEKLDSVEEEISSISRKLESLDKEISRR-TflleekralrgrMERYIEERKSRLSEMERESEEWRSRLTVLEQEMQELE 776
                                    67899999999999999999999996654.36777777777776777777777788888888888888888888888888 PP

                         APG6_N  82 aelaaleeelealee 96 
                                    ++l++     e+le+
  gi|116754465|ref|YP_843583.1| 777 SALSEKGDLREKLER 791
                                    888887776666665 PP

  == domain 6  score: -2.0 bits;  conditional E-value: 8.3
                         APG6_N  11 leeldkqleqaekerdaYeeflkklkkekkeeek.........qdeeleeleee.........leklekeeeelleeLke 72 
                                    +ee +++l+++e+e ++ ++ l  l++e +e e+         +         +         + ++ +  e+l+ e+++
  gi|116754465|ref|YP_843583.1| 744 IEERKSRLSEMERESEEWRSRLTVLEQEMQELESalsekgdlrE---------KlerdmqgsrIPEMMERAEQLEGEIRR 814
                                    78889999999999999999999999998887775555444331.........322223333455577777777777777 PP

                         APG6_N  73 lekereeleaelaaleeelealeeeeerfwreynelqlelleleeelds 121
                                    le+   +l++e+   + ++e+l +  ++  r    l+l++++  +++ s
  gi|116754465|ref|YP_843583.1| 815 LESRIMDLDSEIMRCRLKEENLRNRLDELARTKELLELKKNDAIQRRSS 863
                                    7777777777777777777777777777777777777777766666665 PP

  == domain 7  score: 5.6 bits;  conditional E-value: 0.038
                         APG6_N  46 deeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerf 101
                                     +++e+l+  l++l+++e++l +eL  l+ er +l + +   e+e   +e+  er 
  gi|116754465|ref|YP_843583.1| 865 LSSMEDLRAALDELSRKEKDLDRELHGLKGERGSLMESIIGKEREIGGMERSIERL 920
                                    45778888888888888888888888888888888888888888776666655555 PP

  == domain 8  score: 6.9 bits;  conditional E-value: 0.015
                         APG6_N   11 leeldkqleqaekerdaYeeflkklkkekkeeek....qdeeleeleeeleklekeeeelleeLkelekereeleael 84  
                                     +e+ld +l ++   r++ +  ++ l++e +++         + e +  ++++le+e ++l+     + +e e++++  
  gi|116754465|ref|YP_843583.1|  917 IERLDARLTAVSGAREEISISMQSLRSEIESAGIdpseAPPKSETIAAKIRALEEEMASLEPVNMLAIDEYERVDKRF 994 
                                     788899999999999999999999999877755466663334444555566666666666665556667777777777 PP

                         APG6_N   85 aaleeelealeeeeerfwreyne.lql 110 
                                     ++l+   e l++e e  +++     ql
  gi|116754465|ref|YP_843583.1|  995 RNLSDRREVLHREREGIIEKLERyDQL 1021
                                     777777777777777777776663444 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   4.7     0.015       8.9     347     454 ..     175     286 ..     165     291 .. 0.56
   2 !    5.5   2.2    0.0093       5.4     402     459 ..     298     355 ..     287     379 .. 0.81
   3 !    5.8   9.7     0.008       4.6     283     430 ..     365     508 ..     356     524 .. 0.45
   4 !   17.7   9.6     2e-06    0.0011     267     477 ..     692     934 ..     688     979 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.015
                         AAA_13 347 KrkepfksvelesvkakiesikklvaeineliakhNekvan...l...eeekeeakkklelhlveeleseldeykkkykk 420
                                    K+++ ++  el++v ++i ++  +++e+ ++ ++  +  ++   +    ee+++ +  l l + +e+e+e++++++++ +
  gi|116754465|ref|YP_843583.1| 175 KKQRAMA--ELDVVRERIARVDVILEEVGQQLRRLQAERDRalrYracREERKKQEAYLLLARFKEAEAEISALDDEITS 252
                                    5544444..66666666666666666666666555444332111200023333333344444456667777777777777 PP

                         AAA_13 421 lekaieklekelkeeeaelkkleeeikeLekqlr 454
                                    ++ + ++l ++l++  +el+ lee+ k+ e +++
  gi|116754465|ref|YP_843583.1| 253 ITSEKSQLLQSLEAGREELRRLEERLKAVEGEIS 286
                                    7777777777777777777777777776666665 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0093
                         AAA_13 402 hlveeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpa 459
                                     ++ee++ ++ + ++ +++++++ie+++++l++   e+  +++ei+++ +ql+d+   
  gi|116754465|ref|YP_843583.1| 298 REIEEIRGKIAREETRIEAADADIEEADRSLSQCFIEMDRVRAEIAAISEQLSDKAMR 355
                                    3789999999999999999999999999999999999999999999999999987655 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.008
                         AAA_13 283 ekqerLekliekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfksvelesvka 362
                                    ++ ++L++l +++  + s++ +k+ +    a++ ++ e+ ++++ +++++ +  L++++ra  +K  e++++++  ++ +
  gi|116754465|ref|YP_843583.1| 365 DQRSQLSSLRANISDADSRF-AKYREE--LAQLIKEIEDTRSQIGERLRERDRLLDAIRRASMEKE-EIATEIT--EALS 438
                                    23333333333333332211.222111..1222233334444444444444444555555555554.5555333..2223 PP

                         AAA_13 363 kiesi...kklvaeineliakhNekvanleeekeeakkklelhlveeleseldeykkkykklekaieklek 430
                                     i+++   ++ +++  e+ia+     ++  ee e+ + +l++ +++el+  l++++++y+++e+++  +e+
  gi|116754465|ref|YP_843583.1| 439 SISAAsteSERLEREVESIASEAMDLDKRREELESRRLSLRR-ELAELDRSLQRLQSEYARVEAQVRAAEE 508
                                    333330003444444444444444444444444444555666.5677888888888888888888887774 PP

  == domain 4  score: 17.7 bits;  conditional E-value: 2e-06
                         AAA_13 267 aerkaaLeahFddefeekqerLekliekveskkselleklkavsde...........asensafeedkeelkaeaealee 335
                                    ++r+ +L +  d+ +ee+++++++++e++++++s+ +  l++  +            +s+ s++e++ ee ++++ +le+
  gi|116754465|ref|YP_843583.1| 692 EARRGELLEKLDS-VEEEISSISRKLESLDKEISRRTFLLEEKRALrgrmeryieerKSRLSEMERESEEWRSRLTVLEQ 770
                                    5666666666666.77777777777777766655555444444443444444454467788889999************* PP

                         AAA_13 336 qLkglqraleaKrkepfksvelesvkakiesikklvaeineliakhNekvanleeekeeakkklelhlv........... 404
                                    ++++l++al++K  ++ +++e +   ++i ++ +  ++++  i++   ++ +l++e  +++ k e  +            
  gi|116754465|ref|YP_843583.1| 771 EMQELESALSEKG-DLREKLERDMQGSRIPEMMERAEQLEGEIRRLESRIMDLDSEIMRCRLKEENLRNrldelartkel 849
                                    ************9.888889999999999888888888888888888888888888888876655544345566678888 PP

                         AAA_13 405 ............eeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLkaf.G 471
                                                +++ s ++ +  ++++l+++ ++l++el   + e   l e i  +e+++   ++++e +   L+a+ G
  gi|116754465|ref|YP_843583.1| 850 lelkkndaiqrrSSALSSMEDLRAALDELSRKEKDLDRELHGLKGERGSLMESIIGKEREIGGMERSIERLDARLTAVsG 929
                                    88888888777755666667777888888888888888888888888888888999999999999999999999999988 PP

                         AAA_13 472 lgeleL 477
                                      + e+
  gi|116754465|ref|YP_843583.1| 930 -AREEI 934
                                    .44444 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 ?   -1.2   0.0       4.4   2.6e+03      62      79 ..     185     202 ..     168     209 .. 0.59
   2 ?    4.3   0.0     0.082        47      28      58 ..     236     266 ..     231     290 .. 0.76
   3 ?    5.1   0.0     0.047        27      27      81 ..     369     423 ..     362     443 .. 0.86
   4 ?    0.1   0.1       1.7   9.7e+02      31      58 ..     443     470 ..     428     515 .. 0.54
   5 ?   -1.2   0.0       4.3   2.5e+03      68      87 ..     700     719 ..     683     725 .. 0.61
   6 ?   -2.1   0.0       8.3   4.8e+03      36      86 ..     766     814 ..     747     817 .. 0.47
   7 ?    0.4   0.0       1.4   8.2e+02      23      83 ..     870     933 ..     864     938 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 4.4
                         DUF948  62 dvneklekvdplteavad 79 
                                     v+e++++vd + e+v++
  gi|116754465|ref|YP_843583.1| 185 VVRERIARVDVILEEVGQ 202
                                    455555555555555543 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.082
                         DUF948  28 ldeaaatieelekqvdpilkevedllakvne 58 
                                    ++ea+a i  l +++++i+ e  +ll+  ++
  gi|116754465|ref|YP_843583.1| 236 FKEAEAEISALDDEITSITSEKSQLLQSLEA 266
                                    7899999**************9999998877 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.047
                         DUF948  27 tldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlg 81 
                                     l++++a i +  ++  ++ +e+++l+++++++ +++ e+l + d+l +a++ ++
  gi|116754465|ref|YP_843583.1| 369 QLSSLRANISDADSRFAKYREELAQLIKEIEDTRSQIGERLRERDRLLDAIRRAS 423
                                    5678889999999999999999999999999999999999999999999998877 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 1.7
                         DUF948  31 aaatieelekqvdpilkevedllakvne 58 
                                    a++  e le++v++i  e+ dl +  +e
  gi|116754465|ref|YP_843583.1| 443 ASTESERLEREVESIASEAMDLDKRREE 470
                                    5555566666666666666665555444 PP

  == domain 5  score: -1.2 bits;  conditional E-value: 4.3
                         DUF948  68 ekvdplteavadlgesvsel 87 
                                    ek+d++ e++  +++++++l
  gi|116754465|ref|YP_843583.1| 700 EKLDSVEEEISSISRKLESL 719
                                    44444444444444444443 PP

  == domain 6  score: -2.1 bits;  conditional E-value: 8.3
                         DUF948  36 eelekqvdpilkevedllakvnelledvne..klekvdplteavadlgesvse 86 
                                    ++le++++    e+e +l++  +l e +++  +  ++ +++e +++l   ++ 
  gi|116754465|ref|YP_843583.1| 766 TVLEQEMQ----ELESALSEKGDLREKLERdmQGSRIPEMMERAEQLEGEIRR 814
                                    44443333....33333333333333333322344566666666666666655 PP

  == domain 7  score: 0.4 bits;  conditional E-value: 1.4
                         DUF948  23 klkktldeaaatieelekqvdpilkevedllakvne...lledvneklekvdplteavadlges 83 
                                     l+  lde+++  ++l ++++++  e   l++ +        ++++ +e++d+  +av  + e 
  gi|116754465|ref|YP_843583.1| 870 DLRAALDELSRKEKDLDRELHGLKGERGSLMESIIGkerEIGGMERSIERLDARLTAVSGAREE 933
                                    5788899999999999999999999976666654332223667777788888777777766655 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.3       2.5   1.4e+03      60      91 ..     175     206 ..     158     213 .. 0.44
   2 ?    5.7   1.8     0.024        14      39     117 ..     246     328 ..     234     331 .. 0.71
   3 ?    3.4   0.4      0.13        77      49     115 ..     313     382 ..     297     392 .. 0.59
   4 !   12.7   2.5   0.00016     0.095      46     120 ..     387     464 ..     370     468 .. 0.79
   5 ?    5.3   0.3     0.034        20      49      95 ..     463     509 ..     458     527 .. 0.80
   6 !   11.1   2.7   0.00051       0.3      48     122 ..     700     777 ..     689     779 .. 0.86
   7 ?    4.7   1.5     0.049        29      51     119 ..     755     828 ..     753     834 .. 0.75
   8 ?    2.7   0.4      0.21   1.2e+02      54      93 ..     805     844 ..     791     870 .. 0.64
   9 ?    2.1   0.5      0.32   1.8e+02      68     121 ..     868     921 ..     832     943 .. 0.57
  10 ?    4.3   0.0      0.07        40      62     121 ..     918     977 ..     911     979 .. 0.57

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 2.5
                        DUF1664  60 tkrhLssridrvdkkldeqkeiskeikeevte 91 
                                     k++ ++++d v +++  +  i +e+ +++ +
  gi|116754465|ref|YP_843583.1| 175 KKQRAMAELDVVRERIARVDVILEEVGQQLRR 206
                                    33333333333333333333333333333333 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.024
                        DUF1664  39 lsdavesvskqleqvseslaatk...rhLssridrvdkkldeqke.iskeikeevtevredlseigedvesvkeavegle 114
                                    l d ++s++++  q+ +sl+a +   r+L++r++ v+ ++ +  e  +  +++e++e+r+++++ ++ +e+ ++ +e+ +
  gi|116754465|ref|YP_843583.1| 246 LDDEITSITSEKSQLLQSLEAGReelRRLEERLKAVEGEISHKGEdEQLRVRREIEEIRGKIAREETRIEAADADIEEAD 325
                                    56677777777777777776666111456788999988888765514557888999999988888888887777777766 PP

                        DUF1664 115 skl 117
                                     +l
  gi|116754465|ref|YP_843583.1| 326 RSL 328
                                    665 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.13
                        DUF1664  49 qleqvseslaatkrhLssridrvdkkldeqkeiskeikeevt...evredlseigedvesvkeavegles 115
                                    ++e   ++++++ r Ls+   ++d+   e ++is++++++ +    ++++l++ +++++s+++ +++ +s
  gi|116754465|ref|YP_843583.1| 313 RIEAADADIEEADRSLSQCFIEMDRVRAEIAAISEQLSDKAMrraGIQGELDDQRSQLSSLRANISDADS 382
                                    4555556666666666666666666666666666666555431114566666666666666666655555 PP

  == domain 4  score: 12.7 bits;  conditional E-value: 0.00016
                        DUF1664  46 vskqleqvseslaatkrhLssridrvdkkldeqkeis...keikeevtevredlseigedvesvkeavegleskleri 120
                                      ++l q+ +++++t+ ++ +r+ + d+ ld+  ++s   +ei+ e+te+ + +s+ ++++e +++ ve+++s+  ++
  gi|116754465|ref|YP_843583.1| 387 YREELAQLIKEIEDTRSQIGERLRERDRLLDAIRRASmekEEIATEITEALSSISAASTESERLEREVESIASEAMDL 464
                                    345899999******************9999987765222689999999999999999**********9998876665 PP

  == domain 5  score: 5.3 bits;  conditional E-value: 0.034
                        DUF1664  49 qleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevred 95 
                                    +l++  e+l++ +  L ++++++d++l+  +   + ++++v +++e 
  gi|116754465|ref|YP_843583.1| 463 DLDKRREELESRRLSLRRELAELDRSLQRLQSEYARVEAQVRAAEER 509
                                    68888899999999999999999999999999999999999877654 PP

  == domain 6  score: 11.1 bits;  conditional E-value: 0.00051
                        DUF1664  48 kqleqvseslaatkrh...Lssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleriee 122
                                    ++l++v e++++  r+   L ++i r    l+e  ++   +++ ++e ++ lse+++++e+ ++  + le++++++e+
  gi|116754465|ref|YP_843583.1| 700 EKLDSVEEEISSISRKlesLDKEISRRTFLLEEKRALRGRMERYIEERKSRLSEMERESEEWRSRLTVLEQEMQELES 777
                                    678888877777666511156799999999*********************************************996 PP

  == domain 7  score: 4.7 bits;  conditional E-value: 0.049
                        DUF1664  51 eqvseslaatkrhLssridrvdkkldeqkeiskeikeevt.....evredlseigedvesvkeavegleskler 119
                                    e+ se+ ++    L+++++++++ l e  ++ ++++++++     e+ e  ++++ +++ +++ +++l+s++ r
  gi|116754465|ref|YP_843583.1| 755 ERESEEWRSRLTVLEQEMQELESALSEKGDLREKLERDMQgsripEMMERAEQLEGEIRRLESRIMDLDSEIMR 828
                                    55566666667778999999999999999888888876542222278889999999999999999999998876 PP

  == domain 8  score: 2.7 bits;  conditional E-value: 0.21
                        DUF1664  54 seslaatkrhLssridrvdkkldeqkeiskeikeevtevr 93 
                                     e+l+   r+L+sri  +d+++  +    +++++ ++e+ 
  gi|116754465|ref|YP_843583.1| 805 AEQLEGEIRRLESRIMDLDSEIMRCRLKEENLRNRLDELA 844
                                    3455555566666666666666666666666666665555 PP

  == domain 9  score: 2.1 bits;  conditional E-value: 0.32
                        DUF1664  68 idrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                    ++ + + lde ++  k++++e++ ++++  ++ e +   ++ + g+e ++er++
  gi|116754465|ref|YP_843583.1| 868 MEDLRAALDELSRKEKDLDRELHGLKGERGSLMESIIGKEREIGGMERSIERLD 921
                                    444555555555555555555555555544444444444444444444444443 PP

  == domain 10  score: 4.3 bits;  conditional E-value: 0.07
                        DUF1664  62 rhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                    ++L +r+  v    +e +   +++++e++++  d se   ++e++ + ++ le++++++e
  gi|116754465|ref|YP_843583.1| 918 ERLDARLTAVSGAREEISISMQSLRSEIESAGIDPSEAPPKSETIAAKIRALEEEMASLE 977
                                    345555555555555555555555556666666666666666666666666666666665 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   9.7      0.88   5.1e+02     323     429 ..     174     274 ..     107     284 .. 0.58
   2 !   16.2  15.4   6.4e-06    0.0037     321     486 ..     289     454 ..     279     456 .. 0.86
   3 ?    1.9   4.4      0.14        82     329     384 ..     451     506 ..     443     520 .. 0.61
   4 ?    0.2   0.1      0.44   2.6e+02     328     369 ..     906     947 ..     898    1002 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.88
                         DUF812 323 elkkkreeeleelqeqieeleskieeleeeikklessikqveeeleeekeeneelekevklkkktlellpdaeeniekLq 402
                                    e k++  +el+ ++e+i +++  +ee+ +++++l+++  ++          +ee++k+   +  +l+  ++ae+ i++L 
  gi|116754465|ref|YP_843583.1| 174 EKKQRAMAELDVVRERIARVDVILEEVGQQLRRLQAERDRALRYRA----CREERKKQ--EAYLLLARFKEAEAEISALD 247
                                    3333334444444444444444444444444444333333222111....11111111..11112233356666666666 PP

                         DUF812 403 alveasaqrlvelakqWekhRvpliee 429
                                     ++ + +++  +l +  e+ R+ l + 
  gi|116754465|ref|YP_843583.1| 248 DEITSITSEKSQLLQSLEAGREELRRL 274
                                    666666666666666666666655333 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 6.4e-06
                         DUF812 321 eeelkkkreeeleelqeqieeleskieeleeeikklessikqveeeleeekeeneelekevklkkk....tlellpdaee 396
                                     e+ + +  +e+ee++ +i + e +ie+ +++i++ + s++q   e+++ ++e +   +++  k +    +   l+d+ +
  gi|116754465|ref|YP_843583.1| 289 GEDEQLRVRREIEEIRGKIAREETRIEAADADIEEADRSLSQCFIEMDRVRAEIAAISEQLSDKAMrragIQGELDDQRS 368
                                    3444555555688***************************************998888887666542222677899999* PP

                         DUF812 397 niekLqalveasaqrlvelakqWekhRvplieeyrelkesksekekeaerkleeikklrekmkevaeelrqkeellkqLv 476
                                    +++ L a + ++ +r  +      +  ++li+e+++ ++++ e+  e+ r l+ i++   + +e+a e+ +   +++   
  gi|116754465|ref|YP_843583.1| 369 QLSSLRANISDADSRFAKYR----EELAQLIKEIEDTRSQIGERLRERDRLLDAIRRASMEKEEIATEITEALSSISAAS 444
                                    *************9997655....55578*************************************************** PP

                         DUF812 477 aeleklpkdv 486
                                    +e e+l+++v
  gi|116754465|ref|YP_843583.1| 445 TESERLEREV 454
                                    *****99987 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.14
                         DUF812 329 eeeleelqeqieeleskieeleeeikklessikqveeeleeekeeneelekevklk 384
                                    e+e+e++ ++  +l+++ eele+   +l+ ++ +++ +l+++++e ++ e++v+ +
  gi|116754465|ref|YP_843583.1| 451 EREVESIASEAMDLDKRREELESRRLSLRRELAELDRSLQRLQSEYARVEAQVRAA 506
                                    45555666666666666666666666666666666666666666666666555544 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 0.44
                         DUF812 328 reeeleelqeqieeleskieeleeeikklessikqveeelee 369
                                    +e+e+  +++ ie+l++++ +++   ++++ s++ + +e+e 
  gi|116754465|ref|YP_843583.1| 906 KEREIGGMERSIERLDARLTAVSGAREEISISMQSLRSEIES 947
                                    678888999999999999999999999999999999888875 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 ?    1.4   0.1      0.52     3e+02      40      61 ..     243     264 ..     177     297 .. 0.55
   2 ?    3.5   1.4      0.12        68      27      80 ..     340     399 ..     231     401 .. 0.63
   3 ?    6.8   0.3     0.011       6.6      16      81 ..     431     495 ..     414     506 .. 0.64
   4 ?    4.1   0.1     0.076        44      34     101 ..     696     779 ..     684     782 .. 0.80
   5 ?    0.6   0.1      0.91   5.3e+02      81     101 ..     806     826 ..     750     857 .. 0.50
   6 ?   -0.1   0.1       1.5   8.5e+02      35      88 ..     807     841 ..     784     879 .. 0.58
   7 ?    0.1   0.0       1.3   7.4e+02      69     118 ..     868     920 ..     833     947 .. 0.52

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.52
                   Baculo_PEP_C  40 ldaietqLnalsedlksllael 61 
                                    + a++ ++++++++ ++ll++l
  gi|116754465|ref|YP_843583.1| 243 ISALDDEITSITSEKSQLLQSL 264
                                    2222222222222222222222 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.12
                   Baculo_PEP_C  27 lqnvqilaqlat...lldaietqLnalsedlksllaeldt...rldtlltnLtdalnalq 80 
                                    +  + i+ ql+      + i+++L++  ++l+sl a++++   r+++  ++L + +++++
  gi|116754465|ref|YP_843583.1| 340 AEIAAISEQLSDkamRRAGIQGELDDQRSQLSSLRANISDadsRFAKYREELAQLIKEIE 399
                                    222222223322000233455555555554444444433333355555555555555554 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.011
                   Baculo_PEP_C  16 ldLtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq.d 81 
                                     ++t++L++i + +++    l++ +++i+++  +l+++ ++ l++ +  l   l++L+++l++lq +
  gi|116754465|ref|YP_843583.1| 431 TEITEALSSISAASTES-ERLEREVESIASEAMDLDKRREE-LESRRLSLRRELAELDRSLQRLQsE 495
                                    47777777775555555.77777777777777777766655.4445556666677777777766632 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.076
                   Baculo_PEP_C  34 aqlatlldaietqLnalsedlksllaeldt.............rldtlltnLtdalnalq...dtlrneLtnlnsiltnL 97 
                                    ++l + ld++e++++++s +l+sl +e+++             r++  +++ ++ l +++   ++ r++Lt l++++ +L
  gi|116754465|ref|YP_843583.1| 696 GELLEKLDSVEEEISSISRKLESLDKEISRrtflleekralrgRMERYIEERKSRLSEMEresEEWRSRLTVLEQEMQEL 775
                                    56777888899999999999999988888888888888888888888888888888888788888899999999988888 PP

                   Baculo_PEP_C  98 lssv 101
                                     s +
  gi|116754465|ref|YP_843583.1| 776 ESAL 779
                                    8865 PP

  == domain 5  score: 0.6 bits;  conditional E-value: 0.91
                   Baculo_PEP_C  81 dtlrneLtnlnsiltnLlssv 101
                                    ++l+ e+  l+s + +L s++
  gi|116754465|ref|YP_843583.1| 806 EQLEGEIRRLESRIMDLDSEI 826
                                    333333333333333333333 PP

  == domain 6  score: -0.1 bits;  conditional E-value: 1.5
                   Baculo_PEP_C  35 qlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq...dtlrneLt 88 
                                    ql+  +  +e+++ +l++++ +                           ++lrn+L+
  gi|116754465|ref|YP_843583.1| 807 QLEGEIRRLESRIMDLDSEIMR----------------------CRlkeENLRNRLD 841
                                    3333333333333333333333......................2222222222222 PP

  == domain 7  score: 0.1 bits;  conditional E-value: 1.3
                   Baculo_PEP_C  69 ltnLtdalnalq...dtlrneLtnlnsiltnLlssvtNinstLnnllqalnnl 118
                                    ++ L +al +l+   ++l+ eL +l+ +  +L+ s+ + +  + ++  +++ l
  gi|116754465|ref|YP_843583.1| 868 MEDLRAALDELSrkeKDLDRELHGLKGERGSLMESIIGKEREIGGMERSIERL 920
                                    33444444444444445555555555555555555544444444444433333 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 ?    6.3  17.4     0.016         9       3     124 ..     174     300 ..     172     303 .. 0.77
   2 !   11.6   8.6   0.00036      0.21       2     131 ..     290     416 ..     289     425 .. 0.92
   3 ?    2.4  17.4      0.25   1.4e+02      10     116 ..     403     509 ..     396     525 .. 0.80
   4 ?    2.3  24.1      0.27   1.6e+02       6     120 ..     696     822 ..     691     829 .. 0.79
   5 !   16.3  12.4   1.3e-05    0.0074      11     111 ..     825     925 ..     816     949 .. 0.87
   6 ?    2.5   0.9      0.23   1.4e+02      18      77 ..     958    1017 ..     953    1028 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.016
                 CENP-F_leu_zip   3 kkklhvlekLKeserkadsLkdkvenLerelemseenqekvil....eaEtskaevetlkeeieelaeelreleldLval 78 
                                    +kk+++  +L  ++++ + +    e+  ++l  ++++++++ +      E +k+e+  l +  +e ++e + l  +++++
  gi|116754465|ref|YP_843583.1| 174 EKKQRAMAELDVVRERIARVDVILEEVGQQLRRLQAERDRALRyracREERKKQEAYLLLARFKEAEAEISALDDEITSI 253
                                    55555555665555555555555566666666666666665432222679999*************************** PP

                 CENP-F_leu_zip  79 rsekeeLekelqkkqervseLeslnsslenlleek.Eqekvqmkees 124
                                    +sek +L ++l+  +e+   Le++   +e  +++k E+e+ +++ e 
  gi|116754465|ref|YP_843583.1| 254 TSEKSQLLQSLEAGREELRRLEERLKAVEGEISHKgEDEQLRVRREI 300
                                    ******************************99987577787777665 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00036
                 CENP-F_leu_zip   2 ekkklhvlekLKeserkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrse 81 
                                    e+++l+v+ +  e++ k +  + ++e+ ++++e++++++++  +e++  +ae+ ++ e++   a ++  ++ +L++ rs+
  gi|116754465|ref|YP_843583.1| 290 EDEQLRVRREIEEIRGKIAREETRIEAADADIEEADRSLSQCFIEMDRVRAEIAAISEQLSDKAMRRAGIQGELDDQRSQ 369
                                    6789999999****************************************************9***************** PP

                 CENP-F_leu_zip  82 keeLekelqkkqervseLeslnsslenlleekEqekvqmkeeskaaveeL 131
                                      +L  ++ +  +r     + +++l +l++e E+ + q+ e+  ++  +L
  gi|116754465|ref|YP_843583.1| 370 LSSLRANISDADSRF---AKYREELAQLIKEIEDTRSQIGERLRERDRLL 416
                                    ****99999999886...57899999*********999999988776666 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.25
                 CENP-F_leu_zip  10 ekLKeserkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekel 89 
                                    ++  e  r+ d L d + +   e+e++  + +++      +  e e l+ e+e +a+e  +l    ++l s + +L +el
  gi|116754465|ref|YP_843583.1| 403 SQIGERLRERDRLLDAIRRASMEKEEIATEITEALSSISAASTESERLEREVESIASEAMDLDKRREELESRRLSLRREL 482
                                    55566678899999999999999999999999999999999999999999999999999999999999999999999999 PP

                 CENP-F_leu_zip  90 qkkqervseLeslnsslenlleekEqe 116
                                     +  +  + L+s    +e +++ +E+ 
  gi|116754465|ref|YP_843583.1| 483 AELDRSLQRLQSEYARVEAQVRAAEER 509
                                    998888888888888888888888875 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.27
                 CENP-F_leu_zip   6 lhvlekLKeserkadsLkdkvenLerele.......mseenqekvileaEtskaevetlkeeieelaeelreleldLval 78 
                                     ++lekL  +e++ +s+  k e+L++e+        +  + + ++++  E+ k  +++++ e ee +++l+ le+++++l
  gi|116754465|ref|YP_843583.1| 696 GELLEKLDSVEEEISSISRKLESLDKEISrrtflleEKRALRGRMERYIEERKSRLSEMERESEEWRSRLTVLEQEMQEL 775
                                    567889999999999999999999988652222000444445679999****************************9999 PP

                 CENP-F_leu_zip  79 r...sekeeLekelqkk.q.ervseLeslnsslenlleekEqekvqm 120
                                        sek +L ++l+   q +r+ e+ ++ ++le  ++++E   + +
  gi|116754465|ref|YP_843583.1| 776 EsalSEKGDLREKLERDmQgSRIPEMMERAEQLEGEIRRLESRIMDL 822
                                    98889*********97413369**************99999876655 PP

  == domain 5  score: 16.3 bits;  conditional E-value: 1.3e-05
                 CENP-F_leu_zip  11 kLKeserkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelq 90 
                                    +  + + k+++L+++ ++L r +e +e +++++i    ++   +e l++ ++el+++ ++l  +L  l+ e+ +L++++ 
  gi|116754465|ref|YP_843583.1| 825 EIMRCRLKEENLRNRLDELARTKELLELKKNDAIQRRSSALSSMEDLRAALDELSRKEKDLDRELHGLKGERGSLMESII 904
                                    566778899*********************************************************************** PP

                 CENP-F_leu_zip  91 kkqervseLeslnsslenlle 111
                                     k +++  +e++ + l   l 
  gi|116754465|ref|YP_843583.1| 905 GKEREIGGMERSIERLDARLT 925
                                    ******999999888777775 PP

  == domain 6  score: 2.5 bits;  conditional E-value: 0.23
                 CENP-F_leu_zip   18 kadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLva 77  
                                     k++ +  k+ +Le e+  +e  +  +i e E   +   +l +  e l +e++ +  +L+ 
  gi|116754465|ref|YP_843583.1|  958 KSETIAAKIRALEEEMASLEPVNMLAIDEYERVDKRFRNLSDRREVLHREREGIIEKLER 1017
                                     677788899**********************99999999999999999998887777765 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   4.4      0.43   2.5e+02     193     243 ..     175     225 ..     156     242 .. 0.60
   2 ?    4.1  15.5     0.031        18     143     260 ..     245     331 ..     222     353 .. 0.43
   3 ?   11.0   6.7   0.00024      0.14     156     253 ..     340     436 ..     332     446 .. 0.59
   4 ?    7.7   5.5    0.0024       1.4     142     195 ..     448     501 ..     445     524 .. 0.82
   5 ?   10.2  15.4   0.00043      0.25     156     280 ..     700     824 ..     681     832 .. 0.76
   6 ?    4.1   7.1      0.03        17     145     255 ..     802     908 ..     796     926 .. 0.74
   7 ?    4.0   6.7     0.034        19     143     253 ..     835     941 ..     829     984 .. 0.65
   8 ?   -0.4   0.3      0.73   4.2e+02     146     191 ..     964    1009 ..     958    1040 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.43
                           Spc7 193 lesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqk 243
                                     ++   +eL  +re++a++++ +ee  ++l +lq+++++     +  +e+k
  gi|116754465|ref|YP_843583.1| 175 KKQRAMAELDVVRERIARVDVILEEVGQQLRRLQAERDRALRYRACREERK 225
                                    244455667777777777777777777777777777666554444443333 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.031
                           Spc7 143 gleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkel 222
                                     l++++++++++k++L ++ e   e l +lee+ +++e e+ +  e                                + 
  gi|116754465|ref|YP_843583.1| 245 ALDDEITSITSEKSQLLQSLEAGREELRRLEERLKAVEGEISHKGE--------------------------------DE 292
                                    3344444444444444444444444444444444444444433333................................22 PP

                           Spc7 223 a.elqeqleeleekieelkeqkseleeeiaeaervleec 260
                                    + ++++++ee++ ki+  +++++ + ++i+ea+r l +c
  gi|116754465|ref|YP_843583.1| 293 QlRVRREIEEIRGKIAREETRIEAADADIEEADRSLSQC 331
                                    213333344444444444444444444444443333333 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00024
                           Spc7 156 elLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleek 235
                                    +++++  e+l++   +    + el ++  +l + ++++++    + +++reela+l +eie  + ++ e+ +++++l ++
  gi|116754465|ref|YP_843583.1| 340 AEIAAISEQLSDKAMRRAGIQGELDDQRSQLSSLRANISDA-DSRFAKYREELAQLIKEIEDTRSQIGERLRERDRLLDA 418
                                    33333344444444444444444444444444444444443.45677777777777777777777777777777777777 PP

                           Spc7 236 ieelkeqkseleeeiaea 253
                                    i  ++ +k+e+ +ei ea
  gi|116754465|ref|YP_843583.1| 419 IRRASMEKEEIATEITEA 436
                                    777777777777777766 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.0024
                           Spc7 142 egleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeeles 195
                                    e+le+++e++ +++  L+k++eel++   +l++e ael + l++lq++++ +e+
  gi|116754465|ref|YP_843583.1| 448 ERLEREVESIASEAMDLDKRREELESRRLSLRRELAELDRSLQRLQSEYARVEA 501
                                    678889999999999999999999999999999999999999999998877765 PP

  == domain 5  score: 10.2 bits;  conditional E-value: 0.00043
                           Spc7 156 elLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleek 235
                                    e+L++ eee++++  +le+  +e++++   l+e ++ l    + ++ee +++l+e + e ee + +l+ l+++++ele++
  gi|116754465|ref|YP_843583.1| 700 EKLDSVEEEISSISRKLESLDKEISRRTFLLEE-KRALRGRMERYIEERKSRLSEMERESEEWRSRLTVLEQEMQELESA 778
                                    567788888888888888888888888888887.5567888888888888888888888888888888888888888888 PP

                           Spc7 236 ieelkeqkseleeeiaeaer.vleeckgwsesevsrlkeevkalee 280
                                    ++e  + +++le +++ ++   ++e+ +  e e++rl+++  +l++
  gi|116754465|ref|YP_843583.1| 779 LSEKGDLREKLERDMQGSRIpEMMERAEQLEGEIRRLESRIMDLDS 824
                                    8888888888888888554313444555667788888888777765 PP

  == domain 6  score: 4.1 bits;  conditional E-value: 0.03
                           Spc7 145 eenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelae 224
                                     e+ e+le + ++Le++   ld+   + + ++++l+++l++l + +e le  +++ ++   ++l++    +e +++ l+e
  gi|116754465|ref|YP_843583.1| 802 MERAEQLEGEIRRLESRIMDLDSEIMRCRLKEENLRNRLDELARTKELLELKKNDAIQRRSSALSS----MEDLRAALDE 877
                                    577888999999999999999999999999999999999999986666665556666655555554....3444468888 PP

                           Spc7 225 lqeqleeleekieelkeqkseleeeiaeaer 255
                                    l ++ ++l+ ++  lk ++ +l+e i  +er
  gi|116754465|ref|YP_843583.1| 878 LSRKEKDLDRELHGLKGERGSLMESIIGKER 908
                                    8888888888888888777777777655554 PP

  == domain 7  score: 4.0 bits;  conditional E-value: 0.034
                           Spc7 143 gleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkel 222
                                    +l+++l++l + kelLe +++ + +   +  +  ++l++ l++l +++++l      eL+ l+ e  +l++ i  k++e+
  gi|116754465|ref|YP_843583.1| 835 NLRNRLDELARTKELLELKKNDAIQRRSSALSSMEDLRAALDELSRKEKDL----DRELHGLKGERGSLMESIIGKEREI 910
                                    566666667777777766666666666666666666666666666655443....4467777777777777777777777 PP

                           Spc7 223 aelqeqleeleekieelkeqkseleeeiaea 253
                                      +++ +e+l++++++++  ++e+   +++ 
  gi|116754465|ref|YP_843583.1| 911 GGMERSIERLDARLTAVSGAREEISISMQSL 941
                                    7777777777776666666655554444433 PP

  == domain 8  score: -0.4 bits;  conditional E-value: 0.73
                           Spc7  146 enlegleedkelLekqeeeldellpeleeekaeleeeleklqeaae 191 
                                      ++ +lee+ + Le  + ++ + ++++++++ +l+++ e l +++e
  gi|116754465|ref|YP_843583.1|  964 AKIRALEEEMASLEPVNMLAIDEYERVDKRFRNLSDRREVLHRERE 1009
                                     5667788888888888888888888888888888888777776333 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.3      0.24   1.4e+02      37      84 ..     163     209 ..     159     215 .. 0.85
   2 ?    8.7   2.3     0.004       2.3      11      85 ..     239     313 ..     234     316 .. 0.72
   3 ?   -0.1   0.2       2.2   1.2e+03      31      81 ..     302     351 ..     290     360 .. 0.67
   4 ?    1.1   2.3      0.94   5.4e+02      13      89 ..     396     471 ..     388     472 .. 0.87
   5 ?    0.7   0.9       1.2     7e+02      18      50 ..     464     496 ..     450     525 .. 0.66
   6 ?    3.2   0.1       0.2   1.2e+02      62      87 ..     699     724 ..     691     727 .. 0.87
   7 ?    0.7   1.0       1.2     7e+02      14      50 ..     743     779 ..     733     808 .. 0.74
   8 ?    1.7   2.9      0.61   3.5e+02       9      77 ..     813     880 ..     806     893 .. 0.68
   9 ?   15.2   0.0   3.7e-05     0.021      12      76 ..     914     977 ..     911     981 .. 0.90
  10 ?   -1.7   0.0       7.2   4.1e+03      16      51 ..     988    1023 ..     982    1034 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.24
                Snapin_Pallidin  37 drlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklkk 84 
                                      + + + e+ee ++  ++++l+  +++++++   ++++ ++l++l++
  gi|116754465|ref|YP_843583.1| 163 IDEIAGVSEFEEKKQ-RAMAELDVVRERIARVDVILEEVGQQLRRLQA 209
                                    566777788888888.99*********************999999996 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.004
                Snapin_Pallidin  11 lepkldeldeklkelrqsQeeLleqldrlnekLkeleeaqe.aevlpdlkeya.kKLvnikkrmsslnerlqklkkR 85 
                                     e ++ +ld+++ +++ + ++Ll++l+  +e+L++lee  +  e   ++ +   +   +++++++++  ++ + + R
  gi|116754465|ref|YP_843583.1| 239 AEAEISALDDEITSITSEKSQLLQSLEAGREELRRLEERLKaVE--GEISHKGeDEQLRVRREIEEIRGKIAREETR 313
                                    578999********************************998322..2222221244445666666666666666665 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 2.2
                Snapin_Pallidin  31 eLleqldrlnekLkeleeaqe.aevlpdlkeyakKLvnikkrmsslnerlqk 81 
                                    e + ++ r+ ++++ +    + +e+   l +    + +++ ++ +++e+l+ 
  gi|116754465|ref|YP_843583.1| 302 EIRGKIAREETRIEAADA--DiEEADRSLSQCFIEMDRVRAEIAAISEQLSD 351
                                    566667777777763333..33466777888888888888888888888765 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.94
                Snapin_Pallidin  13 pkldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklkkRaekL 89 
                                     +++++++++ e  ++ + Ll+ ++r + + +e++ +   e+l+ +        +++++++s+ +    l kR e+L
  gi|116754465|ref|YP_843583.1| 396 KEIEDTRSQIGERLRERDRLLDAIRRASMEKEEIATEIT-EALSSISAASTESERLEREVESIASEAMDLDKRREEL 471
                                    57999999******************9999998876555.899****999***************999999998877 PP

  == domain 5  score: 0.7 bits;  conditional E-value: 1.2
                Snapin_Pallidin  18 ldeklkelrqsQeeLleqldrlnekLkeleeaq 50 
                                    ld++ +el+     L+ +l +l ++L++l+ + 
  gi|116754465|ref|YP_843583.1| 464 LDKRREELESRRLSLRRELAELDRSLQRLQSEY 496
                                    555556666666666666666666666666544 PP

  == domain 6  score: 3.2 bits;  conditional E-value: 0.2
                Snapin_Pallidin  62 akKLvnikkrmsslnerlqklkkRae 87 
                                    ++KL +++ ++ss++ +l++l k ++
  gi|116754465|ref|YP_843583.1| 699 LEKLDSVEEEISSISRKLESLDKEIS 724
                                    58999999999999999999988765 PP

  == domain 7  score: 0.7 bits;  conditional E-value: 1.2
                Snapin_Pallidin  14 kldeldeklkelrqsQeeLleqldrlnekLkeleeaq 50 
                                     ++e +++l+e +++ ee +++l+ l ++++ele a 
  gi|116754465|ref|YP_843583.1| 743 YIEERKSRLSEMERESEEWRSRLTVLEQEMQELESAL 779
                                    5666677777777777777777777777777776654 PP

  == domain 8  score: 1.7 bits;  conditional E-value: 0.61
                Snapin_Pallidin   9 ellepkldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslne 77 
                                    + le+ + +ld+++  +r + e L+++ld+l++  kel e+++++++++  + +  +  ++  + +l+ 
  gi|116754465|ref|YP_843583.1| 813 RRLESRIMDLDSEIMRCRLKEENLRNRLDELART-KELLELKKNDAIQRRSSALSSMEDLRAALDELSR 880
                                    568899999********************99875.3455555544455555555555555555555555 PP

  == domain 9  score: 15.2 bits;  conditional E-value: 3.7e-05
                Snapin_Pallidin  12 epkldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmssln 76 
                                    e ++++ld++l ++    ee + ++++l+++++  + ++++e++p+ ++ a+K+++++ +m sl+
  gi|116754465|ref|YP_843583.1| 914 ERSIERLDARLTAVSGAREEISISMQSLRSEIE-SAGIDPSEAPPKSETIAAKIRALEEEMASLE 977
                                    5689****************************8.4555557********************9986 PP

  == domain 10  score: -1.7 bits;  conditional E-value: 7.2
                Snapin_Pallidin   16 deldeklkelrqsQeeLleqldrlnekLkeleeaqe 51  
                                     +++d+++++l +  e L+ + +   ekL+++ ++++
  gi|116754465|ref|YP_843583.1|  988 ERVDKRFRNLSDRREVLHREREGIIEKLERYDQLKK 1023
                                     678999999999999999999999999999888887 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   9.9    0.0037       2.1     750     869 ..     168     281 ..     149     291 .. 0.90
   2 ?    4.1  27.3     0.011       6.4     309     522 ..     295     502 ..     288     522 .. 0.71
   3 ?    2.4   8.3     0.039        22     231     321 ..     699     789 ..     674     795 .. 0.61
   4 ?   15.6  11.4   3.8e-06    0.0022     603     836 ..     784    1020 ..     776    1035 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0037
                        DUF3584 750 rlkeleeaykreLkskdvDpetvkelkrkieeLekkieriekrreevreYraflqetwlkvdslaeerpalkeqveeles 829
                                     ++e ee+ +r ++++dv  e+++++    ee  +++ r + +r+ +++Yra   e+  +      e   l ++ +e e+
  gi|116754465|ref|YP_843583.1| 168 GVSEFEEKKQRAMAELDVVRERIARVDVILEEVGQQLRRLQAERDRALRYRACREERKKQ------EAYLLLARFKEAEA 241
                                    5688999*********************************************98888766......9999999******* PP

                        DUF3584 830 aaeeleqeltrliedtklerkklekerkalekqldqlden 869
                                    +++ l++e t +++++ + ++ le +r+ l+ ++++l++ 
  gi|116754465|ref|YP_843583.1| 242 EISALDDEITSITSEKSQLLQSLEAGREELRRLEERLKAV 281
                                    ****************999999999999999999888765 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.011
                        DUF3584 309 elnqelsaakaklaakeselealeeqkkkyedadieklkadldqlpsirseleeleeeldaltekhqdvqekydrrkqki 388
                                    +++ e+++ ++k+a+ e ++ea++++ ++  d  +++   ++d+   +r+e+++++e+l     +   +q ++d +++++
  gi|116754465|ref|YP_843583.1| 295 RVRREIEEIRGKIAREETRIEAADADIEE-ADRSLSQCFIEMDR---VRAEIAAISEQLSDKAMRRAGIQGELDDQRSQL 370
                                    56789999999999999999999999988.67888888888775...799**********999999********999999 PP

                        DUF3584 389 keeleeeleklkerleaireekdrlkaaieealealesqlrkqleaqkeelneeekelesrlselklrldsatateEele 468
                                    ++ l +++++ ++r ++ ree ++l ++ie+  +++ + lr +++    +++++ +e e+ + e    l s +a + e+e
  gi|116754465|ref|YP_843583.1| 371 SS-LRANISDADSRFAKYREELAQLIKEIEDTRSQIGERLR-ERDRLLDAIRRASMEKEEIATEITEALSSISAASTESE 448
                                    75.78899999****************************99.56666666666666666666666666666666666666 PP

                        DUF3584 469 qieeadealekaqeelekaeaevealqaeeeqlrkkrdeadealqkaerrleql 522
                                    ++e ++e +      l k+++e e+    +++  ++ d  +++lq + +r+e +
  gi|116754465|ref|YP_843583.1| 449 RLEREVESIASEAMDLDKRREELESRRLSLRRELAELDRSLQRLQSEYARVEAQ 502
                                    665554444443333333333333333333333334444444444444444433 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.039
                        DUF3584 231 iediqal.aaiekvrpeieklqeefeqleslelrLsllkgelkadeerlaekqeevqeakaelkqqlrtledelkeaide 309
                                    +e  +++ ++i ++  ++e l +e++ +  l+++ + l g ++  +e+ ++++ e++ +++e +++l  le+e++e +++
  gi|116754465|ref|YP_843583.1| 699 LEKLDSVeEEISSISRKLESLDKEISRRTFLLEEKRALRGRMERYIEERKSRLSEMERESEEWRSRLTVLEQEMQELESA 778
                                    44444431346666666666666666666666666666666666666666666666666666666666666666666666 PP

                        DUF3584 310 lnqelsaakakl 321
                                    l+ e+ ++++kl
  gi|116754465|ref|YP_843583.1| 779 LS-EKGDLREKL 789
                                    54.344444444 PP

  == domain 4  score: 15.6 bits;  conditional E-value: 3.8e-06
                        DUF3584  603 eLrerl..qaleealqsaeakqkqaeeelkqlnaeleeakravaeaatalknardtlerlqnekesekdklekaiaer 678 
                                      Lre+l  +   + + +  ++++q+e e+  l+  + +++ ++ + + + +n r++l  l   ke ++ k++ ai++ 
  gi|116754465|ref|YP_843583.1|  784 DLREKLerDMQGSRIPEMMERAEQLEGEIRRLESRIMDLDSEIMRCRLKEENLRNRLDELARTKELLELKKNDAIQR- 860 
                                     566654114456778888999******************************************************85. PP

                        DUF3584  679 kqqaeeqlqkldaqlkqleeqqkaaleelkedlsee..rlekkakwqevvgeldeqlaelkkaieaartqakarlkel 754 
                                     +++a  ++++l a+l+ l +++k++  el+  + e+   +e     + ++g ++ ++++l++ + a  ++a+++++  
  gi|116754465|ref|YP_843583.1|  861 RSSALSSMEDLRAALDELSRKEKDLDRELHGLKGERgsLMESIIGKEREIGGMERSIERLDARLTA-VSGAREEISIS 937 
                                     6788899***********************99998722456666778899************9986.57889999999 PP

                        DUF3584  755 eeaykreLkskdvDpetv....kelkrkieeLekkierie.krreevreYraflqetwlkvdslaeerpalkeqveel 827 
                                      +  ++e++s ++Dp+      + +++ki++Le++++  e ++  ++ eY++ + +++ +   l ++r+ l  + e +
  gi|116754465|ref|YP_843583.1|  938 MQSLRSEIESAGIDPSEAppksETIAAKIRALEEEMASLEpVNMLAIDEYER-VDKRFRN---LSDRREVLHREREGI 1011
                                     99************986433227899**********9998456778999988.5777855...788888888777777 PP

                        DUF3584  828 esaaeeleq 836 
                                      +++e+ +q
  gi|116754465|ref|YP_843583.1| 1012 IEKLERYDQ 1020
                                     777776555 PP

>> GP41  Retroviral envelope protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00056      0.32      19     151 ..     253     387 ..     239     404 .. 0.80
   2 ?   -1.6   0.0       3.7   2.1e+03      27      59 ..     904     942 ..     899     951 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00056
                                    H...HHHHHHHHHHHHHHHHHHHHHHHCHHHH..........HHHHHHHHS..TTSCCHHHHHCHHH...HH..HHHHHH CS
                           GP41  19 l...qrnvlkvleeqqeldkkleaRlsAleevvrvlgedvaslktrmklqChanykliCvtkvPynasd.sWdkvkksLe 94 
                                    +   + ++l+ le+ +e  ++le+Rl+A+e  +   ged  +l+ r +++    +  i   +    a+d   + ++ sL+
  gi|116754465|ref|YP_843583.1| 253 ItseKSQLLQSLEAGREELRRLEERLKAVEGEISHKGEDE-QLRVRREIEE-IRG-KIAREETRIEAADaDIEEADRSLS 329
                                    333378999999999999*******************996.5999999995.344.5677777777888799******** PP

                                    HHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHH..HHHH CS
                           GP41  95 giWnnt.evsydlaelhnliediqnqqektldeldkldklaqslanwfkllnslWvky 151
                                    + + ++  v+ ++a +++++ d    +     eld+  + + sl  ++   +s + ky
  gi|116754465|ref|YP_843583.1| 330 QCFIEMdRVRAEIAAISEQLSDKAMRRAGIQGELDDQRSQLSSLRANISDADSRFAKY 387
                                    ****9988*************9998888877777776666667777766666555555 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.7
                                    HHHHHHH......HHHHHHHHHCHHHH..........HH CS
                           GP41  27 leeqqel......dkkleaRlsAleevvrvlgedvaslk 59 
                                    +++ +e+      + +l+aRl+A+     ++   ++sl+
  gi|116754465|ref|YP_843583.1| 904 IGKEREIggmersIERLDARLTAVSGAREEISISMQSLR 942
                                    556666666666688999999999887666776666665 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    0.0012      0.67       5      38 ..      24      72 ..      21     135 .. 0.76
   2 ?   -2.4   0.1       9.4   5.4e+03      37      77 ..     407     449 ..     385     466 .. 0.58
   3 ?   -0.6   0.2       2.5   1.5e+03      37      89 ..     742     796 ..     711     804 .. 0.68
   4 ?    4.4   0.1     0.073        42      52     116 ..     937    1001 ..     914    1014 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0012
                         AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaee...............e 38
                                   + ++vvtG+ G+GK+  +  ll +l+  ++ ++               +
  gi|116754465|ref|YP_843583.1| 24 KDFIVVTGPNGSGKSNIIDALLFSLCLTSSRAMraerlpdliyrgddgR 72
                                   789************9999998877766665555555555555555444 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 9.4
                         AAA_22  37 e...erpevvfvtlpsstsskdllrellralglelkaerlssee 77 
                                    e   er++++     +s++ +++++e+ +al +   a   +se+
  gi|116754465|ref|YP_843583.1| 407 ErlrERDRLLDAIRRASMEKEEIATEITEALSSISAA-STESER 449
                                    2555666666666666667777888888877766665.444444 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 2.5
                         AAA_22  37 e....erpevvfvtlpsstsskdllrellralglelkaerlsseellealeqalrar 89 
                                    +    +++++ +++  s++ +++ l+ l +++++  +a   ++ +l+e+le+ ++  
  gi|116754465|ref|YP_843583.1| 742 RyieeRKSRLSEMERESEE-WRSRLTVLEQEMQELESA-LSEKGDLREKLERDMQGS 796
                                    0333245555566666665.888888888888877777.777777888888877765 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.073
                         AAA_22   52 sskdllrellralglelkaerlsseellealeqalrarav....ielliiDEaqhlrseealeeLrsll 116 
                                     s ++l++e+ +a  ++ +a    ++e ++a  +al++ ++    + +l iDE +++  ++ +++L+++ 
  gi|116754465|ref|YP_843583.1|  937 SMQSLRSEIESAGIDPSEA--PPKSETIAAKIRALEEEMAslepVNMLAIDEYERV--DKRFRNLSDRR 1001
                                     4566666666666666666..66677777777777777777888************..56666665544 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0045       2.6       3      31 ..      17      45 ..      15      58 .. 0.82
   2 ?    1.6   0.0      0.56   3.2e+02      92     121 ..     970     997 ..     889    1005 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0045
                         AAA_19  3 eavealkekvllvtaGpGtGKTrvlkhiv 31
                                   +a+ +lk++ ++vt++ G+GK+ ++ + +
  gi|116754465|ref|YP_843583.1| 17 RALVQLKKDFIVVTGPNGSGKSNIIDALL 45
                                   5555899*****************98876 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.56
                         AAA_19  92 eeaeeekklqeeellivDEfqdvdelqyrL 121
                                    e  ee   l+  ++l +DE+  vd+   +L
  gi|116754465|ref|YP_843583.1| 970 E--EEMASLEPVNMLAIDEYERVDKRFRNL 997
                                    2..34455644569*********9887776 PP

>> RNA12  RNA12 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00012     0.072      16      36 ..      23      42 ..      16      47 .. 0.82
   2 ?   -2.0   4.1       1.9   1.1e+03     256     320 ..     366     443 ..     309     461 .. 0.64
   3 ?   -1.6   1.8       1.4   8.2e+02     254     300 ..     786     833 ..     730     865 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                          RNA12 16 vntFivvkGPrGSGkkeLvld 36
                                    + Fivv+GP GSGk++++ d
  gi|116754465|ref|YP_843583.1| 23 KKDFIVVTGPNGSGKSNII-D 42
                                   678*************998.5 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.9
                          RNA12 256 qkkkdkaasak.............leekdlkeldealeklGGRltDLealvrrvksgetpkeAveeiieqsaeeilkm 320
                                    q+++ ++  a+                ++ ke++++ +++G Rl + + l   ++ ++  ke +   i+++ + i  +
  gi|116754465|ref|YP_843583.1| 366 QRSQLSSLRANisdadsrfakyreELAQLIKEIEDTRSQIGERLRERDRLLDAIRRASMEKEEIATEITEALSSISAA 443
                                    2222222222233444555555545667899999999*********************99999999999998888765 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.4
                          RNA12 254 eeqkkkdkaasak.........leekdlkeldealeklGGRltDLealvrrvksge 300
                                    +e+         +           ++  ++l+  +  l  R++DL++ + r +  e
  gi|116754465|ref|YP_843583.1| 786 REKL--------ErdmqgsripEMMERAEQLEGEIRRLESRIMDLDSEIMRCRLKE 833
                                    2221........122333333345677889999999*********99999988754 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00023      0.13      35      67 ..      22      52 ..       6      54 .. 0.81
   2 ?   -2.2   0.1       3.7   2.1e+03     100     125 ..     319     344 ..     312     419 .. 0.56
   3 ?   -0.5   0.6       1.1   6.5e+02     102     153 ..     395     444 ..     386     482 .. 0.71
   4 ?   -0.8   0.3       1.4   7.8e+02      98     134 ..     705     743 ..     698     759 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00023
                                   GGGS-.SEEEE--TTSSHHHHHHHHHHHHHTT- CS
                   FtsK_SpoIIIE 35 lkkmashllvaGatgsGKStalntLilSlatth 67
                                   lkk    ++v G  gsGKS+ + +L+ Sl +t+
  gi|116754465|ref|YP_843583.1| 22 LKKDF--IVVTGPNGSGKSNIIDALLFSLCLTS 52
                                   55544..89********************8875 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.7
                                    -SHHHHHHHHHHHHHHHHHHHHHHHH CS
                   FtsK_SpoIIIE 100 tdperalraleeLvkemeeryalfre 125
                                    +d+e+a r l ++  em+++ a +++
  gi|116754465|ref|YP_843583.1| 319 ADIEEADRSLSQCFIEMDRVRAEIAA 344
                                    57888888888888888888754443 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1.1
                                    HHHHHHHHHHHHHHHHHHHHHHHHTT-SSHHHHHHHHHHHHHTT---B-TT- CS
                   FtsK_SpoIIIE 102 peralraleeLvkemeeryalfreagvrsiaaydgeiaedpldifgdvflvl 153
                                    ++++  +  ++ + ++er +l+++ + +s+++  +eia++++++   +   +
  gi|116754465|ref|YP_843583.1| 395 IKEIEDTRSQIGERLRERDRLLDAIRRASMEK--EEIATEITEALSSISAAS 444
                                    56666677777788999999999999999988..888888888755444444 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 1.4
                                    -B-SHHHHHHHHHHHHHHHHHHHHHHHHTT-SSHHH..H CS
                   FtsK_SpoIIIE  98 vatdperalraleeLvkemeeryalfreagvrsiaa..y 134
                                    v +++  ++r le L ke+ +r  l++e+++   ++  y
  gi|116754465|ref|YP_843583.1| 705 VEEEISSISRKLESLDKEISRRTFLLEEKRALRGRMerY 743
                                    778999*****************9999999887777444 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 ?    1.3  14.4      0.32   1.9e+02      40     167 ..     188     316 ..     167     331 .. 0.69
   2 ?    8.5   9.9    0.0021       1.2      31     188 ..     296     456 ..     284     457 .. 0.87
   3 ?    6.0   8.7     0.012       6.7      26     119 ..     417     507 ..     412     525 .. 0.58
   4 ?    2.8   0.2      0.11        64      98     138 ..     685     725 ..     671     735 .. 0.62
   5 ?    8.9  15.7    0.0015      0.87      27     134 ..     743     859 ..     739     864 .. 0.89
   6 ?    4.7   0.0     0.029        16      25     102 ..     865     942 ..     861     948 .. 0.84
   7 ?    2.6   0.5      0.13        75      27      85 ..     965    1023 ..     960    1040 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.32
                            GAS  40 kkeernekelseisqenkrlkepLkkaeeeveeLrk.qlknyekdkqslknlkarlkelekelkdlkwehevleqrfekv 118
                                    ++ +r +  l+e+ q+ +rl+ +  +a + ++  ++ + ++     +++k+++a+++ l++e+++++ e+ +l q +e+ 
  gi|116754465|ref|YP_843583.1| 188 ERIARVDVILEEVGQQLRRLQAERDRALRYRACREErKKQEAYLLLARFKEAEAEISALDDEITSITSEKSQLLQSLEAG 267
                                    3333333333444444444443333333332222110122222234578999999************************* PP

                            GAS 119 ekerdelykkfeaaiqevqqktglknllLekklkalqeelEkkeaqlee 167
                                     +e  +l+++ +a+  e++ k + ++l + + +++++ ++ + e ++e+
  gi|116754465|ref|YP_843583.1| 268 REELRRLEERLKAVEGEISHKGEDEQLRVRREIEEIRGKIAREETRIEA 316
                                    *******************************999999888888887765 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0021
                            GAS  31 lKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkq....slknlkarlkelekelkdlkw 106
                                     + eiee++ k +r e +++++ ++ ++    L +   e+++ r++++  +++ +    + + ++ +l ++ ++l++l+ 
  gi|116754465|ref|YP_843583.1| 296 VRREIEEIRGKIAREETRIEAADADIEEADRSLSQCFIEMDRVRAEIAAISEQLSdkamRRAGIQGELDDQRSQLSSLRA 375
                                    6899**********************************9999999887666554400003445677899*********** PP

                            GAS 107 ehevleqrfekvekerdelykkfeaaiqevqqktglknllLekklkalqeelEkkeaqleevlaaanldpaalsavsekl 186
                                    +      rf+k  +e  +l k+ e++  ++ ++   +  lL   + + + e E+   +++e+l++ +   ++ +++++++
  gi|116754465|ref|YP_843583.1| 376 NISDADSRFAKYREELAQLIKEIEDTRSQIGERLRERDRLLDA-IRRASMEKEEIATEITEALSSISAASTESERLEREV 454
                                    *****************************************86.7888888888999******99999999999988888 PP

                            GAS 187 ee 188
                                    e 
  gi|116754465|ref|YP_843583.1| 455 ES 456
                                    75 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.012
                            GAS  26 elIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlk 105
                                    + I++   e ee+ ++ +++   +s++s+e +rl+ +++    e   L k+ ++ e+ + sl   +++l el++ l++l+
  gi|116754465|ref|YP_843583.1| 417 DAIRRASMEKEEIATEITEALSSISAASTESERLEREVESIASEAMDLDKRREELESRRLSL---RRELAELDRSLQRLQ 493
                                    55555555666666666666666666666666666666666666666666666666655543...345555555555555 PP

                            GAS 106 wehevleqrfekve 119
                                     e+  +e ++ ++e
  gi|116754465|ref|YP_843583.1| 494 SEYARVEAQVRAAE 507
                                    55555555555444 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.11
                            GAS  98 ekelkdlkwehevleqrfekvekerdelykkfeaaiqevqq 138
                                     + +++++     l +++++ve+e+  +++k e+  +e++ 
  gi|116754465|ref|YP_843583.1| 685 SERISATEARRGELLEKLDSVEEEISSISRKLESLDKEISR 725
                                    45555555555666666666666666666666665555544 PP

  == domain 5  score: 8.9 bits;  conditional E-value: 0.0015
                            GAS  27 lIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrk.........qlknyekdkqslknlkarlkel 97 
                                    +I++ K+ + e++++ e+ + +l  ++qe ++l+  L +    +e+L++          +++ e+   ++++l++r+ +l
  gi|116754465|ref|YP_843583.1| 743 YIEERKSRLSEMERESEEWRSRLTVLEQEMQELESALSEKGDLREKLERdmqgsripeMMERAEQLEGEIRRLESRIMDL 822
                                    688999******************************************9444444444456789999999********** PP

                            GAS  98 ekelkdlkwehevleqrfekvekerdelykkfeaaiq 134
                                    ++e+ + +++ e+l+ r++++ + ++ l+ k ++aiq
  gi|116754465|ref|YP_843583.1| 823 DSEIMRCRLKEENLRNRLDELARTKELLELKKNDAIQ 859
                                    *****************************99999998 PP

  == domain 6  score: 4.7 bits;  conditional E-value: 0.029
                            GAS  25 LelIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelk 102
                                    L+  + l+  + el +ke+  ++el+ ++ e  +l+e +   e+e+  +++ +++ +    +   ++++++ + + l+
  gi|116754465|ref|YP_843583.1| 865 LSSMEDLRAALDELSRKEKDLDRELHGLKGERGSLMESIIGKEREIGGMERSIERLDARLTAVSGAREEISISMQSLR 942
                                    666788999999999999999999999999999999999999999999999999888888888877777776666665 PP

  == domain 7  score: 2.6 bits;  conditional E-value: 0.13
                            GAS   27 lIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkq 85  
                                     +I+ l ee++ l+  +  +  e + + ++ ++l++  + + +e+e   ++l++y++ k+
  gi|116754465|ref|YP_843583.1|  965 KIRALEEEMASLEPVNMLAIDEYERVDKRFRNLSDRREVLHREREGIIEKLERYDQLKK 1023
                                     68899999999999999999999999999999999999999999999999999998886 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0    0.0013      0.74      13      32 ..      26      45 ..      20      71 .. 0.89
   2 ?    0.2   1.5       1.8     1e+03      52      67 ..     333     348 ..     240     513 .. 0.64
   3 ?    1.2   0.8      0.83   4.8e+02      51      80 ..     753     819 ..     709     885 .. 0.61
   4 ?   -0.4   0.0       2.5   1.5e+03     105     119 ..    1077    1091 ..     931    1099 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0013
                                   EEEEEESTTSSHHHHHHHHT CS
                                   xxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran 13 kvaivGenGaGKStLlklla 32
                                    ++++G+nG+GKS ++ +l+
  gi|116754465|ref|YP_843583.1| 26 FIVVTGPNGSGKSNIIDALL 45
                                   57899***********9986 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.8
                                    B-HHHCCHCEEEE-SS CS
                                    xxxxxxxxxxxxxxxx RF
                       ABC_tran  52 qeleslrkeigvlpqe 67 
                                    +e+ ++r+ei+ ++++
  gi|116754465|ref|YP_843583.1| 333 IEMDRVRAEIAAISEQ 348
                                    2222223333322222 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.83
                                    G..B-HHHCCHCEEEE-SS--S-TTSBHHHH....................................H CS
                                    x..xxxxxxxxxxxxxxxxxxxxxxxxxxxx....................................x RF
                       ABC_tran  51 e..qeleslrkeigvlpqepqlfpeltvren....................................e 80 
                                    e  +e e++r+++ vl+qe q  +   + e+                                     
  gi|116754465|ref|YP_843583.1| 753 EmeRESEEWRSRLTVLEQEMQELESA-LSEKgdlreklerdmqgsripemmeraeqlegeirrlesrI 819
                                    24567888899999999994444333.34444566667666555555544444444444444333330 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 2.5
                                     TSGGS-HHHHHHHHH CS
                                     xxxxxxxxxxxxxxx RF
                       ABC_tran  105 spssLSgGqkqrval 119 
                                     + + +SgG+k+  al
  gi|116754465|ref|YP_843583.1| 1077 RLEAMSGGEKSLTAL 1091
                                     225666666666665 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   0.0    0.0019       1.1      26      49 ..      26      49 ..      14      89 .. 0.88
   2 ?   -0.2   3.4         2   1.1e+03      42     135 ..     218     312 ..     212     335 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0019
                         AAA_16 26 lvllsGesGvGKsslvrellrale 49
                                    ++++G+ G+GKs ++++ll +l+
  gi|116754465|ref|YP_843583.1| 26 FIVVTGPNGSGKSNIIDALLFSLC 49
                                   689*************99997776 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 2
                         AAA_16  42 rellralekdggiflrgkcdqlesaipy.sa.laqalareellrqlldeaesaeleawrekleealaavpelagaeasrl 119
                                    r+++++ +k+++++l +++++ e++i+  +  ++++ ++++ l q l++ ++ el++  e+l+++ +++++   +e  r+
  gi|116754465|ref|YP_843583.1| 218 RACREERKKQEAYLLLARFKEAEAEISAlDDeITSITSEKSQLLQSLEAGRE-ELRRLEERLKAVEGEISHKGEDEQLRV 296
                                    5566777777899999999999777666533466666555555555555444.788888888888787778777877999 PP

                         AAA_16 120 lellkrllallsrder 135
                                    ++++ ++  +++r+e 
  gi|116754465|ref|YP_843583.1| 297 RREIEEIRGKIAREET 312
                                    9999888855555343 PP

>> FliJ  Flagellar FliJ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1  12.0   0.00062      0.36       7      94 ..     197     283 ..     194     301 .. 0.89
   2 ?    3.4   0.2      0.15        85      49      91 ..     295     337 ..     284     340 .. 0.84
   3 ?    7.0   5.3     0.011       6.4       6      90 ..     334     413 ..     329     432 .. 0.83
   4 ?    4.7   8.5     0.057        33       1     113 [.     364     471 ..     359     473 .. 0.89
   5 ?    0.3   8.2       1.3   7.6e+02       7      80 ..     440     508 ..     427     525 .. 0.67
   6 ?    6.2   0.5      0.02        12      52     101 ..     700     749 ..     675     751 .. 0.88
   7 ?    5.7  13.5     0.029        17       1     112 [.     745     857 ..     745     860 .. 0.92
   8 ?    0.8   0.0      0.91   5.3e+02       4      73 ..     872     943 ..     866     952 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00062
                           FliJ   7 Laeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvekareewqear 86 
                                    L+e+ ++l++ +++ ++  +yr+  ++++++ea  l  a+++  +a isald++i+++++e +q+ + +e+ ree+   +
  gi|116754465|ref|YP_843583.1| 197 LEEVGQQLRRLQAERDRALRYRACREERKKQEA-YLLLARFKEAEAEISALDDEITSITSEKSQLLQSLEAGREELRRLE 275
                                    567789999999999999999999999999998.899******************************************* PP

                           FliJ  87 qerkklek 94 
                                     ++k++e 
  gi|116754465|ref|YP_843583.1| 276 ERLKAVEG 283
                                    *****995 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.15
                           FliJ  49 nyqafisaldeaiaqqkqelaqaekqvekareewqearqerkk 91 
                                     +++ i+ ++ +ia+ +  ++ a +++e+a + + ++ +e   
  gi|116754465|ref|YP_843583.1| 295 RVRREIEEIRGKIAREETRIEAADADIEEADRSLSQCFIEMDR 337
                                    5667789999999999999999999999999999999998765 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.011
                           FliJ   6 eLaeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvekareewqea 85 
                                    e+ ++++e+++  e+l      r+  q +l ++      ++l  ++a is  d++ a++++elaq+ k++e  r++  e 
  gi|116754465|ref|YP_843583.1| 334 EMDRVRAEIAAISEQLSDKAMRRAGIQGELDDQR-----SQLSSLRANISDADSRFAKYREELAQLIKEIEDTRSQIGER 408
                                    6788899999999999999999999999999999.....99999999999999999999999999999999999988777 PP

                           FliJ  86 rqerk 90 
                                     +er 
  gi|116754465|ref|YP_843583.1| 409 LRERD 413
                                    77765 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.057
                           FliJ   1 deaareLaeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvekare 80 
                                    d+ + +L + ++++ +a ++ ++ +++++++ k+++++      +++  + + +++l +ai ++  e +    ++ +a +
  gi|116754465|ref|YP_843583.1| 364 DDQRSQLSSLRANISDADSRFAKYREELAQLIKEIEDTR-----SQIGERLRERDRLLDAIRRASMEKEEIATEITEALS 438
                                    456778888888888888888888888888888888888.....9*********************************** PP

                           FliJ  81 ewqearqerkklekLkerekkeeqkeenrrEqk 113
                                       +a  e + le+  e  + e+    +rrE+ 
  gi|116754465|ref|YP_843583.1| 439 SISAASTESERLEREVESIASEAMDLDKRREEL 471
                                    ******************************975 PP

  == domain 5  score: 0.3 bits;  conditional E-value: 1.3
                           FliJ   7 Laeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvekare 80 
                                      +a +e ++ e ++e++ ++  ++ k+ ++       ++   +++ ++ ld+ ++++++e a+ e+qv +a+e
  gi|116754465|ref|YP_843583.1| 440 ISAASTESERLEREVESIASEAMDLDKRREELE-----SRRLSLRRELAELDRSLQRLQSEYARVEAQVRAAEE 508
                                    445566666666666666666666666666666.....666666677777777777777777777777766655 PP

  == domain 6  score: 6.2 bits;  conditional E-value: 0.02
                           FliJ  52 afisaldeaiaqqkqelaqaekqvekareewqearqerkklekLkerekk 101
                                    + +++++e+i+++ ++l+ + k+++++   + e+r  r  +e+ +e++k 
  gi|116754465|ref|YP_843583.1| 700 EKLDSVEEEISSISRKLESLDKEISRRTFLLEEKRALRGRMERYIEERKS 749
                                    668999************************************99999875 PP

  == domain 7  score: 5.7 bits;  conditional E-value: 0.029
                           FliJ   1 deaareLaeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvekare 80 
                                    +e + +L e++re ++ +++l+ leq++qe+++ ls+++   +  e  +  + i  + e+ +q++ e+ ++e ++    +
  gi|116754465|ref|YP_843583.1| 745 EERKSRLSEMERESEEWRSRLTVLEQEMQELESALSEKGDLREKLERDMQGSRIPEMMERAEQLEGEIRRLESRIMDLDS 824
                                    577899********************************9666667777778999************************** PP

                           FliJ  81 ewqearqerkkle.kLkerekkeeqkeenrrEq 112
                                    e + +r +++ l+ +L+e ++++e+ e+++++ 
  gi|116754465|ref|YP_843583.1| 825 EIMRCRLKEENLRnRLDELARTKELLELKKNDA 857
                                    ***********98469************99985 PP

  == domain 8  score: 0.8 bits;  conditional E-value: 0.91
                           FliJ   4 areLaeaqrelqqaeekleeleqyrqeyqkqlsgea.q.glsaaelrnyqafisaldeaiaqqkqelaqaek 73 
                                    + +L e  r+ ++   +l  l+ +r ++++++ g+  + g     +  + a + a+  a +++  + + ++ 
  gi|116754465|ref|YP_843583.1| 872 RAALDELSRKEKDLDRELHGLKGERGSLMESIIGKErEiGGMERSIERLDARLTAVSGAREEISISMQSLRS 943
                                    456777777777777778888888888877777777444444444444444444444444444444444444 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   6.5     0.034        20      50     135 ..     224     310 ..     218     316 .. 0.74
   2 ?   11.9   2.9    0.0003      0.17      67     144 ..     333     417 ..     319     422 .. 0.77
   3 ?   10.7   9.8   0.00074      0.43      43     133 ..     414     504 ..     413     508 .. 0.97
   4 ?    2.9   8.0      0.18     1e+02      45     126 ..     716     794 ..     700     798 .. 0.86
   5 ?    1.7   6.4      0.42   2.4e+02      56     104 ..     806     854 ..     795     887 .. 0.43
   6 ?    2.1   0.4      0.32   1.8e+02      60     121 ..     859     920 ..     848     930 .. 0.73
   7 ?    2.1   0.1      0.31   1.8e+02      61     146 ..     930    1015 ..     918    1020 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.034
                           ADIP  50 rdleqreslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqkl.knekeelqrlknalqqi 128
                                    r +++  +l ++ ++ eaei+ l  +i + + + +ql + l++  +++r le +lk+ e  + ++  +e  r ++ +++i
  gi|116754465|ref|YP_843583.1| 224 RKKQEAYLLLARFKEAEAEISALDDEITSITSEKSQLLQSLEAGREELRRLEERLKAVEGEIsHKGEDEQLRVRREIEEI 303
                                    33344445778888999999999999999999999999999999999999999999877554133445556888888888 PP

                           ADIP 129 ktqyahe 135
                                    + + a e
  gi|116754465|ref|YP_843583.1| 304 RGKIARE 310
                                    8877655 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.0003
                           ADIP  67 aeierlqskierlktqleqler.......elalvqakerqlekklktleqklknekeelqrlknalqqiktqyahelkkk 139
                                     e++r +++i   ++ql+++++       el+ + +++ +l++++ ++++   + +eel+ l + +++++ q    l+ +
  gi|116754465|ref|YP_843583.1| 333 IEMDRVRAEIAAISEQLSDKAMrragiqgELDDQRSQLSSLRANISDADSRFAKYREELAQLIKEIEDTRSQIGERLRER 412
                                    5666777777777777776655222222277778899999**************************************** PP

                           ADIP 140 dreie 144
                                    dr ++
  gi|116754465|ref|YP_843583.1| 413 DRLLD 417
                                    *9766 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00074
                           ADIP  43 sLlqardrdleqreslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlk 122
                                    +Ll a +r   ++e+ +++i +  ++i+  +++ erl++++e+ ++e+  + ++  +le +  +l + l ++ ++lqrl+
  gi|116754465|ref|YP_843583.1| 414 RLLDAIRRASMEKEEIATEITEALSSISAASTESERLEREVESIASEAMDLDKRREELESRRLSLRRELAELDRSLQRLQ 493
                                    59999*************************************************************************** PP

                           ADIP 123 nalqqiktqya 133
                                    +  +++++q++
  gi|116754465|ref|YP_843583.1| 494 SEYARVEAQVR 504
                                    ******99975 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.18
                           ADIP  45 lqardrdleqreslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlkna 124
                                    l ++d+++  r+ l e+ r l+  +er    ie  k +l++ ere + + ++++ le+++++le++l ++ +  ++l+++
  gi|116754465|ref|YP_843583.1| 716 LESLDKEISRRTFLLEEKRALRGRMER---YIEERKSRLSEMERESEEWRSRLTVLEQEMQELESALSEKGDLREKLERD 792
                                    678889999999999999999988888...9***********************************99887777777776 PP

                           ADIP 125 lq 126
                                    +q
  gi|116754465|ref|YP_843583.1| 793 MQ 794
                                    65 PP

  == domain 5  score: 1.7 bits;  conditional E-value: 0.42
                           ADIP  56 eslnetirkleaeierlqskierlktqleqlerelalvqakerqlekkl 104
                                    e+l+ +ir+le+ i  l s+i r   + e l+++l+ + +++  le k 
  gi|116754465|ref|YP_843583.1| 806 EQLEGEIRRLESRIMDLDSEIMRCRLKEENLRNRLDELARTKELLELKK 854
                                    3333334444433333333333333333333333332222222222222 PP

  == domain 6  score: 2.1 bits;  conditional E-value: 0.32
                           ADIP  60 etirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrl 121
                                    +++++  +++e l+++ + l+++ ++l+rel  ++ +  +l  ++   e+ + +  ++++rl
  gi|116754465|ref|YP_843583.1| 859 QRRSSALSSMEDLRAALDELSRKEKDLDRELHGLKGERGSLMESIIGKEREIGGMERSIERL 920
                                    55566668899999999999999999999999888877777777666666666666666665 PP

  == domain 7  score: 2.1 bits;  conditional E-value: 0.31
                           ADIP   61 tirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlknalqqiktqyahelkk 138 
                                      +++++ ++++l+s+ie+     ++   + ++  ak r le ++++le  ++   +e +r  +   +++   ++  + 
  gi|116754465|ref|YP_843583.1|  930 AREEISISMQSLRSEIESAGIDPSEAPPKSETIAAKIRALEEEMASLEPVNMLAIDEYERVDKRFRNLSDRREVLHRE 1007
                                     556667788888899999998888999999999999999999999999999999999999988888888877777777 PP

                           ADIP  139 kdreiekL 146 
                                     ++  iekL
  gi|116754465|ref|YP_843583.1| 1008 REGIIEKL 1015
                                     77777776 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   0.2      0.75   4.3e+02      31      71 ..     238     282 ..     224     287 .. 0.48
   2 ?    1.9   0.4      0.47   2.7e+02      49      85 ..     345     381 ..     306     401 .. 0.53
   3 ?    4.4   0.6     0.078        45      11      85 ..     359     434 ..     354     442 .. 0.76
   4 ?    4.6   1.3     0.067        39      33      86 ..     444     501 ..     440     510 .. 0.52
   5 ?    4.2   0.1     0.089        51      51      88 ..     686     723 ..     667     733 .. 0.75
   6 ?    4.9   2.2     0.054        31      35      95 ..     750     819 ..     739     832 .. 0.56
   7 ?    3.1   0.2       0.2   1.2e+02      38      87 ..     877     923 ..     834     928 .. 0.63
   8 ?   11.2   0.3   0.00059      0.34       9      72 ..     960    1023 ..     958    1025 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.75
                        BLOC1_2  31 aasekykklkdvaaslekklekl....nekyeelqpylqqidqie 71 
                                    +a++++ +l+d++ s++++ ++l    ++  eel+ + ++++++e
  gi|116754465|ref|YP_843583.1| 238 EAEAEISALDDEITSITSEKSQLlqslEAGREELRRLEERLKAVE 282
                                    445555555555555555444440000444444444444444444 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.47
                        BLOC1_2  49 kleklnekyeelqpylqqidqiekqvteLeeavseLD 85 
                                     +e+l+ k    +    ++d+   q+++L +++s  D
  gi|116754465|ref|YP_843583.1| 345 ISEQLSDKAMRRAGIQGELDDQRSQLSSLRANISDAD 381
                                    4444444433333333333333333333333333333 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.078
                        BLOC1_2  11 leaeleatvedyklLeklNeaasekykklkdvaaslekkleklnekye.elqpylqqidqiekqvteLeeavseLD 85 
                                    +++el+  +++++ L +    a ++++k+++++a+l k++e+++++    l++  + +d+i +   e ee++ e+ 
  gi|116754465|ref|YP_843583.1| 359 IQGELDDQRSQLSSLRANISDADSRFAKYREELAQLIKEIEDTRSQIGeRLRERDRLLDAIRRASMEKEEIATEIT 434
                                    6788888888888888888889999999999999999999999887654677777777777777777777776665 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.067
                        BLOC1_2  33 sekykklkdvaaslekkleklnekyeelqp....ylqqidqiekqvteLeeavseLDe 86 
                                    s++ + l+++++s+++++ +l+++ eel++    + +++ ++++++++L++  +++++
  gi|116754465|ref|YP_843583.1| 444 STESERLEREVESIASEAMDLDKRREELESrrlsLRRELAELDRSLQRLQSEYARVEA 501
                                    5555566666666666666666666666541111345555555555555544444444 PP

  == domain 5  score: 4.2 bits;  conditional E-value: 0.089
                        BLOC1_2  51 eklnekyeelqpylqqidqiekqvteLeeavseLDeys 88 
                                    e+++++++   ++l+++d +e++++++    + LD+ +
  gi|116754465|ref|YP_843583.1| 686 ERISATEARRGELLEKLDSVEEEISSISRKLESLDKEI 723
                                    55666666777888888888888888888888888654 PP

  == domain 6  score: 4.9 bits;  conditional E-value: 0.054
                        BLOC1_2  35 kykklkdvaaslekkleklnekyeelqpylqqidqiekqvt.........eLeeavseLDeyskeLEakf 95 
                                    +  +++++ ++ ++ l  l+++ +el++ l++  ++ ++++         e+ e +++L+  +++LE+++
  gi|116754465|ref|YP_843583.1| 750 RLSEMERESEEWRSRLTVLEQEMQELESALSEKGDLREKLErdmqgsripEMMERAEQLEGEIRRLESRI 819
                                    5555555556666666666665555555555555554433211111111156666666666666666654 PP

  == domain 7  score: 3.1 bits;  conditional E-value: 0.2
                        BLOC1_2  38 klkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDey 87 
                                    +l+++ ++l ++l+ l+    e  +++++i   e+++  +e  +++LD+ 
  gi|116754465|ref|YP_843583.1| 877 ELSRKEKDLDRELHGLKG---ERGSLMESIIGKEREIGGMERSIERLDAR 923
                                    333333333333333333...55666777777777777777777777765 PP

  == domain 8  score: 11.2 bits;  conditional E-value: 0.00059
                        BLOC1_2    9 kyleaeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiek 72  
                                     + + a++ a  e++  Le +N  a+ +y+ ++++  +l++  e l ++ e + ++l++ dq++k
  gi|116754465|ref|YP_843583.1|  960 ETIAAKIRALEEEMASLEPVNMLAIDEYERVDKRFRNLSDRREVLHREREGIIEKLERYDQLKK 1023
                                     678899999***********************************************99999986 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8  31.3     0.062        36      37     291 ..     172     418 ..     167     431 .. 0.65
   2 ?    6.5   9.1    0.0094       5.4      46     131 ..     423     508 ..     418     524 .. 0.85
   3 ?    4.9  14.9     0.028        16      29     152 ..     784     918 ..     780     948 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.062
                                    XXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXX CS
                       Filament  37 leekksaevsklkelyekeleelrkqldeltkerarlqleldnlreeledlrkkyeke....lnkreevEaelkalrkdl 112
                                     eekk+++ +   ++  + ++ +   l+e+ ++  rlq+e+d++    +   ++ ++e    l++ +e+Eae+ al  ++
  gi|116754465|ref|YP_843583.1| 172 FEEKKQRAMA-ELDVVRERIARVDVILEEVGQQLRRLQAERDRALRYRACREERKKQEayllLARFKEAEAEISALDDEI 250
                                    4444444444.333445555555555666666666666666555433222222222223344444455666666666666 PP

                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXX CS
                       Filament 113 deatlarvdLekkvesLkeelaflkkvheeEvkelqkqvseqvlvevdaarkldLteilkeir...aqyeelaeknreea 189
                                       t ++++L + +e+ +eel+ l    ee +k ++ ++s++      + ++l + + ++eir   a  e+ +e   +++
  gi|116754465|ref|YP_843583.1| 251 TSITSEKSQLLQSLEAGREELRRL----EERLKAVEGEISHK-----GEDEQLRVRREIEEIRgkiAREETRIEAADADI 321
                                    666666666655555555555433....34444444444211.....122334477778888833344688999999999 PP

                                    XXXXXXXXXXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Filament 190 eewykskleelqeaaeknsealrsakeeitelrrqiqsleieleslkkqkasleaqlaeleerleaeleklqeklselee 269
                                    ee   + l++   ++++  +++ +  e++++  ++    + el+++++q +sl+a++++++ r++    k++e+l++l +
  gi|116754465|ref|YP_843583.1| 322 EEA-DRSLSQCFIEMDRVRAEIAAISEQLSDKAMRRAGIQGELDDQRSQLSSLRANISDADSRFA----KYREELAQLIK 396
                                    998.56688899999**********************************************9986....68888888889 PP

                                    HHHHHHHHHHHHHHHHHHHHHH CS
                       Filament 270 elaeireemarqlreYqeLLdv 291
                                    e++++r+++  +lre ++LLd 
  gi|116754465|ref|YP_843583.1| 397 EIEDTRSQIGERLRERDRLLDA 418
                                    9999****************95 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0094
                                    X.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       Filament  46 sklkelyekeleelrkqldeltkerarlqleldnlreeledlrkkyekelnkreevEaelkalrkdldeatlarvdLekk 125
                                    s  ke   +e++e+ + + ++++e +rl+ e+++++ e+ dl k+ e+  ++r ++ +el++l + l+ ++ + + +e++
  gi|116754465|ref|YP_843583.1| 423 SMEKEEIATEITEALSSISAASTESERLEREVESIASEAMDLDKRREELESRRLSLRRELAELDRSLQRLQSEYARVEAQ 502
                                    455677789999999****************************99999999999**********9999998887777877 PP

                                    XXXXXX CS
                       Filament 126 vesLke 131
                                    v + +e
  gi|116754465|ref|YP_843583.1| 503 VRAAEE 508
                                    776666 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.028
                                    XXXXXXXXXXXXX.XXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.......XXXXXX CS
                       Filament  29 eLeakieeleekk.saevsklkelyekeleelrkqldeltkerarlqleldnlreeledlrkkyeke.......lnkree 100
                                    +L+ k+e+  + +  +e  +  e  e e++ l +++ +l +e  r++l  +nlr+ l++l    e         +++r++
  gi|116754465|ref|YP_843583.1| 784 DLREKLERDMQGSrIPEMMERAEQLEGEIRRLESRIMDLDSEIMRCRLKEENLRNRLDELARTKELLelkkndaIQRRSS 863
                                    67777766555433778888889999999999999999999999999999999999988743222112445555999*** PP

                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXX CS
                       Filament 101 vEaelkalrkdldeatlarvdLekkvesLkeelaflkkv...heeEvkelqkqvs 152
                                    + + +++lr  lde++ +  dL++++  Lk e   l +     e E+  ++++++
  gi|116754465|ref|YP_843583.1| 864 ALSSMEDLRAALDELSRKEKDLDRELHGLKGERGSLMESiigKEREIGGMERSIE 918
                                    *****************************98865554431224666777766665 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   7.8       0.3   1.7e+02      68     162 ..     169     268 ..     149     273 .. 0.67
   2 ?   14.7  11.4   5.3e-05     0.031      11     151 ..     270     405 ..     265     416 .. 0.77
   3 ?    6.1  16.3     0.024        14      11     145 ..     390     524 ..     388     529 .. 0.85
   4 ?    0.2  16.5       1.5   8.6e+02      41     141 ..     696     816 ..     675     819 .. 0.66
   5 ?    8.5   8.8    0.0042       2.4      42     159 ..     807     939 ..     794     947 .. 0.67
   6 ?    5.1   0.5     0.049        28      37     151 ..     907    1022 ..     888    1033 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.3
                           Fez1  68 levcenelqrkkseaellrekvekleeelkelreelselsleeeeaalesdeakaqrqe......aeeleelkreverlr 141
                                    + + e++ qr+ +e +++re++ +++  l+e+ ++l++l++e+++a  + ++ +++r++        + +e ++e+  l 
  gi|116754465|ref|YP_843583.1| 169 VSEFEEKKQRAMAELDVVRERIARVDVILEEVGQQLRRLQAERDRAL-RYRACREERKKqeayllLARFKEAEAEISALD 247
                                    56778888999999999999999999999999999998776655544.33333333333235677555666666666666 PP

                           Fez1 142 aeLkeerqkkeeqassFeqER 162
                                     e++    +k +  +s e  R
  gi|116754465|ref|YP_843583.1| 248 DEITSITSEKSQLLQSLEAGR 268
                                    666666666666655555544 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 5.3e-05
                           Fez1  11 EislLKqQLkdsqaevtqkls.eivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekv 89 
                                    E+  L + Lk +  e+++k++ e + ++ ++ e+r k+ ++e++i+ +++ +ee +++l +c  e++r ++e   ++e++
  gi|116754465|ref|YP_843583.1| 270 ELRRLEERLKAVEGEISHKGEdEQLRVRREIEEIRGKIAREETRIEAADADIEEADRSLSQCFIEMDRVRAEIAAISEQL 349
                                    66778899***********96489******************************************************99 PP

                           Fez1  90 ekleeelkelreelselsleeeeaalesdeakaqrqeaeeleelkreverlraeLkeerqkk 151
                                    +      ++++ el ++ ++ ++ +++ ++a       ++ ++ ++e+++l +e++  r + 
  gi|116754465|ref|YP_843583.1| 350 SDKAMRRAGIQGELDDQRSQLSSLRANISDAD------SRFAKYREELAQLIKEIEDTRSQI 405
                                    99999999999999986655444444433333......344444555555555554444443 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.024
                           Fez1  11 EislLKqQLkdsqaevtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekve 90 
                                    E++ L + + d+++++ ++l e   l   +r ++ + ee  +ei+e+ +s++  ++e e++e e++   sea  l+++ e
  gi|116754465|ref|YP_843583.1| 390 ELAQLIKEIEDTRSQIGERLRERDRLLDAIRRASMEKEEIATEITEALSSISAASTESERLEREVESIASEAMDLDKRRE 469
                                    67777777888999999999999999999999888888888999999999999999999999999999999999999999 PP

                           Fez1  91 kleeelkelreelselsleeeeaalesdeakaqrqeaeeleelkreverlraeLk 145
                                    +le+   +lr+el+el ++ ++ ++e  +++aq ++aee +  +r ve +r+++k
  gi|116754465|ref|YP_843583.1| 470 ELESRRLSLRRELAELDRSLQRLQSEYARVEAQVRAAEERSGYSRAVEAVRSAMK 524
                                    9999999999999999988888888888888888888888888888888887765 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 1.5
                           Fez1  41 relrakleekeeeikeleesleektle.....................levcenelqrkkseaellrekvekleeelkel 99 
                                     el +kl++ eeei++++ +le+ ++e                     +e+ +++l++++ e+e  r +++ le+e++el
  gi|116754465|ref|YP_843583.1| 696 GELLEKLDSVEEEISSISRKLESLDKEisrrtflleekralrgrmeryIEERKSRLSEMERESEEWRSRLTVLEQEMQEL 775
                                    46777788888888888888877777777777777777777777777777777777777888888888888888888888 PP

                           Fez1 100 reelselsleeeeaalesdeakaqrqeaeeleelkreverlr 141
                                     ++lse+   +e+ + +++ ++  +  +e++e+l+ e+ rl+
  gi|116754465|ref|YP_843583.1| 776 ESALSEKGDLREKLERDMQGSRIPEM-MERAEQLEGEIRRLE 816
                                    88888755444443322222222222.345555555555555 PP

  == domain 5  score: 8.5 bits;  conditional E-value: 0.0042
                           Fez1  42 elrakleekeeeikeleesleektlelevcenelqrk........kseaellrekvekleeelkelreelselsleeeea 113
                                    +l+ ++++ e++i++l++++    l+ e++ n+l++          ++++ ++   +++ + +++lr +l els++e++ 
  gi|116754465|ref|YP_843583.1| 807 QLEGEIRRLESRIMDLDSEIMRCRLKEENLRNRLDELartkelleLKKNDAIQR-RSSALSSMEDLRAALDELSRKEKDL 885
                                    455566666666666666655555555555554444422222222122222222.2344456888999999999999999 PP

                           Fez1 114 alesdeakaqrqe........aeeleelkreverlraeLkeerqkkeeqassFe 159
                                      e +  k +r +        ++e++ ++r++erl a+L+    ++ee   s +
  gi|116754465|ref|YP_843583.1| 886 DRELHGLKGERGSlmesiigkEREIGGMERSIERLDARLTAVSGAREEISISMQ 939
                                    988888888888899999999999***************999988888766655 PP

  == domain 6  score: 5.1 bits;  conditional E-value: 0.049
                           Fez1   37 kaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselsleeeeaa 114 
                                       ++  ++ ++e+ +++++ ++ ++ee + +++ + +e++ +  + +    k e++ ++++ l ee+++l++ +  a+
  gi|116754465|ref|YP_843583.1|  907 EREIGGMERSIERLDARLTAVSGAREEISISMQSLRSEIESAGIDPSEAPPKSETIAAKIRALEEEMASLEPVNMLAI 984 
                                     555556778889999999999999999999999999999999999999999999999999999999998887777766 PP

                           Fez1  115 lesdeakaq.rqeaeeleelkreverlraeLkeerqkk 151 
                                      e +++ ++ r+ +++ e l+re e + ++L+   q k
  gi|116754465|ref|YP_843583.1|  985 DEYERVDKRfRNLSDRREVLHREREGIIEKLERYDQLK 1022
                                     55555444325556777778888888888887665544 PP

>> Flg_hook  Flagellar hook-length control protein FliK
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.038        22      57      81 ..     123     147 ..     121     150 .. 0.90
   2 ?    1.1   0.1      0.63   3.7e+02      41      62 ..     252     273 ..     240     287 .. 0.87
   3 ?   -1.7   0.6       4.9   2.8e+03      53      67 ..     478     492 ..     468     507 .. 0.58
   4 ?    1.9   0.2      0.36   2.1e+02      51      68 ..     766     783 ..     763     784 .. 0.91
   5 ?    0.1   0.0       1.3   7.5e+02      38      73 ..     920     954 ..     916     956 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.038
                                    HHHHHHHHHCCTTCCEEEEEECS-- CS
                       Flg_hook  57 lprLreaLaaaGlklddlsvsegsp 81 
                                    +++L+e La+aG++ ++ +v ++++
  gi|116754465|ref|YP_843583.1| 123 QAELQEHLARAGITPEGYNVVMQGD 147
                                    689*****************99876 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.63
                                    EEEE-SCHHHHHHHHTHHHHHH CS
                       Flg_hook  41 qltaenpetrelLeqnlprLre 62 
                                    ++t+e+++ ++ Le+ +++Lr+
  gi|116754465|ref|YP_843583.1| 252 SITSEKSQLLQSLEAGREELRR 273
                                    7999************999985 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 4.9
                                    HHHTHHHHHHHHHCC CS
                       Flg_hook  53 LeqnlprLreaLaaa 67 
                                    L+++l++L ++L++ 
  gi|116754465|ref|YP_843583.1| 478 LRRELAELDRSLQRL 492
                                    555555555555554 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.36
                                    HHHHHTHHHHHHHHHCCT CS
                       Flg_hook  51 elLeqnlprLreaLaaaG 68 
                                    + Leq++++L++aL++ G
  gi|116754465|ref|YP_843583.1| 766 TVLEQEMQELESALSEKG 783
                                    579************987 PP

  == domain 5  score: 0.1 bits;  conditional E-value: 1.3
                                    EEEEEEE-SCHHHHHHHHTHHHHHHHHHCCTTCCEE CS
                       Flg_hook  38 lsvqltaenpetrelLeqnlprLreaLaaaGlkldd 73 
                                    l ++lta +  +re +  ++++Lr++ ++aG+  ++
  gi|116754465|ref|YP_843583.1| 920 LDARLTAVSG-AREEISISMQSLRSEIESAGIDPSE 954
                                    6667777665.89999999************98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1696  (0.0945953); expected 358.6 (0.02)
Passed bias filter:                      697  (0.0388756); expected 358.6 (0.02)
Passed Vit filter:                       209  (0.0116571); expected 17.9 (0.001)
Passed Fwd filter:                       150  (0.00836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              31  [number of targets reported over threshold]
# CPU time: 3.26u 0.39s 00:00:03.65 Elapsed: 00:00:00.71
# Mc/sec: 5008.82
//
Query:       gi|116754466|ref|YP_843584.1|  [L=156]
Description: hypothetical protein Mthe_1162 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); 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: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1197.57
//
Query:       gi|116754467|ref|YP_843585.1|  [L=457]
Description: glutamate synthase (NADPH), homotetrameric [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.8e-42  142.3   1.1    7.6e-42  141.7   1.1    1.3  1  Fer4_20         Dihydroprymidine dehydrogenase domain II, 4Fe
    3.9e-37  128.1   0.3    5.5e-37  127.6   0.3    1.1  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.1e-12   48.3   3.6      4e-06   27.3   0.3    3.3  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    1.4e-09   37.6   1.6    7.6e-05   22.1   0.1    3.1  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    2.9e-08   33.8   1.4      5e-08   33.1   0.1    2.0  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
      4e-07   29.6   0.7    0.00062   19.1   0.0    2.2  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
    4.5e-06   27.1   0.1     0.0059   17.0   0.0    2.3  2  NAD_binding_7   Putative NAD(P)-binding
    6.9e-05   22.4   3.1     0.0013   18.1   0.1    2.2  2  FAD_oxidored    FAD dependent oxidoreductase
     0.0002   20.9   0.0       0.16   11.3   0.0    2.5  2  PALP            Pyridoxal-phosphate dependent enzyme
    0.00021   20.5   0.6    0.00021   20.5   0.6    2.4  3  FAD_binding_2   FAD binding domain
    0.00044   19.1   0.3    0.00044   19.1   0.3    1.9  2  HI0933_like     HI0933-like protein
    0.00075   18.8   0.8     0.0013   18.0   0.2    1.6  2  Thi4            Thi4 family
    0.00097   18.4   0.0       0.24   10.5   0.0    2.2  2  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
     0.0012   18.2   0.0        1.9    7.8   0.0    2.4  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
     0.0013   18.4   5.5     0.0023   17.6   0.8    2.6  3  DAO             FAD dependent oxidoreductase
     0.0018   17.4   1.3      0.024   13.7   0.1    2.2  2  GIDA            Glucose inhibited division protein A
     0.0023   18.5   0.2       0.36   11.4   0.1    3.1  2  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
     0.0024   17.2   1.6     0.0098   15.2   0.2    2.0  2  FAD_binding_3   FAD binding domain
      0.004   16.5   0.1      0.004   16.5   0.1    1.5  2  Amino_oxidase   Flavin containing amine oxidoreductase
     0.0096   15.8   0.4        2.1    8.2   0.0    2.2  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
  ------ inclusion threshold ------
      0.014   14.9   0.1        4.3    6.9   0.0    2.2  2  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
      0.016   15.8   0.3      0.016   15.8   0.3    2.4  2  Fer4_7          4Fe-4S dicluster domain
       0.03   13.0   0.1       0.55    8.9   0.0    2.1  2  Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
      0.031   14.0   0.0        2.1    8.0   0.0    2.2  2  ELFV_dehydrog   Glutamate/Leucine/Phenylalanine/Valine dehydr
      0.033   14.3   0.1        4.4    7.4   0.1    3.0  3  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
      0.035   13.7   0.0       0.11   12.1   0.0    1.8  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
      0.079   13.5   0.1        1.7    9.2   0.0    2.3  2  XdhC_C          XdhC Rossmann domain
       0.18   11.4   0.5       0.43   10.2   0.5    1.6  1  ApbA            Ketopantoate reductase PanE/ApbA
       0.34   10.9   1.8       0.56   10.2   0.3    2.1  2  NAD_binding_9   FAD-NAD(P)-binding
        3.4    8.0   7.8       0.85    9.9   2.3    2.5  2  Fer4_2          4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer4_20  Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.7   1.1   1.3e-44   7.6e-42       1     109 [.      15     122 ..      15     125 .. 0.96

  Alignments for each domain:
  == domain 1  score: 141.7 bits;  conditional E-value: 1.3e-44
                                    HTTS-S-SB----HHHHHHHHTT----TT-HHHHCSTT---HHHHHHHHHTT-HHHHHHHHHHH-S-HHHHHHHS-GGGT CS
                        Fer4_20   1 raknfkevalglteeealeeAsRClqCkkapcvkgCPveidipefikkiaegnleeaakiiketnslpavcgrvCpqeel 80 
                                    r++nf+evalg+++e+al+eA+RCl Ckk+ cv+gCPv ++ip+fi+++++g+ +ea++iik++nslp +cgrvCpqee+
  gi|116754467|ref|YP_843585.1|  15 RRRNFSEVALGYSKEDALREADRCLGCKKPGCVEGCPVGVEIPQFIDALRRGDADEALRIIKRRNSLPGICGRVCPQEEQ 94 
                                    5789**************************************************************************** PP

                                    GCCS-GGGTTB.----HHHHHHHHHHHHH CS
                        Fer4_20  81 CegaCvlekkgkepvaigklerfvadaar 109
                                    Ce++Cvl +k+ ep+aig+ler++ad+ r
  gi|116754467|ref|YP_843585.1|  95 CESRCVLARKD-EPIAIGRLERYAADFGR 122
                                    *******8666.**************865 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 !  127.6   0.3   9.2e-40   5.5e-37       1     294 []     134     438 ..     134     440 .. 0.80

  Alignments for each domain:
  == domain 1  score: 127.6 bits;  conditional E-value: 9.2e-40
                                    CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH.HHHHCHHHHCCCCHCCTCEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias.evvkklnqgielllgeevvkid 79 
                                    k+++++G+GpAGl++a +la  g++vt++   ++++  g +l++ + +++ +++i++ ev      ++ + lg   vki+
  gi|116754467|ref|YP_843585.1| 134 KRIAIVGSGPAGLTCAADLALMGHDVTIF---EALHEAGGVLTYGIPEFRLPKSIVKrEV------DYVRSLG---VKIE 201
                                    589**************************...889999****************999543......4555555...6776 PP

                                    ESCEEEEETEEECTCEEEEEESEEEE---EEE-BC.TCTTC.TTBEECCSECHHHHHHCCSS-T..............SE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx..............xx RF
                    Pyr_redox_2  80 pgkkkvklekkkegdeekiaydklvlAtGssprdl.gipGvaenvgklvrtldsaealklkllp..............kr 144
                                     ++  v+   +++ +    +yd+++l +G+ + ++ +ipG++ ++++    +++    + +l++              ++
  gi|116754467|ref|YP_843585.1| 202 LDA--VVG-RTVGVQDLLREYDAIFLGIGAGAPRFlNIPGENLGGIY----SANEYLTRINLMKaymfpdfdtpinkgRK 274
                                    666..222.23445556679*********8655555*****333332....23333333333334444477777****** PP

                                    EEEES-SHHHHHHHHHHHHH.T-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE.......EE CS
                                    xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xx RF
                    Pyr_redox_2 145 ivvvGgGyiGvElAaalakl.gkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgnge.......kl 216
                                    ++v+GgG+++++ A  + +l ++ev++v++r++    ++ +l+++  e  ++eGv + l t++++++g+g        + 
  gi|116754467|ref|YP_843585.1| 275 VAVIGGGNVAMDAARSALRLgAVEVHIVYRRSEAE--MPARLEEI--ENAKEEGVIFDLLTNPVAFEGDGMvramecvR- 349
                                    ********************5558*********96..99999998..888999*****************998776440. PP

                                    EEEETTSCE...............EEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGCTEC CS
                                    xxxxxxxxx...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 217 evvledgee...............idadlvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDvaggk 281
                                     ++l++ +                ++ d+ ++a+G +p++  l    gl ++++g + vde++rt+++ i+a GD+a   
  gi|116754467|ref|YP_843585.1| 350 -MELGEPDAsgrrrpvekkgseftMEIDTAIIAIGTTPNPLVLRSVPGLRTTRWGTVDVDERGRTSIERIWAGGDIA--- 425
                                    .5555555566667777777779*****************9997888******************************... PP

                                    CSS--HHHHHHHH CS
                                    xxxxxxxxxxxxx RF
                    Pyr_redox_2 282 ggpelaqaAvqqG 294
                                    +g +++  A+ +G
  gi|116754467|ref|YP_843585.1| 426 TGSATVISAMGAG 438
                                    7777777777665 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.2   1.8e-06    0.0011       1      70 [.     135     213 ..     135     218 .. 0.73
   2 !   27.3   0.3   6.6e-09     4e-06       1      74 [.     274     343 ..     274     351 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.8e-06
                                    EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTT.........SSHHHHHHHHHHHHHTTEEEECSEEEEEEEEET CS
                      Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrl.........lDeeaskilqeklekngievllntkveeiegse 70 
                                    ++++vG+G  gl +A+ la +g++Vt++e+  +   +         l++ + k+  ++++ +g+++ l+++v + +g +
  gi|116754467|ref|YP_843585.1| 135 RIAIVGSGPAGLTCAADLALMGHDVTIFEALHEAGGVltygipefrLPKSIVKREVDYVRSLGVKIELDAVVGRTVGVQ 213
                                    79**************************998876632111122222567777777777888888887777777666655 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 6.6e-09
                                    EEEEECSSHHHHHHHHHHHHTT.SEEEEEESSSSSSTTSSHHHHHHH..HHHHHHTTEEEECSEEEEEEEEETTSEE CS
                      Pyr_redox   1 kvvvvGgGyiglElAgalaelg.kkVtvversdkllrllDeeaskil..qeklekngievllntkveeiegsedgve 74 
                                    kv+v+GgG++++++A  + +lg  +V++v r+++        + ++l   e+ +++g+ + l t+++++eg++  v+
  gi|116754467|ref|YP_843585.1| 274 KVAVIGGGNVAMDAARSALRLGaVEVHIVYRRSEAE------MPARLeeIENAKEEGVIFDLLTNPVAFEGDGM-VR 343
                                    79********************67***********9......44444225788999**************9987.54 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.2     6e-05     0.036       2      29 ..     138     164 ..     137     174 .. 0.90
   2 !   22.1   0.1   1.3e-07   7.6e-05     162     200 ..     270     309 ..     216     422 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6e-05
                    Pyr_redox_3   2 IiGaGPaGlaaaielkkagledylilEk 29 
                                    I+G GPaGl++a  l  +g  d++i E 
  gi|116754467|ref|YP_843585.1| 138 IVGSGPAGLTCAADLALMGH-DVTIFEA 164
                                    9******************9.7999986 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 1.3e-07
                    Pyr_redox_3 162 yagqkvvViGgknSavDaAlelvrkga.eVtvvtrgseie 200
                                     +g+kv+ViGg+n a+DaA    r ga eV++v+r+se e
  gi|116754467|ref|YP_843585.1| 270 NKGRKVAVIGGGNVAMDAARSALRLGAvEVHIVYRRSEAE 309
                                    3589*********************9759*******9755 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 !   33.1   0.1   8.3e-11     5e-08       1      36 [.     138     173 ..     138     197 .. 0.86
   2 ?   -1.6   0.2       5.4   3.2e+03       1      24 [.     277     301 ..     277     307 .. 0.73

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 8.3e-11
                                    EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG- CS
                  NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraa 36 
                                    IvG+G +Gl++A+ La  g+dv+++e+ +  GG ++
  gi|116754467|ref|YP_843585.1| 138 IVGSGPAGLTCAADLALMGHDVTIFEALHEAGGVLT 173
                                    9********************************765 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 5.4
                                    EE--SHHHHHHHHHHHCCTE.EEEE CS
                  NAD_binding_8   1 IvGaGlsGlvaAylLakagf.dvll 24 
                                    ++G+G  ++ aA+ + + g+ +v++
  gi|116754467|ref|YP_843585.1| 277 VIGGGNVAMDAARSALRLGAvEVHI 301
                                    89***99999998766664436666 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 !    8.8   0.2    0.0015      0.87      29      59 ..     134     164 ..     127     173 .. 0.88
   2 !   19.1   0.0     1e-06   0.00062       4      62 ..     246     307 ..     243     388 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0015
                                    -EEEEESTSHHHHHHHHHHHHTT-EEEEEES CS
                    AlaDh_PNT_C  29 akvlviGgGvaGlqAiatakglgakVtvlDv 59 
                                     ++ ++G G aGl  +a  + +g +Vt+++ 
  gi|116754467|ref|YP_843585.1| 134 KRIAIVGSGPAGLTCAADLALMGHDVTIFEA 164
                                    5899************************986 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 1e-06
                                    HHHHHCSCGCTSEEETTCEETC.B.---EEEEESTSHHHHHHHHHHHHTT-E.EEEEESSHH CS
                    AlaDh_PNT_C   4 eaakalekffggkgtlaGgvpg.v.epakvlviGgGvaGlqAiatakglgak.VtvlDvrpa 62 
                                     a ++l++ + +k  +       + +  kv viGgG + + A++ a +lga+ V ++  r++
  gi|116754467|ref|YP_843585.1| 246 SANEYLTRINLMKAYMFPDFDTpInKGRKVAVIGGGNVAMDAARSALRLGAVeVHIVYRRSE 307
                                    56677777777777777766543314558*********************953666655533 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 !    7.7   0.0    0.0077       4.6       6      36 ..     132     162 ..     130     192 .. 0.92
   2 !   17.0   0.0   9.8e-06    0.0059       6      46 ..     271     316 ..     270     395 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0077
                  NAD_binding_7   6 kgkkvlvvGgGevAarkvrklleagakvtvv 36 
                                    kgk++ +vG G+ +++ +  l+  g +vt+ 
  gi|116754467|ref|YP_843585.1| 132 KGKRIAIVGSGPAGLTCAADLALMGHDVTIF 162
                                    89**************************996 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 9.8e-06
                  NAD_binding_7   6 kgkkvlvvGgGevAarkvrklleaga.kvtvvapevkeele....e 46 
                                    kg+kv v+GgG+vA+  +r+ l+ ga +v++v  ++++e++    e
  gi|116754467|ref|YP_843585.1| 271 KGRKVAVIGGGNVAMDAARSALRLGAvEVHIVYRRSEAEMParleE 316
                                    689********************99548999999965555443321 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   2.2e-06    0.0013       2      42 ..     136     176 ..     135     187 .. 0.95
   2 ?    4.4   0.7     0.032        19       2      28 ..     275     302 ..     274     307 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.2e-06
                   FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsgl 42 
                                    + +vG+gpaG+++A   a +G  v + e     GG lt g+
  gi|116754467|ref|YP_843585.1| 136 IAIVGSGPAGLTCAADLALMGHDVTIFEALHEAGGVLTYGI 176
                                    68************************************986 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.032
                   FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGa.kvlLv 28 
                                    v V+GGg   + AA +A r Ga +v +v
  gi|116754467|ref|YP_843585.1| 275 VAVIGGGNVAMDAARSALRLGAvEVHIV 302
                                    89*******************9556666 PP

>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00027      0.16      48     105 ..     126     201 ..     112     229 .. 0.87
   2 !    7.0   0.0    0.0056       3.4      53      90 ..     270     308 ..     248     346 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00027
                                    HHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-EEEEE..................EETTS-HHHHHHHHHTT-EEE CS
                           PALP  48 rlkegtgaktvveassGNhgralAaaaallGlkvtiv..................vpadaspekvallrllGaevv 105
                                    r++e t++k+++  +sG +g+ +Aa  al+G +vti+                  +p++  +  v+  r+lG +++
  gi|116754467|ref|YP_843585.1| 126 RARESTKGKRIAIVGSGPAGLTCAADLALMGHDVTIFealheaggvltygipefrLPKSIVKREVDYVRSLGVKIE 201
                                    577889*******************************999999999999999999999999999999999998765 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0056
                                    TTTSEEEEEBSSHHHHHHHHHHHHHT-.EEEEEEETTS- CS
                           PALP  53 tgaktvveassGNhgralAaaaallGl.kvtivvpadas 90 
                                    ++++ v++ ++GN ++ +A  a +lG  +v+iv  ++  
  gi|116754467|ref|YP_843585.1| 270 NKGRKVAVIGGGNVAMDAARSALRLGAvEVHIVYRRSEA 308
                                    57899********************966*****777655 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.6   3.5e-07   0.00021       2      37 ..     136     171 ..     135     175 .. 0.91
   2 ?   -0.6   0.9       0.9   5.4e+02       2      29 ..     275     303 ..     274     310 .. 0.88
   3 ?   -1.8   0.0       2.1   1.3e+03     369     405 ..     390     428 ..     357     438 .. 0.66

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 3.5e-07
                                    EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSG CS
                  FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqefgga 37 
                                    + ++GsG AGL++A+ +a  G++v++ e  +e gg 
  gi|116754467|ref|YP_843585.1| 136 IAIVGSGPAGLTCAADLALMGHDVTIFEALHEAGGV 171
                                    67***************************9998885 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.9
                                    EEEE--SHHHHHHHHHHHHTTT.-EEEEE CS
                  FAD_binding_2   2 viViGsGlAGLaAAleaaeaGl.kvavve 29 
                                    v ViG+G   + AA +a + G+ +v +v 
  gi|116754467|ref|YP_843585.1| 275 VAVIGGGNVAMDAARSALRLGAvEVHIVY 303
                                    89***************999999999885 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 2.1
                                    EEEES-EEEBETTSBE..STTEEESSBTEEE-STCEESS CS
                  FAD_binding_2 369 qhytmgGvetdengrv..ldadgqpipGLYAaGevaagg 405
                                    ++ +  G++t+ +g v  ++++ + i+  +A G  a g+
  gi|116754467|ref|YP_843585.1| 390 VLRSVPGLRTTRWGTVdvDERGRTSIERIWAGGDIATGS 428
                                    444455666666666655555555777777777777444 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.3   7.3e-07   0.00044       2      36 ..     135     169 ..     134     173 .. 0.92
   2 ?   -0.2   0.2      0.54   3.2e+02       2      23 ..     274     295 ..     273     306 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 7.3e-07
                                    SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                    HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36 
                                    +++++G G+AGl +A+ +a  g++V+++e+ +++g
  gi|116754467|ref|YP_843585.1| 135 RIAIVGSGPAGLTCAADLALMGHDVTIFEALHEAG 169
                                    689**************************988776 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.54
                                    SEEEE--SHHHHHHHHHHHHTT CS
                    HI0933_like   2 dviviGgGaAGlmaAisaakrg 23 
                                    +v+viGgG   + aA sa + g
  gi|116754467|ref|YP_843585.1| 274 KVAVIGGGNVAMDAARSALRLG 295
                                    79*******9999999986655 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.2   2.3e-06    0.0013      20      84 ..     136     200 ..     129     211 .. 0.81
   2 ?   -2.4   0.0       3.8   2.3e+03      19      45 ..     274     300 ..     264     305 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.3e-06
                                    EEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTB..SEEEEETTTHHHHHHTT--- CS
                           Thi4  20 vvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlf..saivvrkpakelLdelgiky 84 
                                    ++ivG+G++GLt+a  la   +  v+i+e+    GG    G   f   + +v+++ +  ++ lg+k 
  gi|116754467|ref|YP_843585.1| 136 IAIVGSGPAGLTCAADLALM-GHDVTIFEALHEAGGVLTYGIPEFrlPKSIVKREVD-YVRSLGVKI 200
                                    89*****************9.*********999999888887666224777777765.456666665 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.8
                                    EEEEE--SHHHHHHHHHHHHCTTS-EE CS
                           Thi4  19 DvvivGaGssGLtaayylakkpdlkva 45 
                                     v+++G+G   + aa+   +   ++v 
  gi|116754467|ref|YP_843585.1| 274 KVAVIGGGNVAMDAARSALRLGAVEVH 300
                                    589999999999999876555555555 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 ?    5.6   0.0     0.012       7.4     184     214 ..     126     156 ..      77     165 .. 0.78
   2 !   10.5   0.0    0.0004      0.24     180     228 ..     249     308 ..     212     317 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.012
                    K_oxygenase 184 rkeellakkriaVvGsGqSaaeifedllrrq 214
                                    r +e+ ++kria+vGsG  +   + dl+   
  gi|116754467|ref|YP_843585.1| 126 RARESTKGKRIAIVGSGPAGLTCAADLALMG 156
                                    4455999**********99988888877655 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0004
                    K_oxygenase 180 eylerkee............llakkriaVvGsGqSaaeifedllrrqkkvelklvtrseal 228
                                    eyl+r++              ++++++aV+G+G  a + ++ +lr  + ve+++v r+++ 
  gi|116754467|ref|YP_843585.1| 249 EYLTRINLmkaymfpdfdtpINKGRKVAVIGGGNVAMDAARSALRLGA-VEVHIVYRRSEA 308
                                    555555445555555566667899******************998766.9******99875 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 !    7.8   0.0    0.0031       1.9      30      67 ..     127     164 ..     112     182 .. 0.86
   2 !    7.8   0.0    0.0032       1.9      35      73 ..     271     310 ..     255     344 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0031
                                    SBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESS CS
                   2-Hacid_dh_C  30 lgkelsgktvGiiGlGrIGqavakrlkafgmkviaydr 67 
                                      ++ +gk+++i+G G  G + a  l+ +g +v++++ 
  gi|116754467|ref|YP_843585.1| 127 ARESTKGKRIAIVGSGPAGLTCAADLALMGHDVTIFEA 164
                                    556789**************************998876 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0032
                                    TTSEEEEES-SHHHHHHHHHHHHTT-.EEEEESSSHHHHH CS
                   2-Hacid_dh_C  35 sgktvGiiGlGrIGqavakrlkafgm.kviaydrskkkee 73 
                                    +g++v++iG G+++  +a+ +  +g+ +v ++ r+ ++e 
  gi|116754467|ref|YP_843585.1| 271 KGRKVAVIGGGNVAMDAARSALRLGAvEVHIVYRRSEAEM 310
                                    799*******************999877766655544332 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.8   3.8e-06    0.0023       2      33 ..     136     169 ..     135     174 .. 0.91
   2 ?   -3.0   0.0         7   4.2e+03     155     207 ..     192     234 ..     182     255 .. 0.66
   3 ?    2.4   0.1      0.15        92       1      32 [.     274     308 ..     274     312 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.8e-06
                                    EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                            DAO   2 vviiGGGiiGlstAyeLarrg..Vtllekgdiag 33 
                                    ++i+G+G +Gl++A +La  g  Vt++e+ ++ag
  gi|116754467|ref|YP_843585.1| 136 IAIVGSGPAGLTCAADLALMGhdVTIFEALHEAG 169
                                    9*****************99999*****988777 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 7
                                    HHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEE.EEEEEEEE--GGGHH.HH CS
                            DAO 155 aaealGveilegtevtgleeedgkvwgverttpgen.daadavVnaaGawsd.ll 207
                                     +++lGv+i +   v+g        +gv+        +++da+ +  Ga++  +l
  gi|116754467|ref|YP_843585.1| 192 YVRSLGVKIELD-AVVGR------TVGVQ-----DLlREYDAIFLGIGAGAPrFL 234
                                    566777777777.66664......55662.....122357888888888877444 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.15
                                    EEEEECTSHHHHHHHHHHHHTT...EEEEESSSST CS
                            DAO   1 dvviiGGGiiGlstAyeLarrg...Vtllekgdia 32 
                                    +v++iGGG + + +A+ + r g   V ++ ++++a
  gi|116754467|ref|YP_843585.1| 274 KVAVIGGGNVAMDAARSALRLGaveVHIVYRRSEA 308
                                    59****************88899999999888665 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.1     4e-05     0.024       2      62 ..     136     196 ..     135     208 .. 0.77
   2 ?    2.6   0.2     0.096        58       1      23 [.     274     296 ..     274     317 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4e-05
                                    EEEE-SSHHHHHHHHHHHHTT--EEEE..ES-GGGTT--SSSSEEE-TTHHHHHHHHHHHT-S CS
                           GIDA   2 viViGgGhAGceAAlaaarlGakvlLi..thkldtiaelsCnpsiggiakgllvrEidalggl 62 
                                    + ++G G AG+ +A+ +a +G++v+++   h+ + +++    p ++ + k++++rE+d + +l
  gi|116754467|ref|YP_843585.1| 136 IAIVGSGPAGLTCAADLALMGHDVTIFeaLHEAGGVLTY-GIPEFRLP-KSIVKREVDYVRSL 196
                                    789************************655555555554.46777765.77888888777665 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.096
                                    CEEEE-SSHHHHHHHHHHHHTT- CS
                           GIDA   1 dviViGgGhAGceAAlaaarlGa 23 
                                    +v ViGgG   + AA  a rlGa
  gi|116754467|ref|YP_843585.1| 274 KVAVIGGGNVAMDAARSALRLGA 296
                                    699******************96 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 ?    3.4   0.1      0.19   1.1e+02       1      31 [.     135     162 ..     135     169 .. 0.90
   2 !   11.4   0.1   0.00061      0.36       1      45 [.     274     316 ..     274     332 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.19
                                    EEEEETTSHHHHHHHHHHHHTTS-GGCEEEE CS
                  F420_oxidored   1 kigiiGaGnmgealasgllaagaqpheivva 31 
                                    +i+i+G+G  g + a  l+  g   h++++ 
  gi|116754467|ref|YP_843585.1| 135 RIAIVGSGPAGLTCAADLALMG---HDVTIF 162
                                    79********************...999975 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00061
                                    EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHH CS
                  F420_oxidored   1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaee 45 
                                    k+++iG+Gn++   a+ +l+ g  + e+ ++ +r++ ++ +  ee
  gi|116754467|ref|YP_843585.1| 274 KVAVIGGGNVAMDAARSALRLG--AVEVHIVYRRSEAEMPARLEE 316
                                    79********************..667776778877665554444 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.2   1.6e-05    0.0098       4      34 ..     136     166 ..     134     170 .. 0.91
   2 ?    0.9   0.1      0.36   2.1e+02       3      36 ..     274     308 ..     273     318 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.6e-05
                                    EEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                  FAD_binding_3   4 VlIVGaGpaGlmlallLseaGvrvvlvekrs 34 
                                    ++IVG+GpaGl+ a  L+  G +v++ e   
  gi|116754467|ref|YP_843585.1| 136 IAIVGSGPAGLTCAADLALMGHDVTIFEALH 166
                                    68************************99765 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.36
                                    EEEEE--SHHHHHHHHHHHHTT.HHEEEEESSSSS CS
                  FAD_binding_3   3 dVlIVGaGpaGlmlallLseaG.vrvvlvekrstt 36 
                                    +V+++G+G + + +a+   + G v+v++v +rs++
  gi|116754467|ref|YP_843585.1| 274 KVAVIGGGNVAMDAARSALRLGaVEVHIVYRRSEA 308
                                    69*************9766666489****999886 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   6.7e-06     0.004       2      28 ..     144     170 ..     143     173 .. 0.96
   2 ?   -3.1   0.1       5.8   3.5e+03     423     449 ..     419     443 ..     399     445 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.7e-06
                                    HHHHHHHHHHHTTEEEEEEESSSSSBT CS
                  Amino_oxidase   2 aGLaaArqLlsaGfdVtvlEardrvGG 28 
                                    aGL++A  L+  G+dVt++Ea   +GG
  gi|116754467|ref|YP_843585.1| 144 AGLTCAADLALMGHDVTIFEALHEAGG 170
                                    9*************************9 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.8
                                    EE.SGGGCTTTTTSHHHHHHHHHHHHH CS
                  Amino_oxidase 423 ffAGehtsreypgtvegAilSGlraAa 449
                                      AG  ++ +  +tv  A+ +G+raA 
  gi|116754467|ref|YP_843585.1| 419 W-AGGDIA-TGSATVISAMGAGKRAAF 443
                                    3.555544.466889999999999995 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 !    8.2   0.0    0.0035       2.1       2      31 ..     136     165 ..     135     190 .. 0.91
   2 ?    5.8   0.1     0.019        12       1      44 [.     274     319 ..     274     337 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0035
                                    EEEE--SCCHHHHHHHHHHTT-EEEEE-S- CS
                        3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdis 31 
                                    +a++G+G  G   aa +a  g++V++++  
  gi|116754467|ref|YP_843585.1| 136 IAIVGSGPAGLTCAADLALMGHDVTIFEAL 165
                                    8************************99875 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.019
                                    EEEEE--SCCHHHHHHHHHHTT.-EEEEE-S.-HHHHHHHHHHHHH CS
                        3HCDH_N   1 kvaviGaGtmGagiaavfasag.leVvlvdi.seealekalekiek 44 
                                    kvaviG G +    a  +++ g +eV++v + se+ + + le+ie+
  gi|116754467|ref|YP_843585.1| 274 KVAVIGGGNVAMDAARSALRLGaVEVHIVYRrSEAEMPARLEEIEN 319
                                    79*****************997379999887244445555555555 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 ?    6.9   0.0    0.0071       4.3       3      32 ..     132     161 ..     130     169 .. 0.91
   2 ?    5.9   0.0     0.014       8.6       3      47 ..     271     323 ..     269     333 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0071
                                    HTS-EEEES-SHHHHHHHHHHHHTT--EEE CS
                           IlvN   3 kgkkiaviGyGsqGhaqalnlrdsgldvvv 32 
                                    kgk+ia++G G  G + a  l   g dv++
  gi|116754467|ref|YP_843585.1| 132 KGKRIAIVGSGPAGLTCAADLALMGHDVTI 161
                                    89********************99999987 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.014
                                    HTS-EEEES-SHHHHHHH.HHHHHTT--EEEEE-TT-.......HHHHHHHHT CS
                           IlvN   3 kgkkiaviGyGsqGhaqa.lnlrdsgldvvvglregs.......ksvkkAkee 47 
                                    kg+k+aviG G+ +   a   lr   ++v +  r+++       + +++Akee
  gi|116754467|ref|YP_843585.1| 271 KGRKVAVIGGGNVAMDAArSALRLGAVEVHIVYRRSEaemparlEEIENAKEE 323
                                    799*********997766257999999**999998874444444445555555 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   0.3   2.6e-05     0.016      32      52 .]      32      54 ..       6      54 .. 0.80
   2 ?    0.4   0.4       1.7   9.9e+02       7      14 ..      84      91 ..      82     115 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.6e-05
                         Fer4_7 32 eidpekClgCga..CvavCPtga 52
                                     ++++ClgC++  Cv+ CP+g+
  gi|116754467|ref|YP_843585.1| 32 LREADRCLGCKKpgCVEGCPVGV 54
                                   45689****************96 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.7
                         Fer4_7  7 aCvaaCpv 14
                                    C ++Cp+
  gi|116754467|ref|YP_843585.1| 84 ICGRVCPQ 91
                                   56666664 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 ?    1.8   0.0      0.13        79     261     298 ..     122     159 ..     100     167 .. 0.79
   2 ?    8.9   0.0   0.00092      0.55     270     326 ..     270     326 ..     256     333 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.13
                                    HHHHHHHHHHTT-EEEEECSSHHHHHHHHHHHHHT-EE CS
                 Oxidored_nitro 261 daladyheylagkrvaiygdpdrvvalarllkelGmev 298
                                    +  + ++e ++gkr+ai+g +   +  a+ l+ +G +v
  gi|116754467|ref|YP_843585.1| 122 RDCRRARESTKGKRIAIVGSGPAGLTCAADLALMGHDV 159
                                    55667899************999988888888777776 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00092
                                    HTT-EEEEECSSHHHHHHHHHHHHHT-EEEEEEESSS-HHHHHHHHHHS.TT.SEEE CS
                 Oxidored_nitro 270 lagkrvaiygdpdrvvalarllkelGmevvaagtetahrddeerlkaeleegepevi 326
                                     +g++va++g++  ++  ar    lG+  v+++++ ++++  +rl+++  ++e+ vi
  gi|116754467|ref|YP_843585.1| 270 NKGRKVAVIGGGNVAMDAARSALRLGAVEVHIVYRRSEAEMPARLEEIENAKEEGVI 326
                                    579********************************9988877777764444444555 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 ?    3.6   0.0     0.075        45      27      58 ..     128     159 ..     116     173 .. 0.81
   2 ?    8.0   0.0    0.0035       2.1      30      61 ..     270     301 ..     243     306 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.075
                                    TS-STTEEEEEE--SHHHHHHHHHHHHCT-EE CS
                  ELFV_dehydrog  27 ldslegkrvaisGsGnvgsyaallltelgakv 58 
                                     +s++gkr+ai GsG  g  +a  l+ +g+ v
  gi|116754467|ref|YP_843585.1| 128 RESTKGKRIAIVGSGPAGLTCAADLALMGHDV 159
                                    45799*************99998887777765 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0035
                                    STTEEEEEE--SHHHHHHHHHHHHCT-EEEEE CS
                  ELFV_dehydrog  30 legkrvaisGsGnvgsyaallltelgakvvav 61 
                                     +g++va+ G Gnv+  aa+ + +lga  v +
  gi|116754467|ref|YP_843585.1| 270 NKGRKVAVIGGGNVAMDAARSALRLGAVEVHI 301
                                    5899*********************9976655 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.25   1.5e+02       8      41 ..     129     161 ..     124     167 .. 0.81
   2 ?   -0.3   0.0       1.7   9.9e+02      41      88 ..     185     231 ..     184     237 .. 0.71
   3 ?    7.4   0.1    0.0074       4.4      11      47 ..     271     307 ..     266     330 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.25
                                    S..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEE CS
                   Shikimate_DH   8 eslkekkvlliGaGemaelvakhLlakgvkkvvv 41 
                                    es k+k++ ++G G  +   a  L+  g + v++
  gi|116754467|ref|YP_843585.1| 129 ESTKGKRIAIVGSGPAGLTCAADLALMGHD-VTI 161
                                    57899***********99999988876665.655 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.7
                                    EEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS- CS
                   Shikimate_DH  41 vaNRtlerakelaeelkgeeiealkleelkellaeadvvisataseep 88 
                                    ++ R+++ +++l  +++ + + + +   +++ll+e+d ++  +++  p
  gi|116754467|ref|YP_843585.1| 185 IVKREVDYVRSLGVKIELD-AVVGRTVGVQDLLREYDAIFLGIGAGAP 231
                                    5666666666666666433.5566666789999*******99988766 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0074
                                    TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHH CS
                   Shikimate_DH  11 kekkvlliGaGemaelvakhLlakgvkkvvvaNRtle 47 
                                    k++kv +iG G++a  +a+  l+ g+ +v ++ R  e
  gi|116754467|ref|YP_843585.1| 271 KGRKVAVIGGGNVAMDAARSALRLGAVEVHIVYRRSE 307
                                    6799******************9*9999*99988655 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 ?   12.1   0.0   0.00018      0.11       2      28 ..     135     161 ..     134     167 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00018
                                    EEEEE--STTHHHHHHHHHHCTSEEEE CS
                 UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeighevig 28 
                                    +i+++G+G  Gl++aa la +gh+v++
  gi|116754467|ref|YP_843585.1| 135 RIAIVGSGPAGLTCAADLALMGHDVTI 161
                                    8************************97 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.49   2.9e+02       2      30 ..     137     165 ..     136     209 .. 0.86
   2 ?    9.2   0.0    0.0028       1.7       1      44 [.     275     319 ..     275     373 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.49
                                    EEE--STTHHHHHHHHHHHTEEEEEEES- CS
                         XdhC_C   2 vifGaghvaqalarlaaalgfrvtvvdpr 30 
                                    +i+G g+ +  +a+ +a +g +vt++++ 
  gi|116754467|ref|YP_843585.1| 137 AIVGSGPAGLTCAADLALMGHDVTIFEAL 165
                                    79**********************99865 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0028
                                    EEEE--STTHHHHHHHHHHHT.EEEEEEES-GGGG-GGG-TT-SE CS
                         XdhC_C   1 lvifGaghvaqalarlaaalg.frvtvvdpreefatkerfpeade 44 
                                    ++++G+g+va   ar a +lg ++v++v  r+e++ ++r++e ++
  gi|116754467|ref|YP_843585.1| 275 VAVIGGGNVAMDAARSALRLGaVEVHIVYRRSEAEMPARLEEIEN 319
                                    579******************89*********9998888876554 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.5   0.00071      0.43       1      26 [.     136     161 ..     136     173 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00071
                                    EEEES-SHHHHHHHHHHHHHTHCEEE CS
                           ApbA   1 iailGaGaiGsllaakLakagadvtl 26 
                                    iai+G+G  G ++aa La  g+dvt+
  gi|116754467|ref|YP_843585.1| 136 IAIVGSGPAGLTCAADLALMGHDVTI 161
                                    89**********************97 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.3   0.00094      0.56       1      39 [.     137     170 ..     137     177 .. 0.87
   2 ?   -1.7   0.1       4.2   2.5e+03       1      33 [.     276     304 ..     276     317 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00094
                  NAD_binding_9   1 aivGaGprGlavlerLlarakkkspleitlfdp.sepgag 39 
                                    aivG Gp+Gl++++ L+        +++t+f+  +e+g g
  gi|116754467|ref|YP_843585.1| 137 AIVGSGPAGLTCAADLALM-----GHDVTIFEAlHEAG-G 170
                                    8***************988.....59999999988887.4 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4.2
                  NAD_binding_9   1 aivGaGprGlavlerLlarakkkspleitlfdp 33 
                                    a++G+G  ++ +++  l+       +e++++ +
  gi|116754467|ref|YP_843585.1| 276 AVIGGGNVAMDAARSALRL----GAVEVHIVYR 304
                                    7999999999999999988....4677777655 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   2.3    0.0014      0.85       6      21 ..      34      51 ..      29      52 .. 0.84
   2 ?    0.2   0.3       1.7     1e+03      14      22 .]      83      91 ..      83      91 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0014
                         Fer4_2  6 dtdrCigCg..aCvsaCP 21
                                   ++drC+gC+   Cv  CP
  gi|116754467|ref|YP_843585.1| 34 EADRCLGCKkpGCVEGCP 51
                                   689*****6677****** PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.7
                         Fer4_2 14 gaCvsaCPa 22
                                   g+C  +CP+
  gi|116754467|ref|YP_843585.1| 83 GICGRVCPQ 91
                                   78999***5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); 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):              30  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 3382.40
//
Query:       gi|116754468|ref|YP_843586.1|  [L=736]
Description: oligosaccharyl transferase, STT3 subunit [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.3e-25   88.1  40.2    1.9e-24   86.5  40.2    1.7  1  STT3      Oligosaccharyl transferase STT3 subunit
    9.3e-20   70.7   0.2    1.6e-19   70.0   0.2    1.4  1  AglB_L1   Archaeal glycosylation protein B long peripheral do
    9.9e-07   29.1  15.5    9.9e-07   29.1  15.5    3.3  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 !   86.5  40.2   3.2e-28   1.9e-24      25     485 ..      49     509 ..      31     510 .. 0.68

  Alignments for each domain:
  == domain 1  score: 86.5 bits;  conditional E-value: 3.2e-28
                                    CT--S--SSCHHHHHHHCCCHHHT-C.....CCHHSSEETTSSTTT-EEESTTCCH.CCC.CHHHHHHCCHHCHHHHHHH CS
                           STT3  25 dglsylsefDpYYnyRltenllnnGfpGdvvikkknwfdhsqyyPpGsrvdygpli.vlLamlasaiinhsldvsirevc 103
                                    +g  ++   D+YY +R + ++ ++       ++++ wfd +  yP G  ++++pl  + +a +a+ +++++ d s+ +v+
  gi|116754468|ref|YP_843586.1|  49 RGDTIFDGYDEYYHLRRIFYTFHH-------FPQTLWFDSYINYPHGLEITWPPLFdIAVAAIAHLVTPLIGDRSVEAVA 121
                                    677888999**************9.......8**********************98689********************* PP

                                    HCCHHHHHHHHCHHHHHHHHHHS-CCCHHHHHHHCCC-CCCCCTTSTT--STCCCCHHHHHHHHHHHHHHHHCCSTTCHH CS
                           STT3 104 lwlpallgsLlaIpiyflvrelksdiaGllAAlllaiaPgYlsrtvaGfyDtdmfeivlllfvlffflkaiktksnkisl 183
                                     +++++lg++l++++y ++re+++   +l++A+lla+ P  + rt  G+ D++ +ei+l  +++ ++l  i  +     +
  gi|116754468|ref|YP_843586.1| 122 AVISPILGGVLVVVVYAIAREVFDVKTALVSAFLLAVCPYSVIRTSFGSPDHHSLEILLFSLIVLLLLYTIRGGY---IW 198
                                    ***********************************************************************9999...9* PP

                                    HHHHHHHHHHHHTTSCCGGHHHHCCHHHHHHHHHCTTTS-CCHHHHHHHHHHHHHHH..CCCCCCCTTCHHH...STTTC CS
                           STT3 184 aviaaliiflivlaWggyailiyallllfilalLiigrfelklkiavtfsviiaflviaiivllflgfqvva...vseii 260
                                    + +a+++++ + ++W g  i ++++  + +l  +++ r ++ ++       +++ l++a++++l++gf++     +  ii
  gi|116754468|ref|YP_843586.1| 199 SICAGIAVAALAYTWAGAPIYLLIIPSFAVLRAILSLRGNSAFDYR----PLLVCLAVASVLVLPFGFSSWLhvsFLSII 274
                                    *****************84554444444455555554544444433....333333334456666666665546666666 PP

                                    HHCCCCHHHHHH...HHCCCHHC..CCCCCHHCCCHHTT.HHHHTT--GGGHHHHHHHHHHHHC................ CS
                           STT3 261 galgifgllqlv...afgsvvvlvaelkfyqfislfqpgilsevlgligevvtalavlglialw................ 321
                                     ++ i+ l  ++   a+ +  +++   ++  + +l+  +i+  + + +++ +   +++g+ia                  
  gi|116754468|ref|YP_843586.1| 275 IITAIVLLTTIIeklALRKDLPWIVLPASLFAVALIIIFINYSRIQSAVVYLIGGGMTGKIAEAeplfvntdpftplilw 354
                                    666666555544111555555555555555555577777777778887888888899*****995555555555555544 PP

                                    ........CCCCCTS-----TTHHHHHHHHHS---S--CCHHHCCSSSTTTTCCCHHHCHHCCHHCTCHHHHHHHHHHHH CS
                           STT3 322 ........lgilyslldleyaklkikiiilvsvwlpvgllaltkglrfliftvPlgiifvgllleflavfvkiysvsqil 393
                                            +++ly+ +    a +++    l+ +w ++ l++++   rf+  +  +g i++ lll  + +  + y+ s++ 
  gi|116754468|ref|YP_843586.1| 355 lllyilgaAVLLYETV----ASVSRDARLLLLIWAVLALALTFGQKRFIYVSSTVGPILMALLLIRAIIWTRSYP-SRRF 429
                                    4444333333333333....4444444445555555555555555555555555555555554444444444444.2222 PP

                                    HCCC-SCHCCCCCHHHHHHHCCCHHHHHHHHCCHHHHHHHHHHHHHHHHHHCT.TTTTHHH.TTHHHCHHH......... CS
                           STT3 394 fsgvvvillmltllpvlallaavkiskifstykdekeakikvaakavaptksnglkeslew.kantnrdsv......... 463
                                    ++g+     ++ +lp + l  +v  +  + +                       + esl+w +++t++ s+         
  gi|116754468|ref|YP_843586.1| 430 IAGAALA--IMIFLPIMDLPGIVSSEPAITQ----------------------DWVESLQWlRNSTPQTSYfdepfqvpe 485
                                    2222222..3344454444444444433333......................444444444444444443222222222 PP

                                    ..HHHHHHHHHHHHHHHHHHHHHH CS
                           STT3 464 ..vitwwdyghilaveadrpVtfd 485
                                      v++wwdyg  + ++ +rpV+++
  gi|116754468|ref|YP_843586.1| 486 ysVMCWWDYGNWIVYIGERPVVAN 509
                                    238******************986 PP

>> AglB_L1  Archaeal glycosylation protein B long peripheral domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.0   0.2   2.7e-23   1.6e-19       1      92 []     633     724 ..     633     724 .. 0.95

  Alignments for each domain:
  == domain 1  score: 70.0 bits;  conditional E-value: 2.7e-23
                                    -EEEEEEBSSSSEEEEEEEEE-TTS-EEEEEEEEE.-BTTEEEEEE---SS......-SSSSEESS-EEEEETT...... CS
                        AglB_L1   1 GAtitGsaeagatvtasveletnqgrtftYrqeaeadedGefeltvPYstegeedgetnssveaagpYevtagn...... 74 
                                    GA+i+Gsa++++ v+a ++l++n gr f+Y + a + ++G++e++vPYsteg      +++++aagpY+++  +      
  gi|116754468|ref|YP_843586.1| 633 GAVIRGSARDDTIVVAVLNLSSNLGRPFQYVNYA-VPRNGSYEIRVPYSTEG------AYGIKAAGPYQIVEITpatdgw 705
                                    9*********************************.7***************7......99***********977778888 PP

                                    .EEEEE---HHHHHHT-EE CS
                        AglB_L1  75 .vtaeveVpEeaVlsgetv 92 
                                      ++ v+V+Ee+Vl+g++v
  gi|116754468|ref|YP_843586.1| 706 gDVTLVNVTEEDVLKGRIV 724
                                    8999************987 PP

>> PMT_2  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1  15.5   1.6e-10   9.9e-07       6     156 ..     101     260 ..      94     265 .. 0.73
   2 ?   -1.3   2.7      0.39   2.3e+03     120     154 ..     274     308 ..     260     316 .. 0.50
   3 ?   -7.7  20.3         3   1.8e+04      24     156 ..     298     443 ..     279     445 .. 0.47

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 1.6e-10
                          PMT_2   6 iawllalftklfgf..selairlvsalagvltilllyllarrlfgkraallaalllavvplfvalsalftpdaplv..ll 81 
                                    +a +++l+t l+g+   e ++ ++s ++g + ++++y++ar++f+ ++al++a+llav+p+ v+ +  + pd   +  ll
  gi|116754468|ref|YP_843586.1| 101 VAAIAHLVTPLIGDrsVEAVAAVISPILGGVLVVVVYAIAREVFDVKTALVSAFLLAVCPYSVIRTSFGSPDHHSLeiLL 180
                                    67899*******98657888899*************************************99999999999876551044 PP

                          PMT_2  82 walalylllraleknklkywllagvlfGlgflsKy..taalllia.all..yllisarrilkekkpyl.alllalllfsp 155
                                     +l+++lll  +  +   + + ag+++++  ++     + ll+i+ +++  ++l  ++    + +p+l +l++a +l++p
  gi|116754468|ref|YP_843586.1| 181 FSLIVLLLLYTIRGGY-IWSICAGIAVAALAYTWAgaPIYLLIIPsFAVlrAILSLRGNSAFDYRPLLvCLAVASVLVLP 259
                                    4444444444444444.488999988887777754114444554434445444444455666667777799999999999 PP

                          PMT_2 156 v 156
                                    +
  gi|116754468|ref|YP_843586.1| 260 F 260
                                    6 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.39
                          PMT_2 120 llliaallyllis.arr.ilkekkpylalllalllfs 154
                                    +++ a+   ll++  ++  l+++ p+++l   l +++
  gi|116754468|ref|YP_843586.1| 274 IIITAI--VLLTTiIEKlALRKDLPWIVLPASLFAVA 308
                                    222222..33333323337777666664444433333 PP

  == domain 3  score: -7.7 bits;  conditional E-value: 3
                          PMT_2  24 irlvsalagvltilllyllarrlfgkraallaall....lavvplfvalsalftpdaplvllwal.alylllrale..kn 96 
                                    i l++ l++v  i+++ +   r+ ++++ l++  +    +++ plfv++   ftp ++ +ll++l a+ ll++ +   ++
  gi|116754468|ref|YP_843586.1| 298 IVLPASLFAVALIIIF-INYSRIQSAVVYLIGGGMtgkiAEAEPLFVNTDP-FTPLILWLLLYILgAAVLLYETVAsvSR 375
                                    5555555555444443.3333344556555555441111455555555555.4443333333322233344444433434 PP

                          PMT_2  97 klkywllagvlfGlg..flsK......ytaallliaallyllis...arrilkekkpylalllalllfspv 156
                                     ++ +ll+ ++++l+  f  K       t++ +l+a    lli+   + r   +++++++++la+++f+p+
  gi|116754468|ref|YP_843586.1| 376 DARLLLLIWAVLALAltFGQKrfiyvsSTVGPILMA---LLLIRaiiWTRSYPSRRFIAGAALAIMIFLPI 443
                                    445554444444444113334111000333333333...34444444447788888888888888888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (736 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       840  (0.0468515); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.72u 0.27s 00:00:00.99 Elapsed: 00:00:00.45
# Mc/sec: 4896.65
//
Query:       gi|116754469|ref|YP_843587.1|  [L=273]
Description: hypothetical protein Mthe_1165 [Methanosaeta thermophila PT]
Scores for 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-97  324.5  12.3      1e-96  324.3  12.3    1.0  1  DUF63     Membrane protein of unknown function DUF63


Domain annotation for each model (and alignments):
>> DUF63  Membrane protein of unknown function DUF63
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  324.3  12.3  5.8e-101     1e-96       1     272 []       8     273 .]       8     273 .] 0.98

  Alignments for each domain:
  == domain 1  score: 324.3 bits;  conditional E-value: 5.8e-101
                          DUF63   1 iseFiykyYidpivykegYnivntltyaiiLivavyliykllkklkikidekfvlatipyvilgsslRvveDagllkppl 80 
                                    i +F+++yY++pi++++gYn+vnt+t+ai+L+v+++li +++++++i+++++f+lat py+i+gsslRv+eDa+l++ppl
  gi|116754469|ref|YP_843587.1|   8 IVHFVQRYYVEPIINDSGYNPVNTVTWAIVLGVFIVLIQRAFRRYGIEVNSRFILATAPYIIAGSSLRVIEDAELIDPPL 87 
                                    789***************************************************************************** PP

                          DUF63  81 syllitPliyflvflitlavlliskklekklkkdykklyaavGvvlvlvvlllLllteevvnlevlllvlllaavltalv 160
                                    syllitPliy+lv+ +tl++l+is++l     +  ++ly avG+ +++++lllL+  e v++++v+l+v++l + +t +v
  gi|116754469|ref|YP_843587.1|  88 SYLLITPLIYILVASVTLLALFISRRL-----TGGYRLYSAVGISWSALNLLLLI-REGVQHAWVPLAVVALGSSITGCV 161
                                    ***************************.....45578999************999.************************ PP

                          DUF63 161 llllrklklellsdklnlllllahllDasatfvgidllgYvEqHvvpsfLidltGtalvmyplkllvlipvlyildkevk 240
                                    ++ll+ l ++l ++++ l+++l+h+lDas+t++g+d+lgY E+Hvvp++Li+++G+a+vmyplkl+vl+p l+ild++ +
  gi|116754469|ref|YP_843587.1| 162 YILLQILPHSLSMRRCALSVILSHMLDASSTYIGVDWLGYEEKHVVPTLLIHTAGSAAVMYPLKLIVLLPLLVILDESLR 241
                                    ******************************************************************************** PP

                          DUF63 241 eeeelrnlvklailvlGlaPgiRnllrmvlgv 272
                                    ++++++ +++l++lvlGlaP++Rn+lrm+lg+
  gi|116754469|ref|YP_843587.1| 242 NDRDIMGILVLTLLVLGLAPATRNTLRMMLGI 273
                                    ******************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1949.58
//
Query:       gi|116754470|ref|YP_843588.1|  [L=244]
Description: flavoprotein [Methanosaeta thermophila PT]
Scores for complete 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   60.7   0.0    4.2e-16   59.1   0.0    1.7  2  Flavoprotein  Flavoprotein
    2.4e-06   27.1   8.5     0.0043   16.8   0.6    3.4  3  Fer4          4Fe-4S binding domain
    1.6e-05   24.7  14.7      0.002   18.1   5.0    2.6  2  Fer4_2        4Fe-4S binding domain
    3.2e-05   24.4   6.7     0.0057   17.2   0.1    2.6  2  Fer4_7        4Fe-4S dicluster domain
    7.4e-05   22.8   9.6    0.00013   22.0   9.6    1.4  1  Fer4_9        4Fe-4S dicluster domain
    0.00012   22.1   5.3      0.025   14.7   0.2    2.4  2  Fer4_21       4Fe-4S dicluster domain
    0.00041   21.2   5.3      0.059   14.3   0.1    2.5  2  Fer4_16       4Fe-4S double cluster binding domain
    0.00068   20.1   3.6      0.074   13.6   0.2    2.4  2  Fer4_17       4Fe-4S dicluster domain
     0.0036   17.3  13.0       0.26   11.4   1.4    2.4  2  Fer4_6        4Fe-4S binding domain
     0.0041   17.2  10.1     0.0076   16.3  10.1    1.4  1  Fer4_10       4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.02   15.3   2.1       0.99    9.9   0.1    2.5  2  Fer4_8        4Fe-4S dicluster domain
       0.28   11.9   0.1       0.28   11.9   0.1    3.1  3  Fer4_15       4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Flavoprotein  Flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.1   0.0   2.8e-19   4.2e-16       2     112 ..       3     134 ..       2     172 .. 0.77
   2 ?   -1.2   0.0      0.99   1.5e+03     115     136 ..     202     224 ..     194     239 .. 0.70

  Alignments for each domain:
  == domain 1  score: 59.1 bits;  conditional E-value: 2.8e-19
                                    EEEEEE-SSCGGGCH.HHHHHHHHHTTEEEEEEESCHHHHCCHHGGS..........TCSSHHHHHHCT........... CS
                   Flavoprotein   2 killgiTGsvaaika.lellekLkkegievqvvltkaAkkfiskeklklaa......redpilhielrr........... 63 
                                    ++++giTG+   + + ++ ++++   +++v  +++ka++++++     l +       ++ +++i l+            
  gi|116754470|ref|YP_843588.1|   3 RVAWGITGGGQYLAEsVRAMREVAA-QHRVCTFVSKAGEEVLRMY--GLLEelreisGGGYLEEIFLESesgrsfpmtgr 79 
                                    899******9988776777777775.*****************55..333323334444555555554478889999999 PP

                                    ....TESEEEEEEEEHHHHHHHHTT--SSHHHHHHHT..HCCTTEEEEE.--HHC CS
                   Flavoprotein  64 ....wadllviaPasantlakianGiadnlltlilra..takkpiliaPamnpam 112
                                        ++dll+iaPa+ nt+akia+Gi+d+ +t+ + +  +a++p+l++P+   + 
  gi|116754470|ref|YP_843588.1|  80 lmigRYDLLLIAPATSNTVAKIACGISDTIVTNAAALaeKAQVPVLVLPTDVREA 134
                                    9999*****************************994459999*******655554 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.99
                                    CSTCHHHHHHH.HT......... CS
                   Flavoprotein 115 npqtlknlekl.eegvtvikPse 136
                                    + ++++n+e l e+g+t+++  e
  gi|116754470|ref|YP_843588.1| 202 RGIDQRNIEMLrERGYTILESPE 224
                                    56789999999779999998653 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.5    0.0016       2.4       2      14 ..     141     153 ..     140     155 .. 0.92
   2 !    5.7   0.0    0.0094        14      16      24 .]     157     165 ..     156     165 .. 0.87
   3 !   16.8   0.6   2.9e-06    0.0043       3      23 ..     172     192 ..     170     193 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0016
                                    EEETTTSSS-THH CS
                           Fer4   2 videekCigCGaC 14 
                                     ++ e+C +C +C
  gi|116754470|ref|YP_843588.1| 141 AVNREMCNACEIC 153
                                    689********** PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0094
                                    HHSTTTEEE CS
                           Fer4  16 evCPvgAIt 24 
                                     +CP gAI+
  gi|116754470|ref|YP_843588.1| 157 TACPQGAIS 165
                                    59*****96 PP

  == domain 3  score: 16.8 bits;  conditional E-value: 2.9e-06
                                    EETTTSSS-THHHHHSTTTEE CS
                           Fer4   3 ideekCigCGaCvevCPvgAI 23 
                                    id  +C gCG+C   C   AI
  gi|116754470|ref|YP_843588.1| 172 IDLMRCDGCGTCLPLCSSSAI 192
                                    8999************87777 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   5.0   1.3e-06     0.002       1      22 []     138     161 ..     138     161 .. 0.94
   2 !   11.5   2.1   0.00017      0.26       5      20 ..     172     187 ..     169     189 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.3e-06
                         Fer4_2   1 apvvvdtdrCigCgaC..vsaCPa 22 
                                    ap++v++++C++C++C  ++aCP+
  gi|116754470|ref|YP_843588.1| 138 APYAVNREMCNACEICppQTACPQ 161
                                    5899*******************6 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00017
                         Fer4_2   5 vdtdrCigCgaCvsaC 20 
                                    +d  rC gCg+C+  C
  gi|116754470|ref|YP_843588.1| 172 IDLMRCDGCGTCLPLC 187
                                    67779*******9888 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   1.0   0.00059      0.88      27      52 .]     136     163 ..     101     169 .. 0.74
   2 !   17.2   0.1   3.8e-06    0.0057       1      26 [.     176     201 ..     176     225 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00059
                         Fer4_7  27 gtekveidpekClgCgaC..vavCPtga 52 
                                    +++ ++++ e+C  C+ C  +++CP ga
  gi|116754470|ref|YP_843588.1| 136 TRAPYAVNREMCNACEICppQTACPQGA 163
                                    3355678899999999996677999987 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 3.8e-06
                         Fer4_7   1 rCigCgaCvaaCpvkaieldeeenek 26 
                                    rC gCg C + C+++ai+    ++ +
  gi|116754470|ref|YP_843588.1| 176 RCDGCGTCLPLCSSSAIDAVRMNVRR 201
                                    8****************988776554 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   9.6   8.9e-08   0.00013       2      51 .]     147     192 ..     146     192 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 8.9e-08
                         Fer4_9   2 CtgCgaC..veaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                    C+ C  C  ++aCp+g++++d ++ ++ +      +C gCg+C+  C + ai
  gi|116754470|ref|YP_843588.1| 147 CNACEICppQTACPQGAISGDGVRSIDLM------RCDGCGTCLPLCSSSAI 192
                                    *******99999****************9......6***********99887 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.9   0.00092       1.4      34      57 ..     140     164 ..     127     166 .. 0.77
   2 !   14.7   0.2   1.7e-05     0.025       3      31 ..     172     200 ..     170     213 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00092
                        Fer4_21  34 lkvvedeCvGCnlC..ssvCPvedci 57 
                                    ++v  + C +C++C   + CP +++i
  gi|116754470|ref|YP_843588.1| 140 YAVNREMCNACEICppQTACP-QGAI 164
                                    578899********5557999.6887 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.7e-05
                        Fer4_21   3 idedkCigCgkCliaCedtshqaieidak 31 
                                    id  +C gCg Cl  C+ ++++a++++ +
  gi|116754470|ref|YP_843588.1| 172 IDLMRCDGCGTCLPLCSSSAIDAVRMNVR 200
                                    88889*******************98754 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 !    8.3   1.4     0.003       4.4       2      21 ..     147     168 ..     146     175 .. 0.80
   2 !   14.3   0.1     4e-05     0.059       1      26 [.     176     200 ..     176     231 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.003
                        Fer4_16   2 CgtCgkC..aevCPtnaikekk 21 
                                    C  C+ C    +CP++ai+++ 
  gi|116754470|ref|YP_843588.1| 147 CNACEICppQTACPQGAISGDG 168
                                    99*****55579******9984 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 4e-05
                        Fer4_16   1 rCgtCgkCaevCPtnaikekkekeie 26 
                                    rC +Cg C+  C ++ai++  + +++
  gi|116754470|ref|YP_843588.1| 176 RCDGCGTCLPLCSSSAIDAV-RMNVR 200
                                    6*****************98.23332 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.3    0.0043       6.4      42      59 ..     143     162 ..     101     166 .. 0.64
   2 !   13.6   0.2     5e-05     0.074       1      18 [.     176     196 ..     176     229 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0043
                        Fer4_17  42 kaslCieCgeCe..rkCPqg 59 
                                    + + C+ C+ C   ++CPqg
  gi|116754470|ref|YP_843588.1| 143 NREMCNACEICPpqTACPQG 162
                                    44778888888666788876 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 5e-05
                        Fer4_17   1 rCiqCgyClpeCpsyea...y 18 
                                    rC +Cg Clp C+s ++   +
  gi|116754470|ref|YP_843588.1| 176 RCDGCGTCLPLCSSSAIdavR 196
                                    7************97763332 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   4.4   0.00026      0.39       4      24 .]     142     164 ..     141     164 .. 0.95
   2 !   11.4   1.4   0.00017      0.26       8      24 .]     176     192 ..     171     192 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00026
                         Fer4_6   4 idpdkCigCgdC..vrvCPegai 24 
                                    ++++ C+ C+ C   ++CP gai
  gi|116754470|ref|YP_843588.1| 142 VNREMCNACEICppQTACPQGAI 164
                                    89*****************9998 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00017
                         Fer4_6   8 kCigCgdCvrvCPegai 24 
                                    +C+gCg C   C   ai
  gi|116754470|ref|YP_843588.1| 176 RCDGCGTCLPLCSSSAI 192
                                    8********99998887 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3  10.1   5.1e-06    0.0076       5      55 ..     143     187 ..     140     188 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.1e-06
                        Fer4_10   5 dddtCirCgkC..vkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                    +++ C  C+ C  ++aCP+        g++s++++ ++++ +C+gcg C   C
  gi|116754470|ref|YP_843588.1| 143 NREMCNACEICppQTACPQ--------GAISGDGVRSIDLMRCDGCGTCLPLC 187
                                    7889*******65679***........**********************9887 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.2     0.026        39      50      63 ..     146     161 ..     112     167 .. 0.73
   2 ?    9.9   0.1   0.00066      0.99       2      31 ..     174     204 ..     173     232 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.026
                         Fer4_8  50 sCttcgaC..tevCpv 63 
                                     C++c+ C  +++Cp+
  gi|116754470|ref|YP_843588.1| 146 MCNACEICppQTACPQ 161
                                    4555555544455554 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00066
                         Fer4_8   2 lekCieCgaCqsaCpvlrrtk.khlldarge 31 
                                    l++C +Cg C   C +    + +++   rg 
  gi|116754470|ref|YP_843588.1| 174 LMRCDGCGTCLPLCSSSAIDAvRMNVRRRGI 204
                                    789***********75555443444444433 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 ?    0.6   0.8      0.65   9.6e+02       3      15 ..     142     154 ..     141     158 .. 0.87
   2 ?    0.4   0.1      0.77   1.1e+03      58      65 ..     158     165 ..     155     165 .. 0.86
   3 ?   11.9   0.1   0.00019      0.28       3      19 ..     172     188 ..     171     234 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.65
                        Fer4_15   3 vDrdaCigcglCv 15 
                                    v+r+ C  c+ C 
  gi|116754470|ref|YP_843588.1| 142 VNREMCNACEICP 154
                                    7899********6 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.77
                        Fer4_15  58 aCPvdAIr 65 
                                    aCP +AI+
  gi|116754470|ref|YP_843588.1| 158 ACPQGAIS 165
                                    9*****95 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00019
                        Fer4_15   3 vDrdaCigcglCvaeap 19 
                                    +D  +C+gcg C+ +++
  gi|116754470|ref|YP_843588.1| 172 IDLMRCDGCGTCLPLCS 188
                                    8999**********994 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1852.14
//
Query:       gi|116754471|ref|YP_843589.1|  [L=126]
Description: hypothetical protein Mthe_1167 [Methanosaeta thermophila PT]
Scores for complete 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-23   81.7   7.6    3.9e-16   59.5   0.2    2.0  2  Mut7-C      Mut7-C RNAse domain
     0.0035   17.0   0.7     0.0055   16.4   0.7    1.3  1  zf-RRN7     Zinc-finger of RNA-polymerase I-specific TFIIB, R
  ------ inclusion threshold ------
      0.024   14.8   0.0       0.71   10.0   0.0    2.0  2  zf-RRPl_C4  Putative ribonucleoprotein zinc-finger pf C4 type
      0.057   13.4   4.5       0.43   10.6   1.3    2.3  2  ADK_lid     Adenylate kinase, active site lid
       0.18   11.7   0.4        1.6    8.6   0.0    2.2  2  zf-C2H2_3   zinc-finger of acetyl-transferase ESCO


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 !   59.5   0.2   1.1e-19   3.9e-16       8     103 ..       1      94 [.       1      98 [. 0.90
   2 !   26.1   2.5     2e-09   7.3e-06     123     145 ..      98     120 ..      90     121 .. 0.87

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 1.1e-19
                         Mut7-C   8 mlgklakyLRllGydalyasdvedeellalaakekrillTrdreLlkraklkkg..vlltsrdveeqlreviarlglkls 85 
                                    ml +l ++LRl+G+d+   ++++d +l+a+a  ++r+llTrdr+L++  + +    +l++s+++ eqlrev +  g++ls
  gi|116754471|ref|YP_843589.1|   1 MLMRLGRWLRLAGHDVENPRSMSDVDLIAQA-GDRRTLLTRDRSLAELCEREGVrcILIRSSHIDEQLREV-RGRGIDLS 78 
                                    899**************************97.579*********999877775566889************.88899**9 PP

                         Mut7-C  86 lkpelsrCvaCngeleev 103
                                    l+p  +rC+ Cngel  +
  gi|116754471|ref|YP_843589.1|  79 LNP--ERCTICNGELLDM 94 
                                    999..********99876 PP

  == domain 2  score: 26.1 bits;  conditional E-value: 2e-09
                         Mut7-C 123 ftrCekCrkvfWkGshwerveel 145
                                     + C +C+k++W+Gshw+ +e++
  gi|116754471|ref|YP_843589.1|  98 RWMCSECGKIYWRGSHWRGIEAR 120
                                    69****************99987 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 !   16.4   0.7   1.5e-06    0.0055       5      28 ..      82     105 ..      80     108 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.5e-06
                        zf-RRN7   5 ppCgvCgcrsftlddGfyyCrrCh 28 
                                    ++C +C++ + +  +G++ C +C+
  gi|116754471|ref|YP_843589.1|  82 ERCTICNGELLDMGNGRWMCSECG 105
                                    79*********************9 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 ?    3.0   0.0     0.031   1.1e+02      46      80 ..      36      70 ..      16      72 .. 0.83
   2 ?   10.0   0.0    0.0002      0.71       3      29 ..      83     110 ..      81     120 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.031
                     zf-RRPl_C4 46 ekislrdkLCtkCkeknekekeircetfeeylkkl 80
                                   + ++  + L + C+++  +   ir+++++e+l+ +
  gi|116754471|ref|YP_843589.1| 36 TLLTRDRSLAELCEREGVRCILIRSSHIDEQLREV 70
                                   557788999*****99999889*******999875 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0002
                     zf-RRPl_C4   3 kCkyClskklknlnetvyCeaC.eiyfk 29 
                                    +C+ C+ + l++ n  + C++C +iy++
  gi|116754471|ref|YP_843589.1|  83 RCTICNGELLDMGNGRWMCSECgKIYWR 110
                                    8*********************668877 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.017        62      20      31 ..      80      91 ..      71      93 .. 0.88
   2 ?   10.6   1.3   0.00012      0.43       1      11 [.      98     108 ..      98     115 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.017
                                   STTB-TTT--.- CS
                        ADK_lid 20 veglCDkCGepL 31
                                   ++  C  C+++L
  gi|116754471|ref|YP_843589.1| 80 NPERCTICNGEL 91
                                   6889******99 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00012
                                    EEE-TTT--EE CS
                        ADK_lid   1 RrvCpkCGrsY 11 
                                    R++C+ CG++Y
  gi|116754471|ref|YP_843589.1|  98 RWMCSECGKIY 108
                                    9********** 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 ?    0.6   0.1      0.14   5.2e+02      11      20 ..      79      88 ..      75      88 .. 0.72
   2 ?    8.6   0.0   0.00044       1.6       4      27 ..      92     112 ..      91     113 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.14
                      zf-C2H2_3 11 fgasqCkeCg 20
                                    + ++C+ C+
  gi|116754471|ref|YP_843589.1| 79 LNPERCTICN 88
                                   45689****6 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00044
                      zf-C2H2_3   4 LdlgqksfgasqCkeCgMvYnpgs 27 
                                    Ld g+   g   C+eCg +Y +gs
  gi|116754471|ref|YP_843589.1|  92 LDMGN---GRWMCSECGKIYWRGS 112
                                    77774...4588*****9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); 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: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 1083.55
//
Query:       gi|116754472|ref|YP_843590.1|  [L=194]
Description: hypothetical protein Mthe_1168 [Methanosaeta thermophila PT]
Scores for complete 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   32.2   0.1    1.7e-07   31.7   0.1    1.2  1  Transglut_core  Transglutaminase-like superfamily
    9.7e-06   25.5   0.0    1.3e-05   25.1   0.0    1.2  1  Peptidase_C93   Bacterial transglutaminase-like cysteine prot
    0.00072   19.1   1.1      0.052   13.1   1.1    2.1  1  DUF553          Transglutaminase-like domain


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 !   31.7   0.1   2.8e-11   1.7e-07      16     108 ..      33     125 ..      19     129 .. 0.87

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 2.8e-11
                 Transglut_core  16 ekakaiyewvrknveysaprrtpgsrd....aeavletgkGncedfaslfvallRalGi...paRvvtgylsgeeekeqs 88 
                                    e+a ++ ++v++n+ey+++++  g  d    + ++l+ ++G+ced + l+++l+ a+Gi     Rvv+g + ++      
  gi|116754472|ref|YP_843590.1|  33 ERAWKVWKYVAENIEYVSDKKAFGMPDfwlfPAETLTLRRGDCEDSSFLLATLMIASGIsehCVRVVIGRVFTR------ 106
                                    7888999**********99999999999*******************************55448******9975...... PP

                 Transglut_core  89 vasedaHawvevylegygWv 108
                                     ++ + H+wv +  e ++W+
  gi|116754472|ref|YP_843590.1| 107 -NTAYGHCWVVYQNESGTWC 125
                                    .67788***99888888897 PP

>> Peptidase_C93  Bacterial transglutaminase-like cysteine proteinase BTLCP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   2.1e-09   1.3e-05      44     124 ..      37     124 ..      16     134 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 2.1e-09
                  Peptidase_C93  44 evnasvNeeikpvtdkelygveerWeypkdg....aGdCedyallKrkeLieaGlpasallltv...vrdekgegHavLt 116
                                    +v + v e+i+ v+dk+ +g+ + W +p+++    +GdCed   l    +i++G++++ +++ +    ++++  gH  ++
  gi|116754472|ref|YP_843590.1|  37 KVWKYVAENIEYVSDKKAFGMPDFWLFPAETltlrRGDCEDSSFLLATLMIASGISEHCVRVVIgrvFTRNTAYGHCWVV 116
                                    678899**********************98544448*********************98887641103445556888777 PP

                  Peptidase_C93 117 vrtdrGdl 124
                                     + ++G  
  gi|116754472|ref|YP_843590.1| 117 YQNESGTW 124
                                    77777765 PP

>> DUF553  Transglutaminase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   1.1   8.7e-06     0.052      17     115 ..      33     116 ..      22     136 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.7e-06
                         DUF553  17 etiinvlewvdenikYdyekaevvetllvlWatfftlskvdskilklietpkeilktkkgiCrDYaiLTaalLlnlnisk 96 
                                    e +++v ++v+eni+Y  +k      +   W                   p e+l+ + g C+D ++L a l+ +++is+
  gi|116754472|ref|YP_843590.1|  33 ERAWKVWKYVAENIEYVSDKKAFG--MPDFW-----------------LFPAETLTLRRGDCEDSSFLLATLMIASGISE 93 
                                    679999999999999999998877..33333.................35888888888888888888888888888876 PP

                         DUF553  97 vyl..v..svtfenskvgHaava 115
                                      +  v   v  +n+  gH  v+
  gi|116754472|ref|YP_843590.1|  94 HCVrvVigRVFTRNTAYGHCWVV 116
                                    43310111334456666676655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.20s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 1649.16
//
Query:       gi|116754473|ref|YP_843591.1|  [L=82]
Description: exodeoxyribonuclease VII, small subunit [Methanosaeta thermophila PT]
Scores for complete 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-20   71.8   2.7    4.9e-20   71.3   2.7    1.2  1  Exonuc_VII_S  Exonuclease VII small subunit
     0.0075   16.4   0.2     0.0084   16.2   0.2    1.1  1  DUF3461       Protein of unknown function (DUF3461)
  ------ inclusion threshold ------
      0.084   12.8   0.2       0.17   11.8   0.2    1.5  1  HetR_C        Heterocyst differentiation regulator C-terminal


Domain annotation for each model (and alignments):
>> Exonuc_VII_S  Exonuclease VII small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.3   2.7   8.2e-24   4.9e-20       2      51 ..      21      70 ..      21      71 .. 0.98

  Alignments for each domain:
  == domain 1  score: 71.3 bits;  conditional E-value: 8.2e-24
                   Exonuc_VII_S  2 EealaeLeeIvekLEsgelsLeeslklyeeGvkLlkeCekkLdeaeqkve 51
                                   E al+eLeeIv++LEsg lsL+esl+l+e+Gv+L++ C++k++ ae+++e
  gi|116754473|ref|YP_843591.1| 21 ESALNELEEIVRELESGRLSLDESLELFERGVRLVRICSSKIEGAERRIE 70
                                   89**********************************************97 PP

>> DUF3461  Protein of unknown function (DUF3461)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.2   1.4e-06    0.0084      63     125 .]       6      72 ..       1      72 [. 0.82

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.4e-06
                        DUF3461  63 seeykevseis.avlrkvleeLdklte...kkkeekdikekllkdlkhlekvvnskikeierklekl 125
                                    se+y++v eis ++l+++l+eL+++++   + + + d   +l++    l ++ +ski+  er++e+l
  gi|116754473|ref|YP_843591.1|   6 SEKYRSVVEISeQSLESALNELEEIVReleSGRLSLDESLELFERGVRLVRICSSKIEGAERRIESL 72 
                                    789*******83579**********88433444566777788888889****************987 PP

>> HetR_C  Heterocyst differentiation regulator C-terminal Hood domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   2.8e-05      0.17      37      57 ..      13      33 ..       1      38 [. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.8e-05
                         HetR_C 37 ldippekleqaleeldeiire 57
                                   ++i ++ le+al+el+ei+re
  gi|116754473|ref|YP_843591.1| 13 VEISEQSLESALNELEEIVRE 33
                                   67999***************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1277  (0.0712254); expected 358.6 (0.02)
Passed bias filter:                     1065  (0.059401); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 602.35
//
Query:       gi|116754474|ref|YP_843592.1|  [L=150]
Description: HEAT repeat-containing PBS lyase [Methanosaeta thermophila PT]
Scores for complete 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   2.6    2.6e-11   43.7   0.2    2.1  2  HEAT_2         HEAT repeats
    1.3e-14   53.1   3.1    0.00037   20.5   0.0    4.3  4  HEAT           HEAT repeat
    1.5e-12   46.9   1.0      2e-06   27.9   0.1    3.5  3  HEAT_PBS       PBS lyase HEAT-like repeat
    2.7e-08   34.0   1.1    0.00019   21.5   0.1    3.5  3  Cnd1           non-SMC mitotic condensation complex subunit 1
    9.2e-05   22.9   7.7      0.008   16.7   0.1    4.4  5  HEAT_EZ        HEAT-like repeat
    0.00014   21.8   0.1       0.13   12.3   0.0    3.2  3  Arm            Armadillo/beta-catenin-like repeat
      0.005   15.5   0.3      0.068   11.7   0.1    2.3  3  Adaptin_N      Adaptin N terminal region
  ------ inclusion threshold ------
      0.023   14.7   0.1      0.074   13.1   0.1    1.8  2  Aconitase_B_N  Aconitate B N-terminal domain
      0.041   14.5   0.2         31    5.2   0.0    3.1  3  Vac14_Fab1_bd  Vacuolar 14 Fab1-binding region


Domain annotation for each model (and alignments):
>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.5     2e-12   4.1e-09       2      65 ..      27      92 ..      26      94 .. 0.87
   2 !   43.7   0.2   1.3e-14   2.6e-11       2      59 ..      88     144 ..      87     149 .. 0.91

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 2e-12
                         HEAT_2  2 daLlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigd...pealp 65
                                   d L++a  +d++  vr +a+  L     pe+++aL+++++ded  vR +a   L++ g+   +++l+
  gi|116754474|ref|YP_843592.1| 27 DRLIEAT-RDKNMLVRSNAVSILSAREGPEVVEALIQAMKDEDYVVRSNAMVRLSERGTavlDRVLE 92
                                   6799999.9************************************************9722244444 PP

  == domain 2  score: 43.7 bits;  conditional E-value: 1.3e-14
                         HEAT_2   2 daLlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaig 59 
                                    d  l+al ndpd+e+r+ a+++Lg++++p+a++ L ++++de++ vR +a  +L a+g
  gi|116754474|ref|YP_843592.1|  88 DRVLEAL-NDPDEEIRAGAAWVLGELKDPRAIEPLQKAMDDENMVVRIQAKASLMAMG 144
                                    6689999.9**************************************99999999887 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.1   0.00032      0.64       5      25 ..      29      49 ..      27      50 .. 0.88
   2 !    9.8   0.0   0.00053       1.1       2      20 ..      57      75 ..      56      80 .. 0.90
   3 !   20.5   0.0   1.9e-07   0.00037       2      27 ..      87     112 ..      86     113 .. 0.94
   4 !   10.2   0.0   0.00037      0.74       2      27 ..     118     143 ..     117     146 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00032
                                   HHHHHT-SSHHHHHHHHHHHH CS
                           HEAT  5 llkllsDpspeVReaAakaLg 25
                                   l+++ +D+++ VR++A+  L 
  gi|116754474|ref|YP_843592.1| 29 LIEATRDKNMLVRSNAVSILS 49
                                   88999************9886 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00053
                                   HHHHHHHHT-SSHHHHHHH CS
                           HEAT  2 lPlllkllsDpspeVReaA 20
                                   + +l+++++D++  VR++A
  gi|116754474|ref|YP_843592.1| 57 VEALIQAMKDEDYVVRSNA 75
                                   678999***********98 PP

  == domain 3  score: 20.5 bits;  conditional E-value: 1.9e-07
                                    HHHHHHHHT-SSHHHHHHHHHHHHHH CS
                           HEAT   2 lPlllkllsDpspeVReaAakaLgal 27 
                                    l+ +l++l+Dp+ e+R+ Aa+ Lg+l
  gi|116754474|ref|YP_843592.1|  87 LDRVLEALNDPDEEIRAGAAWVLGEL 112
                                    8899********************97 PP

  == domain 4  score: 10.2 bits;  conditional E-value: 0.00037
                                    HHHHHHHHT-SSHHHHHHHHHHHHHH CS
                           HEAT   2 lPlllkllsDpspeVReaAakaLgal 27 
                                    + +l+k++ D+++ VR  A  +L a+
  gi|116754474|ref|YP_843592.1| 118 IEPLQKAMDDENMVVRIQAKASLMAM 143
                                    5689*************998888765 PP

>> HEAT_PBS  PBS lyase HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   8.5e-05      0.17       1      27 []      40      66 ..      40      66 .. 0.97
   2 ?    3.3   0.0     0.091   1.8e+02       1      27 []      71      96 ..      71      96 .. 0.87
   3 !   27.9   0.1     1e-09     2e-06       1      27 []     101     127 ..     101     127 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.5e-05
                                   HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                       HEAT_PBS  1 vRraAakaLgqlgdeeaipaLleaLqd 27
                                   vR +A+  L +   +e+++aL++a +d
  gi|116754474|ref|YP_843592.1| 40 VRSNAVSILSAREGPEVVEALIQAMKD 66
                                   8***********************997 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.091
                                   HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                       HEAT_PBS  1 vRraAakaLgqlgdeeaipaLleaLqd 27
                                   vR +A+  L + g+ +++++ leaL+d
  gi|116754474|ref|YP_843592.1| 71 VRSNAMVRLSERGT-AVLDRVLEALND 96
                                   78899999999999.999999999987 PP

  == domain 3  score: 27.9 bits;  conditional E-value: 1e-09
                                    HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                       HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLqd 27 
                                    +R+ Aa+ Lg+l+d++ai++L++a +d
  gi|116754474|ref|YP_843592.1| 101 IRAGAAWVLGELKDPRAIEPLQKAMDD 127
                                    5999********************997 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 !   14.5   0.2   1.4e-05     0.028       1      46 [.      39      80 ..      24      83 .. 0.87
   2 !   21.5   0.1   9.8e-08   0.00019       1      87 [.      39     114 ..      39     117 .. 0.88
   3 !    7.9   0.0    0.0015         3      23      42 ..     118     137 ..     115     148 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.4e-05
                           Cnd1  1 liRalairtlgcirvpnlveylvepLrkrLkDedpyVRktaaivva 46
                                   l+R++a+  l++   p++ve+l++    ++kDed  VR +a++ ++
  gi|116754474|ref|YP_843592.1| 39 LVRSNAVSILSAREGPEVVEALIQ----AMKDEDYVVRSNAMVRLS 80
                                   699999999999999999998886....568999999999988665 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 9.8e-08
                           Cnd1   1 liRalairtlgcirvpnlveylvepLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanala 80 
                                    l+R++a+  l++   p++ve+l++    ++kDed  VR +a++ +++       +   +l++++++l+D++++++a a  
  gi|116754474|ref|YP_843592.1|  39 LVRSNAVSILSAREGPEVVEALIQ----AMKDEDYVVRSNAMVRLSE-------RGTAVLDRVLEALNDPDEEIRAGAAW 107
                                    69*****************99887....578**********998764.......3344899******************* PP

                           Cnd1  81 alteise 87 
                                    +l e+++
  gi|116754474|ref|YP_843592.1| 108 VLGELKD 114
                                    **99875 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0015
                           Cnd1  23 vepLrkrLkDedpyVRktaa 42 
                                    +epL+k++ De++ VR +a 
  gi|116754474|ref|YP_843592.1| 118 IEPLQKAMDDENMVVRIQAK 137
                                    78999999999999998875 PP

>> HEAT_EZ  HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       4.2   8.3e+03      22      31 ..      11      20 ..       9      20 .. 0.82
   2 ?    3.5   0.0     0.055   1.1e+02      32      53 ..      28      49 ..      26      50 .. 0.85
   3 ?    3.3   0.0     0.061   1.2e+02      27      48 ..      54      75 ..      54      80 .. 0.77
   4 !   16.7   0.1     4e-06     0.008      29      55 .]      86     112 ..      84     112 .. 0.86
   5 ?    0.8   0.0      0.37   7.3e+02      28      48 ..     116     136 ..     115     145 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4.2
                        HEAT_EZ 22 lqplvpeilp 31
                                   ++p++pe+lp
  gi|116754474|ref|YP_843592.1| 11 DEPEIPEVLP 20
                                   6799999998 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.055
                        HEAT_EZ 32 aLlalLnddsdeVRaaAagaLg 53
                                    L+ + +d++ +VR +A+  L+
  gi|116754474|ref|YP_843592.1| 28 RLIEATRDKNMLVRSNAVSILS 49
                                   58888899999*******9987 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.061
                        HEAT_EZ 27 peilpaLlalLnddsdeV.RaaA 48
                                   pe++ aL+++++d +d V R +A
  gi|116754474|ref|YP_843592.1| 54 PEVVEALIQAMKD-EDYVvRSNA 75
                                   799*****99997.444437776 PP

  == domain 4  score: 16.7 bits;  conditional E-value: 4e-06
                        HEAT_EZ  29 ilpaLlalLnddsdeVRaaAagaLgnl 55 
                                    +l+  l +Lnd++ e+Ra Aa+ Lg l
  gi|116754474|ref|YP_843592.1|  86 VLDRVLEALNDPDEEIRAGAAWVLGEL 112
                                    67777889999999***********86 PP

  == domain 5  score: 0.8 bits;  conditional E-value: 0.37
                        HEAT_EZ  28 eilpaLlalLnddsdeV.RaaA 48 
                                    +++ +L +++ d + +V R +A
  gi|116754474|ref|YP_843592.1| 116 RAIEPLQKAMDD-ENMVvRIQA 136
                                    567777766655.445547655 PP

>> Arm  Armadillo/beta-catenin-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.25     5e+02       5      17 ..      36      48 ..      28      50 .. 0.73
   2 ?    4.5   0.0      0.02        39      13      32 ..      56      75 ..      54      76 .. 0.92
   3 !   12.3   0.0   6.7e-05      0.13      14      39 ..      87     112 ..      85     112 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.25
                                   HHHHHHTTHHHHH CS
                            Arm  5 kdavieaGavppL 17
                                   k ++++++av +L
  gi|116754474|ref|YP_843592.1| 36 KNMLVRSNAVSIL 48
                                   5577888888777 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.02
                                   HHHHHHHHTTTSSHHHHHHH CS
                            Arm 13 avppLvrLLssedeevqeeA 32
                                   +v++L++ +++ed  v+ +A
  gi|116754474|ref|YP_843592.1| 56 VVEALIQAMKDEDYVVRSNA 75
                                   89***********9999998 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 6.7e-05
                                    HHHHHHHTTTSSHHHHHHHHHHHHHH CS
                            Arm  14 vppLvrLLssedeevqeeAawALsNL 39 
                                    +++ ++ L+++dee++  Aaw L+ L
  gi|116754474|ref|YP_843592.1|  87 LDRVLEALNDPDEEIRAGAAWVLGEL 112
                                    67778899***************976 PP

>> Adaptin_N  Adaptin N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7   0.0    0.0022       4.5     146     176 ..      16      48 ..      14      51 .. 0.90
   2 !   11.7   0.1   3.4e-05     0.068      84     185 ..      29     117 ..      24     127 .. 0.76
   3 !    3.9   0.0     0.008        16      87     112 ..      93     118 ..      79     143 .. 0.56

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0022
                                    HHCCCCC.H.HHHHHHCTT-SSHHHHHHHHHHH CS
                      Adaptin_N 146 pdllrkq.l.veeikellsdkdpgvvlaAvall 176
                                    p+ l+++ + +++++e+  dk+++v ++Av++l
  gi|116754474|ref|YP_843592.1|  16 PEVLPDEsWpTDRLIEATRDKNMLVRSNAVSIL 48 
                                    67888999999*******************998 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 3.4e-05
                                    HHHHCCSSSHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHT-SSHHHHHHHHHHHHHCCCCCHHCCCCCHHHHHHHCTT- CS
                      Adaptin_N  84 lqkDlkdpnqlirglALrvLssirvpelaedlapaikkllkdrspyvrkkAalailklykkdpdllrkqlveeikellsd 163
                                    l  +  d+n+l+r++A++ Ls    pe++e+l     +++kd++ +vr++A +   +l +          ++++ e+l+d
  gi|116754474|ref|YP_843592.1|  29 LIEATRDKNMLVRSNAVSILSAREGPEVVEAL----IQAMKDEDYVVRSNAMV---RLSERGTAV-----LDRVLEALND 96 
                                    6667789*************999888887765....56788999999999864...444443333.....7889999999 PP

                                    SSHHHHHHHHHHHHHHHCCCCC CS
                      Adaptin_N 164 kdpgvvlaAvalleeikkndrl 185
                                     d  + + A  +l e+ k +r+
  gi|116754474|ref|YP_843592.1|  97 PDEEIRAGAAWVLGEL-KDPRA 117
                                    9999999999999998.55554 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.008
                                    HCCSSSHHHHHHHHHHHCCC--CCCH CS
                      Adaptin_N  87 DlkdpnqlirglALrvLssirvpela 112
                                    +l+dp++ ir+ A  vL+ +++p+  
  gi|116754474|ref|YP_843592.1|  93 ALNDPDEEIRAGAAWVLGELKDPRAI 118
                                    45555555555555555555555433 PP

>> Aconitase_B_N  Aconitate B N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   3.7e-05     0.074      68     120 ..      29      81 ..      26     109 .. 0.85
   2 ?   -0.5   0.0      0.57   1.1e+03      83     107 ..     105     129 ..      86     144 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.7e-05
                  Aconitase_B_N  68 iakgeaesplispeeAvelLgtMlGGynvksLidllkekdeelaeeaaeaLkk 120
                                    +++ +   +++ +++Av++L+   G   v++Li+++k++d  ++++a+  L++
  gi|116754474|ref|YP_843592.1|  29 LIEATRDKNMLVRSNAVSILSAREGPEVVEALIQAMKDEDYVVRSNAMVRLSE 81 
                                    5666777889999************************9999999999999986 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.57
                  Aconitase_B_N  83 AvelLgtMlGGynvksLidllkekd 107
                                    A  +Lg+++   ++++L +++++++
  gi|116754474|ref|YP_843592.1| 105 AAWVLGELKDPRAIEPLQKAMDDEN 129
                                    4445555555566666666666444 PP

>> Vac14_Fab1_bd  Vacuolar 14 Fab1-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.033        66      26      47 ..      54      75 ..      37      80 .. 0.78
   2 ?    5.2   0.0     0.016        31      26      45 ..      84     103 ..      74     110 .. 0.77
   3 ?    1.3   0.0      0.27   5.4e+02      29      52 ..     118     141 ..     113     148 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.033
                  Vac14_Fab1_bd 26 eeivkpvlkcfsDkdsrvRyya 47
                                    e+v+ ++++++D+d  vR  a
  gi|116754474|ref|YP_843592.1| 54 PEVVEALIQAMKDEDYVVRSNA 75
                                   5788999999999999888655 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.016
                  Vac14_Fab1_bd  26 eeivkpvlkcfsDkdsrvRy 45 
                                      +++ vl++++D d+++R 
  gi|116754474|ref|YP_843592.1|  84 TAVLDRVLEALNDPDEEIRA 103
                                    56788899999999998884 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.27
                  Vac14_Fab1_bd  29 vkpvlkcfsDkdsrvRyyacEsly 52 
                                    ++p+ k+++D++  vR  a  sl 
  gi|116754474|ref|YP_843592.1| 118 IEPLQKAMDDENMVVRIQAKASLM 141
                                    78999999****999999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1150.63
//
Query:       gi|116754475|ref|YP_843593.1|  [L=195]
Description: indolepyruvate oxidoreductase subunit beta [Methanosaeta thermophila PT]
Scores for complete 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  132.6   0.1    1.8e-38  132.3   0.1    1.0  1  POR       Pyruvate ferredoxin/flavodoxin oxidoreductase


Domain annotation for each model (and alignments):
>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.3   0.1     1e-42   1.8e-38       1     175 [.      14     189 ..      14     191 .. 0.97

  Alignments for each domain:
  == domain 1  score: 132.3 bits;  conditional E-value: 1e-42
                                    CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEEEEE CS
                            POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglkpgg 80 
                                    GGqGv+++++i+++aa +aG+ v a++++g+++rGg+++ h r++     p+++ g+adllval+++++ ++  +l  gg
  gi|116754475|ref|YP_843593.1|  14 GGQGVILISEIIGRAALKAGLPVRAAETHGMAQRGGSVINHTRLGCI-YGPMVPEGGADLLVALEPAEALRYGRYLSSGG 92 
                                    9********************************************98.88****************9999********** PP

                                    EEEEECTCGTT-CCHHHCTS-HHHHHHH.....T-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHTS-HHHHHHHHH CS
                            POR  81 iiiynseelkpdelkkakeeerelkerl.....gvrvygvdatkiakeiggneraaNtvmlGalaallglplealeeaik 155
                                    ++++n++ + p++++    ++++ +e l       rv+ ++at+ia+++g+ + +aN+vmlGa+++ + +++  +++a++
  gi|116754475|ref|YP_843593.1|  93 VALVNTKPVLPTTVTTGHFRYPDIEEILaplrgVGRVISMNATEIAERAGN-SQTANIVMLGAMSRFMPIEEALILDALR 171
                                    **********************999999****999***********88776.**************************** PP

                                    CCS-CH.HHHHHHHHHHHHH CS
                            POR 156 krfpkkkeviekNlkafrag 175
                                    +++p k   ++ Nlkaf++g
  gi|116754475|ref|YP_843593.1| 172 DSVPAK--YLDVNLKAFELG 189
                                    ****95..9*********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1598.31
//
Query:       gi|116754476|ref|YP_843594.1|  [L=594]
Description: thiamine pyrophosphate binding domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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-23   81.0   0.1    1.3e-22   80.2   0.1    1.4  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    4.7e-12   46.2   0.2      3e-11   43.5   0.2    1.9  1  POR_N         Pyruvate flavodoxin/ferredoxin oxidoreductase, 
    4.4e-07   29.5  15.4    1.3e-05   24.8   4.9    3.4  3  Fer4          4Fe-4S binding domain
    1.4e-05   25.1  11.4    0.00028   21.0  12.3    2.6  3  Fer4_9        4Fe-4S dicluster domain
    6.1e-05   23.1  12.1     0.0011   19.1  12.9    2.4  2  Fer4_21       4Fe-4S dicluster domain
    0.00073   19.5  16.0      0.028   14.5   2.3    3.4  3  Fer4_2        4Fe-4S binding domain
     0.0011   19.3  13.4      0.071   13.6   3.5    2.8  2  Fer4_4        4Fe-4S binding domain
      0.002   18.1  18.1     0.0027   17.7   3.1    3.6  3  Fer4_6        4Fe-4S binding domain
     0.0053   17.3  11.4       0.55   10.8   2.7    2.8  2  Fer4_17       4Fe-4S dicluster domain
     0.0054   17.3  13.2      0.031   14.9   3.6    2.8  3  Fer4_7        4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.019   15.1  13.2      0.019   15.1  13.2    2.4  2  Fer4_10       4Fe-4S dicluster domain
      0.023   15.6  11.8      0.027   15.4   3.3    2.6  2  Fer4_16       4Fe-4S double cluster binding domain
       0.24   10.3   0.2       0.45    9.4   0.2    1.4  1  DUF1702       Protein of unknown function (DUF1702)
        1.7    9.3  11.0       0.85   10.2   1.9    2.6  2  Fer4_13       4Fe-4S single cluster domain of Ferredoxin I
        3.7    8.1  13.5        1.1    9.7   3.2    2.6  3  Fer4_8        4Fe-4S dicluster domain
        3.8    7.7   8.6         19    5.5   8.8    2.0  2  Fer4_18       4Fe-4S dicluster domain
        9.3    7.1  14.0        6.6    7.5   3.4    2.9  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 !   80.2   0.1   1.2e-25   1.3e-22       1     151 [.     384     523 ..     384     525 .. 0.92

  Alignments for each domain:
  == domain 1  score: 80.2 bits;  conditional E-value: 1.2e-25
                                    ESSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEEEEE CS
                   TPP_enzyme_C   1 diGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpitvvv 79 
                                    diGc+t+      ++     +++  ++ +mG ++ +++G+ +   +r++ + +GD++fl+  ++ l +a++++  +t+ +
  gi|116754476|ref|YP_843594.1| 384 DIGCYTI------GI--SMGTVD--TCLCMGASITIGSGIRFGGDERPICCCIGDSTFLHAgMTGLLNAAYNKSRMTIAI 453
                                    7888888......22..334455..99***************87899********************************* PP

                                    EE-SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEEEE CS
                   TPP_enzyme_C  80 lnNegygmtggqqepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgpali 151
                                    l+N++++mtg+q++p +gk+ +g++   +  ++++ +a+alGa  +  ++++++ee  +a+++a++  g +++
  gi|116754476|ref|YP_843594.1| 454 LDNSTTAMTGHQPHPGTGKTATGEE---SVRISLEGIAKALGAGhVECIDPYSLEESINAFARARDFAGLSVV 523
                                    *********************9998...99**************888******************99999998 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 !   43.5   0.2   2.8e-14     3e-11       2     167 ..      14     174 ..      13     189 .. 0.84

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 2.8e-14
                                    HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCCHHH CS
                          POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmienlgl 81 
                                    + ++ag   +a+YP TPssei+++l+  + + ++   +v    +E +a +++iG ++aG+r++ +    Gl  + + ++ 
  gi|116754476|ref|YP_843594.1|  14 GILEAGAGLAAGYPGTPSSEIIDTLSGIASRYDI---HVEWSVNEKAALEVAIGGSWAGTRSVATMKHVGLNVAADPFMT 90 
                                    5667788899*****************9988886...99999*******************************9998888 PP

                                    HHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHHS---EEEE-SSHHHHHHHHHHHHHHHHHCTSEEEEEEEHHHH.HE CS
                          POR_N  82 aageelPvvivvvaRalpstglsirtdqsDlmaardtglivlasenvqeafdlalvAfnlAekvrvPvivlfDgfllshe 161
                                     a   + + +v+v    p    s +++q    +a    +  l +++ qea d+++ Af l+e++ vPv++    +++sh+
  gi|116754476|ref|YP_843594.1|  91 LAYLGVDAGLVIVSADDPYC-HSSQNEQDTRRYAQFASVPCLDPADPQEAKDMTIYAFELSERFGVPVLL-RPTTRVSHA 168
                                    77665555555554444444.56777777777777788999**************************975.568888899 PP

                                    EEEEEC CS
                          POR_N 162 vekvel 167
                                    +++ve 
  gi|116754476|ref|YP_843594.1| 169 RSDVET 174
                                    999985 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.43   4.5e+02       5      12 ..     356     363 ..     353     364 .. 0.90
   2 !    9.0   0.7    0.0012       1.3       5      16 ..     546     557 ..     543     558 .. 0.85
   3 !   24.8   4.9   1.3e-08   1.3e-05       7      24 .]     574     591 ..     571     591 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.43
                                    TTTSSS-T CS
                           Fer4   5 eekCigCG 12 
                                    +++C gCG
  gi|116754476|ref|YP_843594.1| 356 PSLCPGCG 363
                                    789****9 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0012
                                    TTTSSS-THHHH CS
                           Fer4   5 eekCigCGaCve 16 
                                    ++ C+gC +C e
  gi|116754476|ref|YP_843594.1| 546 TDECVGCRQCLE 557
                                    79********65 PP

  == domain 3  score: 24.8 bits;  conditional E-value: 1.3e-08
                                    TSSS-THHHHHSTTTEEE CS
                           Fer4   7 kCigCGaCvevCPvgAIt 24 
                                    +C+gCG C+++CP gAI+
  gi|116754476|ref|YP_843594.1| 574 LCTGCGVCAQICPKGAIE 591
                                    7****************6 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       3.1   3.2e+03      18      40 ..     341     363 ..     336     364 .. 0.61
   2 !    9.0   1.7    0.0015       1.6      22      47 ..     537     561 ..     530     565 .. 0.66
   3 !   21.0  12.3   2.6e-07   0.00028       1      51 []     548     590 ..     548     590 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 3.1
                         Fer4_9  18 vedaaerkarlraaseeaCigCg 40 
                                    v+++ +++  +  +  + C gCg
  gi|116754476|ref|YP_843594.1| 341 VPKDLPGTEIVPPRPPSLCPGCG 363
                                    55555555555555557799998 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0015
                         Fer4_9  22 aerkarlraaseeaCigCgaCvea.Cp 47 
                                    +er++r+r ++e  C+gC++C+e  Cp
  gi|116754476|ref|YP_843594.1| 537 GERFRRYRVTDE--CVGCRQCLEFdCP 561
                                    555666666655..8888888863255 PP

  == domain 3  score: 21.0 bits;  conditional E-value: 2.6e-07
                         Fer4_9   1 kCtgCgaCvea.CpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                    +C+gC++C e  Cpa  + e+a+  +++        C+gCg C+++Cpkgai
  gi|116754476|ref|YP_843594.1| 548 ECVGCRQCLEFdCPAIEFDEKAS--INQ-------LCTGCGVCAQICPKGAI 590
                                    5*******7777**988876654..344.......4**************97 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   1.7   0.00041      0.43      37      53 ..     545     562 ..     531     566 .. 0.77
   2 !   19.1  12.9     1e-06    0.0011       6      58 ..     547     591 ..     544     592 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00041
                        Fer4_21  37 vedeCvGCnlCssv.CPv 53 
                                    v+deCvGC  C++  CP 
  gi|116754476|ref|YP_843594.1| 545 VTDECVGCRQCLEFdCPA 562
                                    69*********9865995 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 1e-06
                        Fer4_21   6 dkCigCgkClia.CedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58 
                                    d+C+gC +Cl   C+     aie+d+k+    +++ C+GC +C+++CP +++ie
  gi|116754476|ref|YP_843594.1| 547 DECVGCRQCLEFdCP-----AIEFDEKAS---INQLCTGCGVCAQICP-KGAIE 591
                                    89*******964398.....9****9887...7899************.79997 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       1.9     2e+03       7      14 ..     356     363 ..     352     364 .. 0.83
   2 !   11.5   2.6   0.00025      0.26       6      22 .]     545     562 ..     541     562 .. 0.88
   3 !   14.5   2.3   2.6e-05     0.028       9      21 ..     574     586 ..     567     587 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.9
                         Fer4_2   7 tdrCigCg 14 
                                    +  C gCg
  gi|116754476|ref|YP_843594.1| 356 PSLCPGCG 363
                                    568****8 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00025
                         Fer4_2   6 dtdrCigCgaCvsa.CPa 22 
                                    +td C+gC+ C+   CPa
  gi|116754476|ref|YP_843594.1| 545 VTDECVGCRQCLEFdCPA 562
                                    6899********999**8 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 2.6e-05
                         Fer4_2   9 rCigCgaCvsaCP 21 
                                     C+gCg C + CP
  gi|116754476|ref|YP_843594.1| 574 LCTGCGVCAQICP 586
                                    5***********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 !   10.1   2.3   0.00089      0.94       2      15 ..     547     561 ..     546     566 .. 0.90
   2 !   13.6   3.5   6.7e-05     0.071       2      16 ..     573     587 ..     572     588 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00089
                         Fer4_4   2 erCigCgsCvaa.CP 15 
                                    + C+gC++C  + CP
  gi|116754476|ref|YP_843594.1| 547 DECVGCRQCLEFdCP 561
                                    78*******999998 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 6.7e-05
                         Fer4_4   2 erCigCgsCvaaCPq 16 
                                    + C+gCg+C  +CP 
  gi|116754476|ref|YP_843594.1| 573 QLCTGCGVCAQICPK 587
                                    57************6 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.3      0.16   1.7e+02       6      13 ..     356     363 ..     356     364 .. 0.88
   2 !    6.4   1.9    0.0096        10       9      21 ..     549     562 ..     546     569 .. 0.83
   3 !   17.7   3.1   2.6e-06    0.0027       7      24 .]     573     590 ..     570     590 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.16
                         Fer4_6   6 pdkCigCg 13 
                                    p++C gCg
  gi|116754476|ref|YP_843594.1| 356 PSLCPGCG 363
                                    79*****9 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0096
                         Fer4_6   9 CigCgdC.vrvCPe 21 
                                    C+gC+ C +  CP+
  gi|116754476|ref|YP_843594.1| 549 CVGCRQClEFDCPA 562
                                    *******5555996 PP

  == domain 3  score: 17.7 bits;  conditional E-value: 2.6e-06
                         Fer4_6   7 dkCigCgdCvrvCPegai 24 
                                    ++C+gCg C+ +CP gai
  gi|116754476|ref|YP_843594.1| 573 QLCTGCGVCAQICPKGAI 590
                                    79**************98 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   1.5   0.00056      0.59      34      58 ..     537     562 ..     511     563 .. 0.80
   2 !   10.8   2.7   0.00052      0.55      42      59 ..     571     588 ..     562     590 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00056
                        Fer4_17  34 leeaekeekaslCieCgeCe.rkCPq 58 
                                     e+  + ++ ++C++C++C   +CP+
  gi|116754476|ref|YP_843594.1| 537 GERFRRYRVTDECVGCRQCLeFDCPA 562
                                    4555667899*********9899995 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00052
                        Fer4_17  42 kaslCieCgeCerkCPqg 59 
                                      +lC++Cg C++ CP+g
  gi|116754476|ref|YP_843594.1| 571 INQLCTGCGVCAQICPKG 588
                                    457899999999999976 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   2.7     0.041        43      34      49 ..     545     561 ..     527     563 .. 0.71
   2 !   12.4  13.6   0.00018      0.19       2      52 .]     549     589 ..     548     589 .. 0.88
   3 !   14.9   3.6     3e-05     0.031       2      19 ..     575     592 ..     574     594 .] 0.75

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.041
                         Fer4_7  34 dpekClgCgaCva.vCP 49 
                                    + ++C+gC++C +  CP
  gi|116754476|ref|YP_843594.1| 545 VTDECVGCRQCLEfDCP 561
                                    56778888888764565 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00018
                         Fer4_7   2 CigCgaCvaa.CpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                    C+gC++C +  Cp  aie+de++            + C+gCg+C++ CP+ga
  gi|116754476|ref|YP_843594.1| 549 CVGCRQCLEFdCP--AIEFDEKA---------SINQLCTGCGVCAQICPKGA 589
                                    ********988**..9***9983.........34579*************98 PP

  == domain 3  score: 14.9 bits;  conditional E-value: 3e-05
                         Fer4_7   2 CigCgaCvaaCpvkaiel 19 
                                    C+gCg C++ Cp +aie+
  gi|116754476|ref|YP_843594.1| 575 CTGCGVCAQICPKGAIEV 592
                                    888888888888888765 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1  13.2   1.8e-05     0.019       6      56 .]     546     586 ..     542     586 .. 0.80
   2 ?   10.5   3.7   0.00048       0.5       7      21 ..     573     587 ..     568     592 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.8e-05
                        Fer4_10   6 ddtCirCgkCvka.CPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                    +d C++C++C ++ CPa       ++++++ + ++     Ctgcg C+++CP
  gi|116754476|ref|YP_843594.1| 546 TDECVGCRQCLEFdCPA-------IEFDEKASINQ----LCTGCGVCAQICP 586
                                    689*********99***.......44444444444....5***********9 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00048
                        Fer4_10   7 dtCirCgkCvkaCPa 21 
                                    + C++Cg C + CP 
  gi|116754476|ref|YP_843594.1| 573 QLCTGCGVCAQICPK 587
                                    679999999999997 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   1.4     0.058        61       2      20 ..     549     568 ..     548     573 .. 0.73
   2 ?   15.4   3.3   2.6e-05     0.027       2      18 ..     575     591 ..     574     594 .] 0.91

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.058
                        Fer4_16   2 CgtCgkCaev.CPtnaikek 20 
                                    C++C++C+e  CP+  ++ek
  gi|116754476|ref|YP_843594.1| 549 CVGCRQCLEFdCPAIEFDEK 568
                                    *******9855997665555 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 2.6e-05
                        Fer4_16   2 CgtCgkCaevCPtnaik 18 
                                    C++Cg Ca++CP +ai+
  gi|116754476|ref|YP_843594.1| 575 CTGCGVCAQICPKGAIE 591
                                    ****************8 PP

>> DUF1702  Protein of unknown function (DUF1702)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.2   0.00043      0.45     219     254 ..      16      51 ..      10      85 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00043
                        DUF1702 219 LwsGvgLAatyAGgvdeeelealrelageyraelaq 254
                                    L +G+gLAa y G+ ++e +++l   a +y  ++  
  gi|116754476|ref|YP_843594.1|  16 LEAGAGLAAGYPGTPSSEIIDTLSGIASRYDIHVEW 51 
                                    779***************************998865 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   2.0     0.097     1e+02       4      17 ..     547     561 ..     545     570 .. 0.77
   2 ?   10.2   1.9    0.0008      0.85       2      18 ..     572     587 ..     571     588 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.097
                        Fer4_13   4 dtCiacgaCvel.aP 17 
                                    d+C++c +C e+ +P
  gi|116754476|ref|YP_843594.1| 547 DECVGCRQCLEFdCP 561
                                    8********998444 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0008
                        Fer4_13   2 DrdtCiacgaCvelaPd 18 
                                    + + C++cg+C++++P+
  gi|116754476|ref|YP_843594.1| 572 N-QLCTGCGVCAQICPK 587
                                    5.78************6 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   2.6      0.14   1.5e+02       3      16 ..     547     561 ..     523     564 .. 0.72
   2 ?    3.3   2.3      0.11   1.2e+02       3      18 ..     547     563 ..     545     572 .. 0.77
   3 ?    9.7   3.2    0.0011       1.1      48      64 ..     572     588 ..     564     589 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.14
                         Fer4_8   3 ekCieCgaCq.saCp 16 
                                    ++C++C  C    Cp
  gi|116754476|ref|YP_843594.1| 547 DECVGCRQCLeFDCP 561
                                    456666666643465 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.11
                         Fer4_8   3 ekCieCgaCq.saCpvl 18 
                                    ++C++C  C    Cp++
  gi|116754476|ref|YP_843594.1| 547 DECVGCRQCLeFDCPAI 563
                                    57999999985568865 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0011
                         Fer4_8  48 lwsCttcgaCtevCpvg 64 
                                     + Ct+cg C++ Cp+g
  gi|116754476|ref|YP_843594.1| 572 NQLCTGCGVCAQICPKG 588
                                    57899999999999986 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       9.9     1e+04      25      63 ..     460     500 ..     446     502 .. 0.52
   2 ?    5.5   8.8     0.018        19      52      96 ..     540     586 ..     524     592 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 9.9
                        Fer4_18  25 llvvydakr..Gekiagrkkekkalkekeerkekgagdcid 63 
                                     ++ ++ +   G++ +g+++ + +l+   +   +g+ +cid
  gi|116754476|ref|YP_843594.1| 460 AMTGHQPHPgtGKTATGEESVRISLEGIAKALGAGHVECID 500
                                    33444444411344445666666666666666677777776 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.018
                        Fer4_18  52 erkekgagdcidcescvkv.cP.tgidirkGlqleciscllcidacd 96 
                                     r+ + + +c+ c++c++  cP ++ d +  +   c  c+ c   c 
  gi|116754476|ref|YP_843594.1| 540 FRRYRVTDECVGCRQCLEFdCPaIEFDEKASINQLCTGCGVCAQICP 586
                                    456677899********966994589999999999********9996 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 ?    4.1   2.9     0.078        82       6      26 ..     547     567 ..     546     573 .. 0.84
   2 ?    7.5   3.4    0.0063       6.6       6      20 ..     573     587 ..     572     591 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.078
                        Fer4_15   6 daCigcglCvaeapevfelde 26 
                                    d+C gc +C++ +   +e+de
  gi|116754476|ref|YP_843594.1| 547 DECVGCRQCLEFDCPAIEFDE 567
                                    89*********9977898886 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0063
                        Fer4_15   6 daCigcglCvaeape 20 
                                    ++C+gcg+C++ +p+
  gi|116754476|ref|YP_843594.1| 573 QLCTGCGVCAQICPK 587
                                    68***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (594 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.60u 0.24s 00:00:00.84 Elapsed: 00:00:00.42
# Mc/sec: 4287.91
//
Query:       gi|116754477|ref|YP_843595.1|  [L=427]
Description: thiamine biosynthesis protein ThiC [Methanosaeta thermophila PT]
Scores for complete 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-175  584.0   0.0   1.7e-175  583.8   0.0    1.0  1  ThiC_Rad_SAM  Radical SAM ThiC family


Domain annotation for each model (and alignments):
>> ThiC_Rad_SAM  Radical SAM ThiC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  583.8   0.0  9.4e-180  1.7e-175       3     417 ..       4     420 ..       2     421 .. 0.99

  Alignments for each domain:
  == domain 1  score: 583.8 bits;  conditional E-value: 9.4e-180
                   ThiC_Rad_SAM   3 leaarkgiiteemeevaekenvepefvreevaeGrivipanknhkekpvaiGkglrtkvnaniGtsadasdieeEveKlk 82 
                                    le+a +g++++em+ va++e+ +pef+r+++a+Grivip    ++++pv+iGkglrtkvna+iGts+d++d+++EveK++
  gi|116754477|ref|YP_843595.1|   4 LEDAAAGRLNDEMRLVAQAEGKSPEFIRRGIASGRIVIPISPYRETRPVGIGKGLRTKVNASIGTSSDIVDVDMEVEKAR 83 
                                    7899**************************************************************************** PP

                   ThiC_Rad_SAM  83 valkagadtvmdLstggdideirekileespvpvgtvpiYqalee...kekkveelteeellevieeqaedGvdfltiHa 159
                                    va++agadt+m+Lstggd++eir++++e ++++vg+vp+Yqa+ e   k+++ +++te+el++++ eqa+ G +f++iH+
  gi|116754477|ref|YP_843595.1|  84 VAESAGADTLMELSTGGDLREIRRRVIEVTSLSVGSVPLYQAFIEairKHGAGVDMTEDELFRAVDEQARMGTNFMAIHT 163
                                    *******************************************99999999***************************** PP

                   ThiC_Rad_SAM 160 gvtlellellkke.kRltgivSrgGsllaawmlanekenplyeefdelleilkeydvtlSlgdglRpGsiaDatdeaqla 238
                                    g+++ +le+lk++ +R+ g++SrgG++++awml+nekenply+efd+lleilke++vtlSlg+g+R+G+i+D+td+aq++
  gi|116754477|ref|YP_843595.1| 164 GINRICLERLKAQgGRFGGLCSRGGAFMIAWMLHNEKENPLYSEFDYLLEILKEHEVTLSLGNGMRAGAIHDSTDRAQIQ 243
                                    **********98868***************************************************************** PP

                   ThiC_Rad_SAM 239 elivlgelvkrareagvqvmveGPGHvpldeieanvklqkklckeaPfyvlGplvtDiapgYDhitsaiGaalaaaaGad 318
                                    el++++el++ra++agvq++veGPGH+p+deiean++++k++++e Pfy+lGplvtDiapgYDhi++aiGa+l++a+Gad
  gi|116754477|ref|YP_843595.1| 244 ELVINAELADRAQAAGVQTIVEGPGHIPVDEIEANIRIMKRMTDERPFYMLGPLVTDIAPGYDHIVAAIGASLSSAYGAD 323
                                    ******************************************************************************** PP

                   ThiC_Rad_SAM 319 llCyvtpaEHlglPdeedvkeGviaakiaahaadlakglkkarerdkalskaRkeldwekqfelaldpekareireeklp 398
                                    ++CyvtpaEHl+lP+ edv+eGviaa+iaa ++d++k   + r+rd ++ +aR++l w+ qf+laldp++ar+ir+e++p
  gi|116754477|ref|YP_843595.1| 324 FICYVTPAEHLALPTPEDVREGVIAARIAAYIGDMIKL--GRRDRDLEMGRARRDLLWDMQFHLALDPQRARQIRAEREP 401
                                    *************************************8..889************************************* PP

                   ThiC_Rad_SAM 399 eeeeaCsmCgekCavkive 417
                                    +++++C+mCg++Ca+ki++
  gi|116754477|ref|YP_843595.1| 402 ADSRVCTMCGDYCALKIIK 420
                                    ****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3082.79
//
Query:       gi|116754478|ref|YP_843596.1|  [L=67]
Description: hypothetical protein Mthe_1174 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0093   16.0   0.0      0.017   15.2   0.0    1.4  1  TPR_2     Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.011   15.5   0.0      0.019   14.8   0.0    1.4  1  TPR_1     Tetratricopeptide repeat
      0.024   14.8   0.2       0.05   13.8   0.2    1.5  1  TPR_8     Tetratricopeptide repeat
      0.038   14.0   0.0      0.051   13.7   0.0    1.1  1  MIT       MIT (microtubule interacting and transport) domain
      0.073   13.2   0.1      0.084   13.0   0.1    1.0  1  KaiA      KaiA C-terminal domain
       0.11   12.6   0.0       0.14   12.2   0.0    1.1  1  DUF1664   Protein of unknown function (DUF1664)


Domain annotation for each model (and alignments):
>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   5.9e-06     0.017       6      29 ..      10      33 ..       7      34 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.9e-06
                          TPR_2  6 nlGlayyklgdyeeAleafekAle 29
                                   +l++ y + + yeeA+ +fe A++
  gi|116754478|ref|YP_843596.1| 10 YLAMMYVYIKSYEEAISDFETAVK 33
                                   89********************86 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   6.2e-06     0.019       6      29 ..      10      33 ..       8      33 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6.2e-06
                                   HHHHHHHHTT-HHHHHHHHHHHHH CS
                          TPR_1  6 nlGnayfklgkydeAleyyekALe 29
                                    l+++y + + y+eA+ ++e A++
  gi|116754478|ref|YP_843596.1| 10 YLAMMYVYIKSYEEAISDFETAVK 33
                                   699******************986 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   1.7e-05      0.05       7      29 ..      11      33 ..      10      33 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.7e-05
                                   HHHHHHHTT-HHHHHHHHHHHHH CS
                          TPR_8  7 lgsiylklgdyeeAkeyyekale 29
                                   l++ y   + yeeA++ +e a++
  gi|116754478|ref|YP_843596.1| 11 LAMMYVYIKSYEEAISDFETAVK 33
                                   7999*****************96 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.7e-05     0.051      24      61 ..      18      57 ..      18      60 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.7e-05
                            MIT 24 lelYkealelLlqalk.e.kneerrellrekieeYleRae 61
                                   ++ Y+ea+  + +a+k    ++   e++rek +e +eR+ 
  gi|116754478|ref|YP_843596.1| 18 IKSYEEAISDFETAVKdTgFADLAIEAVREKFRERIERVS 57
                                   689*************54755599********99999975 PP

>> KaiA  KaiA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   2.8e-05     0.084      32      89 ..       5      62 ..       2      66 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.8e-05
                                   HHHHHHHHHHHHCTSTTSSHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHHHHC CS
                           KaiA 32 elkseyreivleyfkddsevnqkidefvnkaffadlsvskileihmelldefskqlkl 89
                                   + +s y  ++  y k+ +e  +  +  v+ + fadl++  + e   e ++  sk+l +
  gi|116754478|ref|YP_843596.1|  5 KTSSMYLAMMYVYIKSYEEAISDFETAVKDTGFADLAIEAVREKFRERIERVSKELDM 62
                                   56788999999******************************************99975 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.6e-05      0.14      31      77 ..      13      62 ..       8      66 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.6e-05
                        DUF1664 31 lmfvTkrslsdavesvskqleqvs...eslaatkrhLssridrvdkklde 77
                                   +m+v  +s ++a+++  + +++      +++a+++++ +ri+rv k+ld 
  gi|116754478|ref|YP_843596.1| 13 MMYVYIKSYEEAISDFETAVKDTGfadLAIEAVREKFRERIERVSKELDM 62
                                   99***********99999999876444689*****************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       764  (0.0426125); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); 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: 0.34u 0.28s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 499.97
//
Query:       gi|116754479|ref|YP_843597.1|  [L=267]
Description: hypothetical protein Mthe_1175 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 2094.92
//
Query:       gi|116754480|ref|YP_843598.1|  [L=619]
Description: threonyl-tRNA synthetase [Methanosaeta thermophila PT]
Scores for complete 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  174.2   0.2    2.8e-51  173.2   0.0    1.7  2  tRNA-Thr_ED     Archaea-specific editing domain of threonyl-t
      1e-19   70.4   0.7      1e-19   70.4   0.7    2.1  3  HGTP_anticodon  Anticodon binding domain
    4.8e-16   59.2   0.2    9.3e-16   58.3   0.2    1.5  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
  ------ inclusion threshold ------
       0.02   14.9   0.0      0.043   13.9   0.0    1.5  1  TPK_catalytic   Thiamin pyrophosphokinase, catalytic domain


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 !  173.2   0.0   6.3e-55   2.8e-51       1     137 []       1     137 [.       1     137 [. 0.98
   2 ?   -3.5   0.0       2.2     1e+04      21      50 ..     512     541 ..     507     550 .. 0.72

  Alignments for each domain:
  == domain 1  score: 173.2 bits;  conditional E-value: 6.3e-55
                                    -EEEEEEEEEEEEEEEEESSSS-...SS---EEEESSEEEEEEE-BTT--H...HHHHHHHHHHHHHHHHHT-SEEEEEE CS
                    tRNA-Thr_ED   1 mrlLlihadeleyeakkkalkeae..eeeekegrleealvvFiavEkeDeeekekvvekavkeikkvakkvkakkvvlyp 78 
                                    m+lLlih+d +e+eakk++ k ae  +ee ++grl+eal++FiavEk De+++++vv++a+ ei++vak+vka++++lyp
  gi|116754480|ref|YP_843598.1|   1 MQLLLIHSDFIEFEAKKPT-KFAEevPEEARSGRLDEALCAFIAVEKFDEDDPDAVVAQAAGEIEEVAKRVKAERIMLYP 79 
                                    9******************.7777699999************************************************** PP

                                    -STS-SSB--HHHHHHHHHHHHHHHHTT.-EEEE--SSEEEEEEEEE--STTSEEEEE- CS
                    tRNA-Thr_ED  79 yaHLssslaspevakeilkkleeklkekglevkraPFGwykefeisckGhpLaelsrei 137
                                    yaHLss l+spe+a+++l++le++lk++ +ev+raPFGwyk+f+i+ckGhpL+elsr+i
  gi|116754480|ref|YP_843598.1|  80 YAHLSSALSSPETAVRVLRDLESTLKSS-FEVARAPFGWYKSFTIRCKGHPLSELSRSI 137
                                    ***************************8.****************************97 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.2
                                    SS-.SS---EEEESSEEEEEEE-BTT--H. CS
                    tRNA-Thr_ED  21 keaeeeeekegrleealvvFiavEkeDeee 50 
                                    ++ae ++ +  ++ e l   + v+++De+ 
  gi|116754480|ref|YP_843598.1| 512 PVAERHHARAMEVAEQLNFRVDVDDRDETV 541
                                    567777777778888888888888888874 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       1.9   8.7e+03      10      24 ..      59      73 ..      54      73 .. 0.64
   2 ?   -2.8   0.0       1.7   7.4e+03      14      47 ..     358     391 ..     353     395 .. 0.68
   3 !   70.4   0.7   2.3e-23     1e-19       1      93 [.     507     596 ..     507     597 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.9
                                   SHHHHHHHHHHHHHH CS
                 HGTP_anticodon 10 kaeeleeyakklaee 24
                                    a e+ee+ak++++e
  gi|116754480|ref|YP_843598.1| 59 AAGEIEEVAKRVKAE 73
                                   345788999888865 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.7
                                    HHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHH CS
                 HGTP_anticodon  14 leeyakklaeeLraagirvelddsnesigkkire 47 
                                    + + ++   + Lr+ag++ + ++ + ++ k + e
  gi|116754480|ref|YP_843598.1| 358 FRKQYEASISVLRDAGLDLKDYEVAIRFTKDFYE 391
                                    5555666667899999877777777777776665 PP

  == domain 3  score: 70.4 bits;  conditional E-value: 2.3e-23
                                    SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEET...TTC CS
                 HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdr...dtr 77 
                                    qv +ip++e   +++  a+++ae+L+   +rv++dd++e++gkkir+a + ++p++ vvG++el +g +tv  r   ++ 
  gi|116754480|ref|YP_843598.1| 507 QVRIIPVAE---RHHARAMEVAEQLN---FRVDVDDRDETVGKKIRDAGREWVPYVAVVGDEELSTGLLTVTVRsesTSN 580
                                    89*******...9************9...***********************************99*9999999987777 PP

                                    EEEEEETTHHHHHHHH CS
                 HGTP_anticodon  78 eqervsldelveklke 93 
                                    +++++s++el + l++
  gi|116754480|ref|YP_843598.1| 581 QKIKMSVEELRARLQS 596
                                    999*******999986 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 !   58.3   0.2   2.1e-19   9.3e-16       4     178 ..     280     486 ..     277     487 .. 0.80

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 2.1e-19
                                    EETTSEEEEE-SSSHHHHHHHHHHHEEEBGG.SSEEEEEEEEE.EBTTTS.TBCTTTB-SEEEEEEEEEEES.GGGHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx.xxxxxx.xxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                   tRNA-synt_2b   4 edrndreyiLkPtneetfvelirdevlrskr.LPlklyqiqtk.yRdEks.dsrGLlRvreFhqkdgyvfha.easldds 79 
                                    e + ++ + L+  ++ +   ++ d    s+r LPl+++++++  +R+E++ ++ GL R+r F++ d + f+   +s+ ++
  gi|116754480|ref|YP_843598.1| 280 EAD-KKHLFLRFAACFGQFLMGHDM-TFSYRsLPLRMFELTRYsFRREQRgELVGLRRLRAFTMPDMHTFCGdMSSAMEE 357
                                    544.478899999999999999999.667666*******99854******8999******************77999*** PP

                                    HHHHHHHHHHHHHHTT.SC...EEEEEEGTTSC..............................BTTSEEEEEEEEETTTS CS
                                    xxxxxxxxxxxxxxxxxxx...xxxxxxxxxxx..............................xxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2b  80 lrdlikaisriferlglef...raiielmsaks..............................adykdkkefeavseslt 126
                                    +r+  +a   ++++ gl            ++++                              +    k ef+ v+  l+
  gi|116754480|ref|YP_843598.1| 358 FRKQYEASISVLRDAGLDLkdyE---VAIRFTKdfyennktfieglvdivdkpvliemwderfFYFVLKFEFNFVDA-LD 433
                                    *****************874432...333333322245556666666666666666666666333345666666666.** PP

                                    EEEEEEEEEEEETHHHHHTTEEEECTTSSEEEEEEEEEE.EE.HHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.xxxxxxxxxxx RF
                   tRNA-synt_2b 127 kgieigtiqklgtrlserlgatvldennreksvimicaa.ig.veRllsaileq 178
                                    k+  ++t+q +  + +er ++ ++d +++++++i+++ +  g +eRl+ a+le+
  gi|116754480|ref|YP_843598.1| 434 KASALSTVQID-VENAERYDIGYVDAEGNRQRPIILHCSpSGaIERLMYALLEK 486
                                    ***********.999************************9999********997 PP

>> TPK_catalytic  Thiamin pyrophosphokinase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   9.5e-06     0.043      34      84 ..     345     394 ..     330     417 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.5e-06
                  TPK_catalytic  34 dvivGDlDSirpevkefyeskgteivkkpdqdstDlekaialvlekekedk 84 
                                    ++++GD+ S  +e +++ye   + ++++   d  D e ai++ ++ ++++k
  gi|116754480|ref|YP_843598.1| 345 HTFCGDMSSAMEEFRKQYEA-SISVLRDAGLDLKDYEVAIRFTKDFYENNK 394
                                    567****************9.8***********************997766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (619 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); 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: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.39
# Mc/sec: 4808.59
//
Query:       gi|116754481|ref|YP_843599.1|  [L=874]
Description: S-layer-like domain-containing protein [Methanosaeta thermophila PT]
Scores for 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-117  388.7   0.0    1.7e-57  194.4   0.2    2.1  2  S-layer   S-layer protein


Domain annotation for each model (and alignments):
>> S-layer  S-layer protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.2   0.0   4.7e-61   8.4e-57       7     258 .]      38     280 ..      33     280 .. 0.96
   2 !  194.4   0.2   9.7e-62   1.7e-57       9     250 ..     324     576 ..     317     591 .. 0.91

  Alignments for each domain:
  == domain 1  score: 192.2 bits;  conditional E-value: 4.7e-61
                        S-layer   7 seeltwtasnFsgfyydiddglssEsltlelesksdrtieegelvYsttpvekefefeewgsYevigflaekYfagydns 86 
                                    ++e  w+a++F  f yd+++g++sEsl++     ++rtieeg+l+Ys ++v k fe+e+wg+Y  igfl+++Y+agy + 
  gi|116754481|ref|YP_843599.1|  38 TAEGVWNAEDFGWFVYDLKEGMGSESLSII---PTERTIEEGNLIYSCRAVAKRFEYESWGRYLWIGFLGKRYLAGYPEG 114
                                    45566************************8...389*****************************************888 PP

                        S-layer  87 aetsddvsllsdekLskvlidedeektlksgssleLeegYeleikqiDvdgdkvwleLtkdgeevdskvissskadstyv 166
                                    +  ++++s l++++L++vlid+d+++t++s   l L++gY++ ++++  dg k+++eL  dg+ vd +v+++    styv
  gi|116754481|ref|YP_843599.1| 115 P-ITEEISSLEKGELREVLIDSDDRYTISSERPLILGDGYTVALESVSDDGRKAFIELLMDGSTVDRAVVEE---GSTYV 190
                                    8.799*******************************************************************...***** PP

                        S-layer 167 yekdlgdeddvviiavhvdevfrgtedslvviegifqis.ddvleieegdefgkmevksvseneiemenddsitLsrdkt 245
                                     ++    e d+++i +hv++ ++g++++ v ++gifq+s   ++ + +g ++g ++v+++s ++ie++n+d+i Ls d+ 
  gi|116754481|ref|YP_843599.1| 191 WKH---PETDIPLILIHVRSGMHGRDEDRVDVDGIFQVStHPAVVLTDGATIGLLKVNDISGDRIELRNSDDIALSPDSM 267
                                    *97...5788*****************************6667999********************************** PP

                        S-layer 246 ieimddlkfkvaD 258
                                    ++i++ l ++v+D
  gi|116754481|ref|YP_843599.1| 268 VHIAGGLALRVTD 280
                                    **********998 PP

  == domain 2  score: 194.4 bits;  conditional E-value: 9.7e-62
                        S-layer   9 eltwtasnFsgfyydiddglssEsltlelesksdrtie.................egelvYsttpvekefefeewgsYev 71 
                                    ++ w+  n++gfy+d +d+++sE+++l+ +  s r++                    +l Y t +++k fe ++wg+Y v
  gi|116754481|ref|YP_843599.1| 324 STVWDYRNYAGFYFDDEDMIGSETFVLNGS--SRRVVPrfgpivpvemngsvvgsMRGLLYYTYIQPKRFERDSWGEYYV 401
                                    456************************955..4444445555555555555555569*********************** PP

                        S-layer  72 igflaekYfagy.dnsaetsddvsllsdekLskvlidedeektlksgssleLeegYeleikqiDvdgdkvwleLtkdgee 150
                                    + +++e +fagy  n++++  ++s+++ e L +vlid+d + +++sg+ +   +gY+l i+  Dv  d+++++L kd++ 
  gi|116754481|ref|YP_843599.1| 402 LSLFGELWFAGYgRNTSSEIGEKSMFDYERLGRVLIDTDAQDIATSGNIYFFRDGYSLLIR--DVGKDRIFVSLLKDNRI 479
                                    ************866667999****************************************..***************** PP

                        S-layer 151 vdskvissskadstyvyekdlgdeddvviiavhvdevfrgtedslvviegifqisddv.leieegdefgkmevksvsene 229
                                    vd++ iss   +styvy+kd+ d +d++i+avhv e+fr++e +++vi+g+fqisd++ l ie g ++g m + + + + 
  gi|116754481|ref|YP_843599.1| 480 VDNSTISS---NSTYVYKKDVFDIKDLPILAVHVGEIFRDKERQIAVIDGVFQISDQIyLPIEGGSKIGDMVIFT-TPKG 555
                                    ********...********************************************99769***********9987.7888 PP

                        S-layer 230 iemenddsitLsrdktieimd 250
                                    i m nd+s +L +++++ei  
  gi|116754481|ref|YP_843599.1| 556 IYMVNDESKSLGKGSSVEIWP 576
                                    *****************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (874 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 5763.49
//
Query:       gi|116754482|ref|YP_843600.1|  [L=264]
Description: nitrogenase [Methanosaeta thermophila PT]
Scores for complete 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-90  303.5   1.0    1.5e-90  303.4   1.0    1.0  1  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
      1e-09   38.5   0.0    1.6e-09   37.9   0.0    1.3  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    6.7e-09   35.6   0.0    2.1e-08   33.9   0.0    1.8  1  ParA         NUBPL iron-transfer P-loop NTPase
    1.1e-07   31.9   0.3      3e-07   30.5   0.0    1.7  2  AAA_31       AAA domain
    1.2e-06   28.0   0.2    2.3e-06   27.0   0.2    1.4  2  ArsA_ATPase  Anion-transporting ATPase
     0.0004   19.5   0.4    0.00054   19.0   0.4    1.2  1  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
    0.00042   19.7   0.2     0.0035   16.7   0.0    2.0  2  MipZ         ATPase MipZ
    0.00052   19.8   0.0     0.0008   19.2   0.0    1.2  1  AAA_24       AAA domain
     0.0026   18.1   0.1      0.023   15.1   0.1    2.2  3  AAA_16       AAA ATPase domain
     0.0043   16.9   0.2        1.9    8.2   0.1    2.2  2  ATP_bind_1   Conserved hypothetical ATP binding protein
     0.0078   16.1   0.1       0.13   12.1   0.0    2.2  2  NTPase_1     NTPase
  ------ inclusion threshold ------
      0.012   15.2   0.1      0.032   13.8   0.0    1.6  2  AAA_25       AAA domain
      0.037   13.2   0.0      0.059   12.6   0.0    1.2  1  NB-ARC       NB-ARC domain
       0.11   12.2   0.3        0.2   11.4   0.3    1.3  1  IstB_IS21    IstB-like ATP binding protein
        0.2   11.7   0.0       0.29   11.2   0.0    1.2  1  DUF87        Helicase HerA, central domain
       0.26   10.4   0.0       0.35   10.0   0.0    1.2  1  DUF815       Protein of unknown function (DUF815)


Domain annotation for each model (and alignments):
>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  303.4   1.0   1.3e-93   1.5e-90       2     265 ..       6     262 ..       5     264 .] 0.96

  Alignments for each domain:
  == domain 1  score: 303.4 bits;  conditional E-value: 1.3e-93
                      Fer4_NifH   2 kiaiyGkGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrlllggkaqetvldtlrekgavedvkvedvvkkGyggv 81 
                                    ++aiyGkGGiGks  ++n++aa ae+g +vl+vGCDPk+Ds  + l g+ ++t++d++re +   +++ edvv++Gy+gv
  gi|116754482|ref|YP_843600.1|   6 HVAIYGKGGIGKSCIASNVAAACAERGVRVLVVGCDPKSDSS-INLIGRRIPTMMDMIREGK---EIREEDVVFTGYRGV 81 
                                    79***************************************9.89999***********988...69************* PP

                      Fer4_NifH  82 kcvesGGPepGvGCaGrgvitaielleelgayd.dlDfvlyDvLGDvvCGGfalPiredkaqevyivtsgelmalyaann 160
                                    +c+e GGPepGvGCaGrg+i ai++l + +    d+D+vlyDv GD+vCGGf++Pir++   e yi+tsge m +yaann
  gi|116754482|ref|YP_843600.1|  82 RCIEVGGPEPGVGCAGRGIIVAIDFLRKVSRIMdDVDLVLYDVPGDIVCGGFSAPIRKGLVTEAYIITSGEYMPVYAANN 161
                                    ***************************98765527********************************************* PP

                      Fer4_NifH 161 iakgiekyaksggvrlgGliinsrkvddereliekfaeelgtkvlevvPrdeivrkaelrkktvieyapeseqakeyrel 240
                                    i++g+++     g rl+G+++nsr+v+ ere++++fa+++g++++ ++P+d +v++ e r  tvie +pes++a  yr+l
  gi|116754482|ref|YP_843600.1| 162 ICRGLKRL----GARLAGVVCNSRDVEGEREIVDDFARAIGSRMVVFIPKDPVVQRCERRAVTVIEGEPESSIAGVYRAL 237
                                    ****9865....679***************************************************************** PP

                      Fer4_NifH 241 arkilenkklviPkplsedeLeell 265
                                    a+++l+  +  +P+pl +++L e++
  gi|116754482|ref|YP_843600.1| 238 AEHVLSCTDASVPEPLDDESLREIT 262
                                    *********************9986 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 !   37.9   0.0   1.5e-12   1.6e-09       3     123 ..       8     216 ..       6     221 .. 0.81

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 1.5e-12
                                    EEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH.......HTTEB-HHHH..................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxx..................... RF
                           CbiA   3 iastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai.......leglendiep..................... 54 
                                    ++ +kGG GK+ +a n a+a a+rg rVl+v +Dp + ++ i                +                     
  gi|116754482|ref|YP_843600.1|   8 AIYGKGGIGKSCIASNVAAACAERGVRVLVVGCDPKSDSS-InligrriP--------Tmmdmiregkeireedvvftgy 78 
                                    5789********************************6665.334455540........1445555555566666****** PP

                                    ...............................................................................C CS
                                    ...............................................................................x RF
                           CbiA  55 ...............................................................................d 55 
                                                                                                                    
  gi|116754482|ref|YP_843600.1|  79 rgvrcievggpepgvgcagrgiivaidflrkvsrimddvdlvlydvpgdivcggfsapirkglvteayiitsgeympvyA 158
                                    *************************************************************9999999999999998887 PP

                                    CHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA  56 lkrllellealgkkkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeapa 123
                                    +  + + l++lg +      +agvv n  d e  e+++ +++++ +   g + + +ip+d  v +++ 
  gi|116754482|ref|YP_843600.1| 159 ANNICRGLKRLGAR------LAGVVCNSRDVE-GEREIVDDFARAI---GSRMVVFIPKDPVVQRCER 216
                                    77777777777755......899999998887.4555555666655...8888889999987776655 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 !   33.9   0.0   1.9e-11   2.1e-08       9     244 ..       9     240 ..       4     242 .. 0.74

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 1.9e-11
                           ParA   9 lSgKGGVGKStvavnlAlaLakkglkvgllDaD........iyGpsiprllgveeekpeqsekkliPveakgikvmSigf 80 
                                    + gKGG+GKS +a+n+A+a a++g++v ++  D        ++G  ip+++++ +e  e +e+ ++ +  +g++++ +g 
  gi|116754482|ref|YP_843600.1|   9 IYGKGGIGKSCIASNVAAACAERGVRVLVVGCDpksdssinLIGRRIPTMMDMIREGKEIREEDVVFTGYRGVRCIEVGG 88 
                                    469**************************97665555665589*********999888888888999999*****99997 PP

                           ParA  81 llesedeavvwrGpmkskaikqllkdve..wgelDyLiiDlPPG..tgDeqltvaqklplagaviVttpqevaladvkka 156
                                               rG ++  ai ++l++v+   +++D+++ D+P     g  +  + + l +++a i+t+ + + +  ++  
  gi|116754482|ref|YP_843600.1|  89 PE--PGVGCAGRGIIV--AI-DFLRKVSriMDDVDLVLYDVPGDivCGGFSAPIRKGL-VTEAYIITSGEYMPVYAANNI 162
                                    44..466666777665..44.466666422589********95422344445555555.8899999************** PP

                           ParA 157 iemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdegkplvlkepeseaak 236
                                    ++ +k++ +++ Gvv N   +  +          ++ ++++a+++g +++  ip dp ++++  +  ++++ epes++a 
  gi|116754482|ref|YP_843600.1| 163 CRGLKRLGARLAGVVCNSRDVEGE----------REIVDDFARAIGSRMVVFIPKDPVVQRCERRAVTVIEGEPESSIAG 232
                                    **************9996554433..........2334566666666666677777766666666666666667777776 PP

                           ParA 237 aleeiaek 244
                                    +++++ae+
  gi|116754482|ref|YP_843600.1| 233 VYRALAEH 240
                                    66666666 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0   2.6e-10     3e-07       9      49 ..      11      51 ..       4      77 .. 0.78
   2 ?   -1.8   0.2       2.2   2.4e+03     109     127 ..     108     126 ..     103     131 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 2.6e-10
                         AAA_31  9 qKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglg 49
                                    KGG+GK+  + n+aaa a++g +vL+v +Dp + ++++l 
  gi|116754482|ref|YP_843600.1| 11 GKGGIGKSCIASNVAAACAERGVRVLVVGCDPKSDSSINLI 51
                                   5**********************************999763 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.2
                         AAA_31 109 ellekvkdeYDyiiiDcpP 127
                                    ++++++ d+ D+++ D+p 
  gi|116754482|ref|YP_843600.1| 108 RKVSRIMDDVDLVLYDVPG 126
                                    567899999*******985 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.2   2.1e-09   2.3e-06       2      40 ..       5      43 ..       4      51 .. 0.92
   2 ?   -3.6   0.0       4.3   4.9e+03     210     243 ..     146     179 ..     142     186 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 2.1e-09
                                   EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STT CS
                    ArsA_ATPase  2 kvilvgGKGGVGKttvsaatavklsekgkkvllistDPA 40
                                   k + + GKGG+GK+ +++ +a+ ++e g +vl++  DP 
  gi|116754482|ref|YP_843600.1|  5 KHVAIYGKGGIGKSCIASNVAAACAERGVRVLVVGCDPK 43
                                   678899********************************5 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 4.3
                                    EEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEE CS
                    ArsA_ATPase 210 rlVvipEklslkEteRaikeLkkygikvdavivN 243
                                     +++  E ++++  +  ++ Lk++g +   v+ N
  gi|116754482|ref|YP_843600.1| 146 YIITSGEYMPVYAANNICRGLKRLGARLAGVVCN 179
                                    5778889999999999999999999999999988 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.4   4.8e-07   0.00054      31      80 ..       6      54 ..       3     105 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 4.8e-07
                                   EEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE--------------- CS
                           MeaB 31 vvGltGvPGaGkstlvealglelrrrGkrvavlavDPsspftGGsilGDk 80
                                    v + G  G Gks + +++++  ++rG rv v+  DP s  +   ++G +
  gi|116754482|ref|YP_843600.1|  6 HVAIYGKGGIGKSCIASNVAAACAERGVRVLVVGCDPKSDSSI-NLIGRR 54
                                   578999********************************98653.455555 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   3.1e-06    0.0035       8      54 ..      11      57 ..       6      74 .. 0.90
   2 ?    0.6   0.1      0.25   2.7e+02      89     110 ..     106     127 ..      97     130 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.1e-06
                                   SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHHHHHHHH CS
                           MipZ  8 ekGGsGksttavhvavaLlkkGarvaaidldlrqrtlarylenraat 54
                                    kGG Gks +a  va a +++G+rv ++  d +  ++   ++ r  t
  gi|116754482|ref|YP_843600.1| 11 GKGGIGKSCIASNVAAACAERGVRVLVVGCDPKSDSSINLIGRRIPT 57
                                   59******************************999999999988765 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.25
                                    HHHHHHHHHHH-SEEEEE--SS CS
                           MipZ  89 leelvadleaeldfividtPGs 110
                                    + + v++++ ++d+++ d+PG 
  gi|116754482|ref|YP_843600.1| 106 FLRKVSRIMDDVDLVLYDVPGD 127
                                    556789999***********95 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   7.1e-07    0.0008       4      63 ..       6      72 ..       4      85 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 7.1e-07
                         AAA_24  4 kiliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdieswedfldevvelaael 63
                                    ++iyG+ giGK+ +a++        g ++l++ ++  ++s  +  + +i+++ d++ e +e+++e+
  gi|116754482|ref|YP_843600.1|  6 HVAIYGKGGIGKSCIASNVaaacaerGVRVLVVGCDPKSDSSINLIGRRIPTMMDMIREGKEIREED 72
                                   589*********************************9888888888888999999999888887665 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   0.1     2e-05     0.023      25      63 ..       5      43 ..       2      65 .. 0.80
   2 ?   -1.6   0.0       2.7     3e+03      14      35 ..      57      81 ..      49      81 .. 0.70
   3 ?   -0.5   0.0       1.3   1.4e+03      45     104 ..     194     241 ..     186     262 .. 0.49

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2e-05
                         AAA_16 25 elvllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                     v ++G  G+GKs ++  ++ a  ++g+ +l   cd  
  gi|116754482|ref|YP_843600.1|  5 KHVAIYGKGGIGKSCIASNVAAACAERGVRVLVVGCDPK 43
                                   5799*****************988888999988888876 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.7
                         AAA_16 14 salervrsgrp...elvllsGesGv 35
                                   ++++++r+g +   e v+++G++Gv
  gi|116754482|ref|YP_843600.1| 57 TMMDMIREGKEireEDVVFTGYRGV 81
                                   4555555665566699*******97 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1.3
                         AAA_16  45 lralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekleea 104
                                    +ra+  + ++f+  +           +++q ++r + ++ ++ e+es+ ++ +r+  e +
  gi|116754482|ref|YP_843600.1| 194 ARAIGSRMVVFIPKD-----------PVVQRCER-RAVTVIEGEPESSIAGVYRALAEHV 241
                                    444444444443333...........33334423.4455555555555555555444444 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 !    8.2   0.1    0.0017       1.9       1      37 [.       9      45 ..       9      48 .. 0.92
   2 !    6.5   0.0    0.0057       6.4      66     102 ..      98     128 ..      95     136 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0017
                     ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrsvavvNLDPAae 37
                                   + G  G GK+ + ++++  + +rg +v vv  DP ++
  gi|116754482|ref|YP_843600.1|  9 IYGKGGIGKSCIASNVAAACAERGVRVLVVGCDPKSD 45
                                   57999****************************9765 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0057
                     ATP_bind_1  66 galvvaleflresldwldeelekeeddyllfDtPGQi 102
                                    ++++va++flr+    + +++     d++l+D+PG i
  gi|116754482|ref|YP_843600.1|  98 RGIIVAIDFLRKVS-RIMDDV-----DLVLYDVPGDI 128
                                    5899****999875.677777.....*********76 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   0.00012      0.13       1      31 [.       6      36 ..       6      72 .. 0.88
   2 ?    1.7   0.0      0.19   2.2e+02      17      44 ..     160     187 ..     158     202 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00012
                                   EEEEE--TTSSHHHHHHHHHHHH...GGGEE CS
                       NTPase_1  1 kvfiTGppGvGKtTlvkkvlellkssgvkvg 31
                                   +v+i G+ G+GK+ + ++v+ +++++gv+v 
  gi|116754482|ref|YP_843600.1|  6 HVAIYGKGGIGKSCIASNVAAACAERGVRVL 36
                                   78999***********************995 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.19
                                    HHHHHHH...GGGEEEEEEEEE------ CS
                       NTPase_1  17 kkvlellkssgvkvgGfyteevreggrr 44 
                                    +++++ lk+ g +++G++++    +g+r
  gi|116754482|ref|YP_843600.1| 160 NNICRGLKRLGARLAGVVCNSRDVEGER 187
                                    689999*************998888777 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.9e-05     0.032      36      75 ..       7      36 ..       5      50 .. 0.81
   2 ?   -2.4   0.0       2.7     3e+03      73     135 ..     218     239 ..     184     252 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.9e-05
                         AAA_25 36 allaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVl 75
                                   ++++G +g GK+ +a+++a+a+a +G             Vl
  gi|116754482|ref|YP_843600.1|  7 VAIYGKGGIGKSCIASNVAAACAeRGVR-----------VL 36
                                   579********************66654...........44 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.7
                         AAA_25  73 kVlyvsaEdsedelrrRlravgealrddarllvldlagveslpLfakdrggtlltadvdalea 135
                                    +V ++ +E                                          ++ ++++++al++
  gi|116754482|ref|YP_843600.1| 218 AVTVIEGE-----------------------------------------PESSIAGVYRALAE 239
                                    33333333.........................................22333444444444 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.2e-05     0.059      22      42 ..       6      26 ..       2      34 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.2e-05
                                   EEEEEESTTSSHHHHHHHHCC CS
                         NB-ARC 22 vvalvGmgGvGKttlakqiln 42
                                    va++G+gG+GK+ +a+++  
  gi|116754482|ref|YP_843600.1|  6 HVAIYGKGGIGKSCIASNVAA 26
                                   589**************9976 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   0.3   0.00018       0.2      49      80 ..       6      37 ..       3      41 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00018
                      IstB_IS21 49 nivllGpsGvGKshlaialgveavraglsvlf 80
                                    +++ G  G+GKs +a  ++ + +++g++vl 
  gi|116754482|ref|YP_843600.1|  6 HVAIYGKGGIGKSCIASNVAAACAERGVRVLV 37
                                   5899*************************985 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00026      0.29      24      58 ..       5      38 ..       4      45 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00026
                          DUF87 24 rHlAilgsTGsGKSntvavLleellekkgatilil 58
                                   +H+Ai g+ G GKS  ++   +  + ++g+++l++
  gi|116754482|ref|YP_843600.1|  5 KHVAIYGKGGIGKSCIASNVAAACA-ERGVRVLVV 38
                                   7***************999888888.999999985 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00031      0.35      52      87 ..       3      38 ..       1      65 [. 0.90

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00031
                         DUF815 52 pannvLLwGarGtGKSslvkallneyaeegLrliev 87
                                   p ++v ++G+ G GKS +   + +++ae+g+r++ v
  gi|116754482|ref|YP_843600.1|  3 PIKHVAIYGKGGIGKSCIASNVAAACAERGVRVLVV 38
                                   568999************************999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); 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: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 1973.31
//
Query:       gi|116754483|ref|YP_843601.1|  [L=464]
Description: cobyrinic acid a,c-diamide synthase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-39  136.0   0.0      2e-39  135.2   0.0    1.3  1  GATase_3  CobB/CobQ-like glutamine amidotransferase domain
    1.3e-19   70.8   0.1    1.2e-14   54.7   0.0    2.2  2  AAA_26    AAA domain
    1.3e-15   57.5   0.0    2.3e-15   56.8   0.0    1.4  1  CbiA      CobQ/CobB/MinD/ParA nucleotide binding domain
  ------ inclusion threshold ------
      0.033   14.1   0.0       0.09   12.7   0.0    1.7  2  MobB      Molybdopterin guanine dinucleotide synthesis protei


Domain annotation for each model (and alignments):
>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.2   0.0   4.4e-43     2e-39       1     192 [.     253     444 ..     253     447 .. 0.93

  Alignments for each domain:
  == domain 1  score: 135.2 bits;  conditional E-value: 4.4e-43
                       GATase_3   1 kiavirlpaisnyt..dldpLeaepevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpv 78 
                                    +++v++++a+++y+  +l+++e ++++ v f+p++d++++e +d ++++Gg++++ +  l+r+s++  +i++a ++g+p+
  gi|116754483|ref|YP_843601.1| 253 RVGVAQDEAFNFYYrdNLELIELAGAEVVPFSPIHDSRIPE-VDGLYVGGGYPELYAEDLSRNSSMMSSIRDAQTDGMPL 331
                                    699************************************66.************************************** PP

                       GATase_3  79 lgiCGGlqmLGeeiedpegvegeageveglglLdietefekekltgqvegevel....aaegeevkGyEiHsGrtilkek 154
                                    +++CGGl+++++e+e p+  +ge+++++++g++++  + +++++++ v+g         ++g+ + G+E+H+++ + + +
  gi|116754483|ref|YP_843601.1| 332 YAECGGLMYMCRELEWPH--DGEESRYQMVGVVPALARRGRRRIVSYVNGAFVTdtsiGRSGDGFMGHEFHHSELVVDGD 409
                                    **************9887..56899********************99999966688888889****************** PP

                       GATase_3 155 akpllkvkvggnng.ekdGavkksedgnvlGtYlHglfd 192
                                    ++ ++k+++g++++ + dG+v     g+++++Y H++ +
  gi|116754483|ref|YP_843601.1| 410 VRYAIKLNRGTGISnGLDGIVD----GRMIASYSHLHSA 444
                                    *******88777777******5....5*********976 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   5.7e-06     0.026       2      40 ..       5      43 ..       4      72 .. 0.84
   2 !   54.7   0.0   2.6e-18   1.2e-14      86     193 ..      69     182 ..      57     186 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.7e-06
                         AAA_26  2 tifvtgtdtgvGKTvvslgLvralkrkgvkvgyfKPiqt 40
                                   +i+++g + ++GKT++ +gL++al r + +v+ fK    
  gi|116754483|ref|YP_843601.1|  5 RIVIAGDRSSSGKTTIVAGLLSALVRMNLNVQAFKVAMD 43
                                   599***********************9999999996655 PP

  == domain 2  score: 54.7 bits;  conditional E-value: 2.6e-18
                         AAA_26  86 idlekivkelekdadivvVEGagglgvpitee.llnadiaknlgapvilVargglgtinqllltiealr.qknvrvlGvi 163
                                     ++ +i+++ + dadi v+EG+ gl ++   +  ++a+iak+l+apvilV+ +++ t  +++l   ++  +++v+++Gvi
  gi|116754483|ref|YP_843601.1|  69 SRVLEIFNHASRDADIAVIEGVRGLYEGYEGDaGSTAQIAKMLRAPVILVVDARSITRSAAALVRGYMDyDRDVQIRGVI 148
                                    455566688999**************9987777**********************99888877777776589******** PP

                         AAA_26 164 lNkvrnp....envetlekksgipvlGvvPylpd 193
                                    lNk+  +    ++ +++e + g+pv+G++  +++
  gi|116754483|ref|YP_843601.1| 149 LNKLGGErhadKATREIERYAGVPVVGAIQRNDE 182
                                    ***98885554599***************98876 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 !   56.8   0.0   5.1e-19   2.3e-15       1     119 [.       6     184 ..       6     193 .. 0.89

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 5.1e-19
                                    EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH.......................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................... RF
                           CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep.......................... 54 
                                    i+ia+  + +GKTt++a+L+ al r +l+V+++++  +    ++                                    
  gi|116754483|ref|YP_843601.1|   6 IVIAGDRSSSGKTTIVAGLLSALVRMNLNVQAFKVAMDYIDPSY---------Htwitgrfcrnldgylmsesrvleifn 76 
                                    79********************************9999655554.........033333333467777777888****** PP

                                    ...........................................CCHCCCHHHHHHCHCHHHH.....EEEEEEEEESS.. CS
                                    ...........................................xxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxx RF
                           CbiA  55 ...........................................dlkrllellealgkkkall...lkiagvvlnrvdgen 88 
                                                                               d+ ++ ++++al++++ +    ++i gv+ln+ +ge+
  gi|116754483|ref|YP_843601.1|  77 hasrdadiaviegvrglyegyegdagstaqiakmlrapvilvvDARSITRSAAALVRGYMDYdrdVQIRGVILNKLGGER 156
                                    ***********************************************************999*****************9 PP

                                    .-TTCHHHHHHHHHHCTS-EEEEEE--CCHC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA  89 eetllkealeelkqrygvpvlgviprdeava 119
                                    +  +    +e++    gvpv+g i r+++  
  gi|116754483|ref|YP_843601.1| 157 HADKATREIERYA---GVPVVGAIQRNDEMH 184
                                    9998888888887...**********99974 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 ?   12.7   0.0     2e-05      0.09       4      40 ..       8      45 ..       5      51 .. 0.84
   2 ?   -2.7   0.0       1.2   5.2e+03      82      99 ..      72      90 ..      65      92 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2e-05
                           MobB  4 ivg.ksgsGKTtLleklipelkarglrvgtiKhahhgf 40
                                   i+g +s sGKTt++  l+++l + +l+v + K a + +
  gi|116754483|ref|YP_843601.1|  8 IAGdRSSSGKTTIVAGLLSALVRMNLNVQAFKVAMDYI 45
                                   5541599***********************99887765 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.2
                           MobB 82 eellarl.sevDlvlvEGf 99
                                    e++++  +++D+ ++EG 
  gi|116754483|ref|YP_843601.1| 72 LEIFNHAsRDADIAVIEGV 90
                                   4566666356999999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); 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 0.22s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 3558.34
//
Query:       gi|116754484|ref|YP_843602.1|  [L=339]
Description: putative deoxyhypusine synthase [Methanosaeta thermophila PT]
Scores for complete 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-93  313.7   0.0    1.3e-93  313.5   0.0    1.0  1  DS        Deoxyhypusine synthase


Domain annotation for each model (and alignments):
>> DS  Deoxyhypusine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  313.5   0.0     7e-98   1.3e-93       1     287 [.      23     311 ..      23     312 .. 0.97

  Alignments for each domain:
  == domain 1  score: 313.5 bits;  conditional E-value: 7e-98
                             DS   1 ellesyekigfqatslgeaidilnkmrkdekctiflgltsnlissGlreiiadlvkeklvdvivtTaggieeDlikalgk 80 
                                    el++ ++++gfqa +lg++++++++m  ++++t+flgl+++++++Gl+e+ia+l+ +++vd++v+T++++ +Dl++ lg 
  gi|116754484|ref|YP_843602.1|  23 ELVSDMARMGFQAGQLGQSLRVWENML-SRDVTVFLGLAGAMVPAGLQEMIAYLISRRYVDCLVSTGANLFHDLCEGLGI 101
                                    699***********************5.789************************************************* PP

                             DS  81 ktylgdfelddeeLrekginRignllvpnenyckfedwvreildkleeeqkvwspselikelGkeindeeSilywAyknd 160
                                     +y g+  +dd++L+e +i+Ri +++v++ +++++++++++++ +l+++  + s++e+++ lG+e+  e+ il +Ay+++
  gi|116754484|ref|YP_843602.1| 102 MHYRGSSCADDAHLNECKIDRIFDVFVSEVELHRADKYISDLVMSLRTD-IMYSSREIMELLGREL-PETTILGAAYRAG 179
                                    **********************************************984.455*************.699********** PP

                             DS 161 ipvfcpaltDgslGdqlllfhsvkekkklkldivkDirelndialkakktgaiilGGGvpKhhilnanlm.......rng 233
                                    +p+f+pal+D+s+G++++++   ++ +++++d ++D++e+++i+ k+ +tg++++GGGvpK++i++++++       r g
  gi|116754484|ref|YP_843602.1| 180 VPIFVPALSDSSIGIGMVIAW--RNGHRVIVDQIRDVDEITQISEKSAETGVVFIGGGVPKNFIQQTKVIselmgtyRGG 257
                                    ***************999999..79999****************************************999**9*9989* PP

                             DS 234 adyavyittaqefdGslsgatldEavSwgkikaeaksvkvyaDaTivlPLlvaa 287
                                    + ya+++tt++++ G+lsg+t++EavSwgk+++ea+ ++v++DaTi++PL+v+a
  gi|116754484|ref|YP_843602.1| 258 HSYAIQYTTDTPHFGGLSGCTFSEAVSWGKVDKEARMAQVFSDATITVPLVVHA 311
                                    ****************************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); 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 0.20s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 2764.57
//
Query:       gi|116754485|ref|YP_843603.1|  [L=246]
Description: nucleotidyl transferase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-41  141.7   0.0    3.2e-41  141.5   0.0    1.0  1  NTP_transferase  Nucleotidyl transferase
    7.6e-14   52.4   0.0    8.5e-14   52.2   0.0    1.1  1  NTP_transf_3     MobA-like NTP transferase domain
    1.6e-06   28.0   0.0    6.6e-06   26.0   0.0    1.8  2  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
  ------ inclusion threshold ------
      0.039   13.8   0.0       0.05   13.4   0.0    1.2  1  Glycos_transf_2  Glycosyl transferase family 2


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.5   0.0   7.2e-45   3.2e-41       2     245 ..       5     238 ..       4     241 .. 0.95

  Alignments for each domain:
  == domain 1  score: 141.5 bits;  conditional E-value: 7.2e-45
                                    EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEES CS
                NTP_transferase   2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialep 81 
                                    +vI a GsGtRL P t++++k l+pv++k  +i+++++++  sgie+i +v++  h++ + ++l++g +fgv++ +++++
  gi|116754485|ref|YP_843603.1|   5 GVIPAAGSGTRLGPFTNAIPKELLPVGEK-AVIEHVVEAMRLSGIEDIAIVCS-PHKHGLCDYLGSGRRFGVNLVYVMQD 82 
                                    7999*************************.*****************777776.7889999******************* PP

                                    S--BGGHHHHHTHHHHTTSSE..EEEEETTEEEEST.THHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECTTSBEE CS
                NTP_transferase  82 egkgtAdAvalaaelledeksdelvlvLggDhlikd.ayeeavkkaiekaakgtvtfgivpveeateyGvieadeegrve 160
                                    e++g+ dAv+ a++++++++    ++vLg++ +  +  ++e++  + e++a  ++t+g+ +ve+ t+ G+i++++ + + 
  gi|116754485|ref|YP_843603.1|  83 ERRGLGDAVLAAENVIDESF----AVVLGDNFFHPKsFLSELISYHLERRA--DATLGVAEVEDVTRHGIIKPEG-DSIV 155
                                    *****************999....6********9997889***********..9******************998.5999 PP

                                    EEECS-SSHSH.CSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEEXSSHHHHH CS
                NTP_transferase 161 rfvEKPkeaka.selassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsDvGtldsll 239
                                    ++vEKP+ + a s+l + G Yvf +++++ + +  e+  rge ++td+++ ++++g+  l+   ++     DvGt+++l+
  gi|116754485|ref|YP_843603.1| 156 DIVEKPSPEMAfSNLGAIGMYVFSPDIFDAI-RETEPGYRGEIQLTDAVKVMIDRGRSILYRKIDGI--HIDVGTPKDLM 232
                                    ********9999*******************.67**************************9999996..5********** PP

                                    HHHHHH CS
                NTP_transferase 240 eanekl 245
                                    +ane +
  gi|116754485|ref|YP_843603.1| 233 RANEWY 238
                                    **9865 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 !   52.2   0.0   1.9e-17   8.5e-14       1     127 [.       5     140 ..       5     205 .. 0.80

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 1.9e-17
                                    EEEEEESS-TTTTT.....THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSHC.....HHHHHHTTCTS-EEE-TTS.S CS
                   NTP_transf_3   1 aviLAGGrSsRmgg.....dKallplggkpllervldalraagvdevvvvggde.....evlaalarlgvrvvededp.g 69 
                                    +vi A+G ++R+g      +K llp+g+k ++e+v++a+r +g++++ +v+ ++     + l   +r+gv +v+ ++   
  gi|116754485|ref|YP_843603.1|   5 GVIPAAGSGTRLGPftnaiPKELLPVGEKAVIEHVVEAMRLSGIEDIAIVCSPHkhglcDYLGSGRRFGVNLVYVMQDeR 84 
                                    6899*********445679*******************************988633333333344788999888866526 PP

                                    -SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSEE CS
                   NTP_transf_3  70 kgplaslaaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvptyeger 127
                                    +g + +++aa + +  ++ ++v+++D  + +++++ +l+  + +++ad++  ++e e 
  gi|116754485|ref|YP_843603.1|  85 RGLGDAVLAAENVI--DESFAVVLGDNFFHPKSFLSELISYHLERRADATLGVAEVED 140
                                    9**********988..8***********************998888888777666554 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 !   26.0   0.0   1.5e-09   6.6e-06       4      96 ..       6     106 ..       4     151 .. 0.75
   2 ?   -0.4   0.0      0.18   7.8e+02     178     216 ..     197     235 ..     177     241 .. 0.72

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 1.5e-09
                                    EEECTTSSCTT-...SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGG..CCEEEEE.--SSH CS
                           IspD   4 vipAAGsGkRmk...aglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllld..ksiqlva.GGdeR 77 
                                    vipAAGsG+R++   +  pK +l +  ++++eh v+a+   + ++ i +v s+++ +    l +     ++lv    deR
  gi|116754485|ref|YP_843603.1|   6 VIPAAGSGTRLGpftNAIPKELLPVGEKAVIEHVVEAMRL-SGIEDIAIVCSPHKHGLCDYLGSGrrFGVNLVYvMQDER 84 
                                    8*********96443689********************88.679**********99998888877552355553123444 PP

                                    H...HHHHHHHHTTSSTTSEEE CS
                           IspD  78 a...esVlnglkalegeakfVL 96 
                                        ++Vl++ ++++++ ++VL
  gi|116754485|ref|YP_843603.1|  85 RglgDAVLAAENVIDESFAVVL 106
                                    3233667777777666655554 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.18
                                    ---SSHHHHHHHTT--EEEEE--TTG----SHHHHHHHH CS
                           IspD 178 aeitDdaslvekiGlsvkvVeGeednlKittpeDlalAe 216
                                    ++ tD ++++   G s+   + +   + + tp+Dl++A+
  gi|116754485|ref|YP_843603.1| 197 IQLTDAVKVMIDRGRSILYRKIDGIHIDVGTPKDLMRAN 235
                                    567777777777777776666667788899999999984 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 ?   13.4   0.0   1.1e-05      0.05      55     131 ..      75     151 ..      60     217 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.1e-05
                                    TEEEEEESSS-HHHHHHHHHHHH--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-S CS
                Glycos_transf_2  55 rvrvirreenvGkagalnaglraatgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkr 131
                                    ++ ++ ++e++G++ a+ a+    +  + ++l +   +++ +l++l+ +  + +ad+ lg   + ++ ++ i ++++
  gi|116754485|ref|YP_843603.1|  75 NLVYVMQDERRGLGDAVLAAENVIDESFAVVLGDNFFHPKSFLSELISYHLERRADATLGVAEVEDVTRHGIIKPEG 151
                                    7889**************999999999********************************999988888877777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.21s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1948.58
//
Query:       gi|116754486|ref|YP_843604.1|  [L=79]
Description: putative glycosyl transferase, partial [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-10   39.8   0.0    3.8e-10   39.5   0.0    1.1  1  Glycos_transf_1  Glycosyl transferases group 1
    1.1e-07   32.4   0.0    1.6e-07   31.8   0.0    1.3  1  Glyco_trans_1_4  Glycosyl transferases group 1
    0.00011   22.5   0.0    0.00049   20.4   0.0    1.8  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 !   39.5   0.0   6.4e-14   3.8e-10     118     170 ..       4      56 ..       1      58 [. 0.95

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 6.4e-14
                                    -EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHHHHHHHH CS
                Glycos_transf_1 118 pviasnaggpaevvkdgetGllvkpnnaealaeairklledeelrerlgenar 170
                                    pvi+++a+g++e+v dge+G+lv+p ++ alae +++++ ++el  r+g ++r
  gi|116754486|ref|YP_843604.1|   4 PVITTDAPGCRETVIDGENGFLVPPRDVGALAETMERFVLEPELIGRMGAASR 56 
                                    9******************************************9999998877 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 !   31.8   0.0   2.7e-11   1.6e-07      93     130 ..       1      40 [.       1      44 [. 0.93

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 2.7e-11
                                    TT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHH CS
                Glyco_trans_1_4  93 aglpvVatdvggiaevv..gengllvppgdpealaeailr 130
                                    +++pv++td++g++e+v  geng+lvpp+d+ alae ++r
  gi|116754486|ref|YP_843604.1|   1 MARPVITTDAPGCRETVidGENGFLVPPRDVGALAETMER 40 
                                    689************999******************9987 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 !   20.4   0.0   8.2e-08   0.00049      23      84 ..       3      66 ..       1      74 [. 0.93
   2 ?    0.8   0.0      0.11   6.4e+02      11      22 ..      68      79 .]      66      79 .] 0.87

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 8.2e-08
                Glyco_trans_1_2 23 afaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarervlaehtyd 84
                                   ++++t+da+g +e + +g+ ++l+   d+  lae +++++ +pe++ ++++a r+ ++++++++
  gi|116754486|ref|YP_843604.1|  3 RPVITTDAPGCRETVIDGENGFLVPprDVGALAETMERFVLEPELIGRMGAASRRIAEERFDVR 66
                                   799***************************************************9999998765 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.11
                Glyco_trans_1_2 11 pnlrlfEaaacG 22
                                   +n r+ Ea++ G
  gi|116754486|ref|YP_843604.1| 68 INKRMMEAMGLG 79
                                   799******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       217  (0.0121033); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.32u 0.23s 00:00:00.55 Elapsed: 00:00:00.37
# Mc/sec: 642.39
//
Query:       gi|116754487|ref|YP_843605.1|  [L=633]
Description: hypothetical protein Mthe_1183 [Methanosaeta thermophila PT]
Scores for complete 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   0.1     0.0057   16.5   0.0    1.6  2  Peptidase_M10  Matrixin
  ------ inclusion threshold ------
        3.5    8.4   3.9        1.5    9.5   1.0    2.1  2  SRR            Seven Residue Repeat
        4.7    6.3   8.8         15    4.7   0.3    3.1  3  TolB_like      TolB-like 6-blade propeller-like


Domain annotation for each model (and alignments):
>> Peptidase_M10  Matrixin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       1.4   8.5e+03      18      37 ..     332     351 ..     310     361 .. 0.76
   2 !   16.5   0.0   9.5e-07    0.0057      84     124 ..     412     449 ..     369     491 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.4
                                    SXHHHHHHHHHHHHHHHHTT CS
                                    xxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M10  18 leeeevrkairrAfkvwsev 37 
                                    l++++ ++ai+ A ++w+++
  gi|116754487|ref|YP_843605.1| 332 LTAAQAQAAIAAAANTWDDA 351
                                    67788888888888888876 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 9.5e-07
                                    TTTEEEEETTS-EESSTS-.SSSEEHHHHHHHHHHHHTTBE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M10  84 lggdihfdddeqWtlgeekveqgvslflVaaHEiGHalGLe 124
                                    l++d+ ++   +W+++     +++++++Va+HE+GH++GL 
  gi|116754487|ref|YP_843605.1| 412 LESDVSYNTRYSWSTDG---VNHIDVQTVALHELGHTIGLG 449
                                    57888888888898875...589****************96 PP

>> SRR  Seven Residue Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1         3   1.8e+04       6      14 .]     405     413 ..     405     413 .. 0.81
   2 ?    9.5   1.0   0.00025       1.5       2      13 ..     463     474 ..     462     475 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3
                            SRR   6 VknaYeqLs 14 
                                    V+++Y+ L+
  gi|116754487|ref|YP_843605.1| 405 VDGYYSVLE 413
                                    899**9775 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00025
                            SRR   2 nfekVknaYeqL 13 
                                    ++++V+naY+++
  gi|116754487|ref|YP_843605.1| 463 DYDQVMNAYNDI 474
                                    79********98 PP

>> TolB_like  TolB-like 6-blade propeller-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.4    0.0039        23      38      59 ..     509     529 ..     496     541 .. 0.81
   2 ?    4.7   0.3    0.0025        15      39      60 ..     555     576 ..     538     588 .. 0.76
   3 ?    1.9   0.2     0.018   1.1e+02      39      59 ..     601     621 ..     582     629 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0039
                      TolB_like  38 gddffyaysypelqfvssfakr 59 
                                    g d+fy+ sype+qf +s++ r
  gi|116754487|ref|YP_843605.1| 509 G-DHFYTTSYPEVQFANSIGYR 529
                                    3.569999**********9976 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0025
                      TolB_like  39 ddffyaysypelqfvssfakrG 60 
                                     d+fy+ sype+qf +s++ r 
  gi|116754487|ref|YP_843605.1| 555 GDHFYTTSYPEVQFANSIGYRY 576
                                    3679999**********99775 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.018
                      TolB_like  39 ddffyaysypelqfvssfakr 59 
                                     d+fy+  ype+qf +s++ r
  gi|116754487|ref|YP_843605.1| 601 GDHFYTTNYPEVQFANSIGYR 621
                                    3669999**********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (633 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); 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: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 4415.48
//
Query:       gi|116754488|ref|YP_843606.1|  [L=289]
Description: transposase, IS4 family protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.2e-33  113.1   0.0    3.2e-31  107.9   0.0    2.2  2  DDE_Tnp_1_5  Transposase DDE domain
      9e-21   74.5   0.1    1.6e-20   73.7   0.1    1.4  1  DDE_Tnp_1    Transposase DDE domain


Domain annotation for each model (and alignments):
>> DDE_Tnp_1_5  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.9   0.0   3.6e-35   3.2e-31       2     111 ..      18     125 ..      17     126 .. 0.95
   2 ?    2.8   0.0     0.016   1.4e+02      40      67 ..     252     281 ..     246     287 .. 0.82

  Alignments for each domain:
  == domain 1  score: 107.9 bits;  conditional E-value: 3.6e-35
                    DDE_Tnp_1_5   2 kRGsltiwldeeaiaawkek...kkngkrgrpqvysdaaiqtcltvkvlfklplRqlqGfvqsllklaglellvpdystl 78 
                                    +RG  +++l+++++++w+e+    +++k+grp++y++++iq+c +++++++lp+Rql+Gf+q+l+ ++   ll++dystl
  gi|116754488|ref|YP_843606.1|  18 RRG--WFYLSTDFVNNWDEEllkMNKNKNGRPYRYPETFIQFCGLAYAFLHLPYRQLEGFIQALSGFVPG-LLAADYSTL 94 
                                    799..************9987745569******************************************9.99******* PP

                    DDE_Tnp_1_5  79 srraktlevkipvkrkskglhlvvdstGlkvlg 111
                                    ++r ++le++ip+ +++  l+++vdstG+kv++
  gi|116754488|ref|YP_843606.1|  95 WQRITNLELNIPIPDND--LVVAVDSTGMKVTN 125
                                    **************999..99**********97 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.016
                    DDE_Tnp_1_5  40 tcltvkvlfklplRql..qGfvqsllklag 67 
                                    ++  +k++f+ ++R++  +G+++ + ++ +
  gi|116754488|ref|YP_843606.1| 252 VFSAIKRIFGETVRATskEGMIREVRRMFT 281
                                    56789*********9855699999988876 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.7   0.1   1.8e-24   1.6e-20       5     200 ..     112     271 ..     108     285 .. 0.83

  Alignments for each domain:
  == domain 1  score: 73.7 bits;  conditional E-value: 1.8e-24
                      DDE_Tnp_1   5 evlivDattvrvpgtkedarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrprkgklvlaDa 84 
                                     v++vD+t ++v+  + ++r++++  + + ++k+hiavd +++ ++ ++it+  v d++ +k+ll+ +   k    l+D+
  gi|116754488|ref|YP_843606.1| 112 LVVAVDSTGMKVTNRGDWMRESHGVER-RGWIKVHIAVDVETRKPVTFEITDETVTDHEMVKPLLEDV---KLEDSLMDG 187
                                    699******************888666.79************************************99...89******* PP

                      DDE_Tnp_1  85 GYasaelldtleekgvd.yiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgdvyyvtntnsells 163
                                    +Y++++++d+++ekgvd + i+++kn+ ++        r +    +++  +  +++ +++                    
  gi|116754488|ref|YP_843606.1| 188 AYDKEGVFDFMKEKGVDmPGIKIRKNAIVKAG----SSRAEPVLEFMKYGYHSWKIVHGY-------------------- 243
                                    ****************9568899999988866....344445555555555555555555.................... PP

                      DDE_Tnp_1 164 aeevaelyrlRwqiErvFkwlkrkfgldrlryrglnr 200
                                             +Rw  E+vF+ +kr fg + +r+ ++++
  gi|116754488|ref|YP_843606.1| 244 --------GRRWAAESVFSAIKRIFG-ETVRATSKEG 271
                                    ........***************998.6666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 2246.63
//
Query:       gi|116754489|ref|YP_843607.1|  [L=354]
Description: periplasmic binding protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.3e-45  153.6   0.0    7.6e-45  153.3   0.0    1.1  1  Peripla_BP_2  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.3   0.0   4.3e-49   7.6e-45       2     235 ..      54     299 ..      53     302 .. 0.93

  Alignments for each domain:
  == domain 1  score: 153.3 bits;  conditional E-value: 4.3e-49
                                    EE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT....TS-BSBESSSB-HHHHHHH--SEEEE-GGG......GGGH CS
                   Peripla_BP_2   2 aslspsvteillalGatdkvvgvdtttsdpldadklee..aivevgadgeidvEklaalkPDlvilskgl...gltdede 76 
                                    ++l + +++   alGa d++vg d +t+d+ d+  l+e  ++++vg+  e+++Ek+a+lkPD+vi  + +   ++ + ++
  gi|116754489|ref|YP_843607.1|  54 VVLWSNPAKEMRALGAVDRIVGMDQSTKDEVDKGTLPEltNVPVVGTQEEPNYEKIAELKPDVVICLSAGyppEPDEVQK 133
                                    5666666667789**************************************************99655555*99999999 PP

                                    HHHHHHS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT...-EEEEEEEETTE...EEE CS
                   Peripla_BP_2  77 ellksgiptvivessntgeslkeqiralgellgledeaeklvaeidsklaaaksaidse..kpkpvlvfggade.ggyvv 153
                                    +l+  gi++v  ++  t e + ++i +lg +lg+e+eae++++++ s ++ +++ ++++   ++++++f ga +  +y  
  gi|116754489|ref|YP_843607.1| 134 KLEPFGIKVVGLDFYRT-EVWFDEISTLGRMLGKESEAEEYMSFFRSYYDLINQTVATIpdSDRKTVYFEGAKKyLTYGG 212
                                    99999************.******************************************99999*****9999445556 PP

                                    E-TTSTTTHHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEH......HHHT-S--HHHHT-SHHHHTSHHHH CS
                   Peripla_BP_2 154 agsnsyigdlldalgieniaaeskkseyeeisaEqilasdpdvifvsgr......aeadnktgleflkenpllaelpAvk 227
                                    ag +s+i  +++a+g++++++e  ++ + e+++E ++ ++pdvif  ++       +++ k + ++++++p+la+++Avk
  gi|116754489|ref|YP_843607.1| 213 AGYGSGIPNMIRAAGGKDLYPER-SELAFEVDPEDVARRNPDVIFKGTTlgwnaeSDEQFKSIRDEIMSRPELANTKAVK 291
                                    7889999****************.*****************************998889999****************** PP

                                    TT-EEEE- CS
                   Peripla_BP_2 228 ngrVyald 235
                                    ng+Vy + 
  gi|116754489|ref|YP_843607.1| 292 NGQVYVIS 299
                                    *****985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2631.39
//
Query:       gi|116754490|ref|YP_843608.1|  [L=369]
Description: transport system permease protein [Methanosaeta thermophila PT]
Scores for 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-91  305.3  35.1    4.9e-91  305.0  35.1    1.0  1  FecCD     FecCD transport family
  ------ inclusion threshold ------
        9.4    5.1  13.8        1.2    8.0   8.5    2.1  2  MMPL      MMPL 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 !  305.0  35.1   5.5e-95   4.9e-91       1     311 [.      44     362 ..      44     363 .. 0.98

  Alignments for each domain:
  == domain 1  score: 305.0 bits;  conditional E-value: 5.5e-95
                          FecCD   1 llllllllslllgavkispsevfeallgka......dsleaeivlelrlprvlaallvGaaLavaGallQtvtrNpLadP 74 
                                    +llll +ls ++g +k s++evf+++l++       d++ ++iv+ lrlpr+l+++++G +L+vaGa++Q+vtrNpL++P
  gi|116754490|ref|YP_843608.1|  44 ILLLLAILSACTGGAKESWTEVFHSILSRCipsidsDPFVESIVWHLRLPRILMGIVAGSGLGVAGAVMQAVTRNPLVSP 123
                                    578999*********************999**9*9999999*************************************** PP

                          FecCD  75 silGissgaalgavlallll..lgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsallsaltslll 152
                                     ++Giss+aa+ga +a++++  + + +++ ++l af++al   llv++++ + k++sp+ ++LaGia+++++++lt++l+
  gi|116754490|ref|YP_843608.1| 124 FTVGISSAAAFGASMAIMFGigYVGVGTYIIILSAFISALGCGLLVFFIS-RLKRSSPEVMVLAGIALTYFFGSLTAILQ 202
                                    ********************9999**************************.***************************** PP

                          FecCD 153 lllneealesilfwllGslsgaswskvllllvllllllllllllarkldll.algdetAkslGvnvervrllllllvall 231
                                    +++ne++l+++++w++G+lsga+w+k+ ++  ++ll++++++ ++ +l+++ + gde AkslG+nv++vr ++lll++++
  gi|116754490|ref|YP_843608.1| 203 FFANEQQLNAMVNWTFGTLSGADWHKLTIITGAFLLSMPVFIRFSWDLNIMfSGGDEAAKSLGINVAQVRNVALLLSSFI 282
                                    *************************************************98466899*********************** PP

                          FecCD 232 tavavalvGpigFvGLivPhiarllvgadhrkllplsallGallllladllarlllsptelpvgivtaliGapffiylll 311
                                    ta++v+++G+igFvGL++Ph+ r+++g+dhr llp+s+++G++l++ ad+++r++l+p+ +p+giv++++G+p+f+yl++
  gi|116754490|ref|YP_843608.1| 283 TAAIVCFTGIIGFVGLVAPHVGRMVLGSDHRFLLPASCVVGSILVIGADIVGRTILAPVIIPIGIVISFVGVPMFLYLMV 362
                                    ******************************************************************************97 PP

>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.2      0.12   1.1e+03     131     164 ..      18      51 ..       8      55 .. 0.69
   2 ?    8.0   8.5   0.00013       1.2     147     231 ..      99     180 ..      95     197 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.12
                           MMPL 131 aatladlrdasdrdlklievvtlvvilviLlivy 164
                                    a  ++  + +s+  +++i ++++  ++++Ll ++
  gi|116754490|ref|YP_843608.1|  18 ADRVNARQAYSEFVARKILFIAVSFAILLLLAIL 51 
                                    5555556677777778888888888888888776 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00013
                           MMPL 147 lievvtlvvilviLlivyrSlvaallplltvvvsllaalgl.vlilalllglelstfvlgllvvlliavGtDYallLvsR 225
                                    ++   +l v+ +++  v+r+++       tv++s +aa+g  ++i+  +  +++ t ++ l+ +++ a G    ++++sR
  gi|116754490|ref|YP_843608.1|  99 IVAGSGLGVAGAVMQAVTRNPLV---SPFTVGISSAAAFGAsMAIMFGIGYVGVGTYIIILS-AFISALGCGLLVFFISR 174
                                    66667788888889999998754...458*************************99988765.566799999******** PP

                           MMPL 226 yreela 231
                                    ++  + 
  gi|116754490|ref|YP_843608.1| 175 LKRSSP 180
                                    *98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       856  (0.0477439); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:02.03
# Mc/sec: 552.00
//
Query:       gi|116754491|ref|YP_843609.1|  [L=333]
Description: dienelactone hydrolase [Methanosaeta thermophila PT]
Scores for complete 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   67.2   0.0      9e-09   35.1   0.0    2.2  2  Peptidase_S9   Prolyl oligopeptidase family
    4.7e-11   42.4   0.0    3.2e-07   29.9   0.0    2.2  2  Hydrolase_4    Serine aminopeptidase, S33
    2.4e-08   34.9   0.0    3.2e-08   34.4   0.0    1.1  1  Abhydrolase_6  Alpha/beta hydrolase family
    7.3e-08   32.2   0.0    3.8e-05   23.4   0.0    3.1  2  DLH            Dienelactone hydrolase family
    9.4e-07   29.0   0.0    1.9e-05   24.7   0.0    2.1  1  BAAT_C         BAAT / Acyl-CoA thioester hydrolase C terminal
    1.7e-05   24.6   0.0     0.0013   18.5   0.0    2.1  2  Abhydrolase_1  alpha/beta hydrolase fold
    3.3e-05   23.8   0.1    0.00034   20.5   0.1    2.3  2  Abhydrolase_3  alpha/beta hydrolase fold
    0.00011   22.0   0.0    0.00057   19.6   0.0    1.9  1  Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
    0.00048   18.9   0.0    0.00097   17.9   0.0    1.6  1  AXE1           Acetyl xylan esterase (AXE1)
  ------ inclusion threshold ------
      0.019   14.8   0.0      0.045   13.5   0.0    1.5  2  Abhydrolase_2  Phospholipase/Carboxylesterase
      0.027   13.8   0.1       0.11   11.7   0.0    1.9  3  LIP            Secretory lipase


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 !   30.0   0.0   2.1e-10   3.4e-07      11     130 ..      76     186 ..      66     191 .. 0.77
   2 !   35.1   0.0   5.5e-12     9e-09     130     190 ..     233     295 ..     205     307 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 2.1e-10
                                    HCCT-EEEEE--TTSSTTHCHHHHTTSGGGGHHHHHHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHHHHHHH-GGG-S CS
                   Peptidase_S9  11 adrGyvvvvanirGsggyGeafhdagkrklgqnefdDfiaaaealakegyvdserlaitGgSyGGyltgaalnqrpdlFk 90 
                                    a +G++ +  + rG g+      d g+     ++++D +aa +al + ++vd+er+a++G S+G y++g ++  + ++ k
  gi|116754491|ref|YP_843609.1|  76 AREGFATFSWDRRGIGESEPPVFDGGYL----QDAEDAMAAYRALSSLDLVDPERIAVMGQSAGVYTAGLLAK-KENRPK 150
                                    5566666666666666666666665555....4789*********************************9999.888889 PP

                                    EEEEESE---CCCHHCSTTSTHH.HCCCC--TTTCHHHHHH CS
                   Peptidase_S9  91 aavaevpvvdvlrydsdtdllte.eymewgnpeeneegyke 130
                                    a + + + +   + +     ++  ++ e+ ++  ++e+ ++
  gi|116754491|ref|YP_843609.1| 151 AYILQGGLYRDYAKMMI---FNYqRVVEYATK--SPENLRW 186
                                    99999999877777766...666678787776..6666655 PP

  == domain 2  score: 35.1 bits;  conditional E-value: 5.5e-12
                                    HHHHH-CGGG--.---EEEEEEETT-SSS-THHHHHHHHHHH--S-S.EEEEEETTS-SSTTS CS
                   Peptidase_S9 130 elspyspldnvk.aypplLlihGlaDdrvppaealklvaaLqkkgkn.vlllifpdegHgvgk 190
                                    +l +ysp +++k +++p+L+ihG  D +vp++ a+++ + L+++g++ v+l+i pd++H++++
  gi|116754491|ref|YP_843609.1| 233 YLPEYSPKNQFKyIQKPVLVIHGACDLNVPVEDAFMIEQDLKEHGNKnVELVIIPDADHSFQQ 295
                                    6889999999889********************************999***********8875 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0   1.9e-10   3.2e-07      20     119 ..      68     167 ..      65     229 .. 0.81
   2 !   10.4   0.0   0.00017      0.27     186     233 ..     242     292 ..     238     295 .. 0.89

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 1.9e-10
                    Hydrolase_4  20 yaelaeaLaaqGfavyalDhrGhGrse...gkrghvpsfddyvdDlaafvekvkeehpelplfllGhSmGGliallyllr 96 
                                    + e+ ++La++Gfa++ +D rG G+se      g++++ +d ++  +a+ + +    pe+ + ++G+S G ++a l++++
  gi|116754491|ref|YP_843609.1|  68 FLEISKRLAREGFATFSWDRRGIGESEppvFDGGYLQDAEDAMAAYRAL-SSLDLVDPER-IAVMGQSAGVYTAGLLAKK 145
                                    67899**********************7765567778888877777777.4555555555.9********9999999977 PP

                    Hydrolase_4  97 ypdkvaglilsaPalkikaklka 119
                                    + +  ++ il + +++  ak+ +
  gi|116754491|ref|YP_843609.1| 146 ENR-PKAYILQGGLYRDYAKMMI 167
                                    666.79******99998888733 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00017
                    Hydrolase_4 186 raakitlPllllhGeaDkvvdpeas...relyerlgskdktlklypglyHe 233
                                    + + i+ P+l++hG+ D  v+ e++   ++ +++ g k+++l ++p + H+
  gi|116754491|ref|YP_843609.1| 242 QFKYIQKPVLVIHGACDLNVPVEDAfmiEQDLKEHGNKNVELVIIPDADHS 292
                                    5566889******************9998889999999**********997 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.0     2e-11   3.2e-08       1     217 [.      38     302 ..      38     303 .. 0.65

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 2e-11
                                    EEEE--............GC.....G...CHHHH.HHHHCCTCEEEEE--TTSTS-GGCS--HHHCHHHHHHHCCTT... CS
                  Abhydrolase_6   1 vlllHG............agssassW...lvapL.aallaagvhvlapDlpGhGrsdpppldledladlaalldelaa.. 62 
                                    vl++HG             + ++ ++   ++ ++  +l+++g+++++ D++G G+s+pp +d   l+d +++ ++ +a  
  gi|116754491|ref|YP_843609.1|  38 VLMIHGsleqdrdgnllnRPDGRPVFkknFFLEIsKRLAREGFATFSWDRRGIGESEPPVFDGGYLQDAEDAMAAYRAls 117
                                    6788886666665555553344566654323455444555559***********66666655555888888777777778 PP

                                    ......TTSEEEEEETCHHHHHHHHHHCC......EE.EEES-..----TTT...S----TTHHHHHHTT-CCCCHCCH. CS
                  Abhydrolase_6  63 .....gggpvvlvGHSlGGalalaaapla....lvvg.vlldppptalpagl...laaalelllallallrllawlsre. 128
                                         ++ ++ ++G S G + a +   la    +  + +l  +    +++     +  + ++++ ++++   l+w+ ++ 
  gi|116754491|ref|YP_843609.1| 118 sldlvDPERIAVMGQSAGVYTAGL---LAkkenRPKAyILQGG---LYRDYAkmmIFNYQRVVEYATKSPENLRWVEENd 191
                                    888899999*********888888...5555565455577777...5555555544444444445555555589997777 PP

                                    ............S-HSCCCCHHH....C.CCCHCHCCCGHHHHCCHHCHTTCCHHTT-TTGCEEE.CTT-C........H CS
                  Abhydrolase_6 129 ............plprlfladed....a.daawrarlarlaallaglgllpaaawadlpvpllvl.ggeDp........l 182
                                                ++ r ++++++    +   +wr r+++ + l  +        ++ +  p+lv+ g+ D         +
  gi|116754491|ref|YP_843609.1| 192 ilglviglnlqsLMERAMMGEVEhlfnYkGKTWRIRHDPICYLPEYSP---KNQFKYIQKPVLVIhGACDLnvpvedafM 268
                                    777888888887666677777775443157888888877775555444...66777777777776555555323322265 PP

                                    HHHCHHCCCHSTTEEETCE...SSS-HHH.HSHHHH CS
                  Abhydrolase_6 183 vprllerllaqagarlpvvlpgaGHlphl.eepdev 217
                                    + + l++++    ++l v++p+a+H++++ +ep+e+
  gi|116754491|ref|YP_843609.1| 269 IEQDLKEHGN-KNVEL-VIIPDADHSFQQiAEPAEL 302
                                    5566777777.88888.********66666999775 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.016        26      28      47 ..      67      86 ..      62     157 .. 0.56
   2 !   23.4   0.0   2.3e-08   3.8e-05     136     215 ..     239     331 ..     230     333 .] 0.81

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.016
                            DLH 28 nikdiserlaeeGYvalaPd 47
                                   ++ +is+rla+eG++ +  d
  gi|116754491|ref|YP_843609.1| 67 FFLEISKRLAREGFATFSWD 86
                                   55677777777777776533 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 2.3e-08
                            DLH 136 eleeaakikapilalfgeeDefipadevekleealkaa.nvdlelkvYpgagHaFandsre............syneeaa 202
                                    + ++ + i++p+l+++g  D  +p +++  +e+ lk++ n+++el++ p+a+H+F +  ++            s++    
  gi|116754491|ref|YP_843609.1| 239 PKNQFKYIQKPVLVIHGACDLNVPVEDAFMIEQDLKEHgNKNVELVIIPDADHSFQQIAEPaelrlkerisleSFRRPYR 318
                                    66778889***************************9873689*************9987776777777777776666666 PP

                            DLH 203 edawervlelfkq 215
                                    e+ + +v++++k+
  gi|116754491|ref|YP_843609.1| 319 EEYFLAVVSFLKR 331
                                    6666666666665 PP

>> BAAT_C  BAAT / Acyl-CoA thioester hydrolase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   1.1e-08   1.9e-05       9     163 ..     112     293 ..     110     300 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.1e-08
                                    HHHHHHCSTTB--SSEEEEEETHHHHHHHHHHHHSSSEEEEEEES--SB--SSEEEETTE..EE----B-GGG-EE.... CS
                         BAAT_C   9 ainyllrhpkvkkdkigllGiSkGgelalllasflkkisavvlingsavvvegklvykdeskvlpelklsmeklkv.... 84 
                                    a++ l++   v  ++i+++G+S G  +a lla + + ++a +l  g    +++  +++++ +v+++ ++s e+l +    
  gi|116754491|ref|YP_843609.1| 112 AYRALSSLDLVDPERIAVMGQSAGVYTAGLLAKKENRPKAYILQGGLYRDYAKMMIFNYQ-RVVEYATKSPENLRWveen 190
                                    5667888899999*****************************998888888888888877.9****************** PP

                                    ..............................-TTS-EE-TT-B--TTTGGGCCCB--GGG--SEEEEEEETT-SSS-HHHH CS
                         BAAT_C  85 ..............................nknglldivdvlallkeklaekalipvekakgpillvvgedDknwpSkes 134
                                                                   k  ++++  +  l+    ++    ++  ++ p+l++ g  D n+p ++ 
  gi|116754491|ref|YP_843609.1| 191 dilglviglnlqslmerammgevehlfnykGKTWRIRHDPICYLP----EYSPKNQFKYIQKPVLVIHGACDLNVPVEDA 266
                                    *****************9999666655432222222222233333....33333457789****************8887 PP

                                    HHHHHHHHHCTT--.--EEEEETTB-S-- CS
                         BAAT_C 135 aekaserLkkagkkvevqlltYpkaGHli 163
                                      ++++ Lk++g+k +v+l++ p+a H +
  gi|116754491|ref|YP_843609.1| 267 F-MIEQDLKEHGNK-NVELVIIPDADHSF 293
                                    7.************.**********9987 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   7.7e-07    0.0013       1     115 [.      36     168 ..      36     189 .. 0.72
   2 ?    4.3   0.0     0.017        27     195     252 ..     237     293 ..     199     295 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 7.7e-07
                                    SEEEEE-STTT.................CGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHH CS
                  Abhydrolase_1   1 pvlvilhGlpg.................ssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddl 63 
                                    p+++++hG ++                   + + e  + + La++gf ++  D rG g+S+p+       y + + +d +
  gi|116754491|ref|YP_843609.1|  36 PAVLMIHGSLEqdrdgnllnrpdgrpvfKKNFFLE--ISKRLAREGFATFSWDRRGIGESEPPVFD--GGY-LQDAEDAM 110
                                    56777777777766665555554444333334777..88999999*******************96..444.33344444 PP

                                    H...HH..HHHCTTSSEEEEEETHHHHHHHHHHHHHGGGEEEEEEESE..CSSCCHHHH CS
                  Abhydrolase_1  64 d...ri..ldalgddkltlvGhSmGGmialayaaeyperVkalvllga..idpaaslie 115
                                        ++  ld  + ++++++G+S G  +a  +a +  +r ka +l g+   d+a ++i 
  gi|116754491|ref|YP_843609.1| 111 AayrALssLDLVDPERIAVMGQSAGVYTAGLLAKK-ENRPKAYILQGGlyRDYAKMMIF 168
                                    44534478*****************9999999887.66778888888855555555444 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.017
                                    CCHHHHHHHHHCTHHHHSEEEEEEETTCSSSCHHHHHHHHHCHTS.....EEEEEEETCSSSH CS
                  Abhydrolase_1 195 tdsaklllrlrelknvlaptlvisgtsDplvppkaledlaqllpk.....krlvvisdagHla 252
                                    +   + +        + +p+lvi+g+ D  vp +    ++q+l++     ++lv+i+da H  
  gi|116754491|ref|YP_843609.1| 237 YSPKNQFKY------IQKPVLVIHGACDLNVPVEDAFMIEQDLKEhgnknVELVIIPDADHSF 293
                                    333333344......444********9999999777666666333355569********9976 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       3.6   5.9e+03      38      57 ..      20      39 ..      12      45 .. 0.78
   2 !   20.5   0.1   2.1e-07   0.00034      49     210 ..     106     294 ..     101     295 .. 0.58

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.6
                                   --TTTS-TTHHHHHHHHHHH CS
                  Abhydrolase_3 38 rlAPehpfPaavedalaalr 57
                                   rlA   ++Pa ++d   a+ 
  gi|116754491|ref|YP_843609.1| 20 RLAGVLRYPAGIKDPAPAVL 39
                                   78888899999999776665 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 2.1e-07
                                    HHHHHHHHHHHHHTHHHHTETTCEEEEEEETHHHHHHHHHHHHHHHTT---............EEEEEEESE..-SSTSS CS
                  Abhydrolase_3  49 vedalaalrwlaeqawelgadpsrivlaGdSaGGnlaaavalrardegepk............vagqvliyP..vtdler 114
                                     eda+aa+r l +      +dp+ri+++G+SaG   a  +a   ++e++pk             + ++  y   v + ++
  gi|116754491|ref|YP_843609.1| 106 AEDAMAAYRALSSL---DLVDPERIAVMGQSAGVYTAGLLA---KKENRPKayilqgglyrdyAKMMIFNYQrvV-E-YA 177
                                    79*********999...57**************65555444...5555455566777888877444444444421.1.23 PP

                                    TTSHHHHHCHHTTTSSSS..........CHHHHHHHHHHHS.S...GGGGGSTTTSGGGC..S-.SST.---EEEEEETT CS
                  Abhydrolase_3 115 tesesikkaeeladgpll..........traaldlfwrlyl.p...eadrddplasplla..ed.lsg.lpptlvvvaef 176
                                    t+s++  +  e++d   l          +ra++ ++  l+  +      r+dp +       ++ ++   +p+lv+ + +
  gi|116754491|ref|YP_843609.1| 178 TKSPENLRWVEENDILGLviglnlqslmERAMMGEVEHLFNyKgktWRIRHDPICYLPEYspKNqFKYiQKPVLVIHGAC 257
                                    33333322222222111222333322226777777777766432322334466554443334224665467899999999 PP

                                    -TTH..HHHHHHHHHHHHTT.--EEEEEETTEETTGG CS
                  Abhydrolase_3 177 Dplr..degeayaerlraag.vevelieyegmvHgfa 210
                                    D+    +++ +  + l+++g ++vel+ ++++ H+f+
  gi|116754491|ref|YP_843609.1| 258 DLNVpvEDAFMIEQDLKEHGnKNVELVIIPDADHSFQ 294
                                    8765115666677888875426799999999999986 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 !   19.6   0.0   3.5e-07   0.00057      52     262 ..      60     285 ..      19     292 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.5e-07
                                    H..............HHHTT-EEEEEE-TTSTTS-S.---TTTTTHHHHHHHHHHHHHHC.TTEEEEEEEEEECHHHHHH CS
                  Peptidase_S15  52 v..............fvarGYavVvqdvrGtggSeG.eftvgdsdeaedgadvidWlakq.pwsnGkVgmtGiSYlGttq 115
                                                   ++++G+a    d rG g+Se  +f+ g  ++aed+ ++ + l         +++++G S + +t+
  gi|116754491|ref|YP_843609.1|  60 RpvfkknffleiskrLAREGFATFSWDRRGIGESEPpVFDGGYLQDAEDAMAAYRALSSLdLVDPERIAVMGQSAGVYTA 139
                                    0334445677777779*******************725666699***************989999*********999999 PP

                                    HHHCTT--TTEEEEEEECE-S-TCCC.CSECTTEEBCCHHHHHHHHHCCCCHHTSSS-STTHHHHHHHHHHCHCCCCCCT CS
                  Peptidase_S15 116 llaaatgvpalkaivpeaaisdlydd.yyregGlvrapgglswedldllaealtsrradegdalkaaaryeaasdellae 194
                                     l+a+ +  + ka + + ++   y + +++++  v+  ++ s      l  + ++     g  +  + +   +++ +++e
  gi|116754491|ref|YP_843609.1| 140 GLLAK-KENRPKAYILQGGLYRDYAKmMIFNYQRVVEYATKSP---ENLRWVEENDI--LGLVIGLNLQ-SLMERAMMGE 212
                                    88888.9999999999999777777667777766666555555...33333333333..3333333333.3344555555 PP

                                    THHH.THHHHCCCC--SSSHHHHTT-HHHHHCT--S-EEEEEECCSSTTC.CHHHHHHHHHCCTT-...EEEE CS
                  Peptidase_S15 195 ldrq.tpveselletgdydafWkdrnlsedadkvkapvllvgGwnDwnvk.ngaiklyealkapgv...klil 262
                                    ++   +   +++  + d   +  + +++++++ ++ pvl+++G  D nv  + a+ + + lk++g    +l++
  gi|116754491|ref|YP_843609.1| 213 VEHLfNYKGKTWRIRHDPICYLPEYSPKNQFKYIQKPVLVIHGACDLNVPvEDAFMIEQDLKEHGNknvELVI 285
                                    55553333457777888999999999999*******************9999999999999999887776665 PP

>> AXE1  Acetyl xylan esterase (AXE1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0     6e-07   0.00097     141     204 ..      88     155 ..      12     185 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 6e-07
                                    TTTTSTTT-HHHHHHH....HHHHHHHHHHTSTTEEEEEEEEEEETHHHHHHHHHHHH-SS-SEEEEE CS
                           AXE1 141 rGlldkeklyyrrvfl....DavrlveivaslpevDeeRvavlGasqGGalalavaalekrikavvad 204
                                    rG+ + e   +   +l    Da+ + ++++sl+ vD+eR+av+G+s G   a   a  e+r+ka + +
  gi|116754491|ref|YP_843609.1|  88 RGIGESEPPVFDGGYLqdaeDAMAAYRALSSLDLVDPERIAVMGQSAGVYTAGLLAKKENRPKAYILQ 155
                                    55555555555555544444899999*********************988877777777777776544 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       4.2   6.9e+03     102     119 ..     122     139 ..     116     154 .. 0.75
   2 ?   13.5   0.0   2.8e-05     0.045     147     202 ..     239     294 ..     227     297 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 4.2
                                    --GGGEEEEEETHHHHHH CS
                  Abhydrolase_2 102 ipssriiigGFSqGaala 119
                                    ++ +ri+++G S G   a
  gi|116754491|ref|YP_843609.1| 122 VDPERIAVMGQSAGVYTA 139
                                    788999999999996655 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 2.8e-05
                                    TTTS-GGGGG-EEEEEEETT-SSS-HHHHHHHHHHHHTTS-.GEEEEEETT--SS-- CS
                  Abhydrolase_2 147 essatavtkklpilqiHgeeDpvvplalgkaakevlkkllk.kvelksyeglaHsid 202
                                    ++++++   + p+l iHg +D  vp+  + + ++ lk+  + +vel+++++  Hs  
  gi|116754491|ref|YP_843609.1| 239 PKNQFKYI-QKPVLVIHGACDLNVPVEDAFMIEQDLKEHGNkNVELVIIPDADHSFQ 294
                                    55555555.679***************************999************975 PP

>> LIP  Secretory lipase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       2.2   3.6e+03      53      86 ..     111     140 ..      74     155 .. 0.67
   2 ?   -1.5   0.0      0.75   1.2e+03     240     276 ..     151     189 ..     143     190 .. 0.77
   3 ?   11.7   0.0     7e-05      0.11     215     264 ..     247     296 ..     237     309 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.2
                            LIP  53 dsiraalksekvtgiksdakvalwGYSgGslAsa 86 
                                     +     ++ ++  + +  ++a++G S G   ++
  gi|116754491|ref|YP_843609.1| 111 AA----YRALSSLDLVDPERIAVMGQSAGVYTAG 140
                                    33....3344444566778889999888876655 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.75
                            LIP 240 nwcdkgiaslefaedlssg..HlaetlvgapaaltWitd 276
                                     +  +g+   ++a+ ++ +   ++e  +  p  l+W+++
  gi|116754491|ref|YP_843609.1| 151 AYILQGGLYRDYAKMMIFNyqRVVEYATKSPENLRWVEE 189
                                    566667767778888876645899999*********985 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 7e-05
                            LIP 215 qiPvlvyhgvidelipikdakklaknwcdkgiaslefaedlssgHlaetl 264
                                    q Pvlv+hg +d  +p++da  ++++  ++g +++e +    ++H  +++
  gi|116754491|ref|YP_843609.1| 247 QKPVLVIHGACDLNVPVEDAFMIEQDLKEHGNKNVELVIIPDADHSFQQI 296
                                    78**********************************99877777766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        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):              11  [number of targets reported over threshold]
# CPU time: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2293.86
//
Query:       gi|116754492|ref|YP_843610.1|  [L=534]
Description: transposase [Methanosaeta thermophila PT]
Scores for complete 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-44  148.6   0.0    1.7e-43  147.4   0.0    1.7  1  DUF4277    Domain of unknown function (DUF4277)
    3.3e-12   46.5   0.4    3.9e-11   43.0   0.4    2.1  1  DDE_Tnp_1  Transposase DDE domain


Domain annotation for each model (and alignments):
>> DUF4277  Domain of unknown function (DUF4277)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.4   0.0   1.9e-47   1.7e-43       2     109 .]       4     111 ..       3     111 .. 0.98

  Alignments for each domain:
  == domain 1  score: 147.4 bits;  conditional E-value: 1.9e-47
                        DUF4277   2 evksldhlglvaglidelglaelidelipkksqekvsagevvkalilngLgfvsrpLylfpeffedkplerLlgegveae 81 
                                    +++sldhlg+va+++d+lg+a++id+++pk +q+k++++ +vka++lngLgfv ++Lylfpef+e++p+erLlg+gv+a+
  gi|116754492|ref|YP_843610.1|   4 DTRSLDHLGIVAAVFDRLGIADVIDSRMPKLRQHKLEHSVIVKAMVLNGLGFVGQRLYLFPEFYERLPVERLLGDGVNAS 83 
                                    6899**************************************************************************** PP

                        DUF4277  82 hlnddrlgrtLDklyeagvtklfteial 109
                                    +lndd++grtLD++ye+g+t+lf+eial
  gi|116754492|ref|YP_843610.1|  84 DLNDDAIGRTLDAIYEQGATDLFNEIAL 111
                                    **************************96 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   0.4   4.4e-15   3.9e-11      35     213 ..     162     450 ..     124     451 .. 0.86

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 4.4e-15
                      DDE_Tnp_1  35 gyklhiavdtrsglilsvvitpgnvhdskglkq.lldelrpr....kgklvlaDaGYasaelldtleekgvdyiirlkkn 109
                                     + l +++++  g++l ++ ++gn +d++++++ +l  ++      +  +++aD++  ++++++ l  + +++i r++  
  gi|116754492|ref|YP_843610.1| 162 QFVLSLVTNQD-GIPLFAKAHSGNASDRNTIIEsFL-KIKSGlnleDCAYYIADSAVYTEPNIRMLG-REMKWITRVPAT 238
                                    44566777777.9********************644.4555577889999******888***99999.9********777 PP

                      DDE_Tnp_1 110 tklyrkgaeskrrgrlrkhdrnkiltksqkrrnk.............................................. 143
                                     k+ +   +s  ++ ++++ r+++++++    +                                               
  gi|116754492|ref|YP_843610.1| 239 IKECEMLLDSDVEMVECRDARYRCFSTTSDYGGVqqkwvlyqsepmrdlkaerfenhlekdgtkarrslaklkrreface 318
                                    7777777777788888888888888888887777888888888888888999999999999999999999999999**** PP

                      DDE_Tnp_1 144 .............................................................skkekgdvyyvtntnsell 162
                                                                                                 +k+    + ++  tn+   
  gi|116754492|ref|YP_843610.1| 319 adalketelwardhplyrfshislkkvckradkkrgrpkngeklieiyfidadieldqekvEKTKSRLGRFIIATNDLNI 398
                                    ************************************************************999999999*********** PP

                      DDE_Tnp_1 163 saeevaelyrlRwqiErvFkwlkrk.fgldrlryrglnrveaqllllllaln 213
                                    ++ ++  +y+ + ++Er F++lk+k f+   +++++ +r+ea ++++ l+l+
  gi|116754492|ref|YP_843610.1| 399 DPDTLLSYYKGQQEVERGFRFLKDKsFRVAEVYLKKEERIEALAMIMVLSLM 450
                                    ***********************************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (534 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       680  (0.0379274); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); 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: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 3594.14
//
Query:       gi|116754493|ref|YP_843611.1|  [L=423]
Description: acyl-CoA thioester hydrolase/bile acid-CoA amino acid N-acetyltransferase [Methanosaeta thermophila PT]
Scores for complete 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-41  141.8   0.0    3.6e-41  141.4   0.0    1.2  1  BAAT_C           BAAT / Acyl-CoA thioester hydrolase C termin
    3.5e-26   91.7   0.0    5.8e-26   91.0   0.0    1.4  1  Bile_Hydr_Trans  Acyl-CoA thioester hydrolase/BAAT N-terminal
    8.9e-06   25.4   0.0    0.00071   19.2   0.0    2.3  2  DLH              Dienelactone hydrolase family
    1.7e-05   23.7   0.1    0.00015   20.6   0.0    2.0  2  AXE1             Acetyl xylan esterase (AXE1)
    0.00026   20.5   0.0      0.017   14.6   0.0    2.7  3  Peptidase_S9     Prolyl oligopeptidase family
     0.0022   17.9   0.0     0.0034   17.3   0.0    1.3  1  Abhydrolase_3    alpha/beta hydrolase fold
     0.0063   16.2   0.0      0.018   14.7   0.0    1.8  2  Abhydrolase_1    alpha/beta hydrolase fold
     0.0063   16.1   0.0     0.0095   15.6   0.0    1.3  1  Peptidase_S15    X-Pro dipeptidyl-peptidase (S15 family)
  ------ inclusion threshold ------
      0.019   14.7   0.0      0.032   13.9   0.0    1.3  1  Esterase         Putative esterase
      0.064   12.5   0.0        5.8    6.0   0.0    2.1  2  Abhydrolase_7    Abhydrolase family
       0.11   12.1   0.0        0.4   10.2   0.0    1.8  2  DUF2974          Protein of unknown function (DUF2974)


Domain annotation for each model (and alignments):
>> BAAT_C  BAAT / Acyl-CoA thioester hydrolase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.4   0.0   2.2e-44   3.6e-41       1     212 [.     193     422 ..     193     423 .] 0.88

  Alignments for each domain:
  == domain 1  score: 141.4 bits;  conditional E-value: 2.2e-44
                                    EECHHHHHHHHHHHCSTTB--SSEEEEEETHHHHHHHHHHHHSSSEEEEEEES--SB--SSEEEETTE........EE-- CS
                         BAAT_C   1 vdleYFeeainyllrhpkvkkdkigllGiSkGgelalllasflkkisavvlingsavvvegklvykdes......kvlpe 74 
                                    +++e + +ai++l+++p v++d+ig++G S+Ggelall as++++i+avv +++s v+ +g   + d+       +++p+
  gi|116754493|ref|YP_843611.1| 193 IPVETVGKAIEWLNQQPLVARDHIGIVGASRGGELALLAASIYPEIKAVVGYTPSGVIWSGIGENPDAPawtyqgRAFPY 272
                                    5788899****************************************************99888887778899999**** PP

                                    --B-GGG-EE..............-TTS-EE-TT-B--TTTGGGCCCB--GGG--SEEEEEEETT-SSS-HHHHHHHHHH CS
                         BAAT_C  75 lklsmeklkv..............nknglldivdvlallkeklaekalipvekakgpillvvgedDknwpSkesaekase 140
                                    lk  m++ +                ++  l++ ++++++     ++a ipve++k+++ll+    D +wpS+   ++ ++
  gi|116754493|ref|YP_843611.1| 273 LKAMMSEEQGrqfleaqkngtpylDAPSFLYSLEMQRSR----IDEATIPVENSKAAFLLIGNPGDGVWPSDMLSQISID 348
                                    **9999987789999988777555555555555555555....45689******************************** PP

                                    HHHCTT--.--EEEEETTB-S---S.TT-----EEEE.TTTTEEEE--B-HHHHHHHHHHHHHHHHHHHHHH-X CS
                         BAAT_C 141 rLkkagkkvevqlltYpkaGHliep.Pyfplceavla.klvgekvlyGGetkahakAqedsWkkilkFlkkhla 212
                                    rL+++ ++ ++qll+Y+++GH++ p Py p++ + +    v+     GG  +  a+A+edsW ++++Flk+ l+
  gi|116754493|ref|YP_843611.1| 349 RLRAHDHPRQYQLLSYDQGGHMLIPyPYYPTTMRQFYlPTVDVWEGLGGTAEGAARAAEDSWPRVVEFLKRELE 422
                                    *********************87655****98776551556666899***********************9985 PP

>> Bile_Hydr_Trans  Acyl-CoA thioester hydrolase/BAAT N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.0   0.0   3.6e-29   5.8e-26       2     125 ..      14     129 ..      13     130 .. 0.88

  Alignments for each domain:
  == domain 1  score: 91.0 bits;  conditional E-value: 3.6e-29
                Bile_Hydr_Trans   2 epvkikvsglppgqkvtlrasltdekgelfeSfAvykadekGevdlsrdaplgGsYtgvepmGLfwsmkpekekkrrllk 81 
                                    +pv+i++sgl  gq  tlr s +d  g+++ S+A ++ad++G++d srdap++GsY+g+++ GLfwsm  ++  +  ++ 
  gi|116754493|ref|YP_843611.1|  14 DPVSIRASGLDAGQIATLRVSGQDVLGNTWYSEASFRADDAGTIDTSRDAPVEGSYHGIDQAGLFWSMSVNQTGE--FV- 90 
                                    599*****************************************************************7766665..33. PP

                Bile_Hydr_Trans  82 kdvs.tpfvvtlevlekkekegkelasatveRlfvapgVkrieVr 125
                                       s  p++ +l+v     ++g+e++s++v+R+ ++ + +r++V+
  gi|116754493|ref|YP_843611.1|  91 ---SaFPVIHNLTVG--LYVDGREVDSRVVQRI-AQIDLERENVT 129
                                    ...225666666665..5588************.88999999887 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   4.4e-07   0.00071      83     130 ..     199     246 ..     187     263 .. 0.90
   2 ?    3.8   0.0     0.023        37     199     216 ..     403     420 ..     392     421 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 4.4e-07
                            DLH  83 kaavaylksvpevstkkvgvvGfCmGGalalllaaevpevdaavafYG 130
                                      a+++l+++p v  + +g+vG   GG+lall a+  pe++a+v++ +
  gi|116754493|ref|YP_843611.1| 199 GKAIEWLNQQPLVARDHIGIVGASRGGELALLAASIYPEIKAVVGYTP 246
                                    5799*****************************************977 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.023
                            DLH 199 eeaaedawervlelfkqv 216
                                    + aaed+w rv+e++k+ 
  gi|116754493|ref|YP_843611.1| 403 ARAAEDSWPRVVEFLKRE 420
                                    789************985 PP

>> AXE1  Acetyl xylan esterase (AXE1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.11   1.8e+02      67      96 ..     130     160 ..     113     172 .. 0.83
   2 !   20.6   0.0   9.1e-08   0.00015     160     206 ..     200     246 ..     192     249 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.11
                                    EEEEEEEEEES.SSSSEEEEEEEE-TT--.G CS
                           AXE1  67 arikaklvlPkekeeklPavvefhGYegs.r 96 
                                     +i + ++ Pke  e+ Pa++   G eg+ +
  gi|116754493|ref|YP_843611.1| 130 DPIVGVFLIPKEITEPTPAIIVLGGSEGGyK 160
                                    579999**************99888777644 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 9.1e-08
                                    HHHHHHHTSTTEEEEEEEEEEETHHHHHHHHHHHH-SS-SEEEEES- CS
                           AXE1 160 rlveivaslpevDeeRvavlGasqGGalalavaalekrikavvadyP 206
                                    +++e + + p v  + ++++Gas GG lal +a++ ++ikavv + P
  gi|116754493|ref|YP_843611.1| 200 KAIEWLNQQPLVARDHIGIVGASRGGELALLAASIYPEIKAVVGYTP 246
                                    689999999**********************************9887 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.049        80      65      82 ..     148     165 ..     122     171 .. 0.84
   2 !   14.6   0.0     1e-05     0.017      50      85 ..     200     235 ..     189     248 .. 0.87
   3 ?   -2.7   0.0       2.1   3.5e+03     165     187 ..     346     370 ..     313     373 .. 0.64

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.049
                                    GEEEEEETHHHHHHHHHH CS
                   Peptidase_S9  65 rlaitGgSyGGyltgaal 82 
                                     +++ GgS GGy  g+a 
  gi|116754493|ref|YP_843611.1| 148 AIIVLGGSEGGYKEGWAS 165
                                    57899*******999985 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1e-05
                                    HHHHHHHHTTS--GGGEEEEEETHHHHHHHHHHHH- CS
                   Peptidase_S9  50 aaaealakegyvdserlaitGgSyGGyltgaalnqr 85 
                                    +a+e+l+++ +v +++++i G+S GG l++ a+   
  gi|116754493|ref|YP_843611.1| 200 KAIEWLNQQPLVARDHIGIVGASRGGELALLAASIY 235
                                    899*************************99998755 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 2.1
                                    HHHHHH--S-S..EEEEEETTS-SS CS
                   Peptidase_S9 165 lvaaLqkkgkn..vlllifpdegHg 187
                                     +++L+ ++++  ++ll + + gH 
  gi|116754493|ref|YP_843611.1| 346 SIDRLRAHDHPrqYQLLSYDQGGHM 370
                                    4688887776667999999999995 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   2.1e-06    0.0034      19     146 ..     162     287 ..     150     312 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.1e-06
                                    HHHHHHHHHHTSEEEEEE---TTTS-T...THHHHHHHHHHHHHHHTHHHHTETTCEEEEEEETHHHHHHHHHHHHHHHT CS
                  Abhydrolase_3  19 alcrelakelgavvvsvdYrlAPehpf...PaavedalaalrwlaeqawelgadpsrivlaGdSaGGnlaaavalrarde 95 
                                     +++ +a+++++  ++  Y  AP  p      +ve + +a++wl +q     +  ++i ++G S GG la+ +a      
  gi|116754493|ref|YP_843611.1| 162 GWASVIASKTRMPTLALAYFGAPGLPQtleNIPVETVGKAIEWLNQQP---LVARDHIGIVGASRGGELALLAASIYP-- 236
                                    5677899999999999999999655541116899*************5...6999***************98884443.. PP

                                    T---EEEEEEESE....-SST.SSTTSHHHHHCHHTTTSSSSCHHHHHHHHHHHSS CS
                  Abhydrolase_3  96 gepkvagqvliyP....vtdl.ertesesikkaeeladgplltraaldlfwrlylp 146
                                       +++++v + P    +    e+++ ++++  ++ +  p l++ + ++  r++l+
  gi|116754493|ref|YP_843611.1| 237 ---EIKAVVGYTPsgviWSGIgENPDAPAWT--YQGRAFPYLKAMMSEEQGRQFLE 287
                                    ...3666666667655533334566666662..23344455555555555555554 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.1e-05     0.018      53     106 ..     192     246 ..     126     272 .. 0.81
   2 ?   -1.7   0.0       1.1   1.9e+03     207     251 ..     319     370 ..     281     373 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.1e-05
                                    HHSHHHHHHHHHHH.HHHCTTSSEE.EEEETHHHHHHHHHHHHHGGGEEEEEEESE CS
                  Abhydrolase_1  53 dygtasvaddldri.ldalgddklt.lvGhSmGGmialayaaeyperVkalvllga 106
                                    + +  +v + ++++ +++l  +  + +vG S GG +al +a+ ype +ka+v   +
  gi|116754493|ref|YP_843611.1| 192 NIPVETVGKAIEWLnQQPLVARDHIgIVGASRGGELALLAASIYPE-IKAVVGYTP 246
                                    45778889999999877666555555********************.999998777 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.1
                                    THHHHSEEEEEEETTCSSSCHHHHHHHHHC.......HTSEEEEEEETCSSS CS
                  Abhydrolase_1 207 lknvlaptlvisgtsDplvppkaledlaql.......lpkkrlvvisdagHl 251
                                    + n +a  l+i+   D++ p ++l+++  +        ++ +l+ ++++gH+
  gi|116754493|ref|YP_843611.1| 319 VENSKAAFLLIGNPGDGVWPSDMLSQISIDrlrahdhPRQYQLLSYDQGGHM 370
                                    6666666666666666666666655554334333354555777777777776 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 !   15.6   0.0   5.8e-06    0.0095      86     131 ..     198     243 ..     181     309 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.8e-06
                                    HHHHHHHHHHC.TTEEEEEEEEEECHHHHHHHHHCTT--TTEEEEEE CS
                  Peptidase_S15  86 gadvidWlakq.pwsnGkVgmtGiSYlGttqllaaatgvpalkaivp 131
                                    + ++i+Wl++q   + +++g +G S +G ++llaa+   p++ka+v 
  gi|116754493|ref|YP_843611.1| 198 VGKAIEWLNQQpLVARDHIGIVGASRGGELALLAAS-IYPEIKAVVG 243
                                    5578*******88999*****************999.7788888775 PP

>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0     2e-05     0.032     105     195 ..     204     293 ..     202     323 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2e-05
                                    HHHHHCSEECCCEEEEEETHHHHHHHHHHHCSTTTCCEEEEES--S-CCHCHHHC....TTCCHHHCC-CCCCHCHHCHT CS
                       Esterase 105 lldanfrtapdgravaGqSmGGlgALilalkhpdrFgsvssfSpivnpsnamWgq....eekeawqendpvllakelsas 180
                                    +l+++  +a+d   ++G+S GG  AL++a+ +p+  + v+       ps ++W      ++ +aw  ++ ++   ++  s
  gi|116754493|ref|YP_843611.1| 204 WLNQQPLVARDHIGIVGASRGGELALLAASIYPEIKAVVGYT-----PSGVIWSGigenPDAPAWTYQGRAFPYLKAMMS 278
                                    66666667777789*******************987666543.....578888777888888888877777766666666 PP

                                    TSEEEEEEEECTTBC CS
                       Esterase 181 lkalriyldvGtsed 195
                                     ++ r +l++ ++ +
  gi|116754493|ref|YP_843611.1| 279 EEQGRQFLEAQKNGT 293
                                    666666666655555 PP

>> Abhydrolase_7  Abhydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.012        19      51     132 ..      79     165 ..      73     177 .. 0.65
   2 ?    6.0   0.0    0.0036       5.8     212     253 ..     201     242 ..     197     245 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.012
                                    HHHHHHHHHHHHH-----------EEEEEEEETTEEEEEEEE--STTB-EE....EEEEEETT--S-EEEEEEE--T.T- CS
                  Abhydrolase_7  51 wqkevrkameelmkfPelkklpapvcvkteqrdgyrlekwefyPlpkavst....flvliPdnvkkpvpavlciPGs.gk 125
                                    w  +v+++ e + +fP +++l++ + v  ++ d   +++     l++  +t     + liP+++ +p+pa++ + Gs g+
  gi|116754493|ref|YP_843611.1|  79 WSMSVNQTGEFVSAFPVIHNLTVGLYVDGREVDSRVVQRIAQIDLERENVTdpivGVFLIPKEITEPTPAIIVLGGSeGG 158
                                    555666666666666666666666666666666666666555555443333111124599****************9356 PP

                                    -HHHHCT CS
                  Abhydrolase_7 126 tkeelaG 132
                                     ke+ a 
  gi|116754493|ref|YP_843611.1| 159 YKEGWAS 165
                                    7888765 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0036
                                    HHHHHCT-TTEEEEEEEEEEEGGGHHHHHHHHHH-TT--EEE CS
                  Abhydrolase_7 212 vldwmktqslirkdriivsGfslGteplmvlGaldesiyafv 253
                                     ++w+ +q+l+ +d+i + G s G e  +   ++ ++i a v
  gi|116754493|ref|YP_843611.1| 201 AIEWLNQQPLVARDHIGIVGASRGGELALLAASIYPEIKAVV 242
                                    579***********************9888888888888776 PP

>> DUF2974  Protein of unknown function (DUF2974)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       0.8   1.3e+03      85     128 ..     148     190 ..     140     200 .. 0.79
   2 ?   10.2   0.0   0.00025       0.4      65     104 ..     195     234 ..     191     242 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.8
                        DUF2974  85 kiylgGhSkGGnlAvyaamnaeddlqeriskiysfDgpGfskev 128
                                    +i++ G S GG    +a++ a+++     + +y f +pG+++++
  gi|116754493|ref|YP_843611.1| 148 AIIVLGGSEGGYKEGWASVIASKTRMPTLALAY-FGAPGLPQTL 190
                                    4888888****9999999998888887777777.9999998875 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00025
                        DUF2974  65 vpaqesAlkYlnkileesegkiylgGhSkGGnlAvyaamn 104
                                    v+   +A+++ln+      ++i ++G S+GG lA++aa  
  gi|116754493|ref|YP_843611.1| 195 VETVGKAIEWLNQQPLVARDHIGIVGASRGGELALLAASI 234
                                    55566899******999999****************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2926.88
//
Query:       gi|116754494|ref|YP_843612.1|  [L=91]
Description: hypothetical protein Mthe_1190 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.6e-23   81.3   0.8    4.5e-23   81.0   0.8    1.1  1  DUF2116      Uncharacterized protein containing a Zn-ribbon (
  ------ inclusion threshold ------
       0.04   14.0   0.3      0.052   13.6   0.3    1.3  1  DZR          Double zinc ribbon
      0.048   13.1   0.6       0.08   12.4   0.6    1.3  1  zf-ribbon_3  zinc-ribbon domain


Domain annotation for each model (and alignments):
>> DUF2116  Uncharacterized protein containing a Zn-ribbon (DUF2116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.0   0.8   7.6e-27   4.5e-23       1      58 [.      32      85 ..      32      86 .. 0.97

  Alignments for each domain:
  == domain 1  score: 81.0 bits;  conditional E-value: 7.6e-27
                        DUF2116  1 epHkHCivCGkaIpldesfCsekCqeeyekkrkkvarsqqilfgililllavvlvlkf 58
                                   +pH+HC+vCG+aI+++esfC+e C+++++++++k    qqilf+++i+l+a++l+l++
  gi|116754494|ref|YP_843612.1| 32 APHRHCVVCGNAIGSEESFCDELCESRFRSAQRK----QQILFAAFIILMALILFLPS 85
                                   59********************************....*****************987 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.3   8.7e-06     0.052      27      47 ..      28      53 ..       8      59 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.7e-06
                            DZR 27 a.....edrCpsCgekvdpearfCpe 47
                                         +++C+ Cg ++ +e++fC+e
  gi|116754494|ref|YP_843612.1| 28 MaeiapHRHCVVCGNAIGSEESFCDE 53
                                   044555899***************86 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.6   1.3e-05      0.08       2      20 ..      34      52 ..      33      53 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.3e-05
                    zf-ribbon_3  2 tvrCPnCGa.plssddnvCp 20
                                   +++C  CG+ +  s+ ++C 
  gi|116754494|ref|YP_843612.1| 34 HRHCVVCGNaI-GSEESFCD 52
                                   79*******66.*******6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       887  (0.0494729); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 642.38
//
Query:       gi|116754495|ref|YP_843613.1|  [L=102]
Description: hypothetical protein Mthe_1191 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 776.73
//
Query:       gi|116754496|ref|YP_843614.1|  [L=186]
Description: hypothetical protein Mthe_1192 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 1311.58
//
Query:       gi|116754497|ref|YP_843615.1|  [L=659]
Description: acetate--CoA ligase [Methanosaeta thermophila PT]
Scores for complete 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-93  311.9   0.0    6.4e-93  311.6   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    9.7e-28   97.0   3.4    9.7e-28   97.0   3.4    2.4  3  AMP-binding_C  AMP-binding enzyme C-terminal domain
    1.8e-14   53.4   5.6    1.8e-14   53.4   5.6    2.3  2  ACAS_N         Acetyl-coenzyme A synthetase N-terminus


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  311.6   0.0   1.1e-96   6.4e-93       2     422 ..      97     538 ..      96     539 .. 0.89

  Alignments for each domain:
  == domain 1  score: 311.6 bits;  conditional E-value: 1.1e-96
                                    HHHHHHST.TSEEEEE....CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEE CS
                    AMP-binding   2 eeqaaktp.dkvalvd....sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvp 76 
                                    +++a+ ++ +kva+++     g+ +t+TY +l+++vn++A+gL+slGvkkgdrV i+lp+ pe+ +++la++k+Ga++++
  gi|116754497|ref|YP_843615.1|  97 DRHAKSWRrNKVAYYFvgepVGDTKTITYYQLYQAVNKMANGLKSLGVKKGDRVSIYLPMIPELPITMLACAKIGAIHSV 176
                                    5677777779****8899*9889********************************************************* PP

                                    EETTS-HHHHHHHHHHHTESEEE.......ETCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS CS
                    AMP-binding  77 lnptltaeelayiledseakvli.......atvdsel.leklleaaakleavklvivldadellkeeelkeeeeseekae 148
                                    + ++++a  l+  ++d+eakv++       +  +     ++++ea ++ ++v++v+v+++ +l+   ++  +  +++  +
  gi|116754497|ref|YP_843615.1| 177 VFSGFSAGGLQSRVTDAEAKVVVtsdgfyrR-GKPLPlKPNVDEAVQNAPSVEKVVVVKRVGLDVPMKEGRDI-WYH--D 252
                                    ***********************99888742.34555578899999999999999999988877664444333.222..1 PP

                                    ......-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHC..SCCTTT-EEEESS-TTSCHHHHHH CS
                    AMP-binding 149 ......kpeeeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletr..fklkeddvvlsilplahifglile 220
                                           ++ +eel+p+d ++i+YTSGTTGkPKG+ + h+ ++   a     t    +++e+dv+++++++ +i+g+++ 
  gi|116754497|ref|YP_843615.1| 253 lvkdqpAECYTEELDPEDRLFILYTSGTTGKPKGIEHAHGGFCVGPAYT---TAwaLDVHEEDVYWCTADCGWITGHSYV 329
                                    2345567889999**************************9986553332...1222557889****************** PP

                                    HHHHHHTT-EEEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHH CS
                    AMP-binding 221 lllallsGatvvllpkdaa.ldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspel 299
                                    ++++l+ Gat +l+++ ++ +d ++++  ie+++v+v++++P+++++++++g+     k+++l+s+r++ ++gepl+pe+
  gi|116754497|ref|YP_843615.1| 330 VYGPLCLGATSILYEGAPDyPDIGRWWSIIEEYGVSVFYTAPTAIRMFMKAGDQW--PKKYNLKSIRILASVGEPLNPEA 407
                                    *******************888****************************86554..56679****************** PP

                                    HHHHHHHHTC...EEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEET..TS CS
                    AMP-binding 300 lrffralfge...evlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgp..gv 374
                                      +fr+  g+   ++++++++TEt+++v+ +pl+   +k+gsv +plpg    i De+ g+ vp g  G ++ + p  ++
  gi|116754497|ref|YP_843615.1| 408 YVWFRNNIGGgqaPIIDTWWQTETGCHVI-APLPMTPEKPGSVAFPLPGFNTDIYDED-GNSVPLGYGGNIVQKTPwpSM 485
                                    ******99999*****************9.666667789******************9.****************9778* PP

                                    -SEBTT-HHHHHHHEEE.....TCCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                    AMP-binding 375 mkgYlkkpeataeafds.....egrwlrTGDlgrldedGyleivgRkkdlikl 422
                                     + ++++pe+  + +++     +++ +  GD +++d+dGy +i gR++d++k+
  gi|116754497|ref|YP_843615.1| 486 LRAFFRDPERYMKEYWQmywdiKPGTYLAGDKATRDKDGYWWIQGRIDDVLKV 538
                                    ****************899987557**************************98 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 ?   -3.1   0.0       2.7   1.6e+04      42      53 ..      40      51 ..      33      56 .. 0.76
   2 ?   -1.9   0.3       1.1   6.8e+03       2      18 ..     217     233 ..     216     242 .. 0.85
   3 !   97.0   3.4   1.6e-31   9.7e-28       1      76 []     547     625 ..     547     625 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.7
                                   HHHHHHHHHHHH CS
                  AMP-binding_C 42 leeeLkahvrke 53
                                   +e+e +++++++
  gi|116754497|ref|YP_843615.1| 40 TEKEMREWCAQN 51
                                   689*****9985 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.1
                                    HHHHHHSSTTEEEEEEE CS
                  AMP-binding_C   2 vEsalvshpaVaeaaVv 18 
                                    v +a+ + p V+ ++Vv
  gi|116754497|ref|YP_843615.1| 217 VDEAVQNAPSVEKVVVV 233
                                    77899999999999998 PP

  == domain 3  score: 97.0 bits;  conditional E-value: 1.6e-31
                                    HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE---.---..HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                  AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg.sea..leeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                    evEsa vshpaVaeaaV+G+pdevkGe++vaf++lk+g +e+  l++++ +hvr+ lgp+a p+ v+fv+++pktrsGK
  gi|116754497|ref|YP_843615.1| 547 EVESAAVSHPAVAEAAVIGKPDEVKGEVIVAFIILKEGvQESedLKKDIAKHVRSVLGPVAYPEIVYFVKDVPKTRSGK 625
                                    8***********************************99632246**********************************9 PP

>> ACAS_N  Acetyl-coenzyme A synthetase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   5.6     3e-18   1.8e-14       2      55 .]      42      95 ..      41      95 .. 0.97
   2 ?   -1.6   0.4      0.45   2.7e+03       6      37 ..     487     517 ..     484     532 .. 0.54

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 3e-18
                                   HHHHHHHHH-HHHHHHHHHCC.S--SB--S-SECSTTTCT-EESTT-EE-HHHHH CS
                         ACAS_N  2 kelykeSiedpeaFWaeqake.ldWekpfdkvldgskgpfikWFeGGklNicyNc 55
                                   ke+ ++  +++  FW+e+a+   dW+kp++++l++ ++p++kWF GGk N+++N+
  gi|116754497|ref|YP_843615.1| 42 KEMREWCAQNYLDFWDEMAQTyADWFKPYTQILEW-NPPYAKWFLGGKCNVAHNA 95
                                   79******************98*************.9*****************7 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.45
                                    HHHHH-HHHHHHHHHCCS--SB--S-SECSTT CS
                         ACAS_N   6 keSiedpeaFWaeqakeldWekpfdkvldgsk 37 
                                    +   +dpe++ +e ++ ++W+ ++ + l g+k
  gi|116754497|ref|YP_843615.1| 487 RAFFRDPERYMKEYWQ-MYWDIKPGTYLAGDK 517
                                    5556677766666663.566666655554443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (659 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 4702.27
//
Query:       gi|116754498|ref|YP_843616.1|  [L=670]
Description: acetate--CoA ligase [Methanosaeta thermophila PT]
Scores for complete 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-96  321.8   0.0    6.6e-96  321.5   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    4.6e-29  101.2   3.8    4.6e-29  101.2   3.8    2.5  3  AMP-binding_C  AMP-binding enzyme C-terminal domain
      3e-14   52.7   4.1      3e-14   52.7   4.1    2.1  2  ACAS_N         Acetyl-coenzyme A synthetase N-terminus


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  321.5   0.0   1.1e-99   6.6e-96       3     422 ..     108     549 ..     106     550 .. 0.90

  Alignments for each domain:
  == domain 1  score: 321.5 bits;  conditional E-value: 1.1e-99
                                    HHHHHST.TSEEEEE.....CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEE CS
                    AMP-binding   3 eqaaktp.dkvalvd.....sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvp 76 
                                    ++a+  + dkva+++     +++ +++TY +l+++vn++A+gL+slGvkkgdrV i++p+ pe  +a+la++k+Ga++++
  gi|116754498|ref|YP_843616.1| 108 RHAKGAKkDKVAYIFvpeptDQQVRKITYLDLYKAVNKFANGLKSLGVKKGDRVSIYMPMIPETPIAMLACAKIGAIHSV 187
                                    56655555***********9999********************************************************* PP

                                    EETTS-HHHHHHHHHHHTESEEE.......ETCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS CS
                    AMP-binding  77 lnptltaeelayiledseakvli.......atvdsel.leklleaaakleavklvivldadellkeeelkeeeeseekae 148
                                    + ++++a  l+  + d+eakv++       +  +     ++++ea ++ ++v++v+v+++++l+   ++  +  +++  e
  gi|116754498|ref|YP_843616.1| 188 VFSGFSAGGLQSRVLDAEAKVVVttdgfyrR-GKPLPlKPNVDEAVQNAPSVEKVVVVKRAGLDVPMKEGRDI-WYH--E 263
                                    ***********************99887642.34556689999999999**********99988775444443.333..1 PP

                                    ......-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEH.HHHHHHHHHHHHHHC.SCCTTT-EEEESS-TTSCHHHHHH CS
                    AMP-binding 149 ......kpeeeeelkpddlayiiYTSGTTGkPKGVmlsh.rnlvanvaslkletr.fklkeddvvlsilplahifglile 220
                                          +++e+e+ +++d ++i+YTSGTTGkPKG+ + h ++ v+ +++    +  f+lk+ddv+++++++ +i+g+++ 
  gi|116754498|ref|YP_843616.1| 264 lvanqpDECETEKMDSEDRLFILYTSGTTGKPKGIEHVHgGYCVTPAQTT---HWvFDLKDDDVWWCTADVGWITGHSYV 340
                                    344567899999***************************55556665553...33688999******************* PP

                                    HHHHHHTT-EEEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHH CS
                    AMP-binding 221 lllallsGatvvllpkdaa.ldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspel 299
                                    ++++l+ Gat +l+++ ++ +d ++++  i+++kv+v++++P+++++++++g+     +++dlsslrl+ ++gep++pe+
  gi|116754498|ref|YP_843616.1| 341 VYGPLCLGATSILYEGAPDyPDFGRWFSIIQEHKVSVFYTAPTAIRMFMKAGEQW--PQKYDLSSLRLLGSVGEPINPEA 418
                                    *******************888****************************86544..5567******************* PP

                                    HHHHHHHHTC...EEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEET..TS CS
                    AMP-binding 300 lrffralfge...evlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgp..gv 374
                                    + ++r+ fg    ++++++++TEt+++v+  pl+    k+gs  +plpg    i De+  +pvp+g+ G ++   p  ++
  gi|116754498|ref|YP_843616.1| 419 WIWYRKYFGSdrcPIMDTWWQTETGCFVV-SPLPITPLKPGSPTFPLPGFNTDIYDED-ANPVPPGQGGNIVNPTPwpSM 496
                                    ****************************9.6667777799*****************9.9************8888668* PP

                                    -SEBTT-HHHHHHHEEE......TCCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                    AMP-binding 375 mkgYlkkpeataeafds......egrwlrTGDlgrldedGyleivgRkkdlikl 422
                                     + ++k+pe+  + +++      + + +  GD +++d+dGy++i gR++d++k+
  gi|116754498|ref|YP_843616.1| 497 LRAFYKDPERYMKEYWQmywdirP-GVYLAGDKATRDKDGYFFIQGRIDDVLKV 549
                                    ****************89997744.7**************************98 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 ?   -2.0   0.0       1.2   7.3e+03      45      72 ..      38      72 ..      17      73 .. 0.71
   2 ?   -1.7   0.2         1     6e+03       2      18 ..     228     244 ..     227     253 .. 0.85
   3 !  101.2   3.8   7.7e-33   4.6e-29       1      76 []     558     636 ..     558     636 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.2
                                   HHHHHHHH.......HT-TTTS-SEEEE-S---B- CS
                  AMP-binding_C 45 eLkahvrk.......elgpyavpkkvvfvdelpkt 72
                                   +++++++k       e+ ++   ++++f de+ kt
  gi|116754498|ref|YP_843616.1| 38 NVMQWMKKkgftserEMRAWTGQHYIEFWDEMAKT 72
                                   56666644444444588888888889999999887 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1
                                    HHHHHHSSTTEEEEEEE CS
                  AMP-binding_C   2 vEsalvshpaVaeaaVv 18 
                                    v +a+ + p V+ ++Vv
  gi|116754498|ref|YP_843616.1| 228 VDEAVQNAPSVEKVVVV 244
                                    78899999******999 PP

  == domain 3  score: 101.2 bits;  conditional E-value: 7.7e-33
                                    HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE---..---..HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                  AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg..sea..leeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                    evEsalvshpaVaeaaV+G+pdevkGe++vafV+l++g  + +  l++eL +hvr+ lgp+a p+ v+fv+++pktrsGK
  gi|116754498|ref|YP_843616.1| 558 EVESALVSHPAVAEAAVIGKPDEVKGEVIVAFVILREGvkE-SedLKKELAKHVRSVLGPVAYPEIVYFVKDVPKTRSGK 636
                                    8**********************************999532.246**********************************9 PP

>> ACAS_N  Acetyl-coenzyme A synthetase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.7   4.1     5e-18     3e-14       2      55 .]      52     105 ..      51     105 .. 0.96
   2 ?   -2.9   0.1       1.1   6.6e+03       4      20 ..     496     512 ..     495     528 .. 0.71

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 5e-18
                                    HHHHHHHHH-HHHHHHHHHCC.S--SB--S-SECSTTTCT-EESTT-EE-HHHHH CS
                         ACAS_N   2 kelykeSiedpeaFWaeqake.ldWekpfdkvldgskgpfikWFeGGklNicyNc 55 
                                    +e+ ++  +++ +FW+e+ak   dW++p+ ++l++ k+p+++WF+GGk N++yN+
  gi|116754498|ref|YP_843616.1|  52 REMRAWTGQHYIEFWDEMAKTyADWFEPYAQILEW-KPPYARWFVGGKCNVAYNA 105
                                    68999***************98*************.999***************7 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.1
                                    HHHHHHH-HHHHHHHHH CS
                         ACAS_N   4 lykeSiedpeaFWaeqa 20 
                                    + +   +dpe++ +e +
  gi|116754498|ref|YP_843616.1| 496 MLRAFYKDPERYMKEYW 512
                                    66677788877666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (670 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.41
# Mc/sec: 4903.08
//
Query:       gi|116754499|ref|YP_843617.1|  [L=660]
Description: acetate--CoA ligase [Methanosaeta thermophila PT]
Scores for complete 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-93  311.6   0.0    7.8e-93  311.3   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    7.7e-27   94.1   4.0    5.2e-26   91.4   3.0    2.4  2  AMP-binding_C  AMP-binding enzyme C-terminal domain
    5.1e-16   58.3   6.1    5.1e-16   58.3   6.1    2.7  2  ACAS_N         Acetyl-coenzyme A synthetase N-terminus


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  311.3   0.0   1.3e-96   7.8e-93       2     422 ..      98     539 ..      97     540 .. 0.88

  Alignments for each domain:
  == domain 1  score: 311.3 bits;  conditional E-value: 1.3e-96
                                    HHHHHHST.TSEEEEE....CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEE CS
                    AMP-binding   2 eeqaaktp.dkvalvd....sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvp 76 
                                    +++a+ ++ +kva++      g+ +++TY++l+++vn++A+gL+slGv+kgdrV i++p+ pe+ +a+la++k+Ga++++
  gi|116754499|ref|YP_843617.1|  98 DRHAKSWRrNKVAYIGvgepLGDVRKFTYGDLYREVNKFANGLKSLGVEKGDRVSIYMPMIPELPIAMLACAKIGAIHSV 177
                                    56777777799***9999997789******************************************************** PP

                                    EETTS-HHHHHHHHHHHTESEEE.......E.TCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS CS
                    AMP-binding  77 lnptltaeelayiledseakvli.......a.tvdselleklleaaakleavklvivldadellkeeelkeeeeseekae 148
                                    + +++++++ a  + d+e+k+ i       + ++  el ++++ea ++ ++vk+ iv+++ + +     +++++ + +++
  gi|116754499|ref|YP_843617.1| 178 VFSGFSSKAYADRVIDAESKISItvdgfwrRgKIV-ELKKQADEAIQDAPTVKHQIVYKRTGQD----IPWNKDRDIWWH 252
                                    ***********************999888625322.2235556666667889999999976644....444444343332 PP

                                    .......-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHC.SCCTTT-EEEESS-TTSCHHHHHH CS
                    AMP-binding 149 .......kpeeeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletr.fklkeddvvlsilplahifglile 220
                                            ++e+e+l+p++ ++i+YTSGTTGkPKG+ + h+ ++  v +  l    f+lkeddv+++++++ +i+g+++ 
  gi|116754499|ref|YP_843617.1| 253 dlvkdqpAECETEQLDPEHRLFILYTSGTTGKPKGIEHAHGGYCVGVPQT-LH-WvFDLKEDDVWWCTADIGWITGHSYI 330
                                    4556778889999***************************9999998885.33.2588999******************* PP

                                    HHHHHHTT-EEEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHH CS
                    AMP-binding 221 lllallsGatvvllpkdaa.ldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspel 299
                                    ++++l+ Gat ++++++++ +d ++++  ie+++v+v++++P+++++++++g+     ++++++ lrl+ ++gep++pe+
  gi|116754499|ref|YP_843617.1| 331 VYGPLSLGATSIIYEGSPDyPDFGRWWSIIEEFGVNVLYTAPTAIRMFMRAGEQW--PAKYNMKCLRLLGTVGEPINPEA 408
                                    *******************888****************************86554..34457778*************** PP

                                    HHHHHHHHTC...EEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEET..TS CS
                    AMP-binding 300 lrffralfge...evlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgp..gv 374
                                    + ++r+  g+   ++++++++TEt++++   pl+    k+gs+ ++lpg  + + De+ g+pvp+ge G +++  p  ++
  gi|116754499|ref|YP_843617.1| 409 WVWYRKNIGRdelQIMDTWWQTETGTFIG-SPLPITPLKPGSCTFALPGYSMDVWDEA-GKPVPPGEGGNIVILEPypSM 486
                                    *******999*****************96.4555666789*****************9.***************99778* PP

                                    -SEBTT-HHHHHHHEEE.....TCCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                    AMP-binding 375 mkgYlkkpeataeafds.....egrwlrTGDlgrldedGyleivgRkkdlikl 422
                                     + ++k+p++  +++++       + +  GD gr+dedGy++i gR++d+ik+
  gi|116754499|ref|YP_843617.1| 487 LRDFYKDPDRYFRTYWEtywnvRAGTYLAGDKGRRDEDGYFWIQGRIDDVIKV 539
                                    **********999999888866346***************************8 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.18   1.1e+03      47      72 ..      31      63 ..      10      65 .. 0.71
   2 !   91.4   3.0   8.8e-30   5.2e-26       1      76 []     548     626 ..     548     626 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.18
                                   HHHHHH.......HT-TTTS-SEEEE-S---B- CS
                  AMP-binding_C 47 kahvrk.......elgpyavpkkvvfvdelpkt 72
                                   +++++k       e+ ++   ++v+f de+ kt
  gi|116754499|ref|YP_843617.1| 31 MQWMKKkgfktekEMREWCSKNYVEFWDEMAKT 63
                                   555533334444488888666688899999888 PP

  == domain 2  score: 91.4 bits;  conditional E-value: 8.8e-30
                                    HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE---.---..HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                  AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg.sea..leeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                    evEsa vshp+VaeaaV+G+pd+vkGe++++f +l++g +e+  l++++ +h+r++lgp+a p++v+fv+++pktrsGK
  gi|116754499|ref|YP_843617.1| 548 EVESAAVSHPKVAEAAVIGKPDPVKGEVIIVFAILREGvQESeeLKKDIAKHIRETLGPVAMPEAVYFVKDVPKTRSGK 626
                                    8**********************************999632246**********************************9 PP

>> ACAS_N  Acetyl-coenzyme A synthetase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.3   6.1   8.5e-20   5.1e-16       2      55 .]      43      96 ..      42      96 .. 0.97
   2 ?    0.3   0.1      0.11   6.7e+02       1      22 [.     483     504 ..     483     526 .. 0.83

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 8.5e-20
                                   HHHHHHHHH-HHHHHHHHHCC.S--SB--S-SECSTTTCT-EESTT-EE-HHHHH CS
                         ACAS_N  2 kelykeSiedpeaFWaeqake.ldWekpfdkvldgskgpfikWFeGGklNicyNc 55
                                   ke+ ++  +++ +FW+e+ak   dW++p+++vld+ k+p++kWF+GGk+N++yN+
  gi|116754499|ref|YP_843617.1| 43 KEMREWCSKNYVEFWDEMAKTyADWFEPYKQVLDW-KPPYAKWFVGGKVNMAYNA 96
                                   799*****************98*************.999***************7 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.11
                                    HHHHHHHHHH-HHHHHHHHHCC CS
                         ACAS_N   1 ykelykeSiedpeaFWaeqake 22 
                                    y ++ +   +dp+++++  ++ 
  gi|116754499|ref|YP_843617.1| 483 YPSMLRDFYKDPDRYFRTYWET 504
                                    6689999999999999988864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (660 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); 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: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 4473.38
//
Query:       gi|116754500|ref|YP_843618.1|  [L=469]
Description: ATPase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.9e-06   26.4   0.0    1.3e-05   25.0   0.0    1.8  1  AAA_3      ATPase family associated with various cellular act
    0.00021   21.3   0.0    0.00037   20.5   0.0    1.4  1  AAA_5      AAA domain (dynein-related subfamily)
  ------ inclusion threshold ------
       0.11   11.9   0.0       0.92    8.8   0.0    2.1  2  Gtr1_RagA  Gtr1/RagA G protein conserved region
        0.2   11.7   0.0       0.37   10.8   0.0    1.4  1  TsaE       Threonylcarbamoyl adenosine biosynthesis protein T


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 !   25.0   0.0     3e-09   1.3e-05      65     129 ..     175     237 ..     100     239 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 3e-09
                          AAA_3  65 llladeinrappktqsalleameerqvtvegethklpepflvlatqnPieqeGtyplpeaqldrf 129
                                      l +einr p+  q  +le+++ r++t++g+  +     + +at nP e + typ+ ea +dr 
  gi|116754500|ref|YP_843618.1| 175 WKLINEINRFPAGKQNLFLEIIKKRKITYAGQVLEPG-DTCYFATMNP-EFSSTYPVDEALMDRI 237
                                    55889**************************998855.45678*****.999***********96 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   8.2e-08   0.00037       2     137 ..     101     236 ..     100     237 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 8.2e-08
                                    EEEE--SSSSHHHHHHHGGGGB......S--EEEEE--TT--HHHHH--B--...........--------G-SEEEEES CS
                          AAA_5   2 vlLvGppGtgKselaerlaaal......nreveyvqltrdtteedlkgrreik..ngttslvdsplvraaregeilvlDE 73 
                                    vlL G  G  K++l+  l  ++        e ++v ++   tee+++g ++++  ++ ts +  +l +   +++  +++E
  gi|116754500|ref|YP_843618.1| 101 VLLYGGMGANKTTLVNILGGVFmnmsfdDVENLMVTGHPEQTEEKIIGFIDPRqwMQPTSSEIRVLWTPWARSRWKLINE 180
                                    89*******************99999999999************************************************ PP

                                    GGG--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHTT CS
                          AAA_5  74 veraesevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrsR 137
                                    ++r +   +n +l ++ +r++     g++           +  +at+np   s  ++++al +R
  gi|116754500|ref|YP_843618.1| 181 INRFPAGKQNLFLEIIKKRKIT--YAGQVLEPGD------TCYFATMNPEFSSTYPVDEALMDR 236
                                    **********************..6666665555......899*******999999*****999 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 ?    8.8   0.0    0.0002      0.92       2      49 ..     101     151 ..     100     161 .. 0.91
   2 ?    0.3   0.0     0.085   3.8e+02      76     117 ..     335     377 ..     329     378 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0002
                      Gtr1_RagA   2 vLLmGksgsGKtsmrsi...iFdnylardtlrlgatidveksevrflgnlt 49 
                                    vLL G  g+ Kt++ +i   +F n++  d+ +l +t + e++e ++ g+++
  gi|116754500|ref|YP_843618.1| 101 VLLYGGMGANKTTLVNIlggVFMNMSFDDVENLMVTGHPEQTEEKIIGFID 151
                                    8**************997778*********************999999875 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.085
                      Gtr1_RagA  76 nvgvliyVfDvesre.leedletlkeilealrqyspeakvfvl 117
                                    n +v  + +D   ++ +++dl+ ++++++ +  +s+  +++vl
  gi|116754500|ref|YP_843618.1| 335 NPEVCCWQIDEGLSDrVRQDLRAFTKAVSFVCGISNGSRIEVL 377
                                    55666777787766559***********************998 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   8.2e-05      0.37      14      39 ..      91     118 ..      79     130 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 8.2e-05
                                    HHHCH..TEEEEEEESTTSSHHHHHHHH CS
                           TsaE  14 lakal..gdvilLeGdLGaGKTtlvrgl 39 
                                    la+a+  ++++lL+G +Ga KTtlv  l
  gi|116754500|ref|YP_843618.1|  91 LANAClrNRAVLLYGGMGANKTTLVNIL 118
                                    4444456778**************9866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 3417.46
//
Query:       gi|116754501|ref|YP_843619.1|  [L=152]
Description: formylmethanofuran dehydrogenase, subunit C (tungsten) [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-07   31.5  14.6    4.5e-07   29.6  14.6    2.1  1  GXGXG     GXGXG motif


Domain annotation for each model (and alignments):
>> GXGXG  GXGXG motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6  14.6   2.5e-11   4.5e-07      57     152 ..      37     139 ..       2     147 .. 0.69

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 2.5e-11
                                    EEEE-STTTTT-ESSEEEEE--TT-SS-GGG...SB-S-SSTTT...T--SEEEEESSB--SSTTTT-.SS-EEEESEB- CS
                          GXGXG  57 eGdandyvGkglsgGkivikpskeskfkaee...niivGnvvly...gatgGklfirgkageRfavrn.sgatavvegvg 129
                                      da dy+G+g++gG iv +   + +f++ +    +i+G++  +      gGk+ ++g+ageR++  + sg + v ++vg
  gi|116754501|ref|YP_843619.1|  37 MCDAGDYLGQGMTGGGIVASSCGTYAFRNMSggwGVILGDAGSFigvNNSGGKILVKGNAGERVGWLMrSGRITVLGDVG 116
                                    469**************998877666655432225777776443211446778888888888877766567777777778 PP

                                    SSTTTT-EEEEEEE-S-B-SSBT CS
                          GXGXG 130 dhgceYmtGGvvvvLgktgrnfa 152
                                    d+++    GG + + g  g+n +
  gi|116754501|ref|YP_843619.1| 117 DYAGILAKGGLIRIRGGAGENAG 139
                                    88888777887777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      198  (0.0110436); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1102.15
//
Query:       gi|116754502|ref|YP_843620.1|  [L=495]
Description: hypothetical protein Mthe_1199 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.15   12.7   0.0       0.33   11.6   0.0    1.6  1  VWA_2     von Willebrand factor type A domain


Domain annotation for each model (and alignments):
>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   1.8e-05      0.33       1      78 [.     326     401 ..     326     425 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.8e-05
                          VWA_2   1 lvfvlDtSgSmrngdygptrleaakdaveallksl.pgdrvglvtfsdgpevlipltkdkakilnalrnleakgggtnl 78 
                                    l++vlD+S Sm +   g + + a  +a +a   ++ +g  ++ ++fs++  ++ p+++d +++++ l +  +  g tn+
  gi|116754502|ref|YP_843620.1| 326 LLVVLDSSRSMDGHRRGSRTFYATLAAFKAAQFAYeQGAEIAAINFSERF-LVQPWCRDLDAVEDVLIEYLC--GRTNI 401
                                    689********9997776666666666655544442799*******9987.467888888888887776664..56665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 3706.01
//
Query:       gi|116754503|ref|YP_843621.1|  [L=308]
Description: putative deoxyhypusine synthase [Methanosaeta thermophila PT]
Scores for 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-101  337.0   0.0   9.9e-101  336.8   0.0    1.0  1  DS        Deoxyhypusine synthase
  ------ inclusion threshold ------
      0.031   14.7   0.1      0.077   13.5   0.1    1.6  1  Rnk_N     Rnk N-terminus


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 !  336.8   0.0  1.1e-104  9.9e-101       1     287 [.      17     296 ..      17     297 .. 0.97

  Alignments for each domain:
  == domain 1  score: 336.8 bits;  conditional E-value: 1.1e-104
                             DS   1 ellesyekigfqatslgeaidilnkmrkdekctiflgltsnlissGlreiiadlvkeklvdvivtTaggieeDlikalgk 80 
                                    el++ +e +gf a++l++a++i+++m+ +e+   f++l+++++++G+r++i+dl++++++dv+vtT++++ +D+++++++
  gi|116754503|ref|YP_843621.1|  17 ELVRGMEGCGFGARRLAHAAEIYQEMV-EEDYRKFFTLAGAMVPAGMRNLISDLIRRGMIDVLVTTGANLVHDIVESFSH 95 
                                    699***********************5.6899**********************************************99 PP

                             DS  81 ktylgdfelddeeLrekginRignllvpnenyckfedwvreildkleeeqkvwspselikelGkeindeeSilywAyknd 160
                                     + lg  e+dd+eLr++gi Ri+++++ ++++ +fe+ v+++l + e+    +s ++l++e+G+ i+d++Sil++A + +
  gi|116754503|ref|YP_843621.1|  96 -HRLGYLEADDSELRRSGISRIYDVYITDDDFVRFEELVQNLLPDREA---PISGRDLLAEIGSGIDDRRSILRSASDCG 171
                                    .*******************************************9998...49*************************** PP

                             DS 161 ipvfcpaltDgslGdqlllfhsvkekkklkldivkDirelndialkakktgaiilGGGvpKhhilnan.lmrngadyavy 239
                                    +pvfcpa+tD+++G+q++l++   ++kkl++d+++D+re+ di+++++++g++++GGGvpK+++l+++ ++ n +  a++
  gi|116754503|ref|YP_843621.1| 172 VPVFCPAITDSMIGLQAWLHR---QTKKLNIDVLEDVREIVDICYESERAGILMVGGGVPKNFALQSMlVTPNSFRLAIQ 248
                                    ******************999...7888****************************************55579******* PP

                             DS 240 ittaqefdGslsgatldEavSwgkikaeaksvkvyaDaTivlPLlvaa 287
                                    +tt++++ G+lsgatl+Ea+Swgki++e k+v+vy+DaTi+lPLlva+
  gi|116754503|ref|YP_843621.1| 249 LTTDHPEAGGLSGATLSEAISWGKIDPEGKHVTVYGDATITLPLLVAS 296
                                    **********************************************96 PP

>> Rnk_N  Rnk N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   8.6e-06     0.077       3      35 ..     119     153 ..     118     154 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.6e-06
                                    -EEEHHHHHHHHHHHHCT.TTT.SSTTHHHHHHHH CS
                          Rnk_N   3 IyitelDleRLeaLldsl.adr.dppaaeaLeaEL 35 
                                    +yit+ D+ R e L+ +l +dr +p  +++L aE+
  gi|116754503|ref|YP_843621.1| 119 VYITDDDFVRFEELVQNLlPDReAPISGRDLLAEI 153
                                    8***************99999989999999**997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); 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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2208.98
//
Query:       gi|116754504|ref|YP_843622.1|  [L=146]
Description: putative transcriptional regulator [Methanosaeta thermophila PT]
Scores for complete 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   94.7   0.0    3.2e-27   94.3   0.0    1.2  1  TFX_C            DNA_binding protein, TFX, C-term
    7.3e-08   31.8   2.4    1.3e-07   31.0   1.8    1.8  1  Sigma70_r4       Sigma-70, region 4
    5.6e-05   22.6   0.2     0.0001   21.7   0.2    1.4  1  GerE             Bacterial regulatory proteins, luxR family
    0.00017   21.2   0.6    0.00057   19.5   0.6    1.9  1  Sigma70_r4_2     Sigma-70, region 4
    0.00085   19.6   0.1     0.0014   18.9   0.1    1.4  1  KORA             TrfB plasmid transcriptional repressor
    0.00096   19.5   0.7      0.002   18.4   0.7    1.6  1  HTH_31           Helix-turn-helix domain
      0.002   17.8   0.3     0.0044   16.8   0.2    1.5  1  HTH_23           Homeodomain-like domain
     0.0048   16.9   0.2     0.0079   16.2   0.2    1.4  1  HTH_3            Helix-turn-helix
     0.0067   16.4   0.3      0.021   14.8   0.1    2.0  3  HTH_Crp_2        Crp-like helix-turn-helix domain
     0.0085   16.0   0.3      0.013   15.4   0.3    1.3  1  HTH_37           Helix-turn-helix domain
  ------ inclusion threshold ------
      0.057   13.5   0.2       0.11   12.7   0.2    1.6  1  HTH_28           Helix-turn-helix domain
      0.066   13.0   0.5       0.23   11.2   0.1    2.0  2  HTH_38           Helix-turn-helix domain
        0.1   12.6   0.1       0.18   11.8   0.1    1.4  1  HTH_19           Helix-turn-helix domain
       0.15   11.7   0.0       0.16   11.6   0.0    1.1  1  CAP59_mtransfer  Cryptococcal mannosyltransferase 1


Domain annotation for each model (and alignments):
>> TFX_C  DNA_binding protein, TFX, C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.3   0.0   2.5e-30   3.2e-27       1      83 []      52     134 ..      52     134 .. 0.99

  Alignments for each domain:
  == domain 1  score: 94.3 bits;  conditional E-value: 2.5e-30
                                    SS-HHHHHHHH---EEEEE--GGGHHHHHHHHHHHHHHHS-S----HHHHHHHHHHH-SSS-----SSS-EEEEESSSSS CS
                          TFX_C   1 AreTlaflealdapvlvtieeGtdlfdipkiiyaeadkagikvkydtieLikllreeapeaikgrvvkedlevyitedGe 80 
                                    A eTl+++++++apv v+i+eGtdlf +p ii++ead +g+k++ ++i+++  l+e ap+ +++r++++++++y+tedGe
  gi|116754504|ref|YP_843622.1|  52 ALETLKQWKMIHAPVAVSIPEGTDLFALPGIIFREADTRGLKLPVNSIDILAGLKEIAPHLTRRRLIERSFDIYVTEDGE 131
                                    679***************************************************************************** PP

                                    EEE CS
                          TFX_C  81 irv 83 
                                    i+v
  gi|116754504|ref|YP_843622.1| 132 IYV 134
                                    **8 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   1.8     1e-10   1.3e-07       5      47 ..       7      48 ..       6      51 .. 0.93

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 1e-10
                                   S-HHHHHHHHHHHTTT--HHHHHHHHTS-HHHHHHHHHHHHHH CS
                     Sigma70_r4  5 LpererevlelrfgeglTleEIgerlgiSrerVrqiekrAlrk 47
                                   L+er+ +vl+lr+  g+++eE+++ lg +r  V+ +ekrA+++
  gi|116754504|ref|YP_843622.1|  7 LTERQIQVLRLRRS-GMSQEEVAALLGTTRANVSILEKRAMQN 48
                                   99**********95.569***********************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 !   21.7   0.2   8.2e-08    0.0001       3      43 ..       7      47 ..       6      51 .. 0.95

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 8.2e-08
                                   S-HHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHH CS
                           GerE  3 LskRErevLrllaeGksnkeIAeelniSekTVkvhksnimk 43
                                   L++R+ +vLrl  +G+s +e+A+ l+    +V++  +++m+
  gi|116754504|ref|YP_843622.1|  7 LTERQIQVLRLRRSGMSQEEVAALLGTTRANVSILEKRAMQ 47
                                   9*********************************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 !   19.5   0.6   4.4e-07   0.00057      11      52 ..       7      47 ..       7      56 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 4.4e-07
                                   S-HHHHHHHHHHHTS---HHHHHHHHT--HHHHHHHHHHHHH CS
                   Sigma70_r4_2 11 LperqreifllryleglsykEIAellgisegtVksrlsRArk 52
                                   L+erq +++ lr+  g+s++E+A+llg++ ++V    +RA++
  gi|116754504|ref|YP_843622.1|  7 LTERQIQVLRLRR-SGMSQEEVAALLGTTRANVSILEKRAMQ 47
                                   899********75.*******************887777765 PP

>> KORA  TrfB plasmid transcriptional repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   1.1e-06    0.0014      31      73 ..      21      64 ..       7      73 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.1e-06
                           KORA 31 gkkqadvatelgltkqavsqavkrvwaahaere.epaglerVsv 73
                                   g +q++va+ lg t+ +vs ++kr++++ +  + + ++++ + +
  gi|116754504|ref|YP_843622.1| 21 GMSQEEVAALLGTTRANVSILEKRAMQNIDRALeTLKQWKMIHA 64
                                   678*************************9987756677887765 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.7   1.6e-06     0.002       9      36 ..      15      43 ..      10      56 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.6e-06
                         HTH_31  9 lRe.raGLsqeevAerlgvsestlsrlEq 36
                                   lR  r+G+sqeevA++lg +++ +s lE 
  gi|116754504|ref|YP_843622.1| 15 LRLrRSGMSQEEVAALLGTTRANVSILEK 43
                                   444147*****************999986 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.2   3.4e-06    0.0044       6      39 ..      10      43 ..       8      48 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.4e-06
                         HTH_23  6 eRlrillllaeGlsvreIAreLgvsrrTvyrwlk 39
                                   + +++l+l + G+s++e+A++Lg +r  v+   k
  gi|116754504|ref|YP_843622.1| 10 RQIQVLRLRRSGMSQEEVAALLGTTRANVSILEK 43
                                   55799*******************9976665555 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.2   6.2e-06    0.0079       4      31 ..      15      43 ..      12      54 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6.2e-06
                                   HHH.HTTHHHHHHHHHHTSSHHHHHHHHT CS
                          HTH_3  4 lRk.qlglsqeeLAeklGvsrstisriEn 31
                                   lR+   g+sqee+A++lG +r+ +s +E+
  gi|116754504|ref|YP_843622.1| 15 LRLrRSGMSQEEVAALLGTTRANVSILEK 43
                                   566689***************99986665 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   1.7e-05     0.021      21      39 ..      21      39 ..       3      44 .. 0.81
   2 ?   -2.9   0.0       5.7   7.2e+03      38      51 ..      49      62 ..      46      66 .. 0.71
   3 ?   -3.0   0.0         6   7.7e+03      45      54 ..     112     121 ..     108     127 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.7e-05
                                   EHHHHHHHHHTTSSHHHHH CS
                      HTH_Crp_2 21 pltqeelAsmlGltretvs 39
                                    ++qee A++lG+tr  vs
  gi|116754504|ref|YP_843622.1| 21 GMSQEEVAALLGTTRANVS 39
                                   69**************998 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.7
                                   HHHHHHHHHHTTSE CS
                      HTH_Crp_2 38 vsrilseLkregli 51
                                   + r+l  Lk+ ++i
  gi|116754504|ref|YP_843622.1| 49 IDRALETLKQWKMI 62
                                   56888888876665 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 6
                                    HHHTTSEEET CS
                      HTH_Crp_2  45 Lkreglisrg 54 
                                    L r+ li+r+
  gi|116754504|ref|YP_843622.1| 112 LTRRRLIERS 121
                                    6677777764 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.3   1.1e-05     0.013      28      59 ..      18      49 ..      10      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.1e-05
                                   HHCT--HHHHHHHHT--HHHHHHHHTT--TT- CS
                         HTH_37 28 ekrelsqseaaqllgiaqPkvsrllrgklsrf 59
                                   ++ + sq+e+a+llg+++++vs l++   +++
  gi|116754504|ref|YP_843622.1| 18 RRSGMSQEEVAALLGTTRANVSILEKRAMQNI 49
                                   56789********************9888776 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   8.2e-05      0.11       3      29 ..      12      38 ..      10      60 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.2e-05
                         HTH_28  3 leiikllaaGhsvreaArelgisrrtv 29
                                   +++++l  +G+s+ e+A++lg++r  v
  gi|116754504|ref|YP_843622.1| 12 IQVLRLRRSGMSQEEVAALLGTTRANV 38
                                   68999999***************9766 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00018      0.23      10      34 ..      10      35 ..       7      39 .. 0.75
   2 ?   -1.0   0.0       1.2   1.5e+03      22      32 ..     104     114 ..     103     117 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00018
                         HTH_38 10 ReeIerl..laeGlslreIArrLgrsp 34
                                   R +I+ l  +  G+s+ e+A +Lg  +
  gi|116754504|ref|YP_843622.1| 10 R-QIQVLrlRRSGMSQEEVAALLGTTR 35
                                   5.5665531689************887 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.2
                         HTH_38  22 slreIArrLgr 32 
                                    +l+eIA +L r
  gi|116754504|ref|YP_843622.1| 104 GLKEIAPHLTR 114
                                    5789*999987 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00014      0.18      12      35 ..      21      44 ..      17      59 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00014
                         HTH_19 12 gltqeelaerlgisrskisaiEng 35
                                   g++qee+a  lg++r+  s +E+ 
  gi|116754504|ref|YP_843622.1| 21 GMSQEEVAALLGTTRANVSILEKR 44
                                   9****************9999975 PP

>> CAP59_mtransfer  Cryptococcal mannosyltransferase 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00013      0.16      23      70 ..      25      71 ..       9     107 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00013
                CAP59_mtransfer 23 lelirfLgpenvfvSiyesgskdgtkeaLraleaelealgversivln 70
                                    e++ +Lg+ +  vSi+e++  ++   aL++l ++++ ++++  + + 
  gi|116754504|ref|YP_843622.1| 25 EEVAALLGTTRANVSILEKRAMQNIDRALETL-KQWKMIHAPVAVSIP 71
                                   57899***************************.889988888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); 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: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1061.63
//
Query:       gi|116754505|ref|YP_843623.1|  [L=256]
Description: ABC transporter related [Methanosaeta thermophila PT]
Scores for complete 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-32  110.9   0.0    8.8e-32  110.5   0.0    1.2  1  ABC_tran     ABC transporter
    1.9e-10   41.1   0.1    8.1e-05   22.6   0.0    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    0.00037   20.0   0.0      0.018   14.5   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
     0.0017   18.6   0.2        0.2   11.9   0.1    2.2  2  AAA_22       AAA domain
     0.0049   17.4   0.2     0.0078   16.7   0.2    1.2  1  AAA_23       AAA domain
  ------ inclusion threshold ------
      0.014   15.1   0.1      0.026   14.3   0.1    1.4  1  AAA_29       P-loop containing region of AAA domain
      0.028   14.8   0.2      0.062   13.7   0.2    1.8  1  AAA_16       AAA ATPase domain
      0.028   14.3   0.0      0.057   13.3   0.0    1.5  1  RsgA_GTPase  RsgA GTPase
      0.032   13.8   0.3        0.3   10.6   0.1    2.1  2  cobW         CobW/HypB/UreG, nucleotide-binding domain
       0.05   13.3   0.3       0.21   11.3   0.0    1.9  2  AAA_30       AAA domain
       0.06   13.6   0.1       0.86    9.9   0.1    2.2  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
       0.33   10.8   1.4        1.9    8.4   0.1    2.5  3  NACHT        NACHT domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.5   0.0   5.9e-35   8.8e-32       1     137 []      20     165 ..      20     165 .. 0.96

  Alignments for each domain:
  == domain 1  score: 110.5 bits;  conditional E-value: 5.9e-35
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvren 79 
                                    l +++++++ ge+++i+G++GaGK+tLl+++     p +G++l++g+  k+  e+  +r++igv++q p + +++ v++n
  gi|116754505|ref|YP_843623.1|  20 LTDINIEVRTGETLGIIGPTGAGKTTLLRVMDLIDLPSKGRVLFKGEAPKNeGERLAARRRIGVVFQRPVMLRGT-VYDN 98 
                                    6799*****************************************8888886899999***************99.**** PP

                                    .............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    .............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 .............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                                 e de++e+als +glk+ + +++    + LSgG+ qrvalaral+  p+llllDEpta
  gi|116754505|ref|YP_843623.1|  99 vayglrirrlskdEIDERVEAALSDVGLKGYERRPA----KVLSGGEMQRVALARALAISPELLLLDEPTA 165
                                    ************999***************999999....*****************************97 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   2.8e-06    0.0041       3      22 ..      34      53 ..      33     126 .. 0.78
   2 !   22.6   0.0   5.4e-08   8.1e-05     220     298 ..     120     195 ..      68     200 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.8e-06
                         AAA_21  3 vliGpNgsGKSnLLdaldll 22
                                   ++iGp g+GK++LL+ +dl+
  gi|116754505|ref|YP_843623.1| 34 GIIGPTGAGKTTLLRVMDLI 53
                                   69***************998 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 5.4e-08
                         AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                     +  +  +++  +pa  lS G  +  al+ al+  +    lll+DEp ++L+P+    + el+++++ +g   +++TH+
  gi|116754505|ref|YP_843623.1| 120 ALSDVGLKGYERRPAKVLSGGEMQRVALARALAISP---ELLLLDEPTANLDPRTSYVIEELISRAKMRGMTTVVSTHD 195
                                    555555566777888888999777779999999988...9*************8888888999777667*********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 ?    3.7   0.0     0.024        36      27      42 ..      33      48 ..      11      53 .. 0.79
   2 !   14.5   0.0   1.2e-05     0.018     136     210 ..     136     208 ..      65     216 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.024
                                   EEEEESTTSSHHHHHH CS
                                   xxxxxxxxxxxxxxxx RF
                          SMC_N 27 taivGpNGSGKsnlld 42
                                     i+Gp G+GK+ ll 
  gi|116754505|ref|YP_843623.1| 33 LGIIGPTGAGKTTLLR 48
                                   469*********9875 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 1.2e-05
                                    CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSH.HHCCC-SCEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx.xxxxxxxxxxx RF
                          SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislre.emlekadklvg 210
                                    +LSgGe + vala  +Ai       l llDe  a+LD +    + el+ +++ + +  +v +++  + ++ ad++v 
  gi|116754505|ref|YP_843623.1| 136 VLSGGEMQRVALARALAISP----ELLLLDEPTANLDPRTSYVIEELISRAKMRgMTTVVSTHDLpQAVRLADRIVI 208
                                    8**************99964....489*********************97776637777777764145566666655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.1   0.00013       0.2       9      23 ..      34      48 ..      27      60 .. 0.86
   2 ?    4.6   0.0     0.024        36      56     122 ..     116     186 ..      93     200 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                         AAA_22  9 vvtGesGtGKTtllr 23
                                    ++G++G+GKTtllr
  gi|116754505|ref|YP_843623.1| 34 GIIGPTGAGKTTLLR 48
                                   59***********98 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.024
                         AAA_22  56 llrellralglelkaerlsseell.ealeqalrarav...ielliiDEaqh.lr..seealeeLrsllnlsrkg 122
                                      ++ l+++gl++ + r   + l    +++ + ara    +ell++DE    l+  +  ++eeL s+++    g
  gi|116754505|ref|YP_843623.1| 116 RVEAALSDVGLKGYE-RRPAKVLSgGEMQRVALARALaisPELLLLDEPTAnLDprTSYVIEELISRAK--MRG 186
                                    455666777776666.8888888889999999999999**********877798755888888888777..444 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.2   5.2e-06    0.0078      11      38 ..      21      49 ..      12      53 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.2e-06
                         AAA_23 11 rdqeidFskglt.lItGpNGaGKTTildA 38
                                    d +i+   g t  I+Gp+GaGKTT+l+ 
  gi|116754505|ref|YP_843623.1| 21 TDINIEVRTGETlGIIGPTGAGKTTLLRV 49
                                   55666665544416************986 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   1.7e-05     0.026      17      43 ..      25      51 ..      18      66 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.7e-05
                         AAA_29 17 ieidlkgatlltGpsGsGKSTllDAiq 43
                                   ie+++ ++  ++Gp+G+GK+Tll  + 
  gi|116754505|ref|YP_843623.1| 25 IEVRTGETLGIIGPTGAGKTTLLRVMD 51
                                   5555445677************95555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   4.1e-05     0.062      18      63 ..      26      70 ..      16     223 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.1e-05
                         AAA_16 18 rvrsgrpelvllsGesGvGKsslvrellr.alekdggiflrgkcdql 63
                                    vr+g  e + ++G+ G GK++l+r      l  +g ++++g++ ++
  gi|116754505|ref|YP_843623.1| 26 EVRTG--ETLGIIGPTGAGKTTLLRVMDLiDLPSKGRVLFKGEAPKN 70
                                   46666..56889************87664233333344466666665 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.8e-05     0.057      74     119 ..       4      50 ..       1      57 [. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.8e-05
                                    HTTSEEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHH CS
                    RsgA_GTPase  74 algyevllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinal 119
                                    ++++e + ++++ ++ l++++ +++  +t  ++G++G+GK+tL+ ++
  gi|116754505|ref|YP_843623.1|   4 TIQLEGVSIEKNGRQILTDINIEVRTgETLGIIGPTGAGKTTLLRVM 50 
                                    5666667777777888899998888879***************9876 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1    0.0002       0.3       3      18 ..      33      48 ..      31      60 .. 0.88
   2 ?    1.1   0.0      0.17   2.5e+02      89     124 ..     162     196 ..     130     231 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0002
                                   EEEEESTTCCHHHHHH CS
                           cobW  3 tvltGflGsGKTtLln 18
                                   +++ G+ G+GKTtLl+
  gi|116754505|ref|YP_843623.1| 33 LGIIGPTGAGKTTLLR 48
                                   6799***********8 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.17
                                    EECTTTTHHHHHTTSHHHHHCCCECEEEEEEETTTH CS
                           cobW  89 EttGlaePapvafteeelksdltldavvavvDaknl 124
                                    E t +++P ++    eel s++++ ++ +vv+ + l
  gi|116754505|ref|YP_843623.1| 162 EPTANLDPRTS-YVIEELISRAKMRGMTTVVSTHDL 196
                                    67778888888.557788889999999999988554 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00014      0.21      20      49 ..      32      61 ..      24      83 .. 0.78
   2 ?   -0.3   0.0      0.49   7.4e+02      81     109 ..     155     191 ..     112     211 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00014
                         AAA_30 20 vavltGpAGtGKttalkalreaweaaggrv 49
                                   +  + Gp G+GKtt+l+++  +   ++grv
  gi|116754505|ref|YP_843623.1| 32 TLGIIGPTGAGKTTLLRVMDLIDLPSKGRV 61
                                   56789************9877666555555 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.49
                         AAA_30  81 k.......grarlepgtllivDE.agmvdtkqlaall 109
                                             +a+l+p+t +++ E ++ + ++ +++++
  gi|116754505|ref|YP_843623.1| 155 PelllldePTANLDPRTSYVIEElISRAKMRGMTTVV 191
                                    2444444555667777777777732444444444433 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 ?    9.9   0.1   0.00057      0.86      27      81 ..     131     172 ..     103     181 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00057
                        SbcCD_C  27 srssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesi 81 
                                    +r ++ lSGGe q    +    ala ++        +++l++LDE  ++lD++++
  gi|116754505|ref|YP_843623.1| 131 RRPAKVLSGGEMQR---V----ALARALAI------SPELLLLDEPTANLDPRTS 172
                                    67788888888843...2....33333333......5789999999999999876 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1    0.0013       1.9       2      18 ..      32      48 ..      31      59 .. 0.87
   2 ?   -0.5   0.0       0.7     1e+03      90     128 ..     160     194 ..     143     205 .. 0.82
   3 ?   -0.8   0.1      0.86   1.3e+03      77      89 ..     200     212 ..     192     213 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0013
                                   CEEEEC-TTTCHHHHHH CS
                          NACHT  2 lvilqGeaGsGKTtLlq 18
                                   ++ + G+ G GKTtLl+
  gi|116754505|ref|YP_843623.1| 32 TLGIIGPTGAGKTTLLR 48
                                   56699**********97 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.7
                                    STT-SS-TCH.........HHHHHCTTTTT--EEEEEEE CS
                          NACHT  90 lDelvtdlgqkekqpvrtlLselirkkllpeasllltvr 128
                                    lDe  + l++    ++  +++eli+++ +++ + +++++
  gi|116754505|ref|YP_843623.1| 160 LDEPTANLDP----RTSYVIEELISRAKMRGMTTVVSTH 194
                                    4666666666....7788999999999999999999886 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.86
                                    CCSCCCEEEEEE- CS
                          NACHT  77 lelperlLlilDg 89 
                                    ++l++r+++i+Dg
  gi|116754505|ref|YP_843623.1| 200 VRLADRIVIIMDG 212
                                    7899********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 1857.10
//
Query:       gi|116754506|ref|YP_843624.1|  [L=228]
Description: binding-protein-dependent transport systems inner membrane component [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-15   57.1  13.8    2.6e-15   56.6  13.8    1.2  1  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
      0.045   14.4   0.5      0.076   13.7   0.5    1.4  1  AIRS          AIR synthase related protein, N-terminal domain
       0.22   11.3   5.4          2    8.2   0.4    3.1  2  DUF3188       Protein of unknown function (DUF3188)


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 !   56.6  13.8   4.4e-19   2.6e-15       2     179 ..      45     225 ..      44     228 .] 0.87

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 4.4e-19
                   BPD_transp_1   2 illGilaalnrnkkldkllrpliivllslPsfvlaillvlvf.....vilsilghlilpviillllsaapyvrlirraal 76 
                                    ++lG+l+  +++++++  l +li++l+s+P++ ++++++l++         +l ++  ++ii  ++ ++p+++ ++ +al
  gi|116754506|ref|YP_843624.1|  45 VPLGSLIH-FHHFPGRSGLINLIQTLYSIPTVTVGLFVFLLIsregpLGGYGLLYTPYGMIIGQTVLITPVILGLTISAL 123
                                    79999999.999***************************999***654444555666669******************** PP

                   BPD_transp_1  77 rslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseisng 156
                                    +s+++d + +a  lGa r+q++++v++  a  p+++ ++l fg++l +  ++ ++g++    t++l++ ++  +s+++  
  gi|116754506|ref|YP_843624.1| 124 SSVSEDIRDTAVSLGADRFQTMWTVIV-EARGPVLAAVLLGFGRALSEVGVAMMIGGNIRGYTRVLTTAIALETSMGNLE 202
                                    ***********************8888.89999***********************988777777777777777777778 PP

                   BPD_transp_1 157 gvlalviavlllnlvadilqrll 179
                                    +++al+++++ + lv++ ++  l
  gi|116754506|ref|YP_843624.1| 203 ISIALGLILISIALVVNTVVGRL 225
                                    88888888888888887766554 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 ?   13.7   0.5   1.3e-05     0.076      24      88 ..     121     191 ..     100     209 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.3e-05
                                    HHHHHHHHHHHHHH.TTTEEEEEEEEEEEEC....HHHHHHHHHHHHHHHTT-.EEEEEEEEEESSEEEEE CS
                           AIRS  24 iGakavavnlsDla.amGArPlalllslalp....wleevvrglaeaaeelgv.plvgGdtsfsneptisv 88 
                                     +  +v + ++D a + GA+    + +++++     l++v+ g+++a++e+gv  ++gG++  +++++ ++
  gi|116754506|ref|YP_843624.1| 121 SALSSVSEDIRDTAvSLGADRFQTMWTVIVEargpVLAAVLLGFGRALSEVGVaMMIGGNIRGYTRVLTTA 191
                                    5677899999**99678***999999999999*********************456899999998743333 PP

>> DUF3188  Protein of unknown function (DUF3188)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.4   0.00034         2      23      37 ..      64      82 ..      40      86 .. 0.73
   2 ?    4.2   0.6    0.0061        36       2      14 ..     208     220 ..     206     227 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00034
                        DUF3188 23 r....lqslPallvGlgLi 37
                                   +    l+s+P ++vGl++ 
  gi|116754506|ref|YP_843624.1| 64 NliqtLYSIPTVTVGLFVF 82
                                   155559**********986 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0061
                        DUF3188   2 AplLillgllill 14 
                                    ++ Li+++l+++ 
  gi|116754506|ref|YP_843624.1| 208 GLILISIALVVNT 220
                                    5788888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); 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: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1685.51
//
Query:       gi|116754507|ref|YP_843625.1|  [L=293]
Description: ABC transporter tungsten-binding protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-22   80.5   0.0    1.9e-22   80.2   0.0    1.1  1  PBP_like_2      PBP superfamily domain
    9.8e-13   48.4   0.0    1.5e-12   47.8   0.0    1.3  1  SBP_bac_11      Bacterial extracellular solute-binding protei
    1.9e-05   24.2   0.0    0.00034   20.0   0.0    2.1  2  LysR_substrate  LysR substrate binding domain
     0.0082   16.1   0.0       0.31   10.9   0.0    2.2  2  SBP_bac_1       Bacterial extracellular solute-binding protei
  ------ inclusion threshold ------
      0.013   15.0   0.0      0.043   13.2   0.0    1.7  2  SBP_bac_6       Bacterial extracellular solute-binding protei
       0.17   11.6   0.0       0.82    9.4   0.0    1.9  2  SBP_bac_8       Bacterial extracellular solute-binding protei


Domain annotation for each model (and alignments):
>> PBP_like_2  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.2   0.0   6.5e-26   1.9e-22       8     281 ..      27     248 ..      20     249 .. 0.79

  Alignments for each domain:
  == domain 1  score: 80.2 bits;  conditional E-value: 6.5e-26
                     PBP_like_2   8 svgeifgaGstt.papalrklada.fekaapgakvnyastGSgagikalrngdvdfagsdrplteseia.agwaangagg 84 
                                    ++  +++a++t+ +++ l++ ++  fe++ +g++v + s+G+g +++++r gdvd+ +++++++e e++ +g+++ +   
  gi|116754507|ref|YP_843625.1|  27 ER--LRIATTTSlYDTKLLDTLESrFEEK-YGIEVDVISGGTGFALEQGRRGDVDLLLVHDKAREYEFIaEGYGTER--- 100
                                    44..666666551456666666669****.7**********************************************... PP

                     PBP_like_2  85 liqvpvaigaialvvnkdnpln....lsreaLakIfsgkItnWndvlglpadgpIkvvhrsdgsgttflfstalaeqgpw 160
                                       + +a++ + +v++ d+p++     + ea++ I             + ++ ++++v+r+d+sg      t+  e+ +w
  gi|116754507|ref|YP_843625.1| 101 ---RCFAYNYFYIVGPADDPAGikgtNASEAFRMIAD----------AGEKNSNVRFVSRGDNSG------THAREKLLW 161
                                    ...******************9666667777777744..........4458**************......********* PP

                     PBP_like_2 161 tasgigasgsegvasavsnngaigyvsvaywlavkgysladvtngagkfvlptaataasalkvakiasnplawslqpvee 240
                                    +++gi+ sgs+     +s++g+++++ + +++  ++y+l+d       ++ ++    a  l            sl+p++ 
  gi|116754507|ref|YP_843625.1| 162 KSAGIEPSGSWY---LESGQGMGATLIMVDEK--RAYTLTD-----MSTYMAF----AGNL------------SLVPLV- 214
                                    *****9555554...4588**99999999899..79*****.....4566666....6633............345554. PP

                     PBP_like_2 241 niadgayPlsrftyiivyqpyayhgnnaalakaFldyllsd 281
                                         +  l + + +i +++   h    + a+ F+++lls 
  gi|116754507|ref|YP_843625.1| 215 ---TESEELLNVYAAIPVSASE-H---LDDAERFVEFLLSQ 248
                                    ...4677777777777777543.3...67777777777775 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 !   47.8   0.0   4.9e-16   1.5e-12       2     228 ..      30     258 ..      29     259 .. 0.82

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 4.9e-16
                                    EEEE-SST..HHHHHHHHHHHHHHH---EEEEESSHHHHHHHHHHH..-SEEEESSH.HHHHHHHHGGGGGGG-EEEEEE CS
                     SBP_bac_11   2 tvaaagsl..aaalrelaaaFeahtgvkvevsaggsgklarqiadgarpDvwipassawlellaaaglvqaesavplass 79 
                                    ++a+ +sl  ++ l+ l  +Fe+++g++v+v +gg g +++q ++g ++D+++  + a   + +a+g+++  +++ +a++
  gi|116754507|ref|YP_843625.1|  30 RIATTTSLydTKLLDTLESRFEEKYGIEVDVISGGTGFALEQGRRG-DVDLLLVHDKAREYEFIAEGYGT--ERRCFAYN 106
                                    6666677644578999******************************.***********************..******** PP

                                    EEEEEESTT-TT---SHHH......HHHS...S--EEEE--T-TTTTH..H.HHHHGGG--HHHHHHHHHTEEEEESSHH CS
                     SBP_bac_11  80 plviavpkgnpkkikgwad......Llkp...glklavadPttspsGl..aalalleaagaqellkalekkvvklgessr 148
                                       i+ p++ p++ikg ++      ++++   + ++ +++ + ++sG+  + + l++ ag    ++   ++   +g++ +
  gi|116754507|ref|YP_843625.1| 107 YFYIVGPADDPAGIKGTNAseafrmIADAgekNSNVRFVS-RGDNSGThaREKLLWKSAG----IEPSGSWYLESGQGMG 181
                                    ***********99997777444443344355433455554.3455666215557888889....6777889999****** PP

                                    HHHHHHHTTT-SEEEEEHHHHH..HSTTSSEEEE--TTT--...EEEEEEEE-TT--HHHHHHHHHTTSHHHHHHHHHTT CS
                     SBP_bac_11 149 qlltaveageadagivyeseakaaengdkleavylpeglnldpldypaavlkkaakreaAraFlafLrspeaqailrkyG 228
                                     +l  v++++a  ++   +  ++a+n   +++v+ +e+l+    +y+a+ ++ + +   A++F++fL+s+e+q+i++ yG
  gi|116754507|ref|YP_843625.1| 182 ATLIMVDEKRAYTLTDMSTYMAFAGNLSLVPLVTESEELLN---VYAAIPVSASEHLDDAERFVEFLLSQEGQEIIAGYG 258
                                    **********9999999999998777777777777777773...7777777888999********************999 PP

>> LysR_substrate  LysR substrate binding 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   0.00034       2      82 ..      23     103 ..      22     107 .. 0.95
   2 ?    2.1   0.0     0.036   1.1e+02     103     142 ..     141     180 ..     133     248 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.1e-07
                                    TTSCEEEEEEEECCCHHHHHHHHHHHHHHHSTTEEEEEEEESHHHHHHHHHTTSSSEEEEESSSCCTTEEEEEEEEEEEE CS
                 LysR_substrate   2 gglrgrLrigapptlaryllppllarfraryPevelelvegdseelldllaegelDlairagppedsglearpLaeeplv 81 
                                    g+   rLri+++++l  + l + l++  ++  ++e+++ +g +   l++ ++g++Dl ++++  ++ +++a+  ++e+++
  gi|116754507|ref|YP_843625.1|  23 GETDERLRIATTTSLYDTKLLDTLESRFEEKYGIEVDVISGGTGFALEQGRRGDVDLLLVHDKAREYEFIAEGYGTERRC 102
                                    56788********************999999********************************************99998 PP

                                    E CS
                 LysR_substrate  82 l 82 
                                     
  gi|116754507|ref|YP_843625.1| 103 F 103
                                    6 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.036
                                    TSEEEEESTTSTHHHHHHHHHHCTTEECEEEEEESSHHHH CS
                 LysR_substrate 103 deplilleegsglrdlledalreaglkprvalevnsleal 142
                                    + +++ + ++sg++ +   + ++ag++p +++ ++s + +
  gi|116754507|ref|YP_843625.1| 141 NVRFVSRGDNSGTHAREKLLWKSAGIEPSGSWYLESGQGM 180
                                    678999999999999999999*******999999887654 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 ?    3.6   0.0     0.018        53      17      69 ..      49      95 ..      32     118 .. 0.70
   2 !   10.9   0.0   0.00011      0.31     283     315 .]     218     252 ..     105     252 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.018
                                   HHHHHHTTEEEEEEEECHHHHHHHHHHHHHTTS.SSCSEEEECGGHHH..HHHHTT CS
                      SBP_bac_1 17 afekehpgikVeiesvgsgslaqkltlaiaaGd.gpaDviavdndwia..rlakag 69
                                   +fe+ ++gi+V ++s+  g++       +++G+ g+ D+  v +d+ +  +++ +g
  gi|116754507|ref|YP_843625.1| 49 RFEE-KYGIEVDVISG--GTGFA-----LEQGRrGDVDLLLV-HDKAReyEFIAEG 95
                                   3888.68******888..55555.....44555455588888.4444433555555 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00011
                                    E..EEEEEEEEBTTCSTHHHHHHHHHHHTSHHHHH CS
                      SBP_bac_1 283 i..lgayglaipkgsknpeaAkkFldfllspeaqa 315
                                       l++y  + +++s + + A+ F++flls e+q+
  gi|116754507|ref|YP_843625.1| 218 EelLNVYAAIPVSASEHLDDAERFVEFLLSQEGQE 252
                                    15579999*************************96 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 ?   -0.9   0.0      0.29   8.6e+02      47      67 ..     168     191 ..     162     197 .. 0.85
   2 ?   13.2   0.0   1.4e-05     0.043     176     213 ..     220     258 ..     187     270 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.29
                      SBP_bac_6  47 pdgkyy...pygvgplvlavnkdr 67 
                                    p g +y   + g+g+++++v+++r
  gi|116754507|ref|YP_843625.1| 168 PSGSWYlesGQGMGATLIMVDEKR 191
                                    667888898999*********998 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1.4e-05
                      SBP_bac_6 176 lvspifmlvkkg.kkkelakafidfllspevqailakag 213
                                    l+++++++ +++ ++ ++a++f++flls+e+q+i+a  g
  gi|116754507|ref|YP_843625.1| 220 LLNVYAAIPVSAsEHLDDAERFVEFLLSQEGQEIIAGYG 258
                                    56666666666789*********************9876 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 ?   -0.5   0.0      0.28   8.5e+02       5      21 ..      49      65 ..      46      88 .. 0.87
   2 ?    9.4   0.0   0.00027      0.82     158     257 ..     125     256 ..      82     265 .. 0.63

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.28
                                   HHHHH-TEEEEEEE--S CS
                      SBP_bac_8  5 efekktgvkvnvvtaas 21
                                   +fe+k+g++v v++ ++
  gi|116754507|ref|YP_843625.1| 49 RFEEKYGIEVDVISGGT 65
                                   79**********98765 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00027
                                    .HHHHHHHHHHHHTT-...EE....-S..--SSTTTTTSBSEEEE-TTHHHHHH.....................-TTTS CS
                      SBP_bac_8 158 lkealellkklkdngk...ty....dtgadavsefanGevaftingswdiaaaq.....................kagkk 209
                                      ea++++++  ++     ++    ++g++a +++  +++ + ++gsw + + q                          
  gi|116754507|ref|YP_843625.1| 125 ASEAFRMIADAGEKNSnvrFVsrgdNSGTHAREKLLWKSAGIEPSGSWYLESGQgmgatlimvdekraytltdmsT---- 200
                                    3677888888774443244557776788899999999999999999999999997777777665432222222210.... PP

                                    EEEE--.............S--EEEEEEEEEEBTT.S-HHHHHHHHHHHHHTTSHHHHHHHH CS
                      SBP_bac_8 210 lgaivp.............kqgsfaggkglavpkn.aknedlaAldFlkwltspenqaalae 257
                                        ++              +  ++++ + a+p + +++ d  A +F+++l+s e+q+  a 
  gi|116754507|ref|YP_843625.1| 201 ----YMafagnlslvplvtESEELLNV-YAAIPVSaSEHLD-DAERFVEFLLSQEGQEIIAG 256
                                    ....11333333333344334456666.3445554155556.5**************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); 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 0.24s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2265.69
//
Query:       gi|116754508|ref|YP_843626.1|  [L=347]
Description: hypothetical protein Mthe_1205 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 2482.82
//
Query:       gi|116754509|ref|YP_843627.1|  [L=677]
Description: carbohydrate-binding and sugar hydrolysis [Methanosaeta thermophila PT]
Scores for complete 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-94  314.5  63.9    5.8e-47  160.0  14.2    4.1  4  NosD             Periplasmic copper-binding protein (NosD)
    2.1e-59  199.9  78.4    4.6e-22   78.5  20.5    4.5  4  Beta_helix       Right handed beta helix region
      2e-08   34.3  41.2     0.0018   18.1   2.7    5.7  5  Pectate_lyase_3  Pectate lyase superfamily protein
  ------ inclusion threshold ------
      0.061   12.0   0.0       0.16   10.7   0.0    1.8  1  Pectinesterase   Pectinesterase


Domain annotation for each model (and alignments):
>> NosD  Periplasmic copper-binding protein (NosD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   8.3   8.7e-15   3.9e-11      32     148 ..     102     217 ..      84     217 .. 0.86
   2 !   77.5  16.5   2.1e-25   9.2e-22      61     173 ..     197     307 ..     194     309 .. 0.91
   3 !   70.1   8.0   3.8e-23   1.7e-19      17     169 ..     309     458 ..     304     462 .. 0.97
   4 !  160.0  14.2   1.3e-50   5.8e-47      17     240 ..     441     667 ..     438     668 .. 0.95

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 8.7e-15
                           NosD  32 neisnsrdgilldnssnntitgntienlryGihlensesntiedntlssnesGialmsssnntlenNtisnnenyGills 111
                                    n+   + +gi    s+n+ i+++ ++++ +G+ l + +++++  n+++   +Gi+  ss+ nt++ N++ +n+n+Gil+ 
  gi|116754509|ref|YP_843627.1| 102 NASAWGAAGI-RVLSENALISRCNVSDSFAGVLLLGGNGSVVDCNVTECHFAGIVAASSR-NTVKMNRAHENNNAGILIL 179
                                    4445555666.66689999********************777777776666****99999.******************* PP

                           NosD 112 dssnntisnNtis.nnnkGiflensssntitgNriesn 148
                                    +s++n +++N +s n ++Gi++++s++ ++++N+ + n
  gi|116754509|ref|YP_843627.1| 180 RSDENLVEGNDASyNLGSGIKVYKSNDCVVRNNTADTN 217
                                    *********************************97766 PP

  == domain 2  score: 77.5 bits;  conditional E-value: 2.1e-25
                           NosD  61 yGihlensesntiedntlssnesGialmsssnntlenNtisnnenyGillsdssnntisnNtisnnnkGiflensssnti 140
                                    +Gi + +s+++++++nt++ n++Gi+l++s+++t+e+N++ nn++ Gi+   ss ntis+Nt+  n+++++l++s +nti
  gi|116754509|ref|YP_843627.1| 197 SGIKVYKSNDCVVRNNTADTNDYGIVLSESHRCTVEGNILENNDY-GIYPYLSSTNTISRNTARTNDYAVYLYSSWNNTI 275
                                    799999999999999999999999999999999999999999987.9999999999999999999999999999999999 PP

                           NosD 141 tgNriesnqkiGilllsssegntiynNyFinns 173
                                    t+N +  n+ +Gil + +s++nti  N++  n+
  gi|116754509|ref|YP_843627.1| 276 TENDLRMNDAYGIL-IYYSDNNTISSNDLRSNE 307
                                    99999999999999.999999999999996665 PP

  == domain 3  score: 70.1 bits;  conditional E-value: 3.8e-23
                           NosD  17 ngiqlensegseisnneisnsrdgilldnssnntitgntienlryGihlensesntiedntlssnesGialmsssnntle 96 
                                     g+ + +s+g+++ +n + +s++++++++++ n  +gn+i+n+++Gi le s +nt+++nt+s++  Gi+++s ++n++e
  gi|116754509|ref|YP_843627.1| 309 GGLSVRGSRGNRLCGNMMGDSPYSLHIEDAEFNIAEGNRISNGETGIILERSMNNTLSGNTISETLTGISVSSGRGNIIE 388
                                    589999************************************************************************** PP

                           NosD  97 nNtisnnenyGillsdssnntisnNtisnnnkGiflensssntitgNriesnqkiGilllsssegntiynNyF 169
                                    +N++++++  Gi  ++s ++ is N i +++ +++l  s  ++++gN i +  + G+l +++s+g   ++N+F
  gi|116754509|ref|YP_843627.1| 389 GNNLTGCRL-GIEANASIGSIISANIIERCDLCVHLLHSPASRLEGNIIRQG-SSGVL-VEASDGFAAVDNTF 458
                                    *******99.*****************************************9.*****.*************9 PP

  == domain 4  score: 160.0 bits;  conditional E-value: 1.3e-50
                           NosD  17 ngiqlensegseisnneisnsrdgilldnssnntitgntienlryGihlensesntiedntlssnesGialmsssnntle 96 
                                    +g+ +e s+g+   +n+ + ++ +i++++s++ +++++ i+  +++i +++se++++e+n +s++++Gi l  s ++ + 
  gi|116754509|ref|YP_843627.1| 441 SGVLVEASDGFAAVDNTFDGVPRAITITASHGSRVSNSSITGADTAILVNSSEEVVVEGNSMSNSTEGIRLLASYDTEIA 520
                                    69999*************************************************************************** PP

                           NosD  97 nNtisnnenyGillsdssnntisnNtisnnnkGiflensssntitgNriesn.....qkiGilllsssegntiynNyFin 171
                                    +N+i++ +n Gi+l++s++nti++N+is++n+Gi+l++s +n+++ N+i++n      + G++   +s++n+iy N+F++
  gi|116754509|ref|YP_843627.1| 521 GNVITGAKN-GIILDESNENTIEENNISRCNSGITLSRSWRNVLMMNNISYNtnglvLDEGMY-PIESSENQIYLNSFVQ 598
                                    *********.******************************************55555556666.777889********** PP

                           NosD 172 nsenvkydgsnnneWnttktsgtniiggpylg..GNyWsdydgeDadgDGigDtpYeindgviDylplvnp 240
                                    n+++v    s  n W++++  ++ + g ++ +  GNyW+  +geD++gDGi D+  ++  ++ D +pl++p
  gi|116754509|ref|YP_843627.1| 599 NRNDVVSYIS-SNFWSSPTSIRYIYRGRSFESrmGNYWHGLEGEDRNGDGILDSGRSVGLED-DPYPLAEP 667
                                    *****99997.********99*********9999****************************.*****988 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 !   78.5  20.5     1e-25   4.6e-22       2     157 ..     110     257 ..      84     258 .. 0.87
   2 !   54.8  14.4   2.1e-18   9.3e-15      22     128 ..     217     320 ..     215     328 .. 0.90
   3 !   51.7  11.3   1.9e-17   8.5e-14      22     158 .]     329     458 ..     317     458 .. 0.90
   4 !   55.5  18.3   1.3e-18   5.8e-15       2     139 ..     464     601 ..     463     625 .. 0.87

  Alignments for each domain:
  == domain 1  score: 78.5 bits;  conditional E-value: 1e-25
                                    SEEE-SS-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--E CS
                     Beta_helix   2 gisingssnvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasnnl 81 
                                    gi + +++   i+ +++s+ + +G+ l g+++ v++ ++++ + + Gi   + s+nt++ n+ ++nn+ gi +  ++ nl
  gi|116754509|ref|YP_843627.1| 110 GIRVLSENA-LISRCNVSD-SFAGVLLLGGNGSVVD-CNVTECHFAGIVAAS-SRNTVKMNRAHENNNAGILILRSDENL 185
                                    455555555.788888888.6888888888886666.888887888888775.*************************** PP

                                    EES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS--EEES-E CS
                     Beta_helix  82 ienneitdnggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsssnvtvrnNt 157
                                    +e+n+ + n gsGi ++ s++++++nN++d n  +Giv+++s  ++tv++N++ nn+ +Gi+ + ss+ +t+++Nt
  gi|116754509|ref|YP_843627.1| 186 VEGNDASYNLGSGIKVYKSNDCVVRNNTADTND-YGIVLSESH-RCTVEGNILENND-YGIYPYLSST-NTISRNT 257
                                    *********************************.*********.************8.**********.*****98 PP

  == domain 2  score: 54.8 bits;  conditional E-value: 2.1e-18
                                    SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES-EEES-SS-SEE-TT-S CS
                     Beta_helix  22 ggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasnnlienneitdnggsGiylnyss 101
                                    ++yGi l +s+++++e+n ++n +++Giy + ss ntis+nt + n  ++++l+ + nn+i  n+ ++n+ +Gi ++ys+
  gi|116754509|ref|YP_843627.1| 217 NDYGIVLSESHRCTVEGNILEN-NDYGIYPYLSSTNTISRNTARTND-YAVYLYSSWNNTITENDLRMNDAYGILIYYSD 294
                                    789*************999999.9*******9************999.9********************999******** PP

                                    --EEES-EEESTT--SEE---TT---E CS
                     Beta_helix 102 nntienNiidnnagsGividdsssnvt 128
                                    nnti+ N +++n+  G++++ s  +++
  gi|116754509|ref|YP_843627.1| 295 NNTISSNDLRSNEIGGLSVRGSR-GNR 320
                                    ************99999999998.444 PP

  == domain 3  score: 51.7 bits;  conditional E-value: 1.9e-17
                                    SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES-EEES-SS-SEE-TT-S CS
                     Beta_helix  22 ggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasnnlienneitdnggsGiylnyss 101
                                    + y +++++++ ++ e+n+i+n +++Gi +++s nnt+s+ntis+   +gi ++ + +n+ie+n+ t ++  Gi+ n s 
  gi|116754509|ref|YP_843627.1| 329 SPYSLHIEDAEFNIAEGNRISN-GETGIILERSMNNTLSGNTISETL-TGISVSSGRGNIIEGNNLTGCRL-GIEANASI 405
                                    678999****************.*********************999.*********************98.******** PP

                                    --EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS--EEES-E. CS
                     Beta_helix 102 nntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsssnvtvrnNti 158
                                      +i+ Nii+ +    +++  s    + ++N+i + +  G+ v  s++ +  + Nt+
  gi|116754509|ref|YP_843627.1| 406 GSIISANIIERCD-LCVHLLHSP-ASRLEGNIIRQGS-SGVLVEASDG-FAAVDNTF 458
                                    *************.999999999.7777******998.***5555555.99999987 PP

  == domain 4  score: 55.5 bits;  conditional E-value: 1.3e-18
                                    SEEE-SS-E.EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--E CS
                     Beta_helix   2 gisingssnvtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasnnl 81 
                                    +i i+ s++  ++n+ i++  +++i +++s+ vv+e+n ++n s++Gi++l s ++ i +n+i++ +  gi l++++ n+
  gi|116754509|ref|YP_843627.1| 464 AITITASHGSRVSNSSITG-ADTAILVNSSEEVVVEGNSMSN-STEGIRLLASYDTEIAGNVITGAK-NGIILDESNENT 540
                                    57788888889********.6*********************.************************.************ PP

                                    EES-EEES-SS-SEE-TT-S--EEES-EEESTT--SEE---TT.....---EEES-EEES-SS CS
                     Beta_helix  82 ienneitdnggsGiylnyssnntienNiidnnagsGividdss.....snvtvtnNtitnnkg 139
                                    ie n+i+++++ Gi+l+ s +n++  N+i+ n+ +G+v+d++      s++ +  N++++n++
  gi|116754509|ref|YP_843627.1| 541 IEENNISRCNS-GITLSRSWRNVLMMNNISYNT-NGLVLDEGMypiesSENQIYLNSFVQNRN 601
                                    *********87.*****9999999999999999.89999999955555566666666666664 PP

>> Pectate_lyase_3  Pectate lyase superfamily protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1     0.075   3.4e+02     154     211 ..      91     150 ..      49     155 .. 0.72
   2 !   18.1   2.7   4.1e-07    0.0018     132     214 ..     160     243 ..     155     244 .. 0.90
   3 !    8.6   8.6   0.00034       1.5      99     215 .]     267     400 ..     246     400 .. 0.63
   4 !   13.9   0.4   8.3e-06     0.037     145     215 .]     440     510 ..     426     510 .. 0.80
   5 !    9.8   2.9   0.00015      0.66     162     213 ..     523     574 ..     511     577 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.075
                                    -EEEEES-EEES...-SS-SEEES-EEEEEES-EEE-S--SEEE-TT-EEEEEEEEEESSS CS
                Pectate_lyase_3 154 sggflndlvfsg...lgdigiavgnqqftvrnitfnnattgievlwgwgwtlknvkinnce 211
                                     g  ++++++++    g+ gi+v ++++ ++++ ++++  g+ +l g+g ++ ++++ +c 
  gi|116754509|ref|YP_843627.1|  91 DGVNVSEFIITNasaWGAAGIRVLSENALISRCNVSDSFAGVLLLGGNGSVV-DCNVTECH 150
                                    3444466777775556778888878888888888888888888885555444.78888886 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 4.1e-07
                                    S-SSEEE-SSS---TT---SS--EEEE..ES-EEES-SS-SEEE.S-EEEEEES-EEE-S--SEEE-TT-EEEEEEEEEE CS
                Pectate_lyase_3 132 nvefemseasgtkhqgifiengsggfl..ndlvfsglgdigiav.gnqqftvrnitfnnattgievlwgwgwtlknvkin 208
                                    +++++m+ a+++++ gi+i ++ ++ +  nd+ ++   + gi+v ++++ +vrn+t  ++  gi ++++ + t++++ ++
  gi|116754509|ref|YP_843627.1| 160 RNTVKMNRAHENNNAGILILRSDENLVegNDASYNL--GSGIKVyKSNDCVVRNNTADTNDYGIVLSESHRCTVEGNILE 237
                                    56899*****9****************877777766..99****99*********************9999******999 PP

                                    SSSEEE CS
                Pectate_lyase_3 209 ncegGi 214
                                    n   Gi
  gi|116754509|ref|YP_843627.1| 238 NNDYGI 243
                                    998887 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.00034
                                    EEEEGGGG-SS---SSEEEES-EEEEEEEEEEES-SSEEE-SSS.....---TT--............-SS--EEEEES- CS
                Pectate_lyase_3  99 fyrqirnlkiditavapgatgihwqtaqatslenvefemseasg.....tkhqgif............iengsggflndl 161
                                    +y+++ n ++  +   ++a+gi   ++++ ++++++++++e  g       +++++            i        +d+
  gi|116754509|ref|YP_843627.1| 267 LYSSWNNTITENDLRMNDAYGILIYYSDNNTISSNDLRSNEIGGlsvrgSRGNRLCgnmmgdspyslhI--------EDA 338
                                    566677755555554555677777777777777777777776643433322222222222111111113........455 PP

                                    EEES.......-SS-SEEE.S-EEEEEES-EEE-S--SEEE-TT-EEEEEEEEEESSSEEEE CS
                Pectate_lyase_3 162 vfsg.......lgdigiav.gnqqftvrnitfnnattgievlwgwgwtlknvkinncegGid 215
                                    +f+        +g++gi + ++ + t++ +t++++ tgi+v++g+g +++++++ +c  Gi+
  gi|116754509|ref|YP_843627.1| 339 EFNIaegnrisNGETGIILeRSMNNTLSGNTISETLTGISVSSGRGNIIEGNNLTGCRLGIE 400
                                    444444444444999999977************************************99985 PP

  == domain 4  score: 13.9 bits;  conditional E-value: 8.3e-06
                                    -TT---SS--EEEEES-EEES-SS-SEEE.S-EEEEEES-EEE-S--SEEE-TT-EEEEEEEEEESSSEEEE CS
                Pectate_lyase_3 145 hqgifiengsggflndlvfsglgdigiav.gnqqftvrnitfnnattgievlwgwgwtlknvkinncegGid 215
                                     +g+++e + g    d +f+g    +i++  ++ + v+n  +++a t+i v++++++++++++++n+++Gi+
  gi|116754509|ref|YP_843627.1| 440 SSGVLVEASDGFAAVDNTFDG-VPRAITItASHGSRVSNSSITGADTAILVNSSEEVVVEGNSMSNSTEGIR 510
                                    346666665554448******.555566648*********************9999**************95 PP

  == domain 5  score: 9.8 bits;  conditional E-value: 0.00015
                                    EEES-SS-SEEE.S-EEEEEES-EEE-S--SEEE-TT-E.EEEEEEEEESSSEE CS
                Pectate_lyase_3 162 vfsglgdigiav.gnqqftvrnitfnnattgievlwgwg.wtlknvkinncegG 213
                                    v++g  + gi +  +++ t++++ ++ ++ gi ++++w+ + ++n+  +n ++G
  gi|116754509|ref|YP_843627.1| 523 VITG-AKNGIILdESNENTIEENNISRCNSGITLSRSWRnVLMMNNISYN-TNG 574
                                    5677.7788888779************************55555554444.444 PP

>> Pectinesterase  Pectinesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   3.5e-05      0.16       3      48 ..      22      63 ..      20     128 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 3.5e-05
                                   EE-TTS-SSBSSHHHHHHHS-SS-SS-EEEEE-SEEEE--EEE-TT CS
                 Pectinesterase  3 vvakdgsgkfktiseavaavpeksekrfviyvkaGvYeenvevekk 48
                                    v +dg ++f++i++a+a + +      +i v +GvY e v+++k+
  gi|116754509|ref|YP_843627.1| 22 RVDDDGGADFSSIQDALALAGDG----DIIEVMSGVYAESVNITKS 63
                                   5789*************999754....59**************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (677 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); 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: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.43
# Mc/sec: 4682.19
//
Query:       gi|116754510|ref|YP_843628.1|  [L=146]
Description: type I restriction-modification system restriction subunit [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       752  (0.0419432); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); 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: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1128.62
//
Query:       gi|116754511|ref|YP_843629.1|  [L=41]
Description: restriction endonuclease S subunits [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                      1124  (0.0626917); expected 358.6 (0.02)
Passed bias filter:                      614  (0.0342462); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.24s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 330.46
//
Query:       gi|116754512|ref|YP_843630.1|  [L=448]
Description: putative transcriptional regulator [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      7e-18   64.6   0.0    1.4e-17   63.5   0.0    1.5  1  HATPase_c_4     Putative ATP-dependent DNA helicase recG C-te
    3.6e-14   53.1   0.0    6.7e-14   52.3   0.0    1.5  1  AlbA_2          Putative DNA-binding domain
     0.0023   17.6   0.0     0.0056   16.4   0.0    1.6  1  HTH_DeoR        DeoR-like helix-turn-helix domain
  ------ inclusion threshold ------
      0.029   14.6   0.2       0.12   12.6   0.1    2.0  2  PaaX            PaaX-like protein
       0.12   12.5   0.2       0.37   10.9   0.1    1.9  2  NYD-SP28_assoc  Sperm tail C-terminal domain


Domain annotation for each model (and alignments):
>> HATPase_c_4  Putative ATP-dependent DNA helicase recG C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.5   0.0     4e-21   1.4e-17       3      88 .]     284     369 ..     283     369 .. 0.97

  Alignments for each domain:
  == domain 1  score: 63.5 bits;  conditional E-value: 4e-21
                    HATPase_c_4   3 kvqieifdDRleItspGglpggvtveskllegrssaRNelLasllerlrlmeergsGiqrilealeeaglpepefredgs 82 
                                    ++qi++ + Rle+ spG+lp+++t+e +  +++s  RN+l+a+++   +++e++g+G  ri++ ++e+g+ epef   + 
  gi|116754512|ref|YP_843630.1| 284 DIQIRLEEGRLEVWSPGELPPPLTPEALYGPHSSVLRNPLIAQAFYFAGVIERWGTGTTRIIRLCHEQGFLEPEFAHWQG 363
                                    79*************************99***********************************************9999 PP

                    HATPase_c_4  83 sftvtl 88 
                                     ++vt+
  gi|116754512|ref|YP_843630.1| 364 GLRVTF 369
                                    999986 PP

>> AlbA_2  Putative DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.3   0.0   1.9e-17   6.7e-14       1     118 [.       8     110 ..       8     114 .. 0.81

  Alignments for each domain:
  == domain 1  score: 52.3 bits;  conditional E-value: 1.9e-17
                         AlbA_2   1 EdellEfKeslgnklkkrersiakticAfaNsegGtlliGVeDdgkvvGvecsdqeedqlrlelksiikrfkpkvlpdie 80 
                                    E e+lEfK+++ ++        +++++A+aN++gGtll+G+ Ddg++vG+  + ++++ +r+++  i++++   v+p+i+
  gi|116754512|ref|YP_843630.1|   8 EGETLEFKRQWTDR-------ALEDLAALANTRGGTLLVGIRDDGEIVGT--TVDDREVQRITNL-IASHLG--VTPSIQ 75 
                                    8899******9998.......679**************************..6666666666666.666665..778899 PP

                         AlbA_2  81 rvelkgkkvlvvkvekskkkplyeneegvvyiRrggss 118
                                     v++kg+ v++++ve++   +   ++ g++  R+g ++
  gi|116754512|ref|YP_843630.1|  76 VVDMKGRPVIEIQVEPAAGLV---SYGGRYLRRVGTTN 110
                                    999*************99888...44455555555554 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.5e-06    0.0056       1      45 [.     387     431 ..     387     440 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.5e-06
                       HTH_DeoR   1 RieqilellkqqgklsveelvellgvSeaTiRRDLneLeeqgllt 45 
                                    R+ q + ++k++gk++  e  +  gvS++ +R DL+ L+e g+l+
  gi|116754512|ref|YP_843630.1| 387 RQIQAVLYVKEHGKITNREFRAFTGVSDEGARLDLKRLVELGILK 431
                                    66677889**********************************975 PP

>> PaaX  PaaX-like protein
   #    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      31      54 ..     380     402 ..     377     409 .. 0.70
   2 ?   12.6   0.1   3.4e-05      0.12      33      66 ..     410     443 ..     404     446 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.6
                           PaaX  31 aelGiseslvRaalsRlakaGwlv 54 
                                     +lG++e+ + a l  ++++G ++
  gi|116754512|ref|YP_843630.1| 380 RALGLNERQIQAVL-YVKEHGKIT 402
                                    68999999997544.456666655 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 3.4e-05
                           PaaX  33 lGiseslvRaalsRlakaGwlvrekegrrsfYrL 66 
                                     G+s++  R  l Rl++ G l++  +gr ++Y+L
  gi|116754512|ref|YP_843630.1| 410 TGVSDEGARLDLKRLVELGILKPRGKGRSAYYAL 443
                                    59999999************************99 PP

>> NYD-SP28_assoc  Sperm tail C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.2   4.2e+03       5      21 ..     117     133 ..     116     137 .. 0.79
   2 ?   10.9   0.1    0.0001      0.37      16      42 ..     221     247 ..     216     259 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.2
                 NYD-SP28_assoc   5 rlanvipeeklklWdal 21 
                                    +la  i e+  ++Wd l
  gi|116754512|ref|YP_843630.1| 117 ELARHILERSGRTWDGL 133
                                    677788899999**998 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0001
                 NYD-SP28_assoc  16 klWdalekaLekYhevLteRaklieet 42 
                                     lW++le  +e++ +vL+ R ++  e 
  gi|116754512|ref|YP_843630.1| 221 TLWQQLEGVMERFRQVLKVRFEIKVEE 247
                                    59*******************997765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); 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: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 3277.78
//
Query:       gi|116754513|ref|YP_843631.1|  [L=522]
Description: N-6 DNA methylase [Methanosaeta thermophila PT]
Scores for 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  305.2   0.0    6.7e-91  304.8   0.0    1.1  1  N6_Mtase   N-6 DNA Methylase
    1.6e-30  106.5   0.0    3.6e-30  105.4   0.0    1.6  1  HsdM_N     HsdM N-terminal domain
     0.0015   18.2   0.0     0.0033   17.1   0.0    1.6  1  UPF0020    Putative RNA methylase family UPF0020
  ------ inclusion threshold ------
      0.039   13.8   0.3       0.33   10.8   0.0    2.5  2  AAA_lid_2  AAA lid domain


Domain annotation for each model (and alignments):
>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  304.8   0.0   1.5e-94   6.7e-91       3     311 ..     163     487 ..     161     488 .. 0.94

  Alignments for each domain:
  == domain 1  score: 304.8 bits;  conditional E-value: 1.5e-94
                       N6_Mtase   3 kdllGdvYEyllrkfaeeegksgGeffTPrevsklivellepksgesvyDpacGsggllvqaekvlkee........... 71 
                                     d+lG++YEyllrkfae +g+s+Gef+TPrev  l++++lep++g +vyDpacGsggll++ +  l e+           
  gi|116754513|ref|YP_843631.1| 163 PDILGRAYEYLLRKFAEGQGQSAGEFYTPREVAVLMARILEPEPGMTVYDPACGSGGLLIKCHLRLLETrgeqqnghrrl 242
                                    69***********************************************************9987777768888877776 PP

                       N6_Mtase  72 dgktkelsiyGqeknettyrLakmNlllhgieykkvkirlgdtlekpkfe....kdkkfdvvvaNppfnqkewkektlek 147
                                      ++  l ++Gqe+n+tt+++a+mN ++h++e +   irlgdt+ +p f+      ++fd v aNp +nq+ +  +  e+
  gi|116754513|ref|YP_843631.1| 243 PPEHAPLRLFGQEINPTTFAMARMNAVIHDMEAD---IRLGDTMRNPAFRdatgRLMTFDLVTANPMWNQD-FPTEVYEN 318
                                    666778999***********************99...*************999999***************.*9999999 PP

                       N6_Mtase 148 de..rfreavapksnadlafllhiieslkpkGraavvlangvLfrg......gkegkIrkalvekdlveavialpeklFy 219
                                    d+  rfr +v+p+s+ad+ +l+h+++sl++ Gr+avvl+ g+ +rg      ++e +Ir+a+ve+dl+ea i lpe++Fy
  gi|116754513|ref|YP_843631.1| 319 DPyeRFRFGVPPSSSADWGWLQHMLASLNERGRMAVVLDTGAVSRGsgnqgsNRERDIRRAFVENDLIEAAILLPENMFY 398
                                    98889***************************************953344445799************************ PP

                       N6_Mtase 220 ntsiptcilvlkkekaerkgkvlfidaseefkkkdrkknklteediekildtykekskevdkfskvveleeiaendynln 299
                                    nt++p+ i+v+++ k  r g++l+i+as+ f k  r kn l +e+ie+i+  y+ + + +++ ++v++ ee a ndynl+
  gi|116754513|ref|YP_843631.1| 399 NTTAPGFIIVVNRRKR-RPGEILLINASKLFAKG-RPKNYLADEHIETIARLYHDW-RAEEGLAAVITNEEAARNDYNLS 475
                                    ***************5.9***************9.9********************.*********************** PP

                       N6_Mtase 300 vgryveteeeee 311
                                    ++ryv+++++ee
  gi|116754513|ref|YP_843631.1| 476 PSRYVASNDKEE 487
                                    ******998876 PP

>> HsdM_N  HsdM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.4   0.0     8e-34   3.6e-30       1     136 [.       8     150 ..       8     151 .. 0.84

  Alignments for each domain:
  == domain 1  score: 105.4 bits;  conditional E-value: 8e-34
                                    HHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHHHHHHHHHCC.................--..--------...... CS
                         HsdM_N   1 lesklwkaadiLRgkvdaseykeyilgLlFlKrlddveeereekllee..........ykenaleeleeklksk....ea 66 
                                    le +lw+aa+ +Rg +da+++k+yil+L+FlKrl+dv+e++ ++l+ee          ++    +e+e+ + ++      
  gi|116754513|ref|YP_843631.1|   8 LETWLWDAACAIRGPLDAPKFKDYILPLVFLKRLSDVFEDELDRLAEEfgsrdvatriVE----DERERGTIANsrgsVR 83 
                                    789*********************************************666553333222....2333322222455699 PP

                                    ..S-CCCSHHHHHHS--HHHHHHHHHHCHHHHCT--STHHHHHHHS.......S-----SSHHHHHHHHHH CS
                         HsdM_N  67 fyipeelrWkelakkkdddelgenlnkafpaleelnkslkgvfmkd.dfnafalgeitkkspalLskviek 136
                                    fyipe++rW++++k+ ++  lg+ l++a++a++++n+ l+gv++   dfna+a g+ +  +++ L+k+++ 
  gi|116754513|ref|YP_843631.1|  84 FYIPERARWSNIRKQTTG--LGQYLTDAVRAVARENPRLRGVID-LvDFNATAAGQ-HIVPDEYLAKLVNV 150
                                    **************8888..***********************7.46*****9999.5999******9985 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   7.4e-07    0.0033      16     102 ..     194     274 ..     191     311 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 7.4e-07
                                    HHHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHH......HH--EEEEES-HHHH CS
                        UPF0020  16 LAaalvrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeear......aelklygsDldrrvv 89 
                                    +A  + r+ + +pg + +DP CGsG++lI   l   +   g  ++             r      a l+l+g ++++   
  gi|116754513|ref|YP_843631.1| 194 VAVLMARILEPEPGMTVYDPACGSGGLLIKCHLRLLETR-GEQQNG-----------HRrlppehAPLRLFGQEINPTTF 261
                                    6788999999*******************8777666666.222211...........11122211334477777777777 PP

                                    HHHHHHHHHTT-G CS
                        UPF0020  90 qgareNaekagvg 102
                                    + ar Na    ++
  gi|116754513|ref|YP_843631.1| 262 AMARMNAVIHDME 274
                                    7777777655555 PP

>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.38   1.7e+03      30      59 ..     131     161 ..     126     167 .. 0.81
   2 ?   10.8   0.0   7.5e-05      0.33      18      56 ..     417     455 ..     413     470 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.38
                      AAA_lid_2  30 AalegrdyVtpeDvkeaaplVLaHRlr.rep 59 
                                    A  +g++ V +e + +++    +HRl  r+ 
  gi|116754513|ref|YP_843631.1| 131 ATAAGQHIVPDEYLAKLVNVLSRHRLGlRDV 161
                                    6677888899999999999999***987655 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 7.5e-05
                      AAA_lid_2  18 adlallraArAlAalegrdyVtpeDvkeaaplVLaHRlr 56 
                                    +++ l++a++ +A  + ++y ++e+++++a+l    R+ 
  gi|116754513|ref|YP_843631.1| 417 GEILLINASKLFAKGRPKNYLADEHIETIARLYHDWRAE 455
                                    89*****************************98887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (522 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); 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: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 3867.93
//
Query:       gi|116754514|ref|YP_843632.1|  [L=196]
Description: type I restriction-modification system specificity subunit, partial [Methanosaeta thermophila PT]
Scores for complete 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-23   82.4   0.2    1.1e-22   81.2   0.1    1.6  2  HsdM_N    HsdM N-terminal domain


Domain annotation for each model (and alignments):
>> HsdM_N  HsdM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.2   0.1     6e-27   1.1e-22       1     137 []       9     145 ..       9     145 .. 0.90
   2 ?   -1.4   0.0      0.18   3.2e+03      83     103 ..     170     190 ..     164     196 .] 0.72

  Alignments for each domain:
  == domain 1  score: 81.2 bits;  conditional E-value: 6e-27
                                    HHHHHHHHH.HHHHHS-SHHHHHHHHHHHHHHHHHHHHHHHHHHCC..............--..--------....S-CC CS
                         HsdM_N   1 lesklwkaa.diLRgkvdaseykeyilgLlFlKrlddveeereekllee..yken.....aleeleeklkskeafyipee 72 
                                    +++++w +a d LR+ + + +y+++il++++++rld+v+e++++++l+             +++ + ++++++afy++++
  gi|116754514|ref|YP_843632.1|   9 ITNFIWGIAdDVLRDLYVRGKYRDVILPMTVIRRLDAVLEPTKQAVLDMkaS--LdkagiVHQDAALRQAAGQAFYNTSP 86 
                                    679******999**558*****************************999551..334455337888999999******** PP

                                    CSHHHHHHS--HHHHHHHHHHCHHHHCT--STHHHHHHHS......S-----SSHHHHHHHHHHH CS
                         HsdM_N  73 lrWkelakkkdddelgenlnkafpaleelnkslkgvfmkddfnafalgeitkkspalLskviekf 137
                                    +++++l+++++ ++l++++++++++++ +   +++++   d+++f++++ ++ + + L  +iekf
  gi|116754514|ref|YP_843632.1|  87 FTLRDLKARASRQQLEADFRAYLDGFSPN---VQEII---DNFEFRNQIPRLAKADALGTLIEKF 145
                                    *********88889**************9...*****...679********************98 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.18
                                    -HHHHHHHHHHCHHHHCT--S CS
                         HsdM_N  83 dddelgenlnkafpaleelnk 103
                                    d+ ++g  ++++++ ++e+n+
  gi|116754514|ref|YP_843632.1| 170 DNHAMGTIFEELVRRFNEENN 190
                                    455688888888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); 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: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1492.18
//
Query:       gi|116754515|ref|YP_843633.1|  [L=406]
Description: ADP-dependent glucokinase [Methanosaeta thermophila PT]
Scores for complete 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-60  203.3   0.0    8.5e-60  202.5   0.0    1.4  1  ADP_PFK_GK  ADP-specific Phosphofructokinase/Glucokinase cons
    0.00083   18.7   1.6        1.3    8.3   0.0    3.1  3  PfkB        pfkB family carbohydrate kinase
  ------ inclusion threshold ------
       0.22   11.1   0.8       0.97    9.0   0.1    2.2  2  AIRC        AIR carboxylase


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 !  202.5   0.0   1.4e-63   8.5e-60       4     423 ..       2     402 ..       1     403 [. 0.86

  Alignments for each domain:
  == domain 1  score: 202.5 bits;  conditional E-value: 1.4e-63
                                    EEES--EEEEE.....HHHHHHHHCC-HH.HHHHHHC--SSBSSHHHHHHHHHHHHHHT--EEEEB--HHHHHHHH.... CS
                     ADP_PFK_GK   4 avGynanvDai.....vdavelleklgleevkekseedhdeikskedlletfayffkkGaaaErfvenkelfeelvkaak 78 
                                    ++++n+n+D +     ++++ l+++l       +s e ++ i+s +dl+ ++++ + +G ++E+++e +++ +e+++   
  gi|116754515|ref|YP_843633.1|   2 LCAFNVNIDCVhtitgEEIEMLFRDLCPL---LRSLEIPSGITSLSDLAISILHHMGHGTGSELIIEGEKVADEIAS--- 75 
                                    79**********99999999999966633...4788999*************************************7... PP

                                    CC--SEEEEESHHHHHHHHHCCTT-EEEEE-.---HHHHTTS-SSEE........EEEEGGG-S-..---EEEEEEE-TT CS
                     ADP_PFK_GK  79 klkkaelrmGGnagimanrlakegakvllga.klskklkellsekiv........vlgkpseaske.kdeiHlIlEykkg 148
                                     l + e+rmGGnag +an+la++ga+ ++++ +l++++++l+++ ++         l++p+ ask+ ++  H++++y++g
  gi|116754515|ref|YP_843633.1|  76 -LFNWEIRMGGNAGNIANVLAALGAEPVVNVpSLTPRQASLFHHAVRvpvmgggvSLTDPVHASKDgQELRHFVIQYRSG 154
                                    .666668******************9999999*************55566677777789999999988899********* PP

                                    -EE....TEEE-SS-EEEEEE--STCGGTS--HHHCTTHHHHH..-SEEEE--GGG--TB-TTSTCHHHHHHHHHHHHHH CS
                     ADP_PFK_GK 149 ekw....geieapraNRfIissdpenlrlsileefkealkefk..pdllvlsGlqmleeqykegkereerlekvkeqlks 222
                                    e +    g+i apr+NR I++ dp n +++i+  f++ l + +  ++++vlsG+++   +       +e +e+   +++ 
  gi|116754515|ref|YP_843633.1| 155 ECVdtpsGRIMAPRENRIIATFDPLNRMMHINPAFRAFLGRPDpaVKGVVLSGFHLVPYEL-----HREIFEERLGLMRW 229
                                    ******888******************************887777***********99863.....56788888899999 PP

                                    HCCT-EEEEE----S-HHHHHHHHHHCGGG-SEEEE-HHHHHHHHHHTT-HHHCCSS...CC--HHHHHHHHHHHHH... CS
                     ADP_PFK_GK 223 lknkikiHlElAsfqdeellkeilekilpyvdslGlnEqElanllsvlggeekeltevsdkepriakvlealrkllkllk 302
                                    +      H E++sf+ ee+++ +le  + +vds+G+nE+El++l+++     +          +++++  a++++ +   
  gi|116754515|ref|YP_843633.1| 230 WLDTRYSHAEMGSFEREEVMRFLLE--ILEVDSIGMNEDELSMLADSG----E----------NWEDIAGAAEQIQE--- 290
                                    999999*******************..889*****************8....2..........34566677778888... PP

                                    ..HHTT-SEEEEEETTEEEEEEETTSSS-HHHHHHHHHHHHHHHHHHHHH-SH.HHHHHHH..........HS-B-TT.H CS
                     ADP_PFK_GK 303 kskkrkltrihvHtlayqiiltkkesewkneaakkalakaallAarkacnsdl.eklelklddsfsvskskkiplnek.e 380
                                      +  ++ r+ vHt+++ ++++   +   + ++ +al+ +a +A r a++ ++ ++++l+++d+ +   +  ++   +  
  gi|116754515|ref|YP_843633.1| 291 --EF-GIPRVCVHTREFTVSISP--D---PVKEIAALEMGAEIAGRLAATGSIdRSANLGVSDEGRRAVEDLLRAGGRrA 362
                                    ..66.9****************3..3...4445568**************644045667774444444444444444445 PP

                                    HHHHHHHCCEETTEEEEEEE-B--SS-S--TTHHHHHHHHHHH CS
                     ADP_PFK_GK 381 pvscweeeieleevevclaPvlvckkpkkTvGlGDtISaaglv 423
                                     + +++e++   + +vc+ P+ v  +p++TvGlGD+ +aa+l+
  gi|116754515|ref|YP_843633.1| 363 GLGAFREND---GSSVCVHPSFVASDPVTTVGLGDALTAATLY 402
                                    555555555...9***************************986 PP

>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0   0.00021       1.3      22      52 ..      70     100 ..      60     106 .. 0.81
   2 !    3.7   0.0    0.0052        31     180     224 ..     255     298 ..     235     302 .. 0.80
   3 !    4.3   0.2    0.0034        20     243     271 ..     378     406 .]     363     406 .] 0.83

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00021
                                    TTSEEEESEEEEEEESHHHHHHHHHHHTT-E CS
                           PfkB  22 egelvevktveksaGGagaNvAvalarlgad 52 
                                    ++e     ++e ++GG++ N+A +la lga+
  gi|116754515|ref|YP_843633.1|  70 ADEIASLFNWEIRMGGNAGNIANVLAALGAE 100
                                    566667788999*****************76 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0052
                                    HHCTESEEEEEHHHHHHHHTSCT..HSHHHHHHHHHHHHHTTSSEEE CS
                           PfkB 180 llaladllkpneeElealtgekl..edieealaalhklkakgaktvv 224
                                    +l  +d + +ne+El+ l+++    edi+ a++++++  + g+  v 
  gi|116754515|ref|YP_843633.1| 255 IL-EVDSIGMNEDELSMLADSGEnwEDIAGAAEQIQE--EFGIPRVC 298
                                    44.6888999******999888788999999999999..77885554 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.0034
                                    EEE.SSSS-SBGTTHHHHHHHHHHHHHHT CS
                           PfkB 243 vpavpkvkvvDttGAGDsfvggflaalle 271
                                    +p++ + ++v t+G GD+ +++ l+ ll+
  gi|116754515|ref|YP_843633.1| 378 HPSFVASDPVTTVGLGDALTAATLYTLLK 406
                                    56778899*****************9985 PP

>> AIRC  AIR carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1   0.00016      0.97      59      87 ..      81     109 ..      65     131 .. 0.85
   2 ?   -0.5   0.0      0.14   8.5e+02     107     122 ..     386     401 ..     374     403 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00016
                                    EEEEESS--HHHHHHHHSSS-EEEEEE-- CS
                           AIRC  59 IagAGgaahLpgvvaslttlPVigvPvks 87 
                                    I + G+a ++++v+a+l   PV++vP  +
  gi|116754515|ref|YP_843633.1|  81 IRMGGNAGNIANVLAALGAEPVVNVPSLT 109
                                    667899********************866 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.14
                                    --EE-SSTHHHHHHHH CS
                           AIRC 107 pvatvaigkaknAall 122
                                    pv+tv++g+a  Aa l
  gi|116754515|ref|YP_843633.1| 386 PVTTVGLGDALTAATL 401
                                    9*********999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 2827.47
//
Query:       gi|116754516|ref|YP_843634.1|  [L=368]
Description: 4Fe-4S ferredoxin iron-sulfur binding domain-containing protein [Methanosaeta thermophila PT]
Scores for 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-41  140.4   0.1    1.2e-40  140.0   0.1    1.2  1  DUF362    Domain of unknown function (DUF362)
    7.3e-11   41.4  15.3    4.2e-07   29.5   1.6    2.4  2  Fer4      4Fe-4S binding domain
    1.4e-08   34.4  13.3    0.00024   21.1   3.7    2.4  2  Fer4_6    4Fe-4S binding domain
    8.8e-08   32.2   9.6    1.8e-07   31.2   9.6    1.6  1  Fer4_9    4Fe-4S dicluster domain
    1.7e-07   31.7  34.9    1.4e-05   25.6  13.6    2.2  3  Fer4_7    4Fe-4S dicluster domain
    2.7e-07   30.3  13.2    0.00035   20.5   2.5    2.5  2  Fer4_2    4Fe-4S binding domain
    3.4e-07   30.3  12.6      1e-06   28.8  12.6    1.8  1  Fer4_10   4Fe-4S dicluster domain
    4.9e-07   29.8   7.5     0.0034   17.5   1.8    2.3  2  Fer4_21   4Fe-4S dicluster domain
    2.1e-06   28.6   7.2     0.0014   19.6   1.5    2.4  2  Fer4_16   4Fe-4S double cluster binding domain
    1.4e-05   25.2  14.1     0.0042   17.5   3.0    2.4  2  Fer4_4    4Fe-4S binding domain
    0.00057   20.7  11.4       0.04   14.8   2.0    2.5  2  Fer4_22   4Fe-4S dicluster domain
     0.0011   19.8  18.2      0.085   13.8   5.2    2.6  2  Fer4_3    4Fe-4S binding domain
     0.0019   18.6   9.8       0.12   12.8   3.4    2.4  2  Fer4_8    4Fe-4S dicluster domain
     0.0096   15.1   0.4      0.015   14.4   0.4    1.2  1  Lar_N     Lactate racemase N-terminal domain
  ------ inclusion threshold ------
      0.013   15.7   6.2      0.026   14.7   6.2    1.4  1  Fer4_18   4Fe-4S dicluster domain
      0.064   13.8  15.1       0.45   11.1   3.8    2.4  3  Fer4_17   4Fe-4S dicluster domain
       0.85   10.4  11.7       0.33   11.7   1.5    2.5  2  Fer4_15   4Fe-4S single cluster domain
        1.9    9.1  10.1        2.2    8.9   1.3    2.3  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I


Domain annotation for each model (and alignments):
>> DUF362  Domain of unknown function (DUF362)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.0   0.1   1.2e-43   1.2e-40       2     203 .]      43     313 ..      42     313 .. 0.90

  Alignments for each domain:
  == domain 1  score: 140.0 bits;  conditional E-value: 1.2e-43
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx..xxxxxxxxxxxxxxxxx..xxxxxx RF
                         DUF362   2 aiKpNlgeagnpegatthpevvravvellkeagagkiivgdspglyv.srgka..hrevaeeagydelaega..diadgl 76 
                                    aiK+++ge gn ++  ++p +vr+vv+l+ke+g ++++++d+++ly   rg++  h ++a  +g+ +++ +a  +iadgl
  gi|116754516|ref|YP_843634.1|  43 AIKLHFGEVGNDTY--ISPVFVREVVKLVKEKG-ARPFLTDTNTLYSgGRGNSvdHIRTAIGHGFAYAVVDApvIIADGL 119
                                    8**********998..****************9.79*********9666666678************8885557****** PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx............. RF
                         DUF362  77 egedevvvpvkgkhlkkelkiakavleaDviInlpklKgHalagvtgalKn.lfGcisgsgkaeiHs............. 142
                                    +ge+ v v+v+ +h+ + ++ia +++ a ++I+++++K H+ ag++ga+Kn ++Gc++  gkae+H+             
  gi|116754516|ref|YP_843634.1| 120 RGENHVSVDVNLNHFRS-VRIAGDIVSAESMIVISHFKAHMVAGFGGAIKNlGMGCAPPIGKAEQHTakpmvykekcrgc 198
                                    ********998778777.************************************************************** PP

                                    ............................................xx.xxxxxxxxxxxxxxx.x....xxx...xxxxxx RF
                         DUF362 143 ............................................kr.dsekfaekiadlaka.l....kpd...lnvvdg 169
                                                                                +  +   f e+++++a++ +    + +   +n++ +
  gi|116754516|ref|YP_843634.1| 199 grcmkacprsaisvvdgkayidlgvcvgcgecvracleramdfdWAvAIPPFVERMVEYAYGaVlgksG-RvgfFNFLID 277
                                    *******************************************97766889***********8787542.1477799999 PP

                                    x.....xxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxx RF
                         DUF362 170 i.....kamegegpsggskelglv.....laStDpvalDaaaad 203
                                    i     ++ + ++p        +v     laS+Dpva+D+a++d
  gi|116754516|ref|YP_843634.1| 278 ItpdcdCVPWSDAP--------VVpdigiLASRDPVAIDMASYD 313
                                    98888855566888........3344446***********9875 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   1.6   4.2e-10   4.2e-07       3      24 .]     190     211 ..     188     211 .. 0.91
   2 !   17.1   6.2   3.5e-06    0.0035       2      18 ..     218     234 ..     217     234 .. 0.95

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 4.2e-10
                                    EETTTSSS-THHHHHSTTTEEE CS
                           Fer4   3 ideekCigCGaCvevCPvgAIt 24 
                                    + +ekC gCG+C+++CP  AI+
  gi|116754516|ref|YP_843634.1| 190 VYKEKCRGCGRCMKACPRSAIS 211
                                    779*****************95 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 3.5e-06
                                    EEETTTSSS-THHHHHS CS
                           Fer4   2 videekCigCGaCvevC 18 
                                    +id   C+gCG+Cv +C
  gi|116754516|ref|YP_843634.1| 218 YIDLGVCVGCGECVRAC 234
                                    89*************** PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   3.7   2.4e-07   0.00024       7      24 .]     193     210 ..     192     210 .. 0.92
   2 !   18.5   2.1   1.5e-06    0.0015       2      21 ..     217     236 ..     216     239 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.4e-07
                         Fer4_6   7 dkCigCgdCvrvCPegai 24 
                                    +kC gCg+C+++CP  ai
  gi|116754516|ref|YP_843634.1| 193 EKCRGCGRCMKACPRSAI 210
                                    89************9887 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 1.5e-06
                         Fer4_6   2 veidpdkCigCgdCvrvCPe 21 
                                    + id   C+gCg+Cvr+C e
  gi|116754516|ref|YP_843634.1| 217 AYIDLGVCVGCGECVRACLE 236
                                    6678888***********66 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   9.6   1.8e-10   1.8e-07       1      49 [.     194     237 ..     181     239 .. 0.94

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 1.8e-10
                         Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49 
                                    kC gCg+C++aCp  +++  +++ ++ l       C+gCg+Cv aC + 
  gi|116754516|ref|YP_843634.1| 194 KCRGCGRCMKACPRSAISVVDGKAYIDLGV-----CVGCGECVRACLER 237
                                    7******************99999999965.....***********766 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   4.3   1.1e-05     0.011      28      52 .]     185     209 ..     177     209 .. 0.76
   2 !   25.6  13.6   1.4e-08   1.4e-05       1      48 [.     194     234 ..     194     238 .. 0.93
   3 !   16.5   1.7   9.3e-06    0.0093       2      21 ..     224     243 ..     223     265 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.1e-05
                         Fer4_7  28 tekveidpekClgCgaCvavCPtga 52 
                                    t+k+ +  ekC gCg+C+++CP  a
  gi|116754516|ref|YP_843634.1| 185 TAKPMVYKEKCRGCGRCMKACPRSA 209
                                    4566677899999999999999765 PP

  == domain 2  score: 25.6 bits;  conditional E-value: 1.4e-08
                         Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavC 48 
                                    +C gCg+C++aCp +ai++ +        k++id   C+gCg+Cv++C
  gi|116754516|ref|YP_843634.1| 194 KCRGCGRCMKACPRSAISVVDG-------KAYIDLGVCVGCGECVRAC 234
                                    7******************874.......79***************** PP

  == domain 3  score: 16.5 bits;  conditional E-value: 9.3e-06
                         Fer4_7   2 CigCgaCvaaCpvkaielde 21 
                                    C+gCg Cv+aC  +a+++d 
  gi|116754516|ref|YP_843634.1| 224 CVGCGECVRACLERAMDFDW 243
                                    *************9999984 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   2.5   3.5e-07   0.00035       2      21 ..     187     206 ..     186     207 .. 0.88
   2 !   14.9   3.1   2.1e-05     0.021       2      20 ..     216     234 ..     215     234 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 3.5e-07
                         Fer4_2   2 pvvvdtdrCigCgaCvsaCP 21 
                                    ++ v  ++C gCg C +aCP
  gi|116754516|ref|YP_843634.1| 187 KPMVYKEKCRGCGRCMKACP 206
                                    5778889************* PP

  == domain 2  score: 14.9 bits;  conditional E-value: 2.1e-05
                         Fer4_2   2 pvvvdtdrCigCgaCvsaC 20 
                                    ++++d   C+gCg Cv aC
  gi|116754516|ref|YP_843634.1| 216 KAYIDLGVCVGCGECVRAC 234
                                    578999************* PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8  12.6     1e-09     1e-06       6      55 ..     192     234 ..     187     235 .. 0.93

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 1e-09
                        Fer4_10   6 ddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                    +++C +Cg+C+kaCP        +++   +++  ++++ C gcg+Cv+aC
  gi|116754516|ref|YP_843634.1| 192 KEKCRGCGRCMKACPR-------SAISVVDGKAYIDLGVCVGCGECVRAC 234
                                    689*************.......999999999999*************** PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   1.8   3.4e-06    0.0034      35      57 ..     189     210 ..     173     215 .. 0.70
   2 !   15.1   0.3   1.9e-05     0.019       1      24 [.     217     240 ..     217     248 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.4e-06
                        Fer4_21  35 kvvedeCvGCnlCssvCPvedci 57 
                                     v +++C GC  C++ CP   +i
  gi|116754516|ref|YP_843634.1| 189 MVYKEKCRGCGRCMKACP-RSAI 210
                                    345888999999999998.4666 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.9e-05
                        Fer4_21   1 AridedkCigCgkCliaCedtshq 24 
                                    A id   C+gCg+C+ aC + +++
  gi|116754516|ref|YP_843634.1| 217 AYIDLGVCVGCGECVRACLERAMD 240
                                    7799999***********987765 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   1.5   1.4e-06    0.0014       1      19 [.     194     212 ..     194     220 .. 0.88
   2 !   12.0   0.4   0.00032      0.32       2      20 ..     224     242 ..     223     255 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.4e-06
                        Fer4_16   1 rCgtCgkCaevCPtnaike 19 
                                    +C +Cg+C+++CP +ai+ 
  gi|116754516|ref|YP_843634.1| 194 KCRGCGRCMKACPRSAISV 212
                                    5****************86 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00032
                        Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                    C++Cg+C+ +C ++a++ +
  gi|116754516|ref|YP_843634.1| 224 CVGCGECVRACLERAMDFD 242
                                    ************9999876 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   3.0   4.2e-06    0.0042       1      15 [.     192     206 ..     192     214 .. 0.92
   2 !   13.0   3.4   0.00012      0.12       4      14 ..     224     234 ..     221     237 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.2e-06
                         Fer4_4   1 qerCigCgsCvaaCP 15 
                                    +e+C gCg+C+ aCP
  gi|116754516|ref|YP_843634.1| 192 KEKCRGCGRCMKACP 206
                                    69************* PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00012
                         Fer4_4   4 CigCgsCvaaC 14 
                                    C+gCg Cv+aC
  gi|116754516|ref|YP_843634.1| 224 CVGCGECVRAC 234
                                    *********** PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   2.0     4e-05      0.04      76      94 ..     189     207 ..     179     209 .. 0.80
   2 !   10.5   2.1   0.00084      0.84      78      94 ..     220     236 ..     212     238 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4e-05
                        Fer4_22  76 kfgesgCvGCgRCieacpv 94 
                                     + +++C GCgRC++acp 
  gi|116754516|ref|YP_843634.1| 189 MVYKEKCRGCGRCMKACPR 207
                                    456889***********97 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00084
                        Fer4_22  78 gesgCvGCgRCieacpv 94 
                                    +  +CvGCg C++ac +
  gi|116754516|ref|YP_843634.1| 220 DLGVCVGCGECVRACLE 236
                                    5668***********86 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   5.2   8.5e-05     0.085       1      15 []     195     209 ..     195     209 .. 0.92
   2 !   11.3   5.1   0.00056      0.56       1      15 []     224     238 ..     224     238 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.5e-05
                         Fer4_3   1 CtgCgaCvevCPvgA 15 
                                    C gCg+C+++CP  A
  gi|116754516|ref|YP_843634.1| 195 CRGCGRCMKACPRSA 209
                                    99**********866 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00056
                         Fer4_3   1 CtgCgaCvevCPvgA 15 
                                    C+gCg Cv++C ++A
  gi|116754516|ref|YP_843634.1| 224 CVGCGECVRACLERA 238
                                    ***********7766 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   3.4   0.00012      0.12       3      16 ..     193     206 ..     191     223 .. 0.80
   2 !    9.6   0.2    0.0012       1.2       4      15 ..     223     234 ..     219     267 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00012
                         Fer4_8   3 ekCieCgaCqsaCp 16 
                                    ekC +Cg+C++aCp
  gi|116754516|ref|YP_843634.1| 193 EKCRGCGRCMKACP 206
                                    69***********9 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0012
                         Fer4_8   4 kCieCgaCqsaC 15 
                                     C++Cg C  aC
  gi|116754516|ref|YP_843634.1| 223 VCVGCGECVRAC 234
                                    588888888888 PP

>> Lar_N  Lactate racemase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.4   1.5e-05     0.015     144     184 ..     136     176 ..     130     194 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.5e-05
                          Lar_N 144 pveinklvaeadlviltGfiepHyfaGfsGGrKsilpGvas 184
                                     v i   +++a+ +i++   + H++aGf+G  K +  G+a 
  gi|116754516|ref|YP_843634.1| 136 SVRIAGDIVSAESMIVISHFKAHMVAGFGGAIKNLGMGCAP 176
                                    57888999******************************996 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   6.2   2.6e-05     0.026      56      97 ..     190     236 ..     174     247 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.6e-05
                        Fer4_18  56 kgagdcidcescvkvcPt.gidirkGlql....eciscllcidacdk 97 
                                      + +c  c+ c+k cP   i + +G  +     c+ c++c+ ac +
  gi|116754516|ref|YP_843634.1| 190 VYKEKCRGCGRCMKACPRsAISVVDGKAYidlgVCVGCGECVRACLE 236
                                    45679************63688888876533345***********54 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   4.9   0.00079      0.79       1      14 [.     194     207 ..     172     211 .. 0.71
   2 ?   11.1   3.8   0.00045      0.45       1      16 [.     194     209 ..     194     220 .. 0.84
   3 ?    8.8   2.3    0.0023       2.3      44      57 ..     222     235 ..     209     238 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00079
                        Fer4_17   1 rCiqCgyClpeCps 14 
                                    +C++Cg C+++Cp+
  gi|116754516|ref|YP_843634.1| 194 KCRGCGRCMKACPR 207
                                    46666666666665 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00045
                        Fer4_17   1 rCiqCgyClpeCpsye 16 
                                    +C++Cg C+++Cp+ +
  gi|116754516|ref|YP_843634.1| 194 KCRGCGRCMKACPRSA 209
                                    6***********9865 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0023
                        Fer4_17  44 slCieCgeCerkCP 57 
                                    + C++CgeC+r+C 
  gi|116754516|ref|YP_843634.1| 222 GVCVGCGECVRACL 235
                                    56999999999995 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   1.5   0.00033      0.33       5      33 ..     192     220 ..     189     223 .. 0.87
   2 ?    5.3   2.8     0.033        32       3      20 ..     219     236 ..     218     244 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00033
                        Fer4_15   5 rdaCigcglCvaeapevfeldedglasvl 33 
                                    +++C gcg+C++++p+      dg+a+++
  gi|116754516|ref|YP_843634.1| 192 KEKCRGCGRCMKACPRSAISVVDGKAYID 220
                                    689************88888889999987 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.033
                        Fer4_15   3 vDrdaCigcglCvaeape 20 
                                    +D   C gcg Cv+++ e
  gi|116754516|ref|YP_843634.1| 219 IDLGVCVGCGECVRACLE 236
                                    78889*********9954 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   1.3    0.0022       2.2       3      18 ..     192     207 ..     190     208 .. 0.90
   2 ?    4.6   2.0     0.047        46       1      16 [.     219     234 ..     219     236 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0022
                        Fer4_13   3 rdtCiacgaCvelaPd 18 
                                    +++C +cg C +++P 
  gi|116754516|ref|YP_843634.1| 192 KEKCRGCGRCMKACPR 207
                                    79*************5 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.047
                        Fer4_13   1 VDrdtCiacgaCvela 16 
                                    +D   C++cg Cv ++
  gi|116754516|ref|YP_843634.1| 219 IDLGVCVGCGECVRAC 234
                                    67788*********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); 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: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2716.29
//
Query:       gi|116754517|ref|YP_843635.1|  [L=648]
Description: carbon-monoxide dehydrogenase, catalytic subunit [Methanosaeta thermophila PT]
Scores for 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-125  420.4   0.0   1.2e-125  420.2   0.0    1.0  1  Prismane  Prismane/CO dehydrogenase family
  ------ inclusion threshold ------
        3.1    7.5   6.4        6.8    6.4   6.4    1.6  1  zf-tcix   Putative treble-clef, zinc-finger, Zn-binding


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 !  420.2   0.0  1.3e-129  1.2e-125       3     510 ..      68     628 ..      66     629 .. 0.98

  Alignments for each domain:
  == domain 1  score: 420.2 bits;  conditional E-value: 1.3e-129
                                    E-SSTCT-ECSC..S.SS-TTS-BHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHCHTSTTTB-SHHHHHHHHHH CS
                                    xxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Prismane   3 CrqCengpCrit..knkrGvCGkdadtavardlliavlkgaaahaahareladtliakalfktltnvnfddekklkrlae 80 
                                    C +C+ngpCr +  k++rGvCG++ad++++r++l++ ++ga+++  ha+++++tl+a+al++t   +++ ++kkl+rla 
  gi|116754517|ref|YP_843635.1|  68 CDLCSNGPCRADasKDRRGVCGISADGMAMRMMLLRNVMGASTYHYHAEQTIRTLRATALGRT--PFRIVEQKKLRRLAS 145
                                    *************9************************************************9..*************** PP

                                    HHCHHHCCSSHHHHHHHHCCHHHCGGGS-SSHHHHHHHCCCHHHHHHHHHHHCHHTT-HHHHHHHHHHHCCCCTTSTHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Prismane  81 algieeelkdieelaakvaevaledlskeenedirslkellpkglkglyaehaivlgyadeevveflaktlaglesdpld 160
                                    +l+i++++ + e++a ++ +++ +d++++  ++ + +++++p+++k+l++ ++i++g+++ e+  +  ++l+++++++ +
  gi|116754517|ref|YP_843635.1| 146 MLDIDTSG-SPEDTALRLCDAVEADFNRSYYQESQIVEAFAPAERKDLWRALGIFPGGIHGEILLATGSCLTNVDGSYES 224
                                    ********.*********************************************************************** PP

                                    HHHHHHHHHHHH.HHHHHHHHHHHHHHH-----EEEEECGCG-.SSSEEEEEESS-HHHHHHHHHHHCTTCCCCCCC... CS
                                    xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                       Prismane 161 llskalrlGlld.lkgmelldeantslfGtPeppltevnlgvldkdkvnIlvsGHdladleelleqtegkglnvyth... 236
                                    l  ka+rl+++  ++ +++l++++++lfG P+p+++ v+lgvld+d+vn++v+GH++ +  +++  +++++++++++   
  gi|116754517|ref|YP_843635.1| 225 LAMKAMRLSIAMaYQSQMVLEHCQDVLFGVPRPHKMMVDLGVLDPDYVNVVVNGHEPFMGFAMIMLARQPEWQERARsag 304
                                    ************9******************************************************************* PP

                                    ..GCCCCCCHHHHHHHHHCC.....EEEEECSSGGGHHHHHCCHECEEEESSSS--TTHHHHHHCHCCEEEEECTTB-.T CS
                                    ..xxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                       Prismane 237 ..gemLpghcctalklkyrh.....lvgnvGnawqqekaeftgavdaivvdtnCivpplasvaekyktrlittsevak.p 308
                                      g+++++ + t++++ +r      l g  Gn+++qe +++tg +d++ +d+nC +p  +++a++y+ rl+ +se +  +
  gi|116754517|ref|YP_843635.1| 305 arGLRIIASIETGQEIIQRWsmdevLGGFTGNWISQEPMMATGSIDLMACDMNCSLPLDPEYARRYGFRLVPVSELVAfE 384
                                    ***************877778999999************************************************99989 PP

                                    TSEEE-..-CTTCHHHHHHHHHHHHCCHCCTTCGG.-.............................HHHHHTTSS-EEEE CS
                                    xxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............................xxxxxxxxxxxxxx RF
                       Prismane 309 gakhie..eeekadkdaseiiekAielakareekkve.............................idaiksGtIkgvvl 357
                                    g+ +     +e+ +++a +++e+Ai++++ r++ + +                             ++a+ksG+I+g+v+
  gi|116754517|ref|YP_843635.1| 385 GISDRLnyVPEQVEHQAAKLLEMAISNYPSRRSGEKHvrdlpageatvgfstesilellggsldplLNALKSGQIRGIVG 464
                                    9887755778999******************99666678***************************************** PP

                                    E-B---TTCGCC..HHHHHHHHCHHTTEEEEEECHHHHHCCCTTTTECGHHHHSTHC.........EESEEEEESCCCHH CS
                                    xxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxx RF
                       Prismane 358 vvGCdnakkgrd..yytelakelikrdvlvltaGCakyalnklglgtieaaelageg.........iPrvLdvGsCvdny 426
                                    +v+C++ +++++  + + lakelikrdvl+l++GC++ a++ +gl+  eaa lag+g         iP+vL++G+C+d +
  gi|116754517|ref|YP_843635.1| 465 LVSCTTLRDSGQdvHSVALAKELIKRDVLILSMGCGNAAMQLAGLCRKEAAALAGSGlegicsslgIPPVLSYGTCTDVG 544
                                    ******9998887889**************************************************************** PP

                                    HHHHHHHHHHHHTTSSGGGSSEEEEECC--SHHHHHHHHHHHHTT-CEEECSS-TTTT-HHHHHHHHCHHHHHHCEEEEC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Prismane 427 rivvialklaealgvdindLplaalalewyeqKAvailltllalGinihlgptlpafgspnvlkvlvedfedriggivtv 506
                                    r+ ++   ++e lgv ++dLp+aa+a+e++eqKA+++++++la+G+++++ p++ ++g p +l++l + +++ +gg+++v
  gi|116754517|ref|YP_843635.1| 545 RLSELLRSVSEMLGVPVKDLPVAAAAPEYMEQKATIDAIFALAFGLYTYVNPVPTITGAPRLLDLLLRGCREVTGGVISV 624
                                    ******************************************************************************** PP

                                    HCHH CS
                                    xxxx RF
                       Prismane 507 eedp 510
                                    e+dp
  gi|116754517|ref|YP_843635.1| 625 EKDP 628
                                    ***9 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 ?    6.4   6.4   0.00076       6.8      11      34 ..      57      78 ..      57      85 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.00076
                        zf-tcix 11 rkCpkCGtyNGtRglsCkNkaCdq 34
                                   r+Cp C    GtR+ +C+N  C +
  gi|116754517|ref|YP_843635.1| 57 RRCPYC--MAGTRCDLCSNGPCRA 78
                                   79****..78************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (648 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.25s 00:00:00.84 Elapsed: 00:00:00.42
# Mc/sec: 4642.82
//
Query:       gi|116754518|ref|YP_843636.1|  [L=339]
Description: hypothetical protein Mthe_1217 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.8e-11   42.5   0.9     0.0042   17.1   0.0    3.6  3  Nitroreductase  Nitroreductase family
      2e-08   34.1   0.2    5.8e-05   22.8   0.0    2.3  2  TM1586_NiRdase  Putative TM nitroreductase
     0.0058   17.2   0.0       0.02   15.5   0.0    1.9  2  PGM_PMM_II      Phosphoglucomutase/phosphomannomutase, alpha/


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 !   11.7   0.0   3.3e-05       0.2      19      43 ..      24      48 ..      22      59 .. 0.88
   2 !   10.1   0.1   0.00011      0.63     112     139 ..      70      97 ..      53     112 .. 0.82
   3 !   17.1   0.0   7.1e-07    0.0042       1     170 []     130     321 ..     130     321 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.3e-05
                                   HHHHHHHHHHTS--GGG---EEEEE CS
                 Nitroreductase 19 elekileaarraPsagnlqpwrfvv 43
                                   +l+ +l+ a  aPs+ n+qpw+f +
  gi|116754518|ref|YP_843636.1| 24 KLKFVLRYAVLAPSGPNTQPWKFSI 48
                                   6777999****************75 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00011
                                    HHHHHHHHHHHHHHHHHHHHHTT-EEEE CS
                 Nitroreductase 112 yryalldagaaaqnllLaAtalGlgscp 139
                                     r+a++++g+a+ n+l+aA+ ++lg  +
  gi|116754518|ref|YP_843636.1|  70 HRTAYMSLGCAVANMLIAAEHFNLGYSV 97 
                                    57899*******************9765 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 7.1e-07
                                    HHH--B--.-B-S----HHHHHHHHHHH.........HTS--GGG-.....--EEEEEE.-CCCHHHHHHHHHHHHHHHH CS
                 Nitroreductase   1 irkRrSiR.kFddepvpkeelekileaa.........rraPsagnl.....qpwrfvvvqdkelryklaeaalelllkae 65 
                                    i +R++ R  F+++ +++e+l+++ e           ++ P ++n+        + + + +ke r++la +++ ++  a 
  gi|116754518|ref|YP_843636.1| 130 ITERHTNRsRFEEREIEPEKLQRMKELVendgfrldiMTDPDGKNRmaeilARAHKIQLGNKEFRRELASWIRPNTSDAY 209
                                    789*************************999999998889*****95443322233334488888888888888887777 PP

                                    TT-SS-GGGGGG.................HHHHHHHHHHHHSSEEEEE---TTS---HHHHHHHHHHHHHHHHHHHHHHH CS
                 Nitroreductase  66 aqaelaqryrke.................elklkaqkalagapvlivivatldkserkaaerayryalldagaaaqnllL 128
                                      +        +                 ++  k+ ++++++p+  v+          ++++++  +++ +g   + l L
  gi|116754518|ref|YP_843636.1| 210 DGLPGYAFGYSDfesylgkfifgafdtswSRARKESALMRESPAAAVL----------SSDSEDKLTWVRLGVTFEKLFL 279
                                    7766666655558888********************************..........********************** PP

                                    HHHHTT-EEEEE-GGGGGHH...HHHHHHT-S..SEEEEEEEEE- CS
                 Nitroreductase 129 aAtalGlgscpiggfdeaae...evrkllglpdeeeivvliavGy 170
                                     At++++ +   +++ + +e   e++++lg+     +++li++Gy
  gi|116754518|ref|YP_843636.1| 280 LATEMDVRFDLFSQPVAIDElrgEMAEFLGVR---YPQLLIRMGY 321
                                    ***************98888888********9...6888899998 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   9.6e-09   5.8e-05     157     213 ..      22      86 ..      16      94 .. 0.72
   2 !    9.0   0.2   0.00015      0.91       2      34 ..     126     159 ..     125     185 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 9.6e-09
                                    -HHHHHHHHHHHTS--GGG----EEE.E-SSEE..............EEE-S-HHHHHHHHHHHHH CS
                 TM1586_NiRdase 157 pewfkeileaarlAPsAlNqqpwrfelkdddeiki.........kasvlgklskiDlGIallHfel 213
                                     +++k +l+ a lAPs  N+qpw+f++kd+ +i++          ++ +++   + lG a+  + +
  gi|116754518|ref|YP_843636.1|  22 YDKLKFVLRYAVLAPSGPNTQPWKFSIKDS-SISVifdrsrtlpAVDPTHRTAYMSLGCAVANMLI 86 
                                    57788999******************9996.88886777777763333345555555555554444 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00015
                                    HHHHHHH--B---.B--S---HHHHHHHHH---- CS
                 TM1586_NiRdase   2 lyeaiekRhsvRk.Ykdealeeelleelkeaiee 34 
                                    l+ +i++Rh+ R+ ++++++e+e+l+++ke +e+
  gi|116754518|ref|YP_843636.1| 126 LFRQITERHTNRSrFEEREIEPEKLQRMKELVEN 159
                                    7889********66*************9998764 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 ?   -1.6   0.0      0.71   4.2e+03      92      99 ..     105     112 ..      90     117 .. 0.85
   2 !   15.5   0.0   3.4e-06      0.02      39      93 ..     126     172 ..     109     177 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.71
                                    TS-BEEEE CS
                     PGM_PMM_II  92 DaDRlgvv 99 
                                    DaDR++v+
  gi|116754518|ref|YP_843636.1| 105 DADRIAVI 112
                                    9****997 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 3.4e-06
                                    HHHHTT-EEEES-----TT-TTSS----TT-TTTTHHHHGGGGG-SEEEEE-TTS CS
                     PGM_PMM_II  39 llkelgvdvvelnaepdpdfptkapnpeekealkllielvkkegadlglafDgDa 93 
                                    l+++     ++++++    f ++ ++pe+   l+++ elv+++g++l +++D+D+
  gi|116754518|ref|YP_843636.1| 126 LFRQ-----ITERHTNRSRFEEREIEPEK---LQRMKELVENDGFRLDIMTDPDG 172
                                    4444.....56677777789888888888...**********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); 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: 00:00:00.42
# Mc/sec: 2395.45
//
Query:       gi|116754519|ref|YP_843637.1|  [L=445]
Description: adenylosuccinate lyase [Methanosaeta thermophila PT]
Scores for complete 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-53  181.6   0.1    3.5e-53  181.0   0.1    1.2  1  Lyase_1      Lyase
    8.5e-22   77.5   0.4    8.5e-22   77.5   0.4    2.1  2  ADSL_C       Adenylosuccinate lyase C-terminus
     0.0081   16.2   0.4       0.02   15.0   0.1    1.8  2  ASL_C        Adenylosuccinate lyase C-terminal
  ------ inclusion threshold ------
      0.012   16.0   0.0      0.052   14.0   0.0    2.2  1  FumaraseC_C  Fumarase C C-terminus


Domain annotation for each model (and alignments):
>> Lyase_1  Lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.0   0.1   7.8e-57   3.5e-53      23     310 ..      17     292 ..       9     294 .. 0.88

  Alignments for each domain:
  == domain 1  score: 181.0 bits;  conditional E-value: 7.8e-57
                                    GGHHHHHC......HHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHCHCHHCGGHHHBSSSSSHHHHHHHHHHHHHHHHTT CS
                        Lyase_1  23 rlseedik......alaalkkaaakanvdlkeeaaaiikaldevleegklddqfvlkviqegsgtavnmnlnevigellg 96 
                                     ++eed +      ++aal++a +++++++k +a+ai +a++           ++ k i+ ++g+++ +    v++  ++
  gi|116754519|ref|YP_843637.1|  17 AIWEEDYRismlfrVEAALARAEEEVGLIPKGAADAIARAAEMASP-------QRAKEIEAEIGHDMMA---VVLA--MA 84 
                                    5555555566666699**************9999999999876666.......2345778888888766...6777..88 PP

                                    HSSGIIIIITTT--HHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHTTT-EEEEEETTEEEEEEEHHHHHHHHH CS
                        Lyase_1  97 ekvepndkvhtgqSsnDqvpTalrlalkkalsekLlpaleqLidalkekakefkdvvkiGrThlqdAtPvtlgqelsaya 176
                                    e+ +  +++h g++snD+ +Ta  l+lk++l e ++++l++L ++l + a e+++ v +GrTh+q A+P+t g  ++ +a
  gi|116754519|ref|YP_843637.1|  85 EVCDYGEWIHLGATSNDILDTATGLQLKASL-EIIEAKLRELLRVLLDLAMENRNLVCAGRTHGQMAVPTTYGLRFAIWA 163
                                    8999***************************.88********************************************** PP

                                    HHHHHHHHHHHHHHHHHTCEETTTTTTTSSTTTSCC.THHHHHHHHHHHHHCSTEESSSHHHHHHC-HHHHHHHHHHHHH CS
                        Lyase_1 177 ealerdrerlkellkrllvellgggtavgtglnadp.efaelvakelakvtglpvkapnsfeavsdrDavvellgalkll 255
                                     ++ r++ rl+e+++r  v++++g++++ ++++ +    +++v++ l+        + +  ++v +rD+++e++  l+l+
  gi|116754519|ref|YP_843637.1| 164 SEVARHIDRLREIRPRAAVGKISGAVGTQAAFGPHGmTIQRRVMEILG------LNEVDVSNQVVQRDRHAEVICLLALI 237
                                    ************************888888888777344555555555......3667888899**************** PP

                                    HHHHHHHHHHHHHHTSTTTSSEEEEGCCTSSC-TTSTTTEBTHHHHHHHHHHHHH CS
                        Lyase_1 256 atsLskfaeDlrllssgeaglvelslaesepGSSiMPgKvNPvqlElltgvagrv 310
                                    a  L k++ ++r l+ +e+ +ve+s+  ++ GSS+MP+K+NP+ +E + g a+ v
  gi|116754519|ref|YP_843637.1| 238 ASTLDKICVEIRTLQRTEIAEVEESFGRRQVGSSTMPHKRNPIRSEQVCGLARVV 292
                                    ************************************************9999887 PP

>> ADSL_C  Adenylosuccinate lyase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       1.5   6.5e+03      28      53 ..      34      68 ..      21      72 .. 0.55
   2 !   77.5   0.4   1.9e-25   8.5e-22       1      72 [.     358     435 ..     358     436 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.5
                                   HHHHHHHC.......HHHHHHT-HHHH.C.HHCHH CS
                         ADSL_C 28 aamkawee.......llelLaadpevk.k.seeel 53
                                   a ++a ee        ++++a  +e++   +++e+
  gi|116754519|ref|YP_843637.1| 34 ALARAEEEvglipkgAADAIARAAEMAsPqRAKEI 68
                                   44444444554444444555555555533544455 PP

  == domain 2  score: 77.5 bits;  conditional E-value: 1.9e-25
                                    TGGGHHHHHHHHHH.TH-HHHHHHHHHHHHHHHHHC...HHHHHHT-HHHH.C.HHCHHHHHT-GGGCCTTHHHHHHH CS
                         ADSL_C   1 GlifservllaLvk.glgReeAyelVqeaamkawee...llelLaadpevk.k.seeeldalfdpayylgsadeivdr 72 
                                    Gl ++e+v+++L+k g gR++ +e+ ++a+m+a ee   ll++L++d +v+ + se+e+++l+dp++y+g a e+v+r
  gi|116754519|ref|YP_843637.1| 358 GLNMAEAVMVELAKrGAGRQTSHEILRAASMRAFEEgreLLDVLLEDGTVTkYiSEDEIRELLDPHRYTGTAVEQVER 435
                                    899**********66************************************55************************9 PP

>> ASL_C  Adenylosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.1   9.3e+03      33      48 ..     211     226 ..     205     235 .. 0.76
   2 !   15.0   0.1   4.5e-06      0.02       5     114 ..     309     425 ..     307     426 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.1
                                    HHCCEEE-HHHHHHHH CS
                          ASL_C  33 glsklevneealaedL 48 
                                    gl++++v+++++++d 
  gi|116754519|ref|YP_843637.1| 211 GLNEVDVSNQVVQRDR 226
                                    7888999988888874 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 4.5e-06
                                    --TCHHHHHTTC.HHHHHHHHHHHHHHHHHHCCEEE-HHHHHHHHHT-GGG.GHHHHHHHHHHT..T-TTHHHHHHHHHT CS
                          ASL_C   5 RDLtdStvlRnl.gvalahslialksllkglsklevneealaedLdenwev.laEaiqtvlrre..giekpYeklkeltr 80 
                                    RDLt+S+  R +   a+  +   l+ +++ l+ l++ +e+++++L     + +aEa+ + l +   g + ++e l++   
  gi|116754519|ref|YP_843637.1| 309 RDLTNSSCERVIfPEAFVLTDHILNLTIRILKGLRIRKENVERNLTLLKGLnMAEAVMVELAKRgaGRQTSHEILRAASM 388
                                    9*********98346788888889999******************99876559****9999655227899*****99865 PP

                                    TS.---HHHHHHHHHCS-S-HHHH.HHHHC.--CCC- CS
                          ASL_C  81 gk.kitkeslkefieslevseeak.eeLka.ltpatY 114
                                     + +  +e l+ ++e+ +v++ ++ +e+++ l p++Y
  gi|116754519|ref|YP_843637.1| 389 RAfEEGRELLDVLLEDGTVTKYISeDEIRElLDPHRY 425
                                    5548888888888888777665542455552467777 PP

>> FumaraseC_C  Fumarase C C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.2e-05     0.052      20      51 ..     389     424 ..     384     427 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.2e-05
                                    HHHHHT--HHHHHHHTT-.....-HHHHHHHT-HHH CS
                    FumaraseC_C  20 eAlkegktlreavlelgl....lteeeldelldpek 51 
                                    +A++eg+ l ++ le g     ++e+e+ elldp +
  gi|116754519|ref|YP_843637.1| 389 RAFEEGRELLDVLLEDGTvtkyISEDEIRELLDPHR 424
                                    799************6665555************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3298.64
//
Query:       gi|116754520|ref|YP_843638.1|  [L=212]
Description: small GTP-binding protein [Methanosaeta thermophila PT]
Scores for complete 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   58.5   0.0    7.8e-16   58.2   0.0    1.1  1  MMR_HSR1       50S ribosome-binding GTPase
    2.9e-13   49.8   0.1    1.5e-05   24.6   0.0    3.0  2  GTP_EFTU       Elongation factor Tu GTP binding domain
    1.7e-06   27.6   0.0     0.0069   15.9   0.0    2.4  2  Arf            ADP-ribosylation factor family
    2.1e-05   24.5   0.2       0.16   11.8   0.0    2.1  2  RsgA_GTPase    RsgA GTPase
    4.4e-05   23.1   0.2    0.00031   20.3   0.2    2.3  1  FeoB_N         Ferrous iron transport protein B
    0.00016   21.9   0.0        0.1   12.8   0.0    2.2  2  Roc            Ras of Complex, Roc, domain of DAPkinase
    0.00036   21.0   0.0    0.00063   20.2   0.0    1.4  1  AAA            ATPase family associated with various cellular
    0.00066   19.1   0.0    0.00093   18.6   0.0    1.2  1  Septin         Septin
    0.00076   19.3   0.0     0.0012   18.6   0.0    1.5  1  AAA_24         AAA domain
    0.00077   19.1   0.0       0.23   11.1   0.0    2.6  2  Ras            Ras family
     0.0013   18.7   0.0     0.0022   18.0   0.0    1.3  1  MMR_HSR1_Xtn   C-terminal region of MMR_HSR1 domain
     0.0019   17.2   0.3          1    8.3   0.0    2.7  2  MeaB           Methylmalonyl Co-A mutase-associated GTPase Me
     0.0026   16.9   0.1     0.0042   16.2   0.1    1.2  1  Parvo_NS1      Parvovirus non-structural protein NS1
     0.0056   16.1   0.0       0.53    9.7   0.0    2.3  2  SRPRB          Signal recognition particle receptor beta subu
     0.0082   16.7   0.0      0.031   14.8   0.0    1.9  1  AAA_18         AAA domain
  ------ inclusion threshold ------
      0.018   14.9   0.0      0.027   14.4   0.0    1.4  1  ATPase_2       ATPase domain predominantly from Archaea
      0.034   14.5   0.0      0.066   13.6   0.0    1.5  1  RNA_helicase   RNA helicase
      0.035   13.7   0.1      0.072   12.7   0.1    1.5  1  AAA_25         AAA domain
      0.054   14.0   0.0      0.071   13.6   0.0    1.2  1  ABC_tran       ABC transporter
      0.064   12.4   0.0        0.1   11.8   0.0    1.3  1  NB-ARC         NB-ARC domain
      0.069   13.1   0.0        0.2   11.6   0.0    1.7  2  NACHT          NACHT domain
      0.071   13.4   0.0       0.11   12.8   0.0    1.3  1  AAA_28         AAA domain
       0.11   12.8   0.0       0.51   10.6   0.0    2.2  2  AAA_22         AAA domain
       0.15   12.1   0.0         19    5.3   0.0    2.3  2  Dynamin_N      Dynamin family
       0.18   12.1   0.0       0.29   11.4   0.0    1.3  1  YchF-GTPase_C  Protein of unknown function (DUF933)


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 !   58.2   0.0   1.1e-18   7.8e-16       1     114 []      25     169 ..      25     169 .. 0.75

  Alignments for each domain:
  == domain 1  score: 58.2 bits;  conditional E-value: 1.1e-18
                                    EEEEEESTTSSHHHHHHHHHT....S..TEEESSSTTSSSSEEEEE...EEETT..EEEEEEECGGC...........S. CS
                       MMR_HSR1   1 evaivGrpNvGKStLinaltg....e..kaivsdkpgtTrdinegr...vklkg..keielvDtpGl...........i. 57 
                                    +++i+G pN+GK+tL n++++    +     vs  p  Tr  ++++   ++ +g   ++ +vDtpG+           + 
  gi|116754520|ref|YP_843638.1|  25 RIGIYGPPNAGKTTLANRIVKdwsgDgtLGTVSPVPHETRRAVRKEglvINADGasIHLDIVDTPGMatkidfrefmaYg 104
                                    69******************8444414378***********9887643334444346689******87776666665514 PP

                                    ....S...HHHHHH.HHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                       MMR_HSR1  58 ....e...gaseek.glgkaflaleeadlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                        e   +a+e   g+ +a++ l++ d +llv+d++e+ +++++ ++   +e ++ pl++v+nk
  gi|116754520|ref|YP_843638.1| 105 mseeEakrRAKEATeGVIEAIKWLDDLDGVLLVMDSTEDPYTQVNVTVIGNMEARNLPLLIVANK 169
                                    44321323222222577777777889*********8888************999*********98 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0     4e-07   0.00029       4      90 ..      24     104 ..      21     110 .. 0.78
   2 !   24.6   0.0   2.1e-08   1.5e-05      87     189 ..     124     208 ..     118     212 .] 0.81

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 4e-07
                                    EEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEETTCSSEEEEEEEESSSG.. CS
                       GTP_EFTU   4 rnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisleketkkylinliDtPGHv.. 81 
                                      igi g  ++GKtTL  r++++ + +   g+       +   ++E +r +  +  +i+ +  +++ ++ ++DtPG +  
  gi|116754520|ref|YP_843638.1|  24 ARIGIYGPPNAGKTTLANRIVKDWSGDGTLGT-------VSPVPHETRRAVRKEGLVINAD--GASIHLDIVDTPGMAtk 94 
                                    679******************99988777555.......5678888888888888888888..99999********6422 PP

                                    .GGHHHHHHH CS
                       GTP_EFTU  82 .dFskevirg 90 
                                     dF + +  g
  gi|116754520|ref|YP_843638.1|  95 iDFREFMAYG 104
                                    2566666555 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 2.1e-08
                                    HHHHHHT-SEEEEEEETTTBSTHHHH.HHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTT CS
                       GTP_EFTU  87 virglrvlDgavlvvdaveGvepqte.evlrlalkegvpiivfiNKmDrlkaelkeiveevkqklsrkeeklekygekge 165
                                     i+ l  lDg++lv+d++e++ +q + +v+  + ++++p+ ++ NK+D ++a  ++i+ +  q                 
  gi|116754520|ref|YP_843638.1| 124 AIKWLDDLDGVLLVMDSTEDPYTQVNvTVIGNMEARNLPLLIVANKIDLPNAAPSRIKAAFPQ----------------- 186
                                    55668899************999975499*********************9988887766552................. PP

                                    TTEEEEEEBTTTTBTHHHHHHHHH CS
                       GTP_EFTU 166 kevpvvfgSalkgegvktllealv 189
                                       pvv +Sal+g+++++l  a+ 
  gi|116754520|ref|YP_843638.1| 187 --HPVVQISALEGKNLDELYHAIA 208
                                    ..4678888888888888877776 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0    0.0007       0.5       5      37 ..      15      46 ..      11      76 .. 0.78
   2 !   15.9   0.0   9.6e-06    0.0069      80     133 ..     129     178 ..     120     207 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0007
                                   HHGGTT.TTEEEEEEEESTTSSHHHHHHHHHHS CS
                            Arf  5 laklklkkkelrilllGLDnaGKtTilkklkle 37
                                   l+++++ kk +ri + G  naGKtT+ +++ ++
  gi|116754520|ref|YP_843638.1| 15 LSRIFG-KKRARIGIYGPPNAGKTTLANRIVKD 46
                                   566777.999****************9998776 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 9.6e-06
                                    TTESEEEEEEETT-CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS-H CS
                            Arf  80 ektdavifvvDsadreRleeakeeLkalleeeelkevallvlaNKqDlpealse 133
                                    ++ d+v+ v+Ds++    +       +++ + e ++ +ll++aNK+Dlp+a+ +
  gi|116754520|ref|YP_843638.1| 129 DDLDGVLLVMDSTEDPYTQVN----VTVIGNMEARNLPLLIVANKIDLPNAAPS 178
                                    566777777777765433322....356778899****************9754 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00047      0.33     104     162 ..      28      92 ..      20      97 .. 0.82
   2 !   11.8   0.0   0.00023      0.16      17      97 ..     132     207 ..     115     211 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00047
                                    EECSTTSSHHHHHHHHCT..T-----S--------------SEEEEEETTTEE....EESS-SSS CS
                    RsgA_GTPase 104 lvGqSGvGKStLinallp..elelktgevseklgrGkhTTtavellelaeggl....liDtPGfr 162
                                    + G+  +GK+tL n+++   + +   g vs   ++ +   ++  l+  a+g+     ++DtPG+ 
  gi|116754520|ref|YP_843638.1|  28 IYGPPNAGKTTLANRIVKdwSGDGTLGTVSPVPHETRRAVRKEGLVINADGASihldIVDTPGMA 92 
                                    6788999**********944458999****************99998887664233379****96 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00023
                                    -EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHH CS
                    RsgA_GTPase  17 dqllivvslkepelslnlldrfLvlaeekgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkel 96 
                                    d +l+v+  +e+ +++  +  ++  +e+++++++iv nKiDl + +   +++k+++ +   +v+ +sa ++++l+el ++
  gi|116754520|ref|YP_843638.1| 132 DGVLLVMDSTEDPYTQVNV-TVIGNMEARNLPLLIVANKIDLPNAAP--SRIKAAFPQH--PVVQISALEGKNLDELYHA 206
                                    6777777666444444333.58899******************9999..7777777776..9999999999999999876 PP

                                    C CS
                    RsgA_GTPase  97 l 97 
                                    +
  gi|116754520|ref|YP_843638.1| 207 I 207
                                    6 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 !   20.3   0.2   4.4e-07   0.00031       3     156 .]      26     207 ..      24     207 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 4.4e-07
                                    EEEEESTTSSHHHHHHHHH......TTSEEEEESTTSS...SEEEEEEEEETT..EEEEEEE----...........SSS CS
                         FeoB_N   3 valvGnpnvGkttlfnalt......gakqkvgNwpGvt...vekkegklklkg..keveivDlPGi...........Ysl 60 
                                    + + G pn+Gkttl n++       g+  +v+  p  t   v k+   ++ +g   +++ivD PG+           Y +
  gi|116754520|ref|YP_843638.1|  26 IGIYGPPNAGKTTLANRIVkdwsgdGTLGTVSPVPHETrraVRKEGLVINADGasIHLDIVDTPGMatkidfrefmaYGM 105
                                    7789**************822222223334444444442225555556666663356689******87777777555555 PP

                                    .......SSSSHHHHHHHHHHHCTSSSEEEEEEEGGG...HHHHHHHHHHHHHTTSSEEEEEETHHHHHHTTEEE-HHHH CS
                         FeoB_N  61 .......sayseeekvardflleeepdvvvnvvdatn...lernLyLtlqllelgvpvvlalnmideaekkgieidlkkL 130
                                            a    e v + +   ++ d v+ v+d+t+    + n++++ ++   ++p++++ n+id  +++  +i ++  
  gi|116754520|ref|YP_843638.1| 106 seeeakrRAKEATEGVIEAIKWLDDLDGVLLVMDSTEdpyTQVNVTVIGNMEARNLPLLIVANKIDLPNAAPSRIKAAF- 184
                                    55443322233334444445557899*********974435677777778888889***************99998754. PP

                                    HHHHTS-EEEEBTTTTBTHHHHHHHH CS
                         FeoB_N 131 sekLgvpvvktsakkkegieellkai 156
                                        + pvv++sa ++++++el +ai
  gi|116754520|ref|YP_843638.1| 185 ---PQHPVVQISALEGKNLDELYHAI 207
                                    ...457***************99876 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 !   12.8   0.0   0.00014       0.1       2      66 ..      26      91 ..      25     107 .. 0.81
   2 !    7.0   0.0    0.0088       6.3      80     120 .]     131     172 ..     123     172 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00014
                                   EEEESSTTSSHHHHHHCHCT-CCC-EEETTTT.EEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SG CS
                            Roc  2 vvlvGdsgvGKtsllkrfvedkfsekekstig.vdfltkevtkikgvendkkvkkvklniWDtaGq 66
                                   + + G  ++GKt+l++r+v+d   + +  t++ v   t+++++ +g+  + +  +++l+i Dt G 
  gi|116754520|ref|YP_843638.1| 26 IGIYGPPNAGKTTLANRIVKDWSGDGTLGTVSpVPHETRRAVRKEGLVINADGASIHLDIVDTPGM 91
                                   56789***************9998888777762556667777778888888899999999999885 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0088
                                    SCEEEEEEEGHHHHCHHHHHHHHHHH.CSSS-EEEEEE-TTT CS
                            Roc  80 aalailvydsrssenlkeWlkelkkv.agkspvilvgnkiDl 120
                                     + ++lv+ds+++   +  ++ + ++ a++ p+++v+nkiDl
  gi|116754520|ref|YP_843638.1| 131 LDGVLLVMDSTEDPYTQVNVTVIGNMeARNLPLLIVANKIDL 172
                                    5678999999999888888999988724567*********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 !   20.2   0.0   8.8e-07   0.00063       3     118 ..      28     176 ..      26     185 .. 0.66

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 8.8e-07
                                    EESSTTSSHHHHHHHHHHHHTHE......................EEEEETTTCSSS.................STTHHH CS
                            AAA   3 lyGppGtGKTllakavakelgve......................fleisgsellsk.................yvgese 43 
                                    +yGpp  GKT+la+ ++k+++ +                      +++ +g+++  +                   g se
  gi|116754520|ref|YP_843638.1|  28 IYGPPNAGKTTLANRIVKDWSGDgtlgtvspvphetrravrkeglVINADGASIHLDivdtpgmatkidfrefmAYGMSE 107
                                    7******************8533333344455566666667777744444444442255556666666666666999999 PP

                                    HHHHHHHHHHHHTSTS.EEEEEETGGGHHHHHTTCCCHHHHHHHHHH.HHHHHHTTTSSSTEEEEEEESSGGGSTHH CS
                            AAA  44 kkirelfkeakekakp.silfiDEidalaksrsgseseeeervvnqL.lteldgvkkkeskvivigatnrpdkldpa 118
                                    ++ +   kea e      i ++D++d +         +++e+   q  +t++ +++   +++ +++++n++d ++ a
  gi|116754520|ref|YP_843638.1| 108 EEAKRRAKEATEGV-IeAIKWLDDLDGVLLVM-----DSTEDPYTQVnVTVIGNMEA--RNLPLLIVANKIDLPNAA 176
                                    99999999999988.55999******998888.....33333333331455555555..358888888888766555 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.3e-06   0.00093       9      79 ..      28      98 ..      24     113 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.3e-06
                                   EEEBTTSSCCCCCCTTSSSS------------------S-EEEEEEEEETTCEEEEEEEE---BSSSSSHH CS
                         Septin  9 vvGesglGkttlintlfetdlieeekleeasekkkktveikkkkvvieedgvklnltviDtpgfGdavdns 79
                                   + G    Gkttl n ++++   + +  +     +++   ++k+  vi+ dg  ++l ++Dtpg   ++d +
  gi|116754520|ref|YP_843638.1| 28 IYGPPNAGKTTLANRIVKDWSGDGTLGTVSPVPHETRRAVRKEGLVINADGASIHLDIVDTPGMATKIDFR 98
                                   5688889*********9988777754444445788889999***********************9999965 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.7e-06    0.0012       2      59 ..      23     104 ..      22     159 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.7e-06
                         AAA_24   2 klkiliyGpsgiGKTtlakel........................gpkplfidtekGlksldadkfpdieswedfldevv 57 
                                     ++i iyGp+ +GKTtla+++                         ++ l+i+ ++ + +ld  + p + + +df+++++
  gi|116754520|ref|YP_843638.1|  23 RARIGIYGPPNAGKTTLANRIvkdwsgdgtlgtvspvphetrravRKEGLVINADGASIHLDIVDTPGMATKIDFREFMA 102
                                    579*****************988888777777777777777777777777777777777777777777777777777776 PP

                         AAA_24  58 el 59 
                                    + 
  gi|116754520|ref|YP_843638.1| 103 YG 104
                                    65 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.015        11       6      58 ..      30      91 ..      25     111 .. 0.68
   2 !   11.1   0.0   0.00031      0.23      71     157 ..     130     208 ..     124     211 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.015
                                   ESTTSSHHHHHHHHHHSSCSSSCTTTSSEE.......EEEEEEEET.........TEEEEEEEEEETTS CS
                            Ras  6 GdsavGKtslllrfvkdkFkeeyesTigvd.......fytkeievd.........gkevkleiwDTAGq 58
                                   G  + GKt+l +r vkd   +    T+                  +         g +++l+i DT G 
  gi|116754520|ref|YP_843638.1| 30 GPPNAGKTTLANRIVKDWSGDGTLGTVSPVphetrraV-------RkeglvinadGASIHLDIVDTPGM 91
                                   67778888888888888877777777743222222211.......123344444499*********985 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00031
                                    TESEEEEEEETTBHHHHHTHHHHHHHHHHHSTTTSEEEEEEETTTGGGG-SS-HHHHHHHHHHHTSEEEEEBTTTTCTHH CS
                            Ras  71 daegillvyditsresfenvkkwveeikrvaeenvpivLvGnKvDleekravsteegeelakelglkfletSAktnenve 150
                                    d +g+llv d t ++ +++v+  v+ i ++  +n+p+++v+nK+Dl +         +  a   + + +++SA + +n++
  gi|116754520|ref|YP_843638.1| 130 DLDGVLLVMDST-EDPYTQVN--VTVIGNMEARNLPLLIVANKIDLPNAAPS-----RIKAAFPQHPVVQISALEGKNLD 201
                                    566777777754.45677776..333555556789************83332.....22344456778888888888888 PP

                                    HHHHHHH CS
                            Ras 151 eafeell 157
                                    e++++++
  gi|116754520|ref|YP_843638.1| 202 ELYHAIA 208
                                    8887765 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 !   18.0   0.0   3.1e-06    0.0022      54     100 ..     159     207 ..     135     211 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.1e-06
                   MMR_HSR1_Xtn  54 vYipclyvlNKiDl..isleeldelarepnsvviSaekelnldeLkeki 100
                                      +p l+v NKiDl  +  + +++   ++ +v iSa +++nldeL ++i
  gi|116754520|ref|YP_843638.1| 159 RNLPLLIVANKIDLpnAAPSRIKAAFPQHPVVQISALEGKNLDELYHAI 207
                                    56899*********4444445555444668888************9887 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0014         1      29      57 ..      23      51 ..      11      62 .. 0.84
   2 !    6.5   0.0    0.0048       3.5     204     229 ..     186     211 ..     133     212 .] 0.87

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0014
                                   SEEEEEEE-TTSSHHHHHHHHHHHHHCTT CS
                           MeaB 29 aqvvGltGvPGaGkstlvealglelrrrG 57
                                     ++G+ G P aGk tl ++++      G
  gi|116754520|ref|YP_843638.1| 23 RARIGIYGPPNAGKTTLANRIVKDWSGDG 51
                                   469*****************998776666 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0048
                                    --EEEEEBCCCTBSHHHHHHHHHHHH CS
                           MeaB 204 rpkvlktsavegeGidelvdaieehr 229
                                    + +v+++sa+eg+ +del +ai  h+
  gi|116754520|ref|YP_843638.1| 186 QHPVVQISALEGKNLDELYHAIAVHF 211
                                    579*******************9885 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 !   16.2   0.1   5.8e-06    0.0042     105     136 ..      13      45 ..       8      55 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.8e-06
                      Parvo_NS1 105 awlskqlgkrnt.vwfyGpantGktnlaeaIak 136
                                    +wls+ +gk+ + +++yGp+n Gkt la+ I+k
  gi|116754520|ref|YP_843638.1|  13 IWLSRIFGKKRArIGIYGPPNAGKTTLANRIVK 45 
                                    7999998876544****************9987 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0   0.00074      0.53       3      58 ..      23      90 ..      21     109 .. 0.63
   2 ?    4.4   0.0     0.031        23      66     133 ..     121     180 ..     115     200 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00074
                                   --EEEEE-STTSSHHHHHHHHHHS....S---B---SS-EEETTG..........GG..TT-SEEEETT CS
                          SRPRB  3 kpavllvGlsdsGKTslftrLttd....svkktvtSqessaalkv.......ksekg..skltliDfPG 58
                                   + ++ + G+ ++GKT+l +r+ +d      +   +S  ++ + +         + +g   +l+++D PG
  gi|116754520|ref|YP_843638.1| 23 RARIGIYGPPNAGKTTLANRIVKDwsgdG-TLGTVSPVPHETRRAvrkeglvINADGasIHLDIVDTPG 90
                                   5677899***************9976642.222333333333332233444433333003455677777 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.031
                                    HHHHHHHHGGEEEEEEEEETTS-HHHHHHHHHHHHHHHHHHHHHTT---EEEEEE-TTSTT---HHHH CS
                          SRPRB  66 lleklkaksslkglvfvvDStidpkevkevAEllyeilliteklkdavdiliACnKqelflakspkli 133
                                    ++e +k  + l g++ v+DSt dp    +v     +++ ++  +  ++++li  nK +l  a + + i
  gi|116754520|ref|YP_843638.1| 121 VIEAIKWLDDLDGVLLVMDSTEDPYTQVNV-----TVIGNM--EARNLPLLIVANKIDLPNAAP-SRI 180
                                    578888899999999999*99999765554.....333333..355677888888888877643.445 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   4.3e-05     0.031       1      21 [.      26      46 ..      26     154 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.3e-05
                         AAA_18  1 IlltGtpGvGKttlakeLskr 21
                                   I++ G+p +GKttla+++ k 
  gi|116754520|ref|YP_843638.1| 26 IGIYGPPNAGKTTLANRIVKD 46
                                   89**************99776 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   0.0   3.7e-05     0.027      23      43 ..      26      46 ..      15     126 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.7e-05
                       ATPase_2 23 yfiYGpegsGKtaLlkeiien 43
                                   + iYGp + GKt+L ++i++ 
  gi|116754520|ref|YP_843638.1| 26 IGIYGPPNAGKTTLANRIVKD 46
                                   569***************986 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   9.2e-05     0.066       3      25 ..      28      50 ..      26      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.2e-05
                   RNA_helicase  3 lyGpsgeGKStlakeLakallkk 25
                                   +yGp++ GK+tla++++k+++++
  gi|116754520|ref|YP_843638.1| 28 IYGPPNAGKTTLANRIVKDWSGD 50
                                   8****************998854 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1    0.0001     0.072      34     111 ..      24     107 ..      14     143 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0001
                         AAA_25  34 elallaGapgtGKttlaldlalavatGkpwlg........pvapeqgkVlyvsaEdsedelrrRlravgealrd.darll 104
                                    + + ++G+p +GKttla  ++ +++ G+  lg         ++  +   l+++a+++   ++  +  +   ++  d r++
  gi|116754520|ref|YP_843638.1|  24 ARIGIYGPPNAGKTTLANRIVKDWS-GDGTLGtvspvpheTRRAVRKEGLVINADGAS--IHLDIVDTPGMATKiDFREF 100
                                    56678*******************9.44455666733223333345556788887777..66666655544433255555 PP

                         AAA_25 105 vldlagv 111
                                      +++++
  gi|116754520|ref|YP_843638.1| 101 MAYGMSE 107
                                    5555444 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   9.9e-05     0.071      11      67 ..      23      77 ..      20     151 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.9e-05
                                   TSEEEEEESTTSSHHHHHHHHTTSS--..SEEEEEETTCEGGGB-HHHCCHCEEEE-SS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran 11 gekvaivGenGaGKStLlkllagllkp..teGeilldgkdlkeqeleslrkeigvlpqe 67
                                     +++i G+  aGK+tL++ + +  +   t G++     ++ +++++ +rke  v+  +
  gi|116754520|ref|YP_843638.1| 23 RARIGIYGPPNAGKTTLANRIVKDWSGdgTLGTV----SPVPHETRRAVRKEGLVINAD 77
                                   6789*****************9998754455666....677777777777777666666 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00014       0.1      18      44 ..      21      47 ..      10      52 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00014
                                   SCSEEEEEEESTTSSHHHHHHHHCCSH CS
                         NB-ARC 18 lqslvvalvGmgGvGKttlakqilnks 44
                                    ++  ++++G +  GKttla+ i+++ 
  gi|116754520|ref|YP_843638.1| 21 KKRARIGIYGPPNAGKTTLANRIVKDW 47
                                   566679******************995 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00028       0.2       5      28 ..      28      51 ..      24      74 .. 0.81
   2 ?   -1.2   0.0       2.3   1.7e+03      83      99 ..     134     150 ..     110     203 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00028
                                   EEC-TTTCHHHHHHHHHHHHCTS- CS
                          NACHT  5 lqGeaGsGKTtLlqklalawaegk 28
                                   + G++  GKTtL+ +++ +w  + 
  gi|116754520|ref|YP_843638.1| 28 IYGPPNAGKTTLANRIVKDWSGDG 51
                                   7899999*************8765 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.3
                                    EEEEEE-STT-SS-TCH CS
                          NACHT  83 lLlilDglDelvtdlgq 99 
                                    +Ll++D+ ++  t+ + 
  gi|116754520|ref|YP_843638.1| 134 VLLVMDSTEDPYTQVNV 150
                                    67777777766665554 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00015      0.11       1      57 [.      25      99 ..      25     125 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00015
                         AAA_28  1 kivitGgestGKTtlleaLaar.......gyp..vvpEaareileeklakgedalpwv.e........dllafae 57
                                   +i i G++ +GKTtl++++ ++       g++  v +E+ r + +e+l  + d +  + +        ++++f+e
  gi|116754520|ref|YP_843638.1| 25 RIGIYGPPNAGKTTLANRIVKDwsgdgtlGTVspVPHETRRAVRKEGLVINADGASIHlDivdtpgmaTKIDFRE 99
                                   5789***************97777776665433244999999999988444433322212233444443333333 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00071      0.51      10      28 ..      28      46 ..      21     161 .. 0.76
   2 ?   -0.6   0.0       2.1   1.5e+03      29      62 ..     176     209 ..     171     212 .] 0.78

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00071
                         AAA_22 10 vtGesGtGKTtllrrlleq 28
                                   ++G++ +GKTtl++r+++ 
  gi|116754520|ref|YP_843638.1| 28 IYGPPNAGKTTLANRIVKD 46
                                   89*************9875 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.1
                         AAA_22  29 ldeeakaeeerpevvfvtlpsstsskdllrellr 62 
                                    ++ ++ka+ ++ +vv + + +++++++l+++++ 
  gi|116754520|ref|YP_843638.1| 176 APSRIKAAFPQHPVVQISALEGKNLDELYHAIAV 209
                                    5566677778899999999999999999999975 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.026        19       1      20 [.      26      45 ..      26      53 .. 0.90
   2 ?    4.7   0.0     0.038        28     102     140 ..      82     142 ..      73     170 .. 0.60

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.026
                                   EEEEEBTTTTHHHHHHHHHT CS
                      Dynamin_N  1 iavvGsqSsGKSSvlnaLlg 20
                                   i + G  ++GK++++n +++
  gi|116754520|ref|YP_843638.1| 26 IGIYGPPNAGKTTLANRIVK 45
                                   6788999***********96 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.038
                                    SEEEEE---B-SSSGTTS......................HHHHHHHSTTEEEEEEEETTS CS
                      Dynamin_N 102 gltlvDlPGldsvnkrdq......................elvkeyikkadiilavtsanh 140
                                    +l +vD+PG+    + ++                        + + +++ d +l+v+++  
  gi|116754520|ref|YP_843638.1|  82 HLDIVDTPGMATKIDFREfmaygmseeeakrrakeategvIEAIKWLDDLDGVLLVMDSTE 142
                                    5789*****9876665555666666666666666555533222233455555555555555 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 ?   11.4   0.0    0.0004      0.29      10      68 ..      61     120 ..      55     126 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0004
                  YchF-GTPase_C  10 kevraWtikkgttapqaAgviHsDfekgFiraevikyedlvelgs.eaaakeagklrleg 68 
                                    +e+r    k+g  ++     iH D+  +  +a  i++++++++g  e++ak++ k  +eg
  gi|116754520|ref|YP_843638.1|  61 HETRRAVRKEGLVINADGASIHLDIVDTPGMATKIDFREFMAYGMsEEEAKRRAKEATEG 120
                                    67777777888888888999***********************76699999999988887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      612  (0.0341346); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 1602.63
//
Query:       gi|116754521|ref|YP_843639.1|  [L=120]
Description: hypothetical protein Mthe_1220 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-45  152.2   0.8    4.2e-45  151.9   0.8    1.1  1  DUF2073   Uncharacterized protein conserved in archaea (DUF20


Domain annotation for each model (and alignments):
>> DUF2073  Uncharacterized protein conserved in archaea (DUF2073)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.9   0.8   2.4e-49   4.2e-45       1     105 []      14     117 ..      14     117 .. 0.98

  Alignments for each domain:
  == domain 1  score: 151.9 bits;  conditional E-value: 2.4e-49
                        DUF2073   1 lekmtsmekirlildkvkegkivvlEkgLtpeeeakliettmeeikpdeFsGieietypkkekdkgllekllgkkeseer 80 
                                    l++mtsmekirlildkvk+g+ivvlE+gLtpeee +lie+tm+ei++deFsGieie+yp+k++  ++++++lg+ +s+ r
  gi|116754521|ref|YP_843639.1|  14 LNRMTSMEKIRLILDKVKTGRIVVLESGLTPEEEVRLIEMTMTEIRVDEFSGIEIESYPAKRE-GSFVSRILGRGSSKGR 92 
                                    799***********************************************************9.**************** PP

                        DUF2073  81 ltvigPanqlktlkkdkdlisalvs 105
                                    +tvigPanql+t++kd+  is+ vs
  gi|116754521|ref|YP_843639.1|  93 MTVIGPANQLRTVEKDQYQISTKVS 117
                                    *********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1005.67
//
Query:       gi|116754522|ref|YP_843640.1|  [L=142]
Description: hypothetical protein Mthe_1221 [Methanosaeta thermophila PT]
Scores for 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-43  145.8   0.0    9.9e-43  145.6   0.0    1.0  1  DUF2072      Zn-ribbon containing protein
     0.0039   17.2   0.2     0.0065   16.5   0.2    1.3  1  HypA         Hydrogenase/urease nickel incorporation, metallo
  ------ inclusion threshold ------
      0.022   14.7   1.8      0.037   14.0   1.8    1.2  1  Prok-RING_1  Prokaryotic RING finger family 1
      0.032   14.4   0.8      0.072   13.2   0.8    1.5  1  Zn-ribbon_8  Zinc ribbon domain
       0.11   11.9   1.1       0.73    9.2   0.0    2.7  3  zf-TFIIB     Transcription factor zinc-finger


Domain annotation for each model (and alignments):
>> DUF2072  Zn-ribbon containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.6   0.0   2.7e-46   9.9e-43       1     132 [.       2     138 ..       2     139 .. 0.89

  Alignments for each domain:
  == domain 1  score: 145.6 bits;  conditional E-value: 2.7e-46
                        DUF2072   1 PHkCtkCekvfedgskeilkGCpsCGgkkFlyvkeeekkedvseeke.......elvaeaeeeieevldaeeteeeklek 73 
                                    PH+Ct+C+kvf+dg++ ilkGCp+CGg++F+y++e+e+  ++s   +       ++ ++ ++ei++v++ ++ ++ek++k
  gi|116754522|ref|YP_843640.1|   2 PHMCTRCKKVFDDGAD-ILKGCPKCGGRMFEYIRERETLITESMGVRrppkravTTAVRDRNEIKDVMGGDRGASEKIKK 80 
                                    9**************9.******************9987665554443566544444555556***************** PP

                        DUF2072  74 kekekaekekeeedrvesvrilepGsYelNlekLlerdelvmalkeegkYvvdlpsvlk 132
                                    +++ ++++++ e++ +esvri+epG+YelNl++L++rdelvmalke g+Y++dl+s+++
  gi|116754522|ref|YP_843640.1|  81 PAAIQTSQRSPEDRPIESVRITEPGRYELNLPTLFSRDELVMALKE-GTYLIDLNSAFR 138
                                    *******************************************998.**********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 !   16.5   0.2   1.8e-06    0.0065      72     109 ..       4      42 ..       1      44 [. 0.87

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.8e-06
                                    EETTTS-EEECHHH.HHS-TTTSSS-EEEEESSSEEEEE CS
                           HypA  72 rCreCgkefeleek.alrCpkCgsadveivsGeellvks 109
                                    +C++C+k f+  ++    CpkCg++ +e ++ +e l+++
  gi|116754522|ref|YP_843640.1|   4 MCTRCKKVFDDGADiLKGCPKCGGRMFEYIRERETLITE 42 
                                    7*********77666668****************99986 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.8     1e-05     0.037       6      27 ..       4      26 ..       2      29 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1e-05
                    Prok-RING_1  6 kCpvCgkelkeedDiVv.CpeCg 27
                                    C+ C+k ++++ Di   Cp+Cg
  gi|116754522|ref|YP_843640.1|  4 MCTRCKKVFDDGADILKgCPKCG 26
                                   6**************966****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 ?   13.2   0.8     2e-05     0.072       8      35 ..       5      28 ..       4      32 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2e-05
                    Zn-ribbon_8  8 CeeCghefevlqsisdaplta.CPeCgse 35
                                   C++C+++f+  +        + CP+Cg++
  gi|116754522|ref|YP_843640.1|  5 CTRCKKVFDDGAD-----ILKgCPKCGGR 28
                                   *********4442.....4445*****95 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.19     7e+02      21      26 ..       4       9 ..       3      15 .. 0.71
   2 ?    9.2   0.0    0.0002      0.73      20      31 ..      20      31 ..      17      40 .. 0.83
   3 ?   -2.1   0.0      0.69   2.5e+03      31      40 ..      71      80 ..      71      81 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.19
                       zf-TFIIB 21 yCpqCr 26
                                    C++C+
  gi|116754522|ref|YP_843640.1|  4 MCTRCK 9 
                                   566664 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0002
                       zf-TFIIB 20 dyCpqCrGvWld 31
                                   + Cp+C+G +++
  gi|116754522|ref|YP_843640.1| 20 KGCPKCGGRMFE 31
                                   679999998885 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.69
                       zf-TFIIB 31 drgeleklle 40
                                   drg +ek+++
  gi|116754522|ref|YP_843640.1| 71 DRGASEKIKK 80
                                   89*****985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); 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):               5  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1096.87
//
Query:       gi|116754523|ref|YP_843641.1|  [L=50]
Description: hypothetical protein Mthe_1222 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                      316  (0.0176251); 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: 0.32u 0.25s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 387.62
//
Query:       gi|116754524|ref|YP_843642.1|  [L=133]
Description: hypothetical protein Mthe_1223 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1043.80
//
Query:       gi|116754525|ref|YP_843643.1|  [L=523]
Description: D-3-phosphoglycerate dehydrogenase [Methanosaeta thermophila PT]
Scores for complete 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-65  219.4   0.0    4.5e-65  218.3   0.0    1.6  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    3.2e-42  143.4   1.0    7.1e-42  142.3   1.0    1.6  1  2-Hacid_dh      D-isomer specific 2-hydroxyacid dehydrogenase
    4.2e-06   27.0   1.8    2.1e-05   24.8   0.1    2.8  3  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    5.1e-05   23.0   0.5    0.00023   20.9   0.1    2.5  2  ACT             ACT domain
    0.00012   22.2   0.5     0.0016   18.5   0.0    2.4  2  AdoHcyase_NAD   S-adenosyl-L-homocysteine hydrolase, NAD bind
    0.00024   20.7   0.1     0.0025   17.4   0.0    2.4  3  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
    0.00062   20.2   0.2      0.039   14.4   0.0    2.9  3  UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family,
  ------ inclusion threshold ------
      0.038   14.6   0.3       0.29   11.8   0.0    2.5  2  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
       0.11   13.1   2.6       0.67   10.6   0.0    3.2  3  ACT_4           ACT 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 !  218.3   0.0   2.3e-68   4.5e-65       1     178 []     104     278 ..     104     278 .. 0.98

  Alignments for each domain:
  == domain 1  score: 218.3 bits;  conditional E-value: 2.3e-68
                                    HHHHHHHHTTHHHHHHHHHTTCCHTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTC CS
                   2-Hacid_dh_C   1 lalllallrrlaeadeevregewksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgv 80 
                                    +a++l+l+r++++a+++vr+gew ++k+++g e+ +kt+GiiGlGrIG++vakr+kafgm+++ayd++ ++++ ++elg+
  gi|116754525|ref|YP_843643.1| 104 IAMMLSLARNIPQAHASVRRGEW-NRKKYTGVEVFNKTLGIIGLGRIGTEVAKRMKAFGMRILAYDPFITESK-AAELGI 181
                                    68*********************.9*******************************************99776.9***** PP

                                    EECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCEEEES--SSSSSG CS
                   2-Hacid_dh_C  81 elvsleellaesDivslhlpltpetrhlinaeelakmkkgailiNtaRGglvdeeaLleaLksgkiagaalDvfeeeplp 160
                                    +l+slee+++esD++++h+pltpetr++i++ ++++mk+++ +iN+aRGg+++e+aL++a+ +++iagaa+Dv+ +ep+ 
  gi|116754525|ref|YP_843643.1| 182 KLASLEEIYRESDFITVHTPLTPETRNMIDEPQIKMMKPTVRIINCARGGIINEAALAKAVAENRIAGAAVDVYTKEPPV 261
                                    ******************************************************************************** PP

                                    TCHHHHHSTTEEE-SS-T CS
                   2-Hacid_dh_C 161 edspllelpnviltPHia 178
                                      +plle +++i tPH++
  gi|116754525|ref|YP_843643.1| 262 -GNPLLEQERIITTPHLG 278
                                    .55*************97 PP

>> 2-Hacid_dh  D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.3   1.0   3.5e-45   7.1e-42       1     134 []       3     310 ..       3     310 .. 0.99

  Alignments for each domain:
  == domain 1  score: 142.3 bits;  conditional E-value: 3.5e-45
                                    EEEEST.CHHHHHHHHHTTE.EEEEESCSSHHHCHHHHTTESEEEE-TTS-BSHHHHHHHTT--EEEESSSSCTTB-HHH CS
                                    xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     2-Hacid_dh   1 vlileplreeelellkeegv.evevkdellteellekakdadalivrsntkvtaevlealpkLkviaragvGvDnvDlda 79 
                                    vl+++pl ee++++l+     ev+v ++l+ eel+e++k++dal++rs tkvta+v++a+++LkviaragvGvDnvD+da
  gi|116754525|ref|YP_843643.1|   3 VLVSDPLAEEGIRRLET--AaEVDVITNLSPEELVERIKGYDALVIRSGTKVTADVINAADRLKVIARAGVGVDNVDVDA 80 
                                    7999*************..44*********************************************************** PP

                                    HHHTT-EEEE-TTTTHHHHHHHH......................................................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxx......................................................... RF
                     2-Hacid_dh  80 akerGilVtnvpgystesvAElt......................................................... 102
                                    a+++Gi+V+n+pg +t+s+AE+t                                                         
  gi|116754525|ref|YP_843643.1|  81 ATKKGIIVVNAPGGNTISAAEHTiammlslarnipqahasvrrgewnrkkytgvevfnktlgiiglgrigtevakrmkaf 160
                                    ******************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                     2-Hacid_dh 103 ................................................................................ 102
                                                                                                                    
  gi|116754525|ref|YP_843643.1| 161 gmrilaydpfiteskaaelgiklasleeiyresdfitvhtpltpetrnmidepqikmmkptvriincarggiineaalak 240
                                    ******************************************************************************** PP

                                    ......................................T-BHHHHHHHHHHHHHHHHHHHTTCCGTTBCS CS
                                    ......................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     2-Hacid_dh 103 ......................................aaTeeaqeniaeeaaenlvaflkgespanavn 134
                                                                          a+T eaq n+a  +a++++a+ +g+ p++a+n
  gi|116754525|ref|YP_843643.1| 241 avaenriagaavdvytkeppvgnplleqeriittphlgASTAEAQINVALAVADQIIAISRGQLPTTAIN 310
                                    *****************************************************************99987 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1      0.96   1.9e+03     103     132 ..      80     108 ..      30     119 .. 0.72
   2 !   24.8   0.1     1e-08   2.1e-05       2     109 ..     141     247 ..     140     254 .. 0.88
   3 ?   -0.6   0.0      0.69   1.4e+03      36      69 ..     386     420 ..     375     430 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.96
                                    HHHHTT-EEEEEEEESHHHHHHHT-EEEEE CS
                  NAD_binding_2 103 elkekglkfldaPVSGGeegAekGtLsimv 132
                                    ++++kg+ +++aP  G +  A++ t+++m+
  gi|116754525|ref|YP_843643.1|  80 AATKKGIIVVNAP-GGNTISAAEHTIAMML 108
                                    4556666666666.4555666666666665 PP

  == domain 2  score: 24.8 bits;  conditional E-value: 1e-08
                                    EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS.HCCC- CS
                  NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieg.lleal 80 
                                    +g+iGlG +G++ a+++++ g+++ +y+     +e+ +ae    ++s+ee+ ++ d++ +  + +++++++i++  ++ +
  gi|116754525|ref|YP_843643.1| 141 LGIIGLGRIGTEVAKRMKAFGMRILAYDPF--ITESKAAELGIKLASLEEIYRESDFITVHTPLTPETRNMIDEpQIKMM 218
                                    79**************************54..444444444568899***************************99999* PP

                                    -TT-EEEE-S---HHHHHHHHHHHHHTT- CS
                  NAD_binding_2  81 kkgdilidgstsspedtrelakelkekgl 109
                                    k+   +i+++   + +   lak+++e+ +
  gi|116754525|ref|YP_843643.1| 219 KPTVRIINCARGGIINEAALAKAVAENRI 247
                                    *********99999999999999988775 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.69
                                    HHHHHTTEEE-SSHHHHHHHC.SEEEE-SSSHHHH CS
                  NAD_binding_2  36 eelvaegakaaesieelvasl.dvvitmvkagkav 69 
                                      l ++g+k++es  e++++  +++ + +k ++++
  gi|116754525|ref|YP_843643.1| 386 ALLKEKGIKLMESKTEVANGYsNLITMRLKTTSET 420
                                    55778899***********9956666667776665 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       2.8   5.5e+03      22      31 ..     282     291 ..     282     293 .. 0.85
   2 !   20.9   0.1   1.2e-07   0.00023       3      65 ..     452     512 ..     450     514 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.8
                                    HHTTSEEEEE CS
                            ACT  22 adrgiNidsi 31 
                                    a+++iN++ +
  gi|116754525|ref|YP_843643.1| 282 AEAQINVALA 291
                                    799****987 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 1.2e-07
                                    EEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHTT CS
                            ACT   3 lrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkkl 65 
                                    ++v+ +DrP +++ v+ +l++++iNi s+++++     ++   +v+ vd+  ++e+++++ ++
  gi|116754525|ref|YP_843643.1| 452 VLVLHEDRPNIIGPVCVVLGEANINIGSMHVGRISA--GKPQLMVLNVDTPLDDETMKRILSV 512
                                    778999******************************..9*******************99765 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.2      0.19   3.7e+02      53     100 ..      59     106 ..      38     120 .. 0.75
   2 !   18.5   0.0   8.2e-07    0.0016      17     110 ..     132     228 ..     126     272 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.19
                                    -S-HHHHHHHHCTT-EE--HHHCTTT-SEEEE-SSSSSSB-HHHHCCS CS
                  AdoHcyase_NAD  53 evdPicalqaameGfevvtleevvkkadivvtttGnkdiitlehlkkm 100
                                      d +  +  a  G + v ++ ++kk+ ivv + G + i  +eh  +m
  gi|116754525|ref|YP_843643.1|  59 AADRLKVIARAGVGVDNVDVDAATKKGIIVVNAPGGNTISAAEHTIAM 106
                                    4455555555666777888999999999*******9999999998776 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 8.2e-07
                                    H-S--TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-H.HHHHHHHCTT-EE--HHHCTTT-SEEEE-S....SSSSS CS
                  AdoHcyase_NAD  17 tdvllaGkvavvaGyGdvGkGcaaslkglGarvivtevdP.icalqaameGfevvtleevvkkadivvttt....Gnkdi 91 
                                    t v +  k+  ++G G +G   a+ +k++G r++    dP i+  +aa  G +++ lee+ +++d++   t     ++++
  gi|116754525|ref|YP_843643.1| 132 TGVEVFNKTLGIIGLGRIGTEVAKRMKAFGMRILA--YDPfITESKAAELGIKLASLEEIYRESDFITVHTpltpETRNM 209
                                    66667789999********************9875..6885677899999***************88765522235799* PP

                                    B-HHHHCCS-TTEEEEE-S CS
                  AdoHcyase_NAD  92 itlehlkkmkddaivcniG 110
                                    i   ++k mk ++ + n  
  gi|116754525|ref|YP_843643.1| 210 IDEPQIKMMKPTVRIINCA 228
                                    ********99877555543 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.41   8.1e+02      57      76 ..      19      38 ..      14      73 .. 0.62
   2 ?   -1.5   0.0      0.81   1.6e+03      26      88 ..      48     111 ..      38     120 .. 0.62
   3 !   17.4   0.0   1.3e-06    0.0025       4      71 ..     138     203 ..     135     242 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.41
                                   HHHT-SEEEE-S-HHHHHHH CS
                           IlvN 57 avkkadvvmiliPDelqkev 76
                                    +++ dv+++l P+el +++
  gi|116754525|ref|YP_843643.1| 19 TAAEVDVITNLSPEELVERI 38
                                   55666777777776665544 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.81
                                    TT--EEEEE-TT-HHHHHHHHTT-EEEEHH.HHHHT-SEEEE-S-HHHHHHHHHHHTGGG--TT CS
                           IlvN  26 sgldvvvglregsksvkkAkeegfevltva.eavkkadvvmiliPDelqkevyeeeiepnlkeg 88 
                                    sg +v+  + + +  +k   ++g+ v +v+ +a++k  ++++ +P     +  e++i+  l+  
  gi|116754525|ref|YP_843643.1|  48 SGTKVTADVINAADRLKVIARAGVGVDNVDvDAATKKGIIVVNAPGGNTISAAEHTIAMMLSLA 111
                                    5666666666666666666666666666644566666677777777666666666666666555 PP

  == domain 3  score: 17.4 bits;  conditional E-value: 1.3e-06
                                    TS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HH CS
                           IlvN   4 gkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDe 71 
                                    +k++ +iG G  G   a+ ++  g+ +    ++   + +kA e g++ ++++e+ +++d++++ +P +
  gi|116754525|ref|YP_843643.1| 138 NKTLGIIGLGRIGTEVAKRMKAFGMRILA--YDPFITESKAAELGIKLASLEEIYRESDFITVHTPLT 203
                                    799**********************9864..444457899***********************99843 PP

>> UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.083   1.7e+02      33      74 ..       3      48 ..       1     131 [. 0.79
   2 !   14.4   0.0   1.9e-05     0.039      21      93 ..     152     220 ..     150     228 .. 0.80
   3 ?   -3.3   0.0       6.3   1.2e+04      48      71 ..     387     410 ..     377     414 .. 0.64

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.083
                                   EEEE-SSTHHCCCCHHGG.....BTCCEEES-CHHHHTT-SEEEE-S CS
                 UDPG_MGDP_dh_C 33 vkiyDPkvkeeaveaele.....ekgvevvdsleealkgadaivilt 74
                                   v + DP ++e  ++ e++      +++ + ++l e++kg+da+vi  
  gi|116754525|ref|YP_843643.1|  3 VLVSDPLAEEGIRRLETAaevdvITNL-SPEELVERIKGYDALVIRS 48
                                   677888888877777665444432222.2345678899999999865 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 1.9e-05
                                    HHHHHHHHCTSEEEEE-SSTHHCCCCHHGGBTCCEEES-CHHHHTT-SEEEE-S--.GGGGGS.-HHHHHHCCSS CS
                 UDPG_MGDP_dh_C  21 diieeLleegaevkiyDPkvkeeaveaeleekgvevvdsleealkgadaivilteh.defkel.dlaklkelmkp 93 
                                    ++++++++ g+++ +yDP ++e+++++     g++++ slee  +++d i ++t+  +e +++ d  ++ ++mkp
  gi|116754525|ref|YP_843643.1| 152 EVAKRMKAFGMRILAYDPFITESKAAE----LGIKLA-SLEEIYRESDFITVHTPLtPETRNMiDEPQI-KMMKP 220
                                    6899******************99987....589998.7***************864777775233333.34454 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 6.3
                                    HGGBTCCEEES-CHHHHTT-SEEE CS
                 UDPG_MGDP_dh_C  48 eleekgvevvdsleealkgadaiv 71 
                                     l+ekg+++++s +e ++g++ ++
  gi|116754525|ref|YP_843643.1| 387 LLKEKGIKLMESKTEVANGYSNLI 410
                                    344667777777777777776665 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.2         1     2e+03      20      67 ..      47      89 ..      11     106 .. 0.62
   2 ?   11.8   0.0   0.00014      0.29       2      68 ..     141     199 ..     140     214 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1
                                   HTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE CS
                  F420_oxidored 20 aagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvl 67
                                   ++g   ++++ a   n   + +  +++gv+v      +aa++  ++v+
  gi|116754525|ref|YP_843643.1| 47 RSG---TKVT-ADVINAADRLKVIARAGVGVDN-VDVDAATKKGIIVV 89
                                   444...4444.3333333333444445666766.34444445555555 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00014
                                    EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE- CS
                  F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvla 68 
                                    +giiG G++g  +a+++ a g     i+ a   +p   e+ a+elg+k+ +   ee  +e+d++ + 
  gi|116754525|ref|YP_843643.1| 141 LGIIGLGRIGTEVAKRMKAFG---MRIL-A--YDPFITESKAAELGIKLAS--LEEIYRESDFITVH 199
                                    8********************...7777.5..6777778888899887777..99999999987654 PP

>> ACT_4  ACT domain
   #    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      24      49 ..      63      88 ..      54      91 .. 0.83
   2 ?   -3.2   0.0       6.8   1.4e+04      25      47 ..     386     406 ..     381     415 .. 0.69
   3 ?   10.6   0.0   0.00034      0.67      11      80 .]     454     520 ..     450     520 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.46
                          ACT_4 24 tqviseekanivsvnaktrkkdglae 49
                                   ++vi+ +++ + +v +++  k+g+  
  gi|116754525|ref|YP_843643.1| 63 LKVIARAGVGVDNVDVDAATKKGIIV 88
                                   689*************9987777655 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 6.8
                          ACT_4  25 qviseekanivsvnaktrkkdgl 47 
                                    ++++e+++++++ +++    +g+
  gi|116754525|ref|YP_843643.1| 386 ALLKEKGIKLMESKTEVA--NGY 406
                                    567888999999998883..333 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00034
                          ACT_4  11 veaedrkglLaditqviseekanivsvnaktrkkdglaeikitveVkdveh.L.srviakLraipgVisVeR 80 
                                    v  edr+++++ ++ v+ e+++ni s+++   ++     +k ++ V +v+  L ++ ++++ +++gV s++R
  gi|116754525|ref|YP_843643.1| 454 VLHEDRPNIIGPVCVVLGEANINIGSMHVGRISA-----GKPQLMVLNVDTpLdDETMKRILSVSGVLSARR 520
                                    6679************************998654.....444444444443222567777777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (523 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); 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: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 3597.62
//
Query:       gi|116754526|ref|YP_843644.1|  [L=245]
Description: purine phosphorylase family 2 [Methanosaeta thermophila PT]
Scores for 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-38  129.7   0.1    1.2e-37  129.5   0.1    1.0  1  PNP_UDP_1        Phosphorylase superfamily
  ------ inclusion threshold ------
       0.02   14.8   0.0      0.032   14.1   0.0    1.3  1  NAD_binding_10   NAD(P)H-binding
      0.058   13.2   1.3      0.095   12.5   0.1    1.9  2  DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydr


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 !  129.5   0.1   1.9e-41   1.2e-37      23     233 ..      23     225 ..      12     226 .. 0.91

  Alignments for each domain:
  == domain 1  score: 129.5 bits;  conditional E-value: 1.9e-41
                                    EEEEEE.TTEEEEEEEE.TTEEEEEEE--...SSHHHHHHHHHHHHHHHC--SEEEEEEEEEESSTTT-TT-EEEEEEEE CS
                      PNP_UDP_1  23 tpfgregrgfkfvtGtl.kgkpvvivstG...iGkpnaavvaeirllkefgvkaiiriGtaGglnpdlkvGDvvipddai 98 
                                    tp+g++    + +  ++ ++++v+i ++G   + +  ++++a i + ++ g+ +ii+i+t+G++    ++G +vip+d+i
  gi|116754526|ref|YP_843644.1|  23 TPYGNV----RAISSRIsGRDVVFISRHGddhLPPYRVNYRAIICAAESTGAGRIIAINTVGSM--ISPPGSFVIPNDFI 96 
                                    555555....4444455478899********99999999*************************..99************ PP

                                    ESSSCCGCCTHHCCTCCCCTTSSEE--HHHHHHHHHCHHTTTTTEEEEEEEEESESS-CHHHHHHHHHHTC-CEEESSHH CS
                      PNP_UDP_1  99 nfdgrsplygpkeegqyfpdsydapadpelrallkeaaealgikvhrGvvatadgfyaeteaelrllrrlgadaveMEta 178
                                     f+ ++ ++++++  + ++d++++ ++pe+r++l e+++a+g +  +Gv+++++g+++et+a++++lr++g d+v+M+++
  gi|116754526|ref|YP_843644.1|  97 EFTKFRVPTFYEDR-AVHVDMSEP-YCPEIRKVLMESCRAEGHEPYEGVYVCTEGPHFETHAQIKMLRSFG-DVVGMTGY 173
                                    *8888888888887.*********.**********************************************.******** PP

                                    HHHHHHHHTT--EEEEEEEEETTTBETTCTCH.HCCCHHHHHHHHHHHHHHHHHH CS
                      PNP_UDP_1 179 avaqlArelgipfaairvvsdlaaggadaeatheeveefaqeaaknaaalllall 233
                                    ++++lAre+g+++a+i++ +++a++   ++ + + +  + +++  ++a+++++++
  gi|116754526|ref|YP_843644.1| 174 PEVVLARERGLCYASICLATNKAGE---GQFDLRQIVSVERKSMSDLARIIERAV 225
                                    *********************8887...777889999999999999999999987 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 ?   14.1   0.0   5.4e-06     0.032      50     109 ..      27      89 ..      18     108 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.4e-06
                                    -CCHHHHHHTT-SEEEES---TCCHHHH...HHHHHHHHHHCT--EEEEEEETTTTSGCGCHH CS
                 NAD_binding_10  50 dvedlaealkgadaVvsalggggkdeeg...aknivdaakeagvkRfvlvsaigvgdevpgef 109
                                    +v ++ + ++g d+V+++  g++         ++i+ aa+ +g  R++ + ++g+  + pg+f
  gi|116754526|ref|YP_843644.1|  27 NVRAISSRISGRDVVFISRHGDDHLPPYrvnYRAIICAAESTGAGRIIAINTVGSMISPPGSF 89 
                                    67789999*******9999988884444457**********************9987777765 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 ?   12.5   0.1   1.6e-05     0.095      14      39 ..     132     155 ..     131     157 .. 0.74
   2 ?   -2.4   0.1      0.73   4.4e+03       9      21 ..     183     195 ..     183     201 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.6e-05
                                    TEEEETTCTT.CEEETTTT-CEEECC CS
                DHODB_Fe-S_bind  14 CvvktkggdggeykrvCkdGPvFdad 39 
                                    C+ + ++    e ++vC++GP F+ +
  gi|116754526|ref|YP_843644.1| 132 CRAEGHE--PYEGVYVCTEGPHFETH 155
                                    5555544..44799*********987 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.73
                                    SSS-TTEEEETTC CS
                DHODB_Fe-S_bind   9 GaClgCvvktkgg 21 
                                    G+C++  +  +++
  gi|116754526|ref|YP_843644.1| 183 GLCYASICLATNK 195
                                    8899866655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1740.97
//
Query:       gi|116754527|ref|YP_843645.1|  [L=229]
Description: hypothetical protein Mthe_1226 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); 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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1693.96
//
Query:       gi|116754528|ref|YP_843646.1|  [L=249]
Description: ABC-2 type transporter [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-24   86.1  24.5    2.1e-24   86.1  24.5    1.7  2  ABC2_membrane    ABC-2 type transporter
    1.1e-16   60.9  24.9    1.1e-16   60.9  24.9    1.6  1  ABC2_membrane_3  ABC-2 family transporter protein
    7.1e-05   22.2  23.5    7.1e-05   22.2  23.5    2.2  2  ABC2_membrane_2  ABC-2 family transporter protein
     0.0021   18.5   1.4     0.0021   18.5   1.4    2.8  5  AtpR             N-ATPase, AtpR subunit


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 !   86.1  24.5   4.8e-28   2.1e-24      10     208 ..      17     209 ..      10     211 .. 0.84
   2 ?   -0.8   0.4      0.19   8.4e+02     117     139 ..     212     234 ..     208     238 .. 0.51

  Alignments for each domain:
  == domain 1  score: 86.1 bits;  conditional E-value: 4.8e-28
                  ABC2_membrane  10 eflqrwrdpslgllwrliqplllalvfgtvfgnlgnsedglnr......pgllffsvlflafsaltsvapvferergvle 83 
                                    ++  ++       ++ +i+pl+l++ f+              +      pgl++++++f++ +a+  +++ +e + ++le
  gi|116754528|ref|YP_843646.1|  17 DVWIYYAKGPVM-VFGIIFPLFLLMAFTIGRN----------MtvrdlfPGLMGMAIFFTS-TAVGPAILPWEARSRTLE 84 
                                    555555555555.5667777555554444433..........0122345************.9999999*********** PP

                  ABC2_membrane  84 relvsplyslsayvlakvlvelpvsllqalifllivyflvgldlsrfflflllllltalaasslgllisalapsfe..da 161
                                    r+ ++p+   +a +l+ v+++++++++++li l++++++ g+++ ++++fl+ +ll ++++ sl++l+sa+ p+    ++
  gi|116754528|ref|YP_843646.1|  85 RLVTAPV-GIWALLLGDVIASFVFGIMISLIPLAVAVLM-GVEVLHVMIFLVGMLLATFCFASLSILLSAYPPTDVpaTV 162
                                    *******.*******************************.****877************************998661155 PP

                  ABC2_membrane 162 sqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrsn 208
                                    ++l+slv +pl++ sG+f+p+d++p+w ++i+ ++Plty+v++ r++
  gi|116754528|ref|YP_843646.1| 163 MMLSSLVRFPLVFISGVFVPVDQLPGWGRAISSVSPLTYFVDLARYS 209
                                    66669999***********************************9986 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.19
                  ABC2_membrane 117 livyflvgldlsrf.flfllllll 139
                                     ++y+ v++dl  + +lf +++l+
  gi|116754528|ref|YP_843646.1| 212 GVTYYSVNVDLA-VmGLFAIVFLV 234
                                    477777777775.22332222222 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9  24.9   2.5e-20   1.1e-16     157     344 ..      48     237 ..      43     238 .. 0.92

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 2.5e-20
                ABC2_membrane_3 157 snvasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll..afglgip 234
                                    + v + + gl+ + ++f + ++  + +  E +sr++e++++++v  ++++l+ ++++f+ ++ ++l+ l++  + g  ++
  gi|116754528|ref|YP_843646.1|  48 MTVRDLFPGLMGMAIFFTSTAVGPAILPWEARSRTLERLVTAPVGIWALLLGDVIASFVFGIMISLIPLAVavLMG--VE 125
                                    667788999999999999999888888899*************************************999655888..*9 PP

                ABC2_membrane_3 235 fgnlglllllfllfglayialgyllssl..fknsetaqilifivilllsgffgglfpledlpsalkwifsiiPffapglg 312
                                    + +++++l+ +ll  +++++l+ lls+   ++ ++t++ l ++v ++l +++g+++p+++lp++ + i+s+ P++++ ++
  gi|116754528|ref|YP_843646.1| 126 VLHVMIFLVGMLLATFCFASLSILLSAYppTDVPATVMMLSSLVRFPLVFISGVFVPVDQLPGWGRAISSVSPLTYFVDL 205
                                    9***************************77778889899999999999999999999*********************** PP

                ABC2_membrane_3 313 llrlitgdplweillsliilalfavvylllal 344
                                        i+g++++++  +l+++ lfa+v+l+ a+
  gi|116754528|ref|YP_843646.1| 206 ARYSISGVTYYSVNVDLAVMGLFAIVFLVTAI 237
                                    *999*************************997 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 ?    0.1   0.1     0.089     4e+02       2      34 ..      12      43 ..      11      55 .. 0.67
   2 !   22.2  23.5   1.6e-08   7.1e-05      78     284 ..      55     241 ..      40     244 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.089
                ABC2_membrane_2  2 aiakkEfrdlvrsrrfllltvllplidvalayl 34
                                   aia+k++     +  + ++++++pl+ + +a++
  gi|116754528|ref|YP_843646.1| 12 AIARKDVWIYYAKGPVMVFGIIFPLF-LLMAFT 43
                                   56666666666666677777777777.666654 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 1.6e-08
                ABC2_membrane_2  78 stimavlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaigla.iavallatvllalaiilalgivl 156
                                    +++m ++i +  ++ g  ++  E  ++Tl++l + Pv  +++llg +i++++ g++  ++ l ++vl+            
  gi|116754528|ref|YP_843646.1|  55 PGLMGMAIFFTSTAVGPAILPWEARSRTLERLVTAPVGIWALLLGDVIASFVFGIMiSLIPLAVAVLM------------ 122
                                    5678888888899999999999*******************************888666666666555............ PP

                ABC2_membrane_2 157 aledllllvvasvlllllv.vflalglllSsvarssreaaalalglfv.vlailvpivlygvaellagpavpqeindfls 234
                                     + ++l ++++ v +ll++ +f++l++llS+   + + a+ ++l+ +v + ++++++v  +v +l+        +   +s
  gi|116754528|ref|YP_843646.1| 123 -GVEVLHVMIFLVGMLLATfCFASLSILLSAYPPTDVPATVMMLSSLVrFPLVFISGVFVPVDQLPG-------WGRAIS 194
                                    .5555555555555555555************************98772446666777778777777.......55669* PP

                ABC2_membrane_2 235 llsptsayntllneilagsdlnalgstatnllilllllavllvlgyvlFk 284
                                     +sp  ++  l +  ++g     ++s    l+++ l ++v+lv ++ l +
  gi|116754528|ref|YP_843646.1| 195 SVSPLTYFVDLARYSISGVT---YYSVNVDLAVMGLFAIVFLVTAIKLHE 241
                                    ********988888888884...8999999*************9987655 PP

>> AtpR  N-ATPase, AtpR subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.6      0.57   2.6e+03      57      70 ..      46      59 ..       9      71 .. 0.62
   2 ?   -1.0   1.2      0.57   2.5e+03      23      44 ..      42      63 ..      25      99 .. 0.53
   3 ?   -1.3   0.7      0.71   3.2e+03      71      71 ..      93      93 ..      48     124 .. 0.61
   4 !   18.5   1.4   4.6e-07    0.0021       4      54 ..     129     179 ..     126     197 .. 0.88
   5 ?   -3.9   0.1         4   1.8e+04      69      78 ..     225     234 ..     222     242 .. 0.49

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.57
                           AtpR 57 aagglarlLaallG 70
                                    +  ++ l+ +l+G
  gi|116754528|ref|YP_843646.1| 46 RNMTVRDLFPGLMG 59
                                   33333444444444 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.57
                           AtpR 23 ltvrrliaskrpalllvsslll 44
                                   +t+ r ++ +     l++  ++
  gi|116754528|ref|YP_843646.1| 42 FTIGRNMTVRDLFPGLMGMAIF 63
                                   3333333333333333333333 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.71
                           AtpR 71 F 71
                                   +
  gi|116754528|ref|YP_843646.1| 93 I 93
                                   1 PP

  == domain 4  score: 18.5 bits;  conditional E-value: 4.6e-07
                           AtpR   4 llalllGlllGaiyFggLwltvrrliaskrpalllvsslllRlgivlagfy 54 
                                    ++ +l+G+ll ++ F++L + +  ++ +  pa+++++s l+R+ +v+   +
  gi|116754528|ref|YP_843646.1| 129 VMIFLVGMLLATFCFASLSILLSAYPPTDVPATVMMLSSLVRFPLVFISGV 179
                                    678****************************************99976444 PP

  == domain 5  score: -3.9 bits;  conditional E-value: 4
                           AtpR  69 lGFllaRlll 78 
                                    +G++++ +l+
  gi|116754528|ref|YP_843646.1| 225 MGLFAIVFLV 234
                                    3444333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       923  (0.0514808); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1781.33
//
Query:       gi|116754529|ref|YP_843647.1|  [L=309]
Description: daunorubicin resistance ABC transporter ATPase subunit [Methanosaeta thermophila PT]
Scores for complete 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-29  101.7   0.0    7.7e-29  100.9   0.0    1.4  1  ABC_tran     ABC transporter
    9.7e-15   55.2   0.2    2.3e-10   40.8   0.0    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    3.6e-08   34.0   0.1    2.9e-07   31.1   0.0    2.1  2  DUF4162      Domain of unknown function (DUF4162)
    7.5e-05   23.3   0.1    0.00018   22.1   0.1    1.6  2  AAA_23       AAA domain
    0.00022   20.8   0.1        0.2   11.1   0.0    2.2  2  SMC_N        RecF/RecN/SMC N terminal domain
     0.0045   17.3   0.2      0.065   13.5   0.2    2.3  1  AAA_22       AAA domain
     0.0086   15.8   0.1      0.017   14.9   0.1    1.4  1  AAA_29       P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.016   15.6   0.1       0.61   10.4   0.0    2.3  2  AAA_16       AAA ATPase domain
      0.022   15.2   0.3        2.5    8.5   0.0    2.9  2  AAA          ATPase family associated with various cellular a
      0.029   14.0   0.1      0.058   13.0   0.1    1.4  1  AAA_27       AAA domain
       0.14   12.1   0.0       0.35   10.8   0.0    1.6  2  RsgA_GTPase  RsgA GTPase
       0.16   12.1   0.1        1.7    8.7   0.0    2.2  2  MMR_HSR1     50S ribosome-binding GTPase
       0.17   10.5   0.2        5.4    5.5   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 !  100.9   0.0   5.6e-32   7.7e-29       2     136 ..      20     162 ..      19     163 .. 0.97

  Alignments for each domain:
  == domain 1  score: 100.9 bits;  conditional E-value: 5.6e-32
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                    +++s+++ ege+ +++G+nG+GKSt +++l+g ++p+eG+  + g d+ +    ++r +ig++p+ ++   elt+ +n  
  gi|116754529|ref|YP_843647.1|  20 DHISFSVAEGEIFGFLGPNGSGKSTTIRMLTGTVRPDEGTAAIMGYDICK-HPIRARTSIGFVPEMANAYVELTAWRNlm 98 
                                    789*********************************************99.566789*********************** PP

                                    ...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                               e++++++++l+++gl + + + v    + +S+G++qr+ l++al+++p++l+lDEp 
  gi|116754529|ref|YP_843647.1|  99 fmgelygiprrERERRASELLKRFGLYDRRGDQV----RAFSKGMRQRLLLCMALINDPPVLILDEPA 162
                                    **********9999**************999999....*****************************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   0.1   7.7e-05      0.11       2      19 ..      32      49 ..      31      64 .. 0.86
   2 !   40.8   0.0   1.6e-13   2.3e-10     228     298 ..     126     193 ..      90     196 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.7e-05
                         AAA_21  2 nvliGpNgsGKSnLLdal 19
                                    ++ GpNgsGKS+ ++ l
  gi|116754529|ref|YP_843647.1| 32 FGFLGPNGSGKSTTIRML 49
                                   6789*********99987 PP

  == domain 2  score: 40.8 bits;  conditional E-value: 1.6e-13
                         AAA_21 228 dgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                    d++  ++r +S G+++ l l  al+ ++   ++l++DEp +gL+ +  r + e+++el+r+g+ v+ltTH+
  gi|116754529|ref|YP_843647.1| 126 DRRGDQVRAFSKGMRQRLLLCMALINDP---PVLILDEPASGLDVESSRLIKEVIRELNREGTTVFLTTHD 193
                                    4444456778***************999...***************************************8 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.88   1.2e+03      25      57 ..     171     204 ..     156     216 .. 0.72
   2 !   31.1   0.0   2.1e-10   2.9e-07      16      81 .]     232     303 ..     225     303 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.88
                                    -..--.-EEEE-TTS-EEEEE------------- CS
                        DUF4162  25 leepg.veeveeeggelelkledeeaanellkal 57 
                                    + +++ ++e+++eg+++ l+  d e+a++l +++
  gi|116754529|ref|YP_843647.1| 171 RLIKEvIRELNREGTTVFLTTHDIEDASQLCDKV 204
                                    4445657777888888888888877888887765 PP

  == domain 2  score: 31.1 bits;  conditional E-value: 2.1e-10
                                    EEE....-------..---EEEE-TTS-EEEEE--.-----------.----EEEEEEEE---HHHHHHHHH CS
                        DUF4162  16 eve....adaeelleepgveeveeeggelelkled.eeaanellkal.tsgveirsFeeeePsLndIFiekv 81 
                                    ev+     d+  +  + +v+ev + g++l+l ++d ++a  ++ +++ t++++i  ++   PsL+dIF++++
  gi|116754529|ref|YP_843647.1| 232 EVSfsrsVDERRISGIHSVREVMKSGDKLRLYVDDiDTAIASIVEYAkTNNMRILALSTLAPSLEDIFVRLT 303
                                    5556333444555555556666777799*******************88********************975 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.1   1.3e-07   0.00018       6      40 ..      12      50 ..      10      93 .. 0.91
   2 ?   -2.0   0.0         3   4.2e+03      69      87 ..     225     250 ..     178     288 .. 0.59

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.3e-07
                         AAA_23  6 nfrsfrdqe.idF...skgltlItGpNGaGKTTildAik 40
                                    f+sf  ++ i F   +  ++ + GpNG+GK+T ++ ++
  gi|116754529|ref|YP_843647.1| 12 RFGSFTAVDhISFsvaEGEIFGFLGPNGSGKSTTIRMLT 50
                                   69***88766***99999***************998776 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3
                         AAA_23  69 gkvkayveltfenkdgry.......t 87 
                                    g+   ++e++f++  +++        
  gi|116754529|ref|YP_843647.1| 225 GSAHHCIEVSFSRSVDERrisgihsV 250
                                    55556677777664333333333332 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.1    0.0017       2.4      28      41 ..      33      46 ..      10      52 .. 0.75
   2 !   11.1   0.0   0.00014       0.2     148     201 ..     142     196 ..     108     210 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0017
                                   EEEESTTSSHHHHH CS
                                   xxxxxxxxxxxxxx RF
                          SMC_N 28 aivGpNGSGKsnll 41
                                     +GpNGSGKs  +
  gi|116754529|ref|YP_843647.1| 33 GFLGPNGSGKSTTI 46
                                   568********865 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00014
                                    HHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                          SMC_N 148 aLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreem 201
                                     Ll+ +  ++  p+ +lDe ++ LD +  + + e+++e + + + ++ ++++ e 
  gi|116754529|ref|YP_843647.1| 142 RLLLCMALINDPPVLILDEPASGLDVESSRLIKEVIRELNREgTTVFLTTHDIED 196
                                    477778888999*************************987765888888887554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.2   4.7e-05     0.065      12     127 ..      36     189 ..      29     198 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.7e-05
                         AAA_22  12 GesGtGKTtllrrlleqldeeakaee.........................erpevvfvtlpsstsskdllrellralgl 66 
                                    G+ G+GK+t++r+l+ +   ++  +                          +     +v+l++      ++ el      
  gi|116754529|ref|YP_843647.1|  36 GPNGSGKSTTIRMLTGTVRPDEGTAAimgydickhpirartsigfvpemanA-----YVELTAWR-NLMFMGELY----- 104
                                    9***************986555555477888887777555444433222220.....22222222.112222222..... PP

                         AAA_22  67 elka......................erlsseellealeqalrarav....ielliiDEaqh.lr..seealeeLrslln 117
                                       +                      ++++ +++ + ++q l  +++    +++li+DE    l+  s ++++e+ + ln
  gi|116754529|ref|YP_843647.1| 105 ---GiprrererrasellkrfglydrRGDQVRAFSKGMRQRLLLCMAlindPPVLILDEPASgLDveSSRLIKEVIRELN 181
                                    ...13333344577777777777774455555555999999999999999999999999999998876777777766667 PP

                         AAA_22 118 lsrkgvqliL 127
                                      r g++++L
  gi|116754529|ref|YP_843647.1| 182 --REGTTVFL 189
                                    ..77777655 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 !   14.9   0.1   1.2e-05     0.017      11      39 ..      15      46 ..      12      56 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.2e-05
                         AAA_29 11 tfdg.htieidlkg..atlltGpsGsGKSTll 39
                                   +f+    i++++++  ++ + Gp+GsGKST +
  gi|116754529|ref|YP_843647.1| 15 SFTAvDHISFSVAEgeIFGFLGPNGSGKSTTI 46
                                   5555556666665557999***********76 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00044      0.61      25      63 ..      30      68 ..      23     161 .. 0.62
   2 ?    2.6   0.0      0.11   1.5e+02      38     106 ..     170     236 ..     169     288 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00044
                         AAA_16 25 elvllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                   e+  + G+ G+GKs+ +r+l   ++ d+g ++   +d +
  gi|116754529|ref|YP_843647.1| 30 EIFGFLGPNGSGKSTTIRMLTGTVRPDEGTAAIMGYDIC 68
                                   566678**************9999988665544444444 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.11
                         AAA_16  38 sslvrellralekdg.giflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekleeala 106
                                    s+l++e+ r+l+++g  +fl+++  +   a  +   + ++ +++++ +++++++ ++++ +++ +e +++
  gi|116754529|ref|YP_843647.1| 170 SRLIKEVIRELNREGtTVFLTTHDIED--ASQLCDKVAII-NRGVIIAVDRPEALRLAGSAHHCIEVSFS 236
                                    899999999999998666666666666..33333355555.55777777777666555555555555555 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 ?    8.5   0.0    0.0018       2.5       3      35 ..      34      68 ..      32     200 .. 0.66
   2 ?    3.6   0.0     0.061        85      24      94 ..     228     296 ..     205     303 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0018
                                   EESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCS CS
                            AAA  3 lyGppGtGKTllakavakelg..vefleisgsell 35
                                   + Gp G GK+++++ +  ++        i g +++
  gi|116754529|ref|YP_843647.1| 34 FLGPNGSGKSTTIRMLTGTVRpdEGTAAIMGYDIC 68
                                   68*************99987422334444444444 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.061
                                    HEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH..TTCCCHHHHHHHHHHHHHHH CS
                            AAA  24 vefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr..sgseseeeervvnqLlteld 94 
                                     +++e+s s+ +++    + +++re++k+  + +    l +D+id  + s     ++++ +  ++++L + l+
  gi|116754529|ref|YP_843647.1| 228 HHCIEVSFSRSVDERRISGIHSVREVMKSGDKLR----LYVDDIDTAIASIveYAKTNNMRILALSTLAPSLE 296
                                    4678999999998888889999999999888887....99999999888876655666666666666666665 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   4.2e-05     0.058       9      46 ..      11      49 ..       4      52 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.2e-05
                         AAA_27  9 eryGkftdr.sldfsaeeadlhliyGpNEAGKstalrAi 46
                                   +r+G+ft   +++fs +e ++   +GpN +GKst++r +
  gi|116754529|ref|YP_843647.1| 11 KRFGSFTAVdHISFSVAEGEIFGFLGPNGSGKSTTIRML 49
                                   69*****8549*******99999************9865 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00025      0.35      89     123 ..      18      53 ..       3      75 .. 0.84
   2 ?   -2.6   0.0       3.2   4.4e+03      57      84 ..     166     192 ..     134     206 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00025
                                    THHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT- CS
                    RsgA_GTPase  89 gleelkellkd.ktsvlvGqSGvGKStLinallpel 123
                                    ++++++  +++ ++  ++G+ G GKSt i +l+++ 
  gi|116754529|ref|YP_843647.1|  18 AVDHISFSVAEgEIFGFLGPNGSGKSTTIRMLTGTV 53 
                                    567787777776999****************99864 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.2
                                    GG--HHHHHHHHHHHHHHTTSEEEE--T CS
                    RsgA_GTPase  57 Dlleeeeeleelkeelealgyevllvsa 84 
                                    D+ +++  ++e+  el++ g++v+l+  
  gi|116754529|ref|YP_843647.1| 166 DVESSRL-IKEVIRELNREGTTVFLTTH 192
                                    3434444.56666666666666655533 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0    0.0012       1.7       3      22 ..      33      52 ..      31      73 .. 0.84
   2 ?    1.0   0.0      0.31   4.3e+02      18      58 ..     171     208 ..     169     287 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0012
                                   EEEESTTSSHHHHHHHHHTS CS
                       MMR_HSR1  3 aivGrpNvGKStLinaltge 22
                                   +++G   +GKSt i+ ltg+
  gi|116754529|ref|YP_843647.1| 33 GFLGPNGSGKSTTIRMLTGT 52
                                   799***************96 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.31
                                    HHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSS CS
                       MMR_HSR1  18 altgekaivsdkpgtTrdinegrvklkgkeielvDtpGlie 58 
                                    +l++e+ +  ++ gtT   +++ ++  +   +l+D + +i+
  gi|116754529|ref|YP_843647.1| 171 RLIKEVIRELNREGTTVFLTTHDIE--D-ASQLCDKVAIIN 208
                                    5667777777889999999999998..3.456777666543 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1     0.027        37      23      38 ..      36      51 ..      31      64 .. 0.84
   2 ?    5.5   0.0    0.0039       5.4     525     572 ..     151     195 ..     147     205 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.027
                         AAA_13 23 GwNGaGKTtLSrllrs 38
                                   G NG+GK+t  r+l  
  gi|116754529|ref|YP_843647.1| 36 GPNGSGKSTTIRMLTG 51
                                   99*******9998876 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0039
                         AAA_13 525 gkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnle 572
                                    +   + ++D P S LD +s+ ++   i++      +   +f+ TH +e
  gi|116754529|ref|YP_843647.1| 151 NDPPVLILDEPASGLDVESSRLIKEVIRELN---REGTTVFLTTHDIE 195
                                    67889**************999999999996...89999******876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); 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: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2196.66
//
Query:       gi|116754530|ref|YP_843648.1|  [L=68]
Description: hypothetical protein Mthe_1229 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.011   16.8   1.0      0.014   16.4   1.0    1.3  1  DUF5320   Family of unknown function (DUF5320)
      0.016   14.9   1.1       0.17   11.7   0.0    2.3  2  SAP       SAP domain
      0.025   14.9   0.7      0.028   14.7   0.7    1.1  1  DUF4164   Domain of unknown function (DUF4164)
      0.033   14.3   1.3      0.044   13.8   1.3    1.1  1  DUF1192   Protein of unknown function (DUF1192)
        0.1   12.9   0.1       0.13   12.5   0.1    1.1  1  DUF5403   Family of unknown function (DUF5403)
       0.12   12.1   0.0       0.13   12.0   0.0    1.0  1  LXG       LXG domain of WXG superfamily


Domain annotation for each model (and alignments):
>> DUF5320  Family of unknown function (DUF5320)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.4   1.0   4.7e-06     0.014      62      99 .]      20      62 ..       1      62 [. 0.69

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.7e-06
                        DUF5320 62 a.....aaetaeaskeeekelLeeqaeaLeeeleaikkrlkel 99
                                   +     a   + + kee  e L+e+ e L++ele +++rl+ l
  gi|116754530|ref|YP_843648.1| 20 RdfcccAGFGRISGKEEMVERLKEYREELKSELERVEARLRAL 62
                                   122333334467899999*********************9875 PP

>> SAP  SAP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   5.7e-05      0.17      20      34 ..      31      44 ..      30      45 .. 0.88
   2 ?    2.0   0.2     0.059   1.8e+02       8      15 ..      47      54 ..      45      56 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.7e-05
                                   TTS-HHHHHHHHHHH CS
                            SAP 20 tsGkKaeLieRLkey 34
                                   +sG K+e++eRLkey
  gi|116754530|ref|YP_843648.1| 31 ISG-KEEMVERLKEY 44
                                   577.**********9 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.059
                                   HHHHHHHH CS
                            SAP  8 eLKeeLkk 15
                                   eLK+eL++
  gi|116754530|ref|YP_843648.1| 47 ELKSELER 54
                                   99999986 PP

>> DUF4164  Domain of unknown function (DUF4164)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.7   9.5e-06     0.028      37      71 ..      34      68 .]      28      68 .] 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 9.5e-06
                        DUF4164 37 leaeiealgedrsRLaeeLdqaearaarleevnrE 71
                                    e+ +e+l+e r+ L  eL  +ear+++l+++ +E
  gi|116754530|ref|YP_843648.1| 34 KEEMVERLKEYREELKSELERVEARLRALQSGVQE 68
                                   57889************************998766 PP

>> DUF1192  Protein of unknown function (DUF1192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.3   1.5e-05     0.044      22      46 ..      38      62 ..      37      66 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.5e-05
                        DUF1192 22 veELeerIalLeaEIaRleaaiakk 46
                                   ve L+e+ ++L++E +R+ea +++ 
  gi|116754530|ref|YP_843648.1| 38 VERLKEYREELKSELERVEARLRAL 62
                                   677*****************99875 PP

>> DUF5403  Family of unknown function (DUF5403)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   4.5e-05      0.13       8      36 ..      34      62 ..      30      67 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.5e-05
                        DUF5403  8 ldklvahlpgvkaavaeelerraarvrAv 36
                                    +++v +l++ ++++++eler++ar rA 
  gi|116754530|ref|YP_843648.1| 34 KEEMVERLKEYREELKSELERVEARLRAL 62
                                   5889**********************996 PP

>> LXG  LXG domain of WXG superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.4e-05      0.13     155     188 ..      35      68 .]      30      68 .] 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.4e-05
                            LXG 155 qetiekledfdqeqksalanlesdlkalktyvse 188
                                    +e +e l+++ +e+ks+l+ +e+ l+al+++v+e
  gi|116754530|ref|YP_843648.1|  35 EEMVERLKEYREELKSELERVEARLRALQSGVQE 68 
                                    789999**********************999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1415  (0.0789224); expected 358.6 (0.02)
Passed bias filter:                      989  (0.055162); expected 358.6 (0.02)
Passed Vit filter:                       149  (0.00831056); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 494.78
//
Query:       gi|116754531|ref|YP_843649.1|  [L=107]
Description: regulatory protein, ArsR [Methanosaeta thermophila PT]
Scores for complete 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-11   43.6   0.0    3.3e-11   43.1   0.0    1.3  1  HTH_20    Helix-turn-helix domain
    2.4e-06   27.3   0.0    7.8e-06   25.7   0.0    1.9  1  HTH_5     Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
      0.011   15.6   0.1      0.015   15.3   0.1    1.2  1  PadR      Transcriptional regulator PadR-like family
      0.034   14.3   0.0      0.039   14.1   0.0    1.2  1  FUR       Ferric uptake regulator family
      0.038   13.9   0.0      0.052   13.5   0.0    1.3  1  HTH_12    Ribonuclease R winged-helix domain
       0.14   12.7   0.0        0.2   12.2   0.0    1.2  1  HTH_27    Winged helix DNA-binding domain


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   0.0   1.1e-14   3.3e-11       2      57 ..      18      76 ..      17      80 .. 0.90

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 1.1e-14
                                   HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHT....S-HHHHHHHHHHHHHCTTEEEE CS
                         HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerld....lskntlsyHLrvLeeagLvevv 57
                                   ++++AL  P+R +i r + ++++++ +e+ e+l+    +s+  l+yHL +L+eag++ev 
  gi|116754531|ref|YP_843649.1| 18 RYIRALHCPTRWAIIRCI-GKGERSTKEIYEELSsygeISMPGLYYHLSALREAGIIEVA 76
                                   67888888**********.**************44556********************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 !   25.7   0.0   2.6e-09   7.8e-06       1      46 [.      25      74 ..      25      75 .. 0.92

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 2.6e-09
                                   SHHHHHHHHHHTTSSEEHHHHHHHH....TS-HHHHHHHHHHHHHTTSEE CS
                          HTH_5  1 dptRlkILklLaegelcvcelaeel....glsqstvShHLkkLreaGLVe 46
                                   +ptR  I++   +ge++  e+ eel    ++s + + +HL++LreaG++e
  gi|116754531|ref|YP_843649.1| 25 CPTRWAIIRCIGKGERSTKEIYEELssygEISMPGLYYHLSALREAGIIE 74
                                   599****************99999977778******************97 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.1     5e-06     0.015       4      65 ..      34      91 ..      31      94 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5e-06
                                   HHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEE CS
                           PadR  4 lleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrl 65
                                    ++++++   ei +el+ +  g  e+s+  lY  L+ L++ g++e    +++ g p k++rl
  gi|116754531|ref|YP_843649.1| 34 CIGKGERSTKEIYEELSSY--G--EISMPGLYYHLSALREAGIIEVAGYRESGGIPEKVWRL 91
                                   5677777778999999999..8..9********************99999999999999987 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.3e-05     0.039       9      62 ..      27      77 ..      23     101 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.3e-05
                                   HHHHHHHHHHHHSSSBEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEE CS
                            FUR  9 qRekilevlekseehlsaeevykelkeedpeislaTVYrtLklleeaglvkele 62
                                   +R +i++ + k e   s +e+y+el + + eis+  +Y  L  l+eag+++   
  gi|116754531|ref|YP_843649.1| 27 TRWAIIRCIGKGE--RSTKEIYEELSS-YGEISMPGLYYHLSALREAGIIEVAG 77
                                   5666677666665..599******976.678*******************8765 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 ?   13.5   0.0   1.7e-05     0.052       3      61 ..      31      87 ..      29      91 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.7e-05
                         HTH_12  3 ILkilaesdkpigakeiaeeLkkrgydigeravRyrLrkleergltrrvgya.greltEk 61
                                   I++ + + ++  + kei eeL   g+ i+   + y+L +l e g+++  gy     ++Ek
  gi|116754531|ref|YP_843649.1| 31 IIRCIGKGER--STKEIYEELSSYGE-ISMPGLYYHLSALREAGIIEVAGYReSGGIPEK 87
                                   7788888888..99**********97.889*******************99844457776 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 ?   12.2   0.0   6.7e-05       0.2       6      57 ..      29      82 ..      26      91 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.7e-05
                         HTH_27  6 alvLhlir.hrrrrkkl.adlcgrlnvedshisyslkkLtekGLvertgdeadr 57
                                   ++++++i+ ++r +k++ ++l+ +  ++     y l++L e+G +e  g+++++
  gi|116754531|ref|YP_843649.1| 29 WAIIRCIGkGERSTKEIyEELSSYGEISMPGLYYHLSALREAGIIEVAGYRESG 82
                                   899*****99999******************************99888877666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       221  (0.0123264); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 821.15
//
Query:       gi|116754532|ref|YP_843650.1|  [L=254]
Description: hypothetical protein Mthe_1231 [Methanosaeta thermophila PT]
Scores for 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-48  166.0   0.0    1.3e-48  165.7   0.0    1.1  1  DUF169    Uncharacterised ArCR, COG2043
  ------ inclusion threshold ------
       0.29    9.2   0.0       0.41    8.7   0.0    1.1  1  Pox_F12L  Poxvirus F12L protein


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 !  165.7   0.0   1.4e-52   1.3e-48       2     205 ..      14     218 ..      13     219 .. 0.95

  Alignments for each domain:
  == domain 1  score: 165.7 bits;  conditional E-value: 1.4e-52
                         DUF169   2 LaealrlktePVavkfsdekpelpekkekieekkrlCqmvalarakgktvvftaetlgCpgGaaalGfkelpeklksg.. 79 
                                    +   l+l+t+PV+v f+ + +   e+ e + +++r+Cq+ + ar +g++v+++ae ++Cp +a a+Gf++lpe l++g  
  gi|116754532|ref|YP_843650.1|  14 MIAILGLSTSPVGVRFLMDGEV--EGAE-VLHRHRYCQALMRAR-HGRSVILNAEGISCPAAARAFGFRPLPEPLRTGrg 89 
                                    56789**************994..3333.33456**********.*********************************** PP

                         DUF169  80 ...egylkspeaakkfveslprleagevkyvvvapLekaefePdvvvffanpeqlmrLvqlalydrgggrlnvsfpgnga 156
                                        g+++++ +a++++e++p le g+vk + + pLe a+  Pd+vv+ +++e+lm++v ++++ rgg+r+++s++  +a
  gi|116754532|ref|YP_843650.1|  90 lvsFGIVSDESVARRMFEDMPHLEMGAVKQIHLYPLEVAKHPPDLVVVEGEAEKLMWIVLSYMHSRGGERVQSSTAVLQA 169
                                    ******************************************************************************** PP

                         DUF169 157 aCadivaypykegepniglgdpgarkfaklkddelafgiPyelleemve 205
                                    +C d+++ py e++ n++lg++g+r ++++ d+e+++g+P++ l+e+v+
  gi|116754532|ref|YP_843650.1| 170 TCVDSTVVPYIEKRLNFSLGCYGCRDATDMGDGEVVLGFPASYLPEIVK 218
                                    **********************************************996 PP

>> Pox_F12L  Poxvirus F12L protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   4.6e-05      0.41      16      45 ..      38      67 ..      31      72 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 4.6e-05
                       Pox_F12L 16 vtalkevklsivlartreGkgvivsaenle 45
                                    + l++++++ +l+r+r+G++vi++ae+++
  gi|116754532|ref|YP_843650.1| 38 AEVLHRHRYCQALMRARHGRSVILNAEGIS 67
                                   56799**********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 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:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1817.20
//
Query:       gi|116754533|ref|YP_843651.1|  [L=820]
Description: DEAD/DEAH box helicase domain-containing protein [Methanosaeta thermophila PT]
Scores for 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-20   71.1   0.0    1.9e-19   70.1   0.0    1.5  1  DEAD        DEAD/DEAH box helicase
    5.4e-13   49.2   0.0    1.5e-12   47.9   0.0    1.8  1  Helicase_C  Helicase conserved C-terminal domain
    2.6e-07   30.8   0.0    5.5e-07   29.8   0.0    1.5  1  ResIII      Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
       0.22   10.2   0.0        1.1    7.9   0.0    1.9  2  SNF2_N      SNF2 family 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 !   70.1   0.0   4.2e-23   1.9e-19       2     170 ..     212     374 ..     211     379 .. 0.85

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 4.2e-23
                                    HHHHHHHHHHH.TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEE CS
                                    xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD   2 diQaeaiplil.gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvll 80 
                                    ++Qa a+   l +g+++lv  +T++GK+l+  i+ +++++e     + k l+++P+ +La+q +++l+ + + ++ r++ 
  gi|116754533|ref|YP_843651.1| 212 PVQAMAVRKGLlEGKSLLVVSATATGKSLIGEIAGIKNLIE----GRGKLLFLVPLVALANQKFEQLSAYSE-LGFRTSI 286
                                    688888887776***************************75....7779********************999.6778875 PP

                                    EETTSSHHHHHHHH...HTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTST CS
                                    xxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  81 iiggvaardqlskl...dngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgk 157
                                     +g ++ r  +      d ++di+vgt + +d++l++g+ nl ++ ++V+DE+++l d +++  +  ++++l+    +  
  gi|116754533|ref|YP_843651.1| 287 KVGVSRIRLGRGFSlptDLDADIIVGTYEGIDQVLRSGR-NLGKIGTVVIDEVHMLEDPDRGHRLAGMIARLRFVAPR-- 363
                                    55544444443333444466***************8888.9*******************************766554.. PP

                                    TTSEEEEEESSBS CS
                                    xxxxxxxxxxxxx RF
                           DEAD 158 lqrqvivlSATlp 170
                                       q+i lSAT+ 
  gi|116754533|ref|YP_843651.1| 364 --AQFIYLSATVG 374
                                    ..34*******85 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   0.0   3.2e-16   1.5e-12      12     111 .]     426     525 ..     408     525 .. 0.80

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 3.2e-16
                                    HTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEES CS
                     Helicase_C  12 leeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVinf 91 
                                    ++  +g+++if+n+++++  +++   ++   ++++h+ l+  er++i e f +g+++ +++t++++ G+d+p  ++++  
  gi|116754533|ref|YP_843651.1| 426 STGYKGQTIIFTNSRKKC--FSIA--QSIPGAIAYHAGLQYHERKRIEELFAQGKINAVVTTSALAAGVDFPASQVIF-E 500
                                    567799************..3555..554667788999**********************************665555.4 PP

                                    SSS.....SSHHHHHHHHTTSSSTT CS
                     Helicase_C  92 dlp.....rnvtsyiqriGRtgRag 111
                                     l       +v++++q+ GR+gR g
  gi|116754533|ref|YP_843651.1| 501 TLAmgiewLTVHEFNQMLGRAGRPG 525
                                    44436665559************75 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   1.2e-10   5.5e-07       4     169 ..     210     373 ..     197     375 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 1.2e-10
                                    E-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG.. CS
                         ResIII   4 lreyQeeaienlleklkskrdkrglikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkflseay 82 
                                    l + Q+ a+++ l      + k +l++ aT tGK+l+  ++ i++l + ++  k lflvp  +l +q  e+++ +++  +
  gi|116754533|ref|YP_843651.1| 210 LLPVQAMAVRKGL-----LEGKSLLVVSATATGKSLIGeIAGIKNLIEGRG--KLLFLVPLVALANQKFEQLSAYSELGF 282
                                    5556666666665.....3467999***********************877..***********************9998 PP

                                    ..GEEEESSS-B--............-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T.......TT CS
                         ResIII  83 keigkkvsgdkkka.....kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk.......sw 150
                                       + ++ g ++++     +   + +++i+v t++ +d+ +      +     +++  ++iDE+H l + +        +
  gi|116754533|ref|YP_843651.1| 283 R--TSIKVGVSRIRlgrgfSLPTDLDADIIVGTYEGIDQVL------RSGRNLGKIGTVVIDEVHMLEDPDrghrlagMI 354
                                    4..445555555555667777999****************9......7778888999***********986333333233 PP

                                    HHHHHT-.--SEEEEEESS- CS
                         ResIII 151 reilekf.keavllglTATp 169
                                     + l+ + ++a  ++l+AT 
  gi|116754533|ref|YP_843651.1| 355 AR-LRFVaPRAQFIYLSATV 373
                                    33.22222558888999986 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0     0.091   4.1e+02     255     299 ..     152     197 ..     128     241 .. 0.74
   2 ?    7.9   0.0   0.00024       1.1     148     203 ..     305     357 ..     248     371 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.091
                                    HHHHHHHTT-STTEE---GGGT.--S---EEEEEEEEE--HHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                         SNF2_N 255 kgrsrLlqllqrlmlrrakkdv.eknlPpkteeiiflklskverks 299
                                    ++r+ L +++  l+l r+  d+   ++ p +ee+  l+l++ e  +
  gi|116754533|ref|YP_843651.1| 152 ARRRDLDEVMDLLNLQRIDPDLtRYDIVPASEEVASLSLDEIEIPI 197
                                    45666777777799********4456*************9998755 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00024
                                    ----EEEE-HHHHHHHT......TTS-S-S-SEEEES-GGGT--T..TSHHHHHHHH- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxx RF
                         SNF2_N 148 adydvvittYdvlsreaelqkkrsvlkqvewkrvvlDEghtlkns..tskaaeavskL 203
                                     d+d+++ tY+ + ++      rs  +  ++  vv+DE h+l+      ++a ++ +L
  gi|116754533|ref|YP_843651.1| 305 LDADIIVGTYEGIDQVL-----RSGRNLGKIGTVVIDEVHMLEDPdrGHRLAGMIARL 357
                                    589***********777.....56666667789**********984446666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (820 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.45
# Mc/sec: 5463.81
//
Query:       gi|116754534|ref|YP_843652.1|  [L=264]
Description: helix-turn-helix, type 11 domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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   40.0   0.0    9.4e-10   38.2   0.0    1.9  1  MarR_2          MarR family
    4.1e-10   39.1   0.1    2.5e-09   36.6   0.0    2.1  2  HTH_24          Winged helix-turn-helix DNA-binding
    2.4e-06   28.0   0.0    5.7e-06   26.7   0.0    1.7  1  HTH_27          Winged helix DNA-binding domain
    2.5e-06   27.4   0.7    1.7e-05   24.7   0.1    2.6  3  HTH_Crp_2       Crp-like helix-turn-helix domain
    9.4e-06   25.5   0.0    2.6e-05   24.0   0.0    1.7  1  MarR            MarR family
      4e-05   23.5   0.0    8.3e-05   22.5   0.0    1.5  1  HTH_11          HTH domain
    0.00042   20.3   0.0    0.00098   19.1   0.0    1.6  1  HTH_13          HTH DNA binding domain
    0.00044   20.2   0.0    0.00082   19.3   0.0    1.5  1  HTH_45          Winged helix-turn-helix
    0.00045   20.2   0.0     0.0012   18.9   0.0    1.6  1  HTH_3           Helix-turn-helix
    0.00047   20.4   0.1     0.0029   17.9   0.0    2.2  2  Mnd1            Mnd1 HTH domain
    0.00052   20.1   0.3          1    9.6   0.1    2.4  2  HTH_17          Helix-turn-helix domain
    0.00061   19.5   0.0     0.0015   18.3   0.0    1.6  1  HTH_IclR        IclR helix-turn-helix domain
     0.0013   18.9   0.0     0.0037   17.4   0.0    1.7  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
     0.0014   18.4   0.0     0.0033   17.2   0.0    1.7  1  HTH_23          Homeodomain-like domain
     0.0015   18.8   0.0     0.0041   17.4   0.0    1.7  1  Rrf2            Transcriptional regulator
     0.0025   17.4   0.8      0.018   14.7   0.0    2.7  3  GntR            Bacterial regulatory proteins, gntR family
     0.0049   17.0   0.1       0.03   14.5   0.1    2.1  1  Mrr_N           Mrr N-terminal domain
     0.0087   15.9   0.0      0.024   14.5   0.0    1.8  1  TrmB            Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.021   14.6   0.0      0.033   13.9   0.0    1.2  1  DUF4364         Domain of unknown function (DUF4364)
      0.025   14.7   0.0       0.29   11.3   0.0    2.6  2  HTH_28          Helix-turn-helix domain
      0.026   14.4   0.0      0.054   13.4   0.0    1.6  1  HTH_5           Bacterial regulatory protein, arsR family
      0.029   14.4   0.1       0.26   11.4   0.0    2.5  2  HemN_C          HemN C-terminal domain
      0.036   13.9   0.1       0.18   11.7   0.0    2.1  2  HTH_10          HTH DNA binding domain
       0.04   13.9   0.0      0.088   12.8   0.0    1.6  1  HTH_1           Bacterial regulatory helix-turn-helix protein
      0.041   13.7   0.0       0.13   12.1   0.0    1.8  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
      0.055   13.6   0.0       0.28   11.4   0.0    2.3  2  AbiEi_4         Transcriptional regulator, AbiEi antitoxin
      0.062   13.6   0.0       0.14   12.5   0.0    1.6  1  KORA            TrfB plasmid transcriptional repressor
      0.065   13.6   0.1       0.15   12.4   0.1    1.7  1  HTH_Tnp_1       Transposase
      0.085   12.7   0.1       0.19   11.6   0.1    1.6  1  HxlR            HxlR-like helix-turn-helix
       0.12   12.3   0.1        0.5   10.3   0.0    2.0  2  P22_Cro         DNA-binding transcriptional regulator Cro
       0.14   11.8   0.1       0.24   11.0   0.1    1.4  1  SMC_ScpB        Segregation and condensation complex subunit 
       0.14   11.9   0.0       0.21   11.3   0.0    1.2  1  DUF4423         Domain of unknown function (DUF4423)


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 !   38.2   0.0   1.7e-12   9.4e-10       6      53 ..      12      58 ..      10      61 .. 0.94

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 1.7e-12
                                   HHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                         MarR_2  6 aqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                   + +++L +++++ ++ ++++e+a++lg++++a+s  +k+Lva GLve+
  gi|116754534|ref|YP_843652.1| 12 SRFQILVEIAAHQPN-VRQKEVADKLGVTPQAISEYIKELVADGLVET 58
                                   5799*********97.9*****************************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 !   36.6   0.0   4.4e-12   2.5e-09       1      48 []       9      57 ..       9      57 .. 0.93
   2 ?   -0.4   0.0       1.5   8.5e+02      38      46 ..     245     253 ..     244     253 .. 0.88

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 4.4e-12
                         HTH_24  1 ldetdrkILelLqk.nprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                   +d  +++IL ++ + +p+  q+e+A++lg++p+++++++k+L+ +Gl++
  gi|116754534|ref|YP_843652.1|  9 RDSSRFQILVEIAAhQPNVRQKEVADKLGVTPQAISEYIKELVADGLVE 57
                                   58889****888887999*****************************96 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.5
                         HTH_24  38 lkrLeeeGl 46 
                                    l+rLe+eG+
  gi|116754534|ref|YP_843652.1| 245 LNRLESEGI 253
                                    89*****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 !   26.7   0.0     1e-08   5.7e-06       7      68 .]      15      70 ..      11      70 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 1e-08
                         HTH_27  7 lvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                   ++L  i+  +  +++++++++l v+ ++is+ +k+L++ GLv      + ++++r+r+T  G
  gi|116754534|ref|YP_843652.1| 15 QILVEIAAHQPNVRQKEVADKLGVTPQAISEYIKELVADGLV------ETDGRMRYRITKRG 70
                                   677777778888999***************************......556679*****987 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.1     3e-08   1.7e-05      20      61 ..      25      68 ..       5      71 .. 0.80
   2 ?   -1.2   0.1       3.7   2.1e+03      48      64 ..     153     170 ..     152     172 .. 0.72
   3 ?   -2.3   0.0       8.2   4.6e+03      41      50 ..     244     253 ..     233     254 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 3e-08
                                   EEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ETEE.EEES- CS
                      HTH_Crp_2 20 lpltqeelAsmlGltretvsrilseLkreglis.rgrr.irild 61
                                    ++ q+e A+ lG+t++ +s  ++eL  +gl++  gr   ri+ 
  gi|116754534|ref|YP_843652.1| 25 PNVRQKEVADKLGVTPQAISEYIKELVADGLVEtDGRMrYRITK 68
                                   4799*****************************54542377776 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.7
                                    TTSEE.E.TEEEEES-HHH CS
                      HTH_Crp_2  48 eglis.r.grririldlea 64 
                                    +glis   g+ i+i  + +
  gi|116754534|ref|YP_843652.1| 153 RGLISlDeGK-IKICKVPR 170
                                    699**63255.99988765 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 8.2
                                    HHHHHHHTTS CS
                      HTH_Crp_2  41 ilseLkregl 50 
                                    il++L+ eg+
  gi|116754534|ref|YP_843652.1| 244 ILNRLESEGI 253
                                    8999999997 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   4.7e-08   2.6e-05       5      48 ..      13      57 ..      11      58 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 4.7e-08
                                   HHHHHHHHHHSTT.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                           MarR  5 qfviLrilyeqgp.lsvseLakklgvskstvtrvldrLekkGlie 48
                                   +f iL+ ++ ++p  +++e a+klgv++ ++++ +++L+ +Gl+e
  gi|116754534|ref|YP_843652.1| 13 RFQILVEIAAHQPnVRQKEVADKLGVTPQAISEYIKELVADGLVE 57
                                   68888888776666*****************************97 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   1.5e-07   8.3e-05       2      43 ..      13      54 ..      12      69 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.5e-07
                         HTH_11  2 llqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg 43
                                   ++qil  + ++++++  +e A++L+v+ +++  +Ik+L + g
  gi|116754534|ref|YP_843652.1| 13 RFQILVEIAAHQPNVRQKEVADKLGVTPQAISEYIKELVADG 54
                                   68999999788888************************9988 PP

>> HTH_13  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.7e-06   0.00098       4      49 ..      17      65 ..      15      73 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.7e-06
                         HTH_13  4 LvelvlsrPlVsagmvakeLkvtpraalklvkel...glRElTGRgrfr 49
                                   Lve+   +P V  + va +L vtp+a  + +kel   gl E  GR r+r
  gi|116754534|ref|YP_843652.1| 17 LVEIAAHQPNVRQKEVADKLGVTPQAISEYIKELvadGLVETDGRMRYR 65
                                   78999999**************************77778*********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 !   19.3   0.0   1.5e-06   0.00082      32      73 ..      39      82 ..       9      86 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.5e-06
                         HTH_45 32 sykllnkYLdmLvekglikk.skekYvlTekGle.lleklkele 73
                                   + + +++Y++ Lv  gl+++     Y++T++G e lle+  el+
  gi|116754534|ref|YP_843652.1| 39 TPQAISEYIKELVADGLVETdGRMRYRITKRGVEwLLESAAELK 82
                                   5567899***********7736678*******993456666665 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   2.1e-06    0.0012      10      31 ..      27      48 ..      24      51 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.1e-06
                                   HHHHHHHHHHTSSHHHHHHHHT CS
                          HTH_3 10 lsqeeLAeklGvsrstisriEn 31
                                     q+e+A+klGv++++is +++
  gi|116754534|ref|YP_843652.1| 27 VRQKEVADKLGVTPQAISEYIK 48
                                   57*****************986 PP

>> Mnd1  Mnd1 HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   5.1e-06    0.0029      21      48 ..      33      59 ..      28      60 .. 0.86
   2 ?   -1.6   0.0         6   3.3e+03      35      52 ..     193     210 ..     191     216 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 5.1e-06
                           Mnd1 21 apkekgivsqsVkdvlqsLvdDglveve 48
                                   a k  g+++q + +++++Lv+Dglve++
  gi|116754534|ref|YP_843652.1| 33 ADK-LGVTPQAISEYIKELVADGLVETD 59
                                   444.8*********************97 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 6
                           Mnd1  35 vlqsLvdDglveveKiGs 52 
                                    ++ +L  + l++  KiG 
  gi|116754534|ref|YP_843652.1| 193 LVGALGIEALISLRKIGR 210
                                    56677779999999*995 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.1    0.0019         1       5      41 ..      30      69 ..      28      78 .. 0.66
   2 !    8.2   0.0     0.005       2.8      12      47 ..     146     188 ..     138     190 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0019
                         HTH_17  5 eEaAelLgvsrstvyrlir....rgelpaa.kiGrrwriprs 41
                                   +E+A+ Lgv ++ + ++i+    +g    + ++  r+ri++ 
  gi|116754534|ref|YP_843652.1| 30 KEVADKLGVTPQAISEYIKelvaDGLV-ETdGR-MRYRITKR 69
                                   8*****************633322222.33322.34777765 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.005
                         HTH_17  12 gvsrstvyrli..rrgelpaak.....iGrrwriprsdleewl 47 
                                    +v++s ++ li  ++g+++ +k     +G+++r++ ++l + +
  gi|116754534|ref|YP_843652.1| 146 DVGVSDLRGLIslDEGKIKICKvpriqLGGSRRVDLEALARLI 188
                                    58899999999667****999555588***********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 !   18.3   0.0   2.6e-06    0.0015       6      52 .]      14      60 ..      14      60 .. 0.97

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.6e-06
                                   HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE... CS
                       HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveqdg 52
                                   ++iL  +a++++ ++ +e+A+++g+++ + + +++ Lv  G+ve+dg
  gi|116754534|ref|YP_843652.1| 14 FQILVEIAAHQPNVRQKEVADKLGVTPQAISEYIKELVADGLVETDG 60
                                   789999**************************************996 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   6.6e-06    0.0037      22      56 ..      26      60 ..      19      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 6.6e-06
                                   SB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                 Fe_dep_repress 22 vvktkdlaerLnvspssVsemlkkLekdGyveyek 56
                                    v++k++a  L+v p  +se +k+L  dG+ve+ +
  gi|116754534|ref|YP_843652.1| 26 NVRQKEVADKLGVTPQAISEYIKELVADGLVETDG 60
                                   5899***************************9875 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   0.0   5.9e-06    0.0033       7      46 ..      13      55 ..       7      57 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.9e-06
                         HTH_23  7 Rlrillllae...GlsvreIAreLgvsrrTvyrwlkryreeGl 46
                                   R++il   a      +++e+A++Lgv+++ ++ ++k  +++Gl
  gi|116754534|ref|YP_843652.1| 13 RFQILVEIAAhqpNVRQKEVADKLGVTPQAISEYIKELVADGL 55
                                   899999999778************************9887775 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   7.3e-06    0.0041      11      57 ..      14      58 ..       6      61 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 7.3e-06
                                   HHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                           Rrf2 11 lhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvks 57
                                   +++l+++a+++ +  v+ +e+a++ ++ p+ ++  +++L   glv++
  gi|116754534|ref|YP_843652.1| 14 FQILVEIAAHQPN--VRQKEVADKLGVTPQAISEYIKELVADGLVET 58
                                   689********95..8*****************************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 !   14.7   0.0   3.3e-05     0.018      26      59 ..      28      61 ..      15      66 .. 0.90
   2 ?   -0.5   0.0       1.8     1e+03      33      52 ..     172     191 ..     171     198 .. 0.73
   3 ?   -2.0   0.0         5   2.8e+03      45      53 ..     245     253 ..     245     253 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.3e-05
                                   -HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                           GntR 26 sereLaaefgVsrttvReALrrLeaeglverrqg 59
                                   +++e+a+++gV+ + + e +++L+a+glve   +
  gi|116754534|ref|YP_843652.1| 28 RQKEVADKLGVTPQAISEYIKELVADGLVETDGR 61
                                   679**************************98765 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.8
                                    HHTS-HHHHHHHHHHHHHTT CS
                           GntR  33 efgVsrttvReALrrLeaeg 52 
                                    ++g sr +  eAL rL  e+
  gi|116754534|ref|YP_843652.1| 172 QLGGSRRVDLEALARLIPEK 191
                                    56777777789****98554 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 5
                                    HHHHHHTTS CS
                           GntR  45 LrrLeaegl 53 
                                    L+rLe+eg+
  gi|116754534|ref|YP_843652.1| 245 LNRLESEGI 253
                                    89*****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 !   14.5   0.1   5.3e-05      0.03      57      85 ..      46      74 ..      11      76 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.3e-05
                          Mrr_N 57 artyLkkagllespkrgvwkiTekGrevl 85
                                   ++++L+  gl+e++ r  ++iT++G e+l
  gi|116754534|ref|YP_843652.1| 46 YIKELVADGLVETDGRMRYRITKRGVEWL 74
                                   5689999*******************998 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   4.3e-05     0.024      19      60 ..      23      62 ..       7      69 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.3e-05
                                   HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTT CS
                           TrmB 19 klgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpk 60
                                    + + + +e+a +lgv  + + e++++L+  GlVe+    ++
  gi|116754534|ref|YP_843652.1| 23 HQPNVRQKEVADKLGVTPQAISEYIKELVADGLVETDG--RM 62
                                   46677899***************************983..33 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0     6e-05     0.033      36      88 ..      43      92 ..      38      98 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6e-05
                        DUF4364 36 lqqalseLvesglieeeekenktlykiTekGketlelfenripksirekidey 88
                                   ++++++eLv +gl+e+   +++ +y+iT++G e l +   ++    r  ++e 
  gi|116754534|ref|YP_843652.1| 43 ISEYIKELVADGLVET---DGRMRYRITKRGVEWLLESAAELKRYARVVMEEI 92
                                   789************7...9*************99888888887777666555 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00051      0.29       2      40 ..      13      54 ..      12      62 .. 0.81
   2 ?   -0.7   0.0       2.9   1.6e+03      28      41 ..     240     253 ..     238     259 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00051
                         HTH_28  2 RleiikllaaGh...svreaArelgisrrtvyrWikryeegG 40
                                   R++i+ ++aa+    +++e+A +lg++++ ++  ik + + G
  gi|116754534|ref|YP_843652.1| 13 RFQILVEIAAHQpnvRQKEVADKLGVTPQAISEYIKELVADG 54
                                   8899999998644349999************99999877744 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.9
                         HTH_28  28 tvyrWikryeegGi 41 
                                    ++ + ++r+e++Gi
  gi|116754534|ref|YP_843652.1| 240 QIPGILNRLESEGI 253
                                    777899*******8 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   9.6e-05     0.054       4      47 .]      13      58 ..      10      58 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.6e-05
                                   HHHHHHHHTT.SS.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                          HTH_5  4 RlkILklLae.ge.lcvcelaeelglsqstvShHLkkLreaGLVek 47
                                   R +IL   a  ++     e a++lg+++ ++S++ k L   GLVe+
  gi|116754534|ref|YP_843652.1| 13 RFQILVEIAAhQPnVRQKEVADKLGVTPQAISEYIKELVADGLVET 58
                                   55555555555444455789************************85 PP

>> HemN_C  HemN C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00046      0.26      25      65 ..      31      71 ..      27      72 .. 0.85
   2 ?   -0.8   0.1         3   1.7e+03      48      59 ..     153     164 ..     152     165 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00046
                         HemN_C 25 afeqrfgldleellaaaleklqeqGLLeldg.grlrltprGr 65
                                   +++++ g++ +++    +++l ++GL+e dg  r+r t+rG+
  gi|116754534|ref|YP_843652.1| 31 EVADKLGVTPQAI-SEYIKELVADGLVETDGrMRYRITKRGV 71
                                   5677888887777.445**************88*******96 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 3
                         HemN_C  48 qGLLeldggrlr 59 
                                    +GL++ld+g+++
  gi|116754534|ref|YP_843652.1| 153 RGLISLDEGKIK 164
                                    59******9986 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00031      0.18      24      46 ..      27      49 ..      25      52 .. 0.90
   2 ?   -1.3   0.1       3.5     2e+03      22      31 ..     177     186 ..     176     188 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00031
                         HTH_10 24 vtlkeLAkelGIskstlsehLrk 46
                                   v+ ke+A++lG++++++se++++
  gi|116754534|ref|YP_843652.1| 27 VRQKEVADKLGVTPQAISEYIKE 49
                                   6679****************985 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.5
                         HTH_10  22 RrvtlkeLAk 31 
                                    Rrv+l++LA 
  gi|116754534|ref|YP_843652.1| 177 RRVDLEALAR 186
                                    9*******96 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00016     0.088       4      59 ..      14      70 ..      12      71 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00016
                                   HHHHHHHHHHS.SHH..HHHHHHTS-HHHHHHHHHHHHHHHTS-SEEESSS.EEEE-HHH CS
                          HTH_1  4 lrlfvavaeeg.sft..rAAeeLglsqpavsrqikrLEeelgvpLfeRtgr.glrLTeaG 59
                                   ++++v++a ++ +++  + A++Lg+++ a+s  ik+L   + + L+e +gr + r T +G
  gi|116754534|ref|YP_843652.1| 14 FQILVEIAAHQpNVRqkEVADKLGVTPQAISEYIKEL---VADGLVETDGRmRYRITKRG 70
                                   6677777777776652269****************87...77778888777667777776 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00023      0.13      11      29 ..      29      47 ..      24      53 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00023
                 YdaS_antitoxin 11 qkaLAealgvsqqaVsqWl 29
                                   qk++A++lgv++qa+s  +
  gi|116754534|ref|YP_843652.1| 29 QKEVADKLGVTPQAISEYI 47
                                   99**************987 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0005      0.28       2      37 ..      16      55 ..      15      58 .. 0.76
   2 ?   -2.4   0.0       9.9   5.5e+03      20      36 ..     225     252 ..     215     253 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0005
                        AbiEi_4  2 rlpelasrqvGlfttrelea.aGispsa....lrrLvrkGw 37
                                    l+e+a  +++ ++ +e++  +G++p+a    + +Lv  G+
  gi|116754534|ref|YP_843652.1| 16 ILVEIA-AHQPNVRQKEVADkLGVTPQAiseyIKELVADGL 55
                                   577888.55589******999*******6666666666665 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 9.9
                        AbiEi_4  20 ea.aGispsa..........lrrLvrkG 36 
                                    +a +G+s             l+rL ++G
  gi|116754534|ref|YP_843652.1| 225 AAyHGVSSIIvsvdeqipgiLNRLESEG 252
                                    5555665532344444455567776666 PP

>> KORA  TrfB plasmid transcriptional repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00025      0.14      31      54 ..      26      49 ..      11      61 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00025
                           KORA 31 gkkqadvatelgltkqavsqavkr 54
                                   +++q++va++lg+t qa+s+ +k 
  gi|116754534|ref|YP_843652.1| 26 NVRQKEVADKLGVTPQAISEYIKE 49
                                   579****************98886 PP

>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00027      0.15      20      68 ..      23      82 ..       7      89 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00027
                      HTH_Tnp_1 20 lepgksvsevArrhgvspnqLykWrrqyregeeaspae...........feltaleeenr 68
                                    +p ++ +evA ++gv p++ +  +++  ++ +++ +              l++ ++e++
  gi|116754534|ref|YP_843652.1| 23 HQPNVRQKEVADKLGVTPQAISEYIKELVADGLVETDGrmryritkrgvEWLLESAAELK 82
                                   489999*********************995555544433666666555555555555555 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00034      0.19       5      82 ..      13      84 ..      11      93 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00034
                                   TTHHHHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGG.GHHHHHHHHHH CS
                           HxlR  5 kWkllilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrs.lepvlqelkkw 82
                                   + ++l+ ++  + + R +e++++l +++ + +++ ++eL +dgl+e         ++ Y++t++G + l +  +elk +
  gi|116754534|ref|YP_843652.1| 13 RFQILVEIAAHQPNVRQKEVADKL-GVTPQAISEYIKELVADGLVET------DGRMRYRITKRGVEwLLESAAELKRY 84
                                   667777777788899*********.89999**************975......46788888888854255555555555 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 ?   10.3   0.0   0.00089       0.5      12      29 ..      29      46 ..      28      52 .. 0.85
   2 ?   -1.6   0.0       4.6   2.6e+03       8      17 ..     215     224 ..     214     242 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00089
                                   HHHHHHHHTS-HHHHHHH CS
                        P22_Cro 12 vekvAkalgvtksAVsqW 29
                                   ++ vA  lgvt++A+s+ 
  gi|116754534|ref|YP_843652.1| 29 QKEVADKLGVTPQAISEY 46
                                   678*************97 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.6
                                    HHSSHHHHHH CS
                        P22_Cro   8 hFGgvekvAk 17 
                                    +FG++e+v +
  gi|116754534|ref|YP_843652.1| 215 FFGSKEAVVE 224
                                    6999999843 PP

>> SMC_ScpB  Segregation and condensation complex subunit ScpB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00043      0.24      83     130 ..      11      62 ..       3      87 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00043
                       SMC_ScpB  83 qaaletLaiIaykqp.vtraeieeiRGvn...sdsvvrtLlerglieekgrk 130
                                    ++  ++L  Ia +qp v ++e+++  Gv+    ++ +++L++ gl+e  gr 
  gi|116754534|ref|YP_843652.1|  11 SSRFQILVEIAAHQPnVRQKEVADKLGVTpqaISEYIKELVADGLVETDGRM 62 
                                    677889999*****8577899******985556789************9975 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00037      0.21      25      84 ..      16      72 ..      10      93 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00037
                        DUF4423 25 virellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqtekslt 84
                                   ++ e+++ +++    +e+a++l+  ++ + +++ ++ L+  gl++ d+  +yr t++ ++
  gi|116754534|ref|YP_843652.1| 16 ILVEIAAHQPN-VRQKEVADKLG--VTPQAISEYIKELVADGLVETDGRMRYRITKRGVE 72
                                   67787777777.8999*******..******************************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      621  (0.0346366); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); 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: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1883.44
//
Query:       gi|116754535|ref|YP_843653.1|  [L=170]
Description: hypothetical protein Mthe_1234 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-64  216.9   0.0    1.2e-64  216.7   0.0    1.0  1  ArsR      ArsR transcriptional regulator
  ------ inclusion threshold ------
      0.015   14.9   0.1       0.21   11.2   0.0    2.0  2  SMC_ScpB  Segregation and condensation complex subunit ScpB
      0.044   13.7   0.1        1.7    8.6   0.0    2.4  2  HTH_5     Bacterial regulatory protein, arsR family
      0.051   13.6   0.0       0.17   11.9   0.0    1.8  2  HTH_20    Helix-turn-helix domain
      0.095   13.0   0.1       0.16   12.3   0.1    1.3  1  COMMD1_N  COMMD1 N-terminal domain
       0.13   12.1   0.4        2.6    8.0   0.1    2.5  2  DUF4224   Domain of unknown function (DUF4224)


Domain annotation for each model (and alignments):
>> ArsR  ArsR transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  216.7   0.0   4.1e-68   1.2e-64       1     158 [.       9     168 ..       9     169 .. 0.99

  Alignments for each domain:
  == domain 1  score: 216.7 bits;  conditional E-value: 4.1e-68
                           ArsR   1 indpveLvpllqvfdsetkkkvyeelskeWlteeeleeklgee..veealklLkkikliEsqWrmpepgekpekeYhtsY 78 
                                    indp++Lvpllqvf+se++k+v+++l+++Wlte+el e +g++  v+++++lL+k++liE++Wr+pepg++pekeYh+++
  gi|116754535|ref|YP_843653.1|   9 INDPSDLVPLLQVFGSESHKRVFDKLCDQWLTEKELVEIFGDNesVSQSIELLRKSGLIETKWRVPEPGKSPEKEYHSAF 88 
                                    8****************************************9889*********************************** PP

                           ArsR  79 skvqanfqcsledlsdiievafmsdeeleelvekiekeveegntsisdlsrklglsplfiralakrsekldvkGqrlelv 158
                                    s+vqanf  s+edlsd+i+v+fmsd+el++l+ek+ ++v++g tsis+lsr+lg+s+++++a akr++ l+v+Gqr+el+
  gi|116754535|ref|YP_843653.1|  89 SRVQANFFSSMEDLSDLIRVTFMSDDELRDLTEKLREKVRSGMTSISTLSRDLGKSQVYLKAAAKRAKGLTVRGQRIELS 168
                                    *****************************************************************************986 PP

>> SMC_ScpB  Segregation and condensation complex subunit ScpB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   7.2e-05      0.21      96     136 ..      37      79 ..      34     103 .. 0.90
   2 ?    2.3   0.0     0.037   1.1e+02      16      48 ..     102     134 ..      89     169 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.2e-05
                       SMC_ScpB  96 qpvtraeieeiRGvn..sdsvvrtLlerglieekgrkeepgrp 136
                                    q +t +e+ ei G n  +++ ++ L + glie k r +epg++
  gi|116754535|ref|YP_843653.1|  37 QWLTEKELVEIFGDNesVSQSIELLRKSGLIETKWRVPEPGKS 79 
                                    668999*******998899**********************96 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.037
                       SMC_ScpB  16 leeLakilelskeeveealeeLkeeyeeedrgl 48 
                                    l++L +++ +s +e++++ e+L+e+ ++  + +
  gi|116754535|ref|YP_843653.1| 102 LSDLIRVTFMSDDELRDLTEKLREKVRSGMTSI 134
                                    234444444669999999999999996554444 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 ?    8.6   0.0   0.00056       1.7      11      46 ..      34      68 ..      28      69 .. 0.86
   2 ?    2.7   0.0      0.04   1.2e+02      12      29 ..     128     145 ..     118     146 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00056
                                   HTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_5 11 LaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                   L+++ l+  el+e++g ++s vS+    Lr++GL+e
  gi|116754535|ref|YP_843653.1| 34 LCDQWLTEKELVEIFGDNES-VSQSIELLRKSGLIE 68
                                   77777888899999999998.9*************8 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.04
                                    TTSSEEHHHHHHHHTS-H CS
                          HTH_5  12 aegelcvcelaeelglsq 29 
                                    ++g ++++ l+++lg+sq
  gi|116754535|ref|YP_843653.1| 128 RSGMTSISTLSRDLGKSQ 145
                                    457789999********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 ?   11.9   0.0   5.8e-05      0.17       6      56 ..      21      69 ..      18      72 .. 0.91
   2 ?   -2.4   0.0       1.7   5.2e+03      35      45 ..     128     141 ..     116     143 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.8e-05
                                   HHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                         HTH_20  6 ALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                   ++++++  r+++ L  ++ lt +el e + ++  ++s+ ++ L++ gL+e+
  gi|116754535|ref|YP_843653.1| 21 VFGSESHKRVFDKL-CDQWLTEKELVEIF-GDNESVSQSIELLRKSGLIET 69
                                   6677788899****.**************.********************8 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.7
                                    T...S-HHHHHHHH CS
                         HTH_20  35 d...lskntlsyHL 45 
                                    +   +s +tls+ L
  gi|116754535|ref|YP_843653.1| 128 RsgmTSISTLSRDL 141
                                    13446777777765 PP

>> COMMD1_N  COMMD1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   5.3e-05      0.16      16      84 ..      92     160 ..      85     167 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.3e-05
                       COMMD1_N  16 krkyygeeeiteellkeelypdvs.edefaalvekmksLlksiasadmdlaQLeafLtaqtkkqggalsa 84 
                                    +++++ + e   +l++   ++d + +d  ++l ek++s + si++ ++dl   +  L+a  k+ +g l+ 
  gi|116754535|ref|YP_843653.1|  92 QANFFSSMEDLSDLIRVTFMSDDElRDLTEKLREKVRSGMTSISTLSRDLGKSQVYLKAAAKRAKG-LTV 160
                                    677777777677788888888554155567899999*****************************9.554 PP

>> DUF4224  Domain of unknown function (DUF4224)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.079   2.4e+02       2      12 ..      39      49 ..      38      67 .. 0.78
   2 ?    8.0   0.1   0.00086       2.6       1      16 [.     110     125 ..     110     127 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.079
                        DUF4224  2 LtpeElaeLTG 12
                                   Lt  El+e+ G
  gi|116754535|ref|YP_843653.1| 39 LTEKELVEIFG 49
                                   999*****977 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00086
                        DUF4224   1 fLtpeElaeLTGykrr 16 
                                    f++++El++LT + r+
  gi|116754535|ref|YP_843653.1| 110 FMSDDELRDLTEKLRE 125
                                    9**********98665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       708  (0.0394891); expected 358.6 (0.02)
Passed bias filter:                      572  (0.0319036); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1249.85
//
Query:       gi|116754536|ref|YP_843654.1|  [L=367]
Description: UDP-N-acetylglucosamine 2-epimerase [Methanosaeta thermophila PT]
Scores for 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-113  376.8   0.0   9.8e-113  376.5   0.0    1.0  1  Epimerase_2      UDP-N-acetylglucosamine 2-epimerase
    0.00055   20.4   0.1     0.0012   19.3   0.1    1.5  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
     0.0015   18.6   0.0     0.0026   17.8   0.0    1.4  1  Glyco_transf_4   Glycosyltransferase Family 4
  ------ inclusion threshold ------
      0.057   14.0   0.0       0.16   12.6   0.0    1.8  1  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
      0.089   12.0   0.6       0.73    9.0   0.1    2.1  2  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
       0.14   12.1   0.0       0.27   11.2   0.0    1.4  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 !  376.5   0.0  3.3e-116  9.8e-113       7     347 .]      25     350 ..      21     350 .. 0.95

  Alignments for each domain:
  == domain 1  score: 376.5 bits;  conditional E-value: 3.3e-116
                                    -..EEEEEEE-S--SGGGTHHHHHHTT----SEEE---S--HHHHHHHHHHHHHHHHHHH--SEEEEESSSHHHHHHHHH CS
                    Epimerase_2   7 selelqlvvtGqHldremgdtvfeeleiekpdydlnsdsqslakstgrvligleevleeekpDlvlvlGDtnetlagala 86 
                                    +++++++++tGqH+d+em++++f+e++i++pd++l+++s+s++k+tg++l ++e+vl++e+pD+v+vlGDtn+tlagala
  gi|116754536|ref|YP_843654.1|  25 ERFHEVIIHTGQHYDYEMDRIFFDEIGIPEPDHHLGVGSGSHGKQTGEMLARIEDVLMKEEPDAVVVLGDTNTTLAGALA 104
                                    4699**************************************************************************** PP

                                    HHHTT-EEEEET-----S-TT..SHHHHHHHHHHHT-SEEEESSHHHHHHHHHTT--GGGEEE---HHHHHHHHHHHHHH CS
                    Epimerase_2  87 AfklripvaHveAGlRsfdltegmpeEinRhlidklsdlhfapteearenLlkegeeeerifvvGntviDalllskeeie 166
                                    A+kl++  +HveAGlRs+d++  mpeEinR+l+d++sd++++pt++a +nL++eg+  + ++ +G++++Da+ l ++  +
  gi|116754536|ref|YP_843654.1| 105 AAKLHVTLVHVEAGLRSYDRR--MPEEINRVLVDHCSDILCCPTKTAVDNLRREGI-VDGVYLTGDVMVDAMNLCMDISK 181
                                    *********************..*********************************.789************99999885 PP

                                    ...T-HHHHHH..--SS-EEEEE---HHHHTSHHHHHHHHHHHHHHHHHH--EEEEE--..HHHHHHH..HHHHHH-.TT CS
                    Epimerase_2 167 eklkaseilke..lkekkyvlvtlHrrenedeperlkeilealkalakekdvevvvpvhnnprtrkrl..leeleel.en 241
                                        +s+il++  l+ k+y+l+tlHr+en+d++erl  i+ a++++ ++    +v+p+h  prt++rl  l  +++l e 
  gi|116754536|ref|YP_843654.1| 182 ----RSTILERldLRPKEYMLATLHRAENTDDDERLWGIIGAFEDIGSS----LVFPCH--PRTERRLrdLGLWDSLsES 251
                                    ....5578888889**********************************8....8*****..*******76556777766* PP

                                    EEEE----HHHHHHHHHC-SEEEES-HHHHHHHHHCT--EEESSSS-S-THHHHTTSEEE-TT-HHHHHHHHHHHCT-.. CS
                    Epimerase_2 242 vtlieplgyldflsllknaklvltdSgGiqeEapslgvpvvnlReeteRpegveagtnvlvgtdkeeIvaaleklledkk 321
                                    +++i+p+gyld+l+l +na  +ltdSgG+q+Ea++l+vp+v+lR++te++e+v+ g+nvl+g+++e+Iv+ ++ +  +  
  gi|116754536|ref|YP_843654.1| 252 IKVIKPVGYLDMLQLERNALRILTDSGGVQKEAYILRVPCVTLRDRTEWVETVNDGWNVLAGASRESIVRYAKGFAPN-- 329
                                    ****************************************************************************77.. PP

                                    --......--TT-SS-HHHHHHHHHH CS
                    Epimerase_2 322 elekmanaknpYgdGkaseriveile 347
                                         +++++++gdG+as+ri++++e
  gi|116754536|ref|YP_843654.1| 330 -----RSQTHIFGDGEASRRIADVME 350
                                    .....45568*************985 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 !   19.3   0.1     4e-07    0.0012       9     149 ..      18     158 ..      14     162 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 4e-07
                Glyco_trans_4_4   9 elaraLaarGheVtvltpapapgape...leedgvr..vhrlpvprrpspladlaalralrrllrqrrerpdvvhahs.p 82 
                                     l+raL++r heV + t + +  +++    +e g++   h+l v+ ++++  + ++l++ +++l   +e pd v++ +  
  gi|116754536|ref|YP_843654.1|  18 PLSRALRERFHEVIIHTGQHYDYEMDrifFDEIGIPepDHHLGVGSGSHGKQTGEMLARIEDVL--MKEEPDAVVVLGdT 95 
                                    589**************665555443344444443322678999999999999***********..9*****99999868 PP

                Glyco_trans_4_4  83 taglaarlarrrrgiplvvtlhglllrrgsgavrrlyralerrllrr.adavlvvseaeaeelralgv 149
                                     + la++la+++ ++ lv+   gl      + +rr+  +++r l+ +  d + +++   ++ lr+ g+
  gi|116754536|ref|YP_843654.1|  96 NTTLAGALAAAKLHVTLVHVEAGLR-----SYDRRMPEEINRVLVDHcSDILCCPTKTAVDNLRREGI 158
                                    8999999999565666666555542.....23566667888888888667788888888888888775 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   8.7e-07    0.0026      11     153 ..      19     157 ..      16     163 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 8.7e-07
                 Glyco_transf_4  11 LaraLarrGheVtvvtpgddgpleeev....elvvrvprvplpllkrl.lrslaflrrlrrllkrekpDvv.Hahspaal 84 
                                    L+raL++r heV + t ++ + + ++     + + ++     ++++ + +++  +l r+  +l +e+pD v    +  + 
  gi|116754536|ref|YP_843654.1|  19 LSRALRERFHEVIIHTGQHYDYEMDRIffdeIGIPEPDHHLGVGSGSHgKQTGEMLARIEDVLMKEEPDAVvVLGDTNTT 98 
                                    89*************9888887777768887555555555555555541567778899***********88766677778 PP

                 Glyco_transf_4  85 gaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrl.lrradrviavSeatadelreryg 153
                                    +a++la+++ l++ lV+   gl          +  +r+ +++ r l  + +d + ++++++ d+lr+  g
  gi|116754536|ref|YP_843654.1|  99 LAGALAAAK-LHVTLVHVEAGLR---------SYDRRMPEEINRVLvDHCSDILCCPTKTAVDNLRR-EG 157
                                    888888887.7766666655555.........34444444444555244566777779999999998.66 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.3e-05      0.16       8      49 ..      93     137 ..      88     143 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.3e-05
                                    SHHHHHHHHHHHHTTSEEEEEESSSSSS...TTSSHHHHHHHHHH CS
                      Pyr_redox   8 GyiglElAgalaelgkkVtvversdkll...rllDeeaskilqek 49 
                                    G+++  lAgala+ + +Vt+v+ +  l+   r ++ee+ ++l ++
  gi|116754536|ref|YP_843654.1|  93 GDTNTTLAGALAAAKLHVTLVHVEAGLRsydRRMPEEINRVLVDH 137
                                    789999**********************76677777777766665 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 ?    9.0   0.1   0.00024      0.73     129     194 ..      73     135 ..      50     151 .. 0.69
   2 ?    0.7   0.1     0.081   2.4e+02     261     278 ..     151     169 ..     147     183 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00024
                                    ECHHHHHHCCSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 129 tldsaealklkllpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleeale 194
                                     l+  e +  k+ p+ +vv G  ++   lA+ala ++ +vtlv+    l r++d+++ ++++++l 
  gi|116754536|ref|YP_843654.1|  73 MLARIEDVLMKEEPDAVVVLGDTNT--TLAGALAAAKLHVTLVHVEAGL-RSYDRRMPEEINRVLV 135
                                    4555566666777899999995555..5566666666688888887777.4666666666666554 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.081
                                    -TTSBES.STTEEE-GGGC CS
                                    xxxxxxx.xxxxxxxxxxx RF
                    Pyr_redox_2 261 deflrtn.vpgiyaiGDva 278
                                    d   r   v+g+y+ GDv 
  gi|116754536|ref|YP_843654.1| 151 DNLRREGiVDGVYLTGDVM 169
                                    555555559*********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 ?   11.2   0.0   9.1e-05      0.27      15     113 ..      18     123 ..       3     139 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 9.1e-05
                Glyco_trans_4_2  15 rlakeLakrgyeVhvitpkkgakdeleaegihvhrlkvd...........rkgpleylkafklkklikkikPDvvhahya 83 
                                     l ++L++r +eV + t +    d++ +++i + ++ ++           ++g+ +  +++++ +++ k++PD v +   
  gi|116754536|ref|YP_843654.1|  18 PLSRALRERFHEVIIHTGQHY--DYE-MDRIFFDEIGIPepdhhlgvgsgSHGKQTGEMLARIEDVLMKEEPDAVVVLGD 94 
                                    467899999999988887444..444.5556666664444455566643233333333567******************* PP

                Glyco_trans_4_2  84 kpygllgslaarlsgvipvvlsvwGldvlk 113
                                    +   l+g+laa ++  + +v    Gl  ++
  gi|116754536|ref|YP_843654.1|  95 TNTTLAGALAAAKLH-VTLVHVEAGLRSYD 123
                                    **9******998886.66666656665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2722.04
//
Query:       gi|116754537|ref|YP_843655.1|  [L=278]
Description: hypothetical protein Mthe_1236 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.011   15.8   0.0      0.026   14.6   0.0    1.7  1  Cupredoxin_1  Cupredoxin-like domain


Domain annotation for each model (and alignments):
>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.5e-06     0.026      45      96 ..     166     227 ..     116     232 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.5e-06
                   Cupredoxin_1  45 vklkiknkdktp...eefesed......lgee.kvlapgktttitiaplkpGeYeftcdmhm 96 
                                     +++ikn ++++   +++++++       g+e  +++pgk+++i+i++l+  eY+ +c  + 
  gi|116754537|ref|YP_843655.1| 166 SSIEIKNLGDRTaksVSVQITSpvvlrrSGIElGDIPPGKSKSIEIPKLEGEEYPVVCMVNY 227
                                    57999999999633334444447785554444589***********************8775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 2044.92
//
Query:       gi|116754538|ref|YP_843656.1|  [L=48]
Description: 50S ribosomal protein L40e [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00024   20.9   6.6    0.00028   20.7   6.6    1.2  1  Ribosomal_L40e  Ribosomal L40e family
     0.0019   17.8   1.1     0.0028   17.3   1.1    1.2  1  zinc_ribbon_2   zinc-ribbon domain
  ------ inclusion threshold ------
      0.012   15.3   5.4      0.018   14.7   5.4    1.3  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
      0.013   15.6   0.6      0.014   15.5   0.6    1.2  1  DZR             Double zinc ribbon


Domain annotation for each model (and alignments):
>> Ribosomal_L40e  Ribosomal L40e family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   6.6   6.3e-08   0.00028      15      47 ..      13      42 ..       7      45 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 6.3e-08
                 Ribosomal_L40e 15 dKmiCrkCYArlpprAtnCrkkkCghsnnlrpK 47
                                   + +iC +C Ar p+rAt Cr  kC + + lr+K
  gi|116754538|ref|YP_843656.1| 13 NVKICMRCNARNPIRATRCR--KC-RYKGLRMK 42
                                   568*****************..78.34555555 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   1.1   6.3e-07    0.0028       2      22 ..      17      37 ..      16      38 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 6.3e-07
                  zinc_ribbon_2  2 CpnCGaelqdnakFCpyCGtp 22
                                   C +C a ++ +a+ C +C+++
  gi|116754538|ref|YP_843656.1| 17 CMRCNARNPIRATRCRKCRYK 37
                                   ******************997 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 ?   14.7   5.4   3.9e-06     0.018       2      26 ..      16      37 ..      16      43 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.9e-06
                                   B-SSS--B----SSS----SSS--- CS
                 DNA_RNApol_7kD  2 iCgeCgaevslkkgdpiRCkeCGhR 26
                                   iC++C+a++ ++++   RC++C ++
  gi|116754538|ref|YP_843656.1| 16 ICMRCNARNPIRAT---RCRKCRYK 37
                                   8*************...*****765 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.6     3e-06     0.014       1      19 [.      17      35 ..       4      45 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3e-06
                            DZR  1 CpqCgeelppdarfCseCg 19
                                   C +C++ +p +a  C +C+
  gi|116754538|ref|YP_843656.1| 17 CMRCNARNPIRATRCRKCR 35
                                   4455555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.40
# Mc/sec: 362.03
//
Query:       gi|116754539|ref|YP_843657.1|  [L=255]
Description: geranylgeranylglyceryl phosphate synthase-like protein [Methanosaeta thermophila PT]
Scores for complete 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  209.8   0.0    4.1e-62  209.6   0.0    1.0  1  PcrB            PcrB family
    4.5e-06   25.9   0.6    0.00031   19.8   0.1    2.1  2  IMPDH           IMP dehydrogenase / GMP reductase domain
    5.9e-06   25.9   0.1    2.1e-05   24.1   0.0    1.8  2  His_biosynth    Histidine biosynthesis protein
    0.00074   18.9   2.8       0.34   10.2   0.1    2.2  2  ThiG            Thiazole biosynthesis protein ThiG
     0.0047   17.2   0.0      0.058   13.7   0.0    2.1  2  PucR            Purine catabolism regulatory protein-like fam
     0.0099   15.5   0.0        1.1    8.7   0.0    2.1  2  HMGL-like       HMGL-like
  ------ inclusion threshold ------
      0.014   14.5   0.0        1.5    7.9   0.0    2.1  2  Dus             Dihydrouridine synthase (Dus)
      0.027   13.9   0.1      0.047   13.1   0.1    1.4  1  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
      0.054   13.3   0.1      0.097   12.5   0.0    1.5  2  S-methyl_trans  Homocysteine S-methyltransferase
      0.061   13.4   0.2       0.13   12.4   0.2    1.5  1  DpaA_N          Dipicolinate synthase subunit A N-terminal do
       0.09   12.0   0.6       0.34   10.1   0.1    1.9  2  PEP_hydrolase   Phosphoenolpyruvate hydrolase-like
       0.19   10.9   0.4        0.3   10.2   0.4    1.2  1  DHO_dh          Dihydroorotate dehydrogenase
       0.33   11.3   1.2       0.66   10.3   0.1    2.2  2  LEP503          Lens epithelial cell protein LEP503


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 !  209.6   0.0     3e-65   4.1e-62       7     216 ..      25     241 ..      17     253 .. 0.94

  Alignments for each domain:
  == domain 1  score: 209.6 bits;  conditional E-value: 3e-65
                                    SEEEEE-TTSS-CHHHHHHH...HCTT-SEEEEECST...CHHHHHHHHHHHHHCTSSS-EEEEESSGGG--TTSSEEEE CS
                           PcrB   7 rhltklDPeeenpdEiveiv...iesgtDavmigGsq...svtldntvrllkkvsriklPivlepsnvegvvryaDalFv 80 
                                     hlt++DP  + p+ +v+++   ++ gt a+m+gGs    ++ ld+tvr++k+   ++lP++l+ps   g+  +aDa+F+
  gi|116754539|ref|YP_843657.1|  25 AHLTLIDPASQDPERAVQMArsaADAGTTALMVGGSVgatGSALDRTVRAIKDS--VDLPVILFPSSAAGLCDNADAVFF 102
                                    4****************998887999*********98777899**********9..************************ PP

                                    EEETTBSSTTTTTHHHHHHHHHHHHHHHCTEEEEEEEEEBTTTSHHHHHTTB-.B-TTHHHHHHHHHHHHHHTT-SEEEE CS
                           PcrB  81 msllnsanadWivgahalglkkvkklieseeilaegYlvvePdskvaavteak.vdlnkediaayallaakllglrliYl 159
                                    msllns  + +++  +alg+  v ++   +e++++gY+vveP+++v++v++ak v++ k+diaa+++la ++lg+rliYl
  gi|116754539|ref|YP_843657.1| 103 MSLLNSRSTSYLIENQALGAPIVSRYG--IEAIPMGYIVVEPGGTVGWVGDAKlVPRRKPDIAAAYALAGRYLGMRLIYL 180
                                    ***************************..*************************************************** PP

                                    E-.TTSSS-H..HHHHHHHHHHSSSEEEEESS--SHHHHHHHHCC.SSEEEE-CHHHHHHH CS
                           PcrB 160 Ea.sGaledv..eevialkkklekarlivGGGirsaEkAkevvea.ADvivvGnvveekde 216
                                    Ea sGa  +v    v a++  + ++ l+vGGGir+aE A++ v a AD iv+G+ vee+++
  gi|116754539|ref|YP_843657.1| 181 EAgSGAESPVptSMVSAVRDAIGDTLLVVGGGIRDAEAARKLVSAgADLIVTGTGVEESGD 241
                                    *********99778899999**************************************994 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.011        15      79     122 ..      41      84 ..      26      99 .. 0.83
   2 !   19.8   0.1   2.3e-07   0.00031     129     175 ..     188     235 ..     167     241 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.011
                                    HHTSTTSXBXTTSXB-EEEEE-SSTTHHHHHHHHHHTT-SEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH  79 vkrspnaakdekgrllvgaavgvkedalervkalveagvdvlvv 122
                                    v+ +++aa   +  l+vg +vg++ +al+r  + ++  vd+ v+
  gi|116754539|ref|YP_843657.1|  41 VQMARSAADAGTTALMVGGSVGATGSALDRTVRAIKDSVDLPVI 84 
                                    55556666778899**********************99997655 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 2.3e-07
                                    SHHHHHHHHHHHHHTTT.SEEEEEEE-SHHHHHHHHHTT-SEEEE-SS CS
                                    xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 129 sekvleavkeikkkvee.veviaGnvataegakaLieagadavkvGiG 175
                                    s   +++v+++++++ + + v++G + +ae+a++L++agad +  G G
  gi|116754539|ref|YP_843657.1| 188 SPVPTSMVSAVRDAIGDtLLVVGGGIRDAEAARKLVSAGADLIVTGTG 235
                                    4445789********99899***********************99998 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.62   8.5e+02      43      80 ..      24      59 ..       6      85 .. 0.61
   2 !   24.1   0.0   1.5e-08   2.1e-05      55     112 ..     185     243 ..     157     254 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.62
                                   -SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEEEES CS
                   His_biosynth 43 adelhvvDldaakegreanldlveeiaeevfipvqvGG 80
                                   a  l+++D   a++  e+  ++ +  a++ +  ++vGG
  gi|116754539|ref|YP_843657.1| 24 AAHLTLIDP--ASQDPERAVQMARSAADAGTTALMVGG 59
                                   554554443..445555556666666666666666666 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 1.5e-08
                                    CTTHHHHHHHHHHHHHH-S.SEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHH CS
                   His_biosynth  55 kegreanldlveeiaeevf.ipvqvGGGIrsledveelleagadkviigtaavknpeli 112
                                     +++++ +++v+++++++    + vGGGIr+ e++++l++agad ++ gt + ++ +++
  gi|116754539|ref|YP_843657.1| 185 GAESPVPTSMVSAVRDAIGdTLLVVGGGIRDAEAARKLVSAGADLIVTGTGVEESGDVF 243
                                    4567777889999999987466889*************************887776655 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.1   0.00025      0.34     135     195 ..      42     104 ..      17     108 .. 0.82
   2 !    9.0   0.4   0.00057      0.79     164     224 ..     192     253 ..     175     255 .] 0.86

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00025
                                    HHHHHHHHTT-SEBEEBSSSTTS----S-HHHHHHHHHH-SS-BEE....ES---SHHHHHHHHH CS
                           ThiG 135 vlarrleevGcaavmPlaapiGsglGllnkealkiiieeakvPviv....DAGigspsdaaqame 195
                                     +ar   ++G++a+m  ++ +G+  G +   +++ i +++++Pvi+     AG+    da+  m 
  gi|116754539|ref|YP_843657.1|  42 QMARSAADAGTTALMVGGS-VGA-TGSALDRTVRAIKDSVDLPVILfpssAAGLCDNADAVFFMS 104
                                    5799999********7665.664.57777889*************85554588888888877665 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00057
                                    HHHHHHHHHH-.SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHHHHHHHHH CS
                           ThiG 164 kealkiiieea.kvPvivDAGigspsdaaqamelGadavllntavaeakdpvamArafklav 224
                                    + +++ +++ + +  ++v  Gi+ ++ a + +  Gad ++  t v e+ d  +  + + +a+
  gi|116754539|ref|YP_843657.1| 192 TSMVSAVRDAIgDTLLVVGGGIRDAEAARKLVSAGADLIVTGTGVEESGDVFRFVKDIVTAI 253
                                    567788888888999***********************************999988888777 PP

>> PucR  Purine catabolism regulatory protein-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   4.2e-05     0.058      52     103 ..      33      89 ..      21      93 .. 0.86
   2 ?    1.1   0.0      0.32   4.5e+02      45      78 ..     206     238 ..     183     253 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.2e-05
                           PucR  52 lkddpealaelvrelaeagvaaLviklg..r...eipeelieaadelglPlielpee 103
                                     ++dpe   ++ r+ a+ag  aL+++    +   ++++ + ++ d+ +lP+i +p++
  gi|116754539|ref|YP_843657.1|  33 ASQDPERAVQMARSAADAGTTALMVGGSvgAtgsALDRTVRAIKDSVDLPVILFPSS 89 
                                    4679*********************99655256699******************986 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.32
                           PucR  45 llttglalkddpealaelvrelaeagvaaLvikl 78 
                                    ll+ g +++ d ea ++lv + a+  v + +++ 
  gi|116754539|ref|YP_843657.1| 206 LLVVGGGIR-DAEAARKLVSAGADLIVTGTGVEE 238
                                    444455665.666666666666666666666655 PP

>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.013        18     139     189 ..      31      80 ..      18      86 .. 0.85
   2 !    8.7   0.0   0.00082       1.1      35     101 ..     175     238 ..     153     254 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.013
                                    TTBS--HHHHHHHHHHHHHHT-SEEEEEETTS---HHHHHHHHHHHHHHS- CS
                      HMGL-like 139 dasrtdleflaevveaaeeaGatriniaDtvGvltPneaaelisalkervk 189
                                    d    d+e +++++  a++aG t + +  +vG++  ++  + ++a+k+ v+
  gi|116754539|ref|YP_843657.1|  31 DPASQDPERAVQMARSAADAGTTALMVGGSVGAT-GSALDRTVRAIKDSVD 80 
                                    556789**************************75.5788899999999887 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00082
                                    HT-SEE--TSGGGT.THHHHHHHS---TT-B..--EE-SSHHHHHHHHH....TT-SEEEEEEES-H CS
                      HMGL-like  35 agvdeiEvgfpaaseddfevvraiakavkkarilalvrarekdikaavealkgagakrvhvfiatse 101
                                    +++ ++E+g +a s+ ++  v a+ +a++++  l++v   ++d +aa + l+ aga+ + + + + e
  gi|116754539|ref|YP_843657.1| 175 MRLIYLEAGSGAESPVPTSMVSAVRDAIGDT--LLVVGGGIRDAEAARK-LVSAGADLIVTGTGVEE 238
                                    667789**********************999..9999999********9.********999887766 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.011        15     137     187 ..      37      84 ..      27      86 .. 0.79
   2 ?    7.9   0.0    0.0011       1.5     173     223 ..     193     243 ..     183     253 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.011
                                    TC.HHHHHHHHHHCT-SEEEEESSECCCTT-CG--CHHHHHHHHH-SS-EE CS
                            Dus 137 eenalelakiveaaGaqaltvHgRtraqnyegtadweaIkevkqavsipvi 187
                                     e a+++a+ + +aG +al+v g + a++    a  ++++++k++v +pvi
  gi|116754539|ref|YP_843657.1|  37 PERAVQMARSAADAGTTALMVGGSVGATG---SALDRTVRAIKDSVDLPVI 84 
                                    56799****************99776654...4555778888888888887 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0011
                                    HHHHHHHHH-S.S-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHH CS
                            Dus 173 eaIkevkqavs.ipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlf 223
                                    + +++v++a+  + +++ G+I+dae+a++ ++  Gad ++ g g ++   +f
  gi|116754539|ref|YP_843657.1| 193 SMVSAVRDAIGdTLLVVGGGIRDAEAARKLVSA-GADLIVTGTGVEESGDVF 243
                                    56899*****99***************999998.********9998876666 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 ?   13.1   0.1   3.4e-05     0.047     154     197 ..     196     236 ..     183     237 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.4e-05
                                    HHHHHHHHHHT---EEEEESS--T.TTCHHHHHHT--EEEESHHH CS
                 Ribul_P_3_epim 154 kkvrklidekeldlkievDGGvkl.dnieqiaeagadvlVagsav 197
                                    ++vr +i     d+ + v GG+++ ++++++++agad++V+g++v
  gi|116754539|ref|YP_843657.1| 196 SAVRDAIG----DTLLVVGGGIRDaEAARKLVSAGADLIVTGTGV 236
                                    55555555....5999******86267789************986 PP

>> S-methyl_trans  Homocysteine S-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     7e-05     0.097      72     104 ..      38      70 ..      25     127 .. 0.79
   2 ?   -3.0   0.0       3.6     5e+03      40      52 ..     222     234 ..     216     234 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7e-05
                                    HHHHHHHHHHHHHH....HEEEEE--HHHHCTS CS
                 S-methyl_trans  72 raavelareaadeaaaplfvagsvGpygatlsd 104
                                    ++av++ar aad+ +++l+v gsvG +g +l  
  gi|116754539|ref|YP_843657.1|  38 ERAVQMARSAADAGTTALMVGGSVGATGSALDR 70 
                                    68***********999999**********9966 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.6
                                    HHHHT-SEEE-TT CS
                 S-methyl_trans  40 yleaGadiieTnT 52 
                                     + aGad+i T T
  gi|116754539|ref|YP_843657.1| 222 LVSAGADLIVTGT 234
                                    4567777777755 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 ?   12.4   0.2   9.3e-05      0.13       2      32 ..     206     236 ..     205     253 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.3e-05
                                    EEEESB-HHHHHHHHHHHHTT-EEEEES-TS CS
                         DpaA_N   2 iaviGGDaRqlylarkLaekgakvslyglel 32 
                                    ++v+GG  R+++ arkL + ga++ + g   
  gi|116754539|ref|YP_843657.1| 206 LLVVGGGIRDAEAARKLVSAGADLIVTGTGV 236
                                    68**********************9998833 PP

>> PEP_hydrolase  Phosphoenolpyruvate hydrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.36   4.9e+02     158     201 ..      36      76 ..      25      83 .. 0.66
   2 ?   10.1   0.1   0.00024      0.34     156     185 ..     213     242 ..     192     250 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.36
                  PEP_hydrolase 158 neeearamaeaGadvivahlGlttggsigaktalsleeavelvq 201
                                    ++e a +ma+  ad+  +   l  ggs+ga+  + l+++v+ ++
  gi|116754539|ref|YP_843657.1|  36 DPERAVQMARSAADAGTT--ALMVGGSVGAT-GSALDRTVRAIK 76 
                                    567788888888886544..45566666664.345555555554 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00024
                  PEP_hydrolase 156 vfneeearamaeaGadvivahlGlttggsi 185
                                    ++++e ar++++aGad+iv+  G+ ++g++
  gi|116754539|ref|YP_843657.1| 213 IRDAEAARKLVSAGADLIVTGTGVEESGDV 242
                                    778999******************999875 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.4   0.00022       0.3     228     280 ..     189     240 ..     178     253 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00022
                                    HHHHHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHG CS
                         DHO_dh 228 dialkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfeg 280
                                    ++ + ++ ++++ + +++ ++g GGi  +e a   + aGA l+  +t++  +g
  gi|116754539|ref|YP_843657.1| 189 PVPTSMVSAVRDAIGDTLLVVG-GGIRDAEAARKLVSAGADLIVTGTGVEESG 240
                                    788999*********9999998.9***********************996554 PP

>> LEP503  Lens epithelial cell protein LEP503
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       4.7   6.4e+03      19      28 ..      50      59 ..      39      71 .. 0.63
   2 ?   10.3   0.1   0.00048      0.66       5      31 ..     188     214 ..     185     243 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 4.7
                         LEP503 19 lGdaalrvGt 28
                                    G +al vG 
  gi|116754539|ref|YP_843657.1| 50 AGTTALMVGG 59
                                   3556666643 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00048
                         LEP503   5 rPlaqalPssfrralGdaalrvGtGkr 31 
                                     P++ ++ s+ r a+Gd+ l vG G r
  gi|116754539|ref|YP_843657.1| 188 SPVPTSMVSAVRDAIGDTLLVVGGGIR 214
                                    699********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); 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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1966.27
//
Query:       gi|116754540|ref|YP_843658.1|  [L=383]
Description: peptidase M24 [Methanosaeta thermophila PT]
Scores for complete 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-40  138.5   0.0    3.4e-40  138.0   0.0    1.2  1  Peptidase_M24  Metallopeptidase family M24


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.0   0.0   1.9e-44   3.4e-40       3     209 .]     151     367 ..     149     367 .. 0.90

  Alignments for each domain:
  == domain 1  score: 138.0 bits;  conditional E-value: 1.9e-44
                                    HHHHHHHHHHHHHHHHHHHHT.....T........CBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBCSSS CS
                  Peptidase_M24   3 irkaariasaaleavleaikp.....g........vterelaaeieattlkrhgarglafppivasgenaavlhytpndr 69 
                                    i +++++++ a+e +++ ik+     g         t++ +  ++e  +l++ g++ l  ++iv+ g  ++ +h +  + 
  gi|116754540|ref|YP_843658.1| 151 IAEVQEACESAMEVAVSLIKKskptgGilvfdgkpLTSERVRSAVE-LRLAELGCETL--DTIVCGGLMSSSPHSRG-SG 226
                                    6688999999999999989974445414433444459999999999.55899888887..89*************99.59 PP

                                    B--TTEEEEEEEEEEET..TEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTB.. CS
                  Peptidase_M24  70 vlkegdlvlidagaeyd..gyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesagl.. 145
                                     l ++++++id+ ++ +  +y +D+trTv+ G+++ e  e+y+av+ aqea++k++k+Gv++++++ a+++++ + g+  
  gi|116754540|ref|YP_843658.1| 227 LLPADMPIVIDIFPRSKssRYFADMTRTVVRGEPSVEIVEMYQAVKIAQEAGLKCIKEGVSGADVHGAVCRTFDDFGYte 306
                                    9*******************************9999***************************************99999 PP

                                    ..CCGBSSCSEEEESSSSSEEEEEESSSTTCSSB--TTBEEEEEEEEEEETTTEEEEEBEEEEEES CS
                  Peptidase_M24 146 ..akffphglGHgvGlevhdegpsvsresndgrkleeGmvftiEpgiyfapgeggvriedtvlvte 209
                                      +  f h++GHgvGl++h+  ps+s  + +g +l+ G+v+t+Epg+y  p+ ggvr+ed+v+v+e
  gi|116754540|ref|YP_843658.1| 307 reECGFIHSTGHGVGLSIHER-PSLS--E-HGGTLRSGNVVTVEPGLY-YPDIGGVRLEDLVVVRE 367
                                    998999*************98.**99..4.59****************.99*************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        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 0.25s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2982.38
//
Query:       gi|116754541|ref|YP_843659.1|  [L=352]
Description: hypothetical protein Mthe_1240 [Methanosaeta thermophila PT]
Scores for complete 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  112.9  19.8    1.2e-32  112.9  19.8    2.5  3  DUF389      Domain of unknown function (DUF389)
  ------ inclusion threshold ------
        3.1    6.8  18.8       0.72    8.8   3.3    2.2  2  PHO4        Phosphate transporter family
        4.3    7.4   6.1        5.9    6.9   0.2    3.3  3  Holin_BlyA  holin, BlyA family


Domain annotation for each model (and alignments):
>> DUF389  Domain of unknown function (DUF389)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.05     3e+02      63     100 ..     129     166 ..     114     167 .. 0.72
   2 !  112.9  19.8     2e-36   1.2e-32       1     141 [.     168     302 ..     168     303 .. 0.97
   3 ?   -2.5   0.1      0.79   4.7e+03      32      43 ..     334     345 ..     315     350 .. 0.51

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.05
                         DUF389  63 semlsrtepnlvdllvAlasGaagalallsgnssslvG 100
                                    s +++  +++ v++++ ++s +++a  lls+n  +++G
  gi|116754541|ref|YP_843659.1| 129 SSIETAAKLTKVYIAMIVLSSIIAAAGLLSNNVVVIIG 166
                                    44555555666666677789999999999999988888 PP

  == domain 2  score: 112.9 bits;  conditional E-value: 2e-36
                         DUF389   1 MlisPlmgpilaiafglvigdrkllrrglknlliglllallvgflfglllplkvlgeeelptsemlsrtepnlvdllvAl 80 
                                    M+++Plmgp +a+a+++++gd +l+r++lk+ l+g+ la+++++++gl+lp++       + +e++srt++ + +++vA+
  gi|116754541|ref|YP_843659.1| 168 MVVAPLMGPNVALALATTLGDLTLARNALKTNLVGISLAVILSVALGLILPVD------PSMPEISSRTSVGFAEVIVAF 241
                                    ***********************************************998986......5668***************** PP

                         DUF389  81 asGaagalallsgnssslvGvaIaaaLlPPavnaGlglalgewalalgslllllvNivgIv 141
                                    asG ag+la++++  ++++Gva+a++LlPP+v++Gl+l++g +++a+g+lll+lvN++ ++
  gi|116754541|ref|YP_843659.1| 242 ASGCAGVLAFTTAAPAVIIGVAVAVSLLPPLVAFGLLLGAGYVSYATGALLLFLVNLISVN 302
                                    **********************************************************987 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.79
                         DUF389  32 lliglllallvg 43 
                                    +l +llla l++
  gi|116754541|ref|YP_843659.1| 334 MLWALLLAALLS 345
                                    222222222222 PP

>> PHO4  Phosphate transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   7.8    0.0049        29     108     216 ..     154     263 ..     134     273 .. 0.63
   2 ?    8.8   3.3   0.00012      0.72       9      79 ..     274     347 ..     272     351 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.0049
                           PHO4 108 eavkwkklvkivlswvlsPllggiiaallfllvkrlilvkeklknalralpvlvlvtiailalsilfkgesk.kddeete 186
                                     ++  +++v i+ ++v++Pl+g  +a +l++ +  l l +++lk  l    + ++v++++++ +il    s  +++++t+
  gi|116754541|ref|YP_843659.1| 154 AGLLSNNVVVIIGAMVVAPLMGPNVALALATTLGDLTLARNALKTNLVG--ISLAVILSVALGLILPVDPSMpEISSRTS 231
                                    3444578999**************************9977777655544..44445544444444443333346666666 PP

                           PHO4 187 klf..kflqvvsaalvsfahGanDvanaiGpl 216
                                      f   ++   s+++  +a      a +iG+ 
  gi|116754541|ref|YP_843659.1| 232 VGFaeVIVAFASGCAGVLAFTTAAPAVIIGVA 263
                                    66631223334555555565555555566655 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00012
                           PHO4   9 afatsvgskaltlrqAvilaaifeflGavllGaeVaetirkgivdvelf.....dpselmlgmlaallgaavwlll 79 
                                    af+   g++ +++ + ++l  +++++ + l+G  Va +i++gi+  +       ++++++++ml all aa++ ++
  gi|116754541|ref|YP_843659.1| 274 AFGLLLGAGYVSYATGALLLFLVNLISVNLAG--VATFIAQGIFPRNWWeadraKSATFVALMLWALLLAALLSFI 347
                                    79999***********************9984..9*********44433455557778888888877777766554 PP

>> Holin_BlyA  holin, BlyA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.2   0.00099       5.9      22      51 ..     139     168 ..     122     170 .. 0.86
   2 ?   -0.4   0.1      0.19   1.2e+03      18      42 ..     200     225 ..     188     227 .. 0.65
   3 ?    1.1   0.1     0.066     4e+02       5      26 ..     290     311 ..     287     316 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00099
                     Holin_BlyA  22 giFvvllvlgvllllKPllkdiLilliqKl 51 
                                     +++ ++vl  +++   ll ++++++i+ +
  gi|116754541|ref|YP_843659.1| 139 KVYIAMIVLSSIIAAAGLLSNNVVVIIGAM 168
                                    5699***********************965 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.19
                     Holin_BlyA  18 LiilgiFvvl.lvlgvllllKPllkd 42 
                                    L+ +   v+l + lg++l + P + +
  gi|116754541|ref|YP_843659.1| 200 LVGISLAVILsVALGLILPVDPSMPE 225
                                    44444334432679999999998766 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.066
                     Holin_BlyA   5 kllilLitldeiKLiilgiFvv 26 
                                     ll +L++l  + L  +  F+ 
  gi|116754541|ref|YP_843659.1| 290 ALLLFLVNLISVNLAGVATFIA 311
                                    5899**************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       766  (0.0427241); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); 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):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2574.77
//
Query:       gi|116754542|ref|YP_843660.1|  [L=414]
Description: glycine hydroxymethyltransferase [Methanosaeta thermophila PT]
Scores for complete 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-173  576.1   0.0   3.4e-173  575.8   0.0    1.0  1  SHMT             Serine hydroxymethyltransferase
    8.2e-07   28.5   0.0    1.7e-06   27.5   0.0    1.4  1  Aminotran_1_2    Aminotransferase class I and II
    1.5e-06   27.7   0.1    7.6e-06   25.4   0.1    1.8  1  Beta_elim_lyase  Beta-eliminating lyase
    9.8e-06   24.8   0.0    1.4e-05   24.3   0.0    1.2  1  Aminotran_5      Aminotransferase class-V
  ------ inclusion threshold ------
      0.039   12.5   0.0      0.073   11.6   0.0    1.5  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
      0.073   12.4   0.2       0.14   11.5   0.2    1.5  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
       0.11   12.5   0.0       0.25   11.4   0.0    1.5  1  Cullin_Nedd8     Cullin protein neddylation domain


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 !  575.8   0.0  1.3e-176  3.4e-173       2     399 .]       5     380 ..       4     380 .. 0.99

  Alignments for each domain:
  == domain 1  score: 575.8 bits;  conditional E-value: 1.3e-176
                                    HHHTHHHHHHHHHHHHHHHHSEE-STT-----HHHHHHHTSGGGG----EETTEESSST-HHHHHHHHHHHHHHHHHCT- CS
                           SHMT   2 eesdpevaeiikkekerqkeeieliasenftskavlealGsvltnkyaeGyPGkryyGGcefvdeveelaqdrakelfkl 81 
                                    +++dpe+  +i+ke +rq++++ l+a+enfts+av+ea+G v+tnkyaeGyPGkryy Gc f+de+e+la+dr+k+lf++
  gi|116754542|ref|YP_843660.1|   5 DHVDPEISAVIRKELDRQRNTLVLVAAENFTSPAVMEAQGCVMTNKYAEGYPGKRYYRGCAFMDEAENLARDRCKKLFGA 84 
                                    689***************************************************************************** PP

                                    STTTEEEE---SSHHHHHHHHHHHHT-TT-EEEEESCTTTSTGGGT-BTSS-B-SHHHHHSEEEEE-B-TTTSSB-HHHH CS
                           SHMT  82 dpakwgvnvqplsGsqanlavytallepgdrilgldladGGhlthGakveskkisassklfesveykvdketglidydel 161
                                    +    +vnvqp+sGsqan+a y a l+pgd+i+g++l +GGhl+hG++v++     s+kl+++v+y+v+++t+++dy e+
  gi|116754542|ref|YP_843660.1|  85 E----HVNVQPHSGSQANMAAYFATLKPGDTIMGMNLDHGGHLSHGSPVNF-----SGKLYHVVPYGVSRKTEMLDYSEI 155
                                    *....**********************************************.....************************ PP

                                    HHHHHHH--SEEEEE-SST-S---HHHHHHHHHHTT-EEEEE-GGGHHHHHTTSS--GCCTSSEEEEESSSTT-S-S-EE CS
                           SHMT 162 ekkakefkPklivaGtsaysrlidyarlreiadevgayllvdmahiaGlvaagvipsPfeyadvvtttthktlrGprggl 241
                                       a+e +P++iv+G+say+r+id++ +reiadevga l++d+ahiaGlvaagv+psP++yad+vtttthktlrGprgg+
  gi|116754542|ref|YP_843660.1| 156 LDVARECRPQMIVCGASAYPRIIDFKAMREIADEVGALLMADIAHIAGLVAAGVHPSPIPYADIVTTTTHKTLRGPRGGV 235
                                    ******************************************************************************** PP

                                    EEEC-SEEEEETTTEEEEHHHHHHHHHHHTTTT-SS--HHHHHHHHHHHHHCTSHHHHHHHHHHHHHHHHHHHHHHHTT- CS
                           SHMT 242 illrkgvksvdktgkevleelekkinsavfPglqGGPlnhviaakavalkealepefkvyqkqvlknakalaealkekgy 321
                                    i++r              eel++ i+ avfPg+qGGP++h+iaakava+kea++pef+ yq+q+++na ala+ l e+g+
  gi|116754542|ref|YP_843660.1| 236 IMCR--------------EELAQAIDRAVFPGIQGGPMMHTIAAKAVAFKEAMTPEFRRYQEQIVRNAAALADRLIENGF 301
                                    ****..............89************************************************************ PP

                                    EEGGGS-SSSEEEEEGGGGTS-HHHHHHHHHHTTEE-EEE--TTS.STTTT-SEEEEESHHHHHTT--HHHHHHHHHHH CS
                           SHMT 322 klvsgGtdnhlvlvdlrekgldGkraekvlekvnitankntvPgd.ksalvtsGlrlGtpaltsrgfkeedlekvakfi 399
                                    +lvsgGtdnhl+lv+l ++g++Gk+a++ le++ i+ nkn +P+d + ++vtsG+r+Gtpa+tsrg+ke++++++a++i
  gi|116754542|ref|YP_843660.1| 302 DLVSGGTDNHLMLVKLLKEGITGKEADETLESAGIALNKNMIPFDpRTPFVTSGIRIGTPAVTSRGMKENEMREIADLI 380
                                    ****************************************************************************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 !   27.5   0.0   6.6e-10   1.7e-06      54     356 ..      79     368 ..      65     371 .. 0.70

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 6.6e-10
                                    HHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEES...S-THHHHHHHHTTSEEEEEEBEETTTTEE CS
                  Aminotran_1_2  54 akflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdp...tyasyknilrlsggevvryplyseedfhl 130
                                     k++g       ++  +v+  sG++a+ +a ++ lk  pgd i   ++    + s+   ++ sg   + +p+    +++ 
  gi|116754542|ref|YP_843660.1|  79 KKLFG------AEHV-NVQPHSGSQANMAAYFATLK--PGDTIMGMNLdhgGHLSHGSPVNFSGKLYHVVPYG--VSRKT 147
                                    45666......4455.9**********999999999..*****966651115667777777777776666766..44555 PP

                                    -HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTS CS
                  Aminotran_1_2 131 dlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveee 210
                                     + ++ e l+ a e ++    ++v++++     +++ +  +++   a++ ++ll+ D a+ ++   +     +++   ++
  gi|116754542|ref|YP_843660.1| 148 EMLDYSEILDVARECRP---QMIVCGAS-AYPRIIDFKAMREI---ADEVGALLMADIAHIAGLVAA----GVHPSPIPY 216
                                    55555555556555566...56666665.34466666666666...*****************9982....347777777 PP

                                    TTEEEEEESSSTT.SSGGG-EEEEEEEHHHHHHHHHHHHHHTS.SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                  Aminotran_1_2 211 pnllivgslsKaf.GlaGeRvGyilgnaavvsqlrklsrpfls.ssllqaavaaalsdallkqseleemrqrlqkrrkel 288
                                     + +++++  K + G  G   G i + +++++++ +++ p++     +  ++a+a+  ++ +  e+   ++++ +++  l
  gi|116754542|ref|YP_843660.1| 217 AD-IVTTTTHKTLrGPRG---GVIMCREELAQAIDRAVFPGIQgGPMMHTIAAKAVAFKEAMTPEFRRYQEQIVRNAAAL 292
                                    77.777777777546666...**********************666667777777777777778**************** PP

                                    HHHHHHSTEEEECCS..CSSEEEEEETHH....CHHHHHHH...HHHTCTEEEEEGGGGTSTTEEEEECTTS-HHHH CS
                  Aminotran_1_2 289 rdeLaelglkvlasq..sgmflltdlsae....takelskk...LleevgvyvtpgtsftvpgrlRitvAglteeel 356
                                     d+L e g++ ++    +++ l+ +l++     +a+e  ++    l++ + + +  + + v++ +Ri  +++t+  +
  gi|116754542|ref|YP_843660.1| 293 ADRLIENGFDLVSGGtdNHLMLVKLLKEGitgkEADETLESagiALNK-NMIPFDPRTPFVTSGIRIGTPAVTSRGM 368
                                    ****99966666544315666655555558666333333335755555.4444444555555559998877777655 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.1   2.9e-09   7.6e-06      37     278 ..      74     339 ..      46     343 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 2.9e-09
                                    HHHHHHHHTT-SEE.EEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHH CS
                Beta_elim_lyase  37 Ledavaelfgkeaa.lfvpqGtaAnsillkillqrgeevivtepahihfdetgaiaelagvklrdlknkeaGkmdlekle 115
                                      d++++lfg+e++ +  ++G +An  ++ + l++g+ ++  +  h+     g ++ ++g   + ++     k ++ +  
  gi|116754542|ref|YP_843660.1|  74 ARDRCKKLFGAEHVnVQPHSGSQANMAAYFATLKPGDTIMGMNLDHGGHLSHGSPVNFSGKLYHVVPYGVSRKTEMLDYS 153
                                    5789999*****8725788*******************999999**************9987777776665566666666 PP

                                    HHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHHTTSSEEEEE CS
                Beta_elim_lyase 116 aaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslgeivkemfsyvDsvtms 195
                                    ++++   +   ++++i+              +   +++++ia++ g  l+ D A +a   ++ g++++ +  y+D+vt  
  gi|116754542|ref|YP_843660.1| 154 EILDVARE--CRPQMIVCGASAYP------RIIDFKAMREIADEVGALLMADIAHIAGL-VAAGVHPSPI-PYADIVTTT 223
                                    66666444..67788876655553......456677778899*************9975.5889999876.7******** PP

                                    SSSTT--SS-EEEEE-HH.......................................HHHHHHHHHHHHT---SSTHHHH CS
                Beta_elim_lyase 196 lkKdllanvGgvlafrddel...................................edylaerveqrkylggglrqagvla 240
                                      K l  + Ggv++ r++ +                                     y ++ v+ + +l+++l + g+  
  gi|116754542|ref|YP_843660.1| 224 THKTLRGPRGGVIMCREELAqaidravfpgiqggpmmhtiaakavafkeamtpefRRYQEQIVRNAAALADRLIENGFDL 303
                                    ******************88********************************9998999999999*************99 PP

                                    H..HHHHHHHHSSTTHHHHHHHHHHHHHHHHHCT--EE CS
                Beta_elim_lyase 241 aleagiraleeglaslerdhktaeqlaeklelvrlaip 278
                                    +   g    +++l +l ++  t+++  e le   +a++
  gi|116754542|ref|YP_843660.1| 304 V--SGGTDNHLMLVKLLKEGITGKEADETLESAGIALN 339
                                    9..88778888888888888888888888887777765 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   5.4e-09   1.4e-05      37     243 ..      62     272 ..      28     279 .. 0.70

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 5.4e-09
                                    HHHHHHHHHHH.HHHHHHHHHT-STGGGEEEES.SHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTE CS
                    Aminotran_5  37 lgkeatkavee.arekvaelinaeseeeiifts.Gtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtga 114
                                    +g  +++  e+ ar++ ++l++ae     ++++  ++++ n++a+ +  +lkpgd+i   +++h + l     ++ + g 
  gi|116754542|ref|YP_843660.1|  62 RGCAFMDEAENlARDRCKKLFGAEH----VNVQpHSGSQANMAAYFA--TLKPGDTIMGMNLDHGGHLSHGSPVN-FSGK 134
                                    5555555555548999999999997....344312344778888777..69***************997666665.7787 PP

                                    EEEEEEBETTSCBE...GGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHT CS
                    Aminotran_5 115 kvkvipldeegeld...ldelekllnektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavghipidvkklg 191
                                      +v+p     + +    +e+ +  +e    ++++ + ++   i +++++ ++a ++gal+++D a  +g     v+   
  gi|116754542|ref|YP_843660.1| 135 LYHVVPYGVSRKTEmldYSEILDVARECRPQMIVCGA-SAYPRIIDFKAMREIADEVGALLMADIAHIAGLVAAGVHPSP 213
                                    6677766655555500155555555555555555555.5677999*********************98877777776654 PP

                                    E...SEEEEETTT.TTSSTT-EEEEEEHHHHHTS..SS.....STTSEEEEETTEEEEHC CS
                    Aminotran_5 192 v...DflafsghK.llgPtGiGvlyvrkellekleplll....ggemveevsleettfae 243
                                    +   D+++ ++hK l gP G Gv+++r+el +++  + +    gg m++++  +   f+e
  gi|116754542|ref|YP_843660.1| 214 IpyaDIVTTTTHKtLRGPRG-GVIMCREELAQAIDRAVFpgiqGGPMMHTIAAKAVAFKE 272
                                    333399*******999****.***********9965544122266777777766666665 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 ?   11.6   0.0   2.9e-05     0.073      61     224 ..      78     247 ..      48     300 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.9e-05
                                    HHHHHT-SEEEEE.SSHHHHHHHHHHTTS-TTEEEEEESTSSHHHH......HHHHHTHHH....TTCEEEEESTTSHHH CS
                Cys_Met_Meta_PP  61 iaaLeggeaalav.ssGmaAiaaailallkaGdeivvsddlYggtq......rllkkvlkk....lgievkfvdtsdlee 129
                                      +L g+e++ +   sG  A +aa +a lk Gd i+ ++  +gg        ++  k+++     ++ ++++ d s++ +
  gi|116754542|ref|YP_843660.1|  78 CKKLFGAEHVNVQpHSGSQANMAAYFATLKPGDTIMGMNLDHGGHLshgspvNFSGKLYHVvpygVSRKTEMLDYSEILD 157
                                    55666666654431588888888888888888887776655555330010002222222211101333444555555555 PP

                                    HHHHCCTTEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGTTTHTTTS-GGGGT....-SEEEEETTTTTTCSSS CS
                Cys_Met_Meta_PP 130 lekaikentklvylEtptnpllkvvDiekiaklakkagvlvvvDntfaspllqrplklg....aDivvhSaTKylgGhsd 205
                                    +++ ++   +++   + + p  +++D++++ ++a ++g+l++ D + +++l+   ++      aDiv+  + K l G   
  gi|116754542|ref|YP_843660.1| 158 VARECR--PQMIVCGASAYP--RIIDFKAMREIADEVGALLMADIAHIAGLVAAGVHPSpipyADIVTTTTHKTLRGPR- 232
                                    555554..456666665555..79********************99999888776665555569************986. PP

                                    --EEEEEESSCHHHHHHHH CS
                Cys_Met_Meta_PP 206 vvaGvivvkgkeelkkelk 224
                                      +Gvi++ +  el++ + 
  gi|116754542|ref|YP_843660.1| 233 --GGVIMCRE--ELAQAID 247
                                    ..68887544..5554443 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   5.4e-05      0.14      86     203 ..     137     255 ..      78     276 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.4e-05
                                    EEEEE-B-TTTSSB-GGGCGGG--TTE..EEEEEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETTEECCCSSS CS
                DegT_DnrJ_EryC1  86 kpvfvDvdpdtynidpaaieaaitert..kaIlpVhlyGqvadmdalkaiaakhglkvieDaAhAlGatykgkkvGalgd 163
                                     +v+  v ++t ++d ++i  +  e +    +  + +y ++ d++a+++ia++ g  ++ D Ah  G   +g +   +  
  gi|116754542|ref|YP_843660.1| 137 HVVPYGVSRKTEMLDYSEILDVARECRpqMIVCGASAYPRIIDFKAMREIADEVGALLMADIAHIAGLVAAGVHPSPIPY 216
                                    567777888888888888887777766534445689999****************************9999987777777 PP

                                    EEEEE-BTTSSS-SSS-EEEEESTHHHHHHHHHHHBTTCE CS
                DegT_DnrJ_EryC1 164 aavfSFyptKnlttGeGGavvtndeelaekarvlrnhGlk 203
                                    a ++     K+l    GG+++ + eela+ + +    G++
  gi|116754542|ref|YP_843660.1| 217 ADIVTTTTHKTLRGPRGGVIMCR-EELAQAIDRAVFPGIQ 255
                                    77777778888888888877776.4566666655555555 PP

>> Cullin_Nedd8  Cullin protein neddylation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   9.7e-05      0.25       9      54 ..     363     406 ..     358     408 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.7e-05
                   Cullin_Nedd8   9 aIVRiMKsrktlshneLvsevieqlskrftpsiadikkrIesLiek 54 
                                    +  R MK++   ++ +L++evi+++  + + +i+ +++r+  L e+
  gi|116754542|ref|YP_843660.1| 363 VTSRGMKENEMREIADLITEVIRDM--KNPATIESVRSRVRALCER 406
                                    56689********************..5588888899999888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 2787.67
//
Query:       gi|116754543|ref|YP_843661.1|  [L=280]
Description: bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase [Methanosaeta thermophila PT]
Scores for complete 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-65  218.6   2.2    3.7e-65  218.1   2.2    1.2  1  THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase,
    5.5e-35  120.1   0.0    1.3e-34  118.9   0.0    1.6  2  THF_DHG_CYH    Tetrahydrofolate dehydrogenase/cyclohydrolase,
  ------ inclusion threshold ------
      0.071   13.2   0.2       0.56   10.3   0.1    2.2  2  Ldh_1_N        lactate/malate dehydrogenase, NAD binding doma


Domain annotation for each model (and alignments):
>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.1   2.2   6.2e-69   3.7e-65       1     158 [.     117     273 ..     117     275 .. 0.99

  Alignments for each domain:
  == domain 1  score: 218.1 bits;  conditional E-value: 6.2e-69
                                    SHHHHHHHHTT--SS--HHHHHHHHHHHHCT---TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTSCCHHHHHCCS CS
                  THF_DHG_CYH_C   1 hplnlgrlvkgeeallpctpkgvvellketgielegkkvvvvGrsnivgkplallLleknatVtvchsktkdlaeitrea 80 
                                    hp n+g l++g e l+pctp+g+v  l++ g+++eg ++v+vG+sn+vgkpla++Ll++natV+vch  t++l+e+t+ a
  gi|116754543|ref|YP_843661.1| 117 HPENMGALLLGAERLVPCTPRGIVYALEHLGVDIEGSEAVIVGHSNVVGKPLAAMLLNRNATVQVCHVYTRNLKEHTKDA 196
                                    899***************************************************************************** PP

                                    SEEEE-SS-TT-B-GGGS-TT-EEEE---EEC-TTEEE-SB-HHHHCTTSSEE--TTTSCHHHHHHHHHHHHHHHHHC CS
                  THF_DHG_CYH_C  81 divvvavGkpelikaemvkegavviDvGinrvekgklvGDvdfeevkevasaitPvpgGVGpmTvamllkntleaakr 158
                                    +i+vva+G+p+lika+mv++ga v DvGin+v +gk+vGDvdf++vke+a+ itPvpgGVGp+Tvamll++t++aa++
  gi|116754543|ref|YP_843661.1| 197 EILVVAAGVPRLIKADMVRDGAYVFDVGINKV-DGKTVGDVDFDAVKEKAAGITPVPGGVGPLTVAMLLSQTVTAAEM 273
                                    ********************************.******************************************986 PP

>> THF_DHG_CYH  Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.9   0.0   2.1e-38   1.3e-34       1     116 []       2     114 ..       2     114 .. 0.98
   2 ?   -2.5   0.0         1     6e+03      42      59 ..     182     199 ..     163     212 .. 0.62

  Alignments for each domain:
  == domain 1  score: 118.9 bits;  conditional E-value: 2.1e-38
                                    E--HHHHHHHHHHHHHHHHHHHHHHT---EEEEEEES--HHHHHHHHHHHHHHHHTT-EEEEEEE-TT--HHHHHHHHHH CS
                    THF_DHG_CYH   1 lldGkalakeireelkeeveklkekgvkpkLavilvgddpasevYvrnkkkaceevGieseliklpedvseeellkliee 80 
                                    ++dGkala++i++e++e+ve+l    ++p+La+ilvg++pas++Y+r k+ ace+vGi+se i lp d+ e++l+k+i+ 
  gi|116754543|ref|YP_843661.1|   2 IIDGKALASDIEAEVRERVERLG---FNPGLATILVGENPASQMYIRIKHAACERVGIRSENIVLPGDTDESTLIKTIQG 78 
                                    79*****************9886...69**************************************************** PP

                                    HHH-TT--EEEE-SS-STTS-HHHHHCCS-GGGBTT CS
                    THF_DHG_CYH  81 lneddsvdGilvqlPlpkhidekaileaispeKDVD 116
                                    ln++ +v++il+qlPlp h+d ++++ aispeKD D
  gi|116754543|ref|YP_843661.1|  79 LNKRGDVHAILLQLPLPGHLDPRKAMMAISPEKDAD 114
                                    **********************************88 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1
                                    HHHHHHHHHHHHHHTT-E CS
                    THF_DHG_CYH  42 sevYvrnkkkaceevGie 59 
                                     +vY rn k+  +++ i 
  gi|116754543|ref|YP_843661.1| 182 CHVYTRNLKEHTKDAEIL 199
                                    456666666666666554 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 ?    1.7   0.0     0.042   2.5e+02       4      26 ..     156     178 ..     154     184 .. 0.85
   2 ?   10.3   0.1   9.4e-05      0.56      52      81 ..     178     207 ..     168     240 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.042
                                    EEETTTSHHHHHHHHHHHHTTSS CS
                        Ldh_1_N   4 avvGaaGgiGqslalllankkla 26 
                                    ++vG +  +G++la +l+n++ +
  gi|116754543|ref|YP_843661.1| 156 VIVGHSNVVGKPLAAMLLNRNAT 178
                                    699**************999654 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 9.4e-05
                                    CSTS-EEEEESSGGGGTTESEEEE--S-SS CS
                        Ldh_1_N  52 flsvkvkvsekeeealkdadvvvitagvpr 81 
                                    +++v    +++ +e +kda++ v+ agvpr
  gi|116754543|ref|YP_843661.1| 178 TVQVCHVYTRNLKEHTKDAEILVVAAGVPR 207
                                    444444445599*****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); 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 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 2040.79
//
Query:       gi|116754544|ref|YP_843662.1|  [L=192]
Description: hypothetical protein Mthe_1243 [Methanosaeta thermophila PT]
Scores for complete 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-62  210.0   0.0    2.8e-62  209.8   0.0    1.0  1  DUF2121   Uncharacterized protein conserved in archaea (DUF21
  ------ inclusion threshold ------
       0.11   12.8   0.0       0.18   12.1   0.0    1.5  1  DUF779    Protein of unknown function (DUF779)


Domain annotation for each model (and alignments):
>> DUF2121  Uncharacterized protein conserved in archaea (DUF2121)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  209.8   0.0   3.1e-66   2.8e-62       1     196 []       1     186 [.       1     186 [. 0.98

  Alignments for each domain:
  == domain 1  score: 209.8 bits;  conditional E-value: 3.1e-66
                        DUF2121   1 MslviayigkkgaviagDkReiafrgdeeerekLEeeLYsGeiktdeeLkkkaeelgvkikitddreKvrkvgdvlvGEV 80 
                                    Mslvia+ g++ aviagD+R+iaf+gd++    LEeeLYsG+i++d eL+++a el+++i+i+d+reKv++ gdvlvGEV
  gi|116754544|ref|YP_843662.1|   1 MSLVIAFSGRE-AVIAGDRRSIAFAGDCRL---LEEELYSGRIHDDVELLRRAGELSATIYISDGREKVWRDGDVLVGEV 76 
                                    9********98.****************99...*********************************************** PP

                        DUF2121  81 keisaketkrrRiYatkgayaivelegsevtkkkkgesslivfGnkvtkeiankllkkevkkklslkeiekllkeileev 160
                                    +e+sa+++krrR+Y+t+gay iv++++ +++++ +g +sli++Gn++t+++a k+l+   k        +++++++++ev
  gi|116754544|ref|YP_843662.1|  77 TEVSASSSKRRRVYVTSGAYLIVDVVDGNARISGRGGASLIILGNRHTRDAAGKALQGLGK------ISADAIARVMDEV 150
                                    ********************************************************98877......7899********* PP

                        DUF2121 161 aektasvskeydllkkkkkldkkeaalekaikkDie 196
                                    ++ ta++s+e++llk ++++++++++l++++++D+e
  gi|116754544|ref|YP_843662.1| 151 SAGTATMSREHTLLKITAHHKDPASILMQTFSRDCE 186
                                    **********************************96 PP

>> DUF779  Protein of unknown function (DUF779)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     2e-05      0.18      33      75 ..      63     106 ..      33     116 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2e-05
                         DUF779  33 eflvgdadvllgeiegvpfyiskeqfey.wkhtqltidvvpgrg 75 
                                    e + +d dvl+ge+++v+   sk++  y  +   l++dvv+g++
  gi|116754544|ref|YP_843662.1|  63 EKVWRDGDVLVGEVTEVSASSSKRRRVYvTSGAYLIVDVVDGNA 106
                                    5667899*********9999888777661567889******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1395.09
//
Query:       gi|116754545|ref|YP_843663.1|  [L=210]
Description: molybdopterin-guanine dinucleotide biosynthesis protein [Methanosaeta thermophila PT]
Scores for complete 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-31  107.8   1.1    8.2e-31  107.5   1.1    1.1  1  NTP_transf_3     MobA-like NTP transferase domain
    4.5e-06   26.6   0.1    2.8e-05   24.0   0.1    2.0  2  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
     0.0053   16.4   0.0     0.0087   15.7   0.0    1.5  2  NTP_transferase  Nucleotidyl transferase
  ------ inclusion threshold ------
       0.11   12.4   0.0       0.19   11.6   0.0    1.4  1  CTP_transf_3     Cytidylyltransferase


Domain annotation for each model (and alignments):
>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.5   1.1   1.8e-34   8.2e-31       1     156 [.       4     158 ..       4     164 .. 0.87

  Alignments for each domain:
  == domain 1  score: 107.5 bits;  conditional E-value: 1.8e-34
                                    EEEEEESS-TTTTTTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSHCHHHHHHTTC..TS-EEE-TTSS-SHHHHHHH CS
                   NTP_transf_3   1 aviLAGGrSsRmggdKallplggkpllervldalraagvdevvvvggdeevlaalarl..gvrvvededpgkgplaslaa 78 
                                    aviLAGG+++Rmg +Ka + l+g+pl+e+v++++ +a vdevvvv +d e +++l++   g+rv+ d   g gpla+l++
  gi|116754545|ref|YP_843663.1|   4 AVILAGGEGRRMGAEKASVMLCGRPLIEHVIERILDA-VDEVVVVLRDYEQARRLEGAvsGCRVAIDHACGIGPLAGLQT 82 
                                    79***********************************.**********7777777766559******************* PP

                                    HHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSEEEECCEEEGGGHHHHHHHCTHTTHHHCHHH CS
                   NTP_transf_3  79 alraaadadavlvlacDmPlltpelverllaaaaasgadvvvptyegerghpllfrarllsalaallgdqgarrllrr 156
                                    +++ a +  +++ + cDmP+l++++++ l+  a+ ++++v ++ +  er h +++ ar l+++ +++ ++g+rr+ + 
  gi|116754545|ref|YP_843663.1|  83 GMNVA-RGRYAFATGCDMPFLNSDIIDGLFSVADGHDGAVPILNDIPERLHAVYL-ARQLEDACRIAIARGERRISAP 158
                                    ***98.9*************************98666666555555566555555.5555777889999****99875 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.1   6.3e-09   2.8e-05       3      61 ..       4      56 ..       3      69 .. 0.86
   2 ?   -0.4   0.0      0.18   7.9e+02     204     220 ..     183     199 ..     180     200 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 6.3e-09
                                   EEEECTTSSCTT-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHH CS
                           IspD  3 vvipAAGsGkRmkaglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeq 61
                                   +vi A G+G+Rm+a+  K+ + l g++l+eh ++ +l+  avd++vvv+++++  +++ 
  gi|116754545|ref|YP_843663.1|  4 AVILAGGEGRRMGAE--KASVMLCGRPLIEHVIERILD--AVDEVVVVLRDYE--QARR 56
                                   79**********876..78899***************9..9********9888..4444 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.18
                                    ----SHHHHHHHHHHHH CS
                           IspD 204 lKittpeDlalAeailr 220
                                    + + tp+Dl +Ae i+r
  gi|116754545|ref|YP_843663.1| 183 FNVNTPDDLRSAEDIVR 199
                                    56899********9997 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.9e-06    0.0087       2      61 ..       4      56 ..       3     107 .. 0.82
   2 ?   -3.5   0.0       1.4   6.2e+03     203     232 ..     139     164 ..     135     164 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.9e-06
                                   EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHH CS
                NTP_transferase  2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflv 61
                                   avILaGG+G R+        k  v   g  +li+++++r++   ++e++vvl ++++++ 
  gi|116754545|ref|YP_843663.1|  4 AVILAGGEGRRM-----GAEKASVMLCGR-PLIEHVIERIL-DAVDEVVVVLRDYEQARR 56
                                   8**********7.....456666777777.***********.599**9999999887765 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.4
                                    HHHHHHHHHHHTTEEEEEECSTTEE-EEEX CS
                NTP_transferase 203 eitdilpkaleegkvalaflfkdaeyWsDv 232
                                    +++d+++ a+++g++  +  +     W D+
  gi|116754545|ref|YP_843663.1| 139 QLEDACRIAIARGERRIS--APL--AWLDI 164
                                    677889999998888865..333..37775 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   4.2e-05      0.19      16      45 ..      19      46 ..       5      66 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.2e-05
                                   GGGSEETTEEHHHHHHHHHHHTTTTSEEEE CS
                   CTP_transf_3 16 Knlldlggkpliayvleaalkskafekviv 45
                                   K+   l g+pli++v+e++l+  a+++v+v
  gi|116754545|ref|YP_843663.1| 19 KASVMLCGRPLIEHVIERILD--AVDEVVV 46
                                   6667899**************..7788665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); 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: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1561.13
//
Query:       gi|116754546|ref|YP_843664.1|  [L=284]
Description: rubredoxin-type Fe(Cys)4 protein [Methanosaeta thermophila PT]
Scores for 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-34  116.6   0.4    1.2e-33  116.2   0.4    1.1  1  DJ-1_PfpI       DJ-1/PfpI family
    9.5e-23   80.0   5.6    9.5e-23   80.0   5.6    2.0  2  Rubredoxin      Rubredoxin
     0.0078   16.2   0.0      0.016   15.2   0.0    1.5  1  HypA            Hydrogenase/urease nickel incorporation, meta
  ------ inclusion threshold ------
      0.027   14.4   0.6         45    4.1   0.0    3.3  3  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
      0.027   14.6   2.7       0.16   12.2   2.7    2.2  1  Zn-ribbon_8     Zinc ribbon domain
      0.073   13.2   0.1       0.16   12.1   0.1    1.6  1  PHD_4           PHD-finger
       0.14   11.9   2.3        8.3    6.3   0.4    2.4  2  zinc_ribbon_2   zinc-ribbon domain
        0.2   11.6   6.8        1.3    9.0   1.6    2.3  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
       0.41   10.4   8.1        3.7    7.3   0.5    2.3  2  Rubredoxin_2    Rubredoxin metal binding domain
       0.74    9.7   3.4         20    5.2   0.0    2.3  2  zf-HIT          HIT zinc finger


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 !  116.2   0.4   6.8e-37   1.2e-33       2     164 ..      43     205 ..      42     206 .. 0.95

  Alignments for each domain:
  == domain 1  score: 116.2 bits;  conditional E-value: 6.8e-37
                                    EEEEEEE.TTBEHHHHHHHHHHHHHTTEEEEEEESSTSEEEETTSEEEE-SEEGGGCTCCG-SEEEE--BHHHHH.HHHT CS
                      DJ-1_PfpI   2 kvlvlla.dgvedvElivpvdvlkragikvdvvsvdkeevkgsrGlkvtvdaslddvkaaeyDalvlpGGragpe.rlre 79 
                                    ++l+++a +++++ El +p ++++r g++vdv+s++  + ++++G++v +d+ + +++ ++y a+v +GG    e +l++
  gi|116754546|ref|YP_843664.1|  43 SILMVVApKNYQERELNIPKEAFERSGLDVDVASKGVTTATSMSGESVAIDVDVRNADLSKYRAVVFVGGIGVEElNLHK 122
                                    689999989*************************************************************9965535678 PP

                                    SHHHHHHHHHHHHTT-EEEEETTTHHHHHHTTTTTTSEE--SGGGHHHHHHTTSEE-SSSEEEETTEEEESSGGGHHHHH CS
                      DJ-1_PfpI  80 nekvvelvkefaekgklvaaICagpqlLaaagvlkgrrvTsypavkdklekagakyvdkrvvvdgnlvTsrgpgaaiefa 159
                                    ++ +v+l+k++++kg +vaaIC +p +La+ag+l ++++T+  +  ++l +++ +y+d +vv+dg ++T r p+a+ efa
  gi|116754546|ref|YP_843664.1| 123 DSDYVNLAKSAHDKGIIVAAICLAPNILASAGLLANKNATCADS--TYLVQKNVNYIDAPVVRDGTIITGRDPDASAEFA 200
                                    88*****************************************9..9999****************************** PP

                                    HHHHH CS
                      DJ-1_PfpI 160 lelle 164
                                    ++++ 
  gi|116754546|ref|YP_843664.1| 201 ETIVS 205
                                    *9986 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.78   1.4e+03      13      26 ..       7      20 ..       2      23 .. 0.83
   2 !   80.0   5.6   5.3e-26   9.5e-23       1      47 []     235     281 ..     235     281 .. 0.99

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.78
                                   TTTBBGGGTB-TT- CS
                     Rubredoxin 13 pakGdpdegiapgT 26
                                   ++ G+++  ++p T
  gi|116754546|ref|YP_843664.1|  7 EETGEESGAVQPLT 20
                                   789********988 PP

  == domain 2  score: 80.0 bits;  conditional E-value: 5.3e-26
                                    EEEETTT-BEEETTTBBGGGTB-TT--GGGS-TT-BBTTTB-BGGGE CS
                     Rubredoxin   1 kyeCkvCgyvYdpakGdpdegiapgTkFedlPddWvCPdCgvekeqF 47 
                                    ky+C+vCgy+Ydpa Gdp++gi+pgT+F +lP+dW+CP+Cg+ k++F
  gi|116754546|ref|YP_843664.1| 235 KYRCTVCGYEYDPAAGDPSQGIQPGTPFGELPADWKCPQCGAAKDKF 281
                                    7********************************************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 !   15.2   0.0   8.9e-06     0.016      46      98 ..     209     280 ..     196     283 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8.9e-06
                                    HHHHHHHCC.T.TTT-EEEEE.EE--EEEETTTS-EEECHH.H.HH...............S-TTTSSS-EE CS
                           HypA  46 fafellaegtv.legaeLeie.evpvkvrCreCgkefelee.k.al...............rCpkCgsadve 98 
                                      f+ ++ +    +ga + +    + k+rC++Cg+e++ ++ + +                +Cp+Cg+a+ +
  gi|116754546|ref|YP_843664.1| 209 EEFQSMTGQVEeQSGALMPVGiASSPKYRCTVCGYEYDPAAgDpSQgiqpgtpfgelpadwKCPQCGAAKDK 280
                                    5555555444423344444431456799**********77644433799******************98755 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1     0.047        83       9      29 ..       3      23 ..       1      27 [. 0.94
   2 ?    4.1   0.0     0.025        45      44      57 ..     233     246 ..     216     248 .. 0.88
   3 ?    3.4   0.0     0.042        75      46      55 ..     268     277 ..     262     281 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.047
                 OrfB_Zn_ribbon  9 eykakeyGikveevnpayTSk 29
                                   ey a+e G +   v+p  TS+
  gi|116754546|ref|YP_843664.1|  3 EYEAEETGEESGAVQPLTTSQ 23
                                   8*******************9 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.025
                 OrfB_Zn_ribbon  44 grtfkCpnCgfead 57 
                                    + +++C+ Cg+e+d
  gi|116754546|ref|YP_843664.1| 233 SPKYRCTVCGYEYD 246
                                    56899*****9987 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.042
                 OrfB_Zn_ribbon  46 tfkCpnCgfe 55 
                                     +kCp+Cg+ 
  gi|116754546|ref|YP_843664.1| 268 DWKCPQCGAA 277
                                    6788888865 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   2.7   8.7e-05      0.16       6      34 ..     236     276 ..     235     282 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.7e-05
                    Zn-ribbon_8   6 YrCeeCghefe...........vlqsisdap.....lta.CPeCgs 34 
                                    YrC+ Cg e++           +       p         CP+Cg+
  gi|116754546|ref|YP_843664.1| 236 YRCTVCGYEYDpaagdpsqgiqPGT-----PfgelpADWkCPQCGA 276
                                    ***********99888555444333.....2444445556*****8 PP

>> PHD_4  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   8.8e-05      0.16      32      67 ..     237     274 ..     218     275 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.8e-05
                          PHD_4  32 eCsvCyeivHpeClkek..egegvvnedlpnsWeCpkC 67 
                                     C+vC     p+  + +   ++g+   +lp +W+Cp+C
  gi|116754546|ref|YP_843664.1| 237 RCTVCGYEYDPAAGDPSqgIQPGTPFGELPADWKCPQC 274
                                    588887777777666553345678888*********** PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1     0.013        24       1      11 [.     237     247 ..     237     249 .. 0.79
   2 ?    6.3   0.4    0.0046       8.3       1       7 [.     270     276 ..     270     280 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.013
                  zinc_ribbon_2   1 fCpnCGaelqd 11 
                                    +C+ CG+e ++
  gi|116754546|ref|YP_843664.1| 237 RCTVCGYEYDP 247
                                    69999999876 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0046
                  zinc_ribbon_2   1 fCpnCGa 7  
                                    +Cp+CGa
  gi|116754546|ref|YP_843664.1| 270 KCPQCGA 276
                                    6788876 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   1.6   0.00074       1.3       4      15 ..     235     246 ..     235     248 .. 0.87
   2 ?    5.3   0.3      0.01        18       5      11 ..     269     275 ..     268     278 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00074
                 Zn_ribbon_SprT   4 vYrCtgCgreyt 15 
                                    +YrCt Cg ey+
  gi|116754546|ref|YP_843664.1| 235 KYRCTVCGYEYD 246
                                    7*******8886 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.01
                 Zn_ribbon_SprT   5 YrCtgCg 11 
                                    ++C++Cg
  gi|116754546|ref|YP_843664.1| 269 WKCPQCG 275
                                    9*****9 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.5    0.0021       3.7       1      10 [.     236     245 ..     236     250 .. 0.91
   2 ?    6.6   1.9    0.0035       6.3      15      22 ..     269     276 ..     268     276 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0021
                   Rubredoxin_2   1 YvCsqCGfes 10 
                                    Y+C  CG+e+
  gi|116754546|ref|YP_843664.1| 236 YRCTVCGYEY 245
                                    9*******97 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0035
                   Rubredoxin_2  15 GrCpsCgs 22 
                                    ++Cp+Cg+
  gi|116754546|ref|YP_843664.1| 269 WKCPQCGA 276
                                    9*****96 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   1.4     0.024        44      13      23 ..     235     245 ..     231     245 .. 0.69
   2 ?    5.2   0.0     0.011        20      11      21 ..     266     276 ..     263     277 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.024
                                    SEE-TTT--EE CS
                         zf-HIT  13 kYkCpkCntry 23 
                                    kY+C  C+  y
  gi|116754546|ref|YP_843664.1| 235 KYRCTVCGYEY 245
                                    77787777654 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.011
                                    B-SEE-TTT-- CS
                         zf-HIT  11 pakYkCpkCnt 21 
                                    pa  kCp+C++
  gi|116754546|ref|YP_843664.1| 266 PADWKCPQCGA 276
                                    7788*****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); 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: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2005.71
//
Query:       gi|116754547|ref|YP_843665.1|  [L=202]
Description: dTMP kinase [Methanosaeta thermophila PT]
Scores for 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-38  131.3   0.0    4.4e-38  130.8   0.0    1.2  1  Thymidylate_kin  Thymidylate kinase
     0.0004   20.9   0.0    0.00088   19.8   0.0    1.8  1  AAA_18           AAA domain
    0.00043   20.2   0.0     0.0013   18.6   0.0    2.0  1  dNK              Deoxynucleoside kinase
  ------ inclusion threshold ------
      0.023   14.9   0.0      0.048   13.8   0.0    1.8  1  AAA_33           AAA domain
      0.026   14.8   0.0      0.072   13.4   0.0    1.8  2  AAA_22           AAA domain
      0.077   12.5   0.0        4.4    6.8   0.0    2.2  2  Ploopntkinase1   P-loop Nucleotide Kinase1
      0.087   13.2   0.0        5.3    7.5   0.0    2.7  3  AAA_17           AAA domain
      0.091   12.2   0.0       0.15   11.5   0.0    1.3  1  Arf              ADP-ribosylation factor family
       0.14   11.4   0.0       0.33   10.2   0.0    1.6  2  Zeta_toxin       Zeta toxin


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 !  130.8   0.0   2.2e-41   4.4e-38       1     183 [.      11     183 ..      11     185 .. 0.95

  Alignments for each domain:
  == domain 1  score: 130.8 bits;  conditional E-value: 2.2e-41
                                    EEESTTSSHHHHHHHHHHHHHHTTE.EEEESSSTTSHHHHHHHHHHHTCS---HHHHHHHHHHHHHHTTHHHHHHHHHTT CS
                Thymidylate_kin   1 iEGlDGaGKttqaellkerlkeegikvvltrepggteiGekirelllkeeeleeqteallfaadriehleekikpalkqg 80 
                                    +EG+DGaGKtt+a++l++r+++      +trep+++++Ge++r++            ++lf+ad++ hl++ i p++++g
  gi|116754547|ref|YP_843665.1|  11 LEGIDGAGKTTVARMLRKRFPDFV----FTREPTDGPLGEMARRASG-------FEQLFLFMADHANHLRSCILPSINSG 79 
                                    6********************987....9***************955.......44589********************* PP

                                    -EEEEES-HHHHHHHHHT..TTTTTCHHHHHHGGGTTSE-SEEEEEESSHHHHHTSCCTTSSTTTSHHHHHHHHHHHHHH CS
                Thymidylate_kin  81 ktvivdRylfSslaYqga..kegvdldlvlslnedvllkPdltflldvdpevalkRlakrdeldeeeeeqldflrkvrer 158
                                    ++v++dRy++S +aYqga   +++ ++++++l++   l+Pdlt+l+ +dp+val R++ r+     ++e +  lr v  +
  gi|116754547|ref|YP_843665.1|  80 EVVVSDRYIDSRVAYQGAllRRTISMEWIYELHRPWSLMPDLTLLFRIDPSVALMRCKNRGA--TSIFEMEALLRDVSGN 157
                                    *****************988899************999************************..99************** PP

                                    HHHHHH.TTSTEEEEETTS-HHHHHH CS
                Thymidylate_kin 159 ylelak.ederiliidasksieevhe 183
                                    +  la  e+er++ii+a+++i ev e
  gi|116754547|ref|YP_843665.1| 158 FEILASrEPERFVIINAEREISEVAE 183
                                    *********************99976 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   4.4e-07   0.00088       1      25 [.       9      41 ..       9     151 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 4.4e-07
                         AAA_18  1 IlltGtpGvGKttlakeLskrl.gf.......g 25
                                   I l G+ G+GKtt+a+ L+kr   f        
  gi|116754547|ref|YP_843665.1|  9 ITLEGIDGAGKTTVARMLRKRFpDFvftreptD 41
                                   899*****************9744444444441 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   6.4e-07    0.0013       1      33 [.       9      42 ..       9     194 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 6.4e-07
                                   EEEEESTTSSHHHHHHHHHCCST.CEEEE-HHHH CS
                            dNK  1 ivveGnIgaGKstlvklLskklg.vkvfeEpvdk 33
                                   i++eG  gaGK+t++ +L+k+++ +++ +Ep d 
  gi|116754547|ref|YP_843665.1|  9 ITLEGIDGAGKTTVARMLRKRFPdFVFTREPTDG 42
                                   789*******************99******9985 PP

>> AAA_33  AAA 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     0.048       1      33 [.       8      47 ..       8     152 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.4e-05
                         AAA_33  1 lvllvGlpGsGKstlaerllkklg.avllssdt......l 33
                                   l+ l G  G+GK+t+a+ l k+ + +v+ +++t      +
  gi|116754547|ref|YP_843665.1|  8 LITLEGIDGAGKTTVARMLRKRFPdFVFTREPTdgplgeM 47
                                   68899************99988888888887776655551 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   3.6e-05     0.072       7      30 ..       8      31 ..       2      72 .. 0.84
   2 ?   -1.3   0.0       1.2   2.5e+03      39      62 ..     128     152 ..     101     192 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.6e-05
                         AAA_22  7 ilvvtGesGtGKTtllrrlleqld 30
                                   ++++ G  G+GKTt++r+l+++++
  gi|116754547|ref|YP_843665.1|  8 LITLEGIDGAGKTTVARMLRKRFP 31
                                   57899***************9984 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.2
                         AAA_22  39 rpevvfvtlpsstsskdl.lrellr 62 
                                    +p+v+++ +++ +  + + +++llr
  gi|116754547|ref|YP_843665.1| 128 DPSVALMRCKNRGATSIFeMEALLR 152
                                    6667777777777333333444443 PP

>> Ploopntkinase1  P-loop Nucleotide Kinase1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.017        35      15      43 ..       4      32 ..       1      40 [. 0.85
   2 ?    6.8   0.0    0.0022       4.4      96     155 ..      85     147 ..      76     176 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.017
                 Ploopntkinase1 15 argelyyvkgsngsgkstvpsylaekdpe 43
                                    rg l  + g +g+gk+tv   l ++ p+
  gi|116754547|ref|YP_843665.1|  4 DRGILITLEGIDGAGKTTVARMLRKRFPD 32
                                   688899999***********999999887 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0022
                 Ploopntkinase1  96 eeyikydvlfeg.iipatllstwieklnrparrl..vvlfldtpletclsrvdsrnggedfne 155
                                    + yi+  v ++g ++  t+   wi +l rp   +   +l++  +  + l r + r   + f+ 
  gi|116754547|ref|YP_843665.1|  85 DRYIDSRVAYQGaLLRRTISMEWIYELHRPWSLMpdLTLLFRIDPSVALMRCKNRGATSIFEM 147
                                    568888999998356789************764422566667777888889888877766665 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0027       5.3       2      19 ..      13      30 ..      12      36 .. 0.85
   2 ?    2.6   0.0     0.084   1.7e+02      99     124 ..     116     142 ..      95     149 .. 0.86
   3 ?   -1.2   0.0       1.3   2.5e+03      98     118 ..     162     184 ..     140     197 .. 0.60

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0027
                                   E-TTSSHHHHHHHHHHHH CS
                         AAA_17  2 GgPGsGKgtqceklveky 19
                                   G+ G+GK+t+++ l +++
  gi|116754547|ref|YP_843665.1| 13 GIDGAGKTTVARMLRKRF 30
                                   899********9998876 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.084
                                    HH..SEEEEEE--HHHHHHHHHHH.TT CS
                         AAA_17  99 elkpdaiilleadpeeilerrlkd.rt 124
                                    +l pd+ +l+ +dp + l r++++  t
  gi|116754547|ref|YP_843665.1| 116 SLMPDLTLLFRIDPSVALMRCKNRgAT 142
                                    5779*****************998555 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.3
                                    HHH..SEEEEEE--HH..HHHHH CS
                         AAA_17  98 eelkpdaiilleadpe..eiler 118
                                    ++ +p+ +++++a+ e  e+ er
  gi|116754547|ref|YP_843665.1| 162 ASREPERFVIINAEREisEVAER 184
                                    44455555555555553233333 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   7.4e-05      0.15      15      47 ..       7      42 ..       1      50 [. 0.70

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.4e-05
                                   EEEEEEESTTSSHHHHHHHHHH...SSCEECSSSSS CS
                            Arf 15 lrilllGLDnaGKtTilkklkl...eelvttvPTig 47
                                   + i l G+D+aGKtT+  +l++   + + t  PT g
  gi|116754547|ref|YP_843665.1|  7 ILITLEGIDGAGKTTVARMLRKrfpDFVFTREPTDG 42
                                   556777**********99997622134445666665 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   0.00017      0.33      15      40 ..       5      30 ..       1      35 [. 0.86
   2 ?   -2.5   0.0       1.3   2.5e+03     158     158 ..     174     174 ..     129     196 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00017
                     Zeta_toxin 15 rPklillgGqpGAGKselaellkdel 40
                                   r +li l G  GAGK+++a++l++++
  gi|116754547|ref|YP_843665.1|  5 RGILITLEGIDGAGKTTVARMLRKRF 30
                                   66789999**************9876 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.3
                     Zeta_toxin 158 e 158
                                     
  gi|116754547|ref|YP_843665.1| 174 A 174
                                    2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1488.72
//
Query:       gi|116754548|ref|YP_843666.1|  [L=287]
Description: hypothetical protein Mthe_1247 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.55   10.3   8.0        5.2    7.1   0.7    2.3  2  Defensin_int  Platypus intermediate defensin-like peptide


Domain annotation for each model (and alignments):
>> Defensin_int  Platypus intermediate defensin-like peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.7   0.00029       5.2       6      20 ..     226     240 ..     224     243 .. 0.91
   2 ?    6.6   1.5   0.00043       7.7       3      18 ..     251     266 ..     249     269 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00029
                                    --HHHHTT-EEE-SS CS
                   Defensin_int   6 rPPCedvnGqCqPrG 20 
                                     P C+ vnG+C  rG
  gi|116754548|ref|YP_843666.1| 226 NPQCNWVNGKCYCRG 240
                                    599**********99 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.00043
                                    TSS--HHHHTT-EEE- CS
                   Defensin_int   3 rrrrPPCedvnGqCqP 18 
                                      + P C+ vnGqC  
  gi|116754548|ref|YP_843666.1| 251 CEQNPMCQWVNGQCLC 266
                                    557899********75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 2113.76
//
Query:       gi|116754549|ref|YP_843667.1|  [L=157]
Description: response regulator receiver protein [Methanosaeta thermophila PT]
Scores for complete 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-21   76.8   0.0    1.6e-21   76.6   0.0    1.1  1  Response_reg  Response regulator receiver domain
  ------ inclusion threshold ------
       0.16   10.8   0.0       0.22   10.4   0.0    1.1  1  Epimerase_2   UDP-N-acetylglucosamine 2-epimerase


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.6   0.0   1.8e-25   1.6e-21       1     108 [.       4     123 ..       4     127 .. 0.90

  Alignments for each domain:
  == domain 1  score: 76.6 bits;  conditional E-value: 1.8e-25
                                    EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHH...HHHH.........ESEEEEESSCSSSEHHHHHHHHHHC CS
                   Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealell...keek.........vdlillDinmpgmdGlellkeiree 68 
                                    vl+v+Dd+  ++l+ + +ee ++ ++  ++dg+eal++l      k         +dlillD+++p+mdGl+llkei+++
  gi|116754549|ref|YP_843667.1|   4 VLLVEDDENHASLFIRSFEEMKMGKIYWVSDGDEALDYLlhrG--KyvdsngsprPDLILLDLRLPRMDGLDLLKEIKRT 81 
                                    89*************************************7550..2455566778**********************888 PP

                                    T..TTSEEEEEESSTSHHHHHHHHHCTESEEEESSG-HHHHH CS
                   Response_reg  69 d..pelpviiltahseeedavealkagaddflsKpfdpeeLl 108
                                    +  +++pv+ilt+ ++  d+ +a+   a+ +l Kp+  ++ +
  gi|116754549|ref|YP_843667.1|  82 EdlRSIPVVILTTSNNRHDIRNAYMNHANSYLIKPLGYTKFK 123
                                    87999******************************9877765 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 ?   10.4   0.0   2.4e-05      0.22     206     258 ..      74     127 ..      68     131 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 2.4e-05
                                    HHHHHHHH...H--EEEEE--..HHHHHHHHHHHHH-TTEEEE----HHHHHHHHH CS
                    Epimerase_2 206 alkalake...kdvevvvpvhnnprtrkrlleeleelenvtlieplgyldflsllk 258
                                    +lk+++++   ++++vv+ +    + r+ +++++ +++n +li+plgy++f +l +
  gi|116754549|ref|YP_843667.1|  74 LLKEIKRTedlRSIPVVILTT--SNNRHDIRNAYMNHANSYLIKPLGYTKFKELAR 127
                                    555555552115556666666..788999999999999*************98865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.22s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1234.01
//
Query:       gi|116754550|ref|YP_843668.1|  [L=459]
Description: carbohydrate kinase, FGGY [Methanosaeta thermophila PT]
Scores for 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-31  107.9   0.0    1.7e-30  106.4   0.0    1.8  1  FGGY_N       FGGY family of carbohydrate kinases, N-terminal 
    1.5e-23   83.6   0.1    2.3e-23   83.0   0.1    1.3  1  FGGY_C       FGGY family of carbohydrate kinases, C-terminal 
  ------ inclusion threshold ------
      0.012   15.1   0.0      0.037   13.5   0.0    1.8  3  BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
      0.053   13.2   0.0        0.1   12.2   0.0    1.4  1  Fels1        Fels-1 Prophage Protein-like


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 !  106.4   0.0   3.7e-34   1.7e-30       1     244 [.       1     222 [.       1     223 [. 0.95

  Alignments for each domain:
  == domain 1  score: 106.4 bits;  conditional E-value: 3.7e-34
                                    EEEEEEEESSEEEEEEEETTS-EEEEEEEE--EB-SSTT--EE-HHHHHHHHHHHHHHHHHHCT.-GCCEEEEEEEE-SS CS
                         FGGY_N   1 lilglDcGttstkaivldekgkvvasaqaelelsspkegwaeqdpeeiwqalaeairkvleqagisekqikaIgisgqre 80 
                                    ++lg+D+Gtts+ka ++ ++g++v sa   + + +  e+ +e +pe+ w al+ea+r++         +i++I+i+g + 
  gi|116754550|ref|YP_843668.1|   1 MYLGIDIGTTSVKAGLFTHDGDLVRSAVNRYRQFRSYESFVEMNPEAFWLALCEALRELKPP-----PEISGISIGGHGP 75 
                                    89*******************************************************98655.....5************ PP

                                    -EEEEETTTEESSEEE-TT--TTHHHHHHHHHTTCHCCHHHHHSS-SSTTSHHHHHHHHHHHSCCHHCCHCEEEEHHHHH CS
                         FGGY_N  81 glvllDkndkpLynailwkdrrtaeiveklkeegnekklyektglvlstgftlsklkWlkenepevfekiekflliddyL 160
                                    + v+l    +p+ + +lw  rr++ ++  l+            g  ++++  +    Wl++++ e+f++ +k+  + dy+
  gi|116754550|ref|YP_843668.1|  76 SPVFLGASMEPVAPSVLWMNRRAEREASILSD---------LLGRDVQPSWYVPQTMWLRNHKHEIFARLRKVAQPMDYV 146
                                    ******************************99.........567778999999999************************ PP

                                    HHHHCT--EEEHHHHCTTTSEETTTTEE-HHHHHHTT--GGGS-EEE-TCCEEEEEECCCCCCTT.S-EEEEEEEEEHHH CS
                         FGGY_N 161 iwrLtgqfvtdvtnasesmlfnikklewdeellailgipeelLPklvesseiigelkpelaaklGlkegvpvvggggDqq 240
                                     w+Ltg  +   + as+        l w++e +++++++++++P+ +  +e ig+++p +  ++Gl  g+pv +g+ D +
  gi|116754550|ref|YP_843668.1| 147 AWKLTGSLIA--SVASKEI------LPWSDEEIDAAALDPNMFPEHRVMGELIGYTEPDVLDMTGLRGGIPVFAGAPDFV 218
                                    ******9996..6688754......68***************************************************98 PP

                                    HHHH CS
                         FGGY_N 241 aaal 244
                                     a l
  gi|116754550|ref|YP_843668.1| 219 EAIL 222
                                    8876 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 !   83.0   0.1   5.2e-27   2.3e-23       8     196 ..     239     409 ..     235     411 .. 0.83

  Alignments for each domain:
  == domain 1  score: 83.0 bits;  conditional E-value: 5.2e-27
                         FGGY_C   8 ssflllvgtkpvisehglltpvagedgkpeyalegsiavagslvawlldnlglreeirdageveeslaelaaae.avada 86 
                                    s+ + l  + p+   +g++t  + +  ++ ++  +s + +g  ++w+ +   +      ++    +++++++ae a + +
  gi|116754550|ref|YP_843668.1| 239 SEGIELCWDSPI---EGFYTAPH-PLDENLWHTGASLSTTGLSMEWMASL--V------SK---HPWELAEEAEiAPPGS 303
                                    555555555555...44444333.55689999999***********9999..4......11...3455444444156667 PP

                         FGGY_C  87 ggvvfvpafsglrapywdpdargtitglsssttlahiarAaleavalqlrailealekdsgkpldrlavdGGgskndllm 166
                                    gg++f+p++s +r  +   +a g+++++s +++l+++ rA++e++a ++r +++ ++++ g+++++++++G +s ++l++
  gi|116754550|ref|YP_843668.1| 304 GGLIFLPYLSHERHSI---SAMGAMVNISLNHGLSEVSRAIMEGCACAMRMVIDRFKEK-GVQIKEVRTTGTQSISRLWN 379
                                    *************996...88999********************************888.******************** PP

                         FGGY_C 167 qllAdilgvpVerpktaeatalGaAilAav 196
                                    q+ Adi+g+pV+  +  e+  lGaA++Aa+
  gi|116754550|ref|YP_843668.1| 380 QIKADITGLPVVSQRVLEGEMLGAAMIAAY 409
                                    ***********99999*************8 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 ?   13.5   0.0   8.3e-06     0.037       1      36 [.       3      38 ..       3     107 .. 0.81
   2 ?   -2.9   0.0      0.86   3.8e+03      49      71 ..     130     152 ..     119     179 .. 0.78
   3 ?   -2.3   0.0      0.54   2.4e+03     189     224 ..     336     370 ..     294     407 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.3e-06
                                   EEEEE-SSEEEEEEEETTTEEEEEEEE--TTS-HHH CS
                    BcrAD_BadFG  1 vGiDgGsTttkavlmdekgevlgrgitnsanlesvr 36
                                   +GiD+G+T++ka l++ +g+++  ++   ++++s +
  gi|116754550|ref|YP_843668.1|  3 LGIDIGTTSVKAGLFTHDGDLVRSAVNRYRQFRSYE 38
                                   8*********************99999999888654 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.86
                                    HHHHHHHT--GGGECEE..EEES CS
                    BcrAD_BadFG  49 tealerageeeadieetylvgtg 71 
                                    +e+++r+++ ++ +++++  +tg
  gi|116754550|ref|YP_843668.1| 130 HEIFARLRKVAQPMDYVAWKLTG 152
                                    89999999999999988777766 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.54
                                    --HHHHHHHHHHHHHHHHHHHHHTT---SS.EEEES CS
                    BcrAD_BadFG 189 ekaedIlaglhraialrvialisrsggvtdevtltG 224
                                    e++++I++g + a+ + +  + ++  +++ ev  tG
  gi|116754550|ref|YP_843668.1| 336 EVSRAIMEGCACAMRMVIDRFKEKGVQIK-EVRTTG 370
                                    56667777777777666666666665553.355555 PP

>> Fels1  Fels-1 Prophage Protein-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.3e-05       0.1      10      23 ..     224     237 ..     219     251 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.3e-05
                          Fels1  10 ifspanGVfCDvke 23 
                                      s+++GV+CD+ +
  gi|116754550|ref|YP_843668.1| 224 TASFEKGVVCDKAG 237
                                    569********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 3472.53
//
Query:       gi|116754551|ref|YP_843669.1|  [L=1109]
Description: DNA polymerase II large subunit [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
          0 1282.1   0.0          0 1281.2   0.0    1.4  2  PolC_DP2         DNA polymerase II large subunit DP2
  ------ inclusion threshold ------
       0.02   14.9  16.6        1.5    8.9   0.6    2.9  3  DZR              Double zinc ribbon
        1.6    9.0   7.3       0.77   10.0   0.1    2.6  2  DUF2072          Zn-ribbon containing protein
        2.7    8.0  15.5       0.35   10.9   0.2    3.2  2  HypA             Hydrogenase/urease nickel incorporation, met
        5.3    6.9  11.1        1.3    8.8   0.2    3.6  3  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
        7.5    6.1  28.8        1.2    8.6   1.8    5.2  5  zf-ribbon_3      zinc-ribbon domain
        8.6    6.9  15.7        5.5    7.5   0.1    4.9  6  zf-IS66          zinc-finger binding domain of transposase IS


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 ! 1281.2   0.0         0         0       1     864 []       4     859 ..       4     859 .. 0.98
   2 ?   -3.3   0.1      0.57   1.5e+03     619     649 ..    1026    1060 ..    1017    1096 .. 0.53

  Alignments for each domain:
  == domain 1  score: 1281.2 bits;  conditional E-value: 0
                       PolC_DP2   1 eYfeklekeleeayeiaekarskgldpkeevEiplAkdladRvekllgikgvaerirele.kelsreevalkiakeiaeg 79 
                                    eYfe+le++l+e +eia++arskgldp+++vEip+A dla+Rvekl++i+gvaerire+e + lsree+al+i++++aeg
  gi|116754551|ref|YP_843669.1|   4 EYFERLERGLREEMEIARRARSKGLDPETDVEIPIAVDLAERVEKLVSIPGVAERIREFEvQGLSREEAALAIGRDFAEG 83 
                                    6***********************************************************8899**************** PP

                       PolC_DP2  80 kvgeaeskeeavdkavrtalalltegvvaAPleGiakvkikknddgteylkvyyaGPiRsaGGtaqalsvLvaDyvrkkl 159
                                    ++g+ +s+ +a+d a+rt++alltegvvaAP+eGia+v ++knddg+eylkvyyaGPiRsaGGtaqalsvLvaDyvr+++
  gi|116754551|ref|YP_843669.1|  84 RLGKGASRLDAIDMAIRTSVALLTEGVVAAPIEGIARVGLGKNDDGSEYLKVYYAGPIRSAGGTAQALSVLVADYVRRSM 163
                                    ******************************************************************************** PP

                       PolC_DP2 160 gldrykpreeeieRyveEielYervaslqyspsdeeirlivknipveidGeatedeevsgyrdlervetnrvRGGmllvl 239
                                    g++ ykp++eeieRyveEi lY+r ++lqy+psd+eir+i++n+pv+idGe+te+eevsgyrdl+rvetnrvRGG++lv 
  gi|116754551|ref|YP_843669.1| 164 GIAPYKPTDEEIERYVEEIGLYKRLQHLQYTPSDDEIRTIIRNCPVCIDGEPTEEEEVSGYRDLPRVETNRVRGGIALVS 243
                                    ******************************************************************************** PP

                       PolC_DP2 240 aeGialkakKikkkvkklklegWewleelikaekeekkeeeeekkevkpkekylrdliaGRpvlshpsrkGGfRLrYGRs 319
                                    aeGialk +Kikk+v+kl+++gW wl+ l  +    kk+   +      + k+lrdliaGRpv+shpsr+GGfRLrYGRs
  gi|116754551|ref|YP_843669.1| 244 AEGIALKRPKIKKHVSKLGIDGWGWLDVLGGE----KKDGGGS------SGKFLRDLIAGRPVFSHPSRPGGFRLRYGRS 313
                                    ***************************88776....3333333......58***************************** PP

                       PolC_DP2 320 rntglatagihPatmelldeflavGtqlkverPgKaaavvpvdsiegPtvklknGdvvriddveeal......eikkeve 393
                                    rntgla+agi+Patm++l++fla Gtq+kve+PgKaaav+pv+siegPtv+l+nGdvvridd ++        +++++++
  gi|116754551|ref|YP_843669.1| 314 RNTGLAAAGINPATMMVLNQFLAPGTQIKVEQPGKAAAVAPVSSIEGPTVRLTNGDVVRIDDPSSFPwisspeALRRNIS 393
                                    **************************************************************9987655666699***** PP

                       PolC_DP2 394 eildlGeiLvayGeflennhpLvpasyveewwiqelekaaakkeaeekpsaeealelseeldvpLhPkytylwhdisvee 473
                                    +i+dlGeiLv++G+f+enn+pL+pasy++eww++e+++a+ + + +e+++ ++a++ls++++vpLhP++tylwhdi+ +e
  gi|116754551|ref|YP_843669.1| 394 KIIDLGEILVSFGDFMENNRPLAPASYTFEWWAEEFRRAGGDPAGMEHVDGRTAIRLSRDFGVPLHPDHTYLWHDITLDE 473
                                    ******************************************************************************** PP

                       PolC_DP2 474 lekLaeavaekkkleeeklvleleeevkeiLekllvehkvkeekivieealallkslgldleeekleke..eekdalelv 551
                                    l+ La+a ++ + ++ ++l ++++e+vke+Lekllv+hkv++++iv+e+al+ll +lg+d++ ++ ++e  + ++al++v
  gi|116754551|ref|YP_843669.1| 474 LDLLADAASDGE-IDGDALLMDMREDVKEVLEKLLVHHKVRDGMIVVEDALPLLLCLGVDETGRRWRREdlNADNALSAV 552
                                    *********999.888********************************************99998877766677****** PP

                       PolC_DP2 552 nelsglevrekaptrigaRmGRPeKskeRkmkpavhvLfpigeaggkrrsvkeaakkkgeieveiarrkCkkCgketlea 631
                                    n+lsgl +r++aptrig+RmGRPeKs++R+m+p++hvLfp g++ggk+r v+eaa+ +g iev ++rr+C++Cgke++ +
  gi|116754551|ref|YP_843669.1| 553 NQLSGLVIRARAPTRIGCRMGRPEKSDRREMRPPPHVLFPTGSEGGKSRLVNEAAE-HGFIEVVVERRRCPSCGKEGFAF 631
                                    ********************************************************.9********************** PP

                       PolC_DP2 632 rCeeCgekteeklvCkkceeeveeekcekcekeakavkkkkidlkellekaleklgereekleelkgvkgltskekipEp 711
                                    rCe Cg++te + +C +c+ ++ ++kc++c++e++a+++++id+k +l++ale+lge   ++++++gv+glts++ +pEp
  gi|116754551|ref|YP_843669.1| 632 RCE-CGAHTERVRACLSCGVRA-DDKCPRCGTETSAATRMRIDVKGTLARALESLGE---RVDNIRGVMGLTSRDSTPEP 706
                                    ***.***************988.678*******************************...68****************** PP

                       PolC_DP2 712 leKgilRakhdvsvfkdgtvRyDmtdlplthfrpkeigvsveklrelGYteDieGkplesedqivelkvqDivlsedaae 791
                                    leKg+lRakh+v++fkdgt RyD+tdlplthfrp+eig+sv+ l +lGYt+Di+Gkples+dqi+elkvqD+vl+++a++
  gi|116754551|ref|YP_843669.1| 707 LEKGVLRAKHGVFIFKDGTSRYDLTDLPLTHFRPREIGTSVDALLDLGYTHDIHGKPLESDDQILELKVQDVVLCRNAGD 786
                                    ******************************************************************************** PP

                       PolC_DP2 792 yllkvakfvDdlLeklyglerfYnvekkedLiGklviglaPHtsagvlgRiiGftkasvgyahPyfHaakRRn 864
                                    +ll+v+kf+DdlL+k+ygle++Yn+e+ edLiG+l+iglaPHtsagvl+R+iGft+as+gyahPyfHaakRRn
  gi|116754551|ref|YP_843669.1| 787 WLLRVSKFIDDLLVKFYGLEPYYNAERPEDLIGRLMIGLAPHTSAGVLCRLIGFTRASAGYAHPYFHAAKRRN 859
                                    ************************************************************************9 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.57
                       PolC_DP2  619 rkCkkCgke....tlearCeeCgekteeklvCkkc 649 
                                      +C kC+++     l+  C++Cg +   +++  ++
  gi|116754551|ref|YP_843669.1| 1026 VRCVKCNAKyrrpPLSESCPKCGGRLVLTVHEGSV 1060
                                     45555554311113456677776665554443333 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1      0.08   2.1e+02      28      36 ..     618     626 ..     603     631 .. 0.74
   2 ?    8.6   9.8   0.00073       1.9       1      43 [.     621     668 ..     621     669 .. 0.92
   3 ?    8.9   0.6   0.00057       1.5      12      35 ..    1025    1048 ..    1017    1054 .. 0.69

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.08
                            DZR  28 edrCpsCge 36 
                                     +rCpsCg+
  gi|116754551|ref|YP_843669.1| 618 RRRCPSCGK 626
                                    567888876 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00073
                            DZR   1 CpqCgee..........lppdarfCseCgtklkavaaedrCpsCgekvdpear 43 
                                    Cp+Cg+e          ++++ r C  Cg + +     d+Cp+Cg+++++ +r
  gi|116754551|ref|YP_843669.1| 621 CPSCGKEgfafrcecgaHTERVRACLSCGVRAD-----DKCPRCGTETSAATR 668
                                    9******999999999999*************8.....********9988765 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.00057
                            DZR   12 arfCseCgtklkavaaedrCpsCg 35  
                                     +  C +C++k ++++ ++ Cp+Cg
  gi|116754551|ref|YP_843669.1| 1025 SVRCVKCNAKYRRPPLSESCPKCG 1048
                                     555777777777777777777776 PP

>> DUF2072  Zn-ribbon containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   3.5      0.51   1.3e+03      21      45 ..     620     644 ..     614     695 .. 0.60
   2 ?   10.0   0.1    0.0003      0.77       3      47 ..    1027    1069 ..    1026    1104 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.51
                        DUF2072  21 GCpsCGgkkFlyvkeeekkedvsee 45 
                                     CpsCG + F +  e  ++++ +++
  gi|116754551|ref|YP_843669.1| 620 RCPSCGKEGFAFRCECGAHTERVRA 644
                                    5*********996666666555544 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0003
                        DUF2072    3 kCtkCekvfedgskeilkGCpsCGgkkFlyvkeeekkedvseeke 47  
                                     +C+kC+  ++  +  + + Cp+CGg+  l v+e + ++  + +++
  gi|116754551|ref|YP_843669.1| 1027 RCVKCNAKYR--RPPLSESCPKCGGRLVLTVHEGSVRKYLEVSMK 1069
                                     7*****9997..55689***********99999987775544444 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 ?   -2.7  10.0       2.3   5.8e+03      87      96 ..     635     663 ..     599     674 .. 0.61
   2 ?   10.9   0.2   0.00014      0.35      69      97 ..    1024    1052 ..    1017    1064 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.3
                                    H...................S-TTTSSS- CS
                           HypA  87 l...................rCpkCgsad 96 
                                                        +Cp+Cg++ 
  gi|116754551|ref|YP_843669.1| 635 CgahtervraclscgvraddKCPRCGTET 663
                                    12233444444555666666899999865 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00014
                                     -EEEETTTS-EEECHHHHHS-TTTSSS-E CS
                           HypA   69 vkvrCreCgkefeleekalrCpkCgsadv 97  
                                      +vrC +C+++++    +++CpkCg++ v
  gi|116754551|ref|YP_843669.1| 1024 QSVRCVKCNAKYRRPPLSESCPKCGGRLV 1052
                                     689*********97754789*****9854 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 ?    1.4   0.7      0.11   2.7e+02       2       9 ..     619     626 ..     618     628 .. 0.83
   2 ?    1.4   0.6      0.11   2.7e+02       2       9 ..     654     661 ..     653     663 .. 0.81
   3 ?    8.8   0.2   0.00052       1.3       2      13 ..    1042    1053 ..    1041    1055 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.11
                                    EE-SSS-- CS
                 zf-C4_Topoisom   2 ekCPkCgg 9  
                                    + CP+Cg+
  gi|116754551|ref|YP_843669.1| 619 RRCPSCGK 626
                                    67*****7 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.11
                                    EE-SSS-- CS
                 zf-C4_Topoisom   2 ekCPkCgg 9  
                                     kCP Cg 
  gi|116754551|ref|YP_843669.1| 654 DKCPRCGT 661
                                    69****95 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.00052
                                     EE-SSS--EEEE CS
                 zf-C4_Topoisom    2 ekCPkCggdLvl 13  
                                     e CPkCgg Lvl
  gi|116754551|ref|YP_843669.1| 1042 ESCPKCGGRLVL 1053
                                     78********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 ?   -4.0   1.6       4.4   1.1e+04       4       8 ..     206     210 ..     205     210 .. 0.65
   2 ?    5.3   0.4    0.0053        14       3      10 ..     619     626 ..     617     627 .. 0.82
   3 ?    6.8   1.0    0.0018       4.5       7      24 ..     634     650 ..     633     651 .. 0.93
   4 ?    3.8   0.1     0.016        40       4      10 ..     655     661 ..     653     667 .. 0.71
   5 ?    8.6   1.8   0.00048       1.2       3      26 .]    1026    1051 ..    1024    1051 .. 0.88

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 4.4
                    zf-ribbon_3   4 rCPnC 8  
                                    +CP C
  gi|116754551|ref|YP_843669.1| 206 NCPVC 210
                                    57777 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0053
                    zf-ribbon_3   3 vrCPnCGa 10 
                                    +rCP+CG+
  gi|116754551|ref|YP_843669.1| 619 RRCPSCGK 626
                                    68999996 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0018
                    zf-ribbon_3   7 nCGaplssddnvCpyCGt 24 
                                    +CGa+ ++++++C +CG 
  gi|116754551|ref|YP_843669.1| 634 ECGAH-TERVRACLSCGV 650
                                    5****.***********6 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.016
                    zf-ribbon_3   4 rCPnCGa 10 
                                    +CP+CG+
  gi|116754551|ref|YP_843669.1| 655 KCPRCGT 661
                                    5777764 PP

  == domain 5  score: 8.6 bits;  conditional E-value: 0.00048
                    zf-ribbon_3    3 vrCPnCGa.p.lssddnvCpyCGtkl 26  
                                     vrC +C+a     +    Cp+CG++l
  gi|116754551|ref|YP_843669.1| 1026 VRCVKCNAkYrRPPLSESCPKCGGRL 1051
                                     79******768889*********987 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 ?   -3.1   0.2       4.4   1.1e+04       2      15 ..     205     217 ..     205     222 .. 0.59
   2 ?   -3.8   0.0         7   1.8e+04      10      24 ..     491     504 ..     488     504 .. 0.79
   3 ?    4.7   0.3     0.016        42      33      46 .]     612     625 ..     605     625 .. 0.88
   4 ?    3.3   0.1     0.043   1.1e+02       2      12 ..     654     664 ..     653     674 .. 0.68
   5 ?    7.5   0.1    0.0021       5.5       2      24 ..    1042    1065 ..    1041    1071 .. 0.78
   6 ?   -2.9   0.0       3.7   9.4e+03      19      30 ..    1080    1091 ..    1077    1092 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.4
                        zf-IS66   2 rtCpcCGg.llkpig 15 
                                    r+Cp C   +  p +
  gi|116754551|ref|YP_843669.1| 205 RNCPVCIDgE--PTE 217
                                    5799996544..444 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 7
                        zf-IS66  10 llkpigedrvreeld 24 
                                    ll  + ed v e+l+
  gi|116754551|ref|YP_843669.1| 491 LLMDMRED-VKEVLE 504
                                    56689999.***997 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.016
                        zf-IS66  33 iehirpkyaCpcCe 46 
                                    ie + ++++Cp+C+
  gi|116754551|ref|YP_843669.1| 612 IEVVVERRRCPSCG 625
                                    899**********7 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.043
                        zf-IS66   2 rtCpcCGgllk 12 
                                    ++Cp CG++ +
  gi|116754551|ref|YP_843669.1| 654 DKCPRCGTETS 664
                                    68*****9633 PP

  == domain 5  score: 7.5 bits;  conditional E-value: 0.0021
                        zf-IS66    2 rtCpcCGg.llkpigedrvreeld 24  
                                     ++Cp+CGg l+  + e +vr  l+
  gi|116754551|ref|YP_843669.1| 1042 ESCPKCGGrLVLTVHEGSVRKYLE 1065
                                     68******8866777777886665 PP

  == domain 6  score: -2.9 bits;  conditional E-value: 3.7
                        zf-IS66   19 vreeldipPakf 30  
                                     +r++l++++ ++
  gi|116754551|ref|YP_843669.1| 1080 TRQRLELIQMEI 1091
                                     79*****98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); 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):               7  [number of targets reported over threshold]
# CPU time: 0.79u 0.26s 00:00:01.05 Elapsed: 00:00:00.46
# Mc/sec: 7174.56
//
Query:       gi|116754552|ref|YP_843670.1|  [L=135]
Description: hypothetical protein Mthe_1251 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-21   75.9   0.0    3.1e-21   75.8   0.0    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 !   75.8   0.0   1.7e-25   3.1e-21       2     100 ..       4     109 ..       3     116 .. 0.89

  Alignments for each domain:
  == domain 1  score: 75.8 bits;  conditional E-value: 1.7e-25
                                    EEEEEE-TTSBHHHHHHHHHHHHT-SSEEEEEEEEEEEEEE.EEECTTT......EE-S-EEEEEEEEEEEETT....EE CS
                         DUF296   2 phvlrlepGediveaieefarkrgiraacvlsaiGavsnvt.rladgee......kllgrfeilslsGtilpdg....lH 70 
                                    ++++ le G+di++ai  +a +r+i ++++ s+iGa+s+++ +++d++e      +++g +ei s++G+i+ ++    +H
  gi|116754552|ref|YP_843670.1|   4 MMMVGLEYGSDIMDAIRGVAADRSIDSGFF-SVIGALSSANlAYYDQTEkvyrkrSFEGAYEIASCTGNISLKDgerfIH 82 
                                    578889************************.**************9999999999899**************44489*** PP

                                    EEEEEEETTSEEEEEEEEEE.EEEEEEEEE CS
                         DUF296  71 lhvslagedgqvvgGhlaegplvaattvev 100
                                     h++la+e+ + +gGhl+ g  +  + +e+
  gi|116754552|ref|YP_843670.1|  83 AHIVLADENYNLIGGHLLGG-RI--FAAEL 109
                                    ******************77.55..44444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); 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 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 990.94
//
Query:       gi|116754553|ref|YP_843671.1|  [L=332]
Description: phosphoribosylaminoimidazole synthetase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-21   77.6   0.0    2.1e-21   76.7   0.0    1.4  1  AIRS_C    AIR synthase related protein, C-terminal domain
    3.8e-16   59.5   0.3      6e-16   58.9   0.3    1.3  1  AIRS      AIR synthase related protein, N-terminal domain


Domain annotation for each model (and alignments):
>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.7   0.0   2.3e-25   2.1e-21       2     149 ..     170     323 ..     169     328 .. 0.89

  Alignments for each domain:
  == domain 1  score: 76.7 bits;  conditional E-value: 2.3e-25
                                    TTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTT......TSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHH CS
                         AIRS_C   2 pGdvliltgslGlggagtslkrkileeegldds......avqlgdvlleptliyvkralaalkglvkaahDvTgGGLlga 75 
                                     Gd++++++s Gl+++g+ l+r+i+e++g  ++      ++ +g+ ll+pt+iy   ++ +++ +v++++++Tg GLl  
  gi|116754553|ref|YP_843671.1| 170 IGDAVVGVPSTGLHSNGYTLARRIIESSGYTYFdkmpgdSRSIGEILLTPTRIYIEVLELLQRCDVHGLAHITGSGLLK- 248
                                    7****************************9999*****7677************988887778**************95. PP

                                    HHHHHHTTTEEEEEECG..THHHHHHHH.....HHHHHHHCSTTTEEEEEEEHGGH.HHHHHHHHHTTCCCEEEEEEEEE CS
                         AIRS_C  76 laemapasgvgaeidld..kvpifdele.....splemllsensGrllvavppeea.davlaileeeglpeaavIGevta 147
                                    l+++ +   +g+ei+ +    p+f+ l+     ++ em++++n+G ++v+v pee+ d +++i++       +vIG++++
  gi|116754553|ref|YP_843671.1| 249 LHRITD---LGFEITDPiePHPVFKFLQelggvDDVEMYRTFNMGMGFVVVLPEEQaDDACRIMGP----GSKVIGRIVE 321
                                    888855...6777777777777777777777************************99********4....479*****99 PP

                                    SS CS
                         AIRS_C 148 ke 149
                                    ++
  gi|116754553|ref|YP_843671.1| 322 SG 323
                                    75 PP

>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.9   0.3   6.7e-20     6e-16       4      94 .]      54     157 ..      20     157 .. 0.92

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 6.7e-20
                                    EEEEEEEEEE.EECCTCCCC....HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.....HHHHHHHHHHHHHHHTT-EEE CS
                           AIRS   4 avvvttdshnrpvlvepvhf....iGakavavnlsDlaamGArPlalllslalp.....wleevvrglaeaaeelgvplv 74 
                                    a+++ttd++++++l+++       iG  ++a+n++Dl+a GA+Pla++++la++       e+++ gl+++ae  ++++v
  gi|116754553|ref|YP_843671.1|  54 AIAMTTDGVGSKILIANAMRkwdtIGIDCIAMNVNDLLAIGAEPLAFVDYLAVErvdpeVSEQIAVGLQKGAEISNISIV 133
                                    479************764445677**********************************999******************* PP

                                    EEEEEEESS....EEEEEEEEEEE CS
                           AIRS  75 gGdtsfsne....ptisvtavGlv 94 
                                    gG+t++ +e    + ++ ta+G v
  gi|116754553|ref|YP_843671.1| 134 GGETASLPEmirgLDLAGTAIGYV 157
                                    ******999999999******976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); 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: 00:00:00.41
# Mc/sec: 2424.05
//
Query:       gi|116754554|ref|YP_843672.1|  [L=465]
Description: aspartate kinase [Methanosaeta thermophila PT]
Scores for complete 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  165.8   0.4    2.4e-48  164.8   0.0    1.7  2  AA_kinase      Amino acid kinase family
    5.1e-26   90.1   2.6      9e-13   47.7   0.1    3.1  3  ACT            ACT domain
    2.8e-25   87.9   0.5    9.8e-14   50.9   0.2    2.6  2  ACT_7          ACT domain
    7.6e-05   23.6   0.1      0.017   16.1   0.1    2.4  2  LytR_C         LytR cell envelope-related transcriptional att
     0.0015   18.5   0.5      0.048   13.7   0.1    2.8  3  ACT_6          ACT domain
  ------ inclusion threshold ------
      0.059   13.4   0.0       0.11   12.4   0.0    1.4  1  CarS-like      CDP-archaeol synthase
       0.46   10.8   2.2         16    5.9   0.2    2.8  3  Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor


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 !  164.8   0.0   9.5e-52   2.4e-48       2     240 ..       3     286 ..       2     287 .. 0.88
   2 ?   -1.6   0.1      0.65   1.7e+03      25      55 ..     387     422 ..     324     454 .. 0.54

  Alignments for each domain:
  == domain 1  score: 164.8 bits;  conditional E-value: 9.5e-52
                                    EEEEEE-TTCCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--.HHHHHHHHHH.TCCCCCHHHC................ CS
                      AA_kinase   2 rvVvKlGGssltdkeeaslrrlaeqiaalkesgnklvvVhGg.gsftdgllal.ksglssgelaa............glr 67 
                                    r+V+K+GG s++d+ +  lr++ e ++ + +sgn++vvV+++  ++td ll+  +s  + g+               ++ 
  gi|116754554|ref|YP_843672.1|   3 RLVMKFGGVSVADGRR--LRNVGELVRGF-SSGNEIVVVTSAlQGVTDDLLECaRSSAKYGRVSDvddfimrlaekhEQA 79 
                                    89**************..***********.**********************9633333333333566666666666444 PP

                                    E..HHHHHHHHH...............................HHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE. CS
                      AA_kinase  68 stleeagevatr...............................dalaslgerlvaallaaglpavglsaaaldateagr. 115
                                     t+++  e++++                               d++ s+ge+l+a +l+  ++++g+ +++++  e g+ 
  gi|116754554|ref|YP_843672.1|  80 ITDAISDEAIRDeirsdirkkidtlekayvgicylgeltprsiDYISSFGEQLSAPILSGVFRDMGIESRYYTGGEVGIi 159
                                    445554554444888889999999999*************************************************999* PP

                                    .....HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETTTE...EEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESST CS
                      AA_kinase 116 ...degsdgnvesvdaeaieelleagvvpvltgfigldeege...lgrgssDtiaallAealgAdkliiltdVdGVydad 189
                                       d+g+++++e+  +   ++ll  + +pv+tgfi++de+g    lgrg+sD +a+++++a++Ad+++++++++GV++ad
  gi|116754554|ref|YP_843672.1| 160 tnsDYGNAKPLEKSYSLIAKKLLPIKGIPVVTGFIAMDENGIittLGRGGSDFSASIIGAAIDADEIWFWKETSGVLTAD 239
                                    **7777777777777777777775567***************************************************** PP

                                    TTTCCTTCECCEEEHHHCHHCSSS.TTTHHHHCHHHHHHHHHCTT-EEEEE CS
                      AA_kinase 190 pkkvpdarllpeisvdeaeesaselatgGmkvkhpaalaaarrggipvvIt 240
                                    pk++p+a+ +p+is+ ea+e    l+ +G+kv+hp+a+++a r+gipv+++
  gi|116754554|ref|YP_843672.1| 240 PKIDPSAKTIPTISYIEAME----LSFFGAKVLHPRAIEPAIRKGIPVRVK 286
                                    ********************....*************************96 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.65
                                    HHHHHHHHHTTEEEEEE--H.....HHHHHHHHH..TC CS
                      AA_kinase  25 eqiaalkesgnklvvVhGgg.....sftdgllal..ks 55 
                                    + i+    ++  +v V+G g     +++ +l ++  ++
  gi|116754554|ref|YP_843672.1| 387 RGISHN--KDVCVVAVVGSGmagtpGVAGRLFSAmgRA 422
                                    233332..222233333333233444444444444444 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.5   6.3e+03      49      64 ..      80      95 ..      79      98 .. 0.81
   2 !   47.7   0.1   3.5e-16     9e-13       9      64 ..     330     379 ..     326     381 .. 0.87
   3 !   41.3   0.0   3.7e-14   9.5e-11       6      64 ..     404     456 ..     399     459 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.5
                                   EEEHHHHHHHHHHHHT CS
                            ACT 49 vvdeedleevlealkk 64
                                   ++d+ ++e++ +++++
  gi|116754554|ref|YP_843672.1| 80 ITDAISDEAIRDEIRS 95
                                   6889999999999987 PP

  == domain 2  score: 47.7 bits;  conditional E-value: 3.5e-16
                                    SSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHT CS
                            ACT   9 DrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkk 64 
                                    + PG++arvf+ala++g+Ni++i+q+ss      ++++  vv+e+dl++++eal++
  gi|116754554|ref|YP_843672.1| 330 GTPGVAARVFSALANAGVNIIMISQGSS------EANISMVVEEKDLDKAEEALRR 379
                                    68**************************......7788888888888888888875 PP

  == domain 3  score: 41.3 bits;  conditional E-value: 3.7e-14
                                    EEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHT CS
                            ACT   6 gvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkk 64 
                                    g+++ PG+++r+f+a++++giN+++i+q+ss      ++++ +vv ++d + +++++++
  gi|116754554|ref|YP_843672.1| 404 GMAGTPGVAGRLFSAMGRAGINVRMISQGSS------EHNISFVVAAKDGKRAVQKIHR 456
                                    7899***************************......7888888888888888888876 PP

>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.9   0.2   3.8e-17   9.8e-14       5      65 .]     317     379 ..     313     379 .. 0.95
   2 !   34.8   0.0   3.9e-12     1e-08       3      64 ..     392     455 ..     390     456 .. 0.94

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 3.8e-17
                                    EEEEEEE-S-.---SS--HHHHHHHHHHTTT---EEEE...-SS-EEEEEEGGGHHHHHHHHHH CS
                          ACT_7   5 gwiklsvvgsglpfdvtGivaklaspLaeagIsifqiS...tyrtdyiLVpeedlekAveaLhe 65 
                                    +++ l+v+g+ + + ++G++a+++s+La+ag++i +iS   ++  ++ +V+e+dl+kA eaL++
  gi|116754554|ref|YP_843672.1| 317 NVALLNVSGAEMIG-TPGVAARVFSALANAGVNIIMISqgsSEANISMVVEEKDLDKAEEALRR 379
                                    7889********88.***********************************************85 PP

  == domain 2  score: 34.8 bits;  conditional E-value: 3.9e-12
                                    EEEEEEEEE-S-.---SS--HHHHHHHHHHTTT---EEEE...-SS-EEEEEEGGGHHHHHHHHH CS
                          ACT_7   3 edgwiklsvvgsglpfdvtGivaklaspLaeagIsifqiS...tyrtdyiLVpeedlekAveaLh 64 
                                    ++++ ++ vvgsg+++ ++G++ +l+s+  +agI++ +iS   +++ ++++V ++d ++Av+  h
  gi|116754554|ref|YP_843672.1| 392 NKDVCVVAVVGSGMAG-TPGVAGRLFSAMGRAGINVRMISqgsSEHNISFVVAAKDGKRAVQKIH 455
                                    678889********99.********************************************9877 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 !   16.1   0.1   6.8e-06     0.017       4      82 ..     318     402 ..     315     404 .. 0.68
   2 ?    5.2   0.0     0.017        43      10      62 ..     406     458 ..     404     464 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.8e-06
                         LytR_C   4 VeVlNgtg.....vsGlAarvadaLeerGftvgevgn.agnadee.ttivyreaaaaaakalaaalglgelqedsvkdas 76 
                                    V+ lN +g     ++G+Aarv +aL+++G ++  +++ +++a  + + +v +++ ++a +al+++l+  e++   + +++
  gi|116754554|ref|YP_843672.1| 318 VALLNVSGaemigTPGVAARVFSALANAGVNIIMISQgSSEA--NiSMVVEEKDLDKAEEALRRDLP-REIVRGISHNKD 394
                                    6677777777777*********************88525455..2466663333334777******5.554444444444 PP

                         LytR_C  77 ..vtvvlG 82 
                                      v+ v+G
  gi|116754554|ref|YP_843672.1| 395 vcVVAVVG 402
                                    67777777 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.017
                         LytR_C  10 tgvsGlAarvadaLeerGftvgevgnagnadee.ttivyreaaaaaakalaaal 62 
                                    +g++G+A+r+ +a+ ++G +v  +++ ++  ++ + +v+ +++++a +++ +++
  gi|116754554|ref|YP_843672.1| 406 AGTPGVAGRLFSAMGRAGINVRMISQGSSE-HNiSFVVAAKDGKRAVQKIHREF 458
                                    699*******************98854444.22466665333334666766665 PP

>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       3.6   9.2e+03       7      31 ..     193     217 ..     189     217 .. 0.78
   2 !   13.7   0.1   1.9e-05     0.048      12      64 ..     331     383 ..     318     387 .. 0.78
   3 ?    1.9   0.0     0.086   2.2e+02      13      61 ..     409     457 ..     400     463 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.6
                          ACT_6   7 vtGpdrpGltasLtsvlaefgvnil 31 
                                    ++ +d  G++  L +  ++f ++i+
  gi|116754554|ref|YP_843672.1| 193 FIAMDENGIITTLGRGGSDFSASII 217
                                    5668999999999888888888875 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1.9e-05
                          ACT_6  12 rpGltasLtsvlaefgvnilDieqavihgrlsLgllvsgp..edalarlekaLlf 64 
                                     pG+ a+++s+la  gvni+ i q   + + s  ++v+ +  ++a+++l+++L++
  gi|116754554|ref|YP_843672.1| 331 TPGVAARVFSALANAGVNIIMISQGSSEANIS--MVVEEKdlDKAEEALRRDLPR 383
                                    59**********************98777655..566666568888888888887 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.086
                          ACT_6  13 pGltasLtsvlaefgvnilDieqavihgrlsLgllvsgpedalarleka 61 
                                    pG+  +L+s+  + g+n+  i q   + + s+++  +  ++a++++ ++
  gi|116754554|ref|YP_843672.1| 409 PGVAGRLFSAMGRAGINVRMISQGSSEHNISFVVAAKDGKRAVQKIHRE 457
                                    99*********************99999988888776666666666665 PP

>> CarS-like  CDP-archaeol synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   4.4e-05      0.11      34      76 ..      10      52 ..       6      85 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.4e-05
                      CarS-like 34 GktlvdGrrliGdGvtyrGtvaGvlvGvlvgliqglleklsil 76
                                   G +++dGrrl   G   rG+ +G  + v+++ +qg+ ++l   
  gi|116754554|ref|YP_843672.1| 10 GVSVADGRRLRNVGELVRGFSSGNEIVVVTSALQGVTDDLLEC 52
                                   67899*******************************9998653 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 ?    5.9   0.2    0.0064        16      48      93 ..     319     364 ..     290     367 .. 0.84
   2 ?   -1.8   0.0       1.6   4.1e+03      41      64 ..     380     404 ..     359     407 .. 0.61
   3 ?    3.7   0.0      0.03        77      51      73 ..     434     456 ..     417     458 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0064
                                    HHHHHTT-SEEEESSSCHHHHHHHCTTTSEEEES-SSBHHHHHHHH CS
                  Nitro_FeMo-Co  48 qllaeegvdvvivgkiGpralakleaagievykgaggtveealkev 93 
                                    +ll  +g++++ + ++  r + +l++ag+ +++ + g+ e+ +  v
  gi|116754554|ref|YP_843672.1| 319 ALLNVSGAEMIGTPGVAARVFSALANAGVNIIMISQGSSEANISMV 364
                                    345559***************************9999998888765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.6
                                    CSSTHHHHHHHH.TT-SEEEESSSC CS
                  Nitro_FeMo-Co  41 ggggklaqllae.egvdvvivgkiG 64 
                                    + ++ +++ ++  ++v vv v++ G
  gi|116754554|ref|YP_843672.1| 380 DLPREIVRGISHnKDVCVVAVVGSG 404
                                    4555556655555899888888877 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.03
                                    HHTT-SEEEESSSCHHHHHHHCT CS
                  Nitro_FeMo-Co  51 aeegvdvvivgkiGpralaklea 73 
                                    +e++++ v+++k G+ra++k+ +
  gi|116754554|ref|YP_843672.1| 434 SEHNISFVVAAKDGKRAVQKIHR 456
                                    679***************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (465 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); 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: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 3253.57
//
Query:       gi|116754555|ref|YP_843673.1|  [L=1074]
Description: carbamoyl phosphate synthase large subunit [Methanosaeta thermophila PT]
Scores for 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-107  355.3   0.6    9.4e-71  237.7   0.1    2.2  2  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    1.6e-43  147.9   0.0    3.9e-43  146.7   0.0    1.7  1  CPSase_L_D3      Carbamoyl-phosphate synthetase large chain, 
      9e-20   70.7   2.1    4.4e-18   65.3   0.0    4.3  5  MGS              MGS-like domain
    1.5e-19   70.2   0.1    1.4e-09   37.8   0.0    2.6  2  ATP-grasp        ATP-grasp domain
    3.2e-15   56.2   0.0    2.1e-06   27.4   0.0    2.6  2  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    8.6e-15   54.6   0.1      2e-06   27.6   0.0    2.7  2  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T
      2e-13   50.7   0.2    1.4e-05   25.2   0.0    2.6  2  ATP-grasp_3      ATP-grasp domain
    2.2e-07   30.9   0.0      0.018   14.8   0.0    2.5  2  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr
    5.5e-06   26.0   0.1     0.0042   16.6   0.0    3.2  3  ATP-grasp_5      ATP-grasp domain
    2.1e-05   24.2   0.0      0.073   12.6   0.0    2.8  2  ATP-grasp_2      ATP-grasp domain
    0.00055   19.6   0.0      0.021   14.4   0.0    2.7  2  RimK             RimK-like ATP-grasp domain
  ------ inclusion threshold ------
      0.047   14.2   1.2         15    6.2   0.0    4.1  4  MerR-DNA-bind    MerR, DNA binding
      0.082   12.8   0.0       0.24   11.3   0.0    1.7  1  YjeF_N           YjeF-related protein N-terminus
      0.096   12.3   0.0         11    5.7   0.0    2.8  2  STAS             STAS domain
        0.1   12.1   0.0        4.7    6.6   0.0    2.8  3  Epimerase        NAD dependent epimerase/dehydratase family
       0.18   11.7   0.0        1.2    9.0   0.0    2.4  3  PS_pyruv_trans   Polysaccharide pyruvyl transferase


Domain annotation for each model (and alignments):
>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.7   0.1   8.4e-74   9.4e-71       1     210 [.     128     331 ..     128     332 .. 0.99
   2 !  116.1   0.0   1.4e-36   1.5e-33       1     210 [.     669     871 ..     669     872 .. 0.96

  Alignments for each domain:
  == domain 1  score: 237.7 bits;  conditional E-value: 8.4e-74
                                    SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHST CS
                    CPSase_L_D2   1 DkesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgn 80 
                                    D++ +k+a+++i++pv +s a+  ++leea ++ ke+g P i+++a++lGG+G++var++eel+ +++++l+ ++     
  gi|116754555|ref|YP_843673.1| 128 DRDLFKKAMERIGEPVPRSIAV--TSLEEAEEAMKELGLPLIVRPAYTLGGSGGGVARTHEELMRICEMGLKRSR----I 201
                                    9*******************99..**************************************************7....9 PP

                                    S-EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCEC..TCCCCEEEES-SS--HHHHHHHHHHHHHHHHHHT-EEEE CS
                    CPSase_L_D2  81 kqvlvekslkgpkeiEvevlrDakgnvitvcerenslql..rtqkvievAPsqtLtdeerqalreaavkvvrevgvvgag 158
                                    +qvl+e+s+ g+ e+E+ev+rD+++++it+c++en++++  +t+++i+v P qtL+d+e q+lr+aa++++r++g++g++
  gi|116754555|ref|YP_843673.1| 202 HQVLLEESVIGWTEVEYEVMRDSNNTCITICNMENMDPMgiHTGESIVVTPIQTLSDHEIQMLRSAAINIIRALGIEGGC 281
                                    ******************************************************************************** PP

                                    EEEEEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT--GCG CS
                    CPSase_L_D2 159 tveflldpkskeyyviEvNtRlsvesalaekaTGldlvkeaakialgekLee 210
                                    +++f++   ++ey viEvN+R+s++sala+kaTG++++ ++akia g +L+e
  gi|116754555|ref|YP_843673.1| 282 NIQFAVR--NGEYRVIEVNPRVSRSSALASKATGYPIARVTAKIAIGLTLDE 331
                                    ******9..6****************************************97 PP

  == domain 2  score: 116.1 bits;  conditional E-value: 1.4e-36
                                    SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHST CS
                    CPSase_L_D2   1 DkesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgn 80 
                                    D+e+++++l+k+++p  ++ +a   + eea ++akeigyPv++++++ lGG+ m ++++e+ l+  +++a++ ++    +
  gi|116754555|ref|YP_843673.1| 669 DRERFNKLLNKLGIPQPKAGIA--YSPEEAKRVAKEIGYPVLVRPSYVLGGRAMEIVYDESGLELYMREAVRVSH----E 742
                                    9***************999999..9*************************************************6....9 PP

                                    S-EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCEC..TCCCCEEEES-SS--HHHHHHHHHHHHHHHHHHT-EEEE CS
                    CPSase_L_D2  81 kqvlvekslkgpkeiEvevlrDakgnvitvcerenslql..rtqkvievAPsqtLtdeerqalreaavkvvrevgvvgag 158
                                    + vl++ +l++  ei+v+ ++D ++  i    +e + +   + +++  + P qtL ++   +++    +++ +++v+g  
  gi|116754555|ref|YP_843673.1| 743 HPVLIDDFLQNAVEIDVDAVSDGRDVLIGA-IMEHIEEAgiHSGDSACMIPPQTLPEDVIATVKDYVRRIALALDVKGII 821
                                    ************************977765.5777777678*************************************** PP

                                    EEEEEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT--GCG CS
                    CPSase_L_D2 159 tveflldpkskeyyviEvNtRlsvesalaekaTGldlvkeaakialgekLee 210
                                    +++ +++  ++  yv+E N+R s+  +  +ka Gl+l+k+aak+ +g++L+e
  gi|116754555|ref|YP_843673.1| 822 NIQMAYK--DGIVYVLEANPRSSRTIPFVSKAVGLPLAKIAAKVMAGNTLRE 871
                                    ******9..69***************************************97 PP

>> CPSase_L_D3  Carbamoyl-phosphate synthetase large chain, oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.7   0.0   3.5e-46   3.9e-43       3     122 .]     422     537 ..     420     537 .. 0.96

  Alignments for each domain:
  == domain 1  score: 146.7 bits;  conditional E-value: 3.5e-46
                    CPSase_L_D3   3 lkeptdeRifaiaealrrglsveeiheltkidpwFLekleelvelekelkkkkkeldeellreakklGfsDkqiaellee 82 
                                    l++ptdeR+fai++alrrg+sveei++l++idp+F+e++++++++e+elk+    l+++ lr+akk+Gf D++iael++ 
  gi|116754555|ref|YP_843673.1| 422 LRTPTDERLFAIYQALRRGFSVEEISQLSMIDPYFIERIQNIIRMEDELKNG---LTPDRLRRAKKMGFLDSRIAELVG- 497
                                    89**********************************************9987...8*********************87. PP

                    CPSase_L_D3  83 eeeeevrelrkklgilpvykrvDtcAaeFeaetpYlYstY 122
                                     ++eev+++r +lgi p+yk+vDtcAaeF+a+tpY+YstY
  gi|116754555|ref|YP_843673.1| 498 LSREEVTDYRLSLGIIPTYKMVDTCAAEFAASTPYYYSTY 537
                                    67778**********************************9 PP

>> MGS  MGS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.87   9.7e+02      50      76 ..      23      57 ..       6      84 .. 0.74
   2 ?    0.1   0.0      0.85   9.6e+02      48      93 ..     279     327 ..     249     329 .. 0.76
   3 ?   -1.2   0.0       2.1   2.4e+03      51      94 ..     642     685 ..     610     686 .. 0.82
   4 ?   -3.1   0.0       8.3   9.3e+03      50      66 ..     768     791 ..     750     820 .. 0.54
   5 !   65.3   0.0   3.9e-21   4.4e-18       1      95 []     951    1037 ..     951    1037 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.87
                                   H........HHHHHHHTTSCCEEEEE--THHHHHH CS
                            MGS 50 v........eildaikngeidlvintlypfkatva 76
                                            +  + ++++++++v ++ +p + ++ 
  gi|116754555|ref|YP_843673.1| 23 AaefdfsgsQACKSLREEGVEVVLVNSNPATIMTD 57
                                   34555555577788999999999999998876654 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.85
                                    HCHHHHHHHHTTSCCEEEEE--THHHHHH...CHHHHHHHHHHHTTSHE CS
                            MGS  48 grveildaikngeidlvintlypfkatva...kdgykirraaenidIpl 93 
                                    g ++i+ a++nge+ ++ +++   ++        gy i+r+  +i I+l
  gi|116754555|ref|YP_843673.1| 279 GGCNIQFAVRNGEYRVIEVNPRVSRSSALaskATGYPIARVTAKIAIGL 327
                                    4457899999999999988888777665556778999999999999997 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 2.1
                                    HHHHHHHTTSCCEEEEE--THHHHHHCHHHHHHHHHHHTTSHEE CS
                            MGS  51 eildaikngeidlvintlypfkatvakdgykirraaenidIplp 94 
                                     +++++k  + + vi  ++p +  +a+d  ++ ++ ++ +Ip p
  gi|116754555|ref|YP_843673.1| 642 PLEKELKRRGLKTVILGTSPDSIDIAEDRERFNKLLNKLGIPQP 685
                                    6788999999999***9***999999999999999999999965 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 8.3
                                    H...HHHHHHHTTSCC....EEEE CS
                            MGS  50 v...eildaikngeid....lvin 66 
                                    v    i+++i++ +i+    +  +
  gi|116754555|ref|YP_843673.1| 768 VligAIMEHIEEAGIHsgdsACMI 791
                                    255567888888888766653333 PP

  == domain 5  score: 65.3 bits;  conditional E-value: 3.9e-21
                                     THHHHHHHHHHTTCEEEEEHHHHHHHHHTT--EEECCCCHSTGSGGTHCHHHHHHHHTTSCCEEEEE--THHHHHHCH CS
                            MGS    1 glvelakklkelgfellATgGTakllkeagipvtevvektgegerlggrveildaikngeidlvintlypfkatvakd 78  
                                     +++e+a++++++g +++AT GT  +l+ +g+p +e v k+ +g +++    +ld i+ ge++l+int++++++ +  d
  gi|116754555|ref|YP_843673.1|  951 EIAEVARRFVNAGLKIIATDGTSGYLRGSGVP-AERVRKIYHG-SPN----VLDYIRRGEVKLIINTPTTKQSVK--D 1020
                                     5899****************************.9999999999.899....*******************99886..* PP

                                     HHHHHHHHHHTTSHEES CS
                            MGS   79 gykirraaenidIplpt 95  
                                     g++irr a+++++p++t
  gi|116754555|ref|YP_843673.1| 1021 GFQIRRSAVDYHVPYIT 1037
                                     ***************98 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0   4.2e-10   4.7e-07       3     161 ..     138     302 ..     136     310 .. 0.85
   2 !   37.8   0.0   1.2e-12   1.4e-09       2     160 ..     678     841 ..     677     844 .. 0.90

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 4.2e-10
                                    TTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC....GTTCEEEEE----SEEE CS
                      ATP-grasp   3 klglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal....keekvivEefvpfekEl 78 
                                    + g pvpr +av+s ee+eea++elglp++v+ +     G G  v r +e+l ++ e+     + ++v++Ee v   +E+
  gi|116754555|ref|YP_843673.1| 138 RIGEPVPRSIAVTSLEEAEEAMKELGLPLIVR-PAYTLGGSGGGVARTHEELMRICEMGlkrsRIHQVLLEESVIGWTEV 216
                                    56779***************************.99999999999999999999999887777777899******999*** PP

                                    EEEEEEETTC-EEE--EEEEEEETTEEE...EEEECEE-SCH.HHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCTEEEE CS
                      ATP-grasp  79 svlvvrsaeGetafypvvetvqedgilr...lsvapaevsek.aqkkaeeiakkiveeLggvGvfavElFvledgellvn 154
                                       v+r+ + +  ++  +e++   gi     ++v p +  ++ + +  ++ a +i+++Lg+ G   + + v  +ge  v 
  gi|116754555|ref|YP_843673.1| 217 EYEVMRDSNNTCITICNMENMDPMGIHTgesIVVTPIQTLSDhEIQMLRSAAINIIRALGIEGGCNIQFAVR-NGEYRVI 295
                                    *********999999999****9999853336788877666514455555666**********999986665.9**99** PP

                                    EEESS-- CS
                      ATP-grasp 155 ElapRpH 161
                                    E+ pR+ 
  gi|116754555|ref|YP_843673.1| 296 EVNPRVS 302
                                    *****85 PP

  == domain 2  score: 37.8 bits;  conditional E-value: 1.2e-12
                                    HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC....GTTCEEEEE----SEE CS
                      ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal....keekvivEefvpfekE 77 
                                    +klg+p p+  ++ s ee++++a+e+g+pv+v+ +     G+   +v +e+ le  ++++    +e++v++ +f +  +E
  gi|116754555|ref|YP_843673.1| 678 NKLGIPQPKAGIAYSPEEAKRVAKEIGYPVLVR-PSYVLGGRAMEIVYDESGLELYMREAvrvsHEHPVLIDDFLQNAVE 756
                                    68999****************************.99999************999888888888899************** PP

                                    EEEEEEEETTC-EEE--EEEEEEETTEE....EEEEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCTEEE CS
                      ATP-grasp  78 lsvlvvrsaeGetafypvvetvqedgil....rlsvapaevsekaqkkaeeiakkiveeLggvGvfavElFvledgellv 153
                                    + v +v + +  + + +++e+++e gi        + p++++e+  +++++++++i+ +L++ G++ + + ++ dg ++v
  gi|116754555|ref|YP_843673.1| 757 IDVDAVSDGRD-VLIGAIMEHIEEAGIHsgdsACMIPPQTLPEDVIATVKDYVRRIALALDVKGIINIQMAYK-DGIVYV 834
                                    ******98887.8888999999988775222156788999******************************999.999*** PP

                                    EEEESS- CS
                      ATP-grasp 154 nElapRp 160
                                     E  pR 
  gi|116754555|ref|YP_843673.1| 835 LEANPRS 841
                                    ***9995 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   5.3e-09     6e-06      26     174 ..     153     299 ..     141     303 .. 0.79
   2 !   27.4   0.0   1.9e-09   2.1e-06      26     174 ..     694     839 ..     676     849 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 5.3e-09
                                    HHHHHHHHHC-SSEEEEESSS..STTTTEEEESSGGGHHHHHHHHHTT-..SCEEEEE--.ESEEEEEEEEETSSCEEEE CS
                Dala_Dala_lig_C  26 ellekveeelgypvfVKpare..GSSvGvskveseeelkeaieeafkyd..ekvlvEeai.egreievavlgneklevse 100
                                    e  e+ ++elg+p++V+pa +  GS  Gv+  ++ eel +  e  +k+   ++vl Ee +    e+e  v+ + ++++ +
  gi|116754555|ref|YP_843673.1| 153 EEAEEAMKELGLPLIVRPAYTlgGSGGGVA--RTHEELMRICEMGLKRSriHQVLLEESViGWTEVEYEVMRDSNNTCIT 230
                                    55678899**********964326666665..677899999998887663379****998799*********99999988 PP

                                    EEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEES CS
                Dala_Dala_lig_C 101 vgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEvNt 174
                                    + ++   + +      ++++++ ++   +l++++ + ++ +a+++ +al+++G + + f ++ +ge  + EvN+
  gi|116754555|ref|YP_843673.1| 231 ICNMENMDPM----GIHTGESIVVTPIQTLSDHEIQMLRSAAINIIRALGIEGGCNIQFAVR-NGEYRVIEVNP 299
                                    8777655433....33344455555555689999999***********************98.9********96 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 1.9e-09
                                    HHHHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHT..T-SCEEEEE--.ESEEEEE.EEEETSSCEEEEE CS
                Dala_Dala_lig_C  26 ellekveeelgypvfVKpareGSSvGvskveseeelkeaieeafk..ydekvlvEeai.egreiev.avlgneklevsev 101
                                    e  ++v +e+gypv+V+p+       ++ v  e+ l+ +++ea++  +++ vl++ ++ ++ ei+v av +  ++ +  +
  gi|116754555|ref|YP_843673.1| 694 EEAKRVAKEIGYPVLVRPSYVLGGRAMEIVYDESGLELYMREAVRvsHEHPVLIDDFLqNAVEIDVdAVSDGRDVLIGAI 773
                                    4567899************98878899****************86336788*******99******45555566999999 PP

                                    EEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEES CS
                Dala_Dala_lig_C 102 geivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEvNt 174
                                     e++ + g+       s+d+a +  p +l+++v +++++++ ++  ald++G+  + + ++ +g +++ E N+
  gi|116754555|ref|YP_843673.1| 774 MEHIEEAGIH------SGDSACMIPPQTLPEDVIATVKDYVRRIALALDVKGIINIQMAYK-DGIVYVLEANP 839
                                    9999999985......678999999*******************************99987.9********96 PP

>> ATPgrasp_Ter  ATP-grasp in the biosynthetic pathway with Ter operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   2.1e-08   2.3e-05      48     117 ..     263     333 ..     251     347 .. 0.78
   2 !   27.6   0.0   1.8e-09     2e-06      47     112 ..     802     871 ..     741     888 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 2.1e-08
                   ATPgrasp_Ter  48 elielaerlaeefgldglvnvQvrededgpkLLEiNpRasGGlg.ysalaGvnlpylalklllgleteeve 117
                                     l ++a ++++++g++g  n+Q+  ++++++++E+NpR+s      s ++G  ++++ +k + gl  +e++
  gi|116754555|ref|YP_843673.1| 263 MLRSAAINIIRALGIEGGCNIQFAVRNGEYRVIEVNPRVSRSSAlASKATGYPIARVTAKIAIGLTLDEIR 333
                                    5668999********************************96555156677999999999999998544443 PP

  == domain 2  score: 27.6 bits;  conditional E-value: 1.8e-09
                   ATPgrasp_Ter  47 eelielaerlaeefgldglvnvQvrededgpkLLEiNpRasGGlgy.salaGvnlpylalklllgl...e 112
                                    + + ++++r+a ++ ++g++n+Q+ ++++  ++LE NpR s ++   s + G+ l+++a+k + g+   e
  gi|116754555|ref|YP_843673.1| 802 ATVKDYVRRIALALDVKGIINIQMAYKDGIVYVLEANPRSSRTIPFvSKAVGLPLAKIAAKVMAGNtlrE 871
                                    45668999************************************9625566************9974332 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   0.1   5.9e-08   6.7e-05       3     158 ..     128     301 ..     126     304 .. 0.66
   2 !   25.2   0.0   1.2e-08   1.4e-05       2     157 ..     668     840 ..     667     844 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 5.9e-08
                                    SHHHHHHHHTTT.S---.........-EESS--....SSSEEEEESS-------B--SS--TTE...............E CS
                    ATP-grasp_3   3 dKlktykkLkeagvkvP.....tkleaeeleee....ekklvvKprdGaggesvrvveekeeaeaaieeve........l 65 
                                    d   + k++++ g +vP     t le+  +ee+      +l+v p++  gg++  v++ +ee+ +++e+          l
  gi|116754555|ref|YP_843673.1| 128 DRDLFKKAMERIGEPVPrsiavTSLEE--AEEAmkelGLPLIVRPAYTLGGSGGGVARTHEELMRICEMGLkrsrihqvL 205
                                    555677888888999998885533333..333233448899*******************99998887653455544442 PP

                                    EEE---S.EEEEEEEEE.SSSEEEEEEEEEEEET.........TEEEEE...EES----HHHHHH...HHHHHHHTTSTT CS
                    ATP-grasp_3  66 vqefieG.kplSvsllsdgekvlvlavnrqliekaeke.....fvyaGn...vtpietelkeevv...elaeevvekleg 133
                                    + e + G +++  +++ d         n+  i  +++e      + +G+   vtpi+t  ++e++   ++a +++++l g
  gi|116754555|ref|YP_843673.1| 206 LEESVIGwTEVEYEVMRDS--------NNTCITICNMEnmdpmGIHTGEsivVTPIQTLSDHEIQmlrSAAINIIRAL-G 276
                                    2222222144444444444........444444444444444467777633368999888776651116777888888.* PP

                                    --EEEEEEEEESS.SEEEEEEESS- CS
                    ATP-grasp_3 134 laGyvGvDlvlkdeepyviEvNPRl 158
                                    + G   + + ++++e  viEvNPR+
  gi|116754555|ref|YP_843673.1| 277 IEGGCNIQFAVRNGEYRVIEVNPRV 301
                                    ************************8 PP

  == domain 2  score: 25.2 bits;  conditional E-value: 1.2e-08
                                    TSHHHHHHHHTTT.S---.......-EESS--....SSSEEEEESS-------B--SS--TTE...............EE CS
                    ATP-grasp_3   2 sdKlktykkLkeagvkvP...tkleaeeleee....ekklvvKprdGaggesvrvveekeeaeaaieeve........lv 66 
                                    +d  ++ k L++ g++ P     ++ ee++++     +++ v p++  gg ++ +v ++  +e  + e          l+
  gi|116754555|ref|YP_843673.1| 668 EDRERFNKLLNKLGIPQPkagIAYSPEEAKRVakeiGYPVLVRPSYVLGGRAMEIVYDESGLELYMREAVrvshehpvLI 747
                                    5677788999999*****88845555555554555699*************************9999988999******* PP

                                    EE---.SEEEEEEEEE.SSSEEEEEEEEEEEET....TEEEEEEES----HHHHHHHHHHHHHTTST...T--EEEEEEE CS
                    ATP-grasp_3  67 qefie.GkplSvsllsdgekvlvlavnrqliekaekefvyaGnvtpietelkeevvelaeevvekle...glaGyvGvDl 142
                                     +f++   ++ v+++sdg +vl+ a+ + + e  + +   + +++p + +l e+v++++++ v+++    +++G+  + +
  gi|116754555|ref|YP_843673.1| 748 DDFLQnAVEIDVDAVSDGRDVLIGAIMEHIEEA-GIHSGDSACMIPPQ-TLPEDVIATVKDYVRRIAlalDVKGIINIQM 825
                                    ****73579*********999998887766554.33344444555554.679***********9998888999******* PP

                                    EESS.SEEEEEEESS CS
                    ATP-grasp_3 143 vlkdeepyviEvNPR 157
                                     +kd+  yv+E NPR
  gi|116754555|ref|YP_843673.1| 826 AYKDGIVYVLEANPR 840
                                    *************** PP

>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   3.9e-05     0.043       6     105 ..     132     227 ..     127     275 .. 0.87
   2 !   14.8   0.0   1.6e-05     0.018       7     107 ..     674     770 ..     669     841 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.9e-05
                                    HHHHHHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TTCCCCSSEEE CS
                         GARS_A   6 akdllkkagiptaeyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeealkavkeilekkkfGeagekvvi 85 
                                     k+ ++++g p ++  a+t+ eea+e ++e++ +  +v+++   +g g  va+++ee +++ +  l++ +     ++v++
  gi|116754555|ref|YP_843673.1| 132 FKKAMERIGEPVPRSIAVTSLEEAEEAMKELGLPL-IVRPAYTLGGSGGGVARTHEELMRICEMGLKRSR----IHQVLL 206
                                    6899*******************************.8999999999**************9999998544....579*** PP

                                    EE---S.EEEEEEEEECTTEE CS
                         GARS_A  86 EelleG.eEvsllalvdgktv 105
                                    Ee + G +Ev   ++ d +++
  gi|116754555|ref|YP_843673.1| 207 EESVIGwTEVEYEVMRDSNNT 227
                                    *99999669999999987654 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.6e-05
                                    HHHHHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TTCCCCSSEEEE CS
                         GARS_A   7 kdllkkagiptaeyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeealkavkeilekkkfGeagekvviE 86 
                                     +ll+k gip ++     +peeak + +e + ++  v+++ + +g+ + ++ +e+    +++e ++     + ++ v+i+
  gi|116754555|ref|YP_843673.1| 674 NKLLNKLGIPQPKAGIAYSPEEAKRVAKEIGYPV-LVRPSYVLGGRAMEIVYDESGLELYMREAVR----VSHEHPVLID 748
                                    4799******************************.99****************9999999999987....45689***** PP

                                    E---.SEEEEEEEEECTTEEEE CS
                         GARS_A  87 elle.GeEvsllalvdgktvkp 107
                                    ++l+   E+ + a++dg++v  
  gi|116754555|ref|YP_843673.1| 749 DFLQnAVEIDVDAVSDGRDVLI 770
                                    ***7358***********9864 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.13   1.4e+02      11      49 ..     100     143 ..      93     143 .. 0.83
   2 ?    5.4   0.0      0.01        11      16      51 ..     133     168 ..     114     172 .. 0.86
   3 !   16.6   0.0   3.8e-06    0.0042      16      51 ..     674     709 ..     667     742 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.13
                    ATP-grasp_5  11 teaeakelleaygipvvetrl.....assaeeaveaaeeigypv 49 
                                    +e   + +le yg++v+ t++     a++ +   +a+e+ig pv
  gi|116754555|ref|YP_843673.1| 100 SELAEMGVLEKYGVEVLGTKVrsiqeAEDRDLFKKAMERIGEPV 143
                                    6677789*************988888888888888999998887 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.01
                    ATP-grasp_5  16 kelleaygipvvetrlassaeeaveaaeeigypvvl 51 
                                    k+ +e +g pv++++ ++s eea ea++e+g p  +
  gi|116754555|ref|YP_843673.1| 133 KKAMERIGEPVPRSIAVTSLEEAEEAMKELGLPLIV 168
                                    456788999***********************9766 PP

  == domain 3  score: 16.6 bits;  conditional E-value: 3.8e-06
                    ATP-grasp_5  16 kelleaygipvvetrlassaeeaveaaeeigypvvl 51 
                                    ++ll+ +gip ++  +a s+eea ++a+eigypv +
  gi|116754555|ref|YP_843673.1| 674 NKLLNKLGIPQPKAGIAYSPEEAKRVAKEIGYPVLV 709
                                    789******************************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 !    8.4   0.0    0.0013       1.4       8      62 ..     133     184 ..     122     204 .. 0.81
   2 !   12.6   0.0   6.5e-05     0.073       9      53 ..     675     718 ..     672     738 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0013
                                    HHHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSSTCCCTTCEEEE CS
                    ATP-grasp_2   8 keilakygvkvpegevaesaeeaeeaakklgekelvvKaQvlaGGRGKagGvklv 62 
                                    k+ +++ g +vp++  ++s eeaeea+k+lg    +v+     GG G  gGv  +
  gi|116754555|ref|YP_843673.1| 133 KKAMERIGEPVPRSIAVTSLEEAEEAMKELGLPL-IVRPAYTLGGSG--GGVART 184
                                    4556778999*********************998.888888888765..777544 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 6.5e-05
                                    HHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSSTC CS
                    ATP-grasp_2   9 eilakygvkvpegevaesaeeaeeaakklgekelvvKaQvlaGGR 53 
                                    ++l+k g++ p++ +a s+eea+++ak++g  +  v+     GGR
  gi|116754555|ref|YP_843673.1| 675 KLLNKLGIPQPKAGIAYSPEEAKRVAKEIGYPV-LVRPSYVLGGR 718
                                    79*****************************99.66666667887 PP

>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.11   1.3e+02      17      83 ..     142     207 ..     126     224 .. 0.80
   2 !   14.4   0.0   1.9e-05     0.021       1      94 [.     667     763 ..     667     857 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.11
                                    ----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHH.GGG--EEEEE-- CS
                           RimK  17 kvpntalardeedaekliekiklrfPvvvKsvegsqGikvvlakkeqklkqvlea.lkeailvqeyie 83 
                                    +vp++  + + e+ae+ ++++  + P++v+  ++  G +  +a+++++l  + e  lk + + q  +e
  gi|116754555|ref|YP_843673.1| 142 PVPRSIAVTSLEEAEEAMKEL--GLPLIVRPAYTLGGSGGGVARTHEELMRICEMgLKRSRIHQVLLE 207
                                    456666667777888777776..79**************************99866887777776555 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 1.9e-05
                                    HH-HHHHHHHHHHTT-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHH.....GGG- CS
                           RimK   1 ardKlkslklLakakikvpntalardeedaekliekiklrfPvvvKsvegsqGikvvlakkeqklkqvlea.....lkea 75 
                                    a+d+ +  klL k +i+ p++ +a ++e+a+++ ++i  + Pv+v+ ++   G  + +  +e  l+  +        ++ 
  gi|116754555|ref|YP_843673.1| 667 AEDRERFNKLLNKLGIPQPKAGIAYSPEEAKRVAKEI--GYPVLVRPSYVLGGRAMEIVYDESGLELYMREavrvsHEHP 744
                                    67888999*****************************..69********9999999999999999888755466545556 PP

                                    -EEEEE--SS-SEEEEEEE CS
                           RimK  76 ilvqeyieeaenediRvlv 94 
                                    +l+ +++++a + d+  + 
  gi|116754555|ref|YP_843673.1| 745 VLIDDFLQNAVEIDVDAVS 763
                                    7999999999888876655 PP

>> MerR-DNA-bind  MerR, DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.42   4.7e+02      12      21 ..     324     333 ..     324     336 .. 0.90
   2 ?    6.2   0.0     0.013        15       2      23 ..     428     449 ..     428     454 .. 0.90
   3 ?    1.1   0.2      0.51   5.8e+02      20      59 ..     460     499 ..     456     501 .. 0.56
   4 ?   -1.9   0.0       4.4   4.9e+03      11      21 ..     850     860 ..     848     862 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.42
                                    HTT--HHHHH CS
                  MerR-DNA-bind  12 rlGFsLdeIr 21 
                                    ++G++LdeIr
  gi|116754555|ref|YP_843673.1| 324 AIGLTLDEIR 333
                                    58*******9 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.013
                                    HHHHHHHHHHHTT--HHHHHHH CS
                  MerR-DNA-bind   2 eRLkfIrrarrlGFsLdeIrel 23 
                                    eRL  I +a r GFs++eI++l
  gi|116754555|ref|YP_843673.1| 428 ERLFAIYQALRRGFSVEEISQL 449
                                    5888899*************98 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.51
                                    HHHHHHHHHS.TTTBHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                  MerR-DNA-bind  20 IrelLalydd.rappcqdvrallarklaeleeriaeLqalr 59 
                                    I+ ++ + d+ ++   +d++   a+k+  l+ riaeL  l 
  gi|116754555|ref|YP_843673.1| 460 IQNIIRMEDElKNGLTPDRL-RRAKKMGFLDSRIAELVGLS 499
                                    55555555555433344444.34567777777777777665 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 4.4
                                    HHTT--HHHHH CS
                  MerR-DNA-bind  11 rrlGFsLdeIr 21 
                                    +++G++L+ I+
  gi|116754555|ref|YP_843673.1| 850 KAVGLPLAKIA 860
                                    99*******97 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 ?   11.3   0.0   0.00021      0.24      95     152 ..     925     982 ..     911     990 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00021
                         YjeF_N  95 eeklsapvdlviDAllGiglrgelreelaeliewlnsseapvlavDiPSGldadtGav 152
                                    + ++sa+ +l +D+++ i++r+e+++e+ae+++++ +++ +++a D  SG+   +G +
  gi|116754555|ref|YP_843673.1| 925 KAEMSAENNLPLDGIVFISVRDEDKAEIAEVARRFVNAGLKIIATDGTSGYLRGSGVP 982
                                    456778999*****************************************98888866 PP

>> STAS  STAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0      0.01        11      72      94 ..      33      55 ..      31      70 .. 0.89
   2 ?    3.3   0.0     0.054        61      73      98 ..     644     669 ..     629     681 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.01
                                   HHHHHHHTT-EEEEES--HHHHH CS
                           STAS 72 ilkelkrigvevvlvnikpevre 94
                                   ++k+l+  gvevvlvn +p+ + 
  gi|116754555|ref|YP_843673.1| 33 ACKSLREEGVEVVLVNSNPATIM 55
                                   789***************99875 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.054
                                    HHHHHHTT-EEEEES--HHHHHHHHH CS
                           STAS  73 lkelkrigvevvlvnikpevreklek 98 
                                     kelkr+g + v+ +++p+ ++ +e 
  gi|116754555|ref|YP_843673.1| 644 EKELKRRGLKTVILGTSPDSIDIAED 669
                                    59*****************9998765 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0042       4.7       9      70 ..      28      88 ..      27     105 .. 0.81
   2 ?    1.6   0.0      0.14   1.6e+02       2      40 ..      86     125 ..      85     168 .. 0.74
   3 ?    1.6   0.0      0.14   1.6e+02      74     156 ..     972    1053 ..     925    1062 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0042
                                   HHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.EEEE--TT-HHHHHHHHHHHT-SEEEE CS
                      Epimerase  9 fiGsalvkallekgyevigldrlssasntarledl.elveldltdrsalerlfkeeqpdavih 70
                                   f Gs+ +k l e+g+ev+ +++++ +  t   +d  + v+++ + ++ +++++++e+pd +i 
  gi|116754555|ref|YP_843673.1| 28 FSGSQACKSLREEGVEVVLVNSNPATIMTD--PDMaDKVYIEPLVPEIVAKIIEKERPDGIIA 88
                                   67******************9995555443..233588999999999************9985 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.14
                                    EEETTTSHHHHHHHHHHHHCT.SEEEEEES-STTTTCHHC CS
                      Epimerase   2 lVtGatGfiGsalvkallekg.yevigldrlssasntarl 40 
                                    +++G+ G+ G +++ +l+e g  e  g+  l ++ ++ ++
  gi|116754555|ref|YP_843673.1|  86 IIAGIGGQTGLNITSELAEMGvLEKYGVEVLGTKVRSIQE 125
                                    699*****************98345555555444443333 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.14
                                     ---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHH CS
                      Epimerase   74 vggvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlagek 151 
                                      +g+ + s  pa+ ++k  +g+ n+l+++r+ +vk +++  ++    kd  q    ++ + +++  +   aaK+a+e 
  gi|116754555|ref|YP_843673.1|  972 TSGYLRGSGVPAERVRKIYHGSPNVLDYIRRGEVKLIINTPTTKQSVKDGFQ-IRRSAVDYHVPYITTVQAAKAAAEA 1048
                                     6777788888999999999***************999999998888877774.3333323344445555556666665 PP

                                     HHHHH CS
                      Epimerase  152 lveay 156 
                                     + +a+
  gi|116754555|ref|YP_843673.1| 1049 IEKAL 1053
                                     55555 PP

>> PS_pyruv_trans  Polysaccharide pyruvyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       6.4   7.2e+03      13      97 ..      35     110 ..      33     138 .. 0.57
   2 ?    9.0   0.0     0.001       1.2      11     127 ..     574     679 ..     570     681 .. 0.74
   3 ?   -2.3   0.0       2.9   3.2e+03     129     141 ..     940     952 ..     936     956 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 6.4
                                    HHHHHTT-EEEEEESSTTT--HHHHHHHHHTS-GGGEE................EEE--E....EEEETT-HHHHHHHHH CS
                 PS_pyruv_trans  13 klLrelgpdaeiivltpdpsetkkllkvktpilkklskvllkrlrkkdiddaddviivGgdgtlgndgdlsrlpdalrll 92 
                                    k Lre g+++++++ +p +  t+  + +k  i +  + +  k+  k    + d +i++ g++t +n ++       l+ +
  gi|116754555|ref|YP_843673.1|  35 KSLREEGVEVVLVNSNPATIMTDPDMADKVYIEPLVPEIVAKIIEK---ERPDGIIAGIGGQTGLNITSE------LAEM 105
                                    6688888888888888666666655555555554444444443333...356667777776655655555......5555 PP

                                    HHHHS CS
                 PS_pyruv_trans  93 flakk 97 
                                     +++k
  gi|116754555|ref|YP_843673.1| 106 GVLEK 110
                                    55555 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.001
                                    HHHHHHHTT-EEEEEESSTTT--HHHHHHHHHTS....-GGGEE................EEE--E....EEEETT-HHH CS
                 PS_pyruv_trans  11 lvklLrelgpdaeiivltpdpsetkkllkvktpi....lkklskvllkrlrkkdiddaddviivGgdgtlgndgdlsrlp 86 
                                    +v+ Lre+g++a ii+ +p++++t++  ++k +     l++  +v  k ++++       v +  g++t  n+       
  gi|116754555|ref|YP_843673.1| 574 AVTALREMGIEAHIINNNPETVSTDYDTSDKLFFepvtLEDVMNVIEKERYWG-------VMVQFGGQTAVNL------- 639
                                    799***************66666666666665540000455556667777777.......7777774433333....... PP

                                    HHHHHHHHHHS-SSEEEE-SEEE..-S-HHHHHHHHHHHHH CS
                 PS_pyruv_trans  87 dalrllflakkagkpviilgqgiGpflnealrkllkkilak 127
                                     a  l + +k++g +++ilg++  +++  + r+++ k+l+k
  gi|116754555|ref|YP_843673.1| 640 -AVPLEKELKRRGLKTVILGTSPDSIDIAEDRERFNKLLNK 679
                                    .3889999***************669999999999999998 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.9
                                    TEEEESSHHHHH. CS
                 PS_pyruv_trans 129 dlisvRdelSael 141
                                     +isvRde+ ae+
  gi|116754555|ref|YP_843673.1| 940 VFISVRDEDKAEI 952
                                    59******99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1074 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      675  (0.0376485); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); 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 0.32s 00:00:01.13 Elapsed: 00:00:00.44
# Mc/sec: 7266.98
//
Query:       gi|116754556|ref|YP_843674.1|  [L=361]
Description: carbamoyl phosphate synthase small subunit [Methanosaeta thermophila PT]
Scores for complete 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-44  150.4   0.0    3.3e-44  149.8   0.0    1.2  1  CPSase_sm_chain  Carbamoyl-phosphate synthase small chain, CP
    1.9e-40  138.6   0.0    2.8e-40  138.1   0.0    1.2  1  GATase           Glutamine amidotransferase class-I
    1.2e-09   38.2   0.0    4.7e-07   29.8   0.0    2.2  1  Peptidase_C26    Peptidase C26


Domain annotation for each model (and alignments):
>> CPSase_sm_chain  Carbamoyl-phosphate synthase small chain, CPSase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.8   0.0   5.5e-48   3.3e-44       3     127 ..       4     129 ..       3     130 .. 0.97

  Alignments for each domain:
  == domain 1  score: 149.8 bits;  conditional E-value: 5.5e-48
                CPSase_sm_chain   3 vLvLedGtvfeGksfg.akeavGEvvfnTgmtGYqeiltDpsYagqilvltypliGnyGvneedvesekikvaglvvrel 81 
                                    vL LedGt +eG++fg  + ++GE+vf+T m+GY+e+ltDpsY+gqil++typl GnyGv+ ++++s++++ +g+v+r++
  gi|116754556|ref|YP_843674.1|   4 VLGLEDGTLVEGYGFGaPGIVTGEIVFTTVMSGYEEALTDPSYNGQILLFTYPLQGNYGVSGDEFQSDRMWPRGMVCRHI 83 
                                    799*************55999*********************************************************** PP

                CPSase_sm_chain  82 seepsnwraeesLsewlkeekipgisgvDTRaLtkklrekgamkgv 127
                                      +p ++r++++++e+l +e+ pgi+gvDTR+Lt k+r+ gamk++
  gi|116754556|ref|YP_843674.1|  84 WPSPRHHRSSRTIEEFLVDEGRPGIHGVDTRMLTVKIRRLGAMKAA 129
                                    *******************************************997 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.1   0.0   4.7e-44   2.8e-40       2     181 ..     178     346 ..     177     356 .. 0.94

  Alignments for each domain:
  == domain 1  score: 138.1 bits;  conditional E-value: 4.7e-44
                                    EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.TTTHHHHHHHHCTSTS-EEEETHH CS
                         GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg.vegkieaikearenkiPiLGICLG 80 
                                    +iD +  +++ ++++l  +g++++v+p ++s +ei  ++ +pd i++s+Gpg+p+ +  +iea++++++  +Pi+GICLG
  gi|116754556|ref|YP_843674.1| 178 VIDLG--IKRHILKSLECRGFDLHVLPAHSSVSEI--EAVEPDCIFISNGPGDPErAVSAIEAVRYFAG-SMPIFGICLG 252
                                    78888..****************************..489*****************************.********** PP

                                    HHHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEEE CS
                         GATase  81 mQllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelmeiiek 160
                                    +Q++ +++g+ + k k ++hhgg+++++d       ++  ++i++++H+++v p+++e ++le+t  +++d+++++i+ +
  gi|116754556|ref|YP_843674.1| 253 HQVISLALGARTFKLK-FGHHGGNQPVKD------LESRIVYITSQNHNFAVVPESVEGTDLEITQLNANDGTVEGIRSR 325
                                    ****************.************......56669999************************************* PP

                                    TTTEEEESSBTTSTTSTTHHH CS
                         GATase 161 knpfvgvQFHPEststpegpe 181
                                      ++ +vQ+HPE++++p+ +e
  gi|116754556|ref|YP_843674.1| 326 YLKILAVQYHPEAHPGPMCTE 346
                                    ***************998654 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   7.9e-11   4.7e-07      83     216 .]     222     337 ..     217     337 .. 0.71

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 7.9e-11
                  Peptidase_C26  83 eeeadpeRdalelaLiraalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgsllael 162
                                    +++ dpeR    +  +r   + ++Pi+giC+G+q++  alG ++++ ++    + +h        ++ vk  ++++++  
  gi|116754556|ref|YP_843674.1| 222 NGPGDPERAVSAIEAVRY-FAGSMPIFGICLGHQVISLALGARTFK-LK----FGHH------GGNQPVKDLESRIVYIT 289
                                    566778887777777765.5678*****************998775.34....2233......34556665555555544 PP

                  Peptidase_C26 163 lgseeievnslHhqaike...laeelrveAvae.DgviEaieseeakafvlgvQwHPE 216
                                     +         H++a+      +++l+++   + Dg++E i+s+  k  +l+vQ+HPE
  gi|116754556|ref|YP_843674.1| 290 SQ--------NHNFAVVPesvEGTDLEITQLNAnDGTVEGIRSRYLK--ILAVQYHPE 337
                                    44........344444322225788999988777***********77..********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       222  (0.0123822); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); 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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2834.15
//
Query:       gi|116754557|ref|YP_843675.1|  [L=304]
Description: aspartate carbamoyltransferase catalytic subunit [Methanosaeta thermophila PT]
Scores for complete 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-52  175.7   0.0    1.6e-51  174.2   0.0    1.7  2  OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl
    3.4e-27   95.4   0.0    4.8e-27   95.0   0.0    1.2  1  OTCace    Aspartate/ornithine carbamoyltransferase, Asp/Orn b


Domain annotation for each model (and alignments):
>> OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.2   0.0   1.8e-55   1.6e-51       1     147 [.       5     145 ..       5     146 .. 0.95
   2 ?   -0.9   0.0      0.17   1.5e+03      36      74 ..     149     187 ..     145     213 .. 0.75

  Alignments for each domain:
  == domain 1  score: 174.2 bits;  conditional E-value: 1.8e-55
                                    S-BSSGGGS-HHHHHHHHHHHHHHHHHHHTTT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTTSCTT CS
                       OTCace_N   1 rhllsledlskeeieelldlaaelkekvkkekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseaediqls 80 
                                    rh+ls++d+s+eei+e+l++a++l+    + k +++l+gk+lal+F+epStRTr+Sfe+A+krlGgk+++l++a   + s
  gi|116754557|ref|YP_843675.1|   5 RHVLSMKDFSREEIDEILETAESLEPYA-RGKGSDILEGKILALMFFEPSTRTRMSFETAMKRLGGKTINLGSA---EAS 80 
                                    8************************765.59*****************************************66...679 PP

                                    TGGSTTSSCHHHHHHHHHHHTSEEEEEESSHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHHH CS
                       OTCace_N  81 svskgrkEsleDtarvlsryvdaiviRhpgaeeleelakyasvpviNagdgdgeHPtQaLaDlltir 147
                                    s++kg  Esl+Dt+rv+++y+daiviRhp++ +++  a+++ vpv+Nagdg+g+HPtQ+L+Dl+ti+
  gi|116754557|ref|YP_843675.1|  81 SIAKG--ESLADTIRVVGGYADAIVIRHPKEGSARLAAEFSPVPVLNAGDGAGHHPTQTLLDLYTIK 145
                                    999**..**********************77679999****************************97 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.17
                                    TTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEEST CS
                       OTCace_N  36 llkgktlallFeepStRTrvSfevAakrlGgkvlslsea 74 
                                    +l++ ++al+   +  RT  S   A +  G++   +s +
  gi|116754557|ref|YP_843675.1| 149 HLDDLSIALVGDLKYGRTVHSLAYALSLYGADIYLVSPP 187
                                    566667777777777899999999999999998777644 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 !   95.0   0.0   5.3e-31   4.8e-27       2     156 ..     152     300 ..     151     301 .. 0.92

  Alignments for each domain:
  == domain 1  score: 95.0 bits;  conditional E-value: 5.3e-31
                                    C.EEEEESS.TTSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEEE--S CS
                         OTCace   2 glkiafvGd.kknnvanslikllarlgmdvvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvytdvw 80 
                                    +l ia+vGd k++++++sl+++l+ +g+d++lv+P++l++ ++++  ++      g ++   +dl e++k++Dv+y +++
  gi|116754557|ref|YP_843675.1| 152 DLSIALVGDlKYGRTVHSLAYALSLYGADIYLVSPPTLRMPEQIIGDLSR----MGTRVREVSDLREVIKEVDVLYITRI 227
                                    689**********************************9998888866555....69************************ PP

                                    SETTCCGGHH....HHHHHHCCCSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHHHHHHHHHH CS
                         OTCace  81 vsmgeekere....erlkklkdyqvteellklakkdaivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlhtikAllvl 156
                                    +     +er+    e ++  + y +t   l+  k+++ ++H+LP  r +E++ +V++ +++v+f+q  +++ +++All +
  gi|116754557|ref|YP_843675.1| 228 Q-----RERFpdpvEYNRVARSYSITIRDLEGVKPELRIMHPLP--RVDEISPSVDETEHAVYFRQSFYGVPVRMALLKM 300
                                    *.....8888788566666666**********************..*******************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 2168.13
//
Query:       gi|116754558|ref|YP_843676.1|  [L=154]
Description: aspartate carbamoyltransferase regulatory subunit [Methanosaeta thermophila PT]
Scores for complete 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-35  120.0   1.1    4.8e-35  119.7   1.1    1.1  1  PyrI      Aspartate carbamoyltransferase regulatory chain, al
    4.1e-16   58.6   0.8    6.7e-16   57.9   0.8    1.3  1  PyrI_C    Aspartate carbamoyltransferase regulatory chain, me
  ------ inclusion threshold ------
      0.016   14.3   0.1      0.019   14.1   0.1    1.1  1  T2SSE     Type II/IV secretion system 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 !  119.7   1.1     8e-39   4.8e-35       1      93 [.       6      97 ..       6      98 .. 0.97

  Alignments for each domain:
  == domain 1  score: 119.7 bits;  conditional E-value: 8e-39
                                   X-----SCEEEEEEEETT-HHHHHHHCT--T...TS-EEEEEEEEETTTEEEEEEEEET----HHHHHHHCCC-TT-EEEEE CS
                           PyrI  1 lkvkkienGiViDHIkagkalkvlklLkldklkseekvaiiknvkskklgkKdiikiegkelseeeldklaliapnatiniI 82
                                   lkv++i++G+ViDHI+ag+al+vlk+L++++ +++++v++++nv+s+klgkKdi+k+e++el+e+e++k+aliap atini+
  gi|116754558|ref|YP_843676.1|  6 LKVRPIRSGTVIDHIQAGQALNVLKILGISG-TTGATVSVLMNVSSRKLGKKDIVKVEDRELREDEVNKIALIAPGATINIV 86
                                   69****************************8.7777********************************************** PP

                                   ETTEEEEEE-- CS
                           PyrI 83 kdgevveKkkv 93
                                   +d+ vveK+ v
  gi|116754558|ref|YP_843676.1| 87 RDYAVVEKYAV 97
                                   ********987 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 !   57.9   0.8   1.1e-19   6.7e-16       2      46 ..     103     148 ..     102     149 .. 0.95

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 1.1e-19
                                    EESSS--S-TTBGGGT.TS-.-EEEEEETTTTEEEETTT--EEEHH CS
                         PyrI_C   2 iegvlkCpNpnCItnn.epveskFkvedkekvklkCkYCekeisee 46 
                                    i gv++C+Np CI+n+ ep+++k+ v+ k++v+l+C+YC+++++e+
  gi|116754558|ref|YP_843676.1| 103 IVGVVRCQNPSCISNTnEPIKPKMLVKGKNPVVLRCFYCDQPLTER 148
                                    89**************99***********************99985 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 ?   14.1   0.1   3.1e-06     0.019     129     186 ..      29      83 ..       5     113 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.1e-06
                          T2SSE 129 rglilvsGgTgsGKttllyallkeinksderivtvEDpvEiqleganqvqlnakkakv 186
                                     +++ +sG+Tg   ++l+++   ++ k+   iv vED +E++ +++n+++l a  a++
  gi|116754558|ref|YP_843676.1|  29 LKILGISGTTGATVSVLMNVSSRKLGKK--DIVKVED-RELREDEVNKIALIAPGATI 83 
                                    456669********************99..9******.8*********9999873333 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:                      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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 1138.88
//
Query:       gi|116754559|ref|YP_843677.1|  [L=418]
Description: phosphoglucomutase/phosphomannomutase alpha/beta/subunit [Methanosaeta thermophila PT]
Scores for 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-23   82.1   0.0    8.4e-23   80.6   0.0    1.8  2  PGM_PMM_I    Phosphoglucomutase/phosphomannomutase, alpha/bet
    4.2e-18   65.9   0.1    8.8e-18   64.8   0.1    1.5  1  PGM_PMM_II   Phosphoglucomutase/phosphomannomutase, alpha/bet
    7.5e-18   64.8   0.0    1.5e-17   63.8   0.0    1.5  1  PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/bet
    5.9e-10   39.2   0.0    2.1e-09   37.4   0.0    1.9  1  PGM_PMM_IV   Phosphoglucomutase/phosphomannomutase, C-termina


Domain annotation for each model (and alignments):
>> PGM_PMM_I  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.6   0.0   1.9e-26   8.4e-23      25     120 ..       2      93 ..       1     110 [. 0.92
   2 ?   -2.4   0.0      0.77   3.5e+03      15      47 ..     112     145 ..     105     166 .. 0.73

  Alignments for each domain:
  == domain 1  score: 80.6 bits;  conditional E-value: 1.9e-26
                                    HHHHHHHHHCHHCSTS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEEB-HHHHHHHHHHCCECEEEEE--TTS-T CS
                      PGM_PMM_I  25 klgqaiaeylkaeakkkkvvvGrDtRvssrelaealaaglaanGvevillgllptPavsfairklkadagimitaSHnpp 104
                                    ++g+a+++yl+     + + +GrDtR+s++ l++a+++g++++Gv+v+ +g++p+P++ +++ k++  a+ +i+aSHnpp
  gi|116754559|ref|YP_843677.1|   2 RVGAAFGTYLSG----GAISLGRDTRTSGPSLERAFLEGVLRTGVDVHSYGVIPIPILGYITMKMGRRAAAYISASHNPP 77 
                                    6899*******7....9*************************************************************** PP

                                    TCCCEEEEETTTCE-- CS
                      PGM_PMM_I 105 eyngiKvylsnGgpis 120
                                    eyngi++ + +G+ + 
  gi|116754559|ref|YP_843677.1|  78 EYNGIRFRTGDGYGML 93 
                                    *********9998665 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.77
                                    HCTBSCCHHHHHHHHHHHHCHHC.STS-EEEEEE CS
                      PGM_PMM_I  15 egeltpelveklgqaiaeylkae.akkkkvvvGr 47 
                                    +g +t e++ +++  +++y +++ ++++ + v  
  gi|116754559|ref|YP_843677.1| 112 NGSVTVENADRAILEYGDYAAEKvKTTRDLRVVL 145
                                    4567788888888888888888765555555544 PP

>> PGM_PMM_II  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.8   0.1     2e-21   8.8e-18       3     103 .]     127     221 ..     125     221 .. 0.91

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 2e-21
                                    HHHHGGGTS-HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-EEEES-----TT-TTSS----TT-TTTTHHHHGGGGG CS
                     PGM_PMM_II   3 YiealkekvdseaikksglkvvidplhGaggeilkellkelgvdvvelnaepdpdfptkapnpeekealkllielvkkeg 82 
                                    Y +  +ekv+    + ++l+vv+d+++G++ +i++ +  ++g++v  lna+ d+ fp++ + p+  e+l++++e v ++g
  gi|116754559|ref|YP_843677.1| 127 YGDYAAEKVK----TTRDLRVVLDTGNGSACGIAP-IYTRAGIEVELLNATMDGRFPGRGAAPTS-ESLREAAERVVSTG 200
                                    6666666776....8999**************998.55666*****************9999999.9************* PP

                                    -SEEEEE-TTS-BEEEEETTE CS
                     PGM_PMM_II  83 adlglafDgDaDRlgvvderG 103
                                    ad+g+ fD+DaDR +v+d++G
  gi|116754559|ref|YP_843677.1| 201 ADFGVGFDPDADRGMVIDDKG 221
                                    *****************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 !   63.8   0.0   3.3e-21   1.5e-17       2     110 ..     226     328 ..     225     331 .. 0.91

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 3.3e-21
                                    HHHHHHHHHHHHHCHCSTTTCEEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHHHHHHTTECEEEETTCEEEETTTBS CS
                    PGM_PMM_III   2 gdqllallakylleeklkpgagvvktvmtslalervakklgiklvetkvGdkyvleemkeegavlGgEeSghiifldeat 81 
                                    ++++++++a++  +   +++  v++ + +s++ler +++ gi++ + +vGd +v++++ke+gavlG E Sgh++++++++
  gi|116754559|ref|YP_843677.1| 226 PEKIAIIIARRRYK---PGDL-VIAGFDCSMILERELERDGIRVERERVGDVFVANRVKESGAVLGVERSGHFFIPEFQY 301
                                    67899999997755...5555.********************************************************** PP

                                    S--HHHHHHHHHHHHHHHTS-HHHHHHHH CS
                    PGM_PMM_III  82 tkDGilaallvleilaetgkslselleel 110
                                     +D   ++l+++ei++e+  +lse+++e+
  gi|116754559|ref|YP_843677.1| 302 SDDPFAMSLALAEIVSEE--KLSEMADEI 328
                                    ***************986..899999665 PP

>> PGM_PMM_IV  Phosphoglucomutase/phosphomannomutase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.0   4.7e-13   2.1e-09       6      59 ..     350     398 ..     339     402 .. 0.82

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 4.7e-13
                                    HCC-TT..EECCCCCTTHHCCCCCCCCGCCEEEE.EEEETTCCEEEEEEEES.SH CS
                     PGM_PMM_IV   6 veekakvvaalaallkvasikeglkilledGrrlavRpSGTepllrvyvEak.sd 59 
                                    +++    +++la+l  +  + +g+k+  e  ++l +RpS+Tepl+r+yvE+  +d
  gi|116754559|ref|YP_843677.1| 350 MDK---LLEELADLEPD--TTDGIKVMSEGWSVL-IRPSNTEPLIRIYVESVkDD 398
                                    333...59999999888..*******99877777.****************9554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 3177.19
//
Query:       gi|116754560|ref|YP_843678.1|  [L=303]
Description: glycosyl transferase family protein [Methanosaeta thermophila PT]
Scores for complete 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-19   68.1   0.0    1.2e-18   67.6   0.0    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
    2.9e-08   33.9   0.0    4.6e-08   33.2   0.0    1.3  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    0.00054   20.4   0.0    0.00094   19.7   0.0    1.4  1  Glyco_tranf_2_4  Glycosyl transferase family 2
  ------ inclusion threshold ------
       0.14   11.8   0.6       0.21   11.3   0.6    1.2  1  Tetraspanin      Tetraspanin 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 !   67.6   0.0   2.6e-22   1.2e-18       1     132 [.       7     129 ..       7     161 .. 0.88

  Alignments for each domain:
  == domain 1  score: 67.6 bits;  conditional E-value: 2.6e-22
                                    EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--S CS
                Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatg 80 
                                    +v ipt Ne+  ++e++e  +++      +i+v+D  StD+t+++++e+     + rvi ++ + Gk+ al +++   + 
  gi|116754560|ref|YP_843678.1|   7 CVLIPTLNEAGSIREVIEGFRSM---GFQDILVIDGHSTDGTPDLAREA-----GARVIVQS-GSGKGQALLEAFGLIDK 77 
                                    799********************...88889999999************.....9*******.66*************** PP

                                    SEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SS CS
                Glycos_transf_2  81 dyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrv 132
                                    +yi+++D D ++ p  + +l+++l +++ad v+g+r+ +  +   ++ n+  
  gi|116754560|ref|YP_843678.1|  78 EYIVLIDGDGTYLPSEVDRLLDPLMRGRADHVIGNRFSNLRGGSLKRLNLVG 129
                                    **************************************99999988888654 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.0     1e-11   4.6e-08       3     132 ..       5     121 ..       3     167 .. 0.87

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 1e-11
                Glyco_tranf_2_3   3 dlavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnea 82 
                                    d+ vl+pt+ne+  ++ev+e + +   +  ++ v++  s+++t + a+e       ++ rv+v++    s gk +al ea
  gi|116754560|ref|YP_843678.1|   5 DVCVLIPTLNEAGSIREVIEGFRS--MGFQDILVIDGHSTDGTPDLARE-------AGARVIVQSG---S-GKGQALLEA 71 
                                    599********************9..455788888999*******9*99.......3678887755...4.9******** PP

                Glyco_tranf_2_3  83 lravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfllnrstl 132
                                    +  ++ ++++l+D+D    P  ++rll  + + ++++v +++f++ r   
  gi|116754560|ref|YP_843678.1|  72 FGLIDKEYIVLIDGDGTYLPSEVDRLLDPLMRGRADHVIGNRFSNLRGGS 121
                                    ******************************8889*********9976543 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 !   19.7   0.0   2.1e-07   0.00094       2      45 ..      14      58 ..      13      90 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2.1e-07
                Glyco_tranf_2_4  2 neadiLpeflahhlalgfdrilvydndstDgtrailkel.pevkl 45
                                   nea  + e+++  +++gf++ilv+d +stDgt ++ +e  ++v +
  gi|116754560|ref|YP_843678.1| 14 NEAGSIREVIEGFRSMGFQDILVIDGHSTDGTPDLAREAgARVIV 58
                                   89999*****************************99986344443 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.6   4.6e-05      0.21       5      81 ..     228     298 ..     224     300 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.6e-05
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXX.....................XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Tetraspanin   5 lfffnllfwligivllavGvwlrlkhaeaalacllsesaedpailaillivvGvllfllgflGcigalkenkclllt 81 
                                    lf f l+  ++g + + +G+++       +l+     +  + +il+ +li+vG+ lfl+g+ G ++a   + ++  +
  gi|116754560|ref|YP_843678.1| 228 LFYFGLMGAIFGSMGFLLGLYV----VRDWLQGR--IEHIPLTILTAILIIVGFQLFLMGIQGDMMATMHREVMREL 298
                                    7899999999999999999999....33344333..455677888889***************88887777766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); 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: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2317.98
//
Query:       gi|116754561|ref|YP_843679.1|  [L=456]
Description: hypothetical protein Mthe_1260 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00053   19.9   0.0     0.0011   18.9   0.0    1.4  1  Transglut_core3  Transglutaminase-like superfamily


Domain annotation for each model (and alignments):
>> Transglut_core3  Transglutaminase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0     6e-08    0.0011      31      97 ..     325     389 ..     302     394 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 6e-08
                Transglut_core3  31 rpasaeearrlgravraaarllpgrskCLpralalalllrrrgipatlviGvrkeddpfaaHAWvev 97 
                                    ++ ++ +++r+ +    ++r++ +r +C   + +++ +l+  g++a l++G + +  p+  H Wv v
  gi|116754561|ref|YP_843679.1| 325 DSTDRSDLERILKEHSYISRYSESRFDCSNASQVCWSFLKGLGYDAYLMVGAKDH--PLGEHMWVVV 389
                                    56677788888888888999***********************************..********76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 3473.54
//
Query:       gi|116754562|ref|YP_843680.1|  [L=160]
Description: flavodoxin/nitric oxide synthase [Methanosaeta thermophila PT]
Scores for complete 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   56.8   0.4    1.3e-10   41.2   0.0    2.4  3  FMN_red       NADPH-dependent FMN reductase
    2.4e-13   50.5   0.0    3.2e-13   50.1   0.0    1.3  1  Flavodoxin_5  Flavodoxin domain
    3.2e-11   43.6   0.1    4.3e-11   43.2   0.1    1.2  1  Flavodoxin_1  Flavodoxin
    2.9e-07   30.3   0.0    3.7e-07   30.0   0.0    1.3  1  Flavodoxin_3  Flavodoxin domain
    4.5e-05   23.2   0.0    0.00023   20.9   0.0    1.9  1  Flavodoxin_2  Flavodoxin-like fold
  ------ inclusion threshold ------
      0.028   13.3   0.4       0.04   12.8   0.4    1.2  1  DUF917        Protein of unknown function (DUF917)


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 !   13.9   0.0   1.1e-05     0.033       7      42 ..       6      41 ..       3      46 .. 0.85
   2 !   41.2   0.0   4.5e-14   1.3e-10      69     145 ..      45     120 ..      43     127 .. 0.83
   3 ?   -2.6   0.0       1.4   4.2e+03       7      27 ..     133     155 ..     129     157 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.1e-05
                                   ES--STT-HHHHHHHHHHCCT-T.T-CEEEEETTTS CS
                        FMN_red  7 sGSlrkgsntrklaewaaealkeagaevelidladl 42
                                   ++  ++ +nt+k+a+++ae +k aga+v+l ++ d 
  gi|116754562|ref|YP_843680.1|  6 VAYYSRTGNTEKMARAVAEGAKDAGADVDLKRVEDV 41
                                   5666788***********************999886 PP

  == domain 2  score: 41.2 bits;  conditional E-value: 4.5e-14
                                    HHHH-SCEEEEEEECTTCE-HHHHHHHHCHT-.SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHH.HTT-EEEEC CS
                        FMN_red  69 kiaaadaliivtPeYngsysgllKnalDrlsrtrgkkelrgKpvalvavgggrrgglraeeqlrqvla.elgaivvpr 145
                                     +++ad+++i++P+Y g +s+  K ++Dr    + +  l++K++a+++ +++  gg +++      ++ ++g++v ++
  gi|116754562|ref|YP_843680.1|  45 DLKSADGIVIGSPTYYGLMSAEVKQLFDRSA--KVRGKLENKIGAAFTSSASIEGGNQTTLLSIIQAMmIHGMVVAGD 120
                                    5899**************************7..8999**********9999888887766555544442677777665 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.4
                                    ES--STT..-HHHHHHHHHHCCT CS
                        FMN_red   7 sGSlrkg..sntrklaewaaeal 27 
                                    +GS+ ++  +++rkl e++a  +
  gi|116754562|ref|YP_843680.1| 133 IGSPDDNslRTCRKLGERVAMLA 155
                                    67776664467777777777655 PP

>> Flavodoxin_5  Flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1   0.0   1.1e-16   3.2e-13       1      85 [.       5      93 ..       5     119 .. 0.90

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 1.1e-16
                   Flavodoxin_5  1 lilYsSrdGqTkkiaeriaeelreegelvdvedve.kesedlesydavvigasvyygkllpelakFvekh...reaLstkpv 78
                                   l++Y Sr+G+T+k a+++ae  +++g++vd++ ve +e +dl+s+d +vig++ yyg ++ e++++ ++    r +L++k  
  gi|116754562|ref|YP_843680.1|  5 LVAYYSRTGNTEKMARAVAEGAKDAGADVDLKRVEdVEPDDLKSADGIVIGSPTYYGLMSAEVKQLFDRSakvRGKLENKIG 86
                                   79*******************************9835556**************************9988666778999999 PP

                   Flavodoxin_5 79 alfsvsl 85
                                   a+f+ s 
  gi|116754562|ref|YP_843680.1| 87 AAFTSSA 93
                                   9988765 PP

>> Flavodoxin_1  Flavodoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   0.1   1.4e-14   4.3e-11       1      78 [.       6      80 ..       6     110 .. 0.82

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 1.4e-14
                                   EEEETSSSHHHHHHHHHHHHHHHTTTEEEEEEEEGTTSCGGGGGTHSEEEEEEEEETTTBEEGGGHHHHHHHHHHHCH CS
                   Flavodoxin_1  1 ilYgSetGnteklAkqlaeelgehgfnadvvslsdydeslseieeealllvvtsTfgnGdppengesffqdllelkgd 78
                                   + Y+S tGntek+A+++ae+++++g ++d+ +++d++  ++++++ + ++++ +T++ G ++ + ++ f++ ++ +g+
  gi|116754562|ref|YP_843680.1|  6 VAYYSRTGNTEKMARAVAEGAKDAGADVDLKRVEDVE--PDDLKSADGIVIGSPTYY-GLMSAEVKQLFDRSAKVRGK 80
                                   78************************99999999999..679998777777777666.*9999988888887777743 PP

>> Flavodoxin_3  Flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   1.2e-10   3.7e-07       1      64 [.       5      72 ..       5     108 .. 0.90

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 1.2e-10
                   Flavodoxin_3  1 lilysSltGNTkkvAeaikealeeekeivsikeakek....veeadvvfvGfwvdkgtadeealkfle 64
                                   l+ y S+tGNT+k+A+a++e +++  + v++k+++++    +++ad +++G  ++ g +++e++++  
  gi|116754562|ref|YP_843680.1|  5 LVAYYSRTGNTEKMARAVAEGAKDAGADVDLKRVEDVepddLKSADGIVIGSPTYYGLMSAEVKQLFD 72
                                   589********************9878888888888777789999*****************999875 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   7.7e-08   0.00023      67     103 ..      39      74 ..       2     113 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 7.7e-08
                                    HHHHHHHHHHCSSEEEEEEE-BTTB--HHHHHHHHHH CS
                   Flavodoxin_2  67 veseqiekllaadaivlqfPlwwfgvPailKgwiDrv 103
                                    ++ e  ++l++ad iv+++P ++  ++a +K+ +Dr 
  gi|116754562|ref|YP_843680.1|  39 EDVEP-DDLKSADGIVIGSPTYYGLMSAEVKQLFDRS 74 
                                    34456.99***************************95 PP

>> DUF917  Protein of unknown function (DUF917)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.4   1.3e-05      0.04      25     122 ..      20     122 ..      11     123 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.3e-05
                                    HHHHTT-SBTT--EEEE-GGG--SEE...EEEEEEE-HHHHTT-SS-HH........HHHHHHHHHT--EEEEE-SSSSC CS
                         DUF917  25 ylllrqaleegksvrvvsldelpddalv.vvvgamGsptvieeklpsgd....elleavealekllgrkidavislEiGG 99 
                                    +  ++ a ++g++v + +++++++d+l  + + ++Gspt       + +       ++  +le+ +g  ++   s+E G+
  gi|116754562|ref|YP_843680.1|  20 RAVAEGAKDAGADVDLKRVEDVEPDDLKsADGIVIGSPTYYGLMSAEVKqlfdRSAKVRGKLENKIGAAFTSSASIEGGN 99 
                                    44444444455567777777777766652445566777766555544442222446667778888888899999****** PP

                                    CHHHHHHHHHHHHT-EEESB-SS CS
                         DUF917 100 lNglvallaaaklglpvvDaDgm 122
                                      +l  ++ a+     vv +D m
  gi|116754562|ref|YP_843680.1| 100 QTTLLSIIQAMMIHGMVVAGDPM 122
                                    *********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1221.62
//
Query:       gi|116754563|ref|YP_843681.1|  [L=302]
Description: translation initiation factor IF-2B subunit delta [Methanosaeta thermophila PT]
Scores for complete 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-87  291.6   0.1    6.1e-87  291.4   0.1    1.0  1  IF-2B        Initiation factor 2 subunit family
  ------ inclusion threshold ------
      0.032   14.7   0.2       0.82   10.1   0.0    2.8  3  FumaraseC_C  Fumarase C C-terminus


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 !  291.4   0.1   6.8e-91   6.1e-87       1     282 []      13     285 ..      13     285 .. 0.98

  Alignments for each domain:
  == domain 1  score: 291.4 bits;  conditional E-value: 6.8e-91
                                    SS-SHHHHHHHHHHHHHHHHHHCCCSTHHHHHHHHHHHHHHHHTSSTS-HHHHHHHHHHHHHHHCCTTTSSHHHHHHHHH CS
                          IF-2B   1 kvrGspaiaiaalevllevikdaktskvaeLkeelrkaidlLkkarPtavslgnairrllkeiselksssdvkeakksli 80 
                                    ++rG+  ia+aa+ +l++++   + s  +e+ + l+ka+d+L  +rPtavsl+na+r++ +       s+d+++a+ +++
  gi|116754563|ref|YP_843681.1|  13 EIRGAGLIARAAAAALRDFVLTLDVSSLDEFDSALKKAADTLLRTRPTAVSLSNAVRMVAR-----YRSEDLESARREVV 87 
                                    589**********************************************************.....77************ PP

                                    HHHHHHHHHHHHHHHHHHHHHHTTC-TTEEEEEES--SHHHHHHHHHHHTTEEEEEEEEEXTTTTHHHTHHHHHHHTTXE CS
                          IF-2B  81 ekikelikeieeadekigdiaaelikdgdtilTicnsktvlevlraaakekkkfkVivvEsrPrlqGrltakeLvqagip 160
                                     +++++i++ ++a e ig+i++ ++ dgd+ilT+cns+++l+v++ a++++k+++Vi++EsrPr qG+lt+k L + gip
  gi|116754563|ref|YP_843681.1|  88 ANAERFIESSLKAVERIGEIGSRRVRDGDVILTHCNSSAALAVIERAHRDGKRIEVIATESRPRYQGHLTIKRLDEVGIP 167
                                    ******************************************************************************** PP

                                    EEEEEGGGHHHHHHCTESEEEEEXSEEETTSEEEEETTHHHHHHHHHHTTXEEEEEXXGGGBESTSSSGGGSSXXBEXTH CS
                          IF-2B 161 vtlitdsavayvmseevdkvivGAdrilenGaiankiGTsslAvlAkefnipvlvvaeslkfservqldedifieerdpe 240
                                    + li+dsav+ v++  vd v+vGAd +++nG+++nkiGTs++A++A+e++ p++++ae++kfs+ + ++e + ieer+pe
  gi|116754563|ref|YP_843681.1| 168 TELIVDSAVRSVIED-VDLVVVGADVVTANGSLVNKIGTSQIALCAHEARKPFMAAAETYKFSPDTLMGELVEIEERGPE 246
                                    ***************.**************************************************************** PP

                                    HHHEETTEESSTTTEEEEEBSEEEEEGGGXSEEEETTEEEXC CS
                          IF-2B 241 ellnitgeriaeeelkvvnpafDvtPpelItliITevGvlpp 282
                                    e+l    + +    l+v+npafDvtP+++I++i TevG++pp
  gi|116754563|ref|YP_843681.1| 247 EVLDDYMRYK---HLRVRNPAFDVTPHQYIDVICTEVGAIPP 285
                                    **98777666...9**************************98 PP

>> FumaraseC_C  Fumarase C C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0     0.077   6.9e+02      26      48 ..      26      48 ..      17      51 .. 0.82
   2 ?   10.1   0.0   9.2e-05      0.82      14      52 ..     127     170 ..     125     171 .. 0.90
   3 ?   -1.1   0.0      0.29   2.6e+03      15      33 ..     206     224 ..     198     255 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.077
                                   --HHHHHHHTT-.-HHHHHHHT- CS
                    FumaraseC_C 26 ktlreavlelgllteeeldelld 48
                                     lr+ vl l + + +e+d +l+
  gi|116754563|ref|YP_843681.1| 26 AALRDFVLTLDVSSLDEFDSALK 48
                                   479999*************9986 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 9.2e-05
                                    HHHHHHHHHHHT--HHHHHHH.....TT-.-HHHHHHHT-HHHH CS
                    FumaraseC_C  14 AakIAkeAlkegktlreavle.....lgllteeeldelldpekM 52 
                                    A ++  +A+++gk +  ++ e     +g+lt ++lde+  p+++
  gi|116754563|ref|YP_843681.1| 127 ALAVIERAHRDGKRIEVIATEsrpryQGHLTIKRLDEVGIPTEL 170
                                    77899********************************9777766 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.29
                                    HHHHHHHHHHT--HHHHHH CS
                    FumaraseC_C  15 akIAkeAlkegktlreavl 33 
                                    ++IA  A++ +k+   a+ 
  gi|116754563|ref|YP_843681.1| 206 SQIALCAHEARKPFMAAAE 224
                                    5667777776666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2231.97
//
Query:       gi|116754564|ref|YP_843682.1|  [L=348]
Description: histidinol-phosphate aminotransferase [Methanosaeta thermophila PT]
Scores for complete 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  146.2   0.0    3.9e-42  144.7   0.0    1.6  1  Aminotran_1_2  Aminotransferase class I and II
     0.0013   17.7   0.0     0.0024   16.8   0.0    1.3  1  Alliinase_C    Allinase


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.7   0.0   4.4e-46   3.9e-42       4     362 ..      38     337 ..      35     337 .. 0.92

  Alignments for each domain:
  == domain 1  score: 144.7 bits;  conditional E-value: 4.4e-46
                                    EESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHH CS
                  Aminotran_1_2   4 inLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliea 83 
                                    + L+ ne++++    ++pev++a  +      +l +y+ +d   e+ +a a++lg         e+ v+ g G + +i+ 
  gi|116754564|ref|YP_843682.1|  38 VFLSRNENPYG----PSPEVVRAVSR-----ADLSRYPSQD---EFLSAAAEYLG-------VSEDLVIAGAGLDGIIDS 98 
                                    6699*******....********988.....99999*9999...***********.......7777************** PP

                                    HHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT-- CS
                  Aminotran_1_2  84 lifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGt 163
                                    + +l+ l++g+  ++p pty+ y+ ++rl+g++ v  +            +l    +e p+    t + +++sp+NPtG 
  gi|116754564|ref|YP_843682.1|  99 VSRLF-LEKGRSAFIPVPTYTYYELAARLCGATPVLGR------------NL----REIPK---DTSLTFICSPNNPTGG 158
                                    *****.***************************99999............33....33333...5569************ PP

                                    B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHH CS
                  Aminotran_1_2 164 vatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvsql 243
                                    +++ e l+++    +    ++f+DeaYa+f+   +       +ve++ nl++ ++lsKafGlaG+R+Gy+++ ++v++q 
  gi|116754564|ref|YP_843682.1| 159 LIDDELLREV---LEGTDSMVFLDEAYAEFAGVGH-----AEWVERYENLIVGRTLSKAFGLAGIRIGYAVAPEWVAEQY 230
                                    **********...666678************9965.....89************************************** PP

                                    HHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEEEEETHHCHHHHHHH CS
                  Aminotran_1_2 244 rklsrpflsssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmflltdlsaetakelskk 323
                                    ++++  f +s+++ a  +aal+d++    +++ +++r+ ++r+++ ++L        +s+++++++  ++++  ++l + 
  gi|116754564|ref|YP_843682.1| 231 NRAAPVFGISAPAIAGGVAALKDPH----HMKSAVKRILAERERVAAHL-----RTHPSHANFLYVETVRES--SALVRD 299
                                    *************************....9*******************.....667888999999888888..****** PP

                                    HHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHHH CS
                  Aminotran_1_2 324 Lleevgvyvtpgtsftv..pgrlRitvAglteeeleelvea 362
                                    Ll+e g+ v  ++        ++R+t+  +t+ee++ ++ea
  gi|116754564|ref|YP_843682.1| 300 LLKE-GISVKDCSGIPGsdNHHIRVTI--GTPEENDAFLEA 337
                                    ****.****9976443359889*****..******999985 PP

>> Alliinase_C  Allinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   2.7e-07    0.0024     139     208 ..     145     222 ..     132     232 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.7e-07
                                    EEEEEESS-TTT-.....--------TT-EEEEEE-TT-.ST..TTS---S-B--SEEEEEHHHHHS-GGG-EEEEEE CS
                    Alliinase_C 139 fielvtsPnnPdg.....llreavvkgseakviyDlayY.WP..hytpitskadedimLftlskltGhaGsrlGWalv 208
                                     + ++ sPnnP g      l ++v++g+++ v  D ay  +    +++  ++ ++ i+  tlsk  G aG+r+G+a+ 
  gi|116754564|ref|YP_843682.1| 145 SLTFICSPNNPTGgliddELLREVLEGTDSMVFLDEAYAeFAgvGHAEWVERYENLIVGRTLSKAFGLAGIRIGYAVA 222
                                    567899*****76222224567899************95222112334445556667779***************974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2567.15
//
Query:       gi|116754565|ref|YP_843683.1|  [L=757]
Description: anaerobic ribonucleoside-triphosphate reductase [Methanosaeta thermophila PT]
Scores for complete 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-159  530.7   0.0   5.8e-159  530.5   0.0    1.0  1  NRDD      Anaerobic ribonucleoside-triphosphate reductase


Domain annotation for each model (and alignments):
>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  530.5   0.0  3.2e-163  5.8e-159       1     561 []     128     752 ..     128     752 .. 0.94

  Alignments for each domain:
  == domain 1  score: 530.5 bits;  conditional E-value: 3.2e-163
                                    .XHTTHHHHHHHHHHHHHHHHHHHH-H..HHHHHHHHHHHTTSEEETTGGGTTT.S--EEE--SHHHHHH-CTT-SSS.. CS
                           NRDD   1 enanvdskslsglrlklasevskeyalkkllpkevaeaheegdiHiHDldylallttyClgidlkdlleeGlktgngv.. 78 
                                    enan+ +++++++++k a+++ske +l  llp+++++ h +gd+HiHDl+y+ +  ++C+++dl++++ +Gl+  +g   
  gi|116754565|ref|YP_843683.1| 128 ENANL-QDNAETSHKKKADKISKEQYLL-LLPPHLSDHHISGDLHIHDLEYFGT-RPFCQDHDLRYFFYYGLMP-DGRgt 203
                                    8****.*********************5.************************9.77***************65.55556 PP

                                    ....-B---SHHHHHHHHHHHHHHHHTSSSS-EEETTHHHHHHHHHHHHHHTTSS-GHHHHHHHHHHHHHHHTTS-S..S CS
                           NRDD  79 ....srppkhietalalavnilqtlqneqaGgqaissfdtylapfvrkdyekklkkltkkeikqamqefvynlntlpsrr 154
                                        + p+k+ e+a+ +av++l+++q+++aGgq++++f+t++ap++  +      +l+++eikq mq+fvy++++++++r
  gi|116754565|ref|YP_843683.1| 204 kasvAGPAKKPEVAILHAVKALGSAQTNFAGGQGFYNFLTFVAPYL--E------GLDYEEIKQLMQMFVYEMTQMMVAR 275
                                    9999******************************************..6......78*********************** PP

                                    SSS---EEEEEE.-HH......................................HHHHHTTTTS-HCH----SEEEEEEE CS
                           NRDD 155 GaQvpFtninlgldtp.......................tegrfee..kliikallevmleGdgnkgtpftFPilifklk 209
                                    G+Q +F++++l+ ++p                       t+g+fe+  +l +kal+evmleGd++ g+pf+FP++ ++++
  gi|116754565|ref|YP_843683.1| 276 GGQLVFSSVQLTPGVPtiwkdkpvvykgriwngeqaplkTYGEFERevRLAFKALMEVMLEGDYW-GKPFNFPKPEISIE 354
                                    *****************************************************************.************** PP

                                    EETETTH...............HHHHHHHHHHTTT--EEE.......EEES--GGGTT-------....-.......... CS
                           NRDD 210 edfnleeed..........pnydlfklalevtakrgfpyffnlledlepedekevasmgCRlrld....ege........ 267
                                     df ++e+d          ++ dl+ la++++ak+g pyf n+l+++++  +  +++++C ++++    + +        
  gi|116754565|ref|YP_843683.1| 355 PDF-MREDDefnrahpdlpTYRDLYMLAFKLAAKYGAPYFDNQLPEYRGAGKGISCYQCCAYQFSstfqN-Dtefedkly 432
                                    **9.566566**********************************99999999*************65531.123556666 PP

                                    ....S---EEEEEEEEEEHHHHHH..HH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT.-HHH.HTTSS-G.E... CS
                           NRDD 268 ....rlggrgslgvvtiNlprlaleakgdeekffelLdellelakealeerrkilekllakg.lpflmgkgylks.rkkk 341
                                        ++ ++gs++vv++N+pr a++a+g++e +fe L+el+++  e+++ +r+++ k++a+g +pf++ ++  +  ++++
  gi|116754565|ref|YP_843683.1| 433 fkdgKHFSMGSWQVVSLNCPRAAYKARGEDELLFEYLRELMDVSVEIFKVKRDWMDKIIANGrMPFAT-QRPRDPlTGER 511
                                    65555556**********************************************************75.44443223667 PP

                                    ..........EEEEEEE-HHHHHHHTTEEEE..-HHHHHHHHHHHHHHHHHHHHHHHHHSS-EEEEE---TTHHHHHHHH CS
                           NRDD 342 deveevlkngtltiGfiGlaEalkaltgkkigeseeakefalkvlkhmrekadelkeetglnfsleatPaEslsgrfakl 421
                                     +++  l+  ++tiG++G++E+++++tgk+++es++a++fa++++++m+ ++++l++ +g++++l +tPaE++++rfa  
  gi|116754565|ref|YP_843683.1| 512 GTMAVDLDRLVYTIGVVGINEMVQFHTGKQMHESRDAWRFAVRAMTEMQLYVKKLSRDHGMTIALARTPAETTAQRFAVS 591
                                    789999************************************************************************** PP

                                    H....HH...........................HHG-SSSS-TTSSB-HHHHHHHHHHHTGGGTT-S-EEEEBSS--SS CS
                           NRDD 422 dk..kkfgeipgv.dke................pyYtNsfhvpvdekislfekikleaefqklttGGailyieldeekkn 482
                                    d   ++++e  +   k+                +yYtN +hv v+++i ++e+  le+ f ++++GG+i++i+l+e+ ++
  gi|116754565|ref|YP_843683.1| 592 DLlhDEYRECAKRvVKGdlktalenlhrtrdlpVYYTNGTHVCVSADIPIMERAMLEHVFFPIVDGGNIFHIFLGESDPD 671
                                    *97679*7665554555899999999****************************************************** PP

                                    HHHHHHHHH.HHHHTT--EEEEE--EEEETT.--..EESSSB-TTT--BE.EEEEEESSSSEEEHHHHHHHHHHHSGG-- CS
                           NRDD 483 pealeklvk.iakktgigYfsinpkidvCnecgy..kgeiekCpkCgseeevevirRitGYlrpvsswnkgkkaElkdRv 559
                                    pe+l+++   +ak+t+igYf+++ +++vC++c     g++ekCp+C+s+  v++i+RitGYl+ vs wn++k++El+dR+
  gi|116754565|ref|YP_843683.1| 672 PESLMNFGMnLAKNTQIGYFAFTRDMTVCMSCCAisPGLQEKCPRCNSSV-VDHISRITGYLQAVSGWNAAKQQELRDRK 750
                                    *******999**********************99999**********555.***************************** PP

                                    -B CS
                           NRDD 560 kh 561
                                    ++
  gi|116754565|ref|YP_843683.1| 751 RY 752
                                    98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (757 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.26s 00:00:00.91 Elapsed: 00:00:00.44
# Mc/sec: 5159.99
//
Query:       gi|116754566|ref|YP_843684.1|  [L=58]
Description: 4Fe-4S ferredoxin iron-sulfur binding domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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   67.7  17.3    2.1e-10   40.0   4.6    2.1  2  Fer4        4Fe-4S binding domain
    4.2e-14   51.9  17.0    7.3e-08   32.2   4.8    2.1  2  Fer4_6      4Fe-4S binding domain
    1.1e-12   47.2  16.3    1.9e-07   30.7   4.3    2.2  2  Fer4_2      4Fe-4S binding domain
    2.1e-11   43.8  12.8    3.3e-11   43.2  12.9    1.3  1  Fer4_9      4Fe-4S dicluster domain
    4.6e-11   43.1  13.1    6.4e-11   42.7  13.1    1.3  1  Fer4_7      4Fe-4S dicluster domain
      5e-11   42.6  14.1    5.5e-11   42.4  14.1    1.0  1  Fer4_21     4Fe-4S dicluster domain
    3.4e-10   39.9  15.5    7.2e-10   38.8  15.6    1.4  1  Fer4_10     4Fe-4S dicluster domain
    1.8e-09   38.4  14.0    9.8e-05   23.2   4.7    2.0  2  Fer4_16     4Fe-4S double cluster binding domain
    9.9e-08   32.4  16.4    0.00029   21.3   2.7    2.4  2  Fer4_13     4Fe-4S single cluster domain of Ferredoxin I
    4.2e-07   30.0  15.7     0.0006   20.1   5.4    2.1  2  Fer4_4      4Fe-4S binding domain
      8e-06   26.4  18.5     0.0012   19.6   5.3    2.2  2  Fer4_3      4Fe-4S binding domain
    8.3e-06   26.5  15.4    0.00021   21.9   2.5    2.7  2  Fer4_15     4Fe-4S single cluster domain
    1.8e-05   25.2  16.7     0.0051   17.3   3.9    2.1  2  Fer4_17     4Fe-4S dicluster domain
    9.6e-05   22.8  17.4      0.025   15.0   5.1    2.1  2  Fer4_8      4Fe-4S dicluster domain
    0.00017   22.4   7.5      0.074   13.9   1.5    2.0  2  Fer4_22     4Fe-4S dicluster domain
     0.0011   19.1   7.2     0.0012   18.9   7.2    1.1  1  Fer4_11     4Fe-4S dicluster domain
     0.0097   16.1  14.8       0.13   12.5   3.3    2.0  2  Fer4_18     4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.24   11.5   7.7        0.3   11.2   7.7    1.2  1  Fer4_19     Divergent 4Fe-4S mono-cluster
        1.2    9.3   6.8        1.5    9.0   0.7    2.0  2  ETF_QO      Electron transfer flavoprotein-ubiquinone oxidore


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 !   34.1   4.9   1.6e-11   1.5e-08       2      24 .]       4      26 ..       3      26 .. 0.95
   2 !   40.0   4.6   2.2e-13   2.1e-10       2      23 ..      34      55 ..      33      56 .. 0.95

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 1.6e-11
                                   EEETTTSSS-THHHHHSTTTEEE CS
                           Fer4  2 videekCigCGaCvevCPvgAIt 24
                                   v++ e C+ CG+Cve CP +AI+
  gi|116754566|ref|YP_843684.1|  4 VVNREECVSCGTCVEECPEEAIK 26
                                   89********************6 PP

  == domain 2  score: 40.0 bits;  conditional E-value: 2.2e-13
                                   EEETTTSSS-THHHHHSTTTEE CS
                           Fer4  2 videekCigCGaCvevCPvgAI 23
                                   v+d+ekC+ CG+Cve+CP +AI
  gi|116754566|ref|YP_843684.1| 34 VVDPEKCTECGTCVEACPSEAI 55
                                   8********************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 !   26.1   4.3   6.6e-09   6.2e-06       2      24 .]       3      25 ..       2      25 .. 0.95
   2 !   32.2   4.8   7.7e-11   7.3e-08       1      24 []      32      55 ..      32      55 .. 0.95

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 6.6e-09
                         Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                   ++++++ C++Cg Cv  CPe ai
  gi|116754566|ref|YP_843684.1|  3 AVVNREECVSCGTCVEECPEEAI 25
                                   799******************98 PP

  == domain 2  score: 32.2 bits;  conditional E-value: 7.7e-11
                         Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                   ++++dp+kC+ Cg Cv +CP  ai
  gi|116754566|ref|YP_843684.1| 32 IAVVDPEKCTECGTCVEACPSEAI 55
                                   689*****************9998 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   4.1   8.1e-08   7.7e-05       2      22 .]       2      22 ..       1      22 [. 0.92
   2 !   30.7   4.3     2e-10   1.9e-07       2      21 ..      32      51 ..      31      52 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 8.1e-08
                         Fer4_2  2 pvvvdtdrCigCgaCvsaCPa 22
                                   p+vv+++ C++Cg+Cv  CP+
  gi|116754566|ref|YP_843684.1|  2 PAVVNREECVSCGTCVEECPE 22
                                   5799****************5 PP

  == domain 2  score: 30.7 bits;  conditional E-value: 2e-10
                         Fer4_2  2 pvvvdtdrCigCgaCvsaCP 21
                                    +vvd+++C++Cg+Cv aCP
  gi|116754566|ref|YP_843684.1| 32 IAVVDPEKCTECGTCVEACP 51
                                   579***************** PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2  12.9   3.5e-14   3.3e-11       1      51 []       9      55 ..       9      55 .. 0.92

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 3.5e-14
                         Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                   +C++Cg+Cve Cp ++++ d+ e  +   +    +C++Cg+CveaCp++ai
  gi|116754566|ref|YP_843684.1|  9 ECVSCGTCVEECPEEAIKLDDEEIAVVDPE----KCTECGTCVEACPSEAI 55
                                   5********************999988754....7*************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 !   42.7  13.1   6.8e-14   6.4e-11       2      52 .]      10      54 ..       6      54 .. 0.94

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 6.8e-14
                         Fer4_7  2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                   C+ Cg Cv+ Cp +ai+ld+e      e +++dpekC+ Cg Cv++CP++a
  gi|116754566|ref|YP_843684.1| 10 CVSCGTCVEECPEEAIKLDDE------EIAVVDPEKCTECGTCVEACPSEA 54
                                   ******************997......57899****************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 !   42.4  14.1   5.9e-14   5.5e-11       1      58 [.       3      56 ..       3      57 .. 0.95

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 5.9e-14
                        Fer4_21  1 AridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58
                                   A++++++C++Cg C+  C++   +ai++d+++++ v  ++C+ C  C++ CP +++i+
  gi|116754566|ref|YP_843684.1|  3 AVVNREECVSCGTCVEECPE---EAIKLDDEEIAVVDPEKCTECGTCVEACP-SEAIH 56
                                   899****************6...*****************************.58886 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8  15.6   7.6e-13   7.2e-10       3      56 .]       4      51 ..       2      51 .. 0.80

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 7.6e-13
                        Fer4_10  3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrk.kvekCtgcgaCveaCP 56
                                   v++++ C+ Cg+Cv+ CP      +a+  + ++e++ + ++ekCt+cg CveaCP
  gi|116754566|ref|YP_843684.1|  4 VVNREECVSCGTCVEECPE-----EAI--KLDDEEIAVvDPEKCTECGTCVEACP 51
                                   7899***************.....444..44444444337**************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 !   23.2   4.7     1e-07   9.8e-05       2      30 ..      10      40 ..       9      41 .. 0.79
   2 !   20.1   4.4   9.6e-07   0.00091       1      18 [.      39      56 ..      39      58 .] 0.92

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1e-07
                        Fer4_16  2 CgtCgkCaevCPtnaikek..kekeiearec 30
                                   C++Cg C+e CP++aik +  + +++++++c
  gi|116754566|ref|YP_843684.1| 10 CVSCGTCVEECPEEAIKLDdeEIAVVDPEKC 40
                                   *****************98434455666666 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 9.6e-07
                        Fer4_16  1 rCgtCgkCaevCPtnaik 18
                                   +C++Cg C+e+CP++ai+
  gi|116754566|ref|YP_843684.1| 39 KCTECGTCVEACPSEAIH 56
                                   6***************97 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   2.7   3.1e-07   0.00029       1      18 [.       5      22 ..       5      34 .. 0.91
   2 !   17.6   5.2   4.4e-06    0.0042       1      18 [.      35      52 ..      35      53 .. 0.96

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 3.1e-07
                        Fer4_13  1 VDrdtCiacgaCvelaPd 18
                                   V+r++C++cg+Cve +P+
  gi|116754566|ref|YP_843684.1|  5 VNREECVSCGTCVEECPE 22
                                   89***************7 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 4.4e-06
                        Fer4_13  1 VDrdtCiacgaCvelaPd 18
                                   VD ++C++cg+Cve++P 
  gi|116754566|ref|YP_843684.1| 35 VDPEKCTECGTCVEACPS 52
                                   9****************5 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   2.6   1.5e-05     0.014       2      16 ..       8      22 ..       7      29 .. 0.91
   2 !   20.1   5.4   6.4e-07    0.0006       1      16 [.      37      52 ..      37      53 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.5e-05
                         Fer4_4  2 erCigCgsCvaaCPq 16
                                   e C+ Cg Cv  CP 
  gi|116754566|ref|YP_843684.1|  8 EECVSCGTCVEECPE 22
                                   78************5 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 6.4e-07
                         Fer4_4  1 qerCigCgsCvaaCPq 16
                                   +e+C++Cg Cv aCP+
  gi|116754566|ref|YP_843684.1| 37 PEKCTECGTCVEACPS 52
                                   69*************7 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   5.2   0.00017      0.16       1      15 []      10      24 ..      10      24 .. 0.92
   2 !   19.6   5.3   1.3e-06    0.0012       1      15 []      40      54 ..      40      54 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00017
                         Fer4_3  1 CtgCgaCvevCPvgA 15
                                   C+ Cg+Cve CP+ A
  gi|116754566|ref|YP_843684.1| 10 CVSCGTCVEECPEEA 24
                                   99**********866 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 1.3e-06
                         Fer4_3  1 CtgCgaCvevCPvgA 15
                                   Ct Cg+Cve+CP+ A
  gi|116754566|ref|YP_843684.1| 40 CTECGTCVEACPSEA 54
                                   ************876 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   2.5   2.3e-07   0.00021       2      32 ..       4      35 ..       3      37 .. 0.90
   2 !   12.5   4.5    0.0002      0.19       2      19 ..      34      51 ..      33      56 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 2.3e-07
                        Fer4_15  2 vvDrdaCigcglCvaea.pevfeldedglasv 32
                                   vv+r++C +cg Cv+e+ +e ++ld++ +a+v
  gi|116754566|ref|YP_843684.1|  4 VVNREECVSCGTCVEECpEEAIKLDDEEIAVV 35
                                   699**************6679*******9977 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.0002
                        Fer4_15  2 vvDrdaCigcglCvaeap 19
                                   vvD ++C+ cg Cv+++p
  gi|116754566|ref|YP_843684.1| 34 VVDPEKCTECGTCVEACP 51
                                   69***************8 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   4.8   4.2e-05      0.04      44      59 ..       8      23 ..       3      25 .. 0.88
   2 !   17.3   3.9   5.4e-06    0.0051      43      59 ..      37      53 ..      23      55 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.2e-05
                        Fer4_17 44 slCieCgeCerkCPqg 59
                                   ++C++Cg C+++CP++
  gi|116754566|ref|YP_843684.1|  8 EECVSCGTCVEECPEE 23
                                   68***********986 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 5.4e-06
                        Fer4_17 43 aslCieCgeCerkCPqg 59
                                    ++C+eCg C+++CP++
  gi|116754566|ref|YP_843684.1| 37 PEKCTECGTCVEACPSE 53
                                   57899999999999986 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   5.0   0.00013      0.13      50      63 ..       9      22 ..       6      24 .. 0.75
   2 !   15.0   5.1   2.7e-05     0.025       3      17 ..      38      52 ..      36      55 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                         Fer4_8 50 sCttcgaCtevCpv 63
                                   +C++cg C+e+Cp+
  gi|116754566|ref|YP_843684.1|  9 ECVSCGTCVEECPE 22
                                   68888888888886 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 2.7e-05
                         Fer4_8  3 ekCieCgaCqsaCpv 17
                                   ekC+eCg C +aCp+
  gi|116754566|ref|YP_843684.1| 38 EKCTECGTCVEACPS 52
                                   466666666666664 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   1.5   7.8e-05     0.074      77      95 ..       5      23 ..       1      24 [. 0.85
   2 !   12.6   0.5    0.0002      0.19      78      94 ..      36      52 ..      25      54 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.8e-05
                        Fer4_22 77 fgesgCvGCgRCieacpvk 95
                                   ++++ Cv Cg C+e cp++
  gi|116754566|ref|YP_843684.1|  5 VNREECVSCGTCVEECPEE 23
                                   57899***********985 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.0002
                        Fer4_22 78 gesgCvGCgRCieacpv 94
                                   + ++C+ Cg C+eacp+
  gi|116754566|ref|YP_843684.1| 36 DPEKCTECGTCVEACPS 52
                                   55678888888888876 PP

>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   7.2   1.3e-06    0.0012       8      59 ..       8      55 ..       3      58 .] 0.82

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.3e-06
                        Fer4_11  8 eqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykiv 59
                                   e+C  C    Cv+ +p+eai  d+e  + ++d++++  e+ ++veacP +++
  gi|116754566|ref|YP_843684.1|  8 EECVSC--GTCVEECPEEAIKLDDE-EIAVVDPEKCT-ECGTCVEACPSEAI 55
                                   456666..47**********99995.56678999998.9*********8765 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1  14.8   0.00074       0.7      58      95 ..       7      50 ..       3      50 .. 0.70
   2 !   12.5   3.3   0.00014      0.13      51      74 ..      30      53 ..      22      58 .] 0.74

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00074
                        Fer4_18 58 agdcidcescvkvcPtg.idirkG..lql...eciscllcidac 95
                                     +c++c++cv+ cP + i + +     +   +c +c+ c++ac
  gi|116754566|ref|YP_843684.1|  7 REECVSCGTCVEECPEEaIKLDDEeiAVVdpeKCTECGTCVEAC 50
                                   689************752443332112223337*********** PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00014
                        Fer4_18 51 eerkekgagdcidcescvkvcPtg 74
                                   ee +  +  +c++c++cv+ cP +
  gi|116754566|ref|YP_843684.1| 30 EEIAVVDPEKCTECGTCVEACPSE 53
                                   4555666789************74 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 ?   11.2   7.7   0.00031       0.3      10      60 ..       5      56 ..       2      58 .] 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00031
                        Fer4_19 10 dnrelCihsgnCvkglp.evFdpkrkpwikpdeasteeiievverCPSGALs 60
                                    nre C + g Cv + p e  +++++ +   d ++  e    ve CPS A+ 
  gi|116754566|ref|YP_843684.1|  5 VNREECVSCGTCVEECPeEAIKLDDEEIAVVDPEKCTECGTCVEACPSEAIH 56
                                   68999*********8763699***************************9986 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 ?    9.0   0.7    0.0016       1.5      69      92 ..       4      27 ..       2      33 .. 0.87
   2 ?    5.0   0.8     0.028        27      66      91 ..      31      56 ..      23      58 .] 0.78

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0016
                                   EE-CCC--S--HHHHH-TT--EEE CS
                         ETF_QO 69 qinaqnCvhCktCdikdpsqniew 92
                                   ++n ++Cv C tC    p++ i+ 
  gi|116754566|ref|YP_843684.1|  4 VVNREECVSCGTCVEECPEEAIKL 27
                                   5899*********99999999986 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.028
                                   EEEEE-CCC--S--HHHHH-TT--EE CS
                         ETF_QO 66 kklqinaqnCvhCktCdikdpsqnie 91
                                   +  +++ + C  C tC    ps+ i+
  gi|116754566|ref|YP_843684.1| 31 EIAVVDPEKCTECGTCVEACPSEAIH 56
                                   44578899********9888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 443.22
//
Query:       gi|116754567|ref|YP_843685.1|  [L=404]
Description: proteasome-activating nucleotidase [Methanosaeta thermophila PT]
Scores for complete 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-43  148.3   0.5    7.6e-43  146.1   0.0    2.2  2  AAA              ATPase family associated with various cellul
    1.5e-15   56.7   0.5    4.8e-15   55.1   0.5    1.9  1  AAA_lid_3        AAA+ lid domain
    4.1e-05   24.0   3.3    4.5e-05   23.9   0.3    2.7  2  AAA_16           AAA ATPase domain
    0.00024   20.9   0.0      0.001   18.8   0.0    2.0  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00031   20.8   0.9     0.0028   17.7   0.2    2.9  2  AAA_5            AAA domain (dynein-related subfamily)
     0.0004   20.5   0.2     0.0022   18.1   0.0    2.2  2  AAA_2            AAA domain (Cdc48 subfamily)
    0.00091   19.5   2.1      0.038   14.3   0.1    3.1  3  AAA_22           AAA domain
     0.0018   18.7   0.5      0.049   14.1   0.0    2.7  2  AAA_17           AAA domain
     0.0068   16.8   0.0      0.067   13.6   0.0    2.4  2  RNA_helicase     RNA helicase
     0.0079   16.2   0.0      0.018   15.1   0.0    1.6  1  AAA_14           AAA domain
     0.0083   15.5   0.3       0.21   10.9   0.0    2.9  2  ATPase           KaiC
  ------ inclusion threshold ------
       0.01   15.1   0.0      0.027   13.7   0.0    1.6  1  TIP49            TIP49 P-loop domain
      0.011   15.9   0.2      0.028   14.6   0.0    2.0  1  AAA_33           AAA domain
      0.014   15.1   0.1       0.06   13.1   0.0    2.1  2  IstB_IS21        IstB-like ATP binding protein
      0.022   13.9   0.0      0.049   12.8   0.0    1.6  1  DUF815           Protein of unknown function (DUF815)
      0.023   15.2   0.1      0.074   13.6   0.0    2.0  2  AAA_18           AAA domain
      0.069   12.9   1.4       0.23   11.2   1.4    1.8  1  SKA2             Spindle and kinetochore-associated protein 2
       0.07   12.8   0.3       0.35   10.6   0.1    2.2  2  AAA_24           AAA domain
       0.11   12.4   0.0       0.28   11.0   0.0    1.8  1  AAA_3            ATPase family associated with various cellul
       0.13   12.4   8.1       0.23   11.6   0.8    2.7  2  bZIP_1           bZIP transcription factor
       0.32   11.1  10.2       0.85    9.7  10.2    1.7  1  Cep57_CLD_2      Centrosome localisation domain of PPC89
       0.53   10.6   8.6        1.2    9.5   1.3    2.6  2  Mto2_bdg         Micro-tubular organiser Mto1 C-term Mto2-bin
       0.79   10.0  11.5      0.034   14.4   4.6    2.2  2  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
       0.89    9.5   5.6        1.9    8.4   5.6    1.5  1  Ax_dynein_light  Axonemal dynein light chain
        1.8    9.1   9.8         18    5.8   9.9    2.5  1  ZapB             Cell division protein ZapB
        7.2    7.1   7.3        4.3    7.8   2.7    2.4  2  CENP-H           Centromere protein H (CENP-H)


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 !  146.1   0.0   1.1e-45   7.6e-43       1     131 [.     185     317 ..     185     318 .. 0.96
   2 ?   -0.6   0.1       2.4   1.7e+03      31      74 ..     343     389 ..     332     402 .. 0.66

  Alignments for each domain:
  == domain 1  score: 146.1 bits;  conditional E-value: 1.1e-45
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH...TTC CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr...sgs 77 
                                    vllyG pGtGKTllakava+++ ++f+ +sgsel+ k++ge+++ +r++f+ a+ ka psi+fiDEida+++ r    ++
  gi|116754567|ref|YP_843685.1| 185 VLLYGLPGTGKTLLAKAVAHHARATFIHMSGSELVHKFIGEGAQLVRDIFQMARDKA-PSIVFIDEIDAVGSIRthdGTT 263
                                    79******************************************************9.****************987667 PP

                                    CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                            AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                     s e +r++ qLl+e+dg++++ ++v +i+atnr+d ldpallr gRfdr+iei+
  gi|116754567|ref|YP_843685.1| 264 GSAEVNRTMMQLLAEMDGFRER-GDVKIIAATNRIDILDPALLRpGRFDRIIEIP 317
                                    89999****************7.66****************************97 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.4
                                    TTTCSSSSTTHHHHHHHHHHHHHHHTS...TSEEEEEETGGGHHHHH CS
                            AAA  31 gsellskyvgesekkirelfkeakeka...kpsilfiDEidalaksr 74 
                                    +s++ +++ g+s ++++++  ea  +a   + +++ ++++ + +k+ 
  gi|116754567|ref|YP_843685.1| 343 LSSIAKQTEGASGAELKAIAVEAGMNAirrEATVVTMEDFRQAVKKV 389
                                    56666666777777777777777666666545888888877777776 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   0.5     7e-18   4.8e-15       1      44 [.     340     383 ..     340     384 .. 0.98

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 7e-18
                      AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitmedfe 44 
                                    dvdl+ +A++TeG SGA+l+a+  eA+++A+rr  + +tmedf+
  gi|116754567|ref|YP_843685.1| 340 DVDLSSIAKQTEGASGAELKAIAVEAGMNAIRREATVVTMEDFR 383
                                    9******************************************7 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   0.2       5.4   3.7e+03      86      99 ..      28      41 ..       4      82 .. 0.46
   2 !   23.9   0.3   6.5e-08   4.5e-05      24      96 ..     181     244 ..     152     390 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 5.4
                         AAA_16 86 ldeaesaeleawre 99
                                   ++ea   e+e++r+
  gi|116754567|ref|YP_843685.1| 28 EAEALRMEREEARA 41
                                   22222222222222 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 6.5e-08
                         AAA_16  24 p.elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysa.laqalareellrqlldeaesaelea 96 
                                    p + vll+G +G+GK+ l+++++++++++ +i ++g    +         + + +   +l+r++ ++a++++++ 
  gi|116754567|ref|YP_843685.1| 181 PpRGVLLYGLPGTGKTLLAKAVAHHARAT-FIHMSGSELVH-------KfIGEGA---QLVRDIFQMARDKAPSI 244
                                    159********************999988.33344444444.......2233444...55555555544444443 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 !   18.8   0.0   1.5e-06     0.001      35      95 ..     184     252 ..     178     258 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.5e-06
                         RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvleka..gdlaalltnl......eekdvlfideihr 95 
                                     vllyG PG Gkt lak +a+   +++ + sg  l ++  g+ a l+ ++      ++  ++fidei  
  gi|116754567|ref|YP_843685.1| 184 GVLLYGLPGTGKTLLAKAVAHHARATFIHMSGSELVHKfiGEGAQLVRDIfqmardKAPSIVFIDEIDA 252
                                    59**********************999998888765543355555544432212223447999999975 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   0.2     4e-06    0.0028       1      78 [.     184     254 ..     184     307 .. 0.64
   2 ?   -3.0   0.0       9.5   6.6e+03      61      83 ..     368     391 ..     347     392 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4e-06
                                    EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG-- CS
                          AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEverae 78 
                                    +vlL G pGtgK+ la+ +a+  ++++  + +++      l+ +    +g +  +d   +   + ++i+++DE++ + 
  gi|116754567|ref|YP_843685.1| 184 GVLLYGLPGTGKTLLAKAVAHHARATFIHMSGSE------LVHKFI-GEGAQLVRDIFQMARDKAPSIVFIDEIDAVG 254
                                    59********************999888766655......666665.3555556666666666688888888888665 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 9.5
                                    ----.G-SEEEEESGGG--HHHHH CS
                          AAA_5  61 raar.egeilvlDEveraesevln 83 
                                    +a+r e+ ++ ++++ +a ++vl+
  gi|116754567|ref|YP_843685.1| 368 NAIRrEATVVTMEDFRQAVKKVLG 391
                                    344468888888888888888775 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   3.2e-06    0.0022       7     103 ..     186     276 ..     181     290 .. 0.83
   2 ?   -1.0   0.2       2.4   1.7e+03      30      61 ..     364     394 ..     343     399 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.2e-06
                                    EEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG----- CS
                          AAA_2   7 lllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpke 84 
                                    ll g  g+Gkt+laka+a + ++    ++i +  sel      + + +  +  ++  + a ++   iv++DEid + + +
  gi|116754567|ref|YP_843685.1| 186 LLYGLPGTGKTLLAKAVAHHARA----TFIHMSGSELVH----KFIGEGAQLVRDIFQMARDKApsIVFIDEIDAVGSIR 257
                                    678889***************96....999999999999....66666667777777777777788**********9976 PP

                                    --------HHHHHHHHHHH CS
                          AAA_2  85 ssgadvSregVqrdLLqil 103
                                    +      + +V r ++q+l
  gi|116754567|ref|YP_843685.1| 258 THDGTTGSAEVNRTMMQLL 276
                                    6666677889999999998 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.4
                                    ....-EEEEEGGG-------THHHHHHHHHTT CS
                          AAA_2  30 kkekkliradaselleeeevehlvsrligapp 61 
                                    +   + ir +a+ ++  e+ ++ v++ +g+++
  gi|116754567|ref|YP_843685.1| 364 EAGMNAIRREATVVTM-EDFRQAVKKVLGEEE 394
                                    4445678888888887.888888888777665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       6.6   4.6e+03      96     112 ..      25      47 ..       4      70 .. 0.60
   2 !   14.3   0.1   5.5e-05     0.038       8      44 ..     185     212 ..     180     223 .. 0.82
   3 ?    3.3   0.0      0.14        95      78     126 ..     229     291 ..     224     299 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 6.6
                         AAA_22  96 iiDEaqhlr..s....eealeeL 112
                                    + +Ea+ lr  +    ++++e L
  gi|116754567|ref|YP_843685.1|  25 LAEEAEALRmeReearAKLFESL 47 
                                    45666666554122223333333 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 5.5e-05
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvf 44 
                                    ++++G +GtGKT+l++ +++ +         r+++++
  gi|116754567|ref|YP_843685.1| 185 VLLYGLPGTGKTLLAKAVAHHA---------RATFIH 212
                                    689****************998.........555555 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.14
                         AAA_22  78 llealeqalraravielliiDEaqhlr...s...........eealeeLrsllnl.srkgvqli 126
                                    l++ + q +r++a  +++ iDE++ +    +            ++++ L ++  + +r +v++i
  gi|116754567|ref|YP_843685.1| 229 LVRDIFQMARDKAP-SIVFIDEIDAVGsirThdgttgsaevnRTMMQLLAEMDGFrERGDVKII 291
                                    55555566666666.9*********975551455556666766666666666655666666665 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1      0.41   2.8e+02      39     122 ..      47     128 ..      29     138 .. 0.60
   2 !   14.1   0.0   7.1e-05     0.049       1      37 [.     188     226 ..     188     281 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.41
                                    SHSSHHHHCTSHHHHHH.HHHHHH...HHHHHHHHHSSEEEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHH CS
                         AAA_17  39 lakardemrklpleekk.elqkea...aekiaeeakkkgvlvdghprikeqagfldglpkevleelkpdaiilleadpee 114
                                    l+++++++r+l+  +k+ +l++++    +++ e  +++ v++  h    ++++f+ + p e+ e+l+p+  + ++ +   
  gi|116754567|ref|YP_843685.1|  47 LISNKKYLRELERLKKEnALLRRMplfLATVIE-VGDDYVMLRQHG---NNQEFITTAPPEIMEKLQPNSRVAINNSLT- 121
                                    566666666654444431233322011222232.266667888887...578899999999999999999999887763. PP

                                    HHHHHHHH CS
                         AAA_17 115 ilerrlkd 122
                                     + r+l++
  gi|116754567|ref|YP_843685.1| 122 -IVRLLER 128
                                    .3356665 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 7.1e-05
                                    EE-TTSSHHHHHHHHHHHH..TEEEEEHHHHHHHHHHTT CS
                         AAA_17   1 lGgPGsGKgtqceklveky..gfthlsaGdllreeakrg 37 
                                    +G+PG GK+ +++ ++++    f h+s ++l+ + + +g
  gi|116754567|ref|YP_843685.1| 188 YGLPGTGKTLLAKAVAHHAraTFIHMSGSELVHKFIGEG 226
                                    7***********999988755788888777776666544 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   9.7e-05     0.067       1      68 [.     185     243 ..     185     271 .. 0.82
   2 ?   -0.2   0.0       1.9   1.3e+03      49      67 ..     373     392 ..     366     403 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.7e-05
                   RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvvidDfgqvkdeenps 68 
                                    ++lyG +g+GK++lak            +++  ++++ + ++ ++++ g+ + ++ D+ q+  ++ ps
  gi|116754567|ref|YP_843685.1| 185 VLLYGLPGTGKTLLAKA---------VAHHARATFIHMSGSELVHKFIGEGAQLVRDIFQMARDKAPS 243
                                    689**************.........345667788899999999999999999999999999776555 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.9
                   RNA_helicase  49 gqevvvidDfgqvkdee.np 67 
                                    + +vv ++Df q +++   +
  gi|116754567|ref|YP_843685.1| 373 EATVVTMEDFRQAVKKVlGE 392
                                    5689********99875444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.6e-05     0.018       5      79 ..     185     256 ..     182     291 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.6e-05
                         AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevpew 79 
                                    +++ G+  +GKT l+k ++++       ++ ++  +   k + + ++l + i+++++++  +++f+DEi  v ++
  gi|116754567|ref|YP_843685.1| 185 VLLYGLPGTGKTLLAKAVAHHAR---ATFIHMSGSELVHKFIGEGAQLVRDIFQMARDKAPSIVFIDEIDAVGSI 256
                                    6899999***********98877...888888888877766666567888888886667999*******998555 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00031      0.21      14      37 ..     177     200 ..     149     207 .. 0.81
   2 ?    0.9   0.0      0.35   2.4e+02     106     151 ..     228     279 ..     215     291 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00031
                         ATPase  14 gGipegrvvlitGepGtGKtifal 37 
                                     Gi   r vl++G pGtGKt++a+
  gi|116754567|ref|YP_843685.1| 177 IGIEPPRGVLLYGLPGTGKTLLAK 200
                                    68888999**************97 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.35
                         ATPase 106 elieelaeaikeikakrvviDsitgl.a.....yeekeavaReilrqlvrvl 151
                                    +l++++ ++ +++  + v iD i+++ +      ++ +a++ ++++ql+ ++
  gi|116754567|ref|YP_843685.1| 228 QLVRDIFQMARDKAPSIVFIDEIDAVgSirthdGTTGSAEVNRTMMQLLAEM 279
                                    6788888999999999999998877653100002223344555555655555 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   3.9e-05     0.027      51      90 ..     183     220 ..     179     236 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.9e-05
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevys 90 
                                    r+vLl G +gtGkt la a++++      f+++sgse+  
  gi|116754567|ref|YP_843685.1| 183 RGVLLYGLPGTGKTLLAKAVAHHA--RATFIHMSGSELVH 220
                                    89*******************986..589*******9865 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   4.1e-05     0.028       2      33 ..     185     218 ..     185     297 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.1e-05
                         AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtl 33 
                                    vll GlpG+GK+ la+ ++ +    +++ s  +l
  gi|116754567|ref|YP_843685.1| 185 VLLYGLPGTGKTLLAKAVAHHARatFIHMSGSEL 218
                                    7899*************87555544777666664 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   8.7e-05      0.06      47      72 ..     182     207 ..     167     250 .. 0.88
   2 ?   -1.8   0.0       3.3   2.3e+03      56      91 ..     354     387 ..     351     400 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.7e-05
                      IstB_IS21  47 kenivllGpsGvGKshlaialgveav 72 
                                      +++l G +G+GK+ la a++++a 
  gi|116754567|ref|YP_843685.1| 182 PRGVLLYGLPGTGKTLLAKAVAHHAR 207
                                    56899*****************9984 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.3
                      IstB_IS21  56 sGvGKshlaialgveavraglsvlfvrvedLveelk 91 
                                    sG+    +a+  g++a+r++  v  v++ed+ + +k
  gi|116754567|ref|YP_843685.1| 354 SGAELKAIAVEAGMNAIRREATV--VTMEDFRQAVK 387
                                    55555667888899999988877..45555555554 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     7e-05     0.049      24     114 ..     144     248 ..     126     252 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7e-05
                         DUF815  24 evklddLvgidkqkealvente.......qf..leglpannvLLwGarGtGKSslvkallneyaeegLrl..ievekedl 92 
                                    +v+ dd+ g+d+q +++ e +e        f  +  +p + vLL+G  GtGK  l ka+ ++++++ +++   e+ ++ +
  gi|116754567|ref|YP_843685.1| 144 NVTYDDVGGLDSQIQEIRETVElpltrpeLFssIGIEPPRGVLLYGLPGTGKTLLAKAVAHHARATFIHMsgSELVHKFI 223
                                    56667777777777777666541111111121122367889********************9999886662246666666 PP

                         DUF815  93 kelpklvellr...erperfilfvD 114
                                     e  +lv+ +    + +   i+f+D
  gi|116754567|ref|YP_843685.1| 224 GEGAQLVRDIFqmaRDKAPSIVFID 248
                                    6666666555411133445677776 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       6.6   4.5e+03      44      61 ..      38      58 ..      11      94 .. 0.57
   2 ?   13.6   0.0   0.00011     0.074       1      25 [.     185     217 ..     185     297 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 6.6
                         AAA_18 44 e...aldeskrldedkldkll 61
                                   e   +l es++ ++++l +l 
  gi|116754567|ref|YP_843685.1| 38 EaraKLFESLISNKKYLRELE 58
                                   122244444444444444443 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 0.00011
                         AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.......g 25 
                                    +ll G pG+GKt lak+++ +  +         
  gi|116754567|ref|YP_843685.1| 185 VLLYGLPGTGKTLLAKAVAHHArATfihmsgsE 217
                                    799***************887532256556552 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 ?   11.2   1.4   0.00034      0.23      44      91 ..      12      59 ..       8      67 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00034
                           SKA2 44 lerlkkvkeelqaLkeqceellaekkelidkirttlvanrellqqLqa 91
                                    +r++++ +e  aL e++e+l  e++e   k+  +l++n++ l++L++
  gi|116754567|ref|YP_843685.1| 12 TKRIAALERENRALAEEAEALRMEREEARAKLFESLISNKKYLRELER 59
                                   589*****************************************9986 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00051      0.35       5      32 ..     185     214 ..     182     293 .. 0.76
   2 ?   -0.6   0.0       1.3   9.1e+02      29      62 ..     361     394 ..     344     399 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00051
                         AAA_24   5 iliyGpsgiGKTtlakel..gpkplfidte 32 
                                    +l+yG +g+GKT lak      ++ fi + 
  gi|116754567|ref|YP_843685.1| 185 VLLYGLPGTGKTLLAKAVahHARATFIHMS 214
                                    79**************98776666666554 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.3
                         AAA_24  29 idtekGlksldadkfpdieswedfldevvel..aae 62 
                                    i +e+G++++       + ++edf+++v+++  ++e
  gi|116754567|ref|YP_843685.1| 361 IAVEAGMNAIRREAT--VVTMEDFRQAVKKVlgEEE 394
                                    678999988888874..468999*999999866444 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 ?   11.0   0.0   0.00041      0.28       2      27 ..     185     210 ..     184     250 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00041
                          AAA_3   2 vllegvPGlaktllvkalakaldlef 27 
                                    vll g+PG++ktll+ka+a++  ++f
  gi|116754567|ref|YP_843685.1| 185 VLLYGLPGTGKTLLAKAVAHHARATF 210
                                    899****************9988877 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.8   0.00034      0.23      28      60 ..       8      40 ..       4      44 .. 0.86
   2 ?    4.0   1.9     0.078        54      41      60 ..      49      68 ..      38      70 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00034
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         bZIP_1 28 ieeLerrvkaLekeNksLkseleelkkevekLk 60
                                   ie  ++r +aLe eN +L++e+e l+ e+e+ +
  gi|116754567|ref|YP_843685.1|  8 IESFTKRIAALERENRALAEEAEALRMEREEAR 40
                                   677789*******************99998765 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.078
                                   HHHHHHHHHHHHHHHHHHHH CS
                         bZIP_1 41 eNksLkseleelkkevekLk 60
                                    Nk++  ele+lkke++ L+
  gi|116754567|ref|YP_843685.1| 49 SNKKYLRELERLKKENALLR 68
                                   59*************99665 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 ?    9.7  10.2    0.0012      0.85      13      64 ..      16      67 ..       5      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0012
                    Cep57_CLD_2 13 dsltrklqvheeelkrLnkERdsalrqLgvAyeelneLkaevealrkELkeq 64
                                     l+r++ +  ee ++L+ ER++a  +L + +  + +  +e+e+l+kE+   
  gi|116754567|ref|YP_843685.1| 16 AALERENRALAEEAEALRMEREEARAKLFESLISNKKYLRELERLKKENALL 67
                                   4578888888899999999*****************************8765 PP

>> Mto2_bdg  Micro-tubular organiser Mto1 C-term Mto2-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   1.3    0.0017       1.2      26      51 ..      10      35 ..       8      36 .. 0.91
   2 ?    4.6   1.1      0.06        41      30      44 ..      56      70 ..      38      70 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0017
                       Mto2_bdg 26 garerLeelkaeNrlLkaeLerdrsh 51
                                   + ++r++ l++eNr L+ e e +r+ 
  gi|116754567|ref|YP_843685.1| 10 SFTKRIAALERENRALAEEAEALRME 35
                                   779****************9999996 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.06
                       Mto2_bdg 30 rLeelkaeNrlLkae 44
                                   +Le lk+eN+lL+++
  gi|116754567|ref|YP_843685.1| 56 ELERLKKENALLRRM 70
                                   8999*******9985 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 ?   14.4   4.6     5e-05     0.034      11      70 ..       5      64 ..       1      75 [. 0.88
   2 ?   -2.2   0.1         7   4.8e+03      75      97 ..     378     400 ..     364     402 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5e-05
                    TMF_TATA_bd 11 vqlverlsseirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleele 70
                                    +l+e++ ++i  lE E ++l ee e l  er+ear+ + + + +n +  ++ ++l++ +
  gi|116754567|ref|YP_843685.1|  5 ESLIESFTKRIAALERENRALAEEAEALRMEREEARAKLFESLISNKKYLRELERLKKEN 64
                                   5799**************************************999998888777777655 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 7
                    TMF_TATA_bd  75 elqeryetlLellGeksEeveEL 97 
                                     +++  +++ ++lGe +   e L
  gi|116754567|ref|YP_843685.1| 378 TMEDFRQAVKKVLGEEEKADESL 400
                                    44444455555666655555555 PP

>> Ax_dynein_light  Axonemal dynein light chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   5.6    0.0027       1.9     119     182 ..       6      68 ..       1      70 [. 0.84

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0027
                Ax_dynein_light 119 qgkselekkikeLeeekeelekqvaelkaklealekrekerrqeeekkheeeieflkksnqqlk 182
                                       + ++k+i++Le+e++ l ++ + l+ + e+++++  e + + +kk+  e+e lkk+n  l+
  gi|116754567|ref|YP_843685.1|   6 SLIESFTKRIAALERENRALAEEAEALRMEREEARAKLFESL-ISNKKYLRELERLKKENALLR 68 
                                    55567899******************9999888888777765.67788999*********9887 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   9.9     0.026        18      21      53 ..       9      62 ..       5      70 .. 0.53

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.026
                           ZapB 21 tlLqmeieeLkeeneelkeenrele.....................eeneqlke 53
                                   ++  ++i++L++en++l+ee+++l+                     +e+e+lk+
  gi|116754567|ref|YP_843685.1|  9 ESFTKRIAALERENRALAEEAEALRmereearaklfeslisnkkylRELERLKK 62
                                   444556666666666666666666533333335555555555555555555555 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 ?    7.8   2.7    0.0062       4.3      27      76 ..       6      65 ..       1      77 [. 0.76
   2 ?    0.7   0.1      0.99   6.8e+02      35      85 ..     326     377 ..     321     391 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0062
                         CENP-H 27 eeltevekenlrlkrknrelaaellelakekesek..........eklkeelekleaelk 76
                                   + +++ +k + +l+r+nr la+e + l+ e e+ +          +k+ +ele+l++e  
  gi|116754567|ref|YP_843685.1|  6 SLIESFTKRIAALERENRALAEEAEALRMEREEARaklfeslisnKKYLRELERLKKENA 65
                                   556777888999999999999999888888888887788888766666677777777655 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.99
                         CENP-H  35 enlrlkrknrelaael.l.elakekesekeklkeelekleaelkksrqrwrvv 85 
                                    ++l++++k+ +la ++ l   ak++e  +  ++ +  ++ea +++ r++++vv
  gi|116754567|ref|YP_843685.1| 326 KILEIHTKKMKLAGDVdLsSIAKQTEGAS-GAELKAIAVEAGMNAIRREATVV 377
                                    67899999999999994434444444444.45555678899999999988886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1153  (0.0643092); expected 358.6 (0.02)
Passed bias filter:                      796  (0.0443973); expected 358.6 (0.02)
Passed Vit filter:                       139  (0.0077528); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.46
# Mc/sec: 2625.81
//
Query:       gi|116754568|ref|YP_843686.1|  [L=286]
Description: hypothetical protein Mthe_1267 [Methanosaeta thermophila PT]
Scores for complete 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-94  314.4   0.3    5.5e-94  314.1   0.3    1.0  1  DUF2099   Uncharacterized protein conserved in archaea (DUF20


Domain annotation for each model (and alignments):
>> DUF2099  Uncharacterized protein conserved in archaea (DUF2099)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  314.1   0.3   3.1e-98   5.5e-94       1     256 [.       4     259 ..       4     260 .. 0.98

  Alignments for each domain:
  == domain 1  score: 314.1 bits;  conditional E-value: 3.1e-98
                        DUF2099   1 HiiealgkarvvvkdgkvvevgepkikyCPlfkklrgikeitkeaikkniefrikefGlftkkRkleskedfvsfGasEi 80 
                                    H+ e++ ka v+++dgk + +++p i+ CPl ++l+gi+e ++e+++++i+++i+++G+++++R+le +ed vsfGasEi
  gi|116754568|ref|YP_843686.1|   4 HLAEMA-KALVRIRDGKPEVLTSPLIRFCPLRRDLYGIDEESRETVEEVIRSHIEDLGMYSSQRVLELAEDPVSFGASEI 82 
                                    666665.56*********************************************************************** PP

                        DUF2099  81 lstalkeglidaavivcdgaGtvivtnpelvqglggrisGlveTePieevierieeeggivldketaeidqveGvkkAie 160
                                    l+++++egl+daav+vcdgaGtv++t+p+++q++g++++Gl++TePi+e+++ +e++g+i++d++ a+idq++G+ +Ai+
  gi|116754568|ref|YP_843686.1|  83 LMDGMAEGLVDAAVLVCDGAGTVVITRPDVLQAIGAHMTGLIKTEPIAEIQDGLEQKGCILIDRH-ATIDQIRGFVTAID 161
                                    **************************************************************987.************** PP

                        DUF2099 161 kgykkiavtvae..aedakklrelekeegvkilifavhttgiskeeaeelveaaDlvtacAskeireivkkkallqvgks 238
                                    +g++++avt+a   ++da++lr++ +++g + +i+avhttgis++ea  l+e++D++++cAs+++re+v+++a+lq+g s
  gi|116754568|ref|YP_843686.1| 162 AGFERVAVTLAGsmSSDARDLRAIGARSGRRPFILAVHTTGISSDEAAALAETCDIIWSCASRAVREVVGERAVLQIGVS 241
                                    ***********98789**************************************************************** PP

                        DUF2099 239 vpvfaltekGkelilerl 256
                                    +pvfa+t++Gk+l+l+r+
  gi|116754568|ref|YP_843686.1| 242 IPVFAMTQEGKRLVLNRA 259
                                    ***************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 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:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2090.07
//
Query:       gi|116754569|ref|YP_843687.1|  [L=296]
Description: hypothetical protein Mthe_1268 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00035   21.2   0.0     0.0011   19.6   0.0    1.9  1  Methyltransf_25  Methyltransferase domain
    0.00094   19.0   0.0     0.0014   18.4   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      0.002   18.0   0.0     0.0037   17.1   0.0    1.5  1  Methyltransf_23  Methyltransferase domain
     0.0034   16.8   0.0     0.0096   15.3   0.0    1.6  2  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0041   17.7   0.0      0.009   16.6   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
  ------ inclusion threshold ------
      0.044   13.4   0.0      0.069   12.7   0.0    1.3  1  MetW             Methionine biosynthesis protein MetW


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   3.8e-07    0.0011       1      81 [.     149     226 ..     149     235 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.8e-07
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHH.HHHHHHHTTTTEEEEESBCCGBS..SSTTTEEEEEEESTGGGS CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemlea.areraeeeglnvefvqgdaedlp..fedgsfDlvvssgalhhl 77 
                                    vL++GcG+G  t+ l   +   + +++Di+   + +  r+ a   +   +  + da+ lp  f  +sfD+v+ + ++ ++
  gi|116754569|ref|YP_843687.1| 149 VLEVGCGSGIGTMVLRSLG--MNPWAMDIDRCEVCQgLRAGA--LD-PRRTFVLDARLLPrfFSTESFDAVMGF-MVGLI 222
                                    9**************9995..9*******9855554044444..33.5567779999999888*********95.44556 PP

                                    SHHH CS
                Methyltransf_25  78 sded 81 
                                    +d++
  gi|116754569|ref|YP_843687.1| 223 DDSN 226
                                    6555 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 !   18.4   0.0   4.7e-07    0.0014      68      93 ..     138     165 ..     128     182 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 4.7e-07
                                    HTT..--TT-EEEEES-TTSHHHHHHHH CS
                           PCMT  68 lle..lkkgarvLevGsGsGyltavlar 93 
                                    lle  l++g+rvLevG+GsG+ t vl  
  gi|116754569|ref|YP_843687.1| 138 LLEdaLDDGSRVLEVGCGSGIGTMVLRS 165
                                    55678******************99865 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.2e-06    0.0037      18      54 ..     141     177 ..     122     229 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.2e-06
                Methyltransf_23  18 pklraggrvLdiGcGtGillevlrengfsvtgvDlsp 54 
                                    + l+ g+rvL++GcG+Gi + vlr  g +  ++D+++
  gi|116754569|ref|YP_843687.1| 141 DALDDGSRVLEVGCGSGIGTMVLRSLGMNPWAMDIDR 177
                                    3378999*************99*99999988888864 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   3.2e-06    0.0096     154     197 ..     138     180 ..     133     186 .. 0.89
   2 ?   -2.3   0.0      0.77   2.3e+03      10      35 ..     251     276 ..     246     289 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.2e-06
                           PrmA 154 aleklvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAv 197
                                    +le+ +  g++vl vG+GSGi +++   Lg +   a+DiD   v
  gi|116754569|ref|YP_843687.1| 138 LLEDALDDGSRVLEVGCGSGIGTMVLRSLGMNP-WAMDIDRCEV 180
                                    5899999***********************976.7999998655 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.77
                           PrmA  10 kkeaeeavsniLeelgakgvaiedsk 35 
                                    +k+++e+++++L +lg  g  i++s+
  gi|116754569|ref|YP_843687.1| 251 SKREAERLADLLANLGWDGRIIDNSS 276
                                    678899999****9999999998776 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     3e-06     0.009       1      66 [.     150     215 ..     150     221 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3e-06
                                    EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTS..S-TT-EEEEE CS
                Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklp..fednsfDlvv 66 
                                    L+vGcG+G+ +  l + g++  ++D++   + +  +++  ++   +  v da+ lp  f  +sfD+v+
  gi|116754569|ref|YP_843687.1| 150 LEVGCGSGIGTMVLRSLGMNPWAMDIDRCEVCQGLRAGALDP--RRTFVLDARLLPrfFSTESFDAVM 215
                                    89***********************99888844434444444..356899***999999*******97 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.3e-05     0.069       8      56 ..     140     187 ..     133     217 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.3e-05
                           MetW   8 aelikpgsrvldlGcGdGellellkeekqvdgrGleldeegvaecvakG 56 
                                     + +++gsrvl++GcG G    +l+   +++   +++d+  v + +  G
  gi|116754569|ref|YP_843687.1| 140 EDALDDGSRVLEVGCGSGIGTMVLRS-LGMNPWAMDIDRCEVCQGLRAG 187
                                    567899************99999976.8888888888888887777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.23s 00:00:00.68 Elapsed: 00:00:00.78
# Mc/sec: 1147.69
//
Query:       gi|116754570|ref|YP_843688.1|  [L=207]
Description: TrkA domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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-16   58.5   0.0    1.7e-15   57.3   0.0    1.6  1  TrkA_N    TrkA-N domain
    1.1e-08   34.8   1.2    8.6e-08   31.9   0.1    2.2  2  TrkA_C    TrkA-C domain
  ------ inclusion threshold ------
      0.073   13.1   0.1       0.19   11.7   0.0    1.8  1  HTH_46    Winged helix-turn-helix DNA binding


Domain annotation for each model (and alignments):
>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.3   0.0   2.9e-19   1.7e-15      42     114 ..       9      81 ..       2      83 .. 0.95

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 2.9e-19
                                    SEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHHHHHHHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEEE CS
                         TrkA_N  42 levvvgdatdeevLeeagiekadaviaatgddeanilavllakelnpkkkiiaraqdpehaellkklgadvvi 114
                                     ++++gdat+e+vL+++gi +a+++++a++d  a+  +v+la+ ln++++iiar+++ +++e l  lgad+v+
  gi|116754570|ref|YP_843688.1|   9 EPIYYGDATQEQVLRHLGITDARVLVIAISDPVATRQIVELARRLNEDIYIIARTRYIQEVETLHMLGADEVV 81 
                                    5699*******************************************************************98 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1     0.043   2.6e+02       4      33 ..      33      63 ..      30      73 .. 0.76
   2 !   31.9   0.1   1.4e-11   8.6e-08       2      67 ..     142     203 ..     141     206 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.043
                                   EEEE--GGGTTSBHHHHTHHHH...S-EEEEEE CS
                         TrkA_C  4 vtvpagsplvGktlkelnlrar...gvlvvair 33
                                   ++++ + p++ + + e  l +r   ++ ++a  
  gi|116754570|ref|YP_843688.1| 33 LVIAISDPVATRQIVE--LARRlneDIYIIART 63
                                   6778889999999999..766666888888755 PP

  == domain 2  score: 31.9 bits;  conditional E-value: 1.4e-11
                                    EEEEEE--GGGTTSBHHHHTHHHHS-EEEEEE-T-EEES--TT-B--TT-EEEEEEEHHHHHHHHH CS
                         TrkA_C   2 vevtvpagsplvGktlkelnlrargvlvvairRggeliipsgdtvLeeGDvllvvgspsdlaelre 67 
                                    + ++vp gs+ +G+ l+el++++    v+ai Rg+e +  +g ++L+eGDvl+++ +p+ + e+++
  gi|116754570|ref|YP_843688.1| 142 FTIRVPGGSKAAGRNLDELGIEN----VLAINRGDETLRSTGGLRLQEGDVLILIDTPEKMGEIER 203
                                    6799*****************98....****************************99998887776 PP

>> HTH_46  Winged helix-turn-helix DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.3e-05      0.19      15      52 ..      81     118 ..      65     123 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.3e-05
                         HTH_46  15 lpeelreninvlkyIqkrtnLSrSsimkvLseLkkggy 52 
                                    +pee+  +i++   + +r +LSr +i + + + + g+y
  gi|116754570|ref|YP_843688.1|  81 VPEEYETSIKIFARVLERYQLSRDTIERFVEDVRAGDY 118
                                    69**********************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1535.75
//
Query:       gi|116754571|ref|YP_843689.1|  [L=457]
Description: sodium/hydrogen exchanger [Methanosaeta thermophila PT]
Scores for complete 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-63  215.4  55.4    1.4e-63  215.0  55.4    1.0  1  Na_H_Exchanger  Sodium/hydrogen exchanger family
  ------ inclusion threshold ------
      0.022   15.0   0.1      0.044   14.0   0.1    1.5  1  TrkA_N          TrkA-N domain


Domain annotation for each model (and alignments):
>> Na_H_Exchanger  Sodium/hydrogen exchanger family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.0  55.4   1.6e-67   1.4e-63       2     374 ..      24     387 ..      23     391 .. 0.95

  Alignments for each domain:
  == domain 1  score: 215.0 bits;  conditional E-value: 1.6e-67
                                    HHHHHHHHHHHHHHHHTTSXHHHHHHHHHHHHTTTTTS.....HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTHHHHHH CS
                 Na_H_Exchanger   2 vllillallvgllarrlklpeivgliiaGlllGpsglgliepseedlevlselglilllFlaGleldlrelrknlksill 81 
                                    v++++l++ v++l++r++lp i+g++i+G++ Gp +lgli++  +++ vl+e+g+illlF +G+e++l++l++ ++ +l+
  gi|116754571|ref|YP_843689.1|  24 VIIFVLSSAVLFLFHRIRLPAILGYLITGIIAGPQCLGLIRSL-DQVAVLAEIGVILLLFTVGIEISLKDLLQIKRFVLV 102
                                    3444444444447******************************.************************************ PP

                                    HHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHHHHHHCCCCCHH CS
                 Na_H_Exchanger  82 lallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvlnDavavvllav 161
                                    +++l+vl+t+++  +++ +   lg p+ ea+++g+++s++++++vl+i + +g+ +   g+++lg+++++D+++v++  +
  gi|116754571|ref|YP_843689.1| 103 GGFLQVLFTTLA-VVFILV--NLGRPFGEAIAIGFMVSLSSTAIVLRIIQQRGEFDALHGRTILGILIFQDVIVVPMMLL 179
                                    ************.444443..79********************************************************* PP

                                    HHHHTX.XXXXTSSSTSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTHHHHHHHHHHHHHHHHHHHHHTSXXXHHHH CS
                 Na_H_Exchanger 162 llalak.eeaggetslllllliflvvavgglllglvigwllrlitrftdddrelevllvlllallaallaellgvsgilg 240
                                    ++ l +   a++e+ ++ +++++l++av++  ++++++ +l  ++++  +d el++l+++ +++++a++++ +g+s  lg
  gi|116754571|ref|YP_843689.1| 180 IPMLPGaAVATAESPIFIIIKAALLIAVVIAGAKWAVPRILYQVLKT--RDHELFLLFTVGMCFAIAWISSFVGLSLGLG 257
                                    **99989899*************************************..9****************************** PP

                                    HHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHSXHHHHHXXHHHHHHHHHHHHHHHTHHHHHHHHHTTTXSS CS
                 Na_H_Exchanger 241 aflaGlvlseyefsnklseklesfreglfnplfFvlvGlsldlkvlnnhlsvlilvllilvaillgrilavflllrllgl 320
                                    aflaGlv+se+++s ++  +++++r ++f  +fFv++G+ ldl +l   ++++++++++ + ++l++++a  l+++l+gl
  gi|116754571|ref|YP_843689.1| 258 AFLAGLVISESPYSLHAIGNIRPLR-DAFSSFFFVSIGMLLDLDLL---MKNTAYIIALSICVILIKTIACGLATSLIGL 333
                                    *************************.9*******************...9****************************** PP

                                    XHHHHHHCCCCSS.BHHHHHHHHHHHHHHXHHHHTTSSTTTCSTSXHHHHHHHH CS
                 Na_H_Exchanger 321 slrealiigfgglqrgavalalaalgpalgllarelyallivvvlftvlvqGls 374
                                    ++r  ++++++++q+g+++++l  +g ++gll++e+y l++ v+++t+   +++
  gi|116754571|ref|YP_843689.1| 334 PTRLVVLVSLALSQVGEFSFILSKVGLDAGLLSHEVYQLFLDVTVLTMAATTFM 387
                                    ***********************************************9944444 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   4.9e-06     0.044       2      35 ..     421     454 ..     420     456 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.9e-06
                                    EEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHH CS
                         TrkA_N   2 iiiGlGrvGrslaeeLseggkdvvvidkdeerve 35 
                                    ii+G+G  Gr++a   +++g+++vv+d +++ v+
  gi|116754571|ref|YP_843689.1| 421 IIVGFGVNGRNVAMAARAKGIPYVVVDLNPDIVK 454
                                    9*****************9988********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 3369.87
//
Query:       gi|116754572|ref|YP_843690.1|  [L=265]
Description: stationary phase survival protein SurE [Methanosaeta thermophila PT]
Scores for complete 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   0.5    1.6e-52  178.2   0.5    1.0  1  SurE      Survival protein SurE
  ------ inclusion threshold ------
       0.26   11.4   0.5       0.43   10.7   0.5    1.3  1  WW        WW domain


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 !  178.2   0.5   1.8e-56   1.6e-52       1     193 [.       4     199 ..       4     201 .. 0.92

  Alignments for each domain:
  == domain 1  score: 178.2 bits;  conditional E-value: 1.8e-56
                                    EEEE-SS-TT-HHHHHHHHHHTTTTSEEEEEEESSS-TTCTTS--SSSEEEEEEEECSTTTCEEEESS-HHHHHHHHHHT CS
                           SurE   1 iLltNDDGieapgiralvealaaaghevvvvaPdserSgigkaltleeplrveseeeeeeeeeyavsGtPadcvklalee 80 
                                    iL+tNDDGi apg+ra v+++++ g ev+ vaP+ +rSg+g+++++ eplr+ +++  +++++yavsGtP+d v l++  
  gi|116754572|ref|YP_843690.1|   4 ILVTNDDGIYAPGLRAAVRSVEDLG-EVIAVAPSGQRSGVGRSVSVFEPLRMAEVNL-DGKKAYAVSGTPTDSVILGIFV 81 
                                    8*********************888.*************************985554.9********************* PP

                                    TTTTS.SSEEEEEEEES---GGGG.GG-HHHHHHHHHHHTTSEEEEEEEESSS.....SS-SSS---HHHHHHHHHHHHT CS
                           SurE  81 llkekkpdlVvSGiNhGaNlgtdv.lySGTvgAaleaalegipaiAvSlaskk.....eeekkeedtfeaaakvaaklve 154
                                    +++ + pdl vSGiN G+N++td+ ++SGT+gAa+eaa  g+paiA S+++ +     +++++ e +f++a ++++++++
  gi|116754572|ref|YP_843690.1|  82 VMNGELPDLAVSGINVGENISTDTvTTSGTIGAAIEAASYGVPAIAASIQVADqgdkfDNNHSVEYKFDTAMNLLRRVAS 161
                                    ***99*******************9*************************99999999666677778************* PP

                                    TETTS-...SS-EEEEEEE..SS.GCG-SEEEE-B--CCSC CS
                           SurE 155 klieklllekvellnvNvP..eleeeeikgvkvtrlgrrry 193
                                    +++e+ +   v++ln+N+P  ++e++e   + vtrl+r+ +
  gi|116754572|ref|YP_843690.1| 162 RVLERGMPVGVDILNINLPlnATEDTE---IVVTRLARKIF 199
                                    *******************43333444...66999998765 PP

>> WW  WW domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.5   4.8e-05      0.43       6      19 ..     204     216 ..     204     216 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 4.8e-05
                                    EEEE-TTTT-EEEE CS
                             WW   6 eeqwdpdsGrvYYy 19 
                                    ee++dp+ Gr+YY+
  gi|116754572|ref|YP_843690.1| 204 EERRDPR-GRPYYW 216
                                    799****.*****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); 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 0.26s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2018.19
//
Query:       gi|116754573|ref|YP_843691.1|  [L=510]
Description: parallel beta-helix repeat-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.5e-46  157.1  42.9    9.9e-30  103.6  13.6    2.1  2  NosD        Periplasmic copper-binding protein (NosD)
    1.2e-33  116.2  51.8    3.2e-19   69.3  27.8    2.2  2  Beta_helix  Right handed beta helix region


Domain annotation for each model (and alignments):
>> NosD  Periplasmic copper-binding protein (NosD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.6  21.4     1e-22   9.3e-19       3     175 ..      61     243 ..      59     243 .. 0.87
   2 !  103.6  13.6   1.1e-33   9.9e-30      65     238 ..     224     395 ..     223     397 .. 0.94

  Alignments for each domain:
  == domain 1  score: 67.6 bits;  conditional E-value: 1e-22
                           NosD   3 naisgdevlvsargngiqlensegsei.....snneisnsrdgilldnssnntitgntienlryGihlensesntiednt 77 
                                     a+ gd+++v     g++ + + ++++       + + +s+d+    +++ ++i+g t++n+ yGi+l+  +++ i++nt
  gi|116754573|ref|YP_843691.1|  61 AASPGDTIIVG---PGVYGKFTVNKRLnligeGATVVASSSDACISVEADMVNISGFTVRNGLYGIRLSRVSGCSITNNT 137
                                    56778887776...7788888866666666845556666677778889999***************************** PP

                           NosD  78 lssne.sGialmsssnntlenNtisnnen.....yGillsdssnntisnNtis..nnnkGiflens.ssntitgNriesn 148
                                    +++++  Gi+l  ss+n++ nN++s n       yGi+l+dssn ++  N+i   n ++Gi+l+ s  +nti+gN +++n
  gi|116754573|ref|YP_843691.1| 138 VTGCKqPGIVLLTSSGNIIANNNASYNGVvgegwYGIYLTDSSNDNLIVNNIAnnNGAYGIHLSTScLNNTIKGNILNGN 217
                                    *****99********************9999***********99887777775356679*******9************* PP

                           NosD 149 qkiGilllsssegntiynNyFinnsen 175
                                      +G+++++++++n i +N   +n+ n
  gi|116754573|ref|YP_843691.1| 218 -MYGVYMFTGCSKNIIEGNLISGNKAN 243
                                    .********************999865 PP

  == domain 2  score: 103.6 bits;  conditional E-value: 1.1e-33
                           NosD  65 lensesntiedntlssne.sGialmsssnn.tlenNtisnnenyGillsdssnntisnNtis.nnnkGiflens.ssnti 140
                                    ++++++n+ie+n +s+n+ +Gi l  ++n+ t+++N+i++n+ +Gi+l ds +n+i  N i  n   Gi++++  ++nt+
  gi|116754573|ref|YP_843691.1| 224 FTGCSKNIIEGNLISGNKaNGIDLRFNCNRnTIRDNIITDNQVAGISLLDSGENEILSNDIRsNIRFGIQIQGRsDGNTV 303
                                    67899***********************888******************************87*********877***** PP

                           NosD 141 tgNriesnqkiGilllsssegntiynNyFinnsenvkydgsnnneWnttktsgtniiggpylgGNyWsdydg........ 212
                                    +gN+i+++  +Gi+   +s++n ++ N +i+n ++v + g  +n Wn +            +gGN Wsdy+g        
  gi|116754573|ref|YP_843691.1| 304 EGNNISKS-PTGIF--VESSSNIFHSNRLIDNVVQVVDRG--ENAWNAPY----------PVGGNAWSDYSGvdersgpa 368
                                    ********.*****..56668*****************99..9***9999..........789***************** PP

                           NosD 213 eD.adgDGigDtpYeindgviDylplv 238
                                    +D    DG+gDtp ein+ + D +p +
  gi|116754573|ref|YP_843691.1| 369 QDvPGADGFGDTPREINNRSRDMYPVM 395
                                    9*7789*****************9986 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 !   69.3  27.8   3.6e-23   3.2e-19      19     156 ..      95     235 ..      77     235 .. 0.92
   2 !   56.2  19.6     4e-19   3.6e-15      29     146 ..     225     338 ..     222     353 .. 0.90

  Alignments for each domain:
  == domain 1  score: 69.3 bits;  conditional E-value: 3.6e-23
                                    ES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES-EEES-SS-..... CS
                     Beta_helix  19 snsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasnnlienneitdnggs..... 93 
                                     +s++++i ++ ++   i++ ++ n + +Gi+++++s++ i+nnt++++++ gi l  +s+n+i nn+ + ng +     
  gi|116754573|ref|YP_843691.1|  95 ASSSDACISVEADMV-NISGFTVRN-GLYGIRLSRVSGCSITNNTVTGCKQPGIVLLTSSGNIIANNNASYNGVVgegwy 172
                                    455889999999998.999999999.**********************************************55555566 PP

                                    SEE-T.T-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS--EEES- CS
                     Beta_helix  94 Giyln.yssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsssnvtvrnN 156
                                    Giyl+ +s++n i nNi++nn+++Gi+++ s+ n+t+++N++++n+ +G++  +++s++ +++N
  gi|116754573|ref|YP_843691.1| 173 GIYLTdSSNDNLIVNNIANNNGAYGIHLSTSCLNNTIKGNILNGNM-YGVYMFTGCSKNIIEGN 235
                                    *****55888**********************9999**********.************99998 PP

  == domain 2  score: 56.2 bits;  conditional E-value: 4e-19
                                    -SSS-.EEES-EEES-SS-SEEE-TT.-S-EEES-EEE---SEEE-TT--S--EEES-EEES-SS-SEE-T.T-S--EEE CS
                     Beta_helix  29 rgssnvvienneiannsgsGiyilgs.snntisnntisdnngggialfgasnnlienneitdnggsGiyln.yssnntie 106
                                     g+s+++ie+n i++n  +Gi+++   ++nti++n i+dn   gi l +++ n i  n+i+ n + Gi+++  s+ nt+e
  gi|116754573|ref|YP_843691.1| 225 TGCSKNIIEGNLISGNKANGIDLRFNcNRNTIRDNIITDNQVAGISLLDSGENEILSNDIRSNIRFGIQIQgRSDGNTVE 304
                                    577889*****************9888********************************************66888**** PP

                                    S-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT CS
                     Beta_helix 107 nNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvg 146
                                    +N+i+     Gi++++ss n+ ++ N++ +n+   ++vv+
  gi|116754573|ref|YP_843691.1| 305 GNNISKSP-TGIFVESSS-NI-FHSNRLIDNV---VQVVD 338
                                    ********.*********.66.9*******98...44444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (510 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); 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: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 3410.53
//
Query:       gi|116754574|ref|YP_843692.1|  [L=489]
Description: rhodanese domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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   65.9   0.0    2.6e-11   44.0   0.0    2.3  2  Rhodanese  Rhodanese-like domain
  ------ inclusion threshold ------
        0.1   12.5   0.1       0.25   11.2   0.1    1.6  1  FlgD_ig    FlgD Ig-like domain


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.1e-07     0.001      16     107 .]     114     213 ..     105     213 .. 0.71
   2 !   44.0   0.0   2.9e-15   2.6e-11       8      97 ..     247     329 ..     240     336 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.1e-07
                      Rhodanese  16 llDvR.ppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdgggr.aaaa...aallk... 87 
                                    +lDv+  + eY    I gAv+++ + +++++k+ ++ +e+ + l + gi++ ++vv+ + + ++ ++      a++    
  gi|116754574|ref|YP_843692.1| 114 VLDVSnGASEY----IDGAVHINYMEFYNENKELKSVDEIAALLGNAGISPSDRVVLTGTDYNCpTCLGgpfGATFVywl 189
                                    77888555555....*******6666666666666655555555555*****************6666688844444244 PP

                      Rhodanese  88 ..klGy..knvsvldGGfkawkea 107
                                      + G+   ++++ldG  ++wk+a
  gi|116754574|ref|YP_843692.1| 190 mlYIGHdeSKLKLLDGDTEDWKAA 213
                                    4468876455***********985 PP

  == domain 2  score: 44.0 bits;  conditional E-value: 2.9e-15
                      Rhodanese   8 llekgkvallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellel..gidnkktvvvycdgggraaaaaal 85 
                                    +    +v+++D R+++++ +g+IpgA+n+     ++ k +e+  l++ +el++   g++++k+vvvy ++  +a+ ++ +
  gi|116754574|ref|YP_843692.1| 247 NA---DVQIVDSRTFDAFGQGSIPGALNI-----PYDKVTENGRLKDEAELESVfaGLTKDKPVVVYANTEFKASMVWFA 318
                                    33...456*********************.....999999999999999999999******************888899* PP

                      Rhodanese  86 lkklGyknvsvl 97 
                                    l+ +Gy + +++
  gi|116754574|ref|YP_843692.1| 319 LRMMGY-DARIY 329
                                    **9**5.65555 PP

>> FlgD_ig  FlgD Ig-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   2.8e-05      0.25      26      74 ..     427     470 ..     409     474 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.8e-05
                                    EEEEE-SS--EEEEEEEEESSSEEEEEEE-SB-TTS-B--SEEEEEEEE CS
                        FlgD_ig  26 tvtikDasGevVrtidlgaqsaGvvsftWdGtdndGnkladGaYtvkvt 74 
                                    t ++ Da+G +V ++ ++ +s  ++  tWd t+++     +G+Y+v+ +
  gi|116754574|ref|YP_843692.1| 427 TARVMDAQGGEVASVPMERVSDDEYVGTWDATNAS-----PGRYSVSFV 470
                                    77899*************************66665.....999999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (489 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); 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: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 3599.20
//
Query:       gi|116754575|ref|YP_843693.1|  [L=509]
Description: peptidase S8/S53 subtilisin kexin sedolisin [Methanosaeta thermophila PT]
Scores for complete 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  184.5   0.1    3.3e-54  184.2   0.1    1.1  1  Peptidase_S8  Subtilase family


Domain annotation for each model (and alignments):
>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.2   0.1   1.9e-58   3.3e-54       1     298 []     126     392 ..     126     392 .. 0.91

  Alignments for each domain:
  == domain 1  score: 184.2 bits;  conditional E-value: 1.9e-58
                                    -TT-EEEEECS-B-TT-TTTGGGEEE..EEEE---TTSG.GGEETT-SS-TT-SC-SSS....HHHHHHHHHH-B..SSS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Peptidase_S8   1 gkgvlvavlDtGvdpshpdlsvttdgerklvdvideegagfngadsettstnwarddngnsieHGthvAGiaaanapeeg 80 
                                    g+gv+va++DtGvd +h  l + +d ++ ++  i      ++  d+ ++ ++ ++d+ g    HGth+A+++ ++     
  gi|116754575|ref|YP_843693.1| 126 GNGVTVALIDTGVDAEHDSLDDLDDDPATYDPKI------VAFVDMVNGLEKPYDDN-G----HGTHCASLISGT----- 189
                                    79*******************9999888886555......66778999999999886.7....************..... PP

                                    SSB-SSTTSEEEEEE-SSTTSB-HH..HHHHHHHHHHHHCT-S....EEEE-EESCETTCHHCHHHHHHHHHHHH.CCT- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Peptidase_S8  81 ekngvapgakilsvkvldtsggsmetgteliraieeaaedkvd....vinmslgestslpktgrsiealainravnkkgv 156
                                    +  gvapg +++ +kv+d +g+     ++ ++a++++a++k      vi+ s+g++ s +++    e  a+n++v + g+
  gi|116754575|ref|YP_843693.1| 190 KGMGVAPGSRLAVLKVMDRDGSCY--LSDALSALDWCAKNKDTygirVISFSVGGERSSERPTLLDE--ACNKMV-EDGI 264
                                    99***************9999765..59***********66557788*******8888888888888..******.89** PP

                                    EEEEE--SS-T-HHEEE-TTCEECTTTSTTCEEEEEESTTSSB-TT--B-TT.......-EEEE-S-CCCCCCCCCHHHT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Peptidase_S8 157 lvviSaGNngktgsslqagspvgtpstsknvitvgayttegkiapfSsrGpssdgklkpdivapGgnivstwsrqsnnsa 236
                                    +vv++aGN+g      ++ s++  p+ +++vitvga+++ gki + SsrGp+sdg++kpdiv  G++ v+++   ++++ 
  gi|116754575|ref|YP_843693.1| 265 VVVVAAGNSG------PSPSSIVIPGEAEEVITVGAIDSRGKIFERSSRGPTSDGRIKPDIVTIGVD-VPSALAGTKDD- 336
                                    **********......9999***********************************************.55555555333. PP

                                    TTHHEEEE-SHHHCHHHHHHHHHHHHHHHTT--HHHHHHHHHCCS-EE......SSSSSSTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Peptidase_S8 237 glssyqsmsGTSmAsPnaagaaAlllsalpkltpetvraallntAqdlgkadniesfaqGaG 298
                                           msGTSmA P +aga+Alll+++ +l+p++v+++ll++A+dlg+   + ++ +G+G
  gi|116754575|ref|YP_843693.1| 337 ----ESCMSGTSMAVPQVAGAVALLLEGFGNLSPADVKRVLLRSADDLGDT--GADNTFGWG 392
                                    ....357*****************************************666..********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (509 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        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 0.26s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3645.05
//
Query:       gi|116754576|ref|YP_843694.1|  [L=382]
Description: ATP-NAD/AcoX kinase [Methanosaeta thermophila PT]
Scores for complete 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-46  158.5   0.0    2.3e-46  158.3   0.0    1.0  1  NAD_kinase  ATP-NAD kinase
      4e-05   23.2   0.1    9.9e-05   22.0   0.1    1.7  1  DAGK_cat    Diacylglycerol kinase catalytic domain
    0.00029   20.8   0.0    0.00053   20.0   0.0    1.4  1  DeoRC       DeoR C terminal sensor 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 !  158.3   0.0   3.9e-50   2.3e-46       1     289 [.       8     370 ..       8     373 .. 0.94

  Alignments for each domain:
  == domain 1  score: 158.3 bits;  conditional E-value: 3.9e-50
                                    .EEEEESSC........................GGTCSHHHHHHHHHHHCT-.....EEEEECCGGCCSSSTT--HHHHT CS
                     NAD_kinase   1 kvgivvnpi........................kkeaieraeevarwLldals...rvlevtveeklgeslaeaaefrse 53 
                                    k+g++ npi                        ++ +++rae+ +r Ll+ ++    +  +t  + +ge+l ++++ ++ 
  gi|116754576|ref|YP_843694.1|   8 KLGFLINPIagmggavglkgtdgvaalaerlgaAPVSKDRAERAFRRLLELSRgdiPAQLLTAGGPMGEGLLQELDVEHY 87 
                                    67899999999999999999999999999999988899*************76988888999****************** PP

                                    TTT--.......EEECCC-TTTTTSSSEEEEEE-HHHHHHHHHHHHHCT-EEEEEESSS--SS-SE..EGGGHHHHHHHH CS
                     NAD_kinase  54 visvlkkvkttddtrkaleafadagvdliivvGGDGTaldvarllqkaeiPvlgvnaGvkgfltef..epeaaaellekl 131
                                    v+ ++ ++ t +dt++    fa + vdli++ GGDGTa+dva++    ++P+lg++ Gvk+++++f  +peaaa l+  +
  gi|116754576|ref|YP_843694.1|  88 VVHTPREKTTAEDTKRTCSVFASENVDLILFCGGDGTARDVASVSG--DMPILGIPSGVKMHSGVFavSPEAAADLAFGY 165
                                    *****9999999**********************************..8******************************* PP

                                    HHT-SEEEEEEEEE.........................EEEEETTE................EEEEEEESSEEEEEESS CS
                     NAD_kinase 132 legeirvekrevld.........................avimrskgee..........diadiviensvlnevviirgp 176
                                    ++ge r+ + e+ d                         a ++++k+ +          +ia++++e +  ++ ++i+g 
  gi|116754576|ref|YP_843694.1| 166 IKGELRTRETEIADvdeehyrkgelvvrlygtartpylpALVQQRKQVYassdeehfklEIAQFAREFM-SDGSYYILGA 244
                                    ***************************************77777777667777779**99999997776.********** PP

                                    SSS-EE..EEEEETTEEEEEEEESEE........................EEE-TGGGGTHHHHTT--EE-TT---EEEE CS
                     NAD_kinase 177 gstlie..lelyvdtelleadqldgl........................ivstPtGstayslsaGgplisPgvlailiv 230
                                    g+t ++    ++ +++ll++d+++++                        i+++P+G +++ l++G ++isP+vl+    
  gi|116754576|ref|YP_843694.1| 245 GTTTAKiaELIGCEKTLLGVDVIRNGrtvlkdasesdllellgeidggvrIIVSPIGAQGFILGRGSQQISPRVLR---- 320
                                    ******955679****************************************************************.... PP

                                    EESESSS----EEE-TT-EEEEEE-SS--EEEEETTTEEEEE-TT-EEEEEEESSEEEE CS
                     NAD_kinase 231 picPhslssrpiVvssssklrirvasrseallaldGseelelspgdevrvtasdkkfkl 289
                                         +  +++i ++++ klr     + + ll+++G+ e++  + ++ +v+++++ ++l
  gi|116754576|ref|YP_843694.1| 321 ----IVGPEKLILIATPHKLR-----DLKYLLVDTGDVEIDRALAGRRQVVTGYRMAQL 370
                                    ....8999*************.....****************************98765 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.1   1.7e-08   9.9e-05      33      89 ..      90     141 ..      69     154 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.7e-08
                                    EEEEE--STTHHHHHHHHHHHCC-SEEEEEESHHHHHHHHHHHCTHHCTTSEEEEEE CS
                       DAGK_cat  33 lelieteepgdakelakeakeegvdlivvaGGDGtvsevlnglleelatkpplgiiP 89 
                                     + +e + ++d k+ ++  ++e+vdli+ +GGDGt++ v+++  +     +p+  iP
  gi|116754576|ref|YP_843694.1|  90 HTPREKTTAEDTKRTCSVFASENVDLILFCGGDGTARDVASVSGD-----MPILGIP 141
                                    3444555688899999999999*****************987655.....5555555 PP

>> DeoRC  DeoR C terminal sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   8.8e-08   0.00053       6      60 ..     223     280 ..     218     303 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 8.8e-08
                          DeoRC   6 KrrIAkaAaeliedgdtifldaGtTtlelaraLaekk...nltvvTnslnvaeeLsek 60 
                                    K +IA+ A e+  dg+  +l+aGtTt+ +a+ +  +k    + v+ n+ +v +  se+
  gi|116754576|ref|YP_843694.1| 223 KLEIAQFAREFMSDGSYYILGAGTTTAKIAELIGCEKtllGVDVIRNGRTVLKDASES 280
                                    99*******************************9888677778888887777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); 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:                         3  (0.000167327); expected 0.2 (1e-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: 2752.47
//
Query:       gi|116754577|ref|YP_843695.1|  [L=450]
Description: tryptophan synthase subunit beta [Methanosaeta thermophila PT]
Scores for 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-39  133.7   0.0    1.1e-38  133.4   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 !  133.4   0.0     6e-43   1.1e-38       4     294 .]      75     413 ..      72     413 .. 0.80

  Alignments for each domain:
  == domain 1  score: 133.4 bits;  conditional E-value: 6e-43
                                    CSSS--EEEECCTCCCCCCE..EEEEEGGGSTTSBTTHHHHHHHHHH.HHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-E CS
                           PALP   4 gigpTPlvrlprlskelgvp..lflKlEslnptgSfKdRgaeyllar.lkegtgaktvveassGNhgralAaaaallGlk 80 
                                      +pTPl r+ rl+k+l++p  +++K+E+  p gS+K ++a+   ++  keg   +  +e+++G++g alA+a   +Glk
  gi|116754577|ref|YP_843695.1|  75 LWRPTPLYRAVRLEKALKTParIYYKYEGVSPAGSHKPNTAVPQAYYnMKEG-IERIATETGAGQWGSALALATCIFGLK 153
                                    579***************************************8888868888.8999999999***************** PP

                                    EEEEEETTS-...HHHHHHHHHTT-EEEEE..................CCHHHHHHHHHHHHHHH..STTCEE--TTTSH CS
                           PALP  81 vtivvpadas...pekvallrllGaevvev..................ggdydeavaaaaelaae..gegaylvsqfdnp 137
                                    +ti++ +++    p+++ ++r +Gae+  +                  +g+   a + a e aa   ++++ l s  +  
  gi|116754577|ref|YP_843695.1| 154 CTIYMVRSSYdqkPYRRSMMRVWGAECFPSpsnrtnagrrileqfpdtPGSLGIAISEAVEDAAThdDTNYALGSVLN-- 231
                                    ****8877766669****************444444444444333333333333333322222223344444444443.. PP

                                    HHHHHHHTHHHHHHHHTT...TTEEEEEEE-SSSHHHHHHHHHHHH....HSTT-EEEEEEECTTCGGTTCC...S..S. CS
                           PALP 138 tviegygtiglEileqlg...gkpdavvvpvGgGgliaGiaaglke....rrpdvrvigvepegsdalarsl...ragrr 207
                                    +v + ++  glE+++q+    + pd+++ ++GgG+++ G+++++      ++ + r+++ ep+ +++l+++l   + g+ 
  gi|116754577|ref|YP_843695.1| 232 HVLLHQTVEGLEVKKQFElvdDYPDVIYGCCGGGSNFPGVCFPFIPdklnDKKELRLVACEPTACPSLTKGLytyDFGDT 311
                                    566669999999998888887999**********************87644444******************65533333 PP

                                    SS..B...................SSS.CCSTCSCGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHH CS
                           PALP 208 vtvpvs..................dtiadglavgspselafelldrlvdeivtvsdeealeamrllarregivvepssaa 269
                                         +                     a gl+ + +++l  +l+ + + e+ +  + e+++a+ ++ar+egiv+ p sa+
  gi|116754577|ref|YP_843695.1| 312 -----ArltpllkmytlghdfvppGIHAGGLRYHGDAPLLCSLVNAGIIEAQAFHQREVFDAATTFARAEGIVPAPESAH 386
                                    .....134444888*****666666666666666999******************************************* PP

                                    HHHHH..HHHHHHCCTTCEEEEEEE-B CS
                           PALP 270 alaal..klreagelkegdrvvviltg 294
                                    a+  +  ++ ++++ +e ++ ++ l+g
  gi|116754577|ref|YP_843695.1| 387 AIKPAidEAIQCRKTGETKTLLINLSG 413
                                    **9999************999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 3322.28
//
Query:       gi|116754578|ref|YP_843696.1|  [L=473]
Description: Na+/solute symporter [Methanosaeta thermophila PT]
Scores for complete 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-43  148.4  31.9    3.9e-43  147.9  31.9    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 !  147.9  31.9   2.2e-47   3.9e-43       3     404 ..      31     422 ..      29     424 .. 0.88

  Alignments for each domain:
  == domain 1  score: 147.9 bits;  conditional E-value: 2.2e-47
                            SSF   3 lagrsl.tgfvlglslaasnisaasfvGlaGavaasGlavvllelgalllvlllllllaerlr....nagalTlpdylsk 77 
                                    l+ r++ t+  +g++ +a + saasf+G+ G + + G+ +v++   + +++  l +l+a+r      ++ a T+p++l+ 
  gi|116754578|ref|YP_843696.1|  31 LSDRNIaTPAIIGIAYTAAYFSAASFLGGGGYGLTAGMPWVVFCAFFHVAFACLAWLMAGRIWaaakEYDAKTVPQLLER 110
                                    556666366789*******************************99999999999999999987799999*********** PP

                            SSF  78 RfkgkrilvylsalslllvitlklsvdlvggaklielalGlnyetavlllaaltalYtviGGllAvvytdtiqavlmlvg 157
                                    R+++    v+l+a+ +l++ t++l   + g a l++ ++G+ y ++++  ++++a+Y +iGGl A+++   +q+vlml g
  gi|116754578|ref|YP_843696.1| 111 RYGSPLGKVILAAI-MLVLYTVYLVPIFKGCATLLQGLIGVTYVQGLIFTVIIVAIYYAIGGLPAIIWIGFLQGVLMLGG 189
                                    ****9967777766.567778999999***************************************************** PP

                            SSF 158 alilliivllevGgleslveklkeaapkvvdlltpdslkllrdpltalslwlglvlGvaglphilvRflaakdakailkg 237
                                    a++l    l+  G+le   +++ + a++++ +  p +        ++l +   + lG+  lp  l+ +++a d + ++ +
  gi|116754578|ref|YP_843696.1| 190 AVLLYSSMLSTSGALEIW-SRIPAYATSMSGIDIPWQ--------KTLGMAFSISLGLLALPDLLIMIFSARDRRVVRFA 260
                                    *99987777776666655.454444443322222222........23334457889************************ PP

                            SSF 238 vlkltivlilvligmisiilfaiklagavpkavgtevgvsniaypeLvvkllpnllaGlllavmlAaimstltslllsas 317
                                     +++ + +++  i ++s+++ a  +    ++ + + +++++  +p L+   lp+++ +l+l ++++a mst+++++l++ 
  gi|116754578|ref|YP_843696.1| 261 GIYGPVSIAVYSICIFSLGILAYGV--LSGEQISSFIKNPDSLVPFLARTYLPPGFDALVLLAAISAAMSTISAIVLVTT 338
                                    ****999999999988888877655..556************************************************** PP

                            SSF 318 saftkDlYkkirrkasakekelvgvsriivlvvislaillavqeeqkgvlklvelafaglasavlavillalfwkrvneq 397
                                    +++t D+   +r+    ++  ++++ r++ +v+ + a + a+  +++ ++ lv++ ++++a +v+  ++++l+w r n+ 
  gi|116754578|ref|YP_843696.1| 339 TSLTSDILHYMRPGI--SDATVLRLTRLVGVVILATAAVSAIRVPSQ-IVPLVSISMGVIACCVFVPLVFGLYWRRGNSV 415
                                    *******99999988..89999*************************.*******************************9 PP

                            SSF 398 GAlagli 404
                                    G  a+l+
  gi|116754578|ref|YP_843696.1| 416 GFVASLL 422
                                    9877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       896  (0.0499749); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); 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):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 3205.75
//
Query:       gi|116754579|ref|YP_843697.1|  [L=223]
Description: deoxyribonuclease V [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-65  220.5   0.0    1.9e-65  220.3   0.0    1.0  1  Endonuclease_5  Endonuclease V
  ------ inclusion threshold ------
      0.022   14.2   0.1      0.043   13.2   0.0    1.5  2  DUF99           Protein of unknown function DUF99


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 !  220.3   0.0   2.1e-69   1.9e-65      16     196 ..      34     212 ..      20     213 .. 0.94

  Alignments for each domain:
  == domain 1  score: 220.3 bits;  conditional E-value: 2.1e-69
                                    G..-SEEEEEEEEEEECTCEEEEEEEEEEETTTTEEEEEEEEEEE--S-SSTT-CHHHCHHHHHHHHCC-SS--SEEEEE CS
                 Endonuclease_5  16 k..lklvaGvDvsfvkeekkeavaalvvldlpslevvekavavvklsfpYipgfLaFRElpvllkaleklkqkpdvllvD 93 
                                    +  +++vaG+Dvsf   + ++a aa+v+ld++++++++ ++a++++  pYipg+L FRE pv+l+ale +++  dvll+D
  gi|116754579|ref|YP_843697.1|  34 VdrVETVAGADVSF---SGSRAHAAAVLLDYHDMRLLDVSFAEMDVVYPYIPGLLTFREGPVILRALEGIDE-ADVLLFD 109
                                    23379*********...555669***********************************************97.7****** PP

                                    C-SSSSTTS--HHHHHHHHHTS-EEEEESS-SSSBE----SSTTEEEEEEETTEEEEEEEESSTTS--EEEEEECSS-HH CS
                 Endonuclease_5  94 GnGiaHprrlGlAshlGvlldlptiGvaKsllvgkveepekekgsvvplvsegevigaalrtkknvkpiyvSvGhrisle 173
                                    G+GiaHprr+G AshlG+lld p+iG+aKs+l+g+++ep+ e+gs++ lv++gev+gaalrt++nv+p++vS+Gh+ +l+
  gi|116754579|ref|YP_843697.1| 110 GQGIAHPRRFGEASHLGLLLDRPSIGCAKSRLWGEFREPDGERGSFSLLVDRGEVVGAALRTRTNVRPVFVSPGHMSDLS 189
                                    ******************************************************************************** PP

                                    HHHHHHHHCS-T-SS-HHHHHHH CS
                 Endonuclease_5 174 talelvlallkkyrlPepirqAd 196
                                    +a+e++l+++++yr+Pep+r+A+
  gi|116754579|ref|YP_843697.1| 190 SAIEIALNCARGYRVPEPLRLAH 212
                                    **********************9 PP

>> DUF99  Protein of unknown function DUF99
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0      0.52   4.7e+03      29      51 ..      31      53 ..      19      59 .. 0.56
   2 ?   13.2   0.0   4.8e-06     0.043     141     179 ..     176     215 ..     152     218 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.52
                                   EETT.EEEEEEEEEE-TT-S-HH CS
                          DUF99 29 mradrvvdgvafgrvtvdGtDat 51
                                   +++ ++v+ va + v+  G  a 
  gi|116754579|ref|YP_843697.1| 31 FQRVDRVETVAGADVSFSGSRAH 53
                                   44444666666666666666555 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 4.8e-06
                                    ..EEEEEESS.-HHHHHHHHHHC-SSSSS-HHHHHHHHHH CS
                          DUF99 141 eelyvravGi.eleeaaklvrkltlegriPEPlRvAhliA 179
                                    ++++v    + +l+ a ++  ++++  r+PEPlR+Ah+++
  gi|116754579|ref|YP_843697.1| 176 RPVFVSPGHMsDLSSAIEIALNCARGYRVPEPLRLAHILS 215
                                    456666544415678888888888888**********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       175  (0.00976072); expected 358.6 (0.02)
Passed bias filter:                      162  (0.00903564); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1690.41
//
Query:       gi|116754580|ref|YP_843698.1|  [L=504]
Description: NHL repeat-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      9e-30  101.2   0.2    0.00029   20.7   0.0    6.7  6  NHL            NHL repeat
    6.3e-10   39.3   0.0    1.2e-09   38.4   0.0    1.4  1  Thioredoxin_8  Thioredoxin-like
    3.2e-09   36.8   0.0    5.8e-09   35.9   0.0    1.3  1  AhpC-TSA       AhpC/TSA family
    5.4e-06   26.2   0.0    1.3e-05   24.9   0.0    1.6  1  Redoxin        Redoxin
     0.0088   16.0   0.0       0.19   11.7   0.0    2.3  2  Thioredoxin    Thioredoxin
  ------ inclusion threshold ------
      0.021   15.3   7.7         11    6.7   0.1    5.5  6  PQQ_3          PQQ-like domain
       0.13   11.6   2.8        1.1    8.6   0.1    3.5  4  LVIVD          LVIVD repeat
       0.13   12.7   0.0       0.26   11.8   0.0    1.4  1  Thioredoxin_2  Thioredoxin-like domain


Domain annotation for each model (and alignments):
>> NHL  NHL repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0     6e-05      0.13      11      27 ..     202     218 ..     193     219 .. 0.84
   2 !   16.4   0.1   3.1e-06     0.007       3      23 ..     248     267 ..     248     270 .. 0.90
   3 !   14.4   0.0   1.3e-05      0.03       1      27 [.     302     327 ..     302     328 .. 0.92
   4 !    8.7   0.0   0.00085       1.9       1      27 [.     355     380 ..     355     381 .. 0.92
   5 !   20.7   0.0   1.3e-07   0.00029       1      27 [.     408     433 ..     408     433 .. 0.87
   6 !   19.9   0.0   2.4e-07   0.00053       1      28 []     462     488 ..     462     488 .. 0.97

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6e-05
                                    TTTEEEEEECCCTEEEE CS
                            NHL  11 snGdiyVaDsenhrvqv 27 
                                     +++i++aDs+n+r+ +
  gi|116754580|ref|YP_843698.1| 202 GGDNIFIADSNNNRILI 218
                                    589***********975 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 3.1e-06
                                    SEEEEEEETTTEEEEEECCCT CS
                            NHL   3 yPhGvavdsnGdiyVaDsenh 23 
                                    +P+G+a++ ++ +y+aD++nh
  gi|116754580|ref|YP_843698.1| 248 RPQGIAIV-GDVVYIADTGNH 267
                                    6******5.************ PP

  == domain 3  score: 14.4 bits;  conditional E-value: 1.3e-05
                                    BSSEEEEEEETTTEEEEEECCCTEEEE CS
                            NHL   1 fnyPhGvavdsnGdiyVaDsenhrvqv 27 
                                    +++P++++ + ++++y+a  ++h+++ 
  gi|116754580|ref|YP_843698.1| 302 LSSPWDLVFV-QDHLYIAMAGSHQIWR 327
                                    679******5.**************95 PP

  == domain 4  score: 8.7 bits;  conditional E-value: 0.00085
                                    BSSEEEEEEETTTEEEEEECCCTEEEE CS
                            NHL   1 fnyPhGvavdsnGdiyVaDsenhrvqv 27 
                                    +++P+G++  ++++iy  Dse+++++v
  gi|116754580|ref|YP_843698.1| 355 LAQPSGLTT-DGNRIYFVDSESSSLRV 380
                                    689******.6************9998 PP

  == domain 5  score: 20.7 bits;  conditional E-value: 1.3e-07
                                    BSSEEEEEEETTTEEEEEECCCTEEEE CS
                            NHL   1 fnyPhGvavdsnGdiyVaDsenhrvqv 27 
                                    +++P G+ + + G iyVaD++nhr+++
  gi|116754580|ref|YP_843698.1| 408 LQHPLGLFY-KEGSIYVADTYNHRIKK 433
                                    567888888.9**************85 PP

  == domain 6  score: 19.9 bits;  conditional E-value: 2.4e-07
                                    BSSEEEEEEETTTEEEEEECCCTEEEEE CS
                            NHL   1 fnyPhGvavdsnGdiyVaDsenhrvqvF 28 
                                    fn+P+G++ + ++ +++aD++nh v+++
  gi|116754580|ref|YP_843698.1| 462 FNEPSGLTFL-GDSLFIADTNNHAVRIY 488
                                    99*******9.**************997 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.0   5.2e-13   1.2e-09       1      95 []      52     145 ..      52     145 .. 0.88

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 5.2e-13
                                    .SEEEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SS-HHHHH.HHGGGS.-TTSEE.EE-TT-HHHHTT-S CS
                  Thioredoxin_8   1 gkvvlLyfgaswcppckaftpklkelyeklkkkkkveivyvsldkkeeefe.kylkkn.kkpwlsvpfddkkrnklkkky 78 
                                    g+ vl+ f++++c +c++++  lk l+e++     ++++ v+  k e+e++ + ++k  ++  +++p+  ++  +l++ y
  gi|116754580|ref|YP_843698.1|  52 GRFVLIDFWTYCCINCMHVVTDLKMLEERYP---ELVVIGVHTAKFENEMRvENIEKAiMRYGIEHPVIVDSDRTLWRAY 128
                                    5789**************************6...9********98877764344444458899999999999******** PP

                                    --TT-SEEEEE-TT-BE CS
                  Thioredoxin_8  79 nvkaiPtlvvldkngev 95 
                                    ++ a+P++v++ ++ge+
  gi|116754580|ref|YP_843698.1| 129 GIRAWPSFVLIAPDGEI 145
                                    ***************97 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.0   2.6e-12   5.8e-09      11     121 ..      35     145 ..      27     147 .. 0.79

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 2.6e-12
                                    E....STTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCH......HHHHHHHH- CS
                       AhpC-TSA  11 k....nadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspe......shkkfieke 80 
                                         n+d + ++l d++g+ v++ f++   c  C + + +l+ l e++    + vigv + + e      +++k i ++
  gi|116754580|ref|YP_843698.1|  35 DlvwlNTD-RRYTLRDLRGRFVLIDFWTY-CCINCMHVVTDLKMLEERYP--ELVVIGVHTAKFEnemrveNIEKAIMRY 110
                                    44454565.89***************888.66666666666666555555..44567777766666666679******** PP

                                    H.SSEEEE-TTSHHHHHTT-EETTTTECSCEEEEE-TTSBE CS
                       AhpC-TSA  81 slnfpllsDeegkvakaygvlkeekglalratfvidkegki 121
                                    +++ p++ D+++++ +ayg+       a+++ ++i ++g i
  gi|116754580|ref|YP_843698.1| 111 GIEHPVIVDSDRTLWRAYGIR------AWPSFVLIAPDGEI 145
                                    *********************......************98 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   5.8e-09   1.3e-05      18     130 ..      42     148 ..      27     155 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 5.8e-09
                                    EEEEEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH......HHHHHHHTT-TSEEEE CS
                        Redoxin  18 gnsvslsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndaf......vkefwgkeglkfpvls 91 
                                       ++l++++g+ v++ f++   c  C++ + +l+ l+e++ e    v++v +++ +         +++ ++g+ +pv++
  gi|116754580|ref|YP_843698.1|  42 DRRYTLRDLRGRFVLIDFWTY-CCINCMHVVTDLKMLEERYPEL--VVIGVHTAKFENemrvenIEKAIMRYGIEHPVIV 118
                                    56799***************9.9999***999999998887776..5666665555558886667777777********* PP

                                    -TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEE CS
                        Redoxin  92 DgsaaftkalGlrleedaseglrtpryavidedgkvvyl 130
                                    D +  + +a+G+r         + p++++i  dg +  +
  gi|116754580|ref|YP_843698.1| 119 DSDRTLWRAYGIR---------AWPSFVLIAPDGEILGR 148
                                    ***********99.........************99765 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   8.5e-05      0.19      19      70 ..      53     103 ..      41     108 .. 0.82
   2 ?    1.6   0.0      0.12   2.7e+02      58      88 ..     118     149 ..     114     158 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.5e-05
                                    SEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT- CS
                    Thioredoxin  19 klvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyev 70 
                                    + vl++F+   C  C ++   l+ l e++  +++++ v + + e+  +  ++
  gi|116754580|ref|YP_843698.1|  53 RFVLIDFWTYCCINCMHVVTDLKMLEERYP-ELVVIGVHTAKFENEMRVENI 103
                                    679***************************.677777776666666555555 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.12
                                    TTTSHHHHHHTT-SSSSEEEEEE.TTEEEEEE CS
                    Thioredoxin  58 vdenedlakkyevegiPtlklfk.ngkevkky 88 
                                    vd+ ++l + y++++ P ++l+  +g+   ++
  gi|116754580|ref|YP_843698.1| 118 VDSDRTLWRAYGIRAWPSFVLIApDGEILGRT 149
                                    5667788999*********9875155555555 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.23   5.2e+02      17      31 ..     196     213 ..     183     225 .. 0.63
   2 ?    6.7   0.1    0.0047        11      16      35 ..     251     271 ..     238     275 .. 0.80
   3 ?   -2.9   0.0       4.8   1.1e+04      15      27 ..     303     318 ..     296     320 .. 0.75
   4 ?    5.9   0.1    0.0084        19      15      37 ..     359     382 ..     323     388 .. 0.65
   5 ?   -3.1   0.0       5.6   1.3e+04      21      31 ..     418     429 ..     416     431 .. 0.72
   6 ?    0.4   0.1      0.46     1e+03      15      33 ..     466     484 ..     444     492 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.23
                          PQQ_3  17 p..avdg.glvyvgtgdG 31 
                                    p  +++g + ++++++++
  gi|116754580|ref|YP_843698.1| 196 PgkVISGgDNIFIADSNN 213
                                    255565426899998843 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0047
                          PQQ_3  16 spavdgglvyvgtg.dGtlyA 35 
                                    + a++g++vy++++ ++ ++A
  gi|116754580|ref|YP_843698.1| 251 GIAIVGDVVYIADTgNHMVRA 271
                                    459***********6665555 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 4.8
                          PQQ_3  15 ssp...avdgglvyvg 27 
                                    ssp   +++ +++y++
  gi|116754580|ref|YP_843698.1| 303 SSPwdlVFVQDHLYIA 318
                                    5666668888999986 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.0084
                          PQQ_3  15 sspavdgglvyvgtg.dGtlyAlD 37 
                                    s++++dg+++y++++   +l+ +D
  gi|116754580|ref|YP_843698.1| 359 SGLTTDGNRIYFVDSeSSSLRVID 382
                                    455**********99844444444 PP

  == domain 5  score: -3.1 bits;  conditional E-value: 5.6
                          PQQ_3  21 gglvyvgtg.dG 31 
                                    +g +yv+++ ++
  gi|116754580|ref|YP_843698.1| 418 EGSIYVADTyNH 429
                                    688999987555 PP

  == domain 6  score: 0.4 bits;  conditional E-value: 0.46
                          PQQ_3  15 sspavdgglvyvgtgdGtl 33 
                                    s++++ g+ +++++++++ 
  gi|116754580|ref|YP_843698.1| 466 SGLTFLGDSLFIADTNNHA 484
                                    5557779999999995554 PP

>> LVIVD  LVIVD repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.26   5.8e+02      11      22 ..     203     214 ..     199     219 .. 0.78
   2 ?    8.6   0.1   0.00051       1.1       5      24 ..     250     269 ..     249     269 .. 0.90
   3 ?   -3.3   0.1       2.6   5.7e+03      14      20 ..     421     427 ..     418     428 .. 0.78
   4 ?   -0.5   0.0      0.34   7.6e+02      11      21 ..     472     482 ..     466     485 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.26
                          LVIVD  11 GnYaYvAdqdng 22 
                                    G+  ++Ad++n 
  gi|116754580|ref|YP_843698.1| 203 GDNIFIADSNNN 214
                                    67789***9874 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00051
                          LVIVD   5 qdvavsGnYaYvAdqdngLv 24 
                                    q +a+ G+ +Y+Ad +n +v
  gi|116754580|ref|YP_843698.1| 250 QGIAIVGDVVYIADTGNHMV 269
                                    679*************9876 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 2.6
                          LVIVD  14 aYvAdqd 20 
                                     YvAd  
  gi|116754580|ref|YP_843698.1| 421 IYVADTY 427
                                    6***975 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.34
                          LVIVD  11 GnYaYvAdqdn 21 
                                    G+ +++Ad +n
  gi|116754580|ref|YP_843698.1| 472 GDSLFIADTNN 482
                                    8889****998 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00011      0.26       5      98 ..      52     151 ..      49     156 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                  Thioredoxin_2   5 gkpvlvvftdpdCpyCkklkkelkelddvtvrvllfp....lkpsfepkavaiwcakekkkafkd........ieenvel 72 
                                    g+ vl++f++  C +C    ++lk l   ++r   +p    ++ +  +k+++  + ++ +ka+          +++ + l
  gi|116754580|ref|YP_843698.1|  52 GRFVLIDFWTYCCINCMHVVTDLKML---EER---YPelvvIGVH-TAKFENEMRVENIEKAIMRygiehpviVDSDRTL 124
                                    7789999999999*999988888888...444...3333343444.3344444444444444444677779*99****** PP

                  Thioredoxin_2  73 arkygvrgtPtivfldgk.eivarlpG 98 
                                     r+yg+r+ P++v++ ++ ei+ r  G
  gi|116754580|ref|YP_843698.1| 125 WRAYGIRAWPSFVLIAPDgEILGRTSG 151
                                    ************999999888888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (504 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 3728.27
//
Query:       gi|116754581|ref|YP_843699.1|  [L=294]
Description: radical SAM domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-10   41.3   0.0    2.8e-10   40.8   0.0    1.2  1  Radical_SAM  Radical SAM superfamily
    2.7e-07   30.6   1.1     0.0037   17.0   2.8    2.3  2  DUF1848      Domain of unknown function (DUF1848)


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.0   3.1e-14   2.8e-10       2     165 ..      30     190 ..      29     192 .. 0.82

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 3.1e-14
                                    EEESEESS--TTTSCCTT.HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC....CC CS
                                    xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xx RF
                    Radical_SAM   2 vvtrgCnlrCsfCarpet.vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla....vp 76 
                                    +++ gC+++C +C+ ++   +  ++     ++++  e+ +l+    ++e+i+++   + yp+ +++l   + +      +
  gi|116754581|ref|YP_843699.1|  30 NPYTGCAHGCLYCYASSYiRHFSDCRPKGGIDRLSSEIARLR----GDELISLSNSSDPYPPVEKELGITRSCIslikRK 105
                                    6789************97555555555555555555555555....**************9999999888888889999* PP

                                    TEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  77 giritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGen 156
                                    g+r+ v+t    +  + +++l +++   vs+++ ++  ++ l++  + ++   +l+a++kl++ gi++   + +++pG n
  gi|116754581|ref|YP_843699.1| 106 GLRLQVVTKSDIV-LRDVDLLSDMR-AAVSITITSLRLDDRLEP--GAPSSIMRLKAIRKLTDEGIPVAARIDPIIPGMN 181
                                    *************.*********99.777777777766644555..568888999************777777******* PP

                                    HHHHHHHHH CS
                                    xxxxxxxxx RF
                    Radical_SAM 157 deeleelle 165
                                    d+e+++l+e
  gi|116754581|ref|YP_843699.1| 182 DSEIDALVE 190
                                    *****9987 PP

>> DUF1848  Domain of unknown function (DUF1848)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   2.8   4.2e-07    0.0037     241     265 .]      20      44 ..      13      44 .. 0.92
   2 !    9.9   0.0   6.2e-05      0.56      61     126 ..     118     181 ..      98     275 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.2e-07
                        DUF1848 241 eCgCveskDiGayntClhgCvYCYA 265
                                     C+C e   +  y  C hgC+YCYA
  gi|116754581|ref|YP_843699.1|  20 LCTCPEKLSLNPYTGCAHGCLYCYA 44 
                                    5***********************9 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 6.2e-05
                        DUF1848  61 llkkleelkergiklyfqfTltdyekelepnvpsleerietfkelseklgkerviwRyDPilltek 126
                                    +l+ ++ l++++  + + +T    ++ lep+ ps   r++++++l+++     v+ R DPi+   +
  gi|116754581|ref|YP_843699.1| 118 VLRDVDLLSDMRAAVSITITSLRLDDRLEPGAPSSIMRLKAIRKLTDEGI--PVAARIDPIIPGMN 181
                                    567777787655555555555556667*******************9864..5999*****95433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2395.60
//
Query:       gi|116754582|ref|YP_843700.1|  [L=248]
Description: Cna B domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-13   51.4   2.5    3.3e-12   46.6   0.5    2.5  2  SdrD_B           SdrD B-like domain
    8.8e-06   25.9   3.7    1.7e-05   25.0   0.5    2.8  2  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
     0.0015   18.8   0.0     0.0032   17.7   0.0    1.6  1  DUF3823          Protein of unknown function (DUF3823) N-term
     0.0015   18.6   0.3      0.011   15.8   0.0    2.3  2  DUF2012          Protein of unknown function (DUF2012)
     0.0083   16.4   4.0      0.022   15.1   3.7    2.0  1  SpaA             Prealbumin-like fold domain
  ------ inclusion threshold ------
      0.032   14.2   0.6       0.18   11.8   0.2    2.6  2  CarbopepD_reg_2  CarboxypepD_reg-like domain
        0.3   11.7   1.6       0.61   10.7   1.6    1.6  1  LPAM_1           Prokaryotic membrane lipoprotein lipid attac


Domain annotation for each model (and alignments):
>> SdrD_B  SdrD B-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.017        43      40      75 ..      60      95 ..      44     122 .. 0.85
   2 !   46.6   0.5   1.3e-15   3.3e-12       2      86 ..     131     210 ..     130     240 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.017
                         SdrD_B 40 atttTdasGkYkFtnltpGeYkVeftapagytvtak 75
                                   ++++ +++ +++F++ +p e++++  +p +yt+t  
  gi|116754582|ref|YP_843700.1| 60 EQVVVKKEARFSFNSQKPKEFSIATGKPYQYTFTLG 95
                                   4566678899*********************99965 PP

  == domain 2  score: 46.6 bits;  conditional E-value: 1.3e-15
                         SdrD_B   2 siGdfVweDanknGiqdagekgisgvtVtLkdakgevvatttTdasGkYkFtnltpGeYkVeftapagy.tvtakkaGsd 80 
                                    +i  +V+eDan+n ++d++e+g +g t+ L      +  tttT ++G+Y+F +l++G+Y ++++ p +y  v + + + d
  gi|116754582|ref|YP_843700.1| 131 TISGVVYEDANENAVKDENETGLAGWTLDL------SGVTTTTAEDGTYAFADLSAGDYVLSLIVPPEYnPVAPVNVTLD 204
                                    68899*************************......33489************************999955666666666 PP

                         SdrD_B  81 daldSd 86 
                                    +++  d
  gi|116754582|ref|YP_843700.1| 205 SNKTID 210
                                    655444 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.24   6.1e+02      65      81 ..      78      94 ..      47     131 .. 0.60
   2 !   25.0   0.5   6.7e-09   1.7e-05       6      79 ..     145     211 ..     131     214 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.24
                CarboxypepD_reg 65 eevtltagqtttlditL 81
                                   +e++++ g++ + ++tL
  gi|116754582|ref|YP_843700.1| 78 KEFSIATGKPYQYTFTL 94
                                   33334444444444443 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 6.7e-09
                CarboxypepD_reg   6 VtdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtv.sapGyatatreevtltagqtttldi 79 
                                    V+d++ +++ag t+ ++        +ttt++dG++++++l +g+y +     p y +++   v +t + ++t+d+
  gi|116754582|ref|YP_843700.1| 145 VKDENETGLAGWTLDLS------GVTTTTAEDGTYAFADLSAGDYVLSLiVPPEYNPVAP--VNVTLDSNKTIDF 211
                                    67788888899999998......799*********************9768899999996..5555556666665 PP

>> DUF3823  Protein of unknown function (DUF3823) N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.3e-06    0.0032      32      91 .]     155     214 ..     128     214 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.3e-06
                                    -GGG-.--EEEEB-TTSEE.EEEE-SEEEEEEE-TT-SSB-TT---EEEEESSSEE--EE-- CS
                        DUF3823  32 gygkn.epidvyvkqDGtf.ntllFdGeYklvlkegegpfvkavdtievelkgntkldfeVt 91 
                                    g+    +++++++++DGt+  + l +G+Y l l     p +++v  ++v+l++n+++df Vt
  gi|116754582|ref|YP_843700.1| 155 GWTLDlSGVTTTTAEDGTYaFADLSAGDYVLSLI--VPPEYNPVAPVNVTLDSNKTIDFPVT 214
                                    566666889999*********************7..56655799****************98 PP

>> DUF2012  Protein of unknown function (DUF2012)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.19   4.9e+02      22      45 ..      60      83 ..      40     125 .. 0.78
   2 !   15.8   0.0   4.4e-06     0.011      22      61 ..     163     202 ..     117     246 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.19
                        DUF2012 22 fkalvrrDGsFifrdlpegsYlLe 45
                                    +++v++++ F+f+  ++ ++ + 
  gi|116754582|ref|YP_843700.1| 60 EQVVVKKEARFSFNSQKPKEFSIA 83
                                   457888889998887777666555 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 4.4e-06
                        DUF2012  22 fkalvrrDGsFifrdlpegsYlLevespeyvFepyr.Vdvk 61 
                                    +++ +++DG+++f dl++g Y+L +  p  +++p++ V+v+
  gi|116754582|ref|YP_843700.1| 163 VTTTTAEDGTYAFADLSAGDYVLSLIVPP-EYNPVApVNVT 202
                                    57899******************987664.44443224444 PP

>> SpaA  Prealbumin-like fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   3.7   8.5e-06     0.022      13      81 ..     139     206 ..      79     207 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 8.5e-06
                                    EEETTTSCCCHCHHTT.TTCCEE.................SEEE-BTTSEEEEEEEESEEEEEEEEE-STTEEE-SSEEE CS
                           SpaA  13 lykvdtttdgkdaleakktgtev.................ttlttdenGkatfegLplGtYllvEtkaPegYvldkepfe 75 
                                      + +       a         v                  t tt e+G+  f +L +G+Y+l  + +P  Y+ + +p+ 
  gi|116754582|ref|YP_843700.1| 139 DANEN-------A---------VkdenetglagwtldlsgVTTTTAEDGTYAFADLSAGDYVLSLI-VPPEYN-PVAPVN 200
                                    22222.......2.........012222233344555555788999*****************965.666786.899999 PP

                                    EEECEE CS
                           SpaA  76 vtvtat 81 
                                    vt++ +
  gi|116754582|ref|YP_843700.1| 201 VTLDSN 206
                                    999876 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 ?   -2.0   0.0       1.4   3.7e+03      50      60 ..      70      80 ..      53      96 .. 0.56
   2 ?   11.8   0.2   7.1e-05      0.18       6      49 ..     146     186 ..     132     214 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.4
                CarbopepD_reg_2 50 vsyvGyktqek 60
                                   +s+ + k++e 
  gi|116754582|ref|YP_843700.1| 70 FSFNSQKPKEF 80
                                   33333333333 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 7.1e-05
                CarbopepD_reg_2   6 vdketkeplpgatVyvkgtkkgtvTdenGnFelknlpagkytLv 49 
                                    +d++ ++ l+g t     +++ t+T e+G++ + +l ag+y L 
  gi|116754582|ref|YP_843700.1| 146 KDEN-ETGLAGWTL--DLSGVTTTTAEDGTYAFADLSAGDYVLS 186
                                    3333.345555444..44678899*****************886 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   1.6   0.00024      0.61       1      16 [.       1      16 [.       1      16 [. 0.97

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00024
                         LPAM_1  1 MKKillalgalllLsG 16
                                   MKK++l+++ +l++++
  gi|116754582|ref|YP_843700.1|  1 MKKSILVISVVLAVAA 16
                                   **************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); 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: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1786.89
//
Query:       gi|116754583|ref|YP_843701.1|  [L=105]
Description: hypothetical protein Mthe_1283 [Methanosaeta thermophila PT]
Scores for complete sequence (score 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   0.0        0.6   10.0   0.0    2.0  2  DUF1981   Domain of unknown function (DUF1981)


Domain annotation for each model (and alignments):
>> DUF1981  Domain of unknown function (DUF1981)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   3.4e-05       0.6      51      77 ..      48      74 ..      13      81 .. 0.79
   2 ?   -0.0   0.0     0.045   8.1e+02      13      23 ..      83      94 ..      77     102 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 3.4e-05
                        DUF1981 51 niksGWktifgvltaaakeeneslvrl 77
                                     + GW+tif++++a  + ++ ++v  
  gi|116754583|ref|YP_843701.1| 48 IGEVGWNTIFSLFQAFDERHHGEFVFP 74
                                   4478**********9998887777765 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.045
                        DUF1981 13 fQk.efLkPFee 23
                                   fQk e+L+P+e+
  gi|116754583|ref|YP_843701.1| 83 FQKdECLRPWEV 94
                                   787359***996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       195  (0.0108762); expected 358.6 (0.02)
Passed bias filter:                      185  (0.0103185); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 775.91
//
Query:       gi|116754584|ref|YP_843702.1|  [L=188]
Description: hypothetical protein Mthe_1284 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1369.48
//
Query:       gi|116754585|ref|YP_843703.1|  [L=90]
Description: hypothetical protein Mthe_1285 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.4e-07   29.0   0.0    1.1e-06   28.6   0.0    1.2  1  DsrH      DsrH like protein


Domain annotation for each model (and alignments):
>> DsrH  DsrH like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   6.2e-11   1.1e-06       9      84 ..      16      84 ..      10      87 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 6.2e-11
                                   HHHHHHT--TT-EEEE-GGGGGGGBTTBTTHHHHHTSSSEEEEEHHHHHHTT-TTSB-TTSEEE-.HHHHHHHHHHS CS
                           DsrH  9 lksclrllqegDavlLieDgVyaalkgsrllkalkeasvklyaLkeDleARGlteqlsegvkvid.ydgfVeltvkh 84
                                    + clr+l+ + +++L++DgVy  l+g      l  a+++++a  +Dl  RG++   ++g+k +d y+ +V++++  
  gi|116754585|ref|YP_843703.1| 16 AELCLRMLSRNFRLYLLGDGVYNILSG-----CLGGAEGEIFAFTQDLRERGVS---AAGIKELDdYSVMVDDIMDA 84
                                   689*********************996.....68888999**************...688888888******99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       227  (0.0126611); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 678.47
//
Query:       gi|116754586|ref|YP_843704.1|  [L=107]
Description: hypothetical protein Mthe_1286 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00015   22.1   0.0    0.00023   21.5   0.0    1.3  1  DrsE      DsrE/DsrF-like family
    0.00046   20.3   0.0    0.00054   20.0   0.0    1.1  1  DsrH      DsrH like protein


Domain annotation for each model (and alignments):
>> DrsE  DsrE/DsrF-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   2.5e-08   0.00023       3     110 ..       4     100 ..       3     107 .] 0.82

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.5e-08
                                    EEEEE-S-TTTBSHHHHHHHHHHHHHTTT-EEEEEE-GGGGGGGBS---TGGGTS---GGGGGGCGGGT-EEEEEHHHHH CS
                           DrsE   3 vfilvtggpygseaarealelalaaaalghevsvffygdGvllllkgqtanpadeknlaellkalkeygvklyvCgqaak 82 
                                    v++lv ++py+ e+a+ al++a + + +g   +v +y dGv+l+l++q        +la ll a+ e   ++++ + +++
  gi|116754586|ref|YP_843704.1|   4 VVFLVDSPPYSYERAFGALNAAAVCLPIG--SAVALYADGVYLALADQ-RG-----HLAGLLYAYPEI--DVFAHEPSMA 73 
                                    6788889**********************..66999**********44.44.....488888888885..59******** PP

                                    HTT--GGGE-T--EEEE-HHHHHHHHHH CS
                           DrsE  83 argldededlgvgvevsglgelaelqne 110
                                    +rgl + ++l   ve+ +  e++e ++ 
  gi|116754586|ref|YP_843704.1|  74 ERGLLSCDLL-DRVEMLDDLEFVERIKS 100
                                    ****987777.68888777777777665 PP

>> DsrH  DsrH like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0     6e-08   0.00054      19      81 ..      32      98 ..      19     104 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 6e-08
                                   T-EEEE-GGGGGGGBTTBT.THHHHHTS..SSEEEEEHHHHHHTT-T.TSB-TTSEEE-HHHHHHHH CS
                           DsrH 19 gDavlLieDgVyaalkgsr.llkalkea..svklyaLkeDleARGlt.eqlsegvkvidydgfVelt 81
                                   g+av L  DgVy+al+++r  l+ l  a  ++ ++a ++ +  RGl   +l+++v+++d  +fVe +
  gi|116754586|ref|YP_843704.1| 32 GSAVALYADGVYLALADQRgHLAGLLYAypEIDVFAHEPSMAERGLLsCDLLDRVEMLDDLEFVERI 98
                                   68999*********998651334444446******************888**************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       205  (0.011434); expected 358.6 (0.02)
Passed bias filter:                      183  (0.0102069); 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: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 840.31
//
Query:       gi|116754587|ref|YP_843705.1|  [L=121]
Description: DsrE family protein [Methanosaeta thermophila PT]
Scores for complete 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   60.9   0.0    1.6e-16   60.7   0.0    1.0  1  DrsE      DsrE/DsrF-like family


Domain annotation for each model (and alignments):
>> DrsE  DsrE/DsrF-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.7   0.0   8.7e-21   1.6e-16       1     116 [.       2     118 ..       2     119 .. 0.91

  Alignments for each domain:
  == domain 1  score: 60.7 bits;  conditional E-value: 8.7e-21
                                    -EEEEEE-S-TTTBSHHHHHHHHHHHHHTTT-EEEEEE-GGGGGGGBS---TGGGTS---GGGGGGCGGGT-EEEEEHHH CS
                           DrsE   1 kkvfilvtggpygseaarealelalaaaalghevsvffygdGvllllkgqtanpadeknlaellkalkeygvklyvCgqa 80 
                                    k ++i+ t gpy +++a +a+++a+aa++   +v++f+y d+v+++++gq   p +++n+  l+++l+  g+ + +C  +
  gi|116754587|ref|YP_843705.1|   2 KTLTIVLTDGPYINQNAEIAYRIARAALERY-RVNIFLYLDAVHIPKRGQ--RPVQFRNIGGLFHELASLGAIIRACPRC 78 
                                    6789***********************9987.****************77..6777************************ PP

                                    HHHTT--GGG....E-T-..-EEEE-HHHHHHHHHH-SEEEE CS
                           DrsE  81 akargldede....dlgv..gvevsglgelaelqnegdrvit 116
                                    a  rg+++++    +     gv + +l +l +++ e+d+vi+
  gi|116754587|ref|YP_843705.1|  79 ASSRGYASENgvcpE--YidGVLITSLYDLERMIRESDKVIS 118
                                    *******66554431..2479********************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); 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 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 920.91
//
Query:       gi|116754588|ref|YP_843706.1|  [L=262]
Description: Fe-S cluster domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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   50.0   0.8    2.7e-13   49.3   0.8    1.4  1  FeS          Putative Fe-S cluster
    3.7e-05   23.7   0.0    0.00017   21.6   0.0    2.1  2  HTH_20       Helix-turn-helix domain
    8.3e-05   22.4   0.1    0.00028   20.7   0.1    1.9  1  HTH_5        Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
      0.032   14.2   0.5       0.12   12.4   0.0    2.2  3  HTH_12       Ribonuclease R winged-helix domain
      0.037   14.0   0.1      0.068   13.2   0.1    1.4  1  YhfH         YhfH-like protein
       0.05   14.1   0.0        0.4   11.2   0.0    2.2  2  AAA_assoc_C  C-terminal AAA-associated domain
      0.066   13.2   0.1       0.14   12.2   0.1    1.6  1  HTH_45       Winged helix-turn-helix
       0.11   12.9   0.1       0.36   11.2   0.0    1.9  2  DUF2513      Hypothetical protein (DUF2513)


Domain annotation for each model (and alignments):
>> FeS  Putative Fe-S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.3   0.8   1.2e-16   2.7e-13       1      33 []     210     242 ..     210     242 .. 0.98

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 1.2e-16
                            FeS   1 LPgtNCgaCGypgCmafAealvegeaqledCpp 33 
                                    LPgtNC++CG+++C  fA  lv+ge+ le+C+p
  gi|116754588|ref|YP_843706.1| 210 LPGTNCRECGEQSCYSFAIRLVSGEVGLEKCKP 242
                                    9******************************97 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   7.4e-08   0.00017       4      56 ..      11      60 ..       8      62 .. 0.91
   2 ?   -2.1   0.0       1.8   4.1e+03      13      27 ..     173     193 ..     168     195 .. 0.65

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 7.4e-08
                                   HHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                         HTH_20  4 aeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                     A+a+ +Rr+i+ +L  ++ l+ +++ +++   ++ l+yHL++L++agL++ 
  gi|116754588|ref|YP_843706.1| 11 SNAMANTTRRKIMNLL-LEMDLSKEDIGKAV--GQSMLDYHLQILQQAGLIKI 60
                                   679*************.************95..7777*************985 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.8
                                    HHHHHHH......STCTTB-H CS
                         HTH_20  13 rrilraL......araeglta 27 
                                    r+il +L      a ++g+t+
  gi|116754588|ref|YP_843706.1| 173 REILEELkrtindAIEKGVTP 193
                                    778888866666666666665 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.1   1.3e-07   0.00028       3      46 ..      18      59 ..      16      59 .. 0.95

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.3e-07
                                   HHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_5  3 tRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                   tR+kI++lL e  l+  ++ +++g  qs +++HL +L +aGL++
  gi|116754588|ref|YP_843706.1| 18 TRRKIMNLLLEMDLSKEDIGKAVG--QSMLDYHLQILQQAGLIK 59
                                   9*********************88..99**************95 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   5.3e-05      0.12      22      64 ..      30      73 ..      18      75 .. 0.79
   2 ?   -3.2   0.0       3.7   8.3e+03       5      15 ..     112     122 ..     111     127 .. 0.85
   3 ?   -2.3   0.1         2   4.5e+03      16      30 ..     172     187 ..     167     191 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.3e-05
                         HTH_12 22 eLkkr..gydigeravRyrLrkleergltrrvgyagreltEkGle 64
                                   +L k   g ++g+  + y+L++l + gl++   +  + lt+ G +
  gi|116754588|ref|YP_843706.1| 30 DLSKEdiGKAVGQSMLDYHLQILQQAGLIKIENNV-ASLTDFGRN 73
                                   454444599999999**************876665.999998865 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.7
                         HTH_12   5 kilaesdkpig 15 
                                    +i+a+ d p+g
  gi|116754588|ref|YP_843706.1| 112 RIIARMDPPLG 122
                                    79999999998 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2
                         HTH_12  16 akeiaeeLkkr.gydi 30 
                                    a+ei eeLk + + +i
  gi|116754588|ref|YP_843706.1| 172 AREILEELKRTiNDAI 187
                                    6778888887766665 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1     3e-05     0.068       4      22 ..     203     221 ..     201     224 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3e-05
                           YhfH   4 iveFfrnLPkKkCteCGke 22 
                                    ++e +r LP   C eCG++
  gi|116754588|ref|YP_843706.1| 203 PMEVYRYLPGTNCRECGEQ 221
                                    79***************96 PP

>> AAA_assoc_C  C-terminal AAA-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00018       0.4      19      53 ..      50      84 ..      43     109 .. 0.86
   2 ?    0.1   0.0       0.5   1.1e+03      14      67 ..     131     181 ..     126     201 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00018
                    AAA_assoc_C 19 eaaelLglveveegdielTelGrkfveadikerKe 53
                                   ++++  gl+++e+    lT+ Gr+f+e++ +++ +
  gi|116754588|ref|YP_843706.1| 50 QILQQAGLIKIENNVASLTDFGRNFLESKGEKSER 84
                                   5677889********************99877655 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.5
                    AAA_assoc_C  14 LlpiveaaelLglveveegdielTelGrkfveadikerKeifreqllklvplaa 67 
                                    L+p  +  e +g + +++g + +T  G+  v+ ++ +     re l +   l++
  gi|116754588|ref|YP_843706.1| 131 LFPRGRYSERIGALIIQKGTVLITLYGTGNVTMTMIRDEAHAREILEE---LKR 181
                                    566666666666666777777777777766665554444443333333...444 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   6.2e-05      0.14      35      69 ..      44      78 ..      19      86 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.2e-05
                         HTH_45 35 llnkYLdmLvekglikkskekYvlTekGlellekl 69
                                   +l+  L++L++ glik +++  +lT+ G+++le+ 
  gi|116754588|ref|YP_843706.1| 44 MLDYHLQILQQAGLIKIENNVASLTDFGRNFLESK 78
                                   67778***************************975 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   0.00016      0.36      38      62 ..      41      65 ..      14      81 .. 0.76
   2 ?   -2.1   0.0       2.2   4.8e+03       6      17 ..     171     182 ..     167     199 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00016
                        DUF2513 38 skeeiiyhlkllaeagLieaekkka 62
                                    +  + yhl++l++agLi++e++ a
  gi|116754588|ref|YP_843706.1| 41 GQSMLDYHLQILQQAGLIKIENNVA 65
                                   455788*************988654 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.2
                        DUF2513   6 lvRdiLltleel 17 
                                      R+iL +l++ 
  gi|116754588|ref|YP_843706.1| 171 HAREILEELKRT 182
                                    568888888754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       824  (0.0459591); expected 358.6 (0.02)
Passed bias filter:                      714  (0.0398237); 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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1909.35
//
Query:       gi|116754589|ref|YP_843707.1|  [L=354]
Description: arsenical-resistance protein [Methanosaeta thermophila PT]
Scores for complete 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-65  220.9  12.5    1.2e-65  220.9  12.5    2.1  3  SBF       Sodium Bile acid symporter family
  ------ inclusion threshold ------
       0.36   11.1   0.1       0.36   11.1   0.1    3.2  3  KASH      Nuclear envelope localisation domain


Domain annotation for each model (and alignments):
>> SBF  Sodium Bile acid symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.1      0.95   8.5e+03     184     185 ..      20      21 ..       5      44 .. 0.52
   2 !  220.9  12.5   1.3e-69   1.2e-65       1     194 [.      50     247 ..      50     248 .. 0.99
   3 ?   -1.5   1.0      0.18   1.6e+03      48      83 ..     264     321 ..     253     336 .. 0.48

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 0.95
                            SBF 184 if 185
                                    ++
  gi|116754589|ref|YP_843707.1|  20 MV 21 
                                    11 PP

  == domain 2  score: 220.9 bits;  conditional E-value: 1.3e-69
                            SBF   1 ailLilmmfpmglkveveklkellkrpkalllglvlqwvikPllmfilakillrdlklepelavGlilvglapggamsnv 80 
                                    ai+Lilmm+p+++kv++e+l+e+++++k l+l+l+++wvi+P+lmf+la+i+lrd+   p l+ G+il+gla+++am++v
  gi|116754589|ref|YP_843707.1|  50 AIGLILMMYPPLAKVRYEELGEVFNDRKVLALSLIQNWVIGPVLMFALAVIFLRDY---PHLMYGVILIGLARCIAMVIV 126
                                    69******************************************************...********************* PP

                            SBF  81 wtylakGdlelsvvlvalstllailltPlllyllaksl.......eqttlkvpieeivksvlivviiPliaGillryill 153
                                    w++la+G +e+++ lv l++++++ll+++++y++++ l       e+t ++v+i +i++sv+i+++iP++aGi++r  l+
  gi|116754589|ref|YP_843707.1| 127 WNELACGSTEYCAALVGLNSVFQVLLYSVYAYIFITVLpaylgvaEGTVVDVTITQIAESVFIYLGIPFLAGIITRFTLI 206
                                    ******************************************************************************** PP

                            SBF 154 khkGrewfeskllpavspisligllltivvifalkgelive 194
                                    + +Grew+  +++p +spi+li+ll+ti+v+f+lkg++iv+
  gi|116754589|ref|YP_843707.1| 207 RARGREWYDGRFIPRISPITLIALLFTIIVMFSLKGDYIVQ 247
                                    ***************************************97 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.18
                            SBF  48 lakillrdl......................klepelavGlilvglapggamsnvwty 83 
                                    l +++++++                      + e  +av++ + g+a+  a + v++ 
  gi|116754589|ref|YP_843707.1| 264 LLMFFVSFYmafnlgvsyentaavaftaasnNFELAIAVAVAVFGIASQEAFAAVIGP 321
                                    3333333333334444445555555554444445555555555555555555555554 PP

>> KASH  Nuclear envelope localisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   1.5      0.31   2.8e+03       8      26 ..       3      21 ..       1      26 [. 0.72
   2 ?   -2.5   0.2      0.73   6.5e+03      13      20 ..     228     235 ..     221     241 .. 0.41
   3 ?   11.1   0.1     4e-05      0.36       5      27 ..     252     274 ..     250     297 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.31
                           KASH  8 aalpLqllLllllllalLv 26
                                   a lpL   +l l++++ +v
  gi|116754589|ref|YP_843707.1|  3 AKLPLLSRFLTLWIFLAMV 21
                                   7789997777777777665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.73
                           KASH  13 qllLllll 20 
                                     +lL+ ++
  gi|116754589|ref|YP_843707.1| 228 IALLFTII 235
                                    12222222 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 4e-05
                           KASH   5 vlraalpLqllLllllllalLvp 27 
                                    vlr+a+pL + +ll++++++ + 
  gi|116754589|ref|YP_843707.1| 252 VLRVAVPLAIYFLLMFFVSFYMA 274
                                    89***************999874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       828  (0.0461822); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2719.55
//
Query:       gi|116754590|ref|YP_843708.1|  [L=334]
Description: rhodanese-related sulfurtransferase-like [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-19   70.5   0.0    9.5e-10   39.0   0.0    2.2  2  Rhodanese    Rhodanese-like domain
  ------ inclusion threshold ------
       0.19   10.3   0.0       0.39    9.2   0.0    1.5  2  AMP-binding  AMP-binding enzyme


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   9.9e-11   8.9e-07      30     106 ..     101     177 ..      76     178 .. 0.80
   2 !   39.0   0.0   1.1e-13   9.5e-10      11      95 ..     210     290 ..     203     295 .. 0.75

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 9.9e-11
                      Rhodanese  30 IpgAvnvskdtlsrakkseapllelpeellel....gidnkktvvvycdgggraaaaaallkklGyknvsvldGGfkawk 105
                                    ++gA  +     +++  +++  l+ pee+++     g++n +++vvy+d+ ++aa    +lk+ G+ +vs+ldG ++ w+
  gi|116754590|ref|YP_843708.1| 101 VKGAMRL----SRGSLVNQNGTLKSPEEIASAlgsiGVTNSDRIVVYGDDLEDAALGFFALKYVGHRDVSLLDGDVERWQ 176
                                    5566666....2223333444566667766667778*****************888899******666***********9 PP

                      Rhodanese 106 e 106
                                    +
  gi|116754590|ref|YP_843708.1| 177 S 177
                                    6 PP

  == domain 2  score: 39.0 bits;  conditional E-value: 1.1e-13
                      Rhodanese  11 kgkvallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellel..gidnkktvvvycdgggraaaaaallkk 88 
                                    +g+v+++D+Rp+ ++  ++IpgAv++       ++ ++++  +++e l+el   ++ +++vvvy ++ g+a+ ++ +l+ 
  gi|116754590|ref|YP_843708.1| 210 SGEVQIVDARPFRDFGLSRIPGAVHI-----DSERARDGDRIADNETLMELfaPLQIDRPVVVYSENPGHASIVWFALQL 284
                                    56788**********99*********.....33333334444444444444444699*************8888*9**** PP

                      Rhodanese  89 lGyknvs 95 
                                    +Gy+   
  gi|116754590|ref|YP_843708.1| 285 MGYNA-M 290
                                    **654.3 PP

>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   4.4e-05      0.39      33      76 ..     123     166 ..     119     173 .. 0.92
   2 ?   -3.3   0.0      0.28   2.5e+03      47      72 ..     262     287 ..     259     291 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 4.4e-05
                                    HHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEE CS
                    AMP-binding  33 nrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvp 76 
                                    +++A++L s+Gv++ dr++++ +   +  + ++a+ ++G   v 
  gi|116754590|ref|YP_843708.1| 123 EEIASALGSIGVTNSDRIVVYGDDLEDAALGFFALKYVGHRDVS 166
                                    579********************************999988775 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.28
                                    T-EEEEEESSSHHHHHHHHHHHHTT- CS
                    AMP-binding  47 gdrVaillpnspewvvallailkaGa 72 
                                    +  V+++++n  +  ++++a++ +G 
  gi|116754590|ref|YP_843708.1| 262 DRPVVVYSENPGHASIVWFALQLMGY 287
                                    45699999*9999999**99998885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.36
# Mc/sec: 2814.34
//
Query:       gi|116754591|ref|YP_843709.1|  [L=121]
Description: ArsR family transcriptional regulator [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-18   64.8   0.1    1.1e-17   63.6   0.1    1.6  1  HTH_5     Bacterial regulatory protein, arsR family
    3.5e-16   59.0   0.1    1.2e-15   57.3   0.0    1.8  2  HTH_20    Helix-turn-helix domain
    4.8e-05   23.1   0.0    0.00014   21.7   0.0    1.7  2  TrmB      Sugar-specific transcriptional regulator TrmB
     0.0026   17.5   0.0      0.003   17.3   0.0    1.1  1  DUF742    Protein of unknown function (DUF742)
  ------ inclusion threshold ------
      0.029   14.1   0.0      0.047   13.4   0.0    1.3  1  DUF4423   Domain of unknown function (DUF4423)
      0.044   13.8   0.0      0.071   13.1   0.0    1.4  1  HTH_45    Winged helix-turn-helix
      0.059   13.0   0.1       0.28   10.8   0.1    2.1  1  HTH_24    Winged helix-turn-helix DNA-binding
       0.07   12.9   0.0       0.16   11.8   0.0    1.6  1  HTH_IclR  IclR helix-turn-helix domain
      0.083   13.1   0.0       0.18   12.0   0.0    1.6  1  PaaX      PaaX-like protein
        0.1   12.4   0.0       0.36   10.6   0.0    2.0  2  HTH_38    Helix-turn-helix domain
       0.11   12.9   0.0       0.13   12.6   0.0    1.4  1  DUF2513   Hypothetical protein (DUF2513)
       0.13   12.5   0.0       0.23   11.6   0.0    1.4  1  HTH_34    Winged helix DNA-binding domain
       0.13   12.2   0.0       0.22   11.4   0.0    1.4  1  MarR_2    MarR family


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 !   63.6   0.1   7.8e-21   1.1e-17       1      46 [.      44      89 ..      44      90 .. 0.97

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 7.8e-21
                                   SHHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_5  1 dptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                   dp Rl ILklL++ge cvce++ +l+ +qst+ShHL++L++aGL++
  gi|116754591|ref|YP_843709.1| 44 DPCRLAILKLLQNGEFCVCEIMTALDRPQSTTSHHLSILKDAGLIK 89
                                   899*****************************************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 ?   -1.1   0.1       1.5   2.1e+03      32      55 ..       6      29 ..       2      32 .. 0.63
   2 !   57.3   0.0   8.7e-19   1.2e-15       2      61 .]      37      95 ..      36      95 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.5
                                   HHHTS-HHHHHHHHHHHHH.CTTEE CS
                         HTH_20 32 erldlskntlsyHLrvLee.agLve 55
                                   +++ ++   + + ++ L++ ++ +e
  gi|116754591|ref|YP_843709.1|  6 RLI-GDEERAMHKIQRLRSlVDVIE 29
                                   444.445556677777777777777 PP

  == domain 2  score: 57.3 bits;  conditional E-value: 8.7e-19
                                   HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                         HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvregr 61
                                   +i++AL++P R++il++L +++++++ e++ +ld +++t s+HL +L +agL++ +++g+
  gi|116754591|ref|YP_843709.1| 37 KIFKALSDPCRLAILKLL-QNGEFCVCEIMTALDRPQSTTSHHLSILKDAGLIKERKVGK 95
                                   59****************.**************************************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 ?   -1.8   0.0       2.2   3.1e+03       9      16 ..      34      41 ..      19      43 .. 0.61
   2 !   21.7   0.0     1e-07   0.00014      15      58 ..      51      94 ..      49     104 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.2
                                   HCCCHCHH CS
                           TrmB  9 yEakvYla 16
                                    E+k+++a
  gi|116754591|ref|YP_843709.1| 34 DEVKIFKA 41
                                   45555555 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 1e-07
                                   HHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                           TrmB 15 laLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                   l+Ll++g+  + ei  +l++p+s+    L+ L+d+Gl++ +k  
  gi|116754591|ref|YP_843709.1| 51 LKLLQNGEFCVCEIMTALDRPQSTTSHHLSILKDAGLIKERKVG 94
                                   68*************************************99954 PP

>> DUF742  Protein of unknown function (DUF742)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   2.2e-06     0.003      39     103 ..      41     106 ..       7     113 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.2e-06
                         DUF742  39 arlqpehrailrLcre.plsVaelaAelklPvgvvrvLlsdLldaglltvrapvtdraaeqpdrel 103
                                    a   p + ail+L ++    V e+  +l+ P +++   ls L dagl++ r+    ++ + +d ++
  gi|116754591|ref|YP_843709.1|  41 ALSDPCRLAILKLLQNgEFCVCEIMTALDRPQSTTSHHLSILKDAGLIKERKVGKWSNYRLADGAV 106
                                    455677889******9999*****************************999887766666666555 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.4e-05     0.047      15      77 ..      39      97 ..      28     115 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.4e-05
                        DUF4423 15 feyfssWyypvirellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyr 77
                                   f+ +s++  ++i++ll+  +f   + e+  +l    +++ +++ l++L+++gl+k+ + gk+ 
  gi|116754591|ref|YP_843709.1| 39 FKALSDPCRLAILKLLQNGEF--CVCEIMTALD--RPQSTTSHHLSILKDAGLIKERKVGKWS 97
                                   677889999999999999999..999*******..9***********************9996 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.2e-05     0.071      10      53 ..      49      92 ..      46     118 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.2e-05
                         HTH_45 10 dILeaisegeakkTkimykanLsykllnkYLdmLvekglikksk 53
                                   +IL+ +++ge    +im + +   ++++  L++L + glik++k
  gi|116754591|ref|YP_843709.1| 49 AILKLLQNGEFCVCEIMTALDRPQSTTSHHLSILKDAGLIKERK 92
                                   8***************************************8865 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 ?   10.8   0.1   0.00021      0.28      21      48 .]      62      89 ..      44      89 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00021
                         HTH_24 21 reLAerlglSpstvnrrlkrLeeeGlIk 48
                                    e+  +l+ ++st++ +l  L+++GlIk
  gi|116754591|ref|YP_843709.1| 62 CEIMTALDRPQSTTSHHLSILKDAGLIK 89
                                   589999999******************8 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00012      0.16       6      50 ..      48      90 ..      48      92 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                                   HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                       HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                   laiL++l  +     + e+  +++ p St++++L+ L   G+++ 
  gi|116754591|ref|YP_843709.1| 48 LAILKLLQNGEFC--VCEIMTALDRPQSTTSHHLSILKDAGLIKE 90
                                   6788888888887..89************************9985 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00013      0.18      29      68 ..      64     103 ..      61     105 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                           PaaX  29 llaelGiseslvRaalsRlakaGwlvrekegrrsfYrLsd 68 
                                    ++ +l+  +s+    ls l+ aG++++ k+g+ s YrL+d
  gi|116754591|ref|YP_843709.1|  64 IMTALDRPQSTTSHHLSILKDAGLIKERKVGKWSNYRLAD 103
                                    5666666666666678889*******************99 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1         4   5.6e+03      23      31 ..       1       9 [.       1       9 [. 0.80
   2 ?   10.6   0.0   0.00026      0.36       3      41 ..      40      79 ..      39      80 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 4
                         HTH_38 23 lreIArrLg 31
                                   +++ Ar++g
  gi|116754591|ref|YP_843709.1|  1 MKKLARLIG 9 
                                   578999987 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00026
                         HTH_38  3 khLsleeReeIerllaeG.lslreIArrLgrspsTIsREl 41
                                   k Ls   R  I +ll+ G   ++eI   L+r  sT s +l
  gi|116754591|ref|YP_843709.1| 40 KALSDPCRLAILKLLQNGeFCVCEIMTALDRPQSTTSHHL 79
                                   5688888***********9****************87765 PP

>> DUF2513  Hypothetical protein (DUF2513)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   9.3e-05      0.13      34      65 ..      67      98 ..      22     117 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.3e-05
                        DUF2513 34 idgyskeeiiyhlkllaeagLieaekkkakss 65
                                   + ++++ + + hl++l +agLi+  k+ + s+
  gi|116754591|ref|YP_843709.1| 67 ALDRPQSTTSHHLSILKDAGLIKERKVGKWSN 98
                                   4567888999****************999988 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00017      0.23       2      49 ..      47      93 ..      46      99 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00017
                         HTH_34  2 RlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdke 49
                                   Rla+l + +++ e +  e+ +al   ++  s hl++L++ag i+ +k 
  gi|116754591|ref|YP_843709.1| 47 RLAILKL-LQNGEFCVCEIMTALDRPQSTTSHHLSILKDAGLIKERKV 93
                                   8898875.57999******************************98885 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00016      0.22      19      55 ..      58      92 ..      41      95 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00016
                                   TSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                         MarR_2 19 grdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                   +  + v e+  +l+ ++s++s +l  L +aGL+ +r+
  gi|116754591|ref|YP_843709.1| 58 E--FCVCEIMTALDRPQSTTSHHLSILKDAGLIKERK 92
                                   4..667799999*********************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 1039.39
//
Query:       gi|116754592|ref|YP_843710.1|  [L=331]
Description: hypothetical protein Mthe_1292 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.069   11.7   1.1      0.088   11.4   1.1    1.1  1  FapA      Flagellar Assembly Protein A
        0.1   13.0   0.6        8.6    6.7   0.0    2.7  3  FliC      Flagellin protein
        2.4    8.4  16.5          7    6.8  16.5    2.0  1  EI24      Etoposide-induced protein 2.4 (EI24)
        5.2    7.9   6.0         30    5.5   3.3    2.6  2  Big_7     Bacterial Ig domain


Domain annotation for each model (and alignments):
>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.1     2e-05     0.088     223     310 ..      50     138 ..      37     170 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2e-05
                           FapA 223 ikGvvesatieAggnItikgGiigkgkskikAggnisakfv.enaeveaggdievekqilnslikaggkiiv....ngrk 297
                                    i+  v+sa + Agg +t++  i+g     i Agg++  +    +  v ag+ i+++++i  + + +g++i      + ++
  gi|116754592|ref|YP_843710.1|  50 INAPVDSA-VVAGGVVTVNAPIAG---DLILAGGQVVLRSDiGGKLVAAGSRINISSKIQRNAVLMGEDISMlpgtTVGR 125
                                    55555555.668999999999999...99999999999987466667778889999999999999999999988776667 PP

                           FapA 298 gkivggnikalke 310
                                      ++g +  ++++
  gi|116754592|ref|YP_843710.1| 126 DALIGAKRFSNQG 138
                                    7777766554444 PP

>> FliC  Flagellin protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1      0.87   3.9e+03      20      46 ..      28      60 ..      19      72 .. 0.49
   2 ?    3.7   0.0     0.016        73      30      77 ..     119     165 ..      89     176 .. 0.78
   3 ?    6.7   0.0    0.0019       8.6     107     129 .]     308     330 ..     298     330 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.87
                           FliC 20 gttytlaga......tagtvdvtgatvsadall 46
                                   + t+t++        +ag v+  +a v++++++
  gi|116754592|ref|YP_843710.1| 28 DETITIDSPvdddifAAGSVVNINAPVDSAVVA 60
                                   444444433222222223455555555555554 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.016
                           FliC  30 agtvdvtgatvsadallsavksaaftattgtitynvgvltgkvtftag 77 
                                     gt++  +a + a  + ++ + ++ t t+++++++++ + g v+f+  
  gi|116754592|ref|YP_843710.1| 119 PGTTVGRDALIGAKRFSNQGSING-TLTVAAEQFENNGTAGRVEFQRI 165
                                    456888899999999999999987.999******99999****99865 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0019
                           FliC 107 VtngsGkavYvsadGklTTdats 129
                                    V  g+G+ +Yv +dG  TT a++
  gi|116754592|ref|YP_843710.1| 308 VCMGVGALLYVMKDGASTTQAAT 330
                                    55689***************987 PP

>> EI24  Etoposide-induced protein 2.4 (EI24)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8  16.5    0.0016         7      54     177 ..     157     303 ..       1     320 [. 0.61

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0016
                                    H....................HHHHHHHHHHHHHHH....HHHHHHHHHH.HHCCTTSHH.HHHHHHHHHHHHHHHHHHH CS
                           EI24  54 p....................lwlfplvalllaapf....ygllaekvekrhlglvksla.eslkslllllllllvllpl 108
                                    +                    + l++++  ll +++     + l++  e    +++++ a e+l  +l+++++l+++++l
  gi|116754592|ref|YP_843710.1| 157 AgrvefqriesrhedtafmsfFHLLSIIGYLLLGLIglrvAPWLFRSSED---KMLRDPAiETLVGFLAIIVSLILAMIL 233
                                    05555555555555554333344444555555555555556666666666...566777779999999999999999999 PP

                                    HHTTHHH....HHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHCTHHHHHHHH...HHHHHHTTSCCHHCTH CS
                           EI24 109 liPvvglilsplllswltayfycfeyldlaagrsleerrallerrrayflgfG...llvslllliPllnllf 177
                                     i++vg+++s++ll++l   + ++  l  ++    ++ +a++++  +++++f    +++ +l+l P ++++f
  gi|116754592|ref|YP_843710.1| 234 AITIVGIPVSVMLLLLLGVGI-MLSCLLVSFT-LGRKVMAIFRSGTGSAVSFTvgyVILNILFLLPYIGWIF 303
                                    669999999998888877663.3333333331.345667788888888888888888888999999998887 PP

>> Big_7  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   3.3    0.0068        30       2      40 ..      30      72 ..      30      86 .. 0.76
   2 ?    2.1   0.0     0.077   3.4e+02      11      36 ..     137     162 ..     135     172 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0068
                                   EEEEEE--TT--EB.TSEEEEEEEEE-S...S-EEEEEEEETT CS
                          Big_7  2 tvtitsPangatvs.ggtvtisasAsdd...ggvskVefyvdg 40
                                   t+ti+sP + + +  g+ v+i+a +  +   ggv +V   + g
  gi|116754592|ref|YP_843710.1| 30 TITIDSPVDDDIFAaGSVVNINAPVDSAvvaGGVVTVNAPIAG 72
                                   6888888888888888888888877777666888777665555 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.077
                                    T--EBTSEEEEEEEEE-S.S-EEEEEE CS
                          Big_7  11 gatvsggtvtisasAsdd.ggvskVef 36 
                                    + +++ gt+t+ a+   + g+  +Vef
  gi|116754592|ref|YP_843710.1| 137 QGSIN-GTLTVAAEQFENnGTAGRVEF 162
                                    55677.*******99888899999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1248  (0.0696079); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); 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):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.38
# Mc/sec: 2583.89
//
Query:       gi|116754593|ref|YP_843711.1|  [L=127]
Description: 30S ribosomal protein S8e [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-38  131.3   0.5    2.8e-38  131.2   0.5    1.0  1  Ribosomal_S8e  Ribosomal protein S8e
  ------ inclusion threshold ------
      0.019   15.1   0.0      0.023   14.8   0.0    1.2  1  AAA_lid_10     AAA lid domain


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 !  131.2   0.5   3.2e-42   2.8e-38       4     137 .]       2     124 ..       1     124 [. 0.99

  Alignments for each domain:
  == domain 1  score: 131.2 bits;  conditional E-value: 3.2e-42
                                    BXXCCCSEESSTEEXXXSSXXXCCSBXXXXXXXEESSHEEEEEEETTCEEEEEEESESEEEEEETTTTEEEEEEEEEEEC CS
                  Ribosomal_S8e   4 srdskhkrkltGgkakllrkkrkielgrkekatklgaervkvvrvrgGkrkkralrlkkanvthpeekvtkklkIlgVkk 83 
                                    ++++k++rk tGg+  + r krk+elgr++++t +g  rvk++r+rgG++k r+l+++ a+v++p +++tk +kI +V++
  gi|116754593|ref|YP_843711.1|   2 KWQGKSARKPTGGRLVPARGKRKYELGREPAETLVGPIRVKKIRTRGGNQKLRLLKADVASVSDPVTGATKLVKIETVVD 81 
                                    689***************************************************************************** PP

                                    SSSTCHHHHTTC--TTEEEEEESHHHHHHHHTTEEEEEEESEHHHHSSEEEEEE CS
                  Ribosomal_S8e  84 npsnneyvrlgvltKgaiievdvseLgevtqsgkvvAqvtsrPgqdGcvnavlL 137
                                    np+n++yvr++++t+ga+i+++++e           A+v srPgqdG+vnavlL
  gi|116754593|ref|YP_843711.1|  82 NPANRHYVRRNIITRGAVIRTEIGE-----------ARVLSRPGQDGVVNAVLL 124
                                    *************************...........*****************8 PP

>> AAA_lid_10  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   2.6e-06     0.023      35      94 ..      38      99 ..      20     104 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.6e-06
                                   ----------------HHHHHHHHHHT-TTTTHHHHHHHHHHH...HHHHTT-XXXXXXXXXX CS
                     AAA_lid_10 35 PenvkkvrlkisddaieiasrkvAsvsgdarrAlkiCkrAvEi...aekdyvakhGlgydgka 94
                                   P  vkk+r +  ++ +++   +vAsvs+    A k+ k  + +   a+++yv+++ +  +g++
  gi|116754593|ref|YP_843711.1| 38 PIRVKKIRTRGGNQKLRLLKADVASVSDPVTGATKLVKIETVVdnpANRHYVRRNII-TRGAV 99
                                   789*************************98877777776554433399****99877.55655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       255  (0.0142228); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.32u 0.24s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 1058.86
//
Query:       gi|116754594|ref|YP_843712.1|  [L=198]
Description: hypothetical protein Mthe_1294 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-08   35.2   0.7     0.0044   17.3   0.1    2.3  2  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
     0.0041   17.0   0.9       0.96    9.4   0.1    2.4  2  Big_2            Bacterial Ig-like domain (group 2)
  ------ inclusion threshold ------
       0.01   15.8   0.7        2.3    8.2   0.1    2.2  2  DUF1326          Protein of unknown function (DUF1326)
      0.014   15.4   0.2        6.4    6.8   0.0    2.3  2  DUF3005          Protein of unknown function (DUF3005)
      0.027   14.3   0.1        9.7    6.2   0.0    2.3  2  PEGA             PEGA domain
      0.082   12.8   0.0         13    5.7   0.0    2.2  2  CpeS             CpeS-like protein
       0.27   11.5   3.4         13    6.1   0.3    2.2  2  HALZ             Homeobox associated leucine zipper
        0.3   11.1   6.9        7.5    6.6   0.8    2.9  2  Big_1            Bacterial Ig-like domain (group 1)


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 !   17.3   0.1     2e-06    0.0044      10      64 ..      39      91 ..      28     126 .. 0.82
   2 !   16.8   0.1   2.6e-06    0.0059      10      64 ..     128     180 ..     115     193 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2e-06
                CarboxypepD_reg 10 sgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatr 64
                                   +g +++ +++t   +++g++ +++td+ G   ++g+p gt +  ++++Gy+t   
  gi|116754594|ref|YP_843712.1| 39 DGPALSDVHITGV-DGDGKSFEAVTDSGGIAEISGVP-GTWQFAFEKDGYETLYL 91
                                   7888899999977.4899****************987.9************9876 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 2.6e-06
                CarboxypepD_reg  10 sgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatr 64 
                                    +g +++ +++t   +++g++ +++td+ G   ++g+p gt +  ++++Gy+t   
  gi|116754594|ref|YP_843712.1| 128 DGPALSDVHITGV-DGDGKSFEAVTDSGGIAEISGVP-GTWQFAFEKDGYETLYL 180
                                    7888899999977.4899****************987.9************9875 PP

>> Big_2  Bacterial Ig-like domain (group 2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.1   0.00043      0.96      38      73 ..      21      57 ..      19      63 .. 0.90
   2 !    6.1   0.1    0.0046        10      39      73 ..     111     146 ..      94     153 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00043
                                   EEECC-SSEEEE.TCCEECCCSSEEEEEEEEETTTSS CS
                          Big_2 38 wtssngsvAtVs.atGlVtavaaGkatitatskdgnd 73
                                   w+s+++ + tV    G++++ a  ++ it +++dg +
  gi|116754594|ref|YP_843712.1| 21 WSSQDQVTLTVHvHEGSLDGPALSDVHITGVDGDGKS 57
                                   9*********************************654 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0046
                                    EECC-SSEEEE.TCCEECCCSSEEEEEEEEETTTSS CS
                          Big_2  39 tssngsvAtVs.atGlVtavaaGkatitatskdgnd 73 
                                    +s+++ + tV    G++++ a  ++ it +++dg +
  gi|116754594|ref|YP_843712.1| 111 SSQDQVTLTVHvHEGSLDGPALSDVHITGVDGDGKS 146
                                    566666777779*********************654 PP

>> DUF1326  Protein of unknown function (DUF1326)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1     0.001       2.3       8      47 ..      12      50 ..      10      59 .. 0.81
   2 ?    6.2   0.0    0.0044       9.8      23      47 ..     115     139 ..     106     148 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.001
                        DUF1326  8 lCpCqfaepptegkCeallawhideGevgdvdLdGlnval 47
                                   +C C    + +  + +++l++h++eG++++ +L+++++  
  gi|116754594|ref|YP_843712.1| 12 VCLCLTVPAWSSQD-QVTLTVHVHEGSLDGPALSDVHITG 50
                                   67787555555555.79*******************9876 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0044
                        DUF1326  23 eallawhideGevgdvdLdGlnval 47 
                                    +++l++h++eG++++ +L+++++  
  gi|116754594|ref|YP_843712.1| 115 QVTLTVHVHEGSLDGPALSDVHITG 139
                                    6899*****************9876 PP

>> DUF3005  Protein of unknown function (DUF3005)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0032       7.1      19      38 ..      47      66 ..      30      71 .. 0.81
   2 ?    6.8   0.0    0.0029       6.4      19      38 ..     136     155 ..     109     160 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0032
                        DUF3005 19 tDntvDtDgKnleAarease 38
                                   +   vD DgK++eA ++ + 
  gi|116754594|ref|YP_843712.1| 47 HITGVDGDGKSFEAVTDSGG 66
                                   5567**********998765 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0029
                        DUF3005  19 tDntvDtDgKnleAarease 38 
                                    +   vD DgK++eA ++ + 
  gi|116754594|ref|YP_843712.1| 136 HITGVDGDGKSFEAVTDSGG 155
                                    5567**********998765 PP

>> PEGA  PEGA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0    0.0043       9.7      28      53 ..      69      94 ..      68     108 .. 0.75
   2 ?    5.9   0.0    0.0051        11      28      51 ..     158     181 ..     157     195 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0043
                           PEGA 28 tlsleaGnyslrvekeGYedlektvt 53
                                   ++s  +G+ ++  ek+GYe+l+ + +
  gi|116754594|ref|YP_843712.1| 69 EISGVPGTWQFAFEKDGYETLYLKYD 94
                                   567669**************976655 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0051
                           PEGA  28 tlsleaGnyslrvekeGYedlekt 51 
                                    ++s  +G+ ++  ek+GYe+l+ +
  gi|116754594|ref|YP_843712.1| 158 EISGVPGTWQFAFEKDGYETLYLK 181
                                    567669**************9765 PP

>> CpeS  CpeS-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0    0.0057        13     105     143 ..      66     106 ..      46     121 .. 0.84
   2 ?    5.2   0.0    0.0079        18     105     143 ..     155     195 ..     136     197 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0057
                                    ----------..EEEE-TTS-EEEEEE-SS-EEEEEEEEEE CS
                           CpeS 105 gyaeaapvvs..rYrldeddvLtLtteyetvsseEriwfvs 143
                                    g ae+  v +  ++++++d+  tL+ +y+  +seE   +++
  gi|116754594|ref|YP_843712.1|  66 GIAEISGVPGtwQFAFEKDGYETLYLKYDALQSEETAAYLE 106
                                    566666666622578899999**************999876 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0079
                                    ----------..EEEE-TTS-EEEEEE-SS-EEEEEEEEEE CS
                           CpeS 105 gyaeaapvvs..rYrldeddvLtLtteyetvsseEriwfvs 143
                                    g ae+  v +  ++++++d+  tL+ +y+  +seE   +++
  gi|116754594|ref|YP_843712.1| 155 GIAEISGVPGtwQFAFEKDGYETLYLKYDALQSEETAAYLE 195
                                    566666666622578899999**************998875 PP

>> HALZ  Homeobox associated leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.3    0.0059        13      11      27 ..      83      99 ..      82     102 .. 0.77
   2 ?    6.1   0.3    0.0059        13      11      27 ..     172     188 ..     171     191 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0059
                           HALZ 11 KasYdaLksdydsLkke 27
                                   K  Y+ L ++yd+L+ e
  gi|116754594|ref|YP_843712.1| 83 KDGYETLYLKYDALQSE 99
                                   55688888888888877 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0059
                           HALZ  11 KasYdaLksdydsLkke 27 
                                    K  Y+ L ++yd+L+ e
  gi|116754594|ref|YP_843712.1| 172 KDGYETLYLKYDALQSE 188
                                    55688888888888877 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 ?    6.6   0.8    0.0033       7.5       4      50 ..      24      70 ..      23      73 .. 0.83
   2 ?    6.6   0.8    0.0033       7.5       4      50 ..     113     159 ..     112     162 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0033
                          Big_1  4 vdtntltatvkDangnpvagatVtfsvsggalsassgtTdanGkatv 50
                                   +d++tlt++v   +    a   V+++  +g+  + +++Td+ G+a++
  gi|116754594|ref|YP_843712.1| 24 QDQVTLTVHVHEGSLDGPALSDVHITGVDGDGKSFEAVTDSGGIAEI 70
                                   799999999999987777777777777788888899********997 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0033
                          Big_1   4 vdtntltatvkDangnpvagatVtfsvsggalsassgtTdanGkatv 50 
                                    +d++tlt++v   +    a   V+++  +g+  + +++Td+ G+a++
  gi|116754594|ref|YP_843712.1| 113 QDQVTLTVHVHEGSLDGPALSDVHITGVDGDGKSFEAVTDSGGIAEI 159
                                    799999999999987777777777777788888899********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 1629.08
//
Query:       gi|116754595|ref|YP_843713.1|  [L=192]
Description: hypothetical protein Mthe_1295 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       163  (0.00909142); expected 358.6 (0.02)
Passed bias filter:                      143  (0.0079759); 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 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1433.24
//
Query:       gi|116754596|ref|YP_843714.1|  [L=82]
Description: hypothetical protein Mthe_1296 [Methanosaeta thermophila PT]
Scores for complete 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   0.7    1.4e-25   89.3   0.7    1.1  1  Dodecin   Dodecin


Domain annotation for each model (and alignments):
>> Dodecin  Dodecin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.3   0.7   7.8e-30   1.4e-25       1      64 []      15      78 ..      15      78 .. 0.99

  Alignments for each domain:
  == domain 1  score: 89.3 bits;  conditional E-value: 7.8e-30
                                   EEEEEEEEEEESS-HHHHHHHHHHHHHHH-SSEEEEEEEEEEEEECTTCCEEEEEEEEEEEE-S CS
                        Dodecin  1 VyKvielvGsSpkSwedAiqnAiaeAsktlrnirwveVketrahvedgkiaeYqvtlkvgFrle 64
                                   VyK ielvG+S+ +wedA+++ +++Asktlr++r++eV+e+++++++gki+eY++++k++F++e
  gi|116754596|ref|YP_843714.1| 15 VYKFIELVGTSTVGWEDAVKTVVETASKTLRDLRVAEVTELDVRLDKGKIVEYRAKVKLSFKYE 78
                                   9************************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 615.87
//
Query:       gi|116754597|ref|YP_843715.1|  [L=237]
Description: hypothetical protein Mthe_1297 [Methanosaeta thermophila PT]
Scores for complete sequence (score 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   12.2   2.9       0.42   10.1   0.1    2.3  2  ApbE      ApbE family
        0.1   12.8   0.0       0.21   11.8   0.0    1.5  1  YorP      YorP protein


Domain annotation for each model (and alignments):
>> ApbE  ApbE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   4.7e-05      0.42     127     171 ..      84     127 ..      63     154 .. 0.72
   2 ?    2.2   0.2     0.012   1.1e+02     219     235 ..     165     182 ..     160     193 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 4.7e-05
                                    HHHHHHHHHHHHHH.TT-EEEEEETTEEEEEC-ECT-EEEEEE-TT CS
                           ApbE 127 KGyavdrvaellka.giksalvnlGGdiralGpdgkpwrvgiedPr 171
                                     G ++  ++e++ + g + a+v+ GGdi++   d +p  vgi    
  gi|116754597|ref|YP_843715.1|  84 AGAIAAFAVEAMVEaGADYAVVDNGGDIAIFS-D-EPLLVGIYAGS 127
                                    466666777777777**************988.4.79999997443 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.012
                                    EEEEESC.HHHHHHHHHH CS
                           ApbE 219 vtViads.alADalaTal 235
                                    +tVi+ + a ADa aTal
  gi|116754597|ref|YP_843715.1| 165 ATVISRDpAIADAGATAL 182
                                    79**9777********98 PP

>> YorP  YorP protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.4e-05      0.21      34      59 ..      92     117 ..      82     126 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.4e-05
                                    EEE---SS-SEEEEETTS-EEEE-GG CS
                           YorP  34 iehlhsatydyavsdetgdityfkeh 59 
                                    +e +  a  dyav d+ gdi+ f + 
  gi|116754597|ref|YP_843715.1|  92 VEAMVEAGADYAVVDNGGDIAIFSDE 117
                                    677888999************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); 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: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1750.43
//
Query:       gi|116754598|ref|YP_843716.1|  [L=500]
Description: 2-isopropylmalate synthase [Methanosaeta thermophila PT]
Scores for 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-85  284.5   2.4    1.6e-84  283.6   2.4    1.5  1  HMGL-like   HMGL-like
      1e-32  112.8   2.7    2.2e-32  111.8   2.7    1.6  1  LeuA_dimer  LeuA allosteric (dimerisation) domain


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 !  283.6   2.4   1.8e-88   1.6e-84       2     264 .]       2     259 ..       1     259 [. 0.99

  Alignments for each domain:
  == domain 1  score: 283.6 bits;  conditional E-value: 1.8e-88
                                    -EEEE-TTTHHHHTSSS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B..--EE-SSHHHHHHH CS
                      HMGL-like   2 vkivdttLRDGeqalkaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkarilalvrarekdikaa 81 
                                    vki+dttLRDGeq+++++l+ eekl ia++Ld++gv++iE+gfp++s+++fe+vraia+++ +a++++l r  ++di++ 
  gi|116754598|ref|YP_843716.1|   2 VKIFDTTLRDGEQTPGVSLTPEEKLIIARQLDKLGVNVIEAGFPVSSKGEFESVRAIANEGLTATVCGLSRIIKNDIDRC 81 
                                    89****************************************************************************** PP

                                    HH....TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-ETTT-BTTTBS--HHHHHHHHHHHHHHT-S CS
                      HMGL-like  82 vealkgagakrvhvfiatselhlkaklkkdreevakkaeeavkaarslgkdvelsledasrtdleflaevveaaeeaGat 161
                                     +    a + +vhvf++ts++++ + +kk+ree+++ + +av++++++g  + +s++da+rt+++fl e+  a+e aGa+
  gi|116754598|ref|YP_843716.1|  82 LD----ADVGMVHVFVSTSDIQIAHTIKKSREEIVADSIKAVEYVKDHGVLCLFSAMDATRTPPAFLREIFTAVEGAGAD 157
                                    **....************************************************************************** PP

                                    EEEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHHHHTT--EEEEBTTS--SSBBB-BHHHHHH CS
                      HMGL-like 162 riniaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaAveaGadrvdgtvnGlGeraGnaaleelva 241
                                    +ini+DtvGv+ P+++++l++++ + ++  + + vHcHnd+GlAvan+laAveaGa++v +tvnGlGeraGna l e v+
  gi|116754598|ref|YP_843716.1| 158 IINIPDTVGVMAPSAFHRLVKEVCSYMN--ILVDVHCHNDFGLAVANSLAAVEAGAREVQVTVNGLGERAGNANLAETVM 235
                                    ****************************..************************************************** PP

                                    HHHHTT.-B----HHHHHHHHHHH CS
                      HMGL-like 242 alealg.vdtgldlqklrsiaalv 264
                                     l+    ++t + +q l ++a+lv
  gi|116754598|ref|YP_843716.1| 236 SLHSIYgAKTSIRTQYLVETARLV 259
                                    **98655*************9997 PP

>> LeuA_dimer  LeuA allosteric (dimerisation) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.8   2.7   2.4e-36   2.2e-32       1     133 []     356     492 ..     356     492 .. 0.95

  Alignments for each domain:
  == domain 1  score: 111.8 bits;  conditional E-value: 2.4e-36
                                    XXXXXXXXXXXXXXXXX...XX--EEEEEEEEEEETTCEEEEEEEEEE.TTEEEEEEEE-SSHHHHHHHHHHHHHHHT-. CS
                     LeuA_dimer   1 evtdedlealvkdelle...aeerlkleklqvssgedelstatvklevkdgeekeasaeGnGpvdAllnAlrkalgvdi. 76 
                                    +vtd+dl+++++ +l+e    e+ l l++++v++g++ ++tatv++    geek+ + +G+GpvdA+++A+r++lg+d  
  gi|116754598|ref|YP_843716.1| 356 QVTDADLQTIAEVVLGEiakGEQALVLKEVAVMTGNTITPTATVRALF-RGEEKVLANIGVGPVDAAVKAVREILGQDSl 434
                                    69********9999998876779*************************.99999***********************544 PP

                                    .EEEEEEEE--TT-TT--EEEEEEEE--GGGEEEEEEEESSHHHHHHHHHHHHHHHHS CS
                     LeuA_dimer  77 .kLldYsvhaitegtdaqaevrVelevddgkkvsgvGvdsdiveASlkAlisalnrll 133
                                     ++ d++++ait+g+da+aev + +e ++g+kvs++++++div+AS++Al+sa+nrll
  gi|116754598|ref|YP_843716.1| 435 iRVRDFRIEAITGGSDALAEVVIGVEDTEGRKVSARSAREDIVMASVEALVSAINRLL 492
                                    5*******************************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (500 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); 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: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 3461.06
//
Query:       gi|116754599|ref|YP_843717.1|  [L=251]
Description: TatD family hydrolase [Methanosaeta thermophila PT]
Scores for complete 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-66  223.8   0.0    2.6e-66  223.6   0.0    1.0  1  TatD_DNase    TatD related DNase
     0.0012   18.2   0.1     0.0023   17.3   0.1    1.6  1  Amidohydro_1  Amidohydrolase family
  ------ inclusion threshold ------
      0.039   14.1   0.0       0.96    9.6   0.0    2.3  2  Phage_TAC_7   Phage tail assembly chaperone proteins, E, or 4


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 !  223.6   0.0   4.3e-70   2.6e-66       1     254 [.       5     249 ..       5     250 .. 0.95

  Alignments for each domain:
  == domain 1  score: 223.6 bits;  conditional E-value: 4.3e-70
                                    EEEEE-TTSCCCTTTHHHHHHHHHHTTEEEEEEE-SSGGGHHHHHHHHTT.TTTEEEEE---GGGGGCC.CCHHHHHHHH CS
                     TatD_DNase   1 iDaHcHldskefeedreeileraeeagvaavvvvgtsskdskavlelakkypnkvyavlGiHPnevdeasedlleelkel 80 
                                    iDaHcHld+k f++dr +++era+++gv  +++ g+++++++++l+la++++  ++a+lG+ Pn++d+ ++++++ + + 
  gi|116754599|ref|YP_843717.1|   5 IDAHCHLDFKHFNKDRMDVIERARASGVVEMINSGVDLQTNRETLKLARSHEF-IHATLGLSPNSLDQMRPKDVDLVLDE 83 
                                    8*************************************************998.**************988888777666 PP

                                    HHCCCTSEEEEEEEEEET-.CCCCCGHHHHHHHHHHHHHHHHHTTEEEEEEEES-HHHHHHHHHHCGGCCSEEEETT--S CS
                     TatD_DNase  81 anvkhskvvaiGeiGLDyy.sreestkeaqeevFeeqlrlAkelklplviHlrkaeedlleilkeaaeakakvvlHsfsg 159
                                       +  +++++Ge GLDyy  ++++ +++q +vF++ + lA+el++plviH+r++e+   +++k+ +    kvv+H++sg
  gi|116754599|ref|YP_843717.1|  84 IRQNSGEIIGVGEAGLDYYrCSDPALRRQQIDVFRKVILLAEELEKPLVIHARETEDIAFDLVKDME----KVVFHCYSG 159
                                    6899**************645566777**************************************73....79******* PP

                                    -HHHHHHHHHTTEEEEE-GGGGTTTTHHHHHHHHHS-GGGEEE---TTSSEECCCTTSE--GGGHHHHHHHHHHHHTS-H CS
                     TatD_DNase 160 saeeakkflklgyyislsglltfknakelrelvkavpldrlLiETDaPyltpkpyrgkrnepanvayvveklaelkaltl 239
                                    s e+++k++++g+y+s++ +++   + ++++l+++vpld+lLiETD+P+l+p   r  rnep ++  +++ +a+++++++
  gi|116754599|ref|YP_843717.1| 160 SLETMRKIVDRGFYVSIATVVCR--SVKHQALARNVPLDQLLIETDSPFLSP---RRGRNEPSFILDSLNLIARMRGMDP 234
                                    *********************99..7799***********************...558********************** PP

                                    HHHHHHHHHHHHHHH CS
                     TatD_DNase 240 eelaeitaeNakrlf 254
                                    e+la++t  N++r++
  gi|116754599|ref|YP_843717.1| 235 EDLATATVRNTRRIY 249
                                    *************98 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   3.8e-07    0.0023       7     209 ..       5     183 ..       4     251 .] 0.76

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.8e-07
                                    EEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHHHHHHHHHHTSSSEEEEEEESSEG CS
                   Amidohydro_1   7 IDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattstgiealleaaeelplglrilggkvsl 86 
                                    IDaH Hl + ++ ++      +  + ++ a +sg++++++sG+       +    + e l+ a ++    +++ +g    
  gi|116754599|ref|YP_843717.1|   5 IDAHCHLDFKHF-NK------DRMDVIERARASGVVEMINSGVD----LQT----NRETLKLARSHE--FIHATLG---- 63 
                                    9******88875.55......89999999999999999999985....555....444444444443..5788888.... PP

                                    GSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHH........HHHHHHHHHHHHTTEEEEEETSSCHH CS
                   Amidohydro_1  87 drgsaetskasreklkagaaetikgkadgvvkvalapheapafsde........elkealkeakkrdlpvaiHaletkge 158
                                       s+++    r k ++ + + i++++++++ v+ a    + +sd           ++++ +a++  +p++iHa et+ +
  gi|116754599|ref|YP_843717.1|  64 --LSPNSLDQMRPKDVDLVLDEIRQNSGEIIGVGEAGLDYYRCSDPalrrqqidVFRKVILLAEELEKPLVIHARETEDI 141
                                    ..77777888888888888888899999999988888888888888666665556666666******************* PP

                                    HHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHHH CS
                   Amidohydro_1 159 vedaeaafgetiehgthlevaeslglldeiklilahgvhltpteaellker 209
                                     +d +++     +  +h +     g l++++ i+ +g +++ ++  ++ + 
  gi|116754599|ref|YP_843717.1| 142 AFDLVKDME---KVVFHCYS----GSLETMRKIVDRGFYVSIAT--VVCRS 183
                                    999999999...66445555....67899999999999999552..22233 PP

>> Phage_TAC_7  Phage tail assembly chaperone proteins, E, or 41 or 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00016      0.96      39      77 ..      45      83 ..      21      87 .. 0.74
   2 ?    1.9   0.0     0.039   2.4e+02      63      76 ..     229     242 ..     213     248 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00016
                    Phage_TAC_7 39 pdadllmgaeialiarlsglppedlekLdlaDlarlqer 77
                                   + + l++ ++ ++i+   gl+p  l+++ ++D+  + ++
  gi|116754599|ref|YP_843717.1| 45 NRETLKLARSHEFIHATLGLSPNSLDQMRPKDVDLVLDE 83
                                   34445566679*********************9887665 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.039
                    Phage_TAC_7  63 lekLdlaDlarlqe 76 
                                    ++++d++Dla++++
  gi|116754599|ref|YP_843717.1| 229 MRGMDPEDLATATV 242
                                    45667777766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 1911.43
//
Query:       gi|116754600|ref|YP_843718.1|  [L=162]
Description: hypothetical protein Mthe_1300 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-22   80.5   0.0    2.1e-22   80.2   0.0    1.1  1  NYN       NYN domain


Domain annotation for each model (and alignments):
>> NYN  NYN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.2   0.0   1.2e-26   2.1e-22       1     146 [.      22     153 ..      22     154 .. 0.92

  Alignments for each domain:
  == domain 1  score: 80.2 bits;  conditional E-value: 1.2e-26
                            NYN   1 rvavfiDgenlpvpakgkevdyrklleeirskgelvraraygnwedeeqnkfqdalsstgi.kvkhkplkkrggsgkkav 79 
                                    ++++++Dg n+    k+ ++d++++++ +r +g++++ ++++n+++   +k+ +a +++g+ +v              +v
  gi|116754600|ref|YP_843718.1|  22 KIGLLVDGPNMLR--KEFQMDLEEIRNILRDYGDIKVGKVFLNQYA--SEKLVEAVENQGFePVICT----------SDV 87 
                                    6899*********..6668************************444..48999********888444..........67* PP

                            NYN  80 DvelavdalelaydnkydtivLvsgDgDFaplveklrergkrVevllaeeastsseLisaadefisl 146
                                    Dv++av+ ++++y++ +dti Lv++D+D+ p++ k++e+gk++++++ae +  s +L+++ad++i+l
  gi|116754600|ref|YP_843718.1|  88 DVRMAVEGVDMIYNPVIDTIALVTRDADLKPVLMKAMEHGKETIIFGAE-PGFSVALRNSADYVIVL 153
                                    ***************99******************************65.99************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.34
# Mc/sec: 1409.30
//
Query:       gi|116754601|ref|YP_843719.1|  [L=205]
Description: rhomboid family protein [Methanosaeta thermophila PT]
Scores for complete 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-34  116.9  12.6    7.3e-34  116.9  12.6    1.6  2  Rhomboid  Rhomboid family
    1.9e-06   28.4   0.3    1.9e-06   28.4   0.3    1.7  2  DUF1751   Eukaryotic integral membrane protein (DUF1751)


Domain annotation for each model (and alignments):
>> Rhomboid  Rhomboid family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.23   2.1e+03     104     119 ..      24      39 ..      10      47 .. 0.61
   2 !  116.9  12.6   8.1e-38   7.3e-34       4     148 ..      56     201 ..      53     203 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.23
                                    ...CCCCCCCCCCHHH CS
                       Rhomboid 104 llllllfillnlvlgl 119
                                    l  ++l+il+++++++
  gi|116754601|ref|YP_843719.1|  24 LAIIALCILVSIAMAI 39 
                                    3445555555555555 PP

  == domain 2  score: 116.9 bits;  conditional E-value: 8.1e-38
                                    CC-TTHHHHGGG--SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-S...-EESSHHHHHHHH CS
                       Rhomboid   4 rgelwrlltsmflHagwlHllfNmlallvfGsplerrlGslrflllyllsglagsllsllfsaesesplvGaSGaifgll 83 
                                    +++ w+l+t++f+Ha++ Hl+ Nmlall+fG++lerr+G+ +fll++++sg++g+++ +l+      +++GaSGai+g++
  gi|116754601|ref|YP_843719.1|  56 ESRPWTLVTHIFVHADIGHLFWNMLALLFFGTELERRVGERNFLLVFFASGIFGGIIEMLVATG---YMMGASGAIMGVM 132
                                    5689*********************************************************999...8************ PP

                                    HHHHHHHHCCCCGS----HC......CCCCCCCCCCHHHCTSS.STTTHHHHHHHHHHHHHHHHHHCCH CS
                       Rhomboid  84 gallvlvprnrkllrkliia...llllllfillnlvlgllpra.ggvsnlAHlgGllaGlllgllllrr 148
                                    gal++  p+ r  ++ ++i+   +l+++l+++l+l + +  r  +g+ ++AHl+GllaGl++g  + rr
  gi|116754601|ref|YP_843719.1| 133 GALAIIAPEIRVIIFPIPIPlgiPLAIALIAFLDLYYQISLRGaDGIGHMAHLAGLLAGLFFGQSFGRR 201
                                    *****************9999999999999999999988776679*****************9888776 PP

>> DUF1751  Eukaryotic integral membrane protein (DUF1751)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       1.5   1.4e+04      61      71 ..      25      35 ..      19      42 .. 0.51
   2 !   28.4   0.3   2.1e-10   1.9e-06       2      71 ..      53     122 ..      52     140 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.5
                        DUF1751 61 lvvlltlllyl 71
                                    +++l++l+++
  gi|116754601|ref|YP_843719.1| 25 AIIALCILVSI 35
                                   44444444433 PP

  == domain 2  score: 28.4 bits;  conditional E-value: 2.1e-10
                        DUF1751   2 gallpypwtlltasfveqnvwkvlvslltlllggkylErlWgskEllkFilvvnvitnllvvlltlllyl 71 
                                    + +   pwtl+t+ fv + + ++  ++l+ll++g+ lEr  g++ +l  ++  +++ +++ +l+++ +++
  gi|116754601|ref|YP_843719.1|  53 ALVESRPWTLVTHIFVHADIGHLFWNMLALLFFGTELERRVGERNFLLVFFASGIFGGIIEMLVATGYMM 122
                                    555568****************************************999999999999998888765444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); 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: 0.38u 0.21s 00:00:00.59 Elapsed: 00:00:00.35
# Mc/sec: 1759.84
//
Query:       gi|116754602|ref|YP_843720.1|  [L=602]
Description: translation initiation factor IF-2 [Methanosaeta thermophila PT]
Scores for complete 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-33  115.9   0.0    1.4e-32  112.8   0.0    2.2  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    2.9e-32  110.4   1.6    2.9e-32  110.4   1.6    2.0  2  GTP_EFTU_D4  Elongation factor Tu domain 4
    1.1e-18   67.3   0.7      3e-18   65.9   0.1    2.0  2  IF-2         Translation-initiation factor 2
    3.1e-09   37.1   6.5    1.1e-08   35.4   0.1    3.3  3  GTP_EFTU_D2  Elongation factor Tu domain 2
    3.8e-07   30.2   0.1    1.7e-06   28.1   0.0    2.2  2  MMR_HSR1     50S ribosome-binding GTPase
  ------ inclusion threshold ------
      0.044   14.0   0.0       0.14   12.4   0.0    1.9  1  Roc          Ras of Complex, Roc, domain of DAPkinase
      0.072   12.8   0.2       0.66    9.7   0.0    2.7  4  PduV-EutP    Ethanolamine utilisation - propanediol utilisati
       0.08   13.0   0.0        1.4    8.9   0.0    2.4  2  Dynamin_N    Dynamin family
       0.12   12.6   0.4       0.46   10.7   0.0    2.1  2  DapH_N       Tetrahydrodipicolinate succinyltransferase N-ter


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 !  112.8   0.0   6.9e-36   1.4e-32       4     191 ..      21     227 ..      18     230 .. 0.85

  Alignments for each domain:
  == domain 1  score: 112.8 bits;  conditional E-value: 6.9e-36
                                    EEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEETTCSSEEEEEEEESSSGGG CS
                       GTP_EFTU   4 rnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisleketkkylinliDtPGHvdF 83 
                                      ++++ghvDhGKtTL+dr+  +t a  ++g+ ++        ++E    +  + +   ++++     + +iDtPGH  F
  gi|116754602|ref|YP_843720.1|  21 PIVCVMGHVDHGKTTLLDRIRGTTVAQYEAGAITQ-----HIGATEIPLSVIQQFCGSGFKANLMVPGLLFIDTPGHHAF 95 
                                    579******************99888888666554.....4455555555555555555656666789************ PP

                                    HHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGST...........HHHHHHHHHHHHHHHHH CS
                       GTP_EFTU  84 skevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrl...........kaelkeiveevkqklsr 152
                                    ++  +rg + +D+a+l+vd++eG +pqt e ++++++ ++p++v+ NK+Dr+           +++l  + e v ++l++
  gi|116754602|ref|YP_843720.1|  96 TSLRSRGGSLADLAILIVDINEGFQPQTIESINILKRFKTPFVVAANKIDRIpgwrpvenapmEKSLAGQTERVVETLET 175
                                    *************************************************************9977777777777777766 PP

                                    H....HHHHHHHHHTTT.........TTEEEEEEBTTTTBTHHHHHHHHHHH CS
                       GTP_EFTU 153 k....eeklekygekge.........kevpvvfgSalkgegvktllealvel 191
                                    k     ++l kyg++++         k+v ++++Sa++geg+ +ll +lv l
  gi|116754602|ref|YP_843720.1| 176 KiyelVGELYKYGFDSNrydriadftKTVGIIPVSAITGEGIPDLLLVLVGL 227
                                    666667888888888779999999999******************9998865 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 ?   -3.8   0.0       6.4   1.3e+04      30      48 ..     351     369 ..     347     374 .. 0.61
   2 !  110.4   1.6   1.5e-35   2.9e-32       1      86 []     474     559 ..     474     559 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 6.4
                                    EETT-EEEETTE.EEEEEE CS
                    GTP_EFTU_D4  30 ikpgvklikedGrevGeil 48 
                                    i+++++ ++ d  +vG+il
  gi|116754602|ref|YP_843720.1| 351 IRSEIEAVRIDTDTVGVIL 369
                                    5555555666666666665 PP

  == domain 2  score: 110.4 bits;  conditional E-value: 1.5e-35
                                    S-CEEEEEEEEEEETCCCEEEEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEESS-TTTS-- CS
                    GTP_EFTU_D4   1 rPgkikilpgvvfrrsdpaivGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisiegkivGrqik 80 
                                    +Pg ++ilp++vfr+s+paivGv+v+gG+i  +v+li+edG  vG+i+ iq++++++ +a+ Gqevaisi+g++vGrqi+
  gi|116754602|ref|YP_843720.1| 474 KPGCVRILPDCVFRQSKPAIVGVQVVGGTISHNVPLIREDGAVVGTIRGIQQRNENIPMATVGQEVAISIDGPTVGRQIH 553
                                    79****************************************************************************** PP

                                    TT-EEE CS
                    GTP_EFTU_D4  81 egdily 86 
                                    egd ly
  gi|116754602|ref|YP_843720.1| 554 EGDLLY 559
                                    *****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 !   65.9   0.1   1.5e-21     3e-18       4     104 ..     354     453 ..     351     454 .. 0.92
   2 ?   -1.8   0.1       1.7   3.5e+03      40      70 ..     537     570 ..     516     587 .. 0.69

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 1.5e-21
                                    HHHCCCSCSSCCEEEEEESSHHHHHHHHHHHHCTT.SSTEEEECEEEESSB-HHHHHHHHHST....EEEEEESSSCTHH CS
                           IF-2   4 lfeeikeegkelnviikaDvqGsleAlkeaLekleseevkvkvihsgvGaitesDvelasasn....aiiigFnvkvskk 79 
                                    ++e++  ++++++vi+kaD+ Gsle l   L+       ++++  ++vG++t++Dv  a+a +    ++i+gFnv++ ++
  gi|116754602|ref|YP_843720.1| 354 EIEAVRIDTDTVGVILKADTIGSLEGLVGELRAK-----NIPIHVADVGPVTRRDVIRAAAIKdpllSVILGFNVEILPD 428
                                    5677777889***********************8.....599******************9555899************* PP

                                    HHHCCCCCTSEEEEESSHHHHHHHH CS
                           IF-2  80 akklaekegvkirlynvIYkliddv 104
                                    a ++++k ++ +++++vIY l++ +
  gi|116754602|ref|YP_843720.1| 429 ALSEIQKLDIPVFQSDVIYTLLESY 453
                                    **********************987 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.7
                                    SSTEEEECEEEESS.B-HHHHHHHHH..STEEEE CS
                           IF-2  40 eevkvkvihsgvGa.itesDvelasa..snaiii 70 
                                    +ev +++    vG  i+e D  +++   ++a ii
  gi|116754602|ref|YP_843720.1| 537 QEVAISIDGPTVGRqIHEGDLLYVNIpeKHARII 570
                                    6778888888888448888888877743446665 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 !   35.4   0.1   5.3e-12   1.1e-08       1      73 [.     258     335 ..     258     336 .. 0.93
   2 ?   -0.5   0.1      0.86   1.7e+03      49      65 ..     360     376 ..     340     379 .. 0.77
   3 ?    3.1   0.5     0.065   1.3e+02      30      74 .]     514     559 ..     493     559 .. 0.81

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 5.3e-12
                                    EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEE..........ETTSEEEEEEEESSCCSGSSTT CS
                    GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededea..........vaganaGvivaikgledaiivG 70 
                                    Gt+ ++++y+G + +Gd++++   +t++++i+t++++l+++++ ++e            + a+ G++v +++le+a ++G
  gi|116754602|ref|YP_843720.1| 258 GTTLDVILYDGMISVGDTIVV---GTPREPIITKVRALLKPRP-LKEIrseerftpvkHVVAASGIKVSAPKLETA-LAG 332
                                    89*******************...68899************66.66666*********999**************8.*** PP

                                    CEE CS
                    GTP_EFTU_D2  71 dtl 73 
                                    +t+
  gi|116754602|ref|YP_843720.1| 333 STI 335
                                    **8 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.86
                                    ETTSEEEEEEEESSCCS CS
                    GTP_EFTU_D2  49 vaganaGvivaikgled 65 
                                    ++ + +Gvi++++ + +
  gi|116754602|ref|YP_843720.1| 360 IDTDTVGVILKADTIGS 376
                                    89999*****9988765 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.065
                                    E.EEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEEE CS
                    GTP_EFTU_D2  30 e.ivtrissletfhededeavaganaGvivaikgledaiivGdtlt 74 
                                    +  v++i++++  +e+   a +g+ + + + ++ +   i  Gd l+
  gi|116754602|ref|YP_843720.1| 514 GaVVGTIRGIQQRNENIPMATVGQEVAISIDGPTVGRQIHEGDLLY 559
                                    24899*************************9999999999999886 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   8.6e-10   1.7e-06       2     114 .]      23     143 ..      22     143 .. 0.75
   2 ?   -1.8   0.1       1.6   3.2e+03      42      42 ..     409     409 ..     352     473 .. 0.55

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 8.6e-10
                                    EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEE...............EEEEECGGCSSHHHHHHHH CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgke...............ielvDtpGliegaseekgl 66 
                                    v+++G+   GK+tL+ ++ g+++   +    T++i   ++ l+  +               + ++DtpG  +       +
  gi|116754602|ref|YP_843720.1|  23 VCVMGHVDHGKTTLLDRIRGTTVAQYEAGAITQHIGATEIPLSVIQqfcgsgfkanlmvpgLLFIDTPG-HH------AF 95 
                                    89*****************9877666777777777777666443223455556666666669*******.44......22 PP

                                    HHHHHHHHC.TSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                       MMR_HSR1  67 gkaflalee.adlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                    +    +  + adl++l+vd++ e+++p+  e  ++l++ k p+++++nk
  gi|116754602|ref|YP_843720.1|  96 TSLRSRGGSlADLAILIVDIN-EGFQPQTIESINILKRFKTPFVVAANK 143
                                    22222222348********99.77************999*******998 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.6
                                    E CS
                       MMR_HSR1  42 k 42 
                                    +
  gi|116754602|ref|YP_843720.1| 409 A 409
                                    0 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 ?   12.4   0.0   6.8e-05      0.14       2     119 ..      23     145 ..      22     146 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.8e-05
                                    EEEESSTTSSHHHHHHCHCT-CCC-EEE....TTTTEEEEEEECG.GSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHH CS
                            Roc   2 vvlvGdsgvGKtsllkrfvedkfsekek....stigvdfltkevt.kikgvendkkvkkvklniWDtaGqerfrslhply 76 
                                    v+++G    GKt+ll+r+   ++ + e     + ig++ +  +v  ++ g   + ++    l + Dt G+  f sl++  
  gi|116754602|ref|YP_843720.1|  23 VCVMGHVDHGKTTLLDRIRGTTVAQYEAgaitQHIGATEIPLSVIqQFCGSGFKANLMVPGLLFIDTPGHHAFTSLRSRG 102
                                    6889***************9999877651111444544444333202223333444445567899*************** PP

                                    HCTSCEEEEEEEGHHHHCHHHHHHHHHHHCS.SS-EEEEEE-TT CS
                            Roc  77 lreaalailvydsrssenlkeWlkelkkvag.kspvilvgnkiD 119
                                     + a+lail++d ++  +  + +++++   + k+p+++ +nkiD
  gi|116754602|ref|YP_843720.1| 103 GSLADLAILIVDINEGFQ-PQTIESINILKRfKTPFVVAANKID 145
                                    ************766544.344666666555378999999*999 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00033      0.66       4      29 ..      23      49 ..      20      63 .. 0.78
   2 ?   -1.3   0.0      0.83   1.7e+03      40      49 ..      86      95 ..      84     176 .. 0.57
   3 ?   -3.5   0.0         4   8.1e+03     123     138 ..     206     221 ..     204     224 .. 0.84
   4 ?   -3.4   0.0       3.7   7.3e+03      89     101 ..     361     373 ..     349     377 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00033
                      PduV-EutP  4 illiGkvgsGKttLtqalkgeelk.Yk 29
                                   + ++G+v+ GKttL  +++g ++  Y+
  gi|116754602|ref|YP_843720.1| 23 VCVMGHVDHGKTTLLDRIRGTTVAqYE 49
                                   789****************98874144 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.83
                      PduV-EutP 40 viDtPGeyle 49
                                   +iDtPG ++ 
  gi|116754602|ref|YP_843720.1| 86 FIDTPGHHAF 95
                                   5999997643 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 4
                      PduV-EutP 123 ifevsavekegieell 138
                                    i+ vsa++ egi +ll
  gi|116754602|ref|YP_843720.1| 206 IIPVSAITGEGIPDLL 221
                                    7889********9986 PP

  == domain 4  score: -3.4 bits;  conditional E-value: 3.7
                      PduV-EutP  89 nkeviGiitkidl 101
                                      +++G+i k+d+
  gi|116754602|ref|YP_843720.1| 361 DTDTVGVILKADT 373
                                    4567777777775 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00071       1.4       1      34 [.      23      56 ..      23      64 .. 0.91
   2 ?    1.1   0.0      0.19   3.7e+02      98     112 ..      79      93 ..      75     114 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00071
                                   EEEEEBTTTTHHHHHHHHHTS--S---SSS---S CS
                      Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrr 34
                                   ++v+G++ +GK+++l+ + g  +   +++ +T+ 
  gi|116754602|ref|YP_843720.1| 23 VCVMGHVDHGKTTLLDRIRGTTVAQYEAGAITQH 56
                                   78********************999999999875 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.19
                                    TTS-SEEEEE---B- CS
                      Dynamin_N  98 llvkgltlvDlPGld 112
                                    l v+gl ++D+PG +
  gi|116754602|ref|YP_843720.1|  79 LMVPGLLFIDTPGHH 93 
                                    67899********86 PP

>> DapH_N  Tetrahydrodipicolinate succinyltransferase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00023      0.46      10      75 ..     301     363 ..     298     365 .. 0.89
   2 ?   -2.7   0.1       3.5   7.1e+03      47      73 ..     444     470 ..     437     474 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00023
                                    HHH---B-EEEEEEEE-.C.TC----TTSEEEE-SSEEEEEEEHHHHHHHHHHTTTTEEEEEEEE- CS
                         DapH_N  10 IkeakKkTpvkvYvkgelkeeelefpeevkvfgsedsgvvfGdwkeieevleenkdkiedyevend 75 
                                    I++ ++ Tpvk  v ++   ++++   ++++   +++  v+G+ ++ e++ +e +++ie +++++d
  gi|116754602|ref|YP_843720.1| 301 IRSEERFTPVKHVVAASG--IKVSA-PKLETALAGSTIRVVGEGEDPEAIAKEIRSEIEAVRIDTD 363
                                    7888999*******9994..77755.59***********************************987 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.5
                                    EEEEEEHHHHHHHHHHTTTTEEEEEEE CS
                         DapH_N  47 gvvfGdwkeieevleenkdkiedyeve 73 
                                     v+++ +++ ee +ee+k ++e+ ++e
  gi|116754602|ref|YP_843720.1| 444 DVIYTLLESYEEWMEEKKMQMEQERLE 470
                                    566666777788888888888877777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (602 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); 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: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.38
# Mc/sec: 4753.04
//
Query:       gi|116754603|ref|YP_843721.1|  [L=153]
Description: hypothetical protein Mthe_1303 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.13   10.7   0.0       0.16   10.3   0.0    1.1  1  DUF5042   Domain of unknown function (DUF5042)


Domain annotation for each model (and alignments):
>> DUF5042  Domain of unknown function (DUF5042)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   8.9e-06      0.16     260     296 ..     100     136 ..      80     141 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 8.9e-06
                        DUF5042 260 lnfpvlmspsfrendseksqlaasspstekimehtgv 296
                                    l++ vlms  +re d e+ q+a    + ++ime+ g 
  gi|116754603|ref|YP_843721.1| 100 LEMGVLMSLPIREMDLEEDQVAHVYDAMNRIMEQMGC 136
                                    7899*****************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 1272.02
//
Query:       gi|116754604|ref|YP_843722.1|  [L=421]
Description: adenylosuccinate synthetase [Methanosaeta thermophila PT]
Scores for complete 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-159  530.7   0.0   2.8e-159  530.6   0.0    1.0  1  Adenylsucc_synt  Adenylosuccinate synthetase


Domain annotation for each model (and alignments):
>> Adenylsucc_synt  Adenylosuccinate synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  530.6   0.0  1.5e-163  2.8e-159       1     419 []       3     418 ..       3     418 .. 0.97

  Alignments for each domain:
  == domain 1  score: 530.6 bits;  conditional E-value: 1.5e-163
                                    .EEEE-SSS-S-HHHHHHHHHTT-SEEEE-SB-TTSSEEEEETTEEEEESSS-GGGGSTT-EEEE-TTBEE-HHHHHHHH CS
                Adenylsucc_synt   1 vvvvGaqwGDEGKGkivDllaeeadvvvRfqGGanAGHtvvvdgkkyklhllpSGilnpgvvnviGngvvvdpealleEi 80 
                                    +++ Gaq+GDEGKGkivDllae++d+++RfqGG+nAGHtv v++k+yklhl+pSG+l  +++ +iG+gvv++p++l eE+
  gi|116754604|ref|YP_843722.1|   3 TIITGAQFGDEGKGKIVDLLAEKYDIIARFQGGDNAGHTVKVGDKTYKLHLVPSGVLF-DKRLLIGPGVVLNPKVLWEEL 81 
                                    589******************************************************7.7788***************** PP

                                    TTSS-TT......TEEEETTSEE--HHHHHHHHHHHHH----------TTHHHHHHHHHTT---BGGGGGSHHHHHHHHH CS
                Adenylsucc_synt  81 eeleakgvelskerllisdrahlvlpyhkalDkleeaakgkkkiGtTkkGiGpayadkvarrgirvgdlldeeeleekle 160
                                    ++l  +g+++   +l i+ ++ +++pyh+++D+l+e+a++ +kiGtT++GiG ay dk+ar+ ++++d+ d+e l++kle
  gi|116754604|ref|YP_843722.1|  82 QTLWGMGMKV---DLGIDPKTSIIMPYHIEMDALREKART-AKIGTTRRGIGYAYIDKIAREEVQMADITDPEMLKRKLE 157
                                    ********88...8***********************986.9************************************** PP

                                    HHHHHTHHHHHHT.....T-----HHHHHHHHHHHHGGGEE-HHHHHHHHHHTT--EEEE--S-GGG-TTTSSTTSS-SS CS
                Adenylsucc_synt 161 kllelknkllekldk..eeleveelleellkyaerlkpyvvdtvallnealkegkkvLfEGaqgtllDidhGtYPfvTsS 238
                                    +++  k++ ++++    + ++ e+ l+ +l++ ++lk+ ++d++ ++n+al+e+k vL EGaqg++lD+ hGt  fvTsS
  gi|116754604|ref|YP_843722.1| 158 EIAPAKESAIKEMGGdpSVVRDEAQLRAYLEIGRALKNNLTDVSLEINRALDEDKMVLAEGAQGAFLDVIHGTQKFVTSS 237
                                    ************97765555546688999*************************************************** PP

                                    --SHHHHHHHTT--GGGEEEEEEEEESSEEESSSS--TTB--SHHHHHHHHHTT-B-TTT--B-EEE-EEHHHHHHHHHH CS
                Adenylsucc_synt 239 nttaggaltglglapkkidevlgvvKAyttrvGeGpfptelkdevgeklrekGkEfgtttgrpRrcGwlDlvllryavrv 318
                                     ttag+a++ lg++p ++d+v+gvvKAy+trvGeGp+ptelkde+g++lre+G+E+gtttgrpRrcGw+D+vl r+av +
  gi|116754604|ref|YP_843722.1| 238 FTTAGSACANLGVGPVRVDNVVGVVKAYITRVGEGPMPTELKDEIGDRLREAGGEYGTTTGRPRRCGWFDAVLGRKAVYL 317
                                    ******************************************************************************** PP

                                    HT-SEEEEE-GGGGTT-SEEEEEEEEEETTEEESS--S.....-GEEEEEEEEE--.S--TT---GGGS-HHHHHHHHHH CS
                Adenylsucc_synt 319 ngvtelaltklDvldgldeikvcvaYkldgkeldefpasleelekvepvyeelpgWkedisgvrsfedlpenakkyvefi 398
                                    ng+telaltklDvl+gl +ik+cvaY+ldg++l++ p+s+ el+++ pvyee++gW+e+is++ +++dlp+na++yve+i
  gi|116754604|ref|YP_843722.1| 318 NGYTELALTKLDVLTGLRRIKICVAYELDGEILEYPPESTYELARCVPVYEEMEGWSESISEALDYSDLPQNARAYVERI 397
                                    ******************************************************************************** PP

                                    HHHHTS-EEEEE-SSSTT-EE CS
                Adenylsucc_synt 399 eellgvpvkiisvGpereqti 419
                                    +el++v ++ isvGp reqti
  gi|116754604|ref|YP_843722.1| 398 QELMDVDIAAISVGPAREQTI 418
                                    *******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.37
# Mc/sec: 3410.05
//
Query:       gi|116754605|ref|YP_843723.1|  [L=187]
Description: orotate phosphoribosyltransferase [Methanosaeta thermophila PT]
Scores for complete 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   34.0   0.1    2.8e-08   33.4   0.1    1.3  1  Pribosyltran  Phosphoribosyl transferase domain
  ------ inclusion threshold ------
      0.011   15.1   0.0      0.016   14.7   0.0    1.2  1  UPRTase       Uracil phosphoribosyltransferase
      0.034   13.6   0.0       0.05   13.1   0.0    1.3  1  PRTase_2      Phosphoribosyl transferase


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.1   4.7e-12   2.8e-08      58     132 ..      94     160 ..      70     166 .. 0.86

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 4.7e-12
                                    EEEEEE-TTT--EE........EE----TTSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHHH CS
                   Pribosyltran  58 vrkvkyrpdgseeaargssdesrlledpagkkVliVDDildtGgTllaalelLkekgpeevriavlvdkpateee 132
                                    vrk+ +r+++   +          + + ag kV +VDD+++tG++ll+ +e+L+e+g + + + +++d++++ +e
  gi|116754605|ref|YP_843723.1|  94 VRKKAKRHGKRRFIE--------GPLMEAGAKVAVVDDVVTTGNSLLRSIERLEEAGYTPIQTLAVLDRMEGGRE 160
                                    555556665555554........677899****************************************998765 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   2.6e-06     0.016     121     170 ..     115     162 ..      92     174 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.6e-06
                        UPRTase 121 ertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegvkrla 170
                                      +v ++D v+ TG+s+   i++L e+g     I  l+vl   eg ++++
  gi|116754605|ref|YP_843723.1| 115 GAKVAVVDDVVTTGNSLLRSIERLEEAGY--TPIQTLAVLDRMEGGREAL 162
                                    56799*********************665..6899999998888876665 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   8.4e-06      0.05     117     150 ..     111     144 ..      98     171 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.4e-06
                       PRTase_2 117 llaaakelvLvDDEistGktalnliralqeklpr 150
                                    l++a +++ +vDD ++tG+++l+ i++l+e+   
  gi|116754605|ref|YP_843723.1| 111 LMEAGAKVAVVDDVVTTGNSLLRSIERLEEAGYT 144
                                    567778999******************9987443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 1568.38
//
Query:       gi|116754606|ref|YP_843724.1|  [L=297]
Description: branched-chain amino acid aminotransferase [Methanosaeta thermophila PT]
Scores for complete 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-57  194.8   0.0      2e-57  194.6   0.0    1.0  1  Aminotran_4      Amino-transferase class IV
  ------ inclusion threshold ------
       0.12   11.6   0.0       0.93    8.6   0.0    2.1  2  Polysacc_deac_2  Divergent polysaccharide deacetylase


Domain annotation for each model (and alignments):
>> Aminotran_4  Amino-transferase class IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  194.6   0.0   2.3e-61     2e-57       1     223 []      30     256 ..      30     256 .. 0.97

  Alignments for each domain:
  == domain 1  score: 194.6 bits;  conditional E-value: 2.3e-61
                    Aminotran_4   1 glfEtmrvyngeiffldeHleRLrksaellglelpfdeeelrkileelleannsengrlrllvsrgggglg.aatsepsv 79 
                                    g+fE++r+y g++f+l++H+ RL  sa++++l++p+++ee+ +++ e+l++nn + +++r++v+rg g+lg ++ ++++ 
  gi|116754606|ref|YP_843724.1|  30 GVFEGIRAYGGRVFRLEAHVRRLYDSAQAIMLDIPMTQEEMCEAILETLRRNNLRDAYIRPVVTRGVGDLGlDPRKCSKP 109
                                    8**************************9999*****************************************99999999 PP

                    Aminotran_4  80 avyvsalppgpeseke....lplvtssdvrrdapsplpgaKtlnyldnvlarreakergadevllvdedgnvtEgstsNv 155
                                     v+++a+++++ + +     l+++t +++r ++    p++K+lnyl+n+la+ ea+ +g de++++d +g ++Egs  N+
  gi|116754606|ref|YP_843724.1| 110 TVIIIAISWDAMYGDLyevgLNAITVTVRRNSPAALPPNIKSLNYLNNILAKIEANIKGGDEAIFLDAEGTISEGSGDNI 189
                                    999999999999988889**99999999**************************************************** PP

                    Aminotran_4 156 fivkggelitPplssgiLpGitrrallelakalgleveereitlkdleeadeafltntlrgvlpvrsi 223
                                    f+v++g+++tPp  +  L+Gitr+++lela++ g++v+e+++ l dl  a+e+f+t+t++++ pv +i
  gi|116754606|ref|YP_843724.1| 190 FVVRDGKIYTPPTLN-NLKGITREVVLELANRNGIPVHETRLGLFDLYTAEEVFVTGTAAEIAPVARI 256
                                    ***********8877.7************************************************987 PP

>> Polysacc_deac_2  Divergent polysaccharide deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0     0.042   3.8e+02      36      58 ..      47      69 ..      44      87 .. 0.73
   2 ?    8.6   0.0    0.0001      0.93     131     189 ..     211     271 ..     207     287 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.042
                                   HHHHHHHHCT-EEEEEEEE--TT CS
                Polysacc_deac_2 36 elaeaaraaghevllhlPmepks 58
                                   + +++  ++ + ++l +Pm +++
  gi|116754606|ref|YP_843724.1| 47 AHVRRLYDSAQAIMLDIPMTQEE 69
                                   56677888899999999998544 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0001
                                    T-SHHHHHHHCT--EEE-SEETTS..S-SHHHHHHHHHHHHHHHHCCSEEEEEEE-SCCHH CS
                Polysacc_deac_2 131 ksvaakvakelgvpvaerdvfLDn..etdeaairkqlkklaklakkkGsaiaighprpeti 189
                                    + v+ ++a++ g+pv e  + L +  + +e  ++   +++a +a+  G++i+ g p+p+t 
  gi|116754606|ref|YP_843724.1| 211 REVVLELANRNGIPVHETRLGLFDlyTAEEVFVTGTAAEIAPVARIDGRVIGNGKPGPVTK 271
                                    568999**********9999887766555669**************************983 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2172.25
//
Query:       gi|116754607|ref|YP_843725.1|  [L=136]
Description: 6,7-dimethyl-8-ribityllumazine synthase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-33  115.4   0.0    1.8e-33  115.3   0.0    1.0  1  DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase
  ------ inclusion threshold ------
      0.081   12.2   0.7        8.9    5.6   0.1    2.5  3  Metallophos_3  Metallophosphoesterase, calcineurin superfamil


Domain annotation for each model (and alignments):
>> DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.3   0.0   2.1e-37   1.8e-33       3     139 ..       3     132 ..       1     134 [. 0.95

  Alignments for each domain:
  == domain 1  score: 115.3 bits;  conditional E-value: 2.1e-37
                                    EEEEEEESTTHHHHHHHHHHHHHHHHHCTTSSCCEEEEEESSCCCHHHHHHHHCTSTT-.SEEEEEEEEE--SSCHHHHH CS
                  DMRL_synthase   3 riaiVvarfneeitdkllegaldelkeagvaeenidvvtVPGafElplaakklaesskyldavialGvvirGetphfeyv 82 
                                    r+++Vv++fn++it ++    +++++ +g+  e ++++ VPG++++pla++kl++s +++dav+a+G+vi+Get h+e+v
  gi|116754607|ref|YP_843725.1|   3 RLGFVVSEFNRDITYQMELLGREHARFLGA--EVVQTIMVPGVYDMPLAVRKLLKS-DEIDAVVAIGCVIQGETAHDEIV 79 
                                    89***************************7..59*********************6.457******************** PP

                                    HHHHHHHHHHHHHHCTS-EEEEEEEES.SHHCCHHCCTSTCCCHHHHHHHHHHHHHHH CS
                  DMRL_synthase  83 aeavskglmrvsldtgvPvifgvltvd.teeqaleraggkagnkGeeaaeaalemanl 139
                                    a++++++lm++sl+ ++Pv+ g+  +  ++ +a++r+     +++++a+eaa+++++ 
  gi|116754607|ref|YP_843725.1|  80 AQHAARKLMDLSLEFDKPVTLGISGPRmSRPDAHKRV-----DYAKRAVEAAVKLVRR 132
                                    ***************************9999******.....89999*****999876 PP

>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0    0.0015        14      73     104 ..      17      49 ..       8      55 .. 0.78
   2 ?    5.6   0.1   0.00099       8.9      27      60 ..      53      85 ..      49      96 .. 0.81
   3 ?   -1.8   0.0      0.17   1.5e+03     151     172 ..     113     134 ..     105     135 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0015
                                    HHHHHHH.HHHHHHHTT-SEEEEE--TTS--HH CS
                  Metallophos_3  73 eiiklld.klfrelgeldvpafvvPGkrDaPle 104
                                    ++++ll  +  r lg   v++++vPG  D Pl 
  gi|116754607|ref|YP_843725.1|  17 YQMELLGrEHARFLGAEVVQTIMVPGVYDMPLA 49 
                                    566666425568899999*************86 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.00099
                                   HHHHH--SEEEEES-----HHHHHHHHHHHHTT- CS
                  Metallophos_3 27 viedkdpDllvlvGdlvkaeakadeyesaqeerr 60
                                   +++  + D++v +G ++++e+  de   aq + r
  gi|116754607|ref|YP_843725.1| 53 LLKSDEIDAVVAIGCVIQGETAHDEIV-AQHAAR 85
                                   5667789******************99.555555 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.17
                                    SSS-EEEHHHHHHHGGGGGGS- CS
                  Metallophos_3 151 efrLkYPaweveyrLkvlkelk 172
                                    + r+ Y ++ ve ++k+++ l+
  gi|116754607|ref|YP_843725.1| 113 HKRVDYAKRAVEAAVKLVRRLR 134
                                    6778888888888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 994.71
//
Query:       gi|116754608|ref|YP_843726.1|  [L=379]
Description: aspartate aminotransferase [Methanosaeta thermophila PT]
Scores for complete 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-64  218.4   0.0      2e-64  218.1   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    7.1e-09   35.4   0.1      1e-08   34.9   0.1    1.1  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    0.00011   20.9   0.0    0.00017   20.3   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
     0.0094   16.0   0.0      0.051   13.7   0.0    2.0  2  Rsbr_N           Rsbr N terminal
  ------ inclusion threshold ------
       0.12   11.6   0.0        0.2   10.9   0.0    1.4  1  Beta_elim_lyase  Beta-eliminating lyase


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.1   0.0   5.5e-68     2e-64       2     362 ..      30     372 ..      30     373 .. 0.95

  Alignments for each domain:
  == domain 1  score: 218.1 bits;  conditional E-value: 5.5e-68
                                    EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHH CS
                  Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagali 81 
                                    d+i+Lg++e+++d    t+ ++  a+ +   + ++ ++y+p+ g pel+ a+ak l+++++++  +e  v+v++Ga+ + 
  gi|116754608|ref|YP_843726.1|  30 DIIDLGVGEPDFD----TPRHICDAACR--YMLEGKTRYTPTNGIPELRRAIAKKLREENRIPAVPE-DVIVTPGAKMAV 102
                                    689**********....*********99..9999999******************************.************ PP

                                    HHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT CS
                  Aminotran_1_2  82 ealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPt 161
                                     a+i++l l+ gde ++  p++ sy+++++ +gg  v   ++          +l ea++e      +tk ilv+sp NPt
  gi|116754608|ref|YP_843726.1| 103 FAAIQAL-LDEGDEMVLIGPSWVSYEPCIKFAGGRPVWADVD----QDFMPMDLPEAITE------RTKAILVNSPCNPT 171
                                    *******.***************************9999944....56667788999999......9************* PP

                                    --B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHH CS
                  Aminotran_1_2 162 GtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvs 241
                                    G+v+ +e  +++ d+a  + +++++De+Y++  +g ++++++ ++ + ++ +++ +++sK+++++G+R+Gy++g  ++++
  gi|116754608|ref|YP_843726.1| 172 GAVFGHEVMKEIRDIAIDHDIYVVSDEVYEKIIYG-HEHISIASLPDMADRTITINGFSKSYAMTGWRLGYLTGPRDMLK 250
                                    ***********************************.5667755555555559**************************** PP

                                    HHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEEEEETHH.CHH CS
                  Aminotran_1_2 242 qlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmflltdlsae.tak 318
                                    ++ +l ++  s  ++ +q+a  aal+ +++   ++  m +++ +rr+ l+d+L++lg+ +  + ++++++ d+s++   +
  gi|116754608|ref|YP_843726.1| 251 WISRLLSHSVShpTTFVQWAGIAALEGPQD---DVRRMTEEFRARRDILVDGLRSLGIRCALPGGAFYMFPDVSHLgGGD 327
                                    *****************************7...9******************************************8788 PP

                                    HHHHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHHH CS
                  Aminotran_1_2 319 elskkLleevgvyvtpgtsftv..pgrlRitvAglteeeleelvea 362
                                     +++ Ll+e +++vtpg+ f+   +  +Ri++ ++++e ++e++e+
  gi|116754608|ref|YP_843726.1| 328 VFAERLLKEAKIAVTPGSAFGPggEDYIRISY-ATSRERIKEALER 372
                                    88899***************************.***********98 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 !   34.9   0.1   2.9e-12     1e-08      46     144 ..      97     197 ..      86     199 .. 0.83

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 2.9e-12
                                    SHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEE...EB-GGG CS
                DegT_DnrJ_EryC1  46 sGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaaieaaitertkaIl...pVhlyG 122
                                     +  A+  a++al +++gde +    ++v+   ++  +g +pv +Dvd+d +   p ++ +aitertkaIl   p +  G
  gi|116754608|ref|YP_843726.1|  97 GAKMAVFAAIQAL-LDEGDEMVLIGPSWVSYEPCIKFAGGRPVWADVDQDFM---PMDLPEAITERTKAILvnsPCNPTG 172
                                    5556777778875.4568******************************7765...556789*********9444578889 PP

                                    B--...-HHHHHHHHHHCT-EEEEE CS
                DegT_DnrJ_EryC1 123 qva...dmdalkaiaakhglkvieD 144
                                    +v+    m+++++ia +h+++v++D
  gi|116754608|ref|YP_843726.1| 173 AVFgheVMKEIRDIAIDHDIYVVSD 197
                                    9986556****************99 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 !   20.3   0.0   4.7e-08   0.00017      71     175 ..      93     199 ..      82     203 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 4.7e-08
                                    EEESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEESTTSHHHHHHHCCTTEEEEEEESS-TTT CS
                Cys_Met_Meta_PP  71 lavssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdtsdleelekaikentklvylEtptnpl 150
                                    ++++    A++aai+all +Gde+v+    + + +  +k    +  + +++ +   + +l +ai+e+tk++++ +p np+
  gi|116754608|ref|YP_843726.1|  93 IVTPGAKMAVFAAIQALLDEGDEMVLIGPSWVSYEPCIKFAGGR-PVWADVDQDFMPMDLPEAITERTKAILVNSPCNPT 171
                                    56666678999**************9998887655555544444.46666666667789999****************** PP

                                    T----...HHHHHHHHHHTT-EEEEEGT CS
                Cys_Met_Meta_PP 151 lkvvD...iekiaklakkagvlvvvDnt 175
                                      v     +++i ++a ++++ vv D +
  gi|116754608|ref|YP_843726.1| 172 GAVFGhevMKEIRDIAIDHDIYVVSDEV 199
                                    9997533367788888888899888865 PP

>> Rsbr_N  Rsbr N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       0.4   1.4e+03      77      95 ..      65      83 ..      45      92 .. 0.87
   2 !   13.7   0.0   1.4e-05     0.051      11      78 ..     178     244 ..     173     265 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.4
                                   HHHHHHHHHHHHHHHHH.. CS
                         Rsbr_N 77 tkgLqefrkvvlellseed 95
                                   t+g+ e+r+++ ++l+ee+
  gi|116754608|ref|YP_843726.1| 65 TNGIPELRRAIAKKLREEN 83
                                   899************9986 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1.4e-05
                                    HHHHHHHHHHTTSSS-.--HHHHHHHHHHHHHHHHH-SS.-SSTTHHHHHHHHHHHHHTT--HHHHHH CS
                         Rsbr_N  11 ewlkelkelrkeeslqtisdevyektskefvdlilssveegneeleekleefaerlvqlGwpLkyltk 78 
                                    e +ke+++++ ++++ ++sdevyek+   + ++ ++s+  +  + + +++ f++    +Gw L ylt 
  gi|116754608|ref|YP_843726.1| 178 EVMKEIRDIAIDHDIYVVSDEVYEKIIYGHEHISIASLP-DMADRTITINGFSKSYAMTGWRLGYLTG 244
                                    67999*********************************9.66666799******************94 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   5.7e-05       0.2      93     167 ..     132     197 ..      46     199 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.7e-05
                                    CC--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEE CS
                Beta_elim_lyase  93 lagvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlD 167
                                    +ag +++ ++ ++  ++ + +l +ai+e      ++k+i++   +n   G v   e ++e+++ia +++i ++ D
  gi|116754608|ref|YP_843726.1| 132 FAGGRPVWADVDQ--DFMPMDLPEAITE------RTKAILVNSPCNP-TGAVFGHEVMKEIRDIAIDHDIYVVSD 197
                                    5566566666666..8888888888888......699*********5.9***********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); 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:                         5  (0.000278878); expected 0.2 (1e-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: 2606.16
//
Query:       gi|116754609|ref|YP_843727.1|  [L=398]
Description: exodeoxyribonuclease VII, large subunit [Methanosaeta thermophila PT]
Scores for complete 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-76  256.9   0.0    3.5e-68  230.4   0.2    2.1  2  Exonuc_VII_L     Exonuclease VII, large subunit
    1.3e-26   92.6   0.1    2.3e-26   91.8   0.1    1.4  1  tRNA_anti_2      OB-fold nucleic acid binding domain
    1.5e-08   34.5   0.0    2.5e-08   33.8   0.0    1.4  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
  ------ inclusion threshold ------
      0.062   13.6   0.0       0.11   12.7   0.0    1.3  1  RecJ_OB          RecJ OB domain


Domain annotation for each model (and alignments):
>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  230.4   0.2   7.9e-72   3.5e-68       1     214 [.     124     335 ..     124     336 .. 0.94
   2 !   26.9   0.0   7.2e-10   3.2e-06     241     301 ..     327     386 ..     321     389 .. 0.91

  Alignments for each domain:
  == domain 1  score: 230.4 bits;  conditional E-value: 7.9e-72
                   Exonuc_VII_L   1 lfdeerkkplpklpkrigvvtsptgaairDilrtlkrrgplveillfpalvQGeeaaaeiikalekanalkeaDvliiaR 80 
                                    lf++erk+plp++p+rig+vts  gaa+rD++r l r+    +i+l pa+vQG+ aa+++i+al+++    +aDv+i++R
  gi|116754609|ref|YP_843727.1| 124 LFSPERKRPLPRYPERIGIVTSMDGAALRDVIRSLGRYPA--RIILSPATVQGDAAAQSMISALRALR--GRADVIILCR 199
                                    79********************************998766..**********************8876..667******* PP

                   Exonuc_VII_L  81 GGGSleDLwaFndeelaraiaaskiPvisavGHEtDttiaDfvAdlrapTPtaaAelvvpdkaeleeqleelerrlekai 160
                                    GGGS eDL++Fnd +laraia+s  PvisavGHE D+t+aD+vAd ra+TPtaaA+l+vpd +e+e+ l+++e++++ ai
  gi|116754609|ref|YP_843727.1| 200 GGGSAEDLSPFNDVHLARAIAESDAPVISAVGHEVDVTVADLVADARASTPTAAAKLAVPDVREIEQLLRNMEDQMTWAI 279
                                    ******************************************************************************** PP

                   Exonuc_VII_L 161 krlleekkqrleklasrl..kspeellerkrqrldeleerleralkkqlkkkrerl 214
                                    +++le+ ++rl+ l++ +  ++  ++le ++ rl+++++rl  a ++ ++++++rl
  gi|116754609|ref|YP_843727.1| 280 DSHLERIRSRLDYLSRGIeaRKMYAILEMRKLRLRDISRRLLDAERSIVDSRARRL 335
                                    ***************9996448888****************997777777666665 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 7.2e-10
                   Exonuc_VII_L 241 lleekkerleeleeklealsplkvLkrGyaivrkedgkvvtsakdlkkgdeleirladgev 301
                                    +++++ +rle + ++l+++spl+vL+rGy++v   +  vv +a dl+ g+e+++ ++dge+
  gi|116754609|ref|YP_843727.1| 327 IVDSRARRLEIARARLDSASPLAVLSRGYTMVVG-SAGVVCHAVDLAVGEEIRLVFSDGEA 386
                                    46788999*************************8.688*********************97 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 !   91.8   0.1     5e-30   2.3e-26       1      94 [.       5      99 ..       5     100 .. 0.96

  Alignments for each domain:
  == domain 1  score: 91.8 bits;  conditional E-value: 5e-30
                    tRNA_anti_2  1 lsVseltraikell..eaelkkavwvrGeisnlkrkasghvYftLkDekakisavifrsraaklkftledGmkVlvkgrlsv 80
                                   +sVsel+++i+e++  + +l++ vw  Ge+sn+ +++sgh YftLkD++a+is+v+f+++a++l+f l++Gm+V v g + +
  gi|116754609|ref|YP_843727.1|  5 YSVSELCTRIQERItgDVRLHD-VWACGELSNVVNHSSGHRYFTLKDSEAQISCVMFKRHAEELDFVLRNGMNVRVFGDVGF 85
                                   79************88888866.**********8888********************************************* PP

                    tRNA_anti_2 81 YeprGsyqlivedi 94
                                   Y+ rG++ql+v++i
  gi|116754609|ref|YP_843727.1| 86 YKGRGNVQLQVRSI 99
                                   ***********998 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 !   33.8   0.0   5.7e-12   2.5e-08       1      74 [.      27     100 ..      27     102 .. 0.93

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 5.7e-12
                                    EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEECTTS.SEEEEEEEEE CS
                tRNA_anti-codon   1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrrpgg.elelkveeie 74 
                                    V+ +G+++++   +++++ +++l+D +++i +v+f+  a++l   l++G+ vrv+G v++++g+  ++l+v +i+
  gi|116754609|ref|YP_843727.1|  27 VWACGELSNVV-NHSSGHRYFTLKDSEAQISCVMFKRHAEELDFVLRNGMNVRVFGDVGFYKGRgNVQLQVRSIS 100
                                    77899999996.888**********************************************77778****99986 PP

>> RecJ_OB  RecJ OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.5e-05      0.11      44     107 ..      35      97 ..      18      98 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.5e-05
                        RecJ_OB  44 rivgkeknhlklkledesgksleaiaFnlaeklee..lekgdkvdiaytleinefngretlqlrik 107
                                    ++v + + h  ++l+d +  ++++++F+   +  +  l++g +v++ + +    ++gr ++ql+++
  gi|116754609|ref|YP_843727.1|  35 NVVNHSSGHRYFTLKDSE-AQISCVMFKRHAEELDfvLRNGMNVRVFGDVGF--YKGRGNVQLQVR 97 
                                    56778889999*****87.*********888887778888899999998887..888888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2710.53
//
Query:       gi|116754610|ref|YP_843728.1|  [L=98]
Description: hypothetical protein Mthe_1310 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); 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: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 759.60
//
Query:       gi|116754611|ref|YP_843729.1|  [L=142]
Description: hypothetical protein Mthe_1311 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 1152.83
//
Query:       gi|116754612|ref|YP_843730.1|  [L=268]
Description: fructose-bisphosphate aldolase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-63  214.8   0.0    1.5e-63  214.6   0.0    1.0  1  DeoC        DeoC/LacD family aldolase
  ------ inclusion threshold ------
      0.049   12.9   0.0        5.3    6.3   0.0    2.4  2  TMP-TENI    Thiamine monophosphate synthase
      0.072   12.5   0.4         19    4.6   0.0    3.1  4  PEP_mutase  Phosphoenolpyruvate phosphomutase
      0.091   11.9   0.1        9.1    5.4   0.0    2.2  2  DUF561      Protein of unknown function (DUF561)
       0.11   12.8   0.0        5.2    7.4   0.0    2.6  3  PucR        Purine catabolism regulatory protein-like family


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 !  214.6   0.0   4.2e-67   1.5e-63       2     235 .]      20     235 ..      19     235 .. 0.99

  Alignments for each domain:
  == domain 1  score: 214.6 bits;  conditional E-value: 4.2e-67
                                    EEEEECCSHHHHHHHHCTSSHHHHHHHHHHHHHHGGGSSEEEEETTTHHHHHHCSCTTSEEEEETECSSCCTTSTTEEEE CS
                           DeoC   2 vilavDqrvankddtasaqneqledlkalvkealtpgasavlldpgviasaskeyakdiallvkldkgtyllkskqrdvd 81 
                                    vi+++D++v +++++++        +k++v++++++ga+a ++++g +  ++++y++d +l+++l+++t l ++++ +v+
  gi|116754612|ref|YP_843730.1|  20 VIVPMDHGVTLGPIKGI------RSMKNTVDAVASSGADAAVVHKGAAIFGHRGYGRDLGLIIHLSASTSLGPDPNNKVL 93 
                                    89***************......8******************************************************** PP

                                    TTCHHHHHHHTT-SEEEEEEEEHTTTTCHHHHHHHHHHHHHHHHHHHTEEEEEEEEE-CTTBSSTTCHHHHHHHHHHHHT CS
                           DeoC  82 evasveeakalGAdavkvvvyyradgseeeqqklaeikrvkeacheeglplilelylrdeaikdekvdpdlvaeAarvsa 161
                                     va+veea++lGAd v+++v++   g+e+e+q+l  ++ ++  c+e+g+pl++++y+r+ +i++e+ +++ v++Aarv+a
  gi|116754612|ref|YP_843730.1|  94 -VATVEEALKLGADGVSIHVNI---GAEDEAQMLSLLGSISRSCQEWGMPLMAMMYPRGRKISNEY-AEEFVGHAARVGA 168
                                    .*********************...*****************************************.************* PP

                                    CCT-SEEEE--SSCC.B.HHHHHHHHHHHHHCHSSTEEEEETTS...SHHHHHHHHHHHHHHHTHCEEEESHHHHTT CS
                           DeoC 162 elGaDiiKvevpkevvnateedaevfkdvikaapvpgvvlsGGv...seedfletvedAvkeagasGvlsGRaifqk 235
                                    elGaDiiK++++        +d ++f++v++++pvp +v++GG+   se d+l++v+dAv +agasGv++GR+ifq+
  gi|116754612|ref|YP_843730.1| 169 ELGADIIKTSYT--------GDPDSFSRVVDGCPVP-LVVAGGPkvsSEMDLLRMVRDAV-DAGASGVAIGRNIFQH 235
                                    ************........****************.***********************.**************97 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0    0.0015       5.3      11      61 ..      89     141 ..      81     143 .. 0.86
   2 ?    4.2   0.0    0.0068        25     140     181 .]     184     232 ..     166     232 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0015
                       TMP-TENI  11 kneellevveealkggvtlvqlRek..eldarellelaeklaalcrkygvpli 61 
                                    +n+ l+++veealk g++ v +       d++++l l   + + c++ g+pl+
  gi|116754612|ref|YP_843730.1|  89 NNKVLVATVEEALKLGADGVSIHVNigAEDEAQMLSLLGSISRSCQEWGMPLM 141
                                    577899**********99887777766889*****************999986 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0068
                       TMP-TENI 140 eglkelaealeiPvvaiGGitlenvaevl.......eagadgvavvsai 181
                                    + ++++++ + +P+v+ GG + ++  ++l       +aga+gva+ + i
  gi|116754612|ref|YP_843730.1| 184 DSFSRVVDGCPVPLVVAGGPKVSSEMDLLrmvrdavDAGASGVAIGRNI 232
                                    667888999999*******998776666657778889******997765 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.51   1.8e+03      30      43 ..      43      56 ..      12      61 .. 0.69
   2 ?    4.6   0.0    0.0054        19     165     200 ..     100     145 ..      94     160 .. 0.64
   3 ?    3.7   0.0    0.0099        35     166     203 ..     168     205 ..     162     235 .. 0.59
   4 ?    1.0   0.0     0.069   2.5e+02      87     105 ..     211     229 ..     205     251 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.51
                     PEP_mutase 30 fkalatsSlavaas 43
                                   ++a+a+s++  a +
  gi|116754612|ref|YP_843730.1| 43 VDAVASSGADAAVV 56
                                   44555555444443 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0054
                     PEP_mutase 165 YaeAGAdgvfvpgl...qkdaeiaelvaavd.......vplnvvpl 200
                                     ++ GAdgv ++     +++a++ +l+  ++       +pl++++ 
  gi|116754612|ref|YP_843730.1| 100 ALKLGADGVSIHVNigaEDEAQMLSLLGSISrscqewgMPLMAMMY 145
                                    6789*****9998777744444555544443244444499999983 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.0099
                     PEP_mutase 166 aeAGAdgvfvpglqkdaeiaelvaavdvplnvvplkgt 203
                                    ae GAd +      ++++  ++v+ ++vpl+v  +++ 
  gi|116754612|ref|YP_843730.1| 168 AELGADIIKTSYTGDPDSFSRVVDGCPVPLVVAGGPKV 205
                                    56777777777777777777777777777777664332 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.069
                     PEP_mutase  87 vaetvrrliaaGvvgvniE 105
                                    + + vr +++aG++gv i 
  gi|116754612|ref|YP_843730.1| 211 LLRMVRDAVDAGASGVAIG 229
                                    5578999999999999885 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0    0.0046        17     198     236 ..      95     132 ..      90     136 .. 0.84
   2 ?    5.4   0.0    0.0025       9.1     203     226 ..     218     241 ..     172     251 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0046
                         DUF561 198 vtvplalslgasGiGigsavsklndeeemvallseikka 236
                                     tv+ al+lga G+ i  ++   +de +m +ll  i+ +
  gi|116754612|ref|YP_843730.1|  95 ATVEEALKLGADGVSIHVNIGA-EDEAQMLSLLGSISRS 132
                                    58999**************975.7888999998888765 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0025
                         DUF561 203 alslgasGiGigsavsklndeeem 226
                                    a+ +gasG+ ig+++ + ++   +
  gi|116754612|ref|YP_843730.1| 218 AVDAGASGVAIGRNIFQHENPSII 241
                                    7899***********998876554 PP

>> PucR  Purine catabolism regulatory protein-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0         1   3.7e+03      58      79 ..      38      59 ..      30      65 .. 0.79
   2 ?    2.2   0.0     0.057   2.1e+02      55     100 ..      89     143 ..      76     151 .. 0.77
   3 ?    7.4   0.0    0.0015       5.2      44      79 ..     197     231 ..     165     248 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1
                           PucR 58 alaelvrelaeagvaaLviklg 79
                                   +++++v+++a++g+ a v+  g
  gi|116754612|ref|YP_843730.1| 38 SMKNTVDAVASSGADAAVVHKG 59
                                   5678899999999988888765 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.057
                           PucR  55 dpealaelvrelaeagvaaLviklg....r.....eipeelieaadelglPliel 100
                                    + + l ++v+e  + g+ ++ i ++    +     ++  ++ + ++e+g+Pl+++
  gi|116754612|ref|YP_843730.1|  89 NNKVLVATVEEALKLGADGVSIHVNigaeDeaqmlSLLGSISRSCQEWGMPLMAM 143
                                    55667889999999999999998876665145667778999999********998 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0015
                           PucR  44 LllttglalkddpealaelvrelaeagvaaLviklg 79 
                                    L++  g  ++ ++ +l ++vr+ ++ag+++++i+ +
  gi|116754612|ref|YP_843730.1| 197 LVVAGGPKVS-SEMDLLRMVRDAVDAGASGVAIGRN 231
                                    6666666676.7889******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); 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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2169.72
//
Query:       gi|116754613|ref|YP_843731.1|  [L=213]
Description: CODH nickel-insertion accessory protein [Methanosaeta thermophila PT]
Scores for complete 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-05   23.8   0.0    3.9e-05   23.7   0.0    1.2  1  CbiA      CobQ/CobB/MinD/ParA nucleotide binding domain
     0.0009   19.1   0.1     0.0014   18.5   0.1    1.3  1  AAA_26    AAA domain
     0.0042   16.6   0.0       0.13   11.7   0.0    2.0  1  ParA      NUBPL iron-transfer P-loop NTPase


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 !   23.7   0.0   6.6e-09   3.9e-05      27     127 ..      89     188 ..       6     189 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 6.6e-09
                                    T--EEEEEEEESSCCCCHHTTEB-HHHH.................................CCHCCCHHHHHHCHCHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................xxxxxxxxxxxxxxxxxxx RF
                           CbiA  27 glrVllvDaDpqannlaileglendiep.................................dlkrllellealgkkkall 73 
                                    +++V+                                                        +++r+++l e++g++    
  gi|116754613|ref|YP_843731.1|  89 EKDVV----------------------IldmeagiehlgrgtargvdamivvvepglrsieTVERIKRLGENIGIT---- 142
                                    34444......................0444444444444444455557787888777777888888888888877.... PP

                                    ..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS.- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                           CbiA  74 lkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeaparge.p 127
                                       +  v+n+ d +      ke lee     g+pvlg ip+d +++ea+ +g+ p
  gi|116754613|ref|YP_843731.1| 143 --NLLAVINKTDDP---GIVKEKLEEM----GIPVLGTIPFDRNLIEADLSGRaP 188
                                    ..699*******99...7788999986....*******************99866 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   2.3e-07    0.0014     131     196 ..     115     180 ..     109     182 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.3e-07
                         AAA_26 131 vilVargglgtinqllltiealr.qknvrvlGvilNkvrnpenvetlekksgipvlGvvPylpdlea 196
                                    +i+V+ +gl++i+  + +i+ l  + ++  l  ++Nk+ +p  v++  +  gipvlG++P +++l++
  gi|116754613|ref|YP_843731.1| 115 MIVVVEPGLRSIET-VERIKRLGeNIGITNLLAVINKTDDPGIVKEKLEEMGIPVLGTIPFDRNLIE 180
                                    6899999***9985.56666665156998888999******9777777777************9986 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   2.1e-05      0.13      97     241 ..      75     202 ..      69     207 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.1e-05
                           ParA  97 skaikqllkdvewgelDyLiiDlPPGtgDeqltvaqklplagaviVttpqevaladvkkaiemfkkvkvkvlGvveNmsg 176
                                    s+++k ll++v  +e D++i+D+  G   e+l       ++++++V  p   +++ v++  ++ +++ ++      N+  
  gi|116754613|ref|YP_843731.1|  75 SAFLKALLRHVISKEKDVVILDMEAGI--EHLGRGTARGVDAMIVVVEPGLRSIETVERIKRLGENIGIT------NLLA 146
                                    567899999999999999999997655..78888888888999999999999999999988888776543......3333 PP

                           ParA 177 fvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdegkplvlkepeseaakaleei 241
                                    ++ ++ +        g +++  ee+g+p+lg+ip+d ++ ea  +g+  v      +a +a+++i
  gi|116754613|ref|YP_843731.1| 147 VINKT-D------DPGIVKEKLEEMGIPVLGTIPFDRNLIEADLSGRAPVDV--GGPAVEAIKSI 202
                                    33322.2......246678889999999999999999999988888765533..35555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1580.47
//
Query:       gi|116754614|ref|YP_843732.1|  [L=688]
Description: ribonucleoside-diphosphate reductase, adenosylcobalamin-dependent [Methanosaeta thermophila PT]
Scores for 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-154  512.9   0.0   6.1e-152  506.8   0.0    2.2  1  Ribonuc_red_lgC  Ribonucleotide reductase, barrel domain
    2.3e-25   88.4   0.0    6.1e-25   87.0   0.0    1.8  1  Ribonuc_red_lgN  Ribonucleotide reductase, all-alpha domain
    2.7e-24   85.5   0.9    8.5e-24   83.9   0.9    1.9  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 !  506.8   0.0    1e-155  6.1e-152       1     524 []     201     662 ..     201     662 .. 0.97

  Alignments for each domain:
  == domain 1  score: 506.8 bits;  conditional E-value: 1e-155
                                    EEE.....BSS-EEEE-X..............XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                Ribonuc_red_lgC   1 ssCfvlsvedslesIletvkeaallskaggGvGlnlsklRakgslvkgtegaasGpvsfmklidavadvvkqgGkRrGAa 80 
                                    s+Cfv+ veds+ +I++++k +al++++ggG+G+++s+lR+kg++v++t+g asGpvsfm+++da +dv+kqgG+RrGA+
  gi|116754614|ref|YP_843732.1| 201 SACFVVPVEDSIAGIFDALKYMALIHQSGGGTGFSFSRLRPKGDVVRSTGGIASGPVSFMRIFDAATDVIKQGGRRRGAN 280
                                    79****************************************************************************** PP

                                    XXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.................. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                Ribonuc_red_lgC  81 mvylevwHpDiekfidaKekntgeeenrlsnlnisvgvpdlFmeavkedkdwtLfsPrtvvkleklygeefeeeyeelee 160
                                    m++l+v+HpDi +fi +K       +  ++n+nisv ++++Fm++ ++d++++L++Prt +                   
  gi|116754614|ref|YP_843732.1| 281 MGILRVDHPDITEFIACK-D-----RGGMDNFNISVAITEEFMRQCERDGSVELINPRTGE------------------- 335
                                    ******************.4.....568******************************322................... PP

                                    .......XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                Ribonuc_red_lgC 161 kakikkkevkakeLfeeiaesawetgePgvlfkDtiNrrnvlekakggkIratNlCgEiplleyesvavCnLasinLakf 240
                                        ++ e++a++L+  +a+ aw+ g+Pgv+f+D+iN+ +++     g I+atN+CgE+pll+ es   CnL+s+nL+++
  gi|116754614|ref|YP_843732.1| 336 ----ATGEMSARDLMVMMATYAWRRGDPGVVFIDRINALHPV----PGIIEATNPCGEQPLLPFES---CNLGSVNLSRM 404
                                    ....2349**********************************....48******************...*********** PP

                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                Ribonuc_red_lgC 241 vkkdeegkkefdwdelkkviqlvvraLdnvidvnkyplpeiekntkktRriGlGvmgladalaklgipydseealkfark 320
                                    v     ++ e++wd+l+++++l+vr+Ld+vid+n++pl++ie++t +tR+iGlGvmg+a++l++lg+ y s++al++a++
  gi|116754614|ref|YP_843732.1| 405 V-----ERGEISWDRLEETVRLAVRFLDDVIDANRFPLKQIEDATLRTRKIGLGVMGFAEMLIQLGVSYASQDALRIAEE 479
                                    *.....578*********************************************************************** PP

                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX......XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                Ribonuc_red_lgC 321 itelltyyaykaSvelAkergpfplfekskyskgilpvdefeekekedweeLreeikkyGlrnamvtalaPTgsiSliag 400
                                    ++ ++t +a ++S+ l +erg+fplfe+s  +k                +          +rna+vt++aPTg+iS+iag
  gi|116754614|ref|YP_843732.1| 480 LMAFITKTAREESCALGRERGSFPLFEESSLKKW---------------DA---------MRNATVTTIAPTGTISIIAG 535
                                    ****************************998875...............44.........9******************* PP

                                    XXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                    xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                Ribonuc_red_lgC 401 tssgiePifalvykksvtvge.flevnpvfeeeLkklglwseellkki..lesvqgleeipeeikrvfktaldidqedhi 477
                                    tssgieP+fa  +++ v +g  ++e  p fe+   ++g+++ +l++++   +s+q+++ ip++ik++f taldi++e+h+
  gi|116754614|ref|YP_843732.1| 536 TSSGIEPLFAVSFVRHVLEGArLIESSPLFERMASERGIMTPALRAEVarRGSIQEIPGIPDDIKELFLTALDISPEQHV 615
                                    *******************65499************************77777*************************** PP

                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                Ribonuc_red_lgC 478 kaqaaiqkwidqsiSktinlpneatvedvkelyllAwklGlKgvtyY 524
                                    ++qaa qk+ d+++Skt+nlp++a+v+dv ++y lA++lG+Kg+t+Y
  gi|116754614|ref|YP_843732.1| 616 RIQAAFQKHTDNAVSKTVNLPEKASVSDVIKVYRLAYELGCKGITVY 662
                                    **********************************************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 !   87.0   0.0     1e-28   6.1e-25       2      83 .]     119     198 ..     118     198 .. 0.92

  Alignments for each domain:
  == domain 1  score: 87.0 bits;  conditional E-value: 1e-28
                Ribonuc_red_lgN   2 kltynalkvledrYllkdengeivEspqqmfmRvAlalaiaealydkleedkdlaeefydlmssqkflpasPtlmnaGte 81 
                                    kl++na++vl++rYl++de g++vE+p +mf+RvA a+   e+ y  + ++ d  ++f  +m s+ flp+sPtlmnaG +
  gi|116754614|ref|YP_843732.1| 119 KLSVNAIEVLKKRYLKRDEFGNVVETPGEMFERVASAVSAVERRY--EGDADDARKKFLSMMRSLSFLPNSPTLMNAGLP 196
                                    789***************************************987..4566666779*********************99 PP

                Ribonuc_red_lgN  82 lg 83 
                                    lg
  gi|116754614|ref|YP_843732.1| 197 LG 198
                                    86 PP

>> ATP-cone  ATP cone domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.9   0.9   1.4e-27   8.5e-24       2      86 .]      15     104 ..      14     104 .. 0.97

  Alignments for each domain:
  == domain 1  score: 83.9 bits;  conditional E-value: 1.4e-27
                                    EEE-TTS-EEE--HHHHHHHHHHHHHH....-HHHHHHHHHHHHHHHHHHHIIT.-BHHHHHHHHHHHHHHSS-HHHHHH CS
                       ATP-cone   2 kViKRdGtvepfdvekIkraiekAceg....seeeideiaeeveaevrkrlrdg.isteeIqdlvektliehpdyavaaa 76 
                                    +++KRdG++++fd+++I rai+kA+++    +e++  e+a +v++ v +r+rd+ +s+e++qd+ve++li++++ +va+a
  gi|116754614|ref|YP_843732.1|  15 RIRKRDGRIVDFDPSRISRAISKAFNAlgivDEKTPVELAGRVVDVVDERFRDEiPSVEDVQDIVEEVLIDAGYAQVAKA 94 
                                    69****************************99999*******************99************************ PP

                                    HHHHHHHHHH CS
                       ATP-cone  77 yilyrnlrke 86 
                                    yilyr+ r+e
  gi|116754614|ref|YP_843732.1|  95 YILYRQRRSE 104
                                    ******9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (688 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.41
# Mc/sec: 5041.36
//
Query:       gi|116754615|ref|YP_843733.1|  [L=588]
Description: phosphotransferase domain-containing protein [Methanosaeta thermophila PT]
Scores for 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-26   90.0   4.0    5.2e-23   81.2   1.0    3.6  3  HHH_8            Helix-hairpin-helix domain
    9.4e-21   73.8   0.1    2.8e-20   72.2   0.1    1.9  2  DNA_pol_B_thumb  DNA polymerase beta thumb
    7.1e-15   55.4   0.8    1.3e-09   38.6   0.1    3.0  2  HHH_5            Helix-hairpin-helix domain
    1.7e-09   38.2   0.0    4.3e-09   36.9   0.0    1.8  1  PHP              PHP domain
    2.2e-09   37.5   0.3      9e-09   35.5   0.1    2.1  2  DNA_pol_B_palm   DNA polymerase beta palm
    3.9e-07   29.6   0.9      0.044   13.7   0.0    3.8  3  HHH              Helix-hairpin-helix motif
    7.3e-06   26.2   1.3       0.08   13.2   0.0    4.4  4  HHH_3            Helix-hairpin-helix motif
     0.0013   18.8   0.0     0.0084   16.2   0.0    2.4  2  DUF1992          Domain of unknown function (DUF1992)
      0.002   18.3   0.1        2.4    8.5   0.0    2.8  2  Cdd1             Pathogenicity locus
     0.0022   18.1   0.0       0.14   12.3   0.0    2.7  2  HHH_2            Helix-hairpin-helix motif
     0.0053   17.0   0.6        2.8    8.5   0.0    3.6  3  IMS_HHH          IMS family HHH motif
     0.0068   16.2   0.0       0.26   11.1   0.0    2.7  2  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
  ------ inclusion threshold ------
      0.011   16.0   0.0      0.029   14.7   0.0    1.8  1  NTP_transf_2     Nucleotidyltransferase domain
      0.016   14.7   0.0      0.032   13.7   0.0    1.5  1  RNase_P_p30      RNase P subunit p30
      0.016   15.3   0.8        5.2    7.2   0.0    3.1  3  DUF3701          Phage integrase protein
      0.024   14.6   0.0          2    8.4   0.0    2.9  2  HRDC             HRDC domain
       0.13   11.7   0.0       0.37   10.2   0.0    1.7  2  BBS1             Ciliary BBSome complex subunit 1


Domain annotation for each model (and alignments):
>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.2   1.0     5e-26   5.2e-23       1      68 []      20      89 ..      20      89 .. 0.97
   2 !    6.7   0.0    0.0091       9.6      35      65 ..      93     126 ..      91     128 .. 0.83
   3 ?   -0.2   0.0       1.3   1.3e+03      37      59 ..     135     155 ..     130     164 .. 0.61

  Alignments for each domain:
  == domain 1  score: 81.2 bits;  conditional E-value: 5e-26
                                   HHHHHHHHHHHHHHHHHCT--CCCHHHHHHHHCCCCC-SS-HHHH..TTHCTTSTT--HHHHHHHHHHHH CS
                          HHH_8  1 NkeiadaLeeladllelkgedpfrvraYrrAaraiealpeeitsl..eeeltklpgiGkkiaakieeile 68
                                   Nkeia++L e+ +lle++ge+ f+v aY+rAaraie+l+e+i+++  ++el ++pg+Gk+ia+ki e+l+
  gi|116754615|ref|YP_843733.1| 20 NKEIAAILYEMGELLEIRGENRFKVIAYSRAARAIESLKEDIEDVwrRGELDRIPGVGKAIAEKISEYLT 89
                                   9*********************************************6669******************95 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0091
                                    CCC-SS-HHHH.TT..HCTTSTT--HHHHHHHHH CS
                          HHH_8  35 iealpeeitsl.ee..eltklpgiGkkiaakiee 65 
                                    i+a+++ + s  ++  el +l+g+G+k+ a ++e
  gi|116754615|ref|YP_843733.1|  93 IKAYDDLVSSTpKGmkELLQLQGVGPKTVALLHE 126
                                    88888888888755777***********998877 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 1.3
                                    C-SS-HHHHTT.HCTTSTT--HHH CS
                          HHH_8  37 alpeeitslee.eltklpgiGkki 59 
                                    +l+ +    ++ ++++lpg+G+  
  gi|116754615|ref|YP_843733.1| 135 ELEAAA---RQhRIRRLPGMGPTK 155
                                    333333...334699******754 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 !   72.2   0.1   2.7e-23   2.8e-20       2      70 .]     271     332 ..     270     332 .. 0.98
   2 ?   -2.9   0.0       7.4   7.8e+03      44      61 ..     571     588 .]     552     588 .] 0.66

  Alignments for each domain:
  == domain 1  score: 72.2 bits;  conditional E-value: 2.7e-23
                                    HHHHHS-HHHHHHHHHHHHCTTEEEETTEEE.......ETCCCEEEC-SSHHHHHHHCTS----GGGTT CS
                DNA_pol_B_thumb   2 llyfTGsktFnrdlRrlakkkglkLnssglrdekgkaeddddgelvevetErdvfelLglpyipPeeRe 70 
                                    l+yfTGsk++n++lR +a ++g++L+++ l        + d+ge + +++E+dv+++Lg++yipPe+Re
  gi|116754615|ref|YP_843733.1| 271 LQYFTGSKEHNVKLRGIALQRGYSLSEYSLK-------RLDTGEELFFDREEDVYKALGMQYIPPELRE 332
                                    89*****************************.......9*****************************7 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 7.4
                                    CEEEC-SSHHHHHHHCTS CS
                DNA_pol_B_thumb  44 gelvevetErdvfelLgl 61 
                                     + +++ + +d++++Lg+
  gi|116754615|ref|YP_843733.1| 571 SNVINTLSAKDLMRHLGI 588
                                    445666777899999986 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.1   4.7e-05      0.05       3      53 ..      32      86 ..      31     105 .. 0.72
   2 !   38.6   0.1   1.2e-12   1.3e-09       2      55 ..     108     163 ..     107     165 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.7e-05
                                   HHHTSTT--HHHHHHHHTTT--SHHHHHHS.....-HHHHHTSTTS-HHHHHHHHH CS
                          HHH_5  3 eLlsvsGiGpktAlallsaGiesvedlaaa.....dveeLakipGiGkktAeriil 53
                                   eLl++ G ++  ++a  +a  + +e l++       + eL +ipG+Gk  Ae+i +
  gi|116754615|ref|YP_843733.1| 32 ELLEIRGENRFKVIAYSRA-ARAIESLKEDiedvwRRGELDRIPGVGKAIAEKISE 86
                                   5677777777777777777.566666555422112356799999999999999976 PP

  == domain 2  score: 38.6 bits;  conditional E-value: 1.2e-12
                                    HHHHTSTT--HHHHHHHHTT.T--SHHHHHHS-H.HHHHTSTTS-HHHHHHHHHHH CS
                          HHH_5   2 eeLlsvsGiGpktAlallsa.Giesvedlaaadv.eeLakipGiGkktAeriilel 55 
                                    +eLl+++G+Gpkt+  l+++ G+++v++l aa++ +++ ++pG+G+ +  +i+ ++
  gi|116754615|ref|YP_843733.1| 108 KELLQLQGVGPKTVALLHEKlGVSTVDELEAAARqHRIRRLPGMGPTKEANILKAI 163
                                    79******************99*******98886379***************9876 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.0   4.1e-12   4.3e-09       1      74 [.     357     465 ..     357     546 .. 0.71

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 4.1e-12
                                    EEEE--CCC.--.S-H..HHHHHHHHHCT-SEEEEEEEEBTT............HHHHHHHHHHHHTTTTSEEEEEEE.. CS
                                    xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            PHP   1 dlHvHteys.lldgalsieelvkkakelglkaiaiTDhgnlf............gyvefykaakkkykagikpiiGleay 67 
                                    dlHvH++ s ++ g++  ee+v  a++lg++ iaiTDh++              + ve + ++++   +g++++ G+e++
  gi|116754615|ref|YP_843733.1| 357 DLHVHSTWSdGV-GSI--EEMVSHARSLGYEYIAITDHSPSVgiaggiseerllEKVETIYRMNE-GLEGFRILAGTEVD 432
                                    89*******777.888..**********************99*********88866777777743.338*********** PP

                                    ................................. CS
                                    xxxxxx..........................x RF
                            PHP  68 vaddse..........................k 74 
                                    +  d+                           +
  gi|116754615|ref|YP_843733.1| 433 IRADGSldyrdeilercdvvvaaihmaqsqkeR 465
                                    *99998666666666655555555555555331 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 !   35.5   0.1   8.5e-12     9e-09       1      54 [.     172     225 ..     172     254 .. 0.88
   2 ?   -1.4   0.0       2.5   2.7e+03      44      74 ..     450     479 ..     430     484 .. 0.77

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 8.5e-12
                                    -EEHHHHHHHHHHHHHHHHHH-TT-EEEE-HHHHTT-SEESSEEEEEEBTTBST CS
                 DNA_pol_B_palm   1 riPreEvealealvkkaakeldpevevivcGSYRRgaessGDvDvlitkkdaks 54 
                                    riP + + ++ +++ ++++ ++   +++v+GSYRRg+e+ GD+D+l t ++ ++
  gi|116754615|ref|YP_843733.1| 172 RIPLSVAVRIVEHIMRHLEGIEGLSNITVAGSYRRGKETVGDIDILATSSRPSE 225
                                    8999999999************************************99887665 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.5
                                    EEEEEBTTBSTTSS--HHHHHHHHHHHHHTT CS
                 DNA_pol_B_palm  44 Dvlitkkdakseskklkklleklvkklkkkg 74 
                                    Dv++   ++++ s+k++++ ++lv+++++++
  gi|116754615|ref|YP_843733.1| 450 DVVVAAIHMAQ-SQKEREINSRLVAAMENEH 479
                                    77777777777.4578899999999988765 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.1   0.00021      0.22      12      30 .]      69      87 ..      67      87 .. 0.91
   2 !   13.7   0.0   4.2e-05     0.044       9      27 ..     106     124 ..      99     127 .. 0.83
   3 ?   -0.0   0.0      0.92   9.8e+02      16      23 ..     148     155 ..     145     161 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00021
                                   HHHTSTT-SHHHHHHHHHH CS
                            HHH 12 eLlalPGVGpktAeaIlsy 30
                                   eL  +PGVG++ Ae+I +y
  gi|116754615|ref|YP_843733.1| 69 ELDRIPGVGKAIAEKISEY 87
                                   8999************776 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 4.2e-05
                                    SHHHHHTSTT-SHHHHHHH CS
                            HHH   9 sreeLlalPGVGpktAeaI 27 
                                     ++eLl+l GVGpkt    
  gi|116754615|ref|YP_843733.1| 106 GMKELLQLQGVGPKTVALL 124
                                    579************8765 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.92
                                    STT-SHHH CS
                            HHH  16 lPGVGpkt 23 
                                    lPG Gp +
  gi|116754615|ref|YP_843733.1| 148 LPGMGPTK 155
                                    9*****76 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   7.5e-05      0.08      15      47 ..      69     100 ..      67     103 .. 0.89
   2 ?    3.6   0.1     0.076        80      43      61 ..     107     125 ..     105     128 .. 0.81
   3 ?    3.3   0.1     0.097     1e+02      12      38 ..     141     167 ..     139     191 .. 0.86
   4 ?    0.8   0.0      0.56   5.9e+02       8      22 ..     574     588 .]     573     588 .] 0.91

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.5e-05
                          HHH_3  15 eLqklpGlgpklAknIvayReknGpfksreeLl 47 
                                    eL+++pG+g+++A++I +y    G++k  ++L+
  gi|116754615|ref|YP_843733.1|  69 ELDRIPGVGKAIAEKISEYL-TTGHIKAYDDLV 100
                                    8******************9.778888888887 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.076
                          HHH_3  43 reeLlkvkglgpktfeqla 61 
                                    ++eLl+ +g+gpkt+  l 
  gi|116754615|ref|YP_843733.1| 107 MKELLQLQGVGPKTVALLH 125
                                    799**********998766 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.097
                          HHH_3  12 saeeLqklpGlgpklAknIvayReknG 38 
                                        +++lpG+gp++  nI+++ e + 
  gi|116754615|ref|YP_843733.1| 141 RQHRIRRLPGMGPTKEANILKAIERHR 167
                                    5567899*************9998886 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.56
                          HHH_3   8 iNtAsaeeLqklpGl 22 
                                    iNt sa++L+++ G+
  gi|116754615|ref|YP_843733.1| 574 INTLSAKDLMRHLGI 588
                                    9*********99887 PP

>> DUF1992  Domain of unknown function (DUF1992)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0     8e-06    0.0084       5      61 ..      60     126 ..      58     129 .. 0.90
   2 ?   -2.5   0.0       5.8   6.2e+03      50      64 ..     324     339 ..     301     342 .. 0.60

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 8e-06
                        DUF1992   5 rIreAierGeFdnlpgrGKPLpldd..........endplvpeeerlanrilknagvlPpeielrke 61 
                                     I++  +rGe+d +pg GK + ++           ++d lv  + + + ++l+ +gv P++++l +e
  gi|116754615|ref|YP_843733.1|  60 DIEDVWRRGELDRIPGVGKAIAEKIseylttghikAYDDLVSSTPKGMKELLQLQGVGPKTVALLHE 126
                                    5889999**************993345899999999***************************9887 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.8
                        DUF1992  50 gvlPpei.elrkeiee 64 
                                    +++Ppe+ e r eie+
  gi|116754615|ref|YP_843733.1| 324 QYIPPELrEDRGEIEA 339
                                    3667766356667766 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0    0.0045       4.8       7      24 ..      69      86 ..      66     109 .. 0.69
   2 !    8.5   0.0    0.0023       2.4       3      36 ..     105     139 ..     103     149 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0045
                           Cdd1  7 elqdiPniGkalaedlve 24
                                   el +iP++Gka+ae++ e
  gi|116754615|ref|YP_843733.1| 69 ELDRIPGVGKAIAEKISE 86
                                   799**********99764 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0023
                           Cdd1   3 kalkelqdiPniGkalaedlv.elGirsveelkge 36 
                                    k +kel ++ ++G+++ + l+ +lG+++v+el+  
  gi|116754615|ref|YP_843733.1| 105 KGMKELLQLQGVGPKTVALLHeKLGVSTVDELEAA 139
                                    6789****************989*********865 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   0.00013      0.14      36      61 ..      69      94 ..      56      96 .. 0.90
   2 ?    2.6   0.0      0.14   1.5e+02       8      33 ..     113     140 ..     105     170 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                          HHH_2 36 eLlevddiGeeiAqsivefFeneknr 61
                                   eL  ++++G+ iA++i e++++ + +
  gi|116754615|ref|YP_843733.1| 69 ELDRIPGVGKAIAEKISEYLTTGHIK 94
                                   89******************987765 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.14
                          HHH_2   8 IrhVGektAklLakrFk..sldaLkkas 33 
                                    +  VG kt  lL ++ +  ++d+L++a 
  gi|116754615|ref|YP_843733.1| 113 LQGVGPKTVALLHEKLGvsTVDELEAAA 140
                                    4567777777777777666777776654 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0026       2.8       9      28 ..      65      85 ..      60      88 .. 0.83
   2 ?    2.0   0.1      0.31   3.3e+02      18      31 ..     115     129 ..     113     130 .. 0.85
   3 ?    2.3   0.0      0.23   2.5e+02      13      28 ..     145     161 ..     141     163 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0026
                        IMS_HHH  9 wpl.pitkipGiGgklgekLe 28
                                   w + ++  ipG+G+  +ek+ 
  gi|116754615|ref|YP_843733.1| 65 WRRgELDRIPGVGKAIAEKIS 85
                                   6666899***********965 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.31
                        IMS_HHH  18 GiGgklgekLek.lG 31 
                                    G+G+k+ + L+  lG
  gi|116754615|ref|YP_843733.1| 115 GVGPKTVALLHEkLG 129
                                    9********887576 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.23
                        IMS_HHH  13 itkipGiGgklgek.Le 28 
                                    i+ +pG+G+  ++  L+
  gi|116754615|ref|YP_843733.1| 145 IRRLPGMGPTKEANiLK 161
                                    99*******98888776 PP

>> DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.19     2e+02       3      16 ..      70      83 ..      69      87 .. 0.86
   2 !   11.1   0.0   0.00025      0.26       2      30 ..     109     138 ..     108     148 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.19
                DNA_pol_lambd_f  3 FtkvyGVGpktAkk 16
                                   + ++ GVG ++A+k
  gi|116754615|ref|YP_843733.1| 70 LDRIPGVGKAIAEK 83
                                   66899*******98 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00025
                DNA_pol_lambd_f   2 lFtkvyGVGpktAkkwyak.Girtledlra 30 
                                    ++++  GVGpkt   +++k G+ t+++l a
  gi|116754615|ref|YP_843733.1| 109 ELLQLQGVGPKTVALLHEKlGVSTVDELEA 138
                                    677788**********************98 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   2.7e-05     0.029       7      45 ..     185     225 ..     179     280 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.7e-05
                                    HHHHHTT...TSEEEEEHHHHCTTSCTTSSEEEEEEESTTCH CS
                   NTP_transf_2   7 elkelep...vakvvlfGSyarGtalkgSDiDllvvlpeevs 45 
                                    +++ le+      +++ GSy+rG+ +   DiD+l +++++++
  gi|116754615|ref|YP_843733.1| 185 IMRHLEGiegLSNITVAGSYRRGKET-VGDIDILATSSRPSE 225
                                    455555555577899*********55.38***********54 PP

>> RNase_P_p30  RNase P subunit p30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   3.1e-05     0.032      16     145 ..     371     518 ..     356     521 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.1e-05
                                    ...HHHHHHHHH-SEEEEEEEEEESS---HHHHH..........HHHHHHHH..HHSSEEEEEEES-H.HHHHHHHHH-- CS
                    RNase_P_p30  16 s.rtiktlaelgytgvainftveaekekkpnase...pikeelkelkkelsglkllsRvtlvvsdpsklqrlskvrqkfd 91 
                                      ++++++++lgy+ +ai+ +  +   +   + e   ++ e++ + ++ l+g+++l + ++ +    +l    ++  ++d
  gi|116754615|ref|YP_843733.1| 371 IeEMVSHARSLGYEYIAITDHSPSVGIAGGISEErllEKVETIYRMNEGLEGFRILAGTEVDIRADGSLDYRDEILERCD 450
                                    246******************9954444333333667666777788888888***************9************ PP

                                    EE..EEE-....-SHHHHH...HHHHT.T-SEEE-TTTT....SSS-S--HHHH.HHHHHHT-EEEEE CS
                    RNase_P_p30  92 ll..avrP....ttekalr...aacenldvDiisidlts....rlpfglkhkti.raAvergvafEin 145
                                    ++  a+++    +  +++    aa en +vDii +++      r p+ ++  +i + A++ g+ +Ein
  gi|116754615|ref|YP_843733.1| 451 VVvaAIHMaqsqKEREINSrlvAAMENEHVDIIAHPTGRiigrREPYRVDMDLIlETAARTGTIMEIN 518
                                    88333444111133445552225669999*******98877777777788877635677777777775 PP

>> DUF3701  Phage integrase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0049       5.2      30      74 ..      51      94 ..      43     111 .. 0.76
   2 ?    5.2   0.1     0.021        23      24      73 ..     120     167 ..     116     186 .. 0.80
   3 ?   -3.0   0.0       7.5   7.9e+03      43      55 ..     560     572 ..     527     586 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0049
                        DUF3701 30 aagvktLaeLiarinrrgkrWwravprlGaakArrieafLaa.hae 74
                                   a+ ++ L e i+ + rrg      +p++G+a A++i ++L + h +
  gi|116754615|ref|YP_843733.1| 51 ARAIESLKEDIEDVWRRG--ELDRIPGVGKAIAEKISEYLTTgHIK 94
                                   556666777777777777..4689****************875555 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.021
                        DUF3701  24 varrLaaa.gvktLaeLiarinrrgkrWwravprlGaakArrieafLaaha 73 
                                    +++ L+++ gv t++eL a+ ++ +    r +p++G++k  +i + +++h 
  gi|116754615|ref|YP_843733.1| 120 TVALLHEKlGVSTVDELEAAARQHR---IRRLPGMGPTKEANILKAIERHR 167
                                    5555654339*********999888...9*********9998887777765 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 7.5
                        DUF3701  43 inrrgkrWwravp 55 
                                    + ++++ W +  +
  gi|116754615|ref|YP_843733.1| 560 VTVARRGWLEPSN 572
                                    4444545554444 PP

>> HRDC  HRDC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.12   1.2e+02      44      61 ..      68      85 ..      66      89 .. 0.85
   2 ?    8.4   0.0    0.0019         2      34      57 ..      98     121 ..      94     127 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.12
                                   HHHHTSTTT-HHHHHHHH CS
                           HRDC 44 eeLlqiegvgkrklekyg 61
                                   +eL +i+gvgk+ +ek  
  gi|116754615|ref|YP_843733.1| 68 GELDRIPGVGKAIAEKIS 85
                                   79**********999865 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0019
                                    HHHHH---SHHHHHTSTTT-HHHH CS
                           HRDC  34 eiAeklPttleeLlqiegvgkrkl 57 
                                    +++ + P+ ++eLlq+ gvg++ +
  gi|116754615|ref|YP_843733.1|  98 DLVSSTPKGMKELLQLQGVGPKTV 121
                                    78999***************9976 PP

>> BBS1  Ciliary BBSome complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       2.5   2.6e+03     227     242 ..     247     262 ..     244     263 .. 0.89
   2 ?   10.2   0.0   0.00035      0.37     165     213 ..     439     487 ..     404     496 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.5
                           BBS1 227 vfisatGlfdvdyriv 242
                                    ++i++ G+++vd riv
  gi|116754615|ref|YP_843733.1| 247 ASIIIEGTVQVDLRIV 262
                                    57999*********97 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00035
                           BBS1 165 ekykskplkkqtvitcmtslkknsadddaisclvigtEskeiyildsea 213
                                      y+++ l++ +v+++   + +++++++  s lv + E++++ i+ + +
  gi|116754615|ref|YP_843733.1| 439 LDYRDEILERCDVVVAAIHMAQSQKEREINSRLVAAMENEHVDIIAHPT 487
                                    5689999***********************************9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (588 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.39
# Mc/sec: 4515.99
//
Query:       gi|116754616|ref|YP_843734.1|  [L=150]
Description: hypothetical protein Mthe_1316 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); 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: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1150.17
//
Query:       gi|116754617|ref|YP_843735.1|  [L=139]
Description: hypothetical protein Mthe_1317 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.063   13.0   0.0      0.082   12.6   0.0    1.1  1  DUF5435   Family of unknown function (DUF5435)


Domain annotation for each model (and alignments):
>> DUF5435  Family of unknown function (DUF5435)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.6e-06     0.082      91     132 ..      72     113 ..      56     126 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.6e-06
                        DUF5435  91 issaslsnvltesltttqddtanrcsdayaespavlhledvt 132
                                    ++ a+   v ++s t t+++ an c+d    +p+ + le++ 
  gi|116754617|ref|YP_843735.1|  72 VAVAAFGAVAANSKTVTKNQDANACCDLGNAAPTTVNLERIG 113
                                    5667888999*****************************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 1133.32
//
Query:       gi|116754618|ref|YP_843736.1|  [L=267]
Description: hypothetical protein Mthe_1318 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 2009.52
//
Query:       gi|116754619|ref|YP_843737.1|  [L=409]
Description: translation initiation factor IF-2 subunit gamma [Methanosaeta thermophila PT]
Scores for 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-32  109.1   1.3    1.8e-31  108.2   0.2    2.1  2  eIF2_C        Initiation factor eIF2 gamma, C terminal
    2.8e-29  102.1   1.0    2.9e-28   98.7   1.0    2.1  1  GTP_EFTU      Elongation factor Tu GTP binding domain
    7.3e-08   32.7   2.0    2.5e-07   31.0   2.0    2.0  1  GTP_EFTU_D2   Elongation factor Tu domain 2
    1.5e-06   28.2   0.7    3.4e-05   23.8   0.2    2.3  2  RsgA_GTPase   RsgA GTPase
    0.00031   20.7   0.2    0.00059   19.8   0.2    1.4  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
     0.0019   18.2   0.0     0.0046   17.0   0.0    1.7  1  MMR_HSR1      50S ribosome-binding GTPase
  ------ inclusion threshold ------
      0.012   15.2   0.1       0.33   10.5   0.0    2.2  2  cobW          CobW/HypB/UreG, nucleotide-binding domain
      0.078   13.0   1.1       0.14   12.2   1.1    1.4  1  Nop10p        Nucleolar RNA-binding protein, Nop10p family
      0.088   12.6   1.7        3.1    7.6   0.0    2.6  3  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
        0.1   12.2   0.3       0.26   10.9   0.1    1.7  2  Ras           Ras family
       0.13   10.1   0.1       0.19    9.5   0.1    1.2  1  PolC_DP2      DNA polymerase II large subunit DP2


Domain annotation for each model (and alignments):
>> eIF2_C  Initiation factor eIF2 gamma, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1         3   4.9e+03       8      31 ..     133     154 ..     121     155 .. 0.69
   2 !  108.2   0.2   1.1e-34   1.8e-31       3      86 .]     323     407 ..     321     407 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3
                                    EE-SBESSSSSCCC-----TTEEE CS
                         eIF2_C   8 ellerlvgvkeekkveklkkkEvL 31 
                                    + ++++v v+++  ++ ++k+EvL
  gi|116754619|ref|YP_843737.1| 133 TGIDKIVIVQNK--IDLISKEEVL 154
                                    445666776665..8888888876 PP

  == domain 2  score: 108.2 bits;  conditional E-value: 1.1e-34
                                    EEEEEEE-SBESSSSSCCC-----TTEEEEEEETTEEEEEEEEEEESS.EEEEEEEEEEE-STTEEEEEEEEETTSEEEE CS
                         eIF2_C   3 leieyellerlvgvkeekkveklkkkEvLmlniGsastggvvtsvkkd.eakvkLkkPvcaekgekialsRrvekrWrLi 81 
                                    + ++++ll+r+vg++ee +ve+++++E+LmlniG+a+t+gvvts++++ +++v+Lk+Pvcae+g+++a+sRr+++rWrLi
  gi|116754619|ref|YP_843737.1| 323 FVMDMKLLDRVVGSTEEAAVEPIHTSEPLMLNIGTATTVGVVTSARESgKVQVQLKRPVCAEVGDRVAVSRRIGARWRLI 402
                                    66899******************************************659****************************** PP

                                    EEEEE CS
                         eIF2_C  82 GwGei 86 
                                    G+G+i
  gi|116754619|ref|YP_843737.1| 403 GVGTI 407
                                    ***98 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.7   1.0   1.8e-31   2.9e-28       4     193 ..       6     197 ..       3     198 .. 0.90

  Alignments for each domain:
  == domain 1  score: 98.7 bits;  conditional E-value: 1.8e-31
                                    EEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE................... CS
                       GTP_EFTU   4 rnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle................... 64 
                                    +nig++ghvDhGKtTL+ +L    g+             +D+++eE +rgi+i    +                      
  gi|116754619|ref|YP_843737.1|   6 VNIGMVGHVDHGKTTLVRALS---GI------------WTDQHSEEMKRGISIRLGYADATfrkcpncpapdcytvdeic 70 
                                    8****************9998...33............4789999********99999888889**************** PP

                                    ....T.TCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTB.STHHHHHHHHHHHHTTTE.EEEEEESCGST.H CS
                       GTP_EFTU  65 ....k.etkkylinliDtPGHvdFskevirglrvlDgavlvvdaveG.vepqteevlrlalkegvp.iivfiNKmDrl.k 136
                                        + +   ++++++D+PGH+  + ++  g++++Dgavlv++a+e  ++pqt+e+l  ++  g+  i+++ NK+D + k
  gi|116754619|ref|YP_843737.1|  71 khcgSpTNILRTVSFVDSPGHETLMATMLCGAAIMDGAVLVIAANEPcPQPQTKEHLMALNITGIDkIVIVQNKIDLIsK 150
                                    988744777899*********************************9879****************9899999******99 PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHHSH CS
                       GTP_EFTU 137 aelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealvellp 193
                                    +e+ e  +++k  +      ++  +++   + pvv++Sa ++ +++ +++a+ e +p
  gi|116754619|ref|YP_843737.1| 151 EEVLEHYRQIK-AF------VKGTVAE---NAPVVPISAQQNINIDMVIQAIEEVIP 197
                                    99999999999.66......4444444...57********************99988 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   2.0   1.6e-10   2.5e-07       1      62 [.     229     297 ..     229     310 .. 0.86

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 1.6e-10
                                    EEEEEEEEEESEEETTEEEEEEC.TCTTSEE.......EEEEEEEEEEETEEESEEETTSEEEEEEEESS CS
                    GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskke.......ivtrissletfhededeavaganaGvivaikg 62 
                                    G+v++g++ +G+l+kGd+++i++   ++  e       i t+++ l +  ed+ e+ +g+ +Gv++++++
  gi|116754619|ref|YP_843737.1| 229 GGVVGGTLSQGVLRKGDKLEIVPgRLVEA-EgkkqwvpIETKVTNLKAGGEDVAEVTPGGLIGVGTNLDP 297
                                    89********************9765544.2589*******************************99865 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.094   1.5e+02     104     137 ..      10      40 ..       5      42 .. 0.76
   2 !   23.8   0.2   2.1e-08   3.4e-05      13      98 ..     102     193 ..      79     197 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.094
                                    EECSTTSSHHHHHHHHCTT-----S--------- CS
                    RsgA_GTPase 104 lvGqSGvGKStLinallpelelktgevseklgrG 137
                                    +vG+   GK+tL+ al +     t + se+++rG
  gi|116754619|ref|YP_843737.1|  10 MVGHVDHGKTTLVRALSGI---WTDQHSEEMKRG 40 
                                    6889999*********985...555555555555 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 2.1e-08
                                    EES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-.EEEEEEE-GGG--HHH......HHHHHHHHHHHTTSEEEE--TT CS
                    RsgA_GTPase  13 vaNvdqllivvslkepelslnlldrfLvlaeekgi.epvivlnKiDlleeee......eleelkeelealgyevllvsak 85 
                                    +a +d +++v++++ep  ++++ +  L++++ +gi ++viv nKiDl+++ee      +++++ + + a + +v+ +sa+
  gi|116754619|ref|YP_843737.1| 102 AAIMDGAVLVIAANEPCPQPQT-KEHLMALNITGIdKIVIVQNKIDLISKEEvlehyrQIKAFVKGTVAENAPVVPISAQ 180
                                    7889**********88887776.56678888888878999************9998888888888888999999999999 PP

                                    THTTHHHHHHHCT CS
                    RsgA_GTPase  86 tkegleelkellk 98 
                                    ++ +++ + ++++
  gi|116754619|ref|YP_843737.1| 181 QNINIDMVIQAIE 193
                                    9999998877765 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 !   19.8   0.2   3.6e-07   0.00059      58     100 ..     138     192 ..     126     196 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 3.6e-07
                   MMR_HSR1_Xtn  58 clyvlNKiDlisleeldelare............pnsvviSaekelnldeLkeki 100
                                     ++v NKiDlis+ee+ e +r+              +v+iSa++++n+d + ++i
  gi|116754619|ref|YP_843737.1| 138 IVIVQNKIDLISKEEVLEHYRQikafvkgtvaenAPVVPISAQQNINIDMVIQAI 192
                                    68999**********999999778999999997668999**********999887 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   2.9e-06    0.0046       1      99 [.       7     128 ..       7     158 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.9e-06
                                    EEEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEE..ETTEE............................EE CS
                       MMR_HSR1   1 evaivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvk..lkgke............................ie 49 
                                    +++ vG+   GK+tL++al+g  + + s++    + i+ g  +  ++  +                            + 
  gi|116754619|ref|YP_843737.1|   7 NIGMVGHVDHGKTTLVRALSGIwTDQHSEEMKRGISIRLGYADatFR--KcpncpapdcytvdeickhcgsptnilrtVS 84 
                                    5899*****************76556666666666666555442233..13356666777777777777777777777** PP

                                    EEECGGCSSHHHHHHHHHHHHHHHHC.TSEEEEEEETTTTCSHHHHHHHHH CS
                       MMR_HSR1  50 lvDtpGliegaseekglgkaflalee.adlillvvdaseeklkpldeelee 99 
                                    +vD pG  e       l  ++l     +d ++lv+ a+e   +p+ +e   
  gi|116754619|ref|YP_843737.1|  85 FVDSPG-HE------TLMATMLCGAAiMDGAVLVIAANEPCPQPQTKEHLM 128
                                    ******.44......566666654444799999998772223333333333 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   0.0     0.067   1.1e+02       4      22 ..       9      30 ..       6      41 .. 0.73
   2 ?   10.5   0.0    0.0002      0.33     103     166 ..      96     161 ..      82     170 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.067
                                   EEEESTTCCHHHHHHHHH...C CS
                           cobW  4 vltGflGsGKTtLlnhll...e 22
                                   +++G +  GKTtL+++l    +
  gi|116754619|ref|YP_843737.1|  9 GMVGHVDHGKTTLVRALSgiwT 30
                                   57888899******99865552 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0002
                                    SHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEE..E-HHHHCHC..HHHHHHHH CS
                           cobW 103 eeelksdltldavvavvDaknleaeeekieekaedqlaaadllvl..nKtDlldeeallekleerl 166
                                    ++ l+ ++ +d+ v v+ a++   + +++e+++   ++  d +v+  nK+Dl+++e+ le+ +++ 
  gi|116754619|ref|YP_843737.1|  96 ATMLCGAAIMDGAVLVIAANEPCPQPQTKEHLMALNITGIDKIVIvqNKIDLISKEEVLEHYRQIK 161
                                    556777888999*******9998999999999999999999665555*********9888777655 PP

>> Nop10p  Nucleolar RNA-binding protein, Nop10p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.1   8.9e-05      0.14       5      28 ..      52      78 ..      49      82 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.9e-05
                                   -EE-TTT-...-EESSSB-TTT-SB-B CS
                         Nop10p  5 lrkcgkcr...vYTLkkvcpecggptk 28
                                    rkc++c     YT  ++c +cg+pt 
  gi|116754619|ref|YP_843737.1| 52 FRKCPNCPapdCYTVDEICKHCGSPTN 78
                                   689999988889*************96 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0019       3.1       4      23 ..       8      27 ..       6      38 .. 0.87
   2 ?    3.5   0.4     0.034        55      41     142 ..      86     193 ..      77     194 .. 0.55
   3 ?   -3.7   0.0       5.4   8.8e+03      85      99 ..     353     367 ..     338     378 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0019
                      PduV-EutP  4 illiGkvgsGKttLtqalkg 23
                                   i ++G+v+ GKttL +al+g
  gi|116754619|ref|YP_843737.1|  8 IGMVGHVDHGKTTLVRALSG 27
                                   5589**************97 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.034
                      PduV-EutP  41 iDtPGeylenrklysalivtsaeadvialvqdateeesvfppgfasvfnkeviGi......itkidlaedeenieavee. 113
                                    +D+PG    +++l+ ++ + +a  d  +lv +a+e+ +  p++  ++++ ++ Gi        kidl ++ee +e  ++ 
  gi|116754619|ref|YP_843737.1|  86 VDSPG----HETLMATMLCGAAIMDGAVLVIAANEP-CPQPQTKEHLMALNITGIdkivivQNKIDLISKEEVLEHYRQi 160
                                    56666....344555555555555555555554443.4445555555555555532222114688888777777665541 PP

                      PduV-EutP 114 ..lLksaGaek..ifevsavekegieellkyle 142
                                      ++k   ae+  +  +sa ++++i+ +++ +e
  gi|116754619|ref|YP_843737.1| 161 kaFVKGTVAENapVVPISAQQNINIDMVIQAIE 193
                                    113443333332268999999999999988886 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 5.4
                      PduV-EutP  85 asvfnkeviGiitki 99 
                                     ++ +  ++G++t +
  gi|116754619|ref|YP_843737.1| 353 LNIGTATTVGVVTSA 367
                                    444455667777755 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.6   2.6e+03       4      18 ..      10      24 ..       8      42 .. 0.78
   2 ?   10.9   0.1   0.00016      0.26     106     159 ..     137     195 ..     121     198 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.6
                                   EEESTTSSHHHHHHH CS
                            Ras  4 lvGdsavGKtslllr 18
                                   +vG    GKt+l+  
  gi|116754619|ref|YP_843737.1| 10 MVGHVDHGKTTLVRA 24
                                   6899999****9864 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00016
                                    EEEEEEETTTGGGG-SS..-HHHHHHHH...HHHTSEEEEEBTTTTCTHHHHHHHHHHH CS
                            Ras 106 pivLvGnKvDleekrav..steegeela...kelglkfletSAktnenveeafeellre 159
                                    +iv+v nK+Dl +k++v  ++++ +++       +++ + +SA++n n++ +++++ + 
  gi|116754619|ref|YP_843737.1| 137 KIVIVQNKIDLISKEEVleHYRQIKAFVkgtVAENAPVVPISAQQNINIDMVIQAIEEV 195
                                    699**********9988333445566653323456999*************99988765 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 ?    9.5   0.1   0.00012      0.19     615     757 ..      49     194 ..      30     199 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00012
                       PolC_DP2 615 eiarrkCkkC...gketlearCeeCgekteeklvCkkceeeveeek..cekcekeakavkkkkidlkellekaleklger 689
                                    + + rkC++C   +  t+   C++Cg+ t+   + + +++  +e    +  c++     +   i  +e   + ++k ++ 
  gi|116754619|ref|YP_843737.1|  49 DATFRKCPNCpapDCYTVDEICKHCGSPTNILRTVSFVDSPGHETLmaTMLCGAAIMDGAVLVIAANEPCPQPQTKEHL- 127
                                    55678999994445679999***********999999998666544225566666666666666666666665555444. PP

                       PolC_DP2 690 eekleelkgvkgltskekipEpleK.gilRakhdvsvfkdgtvRyDmtdlplthfrpkeigvsveklre 757
                                         ++ g+++++  ++ ++ + K  +l   +++ +f  gtv  ++  +p+++ +  +i++ ++ ++e
  gi|116754619|ref|YP_843737.1| 128 --MALNITGIDKIVIVQNKIDLISKeEVLEHYRQIKAFVKGTVAENAPVVPISAQQNINIDMVIQAIEE 194
                                    ..6678999999988888888888735999999999999999999999999998888888887777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       721  (0.0402142); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); 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: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 2890.77
//
Query:       gi|116754620|ref|YP_843738.1|  [L=127]
Description: nucleotide binding protein, PINc [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-40  138.2   0.1    1.6e-40  138.0   0.1    1.0  1  PIN_9     PIN like domain
     0.0014   18.8   0.2     0.0032   17.6   0.0    1.8  2  PIN_10    PIN like domain
     0.0018   18.8   0.0     0.0066   17.0   0.0    1.7  1  PIN       PIN domain
  ------ inclusion threshold ------
      0.035   14.4   0.0      0.052   13.8   0.0    1.4  1  PIN_4     PIN domain


Domain annotation for each model (and alignments):
>> PIN_9  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.0   0.1   3.6e-44   1.6e-40       1     115 [.       3     115 ..       3     116 .. 0.97

  Alignments for each domain:
  == domain 1  score: 138.0 bits;  conditional E-value: 3.6e-44
                          PIN_9   1 vilDtnaLmipvqfgvdifeelerllgsvelvvpkavleELerlak.agkgkertaakvalsLaerceiveaeeekaDda 79 
                                    v+lDtnaLm+p qfgvdif+elerl g+ +++vp+av++EL++++k a+kgk+++aa+val L +rc++v+a+ + aDd+
  gi|116754620|ref|YP_843738.1|   3 VLLDTNALMMPEQFGVDIFSELERL-GYFDYIVPTAVVRELRAISKfAEKGKDKRAASVALGLLSRCRVVDAD-GVADDV 80 
                                    89***********************.******************9845677**********************.****** PP

                          PIN_9  80 ilelakeldaavlvTnDreLkkrllekgipvilLRq 115
                                    + +la+e++aavl T D+eL+krl ++gi+vi+LRq
  gi|116754620|ref|YP_843738.1|  81 LERLASETGAAVL-TGDKELRKRLSKRGITVIYLRQ 115
                                    *************.*********************9 PP

>> PIN_10  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       1.1   5.1e+03       1       9 [.       1       9 [.       1      12 [. 0.86
   2 !   17.6   0.0   7.1e-07    0.0032       5      68 ..      30     105 ..      28     115 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.1
                         PIN_10 1 MkfflDenl 9
                                  Mk++lD n 
  gi|116754620|ref|YP_843738.1| 1 MKVLLDTNA 9
                                  99****985 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 7.1e-07
                         PIN_10   5 lDenlppalakaLrelleeeg............hevvhlrdkfaagtkDeeWiaalaeggwvvltkDrrirkrpaE 68 
                                    +D  +p a+ + Lr++++ ++              + + r + a g++D  + ++++e+g +vlt D+++rkr  +
  gi|116754620|ref|YP_843738.1|  30 FDYIVPTAVVRELRAISKFAEkgkdkraasvalGLLSRCRVVDADGVADDVLERLASETGAAVLTGDKELRKRLSK 105
                                    7888999999999999995444677776665554455555555********999999***************9544 PP

>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.5e-06    0.0066       1      90 [.       3      92 ..       3     101 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.5e-06
                                   EEE-HHHHHHHHTTSHHHHHHHHHHHTS..SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHHHHHH CS
                            PIN  1 ivlDTsvliallrgeekaeaarklleel..eelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidaeiaee 80
                                   ++lDT++l     +e +   +   le+l   + +++ +v+ El+++ +   +k + +++   +l lls++++++ d  + + 
  gi|116754620|ref|YP_843738.1|  3 VLLDTNALM---MPEQFGVDIFSELERLgyFDYIVPTAVVRELRAISKF-AEKGKDKRAASVALGLLSRCRVVDADGVADDV 80
                                   689******...99999999*****************************.55555555555566669*******77777777 PP

                                   HHHHHHHHH..S CS
                            PIN 81 aaeialkyg..l 90
                                    +++a++ g  +
  gi|116754620|ref|YP_843738.1| 81 LERLASETGaaV 92
                                   777776666554 PP

>> PIN_4  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.2e-05     0.052       2      57 ..       4      65 ..       3     109 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.2e-05
                          PIN_4  2 VlDTnvlLhdpealksf......keehdvviPitVleELdklKkgsserelarlarqanrll 57
                                    lDTn l+   ++   +       +  d ++P  V++EL+++ k  ++ + +r+a+ a+ ll
  gi|116754620|ref|YP_843738.1|  4 LLDTNALMMPEQFGVDIfselerLGYFDYIVPTAVVRELRAISKFAEKGKDKRAASVALGLL 65
                                   59****999888755556777877999***************99998644444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 879.28
//
Query:       gi|116754621|ref|YP_843739.1|  [L=206]
Description: DNA-directed RNA polymerase subunit E' [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.4e-19   68.6   0.1    9.6e-19   67.5   0.1    1.6  1  SHS2_Rpb7-N    SHS2 domain found in N terminus of Rpb7p/Rpc25
      5e-14   52.4   0.3    1.4e-13   51.0   0.3    1.8  1  S1             S1 RNA binding domain
    0.00026   21.3   1.1    0.00078   19.7   1.1    1.9  1  RNA_pol_Rbc25  RNA polymerase III subunit Rpc25
  ------ inclusion threshold ------
      0.085   12.9   0.0       0.41   10.7   0.0    2.2  1  S1_2           S1 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 !   67.5   0.1   2.1e-22   9.6e-19       2      70 .]       9      77 ..       8      77 .. 0.98

  Alignments for each domain:
  == domain 1  score: 67.5 bits;  conditional E-value: 2.1e-22
                                   EEEEE-GGGTTSTHHHHHHHHHHHHHTTBEETTTEEEEEEEEEEEECCEEE-TTTSSEEEEEEEEEEEE CS
                    SHS2_Rpb7-N  2 dtvrlePsylgstledallerllekyegkvvpslGvivavldiaeysegkvlggsGsvyvrVtfralvF 70
                                    +vr++P+++g++l+da++ +l++kye +v++ lG iva+l + +++eg+++ g+G+vy++V f+a+vF
  gi|116754621|ref|YP_843739.1|  9 GVVRIPPEDMGNPLNDAVEMALRNKYEARVDRTLGAIVAILGVDSIGEGRIIAGDGAVYYDVIFDAVVF 77
                                   69******************************************************************9 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   0.3   3.1e-17   1.4e-13       1      69 [.      78     155 ..      78     161 .. 0.92

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 3.1e-17
                                    HSTTTCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSS..........CEESCHHHCEETTEEEEEEEEEEETTTTE CS
                             S1   1 kpekgevveGeVtsvtkgGafVelgngvegfvpaselsrd..........arvedpdevlkvGdevkvkvlkvdkdrrr 69 
                                    kpe  evveGeV++++k+GafV +g + +g++++s++ ++             +d ++ l +Gd+v+++++ v  ++r 
  gi|116754621|ref|YP_843739.1|  78 KPEMQEVVEGEVVEIVKFGAFVSIG-PFDGLLHVSQITDEymaydeknarLVSKDTNKFLAEGDRVRARIIAVSLNERD 155
                                    67888********************.**********************987789999999************9988775 PP

>> RNA_pol_Rbc25  RNA polymerase III subunit Rpc25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   1.1   1.7e-07   0.00078       1      93 [.      79     186 ..      79     205 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.7e-07
                                    -STTSEEEEEEEEEETTCEEEEBTTBSEEEEECCCCSTTEEEECCCTCEEEEESSSEEEEE-TTSEEEEEEEEEEE---- CS
                  RNA_pol_Rbc25   1 PfvgevltgkiksstregikvslgffddifvpkelLfepsefdeeeqawvweveeeeelyldvgeeirfrveeeifvdvk 80 
                                    P ++ev++g + +  + g +vs+g fd ++   +   e++++de++   v +   +++ +l  g+++r r+  ++ ++++
  gi|116754621|ref|YP_843739.1|  79 PEMQEVVEGEVVEIVKFGAFVSIGPFDGLLHVSQITDEYMAYDEKNARLVSK---DTNKFLAEGDRVRARIIAVSLNERD 155
                                    7789************************99999999********99887655...589999******************* PP

                                    ---HHHHHCHHH..................C CS
                  RNA_pol_Rbc25  81 pkspkeaeleee..................e 93 
                                    pk +k   + ++                  e
  gi|116754621|ref|YP_843739.1| 156 PKGSKIGLTMRQtglgkiewlealrrgeisE 186
                                    *999877666666777777777666664332 PP

>> S1_2  S1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   9.1e-05      0.41       4      38 ..      84     117 ..      83     144 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 9.1e-05
                           S1_2   4 intlkvlretdfgyfLqkdesgevlLpkkevpeel 38 
                                    +++ +v+++ +fg+f++ +   + lL+ +++++e 
  gi|116754621|ref|YP_843739.1|  84 VVEGEVVEIVKFGAFVSIGP-FDGLLHVSQITDEY 117
                                    67889***************.**********9653 PP



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:                      490  (0.02733); 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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1521.50
//
Query:       gi|116754622|ref|YP_843740.1|  [L=61]
Description: DNA-directed RNA polymerase subunit E, RpoE2 [Methanosaeta thermophila PT]
Scores for complete 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-12   47.6   0.0    1.7e-12   47.3   0.0    1.1  1  Spt4          Spt4/RpoE2 zinc finger
  ------ inclusion threshold ------
      0.012   15.2   1.9      0.017   14.7   1.9    1.2  1  RecR          RecR protein
      0.025   14.1   0.2       0.12   11.9   0.0    2.0  2  TF_Zn_Ribbon  TFIIB zinc-binding
      0.052   13.0   1.8      0.071   12.5   0.1    1.9  2  zf-ribbon_3   zinc-ribbon domain
      0.054   13.2   3.4       0.29   10.8   0.2    2.1  2  zf-RRN7       Zinc-finger of RNA-polymerase I-specific TFIIB,
       0.22   11.6   2.6       0.79    9.9   2.6    1.8  1  Zn-ribbon_8   Zinc ribbon domain


Domain annotation for each model (and alignments):
>> Spt4  Spt4/RpoE2 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   0.0   5.6e-16   1.7e-12       2      77 .]       4      61 .]       3      61 .] 0.97

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 5.6e-16
                           Spt4  2 rACllCklvktedqFeeegCpnCeilelkgdkekvsectseefeGlvaildpekSwvAkwqrldkkvpglYAlkve 77
                                   +AC++C+++++        Cp+C           +s+++s+++ G+++++dp+ S++A +  l+ + pg YAlkv+
  gi|116754622|ref|YP_843740.1|  4 QACRECHRIVEGLV-----CPIC-----------GSSSLSKDWAGYIVVIDPRGSEIAAK--LGITLPGRYALKVR 61
                                   8**********999.....****...........**************************..************96 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   1.9   5.6e-06     0.017      18      37 ..       5      24 ..       4      25 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.6e-06
                                   E-TTT--EESSSS-CCCCST CS
                           RecR 18 hCsrCgnlteedlCaICsdp 37
                                    C++C+ + e  +C+IC ++
  gi|116754622|ref|YP_843740.1|  5 ACRECHRIVEGLVCPICGSS 24
                                   5****************875 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.17     5e+02       3       7 ..       6      10 ..       4      14 .. 0.76
   2 ?   11.9   0.0     4e-05      0.12       2      14 ..      17      29 ..      16      44 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.17
                                   ETTTT CS
                   TF_Zn_Ribbon  3 CPnCg 7 
                                   C +C+
  gi|116754622|ref|YP_843740.1|  6 CRECH 10
                                   99997 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 4e-05
                                   EETTTTCEECHEE CS
                   TF_Zn_Ribbon  2 kCPnCgstnlveD 14
                                   +CP+Cgs++l  D
  gi|116754622|ref|YP_843740.1| 17 VCPICGSSSLSKD 29
                                   8******998444 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1       0.3   8.9e+02      17      22 ..       4       9 ..       2       9 .. 0.77
   2 ?   12.5   0.1   2.4e-05     0.071       4      16 ..      17      30 ..      14      31 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.3
                    zf-ribbon_3 17 nvCpyC 22
                                   ++C  C
  gi|116754622|ref|YP_843740.1|  4 QACREC 9 
                                   679988 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 2.4e-05
                    zf-ribbon_3  4 rCPnCGa.plssdd 16
                                    CP CG+  ls+d+
  gi|116754622|ref|YP_843740.1| 17 VCPICGSsSLSKDW 30
                                   5******8899997 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.4     0.019        58      24      28 ..       6      10 ..       6      14 .. 0.85
   2 ?   10.8   0.2   9.8e-05      0.29       4      15 ..      15      30 ..      13      31 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.019
                        zf-RRN7 24 CrrCh 28
                                   Cr+Ch
  gi|116754622|ref|YP_843740.1|  6 CRECH 10
                                   ***** PP

  == domain 2  score: 10.8 bits;  conditional E-value: 9.8e-05
                        zf-RRN7  4 gppCgvCgc....rsf 15
                                   g +C++Cg+    +++
  gi|116754622|ref|YP_843740.1| 15 GLVCPICGSsslsKDW 30
                                   78*******6666666 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   2.6   0.00027      0.79       8      38 ..       6      28 ..       3      30 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00027
                    Zn-ribbon_8  8 CeeCghefevlqsisdapltaCPeCgs.evrr 38
                                   C+eC++  e l+         CP Cgs  + +
  gi|116754622|ref|YP_843740.1|  6 CRECHRIVEGLV---------CPICGSsSLSK 28
                                   999999999777.........******88877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 482.20
//
Query:       gi|116754623|ref|YP_843741.1|  [L=178]
Description: hypothetical protein Mthe_1323 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-41  140.2   0.0    3.2e-41  139.9   0.0    1.1  1  DUF359    Protein of unknown function (DUF359)


Domain annotation for each model (and alignments):
>> DUF359  Protein of unknown function (DUF359)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.9   0.0   1.8e-45   3.2e-41       1     125 [.      50     172 ..      50     173 .. 0.96

  Alignments for each domain:
  == domain 1  score: 139.9 bits;  conditional E-value: 1.8e-45
                         DUF359   1 vtknllkagikPdlaivDgktkReeveeeekeeekekekekevievkNpaGtiteelieaikealeseekvlilVdGEED 80 
                                    +t +llka+++Pdl+ivD+ktkR++ve++ k+++   e +++v++v+NpaGt+teel++a++e+l+  +++ i+VdGEED
  gi|116754623|ref|YP_843741.1|  50 TTFYLLKASFIPDLMIVDHKTKRSPVEDSIKRRH--LEGSYRVVNVENPAGTLTEELLDAVRESLNGCTPTEIIVDGEED 127
                                    7999********************9999555555..699***************************************** PP

                         DUF359  81 LavlpaillapegsvvvYGqpdeGvvlvkvteeakeeaeellekf 125
                                    La+lpail+ap gs+vvYGqp+ G vlv vt e+k+e+e +l+++
  gi|116754623|ref|YP_843741.1| 128 LAALPAILYAPLGSAVVYGQPSVGSVLVMVTPEKKREIEGILRRM 172
                                    ******************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 1528.89
//
Query:       gi|116754624|ref|YP_843742.1|  [L=99]
Description: ribosomal protein S24e [Methanosaeta thermophila PT]
Scores for complete 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   73.4   0.1    1.3e-20   73.1   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 !   73.1   0.1   7.2e-25   1.3e-20       1      78 [.      20      97 ..      20      98 .. 0.98

  Alignments for each domain:
  == domain 1  score: 73.1 bits;  conditional E-value: 7.2e-25
                                   EEEEE-SSS-S--HHHHHHHHHHHHTS-CTTEEEEEEEE-SSSSEEEEEEEEES-HHHHHHHS-HHHHHHTTSS---S CS
                 Ribosomal_S24e  1 vvdvlHpgkatpskteireklakmykvdpdlvvvfgfrthfGggkttGfakiYdsleaakkfEpkhrlaRnglaekkk 78
                                   v++v+H + +tp+++++ e+la++ +++p lvvv+++++ fG++++ ++a+iY+s+e+++++E+ h+++Rn ++e+k+
  gi|116754624|ref|YP_843742.1| 20 VLKVIHGEGPTPTRKSVVERLAAIKDSKPGLVVVRKMNSLFGRRESIAHARIYESEERMRQVENPHIVKRNVFTEQKE 97
                                   689************************************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 729.05
//
Query:       gi|116754625|ref|YP_843743.1|  [L=49]
Description: ribosomal protein S27a [Methanosaeta thermophila PT]
Scores for complete 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-19   67.8   1.9    7.6e-19   67.6   1.9    1.0  1  Ribosomal_S27   Ribosomal protein S27a
    0.00071   19.6   0.8    0.00072   19.6   0.8    1.0  1  DUF1451         Zinc-ribbon containing domain
     0.0013   18.3   2.8     0.0019   17.8   2.8    1.3  1  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
     0.0014   18.8   0.7     0.0017   18.5   0.7    1.2  1  Ribosomal_L37e  Ribosomal protein L37e
      0.009   16.2   0.3     0.0097   16.1   0.3    1.1  1  IBR             IBR domain, a half RING-finger domain
  ------ inclusion threshold ------
      0.015   15.0   2.9       0.27   11.0   0.2    2.2  2  zinc_ribbon_2   zinc-ribbon domain
      0.031   14.3   3.5      0.058   13.4   3.3    1.6  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
      0.041   14.1   3.1       0.21   11.8   0.3    2.2  2  zinc_ribbon_13  Nucleic-acid-binding protein containing Zn-ri
      0.063   13.3   0.3      0.063   13.3   0.3    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.066   13.1   4.0       0.37   10.8   4.0    2.0  1  Nudix_N_2       Nudix N-terminal
      0.074   13.0   0.6      0.081   12.9   0.6    1.3  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
      0.078   13.1   0.2      0.089   12.9   0.2    1.3  1  MqsA_antitoxin  Antitoxin component of bacterial toxin-antito
       0.12   12.7   3.5       0.35   11.2   0.4    2.1  2  zinc_ribbon_9   zinc-ribbon
       0.16   11.5   3.5       0.27   10.8   3.5    1.4  1  TF_Zn_Ribbon    TFIIB zinc-binding
       0.22   11.0   5.0       0.34   10.4   0.3    2.1  2  zf-ribbon_3     zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Ribosomal_S27  Ribosomal protein S27a
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.6   1.9   6.4e-22   7.6e-19       1      45 []       3      45 ..       3      45 .. 0.99

  Alignments for each domain:
  == domain 1  score: 67.6 bits;  conditional E-value: 6.4e-22
                                   SSSSCCESSSSSEEESS-B-SS-S-TTSBEEECTTEEEESSTTTE CS
                  Ribosomal_S27  1 vlkyYkvddsgkverlrkeCpreCGaGvfMAehkdRkyCGkCglT 45
                                   v+kyY++ + ++++  +  Cpr CG+Gvf+Aeh+dR +CG+Cg+T
  gi|116754625|ref|YP_843743.1|  3 VHKYYQLSG-ETIKARKPICPR-CGNGVFLAEHEDRMSCGRCGYT 45
                                   89*******.9***********.*********************9 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.8     6e-07   0.00072     101     144 ..       4      48 ..       1      49 [] 0.91

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 6e-07
                        DUF1451 101 agvyq.sGevvglGtlvCekCgkelalkkteeippCpkCgateFr 144
                                    +++yq sGe + + + +C +Cg+ + l + e    C +Cg teF+
  gi|116754625|ref|YP_843743.1|   4 HKYYQlSGETIKARKPICPRCGNGVFLAEHEDRMSCGRCGYTEFK 48 
                                    5666659*************************************7 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   2.8   1.6e-06    0.0019       4      32 .]      19      47 ..      16      47 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.6e-06
                  zf-NADH-PPase  4 rFCgrCGaptepaeggwarvCpaCglehY 32
                                   + C+rCG  + +ae++  + C  Cg+  +
  gi|116754625|ref|YP_843743.1| 19 PICPRCGNGVFLAEHEDRMSCGRCGYTEF 47
                                   57***********************9766 PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.7   1.4e-06    0.0017      18      43 ..      20      48 ..       9      49 .] 0.80

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.4e-06
                 Ribosomal_L37e 18 lCrrCgkrsy...hvqkktCascGypsak 43
                                   +C rCg+  +   h  + +C+ cGy + k
  gi|116754625|ref|YP_843743.1| 20 ICPRCGNGVFlaeHEDRMSCGRCGYTEFK 48
                                   7*********666666789******7654 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 !   16.1   0.3   8.1e-06    0.0097      18      46 ..      18      44 ..       4      47 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.1e-06
                            IBR 18 lkwCprpdCeaiieksegcksvtCskCgf 46
                                   +  Cp   C++ +   e++++++C +Cg+
  gi|116754625|ref|YP_843743.1| 18 KPICP--RCGNGVFLAEHEDRMSCGRCGY 44
                                   447**..9*******************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 ?   11.0   0.2   0.00022      0.27       6      21 ..      11      26 ..      11      28 .. 0.70
   2 ?    4.9   0.2     0.019        23      16      21 ..      39      44 ..      32      45 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00022
                  zinc_ribbon_2  6 GaelqdnakFCpyCGt 21
                                   G++++ + + Cp+CG 
  gi|116754625|ref|YP_843743.1| 11 GETIKARKPICPRCGN 26
                                   6677777777888886 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.019
                  zinc_ribbon_2 16 CpyCGt 21
                                   C +CG+
  gi|116754625|ref|YP_843743.1| 39 CGRCGY 44
                                   888886 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   3.3   4.9e-05     0.058      18      46 .]      18      45 ..      12      47 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.9e-05
                  Zn_Tnp_IS1595 18 gfvCPhCgsrkayriktrglfqCkeCrkq 46
                                   +++CP+Cg+  ++  ++  +  C +C+++
  gi|116754625|ref|YP_843743.1| 18 KPICPRCGNG-VFLAEHEDRMSCGRCGYT 45
                                   699*****65.34444468*******985 PP

>> zinc_ribbon_13  Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.064        77       2       8 ..      21      27 ..      20      35 .. 0.80
   2 ?   11.8   0.3   0.00017      0.21      36      46 ..      37      47 ..      28      49 .] 0.91

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.064
                 zinc_ribbon_13  2 CpKCgnt 8 
                                   Cp+Cgn 
  gi|116754625|ref|YP_843743.1| 21 CPRCGNG 27
                                   9***996 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00017
                 zinc_ribbon_13 36 vsCknCgYtel 46
                                    sC +CgYte+
  gi|116754625|ref|YP_843743.1| 37 MSCGRCGYTEF 47
                                   69********8 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3   5.2e-05     0.063      65      97 ..      12      47 ..       2      49 .] 0.73

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.2e-05
                                   EEE--.EEEETTTS-EEECHH.H.HHS-TTTSSS-E CS
                           HypA 65 eevpv.kvrCreCgkefelee.k.alrCpkCgsadv 97
                                   e++++ k  C +Cg+ + l+e + +++C++Cg +++
  gi|116754625|ref|YP_843743.1| 12 ETIKArKPICPRCGNGVFLAEhEdRMSCGRCGYTEF 47
                                   555551458*****999977743689*****98765 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   4.0   0.00031      0.37       3      32 ..      21      46 ..      20      48 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00031
                                   -TTT--B-EEE--TT-SS-EEEETTTTEEE CS
                      Nudix_N_2  3 CsqCGtpvelripdgDnreRlvCpaCgtih 32
                                   C+ CG+ v l+    +++ R  C +Cg++ 
  gi|116754625|ref|YP_843743.1| 21 CPRCGNGVFLA----EHEDRMSCGRCGYTE 46
                                   9******8776....6899********975 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 ?   12.9   0.6   6.8e-05     0.081      30      55 ..      20      45 ..       5      48 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.8e-05
                 OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgfe 55
                                    C++Cg  +  a +++++ C +Cg++
  gi|116754625|ref|YP_843743.1| 20 ICPRCGNGVFLAEHEDRMSCGRCGYT 45
                                   6******999999***********97 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 ?   12.9   0.2   7.5e-05     0.089      34      57 ..      18      41 ..       3      49 .] 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.5e-05
                 MqsA_antitoxin 34 gdfCarCGegvldeeeedrlseel 57
                                      C+rCG+gv+ +e+edr+s   
  gi|116754625|ref|YP_843743.1| 18 KPICPRCGNGVFLAEHEDRMSCGR 41
                                   457****************98654 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.4   0.00029      0.35      21      30 ..      18      27 ..       9      32 .. 0.70
   2 ?    3.7   0.2     0.063        75      15      28 ..      31      43 ..      28      47 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00029
                  zinc_ribbon_9 21 dvlCPhCggg 30
                                    ++CP+Cg+g
  gi|116754625|ref|YP_843743.1| 18 KPICPRCGNG 27
                                   458****865 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.063
                  zinc_ribbon_9 15 spdedsdvlCPhCg 28
                                   +++ed+ + C +Cg
  gi|116754625|ref|YP_843743.1| 31 AEHEDRMS-CGRCG 43
                                   56777778.****8 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   3.5   0.00023      0.27       2      27 ..      20      44 ..      19      46 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00023
                                   EETTTTC.EECHEETSTTCEEESSSSB CS
                   TF_Zn_Ribbon  2 kCPnCgs.tnlveDpergelvCtdCGl 27
                                   +CP Cg+  + + ++e   + C++CG+
  gi|116754625|ref|YP_843743.1| 20 ICPRCGNgVF-LAEHE-DRMSCGRCGY 44
                                   6*****9444.44433.256******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 ?   10.4   0.3   0.00029      0.34      13      24 ..      15      26 ..      11      28 .. 0.67
   2 ?    6.6   5.4    0.0046       5.4       5      24 ..      21      44 ..      17      45 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00029
                    zf-ribbon_3 13 ssddnvCpyCGt 24
                                   +++ ++Cp CG 
  gi|116754625|ref|YP_843743.1| 15 KARKPICPRCGN 26
                                   777778888875 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0046
                    zf-ribbon_3  5 CPnCGa.p.ls..sddnvCpyCGt 24
                                   CP+CG+ + l+  +d + C  CG+
  gi|116754625|ref|YP_843743.1| 21 CPRCGNgVfLAehEDRMSCGRCGY 44
                                   9****9987762246677888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); 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: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 356.07
//
Query:       gi|116754626|ref|YP_843744.1|  [L=95]
Description: hypothetical protein Mthe_1326 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-07   31.7   0.2    6.9e-06   26.9   0.0    2.0  2  Fic       Fic/DOC family


Domain annotation for each model (and alignments):
>> Fic  Fic/DOC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.3   0.0    0.0088   1.6e+02       2      19 ..       6      23 ..       5      32 .. 0.75
   2 !   26.9   0.0   3.9e-10   6.9e-06      49      97 .]      33      78 ..      28      78 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.0088
                                   -SHHHHHHHHCHS-S--- CS
                            Fic  2 ltledllelhrlllqdig 19
                                   +t+e ++e+h+ll  d++
  gi|116754626|ref|YP_843744.1|  6 ITAEMIIEIHDLLGPDLE 23
                                   799*********966654 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 3.9e-10
                                   HHHHHHHHCHHT-S-HHHHHHHHHHHHHHH--SSS-HHHHHHHHHHHHH CS
                            Fic 49 leelleylnelekeeplekaaalhyefekiHPFaDGNgRtarlllnllL 97
                                   l+ l+e +n  ++ +++++aa+++y ++  HPF DG +Rta+ l++++L
  gi|116754626|ref|YP_843744.1| 33 LDYLVERIN--KERDVFKRAAWALY-LADQHPFWDGQKRTAFYLADMIL 78
                                   566788888..88889999999765.8999***************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 775.25
//
Query:       gi|116754627|ref|YP_843745.1|  [L=224]
Description: hypothetical protein Mthe_1329 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1780.86
//
Query:       gi|116754628|ref|YP_843746.1|  [L=195]
Description: phosphatidylserine decarboxylase related protein [Methanosaeta thermophila PT]
Scores for complete 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-27   95.7   0.2    3.6e-23   82.2   0.1    2.1  2  PS_Dcarbxylase  Phosphatidylserine decarboxylase
     0.0072   16.3   0.0      0.055   13.4   0.0    2.1  2  RnfC_N          RnfC Barrel sandwich hybrid domain
  ------ inclusion threshold ------
      0.017   15.3   0.0        4.5    7.6   0.0    3.1  3  Peptidase_M23   Peptidase family M23


Domain annotation for each model (and alignments):
>> PS_Dcarbxylase  Phosphatidylserine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   1.4e-05     0.086       2      34 ..      38      68 ..      37      73 .. 0.88
   2 !   82.2   0.1     6e-27   3.6e-23      71     199 ..      71     190 ..      68     191 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.4e-05
                 PS_Dcarbxylase  2 neffvrklkdgaRpidddpgaivsPaDgrilqi 34
                                   ++f++ +++d++R + +++g ++sPaDgri++ 
  gi|116754628|ref|YP_843746.1| 38 TAFMIHFHRDPERFP-EGEG-MLSPADGRIVEA 68
                                   589**********99.8887.*********987 PP

  == domain 2  score: 82.2 bits;  conditional E-value: 6e-27
                 PS_Dcarbxylase  71 yfvviyLspgdyHryhaPvsgkveerrhipGellsvnpsalkelrglftlneRvvlvie.wkGkvavvpvGatnvgsivl 149
                                     ++ i+++p d+H+++aP +g+v++++   G+    +p++ + l     +n   +++ie + G++ + +++++ ++++v+
  gi|116754628|ref|YP_843746.1|  71 KHIYIFMGPMDVHVNRAPLDGVVRSVEFRGGD---HSPAFRHPL-----KNAHSIIEIEsEMGRFTLKQISGMAARRVVC 142
                                    5789**********************999999...555555555.....899*******559****************** PP

                 PS_Dcarbxylase 150 nvlkgdelkkGeelGyFqfGStvvlvfeagkfieslvekgqkvkmGeklg 199
                                    +v++gd+l++G+++G+++fGS v++  ++g  ++   +kg +v++G++++
  gi|116754628|ref|YP_843746.1| 143 WVSPGDRLRRGQRIGMIRFGSGVIVTAPPG--YRIIARKGSRVRAGQTVI 190
                                    ******************************..****************97 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 !   13.4   0.0   9.2e-06     0.055       2      61 ..      97     159 ..      96     175 .. 0.73
   2 ?    0.3   0.0      0.12     7e+02      44      58 ..     175     189 ..     171     194 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.2e-06
                         RnfC_N   2 tfkgGvhppenkels.kekpieklplpkelvlplsqhiGapakpl...vkvgdkVlkGqkiaea 61 
                                    +f+gG h p  ++   ++++i +++  +   + l+q  G++a+ +   v+ gd+ ++Gq+i+  
  gi|116754628|ref|YP_843746.1|  97 EFRGGDHSPAFRHPLkNAHSIIEIES-EMGRFTLKQISGMAARRVvcwVSPGDRLRRGQRIGMI 159
                                    68999998888776514555655554.4457899*****99985522379***********975 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.12
                         RnfC_N  44 plvkvgdkVlkGqki 58 
                                    ++  +g +V+ Gq +
  gi|116754628|ref|YP_843746.1| 175 IIARKGSRVRAGQTV 189
                                    67889********75 PP

>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.019   1.2e+02      11      30 ..      52      71 ..      49      85 .. 0.85
   2 ?    7.6   0.0   0.00075       4.5      31      72 ..     103     159 ..      80     171 .. 0.62
   3 ?    1.3   0.0     0.067     4e+02      57      68 ..     177     188 ..     158     192 .. 0.54

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.019
                                   TTT-EEEESSSEEEEEEEEE CS
                  Peptidase_M23 11 pkgtpVlAaadGtVvfagkk 30
                                   p+g+  l++adG++v+a++k
  gi|116754628|ref|YP_843746.1| 52 PEGEGMLSPADGRIVEADEK 71
                                   6788899*********9885 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00075
                                    T.........TTEEEEEEEECTC..EEEEEEEESEES....S-TTEEE-TTCEEEEE CS
                  Peptidase_M23  31 e.........gyGnvviidhgdg..ystlyahlskis....vkegqkVkaGqvIGtv 72 
                                    +         ++  ++ i+ + g  +   +  + + +    v++g++ ++Gq IG +
  gi|116754628|ref|YP_843746.1| 103 HspafrhplkNAHSIIEIESEMGrfTLKQISGMAARRvvcwVSPGDRLRRGQRIGMI 159
                                    1455555554556666666655533333344444433456799************87 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.067
                                    S-TTEEE-TTCE CS
                  Peptidase_M23  57 vkegqkVkaGqv 68 
                                     ++g +V+aGq+
  gi|116754628|ref|YP_843746.1| 177 ARKGSRVRAGQT 188
                                    345555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1424.54
//
Query:       gi|116754629|ref|YP_843747.1|  [L=213]
Description: CDP-diacylglycerol--serine O-phosphatidyltransferase [Methanosaeta thermophila PT]
Scores for 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-10   39.2   0.6    9.2e-10   39.2   0.6    3.3  2  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
  ------ inclusion threshold ------
       0.78    9.3  10.3      0.024   14.3   2.4    2.1  2  CbiQ             Cobalt transport protein


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 !   39.2   0.6     1e-13   9.2e-10       5      66 .]       8      67 ..       6      67 .. 0.92
   2 ?   -5.0  10.1         2   1.8e+04       6      43 ..     121     137 ..      73     206 .. 0.69

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 1e-13
                                   HHHHHHHHHHHHHHHGGGS-H..HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
                CDP-OH_P_transf  5 aiTllrlllsvlailllltyyplvlailllliasltDalDGklARrlnqvstlGkllDslaD 66
                                   +++l++ +++++a++ l+ ++   l +l+l++a+l+D+ DG +ARr +q s+lG  lDslaD
  gi|116754629|ref|YP_843747.1|  8 LLSLMNAISGFSAMI-LAHLQIRDLSVLMLMAAALFDGADGIVARRSEQ-SELGPHLDSLAD 67
                                   799***********6.55777789***********************88.***********9 PP

  == domain 2  score: -5.0 bits;  conditional E-value: 2
                                    HHHHHHHHHHHHHHGGGS-H..HHHHHHHHHHHHHTTH CS
                CDP-OH_P_transf   6 iTllrlllsvlailllltyyplvlailllliasltDal 43 
                                    iT ++l+l+                     +++l+D+l
  gi|116754629|ref|YP_843747.1| 121 ITAAGLMLG---------------------VSMLLDSL 137
                                    444455444.....................44444432 PP

>> CbiQ  Cobalt transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   2.4   2.7e-06     0.024      56     122 ..      88     156 ..      64     162 .. 0.78
   2 ?   -1.1   1.6      0.13   1.2e+03      27      47 ..     177     197 ..     150     210 .. 0.45

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.7e-06
                                    HHCCCHCHHHHHHHHHHE.......EECTTEEE...E-TTHHHHHHHHHHHHHHHHHHHHH.....HHHHS- CS
                           CbiQ  56 alilpllflllgllillfqlittegefvfagggqisitseGllrglllalRiltllsllll.....lalTTp 122
                                     l+l  l +l g+l l++ +i+++++  f g+    it  Gl+ g++++l +l+++s+l++     ++ T p
  gi|116754629|ref|YP_843747.1|  88 LLMLSALYMLCGMLRLARYNISPKEWAHFEGLP---ITAAGLMLGVSMLLDSLIFTSCLMIllsalMVSTLP 156
                                    345567888889999999***************...*****************9999999955554444544 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.13
                                    -HHHHHHHHHHHHHHHHHTTS CS
                           CbiQ  27 apnlvtlliiiallllllllv 47 
                                    +++l++ ++ ++++++l+ ++
  gi|116754629|ref|YP_843747.1| 177 LSALHLSGMRASAIVILISMA 197
                                    222222222222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); 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):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1684.68
//
Query:       gi|116754630|ref|YP_843748.1|  [L=108]
Description: hypothetical protein Mthe_1332 [Methanosaeta thermophila PT]
Scores for complete 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-42  142.5   0.0      7e-42  142.3   0.0    1.0  1  DHNA      Dihydroneopterin aldolase
  ------ inclusion threshold ------
       0.11   12.3   0.0       0.15   11.9   0.0    1.2  1  Ski2_N    Ski2 N-terminal region


Domain annotation for each model (and alignments):
>> DHNA  Dihydroneopterin aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.3   0.0   7.8e-46     7e-42       1     108 []       3     108 .]       3     108 .] 0.98

  Alignments for each domain:
  == domain 1  score: 142.3 bits;  conditional E-value: 7.8e-46
                                    -HHHHHHHHHHHHHHHHHHHHTT-EESTTTHHHHHHHHHHHHHTSTTEEEEEEEE-S-..GGCC-STS-EE--TTTEEEE CS
                           DHNA   1 tdrerAvFEagiklgalyHqfvGtPvseesaeslekaieesielQPfvedvkvkidrekleekleefgYteLtgemldve 80 
                                    t re A+FEagiklgalyHqfvGtPvs ++a+sle+aie+si+lQP+v++v+v+idr++l+ ++  fgY+eL+g+m+++ 
  gi|116754630|ref|YP_843748.1|   3 TPREIAAFEAGIKLGALYHQFVGTPVSVKTADSLERAIERSISLQPYVKSVSVRIDRSMLSGNV--FGYSELSGKMIRAA 80 
                                    57999********************************************************999..************** PP

                                    EEEEETTEEEEEEEEEETTTTEEEEEEE CS
                           DHNA  81 itvkyeeaevkarleyieeldYplmkve 108
                                    +++ ye+a+v+a ley+ e+dYp+m++e
  gi|116754630|ref|YP_843748.1|  81 VEIAYEGARVRAVLEYDPEKDYPMMHLE 108
                                    *************************975 PP

>> Ski2_N  Ski2 N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.7e-05      0.15      11      45 ..      38      72 ..      29      82 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.7e-05
                         Ski2_N 11 kdyksllkippsasrtslefkRkgleGkivgykev 45
                                   + ++  + ++p  ++ s++ +R+ l+G++ gy+e 
  gi|116754630|ref|YP_843748.1| 38 RAIERSISLQPYVKSVSVRIDRSMLSGNVFGYSEL 72
                                   567888999*************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 786.43
//
Query:       gi|116754631|ref|YP_843749.1|  [L=371]
Description: hypothetical protein Mthe_1333 [Methanosaeta thermophila PT]
Scores for complete 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-179  596.9   0.0   1.6e-179  596.7   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 !  596.7   0.0  8.9e-184  1.6e-179       1     361 []       3     368 ..       3     368 .. 0.99

  Alignments for each domain:
  == domain 1  score: 596.7 bits;  conditional E-value: 8.9e-184
                       FBPase_3   1 kvtlsvikaDvGslaGhtkvheellekveevleeakkkgllidfyvtkvGDDielimthtkgvdneevhklawdafkeat 80 
                                    kvt+s+ikaDvG+++Gh++vh++l++k+eevl+eak++g+lidf+v+++GDD+el+mth+ g+d+ e+h +aw++f++at
  gi|116754631|ref|YP_843749.1|   3 KVTVSLIKADVGGWPGHASVHPALIDKAEEVLSEAKSAGTLIDFKVMACGDDLELLMTHRLGTDEAEIHAIAWETFEKAT 82 
                                    89****************************************************************************** PP

                       FBPase_3  81 evakelklygaGqDlLkdafsGnvkGlGPgvaelefeeRksepvvvfaaDktepgafnlplykifadpfntaGlvidpkl 160
                                    + ak+lklygaGqDlL dafsGn++G+GPgvae++f+eR++ep+v f++Dktepgafnlp++++fadpfntaGlvidp+l
  gi|116754631|ref|YP_843749.1|  83 AEAKSLKLYGAGQDLLCDAFSGNIRGMGPGVAEMQFTERDAEPLVAFMMDKTEPGAFNLPIFRMFADPFNTAGLVIDPSL 162
                                    ******************************************************************************** PP

                       FBPase_3 161 heGfkfevlDvieekkillsapeelydllallgakeryvikrvysk.....kdeeiaavvsterlsliaGkYvGkDDPva 235
                                    h+Gf fe++D+ ++kk+ +s+pee+y++lal+gak+ryvikrvy k      +ee++avvste+l ++aG+YvGkDDPva
  gi|116754631|ref|YP_843749.1| 163 HNGFIFEIWDILDHKKVFMSCPEEMYNILALIGAKSRYVIKRVYPKpggklPSEEPVAVVSTEKLYQTAGTYVGKDDPVA 242
                                    **********************************************998877899************************* PP

                       FBPase_3 236 ivRaqsglPavgevlepfalphlvaGwmrGshngplmPvslkdakptrfdgpprvvalgfqlkegklvgpvDlfddpafd 315
                                    +vRaqsglPa+gevlepfal hlv+GwmrGshngplmP++++da+ptrfdgpprv+a gfql++g l+gpvDlf+d afd
  gi|116754631|ref|YP_843749.1| 243 LVRAQSGLPALGEVLEPFALGHLVSGWMRGSHNGPLMPCAFEDAHPTRFDGPPRVIAAGFQLCNGLLIGPVDLFADVAFD 322
                                    ******************************************************************************** PP

                       FBPase_3 316 eaRekaaeiadelRrqGpfephrlpeeeleYttlpevleklkerfe 361
                                     +R ++ ei+d++R++Gpfephrlp e++eYttlp+vl++l+erfe
  gi|116754631|ref|YP_843749.1| 323 LTRMRVLEITDYMRAHGPFEPHRLPLEDMEYTTLPHVLKRLAERFE 368
                                    ********************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       242  (0.0134977); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); 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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2863.51
//
Query:       gi|116754632|ref|YP_843750.1|  [L=202]
Description: hypothetical protein Mthe_1334 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0061   16.4   0.1      0.023   14.6   0.0    2.0  3  Clathrin  Region in Clathrin and VPS
  ------ inclusion threshold ------
       0.35   11.8   2.4        2.7    9.1   0.2    3.4  4  TPR_14    Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> Clathrin  Region in Clathrin and VPS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   2.6e-06     0.023      75     134 ..      31      90 ..       9      97 .. 0.88
   2 ?   -1.3   0.0      0.21   1.9e+03      93     118 ..      95     120 ..      91     125 .. 0.81
   3 ?   -2.9   0.0      0.63   5.6e+03     100     117 ..     146     163 ..     129     169 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.6e-06
                                    HHHHHHHT-SSHHHHHHHHHTTXTHSSHSSXSSSSHCSCHHHHTTTTTXXSHHHHHHHHH CS
                       Clathrin  75 kvaklcekadlyeeavilykkinefkkaisllkklkdfddaieyaakvsnpelwekllea 134
                                     +++l+  a+ +e av+l + ++++++a+++l + +d+  a+++ + + +pe +e+ll+ 
  gi|116754632|ref|YP_843750.1|  31 PAIDLLLRANEIEYAVVLCREHGMIQRAVDILVDAGDYLWAAQITKSAGSPEEAERLLRS 90 
                                    578999999**********************9999****************999999875 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.21
                                    HHTTXTHSSHSSXSSSSHCSCHHHHT CS
                       Clathrin  93 ykkinefkkaisllkklkdfddaiey 118
                                    y  ++++ +ais +  l++++d+i++
  gi|116754632|ref|YP_843750.1|  95 YISMEMYGRAISAATALNLPPDQIDA 120
                                    77889999999998999999988875 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 0.63
                                    SSHSSXSSSSHCSCHHHH CS
                       Clathrin 100 kkaisllkklkdfddaie 117
                                      a+ +l+++++ ++++ 
  gi|116754632|ref|YP_843750.1| 146 MSAVAMLETDEEVKRELM 163
                                    456666666666666663 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.4   1.2e+04      18      27 ..      30      39 ..      21      43 .. 0.76
   2 ?   -1.6   0.0       0.8   7.2e+03      12      25 ..      50      63 ..      38      71 .. 0.66
   3 ?    9.1   0.2    0.0003       2.7       4      29 ..      68      93 ..      59     125 .. 0.91
   4 ?    0.4   0.1      0.18   1.6e+03      16      40 ..     134     161 ..     116     165 .. 0.54

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.4
                         TPR_14 18 deAiallrra 27
                                   + Ai+ll ra
  gi|116754632|ref|YP_843750.1| 30 EPAIDLLLRA 39
                                   5688888877 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.8
                         TPR_14 12 lalGdpdeAiallr 25
                                   ++ G  ++A+++l 
  gi|116754632|ref|YP_843750.1| 50 REHGMIQRAVDILV 63
                                   55566666666654 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0003
                         TPR_14  4 llalaeallalGdpdeAiallrrala 29
                                   +l +a++   +G p+eA++llr  l+
  gi|116754632|ref|YP_843750.1| 68 YLWAAQITKSAGSPEEAERLLRSGLE 93
                                   56677888889***********9986 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 0.18
                         TPR_14  16 dpdeAiallrr...alalaPddaeawll 40 
                                    d+ +A a+l+    a+a   +d+e+ ++
  gi|116754632|ref|YP_843750.1| 134 DLSRAHAALESmmsAVAMLETDEEVKRE 161
                                    4555555555522234444555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       935  (0.0521501); expected 358.6 (0.02)
Passed bias filter:                      702  (0.0391544); 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: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1446.92
//
Query:       gi|116754633|ref|YP_843751.1|  [L=636]
Description: serine phosphatase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-23   82.6   0.0    5.7e-23   81.8   0.0    1.4  1  SpoIIE    Stage II sporulation protein E (SpoIIE)
    2.3e-15   57.1   0.1    3.7e-15   56.4   0.1    1.3  1  dCache_1  Cache domain


Domain annotation for each model (and alignments):
>> SpoIIE  Stage II sporulation protein E (SpoIIE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.8   0.0   6.4e-27   5.7e-23       2     177 ..     462     625 ..     461     635 .. 0.91

  Alignments for each domain:
  == domain 1  score: 81.8 bits;  conditional E-value: 6.4e-27
                                    TTEEEEEEEECSSSSHHHHHHHHHHHHHHHHHHHTTTSHHHHHHHHHHHCHCTTSTT.TTCEEEEEEEETTTTEEEEEEE CS
                         SpoIIE   2 dgrlalvvgDvvGhGleAalimgllrsalrelataglepaevlkrlnralardleeeerfaTavlavydpstgkleyana 81 
                                    +g++al +g + G  +e+a++++ +r ++r+l +++  p+ev+kr+n++la++  +    +++++av+d  +g+l y+na
  gi|116754633|ref|YP_843751.1| 462 HGKVALCMGRANGEEMESAVLAAIARAVIRALPSQH--PDEVIKRANSILAKSSSSP---ISCFYAVLDHGQGELVYSNA 536
                                    588999**************************9998..9***********6555555...******************** PP

                                    SSSSEEEEETTSTEEEEE--SS--TTTSSST-EEEEEEE--TTEEEEEESCCCCSSSHHHHHHCCCHHCHHHHCT..... CS
                         SpoIIE  82 GhpppllvrpdggtklllastglplGilpeadyetaelelepgdtlllyTDGvtEardsdgelfgkerllallasaeges 161
                                    Gh pp++v++ +g +  l + g+p+ i ++++   ++ ++ +gd+l++y+ G++Ea+    ++ ++erl+ +++ ++++s
  gi|116754633|ref|YP_843751.1| 537 GHAPPFVVSR-DGSVDTLCGDGIPMTIRDDLKLGYERRPISKGDVLVIYSEGMIEAQ----GF-DLERLIGVARGSRTKS 610
                                    **********.77888889*************************************9....44.7799******999999 PP

                                    HCCHHHHHHHHHHHHT CS
                         SpoIIE 162 leelldalveellelg 177
                                    ++e++d + +++ + g
  gi|116754633|ref|YP_843751.1| 611 ASEIADDIERAVPK-G 625
                                    *******9999988.3 PP

>> dCache_1  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.4   0.1   4.1e-19   3.7e-15      11     248 ..      61     294 ..      58     295 .. 0.83

  Alignments for each domain:
  == domain 1  score: 56.4 bits;  conditional E-value: 4.1e-19
                       dCache_1  11 llglaeqlanniedvldslenlaetlasnpslqdlleepnra...neasreslqallksilksnpdisgvylvdadGqvi 87 
                                    ++ ++ ++a + e++++++   ++++  +  ++++++ ++r    n    + l ++l    k+n+ i+ +yl++adG++ 
  gi|116754633|ref|YP_843751.1|  61 QELIVSSKAMQYEEFFRRIA-ESNQFVADY-AASGFSDIDRVadpN----SPLSQTLARAIKRNSAIERIYLATADGRI- 133
                                    67788999999999999986.677777765.566778777745432....468899999999****************9. PP

                       dCache_1  88 assdpssppnleg...tddpadrdwykealaggggkpvisdpyvdqtggkpvitiavpiyddsgkfiGvlaadldldnlq 164
                                     +s+p++++  ++     + ++ +wy++a a+g   +v+ +     + ++  +++a+p y  + +   v+a  ++l++l+
  gi|116754633|ref|YP_843751.1| 134 -ASWPETDGIRNYainASELRSLGWYNAAQAAG--GTVWIP-----G-DEMHMMCATPAYW-NITLYCVAASEVSLSDLY 203
                                    .57777776665598978888899*********..799993.....5.9***********8.699999999999999999 PP

                       dCache_1 165 dllsniklgetgyvfivdsdGniiahpd...kdl.......lgknlrdelkaq.ealekalakiesgvssvklngeeylv 233
                                    + ls ++  ++gy fiv+++G +++ p+     +       l +nl++++ +    l ++++k +sg+ + +++g+ ++v
  gi|116754633|ref|YP_843751.1| 204 SDLSMLR--GSGYPFIVNRSGDVVMIPKvrrG-DapwdnllLSGNLYKSNISAlAELGDRISKGKSGSDYLMIDGRGWFV 280
                                    9999997..569***************98651.15667788666666665544889**********************99 PP

                       dCache_1 234 ayapiptglgWylvv 248
                                     y+p+++  gW++vv
  gi|116754633|ref|YP_843751.1| 281 VYSPVKS-VGWTVVV 294
                                    9*****8.******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (636 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); 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 0.30s 00:00:00.90 Elapsed: 00:00:00.45
# Mc/sec: 4255.27
//
Query:       gi|116754634|ref|YP_843752.1|  [L=126]
Description: 4Fe-4S ferredoxin, iron-sulfur binding [Methanosaeta thermophila PT]
Scores for complete 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   18.9  13.8     0.0017   18.1   1.8    3.7  4  Fer4         4Fe-4S binding domain
     0.0031   18.2   1.5      0.074   13.8   1.5    2.5  1  Fer4_15      4Fe-4S single cluster domain
      0.004   17.7   2.5      0.004   17.7   2.5    2.3  2  Fer4_13      4Fe-4S single cluster domain of Ferredoxin I
     0.0078   16.2   1.4     0.0078   16.2   1.4    3.6  4  Fer4_6       4Fe-4S binding domain
     0.0092   16.0   0.7     0.0092   16.0   0.7    3.3  4  Fer4_2       4Fe-4S binding domain
  ------ inclusion threshold ------
      0.011   15.9   4.4       0.06   13.5   0.1    2.8  3  Fer4_10      4Fe-4S dicluster domain
       0.02   14.3   3.6       0.14   11.6   0.0    2.9  2  zf-ribbon_3  zinc-ribbon domain
      0.087   13.8   3.9        2.9    8.9   0.6    2.7  2  Fer4_16      4Fe-4S double cluster binding domain
      0.091   12.9   6.3        1.1    9.5   0.1    2.9  2  Fer4_9       4Fe-4S dicluster domain
        0.4   11.6   0.0        0.4   11.6   0.0    3.0  3  zf-C2H2_4    C2H2-type zinc finger
       0.47   11.1  10.1         17    6.1  10.1    2.9  1  Fer4_7       4Fe-4S dicluster domain
        1.1    9.3   0.1        1.1    9.3   0.1    3.1  3  zf-C2HC_2    zinc-finger of a C2HC-type
        1.9    8.6   9.1         17    5.6   9.1    2.5  1  DZR          Double zinc ribbon


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 !   18.1   1.8   1.2e-06    0.0017       2      15 ..       2      15 ..       1      17 [. 0.89
   2 !    7.7   0.1    0.0024       3.3      16      24 .]      46      54 ..      45      54 .. 0.85
   3 ?   -0.7   0.2         1   1.4e+03       7      12 ..      70      75 ..      66      76 .. 0.71
   4 ?   -0.7   0.1         1   1.4e+03       6      11 ..     101     106 ..      99     108 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.2e-06
                                   EEETTTSSS-THHH CS
                           Fer4  2 videekCigCGaCv 15
                                   +ide kCigC aC 
  gi|116754634|ref|YP_843752.1|  2 KIDEKKCIGCRACS 15
                                   79***********6 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0024
                                   HHSTTTEEE CS
                           Fer4 16 evCPvgAIt 24
                                   e CP+gAI+
  gi|116754634|ref|YP_843752.1| 46 ETCPTGAIS 54
                                   78*****96 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1
                                   TSSS-T CS
                           Fer4  7 kCigCG 12
                                   +C  CG
  gi|116754634|ref|YP_843752.1| 70 RCSICG 75
                                   677777 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 1
                                    TTSSS- CS
                           Fer4   6 ekCigC 11 
                                    ++C +C
  gi|116754634|ref|YP_843752.1| 101 DLCPNC 106
                                    678777 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 !   13.8   1.5   5.4e-05     0.074       2      64 ..       2      53 ..       1      55 [. 0.65

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.4e-05
                        Fer4_15  2 vvDrdaCigcglCvaeapevfeldedglasvllddgeiaegevpddeeeaaqeAaraCPvdAI 64
                                   ++D+++Cigc +C a ++ +   +++ + s++               e+ +++  ++CP++AI
  gi|116754634|ref|YP_843752.1|  2 KIDEKKCIGCRACSAISSSISISEDAEMRSITFH-----------PHEDLTDRLIETCPTGAI 53
                                   69*************9876655555566666542...........233344444555666665 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 !   17.7   2.5   2.9e-06     0.004       1      57 [.       3      54 ..       3      55 .. 0.79
   2 ?   -2.8   0.0       7.1   9.8e+03       9      18 ..      71      76 ..      69      88 .. 0.57

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.9e-06
                        Fer4_13  1 VDrdtCiacgaCvelaPdvFeeddeggasvvaeqptseeekadaeeAadaCPvesIg 57
                                   +D+++Ci+c aC ++   +   +d  ++  ++ +p+    +++  + +++CP+ +I 
  gi|116754634|ref|YP_843752.1|  3 IDEKKCIGCRACSAISSSISISEDA-EMRSITFHPH----EDLTDRLIETCPTGAIS 54
                                   89****************9766666.5555666677....346677799*****996 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 7.1
                        Fer4_13  9 cgaCvelaPd 18
                                   c +C     +
  gi|116754634|ref|YP_843752.1| 71 CSIC----GE 76
                                   3333....33 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   1.4   5.7e-06    0.0078       3      17 ..       2      16 ..       1      17 [. 0.88
   2 ?    3.7   0.1     0.052        71      17      24 .]      46      53 ..      45      53 .. 0.85
   3 ?   -3.3   0.3       8.3   1.1e+04      13      15 ..      72      74 ..      69      76 .. 0.50
   4 ?    1.8   0.5      0.21   2.9e+02       7      14 ..     101     108 ..     100     108 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.7e-06
                         Fer4_6  3 eidpdkCigCgdCvr 17
                                    id+ kCigC++C +
  gi|116754634|ref|YP_843752.1|  2 KIDEKKCIGCRACSA 16
                                   69***********76 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.052
                         Fer4_6 17 rvCPegai 24
                                     CP+gai
  gi|116754634|ref|YP_843752.1| 46 ETCPTGAI 53
                                   57*****8 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 8.3
                         Fer4_6 13 gdC 15
                                     C
  gi|116754634|ref|YP_843752.1| 72 SIC 74
                                   333 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.21
                         Fer4_6   7 dkCigCgd 14 
                                    d+C  C++
  gi|116754634|ref|YP_843752.1| 101 DLCPNCRR 108
                                    89****86 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.7   6.7e-06    0.0092       4      17 ..       2      15 ..       1      17 [. 0.88
   2 ?   -2.0   0.1       3.5   4.8e+03      19      22 .]      47      50 ..      45      50 .. 0.73
   3 ?   -1.3   0.8       2.2   3.1e+03      12      16 ..      70      74 ..      69      75 .. 0.80
   4 ?    0.7   0.3      0.51   7.1e+02       8      14 ..     101     107 ..     100     108 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6.7e-06
                         Fer4_2  4 vvdtdrCigCgaCv 17
                                   ++d+ +CigC+aC 
  gi|116754634|ref|YP_843752.1|  2 KIDEKKCIGCRACS 15
                                   79***********4 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.5
                         Fer4_2 19 aCPa 22
                                    CP+
  gi|116754634|ref|YP_843752.1| 47 TCPT 50
                                   6997 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 2.2
                         Fer4_2 12 gCgaC 16
                                   +C++C
  gi|116754634|ref|YP_843752.1| 70 RCSIC 74
                                   68888 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.51
                         Fer4_2   8 drCigCg 14 
                                    d C +C+
  gi|116754634|ref|YP_843752.1| 101 DLCPNCR 107
                                    6799997 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   4.3e-05      0.06       2      17 ..       1      16 [.       1      40 [. 0.91
   2 ?    3.2   0.0      0.07        96      18      49 ..      47      75 ..      41      81 .. 0.80
   3 ?   -0.8   0.1       1.2   1.7e+03      19      48 ..     103     106 ..      96     121 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.3e-05
                        Fer4_10  2 vvidddtCirCgkCvk 17
                                   ++id+++Ci+C++C +
  gi|116754634|ref|YP_843752.1|  1 MKIDEKKCIGCRACSA 16
                                   579***********86 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.07
                        Fer4_10 18 aCPadltsvgakgeaseeeavrkkvekCtgcg 49
                                    CP+   +   ++ ++e+ +    +++C  cg
  gi|116754634|ref|YP_843752.1| 47 TCPT---GAISSALTTESITLAFRMKRCSICG 75
                                   7999...7777777888888888999999887 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.2
                        Fer4_10  19 CPadltsvgakgeaseeeavrkkvekCtgc 48 
                                    CP                          +c
  gi|116754634|ref|YP_843752.1| 103 CP--------------------------NC 106
                                    22..........................22 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   9.9e-05      0.14       2      15 ..      68      82 ..      67      84 .. 0.78
   2 ?    1.4   1.4      0.16   2.3e+02      19      22 ..     103     106 ..     102     106 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.9e-05
                    zf-ribbon_3  2 tvrCPnCGa.plssd 15
                                   ++rC+ CG+  ++++
  gi|116754634|ref|YP_843752.1| 68 MKRCSICGEpFATER 82
                                   99*******557665 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.16
                    zf-ribbon_3  19 CpyC 22 
                                    Cp+C
  gi|116754634|ref|YP_843752.1| 103 CPNC 106
                                    5555 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1     0.028        38      53      61 ..       7      15 ..       2      34 .. 0.72
   2 ?    8.9   0.6    0.0021       2.9       9      60 ..      45     106 ..      45     108 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.028
                        Fer4_16 53 aitgCdiCq 61
                                   +++gC++C 
  gi|116754634|ref|YP_843752.1|  7 KCIGCRACS 15
                                   455666654 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0021
                        Fer4_16   9 aevCPtnaikek.kekeiearecisy.........ntaekkdlaedeekckkqeaitgCdiC 60 
                                    +e+CPt+ai++  + ++i     ++          +++e + +a    ++ ++ ++  C +C
  gi|116754634|ref|YP_843752.1|  45 IETCPTGAISSAlTTESITLAFRMKRcsicgepfaTEREIEHVAALMPARFQKSWLDLCPNC 106
                                    589*******9865555655555555556677776555555555555555557788888888 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1    0.0008       1.1       1      10 [.       7      16 ..       2      39 .. 0.71
   2 ?    3.8   2.5     0.047        65      10      41 ..      46      76 ..      45     121 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0008
                         Fer4_9  1 kCtgCgaCve 10
                                   kC+gC+aC +
  gi|116754634|ref|YP_843752.1|  7 KCIGCRACSA 16
                                   5666666655 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.047
                         Fer4_9 10 eaCpagvvvedaaerkarlraaseeaCigCga 41
                                   e Cp+g+++    ++ + l  +  ++C  Cg+
  gi|116754634|ref|YP_843752.1| 46 ETCPTGAISSALTTESITLAFRM-KRCSICGE 76
                                   67999999999999999986655.48988985 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.5       3.1   4.3e+03       3       6 ..      11      14 ..       6      21 .. 0.57
   2 ?   11.6   0.0   0.00029       0.4       2      20 ..      70      87 ..      69      90 .. 0.85
   3 ?   -0.6   0.3       2.5   3.4e+03       3       8 ..     103     108 ..     102     109 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 3.1
                      zf-C2H2_4  3 CpiC 6 
                                   C+ C
  gi|116754634|ref|YP_843752.1| 11 CRAC 14
                                   4445 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00029
                      zf-C2H2_4  2 kCpiCgksFsskkaLlrHl 20
                                   +C+iCg++F + ++   H+
  gi|116754634|ref|YP_843752.1| 70 RCSICGEPFATERE-IEHV 87
                                   7**********999.6666 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 2.5
                      zf-C2H2_4   3 CpiCgk 8  
                                    Cp C++
  gi|116754634|ref|YP_843752.1| 103 CPNCRR 108
                                    9***75 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1  10.1     0.012        17       1      42 [.       7      75 ..       1     122 [. 0.67

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.012
                         Fer4_7  1 rCigCgaCvaaC.........pvkaieldeeenek..................gtekveidpekClgCg 42
                                   +CigC+aC a            ++ i+++++e+                    +  ++++++ +C+ Cg
  gi|116754634|ref|YP_843752.1|  7 KCIGCRACSAISssisisedaEMRSITFHPHEDLTdrlietcptgaissalttESITLAFRMKRCSICG 75
                                   799999999998666666655333333333322223333333333333333222244477788888886 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 ?    9.3   0.1   0.00078       1.1       2      20 ..      68      86 ..      67      89 .. 0.82
   2 ?    2.2   0.9      0.13   1.8e+02       5      10 ..     103     108 ..     102     109 .. 0.91
   3 ?   -3.2   0.2       6.2   8.5e+03      20      24 ..     115     119 ..     115     119 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00078
                      zf-C2HC_2  2 lvpCpkCgRsFnpdrlekH 20
                                   +  C +Cg  F+++r   H
  gi|116754634|ref|YP_843752.1| 68 MKRCSICGEPFATEREIEH 86
                                   679*********9995555 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.13
                      zf-C2HC_2   5 CpkCgR 10 
                                    Cp+C R
  gi|116754634|ref|YP_843752.1| 103 CPNCRR 108
                                    ****98 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 6.2
                      zf-C2HC_2  20 HepvC 24 
                                    H ++C
  gi|116754634|ref|YP_843752.1| 115 HARQC 119
                                    88898 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   9.1     0.012        17      12      40 ..      68     112 ..       2     120 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.012
                            DZR  12 arfCseCgtklkavaa................edrCpsCgekvdp 40 
                                     + Cs Cg++   + +                 d Cp+C ++ + 
  gi|116754634|ref|YP_843752.1|  68 MKRCSICGEPFATEREiehvaalmparfqkswLDLCPNCRRDGQR 112
                                    578*******976555899999*****************998654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       728  (0.0406046); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); 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):              13  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 949.58
//
Query:       gi|116754635|ref|YP_843753.1|  [L=147]
Description: 4Fe-4S ferredoxin iron-sulfur binding domain-containing protein [Methanosaeta thermophila PT]
Scores for 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-15   54.0  31.2    1.2e-08   34.7   2.2    4.3  4  Fer4_6    4Fe-4S binding domain
    5.6e-14   51.3  32.2    9.6e-10   37.9   2.2    5.2  6  Fer4      4Fe-4S binding domain
    6.7e-10   38.5  34.3    5.3e-06   26.2   2.1    4.3  4  Fer4_2    4Fe-4S binding domain
      1e-09   38.4  10.4      1e-09   38.4  10.4    1.9  2  Fer4_11   4Fe-4S dicluster domain
    1.4e-09   38.4  29.0     0.0029   18.2   4.1    4.0  5  Fer4_7    4Fe-4S dicluster domain
    7.2e-08   32.5  26.5    0.00082   19.5  10.6    3.4  4  Fer4_9    4Fe-4S dicluster domain
    1.7e-07   31.2  27.4    0.00091   19.3   9.3    3.5  2  Fer4_10   4Fe-4S dicluster domain
    2.7e-07   30.6  34.8    0.00066   20.0   3.3    4.5  4  Fer4_4    4Fe-4S binding domain
    1.2e-05   26.2  24.8     0.0065   17.4   4.4    4.3  4  Fer4_16   4Fe-4S double cluster binding domain
    2.9e-05   24.1  27.6      0.019   15.1   9.3    3.4  3  Fer4_21   4Fe-4S dicluster domain
    0.00041   21.0  14.3     0.0077   16.9   1.3    3.4  3  Fer4_15   4Fe-4S single cluster domain
     0.0042   17.9   5.9     0.0042   17.9   5.9    4.4  4  Fer4_3    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.059   13.9   1.6      0.059   13.9   1.6    4.2  4  Fer4_17   4Fe-4S dicluster domain
       0.66   10.5  32.1        3.5    8.2   9.4    4.0  2  Fer4_8    4Fe-4S dicluster domain
        3.7    8.2  20.8       0.33   11.5   1.1    3.5  3  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I


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 !   21.4   1.7   1.5e-07   0.00018       5      20 ..       7      22 ..       3      27 .. 0.90
   2 ?    5.5   2.3     0.016        19       9      22 ..      45      60 ..      41      62 .. 0.86
   3 !   34.7   2.2   9.8e-12   1.2e-08       2      24 .]      69      91 ..      68      91 .. 0.96
   4 !    9.8   2.5   0.00074      0.88       7      24 .]      98     120 ..      96     120 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.5e-07
                         Fer4_6  5 dpdkCigCgdCvrvCP 20
                                   dp++CigC+ C+++C 
  gi|116754635|ref|YP_843753.1|  7 DPERCIGCRSCEVACE 22
                                   9**************6 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.016
                         Fer4_6  9 CigCgd..CvrvCPeg 22
                                   C +C+   C++vC +g
  gi|116754635|ref|YP_843753.1| 45 CHQCDTspCTAVCYTG 60
                                   999*9999*****887 PP

  == domain 3  score: 34.7 bits;  conditional E-value: 9.8e-12
                         Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                   v++d+d+C+ Cg Cv++CP+gai
  gi|116754635|ref|YP_843753.1| 69 VAFDQDLCTRCGLCVVACPFGAI 91
                                   89********************8 PP

  == domain 4  score: 9.8 bits;  conditional E-value: 0.00074
                         Fer4_6   7 dkCigC.gd....CvrvCPegai 24 
                                    ++C+ C ++    Cv+ CP+ a+
  gi|116754635|ref|YP_843753.1|  98 QRCDLCiEKetpiCVMTCPAEAL 120
                                    689999888999********996 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   3.3   4.8e-08   5.8e-05       1      18 [.       4      21 ..       4      24 .. 0.91
   2 ?   -1.2   0.1       1.7   2.1e+03      10      14 ..      44      48 ..      43      50 .. 0.69
   3 ?   -0.1   0.0      0.76   9.1e+02      14      22 ..      53      61 ..      53      63 .. 0.81
   4 !   37.9   2.2   8.1e-13   9.6e-10       2      24 .]      70      92 ..      69      92 .. 0.94
   5 ?    0.2   0.1      0.65   7.8e+02      10      16 ..      99     105 ..      98     106 .. 0.73
   6 !    8.3   0.5    0.0018       2.1      13      23 ..     110     120 ..     110     121 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 4.8e-08
                                   EEEETTTSSS-THHHHHS CS
                           Fer4  1 vvideekCigCGaCvevC 18
                                   ++ d+e+CigC  C+ +C
  gi|116754635|ref|YP_843753.1|  4 IYLDPERCIGCRSCEVAC 21
                                   589*************** PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.7
                                   S-THH CS
                           Fer4 10 gCGaC 14
                                   +C +C
  gi|116754635|ref|YP_843753.1| 44 YCHQC 48
                                   67777 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.76
                                   HHHHSTTTE CS
                           Fer4 14 CvevCPvgA 22
                                   C  vC +g 
  gi|116754635|ref|YP_843753.1| 53 CTAVCYTGS 61
                                   999**9885 PP

  == domain 4  score: 37.9 bits;  conditional E-value: 8.1e-13
                                   EEETTTSSS-THHHHHSTTTEEE CS
                           Fer4  2 videekCigCGaCvevCPvgAIt 24
                                    +d+++C++CG+Cv +CP+gAI+
  gi|116754635|ref|YP_843753.1| 70 AFDQDLCTRCGLCVVACPFGAIE 92
                                   58********************6 PP

  == domain 5  score: 0.2 bits;  conditional E-value: 0.65
                                    S-THHHH CS
                           Fer4  10 gCGaCve 16 
                                    +C +C+e
  gi|116754635|ref|YP_843753.1|  99 RCDLCIE 105
                                    5888876 PP

  == domain 6  score: 8.3 bits;  conditional E-value: 0.0018
                                    HHHHHSTTTEE CS
                           Fer4  13 aCvevCPvgAI 23 
                                    +Cv+ CP +A+
  gi|116754635|ref|YP_843753.1| 110 ICVMTCPAEAL 120
                                    6*********8 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   2.5   3.7e-08   4.5e-05       2      20 ..       3      21 ..       2      23 .. 0.93
   2 ?    1.0   4.1      0.46   5.5e+02      10      20 ..      45      57 ..      41      59 .. 0.78
   3 !   26.2   2.1   4.5e-09   5.3e-06       3      21 ..      69      87 ..      67      88 .. 0.93
   4 ?    5.8   2.6     0.013        16       9      22 .]      99     117 ..      97     117 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 3.7e-08
                         Fer4_2  2 pvvvdtdrCigCgaCvsaC 20
                                   +++ d++rCigC++C  aC
  gi|116754635|ref|YP_843753.1|  3 KIYLDPERCIGCRSCEVAC 21
                                   799**************** PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.46
                         Fer4_2 10 CigC..gaCvsaC 20
                                   C +C  ++C+ +C
  gi|116754635|ref|YP_843753.1| 45 CHQCdtSPCTAVC 57
                                   5578445****9* PP

  == domain 3  score: 26.2 bits;  conditional E-value: 4.5e-09
                         Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                   v++d d C++Cg Cv aCP
  gi|116754635|ref|YP_843753.1| 69 VAFDQDLCTRCGLCVVACP 87
                                   789**************** PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.013
                         Fer4_2   9 rCigC..g...aCvsaCPa 22 
                                    rC  C  +   +Cv  CPa
  gi|116754635|ref|YP_843753.1|  99 RCDLCieKetpICVMTCPA 117
                                    89999862577*******8 PP

>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.4      0.55   6.5e+02       3      25 ..       4      24 ..       2      35 .. 0.63
   2 !   38.4  10.4   8.5e-13     1e-09       5      99 ..      40     124 ..      37     125 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.55
                        Fer4_11  3 wlflpeqCrhCleppCvasapse 25
                                   +++ pe C  C   +C  ++++e
  gi|116754635|ref|YP_843753.1|  4 IYLDPERCIGCR--SCEVACERE 24
                                   566788888885..466666555 PP

  == domain 2  score: 38.4 bits;  conditional E-value: 8.5e-13
                        Fer4_11   5 flpeqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivrkneetgkvekCdmcldrveaGllp 84 
                                     +p +C++C + pC a++ ++++  d    +V +d++ +  ++  +v acP+ ++      +++++Cd+c+++ +    p
  gi|116754635|ref|YP_843753.1|  40 AVPVYCHQCDTSPCTAVCYTGSLRLDG--DMVAFDQDLCT-RCGLCVVACPFGAIEL---RSMIQRCDLCIEKET----P 109
                                    5799****************9999998..79********8.************9976...56789*******998....* PP

                        Fer4_11  85 acvescptgalnfgd 99 
                                    +cv +cp++al++gd
  gi|116754635|ref|YP_843753.1| 110 ICVMTCPAEALRLGD 124
                                    ************998 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   3.0   1.2e-05     0.015      30      48 ..       3      21 ..       1      25 [. 0.76
   2 !   11.9  15.0   0.00022      0.26       1      51 [.      10      60 ..      10      61 .. 0.81
   3 !   17.5  13.4   3.9e-06    0.0046       2      52 .]      45      90 ..      44      90 .. 0.91
   4 !   18.2   4.1   2.4e-06    0.0029       2      20 ..      76      94 ..      75     101 .. 0.89
   5 !   10.6   0.6   0.00056      0.67       2      25 ..     100     128 ..      99     140 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.2e-05
                         Fer4_7 30 kveidpekClgCgaCvavC 48
                                   k+++dpe+C+gC++C+ +C
  gi|116754635|ref|YP_843753.1|  3 KIYLDPERCIGCRSCEVAC 21
                                   6778888888888888888 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00022
                         Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCga..CvavCPtg 51
                                   rCigC+ C++aC  +    + +     + +++ +p +C +C+   C avC tg
  gi|116754635|ref|YP_843753.1| 10 RCIGCRSCEVACEREHGHPRISVGI--VGDLAAVPVYCHQCDTspCTAVCYTG 60
                                   8***********9665555444333..36999**********999*****887 PP

  == domain 3  score: 17.5 bits;  conditional E-value: 3.9e-06
                         Fer4_7  2 CigCg..aCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                   C +C    C+a+C ++ ++ld +        v++d++ C+ Cg Cv +CP+ga
  gi|116754635|ref|YP_843753.1| 45 CHQCDtsPCTAVCYTGSLRLDGD-------MVAFDQDLCTRCGLCVVACPFGA 90
                                   89995559************886.......489******************98 PP

  == domain 4  score: 18.2 bits;  conditional E-value: 2.4e-06
                         Fer4_7  2 CigCgaCvaaCpvkaield 20
                                   C+ Cg Cv+aCp +aiel+
  gi|116754635|ref|YP_843753.1| 76 CTRCGLCVVACPFGAIELR 94
                                   ****************986 PP

  == domain 5  score: 10.6 bits;  conditional E-value: 0.00056
                         Fer4_7   2 CigC.....gaCvaaCpvkaieldeeene 25 
                                    C  C       Cv +Cp++a++l ++++ 
  gi|116754635|ref|YP_843753.1| 100 CDLCieketPICVMTCPAEALRLGDVDVV 128
                                    55554333359***********9887654 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9  12.2     4e-05     0.047       1      49 [.      10      60 ..      10      62 .. 0.82
   2 !   19.5  10.6   6.8e-07   0.00082       1      51 []      44      91 ..      44      91 .. 0.86
   3 !   13.3  10.3   5.8e-05      0.07       2      50 ..      76     119 ..      75     120 .. 0.79
   4 !    7.7   0.7    0.0032       3.9       2      26 ..     100     129 ..      98     137 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4e-05
                         Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCga..CveaCpkg 49
                                   +C+gC++C+ aC+ ++  ++ + +++   aa    C++C +  C+++C +g
  gi|116754635|ref|YP_843753.1| 10 RCIGCRSCEVACEREHGHPRISVGIVGDLAAVPVYCHQCDTspCTAVCYTG 60
                                   6***********88888777777776665555578*************876 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 6.8e-07
                         Fer4_9  1 kCtgCga..CveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                   +C +C++  C+++C +g  + d       ++      C+ Cg Cv aCp gai
  gi|116754635|ref|YP_843753.1| 44 YCHQCDTspCTAVCYTGSLRLDGDMVAFDQD-----LCTRCGLCVVACPFGAI 91
                                   6999*8777*****99999998888777763.....6************9987 PP

  == domain 3  score: 13.3 bits;  conditional E-value: 5.8e-05
                         Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCga.....CveaCpkga 50 
                                    Ct+Cg Cv aCp+g+++ ++  +   l       Ci   +     Cv  Cp +a
  gi|116754635|ref|YP_843753.1|  76 CTRCGLCVVACPFGAIELRSMIQRCDL-------CI---EketpiCVMTCPAEA 119
                                    ****************99887666443.......55...445599999999876 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.0032
                         Fer4_9   2 CtgCga.....CveaCpagvvvedaaerka 26 
                                    C  C +     Cv  Cpa++ +  ++    
  gi|116754635|ref|YP_843753.1| 100 CDLCIEketpiCVMTCPAEALRLGDVDVVS 129
                                    777733344569999999998887776555 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9  10.0   1.8e-05     0.021       1      55 [.       3      57 ..       3      58 .. 0.80
   2 !   19.3   9.3   7.6e-07   0.00091       2      56 .]      69     116 ..      68     142 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.8e-05
                        Fer4_10  1 kvvidddtCirCgkCvkaCPadltsvgakgeaseeeavrk..kvekCtgcg..aCveaC 55
                                   k+++d+++Ci+C+ C  aC    ++  + + +s + + +   ++  C++c    C+++C
  gi|116754635|ref|YP_843753.1|  3 KIYLDPERCIGCRSCEVAC----EREHGHPRISVGIVGDLaaVPVYCHQCDtsPCTAVC 57
                                   5789***************....46666666666666554458999****7679***** PP

  == domain 2  score: 19.3 bits;  conditional E-value: 7.6e-07
                        Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgc...g..aCveaCP 56 
                                    v +d+d C+rCg Cv aCP+        g+++     r  +++C+ c   +   Cv  CP
  gi|116754635|ref|YP_843753.1|  69 VAFDQDLCTRCGLCVVACPF--------GAIEL----RSMIQRCDLCiekEtpICVMTCP 116
                                    6789****************........44444....44445566664332568999998 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   3.3   5.5e-07   0.00066       1      15 [.       8      22 ..       8      29 .. 0.93
   2 ?    3.7   3.6     0.095   1.1e+02       4      14 ..      45      57 ..      43      60 .. 0.92
   3 !   19.7   2.2   6.9e-07   0.00082       1      17 []      73      89 ..      73      89 .. 0.93
   4 ?    4.7   2.5     0.045        53       3      16 ..     102     117 ..      98     126 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 5.5e-07
                         Fer4_4  1 qerCigCgsCvaaCP 15
                                   +erCigC+sC+ aC+
  gi|116754635|ref|YP_843753.1|  8 PERCIGCRSCEVACE 22
                                   69************8 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.095
                         Fer4_4  4 CigCgs..CvaaC 14
                                   C +C+   C+a+C
  gi|116754635|ref|YP_843753.1| 45 CHQCDTspCTAVC 57
                                   99***99****** PP

  == domain 3  score: 19.7 bits;  conditional E-value: 6.9e-07
                         Fer4_4  1 qerCigCgsCvaaCPqg 17
                                   q+ C++Cg Cv aCP+g
  gi|116754635|ref|YP_843753.1| 73 QDLCTRCGLCVVACPFG 89
                                   799************86 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.045
                         Fer4_4   3 rCigCgs..CvaaCPq 16 
                                     Ci+     Cv +CP 
  gi|116754635|ref|YP_843753.1| 102 LCIEKETpiCVMTCPA 117
                                    466555566******6 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   2.9     0.027        33       1      12 [.      10      21 ..       7      25 .. 0.78
   2 !    7.2   0.4    0.0082       9.8       2      20 ..      45      65 ..      44      73 .. 0.85
   3 !   17.4   4.4   5.5e-06    0.0065       2      24 ..      76      96 ..      75     109 .. 0.79
   4 !    7.2   1.0    0.0079       9.5       7      20 ..     110     123 ..      98     139 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.027
                        Fer4_16  1 rCgtCgkCaevC 12
                                   rC++C+ C  +C
  gi|116754635|ref|YP_843753.1| 10 RCIGCRSCEVAC 21
                                   588888888888 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0082
                        Fer4_16  2 CgtCgk..CaevCPtnaikek 20
                                   C++C    C+ vC t+ ++ +
  gi|116754635|ref|YP_843753.1| 45 CHQCDTspCTAVCYTGSLRLD 65
                                   ****9889*******999877 PP

  == domain 3  score: 17.4 bits;  conditional E-value: 5.5e-06
                        Fer4_16  2 CgtCgkCaevCPtnaikekkeke 24
                                   C++Cg C+ +CP +ai+ +   +
  gi|116754635|ref|YP_843753.1| 76 CTRCGLCVVACPFGAIELR--SM 96
                                   ****************998..33 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.0079
                        Fer4_16   7 kCaevCPtnaikek 20 
                                     C+++CP++a++  
  gi|116754635|ref|YP_843753.1| 110 ICVMTCPAEALRLG 123
                                    5*********9987 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   9.3   1.6e-05     0.019       3      51 ..       6      57 ..       4      64 .. 0.85
   2 !   15.0   9.5   1.7e-05      0.02       8      58 ..      45      92 ..      41      93 .. 0.72
   3 !   10.5  10.8   0.00044      0.52       3      55 ..      71     118 ..      69     122 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.6e-05
                        Fer4_21  3 idedkCigCgkCliaCe.dtshqaieidaktvlkvvedeCvGCnl..CssvC 51
                                   +d+++CigC +C +aCe + +h  i++     l+ v   C  C+   C++vC
  gi|116754635|ref|YP_843753.1|  6 LDPERCIGCRSCEVACErEHGHPRISVGIVGDLAAVPVYCHQCDTspCTAVC 57
                                   689*************8467999**998888888889999999865599999 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.7e-05
                        Fer4_21  8 CigCgk..CliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58
                                   C +C    C+ +C +     +++d+  +++  +d C+ C lC+  CP  ++ie
  gi|116754635|ref|YP_843753.1| 45 CHQCDTspCTAVCYT---GSLRLDG-DMVAFDQDLCTRCGLCVVACPF-GAIE 92
                                   555543337777774...3456664.466999***************7.9987 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.00044
                        Fer4_21   3 idedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCn..lCssvCPved 55 
                                    +d+d C  Cg+C++aC+     aie+ +   +  + d C+  +  +C+  CP  +
  gi|116754635|ref|YP_843753.1|  71 FDQDLCTRCGLCVVACP---FGAIELRS---MIQRCDLCIEKEtpICVMTCPA-E 118
                                    68999999999999999...66776642...2334566654332278888885.4 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 !   11.7   0.6   0.00029      0.34       1      19 [.       4      22 ..       4      35 .. 0.89
   2 !   16.9   1.3   6.5e-06    0.0077       1      19 [.      69      87 ..      69      95 .. 0.91
   3 ?   -0.2   0.1       1.4   1.7e+03      58      65 ..     114     121 ..     108     122 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00029
                        Fer4_15  1 VvvDrdaCigcglCvaeap 19
                                   +++D ++Cigc  C  +++
  gi|116754635|ref|YP_843753.1|  4 IYLDPERCIGCRSCEVACE 22
                                   799***********99985 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 6.5e-06
                        Fer4_15  1 VvvDrdaCigcglCvaeap 19
                                   V +D+d+C+ cglCv ++p
  gi|116754635|ref|YP_843753.1| 69 VAFDQDLCTRCGLCVVACP 87
                                   789***************8 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 1.4
                        Fer4_15  58 aCPvdAIr 65 
                                    +CP++A+r
  gi|116754635|ref|YP_843753.1| 114 TCPAEALR 121
                                    79999986 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   4.6    0.0054       6.5       1      11 [.      11      21 ..      11      23 .. 0.97
   2 ?    4.0   4.4     0.096   1.2e+02       1      11 [.      45      57 ..      45      60 .. 0.85
   3 !   17.9   5.9   3.5e-06    0.0042       1      15 []      76      90 ..      76      90 .. 0.98
   4 ?    4.6   0.5     0.064        77       1      12 [.     100     116 ..     100     119 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0054
                         Fer4_3  1 CtgCgaCvevC 11
                                   C+gC+ C+++C
  gi|116754635|ref|YP_843753.1| 11 CIGCRSCEVAC 21
                                   *********** PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.096
                         Fer4_3  1 CtgCg..aCvevC 11
                                   C++C   +C  vC
  gi|116754635|ref|YP_843753.1| 45 CHQCDtsPCTAVC 57
                                   ****5459***** PP

  == domain 3  score: 17.9 bits;  conditional E-value: 3.5e-06
                         Fer4_3  1 CtgCgaCvevCPvgA 15
                                   Ct Cg+Cv++CP gA
  gi|116754635|ref|YP_843753.1| 76 CTRCGLCVVACPFGA 90
                                   *************98 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.064
                         Fer4_3   1 CtgC.g....aCvevCP 12 
                                    C+ C +     Cv  CP
  gi|116754635|ref|YP_843753.1| 100 CDLCiEketpICVMTCP 116
                                    99995344434*****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 ?   11.3   1.9   0.00032      0.38      44      58 ..       9      23 ..       3      26 .. 0.86
   2 ?    2.7   2.2      0.16   1.9e+02       2      15 ..      45      60 ..      44      73 .. 0.83
   3 ?   13.9   1.6     5e-05     0.059      44      58 ..      74      88 ..      63      91 .. 0.80
   4 ?    1.4   2.3      0.41   4.9e+02      42      59 ..      99     118 ..      90     120 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00032
                        Fer4_17 44 slCieCgeCerkCPq 58
                                   ++Ci+C+ Ce +C  
  gi|116754635|ref|YP_843753.1|  9 ERCIGCRSCEVACER 23
                                   689999999999975 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.16
                        Fer4_17  2 CiqCgy..ClpeCpsy 15
                                   C+qC    C+++C ++
  gi|116754635|ref|YP_843753.1| 45 CHQCDTspCTAVCYTG 60
                                   99**9888**999865 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 5e-05
                        Fer4_17 44 slCieCgeCerkCPq 58
                                   +lC+ Cg+C+ +CP 
  gi|116754635|ref|YP_843753.1| 74 DLCTRCGLCVVACPF 88
                                   679999999999985 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.41
                        Fer4_17  42 kaslCieCge..CerkCPqg 59 
                                    +++lCie +   C++ CP++
  gi|116754635|ref|YP_843753.1|  99 RCDLCIEKETpiCVMTCPAE 118
                                    45556654434499999975 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3  14.7      0.19   2.3e+02       3      63 ..       9      59 ..       7      61 .. 0.69
   2 ?    8.2   9.4    0.0029       3.5       4      18 ..      75      89 ..      72     143 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.19
                         Fer4_8  3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcga..CtevCpv 63
                                   e+Ci+C  C+ aC       +++ ++r  +   v +  +        +C++c    Ct vC +
  gi|116754635|ref|YP_843753.1|  9 ERCIGCRSCEVACE------REHGHPRISVGI-VGDLAA-----VPVYCHQCDTspCTAVCYT 59
                                   69***********3......444444444444.333333.....4679999998899999965 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0029
                         Fer4_8  4 kCieCgaCqsaCpvl 18
                                    C++Cg+C  aCp+ 
  gi|116754635|ref|YP_843753.1| 75 LCTRCGLCVVACPFG 89
                                   588888888888854 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   2.6    0.0042         5       2      16 ..       7      21 ..       6      23 .. 0.89
   2 ?   11.5   1.1   0.00028      0.33       2      17 ..      72      87 ..      71      88 .. 0.96
   3 ?   -1.0   2.5       2.3   2.7e+03      11      17 ..     110     116 ..      99     119 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0042
                        Fer4_13  2 DrdtCiacgaCvela 16
                                   D ++Ci+c +C  ++
  gi|116754635|ref|YP_843753.1|  7 DPERCIGCRSCEVAC 21
                                   889********9888 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00028
                        Fer4_13  2 DrdtCiacgaCvelaP 17
                                   D+d C+ cg+Cv ++P
  gi|116754635|ref|YP_843753.1| 72 DQDLCTRCGLCVVACP 87
                                   899************9 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 2.3
                        Fer4_13  11 aCvelaP 17 
                                    +Cv+++P
  gi|116754635|ref|YP_843753.1| 110 ICVMTCP 116
                                    5999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1130.92
//
Query:       gi|116754636|ref|YP_843754.1|  [L=662]
Description: formate dehydrogenase, alpha subunit [Methanosaeta thermophila PT]
Scores for complete 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-79  268.0   0.0    1.8e-79  267.7   0.0    1.1  1  Molybdopterin    Molybdopterin oxidoreductase
    2.1e-23   82.4   0.0    4.1e-23   81.5   0.0    1.5  1  Molydop_binding  Molydopterin dinucleotide binding domain
    3.5e-12   46.1   0.3      9e-12   44.8   0.3    1.7  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 !  267.7   0.0     3e-83   1.8e-79       1     431 [.      54     467 ..      54     468 .. 0.89

  Alignments for each domain:
  == domain 1  score: 267.7 bits;  conditional E-value: 3e-83
                                    B--S-EEECTTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEEEEEBTSSCSHHHHHHHHHHHHHTT-EEE-BEECC CS
                  Molybdopterin   1 RlkyPmvRkqargeGkFvrvsWdeAleliaaslkytikkygpdrvagfssgplmsmeslaslkkllsllggknlsfydwy 80 
                                    Rl+yPm+R    g++ + rvsWdeAl+ +a++++++  + gp++ a+ +s + + +e+ ++++k ++l+g    +++d++
  gi|116754636|ref|YP_843754.1|  54 RLRYPMMR---VGKD-WIRVSWDEALDRVAEEMEKVLRERGPKALAFLGSAKCT-NEENYIFQKIARLMGT---NNIDNC 125
                                    9*******...6554.******************************99998888.999999***9999998...788888 PP

                                    GGGTTHHHHCHHCCCCCTTTS-SS-CCGGGG-SEEEEESS-HHHHSHHHHHHHHHHHHTTC-EEEEECSSB-HCGGGCSE CS
                  Molybdopterin  81 adlppasaqqtigsdsrsnyessnpledlensdliilwGsNvreerpilnarirkaalkkkakvivigpryaellkfade 160
                                    a+ +++ +  ++  +   +++++np++dl+ sd i+++GsN++e++p++ ar + +a+ ++a viv +pr++ ++  ad+
  gi|116754636|ref|YP_843754.1| 126 ARRCHSPTIIALREM-LGTPAMTNPISDLALSDCILVIGSNLAENHPVV-ARWILRAKDRGAVVIVADPRVTPTSWLADL 203
                                    888875554455444.568999***************************.88888889989************7788*** PP

                                    EEEEHTTTHHHHHHHHHHHHHHCCCCTCHHHHHHEECHHHCCCCCCCEECCSHHHHHHCCHHHHHHHHHHHHHHTSSEEE CS
                  Molybdopterin 161 wlaikpgtdaalalamghvilqelkvdkeflrkytygkeetdmpllvtleeetgkkkevvariarelarnaaktagksmi 240
                                    ++ ++pgtd al+++m +vil+e+++  +f++ +t g+e++d  l  +++e+++++++  a  +++ ar +a     s i
  gi|116754636|ref|YP_843754.1| 204 HMQLNPGTDIALINGMINVILREGLEKRAFINERTIGFENLD--LRDYTPERVSAITGLSAGDIIRAARLYARSPA-SSI 280
                                    ***************************************998..6799******************9999998888.777 PP

                                    EECHHHHTSTTHHHHHHHHHHHHHHCTHCSSTTCEEEEESSCTTHHHCHHHHTCCTTCCCCCCCTT......HHHHHCCC CS
                  Molybdopterin 241 ivGaglnhrqdgdaiyravinLallvgnvgqpgGgwahlnGqlilagaaekvgalpvllsvkslke......ekikfaae 314
                                    ++ +g+++++ g+++++a +nLal +g++g+pg+g + l+Gq++++g a+++gal+  ++  +++e         +++  
  gi|116754636|ref|YP_843754.1| 281 VYCMGITQHTCGTDNVAACANLALVCGQIGRPGAGIFPLRGQNNVQG-ACDMGALADFYPGWRSVEdsraidDLRRLW-- 357
                                    77*********************************************.******************555443333333.. PP

                                    TTTCSTSS--ECGGCHHHHHHTTSSSEEEEESH.HHHHSTTSCCCHCHHHCSSEEEEEESCSSHHHHTSSEEEEBE-CCG CS
                  Molybdopterin 315 qpgnlgnfprnlfversnllkssgkkvlyllgnnpevdhadenevekalekldlvvvldgrltstalyaDiiLPaatwyE 394
                                       n    p  +   +++l+ + ++k+ly++g +++v+   ++ +     k  + vv d+++t+ta+ aD++LPa++w E
  gi|116754636|ref|YP_843754.1| 358 ---NARSLPMGRGL-TADLMPDADLKFLYVMG-EDIVNSDPTVSR--RRLKRGFMVVQDIFMTDTAKLADLVLPATAWAE 430
                                    ...33444444454.5788899**********.555555555555..3559***************************** PP

                                    SEEEEE-TTSEEEEEEESSS-STT-BEHHHHHHHHHH CS
                  Molybdopterin 395 kedlytndegrfqhlkqavsppgeaksdwkIlkaLak 431
                                    ke++ t++e+r+q + +a +ppgea+ d +Il+++a 
  gi|116754636|ref|YP_843754.1| 431 KEGTITSTERRVQWIYRAGEPPGEARMDLWILSEVAA 467
                                    **********************************986 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.5   0.0   6.9e-27   4.1e-23       1     110 [.     551     654 ..     551     655 .. 0.97

  Alignments for each domain:
  == domain 1  score: 81.5 bits;  conditional E-value: 6.9e-27
                                    EEEEEE-BTTBSTTTTTCGCCHHHHCSSS.-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEEEEESS CS
                Molydop_binding   1 lrLitgrsldqlhsqtrtrpvlrlakpep.evveinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvvfmpfg 79 
                                    l+Litgr+  +++s+ +t++++ l k+ep   + +np+dA + G++dGd V ve+r+G++++ra++t++ ++G++fmpf+
  gi|116754636|ref|YP_843754.1| 551 LILITGRVALHYNSGSMTMRSEGLVKREPeIHIDVNPDDAMRFGLADGDAVMVETRWGRARARAQITQGQKRGTLFMPFH 630
                                    79***************************99************************************************* PP

                                    HCC.....S-GHCTS--SCSTTT--CSTT-E CS
                Molydop_binding  80 wweagekggnaNaltddatdplsgtpefksv 110
                                    ++e       +N + ++ +d  + +pe+k++
  gi|116754636|ref|YP_843754.1| 631 FPE-------TNLIASELLDRKAMMPELKVA 654
                                    ***.......99999************9975 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   0.3   1.5e-15     9e-12       4      55 .]       5      51 ..       3      51 .. 0.95

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 1.5e-15
                                   EEEE-SSBTT--EEEEEEETTEEEEEEE-TTSTTTTT---HHHHTCHHCCCB CS
                 Molybdop_Fe4S4  4 vktaCpyCgvgCglevhvkdgkivkvegdpdhpvnegrlCvKGrtllervyn 55
                                   ++t+CpyC vgCg+ ++ ++ +       pdhpvneg lC+KG+++l+++++
  gi|116754636|ref|YP_843754.1|  5 TPTVCPYCAVGCGFYITRNGMEY-----MPDHPVNEGALCAKGNAALDILNH 51
                                   89*****************9999.....9*******************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (662 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); 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: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 4598.49
//
Query:       gi|116754637|ref|YP_843755.1|  [L=168]
Description: 4Fe-4S ferredoxin iron-sulfur binding domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-15   57.1  10.0    1.5e-15   57.1  10.0    2.0  2  Fer4_11        4Fe-4S dicluster domain
      5e-12   46.2  27.1      2e-06   28.3   9.3    3.1  4  Fer4_7         4Fe-4S dicluster domain
    9.4e-12   44.9  22.8    1.8e-05   24.8   8.8    2.7  2  Fer4_9         4Fe-4S dicluster domain
    9.9e-10   37.8  39.1    0.00015   21.5   2.7    5.5  6  Fer4           4Fe-4S binding domain
    1.7e-09   37.4  37.6     0.0021   18.0   2.4    4.7  4  Fer4_6         4Fe-4S binding domain
    2.5e-09   37.1  26.6    0.00039   20.5  10.8    3.3  3  Fer4_10        4Fe-4S dicluster domain
    9.8e-09   36.0  21.0      0.046   14.7   1.1    4.4  4  Fer4_16        4Fe-4S double cluster binding domain
    1.2e-08   34.5  33.4      0.012   15.6   2.4    4.3  4  Fer4_2         4Fe-4S binding domain
    4.4e-07   29.9  32.6     0.0073   16.7   4.0    4.4  4  Fer4_4         4Fe-4S binding domain
     0.0056   16.4  20.7      0.041   13.7   0.4    3.6  3  Fer4_20        Dihydroprymidine dehydrogenase domain II, 4Fe-
     0.0073   17.2  43.0      0.048   14.6   6.5    4.3  4  Fer4_3         4Fe-4S binding domain
     0.0095   16.5  24.7       0.93   10.1   0.7    4.2  4  Fer4_17        4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.023   14.8  32.2       0.56   10.4  12.5    3.7  3  Fer4_21        4Fe-4S dicluster domain
      0.024   15.1  24.5      0.037   14.5   7.3    3.4  2  Fer4_8         4Fe-4S dicluster domain
       0.12   12.5   0.1       0.25   11.4   0.1    1.6  1  Fe_dep_repr_C  Iron dependent repressor, metal binding and di
        1.8    8.6   6.5         17    5.5   0.1    2.7  2  DUF4033        Domain of unknown function (DUF4033)


Domain annotation for each model (and alignments):
>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.6      0.61   6.8e+02       4      21 ..       5      20 ..       2      34 .. 0.63
   2 !   57.1  10.0   1.4e-18   1.5e-15       6      99 ..      55     143 ..      51     144 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.61
                        Fer4_11  4 lflpeqCrhCleppCvas 21
                                   l+ pe C+ C +  C  +
  gi|116754637|ref|YP_843755.1|  5 LVRPERCMGCRS--CEIA 20
                                   556888888853..3333 PP

  == domain 2  score: 57.1 bits;  conditional E-value: 1.4e-18
                        Fer4_11   6 lpeqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivrkneetgkvekCdmcldrveaGllpa 85 
                                    +p  CrhC+++pCva++p++a+++d   G+V  +++ +  ++ +++++c y ++ +++++ ++ kCd c d       pa
  gi|116754637|ref|YP_843755.1|  55 VPILCRHCEDAPCVAVCPTGALTQDAISGVVRHNKDICI-GCWTCASVCTYGVIGRDRRARVAIKCDRCPDLEV----PA 129
                                    7899**********************************7.*****************************99865....** PP

                        Fer4_11  86 cvescptgalnfgd 99 
                                    cv++cpt+al +gd
  gi|116754637|ref|YP_843755.1| 130 CVSACPTRALIYGD 143
                                    *********99987 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   3.7   0.00011      0.12      33      50 ..       6      23 ..       2      25 .. 0.75
   2 !   28.3   9.3   1.8e-09     2e-06       1      52 []      10      75 ..      10      75 .. 0.63
   3 !   21.2  10.9     3e-07   0.00034       2      52 .]      92     138 ..      91     138 .. 0.87
   4 !   10.4   2.1   0.00069      0.77       1      23 [.     118     145 ..     117     156 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00011
                         Fer4_7 33 idpekClgCgaCvavCPt 50
                                   ++pe+C+gC++C+ +C +
  gi|116754637|ref|YP_843755.1|  6 VRPERCMGCRSCEIACAV 23
                                   678888888888888865 PP

  == domain 2  score: 28.3 bits;  conditional E-value: 1.8e-09
                         Fer4_7  1 rCigCgaCvaaCpvkaield...eeenekgt........ekvei.dpekClgCga..CvavCPtga 52
                                   rC+gC+ C+ aC v+  + +    + +e ++        +++ + +p  C +C+   CvavCPtga
  gi|116754637|ref|YP_843755.1| 10 RCMGCRSCEIACAVEHSQSRdlfRALSEMPQkrlfvehvPEYSLaVPILCRHCEDapCVAVCPTGA 75
                                   8***********8555554411122222222222233225555525888*****999*******98 PP

  == domain 3  score: 21.2 bits;  conditional E-value: 3e-07
                         Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCga..CvavCPtga 52 
                                    CigC  C+++C +++i  d +      ++v+i+ ++C + ++  Cv++CPt a
  gi|116754637|ref|YP_843755.1|  92 CIGCWTCASVCTYGVIGRDRR------ARVAIKCDRCPDLEVpaCVSACPTRA 138
                                    *****************9886......679*******7655444******976 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 0.00069
                         Fer4_7   1 rCigCg.....aCvaaCpvkaieldeee 23 
                                    +C  C      aCv+aCp++a+ + ++e
  gi|116754637|ref|YP_843755.1| 118 KCDRCPdlevpACVSACPTRALIYGDVE 145
                                    688895555669******9998766655 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   6.4   1.6e-08   1.8e-05       1      50 [.      10      75 ..      10      76 .. 0.78
   2 !   24.8   8.8   1.6e-08   1.8e-05       2      50 ..      92     138 ..      91     140 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.6e-08
                         Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase..............eaCigCga..CveaCpkga 50
                                   +C+gC++C+ aC  ++ + ++  r  +   ++                 C +C++  Cv++Cp+ga
  gi|116754637|ref|YP_843755.1| 10 RCMGCRSCEIACAVEHSQSRDLFRALSEMPQKRlfvehvpeyslavpILCRHCEDapCVAVCPTGA 75
                                   6***********8877765555555443333335888888899999999***************97 PP

  == domain 2  score: 24.8 bits;  conditional E-value: 1.6e-08
                         Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCga.....CveaCpkga 50 
                                    C+gC +C ++C +gv+ +d+ +r a        +C  C +     Cv aCp+ a
  gi|116754637|ref|YP_843755.1|  92 CIGCWTCASVCTYGVIGRDRRARVAI-------KCDRCPDlevpaCVSACPTRA 138
                                    ***********************999.......5*****************976 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   3.0     6e-06    0.0067       3      18 ..       6      21 ..       4      21 .. 0.92
   2 ?   -0.5   0.1       1.1   1.2e+03       9      17 ..      57      65 ..      57      65 .. 0.78
   3 !   12.8   0.7   7.2e-05      0.08      14      24 .]      67      77 ..      67      77 .. 0.94
   4 !   21.5   2.7   1.3e-07   0.00015       3      23 ..      87     107 ..      85     108 .. 0.91
   5 ?   -1.6   0.7       2.6   2.9e+03      10      14 ..     118     122 ..     117     122 .. 0.51
   6 !   11.6   0.6   0.00017      0.19      13      23 ..     129     139 ..     129     140 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6e-06
                                   EETTTSSS-THHHHHS CS
                           Fer4  3 ideekCigCGaCvevC 18
                                   + +e+C+gC  C+ +C
  gi|116754637|ref|YP_843755.1|  6 VRPERCMGCRSCEIAC 21
                                   789************* PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.1
                                   SS-THHHHH CS
                           Fer4  9 igCGaCvev 17
                                   i C  C+++
  gi|116754637|ref|YP_843755.1| 57 ILCRHCEDA 65
                                   679999886 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 7.2e-05
                                   HHHHSTTTEEE CS
                           Fer4 14 CvevCPvgAIt 24
                                   Cv vCP+gA+t
  gi|116754637|ref|YP_843755.1| 67 CVAVCPTGALT 77
                                   *********96 PP

  == domain 4  score: 21.5 bits;  conditional E-value: 1.3e-07
                                    EETTTSSS-THHHHHSTTTEE CS
                           Fer4   3 ideekCigCGaCvevCPvgAI 23 
                                     +++ CigC +C++vC +g+I
  gi|116754637|ref|YP_843755.1|  87 HNKDICIGCWTCASVCTYGVI 107
                                    699*************99998 PP

  == domain 5  score: -1.6 bits;  conditional E-value: 2.6
                                    S-THH CS
                           Fer4  10 gCGaC 14 
                                    +C +C
  gi|116754637|ref|YP_843755.1| 118 KCDRC 122
                                    55555 PP

  == domain 6  score: 11.6 bits;  conditional E-value: 0.00017
                                    HHHHHSTTTEE CS
                           Fer4  13 aCvevCPvgAI 23 
                                    aCv++CP+ A+
  gi|116754637|ref|YP_843755.1| 129 ACVSACPTRAL 139
                                    7*******997 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   1.7   1.1e-05     0.012       4      20 ..       6      22 ..       3      27 .. 0.87
   2 !   15.9   4.3   8.7e-06    0.0098       8      24 .]      58      76 ..      57      76 .. 0.94
   3 !   18.0   2.4   1.9e-06    0.0021       1      24 []      84     107 ..      84     107 .. 0.94
   4 ?    4.9   6.0     0.027        30       8      24 .]     118     139 ..     117     139 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-05
                         Fer4_6  4 idpdkCigCgdCvrvCP 20
                                   + p++C gC+ C+++C 
  gi|116754637|ref|YP_843755.1|  6 VRPERCMGCRSCEIACA 22
                                   779*************7 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 8.7e-06
                         Fer4_6  8 kCigCgd..CvrvCPegai 24
                                   +C +C+d  Cv+vCP+ga+
  gi|116754637|ref|YP_843755.1| 58 LCRHCEDapCVAVCPTGAL 76
                                   6****999*********97 PP

  == domain 3  score: 18.0 bits;  conditional E-value: 1.9e-06
                         Fer4_6   1 vveidpdkCigCgdCvrvCPegai 24 
                                    vv++++d CigC  C++vC +g+i
  gi|116754637|ref|YP_843755.1|  84 VVRHNKDICIGCWTCASVCTYGVI 107
                                    799****************99987 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.027
                         Fer4_6   8 kCigC.gd....CvrvCPegai 24 
                                    kC+ C +     Cv++CP+ a+
  gi|116754637|ref|YP_843755.1| 118 KCDRCpDLevpaCVSACPTRAL 139
                                    577774447777*******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 !   15.7   0.2   1.1e-05     0.012       4      30 ..       6      31 ..       3      44 .. 0.69
   2 !   16.0  13.1   8.4e-06    0.0094       8      55 ..      58     102 ..      53     103 .. 0.94
   3 !   20.5  10.8   3.5e-07   0.00039       2      56 .]      85     135 ..      84     135 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-05
                        Fer4_10  4 idddtCirCgkCvkaCPadltsvgakg 30
                                   + +++C++C+ C  aC a  +s++   
  gi|116754637|ref|YP_843755.1|  6 VRPERCMGCRSCEIAC-AVEHSQSRDL 31
                                   6789************.5345555544 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 8.4e-06
                        Fer4_10   8 tCirCg..kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                     C +C+   Cv++CP+     ga  ++ ++++vr++ + C+gc  C+++C
  gi|116754637|ref|YP_843755.1|  58 LCRHCEdaPCVAVCPT-----GALTQDAISGVVRHNKDICIGCWTCASVC 102
                                    6****9999*******.....***************************** PP

  == domain 3  score: 20.5 bits;  conditional E-value: 3.5e-07
                        Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcg..aCveaCP 56 
                                    v++++d Ci+C +C ++C +    +g++  +++ ++v +k+++C++ +  aCv+aCP
  gi|116754637|ref|YP_843755.1|  85 VRHNKDICIGCWTCASVC-T----YGVI-GRDRRARVAIKCDRCPDLEvpACVSACP 135
                                    57899*************.4....4444.456667777889999997777******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 !    8.7   0.4     0.003       3.4      53      65 ..      10      22 ..       4      41 .. 0.73
   2 !   14.7   1.1   4.1e-05     0.046       2      20 ..      59      79 ..      58      90 .. 0.84
   3 !   12.3   3.3   0.00023      0.26       2      28 ..      92     118 ..      91     128 .. 0.85
   4 !   10.7   1.1   0.00071      0.79       7      33 ..     129     155 ..     117     167 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.003
                        Fer4_16 53 aitgCdiCqdvCP 65
                                   +++gC+ C+ +C 
  gi|116754637|ref|YP_843755.1| 10 RCMGCRSCEIACA 22
                                   4555555555554 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 4.1e-05
                        Fer4_16  2 CgtCgk..CaevCPtnaikek 20
                                   C  C+   C+ vCPt+a++++
  gi|116754637|ref|YP_843755.1| 59 CRHCEDapCVAVCPTGALTQD 79
                                   99999889***********98 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00023
                        Fer4_16   2 CgtCgkCaevCPtnaikekkekeiear 28 
                                    C++C  Ca+vC  ++i  +++++++++
  gi|116754637|ref|YP_843755.1|  92 CIGCWTCASVCTYGVIGRDRRARVAIK 118
                                    ******************988777655 PP

  == domain 4  score: 10.7 bits;  conditional E-value: 0.00071
                        Fer4_16   7 kCaevCPtnaikekkekeiearecisy 33 
                                    +C+++CPt+a+     +ei + +  ++
  gi|116754637|ref|YP_843755.1| 129 ACVSACPTRALIYGDVEEISSSKRAES 155
                                    7*********98775666666555544 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   2.4   1.1e-05     0.012       5      20 ..       6      21 ..       2      23 .. 0.86
   2 !   12.2   3.1   0.00014      0.16       9      22 .]      58      73 ..      50      73 .. 0.90
   3 !   13.2   2.6   6.3e-05     0.071       3      21 ..      85     103 ..      83     104 .. 0.87
   4 !   11.4   2.4   0.00024      0.26       9      22 .]     118     136 ..     107     136 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-05
                         Fer4_2  5 vdtdrCigCgaCvsaC 20
                                   v ++rC+gC++C  aC
  gi|116754637|ref|YP_843755.1|  6 VRPERCMGCRSCEIAC 21
                                   5699**********99 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00014
                         Fer4_2  9 rCigCg..aCvsaCPa 22
                                    C +C+  +Cv +CP+
  gi|116754637|ref|YP_843755.1| 58 LCRHCEdaPCVAVCPT 73
                                   5****889*******7 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 6.3e-05
                         Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                    v  + d+CigC +C s+C 
  gi|116754637|ref|YP_843755.1|  85 VRHNKDICIGCWTCASVCT 103
                                    56799*************6 PP

  == domain 4  score: 11.4 bits;  conditional E-value: 0.00024
                         Fer4_2   9 rCigCg.....aCvsaCPa 22 
                                    +C +C      aCvsaCP+
  gi|116754637|ref|YP_843755.1| 118 KCDRCPdlevpACVSACPT 136
                                    79999445688*******7 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   4.0   6.6e-06    0.0073       1      14 [.       8      21 ..       8      24 .. 0.91
   2 !   10.0   1.8   0.00096       1.1       4      17 .]      59      74 ..      51      74 .. 0.91
   3 !    8.1   2.8    0.0038       4.2       2      16 ..      90     104 ..      89     105 .. 0.86
   4 !   11.8   1.5   0.00024      0.27       3      17 .]     118     137 ..     115     141 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.6e-06
                         Fer4_4  1 qerCigCgsCvaaC 14
                                   +erC gC+sC++aC
  gi|116754637|ref|YP_843755.1|  8 PERCMGCRSCEIAC 21
                                   69************ PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00096
                         Fer4_4  4 CigCgs..CvaaCPqg 17
                                   C +C    Cva+CP+g
  gi|116754637|ref|YP_843755.1| 59 CRHCEDapCVAVCPTG 74
                                   99***779******86 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0038
                         Fer4_4   2 erCigCgsCvaaCPq 16 
                                    + CigC  C ++C +
  gi|116754637|ref|YP_843755.1|  90 DICIGCWTCASVCTY 104
                                    67***********76 PP

  == domain 4  score: 11.8 bits;  conditional E-value: 0.00024
                         Fer4_4   3 rCigCg.....sCvaaCPqg 17 
                                    +C +C+     +Cv+aCP++
  gi|116754637|ref|YP_843755.1| 118 KCDRCPdlevpACVSACPTR 137
                                    699999777777******85 PP

>> Fer4_20  Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.9     0.017        19      19      40 ..       6      25 ..       1      38 [. 0.80
   2 ?    5.6   7.1     0.011        13      24      53 ..      59      88 ..      57     102 .. 0.86
   3 !   13.7   0.4   3.6e-05     0.041      20      59 ..     118     157 ..     107     166 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.017
                                   HHHTT----TT-HHHHCSTT-- CS
                        Fer4_20 19 eeAsRClqCkkapcvkgCPvei 40
                                      +RC+ C  + c+ +C ve 
  gi|116754637|ref|YP_843755.1|  6 VRPERCMGC--RSCEIACAVEH 25
                                   56689****..78999999875 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.011
                                   ----TT-HHHHCSTT---HHHHHHHHHTT- CS
                        Fer4_20 24 ClqCkkapcvkgCPveidipefikkiaegn 53
                                   C +C++apcv+ CP+    ++ i+ + ++n
  gi|116754637|ref|YP_843755.1| 59 CRHCEDAPCVAVCPTGALTQDAISGVVRHN 88
                                   99*************998888887776655 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 3.6e-05
                                    HHTT----TT-HHHHCSTT---HHHHHHHHHTT-HHHHHH CS
                        Fer4_20  20 eAsRClqCkkapcvkgCPveidipefikkiaegnleeaak 59 
                                    + +RC + + + cv++CP++  i + +++i++++ +e+a 
  gi|116754637|ref|YP_843755.1| 118 KCDRCPDLEVPACVSACPTRALIYGDVEEISSSKRAESAL 157
                                    567888888999******************9876555443 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   5.0     0.084        94       1      11 [.      11      21 ..      11      24 .. 0.91
   2 !   14.6   6.5   4.3e-05     0.048       1      15 []      59      75 ..      59      75 .. 0.92
   3 ?    5.6   4.0     0.032        36       1      14 [.      92     105 ..      92     106 .. 0.90
   4 !   11.3   3.8   0.00049      0.55       1      15 []     119     138 ..     119     138 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.084
                         Fer4_3  1 CtgCgaCvevC 11
                                   C+gC+ C+ +C
  gi|116754637|ref|YP_843755.1| 11 CMGCRSCEIAC 21
                                   **********9 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 4.3e-05
                         Fer4_3  1 CtgCg..aCvevCPvgA 15
                                   C +C+  +Cv vCP+gA
  gi|116754637|ref|YP_843755.1| 59 CRHCEdaPCVAVCPTGA 75
                                   99**8778********9 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.032
                         Fer4_3   1 CtgCgaCvevCPvg 14 
                                    C+gC +C  vC +g
  gi|116754637|ref|YP_843755.1|  92 CIGCWTCASVCTYG 105
                                    ****77*****987 PP

  == domain 4  score: 11.3 bits;  conditional E-value: 0.00049
                         Fer4_3   1 CtgCg.....aCvevCPvgA 15 
                                    C+ C      aCv +CP++A
  gi|116754637|ref|YP_843755.1| 119 CDRCPdlevpACVSACPTRA 138
                                    99996678999******998 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   2.0    0.0018         2      44      57 ..       9      22 ..       3      26 .. 0.87
   2 !    8.9   0.7    0.0019       2.1       2      20 ..      59      79 ..      58      89 .. 0.81
   3 !   10.1   0.7   0.00083      0.93      44      60 ..      90     106 ..      78     107 .. 0.75
   4 ?    4.7   7.9     0.041        46       2      26 ..      92     116 ..      91     162 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0018
                        Fer4_17 44 slCieCgeCerkCP 57
                                   ++C++C+ Ce +C 
  gi|116754637|ref|YP_843755.1|  9 ERCMGCRSCEIACA 22
                                   68********9995 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0019
                        Fer4_17  2 CiqCgy..ClpeCpsyeaydn 20
                                   C++C+   C+++Cp+++ +++
  gi|116754637|ref|YP_843755.1| 59 CRHCEDapCVAVCPTGALTQD 79
                                   *****889******9988766 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00083
                        Fer4_17  44 slCieCgeCerkCPqgl 60 
                                    + Ci+C  C+++C +g+
  gi|116754637|ref|YP_843755.1|  90 DICIGCWTCASVCTYGV 106
                                    66888888888887765 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.041
                        Fer4_17   2 CiqCgyClpeCpsyeaydnepkkll 26 
                                    Ci+C  C+ +C ++ + ++++++++
  gi|116754637|ref|YP_843755.1|  92 CIGCWTCASVCTYGVIGRDRRARVA 116
                                    9999999999999988777777665 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1  12.0    0.0054         6       3      56 ..       6      75 ..       4      82 .. 0.65
   2 ?   10.4  12.5    0.0005      0.56       8      52 ..      59     103 ..      55     108 .. 0.73
   3 ?    9.0  12.4    0.0013       1.5       4      55 ..      88     138 ..      84     142 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0054
                        Fer4_21  3 idedkCigCgkCliaCedtshqai.......eidaktvl........kvvedeCvGCn..lCssvCPvedc 56
                                   + +++C+gC +C iaC  +  q         e+ +k+ +          v   C  C+   C++vCP+ ++
  gi|116754637|ref|YP_843755.1|  6 VRPERCMGCRSCEIACAVEHSQSRdlfralsEMPQKRLFvehvpeysLAVPILCRHCEdaPCVAVCPT-GA 75
                                   67899***********9776665544565553333332244444332345668999973369999996.55 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0005
                        Fer4_21   8 CigCgk..CliaCedtshqaieida.ktvlkvvedeCvGCnlCssvCP 52 
                                    C +C+   C+ +C++++   ++ da + v+++ +d C+GC  C+svC 
  gi|116754637|ref|YP_843755.1|  59 CRHCEDapCVAVCPTGA---LTQDAiSGVVRHNKDICIGCWTCASVCT 103
                                    777864449*****754...44333034677889*************5 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0013
                        Fer4_21   4 dedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnl..CssvCPved 55 
                                    ++d CigC  C+ +C    +  i  d ++++++  d+C   ++  C+s CP+  
  gi|116754637|ref|YP_843755.1|  88 NKDICIGCWTCASVCT---YGVIGRDRRARVAIKCDRCPDLEVpaCVSACPTRA 138
                                    6899***********9...899*99999999999****7765444******865 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   7.3   3.3e-05     0.037       3      64 ..       9      74 ..       8      75 .. 0.78
   2 ?    6.1   2.3     0.014        15       5      62 ..      92     103 ..      82     106 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.3e-05
                         Fer4_8  3 ekCieCgaCqsaCpvlrrtkkhlldargeaae........dvqeeqvleeeealwsCttcga..CtevCpvg 64
                                   e+C++C  C+ aC v +++ ++l+ a  e  +         + +            C +c+   C+ vCp+g
  gi|116754637|ref|YP_843755.1|  9 ERCMGCRSCEIACAVEHSQSRDLFRALSEMPQkrlfvehvPEYS------LAVPILCRHCEDapCVAVCPTG 74
                                   68***********9888888999999988777555544332223......45689******999******87 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.014
                         Fer4_8   5 CieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCp 62 
                                    Ci+C  C s C                                               
  gi|116754637|ref|YP_843755.1|  92 CIGCWTCASVC----------------------------------------------T 103
                                    66666666666..............................................3 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 ?   11.4   0.1   0.00023      0.25      33      55 ..      16      38 ..       5      50 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00023
                                   HHHHCCCCGGGS-HHHHHHHHHH CS
                  Fe_dep_repr_C 33 aheeAerlEhalseelierldel 55
                                    +e A++ Eh  s++l+++l e+
  gi|116754637|ref|YP_843755.1| 16 SCEIACAVEHSQSRDLFRALSEM 38
                                   699*****************987 PP

>> DUF4033  Domain of unknown function (DUF4033)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.015        17      33      45 ..      59      71 ..      31      79 .. 0.87
   2 ?    3.9   2.8     0.048        53      18      45 ..     107     134 ..      92     139 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.015
                        DUF4033 33 CryLeesgCagvC 45
                                   Cr+ e++ C++vC
  gi|116754637|ref|YP_843755.1| 59 CRHCEDAPCVAVC 71
                                   ************* PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.048
                        DUF4033  18 slekkkeksgvkvkkCryLeesgCagvC 45 
                                    ++++++++ ++k ++C  Le   C++ C
  gi|116754637|ref|YP_843755.1| 107 IGRDRRARVAIKCDRCPDLEVPACVSAC 134
                                    55666777899999*************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); 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: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1183.64
//
Query:       gi|116754638|ref|YP_843756.1|  [L=623]
Description: carbon-monoxide dehydrogenase, catalytic subunit [Methanosaeta thermophila PT]
Scores for complete 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-174  581.1   0.0   2.2e-174  580.9   0.0    1.0  1  Prismane  Prismane/CO dehydrogenase family


Domain annotation for each model (and alignments):
>> Prismane  Prismane/CO dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  580.9   0.0  1.2e-178  2.2e-174       1     510 [.      47     601 ..      47     602 .. 0.99

  Alignments for each domain:
  == domain 1  score: 580.9 bits;  conditional E-value: 1.2e-178
                                    -EE-SSTCT-ECSC....S.SS-TTS-BHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHCHTSTTTB-SHHHHHH CS
                                    xxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Prismane   1 mfCrqCengpCrit....knkrGvCGkdadtavardlliavlkgaaahaahareladtliakalfktltnvnfddekklk 76 
                                    ++Cr+C++gpCri+    ++++GvCG++ad++var+ll+++++gaaaha+har+++  ++++ ++++  +++++de+kl+
  gi|116754638|ref|YP_843756.1|  47 ICCRNCNMGPCRIDpfgdGPDKGVCGATADIIVARNLLRMIAAGAAAHADHARDAVIVFKEALEGRA-RSYQIRDEAKLR 125
                                    6*************************************************************99999.************ PP

                                    HHHHHHCHHHCCSSHHHHHHHHCCHHHCGGGS-SSHHHHHHHCCCHHHHHHHHHHHCHHTT-HHHHHHHHHHHCCCCTTS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Prismane  77 rlaealgieeelkdieelaakvaevaledlskeenedirslkellpkglkglyaehaivlgyadeevveflaktlagles 156
                                    +la++++i + +  ++  aa++a++ l+d++++e    ++l+ ++p+++++++++++i ++++d+e+ve++++t++g+++
  gi|116754638|ref|YP_843756.1| 126 ELAAEYNISSWG--EQGGAADLANALLSDFGRQE--GYVTLTRRAPEKRRKIWESLGISPRGIDREIVECMHRTHMGVDN 201
                                    ***********9..9999*************996..******************************************** PP

                                    THHHHHHHHHHHHHHH.HHHHHHHHHHHHHHH-----EEEEECGCG-.SSSEEEEEESS-HHHHHHHHHHHCTTCCCCCC CS
                                    xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Prismane 157 dpldllskalrlGlld.lkgmelldeantslfGtPeppltevnlgvldkdkvnIlvsGHdladleelleqtegkglnvyt 235
                                    dpl++l++ lr++++d ++ +++++e++++lfGtP+p+++e+nlgvl++d+vnI+v+GH++ ++e+++e+++++++ + +
  gi|116754638|ref|YP_843756.1| 202 DPLHILQHGLRTSIADgWGSSMIATEVQDILFGTPSPRRSEANLGVLKEDEVNIIVHGHEPILSEMIVEAASDPEMIKLA 281
                                    ******************************************************************************** PP

                                    C.....GCCCCCCHHHHHHHHHCCEEEEECSSGGGHHHHHCCHECEEEESSSS--TTHHHHHHCHCCEEEEECTTB-.TT CS
                                    x.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                       Prismane 236 h.....gemLpghcctalklkyrhlvgnvGnawqqekaeftgavdaivvdtnCivpplasvaekyktrlittsevak.pg 309
                                    +     g++++g+cct++++ +rh+++++Gn++qqe+a++tgav+a+vvd++Ci+p+l  +a++y+t++i+ts++a  pg
  gi|116754638|ref|YP_843756.1| 282 KsvganGINVAGICCTGNEVLMRHGIPVAGNFLQQELAVITGAVEAMVVDVQCIMPSLGGLAACYHTKFISTSPKAEfPG 361
                                    ******************************************************************************** PP

                                    SEEE-.-CTTCHHHHHHHHHHHHCCHCCTTCGG.-............................HHHHHTTSS-EEEEE-B CS
                                    xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................xxxxxxxxxxxxxxxxx RF
                       Prismane 310 akhie.eeekadkdaseiiekAielakareekkve............................idaiksGtIkgvvlvvG 360
                                    a ++e +ee+a + a+ei+++A+e++++r+  +v                             idai++G Ikg+++vvG
  gi|116754638|ref|YP_843756.1| 362 ALRMEfSEERAAEIAREIVRTAVENYPKRDRGRVLiprersecmvgfsveailkalggtpqplIDAIVNGSIKGIAAVVG 441
                                    *****999*********************998888999****************************************** PP

                                    ---TTCGCC.HHHHHHHHCHHTTEEEEEECHHHHHCCCTTTTECGHHHHSTHC.........EESEEEEESCCCHHHHHH CS
                                    xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxx RF
                       Prismane 361 Cdnakkgrd.yytelakelikrdvlvltaGCakyalnklglgtieaaelageg.........iPrvLdvGsCvdnyrivv 430
                                    C+n+k  +d  +++l++eli+++vlv+t+GC+++a++k+gl+ ++aa+ ag+g         +P+vL++GsCvd++ri+v
  gi|116754638|ref|YP_843756.1| 442 CNNPKVPHDhGHVNLVRELIRNNVLVVTTGCNAIACAKAGLLRPAAAKEAGDGlrgvceslgVPPVLHMGSCVDISRILV 521
                                    *********9********************************************************************** PP

                                    HHHHHHHHTTSSGGGSSEEEEECC--SHHHHHHHHHHHHTT-CEEECSS-TTTT-HHHHHHHHCHHHHHHCEEEECHCHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Prismane 431 ialklaealgvdindLplaalalewyeqKAvailltllalGinihlgptlpafgspnvlkvlvedfedriggivtveedp 510
                                    +a+++a++lgvdi+dLp+a +a+ew+++KAv+i+++++a+G+ ++lg+++p++gsp v+++l++d+ d +g+++ ve+dp
  gi|116754638|ref|YP_843756.1| 522 VAAAIANKLGVDISDLPVAGAAPEWMSEKAVSIGAYVVASGVFTVLGTVPPVLGSPVVTRILTKDLGDAVGATFAVEPDP 601
                                    *******************************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (623 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 4186.03
//
Query:       gi|116754639|ref|YP_843757.1|  [L=127]
Description: hypothetical protein Mthe_1342 [Methanosaeta thermophila PT]
Scores for complete 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-33  112.5   0.9    9.4e-33  112.1   0.9    1.1  1  DUF2111   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2111  Uncharacterized protein conserved in archaea (DUF2111)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.1   0.9   5.2e-37   9.4e-33       1      83 []      22     102 ..      22     102 .. 0.98

  Alignments for each domain:
  == domain 1  score: 112.1 bits;  conditional E-value: 5.2e-37
                        DUF2111   1 vhelvgklPvtirsknkkGvriekgkvvdedYtgpvLeevleegkvikkvpkeGaYkGvpvvvaPikekegkviaaiGvV 80 
                                    ++e+++ lPvt+rs   +Gvr+e+gkvvd+dYtgpvLe+vl++g++++++p++Ga+kGvpv vaPi+  +++v+aa+GvV
  gi|116754639|ref|YP_843757.1|  22 INEILN-LPVTMRSAGARGVRVERGKVVDDDYTGPVLEDVLRSGRAMRTIPSSGAFKGVPVSVAPIRL-KDRVLAAVGVV 99 
                                    789999.*************************************************************.9********** PP

                        DUF2111  81 Dit 83 
                                    D++
  gi|116754639|ref|YP_843757.1| 100 DVV 102
                                    *96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); 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: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.43
# Mc/sec: 879.69
//
Query:       gi|116754640|ref|YP_843758.1|  [L=142]
Description: GCN5-related N-acetyltransferase [Methanosaeta thermophila PT]
Scores for complete 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   0.1    3.4e-17   62.8   0.1    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
      2e-12   47.1   0.0    2.6e-12   46.8   0.0    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    3.8e-11   43.3   0.0    5.4e-11   42.8   0.0    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    4.9e-09   36.0   0.0    6.3e-09   35.7   0.0    1.3  1  FR47             FR47-like protein
    8.2e-07   29.3   0.3    1.1e-06   28.8   0.3    1.3  1  Acetyltransf_6   Acetyltransferase (GNAT) domain
    8.4e-07   29.1   0.0      4e-05   23.7   0.0    2.1  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
     0.0046   16.7   0.1     0.0056   16.4   0.1    1.3  1  PanZ             Acetyltransferase (GNAT) domain, PanZ
     0.0061   16.3   0.1       0.01   15.5   0.1    1.4  1  Acetyltransf_8   Acetyltransferase (GNAT) domain
     0.0071   16.3   0.0      0.012   15.6   0.0    1.3  1  Acetyltransf_13  ESCO1/2 acetyl-transferase
  ------ inclusion threshold ------
      0.012   15.7   0.0      0.022   14.9   0.0    1.4  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
      0.028   15.1   0.1      0.072   13.8   0.0    1.9  2  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 !   62.8   0.1   2.1e-20   3.4e-17       2     117 .]      12     119 ..      11     119 .. 0.82

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 2.1e-20
                                    HHHHHHHHHHTHHHHHHHHHHHHHHHHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHH CS
                 Acetyltransf_1   2 rdlvellvesffppnedaseeefeesfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaL 81 
                                    +++ve+++++f++   +  + +   sf l + + lva++d e+ Gf+ ++        +++i+ l V+p++r++G+GsaL
  gi|116754640|ref|YP_843758.1|  12 DRIVEIERLCFPE---EVLFTRGLFSFLLRNATALVACDD-EIMGFVIGYLSGR----TGVIYTLDVHPDHRRRGVGSAL 83 
                                    5678888888664...222223233355667767776666.8*****9998888....9********************* PP

                                    HHHHHHHHHHTTESEEEEEEETTEHHHHHHHHHTTE CS
                 Acetyltransf_1  82 lealeerareegikkivlaveedndaairlYeklGF 117
                                    l+a+e+++r  g+++  l+ + +n+aa +lY + G+
  gi|116754640|ref|YP_843758.1|  84 LDAIEREMRAAGARRFRLEADTSNRAALELYHRSGY 119
                                    *******************************99997 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.0   1.6e-15   2.6e-12      34     109 ..      43     122 ..      30     131 .. 0.85

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 1.6e-15
                Acetyltransf_10  34 lvaeeggkivGvi..el.rdgshisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavpfYeklGFka 108
                                    l + ++++i+G++   l  +++ i+ l V+p++r++G+g+aLl+a+e+e++ +g +  +l+++ s+ +a ++Y++ G+++
  gi|116754640|ref|YP_843758.1|  43 L-VACDDEIMGFVigYLsGRTGVIYTLDVHPDHRRRGVGSALLDAIEREMRAAGARRfRLEADTSNrAALELYHRSGYVE 121
                                    3.33567899998765566777*******************************9999*********9***********97 PP

                Acetyltransf_10 109 v 109
                                     
  gi|116754640|ref|YP_843758.1| 122 G 122
                                    5 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.8   0.0   3.3e-14   5.4e-11       3      76 .]      40     121 ..      33     121 .. 0.69

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 3.3e-14
                                    EEEEEEEETTEEEEEEEEEEES..TCTEEEEE-GGGTTSSHHHHHHHHTT.....SEEE...EEEEEETHHHHHHHHHHT CS
                 Acetyltransf_7   3 gevfVaeddgkivGfialslld..aeitrlaVdpeyrgkGiGraLleaae.....kgii...leqlelnaekaikfYekl 72 
                                    ++ +Va  d++i+Gf++ +l++  + i  l V+p++r++G+G+aLl+a+e      g +   le + +++++a+++Y + 
  gi|116754640|ref|YP_843758.1|  40 ATALVA-CDDEIMGFVIGYLSGrtGVIYTLDVHPDHRRRGVGSALLDAIEremraAGARrfrLE-ADTSNRAALELYHRS 117
                                    555666.569999999999987544444466****************83333445443322233.3333348999***** PP

                                    TEEE CS
                 Acetyltransf_7  73 GFee 76 
                                    G++e
  gi|116754640|ref|YP_843758.1| 118 GYVE 121
                                    **86 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.0   3.9e-12   6.3e-09      17      79 ..      58     121 ..      31     129 .. 0.88

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 3.9e-12
                                    EE-TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EE.EEEETT-HHHHHHHHHHT-EE CS
                           FR47  17 lrkdggelgalqvlpehrrrGlgsrlvkalakeiaergktvl.lvvvasNtpsirlyeklGfek 79 
                                    l    g ++ l v+p+hrrrG gs l  a+ +e++++g   + l + +sN ++ +ly + G+ +
  gi|116754640|ref|YP_843758.1|  58 LSGRTGVIYTLDVHPDHRRRGVGSALLDAIEREMRAAGARRFrLEADTSNRAALELYHRSGYVE 121
                                    566789******************************998877377899***********99965 PP

>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.3   6.9e-10   1.1e-06      75     133 ..      43     101 ..      21     114 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 6.9e-10
                 Acetyltransf_6  75 vlrldgrpvAvalglrsgdrlyywlggydpelaklspgllllweliedaaeeGlrrfdl 133
                                     + +d++++++++g+ sg++   +   ++p++++ ++g  ll  + +++++ G rrf l
  gi|116754640|ref|YP_843758.1|  43 LVACDDEIMGFVIGYLSGRTGVIYTLDVHPDHRRRGVGSALLDAIEREMRAAGARRFRL 101
                                    4557*****************************************************87 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   2.5e-08     4e-05       3     125 ..       4     119 ..       2     122 .. 0.67

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2.5e-08
                                    EEE-GGGHHHHHHHHHHHTT----H..HHHHHHHHHHTTSEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEEEEE- CS
                 Acetyltransf_9   3 relteedldevlellkyaFqdeespleeireyfrklleesrvlgaedngelvgqlallplelnvpGktlkaagvtgVava 82 
                                    r++  edld ++e+ + +F +e   +   r  f+ ll ++ + ++ +++e++g +  +         + +++ ++   v+
  gi|116754640|ref|YP_843758.1|   4 RRACIEDLDRIVEIERLCFPEEVLFT---RGLFSFLL-RNATALVACDDEIMGFVIGY--------LSGRTGVIYTLDVH 71 
                                    55556666666666666666666553...23333333.33333333455555544433........234678999999** PP

                                    CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--.....SSHHHHHTTT- CS
                 Acetyltransf_9  83 pehrgrgvlskLlaraleemreegqplsllfP.....ssipiYrrfGy 125
                                    p+hr+rgv s+Ll++  +emr+ g++   l +     ++ ++Y+r Gy
  gi|116754640|ref|YP_843758.1|  72 PDHRRRGVGSALLDAIEREMRAAGARRFRLEAdtsnrAALELYHRSGY 119
                                    *************************99999998877666788999888 PP

>> PanZ  Acetyltransferase (GNAT) domain, PanZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   3.4e-06    0.0056      57      94 ..      58      95 ..      10     122 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.4e-06
                           PanZ 57 ledkeaelsdlcVRevTRrRGVgsyLleearrqaPevk 94
                                   l+++++ +  l V    RrRGVgs Ll+ + r++ +  
  gi|116754640|ref|YP_843758.1| 58 LSGRTGVIYTLDVHPDHRRRGVGSALLDAIEREMRAAG 95
                                   667788999999******************99985444 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   6.4e-06      0.01      89     140 ..      72     122 ..      57     126 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.4e-06
                                    HHHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-EEE CS
                 Acetyltransf_8  89 aeargkglttallralvhylfadprtrrvvvEPdvrNerairllekaGfeke 140
                                    +++r++g+++all a+ + + a  ++rr  +E d +N++a++l+++ G+++ 
  gi|116754640|ref|YP_843758.1|  72 PDHRRRGVGSALLDAIEREMRAA-GARRFRLEADTSNRAALELYHRSGYVEG 122
                                    7899***********99999888.9***********************9876 PP

>> Acetyltransf_13  ESCO1/2 acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   7.3e-06     0.012      12      33 ..      70      91 ..      64     103 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 7.3e-06
                Acetyltransf_13 12 vssshRrkgiAtkLldaarenf 33
                                   v+++hRr+g+ ++Llda+ +++
  gi|116754640|ref|YP_843758.1| 70 VHPDHRRRGVGSALLDAIEREM 91
                                   89***************98765 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.4e-05     0.022      16      58 ..      56      96 ..      40      98 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.4e-05
                Acetyltransf_CG 16 eYevrkegvldfthTeVpeelrGkGiAkkLvkaalddareegl 58
                                    Y    + + +++   V++ +r++G++++L +a+  ++r++g 
  gi|116754640|ref|YP_843758.1| 56 GYL--SGRTGVIYTLDVHPDHRRRGVGSALLDAIEREMRAAGA 96
                                   663..4557789999*******************999999986 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.4e-05     0.072      65     137 ..      50     119 ..       1     120 [. 0.80
   2 ?   -3.1   0.0       7.2   1.2e+04      95     104 ..     130     139 ..     125     141 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.4e-05
                 Acetyltransf_3  65 viGsvglrdleeedeeaelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGf 137
                                    ++G+v  + l+++++ +   + ++p+++++G+++  + a+ + + +  g++r++ ++d++N+a   ++ + G+
  gi|116754640|ref|YP_843758.1|  50 IMGFVIGY-LSGRTG-VIYTLDVHPDHRRRGVGSALLDAIEREM-RAAGARRFRLEADTSNRAALELYHRSGY 119
                                    46666322.344433.5555667899*********999999999.8888*******************99996 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 7.2
                 Acetyltransf_3  95 Gyateavral 104
                                    Gy+++avr +
  gi|116754640|ref|YP_843758.1| 130 GYGKDAVRLW 139
                                    9999999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); 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: 1000.61
//
Query:       gi|116754641|ref|YP_843759.1|  [L=175]
Description: hypothetical protein Mthe_1344 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1307.51
//
Query:       gi|116754642|ref|YP_843760.1|  [L=230]
Description: beta-lactamase domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-18   66.4   6.2    1.2e-17   64.6   6.2    1.8  1  Lactamase_B    Metallo-beta-lactamase superfamily
      1e-07   31.7   0.2    1.4e-07   31.3   0.2    1.2  1  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
       0.24   10.5   0.2        0.3   10.1   0.2    1.1  1  PDEase_II      cAMP phosphodiesterases class-II


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 !   64.6   6.2     2e-21   1.2e-17       2     197 .]      20     204 ..      19     204 .. 0.86

  Alignments for each domain:
  == domain 1  score: 64.6 bits;  conditional E-value: 2e-21
                                    CCCSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHC CS
                    Lactamase_B   2 gpdpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapa 81 
                                    g+d + +yl++ + ++ LiD+G++ + + ++++ +++g++p  ++++i TH H+DHiGg + +v+ ++ +v+a++++ + 
  gi|116754642|ref|YP_843760.1|  20 GGDDCCVYLVDCGADLALIDAGLGRSVDNILRNVQSAGYEPHWIKYIIATHCHIDHIGGIAPIVNLYGPKVIAHELDRKG 99 
                                    5666779999999*************************************************************999988 PP

                                    CHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEE..TTCCEEEECTTTSSHHCCC CS
                    Lactamase_B  82 lfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvvey..gggkvlftGDallagetgr 159
                                     ++ + d  a    +  ++ + + ++  + e++ ++ g+++++++++pgh++g+++ ++  ++g+vlf  D    +  + 
  gi|116754642|ref|YP_843760.1| 100 IEEVHDDLTAADLYG-VKYTPTKVDISLRGEHEMIRIGDVDFHMIHTPGHTPGSISPFIdtDDGRVLFGQDIHG-PFSP- 176
                                    888888766665544.7778889999999999999********************9887657778887666555.3333. PP

                                    CCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                    Lactamase_B 160 idltlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                              r +sd +k+ +s++k+  l+++vl+ gH
  gi|116754642|ref|YP_843760.1| 177 ----------RWGSDLAKWKESMEKILSLNIDVLCEGH 204
                                    ..........4444799999999999999999998777 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 !   31.3   0.2   2.3e-11   1.4e-07       4     143 ..      37     170 ..      27     190 .. 0.73

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 2.3e-11
                                    EES--TTHHHHHTCGGS--S.SS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEE.......HHHHHHCCTTCG CS
                  Lactamase_B_2   4 LiDagpdlrqqalralqPve.lrdelppidaVllthaHyDHlaglltlrelrpkklplyap.......kgvlavleanfv 75 
                                    LiDag++        l++v+ +  e++ i+ ++ th+H+DH+ g+  +  l++ k  ++a+       ++v+++l+a   
  gi|116754642|ref|YP_843760.1|  37 LIDAGLGRSVD--NILRNVQsAGYEPHWIKYIIATHCHIDHIGGIAPIVNLYGPK--VIAHeldrkgiEEVHDDLTAADL 112
                                    78888883333..333456668999*******************99999955543..44544444444666666666655 PP

                                    HHHCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS- CS
                  Lactamase_B_2  76 ylaleeepavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDt 143
                                    y ++  + +v++     +e +++gd  ++++++  ++ ++          ++  i++++ rv+++ D 
  gi|116754642|ref|YP_843760.1| 113 YGVKYTPTKVDISLRGEHEMIRIGD--VDFHMIHTPGHTPG--------SISPFIDTDDGRVLFGQDI 170
                                    5555555666666666888888885..56999999999998........8888888888888888776 PP

>> PDEase_II  cAMP phosphodiesterases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.2   5.1e-05       0.3      83      97 ..      64      79 ..      47     117 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 5.1e-05
                                   EEE-.S---GGGTHHH CS
                      PDEase_II 83 sylI.tHsHLDHvsgl 97
                                   +y I tH+H+DH++g+
  gi|116754642|ref|YP_843760.1| 64 KYIIaTHCHIDHIGGI 79
                                   676658********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); 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: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1641.75
//
Query:       gi|116754643|ref|YP_843761.1|  [L=80]
Description: hypothetical protein Mthe_1346 [Methanosaeta thermophila PT]
Scores for complete 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-08   34.2  19.6    2.6e-08   34.0  19.6    1.1  1  BofA           SigmaK-factor processing regulatory protein Bo
  ------ inclusion threshold ------
       0.13   12.4   1.2       0.13   12.4   1.2    1.9  2  Pox_A9         A9 protein conserved region


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 !   34.0  19.6   2.9e-12   2.6e-08       3      74 ..       7      75 ..       5      76 .. 0.91

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 2.9e-12
                           BofA  3 illlllvikllkkplkillkllinavlGlvlLflvNllgavfglhipiNlitaliagflGipGvilLillkl 74
                                   +lll++v+  l+  lk l ++++na++Gl +L+l+N   a+ gl i++++  +li++f+G  G++++i l++
  gi|116754643|ref|YP_843761.1|  7 LLLLIAVLIGLFVILKSLRTFVVNALIGLFVLYLAN---AAAGLGIGYSWPVVLICAFGGALGALMVIALHI 75
                                   567777777778889999999***************...9******************************97 PP

>> Pox_A9  A9 protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.2      0.27   2.4e+03      40      46 ..       5      11 ..       2      18 .. 0.57
   2 ?   12.4   1.2   1.4e-05      0.13      24      49 ..      18      43 ..      15      45 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.27
                         Pox_A9 40 GvaLlyi 46
                                   G+ Ll i
  gi|116754643|ref|YP_843761.1|  5 GMLLLLI 11
                                   5555544 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 1.4e-05
                         Pox_A9 24 fVvlksiisMvmyLvlGvaLlyissn 49
                                   fV+lks+ + v+  ++G+  ly+++ 
  gi|116754643|ref|YP_843761.1| 18 FVILKSLRTFVVNALIGLFVLYLANA 43
                                   9**********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1147  (0.0639746); 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:                         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: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 629.30
//
Query:       gi|116754644|ref|YP_843762.1|  [L=414]
Description: citrate transporter [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-33  116.7  30.8    1.7e-33  116.1  30.8    1.3  1  CitMHS    Citrate transporter


Domain annotation for each model (and alignments):
>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.1  30.8   9.5e-38   1.7e-33      17     294 ..      35     353 ..       4     366 .. 0.78

  Alignments for each domain:
  == domain 1  score: 116.1 bits;  conditional E-value: 9.5e-38
                                    xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                         CitMHS  17 lvlvll.vltieealsgiaspiillllgamiigaaleetGlfdrlaakllrlaggkrd.llvllvlltallsafvsndgv 94 
                                    +++v+l  +++ +a+  i ++++++l+g++++g+a+ ++G   +l+++l  +a + +d ll++l +++++lsaf+ nd+ 
  gi|116754644|ref|YP_843762.1|  35 IAAVALgEISPVDAIRSINADVMIFLAGMFVVGEAMRQSGYLFYLTNRLFGRADS-TDeLLIMLLFGMGMLSAFLMNDTI 113
                                    2333336788888*****************************************6.788********************* PP

                                    xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..................xx RF
                         CitMHS  95 vlimipivlslakrlkklppl.lliplalaaniggaltpiGtpttraaarpglslpnlll..................la 155
                                    ++i +p+vl l + l++  p+ +l+ la+a  ig+a++piG+p            +nll+                  ++
  gi|116754644|ref|YP_843762.1| 114 AIIGTPVVLYLSR-LHRVAPAlMLLSLAFAVTIGSAMSPIGNP------------QNLLIaidggldnpfadffgnlfIP 180
                                    ************9.6777777799*******************............9999999999999999998888877 PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxx...................... RF
                         CitMHS 156 lllvgllplvllfmfgvalalpvnapkvkkqkaiieaiarsllpv......atillla...................... 207
                                     +++ l++++ll+      a+  n  +  +q ++  +++   l        ati++l+                      
  gi|116754644|ref|YP_843762.1| 181 TCIN-LFIVYLLM-----KAFYRNEFRRLDQIHVSCSLSDENLARvcrislATIVVLIllkivavmlgagesfrltyiav 254
                                    7777.44444444.....45555555555555555555554444455555533333335556666666677777777777 PP

                                    ................xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         CitMHS 208 ................ykkveWsvlllfaGvfllvgaleqtG.ilealadllgaggplvalalvlgliallsafisnvav 270
                                                    ++ ++W++l++fa +f+l++a+ ++G i e+l+  l+++g+ +++++vlgl++ ls+++snv++
  gi|116754644|ref|YP_843762.1| 255 aaalpvitlsnrrwemLRGIDWETLIFFASMFVLMEAVWRSGfIQESLS--LESDGI-ASVSMVLGLSVTLSQLVSNVPF 331
                                    77788888889999999*************************6666664..644566.7789****************** PP

                                    xxxxxxxxxxxxxxxxxxxxxxxx RF
                         CitMHS 271 aalmapialgmapalgllspspla 294
                                    +al +p++ ++ ++++  ++++la
  gi|116754644|ref|YP_843762.1| 332 VALYLPVLDQIGATAQ--TMVALA 353
                                    *******999887544..333344 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       871  (0.0485805); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2785.99
//
Query:       gi|116754645|ref|YP_843763.1|  [L=142]
Description: hypothetical protein Mthe_1348 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); 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: 0.34u 0.27s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1127.74
//
Query:       gi|116754646|ref|YP_843764.1|  [L=206]
Description: hypothetical protein Mthe_1349 [Methanosaeta thermophila PT]
Scores for complete 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   17.8   0.1     0.0072   16.9   0.1    1.4  1  DUF4405   Domain of unknown function (DUF4405)
     0.0038   17.6   0.0     0.0092   16.4   0.0    1.6  2  MG2       MG2 domain


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 !   16.9   0.1     8e-07    0.0072       3      27 ..       4      28 ..       3      55 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 8e-07
                        DUF4405  3 dlllllsflvlaiSGillsfavlps 27
                                   d+lll+++l+l+iSG l +++++ +
  gi|116754646|ref|YP_843764.1|  4 DALLLVCMLFLMISGSLAWAHISYG 28
                                   789****************996543 PP

>> MG2  MG2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.64   5.7e+03      58      80 ..      67      89 ..      56     114 .. 0.70
   2 !   16.4   0.0     1e-06    0.0092      34      81 ..     115     170 ..      99     182 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.64
                                   TTEEEEEEE--TT--SEEEEEEE CS
                            MG2 58 tggaesefalpeaaklGeysvel 80
                                   +gg+   ++ + +a lG y ++l
  gi|116754646|ref|YP_843764.1| 67 SGGVAEGIDSQFDARLGPYLLNL 89
                                   55555666666678888888777 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 1e-06
                                    EEEEEEEE-TTSSEEEEEEE....EE-CTTE..EEEEEE--TT--SEEEEEEE..E CS
                            MG2  34 lplkltirdpdgkevkelpl....atdetgg..aesefalpeaaklGeysvel..s 81 
                                     p  +++++p+g+   e +l    ++d+tgg  + +++++p++a+ G+++++    
  gi|116754646|ref|YP_843764.1| 115 SPPLIKLVSPSGGMSAEVQLnqtsTADSTGGvvYRGDIRIPADAEPGRWRISWlrA 170
                                    5666777788777666666665567778887899*****************98443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1539.09
//
Query:       gi|116754647|ref|YP_843765.1|  [L=183]
Description: hypothetical protein Mthe_1350 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1361.18
//
Query:       gi|116754648|ref|YP_843766.1|  [L=180]
Description: glutamine amidotransferase class-I [Methanosaeta thermophila PT]
Scores for 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-08   32.1   0.0    1.2e-07   31.7   0.0    1.1  1  GATase    Glutamine amidotransferase class-I


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 !   31.7   0.0   6.7e-12   1.2e-07      13     174 ..      23     167 ..      16     169 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 6.7e-12
                                    HHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.TTTHHHHHHHHCTSTS-EEEETHHHHHHHHHTTTE CS
                         GATase  13 lvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg.vegkieaikearenkiPiLGICLGmQllaiefgrk 91 
                                    ++ al+++g++++v+ +++  +       ++d+i++ g   +   +    + ++++re k+P+LGI  G  l++  +g++
  gi|116754648|ref|YP_843766.1|  23 VAAALRRAGAEIDVLHYSE-LDDP----HGYDKIVLCGTALKDRrCFDDADQLSWIRECKLPMLGISTGAALICSILGGS 97 
                                    67899999*******9995.4444....49*******98655555*********************************** PP

                                    EEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEEETTTEEEESSBT CS
                         GATase  92 vvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelmeiiekknpfvgvQFHP 171
                                    v +  + ++ g    + +     l g+++++ + h H + +     +p++l+ + ++      ++++ +++p++g+ F P
  gi|116754648|ref|YP_843766.1|  98 VLPYIHIGM-GDVKIIAE---TPLLGEPRTIPVFHLHAFRLV----LPSELRAIEEN-----CEAFVGRDRPVYGILFSP 164
                                    ***995444.43333443...4799***************99....79998874444.....578888888999999999 PP

                                    TST CS
                         GATase 172 Est 174
                                    E++
  gi|116754648|ref|YP_843766.1| 165 EVR 167
                                    975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1320.10
//
Query:       gi|116754649|ref|YP_843767.1|  [L=238]
Description: putative ATP binding protein [Methanosaeta thermophila PT]
Scores for complete 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-68  229.0   0.0    5.3e-68  228.8   0.0    1.0  1  Diphthami_syn_2  Diphthamide synthase


Domain annotation for each model (and alignments):
>> Diphthami_syn_2  Diphthamide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  228.8   0.0     3e-72   5.3e-68       1     218 [.       4     225 ..       4     226 .. 0.98

  Alignments for each domain:
  == domain 1  score: 228.8 bits;  conditional E-value: 3e-72
                Diphthami_syn_2   1 mkvavlysGGkDsilaLykalkesevesLvsvisenkesymfhvvnvhlvellaesvGiplikletaGeeekevedLkgt 80 
                                    mk  vl+sGGkDs++a y+a+++ +v+ L+++isen+esymfh++n+ l +l+a ++G+++ k +t G+ee e edL++ 
  gi|116754649|ref|YP_843767.1|   4 MKLGVLFSGGKDSVFACYRAMEHEDVRCLITLISENEESYMFHTPNIGLADLVASAIGVDILKWRTPGVEEMELEDLRDA 83 
                                    8999**************************************************************************99 PP

                Diphthami_syn_2  81 lkkld....veavviGaieseyqksriervCrelGlksvaPLWkkdpeelleeiveekfevivvavkaegldeslLGrri 156
                                    + + +    +e++v+Gaies yq sri+r+C  l l  + PLW+ d  e+l    + +f+viv++v a+ ldes+LG  i
  gi|116754649|ref|YP_843767.1|  84 IIEARrlygIEGIVTGAIESVYQSSRIQRICSSLDLWCFNPLWQLDQIEYLRMLRAYGFRVIVTGVFAYPLDESFLGAEI 163
                                    977766778*********************************************************************** PP

                Diphthami_syn_2 157 dkklidelkklsekygidkagegGeaetlvlDaPlfkkrlevkelekkwderrgyldierak 218
                                    d  +i +l+ l+++ygi ++gegGe etlvlD+P+f++rle+  +  + +++rg + ie a+
  gi|116754649|ref|YP_843767.1| 164 DDGMIAKLQGLQKRYGISPSGEGGELETLVLDGPIFRRRLEILRAASHFSGNRGRYVIESAR 225
                                    **********************************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1823.90
//
Query:       gi|116754650|ref|YP_843768.1|  [L=95]
Description: chorismate mutase [Methanosaeta thermophila PT]
Scores for complete 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-16   59.0   1.3    5.1e-16   58.8   1.3    1.0  1  CM_2      Chorismate mutase type II


Domain annotation for each model (and alignments):
>> CM_2  Chorismate mutase type II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   1.3   2.8e-20   5.1e-16       1      75 []       8      86 ..       8      86 .. 0.95

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 2.8e-20
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSGSS-HHHHHHHHHHHHHHH....S-HHHHHHHHHHHHHHHHHHHH CS
                           CM_2  1 RkeIdeiDdeileLLaeRaelakevgeyKkeeglpvydpeReaevlerleega....ldeeaierifreiisasralqk 75
                                   R e+ +iD+eil+L+++R++la+++ + K++ gl++ dp++ea vl+r  + a    ld+ +i++ifr +i++s++ q+
  gi|116754650|ref|YP_843768.1|  8 RLEVQKIDEEILRLIQKRMALAEKIYRDKAALGLSISDPDQEALVLSRAVDMAtelgLDPGSIKSIFRILIDMSLQKQH 86
                                   77899**********************************************556678******************9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); 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: 0.32u 0.23s 00:00:00.55 Elapsed: 00:00:00.35
# Mc/sec: 810.71
//
Query:       gi|116754651|ref|YP_843769.1|  [L=288]
Description: shikimate kinase [Methanosaeta thermophila PT]
Scores for complete 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-11   43.8   2.8    2.2e-11   43.8   2.8    1.9  2  GHMP_kinases_N  GHMP kinases N terminal domain
    4.3e-05   23.8   0.4    0.00032   21.0   0.1    2.5  3  GHMP_kinases_C  GHMP kinases C terminal
  ------ inclusion threshold ------
      0.029   14.6   0.0       0.05   13.8   0.0    1.3  1  NusG_add        NusG additional 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 ?   -2.8   0.0       1.3   7.8e+03      22      33 ..      11      22 ..       7      47 .. 0.57
   2 !   43.8   2.8   3.6e-15   2.2e-11       2      66 .]      74     142 ..      73     142 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.3
                                   HHHHHHHHHHTT CS
                 GHMP_kinases_N 22 valvaAllallg 33
                                   ++++ A++++ g
  gi|116754651|ref|YP_843769.1| 11 ATVLNAIANWKG 22
                                   445555555443 PP

  == domain 2  score: 43.8 bits;  conditional E-value: 3.6e-15
                                    EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHH...HHHHHHHHHHHHHHHHHSHHH.HHHHHSS CS
                 GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglslee...aklaleaerlaqggngsggDv.aasvyGg 66 
                                    ++++seiPv++GL SS+A+a a+v+A  ++lg ++++   +++++ea   a++++++ +D+ +as++Gg
  gi|116754651|ref|YP_843769.1|  74 VRTRSEIPVASGLKSSSAAANAAVLATVDALGEEIDMidaVRIGVEAALDAGVTVTGAFDDaCASMLGG 142
                                    5689***************************999755567*********************78888887 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 ?   -1.9   0.0      0.73   4.4e+03      39      56 ..     117     131 ..     102     133 .. 0.73
   2 ?   -1.3   0.0      0.49   2.9e+03      28      54 ..     181     206 ..     173     210 .. 0.81
   3 !   21.0   0.1   5.3e-08   0.00032      43      83 ..     226     263 ..     216     265 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.73
                 GHMP_kinases_C  39 llealselGalgaklsGa 56 
                                     +ea++++G   + ++Ga
  gi|116754651|ref|YP_843769.1| 117 GVEAALDAG---VTVTGA 131
                                    467888888...777777 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.49
                 GHMP_kinases_C  28 vvgilppeleellealselGalgakls 54 
                                    +++ l+++ +++ e++ e + +++ ++
  gi|116754651|ref|YP_843769.1| 181 RCRALSRVADAVFEMAIEGD-YAGAMT 206
                                    67888999999999999999.888887 PP

  == domain 3  score: 21.0 bits;  conditional E-value: 5.3e-08
                 GHMP_kinases_C  43 lselGalgaklsGaGgGptvfalfkdkdeaeqvaralreef 83 
                                    ++++Ga ga lsG+  Gp+ +al+ d+   ++v++a+++++
  gi|116754651|ref|YP_843769.1| 226 ALRAGAAGATLSGT--GPAYAALV-DDISGDDVVEAWSSLG 263
                                    689***********..********.************8865 PP

>> NusG_add  NusG additional domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   8.4e-06      0.05      47     105 ..     116     176 ..     103     179 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.4e-06
                       NusG_add  47 lkigarvkqGmplaadgeyice.ldGkiveveklkrivvkredneldvy.vipldvfdsaa 105
                                    + ++a +  G+ ++  ++  c+ + G +v +++lkr  +kr++ + dv   ip ++f s+ 
  gi|116754651|ref|YP_843769.1| 116 IGVEAALDAGVTVTGAFDDACAsMLGGVVVTDNLKRCLLKRDELHSDVVlLIPEEQFFSRD 176
                                    456788999999999999888648899****************999975268888888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1971.03
//
Query:       gi|116754652|ref|YP_843770.1|  [L=174]
Description: hypothetical protein Mthe_1355 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); 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: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1261.71
//
Query:       gi|116754653|ref|YP_843771.1|  [L=61]
Description: hypothetical protein Mthe_1356 [Methanosaeta thermophila PT]
Scores for complete 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-18   66.2   4.1    2.5e-18   66.1   4.1    1.0  1  CooT      CO dehydrogenase accessory protein CooT


Domain annotation for each model (and alignments):
>> CooT  CO dehydrogenase accessory protein CooT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.1   4.1   1.4e-22   2.5e-18       1      61 []       1      60 [.       1      60 [. 0.98

  Alignments for each domain:
  == domain 1  score: 66.1 bits;  conditional E-value: 1.4e-22
                           CooT  1 MCeanvyllkngkeeelvmedVdkiepeedgvvltdifGeekevegkIkeidLvehkiile 61
                                   MCe++vy++ +gk+ elvme+V++i + ++++++++i+G  +ev+gk+ke++++++++++e
  gi|116754653|ref|YP_843771.1|  1 MCELSVYMVAGGKK-ELVMESVVRIVVMDGRILFEGILGGSMEVDGKLKEVNILSQEVLIE 60
                                   *********99987.********************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); 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: 0.31u 0.25s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 475.61
//
Query:       gi|116754654|ref|YP_843772.1|  [L=120]
Description: prefoldin, beta subunit [Methanosaeta thermophila PT]
Scores for complete 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   79.7  16.9    1.5e-22   79.5  16.9    1.0  1  Prefoldin_2   Prefoldin subunit
  ------ inclusion threshold ------
      0.022   14.4   7.7      0.033   13.8   7.7    1.2  1  DUF4795       Domain of unknown function (DUF4795)
      0.056   13.8   0.5      0.056   13.8   0.5    1.9  2  TINF2_N       TERF1-interacting nuclear factor 2 N-terminus
      0.096   12.6   5.6       0.19   11.7   0.6    2.1  2  DUF1706       Protein of unknown function (DUF1706)
       0.12   12.9  10.2       0.17   12.4  10.2    1.2  1  FlgN          FlgN protein
       0.16   12.2   3.6       0.37   11.0   0.1    2.4  2  CinA_KH       Damage-inducible protein CinA KH domain
       0.27   11.8   8.6         22    5.6   5.0    3.0  2  HisKA_3       Histidine kinase
       0.41   10.2  11.7        2.3    7.7  11.4    1.9  1  DUF3053       Protein of unknown function (DUF3053)
       0.52    9.6  11.8       0.21   10.9   3.8    2.1  2  DUF4763       Domain of unknown function (DUF4763)
       0.89    9.6  17.6        0.6   10.2   1.7    2.1  2  TPR_MLP1_2    TPR/MLP1/MLP2-like protein
        1.1   10.0  10.5        0.4   11.4   4.8    2.1  2  KfrA_N        Plasmid replication region DNA-binding N-term
        1.5    8.0  17.1       0.44    9.8   7.3    2.0  2  DUF3450       Protein of unknown function (DUF3450)
        1.5    8.6  14.1       0.13   12.0   4.5    2.2  2  DivIC         Septum formation initiator
        1.8    8.8  13.3        5.6    7.2   0.8    2.2  2  Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
        1.9    6.3   4.5        2.5    5.9   4.5    1.2  1  V_ATPase_I    V-type ATPase 116kDa subunit family
        2.1    8.8   6.1       0.99    9.8   0.4    2.5  2  FlaC_arch     Flagella accessory protein C (FlaC)
        4.3    7.5   9.9        3.4    7.8   0.5    2.1  1  Fib_alpha     Fibrinogen alpha/beta chain family
        4.7    7.5  11.1        2.8    8.2   5.1    2.0  2  Spc24         Spc24 subunit of Ndc80
        6.7    7.2   7.9         21    5.6   8.0    1.7  1  NBD_C         Nucleotide-binding C-terminal domain
        7.7    6.7  11.7          6    7.0   4.2    2.2  2  PilO          Pilus assembly protein, PilO
        9.4    6.3   8.4          2    8.5   0.8    2.1  2  DUF1664       Protein of unknown function (DUF1664)


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 !   79.5  16.9   1.8e-25   1.5e-22       1     105 [.      10     114 ..      10     115 .. 0.99

  Alignments for each domain:
  == domain 1  score: 79.5 bits;  conditional E-value: 1.8e-25
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT--EEEEETTEEEEE-HHHHHHHHHHHHHHHHHHHHH CS
                    Prefoldin_2   1 qelinkfqqlqqqlqqlaqqikqletqlkelelvleelelldedtkvyklvGdvlvkqdkeevkeeLeerketlekeikt 80 
                                    q++++++qqlqqq q+l++q+ q+e  +ke+e +++el++ ++d  vyk+vG++++  dk+++ +eL+er + l+ ++kt
  gi|116754654|ref|YP_843772.1|  10 QNQLAQLQQLQQQAQALVAQKSQIELLKKEAEAAIKELDKSPDDVVVYKNVGELMLRSDKATLMTELKERVDLLDLRLKT 89 
                                    89****************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHHCCTS- CS
                    Prefoldin_2  81 lekqleklekeleelkeelqkklqq 105
                                    + kq+e+++ ++++l+++l++ l+q
  gi|116754654|ref|YP_843772.1|  90 VAKQEERIQSRFNQLQDQLRQSLGQ 114
                                    *********************9986 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   7.7   3.8e-05     0.033       3     104 ..      10     115 ..       5     117 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.8e-05
                        DUF4795   3 vnsaellkklqeaieklqeelekleekvkelekrledkekkle..alkkqieelekvkadkeeveeelaekadkeaLatk 80 
                                    +n+   l++lq++ + l ++++++e  +ke e  +++++k+ +  +++k + el     dk ++ +el+e +d  +L+ k
  gi|116754654|ref|YP_843772.1|  10 QNQLAQLQQLQQQAQALVAQKSQIELLKKEAEAAIKELDKSPDdvVVYKNVGELML-RSDKATLMTELKERVDLLDLRLK 88 
                                    44444577888888888888877777777777777766665431156677777754.4889****************999 PP

                        DUF4795  81 vsrdq...fDeakkeLekmleellekl 104
                                    +  +q   +++++++L+ +l++ l ++
  gi|116754654|ref|YP_843772.1|  89 TVAKQeerIQSRFNQLQDQLRQSLGQM 115
                                    887778899999999999998877766 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 ?    1.0   0.7      0.59     5e+02      63     103 ..      10      52 ..       3      55 .. 0.58
   2 ?   13.8   0.5   6.5e-05     0.056      21      73 ..      55     108 ..      52     115 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.59
                        TINF2_N  63 qshlerlrasaa..kstkkkdekveeaqenflklvqsLledpe 103
                                    q+ l +l++ ++  ++  ++++++e  +++    +++L ++p+
  gi|116754654|ref|YP_843772.1|  10 QNQLAQLQQLQQqaQALVAQKSQIELLKKEAEAAIKELDKSPD 52 
                                    4444444443333355556666777777777777777776665 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 6.5e-05
                        TINF2_N  21 lvteavPeLlssrqkakLilGLrarl.ilellrkekaadlkaiqshlerlrasa 73 
                                    +v+++v eL+ ++ ka+L+  L++r+ +l+l +k  a++ + iqs +++l+ + 
  gi|116754654|ref|YP_843772.1|  55 VVYKNVGELMLRSDKATLMTELKERVdLLDLRLKTVAKQEERIQSRFNQLQDQL 108
                                    68999********************956677777779************99864 PP

>> DUF1706  Protein of unknown function (DUF1706)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.6   0.00022      0.19       9      54 ..      14      58 ..       6      65 .. 0.82
   2 ?    3.8   0.5     0.057        48       5      45 ..      67     106 ..      63     115 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00022
                                   HHHHHHHHHHHHHHHTTTTS-GGGT...T--BTTCSS-HHHHHHHH CS
                        DUF1706  9 eLleaieknfekLiklidsipeeekkapeeavkgrdktvadvlayl 54
                                   + l++ +++++ L ++ ++i+  +k+a e a+k+ dk++ dv++y 
  gi|116754654|ref|YP_843772.1| 14 AQLQQLQQQAQALVAQKSQIELLKKEA-EAAIKELDKSPDDVVVYK 58
                                   446789999999999999999998855.579*************96 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.057
                                    SSHHHHHHHHHHHHHHHHHTTTTS-GGGT...T--BTTCSS CS
                        DUF1706   5 qsKeeLleaieknfekLiklidsipeeekkapeeavkgrdk 45 
                                    ++K+ L+++ +++++ L   ++++ ++e++ +  ++++ + 
  gi|116754654|ref|YP_843772.1|  67 SDKATLMTELKERVDLLDLRLKTVAKQEERIQ-SRFNQLQD 106
                                    6899***************9999999998666.23333333 PP

>> FlgN  FlgN protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4  10.2    0.0002      0.17      34     125 ..      10     112 ..       8     117 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0002
                                    TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--........SCHHHHHHHHCT...TCCHHHHHHHHHHHHHHHH CS
                           FlgN  34 agdieaLeelleekqellekleqleqkrakllaelgls........aeeatlsellak...eedeelkelwqelkellee 102
                                    ++++++L++l ++ q+l+++ +q+e    ++ a++++           +   + +l++   + ++elke ++ l+ +l++
  gi|116754654|ref|YP_843772.1|  10 QNQLAQLQQLQQQAQALVAQKSQIELLKKEAEAAIKELdkspddvvVYKNVGELMLRSdkaTLMTELKERVDLLDLRLKT 89 
                                    789999************9888877776666666666666687776333333344444789******************* PP

                                    HHHHHHHHHHHHHHCCHHHHHHH CS
                           FlgN 103 lkelnelNgrlieqslefnqrll 125
                                    + ++ e+ ++  +q +++++++l
  gi|116754654|ref|YP_843772.1|  90 VAKQEERIQSRFNQLQDQLRQSL 112
                                    ********************998 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 ?    1.6   0.8      0.37   3.2e+02      13      40 ..       8      35 ..       7      50 .. 0.74
   2 ?   11.0   0.1   0.00043      0.37      18      69 ..      60     114 ..      54     115 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.37
                                   HHHHHHGGGS-BSSSEEEEEEETTEEEE CS
                        CinA_KH 13 avaekladlidrenptlAiyakegevtv 40
                                   +v+++la l + +++  A+ a+++++++
  gi|116754654|ref|YP_843772.1|  8 QVQNQLAQLQQLQQQAQALVAQKSQIEL 35
                                   6788888888888888888888888775 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00043
                                    HGGGS-BSSS.EEEEEEET..TEEEEEEE...EEHHHHHHHHH....HHHHHTTT CS
                        CinA_KH  18 ladlidrenp.tlAiyake..gevtvRltakaaneeeaealiapveeeirerlgd 69 
                                    +++l+ r++  tl +  ke  +  ++Rl   a++ee  + + +++++++r+ lg+
  gi|116754654|ref|YP_843772.1|  60 VGELMLRSDKaTLMTELKErvDLLDLRLKTVAKQEERIQSRFNQLQDQLRQSLGQ 114
                                    6677777555577666666445789****************************97 PP

>> HisKA_3  Histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.3      0.15   1.3e+02      34      54 ..       5      25 ..       2      27 .. 0.83
   2 ?    5.6   5.0     0.026        22      36      65 ..      88     117 ..      21     119 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.15
                                   -HHHHHHHHHHHHHHHHHHHH CS
                        HisKA_3 34 dpekaaeqlreieelarealq 54
                                    p+++++ql+++++l ++a++
  gi|116754654|ref|YP_843772.1|  5 LPPQVQNQLAQLQQLQQQAQA 25
                                   688999999999999999876 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.026
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                        HisKA_3  36 ekaaeqlreieelarealqevRrllhnLrp 65 
                                    + +a+q ++i+++ ++ ++++R+ l+++ p
  gi|116754654|ref|YP_843772.1|  88 KTVAKQEERIQSRFNQLQDQLRQSLGQMPP 117
                                    266667777777777777777777777655 PP

>> DUF3053  Protein of unknown function (DUF3053)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7  11.4    0.0027       2.3      89     164 ..       9      84 ..       7     111 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0027
                        DUF3053  89 pqdyltrrdelrqaagalneleqqlqnakaqadkaraaLkqpddlkavydkayektVtqpanaltpllplaeallq 164
                                    +q+ l++ ++l+q+a+al + ++q++  k++a++a   L +++d  +vy ++ e +    +++l++ l+ +  ll+
  gi|116754654|ref|YP_843772.1|   9 VQNQLAQLQQLQQQAQALVAQKSQIELLKKEAEAAIKELDKSPDDVVVYKNVGELMLRSDKATLMTELKERVDLLD 84 
                                    68999**********************************7766666999999888888777777766666555555 PP

>> DUF4763  Domain of unknown function (DUF4763)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   3.8   0.00025      0.21      98     136 ..      12      50 ..       3      53 .. 0.87
   2 ?    3.8   1.1     0.036        31     120     152 ..      77     109 ..      61     116 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00025
                        DUF4763  98 eqpeileLqrnnhkLrqqlaelqqhlkasrkslkelres 136
                                    +  ++++Lq++ + L+ q +++++ +k+ ++++kel++s
  gi|116754654|ref|YP_843772.1|  12 QLAQLQQLQQQAQALVAQKSQIELLKKEAEAAIKELDKS 50 
                                    55799******************************9976 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.036
                        DUF4763 120 qqhlkasrkslkelreslcqekkrlrklqkrln 152
                                    +++    +  lk + ++  + ++r ++lq +l 
  gi|116754654|ref|YP_843772.1|  77 KERVDLLDLRLKTVAKQEERIQSRFNQLQDQLR 109
                                    333334444444444444444444444444433 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   8.4     0.027        23      49      90 ..       9      50 ..       7      59 .. 0.58
   2 ?   10.2   1.7    0.0007       0.6      48      96 ..      62     110 ..      56     115 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.027
                     TPR_MLP1_2 49 lvkhaedvkelqalreelnelkaeiaelkaeaesakaelees 90
                                   ++++ +++++lq+  + l   k++i+ lk+eae+a +el++s
  gi|116754654|ref|YP_843772.1|  9 VQNQLAQLQQLQQQAQALVAQKSQIELLKKEAEAAIKELDKS 50
                                   444445555555555555555666666666666666666554 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0007
                     TPR_MLP1_2  48 elvkhaedvkelqalreelnelkaeiaelkaeaesakaeleeseeswee 96 
                                    el++ ++ ++ +++l+e+++ l  +++++ ++ e+ ++ +++ + ++ +
  gi|116754654|ref|YP_843772.1|  62 ELMLRSDKATLMTELKERVDLLDLRLKTVAKQEERIQSRFNQLQDQLRQ 110
                                    9***************************************999988766 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 ?   11.4   4.8   0.00047       0.4      58     100 ..       4      50 ..       1      56 [. 0.79
   2 ?    2.4   0.3      0.29   2.5e+02      81     101 ..      88     108 ..      58     115 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00047
                         KfrA_N  58 elPealaeal..laalwqaale..eaeeelaaaraelqaaraaleae 100
                                    elP +++++l  l++l q+a++  +++++++ +++e++aa+++l++ 
  gi|116754654|ref|YP_843772.1|   4 ELPPQVQNQLaqLQQLQQQAQAlvAQKSQIELLKKEAEAAIKELDKS 50 
                                    89*****9998888888888885444448999999999999998875 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.29
                         KfrA_N  81 eelaaaraelqaaraaleaer 101
                                    +++a++++++q++ ++l+ ++
  gi|116754654|ref|YP_843772.1|  88 KTVAKQEERIQSRFNQLQDQL 108
                                    233333333333333333333 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   7.3   0.00052      0.44      45      96 ..       8      59 ..       3      74 .. 0.87
   2 ?    4.0   2.8     0.031        27      53      90 ..      73     110 ..      63     115 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00052
                        DUF3450 45 ekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeier 96
                                   + q+ la++++l++++++l ++++q e l +++e+ i++l+++ +++   ++
  gi|116754654|ref|YP_843772.1|  8 QVQNQLAQLQQLQQQAQALVAQKSQIELLKKEAEAAIKELDKSPDDVVVYKN 59
                                   678999************************************9999876665 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.031
                        DUF3450  53 yralkeeleslevyneqlerlvasqeqeiasleeqiee 90 
                                    +++lke+++ l++  + ++++ +  ++++++l+ q+ +
  gi|116754654|ref|YP_843772.1|  73 MTELKERVDLLDLRLKTVAKQEERIQSRFNQLQDQLRQ 110
                                    66777888888888888888888888888888877754 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   4.5   0.00016      0.13      12      55 ..       9      52 ..       5      55 .. 0.86
   2 ?    2.0   2.1       0.2   1.7e+02      22      53 ..      76     106 ..      69     111 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
                                   XXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXX CS
                          DivIC 12 gkkgllaykqlkqeiaalqaelaklkaeneeLeaevkdLksded 55
                                   + ++l +++ql+q+ +al a+  ++   ++e ea +k+L +++d
  gi|116754654|ref|YP_843772.1|  9 VQNQLAQLQQLQQQAQALVAQKSQIELLKKEAEAAIKELDKSPD 52
                                   67899999999999999999999999999999999999988887 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.2
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXX CS
                          DivIC  22 lkqeiaalqaelaklkaeneeLeaevkdLksd 53 
                                    lk+ ++ l   l+++ +++e+ +++ ++L +d
  gi|116754654|ref|YP_843772.1|  76 LKERVDLLDLRLKTVAKQEERIQSRFNQL-QD 106
                                    45555555555555555555555555555.33 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   5.5    0.0084       7.2      55      99 ..       9      53 ..       7      57 .. 0.76
   2 ?    7.2   0.8    0.0066       5.6      60     101 ..      61     105 ..      55     116 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0084
                                   HHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH CS
                   Seryl_tRNA_N 55 lskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelek 99
                                   ++++ +++ + +++a++l+a+ +++    k++ea+ kel++  ++
  gi|116754654|ref|YP_843772.1|  9 VQNQLAQLQQLQQQAQALVAQKSQIELLKKEAEAAIKELDKSPDD 53
                                   667777777777888888888888888888888888888887665 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0066
                                    CCCCCTT...S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Seryl_tRNA_N  60 gkakkkk...edaeeliaevkelkeelkaleaelkeleaelekll 101
                                    g+++ +       +el+++v+ l  +lk++ ++++ +++++++l 
  gi|116754654|ref|YP_843772.1|  61 GELMLRSdkaTLMTELKERVDLLDLRLKTVAKQEERIQSRFNQLQ 105
                                    555544433344556666666677777777777777776666654 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 ?    5.9   4.5    0.0029       2.5      29     105 ..      30     107 ..       7     114 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0029
                     V_ATPase_I  29 vrrcdemerklrfleeeieklekavikeeea............eesleapeekeldeleeelekleeelkelnenleklk 96 
                                      +++ ++++ +   +e++           +            e +l++++++ + el+e+++ l+ +lk++ +++e+++
  gi|116754654|ref|YP_843772.1|  30 KSQIELLKKEAEAAIKELD-----------KspddvvvyknvgELMLRSDKATLMTELKERVDLLDLRLKTVAKQEERIQ 98 
                                    2333333333333333333...........033345666666777889999999************************** PP

                     V_ATPase_I  97 kelnelvel 105
                                    +++n+l+++
  gi|116754654|ref|YP_843772.1|  99 SRFNQLQDQ 107
                                    *****9865 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.9      0.53   4.6e+02      13      24 ..      30      41 ..       4      64 .. 0.60
   2 ?    9.8   0.4    0.0012      0.99       2      38 ..      73     109 ..      73     113 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.53
                      FlaC_arch 13 steletvkkene 24
                                   ++++e +kke e
  gi|116754654|ref|YP_843772.1| 30 KSQIELLKKEAE 41
                                   234444444444 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0012
                      FlaC_arch   2 idelEnklsklsteletvkkeneelsksveelkenVk 38 
                                    + el ++++ l+ +l+tv k+ e +++  ++l+++ +
  gi|116754654|ref|YP_843772.1|  73 MTELKERVDLLDLRLKTVAKQEERIQSRFNQLQDQLR 109
                                    67999***************************99886 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 ?    7.8   0.5     0.004       3.4      31      72 ..      74     115 ..      68     118 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.004
                                    CCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH CS
                      Fib_alpha  31 kdvkkdlekleneleeisnstkeaeelvkeikdslrekqksk 72 
                                    +++k++++ l  +l++++++++ +++  ++++d+lr+   + 
  gi|116754654|ref|YP_843772.1|  74 TELKERVDLLDLRLKTVAKQEERIQSRFNQLQDQLRQSLGQM 115
                                    6889999999999*******************9999987665 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   5.1    0.0033       2.8      13      88 ..       9      84 ..       4      89 .. 0.74
   2 ?    3.7   1.2     0.083        71      10      43 ..      77     110 ..      70     115 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0033
                          Spc24 13 lsdleselesleselaelkeeleeleeeseekeserve.detllklklYrsL.Gielekdvnkvlirnkekgdvnvln 88
                                   ++++ ++l++l+++ + l ++  ++e  ++e e++++e d++   + +Y+++  + l  d  k+   ++ k+ v+ l+
  gi|116754654|ref|YP_843772.1|  9 VQNQLAQLQQLQQQAQALVAQKSQIELLKKEAEAAIKElDKSPDDVVVYKNVgELMLRSD--KATLMTELKERVDLLD 84
                                   555667888888999999999999888888888888999***9*********55777777..4444444444466555 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.083
                          Spc24  10 akelsdleselesleselaelkeeleeleeesee 43 
                                     + ++ l+  l+ + ++ ++ ++++++l+++  +
  gi|116754654|ref|YP_843772.1|  77 KERVDLLDLRLKTVAKQEERIQSRFNQLQDQLRQ 110
                                    5566667777777888888888888888887655 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 ?    5.6   8.0     0.025        21      10      82 ..       8      72 ..       1     115 [. 0.65

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.025
                                   HHHHHHHHHCTS.CTSEEEEEEHHHHHSCCTCHHHHHHHHHHHHHCCTCCTSSEEEEEECTGHHHH.HH---H CS
                          NBD_C 10 kTtaQlaallkegesvpvleldvealledeesaeaeieraleqaeeallaagkdvlvytsrepedvrdalesl 82
                                     + Qla+l++        + +++al++ ++s+ +++++ +e+a ++l ++ +dv+vy + ++  +r++ + l
  gi|116754654|ref|YP_843772.1|  8 QVQNQLAQLQQL-------QQQAQALVA-QKSQIELLKKEAEAAIKELDKSPDDVVVYKNVGELMLRSDKATL 72
                                   557788888643.......445555553.3444455555555555553324779******9999998443333 PP

>> PilO  Pilus assembly protein, PilO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   4.2     0.007         6       9      47 ..      10      48 ..       4      55 .. 0.87
   2 ?    4.5   0.8     0.043        37      24      46 ..      86     108 ..      62     118 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.007
                           PilO  9 keLkkefeekkekaanLeklkkqleeleeeleellkqLP 47
                                   ++  +++++ +++a++L + k+q+e l++e e+++k+L 
  gi|116754654|ref|YP_843772.1| 10 QNQLAQLQQLQQQAQALVAQKSQIELLKKEAEAAIKELD 48
                                   5667889999**************************995 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.043
                           PilO  24 nLeklkkqleeleeeleellkqL 46 
                                    +L+++ kq e++++++++l +qL
  gi|116754654|ref|YP_843772.1|  86 RLKTVAKQEERIQSRFNQLQDQL 108
                                    56666666677777777666666 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   1.5      0.19   1.6e+02      83     113 ..      17      47 ..       4      63 .. 0.44
   2 ?    8.5   0.8    0.0023         2      62      98 ..      74     110 ..      54     116 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.19
                        DUF1664  83 keikeevtevredlseigedvesvkeavegl 113
                                    ++++++ +++  + s+i+   ++ ++a+++l
  gi|116754654|ref|YP_843772.1|  17 QQLQQQAQALVAQKSQIELLKKEAEAAIKEL 47 
                                    2222222222222333332222233333333 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0023
                        DUF1664  62 rhLssridrvdkkldeqkeiskeikeevtevredlse 98 
                                     +L++r+d +d +l+ +++  + i++  ++++++l++
  gi|116754654|ref|YP_843772.1|  74 TELKERVDLLDLRLKTVAKQEERIQSRFNQLQDQLRQ 110
                                    6899999999999999999999999999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2526  (0.140889); expected 358.6 (0.02)
Passed bias filter:                      978  (0.0545485); expected 358.6 (0.02)
Passed Vit filter:                       117  (0.00652574); expected 17.9 (0.001)
Passed Fwd filter:                        36  (0.00200792); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.40
# Mc/sec: 900.84
//
Query:       gi|116754655|ref|YP_843773.1|  [L=75]
Description: hypothetical protein Mthe_1358 [Methanosaeta thermophila PT]
Scores for complete 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-09   36.0   0.1    6.4e-09   35.8   0.1    1.1  1  Pcc1      Transcription factor Pcc1


Domain annotation for each model (and alignments):
>> Pcc1  Transcription factor Pcc1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.1   3.6e-13   6.4e-09      13      74 .]      13      74 ..       4      74 .. 0.88

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 3.6e-13
                                   HHHHHHHHHHHHCHC-TTECEEEEEEETTEEEEEEEESSHHHHHHHHHHHHHHHHHHHHHHH CS
                           Pcc1 13 lAsialrtLqvDkelsplavkrslslegnvLqveykAttnrmLRvavngfleslglvletme 74
                                   + +++l++L+++     +  +++++ ++n L ++++  +  +LR+a+n++l+++ +++e++e
  gi|116754655|ref|YP_843773.1| 13 DSEVVLNALKPELDDDLHRGRVEIRAANNGLLLTVEGDDVVSLRAALNTWLRLVRICVEMIE 74
                                   579*********87755558***************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.21s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 631.09
//
Query:       gi|116754656|ref|YP_843774.1|  [L=45]
Description: DNA-directed RNA polymerase subunit P [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.1e-10   39.2   8.0    5.2e-10   38.8   8.0    1.2  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
    5.6e-05   22.6   1.4       0.19   11.4   0.2    2.1  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
    0.00054   19.4   1.1    0.00067   19.1   1.1    1.2  1  TF_Zn_Ribbon    TFIIB zinc-binding
     0.0014   17.9   0.4     0.0095   15.3   0.1    2.0  2  zf-ribbon_3     zinc-ribbon domain
     0.0021   17.9   0.6     0.0026   17.6   0.6    1.2  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
     0.0023   17.9   0.5     0.0023   17.9   0.5    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
     0.0036   17.2   4.2       0.11   12.5   0.1    2.1  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
     0.0039   17.1   1.4      0.071   13.0   0.1    2.1  2  Cys_rich_CPXG   Cysteine-rich CPXCG
     0.0061   16.5   0.1     0.0063   16.5   0.1    1.1  1  Anti-TRAP       Tryptophan RNA-binding attenuator protein inh
     0.0087   15.6   1.8       0.86    9.2   0.3    2.1  2  Sgf11           Sgf11 (transcriptional regulation protein)
  ------ inclusion threshold ------
      0.015   15.3   1.0      0.024   14.7   1.0    1.4  1  DZR             Double zinc ribbon
      0.015   15.0   2.3      0.034   13.9   2.3    1.6  1  zinc_ribbon_2   zinc-ribbon domain
      0.016   15.2   1.5      0.024   14.7   1.5    1.2  1  zinc_ribbon_6   Zinc-ribbon
      0.023   14.9   1.4      0.036   14.3   1.4    1.3  1  zinc_ribbon_9   zinc-ribbon
       0.03   14.1   0.7       0.84    9.4   0.1    2.0  2  YacG            DNA gyrase inhibitor YacG
      0.033   14.3   5.4      0.074   13.2   5.3    1.7  1  Zn-ribbon_8     Zinc ribbon domain
      0.038   13.9   3.3       0.12   12.2   0.3    2.0  2  DUF951          Bacterial protein of unknown function (DUF951
      0.039   13.8   1.3        3.8    7.5   0.2    1.7  2  C1_1            Phorbol esters/diacylglycerol binding domain 
      0.052   13.6   1.5          1    9.4   0.1    2.0  2  CpXC            CpXC protein
      0.081   12.9   4.0        4.6    7.3   0.1    2.2  2  zf-C2HC_2       zinc-finger of a C2HC-type
      0.099   12.9   0.3      0.099   12.9   0.3    1.1  1  DUF2072         Zn-ribbon containing protein
       0.15   12.0   4.6        3.7    7.6   4.6    2.2  1  zinc_ribbon_4   zinc-ribbon domain
       0.19   12.5   3.9       0.39   11.5   4.0    1.4  1  zinc_ribbon_15  zinc-ribbon family
       0.23   11.8   2.5       0.78   10.1   0.1    2.0  2  DUF3268         zinc-finger-containing domain
       0.43   10.7   6.3          3    8.0   6.3    2.0  1  UPF0547         Uncharacterised protein family UPF0547
       0.43   10.7   2.5        9.4    6.4   0.1    2.0  2  DiS_P_DiS       Bacterial Peptidase A24 N-terminal domain
       0.44   10.3   4.8        2.7    7.8   0.2    2.4  3  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal


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 !   38.8   8.0   7.8e-13   5.2e-10       1      32 []       3      35 ..       3      35 .. 0.95

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 7.8e-13
                                   -B-SSS--B--.--SSS----SSS-----B--- CS
                 DNA_RNApol_7kD  1 YiCgeCgaevs.lkkgdpiRCkeCGhRilYKkR 32
                                   Y+C++C+  v+ + + + +RC +CGhRil+K+R
  gi|116754656|ref|YP_843774.1|  3 YKCARCKRTVEvDYEYAGVRCPYCGHRILMKER 35
                                   9**********7778899**************9 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.2   0.00028      0.19       3      15 ..       3      15 ..       2      19 .. 0.86
   2 !   11.0   0.1   0.00037      0.25       3      18 ..      21      36 ..      19      37 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00028
                         zf_UBZ  3 ylCerCgkeipes 15
                                   y C+rC+++++++
  gi|116754656|ref|YP_843774.1|  3 YKCARCKRTVEVD 15
                                   99*******9987 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00037
                         zf_UBZ  3 ylCerCgkeipeselq 18
                                   + C+ Cg++i++ e++
  gi|116754656|ref|YP_843774.1| 21 VRCPYCGHRILMKERP 36
                                   67**********9997 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   1.1     1e-06   0.00067       1      27 [.       3      28 ..       3      33 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1e-06
                                   EEETTTTCEECHEETSTTCEEESSSSB CS
                   TF_Zn_Ribbon  1 ykCPnCgstnlveDpergelvCtdCGl 27
                                   ykC  C+ t +++D+e + ++C+ CG 
  gi|116754656|ref|YP_843774.1|  3 YKCARCKRT-VEVDYEYAGVRCPYCGH 28
                                   89*****87.9***************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 ?    1.2   0.0      0.39   2.6e+02       3       9 ..       3       9 ..       1      15 [. 0.66
   2 !   15.3   0.1   1.4e-05    0.0095       3      11 ..      21      30 ..      19      35 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.39
                    zf-ribbon_3 3 vrCPnCG 9
                                  ++C +C+
  gi|116754656|ref|YP_843774.1| 3 YKCARCK 9
                                  5666665 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.4e-05
                    zf-ribbon_3  3 vrCPnCGa.p 11
                                   vrCP+CG+ +
  gi|116754656|ref|YP_843774.1| 21 VRCPYCGHrI 30
                                   7999999977 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.6   3.9e-06    0.0026       9      38 ..       2      30 ..       1      43 [. 0.76

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.9e-06
                 OrfB_Zn_ribbon  9 eykakeyGikveevnpayTSktCseCgskn 38
                                   +yk+ +  + ++ev+ +y   +C+ Cg++ 
  gi|116754656|ref|YP_843774.1|  2 AYKCARC-KRTVEVDYEYAGVRCPYCGHRI 30
                                   6888854.567789*************986 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.5   3.5e-06    0.0023      71      95 ..       3      29 ..       1      44 [. 0.78

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.5e-06
                                   EEETTTS-EEECHHH..HHS-TTTSSS CS
                           HypA 71 vrCreCgkefeleek..alrCpkCgsa 95
                                   ++C +C++++e++ +   +rCp Cg++
  gi|116754656|ref|YP_843774.1|  3 YKCARCKRTVEVDYEyaGVRCPYCGHR 29
                                   79*********98744678*****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 ?    6.6   0.8     0.012       7.8      38      46 .]       3      11 ..       1      11 [. 0.87
   2 !   12.5   0.1   0.00016      0.11      18      28 ..      20      35 ..      18      44 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.012
                  Zn_Tnp_IS1595 38 fqCkeCrkq 46
                                   ++C++C+++
  gi|116754656|ref|YP_843774.1|  3 YKCARCKRT 11
                                   9******85 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00016
                  Zn_Tnp_IS1595 18 gfvCPhCgsr.....k 28
                                   g++CP+Cg+r     +
  gi|116754656|ref|YP_843774.1| 20 GVRCPYCGHRilmkeR 35
                                   799*****98554433 PP

>> Cys_rich_CPXG  Cysteine-rich CPXCG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.095        63       1      13 [.       3      15 ..       3      20 .. 0.79
   2 !   13.0   0.1   0.00011     0.071       1      11 [.      21      31 ..      21      33 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.095
                  Cys_rich_CPXG  1 iqCPyCgeeievl 13
                                   ++C+ C  ++ev+
  gi|116754656|ref|YP_843774.1|  3 YKCARCKRTVEVD 15
                                   6899999998876 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00011
                  Cys_rich_CPXG  1 iqCPyCgeeie 11
                                   + CPyCg++i 
  gi|116754656|ref|YP_843774.1| 21 VRCPYCGHRIL 31
                                   68******985 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 !   16.5   0.1   9.5e-06    0.0063      12      42 ..       4      31 ..       1      39 [. 0.84

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 9.5e-06
                                   E-TTTTTTSEETTE......E-TTTTTSSEE CS
                      Anti-TRAP 12 kCdaCngsGkiepeeprasleCPkCsGkgli 42
                                   kC  C+++ +++ e   a++ CP C G+ ++
  gi|116754656|ref|YP_843774.1|  4 KCARCKRTVEVDYE--YAGVRCPYC-GHRIL 31
                                   8***********99..9********.55555 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.3    0.0013      0.86       4      14 ..       2      12 ..       1      14 [. 0.86
   2 ?    6.3   0.1     0.011       7.2       5      14 ..      21      30 ..      17      32 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0013
                                   EEE-TTTSSEE CS
                          Sgf11  4 yvtCpnCgRqi 14
                                    ++C  C+R++
  gi|116754656|ref|YP_843774.1|  2 AYKCARCKRTV 12
                                   589*******9 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.011
                                   EE-TTTSSEE CS
                          Sgf11  5 vtCpnCgRqi 14
                                   v+Cp+Cg  i
  gi|116754656|ref|YP_843774.1| 21 VRCPYCGHRI 30
                                   89****9766 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   1.0   3.6e-05     0.024      14      36 ..       4      28 ..       1      37 [. 0.54

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.6e-05
                            DZR 14 fCseCgtklkavaa..edrCpsCge 36
                                    C +C+ +++   +    rCp Cg+
  gi|116754656|ref|YP_843774.1|  4 KCARCKRTVEVDYEyaGVRCPYCGH 28
                                   3555555554333344555555555 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   2.3   5.1e-05     0.034       1      22 [.       4      29 ..       4      30 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.1e-05
                  zinc_ribbon_2  1 fCpnCGaelqdnakF....CpyCGtp 22
                                   +C +C ++++ +  +    CpyCG+ 
  gi|116754656|ref|YP_843774.1|  4 KCARCKRTVEVDYEYagvrCPYCGHR 29
                                   7999999998666666999*****96 PP

>> zinc_ribbon_6  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   1.5   3.6e-05     0.024      32      54 ..       5      27 ..       2      28 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.6e-05
                  zinc_ribbon_6 32 CnDCekksevkfhvlglkCkeCg 54
                                   C  C+++ ev++ ++g++C  Cg
  gi|116754656|ref|YP_843774.1|  5 CARCKRTVEVDYEYAGVRCPYCG 27
                                   999*******************7 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   1.4   5.4e-05     0.036       5      30 ..       5      29 ..       3      32 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.4e-05
                  zinc_ribbon_9  5 ChqCdrfVsvspdedsdvlCPhCggg 30
                                   C +C+r+V+v  +      CP+Cg  
  gi|116754656|ref|YP_843774.1|  5 CARCKRTVEVDYEYAGVR-CPYCGHR 29
                                   679*******87766667.****976 PP

>> YacG  DNA gyrase inhibitor YacG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1      0.07        47       2      13 ..       4      15 ..       3      19 .. 0.83
   2 ?    9.4   0.1    0.0013      0.84       1      14 [.      21      34 ..      21      45 .] 0.83

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.07
                           YacG  2 kCPtCkkevews 13
                                   kC  Ck++ve++
  gi|116754656|ref|YP_843774.1|  4 KCARCKRTVEVD 15
                                   7999**999976 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0013
                           YacG  1 vkCPtCkkevewse 14
                                   v+CP C++++ ++e
  gi|116754656|ref|YP_843774.1| 21 VRCPYCGHRILMKE 34
                                   89******999988 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   5.3   0.00011     0.074       6      34 ..       3      28 ..       2      34 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00011
                    Zn-ribbon_8  6 YrCeeCghefevlqsisdapltaCPeCgs 34
                                   Y+C +C+++ ev     + + + CP Cg+
  gi|116754656|ref|YP_843774.1|  3 YKCARCKRTVEVDY---EYAGVRCPYCGH 28
                                   ***********666...555889*****8 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 ?    3.2   0.2      0.12        83      32      42 ..       4      14 ..       1      19 [. 0.84
   2 ?   12.2   0.3   0.00019      0.12      31      54 ..      21      45 .]      17      45 .] 0.85

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.12
                         DUF951 32 kClgcgrevml 42
                                   kC +c+r v +
  gi|116754656|ref|YP_843774.1|  4 KCARCKRTVEV 14
                                   9******9965 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00019
                         DUF951 31 lkClgcgrevml.pRskfekkikkv 54
                                   ++C  cg+ +++ +R +  k++k +
  gi|116754656|ref|YP_843774.1| 21 VRCPYCGHRILMkERPTTVKRMKAI 45
                                   79******99963699999999986 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 ?    7.5   0.2    0.0057       3.8      28      38 ..       2      12 ..       1      15 [. 0.84
   2 ?    5.5   0.0     0.024        16      11      23 ..      20      32 ..      14      42 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0057
                                   EEEETTT--EE CS
                           C1_1 28 glkCswCkllv 38
                                   ++kC+ Ck++v
  gi|116754656|ref|YP_843774.1|  2 AYKCARCKRTV 12
                                   79******998 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.024
                                   --B-TTT-SB--S CS
                           C1_1 11 ptfCkhCgeflwg 23
                                     +C +Cg  + +
  gi|116754656|ref|YP_843774.1| 20 GVRCPYCGHRILM 32
                                   4578888888844 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.055        37      38      52 ..       3      17 ..       1      20 [. 0.80
   2 ?    9.4   0.1    0.0015         1      38      51 ..      21      34 ..      17      44 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.055
                           CpXC 38 atCpkCgatakleap 52
                                   ++C +C +t++++++
  gi|116754656|ref|YP_843774.1|  3 YKCARCKRTVEVDYE 17
                                   789999999988886 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0015
                           CpXC 38 atCpkCgataklea 51
                                   ++Cp+Cg+++ ++ 
  gi|116754656|ref|YP_843774.1| 21 VRCPYCGHRILMKE 34
                                   79*****9998764 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 ?    7.3   0.1    0.0069       4.6       4      15 ..       4      15 ..       3      16 .. 0.86
   2 ?    6.6   1.1     0.011       7.1       3       9 ..      21      27 ..      21      27 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0069
                      zf-C2HC_2  4 pCpkCgRsFnpd 15
                                   +C  C+R+  +d
  gi|116754656|ref|YP_843774.1|  4 KCARCKRTVEVD 15
                                   799*****9887 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.011
                      zf-C2HC_2  3 vpCpkCg 9 
                                   v Cp+Cg
  gi|116754656|ref|YP_843774.1| 21 VRCPYCG 27
                                   78****9 PP

>> DUF2072  Zn-ribbon containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   0.00015     0.099       2      30 ..       3      31 ..       2      44 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00015
                        DUF2072  2 HkCtkCekvfedgskeilkGCpsCGgkkF 30
                                    kC++C+++ e   +     Cp CG +  
  gi|116754656|ref|YP_843774.1|  3 YKCARCKRTVEVDYEYAGVRCPYCGHRIL 31
                                   59*********999999999*****8754 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   4.6    0.0055       3.7       4      35 ..       4      30 ..       1      31 [. 0.72

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0055
                  zinc_ribbon_4  4 tCpsCkakyeiddeklpakgvkvrCskCghvF 35
                                    C +Ck + e+d e      + vrC+ Cgh +
  gi|116754656|ref|YP_843774.1|  4 KCARCKRTVEVDYE-----YAGVRCPYCGHRI 30
                                   57777777777664.....5679*******86 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   4.0   0.00058      0.39      66      86 .]       3      27 ..       2      27 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00058
                 zinc_ribbon_15 66 keCknCgkeveeefky....CpkCg 86
                                   ++C++C+++ve +++y    Cp+Cg
  gi|116754656|ref|YP_843774.1|  3 YKCARCKRTVEVDYEYagvrCPYCG 27
                                   68*************99999****9 PP

>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.4      0.26   1.7e+02      29      43 ..       1      15 [.       1      20 [. 0.84
   2 ?   10.1   0.1    0.0012      0.78       3      16 ..      21      34 ..      19      44 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.26
                        DUF3268 29 llylCpkCdayvgvh 43
                                   ++y C +C   v v 
  gi|116754656|ref|YP_843774.1|  1 MAYKCARCKRTVEVD 15
                                   6899****9999886 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0012
                        DUF3268  3 trCpyCGekvilvs 16
                                   +rCpyCG+++ +++
  gi|116754656|ref|YP_843774.1| 21 VRCPYCGHRILMKE 34
                                   79******998876 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   6.3    0.0046         3       3      23 ..       5      29 ..       4      29 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0046
                        UPF0547  3 CPeCeakvPvaa....qfCphCGyv 23
                                   C +C ++v v+     ++Cp+CG++
  gi|116754656|ref|YP_843774.1|  5 CARCKRTVEVDYeyagVRCPYCGHR 29
                                   777888887754222269*****95 PP

>> DiS_P_DiS  Bacterial Peptidase A24 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.3     0.036        24      54      67 ..       4      17 ..       1      21 [. 0.82
   2 ?    6.4   0.1     0.014       9.4      29      39 ..      22      32 ..      18      36 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.036
                      DiS_P_DiS 54 rCraCkakislryp 67
                                   +C++Ck+++++ y 
  gi|116754656|ref|YP_843774.1|  4 KCARCKRTVEVDYE 17
                                   89999999998885 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.014
                      DiS_P_DiS 29 rCpkCghklkw 39
                                   rCp Cgh++ +
  gi|116754656|ref|YP_843774.1| 22 RCPYCGHRILM 32
                                   78888888765 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.6      0.04        27      44      52 ..       2      10 ..       1      12 [. 0.83
   2 ?    7.8   0.2    0.0041       2.7      38      53 ..      14      29 ..      10      30 .. 0.80
   3 ?   -1.2   0.0       2.5   1.7e+03       8      23 ..      30      45 .]      29      45 .] 0.76

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.04
                 zinc_ribbon_10 44 kyrCpkCga 52
                                    y+C+ C+ 
  gi|116754656|ref|YP_843774.1|  2 AYKCARCKR 10
                                   7******86 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0041
                 zinc_ribbon_10 38 eeleevkyrCpkCgal 53
                                    ++e+   rCp+Cg+ 
  gi|116754656|ref|YP_843774.1| 14 VDYEYAGVRCPYCGHR 29
                                   677888889*****96 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 2.5
                 zinc_ribbon_10  8 vLvGddetsaknryal 23
                                   +L+ + +t +k ++a+
  gi|116754656|ref|YP_843774.1| 30 ILMKERPTTVKRMKAI 45
                                   5777888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 325.91
//
Query:       gi|116754657|ref|YP_843775.1|  [L=94]
Description: 50S ribosomal protein L37Ae [Methanosaeta thermophila PT]
Scores for complete 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-29  101.3   4.3    2.6e-29  101.1   4.3    1.0  1  Ribosomal_L37ae  Ribosomal L37ae protein family
    0.00096   19.1   3.8     0.0015   18.5   3.8    1.3  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.003   17.7   0.4       0.57   10.3   0.2    2.3  2  Zn-ribbon_8      Zinc ribbon domain
  ------ inclusion threshold ------
      0.013   15.4   0.6      0.021   14.8   0.6    1.4  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.014   15.2   0.9       0.81    9.5   0.1    2.2  2  zinc_ribbon_10   Predicted integral membrane zinc-ribbon meta
      0.015   15.5   0.2      0.023   14.9   0.2    1.2  1  IBR              IBR domain, a half RING-finger domain
      0.038   13.8   0.2      0.044   13.5   0.2    1.1  1  Rep_fac-A_C      Replication factor-A C terminal domain
      0.049   13.7   1.1       0.12   12.5   1.1    1.6  1  Elf1             Transcription elongation factor Elf1 like
       0.05   13.5   3.7       0.15   12.0   3.7    1.8  1  HalOD2           Halobacterial output domain 2
      0.093   12.8   5.2       0.56   10.3   5.2    2.0  1  UPF0547          Uncharacterised protein family UPF0547
      0.099   12.3   2.2        3.8    7.2   0.4    2.2  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
        0.1   13.1   0.1       0.13   12.8   0.1    1.2  1  RPA_interact_C   Replication protein A interacting C-terminal
       0.21   11.6   2.7        1.5    8.9   2.7    1.9  1  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
       0.23   10.8   2.7       0.69    9.3   2.7    1.7  1  zf-TFIIB         Transcription factor zinc-finger
       0.27   11.0   4.9       0.53   10.0   1.1    2.2  2  Rubredoxin_2     Rubredoxin metal binding domain
       0.35   10.6   3.1        4.4    7.2   0.7    2.3  2  zinc_ribbon_2    zinc-ribbon domain
       0.47   11.0   4.2        0.9   10.1   0.3    2.2  2  zf-H2C2_2        Zinc-finger double domain
       0.53   10.7   5.1       0.73   10.2   0.6    2.2  2  DUF4379          Probable Zinc-ribbon domain
       0.55   10.2   5.4        5.5    7.0   4.5    2.1  2  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
       0.66   10.1   2.5        2.2    8.4   0.1    2.1  2  zf-Mss51         Zinc-finger of mitochondrial splicing suppre


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 !  101.1   4.3     3e-32   2.6e-29       2      84 ..       8      91 ..       7      92 .. 0.93

  Alignments for each domain:
  == domain 1  score: 101.1 bits;  conditional E-value: 3e-32
                                   XXXXX-GGGGTTSS-HHHHHHHHHHHHHHHS-BEESSSSSSEEEEEETTEEEETTTTEEEE-BSSSSS-HHHHHHHH-.XXX CS
                Ribosomal_L37ae  2 tkkvgiaGkygtrYGaslrkrvkkieisqhakytCpfcgktkvkRkavgiwkCkkcgktvaGgAytpettsaktvksa.irr 82
                                    +k+++a ++g+rYG+++rk v++ie++++ +y Cp+c++t+v+R+++ iw+C+kcg+++aGg+y p t+++++v ++ i+r
  gi|116754657|ref|YP_843775.1|  8 GRKTRSAARFGPRYGRKIRKLVADIEEKSRVRYDCPRCNRTRVRRVGTAIWQCSKCGYEFAGGTYLPVTSAGRSVVRSmIKR 89
                                   689*******************************************************************998765554988 PP

                                   XX CS
                Ribosomal_L37ae 83 lk 84
                                   + 
  gi|116754657|ref|YP_843775.1| 90 AM 91
                                   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 !   18.5   3.8   1.7e-06    0.0015      20      45 ..      41      65 ..      33      66 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.7e-06
                  Zn_Tnp_IS1595 20 vCPhCgsrkayriktrglfqCkeCrk 45
                                    CP+C  ++++r+ t   +qC++C++
  gi|116754657|ref|YP_843775.1| 41 DCPRCNRTRVRRVGT-AIWQCSKCGY 65
                                   4*****99******9.********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 !   10.3   0.2   0.00064      0.57      28      39 ..      40      53 ..      22      53 .. 0.78
   2 ?    5.6   0.0     0.019        17       7      15 ..      59      67 ..      58      92 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00064
                    Zn-ribbon_8 28 a.CPeCgs.evrrv 39
                                     CP+C+  +vrrv
  gi|116754657|ref|YP_843775.1| 40 YdCPRCNRtRVRRV 53
                                   44**********97 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.019
                    Zn-ribbon_8  7 rCeeCghef 15
                                   +C +Cg ef
  gi|116754657|ref|YP_843775.1| 59 QCSKCGYEF 67
                                   7*****999 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 ?   14.8   0.6   2.3e-05     0.021      30      56 ..      41      67 ..      21      68 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.3e-05
                 OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgfea 56
                                   +C++C ++  +++ +  ++C++Cg+e+
  gi|116754657|ref|YP_843775.1| 41 DCPRCNRTRVRRVGTAIWQCSKCGYEF 67
                                   7***********************985 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 ?    9.5   0.1    0.0009      0.81      38      52 ..      33      47 ..      28      49 .. 0.86
   2 ?    4.4   0.1     0.034        30      44      52 ..      57      65 ..      50      66 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0009
                 zinc_ribbon_10 38 eeleevkyrCpkCga 52
                                   ee+++v+y Cp C+ 
  gi|116754657|ref|YP_843775.1| 33 EEKSRVRYDCPRCNR 47
                                   7999*********96 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.034
                 zinc_ribbon_10 44 kyrCpkCga 52
                                    ++C+kCg 
  gi|116754657|ref|YP_843775.1| 57 IWQCSKCGY 65
                                   79*****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 ?   14.9   0.2   2.5e-05     0.023      11      48 ..      31      67 ..      20      69 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.5e-05
                            IBR 11 sles.dpnlkwCprpdCeaiieksegcksvtCskCgfef 48
                                    +e+ ++ +  Cp   C++      g++  +CskCg+ef
  gi|116754657|ref|YP_843775.1| 31 DIEEkSRVRYDCP--RCNRTRVRRVGTAIWQCSKCGYEF 67
                                   35663555778**..9**99888888999*********9 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 ?   13.5   0.2     5e-05     0.044       7      49 ..      28      69 ..      23      78 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5e-05
                                   EEEEEETTTTEEEB--STT---B-EEE.TTTEEEETTTTEEESS CS
                    Rep_fac-A_C  7 tvsfikkdnlvYkACpsedCnkKvvee.edgewrCekCdkevee 49
                                    v  i++++ v   Cp   Cn+  v++ +   w+C kC  e++ 
  gi|116754657|ref|YP_843775.1| 28 LVADIEEKSRVRYDCP--RCNRTRVRRvGTAIWQCSKCGYEFAG 69
                                   56667777666667**..****9888868899******988865 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.1   0.00013      0.12      15      55 ..      33      67 ..      20      78 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                           Elf1 15 kkklptkFdCpfCnheksvevkldkkekiaevsCkvCgesf 55
                                    +k   ++dCp+Cn +   +    ++ ++a+ +C++Cg +f
  gi|116754657|ref|YP_843775.1| 33 EEKSRVRYDCPRCNRT---R---VRRVGTAIWQCSKCGYEF 67
                                   4556789*********...2...2456899*******9887 PP

>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   3.7   0.00016      0.15      24      41 ..      50      67 ..      40      72 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
                         HalOD2 24 yrqLGayvWkCtrCGevq 41
                                   +r+ G+ +W+C++CG   
  gi|116754657|ref|YP_843775.1| 50 VRRVGTAIWQCSKCGYEF 67
                                   7899***********755 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   5.2   0.00062      0.56       3      24 ..      42      67 ..      41      68 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00062
                        UPF0547  3 CPeCeak....vPvaaqfCphCGyvF 24
                                   CP+C ++    v +a   C+ CGy+F
  gi|116754657|ref|YP_843775.1| 42 CPRCNRTrvrrVGTAIWQCSKCGYEF 67
                                   999997666669*************9 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.4    0.0042       3.8       3      10 ..      40      47 ..      38      48 .. 0.86
   2 ?    4.8   0.1     0.024        21       3      12 ..      58      67 ..      56      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0042
                         zf_UBZ  3 ylCerCgk 10
                                   y C+rC++
  gi|116754657|ref|YP_843775.1| 40 YDCPRCNR 47
                                   99****97 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.024
                         zf_UBZ  3 ylCerCgkei 12
                                   ++C++Cg e+
  gi|116754657|ref|YP_843775.1| 58 WQCSKCGYEF 67
                                   79****9765 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 ?   12.8   0.1   0.00015      0.13       2      27 ..      42      69 ..      41      93 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00015
                 RPA_interact_C  2 CPvCkkrklkets.evifCe.Cglrlet 27
                                   CP C+++++++    + +C+ Cg +++ 
  gi|116754657|ref|YP_843775.1| 42 CPRCNRTRVRRVGtAIWQCSkCGYEFAG 69
                                   ***********9857779*99**99986 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   2.7    0.0016       1.5      15      29 ..      53      67 ..      41      68 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0016
                 PhnA_Zn_Ribbon 15 edgallvCpeCahEw 29
                                   +++a++ C++C++E+
  gi|116754657|ref|YP_843775.1| 53 VGTAIWQCSKCGYEF 67
                                   6789**********8 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   2.7   0.00077      0.69       1      26 [.      41      64 ..      41      64 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00077
                       zf-TFIIB  1 kCPkCqdeleeserggveidyCpqCr 26
                                   +CP+C+ +   ++r g  i++C +C+
  gi|116754657|ref|YP_843775.1| 41 DCPRCNRT--RVRRVGTAIWQCSKCG 64
                                   5****986..68999**********7 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1      0.14   1.2e+02      17      21 ..      42      46 ..      40      54 .. 0.76
   2 ?   10.0   1.1    0.0006      0.53       1      11 [.      58      68 ..      58      69 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.14
                   Rubredoxin_2 17 CpsCg 21
                                   Cp C+
  gi|116754657|ref|YP_843775.1| 42 CPRCN 46
                                   77776 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0006
                   Rubredoxin_2  1 YvCsqCGfesa 11
                                   ++Cs+CG+e+a
  gi|116754657|ref|YP_843775.1| 58 WQCSKCGYEFA 68
                                   89******975 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   0.1     0.065        58       2       6 ..      42      46 ..      34      50 .. 0.71
   2 ?    7.2   0.7    0.0049       4.4      16      22 ..      60      66 ..      59      67 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.065
                  zinc_ribbon_2  2 CpnCG 6 
                                   Cp+C 
  gi|116754657|ref|YP_843775.1| 42 CPRCN 46
                                   66665 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0049
                  zinc_ribbon_2 16 CpyCGtp 22
                                   C++CG++
  gi|116754657|ref|YP_843775.1| 60 CSKCGYE 66
                                   7777775 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 ?    2.6   0.4      0.24   2.1e+02      14      22 ..      39      47 ..      33      51 .. 0.79
   2 ?   10.1   0.3     0.001       0.9      14      25 ..      57      68 ..      48      68 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.24
                      zf-H2C2_2 14 pyeCplCdk 22
                                   +y Cp C+ 
  gi|116754657|ref|YP_843775.1| 39 RYDCPRCNR 47
                                   499****97 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.001
                      zf-H2C2_2 14 pyeCplCdkaFk 25
                                   +++C++C++ F+
  gi|116754657|ref|YP_843775.1| 57 IWQCSKCGYEFA 68
                                   68*******995 PP

>> DUF4379  Probable Zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.3      0.32   2.9e+02      45      56 .]      36      45 ..      22      45 .. 0.68
   2 ?   10.2   0.6   0.00081      0.73      28      39 ..      56      67 ..      49      72 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.32
                        DUF4379 45 nrtkgsskCpkC 56
                                   +r+  + +Cp C
  gi|116754657|ref|YP_843775.1| 36 SRV--RYDCPRC 45
                                   333..3349999 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00081
                        DUF4379 28 vwWkCakCgheW 39
                                   + W+C+kCg+e+
  gi|116754657|ref|YP_843775.1| 56 AIWQCSKCGYEF 67
                                   78*******997 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 ?    2.8   0.7      0.12   1.1e+02      21      27 ..      37      45 ..      28      49 .. 0.67
   2 ?    7.0   4.5    0.0061       5.5       4      31 ..      42      67 ..      42      69 .. 0.66

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.12
                                   E..EEESSS CS
                 RNA_POL_M_15KD 21 n..feCrqC 27
                                   +  ++C  C
  gi|116754657|ref|YP_843775.1| 37 RvrYDCPRC 45
                                   335888888 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0061
                                   ESTTTSBEEEEECSCCCEEEESSSS-EE CS
                 RNA_POL_M_15KD  4 CpkCgNlLlpkedkegknfeCrqCgYee 31
                                   Cp C+     +++   +   C++CgYe+
  gi|116754657|ref|YP_843775.1| 42 CPRCNRTRVRRVGTAIW--QCSKCGYEF 67
                                   66666555555555554..6******97 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 ?    8.4   0.1    0.0025       2.2      11      22 ..      34      45 ..       6      51 .. 0.83
   2 ?    2.1   0.3      0.24   2.2e+02      17      24 ..      58      65 ..      49      68 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0025
                       zf-Mss51 11 apkhvdfeCpdC 22
                                   ++++v+++Cp+C
  gi|116754657|ref|YP_843775.1| 34 EKSRVRYDCPRC 45
                                   789********* PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.24
                       zf-Mss51 17 feCpdCGi 24
                                    +C +CG+
  gi|116754657|ref|YP_843775.1| 58 WQCSKCGY 65
                                   68*****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 678.56
//
Query:       gi|116754658|ref|YP_843776.1|  [L=257]
Description: exosome complex RNA-binding protein Rrp42 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.9e-26   92.1   0.0    6.1e-26   91.5   0.0    1.3  1  RNase_PH    3' exoribonuclease family, domain 1
    2.5e-08   33.8   0.2    3.9e-08   33.2   0.2    1.3  1  RNase_PH_C  3' exoribonuclease family, domain 2


Domain annotation for each model (and alignments):
>> RNase_PH  3' exoribonuclease family, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.5   0.0   6.8e-30   6.1e-26       1     132 []      30     165 ..      30     165 .. 0.93

  Alignments for each domain:
  == domain 1  score: 91.5 bits;  conditional E-value: 6.8e-30
                                    EEEEEEEEESSSSTTSEEEEEEECCEEEEEEEEEEEEEE-TCCG--CCEEEECCCCECCCCEC-C...S...HHHHHHHH CS
                       RNase_PH   1 elRslsietgvlsqanGSaylelGdtkvlasvtgpieerpseerddaegaldveveyapfasgerrregrpsdeeielsr 80 
                                    ++R+++ie +++++a+GSa+++lG+t+v+++++ +  e p++++ ++ g+++++ e+ p+as+ ++  g p++  iel+r
  gi|116754658|ref|YP_843776.1|  30 QYRPIEIERNIIKKAEGSALVKLGKTQVMVGIKIQPGE-PFPDA-PNRGVIVTNAELVPLASPIFEP-GPPNEYGIELAR 106
                                    68**********************************99.66664.33489***************77.9*********** PP

                                    HHHHHHCCTC-C........CGCCTCEEEEEEEEEECCCS-CHHHCHHHHHHHHHCTCEE CS
                       RNase_PH  81 lleralrpsill........ekkpkstididitvlssdggslldalinaaslALadagip 132
                                    +++r +r+s+++        ++++ + i idi++l++ g +++da++++a++AL+ a +p
  gi|116754658|ref|YP_843776.1| 107 VVDRGVRESGSVdldalcivPGEKVWIIFIDIHILDDCG-NIMDASSLGAIAALLGATVP 165
                                    ***********88888888899999**************.**************999887 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 !   33.2   0.2   4.3e-12   3.9e-08       1      66 [.     181     246 ..     181     247 .. 0.97

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 4.3e-12
                                    S--EEEEEEEETTEEEES--HHHHHHSSEEEEEEEETTSEEEEEEEECSSCEEHHHHHHHHHHHHH CS
                     RNase_PH_C   1 apviavtvgkvddqfvlDptkeEedlsegdltlavagtkevvtlmkeggsqldeetlleaielAkk 66 
                                    +++ia t   ++d ++ Dp+ +Ee++++++lt+    ++ ++ ++k+g + l+e+++ + +++A +
  gi|116754658|ref|YP_843776.1| 181 DIPIATTAVEFGDVVLFDPDVDEEAIADAKLTVITKADGTICGMQKSGPGMLSEDQVYRIVDIACD 246
                                    689***********************************************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1927.68
//
Query:       gi|116754659|ref|YP_843777.1|  [L=245]
Description: exosome complex exonuclease Rrp41 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      6e-35  120.6   0.0    8.3e-35  120.2   0.0    1.2  1  RNase_PH    3' exoribonuclease family, domain 1
    8.7e-17   60.9   0.0    1.8e-16   59.9   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 !  120.2   0.0   9.3e-39   8.3e-35       1     132 []      20     149 ..      20     149 .. 0.93

  Alignments for each domain:
  == domain 1  score: 120.2 bits;  conditional E-value: 9.3e-39
                                    EEEEEEEEESSSSTTSEEEEEEECCEEEEEEEEEEEEEE-TCCG--CC.EEEECCCCECCCCEC-C...S...HHHHHHH CS
                       RNase_PH   1 elRslsietgvlsqanGSaylelGdtkvlasvtgpieerpseerddae.galdveveyapfasgerrregrpsdeeiels 79 
                                    elR++++e gvl++a+GS+y+e+Gd+kv+a+v+gp+e++p+  + +++   +  ++++a+f+ +errr   p++++ els
  gi|116754659|ref|YP_843777.1|  20 ELRPIKMEVGVLKRADGSCYMEMGDNKVIAAVYGPREVHPRHLQ-EVNrAIIRYRYNMASFSVEERRR-PGPDRRSYELS 97 
                                    79************************************777663.333244***************88.56********* PP

                                    HHHHHHHCCTC-CCGCCTCEEEEEEEEEECCCS-CHHHCHHHHHHHHHCTCEE CS
                       RNase_PH  80 rlleralrpsillekkpkstididitvlssdggslldalinaaslALadagip 132
                                    ++  +al+p+il++ +pks idi+++vl++d  ++  a inaas+ALadagip
  gi|116754659|ref|YP_843777.1|  98 KVSREALEPVILTSYFPKSVIDIFVEVLQADA-GTRTAGINAASVALADAGIP 149
                                    ********************************.*******************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 !   59.9   0.0     2e-20   1.8e-16       2      67 .]     153     216 ..     152     216 .. 0.98

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 2e-20
                                    --EEEEEEEETTEEEES--HHHHHHSSEEEEEEEETTSEEEEEEEECSSCEEHHHHHHHHHHHHHH CS
                     RNase_PH_C   2 pviavtvgkvddqfvlDptkeEedlsegdltlavagtkevvtlmkeggsqldeetlleaielAkkg 67 
                                    +v++++ gkvd+q+vlDp k+E++ +++d+++a++ t+e+ tl++++g  l+++++ +a+elAkkg
  gi|116754659|ref|YP_843777.1| 153 LVSSCAAGKVDGQIVLDPMKDEDNFGQADMPIAITPTGEI-TLLQMDGI-LTRDEFRQAMELAKKG 216
                                    799***********************************99.********.**************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1892.65
//
Query:       gi|116754660|ref|YP_843778.1|  [L=221]
Description: exosome complex RNA-binding protein Rrp4 [Methanosaeta thermophila PT]
Scores for 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-10   38.8   0.4    2.3e-09   37.5   0.4    1.7  1  KH_6      KH domain
    1.9e-08   34.0   0.0    3.3e-08   33.2   0.0    1.4  1  ECR1_N    Exosome complex exonuclease RRP4 N-terminal region
    3.5e-08   33.2   0.0    6.6e-08   32.3   0.0    1.5  1  KH_1      KH domain
    5.3e-07   29.9   0.0    1.3e-06   28.6   0.0    1.7  1  S1        S1 RNA binding domain
    8.3e-05   22.3   0.2    0.00017   21.3   0.2    1.6  1  KH_2      KH domain


Domain annotation for each model (and alignments):
>> KH_6  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.5   0.4   6.4e-13   2.3e-09       1      45 [.     137     184 ..     137     185 .. 0.89

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 6.4e-13
                           KH_6   1 GmlfeVslslvrRll...nhvLeeLgkagpfeiavGlNGriWvksesp 45 
                                    G ++e+s   v+Rl+     ++++L+k++ ++i vG+NGriWv+++++
  gi|116754660|ref|YP_843778.1| 137 GRVVEISHTRVPRLIgkgGSMISMLKKELNCNIFVGQNGRIWVSGNEE 184
                                    789************999555599999999*************99875 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 !   33.2   0.0   9.3e-12   3.3e-08       1      34 [.       5      37 ..       5      40 .. 0.95

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 9.3e-12
                                   EE-TT-EEEETTTSEE-TTEEEETTEEEESSSEE CS
                         ECR1_N  1 iVtPGevlttdeefmrGhGTYvrggtiyAsvaGt 34
                                   iV+PG+ l ++++  +G+GTYvr+g++y+ + G+
  gi|116754660|ref|YP_843778.1|  5 IVIPGDLL-SEDTRRAGEGTYVRNGKVYSLLYGI 37
                                   9*******.9999*******************97 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.0   1.9e-11   6.6e-08       3      64 ..     139     193 ..     137     195 .. 0.88

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 1.9e-11
                                    EEEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEEESHHHHHHHHHHH CS
                           KH_1   3 rilvPsslvgriIGkgGsnIkeIreetgakIkvpksedegsderevtisGspeavekAkeli 64 
                                    ++++ +  v+r+IGkgGs+I  +++e +++I v  +      +  + +sG++e+ + A++ i
  gi|116754660|ref|YP_843778.1| 139 VVEISHTRVPRLIGKGGSMISMLKKELNCNIFVG-Q------NGRIWVSGNEEDMDLALKTI 193
                                    5799999******************88*****75.3......357*****9999**999887 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   3.7e-10   1.3e-06       2      68 ..      55     121 ..      54     126 .. 0.94

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 3.7e-10
                                    STTTCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTT CS
                             S1   2 pekgevveGeVtsvtkgGafVelgngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrr 68 
                                    p++g+ v G+V+++t  + + ++  + +g++++se + + +ved ++ l++G  v ++v +vd + +
  gi|116754660|ref|YP_843778.1|  55 PAVGDNVIGVVKDITFSNWILDINSPYDGLLHISEFPKKIDVEDMSKYLRIGSSVMARVKDVDPAMK 121
                                    789************************************************************8755 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.2   4.7e-08   0.00017      28      68 ..     139     179 ..     112     183 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 4.7e-08
                                    EEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEE CS
                           KH_2  28 iiviresqpgivIGkgGsnikkigkelrkdieklegkkVkl 68 
                                    ++ i   +  ++IGkgGs+i +++kel+ +i + +++++++
  gi|116754660|ref|YP_843778.1| 139 VVEISHTRVPRLIGKGGSMISMLKKELNCNIFVGQNGRIWV 179
                                    566788899*********************99999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 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:                        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: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1803.81
//
Query:       gi|116754661|ref|YP_843779.1|  [L=232]
Description: putative RNA-associated protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-22   78.6   0.0    4.8e-22   77.8   0.0    1.4  1  SBDS      Shwachman-Bodian-Diamond syndrome (SBDS) protein
    1.6e-19   70.0   0.1    2.6e-19   69.4   0.1    1.3  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 !   77.8   0.0   5.3e-26   4.8e-22       5      88 .]      10      93 ..       6      93 .. 0.97

  Alignments for each domain:
  == domain 1  score: 77.8 bits;  conditional E-value: 5.3e-26
                                   EEEEETTEEEEEEE-HHHHHHHHCTT---HHHHBSSSS-EEETTTTEE--HHHHHHHHS---HHHHHHHHHHHSEEE--HHH CS
                           SBDS  5 vrykkgkkrFeiavyknklleyregkeidLsevlqsekiFtnaskGetaskselekafgteskdeiikeILkkGeiqvsaee 86
                                   +r+k+++  Fe++v+++ +l  r+g+++ ++++l++e++F+nas+G++  +++l kafgt++   i+++I+kkGei ++ae+
  gi|116754661|ref|YP_843779.1| 10 ARLKSHGAVFEVLVDPDGALAMRRGEDVRIEDILAVEDVFENASRGDRSAEEDLLKAFGTTDPLAIAEIIIKKGEISLTAEQ 91
                                   79*******************************************************************************9 PP

                                   HH CS
                           SBDS 87 rk 88
                                   r+
  gi|116754661|ref|YP_843779.1| 92 RR 93
                                   96 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 !   69.4   0.1   2.8e-23   2.6e-19       2     115 ..     100     217 ..      99     218 .. 0.82

  Alignments for each domain:
  == domain 1  score: 69.4 bits;  conditional E-value: 2.8e-23
                                    HHHHHHHHHHHEEBTTTTB---HHHHHHHHHHTT----TTS-CCCCHHHHHHHHTTTS--EE-EEEEEEEE-...CCCHH CS
                         SBDS_C   2 ekeiieivaeklvnpqtkrpytttmIekalkelgtsvktnksaksQalevikaLiqeipiqrarmrlritcptsikdkil 81 
                                    ++++ie++a++++npqt++p+++++Ie+a+ e++++++++ks ++ ++  +ka++ +ipi+++++++++++p   ++++ 
  gi|116754661|ref|YP_843779.1| 100 KRQVIELIARNAINPQTRTPHPPSRIEQAMAEAKVHIDPTKSLEELVAITMKAIRPIIPIRFEEVEVAVKVP---ASYAA 176
                                    799*********************************************************************...55555 PP

                                    HHHHHH.HH.....S.EE.....EEEE.EEGGGHHHHHHHH CS
                         SBDS_C  82 klieqv.esqkvaekewe.....vvvl.iePgaykeleefv 115
                                    k + ++ +  k++ + w+     + v+ i++g++ e+ ++v
  gi|116754661|ref|YP_843779.1| 177 KSYGEIsTFGKLVREAWQndgswIGVIrIPAGMQTEFYSLV 217
                                    55555545545444444444444444459999999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1629.35
//
Query:       gi|116754662|ref|YP_843780.1|  [L=240]
Description: proteasome subunit alpha [Methanosaeta thermophila PT]
Scores for complete 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-57  193.3   0.4    3.4e-57  193.0   0.4    1.1  1  Proteasome      Proteasome subunit
    1.1e-14   53.8   0.5    3.9e-14   52.0   0.1    2.1  2  Proteasome_A_N  Proteasome subunit A N-terminal signature


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.0   0.4   3.8e-61   3.4e-57       1     190 []      26     210 ..      26     210 .. 0.97

  Alignments for each domain:
  == domain 1  score: 193.0 bits;  conditional E-value: 3.8e-61
                                    HHHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTC CS
                     Proteasome   1 vkkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrpip 80 
                                    v++Gtt+vGik++dgv++ +dkr+t  s l++++++eKif+id hig+a++Gl+aDar+lv+rar+e+q  rl y+++i 
  gi|116754662|ref|YP_843780.1|  26 VRRGTTAVGIKATDGVAVLVDKRIT--SRLMEPESIEKIFQIDTHIGAATSGLVADARILVDRARVECQINRLIYDERIG 103
                                    679**********************..***************************************************** PP

                                    HHHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHSTTBSH CS
                     Proteasome  81 verlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekeykedltl 160
                                    ve l +++++ +q ytq++g+rpfg +lli+g  ++   +L+++dpsG+++e+k a+ iG g+ a+++++e++y+ed+++
  gi|116754662|ref|YP_843780.1| 104 VEALSKKICDFKQTYTQYGGVRPFGTALLIIGAEDNR-VRLFETDPSGALLEYK-ATGIGAGRAAVMEVFEAKYREDMNM 181
                                    **********************************555.9**************8.************************* PP

                                    HHHHHHHHHHHHHHHHHBTTSCSSEEEEEE CS
                     Proteasome 161 eeavelavkalkealerdklsgknievavi 190
                                     ea+ l ++al+ a+e+  l  ++ e++vi
  gi|116754662|ref|YP_843780.1| 182 REAILLGLEALYRASEGK-LDASTTEIGVI 210
                                    ****************55.99999999886 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 !   52.0   0.1   4.4e-18   3.9e-14       1      23 []       3      25 ..       3      25 .. 0.99
   2 ?   -0.8   0.0      0.15   1.3e+03      13      18 ..      61      66 ..      61      66 .. 0.88

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 4.4e-18
                 Proteasome_A_N  1 YDrslttFSPdGRLfQVEYAmkA 23
                                   YDr++t+FSPdGRLfQVEYA +A
  gi|116754662|ref|YP_843780.1|  3 YDRAITVFSPDGRLFQVEYAREA 25
                                   *********************99 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.15
                 Proteasome_A_N 13 RLfQVE 18
                                   ++fQ++
  gi|116754662|ref|YP_843780.1| 61 KIFQID 66
                                   79**97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); 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 0.22s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1881.00
//
Query:       gi|116754663|ref|YP_843781.1|  [L=174]
Description: ribonuclease P-related protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      3e-15   56.3   0.0    4.2e-15   55.9   0.0    1.2  1  RNase_P_Rpp14  Rpp14/Pop5 family


Domain annotation for each model (and alignments):
>> RNase_P_Rpp14  Rpp14/Pop5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.9   0.0   2.3e-19   4.2e-15       1     103 []      13     106 ..      13     106 .. 0.95

  Alignments for each domain:
  == domain 1  score: 55.9 bits;  conditional E-value: 2.3e-19
                                    EEEEEEEEESS......-HHHHHHHHHHHHHHHHHHHHHHH--..EEEEEETTTTEEEEEEEGGGHHHHHHHHHT--EET CS
                  RNase_P_Rpp14   1 RYllveilypdeeeelteksllkairesvqelfGdyglgklgsslsvkyfspatstaiiRcsresyrlvwaaLtlitkie 80 
                                    RYl++e+ ++    +l+++++  +i++s  +lfGd g ++ +       +s + + +i+Rc+++++++++a+L++i+ i 
  gi|116754663|ref|YP_843781.1|  13 RYLVFELESEG---HLDARDVSIEIQSSYLSLFGDSGGASPRL------ISFDGRFGIVRCRNGHVEELRASLATIHAIA 83 
                                    9**********...5889*******************888887......567779************************* PP

                                    TEEEEEEEEEEESSHHHHHHHTT CS
                  RNase_P_Rpp14  81 grpvvfrvvrvsGTikkaeeeai 103
                                    g ++ +r+ +vsGTik+a e++i
  gi|116754663|ref|YP_843781.1|  84 GFRAAIRIRGVSGTIKTATEKYI 106
                                    *******************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       247  (0.0137766); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1364.29
//
Query:       gi|116754664|ref|YP_843782.1|  [L=233]
Description: RNase P subunit p30 [Methanosaeta thermophila PT]
Scores for complete 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-36  125.6   0.0    2.2e-36  125.3   0.0    1.1  1  RNase_P_p30    RNase P subunit p30
     0.0036   16.8   0.0     0.0058   16.1   0.0    1.3  1  CutC           CutC family
  ------ inclusion threshold ------
      0.063   13.0   0.5         17    5.2   0.1    2.7  2  PEP-utilizers  PEP-utilising enzyme, mobile domain


Domain annotation for each model (and alignments):
>> RNase_P_p30  RNase P subunit p30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.3   0.0   3.8e-40   2.2e-36       1     213 [.       3     202 ..       3     204 .. 0.94

  Alignments for each domain:
  == domain 1  score: 125.3 bits;  conditional E-value: 3.8e-40
                                    EEEEE-SH.........HHHHHHHHH-SEEEEEEEEEESS---HHHHH.......HHHHHHHH..HHSSEEEEEEES-H. CS
                    RNase_P_p30   1 ydlnipwpsddskkksrtiktlaelgytgvainftveaekekkpnasepikeelkelkkelsglkllsRvtlvvsdpskl 80 
                                    y+ +++  +++s+++sr++  +++lg++g+++  ++ + + +  +a             ++ g+ + ++v++  +dp++l
  gi|116754664|ref|YP_843782.1|   3 YEPRVHVMPQGSSSPSRMAIVARRLGFSGIIVMGINGSGDLQGLDAAY-----------RIGGISVARGVEVASKDPRSL 71 
                                    678999*****************************9955555555555...........8999***************99 PP

                                    .HHHHHHHHH--EEEEE--SHHHHHHHHHT.T-SEEE-TTTTSSS-S--HHHHHHHHHHT-EEEEESHHHHHS-HHHHHH CS
                    RNase_P_p30  81 .qrlskvrqkfdllavrPttekalraacenldvDiisidltsrlpfglkhktiraAvergvafEinyspllrdsglaRrn 159
                                     +r+s +r+++  lav+ t+e +lr a+ +++vD++         f l+ +++r+A++++va+ i+++p++r +g +R++
  gi|116754664|ref|YP_843782.1|  72 kGRISSLRDRYPFLAVHATSEPVLREALDDPRVDLVLNAG-----FRLTVPEARSARRNQVALAIDLQPMIRLRGVSRSR 146
                                    9**********************************98777.....779******************************** PP

                                    HHHHHHHHHHHHHH..--EEEE--BSSGGG---HHHHHHHHHHHT--HHHHHHTTT CS
                    RNase_P_p30 160 fisnarkllrltrg..kgvviSSgAesplelRnpydiinLlktlGLeedrakeavs 213
                                    ++   r ++r++r+   ++vi+++++s+l+lR+p+d+i+++++lG++ ++a +a++
  gi|116754664|ref|YP_843782.1| 147 WLDLQRYNVRVARKfgIPLVITASPRSHLDLRAPRDMIAMAHILGITREEAIDALR 202
                                    **************9999**********************************9985 PP

>> CutC  CutC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   9.6e-07    0.0058      46     134 ..     126     209 ..      97     221 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 9.6e-07
                           CutC  46 aeeakipvyvmiRPRgGdFvysdeelkamleDieaarelgldgvvlGaltadgeiDlkaleklieaaegLgvtfHrAfDv 125
                                    +    i +++miR Rg   v  ++ l+  + +++ ar+ g++ v++    + +++Dl a + +i++a+ Lg+t   A+D 
  gi|116754664|ref|YP_843782.1| 126 QVALAIDLQPMIRLRG---VSRSRWLDLQRYNVRVARKFGIPLVIT--ASPRSHLDLRAPRDMIAMAHILGITREEAIDA 200
                                    3467899999999998...6789999999*************8876..468899************************** PP

                           CutC 126 vadpeeale 134
                                     + p + le
  gi|116754664|ref|YP_843782.1| 201 LRLPGRILE 209
                                    998888776 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 ?    5.2   0.1    0.0028        17      35      50 ..      17      32 ..       9      40 .. 0.79
   2 ?    5.0   0.0    0.0034        20      41      55 ..     157     171 ..     155     186 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0028
                                   HHHHHHHHHHTT--EE CS
                  PEP-utilizers 35 tSHaAivArelgiPaV 50
                                    S +AivAr lg   +
  gi|116754664|ref|YP_843782.1| 17 PSRMAIVARRLGFSGI 32
                                   589********98765 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0034
                                    HHHHTT--EEE--SS CS
                  PEP-utilizers  41 vArelgiPaVvgvge 55 
                                    vAr++giP V+ ++ 
  gi|116754664|ref|YP_843782.1| 157 VARKFGIPLVITASP 171
                                    8*********98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); 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: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.36
# Mc/sec: 1919.04
//
Query:       gi|116754665|ref|YP_843783.1|  [L=138]
Description: hypothetical protein Mthe_1368 [Methanosaeta thermophila PT]
Scores for 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-38  129.2   0.0      1e-37  129.0   0.0    1.0  1  RNA_binding  RNA binding


Domain annotation for each model (and alignments):
>> RNA_binding  RNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.0   0.0   5.8e-42     1e-37       1     118 [.       4     119 ..       4     120 .. 0.97

  Alignments for each domain:
  == domain 1  score: 129.0 bits;  conditional E-value: 5.8e-42
                                    EEEEEEEE-TTC-HHHHHHHHHTTSTTSE---EEEEEE-CCC-EEEEEEEEESSHHHHHHHHHHHHHHCCCCHHHHHHCC CS
                    RNA_binding   1 kievrafvhaTEdeekVlealsnllpeeeveieeeeaeGhygnpitileaelekkkakkvlkkllellreeeikeLlkel 80 
                                    ++ +rafv  TEdee+V++als ++p +  +i++++a+G+ygnpitileael++k+ +++++ l+e+l+  e+++L++e+
  gi|116754665|ref|YP_843783.1|   4 RVHFRAFVSVTEDEERVRRALSIFVPLD--HIRSTRASGYYGNPITILEAELRRKEGLEFIHMLREQLSAGELSRLRREI 81 
                                    689***********************88..69**********************999*********************** PP

                                    HCCB-TTSEEEEEEEHHHHHTT---BESSSSEEEEEEE CS
                    RNA_binding  81 eervdekgklylrldKQaaylgklslvegddvIkvkik 118
                                    +ervde++kl+lrldKQaay+g ++l+e +d+I v ++
  gi|116754665|ref|YP_843783.1|  82 PERVDEDCKLHLRLDKQAAYRGMVRLSEAGDAIDVSVH 119
                                    ***********************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 977.70
//
Query:       gi|116754666|ref|YP_843784.1|  [L=203]
Description: 50S ribosomal protein L15e [Methanosaeta thermophila PT]
Scores for 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-81  270.2   9.9      1e-80  270.0   9.9    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 !  270.0   9.9   5.6e-85     1e-80       1     191 []      11     198 ..      11     198 .. 0.99

  Alignments for each domain:
  == domain 1  score: 270.0 bits;  conditional E-value: 5.6e-85
                                    -SHHHHHHHTTSTTSHHHHHHHHHHHHHHTTS-SEEEESS-SSHHHHHHHT--SSTTEEEEEEEEE-SS---..---SS- CS
                 Ribosomal_L15e   1 gaykylrelwkkkqsdvlrellrerlweyrqepavvrverptrldrArrLGYkakqGivvvrvrvrrGgrkkkvskgktg 80 
                                    ++y y++++w+++ ++++  l  +r++ +r+e +v+r+erptrldrAr+LGYkakqGiv++rvrvrrG+ +k  s+++++
  gi|116754666|ref|YP_843784.1|  11 SFYGYIKDAWNSPAKSYVGRLRAQRMIAWRREMSVQRIERPTRLDRARALGYKAKQGIVLARVRVRRGALRK--SRYVRN 88 
                                    689*********************************************************************..****** PP

                                    --GGGG-SSS---SS-HHHHHHHHHHHHSTTSEEEEEEEEEEESSEEEEEEEEE-TTSHHHHT-TTTGGGGSGGGTTGGG CS
                 Ribosomal_L15e  81 rkpkrqgvnklkpakslqaiaeervgrklpnlrvLnSYwvgeDgtykyyEvilvDpshkairndkkinwickkvhkhRel 160
                                    r++k++++++++p kslq+iaeer++r+++n++vLnSYwvg+Dg++k++EvilvDp+h+ai++d++++wic  +h++R+ 
  gi|116754666|ref|YP_843784.1|  89 RRTKHMAMHRQNPGKSLQRIAEERASRRFRNMEVLNSYWVGQDGRHKWFEVILVDPNHPAIKSDRDLSWICGGSHRGRAE 168
                                    ******************************************************************************** PP

                                    GT-SHHHHHHTT-S-SS.TT-TTTSS-TGGG CS
                 Ribosomal_L15e 161 rGltsagkksRGlrkkglkgaekirgsrran 191
                                    rG+tsagkk+RGlr+kg  g+ek+r+s+ra+
  gi|116754666|ref|YP_843784.1| 169 RGKTSAGKKGRGLRRKG-FGTEKTRPSIRAH 198
                                    *****************.9*********995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1455.34
//
Query:       gi|116754667|ref|YP_843785.1|  [L=226]
Description: hypothetical protein Mthe_1370 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-08   32.8   0.1      2e-07   30.7   0.0    2.0  2  DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large s


Domain annotation for each model (and alignments):
>> DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.0   1.1e-11     2e-07     101     162 ..      30      92 ..      26     129 .. 0.83
   2 ?   -3.4   0.0      0.28   4.9e+03      58      79 ..     171     190 ..     161     208 .. 0.59

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 1.1e-11
                                    SHHHHTT--HHHHCCHHHHCCCSS--CHHHHHHHHHHHHCT--CHHHHCCCHCHST.....HHHH CS
                DNA_primase_lrg 101 dklakesfPpCmrelleglkknghlkhegrlqltlFlkdiglsldeilelwkeaftr...teekF 162
                                    +++ +e fPpC+r++l +  ++g+  + +   l++Fl ++g+s+ ++l+lwk +++r   +e  F
  gi|116754667|ref|YP_843785.1|  30 ERIPEERFPPCIRNMLHRASEEGS--NRAGAVLASFLGQAGWSEGDALKLWKIFAERtglSESLF 92 
                                    67899************9965555..55666799******************9988866444434 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.28
                                    HHGGGSSS---HHHHHHHCT-- CS
                DNA_primase_lrg  58 eleeeikederekleelleals 79 
                                    el  e+ +d r ++e++l ++ 
  gi|116754667|ref|YP_843785.1| 171 EL--EVSDDLRGEIEKILAEIG 190
                                    33..446666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); 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: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1681.90
//
Query:       gi|116754668|ref|YP_843786.1|  [L=504]
Description: hypothetical protein Mthe_1371 [Methanosaeta thermophila PT]
Scores for complete 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-229  761.5   0.6   2.6e-229  761.3   0.6    1.0  1  DUF2114   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2114  Uncharacterized protein conserved in archaea (DUF2114)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  761.3   0.6  1.4e-233  2.6e-229       1     448 [.      29     474 ..      29     475 .. 0.99

  Alignments for each domain:
  == domain 1  score: 761.3 bits;  conditional E-value: 1.4e-233
                        DUF2114   1 eyyivasvelGntttkciltatnletgktyllnktvkmtrdvrkpkegeevfgktlagveltresvaelvrdtlleslkk 80 
                                    +yyivasve+Gntttk+iltat+++tgkt+++nktv+mtrdvr+pk+gee+fg+t++g++lt+es+aelvrdtlles+++
  gi|116754668|ref|YP_843786.1|  29 PYYIVASVEVGNTTTKSILTATDMDTGKTQIVNKTVRMTRDVRPPKPGEEIFGRTICGTPLTKESIAELVRDTLLESHQA 108
                                    7******************************************************************************* PP

                        DUF2114  81 akldieedldfvvrstGvvagfdspeevgelikaladGCleagvppkkmtpamskenlpeklrkyslldkvvfdGavasv 160
                                    a l ie+dl+fvvrstGvva+fdspeevg +i+ala+GCl+agvpp+ mtpams+ n+pe++r+ysl++k+vf+G vasv
  gi|116754668|ref|YP_843786.1| 109 AGLLIERDLNFVVRSTGVVAEFDSPEEVGIFIQALAQGCLDAGVPPRLMTPAMSIYNIPERFRRYSLIEKIVFNGPVASV 188
                                    ******************************************************************************** PP

                        DUF2114 161 vpPkgktgvevvanemegeLvtaGikegakwtdvdfrnPcisidfGttLdGrivndeePyaktvgnfcGlaGaipdaivr 240
                                    +pP+g+tgve+vanemegeL+taGik+gakwtdvdfrnPc+++dfGttLdGri+++e Pya+t+gnfcG+aGaipda+vr
  gi|116754668|ref|YP_843786.1| 189 WPPMGATGVEIVANEMEGELATAGIKQGAKWTDVDFRNPCLAMDFGTTLDGRITSEEIPYARTIGNFCGVAGAIPDAVVR 268
                                    ******************************************************************************** PP

                        DUF2114 241 GtglvdkklgaaldlfkekkkkkkkkkkikeyaekihelidiekvPkdrerfGtvPvdakaaeeagvvliGcdvgengsd 320
                                    Gtglvd+++g+ald+fk+k+  +  +kk++ yae+i+ li+ie+vP +++r+G vP+da+aa++ gvvliGcd+gengs+
  gi|116754668|ref|YP_843786.1| 269 GTGLVDATTGTALDIFKDKN--SGVNKKARLYAEEIDLLIKIERVPVGTKRYGYVPLDAAAAQKLGVVLIGCDCGENGSK 346
                                    *****************988..788999**************************************************** PP

                        DUF2114 321 lekleeigaeilekeglkvllavldevsakivkrlievaveeglveektaiGitGragitGkkpelilekieelglyddk 400
                                    l++l+eig ei++++glkvl a+ld vsaki++rl+eva eeglv+++taiG+tGragi+G+kpelile+i +lglyd++
  gi|116754668|ref|YP_843786.1| 347 LNELSEIGGEIYRRDGLKVLSATLDLVSAKIARRLVEVAIEEGLVTKRTAIGVTGRAGISGNKPELILEEIGKLGLYDEP 426
                                    ******************************************************************************** PP

                        DUF2114 401 eenvvfvddgLarGaavmarCmnslGtpknPlGGvrggkCilkkrikl 448
                                    e+n+vfvddgLarGaavmarCmns+GtpknP+GG rgg+Cilk+ri++
  gi|116754668|ref|YP_843786.1| 427 EKNIVFVDDGLARGAAVMARCMNSMGTPKNPMGGIRGGRCILKERIEY 474
                                    *********************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (504 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 3673.34
//
Query:       gi|116754669|ref|YP_843787.1|  [L=298]
Description: radical SAM domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.1e-09   37.0   0.1    1.8e-06   28.4   0.0    2.3  2  Radical_SAM  Radical SAM superfamily
    0.00013   22.3   0.1    0.00022   21.5   0.1    1.3  1  Fer4_12      4Fe-4S single cluster domain
      0.003   17.7   0.1     0.0087   16.2   0.1    1.7  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 !   28.4   0.0     3e-10   1.8e-06       2     142 ..      75     208 ..      74     243 .. 0.83
   2 !    6.7   0.1    0.0014       8.5      91     143 ..     237     292 ..     210     297 .. 0.72

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 3e-10
                                    EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgirit 81 
                                    +++ gCnl+C+fC+++e  ++ + g +++ e+++ ++  l +  g++++ l+  +  + p + e+l  +++    g++i 
  gi|116754669|ref|YP_843787.1|  75 IFFAGCNLACVFCQNYEI-SQLDMGVEVTAERLAGIMMHL-QLTGCHNINLVTPTHVV-PQILEALVIASEM---GLSIP 148
                                    6899*************7.*********************.9************8888.9999999999998...88888 PP

                                    EEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  82 vetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagi 142
                                    ++ n +  d     rll+  vd +  +++ ++de+  ++ n ++ +   ++a++ +++  +
  gi|116754669|ref|YP_843787.1| 149 LVYNSGGYDSVDTLRLLDGIVDIYMPDAKYGSDEMAMRYSNAPGYVGVMKAAIKEMHRQ-V 208
                                    888888876444444555468*************7777776667777777777777766.4 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0014
                                    HHHHHHHHHTT.-SEEEEEEBSSSHH...HHHHHHTCTSHHHHHHHHHHHHHHTTSE CS
                                    xxxxxxxxxxx.xxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  91 eeklerllelg.vdrvslgleaadde...kvlklmnrghtfeevlealeklreagik 143
                                    +e+++ + el   +++++  +   +    ++++l  r+ t++e+ eal+++r+ag+ 
  gi|116754669|ref|YP_843787.1| 237 DEVVRFISELSkNTYINIMDQYRPEYradRYRELS-RRITLSEYREALRLARAAGLS 292
                                    66666666666445555544433333777799999.89****************986 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 !   21.5   0.1   3.7e-08   0.00022       9      50 ..      74     115 ..      66     125 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 3.7e-08
                        Fer4_12   9 slfvsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkk 50 
                                    ++f++gCnl+C +C n e+ + + g e+t e l+ i+ +l+ 
  gi|116754669|ref|YP_843787.1|  74 TIFFAGCNLACVFCQNYEISQLDMGVEVTAERLAGIMMHLQL 115
                                    79****************************999999988865 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 !   16.2   0.1   1.5e-06    0.0087       2      46 ..      76     118 ..      75     125 .. 0.84
   2 ?   -2.6   0.0      0.96   5.8e+03      65      92 ..     237     261 ..     233     281 .. 0.60

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.5e-06
                        Fer4_14   2 fvrlsgCnlsCkgCdnketwkselgkpqteelleqilkdlkksei 46 
                                    f  ++gCnl+C++C n e  + ++g + t e l  i+ +l+ + +
  gi|116754669|ref|YP_843787.1|  76 F--FAGCNLACVFCQNYEISQLDMGVEVTAERLAGIMMHLQLTGC 118
                                    4..5*****************************999988776665 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.96
                        Fer4_14  65 kellklvkrlkeeypekkiwletngtle 92 
                                    +e+++++++l +++    i +   +  e
  gi|116754669|ref|YP_843787.1| 237 DEVVRFISELSKNT---YINIMDQYRPE 261
                                    56777777777776...45555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2427.79
//
Query:       gi|116754670|ref|YP_843788.1|  [L=141]
Description: hypothetical protein Mthe_1373 [Methanosaeta thermophila PT]
Scores for complete 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-42  144.7   0.3    2.3e-42  144.5   0.3    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 !  144.5   0.3   1.3e-46   2.3e-42       1     138 []       3     141 .]       3     141 .] 0.95

  Alignments for each domain:
  == domain 1  score: 144.5 bits;  conditional E-value: 1.3e-46
                                    EEE---SSEEEEEEE-SSSHHHHHHHHHHHHHHHS--TT---S-EEEEEEEESSSHHHHHHHHHHHHHHHHHT--S---- CS
                       Archease   1 yeyldhtADviieawGksleeafesaalalfeymtdlskvepkeekeieveaedledlLfdfLdellylfdteyfvfkev 80 
                                    ye+l+htADv+++a+G+s ee++ +aala+f++m+d+++v+ +   e+e+eaed+e+l +++L+ell+lf++e  vf+++
  gi|116754670|ref|YP_843788.1|   3 YEFLEHTADVKFRAYGTSPEEMLRNAALAMFSAMIDTKTVRHEMVWEVELEAEDMESLAYKWLSELLFLFSAELAVFSDF 82 
                                    9******************************************999********************************** PP

                                    EEEE.E-SSSEEEEEEEE----.-TT--------B--S---EEEE..ETTEEEEEEEEE- CS
                       Archease  81 kvdeeeeeeeleleaeargekfdkekhevqtevKAvTyhelriee..eddgweayvvvDi 138
                                    +++   +++ ++l+a+++ge++d+++h+++tevKAvT+h+++++   +d  w ++vv+D+
  gi|116754670|ref|YP_843788.1|  83 DISL-SHNSVWRLNARVHGEHIDRKRHSFETEVKAVTLHQFEVRPgdSDRPWIMQVVLDV 141
                                    7754.66889*********************************99445567********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1060.07
//
Query:       gi|116754671|ref|YP_843789.1|  [L=473]
Description: hypothetical protein Mthe_1374 [Methanosaeta thermophila PT]
Scores for complete 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-164  547.2   0.0   3.2e-164  547.0   0.0    1.0  1  RtcB      tRNA-splicing ligase RtcB


Domain annotation for each model (and alignments):
>> RtcB  tRNA-splicing ligase RtcB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  547.0   0.0  1.8e-168  3.2e-164       1     412 []      43     473 .]      43     473 .] 0.99

  Alignments for each domain:
  == domain 1  score: 547.0 bits;  conditional E-value: 1.8e-168
                                    HHHHHTTSTTB-S-EEEEEEEE--SSS-EEEEEEE-...-EE-HHHC-SST.-EEEEEEEEEEHHHHGGGHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           RtcB   1 qlknvaslpgivkhvaamPDvHlGkgapiGsViatk...gviiPaaVGvDI.CGvrllktnltaeeleeklkelvkelek 76 
                                    q++nva+lpgivk+++amPD+HlG+g+piG+V+a++   gvi+P++VG+DI CGvrll+t+lt ee+++ +++l+++l+k
  gi|116754671|ref|YP_843789.1|  43 QVANVATLPGIVKYSMAMPDAHLGYGFPIGGVAAFRedgGVISPGGVGFDInCGVRLLRTDLTVEEVRPVISDLIEALFK 122
                                    89****************************************************************************** PP

                                    HS-------------HHHHHHHHHHTHHHHHHTTSS-GGGGGGBGGGG--TT--GGGS-HHHHHHHGGGTT---STT-EE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           RtcB  77 avpvglgskkkvklskkeleevleegakwaveeglgeeedlekieeegalkeadlekvskkakerarkqlGtlGsGNHFi 156
                                    ++p+g+g ++++++s++el+e++  ga+waveeg+g+e dle++ee+g+lk+ad+++vs+ka++r+r+q+GtlGsGNHF+
  gi|116754671|ref|YP_843789.1| 123 EIPSGVGATSRLHVSDSELTEAFIAGARWAVEEGYGTEGDLEHCEENGCLKGADPSQVSTKARKRGRPQFGTLGSGNHFL 202
                                    *******99*********************************************************************** PP

                                    EEEEEEEES-HHHHHHHT--TTEEEEEEEE--HHHHHHHHHHHHHHHHCCHHHCT---SSGGG--EETTSHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           RtcB 157 EvqlveeildeeaakalgleegqvvvmlHsGSRglGhqiaedylkiakkalkkkgiklpdrdLaylpagseegqaYlkam 236
                                    Evq+v e++de++a+++gl +gqv+vm+H+GSRg Ghqi++d+l+++ ka++k++i+lpd++La++p+g++e+ +Y+ am
  gi|116754671|ref|YP_843789.1| 203 EVQYVGEVYDERIARRFGLFKGQVTVMIHCGSRGAGHQICTDHLEVLAKAVRKYNIDLPDKQLACAPIGTPEATNYFGAM 282
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHT.T--HHHH--EEEEEEESEEEEEEEE..T...EEEEEEEES-EE-.......... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x...xxxxxxxxxxxxx.......... RF
                           RtcB 237 qaaanyAkaNRqvitervreilekvlkkekedlelelvvdvaHNiakkEehe.d...ekvlVhRKGAtrA.......... 302
                                    +aaanyA+aNRq+i++++re+++k+++    d+e+ lv+dvaHN+ak Eeh+ d   e+++VhRKGAtr+          
  gi|116754671|ref|YP_843789.1| 283 AAAANYAWANRQIIAHWTREVFAKYFG----DVEMPLVYDVAHNVAKIEEHMvDgrlERLYVHRKGATRSfgpsrrevpq 358
                                    **************************6....78999****************9679************************ PP

                                    ...TT--EEEE--STTS-EEEEE--HHHH..SSSEE---S-----------------TTTTTCCCT-EEEE--------- CS
                                    ...xxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           RtcB 303 ...kvgqpviipGsmgtkSyivkGkgnae..sfgStsHGAGRlmsRakakkkfkleevkkdleeqgigvearkkegvleE 377
                                       +vgqp +ipGsmgt Sy++ G+++a   +fgS++HG+GR+msR++akk+++++evk++l+++gi+v+a+++++++eE
  gi|116754671|ref|YP_843789.1| 359 dyrDVGQPLLIPGSMGTPSYVLCGQDRALelTFGSACHGSGRIMSRSQAKKTYRGSEVKASLQREGIKVMATESAVLAEE 438
                                    **************************99999************************************************* PP

                                    ---------HHHHHHHHCTS-EEEEEEEEEEEEE- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           RtcB 378 apeaYKdideVveaqaeaglvevvarlkpvlvvkg 412
                                    ape YK+ +eVve++++ gl+++va+  p++v kg
  gi|116754671|ref|YP_843789.1| 439 APEVYKPSHEVVEVVHALGLAKKVAKTIPLGVSKG 473
                                    ********************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 3284.31
//
Query:       gi|116754672|ref|YP_843790.1|  [L=243]
Description: RNA methyltransferase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-31  109.9   0.0    1.5e-31  109.5   0.0    1.2  1  SpoU_methylase   SpoU rRNA Methylase family
     0.0028   17.5   0.0     0.0087   15.9   0.0    1.8  1  Methyltrn_RNA_4  SAM-dependent RNA methyltransferase


Domain annotation for each model (and alignments):
>> SpoU_methylase  SpoU rRNA Methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.5   0.0   1.7e-35   1.5e-31       2     142 .]       3     158 ..       2     158 .. 0.83

  Alignments for each domain:
  == domain 1  score: 109.5 bits;  conditional E-value: 1.7e-35
                                    EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHH.EEEESSHHHHHHHHCCCTEEEEE CS
                 SpoU_methylase   2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevle.lkvvdsleealkelkeegfalva 80 
                                    l+vvlve++++gN+Ga+aR++k+fg+++lvlv+p+      +  +++aa+a+++l+ +k vd le+al+ ++      v+
  gi|116754672|ref|YP_843790.1|   3 LRVVLVEPRYEGNVGAVARSMKNFGFNDLVLVRPCDI---GSFGMAMAAHAKDILQsAKSVDRLEDALEGVNLI----VG 75 
                                    89*******************************9886...6677899***********************9988....55 PP

                                    EST..T-SEGC......CSHHH...............TTEEEEEEBTTTBS-HHHHCTSSEEEE----TTSSS--HHHHH CS
                 SpoU_methylase  81 tsl..kgksls......eidlk...............ekvalvfGnEdkGlsnelleladrlvkIpmsgeveSLNvavAv 137
                                    t++   +++ +      +  ++               + val++G+Ed+Gl+n++l ++d lv+Ip+s e++ +N+++A+
  gi|116754672|ref|YP_843790.1|  76 TTGkrLSRDHHhlrlhlR--VPfltpselaerlrdkdGTVALLLGREDWGLTNDELMACDVLVSIPTSDEYPVMNLSHAA 153
                                    555332223331324231..11334455556677777******************************************* PP

                                    HHHHH CS
                 SpoU_methylase 138 ailly 142
                                     +lly
  gi|116754672|ref|YP_843790.1| 154 TVLLY 158
                                    ***98 PP

>> Methyltrn_RNA_4  SAM-dependent RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   9.7e-07    0.0087      67     177 ..      42     157 ..      14     161 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9.7e-07
                                    GGGGT-SSSHHHHTTEEEESSHHHHHHHHHHHHSS--EEEE--SS.....--SS-B-HHHHHHHHHH--S-EEEEE--.T CS
                Methyltrn_RNA_4  67 agaeynpdRkealslvkvvesleealeeiekeegkkplvvatsAr.....kkentvsyeelrelleeeekpvlllfGt.g 140
                                    +g ++ ++ k+ l+  k v++le+ale ++   g++ + +  + +      +   ++ +el e+l++++ +v ll+G   
  gi|116754672|ref|YP_843790.1|  42 FGMAMAAHAKDILQSAKSVDRLEDALEGVNLIVGTTGKRLSRDHHhlrlhLRVPFLTPSELAERLRDKDGTVALLLGReD 121
                                    577778888999999999999999999999999999988888887555555566778899*****************737 PP

                                    T---HHHHTT-SEEB--TTTTSS-----HHHHHHHHH CS
                Methyltrn_RNA_4 141 wGlaeevlekadyiLepirgaseynHLsvrsAvaiil 177
                                    wGl+++ l ++d+ L +i + +ey  +    A++++l
  gi|116754672|ref|YP_843790.1| 122 WGLTNDELMACDV-LVSIPTSDEYPVMNLSHAATVLL 157
                                    ***********96.67899999999999888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); 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: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1865.56
//
Query:       gi|116754673|ref|YP_843791.1|  [L=1261]
Description: TPR repeat-containing protein [Methanosaeta thermophila PT]
Scores for complete 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-142  462.9  96.9    1.9e-15   56.9   0.4   16.0 16  TPR_12          Tetratricopeptide repeat
    2.5e-96  311.9  43.6      2e-05   24.2   0.1   25.6 25  TPR_1           Tetratricopeptide repeat
    6.5e-86  275.7  75.1    0.00016   21.5   0.1   26.5 27  TPR_2           Tetratricopeptide repeat
    1.4e-76  247.0  76.3    5.9e-06   25.9   0.0   26.9 27  TPR_7           Tetratricopeptide repeat
    3.1e-68  224.0  92.7    2.8e-05   23.8   0.1   25.3 25  TPR_10          Tetratricopeptide repeat
    2.7e-53  181.2  19.3    2.8e-10   40.1   0.5   10.3 10  SNAP            Soluble NSF attachment protein, SNAP
    9.3e-44  150.2  45.5    1.2e-07   31.4   0.2   10.6 10  TPR_MalT        MalT-like TPR region
      4e-43  142.0  63.6    0.00088   19.3   0.1   24.5 24  TPR_8           Tetratricopeptide repeat
    2.9e-33  111.7  76.9      0.071   14.0   0.0   24.3 24  TPR_14          Tetratricopeptide repeat
    6.7e-33  113.1  65.8    4.7e-05   23.9   0.5   17.0 18  TPR_16          Tetratricopeptide repeat
      6e-28   96.2  32.1       0.13   12.0   0.0   19.1 18  TPR_11          TPR repeat
      8e-18   64.7  53.8       0.02   15.4   0.0   16.8 20  TPR_19          Tetratricopeptide repeat
    1.7e-17   63.2  26.7        1.6    8.8   0.0   16.6 16  MIT             MIT (microtubule interacting and transport) d
    1.9e-17   63.6  23.8      0.036   13.8   0.1   11.2 11  RPN7            26S proteasome subunit RPN7
    7.3e-17   60.8  61.9        2.5    8.9   0.0   24.0 23  TPR_6           Tetratricopeptide repeat
    5.1e-16   57.8  25.0        4.5    7.9   0.0   19.7 20  TPR_17          Tetratricopeptide repeat
      4e-09   36.7  34.6        0.1   12.7   1.1   11.1 12  DUF3856         Domain of Unknown Function (DUF3856)
    8.1e-09   35.6  31.3        1.2    9.5   0.2   12.5 14  ANAPC3          Anaphase-promoting complex, cyclosome, subuni
    2.3e-07   30.9  58.5      0.013   15.6   0.1   14.3 16  TPR_9           Tetratricopeptide repeat
      2e-06   27.9  57.3       0.19   12.4   0.2   18.1 15  TPR_4           Tetratricopeptide repeat
      2e-05   24.5  20.6        4.1    7.9   0.0   13.8 12  PPR             PPR repeat
    5.2e-05   23.1   3.4        1.1    9.3   0.1    7.7  9  TPR_3           Tetratricopeptide repeat
    0.00041   20.0  23.2        0.8    9.2   0.1    9.1 11  Foie-gras_1     Foie gras liver health family 1
     0.0024   17.6  27.4        3.4    7.4   0.1    9.6  9  TPR_21          Tetratricopeptide repeat-like domain
     0.0098   15.5   1.0        5.1    6.6   0.0    5.1  7  ComR_TPR        ComR tetratricopeptide
  ------ inclusion threshold ------
      0.056   13.6   0.8         21    5.4   0.1    5.4  4  PPR_2           PPR repeat family
      0.099   11.9   5.0       0.24   10.7   0.2    3.5  4  CorA            CorA-like Mg2+ transporter protein
       0.12   11.4   9.3       0.93    8.4   0.0    5.5  7  SRP68           RNA-binding signal recognition particle 68
       0.12   10.7   1.9         16    3.8   0.1    3.6  3  Cohesin_load    Cohesin loading factor
       0.17   10.4   0.1        0.3    9.6   0.1    1.3  1  Het-C           Heterokaryon incompatibility protein Het-C
       0.22   11.3   2.1        2.5    7.8   0.1    3.6  3  Vta1_C          Vta1 C-terminal domain
       0.73   10.5   4.9        5.1    7.8   0.2    4.3  2  DUF4398         Domain of unknown function (DUF4398)
       0.81    9.8  17.9          1    9.5   0.1    7.7  7  ANAPC5          Anaphase-promoting complex subunit 5
        1.4    8.6  12.5         53    3.4   0.0    5.9  5  YfiO            Outer membrane lipoprotein
        2.7    7.4  23.2        5.7    6.3   3.6    6.3  8  SPO22           Meiosis protein SPO22/ZIP4 like
        3.5    7.2  21.7         20    4.8   0.0    9.3  9  SHNi-TPR        SHNi-TPR
          6    7.3  11.7       0.48   10.8   0.4    5.1  2  TPR_20          Tetratricopeptide repeat
        7.7    6.7   9.2        2.1    8.5   0.1    4.6  3  Fis1_TPR_C      Fis1 C-terminal 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 !   25.7   0.3   2.2e-08     1e-05       8      76 ..      66     128 ..      59     129 .. 0.91
   2 !   28.7   1.1   2.6e-09   1.2e-06       2      73 ..     134     203 ..     133     207 .. 0.94
   3 !   23.9   0.2   7.9e-08   3.7e-05       3      76 ..     175     246 ..     173     247 .. 0.92
   4 !   47.5   0.9   3.5e-15   1.6e-12       4      76 ..     257     326 ..     254     327 .. 0.94
   5 !   45.1   1.9     2e-14   9.4e-12       1      76 [.     332     405 ..     332     406 .. 0.95
   6 !   53.9   0.8   3.5e-17   1.6e-14       3      77 .]     415     486 ..     413     486 .. 0.95
   7 !   50.1   0.4   5.5e-16   2.6e-13       2      74 ..     493     563 ..     492     564 .. 0.96
   8 !   42.8   0.2     1e-13   4.9e-11       2      75 ..     570     641 ..     569     643 .. 0.92
   9 !   50.1   0.2   5.4e-16   2.6e-13       3      76 ..     648     719 ..     646     720 .. 0.94
  10 !   56.9   0.4   4.1e-18   1.9e-15       2      76 ..     687     759 ..     686     760 .. 0.95
  11 !   26.2   0.0   1.5e-08   7.1e-06       2      39 ..     727     763 ..     726     772 .. 0.85
  12 !   51.4   0.6   2.1e-16   9.8e-14       4      73 ..     769     836 ..     766     840 .. 0.94
  13 !   46.3   1.1   7.9e-15   3.7e-12       3      72 ..     888     955 ..     886     960 .. 0.94
  14 !    8.8   1.8    0.0042         2       2      77 .]    1005    1077 ..    1004    1077 .. 0.92
  15 !   28.8   2.3   2.3e-09   1.1e-06      20      76 ..    1062    1116 ..    1045    1117 .. 0.83
  16 !   17.0   4.9   1.1e-05    0.0052       3      76 ..    1125    1196 ..    1123    1197 .. 0.94

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 2.2e-08
                         TPR_12   8 nlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                     l+++ ++lg ++ A ++l +ale+a    G d   ++ +l  Lg +y   ++++ A++l+++al ++e
  gi|116754673|ref|YP_843791.1|  66 SLGMISQQLGSLERAVSHLSRALERA---SGAD---AVKVLSRLGSIYANVEDLDRAISLYRDALSRLE 128
                                    69************************...5666...799**************************9987 PP

  == domain 2  score: 28.7 bits;  conditional E-value: 2.6e-09
                         TPR_12   2 vatalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                                    +a +l nl +++r++ r+d+Al++   a+ + r++  +d+  +a++    +++ r++g++  A+el++ +l+
  gi|116754673|ref|YP_843791.1| 134 RAGILINLSMAYREARRWDDALQCSSDAIYLLRSS--GDRSSVARAIMEEAEIRREMGDLSSAEELYRTCLE 203
                                    577899**************************999..8888***************************9997 PP

  == domain 3  score: 23.9 bits;  conditional E-value: 7.9e-08
                         TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                    a+a  + a++ r++g++  A+el++++le ++rl  ++ p ++++l  Lgr+ +++g+ + A++l+  a+ ++e
  gi|116754673|ref|YP_843791.1| 175 ARAIMEEAEIRREMGDLSSAEELYRTCLEEFERL--GEIPFVCRSLEMLGRISQLRGESRRAEDLFDMAMHRYE 246
                                    66666789**************************..899***************************99987665 PP

  == domain 4  score: 47.5 bits;  conditional E-value: 3.5e-15
                         TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                    tal  l+++++  gr+  A+e++ kale +r++   d++ +a+tl  L+rly  +g+++ A+e+++eal+i++
  gi|116754673|ref|YP_843791.1| 257 TAL-LLGDLHAIEGRFSSAEECYLKALEGFREV--SDRESVANTLLSLARLYGSMGEWRGAVERYREALDILQ 326
                                    344.9****************************..99999*******************************87 PP

  == domain 5  score: 45.1 bits;  conditional E-value: 2e-14
                         TPR_12   1 dvatalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                    d+a+al++++++++rl +y+ A+ ++ k+le+ ++l  +++++ a++  ++g +++ lg+++ A+e++e+  ++++
  gi|116754673|ref|YP_843791.1| 332 DLARALREMGTACYRLRDYEMAQNYFMKSLELSEAL--GERDGMAASHTGMGHMLSDLGDWDGAVEHYERGAELLR 405
                                    5799**99**************************99..77889***************************999987 PP

  == domain 6  score: 53.9 bits;  conditional E-value: 3.5e-17
                         TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiaek 77 
                                    a++  n+a+v++ +g++++Al++++ al+i++rl  +d  +++ tl+n+g +y+ +g+ e+A++ + ++l+++e+
  gi|116754673|ref|YP_843791.1| 415 ACTS-NIASVYQMMGDLEKALDIYHDALQIQERL--GDMQGASKTLNNMGLVYQHMGEIEAAERNYMRCLELKEQ 486
                                    6777.*****************************..88999******************************9986 PP

  == domain 7  score: 50.1 bits;  conditional E-value: 5.5e-16
                         TPR_12   2 vatalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                    +a+++ nla+++  + r+d+A+++++ ale ++++  +d+ + a++++nLg +y++ g+  +A++ ++ ++++
  gi|116754673|ref|YP_843791.1| 493 AANTHINLATLYEIQRRWDDAITHYQDALETFEAI--GDRRGMAAVMNNLGNVYEEKGDILQAIKSYRMSMEL 563
                                    588999*****************************..9999*****************************997 PP

  == domain 8  score: 42.8 bits;  conditional E-value: 1e-13
                         TPR_12   2 vatalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                    +a++  nl+ +++r g+ + A+++++++le+++++  +d  ++a +l +Lg + +++g +++Al+ ++++++++
  gi|116754673|ref|YP_843791.1| 570 IAKISWNLGGLYQRIGDAESAEKCYRASLEAFQSI--GDERGAAYALMGLGSIALERGLWDDALDCFKRCVDLR 641
                                    567777***************************99..55559****************************9987 PP

  == domain 9  score: 50.1 bits;  conditional E-value: 5.4e-16
                         TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                    +++l  +a+v+ r g ++eAl+ ++k+le++r    +d++++a++l ++g l+ ++g++++Ale++ e+l+i+e
  gi|116754673|ref|YP_843791.1| 648 LRVLGSIASVYERKGMWQEALAEYRKVLERFRG--MGDSLGVAAVLSTIGNLLAEQGHWDDALEHYSESLEIFE 719
                                    678888*************************85..59***********************************98 PP

  == domain 10  score: 56.9 bits;  conditional E-value: 4.1e-18
                         TPR_12   2 vatalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                    va++l+ ++++l+++g +d+Ale++ ++lei++rl  +d + ta t +n++ +++++g+++ Al+l+ +a++ ++
  gi|116754673|ref|YP_843791.1| 687 VAAVLSTIGNLLAEQGHWDDALEHYSESLEIFERL--GDGYSTAVTTNNMANVLYRRGEWDRALNLYSKAMEHFQ 759
                                    7899999****************************..88889*****************************9876 PP

  == domain 11  score: 26.2 bits;  conditional E-value: 1.5e-08
                         TPR_12   2 vatalnnlaavlrrlgrydeAlellekaleiarrllGp 39 
                                    +a + nn+a+vl+r+g++d Al l+ ka+e ++r+ G+
  gi|116754673|ref|YP_843791.1| 727 TAVTTNNMANVLYRRGEWDRALNLYSKAMEHFQRV-GD 763
                                    788999****************************9.33 PP

  == domain 12  score: 51.4 bits;  conditional E-value: 2.1e-16
                         TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                                    ++l+n+a++++r+g+++ A+el++k+lei++ l  +d+ + a +l+nLg ly+++g++  A+++++ a +
  gi|116754673|ref|YP_843791.1| 769 ATLSNIASIHYRRGEWERAIELYHKSLEIFEGL--EDSGASAMVLNNLGLLYHRRGEWSLAVDHFRLAAE 836
                                    6899*****************************..99****************************98876 PP

  == domain 13  score: 46.3 bits;  conditional E-value: 7.9e-15
                         TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeal 72 
                                    a ++  la++++   r++eAl++++k+le+++r+  +d++ +a+t++n++ +yr +g++  A++ll +++
  gi|116754673|ref|YP_843791.1| 888 AEMHGILANAYADIFRWEEALDHYQKSLELFERT--GDRYSAAETMFNMALIYRDRGEWSIAEDLLSRSM 955
                                    567756****************************..9999**************************9986 PP

  == domain 14  score: 8.8 bits;  conditional E-value: 0.0042
                         TPR_12    2 vatalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiaek 77  
                                     ++ a+  +a v + +g++ eA+ +l +a  ++ ++ G d+   ++ ++  g+ y+ +  + eA++ +++ala+a+k
  gi|116754673|ref|YP_843791.1| 1005 LCEAYLAMARVKLNRGEMSEARFYLSEAETLILKT-GYDS-MKIRLYIEWGDFYLSQ-APFEARSSYQKALALARK 1077
                                     6789999*************************999.5555.99***********888.***************986 PP

  == domain 15  score: 28.8 bits;  conditional E-value: 2.3e-09
                         TPR_12   20 deAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76  
                                      eA++ ++kal++ar+  G    ++  +lr Lg + + +g+y+eA+e+l++al +++
  gi|116754673|ref|YP_843791.1| 1062 FEARSSYQKALALARKM-GL-TRDEGVALRSLGAASLNAGDYDEAEEHLQKALTLFK 1116
                                     79************876.55.559***********99*****************987 PP

  == domain 16  score: 17.0 bits;  conditional E-value: 1.1e-05
                         TPR_12    3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76  
                                     ++++  +a++++ ++++  A+e      ++arrl  ++++l + +l  ++ + +a+ r+++A++ + eal+ia+
  gi|116754673|ref|YP_843791.1| 1125 LSTYALMATLYFNRKDHSRAEETALLLERQARRL--GYRDLQVKALEVIAGCELATSRTDAAVSTYLEALNIAQ 1196
                                     567767****************************..9***********************************98 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00038      0.18       3      30 ..      63      90 ..      61      93 .. 0.93
   2 !   13.0   0.0   0.00015     0.069       2      29 ..      98     125 ..      97     129 .. 0.93
   3 ?    1.2   0.0      0.76   3.6e+02       9      23 ..     143     157 ..     136     164 .. 0.87
   4 ?    4.5   0.0     0.069        33       8      29 ..     182     203 ..     175     207 .. 0.85
   5 !   11.5   0.1   0.00043       0.2       7      29 ..     261     283 ..     257     283 .. 0.94
   6 !    7.3   0.0    0.0096       4.5       1      30 [.     295     324 ..     295     327 .. 0.92
   7 !   16.2   0.2   1.4e-05    0.0067       1      31 [.     334     364 ..     334     366 .. 0.95
   8 !   15.2   0.0   2.9e-05     0.014       1      30 [.     374     403 ..     374     406 .. 0.91
   9 !   17.0   0.1   8.2e-06    0.0039       5      32 ..     418     445 ..     414     447 .. 0.92
  10 !   24.2   0.1   4.2e-08     2e-05       2      32 ..     455     485 ..     454     487 .. 0.94
  11 !   19.4   0.0   1.4e-06   0.00067       1      29 [.     494     522 ..     494     525 .. 0.95
  12 !   18.4   0.0   2.9e-06    0.0014       2      31 ..     535     564 ..     534     567 .. 0.91
  13 !    7.8   0.1    0.0065       3.1       6      29 ..     576     599 ..     576     603 .. 0.94
  14 !   16.7   0.0     1e-05    0.0048       1      30 [.     611     640 ..     611     641 .. 0.95
  15 !   11.2   0.0   0.00055      0.26       3      30 ..     650     677 ..     649     680 .. 0.90
  16 !   19.5   0.0   1.3e-06   0.00062       1      31 [.     688     718 ..     688     720 .. 0.91
  17 !   15.7   0.0   2.1e-05    0.0097       5      30 ..     732     757 ..     728     760 .. 0.92
  18 !   19.0   0.0   1.8e-06   0.00085       3      31 ..     770     798 ..     769     800 .. 0.93
  19 !   15.9   0.1   1.8e-05    0.0086       2      28 ..     809     835 ..     808     849 .. 0.93
  20 !   18.7   0.2   2.4e-06    0.0011       2      31 ..     889     918 ..     888     920 .. 0.89
  21 ?    5.1   0.0     0.046        22       1      26 [.     928     953 ..     928     956 .. 0.87
  22 ?   -0.3   0.1       2.3   1.1e+03       2      27 ..    1007    1032 ..    1006    1035 .. 0.88
  23 ?    1.7   0.1      0.53   2.5e+02      19      32 ..    1063    1076 ..    1063    1078 .. 0.84
  24 !   21.0   0.1   4.5e-07   0.00021       3      30 ..    1087    1114 ..    1086    1117 .. 0.91
  25 ?    2.5   0.0      0.29   1.4e+02       3      22 ..    1127    1146 ..    1126    1147 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00038
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                          TPR_1  3 alynlGnayfklgkydeAleyyekALel 30
                                    ++ lG++ ++lg ++ A+ + ++ALe 
  gi|116754673|ref|YP_843791.1| 63 LWFSLGMISQQLGSLERAVSHLSRALER 90
                                   69************************97 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00015
                                    HHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                          TPR_1   2 kalynlGnayfklgkydeAleyyekALe 29 
                                    k+l +lG +y + +++d A+  y+ AL+
  gi|116754673|ref|YP_843791.1|  98 KVLSRLGSIYANVEDLDRAISLYRDALS 125
                                    799***********************97 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.76
                                    HHHHHTT-HHHHHHH CS
                          TPR_1   9 nayfklgkydeAley 23 
                                    +ay++  ++d+Al++
  gi|116754673|ref|YP_843791.1| 143 MAYREARRWDDALQC 157
                                    79***********99 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.069
                                    HHHHHHTT-HHHHHHHHHHHHH CS
                          TPR_1   8 GnayfklgkydeAleyyekALe 29 
                                    + + +++g++  A+e y+ +Le
  gi|116754673|ref|YP_843791.1| 182 AEIRREMGDLSSAEELYRTCLE 203
                                    567789***************8 PP

  == domain 5  score: 11.5 bits;  conditional E-value: 0.00043
                                    HHHHHHHTT-HHHHHHHHHHHHH CS
                          TPR_1   7 lGnayfklgkydeAleyyekALe 29 
                                    lG ++   g++  A+e+y kALe
  gi|116754673|ref|YP_843791.1| 261 LGDLHAIEGRFSSAEECYLKALE 283
                                    899999****************8 PP

  == domain 6  score: 7.3 bits;  conditional E-value: 0.0096
                                    HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                          TPR_1   1 akalynlGnayfklgkydeAleyyekALel 30 
                                    a++l  l+ +y ++g++  A+e y++AL +
  gi|116754673|ref|YP_843791.1| 295 ANTLLSLARLYGSMGEWRGAVERYREALDI 324
                                    678999**********************97 PP

  == domain 7  score: 16.2 bits;  conditional E-value: 1.4e-05
                                    HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                          TPR_1   1 akalynlGnayfklgkydeAleyyekALeln 31 
                                    a+al  +G a+++l +y+ A  y+ k Lel 
  gi|116754673|ref|YP_843791.1| 334 ARALREMGTACYRLRDYEMAQNYFMKSLELS 364
                                    789999***********************95 PP

  == domain 8  score: 15.2 bits;  conditional E-value: 2.9e-05
                                    HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                          TPR_1   1 akalynlGnayfklgkydeAleyyekALel 30 
                                    a ++ ++G+++  lg++d A+e+ye+  el
  gi|116754673|ref|YP_843791.1| 374 AASHTGMGHMLSDLGDWDGAVEHYERGAEL 403
                                    66899********************98776 PP

  == domain 9  score: 17.0 bits;  conditional E-value: 8.2e-06
                                    HHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                          TPR_1   5 ynlGnayfklgkydeAleyyekALelnP 32 
                                     n++ +y+ +g++++Al+ y  AL++++
  gi|116754673|ref|YP_843791.1| 418 SNIASVYQMMGDLEKALDIYHDALQIQE 445
                                    69***********************975 PP

  == domain 10  score: 24.2 bits;  conditional E-value: 4.2e-08
                                    HHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                          TPR_1   2 kalynlGnayfklgkydeAleyyekALelnP 32 
                                    k+l+n+G++y+++g+ + A+  y ++Lel +
  gi|116754673|ref|YP_843791.1| 455 KTLNNMGLVYQHMGEIEAAERNYMRCLELKE 485
                                    79**************************986 PP

  == domain 11  score: 19.4 bits;  conditional E-value: 1.4e-06
                                    HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                          TPR_1   1 akalynlGnayfklgkydeAleyyekALe 29 
                                    a+++ nl+ +y  + ++d+A+ +y+ ALe
  gi|116754673|ref|YP_843791.1| 494 ANTHINLATLYEIQRRWDDAITHYQDALE 522
                                    6899************************8 PP

  == domain 12  score: 18.4 bits;  conditional E-value: 2.9e-06
                                    HHHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                          TPR_1   2 kalynlGnayfklgkydeAleyyekALeln 31 
                                     + +nlGn+y ++g+  +A++ y+   el+
  gi|116754673|ref|YP_843791.1| 535 AVMNNLGNVYEEKGDILQAIKSYRMSMELD 564
                                    6789*********************99998 PP

  == domain 13  score: 7.8 bits;  conditional E-value: 0.0065
                                    HHHHHHHHTT-HHHHHHHHHHHHH CS
                          TPR_1   6 nlGnayfklgkydeAleyyekALe 29 
                                    nlG +y++ g+ + A+++y+  Le
  gi|116754673|ref|YP_843791.1| 576 NLGGLYQRIGDAESAEKCYRASLE 599
                                    89******************9998 PP

  == domain 14  score: 16.7 bits;  conditional E-value: 1e-05
                                    HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                          TPR_1   1 akalynlGnayfklgkydeAleyyekALel 30 
                                    a+al +lG + ++ g +d+Al+++++++ l
  gi|116754673|ref|YP_843791.1| 611 AYALMGLGSIALERGLWDDALDCFKRCVDL 640
                                    79*************************987 PP

  == domain 15  score: 11.2 bits;  conditional E-value: 0.00055
                                    HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                          TPR_1   3 alynlGnayfklgkydeAleyyekALel 30 
                                    +l  ++ +y ++g+++eAl+ y+k+Le 
  gi|116754673|ref|YP_843791.1| 650 VLGSIASVYERKGMWQEALAEYRKVLER 677
                                    577899********************96 PP

  == domain 16  score: 19.5 bits;  conditional E-value: 1.3e-06
                                    HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                          TPR_1   1 akalynlGnayfklgkydeAleyyekALeln 31 
                                    a +l  +Gn++ ++g +d+Ale+y++ Le+ 
  gi|116754673|ref|YP_843791.1| 688 AAVLSTIGNLLAEQGHWDDALEHYSESLEIF 718
                                    567889***********************95 PP

  == domain 17  score: 15.7 bits;  conditional E-value: 2.1e-05
                                    HHHHHHHHHTT-HHHHHHHHHHHHHH CS
                          TPR_1   5 ynlGnayfklgkydeAleyyekALel 30 
                                    +n++n++++ g++d Al  y+kA e+
  gi|116754673|ref|YP_843791.1| 732 NNMANVLYRRGEWDRALNLYSKAMEH 757
                                    8**********************886 PP

  == domain 18  score: 19.0 bits;  conditional E-value: 1.8e-06
                                    HHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                          TPR_1   3 alynlGnayfklgkydeAleyyekALeln 31 
                                    +l n++ ++++ g+++ A+e y k Le+ 
  gi|116754673|ref|YP_843791.1| 770 TLSNIASIHYRRGEWERAIELYHKSLEIF 798
                                    689************************95 PP

  == domain 19  score: 15.9 bits;  conditional E-value: 1.8e-05
                                    HHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                          TPR_1   2 kalynlGnayfklgkydeAleyyekAL 28 
                                     +l+nlG++y++ g++  A+++++ A 
  gi|116754673|ref|YP_843791.1| 809 MVLNNLGLLYHRRGEWSLAVDHFRLAA 835
                                    589********************9875 PP

  == domain 20  score: 18.7 bits;  conditional E-value: 2.4e-06
                                    HHHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                          TPR_1   2 kalynlGnayfklgkydeAleyyekALeln 31 
                                    + +  l+nay    +++eAl++y+k Lel 
  gi|116754673|ref|YP_843791.1| 889 EMHGILANAYADIFRWEEALDHYQKSLELF 918
                                    556779**********************95 PP

  == domain 21  score: 5.1 bits;  conditional E-value: 0.046
                                    HHHHHHHHHHHHHTT-HHHHHHHHHH CS
                          TPR_1   1 akalynlGnayfklgkydeAleyyek 26 
                                    a++ +n++++y+  g++  A++  ++
  gi|116754673|ref|YP_843791.1| 928 AETMFNMALIYRDRGEWSIAEDLLSR 953
                                    68889************999987665 PP

  == domain 22  score: -0.3 bits;  conditional E-value: 2.3
                                     HHHHHHHHHHHHTT-HHHHHHHHHHH CS
                          TPR_1    2 kalynlGnayfklgkydeAleyyekA 27  
                                     +a+  ++ + ++ g+  eA  y ++A
  gi|116754673|ref|YP_843791.1| 1007 EAYLAMARVKLNRGEMSEARFYLSEA 1032
                                     68999999999*********999998 PP

  == domain 23  score: 1.7 bits;  conditional E-value: 0.53
                                     HHHHHHHHHHHHST CS
                          TPR_1   19 eAleyyekALelnP 32  
                                     eA   y+kAL l  
  gi|116754673|ref|YP_843791.1| 1063 EARSSYQKALALAR 1076
                                     68889*****9976 PP

  == domain 24  score: 21.0 bits;  conditional E-value: 4.5e-07
                                     HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                          TPR_1    3 alynlGnayfklgkydeAleyyekALel 30  
                                     al  lG+a ++ g+ydeA+e+ +kAL+l
  gi|116754673|ref|YP_843791.1| 1087 ALRSLGAASLNAGDYDEAEEHLQKALTL 1114
                                     67789*********************98 PP

  == domain 25  score: 2.5 bits;  conditional E-value: 0.29
                                     HHHHHHHHHHHTT-HHHHHH CS
                          TPR_1    3 alynlGnayfklgkydeAle 22  
                                     ++  ++ +yf+ +++  A+e
  gi|116754673|ref|YP_843791.1| 1127 TYALMATLYFNRKDHSRAEE 1146
                                     58889*************97 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   0.00032      0.15       3      31 ..      63      91 ..      61      94 .. 0.93
   2 !   11.9   0.0    0.0004      0.19       2      29 ..      98     125 ..      97     128 .. 0.93
   3 ?    7.6   0.1      0.01       4.7       3      23 ..     137     157 ..     135     164 .. 0.91
   4 ?    6.6   0.1      0.02       9.5       2      31 ..     176     205 ..     175     208 .. 0.87
   5 ?   -1.2   0.0       6.5     3e+03       4      27 ..     218     241 ..     216     248 .. 0.82
   6 !   11.8   0.1   0.00044      0.21       6      29 ..     260     283 ..     256     283 .. 0.94
   7 !    7.7   0.1    0.0093       4.4       3      30 ..     297     324 ..     295     326 .. 0.90
   8 !   17.9   0.5   4.8e-06    0.0023       1      31 [.     334     364 ..     334     367 .. 0.94
   9 !   12.2   0.0   0.00033      0.16       3      30 ..     376     403 ..     374     407 .. 0.88
  10 !   12.4   0.0   0.00028      0.13       5      32 ..     418     445 ..     414     447 .. 0.90
  11 !   13.8   0.1    0.0001     0.049       2      32 ..     455     485 ..     454     487 .. 0.92
  12 !   17.0   0.1   9.7e-06    0.0046       2      29 ..     495     522 ..     494     526 .. 0.92
  13 !   14.4   0.0   6.4e-05      0.03       1      32 [.     534     565 ..     534     567 .. 0.91
  14 !   10.2   0.1    0.0014      0.66       3      30 ..     573     600 ..     571     603 .. 0.89
  15 !   13.3   0.0   0.00015      0.07       1      30 [.     611     640 ..     611     643 .. 0.94
  16 !   13.3   0.0   0.00014     0.067       7      30 ..     654     677 ..     649     680 .. 0.88
  17 !   21.3   0.0   3.9e-07   0.00018       1      32 [.     688     719 ..     688     721 .. 0.92
  18 !   16.5   0.0   1.3e-05    0.0063       5      30 ..     732     757 ..     730     760 .. 0.92
  19 !   20.0   0.0   1.1e-06   0.00051       3      32 ..     770     799 ..     768     801 .. 0.91
  20 !   13.9   0.1   9.4e-05     0.044       2      29 ..     809     836 ..     808     841 .. 0.91
  21 !   18.2   0.4   4.1e-06    0.0019       5      31 ..     892     918 ..     888     920 .. 0.89
  22 ?    5.8   0.0     0.036        17       1      27 [.     928     954 ..     928     959 .. 0.89
  23 ?    3.4   0.2      0.22     1e+02       2      27 ..    1007    1032 ..    1006    1035 .. 0.92
  24 ?    4.6   0.1     0.089        42      18      31 ..    1062    1075 ..    1053    1077 .. 0.85
  25 !   21.5   0.1   3.5e-07   0.00016       3      31 ..    1087    1115 ..    1086    1117 .. 0.92
  26 ?   -0.8   0.0       4.7   2.2e+03       4      22 ..    1128    1146 ..    1127    1148 .. 0.86
  27 ?   -1.7   0.0       9.5   4.5e+03      14      31 ..    1178    1195 ..    1166    1198 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00032
                          TPR_2  3 alynlGlayyklgdyeeAleafekAleld 31
                                   +++ lG++  +lg +e+A+ ++ +Ale +
  gi|116754673|ref|YP_843791.1| 63 LWFSLGMISQQLGSLERAVSHLSRALERA 91
                                   7*************************975 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.0004
                          TPR_2   2 ealynlGlayyklgdyeeAleafekAle 29 
                                    ++l +lG +y++  d+++A+ +++ Al+
  gi|116754673|ref|YP_843791.1|  98 KVLSRLGSIYANVEDLDRAISLYRDALS 125
                                    6899**********************96 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.01
                          TPR_2   3 alynlGlayyklgdyeeAlea 23 
                                    +l nl +ay+++ ++++Al++
  gi|116754673|ref|YP_843791.1| 137 ILINLSMAYREARRWDDALQC 157
                                    789****************97 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.02
                          TPR_2   2 ealynlGlayyklgdyeeAleafekAleld 31 
                                    +a ++ +++ +++gd+  A+e+++ +le  
  gi|116754673|ref|YP_843791.1| 176 RAIMEEAEIRREMGDLSSAEELYRTCLEEF 205
                                    5667889999*****************975 PP

  == domain 5  score: -1.2 bits;  conditional E-value: 6.5
                          TPR_2   4 lynlGlayyklgdyeeAleafekA 27 
                                    l +lG++   +g+  +A+++f+ A
  gi|116754673|ref|YP_843791.1| 218 LEMLGRISQLRGESRRAEDLFDMA 241
                                    668999999999999999999876 PP

  == domain 6  score: 11.8 bits;  conditional E-value: 0.00044
                          TPR_2   6 nlGlayyklgdyeeAleafekAle 29 
                                     lG++++  g++  A+e++ kAle
  gi|116754673|ref|YP_843791.1| 260 LLGDLHAIEGRFSSAEECYLKALE 283
                                    69********************97 PP

  == domain 7  score: 7.7 bits;  conditional E-value: 0.0093
                          TPR_2   3 alynlGlayyklgdyeeAleafekAlel 30 
                                     l  l+++y  +g++  A+e +++Al +
  gi|116754673|ref|YP_843791.1| 297 TLLSLARLYGSMGEWRGAVERYREALDI 324
                                    57789*********************86 PP

  == domain 8  score: 17.9 bits;  conditional E-value: 4.8e-06
                          TPR_2   1 aealynlGlayyklgdyeeAleafekAleld 31 
                                    a+al ++G a+y+l dye A ++f k+lel 
  gi|116754673|ref|YP_843791.1| 334 ARALREMGTACYRLRDYEMAQNYFMKSLELS 364
                                    789**************************97 PP

  == domain 9  score: 12.2 bits;  conditional E-value: 0.00033
                          TPR_2   3 alynlGlayyklgdyeeAleafekAlel 30 
                                     +  +G  +  lgd++ A+e++e+  el
  gi|116754673|ref|YP_843791.1| 376 SHTGMGHMLSDLGDWDGAVEHYERGAEL 403
                                    67789999****************9998 PP

  == domain 10  score: 12.4 bits;  conditional E-value: 0.00028
                          TPR_2   5 ynlGlayyklgdyeeAleafekAleldP 32 
                                     n++ +y  +gd+e+Al+ +  Al++ +
  gi|116754673|ref|YP_843791.1| 418 SNIASVYQMMGDLEKALDIYHDALQIQE 445
                                    58999********************975 PP

  == domain 11  score: 13.8 bits;  conditional E-value: 0.0001
                          TPR_2   2 ealynlGlayyklgdyeeAleafekAleldP 32 
                                    + l+n+Gl+y ++g+ e A++ + ++lel +
  gi|116754673|ref|YP_843791.1| 455 KTLNNMGLVYQHMGEIEAAERNYMRCLELKE 485
                                    5799************************975 PP

  == domain 12  score: 17.0 bits;  conditional E-value: 9.7e-06
                          TPR_2   2 ealynlGlayyklgdyeeAleafekAle 29 
                                      + nl+ +y+ + ++++A+ +++ Ale
  gi|116754673|ref|YP_843791.1| 495 NTHINLATLYEIQRRWDDAITHYQDALE 522
                                    6799***********************8 PP

  == domain 13  score: 14.4 bits;  conditional E-value: 6.4e-05
                          TPR_2   1 aealynlGlayyklgdyeeAleafekAleldP 32 
                                    a + +nlG++y+++gd  +A++ ++ + eld 
  gi|116754673|ref|YP_843791.1| 534 AAVMNNLGNVYEEKGDILQAIKSYRMSMELDG 565
                                    57899********************9999985 PP

  == domain 14  score: 10.2 bits;  conditional E-value: 0.0014
                          TPR_2   3 alynlGlayyklgdyeeAleafekAlel 30 
                                    + +nlG +y + gd e A+++++++le 
  gi|116754673|ref|YP_843791.1| 573 ISWNLGGLYQRIGDAESAEKCYRASLEA 600
                                    5689********************9985 PP

  == domain 15  score: 13.3 bits;  conditional E-value: 0.00015
                          TPR_2   1 aealynlGlayyklgdyeeAleafekAlel 30 
                                    a+al+ lG +++++g +++Al++f++++ l
  gi|116754673|ref|YP_843791.1| 611 AYALMGLGSIALERGLWDDALDCFKRCVDL 640
                                    789***********************9987 PP

  == domain 16  score: 13.3 bits;  conditional E-value: 0.00014
                          TPR_2   7 lGlayyklgdyeeAleafekAlel 30 
                                    ++ +y+++g ++eAl+ ++k+le 
  gi|116754673|ref|YP_843791.1| 654 IASVYERKGMWQEALAEYRKVLER 677
                                    7899******************96 PP

  == domain 17  score: 21.3 bits;  conditional E-value: 3.9e-07
                          TPR_2   1 aealynlGlayyklgdyeeAleafekAleldP 32 
                                    a +l  +G++++++g++++Ale++ ++le+ +
  gi|116754673|ref|YP_843791.1| 688 AAVLSTIGNLLAEQGHWDDALEHYSESLEIFE 719
                                    678999***********************975 PP

  == domain 18  score: 16.5 bits;  conditional E-value: 1.3e-05
                          TPR_2   5 ynlGlayyklgdyeeAleafekAlel 30 
                                    +n+++++y++g++++Al+++ kA e+
  gi|116754673|ref|YP_843791.1| 732 NNMANVLYRRGEWDRALNLYSKAMEH 757
                                    689********************986 PP

  == domain 19  score: 20.0 bits;  conditional E-value: 1.1e-06
                          TPR_2   3 alynlGlayyklgdyeeAleafekAleldP 32 
                                     l n++ ++y++g++e+A+e++ k+le+ +
  gi|116754673|ref|YP_843791.1| 770 TLSNIASIHYRRGEWERAIELYHKSLEIFE 799
                                    5889***********************975 PP

  == domain 20  score: 13.9 bits;  conditional E-value: 9.4e-05
                          TPR_2   2 ealynlGlayyklgdyeeAleafekAle 29 
                                     +l+nlGl+y ++g++  A+++f+ A e
  gi|116754673|ref|YP_843791.1| 809 MVLNNLGLLYHRRGEWSLAVDHFRLAAE 836
                                    589*********************9987 PP

  == domain 21  score: 18.2 bits;  conditional E-value: 4.1e-06
                          TPR_2   5 ynlGlayyklgdyeeAleafekAleld 31 
                                      l++ay+   ++eeAl++++k+lel 
  gi|116754673|ref|YP_843791.1| 892 GILANAYADIFRWEEALDHYQKSLELF 918
                                    569**********************97 PP

  == domain 22  score: 5.8 bits;  conditional E-value: 0.036
                          TPR_2   1 aealynlGlayyklgdyeeAleafekA 27 
                                    ae  +n++l+y+ +g++  A++++ ++
  gi|116754673|ref|YP_843791.1| 928 AETMFNMALIYRDRGEWSIAEDLLSRS 954
                                    7899**************999998776 PP

  == domain 23  score: 3.4 bits;  conditional E-value: 0.22
                          TPR_2    2 ealynlGlayyklgdyeeAleafekA 27  
                                     ea+ +++++ +++g+  eA+ ++ +A
  gi|116754673|ref|YP_843791.1| 1007 EAYLAMARVKLNRGEMSEARFYLSEA 1032
                                     8999*******************999 PP

  == domain 24  score: 4.6 bits;  conditional E-value: 0.089
                          TPR_2   18 eeAleafekAleld 31  
                                      eA+  ++kAl+l+
  gi|116754673|ref|YP_843791.1| 1062 FEARSSYQKALALA 1075
                                     59**********97 PP

  == domain 25  score: 21.5 bits;  conditional E-value: 3.5e-07
                          TPR_2    3 alynlGlayyklgdyeeAleafekAleld 31  
                                     al  lG a +++gdy+eA+e+++kAl l 
  gi|116754673|ref|YP_843791.1| 1087 ALRSLGAASLNAGDYDEAEEHLQKALTLF 1115
                                     6788**********************986 PP

  == domain 26  score: -0.8 bits;  conditional E-value: 4.7
                          TPR_2    4 lynlGlayyklgdyeeAle 22  
                                     +  ++ +y++++d+ +A+e
  gi|116754673|ref|YP_843791.1| 1128 YALMATLYFNRKDHSRAEE 1146
                                     5678999********9987 PP

  == domain 27  score: -1.7 bits;  conditional E-value: 9.5
                          TPR_2   14 lgdyeeAleafekAleld 31  
                                       + + A+  + +Al ++
  gi|116754673|ref|YP_843791.1| 1178 TSRTDAAVSTYLEALNIA 1195
                                     5577899999*****987 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.78   3.7e+02       2      29 ..      64      89 ..      63      93 .. 0.85
   2 !   17.6   0.1   5.8e-06    0.0028       2      32 ..     100     131 ..      99     135 .. 0.87
   3 ?    3.8   0.1      0.15        69       2      21 ..     138     157 ..     137     157 .. 0.91
   4 ?    7.4   0.0     0.011       5.1       6      29 ..     182     206 ..     182     212 .. 0.87
   5 ?    3.6   0.1      0.17        81       1      29 [.     217     243 ..     217     249 .. 0.90
   6 !   10.0   0.1    0.0016      0.74       3      35 ..     259     291 ..     257     292 .. 0.86
   7 !   19.7   0.2   1.2e-06   0.00058       1      32 [.     297     328 ..     297     332 .. 0.88
   8 !    9.6   0.3    0.0021      0.97       1      34 [.     336     369 ..     336     371 .. 0.89
   9 !   15.5   0.0   2.7e-05     0.013       4      25 ..     379     400 ..     376     413 .. 0.81
  10 !   10.5   0.1    0.0011      0.51       3      34 ..     418     449 ..     415     451 .. 0.87
  11 !   11.9   0.0   0.00039      0.18       1      34 [.     456     489 ..     456     490 .. 0.93
  12 !   14.7   0.1   4.9e-05     0.023       2      35 ..     497     530 ..     496     531 .. 0.87
  13 !   10.3   0.0    0.0012      0.57       3      31 ..     538     564 ..     536     569 .. 0.83
  14 !   14.8   0.1   4.6e-05     0.022       4      31 ..     576     603 ..     575     608 .. 0.86
  15 !   11.0   0.0   0.00076      0.36       1      32 [.     613     644 ..     613     648 .. 0.85
  16 !   12.6   0.0   0.00023      0.11       2      27 ..     651     676 ..     650     685 .. 0.88
  17 !   13.4   0.0   0.00013      0.06       2      31 ..     691     720 ..     690     723 .. 0.87
  18 !   12.9   0.0   0.00019     0.088       3      28 ..     732     755 ..     730     764 .. 0.87
  19 !   25.9   0.0   1.3e-08   5.9e-06       1      30 [.     770     799 ..     770     805 .. 0.89
  20 !   14.0   0.1   8.3e-05     0.039       2      25 ..     811     834 ..     810     850 .. 0.89
  21 !   15.7   0.2   2.3e-05     0.011       5      34 ..     894     923 ..     879     925 .. 0.92
  22 ?    6.8   0.0     0.016       7.5       2      26 ..     931     955 ..     930     968 .. 0.85
  23 ?   -0.2   0.0       2.7   1.3e+03       1      18 [.    1008    1025 ..    1008    1026 .. 0.93
  24 ?   -0.9   0.0       4.6   2.2e+03      17      31 ..    1063    1077 ..    1063    1085 .. 0.79
  25 !   13.4   0.2   0.00013     0.061       1      33 [.    1087    1119 ..    1087    1122 .. 0.85
  26 ?    0.4   0.0       1.8   8.5e+02       1      20 [.    1127    1146 ..    1127    1148 .. 0.91
  27 ?    1.3   0.0      0.93   4.4e+02      13      33 ..    1179    1199 ..    1176    1202 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.78
                          TPR_7  2 LlnLarlysrlGdyeeAielyeqsLalt 29
                                   ++ L+ + ++lG  e+A++++ +  al+
  gi|116754673|ref|YP_843791.1| 64 WFSLGMISQQLGSLERAVSHLSR--ALE 89
                                   57899999*************99..555 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 5.8e-06
                          TPR_7   2 LlnLarlysrlGdyeeAielyeqsL.altkdp 32 
                                    L++L+++y ++ d ++Ai+ly+ +L +l++ +
  gi|116754673|ref|YP_843791.1| 100 LSRLGSIYANVEDLDRAISLYRDALsRLESGD 131
                                    899********************888887665 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.15
                          TPR_7   2 LlnLarlysrlGdyeeAiel 21 
                                    L nL  +y++ +++++A+++
  gi|116754673|ref|YP_843791.1| 138 LINLSMAYREARRWDDALQC 157
                                    679999***********986 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.011
                          TPR_7   6 arlysrlGdyeeAielyeqsL.alt 29 
                                    a++++++Gd + A+ely+ +L +++
  gi|116754673|ref|YP_843791.1| 182 AEIRREMGDLSSAEELYRTCLeEFE 206
                                    7899***************996665 PP

  == domain 5  score: 3.6 bits;  conditional E-value: 0.17
                          TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLalt 29 
                                    +L  L+r+ + +G+ ++A++l+    a++
  gi|116754673|ref|YP_843791.1| 217 SLEMLGRISQLRGESRRAEDLFDM--AMH 243
                                    5778******************99..887 PP

  == domain 6  score: 10.0 bits;  conditional E-value: 0.0016
                          TPR_7   3 lnLarlysrlGdyeeAielyeqsLaltkdpeda 35 
                                    l L++l+  +G+++ A+e+y ++L+  ++ +d+
  gi|116754673|ref|YP_843791.1| 259 LLLGDLHAIEGRFSSAEECYLKALEGFREVSDR 291
                                    6799******************99877777765 PP

  == domain 7  score: 19.7 bits;  conditional E-value: 1.2e-06
                          TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdp 32 
                                    +Ll Larly ++G+++ A+e y+++L +  ++
  gi|116754673|ref|YP_843791.1| 297 TLLSLARLYGSMGEWRGAVERYREALDILQSE 328
                                    799*********************88777666 PP

  == domain 8  score: 9.6 bits;  conditional E-value: 0.0021
                          TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdped 34 
                                    aL  ++ ++ rl+dye A  ++ +sL+l ++ ++
  gi|116754673|ref|YP_843791.1| 336 ALREMGTACYRLRDYEMAQNYFMKSLELSEALGE 369
                                    577899*********************9988776 PP

  == domain 9  score: 15.5 bits;  conditional E-value: 2.7e-05
                          TPR_7   4 nLarlysrlGdyeeAielyeqs 25 
                                     ++++ s+lGd++ A+e+ye+ 
  gi|116754673|ref|YP_843791.1| 379 GMGHMLSDLGDWDGAVEHYERG 400
                                    5899*****************3 PP

  == domain 10  score: 10.5 bits;  conditional E-value: 0.0011
                          TPR_7   3 lnLarlysrlGdyeeAielyeqsLaltkdped 34 
                                    +n+a++y+ +Gd e+A+++y  +L++ ++ +d
  gi|116754673|ref|YP_843791.1| 418 SNIASVYQMMGDLEKALDIYHDALQIQERLGD 449
                                    8********************99988777766 PP

  == domain 11  score: 11.9 bits;  conditional E-value: 0.00039
                          TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdped 34 
                                    +L+n++ +y+ +G+ e A++ y ++L+l ++ +d
  gi|116754673|ref|YP_843791.1| 456 TLNNMGLVYQHMGEIEAAERNYMRCLELKEQLGD 489
                                    79*************************9998876 PP

  == domain 12  score: 14.7 bits;  conditional E-value: 4.9e-05
                          TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdpeda 35 
                                    + nLa ly+ ++++++Ai++y+ +L++ ++ +d+
  gi|116754673|ref|YP_843791.1| 497 HINLATLYEIQRRWDDAITHYQDALETFEAIGDR 530
                                    67*********************99887777665 PP

  == domain 13  score: 10.3 bits;  conditional E-value: 0.0012
                          TPR_7   3 lnLarlysrlGdyeeAielyeqsLaltkd 31 
                                    +nL+++y++ Gd  +Ai+ y+ s++l  d
  gi|116754673|ref|YP_843791.1| 538 NNLGNVYEEKGDILQAIKSYRMSMEL--D 564
                                    8*********************5555..4 PP

  == domain 14  score: 14.8 bits;  conditional E-value: 4.6e-05
                          TPR_7   4 nLarlysrlGdyeeAielyeqsLaltkd 31 
                                    nL+ ly+r Gd e A+++y++sL+   +
  gi|116754673|ref|YP_843791.1| 576 NLGGLYQRIGDAESAEKCYRASLEAFQS 603
                                    9**********************66555 PP

  == domain 15  score: 11.0 bits;  conditional E-value: 0.00076
                          TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdp 32 
                                    aL  L+++  ++G +++A+++++++  l+ d 
  gi|116754673|ref|YP_843791.1| 613 ALMGLGSIALERGLWDDALDCFKRCVDLRLDT 644
                                    5778********************87777765 PP

  == domain 16  score: 12.6 bits;  conditional E-value: 0.00023
                          TPR_7   2 LlnLarlysrlGdyeeAielyeqsLa 27 
                                    L  +a++y+r G ++eA+  y+++L+
  gi|116754673|ref|YP_843791.1| 651 LGSIASVYERKGMWQEALAEYRKVLE 676
                                    789********************773 PP

  == domain 17  score: 13.4 bits;  conditional E-value: 0.00013
                          TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkd 31 
                                    L+ +++l  ++G++++A+e+y +sL++ ++
  gi|116754673|ref|YP_843791.1| 691 LSTIGNLLAEQGHWDDALEHYSESLEIFER 720
                                    7789*******************9998665 PP

  == domain 18  score: 12.9 bits;  conditional E-value: 0.00019
                          TPR_7   3 lnLarlysrlGdyeeAielyeqsLal 28 
                                    +n+a++  r+G++++A+ ly +  a+
  gi|116754673|ref|YP_843791.1| 732 NNMANVLYRRGEWDRALNLYSK--AM 755
                                    8*****9*************99..55 PP

  == domain 19  score: 25.9 bits;  conditional E-value: 1.3e-08
                          TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltk 30 
                                    +L+n+a+++ r+G++e+Aiely +sL++ +
  gi|116754673|ref|YP_843791.1| 770 TLSNIASIHYRRGEWERAIELYHKSLEIFE 799
                                    79************************9865 PP

  == domain 20  score: 14.0 bits;  conditional E-value: 8.3e-05
                          TPR_7   2 LlnLarlysrlGdyeeAielyeqs 25 
                                    L+nL+ ly+r+G+++ A+++++ +
  gi|116754673|ref|YP_843791.1| 811 LNNLGLLYHRRGEWSLAVDHFRLA 834
                                    9*******************9974 PP

  == domain 21  score: 15.7 bits;  conditional E-value: 2.3e-05
                          TPR_7   5 LarlysrlGdyeeAielyeqsLaltkdped 34 
                                    La++y +  ++eeA+++y++sL+l ++ +d
  gi|116754673|ref|YP_843791.1| 894 LANAYADIFRWEEALDHYQKSLELFERTGD 923
                                    9*********************99777666 PP

  == domain 22  score: 6.8 bits;  conditional E-value: 0.016
                          TPR_7   2 LlnLarlysrlGdyeeAielyeqsL 26 
                                     +n+a +y+++G+++ A++l+ +s+
  gi|116754673|ref|YP_843791.1| 931 MFNMALIYRDRGEWSIAEDLLSRSM 955
                                    68************99999887765 PP

  == domain 23  score: -0.2 bits;  conditional E-value: 2.7
                          TPR_7    1 aLlnLarlysrlGdyeeA 18  
                                     a+l++ar+  ++G+++eA
  gi|116754673|ref|YP_843791.1| 1008 AYLAMARVKLNRGEMSEA 1025
                                     799************998 PP

  == domain 24  score: -0.9 bits;  conditional E-value: 4.6
                          TPR_7   17 eAielyeqsLaltkd 31  
                                     eA + y+++Lal++ 
  gi|116754673|ref|YP_843791.1| 1063 EARSSYQKALALARK 1077
                                     577889999999865 PP

  == domain 25  score: 13.4 bits;  conditional E-value: 0.00013
                          TPR_7    1 aLlnLarlysrlGdyeeAielyeqsLaltkdpe 33  
                                     aL  L+ +  + Gdy+eA+e+++++L l k+ +
  gi|116754673|ref|YP_843791.1| 1087 ALRSLGAASLNAGDYDEAEEHLQKALTLFKSIN 1119
                                     6778999999**************887777665 PP

  == domain 26  score: 0.4 bits;  conditional E-value: 1.8
                          TPR_7    1 aLlnLarlysrlGdyeeAie 20  
                                     ++  +a ly+++ d+++A+e
  gi|116754673|ref|YP_843791.1| 1127 TYALMATLYFNRKDHSRAEE 1146
                                     6889**************97 PP

  == domain 27  score: 1.3 bits;  conditional E-value: 0.93
                          TPR_7   13 GdyeeAielyeqsLaltkdpe 33  
                                      +++ A++ y ++L ++ +++
  gi|116754673|ref|YP_843791.1| 1179 SRTDAAVSTYLEALNIAQSDG 1199
                                     6899********999998887 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.32   1.5e+02       8      31 ..      67      90 ..      66      91 .. 0.93
   2 !    9.9   0.0    0.0015      0.69       5      32 ..     100     127 ..      98     129 .. 0.91
   3 !   12.5   0.2   0.00021       0.1       2      23 ..     135     156 ..     134     166 .. 0.89
   4 ?    4.1   0.5     0.098        46      13      33 ..     186     206 ..     175     210 .. 0.87
   5 ?    4.0   0.1      0.11        50       3      33 ..     216     246 ..     214     247 .. 0.92
   6 ?    2.7   0.1      0.26   1.2e+02       8      35 ..     261     288 ..     256     293 .. 0.83
   7 !   18.6   0.2   2.6e-06    0.0012       1      33 [.     294     326 ..     294     328 .. 0.94
   8 !    8.9   0.7    0.0029       1.3       1      37 [.     333     369 ..     333     372 .. 0.91
   9 !   10.8   0.0   0.00072      0.34       8      34 ..     380     406 ..     374     407 .. 0.88
  10 !   23.8   0.1     6e-08   2.8e-05       2      35 ..     414     447 ..     413     449 .. 0.96
  11 !   19.8   0.2   1.1e-06   0.00053       4      35 ..     456     487 ..     455     491 .. 0.94
  12 !   12.8   0.1   0.00017      0.08       7      33 ..     499     525 ..     494     528 .. 0.91
  13 !    7.8   0.1    0.0063         3       2      24 ..     534     556 ..     533     563 .. 0.79
  14 ?    7.1   0.1     0.011       5.2       7      31 ..     576     600 ..     576     604 .. 0.94
  15 ?    5.6   0.0     0.032        15       2      32 ..     611     641 ..     610     643 .. 0.92
  16 ?    4.8   0.0     0.057        27       5      31 ..     651     677 ..     648     679 .. 0.83
  17 !   17.2   0.0   7.4e-06    0.0035       1      35 [.     687     721 ..     687     722 .. 0.95
  18 !   22.5   0.2   1.5e-07   7.2e-05       1      30 [.     727     756 ..     727     761 .. 0.94
  19 !   19.7   0.0   1.2e-06   0.00057       3      31 ..     769     797 ..     768     801 .. 0.94
  20 !   17.4   0.3   6.4e-06     0.003       2      31 ..     808     837 ..     807     841 .. 0.92
  21 !   14.4   0.1   5.6e-05     0.027       8      34 ..     894     920 ..     894     923 .. 0.94
  22 !    9.0   0.0    0.0028       1.3       4      29 ..     930     955 ..     928     961 .. 0.85
  23 ?   -0.9   0.0       3.6   1.7e+03      20      34 ..    1063    1077 ..    1061    1078 .. 0.83
  24 !   14.4   0.1   5.6e-05     0.026       4      31 ..    1087    1114 ..    1086    1118 .. 0.91
  25 ?    3.2   0.4      0.18        85       2      23 ..    1125    1146 ..    1124    1159 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.32
                         TPR_10  8 LanalrqrgrydeAealleealai 31
                                   L+++ +q+g +++A+ +l +al++
  gi|116754673|ref|YP_843791.1| 67 LGMISQQLGSLERAVSHLSRALER 90
                                   9******************99986 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0015
                         TPR_10   5 lnNLanalrqrgrydeAealleealair 32 
                                    l+ L+ ++ ++ ++d+A  l+++al++ 
  gi|116754673|ref|YP_843791.1| 100 LSRLGSIYANVEDLDRAISLYRDALSRL 127
                                    788**********************975 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 0.00021
                         TPR_10   2 AsslnNLanalrqrgrydeAea 23 
                                    A +l NL++a+r+ +r+d+A++
  gi|116754673|ref|YP_843791.1| 135 AGILINLSMAYREARRWDDALQ 156
                                    889*****************98 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.098
                         TPR_10  13 rqrgrydeAealleealairr 33 
                                    r++g++  Ae+l++ +l+  +
  gi|116754673|ref|YP_843791.1| 186 REMGDLSSAEELYRTCLEEFE 206
                                    789**************8655 PP

  == domain 5  score: 4.0 bits;  conditional E-value: 0.11
                         TPR_10   3 sslnNLanalrqrgrydeAealleealairr 33 
                                    +sl  L+++ + rg+  +Ae+l++ a+ +++
  gi|116754673|ref|YP_843791.1| 216 RSLEMLGRISQLRGESRRAEDLFDMAMHRYE 246
                                    68899********************999997 PP

  == domain 6  score: 2.7 bits;  conditional E-value: 0.26
                         TPR_10   8 LanalrqrgrydeAealleealairrrl 35 
                                    L+ ++   gr+  Ae+ + +al+  r++
  gi|116754673|ref|YP_843791.1| 261 LGDLHAIEGRFSSAEECYLKALEGFREV 288
                                    666677779*************998887 PP

  == domain 7  score: 18.6 bits;  conditional E-value: 2.6e-06
                         TPR_10   1 tAsslnNLanalrqrgrydeAealleealairr 33 
                                    +A++l  La+++ ++g++ +A++ ++eal+i +
  gi|116754673|ref|YP_843791.1| 294 VANTLLSLARLYGSMGEWRGAVERYREALDILQ 326
                                    699**************************9965 PP

  == domain 8  score: 8.9 bits;  conditional E-value: 0.0029
                         TPR_10   1 tAsslnNLanalrqrgrydeAealleealairrrllG 37 
                                    +A++l  ++ a +++++y+ A +++ ++l++ ++l +
  gi|116754673|ref|YP_843791.1| 333 LARALREMGTACYRLRDYEMAQNYFMKSLELSEALGE 369
                                    599****************************998755 PP

  == domain 9  score: 10.8 bits;  conditional E-value: 0.00072
                         TPR_10   8 LanalrqrgrydeAealleealairrr 34 
                                    ++++l+++g++d+A++++e+  ++ r+
  gi|116754673|ref|YP_843791.1| 380 MGHMLSDLGDWDGAVEHYERGAELLRE 406
                                    799****************98887665 PP

  == domain 10  score: 23.8 bits;  conditional E-value: 6e-08
                         TPR_10   2 AsslnNLanalrqrgrydeAealleealairrrl 35 
                                    A++ +N+a +++ +g++++A++++++al+i++rl
  gi|116754673|ref|YP_843791.1| 414 AACTSNIASVYQMMGDLEKALDIYHDALQIQERL 447
                                    8999**************************9997 PP

  == domain 11  score: 19.8 bits;  conditional E-value: 1.1e-06
                         TPR_10   4 slnNLanalrqrgrydeAealleealairrrl 35 
                                    +lnN++ +++++g+ ++Ae+ + ++l++ ++l
  gi|116754673|ref|YP_843791.1| 456 TLNNMGLVYQHMGEIEAAERNYMRCLELKEQL 487
                                    89**************************9987 PP

  == domain 12  score: 12.8 bits;  conditional E-value: 0.00017
                         TPR_10   7 NLanalrqrgrydeAealleealairr 33 
                                    NLa ++  ++r+d+A  ++++al++ +
  gi|116754673|ref|YP_843791.1| 499 NLATLYEIQRRWDDAITHYQDALETFE 525
                                    9**********************9865 PP

  == domain 13  score: 7.8 bits;  conditional E-value: 0.0063
                         TPR_10   2 AsslnNLanalrqrgrydeAeal 24 
                                    A+ +nNL+n++ + g+  +A + 
  gi|116754673|ref|YP_843791.1| 534 AAVMNNLGNVYEEKGDILQAIKS 556
                                    899********999987666665 PP

  == domain 14  score: 7.1 bits;  conditional E-value: 0.011
                         TPR_10   7 NLanalrqrgrydeAealleealai 31 
                                    NL+ ++++ g+ + Ae+ ++ +l++
  gi|116754673|ref|YP_843791.1| 576 NLGGLYQRIGDAESAEKCYRASLEA 600
                                    9*********************986 PP

  == domain 15  score: 5.6 bits;  conditional E-value: 0.032
                         TPR_10   2 AsslnNLanalrqrgrydeAealleealair 32 
                                    A +l  L+ +  +rg +d+A++ +++++++r
  gi|116754673|ref|YP_843791.1| 611 AYALMGLGSIALERGLWDDALDCFKRCVDLR 641
                                    678889*********************9986 PP

  == domain 16  score: 4.8 bits;  conditional E-value: 0.057
                         TPR_10   5 lnNLanalrqrgrydeAealleealai 31 
                                    l  +a ++ + g ++eA+a ++++l++
  gi|116754673|ref|YP_843791.1| 651 LGSIASVYERKGMWQEALAEYRKVLER 677
                                    6678899999999999***99999986 PP

  == domain 17  score: 17.2 bits;  conditional E-value: 7.4e-06
                         TPR_10   1 tAsslnNLanalrqrgrydeAealleealairrrl 35 
                                    +A+ l+ ++n+l ++g +d+A++++ e+l+i +rl
  gi|116754673|ref|YP_843791.1| 687 VAAVLSTIGNLLAEQGHWDDALEHYSESLEIFERL 721
                                    6999***************************9986 PP

  == domain 18  score: 22.5 bits;  conditional E-value: 1.5e-07
                         TPR_10   1 tAsslnNLanalrqrgrydeAealleeala 30 
                                    tA + nN+an+l++rg++d+A++l+ +a++
  gi|116754673|ref|YP_843791.1| 727 TAVTTNNMANVLYRRGEWDRALNLYSKAME 756
                                    8999*********************99976 PP

  == domain 19  score: 19.7 bits;  conditional E-value: 1.2e-06
                         TPR_10   3 sslnNLanalrqrgrydeAealleealai 31 
                                    ++l+N+a ++++rg++++A +l++++l+i
  gi|116754673|ref|YP_843791.1| 769 ATLSNIASIHYRRGEWERAIELYHKSLEI 797
                                    69*************************98 PP

  == domain 20  score: 17.4 bits;  conditional E-value: 6.4e-06
                         TPR_10   2 AsslnNLanalrqrgrydeAealleealai 31 
                                    A+ lnNL+ ++++rg++  A+++++ a ++
  gi|116754673|ref|YP_843791.1| 808 AMVLNNLGLLYHRRGEWSLAVDHFRLAAEC 837
                                    99**********************999877 PP

  == domain 21  score: 14.4 bits;  conditional E-value: 5.6e-05
                         TPR_10   8 LanalrqrgrydeAealleealairrr 34 
                                    Lana+ + +r++eA+++++++l++ +r
  gi|116754673|ref|YP_843791.1| 894 LANAYADIFRWEEALDHYQKSLELFER 920
                                    9**********************9887 PP

  == domain 22  score: 9.0 bits;  conditional E-value: 0.0028
                         TPR_10   4 slnNLanalrqrgrydeAealleeal 29 
                                    ++ N+a ++r+rg++  Ae+ll +++
  gi|116754673|ref|YP_843791.1| 930 TMFNMALIYRDRGEWSIAEDLLSRSM 955
                                    6669****************987665 PP

  == domain 23  score: -0.9 bits;  conditional E-value: 3.6
                         TPR_10   20 eAealleealairrr 34  
                                     eA+  +++ala+ r+
  gi|116754673|ref|YP_843791.1| 1063 EARSSYQKALALARK 1077
                                     788889999999886 PP

  == domain 24  score: 14.4 bits;  conditional E-value: 5.6e-05
                         TPR_10    4 slnNLanalrqrgrydeAealleealai 31  
                                     +l  L++a  + g+ydeAe++l++al +
  gi|116754673|ref|YP_843791.1| 1087 ALRSLGAASLNAGDYDEAEEHLQKALTL 1114
                                     6789*********************986 PP

  == domain 25  score: 3.2 bits;  conditional E-value: 0.18
                         TPR_10    2 AsslnNLanalrqrgrydeAea 23  
                                     +s++  +a ++++r+++ +Ae+
  gi|116754673|ref|YP_843791.1| 1125 LSTYALMATLYFNRKDHSRAEE 1146
                                     789999**************96 PP

>> SNAP  Soluble NSF attachment protein, SNAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.034        16      96     144 ..      76     126 ..      52     135 .. 0.70
   2 !   10.3   0.0   0.00072      0.34      82     146 ..     142     206 ..     131     211 .. 0.86
   3 !   16.4   0.0   9.7e-06    0.0046      89     155 ..     270     335 ..     226     342 .. 0.63
   4 !   34.2   0.1   3.8e-11   1.8e-08      41     145 ..     341     444 ..     326     462 .. 0.88
   5 !   40.1   0.5   5.9e-13   2.8e-10      40     184 ..     459     607 ..     447     611 .. 0.87
   6 ?    5.2   0.0     0.025        12      85     143 ..     581     639 ..     567     643 .. 0.75
   7 !   21.8   0.0   2.3e-07   0.00011      80     153 ..     734     807 ..     713     814 .. 0.82
   8 !   26.6   0.6   7.8e-09   3.7e-06      44     172 ..     817     945 ..     807     953 .. 0.88
   9 !   14.2   1.0   4.8e-05     0.023      55     175 ..    1025    1145 ..    1004    1154 .. 0.87
  10 ?   -0.8   0.0       1.7     8e+02      57      88 ..    1167    1198 ..    1165    1210 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.034
                                    HHHHHHHHHHH...TT-HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHH CS
                           SNAP  96 alekAieiyte...kgrfrraAklkkeiaelyekelgdlekAieaYekAael 144
                                    +le+A++++ +   + +   a k    ++ +y +  +dl++Ai+ Y++A   
  gi|116754673|ref|YP_843791.1|  76 SLERAVSHLSRaleRASGADAVKVLSRLGSIYANV-EDLDRAISLYRDALSR 126
                                    45555555543000334445667778889999988.9999999999998765 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00072
                                    HHHHHHT.-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHH CS
                           SNAP  82 akcykkv.speeAvealekAieiytekgrfrraAklkkeiaelyekelgdlekAieaYekAaelye 146
                                    + +y++  + ++A ++ + Ai ++ ++g  +  A+  +e ae+  +  gdl++A e Y++  e +e
  gi|116754673|ref|YP_843791.1| 142 SMAYREArRWDDALQCSSDAIYLLRSSGDRSSVARAIMEEAEIRREM-GDLSSAEELYRTCLEEFE 206
                                    556666647789*******************************9966.**********99998887 PP

  == domain 3  score: 16.4 bits;  conditional E-value: 9.7e-06
                                    -HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT-HHHHH CS
                           SNAP  89 speeAvealekAieiytekgrfrraAklkkeiaelyekelgdlekAieaYekAaelyeqeeakalan 155
                                    + ++A e++ kA e + e    +  A+   ++a ly +  g+++ A+e Y++A ++ ++e+++ la 
  gi|116754673|ref|YP_843791.1| 270 RFSSAEECYLKALEGFREVSDRESVANTLLSLARLYGSM-GEWRGAVERYREALDILQSEQSQDLAR 335
                                    456677777777777777777777777777777777766.777777777777777777777766655 PP

  == domain 4  score: 34.2 bits;  conditional E-value: 3.8e-11
                                    HHHHHHHTT-THHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHT.-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHH CS
                           SNAP  41 AAnayklakkweeAgeaflkaAecqeklkekdeaanayveAakcykkv.speeAvealekAieiytekgrfrraAklkke 119
                                       +y+l +++e A + f+k  e+ e l+e+d  a +++  +++++   + + Ave++e+ +e++ e+g +r aA  + +
  gi|116754673|ref|YP_843791.1| 341 GTACYRL-RDYEMAQNYFMKSLELSEALGERDGMAASHTGMGHMLSDLgDWDGAVEHYERGAELLREMGDLRGAAACTSN 419
                                    5567888.5799*********************************998899***************************** PP

                                    HHHHHHHTT--HHHHHHHHHHHHHHH CS
                           SNAP 120 iaelyekelgdlekAieaYekAaely 145
                                    ia +y+   gdlekA++ Y++A ++ 
  gi|116754673|ref|YP_843791.1| 420 IASVYQMM-GDLEKALDIYHDALQIQ 444
                                    ******99.*************8765 PP

  == domain 5  score: 40.1 bits;  conditional E-value: 5.9e-13
                                    HHHHHHHHTT-THHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHT.-HHHHHHHHHHHHHHHHHTT-HHHHHHHHH CS
                           SNAP  40 qAAnayklakkweeAgeaflkaAecqeklkekdeaanayveAakcykkv.speeAvealekAieiytekgrfrraAklkk 118
                                    + +  y+   ++e+A + ++++ e++e+l++ + aan++++ a+ y+ + + ++A+++++ A e++   g  r  A   +
  gi|116754673|ref|YP_843791.1| 459 NMGLVYQHMGEIEAAERNYMRCLELKEQLGDVHGAANTHINLATLYEIQrRWDDAITHYQDALETFEAIGDRRGMAAVMN 538
                                    556667888899999*******************************9886889*************************** PP

                                    HHHHHHHHTT--HHHHHHHHHHHHHHHHHTT-HHHHH....HHHHHHHHHHHHTT-HHHHHHHHHHHHHT CS
                           SNAP 119 eiaelyekelgdlekAieaYekAaelyeqeeakalan....kcllkvAelsaelekyekAieiyekvakk 184
                                    +++++ye++ gd+ +Ai++Y+   el  ++ + a+ +     +++++ + ++ ++ y +++e++++++++
  gi|116754673|ref|YP_843791.1| 539 NLGNVYEEK-GDILQAIKSYRMSMELDGGDASIAKISwnlgGLYQRIGDAESAEKCYRASLEAFQSIGDE 607
                                    *******99.***************999999766654224468899999999999999999999999876 PP

  == domain 6  score: 5.2 bits;  conditional E-value: 0.025
                                    HHHT.-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHH CS
                           SNAP  85 ykkv.speeAvealekAieiytekgrfrraAklkkeiaelyekelgdlekAieaYekAae 143
                                    y++  ++e+A ++++++ e +++ g  r aA   + ++ +  +  g +++A++++++  +
  gi|116754673|ref|YP_843791.1| 581 YQRIgDAESAEKCYRASLEAFQSIGDERGAAYALMGLGSIALER-GLWDDALDCFKRCVD 639
                                    44444778888888888888888888888888888888888877.888888888877665 PP

  == domain 7  score: 21.8 bits;  conditional E-value: 2.3e-07
                                    HHHHHHHHT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT.-HHH CS
                           SNAP  80 eAakcykkvspeeAvealekAieiytekgrfrraAklkkeiaelyekelgdlekAieaYekAaelyeqee.akal 153
                                     A   y++ + ++A + ++kA+e++++ g ++  +    +ia +     g++e+Aie Y+k  e++e+ e + a+
  gi|116754673|ref|YP_843791.1| 734 MANVLYRRGEWDRALNLYSKAMEHFQRVGDMHSYGATLSNIASIHYRR-GEWERAIELYHKSLEIFEGLEdSGAS 807
                                    46667899999**********************9999*******9999.*****************985525444 PP

  == domain 8  score: 26.6 bits;  conditional E-value: 7.8e-09
                                    HHHHTT-THHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHT-HHHHHHH..HHHHHHHHHHTT-HHHHHHHHHHHH CS
                           SNAP  44 ayklakkweeAgeaflkaAecqeklkekdeaanayveAakcykkvspeeAvea..lekAieiytekgrfrraAklkkeia 121
                                    +y  + +w+ A + f  aAec  +++ ++eaa+ +     ++++++ e++v+   + k  e   ++g +++aA+++  +a
  gi|116754673|ref|YP_843791.1| 817 LYHRRGEWSLAVDHFRLAAECAMRAG-DHEAATEFRANIDMVRSCRGEASVDIdgYLKKLEEIERAGDVEMAAEMHGILA 895
                                    5777899****************887.5899**************888887543388899999***************** PP

                                    HHHHHTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HH CS
                           SNAP 122 elyekelgdlekAieaYekAaelyeqeeakalankcllkvAelsaelekye 172
                                    + y +   ++e+A+++Y+k  el+e  +   +a + + ++A ++ + ++++
  gi|116754673|ref|YP_843791.1| 896 NAYADI-FRWEEALDHYQKSLELFERTGDRYSAAETMFNMALIYRDRGEWS 945
                                    ***976.9********************99999999999999887777665 PP

  == domain 9  score: 14.2 bits;  conditional E-value: 4.8e-05
                                     HHHHHHHHHHHH.HTT-HHHHHHHHHHHHHHHHHT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT--H CS
                           SNAP   55 geaflkaAecqe.klkekdeaanayveAakcykkvspeeAvealekAieiytekgrfrraAklkkeiaelyekelgdl 131 
                                     ++ +l  Ae+   k++ ++   + y+e +  y ++ p eA ++++kA ++  ++g  r  +   ++++    ++ gd+
  gi|116754673|ref|YP_843791.1| 1025 ARFYLSEAETLIlKTGYDSMKIRLYIEWGDFYLSQAPFEARSSYQKALALARKMGLTRDEGVALRSLGAASLNA-GDY 1101
                                     566777666554158888888899*************************************************9.*** PP

                                     HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHHH CS
                           SNAP  132 ekAieaYekAaelyeqeeakalankcllkvAelsaelekyekAi 175 
                                     ++A e+ +kA  l+++ ++  +  + +  +A l+ + ++ ++A 
  gi|116754673|ref|YP_843791.1| 1102 DEAEEHLQKALTLFKSINSMYDLLSTYALMATLYFNRKDHSRAE 1145
                                     *********************99999999999999999888885 PP

  == domain 10  score: -0.8 bits;  conditional E-value: 1.7
                                     HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHT CS
                           SNAP   57 aflkaAecqeklkekdeaanayveAakcykkv 88  
                                     a + +A c+  ++ +d a ++y+eA ++ +++
  gi|116754673|ref|YP_843791.1| 1167 ALEVIAGCELATSRTDAAVSTYLEALNIAQSD 1198
                                     56678999999999999999999999987765 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.2   2.6e-10   1.2e-07      10     191 ..      70     245 ..      65     254 .. 0.88
   2 !   18.4   2.5   2.4e-06    0.0011      43     192 ..     258     405 ..     246     406 .. 0.91
   3 !   17.0   1.8   6.5e-06    0.0031     114     185 ..     387     458 ..     332     460 .. 0.61
   4 !   20.8   0.9   4.3e-07    0.0002      44     150 ..     458     562 ..     454     568 .. 0.90
   5 !   10.6   0.0   0.00055      0.26      42     109 ..     573     640 ..     567     652 .. 0.90
   6 !   20.5   0.1   5.6e-07   0.00026      82     187 ..     650     754 ..     643     756 .. 0.84
   7 !   22.0   0.6   1.9e-07   8.8e-05      38     190 ..     726     878 ..     722     888 .. 0.85
   8 !   17.3   1.9     5e-06    0.0024      11     186 ..     778     953 ..     775     964 .. 0.82
   9 !   14.0   0.0   5.2e-05     0.025     161     197 ..    1006    1042 ..     992    1052 .. 0.87
  10 !   23.2   2.7   8.1e-08   3.8e-05      98     228 ..    1063    1192 ..    1053    1216 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 2.6e-10
                       TPR_MalT  10 laiasgdaeralelArqALallpeddllariaatavlGeasllqGdleaAlqalqeaeklarqadslhvallallqqaei 89 
                                    +  + g  era+ +  +AL++ +  d    + +++ lG ++   +dl++A + ++ a + + + d  +  +  l+ +++ 
  gi|116754673|ref|YP_843791.1|  70 ISQQLGSLERAVSHLSRALERASGAD---AVKVLSRLGSIYANVEDLDRAISLYRDALSRLESGDPER--AGILINLSMA 144
                                    555678899999999********999...6788899*************************9999998..7778888*** PP

                       TPR_MalT  90 lvaqGrLheAletyeqalqlateqglqqlplvgfllvlladllyEwndLeeAeqhlqeGielleql.epeaaldayvlla 168
                                    +++  r ++Al+   +a+ l + +g +   ++  +  + a++ +E++dL  Ae+  +  +e  e+l e     +++ +l 
  gi|116754673|ref|YP_843791.1| 145 YREARRWDDALQCSSDAIYLLRSSGDR-SSVARAI-MEEAEIRREMGDLSSAEELYRTCLEEFERLgEIPFVCRSLEMLG 222
                                    *******************99998888.4666666.466**********************9999845577779****** PP

                       TPR_MalT 169 rialaqGdleeAetllekaeela 191
                                    ri++ +G+ + Ae+l++ a   +
  gi|116754673|ref|YP_843791.1| 223 RISQLRGESRRAEDLFDMAMHRY 245
                                    ****************9987666 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 2.4e-06
                       TPR_MalT  43 tavlGeasllqGdleaAlqalqeaeklarqadslhvallallqqaeilvaqGrLheAletyeqalqlateqglqqlplvg 122
                                     ++lG  + ++G++ +A++ + +a +  r+      ++ +ll++a ++   G+ + A+e y++al   + ++ q      
  gi|116754673|ref|YP_843791.1| 258 ALLLGDLHAIEGRFSSAEECYLKALEGFREVSDRESVANTLLSLARLYGSMGEWRGAVERYREALDILQSEQSQD---LA 334
                                    3589**********************9999999999******************************999999997...55 PP

                       TPR_MalT 123 fllvlladllyEwndLeeAeqhlqeGielleql.epeaaldayvllarialaqGdleeAetllekaeelar 192
                                     +l++++   y   d e A+++  +++el+e l e++  +++ + + +     Gd+++A +  e+  el+r
  gi|116754673|ref|YP_843791.1| 335 RALREMGTACYRLRDYEMAQNYFMKSLELSEALgERDGMAASHTGMGHMLSDLGDWDGAVEHYERGAELLR 405
                                    67799***************************96779999999****************999999988876 PP

  == domain 3  score: 17.0 bits;  conditional E-value: 6.5e-06
                       TPR_MalT 114 glqqlplvgfllvlladllyEwndLeeAeqhlqeGielleql.epeaaldayvllarialaqGdleeAetlle 185
                                     +    +v+++ ++ a+ll+E++dL++A+ +  +   + +++ + e ald+y    +i+   Gd+++A ++l+
  gi|116754673|ref|YP_843791.1| 387 LGDWDGAVEHYERG-AELLREMGDLRGAAACTSNIASVYQMMgDLEKALDIYHDALQIQERLGDMQGASKTLN 458
                                    33333456667666.7777777777777777777777777774557777777777777777777777777776 PP

  == domain 4  score: 20.8 bits;  conditional E-value: 4.3e-07
                       TPR_MalT  44 avlGeasllqGdleaAlqalqeaeklarqadslhvallallqqaeilvaqGrLheAletyeqalqlateqglqqlplvgf 123
                                     ++G ++++ G+ eaA++ ++   +l  q + +h a+ + + +a ++  q r ++A+ +y++al+  +  g ++  ++ +
  gi|116754673|ref|YP_843791.1| 458 NNMGLVYQHMGEIEAAERNYMRCLELKEQLGDVHGAANTHINLATLYEIQRRWDDAITHYQDALETFEAIGDRR-GMAAV 536
                                    589**************************************************************999999986.66666 PP

                       TPR_MalT 124 llvlladllyEwndLeeAeqhlqeGie 150
                                    +   l++++ E++d  +A +  + ++e
  gi|116754673|ref|YP_843791.1| 537 M-NNLGNVYEEKGDILQAIKSYRMSME 562
                                    6.778*********9999766666555 PP

  == domain 5  score: 10.6 bits;  conditional E-value: 0.00055
                       TPR_MalT  42 atavlGeasllqGdleaAlqalqeaeklarqadslhvallallqqaeilvaqGrLheAletyeqalql 109
                                    ++++lG+ ++  Gd e+A++ +++  ++ ++++  + a++al++++ i+ ++G  ++Al+ +++   l
  gi|116754673|ref|YP_843791.1| 573 ISWNLGGLYQRIGDAESAEKCYRASLEAFQSIGDERGAAYALMGLGSIALERGLWDDALDCFKRCVDL 640
                                    68999******************************************************999987766 PP

  == domain 6  score: 20.5 bits;  conditional E-value: 5.6e-07
                       TPR_MalT  82 allqqaeilvaqGrLheAletyeqalqlateqglqqlplvgfllvlladllyEwndLeeAeqhlqeGielleqlep.eaa 160
                                     l ++a ++  +G  +eAl  y++ l+  +  g + l ++ +l ++ ++ll E+++ + A +h  e++e+ e+l+    +
  gi|116754673|ref|YP_843791.1| 650 VLGSIASVYERKGMWQEALAEYRKVLERFRGMGDS-LGVAAVLSTI-GNLLAEQGHWDDALEHYSESLEIFERLGDgYST 727
                                    566788999******************76655555.7888888666.**************************9772555 PP

                       TPR_MalT 161 ldayvllarialaqGdleeAetlleka 187
                                    +  +  +a + + +G+++ A++l  ka
  gi|116754673|ref|YP_843791.1| 728 AVTTNNMANVLYRRGEWDRALNLYSKA 754
                                    558889****************99988 PP

  == domain 7  score: 22.0 bits;  conditional E-value: 1.9e-07
                       TPR_MalT  38 ariaatavlGeasllqGdleaAlqalqeaeklarqadslhvallallqqaeilvaqGrLheAletyeqalqlateqglqq 117
                                    + +++t +++ +   +G+ ++Al+ +++a ++ ++ + +h    +l  +a i+  +G+ + A+e+y+++l+    +gl+ 
  gi|116754673|ref|YP_843791.1| 726 STAVTTNNMANVLYRRGEWDRALNLYSKAMEHFQRVGDMHSYGATLSNIASIHYRRGEWERAIELYHKSLEIF--EGLED 803
                                    5567788899999999*******************************************************55..67777 PP

                       TPR_MalT 118 lplvgfllvlladllyEwndLeeAeqhlqeGielleql.epeaaldayvllarialaqGdle.eAetllekaeel 190
                                      ++ ++l  l+ l++ +++   A +h + + e++ +  + eaa++ ++ +  ++ ++G+++ + + +l+k+ee 
  gi|116754673|ref|YP_843791.1| 804 SGASAMVLNNLGLLYHRRGEWSLAVDHFRLAAECAMRAgDHEAATEFRANIDMVRSCRGEASvDIDGYLKKLEEI 878
                                    899999999************************999984668888999999999999999863455566666665 PP

  == domain 8  score: 17.3 bits;  conditional E-value: 5e-06
                       TPR_MalT  11 aiasgdaeralelArqALallpe.ddllariaatavlGeasllqGdleaAlqalqeaeklarqadslhvallallqqaei 89 
                                       +g+ era+el  + L++++  +d  a+++++ +lG  ++ +G+   A+++++ a + a +a+   +a      + ++
  gi|116754673|ref|YP_843791.1| 778 HYRRGEWERAIELYHKSLEIFEGlEDSGASAMVLNNLGLLYHRRGEWSLAVDHFRLAAECAMRAGDHEAATEFRANIDMV 857
                                    56789999999999999999986588999999***********************9999997777766554444556668 PP

                       TPR_MalT  90 lvaqGrLheAletyeqalqlateqglqqlplvgfllvlladllyEwndLeeAeqhlqeGielleql.epeaaldayvlla 168
                                    +  +G+    ++ y + l+ ++++g    +++  ++ +la+ + +  + eeA +h q+++el e+  ++  a++    +a
  gi|116754673|ref|YP_843791.1| 858 RSCRGEASVDIDGYLKKLEEIERAGDV--EMAAEMHGILANAYADIFRWEEALDHYQKSLELFERTgDRYSAAETMFNMA 935
                                    888888888888888888877777644..56666666677777777789****************8455677778889** PP

                       TPR_MalT 169 rialaqGdleeAetllek 186
                                     i+  +G+++ Ae+ll +
  gi|116754673|ref|YP_843791.1| 936 LIYRDRGEWSIAEDLLSR 953
                                    ***************987 PP

  == domain 9  score: 14.0 bits;  conditional E-value: 5.2e-05
                       TPR_MalT  161 ldayvllarialaqGdleeAetllekaeelaresnfh 197 
                                      +ay+++ar++l +G+++eA  +l +ae l  ++ ++
  gi|116754673|ref|YP_843791.1| 1006 CEAYLAMARVKLNRGEMSEARFYLSEAETLILKTGYD 1042
                                     589**************************98888775 PP

  == domain 10  score: 23.2 bits;  conditional E-value: 8.1e-08
                       TPR_MalT   98 eAletyeqalqlateqglqqlplvgfllvlladllyEwndLeeAeqhlqeGielleql.epeaaldayvllarialaq 174 
                                     eA   y++al+la++ gl++ +  g++l++l+   +  +d +eAe+hlq++++l ++  +    l  y+l+a +++ +
  gi|116754673|ref|YP_843791.1| 1063 EARSSYQKALALARKMGLTRDE--GVALRSLGAASLNAGDYDEAEEHLQKALTLFKSInSMYDLLSTYALMATLYFNR 1138
                                     5778899999999999999755..677889999999999999999999999999999945588889999999999999 PP

                       TPR_MalT  175 GdleeAetllekaeelaresnfhvdwlanaeevrvrlwlaqgdlaaaer.wleaa 228 
                                      d++ Ae++   +e++ar+  + +d + +a ev     la+ +++aa+   lea 
  gi|116754673|ref|YP_843791.1| 1139 KDHSRAEETALLLERQARRLGY-RDLQVKALEVIAGCELATSRTDAAVStYLEAL 1192
                                     9999999999999999999999.57777788888788888888888876345544 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   0.00016     0.075       2      31 ..      62      91 ..      61      93 .. 0.93
   2 !   12.6   0.0   0.00025      0.12       2      29 ..      98     125 ..      97     126 .. 0.92
   3 ?    6.7   0.1      0.02       9.7       2      29 ..     176     203 ..     175     205 .. 0.86
   4 !   12.5   0.1   0.00028      0.13       5      29 ..     259     283 ..     255     283 .. 0.92
   5 ?    1.9   0.0      0.69   3.2e+02       3      30 ..     297     324 ..     295     324 .. 0.88
   6 !   14.0   0.2   9.5e-05     0.045       7      32 ..     340     365 ..     334     367 .. 0.88
   7 ?    3.1   0.0       0.3   1.4e+02       5      29 ..     378     402 ..     374     403 .. 0.85
   8 ?    7.4   0.1     0.012       5.9       6      32 ..     419     445 ..     418     447 .. 0.93
   9 !   19.3   0.1   1.9e-06   0.00088       2      33 ..     455     486 ..     454     487 .. 0.93
  10 ?    2.0   0.0      0.67   3.2e+02       3      29 ..     496     522 ..     494     525 .. 0.91
  11 !   14.8   0.0   5.3e-05     0.025       2      31 ..     535     564 ..     534     567 .. 0.89
  12 !   14.4   0.1   6.8e-05     0.032       2      30 ..     572     600 ..     571     603 .. 0.90
  13 ?    3.2   0.0      0.27   1.3e+02       2      31 ..     612     641 ..     611     644 .. 0.89
  14 ?    7.5   0.0     0.012       5.5       2      29 ..     649     676 ..     648     679 .. 0.92
  15 ?   -0.5   0.0       4.2     2e+03       4      30 ..     691     717 ..     688     720 .. 0.84
  16 ?    3.3   0.0      0.25   1.2e+02       5      30 ..     772     797 ..     769     799 .. 0.92
  17 ?    0.7   0.0       1.7   7.9e+02       4      27 ..     811     834 ..     810     838 .. 0.80
  18 ?    3.8   0.1      0.18        83       1      30 [.     888     917 ..     888     920 .. 0.91
  19 ?   -0.3   0.0       3.7   1.7e+03       1      15 [.     928     942 ..     928     943 .. 0.87
  20 ?    3.9   0.2      0.16        74       2      29 ..    1007    1034 ..    1007    1038 .. 0.91
  21 ?    1.6   0.2       0.9   4.2e+02      19      33 ..    1063    1077 ..    1063    1078 .. 0.90
  22 !   11.5   0.1   0.00057      0.27       7      30 ..    1091    1114 ..    1090    1117 .. 0.86
  23 ?    3.4   0.0      0.23   1.1e+02       3      23 ..    1127    1147 ..    1125    1150 .. 0.90
  24 ?    3.0   0.0      0.31   1.5e+02      16      33 ..    1180    1197 ..    1166    1198 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00016
                                   CHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                          TPR_8  2 eayynlgsiylklgdyeeAkeyyekaleld 31
                                   ++++ lg+i ++lg +e A++ + +ale +
  gi|116754673|ref|YP_843791.1| 62 SLWFSLGMISQQLGSLERAVSHLSRALERA 91
                                   58*************************975 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00025
                                    CHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                          TPR_8   2 eayynlgsiylklgdyeeAkeyyekale 29 
                                    +++ +lgsiy + +d++ A++ y+ al+
  gi|116754673|ref|YP_843791.1|  98 KVLSRLGSIYANVEDLDRAISLYRDALS 125
                                    57789*********************97 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.02
                                    CHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                          TPR_8   2 eayynlgsiylklgdyeeAkeyyekale 29 
                                    +a +  + i +++gd+ +A+e y+ +le
  gi|116754673|ref|YP_843791.1| 176 RAIMEEAEIRREMGDLSSAEELYRTCLE 203
                                    55666688999***************98 PP

  == domain 4  score: 12.5 bits;  conditional E-value: 0.00028
                                    HHHHHHHHHTT-HHHHHHHHHHHHH CS
                          TPR_8   5 ynlgsiylklgdyeeAkeyyekale 29 
                                    ++lg+++   g++ +A+e+y kale
  gi|116754673|ref|YP_843791.1| 259 LLLGDLHAIEGRFSSAEECYLKALE 283
                                    78*********************97 PP

  == domain 5  score: 1.9 bits;  conditional E-value: 0.69
                                    HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                          TPR_8   3 ayynlgsiylklgdyeeAkeyyekalel 30 
                                     ++ l+++y ++g+   A+e y++al++
  gi|116754673|ref|YP_843791.1| 297 TLLSLARLYGSMGEWRGAVERYREALDI 324
                                    6789**********99999999999976 PP

  == domain 6  score: 14.0 bits;  conditional E-value: 9.5e-05
                                    HHHHHHHTT-HHHHHHHHHHHHHHHH CS
                          TPR_8   7 lgsiylklgdyeeAkeyyekaleldp 32 
                                    +g ++  l dye+A+ y++k lel++
  gi|116754673|ref|YP_843791.1| 340 MGTACYRLRDYEMAQNYFMKSLELSE 365
                                    6889999*****************97 PP

  == domain 7  score: 3.1 bits;  conditional E-value: 0.3
                                    HHHHHHHHHTT-HHHHHHHHHHHHH CS
                          TPR_8   5 ynlgsiylklgdyeeAkeyyekale 29 
                                      +g+ +++lgd + A+e ye+  e
  gi|116754673|ref|YP_843791.1| 378 TGMGHMLSDLGDWDGAVEHYERGAE 402
                                    5689*****************9766 PP

  == domain 8  score: 7.4 bits;  conditional E-value: 0.012
                                    HHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                          TPR_8   6 nlgsiylklgdyeeAkeyyekaleldp 32 
                                    n++s+y+ +gd+e+A   y  al++++
  gi|116754673|ref|YP_843791.1| 419 NIASVYQMMGDLEKALDIYHDALQIQE 445
                                    89*****************99999975 PP

  == domain 9  score: 19.3 bits;  conditional E-value: 1.9e-06
                                    CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                          TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                    + ++n+g++y+ +g++e+A+  y+++lel+++
  gi|116754673|ref|YP_843791.1| 455 KTLNNMGLVYQHMGEIEAAERNYMRCLELKEQ 486
                                    6799*************************975 PP

  == domain 10  score: 2.0 bits;  conditional E-value: 0.67
                                    HHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                          TPR_8   3 ayynlgsiylklgdyeeAkeyyekale 29 
                                     + nl+ +y+ + + + A+  y+ ale
  gi|116754673|ref|YP_843791.1| 496 THINLATLYEIQRRWDDAITHYQDALE 522
                                    6789*********************97 PP

  == domain 11  score: 14.8 bits;  conditional E-value: 5.3e-05
                                    CHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                          TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleld 31 
                                     +++nlg++y+++gd+ +A+++y+   eld
  gi|116754673|ref|YP_843791.1| 535 AVMNNLGNVYEEKGDILQAIKSYRMSMELD 564
                                    5789*******************9877776 PP

  == domain 12  score: 14.4 bits;  conditional E-value: 6.8e-05
                                    CHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                          TPR_8   2 eayynlgsiylklgdyeeAkeyyekalel 30 
                                    ++ +nlg +y+  gd e+A+++y+  le+
  gi|116754673|ref|YP_843791.1| 572 KISWNLGGLYQRIGDAESAEKCYRASLEA 600
                                    56689********************9985 PP

  == domain 13  score: 3.2 bits;  conditional E-value: 0.27
                                    CHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                          TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleld 31 
                                     a++ lgsi l+ g  + A  +++++++l+
  gi|116754673|ref|YP_843791.1| 612 YALMGLGSIALERGLWDDALDCFKRCVDLR 641
                                    578899*********************997 PP

  == domain 14  score: 7.5 bits;  conditional E-value: 0.012
                                    CHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                          TPR_8   2 eayynlgsiylklgdyeeAkeyyekale 29 
                                    +++  ++s+y+ +g  +eA + y+k+le
  gi|116754673|ref|YP_843791.1| 649 RVLGSIASVYERKGMWQEALAEYRKVLE 676
                                    78889*********************98 PP

  == domain 15  score: -0.5 bits;  conditional E-value: 4.2
                                    HHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                          TPR_8   4 yynlgsiylklgdyeeAkeyyekalel 30 
                                    +  +g+++ ++g  + A e y + le+
  gi|116754673|ref|YP_843791.1| 691 LSTIGNLLAEQGHWDDALEHYSESLEI 717
                                    557999999999999999999999997 PP

  == domain 16  score: 3.3 bits;  conditional E-value: 0.25
                                    HHHHHHHHHTT-HHHHHHHHHHHHHH CS
                          TPR_8   5 ynlgsiylklgdyeeAkeyyekalel 30 
                                     n++si+   g+ e A+e y k le+
  gi|116754673|ref|YP_843791.1| 772 SNIASIHYRRGEWERAIELYHKSLEI 797
                                    599********************998 PP

  == domain 17  score: 0.7 bits;  conditional E-value: 1.7
                                    HHHHHHHHHHTT-HHHHHHHHHHH CS
                          TPR_8   4 yynlgsiylklgdyeeAkeyyeka 27 
                                    ++nlg++y+  g+   A+  ++ a
  gi|116754673|ref|YP_843791.1| 811 LNNLGLLYHRRGEWSLAVDHFRLA 834
                                    79*******999877777777766 PP

  == domain 18  score: 3.8 bits;  conditional E-value: 0.18
                                    CCHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                          TPR_8   1 aeayynlgsiylklgdyeeAkeyyekalel 30 
                                    ae++  l+++y +  + eeA   y+k lel
  gi|116754673|ref|YP_843791.1| 888 AEMHGILANAYADIFRWEEALDHYQKSLEL 917
                                    5778889*********************98 PP

  == domain 19  score: -0.3 bits;  conditional E-value: 3.7
                                    CCHHHHHHHHHHHTT CS
                          TPR_8   1 aeayynlgsiylklg 15 
                                    ae ++n+++iy++ g
  gi|116754673|ref|YP_843791.1| 928 AETMFNMALIYRDRG 942
                                    6899*******9977 PP

  == domain 20  score: 3.9 bits;  conditional E-value: 0.16
                                     CHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                          TPR_8    2 eayynlgsiylklgdyeeAkeyyekale 29  
                                     eay+ ++++ l+ g++ eA  y+ +a +
  gi|116754673|ref|YP_843791.1| 1007 EAYLAMARVKLNRGEMSEARFYLSEAET 1034
                                     69*********************99865 PP

  == domain 21  score: 1.6 bits;  conditional E-value: 0.9
                                     HHHHHHHHHHHHHHH CS
                          TPR_8   19 eAkeyyekaleldpd 33  
                                     eA ++y+kal l+++
  gi|116754673|ref|YP_843791.1| 1063 EARSSYQKALALARK 1077
                                     799*******99986 PP

  == domain 22  score: 11.5 bits;  conditional E-value: 0.00057
                                     HHHHHHHTT-HHHHHHHHHHHHHH CS
                          TPR_8    7 lgsiylklgdyeeAkeyyekalel 30  
                                     lg + l+ gdy+eA+e ++kal+l
  gi|116754673|ref|YP_843791.1| 1091 LGAASLNAGDYDEAEEHLQKALTL 1114
                                     56677899**************98 PP

  == domain 23  score: 3.4 bits;  conditional E-value: 0.23
                                     HHHHHHHHHHHTT-HHHHHHH CS
                          TPR_8    3 ayynlgsiylklgdyeeAkey 23  
                                      y +++ +y++ +d+  A+e+
  gi|116754673|ref|YP_843791.1| 1127 TYALMATLYFNRKDHSRAEET 1147
                                     799***************986 PP

  == domain 24  score: 3.0 bits;  conditional E-value: 0.31
                                     -HHHHHHHHHHHHHHHHH CS
                          TPR_8   16 dyeeAkeyyekaleldpd 33  
                                     + ++A+++y +al ++++
  gi|116754673|ref|YP_843791.1| 1180 RTDAAVSTYLEALNIAQS 1197
                                     789***********9876 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1      0.12        56       4      35 ..      64      95 ..      61     100 .. 0.80
   2 !   12.8   0.0   0.00035      0.16       3      31 ..      99     127 ..      97     142 .. 0.79
   3 ?   -0.5   0.0       6.6   3.1e+03       9      24 ..     143     158 ..     135     162 .. 0.81
   4 ?    4.8   0.1      0.13        62       5      31 ..     179     205 ..     175     211 .. 0.83
   5 ?    5.1   0.1      0.11        51       4      29 ..     258     283 ..     255     292 .. 0.89
   6 ?    7.8   0.4     0.014       6.6       2      38 ..     296     337 ..     295     342 .. 0.73
   7 ?    2.6   0.1      0.67   3.2e+02       2      30 ..     335     363 ..     334     369 .. 0.88
   8 ?    7.4   0.0     0.019       9.1       7      30 ..     380     403 ..     374     415 .. 0.83
   9 ?    6.8   0.0     0.031        14       7      31 ..     420     444 ..     414     452 .. 0.89
  10 ?   -1.0   0.0       9.3   4.4e+03       8      30 ..     461     483 ..     459     493 .. 0.82
  11 !   12.3   0.1    0.0005      0.24       7      32 ..     500     525 ..     494     537 .. 0.87
  12 ?    2.2   0.0      0.93   4.4e+02       7      35 ..     540     568 ..     534     572 .. 0.88
  13 ?    5.7   0.1     0.068        32       7      31 ..     577     601 ..     575     616 .. 0.80
  14 !   14.0   0.0   0.00015     0.071       3      42 ..     613     652 ..     610     654 .. 0.93
  15 !    9.0   0.0    0.0059       2.8       8      31 ..     655     678 ..     653     693 .. 0.87
  16 ?    7.8   0.0     0.015         7       4      31 ..     691     718 ..     687     723 .. 0.86
  17 !    8.5   0.0    0.0085         4       7      29 ..     734     756 ..     732     762 .. 0.89
  18 !   10.0   0.0    0.0028       1.3       7      32 ..     774     799 ..     769     806 .. 0.88
  19 ?    2.9   0.3      0.55   2.6e+02       7      39 ..     814     849 ..     808     854 .. 0.77
  20 ?    3.3   0.1      0.39   1.8e+02       7      32 ..     894     919 ..     888     925 .. 0.81
  21 ?    0.5   0.0       3.1   1.5e+03       7      27 ..     934     954 ..     928     969 .. 0.87
  22 ?    7.3   0.1     0.021       9.8       2      27 ..    1007    1032 ..    1007    1041 .. 0.93
  23 !   12.8   0.1   0.00035      0.17       3      31 ..    1087    1115 ..    1086    1123 .. 0.90
  24 ?    0.5   0.2       3.3   1.6e+03       4      23 ..    1128    1147 ..    1125    1156 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.12
                         TPR_14  4 llalaeallalGdpdeAiallrralalaPdda 35
                                   +  l+ +  +lG +++A+ +l ral++a + +
  gi|116754673|ref|YP_843791.1| 64 WFSLGMISQQLGSLERAVSHLSRALERASGAD 95
                                   66677777899***************976544 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00035
                         TPR_14   3 allalaeallalGdpdeAiallrralala 31 
                                    +l +l++++++ +d+d+Ai l+r+al++ 
  gi|116754673|ref|YP_843791.1|  99 VLSRLGSIYANVEDLDRAISLYRDALSRL 127
                                    5779**********************973 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 6.6
                         TPR_14   9 eallalGdpdeAiall 24 
                                     a+++++++d+A+++ 
  gi|116754673|ref|YP_843791.1| 143 MAYREARRWDDALQCS 158
                                    6899********9875 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.13
                         TPR_14   5 lalaeallalGdpdeAiallrralala 31 
                                    ++ ae+ ++ Gd+  A++l+r +l+ +
  gi|116754673|ref|YP_843791.1| 179 MEEAEIRREMGDLSSAEELYRTCLEEF 205
                                    5568888999*************9987 PP

  == domain 5  score: 5.1 bits;  conditional E-value: 0.11
                         TPR_14   4 llalaeallalGdpdeAiallrrala 29 
                                     l+l+++++  G++  A++++ +al+
  gi|116754673|ref|YP_843791.1| 258 ALLLGDLHAIEGRFSSAEECYLKALE 283
                                    6899*******************998 PP

  == domain 6  score: 7.8 bits;  conditional E-value: 0.014
                         TPR_14   2 eallalaeallalGdpdeAiallrrala.....laPddaeaw 38 
                                    + ll la+++   G++++A++ +r+al+     +  d a+a+
  gi|116754673|ref|YP_843791.1| 296 NTLLSLARLYGSMGEWRGAVERYREALDilqseQSQDLARAL 337
                                    57899**********************965332223334444 PP

  == domain 7  score: 2.6 bits;  conditional E-value: 0.67
                         TPR_14   2 eallalaeallalGdpdeAiallrralal 30 
                                    +al++++ a+++l+d++ A +++ + l+l
  gi|116754673|ref|YP_843791.1| 335 RALREMGTACYRLRDYEMAQNYFMKSLEL 363
                                    7999****************999888876 PP

  == domain 8  score: 7.4 bits;  conditional E-value: 0.019
                         TPR_14   7 laeallalGdpdeAiallrralal 30 
                                    +++ l  lGd+d+A+++++r  +l
  gi|116754673|ref|YP_843791.1| 380 MGHMLSDLGDWDGAVEHYERGAEL 403
                                    6788999*************9775 PP

  == domain 9  score: 6.8 bits;  conditional E-value: 0.031
                         TPR_14   7 laeallalGdpdeAiallrralala 31 
                                    +a+++   Gd+++A++++++al+ +
  gi|116754673|ref|YP_843791.1| 420 IASVYQMMGDLEKALDIYHDALQIQ 444
                                    5899999***************975 PP

  == domain 10  score: -1.0 bits;  conditional E-value: 9.3
                         TPR_14   8 aeallalGdpdeAiallrralal 30 
                                    + ++ + G+ ++A++ + r+l+l
  gi|116754673|ref|YP_843791.1| 461 GLVYQHMGEIEAAERNYMRCLEL 483
                                    67899999999999988888875 PP

  == domain 11  score: 12.3 bits;  conditional E-value: 0.0005
                         TPR_14   7 laeallalGdpdeAiallrralalaP 32 
                                    la +++ ++++d+Ai+++++al+++ 
  gi|116754673|ref|YP_843791.1| 500 LATLYEIQRRWDDAITHYQDALETFE 525
                                    899********************986 PP

  == domain 12  score: 2.2 bits;  conditional E-value: 0.93
                         TPR_14   7 laeallalGdpdeAiallrralalaPdda 35 
                                    l+ ++++ Gd  +Ai+ +r   +l+ +da
  gi|116754673|ref|YP_843791.1| 540 LGNVYEEKGDILQAIKSYRMSMELDGGDA 568
                                    799****************9988888776 PP

  == domain 13  score: 5.7 bits;  conditional E-value: 0.068
                         TPR_14   7 laeallalGdpdeAiallrralala 31 
                                    l+ ++ + Gd + A++++r+ l+++
  gi|116754673|ref|YP_843791.1| 577 LGGLYQRIGDAESAEKCYRASLEAF 601
                                    67789999**************987 PP

  == domain 14  score: 14.0 bits;  conditional E-value: 0.00015
                         TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                    al+ l+++ l++G +d+A+++++r+++l  d +ea++ l+
  gi|116754673|ref|YP_843791.1| 613 ALMGLGSIALERGLWDDALDCFKRCVDLRLDTPEALRVLG 652
                                    677899*******************************998 PP

  == domain 15  score: 9.0 bits;  conditional E-value: 0.0059
                         TPR_14   8 aeallalGdpdeAiallrralala 31 
                                    a+++++ G ++eA+a +r++l+++
  gi|116754673|ref|YP_843791.1| 655 ASVYERKGMWQEALAEYRKVLERF 678
                                    89*******************987 PP

  == domain 16  score: 7.8 bits;  conditional E-value: 0.015
                         TPR_14   4 llalaeallalGdpdeAiallrralala 31 
                                    l  ++ +l+++G +d+A++++ + l+ +
  gi|116754673|ref|YP_843791.1| 691 LSTIGNLLAEQGHWDDALEHYSESLEIF 718
                                    5567899*****************9976 PP

  == domain 17  score: 8.5 bits;  conditional E-value: 0.0085
                         TPR_14   7 laeallalGdpdeAiallrrala 29 
                                    +a +l+++G++d+A++l+ +a +
  gi|116754673|ref|YP_843791.1| 734 MANVLYRRGEWDRALNLYSKAME 756
                                    699***************99866 PP

  == domain 18  score: 10.0 bits;  conditional E-value: 0.0028
                         TPR_14   7 laeallalGdpdeAiallrralalaP 32 
                                    +a++++++G++++Ai+l+++ l+ + 
  gi|116754673|ref|YP_843791.1| 774 IASIHYRRGEWERAIELYHKSLEIFE 799
                                    6899******************9875 PP

  == domain 19  score: 2.9 bits;  conditional E-value: 0.55
                         TPR_14   7 laeallalGdpdeAiallrrala...laPddaeawl 39 
                                    l+ ++ ++G++  A++++r a +   +a d+++a  
  gi|116754673|ref|YP_843791.1| 814 LGLLYHRRGEWSLAVDHFRLAAEcamRAGDHEAATE 849
                                    678899999999999999999776666667666665 PP

  == domain 20  score: 3.3 bits;  conditional E-value: 0.39
                         TPR_14   7 laeallalGdpdeAiallrralalaP 32 
                                    la a++   +++eA++++++ l+l+ 
  gi|116754673|ref|YP_843791.1| 894 LANAYADIFRWEEALDHYQKSLELFE 919
                                    78888888899999999999998875 PP

  == domain 21  score: 0.5 bits;  conditional E-value: 3.1
                         TPR_14   7 laeallalGdpdeAiallrra 27 
                                    +a +++ +G++  A++ll r 
  gi|116754673|ref|YP_843791.1| 934 MALIYRDRGEWSIAEDLLSRS 954
                                    6889**************986 PP

  == domain 22  score: 7.3 bits;  conditional E-value: 0.021
                         TPR_14    2 eallalaeallalGdpdeAiallrra 27  
                                     ea+la+a++ l++G+  eA+ +l +a
  gi|116754673|ref|YP_843791.1| 1007 EAYLAMARVKLNRGEMSEARFYLSEA 1032
                                     79*********************998 PP

  == domain 23  score: 12.8 bits;  conditional E-value: 0.00035
                         TPR_14    3 allalaeallalGdpdeAiallrralala 31  
                                     al+ l++a l++Gd+deA+++l++al l+
  gi|116754673|ref|YP_843791.1| 1087 ALRSLGAASLNAGDYDEAEEHLQKALTLF 1115
                                     6788999******************9877 PP

  == domain 24  score: 0.5 bits;  conditional E-value: 3.3
                         TPR_14    4 llalaeallalGdpdeAial 23  
                                     ++++a +++++ d+ +A++ 
  gi|116754673|ref|YP_843791.1| 1128 YALMATLYFNRKDHSRAEET 1147
                                     67889************986 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.2     0.005       2.3      12      67 ..      40      94 ..      34      95 .. 0.88
   2 !   20.5   0.3   1.2e-06   0.00055       3      62 ..      67     126 ..      65     132 .. 0.89
   3 !   15.2   0.7   5.2e-05     0.025       3      54 ..     103     155 ..     101     157 .. 0.94
   4 ?    5.5   0.2     0.057        27       3      59 ..     141     200 ..     139     206 .. 0.77
   5 ?    3.2   0.1      0.29   1.4e+02      38      62 ..     259     283 ..     252     289 .. 0.86
   6 !    9.0   1.5    0.0045       2.1       1      51 [.     299     351 ..     299     354 .. 0.86
   7 ?    1.7   0.0      0.92   4.3e+02      34      59 ..     374     399 ..     362     407 .. 0.69
   8 ?    1.0   0.0       1.5     7e+02       9      23 ..     386     400 ..     378     444 .. 0.71
   9 !   15.6   0.0   4.1e-05     0.019       2      59 ..     499     559 ..     498     568 .. 0.89
  10 !   23.9   0.5     1e-07   4.7e-05       3      55 ..     577     632 ..     576     636 .. 0.91
  11 !   20.7   0.1     1e-06   0.00049       3      63 ..     617     677 ..     617     682 .. 0.94
  12 ?    7.1   0.0     0.018       8.5       4      25 ..     695     716 ..     692     724 .. 0.85
  13 ?    7.8   0.0     0.011       5.4       2      25 ..     733     756 ..     732     766 .. 0.85
  14 !   23.3   0.1   1.6e-07   7.6e-05       3      65 ..     774     839 ..     772     844 .. 0.93
  15 ?    3.0   0.1      0.34   1.6e+02      32      62 ..     886     916 ..     872     922 .. 0.79
  16 ?    5.1   0.5     0.079        37       3      57 ..     894     951 ..     893     958 .. 0.83
  17 !    8.1   2.3    0.0092       4.3      35      62 ..    1086    1113 ..    1059    1117 .. 0.64
  18 ?    5.3   1.7     0.068        32       4      61 ..    1132    1192 ..    1129    1199 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.005
                         TPR_16 12 dyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67
                                   + + A+  l++  +++ s ++++  ++ lg +  ++g l++A+  + +al+ a++a
  gi|116754673|ref|YP_843791.1| 40 NRAGALSHLDEIAEQN-SASRDHSLWFSLGMISQQLGSLERAVSHLSRALERASGA 94
                                   6677899999999999.66679****************************999876 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 1.2e-06
                         TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraal.r 62 
                                    l+++  ++g  ++A+  l +al+r+ s  da+  l  lg +++   +l++A+ lyr al r
  gi|116754673|ref|YP_843791.1|  67 LGMISQQLGSLERAVSHLSRALERA-SGADAVKVLSRLGSIYANVEDLDRAISLYRDALsR 126
                                    66677899*****************.8889***************************9944 PP

  == domain 3  score: 15.2 bits;  conditional E-value: 5.2e-05
                         TPR_16   3 laraalragdyddAaaal.eaalkrdpssPdaaeAllllgdaalrqgrlaeAa 54 
                                    l+ ++++  d d+A+ ++ +a+ ++ +++P++a  l +l  a+ ++ r+++A+
  gi|116754673|ref|YP_843791.1| 103 LGSIYANVEDLDRAISLYrDALSRLESGDPERAGILINLSMAYREARRWDDAL 155
                                    7899**************9999999***************************7 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.057
                         TPR_16   3 laraalragdyddAaaa...leaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyra 59 
                                    l +a+++a+++ddA+     +  +l++ ++ +  a+A ++ ++++ + g+l  A++lyr 
  gi|116754673|ref|YP_843791.1| 141 LSMAYREARRWDDALQCssdAIYLLRSSGDRSSVARAIMEEAEIRREMGDLSSAEELYRT 200
                                    668999999999999862224455666666666999999999999999999999999986 PP

  == domain 5  score: 3.2 bits;  conditional E-value: 0.29
                         TPR_16  38 lllgdaalrqgrlaeAaalyraalr 62 
                                    lllgd+++  gr+  A++ y++al+
  gi|116754673|ref|YP_843791.1| 259 LLLGDLHAIEGRFSSAEECYLKALE 283
                                    899***********99999998885 PP

  == domain 6  score: 9.0 bits;  conditional E-value: 0.0045
                         TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPd..aaeAllllgdaalrqgrla 51 
                                    l lar++   g+++ A++++++al+   s+     a+Al + g a++r+ +++
  gi|116754673|ref|YP_843791.1| 299 LSLARLYGSMGEWRGAVERYREALDILQSEQSqdLARALREMGTACYRLRDYE 351
                                    679*********************96654444569************999997 PP

  == domain 7  score: 1.7 bits;  conditional E-value: 0.92
                         TPR_16  34 aeAllllgdaalrqgrlaeAaalyra 59 
                                    a+++ + g ++  +g++++A++ y++
  gi|116754673|ref|YP_843791.1| 374 AASHTGMGHMLSDLGDWDGAVEHYER 399
                                    55666666667777777777777766 PP

  == domain 8  score: 1.0 bits;  conditional E-value: 1.5
                         TPR_16   9 ragdyddAaaaleaa 23 
                                    ++gd+d A++ +e+ 
  gi|116754673|ref|YP_843791.1| 386 DLGDWDGAVEHYERG 400
                                    566666666666653 PP

  == domain 9  score: 15.6 bits;  conditional E-value: 4.1e-05
                         TPR_16   2 alaraalragdyddAaaaleaalkrdpssPd......aaeAllllgdaalrqgrlaeAaalyra 59 
                                    +la+++  ++++ddA+  ++ al+ +    +       a+ +++lg+++ ++g+   A+  yr 
  gi|116754673|ref|YP_843791.1| 499 NLATLYEIQRRWDDAITHYQDALETF---EAigdrrgMAAVMNNLGNVYEEKGDILQAIKSYRM 559
                                    688889999*****************...77788999**********************88875 PP

  == domain 10  score: 23.9 bits;  conditional E-value: 1e-07
                         TPR_16   3 laraalragdyddAaaaleaalkrdpssPd......aaeAllllgdaalrqgrlaeAaa 55 
                                    l+ ++ r gd + A++ ++a l+++           aa Al++lg +al++g +++A++
  gi|116754673|ref|YP_843791.1| 577 LGGLYQRIGDAESAEKCYRASLEAF---QSigdergAAYALMGLGSIALERGLWDDALD 632
                                    899**********************...66677999*********************86 PP

  == domain 11  score: 20.7 bits;  conditional E-value: 1e-06
                         TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalra 63 
                                    l+ +al++g +ddA+  +++ ++++ ++P+a + l   + ++ r+g ++eA+a yr+ l+ 
  gi|116754673|ref|YP_843791.1| 617 LGSIALERGLWDDALDCFKRCVDLRLDTPEALRVLGSIASVYERKGMWQEALAEYRKVLER 677
                                    5789****************************************************98865 PP

  == domain 12  score: 7.1 bits;  conditional E-value: 0.018
                         TPR_16   4 araalragdyddAaaaleaalk 25 
                                    +++++++g++ddA++ + + l+
  gi|116754673|ref|YP_843791.1| 695 GNLLAEQGHWDDALEHYSESLE 716
                                    8999***********9988776 PP

  == domain 13  score: 7.8 bits;  conditional E-value: 0.011
                         TPR_16   2 alaraalragdyddAaaaleaalk 25 
                                    ++a+ ++r+g++d+A++++  a +
  gi|116754673|ref|YP_843791.1| 733 NMANVLYRRGEWDRALNLYSKAME 756
                                    5799***************88755 PP

  == domain 14  score: 23.3 bits;  conditional E-value: 1.6e-07
                         TPR_16   3 laraalragdyddAaaaleaalkrdpssPd...aaeAllllgdaalrqgrlaeAaalyraalraap 65 
                                     a +++r+g++++A+++++  l+ + +  d    a  l++lg+++ r+g++ +A++ +r a+++a+
  gi|116754673|ref|YP_843791.1| 774 IASIHYRRGEWERAIELYHKSLEIFEGLEDsgaSAMVLNNLGLLYHRRGEWSLAVDHFRLAAECAM 839
                                    58899********************88888999****************************99876 PP

  == domain 15  score: 3.0 bits;  conditional E-value: 0.34
                         TPR_16  32 daaeAllllgdaalrqgrlaeAaalyraalr 62 
                                     aae++  l++a++   r++eA++ y++ l+
  gi|116754673|ref|YP_843791.1| 886 MAAEMHGILANAYADIFRWEEALDHYQKSLE 916
                                    5899999999999999999999999988765 PP

  == domain 16  score: 5.1 bits;  conditional E-value: 0.079
                         TPR_16   3 laraalragdyddAaaaleaalkrdpssPd...aaeAllllgdaalrqgrlaeAaaly 57 
                                    la+a+++  ++++A+  ++  l+++ ++ d   aae +++ ++++  +g++  A++l+
  gi|116754673|ref|YP_843791.1| 894 LANAYADIFRWEEALDHYQKSLELFERTGDrysAAETMFNMALIYRDRGEWSIAEDLL 951
                                    68888888899**************999998888888888888888888887777665 PP

  == domain 17  score: 8.1 bits;  conditional E-value: 0.0092
                         TPR_16   35 eAllllgdaalrqgrlaeAaalyraalr 62  
                                      Al  lg a l +g+++eA++ +++al+
  gi|116754673|ref|YP_843791.1| 1086 VALRSLGAASLNAGDYDEAEEHLQKALT 1113
                                     4777777777777777777777777664 PP

  == domain 18  score: 5.3 bits;  conditional E-value: 0.068
                         TPR_16    4 araalragdyddAaa...al.eaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraal 61  
                                     a+++++++d  +A++   +l ++a+++++++   + Al   + + l+ +r ++A+  y++al
  gi|116754673|ref|YP_843791.1| 1132 ATLYFNRKDHSRAEEtalLLeRQARRLGYRDL-QVKALEVIAGCELATSRTDAAVSTYLEAL 1192
                                     67777777777777522234456666666665.8*********************8888887 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.59   2.8e+02       6      22 ..      73      89 ..      72      90 .. 0.94
   2 ?   -1.9   0.0       5.9   2.8e+03       2      21 ..     105     124 ..     104     125 .. 0.77
   3 ?    3.0   0.0      0.17        83       1      22 [.     262     283 ..     262     283 .. 0.93
   4 !    9.4   0.0    0.0018      0.85       3      23 ..     304     324 ..     302     347 .. 0.79
   5 !    8.8   0.0    0.0027       1.3       1      22 [.     381     402 ..     381     404 .. 0.88
   6 ?    1.6   0.0      0.49   2.3e+02       7      24 ..     427     444 ..     422     447 .. 0.88
   7 ?   -0.1   0.0       1.6   7.7e+02       1      23 [.     461     483 ..     456     491 .. 0.57
   8 ?    5.0   0.0     0.042        20       9      22 ..     509     522 ..     503     523 .. 0.90
   9 !    9.0   0.0    0.0024       1.1       1      42 []     541     585 ..     541     585 .. 0.80
  10 ?    5.2   0.0     0.036        17       1      35 [.     618     652 ..     618     654 .. 0.89
  11 ?    4.3   0.1     0.069        32       6      22 ..     660     676 ..     655     676 .. 0.85
  12 !   12.0   0.0   0.00027      0.13       1      23 [.     695     717 ..     695     720 .. 0.96
  13 !   11.2   0.0   0.00048      0.23       2      21 ..     736     755 ..     735     756 .. 0.92
  14 !   10.7   0.2    0.0007      0.33       3      40 ..     777     820 ..     775     822 .. 0.73
  15 ?    6.7   0.1     0.012       5.7       2      23 ..     896     917 ..     895     919 .. 0.85
  16 ?    0.2   0.3       1.4   6.4e+02      12      23 ..    1063    1074 ..    1063    1077 .. 0.87
  17 ?    4.9   0.1     0.044        21       8      23 ..    1099    1114 ..    1094    1115 .. 0.92
  18 ?    1.5   0.1       0.5   2.4e+02       9      25 ..    1180    1196 ..    1176    1198 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.59
                         TPR_11  6 eqGkyeeAieaYkkAlk 22
                                   ++G +e A+ ++++Al+
  gi|116754673|ref|YP_843791.1| 73 QLGSLERAVSHLSRALE 89
                                   79*************97 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.9
                         TPR_11   2 dayyeqGkyeeAieaYkkAl 21 
                                     +y    +++ Ai  Y+ Al
  gi|116754673|ref|YP_843791.1| 105 SIYANVEDLDRAISLYRDAL 124
                                    56666678999999999997 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.17
                         TPR_11   1 GdayyeqGkyeeAieaYkkAlk 22 
                                    Gd+    G++  A e+Y kAl+
  gi|116754673|ref|YP_843791.1| 262 GDLHAIEGRFSSAEECYLKALE 283
                                    8888999*************97 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.0018
                         TPR_11   3 ayyeqGkyeeAieaYkkAlkl 23 
                                    +y + G++ +A+e+Y++Al++
  gi|116754673|ref|YP_843791.1| 304 LYGSMGEWRGAVERYREALDI 324
                                    56689**************87 PP

  == domain 5  score: 8.8 bits;  conditional E-value: 0.0027
                         TPR_11   1 GdayyeqGkyeeAieaYkkAlk 22 
                                    G+++ ++G++++A+e+Y++  +
  gi|116754673|ref|YP_843791.1| 381 GHMLSDLGDWDGAVEHYERGAE 402
                                    788999***********99766 PP

  == domain 6  score: 1.6 bits;  conditional E-value: 0.49
                         TPR_11   7 qGkyeeAieaYkkAlkld 24 
                                     G++e+A+  Y  Al++ 
  gi|116754673|ref|YP_843791.1| 427 MGDLEKALDIYHDALQIQ 444
                                    69*************997 PP

  == domain 7  score: -0.1 bits;  conditional E-value: 1.6
                         TPR_11   1 GdayyeqGkyeeAieaYkkAlkl 23 
                                    G +y   G++e+A  +Y + l+l
  gi|116754673|ref|YP_843791.1| 461 GLVYQHMGEIEAAERNYMRCLEL 483
                                    33444456666666666555555 PP

  == domain 8  score: 5.0 bits;  conditional E-value: 0.042
                         TPR_11   9 kyeeAieaYkkAlk 22 
                                    ++++Ai++Y+ Al+
  gi|116754673|ref|YP_843791.1| 509 RWDDAITHYQDALE 522
                                    79**********97 PP

  == domain 9  score: 9.0 bits;  conditional E-value: 0.0024
                         TPR_11   1 GdayyeqGkyeeAieaYkkAlkld...PdnaeayynLGlayykqG 42 
                                    G++y e+G++ +Ai++Y+   +ld    + a + +nLG +y++ G
  gi|116754673|ref|YP_843791.1| 541 GNVYEEKGDILQAIKSYRMSMELDggdASIAKISWNLGGLYQRIG 585
                                    9******************99997222444567888888888776 PP

  == domain 10  score: 5.2 bits;  conditional E-value: 0.036
                         TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLG 35 
                                    G +  e+G +++A+ ++k+ ++l+ d +ea+  LG
  gi|116754673|ref|YP_843791.1| 618 GSIALERGLWDDALDCFKRCVDLRLDTPEALRVLG 652
                                    5566799***********************98877 PP

  == domain 11  score: 4.3 bits;  conditional E-value: 0.069
                         TPR_11   6 eqGkyeeAieaYkkAlk 22 
                                     +G + eA+++Y+k l+
  gi|116754673|ref|YP_843791.1| 660 RKGMWQEALAEYRKVLE 676
                                    6899**********986 PP

  == domain 12  score: 12.0 bits;  conditional E-value: 0.00027
                         TPR_11   1 GdayyeqGkyeeAieaYkkAlkl 23 
                                    G+++ eqG +++A+e+Y++ l++
  gi|116754673|ref|YP_843791.1| 695 GNLLAEQGHWDDALEHYSESLEI 717
                                    9******************9987 PP

  == domain 13  score: 11.2 bits;  conditional E-value: 0.00048
                         TPR_11   2 dayyeqGkyeeAieaYkkAl 21 
                                    +++y +G+++ A++ Y+kA 
  gi|116754673|ref|YP_843791.1| 736 NVLYRRGEWDRALNLYSKAM 755
                                    99****************95 PP

  == domain 14  score: 10.7 bits;  conditional E-value: 0.0007
                         TPR_11   3 ayyeqGkyeeAieaYkkAlkl......dPdnaeayynLGlayyk 40 
                                    + y +G++e Aie Y k l++      +  +a +++nLGl+y++
  gi|116754673|ref|YP_843791.1| 777 IHYRRGEWERAIELYHKSLEIfegledSGASAMVLNNLGLLYHR 820
                                    789**************999833333344666677777777776 PP

  == domain 15  score: 6.7 bits;  conditional E-value: 0.012
                         TPR_11   2 dayyeqGkyeeAieaYkkAlkl 23 
                                    +ay +  ++eeA+ +Y+k l+l
  gi|116754673|ref|YP_843791.1| 896 NAYADIFRWEEALDHYQKSLEL 917
                                    66666669**********9997 PP

  == domain 16  score: 0.2 bits;  conditional E-value: 1.4
                         TPR_11   12 eAieaYkkAlkl 23  
                                     eA  +Y+kAl+l
  gi|116754673|ref|YP_843791.1| 1063 EARSSYQKALAL 1074
                                     78889*****98 PP

  == domain 17  score: 4.9 bits;  conditional E-value: 0.044
                         TPR_11    8 GkyeeAieaYkkAlkl 23  
                                     G+y+eA e+++kAl l
  gi|116754673|ref|YP_843791.1| 1099 GDYDEAEEHLQKALTL 1114
                                     9************976 PP

  == domain 18  score: 1.5 bits;  conditional E-value: 0.5
                         TPR_11    9 kyeeAieaYkkAlkldP 25  
                                     + ++A+  Y +Al++ +
  gi|116754673|ref|YP_843791.1| 1180 RTDAAVSTYLEALNIAQ 1196
                                     5799*********9966 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1      0.24   1.1e+02       5      26 ..      75      96 ..      35     103 .. 0.54
   2 ?    4.6   0.1       0.1        48       5      45 ..      75     117 ..      71     119 .. 0.81
   3 !   15.1   0.2   5.1e-05     0.024       6      47 ..     112     157 ..     108     162 .. 0.89
   4 ?   -0.9   0.0       5.1   2.4e+03       3      20 ..     187     204 ..     185     208 .. 0.83
   5 ?    1.2   0.0       1.1   5.3e+02       7      53 ..     238     283 ..     228     301 .. 0.74
   6 ?    3.6   0.7      0.21        99       8      46 ..     312     355 ..     306     363 .. 0.67
   7 ?    1.0   0.0       1.4   6.4e+02      14      50 ..     363     399 ..     348     406 .. 0.74
   8 ?    4.7   0.5      0.09        42       5      48 ..     388     437 ..     384     444 .. 0.74
   9 ?    4.8   0.6     0.085        40       4      45 ..     427     474 ..     424     477 .. 0.77
  10 !   10.6   0.0    0.0013      0.61       7      60 ..     517     569 ..     505     573 .. 0.80
  11 ?    5.4   0.1     0.055        26       8      61 ..     595     647 ..     583     654 .. 0.74
  12 ?    4.1   0.0      0.14        65       1      56 [.     621     679 ..     621     689 .. 0.83
  13 !   15.4   0.0   4.3e-05      0.02       1      57 [.     698     760 ..     698     772 .. 0.80
  14 ?   -0.3   0.0       3.4   1.6e+03       4      41 ..     781     824 ..     778     829 .. 0.62
  15 ?   -0.4   0.1       3.7   1.8e+03      30      45 ..     833     848 ..     827     850 .. 0.82
  16 ?    2.7   0.0      0.38   1.8e+02       8      56 ..     905     959 ..     902     963 .. 0.73
  17 ?    7.0   0.0     0.018       8.3       6      50 ..     988    1031 ..     986    1034 .. 0.81
  18 !   11.1   1.1   0.00093      0.44       5      53 ..    1066    1113 ..    1063    1125 .. 0.80
  19 !   12.2   1.3   0.00041      0.19       4      56 ..    1098    1156 ..    1095    1168 .. 0.75
  20 ?    0.2   0.1       2.3   1.1e+03      32      66 ..    1172    1206 ..    1162    1208 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.24
                         TPR_19  5 gdyaeAlalleqalqedpknae 26
                                   g +++A+++l++al+ + + ++
  gi|116754673|ref|YP_843791.1| 75 GSLERAVSHLSRALERASGADA 96
                                   4455555555555555544444 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.1
                         TPR_19   5 gdyaeAlalleqalqedpknaearl..lLAeallalgqldeAe 45 
                                    g +++A+++l++al+ + + ++++   +L  ++ +  +ld A+
  gi|116754673|ref|YP_843791.1|  75 GSLERAVSHLSRALERASGADAVKVlsRLGSIYANVEDLDRAI 117
                                    8899************999888877557788888877777776 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 5.1e-05
                         TPR_19   6 dyaeAlalleqalqe....dpknaearllLAeallalgqldeAeal 47 
                                    d+++A++l++ al+     dp+ a ++++L  a+ ++ ++d+A ++
  gi|116754673|ref|YP_843791.1| 112 DLDRAISLYRDALSRlesgDPERAGILINLSMAYREARRWDDALQC 157
                                    8999999999999666666************************986 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 5.1
                         TPR_19   3 aegdyaeAlalleqalqe 20 
                                    ++gd+ +A +l++  l+e
  gi|116754673|ref|YP_843791.1| 187 EMGDLSSAEELYRTCLEE 204
                                    789999999999988876 PP

  == domain 5  score: 1.2 bits;  conditional E-value: 1.1
                         TPR_19   7 yaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpe 53 
                                    ++ A+ ++e   + +   ++ +llL +++   g++  Ae++  +++e
  gi|116754673|ref|YP_843791.1| 238 FDMAMHRYEHCHEIEG-ASRTALLLGDLHAIEGRFSSAEECYLKALE 283
                                    4455566666544444.5556666***************99877766 PP

  == domain 6  score: 3.6 bits;  conditional E-value: 0.21
                         TPR_19   8 aeAlalleqal.....qedpknaearllLAeallalgqldeAea 46 
                                      A++++++al     +++ + a+a+  +  a++ l +++ A++
  gi|116754673|ref|YP_843791.1| 312 RGAVERYREALdilqsEQSQDLARALREMGTACYRLRDYEMAQN 355
                                    55555566655222215577777777788999999999998875 PP

  == domain 7  score: 1.0 bits;  conditional E-value: 1.4
                         TPR_19  14 leqalqedpknaearllLAeallalgqldeAealLda 50 
                                    l++al e  ++a+   ++   l  lg++d A +  ++
  gi|116754673|ref|YP_843791.1| 363 LSEALGERDGMAASHTGMGHMLSDLGDWDGAVEHYER 399
                                    4457777778999999999999999999999876555 PP

  == domain 8  score: 4.7 bits;  conditional E-value: 0.09
                         TPR_19   5 gdyaeAlalleqalqedpknaearllL......AeallalgqldeAealL 48 
                                    gd + A++++e+  +   +++++r +       A ++  +g+l++A ++ 
  gi|116754673|ref|YP_843791.1| 388 GDWDGAVEHYERGAELLREMGDLRGAAactsniASVYQMMGDLEKALDIY 437
                                    89999999999988888887777774444444488888889999888775 PP

  == domain 9  score: 4.8 bits;  conditional E-value: 0.085
                         TPR_19   4 egdyaeAlalleqalqe......dpknaearllLAeallalgqldeAe 45 
                                    +gd++ Al+++  alq         + +  + ++  ++  +g++++Ae
  gi|116754673|ref|YP_843791.1| 427 MGDLEKALDIYHDALQIqerlgdMQGASKTLNNMGLVYQHMGEIEAAE 474
                                    8**************886664444446666667799999999999887 PP

  == domain 10  score: 10.6 bits;  conditional E-value: 0.0013
                         TPR_19   7 yaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddar 60 
                                    y++Al+ +e++  +  ++a++  +L +++ + g++ +A++     +e d  da 
  gi|116754673|ref|YP_843791.1| 517 YQDALETFEAI-GDRRGMAAVMNNLGNVYEEKGDILQAIKSYRMSMELDGGDAS 569
                                    66666666664.66788***********************99999999988765 PP

  == domain 11  score: 5.4 bits;  conditional E-value: 0.055
                         TPR_19   8 aeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddary 61 
                                     + l++++++  ++ + a+a+++L  + l+ g +d+A ++ ++  +   d++++
  gi|116754673|ref|YP_843791.1| 595 RASLEAFQSI-GDERGAAYALMGLGSIALERGLWDDALDCFKRCVDLRLDTPEA 647
                                    3336666664.5678899*********************999877766666555 PP

  == domain 12  score: 4.1 bits;  conditional E-value: 0.14
                         TPR_19   1 llaegdyaeAlalleqalqedpknaearllL...AeallalgqldeAealLdalpeedp 56 
                                    +l++g  ++Al+ +++  +   + +ea+  L   A ++   g ++eA a   +++e ++
  gi|116754673|ref|YP_843791.1| 621 ALERGLWDDALDCFKRCVDLRLDTPEALRVLgsiASVYERKGMWQEALAEYRKVLERFR 679
                                    688999999*999***888866666666666666**************99999888765 PP

  == domain 13  score: 15.4 bits;  conditional E-value: 4.3e-05
                         TPR_19   1 llaegdyaeAlalleqalqe.....dpknaearl..lLAeallalgqldeAealLdalpeedpd 57 
                                    l ++g  ++Al+++++ l+      d  ++ a    ++A++l+  g++d A +l ++++e+++ 
  gi|116754673|ref|YP_843791.1| 698 LAEQGHWDDALEHYSESLEIferlgDG-YSTAVTtnNMANVLYRRGEWDRALNLYSKAMEHFQR 760
                                    679*************99885554322.333333479**********************99986 PP

  == domain 14  score: -0.3 bits;  conditional E-value: 3.4
                         TPR_19   4 egdyaeAlalleqalqe......dpknaearllLAeallalgql 41 
                                    +g  ++A++l+ + l+       +  +a ++ +L  ++   g++
  gi|116754673|ref|YP_843791.1| 781 RGEWERAIELYHKSLEIfegledSGASAMVLNNLGLLYHRRGEW 824
                                    68888999999997755222221555666666666666666666 PP

  == domain 15  score: -0.4 bits;  conditional E-value: 3.7
                         TPR_19  30 lLAeallalgqldeAe 45 
                                    l Ae+ + +g+ ++A 
  gi|116754673|ref|YP_843791.1| 833 LAAECAMRAGDHEAAT 848
                                    4799999999999996 PP

  == domain 16  score: 2.7 bits;  conditional E-value: 0.38
                         TPR_19   8 aeAlalleqalqedpk......naearllLAeallalgqldeAealLdalpeedp 56 
                                    +eAl+++++ l+           ae   ++A ++   g++  Ae+lL++ + e++
  gi|116754673|ref|YP_843791.1| 905 EEALDHYQKSLELFERtgdrysAAETMFNMALIYRDRGEWSIAEDLLSRSMSEFR 959
                                    566666666665533333343467777789*****************99888765 PP

  == domain 17  score: 7.0 bits;  conditional E-value: 0.018
                         TPR_19    6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealLda 50  
                                     d  +A+  +e++  + p+  ea l++A++ l+ g+  eA+  L++
  gi|116754673|ref|YP_843791.1|  988 DILSAITTFESI-GAIPDLCEAYLAMARVKLNRGEMSEARFYLSE 1031
                                     566677778885.55688889*******************99876 PP

  == domain 18  score: 11.1 bits;  conditional E-value: 0.00093
                         TPR_19    5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpe 53  
                                       y+ Alal +++     +  ++r  L  a l++g++deAe+ L++++ 
  gi|116754673|ref|YP_843791.1| 1066 SSYQKALALARKMGLTRDEGVALRS-LGAASLNAGDYDEAEEHLQKALT 1113
                                     5799999999998555555666666.9*****************99876 PP

  == domain 19  score: 12.2 bits;  conditional E-value: 0.00041
                         TPR_19    4 egdyaeAlalleqalqedpk.....naearl...lLAeallalgqldeAealLdalpeedp 56  
                                     +gdy+eA ++l++al+         +  ++    l+A ++++ ++   Ae++   l ++++
  gi|116754673|ref|YP_843791.1| 1098 AGDYDEAEEHLQKALTLFKSinsmyD--LLStyaLMATLYFNRKDHSRAEETALLLERQAR 1156
                                     8**************99666666433..33324577**************99766666655 PP

  == domain 20  score: 0.2 bits;  conditional E-value: 2.3
                         TPR_19   32 AeallalgqldeAealLdalpeedpddaryasLlA 66  
                                     A + la+ ++d+A  +  ++++ ++ d   ++Ll 
  gi|116754673|ref|YP_843791.1| 1172 AGCELATSRTDAAVSTYLEALNIAQSDGVSKRLLT 1206
                                     8899***********99999999998877666665 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 ?    2.2   0.0      0.41   1.9e+02      16      35 ..     109     128 ..     105     131 .. 0.83
   2 ?    2.6   0.0      0.31   1.5e+02       7      35 ..     178     206 ..     173     210 .. 0.79
   3 ?    1.5   0.0      0.68   3.2e+02      17      40 ..     268     292 ..     267     305 .. 0.81
   4 ?    5.7   0.0     0.033        16      16      35 ..     307     326 ..     294     340 .. 0.82
   5 ?    2.8   0.0      0.26   1.2e+02      18      36 ..     388     406 ..     384     413 .. 0.90
   6 ?    0.9   0.1         1   4.9e+02      17      32 ..     427     442 ..     412     447 .. 0.83
   7 !    8.7   0.0    0.0038       1.8       4      36 ..     494     526 ..     492     535 .. 0.89
   8 ?   -0.8   0.0       3.5   1.7e+03      14      32 ..     544     562 ..     539     563 .. 0.88
   9 ?    0.6   0.0       1.3   6.1e+02      18      37 ..     585     604 ..     582     611 .. 0.86
  10 ?   -2.0   0.0       8.1   3.8e+03      17      33 ..     624     640 ..     621     641 .. 0.85
  11 ?    2.2   0.0       0.4   1.9e+02       9      34 ..     653     678 ..     649     681 .. 0.86
  12 ?    6.3   0.0     0.022        10      16      36 ..     700     720 ..     696     731 .. 0.89
  13 !    8.8   0.0    0.0034       1.6       4      37 ..     728     761 ..     725     766 .. 0.81
  14 ?    7.2   0.0     0.011       5.1      17      35 ..     781     799 ..     768     807 .. 0.88
  15 ?    6.7   0.0     0.016       7.7      20      35 ..     904     919 ..     902     930 .. 0.89
  16 ?    4.8   0.1     0.064        30       6      37 ..    1087    1118 ..    1083    1124 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.41
                            MIT  16 nagnyeeAlelYkealelLl 35 
                                    n ++ + A++lY++al  L 
  gi|116754673|ref|YP_843791.1| 109 NVEDLDRAISLYRDALSRLE 128
                                    5678999********98775 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.31
                            MIT   7 lvkkAveeDnagnyeeAlelYkealelLl 35 
                                    + ++A  + + g+ + A elY+++le + 
  gi|116754673|ref|YP_843791.1| 178 IMEEAEIRREMGDLSSAEELYRTCLEEFE 206
                                    556666666779999***********997 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.68
                            MIT  17 agnyeeAlelYkealelLlqalk.e 40 
                                    +g ++ A e+Y +ale + ++   e
  gi|116754673|ref|YP_843791.1| 268 EGRFSSAEECYLKALEGFREVSDrE 292
                                    578999************9998733 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.033
                            MIT  16 nagnyeeAlelYkealelLl 35 
                                    + g++  A+e Y+eal++L+
  gi|116754673|ref|YP_843791.1| 307 SMGEWRGAVERYREALDILQ 326
                                    668999************97 PP

  == domain 5  score: 2.8 bits;  conditional E-value: 0.26
                            MIT  18 gnyeeAlelYkealelLlq 36 
                                    g+++ A+e Y+ + elL +
  gi|116754673|ref|YP_843791.1| 388 GDWDGAVEHYERGAELLRE 406
                                    899*************975 PP

  == domain 6  score: 0.9 bits;  conditional E-value: 1
                            MIT  17 agnyeeAlelYkeale 32 
                                     g+ e+Al+ Y +al+
  gi|116754673|ref|YP_843791.1| 427 MGDLEKALDIYHDALQ 442
                                    58999********997 PP

  == domain 7  score: 8.7 bits;  conditional E-value: 0.0038
                            MIT   4 AlelvkkAveeDnagnyeeAlelYkealelLlq 36 
                                    A   ++ A+ ++ +  +++A+  Y++ale +  
  gi|116754673|ref|YP_843791.1| 494 ANTHINLATLYEIQRRWDDAITHYQDALETFEA 526
                                    6667999**********************9975 PP

  == domain 8  score: -0.8 bits;  conditional E-value: 3.5
                            MIT  14 eDnagnyeeAlelYkeale 32 
                                    ++++g++  A++ Y+ ++e
  gi|116754673|ref|YP_843791.1| 544 YEEKGDILQAIKSYRMSME 562
                                    7999**********98877 PP

  == domain 9  score: 0.6 bits;  conditional E-value: 1.3
                            MIT  18 gnyeeAlelYkealelLlqa 37 
                                    g+ e A ++Y+ +le ++ +
  gi|116754673|ref|YP_843791.1| 585 GDAESAEKCYRASLEAFQSI 604
                                    67899************976 PP

  == domain 10  score: -2.0 bits;  conditional E-value: 8.1
                            MIT  17 agnyeeAlelYkealel 33 
                                    +g +++Al+++k +++l
  gi|116754673|ref|YP_843791.1| 624 RGLWDDALDCFKRCVDL 640
                                    567899*******9986 PP

  == domain 11  score: 2.2 bits;  conditional E-value: 0.4
                            MIT   9 kkAveeDnagnyeeAlelYkealelL 34 
                                    + A  ++++g ++eAl  Y++ le +
  gi|116754673|ref|YP_843791.1| 653 SIASVYERKGMWQEALAEYRKVLERF 678
                                    67899**************9988766 PP

  == domain 12  score: 6.3 bits;  conditional E-value: 0.022
                            MIT  16 nagnyeeAlelYkealelLlq 36 
                                    ++g++++Ale Y+e+le++  
  gi|116754673|ref|YP_843791.1| 700 EQGHWDDALEHYSESLEIFER 720
                                    6899**************975 PP

  == domain 13  score: 8.8 bits;  conditional E-value: 0.0034
                            MIT   4 AlelvkkAveeDnagnyeeAlelYkealelLlqa 37 
                                    A+   ++A  + ++g+++ Al+lY++a+e+++ +
  gi|116754673|ref|YP_843791.1| 728 AVTTNNMANVLYRRGEWDRALNLYSKAMEHFQRV 761
                                    555566666667899****************975 PP

  == domain 14  score: 7.2 bits;  conditional E-value: 0.011
                            MIT  17 agnyeeAlelYkealelLl 35 
                                    +g++e A+elY ++le++ 
  gi|116754673|ref|YP_843791.1| 781 RGEWERAIELYHKSLEIFE 799
                                    799*************996 PP

  == domain 15  score: 6.7 bits;  conditional E-value: 0.016
                            MIT  20 yeeAlelYkealelLl 35 
                                    +eeAl+ Y+++lel+ 
  gi|116754673|ref|YP_843791.1| 904 WEEALDHYQKSLELFE 919
                                    79************97 PP

  == domain 16  score: 4.8 bits;  conditional E-value: 0.064
                            MIT    6 elvkkAveeDnagnyeeAlelYkealelLlqa 37  
                                     +l +  + + nag+y+eA e  ++al l++ +
  gi|116754673|ref|YP_843791.1| 1087 ALRSLGAASLNAGDYDEAEEHLQKALTLFKSI 1118
                                     55566677889*****************9865 PP

>> RPN7  26S proteasome subunit RPN7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.16        74      20      66 ..      85     127 ..      69     145 .. 0.75
   2 ?    0.8   0.0      0.73   3.4e+02      31      70 ..     170     209 ..     160     218 .. 0.85
   3 !   11.5   0.1   0.00038      0.18      37     140 ..     256     361 ..     224     370 .. 0.78
   4 !   11.6   0.1   0.00036      0.17      24     134 ..     283     395 ..     276     397 .. 0.79
   5 ?    6.4   1.1     0.014       6.5      37     144 ..     415     525 ..     389     527 .. 0.80
   6 !    8.6   0.1    0.0029       1.4       7      61 ..     505     559 ..     499     564 .. 0.91
   7 !    9.8   0.0    0.0013       0.6      29      69 ..     564     604 ..     560     632 .. 0.90
   8 ?    0.2   0.0       1.2   5.5e+02      41      70 ..     653     682 ..     640     694 .. 0.84
   9 !    9.2   0.1    0.0019       0.9      11     136 ..     703     831 ..     696     838 .. 0.84
  10 ?    6.1   0.1     0.017       8.2      15      90 ..     867     942 ..     854     960 .. 0.77
  11 !   13.8   0.1   7.7e-05     0.036      74     170 ..    1007    1140 ..     994    1143 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.16
                                    HHHHHHHHHTT-HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTCCCC- CS
                           RPN7  20 daelkdakenlgkeeirrakldlaehYlkigdleeAlkaysrireyc 66 
                                     + l++        +  +   +l+  Y+++ dl+ A+ +y+ ++  +
  gi|116754673|ref|YP_843791.1|  85 SRALER----ASGADAVKVLSRLGSIYANVEDLDRAISLYRDALSRL 127
                                    444443....4444555667889*****************9988766 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.73
                                    -HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTCCCC--SHH CS
                           RPN7  31 gkeeirrakldlaehYlkigdleeAlkaysrireyctslk 70 
                                      ++++ra  + ae   ++gdl++A ++y+ ++e+   l+
  gi|116754673|ref|YP_843791.1| 170 DRSSVARAIMEEAEIRREMGDLSSAEELYRTCLEEFERLG 209
                                    5689999999********************9999876665 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00038
                                    HHHHHHHHHHHHCT-HHHHHHHHHTCCC...C--SHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHCSSS---.HHHHH CS
                           RPN7  37 rakldlaehYlkigdleeAlkaysrire...yctslkhkidmllnlirvaiffndwdlvskylekakellekggdwerkn 113
                                    r+ l l++ ++  g +++A ++y +++e   +++  +++++ ll+l r+   +++w  + +   +a ++l++ ++ +  +
  gi|116754673|ref|YP_843791.1| 256 RTALLLGDLHAIEGRFSSAEECYLKALEgfrEVSDRESVANTLLSLARLYGSMGEWRGAVERYREALDILQS-EQSQDLA 334
                                    556667888888888888888888887633356677788888888888888888888888888888888888.6777888 PP

                                    HHHHHHHHHHHHTT-HHHHHHHHCTS- CS
                           RPN7 114 rlkvyeGlallairkfkeAaellldil 140
                                    r     G+a+ + r+++ A + ++++l
  gi|116754673|ref|YP_843791.1| 335 RALREMGTACYRLRDYEMAQNYFMKSL 361
                                    888888999999999998888888876 PP

  == domain 4  score: 11.6 bits;  conditional E-value: 0.00036
                                    HHHHHTT-HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTCCCC--S..HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHC CS
                           RPN7  24 kdakenlgkeeirrakldlaehYlkigdleeAlkaysrireycts..lkhkidmllnlirvaiffndwdlvskylekake 101
                                    ++ +e +  e+++++ l la+ Y ++g+ + A++ y+++++ + s  ++  +  l ++   ++ + d++++++y  k  e
  gi|116754673|ref|YP_843791.1| 283 EGFREVSDRESVANTLLSLARLYGSMGEWRGAVERYREALDILQSeqSQDLARALREMGTACYRLRDYEMAQNYFMKSLE 362
                                    5556667789*****************************99765511444555555666668889999999999999999 PP

                                    SSS---.HHHHHHHHHHHHHHHHHTT-HHHHHH CS
                           RPN7 102 llekggdwerknrlkvyeGlallairkfkeAae 134
                                    l e  g+++ ++  ++  G  l   +++  A+e
  gi|116754673|ref|YP_843791.1| 363 LSEALGERDGMAASHTGMGHMLSDLGDWDGAVE 395
                                    999999988888888888877777777777766 PP

  == domain 5  score: 6.4 bits;  conditional E-value: 0.014
                                    HHHHHHHHHHHHCT-HHHHHHHHHTCCCC--SHHHHHHHHHHHHHHHHHTT...-HHHHHHHHHHHHCSSS---.HHHHH CS
                           RPN7  37 rakldlaehYlkigdleeAlkaysrireyctslkhkidmllnlirvaiffn...dwdlvskylekakellekggdwerkn 113
                                    ++  ++a  Y ++gdle+Al  y  +++    l+       +l  +++ ++   +++ ++++  ++ el e+ gd+   +
  gi|116754673|ref|YP_843791.1| 415 ACTSNIASVYQMMGDLEKALDIYHDALQIQERLGDMQGASKTLNNMGLVYQhmgEIEAAERNYMRCLELKEQLGDVHGAA 494
                                    567789999**************998877777776666666666666555411156667788999999999999999999 PP

                                    HHHHHHHHHHHHTT-HHHHHHHHCTS-GGGT CS
                           RPN7 114 rlkvyeGlallairkfkeAaellldilstft 144
                                      ++  ++++  +r++ +A  +  d+l+tf+
  gi|116754673|ref|YP_843791.1| 495 NTHINLATLYEIQRRWDDAITHYQDALETFE 525
                                    9999999999999999999999999999985 PP

  == domain 6  score: 8.6 bits;  conditional E-value: 0.0029
                                    HHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHCT-HHHHHHHHHT CS
                           RPN7   7 elrkknekeleeLdaelkdakenlgkeeirrakldlaehYlkigdleeAlkaysr 61 
                                    e+++++++ + + +  l+  +  +    +++ +++l++ Y + gd+ +A+k y+ 
  gi|116754673|ref|YP_843791.1| 505 EIQRRWDDAITHYQDALETFEAIGDRRGMAAVMNNLGNVYEEKGDILQAIKSYRM 559
                                    78899*****************9******************************86 PP

  == domain 7  score: 9.8 bits;  conditional E-value: 0.0013
                                    TT-HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTCCCC--SH CS
                           RPN7  29 nlgkeeirrakldlaehYlkigdleeAlkaysrireyctsl 69 
                                    ++g+ +i++   +l+  Y +igd e+A k+y++ +e   s 
  gi|116754673|ref|YP_843791.1| 564 DGGDASIAKISWNLGGLYQRIGDAESAEKCYRASLEAFQSI 604
                                    5799****************************998877766 PP

  == domain 8  score: 0.2 bits;  conditional E-value: 1.2
                                    HHHHHHHHCT-HHHHHHHHHTCCCC--SHH CS
                           RPN7  41 dlaehYlkigdleeAlkaysrireyctslk 70 
                                     +a  Y + g  +eAl+ y++++e    ++
  gi|116754673|ref|YP_843791.1| 653 SIASVYERKGMWQEALAEYRKVLERFRGMG 682
                                    67899****************999876665 PP

  == domain 9  score: 9.2 bits;  conditional E-value: 0.0019
                                    HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTCCCC--SHHHHHH...HHHHHHHHHHHTT CS
                           RPN7  11 knekeleeLdaelkdakenlgkeeirrakldlaehYlkigdleeAlkaysrireyctslkhkid...mllnlirvaiffn 87 
                                    ++++ le+  + l+  +  +   +++ + ++ a+  ++ g+ + Al++ys+++e+    +   +    l n+  + + ++
  gi|116754673|ref|YP_843791.1| 703 HWDDALEHYSESLEIFERLGDGYSTAVTTNNMANVLYRRGEWDRALNLYSKAMEHFQRVGDMHSygaTLSNIASIHYRRG 782
                                    6888888888888887777778899999**************************99887766551114556778889999 PP

                                    -HHHHHHHHHHHHCSSS---.HHHHHHHHHHHHHHHHHTT-HHHHHHHH CS
                           RPN7  88 dwdlvskylekakellekggdwerknrlkvyeGlallairkfkeAaell 136
                                    +w+ + +  +k  e+ e  +d  + + +    Gl++ + ++++ A++++
  gi|116754673|ref|YP_843791.1| 783 EWERAIELYHKSLEIFEGLEDSGASAMVLNNLGLLYHRRGEWSLAVDHF 831
                                    9999999999999999999999999999999999999999999998887 PP

  == domain 10  score: 6.1 bits;  conditional E-value: 0.017
                                    HHHHHHHHHHHHHHTT-HHHHH.HHHHHHHHHHHHCT-HHHHHHHHHTCCCC--SHHHHHHHHHHHHHHHHHTT-HH CS
                           RPN7  15 eleeLdaelkdakenlgkeeir.rakldlaehYlkigdleeAlkaysrireyctslkhkidmllnlirvaiffndwd 90 
                                     ++   ++l++  e  g+ e++ + +  la+ Y++i   eeAl  y++ +e    ++   +   ++  +a+ + d +
  gi|116754673|ref|YP_843791.1| 867 DIDGYLKKLEEI-ERAGDVEMAaEMHGILANAYADIFRWEEALDHYQKSLELFERTGDRYSAAETMFNMALIYRDRG 942
                                    555555666664.45566666515556799******************99999999999999999999999998865 PP

  == domain 11  score: 13.8 bits;  conditional E-value: 7.7e-05
                                     HHHHHHHHHHHHTT-HHHHHHHHHHHHCSSS---.HHHHHH..................................... CS
                           RPN7   74 dmllnlirvaiffndwdlvskylekakellekggdwerknr..................................... 114 
                                     + +l++ rv++ +++++ +  yl++a++l+ k+g  ++k r                                     
  gi|116754673|ref|YP_843791.1| 1007 EAYLAMARVKLNRGEMSEARFYLSEAETLILKTGYDSMKIRlyiewgdfylsqapfearssyqkalalarkmgltrde 1084
                                     67999***************************99999999999999999999999999999999999999******** PP

                                     ..HHHHHHHHHHHTT-HHHHHHHHCTS-GGGT.TTT--HHHHHHHHHHHHHHH--HHH CS
                           RPN7  115 ..lkvyeGlallairkfkeAaellldilstftskellsyedlavyavlcalatldRkd 170 
                                          + G a+l  +++ eA e+l ++l+ f  k + s  dl    +l+a + ++Rkd
  gi|116754673|ref|YP_843791.1| 1085 gvALRSLGAASLNAGDYDEAEEHLQKALTLF--KSINSMYDLLSTYALMATLYFNRKD 1140
                                     *99999*************************..8999999999999999999999997 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       4.9   2.3e+03       4      29 ..      65      90 ..      63      93 .. 0.85
   2 ?    3.6   0.0      0.26   1.2e+02       5      28 ..     102     125 ..      98     127 .. 0.87
   3 ?    2.3   0.0      0.69   3.2e+02       5      21 ..     140     156 ..     138     162 .. 0.87
   4 ?    4.8   0.0      0.11        53       6      30 ..     181     205 ..     176     206 .. 0.89
   5 ?    7.3   0.1     0.017         8       3      28 ..     298     323 ..     297     324 .. 0.90
   6 ?   -0.0   0.4       3.8   1.8e+03       3      24 ..     337     358 ..     335     363 .. 0.82
   7 ?    1.8   0.0         1   4.8e+02      12      25 ..     386     399 ..     372     399 .. 0.81
   8 ?    6.6   0.0      0.03        14       6      28 ..     420     442 ..     419     444 .. 0.88
   9 ?    1.5   0.0       1.2   5.7e+02       5      28 ..     459     482 ..     459     483 .. 0.88
  10 ?    4.1   0.0      0.18        83       6      30 ..     500     524 ..     498     525 .. 0.79
  11 ?    0.7   0.0       2.2   1.1e+03       5      24 ..     539     558 ..     539     559 .. 0.89
  12 ?   -0.5   0.0       5.2   2.5e+03       4      25 ..     575     596 ..     574     601 .. 0.84
  13 ?    7.3   0.0     0.017       8.1       1      28 [.     612     639 ..     612     641 .. 0.92
  14 !    8.9   0.0    0.0054       2.5       6      30 ..     654     678 ..     653     680 .. 0.92
  15 ?    2.1   0.0      0.78   3.7e+02       6      24 ..     694     712 ..     693     726 .. 0.77
  16 ?    7.7   0.0     0.013       5.9       2      26 ..     737     761 ..     735     764 .. 0.91
  17 ?    6.1   0.0     0.041        19       5      25 ..     773     793 ..     771     798 .. 0.86
  18 ?    1.7   0.0       1.1     5e+02       5      24 ..     813     832 ..     813     836 .. 0.89
  19 ?    1.2   0.1       1.5   7.2e+02      15      27 ..     903     915 ..     893     926 .. 0.52
  20 ?    4.3   0.0      0.16        76       2      25 ..     930     953 ..     929     958 .. 0.86
  21 ?    0.7   0.4       2.2     1e+03       1      23 [.    1007    1029 ..    1007    1032 .. 0.84
  22 ?    4.5   0.4      0.14        64       6      29 ..    1091    1114 ..    1065    1116 .. 0.75
  23 ?    0.5   0.1       2.6   1.2e+03       5      22 ..    1130    1147 ..    1128    1152 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 4.9
                                   HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          TPR_6  4 yklalsyrklgdtdkAlealerlike 29
                                   + l++  ++lg  ++A+  l r +++
  gi|116754673|ref|YP_843791.1| 65 FSLGMISQQLGSLERAVSHLSRALER 90
                                   56888899999*******99999987 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.26
                                    HHHHHHHH.HHHHHHHHHHHHHHHH CS
                          TPR_6   5 klalsyrk.lgdtdkAlealerlik 28 
                                    +l+  y +   d d+A+ ++++ ++
  gi|116754673|ref|YP_843791.1| 102 RLGSIYANvE-DLDRAISLYRDALS 125
                                    89999***77.**********9886 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.69
                                    HHHHHHHHHHHHHHHHH CS
                          TPR_6   5 klalsyrklgdtdkAle 21 
                                    +l ++yr++ ++d+Al+
  gi|116754673|ref|YP_843791.1| 140 NLSMAYREARRWDDALQ 156
                                    689*****88*****97 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.11
                                    HHHHHHHHHHHHHHHHHHHHHHHH- CS
                          TPR_6   6 lalsyrklgdtdkAlealerlikeY 30 
                                     a+ +r++gd + A e+++ +++e+
  gi|116754673|ref|YP_843791.1| 181 EAEIRREMGDLSSAEELYRTCLEEF 205
                                    58999*****************997 PP

  == domain 5  score: 7.3 bits;  conditional E-value: 0.017
                                    HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          TPR_6   3 lyklalsyrklgdtdkAlealerlik 28 
                                    l+ la++y ++g+++ A+e +++ ++
  gi|116754673|ref|YP_843791.1| 298 LLSLARLYGSMGEWRGAVERYREALD 323
                                    6789*****************99875 PP

  == domain 6  score: -0.0 bits;  conditional E-value: 3.8
                                    HHHHHHHHHHHHHHHHHHHHHH CS
                          TPR_6   3 lyklalsyrklgdtdkAleale 24 
                                    l  ++ + ++l d++ A  ++ 
  gi|116754673|ref|YP_843791.1| 337 LREMGTACYRLRDYEMAQNYFM 358
                                    557899999988****999986 PP

  == domain 7  score: 1.8 bits;  conditional E-value: 1
                                    HHHHHHHHHHHHHH CS
                          TPR_6  12 klgdtdkAlealer 25 
                                     lgd+d A+e +er
  gi|116754673|ref|YP_843791.1| 386 DLGDWDGAVEHYER 399
                                    379*********97 PP

  == domain 8  score: 6.6 bits;  conditional E-value: 0.03
                                    HHHHHHHHHHHHHHHHHHHHHHH CS
                          TPR_6   6 lalsyrklgdtdkAlealerlik 28 
                                    +a  y+++gd +kAl+++ + ++
  gi|116754673|ref|YP_843791.1| 420 IASVYQMMGDLEKALDIYHDALQ 442
                                    8999**************98775 PP

  == domain 9  score: 1.5 bits;  conditional E-value: 1.2
                                    HHHHHHHHHHHHHHHHHHHHHHHH CS
                          TPR_6   5 klalsyrklgdtdkAlealerlik 28 
                                    +++l y+ +g+ ++A + + r+++
  gi|116754673|ref|YP_843791.1| 459 NMGLVYQHMGEIEAAERNYMRCLE 482
                                    69*************999988875 PP

  == domain 10  score: 4.1 bits;  conditional E-value: 0.18
                                    HHHHHHHHHHHHHHHHHHHHHHHH- CS
                          TPR_6   6 lalsyrklgdtdkAlealerlikeY 30 
                                    la +y+ + ++d+A++ +++ ++ +
  gi|116754673|ref|YP_843791.1| 500 LATLYEIQRRWDDAITHYQDALETF 524
                                    566565366***********99876 PP

  == domain 11  score: 0.7 bits;  conditional E-value: 2.2
                                    HHHHHHHHHHHHHHHHHHHH CS
                          TPR_6   5 klalsyrklgdtdkAleale 24 
                                    +l+  y++ gd  +A++ ++
  gi|116754673|ref|YP_843791.1| 539 NLGNVYEEKGDILQAIKSYR 558
                                    58999***88*******997 PP

  == domain 12  score: -0.5 bits;  conditional E-value: 5.2
                                    HHHHHHHHHHHHHHHHHHHHHH CS
                          TPR_6   4 yklalsyrklgdtdkAlealer 25 
                                    ++l+ +y++ gd++ A + ++ 
  gi|116754673|ref|YP_843791.1| 575 WNLGGLYQRIGDAESAEKCYRA 596
                                    57888999*88*****999985 PP

  == domain 13  score: 7.3 bits;  conditional E-value: 0.017
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          TPR_6   1 dAlyklalsyrklgdtdkAlealerlik 28 
                                    +Al+ l+   ++ g +d+Al+ ++r+++
  gi|116754673|ref|YP_843791.1| 612 YALMGLGSIALERGLWDDALDCFKRCVD 639
                                    79*****9999988***********987 PP

  == domain 14  score: 8.9 bits;  conditional E-value: 0.0054
                                    HHHHHHHHHHHHHHHHHHHHHHHH- CS
                          TPR_6   6 lalsyrklgdtdkAlealerlikeY 30 
                                    +a  y++ g +++Al+ ++++++++
  gi|116754673|ref|YP_843791.1| 654 IASVYERKGMWQEALAEYRKVLERF 678
                                    68899*988**************98 PP

  == domain 15  score: 2.1 bits;  conditional E-value: 0.78
                                    HHHHHHHHHHHHHHHHHHH CS
                          TPR_6   6 lalsyrklgdtdkAleale 24 
                                    ++ ++ ++g +d+Ale + 
  gi|116754673|ref|YP_843791.1| 694 IGNLLAEQGHWDDALEHYS 712
                                    5777888889999998775 PP

  == domain 16  score: 7.7 bits;  conditional E-value: 0.013
                                    HHHHHHHHHHHHHHHHHHHHHHHHH CS
                          TPR_6   2 AlyklalsyrklgdtdkAlealerl 26 
                                    +ly++++  r+l+ ++kA+e ++r+
  gi|116754673|ref|YP_843791.1| 737 VLYRRGEWDRALNLYSKAMEHFQRV 761
                                    699****99*999*********998 PP

  == domain 17  score: 6.1 bits;  conditional E-value: 0.041
                                    HHHHHHHHHHHHHHHHHHHHH CS
                          TPR_6   5 klalsyrklgdtdkAlealer 25 
                                    ++a  +++ g++++A+e++ +
  gi|116754673|ref|YP_843791.1| 773 NIASIHYRRGEWERAIELYHK 793
                                    689999*989********987 PP

  == domain 18  score: 1.7 bits;  conditional E-value: 1.1
                                    HHHHHHHHHHHHHHHHHHHH CS
                          TPR_6   5 klalsyrklgdtdkAleale 24 
                                    +l+l+y + g+++ A++ ++
  gi|116754673|ref|YP_843791.1| 813 NLGLLYHRRGEWSLAVDHFR 832
                                    59******99******9887 PP

  == domain 19  score: 1.2 bits;  conditional E-value: 1.5
                                    HHHHHHHHHHHHH CS
                          TPR_6  15 dtdkAlealerli 27 
                                    ++++Al+ +++ +
  gi|116754673|ref|YP_843791.1| 903 RWEEALDHYQKSL 915
                                    5555555555533 PP

  == domain 20  score: 4.3 bits;  conditional E-value: 0.16
                                    HHHHHHHHHHHHHHHHHHHHHHHH CS
                          TPR_6   2 AlyklalsyrklgdtdkAlealer 25 
                                     ++++al yr  g+++ A ++l r
  gi|116754673|ref|YP_843791.1| 930 TMFNMALIYRDRGEWSIAEDLLSR 953
                                    59*********88***99998866 PP

  == domain 21  score: 0.7 bits;  conditional E-value: 2.2
                                     HHHHHHHHHHHHHHHHHHHHHHH CS
                          TPR_6    1 dAlyklalsyrklgdtdkAleal 23  
                                     +A++ +a+  ++ g+ ++A+ +l
  gi|116754673|ref|YP_843791.1| 1007 EAYLAMARVKLNRGEMSEARFYL 1029
                                     68999999999989*****9877 PP

  == domain 22  score: 4.5 bits;  conditional E-value: 0.14
                                     HHHHHHHHHHHHHHHHHHHHHHHH CS
                          TPR_6    6 lalsyrklgdtdkAlealerlike 29  
                                     l+ + +++gd+d+A e l++ ++ 
  gi|116754673|ref|YP_843791.1| 1091 LGAASLNAGDYDEAEEHLQKALTL 1114
                                     344444559***********9875 PP

  == domain 23  score: 0.5 bits;  conditional E-value: 2.6
                                     HHHHHHHHHHHHHHHHHH CS
                          TPR_6    5 klalsyrklgdtdkAlea 22  
                                     ++a +y++ +d+++A e+
  gi|116754673|ref|YP_843791.1| 1130 LMATLYFNRKDHSRAEET 1147
                                     599*****99****9875 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       6.6   3.1e+03      14      33 ..      62      81 ..      53      82 .. 0.87
   2 ?    3.1   0.0      0.32   1.5e+02      13      33 ..      97     117 ..      85     118 .. 0.85
   3 ?    1.1   0.0       1.4   6.6e+02       9      34 .]     131     156 ..     119     156 .. 0.81
   4 ?   -0.7   0.0       5.2   2.5e+03      15      33 ..     217     235 ..     212     236 .. 0.89
   5 ?    2.1   0.0      0.65   3.1e+02       1      33 [.     277     315 ..     277     316 .. 0.71
   6 ?    0.3   0.1       2.6   1.2e+03       9      33 ..     330     354 ..     327     355 .. 0.86
   7 ?    1.5   0.0         1   4.8e+02       6      29 ..     414     437 ..     410     442 .. 0.65
   8 ?    1.3   0.0       1.2   5.6e+02      14      33 ..     455     474 ..     453     475 .. 0.89
   9 ?    4.9   0.0     0.083        39       2      33 ..     477     514 ..     476     515 .. 0.73
  10 !    7.9   0.0    0.0096       4.5      14      33 ..     535     554 ..     533     555 .. 0.89
  11 ?   -1.5   0.0       9.1   4.3e+03      15      33 ..     650     668 ..     633     669 .. 0.74
  12 ?    0.7   0.0       1.8   8.6e+02      15      34 .]     690     709 ..     683     709 .. 0.86
  13 ?    4.2   0.1      0.14        66      17      33 ..     732     748 ..     728     749 .. 0.91
  14 ?    1.2   0.0       1.3   6.3e+02      15      34 .]     770     789 ..     750     789 .. 0.78
  15 ?    7.1   0.0     0.017       7.9      12      32 ..     807     827 ..     793     829 .. 0.85
  16 ?    3.8   0.0       0.2        93      13      29 ..     928     944 ..     910     949 .. 0.69
  17 ?    1.5   0.0       1.1     5e+02       4      24 ..     959     979 ..     959     987 .. 0.85
  18 ?   -0.9   0.0         6   2.8e+03      10      33 ..    1003    1026 ..    1002    1027 .. 0.85
  19 ?    4.4   0.1      0.12        57      14      34 .]    1086    1106 ..    1068    1106 .. 0.90
  20 ?    1.8   0.0      0.85     4e+02      16      34 .]    1128    1146 ..    1125    1146 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 6.6
                         TPR_17 14 daynnLAelllknGdlmtAr 33
                                    +++ L+ +  ++G l++A+
  gi|116754673|ref|YP_843791.1| 62 SLWFSLGMISQQLGSLERAV 81
                                   68************999995 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.32
                         TPR_17  13 adaynnLAelllknGdlmtAr 33 
                                    ++++  L+ ++++  dl++A+
  gi|116754673|ref|YP_843791.1|  97 VKVLSRLGSIYANVEDLDRAI 117
                                    678899*************97 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 1.4
                         TPR_17   9 dPnnadaynnLAelllknGdlmtArq 34 
                                    dP  a  + nL  +++++ ++++A+q
  gi|116754673|ref|YP_843791.1| 131 DPERAGILINLSMAYREARRWDDALQ 156
                                    8999999***************9987 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 5.2
                         TPR_17  15 aynnLAelllknGdlmtAr 33 
                                    ++ +L+++   +G++++A+
  gi|116754673|ref|YP_843791.1| 217 SLEMLGRISQLRGESRRAE 235
                                    56789************98 PP

  == domain 5  score: 2.1 bits;  conditional E-value: 0.65
                         TPR_17   1 lylkaleldPnn......adaynnLAelllknGdlmtAr 33 
                                    +ylkale           a+ +  LA+l+ + G+++ A+
  gi|116754673|ref|YP_843791.1| 277 CYLKALEGFREVsdresvANTLLSLARLYGSMGEWRGAV 315
                                    6778888753322334469999999***99999998886 PP

  == domain 6  score: 0.3 bits;  conditional E-value: 2.6
                         TPR_17   9 dPnnadaynnLAelllknGdlmtAr 33 
                                      + a a+ +++++ +++ d+++A+
  gi|116754673|ref|YP_843791.1| 330 SQDLARALREMGTACYRLRDYEMAQ 354
                                    5677899999999999*******97 PP

  == domain 7  score: 1.5 bits;  conditional E-value: 1
                         TPR_17   6 leldPnnadaynnLAelllknGdl 29 
                                    +++  n a +y++++ l + +  +
  gi|116754673|ref|YP_843791.1| 414 AACTSNIASVYQMMGDLEKALDIY 437
                                    566677777777777777666555 PP

  == domain 8  score: 1.3 bits;  conditional E-value: 1.2
                         TPR_17  14 daynnLAelllknGdlmtAr 33 
                                    + +nn++ ++ + G+ + A+
  gi|116754673|ref|YP_843791.1| 455 KTLNNMGLVYQHMGEIEAAE 474
                                    679***********999987 PP

  == domain 9  score: 4.9 bits;  conditional E-value: 0.083
                         TPR_17   2 ylkaleldPnn......adaynnLAelllknGdlmtAr 33 
                                    y ++lel          a+ + nLA+l++ + ++++A+
  gi|116754673|ref|YP_843791.1| 477 YMRCLELKEQLgdvhgaANTHINLATLYEIQRRWDDAI 514
                                    55666665444444444999***********9999996 PP

  == domain 10  score: 7.9 bits;  conditional E-value: 0.0096
                         TPR_17  14 daynnLAelllknGdlmtAr 33 
                                     ++nnL+++++++Gd  +A+
  gi|116754673|ref|YP_843791.1| 535 AVMNNLGNVYEEKGDILQAI 554
                                    69*************99987 PP

  == domain 11  score: -1.5 bits;  conditional E-value: 9.1
                         TPR_17  15 aynnLAelllknGdlmtAr 33 
                                    ++   A +++++G +++A+
  gi|116754673|ref|YP_843791.1| 650 VLGSIASVYERKGMWQEAL 668
                                    5666799999***999997 PP

  == domain 12  score: 0.7 bits;  conditional E-value: 1.8
                         TPR_17  15 aynnLAelllknGdlmtArq 34 
                                    ++   ++ll+++G +++A++
  gi|116754673|ref|YP_843791.1| 690 VLSTIGNLLAEQGHWDDALE 709
                                    566789***********985 PP

  == domain 13  score: 4.2 bits;  conditional E-value: 0.14
                         TPR_17  17 nnLAelllknGdlmtAr 33 
                                    nn+A++l+++G++++A+
  gi|116754673|ref|YP_843791.1| 732 NNMANVLYRRGEWDRAL 748
                                    9**************96 PP

  == domain 14  score: 1.2 bits;  conditional E-value: 1.3
                         TPR_17  15 aynnLAelllknGdlmtArq 34 
                                     + n A +++++G++++A++
  gi|116754673|ref|YP_843791.1| 770 TLSNIASIHYRRGEWERAIE 789
                                    5678999999*******986 PP

  == domain 15  score: 7.1 bits;  conditional E-value: 0.017
                         TPR_17  12 nadaynnLAelllknGdlmtA 32 
                                    +a ++nnL+ l++++G++  A
  gi|116754673|ref|YP_843791.1| 807 SAMVLNNLGLLYHRRGEWSLA 827
                                    799*************97665 PP

  == domain 16  score: 3.8 bits;  conditional E-value: 0.2
                         TPR_17  13 adaynnLAelllknGdl 29 
                                    a+ ++n+A +++ +G++
  gi|116754673|ref|YP_843791.1| 928 AETMFNMALIYRDRGEW 944
                                    999***********986 PP

  == domain 17  score: 1.5 bits;  conditional E-value: 1.1
                         TPR_17   4 kaleldPnnadaynnLAelll 24 
                                    +al+  P ++ +  nL+ l +
  gi|116754673|ref|YP_843791.1| 959 RALKASPCYSMSRLNLGLLKE 979
                                    79***************9865 PP

  == domain 18  score: -0.9 bits;  conditional E-value: 6
                         TPR_17   10 PnnadaynnLAelllknGdlmtAr 33  
                                     P+  +ay  +A++ l++G+  +Ar
  gi|116754673|ref|YP_843791.1| 1003 PDLCEAYLAMARVKLNRGEMSEAR 1026
                                     78899********99999866665 PP

  == domain 19  score: 4.4 bits;  conditional E-value: 0.12
                         TPR_17   14 daynnLAelllknGdlmtArq 34  
                                     +a+  L+ + l++Gd+++A++
  gi|116754673|ref|YP_843791.1| 1086 VALRSLGAASLNAGDYDEAEE 1106
                                     678899*************96 PP

  == domain 20  score: 1.8 bits;  conditional E-value: 0.85
                         TPR_17   16 ynnLAelllknGdlmtArq 34  
                                     y ++A+l+ +++d+ +A++
  gi|116754673|ref|YP_843791.1| 1128 YALMATLYFNRKDHSRAEE 1146
                                     8899************986 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0        10   4.7e+03      67     127 ..      66     124 ..      61     138 .. 0.75
   2 ?    2.8   0.2      0.24   1.1e+02      59     137 ..     139     211 ..     104     213 .. 0.82
   3 ?   -1.2   0.0       4.2     2e+03      24      49 ..     270     295 ..     254     334 .. 0.51
   4 ?    5.2   0.6     0.044        21      61     132 ..     333     406 ..     292     413 .. 0.82
   5 !    8.9   1.2    0.0031       1.5      52     139 ..     372     452 ..     326     456 .. 0.65
   6 ?    4.5   0.1     0.071        33      55     124 ..     414     478 ..     409     494 .. 0.73
   7 ?    4.6   0.2     0.065        31      55     129 ..     494     563 ..     463     566 .. 0.80
   8 ?    3.2   0.0      0.19        87      62     128 ..     611     676 ..     596     681 .. 0.83
   9 ?    5.5   0.1     0.036        17      22      90 ..     661     723 ..     650     727 .. 0.78
  10 !    9.3   0.1    0.0023       1.1      55      98 ..     728     771 ..     722     800 .. 0.79
  11 !   12.7   1.1   0.00022       0.1      27      99 ..     845     932 ..     826     949 .. 0.70
  12 ?    4.7   0.0     0.064        30      14      43 ..    1090    1119 ..    1081    1125 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 10
                                    HTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                        DUF3856  67 klgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmag 127
                                     lg   + l s ++a+ ++ r   le++ G   ++++ + +  ++++   d a+  +r a 
  gi|116754673|ref|YP_843791.1|  66 SLGMISQQLGSLERAVSHLSR--ALERASGADAVKVLSRLGSIYANVEDLDRAISLYRDAL 124
                                    577777788888888888887..47778888888888777888888888888888777765 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.24
                                    HHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH--S-- CS
                        DUF3856  59 aglsealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagemiaerkGel 137
                                      ls a+ + +r+d+al+++  a++ +   G+  +       +a+++ a    e+G  + a + +r+  e   er Ge+
  gi|116754673|ref|YP_843791.1| 139 INLSMAYREARRWDDALQCSSDAIYLLRSSGDRSS-----VARAIMEEAEIRREMGDLSSAEELYRTCLEEF-ERLGEI 211
                                    57999******************998888887544.....45788888888888888888888888877764.566665 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 4.2
                                    -HHHHHHHHHHHHHHHTTS-TTS--- CS
                        DUF3856  24 ayeeaaasyrkalevsrtipaeeafd 49 
                                    +++ a++ y kale  r ++  e+  
  gi|116754673|ref|YP_843791.1| 270 RFSSAEECYLKALEGFREVSDRESVA 295
                                    55555555555555555555544433 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.044
                                    HHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHH..HHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                        DUF3856  61 lsealaklgrydealesadkalryfnrrGeleqdeGklWiaav..fsravaleelGrkdealkafrmagemiae 132
                                    l+ al ++g     l+  + a +yf +  el ++ G+    a      ++ l++lG  d a+++++  +e++ e
  gi|116754673|ref|YP_843791.1| 333 LARALREMGTACYRLRDYEMAQNYFMKSLELSEALGERDGMAAshTGMGHMLSDLGDWDGAVEHYERGAELLRE 406
                                    77778888887788888899999999999999998877544440145677899999999999999999999987 PP

  == domain 5  score: 8.9 bits;  conditional E-value: 0.0031
                                    HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHH..HHHHHHHHTT-HHHHHHHHHHHHHH CS
                        DUF3856  52 GfdalchaglsealaklgrydealesadkalryfnrrGeleqdeGklWiaavf..sravaleelGrkdealkafrmagem 129
                                    G  a  h+g+ + l  lg++d a+e       +++r  el ++ G l  aa +  + a  ++ +G  ++al+ ++ a + 
  gi|116754673|ref|YP_843791.1| 372 G-MAASHTGMGHMLSDLGDWDGAVE-------HYERGAELLREMGDLRGAAACtsNIASVYQMMGDLEKALDIYHDALQ- 442
                                    3.34566666666666666666555.......55555555555555555444411445667889999999999998875. PP

                                    HHH--S--TT CS
                        DUF3856 130 iaerkGelkg 139
                                    i+er G+++g
  gi|116754673|ref|YP_843791.1| 443 IQERLGDMQG 452
                                    7899999887 PP

  == domain 6  score: 4.5 bits;  conditional E-value: 0.071
                                    HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHH CS
                        DUF3856  55 alchaglsealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafr 124
                                    a c + +++ +  +g+ ++al   + al+  +r G+++ +        + + +  ++ +G  + a +++ 
  gi|116754673|ref|YP_843791.1| 414 AACTSNIASVYQMMGDLEKALDIYHDALQIQERLGDMQGASKT-----LNNMGLVYQHMGEIEAAERNYM 478
                                    67999999***************************99876543.....3455555566666555555555 PP

  == domain 7  score: 4.6 bits;  conditional E-value: 0.065
                                    HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHH.HHHHHHHHTT-HHHHHHHHHHHHHH CS
                        DUF3856  55 alchaglsealaklgrydealesadkalryfnrrGeleqdeGklWiaavf.sravaleelGrkdealkafrmagem 129
                                    a +h  l+  +   +r+d+a++  + al+ f+  G+ +       +aav+ + +  +ee G   +a+k++rm+ e+
  gi|116754673|ref|YP_843791.1| 494 ANTHINLATLYEIQRRWDDAITHYQDALETFEAIGDRR------GMAAVMnNLGNVYEEKGDILQAIKSYRMSMEL 563
                                    66788999999999999999999999999999998753......3455551669999***************9985 PP

  == domain 8  score: 3.2 bits;  conditional E-value: 0.19
                                    HHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                        DUF3856  62 sealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmage 128
                                    + al++lg+        d al  f r  +l+ d  +  ++++ s a  +e  G  +eal ++r++ e
  gi|116754673|ref|YP_843791.1| 611 AYALMGLGSIALERGLWDDALDCFKRCVDLRLDTPE-ALRVLGSIASVYERKGMWQEALAEYRKVLE 676
                                    56777777766555667999999*999999999876.5899999999***************99987 PP

  == domain 9  score: 5.5 bits;  conditional E-value: 0.036
                                    HT-HHHHHHHHHHHHHHHTTS-TTS---HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH-- CS
                        DUF3856  22 egayeeaaasyrkalevsrtipaeeafdheGfdalchaglsealaklgrydealesadkalryfnrrGe 90 
                                    +g ++ea a+yrk le  r +      d  G  a + +++ + la+ g++d+ale   ++l+ f+r G+
  gi|116754673|ref|YP_843791.1| 661 KGMWQEALAEYRKVLERFRGMG-----DSLGVAA-VLSTIGNLLAEQGHWDDALEHYSESLEIFERLGD 723
                                    6778888888888888888876.....5566655.4577888899999999999999999999999886 PP

  == domain 10  score: 9.3 bits;  conditional E-value: 0.0023
                                    HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHH CS
                        DUF3856  55 alchaglsealaklgrydealesadkalryfnrrGeleqdeGkl 98 
                                    a++   +++ l + g++d al+   ka+++f r G++++ +  l
  gi|116754673|ref|YP_843791.1| 728 AVTTNNMANVLYRRGEWDRALNLYSKAMEHFQRVGDMHSYGATL 771
                                    5667789999****************************977665 PP

  == domain 11  score: 12.7 bits;  conditional E-value: 0.00022
                                    HHHHHHHHHHHHHTTS-TTS---HHHH...............HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--T CS
                        DUF3856  27 eaaasyrkalevsrtipaeeafdheGf...............dalchaglsealaklgrydealesadkalryfnrrGel 91 
                                    eaa ++r  +++ r+   e + d +G+                a +h  l++a+a + r++eal   +k+l+ f+r G+ 
  gi|116754673|ref|YP_843791.1| 845 EAATEFRANIDMVRSCRGEASVDIDGYlkkleeieragdvemAAEMHGILANAYADIFRWEEALDHYQKSLELFERTGDR 924
                                    566666666666666666666666665444433333332222467899******************************97 PP

                                    TSTHHHHH CS
                        DUF3856  92 eqdeGklW 99 
                                     ++   ++
  gi|116754673|ref|YP_843791.1| 925 YSAAETMF 932
                                    66555444 PP

  == domain 12  score: 4.7 bits;  conditional E-value: 0.064
                                     HHHHHHHHHT-HHHHHHHHHHHHHHHTTS- CS
                        DUF3856   14 seaekqleegayeeaaasyrkalevsrtip 43  
                                     s +   l++g y+ea+++ +kal++ ++i 
  gi|116754673|ref|YP_843791.1| 1090 SLGAASLNAGDYDEAEEHLQKALTLFKSIN 1119
                                     557788999999***999999999999886 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 ?   -1.7   0.0       7.6   3.6e+03      37      49 ..     111     123 ..      73     161 .. 0.53
   2 ?    3.3   0.2      0.21        99       6      75 ..     272     353 ..     267     360 .. 0.56
   3 ?   -0.2   0.1       2.5   1.2e+03      30      79 ..     341     397 ..     322     400 .. 0.57
   4 ?   -0.2   0.0       2.5   1.2e+03      30      49 ..     421     440 ..     388     449 .. 0.73
   5 ?    4.5   0.2     0.087        41      37      81 ..     475     519 ..     437     520 .. 0.82
   6 ?    2.8   0.0       0.3   1.4e+02      18      79 ..     606     671 ..     585     674 .. 0.69
   7 ?    0.8   0.0       1.3   5.9e+02       8      79 ..     630     711 ..     623     714 .. 0.45
   8 !    8.4   0.1    0.0051       2.4      29      49 ..     734     754 ..     700     763 .. 0.66
   9 ?    7.0   0.0     0.015         7      30      49 ..     775     794 ..     763     802 .. 0.86
  10 ?    1.0   0.0       1.1     5e+02      59      81 ..     891     913 ..     878     914 .. 0.84
  11 ?    4.7   0.0     0.077        36       5      72 ..     911     972 ..     900     977 .. 0.74
  12 ?   -0.8   0.0       3.9   1.8e+03       8      49 ..     992    1032 ..     987    1038 .. 0.62
  13 !    9.5   0.2    0.0024       1.2      27      82 .]    1055    1111 ..    1054    1111 .. 0.84
  14 ?    4.5   0.4     0.084        40      21      77 ..    1122    1186 ..    1112    1191 .. 0.66

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 7.6
                                    T-HHHHHHHHHCT CS
                         ANAPC3  37 gqykrAyellrka 49 
                                    ++ +rA+ l+r+a
  gi|116754673|ref|YP_843791.1| 111 EDLDRAISLYRDA 123
                                    4444444444444 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.21
                                    HHHHHHHHHHH......HHH--HHHHHH.HHHHHHHTT-.......HHHHHHHHHCTSHHHC-H.HHHHHHHHHHHHTT- CS
                         ANAPC3   6 knAiflaerlla.....aetespedayl.lAlclylngq.......ykrAyellrkaklnsksl.gcrylfAqcllkLkk 71 
                                     +A+ ++ ++l+     +++es  +++l lA  + ++g+       y +A+++l++   +s++l +++  ++ +++ L  
  gi|116754673|ref|YP_843791.1| 272 SSAEECYLKALEgfrevSDRESVANTLLsLARLYGSMGEwrgaverYREALDILQSE--QSQDLaRALREMGTACYRLRD 349
                                    566666666663333345566655655547888888888333333355555555555..223334666666677777777 PP

                                    HHHH CS
                         ANAPC3  72 yeeA 75 
                                    ye A
  gi|116754673|ref|YP_843791.1| 350 YEMA 353
                                    7766 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 2.5
                                    HHHHHHTT-HHHHHHHHHCT.SHHHC-H.......HHHHHHHHHHHHTT-HHHHHHHH CS
                         ANAPC3  30 AlclylngqykrAyellrka.klnsksl.......gcrylfAqcllkLkkyeeAiaaL 79 
                                    + + y++ +y+ A++++ k+ +l s+ l       +++  +++ l +L+ ++ A+ ++
  gi|116754673|ref|YP_843791.1| 341 GTACYRLRDYEMAQNYFMKSlEL-SEALgerdgmaASHTGMGHMLSDLGDWDGAVEHY 397
                                    56677777777777776655222.2111122222255555666666666666666665 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 2.5
                                    HHHHHHTT-HHHHHHHHHCT CS
                         ANAPC3  30 AlclylngqykrAyellrka 49 
                                    A ++  +g+ ++A++++++a
  gi|116754673|ref|YP_843791.1| 421 ASVYQMMGDLEKALDIYHDA 440
                                    67777788888888877766 PP

  == domain 5  score: 4.5 bits;  conditional E-value: 0.087
                                    T-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                         ANAPC3  37 gqykrAyellrkaklnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                     +y r++el ++++  +   + ++ +A  +  + ++++Ai++++ 
  gi|116754673|ref|YP_843791.1| 475 RNYMRCLELKEQLGDVHGAANTHINLATLYEIQRRWDDAITHYQD 519
                                    5699*********88888889999999999999********9875 PP

  == domain 6  score: 2.8 bits;  conditional E-value: 0.3
                                    HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHH..HHHHHT.T-HHHHHHHH CS
                         ANAPC3  18 aetespedayllAlclylngqykrAyellrka.klnskslgcrylfA..qcllkL.kkyeeAiaaL 79 
                                     e+  +++++ l+   +++g ++ A++ ++++ +l+  +++++ +++   + ++  + ++eA+a +
  gi|116754673|ref|YP_843791.1| 606 DERGAAYALMGLGSIALERGLWDDALDCFKRCvDLRLDTPEALRVLGsiASVYERkGMWQEALAEY 671
                                    455555666667999999999999999999999999999999988884422232247888888765 PP

  == domain 7  score: 0.8 bits;  conditional E-value: 1.3
                                    HHHHHHHHH.HHH--HHHHHHH...HHHHHHTT-HHHHHHHHHCT.SHHHC-H.......HHHHHHHHHHHHTT-HHHHH CS
                         ANAPC3   8 Aiflaerllaaetespedayll...AlclylngqykrAyellrka.klnsksl.......gcrylfAqcllkLkkyeeAi 76 
                                    A+ ++ r +    + pe++  l   A ++ + g +++A+  +rk  + + + +       +++ +++  l +++++++A+
  gi|116754673|ref|YP_843791.1| 630 ALDCFKRCVDLRLDTPEALRVLgsiASVYERKGMWQEALAEYRKVlE-RFRGMgdslgvaAVLSTIGNLLAEQGHWDDAL 708
                                    44444444444444444444444445555555666666554444422.22222111222223333335566777777777 PP

                                    HHH CS
                         ANAPC3  77 aaL 79 
                                     ++
  gi|116754673|ref|YP_843791.1| 709 EHY 711
                                    766 PP

  == domain 8  score: 8.4 bits;  conditional E-value: 0.0051
                                    HHHHHHHTT-HHHHHHHHHCT CS
                         ANAPC3  29 lAlclylngqykrAyellrka 49 
                                     A +ly++g+++rA++l++ka
  gi|116754673|ref|YP_843791.1| 734 MANVLYRRGEWDRALNLYSKA 754
                                    49***************9998 PP

  == domain 9  score: 7.0 bits;  conditional E-value: 0.015
                                    HHHHHHTT-HHHHHHHHHCT CS
                         ANAPC3  30 AlclylngqykrAyellrka 49 
                                    A  +y++g+++rA+el++k+
  gi|116754673|ref|YP_843791.1| 775 ASIHYRRGEWERAIELYHKS 794
                                    889*************9997 PP

  == domain 10  score: 1.0 bits;  conditional E-value: 1.1
                                    HHHHHHHHHHTT-HHHHHHHH-S CS
                         ANAPC3  59 rylfAqcllkLkkyeeAiaaLek 81 
                                    + ++A ++ ++ ++eeA+++++k
  gi|116754673|ref|YP_843791.1| 891 HGILANAYADIFRWEEALDHYQK 913
                                    568999999***********987 PP

  == domain 11  score: 4.7 bits;  conditional E-value: 0.077
                                    HHHHHHHHHHHH.HHH--HHHHHH.HHHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-H CS
                         ANAPC3   5 yknAiflaerllaaetespedayl.lAlclylngqykrAyellrkaklnskslgcrylfAqcllkLkky 72 
                                    y++ + l+er    +++s+  +++  Al +  +g++  A +ll+++       + r l+A  ++ ++++
  gi|116754673|ref|YP_843791.1| 911 YQKSLELFERTG--DRYSAAETMFnMALIYRDRGEWSIAEDLLSRS-----MSEFRALKASPCYSMSRL 972
                                    555555666665..666666666636******************99.....556888888888877766 PP

  == domain 12  score: -0.8 bits;  conditional E-value: 3.9
                                     HHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT CS
                         ANAPC3    8 AiflaerllaaetespedayllAlclylngqykrAyellrka 49  
                                     Ai  +e +  a ++ +e+ ++ A + +++g+  +A  +l++a
  gi|116754673|ref|YP_843791.1|  992 AITTFESIG-AIPDLCEAYLAMARVKLNRGEMSEARFYLSEA 1032
                                     455555555.55666666666677777777776666666655 PP

  == domain 13  score: 9.5 bits;  conditional E-value: 0.0024
                                     HHHHHHHHHTT-.HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-SS CS
                         ANAPC3   27 yllAlclylngq.ykrAyellrkaklnskslgcrylfAqcllkLkkyeeAiaaLekl 82  
                                     ++l+++ +++   y++A+ l+rk++l      ++  ++ ++l  + y+eA+ +L+k+
  gi|116754673|ref|YP_843791.1| 1055 FYLSQAPFEARSsYQKALALARKMGLTRDEGVALRSLGAASLNAGDYDEAEEHLQKA 1111
                                     5677888877666***********77777777888899999*************985 PP

  == domain 14  score: 4.5 bits;  conditional E-value: 0.084
                                     --HHHHHHH.HHHHHHTT-HHHHHHHHHCTSHHHC-H.......HHHHHHHHHHHHTT-HHHHHH CS
                         ANAPC3   21 espedayll.AlclylngqykrAyellrkaklnsksl.......gcrylfAqcllkLkkyeeAia 77  
                                     +++ ++y+l A  +++++++ rA e +  ++ + + l       +++ ++A c l+ ++ + A++
  gi|116754673|ref|YP_843791.1| 1122 YDLLSTYALmATLYFNRKDHSRAEETALLLERQARRLgyrdlqvKALEVIAGCELATSRTDAAVS 1186
                                     6777889988************9987654433333332333355666666666666666666655 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   2.9e-05     0.013      25      67 ..      57      99 ..      32     104 .. 0.84
   2 ?   -0.3   0.0       2.7   1.3e+03      41      62 ..     102     123 ..      98     129 .. 0.69
   3 !    7.9   1.1    0.0073       3.5       3      57 ..     143     203 ..     141     209 .. 0.91
   4 ?    4.2   0.4       0.1        48      35      70 ..     301     336 ..     293     342 .. 0.73
   5 ?    1.2   0.1      0.88   4.1e+02      27      61 ..     332     366 ..     330     375 .. 0.82
   6 ?   -0.5   0.1       3.1   1.4e+03      42      60 ..     387     405 ..     380     418 .. 0.51
   7 ?    0.6   0.5       1.4   6.4e+02      36      58 ..     421     443 ..     389     458 .. 0.66
   8 !    9.2   0.4    0.0028       1.3      34      66 ..     459     491 ..     420     496 .. 0.83
   9 ?    3.1   0.1      0.23   1.1e+02       3      69 ..     542     615 ..     540     617 .. 0.72
  10 !   10.6   0.4     0.001      0.47       2      56 ..     618     675 ..     617     684 .. 0.83
  11 ?   -1.2   0.0       4.8   2.2e+03      36      51 ..     695     710 ..     693     723 .. 0.69
  12 ?   -2.1   0.0       9.1   4.3e+03      37      51 ..     736     750 ..     731     759 .. 0.66
  13 !    8.7   1.0    0.0041       1.9       2      68 ..     775     847 ..     774     852 .. 0.83
  14 ?   -0.3   0.2       2.7   1.3e+03       3      50 ..     896     949 ..     894     956 .. 0.71
  15 ?    0.9   0.0       1.1   5.1e+02      26      53 ..    1003    1030 ..     986    1032 .. 0.86
  16 ?   -0.7   0.2       3.5   1.6e+03      32      54 ..    1088    1110 ..    1066    1115 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.9e-05
                          TPR_9 25 aPddpeerrdRGlllaqlGclsaAladLeaylalapdapdaea 67
                                   a++d+++++  G++ +qlG l+ A+  L ++l+ a  a+++  
  gi|116754673|ref|YP_843791.1| 57 ASRDHSLWFSLGMISQQLGSLERAVSHLSRALERASGADAVKV 99
                                   6799*****************************9976655544 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 2.7
                          TPR_9  41 qlGclsaAladLeaylalapda 62 
                                    +lG + a ++dL+++++l  da
  gi|116754673|ref|YP_843791.1| 102 RLGSIYANVEDLDRAISLYRDA 123
                                    6677777777777777776655 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0073
                          TPR_9   3 aiaireedweralavverllll......aPddpeerrdRGlllaqlGclsaAladLeayla 57 
                                     ++ ++++w+ al+++   ++l       +  ++ +++ + ++ ++G+ls A +   ++l+
  gi|116754673|ref|YP_843791.1| 143 MAYREARRWDDALQCSSDAIYLlrssgdRSSVARAIMEEAEIRREMGDLSSAEELYRTCLE 203
                                    57999***********9999999*****************************988888776 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.1
                          TPR_9  35 RGlllaqlGclsaAladLeaylalapdapdaeaira 70 
                                     ++l+  +G +++A++    +l++  + +  +++ra
  gi|116754673|ref|YP_843791.1| 301 LARLYGSMGEWRGAVERYREALDILQSEQSQDLARA 336
                                    6999******************66553333333333 PP

  == domain 5  score: 1.2 bits;  conditional E-value: 0.88
                          TPR_9  27 ddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                    d ++ +r+ G + ++l +++ A + +   l+l+++
  gi|116754673|ref|YP_843791.1| 332 DLARALREMGTACYRLRDYEMAQNYFMKSLELSEA 366
                                    568999****************9999888887775 PP

  == domain 6  score: -0.5 bits;  conditional E-value: 3.1
                          TPR_9  42 lGclsaAladLeaylalap 60 
                                    lG++ +A++  e+ ++l  
  gi|116754673|ref|YP_843791.1| 387 LGDWDGAVEHYERGAELLR 405
                                    5555555555555443333 PP

  == domain 7  score: 0.6 bits;  conditional E-value: 1.4
                          TPR_9  36 GlllaqlGclsaAladLeaylal 58 
                                    + +++ +G+l++Al+    +l++
  gi|116754673|ref|YP_843791.1| 421 ASVYQMMGDLEKALDIYHDALQI 443
                                    45556666666665555555544 PP

  == domain 8  score: 9.2 bits;  conditional E-value: 0.0028
                          TPR_9  34 dRGlllaqlGclsaAladLeaylalapdapdae 66 
                                      Gl+++++G ++aA +   ++l+l ++  d++
  gi|116754673|ref|YP_843791.1| 459 NMGLVYQHMGEIEAAERNYMRCLELKEQLGDVH 491
                                    57**********************999877765 PP

  == domain 9  score: 3.1 bits;  conditional E-value: 0.23
                          TPR_9   3 aiaireedweralavverllll...aPddpeerrdRGlllaqlGclsaA....ladLeaylalapdapdaeair 69 
                                    +++ ++ d  +a++ + + + l   +   +   +  G l+++ G+ + A    +a Lea+ ++ +++ +a+a++
  gi|116754673|ref|YP_843791.1| 542 NVYEEKGDILQAIKSYRMSMELdggDASIAKISWNLGGLYQRIGDAESAekcyRASLEAFQSIGDERGAAYALM 615
                                    56777777777777777777773333333445688999999999999995555567888889999999999887 PP

  == domain 10  score: 10.6 bits;  conditional E-value: 0.001
                          TPR_9   2 kaiaireedweralavverllllaPddpeerrdRG...lllaqlGclsaAladLeayl 56 
                                     +ia+++  w+ al +  r + l  d+pe +r  G    ++++ G +++Ala+    l
  gi|116754673|ref|YP_843791.1| 618 GSIALERGLWDDALDCFKRCVDLRLDTPEALRVLGsiaSVYERKGMWQEALAEYRKVL 675
                                    6899*******************888888888765222689**********9987655 PP

  == domain 11  score: -1.2 bits;  conditional E-value: 4.8
                          TPR_9  36 GlllaqlGclsaAlad 51 
                                    G lla++G++  Al+ 
  gi|116754673|ref|YP_843791.1| 695 GNLLAEQGHWDDALEH 710
                                    5567777777777654 PP

  == domain 12  score: -2.1 bits;  conditional E-value: 9.1
                          TPR_9  37 lllaqlGclsaAlad 51 
                                     +l+++G +  Al+ 
  gi|116754673|ref|YP_843791.1| 736 NVLYRRGEWDRALNL 750
                                    466777777777654 PP

  == domain 13  score: 8.7 bits;  conditional E-value: 0.0041
                          TPR_9   2 kaiaireedweralavverllll......aPddpeerrdRGlllaqlGclsaAladLeaylalapdapdaeai 68 
                                     +i+ r+ +wera++ +   l +         ++  +   Gll++++G +s A++ +  +++ a  a d ea+
  gi|116754673|ref|YP_843791.1| 775 ASIHYRRGEWERAIELYHKSLEIfegledSGASAMVLNNLGLLYHRRGEWSLAVDHFRLAAECAMRAGDHEAA 847
                                    578999999999999999999998888866667888889******************9999877777766665 PP

  == domain 14  score: -0.3 bits;  conditional E-value: 2.7
                          TPR_9   3 aiaireedweralavverllll......aPddpeerrdRGlllaqlGclsaAla 50 
                                    ++++   +we+al  ++  l l         ++e  +  +l++  +G +s A +
  gi|116754673|ref|YP_843791.1| 896 NAYADIFRWEEALDHYQKSLELfertgdRYSAAETMFNMALIYRDRGEWSIAED 949
                                    566666788888888888888877777666677777788888888888877765 PP

  == domain 15  score: 0.9 bits;  conditional E-value: 1.1
                          TPR_9   26 PddpeerrdRGlllaqlGclsaAladLe 53  
                                     Pd +e ++  +++   +G +s+A++ L 
  gi|116754673|ref|YP_843791.1| 1003 PDLCEAYLAMARVKLNRGEMSEARFYLS 1030
                                     8889999999**************9996 PP

  == domain 16  score: -0.7 bits;  conditional E-value: 3.5
                          TPR_9   32 rrdRGlllaqlGclsaAladLea 54  
                                     +r  G +    G++ +A + L+ 
  gi|116754673|ref|YP_843791.1| 1088 LRSLGAASLNAGDYDEAEEHLQK 1110
                                     34445555555555555555555 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.67   3.1e+02       4      25 ..     218     239 ..     216     240 .. 0.87
   2 ?    0.3   0.0       3.4   1.6e+03       2      22 ..     256     276 ..     255     278 .. 0.83
   3 ?    1.8   0.1       1.1   5.2e+02       3      26 .]     297     320 ..     295     320 .. 0.89
   4 !    8.5   0.0    0.0078       3.7       2      26 .]     375     399 ..     374     399 .. 0.91
   5 ?   -0.7   0.2       7.2   3.4e+03       8      22 ..     401     415 ..     401     417 .. 0.91
   6 ?   -0.1   0.0       4.6   2.2e+03       8      23 ..     421     436 ..     414     438 .. 0.79
   7 ?    1.8   0.0       1.1   5.3e+02       6      22 ..     459     475 ..     456     475 .. 0.89
   8 ?    3.1   0.1      0.41   1.9e+02       1      23 [.     611     633 ..     611     636 .. 0.89
   9 ?    5.7   0.1     0.059        28       8      23 ..     695     710 ..     688     713 .. 0.87
  10 !    8.3   0.0    0.0089       4.2       2      22 ..     729     749 ..     728     751 .. 0.86
  11 ?    0.7   0.0       2.5   1.2e+03       9      23 ..     776     790 ..     769     793 .. 0.80
  12 ?    5.9   0.1     0.051        24       3      25 ..     810     832 ..     808     833 .. 0.87
  13 ?    1.5   1.2       1.4   6.5e+02       7      21 ..     834     848 ..     832     851 .. 0.86
  14 ?   -0.8   0.0       7.4   3.5e+03       3      24 ..     930     951 ..     928     953 .. 0.78
  15 !   12.4   0.2   0.00041      0.19       2      25 ..    1086    1109 ..    1085    1110 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.67
                          TPR_4   4 llaLArallalGdldeAralle 25 
                                    l +L+r  +++G++ +A++l++
  gi|116754673|ref|YP_843791.1| 218 LEMLGRISQLRGESRRAEDLFD 239
                                    67899*************9975 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 3.4
                          TPR_4   2 rallaLArallalGdldeAra 22 
                                    r++l+L+ +++  G++  A++
  gi|116754673|ref|YP_843791.1| 256 RTALLLGDLHAIEGRFSSAEE 276
                                    678999999999999987775 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 1.1
                          TPR_4   3 allaLArallalGdldeAraller 26 
                                    +ll LAr++   G++  A +  ++
  gi|116754673|ref|YP_843791.1| 297 TLLSLARLYGSMGEWRGAVERYRE 320
                                    6899**************999886 PP

  == domain 4  score: 8.5 bits;  conditional E-value: 0.0078
                          TPR_4   2 rallaLArallalGdldeAraller 26 
                                    + + +++  l +lGd+d A ++ er
  gi|116754673|ref|YP_843791.1| 375 ASHTGMGHMLSDLGDWDGAVEHYER 399
                                    678999****************997 PP

  == domain 5  score: -0.7 bits;  conditional E-value: 7.2
                          TPR_4   8 ArallalGdldeAra 22 
                                    A++l + Gdl  A+a
  gi|116754673|ref|YP_843791.1| 401 AELLREMGDLRGAAA 415
                                    89999********98 PP

  == domain 6  score: -0.1 bits;  conditional E-value: 4.6
                          TPR_4   8 ArallalGdldeAral 23 
                                    A +++  Gdl+ A+++
  gi|116754673|ref|YP_843791.1| 421 ASVYQMMGDLEKALDI 436
                                    7789999******986 PP

  == domain 7  score: 1.8 bits;  conditional E-value: 1.1
                          TPR_4   6 aLArallalGdldeAra 22 
                                    +++ ++++ G+ ++A++
  gi|116754673|ref|YP_843791.1| 459 NMGLVYQHMGEIEAAER 475
                                    7899***********97 PP

  == domain 8  score: 3.1 bits;  conditional E-value: 0.41
                          TPR_4   1 arallaLArallalGdldeAral 23 
                                    a+al +L+  +l++G +d+A++ 
  gi|116754673|ref|YP_843791.1| 611 AYALMGLGSIALERGLWDDALDC 633
                                    579999**************986 PP

  == domain 9  score: 5.7 bits;  conditional E-value: 0.059
                          TPR_4   8 ArallalGdldeAral 23 
                                    + +l+++G++d+A+++
  gi|116754673|ref|YP_843791.1| 695 GNLLAEQGHWDDALEH 710
                                    578***********98 PP

  == domain 10  score: 8.3 bits;  conditional E-value: 0.0089
                          TPR_4   2 rallaLArallalGdldeAra 22 
                                    +++ ++A +l+++G++d+A+ 
  gi|116754673|ref|YP_843791.1| 729 VTTNNMANVLYRRGEWDRALN 749
                                    567799*************86 PP

  == domain 11  score: 0.7 bits;  conditional E-value: 2.5
                          TPR_4   9 rallalGdldeAral 23 
                                      ++++G++++A +l
  gi|116754673|ref|YP_843791.1| 776 SIHYRRGEWERAIEL 790
                                    5799*******9766 PP

  == domain 12  score: 5.9 bits;  conditional E-value: 0.051
                          TPR_4   3 allaLArallalGdldeAralle 25 
                                    +l +L+ +++++G++  A ++++
  gi|116754673|ref|YP_843791.1| 810 VLNNLGLLYHRRGEWSLAVDHFR 832
                                    6789***********99999876 PP

  == domain 13  score: 1.5 bits;  conditional E-value: 1.4
                          TPR_4   7 LArallalGdldeAr 21 
                                     A+ + ++Gd+++A 
  gi|116754673|ref|YP_843791.1| 834 AAECAMRAGDHEAAT 848
                                    799999*******95 PP

  == domain 14  score: -0.8 bits;  conditional E-value: 7.4
                          TPR_4   3 allaLArallalGdldeArall 24 
                                    +  ++A  + ++G++  A++ll
  gi|116754673|ref|YP_843791.1| 930 TMFNMALIYRDRGEWSIAEDLL 951
                                    67899********986666665 PP

  == domain 15  score: 12.4 bits;  conditional E-value: 0.00041
                          TPR_4    2 rallaLArallalGdldeAralle 25  
                                     +al  L+ a l +Gd+deA+++l+
  gi|116754673|ref|YP_843791.1| 1086 VALRSLGAASLNAGDYDEAEEHLQ 1109
                                     68999*****************97 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       3.2   1.5e+03       8      25 ..     105     122 ..     102     126 .. 0.85
   2 ?    0.8   0.0       1.5   7.3e+02       5      25 ..     300     320 ..     297     323 .. 0.85
   3 ?   -1.2   0.1       6.6   3.1e+03       9      25 ..     343     359 ..     340     363 .. 0.85
   4 ?   -1.2   0.0       6.9   3.2e+03       9      24 ..     383     398 ..     376     408 .. 0.73
   5 ?    2.7   0.0      0.39   1.8e+02       8      25 ..     422     439 ..     418     442 .. 0.84
   6 ?    2.1   0.0      0.59   2.8e+02      13      27 ..     624     638 ..     622     642 .. 0.85
   7 ?    2.0   0.0      0.66   3.1e+02       5      20 ..     653     668 ..     650     669 .. 0.87
   8 ?   -0.1   0.0         3   1.4e+03       8      25 ..     696     713 ..     691     717 .. 0.83
   9 !    7.9   0.0    0.0087       4.1       1      25 [.     729     753 ..     729     757 .. 0.91
  10 ?    3.6   0.0       0.2        93       6      25 ..     774     793 ..     769     797 .. 0.82
  11 ?    0.3   0.0       2.3   1.1e+03       5      25 ..     893     913 ..     889     917 .. 0.84
  12 ?   -0.4   0.0       3.7   1.7e+03      13      24 ..    1098    1109 ..    1094    1117 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 3.2
                            PPR   8 sgycknGkleeAlelfke 25 
                                    s y+   +l+ A++l+++
  gi|116754673|ref|YP_843791.1| 105 SIYANVEDLDRAISLYRD 122
                                    5799999********987 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1.5
                            PPR   5 slIsgycknGkleeAlelfke 25 
                                    sl + y++ G+++ A+e ++e
  gi|116754673|ref|YP_843791.1| 300 SLARLYGSMGEWRGAVERYRE 320
                                    78899**********997766 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 6.6
                            PPR   9 gycknGkleeAlelfke 25 
                                    ++ + +++e+A  +f +
  gi|116754673|ref|YP_843791.1| 343 ACYRLRDYEMAQNYFMK 359
                                    899********999976 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 6.9
                            PPR   9 gycknGkleeAlelfk 24 
                                     ++  G+++ A+e ++
  gi|116754673|ref|YP_843791.1| 383 MLSDLGDWDGAVEHYE 398
                                    6677788888887665 PP

  == domain 5  score: 2.7 bits;  conditional E-value: 0.39
                            PPR   8 sgycknGkleeAlelfke 25 
                                    s+y   G+le+Al+++++
  gi|116754673|ref|YP_843791.1| 422 SVYQMMGDLEKALDIYHD 439
                                    677789*********985 PP

  == domain 6  score: 2.1 bits;  conditional E-value: 0.59
                            PPR  13 nGkleeAlelfkeMk 27 
                                     G++++Al++fk+ +
  gi|116754673|ref|YP_843791.1| 624 RGLWDDALDCFKRCV 638
                                    59*********9865 PP

  == domain 7  score: 2.0 bits;  conditional E-value: 0.66
                            PPR   5 slIsgycknGkleeAl 20 
                                    s+ s+y ++G+++eAl
  gi|116754673|ref|YP_843791.1| 653 SIASVYERKGMWQEAL 668
                                    56789**********8 PP

  == domain 8  score: -0.1 bits;  conditional E-value: 3
                            PPR   8 sgycknGkleeAlelfke 25 
                                    + ++  G +++Ale + e
  gi|116754673|ref|YP_843791.1| 696 NLLAEQGHWDDALEHYSE 713
                                    678999*******98877 PP

  == domain 9  score: 7.9 bits;  conditional E-value: 0.0087
                            PPR   1 vtynslIsgycknGkleeAlelfke 25 
                                    vt n + +++ + G+++ Al l+ +
  gi|116754673|ref|YP_843791.1| 729 VTTNNMANVLYRRGEWDRALNLYSK 753
                                    788*******************987 PP

  == domain 10  score: 3.6 bits;  conditional E-value: 0.2
                            PPR   6 lIsgycknGkleeAlelfke 25 
                                    + s + + G++e A+el+++
  gi|116754673|ref|YP_843791.1| 774 IASIHYRRGEWERAIELYHK 793
                                    5677889***********87 PP

  == domain 11  score: 0.3 bits;  conditional E-value: 2.3
                            PPR   5 slIsgycknGkleeAlelfke 25 
                                    +l ++y+   ++eeAl+ +++
  gi|116754673|ref|YP_843791.1| 893 ILANAYADIFRWEEALDHYQK 913
                                    788999999*******97765 PP

  == domain 12  score: -0.4 bits;  conditional E-value: 3.7
                            PPR   13 nGkleeAlelfk 24  
                                     +G+++eA+e ++
  gi|116754673|ref|YP_843791.1| 1098 AGDYDEAEEHLQ 1109
                                     799999998665 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       4.3     2e+03       7      27 ..     103     121 ..      99     121 .. 0.86
   2 ?   -2.0   0.0       8.4     4e+03      14      27 ..     188     199 ..     187     199 .. 0.86
   3 !    9.3   0.1    0.0024       1.1       8      25 ..     421     438 ..     420     444 .. 0.91
   4 ?   -2.0   0.0       7.9   3.7e+03       8      21 ..     461     474 ..     460     477 .. 0.86
   5 ?   -2.2   0.0       9.7   4.6e+03      14      33 ..     547     564 ..     544     564 .. 0.85
   6 ?   -1.6   0.0       6.2   2.9e+03      10      25 ..     737     752 ..     735     753 .. 0.85
   7 ?   -1.1   0.0       4.4   2.1e+03      12      30 ..     779     795 ..     765     799 .. 0.72
   8 ?   -1.8   0.0         7   3.3e+03      15      33 ..     923     939 ..     922     940 .. 0.83
   9 ?    4.2   0.1     0.091        43       7      34 ..    1091    1116 ..    1088    1117 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 4.3
                                    HHHHHHHTT-HHHHHHH..HH CS
                          TPR_3   7 yAaefynkkkyqeArelfsYa 27 
                                    ++  + n ++++ A+ l  Y+
  gi|116754673|ref|YP_843791.1| 103 LGSIYANVEDLDRAISL--YR 121
                                    7889999**********..75 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 8.4
                                    TT-HHHHHHH..HH CS
                          TPR_3  14 kkkyqeArelfsYa 27 
                                    +++++ A+el  Y+
  gi|116754673|ref|YP_843791.1| 188 MGDLSSAEEL--YR 199
                                    8999******..75 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0024
                                    HHHHHHTT-HHHHHHH.. CS
                          TPR_3   8 AaefynkkkyqeArelfs 25 
                                    A ++++++++++A++ ++
  gi|116754673|ref|YP_843791.1| 421 ASVYQMMGDLEKALDIYH 438
                                    889*************66 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 7.9
                                    HHHHHHTT-HHHHH CS
                          TPR_3   8 AaefynkkkyqeAr 21 
                                    + +++ +++++ A+
  gi|116754673|ref|YP_843791.1| 461 GLVYQHMGEIEAAE 474
                                    5799*******997 PP

  == domain 5  score: -2.2 bits;  conditional E-value: 9.7
                                    TT-HHHHHHH..HHHHHHH- CS
                          TPR_3  14 kkkyqeArelfsYallaild 33 
                                    k+++ +A+    Y+ +  ld
  gi|116754673|ref|YP_843791.1| 547 KGDILQAIKS--YRMSMELD 564
                                    99******99..98887775 PP

  == domain 6  score: -1.6 bits;  conditional E-value: 6.2
                                    HHHHTT-HHHHHHH.. CS
                          TPR_3  10 efynkkkyqeArelfs 25 
                                    ++y  ++ + A++l+s
  gi|116754673|ref|YP_843791.1| 737 VLYRRGEWDRALNLYS 752
                                    6788899999****88 PP

  == domain 7  score: -1.1 bits;  conditional E-value: 4.4
                                    HHTT-HHHHHHH..HHHHH CS
                          TPR_3  12 ynkkkyqeArelfsYalla 30 
                                    y  ++ + A+el++   + 
  gi|116754673|ref|YP_843791.1| 779 YRRGEWERAIELYH--KSL 795
                                    555667789***55..555 PP

  == domain 8  score: -1.8 bits;  conditional E-value: 7
                                    T-HHHHHHH..HHHHHHH- CS
                          TPR_3  15 kkyqeArelfsYallaild 33 
                                    ++y+ A+  f    + i++
  gi|116754673|ref|YP_843791.1| 923 DRYSAAETMFN--MALIYR 939
                                    69*******55..999997 PP

  == domain 9  score: 4.2 bits;  conditional E-value: 0.091
                                     HHHHHHHTT-HHHHHHH..HHHHHHH-T CS
                          TPR_3    7 yAaefynkkkyqeArelfsYallaildk 34  
                                     ++a+  n ++y+eA+e ++   + +l+k
  gi|116754673|ref|YP_843791.1| 1091 LGAASLNAGDYDEAEEHLQ--KALTLFK 1116
                                     66666688********999..8888887 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 ?   -0.1   0.0       1.2   5.8e+02     160     223 ..     107     168 ..      87     179 .. 0.83
   2 ?    1.8   0.4      0.32   1.5e+02     171     223 ..     276     328 ..     271     362 .. 0.81
   3 ?    2.5   0.0       0.2        93     170     215 ..     394     439 ..     375     446 .. 0.79
   4 ?   -0.6   0.0       1.7   7.9e+02     167     216 ..     511     560 ..     500     576 .. 0.88
   5 ?    1.5   0.0      0.38   1.8e+02     162     215 ..     583     636 ..     571     643 .. 0.89
   6 ?   -2.7   0.0       7.7   3.6e+03     195     220 ..     653     678 ..     647     682 .. 0.81
   7 ?    6.6   0.0     0.011       5.2     165     217 ..     703     755 ..     696     762 .. 0.89
   8 !    9.2   0.1    0.0017       0.8     165     214 ..     743     792 ..     739     798 .. 0.88
   9 ?    2.8   0.0      0.15        72     212     249 ..     810     847 ..     801     854 .. 0.86
  10 !    7.1   0.3    0.0077       3.6     165     221 ..     903     959 ..     877     962 .. 0.89
  11 ?   -0.7   0.3       1.8   8.5e+02     174     219 ..    1069    1114 ..    1063    1193 .. 0.65

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.2
                    Foie-gras_1 160 ekgvahskliidlLekaleeFskrkqtRlaeelsleiAeeylrlgdwkkalellqpltlsyrke 223
                                    + +v++   +i l++ al   ++ + +R    + l +A  y ++++w++al+  + +  ++r++
  gi|116754673|ref|YP_843791.1| 107 YANVEDLDRAISLYRDALSRLESGDPERAGILINLSMA--YREARRWDDALQCSSDAIYLLRSS 168
                                    56788888999999999999999999998888888887..9999******99877776666665 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.32
                    Foie-gras_1 171 dlLekaleeFskrkqtRlaeelsleiAeeylrlgdwkkalellqpltlsyrke 223
                                    +++ kale F++   +  +++  l +A+ y  +g+w  a+e ++ +  ++ +e
  gi|116754673|ref|YP_843791.1| 276 ECYLKALEGFREVSDRESVANTLLSLARLYGSMGEWRGAVERYREALDILQSE 328
                                    6888999999999999999999******************9999876555555 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.2
                    Foie-gras_1 170 idlLekaleeFskrkqtRlaeelsleiAeeylrlgdwkkalellqp 215
                                    ++ +e+  e  ++ +  R a+ ++ +iA  y ++gd +kal+++  
  gi|116754673|ref|YP_843791.1| 394 VEHYERGAELLREMGDLRGAAACTSNIASVYQMMGDLEKALDIYHD 439
                                    55666666666677778999*********************99865 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 1.7
                    Foie-gras_1 167 kliidlLekaleeFskrkqtRlaeelsleiAeeylrlgdwkkalellqpl 216
                                     ++i  ++ ale F+  + +R  + ++ ++++ y + gd  +a++ +++ 
  gi|116754673|ref|YP_843791.1| 511 DDAITHYQDALETFEAIGDRRGMAAVMNNLGNVYEEKGDILQAIKSYRMS 560
                                    5688999***************************9999999999999885 PP

  == domain 5  score: 1.5 bits;  conditional E-value: 0.38
                    Foie-gras_1 162 gvahskliidlLekaleeFskrkqtRlaeelsleiAeeylrlgdwkkalellqp 215
                                    ++ +++ + ++++++le F++ + +R a+   + ++   l+ g w++al+ ++ 
  gi|116754673|ref|YP_843791.1| 583 RIGDAESAEKCYRASLEAFQSIGDERGAAYALMGLGSIALERGLWDDALDCFKR 636
                                    6667778889***************************************99875 PP

  == domain 6  score: -2.7 bits;  conditional E-value: 7.7
                    Foie-gras_1 195 eiAeeylrlgdwkkalellqpltlsy 220
                                     iA  y r g w++al+ ++ +   +
  gi|116754673|ref|YP_843791.1| 653 SIASVYERKGMWQEALAEYRKVLERF 678
                                    689999999*******9999886555 PP

  == domain 7  score: 6.6 bits;  conditional E-value: 0.011
                    Foie-gras_1 165 hskliidlLekaleeFskrkqtRlaeelsleiAeeylrlgdwkkalellqplt 217
                                    h+ ++++ ++++le F++ +    ++  + ++A+ ++r g+w+ al+l++ ++
  gi|116754673|ref|YP_843791.1| 703 HWDDALEHYSESLEIFERLGDGYSTAVTTNNMANVLYRRGEWDRALNLYSKAM 755
                                    8999999**********9999999999999******************99875 PP

  == domain 8  score: 9.2 bits;  conditional E-value: 0.0017
                    Foie-gras_1 165 hskliidlLekaleeFskrkqtRlaeelsleiAeeylrlgdwkkalellq 214
                                    ++  +++l++ka+e F++ +          +iA  ++r g+w+ a+el+ 
  gi|116754673|ref|YP_843791.1| 743 EWDRALNLYSKAMEHFQRVGDMHSYGATLSNIASIHYRRGEWERAIELYH 792
                                    567889***********8888777777778*****************986 PP

  == domain 9  score: 2.8 bits;  conditional E-value: 0.15
                    Foie-gras_1 212 llqpltlsyrkegWwsLleevlwalrecalkvqdvkdv 249
                                    +l+ l l+y + g wsL+ +    + eca++++d +++
  gi|116754673|ref|YP_843791.1| 810 VLNNLGLLYHRRGEWSLAVDHFRLAAECAMRAGDHEAA 847
                                    6788899999999999999999999*********9986 PP

  == domain 10  score: 7.1 bits;  conditional E-value: 0.0077
                    Foie-gras_1 165 hskliidlLekaleeFskrkqtRlaeelsleiAeeylrlgdwkkalellqpltlsyr 221
                                     +++++d ++k+le F++ + +  a+e ++++A  y + g+w+ a +ll+  ++ +r
  gi|116754673|ref|YP_843791.1| 903 RWEEALDHYQKSLELFERTGDRYSAAETMFNMALIYRDRGEWSIAEDLLSRSMSEFR 959
                                    578999***********8777778999**********************99888777 PP

  == domain 11  score: -0.7 bits;  conditional E-value: 1.8
                    Foie-gras_1  174 ekaleeFskrkqtRlaeelsleiAeeylrlgdwkkalellqpltls 219 
                                     +kal+ ++k + tR +      ++ + l++gd+++a e lq + ++
  gi|116754673|ref|YP_843791.1| 1069 QKALALARKMGLTRDEGVALRSLGAASLNAGDYDEAEEHLQKALTL 1114
                                     5566666666666655555556666666666666666666665333 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.1    0.0071       3.4      87     181 ..      36     134 ..      24     144 .. 0.74
   2 ?    5.0   0.0     0.037        18     126     184 ..     235     294 ..     223     303 .. 0.83
   3 ?    0.3   0.1         1   4.9e+02      85     116 ..     304     335 ..     287     413 .. 0.62
   4 ?   -1.6   0.0       3.9   1.8e+03     154     176 ..     422     444 ..     393     459 .. 0.79
   5 ?    4.8   0.1     0.044        21     128     176 ..     516     564 ..     463     580 .. 0.87
   6 ?    3.3   0.0      0.12        57     146     174 ..     688     716 ..     579     722 .. 0.67
   7 ?   -0.2   0.0       1.4   6.7e+02     113     173 ..     728     755 ..     715     796 .. 0.73
   8 ?    5.1   0.1     0.036        17     116     176 ..    1009    1075 ..    1006    1090 .. 0.81
   9 ?    1.6   0.8       0.4   1.9e+02      85     105 ..    1094    1114 ..    1085    1207 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0071
                         TPR_21  87 veagdlaaAkaqLewvlekakdeelkalarlRLarvllaekkydeAlktLeakkeeaf...aalvaelrGDilvaqgkld 163
                                    v a + a A ++L++++e+++    ++     L  +  + + +++A++ L+++ e a    a++v  + G i+++ ++ld
  gi|116754673|ref|YP_843791.1|  36 VLASNRAGALSHLDEIAEQNSAS-RDHSLWFSLGMISQQLGSLERAVSHLSRALERASgadAVKVLSRLGSIYANVEDLD 114
                                    55566677777787777777444.555566778888888899999999997665544411156778889*********** PP

                         TPR_21 164 eAraaYqaAlaaleeka..r 181
                                     A + Y++Al++le+++  r
  gi|116754673|ref|YP_843791.1| 115 RAISLYRDALSRLESGDpeR 134
                                    ************99987654 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.037
                         TPR_21 126 ekkydeAlktLeakkeeafaalvaelrGDilvaqgkldeAraaYqaAlaaleeka.rell 184
                                    e+ +d A+++ e+ +e + a++ a l GD+++ +g++  A + Y +Al+   e + re +
  gi|116754673|ref|YP_843791.1| 235 EDLFDMAMHRYEHCHEIEGASRTALLLGDLHAIEGRFSSAEECYLKALEGFREVSdRESV 294
                                    566788888888888888889999999*********************998877665555 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 1
                         TPR_21  85 aaveagdlaaAkaqLewvlekakdeelkalar 116
                                       + g++  A ++++++l+  ++e+ ++lar
  gi|116754673|ref|YP_843791.1| 304 LYGSMGEWRGAVERYREALDILQSEQSQDLAR 335
                                    44444444455444444444444444444444 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 3.9
                         TPR_21 154 DilvaqgkldeAraaYqaAlaal 176
                                     ++  +g+l++A + Y++Al+ +
  gi|116754673|ref|YP_843791.1| 422 SVYQMMGDLEKALDIYHDALQIQ 444
                                    57888999999999999998755 PP

  == domain 5  score: 4.8 bits;  conditional E-value: 0.044
                         TPR_21 128 kydeAlktLeakkeeafaalvaelrGDilvaqgkldeAraaYqaAlaal 176
                                    +y++Al+t ea  +    a+v +  G+++ ++g++ +A + Y+ +++  
  gi|116754673|ref|YP_843791.1| 516 HYQDALETFEAIGDRRGMAAVMNNLGNVYEEKGDILQAIKSYRMSMELD 564
                                    6899999999999999999999999999999999999999999988765 PP

  == domain 6  score: 3.3 bits;  conditional E-value: 0.12
                         TPR_21 146 alvaelrGDilvaqgkldeAraaYqaAla 174
                                    a+v    G++l++qg+ d+A ++Y+++l+
  gi|116754673|ref|YP_843791.1| 688 AAVLSTIGNLLAEQGHWDDALEHYSESLE 716
                                    5666778999**************99986 PP

  == domain 7  score: -0.2 bits;  conditional E-value: 1.4
                         TPR_21 113 alarlRLarvllaekkydeAlktLeakkeeafaalvaelrGDilvaqgkldeAraaYqaAl 173
                                    a+ +  +a+vl   ++ d+Al++ +                                 +A+
  gi|116754673|ref|YP_843791.1| 728 AVTTNNMANVLYRRGEWDRALNLYS---------------------------------KAM 755
                                    5555566666666666666665443.................................333 PP

  == domain 8  score: 5.1 bits;  conditional E-value: 0.036
                         TPR_21  116 rlRLarvllaekkydeAlktLeakkeeafaalvaelr.......GDilvaqgkldeAraaYqaAlaal 176 
                                      l +arv l+ +++ eA   L+++++   +  ++ ++       GD +++q    eAr+ Yq+Ala  
  gi|116754673|ref|YP_843791.1| 1009 YLAMARVKLNRGEMSEARFYLSEAETLILKTGYDSMKirlyiewGDFYLSQAP-FEARSSYQKALALA 1075
                                     57799999999999999999999998888888888776666777999998865.58********9865 PP

  == domain 9  score: 1.6 bits;  conditional E-value: 0.4
                         TPR_21   85 aaveagdlaaAkaqLewvlek 105 
                                     a+ +agd+++A+++L+++l  
  gi|116754673|ref|YP_843791.1| 1094 ASLNAGDYDEAEEHLQKALTL 1114
                                     567889999999999998764 PP

>> ComR_TPR  ComR tetratricopeptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0       0.6   2.8e+02     136     213 ..     294     369 ..     269     371 .. 0.66
   2 ?   -1.0   0.1       2.3   1.1e+03     144     213 ..     421     489 ..     414     499 .. 0.61
   3 ?   -1.9   0.0       4.1   1.9e+03     187     213 ..     504     529 ..     453     531 .. 0.64
   4 ?   -3.0   0.0       9.2   4.3e+03     193     214 ..     586     607 ..     582     608 .. 0.89
   5 ?   -2.8   0.0         8   3.8e+03     195     213 ..     745     763 ..     690     804 .. 0.59
   6 ?    6.6   0.0     0.011       5.1     138     211 ..    1007    1078 ..     987    1082 .. 0.84
   7 ?   -0.0   0.0       1.1   5.3e+02     145     199 ..    1093    1146 ..    1086    1148 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.6
                                    HHHHHHHHHHHHHHTT--TTHHHHHHHHHHHHHHHT--TTHHHHHHHHHHHHHHTS--HHHHHHHHHHHHHHHHHTT- CS
                       ComR_TPR 136 lrdvllsaltvllklkeyeklekllkvlnkimektqdfqkkpivlmlewKyylkvkkdiekAkelYqkAilfakllgd 213
                                    + ++lls++ ++ +++e +   +   ++ +i+++ q       +  +      +  +d+e+A++++ k++ +++ lg+
  gi|116754673|ref|YP_843791.1| 294 VANTLLSLARLYGSMGEWRGAVERYREALDILQSEQSQDLARALREMGTA--CYRLRDYEMAQNYFMKSLELSEALGE 369
                                    45666666666666666555555555555555555554444444433333..33369************999999887 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.3
                                    HHHHHHTT--TTHHHHHHHHHHHHHHHT--TTHHHHHHHHHHHHHHTS--HHHHHHHHHHHHHHHHHTT- CS
                       ComR_TPR 144 ltvllklkeyeklekllkvlnkimektqdfqkkpivlmlewKyylkvkkdiekAkelYqkAilfakllgd 213
                                    ++v+ ++++ ek  ++ + + +i e+  d+q    +l     +y  +  +ie A++ Y + + + + lgd
  gi|116754673|ref|YP_843791.1| 421 ASVYQMMGDLEKALDIYHDALQIQERLGDMQGASKTLNNMGLVYQ-HMGEIEAAERNYMRCLELKEQLGD 489
                                    555666666666666666666666666666655554444444443.566666666666666666666665 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 4.1
                                    HHHTS--HHHHHHHHHHHHHHHHHTT- CS
                       ComR_TPR 187 ylkvkkdiekAkelYqkAilfakllgd 213
                                    y  +++  + A ++Yq+A+   + +gd
  gi|116754673|ref|YP_843791.1| 504 YE-IQRRWDDAITHYQDALETFEAIGD 529
                                    33.677788888889988888777777 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 9.2
                                    -HHHHHHHHHHHHHHHHHTT-H CS
                       ComR_TPR 193 diekAkelYqkAilfakllgde 214
                                    d e+A+++Y +++   + +gde
  gi|116754673|ref|YP_843791.1| 586 DAESAEKCYRASLEAFQSIGDE 607
                                    7899*********999999997 PP

  == domain 5  score: -2.8 bits;  conditional E-value: 8
                                    HHHHHHHHHHHHHHHHTT- CS
                       ComR_TPR 195 ekAkelYqkAilfakllgd 213
                                    ++A +lY kA+   + +gd
  gi|116754673|ref|YP_843791.1| 745 DRALNLYSKAMEHFQRVGD 763
                                    4444444444433333333 PP

  == domain 6  score: 6.6 bits;  conditional E-value: 0.011
                                     HHHHHHHHHHHHTT--TTHHHHHHHHHHHHHHHT--TTHHHHHHHHHHHHHHTS--HHHHHHHHHHHHHHHHHT CS
                       ComR_TPR  138 dvllsaltvllklkeyeklekllkvlnkimektqdfqkkpivlmlewKyylkvkkdiekAkelYqkAilfakll 211 
                                     +++l+++ v+l+ +e+++ + +l+++++++ kt   + + i l +ew  +  + +   +A ++YqkA+++a+ +
  gi|116754673|ref|YP_843791.1| 1007 EAYLAMARVKLNRGEMSEARFYLSEAETLILKTGYDS-MKIRLYIEWGDFY-LSQAPFEARSSYQKALALARKM 1078
                                     5778899999**********************97555.5566677887665.5888889***********9865 PP

  == domain 7  score: -0.0 bits;  conditional E-value: 1.1
                                     HHHHHTT--TTHHHHHHHHHHHHHHHT--TTHHHHHHHHHHHHHHTS--HHHHHH CS
                       ComR_TPR  145 tvllklkeyeklekllkvlnkimektqdfqkkpivlmlewKyylkvkkdiekAke 199 
                                     + +l+ ++y++ e+ l+++ ++ ++++ + +   ++ l +  y   +kd ++A+e
  gi|116754673|ref|YP_843791.1| 1093 AASLNAGDYDEAEEHLQKALTLFKSINSMYDLLSTYALMATLYF-NRKDHSRAEE 1146
                                     56778888999999999999999999999999988888888888.7788888876 PP

>> PPR_2  PPR repeat family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       7.8   3.7e+03      12      28 ..     106     122 ..     105     126 .. 0.87
   2 ?   -1.0   0.0       4.4   2.1e+03      15      28 ..     426     439 ..     414     440 .. 0.79
   3 ?    5.4   0.1     0.044        21       3      28 ..     728     753 ..     726     767 .. 0.92
   4 ?    0.4   0.0       1.6   7.5e+02      11      27 ..     776     792 ..     769     793 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 7.8
                          PPR_2  12 glckkgkveeAfklfne 28 
                                     +++ ++++ A++l+ +
  gi|116754673|ref|YP_843791.1| 106 IYANVEDLDRAISLYRD 122
                                    68999**********87 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 4.4
                          PPR_2  15 kkgkveeAfklfne 28 
                                      g++e+A++++++
  gi|116754673|ref|YP_843791.1| 426 MMGDLEKALDIYHD 439
                                    389********987 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.044
                          PPR_2   3 vvtyNtlIsglckkgkveeAfklfne 28 
                                     vt N + + l+++g+++ A+ l+++
  gi|116754673|ref|YP_843791.1| 728 AVTTNNMANVLYRRGEWDRALNLYSK 753
                                    69*********************975 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 1.6
                          PPR_2  11 sglckkgkveeAfklfn 27 
                                    s ++++g++e A++l++
  gi|116754673|ref|YP_843791.1| 776 SIHYRRGEWERAIELYH 792
                                    56899**********97 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   0.00052      0.24     133     219 ..      47     128 ..      44     131 .. 0.86
   2 ?    1.2   0.1       0.4   1.9e+02     138     204 ..     286     347 ..     236     369 .. 0.78
   3 ?   -3.2   0.1       8.5     4e+03     142     142 ..     449     449 ..     415     525 .. 0.46
   4 ?   -3.1   0.0       7.8   3.7e+03     152     225 ..     653     728 ..     643     740 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00052
                           CorA 133 eldeledeledstkkeilrelaqlrrrlvklrralapnrevlkrllakaddkllddedkeylrdlldelerllemlealr 212
                                    +lde+ ++ + s+++++  +l  + ++l+ l+ra++++ ++l ++ + ad+ ++      +l  ++ ++e l++ ++ +r
  gi|116754673|ref|YP_843791.1|  47 HLDEIAEQNSASRDHSLWFSLGMISQQLGSLERAVSHLSRAL-ERASGADAVKVL-S---RLGSIYANVEDLDRAISLYR 121
                                    899***************************************.666623333333.3...38****************** PP

                           CorA 213 erleslq 219
                                    + l++l 
  gi|116754673|ref|YP_843791.1| 122 DALSRLE 128
                                    **99985 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.4
                           CorA 138 edeledstkkeilrelaqlrrrlvklrralapnrevlkrllakaddkllddedkeylrdlldelerl 204
                                     +  ++++ ++ l +la+l  +++++r a+ + re+l ++l+    ++ +++ ++ lr++     rl
  gi|116754673|ref|YP_843791.1| 286 REVSDRESVANTLLSLARLYGSMGEWRGAVERYREAL-DILQ----SEQSQDLARALREMGTACYRL 347
                                    444478889999999999999****************.9999....666666666677777776664 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 8.5
                           CorA 142 e 142
                                    +
  gi|116754673|ref|YP_843791.1| 449 D 449
                                    2 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 7.8
                           CorA 152 elaqlrrrlvklrralapnrevlkrllakaddkllddedkey.lrdlldelerllemlealrerl...eslqdtyssl 225
                                    ++a + +r + +++ala+ r+vl ++ + + ++ l  ++ +  + +ll e  + ++ le+++e l   e+l d ys+ 
  gi|116754673|ref|YP_843791.1| 653 SIASVYERKGMWQEALAEYRKVL-ERFR-GMGDSLGVAAVLStIGNLLAEQGHWDDALEHYSESLeifERLGDGYSTA 728
                                    55555566666788888888888.6666.3333333333222277777777775555555554441114555555554 PP

>> SRP68  RNA-binding signal recognition particle 68
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       6.4     3e+03     373     440 ..     238     327 ..     234     336 .. 0.59
   2 ?   -1.0   0.0       1.4   6.8e+02     136     152 ..     507     524 ..     414     558 .. 0.66
   3 ?    1.6   0.0      0.22   1.1e+02     122     148 ..     611     637 ..     608     641 .. 0.91
   4 ?   -3.3   0.0       6.9   3.2e+03     408     435 ..     647     675 ..     646     679 .. 0.72
   5 ?    8.4   0.0     0.002      0.93     129     157 ..     695     723 ..     683     741 .. 0.87
   6 ?    1.6   0.0      0.22   1.1e+02     130     159 ..     776     805 ..     762     814 .. 0.75
   7 ?   -2.2   0.1       3.3   1.5e+03     127     153 ..     890     919 ..     886     929 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 6.4
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX......................XXXXXXXXXXXXXXXXXXXX CS
                          SRP68 373 ydallqslesikelpgvaadeelaeeleakkayfrAlr......................clyiarshalaskyaeAlAL 430
                                    +d+ ++ +e   e++g+ + + l  +l a + +f +                         l++ar++ + ++++ A+  
  gi|116754673|ref|YP_843791.1| 238 FDMAMHRYEHCHEIEGASRTALLLGDLHAIEGRFSSAEecylkalegfrevsdresvantLLSLARLYGSMGEWRGAVER 317
                                    56666666666666666666666666666555555554444444445555555555555577777777777777777776 PP

                                    XXXXXXXXXX CS
                          SRP68 431 lkrAlelaee 440
                                    + +Al+ +++
  gi|116754673|ref|YP_843791.1| 318 YREALDILQS 327
                                    6666666655 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.4
                                    T.-HHHHHHHHHHHHHHH CS
                          SRP68 136 q.qWekalesyskaraiy 152
                                    q +W++a+++y+ a   +
  gi|116754673|ref|YP_843791.1| 507 QrRWDDAITHYQDALETF 524
                                    123444444444443333 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.22
                                    HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                          SRP68 122 AYaallrGallfekqqWekalesyska 148
                                    AYa +  G++++e+  W++al+ ++++
  gi|116754673|ref|YP_843791.1| 611 AYALMGLGSIALERGLWDDALDCFKRC 637
                                    999999******************998 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 6.9
                                    XXXXX.XXXXXXXXXXXXXXXXXXXXXXX CS
                          SRP68 408 Alrcl.yiarshalaskyaeAlALlkrAl 435
                                    Alr l +ia ++  ++ + eAlA + ++l
  gi|116754673|ref|YP_843791.1| 647 ALRVLgSIASVYERKGMWQEALAEYRKVL 675
                                    55555468999999999999998776665 PP

  == domain 5  score: 8.4 bits;  conditional E-value: 0.002
                                    HHHHHHTT-HHHHHHHHHHHHHHHHHHHH CS
                          SRP68 129 GallfekqqWekalesyskaraiyeaLak 157
                                    G+ll e+ +W++ale+ys++  i+e L+ 
  gi|116754673|ref|YP_843791.1| 695 GNLLAEQGHWDDALEHYSESLEIFERLGD 723
                                    99************************986 PP

  == domain 6  score: 1.6 bits;  conditional E-value: 0.22
                                    HHHHHTT-HHHHHHHHHHHHHHHHHHHHHH CS
                          SRP68 130 allfekqqWekalesyskaraiyeaLakvt 159
                                    +++  + +We+a+e y k+  i+e L  ++
  gi|116754673|ref|YP_843791.1| 776 SIHYRRGEWERAIELYHKSLEIFEGLEDSG 805
                                    4455566*******************9887 PP

  == domain 7  score: -2.2 bits;  conditional E-value: 3.3
                                    HHHHHHHHTT...-HHHHHHHHHHHHHHHH CS
                          SRP68 127 lrGallfekq...qWekalesyskaraiye 153
                                    ++G+l+       +We+al++y+k+  ++e
  gi|116754673|ref|YP_843791.1| 890 MHGILANAYAdifRWEEALDHYQKSLELFE 919
                                    66666655556669*********9987766 PP

>> Cohesin_load  Cohesin loading factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.98   4.6e+02     412     430 ..     423     441 ..     420     455 .. 0.82
   2 ?    3.8   0.1     0.034        16     410     458 ..     461     509 ..     450     542 .. 0.84
   3 ?    3.4   0.1     0.044        21      76     117 ..    1100    1141 ..    1097    1150 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.98
                   Cohesin_load 412 yaqskgdlkaAlaqyketa 430
                                     +q +gdl++Al++y +++
  gi|116754673|ref|YP_843791.1| 423 VYQMMGDLEKALDIYHDAL 441
                                    6899***********8554 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.034
                   Cohesin_load 410 glyaqskgdlkaAlaqyketaarkskerelyilsllNlviIlesevsed 458
                                    gl +q +g+++aA++ y+  +  k++  ++  +++ ++ + + +e+++ 
  gi|116754673|ref|YP_843791.1| 461 GLVYQHMGEIEAAERNYMRCLELKEQLGDVHGAANTHINLATLYEIQRR 509
                                    99****************9999999999999999998888888877764 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.044
                   Cohesin_load   76 nideAeeylskailiaek.nrlidlkfvcqfLlarllektnpk 117 
                                     ++deAee+l+ka+++ ++ n+++dl +++  L a l++++  +
  gi|116754673|ref|YP_843791.1| 1100 DYDEAEEHLQKALTLFKSiNSMYDL-LSTYALMATLYFNRKDH 1141
                                     69**********************9.55555666666665554 PP

>> Het-C  Heterokaryon incompatibility protein Het-C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   0.00063       0.3     198     233 ..     326     361 ..     314     385 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00063
                          Het-C 198 kkgkeedllealRllGqalhtleDfaahsnyvelaL 233
                                    ++++++dl  alR +G+a++ l D+    ny   +L
  gi|116754673|ref|YP_843791.1| 326 QSEQSQDLARALREMGTACYRLRDYEMAQNYFMKSL 361
                                    678899*************************75443 PP

>> Vta1_C  Vta1 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1       1.5   7.2e+02      21      37 ..     111     127 ..     110     128 .. 0.91
   2 ?   -1.4   0.0       4.1   1.9e+03      25      38 .]     313     326 ..     312     326 .. 0.87
   3 ?    7.8   0.1    0.0054       2.5      22      36 ..    1100    1114 ..    1094    1116 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 1.5
                         Vta1_C  21 eDvetAiknLqeALklL 37 
                                    eD + Ai+  ++AL+ L
  gi|116754673|ref|YP_843791.1| 111 EDLDRAISLYRDALSRL 127
                                    8*************977 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.1
                         Vta1_C  25 tAiknLqeALklLt 38 
                                    +A++  +eAL++L+
  gi|116754673|ref|YP_843791.1| 313 GAVERYREALDILQ 326
                                    6889999******8 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0054
                         Vta1_C   22 DvetAiknLqeALkl 36  
                                     D+++A ++Lq+AL+l
  gi|116754673|ref|YP_843791.1| 1100 DYDEAEEHLQKALTL 1114
                                     9************98 PP

>> DUF4398  Domain of unknown function (DUF4398)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0       1.3   6.1e+02      32      56 ..    1009    1033 ..    1004    1051 .. 0.75
   2 ?    7.8   0.2     0.011       5.1      12      73 ..    1087    1155 ..    1077    1159 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 1.3
                        DUF4398   32 aLaqAeaamaekdyeeAdhlaylAe 56  
                                     +La A+ + ++++ +eA+ ++ +Ae
  gi|116754673|ref|YP_843791.1| 1009 YLAMARVKLNRGEMSEARFYLSEAE 1033
                                     6777777777777777777777776 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.011
                        DUF4398   12 aAraagaeeyApaeleeAreaLaqAea..amaekdyeeAdhlaylAer.....daelAearAkaakaea 73  
                                     a+r+ ga+ + + ++ eA+e L++A    +  ++ y+    +a++A       d   Ae++A     +a
  gi|116754673|ref|YP_843791.1| 1087 ALRSLGAASLNAGDYDEAEEHLQKALTlfKSINSMYDLLSTYALMATLyfnrkDHSRAEETALLLERQA 1155
                                     56788999999999*************996779999999999999999555554556666666555554 PP

>> ANAPC5  Anaphase-promoting complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0       1.3   5.9e+02      25      71 ..      48      91 ..      44     110 .. 0.81
   2 ?    0.9   0.0         1   4.7e+02      44      85 ..     138     179 ..     134     187 .. 0.84
   3 ?    9.5   0.1    0.0022         1      37      77 ..     291     331 ..     236     351 .. 0.80
   4 ?   -1.9   0.0       7.8   3.7e+03      46      76 ..     419     449 ..     389     460 .. 0.84
   5 ?    1.1   0.0      0.89   4.2e+02      38      63 ..     765     790 ..     693     847 .. 0.68
   6 ?   -0.6   0.0         3   1.4e+03      51      51 ..     978     978 ..     904    1052 .. 0.52
   7 ?    1.0   1.2      0.95   4.5e+02       8      73 ..    1095    1197 ..    1092    1209 .. 0.58

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 1.3
                         ANAPC5 25 FDyvlsqnessqkksyqyalLnlaslhadfghneeAvkaleeairlA 71
                                    D + +qn+ s   + ++  ++l ++++++g  e Av+ l+ a + A
  gi|116754673|ref|YP_843791.1| 48 LDEIAEQNSAS---RDHSLWFSLGMISQQLGSLERAVSHLSRALERA 91
                                   67777777777...77888999****************999887655 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1
                         ANAPC5  44 lLnlaslhadfghneeAvkaleeairlArenkDkscLalala 85 
                                    l+nl +   +   +++A++  ++ai l r ++D s++a a++
  gi|116754673|ref|YP_843791.1| 138 LINLSMAYREARRWDDALQCSSDAIYLLRSSGDRSSVARAIM 179
                                    6777778888888999********************998876 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0022
                         ANAPC5  37 kksyqyalLnlaslhadfghneeAvkaleeairlArenkDk 77 
                                    ++s    lL+la+l  ++g++  Av++ +ea  + + ++++
  gi|116754673|ref|YP_843791.1| 291 RESVANTLLSLARLYGSMGEWRGAVERYREALDILQSEQSQ 331
                                    55667789**************************9998876 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 7.8
                         ANAPC5  46 nlaslhadfghneeAvkaleeairlArenkD 76 
                                    n as+ + +g+ e+A++  ++a ++    +D
  gi|116754673|ref|YP_843791.1| 419 NIASVYQMMGDLEKALDIYHDALQIQERLGD 449
                                    7788999999999999999999888666555 PP

  == domain 5  score: 1.1 bits;  conditional E-value: 0.89
                         ANAPC5  38 ksyqyalLnlaslhadfghneeAvka 63 
                                    +sy   l n as+h++ g++e A++ 
  gi|116754673|ref|YP_843791.1| 765 HSYGATLSNIASIHYRRGEWERAIEL 790
                                    46666666777777777777777654 PP

  == domain 6  score: -0.6 bits;  conditional E-value: 3
                         ANAPC5  51 h 51 
                                    +
  gi|116754673|ref|YP_843791.1| 978 K 978
                                    2 PP

  == domain 7  score: 1.0 bits;  conditional E-value: 0.95
                         ANAPC5    8 alrakdYqqaldsLhryFDyvlsqnessq....................................kksyqyalLnl.a 48  
                                     +l+a dY++a ++L +    + s n+ ++                                     + +q+ +L++ a
  gi|116754673|ref|YP_843791.1| 1095 SLNAGDYDEAEEHLQKALTLFKSINSMYDllstyalmatlyfnrkdhsraeetalllerqarrlgYRDLQVKALEViA 1172
                                     678889999999988887777666666655555555555555555555555555666655444443334443333212 PP

                         ANAPC5   49 slhadfghneeAvkaleeairlAre 73  
                                       + + +  ++Av++  ea ++A+ 
  gi|116754673|ref|YP_843791.1| 1173 GCELATSRTDAAVSTYLEALNIAQS 1197
                                     2333335556666666666666665 PP

>> YfiO  Outer membrane lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.2      0.13        63     137     193 ..     291     349 ..     285     358 .. 0.75
   2 ?   -0.9   0.0       2.5   1.2e+03     141     184 ..     494     537 ..     482     555 .. 0.81
   3 ?    3.4   0.0      0.11        53     147     174 ..     654     681 ..     651     692 .. 0.91
   4 ?    0.8   0.0      0.71   3.4e+02       4      40 ..     734     770 ..     731     798 .. 0.78
   5 ?    3.3   0.2      0.13        60      12      64 ..    1092    1147 ..    1087    1153 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.13
                                    HHHHHHHHHHHHHHHHHHT-HHHHHHHHHHHHHHSTTSHHH..HHHHHHHHHHHHHTT- CS
                           YfiO 137 rerLArhElevaefylkreayvaainRvkevlknypdtesv..eeaLaimveayralgl 193
                                    re +A+  l+ a+ y   +++  a++R++e l   ++ +s   + aL  m  a ++l  
  gi|116754673|ref|YP_843791.1| 291 RESVANTLLSLARLYGSMGEWRGAVERYREALDILQSEQSQdlARALREMGTACYRLRD 349
                                    789999999*********************99877766555004566666666555554 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.5
                                    HHHHHHHHHHHHHHT-HHHHHHHHHHHHHHSTTSHHHHHHHHHH CS
                           YfiO 141 ArhElevaefylkreayvaainRvkevlknypdtesveeaLaim 184
                                    A+  ++ a  y  ++++  ai  ++  l+++++  + +   a+m
  gi|116754673|ref|YP_843791.1| 494 ANTHINLATLYEIQRRWDDAITHYQDALETFEAIGDRRGMAAVM 537
                                    77788999999999999999999999999999887776555555 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.11
                                    HHHHHHHHT-HHHHHHHHHHHHHHSTTS CS
                           YfiO 147 vaefylkreayvaainRvkevlknypdt 174
                                    +a  y ++++++ a+  +++vl+ +  +
  gi|116754673|ref|YP_843791.1| 654 IASVYERKGMWQEALAEYRKVLERFRGM 681
                                    999*********************9866 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.71
                                    -HHHHHHHHHHHHHHT-HHHHHHHHHHHHHHSTTSTT CS
                           YfiO   4 taselYekgqealqkgdyaeAikklealdsryPfspy 40 
                                     a+ lY+ g+ + + + y++A ++++ + +++  +  
  gi|116754673|ref|YP_843791.1| 734 MANVLYRRGEWDRALNLYSKAMEHFQRVGDMHSYGAT 770
                                    5678899999999999999999999999888877765 PP

  == domain 5  score: 3.3 bits;  conditional E-value: 0.13
                                     HHHHHHHT-HHHHHHHHHHHHHHST..TSTTHHHHHHHHHHH.HHHTT-HHHHHHH CS
                           YfiO   12 gqealqkgdyaeAikklealdsryP..fspyaeqaqldliyA.yykdadyaealas 64  
                                     g  +l++gdy eA ++l+++ + +   +s y   + ++l+   y++++d + a+++
  gi|116754673|ref|YP_843791.1| 1092 GAASLNAGDYDEAEEHLQKALTLFKsiNSMYDLLSTYALMATlYFNRKDHSRAEET 1147
                                     67899****************99853368888888888766525566777777665 PP

>> SPO22  Meiosis protein SPO22/ZIP4 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       6.2   2.9e+03     220     241 ..      73      94 ..      28     134 .. 0.44
   2 ?    5.6   0.1      0.02       9.3      16      67 ..     316     365 ..     268     379 .. 0.84
   3 ?   -1.6   0.0       3.2   1.5e+03      39      79 ..     691     731 ..     685     749 .. 0.74
   4 ?   -1.1   0.0       2.2     1e+03     253     275 ..     733     755 ..     732     762 .. 0.91
   5 ?    4.2   0.1     0.054        25     249     275 ..     769     795 ..     747     796 .. 0.88
   6 ?   -2.4   0.1       5.5   2.6e+03      30      67 ..     885     919 ..     871     937 .. 0.54
   7 ?    0.3   0.1      0.84     4e+02      34     109 ..    1004    1074 ..     993    1091 .. 0.72
   8 ?    6.3   3.6     0.012       5.7      43     188 ..    1092    1240 ..    1085    1258 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 6.2
                          SPO22 220 aiealedilaalehslgkqlsk 241
                                    ++ +le ++++l++ l++  ++
  gi|116754673|ref|YP_843791.1|  73 QLGSLERAVSHLSRALERASGA 94 
                                    2333333333333333332222 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.02
                          SPO22  16 skakceenllrldpeeaeeLarllyniGksllskkkyeeavkWLqraldile 67 
                                    ++   +e l+ l+ e  + Lar l ++G + +  ++ye+a  ++ ++l++ e
  gi|116754673|ref|YP_843791.1| 316 ER--YREALDILQSEQSQDLARALREMGTACYRLRDYEMAQNYFMKSLELSE 365
                                    45..567788888889999999999999999999999999999999998877 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 3.2
                          SPO22  39 lyniGksllskkkyeeavkWLqraldilekqesesksssdl 79 
                                    l  iG  l +++ +++a+   +++l+i+e++ ++ +++ + 
  gi|116754673|ref|YP_843791.1| 691 LSTIGNLLAEQGHWDDALEHYSESLEIFERLGDGYSTAVTT 731
                                    55678888888888888888888888888877766666444 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 2.2
                          SPO22 253 nkgekhykaknydeAaewyelsl 275
                                    n++  +y+ +++d A+++y +++
  gi|116754673|ref|YP_843791.1| 733 NMANVLYRRGEWDRALNLYSKAM 755
                                    678889**************998 PP

  == domain 5  score: 4.2 bits;  conditional E-value: 0.054
                          SPO22 249 tLLWnkgekhykaknydeAaewyelsl 275
                                    + L n ++ hy+ ++++ A+e+y++sl
  gi|116754673|ref|YP_843791.1| 769 ATLSNIASIHYRRGEWERAIELYHKSL 795
                                    56778999*****************98 PP

  == domain 6  score: -2.4 bits;  conditional E-value: 5.5
                          SPO22  30 eeaeeLarllyniGksllskkkyeeavkWLqraldile 67 
                                    e+a e++ +l n+  +++   ++eea+   q++l+++e
  gi|116754673|ref|YP_843791.1| 885 EMAAEMHGILANAYADIF---RWEEALDHYQKSLELFE 919
                                    444444444444444444...44444444444444444 PP

  == domain 7  score: 0.3 bits;  conditional E-value: 0.84
                          SPO22   34 eLarllyniGksllskkkyeeavkWLqraldilekqesesksssdlselrlsvlrllarayle...ldqeesyekalk 108 
                                      L++ ++ +++  l++++ +ea ++L++a  ++       k+   + +++++ +      yl     + ++sy+kal+
  gi|116754673|ref|YP_843791.1| 1004 DLCEAYLAMARVKLNRGEMSEARFYLSEAETLIL------KT--GYDSMKIRLYIEWGDFYLSqapFEARSSYQKALA 1073
                                     79999999999999999999999***99988776......22..3555666555555555555444446666666666 PP

                          SPO22  109 a 109 
                                     +
  gi|116754673|ref|YP_843791.1| 1074 L 1074
                                     5 PP

  == domain 8  score: 6.3 bits;  conditional E-value: 0.012
                          SPO22   43 GksllskkkyeeavkWLqraldilekqesesksssdlselrlsvlrllarayleldqeesyekalkavellqkeygkk 120 
                                     G + l+ ++y+ea   Lq+al +++     s +s    +  ls++ l+a+ y+   +++++ +a+++  ll+ +    
  gi|116754673|ref|YP_843791.1| 1092 GAASLNAGDYDEAEEHLQKALTLFK-----SINS--MYD-LLSTYALMATLYF---NRKDHSRAEETALLLERQAR-- 1156
                                     566778999****************.....4444..333.4799*********...6**************87777.. PP

                          SPO22  121 ehpsllllklkill...kreadeeeieealeemidsve..lseanfklilslikrla............eksaalavr 181 
                                      +   + l++k+l     +e  ++   +a++ ++++++  +s+   k +l ++ r +            + s+  a++
  gi|116754673|ref|YP_843791.1| 1157 -RLGYRDLQVKALEviaGCELATSRTDAAVSTYLEALNiaQSDGVSKRLLTELTRNIvsslqdilreraNLSDLSAIK 1233
                                     .66666666666666668888888888888888888887755544444444444433366666667776667777777 PP

                          SPO22  182 vldylld 188 
                                     ++++ll+
  gi|116754673|ref|YP_843791.1| 1234 TVECLLE 1240
                                     7777777 PP

>> SHNi-TPR  SHNi-TPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       3.4   1.6e+03      21      32 ..     110     121 ..     110     124 .. 0.89
   2 ?   -1.2   0.1         3   1.4e+03      20      32 ..     314     326 ..     314     327 .. 0.85
   3 ?   -1.5   0.1       3.7   1.7e+03      23      31 ..     429     437 ..     428     449 .. 0.60
   4 ?    4.8   0.0     0.041        20      22      35 ..     475     488 ..     471     491 .. 0.80
   5 ?   -1.2   0.0       3.1   1.5e+03      17      29 ..     510     522 ..     508     522 .. 0.89
   6 ?    3.4   0.0      0.11        52       5      32 ..     615     642 ..     611     647 .. 0.86
   7 ?    2.4   0.0      0.22     1e+02       3      30 ..     690     717 ..     688     722 .. 0.83
   8 ?    0.9   0.0      0.67   3.1e+02      18      30 ..     905     917 ..     903     921 .. 0.87
   9 ?    1.1   0.1      0.58   2.7e+02       7      30 ..    1091    1114 ..    1088    1114 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3.4
                       SHNi-TPR  21 veDlrkaLeLre 32 
                                    veDl++a+ L++
  gi|116754673|ref|YP_843791.1| 110 VEDLDRAISLYR 121
                                    79*******997 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3
                       SHNi-TPR  20 AveDlrkaLeLre 32 
                                    Ave +r+aL++ +
  gi|116754673|ref|YP_843791.1| 314 AVERYREALDILQ 326
                                    7888******987 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 3.7
                       SHNi-TPR  23 DlrkaLeLr 31 
                                    Dl+kaL+++
  gi|116754673|ref|YP_843791.1| 429 DLEKALDIY 437
                                    566666654 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.041
                       SHNi-TPR  22 eDlrkaLeLreqll 35 
                                     ++ ++LeL+eql 
  gi|116754673|ref|YP_843791.1| 475 RNYMRCLELKEQLG 488
                                    5899********96 PP

  == domain 5  score: -1.2 bits;  conditional E-value: 3.1
                       SHNi-TPR  17 FpqAveDlrkaLe 29 
                                     ++A++ ++ aLe
  gi|116754673|ref|YP_843791.1| 510 WDDAITHYQDALE 522
                                    689********97 PP

  == domain 6  score: 3.4 bits;  conditional E-value: 0.11
                       SHNi-TPR   5 dlLGEislEnenFpqAveDlrkaLeLre 32 
                                      LG i lE++  ++A+  ++++++Lr+
  gi|116754673|ref|YP_843791.1| 615 MGLGSIALERGLWDDALDCFKRCVDLRL 642
                                    56899999*******************8 PP

  == domain 7  score: 2.4 bits;  conditional E-value: 0.22
                       SHNi-TPR   3 vydlLGEislEnenFpqAveDlrkaLeL 30 
                                    v+ ++G++  E++  ++A+e + ++Le+
  gi|116754673|ref|YP_843791.1| 690 VLSTIGNLLAEQGHWDDALEHYSESLEI 717
                                    566677788899999************9 PP

  == domain 8  score: 0.9 bits;  conditional E-value: 0.67
                       SHNi-TPR  18 pqAveDlrkaLeL 30 
                                    ++A+  ++k+LeL
  gi|116754673|ref|YP_843791.1| 905 EEALDHYQKSLEL 917
                                    899999******9 PP

  == domain 9  score: 1.1 bits;  conditional E-value: 0.58
                       SHNi-TPR    7 LGEislEnenFpqAveDlrkaLeL 30  
                                     LG  sl ++ +++A e l+kaL L
  gi|116754673|ref|YP_843791.1| 1091 LGAASLNAGDYDEAEEHLQKALTL 1114
                                     6666899999************87 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.4     0.001      0.48      16      88 ..      55     127 ..      38     127 .. 0.86
   2 ?   -0.4   0.0       3.3   1.5e+03      11      49 ..     483     521 ..     478     540 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.001
                         TPR_20  16 aanpddldarldlAlallaagryeeAleqLleilkrdrkweddaarkqllkifealgsqdplvakyRrkLssl 88 
                                    +++  d+ + + l     + g  e A+++L + l+r ++++  ++  +l  i + +++ d +++ yR  Ls+l
  gi|116754673|ref|YP_843791.1|  55 NSASRDHSLWFSLGMISQQLGSLERAVSHLSRALERASGADAVKVLSRLGSIYANVEDLDRAISLYRDALSRL 127
                                    3446799999************************************************************986 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 3.3
                         TPR_20  11 leaalaanpddldarldlAlallaagryeeAleqLleil 49 
                                    l+++l +     +++++lA+++  + r ++A+++  + l
  gi|116754673|ref|YP_843791.1| 483 LKEQLGDVHGAANTHINLATLYEIQRRWDDAITHYQDAL 521
                                    566666666677788899999999999999988755555 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1    0.0045       2.1       9      29 ..     342     362 ..     340     366 .. 0.85
   2 ?   -1.8   0.0       7.3   3.4e+03      11      29 ..     778     796 ..     773     797 .. 0.79
   3 ?    0.0   0.0       1.9   9.1e+02       8      28 ..    1092    1112 ..    1090    1124 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0045
                                    HHHHHHT-HHHHHHHHHHHHH CS
                     Fis1_TPR_C   9 lGhyklgeYseArryvdalLe 29 
                                     ++y+l++Y++A +y    Le
  gi|116754673|ref|YP_843791.1| 342 TACYRLRDYEMAQNYFMKSLE 362
                                    59************9877666 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 7.3
                                    HHHHT-HHHHHHHHHHHHH CS
                     Fis1_TPR_C  11 hyklgeYseArryvdalLe 29 
                                    hy+ ge ++A ++    Le
  gi|116754673|ref|YP_843791.1| 778 HYRRGEWERAIELYHKSLE 796
                                    9*********988766665 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 1.9
                                     HHHHHHHT-HHHHHHHHHHHH CS
                     Fis1_TPR_C    8 AlGhyklgeYseArryvdalL 28  
                                       +++  g+Y+eA + ++  L
  gi|116754673|ref|YP_843791.1| 1092 GAASLNAGDYDEAEEHLQKAL 1112
                                     6789999******99888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); 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: 1.24u 0.32s 00:00:01.56 Elapsed: 00:00:00.63
# Mc/sec: 6011.76
//
Query:       gi|116754674|ref|YP_843792.1|  [L=210]
Description: hypothetical protein Mthe_1377 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-11   43.9   0.2    8.8e-11   42.3   0.2    1.8  1  CxxCxxCC  Putative zinc- or iron-chelating domain


Domain annotation for each model (and alignments):
>> CxxCxxCC  Putative zinc- or iron-chelating domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.2   4.9e-15   8.8e-11       1      74 [.      16     132 ..      16     148 .. 0.85

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 4.9e-15
                       CxxCxxCC   1 eCkeCgaCCk......................elkvklteedlerlkaaevaeeeeeskkiak................. 41 
                                    +C++CgaCC+                      ++ + l+e+++ r++++   + +e+  +++                  
  gi|116754674|ref|YP_843792.1|  16 KCQRCGACCHhrrpsefpdlippelvqrfverSNLIHLNEDEVTRISRVYGLRPDEFVDTLYPyngrtvrvsddglkvvl 95 
                                    6*********9999988888888888888877777788888888887777777777777766699*************** PP

                       CxxCxxCC  42 ........adgrCvfldeetklCkiYeeRpkicrlfpasek 74 
                                             d  Cvf+d+    C+iY +Rp +crlfp+   
  gi|116754674|ref|YP_843792.1|  96 dipvlkskPDTTCVFYDNG---CRIYPHRPRACRLFPFR-I 132
                                    *******999*******99...***************95.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1616.57
//
Query:       gi|116754675|ref|YP_843793.1|  [L=311]
Description: tetrahydromethanopterin S-methyltransferase subunit H [Methanosaeta thermophila PT]
Scores for complete 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-129  430.1   1.5   4.2e-129  430.0   1.5    1.0  1  MtrH      Tetrahydromethanopterin S-methyltransferase MtrH su


Domain annotation for each model (and alignments):
>> MtrH  Tetrahydromethanopterin S-methyltransferase MtrH subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  430.0   1.5  2.3e-133  4.2e-129       1     298 [.       6     300 ..       6     301 .. 0.99

  Alignments for each domain:
  == domain 1  score: 430.0 bits;  conditional E-value: 2.3e-133
                           MtrH   1 keqkvleiaGvkiGGqpGeyPtvlvgtifyakhkivedekkGifdkeaaealikkqeelsdktGnPalvqvvGeteeaiv 80 
                                    ++q+v++ +  kiGGqpGeyPt  +gt+fya+hkiv d ++G+fdk+aae+l+++q+e+s++tGn  ++q+v et+ea+ 
  gi|116754675|ref|YP_843793.1|   6 RKQEVFDFGKFKIGGQPGEYPTCCIGTMFYARHKIVSDPEHGVFDKNAAEKLWNQQVEMSEITGNTCMNQIVAETNEAMQ 85 
                                    68****************************************************************************** PP

                           MtrH  81 kyidfvadvtdaPllidstsaevklaaakyatevGladrviynsinasiedaeiealkesdveaaivlafnpmdptvegk 160
                                    k id+++++ d P+lids++ ev++ ++kyate+G+adr+i+nsinasi d+e++alkesd++aaivlafn+m+  ++gk
  gi|116754675|ref|YP_843793.1|  86 KEIDWFVEISDYPFLIDSSAPEVRAFGVKYATEIGVADRAIHNSINASITDEELQALKESDLDAAIVLAFNAMEKGTKGK 165
                                    ******************************************************************************** PP

                           MtrH 161 lkileegegtaekgllelaeeaGiekplidvavtplgsgagaavkaslavkaklGlPvGsgihnvpsaWdwlrefkkkek 240
                                    ++il++++g+a+kg+le a+++Gi++ lid+a++plg+g+ga+++a +avka lGlPvG+g hn++saWdw++++kk++k
  gi|116754675|ref|YP_843793.1| 166 MDILTKAAGGAKKGMLEYAKDCGITRILIDTAAMPLGAGSGATYRACIAVKAMLGLPVGGGFHNAASAWDWMKKWKKTHK 245
                                    ******************************************************************************** PP

                           MtrH 241 ekaaeyevadvganlvqvilgsdfvlyGPienakkvfPavamvdilikeaakelgvel 298
                                    e+ a   + d+g+nlv+ i+g+df lyGPiena ++fPa amvdi+ +e  +elg+e+
  gi|116754675|ref|YP_843793.1| 246 EAFA---PVDIGSNLVAGIVGADFYLYGPIENAPMIFPAAAMVDIMKAESIQELGLEV 300
                                    *999...99**********************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); 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 0.23s 00:00:00.66 Elapsed: 00:00:00.36
# Mc/sec: 2567.86
//
Query:       gi|116754676|ref|YP_843794.1|  [L=84]
Description: tetrahydromethanopterin S-methyltransferase subunit G [Methanosaeta thermophila PT]
Scores for 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-29  100.0   0.7    5.8e-29   99.7   0.7    1.1  1  MtrG      Tetrahydromethanopterin S-methyltransferase, subuni
  ------ inclusion threshold ------
      0.013   15.3   0.0       0.02   14.8   0.0    1.2  1  DUF2536   Protein of unknown function (DUF2536)


Domain annotation for each model (and alignments):
>> MtrG  Tetrahydromethanopterin S-methyltransferase, subunit G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.7   0.7   6.5e-33   5.8e-29       2      63 ..      12      73 ..      11      74 .. 0.98

  Alignments for each domain:
  == domain 1  score: 99.7 bits;  conditional E-value: 6.5e-33
                           MtrG  2 iPsvvvdpddfnevkkrLdeieekvefvnsEiaqriGkkvGRdiGilYGlviGliillvyil 63
                                   +P +vvd+d+++e+++rLd+ieek+ef+++E ++r+Gk+vGRd+G++YG+++Glii+l+yil
  gi|116754676|ref|YP_843794.1| 12 VPVAVVDRDQYREIMARLDKIEEKIEFYSAEKFMRAGKSVGRDLGVAYGVCAGLIIILAYIL 73
                                   8***********************************************************97 PP

>> DUF2536  Protein of unknown function (DUF2536)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   2.3e-06      0.02       4      22 ..      28      46 ..      26      55 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.3e-06
                        DUF2536  4 qldliedKvEfFEAedlke 22
                                   +ld+ie+K+Ef+ Ae++  
  gi|116754676|ref|YP_843794.1| 28 RLDKIEEKIEFYSAEKFMR 46
                                   79*************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       764  (0.0426125); expected 358.6 (0.02)
Passed bias filter:                      568  (0.0316805); 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: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 713.57
//
Query:       gi|116754677|ref|YP_843795.1|  [L=75]
Description: tetrahydromethanopterin S-methyltransferase subunit F [Methanosaeta thermophila PT]
Scores for complete 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   90.9   0.1    2.9e-26   90.7   0.1    1.1  1  MtrF      Tetrahydromethanopterin S-methyltransferase, F subu
  ------ inclusion threshold ------
        0.1   12.4   0.1       0.12   12.1   0.1    1.1  1  DDDD      Putative mitochondrial precursor protein


Domain annotation for each model (and alignments):
>> MtrF  Tetrahydromethanopterin S-methyltransferase, F subunit (MtrF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.7   0.1   3.2e-30   2.9e-26       1      62 []      11      72 ..      11      72 .. 0.97

  Alignments for each domain:
  == domain 1  score: 90.7 bits;  conditional E-value: 3.2e-30
                           MtrF  1 gvptvnkpnmkaiksvvedirYraqLiaReqkLdSGvsatgivGfaiGfvlAllLvvlPvll 62
                                   g p+v++p m  ++++v+di+Y+aqL+aRe+kL+SGv+a++ +GfaiGf+lA+++v+ P+ll
  gi|116754677|ref|YP_843795.1| 11 GTPAVIEPAMPLFDQIVDDIKYKAQLLARETKLSSGVIAAAPQGFAIGFFLAVAMVLGPFLL 72
                                   6799*******************************************************986 PP

>> DDDD  Putative mitochondrial precursor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   1.4e-05      0.12      16      50 ..      39      74 ..      27      75 .] 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.4e-05
                           DDDD 16 savttrsGaikpkPkktpFgL.lrvilvVipgllvG 50
                                   +++  +sG i + P+  + g+ l+v +v  p+ll+G
  gi|116754677|ref|YP_843795.1| 39 RETKLSSGVIAAAPQGFAIGFfLAVAMVLGPFLLMG 74
                                   567889**************6378999999****99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.31u 0.23s 00:00:00.54 Elapsed: 00:00:00.36
# Mc/sec: 627.57
//
Query:       gi|116754678|ref|YP_843796.1|  [L=243]
Description: tetrahydromethanopterin S-methyltransferase subunit A [Methanosaeta thermophila PT]
Scores for 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-86  288.0   3.2    2.7e-86  287.6   3.2    1.1  1  MtrA      Tetrahydromethanopterin S-methyltransferase, subuni


Domain annotation for each model (and alignments):
>> MtrA  Tetrahydromethanopterin S-methyltransferase, subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  287.6   3.2   1.5e-90   2.7e-86       1     172 [.       4     175 ..       4     176 .. 0.99

  Alignments for each domain:
  == domain 1  score: 287.6 bits;  conditional E-value: 1.5e-90
                                    -----TTSS-S--S-EE--TT-SEEEE-TT-SS-HHHHHHCT-SEEE----TTHHHHHHHHHHHT-TT--EEEEEE---T CS
                           MtrA   1 kkepaegWPvvkGdyevGdaespvavvtlgshleeeavleaGaaiaGplktenlGiekvvanvisnpnirflivtGaevk 80 
                                    kk+pae WPv++G+yevG++espvavvt+gshl+++++++aGaa+aGp+kten+Giek+vanvisnpnir+li+tG+evk
  gi|116754678|ref|YP_843796.1|   4 KKKPAEPWPVITGEYEVGNPESPVAVVTCGSHLNNAELVAAGAALAGPCKTENIGIEKMVANVISNPNIRYLIITGMEVK 83 
                                    89****************************************************************************** PP

                                    TT-HHHHHHHHHHH-B-TTSBBTT--SSS-B-SSS-HHHHHHHHHH-EEEEEET---HHHHHHHHHHHHHT-----SS-- CS
                           MtrA  81 GhitGqalkalhenGvdkekkivgakGaiPfienlteeaverfqeqvelvdlidtedvgaikakikelvakdpgafeeep 160
                                    GhitGqa++a++++G+dke++ivgakGaiPfi+nlt ea+er+++q+ ++++idted+gai+akikelvakdpga++ ep
  gi|116754678|ref|YP_843796.1|  84 GHITGQAIEAFTASGIDKEGRIVGAKGAIPFIQNLTPEAIERWRQQITTINMIDTEDMGAITAKIKELVAKDPGALDVEP 163
                                    ******************************************************************************** PP

                                    -----XXXXXXX CS
                           MtrA 161 lvievkeeeeee 172
                                    +++e+ke+++ee
  gi|116754678|ref|YP_843796.1| 164 MIVEIKEGAGEE 175
                                    *******98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1766.18
//
Query:       gi|116754679|ref|YP_843797.1|  [L=116]
Description: tetrahydromethanopterin S-methyltransferase subunit B [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-36  123.9   0.1      3e-36  123.7   0.1    1.1  1  MtrB      Tetrahydromethanopterin S-methyltransferase subunit


Domain annotation for each model (and alignments):
>> MtrB  Tetrahydromethanopterin S-methyltransferase subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.7   0.1   1.7e-40     3e-36       1      94 []       3      96 ..       3      96 .. 0.98

  Alignments for each domain:
  == domain 1  score: 123.7 bits;  conditional E-value: 1.7e-40
                           MtrB  1 lvkvlpelnlvldpetgvvaearedvvllsldpvleeidkLekiaddlvnsLdpetallesypgRektlviaGlltnlfyGf 82
                                   +v++ pel+l +dp +gvvae+redvvl+++dpv+++id+L++iaddlvn+L p+++llesy++R kt++i+Gl+tn++ Gf
  gi|116754679|ref|YP_843797.1|  3 YVRISPELGLLFDPLKGVVAEQREDVVLYTFDPVMDRIDRLDAIADDLVNQLVPDNELLESYKNRGKTSLIGGLYTNIWVGF 84
                                   79******************************************************************************** PP

                           MtrB 83 ivglviaallal 94
                                   i+glvi++++++
  gi|116754679|ref|YP_843797.1| 85 IIGLVISFVVLI 96
                                   ********9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 879.05
//
Query:       gi|116754680|ref|YP_843798.1|  [L=275]
Description: tetrahydromethanopterin S-methyltransferase subunit C [Methanosaeta thermophila PT]
Scores for complete 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-99  331.9  27.9    2.5e-99  331.7  27.9    1.0  1  MtrC      Tetrahydromethanopterin S-methyltransferase, subuni
  ------ inclusion threshold ------
      0.082   13.2   0.2      0.082   13.2   0.2    4.0  4  Ost5      Oligosaccharyltransferase subunit 5
        3.1    7.7  12.9      0.073   13.0   2.3    3.0  3  DUF418    Protein of unknown function (DUF418)


Domain annotation for each model (and alignments):
>> MtrC  Tetrahydromethanopterin S-methyltransferase, subunit C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  331.7  27.9  4.1e-103   2.5e-99       1     265 [.       1     271 [.       1     274 [. 0.98

  Alignments for each domain:
  == domain 1  score: 331.7 bits;  conditional E-value: 4.1e-103
                           MtrC   1 msaggggkeaeeaipekkllalgivggligiylasvl....epalgsllaalgaicaivwGadavrrvasYglGTGVPSi 76 
                                    m+++gg+ +a +aip++kl ++g+ g+l+giyla+vl    +++++s+laa+ga++a v+Ga+avrrv+ Yg+GTGVPSi
  gi|116754680|ref|YP_843798.1|   1 MTVAGGAPTAPAAIPAEKLRIYGLGGALVGIYLAAVLnsvlDTDIFSVLAAVGAVAAAVTGANAVRRVCGYGIGTGVPSI 80 
                                    7899********************************99999999************************************ PP

                           MtrC  77 gmlalgmGivaalaglavgsalkl.lagpiialvvaliiglvvgvlakkvikmkipileksttelaaagalsiiglsvai 155
                                    gmlalgmGiv+a +g++++++l   +ag iialv+a+++g++vg++a+kv++++ipi+e+++t+l++aga++iig+s+ai
  gi|116754680|ref|YP_843798.1|  81 GMLALGMGIVGASFGFSTAQQLGVsMAGVIIALVYAMVFGYIVGTIANKVLGFGIPIMEEGLTDLSGAGAMAIIGWSYAI 160
                                    *********************9999******************************************************* PP

                           MtrC 156 agsfeikailskviatGliallfilaglailhPfNaclGPdEkqdRTLklalekgalaliivgivsletesaaa.lvvii 234
                                    +gs+++ ++++kv++tG++a++fi++glailhPfNa+lGPdEkqdRTL+++l+ g+la+++vg++sl+t saaa l++ii
  gi|116754680|ref|YP_843798.1| 161 SGSLAYVDLVDKVFNTGYLAIVFICGGLAILHPFNANLGPDEKQDRTLVNGLMVGSLAVVAVGLCSLATLSAAAaLITII 240
                                    *******************************************************************9988766599*** PP

                           MtrC 235 vgliiWlisfkkfvklvkrdaakvkgtgllP 265
                                    +g+++W+++++++++lvkrdaa+v+gtgllP
  gi|116754680|ref|YP_843798.1| 241 IGAAAWYYFYVWYYRLVKRDAAAVVGTGLLP 271
                                    ******************************9 PP

>> Ost5  Oligosaccharyltransferase subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.5     0.029   1.8e+02       8      63 ..      15      65 ..      10      73 .. 0.62
   2 ?   -2.2   3.8      0.89   5.3e+03      15      33 ..      80      98 ..      76     137 .. 0.49
   3 ?   13.2   0.2   1.4e-05     0.082      13      68 ..     177     232 ..     166     237 .. 0.92
   4 ?   -1.5   0.1      0.54   3.2e+03      15      31 ..     234     250 ..     228     266 .. 0.65

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.029
                           Ost5  8 ppslqptlafvllligllltalfflyevtstkkkrslvkelllalvASlflGfGvv 63
                                   p + + ++++   l+g+ l+a+   +   s + ++ +   +++++vA++  G  +v
  gi|116754680|ref|YP_843798.1| 15 PAEKLRIYGLGGALVGIYLAAVL--N---SVLDTDIFSVLAAVGAVAAAVTGANAV 65
                                   55555566666666666666666..3...334445577778888888888887666 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.89
                           Ost5 15 lafvllligllltalffly 33
                                   +++++l +g++ +++ f  
  gi|116754680|ref|YP_843798.1| 80 IGMLALGMGIVGASFGFST 98
                                   5555555555555444332 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 1.4e-05
                           Ost5  13 ptlafvllligllltalfflyevtstkkkrslvkelllalvASlflGfGvvfllla 68 
                                     +la+v++  gl+++  f  +    +k+ r+lv+ l+++ +A +++G+ ++++l a
  gi|116754680|ref|YP_843798.1| 177 GYLAIVFICGGLAILHPFNANLGPDEKQDRTLVNGLMVGSLAVVAVGLCSLATLSA 232
                                    79****************99999999999*********************999866 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 0.54
                           Ost5  15 lafvllligllltalff 31 
                                     a+++++ig +   +f 
  gi|116754680|ref|YP_843798.1| 234 AALITIIIGAAAWYYFY 250
                                    45566666666666654 PP

>> DUF418  Protein of unknown function (DUF418)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1       0.2   1.2e+03      24      62 ..      26      56 ..      16      62 .. 0.43
   2 ?   13.0   2.3   1.2e-05     0.073      12      81 ..      60     129 ..      49     152 .. 0.90
   3 ?    0.4   1.2     0.093   5.6e+02      24      51 ..     216     234 ..     176     266 .. 0.53

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.2
                         DUF418 24 gllvglplnlllavlaeaaeesallelllsvlrylagll 62
                                   g+lvg+ l+++l         s+l + ++svl ++++++
  gi|116754680|ref|YP_843798.1| 26 GALVGIYLAAVLN--------SVLDTDIFSVLAAVGAVA 56
                                   3333333333332........444444444444444444 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 1.2e-05
                         DUF418  12 ehkrllrrllligllvglplnlllavlaeaaeesallelllsvlrylaglllalgyvalillllakekrr 81 
                                       +++rr++++g+  g+p   +la+ +++   s++ ++++++  ++ag+++al+y++++++++ + +++
  gi|116754680|ref|YP_843798.1|  60 TGANAVRRVCGYGIGTGVPSIGMLALGMGIVGASFGFSTAQQLGVSMAGVIIALVYAMVFGYIVGTIANK 129
                                    567789********************************************************99888775 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.093
                         DUF418  24 gllvglplnlllavlaeaaeesallell 51 
                                    +l+v +++ + la         +l + +
  gi|116754680|ref|YP_843798.1| 216 SLAVVAVGLCSLA---------TLSAAA 234
                                    2222222222222.........222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       889  (0.0495845); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 1930.70
//
Query:       gi|116754681|ref|YP_843799.1|  [L=229]
Description: tetrahydromethanopterin S-methyltransferase subunit D [Methanosaeta thermophila PT]
Scores for complete 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-92  309.5  22.8    1.5e-92  309.2  22.8    1.1  1  MtrD      Tetrahydromethanopterin S-methyltransferase, subuni
  ------ inclusion threshold ------
      0.027   13.3   0.2       0.05   12.4   0.2    1.4  1  EcsB      Bacterial ABC transporter protein EcsB


Domain annotation for each model (and alignments):
>> MtrD  Tetrahydromethanopterin S-methyltransferase, subunit D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  309.2  22.8   1.7e-96   1.5e-92       2     218 .]       8     215 ..       7     215 .. 0.98

  Alignments for each domain:
  == domain 1  score: 309.2 bits;  conditional E-value: 1.7e-96
                           MtrD   2 illliliviggvligvgvhfvPvGGapaamaqatGvgtGtaqlaaGagltGlltaaalaektdslllillsGavgamlml 81 
                                    i+++++i++gg+l+gvgvhfvPvGGapaamaqatGvgtGt+qlaaG+gltGll+a++++++td+++ il+sGavgam+m+
  gi|116754681|ref|YP_843799.1|   8 IVYILEIIVGGLLVGVGVHFVPVGGAPAAMAQATGVGTGTVQLAAGSGLTGLLAAGLMMSVTDNIWPILASGAVGAMIMI 87 
                                    899***************************************************************************** PP

                           MtrD  82 aitmlvgnliyvygvGvvaasakvekdpitgdkqekyvsqGteGhgiPtvsfvsGviGgllgGiGGalvyyallellkaa 161
                                    + tm+vg +iy y+vG + asakv++dpitg++q  yv++Gt G+giPtvsfvsG+iGg++gG+GGal+yy l+ +++  
  gi|116754681|ref|YP_843799.1|  88 DATMMVGGWIYAYAVGAPFASAKVNYDPITGYSQPPYVAPGTVGQGIPTVSFVSGTIGGFMGGLGGALIYYPLMMINH-- 165
                                    *************************************************************************96655.. PP

                           MtrD 162 lklaaaaavalaailavglflvnavlasynigGtieGfhdpkfkrlpkavvaslvas 218
                                           + +l+a++a+g+flvnavlas+ni+GtieGfhdpkfkr++ka+ ++lva+
  gi|116754681|ref|YP_843799.1| 166 -------NPSLSALFAIGIFLVNAVLASWNIQGTIEGFHDPKFKRWTKAFRSCLVAT 215
                                    .......799********************************************986 PP

>> EcsB  Bacterial ABC transporter protein EcsB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   5.6e-06      0.05     114     185 ..     154     225 ..     138     229 .] 0.72

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.6e-06
                           EcsB 114 llillPlllettglsiaelllllllllllkl..lnlllkweelrlqgkkkrridrlirlllnalllylllalap 185
                                    +li +Pl+++ ++ s+++l+++ ++l+ + l  +n++   e ++  ++k +r+ + +r +l a l+ +l+a+++
  gi|116754681|ref|YP_843799.1| 154 ALIYYPLMMINHNPSLSALFAIGIFLVNAVLasWNIQGTIEGFH--DPKFKRWTKAFRSCLVATLILALVAVTI 225
                                    789****************9999998866661255555555555..6666666666666666666666665554 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:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1759.66
//
Query:       gi|116754682|ref|YP_843800.1|  [L=301]
Description: tetrahydromethanopterin S-methyltransferase subunit E [Methanosaeta thermophila PT]
Scores for 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-129  430.1   9.1   3.5e-129  429.9   9.1    1.0  1  MtrE      Tetrahydromethanopterin S-methyltransferase, subuni
  ------ inclusion threshold ------
        1.3    9.3   9.6       0.18   12.1   4.9    2.0  2  GtrA      GtrA-like protein


Domain annotation for each model (and alignments):
>> MtrE  Tetrahydromethanopterin S-methyltransferase, subunit E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  429.9   9.1  3.9e-133  3.5e-129       1     271 []       6     278 ..       6     278 .. 0.99

  Alignments for each domain:
  == domain 1  score: 429.9 bits;  conditional E-value: 3.9e-133
                           MtrE   1 lGvlalmgalatiagaaedlesdvgsqsnpnsqvqLapqmgylhrifnkaisGePvaygllaavagavalvllsalklnv 80 
                                    +G++a+mgalat+aga+ed+esdvgsqsnpnsqvqLa+q+g++hri+nkaisGeP+a++l+a++a++va++l++++ +++
  gi|116754682|ref|YP_843800.1|   6 MGLVAAMGALATVAGASEDIESDVGSQSNPNSQVQLAAQVGNPHRIYNKAISGEPPANALWATTAAVVAYTLITKFAMPA 85 
                                    8******************************************************************************* PP

                           MtrE  81 vlaivlgalvaalvhgvyavtaylGriasqakfkqpvyldvlkshlgaivahafiavfaivvlsylmtlvlk..hpfplp 158
                                    ++ai++ga+vaal++gv++++ay+Gr+asq++f+q++yld+++ ++++i+aha+i++f+i++++y++t++l+  hpfp+p
  gi|116754682|ref|YP_843800.1|  86 LFAIAVGASVAALFNGVFSTSAYFGRNASQRRFNQWIYLDIVRYTTPSIMAHAWITAFCITCIAYIQTQILMphHPFPMP 165
                                    ***********************************************************************888****** PP

                           MtrE 159 llaliwGitvGaiGsstGdvhyGaereyqkkefGaGvpvaasGdivrkaeaGlrnsidnalfcakfggpltGlafglivf 238
                                    ++a+iwGi+vGaiGss+Gd+hyG ere+q + fG+G++++ sG+ivrkaeaGlrnsidna+fcak+ggp+tGlafgl+vf
  gi|116754682|ref|YP_843800.1| 166 VIAMIWGIAVGAIGSSVGDIHYGGEREFQWRIFGQGLNTMLSGQIVRKAEAGLRNSIDNAWFCAKLGGPFTGLAFGLVVF 245
                                    ******************************************************************************** PP

                           MtrE 239 lelWrtivfekvtagwlavivgliivllliiln 271
                                    l++Wrt+vf++vt++ la+ +gl++v+l+ ++n
  gi|116754682|ref|YP_843800.1| 246 LDSWRTTVFDPVTQSGLAIGMGLFFVILMNLYN 278
                                    *****************************9987 PP

>> GtrA  GtrA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   4.9     2e-05      0.18      10     106 ..      68     178 ..      64     204 .. 0.70
   2 ?   -1.9   0.1      0.41   3.7e+03       9      21 ..     261     273 ..     237     283 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2e-05
                           GtrA  10 tlvdlallllllellglsyllAnaiafivailfnFilnrrwtFkdrekakl.....lkqflkFvlvsllglllnllilwl 84 
                                    t   +++++l++  + +++l+A a++  va+lfn +++    F ++ ++++       +++++   s+++ +  +++   
  gi|116754682|ref|YP_843800.1|  68 TTAAVVAYTLIT-KFAMPALFAIAVGASVAALFNGVFSTSAYFGRNASQRRfnqwiYLDIVRYTTPSIMAHAWITAFCIT 146
                                    555566666776.56*****************************999987744444444455555555555555555555 PP

                           GtrA  85 lveklgleall..........aklvgiivalv 106
                                    ++ +++ + l+          a++ gi+v+++
  gi|116754682|ref|YP_843800.1| 147 CIAYIQTQILMphhpfpmpviAMIWGIAVGAI 178
                                    55555543333777777666666666666655 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.41
                           GtrA   9 gtlvdlallllll 21 
                                    g ++ ++l++++l
  gi|116754682|ref|YP_843800.1| 261 GLAIGMGLFFVIL 273
                                    3344444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2363.57
//
Query:       gi|116754683|ref|YP_843801.1|  [L=178]
Description: hypothetical protein Mthe_1386 [Methanosaeta thermophila PT]
Scores for 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-53  180.9   4.8    2.2e-53  180.8   4.8    1.0  1  CarS-like     CDP-archaeol synthase
    7.3e-07   29.2   3.4    7.3e-07   29.2   3.4    1.9  2  CTP_transf_1  Cytidylyltransferase family
  ------ inclusion threshold ------
      0.091   12.2   2.8       0.15   11.5   2.8    1.3  1  DUF92         Integral membrane protein DUF92


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 !  180.8   4.8   3.7e-57   2.2e-53       2     175 .]       1     178 []       1     178 [] 0.94

  Alignments for each domain:
  == domain 1  score: 180.8 bits;  conditional E-value: 3.7e-57
                      CarS-like   2 ldlilksiylllpayvanasavlvGGGtpvdlGktlvdGrrliGdGvtyrGtvaGvlvGvlvgliqglleklsilaldss 81 
                                    +++i++si+l+lpayv+n++a l+GGGtp+d+G++l dG+r+ G+G+t rGt+aGv++G++vgl+q  +    +  l s+
  gi|116754683|ref|YP_843801.1|   1 MNIIVHSIWLMLPAYVPNNFAALFGGGTPLDMGMSLPDGHRVFGNGKTIRGTIAGVAGGIIVGLLQNSI--AGVFGLPSF 78 
                                    589******************************************************************..456889999 PP

                      CarS-like  82 gsvlefvilalllafGallGdavGsfikrrlkierGkpalildqldfvlgalllayp......vkllpieliilivlitl 155
                                    g  +e +++ + l+ G++lGd++ sfikrrl+++rG  + ++dqldfv+ga +l++        + ++  +iil++lit+
  gi|116754683|ref|YP_843801.1|  79 GDGMELFLVLFGLSAGSMLGDLTASFIKRRLGMKRGASFFLVDQLDFVMGAWALTFLlapewfNAQFTSPVIILVLLITP 158
                                    999************************************************99885433354457899************ PP

                      CarS-like 156 vlhlsaniiayklglkdvwy 175
                                    vlh  an+i y +g k+ ++
  gi|116754683|ref|YP_843801.1| 159 VLHRFANVIGYMIGAKKEPW 178
                                    ***************99887 PP

>> CTP_transf_1  Cytidylyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   3.4   1.2e-10   7.3e-07     170     233 ..      46     112 ..      45     118 .. 0.83
   2 ?    0.2   0.4     0.085   5.1e+02     118     153 ..     133     166 ..     113     176 .. 0.40

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 1.2e-10
                                    --BHHHHHHHHHHHHHHHHHHHHHHHCTS---TTSHHHHHHH...HHHHHHHHHHHHHHHHHHHT-S CS
                   CTP_transf_1 170 kKTveGfigGlvaavvvglllalvlskalalsllhllllsll...lslvavfGDLveSglKRafgiK 233
                                    +KT+ G i+G+++ ++vgll  ++++ +  +s+  ++ l l+   ls  +++GDL++S +KR++g K
  gi|116754683|ref|YP_843801.1|  46 GKTIRGTIAGVAGGIIVGLLQNSIAGVFGLPSFGDGMELFLVlfgLSAGSMLGDLTASFIKRRLGMK 112
                                    6***********************99988777766554433311267889***************99 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.085
                                    HHHH.TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   CTP_transf_1 118 vlllqslllienikeglllvllllalvvaaDigaYf 153
                                    ++ll +  ++++++++ + ++l+l+++ +   +a +
  gi|116754683|ref|YP_843801.1| 133 TFLL-APEWFNAQFTSPV-IILVLLITPVLHRFANV 166
                                    2222.2222222222222.22222223333333333 PP

>> DUF92  Integral membrane protein DUF92
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   2.8   2.4e-05      0.15     145     188 ..      48     103 ..      44     113 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.4e-05
                          DUF92 145 sllGllasllGalliall..avlllllel..........lillltla.GllGsllDS 188
                                    ++ G++a+++G+++++ll  + ++ ++ l          l+l+++ a  +lG l+ S
  gi|116754683|ref|YP_843801.1|  48 TIRGTIAGVAGGIIVGLLqnS-IAGVFGLpsfgdgmelfLVLFGLSAgSMLGDLTAS 103
                                    899*************99752.44444446778886654333333331445555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 1284.27
//
Query:       gi|116754684|ref|YP_843802.1|  [L=170]
Description: nitroreductase [Methanosaeta thermophila PT]
Scores for complete 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   86.4   2.2    1.3e-12   48.1   0.5    2.4  3  Nitroreductase  Nitroreductase family
      1e-08   35.1   0.0      8e-08   32.1   0.0    2.7  1  TM1586_NiRdase  Putative TM nitroreductase
  ------ inclusion threshold ------
      0.022   14.6   0.0      0.043   13.7   0.0    1.4  1  DUF5547         Family of unknown function (DUF5547)


Domain annotation for each model (and alignments):
>> Nitroreductase  Nitroreductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   0.5   2.1e-16   1.3e-12       1      55 [.       5      59 ..       5      64 .. 0.95
   2 !   38.2   0.0   2.5e-13   1.5e-09      81     170 .]      62     149 ..      58     149 .. 0.87
   3 ?   -2.6   0.1      0.86   5.1e+03      13      21 ..     155     163 ..     153     164 .. 0.78

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 2.1e-16
                                   HHH--B---B-S----HHHHHHHHHHHHTS--GGG---EEEEEE.-CCCHHHHHH CS
                 Nitroreductase  1 irkRrSiRkFddepvpkeelekileaarraPsagnlqpwrfvvvqdkelryklae 55
                                   +r+RrSiR ++++ +++e++e + eaa r+P++ +++pwrf+ ++d++++++l  
  gi|116754684|ref|YP_843802.1|  5 LRSRRSIRRYKAKDIEPEKVELLKEAALRSPTSRGINPWRFFFIRDRKTLEELSR 59
                                   589***********************************************99976 PP

  == domain 2  score: 38.2 bits;  conditional E-value: 2.5e-13
                                    HHHHHHHHHSSEEEEE---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGG.........GGHHHHH CS
                 Nitroreductase  81 lkaqkalagapvlivivatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfd.........eaaeevr 151
                                    ++  ++l++a + +v+          a+e++ ++ + d+++a   + L+A++lGlgsc+i   +         e+   vr
  gi|116754684|ref|YP_843802.1|  62 ESGSSFLKDARLGVVV---------CAKESESDVWIEDCSIASIIMHLTAHSLGLGSCWIQIRNrmhnasktsEE--YVR 130
                                    6667788888888888.........788888888899***************************88877764444..6** PP

                                    HHHT-S..SEEEEEEEEE- CS
                 Nitroreductase 152 kllglpdeeeivvliavGy 170
                                    ++lglp++ ++  +ia+Gy
  gi|116754684|ref|YP_843802.1| 131 EVLGLPEDLRVESIIAFGY 149
                                    ******************9 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.86
                                    ----HHHHH CS
                 Nitroreductase  13 epvpkeele 21 
                                     pvpkeele
  gi|116754684|ref|YP_843802.1| 155 PPVPKEELE 163
                                    56*****98 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0   1.3e-11     8e-08       4     141 ..       3     160 ..       1     169 [. 0.69

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 1.3e-11
                                    HHHHH--B---B--S---HHHHHHHHH-----S...S--...---EE.E................-SSSSEEEE----SS CS
                 TM1586_NiRdase   4 eaiekRhsvRkYkdealeeelleelkeaieeinkesgle...lqlvidenkafk...skvaklgkfkgvpnyialvgekk 77 
                                    + ++ R+s+R+Yk + +e+e++e lkea+ +  +  g++   + ++ d ++ ++   +k ++  + k+++  ++++++++
  gi|116754684|ref|YP_843802.1|   3 DLLRSRRSIRRYKAKDIEPEKVELLKEAALRSPTSRGINpwrFFFIRDRKTLEElsrAKESGSSFLKDARLGVVVCAKES 82 
                                    67899***********************9999888888732233333333332210023333445666666566665555 PP

                                    ..HHHHHHHHHHHHHHHHHHHHTT-EEEEES--SST.....................T-S-EEEEE-BS---..-.-- CS
                 TM1586_NiRdase  78 ..edleekaGYygeqlvLkltalGlgtcWvggtykk..........kkakvelkkgeklvivIalGyaktkl..veak 141
                                      + + e +      + L + +lGlg+cW+ +              +++ + l+++ ++  +Ia+Gy+++++  v+++
  gi|116754684|ref|YP_843802.1|  83 esDVWIEDCSIASIIMHLTAHSLGLGSCWIQIRNRMhnasktseeyVREVLGLPEDLRVESIIAFGYPDETKppVPKE 160
                                    34778999*********************9865433223334444555667889999***********9987333444 PP

>> DUF5547  Family of unknown function (DUF5547)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   7.1e-06     0.043      87     115 ..      55      83 ..      46      91 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.1e-06
                        DUF5547  87 enftrsegtGtGylsekalGsvvyvkesd 115
                                    e+++r++++G+ +l +  lG vv+ kes+
  gi|116754684|ref|YP_843802.1|  55 EELSRAKESGSSFLKDARLGVVVCAKESE 83 
                                    789************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1307.98
//
Query:       gi|116754685|ref|YP_843803.1|  [L=456]
Description: hypothetical protein Mthe_1388 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    0.00024   20.8   0.0    0.00051   19.7   0.0    1.6  1  cobW        CobW/HypB/UreG, nucleotide-binding domain
  ------ inclusion threshold ------
       0.02   14.1   0.0      0.042   13.1   0.0    1.5  1  Zeta_toxin  Zeta toxin


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 !   19.7   0.0   5.7e-08   0.00051     110     176 ..     246     309 ..     224     310 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 5.7e-08
                                    CCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHHHCHC..HHHHHHHHHHHHTTS-EE CS
                           cobW 110 ltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDlldeeallekleerlrqlnpeakvl 176
                                    ++ d  v+v Da +    +e +   +   + +ad++v+nK++ ++e+ +++ +e+ + +lnp+akv+
  gi|116754685|ref|YP_843803.1| 246 VRPDLWVTVADAMR--PGHELTYYPGSINFRCADIIVINKVNSASED-DVAIIERNAARLNPRAKVF 309
                                    56688899999944..5667777788889****************99.66**************997 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.6e-06     0.042       9      59 ..     130     177 ..     125     195 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.6e-06
                     Zeta_toxin   9 k.ypsqerPklillgGqpGAGKselaellkdelerqgnvvrldpDdlRelhP 59 
                                    + ++++++P++ + +  +GAGKs++ ++++d l    + ++l+p  +R   P
  gi|116754685|ref|YP_843803.1| 130 RtMIRSSKPVVAVCAVRTGAGKSQTTRYVADVL----RSLHLKPAVIRHPMP 177
                                    336889*************************99....678888877776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 3550.49
//
Query:       gi|116754686|ref|YP_843804.1|  [L=239]
Description: XRE family transcriptional regulator [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.8e-12   45.1   0.0    2.2e-11   43.6   0.0    1.8  1  HTH_3           Helix-turn-helix
    7.5e-08   32.3   0.0    1.7e-07   31.1   0.0    1.6  1  HTH_19          Helix-turn-helix domain
    1.8e-06   28.2   0.0    4.1e-06   27.1   0.0    1.6  1  HTH_31          Helix-turn-helix domain
  ------ inclusion threshold ------
       0.02   15.0   0.0      0.047   13.8   0.0    1.6  2  MqsA_antitoxin  Antitoxin component of bacterial toxin-antito
      0.044   14.2   0.0       0.13   12.8   0.0    1.8  1  HTH_26          Cro/C1-type HTH DNA-binding domain
       0.12   12.3   0.1       0.72    9.8   0.0    2.3  3  HTH_25          Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   0.0   7.4e-15   2.2e-11       1      48 [.      32      80 ..      32      84 .. 0.98

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 7.4e-15
                                   HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTT.SSCSBHHHHHHHHHHH CS
                          HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnG.ernPsletlkklakaL 48
                                   l+++R   g+sq+eL+ +lG+s+s is++E+G +r+P + ++ k+ +aL
  gi|116754686|ref|YP_843804.1| 32 LRKWRRNFGISQTELSNYLGISPSVISDYESGrRRSPGILIVSKIIDAL 80
                                   89*******************************************9998 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.0   5.8e-11   1.7e-07       1      53 [.      29      88 ..      29      94 .. 0.83

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 5.8e-11
                         HTH_19  1 GerLkeaReelgltqeelaerlgisrskisaiEngkkdvps.......aelllkiaealg 53
                                   Ge L++ R+++g++q el++ lgis+s is +E+g++  p+       ++ llki e+ g
  gi|116754686|ref|YP_843804.1| 29 GETLRKWRRNFGISQTELSNYLGISPSVISDYESGRRRSPGilivskiIDALLKIDELRG 88
                                   899********************************8879996665555555577777666 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   1.4e-09   4.1e-06       3      43 ..      29      69 ..      29      83 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 1.4e-09
                         HTH_31  3 GalLralReraGLsqeevAerlgvsestlsrlEqGrrgrps 43
                                   G++Lr +R+  G+sq+e+   lg+s+s +s++E+Grr  p 
  gi|116754686|ref|YP_843804.1| 29 GETLRKWRRNFGISQTELSNYLGISPSVISDYESGRRRSPG 69
                                   899**********************************6554 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 ?   13.8   0.0   1.6e-05     0.047      66     114 ..      24      72 ..       4      87 .. 0.82
   2 ?   -2.9   0.0       2.2   6.7e+03      72      93 ..     144     165 ..     120     185 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.6e-05
                 MqsA_antitoxin  66 aelvdpafiarvrkkleldqreaaeifGgGvnafsryekGkvrpplalv 114
                                     ++  ++++++ r++++++q e+++ +G      s ye+G+ r+p  l+
  gi|116754686|ref|YP_843804.1|  24 LSQNPGETLRKWRRNFGISQTELSNYLGISPSVISDYESGRRRSPGILI 72 
                                    4455678899********************************9997665 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.2
                 MqsA_antitoxin  72 afiarvrkkleldqreaaeifG 93 
                                    + i +++  lel  ++  +i+G
  gi|116754686|ref|YP_843804.1| 144 TIIDSIKAILELLPEQFYKIYG 165
                                    3455555566666666666665 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 ?   12.8   0.0   4.2e-05      0.13       2      49 ..      32      79 ..      31      83 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.2e-05
                         HTH_26  2 LrelmadrgitkseLargtgisaatlsrlvkgkpervsldtLdkiCda 49
                                   Lr++ +  gi+++eL+  +gis + +s + +g+ +++ +   +ki da
  gi|116754686|ref|YP_843804.1| 32 LRKWRRNFGISQTELSNYLGISPSVISDYESGRRRSPGILIVSKIIDA 79
                                   788888899**********************99766666666666555 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00024      0.72       2      33 ..      32      63 ..      31      66 .. 0.91
   2 ?   -1.7   0.1      0.94   2.8e+03      35      55 ..     153     172 ..     151     174 .. 0.74
   3 ?   -3.4   0.0         3     9e+03      26      36 ..     198     208 ..     196     210 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00024
                                   HHHHHHTTT--HHHHHHHSS--HHHHHHHHCT CS
                         HTH_25  2 LraaRearglsleevaketkIrkdylealEed 33
                                   Lr+ R+  g+s  e+++ + I+++++   E++
  gi|116754686|ref|YP_843804.1| 32 LRKWRRNFGISQTELSNYLGISPSVISDYESG 63
                                   999**********************9887776 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.94
                                    -TTSS-HHHHHHHHHHHHHHT CS
                         HTH_25  35 fdalpepvylrgylrnYArlL 55 
                                    +++lpe+ + + y r+ Ar+L
  gi|116754686|ref|YP_843804.1| 153 LELLPEQ-FYKIYGRSTARAL 172
                                    5778888.4588888888877 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 3
                                    HHHHHHCT--T CS
                         HTH_25  26 ylealEeddfd 36 
                                    +l+ +E++++d
  gi|116754686|ref|YP_843804.1| 198 ILQGIEAERVD 208
                                    68999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1936.15
//
Query:       gi|116754687|ref|YP_843805.1|  [L=345]
Description: hypothetical protein Mthe_1390 [Methanosaeta thermophila PT]
Scores for complete 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-10   40.5   0.0    4.8e-10   39.5   0.0    1.6  1  ACP_syn_III_C   3-Oxoacyl-[acyl-carrier-protein (ACP)] syntha
    1.6e-06   27.9   0.0    3.8e-05   23.5   0.0    2.3  3  HMG_CoA_synt_C  Hydroxymethylglutaryl-coenzyme A synthase C t
      5e-05   22.8   0.3    7.6e-05   22.2   0.3    1.2  1  Thiolase_N      Thiolase, N-terminal domain
     0.0097   15.8   0.1      0.014   15.3   0.1    1.2  1  HMG_CoA_synt_N  Hydroxymethylglutaryl-coenzyme A synthase N t
  ------ inclusion threshold ------
       0.23   11.3   6.5      0.048   13.5   2.8    1.8  2  ACP_syn_III     3-Oxoacyl-[acyl-carrier-protein (ACP)] syntha


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 !   39.5   0.0   1.3e-13   4.8e-10       5      86 ..     222     303 ..     218     307 .. 0.90

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 1.3e-13
                                    T--GGG-SEEEE-SSSHHHHHHHHHHHT--GGGB--TH..HHH-B-GGGHHHHHHHHHHHTTSS-TT-EEEEEEEETTTE CS
                  ACP_syn_III_C   5 gltpedidalvphqanlriidavakklglpeekvvvnl..deyGntsaasiplaLdeaveegklkpgdlvllvgfGaGlt 82 
                                    g +ped d+ v+hq n ++   va klg+++e+++  l   ++Gnt + s ++ L+  ++  + +pg+ + +++fG G  
  gi|116754687|ref|YP_843805.1| 222 GKKPEDYDYAVFHQPNGKFPVRVAAKLGFTKEQIAPGLvvPHIGNTYSGSTLIGLAATLD--QAEPGESIFVTSFGSGAG 299
                                    6799****************************999665559*******************..89**************87 PP

                                    EEEE CS
                  ACP_syn_III_C  83 wgaa 86 
                                      a 
  gi|116754687|ref|YP_843805.1| 300 SDAF 303
                                    6665 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 ?   -2.7   0.0         1   3.6e+03     128     161 ..      46      79 ..      36      80 .. 0.79
   2 ?    2.8   0.0     0.022        77      68      92 ..     226     250 ..     208     252 .. 0.86
   3 !   23.5   0.0   1.1e-08   3.8e-05     138     207 ..     249     313 ..     241     336 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1
                                    HHHHHHHHHHHHHHHHTGGGGHHHHHH---GGGH CS
                 HMG_CoA_synt_C 128 lekallkiakelfkkkvkpsllvptevGnmYtas 161
                                    l+     ia e   + ++ + + p+++G +Yt s
  gi|116754687|ref|YP_843805.1|  46 LDEDTATIAVEAARNAISRANIDPHRIGAIYTGS 79 
                                    5556667777888888888889999999999987 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.022
                                    GG-SEEEE--SSHHHHHHHHHHHHH CS
                 HMG_CoA_synt_C  68 ddfdyvifhsPfcklvqkslarlly 92 
                                    +d+dy +fh P  k+  +  a+l +
  gi|116754687|ref|YP_843805.1| 226 EDYDYAVFHQPNGKFPVRVAAKLGF 250
                                    689**********998888887766 PP

  == domain 3  score: 23.5 bits;  conditional E-value: 1.1e-08
                                    HHHHHHTGGGGHHHHHH---GGGHHHHHHHHHHHHS-HHHHTT-EEEEEEEETTTEEEEEEEEE-S--ST CS
                 HMG_CoA_synt_C 138 elfkkkvkpsllvptevGnmYtaslyaalasllskvsadelagkriglfsYGsGlaaslfslrvkqdvse 207
                                     ++k++++p l+vp ++Gn Y  s    la+ l    ++   g++i + s+GsG  +  fs+rv++  + 
  gi|116754687|ref|YP_843805.1| 249 GFTKEQIAPGLVVP-HIGNTYSGSTLIGLAATL----DQAEPGESIFVTSFGSGAGSDAFSIRVTERIND 313
                                    47899999**9998.79****************....566679*********************998877 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.3   2.1e-08   7.6e-05      25     112 ..      52     139 ..      45     150 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 2.1e-08
                                    HHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-TTSEEEEEEHGGGHHHHHHHHHHHHHHTTSH CS
                     Thiolase_N  25 eLlaealkallekagvdpeevdevivGnvlqagegqniarqaalkagipeevpavtvnkvcsSglkavalaaqsiaagea 104
                                     ++ ea+++++++a++dp+ +  ++ G   +  + +     +  ++g +++ ++  ++ +c  g +a+ ++++ +++g +
  gi|116754687|ref|YP_843805.1|  52 TIAVEAARNAISRANIDPHRIGAIYTGSESHPYAVKPTGTIVGEAIGCSHSHTVADMEFACKAGTAALQACMGLVRSGMI 131
                                    6778999*************************999999999*************************************** PP

                                    SEEEEEEE CS
                     Thiolase_N 105 dvvvagGv 112
                                    d  +a+G+
  gi|116754687|ref|YP_843805.1| 132 DLGLAIGA 139
                                    ******97 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 !   15.3   0.1   3.9e-06     0.014       5     170 ..       3     164 ..       1     167 [. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.9e-06
                 HMG_CoA_synt_N   5 vgilaleiylpaqyvdqaelekfdgveagkytiglgqtrmgfvsdredinslsltvvqkllertkldydaigrlevgtet 84 
                                    vgi++  +y+p   ++  e+ +  g e    + gl   + +  +  ed  ++++   ++ + r ++d + ig +  g+e+
  gi|116754687|ref|YP_843805.1|   3 VGIVSYGVYIPRYRIKVDEIARVWG-EVEDIARGLNVYEKAVPDLDEDTATIAVEAARNAISRANIDPHRIGAIYTGSES 81 
                                    9***************999988654.334577899999999999************************************ PP

                 HMG_CoA_synt_N  85 iidksksvksvlmqlfeesgntdiegidtlnacyggtaalfnavnwiessawdgryalvvagdiaiydsgna.rptggag 163
                                         k   +++ + ++ s    +   d   ac  gtaal  ++  + s + d    l +  d++  + g+a   t  ag
  gi|116754687|ref|YP_843805.1|  82 HPYAVKPTGTIVGEAIGCSHSHTVA--DMEFACKAGTAALQACMGLVRSGMIDLG--LAIGADVSQGAPGDAlEYTAAAG 157
                                    9998899889888888887776664..7778*******************99965..55677888888877624577777 PP

                 HMG_CoA_synt_N 164 avallig 170
                                      a ++g
  gi|116754687|ref|YP_843805.1| 158 GAAYVVG 164
                                    7777776 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 ?   13.5   2.8   1.3e-05     0.048       2      64 ..     107     166 ..     106     180 .. 0.84
   2 ?   -3.8   0.1       3.3   1.2e+04      49      57 ..     291     299 ..     277     302 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.3e-05
                                    EEE-GGGHHHHHHHHHHHHHHTTS-SEEEEEEEEEGGGCS-TTTHHHHTTB-EEEEEEEEEEE CS
                    ACP_syn_III   2 DlnaaCsgfvyalsvAdaliesgaakrvLvigaetlskilDwkdrstavlfGDGAgAvvleas 64 
                                    D++ aC++ ++al+   +l++sg++   L iga++ s+       +  ++ + G++A v++a 
  gi|116754687|ref|YP_843805.1| 107 DMEFACKAGTAALQACMGLVRSGMIDLGLAIGADV-SQG--APGDALEYTAAAGGAAYVVGAA 166
                                    9999******************************9.553..3345677777888888888875 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 3.3
                                    HTTB-EEEE CS
                    ACP_syn_III  49 avlfGDGAg 57 
                                    ++ fG GAg
  gi|116754687|ref|YP_843805.1| 291 VTSFGSGAG 299
                                    456888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2569.37
//
Query:       gi|116754688|ref|YP_843806.1|  [L=387]
Description: acetyl-CoA acetyltransferase [Methanosaeta thermophila PT]
Scores for 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  100.5   0.1    1.5e-28   99.9   0.1    1.3  1  Thiolase_N       Thiolase, N-terminal domain
    7.3e-12   45.0   1.3    1.6e-11   44.0   0.5    2.0  2  Thiolase_C       Thiolase, C-terminal domain
      3e-06   27.0   3.3      3e-06   27.0   3.3    3.2  4  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal domain
  ------ inclusion threshold ------
      0.048   13.5   2.1        9.1    6.2   0.0    2.5  2  ACP_syn_III      3-Oxoacyl-[acyl-carrier-protein (ACP)] synth
      0.078   13.0   1.1        2.9    7.9   0.0    2.8  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 !   99.9   0.1   4.2e-32   1.5e-28       3     258 ..       6     224 ..       4     226 .. 0.89

  Alignments for each domain:
  == domain 1  score: 99.9 bits;  conditional E-value: 4.2e-32
                                    EEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCT.TSTSC.HHHHHHHHTTS-T.TSEEE CS
                     Thiolase_N   3 ivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqa.gegqn.iarqaalkagipe.evpav 79 
                                    i++   t +g+        s ++L  e++ a++e+agv+ e++d +++Gn+  + + +q  i   +a  ag+++ ++p++
  gi|116754688|ref|YP_843806.1|   6 IIGIGCTRFGE----RWGSSLRDLVVETGIAAIEDAGVTGEAIDALYIGNMSGGrFVEQEhIGALIADYAGLSRlHIPST 81 
                                    56666666666....44557889999**************************99988887699999999***86589*** PP

                                    EEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTT.TGGSSSSEEEEEHHHHHHTEETTTTSEHHHH CS
                     Thiolase_N  80 tvnkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvr.sglklgdekakdllipdgladafneehmGlt 158
                                    +v+ +c+Sg  a+ +a  ++a+g ad+v+a GvE+m++++  +++d+  + +  + e   + + p            ++ 
  gi|116754688|ref|YP_843806.1|  82 RVEAACASGGLALREAFLAVASGYADIVIAAGVEKMTDVSSGVAADALaAAADREWECFFGATFPA---------LYAMI 152
                                    *****************************************9998876244455556677778777.........889** PP

                                    HHHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHHTS-BSSSTTSS CS
                     Thiolase_N 159 aenlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLaklkpaFkkeGt 238
                                    a+   ++y+ +Re+++++Avk+h++++ ++ a+ ++ ei              + d+ i+s+++a++L+ l         
  gi|116754688|ref|YP_843806.1| 153 ARLHMRRYGTTREQLAQVAVKNHHHGHMNPIAQ-YHTEI--------------KVDDVINSPLVADPLRIL--------- 208
                                    *********************************.9999*..............89****************......... PP

                                    -BTTSB--BEEEEEEEEEEE CS
                     Thiolase_N 239 vtAgnasqisDGaaavllms 258
                                        ++s+i+DGaaav+l++
  gi|116754688|ref|YP_843806.1| 209 ----DCSPITDGAAAVVLAP 224
                                    ....*************986 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0       3.1   1.1e+04      31      44 ..      33      46 ..      28      49 .. 0.71
   2 !   44.0   0.5   4.4e-15   1.6e-11      23     113 ..     261     369 ..     238     383 .. 0.90

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 3.1
                                   HHHHHT--GGGESE CS
                     Thiolase_C 31 vlkkagltvedidl 44
                                   ++++ag+t e id+
  gi|116754688|ref|YP_843806.1| 33 AIEDAGVTGEAIDA 46
                                   67778888777776 PP

  == domain 2  score: 44.0 bits;  conditional E-value: 4.4e-15
                                    HHHHHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--G..................GGBSTT--HHHH-B-TTT CS
                     Thiolase_C  23 gPayaikkvlkkagltvedidlfEinEAFaaqaLavakaldldl..................ekvNvnGGaialGHPlGa 84 
                                    + +ya+kk+  +a lt +did+ E+++ F+   + ++++l++ +                    vN  GG  a GHP+Ga
  gi|116754688|ref|YP_843806.1| 261 ATVYAAKKAFAQARLTPADIDIAEVHDCFTIGEILAIEDLGFFPkgeggiateegrtsiggdVAVNTSGGLKACGHPVGA 340
                                    569***************************************999****************999**************** PP

                                    HHHHHHHHHHHHHHHCTTSEEEEEEEETT CS
                     Thiolase_C  85 sGaRivvtllselkkeggklgvaalCigg 113
                                    +G +++  ++ +l+ e gk  v+ + ig 
  gi|116754688|ref|YP_843806.1| 341 TGIKQAYEIVLQLRGEAGKRQVSDAEIGL 369
                                    **************999998887766654 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 ?   -3.1   0.1       1.3   4.5e+03       1      12 [.       1      12 [.       1      15 [. 0.87
   2 ?    2.6   0.0     0.023        83      91     128 ..      25      62 ..      20      77 .. 0.80
   3 !   27.0   3.3   8.5e-10     3e-06     167     222 ..      79     134 ..      73     143 .. 0.89
   4 ?   -1.8   0.0      0.52   1.9e+03      95     113 ..     265     283 ..     260     296 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.3
                                   X--EEEEEEEEE CS
                  ketoacyl-synt  1 aepvaivGmgar 12
                                   +++v i+G+g++
  gi|116754688|ref|YP_843806.1|  1 MRSVSIIGIGCT 12
                                   578*******96 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.023
                                    HHHHHHHHHHHHHTS-HHTCTTGGEEEEEEESSTHHHH CS
                  ketoacyl-synt  91 llleaawealedagltpeeldgsrvgvfiGvgagdyaa 128
                                    l++e+   a+edag+t e++d   +g++ G    ++++
  gi|116754688|ref|YP_843806.1|  25 LVVETGIAAIEDAGVTGEAIDALYIGNMSGGRFVEQEH 62 
                                    78899999************998888888877666654 PP

  == domain 3  score: 27.0 bits;  conditional E-value: 8.5e-10
                                    SEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHHHHHHHHTTBB-T CS
                  ketoacyl-synt 167 psvtvdtACsSslvavhaavqslrsgeadvalaGGvellltpeavagfsaagllsp 222
                                    ps  v++AC+S+  a+  a  ++ sg ad+++a Gve ++  ++ ++ +a+++ ++
  gi|116754688|ref|YP_843806.1|  79 PSTRVEAACASGGLALREAFLAVASGYADIVIAAGVEKMTDVSSGVAADALAAAAD 134
                                    8999********99999999************************999999996554 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 0.52
                                    HHHHHHHHHTS-HHTCTTG CS
                  ketoacyl-synt  95 aawealedagltpeeldgs 113
                                    aa++a+++a ltp+++d  
  gi|116754688|ref|YP_843806.1| 265 AAKKAFAQARLTPADIDIA 283
                                    899**********998755 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 ?    5.7   1.0    0.0037        13       3      39 ..      83     119 ..      82     134 .. 0.93
   2 ?    6.2   0.0    0.0025       9.1      52      78 ..     213     245 ..     199     247 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0037
                                    EE-GGGHHHHHHHHHHHHHHTTS-SEEEEEEEEEGGG CS
                    ACP_syn_III   3 lnaaCsgfvyalsvAdaliesgaakrvLvigaetlsk 39 
                                    ++aaC++   al  A  +++sg a  v+  g e++++
  gi|116754688|ref|YP_843806.1|  83 VEAACASGGLALREAFLAVASGYADIVIAAGVEKMTD 119
                                    689******************************9986 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0025
                                    B-EEEEEEEEEEE......SSSSCEEEEEEEEE CS
                    ACP_syn_III  52 fGDGAgAvvleas......eeegarildselgs 78 
                                      DGA+Avvl ++       ++ +ril+s++ s
  gi|116754688|ref|YP_843806.1| 213 ITDGAAAVVLAPTdiasrySDTPIRILASAQAS 245
                                    57********99955444433445566666555 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 ?   -4.1   0.0       4.3   1.6e+04      33      46 ..      33      46 ..      32      48 .. 0.81
   2 ?    7.9   0.0   0.00081       2.9      24      51 ..     260     287 ..     238     291 .. 0.84
   3 ?    2.7   0.1     0.034   1.2e+02      87     108 ..     334     355 ..     330     362 .. 0.90

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 4.3
                                   HHHHHT--GGGEEE CS
                Ketoacyl-synt_C 33 alaeagvdpedvdy 46
                                   a+++agv+ e +d 
  gi|116754688|ref|YP_843806.1| 33 AIEDAGVTGEAIDA 46
                                   78999999999885 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00081
                                    HHHHHHHHHHHHHHT--GGGEEEEE-SS CS
                Ketoacyl-synt_C  24 eaqaraiekalaeagvdpedvdyveahg 51 
                                    +a   a +ka+a+a+++p+d+d+ e h+
  gi|116754688|ref|YP_843806.1| 260 DATVYAAKKAFAQARLTPADIDIAEVHD 287
                                    5667789********************8 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.034
                                    H-B-GGGHHHHHHHHHHHHHHH CS
                Ketoacyl-synt_C  87 iGHleaAaGvaelikvvlalkh 108
                                     GH  +A G+ ++  +vl+l+ 
  gi|116754688|ref|YP_843806.1| 334 CGHPVGATGIKQAYEIVLQLRG 355
                                    7*****************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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: 2933.57
//
Query:       gi|116754689|ref|YP_843807.1|  [L=152]
Description: hypothetical protein Mthe_1392 [Methanosaeta thermophila PT]
Scores for complete 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-17   62.4   0.0    4.4e-17   61.8   0.0    1.2  1  OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
    2.6e-12   46.4   2.0    2.6e-12   46.4   2.0    1.9  2  DUF35_N        Rubredoxin-like zinc ribbon domain (DUF35_N)
  ------ inclusion threshold ------
       0.21   11.4   0.1       0.27   11.1   0.1    1.1  1  FdhE           Protein involved in formate dehydrogenase form


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 !   61.8   0.0   7.3e-21   4.4e-17       6      65 .]      70     128 ..      66     128 .. 0.94

  Alignments for each domain:
  == domain 1  score: 61.8 bits;  conditional E-value: 7.3e-21
                                    GG-EEEEEEEEEE-TTS-EEEEEEEEEEEE-TT...-EE-EEEEEEES..TT-B-EEE-S CS
                  OB_aCoA_assoc   6 grGtvysftvvhrappgfaeeaPyvvgvVeLdegvrimarlvgvdpdevriGmrVravfr 65 
                                    g+Gtv ++t+++   + f+  +Py +++++Ldeg+++++++v+  p+ ++iGmrVr vfr
  gi|116754689|ref|YP_843807.1|  70 GTGTVITYTTIYSGTEDFERLTPYNLAIIQLDEGPKLTGQVVC-SPEKMKIGMRVRPVFR 128
                                    9*****************************************6.56789*********97 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.1   6.8e+03      26      35 ..       8      17 ..       6      19 .. 0.76
   2 !   46.4   2.0   4.4e-16   2.6e-12       4      34 ..      30      60 ..      29      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.1
                        DUF35_N 26 avCphCgsdd 35
                                   + C++ ++d+
  gi|116754689|ref|YP_843807.1|  8 HWCTYSRGDT 17
                                   6799988875 PP

  == domain 2  score: 46.4 bits;  conditional E-value: 4.4e-16
                        DUF35_N  4 aaegrLvgqrCpdCGtvqfPPravCphCgsd 34
                                    +++ L+g++C++CG ++fPPr  Cp+C+++
  gi|116754689|ref|YP_843807.1| 30 PQRYNLIGTHCKSCGEYYFPPRTLCPNCRRT 60
                                   589*************************665 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 ?   11.1   0.1   4.5e-05      0.27     195     228 ..      38      71 ..      30      79 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.5e-05
                                    EEETTT--EEE--TTS-TTT---SS-EEE----- CS
                           FdhE 195 lhCslCeteWhvvRvkCsnCeetkelaylslede 228
                                     hC  C   +   R+ C nC  t +++ +s+ ++
  gi|116754689|ref|YP_843807.1|  38 THCKSCGEYYFPPRTLCPNCRRTGQMEEHSFRGT 71 
                                    59************************99998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); 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: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1170.24
//
Query:       gi|116754690|ref|YP_843808.1|  [L=628]
Description: DNA gyrase, B subunit [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-62  209.9   0.1    2.9e-62  209.2   0.1    1.3  1  DNA_gyraseB    DNA gyrase B
    3.8e-31  107.1   0.1    7.9e-31  106.0   0.1    1.6  1  DNA_gyraseB_C  DNA gyrase B subunit, carboxyl terminus
    6.1e-23   81.5   0.1    1.6e-22   80.1   0.1    1.8  1  HATPase_c      Histidine kinase-, DNA gyrase B-, and HSP90-li
    1.3e-19   70.3   0.0      4e-19   68.7   0.0    1.9  2  Toprim         Toprim domain
     0.0016   18.3   0.3     0.0038   17.0   0.0    1.8  2  HATPase_c_3    Histidine kinase-, DNA gyrase B-, and HSP90-li


Domain annotation for each model (and alignments):
>> DNA_gyraseB  DNA gyrase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  209.2   0.1     8e-66   2.9e-62       1     173 [.     220     388 ..     220     389 .. 0.99

  Alignments for each domain:
  == domain 1  score: 209.2 bits;  conditional E-value: 8e-66
                    DNA_gyraseB   1 GlkdfveelnkdkkelikevlsvegekaveevievevalqwtssysenilsFvNniatpeGGtHvdgfksaltktlneya 80 
                                    G+ +fv++lnk+k+ l+ +++++++    ++ + veva+q+++sy+e++++F+Nni+t+eGGtH++gf++altkt+n+++
  gi|116754690|ref|YP_843808.1| 220 GIISFVQYLNKSKEVLHPNPIYFSRVR--DD-VSVEVAMQYNTSYNESVFTFANNINTREGGTHLSGFRAALTKTVNDFV 296
                                    899**********************99..89.************************************************ PP

                    DNA_gyraseB  81 kkkkllkkkeekisgediregltavvsvkipepqFeGQTKekLgnsevksivekvvseeleafleenkeeakkilekave 160
                                    ++kkllk ++ k++g+d+regl+avvsv++p+pqFeGQTK++Lgns+v+++ve++vse l +++e n+++a++i+eka e
  gi|116754690|ref|YP_843808.1| 297 REKKLLKGDA-KLTGDDLREGLVAVVSVRLPDPQFEGQTKTRLGNSAVRGLVESLVSEGLMEYFELNPQVAEAIVEKATE 375
                                    *****99988.********************************************************************* PP

                    DNA_gyraseB 161 aakareaarkare 173
                                    a++areaarka+e
  gi|116754690|ref|YP_843808.1| 376 AMRAREAARKAKE 388
                                    ***********98 PP

>> DNA_gyraseB_C  DNA gyrase B subunit, carboxyl terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.0   0.1   2.2e-34   7.9e-31       3      63 .]     557     617 ..     555     617 .. 0.97

  Alignments for each domain:
  == domain 1  score: 106.0 bits;  conditional E-value: 2.2e-34
                  DNA_gyraseB_C   3 kveiqRfKGLGEmnpeqLweTTmdpetRrLlqvtiedaeeadelfstLmGkkvepRrefie 63 
                                    k+ +qR+KGLGEmnpeqLweTTm+pe+R+Ll+vt++da eade+fs+LmG++vepRr fie
  gi|116754690|ref|YP_843808.1| 557 KAVVQRYKGLGEMNPEQLWETTMNPEKRTLLRVTLKDAVEADEIFSVLMGEQVEPRRVFIE 617
                                    778*********************************************************8 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.1   0.1   4.5e-26   1.6e-22       2     111 ..      32     174 ..      31     175 .. 0.85

  Alignments for each domain:
  == domain 1  score: 80.1 bits;  conditional E-value: 4.5e-26
                                    HHHHHHHHHHHHHHHHHHH..HSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHT..............GTCSTTCHHC CS
                      HATPase_c   2 dekrLrqiisnlvdNavkf..atkageieveikaseddlvisveDnGiGipkedlk..............klfekfsqdd 65 
                                    d  +L++++ ++vdN+v++  a++++ei+v i+   +d ++sv+D+G+Gip+++++              + ++kf+  d
  gi|116754690|ref|YP_843808.1|  32 DVHGLHHLVYEVVDNSVDEamAGYCKEISVVIH---GDGSVSVKDDGRGIPVDIHPqynrpaveivmtvlHAGGKFDH-D 107
                                    7889***************6666**********...5*******************************877777****.* PP

                                    STCHTSTSSSHHHHHHHHHHHHTTTEEEE...................EEETTT......EEEEEEEEESS CS
                      HATPase_c  66 stkrggggtGlGlsivkklvelmgGeiwv...................esepgr......Gttftftlple 111
                                    ++ ++gg +G+G+s+v++l+e ++ e+++                   e           Gtt++f+++ e
  gi|116754690|ref|YP_843808.1| 108 TYHVSGGLHGVGVSVVNALSEWLEVEVSRegrvyrqryergrpvsdlqE----TgvsentGTTVRFKPDPE 174
                                    *********************9887777777777676665555554441....0344444*******9986 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.2     8e+03       4      17 ..     369     382 ..     343     392 .. 0.67
   2 !   68.7   0.0   1.1e-22     4e-19       1     102 [.     417     528 ..     417     529 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.2
                                    EESSHHHHHHHHHT CS
                         Toprim   4 ivEgpsdaktiaka 17 
                                    ivE+ + a+ +++a
  gi|116754690|ref|YP_843808.1| 369 IVEKATEAMRAREA 382
                                    55555555544443 PP

  == domain 2  score: 68.7 bits;  conditional E-value: 1.1e-22
                                    EEEEESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHS.TTEEEEE..ECTTTHHHHHH.....HHHHHHHHSEEEEECSS CS
                         Toprim   1 elvivEgpsdaktiakalgsgfqavtaslGhildlet.efkpvye..eiedkkkvlka.....lkelakradeiilatDp 72 
                                    el+ivEg+s+ +++++ +++ fqav++++G+il++e  +++++++  ei++ +++l++     ++  + r+++ii++tD+
  gi|116754690|ref|YP_843808.1| 417 ELYIVEGESAGGSAKQGRNRHFQAVLPLRGKILNVERaRLDKMLKneEIRNLITALGTgigddFDITKARYHKIIIMTDA 496
                                    69***********************************988888889999999999999********************** PP

                                    SHHHHHHHHHHHHHHT....HHHTTTEEEEEESS CS
                         Toprim  73 DreGeaiawellevlk....ellenkigrvefse 102
                                    D++G++i+++ll++++    +l+e+  g+v++++
  gi|116754690|ref|YP_843808.1| 497 DVDGSHIRTLLLTFFYrymqPLIEA--GYVYIAQ 528
                                    ****************555555555..8888876 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.1e-06    0.0038       7      46 ..      40      79 ..      34     129 .. 0.87
   2 ?   -3.5   0.1       2.4   8.7e+03      52      81 ..     378     407 ..     372     409 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.1e-06
                    HATPase_c_3  7 laelvdNsld....AdaenvkievnknrgktgeivieDdGkGms 46
                                   + e+vdNs+d    + +++++++++ +    g+++++DdG G++
  gi|116754690|ref|YP_843808.1| 40 VYEVVDNSVDeamaGYCKEISVVIHGD----GSVSVKDDGRGIP 79
                                   89********95544556688998886....69*********97 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.4
                    HATPase_c_3  52 nalrlatsskeakrkstslGkkGi.GlklAs 81 
                                    +a + a+++ke +r +t l + G+ G klA 
  gi|116754690|ref|YP_843808.1| 378 RAREAARKAKEITRRKTALTSSGLpG-KLAD 407
                                    44556777777778888888888866.8876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (628 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.42
# Mc/sec: 4457.61
//
Query:       gi|116754691|ref|YP_843809.1|  [L=796]
Description: DNA gyrase, A subunit [Methanosaeta thermophila PT]
Scores for 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-163  544.2   0.0   2.6e-163  543.9   0.0    1.1  1  DNA_topoisoIV  DNA gyrase/topoisomerase IV, subunit A
    8.3e-73  239.7  19.2    2.3e-16   59.0   0.2    7.0  7  DNA_gyraseA_C  DNA gyrase C-terminal domain, beta-propeller


Domain annotation for each model (and alignments):
>> DNA_topoisoIV  DNA gyrase/topoisomerase IV, subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  543.9   0.0  2.9e-167  2.6e-163       1     425 [.      27     465 ..      27     466 .. 0.99

  Alignments for each domain:
  == domain 1  score: 543.9 bits;  conditional E-value: 2.9e-167
                  DNA_topoisoIV   1 RaiPsvrDGlKPvqRriLyamfkl.lnldkkekKvaqlvGevlgkYhPHGdaslydaivrlaqdfvgniplldpqGnfGs 79 
                                    Ra+P+vrDGlKPv+RriLyam+++  + d+++kK+a++vG+v+gkYhPHGd ++yd++vr+aqdf+++++l+d+qGnfGs
  gi|116754691|ref|YP_843809.1|  27 RALPDVRDGLKPVHRRILYAMYEQgVTFDQPYKKSARIVGDVMGKYHPHGDVAIYDTMVRMAQDFSMRYTLIDGQGNFGS 106
                                    9******************************************************************************* PP

                  DNA_topoisoIV  80 ildgdkdAaaRYietrLskiarellkeidketvdyqenyDgsekEPevlppiiPnlLvnGaeGIavGmatkipphnlkei 159
                                    + dgd++Aa+RY+e+rLskia e+l++i+k+tvd+++nyDgs kEP+vlp+++PnlLvnG++GIavGmat+ipphnl+e+
  gi|116754691|ref|YP_843809.1| 107 V-DGDPPAAMRYTEVRLSKIAGEMLADIEKDTVDFVPNYDGSLKEPTVLPSRLPNLLVNGSTGIAVGMATNIPPHNLREV 185
                                    *.****************************************************************************** PP

                  DNA_topoisoIV 160 idaliallkgeea...ellelvlgPdfptgggiigkeeikeayetgrGkikvrakveie...e.ktivitElPigvntsk 232
                                    + ali+l+++++a   +l++++ gPdfptgg i+g+++i++ay tgrG+i++ra+ eie   + ++i+ tElP++vn++k
  gi|116754691|ref|YP_843809.1| 186 VYALIHLIENPDAsvtDLMNFIRGPDFPTGGYIVGRSGIESAYSTGRGTITIRARSEIEegrRgSRIIFTELPYQVNKAK 265
                                    ***********999********************************************9999569*************** PP

                  DNA_topoisoIV 233 liekieelvkkkkik.isdirdesdr.gvrivielkrgaseekvleklykktkLessisvnnlvlfdkkpkylslkeilk 310
                                    ++e i+elvk+++++ is+irdesdr g+r+v+elk+g+++++vl++l+k+t+Le+++ + nlvl+d++p++l+lke l+
  gi|116754691|ref|YP_843809.1| 266 VVEDIAELVKAGRVDgISEIRDESDReGIRLVVELKQGVNPQVVLNQLHKHTQLETTYGIINLVLVDGQPRTLTLKETLE 345
                                    ***********************9999***************************************************** PP

                  DNA_topoisoIV 311 eflevrlevyerrkeyllekleerleilegllkalnkidevievirkskkekkakkeLiee..lseeqaeyllemrlrrL 388
                                    ++++ r ev+err++++le++e+r++il g+l+al +idevi++ir+s + ++a++ L+++  lseeqa+++l+mrl+rL
  gi|116754691|ref|YP_843809.1| 346 QYINYRAEVIERRTRFELEQAEKRAHILAGILIALRDIDEVIALIRGSPSPSDARNLLMNRfgLSEEQARAILDMRLQRL 425
                                    ******************************************************************************** PP

                  DNA_topoisoIV 389 tkeeveklekeieelekeikelekllak...lkklikeel 425
                                    t +e+ek+ +e +ele++i++l+ +la+   + ++ik+el
  gi|116754691|ref|YP_843809.1| 426 TGLEQEKVASEARELESTIARLKGILASrteVLDIIKNEL 465
                                    ***************************9777778888776 PP

>> DNA_gyraseA_C  DNA gyrase C-terminal domain, beta-propeller
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.2       0.3   2.7e+03      31      45 ..     376     390 ..     376     391 .. 0.86
   2 !   38.2   0.1   8.2e-14   7.3e-10       4      47 ..     500     543 ..     498     544 .. 0.95
   3 !   25.7   0.0   6.6e-10   5.9e-06       1      47 [.     547     596 ..     547     597 .. 0.98
   4 !   28.7   0.1   7.6e-11   6.8e-07       1      47 [.     603     646 ..     603     647 .. 0.92
   5 !   59.0   0.2   2.6e-20   2.3e-16       2      48 .]     651     697 ..     650     697 .. 0.97
   6 !   49.8   0.2   1.9e-17   1.7e-13       2      46 ..     701     745 ..     700     747 .. 0.92
   7 !   47.2   0.3   1.3e-16   1.1e-12       3      47 ..     751     795 ..     748     796 .] 0.96

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.3
                                    EGSETTTTSSEEEEE CS
                  DNA_gyraseA_C  31 kgiklkegdklvsvl 45 
                                    ++i l++ d++++++
  gi|116754691|ref|YP_843809.1| 376 ILIALRDIDEVIALI 390
                                    57899*******986 PP

  == domain 2  score: 38.2 bits;  conditional E-value: 8.2e-14
                                    EEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEEEEE CS
                  DNA_gyraseA_C   4 lliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsvlvv 47 
                                    ++iT+nGy+kr pls ++ q+Rg+kG +g  +k +d++++++ +
  gi|116754691|ref|YP_843809.1| 500 VIITNNGYIKRQPLSVYRMQRRGGKGSIGAETKSEDFVTDIFTA 543
                                    79*************************************99875 PP

  == domain 3  score: 25.7 bits;  conditional E-value: 6.6e-10
                                    SEEEEEETTSEEEEEEGGGS-BT-TTSCTEEGS...ETTTTSSEEEEEEE CS
                  DNA_gyraseA_C   1 dellliTsnGyvkrfplselpeqgRgakGvkgi...klkegdklvsvlvv 47 
                                    d+l+++T++G++ +++++e+p  ++ a+G ++    +l+e+++++ +++v
  gi|116754691|ref|YP_843809.1| 547 DYLMIFTDRGKAHWLRVYEIPMVSKVARGRPIAsllQLEENERITEAIPV 596
                                    8********************************************99998 PP

  == domain 4  score: 28.7 bits;  conditional E-value: 7.6e-11
                                    SEEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEEEEE CS
                  DNA_gyraseA_C   1 dellliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsvlvv 47 
                                    ++++l+T+nG ++++pl  +++ +Rg  G+k+++l  gd+lv++ ++
  gi|116754691|ref|YP_843809.1| 603 EYIVLATRNGSIVKTPLRAFSNPRRG--GIKAVNL-RGDSLVAARLT 646
                                    59************************..*******.77999988775 PP

  == domain 5  score: 59.0 bits;  conditional E-value: 2.6e-20
                                    EEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEEEEES CS
                  DNA_gyraseA_C   2 ellliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsvlvvs 48 
                                    el+++T++G+++rf +s+++++gRg++Gvk+i+l+egd+l+s+ vv+
  gi|116754691|ref|YP_843809.1| 651 ELIVATKKGKAIRFHESDVRSSGRGSMGVKAINLSEGDELISMDVVK 697
                                    79******************************************995 PP

  == domain 6  score: 49.8 bits;  conditional E-value: 1.9e-17
                                    EEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEEEE CS
                  DNA_gyraseA_C   2 ellliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsvlv 46 
                                     l++iT +Gy+kr+ lse+p q+Rg+kGvk i+++ gd + ++ v
  gi|116754691|ref|YP_843809.1| 701 TLFTITTQGYGKRTELSEYPLQRRGGKGVKNIDTRRGDVVAAITV 745
                                    599*******************************99999988766 PP

  == domain 7  score: 47.2 bits;  conditional E-value: 1.3e-16
                                    EEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEEEEE CS
                  DNA_gyraseA_C   3 llliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsvlvv 47 
                                    ll+ T+ G ++r+ +s++++qgR+++Gvk+++ k+gd++ +v+ v
  gi|116754691|ref|YP_843809.1| 751 LLITTKEGVMIRIAASDVRVQGRATQGVKIMDVKPGDEISDVARV 795
                                    89***************************************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (796 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); 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: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.42
# Mc/sec: 5734.95
//
Query:       gi|116754692|ref|YP_843810.1|  [L=233]
Description: IS605 family transposase OrfB [Methanosaeta thermophila PT]
Scores for complete 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   64.4   1.3    6.8e-18   64.4   1.3    2.0  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    2.4e-14   53.6   1.5    3.5e-14   53.1   1.5    1.2  1  OrfB_IS605      Probable transposase
  ------ inclusion threshold ------
      0.015   15.3   1.6      0.027   14.5   1.6    1.4  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.022   14.5   0.8       0.14   11.9   0.1    2.5  2  zinc_ribbon_2   zinc-ribbon domain
      0.024   14.9   4.7       0.06   13.6   4.7    1.7  1  IBR             IBR domain, a half RING-finger domain
      0.054   13.7   0.8       0.11   12.7   0.8    1.5  1  Ntox28          Bacterial toxin 28
       0.06   13.7   5.2       0.18   12.1   5.2    1.9  1  C1_2            C1 domain
      0.098   12.2   0.2      0.098   12.2   0.2    2.6  3  TF_Zn_Ribbon    TFIIB zinc-binding
        0.4   11.1   4.1       0.64   10.4   4.1    1.4  1  ESM4            Enhancer of split M4 family


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 ?   -2.4   0.0       2.4   4.8e+03      54      61 ..     110     117 ..      95     120 .. 0.69
   2 !   64.4   1.3   3.4e-21   6.8e-18       1      67 [.     121     187 ..     121     189 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.4
                 OrfB_Zn_ribbon  54 feadrDvn 61 
                                     +++rD++
  gi|116754692|ref|YP_843810.1| 110 KSMHRDIH 117
                                    45899986 PP

  == domain 2  score: 64.4 bits;  conditional E-value: 3.4e-21
                 OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNil 67 
                                    +++++ +l+y a+ +G+ ++evnp +T ++Cs C s+++++ls+r+++Cp+Cgf++d D nA++ i+
  gi|116754692|ref|YP_843810.1| 121 WSRFMFMLSYEAECAGRRLIEVNPMNTTQRCSACRSIVEKELSDRVHECPHCGFSCDIDCNASMHIA 187
                                    99*************************************************************9887 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.1   1.5   1.8e-17   3.5e-14      29     117 ..      16     104 ..      12     106 .. 0.96

  Alignments for each domain:
  == domain 1  score: 53.1 bits;  conditional E-value: 1.8e-17
                     OrfB_IS605  29 atvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrsrrrkhllhklathliktlkevgv 108
                                     + v+ +g+  + ++ ++ +   ++++  ++l++  k+skn++    kl ++  k++++r+++lhkl++h ++++k + v
  gi|116754692|ref|YP_843810.1|  16 KSFVVDTGNNSVENPGFAEKVSTKVKNIHRRLSRAEKGSKNRQTLIDKLNKVNYKIKNQRNDFLHKLSRHYVNNYKIICV 95 
                                    5678999999********************************************************************** PP

                     OrfB_IS605 109 etLnvgnmk 117
                                    e+L+v+ mk
  gi|116754692|ref|YP_843810.1|  96 EDLDVKRMK 104
                                    ********9 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   1.6   1.4e-05     0.027      46      95 ..     124     175 ..     112     191 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.4e-05
                                    HHHHHHHCC.TTTT-EEEEEEE--EEEETTTS-EEECHH.H.HHS-TTTSSS CS
                           HypA  46 fafellaegtvlegaeLeieevpvkvrCreCgkefelee.k.alrCpkCgsa 95 
                                    f+f l  e +++ +  +e++ ++ + rC+ C++ +e+e  +   +Cp+Cg +
  gi|116754692|ref|YP_843810.1| 124 FMFMLSYEAECAGRRLIEVNPMNTTQRCSACRSIVEKELsDrVHECPHCGFS 175
                                    5555555555555566789999***********999766445779****963 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.46   9.1e+02      14      20 ..     149     155 ..     143     157 .. 0.71
   2 ?   11.9   0.1   7.1e-05      0.14       7      21 ..     160     174 ..     159     175 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.46
                  zinc_ribbon_2  14 kFCpyCG 20 
                                    + C+ C+
  gi|116754692|ref|YP_843810.1| 149 QRCSACR 155
                                    4599996 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 7.1e-05
                  zinc_ribbon_2   7 aelqdnakFCpyCGt 21 
                                    +el+d++  Cp+CG+
  gi|116754692|ref|YP_843810.1| 160 KELSDRVHECPHCGF 174
                                    799***********7 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   4.7     3e-05      0.06      12      57 ..     140     185 ..     131     189 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3e-05
                            IBR  12 lesdpn..lkwCprpdCeaiieksegcksvtCskCgfefCfnCkkewH 57 
                                    +e +p   ++ C    C +i+ek+ +    +C++Cgf+  ++C++++H
  gi|116754692|ref|YP_843810.1| 140 IEVNPMntTQRCS--ACRSIVEKELSDRVHECPHCGFSCDIDCNASMH 185
                                    44444334999*9..9*****9998844446***************99 PP

>> Ntox28  Bacterial toxin 28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.8   5.6e-05      0.11      64     103 ..      40      80 ..      33      81 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.6e-05
                         Ntox28  64 rralekelenppdsdteRevLerklkeavleLd.rvedfle 103
                                     ++++++l +++++  +R++L++kl++ +++++ + +dfl+
  gi|116754692|ref|YP_843810.1|  40 VKNIHRRLSRAEKGSKNRQTLIDKLNKVNYKIKnQRNDFLH 80 
                                    46799*************************99725688988 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   5.2   9.1e-05      0.18      14      46 ..     144     180 ..     127     181 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.1e-05
                           C1_2  14 dssesfnCsaCgrkidgff....YsCseCdfslhvrC 46 
                                    + + + +CsaC+  ++++      +C+ C fs +++C
  gi|116754692|ref|YP_843810.1| 144 PMNTTQRCSACRSIVEKELsdrvHECPHCGFSCDIDC 180
                                    567789******99544445678************** PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       3.4   6.7e+03       9      18 ..      16      25 ..      14      26 .. 0.66
   2 ?   12.2   0.2   4.9e-05     0.098       5      32 ..     133     161 ..     133     165 .. 0.89
   3 ?   -0.4   1.4      0.44   8.7e+02       3       7 ..     169     173 ..     167     178 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.4
                                   EECHEETSTT CS
                   TF_Zn_Ribbon  9 tnlveDperg 18
                                   +++v+D+ ++
  gi|116754692|ref|YP_843810.1| 16 KSFVVDTGNN 25
                                   3479998775 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 4.9e-05
                                    TTTCEE.CHEETSTTCEEESSSSBEEEEC CS
                   TF_Zn_Ribbon   5 nCgstn.lveDpergelvCtdCGlVledn 32 
                                    +C +++ ++++p++++ +C++C +++e +
  gi|116754692|ref|YP_843810.1| 133 ECAGRRlIEVNPMNTTQRCSACRSIVEKE 161
                                    79999989**************9999876 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.44
                                    ETTTT CS
                   TF_Zn_Ribbon   3 CPnCg 7  
                                    CP Cg
  gi|116754692|ref|YP_843810.1| 169 CPHCG 173
                                    99998 PP

>> ESM4  Enhancer of split M4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   4.1   0.00032      0.64      20     109 ..      30     158 ..      14     201 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00032
                           ESM4  20 ansekkavrrlkkvlkpLrrllkkggkgrkteltlahpnnvdlentqqqqqqqqeeldednssn...aeLeqqlveee.. 94 
                                       ++k + ++k++ + L r  +kg k+r+t + + ++ n  ++n++++  ++++    +n +    ++L  + ++e   
  gi|116754692|ref|YP_843810.1|  30 PGFAEKVSTKVKNIHRRLSR-AEKGSKNRQTLIDKLNKVNYKIKNQRNDFLHKLSRHYVNNYKIicvEDLDVKRMKENgh 108
                                    455679999***********.899*******999***********88778888786666666664445555555555566 PP

                           ESM4  95 ...................................veksaqscaacahgr 109
                                                                         +++q+c+ac  ++
  gi|116754692|ref|YP_843810.1| 109 nksmhrdihdafwsrfmfmlsyeaecagrrlievnPMNTTQRCSACRSIV 158
                                    66666666666666666666666666666666643122355555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1401  (0.0781416); expected 358.6 (0.02)
Passed bias filter:                      675  (0.0376485); 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: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 1830.35
//
Query:       gi|116754693|ref|YP_843811.1|  [L=197]
Description: hypothetical protein Mthe_1396 [Methanosaeta thermophila PT]
Scores for 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-10   41.9  27.7    9.1e-07   29.0  10.3    2.0  2  VIT1      VIT family
  ------ inclusion threshold ------
      0.073   12.9   0.1      0.073   12.9   0.1    2.6  3  IncD      Inclusion membrane protein D
          3    8.0  22.8       0.05   13.8  11.6    2.5  3  DUF3792   Protein of unknown function (DUF3792)


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 !   21.0   8.6   4.1e-08   0.00024       2      60 ..      24      82 ..      23      92 .. 0.93
   2 !   29.0  10.3   1.5e-10   9.1e-07     110     213 ..      85     191 ..      80     193 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 4.1e-08
                           VIT1  2 rdavlGanDGLvspfalvaGlsaaslgssktvllaGlaellAGaiSMgiGeYlsvkser 60
                                   r +v+ a DG+++++++v+G   +++++s  v++aG+ + +A  iS   G+Y++ ++er
  gi|116754693|ref|YP_843811.1| 24 RLFVMNAFDGVLTIMGVVLGAYLSGVQDSGFVITAGMGGSIAMGISGMSGAYMAERAER 82
                                   568999**************************************************998 PP

  == domain 2  score: 29.0 bits;  conditional E-value: 1.5e-10
                           VIT1 110 npdallelmlreelgpsaseel.asplkaAlssalsfliGgliPllpylfve..svglalvvsiavtllalllfGavkal 186
                                    + ++l+++mlr+  g +  ++  + ++  Al+ ++s +i +l+ +lp+++v+  s g a ++s+a+ l++l+++G++ a+
  gi|116754693|ref|YP_843811.1|  85 DIKKLESAMLRDLNGTHVVRAFrTASVVVALVDGISPAIAALLLILPFFMVPmiSIGVAAMLSLALGLVVLFFLGLFLAR 164
                                    4556677888877774443444577899************************888************************* PP

                           VIT1 187 ltgssklvsalrmlliGalAaaaayli 213
                                    +++   l+s+l+m+l+G+l+ ++  l 
  gi|116754693|ref|YP_843811.1| 165 ISEEVALISGLKMMLVGVLTILIVSLA 191
                                    *******************98876665 PP

>> IncD  Inclusion membrane protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   1.2e-05     0.073      14      70 ..       2      58 ..       1      97 [. 0.75
   2 ?   -3.0   5.0      0.92   5.5e+03      37      62 ..     137     161 ..      86     175 .. 0.70
   3 ?   -3.7   6.7       1.5   9.1e+03      37      83 ..     137     181 ..     129     192 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.2e-05
                           IncD 14 vvdriallercldpsnslptakrlvav.avatilavallvvagllfsgvlcspvsvla 70
                                   v+ ri l  r l  s +l  a+rl  + a   +l++ + vv g  +sgv  s   + a
  gi|116754693|ref|YP_843811.1|  2 VIPRIELYRRYLKASGALEIARRLFVMnAFDGVLTI-MGVVLGAYLSGVQDSGFVITA 58
                                   789********************9766155666655.678889999**9988765544 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.92
                           IncD  37 lvavavatilavallvvagllfsgvl 62 
                                    ++++ va++l++al +v  l+f g++
  gi|116754693|ref|YP_843811.1| 137 MISIGVAAMLSLALGLVV-LFFLGLF 161
                                    455666667666664443.4455544 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 1.5
                           IncD  37 lvavavatilavallvvagllfsgvlcspvsvlaaslffgvgafllg 83 
                                    ++++ va++l++al +v  l+f g++ + +s    +l+ g+  +l+g
  gi|116754693|ref|YP_843811.1| 137 MISIGVAAMLSLALGLVV-LFFLGLFLARISEEV-ALISGLKMMLVG 181
                                    577889999999986654.677777777776543.344555544444 PP

>> DUF3792  Protein of unknown function (DUF3792)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   3.0      0.35   2.1e+03      38      59 ..      29      50 ..      25      71 .. 0.65
   2 ?   -0.7   0.3      0.26   1.5e+03      41      59 ..      62      80 ..      55      87 .. 0.70
   3 ?   13.8  11.6   8.3e-06      0.05      16      87 ..     123     193 ..     109     197 .] 0.89

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.35
                        DUF3792 38 sililiililsvfigGflagkk 59
                                   +++  +++i++v++g++l+g +
  gi|116754693|ref|YP_843811.1| 29 NAFDGVLTIMGVVLGAYLSGVQ 50
                                   5566678888888888888654 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.26
                        DUF3792 41 iliililsvfigGflagkk 59
                                    +i +++s + g+++a + 
  gi|116754693|ref|YP_843811.1| 62 GSIAMGISGMSGAYMAERA 80
                                   4677778888777777665 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 8.3e-06
                        DUF3792  16 tlilllilalllyftslsekvlsililiililsvfigGflagkkakkkgllnGllvGllyflillllsllik 87 
                                    +++lllil +++  + +s  v  +l+l++ ++ +f+ G+++++++++  l++Gl ++l+ +l +l++sl+++
  gi|116754693|ref|YP_843811.1| 123 IAALLLILPFFMVPM-ISIGVAAMLSLALGLVVLFFLGLFLARISEEVALISGLKMMLVGVLTILIVSLAVS 193
                                    567888888888886.99999999********************************************9984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1105  (0.061632); 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:                         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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.37
# Mc/sec: 1581.42
//
Query:       gi|116754694|ref|YP_843812.1|  [L=941]
Description: DNA polymerase Pol2 [Methanosaeta thermophila PT]
Scores for complete 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-104  350.2   0.0   4.4e-104  348.8   0.0    1.7  1  DNA_pol_B       DNA polymerase family B
    1.3e-47  162.6   0.0    2.5e-46  158.4   0.0    2.2  1  DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
    1.3e-05   25.0   0.0    2.3e-05   24.2   0.0    1.3  1  DNA_pol_B_exo2  Predicted 3'-5' exonuclease related to the ex
  ------ inclusion threshold ------
      0.044   12.6   0.1       0.19   10.6   0.0    1.8  2  DNA_pol_B_2     DNA polymerase type B, organellar and viral
        0.1   12.6   0.0       0.22   11.5   0.0    1.5  1  RNase_H_2       RNase_H superfamily
       0.15   12.0   0.0       0.81    9.6   0.0    2.2  2  Nuc_rec_co-act  Nuclear receptor coactivator


Domain annotation for each model (and alignments):
>> DNA_pol_B  DNA polymerase family B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  348.8   0.0  1.5e-107  4.4e-104       6     457 ..     426     907 ..     422     909 .. 0.91

  Alignments for each domain:
  == domain 1  score: 348.8 bits;  conditional E-value: 1.5e-107
                                    HHHS-HHHHHHHHHHHHHHHTTBE-B-----.--SS......-S----BE----EEESS-EEEEEETTHHHHHHHHTT-S CS
                      DNA_pol_B   6 vledgqqirveslLlrlakeegfilpdrtekkgkeee.....gYqGatVlePkkglydkpvlvlDFaSLYPsiiqahNlc 80 
                                    ++++gq+  ve l+lr +++++++lp +++++++ e+     + +G+ Vl P kgl + +v++lD++SLYP i++ahNlc
  gi|116754694|ref|YP_843812.1| 426 IVNGGQSGMVENLILRRFRSHKRVLPPKPDSEESGERftdadELKGGAVLPPVKGLVE-NVVILDYKSLYPTIMMAHNLC 504
                                    6789**********************86666555544777757************965.7899***************** PP

                                    TTTCE-HCCHCCT--BTT...TEEE-TCC-EEE-TTS---HHHHHHHHHHHHHHHHHHHHHCS--HHHHHHHHHHHHHHH CS
                      DNA_pol_B  81 yttlvaseeeakeleaedeyleveveprlvefvkksvregllpklLkdllakRkaikkelkeekdefekalldkqQlalK 160
                                    y+t+v++e+  +             +p++ +f+++sv +g++p++L++ll+kR++ k  +k++ ++ e+a ld++Q+alK
  gi|116754694|ref|YP_843812.1| 505 YSTVVTKERPPEV----------VKSPSGGYFASPSVCKGIVPEILRELLEKRTETKMLMKSAGED-ERAFLDAKQYALK 573
                                    *****99988654..........4468899*******************************99998.9************ PP

                                    HHHHHHHHHHTSTTSTT--HHHHHHHHHHHHHHHHHHHHHHHHT.....SSGGGT-SS...................... CS
                      DNA_pol_B 161 vtaNsvYGftGvansrlpclalAasvTtiGRemLektkelvekk..aellskllalpeeae..................e 220
                                    ++ Ns+YG+ G+a  rl++l lA+ vT+ GR+++++tke++e+   +  +  ++ lpee++                   
  gi|116754694|ref|YP_843812.1| 574 ILLNSFYGYSGYARARLYSLTLANAVTSFGRHNILRTKEMIEEIgsVYIVDGKALLPEETSvssnpkppdtielnsagrR 653
                                    ******************************************99533333345556665434567889999999998744 PP

                                    .T-EEEEEBSSEEEEE-S-...SSHHHHHHHHHHHHHHHHT.TSTTT--EEEEEEEEEEEEEETTEEEEEEEEESSTTS. CS
                      DNA_pol_B 221 eklkviYGDTDSvfielkv...kdveellkigkelaeevseklfkkplklefekvykkllLisKKkYaglkvektskan. 296
                                    ++l+v+YGDTDSvf++++     + e++  ig+++ae +++ +++kp++l fe+   + ++++KK+Ya   +e+ s+++ 
  gi|116754694|ref|YP_843812.1| 654 YDLSVVYGDTDSVFVRISSgysITPEDAELIGRKIAETITS-KLPKPMELVFEAFARRAIFLAKKRYALWLFERVSTQSk 732
                                    4****************76534677999*************.99**************************9998888778 PP

                                    ......................EEEEESSGGGSTTS-HHHHHHHHHHHHHHSSS....S-HHHHHHHHHHHHHHHH.HHH CS
                      DNA_pol_B 297 ......................klliKGvdlvRrdncklvkevikkvlelllkdeteersleeglealksilkdvl.eel 353
                                                          ++ ++G+++vRrd+c+l++++ +++lel+lk+     +++++++ +++++++++  ++
  gi|116754694|ref|YP_843812.1| 733 pldgvegssktpsegsgiiwrdRIKVRGMETVRRDWCDLTSKTLRRCLELILKE----GRVDDAVQHVRDVIQRLRdMDI 808
                                    89999***************977*******************************....**************99998899 PP

                                    HTT-S-GGGG-EEEEESS.CCCSSGCCSHHHHHHHHHHHHCSS---TTCEEEEEEBETSS.....SS-GGGTEEEHHHHH CS
                      DNA_pol_B 354 eenkvplekfvlskelskepenyksknlphlevakrlkkrneeapevgdrisYvivekkkevkkknllaseraedpeyvl 433
                                    +  +  l+++vl+++++k+p++y +k+ ph+++++++++r +++p vgdr++++iv+  k     ++l  +raedpey+ 
  gi|116754694|ref|YP_843812.1| 809 RRDRELLDDLVLTRRFTKDPSSYRNKQ-PHIQLVEKMRRRGGRVPGVGDRVPFIIVKGGK-----KTLFVDRAEDPEYAV 882
                                    99999*********************9.******************************97.....9************** PP

                                    HCCSEB-HHHHHH.TTHHHHHHHHT CS
                      DNA_pol_B 434 eknlpidieyYls.qllkevarlle 457
                                    e+nlpid+eyY++ qll++v rl+ 
  gi|116754694|ref|YP_843812.1| 883 ENNLPIDTEYYIEkQLLPPVLRLFM 907
                                    ***********************97 PP

>> DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.4   0.0   8.4e-50   2.5e-46       2     336 ..      26     357 ..      25     358 .. 0.88

  Alignments for each domain:
  == domain 1  score: 158.4 bits;  conditional E-value: 8.4e-50
                                    ECTTSEEEEEEEE---EEEEEESSCGGHHHHHHHHHHHCCTTCCCEEEEEEEECCCCEECCTSSCCHHCEEEEEESSTCH CS
                 DNA_pol_B_exo1   2 teegksvcvnvfgfkpyfYceapdgkeleevkeelkelyeelskkvtkivkvelvlkkslygyekkpvpylkvsvsnpne 81 
                                     ++g+s++++v gf+pyfY++a       + +++ +e +e+ + +      ve+v++ + +gy+ kp+++l++  ++p+ 
  gi|116754694|ref|YP_843812.1|  26 RDNGDSIICRVSGFRPYFYASAH------D-ITSAAEAVESMDLD------VEIVERYEPIGYQSKPIKMLRIIAKDPKS 92 
                                    5899*******************......2.34445555555544......66*************************** PP

                                    HHHHHHHHHHCCCCCCCCSSS--HHHHHHHHCTS-TTCEEEEE....................................T CS
                 DNA_pol_B_exo1  82 lkkirkelspleeivdvyeydvdylerflidnkivgfgwysvk....................................k 125
                                    +++ir++++++ ++  vye+d+ +  rflid ++ g++w +v                                      
  gi|116754694|ref|YP_843812.1|  93 VREIRDRVREIPSVRAVYETDILFKNRFLIDTGLGGMAWVKVLdverdstsakesrdglswyglanyreverdstsakeS 172
                                    ****************************************999999*********9999999999999999988887554 PP

                                    EEEEGCC--C-.SEEEEEETTTSCEETTTCCS-EEEEEEEEEETEETTSEETTTT..--EEEEEEEECCTC.SS.SEEEE CS
                 DNA_pol_B_exo1 126 ylvraegkisncdveidcdvddliakpkesepplrvlsFDIeckskkgkfpdaensedpiiqIscvldglgekepearkl 205
                                    +  +  +     ++ +d+ v++l +++ es++plr +sFDIec  ++g++p +e    p+i Is++++          ++
  gi|116754694|ref|YP_843812.1| 173 RVLEGCEMRERRRFIVDVPVEKLAPEDLESTAPLRFMSFDIECLPQNGEMPRPES--SPVILISMAFHPPY--HGMSDLV 248
                                    5555555667788999999999999999999************************..**********6544..2445577 PP

                                    EEECCCTSS----EE--SSTCSTTEEEEEESSHHHHHHHHHHHHHHH--SEEEESSTTTTHHHHHHHHHHHCCTCCHCG. CS
                 DNA_pol_B_exo1 206 ftlrecaseeeedfeltpkpeypgvkvlefdsEkelLqaflefikqydPdvitgYNidnFDlpYilnRakelykvklskl 285
                                    ++ re +                +++v  +++E++l+++f+++i +ydPd+i gYN ++FD+pY+ +Ra+ l +    ++
  gi|116754694|ref|YP_843812.1| 249 LVGRELE--------------CDRPDVEGCADERALISRFVSVIDDYDPDIIAGYNSNEFDIPYLRERASRLGIEM--NV 312
                                    7777777..............35778********************************************999843..45 PP

                                    SCCSCTCEECCCCESEEEEEECEEEETTSEEEEHHHHHHHHSSSSG-SHHH CS
                 DNA_pol_B_exo1 286 grlnkggrskvseigfskqarekvkisgrihlDlyrvvkrklklpsYkLna 336
                                    gr  +g    +++ g +    ++v++ gr+++Dl+++++ +++l+ Y+L +
  gi|116754694|ref|YP_843812.1| 313 GR--DGSTWLIRSMGSN----KNVAVTGRVVVDLLPIIRSSFSLKQYTLRN 357
                                    54..6788888999999....***************************975 PP

>> DNA_pol_B_exo2  Predicted 3'-5' exonuclease related to the exonuclease domain of PolB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   7.7e-09   2.3e-05      35     181 ..     265     414 ..     251     428 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 7.7e-09
                 DNA_pol_B_exo2  35 ssekelikkffegvekkkpqlV.sfngrgfDlpvleyralkhgvsapkyfdegded.rekkwnnylsrystrhlDLmdll 112
                                    ++e++li++f ++++ + p ++ ++n+++fD+p l  ra + g++++   d +    r++  n  ++   +  +DL+ ++
  gi|116754694|ref|YP_843812.1| 265 ADERALISRFVSVIDDYDPDIIaGYNSNEFDIPYLRERASRLGIEMNVGRDGSTWLiRSMGSNKNVAVTGRVVVDLLPII 344
                                    679*****************9846********************998877766644577777777777777799999998 PP

                 DNA_pol_B_exo2 113 seygaranakLdelakllglPGKlgvdGskVaelyqegk.lkeireYcetDvlnTYlvylrlellrgkls 181
                                     +  + ++  L ++a  l    K ++d ++  +++  g+ l+++ +Y + D++    + lrl+l+   + 
  gi|116754694|ref|YP_843812.1| 345 RSSFSLKQYTLRNAAMELIGEEKRDMDPARMESIWLGGDgLADLIRYSRRDAVLVMQLLLRLRLMDKYIA 414
                                    5444677888888887777778999999999999998865889999999999999999999988876665 PP

>> DNA_pol_B_2  DNA polymerase type B, organellar and viral
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   6.2e-05      0.19     213     252 ..     469     507 ..     467     523 .. 0.85
   2 ?   -1.0   0.0       0.2     6e+02     369     383 ..     567     581 ..     559     634 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 6.2e-05
                    DNA_pol_B_2 213 yrGGrcypsvlgiyeeniyvyDvnSlYPsamthypmPygk 252
                                    + GG + p v+g + en+++ D +SlYP++m+   + y +
  gi|116754694|ref|YP_843812.1| 469 LKGGAVLPPVKGLV-ENVVILDYKSLYPTIMMAHNLCYST 507
                                    679***99999977.****************987777665 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.2
                    DNA_pol_B_2 369 vkrsiaKlllNsLYG 383
                                    +k++  K+llNs YG
  gi|116754694|ref|YP_843812.1| 567 AKQYALKILLNSFYG 581
                                    567788********9 PP

>> RNase_H_2  RNase_H superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   7.5e-05      0.22      42     125 ..     266     372 ..     258     403 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.5e-05
                      RNase_H_2  42 eeekailelflellekk..kalvtfngksFDvpflkrlfkkyklde......................eefrhiDLlkel 97 
                                    +e++ i++ f++++ ++  + +  +n ++FD+p+l++++++  ++                         +  +DLl ++
  gi|116754694|ref|YP_843812.1| 266 DERALISR-FVSVIDDYdpDIIAGYNSNEFDIPYLRERASRLGIEMnvgrdgstwlirsmgsnknvavTGRVVVDLLPII 344
                                    44555555.668888885455888***************88887777788889899988888766655555888999999 PP

                      RNase_H_2  98 rkkkl.esysLksvekelgierreedlsG 125
                                    r++   ++y L + + el  e +  d++ 
  gi|116754694|ref|YP_843812.1| 345 RSSFSlKQYTLRNAAMELIGEEK-RDMDP 372
                                    88766688899999998766665.45555 PP

>> Nuc_rec_co-act  Nuclear receptor coactivator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00027      0.81       1      21 [.     262     282 ..     262     285 .. 0.95
   2 ?   -1.5   0.0      0.79   2.4e+03       4      11 ..     559     566 ..     557     574 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00027
                 Nuc_rec_co-act   1 EgrsDEkALLdQLvslLkntD 21 
                                    Eg +DE+AL++  vs+  ++D
  gi|116754694|ref|YP_843812.1| 262 EGCADERALISRFVSVIDDYD 282
                                    899****************99 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.79
                 Nuc_rec_co-act   4 sDEkALLd 11 
                                     DE+A Ld
  gi|116754694|ref|YP_843812.1| 559 EDERAFLD 566
                                    6******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (941 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        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):               6  [number of targets reported over threshold]
# CPU time: 0.68u 0.32s 00:00:01.00 Elapsed: 00:00:00.47
# Mc/sec: 5999.32
//
Query:       gi|116754695|ref|YP_843813.1|  [L=316]
Description: elongation factor Tu domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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-11   42.3   0.2    1.4e-10   41.4   0.2    1.5  1  GTP_EFTU_D2   Elongation factor Tu domain 2
     0.0048   16.8   0.0     0.0082   16.0   0.0    1.3  1  GTP_EFTU_D4   Elongation factor Tu domain 4
  ------ inclusion threshold ------
       0.03   14.9   0.0      0.059   13.9   0.0    1.4  1  3-dmu-9_3-mt  3-demethylubiquinone-9 3-methyltransferase


Domain annotation for each model (and alignments):
>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   0.2   2.4e-14   1.4e-10       1      74 []     158     225 ..     158     225 .. 0.95

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 2.4e-14
                                    EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEEE CS
                    GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtlt 74 
                                    Gtv+lg v +Gt++k d +r+l+ d  k     +i+s++++ ed + a ag++aG+ ++++++++ + +G +lt
  gi|116754695|ref|YP_843813.1| 158 GTVVLGNVAEGTIRKHDLLRVLPGD--KN---AQIRSIQKHDEDFESASAGERAGLALKGIEVSE-LDRGTVLT 225
                                    9********************8844..66...9********************************.9****996 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 !   16.0   0.0   1.4e-06    0.0082      18      73 ..     159     213 ..     147     225 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.4e-06
                                    CEEEEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEESS CS
                    GTP_EFTU_D4  18 paivGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisiegk 73 
                                     ++ G +v +G+i+    l    G +  +i++iq++++  e a+aG++ +++++g 
  gi|116754695|ref|YP_843813.1| 159 TVVLG-NVAEGTIRKHDLLRVLPGDKNAQIRSIQKHDEDFESASAGERAGLALKGI 213
                                    57889.*********9999999****************************999985 PP

>> 3-dmu-9_3-mt  3-demethylubiquinone-9 3-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   9.8e-06     0.059      25      98 ..     183     255 ..     180     264 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.8e-06
                   3-dmu-9_3-mt  25 enseilsvarypeeepskegkvltveFtlagqefvalnggpefkfneavSllveckdqeevdrlwnalseegge 98 
                                    +n +i s+++ +e+++s + +   +  +l+g e+  l+ g+ ++ n+av  + + ++++e+ r+w++   eg  
  gi|116754695|ref|YP_843813.1| 183 KNAQIRSIQKHDEDFESAS-AGERAGLALKGIEVSELDRGTVLTTNDAVKTSTSLRSRAEIVRYWQSPLREGMV 255
                                    5889999999999997733.44578899**************************************98888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 2454.47
//
Query:       gi|116754696|ref|YP_843814.1|  [L=717]
Description: alpha-glucan phosphorylases [Methanosaeta thermophila PT]
Scores for complete 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-35  121.2   0.0    7.1e-29  100.6   0.0    3.2  3  Phosphorylase  Carbohydrate phosphorylase
    7.3e-35  119.7   0.2    2.6e-34  118.0   0.0    2.1  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 !   15.9   0.0   3.4e-07    0.0031      23      69 ..     122     169 ..     115     183 .. 0.91
   2 !  100.6   0.0     8e-33   7.1e-29     217     578 ..     265     616 ..     257     622 .. 0.82
   3 ?   -2.2   0.0     0.099   8.9e+02     681     707 ..     670     697 ..     666     699 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.4e-07
                                    SHHHHHHHHHHHHHHHTT-EEEEEEE--SCESEEEEE.ETTEEEEEEE CS
                  Phosphorylase  23 GGLGRLAacfldslatlelpavGygirYeyGlFkQki.edgaqveepd 69 
                                    GGLG LA  +l  ++ l lp++G+g  Y  G  +Q++  dg+q  e++
  gi|116754696|ref|YP_843814.1| 122 GGLGFLAGDYLKECSDLRLPVIGVGFMYPGGYLRQRLsPDGWQLSESE 169
                                    9************************************679***87765 PP

  == domain 2  score: 100.6 bits;  conditional E-value: 8e-33
                                    HEEEEEESSTTTTHHHHHHHHHHHCC---HHHHHHHHCCCEEEEE--SSGGGS-EEEHHHHHHHSHHHHHHHHHHHHHHH CS
                  Phosphorylase 217 kvaiqlnDtHPalaipelmriLvdeeglewdeaweitkktfaytnhtvlpealekwpvellekllprhleiieeinerfl 296
                                    +++++ln+ HPa+a+ e +r L+  +g++ +ea++ +++t+ +t ht +p   + +p +l+ek +   l  i    ++f 
  gi|116754696|ref|YP_843814.1| 265 NLVLHLNEGHPAFAVLERLRYLIG-NGMSCREAIDYVRRTTVFTTHTPVPAGHDIFPFHLMEKYFNSYLPTIGLTRDQFF 343
                                    6789******************86.59*******************************************9998877777 PP

                                    HHHHHHSTT-HHHHHHHSSEETSCEEEHHHHHHHCCSEEEESSHHHHHHHHHTTTHHHHHHS..GGGEEE----B-CHHH CS
                  Phosphorylase 297 eevekklpedeeklerlsiieeekkvrmanlaivgshsvngvaalhsellkkevlkdfyely..pekfnnktnGitprrw 374
                                    +   +  +              +   +m  +a+ +s   n v++ h e+ ++   +   el    + +  +tnG+    w
  gi|116754696|ref|YP_843814.1| 344 RLGIDPANP-------------QVGFNMTAFAMRMSLYRNCVSRRHLEVTESMWRHLLSELKsnGTVIDHVTNGVHVLTW 410
                                    655554222.............23468999****************99887766666666652156799********999 PP

                                    CCCTSHHHHHHHHHHCSSGGCCSGGGGGGGGGGCCSHHHHHHHHHHHHHHHHHHHHHHHHHHSS-...........--TT CS
                  Phosphorylase 375 lllanpelaelitekigeewvkdleeLkkLekladdkefleelaeikqenKerlaelikekegve...........vdpe 443
                                    l    +++ +l ++ +g +w+++ ++  ++ +l+dd   +e +++ ++  K+rl ++i+e+ +++           v + 
  gi|116754696|ref|YP_843814.1| 411 LD---RSMEDLFNRYLGLGWLEEHDD-PSIWALVDDIPDRELWMA-HRMAKMRLITTIRERARLRwsmdgadpriiVASG 485
                                    96...56888999********99987.556666766665555554.4566788888888766555444555555558888 PP

                                    SEEEEEE......S-SCCCCTHHHHHHHHHHHHHHHHHSTTS----EEEEEE----TT-HHHHHHHHHHHHHHHHHCC-T CS
                  Phosphorylase 444 slfdvqv......kRlheYkRqlLnvLhiitlYneikenpekkvvprtvifggkaapgYalAkkiiklinsvaevvnndp 517
                                     lfd  v      +R+  YkR +L +L+ +++ ++i +n   + +p  +if+gka p+  +Ak+ii+ + +va    +dp
  gi|116754696|ref|YP_843814.1| 486 VLFDPSVftigfaRRFATYKRATL-ILQDLNRLRSILNN---EDMPVQIIFAGKAHPADDTAKQIIQKVYNVA----KDP 557
                                    899977544455599******999.56666666666666...589************************9987....6** PP

                                    TTCCCEEEEEETT-SHHHHHHHGGG-SEEEE---TTTSSS-SHHHHHHHTT-EEEEESSTC CS
                  Phosphorylase 518 evkdklkvvflenynvslaekiipaadlseqistagkeASGTgnmkfmlnGaltigtlDGa 578
                                    + +++  ++f+e+y+ +la+ ++ + dl  +      eASGT+ mk m+nG   ++ lDG 
  gi|116754696|ref|YP_843814.1| 558 SFGGR--IAFVEDYDEQLAQYMVHGVDLWLNTPQPPLEASGTSGMKAMVNGVPQLSILDGW 616
                                    ***97..79**************************************************95 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.099
                                    HHHHHHHHH.HCGGGGBHHHHHHHHHHH CS
                  Phosphorylase 681 wakksilni.aksgkFssDrtikeYaee 707
                                    w + +  +i +++ +Fss r +keY+++
  gi|116754696|ref|YP_843814.1| 670 WVRVMKEAIkSTAPRFSSRRMVKEYTNK 697
                                    555555555134579**********987 PP

>> DUF3417  Protein of unknown function (DUF3417)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.0   0.0   2.9e-38   2.6e-34       1     109 []       8     117 ..       8     117 .. 0.99
   2 ?   -2.8   0.1         1     9e+03      30      50 ..     443     464 ..     411     471 .. 0.62

  Alignments for each domain:
  == domain 1  score: 118.0 bits;  conditional E-value: 2.9e-38
                        DUF3417   1 lpeeLekLeeLaknlwwswneeareLFksldpelweevghnPvklLeevsqerleelaedeeflarleavveefeeylee 80 
                                    +p+++e L+eLa nlwwsw+++ar+LF+ l+p++w+ + hnPvklL+e++++ le++ae+++fl++++av+++f++ ++ 
  gi|116754696|ref|YP_843814.1|   8 IPARIEGLRELACNLWWSWHHPARDLFNMLNPAAWQLSVHNPVKLLHEIDRSVLERAAENDHFLRHYDAVISRFRSEMRG 87 
                                    79****************************************************************************** PP

                        DUF3417  81 k.twfqkkaeeekkeaiAYFsaEfGlhesL 109
                                    k  wf ++ +++ +  iAYFsaE+Glh+s+
  gi|116754696|ref|YP_843814.1|  88 KgGWFPSHIRNPMNVPIAYFSAEYGLHHSM 117
                                    *9*************************985 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1
                        DUF3417  30 l.dpelweevghnPvklLeevs 50 
                                    + d+elw + +   ++l+++++
  gi|116754696|ref|YP_843814.1| 443 IpDRELWMAHRMAKMRLITTIR 464
                                    3355777777776666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (717 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.41
# Mc/sec: 5209.80
//
Query:       gi|116754697|ref|YP_843815.1|  [L=336]
Description: hypothetical protein Mthe_1400 [Methanosaeta thermophila PT]
Scores for complete sequence (score 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   12.2   0.0       0.18   11.2   0.0    1.5  1  BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
        7.7    6.5   8.8         34    4.5   0.2    3.7  3  FhuF_C       FhuF 2Fe-2S C-terminal domain


Domain annotation for each model (and alignments):
>> BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   2.1e-05      0.18      11     105 ..      48     147 ..      45     154 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.1e-05
                                    EEEEEETTTEEEEEEEE--TTS-HHH.........HHHHHHHHHHT--GGGECEE..EEESTTCCCTCTTBSEEE-.... CS
                    BcrAD_BadFG  11 kavlmdekgevlgrgitnsanlesvrfeaaekvleealtealerageeeadieetylvgtgyGratlpekfekeiirs.. 88 
                                     a++ d+kgev+g+g+    +      e  ++ + + l++ l+r g++ +di+  +  + gyGr+  p  ++ +++++  
  gi|116754697|ref|YP_843815.1|  48 LARITDDKGEVIGEGFGIVWSPAVLAAELDAGIVPDDLEDRLRRDGTSSQDIVDKVAALFGYGRVVTPAVIALNMVKEmg 127
                                    6899**********98777666666777899**************************************99*99999999 PP

                                    ...HHHHHHHHHHHH-TT-- CS
                    BcrAD_BadFG  89 ...eilvhgdGavalypgtr 105
                                        i  +g+G+va + +++
  gi|116754697|ref|YP_843815.1| 128 grtLIRREGLGVVATFFDSK 147
                                    98878888888888776665 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 ?    4.5   0.2    0.0038        34      10      19 ..      14      24 ..      13      25 .. 0.81
   2 ?    1.5   0.9     0.032   2.9e+02      12      19 ..     155     162 ..     153     163 .. 0.85
   3 ?    3.6   0.1    0.0075        67       3       9 ..     225     231 ..     224     236 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0038
                         FhuF_C 10 l.pggeyCgsC 19
                                   + p ++ Cg+C
  gi|116754697|ref|YP_843815.1| 14 InPREGVCGTC 24
                                   5588999**** PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.032
                         FhuF_C  12 ggeyCgsC 19 
                                    ++ yC +C
  gi|116754697|ref|YP_843815.1| 155 PSSYCPTC 162
                                    578***** PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.0075
                         FhuF_C   3 sCCLyYr 9  
                                    +CC+ Y 
  gi|116754697|ref|YP_843815.1| 225 GCCMAYA 231
                                    6*****6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); 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 0.23s 00:00:00.65 Elapsed: 00:00:00.36
# Mc/sec: 2777.07
//
Query:       gi|116754698|ref|YP_843816.1|  [L=403]
Description: hypothetical protein Mthe_1401 [Methanosaeta thermophila PT]
Scores for complete 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-94  316.9   2.0    1.7e-94  316.7   1.3    1.4  2  YcaO      YcaO cyclodehydratase, ATP-ad Mg2+-binding


Domain annotation for each model (and alignments):
>> YcaO  YcaO cyclodehydratase, ATP-ad Mg2+-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.15   2.6e+03     282     320 ..      20      58 ..       8      61 .. 0.62
   2 !  316.7   1.3   9.7e-99   1.7e-94       1     323 []      69     375 ..      69     375 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.15
                           YcaO 282 leedletllerlkaagld.vlvvdltrp.dlglpvvkvivP 320
                                    +ee le + +++ aag+  v  +d+t+   +g+pv   i P
  gi|116754698|ref|YP_843816.1|  20 PEETLEIVEKKMPAAGITrV--ADITNLdRIGIPVFTSIRP 58 
                                    55666666666666776633..5665544677887776666 PP

  == domain 2  score: 316.7 bits;  conditional E-value: 9.7e-99
                           YcaO   1 nGkGateeaArasalgEalErysaegffrgdekrvrasyrelegegaldpeelglyseeekdaadfvlepfdpdrpidwv 80 
                                    nGkGat+++A++sa++E++Erysae    ++++  +a+++el +e+al+p+el l+            ++ dpd  i+wv
  gi|116754698|ref|YP_843816.1|  69 NGKGATPTEAKVSAIMEGIERYSAE---VRNADLRTARFSEL-RENALNPAELILP------------RDADPDAVIPWV 132
                                    8*********************999...44555556******.*************............89********** PP

                           YcaO  81 pgwsltdgeevlvPanlvylyeppegea.rlfletsnGlAaGntleeAilhGllEliERdafalawyerlplpridlasd 159
                                     g++l+ +ee+lvPan+v++  p +++  rlf+++++GlA+Gn leeAi+hGl E++ERda ++a ++r   p ++   d
  gi|116754698|ref|YP_843816.1| 133 TGYDLMGDEEILVPANAVFH--PLPSSYtRLFRTNTTGLASGNQLEEAIFHGLAEVVERDAWSIAEHARSMGPLLRYNGD 210
                                    ********************..7777777****************************************99999999899 PP

                           YcaO 160 peirellerlreagievrlldatldlgipvvaavlvd....pklllvagaGahldpevAlerAltElaqsrltlisgare 235
                                      + elle +++a ++v++ d+t+d+g+p++aav++d    +++ll+ag+G+h dpevAl+rAltE+aqsrlt+i+gare
  gi|116754698|ref|YP_843816.1| 211 GLAGELLEMFQRAEVQVYVRDITSDVGVPTFAAVSDDvklkDPALLTAGMGTHTDPEVALLRALTEVAQSRLTQIHGARE 290
                                    *************************************877444999********************************** PP

                           YcaO 236 dpdfdeeladvatleradreallwlpeaaakrldfllfaewassgdleedletllerlkaagld.vlvvdltrpdlglpv 314
                                    d+   +e+++  +++r +r +++w+ e ++ + df+   ++ +++d+ +d++++l+rl+ ag++ ++vvdlt  ++ +pv
  gi|116754698|ref|YP_843816.1| 291 DTVS-AEFRRMMGYDRLKRLNRHWF-EYER-EEDFSSL-NSYNTDDFLDDIRYMLDRLQTAGFErAIVVDLTASEIMVPV 366
                                    ****.89*****************6.4444.3344332.455669*********************************** PP

                           YcaO 315 vkvivPgle 323
                                    v+vivPgle
  gi|116754698|ref|YP_843816.1| 367 VRVIVPGLE 375
                                    *******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.36
# Mc/sec: 3379.22
//
Query:       gi|116754699|ref|YP_843817.1|  [L=208]
Description: TfuA domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-46  155.6   0.0    6.3e-46  155.0   0.0    1.3  1  TfuA      TfuA-like protein


Domain annotation for each model (and alignments):
>> TfuA  TfuA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.0   0.0   3.5e-50   6.3e-46       1     120 []      38     155 ..      38     155 .. 0.99

  Alignments for each domain:
  == domain 1  score: 155.0 bits;  conditional E-value: 3.5e-50
                           TfuA   1 DGvfeqepavahkEilaalkegvavvGaasmGALRAaElaafGmigvGeiyeayrsgeledDdeVavlhapaelgyeals 80 
                                    DGvf+q+++vahkEil+al+ gv+v+Ga+smGALRAaE++ +Gm+gvGeiy+ayrsge+ +DdeVa++++p   ++++ls
  gi|116754699|ref|YP_843817.1|  38 DGVFFQDSSVAHKEILEALRMGVRVIGASSMGALRAAEMDVYGMEGVGEIYRAYRSGEIVADDEVALVFDPV--TLAPLS 115
                                    9**********************************************************************9..9***** PP

                           TfuA  81 ealvnlratlkaaveegiiseeeaaallelakelyykert 120
                                    e+lvn+r++l+ av+eg i++++aa ll++a++ y+++r+
  gi|116754699|ref|YP_843817.1| 116 EPLVNIRHNLRLAVSEGWIDKQTAADLLDIARSRYFPSRS 155
                                    *************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); 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 0.29s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1441.80
//
Query:       gi|116754700|ref|YP_843818.1|  [L=364]
Description: S-adenosylmethionine synthetase [Methanosaeta thermophila PT]
Scores for complete 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-118  394.5   0.0   5.1e-118  394.3   0.0    1.0  1  AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synt
     0.0058   16.6   0.0      0.021   14.8   0.0    1.9  2  Nup35_RRM_2      Nup53/35/40-type RNA recognition motif
  ------ inclusion threshold ------
      0.021   15.1   0.5      0.078   13.3   0.3    1.9  2  AMP-binding_C_2  AMP-binding enzyme C-terminal domain
       0.11   13.2   0.3       0.54   11.0   0.0    2.2  3  S-AdoMet_synt_N  S-adenosylmethionine synthetase, N-terminal 


Domain annotation for each model (and alignments):
>> AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synthetase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  394.3   0.0  1.1e-121  5.1e-118      12     395 ..      10     359 ..       4     360 .. 0.94

  Alignments for each domain:
  == domain 1  score: 394.3 bits;  conditional E-value: 1.1e-121
                                    -GTTSSEEEEEEE-TTSHHHHHHHHHHHHHHHHHHHHHHHHSS---EEEEEEEEE--EEEEETTEEEEEE-EEEEEEEEE CS
                AdoMet_Synthase  12 pveeqevEivErKGiGHPDsiaDgiaeavsralskeylekfgailhhniDkvllvaGesepkfgGGeviepieillsgra 91 
                                    ++e  ++E+vErK++GHPD++aDgi+e++sr+l++ y+e+fg+i+hhn+Dkvl+++G++ep+fgGG+++ep  i+++gra
  gi|116754700|ref|YP_843818.1|  10 NFELPRFEVVERKCTGHPDTLADGISESISRELCRIYMEEFGEIMHHNVDKVLIIGGRAEPQFGGGRILEPPAIVVGGRA 89 
                                    5666789************************************************************************* PP

                                    EEEE.EEE--HHHHHHHHHHHHHHHH-SS--TTTSEEEEEEEEEEEEHHHHHHCH-SS..-BESSSEEEEEEES--HHHH CS
                AdoMet_Synthase  92 tkevegekipveeialeaakeylkenlraldlekdvivdvklgkgsadLkdvferkkkevplaNDtSfgvgyaplselek 171
                                    t+     +  +++++ eaa +yl++ +r+l+   + +v+ + ++g+ +L++++ r       aNDtS+g g+apl  le+
  gi|116754700|ref|YP_843818.1|  90 TS----VRSSMSDVVREAASSYLRKAVRHLN---EFVVEPRTREGAPELRSLIGR------GANDTSIGSGFAPLRPLES 156
                                    *9....455789****************997...679****************99......69***************** PP

                                    HHHHHHHHHTSHHHHHH-TTEEEEEEEEEEEETTEEEEEEEEEEEGGG--SHHHHHHHHHHHHHHHHHHHHHHSTTSEEE CS
                AdoMet_Synthase 172 lvleterllnskelkkklpevGeDiKvmglRekkkielTvavalvdrlvkdleeYlevkeeikeeveelakkltkereve 251
                                    +vle++r+l+       ++ vGeD K+m++R ++++++ va+a ++r++ ++++Y+e+k++i+e++++         +ve
  gi|116754700|ref|YP_843818.1| 157 MVLEIDRMLEG------MKGVGEDRKIMAVRFDDRVKVVVAAAAISRYMFSMDDYIEMKSRIRETIQSAC-------DVE 223
                                    *********97......679****************************************9999987654.......599 PP

                                    EEE-TT-BGGGTB--EESSSSGGGTT--EETTSS--TTSSB-TTS----S--TTS-TTT-HHHHHHHHHHHHHHHHHHH- CS
                AdoMet_Synthase 252 vevNtaDkkeeesvyltvtGtsaEegDdGsvGRGNRvnGlitpnrpmslEAaaGKNPvsHvGKiYnvlaneiakeiveev 331
                                    v+vN+aD  ++++++ltvtGtsaE+gDdG++GRGNR+nGlitp+rpm++EA aGKNPv+HvGKiYnv+a++ a++i + +
  gi|116754700|ref|YP_843818.1| 224 VDVNAAD--HDSNIFLTVTGTSAEMGDDGATGRGNRANGLITPMRPMTMEAVAGKNPVNHVGKIYNVIAQRAAEDISK-L 300
                                    *******..7899**************************************************************987.9 PP

                                    TTEEEEEEEEEE-TTSBTTS-SEEEEEEEESSS---HHSHHHHHHHHHHHHT-HHHHHHHHTTT CS
                AdoMet_Synthase 332 egvkevyvrllsqiGkpidePlvasvqvilekgvsleevekeveeiideelekieeiteelieg 395
                                    +gv+e+yv+l+s+iG+p+d+Pl+ +++++ +     e+   e+e+i++++l + e++++e+++g
  gi|116754700|ref|YP_843818.1| 301 DGVQEAYVTLVSRIGSPLDQPLMKALSIAGS-----ESAGYEAESILEDWLGRAESLVDEFVSG 359
                                    ***************************9543.....34456899***************99987 PP

>> Nup35_RRM_2  Nup53/35/40-type RNA recognition motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   4.7e-06     0.021      14      34 ..      40      60 ..      32      73 .. 0.84
   2 ?   -4.0   0.0       3.4   1.5e+04      35      47 ..     174     186 ..     169     187 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.7e-06
                    Nup35_RRM_2 14 ielVlehFasfGeIvkhyvpk 34
                                   +el + ++++fGeI++h+v+k
  gi|116754700|ref|YP_843818.1| 40 RELCRIYMEEFGEIMHHNVDK 60
                                   567788*************83 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 3.4
                    Nup35_RRM_2  35 evsvmyvkfesek 47 
                                     + +m v+f +++
  gi|116754700|ref|YP_843818.1| 174 DRKIMAVRFDDRV 186
                                    5778889998875 PP

>> AMP-binding_C_2  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3   1.7e-05     0.078       8      79 ..     160     231 ..     159     235 .. 0.84
   2 ?   -1.4   0.0      0.67     3e+03      13      29 ..     297     313 ..     267     323 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.7e-05
                                    HHHHHHHT-TTEEEEEEEEEEEETTEEEEEEEEEE-TT----HHHHHHHHHHHHHHHHHHHSS--EEEEE-T CS
                AMP-binding_C_2   8 qieevlkeieevepeYqivvtregelDelevkvEvkegfsdelkelealekkiakklksklgvsvkvelvep 79 
                                    +i+++l+ +++v++  +i++ r +++ ++ v   + ++++ ++++  +++++i++ ++s++ v+v+v+  ++
  gi|116754700|ref|YP_843818.1| 160 EIDRMLEGMKGVGEDRKIMAVRFDDRVKVVVAAAAISRYMFSMDDYIEMKSRIRETIQSACDVEVDVNAADH 231
                                    6999****************998766666666655556667899***********************98765 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.67
                                    HHT-TTEEEEEEEEEEE CS
                AMP-binding_C_2  13 lkeieevepeYqivvtr 29 
                                    ++++++v++ Y   v+r
  gi|116754700|ref|YP_843818.1| 297 ISKLDGVQEAYVTLVSR 313
                                    45555666666666655 PP

>> S-AdoMet_synt_N  S-adenosylmethionine synthetase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00012      0.54      10      25 ..      23      38 ..      17      65 .. 0.88
   2 ?   -3.5   0.0       3.8   1.7e+04      49      70 ..      83     103 ..      78     107 .. 0.66
   3 ?   -2.0   0.1       1.4   6.1e+03      56      73 ..     201     218 ..     177     232 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00012
                S-AdoMet_synt_N 10 seGHPDkvadqisdai 25
                                     GHPD +ad is++i
  gi|116754700|ref|YP_843818.1| 23 CTGHPDTLADGISESI 38
                                   57***********998 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.8
                S-AdoMet_synt_N  49 vvvageittkakvdiekivrev 70 
                                    +vv g+  t+++ +++++vre+
  gi|116754700|ref|YP_843818.1|  83 IVVGGRA-TSVRSSMSDVVREA 103
                                    4444444.55677888888876 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.4
                S-AdoMet_synt_N  56 ttkakvdiekivrevike 73 
                                    + + ++++++ +re+i++
  gi|116754700|ref|YP_843818.1| 201 SMDDYIEMKSRIRETIQS 218
                                    445566777777777764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); 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: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2556.22
//
Query:       gi|116754701|ref|YP_843819.1|  [L=560]
Description: hydantoinase/oxoprolinase [Methanosaeta thermophila PT]
Scores for 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-48  166.1   4.1      5e-47  160.5   0.7    2.3  2  Hydantoinase_A  Hydantoinase/oxoprolinase
    1.1e-24   87.1   6.4      2e-21   76.5   4.0    3.3  2  Hydant_A_N      Hydantoinase/oxoprolinase N-terminal region
    8.2e-06   26.2   1.3       0.12   12.8   0.0    3.2  2  FtsA            Cell division protein FtsA
    2.4e-05   23.9   2.0     0.0038   16.8   0.8    3.2  2  BcrAD_BadFG     BadF/BadG/BcrA/BcrD ATPase family
    3.7e-05   22.5   2.5     0.0051   15.5   0.1    2.3  2  MutL            MutL protein
     0.0059   16.1   1.3      0.089   12.2   0.1    2.4  2  Ppx-GppA        Ppx/GppA phosphatase family
  ------ inclusion threshold ------
      0.025   13.5   1.5        1.9    7.2   0.1    2.2  2  EutA            Ethanolamine utilisation protein EutA
       0.43    9.8   1.3        1.2    8.3   0.1    2.0  2  StbA            StbA protein
       0.84    8.4   5.8       0.16   10.7   0.2    2.3  3  MreB_Mbl        MreB/Mbl 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 !    6.4   0.1    0.0023       4.5      82     102 ..       3      22 ..       1      45 [. 0.83
   2 !  160.5   0.7   2.5e-50     5e-47       1     288 [.     180     460 ..     180     462 .. 0.94

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0023
                 Hydantoinase_A  82 ItfDmGGTstDvslikdgeve 102
                                    +++D+GGT+t ++l++ g+  
  gi|116754701|ref|YP_843819.1|   3 VGIDVGGTTTNAALVD-GNKV 22 
                                    789***********99.5443 PP

  == domain 2  score: 160.5 bits;  conditional E-value: 2.5e-50
                 Hydantoinase_A   1 rtetavvnAylspilreylesvekslekrgakarlmvmqsdGglvsadearkkpvetilSGPaaGvvgaaatsklagekk 80 
                                    r+ t++++ +  + +r+++e+ e ++++rg+ a+++++++dGg++++d+   kpveti SGPaa+v+g+ a   +++ + 
  gi|116754701|ref|YP_843819.1| 180 RAATTMLTLATRDHYRRFAEQAERAMRDRGIRAPIYILKADGGTLPLDKSLDKPVETIFSGPAASVMGVMA--LTPKGQT 257
                                    78899999999************************************************************..7777778 PP

                 Hydantoinase_A  81 vItfDmGGTstDvslikdgevevsle.teiagvkvrlpaldirtvgagGgsilvvdeggklrvgpesagadpgpacyrkG 159
                                     +++D+GGT+tD++li +g++  s++  +i ++ ++++a ++r++g+gG+s++ +   gk+ vgp+ ag +        G
  gi|116754701|ref|YP_843819.1| 258 SVVVDIGGTTTDLALILSGKPLLSSKgAKIEDMLTHVRAFAVRSIGIGGDSVV-RVSDGKITVGPDRAGPAFAL-----G 331
                                    9********************998762678***********************.55559*******99866665.....9 PP

                 Hydantoinase_A 160 gteltvTDanlvLGrlqpedflsgpdgdqkldvelarrafeelakelnlkveevAegilsvavenmanavrkl....... 232
                                    g e+t TDa +vLG  +              dv lar+ +  +ak l  + e++A  i++++ve ++  v+ +       
  gi|116754701|ref|YP_843819.1| 332 GPEPTPTDALMVLGHTNLG------------DVALARKGIGIIAKILRCSTEDAARMIVDTVVERIVDTVNMMfleweqe 399
                                    99************87665............778********************************************** PP

                 Hydantoinase_A 233 ......svergldpkeltlvvfGGaGaqhaaalaeelgvkkvivppyagvlsalGmalAdvr 288
                                          +  ++ + +  ++v++GGa++ +++ +a++l+ + +i +++  v++a+G+a+A+ +
  gi|116754701|ref|YP_843819.1| 400 payriwELLQRTKARPQNVVGVGGASPPLVPLVAKRLNANAIIPEHA-PVANAIGAAVARPT 460
                                    ******99999****************************99988888.9**********975 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 !   76.5   4.0     1e-24     2e-21       2     176 ..       3     158 ..       2     160 .. 0.91
   2 !    7.7   0.0    0.0014       2.7       2      19 ..     259     276 ..     258     301 .. 0.78

  Alignments for each domain:
  == domain 1  score: 76.5 bits;  conditional E-value: 1e-24
                     Hydant_A_N   2 igIDvGGTfTDavaldekeeevavlKllstpdavaegirealeevleesiprtskidvvrmGTTvatNallerkgervaL 81 
                                    +gIDvGGT T a ++d++ ++v+++  ++  +++   +++ +++++e    + ++i+ v+++TT+ tN + e+k ++v+L
  gi|116754701|ref|YP_843819.1|   3 VGIDVGGTTTNAALVDGN-KVVKTAIGPTDHQEILGSLLRTMDRLIEG--VDVERIERVVLSTTLITNLIAEGKADKVGL 79 
                                    8***************98.*9*********9999999*******9876..668*************************** PP

                     Hydant_A_N  82 ittkgfrdlleigrqnrpdlfelrikkplvlyeevvevderveadgevlkpldeeevrealkalkaagvesiavvllhSy 161
                                    + + g           r + f+          +e v +d+ ++++g+++ pl+ +++r+a+++l ++g++ +avv  +  
  gi|116754701|ref|YP_843819.1|  80 VLIPGPGVNP------RDYRFR----------TEPVILDGAIDYRGREIAPLRDDQIRAAAQSLADQGYRKVAVVGKFCQ 143
                                    ***9976443......334444..........566889****************************************** PP

                     Hydant_A_N 162 lnpehElrvaeiare 176
                                    +n ehE  v+ei+++
  gi|116754701|ref|YP_843819.1| 144 RNHEHETHVREIFSK 158
                                    ************987 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0014
                     Hydant_A_N   2 igIDvGGTfTDavaldek 19 
                                    + +D+GGT TD+ ++  +
  gi|116754701|ref|YP_843819.1| 259 VVVDIGGTTTDLALILSG 276
                                    78*********9887655 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.3   0.00027      0.53       1      32 [.       3      34 ..       3      69 .. 0.86
   2 !   12.8   0.0   5.9e-05      0.12       1      52 [.     259     377 ..     259     525 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00027
                                   EEEEE-SSSEEEEEEETTEEEEEEEES--HHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           FtsA  1 alvDiGagktdvavaedgalvhlrvigvggng 32
                                   +++D+G+++t++a+++++++v++++ ++  + 
  gi|116754701|ref|YP_843819.1|  3 VGIDVGGTTTNAALVDGNKVVKTAIGPTDHQE 34
                                   68********************9998875544 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 5.9e-05
                                    EEEEE-SSSEEEEEEETTEEEE..................EEEES--HHHHHHH.......................... CS
                                    xxxxxxxxxxxxxxxxxxxxxx..................xxxxxxxxxxxxxx.......................... RF
                           FtsA   1 alvDiGagktdvavaedgalvh..................lrvigvggngitkd.......................... 36 
                                    ++vDiG+++td+a++  g++                    +r+ig+gg+ + +                           
  gi|116754701|ref|YP_843819.1| 259 VVVDIGGTTTDLALILSGKPLLsskgakiedmlthvrafaVRSIGIGGDSVVRVsdgkitvgpdragpafalggpeptpt 338
                                    79*************99996556677777778878888888888888887766556666666666666666666666666 PP

                                    .......................HHHHHT--HHHHHHHH CS
                                    .......................xxxxxxxxxxxxxxxx RF
                           FtsA  37 .......................iakalrtaveeAerik 52 
                                                           iak+lr + e+A r+ 
  gi|116754701|ref|YP_843819.1| 339 dalmvlghtnlgdvalarkgigiIAKILRCSTEDAARMI 377
                                    666666666666666666666666666666666666665 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 !   16.8   0.8   1.9e-06    0.0038       1      43 [.       3      58 ..       3     280 .. 0.53
   2 ?    3.7   0.0     0.018        36     203     265 ..     401     456 ..     344     457 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.9e-06
                                   EEEEE-SSEEEEEEEETTTEEEEEEEE--..............TTS-HHH....... CS
                    BcrAD_BadFG  1 vGiDgGsTttkavlmdekgevlgrgitns..............anlesvrfeaaekv 43
                                   vGiD+G+Ttt a+l+d ++  ++++i  +              + +e+v++e  e+v
  gi|116754701|ref|YP_843819.1|  3 VGIDVGGTTTNAALVDGNKV-VKTAIGPTdhqeilgsllrtmdRLIEGVDVERIERV 58
                                   8***************7754.444444334455555555555533344444433333 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.018
                                    HHHHHHHHHTT---SS.EEEESGGGG-HHHHHHH.....HHHH-S-EE--GGGGGHHHHHHHH CS
                    BcrAD_BadFG 203 alrvialisrsggvtdevtltGGvakneaavkelrklvkenygevkininpdsiytgalGAal 265
                                    a r+++l +r ++++++v+ +GG +        l +lv ++ +  +  i+ ++ ++ a+GAa+
  gi|116754701|ref|YP_843819.1| 401 AYRIWELLQRTKARPQNVVGVGGASPP------LVPLVAKRLNA-NAIIPEHAPVANAIGAAV 456
                                    66999**********************......99999999999.578999999999****85 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.2    0.0012       2.4       3      55 ..       4      50 ..       2      69 .. 0.62
   2 !   15.5   0.1   2.6e-06    0.0051     223     273 ..     236     282 ..     226     295 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0012
                           MutL  3 viDiGSttTkvtlvdlekvderllgqaeapTtveeedvleGleealeeleekl 55
                                    iD+G ttT ++lvd +    +++ +a  pT  +  ++l  l + +++l e  
  gi|116754701|ref|YP_843819.1|  4 GIDVGGTTTNAALVDGN----KVVKTAIGPTDHQ--EILGSLLRTMDRLIEGV 50
                                   47888888888888884....4777777777664..55555555555555444 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 2.6e-06
                           MutL 223 eimpTPaAvlkavellaeeeekglgdllvvDvGGaTTdvhsvaegspekek 273
                                    +i   PaA + +v +l  +  +     +vvD+GG+TTd+  +++g+p  ++
  gi|116754701|ref|YP_843819.1| 236 TIFSGPAASVMGVMALTPK-GQ---TSVVVDIGGTTTDLALILSGKPLLSS 282
                                    5667788888888888773.33...68***************999987665 PP

>> Ppx-GppA  Ppx/GppA phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1     0.055   1.1e+02     115     136 ..       3      24 ..       1      27 [. 0.89
   2 !   12.2   0.1   4.5e-05     0.089     100     134 ..     244     278 ..     235     284 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.055
                                    EEEEEETTEEEEEEEETTEEEE CS
                       Ppx-GppA 115 lviDiGGGStElvlgeekevsk 136
                                    + iD+GG  t  +l+++++v+k
  gi|116754701|ref|YP_843819.1|   3 VGIDVGGTTTNAALVDGNKVVK 24 
                                    779**************99987 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 4.5e-05
                                    HHHHHHHHT---SSEEEEEEETTEEEEEEEETTEE CS
                       Ppx-GppA 100 iylgvvssllekgrglviDiGGGStElvlgeekev 134
                                    +++gv++ +++ +  +v+DiGG  t+l+l+ + ++
  gi|116754701|ref|YP_843819.1| 244 SVMGVMALTPKGQTSVVVDIGGTTTDLALILSGKP 278
                                    5789***999*******************988776 PP

>> EutA  Ethanolamine utilisation protein EutA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1   0.00096       1.9     146     169 ..       3      26 ..       1      69 [. 0.88
   2 ?    5.5   0.1    0.0033       6.6     133     165 ..     247     278 ..     233     319 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00096
                           EutA 146 lniDiGGGtsnlalfkeGevidta 169
                                    + iD+GG t+n+al++  +v++ta
  gi|116754701|ref|YP_843819.1|   3 VGIDVGGTTTNAALVDGNKVVKTA 26 
                                    679*************99999987 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0033
                           EutA 133 gaaalskekstrvlniDiGGGtsnlalfkeGev 165
                                    g++al  + +t+v  +DiGG t+ lal+ +G+ 
  gi|116754701|ref|YP_843819.1| 247 GVMALTPKGQTSV-VVDIGGTTTDLALILSGKP 278
                                    4555555555555.59***********999986 PP

>> StbA  StbA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.25   5.1e+02     168     183 ..       5      20 ..       2      64 .. 0.90
   2 ?    8.3   0.1   0.00061       1.2     162     182 ..     255     275 ..     239     283 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.25
                           StbA 168 iDlGGttLDvakvrgk 183
                                    iD+GGtt + a v g+
  gi|116754701|ref|YP_843819.1|   5 IDVGGTTTNAALVDGN 20 
                                    8********9999885 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00061
                           StbA 162 leslLiiDlGGttLDvakvrg 182
                                     + ++++D+GGtt D+a + +
  gi|116754701|ref|YP_843819.1| 255 GQTSVVVDIGGTTTDLALILS 275
                                    56799************9976 PP

>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1       0.2     4e+02     150     170 ..       5      25 ..       2      54 .. 0.88
   2 ?   10.7   0.2   8.2e-05      0.16     135     165 ..     246     276 ..     233     290 .. 0.73
   3 ?   -3.5   0.1       1.7   3.4e+03     116     139 ..     433     456 ..     429     465 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.2
                                    EEE-SS-EEEEEEETTEEEEE CS
                       MreB_Mbl 150 vdiGggttevavislggivts 170
                                    +d+Gg tt+ a++  + +v++
  gi|116754701|ref|YP_843819.1|   5 IDVGGTTTNAALVDGNKVVKT 25 
                                    899**9999999988888765 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 8.2e-05
                                    HHTT--TTSSS-EEEEEE-SS-EEEEEEETT CS
                       MreB_Mbl 135 iGaglpveepsgnmvvdiGggttevavislg 165
                                    +G      + + ++vvdiGg tt++a+i  g
  gi|116754701|ref|YP_843819.1| 246 MGVMALTPKGQTSVVVDIGGTTTDLALILSG 276
                                    4555555567889*************88655 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 1.7
                                    HHHTT-SEEEEEEHHHHHHHHTT- CS
                       MreB_Mbl 116 akkaGarevllieeplaAAiGagl 139
                                    ak++ a+ ++ +  p+a AiGa +
  gi|116754701|ref|YP_843819.1| 433 AKRLNANAIIPEHAPVANAIGAAV 456
                                    667778888888999999999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (560 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); 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:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 3909.26
//
Query:       gi|116754702|ref|YP_843820.1|  [L=478]
Description: histone deacetylase superfamily protein [Methanosaeta thermophila PT]
Scores for complete 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-62  210.7   0.0      5e-62  210.1   0.0    1.3  1  Hist_deacetyl  Histone deacetylase domain


Domain annotation for each model (and alignments):
>> Hist_deacetyl  Histone deacetylase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.1   0.0   2.8e-66     5e-62      83     296 ..      98     307 ..      50     318 .. 0.91

  Alignments for each domain:
  == domain 1  score: 210.1 bits;  conditional E-value: 2.8e-66
                                    CTTTCCHHHHHHHHHHHHHHHHHHTTSSSEEEETTSS--TT-BTTB-B..TTBSS-HHHHHHHHHHHCC-SS-EEEEE-S CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Hist_deacetyl  83 vspktlkaallavgavleavdavlsgsvkaafvlvrPpgHHakaseas..GFClvNnvaiaikylqakhelkrvailDvD 160
                                    v++++ +a l+a+g++l ++da+++g+++++f+lvrPpgHH+++   +  GFC +Nn ai ++y+++k++++r+ai+D D
  gi|116754702|ref|YP_843820.1|  98 VQSQVTEAHLIAAGSTLVLADALMNGEIRNGFALVRPPGHHSMRVVHGnrGFCNINNEAIMVEYIRRKYGVRRIAIVDTD 177
                                    67889999**********************************87776668****************************** PP

                                    SS--HHHHHHCTT-TTEEEEEEEE-CCTSTTSS--TT---SGGGTTSEEEEEE-TT-BHHHHHHHHHHCHHHHHCCH--S CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Hist_deacetyl 161 vHhGnGteeafysdpdvltlSiHryegifyPgtgaledlgegkgkgfnlnvpleegtgdeeylkvfeeilrpvleefkPd 240
                                    vHhG+Gt+++f++dpdvl++S+H+ ++++yPg+g ++++g   + g +lnvpl++gt+de +l+v+e+++ pvl ef+P+
  gi|116754702|ref|YP_843820.1| 178 VHHGDGTQDIFWHDPDVLFISFHQDGRTLYPGSGFTNEMGGPLALGRTLNVPLPPGTTDEGILYVLENLVLPVLDEFDPQ 257
                                    ****************************************99999*********************************** PP

                                    EEEEEE-STTBTTSTT-S-BB-HHHHHHHHHHHCCCHGS-G.EEEEE-S---H.HHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                  Hist_deacetyl 241 lilvsaGfDalkgdplgelnlsvegykeltkklaeladkvkkvvllleGGYnl.eal 296
                                    l+  saG D + +dpl++++ +++gy++l + la         +++leGGY + +al
  gi|116754702|ref|YP_843820.1| 258 LVFNSAGQDNHYTDPLANMRFTAQGYAKLNEVLAP-------DMAVLEGGYAIeSAL 307
                                    **************************998877754.......3679*****994444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (478 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 3478.84
//
Query:       gi|116754703|ref|YP_843821.1|  [L=175]
Description: hypothetical protein Mthe_1406 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.1   12.4   0.2       0.23   11.3   0.0    1.6  2  CdvA      CdvA-like coiled-coil domain


Domain annotation for each model (and alignments):
>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   1.3e-05      0.23      27      70 ..       4      47 ..       2      49 .. 0.93
   2 ?   -2.9   0.0      0.31   5.6e+03      78      97 ..     111     130 ..     108     136 .. 0.48

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.3e-05
                           CdvA 27 leealkklkekakelkeklkkrlkeledqikslekalanlkisy 70
                                   ++ a+++  e+  ++  +++++l+ + d+ ++l++ala l++ y
  gi|116754703|ref|YP_843821.1|  4 VRGAIRARAEEFLKVLAEVEQSLSRCSDETTRLARALALLELAY 47
                                   6778999999999****************************998 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.31
                           CdvA  78 eaYksaieairellesalee 97 
                                    e+ +s+i++ r + + +l+e
  gi|116754703|ref|YP_843821.1| 111 ENIQSSISSARMATDALLSE 130
                                    44444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); 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: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1311.44
//
Query:       gi|116754704|ref|YP_843822.1|  [L=456]
Description: AIR synthase related protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-15   58.0   3.6    2.7e-15   56.9   3.6    1.7  1  AIRS_C    AIR synthase related protein, C-terminal domain
    3.3e-09   37.3   1.2    8.2e-09   36.0   1.2    1.6  1  AIRS      AIR synthase related protein, N-terminal domain


Domain annotation for each model (and alignments):
>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.9   3.6     3e-19   2.7e-15       2     153 ..     242     389 ..     241     392 .. 0.79

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 3e-19
                                    TTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHHHHHHH CS
                         AIRS_C   2 pGdvliltgslGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaalkglvkaahDvTgGGLlgalaemap 81 
                                    pGdv+i+t++ G g +  +++   + ++        ++++ l  + ++++ al+ ++ +++a++DvT+GG+ g+++e+ +
  gi|116754704|ref|YP_843822.1| 242 PGDVIIMTEGAGGGTIC-AAALYYGMHD--------VVEETLNIKFLEAAGALIDEGPEIHAMTDVTNGGIRGDAKEISH 312
                                    9*********9988888.4444444444........67788888999999999999************************ PP

                                    TTTEEEEEECG......THHHHHHHH.HHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEESSSEEE CS
                         AIRS_C  82 asgvgaeidld......kvpifdele.splemllsensGrllvavppeeadavlaileeeglpeaavIGevtakeelsv 153
                                     +gv++++ ++      + ++++ le +++++l   +   ll+++p+ ead +l ++e++g+  a +IG+v+ + ++++
  gi|116754704|ref|YP_843822.1| 313 TAGVKMVFFEErmrslvNHRVLEMLErLEIDYLG-VSIDALLIIAPEREADVILGVIEKAGV-AADIIGRVERGSGVEL 389
                                    ***********65555544444444344444444.455558888888888************.7********9988776 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 !   36.0   1.2   9.1e-13   8.2e-09       5      93 ..     130     230 ..     117     231 .. 0.76

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 9.1e-13
                                    EEEEEEEEE.EECCTCCCC.HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HHHHHHHHHHHHHHHTT-EEEEEE CS
                           AIRS   5 vvvttdshnrpvlvepvhf.iGakavavnlsDlaamGArPlalllslalp......wleevvrglaeaaeelgvplvgGd 77 
                                    ++vt+d++   + ++++ f +G  +  ++l+D+++mGArP+al+  + l       ++ + ++g+a  +e ++vpl++G 
  gi|116754704|ref|YP_843822.1| 130 LIVTVDGMH--SRLSDYPFlAGFHVTRAALRDILVMGARPVALFSDIHLAddgdvaKVLDHIAGIATVGELVNVPLITGS 207
                                    478888444..4444444566********************9888888888**999899999*****************9 PP

                                    EEEESS.......EEEEEEEEEE CS
                           AIRS  78 tsfsne.......ptisvtavGl 93 
                                    t +  +       +t +v+avG+
  gi|116754704|ref|YP_843822.1| 208 TLRIGGdmvigdrLTGCVGAVGI 230
                                    98764456666668888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 3509.10
//
Query:       gi|116754705|ref|YP_843823.1|  [L=150]
Description: hypothetical protein Mthe_1408 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.096   12.8   0.0       0.12   12.5   0.0    1.1  1  DUF5518   Family of unknown function (DUF5518)


Domain annotation for each model (and alignments):
>> DUF5518  Family of unknown function (DUF5518)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.6e-06      0.12      23      64 ..      91     132 ..      81     139 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.6e-06
                        DUF5518  23 psvgsllgllvgGlvaGylaggdskdgavaGalaGligaipv 64 
                                    ++ +s++ +++++l+ G  +++++ ++a+aG l+Gl++ + +
  gi|116754705|ref|YP_843823.1|  91 EYLVSMAIVFLTSLLMGRKTRDKKVEAAIAGGLSGLFALLLG 132
                                    567889999****************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 1104.49
//
Query:       gi|116754706|ref|YP_843824.1|  [L=215]
Description: RNA 2'-phosphotransferase-like protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.3e-24   85.0   0.0    7.9e-24   84.7   0.0    1.0  1  PTS_2-RNA  RNA 2'-phosphotransferase, Tpt1 / KptA family


Domain annotation for each model (and alignments):
>> PTS_2-RNA  RNA 2'-phosphotransferase, Tpt1 / KptA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.7   0.0   4.4e-28   7.9e-24       2     179 ..      35     198 ..      34     199 .. 0.89

  Alignments for each domain:
  == domain 1  score: 84.7 bits;  conditional E-value: 4.4e-28
                      PTS_2-RNA   2 revqlskaLsyiLRhgaekegLkiredGyvkvedlLelpklkslkvtleeikevVesndKqRFelveleelliranqghs 81 
                                    r+++l++ L+  LRh +++ gL+++++G+v++  l++  +++ + ++++ + ++V+s++K R+e   ++++ ira  ghs
  gi|116754706|ref|YP_843824.1|  35 RTEKLGRLLAGALRHFPDDLGLAMSPQGWVEIPVLVDAIRTRYRWANENLVMALVRSDPKGRYE---INGTRIRARYGHS 111
                                    56899********************************888887779999***************...77799******** PP

                      PTS_2-RNA  82 i.kkvesselllepiesaeelpevvvHgTylkawesilasggLkrmsrnhihlatglpgekevisgmrksaevliyidve 160
                                    + ++       l+    ++elp+ +++gT+ ++ e++l + gLk ++++++hl+t+ p+++  +   r+s+  +i++d++
  gi|116754706|ref|YP_843824.1| 112 VgVD-------LDYP--ENELPT-LYYGTAEEEAERLL-EVGLKSATQRYVHLSTT-PDKAWEVGTFRTSNPKIIVVDAA 179
                                    6332.......6663..346787.**************.99**************7.65666667789999********* PP

                      PTS_2-RNA 161 kaladgikfyvsengviLt 179
                                     a ++g+++++ ++ ++++
  gi|116754706|ref|YP_843824.1| 180 GAQREGVRMMKVNESMVIS 198
                                    **********999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       264  (0.0147247); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); 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 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1665.31
//
Query:       gi|116754707|ref|YP_843825.1|  [L=231]
Description: multiple antibiotic resistance (MarC)-related proteins [Methanosaeta thermophila PT]
Scores for complete 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-59  199.9  11.4    3.2e-59  199.8  11.4    1.0  1  MarC             MarC family integral membrane protein
    0.00059   19.6   5.9     0.0018   18.0   5.3    2.1  1  TerC             Integral membrane protein TerC family
  ------ inclusion threshold ------
       0.15   11.7   0.0       0.34   10.6   0.0    1.6  1  N_formyltrans_C  N-formyltransferase dimerization C-terminal 


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 !  199.8  11.4   5.3e-63   3.2e-59       2     201 ..      24     222 ..      23     224 .. 0.98

  Alignments for each domain:
  == domain 1  score: 199.8 bits;  conditional E-value: 5.3e-63
                           MarC   2 kaiikafvsLlaiinplgnvpvflslleevskeerkrialkasilallillvfllfGelilklfgisidalkiaGgillf 81 
                                    ++++++f+sL++i+ p+ +  vf+sl++  s +er+ri ++++++a+ i +vf+l+G++il++fgi++d+l++aGgillf
  gi|116754707|ref|YP_843825.1|  24 QYFVYVFTSLFIIVSPIEATMVFVSLTQDASPAERDRICVRTTLVAFSIAMVFALAGDMILRFFGITVDSLRVAGGILLF 103
                                    789***************************************************************************** PP

                           MarC  82 liaidmlkakqkkekkkkseeeeseekdeiavvPLAlPliaGPgaittvlvlaseassivekvavvlaillaalitllil 161
                                    l+aidml+ak +k k  + e e+++++++i+++PLA+Pl++GPg+ittv+v++   +++ ek++v+lai l    t+ il
  gi|116754707|ref|YP_843825.1| 104 LVAIDMLRAKPHK-KVTQAEIEDATTREDISIFPLAIPLLTGPGTITTVIVHMGASNTLPEKMIVLLAICLTFGATYAIL 182
                                    ************5.99999************************************************************* PP

                           MarC 162 llsslilrllgktginaleRlmGllLvalavqlivdGike 201
                                    ++++ i + lg tgi +++R++Gl+L a+av+++  G  +
  gi|116754707|ref|YP_843825.1| 183 KSAEHIHDILGVTGIMVFTRILGLILGAIAVDFVSVGAWN 222
                                    **********************************988765 PP

>> TerC  Integral membrane protein TerC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   5.3     3e-07    0.0018      16      99 ..      44     130 ..      39     218 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3e-07
                           TerC  16 vviallvkklpeeqqkkalllGilgAlvlRillillavallelf....dlilligglfLlytavkellekrlenklvkee 91 
                                    +v++ l++   +++++++ +  +l+A+ + +++ l++ ++l++f    d + ++gg++L+++a+++l++k  ++k+ + e
  gi|116754707|ref|YP_843825.1|  44 MVFVSLTQDASPAERDRICVRTTLVAFSIAMVFALAGDMILRFFgitvDSLRVAGGILLFLVAIDMLRAKP-HKKVTQAE 122
                                    688889999999*******************************77778*******************9865.43444443 PP

                           TerC  92 kkkkkktk 99 
                                     ++  + +
  gi|116754707|ref|YP_843825.1| 123 IEDATTRE 130
                                    33333333 PP

>> N_formyltrans_C  N-formyltransferase dimerization C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   5.7e-05      0.34      19      40 ..     106     127 ..     100     132 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5.7e-05
                                    HHHHHHHT--TT---EEEE-TT CS
                N_formyltrans_C  19 lidlLRAltfgpyknAyfiddt 40 
                                    +id+LRA+ ++    A+++d t
  gi|116754707|ref|YP_843825.1| 106 AIDMLRAKPHKKVTQAEIEDAT 127
                                    8*****************9954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1641.60
//
Query:       gi|116754708|ref|YP_843826.1|  [L=454]
Description: FAD dependent oxidoreductase [Methanosaeta thermophila PT]
Scores for complete 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   64.0   0.2    3.9e-07   29.6   0.0    3.1  3  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
      4e-15   55.8   2.5    1.2e-07   31.2   0.8    3.1  3  FAD_binding_2  FAD binding domain
    6.6e-12   45.2   1.2    0.00068   18.8   0.0    3.2  3  GIDA           Glucose inhibited division protein A
    1.2e-11   44.0   0.1    1.9e-07   30.2   0.1    2.2  2  HI0933_like    HI0933-like protein
    8.7e-09   35.4   0.2    9.9e-07   28.7   0.0    2.7  2  DAO            FAD dependent oxidoreductase
    6.6e-08   32.2   0.1      1e-07   31.5   0.1    1.3  1  FAD_binding_3  FAD binding domain
    2.8e-06   27.5   0.0    1.3e-05   25.3   0.0    2.2  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    2.4e-05   23.9   0.9    0.00011   21.8   1.2    1.7  2  FAD_oxidored   FAD dependent oxidoreductase
    9.1e-05   22.9   0.1      0.021   15.4   0.1    2.5  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    0.00038   19.8   0.1    0.00062   19.1   0.1    1.3  1  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    0.00055   19.1   0.1      0.001   18.2   0.1    1.4  1  Lycopene_cycl  Lycopene cyclase protein
     0.0047   16.2   0.2     0.0095   15.2   0.2    1.5  1  Thi4           Thi4 family
  ------ inclusion threshold ------
      0.086   12.1   0.1       0.61    9.3   0.1    2.0  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 !   29.6   0.0   2.8e-10   3.9e-07       2      45 ..       3      46 ..       2      54 .. 0.93
   2 !   14.3   0.0   1.3e-05     0.018     176     252 ..     137     217 ..     119     234 .. 0.74
   3 !   16.6   0.0   2.6e-06    0.0036     236     290 ..     390     439 ..     387     443 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 2.8e-10
                                   SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllska 45
                                   dvvv+G+GpAGl aal+l+ +g  v++v++++ +  + c+++k+
  gi|116754708|ref|YP_843826.1|  3 DVVVVGAGPAGLFAALELSVHGKSVVVVDKGRDISERNCPMKKW 46
                                   8****************************999999999999986 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 1.3e-05
                                    SSS.TTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEE.EEETTSCEEEESEEEE-S-EEES-HHCS..HCCT-E CS
                                    xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxx RF
                    Pyr_redox_2 176 rll.raldkelsaaleealekeGvevklgtsvkeidgngekle.vvledgeeidadlvvvavGvrpstelle..eklgle 251
                                    r + +   +e+ ++  + l+++Gv+++l++s+ +++ +++    v l+dg ei a+  ++a G+     + e  e+ g++
  gi|116754708|ref|YP_843826.1| 137 RHMgSDRTPEIIREFSNDLKRRGVRFVLNSSAADLIIEKDVCMgVRLSDGGEIRAESTLLAPGRIGAEWIGEviERYGIK 216
                                    44545667888899999******************999994447******************998776554455666665 PP

                                    E CS
                                    x RF
                    Pyr_redox_2 252 l 252
                                     
  gi|116754708|ref|YP_843826.1| 217 A 217
                                    5 PP

  == domain 3  score: 16.6 bits;  conditional E-value: 2.6e-06
                                    -EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGCTECCSS--HHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 236 GvrpstelleeklglelderggivvdeflrtnvpgiyaiGDvaggkggpelaqaA 290
                                    Gv ++++ll  +  ++   ++ i vd+ l+t+++++ya+GD a   g  + ++aA
  gi|116754708|ref|YP_843826.1| 390 GVNADSTLL-YAPEIKF-YAREISVDKDLQTSIQSLYAAGDGA---GLSRGIVAA 439
                                    777777777.7778887.8899*******************99...544444444 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.8   8.5e-11   1.2e-07       1      32 [.       3      34 ..       3      38 .. 0.95
   2 !   21.4   0.0   8.4e-08   0.00012     112     214 ..     116     213 ..      92     342 .. 0.82
   3 ?    1.2   0.0      0.11   1.6e+02     377     415 ..     411     442 ..     401     444 .. 0.78

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 8.5e-11
                                   SEEEE--SHHHHHHHHHHHHTTT-EEEEESSS CS
                  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeq 32
                                   Dv+V+G+G AGL AAle++ +G++v+vv+k+ 
  gi|116754708|ref|YP_843826.1|  3 DVVVVGAGPAGLFAALELSVHGKSVVVVDKGR 34
                                   9*****************************86 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 8.4e-08
                                    -EEE-TT-SSTEEEE-.STT-.......HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEE CS
                  FAD_binding_2 112 dvrelGglsatartlhdaadarr.etlvtghallarlvesarkagvdfqerteadeLivedgrvtGavvenpesgrevri 190
                                    dv el    a    ++  + ++r +     ++++  + + ++++gv+f  + +a++Li+e++ + G+ ++  ++g+   i
  gi|116754708|ref|YP_843826.1| 116 DVEELSRRAAS-VGARFIPIKQRhMGSDRTPEIIREFSNDLKRRGVRFVLNSSAADLIIEKDVCMGVRLS--DGGE---I 189
                                    44444444444.33333444444466667899*************************************9..5555...5 PP

                                    EESEEEE-----GG.......... CS
                  FAD_binding_2 191 rakavvlatgGfgrallkellgaa 214
                                    ra  ++la g +g++++ e+++++
  gi|116754708|ref|YP_843826.1| 190 RAESTLLAPGRIGAEWIGEVIERY 213
                                    69************8887776665 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.11
                                    EBETTSBESTTEEESSBTEEE-STCEESSSSTTS--TTH CS
                  FAD_binding_2 377 etdengrvldadgqpipGLYAaGevaaggvhganrlgGn 415
                                     +d ++++       i+ LYAaG  a g   g+ + +++
  gi|116754708|ref|YP_843826.1| 411 SVDKDLQT------SIQSLYAAGDGA-GLSRGIVAAAAT 442
                                    57777777......9********999.777776666655 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   2.8e-06    0.0039       1      40 [.       3      41 ..       3      72 .. 0.89
   2 !    6.9   0.0     0.002       2.8     113     159 ..     163     207 ..     142     218 .. 0.83
   3 !   18.8   0.0   4.9e-07   0.00068     305     384 ..     365     450 ..     351     453 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.8e-06
                                   CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--SS CS
                           GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkldtiaelsC 40
                                   dv+V+G+G AG+ AAl+++  G +v+ +  k  +i e  C
  gi|116754708|ref|YP_843826.1|  3 DVVVVGAGPAGLFAALELSVHGKSVVVV-DKGRDISERNC 41
                                   79***********************998.67777777666 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.002
                                    EEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT-BT-EEEET CS
                           GIDA 113 iieeeveeliveekkvkgvvtedgetikakavviatGtflkgkihig 159
                                    +++ ++++li+e++ + gv+++dg +i+a+++ +a G    g  +ig
  gi|116754708|ref|YP_843826.1| 163 VLNSSAADLIIEKDVCMGVRLSDGGEIRAESTLLAPGR--IGAEWIG 207
                                    67788999***************************998..5555555 PP

  == domain 3  score: 18.8 bits;  conditional E-value: 4.9e-07
                                    ----S-HHHHHHHHTTSTT-TT--EEE--EEEEEEEE-GGGB-........T.TSBBSSSBTEEE-CGGGTB.-SHHHHH CS
                           GIDA 305 fstslpeevqkevlrsipGLenaeivrpGyaieydyvdprqll........n.tLetkkvkgLflAGqinGt.eGYeEaa 374
                                    +s  lp+   + v+  i+GLe ++ + pG+  + + + +++++        + +L+t+ ++ L++AG+  G   G ++aa
  gi|116754708|ref|YP_843826.1| 365 ISMALPH---RIVMDVIEGLEILNEIIPGVNADSTLLYAPEIKfyareisvDkDLQTS-IQSLYAAGDGAGLsRGIVAAA 440
                                    5556665...345777888888888888887777777666654332222233378888.9************99****** PP

                                    HHHHHHHHHH CS
                           GIDA 375 aqGllAGina 384
                                    a+GllA++ +
  gi|116754708|ref|YP_843826.1| 441 ATGLLAARGI 450
                                    ******9865 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.1   1.4e-10   1.9e-07       2      36 ..       3      37 ..       2      40 .. 0.93
   2 !   11.6   0.0   5.8e-05      0.08     106     164 ..     142     200 ..     135     220 .. 0.90

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 1.4e-10
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                    HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                   dv+v+G+G+AGl+aA++++ +gk+V++++k++ + 
  gi|116754708|ref|YP_843826.1|  3 DVVVVGAGPAGLFAALELSVHGKSVVVVDKGRDIS 37
                                   8*****************************99875 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 5.8e-05
                                    .-CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE---- CS
                    HI0933_like 106 dkaedivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGG 164
                                    d+  +i++ + + lk++gv++ l+++ +++  e+d  + v++++++e++a++++lA G 
  gi|116754708|ref|YP_843826.1| 142 DRTPEIIREFSNDLKRRGVRFVLNSSAADLIIEKDVCMGVRLSDGGEIRAESTLLAPGR 200
                                    56779***************************************************884 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   7.2e-10   9.9e-07       1      33 [.       3      37 ..       3      51 .. 0.91
   2 ?    3.8   0.0     0.025        35     148     201 ..     147     199 ..      91     281 .. 0.67

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 7.2e-10
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                            DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                                   dvv++G+G +Gl++A+eL+ +g  V++++kg++++
  gi|116754708|ref|YP_843826.1|  3 DVVVVGAGPAGLFAALELSVHGksVVVVDKGRDIS 37
                                   9********************99********9998 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.025
                                    HHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--G CS
                            DAO 148 ltaalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaG 201
                                     ++ + ++++++Gv++++++ + +l  e +  +gv r ++ ge++a +   +a G
  gi|116754708|ref|YP_843826.1| 147 IIREFSNDLKRRGVRFVLNSSAADLIIEKDVCMGV-RLSDgGEIRA-ESTLLAPG 199
                                    56667788999*************75555678999.6667676433.55888888 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.1   7.5e-11     1e-07       3      37 ..       3      37 ..       1      65 [. 0.87

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 7.5e-11
                                   EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSC CS
                  FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekrsttv 37
                                   dV++VGaGpaGl +al+Ls +G +vv+v+k ++ +
  gi|116754708|ref|YP_843826.1|  3 DVVVVGAGPAGLFAALELSVHGKSVVVVDKGRDIS 37
                                   8*****************************88755 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   9.7e-09   1.3e-05       1      32 [.       6      37 ..       6      57 .. 0.96
   2 ?   -2.5   0.0       4.7   6.5e+03      27      41 ..      74      88 ..      71     109 .. 0.70

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 9.7e-09
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSS CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlG 32
                                   +vGaG +Gl aA +L+ +g++v++++k+++++
  gi|116754708|ref|YP_843826.1|  6 VVGAGPAGLFAALELSVHGKSVVVVDKGRDIS 37
                                   8***************************9986 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.7
                                   SSSSSSGGG-EECET CS
                  NAD_binding_8 27 krdrlGGraasyevp 41
                                    ++ +GG++++ +++
  gi|116754708|ref|YP_843826.1| 74 LHPAIGGDLTRLTDD 88
                                   688999999987774 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   1.2   7.7e-08   0.00011       1      31 [.       3      33 ..       3      36 .. 0.95
   2 ?   -0.9   0.0      0.58     8e+02      85     169 ..     144     230 ..     113     326 .. 0.65

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 7.7e-08
                   FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveer 31
                                   DvvVvG+gpaG+ AA+    +G++v++v++ 
  gi|116754708|ref|YP_843826.1|  3 DVVVVGAGPAGLFAALELSVHGKSVVVVDKG 33
                                   9***************************986 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.58
                   FAD_oxidored  85 epevakavleemlaeagvtvllntrlvevekegkriesvtveskeg...rktirAkvfiDATgdGdlaalaGvpyrvGre 161
                                     pe+ ++  +++ ++ gv+ +ln+ + + + e++ + +v++ +  +   + t+ A+  i A   G++++  G++ r+G  
  gi|116754708|ref|YP_843826.1| 144 TPEIIREFSNDLKRR-GVRFVLNSSAADLIIEKDVCMGVRLSDGGEiraESTLLAPGRIGAEWIGEVIERYGIKARYGPL 222
                                    566666655555555.8888888888888888767888888654433355666666677777777777777777777766 PP

                   FAD_oxidored 162 sreetgep 169
                                    + +   e 
  gi|116754708|ref|YP_843826.1| 223 DVGVRVEV 230
                                    66644444 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   1.5e-05     0.021       2      34 ..       4      36 ..       3      43 .. 0.90
   2 ?    4.9   0.0     0.029        40      40      78 ..     145     183 ..     124     186 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.5e-05
                                   EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSS CS
                      Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkl 34
                                   vvvvG+G  gl +A +l+ +gk+V vv+ +  +
  gi|116754708|ref|YP_843826.1|  4 VVVVGAGPAGLFAALELSVHGKSVVVVDKGRDI 36
                                   8**************************987655 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.029
                                    HHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEEE CS
                      Pyr_redox  40 eeaskilqeklekngievllntkveeiegsedgvesvkl 78 
                                    +e+ +++ + l+++g++++ln++++ +  ++d   +v+l
  gi|116754708|ref|YP_843826.1| 145 PEIIREFSNDLKRRGVRFVLNSSAADLIIEKDVCMGVRL 183
                                    6788899999************99987755544445555 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1   4.5e-07   0.00062       1      31 [.       5      34 ..       5      41 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 4.5e-07
                    Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgn 31
                                   +++GaGPaGl aa+el  +g  ++++++kg+
  gi|116754708|ref|YP_843826.1|  5 VVVGAGPAGLFAALELSVHGK-SVVVVDKGR 34
                                   79******************9.8******94 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   7.4e-07     0.001       1      36 [.       3      36 ..       3      48 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 7.4e-07
                  Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieaspsl 36
                                   Dvvv+GaGpAgl  A +l  +  g +vv+++ + ++
  gi|116754708|ref|YP_843826.1|  3 DVVVVGAGPAGLFAALEL--SVHGKSVVVVDKGRDI 36
                                   9*****************..9**********99887 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.2   6.9e-06    0.0095      18      48 ..       2      31 ..       1      37 [. 0.87

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6.9e-06
                                   EEEEEE--SHHHHHHHHHHHHCTTS-EEEEE CS
                           Thi4 18 sDvvivGaGssGLtaayylakkpdlkvaile 48
                                   +Dvv+vGaG++GL aa  l+ + +  v++++
  gi|116754708|ref|YP_843826.1|  2 QDVVVVGAGPAGLFAALELSVH-GKSVVVVD 31
                                   6******************998.77777765 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 ?    9.3   0.1   0.00044      0.61      30      62 ..       3      35 ..       1      45 [. 0.89
   2 ?    0.0   0.0      0.32   4.4e+02     165     194 ..     391     420 ..     384     437 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00044
                                   EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHH CS
                    AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrpa 62
                                    v+v+G+G aGl A+   +  g +V+v+D+  +
  gi|116754708|ref|YP_843826.1|  3 DVVVVGAGPAGLFAALELSVHGKSVVVVDKGRD 35
                                   59***************************8766 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.32
                                    SHHHHHHHHHHHHHHHHHHHCHHHTCCHHH CS
                    AlaDh_PNT_C 165 vprtasalltnntlpyleelladkglkkal 194
                                    v ++++ l++ ++  y++e+  dk+l++ +
  gi|116754708|ref|YP_843826.1| 391 VNADSTLLYAPEIKFYAREISVDKDLQTSI 420
                                    6789****************9999986655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); 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 0.27s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3194.33
//
Query:       gi|116754709|ref|YP_843827.1|  [L=145]
Description: hypothetical protein Mthe_1412 [Methanosaeta thermophila PT]
Scores for complete 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-46  155.9   0.0    8.7e-46  155.7   0.0    1.0  1  SPOUT_MTase  Predicted SPOUT methyltransferase


Domain annotation for each model (and alignments):
>> SPOUT_MTase  Predicted SPOUT methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.7   0.0   4.8e-50   8.7e-46       1     154 []       1     144 [.       1     144 [. 0.96

  Alignments for each domain:
  == domain 1  score: 155.7 bits;  conditional E-value: 4.8e-50
                                    XEEEEEEES---H.HHHHHHHHHHHHHTTT-EEEEEEE....---S-HHHHHHHHHHT--....TT-EEEEE-TTSEE-- CS
                    SPOUT_MTase   1 mkikiiavgklkekylkelieeYlkrlkkyakleiielkkekksekeeekakekegerilkklkkkayvillderGkels 80 
                                    m+++iiavg+++e++++++++ Yl+rl++y++l+++e++         e+   keg+ il++l  + ++++lde+G+++s
  gi|116754709|ref|YP_843827.1|   1 MHMRIIAVGRIRERFWQDAASYYLRRLSPYTRLDVVEVR---------EEDPIKEGRGILAHLC-GGVTVALDEHGESMS 70 
                                    899***********************************4.........667789999***8765.7899*********** PP

                                    HHHHHHHHHHHHHHT-.-EEEEE--TT---GGGGGG-SEEEE--SS---HHHHHHHHHHHHHHHHHHHT--XXX CS
                    SPOUT_MTase  81 SeelakkleklaeegkselvfvIGGsdGlseevkkradeklslsklTfpHqlvrvvllEQiYRaftIlkgepYH 154
                                    S+ela +l++   eg  +++ +IGG++Gls++v++r+d +lslsk+Tfp+q++r++llEQ+YRaf+I+k+epYH
  gi|116754709|ref|YP_843827.1|  71 SQELALWLQNRIVEGCGSINWIIGGPEGLSQDVLNRSDLQLSLSKMTFPYQMARILLLEQLYRAFKIIKNEPYH 144
                                    ************************************************************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 1117.73
//
Query:       gi|116754710|ref|YP_843828.1|  [L=656]
Description: acetate--CoA ligase [Methanosaeta thermophila PT]
Scores for 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-90  303.4   0.0    2.4e-90  303.2   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    3.2e-26   92.1   0.1    5.8e-25   88.1   0.1    2.3  2  AMP-binding_C  AMP-binding enzyme C-terminal domain
    8.4e-15   54.4   4.8    8.4e-15   54.4   4.8    2.4  2  ACAS_N         Acetyl-coenzyme A synthetase N-terminus


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  303.2   0.0     4e-94   2.4e-90       2     422 ..      95     536 ..      94     537 .. 0.90

  Alignments for each domain:
  == domain 1  score: 303.2 bits;  conditional E-value: 4e-94
                                    HHHHHHST.TSEEEEE....CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEE CS
                    AMP-binding   2 eeqaaktp.dkvalvd....sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvp 76 
                                    +++a+ ++ +kva+++     g+ + +TY +l++ vn+lA+gL+slGvkkgdrV+i+lp+ pe+ va+la++k+Ga++v+
  gi|116754710|ref|YP_843828.1|  95 DRHARSWRrNKVAYYFvgepVGDTRAITYYQLYRDVNKLANGLKSLGVKKGDRVGIYLPMIPELPVAMLACAKIGAIHVV 174
                                    56777777799***889999889********************************************************* PP

                                    EETTS-HHHHHHHHHHHTESEEE......ETCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS. CS
                    AMP-binding  77 lnptltaeelayiledseakvli......atvdsel.leklleaaakleavklvivldadellkeeelkeeeeseekae. 148
                                    + ++++a +l+  ++d++a+vli      +  + +   ++++ea ++ ++v+  iv+ + + + e++  ++  + e  + 
  gi|116754710|ref|YP_843828.1| 175 VFSGFSAGALRERINDAGARVLItcdgsyRRGKPIPiKAQADEALQDAPSVERQIVYRRTGQSIEWKDGFDIWWHELVKn 254
                                    ***********************9988762445777788899999999999*****999998877777666655543325 PP

                                    ..-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHC.SCCTTT-EEEESS-TTSCHHHHHHHHHHH CS
                    AMP-binding 149 ..kpeeeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletr.fklkeddvvlsilplahifglilelllal 225
                                      +++e+ + +++d+++i+YT G  GkP GV++ h+ ++   a    +   f++k++dv++s++++ +i+g+++ ++++l
  gi|116754710|ref|YP_843828.1| 255 qpDECETLQMDSEDPLFILYTAGAGGKPRGVVHAHGGFCVGPAYT--TSWvFDIKDTDVYWSTADIGWITGHTYIVYGPL 332
                                    6678888899*************************8886653332..222477889************************ PP

                                    HTT-EEEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHH CS
                    AMP-binding 226 lsGatvvllpkdaa.ldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffr 304
                                    + Gat v+++++++ +d +++++ ie+++v+vi+++P+++++++++g++    +++dl s+rl+ ++ge+++p++  ++r
  gi|116754710|ref|YP_843828.1| 333 CLGATSVMYEGSPDyPDFGRWFQIIEDYGVSVIYTAPTAIRMFMKEGEEW--PRKYDLRSVRLMGSVGEAMNPDAFLWWR 410
                                    **************888****************************76554..5567************************ PP

                                    HHHTC...EEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEET..TS-SEBT CS
                    AMP-binding 305 alfge...evlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgp..gvmkgYl 379
                                    +++g+   ++++++ ++Et+++v+ +pl+    k+gs  +plpg  v ++D + g+ v++ge+G +++  p  ++ +g +
  gi|116754710|ref|YP_843828.1| 411 KHVGNdwaPIMDTWFQSETGCHVI-APLPITPLKPGSPAFPLPGYNVDLLDVN-GRAVGPGESGNIVLTAPwpTMLRGIY 488
                                    ***********************9.7777777899*****************9.***************99667****** PP

                                    T-HHHHHHHEEE.....TCCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                    AMP-binding 380 kkpeataeafds.....egrwlrTGDlgrldedGyleivgRkkdlikl 422
                                    ++pe+ +e + +     +++ + +GD +r+d+dGy +i+gR++d++k+
  gi|116754710|ref|YP_843828.1| 489 GEPEKLREIYYDyywsiKPGIYLSGDRARRDADGYWWILGRIDDVLKV 536
                                    **********9899987557**************************98 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 ?    1.3   0.0      0.11   6.8e+02      51      72 ..      39      60 ..      14      62 .. 0.69
   2 !   88.1   0.1   9.7e-29   5.8e-25       1      76 []     545     623 ..     545     623 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.11
                                   HHHT-TTTS-SEEEE-S---B- CS
                  AMP-binding_C 51 rkelgpyavpkkvvfvdelpkt 72
                                   +kel ++   ++v+f de+ kt
  gi|116754710|ref|YP_843828.1| 39 EKELRAWCSENYVEFWDEMAKT 60
                                   3488888777788888888887 PP

  == domain 2  score: 88.1 bits;  conditional E-value: 9.7e-29
                                    HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE---..-.--HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                  AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg..s.ealeeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                    evEsa +shp+Va+aaV+G pd+vkGe ++ fVvlk+g  + e+l+++++ hvr+++gp+a p++v+fv+++pk r+GK
  gi|116754710|ref|YP_843828.1| 545 EVESAALSHPNVADAAVIGRPDKVKGENIILFVVLKEGinPsEELKKDIRNHVRATMGPIAMPSEVYFVSAIPKDRTGK 623
                                    8***********************************99753355**********************************9 PP

>> ACAS_N  Acetyl-coenzyme A synthetase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.4   4.8   1.4e-18   8.4e-15       2      55 .]      40      93 ..      39      93 .. 0.96
   2 ?   -1.4   0.1      0.37   2.2e+03      12      44 ..     309     354 ..     299     355 .. 0.48

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 1.4e-18
                                   HHHHHHHHH-HHHHHHHHHCC.S--SB--S-SECSTTTCT-EESTT-EE-HHHHH CS
                         ACAS_N  2 kelykeSiedpeaFWaeqake.ldWekpfdkvldgskgpfikWFeGGklNicyNc 55
                                   kel ++  e++ +FW+e+ak   dW+ p++kvl++ ++p+++WF+GGk N+++N+
  gi|116754710|ref|YP_843828.1| 40 KELRAWCSENYVEFWDEMAKTyADWFVPYEKVLEW-NPPHARWFVGGKCNVAHNA 93
                                   68999***************98*************.9*****************7 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.37
                                    HHHHHHHHHCCS--SB--S-SE.............CST.TTC.T-EES CS
                         ACAS_N  12 peaFWaeqakeldWekpfdkvl.............dgs.kgp.fikWF 44 
                                     + +W+   +++ W++  ++++             +gs + p f +WF
  gi|116754710|ref|YP_843828.1| 309 TDVYWST--ADIGWITGHTYIVygplclgatsvmyEGSpDYPdFGRWF 354
                                    5555553..345555555543322222222222223333344577888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (656 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.42
# Mc/sec: 4707.33
//
Query:       gi|116754711|ref|YP_843829.1|  [L=135]
Description: hypothetical protein Mthe_1414 [Methanosaeta thermophila PT]
Scores for complete 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-59  199.2   0.3    1.9e-59  199.0   0.3    1.0  1  DUF1699   Protein of unknown function (DUF1699)
  ------ inclusion threshold ------
      0.033   14.6   0.1        2.8    8.4   0.0    2.2  2  EnY2      Transcription factor e(y)2
       0.12   12.2   0.0       0.44   10.3   0.0    1.9  2  HTH_38    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> DUF1699  Protein of unknown function (DUF1699)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.0   0.3   3.1e-63   1.9e-59       1     130 []       1     130 [.       1     130 [. 0.99

  Alignments for each domain:
  == domain 1  score: 199.0 bits;  conditional E-value: 3.1e-63
                        DUF1699   1 mkirvvsskeeietlnenekivHlafrpsntdilslvkkcpklkaiqvpeSykktlsksakmfleiqgiellegdvwghr 80 
                                    m+irvvssk+ei++ln+ne++vHlafr+sn d+l+l+++cp+l++iqvp+Sykkt+s+++++fle+qgiellegdvwghr
  gi|116754711|ref|YP_843829.1|   1 MRIRVVSSKSEIAQLNPNERMVHLAFRASNVDFLNLMQRCPRLRVIQVPPSYKKTMSNAIQVFLEMQGIELLEGDVWGHR 80 
                                    9******************************************************************************* PP

                        DUF1699  81 kdineyyevseevierikelkseglseeeiaeklsketklspdlikfllk 130
                                    kd++ey++vs+++ie+i++++++g+s e++ae+l+k++++ pdlik+++k
  gi|116754711|ref|YP_843829.1|  81 KDLDEYFTVSDTTIEEIRSMINKGVSFEQMAEELQKKARIGPDLIKYIVK 130
                                    ************************************************86 PP

>> EnY2  Transcription factor e(y)2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0    0.0081        48      48      84 .]      28      64 ..       8      64 .. 0.85
   2 ?    8.4   0.0   0.00046       2.8      34      65 ..      89     119 ..      86     134 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0081
                                   TSS.CHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHH CS
                           EnY2 48 eeevsveelveeitpkaralVPdevkkellqrIrefL 84
                                    ++v++ +l++++      +VP + kk + + I+ fL
  gi|116754711|ref|YP_843829.1| 28 ASNVDFLNLMQRCPRLRVIQVPPSYKKTMSNAIQVFL 64
                                   5668999999999999999**************9997 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00046
                                    HHHHHHHHHHH..HTSS.CHHHHHHHHHHHHH CS
                           EnY2  34 vkelckeiirekgleeevsveelveeitpkar 65 
                                    v++++ e+ir+   ++ vs+e++ ee+++kar
  gi|116754711|ref|YP_843829.1|  89 VSDTTIEEIRS-MINKGVSFEQMAEELQKKAR 119
                                    56677788886.56778**************8 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       0.4   2.4e+03       4      11 ..      14      21 ..      11      22 .. 0.81
   2 ?   10.3   0.0   7.4e-05      0.44      11      33 ..      95     117 ..      89     119 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.4
                         HTH_38  4 hLsleeRe 11
                                   +L+++eR 
  gi|116754711|ref|YP_843829.1| 14 QLNPNERM 21
                                   79999995 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 7.4e-05
                         HTH_38  11 eeIerllaeGlslreIArrLgrs 33 
                                    eeI  ++++G s+ ++A +L ++
  gi|116754711|ref|YP_843829.1|  95 EEIRSMINKGVSFEQMAEELQKK 117
                                    89******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); 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: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 969.67
//
Query:       gi|116754712|ref|YP_843830.1|  [L=93]
Description: hypothetical protein Mthe_1415 [Methanosaeta thermophila PT]
Scores for 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-11   41.8   1.0    1.1e-10   41.6   1.0    1.1  1  2TM       2TM domain
  ------ inclusion threshold ------
      0.022   14.6   0.3      0.032   14.1   0.3    1.3  1  CAAD      CAAD domains of cyanobacterial aminoacyl-tRNA synth


Domain annotation for each model (and alignments):
>> 2TM  2TM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   1.0   1.3e-14   1.1e-10       8      73 ..      19      90 ..      13      93 .] 0.79

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 1.3e-14
                            2TM  8 keikgFyrhlvvYlivniflilinl......gsswf.lwpilfWgiglllhalkvFgtekffgk.eWeerkiek 73
                                   ++ k F+ h+++Y++vn++ i++n          w+ ++pi++Wg+ +++h++        ++  +  er+ie 
  gi|116754712|ref|YP_843830.1| 19 DQVKLFQLHIAIYIVVNAIWIALNAmgtiktIPGWAmYYPIVGWGLLVVVHYWFYVR--GAENLcKLREREIES 90
                                   57799*******************889999844455477**************7443..333335688888876 PP

>> CAAD  CAAD domains of cyanobacterial aminoacyl-tRNA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.3   3.5e-06     0.032      12      61 ..      22      75 ..      12      87 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.5e-06
                           CAAD 12 rklkviglilaaivalklalavldaiddiPllpplleLvG....lgytgwFvyr 61
                                   + +++   i +++ a+++al+++ +i+ iP  +    +vG    +++  wF +r
  gi|116754712|ref|YP_843830.1| 22 KLFQLHIAIYIVVNAIWIALNAMGTIKTIPGWAMYYPIVGwgllVVVHYWFYVR 75
                                   456667778888999************************933322344566655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 724.06
//
Query:       gi|116754713|ref|YP_843831.1|  [L=220]
Description: peroxidase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-29  102.8   0.0    1.8e-29  102.1   0.0    1.3  1  AhpC-TSA    AhpC/TSA family
    2.3e-14   52.9   0.2      4e-14   52.2   0.2    1.3  1  1-cysPrx_C  C-terminal domain of 1-Cys peroxiredoxin
    9.6e-11   41.6   0.0    1.3e-10   41.1   0.0    1.2  1  Redoxin     Redoxin


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.1   0.0   3.1e-33   1.8e-29       2     123 ..      15     142 ..      14     143 .. 0.96

  Alignments for each domain:
  == domain 1  score: 102.1 bits;  conditional E-value: 3.1e-33
                                    TSB----EEESTTCEEEEC.HHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH- CS
                       AhpC-TSA   2 gdkapdfelknadgetvsl.sdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfieke 80 
                                    gd+ p +e+ +++ ++++l +d++gk+ vlf +p+d++pvCtte  a++k+ e+fk++++e+ig+svd+ +sh k+ e +
  gi|116754713|ref|YP_843831.1|  15 GDRLPRMEVRTTH-GPITLpDDLAGKWFVLFSHPADFTPVCTTEFIAFQKRREDFKKLNCELIGLSVDQIFSHMKWTEWI 93 
                                    8999*****9998.999998999********************************************************* PP

                                    H.......SSEEEE-TTSHHHHHTT-EETT.TTECSCEEEEE-TTSBEEE CS
                       AhpC-TSA  81 s......lnfpllsDeegkvakaygvlkee.kglalratfvidkegkiry 123
                                    +      ++fp+++D +g+va+ +g++++     ++ra+fv+d+ g+ir 
  gi|116754713|ref|YP_843831.1|  94 RekmgveIKFPIIAD-TGEVADLLGMIHPGkGSNTVRAVFVVDPSGIIRL 142
                                    99*************.9**********99978899*************95 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 !   52.2   0.2   6.7e-18     4e-14       1      37 [.     163     203 ..     163     204 .. 0.97

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 6.7e-18
                                    HHHHHHHHT-BB-TTT.T.....BT-EEE---SSHHHHHHHH CS
                     1-cysPrx_C   1 ALQladkhgvatPAnWkp.....GdkvivpPpateedavkry 37 
                                    ALQ++dk++vatPAnW p     Gd+vi+pPp++e+ a++r+
  gi|116754713|ref|YP_843831.1| 163 ALQVVDKNKVATPANW-PnndliGDEVIIPPPSDEKSAKERL 203
                                    9***************.99******************99997 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.0   2.2e-14   1.3e-10       3     135 ..      15     148 ..      13     160 .. 0.81

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 2.2e-14
                                    TSBB---ECCEETTCEEEEEHHH.HTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHHHHHHHH CS
                        Redoxin   3 gdkaPdftlplaatdgnsvslse.fkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndafvkefwg 81 
                                    gd++P  +   + t   +++l + ++gk  v+++ p+ f+P+C++e ++++k  e +k+ + + +++++d+    +++ +
  gi|116754713|ref|YP_843831.1|  15 GDRLPRME---VRTTHGPITLPDdLAGKWFVLFSHPADFTPVCTTEFIAFQKRREDFKKLNCELIGLSVDQIFSHMKWTE 91 
                                    88889888...5678889999999*******************************************9988776444333 PP

                                    H......TT-TSEEEE-TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEEESSS CS
                        Redoxin  82 k......eglkfpvlsDgsaaftkalGlrleedaseglrtpryavidedgkvvylevepe 135
                                            ++kfp+++D  ++++  lG+     +++    ++++v+d  g ++ + + p 
  gi|116754713|ref|YP_843831.1|  92 WirekmgVEIKFPIIADT-GEVADLLGMIHP-GKGS-NTVRAVFVVDPSGIIRLILYYPQ 148
                                    3556999777*******8.9*******6643.3344.49***********9986655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1570.93
//
Query:       gi|116754714|ref|YP_843832.1|  [L=102]
Description: 4Fe-4S ferredoxin iron-sulfur binding domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-05   24.1   7.3      0.022   15.3   0.3    2.3  2  Fer4_7    4Fe-4S dicluster domain
    7.1e-05   22.7  12.3     0.0012   18.8   2.1    2.3  2  Fer4_6    4Fe-4S binding domain
    0.00065   19.6  12.5     0.0063   16.6   2.0    2.5  2  Fer4_2    4Fe-4S binding domain
     0.0019   18.3  11.4     0.0033   17.5  11.4    1.4  1  Fer4_9    4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.011   15.9  12.2      0.029   14.5  12.2    1.7  1  Fer4_21   4Fe-4S dicluster domain
      0.012   15.4   3.4      0.012   15.4   3.4    2.6  3  Fer4      4Fe-4S binding domain
      0.017   15.7   0.9      0.017   15.7   0.9    2.2  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
      0.055   13.6  13.5          2    8.6   2.3    2.1  2  Fer4_10   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 !   11.9   1.9   0.00012      0.27      30      46 ..      15      31 ..       3      36 .. 0.81
   2 !   15.3   0.3     1e-05     0.022       2      25 ..      52      76 ..      51      97 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                         Fer4_7 30 kveidpekClgCgaCva 46
                                   +++id ekCl Cg+C++
  gi|116754714|ref|YP_843832.1| 15 HPTIDREKCLKCGMCMN 31
                                   5699***********96 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1e-05
                         Fer4_7  2 Ci.gCgaCvaaCpvkaieldeeene 25
                                   Ci gC+ C++ C+ +ai++++ +  
  gi|116754714|ref|YP_843832.1| 52 CIvGCNTCANLCMGEAISFPDIKPI 76
                                   766***************9874333 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   2.1   5.3e-07    0.0012       2      17 ..      16      31 ..      15      34 .. 0.92
   2 !    9.3   2.8   0.00056       1.3       2      19 ..      45      63 ..      44      68 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 5.3e-07
                         Fer4_6  2 veidpdkCigCgdCvr 17
                                   ++id++kC+ Cg C++
  gi|116754714|ref|YP_843832.1| 16 PTIDREKCLKCGMCMN 31
                                   89************85 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00056
                         Fer4_6  2 veidpdkCi.gCgdCvrvC 19
                                   v+  p+ Ci gC+ C++ C
  gi|116754714|ref|YP_843832.1| 45 VVARPNQCIvGCNTCANLC 63
                                   67789***88*****9988 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   2.0   2.8e-06    0.0063       1      20 [.      14      32 ..      14      33 .. 0.93
   2 !    8.2   3.1    0.0013       2.9       3      20 ..      45      63 ..      43      64 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.8e-06
                         Fer4_2  1 apvvvdtdrCigCgaCvsaC 20
                                   +++ +d+++C+ Cg C  +C
  gi|116754714|ref|YP_843832.1| 14 WHPTIDREKCLKCGMC-MNC 32
                                   79**************.777 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0013
                         Fer4_2  3 vvvdtdrCi.gCgaCvsaC 20
                                   vv+ ++ Ci gC++C + C
  gi|116754714|ref|YP_843832.1| 45 VVARPNQCIvGCNTCANLC 63
                                   6667889*66*****9999 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5  11.4   1.5e-06    0.0033       1      51 []      22      68 ..      22      68 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.5e-06
                         Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaC.igCgaCveaCpkgai 51
                                   kC +Cg C++ C ++v+   + +  ++  +    +C +gC++C++ C  +ai
  gi|116754714|ref|YP_843832.1| 22 KCLKCGMCMN-CGMNVYDWTEDGPVVARPN----QCiVGCNTCANLCMGEAI 68
                                   7*********.*******999999998754....6*999********98776 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5  12.2   1.3e-05     0.029       2      52 ..      17      64 ..      16      70 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.3e-05
                        Fer4_21  2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeC.vGCnlCssvCP 52
                                   +id++kC++Cg C+  C    ++  + +++  +  + ++C vGCn C++ C 
  gi|116754714|ref|YP_843832.1| 17 TIDREKCLKCGMCM-NCG---MNVYDWTEDGPVVARPNQCiVGCNTCANLCM 64
                                   69***********7.577...455566667777778889957*********5 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   3.4   5.4e-06     0.012       1      15 [.      16      30 ..      16      33 .. 0.92
   2 ?   -3.7   0.1       5.9   1.3e+04       7       9 ..      51      53 ..      49      53 .. 0.46
   3 ?    6.6   1.7    0.0033       7.5       9      18 ..      54      63 ..      54      69 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.4e-06
                                   EEEETTTSSS-THHH CS
                           Fer4  1 vvideekCigCGaCv 15
                                   ++id ekC +CG C+
  gi|116754714|ref|YP_843832.1| 16 PTIDREKCLKCGMCM 30
                                   68************8 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 5.9
                                   TSS CS
                           Fer4  7 kCi 9 
                                    Ci
  gi|116754714|ref|YP_843832.1| 51 QCI 53
                                   455 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0033
                                   SS-THHHHHS CS
                           Fer4  9 igCGaCvevC 18
                                   +gC++C++ C
  gi|116754714|ref|YP_843832.1| 54 VGCNTCANLC 63
                                   79*******9 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   0.9   7.5e-06     0.017       1      26 [.      18      43 ..      18      51 .. 0.87
   2 ?    0.6   4.4      0.37   8.3e+02       5      16 ..      51      63 ..      49      65 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 7.5e-06
                        Fer4_13  1 VDrdtCiacgaCvelaPdvFeeddeg 26
                                   +Dr++C  cg C +   +v++  ++g
  gi|116754714|ref|YP_843832.1| 18 IDREKCLKCGMCMNCGMNVYDWTEDG 43
                                   8********************99986 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.37
                        Fer4_13  5 tCi.acgaCvela 16
                                   +Ci +c++C++l+
  gi|116754714|ref|YP_843832.1| 51 QCIvGCNTCANLC 63
                                   67659******99 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7  14.9    0.0035       7.9       1      55 [.      15      63 ..      15      63 .. 0.86
   2 ?    8.6   2.3   0.00088         2       3      21 ..      46      64 ..      44      98 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0035
                        Fer4_10  1 kvvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtg.cgaCveaC 55
                                   ++ id+++C++Cg C++ C +      + +  +e+++v   + +C+  c  C+  C
  gi|116754714|ref|YP_843832.1| 15 HPTIDREKCLKCGMCMN-CGM------NVYDWTEDGPVVARPNQCIVgCNTCANLC 63
                                   5789*************.955......77788888889999****95599**9988 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00088
                        Fer4_10  3 vidddtCi.rCgkCvkaCPa 21
                                   v  +++Ci +C++C + C +
  gi|116754714|ref|YP_843832.1| 46 VARPNQCIvGCNTCANLC-M 64
                                   678999*77*********.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       913  (0.0509231); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 772.07
//
Query:       gi|116754715|ref|YP_843833.1|  [L=300]
Description: hypothetical protein Mthe_1418 [Methanosaeta thermophila PT]
Scores for complete 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  148.4  45.0    2.5e-43  148.4  45.0    1.7  2  TauE      Sulfite exporter TauE/SafE


Domain annotation for each model (and alignments):
>> TauE  Sulfite exporter TauE/SafE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.3      0.05     9e+02      97     108 ..      14      25 ..       5      49 .. 0.43
   2 !  148.4  45.0   1.4e-47   2.5e-43       1     235 [.      48     289 ..      47     290 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.05
                           TauE  97 gvlllllallml 108
                                    ++l++++al ++
  gi|116754715|ref|YP_843833.1|  14 VLLIVIVALAIW 25 
                                    222222222221 PP

  == domain 2  score: 148.4 bits;  conditional E-value: 1.4e-47
                           TauE   1 lllagllaGfvagllGiGggliavPlLll.l.lppavavatsllavvatslsgalahrrrgnvdwrlllllllgsliGal 78 
                                    l+++gl+aGf++gl+G Gg  i++P+  + + +++++a++t+++av++t++sg + h+ r+n+d r++l+l+ g+++G++
  gi|116754715|ref|YP_843833.1|  48 LIAVGLAAGFLGGLIGTGGCSIMLPVIHFwMgYSAPIAIGTTIFAVIFTAISGGYGHLIRKNLDRRATLWLAGGGILGVI 127
                                    589**********************99998888************************9999******************* PP

                           TauE  79 lGallllllpse..llkllfgvlllllallmll...rkkrsrakgrerrptaillvligglvGllsGllGiGgGfllvpl 153
                                    +G++l++ l ++  ll+l++g++ ll a++m++    +++ +++g + + ++ +++++g+++G+l+G++G GgG  lvp 
  gi|116754715|ref|YP_843833.1| 128 FGSWLFTILVEHidLLQLILGLAFLLPAIRMIYegiGRSKPKQEGDTIPGGSSGFAVFGFAIGVLTGIVGLGGGYALVPG 207
                                    *********999778****************997553332444467888888888899888******************* PP

                           TauE 154 lllllglplkkavatslllilvislagalgyalagavdwpllllllpgallGallGarlarrlsertlrrlfallllvlg 233
                                    l++l+g p+  + +tsl++++++++++  + +++g v ++++l+l++g+++Ga++Ga + +r+ + tl+++f++  l+++
  gi|116754715|ref|YP_843833.1| 208 LIYLFGAPVYITMGTSLAVMIPMAVVAGGIKLVQGFVALTTALILAAGTIVGAQIGAAVIKRFRPNTLKLIFGIYFLYVS 287
                                    ***************************999999*********************************************99 PP

                           TauE 234 vk 235
                                    +k
  gi|116754715|ref|YP_843833.1| 288 LK 289
                                    87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       861  (0.0480228); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); 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):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2049.42
//
Query:       gi|116754716|ref|YP_843834.1|  [L=105]
Description: 50S ribosomal protein L12P [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-19   69.9  17.0    2.4e-19   69.7  17.0    1.0  1  Ribosomal_60s  60s Acidic ribosomal protein
     0.0017   18.5   0.5     0.0024   18.1   0.5    1.2  1  TetR_C_31      Tetracyclin repressor-like, C-terminal domain
  ------ inclusion threshold ------
       0.17   10.3   3.3        0.2   10.1   3.3    1.0  1  DUF1631        Protein of unknown function (DUF1631)
       0.21   11.4   3.5        6.7    6.4   0.1    2.0  2  DSBA           DSBA-like thioredoxin domain


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 !   69.7  17.0   5.4e-23   2.4e-19       1      88 []      16     104 ..      16     104 .. 0.74

  Alignments for each domain:
  == domain 1  score: 69.7 bits;  conditional E-value: 5.4e-23
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XX-- CS
                  Ribosomal_60s   1 eptaenikkvlkaagveveaarvkllvkalegkdieellangaaklaaaaaaaaaaaaaaaaaaaaeekkkeeeeeEeed 80 
                                    e++ + ikkvl+aagv  +++r+k+lv+aleg+di+++l++++a   ++aaaa aaaaa+ +a++ ++k++eeee+Ee +
  gi|116754716|ref|YP_843834.1|  16 EVSDDGIKKVLEAAGVAPDEVRIKALVSALEGVDIDKILSQATAM--PVAAAAPAAAAAETEAKKPAAKAEEEEEKEEAE 93 
                                    578999************************************988..444444444444444444444444444446666 PP

                                    S..S--.STTT CS
                  Ribosomal_60s  81 d..dmG.fgLF 88 
                                    +   +G ++LF
  gi|116754716|ref|YP_843834.1|  94 EsgIEGlGALF 104
                                    66788988999 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 !   18.1   0.5   5.3e-07    0.0024      52      93 ..      19      67 ..       9      77 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 5.3e-07
                                   HHHHHHHHHHHCS.S-HHHHHHHHHHHHHHHHHHHHHSG.......TS-H CS
                      TetR_C_31 52 realaallaalGl.pdpeeaarllvaaldGllldrLagp.......aadp 93
                                   ++ +  +l+a+G+ p +e ++ +lv al+G+ +d +  +       aa+p
  gi|116754716|ref|YP_843834.1| 19 DDGIKKVLEAAGVaP-DEVRIKALVSALEGVDIDKILSQatampvaAAAP 67
                                   677889*******66.677***************9988753232332222 PP

>> DUF1631  Protein of unknown function (DUF1631)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   3.3   4.4e-05       0.2     578     646 ..      24      93 ..      20     100 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 4.4e-05
                        DUF1631 578 egLasisydede..teaffkeLealhaaafrakaaelaaaakaaaakpaaaaataspveaeeeealaeeda 646
                                    + L+++++++de   +a+++ Le +  + + ++a++ + aa+a aa +aa++++++p++++eee ++ee++
  gi|116754716|ref|YP_843834.1|  24 KVLEAAGVAPDEvrIKALVSALEGVDIDKILSQATAMPVAAAAPAA-AAAETEAKKPAAKAEEEEEKEEAE 93 
                                    55677766666522679999**********9999888888766666.444444444555444444433333 PP

>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1    0.0015       6.7     113     158 ..      10      59 ..       5      66 .. 0.77
   2 ?    5.7   2.0    0.0025        11     130     168 ..      63     100 ..      48     104 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0015
                                    HHTSSS-TSSHHHHHHHHHHTTS.HHH.....HHHHHTSHHHHHHHHHHHH CS
                           DSBA 113 lwsegqaitddqellevaekaGldaee.....ldealeseavkeavrenta 158
                                    l+s g++++dd  +++v+e+aG+  +e     l  ale+ ++ +++++ ta
  gi|116754716|ref|YP_843834.1|  10 LHSSGKEVSDDG-IKKVLEAAGVAPDEvrikaLVSALEGVDIDKILSQATA 59 
                                    578899999998.**********9999555555666666777777766665 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0025
                                    HHHTTS.HHHHHHHHTSHHHHHHHHHHHHHHHHTT-SSS CS
                           DSBA 130 aekaGldaeeldealeseavkeavrentaaaqslgvtGv 168
                                    a +a   a+++++  +++a+k + +e+ ++a++ g+ G+
  gi|116754716|ref|YP_843834.1|  63 AAAAPA-AAAAETEAKKPAAKAEEEEEKEEAEESGIEGL 100
                                    444444.7899999**********************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1119  (0.0624129); expected 358.6 (0.02)
Passed bias filter:                      624  (0.0348039); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 808.46
//
Query:       gi|116754717|ref|YP_843835.1|  [L=321]
Description: acidic ribosomal protein P0 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-19   69.7   0.2    2.7e-19   69.0   0.2    1.3  1  RL10P_insert   Insertion domain in 60S ribosomal protein L10P
    5.1e-18   65.1   0.3    1.2e-17   63.9   0.0    1.8  2  Ribosomal_L10  Ribosomal protein L10
  ------ inclusion threshold ------
      0.086   13.4   7.9       0.28   11.8   7.9    1.9  1  Ribosomal_60s  60s Acidic ribosomal protein
       0.26   12.1   1.9       0.48   11.3   0.2    2.1  2  FliT           Flagellar protein FliT


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 !   69.0   0.2   5.9e-23   2.7e-19       2      71 .]     114     183 ..     114     183 .. 0.99

  Alignments for each domain:
  == domain 1  score: 69.0 bits;  conditional E-value: 5.9e-23
                   RL10P_insert   2 raGtiAtedviipagplelaPgsiepeLrklglptklkkGkivleedylvckkGetltseqaqlLklLgi 71 
                                    +aG++A+ d+++++g+++  Pg+++ +L+++g+p+ +k Gk+v++++++++k+G+++t++ a++Lkl++i
  gi|116754717|ref|YP_843835.1| 114 KAGAVAPVDIVVESGETSFSPGPMVGKLQSAGIPAAIKGGKVVINQRVVLAKQGDVITPKVAEVLKLMEI 183
                                    89******************************************************************98 PP

>> Ribosomal_L10  Ribosomal protein L10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.9   0.0   2.7e-21   1.2e-17       3      97 ..      12     106 ..      10     108 .. 0.95
   2 ?   -3.3   0.4       2.3     1e+04       7      21 ..     297     311 ..     293     314 .. 0.67

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 2.7e-21
                                    CCCHCCCCCCCCCCCTTSSEEEEEE-TTS-HHHHHHCCCHHHHHGCEEEEESCCCCCCCCHCCTSS.S..SCGCCSSSEE CS
                  Ribosomal_L10   3 kekKeelvkelkellkkyksvvvvdyegltvaqlqelRkklrengaelkvvKntlmrrAleetgeeek..lkellkgpva 80 
                                    +e+K + v+el e++ ++++v v+ +++l++ ++q lR  lr   +e++vv n+++rrA+ +++e+    l ++++ ++a
  gi|116754717|ref|YP_843835.1|  12 PEWKLREVDELVERIRSSRVVGVAGIRELPADEFQRLRGLLRPI-SEVRVVNNNIARRAILKSDES-IrpLVDYIEDQTA 89 
                                    79*****************************************9.*****************9996.447********** PP

                                    EEEESS-TCHHHHCCCC CS
                  Ribosomal_L10  81 lvftnedpvalakvlee 97 
                                    l+f++ +p+al+k+l++
  gi|116754717|ref|YP_843835.1|  90 LIFSDANPFALKKMLDA 106
                                    *************9975 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.3
                                    CCCCCCCCCCCTTSS CS
                  Ribosomal_L10   7 eelvkelkellkkyk 21 
                                    ee+v+e++e+ ++ +
  gi|116754717|ref|YP_843835.1| 297 EEVVEEVEEKKEEED 311
                                    567777777766655 PP

>> Ribosomal_60s  60s Acidic ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   7.9   6.2e-05      0.28      38      88 .]     269     320 ..     209     320 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.2e-05
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XX--SS--.STTT CS
                  Ribosomal_60s  38 llangaaklaaaaaaaaaaaaaaaaaaaaeekkkeeeeeEeedddmG.fgLF 88 
                                    ++++++a+++a a+   +++ a ++ + +e  ++ ee++Eeed ++G ++LF
  gi|116754717|ref|YP_843835.1| 269 VIMKAHANAQAIAGLMSPGGSAPEQRQVEEVVEEVEEKKEEEDAAAGlGSLF 320
                                    33444444333333333444444444444444444444479999*******9 PP

>> FliT  Flagellar protein FliT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00011      0.48      18      61 ..      17      81 ..      15      92 .. 0.92
   2 ?   -1.0   0.1      0.74   3.3e+03      28      52 ..     281     305 ..     271     311 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                                   HHHHHHHHHHHCS-......-ST--HHHHHHHHHHHH...............HHHHHHHHHHHHH CS
                           FliT 18 aerqqlverlreld......aaplspaereekrellr...............rilandaeirall 61
                                   +e  +lver+r+ +        +l+++e +++r llr                il+ d+ ir l+
  gi|116754717|ref|YP_843835.1| 17 REVDELVERIRSSRvvgvagIRELPADEFQRLRGLLRpisevrvvnnniarrAILKSDESIRPLV 81
                                   67889999999999999999999*******************99999999999999999999987 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.74
                                    HCS--ST--HHHHHHHHHHHHHHHH CS
                           FliT  28 reldaaplspaereekrellrrila 52 
                                    + l ++  s++e+++ +e+ +++ +
  gi|116754717|ref|YP_843835.1| 281 AGLMSPGGSAPEQRQVEEVVEEVEE 305
                                    3344667888888888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2307.02
//
Query:       gi|116754718|ref|YP_843836.1|  [L=212]
Description: 50S ribosomal protein L1P [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.4e-48  163.0   0.0    1.3e-47  162.2   0.0    1.4  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 !  162.2   0.0     7e-52   1.3e-47       7     204 .]      19     207 ..       1     207 [. 0.96

  Alignments for each domain:
  == domain 1  score: 162.2 bits;  conditional E-value: 7e-52
                                    SSS--EEEEEEEESSS-TTSGGG--EEEEE-STSTSSCS-EEEEE-HHHHH...HHHHTT..-SEEETCHHHHHHT-HHH CS
                   Ribosomal_L1   7 kkfdesveialnlttkkpkkadqrkpgkipLphplgkevkiclitkdpqaeyakeakeagriakviglkklkkkyksfea 86 
                                    + f+esv++a+nl +++  ++ +r+  ++ Lph+ g++ +i++++++++a    +ak+ag  + vi+ ++lk   +++++
  gi|116754718|ref|YP_843836.1|  19 RGFKESVDLAINLHNIDLTQPGNRVDTEVILPHGRGRPNRIAVFAAGDTAL---KAKAAG-ADYVISPEELKLLGENRKN 94 
                                    4599***********************************************...99****.8899*************** PP

                                    HHHTCCH-SEEEEEGGGHHHHHHHCHHHHGGGT-S-ECC..CT.BTS-HHHHHHHHCTTEEEEE-TTTSEEEEEEEETTS CS
                   Ribosomal_L1  87 krkllkefdlfladdrimpllpklLGkvfgkrkkmPipvltkgtvkedvkkevekalkstvvvrldkgtclsvkvGklsf 166
                                     rkl++e+d+f+a+ + mp ++k+LG+++gkr+kmP+p       ++dv++ + ++++  v +r+++  +++++vG+ ++
  gi|116754718|ref|YP_843836.1|  95 ARKLADEYDFFIAETQFMPVIGKTLGPILGKRGKMPTPL--P--PNADVAQMISRLKN-IVRIRSRDRPTFHIAVGRRDM 169
                                    ***************************************..4..3579**********.********************* PP

                                    SHHHHHHHHHHHHHHHHHTSTTTSGSEEEEEEEETTS- CS
                   Ribosomal_L1 167 taeelaeNieavvkalvekvpkkwkniksiylkttmsp 204
                                    +a +laeNie+v+++l++ ++ + +n+ks+y+kttm+p
  gi|116754718|ref|YP_843836.1| 170 DARQLAENIESVITKLEQTLKDGRRNLKSVYVKTTMGP 207
                                    *************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      748  (0.0417201); 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: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1503.17
//
Query:       gi|116754719|ref|YP_843837.1|  [L=159]
Description: 50S ribosomal protein L11 [Methanosaeta thermophila PT]
Scores for complete 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   76.7   1.4      2e-21   76.3   0.3    1.7  2  Ribosomal_L11    Ribosomal protein L11, RNA binding domain
    6.2e-21   74.0   0.8    1.1e-20   73.2   0.8    1.5  1  Ribosomal_L11_N  Ribosomal protein L11, N-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_L11  Ribosomal protein L11, RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       0.4   3.5e+03      36      58 ..      36      58 ..      29      58 .. 0.64
   2 !   76.3   0.3   2.2e-25     2e-21       2      70 .]      68     134 ..      67     134 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.4
                                   HHHHHHHGGGHT.XS.SHHHHHHH CS
                  Ribosomal_L11 36 yeIAkiKksdln.aalsleaavks 58
                                    +I +  k dln ++++++ +vks
  gi|116754719|ref|YP_843837.1| 36 AKINELTK-DLNgMQVPVKIIVKS 58
                                   44444444.777777777777775 PP

  == domain 2  score: 76.3 bits;  conditional E-value: 2.2e-25
                                    --SHHHHHHHHHTXSSXXSSTTTSXXEEEEHHHHHHHHHHHGGGHTXS.SHHHHHHHHHHHHCTTTEEE CS
                  Ribosomal_L11   2 tPptsylLkkaagiekgsgkpgketvGtvslkqvyeIAkiKksdlnaalsleaavksilgtArsmGikV 70 
                                    tPpts+lL+k+ag+ekgsg  +k++vG++s++qv+++A+iK+++l ++ +l++av +i+gt+  +Gik+
  gi|116754719|ref|YP_843837.1|  68 TPPTSALLLKEAGVEKGSGD-KKNFVGDISMDQVIKVAEIKRKNLLSS-NLKSAVSEIVGTCGTLGIKI 134
                                    9*******************.599******************999988.9*****************97 PP

>> 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 !   73.2   0.8   1.3e-24   1.1e-20       5      61 ..       2      58 ..       1      62 [. 0.93

  Alignments for each domain:
  == domain 1  score: 73.2 bits;  conditional E-value: 1.3e-24
                Ribosomal_L11_N  5 vkvvklrvpaGkAtpaPplGpaLGplGlnikkfckefnkaTkdkkglripVkitvyq 61
                                   ++vv+  v +GkAt++PplGpaLGplG+n++ ++ ++n+ Tkd +g+++pVki v++
  gi|116754719|ref|YP_843837.1|  2 ANVVEALVSGGKATAGPPLGPALGPLGVNVAAVVAKINELTKDLNGMQVPVKIIVKS 58
                                   579999*************************************************54 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); 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: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1110.47
//
Query:       gi|116754720|ref|YP_843838.1|  [L=153]
Description: transcription antitermination protein NusG [Methanosaeta thermophila PT]
Scores for complete 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   84.6   0.3    4.9e-24   84.0   0.3    1.3  1  Spt5-NGN         Early transcription elongation factor of RNA
    1.3e-07   31.4   0.5    2.5e-05   24.0   0.1    2.4  2  KOW              KOW motif
  ------ inclusion threshold ------
      0.014   15.2   0.3      0.026   14.4   0.3    1.4  1  Glyco_hydro_65C  Glycosyl hydrolase family 65, C-terminal dom


Domain annotation for each model (and alignments):
>> Spt5-NGN  Early transcription elongation factor of RNA pol II, NGN section
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.0   0.3   8.2e-28   4.9e-24       1      84 []       5      84 ..       5      84 .. 0.98

  Alignments for each domain:
  == domain 1  score: 84.0 bits;  conditional E-value: 8.2e-28
                       Spt5-NGN  1 siwavkctagqErevalslmkkilelakkenleIkSvfapdelkGyiyvEAdrkaaveralegipnvrgvvqglvpikEved 82
                                   si+ vk+ta+qEr+va  +++     a+ke+l+I+++++pd lkGy++vEA+ ++ ve+a++g+p++r+v +g ++++E+e+
  gi|116754720|ref|YP_843838.1|  5 SIYVVKTTANQERAVANLVAQV----ARKEKLDIRAILVPDVLKGYVLVEASAPEIVEQAIQGVPHARSVIKGASSFAEIEH 82
                                   69*****************988....99999*************************************************** PP

                       Spt5-NGN 83 ll 84
                                   +l
  gi|116754720|ref|YP_843838.1| 83 FL 84
                                   98 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.1   4.3e-09   2.5e-05       2      32 .]      96     126 ..      95     126 .. 0.94
   2 !    5.4   0.0    0.0032        19       1       9 [.     139     147 ..     139     147 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 4.3e-09
                                    TSEEEESSSTTTTCEEEEEEEETTTTEEEEE CS
                            KOW   2 GdhVkVvsGphkGktGkVvkvdqhkvrVfvd 32 
                                    G +V+ +sGp+kG+ ++V++vd  k+ ++v+
  gi|116754720|ref|YP_843838.1|  96 GAIVELISGPFKGEMARVKRVDIAKEEITVE 126
                                    999********************99999987 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0032
                                    TTSEEEESS CS
                            KOW   1 pGdhVkVvs 9  
                                    +GdhV+V+s
  gi|116754720|ref|YP_843838.1| 139 RGDHVRVLS 147
                                    6******97 PP

>> Glyco_hydro_65C  Glycosyl hydrolase family 65, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.3   4.4e-06     0.026      22      51 .]     115     145 ..     112     145 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.4e-06
                                    EEEEESSEEEEEEES.SSTEEEEETTEEEEE CS
                Glyco_hydro_65C  22 rVrvtpeevtvtles.gepltievyGeevtL 51 
                                    rV++++ee+tv+l +   p++i+v+G  v++
  gi|116754720|ref|YP_843838.1| 115 RVDIAKEEITVELFEaMVPIPITVRGDHVRV 145
                                    79************8455*********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); 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: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1202.52
//
Query:       gi|116754721|ref|YP_843839.1|  [L=89]
Description: hypothetical protein Mthe_1424 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00033   20.4   1.4     0.0098   15.7   0.3    2.2  2  Cys_rich_KTR    Cysteine-rich KTR
     0.0044   17.2   0.3        3.7    7.8   0.1    2.3  2  zf-RING_7       C4-type zinc ribbon domain
     0.0055   16.3   0.5        1.1    8.9   0.0    2.4  2  RecR            RecR protein
     0.0078   15.9   5.5      0.053   13.3   1.6    2.4  2  zinc_ribbon_2   zinc-ribbon domain
  ------ inclusion threshold ------
      0.019   14.9   3.5       0.12   12.3   0.9    2.5  2  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
      0.019   14.3   4.3       0.57    9.7   0.6    2.4  2  zf-ribbon_3     zinc-ribbon domain
      0.021   14.7   1.1        3.2    7.7   0.2    2.5  2  DUF3797         Domain of unknown function (DUF3797)
      0.026   14.2   3.4       0.45   10.2   0.4    2.8  3  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
      0.029   15.1   1.3        5.5    7.8   0.1    2.3  2  zf-3CxxC_2      Zinc-binding domain
      0.039   14.7   2.2        1.7    9.4   0.3    2.2  2  TniQ            TniQ
      0.052   13.8   1.7        5.2    7.4   0.1    2.4  2  zinc_ribbon_9   zinc-ribbon
      0.074   11.6   0.8      0.078   11.5   0.8    1.0  1  Terminase_GpA   Phage terminase large subunit (GpA)
        0.1   12.8   5.1       0.13   12.5   0.6    2.1  2  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
       0.25   11.4   4.9          2    8.5   4.9    2.1  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
       0.43   10.2   4.0        8.9    6.0   0.1    2.3  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
        1.3    8.4   7.7         23    4.4   7.7    2.3  1  zf-TFIIB        Transcription factor zinc-finger
        5.6    7.4   7.9         49    4.4   7.9    2.2  1  zf-IS66         zinc-finger binding domain of transposase IS6


Domain annotation for each model (and alignments):
>> Cys_rich_KTR  Cysteine-rich KTR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.3   9.3e-06    0.0098      20      38 ..      30      48 ..      14      53 .. 0.82
   2 ?    4.1   0.0     0.039        41      28      34 ..      70      76 ..      61      84 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 9.3e-06
                   Cys_rich_KTR 20 dTvLknfpLfCPKCkqetl 38
                                   + vL +f  fCPKC +e+l
  gi|116754721|ref|YP_843839.1| 30 QSVLDQFVPFCPKCGNECL 48
                                   579************9998 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.039
                   Cys_rich_KTR 28 LfCPKCk 34
                                    +CP+C 
  gi|116754721|ref|YP_843839.1| 70 YYCPRCD 76
                                   5788884 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.1    0.0035       3.7      22      30 ..      30      44 ..      20      44 .. 0.61
   2 !    7.6   0.0     0.004       4.2       8      29 ..      55      75 ..      48      76 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0035
                                   B......-EE-TTT- CS
                      zf-RING_7 22 e......vvtCpeCG 30
                                   +      v++Cp CG
  gi|116754721|ref|YP_843839.1| 30 QsvldqfVPFCPKCG 44
                                   23444479******9 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.004
                                   B--CCHHHHHCCSTB-EE-TTT CS
                      zf-RING_7  8 elppqvlselragdevvtCpeC 29
                                   +l+ q+++++     + +Cp C
  gi|116754721|ref|YP_843839.1| 55 ALDAQSWKKIIVE-TIYYCPRC 75
                                   4677777777777.5******* PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1     0.011        12      16      24 ..      37      45 ..      23      47 .. 0.88
   2 !    8.9   0.0     0.001       1.1      14      25 ..      67      78 ..      64      83 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.011
                                   -EE-TTT-- CS
                           RecR 16 vrhCsrCgn 24
                                   v +C++Cgn
  gi|116754721|ref|YP_843839.1| 37 VPFCPKCGN 45
                                   779*****9 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.001
                                   HH-EE-TTT--E CS
                           RecR 14 ekvrhCsrCgnl 25
                                   e++ +C+rC n+
  gi|116754721|ref|YP_843839.1| 67 ETIYYCPRCDNY 78
                                   7899*******9 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   1.6     5e-05     0.053       1       9 [.      39      47 ..      34      51 .. 0.75
   2 ?    4.1   0.1     0.039        41       1       5 [.      71      75 ..      65      77 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5e-05
                  zinc_ribbon_2  1 fCpnCGael 9 
                                   fCp+CG+e 
  gi|116754721|ref|YP_843839.1| 39 FCPKCGNEC 47
                                   677777775 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.039
                  zinc_ribbon_2  1 fCpnC 5 
                                   +Cp+C
  gi|116754721|ref|YP_843839.1| 71 YCPRC 75
                                   56666 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 ?   12.3   0.9   0.00011      0.12       3      14 ..      39      50 ..      37      54 .. 0.82
   2 ?    2.5   0.1      0.13   1.3e+02       3       9 ..      71      77 ..      69      78 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                                   BESTTTSBEEEE CS
                 RNA_POL_M_15KD  3 FCpkCgNlLlpk 14
                                   FCpkCgN  lpk
  gi|116754721|ref|YP_843839.1| 39 FCPKCGNECLPK 50
                                   *******76666 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.13
                                   BESTTTS CS
                 RNA_POL_M_15KD  3 FCpkCgN 9 
                                    Cp C N
  gi|116754721|ref|YP_843839.1| 71 YCPRCDN 77
                                   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 ?    9.7   0.6   0.00054      0.57      17      24 ..      38      45 ..      30      47 .. 0.76
   2 ?    6.0   0.2     0.008       8.4       3      10 ..      70      77 ..      69      82 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00054
                    zf-ribbon_3 17 nvCpyCGt 24
                                   ++Cp+CG 
  gi|116754721|ref|YP_843839.1| 38 PFCPKCGN 45
                                   68888885 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.008
                    zf-ribbon_3  3 vrCPnCGa 10
                                   ++CP+C++
  gi|116754721|ref|YP_843839.1| 70 YYCPRCDN 77
                                   69****87 PP

>> DUF3797  Domain of unknown function (DUF3797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.2    0.0031       3.2      15      22 ..      39      46 ..      22      50 .. 0.83
   2 ?    5.6   0.1     0.014        14      14      21 ..      70      77 ..      57      81 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0031
                        DUF3797 15 qCPeCgNn 22
                                    CP+CgN+
  gi|116754721|ref|YP_843839.1| 39 FCPKCGNE 46
                                   6******7 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.014
                        DUF3797 14 vqCPeCgN 21
                                    +CP C N
  gi|116754721|ref|YP_843839.1| 70 YYCPRCDN 77
                                   49****99 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 ?   -0.8   0.0       1.2   1.3e+03      20      29 ..      11      20 ..       8      22 .. 0.79
   2 ?   10.2   0.4   0.00043      0.45       4      16 ..      38      50 ..      38      52 .. 0.82
   3 ?    3.0   0.2      0.08        84       5       9 ..      71      75 ..      69      77 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.2
                  zf-NADH-PPase 20 warvCpaCgl 29
                                   +ar C  +g+
  gi|116754721|ref|YP_843839.1| 11 TARSCLITGA 20
                                   7999988875 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00043
                  zf-NADH-PPase  4 rFCgrCGaptepa 16
                                   +FC++CG ++ p+
  gi|116754721|ref|YP_843839.1| 38 PFCPKCGNECLPK 50
                                   5******887776 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.08
                  zf-NADH-PPase  5 FCgrC 9 
                                   +C+rC
  gi|116754721|ref|YP_843839.1| 71 YCPRC 75
                                   78888 PP

>> zf-3CxxC_2  Zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1    0.0052       5.5      30      46 ..      40      56 ..      34      67 .. 0.81
   2 ?    6.4   0.1     0.014        15       8      20 ..      70      82 ..      68      88 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0052
                     zf-3CxxC_2 30 CkkCkekvepyklrekd 46
                                   C kC++++ p++lr   
  gi|116754721|ref|YP_843839.1| 40 CPKCGNECLPKELRRAL 56
                                   9************9843 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.014
                     zf-3CxxC_2  8 fkCekCgkeWsSa 20
                                   + C++C ++Ws +
  gi|116754721|ref|YP_843839.1| 70 YYCPRCDNYWSEG 82
                                   88********976 PP

>> TniQ  TniQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.3    0.0016       1.7      89     120 ..      23      54 ..       4      62 .. 0.78
   2 ?    6.5   0.6     0.012        13      87     109 ..      53      75 ..      46      82 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0016
                           TniQ  89 lgeaisrrglrrsgrryCplClaedgepywrl 120
                                    + e   ++++  +++ +Cp+C +e+  ++ r+
  gi|116754721|ref|YP_843839.1|  23 VAELEEDQSVLDQFVPFCPKCGNECLPKELRR 54 
                                    5566667788999**********998666554 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.012
                           TniQ  87 kllgeaisrrglrrsgrryCplC 109
                                    +++  a+s++++  ++  yCp+C
  gi|116754721|ref|YP_843839.1|  53 RRALDAQSWKKIIVETIYYCPRC 75 
                                    66677899999************ PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1    0.0049       5.2      21      29 ..      32      45 ..      20      48 .. 0.67
   2 ?    5.8   0.1     0.016        17      23      29 ..      71      77 ..      59      82 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0049
                  zinc_ribbon_9 21 d.....vlCPhCgg 29
                                         ++CP Cg+
  gi|116754721|ref|YP_843839.1| 32 VldqfvPFCPKCGN 45
                                   35555359****97 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.016
                  zinc_ribbon_9 23 lCPhCgg 29
                                   +CP+C++
  gi|116754721|ref|YP_843839.1| 71 YCPRCDN 77
                                   5777775 PP

>> Terminase_GpA  Phage terminase large subunit (GpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.8   7.4e-05     0.078     180     239 ..      18      81 ..       4      86 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.4e-05
                  Terminase_GpA 180 kgtsriealyeesdqr.ryyvpCphCgelqels.fer....lkwpegeaeekaryvCphcgsliee 239
                                     g+ ++ +l e+     +++  Cp+Cg++   +  +r      w++     ++ y Cp c+  ++e
  gi|116754721|ref|YP_843839.1|  18 TGAKEVAELEEDQSVLdQFVPFCPKCGNECLPKeLRRaldaQSWKK--IIVETIYYCPRCDNYWSE 81 
                                    5555555555443333389999*******99554444322245555..588999********9998 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 ?   12.5   0.6   0.00012      0.13      24      36 ..      38      50 ..      30      70 .. 0.82
   2 ?    2.9   0.2      0.11   1.2e+02      23      31 ..      69      77 ..      62      79 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                   NOB1_Zn_bind 24 kFCpkCGnktLkr 36
                                    FCpkCGn+ L +
  gi|116754721|ref|YP_843839.1| 38 PFCPKCGNECLPK 50
                                   5*******99976 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.11
                   NOB1_Zn_bind 23 kkFCpkCGn 31
                                     +Cp+C n
  gi|116754721|ref|YP_843839.1| 69 IYYCPRCDN 77
                                   579****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 ?    8.5   4.9    0.0019         2      19      43 ..      38      75 ..      30      77 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0019
                  Zn_Tnp_IS1595 19 fvCPhCgsr.kayrikt............rglfqCkeC 43
                                   + CP+Cg++  + ++++               + C +C
  gi|116754721|ref|YP_843839.1| 38 PFCPKCGNEcLPKELRRaldaqswkkiivETIYYCPRC 75
                                   45********8888888888999999999999999999 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   1.0     0.018        19       4      15 ..      39      50 ..      38      53 .. 0.79
   2 ?    6.0   0.1    0.0084       8.9       3      10 ..      70      77 ..      68      83 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.018
                         zf_UBZ  4 lCerCgkeipes 15
                                   +C++Cg e ++ 
  gi|116754721|ref|YP_843839.1| 39 FCPKCGNECLPK 50
                                   7*****987665 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0084
                         zf_UBZ  3 ylCerCgk 10
                                   y C+rC+ 
  gi|116754721|ref|YP_843839.1| 70 YYCPRCDN 77
                                   89****96 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   7.7     0.022        23       2      26 ..      40      76 ..      39      79 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.022
                       zf-TFIIB  2 CPkCqde..leeser..........ggveidyCpqCr 26
                                   CPkC++e  ++e++r             +i+yCp+C 
  gi|116754721|ref|YP_843839.1| 40 CPKCGNEclPKELRRaldaqswkkiIVETIYYCPRCD 76
                                   9***998555577778888888544223799*****5 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 ?    4.4   7.9     0.047        49       3      46 .]      39      76 ..      38      76 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.047
                        zf-IS66  3 tCpcCGgllkpigedrvreeldipPakfrViehirpkyaCpcCe 46
                                    Cp+CG +  +++++  r+ ld    k +++e+i   y Cp+C+
  gi|116754721|ref|YP_843839.1| 39 FCPKCGNE--CLPKE-LRRALDAQSWKKIIVETI---YYCPRCD 76
                                   5*****98..89***.9*****777666666665...7899995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 636.46
//
Query:       gi|116754722|ref|YP_843840.1|  [L=370]
Description: histone deacetylase superfamily protein [Methanosaeta thermophila PT]
Scores for 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-75  251.9   0.0    1.2e-74  251.5   0.0    1.1  1  Hist_deacetyl  Histone deacetylase domain


Domain annotation for each model (and alignments):
>> Hist_deacetyl  Histone deacetylase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  251.5   0.0     7e-79   1.2e-74       1     306 [.      19     308 ..      19     309 .. 0.91

  Alignments for each domain:
  == domain 1  score: 251.5 bits;  conditional E-value: 7e-79
                                    SCCGTHHHHHHHHHHHHT.THHHHCCE..EE-----HHHHTTTS-HHHHHHHHCHHHHCHHT.TTHCCHHHCCTSTSSSS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Hist_deacetyl   1 hpenpkRlsaileslaesvglldelel.liqpseatkeellkvHskeYlelleslsnelkkkeeakekeleeiasklldd 79 
                                    hp +p R+  ++++++e +g +  + + ++ p  a++++ll vH++ Y++++++   +           l      l + 
  gi|116754722|ref|YP_843840.1|  19 HPLQPARIM-LTYRMIEEYGFFLGYDTeVQMPYYASEDDLLMVHDPGYIQAVKEERPDP---------AL-----GLDEP 83 
                                    677889998.77777777785554444256677778****************9743322.........22.....24468 PP

                                    STHCTTTCCHHHHHHHHHHHHHHHHHHTTSSSEEEETTSS--TT-BTTB-BTTBSS-HHHHHHHHHHHCC-SS-EEEEE- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Hist_deacetyl  80 dtpvspktlkaallavgavleavdavlsgsvkaafvlvrPpgHHakaseasGFClvNnvaiaikylqakhelkrvailDv 159
                                    dtpv+p++++a+ l +ga++ea+++v+s+  ++      ++ HHa + +a GFC++N+ a++i++l++  +++rv+++D+
  gi|116754722|ref|YP_843840.1|  84 DTPVFPGIYDASALIAGASIEAAKRVASE--PCVAFNLAGGLHHAFPARAAGFCVFNDCALGIRTLRK--RFDRVLYIDI 159
                                    9**************************99..88777779*****************************..688******* PP

                                    SSS--HHHHHHCTT-TTEEEEEEEE-CCTSTTSS--TT---SGGGTTSEEEEEE-TT-BHHHHHHHHHHCHHHHHCCH-- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Hist_deacetyl 160 DvHhGnGteeafysdpdvltlSiHryegifyPgtgaledlgegkgkgfnlnvpleegtgdeeylkvfeeilrpvleefkP 239
                                    D+HhG+G++ +fy+dp+vlt+SiH++++ ++Pgtg ++++g+g+g g++ n+p++ + +de y ++fe+++  +++ fkP
  gi|116754722|ref|YP_843840.1| 160 DAHHGDGVQYIFYEDPSVLTISIHESGKYLFPGTGFVDEIGSGDGYGYSANIPMPLNADDECYRYAFESVIPALFRWFKP 239
                                    ******************************************************************************** PP

                                    SEEEEEE-STTBTTSTT-S-BB-HHHHHHHHHHHCCCHGS-.G..EEEEE-S---HHHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Hist_deacetyl 240 dlilvsaGfDalkgdplgelnlsvegykeltkklaeladkv.k.kvvllleGGYnlealaravtavlsa 306
                                    d+++ ++G+D++  dpl++l+l+ egy++l+++++el d++   ++++l++GGYnle ++ a+t ++++
  gi|116754722|ref|YP_843840.1| 240 DAVVAQLGVDTHYADPLASLDLTLEGYGYLVRRIKELTDEYaAgRMLALGGGGYNLEVVPLAWTLAFQT 308
                                    *****************************************989*******************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       248  (0.0138323); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 2817.41
//
Query:       gi|116754723|ref|YP_843841.1|  [L=350]
Description: tRNA (guanine-N(2)-)-methyltransferase [Methanosaeta thermophila PT]
Scores for complete 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-105  351.6   0.0   6.6e-105  351.4   0.0    1.0  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
    7.2e-05   22.6   0.0    9.9e-05   22.2   0.0    1.2  1  Met_10           Met-10+ like-protein
  ------ inclusion threshold ------
      0.072   12.7   0.0       0.11   12.2   0.0    1.2  1  Cons_hypoth95    Conserved hypothetical protein 95
      0.091   13.5   0.0       0.25   12.0   0.0    1.7  1  Methyltransf_25  Methyltransferase domain
       0.12   12.0   0.0       0.19   11.3   0.0    1.2  1  MTS              Methyltransferase small domain


Domain annotation for each model (and alignments):
>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  351.4   0.0  1.8e-108  6.6e-105      16     374 ..      10     348 ..       2     350 .] 0.92

  Alignments for each domain:
  == domain 1  score: 351.4 bits;  conditional E-value: 1.8e-108
                                    TT--SS--GGGHHHHHHHHHH...HHHHHHHH-S-EEEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHHH CS
                            TRM  16 kkeeVFYNPvqefnRDlsvlvirqlellkkklgekikvldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeNvk 95 
                                    +++ VFYNP++++nRD+ v++    + l+ +     ++lda+sasG+R+iR  +E +gv++v++NDis+ A   i+eN  
  gi|116754723|ref|YP_843841.1|  10 NTDGVFYNPRMKTNRDICVAM---ASELGVN-----EYLDAFSASGIRGIRVRKE-AGVERVVMNDISPSACRRIRENLA 80 
                                    4578****************9...3434444.....69*****************.************************ PP

                                    HTT--GGEEEE-S-HHHHHC--SS-EEEEEE--SS--GGGHHHHHHHEEEEEEEEEEE--HHHHTTSSHHHHHHHHSSB- CS
                            TRM  96 lneveeivvineddAnvllaekkkrfdviDlDPfGspapfldsavqsvkekglLlvTaTDtavLaGaspekclrkYgava 175
                                    ln++++  ++  + A++l+   ++rf++iDlDPfGspa+fl  a+ s+++  +L +TaTDta+L+Ga+ ++++rkY av+
  gi|116754723|ref|YP_843841.1|  81 LNDISD-CEVTCESASALM--SRRRFEAIDLDPFGSPAQFLAPAASSARS--YLFITATDTAPLCGAHLKSGVRKYLAVP 155
                                    ******.5555568*****..789********************999876..**************************** PP

                                    --STTHHHHHHHHHHHHHHHHHHTTTEEEEEEEEEEETTEEEEEEEEEE-HHHHHHHHTTEEEEEEETTT--EEEE--GG CS
                            TRM 176 lkselcHEvalRillkavareaakYekavepllslsadfYvrvfvkvktgaakvkkvleklglvlhCsgClseekvkgla 255
                                    l++e+  E+++Ril++av re a+ ++   plls+++++Yvrv++++k+ga+++++ le++g+v hC+gC   +   g+ 
  gi|116754723|ref|YP_843841.1| 156 LNTEYHREMGVRILMGAVIREMARVDRRGIPLLSYATEHYVRVHMRIKKGAREADEALESMGYVEHCFGCGGWSLRMGMG 235
                                    **********************************************************************6665555554 PP

                                    G--.SB-TTT-SBEEEEEEEE-S-S--HHHHHHHHHHHCT..-TTS-HHHHHHHHHHHHHHS--SS-EEHHHHHHHHT-S CS
                            TRM 256 kfk.aecehcgaklhlaGPlwlgplkdkefveevleeaekekeeelkkrvkklLklikeElldaplyydlsqlasvlkls 334
                                      +   c++cg ++  aGPlwlgpl+dk+++   l++++       + r ++l  l++eE +d+p+yyd+++++++l+++
  gi|116754723|ref|YP_843841.1| 236 CRSsGTCSFCGGRTCTAGPLWLGPLHDKDLLRASLKRLDP------ESRAHRLVLLCSEE-IDVPFYYDHHKICRRLRIT 308
                                    433399***************************9999999......5788889999****.******************* PP

                                    S---HHHHHHH....TT-EE-TTSTTEEE-SS-HHHHHHH CS
                            TRM 335 vpplkkvvsalkelgfevsrtHakpkaikTnapleavvev 374
                                      +++kv+s+l+e g+++srtH+++ +ikT+ap+  ++  
  gi|116754723|ref|YP_843841.1| 309 PSKVEKVISDLLEHGYRASRTHFNGVGIKTDAPMGDLISL 348
                                    **********************************998876 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   2.8e-08   9.9e-05      74     155 ..       7      90 ..       3     182 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 2.8e-08
                                    EEEETTTS---GGGHHHHHHHHTT--T.T.-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TT CS
                         Met_10  74 fklDvskvyfsskleaErerlaklvee.g.evVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvek 151
                                     ++ +  v+++++ ++ r   +++++e g +  +d f   G   i + k +  +rv+ +d+ P++ + ++en++lN++++
  gi|116754723|ref|YP_843841.1|   7 VRVNTDGVFYNPRMKTNRDICVAMASElGvNEYLDAFSASGIRGIRVRKEAGVERVVMNDISPSACRRIRENLALNDISD 86 
                                    5677888************999996662324479********************************************98 PP

                                    CEEE CS
                         Met_10 152 vvkp 155
                                       +
  gi|116754723|ref|YP_843841.1|  87 CEVT 90 
                                    7533 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0     3e-05      0.11      38     121 ..      32     110 ..      18     122 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3e-05
                                    CCHCC-EEEETT-TTSHHHHHHHH.TT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEE CS
                  Cons_hypoth95  38 aeiegarvLDlfaGsGalglEAlS.Rgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdi 116
                                    +e+  +++LD f+ sG  g+      g++++v+ + +++a++ ++enl+  ++++ +++  e+a+  ++++     +f+ 
  gi|116754723|ref|YP_843841.1|  32 SELGVNEYLDAFSASGIRGIRVRKeAGVERVVMNDISPSACRRIRENLALNDISD-CEVTCESASALMSRR-----RFEA 105
                                    55667789*********99965331389************************997.888888888777666.....5777 PP

                                    EEE-- CS
                  Cons_hypoth95 117 vflDP 121
                                    + lDP
  gi|116754723|ref|YP_843841.1| 106 IDLDP 110
                                    77776 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.1e-05      0.25       3      59 ..      41      98 ..      40     109 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.1e-05
                                   EET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBS CS
                Methyltransf_25  3 dlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlp 59
                                   d+   +G   +++ k+ g ++v++ Dis+++++++re+++ +++ ++e+ + +a++l 
  gi|116754723|ref|YP_843841.1| 41 DAFSASGIRGIRVRKEAGVERVVMNDISPSACRRIRENLALNDIsDCEVTCESASALM 98
                                   6666778888888999889********************9999899999999988875 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   5.2e-05      0.19      28     101 ..      32     106 ..       8     113 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.2e-05
                                    HCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTSTTS-EEEE CS
                            MTS  28 pkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeveekkfdli 101
                                    ++   ++ lD  +  G+ g+ + ke    +v++ d++  A +  +enl+ n+++ +ev+ +++ + ++ ++f++i
  gi|116754723|ref|YP_843841.1|  32 SELGVNEYLDAFSASGIRGIRVRKEAGVERVVMNDISPSACRRIRENLALNDISdCEVTCESASALMSRRRFEAI 106
                                    444445678888889999***********************************9999999988888888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); 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: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 2332.29
//
Query:       gi|116754724|ref|YP_843842.1|  [L=109]
Description: hypothetical protein Mthe_1427 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0064   16.9  11.2     0.0078   16.6  11.2    1.1  1  DUF3147        Protein of unknown function (DUF3147)
  ------ inclusion threshold ------
       0.16   11.0  11.6       0.18   10.9  10.4    1.6  1  Acyl_transf_3  Acyltransferase family
        2.8    8.1  14.2          2    8.5   5.1    2.3  2  DUF4229        Protein of unknown function (DUF4229)


Domain annotation for each model (and alignments):
>> DUF3147  Protein of unknown function (DUF3147)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6  11.2   1.3e-06    0.0078       1     104 [.       3     102 ..       3     108 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.3e-06
                        DUF3147   1 lllrFvlGGlavllstivavllggklgGifaafPavylaaliilglevkgkelvsvavnvsrGavvGmisvlvcvlatll 80 
                                    ll+ F+lGG+  +l   +     g l+  +a+fP     ++i +++e  + +      + +rG ++   + +  vl++l+
  gi|116754724|ref|YP_843842.1|   3 LLIYFLLGGIITALVVHLGSSGRGTLSAFIATFPVLTALTFILISMEGSSAD----FCEYARGLLIFTPAWIAYVLTVLI 78 
                                    5899********9999999999999*********988888888888888888....78899******************* PP

                        DUF3147  81 llkkkgwkkgivvalvaWfvaavv 104
                                    + ++ g+ ++i++++v+++va+ +
  gi|116754724|ref|YP_843842.1|  79 TFERIGVWLSIALGMVVYAVASWL 102
                                    ********************9976 PP

>> Acyl_transf_3  Acyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9  10.4     3e-05      0.18     199     296 ..       4      98 ..       1      98 [. 0.95

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3e-05
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Acyl_transf_3 199 llfflfGalladaddrdrnlsrglkislllsllllalillalfgqtdggglvasvliqsaslllvslgimllllllfalp 278
                                    l++fl+G+++  +  + +++ rg++ ++++ + +l +  + l ++    g+ a    + + ll+++ + ++ +l++++  
  gi|116754724|ref|YP_843842.1|   4 LIYFLLGGIITALVVHLGSSGRGTLSAFIATFPVLTALTFILISME---GSSADFCEYARGLLIFTPAWIAYVLTVLITF 80 
                                    89********************************************...9****************************** PP

                                    xxxxxxxxxxxxxxxxxx RF
                  Acyl_transf_3 279 srsafkllrylgkiSygi 296
                                     r++++l + lg   y++
  gi|116754724|ref|YP_843842.1|  81 ERIGVWLSIALGMVVYAV 98 
                                    ******999999998875 PP

>> DUF4229  Protein of unknown function (DUF4229)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   1.7    0.0047        28       6      37 ..       1      43 [.       1      52 [. 0.73
   2 ?    8.5   5.1   0.00034         2       6      49 ..      59     103 ..      57     104 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0047
                        DUF4229  6 aRlaLfvvltavillvarliglp...........vpllvaall 37
                                   +Rl++  +l ++i ++++ +g +           +p+l a+++
  gi|116754724|ref|YP_843842.1|  1 MRLLIYFLLGGIITALVVHLGSSgrgtlsafiatFPVLTALTF 43
                                   79*********99999988887766666666555555555555 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00034
                        DUF4229   6 aRlaLfvvltavillvarliglp.vpllvaallAlvvalplSmvl 49 
                                    aR +L+   +++ +++ +li+ + +++++++ l++vv ++ S++l
  gi|116754724|ref|YP_843842.1|  59 ARGLLIFTPAWIAYVLTVLITFErIGVWLSIALGMVVYAVASWLL 103
                                    78889999999*******************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 866.96
//
Query:       gi|116754725|ref|YP_843843.1|  [L=220]
Description: NADPH-dependent F420 reductase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-13   51.4   0.0    1.9e-13   50.8   0.0    1.3  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
        0.1   11.6   0.0       0.14   11.1   0.0    1.2  1  PDH              Prephenate dehydrogenase
       0.18   12.1   0.0       0.29   11.4   0.0    1.3  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma


Domain annotation for each model (and alignments):
>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   0.0   3.1e-17   1.9e-13       1      97 []       2     102 ..       2     102 .. 0.95

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 3.1e-17
                                    EEEEE.TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.........-EEECECHHHHHHH-SEEEE-S- CS
                  F420_oxidored   1 kigii.GaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.........vkvtavdneeaaeeadvvvlavk 70 
                                    +++++ G+G++g ++a +++ +    ++++++ sr+ e+a+e a+el+         + + ++dn+ a+ +a+vvvl+v+
  gi|116754725|ref|YP_843843.1|   2 RVALVgGTGDIGNGFAVRWAPH----YDVIIG-SRKAERAQESAAELSrymrslgidAMMHGTDNANAIMDAEVVVLCVP 76 
                                    689999***************9....8***88.**********************99888899***************** PP

                                    HHHHHHHHHHCGHHHHTTSEEEEESSS CS
                  F420_oxidored  71 pedveevlselakdalkgklvisvlag 97 
                                    pe +  v  +l kd  ++++vis +++
  gi|116754725|ref|YP_843843.1|  77 PESLGMVTFDL-KDCYSNQIVISPVVP 102
                                    ***********.999********9875 PP

>> PDH  Prephenate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   2.4e-05      0.14      30      65 ..      52      87 ..      30     100 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.4e-05
                                   TTSSSEEES-GGGGCCGSEEEE-S-GGGHHHHHHHH CS
                            PDH 30 lglvdeatddieavkeadivvlavPvevilevlkel 65
                                   ++++ + td+ +a+ +a++vvl+vP+e +  v  +l
  gi|116754725|ref|YP_843843.1| 52 IDAMMHGTDNANAIMDAEVVVLCVPPESLGMVTFDL 87
                                   566677778899***************998876655 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 ?   11.4   0.0   4.9e-05      0.29       2      79 ..       4      77 ..       3      86 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.9e-05
                                   EEE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SSG CS
                Sacchrp_dh_NADP  2 liiGa.GsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnlspp 79
                                    ++G+ G +G ++a   a h dv    ++ +r+ e++++ aa++ +  + +  +da+ +    a ++ ++++vv ++pp
  gi|116754725|ref|YP_843843.1|  4 ALVGGtGDIGNGFAVRWAPHYDV----IIGSRKAERAQESAAEL-SRYMRSLGIDAMMHGTDNANAIMDAEVVVLCVPP 77
                                   567888**************876....9********99999885.5556666667666666566667777777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1539.77
//
Query:       gi|116754726|ref|YP_843844.1|  [L=262]
Description: methyltransferase type 11 [Methanosaeta thermophila PT]
Scores for complete 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-36  124.2   0.0    6.2e-36  123.5   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    1.2e-24   86.8   0.5    7.1e-24   84.3   0.0    2.4  2  Methyltransf_11  Methyltransferase domain
    3.6e-24   85.3   0.7    1.6e-23   83.3   0.0    2.4  2  Methyltransf_25  Methyltransferase domain
    6.8e-20   71.4   0.0    1.2e-19   70.5   0.0    1.4  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    2.1e-13   50.4   0.0    5.2e-13   49.2   0.0    1.7  2  Methyltransf_23  Methyltransferase domain
    1.2e-12   48.4   0.0    3.8e-12   46.8   0.0    1.9  1  Methyltransf_12  Methyltransferase domain
    5.1e-12   46.0   0.0    8.4e-12   45.3   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      5e-08   32.7   0.0    7.1e-08   32.2   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    5.8e-06   26.0   0.0    1.1e-05   25.1   0.0    1.5  1  MTS              Methyltransferase small domain
    1.8e-05   24.2   0.0    2.4e-05   23.8   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
    2.7e-05   24.1   0.0    5.5e-05   23.1   0.0    1.4  1  Methyltransf_8   Hypothetical methyltransferase
    4.3e-05   23.3   0.0    8.2e-05   22.4   0.0    1.4  1  UPF0020          Putative RNA methylase family UPF0020
    0.00023   21.2   0.0    0.00047   20.2   0.0    1.5  1  Methyltransf_32  Methyltransferase domain
  ------ inclusion threshold ------
      0.014   14.8   0.0      0.032   13.7   0.0    1.7  1  Methyltransf_4   Putative methyltransferase
      0.017   14.8   0.0      0.052   13.2   0.0    1.7  2  GCD14            tRNA methyltransferase complex GCD14 subunit
      0.029   13.6   0.0      0.039   13.1   0.0    1.2  1  Methyltransf_3   O-methyltransferase
      0.071   12.2   0.0       0.17   11.0   0.0    1.5  2  Fibrillarin      Fibrillarin
       0.14   11.3   0.0        1.1    8.3   0.0    2.0  2  NNMT_PNMT_TEMT   NNMT/PNMT/TEMT family
       0.15   11.6   0.0       0.25   10.8   0.0    1.3  1  Methyltransf_PK  AdoMet dependent proline di-methyltransferas
       0.15   12.1   0.0       0.51   10.4   0.0    1.8  1  FtsJ             FtsJ-like methyltransferase


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 !  123.5   0.0   6.9e-39   6.2e-36       2     136 ..      75     208 ..      74     229 .. 0.93

  Alignments for each domain:
  == domain 1  score: 123.5 bits;  conditional E-value: 6.9e-39
                Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsn 81 
                                    ++g +vlD G+G+G+++f +a+ +gp++ v+G+D++ e++ +Arena+k g+ nv F+qg+ e+l+  ++d+ +D+i+sn
  gi|116754726|ref|YP_843844.1|  75 KRGEYVLDMGSGAGFDCFLAARAVGPEGMVIGVDMTSEMVDRARENARKGGYRNVDFRQGELENLP--VADNYVDVIMSN 152
                                    67899*************************************************************..9*********** PP

                Methyltransf_31  82 evlnaladpdkileeiervlkpggilliedprllaelpakveeeskay.evvegak 136
                                    +v+n+++d+  +++e++rvlkpgg+l+i+d+ l +e p+ v+++ +ay +++ ga 
  gi|116754726|ref|YP_843844.1| 153 CVINLVPDKRRVFREAFRVLKPGGRLIISDIVLKREIPEAVRRSKEAYvGCLAGAV 208
                                    **********************************************9998888776 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.3   0.0   7.9e-27   7.1e-24       1      96 []      81     180 ..      81     180 .. 0.97
   2 ?   -0.5   0.0       2.3   2.1e+03      19      30 ..     240     251 ..     201     260 .. 0.70

  Alignments for each domain:
  == domain 1  score: 84.3 bits;  conditional E-value: 7.9e-27
                                    EEET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEEEES-CCC-CC CS
                Methyltransf_11   1 LdvGcGtGrlaealakrg...arvvgvDlskemlklakekaseegl.kvefvvadaeklpfednsfDlvvssevlhhved 76 
                                    Ld+G+G+G  +   a+++   + v+gvD++ em+++a+e+a++ g  +v+f+++++e+lp++dn++D+++s+ v++ v+d
  gi|116754726|ref|YP_843844.1|  81 LDMGSGAGFDCFLAARAVgpeGMVIGVDMTSEMVDRARENARKGGYrNVDFRQGELENLPVADNYVDVIMSNCVINLVPD 160
                                    8**************7778************************************************************* PP

                                    HHHHHHHHHHHEEEEEEEEE CS
                Methyltransf_11  77 pekalkeiaRvLkpgGllvi 96 
                                     +++++e+ RvLkpgG+l+i
  gi|116754726|ref|YP_843844.1| 161 KRRVFREAFRVLKPGGRLII 180
                                    ******************96 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 2.3
                                    SEEEEEES-HHH CS
                Methyltransf_11  19 arvvgvDlskem 30 
                                    a+++ vDls+ +
  gi|116754726|ref|YP_843844.1| 240 ANITKVDLSESV 251
                                    556666666655 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1         5   4.5e+03       5      13 ..      32      40 ..      31      49 .. 0.74
   2 !   83.3   0.0   1.7e-26   1.6e-23       1      97 []      80     176 ..      80     176 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 5
                                   T-TTSHHHH CS
                Methyltransf_25  5 GcGtGrltl 13
                                   +cGtG  ++
  gi|116754726|ref|YP_843844.1| 32 CCGTGSAAE 40
                                   7****7654 PP

  == domain 2  score: 83.3 bits;  conditional E-value: 1.7e-26
                                    EEEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEEST.GGGS CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssga.lhhl 77 
                                    vLd+G G G +++ +a+++g ++ v+gvD+++em+++are+a++ g+ nv+f+qg++e+lp +d+ +D+++s+ + ++++
  gi|116754726|ref|YP_843844.1|  80 VLDMGSGAGFDCFLAARAVGpEGMVIGVDMTSEMVDRARENARKGGYrNVDFRQGELENLPVADNYVDVIMSN-CvINLV 158
                                    9******************66*********************99999*************************5.659888 PP

                                    SHHHHHHHHHHHHHHEEEEE CS
                Methyltransf_25  78 sdedlekalkeiarvLkpgG 97 
                                    +  d +++++e++rvLkpgG
  gi|116754726|ref|YP_843844.1| 159 P--DKRRVFREAFRVLKPGG 176
                                    7..7789************9 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.5   0.0   1.4e-22   1.2e-19      43     152 ..      72     181 ..      68     204 .. 0.93

  Alignments for each domain:
  == domain 1  score: 70.5 bits;  conditional E-value: 1.4e-22
                                    --S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEE CS
                Ubie_methyltran  43 vavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtv 122
                                     + krg+ vlD+ +G+g   f  +++vg +g v+++D+ ++m++ +++ +++ g+ n++f q++ e+Lp  d+  Dv+  
  gi|116754726|ref|YP_843844.1|  72 ASLKRGEYVLDMGSGAGFDCFLAARAVGPEGMVIGVDMTSEMVDRARENARKGGYRNVDFRQGELENLPVADNYVDVIMS 151
                                    56799*************************************************************************99 PP

                                    ES-GGG-S-HHHHHHHHHHHEEEEEEEEEE CS
                Ubie_methyltran 123 sfGlrnvtDklkaLkeayrvlkpGGrlvvl 152
                                       +  v+Dk ++++ea+rvlkpGGrl++ 
  gi|116754726|ref|YP_843844.1| 152 NCVINLVPDKRRVFREAFRVLKPGGRLIIS 181
                                    999999********************9875 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       5.7   5.1e+03      31      45 ..      33      47 ..      32      53 .. 0.82
   2 !   49.2   0.0   5.8e-16   5.2e-13      19     127 ..      73     194 ..      64     227 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 5.7
                Methyltransf_23 31 cGtGillevlrengf 45
                                   cGtG+ +e+ r+ g+
  gi|116754726|ref|YP_843844.1| 33 CGTGSAAEISRRIGY 47
                                   9***99998888877 PP

  == domain 2  score: 49.2 bits;  conditional E-value: 5.8e-16
                Methyltransf_23  19 klraggrvLdiGcGtG.illevlrengf..svtgvDlspeaveiae......kakkaqkdqfdeqeaaepqgkfdlIvlr 89 
                                     l++g  vLd+G G G      +r+ g    v+gvD+ +e+v++a+      + ++  + q   ++ ++ +++ d+I ++
  gi|116754726|ref|YP_843844.1|  73 SLKRGEYVLDMGSGAGfDCFLAARAVGPegMVIGVDMTSEMVDRARenarkgGYRNVDFRQGELENLPVADNYVDVIMSN 152
                                    478999**********55666668889977788************999988855666666665668888999******** PP

                Methyltransf_23  90 evlehvpdppellrqiatllkpgGylllseplasl....ked 127
                                     v++ vpd  +++r +++ lkpgG+l++s++  +     + +
  gi|116754726|ref|YP_843844.1| 153 CVINLVPDKRRVFREAFRVLKPGGRLIISDIVLKReipeAVR 194
                                    ******************************643332443233 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.0   4.2e-15   3.8e-12       1      99 []      81     178 ..      81     178 .. 0.88

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 4.2e-15
                Methyltransf_12   1 LeiGcGtGsllrallekl.pdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhl 79 
                                    L+ G+G G   +  +++  p+  ++gvD  ++++++a+e  +k + +n+++ + e ++l   d  +++D++ +++v++ +
  gi|116754726|ref|YP_843844.1|  81 LDMGSGAGFDCFLAARAVgPEGMVIGVDMTSEMVDRARENARKGGYRNVDFRQGELENLPVAD--NYVDVIMSNCVINLV 158
                                    899*****99999999999999999*********88888888888777776666666666555..4************** PP

                Methyltransf_12  80 kdirevldnirklLkpgGrl 99 
                                    +d+r+v++++ ++LkpgGrl
  gi|116754726|ref|YP_843844.1| 159 PDKRRVFREAFRVLKPGGRL 178
                                    ******************97 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 !   45.3   0.0   9.4e-15   8.4e-12      70     171 ..      73     180 ..      54     202 .. 0.84

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 9.4e-15
                                    T--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTGGG-SEEEEEES CS
                           PCMT  70 elkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGyeekaPYdaihvg 149
                                    +lk+g+ vL++GsG+G+   + ar vg++g v++++ + e+v++a++n +k +++nv ++ g+ ++   +    d+i+  
  gi|116754726|ref|YP_843844.1|  73 SLKRGEYVLDMGSGAGFDCFLAARAVGPEGMVIGVDMTSEMVDRARENARKGGYRNVDFRQGELENLPVADNYVDVIMSN 152
                                    599**********************************************************9976654455555777777 PP

                                    SBBSS--......HHHHHTEEEEEEEEE CS
                           PCMT 150 aaapeiP......ealidQLkeGGrlvv 171
                                       + +P      ++ ++ Lk+GGrl++
  gi|116754726|ref|YP_843844.1| 153 CVINLVPdkrrvfREAFRVLKPGGRLII 180
                                    7777788333222467899*******98 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.0     8e-11   7.1e-08     159     266 ..      74     188 ..      68     202 .. 0.84

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 8e-11
                           PrmA 159 vkegeevlDvGtGSGiLa.iaaakLgak.kvvavDiDevAvkvakeNaelNkvea.klevalseellk.eekadvivaNI 234
                                    +k+ge vlD+G G+G    +aa  +g +  v++vD+ +  v+ a+eNa++ + ++  ++    e+l+  ++ +dvi++N 
  gi|116754726|ref|YP_843844.1|  74 LKRGEYVLDMGSGAGFDCfLAARAVGPEgMVIGVDMTSEMVDRARENARKGGYRNvDFRQGELENLPVaDNYVDVIMSNC 153
                                    68899**********96537899999873689*******************9999777665566666447889******* PP

                           PrmA 235 Laevl...ielaedikklvkeggllilSGilkeka 266
                                    + + +    +   ++ +++k+gg+li+S i+ +++
  gi|116754726|ref|YP_843844.1| 154 VINLVpdkRRVFREAFRVLKPGGRLIISDIVLKRE 188
                                    9999955568999****************987764 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   1.2e-08   1.1e-05      32     137 ..      77     180 ..      58     200 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.2e-08
                                    CSEEEEET-TTSHHHHHHHHH.TTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTT.TSTTS-EEEEEE---ST CS
                            MTS  32 sgkvlDlGcGaGvlgaalake.speaevtlvdvdarAlesakenleankle.vevvasdvle.eveekkfdlivsNPPfh 108
                                     + vlD+G+GaG+    +a++  pe  v  vd   + ++ a+en+++ + + v++++ ++ +  v+++ +d+i+sN  + 
  gi|116754726|ref|YP_843844.1|  77 GEYVLDMGSGAGFDCFLAARAvGPEGMVIGVDMTSEMVDRARENARKGGYRnVDFRQGELENlPVADNYVDVIMSNCVIN 156
                                    567*********987766665168888***********************99999999998734669999*******999 PP

                                    TTCHCHHHHHHHHHHHHHHHEEEEEEEEE CS
                            MTS 109 agkatelavaeeliaeAkeaLkegGeLli 137
                                       +      +++++eA ++Lk+gG+L+i
  gi|116754726|ref|YP_843844.1| 157 LVPD-----KRRVFREAFRVLKPGGRLII 180
                                    8888.....799***************96 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   2.7e-08   2.4e-05      58     183 ..      72     199 ..      67     223 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 2.7e-08
                                    TT--TT-EEEEES-TTSHHHHHHHHHH-..-EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---...--SEEE CS
                           CMAS  58 lelkpGmtlLdiGcGWGslvrraveryd..vkvvglTlSkeqaklakkrvdeldlerkvevklldyedlde...kvdrvv 132
                                    ++lk G+++Ld+G G G  +  a++  +    v+g+ + +e   +a+++  + +  r+v+ +  + e+l+     vd + 
  gi|116754726|ref|YP_843844.1|  72 ASLKRGEYVLDMGSGAGFDCFLAARAVGpeGMVIGVDMTSEMVDRARENARKGG-YRNVDFRQGELENLPVadnYVDVIM 150
                                    679**************999888888762156****************998877.7889999999999865445899999 PP

                                    EES-GGGTSGGGHHHHHHHHHHHS-TT-EEEEEEEEE--HHHHHCTTCCCH CS
                           CMAS 133 svgafehvgkenydtffkklkkllkedGllllhtitslhkkelaerglklk 183
                                    s  +++ v  ++  + f++++++lk++G+l++  i+ +++   a r+ k +
  gi|116754726|ref|YP_843844.1| 151 SNCVINLVPDKR--RVFREAFRVLKPGGRLIISDIVLKREIPEAVRRSKEA 199
                                    999999998886..789****************999988777666666554 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   6.1e-08   5.5e-05     111     160 ..     134     184 ..     127     198 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 6.1e-08
                                    S-TTS-S--TT-EEEEE.EES---SS-HHHHHHHHHHHEEEEEEEEEEEEG CS
                 Methyltransf_8 111 cdlakvPledesvdvav.fclslmgtnladflkeanrvlkvGGllkvaevk 160
                                     +l ++P++d+ vdv++  c+  ++ + +   +ea rvlk+GG l ++++ 
  gi|116754726|ref|YP_843844.1| 134 GELENLPVADNYVDVIMsNCVINLVPDKRRVFREAFRVLKPGGRLIISDIV 184
                                    57899*********988459999999*********************9985 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   9.1e-08   8.2e-05      76     128 ..     101     152 ..      85     153 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 9.1e-08
                                    H--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE- CS
                        UPF0020  76 elklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtn 128
                                    e  ++g+D+ +++v++areNa+k g    ++f+q +  +L+ +++ vdvi +n
  gi|116754726|ref|YP_843844.1| 101 EGMVIGVDMTSEMVDRARENARKGGYR-NVDFRQGELENLPVADNYVDVIMSN 152
                                    45589******************9986.69***********88889******9 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   5.3e-07   0.00047      24      91 ..      75     138 ..      68     173 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 5.3e-07
                Methyltransf_32  24 sgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsfaelsiee 91 
                                    ++ ++v+D+G+G g+  f  a  ++  +  v+g+d+ +e+v++a++ a+k g  + +++ f +++ e+
  gi|116754726|ref|YP_843844.1|  75 KRGEYVLDMGSGAGFDCFLAAR-AVGPEGMVIGVDMTSEMVDRARENARKGG--Y-RNVDFRQGELEN 138
                                    55689**********9998888.77789**********************99..7.888888887665 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   3.6e-05     0.032       4      62 ..      79     137 ..      76     184 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.6e-05
                                    EEEEET-TTS.HHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCC CS
                 Methyltransf_4   4 vvleiGcGkG.eflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgdalk 62 
                                     vl++G+G G +  +a     P+  ++G+++ +++v+++ +++++ +++N+   +g+  +
  gi|116754726|ref|YP_843844.1|  79 YVLDMGSGAGfDCFLAARAVGPEGMVIGVDMTSEMVDRARENARKGGYRNVDFRQGEL-E 137
                                    6899****9944444555568******************************9988873.4 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   5.9e-05     0.052      37      89 ..      73     125 ..      69     147 .. 0.92
   2 ?   -1.6   0.0       1.9   1.7e+03      95     170 ..     209     228 ..     166     254 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.9e-05
                          GCD14  37 elkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehe 89 
                                     lk G  v++ G G+g      ar+v+P G +  ++   + +++are+ r+ +
  gi|116754726|ref|YP_843844.1|  73 SLKRGEYVLDMGSGAGFDCFLAARAVGPEGMVIGVDMTSEMVDRARENARKGG 125
                                    5899*******************************************998865 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.9
                          GCD14  95 tvthrDvckeGfdeevsgkvDavfLDlPaPweaiphaakalkkeggrlCsfsPCieqvqrtceaLrelgfteietl 170
                                    tv                                                         + ++a+r+ gf ei+ l
  gi|116754726|ref|YP_843844.1| 209 TV--------------------------------------------------------EEYIDAMRSAGFEEISIL 228
                                    33........................................................334444455555554443 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.4e-05     0.039      48     108 ..      77     136 ..      69     187 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.4e-05
                                    --EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEEEES-H CS
                 Methyltransf_3  48 akrvleiGvftGyslLatalalPeDGkilaididreayeialkfiqkagvaekieliegda 108
                                       vl++G   G+  +  a a+ ++G ++ +d+  e ++ a++  +k g+   +++++g+ 
  gi|116754726|ref|YP_843844.1|  77 GEYVLDMGSGAGFDCFLAARAVGPEGMVIGVDMTSEMVDRARENARKGGYR-NVDFRQGEL 136
                                    56799*****************************************99985.699999963 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00019      0.17      49     108 ..      55     114 ..      35     123 .. 0.86
   2 ?   -2.7   0.0       2.9   2.6e+03     179     198 ..     154     173 ..     143     186 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00019
                                    -TTTSHHHHHHHTT-S--S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHH CS
                    Fibrillarin  49 npfrsKlaaailkglkelpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvl 108
                                     p  s l+ +  + ++   +k+g+ vL +G+++G      +  vg+eg+v +v++++ ++
  gi|116754726|ref|YP_843844.1|  55 APPESNLGLGCGNPVAIASLKRGEYVLDMGSGAGFDCFLAARAVGPEGMVIGVDMTSEMV 114
                                    56678999999999999*************************************987665 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.9
                                    HHHSSSSHHHHHHHHHHHHH CS
                    Fibrillarin 179 sidvtkepeevfkeeveklk 198
                                     i+ + + ++vf+e  + lk
  gi|116754726|ref|YP_843844.1| 154 VINLVPDKRRVFREAFRVLK 173
                                    24445555555555555555 PP

>> NNMT_PNMT_TEMT  NNMT/PNMT/TEMT family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.27   2.4e+02      55      76 ..      75      96 ..      69     105 .. 0.79
   2 ?    8.3   0.0    0.0013       1.1     155     202 ..     139     185 ..     101     223 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.27
                                   S-ECEEEEET-TT--GGGTTGG CS
                 NNMT_PNMT_TEMT 55 kkgdtllDiGaGPTvyqllsar 76
                                   k+g+ +lD+G+G      l+ar
  gi|116754726|ref|YP_843844.1| 75 KRGEYVLDMGSGAGFDCFLAAR 96
                                   6799********8777777666 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0013
                                    SS..EEEEEEESSHHHH-SSHHHHHHHHHHHHTTEEEEEEEEEEEECS CS
                 NNMT_PNMT_TEMT 155 lpkkadvvvtifcleaacedleeylralrnlasllkpGGhlvlggvle 202
                                    lp  ad  v ++  +++ + +   +r  r++ ++lkpGG+l++ +++ 
  gi|116754726|ref|YP_843844.1| 139 LPV-ADNYVDVIMSNCVINLVPDKRRVFREAFRVLKPGGRLIISDIVL 185
                                    554.677777777788888888889999**************998754 PP

>> Methyltransf_PK  AdoMet dependent proline di-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00028      0.25      54     166 ..      75     187 ..      68     198 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00028
                Methyltransf_PK  54 revkvaldcGaGiGrvtknlLlkll....skvDlvepvekflekakeelaeekkkvgkvyvvglqeftPeegrYdliWiq 129
                                    ++ +++ld+G+G G   + +L   +    + v  v+ +++++++a+e+  ++  +  ++ +  l++   +++  d+i   
  gi|116754726|ref|YP_843844.1|  75 KRGEYVLDMGSGAGF--DCFLAARAvgpeGMVIGVDMTSEMVDRARENARKGGYRNVDFRQGELENLPVADNYVDVIMSN 152
                                    667889999999984..445554444665667778999*************99999999999999998888888999999 PP

                Methyltransf_PK 130 WcvghLtDedlvaflkrckkalkpnGlivvkenvake 166
                                     ++  ++D+  v  ++ + + lkp+G +++ + v k 
  gi|116754726|ref|YP_843844.1| 153 CVINLVPDKRRV--FREAFRVLKPGGRLIISDIVLKR 187
                                    999999999866..9**************99877665 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00057      0.51      19      96 ..      74     154 ..      69     219 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00057
                                    S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEES.SSSHHHTTEEEE.....CS-CCCSSHHHHHCHCHHHSSEEEEE CS
                           FtsJ  19 fkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDl.qpmaplpgvtti.....qgditdpetiekikealserkvdlvv 92 
                                    +k+g+ v+D g++ G  +  +++ +g++g+v++vD+  +m  + + +       + d+++ e +++      +++vd+++
  gi|116754726|ref|YP_843844.1|  74 LKRGEYVLDMGSGAGFDCFLAARAVGPEGMVIGVDMtSEMVDRARENARkggyrNVDFRQGELENLPV---ADNYVDVIM 150
                                    678999*******99999999999999*********88885444444442233455555555555333...245677777 PP

                                    E--S CS
                           FtsJ  93 sDga 96 
                                    s  +
  gi|116754726|ref|YP_843844.1| 151 SNCV 154
                                    7665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); 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: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 1964.23
//
Query:       gi|116754727|ref|YP_843845.1|  [L=289]
Description: imidazoleglycerol phosphate synthase, cyclase subunit [Methanosaeta thermophila PT]
Scores for complete 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-79  264.5   0.3    7.8e-79  264.3   0.3    1.0  1  His_biosynth  Histidine biosynthesis protein
    4.3e-09   36.2   2.1    6.2e-05   22.5   0.3    2.2  2  NMO           Nitronate monooxygenase
    2.9e-08   33.3   1.8    0.00063   19.1   0.4    2.1  2  ThiG          Thiazole biosynthesis protein ThiG
    4.7e-08   32.5   0.1    2.1e-05   23.8   0.1    2.1  2  Dus           Dihydrouridine synthase (Dus)
    1.7e-05   24.2   0.2      0.084   12.2   0.1    2.2  2  TMP-TENI      Thiamine monophosphate synthase
     0.0001   21.4   1.5       0.09   11.8   0.2    2.1  2  IMPDH         IMP dehydrogenase / GMP reductase domain
     0.0007   18.9   0.6       0.22   10.7   0.1    2.1  2  DHO_dh        Dihydroorotate dehydrogenase
     0.0087   15.5   0.7       0.13   11.7   0.1    2.5  3  G3P_antiterm  Glycerol-3-phosphate responsive antiterminator


Domain annotation for each model (and alignments):
>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  264.3   0.3   3.5e-82   7.8e-79       1     229 []      24     273 ..      24     273 .. 0.94

  Alignments for each domain:
  == domain 1  score: 264.3 bits;  conditional E-value: 3.5e-82
                                    EEEEEEEEE..TTEEEEECTTCSTCEEEETTSHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEEE CS
                   His_biosynth   1 riipalDlk..dGkvVrlvkGdrfqelryagdpvelakryeeegadelhvvDldaakegreanldlveeiaeevfipvqv 78 
                                    +i+p+lD+k  dG    +vkG++f +l+++gdpv++a+ry+e+gadel+++D++a++egr+++ d+ +++a++v+ip++v
  gi|116754727|ref|YP_843845.1|  24 KIVPCLDVKvvDGV-PSVVKGVKFVDLKHQGDPVAFARRYQEQGADELVFLDITASHEGRKTMVDVARRVADAVDIPFTV 102
                                    59******622563.2357************************************************************* PP

                                    ESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEE......C.............EEEEET CS
                   His_biosynth  79 GGGIrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarr......g.............ykvaik 139
                                    GGGI+s++ ++e+l+agad+v i+taav+np+l++++a++fgs++i+va+Darr      g             ++v+i+
  gi|116754727|ref|YP_843845.1| 103 GGGISSIQGIKEILDAGADRVGINTAAVRNPDLVRSAAQAFGSERITVAVDARRnaeiipGvnvyeledgsrawFEVVIY 182
                                    ******************************************************665555166777888899*9****** PP

                                    TTTEEEEEEHHHHHHHHHHTT-SEEEEEETTTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHHHHTTC.SEEE CS
                   His_biosynth 140 gwreetgldavelakkleelgageilltdidrdGtlsGpdleltkelaeavkipviasGGvgsledlkelksegv.davi 218
                                    g+re tg+da+e+ +++e+lgageil t++drdGt  G+dl+ltk++++av++pv+asGG+++++++ e+++ g  d ++
  gi|116754727|ref|YP_843845.1| 183 GGREPTGIDAIEWCRRVERLGAGEILPTSMDRDGTNIGYDLPLTKAICDAVDVPVTASGGASTPQHILEAFTVGGaDKAL 262
                                    ***********************************************************************88777**** PP

                                    ESHHHHTTSS- CS
                   His_biosynth 219 vgsalyegelt 229
                                    ++ +++ ge+t
  gi|116754727|ref|YP_843845.1| 263 AAGMFHRGEYT 273
                                    ********986 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.3   2.8e-08   6.2e-05     151     224 ..      61     128 ..      46     141 .. 0.83
   2 !   13.5   0.1   1.6e-05     0.036     182     222 ..     223     263 ..     188     282 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 2.8e-08
                            NMO 151 kvearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtr 224
                                      +++GaD l+     a  h+G +    k  + +  +v+davdiP    GGi   +g++ +L +GA  v i t+
  gi|116754727|ref|YP_843845.1|  61 RYQEQGADELVFLDITA-SHEG-R----KTMVDVARRVADAVDIPFTVGGGISSIQGIKEILDAGADRVGINTA 128
                                    55566666666655544.4666.3....3479999**********************************99998 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 1.6e-05
                            NMO 182 faLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqig 222
                                    + L + + davd+Pv A GG  + + +  a+++G +  +++
  gi|116754727|ref|YP_843845.1| 223 LPLTKAICDAVDVPVTASGGASTPQHILEAFTVGGADKALA 263
                                    5688899********************99999997655555 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.4   2.8e-07   0.00063     130     221 ..      52     144 ..      33     164 .. 0.78
   2 !   13.5   0.0   1.4e-05     0.032     135     197 ..     194     256 ..     176     270 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2.8e-07
                                    E-S-HHHHHHHHHTT-SEBEEBSSSTTS----S-HHHH.HHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHH CS
                           ThiG 130 vsdDlvlarrleevGcaavmPlaapiGsglGllnkeal.kiiieeakvPvivDAGigspsdaaqamelGadavllntava 208
                                      d + +arr +e G+  ++ l     s +G +++  + + + + +++P  v  Gi s + + + ++ Gad v +nta  
  gi|116754727|ref|YP_843845.1|  52 QGDPVAFARRYQEQGADELVFLD-ITASHEGRKTMVDVaRRVADAVDIPFTVGGGISSIQGIKEILDAGADRVGINTAAV 130
                                    45556689999999999998775.4568899999887725567777********************************** PP

                                    TSSSHHHH.HHHHH CS
                           ThiG 209 eakdpvam.Arafk 221
                                    +  d v+  A+af 
  gi|116754727|ref|YP_843845.1| 131 RNPDLVRSaAQAFG 144
                                    *9999976156764 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 1.4e-05
                                    HHHHHHHHTT-SEBEEBSS.STTS----S-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT CS
                           ThiG 135 vlarrleevGcaavmPlaa.piGsglGllnkealkiiieeakvPvivDAGigspsdaaqamelG 197
                                      +rr+e +G+  ++P +    G++ G   +   k i++ ++vPv    G  +p+++ +a+ +G
  gi|116754727|ref|YP_843845.1| 194 EWCRRVERLGAGEILPTSMdRDGTNIGYDLPL-TKAICDAVDVPVTASGGASTPQHILEAFTVG 256
                                    579*************9862579****98775.699************************9987 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.1   9.4e-09   2.1e-05     118     244 ..      31     158 ..      11     165 .. 0.79
   2 !    6.7   0.0    0.0014       3.2     165     210 ..     216     261 ..     184     274 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 9.4e-09
                                    HCCSS.S-EEEEEESESS.TTTC.HHHHHHHHHHCT-SEEEEESSECCCTT-CG--CHHHHHHHHH-SS-EEEESS--SH CS
                            Dus 118 vkave.iPvtvkirigid.deeenalelakiveaaGaqaltvHgRtraqnyegtadweaIkevkqavsipviaNGdIkda 195
                                    vk v+ +P  vk   ++d +++ + + +a++ +++Ga++l+    t+ ++ ++t   +  + v +av ip+ + G+I ++
  gi|116754727|ref|YP_843845.1|  31 VKVVDgVPSVVKGVKFVDlKHQGDPVAFARRYQEQGADELVFLDITASHEGRKT-MVDVARRVADAVDIPFTVGGGISSI 109
                                    4555579999998888997888899***************99888888777774.3456689****************** PP

                                    HHHHHHHHHH--SEEEESCHHCCSTTHHHH.HHHHHHSC------HHHHH CS
                            Dus 196 edaqaileetGadgvmigrgalgnPwlfae.stavktgeaepapplaeea 244
                                    + +++il+  Gad v i  +a +nP l+++  +a+  +++  a  +++ a
  gi|116754727|ref|YP_843845.1| 110 QGIKEILDA-GADRVGINTAAVRNPDLVRSaAQAFGSERITVAVDARRNA 158
                                    ********9.******************9855555554444444455555 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0014
                                    TT-CG--CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEE CS
                            Dus 165 nyegtadweaIkevkqavsipviaNGdIkdaedaqaileetGadgv 210
                                    + ++  d+   k++++av +pv a G+  +++ + ++    Gad  
  gi|116754727|ref|YP_843845.1| 216 GTNIGYDLPLTKAICDAVDVPVTASGGASTPQHILEAFTVGGADKA 261
                                    4444667777899*************************99999854 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.1   3.7e-05     0.084     109     176 ..      59     124 ..      54     129 .. 0.82
   2 !    9.9   0.0   0.00019      0.43     120     161 ..     202     245 ..     195     262 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.7e-05
                       TMP-TENI 109 aeeaealgadYigvGpifpTdtKkdaeplgleglkelaealeiPvvaiGGitl.envaevleagadgva 176
                                    a++ +++gad +++  i  T++++++++  ++ ++++a+a+ iP+ + GGi+  + ++e+l+agad+v 
  gi|116754727|ref|YP_843845.1|  59 ARRYQEQGADELVFLDI--TASHEGRKT-MVDVARRVADAVDIPFTVGGGISSiQGIKEILDAGADRVG 124
                                    56677888888888888..888888744.478899****************85378**********986 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00019
                       TMP-TENI 120 igvGpifpTdtKkdaeplgle..glkelaealeiPvvaiGGitl 161
                                    +g+G i pT+   d + +g +  + k++++a+ +Pv a GG ++
  gi|116754727|ref|YP_843845.1| 202 LGAGEILPTSMDRDGTNIGYDlpLTKAICDAVDVPVTASGGAST 245
                                    799***********98888652268****************753 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.2     4e-05      0.09     113     174 ..      63     125 ..      50     157 .. 0.79
   2 !    8.9   0.1   0.00029      0.66     201     242 ..     228     270 ..     222     283 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4e-05
                                    HHTT-SEEE.EE-..STSSSHHHHHHHHHHHHHTTTSEEEEEEE-SHHHHHHHHHTT-SEEEE-S CS
                                    xxxxxxxxx.xxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 113 veagvdvlv.vds..ahghsekvleavkeikkkveeveviaGnvataegakaLieagadavkvGi 174
                                     e+g+d lv +d+  +h   ++++++ +++ ++v+    ++G + + +g+k++++agad v  Gi
  gi|116754727|ref|YP_843845.1|  63 QEQGADELVfLDItaSHEGRKTMVDVARRVADAVDIPFTVGGGISSIQGIKEILDAGADRV--GI 125
                                    5667774443565115666788999999999999555679*******************65..44 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00029
                                    HHHCTCT-EEEEES---SHHHHHHHHHTT.-SEEEESCCCTTB CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx RF
                          IMPDH 201 eaakkagvpviaDGGikysgdivkAlaaG.adavmlGsllagt 242
                                    ++++  +vpv a GG ++ ++i  A+++G ad  +   ++ + 
  gi|116754727|ref|YP_843845.1| 228 AICDAVDVPVTASGGASTPQHILEAFTVGgADKALAAGMFHRG 270
                                    568889********************99637777777666655 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.1   9.6e-05      0.22     231     280 ..      86     132 ..      80     143 .. 0.82
   2 !    6.5   0.0    0.0018       4.1     244     292 ..     234     282 ..     225     284 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 9.6e-05
                                    HHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHG CS
                         DHO_dh 231 lkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfeg 280
                                    + v r++++ ++  ip    GGi+s +   e + aGA  v + ta v ++
  gi|116754727|ref|YP_843845.1|  86 VDVARRVADAVD--IPFTVGGGISSIQGIKEILDAGADRVGINTAAV-RN 132
                                    566777777777..999999************************984.44 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0018
                                    .S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHHHHHHHH CS
                         DHO_dh 244 eipiIgvGGiesgeDalekieaGAslvqvytalvfegpkiakkikkele 292
                                    ++p+ ++GG ++ +  le ++ G +  ++ +++  +g + + ++k+ l 
  gi|116754727|ref|YP_843845.1| 234 DVPVTASGGASTPQHILEAFTVGGADKALAAGMFHRGEYTVGQVKDYLR 282
                                    59*****************************************999876 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       2.6   5.8e+03      47      67 ..      28      48 ..      18      54 .. 0.70
   2 !   11.7   0.1   5.6e-05      0.13     127     166 ..      85     124 ..      83     130 .. 0.90
   3 ?    1.1   0.0       0.1   2.3e+02     131     161 ..     226     256 ..     220     260 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.6
                                   EEEGGGEET--SSHHHHHHHH CS
                   G3P_antiterm 47 fvhiDlieGlskdeaaveflk 67
                                   ++++ +++G+ +  ++v+f+ 
  gi|116754727|ref|YP_843845.1| 28 CLDVKVVDGVPSVVKGVKFVD 48
                                   567777888888888888765 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 5.6e-05
                                    GHHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEE CS
                   G3P_antiterm 127 vpkvikeikkelkipiiaGGLietkedveealkaGaiavs 166
                                    + +v++++ ++++ip+  GG i++ + ++e+l+aGa+ v 
  gi|116754727|ref|YP_843845.1|  85 MVDVARRVADAVDIPFTVGGGISSIQGIKEILDAGADRVG 124
                                    78999*******************************9886 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.1
                                    HCTSTTS...EEEEESS--SHHHHHHHCTT. CS
                   G3P_antiterm 131 ikeikkelkipiiaGGLietkedveealkaG 161
                                    +k+i++++++p+ a+G  +t +++ ea+  G
  gi|116754727|ref|YP_843845.1| 226 TKAICDAVDVPVTASGGASTPQHILEAFTVG 256
                                    688999*************999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 2245.04
//
Query:       gi|116754728|ref|YP_843846.1|  [L=74]
Description: deoxyribonuclease [Methanosaeta thermophila PT]
Scores for complete 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   53.1   0.8    2.8e-14   52.8   0.8    1.1  1  TRAM      TRAM domain


Domain annotation for each model (and alignments):
>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.8   0.8   1.6e-18   2.8e-14       3      61 ..      19      73 ..      17      74 .] 0.95

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 1.6e-18
                                   XXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEEE CS
                           TRAM  3 yvGstqeVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGel 61
                                    vGs+++V++e+ + +eg+gi+r++ g+v+fvp ++   Gd V ++I++v r+++ G+ 
  gi|116754728|ref|YP_843846.1| 19 AVGSEYNVKIEDIA-REGDGIARVE-GFVIFVPETQV--GDQVRIQIDRVMRRFAIGHK 73
                                   69***********9.**********.*********99..****************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 565.00
//
Query:       gi|116754729|ref|YP_843847.1|  [L=412]
Description: bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.4e-49  166.9   0.1      3e-48  164.1   0.0    2.0  2  DFP             DNA / pantothenate metabolism flavoprotein
    1.8e-39  135.0   0.4    2.9e-39  134.4   0.4    1.3  1  Flavoprotein    Flavoprotein
  ------ inclusion threshold ------
      0.014   15.4   0.7        3.6    7.6   0.1    3.2  4  Glyco_transf_4  Glycosyltransferase Family 4


Domain annotation for each model (and alignments):
>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       0.1   6.1e+02      35      54 ..      41      60 ..      38      80 .. 0.80
   2 !  164.1   0.0     5e-52     3e-48       2     186 .]     198     377 ..     197     377 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.1
                                   HHHHHHHTT-EEEEEE-S-S CS
                            DFP 35 lAeaaaarGaeVtlvsgpvs 54
                                   l + +++rGa+V+ v ++ +
  gi|116754729|ref|YP_843847.1| 41 LVRDLIRRGADVHCVMSEAA 60
                                   6678899********98853 PP

  == domain 2  score: 164.1 bits;  conditional E-value: 5e-52
                                    TT-EEEEEES-EEEECCTTEEEEE----HHHHHHHHHHHHTT-EEEEEE-S-SS---TT-EEEE--SHHHHHHHHHHHHT CS
                            DFP   2 egkkvlvtaGpTrEaiDpVRfisNrSSGkmGyalAeaaaarGaeVtlvsgpvsletpegvevvkvesaeemleaveealk 81 
                                    + +++lvt+G+T E+iDp+R+i+Nr+SG++G+++A++a++rGa+Vt+++   +l  p  ++ + vesa++ l+av+++l+
  gi|116754729|ref|YP_843847.1| 198 RSRRILVTSGATAESIDPIRIITNRASGRTGVEIAREAYRRGADVTIIHRA-RLGLP--FKEIYVESAQDTLDAVMKELS 274
                                    679**********************************************98.67777..899**************9986 PP

                                    T-.SEEEE---S--EEES-------------..----EEE---HHHHHHHC-S.S-EEEEEEE-S.S...-HHHHHHHHH CS
                            DFP  82 ea.divimaAAvaDyrpkeaaeeKikkeeeeeeltleleknpdilaelaekkkkkqllvGFaaet.e...ellenarekl 156
                                       d++i aAAv D+++++ +++Kik    +eel l+l++ p+il+++ ++  ++ +++GF+aet     +ll++are +
  gi|116754729|ref|YP_843847.1| 275 GGyDALIGAAAVGDFTVDT-EQRKIKS---KEELVLRLKPAPKILRSV-RSMYPDLTIIGFKAETfVsdeDLLRSARESM 349
                                    555**************86.678**96...568***************.56667778*******863577********** PP

                                    HHTT-SEEEEEEGGGTTGGG-SS-EEEEE. CS
                            DFP 157 erkgldlivaNdvskeeagfgsdenevtll 186
                                     + +ldl++aNdv+    g+g+d+n+v++l
  gi|116754729|ref|YP_843847.1| 350 DASRLDLVIANDVGAG--GMGTDDNRVLIL 377
                                    **************87..*********985 PP

>> Flavoprotein  Flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.4   0.4   4.8e-43   2.9e-39       2     156 ..      24     190 ..      23     192 .. 0.92

  Alignments for each domain:
  == domain 1  score: 134.4 bits;  conditional E-value: 4.8e-43
                                    EEEEEE-SSCGGGCHHHHHHHHHHTTEEEEEEESCHHHHCCHHGGS...........TCSSHHHHHH...CTTESEEEEE CS
                   Flavoprotein   2 killgiTGsvaaikalellekLkkegievqvvltkaAkkfiskeklklaa.......redpilhiel...rrwadllvia 71 
                                     ++lg+TGs+aa+ +++l++ L+++g++v++v+++aA++++++  l+ a+       ++++++h+el   + +ad+l+ia
  gi|116754729|ref|YP_843847.1|  24 TVALGVTGSIAAVRVVDLVRDLIRRGADVHCVMSEAAQRILHPYALEYASgnpviteITGRVEHVELcgvEGRADMLLIA 103
                                    589***************************************776666659999999**********88888******** PP

                                    EEEHHHHHHHHTT--SSHHHHHHHT..HCCTTEEEEE.--HHCCTCSTCHHHHHHH.HT................GHHHH CS
                   Flavoprotein  72 PasantlakianGiadnlltlilra..takkpiliaPamnpamyenpqtlknlekl.eegvtvikPsegdigkgkmaeie 148
                                    Pa+ant++kia+Gi d+++t+++    ++ kp+ ++Pam+ amy++ ++++nl++l + gv+ i+P   ++ k+k+ae +
  gi|116754729|ref|YP_843847.1| 104 PATANTIGKIACGIDDTPVTTFATTaiGSGKPVAVVPAMHEAMYRHHAVVENLNRLrSMGVVCIDPR-IEESKAKIAENS 182
                                    *******************999944479****************************66*********.8889999***99 PP

                                    HHHHHHCH CS
                   Flavoprotein 149 eivgkild 156
                                    +iv ++ +
  gi|116754729|ref|YP_843847.1| 183 RIVAEVER 190
                                    99999875 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1    0.0006       3.6       5      33 ..      35      63 ..      34      92 .. 0.82
   2 ?   -3.3   0.0       1.3     8e+03     132     147 ..     197     212 ..     179     214 .. 0.71
   3 ?    4.0   0.0    0.0074        44       9      36 ..     229     256 ..     224     287 .. 0.85
   4 ?   -0.5   0.0      0.18   1.1e+03      60      86 ..     341     367 ..     290     373 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0006
                 Glyco_transf_4  5 erhvleLaraLarrGheVtvvtpgddgpl 33
                                   ++ v++L+r L rrG +V+ v ++  +++
  gi|116754729|ref|YP_843847.1| 35 AVRVVDLVRDLIRRGADVHCVMSEAAQRI 63
                                   789*****************977766655 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.3
                 Glyco_transf_4 132 rradrviavSeatade 147
                                     r++r++++S ata+ 
  gi|116754729|ref|YP_843847.1| 197 LRSRRILVTSGATAES 212
                                    5788999999999886 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.0074
                 Glyco_transf_4   9 leLaraLarrGheVtvvtpgddgpleee 36 
                                    +e+ar+  rrG +Vt++ +++ g + +e
  gi|116754729|ref|YP_843847.1| 229 VEIAREAYRRGADVTIIHRARLGLPFKE 256
                                    689**************99998888777 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.18
                 Glyco_transf_4  60 flrrlrrllkrekpDvvHahspaalga 86 
                                     lr++r+ +++ + D+v a++ +a+g 
  gi|116754729|ref|YP_843847.1| 341 LLRSARESMDASRLDLVIANDVGAGGM 367
                                    567788888888999999999887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); 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: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3029.16
//
Query:       gi|116754730|ref|YP_843848.1|  [L=305]
Description: GHMP kinase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-07   31.6   1.8    3.4e-07   30.4   1.8    1.6  1  GHMP_kinases_N  GHMP kinases N terminal domain
  ------ inclusion threshold ------
      0.066   13.6   0.1      0.066   13.6   0.1    2.8  3  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 !   30.4   1.8   3.8e-11   3.4e-07       2      66 .]     101     165 ..     100     165 .. 0.89

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 3.8e-11
                                    EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                 GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglsleeaklaleaerlaqggngsggDvaasvyGg 66 
                                    ++++ ++ +gaG+G S+A a++ ++Al++l++l l  ++ a+ a+r+ +   ++ gDv a   Gg
  gi|116754730|ref|YP_843848.1| 101 VETELDMIMGAGFGASGAGALSCAYALNQLFNLALTSNQVAAIAHRAEVINGTGLGDVIAQNTGG 165
                                    556667789**********************9999779*******9999888******9987776 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 ?   -1.3   1.5      0.32   2.9e+03      55      64 ..     110     119 ..     100     147 .. 0.70
   2 ?   -0.8   0.0      0.23   2.1e+03      52      62 ..     149     159 ..     127     160 .. 0.84
   3 ?   13.6   0.1   7.3e-06     0.066       3      66 ..     223     278 ..     221     292 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.32
                 GHMP_kinases_C  55 GaGgGptvfa 64 
                                    GaG+G++ ++
  gi|116754730|ref|YP_843848.1| 110 GAGFGASGAG 119
                                    4444444332 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.23
                 GHMP_kinases_C  52 klsGaGgGptv 62 
                                    ++ G+G+G+ +
  gi|116754730|ref|YP_843848.1| 149 VINGTGLGDVI 159
                                    68899999988 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 7.3e-06
                 GHMP_kinases_C   3 ealergdlellgellnlsqrselkavvgilppeleellealselGalgaklsGaGgGptvfalf 66 
                                    e l+r  ++++ +l  +++      +++  + +  +++ea ++ G   +  s+ ++G++vfa++
  gi|116754730|ref|YP_843848.1| 223 EILRRPTMGEFMRLSKRFTC-----ETELASSWAMDAIEAVESSG---GMASMIMLGDSVFAVG 278
                                    66777556666666666666.....9******************9...88888888******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); 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: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2212.53
//
Query:       gi|116754731|ref|YP_843849.1|  [L=261]
Description: hypothetical protein Mthe_1434 [Methanosaeta thermophila PT]
Scores for complete 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  248.3   0.1    4.1e-74  247.9   0.1    1.1  1  PPS_PS    Phosphopantothenate/pantothenate synthetase
  ------ inclusion threshold ------
       0.14   10.8   0.0       0.19   10.5   0.0    1.1  1  DUF773    CDK5 regulatory subunit-associated protein 3


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 !  247.9   0.1   4.6e-78   4.1e-74       1     174 [.      66     239 ..      66     241 .. 0.99

  Alignments for each domain:
  == domain 1  score: 247.9 bits;  conditional E-value: 4.6e-78
                         PPS_PS   1 lllakkpvisvNGNtaaLvaeeiveLaealgaklevNlfyrteeRvekiaellkeagaeevlgleedaripeleseRakv 80 
                                    llla++p +svNGN+aaLv+ e+veLa+ l+a+levNlf+r+e+Rv+kia+ll+++ga+ vlg++ d r+p+le++Ra +
  gi|116754731|ref|YP_843849.1|  66 LLLAERPALSVNGNVAALVPAEMVELASLLNAPLEVNLFHRSEDRVRKIADLLRSHGARMVLGESPDCRVPGLEHSRALA 145
                                    79****************************************************************************** PP

                         PPS_PS  81 skeGiysaDvvlvplEDGDRaeaLvkmgKkviaiDLNPlsRtartatitivdnvvRalpnlteavkelkkkskeeleeiv 160
                                    ++ Giy+aDvvl+plEDGDR+eaLv+mgK+viaiDLNPlsRt+++a+i+ivdn++Ra+pnl+ ++++l+ + +e+l++i+
  gi|116754731|ref|YP_843849.1| 146 TRGGIYDADVVLIPLEDGDRCEALVRMGKTVIAIDLNPLSRTSMKASISIVDNIMRAVPNLIGKIRSLSGSPREDLQAIL 225
                                    ******************************************************************************** PP

                         PPS_PS 161 kefdnkkvlkealk 174
                                    ++++n+++l++al 
  gi|116754731|ref|YP_843849.1| 226 RDYSNRNTLSDALL 239
                                    **********9975 PP

>> DUF773  CDK5 regulatory subunit-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   2.1e-05      0.19     342     378 ..     219     255 ..     174     259 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 2.1e-05
                         DUF773 342 eealsllddteyRnkllddLlELeaFLkqRlvElsne 378
                                    e+   +l d   Rn l d LlE++ +++ R++El+++
  gi|116754731|ref|YP_843849.1| 219 EDLQAILRDYSNRNTLSDALLEMQEYITARMRELDTA 255
                                    4445899***************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1986.28
//
Query:       gi|116754732|ref|YP_843850.1|  [L=63]
Description: hypothetical protein Mthe_1435 [Methanosaeta thermophila PT]
Scores for complete sequence (score 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   12.4   2.5       0.18   12.2   2.5    1.1  1  DUF2583   Protein of unknown function (DUF2583)


Domain annotation for each model (and alignments):
>> DUF2583  Protein of unknown function (DUF2583)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   2.5     1e-05      0.18       1      54 [.       1      54 [.       1      62 [. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1e-05
                        DUF2583  1 mkrkkalllGnvlmglGlllmvaslaysvlnqlpelelpellaeaallgifiGa 54
                                   m rk+  ++  + m+l l++m+ ++  ++ +++  l++   ++   ++  +iG 
  gi|116754732|ref|YP_843850.1|  1 MDRKQLEIVTSTGMVLALIVMLLAIQLVLPENMRPLGFVGAVTLYIIMMSLIGL 54
                                   899*********************************999888777777666775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       914  (0.0509789); 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: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 460.59
//
Query:       gi|116754733|ref|YP_843851.1|  [L=119]
Description: hypothetical protein Mthe_1436 [Methanosaeta thermophila PT]
Scores for complete 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   46.0   0.3    6.3e-12   45.6   0.3    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 !   45.6   0.3   3.5e-16   6.3e-12       3      72 .]      38     109 ..      36     109 .. 0.97

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 3.5e-16
                                    EEE-SSGGGHHHHHHHHHTT-EEEEE-CCCTC..HHHHHHHHHHHHHHHHCT-EEEEECTTEEEEE-TT-EE CS
                           SepF   3 vveprsfedaqeiadalkegkiVilnledldk..eeakrivdflsgvvyaldGdiqkvgkkvflitPknvdi 72 
                                    v+e++s++  +ei++++++++i+++++  +++  +++ r++ +l+++v ++ Gdi+ vg++ ++i+P++++i
  gi|116754733|ref|YP_843851.1|  38 VAELTSLDVLPEIKQEIRSQNILLIDIAPMKRdkASLDRAIGELRKIVEDMAGDIAGVGDDLVIIVPSGIRI 109
                                    8999****************************889999*******************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 938.84
//
Query:       gi|116754734|ref|YP_843852.1|  [L=191]
Description: ZPR1-related zinc finger protein [Methanosaeta thermophila PT]
Scores for complete 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  122.1   0.0    2.3e-35  121.8   0.0    1.1  1  zf-ZPR1   ZPR1 zinc-finger domain
      0.008   14.9   0.0      0.012   14.4   0.0    1.2  1  AtuA      Acyclic terpene utilisation family protein AtuA


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 !  121.8   0.0   2.5e-39   2.3e-35       2     158 ..       8     162 ..       7     163 .. 0.92

  Alignments for each domain:
  == domain 1  score: 121.8 bits;  conditional E-value: 2.5e-39
                        zf-ZPR1   2 lCpsCgkengetrllltkiPyfkeviimsfeCehCgyknnevksageieekGkritlkveseedlnrqvlkSetatveip 81 
                                    +Cp Cg +++e +  +t++Pyf++ +i+  +Ce Cg+++++++ +++ e+   r tl v++ edln +vl+S+++t++ip
  gi|116754734|ref|YP_843852.1|   8 SCPMCG-ATMEFNWETTELPYFGDALIIGGVCE-CGFRHSDTMLLSQREP--YRHTLVVREIEDLNARVLRSSSGTIHIP 83 
                                    7****7.8899999999****************.****************..**************************** PP

                        zf-ZPR1  82 eleleippg.tlegrlttvEGlLeqikeele..keegdqaered.eekekieeflekleeliegeepftlildDpagnSf 157
                                    e++++i+pg ++e+++t++EG+L ++k+ +e  + +   ++ +d e ++k ee+l+k+e +++ge ++t+il+Dp+gnS+
  gi|116754734|ref|YP_843852.1|  84 EIGVDIEPGyASEAYITNIEGVLVRVKNIVEfaT-NAARQA-RDvERTAKGEEILSKIEMALRGEFSLTVILEDPFGNSA 161
                                    ******************************8532.222223.455899*******************************9 PP

                        zf-ZPR1 158 i 158
                                    i
  gi|116754734|ref|YP_843852.1| 162 I 162
                                    8 PP

>> AtuA  Acyclic terpene utilisation family protein AtuA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   1.3e-06     0.012     165     201 ..       8      44 ..       5      69 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.3e-06
                           AtuA 165 slvlapaawefgWkeddydelAgalvaGhllECgaqv 201
                                    s  +  a +ef+W+++++   + al++G + ECg   
  gi|116754734|ref|YP_843852.1|   8 SCPMCGATMEFNWETTELPYFGDALIIGGVCECGFRH 44 
                                    544555666************************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 1475.34
//
Query:       gi|116754735|ref|YP_843853.1|  [L=295]
Description: LPPG:FO 2-phospho-L-lactate transferase [Methanosaeta thermophila PT]
Scores for 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  156.4   0.0    1.1e-45  156.2   0.0    1.0  1  UPF0052   Uncharacterised protein family UPF0052


Domain annotation for each model (and alignments):
>> UPF0052  Uncharacterised protein family UPF0052
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.2   0.0   5.9e-50   1.1e-45       3     263 ..       3     271 ..       1     290 [. 0.89

  Alignments for each domain:
  == domain 1  score: 156.2 bits;  conditional E-value: 5.9e-50
                                    EEE-CHHHHHHHHHHCCSS..CEEEEEE-----SHHHHHHHHHHTS---HHHHHHHHHH...--S-C..........HHH CS
                        UPF0052   3 vlgGGtGlskllrglkevt..aeltavvtvaDdggssGelrrelgllaigDirnvlval...idder..........lle 67 
                                    +l+GGtG++kllrgl +v   +e+t+vv++a+d + sG        l+ +Di++v+++l   idder          +++
  gi|116754735|ref|YP_843853.1|   3 ILSGGTGTPKLLRGLVRVLdpDEITIVVNTAEDLWVSG-------NLVSPDIDTVIYTLaglIDDERwwgirgdsfiTHT 75 
                                    79*****************99*****************.......9************************9999999777 PP

                                    HHCH-B-SS.....SSSSTT-BHHHHHHHHHHHHHS.-HHHHHHHHHHHTT-SSEEEES-SS--EEEEEETTS-EEESTT CS
                        UPF0052  68 eLfqyRfkg.....dgdlaghslgnllLaalaeltg.sleeaiealskilkvrgrvlPatddpvelsaeledGeeitges 141
                                    +L +  +k+     d+d a h+l+  +++      g +l++a+e ++++l++r rv+P++d++v++ + +  Ge+  +e 
  gi|116754735|ref|YP_843853.1|  76 RLREMGVKEmlaigDADRAFHILRSDIIRR-----GgTLSDATEMMRAALGIRSRVFPMSDESVSTIIATPLGEMHFQEF 150
                                    77777666688888****************.....55*************************************655*** PP

                                    TGGGG-S....-EEE.EEEESTT----HHHHHHHHH-SEEEE-SS-IIIIIHHHHTSCCHHHHHHH-SSEEEEE--SB-- CS
                        UPF0052 142 kiseark.lkapikr.vflepegaeaapevleaikeAdlivlgpGslytSiiPiLlvpgiaealreskakkvlvsnimtq 219
                                    ++   ++  ++++    f + ++a++ ++ l+a+++ + +v+gp++++tSi PiL ++g++ a+  + +++v+vs++ + 
  gi|116754735|ref|YP_843853.1| 151 WV---ERrGEPEVLGvRFDGIDDARPSKGFLDALRRENTVVIGPSNPVTSISPILSLKGVRGAM--AGKTVVAVSPLDG- 224
                                    **...33357999999999*********************************************..779*********9. PP

                                    TTTSTT-BHHHHHHHHHHCH-.....SS....S..-SEEEEE-S.---HHHH CS
                        UPF0052 220 kGetdgfsvsdhvkaieravg.....kgvakay..vdavlvnts.evpeell 263
                                         + ++s+++++ ++a+g     +gv++ +  vd+++v +s + p +++
  gi|116754735|ref|YP_843853.1| 225 -----DRPFSGPAARFMKAAGfepndEGVISILgdVDHFIVSRSsSYPGRCI 271
                                    .....****************97765554444499*****977635555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       233  (0.0129957); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 2147.03
//
Query:       gi|116754736|ref|YP_843854.1|  [L=88]
Description: hypothetical protein Mthe_1440 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       593  (0.0330749); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.28s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 628.08
//
Query:       gi|116754737|ref|YP_843855.1|  [L=469]
Description: phosphoesterase domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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-15   56.2   0.2    8.2e-15   55.4   0.2    1.4  1  DHHA1     DHHA1 domain
  ------ inclusion threshold ------
      0.047   12.7   0.0       0.83    8.6   0.0    2.2  2  SelA      L-seryl-tRNA selenium transferase
      0.048   13.9   0.1      0.097   12.9   0.1    1.5  1  DHH       DHH family


Domain annotation for each model (and alignments):
>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.4   0.2   1.4e-18   8.2e-15      18     138 .]     341     460 ..     325     460 .. 0.78

  Alignments for each domain:
  == domain 1  score: 55.4 bits;  conditional E-value: 1.4e-18
                                    HHHHHHHHHHHHHHHTCEEECTCEEEEEECHCCHHHHHHHHHHHHHHTHG.BT.TCEEEEEEEECTEEEEEEEESSH... CS
                          DHHA1  18 lkealaklkaeellekaeevkgvkvlvaevgeewdagalgiaadklkskl.kk.pvivfvakeegdkvkvsarskkd... 92 
                                    l + ++ +k+ +l++       +  ++ +  ee+  +++gi+a+++ +    + p+ +f+a+ +g   kvsar ++d   
  gi|116754737|ref|YP_843855.1| 341 LLNGIKLVKERGLVQL-----SHIQYFDAG-EEILDTIVGIVAGMVFQIAdRSkPILAFAATPDG-MLKVSARGTQDlvr 413
                                    4444444454444433.....555555666.7777789999999999966644488888888888.************** PP

                                    .SS-HHHHHHHHHHHTTCCEEEETCEEEEEEEHCHHHHHHHHHHHHH CS
                          DHHA1  93 .gvdagelakeaaaklgggGGGHdlAaGagipaekleealealeeai 138
                                     g+d++ ++++ a ++gg GGGH  AaGa+ip+++ +e+l+ ++++i
  gi|116754737|ref|YP_843855.1| 414 aGLDLSRAVSASANEVGGVGGGHSIAAGATIPPQSRDEFLSIIDRVI 460
                                    ****************************************9998765 PP

>> SelA  L-seryl-tRNA selenium transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0   0.00014      0.83     154     191 ..      60      98 ..      56     134 .. 0.85
   2 ?    1.6   0.0     0.019   1.1e+02     159     190 ..     148     179 ..     141     190 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00014
                                    -B---HHHHHHHHH.HHT--EEEEEES-B-S-GGGGT-- CS
                           SelA 154 tkevelaeLvelgk.ekglpvleDlGsGllvdlseygls 191
                                     k+++ + + ++++   +l++++DlGsG++ ++s++g+ 
  gi|116754737|ref|YP_843855.1|  60 FKQLDSRAIERIADaGSDLVIFTDLGSGMIQEISSFGIR 98 
                                    566666777777762579*******************96 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.019
                                    HHHHHHHHHHHT--EEEEEES-B-S-GGGGT- CS
                           SelA 159 laeLvelgkekglpvleDlGsGllvdlseygl 190
                                    +++L +l+    +  l+Dl sG lv l++  +
  gi|116754737|ref|YP_843855.1| 148 NEDLSALAVVGAVGDLQDLSSGRLVGLNRRII 179
                                    689999**999****************98766 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   1.6e-05     0.097       2      70 ..      27     122 ..      26     152 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.6e-05
                                    EEEE-ECSSSHHHHHHHHHHHH.................................CECS--TCGGCGCCHHCCCSEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxx.................................xxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DHH   2 ilivghknpDtDsigSaialan.................................llvDhneksqavegeakeeaedvii 48 
                                    +l+  + + D+D++++a ++                                   +  D ++   +++    + + + +i
  gi|116754737|ref|YP_843855.1|  27 VLV--VSHIDADGLTAAGVICTalsrkgidytplffkqldsraieriadagsdlvIFTDLGSGMIQEIS---SFGIRAVI 101
                                    455..8899******976666656788888888877777777777777777776667888877777766...99****** PP

                                    EE-S---SS---SS--EEEE-S CS
                                    xxxxxxxxxxxxxxxxxxxxxx RF
                            DHH  49 iDHHrlgeefetlapilflnep 70 
                                     DHHr+g ++e +  i+ +n++
  gi|116754737|ref|YP_843855.1| 102 ADHHRPG-SAEIYRGIVHINPH 122
                                    ******9.77777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 3578.61
//
Query:       gi|116754738|ref|YP_843856.1|  [L=146]
Description: hypothetical protein Mthe_1442 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       447  (0.0249317); 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:                         0  (0); expected 0.2 (1e-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: 1066.31
//
Query:       gi|116754739|ref|YP_843857.1|  [L=405]
Description: replication factor A [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      0.004   16.9   0.0        3.3    7.6   0.0    2.9  2  NTR              UNC-6/NTR/C345C module
     0.0045   16.9   0.2        3.8    7.6   0.0    2.9  2  tRNA_anti-codon  OB-fold nucleic acid binding domain
     0.0058   16.5   0.1      0.013   15.4   0.1    1.5  1  RMI1_C           Recq-mediated genome instability protein 1, 


Domain annotation for each model (and alignments):
>> NTR  UNC-6/NTR/C345C module
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   0.0    0.0016       9.9      12      82 ..      64     139 ..      63     158 .. 0.72
   2 !    7.6   0.0   0.00055       3.3      44      95 ..     206     258 ..     169     267 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0016
                                    EEEEEEEEEETTEEEEEEEEEEEEEES......STTTSTTTSEEEEEEETTSSSS-C-TTSEEEEEEEEEEETSSEE CS
                            NTR  12 kvkVlsveeegsfdkytvkvkevlKeg......stdkvrkgkerlfvkrkdCrcpkLklgkeYLimGksskeegrgr 82 
                                    +vk+++++e g+++ +++kv++ + +       +    + + +  fvk ++  +p+L +gk+YL+   ++ +e +gr
  gi|116754739|ref|YP_843857.1|  64 QVKINQIREPGRWVDLEAKVLSLFESPspaisqAGILGDDTGNIRFVKWAKSGQPDLVEGKSYLLKNLVT-DEFQGR 139
                                    68999999999999999999999999866553333333445566788888899999999****9976666.555554 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00055
                                    TTTSEEEEEEETTSSSS-C-TTSEEEEEEEEEEETSSEE..EEESTTCEEEEE- CS
                            NTR  44 rkgkerlfvkrkdCrcpkLklgkeYLimGksskeegrgr..yvlgkkslveewp 95 
                                    +++ ++ fvk ++  +p+L +gk+YL+   ++ +e +gr  + +++++++ee  
  gi|116754739|ref|YP_843857.1| 206 DETGVVRFVKWAKSGQPDLVEGKSYLLKNLVT-DEFQGRfsVKINRSTVIEETD 258
                                    4566778888888999***********98888.666666669999999999865 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 !    7.6   0.0   0.00064       3.8      22      71 ..      99     145 ..      94     150 .. 0.76
   2 !    6.3   0.0    0.0016       9.3      23      72 ..     204     250 ..     181     254 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00064
                                    EEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEEC.TTSSEEEEEE CS
                tRNA_anti-codon  22 dlrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrr.pggelelkve 71 
                                    +l D+tg+i+ v +    ++ + +l eG+ +  +  v+   +g+ +++k++
  gi|116754739|ref|YP_843857.1|  99 ILGDDTGNIRFVKWA---KSGQPDLVEGKSYLLKNLVTDEfQGR-FSVKIN 145
                                    699************...77777777777777776666663444.777776 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0016
                                    EEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEEC.TTSSEEEEEEE CS
                tRNA_anti-codon  23 lrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrr.pggelelkvee 72 
                                    l D+tg ++ v +    ++ + +l eG+ +  +  v+   +g+ +++k+++
  gi|116754739|ref|YP_843857.1| 204 LGDETGVVRFVKWA---KSGQPDLVEGKSYLLKNLVTDEfQGR-FSVKINR 250
                                    88************...88888888888888887777663554.8888776 PP

>> RMI1_C  Recq-mediated genome instability protein 1, C-terminal OB-fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   2.1e-06     0.013      46      82 ..     311     347 ..     297     363 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.1e-06
                         RMI1_C  46 qlkakisDGsaildvdlssevlteligfspaelkesl 82 
                                    ++ka+i+DG  + d+ +++e ++elig++ ++ ke++
  gi|116754739|ref|YP_843857.1| 311 RVKAVIDDGLVAQDILINRERVEELIGLTMEQAKEMA 347
                                    46789**************************876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); 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: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2879.96
//
Query:       gi|116754740|ref|YP_843858.1|  [L=332]
Description: nucleic acid binding, OB-fold, tRNA/helicase-type [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       680  (0.0379274); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2448.73
//
Query:       gi|116754741|ref|YP_843859.1|  [L=394]
Description: argininosuccinate synthase [Methanosaeta thermophila PT]
Scores for complete 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-164  548.0   0.0   1.6e-164  547.8   0.0    1.0  1  Arginosuc_synth  Arginosuccinate synthase
  ------ inclusion threshold ------
       0.03   13.4   0.0       0.05   12.7   0.0    1.2  1  NAD_synthase     NAD synthase
       0.17   11.3   0.1       0.44   10.0   0.0    1.6  2  Diphthami_syn_2  Diphthamide synthase


Domain annotation for each model (and alignments):
>> Arginosuc_synth  Arginosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  547.8   0.0  2.7e-168  1.6e-164       2     386 ..       9     388 ..       8     390 .. 0.99

  Alignments for each domain:
  == domain 1  score: 547.8 bits;  conditional E-value: 2.7e-168
                Arginosuc_synth   2 LaysGGlDtsviikllkeklg.eeviavavdvGqeeedldevkekalklgavksvvvDakeefvedyifpaikanalYed 80 
                                    LaysGGlDtsv+i+ll+e++g + v++v+vdvGq+ ed+++ +++a+kl++ +++++Dak+efv+dyifp ikan+ Ye+
  gi|116754741|ref|YP_843859.1|   9 LAYSGGLDTSVCIPLLRERYGmKRVVTVLVDVGQPPEDIERGNRRAEKLSD-EHYIIDAKDEFVRDYIFPLIKANGSYEG 87 
                                    9********************889**************************9.**************************** PP

                Arginosuc_synth  81 rYllgtalaRPliakklvevakkegaeavahGctGkGnDqvRfevsirslaPdlkviaPvReleltReeeieyakekgip 160
                                     Y+lgta+aRPlia+k+v+va+k g +a+ahGctG+GnDq+Rfe+++r++   + viaP+R+l+l+Re+ei+ya+e+gi+
  gi|116754741|ref|YP_843859.1|  88 -YVLGTAIARPLIARKVVDVARKLGINALAHGCTGRGNDQLRFEAVFRATG--MRVIAPMRDLDLSREWEIDYAREHGID 164
                                    .*************************************************9..*************************** PP

                Arginosuc_synth 161 vevtkkkpysiDenllgrsieagiLedpknappediyeltkdpakapdepeeveiefekGvPvaldgeelsvleliekln 240
                                    v+v+kk+p+siDenl++rsie+g+Ledp ++ppe+iy++t+ p  +   pe+veiefe+GvPv+l++e+l+ +eli++ln
  gi|116754741|ref|YP_843859.1| 165 VQVSKKRPWSIDENLWSRSIEGGMLEDPFFEPPEEIYAWTRTPDGSV-PPEIVEIEFERGVPVSLNNERLDGVELIRRLN 243
                                    *******************************************9888.9******************************* PP

                Arginosuc_synth 241 eiagkhGvGRiDivedRlvglksReiYeapaalvLikahkdlekltlerevakfkkiveekyaelvYkGlwfsPlkeald 320
                                     iagkhG+GR+D++edR++glk+Re+Ye+paa+vL++ah+dle+l+l+r +++fk +v+e +ae+ Y Gl  +Pl ++l+
  gi|116754741|ref|YP_843859.1| 244 LIAGKHGIGRTDMIEDRVLGLKARENYEHPAATVLLTAHRDLEQLVLSRAELRFKASVDEAWAEMAYMGLLDDPLFADLN 323
                                    ******************************************************************************** PP

                Arginosuc_synth 321 afiektqervtGtvrvklfkGsvvvlgReseeslYdeelasydeedefdqkeaeGfikihglqakl 386
                                    afi++++ rv+G vr+klf G+++ +gR+s+ +lY++e++s+d ++++ q++aeGf+k+hg+qa+l
  gi|116754741|ref|YP_843859.1| 324 AFIDQANSRVNGVVRMKLFCGNAMPVGRRSPDALYSQEMVSFD-SQTLSQRDAEGFAKYHGFQARL 388
                                    *******************************************.99*****************986 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   8.3e-06      0.05      20      83 ..       6      68 ..       2      77 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.3e-06
                                   EEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE---HH CS
                   NAD_synthase 20 gvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktidikp 83
                                   +v l  SGG+D s+   l ++  g ++v+++l+ ++ +++ed+e     ae+l++e   id k+
  gi|116754741|ref|YP_843859.1|  6 EVALAYSGGLDTSVCIPLLRERYGMKRVVTVLV-DVGQPPEDIERGNRRAEKLSDEHYIIDAKD 68
                                   577889**************************9.9999******************99999876 PP

>> Diphthami_syn_2  Diphthamide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0      0.74   4.4e+03       3      30 ..       7      34 ..       6      40 .. 0.62
   2 ?   10.0   0.0   7.4e-05      0.44      80     161 ..     106     189 ..      98     193 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.74
                Diphthami_syn_2  3 vavlysGGkDsilaLykalkesevesLv 30
                                   va  ysGG D  + +    +++ ++ +v
  gi|116754741|ref|YP_843859.1|  7 VALAYSGGLDTSVCIPLLRERYGMKRVV 34
                                   5667899998877665544445555555 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 7.4e-05
                Diphthami_syn_2  80 tlkkldveavviGaieseyqksriervCrelGlksvaPLWkkdp.eel.leeiveekfevivvavkaegldeslLGrrid 157
                                      +kl+++a+  G     +++ r+e v r  G++ +aP+ + d  +e+ + +  e++ +v v   +    de+l  r i+
  gi|116754741|ref|YP_843859.1| 106 VARKLGINALAHGCTGRGNDQLRFEAVFRATGMRVIAPMRDLDLsREWeIDYAREHGIDVQVSKKRPWSIDENLWSRSIE 185
                                    5678999*******************************988774133325556666777777777777777777777776 PP

                Diphthami_syn_2 158 kkli 161
                                      ++
  gi|116754741|ref|YP_843859.1| 186 GGML 189
                                    6555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 2736.10
//
Query:       gi|116754742|ref|YP_843860.1|  [L=334]
Description: XRE family transcriptional regulator [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.4e-12   45.1   0.8    2.4e-11   43.5   0.6    2.0  1  HTH_3          Helix-turn-helix
    5.9e-09   35.8   2.9    5.9e-09   35.8   0.4    2.2  2  HTH_19         Helix-turn-helix domain
    1.6e-06   28.0   0.1    7.3e-06   25.8   0.1    2.1  2  HTH_11         HTH domain
    3.3e-06   27.3   1.1    1.5e-05   25.3   0.1    2.6  3  HTH_31         Helix-turn-helix domain
    7.3e-05   22.4   0.0    0.00026   20.7   0.0    1.9  1  HTH_23         Homeodomain-like domain
    0.00053   19.7   0.3     0.0058   16.4   0.1    2.6  2  MerR           MerR family regulatory protein
     0.0011   19.3   0.1     0.0033   17.8   0.1    1.9  1  HTH_26         Cro/C1-type HTH DNA-binding domain
     0.0015   18.2   0.0     0.0041   16.8   0.0    1.8  1  HTH_DeoR       DeoR-like helix-turn-helix domain
     0.0018   17.8   1.7     0.0094   15.5   0.5    2.6  2  Sigma70_r4     Sigma-70, region 4
     0.0028   17.2   0.4     0.0081   15.7   0.0    2.0  2  HTH_24         Winged helix-turn-helix DNA-binding
     0.0037   17.0   0.2      0.012   15.4   0.2    1.8  1  HTH_38         Helix-turn-helix domain
      0.004   17.2   0.1      0.011   15.8   0.1    1.7  1  HTH_7          Helix-turn-helix domain of resolvase
     0.0044   17.0   0.2      0.087   12.9   0.0    2.9  3  HTH_20         Helix-turn-helix domain
     0.0068   16.5   0.1      0.018   15.2   0.1    1.7  1  HTH_28         Helix-turn-helix domain
  ------ inclusion threshold ------
      0.014   15.3   0.0       0.58   10.2   0.0    2.9  2  HTH_Crp_2      Crp-like helix-turn-helix domain
      0.018   14.9   0.1      0.053   13.4   0.1    1.8  1  HTH_25         Helix-turn-helix domain
      0.021   14.6   0.0      0.051   13.4   0.0    1.6  1  HTH_10         HTH DNA binding domain
      0.028   14.5   0.0      0.087   12.9   0.0    1.9  1  MerR_1         MerR HTH family regulatory protein
      0.046   13.6   0.2       0.28   11.1   0.0    2.4  3  MarR_2         MarR family
      0.047   13.5   0.1       0.11   12.3   0.1    1.7  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain
      0.054   13.5   0.0       0.16   12.0   0.0    1.8  1  HTH_29         Winged helix-turn helix
       0.11   12.7   0.0       0.23   11.8   0.0    1.5  1  NUMOD1         NUMOD1 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 !   43.5   0.6   2.9e-14   2.4e-11       1      50 [.     155     204 ..     155     207 .. 0.95

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 2.9e-14
                                    HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTS CS
                          HTH_3   1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgv 50 
                                    l++lR ++g+s+ eLA++lGvsr+t+s++E+     s+++++kl++ ++ 
  gi|116754742|ref|YP_843860.1| 155 LQRLRIERGISIGELAAELGVSRRTVSKYESESMDTSIDIALKLEEIFQE 204
                                    6789******************************************9985 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.4   7.3e-12   5.9e-09       1      52 [.     152     202 ..     152     210 .. 0.93
   2 ?   -1.2   0.1       2.6   2.1e+03       5      48 ..     272     315 ..     269     318 .. 0.58

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 7.3e-12
                         HTH_19   1 GerLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaeal 52 
                                    Ge+L+++R+e+g+++ ela +lg+sr+  s++E++++ ++s++  lk+ e++
  gi|116754742|ref|YP_843860.1| 152 GEMLQRLRIERGISIGELAAELGVSRRTVSKYESESM-DTSIDIALKLEEIF 202
                                    9************************************.99999998887776 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.6
                         HTH_19   5 keaReelgltqeelae.rlgis.rskisaiEngkkdvpsaelllki 48 
                                    k+aR +  l+   l +  l+++  +ki  iE  ++ v++++++ ki
  gi|116754742|ref|YP_843860.1| 272 KRARLMSSLSSVTLTHsALIVDgETKIDRIE--RTAVIGRKEIEKI 315
                                    5555555554444444455666777777777..5567766666665 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       9.6   7.8e+03      15      25 ..     121     131 ..     120     131 .. 0.84
   2 !   25.8   0.1     9e-09   7.3e-06       5      35 ..     154     183 ..     153     183 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 9.6
                         HTH_11  15 pisgeeLAeeL 25 
                                    ++s  +LA++L
  gi|116754742|ref|YP_843860.1| 121 TVSLPTLADYL 131
                                    59999****98 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 9e-09
                         HTH_11   5 ilelLleargpisgeeLAeeLnvSrrtvrrd 35 
                                    +l++L+ +rg is+ eLA eL+vSrrtv ++
  gi|116754742|ref|YP_843860.1| 154 MLQRLRIERG-ISIGELAAELGVSRRTVSKY 183
                                    799**9***9.*****************986 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       5.1   4.1e+03      25      25 ..      90      90 ..      57     137 .. 0.56
   2 !   25.3   0.1   1.8e-08   1.5e-05       3      36 ..     152     185 ..     152     197 .. 0.95
   3 ?   -2.7   0.0       9.4   7.7e+03      28      37 ..     295     304 ..     294     315 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 5.1
                         HTH_31 25 g 25
                                   g
  gi|116754742|ref|YP_843860.1| 90 G 90
                                   2 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 1.8e-08
                         HTH_31   3 GalLralReraGLsqeevAerlgvsestlsrlEq 36 
                                    G+ L++lR ++G+s  e+A+ lgvs+ t+s++E+
  gi|116754742|ref|YP_843860.1| 152 GEMLQRLRIERGISIGELAAELGVSRRTVSKYES 185
                                    789******************************7 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 9.4
                         HTH_31  28 estlsrlEqG 37 
                                    e+++ r+E+ 
  gi|116754742|ref|YP_843860.1| 295 ETKIDRIERT 304
                                    6899999994 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   3.1e-07   0.00026      10      38 ..     154     184 ..     152     187 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 3.1e-07
                         HTH_23  10 illllae..GlsvreIAreLgvsrrTvyrwl 38 
                                    +l+ l+   G+s+ e A+eLgvsrrTv+++ 
  gi|116754742|ref|YP_843860.1| 154 MLQRLRIerGISIGELAAELGVSRRTVSKYE 184
                                    566666457******************9875 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   7.1e-06    0.0058       1      22 [.     165     186 ..     165     187 .. 0.95
   2 ?    0.0   0.0      0.93   7.6e+02      10      24 ..     224     238 ..     220     243 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.1e-06
                                    EHHHHHHHHTTTHHHHHHHHHT CS
                           MerR   1 tIgevAeltGvsprtLRyYEre 22 
                                    +Ige+A  +Gvs rt+  YE+e
  gi|116754742|ref|YP_843860.1| 165 SIGELAAELGVSRRTVSKYESE 186
                                    7*******************87 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.93
                                    TTTHHHHHHHHHTTS CS
                           MerR  10 GvsprtLRyYEreGL 24 
                                     v  + LR++ ++GL
  gi|116754742|ref|YP_843860.1| 224 EVKDSILRRLVEIGL 238
                                    577788********9 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 !   17.8   0.1   4.1e-06    0.0033       2      35 ..     155     188 ..     154     203 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.1e-06
                         HTH_26   2 LrelmadrgitkseLargtgisaatlsrlvkgkp 35 
                                    L++l ++rgi++ eLa  +g+s+ t+s++ ++ +
  gi|116754742|ref|YP_843860.1| 155 LQRLRIERGISIGELAAELGVSRRTVSKYESESM 188
                                    8999*************************99875 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0     5e-06    0.0041       3      31 ..     152     180 ..     151     182 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5e-06
                       HTH_DeoR   3 eqilellkqqgklsveelvellgvSeaTi 31 
                                     ++l+ l+ ++ +s+ el+++lgvS  T+
  gi|116754742|ref|YP_843860.1| 152 GEMLQRLRIERGISIGELAAELGVSRRTV 180
                                    58**************************8 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   0.5   1.1e-05    0.0094      14      45 ..     157     188 ..     155     190 .. 0.90
   2 ?   -0.2   0.0      0.93   7.5e+02      11      23 ..     211     223 ..     210     224 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.1e-05
                                    HHHHTTT--HHHHHHHHTS-HHHHHHHHHHHH CS
                     Sigma70_r4  14 elrfgeglTleEIgerlgiSrerVrqiekrAl 45 
                                    +lr ++g +  E++++lg+Sr +V+  e++ +
  gi|116754742|ref|YP_843860.1| 157 RLRIERGISIGELAAELGVSRRTVSKYESESM 188
                                    578899*******************9998876 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.93
                                    HHHHHHHTTT--H CS
                     Sigma70_r4  11 evlelrfgeglTl 23 
                                    +++++rf+e+ T 
  gi|116754742|ref|YP_843860.1| 211 DIFRQRFVEEATT 223
                                    599******9996 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 !   15.7   0.0   9.9e-06    0.0081       7      37 ..     153     183 ..     149     183 .. 0.82
   2 ?   -3.3   0.1       8.8   7.2e+03      38      46 ..     230     238 ..     229     238 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 9.9e-06
                         HTH_24   7 kILelLqknprisqreLAerlglSpstvnrr 37 
                                    + L+ L+ + +is+ eLA +lg+S+ tv+++
  gi|116754742|ref|YP_843860.1| 153 EMLQRLRIERGISIGELAAELGVSRRTVSKY 183
                                    55666666899*****************986 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 8.8
                         HTH_24  38 lkrLeeeGl 46 
                                    l+rL+e Gl
  gi|116754742|ref|YP_843860.1| 230 LRRLVEIGL 238
                                    899999886 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.2   1.4e-05     0.012      11      39 ..     153     182 ..     152     183 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.4e-05
                         HTH_38  11 eeIerll.aeGlslreIArrLgrspsTIsR 39 
                                    e+++rl+ ++G s+ e A +Lg+s+ T+s+
  gi|116754742|ref|YP_843860.1| 153 EMLQRLRiERGISIGELAAELGVSRRTVSK 182
                                    578999549*******************96 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 !   15.8   0.1   1.3e-05     0.011      17      41 ..     159     183 ..     155     187 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.3e-05
                                    STTTT--STTTSSSS---SSSS--S CS
                          HTH_7  17 LleeGisiskIAkevnisRsTvYRy 41 
                                    ++e Gisi ++A e+++sR Tv +y
  gi|116754742|ref|YP_843860.1| 159 RIERGISIGELAAELGVSRRTVSKY 183
                                    7899******************888 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0       1.2   9.5e+02      45      54 ..      34      43 ..      31      46 .. 0.86
   2 !   12.9   0.0   0.00011     0.087      15      42 ..     154     181 ..     153     182 .. 0.94
   3 ?   -2.5   0.0         7   5.7e+03      51      60 ..     322     331 ..     320     332 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 1.2
                                   HHHHHHCTTE CS
                         HTH_20 45 LrvLeeagLv 54
                                   ++vL+eag++
  gi|116754742|ref|YP_843860.1| 34 INVLREAGFL 43
                                   689*****97 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00011
                                    HHHHHSTCTTB-HHHHHHHHTS-HHHHH CS
                         HTH_20  15 ilraLaraegltaselaerldlskntls 42 
                                    +l+ L+ ++g + +ela++l++s+ t+s
  gi|116754742|ref|YP_843860.1| 154 MLQRLRIERGISIGELAAELGVSRRTVS 181
                                    7999**********************99 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 7
                                    CTTEEEECTE CS
                         HTH_20  51 agLvevvreg 60 
                                    a+L+ ++re+
  gi|116754742|ref|YP_843860.1| 322 ADLLMTRRES 331
                                    8999999996 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   2.2e-05     0.018       9      30 ..     158     181 ..     153     184 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.2e-05
                         HTH_28   9 la..aGhsvreaArelgisrrtvy 30 
                                    l   +G s+ e+A+elg+srrtv+
  gi|116754742|ref|YP_843860.1| 158 LRieRGISIGELAAELGVSRRTVS 181
                                    4443677****************7 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 ?   10.2   0.0   0.00071      0.58      17      40 ..     159     182 ..     127     186 .. 0.80
   2 ?    1.8   0.0      0.29   2.4e+02      23      37 ..     317     331 ..     300     333 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00071
                                    EEEEEHHHHHHHHHTTSSHHHHHH CS
                      HTH_Crp_2  17 eielpltqeelAsmlGltretvsr 40 
                                    +ie  ++  elA+ lG++r tvs+
  gi|116754742|ref|YP_843860.1| 159 RIERGISIGELAAELGVSRRTVSK 182
                                    567788999*************97 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.29
                                    HHHHHHHHTTSSHHH CS
                      HTH_Crp_2  23 tqeelAsmlGltret 37 
                                    ++++ A++l ++re+
  gi|116754742|ref|YP_843860.1| 317 SRKDFADLLMTRRES 331
                                    899**********98 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   6.5e-05     0.053       1      33 [.     154     186 ..     154     191 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.5e-05
                                    HHHHHHHTTT--HHHHHHHSS--HHHHHHHHCT CS
                         HTH_25   1 rLraaRearglsleevaketkIrkdylealEed 33 
                                    +L++ R +rg+s+ e+a+e+ ++ +++ + E++
  gi|116754742|ref|YP_843860.1| 154 MLQRLRIERGISIGELAAELGVSRRTVSKYESE 186
                                    699**********************99887776 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   6.3e-05     0.051      22      43 ..     162     183 ..     160     188 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.3e-05
                         HTH_10  22 RrvtlkeLAkelGIskstlseh 43 
                                    R +++ eLA elG+s+ t+s++
  gi|116754742|ref|YP_843860.1| 162 RGISIGELAAELGVSRRTVSKY 183
                                    899****************986 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 ?   12.9   0.0   0.00011     0.087       2      23 ..     165     186 ..     164     208 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                                    EHHHHHHHHTS-HHHHHHHHHH CS
                         MerR_1   2 sigevakilgvtthtlryweke 23 
                                    sige+a +lgv+ +t+  +e e
  gi|116754742|ref|YP_843860.1| 165 SIGELAAELGVSRRTVSKYESE 186
                                    8*******************88 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       9.1   7.4e+03      41      54 ..      33      46 ..      30      49 .. 0.73
   2 ?   -2.7   0.0       6.8   5.6e+03      11      30 ..      71      88 ..      67      91 .. 0.67
   3 ?   11.1   0.0   0.00034      0.28      16      40 ..     160     182 ..     152     183 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 9.1
                                   HHHHHHHTTSEEEE CS
                         MarR_2 41 ilkrLvaaGLverr 54
                                   +++ L +aG+++ +
  gi|116754742|ref|YP_843860.1| 33 VINVLREAGFLVSS 46
                                   57888889887655 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6.8
                                   HHHHHCTTTSEEEHHHHHHH CS
                         MarR_2 11 LaaLgrrpgrdltvgelarr 30
                                   L ++    +   t++e++r 
  gi|116754742|ref|YP_843860.1| 71 LSNIDGLNE--RTAREITRL 88
                                   555555555..599999986 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00034
                                    CTTTSEEEHHHHHHHHTSSHHHHHH CS
                         MarR_2  16 rrpgrdltvgelarrlglsksavsr 40 
                                     + g  +++gela++lg+s+ +vs+
  gi|116754742|ref|YP_843860.1| 160 IERG--ISIGELAAELGVSRRTVSK 182
                                    5556..99***************96 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00014      0.11       4      35 ..     150     181 ..     149     182 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                  HTH_AsnC-type   4 iDrkILeaLqedaRisyaeLAervGlSestvl 35 
                                    iD   L+ L+    is  eLA+++G+S+ tv 
  gi|116754742|ref|YP_843860.1| 150 IDGEMLQRLRIERGISIGELAAELGVSRRTVS 181
                                    89999999999999****************96 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0    0.0002      0.16       7      32 ..     159     183 ..     158     184 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0002
                         HTH_29   7 llaeGvstvsqiAkllglsrrtvyrw 32 
                                     +++G s + ++A+ lg+srrtv ++
  gi|116754742|ref|YP_843860.1| 159 RIERGIS-IGELAAELGVSRRTVSKY 183
                                    5789998.***************876 PP

>> NUMOD1  NUMOD1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00028      0.23      18      36 ..     165     183 ..     164     183 .. 0.96

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00028
                         NUMOD1  18 SireAakyLgishntInky 36 
                                    Si e+a  Lg+s++t++ky
  gi|116754742|ref|YP_843860.1| 165 SIGELAAELGVSRRTVSKY 183
                                    9*****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); 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: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2274.07
//
Query:       gi|116754743|ref|YP_843861.1|  [L=325]
Description: phosphoribulokinase/uridine kinase [Methanosaeta thermophila PT]
Scores for complete 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-45  153.2   0.0    1.1e-44  152.5   0.0    1.3  1  PRK             Phosphoribulokinase / Uridine kinase family
    0.00066   19.7   0.0     0.0012   18.8   0.0    1.4  1  TsaE            Threonylcarbamoyl adenosine biosynthesis prot
     0.0016   18.9   0.2     0.0069   16.9   0.1    2.2  2  AAA_18          AAA domain
     0.0048   16.8   0.0      0.011   15.7   0.0    1.6  2  NACHT           NACHT domain
     0.0062   16.9   0.0      0.013   15.9   0.0    1.6  1  AAA_16          AAA ATPase domain
  ------ inclusion threshold ------
      0.014   15.1   0.0        5.4    6.7   0.0    2.2  2  Cytidylate_kin  Cytidylate kinase
      0.056   13.6   0.0        0.1   12.7   0.0    1.5  1  AAA_33          AAA domain
      0.094   12.8   0.0       0.15   12.1   0.0    1.8  1  CbiA            CobQ/CobB/MinD/ParA nucleotide binding domain
      0.096   11.9   0.0       0.17   11.1   0.0    1.3  1  Zeta_toxin      Zeta toxin
        0.1   12.3   0.0       0.15   11.7   0.0    1.3  1  AAA_30          AAA domain
        0.1   12.9   0.0       0.32   11.3   0.0    1.8  2  AAA_22          AAA domain
       0.13   12.8   0.0       0.24   11.9   0.0    1.4  1  ABC_tran        ABC transporter
       0.19   10.8   0.1       0.29   10.2   0.1    1.2  1  IIGP            Interferon-inducible GTPase (IIGP)
       0.19   10.9   0.0       0.27   10.4   0.0    1.2  1  TIP49           TIP49 P-loop domain
        0.2   11.4   0.0       0.34   10.7   0.0    1.3  1  AAA_29          P-loop containing region of AAA domain
       0.21   12.0   0.0       0.45   11.0   0.0    1.5  1  AAA_23          AAA domain


Domain annotation for each model (and alignments):
>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.5   0.0     1e-47   1.1e-44       1     189 [.      15     189 ..      15     195 .. 0.95

  Alignments for each domain:
  == domain 1  score: 152.5 bits;  conditional E-value: 1e-47
                            PRK   1 vIgvagsSGaGkttvarklekifgrekvkaaeiegdsflrldraekdleleerkrakekevsflspeandfdllyevlke 80 
                                    v++vag+SG+Gktt++r ++ ++g e v        s +      +d+++ +r+++k   ++ l pean fdll e l  
  gi|116754743|ref|YP_843861.1|  15 VVAVAGDSGSGKTTFTRGIRRLLG-EDVV-------STF----SMDDYHSLDRRQRKTLGITPLRPEANRFDLLAEHLAM 82 
                                    79**********************.3333.......344....4579********************************* PP

                            PRK  81 lkegkkvdkpiYsheteeaapdkeeliegadvlviEGlhalydervaelldlkiyvdisidlelarklqRDiaeRGrsle 160
                                    l+ g +++kp+Y+h+t+e+    + + +++ v+++EGlh++y e++++l d+ki+vd+s  ++  +kl RD+ eRG+  e
  gi|116754743|ref|YP_843861.1|  83 LRRGLAIEKPVYDHTTGEIRG--PVIFKPSPVIIVEGLHPFYTEELRKLSDFKIFVDPSRAVKRRWKLRRDVGERGYAPE 160
                                    *******************99..9999***************************************************** PP

                            PRK 161 avldsilrrkpdyvnyikpqfseadliiq 189
                                    +v+ +il r pdy+ y++ q+ +a+++i+
  gi|116754743|ref|YP_843861.1| 161 DVMREILEREPDYKLYVDVQKVYAEMVIK 189
                                    ***************************97 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.1e-06    0.0012      20      55 ..      14      47 ..       1      61 [. 0.73

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.1e-06
                                   EEEEEEESTTSSHHHHHHHHHHHTT------TTTTS CS
                           TsaE 20 dvilLeGdLGaGKTtlvrglakalgveevkSPTFtl 55
                                    v++  Gd G+GKTt++rg+ + lg  +v S TF++
  gi|116754743|ref|YP_843861.1| 14 FVVAVAGDSGSGKTTFTRGIRRLLGE-DVVS-TFSM 47
                                   3699******************9986.4555.6665 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   6.2e-06    0.0069       1      39 [.      16      52 ..      16     167 .. 0.87
   2 ?   -0.7   0.0       1.7   1.9e+03      69      89 ..     204     226 ..     169     242 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.2e-06
                         AAA_18  1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglll 39
                                   ++++G +G+GKtt+++ ++++l  g+ + ++++ +++  
  gi|116754743|ref|YP_843861.1| 16 VAVAGDSGSGKTTFTRGIRRLL--GEDVVSTFSMDDYHS 52
                                   689******************9..888877777666655 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.7
                         AAA_18  69 s..aleegknlvidghlaelese 89 
                                    +  a+e+ ++ +i+++l ++++e
  gi|116754743|ref|YP_843861.1| 204 RgsAREKYSVRIIQQILDHPLDE 226
                                    25568899999999999999987 PP

>> NACHT  NACHT domain
   #    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       2      47 ..      15      58 ..      14      79 .. 0.83
   2 ?   -3.1   0.0       5.7   6.4e+03      52      67 ..     277     292 ..     267     314 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 9.5e-06
                                   CEEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTT CS
                          NACHT  2 lvilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsr 47
                                   +v++ G++GsGKTt+ +++ +++ e+      f++  ++sl +++r
  gi|116754743|ref|YP_843861.1| 15 VVAVAGDSGSGKTTFTRGIRRLLGEDVVST--FSMDDYHSLDRRQR 58
                                   689*****************9999988766..66666666666555 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.7
                                    .-HCHHHCCCCTS--S CS
                          NACHT  52 rsladllfsqlpepaa 67 
                                    r l+d+l ++ p   +
  gi|116754743|ref|YP_843861.1| 277 RKLCDFLGRDVPSVTE 292
                                    6789999888887665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.2e-05     0.013      16      63 ..       4      50 ..       1     102 [. 0.73

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.2e-05
                         AAA_16 16 lervrsgrp.elvllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                   le++r+++   +v + G+sG+GK++  r ++r l +d  ++ +   d++
  gi|116754743|ref|YP_843861.1|  4 LEKIRESGRvFVVAVAGDSGSGKTTFTRGIRRLLGED--VVSTFSMDDY 50
                                   55554444448899*****************999988..4444444444 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0048       5.4       1      32 [.      16      47 ..      16      84 .. 0.88
   2 ?    6.5   0.0    0.0057       6.4     130     171 ..     130     170 ..     109     191 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0048
                                   EEEE-STTSSHHHHHHHHHHHHT-EEEEHHHH CS
                 Cytidylate_kin  1 iaiDGPagsGKssvaralaeklglkyldtgal 32
                                   +a+ G +gsGK + +r + + lg  +++t ++
  gi|116754743|ref|YP_843861.1| 16 VAVAGDSGSGKTTFTRGIRRLLGEDVVSTFSM 47
                                   7999******************9999999777 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0057
                                    -SEEEEEE--HHHHHHHHHHHHHHTT--.--HHHHHHHHHHHH CS
                 Cytidylate_kin 130 aelKifldAsveeRakRRlkqlkakgts.vsleellaeikeRD 171
                                    +++Kif+d s    +kRR+k +++ g    + e++++ei eR 
  gi|116754743|ref|YP_843861.1| 130 SDFKIFVDPSRA--VKRRWKLRRDVGERgYAPEDVMREILERE 170
                                    799****98754..79*****99999998999********996 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   9.4e-05       0.1       1      35 [.      15      52 ..      15      98 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.4e-05
                         AAA_33  1 lvllvGlpGsGKstlaerllkklg...avllssdtlrr 35
                                   +v + G +GsGK+t+ +++ + lg   + + s d++++
  gi|116754743|ref|YP_843861.1| 15 VVAVAGDSGSGKTTFTRGIRRLLGedvVSTFSMDDYHS 52
                                   78899************998888854444455555443 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   0.0   0.00014      0.15       2      25 ..      16      39 ..      15     261 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                                   EEEESSTTSSHHHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA  2 aiastkGGvGKTtlaanLaralar 25
                                   +++++ +G+GKTt++ ++ r+l +
  gi|116754743|ref|YP_843861.1| 16 VAVAGDSGSGKTTFTRGIRRLLGE 39
                                   7899************99999987 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00015      0.17      13      57 ..      10      53 ..       2      63 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00015
                     Zeta_toxin 13 qerPklillgGqpGAGKselaellkdelerqgnvv.rldpDdlRel 57
                                   + r  ++ ++G +G+GK++  + +++ l  +++vv +++ Dd+ +l
  gi|116754743|ref|YP_843861.1| 10 SGRVFVVAVAGDSGSGKTTFTRGIRRLL--GEDVVsTFSMDDYHSL 53
                                   56667899******************99..6666636888888765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00014      0.15       9      43 ..       3      38 ..       1      81 [. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00014
                         AAA_30  9 avealltsgdrv.avltGpAGtGKttalkalreawe 43
                                   ++e++ +sg+ + +++ G  G+GKtt  +++r+++ 
  gi|116754743|ref|YP_843861.1|  3 LLEKIRESGRVFvVAVAGDSGSGKTTFTRGIRRLLG 38
                                   5677888888651557799************99876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00028      0.32       8     103 ..      16     121 ..      14     144 .. 0.60
   2 ?   -2.3   0.0       4.4     5e+03      52      75 ..     271     291 ..     234     313 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00028
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee..........erpevvfvtlpsst.sskdllrellralglelkaerlsse 76 
                                    ++v G sG+GKTt  r +++ l e+   +           ++++++ +t+  ++ ++ dll e l  l ++l      ++
  gi|116754743|ref|YP_843861.1|  16 VAVAGDSGSGKTTFTRGIRRLLGEDVVSTFsmddyhsldrRQRKTLGITPLRPEaNRFDLLAEHLAMLRRGLAI----EK 91 
                                    6899***********99999996543333355666666666666665555555555555555555555554444....44 PP

                         AAA_22  77 ellealeqalrarav...ielliiDEaqhl 103
                                     ++++ +  +r        +++i++  + +
  gi|116754743|ref|YP_843861.1|  92 PVYDHTTGEIRGPVIfkpSPVIIVEGLHPF 121
                                    444555555555555555566666666655 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.4
                         AAA_22  52 sskdllrellralglelkaerlss 75 
                                      kdl r+l+ +lg++  +    +
  gi|116754743|ref|YP_843861.1| 271 MIKDLERKLCDFLGRDVPS---VT 291
                                    5667777777777776666...33 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00022      0.24      13      36 ..      15      38 ..      10      98 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00022
                                   EEEEEESTTSSHHHHHHHHTTSS- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran 13 kvaivGenGaGKStLlkllagllk 36
                                   +va+ G++G+GK+t+ + + +ll 
  gi|116754743|ref|YP_843861.1| 15 VVAVAGDSGSGKTTFTRGIRRLLG 38
                                   689*************99998875 PP

>> IIGP  Interferon-inducible GTPase (IIGP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00025      0.29      35      60 ..      13      39 ..       3      44 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00025
                                   -EEEEEEESTTSSHHHHHHHHT.T--T CS
                           IIGP 35 klkiavtGdsGnGkssFinaLR.liGh 60
                                   +  +av GdsG+Gk +F   +R l+G+
  gi|116754743|ref|YP_843861.1| 13 VFVVAVAGDSGSGKTTFTRGIRrLLGE 39
                                   4569*************9998714454 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00024      0.27      43      79 ..       4      42 ..       1      61 [. 0.76

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00024
                                   XXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49 43 ikekklaGra..vLlaGpsgtGktalaiaiskelgedvp 79
                                   +++ + +Gr+  v +aG+sg+Gkt    +i + lgedv 
  gi|116754743|ref|YP_843861.1|  4 LEKIRESGRVfvVAVAGDSGSGKTTFTRGIRRLLGEDVV 42
                                   5555667775226689*******************9985 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 ?   10.7   0.0   0.00031      0.34      24      39 ..      15      30 ..       5      40 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00031
                         AAA_29 24 atlltGpsGsGKSTll 39
                                   ++ ++G+sGsGK+T+ 
  gi|116754743|ref|YP_843861.1| 15 VVAVAGDSGSGKTTFT 30
                                   57899*********86 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0004      0.45      23      47 ..      17      41 ..      14      63 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0004
                         AAA_23 23 lItGpNGaGKTTildAiklaLyget 47
                                   ++ G+ G+GKTT+ + i+  L++++
  gi|116754743|ref|YP_843861.1| 17 AVAGDSGSGKTTFTRGIRRLLGEDV 41
                                   678***************9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); 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: 00:00:00.43
# Mc/sec: 2269.36
//
Query:       gi|116754744|ref|YP_843862.1|  [L=170]
Description: nitroreductase [Methanosaeta thermophila PT]
Scores for complete 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-38  132.7   3.6    2.7e-22   79.6   1.4    2.0  2  Nitroreductase  Nitroreductase family
    3.2e-24   85.7   0.2    3.9e-11   42.9   0.0    3.1  3  TM1586_NiRdase  Putative TM nitroreductase
  ------ inclusion threshold ------
      0.021   14.8   0.6       0.04   13.9   0.6    1.5  1  Lentiviral_Tat  Lentiviral Tat protein


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 !   79.6   1.4   4.5e-26   2.7e-22       1      66 [.       7      72 ..       7      73 .. 0.96
   2 !   56.7   0.1   5.1e-19     3e-15      84     170 .]      66     147 ..      64     147 .. 0.97

  Alignments for each domain:
  == domain 1  score: 79.6 bits;  conditional E-value: 4.5e-26
                                   HHH--B---B-S----HHHHHHHHHHHHTS--GGG---EEEEEE.-CCCHHHHHHHHHHHHHHHHT CS
                 Nitroreductase  1 irkRrSiRkFddepvpkeelekileaarraPsagnlqpwrfvvvqdkelryklaeaalelllkaea 66
                                   irkRrSiRk++++pv++e+l +ilea+r aPsa+nlq w+fvvv+dke r++laeaa++++  aea
  gi|116754744|ref|YP_843862.1|  7 IRKRRSIRKYQERPVEEEKLNRILEAGRLAPSAKNLQDWKFVVVRDKERRKRLAEAAKNQWFIAEA 72
                                   89**********************************************************987765 PP

  == domain 2  score: 56.7 bits;  conditional E-value: 5.1e-19
                                    HHHHHHSSEEEEE---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGGGGHHHHHHHHT-S..SEEE CS
                 Nitroreductase  84 qkalagapvlivivatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfdeaaeevrkllglpdeeeiv 163
                                    q ++a+apv+iv+   +++ +++ +  ++++  +d+++a+  + L+At+lGlg+c+ig+f+e++  v+k+l++p++ ++v
  gi|116754744|ref|YP_843862.1|  66 QWFIAEAPVVIVA---CGTETKYVMTCGQHTYTIDVSIAVDHMTLEATELGLGTCWIGAFYEDR--VKKILDVPENIRVV 140
                                    66899********...************************************************..************** PP

                                    EEEEEE- CS
                 Nitroreductase 164 vliavGy 170
                                    +l+++Gy
  gi|116754744|ref|YP_843862.1| 141 ALLPLGY 147
                                    ******9 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.9   1.3e-07   0.00075       1      28 [.       2      29 ..       2      30 .. 0.92
   2 !   24.2   0.0   3.6e-09   2.2e-05     157     188 ..      23      54 ..      22      71 .. 0.84
   3 !   42.9   0.0   6.5e-15   3.9e-11      68     152 ..      84     167 ..      56     169 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.3e-07
                                   -HHHHHHH--B---B--S---HHHHHHH CS
                 TM1586_NiRdase  1 nlyeaiekRhsvRkYkdealeeelleel 28
                                   +++eai+kR+s+RkY+++++eee+l+++
  gi|116754744|ref|YP_843862.1|  2 DVIEAIRKRRSIRKYQERPVEEEKLNRI 29
                                   579********************99876 PP

  == domain 2  score: 24.2 bits;  conditional E-value: 3.6e-09
                                    -HHHHHHHHHHHTS--GGG----EEE.E-SSE CS
                 TM1586_NiRdase 157 pewfkeileaarlAPsAlNqqpwrfelkddde 188
                                    +e++++ilea rlAPsA N q w+f ++ d+e
  gi|116754744|ref|YP_843862.1|  23 EEKLNRILEAGRLAPSAKNLQDWKFVVVRDKE 54 
                                    57899*********************998764 PP

  == domain 3  score: 42.9 bits;  conditional E-value: 6.5e-15
                                    EEEE----SSHHHHHHHHHHHHHHHHHHHHTT-EEEEES--SST............T-S-EEEEE-BS----.-----HH CS
                 TM1586_NiRdase  68 nyialvgekkedleekaGYygeqlvLkltalGlgtcWvggtykk.kkakvelkkgeklvivIalGyaktklveakrkple 146
                                    +y++ +g+    +   +     ++ L++t+lGlgtcW+g+ y+  +k+ ++++++ ++v+++ lGy++++  ++ rkp+e
  gi|116754744|ref|YP_843862.1|  84 KYVMTCGQHT--YTIDVSIAVDHMTLEATELGLGTCWIGAFYEDrVKKILDVPENIRVVALLPLGYPAEDPEPRPRKPVE 161
                                    4555555443..33334446789*****************9988688889****************************** PP

                                    HHBSS- CS
                 TM1586_NiRdase 147 elcevk 152
                                    e++ ++
  gi|116754744|ref|YP_843862.1| 162 EIVCYE 167
                                    *98665 PP

>> Lentiviral_Tat  Lentiviral Tat protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.6   6.8e-06      0.04      37      77 ..      40      81 ..       4      85 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.8e-06
                 Lentiviral_Tat 37 eilqrwlamlrngrlrrkvlremqkwlwrhpkapv.irncGc 77
                                   + lq w  ++  +++rrk l e+ k  w   +apv i +cG 
  gi|116754744|ref|YP_843862.1| 40 KNLQDWKFVVVRDKERRKRLAEAAKNQWFIAEAPVvIVACGT 81
                                   679*****************************9963689996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 1191.04
//
Query:       gi|116754745|ref|YP_843863.1|  [L=80]
Description: putative transcriptional regulator [Methanosaeta thermophila PT]
Scores for 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-05   23.9   0.0      5e-05   23.6   0.0    1.2  1  Rrf2            Transcriptional regulator
    5.5e-05   23.0   0.0    7.4e-05   22.6   0.0    1.1  1  TFIIE_alpha     TFIIE alpha subunit
    5.6e-05   23.0   0.1    0.00013   21.8   0.1    1.6  1  HTH_12          Ribonuclease R winged-helix domain
    9.7e-05   22.2   0.0    0.00015   21.6   0.0    1.3  1  MarR_2          MarR family
     0.0002   21.2   0.0    0.00025   20.9   0.0    1.2  1  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00021   21.1   0.0    0.00027   20.8   0.0    1.2  1  MarR            MarR family
    0.00025   21.0   0.1    0.00032   20.7   0.1    1.2  1  HemN_C          HemN C-terminal domain
    0.00034   20.6   0.0    0.00045   20.2   0.0    1.2  1  HTH_20          Helix-turn-helix domain
    0.00037   20.4   0.0    0.00045   20.2   0.0    1.3  1  HTH_45          Winged helix-turn-helix
    0.00049   19.6   0.0    0.00072   19.1   0.0    1.3  1  HTH_24          Winged helix-turn-helix DNA-binding
     0.0085   16.1   0.0       0.01   15.8   0.0    1.2  1  HTH_Crp_2       Crp-like helix-turn-helix domain
  ------ inclusion threshold ------
      0.026   14.4   0.0      0.031   14.2   0.0    1.2  1  HTH_5           Bacterial regulatory protein, arsR family
      0.033   14.1   0.0      0.053   13.5   0.0    1.3  1  HTH_11          HTH domain
       0.05   13.7   0.0      0.057   13.5   0.0    1.1  1  Replic_Relax    Replication-relaxation
      0.054   13.2   0.0       0.11   12.2   0.0    1.6  2  Ribosomal_S19e  Ribosomal protein S19e
      0.056   13.6   0.0      0.064   13.4   0.0    1.2  1  DUF2250         Uncharacterized protein conserved in archaea 
      0.063   13.4   0.0      0.089   12.9   0.0    1.2  1  DprA_WH         DprA winged helix domain


Domain annotation for each model (and alignments):
>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   4.8e-08     5e-05      21      65 ..      22      63 ..      17      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 4.8e-08
                                   STCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCE CS
                           Rrf2 21 eeeepvsseeiaerqnispsylekilakLrkaglvksvrGkgGGy 65
                                    +++p+s+++ia+   i p+ ++k+l+ L + gl++   G+   +
  gi|116754745|ref|YP_843863.1| 22 GSKGPMSADKIAKIERITPPAIRKVLQDLDERGLIEELDGA---W 63
                                   56789*******************************99997...4 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0     7e-08   7.4e-05      13      58 ..      12      57 ..       2      60 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 7e-08
                                   HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEE CS
                    TFIIE_alpha 13 eeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvk 58
                                   ++   v++vL +kg ++ + +ak  +i ++ +rk+L +L e +l++
  gi|116754745|ref|YP_843863.1| 12 KHRGRVIEVLGSKGPMSADKIAKIERITPPAIRKVLQDLDERGLIE 57
                                   34479***************************************96 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 !   21.8   0.1   1.3e-07   0.00013      11      64 ..      24      71 ..      16      72 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.3e-07
                         HTH_12 11 dkpigakeiaeeLkkrgydigeravRyrLrkleergltrrvgyagreltEkGle 64
                                   + p++a +ia+      + i   a+R  L+ l+ergl++    a  +ltE+G+e
  gi|116754745|ref|YP_843863.1| 24 KGPMSADKIAK-----IERITPPAIRKVLQDLDERGLIEELDGA-WRLTERGVE 71
                                   55777777775.....3788899*****************9999.99*****97 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   1.4e-07   0.00015       9      55 ..      16      60 ..      13      65 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.4e-07
                                   HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                         MarR_2  9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                   rv+ +Lg  ++  +++  +a+  +++++a+ ++l++L ++GL+e+ +
  gi|116754745|ref|YP_843863.1| 16 RVIEVLGSKGP--MSADKIAKIERITPPAIRKVLQDLDERGLIEELD 60
                                   89999*****9..*******************************875 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   2.3e-07   0.00025      17      56 ..      21      60 ..      16      73 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.3e-07
                                   HHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                           TrmB 17 LlklgpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                   L ++gp++ad+ia++  +  + + +vL+ L ++Gl+e  +
  gi|116754745|ref|YP_843863.1| 21 LGSKGPMSADKIAKIERITPPAIRKVLQDLDERGLIEELD 60
                                   3389********************************9866 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   2.5e-07   0.00027       7      48 ..      16      57 ..      11      60 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.5e-07
                                   HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                           MarR  7 viLrilyeqgplsvseLakklgvskstvtrvldrLekkGlie 48
                                   ++++ l ++gp+s  ++ak   ++++++ +vl  L ++Glie
  gi|116754745|ref|YP_843863.1| 16 RVIEVLGSKGPMSADKIAKIERITPPAIRKVLQDLDERGLIE 57
                                   6788999**********************************8 PP

>> HemN_C  HemN C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.1     3e-07   0.00032      38      65 ..      43      70 ..      31      71 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 3e-07
                         HemN_C 38 laaaleklqeqGLLeldggrlrltprGr 65
                                    +++l++l e+GL+e  +g +rlt+rG+
  gi|116754745|ref|YP_843863.1| 43 IRKVLQDLDERGLIEELDGAWRLTERGV 70
                                   5899***********************6 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   4.3e-07   0.00045       5      56 ..       7      58 ..       3      63 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 4.3e-07
                                   HHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                         HTH_20  5 eALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                    +L+++ R r+   L ++++++a  +a+  ++++  +++ L+ L e gL+e 
  gi|116754745|ref|YP_843863.1|  7 FVLGNKHRGRVIEVLGSKGPMSADKIAKIERITPPAIRKVLQDLDERGLIEE 58
                                   5799**********************************************96 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   4.2e-07   0.00045      36      71 ..      43      78 ..      17      80 .] 0.89

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 4.2e-07
                         HTH_45 36 lnkYLdmLvekglikkskekYvlTekGlelleklke 71
                                   ++k L+ L e+gli++ ++ ++lTe+G el ++lk+
  gi|116754745|ref|YP_843863.1| 43 IRKVLQDLDERGLIEELDGAWRLTERGVELERELKR 78
                                   6799**************************999987 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   6.9e-07   0.00072       2      48 .]      11      57 ..      10      57 .. 0.95

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 6.9e-07
                         HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                   ++ + +++e+L  ++ +s   +A+   ++p+++++ l+ L e GlI+
  gi|116754745|ref|YP_843863.1| 11 NKHRGRVIEVLGSKGPMSADKIAKIERITPPAIRKVLQDLDERGLIE 57
                                   5677899***************************************7 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 !   15.8   0.0   9.5e-06      0.01      21      54 ..      26      61 ..       4      72 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 9.5e-06
                                   EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.E.T CS
                      HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglis.r.g 54
                                   p++ + +A +  +t+  + ++l++L ++gli+   g
  gi|116754745|ref|YP_843863.1| 26 PMSADKIAKIERITPPAIRKVLQDLDERGLIEeLdG 61
                                   99******************************6424 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 ?   14.2   0.0   2.9e-05     0.031      12      46 ..      23      57 ..      11      58 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.9e-05
                                   TTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_5 12 aegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                   ++g++++  +a++ ++++++++  L  L e GL+e
  gi|116754745|ref|YP_843863.1| 23 SKGPMSADKIAKIERITPPAIRKVLQDLDERGLIE 57
                                   45*******************************97 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     5e-05     0.053       6      43 ..      18      54 ..      14      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5e-05
                         HTH_11  6 lelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg 43
                                   +e L  ++gp+s++++A+   ++  ++r+ +++L e g
  gi|116754745|ref|YP_843863.1| 18 IEVL-GSKGPMSADKIAKIERITPPAIRKVLQDLDERG 54
                                   6667.99***************************9998 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   5.4e-05     0.057       3      46 ..      20      62 ..      18      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.4e-05
                   Replic_Relax  3 lLaehrvlTtrqiarllfashratarrrLarLrelgllsrlrkr 46
                                   +L  +++++++ ia++   +  a +r++L++L e+gl++ l+  
  gi|116754745|ref|YP_843863.1| 20 VLGSKGPMSADKIAKIERITPPA-IRKVLQDLDERGLIEELDGA 62
                                   688899*****************.**************997754 PP

>> Ribosomal_S19e  Ribosomal protein S19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.87   9.2e+02     107     132 ..       6      34 ..       4      39 .. 0.61
   2 ?   12.2   0.0   0.00011      0.11      94     126 ..      41      72 ..      15      79 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.87
                                    -SS-HHHHHTHHH...HH--SS--S--XX CS
                 Ribosomal_S19e 107 glvkkekkkgrrl...tkkGqrlldriae 132
                                    g+v  +k++gr++    +kG    d+ia+
  gi|116754745|ref|YP_843863.1|   6 GFVLGNKHRGRVIevlGSKGPMSADKIAK 34 
                                    56644556677652125666677777775 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00011
                                    HTTSSS--SSS---SS-HHHHHTHHHHH--SS- CS
                 Ribosomal_S19e  94 svirkilqqLeklglvkkekkkgrrltkkGqrl 126
                                      irk+lq+L++ gl+++ ++   rlt++G +l
  gi|116754745|ref|YP_843863.1|  41 PAIRKVLQDLDERGLIEELDG-AWRLTERGVEL 72 
                                    579*************99977.999****9875 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 ?   13.4   0.0   6.1e-05     0.064      12      58 ..      16      62 ..       8      79 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.1e-05
                        DUF2250 12 kvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlervegk 58
                                   +v++ l   ++  a  iak  +i    +r++l++L e GL+e+ +g+
  gi|116754745|ref|YP_843863.1| 16 RVIEVLGSKGPMSADKIAKIERITPPAIRKVLQDLDERGLIEELDGA 62
                                   67888888888889999999**********************98764 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   8.5e-05     0.089      14      60 ..      14      61 ..      11      62 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.5e-05
                        DprA_WH 14 errvLaaLgp.ePvhvDqLvrrtglpaaevsaaLleLELaGlverlpG 60
                                   ++rv + Lg+  P++ D +++   +++ ++  +L  L   Gl+e l G
  gi|116754745|ref|YP_843863.1| 14 RGRVIEVLGSkGPMSADKIAKIERITPPAIRKVLQDLDERGLIEELDG 61
                                   79******9757********************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); 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: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 606.40
//
Query:       gi|116754746|ref|YP_843864.1|  [L=186]
Description: L-fuculose phosphate aldolase [Methanosaeta thermophila PT]
Scores for complete 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  123.0   0.0    1.4e-35  122.9   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 !  122.9   0.0   8.1e-40   1.4e-35       2     185 ..       5     174 ..       4     175 .. 0.92

  Alignments for each domain:
  == domain 1  score: 122.9 bits;  conditional E-value: 8.1e-40
                                    HHHHHHHHHHHTTSSCTTBCEEEEEETSTTEEEEEBTSS-GGGHTGGGEEEEETTSCEEEECECSSSTB-TTHHHHHHHH CS
                    Aldolase_II   2 elaeasrllarrglvegtgGniSvrvpeedsflitpsgvdfeeltaedlvvvdldsgevvegkekggkpssetplHlaiy 81 
                                    e+a+ +++l ++gl+    GniSv  + ed+++it +g  +++++++++v+v+ d ge  ++   +  +s etp+H+aiy
  gi|116754746|ref|YP_843864.1|   5 EIARFGKKLVEQGLTGSRFGNISVL-T-EDGIIITCTGSMLDDIDERQVVLVERD-GECADD---S-LASCETPVHRAIY 77 
                                    689999******************9.4.69**********************966.998833...3.59*********** PP

                                    HH-TT-SEEEEE--HHHHHHHTCCSTSCHCCSSHHHHC.HSSSEEEEES-SSTTCHHHHHHHHHHHHHS-SEEEETTTEE CS
                    Aldolase_II  82 karpdaravvHtHspaavalsalagkeglppltqeaaklllgdevpvipyaapgteelgealaealkedakavllrnHGl 161
                                    +  +darav+HtHsp+avals+l  ++ + p++ e+ ++l  +e+pv+ + ++g+e+l+ a+++al  d++a++ r+HG+
  gi|116754746|ref|YP_843864.1|  78 RS-TDARAVIHTHSPYAVALSLL--EDVVMPIDSEGIAFL--GEMPVV-DGQFGSEKLASAVSDALM-DHRACIARGHGV 150
                                    *7.9*****************77..788999*******77..78***8.6777*************8.88********** PP

                                    EEEESSHHHHHHHHHHHHHHHHHH CS
                    Aldolase_II 162 ltvGetleeAvalaetleeaaeiq 185
                                    ++ G +l++A+  a ++e++ +i+
  gi|116754746|ref|YP_843864.1| 151 FAKGGDLRDAYITASMAEHSSKIR 174
                                    ******************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 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:                        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 0.28s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1324.67
//
Query:       gi|116754747|ref|YP_843865.1|  [L=244]
Description: TPR repeat-containing protein [Methanosaeta thermophila PT]
Scores for complete 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-56  185.5   9.0    6.2e-10   38.5   0.5    6.1  6  TPR_1         Tetratricopeptide repeat
    8.9e-44  144.1  15.7    3.3e-08   33.0   0.2    6.4  6  TPR_2         Tetratricopeptide repeat
    3.3e-38  126.7   6.1    1.1e-06   28.4   0.0    6.1  6  TPR_8         Tetratricopeptide repeat
    7.7e-35  119.3  17.6      1e-10   42.1   5.6    3.6  4  TPR_16        Tetratricopeptide repeat
    1.4e-29  101.5   5.9    8.3e-08   31.8   0.1    6.1  6  TPR_11        TPR repeat
    1.2e-27   94.3  10.2    5.2e-05   23.3   0.0    7.0  7  TPR_17        Tetratricopeptide repeat
      8e-26   88.5  17.6    9.5e-07   29.1   2.6    6.1  6  TPR_14        Tetratricopeptide repeat
    4.1e-23   81.4  16.1      1e-07   32.1   0.1    4.9  4  TPR_12        Tetratricopeptide repeat
    2.1e-20   73.0   6.1    8.4e-08   32.6   0.8    3.5  3  TPR_19        Tetratricopeptide repeat
    1.6e-19   68.4  10.0     0.0074   16.2   0.0    6.3  6  TPR_7         Tetratricopeptide repeat
    7.1e-19   67.7   9.4      3e-08   33.7   0.4    4.2  4  TPR_9         Tetratricopeptide repeat
    3.6e-13   49.2   2.8       0.24   12.1   0.0    6.1  6  TPR_6         Tetratricopeptide repeat
      1e-12   47.5  19.7      0.098   12.6   0.0    6.2  6  TPR_10        Tetratricopeptide repeat
    1.1e-11   45.0   7.0      0.005   16.9   0.1    5.4  4  DUF3856       Domain of Unknown Function (DUF3856)
    7.9e-09   35.5   3.6      0.061   13.4   0.2    5.1  5  Fis1_TPR_C    Fis1 C-terminal tetratricopeptide repeat
    2.4e-08   34.1   3.1    0.00027   21.1   0.2    3.5  3  ANAPC3        Anaphase-promoting complex, cyclosome, subunit 
    3.9e-08   33.2   5.5       0.98    9.5   0.0    5.2  6  MIT           MIT (microtubule interacting and transport) dom
    3.1e-07   30.9   8.7     0.0057   17.1   1.2    3.2  3  BTAD          Bacterial transcriptional activator domain
    2.4e-06   27.5   0.1      0.011   15.8   0.0    3.3  4  SRP_TPR_like  Putative TPR-like repeat
    4.9e-06   26.7   9.9        1.7    9.5   0.7    6.3  6  TPR_4         Tetratricopeptide repeat
    1.6e-05   24.1   0.0       0.34    9.8   0.0    3.1  3  NARP1         NMDA receptor-regulated protein 1
     0.0005   19.9   0.7        2.8    7.7   0.1    4.1  4  DUF5113       Domain of unknown function (DUF5113)
    0.00061   20.0   0.6     0.0073   16.5   0.0    2.8  3  TPR_5         Tetratrico peptide repeat
  ------ inclusion threshold ------
      0.011   15.3   3.9         22    4.7   0.0    5.1  5  HTH_Bact      Helix-turn-helix bacterial domain
      0.018   13.4   0.0      0.075   11.4   0.0    1.9  2  NYD-SP12_N    Spermatogenesis-associated, N-terminal
      0.024   14.7   0.0       0.14   12.2   0.0    2.2  2  DUF627        Protein of unknown function (DUF627)
      0.032   14.2   3.4        9.2    6.1   0.0    3.8  4  Wzy_C_2       Virulence factor membrane-bound polymerase, C-t
      0.033   14.2   0.3         22    5.2   0.0    4.0  3  ANAPC5        Anaphase-promoting complex subunit 5
      0.033   13.6   0.1        5.4    6.3   0.0    2.4  2  Coatomer_E    Coatomer epsilon subunit
       0.83    9.2   3.4         59    3.2   0.0    3.9  4  SHNi-TPR      SHNi-TPR
       0.87    8.4   2.4         43    2.8   0.1    3.1  2  DUF5588       Family of unknown function (DUF5588)


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   1.7e-08     1e-05      13      34 .]      51      72 ..      50      72 .. 0.94
   2 !   34.4   0.8   2.1e-11   1.2e-08       1      34 []      73     106 ..      73     106 .. 0.96
   3 !   33.6   0.0   3.7e-11   2.2e-08       2      32 ..     108     138 ..     107     139 .. 0.95
   4 !   32.6   0.0   7.7e-11   4.5e-08       2      32 ..     145     175 ..     145     177 .. 0.95
   5 !   38.5   0.5   1.1e-12   6.2e-10       1      34 []     178     211 ..     178     211 .. 0.96
   6 !   21.1   0.0   3.3e-07   0.00019       3      29 ..     214     240 ..     212     242 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.7e-08
                                   HTT-HHHHHHHHHHHHHHSTTH CS
                          TPR_1 13 klgkydeAleyyekALelnPnn 34
                                    lg+y +Al+++e+A+el+P++
  gi|116754747|ref|YP_843865.1| 51 ALGRYSDALDAFERAIELDPSH 72
                                   69******************86 PP

  == domain 2  score: 34.4 bits;  conditional E-value: 2.1e-11
                                    HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                          TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                    a+a+ ++++a+ +l +y eAle++++ALel+P n
  gi|116754747|ref|YP_843865.1|  73 ARAWRGKAAALNNLDRYSEALEACKRALELDPFN 106
                                    89******************************65 PP

  == domain 3  score: 33.6 bits;  conditional E-value: 3.7e-11
                                    HHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                          TPR_1   2 kalynlGnayfklgkydeAleyyekALelnP 32 
                                    +++  +G a+++lg+y+eA++ y++A+el+P
  gi|116754747|ref|YP_843865.1| 108 RSWIVKGFAHHSLGEYEEAVKSYDRAIELDP 138
                                    67999*************************9 PP

  == domain 4  score: 32.6 bits;  conditional E-value: 7.7e-11
                                    HHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                          TPR_1   2 kalynlGnayfklgkydeAleyyekALelnP 32 
                                    +a++n+G+a+ +lg++++Al  y++A+ l+P
  gi|116754747|ref|YP_843865.1| 145 RAWNNRGAALDNLGRHEDALRSYDEAIMLEP 175
                                    69***************************99 PP

  == domain 5  score: 38.5 bits;  conditional E-value: 1.1e-12
                                    HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                          TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                    a+a++n+G+ +  l++yd+Al ++ekA++++P +
  gi|116754747|ref|YP_843865.1| 178 AYAWNNKGVSLVALKRYDDALLCFEKAIKIYPGY 211
                                    79******************************75 PP

  == domain 6  score: 21.1 bits;  conditional E-value: 3.3e-07
                                    HHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                          TPR_1   3 alynlGnayfklgkydeAleyyekALe 29 
                                    a+ n+G ++ +lg+++eA+e  e A +
  gi|116754747|ref|YP_843865.1| 214 AWMNRGGCLKSLGRHEEAEESLEMARR 240
                                    9*********************99965 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.1   5.3e-08     3e-05      10      34 .]      47      72 ..      38      72 .. 0.78
   2 !   21.9   1.5   2.1e-07   0.00012       1      33 [.      73     105 ..      73     106 .. 0.94
   3 !   28.3   0.0   1.8e-09   1.1e-06       3      32 ..     109     138 ..     107     139 .. 0.94
   4 !   27.7   0.1     3e-09   1.7e-06       2      32 ..     145     175 ..     144     177 .. 0.95
   5 !   33.0   0.2   5.7e-11   3.3e-08       1      33 [.     178     210 ..     178     211 .. 0.96
   6 !   15.1   0.0   3.1e-05     0.018       2      29 ..     213     240 ..     212     242 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 5.3e-08
                          TPR_2 10 ayy.klgdyeeAleafekAleldPnn 34
                                    ++ +lg+y +Al+afe+A+eldP +
  gi|116754747|ref|YP_843865.1| 47 YLMkALGRYSDALDAFERAIELDPSH 72
                                   554169******************86 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 2.1e-07
                          TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                    a+a+   + a+ +l++y eAlea+++AleldP 
  gi|116754747|ref|YP_843865.1|  73 ARAWRGKAAALNNLDRYSEALEACKRALELDPF 105
                                    789999**************************6 PP

  == domain 3  score: 28.3 bits;  conditional E-value: 1.8e-09
                          TPR_2   3 alynlGlayyklgdyeeAleafekAleldP 32 
                                     +   G a+  lg+yeeA++ +++A+eldP
  gi|116754747|ref|YP_843865.1| 109 SWIVKGFAHHSLGEYEEAVKSYDRAIELDP 138
                                    68889************************9 PP

  == domain 4  score: 27.7 bits;  conditional E-value: 3e-09
                          TPR_2   2 ealynlGlayyklgdyeeAleafekAleldP 32 
                                    +a++n+G a+ +lg++e+Al+ +++A+ l+P
  gi|116754747|ref|YP_843865.1| 145 RAWNNRGAALDNLGRHEDALRSYDEAIMLEP 175
                                    69***************************99 PP

  == domain 5  score: 33.0 bits;  conditional E-value: 5.7e-11
                          TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                    a+a++n G ++ +l++y++Al +fekA++++P+
  gi|116754747|ref|YP_843865.1| 178 AYAWNNKGVSLVALKRYDDALLCFEKAIKIYPG 210
                                    78******************************7 PP

  == domain 6  score: 15.1 bits;  conditional E-value: 3.1e-05
                          TPR_2   2 ealynlGlayyklgdyeeAleafekAle 29 
                                     a++n+G ++  lg++eeA+e +e A +
  gi|116754747|ref|YP_843865.1| 213 TAWMNRGGCLKSLGRHEEAEESLEMARR 240
                                    59********************998866 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.3e-06   0.00077       1      34 []      38      72 ..      38      72 .. 0.93
   2 !   17.7   0.1   4.9e-06    0.0028       2      34 .]      74     106 ..      73     106 .. 0.88
   3 !   28.4   0.0   1.8e-09   1.1e-06       2      32 ..     108     138 ..     107     138 .. 0.97
   4 !   20.5   0.0   6.4e-07   0.00037       2      33 ..     145     176 ..     145     177 .. 0.96
   5 !   23.2   0.2   8.6e-08     5e-05       1      32 [.     178     209 ..     178     211 .. 0.94
   6 !   15.3   0.0   2.9e-05     0.017       3      25 ..     214     236 ..     213     238 .. 0.95

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.3e-06
                                   CCHHHHHHHHH.HHTT-HHHHHHHHHHHHHHHHH. CS
                          TPR_8  1 aeayynlgsiy.lklgdyeeAkeyyekaleldpdn 34
                                   a++++  g+ + + lg+y  A  ++e+a+eldp++
  gi|116754747|ref|YP_843865.1| 38 ADLWVARGRYLmKALGRYSDALDAFERAIELDPSH 72
                                   689999**8888*********************86 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 4.9e-06
                                    CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                          TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                    +a+  ++ ++ +l +y eA e++++aleldp n
  gi|116754747|ref|YP_843865.1|  74 RAWRGKAAALNNLDRYSEALEACKRALELDPFN 106
                                    6666788899*********************75 PP

  == domain 3  score: 28.4 bits;  conditional E-value: 1.8e-09
                                    CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                          TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldp 32 
                                    +++  +g ++++lg+yeeA+++y +a+eldp
  gi|116754747|ref|YP_843865.1| 108 RSWIVKGFAHHSLGEYEEAVKSYDRAIELDP 138
                                    89****************************9 PP

  == domain 4  score: 20.5 bits;  conditional E-value: 6.4e-07
                                    CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                          TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                    +a++n g ++++lg++e A  +y +a+ l+p 
  gi|116754747|ref|YP_843865.1| 145 RAWNNRGAALDNLGRHEDALRSYDEAIMLEPF 176
                                    79***************************996 PP

  == domain 5  score: 23.2 bits;  conditional E-value: 8.6e-08
                                    CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                          TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldp 32 
                                    a a++n+g  +  l++y+ A  ++eka+++ p
  gi|116754747|ref|YP_843865.1| 178 AYAWNNKGVSLVALKRYDDALLCFEKAIKIYP 209
                                    569***************************99 PP

  == domain 6  score: 15.3 bits;  conditional E-value: 2.9e-05
                                    HHHHHHHHHHHTT-HHHHHHHHH CS
                          TPR_8   3 ayynlgsiylklgdyeeAkeyye 25 
                                    a++n g ++++lg++eeA+e++e
  gi|116754747|ref|YP_843865.1| 214 AWMNRGGCLKSLGRHEEAEESLE 236
                                    8********************98 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   5.6   1.7e-13     1e-10      10      67 ..      52     106 ..      38     107 .. 0.93
   2 !   34.3   2.5   4.6e-11   2.7e-08      10      61 ..     120     171 ..     117     180 .. 0.92
   3 !   30.7   0.0   6.2e-10   3.6e-07      10      66 ..     157     210 ..     156     210 .. 0.97
   4 !   36.9   0.0   7.4e-12   4.3e-09       3      61 ..     184     239 ..     182     241 .. 0.93

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 1.7e-13
                         TPR_16  10 agdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                    +g+y dA+ a+e+a+++d   P +a+A+ +++ a+  + r+ eA++++++al+ +p++
  gi|116754747|ref|YP_843865.1|  52 LGRYSDALDAFERAIELD---PSHARAWRGKAAALNNLDRYSEALEACKRALELDPFN 106
                                    699***************...***********************************97 PP

  == domain 2  score: 34.3 bits;  conditional E-value: 4.6e-11
                         TPR_16  10 agdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraal 61 
                                    +g+y++A++ +++a+++dp   da++A++++g a+  +gr+++A+  y++a+
  gi|116754747|ref|YP_843865.1| 120 LGEYEEAVKSYDRAIELDPMGQDARRAWNNRGAALDNLGRHEDALRSYDEAI 171
                                    699***************99999**********************9999986 PP

  == domain 3  score: 30.7 bits;  conditional E-value: 6.2e-10
                         TPR_16  10 agdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                    +g+ +dA++ +++a+ +    P++a A++++g+++ +++r+++A+  +++a++ +p+
  gi|116754747|ref|YP_843865.1| 157 LGRHEDALRSYDEAIMLE---PFDAYAWNNKGVSLVALKRYDDALLCFEKAIKIYPG 210
                                    79****************...*********************************996 PP

  == domain 4  score: 36.9 bits;  conditional E-value: 7.4e-12
                         TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraal 61 
                                    ++ +++++++yddA+  +e a+k +   P  + A++++g ++  +gr++eA++ ++ a 
  gi|116754747|ref|YP_843865.1| 184 KGVSLVALKRYDDALLCFEKAIKIY---PGYWTAWMNRGGCLKSLGRHEEAEESLEMAR 239
                                    577899*******************...************************9888875 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   5.3e-08   3.1e-05       6      38 ..      51      83 ..      48      87 .. 0.91
   2 !   13.8   0.0   5.9e-05     0.034       9      42 .]      88     121 ..      82     121 .. 0.90
   3 !   31.8   0.1   1.4e-10   8.3e-08       3      41 ..     116     157 ..     114     158 .. 0.79
   4 !   20.3   0.0   5.7e-07   0.00033       7      39 ..     157     189 ..     156     192 .. 0.92
   5 !   15.2   0.0   2.2e-05     0.013       4      35 ..     188     219 ..     187     226 .. 0.90
   6 ?   -0.8   0.0       2.2   1.3e+03       6      17 ..     224     235 ..     221     241 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 5.3e-08
                         TPR_11  6 eqGkyeeAieaYkkAlkldPdnaeayynLGlay 38
                                   ++G+y +A+ a+++A++ldP+ a+a+ + ++a+
  gi|116754747|ref|YP_843865.1| 51 ALGRYSDALDAFERAIELDPSHARAWRGKAAAL 83
                                   68***********************99888876 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 5.9e-05
                         TPR_11   9 kyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                    +y eA+ea k+Al+ldP n + +   G+a++ +G
  gi|116754747|ref|YP_843865.1|  88 RYSEALEACKRALELDPFNSRSWIVKGFAHHSLG 121
                                    8****************99999999999999887 PP

  == domain 3  score: 31.8 bits;  conditional E-value: 1.4e-10
                         TPR_11   3 ayyeqGkyeeAieaYkkAlkldP...dnaeayynLGlayykq 41 
                                    a +++G+yeeA+++Y +A++ldP   d  +a++n+G+a+ ++
  gi|116754747|ref|YP_843865.1| 116 AHHSLGEYEEAVKSYDRAIELDPmgqDARRAWNNRGAALDNL 157
                                    6799*******************4434455788888887655 PP

  == domain 4  score: 20.3 bits;  conditional E-value: 5.7e-07
                         TPR_11   7 qGkyeeAieaYkkAlkldPdnaeayynLGlayy 39 
                                    +G+ e+A+ +Y +A+ l P +a a++n G+ + 
  gi|116754747|ref|YP_843865.1| 157 LGRHEDALRSYDEAIMLEPFDAYAWNNKGVSLV 189
                                    69***************************8765 PP

  == domain 5  score: 15.2 bits;  conditional E-value: 2.2e-05
                         TPR_11   4 yyeqGkyeeAieaYkkAlkldPdnaeayynLG 35 
                                    ++++ +y++A+ +++kA+k+ P + +a+ n+G
  gi|116754747|ref|YP_843865.1| 188 LVALKRYDDALLCFEKAIKIYPGYWTAWMNRG 219
                                    67899***********************9999 PP

  == domain 6  score: -0.8 bits;  conditional E-value: 2.2
                         TPR_11   6 eqGkyeeAieaY 17 
                                    ++G+ eeA e++
  gi|116754747|ref|YP_843865.1| 224 SLGRHEEAEESL 235
                                    79*****97666 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.085        49      12      33 ..      37      59 ..      37      60 .. 0.84
   2 !   20.1   0.1   9.9e-07   0.00057       2      34 .]      62      94 ..      61      94 .. 0.95
   3 !   20.9   0.0   5.6e-07   0.00032       2      33 ..      96     127 ..      95     128 .. 0.95
   4 ?    1.8   0.0      0.66   3.8e+02       2      10 ..     130     138 ..     129     138 .. 0.95
   5 !    9.6   0.1    0.0022       1.3      15      33 ..     146     164 ..     145     165 .. 0.93
   6 !   14.2   0.1   7.7e-05     0.045       2      32 ..     167     197 ..     166     198 .. 0.93
   7 !   23.3   0.0   8.9e-08   5.2e-05       1      34 []     200     233 ..     200     233 .. 0.97

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.085
                         TPR_17 12 nadaynnLAell.lknGdlmtAr 33
                                   nad++  ++++l + +G++ +A+
  gi|116754747|ref|YP_843865.1| 37 NADLWVARGRYLmKALGRYSDAL 59
                                   9*********8835779998886 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 9.9e-07
                         TPR_17  2 ylkaleldPnnadaynnLAelllknGdlmtArq 34
                                   +++a+eldP++a a+  +A +l ++ ++ +A++
  gi|116754747|ref|YP_843865.1| 62 FERAIELDPSHARAWRGKAAALNNLDRYSEALE 94
                                   9***************************99975 PP

  == domain 3  score: 20.9 bits;  conditional E-value: 5.6e-07
                         TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                    +++aleldP n+ ++  ++ +++++G++++A+
  gi|116754747|ref|YP_843865.1|  96 CKRALELDPFNSRSWIVKGFAHHSLGEYEEAV 127
                                    89****************************97 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.66
                         TPR_17   2 ylkaleldP 10 
                                    y +a+eldP
  gi|116754747|ref|YP_843865.1| 130 YDRAIELDP 138
                                    99******9 PP

  == domain 5  score: 9.6 bits;  conditional E-value: 0.0022
                         TPR_17  15 aynnLAelllknGdlmtAr 33 
                                    a+nn++ +l ++G++++A+
  gi|116754747|ref|YP_843865.1| 146 AWNNRGAALDNLGRHEDAL 164
                                    8***************996 PP

  == domain 6  score: 14.2 bits;  conditional E-value: 7.7e-05
                         TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtA 32 
                                    y +a+ l+P +a+a+nn+++ l  ++++++A
  gi|116754747|ref|YP_843865.1| 167 YDEAIMLEPFDAYAWNNKGVSLVALKRYDDA 197
                                    8889999*********************999 PP

  == domain 7  score: 23.3 bits;  conditional E-value: 8.9e-08
                         TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                    +++ka++++P ++ a+ n++ +l+++G++++A++
  gi|116754747|ref|YP_843865.1| 200 CFEKAIKIYPGYWTAWMNRGGCLKSLGRHEEAEE 233
                                    89******************************96 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   2.6   1.7e-09   9.5e-07       2      43 ..      39      81 ..      38      82 .. 0.91
   2 !   19.3   0.3   2.3e-06    0.0013       2      42 ..      74     114 ..      74     116 .. 0.91
   3 !   16.6   0.0   1.8e-05      0.01       9      38 ..     115     147 ..     107     151 .. 0.83
   4 !   17.1   0.4   1.2e-05     0.007       2      39 ..     145     182 ..     144     187 .. 0.91
   5 !   15.2   0.0   4.9e-05     0.029      11      40 ..     188     217 ..     184     221 .. 0.91
   6 ?    5.9   0.1     0.047        27      11      29 ..     222     240 ..     216     243 .. 0.85

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 1.7e-09
                         TPR_14  2 eallalaeall.alGdpdeAiallrralalaPddaeawlllaq 43
                                   +++ a++++l+ alG++ +A+++++ra++l+P++a+aw+  a 
  gi|116754747|ref|YP_843865.1| 39 DLWVARGRYLMkALGRYSDALDAFERAIELDPSHARAWRGKAA 81
                                   79******986489************************98875 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 2.3e-06
                         TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                    +a++  a+al +l+++ eA+++++ral+l+P + + w+  +
  gi|116754747|ref|YP_843865.1|  74 RAWRGKAAALNNLDRYSEALEACKRALELDPFNSRSWIVKG 114
                                    589999*************************9999888766 PP

  == domain 3  score: 16.6 bits;  conditional E-value: 1.8e-05
                         TPR_14   9 eallalGdpdeAiallrralalaP...ddaeaw 38 
                                     a+  lG+++eA++ ++ra++l+P   d ++aw
  gi|116754747|ref|YP_843865.1| 115 FAHHSLGEYEEAVKSYDRAIELDPmgqDARRAW 147
                                    57889******************9885556777 PP

  == domain 4  score: 17.1 bits;  conditional E-value: 1.2e-05
                         TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawl 39 
                                    +a+  +++al +lG++++A++ +++a+ l P da aw 
  gi|116754747|ref|YP_843865.1| 145 RAWNNRGAALDNLGRHEDALRSYDEAIMLEPFDAYAWN 182
                                    688889*************************9999995 PP

  == domain 5  score: 15.2 bits;  conditional E-value: 4.9e-05
                         TPR_14  11 llalGdpdeAiallrralalaPddaeawll 40 
                                    l al ++d+A+ ++++a++ +P+ ++aw+ 
  gi|116754747|ref|YP_843865.1| 188 LVALKRYDDALLCFEKAIKIYPGYWTAWMN 217
                                    7899************************86 PP

  == domain 6  score: 5.9 bits;  conditional E-value: 0.047
                         TPR_14  11 llalGdpdeAiallrrala 29 
                                    l  lG+++eA++ l+ a +
  gi|116754747|ref|YP_843865.1| 222 LKSLGRHEEAEESLEMARR 240
                                    6789***********9865 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.1   0.00013     0.077      50      76 ..      43      70 ..      28      71 .. 0.78
   2 !   13.7   0.8   9.7e-05     0.056       3      32 ..      73     102 ..      71     104 .. 0.93
   3 !   29.8   0.9   9.5e-10   5.5e-07       9      72 ..     113     171 ..     107     173 .. 0.92
   4 !   32.1   0.1   1.7e-10     1e-07       4      74 ..     179     241 ..     176     241 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00013
                         TPR_12 50 nLgrly.ralgryeeAlelleealaiae 76
                                   + gr++  algry +Al+++e+a+++++
  gi|116754747|ref|YP_843865.1| 43 ARGRYLmKALGRYSDALDAFERAIELDP 70
                                   5566755789999999999999999875 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 9.7e-05
                         TPR_12   3 atalnnlaavlrrlgrydeAlellekalei 32 
                                    a+a++  aa+l+ l ry eAle +++ale+
  gi|116754747|ref|YP_843865.1|  73 ARAWRGKAAALNNLDRYSEALEACKRALEL 102
                                    789999**********************97 PP

  == domain 3  score: 29.8 bits;  conditional E-value: 9.5e-10
                         TPR_12   9 laavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeal 72 
                                     + +++ lg+y+eA + +++a+e+    + ++   + ++ +n g +++ lgr+e+Al+ + ea+
  gi|116754747|ref|YP_843865.1| 113 KGFAHHSLGEYEEAVKSYDRAIELD---PMGQD--ARRAWNNRGAALDNLGRHEDALRSYDEAI 171
                                    588999*******************...88887..9**************************97 PP

  == domain 4  score: 32.1 bits;  conditional E-value: 1.7e-10
                         TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                     a+nn ++ l +l+ryd+Al ++eka+ i+     p + +t  +  n g ++  lgr+eeA+e le a +i
  gi|116754747|ref|YP_843865.1| 179 YAWNNKGVSLVALKRYDDALLCFEKAIKIY-----PGY-WT--AWMNRGGCLKSLGRHEEAEESLEMARRI 241
                                    5899**************************.....544.55..889*********************9986 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.8   1.5e-10   8.4e-08       5      59 ..      53     107 ..      50     113 .. 0.94
   2 !   12.9   0.6   0.00021      0.12       5      62 ..     121     181 ..     118     185 .. 0.90
   3 !   28.0   0.0   4.1e-09   2.4e-06       2      52 ..     189     239 ..     188     242 .. 0.93

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 1.5e-10
                         TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdda 59 
                                    g+y +Al+++e+a++ dp +a+a+ + A al +l ++ eA +++++++e dp ++
  gi|116754747|ref|YP_843865.1|  53 GRYSDALDAFERAIELDPSHARAWRGKAAALNNLDRYSEALEACKRALELDPFNS 107
                                    99************************************************99765 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00021
                         TPR_19   5 gdyaeAlalleqalqedpknaearl...lLAeallalgqldeAealLdalpeedpddarya 62 
                                    g y+eA++ + +a++ dp  ++ar    +   al +lg+ ++A +  d++   +p da+++
  gi|116754747|ref|YP_843865.1| 121 GEYEEAVKSYDRAIELDPMGQDARRawnNRGAALDNLGRHEDALRSYDEAIMLEPFDAYAW 181
                                    89*****************88888865577********************99999999887 PP

  == domain 3  score: 28.0 bits;  conditional E-value: 4.1e-09
                         TPR_19   2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalp 52 
                                    +a ++y++Al  +e+a++ +p+++ a+++   +l +lg+ +eAe+ L+ + 
  gi|116754747|ref|YP_843865.1| 189 VALKRYDDALLCFEKAIKIYPGYWTAWMNRGGCLKSLGRHEEAEESLEMAR 239
                                    67789******************************************9875 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.1   6.4e-05     0.037       9      35 ..      48      73 ..      38      74 .. 0.83
   2 !   10.2   0.0    0.0011      0.64      10      34 ..      84     106 ..      78     108 .. 0.82
   3 !   16.2   0.0   1.3e-05    0.0074       8      32 ..     116     138 ..     115     142 .. 0.88
   4 !   14.5   0.1   4.8e-05     0.028       1      35 [.     146     178 ..     146     179 .. 0.94
   5 !    8.8   0.0    0.0029       1.7       1      28 [.     180     205 ..     180     208 .. 0.90
   6 ?    6.0   0.0     0.023        13       2      24 ..     215     237 ..     214     242 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.4e-05
                          TPR_7  9 ysr.lGdyeeAielyeqsLaltkdpeda 35
                                     + lG+y++A++ +e+  a++ dp++a
  gi|116754747|ref|YP_843865.1| 48 LMKaLGRYSDALDAFER--AIELDPSHA 73
                                   55559************..***999987 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0011
                          TPR_7  10 srlGdyeeAielyeqsLaltkdped 34 
                                     +l +y+eA+e +++  al+ dp++
  gi|116754747|ref|YP_843865.1|  84 NNLDRYSEALEACKR--ALELDPFN 106
                                    57889**********..88888876 PP

  == domain 3  score: 16.2 bits;  conditional E-value: 1.3e-05
                          TPR_7   8 lysrlGdyeeAielyeqsLaltkdp 32 
                                    ++++lG+yeeA++ y +  a++ dp
  gi|116754747|ref|YP_843865.1| 116 AHHSLGEYEEAVKSYDR--AIELDP 138
                                    699**************..777665 PP

  == domain 4  score: 14.5 bits;  conditional E-value: 4.8e-05
                          TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdpeda 35 
                                    a++n + +  +lG++e+A++ y +  a+  +p+da
  gi|116754747|ref|YP_843865.1| 146 AWNNRGAALDNLGRHEDALRSYDE--AIMLEPFDA 178
                                    799*********************..*99999986 PP

  == domain 5  score: 8.8 bits;  conditional E-value: 0.0029
                          TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLal 28 
                                    a++n ++  ++l +y++A+ ++e+  a+
  gi|116754747|ref|YP_843865.1| 180 AWNNKGVSLVALKRYDDALLCFEK--AI 205
                                    78999*******************..54 PP

  == domain 6  score: 6.0 bits;  conditional E-value: 0.023
                          TPR_7   2 LlnLarlysrlGdyeeAielyeq 24 
                                    + n + +  +lG++eeA+e +e 
  gi|116754747|ref|YP_843865.1| 215 WMNRGGCLKSLGRHEEAEESLEM 237
                                    5677888999*********9997 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   2.4   5.2e-09     3e-06       9      60 ..      53     104 ..      43     109 .. 0.92
   2 !   33.7   0.4   5.2e-11     3e-08       6      68 ..      84     146 ..      79     148 .. 0.93
   3 !   16.4   0.0   1.3e-05    0.0075       9      60 ..     158     209 ..     151     210 .. 0.94
   4 !   14.7   0.0   4.2e-05     0.025       9      53 ..     192     236 ..     187     241 .. 0.94

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 5.2e-09
                          TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap 60 
                                     +++ al + er + l+P +++ +r  + +l  l+++s+Al++  ++l+l+p
  gi|116754747|ref|YP_843865.1|  53 GRYSDALDAFERAIELDPSHARAWRGKAAALNNLDRYSEALEACKRALELDP 104
                                    68899*********************************************99 PP

  == domain 2  score: 33.7 bits;  conditional E-value: 5.2e-11
                          TPR_9   6 ireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapdaeai 68 
                                     + +++++al+++ r l l+P   + +   G++++ lG +++A++  +++++l+p  +da+++
  gi|116754747|ref|YP_843865.1|  84 NNLDRYSEALEACKRALELDPFNSRSWIVKGFAHHSLGEYEEAVKSYDRAIELDPMGQDARRA 146
                                    46699******************************************************9986 PP

  == domain 3  score: 16.4 bits;  conditional E-value: 1.3e-05
                          TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap 60 
                                     ++e al+ ++  ++l P d++ +   G+ l+ l ++  Al ++e ++ + p
  gi|116754747|ref|YP_843865.1| 158 GRHEDALRSYDEAIMLEPFDAYAWNNKGVSLVALKRYDDALLCFEKAIKIYP 209
                                    6899******************************************998877 PP

  == domain 4  score: 14.7 bits;  conditional E-value: 4.2e-05
                          TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLe 53 
                                    ++++ al + e  + + P  +  ++ RG +l  lG+ ++A + Le
  gi|116754747|ref|YP_843865.1| 192 KRYDDALLCFEKAIKIYPGYWTAWMNRGGCLKSLGRHEEAEESLE 236
                                    7999**************************************998 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   0.00044      0.25       9      32 ..      48      71 ..      39      72 .. 0.83
   2 ?    3.1   0.1       0.3   1.7e+02      10      31 ..      83     104 ..      73     105 .. 0.75
   3 !    8.7   0.0    0.0049       2.8       7      31 ..     114     138 ..     113     138 .. 0.87
   4 ?    2.8   0.0      0.39   2.2e+02       7      27 ..     151     171 ..     149     171 .. 0.83
   5 !   12.1   0.0   0.00041      0.24       7      32 ..     185     210 ..     183     211 .. 0.92
   6 ?    4.4   0.0      0.12        67       2      27 ..     214     239 ..     213     241 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00044
                                   HHHHHHHHHHHHHHHHHHHHH-TT CS
                          TPR_6  9 syrklgdtdkAlealerlikeYPd 32
                                   ++++lg++++Al+a+er i+  P 
  gi|116754747|ref|YP_843865.1| 48 LMKALGRYSDALDAFERAIELDPS 71
                                   45568***************9986 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.3
                                    HHHHHHHHHHHHHHHHHHHH-T CS
                          TPR_6  10 yrklgdtdkAlealerlikeYP 31 
                                    + +l+++++Alea +r ++  P
  gi|116754747|ref|YP_843865.1|  83 LNNLDRYSEALEACKRALELDP 104
                                    33468999*****999998766 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0049
                                    HHHHHHHHHHHHHHHHHHHHHHH-T CS
                          TPR_6   7 alsyrklgdtdkAlealerlikeYP 31 
                                    + ++ +lg++++A++ ++r i+  P
  gi|116754747|ref|YP_843865.1| 114 GFAHHSLGEYEEAVKSYDRAIELDP 138
                                    56788899*************9766 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.39
                                    HHHHHHHHHHHHHHHHHHHHH CS
                          TPR_6   7 alsyrklgdtdkAlealerli 27 
                                    + ++ +lg++++Al+ +++ i
  gi|116754747|ref|YP_843865.1| 151 GAALDNLGRHEDALRSYDEAI 171
                                    67888999********99865 PP

  == domain 5  score: 12.1 bits;  conditional E-value: 0.00041
                                    HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                          TPR_6   7 alsyrklgdtdkAlealerlikeYPd 32 
                                    + s+ +l+++d+Al  +e+ ik YP+
  gi|116754747|ref|YP_843865.1| 185 GVSLVALKRYDDALLCFEKAIKIYPG 210
                                    78899999*****************6 PP

  == domain 6  score: 4.4 bits;  conditional E-value: 0.12
                                    HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          TPR_6   2 AlyklalsyrklgdtdkAlealerli 27 
                                    A ++++ ++++lg++++A e le  +
  gi|116754747|ref|YP_843865.1| 214 AWMNRGGCLKSLGRHEEAEESLEMAR 239
                                    678889999**99*******999865 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.2    0.0048       2.8      13      30 ..      50      67 ..      44      68 .. 0.85
   2 !    8.1   0.5    0.0042       2.5       9      30 ..      80     101 ..      79     102 .. 0.93
   3 !   10.8   0.0    0.0006      0.35       9      30 ..     114     135 ..     114     136 .. 0.92
   4 !   12.3   0.7   0.00021      0.12       6      29 ..     148     171 ..     145     171 .. 0.96
   5 !   12.6   0.0   0.00017     0.098       6      32 ..     182     208 ..     178     208 .. 0.94
   6 ?    5.7   0.1     0.025        14      12      28 ..     222     238 ..     216     242 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0048
                         TPR_10 13 rqrgrydeAealleeala 30
                                    ++gry +A++ +e+a++
  gi|116754747|ref|YP_843865.1| 50 KALGRYSDALDAFERAIE 67
                                   789*************98 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0042
                         TPR_10   9 analrqrgrydeAealleeala 30 
                                    a+al ++ ry eA++ +++al+
  gi|116754747|ref|YP_843865.1|  80 AAALNNLDRYSEALEACKRALE 101
                                    789*****************98 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.0006
                         TPR_10   9 analrqrgrydeAealleeala 30 
                                    + a++++g+y+eA++ +++a++
  gi|116754747|ref|YP_843865.1| 114 GFAHHSLGEYEEAVKSYDRAIE 135
                                    6799****************98 PP

  == domain 4  score: 12.3 bits;  conditional E-value: 0.00021
                         TPR_10   6 nNLanalrqrgrydeAealleeal 29 
                                    nN ++al ++gr+++A++ ++ea+
  gi|116754747|ref|YP_843865.1| 148 NNRGAALDNLGRHEDALRSYDEAI 171
                                    9*********************97 PP

  == domain 5  score: 12.6 bits;  conditional E-value: 0.00017
                         TPR_10   6 nNLanalrqrgrydeAealleealair 32 
                                    nN ++ l +++ryd+A+  +e+a+ i+
  gi|116754747|ref|YP_843865.1| 182 NNKGVSLVALKRYDDALLCFEKAIKIY 208
                                    9999********************998 PP

  == domain 6  score: 5.7 bits;  conditional E-value: 0.025
                         TPR_10  12 lrqrgrydeAealleea 28 
                                    l ++gr++eAe+ le a
  gi|116754747|ref|YP_843865.1| 222 LKSLGRHEEAEESLEMA 238
                                    6789*******998876 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.099        57     110     129 ..      49      68 ..      32      72 .. 0.78
   2 !   14.4   0.2   5.2e-05      0.03      57     129 ..      75     136 ..      69     139 .. 0.87
   3 !   16.9   0.1   8.7e-06     0.005      63     126 ..     115     170 ..     103     174 .. 0.78
   4 !   14.4   0.2   5.3e-05     0.031      45     127 ..     168     239 ..     166     242 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.099
                                    HHHTT-HHHHHHHHHHHHHH CS
                        DUF3856 110 leelGrkdealkafrmagem 129
                                    ++ lGr+++al+af+ a e+
  gi|116754747|ref|YP_843865.1|  49 MKALGRYSDALDAFERAIEL 68 
                                    57789999999999998885 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 5.2e-05
                                    HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                        DUF3856  57 chaglsealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagem 129
                                    ++ g + al +l ry eale+ ++al       el+  + + Wi     ++ a ++lG ++ea+k++  a e+
  gi|116754747|ref|YP_843865.1|  75 AWRGKAAALNNLDRYSEALEACKRAL-------ELDPFNSRSWIV----KGFAHHSLGEYEEAVKSYDRAIEL 136
                                    56778999**************9999.......688888889*95....89999*************999885 PP

  == domain 3  score: 16.9 bits;  conditional E-value: 8.7e-06
                                    HHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                        DUF3856  63 ealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrma 126
                                     a   lg+y+ea++s d+a++       + qd  + W     +r++al++lGr+++al+++  a
  gi|116754747|ref|YP_843865.1| 115 FAHHSLGEYEEAVKSYDRAIEL----DPMGQDARRAW----NNRGAALDNLGRHEDALRSYDEA 170
                                    5778899999999999998864....34556766666....79*****************9877 PP

  == domain 4  score: 14.4 bits;  conditional E-value: 5.3e-05
                                    TS---HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHH CS
                        DUF3856  45 eeafdheGfdalchaglsealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafr 124
                                    +ea   e fda ++     +l+ l+ryd+al + +ka++ +             W +a ++r+ +l++lGr++ea ++++
  gi|116754747|ref|YP_843865.1| 168 DEAIMLEPFDAYAWNNKGVSLVALKRYDDALLCFEKAIKIYP----------GYW-TAWMNRGGCLKSLGRHEEAEESLE 236
                                    68888999******************************9885..........246.456799999999999999999999 PP

                                    HHH CS
                        DUF3856 125 mag 127
                                    ma 
  gi|116754747|ref|YP_843865.1| 237 MAR 239
                                    885 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.042        24      14      33 ..      52      71 ..      50      75 .. 0.92
   2 !   13.4   0.2   0.00011     0.061      11      34 ..      83     106 ..      80     108 .. 0.87
   3 !    9.8   0.0    0.0014      0.84       9      36 ..     115     142 ..     114     145 .. 0.87
   4 ?    1.1   0.0      0.74   4.3e+02      14      32 ..     157     175 ..     152     180 .. 0.88
   5 ?    1.7   0.0      0.47   2.7e+02      14      33 ..     191     210 ..     186     212 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.042
                                   HT-HHHHHHHHHHHHHHTTS CS
                     Fis1_TPR_C 14 lgeYseArryvdalLeiEPe 33
                                   lg+Ys+A+   ++ +e++P+
  gi|116754747|ref|YP_843865.1| 52 LGRYSDALDAFERAIELDPS 71
                                   89****************97 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00011
                                    HHHHT-HHHHHHHHHHHHHHTTS- CS
                     Fis1_TPR_C  11 hyklgeYseArryvdalLeiEPen 34 
                                       l +YseA++ +++ Le++P n
  gi|116754747|ref|YP_843865.1|  83 LNNLDRYSEALEACKRALELDPFN 106
                                    567899****************99 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.0014
                                    HHHHHHT-HHHHHHHHHHHHHHTTS-HH CS
                     Fis1_TPR_C   9 lGhyklgeYseArryvdalLeiEPenrQ 36 
                                    ++h  lgeY+eA +  d+ +e++P  + 
  gi|116754747|ref|YP_843865.1| 115 FAHHSLGEYEEAVKSYDRAIELDPMGQD 142
                                    68899******************97655 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.74
                                    HT-HHHHHHHHHHHHHHTT CS
                     Fis1_TPR_C  14 lgeYseArryvdalLeiEP 32 
                                    lg++++A+r  d  + +EP
  gi|116754747|ref|YP_843865.1| 157 LGRHEDALRSYDEAIMLEP 175
                                    899*********9999999 PP

  == domain 5  score: 1.7 bits;  conditional E-value: 0.47
                                    HT-HHHHHHHHHHHHHHTTS CS
                     Fis1_TPR_C  14 lgeYseArryvdalLeiEPe 33 
                                    l++Y++A+ + +  ++i P+
  gi|116754747|ref|YP_843865.1| 191 LKRYDDALLCFEKAIKIYPG 210
                                    899*******9999999885 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 ?    3.1   0.0      0.19   1.1e+02      68      81 ..      51      64 ..      41      65 .. 0.85
   2 !   21.1   0.2   4.7e-07   0.00027       3      80 ..      53     131 ..      51     133 .. 0.93
   3 !   11.4   0.2   0.00049      0.28       4      80 ..     159     236 ..     156     238 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.19
                                   HTT-HHHHHHHH-S CS
                         ANAPC3 68 kLkkyeeAiaaLek 81
                                   +L++y +A++a+e+
  gi|116754747|ref|YP_843865.1| 51 ALGRYSDALDAFER 64
                                   68*********997 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 4.7e-07
                                    T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                         ANAPC3   3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                    ++y +A+  +er+ + ++ ++ +   +A +l ++ +y +A+e +++a +l++ + +++++++ +   L++yeeA++ ++
  gi|116754747|ref|YP_843865.1|  53 GRYSDALDAFERAIELDPSHARAWRGKAAALNNLDRYSEALEACKRAlELDPFNSRSWIVKGFAHHSLGEYEEAVKSYD 131
                                    58999*********8888888888889***********************************************99876 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00049
                                    -HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                         ANAPC3   4 nyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                    ++++A+  ++ +   e+ ++++   ++ +l  +++y+ A+  ++ka k+++    +++  + cl  L+++eeA+  Le
  gi|116754747|ref|YP_843865.1| 159 RHEDALRSYDEAIMLEPFDAYAWNNKGVSLVALKRYDDALLCFEKAiKIYPGYWTAWMNRGGCLKSLGRHEEAEESLE 236
                                    6788888888888788888888888999999999************999999999999999************99998 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0      0.01       5.9      22      53 ..      50      80 ..      46      85 .. 0.81
   2 ?    3.4   0.3      0.14        82      10      33 ..      79     102 ..      71     102 .. 0.81
   3 ?    2.3   0.1      0.31   1.8e+02      25      39 ..      87     101 ..      82     109 .. 0.63
   4 !    9.5   0.0    0.0017      0.98      17      33 ..     120     136 ..     111     136 .. 0.90
   5 !    8.9   0.0    0.0027       1.5      11      31 ..     151     171 ..     148     173 .. 0.88
   6 ?    3.0   0.0      0.18     1e+02      23      39 ..     190     206 ..     182     210 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.01
                            MIT 22 eAlelYkealelLlqalkekneerrellreki 53
                                   +Al  Y++al+ +  a+   ++++  ++r k+
  gi|116754747|ref|YP_843865.1| 50 KALGRYSDALDAFERAIE-LDPSHARAWRGKA 80
                                   69999********99996.6777777777765 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.14
                            MIT  10 kAveeDnagnyeeAlelYkealel 33 
                                    kA+ + n   y+eAle+ k alel
  gi|116754747|ref|YP_843865.1|  79 KAAALNNLDRYSEALEACKRALEL 102
                                    677888888899999988888875 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.31
                            MIT  25 elYkealelLlqalk 39 
                                    + Y+eale ++ al 
  gi|116754747|ref|YP_843865.1|  87 DRYSEALEACKRALE 101
                                    456666666555554 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.0017
                            MIT  17 agnyeeAlelYkealel 33 
                                     g+yeeA++ Y  a+el
  gi|116754747|ref|YP_843865.1| 120 LGEYEEAVKSYDRAIEL 136
                                    699************96 PP

  == domain 5  score: 8.9 bits;  conditional E-value: 0.0027
                            MIT  11 AveeDnagnyeeAlelYkeal 31 
                                     + +Dn g  e+Al+ Y ea+
  gi|116754747|ref|YP_843865.1| 151 GAALDNLGRHEDALRSYDEAI 171
                                    5789****************8 PP

  == domain 6  score: 3.0 bits;  conditional E-value: 0.18
                            MIT  23 AlelYkealelLlqalk 39 
                                    Al+ Y +al  + +a+k
  gi|116754747|ref|YP_843865.1| 190 ALKRYDDALLCFEKAIK 206
                                    88888888888888887 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   1.2   9.8e-06    0.0057      74     122 ..      51      99 ..      40     103 .. 0.92
   2 !   16.0   0.5   2.1e-05     0.012      71     122 ..     116     170 ..      97     173 .. 0.82
   3 ?    0.7   0.0       1.1   6.5e+02      87     122 ..     203     238 ..     184     242 .. 0.50

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 9.8e-06
                                    HTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                           BTAD  74 rlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                    +lGr+++al+  e++++++P + r++r   +Al  ++r +eALe+ +r+
  gi|116754747|ref|YP_843865.1|  51 ALGRYSDALDAFERAIELDPSHARAWRGKAAALNNLDRYSEALEACKRA 99 
                                    89*****************************************987765 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 2.1e-05
                                    HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHH...HHHHHHHTT-HHHHHHHHHHH CS
                           BTAD  71 aelrlGraeealaelealvaehPlrErlhrq...lmrAlarsGrqaeALevYerl 122
                                    a+ +lG++eea++ ++++++++P+  +++r+     +Al  +Gr ++AL+ Y+++
  gi|116754747|ref|YP_843865.1| 116 AHHSLGEYEEAVKSYDRAIELDPMGQDARRAwnnRGAALDNLGRHEDALRSYDEA 170
                                    6789********************9877665111678***************986 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 1.1
                                    HHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                           BTAD  87 alvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                                    ++++ +P   +++     +l  +Gr +eA e  e +
  gi|116754747|ref|YP_843865.1| 203 KAIKIYPGYWTAWMNRGGCLKSLGRHEEAEESLEMA 238
                                    444444444444444444555556666665555555 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 ?   -0.2   0.0       1.7   9.9e+02      27      39 ..      52      64 ..      47      73 .. 0.78
   2 !   15.8   0.0   1.9e-05     0.011       5      68 ..      62     130 ..      58     140 .. 0.78
   3 ?    0.4   0.0       1.1   6.3e+02      20      39 ..     150     169 ..     128     180 .. 0.75
   4 !    7.5   0.0    0.0067       3.9      19      40 ..     179     204 ..     163     232 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.7
                   SRP_TPR_like 27 lekyeeaLkllkk 39
                                   l++y++aL + + 
  gi|116754747|ref|YP_843865.1| 52 LGRYSDALDAFER 64
                                   7899999988765 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1.9e-05
                   SRP_TPR_like   5 yekilrlegkelkkf..kvvaliklekyeeaLkllkkgs...alsedvrfEkaYvlYklkkykkalkil 68 
                                    +e+ ++l+ ++   +  k+ al +l++y+eaL+++k +      ++     k +++  l +y++a+k  
  gi|116754747|ref|YP_843865.1|  62 FERAIELDPSHARAWrgKAAALNNLDRYSEALEACKRALeldPFNSRSWIVKGFAHHSLGEYEEAVKSY 130
                                    566666655444444449*****************9987444668888999*************99865 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 1.1
                   SRP_TPR_like  20 kvvaliklekyeeaLkllkk 39 
                                    +  al +l+++e+aL+  ++
  gi|116754747|ref|YP_843865.1| 150 RGAALDNLGRHEDALRSYDE 169
                                    667888999******98776 PP

  == domain 4  score: 7.5 bits;  conditional E-value: 0.0067
                   SRP_TPR_like  19 f....kvvaliklekyeeaLkllkkg 40 
                                    +    k v+l+ l +y++aL   +k+
  gi|116754747|ref|YP_843865.1| 179 YawnnKGVSLVALKRYDDALLCFEKA 204
                                    2445699*************999886 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0         2   1.2e+03       5      17 ..      35      47 ..      32      47 .. 0.83
   2 ?    1.9   0.0      0.85   4.9e+02      13      26 .]      51      64 ..      48      64 .. 0.90
   3 ?    2.8   0.6      0.44   2.5e+02       1      23 [.      73      95 ..      73      98 .. 0.88
   4 ?    5.4   0.0     0.063        37       4      20 ..     110     126 ..     107     129 .. 0.86
   5 !    9.5   0.7    0.0029       1.7       2      24 ..     145     167 ..     144     169 .. 0.87
   6 ?    5.8   0.0     0.046        26      14      25 ..     225     236 ..     213     237 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 2
                          TPR_4  5 laLArallalGdl 17
                                   l+ A ++ a+G++
  gi|116754747|ref|YP_843865.1| 35 LMNADLWVARGRY 47
                                   67799******96 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.85
                          TPR_4 13 alGdldeAraller 26
                                   alG++ +A++++er
  gi|116754747|ref|YP_843865.1| 51 ALGRYSDALDAFER 64
                                   89********9997 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.44
                          TPR_4  1 arallaLArallalGdldeAral 23
                                   ara  + A al  l ++ eA+++
  gi|116754747|ref|YP_843865.1| 73 ARAWRGKAAALNNLDRYSEALEA 95
                                   6889999*************986 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.063
                          TPR_4   4 llaLArallalGdldeA 20 
                                     ++ + a++ lG+++eA
  gi|116754747|ref|YP_843865.1| 110 WIVKGFAHHSLGEYEEA 126
                                    677899**********9 PP

  == domain 5  score: 9.5 bits;  conditional E-value: 0.0029
                          TPR_4   2 rallaLArallalGdldeArall 24 
                                    ra  +++ al  lG++++A++  
  gi|116754747|ref|YP_843865.1| 145 RAWNNRGAALDNLGRHEDALRSY 167
                                    677899**************965 PP

  == domain 6  score: 5.8 bits;  conditional E-value: 0.046
                          TPR_4  14 lGdldeAralle 25 
                                    lG+++eA++ le
  gi|116754747|ref|YP_843865.1| 225 LGRHEEAEESLE 236
                                    8*******9887 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.011       6.5     204     256 ..      51     103 ..      27     104 .. 0.87
   2 !    9.4   0.0   0.00075      0.43     202     256 ..      83     137 ..      79     152 .. 0.93
   3 !    9.8   0.0   0.00058      0.34     205     256 ..     191     242 ..     187     244 .] 0.94

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.011
                                    HHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
                          NARP1 204 klgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                                     lg+++ Al+  ++aie +p+    +  Ka  l      ++A e+ ++a +lD
  gi|116754747|ref|YP_843865.1|  51 ALGRYSDALDAFERAIELDPSHARAWRGKAAALNNLDRYSEALEACKRALELD 103
                                    5788999*************************999999999999999999998 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00075
                                    HHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
                          NARP1 202 ydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                                     ++l ++++Ale   +a+e +p     +++K+  +   G+ ++A++  ++a +lD
  gi|116754747|ref|YP_843865.1|  83 LNNLDRYSEALEACKRALELDPFNSRSWIVKGFAHHSLGEYEEAVKSYDRAIELD 137
                                    67889999**********************************************9 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00058
                                    HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
                          NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                                    l++++ Al + +kai+  p     +++++  lk  G  ++A e +e ar++ 
  gi|116754747|ref|YP_843865.1| 191 LKRYDDALLCFEKAIKIYPGYWTAWMNRGGCLKSLGRHEEAEESLEMARRIE 242
                                    57899********************************************875 PP

>> DUF5113  Domain of unknown function (DUF5113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.1    0.0048       2.8      16      60 ..      47      90 ..      31     103 .. 0.70
   2 ?    4.8   0.1     0.039        23       8      36 ..      73     101 ..      70     137 .. 0.87
   3 ?   -0.0   0.0       1.2   6.8e+02      11      36 ..     147     172 ..     141     179 .. 0.84
   4 ?    5.5   0.0     0.024        14      10      61 ..     180     230 ..     172     239 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0048
                        DUF5113 16 yylnvegeyeeALeyldsaleylNahyekYakkkadtldklkmll 60
                                   y + + g+y++AL+ ++ a+e+   h + +  k+a  l++l  + 
  gi|116754747|ref|YP_843865.1| 47 YLMKALGRYSDALDAFERAIELDPSHARAWRGKAA-ALNNLDRYS 90
                                   45677899999999999999998888888888874.666665544 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.039
                        DUF5113   8 andYanlayylnvegeyeeALeyldsale 36 
                                    a +++  a +ln  ++y+eALe  + ale
  gi|116754747|ref|YP_843865.1|  73 ARAWRGKAAALNNLDRYSEALEACKRALE 101
                                    677888899999999********999997 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 1.2
                        DUF5113  11 YanlayylnvegeyeeALeyldsale 36 
                                    + n + +l   g++e+AL+  d+a+ 
  gi|116754747|ref|YP_843865.1| 147 WNNRGAALDNLGRHEDALRSYDEAIM 172
                                    667788888899**********9985 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.024
                        DUF5113  10 dYanlayylnvegeyeeALeyldsaleylNahyekYakkkadtldklkmlle 61 
                                    ++ n +  l + ++y++AL ++++a+++   +++ ++++  + l++l   +e
  gi|116754747|ref|YP_843865.1| 180 AWNNKGVSLVALKRYDDALLCFEKAIKIYPGYWTAWMNRG-GCLKSLGRHEE 230
                                    45677788888899************99999999998887.67776654444 PP

>> TPR_5  Tetratrico peptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1       2.8   1.6e+03      45      45 ..      80      80 ..      48     102 .. 0.44
   2 !   16.5   0.0   1.3e-05    0.0073      10      62 ..     116     168 ..     108     204 .. 0.88
   3 ?   -0.3   0.0       2.2   1.2e+03       7      22 ..     218     233 ..     213     240 .. 0.56

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2.8
                          TPR_5 45 a 45
                                   a
  gi|116754747|ref|YP_843865.1| 80 A 80
                                   2 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.3e-05
                          TPR_5  10 arDstGhedkavplYrraLaeGLagarrrratiqLassLRnlGeaeealaLLr 62 
                                    a+ s G+ ++av+ Y ra++    g+ +rra     ++L nlG+ e+al+  +
  gi|116754747|ref|YP_843865.1| 116 AHHSLGEYEEAVKSYDRAIELDPMGQDARRAWNNRGAALDNLGRHEDALRSYD 168
                                    67899*******************************************98654 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 2.2
                          TPR_5   7 ragarDstGhedkavp 22 
                                    r+g   s G++++a++
  gi|116754747|ref|YP_843865.1| 218 RGGCLKSLGRHEEAEE 233
                                    5555555555555544 PP

>> HTH_Bact  Helix-turn-helix bacterial domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.36   2.1e+02       1      15 [.      54      68 ..      54      69 .. 0.92
   2 ?    2.0   0.0      0.27   1.6e+02       1      14 [.      88     101 ..      88     103 .. 0.91
   3 ?    2.7   0.1      0.16        94       1      15 [.     122     136 ..     122     137 .. 0.92
   4 ?    4.7   0.0     0.038        22       1      15 [.     193     207 ..     193     208 .. 0.95
   5 ?   -0.2   0.0       1.3   7.8e+02      32      44 ..     218     230 ..     215     235 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.36
                                   -HHHHHHHHHHHHHH CS
                       HTH_Bact  1 rYeeaLeqvnkAiei 15
                                   rY  aL   ++Aie+
  gi|116754747|ref|YP_843865.1| 54 RYSDALDAFERAIEL 68
                                   79***********95 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.27
                                    -HHHHHHHHHHHHH CS
                       HTH_Bact   1 rYeeaLeqvnkAie 14 
                                    rY eaLe  ++A+e
  gi|116754747|ref|YP_843865.1|  88 RYSEALEACKRALE 101
                                    7***********98 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.16
                                    -HHHHHHHHHHHHHH CS
                       HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                    +Yeea +  ++Aie+
  gi|116754747|ref|YP_843865.1| 122 EYEEAVKSYDRAIEL 136
                                    6************95 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.038
                                    -HHHHHHHHHHHHHH CS
                       HTH_Bact   1 rYeeaLeqvnkAiei 15 
                                    rY+ aL   +kAi+i
  gi|116754747|ref|YP_843865.1| 193 RYDDALLCFEKAIKI 207
                                    7************97 PP

  == domain 5  score: -0.2 bits;  conditional E-value: 1.3
                                    HHHHHHHTT--HH CS
                       HTH_Bact  32 kgecleklgfsee 44 
                                    +g cl+ lg  ee
  gi|116754747|ref|YP_843865.1| 218 RGGCLKSLGRHEE 230
                                    99****9998765 PP

>> NYD-SP12_N  Spermatogenesis-associated, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00013     0.075     211     279 ..      16      94 ..      11     129 .. 0.81
   2 ?   -0.5   0.0      0.53     3e+02     236     281 ..     190     235 ..     167     240 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00013
                     NYD-SP12_N 211 pfeasaedissvasfietklvtcylrmr..........kpdlalnhahrsivlnpayfrnhlrqaavfrcleryseaar 279
                                     f  sa d+ +  sf et l+   l +           +   al+   r+i l+p++ r    +aa ++ l+rysea  
  gi|116754747|ref|YP_843865.1|  16 TFAVSAPDMPCDQSFFETDLMNADLWVArgrylmkalgRYSDALDAFERAIELDPSHARAWRGKAAALNNLDRYSEALE 94 
                                    58889999999999999999987664330001111112445689999*****************************965 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.53
                     NYD-SP12_N 236 rmrkpdlalnhahrsivlnpayfrnhlrqaavfrcleryseaarsa 281
                                     +++ d al    ++i + p y+   + +   +++l r+ ea  s 
  gi|116754747|ref|YP_843865.1| 190 ALKRYDDALLCFEKAIKIYPGYWTAWMNRGGCLKSLGRHEEAEESL 235
                                    567888899999999999*********************9998875 PP

>> DUF627  Protein of unknown function (DUF627)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00024      0.14      62     105 ..      58     101 ..      48     103 .. 0.95
   2 ?   -1.4   0.0       4.1   2.4e+03      62      96 ..     126     170 ..     123     173 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00024
                         DUF627  62 svecfseavelsrfyArsLfelasqlgsklyYkkavkkakraLs 105
                                    ++++f++a el   +Ar     a  l++   Y +a++ +kraL 
  gi|116754747|ref|YP_843865.1|  58 ALDAFERAIELDPSHARAWRGKAAALNNLDRYSEALEACKRALE 101
                                    89****************************************97 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.1
                         DUF627  62 svecfseavels..........rfyArsLfelasqlgsklyYkka 96 
                                    +v+++ +a el                 L +l+++ +  + Y +a
  gi|116754747|ref|YP_843865.1| 126 AVKSYDRAIELDpmgqdarrawNNRGAALDNLGRHEDALRSYDEA 170
                                    677777777776666666655544455566666666666666665 PP

>> Wzy_C_2  Virulence factor membrane-bound polymerase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.2     0.068        40     120     169 ..      49      99 ..      41     114 .. 0.54
   2 ?    1.9   0.0      0.32   1.8e+02     151     181 ..     152     182 ..     143     187 .. 0.86
   3 ?    6.1   0.0     0.016       9.2     151     181 ..     186     216 ..     181     219 .. 0.91
   4 ?   -1.6   0.0       3.8   2.2e+03     153     170 ..     222     239 ..     221     241 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.068
                        Wzy_C_2 120 plspenlaaklalarklihlsPep.avierlilslallGdedeAeqilara 169
                                    ++    + + l++ +++i+l P   +  +  + +l  l++ +eA+   +ra
  gi|116754747|ref|YP_843865.1|  49 MKALGRYSDALDAFERAIELDPSHaRAWRGKAAALNNLDRYSEALEACKRA 99 
                                    334444445555555555555543133444555555666666666666555 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.32
                        Wzy_C_2 151 lslallGdedeAeqilararalfpeedakwv 181
                                     +l  lG++++A++ +++a+ l p ++++w+
  gi|116754747|ref|YP_843865.1| 152 AALDNLGRHEDALRSYDEAIMLEPFDAYAWN 182
                                    577899**************99999999995 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.016
                        Wzy_C_2 151 lslallGdedeAeqilararalfpeedakwv 181
                                    +sl++l + d+A+   ++a++++p ++ +w 
  gi|116754747|ref|YP_843865.1| 186 VSLVALKRYDDALLCFEKAIKIYPGYWTAWM 216
                                    789999***********************94 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 3.8
                        Wzy_C_2 153 lallGdedeAeqilarar 170
                                    l  lG+++eAe  l+ ar
  gi|116754747|ref|YP_843865.1| 222 LKSLGRHEEAEESLEMAR 239
                                    5679*******9999887 PP

>> ANAPC5  Anaphase-promoting complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.34     2e+02      50      70 ..      48      68 ..      32      75 .. 0.88
   2 ?    5.2   0.0     0.038        22      49      71 ..     115     137 ..      80     145 .. 0.83
   3 ?    2.1   0.0      0.35     2e+02      42      69 ..     179     206 ..     146     241 .. 0.56

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.34
                         ANAPC5 50 lhadfghneeAvkaleeairl 70
                                   l  ++g + +A++a+e ai+l
  gi|116754747|ref|YP_843865.1| 48 LMKALGRYSDALDAFERAIEL 68
                                   667899************987 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.038
                         ANAPC5  49 slhadfghneeAvkaleeairlA 71 
                                      h+++g++eeAvk+   ai+l 
  gi|116754747|ref|YP_843865.1| 115 FAHHSLGEYEEAVKSYDRAIELD 137
                                    5699************9999885 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.35
                         ANAPC5  42 yalLnlaslhadfghneeAvkaleeair 69 
                                    ya  n  +   ++  +++A+  +e ai+
  gi|116754747|ref|YP_843865.1| 179 YAWNNKGVSLVALKRYDDALLCFEKAIK 206
                                    3333333333444445555555555554 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0    0.0093       5.4     178     233 ..      50     105 ..      35     130 .. 0.84
   2 ?    4.8   0.0     0.027        16     178     227 ..     189     238 ..     156     240 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0093
                                    H-TTHHHHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT CS
                     Coatomer_E 178 vggekiqdAyyifqelsekykstplllngkAvvslllgryeeAeslLkeaLdkdak 233
                                    ++ +++ dA+  f+   e  +s      gkA++   l+ry eA +  k aL+ d+ 
  gi|116754747|ref|YP_843865.1|  50 KALGRYSDALDAFERAIELDPSHARAWRGKAAALNNLDRYSEALEACKRALELDPF 105
                                    556789999999999999989999999************************98875 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.027
                                    H-TTHHHHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                     Coatomer_E 178 vggekiqdAyyifqelsekykstplllngkAvvslllgryeeAeslLkea 227
                                    v+ +++ dA++ f+     y+      + +  +   lgr+eeAe++L+ a
  gi|116754747|ref|YP_843865.1| 189 VALKRYDDALLCFEKAIKIYPGYWTAWMNRGGCLKSLGRHEEAEESLEMA 238
                                    45577889999999999999888888888888888999999999999866 PP

>> SHNi-TPR  SHNi-TPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.46   2.7e+02      16      30 ..      54      68 ..      52      69 .. 0.92
   2 ?    2.2   0.1      0.22   1.3e+02      15      30 ..      87     102 ..      86     102 .. 0.93
   3 ?    3.2   0.0       0.1        59      17      30 ..     123     136 ..     121     136 .. 0.93
   4 ?   -1.8   0.0       3.8   2.2e+03      16      30 ..     193     207 ..     192     208 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.46
                       SHNi-TPR 16 nFpqAveDlrkaLeL 30
                                   ++++A+  +++a+eL
  gi|116754747|ref|YP_843865.1| 54 RYSDALDAFERAIEL 68
                                   9***********998 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.22
                       SHNi-TPR  15 enFpqAveDlrkaLeL 30 
                                    +++++A+e  ++aLeL
  gi|116754747|ref|YP_843865.1|  87 DRYSEALEACKRALEL 102
                                    59************98 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.1
                       SHNi-TPR  17 FpqAveDlrkaLeL 30 
                                    +++Av+ +++a+eL
  gi|116754747|ref|YP_843865.1| 123 YEEAVKSYDRAIEL 136
                                    99**********98 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 3.8
                       SHNi-TPR  16 nFpqAveDlrkaLeL 30 
                                    ++++A+  ++ka+++
  gi|116754747|ref|YP_843865.1| 193 RYDDALLCFEKAIKI 207
                                    789998888899887 PP

>> DUF5588  Family of unknown function (DUF5588)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.088        51      63     109 ..     121     165 ..     111     217 .. 0.73
   2 ?    2.8   0.1     0.075        43      95     113 ..     219     240 ..     216     243 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.088
                        DUF5588  63 qeyqkalqeyssiseklsstnfamkrdvqegqarclahlgrhaeale 109
                                     ey+ a++ y    e  ++ + a +r   + +   l  lgrh++al+
  gi|116754747|ref|YP_843865.1| 121 GEYEEAVKSYDRAIELDPMGQDA-RR-AWNNRGAALDNLGRHEDALR 165
                                    68888888888877766655544.33.34455667999999999996 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.075
                        DUF5588  95 arclahlgrhaea...leiaad 113
                                      cl  lgrh+ea   le+a  
  gi|116754747|ref|YP_843865.1| 219 GGCLKSLGRHEEAeesLEMARR 240
                                    56********987333666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); 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: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 1535.11
//
Query:       gi|116754748|ref|YP_843866.1|  [L=414]
Description: cell division control protein 6 [Methanosaeta thermophila PT]
Scores for complete 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   0.1    6.2e-21   74.2   0.1    1.7  1  Cdc6_C           CDC6, C terminal winged helix domain
      4e-13   49.8   0.0      1e-12   48.5   0.0    1.6  1  AAA_22           AAA domain
    1.1e-12   48.7   0.9    7.2e-11   42.8   0.1    2.8  2  AAA_16           AAA ATPase domain
    1.7e-09   38.2   0.1    5.2e-09   36.6   0.0    1.9  1  AAA              ATPase family associated with various cellul
    2.9e-06   27.4   2.1    1.8e-05   24.8   0.3    2.7  2  ATPase_2         ATPase domain predominantly from Archaea
    1.2e-05   24.9   0.0    2.2e-05   24.0   0.0    1.4  1  TniB             Bacterial TniB protein
    4.8e-05   23.3   0.0    0.00011   22.2   0.0    1.6  1  NACHT            NACHT domain
    0.00021   20.6   0.0     0.0003   20.1   0.0    1.2  1  DUF2075          Uncharacterized conserved protein (DUF2075)
    0.00023   21.0   0.1      0.096   12.4   0.0    2.5  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00024   20.9   0.1    0.00056   19.6   0.0    1.6  2  Sigma54_activat  Sigma-54 interaction domain
    0.00048   19.4   0.0    0.00099   18.3   0.0    1.5  1  DUF815           Protein of unknown function (DUF815)
     0.0022   18.6   0.2       0.01   16.4   0.1    2.1  2  AAA_18           AAA domain
     0.0024   17.1   0.0     0.0047   16.1   0.0    1.5  1  NB-ARC           NB-ARC domain
     0.0025   17.1   0.1      0.054   12.8   0.0    2.2  2  Zeta_toxin       Zeta toxin
     0.0031   16.8   0.5       0.26   10.5   0.0    2.2  2  KAP_NTPase       KAP family P-loop domain
     0.0035   17.3   0.0      0.006   16.6   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
     0.0077   16.0   0.3       0.02   14.6   0.3    1.7  1  AAA_24           AAA domain
     0.0085   15.6   0.0      0.018   14.6   0.0    1.5  1  AAA_7            P-loop containing dynein motor region
     0.0093   16.3   0.3      0.024   15.0   0.3    1.7  1  AAA_assoc_2      AAA C-terminal domain
  ------ inclusion threshold ------
      0.016   15.4   0.1       0.18   11.9   0.0    2.4  2  Sigma54_activ_2  Sigma-54 interaction domain
      0.018   14.1   0.0      0.041   12.9   0.0    1.6  1  T2SSE            Type II/IV secretion system protein
      0.019   15.1   0.1       0.14   12.3   0.1    2.2  1  AAA_2            AAA domain (Cdc48 subfamily)
      0.033   14.2   0.0      0.072   13.1   0.0    1.6  1  ResIII           Type III restriction enzyme, res subunit
      0.033   14.6   0.0      0.073   13.5   0.0    1.6  1  RNA_helicase     RNA helicase
      0.034   13.9   0.1       0.12   12.1   0.0    1.9  2  IstB_IS21        IstB-like ATP binding protein
      0.058   13.4   0.0       0.12   12.4   0.0    1.5  1  AAA_14           AAA domain
       0.22   10.2   1.6        7.6    5.2   0.4    2.4  2  AAA_32           AAA domain
       0.33   10.7   3.2        0.6    9.8   1.0    2.3  2  DEAD             DEAD/DEAH box helicase


Domain annotation for each model (and alignments):
>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.2   0.1   9.6e-24   6.2e-21       1      81 [.     309     387 ..     309     389 .. 0.97

  Alignments for each domain:
  == domain 1  score: 74.2 bits;  conditional E-value: 9.6e-24
                                    HHHHHHHHCHCSSS-EEHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSSCHH CS
                         Cdc6_C   1 LcalvlllrksgkeevttgevyevYkslCesegvdpltqrevsdllseLemlgileleksskGrregrtrkisLnvdpdd 80 
                                    L++++ll++ +  + +tt+ vy +Yk+lC   +v+ lt+r++ dl++eL+mlgil + + skGr +grt++isL+v+p +
  gi|116754748|ref|YP_843866.1| 309 LYSILLLEE-QAARNITTSAVYGMYKQLCPLVEVESLTHRRITDLIAELDMLGILHTVVISKGR-YGRTKEISLSVHPPK 386
                                    89*******.*****************************************************9.************976 PP

                                    H CS
                         Cdc6_C  81 v 81 
                                    +
  gi|116754748|ref|YP_843866.1| 387 L 387
                                    5 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   0.0   1.6e-15     1e-12       4     129 ..      61     185 ..      58     191 .. 0.85

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 1.6e-15
                         AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee.erpevvfvtlpsstsskdllrellralglelkaerlsseelleal 82 
                                    t + ++++G +GtGKT +++ + ++l+e  +       +v++ ++ +  ++  +l +l+r ++ +    +  ++++++ +
  gi|116754748|ref|YP_843866.1|  61 TPSNILIYGKTGTGKTAVAKYVGKELEE--AD-AgSTCSVIYLNCEVVDTQYRVLAHLARHFDKDIPMTGWPTDQVYSEF 137
                                    56789*********************53..33.34899*************************99999899999999*** PP

                         AAA_22  83 eqalraravielliiDEaqhlr..seealeeLrsl.lnlsrkgvqliLvG 129
                                    ++al+++++++++++DE+++l    +++l +L+++ ++    + ++ L+G
  gi|116754748|ref|YP_843866.1| 138 RNALDEKKRVVVIMLDEVDKLVrkGDDVLYNLSRInSD--LVQARVSLIG 185
                                    ********************876559999999555255..5555555555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.8   0.1   1.1e-13   7.2e-11       2     161 ..      39     172 ..      38     185 .. 0.69
   2 ?   -1.6   0.1       4.7     3e+03     106     106 ..     256     256 ..     197     323 .. 0.55

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 1.1e-13
                         AAA_16   2 lvGReeeleqLlsalervrsgrp.elvllsGesGvGKsslvrellralekd....ggiflrgkcdqlesaipysalaqal 76 
                                    l+ Ree++++L+s+l ++  g++ +++l++G  G+GK+++++ + ++le++     + +++ +c+    ++ y    ++l
  gi|116754748|ref|YP_843866.1|  39 LPHREEQIQELASVLAPALHGETpSNILIYGKTGTGKTAVAKYVGKELEEAdagsTCSVIYLNCEVV--DTQY----RVL 112
                                    889******************999***************************7654344588888888..4444....333 PP

                         AAA_16  77 areellrqlldeaesaeleawrekleealaavpelagaeasrllellkrllallsrderplvlvlDdlqwadeaslqlla 156
                                     + +l r  + +        w++                  +++ +++++l    +++r +v+ lD+++++     ++l+
  gi|116754748|ref|YP_843866.1| 113 -A-HLARHFDKD---IPMTGWPT-----------------DQVYSEFRNAL---DEKKRVVVIMLDEVDKLVRKGDDVLY 167
                                    .2.333333333...22334444.................34455555555...33344477777777777777777777 PP

                         AAA_16 157 aLlrl 161
                                    +L r 
  gi|116754748|ref|YP_843866.1| 168 NLSRI 172
                                    77665 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.7
                         AAA_16 106 a 106
                                    +
  gi|116754748|ref|YP_843866.1| 256 R 256
                                    1 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.0   8.1e-12   5.2e-09       1     112 [.      65     190 ..      65     206 .. 0.77

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 8.1e-12
                                    EEEESSTTSSHHHHHHHHHHHH.......THEEEEEETTTCSSS................STTHHHHHHHHHHHHHHHTS CS
                            AAA   1 vllyGppGtGKTllakavakel.......gvefleisgsellsk................yvgesekkirelfkeakeka 57 
                                    +l+yG  GtGKT++ak v kel         +++ +++  +  +                + g   +++   f++a  ++
  gi|116754748|ref|YP_843866.1|  65 ILIYGKTGTGKTAVAKYVGKELeeadagsTCSVIYLNCEVVDTQyrvlahlarhfdkdipMTGWPTDQVYSEFRNALDEK 144
                                    699******************844444333667888887776557899999999999***77777777777777764444 PP

                                    .TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSG CS
                            AAA  58 .kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrp 112
                                     + +++++DE+d+l+++         ++v+  L +  +++ +  ++v +ig++n+ 
  gi|116754748|ref|YP_843866.1| 145 kRVVVIMLDEVDKLVRKG--------DDVLYNLSRINSDLVQ--ARVSLIGISNDL 190
                                    246************999........7777777777777766..689999999984 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 !   24.8   0.3   2.8e-08   1.8e-05       4     148 ..      42     172 ..      40     184 .. 0.76
   2 ?   -1.9   0.1       3.9   2.5e+03      79     112 ..     282     318 ..     261     327 .. 0.64

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 2.8e-08
                       ATPase_2   4 Rekelkeleeil....erepneiyfiYGpegsGKtaLlkeiienledkdk....yviyyialreesiskldefieeeeek 75 
                                    Re+ ++el ++l      e+ + ++iYG  g GKta+ k + ++le+ d      viy  + + +++++           
  gi|116754748|ref|YP_843866.1|  42 REEQIQELASVLapalHGETPSNILIYGKTGTGKTAVAKYVGKELEEADAgstcSVIY-LNCEVVDTQYRVL-------- 112
                                    89999998887522226899999**********************9998877745555.4555555544444........ PP

                       ATPase_2  76 kklekalgiavpkaeleeilkeksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLlnl 148
                                      l++++ +++p +             ++  +++ +++ +k++ ++i++De+ kl+    ++  +++++L ++
  gi|116754748|ref|YP_843866.1| 113 AHLARHFDKDIPMTGW---------PTDQVYSEFRNALDEKKRVVVIMLDEVDKLV----RKGDDVLYNLSRI 172
                                    4677777777788666.........5588899999999999999***********9....6667777777665 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.9
                       ATPase_2  79 ekalgiavpkaeleeilk...eksklvfkaielllek 112
                                     ka+ ++++++++ee++k   ++sklv  +i ll e+
  gi|116754748|ref|YP_843866.1| 282 VKAARDKIEQDRVEEVIKtlpTQSKLVLYSILLLEEQ 318
                                    3444667777777777776666666666666555554 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   3.4e-08   2.2e-05      17     132 ..      43     159 ..      37     190 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 3.4e-08
                           TniB  17 keilerLeeLley.pkrkrmpnlllvGdsnnGKtmivekFarlhppekdedaekvpvlvvqappkpdekrlyaaiLealg 95 
                                    +e +++L+++l+   + + ++n+l++G++ +GKt++++   ++  +e     +++ v+++++    ++ r  a++ +++ 
  gi|116754748|ref|YP_843866.1|  43 EEQIQELASVLAPaLHGETPSNILIYGKTGTGKTAVAKYVGKEL-EEA-DAGSTCSVIYLNCEVVDTQYRVLAHLARHFD 120
                                    4556667666655145566789************9876554444.433.356789************************* PP

                           TniB  96 aplkar.arvskleqqvlrllre.lkvrvLiiDEihnll 132
                                    +++  + + +++ +++  + l+e  +v v+++DE+++l+
  gi|116754748|ref|YP_843866.1| 121 KDIPMTgWPTDQVYSEFRNALDEkKRVVVIMLDEVDKLV 159
                                    *998773588999999999997615689999*****997 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   1.7e-07   0.00011       3      99 ..      65     164 ..      63     185 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.7e-07
                                    EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-....-HCHHHCCCCTS--SSS-C....CHHHHC CS
                          NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgna.rsladllfsqlpepaapvse....vwavll 77 
                                    +++ G+ G GKT+ ++ +  ++ e +  +   + v++l++  + ++ ++  +la++  ++ p  + p ++    +++ l 
  gi|116754748|ref|YP_843866.1|  65 ILIYGKTGTGKTAVAKYVGKELEEADAGS--TCSVIYLNCEVVDTQYRVlAHLARHFDKDIPMTGWPTDQvyseFRNALD 142
                                    799***********************777..6*************99888888888888888888777777665777777 PP

                                    CSCCCEEEEEE-STT-SS-TCH CS
                          NACHT  78 elperlLlilDglDelvtdlgq 99 
                                    e ++ +++ lD +D+lv++ + 
  gi|116754748|ref|YP_843866.1| 143 EKKRVVVIMLDEVDKLVRKGDD 164
                                    777778899*******996655 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   4.8e-07    0.0003       3     105 ..      64     163 ..      62     182 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.8e-07
                        DUF2075   3 vvlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakkeekkkkkeafeklss.finnlsefkkae 81 
                                     +l+ G++GtGKt v+  +  ele+ + ++t  +++ N + v++ ++ la  +  +++++++        + +sef+  +
  gi|116754748|ref|YP_843866.1|  64 NILIYGKTGTGKTAVAKYVGKELEEADAGSTCSVIYLNCEVVDTQYRVLAHLA--RHFDKDIPMTGWpTDQVYSEFR--N 139
                                    689**********************************************9988..6666666555440344444333..4 PP

                        DUF2075  82 ekkeepkedvvivDEAhrlltksd 105
                                    + +e++++ v+  DE  +l  k+d
  gi|116754748|ref|YP_843866.1| 140 ALDEKKRVVVIMLDEVDKLVRKGD 163
                                    445667888999999999988766 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 !   12.4   0.0   0.00015     0.096      25      60 ..      54      89 ..      37     107 .. 0.78
   2 ?    5.8   0.0     0.016        10      53     106 ..     115     168 ..     106     177 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00015
                         RuvB_N 25 aakkreealdhvllyGpPGlGkttlakiiakelgvk 60
                                   a    +e+   +l+yG  G Gkt++ak + kel+  
  gi|116754748|ref|YP_843866.1| 54 APALHGETPSNILIYGKTGTGKTAVAKYVGKELEEA 89
                                   44456788899*********************9865 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.016
                         RuvB_N  53 iakelgvklkitsgPvlekagdlaalltnleekdvlfideihrlsraveevlys 106
                                    +a+ ++ ++ +t  P+ +  +++   l + ++  v+++de+ +l r+ ++vly+
  gi|116754748|ref|YP_843866.1| 115 LARHFDKDIPMTGWPTDQVYSEFRNALDEKKRVVVIMLDEVDKLVRKGDDVLYN 168
                                    5778888889999999999999999999999999*******************6 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   8.8e-07   0.00056       7      60 ..      45     104 ..      39     115 .. 0.71
   2 ?   -3.2   0.0       9.4     6e+03      96     110 ..     149     163 ..     143     169 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 8.8e-07
                                    HHHHHHHHHHHHC..TSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS....-EEEEETTT CS
                Sigma54_activat   7 alkelleqikkva..ktdlsvlitGesGtGKellaraiheaskrkek....pfvavncaa 60 
                                    +++el + ++ +   +t++++li G++GtGK+ +a+ + ++ +++++    +++ +nc  
  gi|116754748|ref|YP_843866.1|  45 QIQELASVLAPALhgETPSNILIYGKTGTGKTAVAKYVGKELEEADAgstcSVIYLNCEV 104
                                    5555555555554225679******************98866665543344778888865 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 9.4
                                    EEEEETGGGS-HHHH CS
                Sigma54_activat  96 tlfLDeigelplelQ 110
                                    +++LDe+ +l  ++ 
  gi|116754748|ref|YP_843866.1| 149 VIMLDEVDKLVRKGD 163
                                    689999999977665 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   1.5e-06   0.00099      28      81 ..      37      90 ..      28     123 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.5e-06
                         DUF815 28 ddLvgidkqkealventeqfleglpannvLLwGarGtGKSslvkallneyaeeg 81
                                   ++L   ++q ++l +  +  l+g++ +n+L++G+ GtGK ++ k + +e++e+ 
  gi|116754748|ref|YP_843866.1| 37 KELPHREEQIQELASVLAPALHGETPSNILIYGKTGTGKTAVAKYVGKELEEAD 90
                                   677788999************************************999988765 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   1.6e-05      0.01       1      25 [.      65     105 ..      65     182 .. 0.61
   2 ?   -1.1   0.0       4.1   2.7e+03      47      72 ..     284     308 ..     248     339 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.6e-05
                         AAA_18   1 IlltGtpGvGKttlakeLskrl.gf...............g 25 
                                    Il+ G+ G+GKt +ak++ k+l +                +
  gi|116754748|ref|YP_843866.1|  65 ILIYGKTGTGKTAVAKYVGKELeEAdagstcsviylncevV 105
                                    99****************99975556666666554444441 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 4.1
                         AAA_18  47 deskrldedkldklldaleenssale 72 
                                       +++++d++++++++l  +s+ l 
  gi|116754748|ref|YP_843866.1| 284 AARDKIEQDRVEEVIKTLPTQSK-LV 308
                                    34556666666666666666554.33 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   7.3e-06    0.0047      22     112 ..      64     155 ..      42     170 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 7.3e-06
                                    EEEEEESTTSSHHHHHHHHCCSHCCCCCCBT.EEEEEEEESXXHHHHHHHXXHHHHHCCCTTSSSS-STTSHHHHHHHHC CS
                         NB-ARC  22 vvalvGmgGvGKttlakqilnksdevegrFd.svawvvvsktdkseeiletilkeLslseddleekeeveslkrklvrlL 100
                                     + ++G+ G GKt +ak + ++++e +     sv+++     d+++++l ++++++ +    +   ++ +    + +++L
  gi|116754748|ref|YP_843866.1|  64 NILIYGKTGTGKTAVAKYVGKELEEADAGSTcSVIYLNCEVVDTQYRVLAHLARHFDKD-IPMTGWPTDQ-VYSEFRNAL 141
                                    578***********************9955559***********************655.5555555555.89******* PP

                                    CCT.TEEEE.EEEE CS
                         NB-ARC 101 ltk.rfllv.lDDV 112
                                     +k r++++ lD V
  gi|116754748|ref|YP_843866.1| 142 DEKkRVVVImLDEV 155
                                    99977665515655 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   8.4e-05     0.054      12      42 ..      58      88 ..      47     101 .. 0.85
   2 ?    1.8   0.0      0.19   1.2e+02      33      82 ..     134     183 ..     132     186 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.4e-05
                     Zeta_toxin 12 sqerPklillgGqpGAGKselaellkdeler 42
                                    +e+P  il+ G +G GK+++a+++ +ele+
  gi|116754748|ref|YP_843866.1| 58 HGETPSNILIYGKTGTGKTAVAKYVGKELEE 88
                                   5799***********************9974 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.19
                     Zeta_toxin  33 aellkdelerqgnvvrldpDdlRelhPeyeeilkadpkkaseltqkdase 82 
                                     ++++++l+++++vv++  D++ +l ++ +++l + ++ +s+l+q+ +s 
  gi|116754748|ref|YP_843866.1| 134 YSEFRNALDEKKRVVVIMLDEVDKLVRKGDDVLYNLSRINSDLVQARVSL 183
                                    6778999999*************999999999999999999999988775 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 !   10.5   0.0   0.00041      0.26       3      51 ..      44      93 ..      42     124 .. 0.79
   2 ?    4.5   0.2     0.026        17     158     185 ..     131     158 ..     113     170 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00041
                     KAP_NTPase  3 lyasaladilseptl..atpivvgLygkWGsGKssllnkledelkefakpv 51
                                     ++ la +l  p+l  +tp+ + +ygk G+GK+++ + + +el+e  +  
  gi|116754748|ref|YP_843866.1| 44 EQIQELASVLA-PALhgETPSNILIYGKTGTGKTAVAKYVGKELEEADAGS 93
                                   56777888887.6677789*********************99999985444 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.026
                     KAP_NTPase 158 eelladmektLdalqkrlVvviDdLDrc 185
                                    +++++++ ++Ld++++ +V+ +D+ D +
  gi|116754748|ref|YP_843866.1| 131 DQVYSEFRNALDEKKRVVVIMLDEVDKL 158
                                    567899********************86 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   9.3e-06     0.006       3      46 ..      42      89 ..      40     150 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 9.3e-06
                                   SHHHHHHHHHHHHHCH....TEEEEEEESTTSSHHHHHHHHHHHTT-- CS
                           TsaE  3 seeetealgkklakal....gdvilLeGdLGaGKTtlvrglakalgve 46
                                   +ee++++l++ la al     + il++G+ G+GKT+ ++ + k+l+ +
  gi|116754748|ref|YP_843866.1| 42 REEQIQELASVLAPALhgetPSNILIYGKTGTGKTAVAKYVGKELEEA 89
                                   68999********9988544345*******************999764 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.3   3.1e-05      0.02       3      79 ..      63     160 ..      61     175 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.1e-05
                         AAA_24   3 lkiliyGpsgiGKTtlakel...........gpkplfidtekGlksldadkfpdie......................sw 49 
                                     +iliyG+ g+GKT +ak             + +++++++e                                       
  gi|116754748|ref|YP_843866.1|  63 SNILIYGKTGTGKTAVAKYVgkeleeadagsTCSVIYLNCEVV------------DtqyrvlahlarhfdkdipmtgwPT 130
                                    589***************9955555555544444444444431............1211111122233444445665544 PP

                         AAA_24  50 edfldevvelaaeladyktlviDtidelee 79 
                                    +++++e+    +e+++  ++ +D +d+l++
  gi|116754748|ref|YP_843866.1| 131 DQVYSEFRNALDEKKRVVVIMLDEVDKLVR 160
                                    555666666677777777777788887776 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   2.8e-05     0.018      34      62 ..      63      91 ..      52     123 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.8e-05
                          AAA_7 34 kpvllvGptGtGKtviikdllkkldkeky 62
                                    ++l++G+tGtGKt+++k + k+l++ + 
  gi|116754748|ref|YP_843866.1| 63 SNILIYGKTGTGKTAVAKYVGKELEEADA 91
                                   689***************99999986544 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.3   3.7e-05     0.024      16      56 ..     248     287 ..     235     300 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.7e-05
                                    XXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXX CS
                    AAA_assoc_2  16 aeladGDaRkaLnlLElaaeaaeakegkieitledleealq 56 
                                    a+  +GDaR+aL lL +a e ae+ ++++ it+e++++a +
  gi|116754748|ref|YP_843866.1| 248 AAREHGDARRALDLLRIAGEIAER-ARSQMITEEHVKAARD 287
                                    44457**************99986.8889999999997654 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00029      0.18       6      44 ..      45      85 ..      42     107 .. 0.82
   2 ?    0.3   0.1       1.1     7e+02      82     122 ..     287     326 ..     257     337 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00029
                                   HHHHHHHHHHHHH..T-SS-EEEEEETT--HHHHHHCC--T CS
                Sigma54_activ_2  6 aiqelkerLeqaa..qsklpvfltGekGsgkelvArlLhkn 44
                                    iqel++ L+ a   +  +++++ G  G+gk+ vA++  k+
  gi|116754748|ref|YP_843866.1| 45 QIQELASVLAPALhgETPSNILIYGKTGTGKTAVAKYVGKE 85
                                   68999999999883345567****************98765 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.1
                                    -HHHHHHHHHHHHHHTTTT-EEEEEEEE-TTT..----HHH CS
                Sigma54_activ_2  82 skaeqkeLlellakaeksslrlVstsskdleqlleagafde 122
                                    +k eq +  e+++   + +++lV  s   le++++ +   +
  gi|116754748|ref|YP_843866.1| 287 DKIEQDRVEEVIKTL-PTQSKLVLYSILLLEEQAARNITTS 326
                                    577899999999999.99999**999999999777765555 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 ?   12.9   0.0   6.4e-05     0.041     101     156 ..      32      89 ..      18      96 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.4e-05
                          T2SSE 101 keltlddlgaeealkekiaevlrkavr..erglilvsGgTgsGKttllyallkeinks 156
                                    + +t ++l  +e++ +++a+vl+ a++  +  +il+ G Tg+GKt ++  + ke+++ 
  gi|116754748|ref|YP_843866.1|  32 STYTPKELPHREEQIQELASVLAPALHgeTPSNILIYGKTGTGKTAVAKYVGKELEEA 89 
                                    55677888889999999999999998622457*************9998887777765 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00022      0.14       4      84 ..      63     163 ..      60     178 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00022
                                    --EEEE--TTSSHHHHHHHHHHHTT-.......-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS.......... CS
                          AAA_2   4 isilllgptgvGktelakalaellfv...kkekkliradaselleeeevehlvsrligappgyvgaeegG.......... 70 
                                    ++il+ g+tg+Gkt +ak + + l+    +++ ++i +++  + ++     ++++   a+ +++     G          
  gi|116754748|ref|YP_843866.1|  63 SNILIYGKTGTGKTAVAKYVGKELEEadaGSTCSVIYLNCEVVDTQYR---VLAH--LARHFDKDIPMTGwptdqvysef 137
                                    799************888888877755555566666666665555222...2222..23333333333444455567777 PP

                                    ...........EEEEETGGG----.- CS
                          AAA_2  71 ...........ivllDEidKihpk.e 84 
                                               +++lDE+dK  +k +
  gi|116754748|ref|YP_843866.1| 138 rnaldekkrvvVIMLDEVDKLVRKgD 163
                                    88889999**9**********99432 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 ?   13.1   0.0   0.00011     0.072       4      52 ..      41      90 ..      38     176 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
                                   E-HHHHHHHHHHT.......TTSEEEEEESTTSTHHHHHHHHHHHH-S.. CS
                         ResIII  4 lreyQeeaienll.eklkskrdkrglikmaTGtGKTlvaaklierllkkg 52
                                    re Q++ + ++l  +l+ +   ++li   TGtGKT va  + ++l ++ 
  gi|116754748|ref|YP_843866.1| 41 HREEQIQELASVLaPALHGETPSNILIYGKTGTGKTAVAKYVGKELEEAD 90
                                   57888888888884466668889***************977777776655 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   0.00011     0.073       1      26 [.      65      90 ..      65     110 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00011
                   RNA_helicase  1 iwlyGpsgeGKStlakeLakallkkl 26
                                   i++yG++g+GK+ +ak++ k+l+++ 
  gi|116754748|ref|YP_843866.1| 65 ILIYGKTGTGKTAVAKYVGKELEEAD 90
                                   789**************999998544 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00019      0.12      43      75 ..      58      90 ..      30     118 .. 0.76
   2 ?   -2.0   0.1         4   2.6e+03      99     120 ..     137     158 ..     131     195 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00019
                      IstB_IS21 43 fiekkenivllGpsGvGKshlaialgveavrag 75
                                   + e+  ni++ G +G+GK+ +a  +g+e  +a+
  gi|116754748|ref|YP_843866.1| 58 HGETPSNILIYGKTGTGKTAVAKYVGKELEEAD 90
                                   556779****************99999876644 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4
                      IstB_IS21  99 laralkrllkvdllilDdlgll 120
                                    + +al++  +v +++lD++  l
  gi|116754748|ref|YP_843866.1| 137 FRNALDEKKRVVVIMLDEVDKL 158
                                    6677888889999999998543 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00019      0.12       5      76 ..      65     158 ..      62     194 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00019
                         AAA_14   5 lvitGaRrvGKTtllkqlikell....vkkesilyinldderd...........kkladpe...........kllelile 58 
                                    ++i G   +GKT ++k + kel      +  s++y+n++  ++                 +           ++++++++
  gi|116754748|ref|YP_843866.1|  65 ILIYGKTGTGKTAVAKYVGKELEeadaGSTCSVIYLNCEVVDTqyrvlahlarhF-----DkdipmtgwptdQVYSEFRN 139
                                    6899999********99999999999878899*******9888666665543321.....13355566666677777777 PP

                         AAA_14  59 klke.ekktylflDEiqev 76 
                                     l e ++  +++lDE+ ++
  gi|116754748|ref|YP_843866.1| 140 ALDEkKRVVVIMLDEVDKL 158
                                    743335666799****886 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.039        25      32      57 ..      64      89 ..      59     108 .. 0.79
   2 ?    5.2   0.4     0.012       7.6     478     510 ..     256     288 ..     248     294 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.039
                         AAA_32 32 NifvlGesgtGrttlvkrlleeiakk 57
                                   Ni + G++gtG+t ++k + +e ++ 
  gi|116754748|ref|YP_843866.1| 64 NILIYGKTGTGKTAVAKYVGKELEEA 89
                                   9*************999988887554 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.012
                         AAA_32 478 seiadllrEAdywakkegaevveaehVekAlee 510
                                    ++  dllr A  +a++++++++++ehV++A ++
  gi|116754748|ref|YP_843866.1| 256 RRALDLLRIAGEIAERARSQMITEEHVKAARDK 288
                                    56789**********************999765 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   1.0   0.00094       0.6      12     116 ..      57     163 ..      44     177 .. 0.68
   2 ?   -2.6   0.0       6.1   3.9e+03      51      73 ..     307     329 ..     284     379 .. 0.53

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00094
                                    HTT...CEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST..SEEEEEETTSS CS
                                    xxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxx RF
                           DEAD  12 lgg...gdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyid..lrvlliiggva 86 
                                    l+g    ++l+ ++TG+GKT+++   v +++   + + g  + ++    e +  +++ l  +  + d  + +  + +++ 
  gi|116754748|ref|YP_843866.1|  57 LHGetpSNILIYGKTGTGKTAVAKY-VGKELE--EADAGSTCSVIYLNCEVVDTQYRVLAHLARHFDkdIPMTGWPTDQV 133
                                    433233699***********99654.444553..4777777777777888888888888888887664455555566666 PP

                                    HHHHHHHHHTTCSEEEEEHHHHHHHHHCTS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  87 ardqlskldngvdivvgtpgrlddllstgk 116
                                    +++ +++ld++ ++vv   + +d+l+++g 
  gi|116754748|ref|YP_843866.1| 134 YSEFRNALDEKKRVVVIMLDEVDKLVRKGD 163
                                    677777777778888888888888885444 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6.1
                                    EEEESSHHHHHHHHHHHHHHTTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  51 livePtreLaeqtlnnlkkfkky 73 
                                    l++     L eq ++n++++  y
  gi|116754748|ref|YP_843866.1| 307 LVLYSILLLEEQAARNITTSAVY 329
                                    44444445555555555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       870  (0.0485247); expected 358.6 (0.02)
Passed bias filter:                      750  (0.0418317); expected 358.6 (0.02)
Passed Vit filter:                       123  (0.00686039); 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: 0.66u 0.33s 00:00:00.99 Elapsed: 00:00:00.49
# Mc/sec: 2553.36
//
Query:       gi|116754749|ref|YP_843867.1|  [L=154]
Description: hypothetical protein Mthe_1453 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-10   41.4   0.2    1.9e-10   40.7   0.2    1.4  1  Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (


Domain annotation for each model (and alignments):
>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   0.2   1.1e-14   1.9e-10       2      39 ..      28      62 ..      27      63 .. 0.90

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 1.1e-14
                  Auto_anti-p27  2 kmgelLlkGwtMLaetCpvCgvPLmrdrkggkvyCvaC 39
                                   ++ +++  G tMLae+++ Cg+PL+r+  +g+++C++C
  gi|116754749|ref|YP_843867.1| 28 RITRMMEIGGTMLAEHHD-CGAPLFRY--KGEIICPVC 62
                                   6899***********995.*******6..58******* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       876  (0.0488594); expected 358.6 (0.02)
Passed bias filter:                      590  (0.0329076); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1137.53
//
Query:       gi|116754750|ref|YP_843868.1|  [L=85]
Description: hypothetical protein Mthe_1454 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-36  122.5   1.5    5.9e-36  122.4   1.5    1.0  1  UPF0147   Uncharacterised protein family (UPF0147)
     0.0062   16.8   0.2        2.1    8.7   0.1    2.1  2  UPF0253   Uncharacterised protein family (UPF0253)
     0.0078   14.2   0.1     0.0083   14.1   0.1    1.0  1  FSIP2     Fibrous sheath-interacting protein 2


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 !  122.4   1.5   9.9e-40   5.9e-36       2      81 .]       3      82 ..       2      82 .. 0.98

  Alignments for each domain:
  == domain 1  score: 122.4 bits;  conditional E-value: 9.9e-40
                                   HHHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHHHH CS
                        UPF0147  2 eekikevielLeeiiedtsvPrniRraakeakekLkdekeslavraataisiLdeisnDpnmPlhaRtliwevvskLEti 81
                                   e++ik+++e+Le+i++d++vPrniRr+a+++k  L +e  + av+aa+aisiLdeisnDpn+Plh+Rtliw+v s+LEti
  gi|116754750|ref|YP_843868.1|  3 EKVIKQCVEILERIMSDDTVPRNIRRSAENVKGILLQEGLAEAVKAASAISILDEISNDPNIPLHTRTLIWNVASQLETI 82
                                   789***************************************************************************98 PP

>> UPF0253  Uncharacterised protein family (UPF0253)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.1   0.00036       2.1      25      51 ..       4      30 ..       2      33 .. 0.90
   2 !    6.4   0.0    0.0018        11      29      48 ..      50      69 ..      41      77 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00036
                        UPF0253 25 dAiscalktLdevaanealpeevrekA 51
                                   + i+  ++ L+++ +++ +p+++r +A
  gi|116754750|ref|YP_843868.1|  4 KVIKQCVEILERIMSDDTVPRNIRRSA 30
                                   6688899*****************887 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0018
                        UPF0253 29 calktLdevaanealpeevr 48
                                    a+  Lde+ ++ ++p ++r
  gi|116754750|ref|YP_843868.1| 50 SAISILDEISNDPNIPLHTR 69
                                   5799***********98887 PP

>> FSIP2  Fibrous sheath-interacting protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.1   1.4e-06    0.0083      14      90 ..       3      78 ..       1      83 [. 0.92

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.4e-06
                          FSIP2 14 nkvvhssvcnilkeyrsqdsickninsngenLarrLtsavieeifqhqlnlllsdevpasaclPLeskdvvkkvqkv 90
                                   +kv++ +v +il+   s d++ +ni+ + en+   L +  + e  +    + + de++++  +PL ++ ++  v   
  gi|116754750|ref|YP_843868.1|  3 EKVIKQCV-EILERIMSDDTVPRNIRRSAENVKGILLQEGLAEAVKAASAISILDEISNDPNIPLHTRTLIWNVASQ 78
                                   68888887.8**********************************************************999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 648.00
//
Query:       gi|116754751|ref|YP_843869.1|  [L=253]
Description: hypothetical protein Mthe_1455 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-09   36.9   1.1    4.1e-09   36.3   0.3    1.6  2  Ada_Zn_binding  Metal binding domain of Ada


Domain annotation for each model (and alignments):
>> Ada_Zn_binding  Metal binding domain of Ada
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       0.4   7.1e+03      48      56 ..      23      31 ..      20      32 .. 0.82
   2 !   36.3   0.3   2.3e-13   4.1e-09      11      64 ..     199     253 .]     191     253 .] 0.91

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.4
                                   HHHHHHTT- CS
                 Ada_Zn_binding 48 aaeAeaagf 56
                                    ++Ae++gf
  gi|116754751|ref|YP_843869.1| 23 QKAAEQSGF 31
                                   579999999 PP

  == domain 2  score: 36.3 bits;  conditional E-value: 2.3e-13
                                    TTCCTTBEEEETTTTEEE-TT-S.SS-S-SCCEEEESSHHHHHHTT-EEETTTTT CS
                 Ada_Zn_binding  11 aradgsFvyavkttgiyCrpsCp.arlPkrenveFfdtaaeAeaagfrpCkrcrP 64 
                                    +  dg+ +++  t + y  p+C+ ar+ k+e+ + f++ +eAea g+ pCk c+P
  gi|116754751|ref|YP_843869.1| 199 PGQDGAKYVGSATSRKYHLPDCRyARKIKPEHLVVFSSKEEAEARGYEPCKVCNP 253
                                    6679999***************7689999************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2032.05
//
Query:       gi|116754752|ref|YP_843870.1|  [L=256]
Description: ABC transporter related [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.7e-34  117.1   0.0    1.1e-33  116.6   0.0    1.3  1  ABC_tran       ABC transporter
    1.3e-11   44.4   0.5      6e-10   38.9   0.5    2.1  1  SMC_N          RecF/RecN/SMC N terminal domain
    9.9e-06   25.6   0.7       0.02   14.7   0.7    2.2  2  AAA_21         AAA domain, putative AbiEii toxin, Type IV TA 
    6.2e-05   22.7   0.2    0.00012   21.7   0.2    1.4  1  AAA_29         P-loop containing region of AAA domain
    0.00024   21.0   0.0    0.00054   19.9   0.0    1.6  1  RsgA_GTPase    RsgA GTPase
    0.00033   21.1   0.2      0.001   19.5   0.2    1.7  1  AAA_16         AAA ATPase domain
    0.00036   20.8   0.3     0.0018   18.5   0.3    2.0  1  AAA_22         AAA domain
    0.00044   19.9   0.3      0.023   14.2   0.3    2.5  1  AAA_25         AAA domain
     0.0021   18.6   0.2     0.0046   17.5   0.1    1.6  2  AAA_23         AAA domain
     0.0061   15.7   0.9      0.018   14.1   0.1    1.9  2  T2SSE          Type II/IV secretion system protein
     0.0074   16.0   0.0      0.013   15.3   0.0    1.6  1  AAA_15         AAA ATPase domain
      0.009   15.4   0.9        1.7    8.0   0.1    2.2  2  ATPase         KaiC
  ------ inclusion threshold ------
      0.015   15.8   0.3        2.1    8.8   0.1    2.4  2  AAA            ATPase family associated with various cellular
      0.015   14.9   0.1       0.15   11.6   0.0    2.2  2  cobW           CobW/HypB/UreG, nucleotide-binding domain
      0.017   14.9   0.2      0.058   13.2   0.1    1.8  2  Bclx_interact  Bcl-x interacting, BH3 domain
      0.024   14.7   0.2      0.073   13.1   0.1    2.0  2  MMR_HSR1       50S ribosome-binding GTPase
      0.028   14.6   0.0      0.047   13.9   0.0    1.6  1  AAA_33         AAA domain
      0.034   13.9   0.1       0.56    9.9   0.0    2.2  2  IstB_IS21      IstB-like ATP binding protein
      0.037   13.8   0.0       0.14   11.9   0.0    1.9  2  AAA_30         AAA domain
      0.048   13.7   0.1        2.6    8.0   0.0    2.2  2  MutS_V         MutS domain V
      0.056   12.9   0.1      0.091   12.2   0.1    1.4  1  KdpD           Osmosensitive K+ channel His kinase sensor dom
       0.06   13.2   0.1       0.61   10.0   0.0    2.0  2  ATPase_2       ATPase domain predominantly from Archaea
      0.065   12.1   0.0       0.18   10.7   0.0    1.7  2  AAA_10         AAA-like domain
      0.094   12.6   0.2       0.43   10.5   0.1    1.9  2  NACHT          NACHT domain
        0.1   12.3   0.1       0.31   10.7   0.0    1.8  2  AAA_24         AAA domain
       0.12   11.9   0.1        0.7    9.4   0.0    2.0  2  AAA_7          P-loop containing dynein motor region
       0.12   11.6   0.0       0.12   11.5   0.0    1.3  1  G-alpha        G-protein alpha subunit
       0.12   11.5   0.2       0.29   10.3   0.1    1.6  2  NB-ARC         NB-ARC domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.6   0.0   1.8e-36   1.1e-33       1     136 [.      32     180 ..      32     181 .. 0.92

  Alignments for each domain:
  == domain 1  score: 116.6 bits;  conditional E-value: 1.8e-36
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS--S-TTSBH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke....qeleslrkeigvlpqepqlfpeltv 76 
                                    l++++l++kege +aivG++G+GKStLl+++  l +pt+G+ill++ d+++    ++ +  ++e+g+++q ++l pe t+
  gi|116754752|ref|YP_843870.1|  32 LDHINLTIKEGEFLAIVGPSGSGKSTLLNMIGLLDTPTNGTILLKDIDVTKisanERARLRNRELGFVFQYHHLLPEFTA 111
                                    789******************************************9999999997777778899***************9 PP

                                    HHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    xxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  77 ren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                     en             e++e+++++l+++gl +      +++ps+LSgGq qrva+aral+++p++++ DE t
  gi|116754752|ref|YP_843870.1| 112 VENvmmpmliagverkEARERATALLKEVGLGDRL----DHKPSQLSGGQNQRVAVARALANRPSIVIGDELT 180
                                    999**********8888888899999999988855....5556****************************77 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 !   38.9   0.5   9.3e-13     6e-10       3     211 ..      20     225 ..      18     230 .. 0.72

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 9.3e-13
                                    EEEEEESETTEECEEEEEETTS.SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCC.CCC--BTTCSSTTEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                          SMC_N   3 krleienFksyagktvilpfsk.sftaivGpNGSGKsnlldAilFvLGersakklrsekls.dlihkskekasvkkaeve 80 
                                    +++  +++k  a +++ l +++ +f aivGp GSGKs ll+ i  +L + ++ ++  ++++   i++ +e+a++ + e+ 
  gi|116754752|ref|YP_843870.1|  20 TKIYSDGVKVVALDHINLTIKEgEFLAIVGPSGSGKSTLLNMI-GLLDTPTNGTILLKDIDvTKISA-NERARLRNRELG 97 
                                    6677778888888888888876369******************.55655555454444444133555.799999999999 PP

                                    EEEEETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--S CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  81 itfdnedkklkiekeevsisrrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpap 160
                                     +f+ +    + ++ e +++  ++ + e + + ++ ++  kev  l  + + ++++LSgG+ + va+a  +A    ++ +
  gi|116754752|ref|YP_843870.1|  98 FVFQYHHLLPEFTAVENVMMPMLIAGVERKEARERATALLKEV-GLGDRLDHKPSQLSGGQNQRVAVARALA----NRPS 172
                                    9999887763333333333333333333333444444444554.35556666788**********9998876....5668 PP

                                    EEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC-SCEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 161 lyllDeidaaLDeknvkkvaellkekskn..aQfivislreemlekadklvgv 211
                                    +++ De+  +LD k  + + e+l+e +k+    fi ++++ em ek d+++++
  gi|116754752|ref|YP_843870.1| 173 IVIGDELTGNLDTKTSRMIYEMLRELNKKinQTFILVTHDMEMAEKTDRILRL 225
                                    9999********************999876355899*************9987 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.7     3e-05      0.02       2      22 ..      45      65 ..      44      96 .. 0.81
   2 !    8.8   0.0     0.002       1.3     234     300 ..     150     214 ..     121     217 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3e-05
                         AAA_21  2 nvliGpNgsGKSnLLdaldll 22
                                    +++Gp gsGKS+LL  + ll
  gi|116754752|ref|YP_843870.1| 45 LAIVGPSGSGKSTLLNMIGLL 65
                                   68**************99887 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.002
                         AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQv.iltTHSpl 300
                                    +++lS G+ +  a++ al+ ++   s+++ DE+  +L+ k  r ++e+l+el+++  Q  il+TH+ +
  gi|116754752|ref|YP_843870.1| 150 PSQLSGGQNQRVAVARALANRP---SIVIGDELTGNLDTKTSRMIYEMLRELNKKINQTfILVTHDME 214
                                    4667888877768888888877...99999*******************99999999999*****975 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 !   21.7   0.2   1.9e-07   0.00012      17      45 ..      37      65 ..      31      73 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.9e-07
                         AAA_29 17 ieidlkgatlltGpsGsGKSTllDAiqal 45
                                   ++i++ ++  ++GpsGsGKSTll  i  l
  gi|116754752|ref|YP_843870.1| 37 LTIKEGEFLAIVGPSGSGKSTLLNMIGLL 65
                                   6677555999************9655544 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   8.4e-07   0.00054      89     119 ..      31      62 ..       5      89 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 8.4e-07
                                    THHHHHHHCTT.SEEEEECSTTSSHHHHHHHH CS
                    RsgA_GTPase  89 gleelkellkd.ktsvlvGqSGvGKStLinal 119
                                    +l++++  +k+ ++ ++vG+SG GKStL+n++
  gi|116754752|ref|YP_843870.1|  31 ALDHINLTIKEgEFLAIVGPSGSGKSTLLNMI 62 
                                    6778888888889*****************97 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.2   1.6e-06     0.001      23     144 ..      41     213 ..      30     227 .. 0.51

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.6e-06
                         AAA_16  23 rpelvllsGesGvGKsslvrellralekd..........................ggiflrgkcdqlesaipysalaqal 76 
                                    ++e + ++G+sG+GKs+l++++   l +                           +                   l  ++
  gi|116754752|ref|YP_843870.1|  41 EGEFLAIVGPSGSGKSTLLNMIG-LLDTPtngtillkdidvtkisanerarlrnrE-------------------LGFVF 100
                                    45899**************9998.55555444344443322222222222222211...................22222 PP

                         AAA_16  77 areellrqllde...........aesaeleawrekleeala.................................avpela 112
                                      ++ll +  +             e +e+++ +++l+++++                                 +++el+
  gi|116754752|ref|YP_843870.1| 101 QYHHLLPEFTAVenvmmpmliagVERKEARERATALLKEVGlgdrldhkpsqlsggqnqrvavaralanrpsivIGDELT 180
                                    22233333333344444444444666666666666666666666666655555555555555555555555555555555 PP

                         AAA_16 113 gaea...srllellkrll.allsrderplvlvlDdl 144
                                    g +    sr+ +++ r l +++    ++++lv  d+
  gi|116754752|ref|YP_843870.1| 181 GNLDtktSRMIYEMLRELnKKIN---QTFILVTHDM 213
                                    55554554555444444422222...2355555555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.3   2.8e-06    0.0018       4      29 ..      41      66 ..      37     218 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.8e-06
                         AAA_22  4 tagilvvtGesGtGKTtllrrlleql 29
                                   +  +l+++G+sG+GK+tll+++   +
  gi|116754752|ref|YP_843870.1| 41 EGEFLAIVGPSGSGKSTLLNMIGLLD 66
                                   6789***************9987765 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.3   3.7e-05     0.023      29     188 ..      38     211 ..      32     213 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.7e-05
                         AAA_25  29 llpagelallaGapgtGKttlaldlalava..tGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal......... 97 
                                     + +ge+ +++G++g+GK+tl+  ++l  +   G  +      + + V  +sa +++ +lr+R      ++         
  gi|116754752|ref|YP_843870.1|  38 TIKEGEFLAIVGPSGSGKSTLLNMIGLLDTptNGTIL-----LKDIDVTKISANERA-RLRNRELGFVFQYhhllpefta 111
                                    5789*****************8766654333133322.....256677777777777.7776666655444466777777 PP

                         AAA_25  98 ..............rddarllvldlagveslpLfak.drggtlltadvdaleaaieeveg.vrlvviDplsralggdens 161
                                                  r  ar++++ l +  ++ L +  d++ ++l +  ++  a++++ ++ +  v+ D l+       n 
  gi|116754752|ref|YP_843870.1| 112 venvmmpmliagveRKEARERATALLK--EVGLGDRlDHKPSQLSGGQNQRVAVARALANrPSIVIGDELTG------NL 183
                                    777777777776664444444444433..2444444133333355555555555555544466666666653......33 PP

                         AAA_25 162 nsdv.galvealeriarrtgaavllvhH 188
                                    ++++ ++++e+l+++ ++ + +++lv H
  gi|116754752|ref|YP_843870.1| 184 DTKTsRMIYEMLRELNKKINQTFILVTH 211
                                    3333377777777777777777777777 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   7.2e-06    0.0046      19      40 ..      42      63 ..      21      68 .. 0.82
   2 ?   -2.2   0.0       7.5   4.8e+03     152     152 ..     192     192 ..     125     221 .. 0.60

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 7.2e-06
                         AAA_23 19 kgltlItGpNGaGKTTildAik 40
                                     + +I+Gp G+GK+T+l+ i 
  gi|116754752|ref|YP_843870.1| 42 GEFLAIVGPSGSGKSTLLNMIG 63
                                   45668*************9986 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 7.5
                         AAA_23 152 k 152
                                     
  gi|116754752|ref|YP_843870.1| 192 Y 192
                                    1 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 !   14.1   0.1   2.8e-05     0.018     118     182 ..      31      94 ..       4     106 .. 0.70
   2 ?    0.1   0.1      0.53   3.4e+02     118     179 ..     159     225 ..     106     238 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.8e-05
                          T2SSE 118 iaevlrkavrerglilvsGgTgsGKttllyallkeinksderivtvEDpvEiqleganqvqlnak 182
                                      + ++  ++e   + + G+ gsGK+tll+++   +++ ++  +++ D   ++++++++ +l+++
  gi|116754752|ref|YP_843870.1|  31 ALDHINLTIKEGEFLAIVGPSGSGKSTLLNMI-GLLDTPTNGTILLKDIDVTKISANERARLRNR 94 
                                    4567888888889999*************964.66677666677777776666666666666665 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.53
                          T2SSE 118 iaevlrkavrerglilv....sGgTgsGKttllyallkeinks.derivtvEDpvEiqleganqvql 179
                                    ++ ++++a+++r +i++    +G   +  + ++y +l e+nk+ ++ +++v   +E+  + +  ++l
  gi|116754752|ref|YP_843870.1| 159 QRVAVARALANRPSIVIgdelTGNLDTKTSRMIYEMLRELNKKiNQTFILVTHDMEMAEKTDRILRL 225
                                    4455555555555555422224444444445668888888888777788777777776666655555 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0     2e-05     0.013      16      66 ..      34      81 ..      31     222 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2e-05
                         AAA_15 16 dveidlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedle 66
                                   ++ + ++e  +  ++G+ +sGKS++l+++ l+ + +    + +i +++ d+ 
  gi|116754752|ref|YP_843870.1| 34 HINLTIKEGeFLAIVGPSGSGKSTLLNMIGLLDTPT----NGTILLKDIDVT 81
                                   555556665799*****************8887766....444444444433 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1     0.011       6.9       8      35 ..      32      58 ..      26      61 .. 0.83
   2 !    8.0   0.1    0.0026       1.7     139     195 ..     187     240 ..     161     245 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.011
                         ATPase  8 lDeilkgGipegrvvlitGepGtGKtif 35
                                   lD+i +  i eg+   i+G +G+GK+++
  gi|116754752|ref|YP_843870.1| 32 LDHI-NLTIKEGEFLAIVGPSGSGKSTL 58
                                   5555.467999**************987 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0026
                         ATPase 139 vaReilrqlvrvl.kklgvTailvsekssseeaaggygveefivdgvivLdlkeieee 195
                                    +  + + +++r+l kk+++T ilv+   + e a ++ ++   +vdg iv +l+++ +e
  gi|116754752|ref|YP_843870.1| 187 TS-RMIYEMLRELnKKINQTFILVTH--DMEMAEKTDRILR-LVDGRIVCELRRVGDE 240
                                    33.45566777777999********9..4556777888999.9*****9999888765 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 ?    5.1   0.0     0.044        28       3      18 ..      47      62 ..      45      94 .. 0.89
   2 ?    8.8   0.1    0.0032       2.1      47     128 ..     158     230 ..     112     234 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.044
                                   EESSTTSSHHHHHHHH CS
                            AAA  3 lyGppGtGKTllakav 18
                                   ++Gp G GK++l + +
  gi|116754752|ref|YP_843870.1| 47 IVGPSGSGKSTLLNMI 62
                                   79*********98876 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0032
                                    HHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTS CS
                            AAA  47 relfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRf 124
                                    ++ ++ a++ a +psi++ DE+     ++       ++r++ ++l+el++  +     ++i++t+++++ ++  +  + +
  gi|116754752|ref|YP_843870.1| 158 NQRVAVARALAnRPSIVIGDELTGNLDTK-------TSRMIYEMLRELNKKIN----QTFILVTHDMEMAEKTDRIlRLV 226
                                    34444455555569999999999988888.......78888888888888777....599******99988877655556 PP

                                    SEEE CS
                            AAA 125 drki 128
                                    d +i
  gi|116754752|ref|YP_843870.1| 227 DGRI 230
                                    6555 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00024      0.15       3      36 ..      45      78 ..      43      95 .. 0.75
   2 ?    1.1   0.0       0.4   2.6e+02      39      66 ..     209     235 ..     161     243 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00024
                                   EEEEESTTCCHHHHHHHHHCT--SS-EEEEESS- CS
                           cobW  3 tvltGflGsGKTtLlnhllenraglklavivNef 36
                                   + ++G+ GsGK+tLln +       +  +++ ++
  gi|116754752|ref|YP_843870.1| 45 LAIVGPSGSGKSTLLNMIGLLDTPTNGTILLKDI 78
                                   5799************986555555555555555 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.4
                                    CHCCCCCCHCCCT.EEEETTTTECCHCT CS
                           cobW  39 vsiDaellretgveivelenGciCctlr 66 
                                    v +D e+ ++t + i+ l +G i c lr
  gi|116754752|ref|YP_843870.1| 209 VTHDMEMAEKT-DRILRLVDGRIVCELR 235
                                    66777777777.5699999999988876 PP

>> Bclx_interact  Bcl-x interacting, BH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       6.1   3.9e+03      15      22 ..     171     178 ..     162     179 .. 0.64
   2 ?   13.2   0.1   9.1e-05     0.058      21      30 ..     232     241 ..     229     244 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 6.1
                                    HHHHHHHH CS
                  Bclx_interact  15 PEiwiAqE 22 
                                    P i+i  E
  gi|116754752|ref|YP_843870.1| 171 PSIVIGDE 178
                                    55555555 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 9.1e-05
                                    HHHHHHHHHH CS
                  Bclx_interact  21 qELRRIGDEF 30 
                                     ELRR+GDEF
  gi|116754752|ref|YP_843870.1| 232 CELRRVGDEF 241
                                    5********* PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   0.00011     0.073       2      19 ..      45      62 ..      44      99 .. 0.88
   2 ?   -1.8   0.0       5.1   3.2e+03      67      67 ..     210     210 ..     177     237 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
                                   EEEEESTTSSHHHHHHHH CS
                       MMR_HSR1  2 vaivGrpNvGKStLinal 19
                                    aivG + +GKStL+n +
  gi|116754752|ref|YP_843870.1| 45 LAIVGPSGSGKSTLLNMI 62
                                   59**************86 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 5.1
                                    H CS
                       MMR_HSR1  67 g 67 
                                    +
  gi|116754752|ref|YP_843870.1| 210 T 210
                                    1 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   7.3e-05     0.047       4      46 ..      47      92 ..      45     201 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.3e-05
                         AAA_33  4 lvGlpGsGKstlaerl..lkklg.avllssdtlrrrlfgtdqqskt 46
                                   +vG++GsGKstl+  +  l   + +++l +d+  +++ ++++ +++
  gi|116754752|ref|YP_843870.1| 47 IVGPSGSGKSTLLNMIglLDTPTnGTILLKDIDVTKISANERARLR 92
                                   79**********9864325444478888888877777776666655 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00087      0.56      44      68 ..      39      63 ..      12      81 .. 0.84
   2 ?    1.6   0.0       0.3   1.9e+02     102     153 ..     164     217 ..     152     224 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00087
                      IstB_IS21 44 iekkenivllGpsGvGKshlaialg 68
                                   i++ e ++++GpsG GKs l   +g
  gi|116754752|ref|YP_843870.1| 39 IKEGEFLAIVGPSGSGKSTLLNMIG 63
                                   678899************9987776 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.3
                      IstB_IS21 102 alkrllkvdllilDdlgllpldqaeaellfevi...ekryerrsiiitsnlpfae 153
                                    a +   +++++i D+l   +ld + +++++e++   +k+ +++ i++t ++++ae
  gi|116754752|ref|YP_843870.1| 164 ARALANRPSIVIGDELT-GNLDTKTSRMIYEMLrelNKKINQTFILVTHDMEMAE 217
                                    44445677888888885.5788888888888862225678888899998888776 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00022      0.14      16      40 ..      40      64 ..      32      95 .. 0.81
   2 ?   -0.7   0.0       1.6     1e+03      13     113 ..     166     196 ..     127     230 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00022
                         AAA_30 16 sgdrvavltGpAGtGKttalkalre 40
                                   ++  + +++Gp G+GK+t+l+ +  
  gi|116754752|ref|YP_843870.1| 40 KEGEFLAIVGPSGSGKSTLLNMIGL 64
                                   3445999*************98755 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.6
                         AAA_30  13 lltsgdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieastiakllkrlkgrarlepgtll 92 
                                    +l+++                                                                        +++
  gi|116754752|ref|YP_843870.1| 166 ALANR-----------------------------------------------------------------------PSIV 174
                                    22222.......................................................................2444 PP

                         AAA_30  93 ivDE.agmvdtkqlaallkaae 113
                                    i DE +g +dtk+ + + + ++
  gi|116754752|ref|YP_843870.1| 175 IGDElTGNLDTKTSRMIYEMLR 196
                                    4444223444444444444333 PP

>> MutS_V  MutS domain V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.093        59       3      21 ..      47      65 ..      45      68 .. 0.88
   2 ?    8.0   0.0     0.004       2.6      46     133 ..     138     225 ..     115     242 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.093
                                   EE-STTSSHHHHHHHHHHH CS
                         MutS_V  3 itGpnmaGkstylrqvali 21
                                   i Gp  +Gkst+l  ++l+
  gi|116754752|ref|YP_843870.1| 47 IVGPSGSGKSTLLNMIGLL 65
                                   89***********999875 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.004
                                    EEE--------SS-HHHHHHHH.HHHHHTT--TTSEEEEESTS-SS-HHHHHHHHHHHHHHHHHTT--EEEEEES-GGGG CS
                         MutS_V  46 tRvgasDdlakgkstFmvEmlE.tasilknatekslvilDElGRGtstydGlaialavaeyllekikaktlfatHyhelt 124
                                      vg +D+l ++ s      +  +a     a++ s+vi DEl     t     + + +++ l +ki+ + ++ tH +e++
  gi|116754752|ref|YP_843870.1| 138 KEVGLGDRLDHKPSQLSGGQNQrVAVARALANRPSIVIGDELTGNLDT-KTSRMIYEMLRELNKKINQTFILVTHDMEMA 216
                                    5667777777777766654443144444558899********755555.55667789999*******************9 PP

                                    GHHHHSTTE CS
                         MutS_V 125 klaekleev 133
                                    + ++++ ++
  gi|116754752|ref|YP_843870.1| 217 EKTDRILRL 225
                                    998877665 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 ?   12.2   0.1   0.00014     0.091      35     111 ..     119     198 ..     102     225 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                           KdpD  35 vviglve.thgrketeallegl...eviprkeveykgkeleeldldailarkpevvlvDelahtnapgsrhekryqdvee 110
                                    ++i+ ve ++ r++ +all+++   + +++k  + +g + +++ +  +la++p++v+ Del   n +    +  y+  +e
  gi|116754752|ref|YP_843870.1| 119 MLIAGVErKEARERATALLKEVglgDRLDHKPSQLSGGQNQRVAVARALANRPSIVIGDELTG-NLDTKTSRMIYEMLRE 197
                                    556555515567888888888733345788889999*************************75.4555566666666666 PP

                           KdpD 111 l 111
                                    l
  gi|116754752|ref|YP_843870.1| 198 L 198
                                    5 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 ?   10.0   0.0   0.00096      0.61      13      40 ..      37      62 ..      28      95 .. 0.84
   2 ?    1.4   0.0      0.38   2.4e+02      92     131 ..     177     217 ..     112     230 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00096
                       ATPase_2 13 eilerepneiyfiYGpegsGKtaLlkei 40
                                     +++   e++ i Gp gsGK++Ll+ i
  gi|116754752|ref|YP_843870.1| 37 LTIKE--GEFLAIVGPSGSGKSTLLNMI 62
                                   55555..6788999***********865 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.38
                       ATPase_2  92 eeilkeksklvfkaielllekikkkgkk.iiiiiDelqkli 131
                                    +e+  +  ++  + i ++l++++kk  +  i++  ++ ++ 
  gi|116754752|ref|YP_843870.1| 177 DELTGNLDTKTSRMIYEMLRELNKKINQtFILVTHDMEMAE 217
                                    33333444445556666666666666665666666666665 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00028      0.18      24     112 ..      45     139 ..      31     201 .. 0.77
   2 ?   -0.9   0.0      0.95   6.1e+02     256     284 ..     186     214 ..     159     224 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00028
                         AAA_10  24 sliiGdlGnGKSvlakllvlyisllggkali..iDpkkerekfketl..peiakkinvvtLdse.eenegvLdPlvllk. 97 
                                     +i+G+ G GKS l +++ l  +  +g +l+  iD +k   + + +l  +e+   +++ +L +e +  e v+ P++++  
  gi|116754752|ref|YP_843870.1|  45 LAIVGPSGSGKSTLLNMIGLLDTPTNGTILLkdIDVTKISANERARLrnRELGFVFQYHHLLPEfTAVENVMMPMLIAGv 124
                                    48************************999985566665543333333334455568888887776777888888888876 PP

                         AAA_10  98 eekeaeslaedilel 112
                                    e kea + a ++l+ 
  gi|116754752|ref|YP_843870.1| 125 ERKEARERATALLKE 139
                                    667777777777765 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.95
                         AAA_10 256 aeGkkllkelvRiG.Rsynaavylvtqsad 284
                                    +  + +  e++R   ++ n   +lvt++++
  gi|116754752|ref|YP_843870.1| 186 KTSRMI-YEMLRELnKKINQTFILVTHDME 214
                                    444444.44555443888888899998875 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00067      0.43       3      20 ..      45      62 ..      43      65 .. 0.88
   2 ?   -0.6   0.0       1.7   1.1e+03      91     134 ..     177     218 ..     173     237 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00067
                                   EEEEC-TTTCHHHHHHHH CS
                          NACHT  3 vilqGeaGsGKTtLlqkl 20
                                   +++ G++GsGK+tLl  +
  gi|116754752|ref|YP_843870.1| 45 LAIVGPSGSGKSTLLNMI 62
                                   789************876 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.7
                                    TT-SS-TCH.........HHHHHCTTTTT--EEEEEEECCCHHH CS
                          NACHT  91 DelvtdlgqkekqpvrtlLselirkkllpeasllltvrpralrd 134
                                    Del   l+ k+ + + ++L+el +k  + ++ +l+t   +  ++
  gi|116754752|ref|YP_843870.1| 177 DELTGNLDTKTSRMIYEMLRELNKK--INQTFILVTHDMEMAEK 218
                                    6777777777777778888888777..88888888765555544 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00048      0.31       5      22 ..      45      62 ..      42     112 .. 0.85
   2 ?   -1.4   0.1       2.6   1.7e+03     111     133 ..     187     214 ..     181     224 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00048
                         AAA_24  5 iliyGpsgiGKTtlakel 22
                                   ++i+Gpsg+GK+tl++++
  gi|116754752|ref|YP_843870.1| 45 LAIVGPSGSGKSTLLNMI 62
                                   589***********9988 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.6
                         AAA_24 111 frrllkk.lqelrk....nvifiahekt 133
                                     +r++   l+el+k    ++i++ h  +
  gi|116754752|ref|YP_843870.1| 187 TSRMIYEmLRELNKkinqTFILVTHDME 214
                                    4454444467777655567777777555 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 ?    9.4   0.0    0.0011       0.7      26      52 ..      35      61 ..      19      86 .. 0.83
   2 ?    0.0   0.0      0.81   5.2e+02      40      81 ..     181     222 ..     166     227 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0011
                          AAA_7 26 lelllknkkpvllvGptGtGKtviikd 52
                                   ++l +k++  + +vGp+G+GK+++++ 
  gi|116754752|ref|YP_843870.1| 35 INLTIKEGEFLAIVGPSGSGKSTLLNM 61
                                   578899999999***********9886 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.81
                          AAA_7  40 GptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdi 81 
                                    G+  t  + +i ++l++l+k+  ++ ++  + +  a+++ +i
  gi|116754752|ref|YP_843870.1| 181 GNLDTKTSRMIYEMLRELNKKINQTFILVTHDMEMAEKTDRI 222
                                    444444456777799999966555555555555555555555 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00019      0.12      26      51 ..      45      83 ..      33     222 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00019
                                   EEEEESTTSSHHHHHHHHHHHCS--.............- CS
                        G-alpha 26 llllGqseSGKsTilkqlkllykkg.............f 51
                                   l ++G s+SGKsT+l+ + ll +++             +
  gi|116754752|ref|YP_843870.1| 45 LAIVGPSGSGKSTLLNMIGLLDTPTngtillkdidvtkI 83
                                   6789***************99998866655555555444 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   0.00045      0.29      19      40 ..      43      62 ..      33      65 .. 0.86
   2 ?   -2.2   0.0       2.9   1.9e+03     217     225 ..     195     203 ..     145     226 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00045
                                   CSEEEEEEESTTSSHHHHHHHH CS
                         NB-ARC 19 qslvvalvGmgGvGKttlakqi 40
                                   +  ++a+vG  G+GK+tl++ i
  gi|116754752|ref|YP_843870.1| 43 E--FLAIVGPSGSGKSTLLNMI 62
                                   4..99*************9765 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.9
                                    HHHHHHHHH CS
                         NB-ARC 217 wkkvlekle 225
                                    ++++++k++
  gi|116754752|ref|YP_843870.1| 195 LRELNKKIN 203
                                    222333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       770  (0.0429472); expected 358.6 (0.02)
Passed bias filter:                      663  (0.0369792); expected 358.6 (0.02)
Passed Vit filter:                       108  (0.00602376); 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: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 1792.74
//
Query:       gi|116754753|ref|YP_843871.1|  [L=390]
Description: UDP-glucose/GDP-mannose dehydrogenase [Methanosaeta thermophila PT]
Scores for complete 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-34  118.7   0.0    3.1e-34  118.2   0.0    1.2  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
    3.1e-18   65.8   0.0    4.9e-18   65.1   0.0    1.3  1  UDPG_MGDP_dh    UDP-glucose/GDP-mannose dehydrogenase family,
    0.00027   21.3   0.0    0.00053   20.4   0.0    1.5  1  UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family,
      0.007   16.5   0.0      0.074   13.2   0.0    2.4  2  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
  ------ inclusion threshold ------
      0.035   13.5   0.0         21    4.4   0.0    3.0  3  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase


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 !  118.2   0.0   8.7e-38   3.1e-34       6     179 ..       1     172 [.       1     178 [. 0.96

  Alignments for each domain:
  == domain 1  score: 118.2 bits;  conditional E-value: 8.7e-38
                                    E--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS.--TTHHHHHHHHCHTTTEEEES-HHHHHHC-SEEEE-- CS
                 UDPG_MGDP_dh_N   6 iGlGYvGlvtaavlaeighevigvDideekvdklnsgkipi.yepgLeelvkkavesgrlsfttdvekaveeadvifiaV 84 
                                    +GlG  Gl+ aav+a +g++v+gvDid+++ d +nsgk pi  e gL+el+ +    + l +tt+++  + +++v+++ V
  gi|116754753|ref|YP_843871.1|   1 MGLGNAGLPLAAVIADHGIQVVGVDIDRRRCDLINSGKNPIpQEVGLDELISRYG-GKGLVATTEYRD-AVSCNVFIVIV 78 
                                    59***************************************6699********99.8**********9.568******** PP

                                    ---B-TTTTCB-THHHHHHHHHHHHHHHCEEEEEE-S---TTHHHHCHHHHHHHHCSS-TTCEEEEE------TTSHHHH CS
                 UDPG_MGDP_dh_N  85 gTPskkkgkaaDlkyvesaarsiaealkkgkvvvvkSTvpvgtaeelvkkileeaskkkgvdfdvvsnPEflregsavkd 164
                                    +   +k ++++D + +esa rs++++lk+g++vv++ Tvp+gt+e l+ + +ee s+ k  +f+++++PE++  g  +  
  gi|116754753|ref|YP_843871.1|  79 PLFIDK-NHNPDFRTLESAFRSLGSVLKRGDLVVLETTVPPGTTEGLALRWIEESSELKLGQFYLAHSPERIMTGCSISR 157
                                    **9999.999***********************************************999******************** PP

                                    HHS-S-EEEEESSCH CS
                 UDPG_MGDP_dh_N 165 llnpdrvviGveekk 179
                                    l + ++v++Gv+e++
  gi|116754753|ref|YP_843871.1| 158 LREFPKVIGGVDERS 172
                                    ***********9875 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 !   65.1   0.0   1.4e-21   4.9e-18       2      93 ..     195     285 ..     194     286 .. 0.91

  Alignments for each domain:
  == domain 1  score: 65.1 bits;  conditional E-value: 1.4e-21
                   UDPG_MGDP_dh   2 tAEliKlaaNaflatkIsfiNelanlcealgidveeVieavgldprigpkflkpglGvGGsclpkDvkaLvala..eelg 79 
                                     AE+iK+++ ++++++I+++Nel ++ ++lgid +e +e ++++     +++ p+ GvGG+c+p+ +++L++ +  +e  
  gi|116754753|ref|YP_843871.1| 195 VAEMIKVMEGCYRDVNIALANELFKISNELGIDFHEAREHANHEYC---HIHMPSTGVGGHCIPVYPWFLINEMvrRERA 271
                                    7****************************************99987...89********************954225566 PP

                   UDPG_MGDP_dh  80 leaelleavrevNe 93 
                                     +a +l+++re N+
  gi|116754753|ref|YP_843871.1| 272 EDAVMLRTARELND 285
                                    679*********97 PP

>> UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   1.5e-07   0.00053       2      47 ..     313     358 ..     312     379 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.5e-07
                                    EE-SSSSTT-S--TT-HHHHHHHHHHHCTSEEEEE-SSTHHCCCCH CS
                 UDPG_MGDP_dh_C   2 ilGlafKkdtdDlReSpaldiieeLleegaevkiyDPkvkeeavea 47 
                                    i G+++++++ +l +S+ l++++ L+++g +v +yD   ++e+v +
  gi|116754753|ref|YP_843871.1| 313 IHGITYRPGVRELHHSRNLALAKLLKSRGLKVGAYDETLSKEEVLK 358
                                    78**************************************999876 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   2.1e-05     0.074       6      98 ..       2     122 ..       1     133 [. 0.65
   2 ?   -0.1   0.0      0.25   9.1e+02      14      43 ..     333     361 ..     331     376 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.1e-05
                                    --SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT....................EEE-SSHHHHHHHC...SEEEE- CS
                  NAD_binding_2   6 GlGvMGsnmalnllkagykvavynrtkekveelvaeg....................akaaesieelvasl...dvvitm 62 
                                    GlG+ G ++a  ++++g++v++++ ++ +++ + + +                    ++a+++ +++v+      +v ++
  gi|116754753|ref|YP_843871.1|   2 GLGNAGLPLAAVIADHGIQVVGVDIDRRRCDLINSGKnpipqevgldelisryggkgLVATTEYRDAVSCNvfiVIVPLF 81 
                                    **************************999987766657777777777777777777666666666665433222222223 PP

                                    SSSHHHHH.HHHHS....HCCC--TT-EEEE-S---HHHHH CS
                  NAD_binding_2  63 vkagkavd.evieg....llealkkgdilidgstsspedtr 98 
                                    + ++++ d  ++e+    l + lk+gd+++  +t+ p +t+
  gi|116754753|ref|YP_843871.1|  82 IDKNHNPDfRTLESafrsLGSVLKRGDLVVLETTVPPGTTE 122
                                    33222222112222333466666777777777777776666 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.25
                                    HHHHHHHTT-EEEEE-SSHHHHHHHHHTTE CS
                  NAD_binding_2  14 malnllkagykvavynrtkekveelvaega 43 
                                    +a+ l+++g kv +y+ t +k  e++++g+
  gi|116754753|ref|YP_843871.1| 333 LAKLLKSRGLKVGAYDETLSKE-EVLKTGL 361
                                    788999**********997764.4455555 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 ?    4.2   0.0    0.0067        24      42      89 ..       1      51 [.       1      54 [. 0.78
   2 ?    0.7   0.0     0.083     3e+02      68     106 ..      85     121 ..      67     129 .. 0.79
   3 ?    4.4   0.0    0.0059        21      50      87 ..     332     368 ..     331     384 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0067
                                   ES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH..CHHHHTC.EECSHHHHH CS
                   2-Hacid_dh_C 42 iGlGrIGqavakrlkafgmkviaydrskkkee..eeeelgv.elvsleell 89
                                   +GlG+ G  +a +++  g++v+++d  +++ +  +  ++ + + v l+el+
  gi|116754753|ref|YP_843871.1|  1 MGLGNAGLPLAAVIADHGIQVVGVDIDRRRCDliNSGKNPIpQEVGLDELI 51
                                   7*************************9998776644444444666777766 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.083
                                    SHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S--STTTT CS
                   2-Hacid_dh_C  68 skkkeeeeeelgvelvsleellaesDivslhlpltpetr 106
                                    +++   ++++l+  + sl  +l++ D v+l + + p t+
  gi|116754753|ref|YP_843871.1|  85 NHN--PDFRTLESAFRSLGSVLKRGDLVVLETTVPPGTT 121
                                    333..24677778899**************998887775 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.0059
                                    HHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHH CS
                   2-Hacid_dh_C  50 avakrlkafgmkviaydrskkkeeeeeelgvelvslee 87 
                                    a+ak+lk+ g+kv ayd + +kee + ++g+e+++ e+
  gi|116754753|ref|YP_843871.1| 332 ALAKLLKSRGLKVGAYDETLSKEE-VLKTGLEWMDPED 368
                                    689****************99887.7777888887664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); 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: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2924.10
//
Query:       gi|116754754|ref|YP_843872.1|  [L=189]
Description: hexapaptide repeat-containing transferase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-28   97.3  13.4    1.7e-10   40.2   0.4    3.2  3  Hexapep          Bacterial transferase hexapeptide (six repea
    4.4e-17   61.5  10.5    1.7e-07   30.9   1.1    3.5  3  Hexapep_2        Hexapeptide repeat of succinyl-transferase
  ------ inclusion threshold ------
      0.085   13.3   0.1       0.15   12.6   0.1    1.3  1  Acetyltransf_11  Udp N-acetylglucosamine O-acyltransferase; D
        0.6    9.9   2.7          1    9.2   2.7    1.3  1  Sas6_CC          Sas6/XLF/XRCC4 coiled-coil domain
       0.83    9.9   2.9       0.96    9.7   0.0    2.3  2  CART             Cocaine and amphetamine regulated transcript


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 !   37.6   0.5   3.2e-13   1.1e-09       1      35 [.      13      47 ..      13      48 .. 0.95
   2 !   40.2   0.4   4.7e-14   1.7e-10       1      35 [.      49      83 ..      49      84 .. 0.95
   3 !   27.4   1.4   5.1e-10   1.8e-06       2      35 ..     101     134 ..     100     135 .. 0.95

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 3.2e-13
                                   TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                        Hexapep  1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35
                                   s+ IG+++ I++fa+i++++ IG+n+ Ig gv+i 
  gi|116754754|ref|YP_843872.1| 13 SAEIGEGTSIWHFAHIREGARIGRNCNIGKGVYID 47
                                   689*****************************996 PP

  == domain 2  score: 40.2 bits;  conditional E-value: 4.7e-14
                                   TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                        Hexapep  1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35
                                   +++IG+nv+I +f+ ++++V+I d+v Ig+ +v +
  gi|116754754|ref|YP_843872.1| 49 DVKIGDNVKIQNFVSVYHGVEIEDDVFIGPSAVFT 83
                                   589****************************9987 PP

  == domain 3  score: 27.4 bits;  conditional E-value: 5.1e-10
                                    EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                        Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                    t++  ++ Ig++a+i  +++IG+++ +gag+v++
  gi|116754754|ref|YP_843872.1| 101 TKVCRGASIGANATIICGTTIGEYAMVGAGSVVT 134
                                    78999***************************97 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   1.1   4.7e-11   1.7e-07       3      32 ..      33      64 ..      31      66 .. 0.89
   2 !   10.7   0.0   9.2e-05      0.33       2      15 ..      68      81 ..      67      83 .. 0.90
   3 !   24.1   1.5   6.3e-09   2.3e-05      10      34 .]     109     135 ..     100     135 .. 0.89

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 4.7e-11
                                   EE-TT-EE-TT-EE..SEEE-TT-EE-TT-EE CS
                      Hexapep_2  3 iIGdnCliGanagi..GvslGdncvvgaGvvi 32
                                   +IG nC+iG+  +i   v++Gdn+++++ v +
  gi|116754754|ref|YP_843872.1| 33 RIGRNCNIGKGVYIdrDVKIGDNVKIQNFVSV 64
                                   8*************888*********996665 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 9.2e-05
                                   EEE-TT-EE-TT-E CS
                      Hexapep_2  2 viIGdnCliGanag 15
                                   v I+d+++iG++a+
  gi|116754754|ref|YP_843872.1| 68 VEIEDDVFIGPSAV 81
                                   78*********997 PP

  == domain 3  score: 24.1 bits;  conditional E-value: 6.3e-09
                                    E-TT-EE..SEEE-TT-EE-TT-EE-S CS
                      Hexapep_2  10 iGanagi..GvslGdncvvgaGvvita 34 
                                    iGana+i  G+++G+ + vgaG+v+t+
  gi|116754754|ref|YP_843872.1| 109 IGANATIicGTTIGEYAMVGAGSVVTE 135
                                    9*****669****************95 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 ?   12.6   0.1     4e-05      0.15       1      17 [.     136     152 ..     136     153 .. 0.96

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4e-05
                                    BB-TTEEEETTTTEEEE CS
                Acetyltransf_11   1 DVpPfvlvagnparlrg 17 
                                    DVpP+ lv gnpa lrg
  gi|116754754|ref|YP_843872.1| 136 DVPPYGLVYGNPAVLRG 152
                                    9*************998 PP

>> Sas6_CC  Sas6/XLF/XRCC4 coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   2.7   0.00028         1       1      11 [.     167     177 ..     167     177 .. 0.98

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00028
                                    HHHHHHHHCCH CS
                        Sas6_CC   1 DseVKKYLAvC 11 
                                    Ds+VK+YL +C
  gi|116754754|ref|YP_843872.1| 167 DSDVKEYLCDC 177
                                    9*********9 PP

>> CART  Cocaine and amphetamine regulated transcript protein (CART)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00027      0.96      44      60 ..      28      44 ..       3      50 .. 0.87
   2 ?   -1.9   2.1       1.1   3.9e+03      52      57 ..     173     178 ..     151     185 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00027
                           CART 44 vrkgsRiGklCdCprgt 60
                                   +r+g+RiG+ C+  +g 
  gi|116754754|ref|YP_843872.1| 28 IREGARIGRNCNIGKGV 44
                                   8***********99986 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.1
                           CART  52 klCdCp 57 
                                     lCdC 
  gi|116754754|ref|YP_843872.1| 173 YLCDCG 178
                                    578886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1492.62
//
Query:       gi|116754755|ref|YP_843873.1|  [L=303]
Description: oxidoreductase domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.4e-22   78.6   0.1    1.1e-21   77.9   0.1    1.4  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
    1.3e-06   28.7   0.0    2.1e-06   28.0   0.0    1.4  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
    4.9e-06   26.0   0.0    9.2e-06   25.1   0.0    1.4  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
     0.0005   20.6   0.1     0.0026   18.3   0.0    2.2  3  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    0.00086   18.9   0.0     0.0019   17.8   0.0    1.5  2  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
     0.0024   18.5   0.0     0.0048   17.5   0.0    1.5  1  CoA_binding      CoA binding domain
  ------ inclusion threshold ------
      0.014   15.7   1.3       0.33   11.2   0.9    2.9  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
       0.12   11.3   0.0       0.19   10.6   0.0    1.3  1  OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin famil


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 !   77.9   0.1   4.9e-25   1.1e-21       2     120 .]       2     115 ..       1     115 [. 0.93

  Alignments for each domain:
  == domain 1  score: 77.9 bits;  conditional E-value: 4.9e-25
                                    EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHHHHHHH CS
                   GFO_IDH_MocA   2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpeidavivatpngtheelaka 81 
                                     v++iG+G +g++h+r + e  ++ +   ++d+ +++aea+  +  +  +  ++ell+  + +av++++p+++h+++a+ 
  gi|116754755|ref|YP_843873.1|   2 DVGVIGVGSMGRNHVRVYSEL-KGVDNLYVYDSLEKNAEAA--KEYATICRTIDELLD--ASEAVSICVPTKHHYDVAMC 76 
                                    69*************888888.8888888**********65..566667899******..88****************** PP

                                    HHHTT-EEEEESSS-SSHHHHHHHHHHHHHHTS-EEEE- CS
                   GFO_IDH_MocA  82 aleagkhvllEKPlattveeakelvelaekkgklvsvgy 120
                                    ++eag+h l+EKP+++t++ea++l+++ ++++ +v+vg+
  gi|116754755|ref|YP_843873.1|  77 VIEAGVHCLIEKPMTLTLDEAERLLNAIRSRDLVVGVGH 115
                                    *************************************97 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 !   28.0   0.0   9.4e-10   2.1e-06       1      72 [.       2      74 ..       2     108 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 9.4e-10
                                   EEEEE--SHHHHHHHHHH..HHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHH CS
                  NAD_binding_2  1 kigfiGlGvMGsnmalnl..lkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdev 72
                                   ++g+iG+G MG+n ++    lk   +++vy+   ek  e+++e a+++ +i el+++ ++v ++v+ +++ d  
  gi|116754755|ref|YP_843873.1|  2 DVGVIGVGSMGRNHVRVYseLKGVDNLYVYDSL-EKNAEAAKEYATICRTIDELLDASEAVSICVPTKHHYDVA 74
                                   59*************99965677789*****77.55666677889**********************9987755 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 !   25.1   0.0   4.1e-09   9.2e-06      38     103 ..       2      69 ..       1      74 [. 0.87

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 4.1e-09
                                    EEEEES-SHHHHHHHHHHHHTT-..EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S--ST CS
                   2-Hacid_dh_C  38 tvGiiGlGrIGqavakrlkafgm..kviaydrskkkeeeeeelgvelvsleellaesDivslhlpltp 103
                                     vG+iG+G++G++  ++ ++++   ++++yd  +k+ e+++e+   + +++ell  s+ vs+++p ++
  gi|116754755|ref|YP_843873.1|   2 DVGVIGVGSMGRNHVRVYSELKGvdNLYVYDSLEKNAEAAKEYATICRTIDELLDASEAVSICVPTKH 69 
                                    69***************9987655899999999998887777777788*****************775 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 !   18.3   0.0   1.2e-06    0.0026       2      78 ..       3      74 ..       2      81 .. 0.89
   2 ?   -2.4   0.0       3.4   7.6e+03      24      51 ..     105     131 ..      97     139 .. 0.61
   3 ?   -2.3   0.0       3.1     7e+03      22      45 ..     224     246 ..     218     261 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.2e-06
                                   EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHH CS
                  F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevl 78
                                   +g+iG G+mg+  ++  ++      +++v    + ek +e+a+e+  +++  +  e+++ ++ v ++v+++++ +v+
  gi|116754755|ref|YP_843873.1|  3 VGVIGVGSMGRNHVRVYSELK-GVDNLYVY--DSLEKNAEAAKEYA-TICR-TIDELLDASEAVSICVPTKHHYDVA 74
                                   89*************999986.8999**55..88888889999996.7777.89*******************9997 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.4
                                    -GGCEEEEEESSCCCHHHHHHHHC-EEE CS
                  F420_oxidored  24 qpheivvansrnpekaeelaeelgvkvt 51 
                                    + +++vv+   + e+ + + +e+++ +t
  gi|116754755|ref|YP_843873.1| 105 RSRDLVVG-VGHIERFNPIVAEIKRIIT 131
                                    44556655.7777777777777764444 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 3.1
                                    TS.-GGCEEEEEESSCCCHHHHHHH CS
                  F420_oxidored  22 ga.qpheivvansrnpekaeelaee 45 
                                    g    +e+++   r+pek  +  e+
  gi|116754755|ref|YP_843873.1| 224 GDfMTQEVYI--YRKPEKYFKEGER 246
                                    4446788884..4888877665544 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 !   17.8   0.0   8.5e-07    0.0019       7      81 ..       3      78 ..       1      92 [. 0.91
   2 ?   -2.7   0.0       1.7   3.9e+03      97     134 ..     184     220 ..     173     222 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 8.5e-07
                                   EEEES-SHHHHHHHHHHHH.TT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHHHHHHHHT CS
                           IlvN  7 iaviGyGsqGhaqalnlrd.sgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelqkevyeeei 81
                                   + viG Gs G+++ +   +  g+d  +   + +k+++ Ake +    t++e+ ++++ v i +P +++ +v    i
  gi|116754755|ref|YP_843873.1|  3 VGVIGVGSMGRNHVRVYSElKGVDNLYVYDSLEKNAEAAKEYATICRTIDELLDASEAVSICVPTKHHYDVAMCVI 78
                                   89************99988579**9999999999********************************9999876555 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.7
                                    HHHHTTSS---TTSEEEEEEESS-SHHHHHHHHTT--- CS
                           IlvN  97 fnihfglikppkdvdvvlvAPkgpGhlvreeyeegkGv 134
                                     n+   li+  +++ v l A +   +  r+ y e +Gv
  gi|116754755|ref|YP_843873.1| 184 RNVCEALIRFDSSI-VSLSASRLSSKKFRTFYVEEEGV 220
                                    56666666665554.77888888999999999999998 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   2.2e-06    0.0048       5      88 ..       2      83 ..       1      86 [. 0.96

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.2e-06
                                   EEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHHHHHHHTT CS
                    CoA_binding  5 kviviGagglgiaglyhfkeklkygikavfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqeavdelveag 86
                                    v+viG+g +g+  + + +e +++ +  v++  ++ +    +  ++  ++del +    ++  i+vP ++ +++++ ++eag
  gi|116754755|ref|YP_843873.1|  2 DVGVIGVGSMGRNHVRVYSELKGVDNLYVYDSLEKNAEAAKEYATICRTIDELLDA--SEAVSICVPTKHHYDVAMCVIEAG 81
                                   599*****************************************************..99999******************* PP

                                   -S CS
                    CoA_binding 87 ik 88
                                   + 
  gi|116754755|ref|YP_843873.1| 82 VH 83
                                   96 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 ?   11.2   0.9   0.00015      0.33       1      96 [.       3      84 ..       3     107 .. 0.73
   2 ?   -0.8   0.0      0.76   1.7e+03      51      76 ..      89     113 ..      87     123 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00015
                                   EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SSGGGH CS
                Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnlsppiss 82
                                   v +iG Gs+G+  ++++++ + vd ++ v d  ++++ea+++ a+  r + + lda++  ++             ++p   +
  gi|116754755|ref|YP_843873.1|  3 VGVIGVGSMGRNHVRVYSELKGVD-NLYVYDSLEKNAEAAKEYATICRTIDELLDASEAVSI-------------CVPTKHH 70
                                   679********************7.******9999988876655444444444444444433.............4444466 PP

                                   HHHHHHHHHHT-EE CS
                Sacchrp_dh_NADP 83 ldvlkaCietgvhy 96
                                    dv+ + ie+gvh+
  gi|116754755|ref|YP_843873.1| 71 YDVAMCVIEAGVHC 84
                                   66666666666665 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.76
                                    EEE--TTTHHHHHHHHHTTSSEEEE- CS
                Sacchrp_dh_NADP  51 aialdaenyeavLaallkegdlvvnl 76 
                                    +++l+ ++ e  L  +++++dlvv +
  gi|116754755|ref|YP_843873.1|  89 PMTLTLDEAER-LLNAIRSRDLVVGV 113
                                    57789999999.77779999999965 PP

>> OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   8.4e-05      0.19     132     191 ..       3      61 ..       2      86 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 8.4e-05
                                    EEEE--SHHHHHHHHHHCCCS--SEEEEE-SSHHHHHHHHHHCCS.CTT-EEECSCHHHH CS
                OCD_Mu_crystall 132 laiiGaGvqaetqlealkavldikevriydrdeeaaekfaenlqefefevsackseeeav 191
                                    +++iG G + + ++++ +++ +++++ +yd  e++ae++ e++    + +    ++ eav
  gi|116754755|ref|YP_843873.1|   3 VGVIGVGSMGRNHVRVYSELKGVDNLYVYDSLEKNAEAAKEYATI-CRTIDELLDASEAV 61 
                                    589**********************************99888873.44444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); 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:                         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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.36
# Mc/sec: 2508.77
//
Query:       gi|116754756|ref|YP_843874.1|  [L=363]
Description: DegT/DnrJ/EryC1/StrS aminotransferase [Methanosaeta thermophila PT]
Scores for 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-129  431.4   0.0   3.4e-129  431.3   0.0    1.0  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
      8e-07   28.5   0.0    1.3e-06   27.9   0.0    1.2  1  Aminotran_1_2    Aminotransferase class I and II
    7.8e-05   22.1   0.0    0.00037   19.9   0.0    2.1  1  Beta_elim_lyase  Beta-eliminating lyase
    0.00087   18.3   0.0     0.0014   17.7   0.0    1.2  1  Aminotran_5      Aminotransferase class-V
     0.0023   16.5   0.0     0.0033   16.0   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme


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 !  431.3   0.0  9.4e-133  3.4e-129       3     360 ..      12     359 ..      10     360 .. 0.96

  Alignments for each domain:
  == domain 1  score: 431.3 bits;  conditional E-value: 9.4e-133
                                    HHHHHHHHHHHHTSS-SSSSHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHH CS
                DegT_DnrJ_EryC1   3 keeeleaveevlksgwltsgpeveeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavle 82 
                                    ++ee+e v +v++sg+l +g+ v++FE++f+ y+gvk +iavssGt Al laL+a+g++pgdeVI p++tF+at navl+
  gi|116754756|ref|YP_843874.1|  12 GDEEIEVVSQVIRSGMLVQGEMVRRFEEEFSSYVGVKDSIAVSSGTVALDLALKAFGLDPGDEVICPAFTFIATSNAVLY 91 
                                    689***************************************************************************** PP

                                    TT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEEEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETTEECCCSS CS
                DegT_DnrJ_EryC1  83 lgakpvfvDvdpdtynidpaaieaaitertkaIlpVhlyGqvadmdalkaiaakhglkvieDaAhAlGatykgkkvGalg 162
                                     g++pvf+Dvdp t+n++p+++ ++++++tkaIl VhlyGq++d++a+ +i+++h+l++ieD+A+A+Ga+y+gk++G++g
  gi|116754756|ref|YP_843874.1|  92 QGLRPVFADVDPRTFNLNPEDVLEKVNSNTKAILGVHLYGQPFDVKAIHEICEDHDLILIEDCAQAHGAEYEGKRAGSFG 171
                                    ******************************************************************************** PP

                                    SEEEEE-BTTSSS-SSS-EEEEESTHHHHHHHHHHHBTTCECCTCSSCECCSS---B-B-BHHHHHHHHHHHCTHHHHHH CS
                DegT_DnrJ_EryC1 163 daavfSFyptKnlttGeGGavvtndeelaekarvlrnhGlkrkaekryvgevelGynyrlteiqAAiglaqLerldelva 242
                                     +++fSFyptKn+ttGeGG+++t+d+ lae++r+lrnhG +     +y + + lGynyr+t+iq Aigl+qL++ld +++
  gi|116754756|ref|YP_843874.1| 172 -TGCFSFYPTKNMTTGEGGMITTDDDMLAERLRLLRNHGDR----GKYNHVM-LGYNYRMTNIQGAIGLVQLRKLDAFID 245
                                    .9*************************************77....8999999.*************************** PP

                                    HHHHHHHHHHHHHHTCCCCEESCGGTTSSSEEESCEEEEEHCCHHHCHHHHHHHHHHCCEE-B-SGSCHGGGSCCHHHHH CS
                DegT_DnrJ_EryC1 243 rRreiaelykeeLaelegtaelttpketkkhawhlyavlveeeaevkrdelvealkeegigtrvhypnplhrqpvyaerk 322
                                     R ++ae+++  ++  + t ++  +++ k h++ +y+++ve+++ ++rd+l+  l+++gigt +hyp p+++qp+y++  
  gi|116754756|ref|YP_843874.1| 246 ARIKNAEYLSAHISRDGIT-TPWRDPRCK-HVYNQYVLRVEDDFPMSRDDLASYLQSKGIGTGIHYPMPVYEQPLYRQLG 323
                                    *************996654.445555555.9************99**********************************7 PP

                                    HCCCHC-HHHHHHHHHEEEEEGGTTGSHHHHHHHHHHH CS
                DegT_DnrJ_EryC1 323 eeasgdlpnaerlaervlsLplypelteedvdrVveal 360
                                     +    +p+ae++++rv+s p++p+l++ed++r+++a+
  gi|116754756|ref|YP_843874.1| 324 IR--SICPVAEEISRRVISVPVHPGLSDEDLKRIADAV 359
                                    55..46*****************************998 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 !   27.9   0.0   3.6e-10   1.3e-06      48     189 ..      36     155 ..      30     179 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 3.6e-10
                                    HHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTT CS
                  Aminotran_1_2  48 eleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseed 127
                                     +ee+  +++g         ++++ v+sG+ al+ al+++  l+pgde++ p+ t+   +n++ + g+  v     ++ +
  gi|116754756|ref|YP_843874.1|  36 RFEEEFSSYVG--------VKDSIAVSSGTVALDLALKAFG-LDPGDEVICPAFTFIATSNAVLYQGLRPVFAD-VDPRT 105
                                    58899999999........888*******************.********************************.55*** PP

                                    TEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEET CS
                  Aminotran_1_2 128 fhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDea 189
                                    f+l+ e+++e++++       tk il        G+ ++ + ++++   ++ + l+l+ D a
  gi|116754756|ref|YP_843874.1| 106 FNLNPEDVLEKVNS------NTKAILGVHL---YGQPFDVKAIHEI---CEDHDLILIEDCA 155
                                    **************......7777775433...4666666666666...6666666666655 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0     1e-07   0.00037      33     240 ..      33     265 ..      28     326 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1e-07
                                    HHHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH-.-TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTT.TBE- CS
                Beta_elim_lyase  33 tvnrLedavaelfgkeaalfvpqGtaAnsillkill.qrgeevivtepahihfdetgaiaelagvklrdlknkea.Gkmd 110
                                     v+r+e+++  ++g +  + v +Gt A  ++lk++   +g+evi+     + f  t +++ ++g +++ ++ +    +++
  gi|116754756|ref|YP_843874.1|  33 MVRRFEEEFSSYVGVKDSIAVSSGTVALDLALKAFGlDPGDEVICPA---FTFIATSNAVLYQGLRPVFADVDPRtFNLN 109
                                    6899****************************99988********65...455566677789999999888777335666 PP

                                    HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHHTTSS CS
                Beta_elim_lyase 111 lekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslgeivkemfsyvD 190
                                    +e++ ++++       ++k+i+  v + +  Gq+  +   +++++i++++++ l+ D A    a    g  + +   ++ 
  gi|116754756|ref|YP_843874.1| 110 PEDVLEKVNS------NTKAILG-V-HLY--GQPFDV---KAIHEICEDHDLILIEDCAQAHGAE-YEGKRAGSFGTGC- 174
                                    6666666666......6777753.3.444..999975...677889***********99866655.5555555555554. PP

                                    EEEEESSSTT--SS-EEEEE-HH..............................................HHHHHHHHHHH CS
                Beta_elim_lyase 191 svtmslkKdllanvGgvlafrddel..........................................edylaerveqrky 228
                                     +++  +K++++  Gg++ ++dd l                                          + +++ r++ ++y
  gi|116754756|ref|YP_843874.1| 175 -FSFYPTKNMTTGEGGMITTDDDMLaerlrllrnhgdrgkynhvmlgynyrmtniqgaiglvqlrklDAFIDARIKNAEY 253
                                    .89999*****************668888888888888888888888888888888888888888888888888888888 PP

                                    HT---SSTHHHH CS
                Beta_elim_lyase 229 lggglrqagvla 240
                                    l  +++  g+  
  gi|116754756|ref|YP_843874.1| 254 LSAHISRDGITT 265
                                    888888877765 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   3.8e-07    0.0014      44     181 ..      33     159 ..      17     162 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.8e-07
                                    HHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBET CS
                    Aminotran_5  44 aveearekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkviplde 123
                                    +v+  +e++   +++++    i +s++t a+ l++++++  l+pgde++  +    a+     ++   +g++ +++ +d+
  gi|116754756|ref|YP_843874.1|  33 MVRRFEEEFSSYVGVKD---SIAVSSGTVALDLALKAFG--LDPGDEVICPAFTFIATS----NAVLYQGLRPVFADVDP 103
                                    56666777777777776...678899999*********5..9**********9988888....55557899999999998 PP

                                    TS.CBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTT CS
                    Aminotran_5 124 eg.eldldelekllnektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavg 181
                                    +  +l+++++ +++n +tk++   h     G  ++v++i +++ +++ +++ D aqa g
  gi|116754756|ref|YP_843874.1| 104 RTfNLNPEDVLEKVNSNTKAILGVHL---YGQPFDVKAIHEICEDHDLILIEDCAQAHG 159
                                    753899**************999885...8**************************976 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   9.3e-07    0.0033      55     173 ..      35     153 ..      29     162 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 9.3e-07
                                    HHHHHHHHHHHT-SEEEEESSHHHHHHHHHHTT.S-TTEEEEEESTSSHHHHHHH.HHTHHHTTCEEE..EESTTSHHHH CS
                Cys_Met_Meta_PP  55 svleeriaaLeggeaalavssGmaAiaaailal.lkaGdeivvsddlYggtqrll.kkvlkklgievk..fvdtsdleel 130
                                    + +ee+ +   g++ ++avssG+ A+++a+ a+ l  Gde+++    +  t++ +  + l+ +  +v+   ++  ++e++
  gi|116754756|ref|YP_843874.1|  35 RRFEEEFSSYVGVKDSIAVSSGTVALDLALKAFgLDPGDEVICPAFTFIATSNAVlYQGLRPVFADVDprTFN-LNPEDV 113
                                    5688999999999*******************96677***********9998765144455554444410444.489999 PP

                                    HHHCCTTEEEEE.EESS-TTTT----HHHHHHHHHHTT-EEEEE CS
                Cys_Met_Meta_PP 131 ekaikentklvy.lEtptnpllkvvDiekiaklakkagvlvvvD 173
                                     +++++ntk+++ +   +    +  D+++i +++ +++++++ D
  gi|116754756|ref|YP_843874.1| 114 LEKVNSNTKAILgVHLYG----QPFDVKAIHEICEDHDLILIED 153
                                    999*******98233333....3457777777777777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); 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: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2603.20
//
Query:       gi|116754757|ref|YP_843875.1|  [L=402]
Description: major facilitator transporter [Methanosaeta thermophila PT]
Scores for complete 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   96.8  48.9    2.8e-15   56.1  18.3    2.1  2  MFS_1       Major Facilitator Superfamily
  ------ inclusion threshold ------
        4.4    6.1  21.5        2.3    7.0  18.8    1.9  2  MFS_1_like  MFS_1 like family
        9.3    5.9  18.4      0.016   14.9   4.6    2.8  3  UNC-93      Ion channel regulatory protein UNC-93


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.1  18.3   4.6e-19   2.8e-15       3     241 ..      20     242 ..      18     256 .. 0.82
   2 !   45.3  25.1   9.1e-16   5.4e-12      36     164 ..     250     378 ..     242     395 .. 0.91

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 4.6e-19
                          MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalg.lllll 80 
                                    l+ +++ +++ i+ p++p +  ++lg  + ++gl+ +l     +++ ++ G+ +d +Grr+ ++l+g+ l+a++ +ll+l
  gi|116754757|ref|YP_843875.1|  20 LVSLFNDTSSEIIQPIMP-LFITSLGGGALAVGLVGGLSEGIPSILKILSGYAGDIMGRRKpFVLAGYGLSAAAkTLLPL 98 
                                    78889999**********.55599**************************************************888888 PP

                          MFS_1  81 fasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllgglla.sslgWravfyila 158
                                      s  w  +++l  +   g g+ ++   a+iad + +++ gr++g + a   +Ga+lg +++ ll  + l++r +  ++a
  gi|116754757|ref|YP_843875.1|  99 --SLTWqHVVLLKSIERCGKGVRAAPKDAIIADSAEPSRIGRGFGTVRALDTFGAVLGSVIAYLLWsAGLSFRDILAVAA 176
                                    ..667768999999**************************************************9988899********* PP

                          MFS_1 159 ivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevl 238
                                    ++sl+afv   l+++++ ++++ +  ++       ++l+p        +  w +++++ +f+++++++++++   +qe +
  gi|116754757|ref|YP_843875.1| 177 ALSLMAFV--PLFYVRDIRRSPVVVLRPG-----ISSLSP--------RLRW-FILVASVFSLANFSYMFFMLR-AQELF 239
                                    ******88..3566555555555554444.....455555........4457.666666666677776666655.36666 PP

                          MFS_1 239 gls 241
                                      +
  gi|116754757|ref|YP_843875.1| 240 TGA 242
                                    666 PP

  == domain 2  score: 45.3 bits;  conditional E-value: 9.1e-16
                          MFS_1  36 llltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslwlllvlrvlqGlgagalfpagaaliadwfp 115
                                    ll+ l+ ++++ +++p G++sd +Grr++l +g++lf+l +l ++f+ss+ +l++l v+ Gl  +++  +  a+++d++ 
  gi|116754757|ref|YP_843875.1| 250 LLYILFNVVYSGMAIPSGAVSDLIGRRWILAIGYALFSLVALGFVFVSSSEWLVLLFVMYGLVFAVVDGGQSAYVSDLSC 329
                                    46778999********************************666669666669**************************** PP

                          MFS_1 116 keergraigllsagfslGailgpllggllasslgWravfyilaivslla 164
                                    +e r  a+g + +++++++i   l++g + + +g  a+f++ a+++++a
  gi|116754757|ref|YP_843875.1| 330 DEIRCTALGAYHGMVGIASIASGLIAGTVWQIYGPAATFLLSALLAAVA 378
                                    ***********************************************99 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 ?   -1.5   0.0      0.15   8.9e+02      18      80 ..      32      94 ..      23     118 .. 0.82
   2 ?    7.0  18.8   0.00039       2.3     225     384 ..     209     369 ..     137     370 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.15
                     MFS_1_like 18 llPYltiylkskglkaseigiitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavlfl 80
                                   ++P + ++++s g  a  +g++  +   +  + + + g   D +g+rk+ v+++  lsa++  
  gi|116754757|ref|YP_843875.1| 32 IQPIMPLFITSLGGGALAVGLVGGLSEGIPSILKILSGYAGDIMGRRKPFVLAGYGLSAAAKT 94
                                   678888888888888888888888888888888888899999999999999998888887655 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00039
                     MFS_1_like 225 peviifllvalilgmswgiienFlflYLkelgasntllGslvalgvvaeip...lfffaeklleklGhvklliiallayi 301
                                    p++ +f+lva +     ++ + F+ l  +el      +G+ + l  + +++   + + +  + + +G +++l i+  ++ 
  gi|116754757|ref|YP_843875.1| 209 PRLRWFILVASVFSL-ANFSYMFFMLRAQELFTGALAVGAPLLLYILFNVVysgMAIPSGAVSDLIGRRWILAIGYALFS 287
                                    566666666655543.3444444444444444444445555444444444311123334667788999999999999999 PP

                     MFS_1_like 302 lrfllyaiienawlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsglyfglGralGsliGGllwdlksaif 381
                                    l  l+  ++++  +++++ v++g+ f+++ +    yvs++  ++++ t  g ++g+ +g+ +    li+G +w++++++ 
  gi|116754757|ref|YP_843875.1| 288 LVALGFVFVSSSEWLVLLFVMYGLVFAVVDGGQSAYVSDLSCDEIRCTALGAYHGM-VGIASIASGLIAGTVWQIYGPAA 366
                                    9888888888888888888************************************9.6777777778888*********9 PP

                     MFS_1_like 382 lFr 384
                                    +F 
  gi|116754757|ref|YP_843875.1| 367 TFL 369
                                    996 PP

>> UNC-93  Ion channel regulatory protein UNC-93
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   1.4      0.16   9.7e+02      69     101 ..     215     247 ..     202     258 .. 0.73
   2 ?   14.9   4.6   2.7e-06     0.016      50     149 ..     259     359 ..     249     367 .. 0.77
   3 ?   -1.1   0.5      0.23   1.4e+03     127     144 ..     371     388 ..     368     391 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.16
                         UNC-93  69 alvigallyaifqlgFlllnkyylyissallGv 101
                                     lv++ ++ a f   F++l    l++++  +G+
  gi|116754757|ref|YP_843875.1| 215 ILVASVFSLANFSYMFFMLRAQELFTGALAVGA 247
                                    355566778889999999988888887766665 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 2.7e-06
                         UNC-93  50 ftvanlvapsvvdlltakwalvigallyaifqlgFlllnk.yylyissallGvgaallwtgqGsyLsenstretiernss 128
                                    ++ +++ +  v dl++ +w l ig +l++++ lgF+++ +  +l +  ++ G+ +a++  gq  y+s  s +e + +  +
  gi|116754757|ref|YP_843875.1| 259 YSGMAIPSGAVSDLIGRRWILAIGYALFSLVALGFVFVSSsEWLVLLFVMYGLVFAVVDGGQSAYVSDLSCDEIRCTALG 338
                                    333344445699***********************998751567777899******************999998888877 PP

                         UNC-93 129 ilwallksslliGgiflilvf 149
                                       +++ ++ +  g++  +v+
  gi|116754757|ref|YP_843875.1| 339 AYHGMVGIASIASGLIAGTVW 359
                                    777777666666666555555 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.23
                         UNC-93 127 ssilwallksslliGgif 144
                                    s++l a+ ++ +++Gg++
  gi|116754757|ref|YP_843875.1| 371 SALLAAVASCGMILGGVI 388
                                    678889999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); 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:                         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: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 3004.49
//
Query:       gi|116754758|ref|YP_843876.1|  [L=388]
Description: hypothetical protein Mthe_1462 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-64  217.1   0.6    1.5e-64  216.7   0.6    1.2  1  DUF2202        Uncharacterized protein domain (DUF2202)
    2.5e-27   95.6   0.0    4.5e-27   94.7   0.0    1.4  1  DOMON          DOMON domain
     0.0079   16.6   0.0      0.016   15.6   0.0    1.4  1  Rubrerythrin   Rubrerythrin
  ------ inclusion threshold ------
      0.062   11.9   0.0        0.1   11.2   0.0    1.2  1  PhoPQ_related  PhoPQ-activated pathogenicity-related protein
      0.065   13.2   0.1        0.1   12.6   0.1    1.3  1  EB_dh          Ethylbenzene dehydrogenase
       0.12   12.5   0.0       0.19   11.9   0.0    1.3  1  Ferritin_2     Ferritin-like domain


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 !  216.7   0.6   5.2e-68   1.5e-64       1     161 [.     231     387 ..     231     388 .] 0.99

  Alignments for each domain:
  == domain 1  score: 216.7 bits;  conditional E-value: 5.2e-68
                        DUF2202   1 ekdsllymreeeklarDvYlelYdrwklqiflniakseqthtdavksllekYeledpvkederGkfedeelqelYnkLve 80 
                                    ++d++l++++eek+arD+Y++lY+r++l++fl++++seq+h+d+++sl+e+Y++e+p++e+  G+f++++lq +Yn+L++
  gi|116754758|ref|YP_843876.1| 231 DADWMLFIWKEEKAARDLYESLYERTGLTLFLDLVRSEQSHMDQIRSLMERYGMETPDLER--GVFDNQTLQGIYNDLLS 308
                                    689*******************************************************988..***************** PP

                        DUF2202  81 kgsksledaLkvgatiedldiaDlekalketdnkdikevYenllkGsrnhlRsfvrkleergkeYepqyiseeefdeivs 160
                                     +s++  daL+++at+e+++i+Dle+a++et+nk++++vY++ll+Gsr+hlRs+vr+le+rg+eY+p+y+s++efdeiv+
  gi|116754758|ref|YP_843876.1| 309 ISSDD--DALRAAATFEEISISDLERAISETSNKEAIDVYSGLLAGSRKHLRSYVRDLEDRGIEYTPVYLSRSEFDEIVR 386
                                    ****9..************************************************************************9 PP

                        DUF2202 161 s 161
                                    +
  gi|116754758|ref|YP_843876.1| 387 A 387
                                    7 PP

>> DOMON  DOMON domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.7   0.0   1.5e-30   4.5e-27       4     125 .]      66     183 ..      63     183 .. 0.96

  Alignments for each domain:
  == domain 1  score: 94.7 bits;  conditional E-value: 1.5e-30
                          DOMON   4 eykvswkvdgdgdeiefelsgkvntngyvaiGfsddgkMsnadvvvgwvdngrvyvqdyystggkgapriddt...gsqd 80 
                                     +++swk+d  +++++++l+g +  +g++aiGf ++++M +ad+v+g+vd g+++v d ystg++g p+i+dt   g++d
  gi|116754758|ref|YP_843876.1|  66 VMTISWKID--DEYLYMALNGST--RGWLAIGFEPTEWMRDADMVLGVVD-GNARVLDEYSTGNYG-PHIEDTllgGTDD 139
                                    689******..999******876..7***********************8.99*******999999.****9******** PP

                          DOMON  81 itllsgseengvttlkfrRkldtcdpkqdnkidldttvyviwaag 125
                                    i  + g++ +++t ++frR+ldt+d+  d+++ l++ v++iwa++
  gi|116754758|ref|YP_843876.1| 140 ILEYGGKSYGTHTVAEFRRRLDTGDR-FDKVLRLGKDVSIIWAMS 183
                                    **************************.****************95 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   5.4e-06     0.016       9     133 ..     241     360 ..     239     363 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.4e-06
                                    HHHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS-------TTGGHHHHHH.. CS
                   Rubrerythrin   9 gEssarrlYkelaekakegypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakpkflttaknLe.. 86 
                                     E  ar lY++l+e++         lF++l + E+ H + ++ l+e +  e      +  r+++  ++   ++++ L+  
  gi|116754758|ref|YP_843876.1| 241 EEKAARDLYESLYERTG------LTLFLDLVRSEQSHMDQIRSLMERYGMETP----DLERGVFDNQTLQGIYNDLLSis 310
                                    69999***********9......56**********************998887....55788888888888999988888 PP

                                    ...HHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHH CS
                   Rubrerythrin  87 ...eaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerl 133
                                       +a++ a + ee ++  +e++ +++ n+ea ++   l    +kH +++
  gi|116754758|ref|YP_843876.1| 311 sddDALRAAATFEEISISDLERAISETSNKEAIDVYSGLLAGSRKHLRSY 360
                                    99999999999999999*************99988888887777777765 PP

>> PhoPQ_related  PhoPQ-activated pathogenicity-related protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.5e-05       0.1      31      74 ..      31      73 ..      21      86 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.5e-05
                  PhoPQ_related 31 eltSQkWskeklvdpslwkHkltivvPkekkleetalllisggs 74
                                   +++S +W+++  v  ++++H l+++ P++ +  + ++++is ++
  gi|116754758|ref|YP_843876.1| 31 SVVSEEWQPDGIVGVNEYSHSLKLYSPAR-QGYTGGVMTISWKI 73
                                   579**************************.89999999998665 PP

>> EB_dh  Ethylbenzene dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   3.4e-05       0.1     155     234 ..      98     180 ..      33     192 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.4e-05
                                    .........................................---EEEEEEETTEEEE.EEEEES---TTS..---TTEEE CS
                          EB_dh 155 nvenekdepaamfskegfraddenesvpfdpewkegdt...advkaeakykdGkWtV.elvRpLkagnpldvalepgkvy 230
                                    ++ +++d+  ++ ++   r  de++++ + p++++  +    d+ + + +++G+ tV e+ R+L++g+++d+ l+ gk++
  gi|116754758|ref|YP_843876.1|  98 EWMRDADMVLGV-VDGNARVLDEYSTGNYGPHIEDTLLggtDDILEYGGKSYGTHTVaEFRRRLDTGDRFDKVLRLGKDV 176
                                    333444444333.4444555558888888885554443444***************988********************9 PP

                                    EEEE CS
                          EB_dh 231 dvaf 234
                                    ++  
  gi|116754758|ref|YP_843876.1| 177 SIIW 180
                                    9855 PP

>> Ferritin_2  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   6.4e-05      0.19      32     121 ..     250     351 ..     215     365 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.4e-05
                     Ferritin_2  32 kalldaevrevaeeiakheeaHveflkaale..Gaaav..akptfdf........afdpfadeksflalaavlEdvgvsA 99 
                                    ++l++ + ++++ ++   e++H++ +++  e  G ++   ++  fd         +   ++++++ l++aa++E++ +s 
  gi|116754758|ref|YP_843876.1| 250 ESLYERTGLTLFLDLVRSEQSHMDQIRSLMEryGMETPdlERGVFDNqtlqgiynDLLSISSDDDALRAAATFEEISISD 329
                                    5667777789999999**************876655532233344448888888888999******************** PP

                     Ferritin_2 100 YlgaapllsnkelltaaasIls 121
                                       a+   snke + +  ++l+
  gi|116754758|ref|YP_843876.1| 330 LERAISETSNKEAIDVYSGLLA 351
                                    ***********99998888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); 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 0.22s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2776.52
//
Query:       gi|116754759|ref|YP_843877.1|  [L=242]
Description: hypothetical protein Mthe_1463 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.12   12.4   2.7        0.5   10.4   0.2    2.5  2  Antirestrict  Antirestriction protein
       0.56    9.8   4.5          1    9.0   0.7    2.1  2  FNIP_C        Folliculin-interacting protein C-terminus


Domain annotation for each model (and alignments):
>> Antirestrict  Antirestriction protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   5.6e-05       0.5       9      54 ..      26      71 ..      16      79 .. 0.85
   2 ?    0.9   0.1     0.055   4.9e+02      25      47 ..     102     124 ..      86     128 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 5.6e-05
                   Antirestrict  9 efyelsngglymaPesderlrlvvkengfegevSadAaGiivtlla 54
                                   + + +s +g y+   ++++ ++v ++n++++++S+ A G  vt  a
  gi|116754759|ref|YP_843877.1| 26 QSIDMSASGGYVSQSASNAAVVVGDNNNVNQKISQSASGNYVTQSA 71
                                   67889999********9**********************9999764 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.055
                   Antirestrict  25 derlrlvvkengfegevSadAaG 47 
                                    ++++++v + n +++ vS+ A G
  gi|116754759|ref|YP_843877.1| 102 ANAVAVVGDLNTVNQLVSQSATG 124
                                    57788999999999999999988 PP

>> FNIP_C  Folliculin-interacting protein C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.3     0.013   1.1e+02      53     103 ..      24      74 ..      14      84 .. 0.75
   2 ?    9.0   0.7   0.00011         1      55      98 ..      86     129 ..      74     174 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.013
                         FNIP_C  53 lskdlssavessvldepvaEavcivaDtdkwtvkvlssessklskskklde 103
                                    +s+++ +++    ++++ + a ++v D ++++ k+  s s +  +++  + 
  gi|116754759|ref|YP_843877.1|  24 VSQSIDMSASGGYVSQSASNAAVVVGDNNNVNQKISQSASGNYVTQSAANA 74 
                                    5667778888888999999************99997777554444444444 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00011
                         FNIP_C  55 kdlssavessvldepvaEavcivaDtdkwtvkvlssessklsks 98 
                                    +++s++++  +++++ a av++v D+++++  v  s + +   +
  gi|116754759|ref|YP_843877.1|  86 QSTSQSANGNTISQSAANAVAVVGDLNTVNQLVSQSATGNEIYQ 129
                                    6788899999*****************99977766654333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       917  (0.0511462); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1851.25
//
Query:       gi|116754760|ref|YP_843878.1|  [L=483]
Description: hypothetical protein Mthe_1464 [Methanosaeta thermophila PT]
Scores for 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   22.9   0.0     0.0003   21.0   0.0    2.0  1  DUF11     Domain of unknown function DUF11


Domain annotation for each model (and alignments):
>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.7e-08    0.0003       3      76 ..     213     286 ..     212     350 .. 0.66

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.7e-08
                          DUF11   3 KtvdksevrpGdtvtytltvtNtgpasangvvvtDtl.......................Paglayvsvsasqgtasalt 59 
                                    K  ++s v pG t+tyt+t  N+  ++a ++vv+                                              
  gi|116754760|ref|YP_843878.1| 213 KKAKQSSVSPGSTITYTITYGNNLEVPA-DIVVREFYdqrtffleaypppdpgttnvwtiR------------------- 272
                                    4445566*********************.****9988555555555554443333333330................... PP

                          DUF11  60 svgsLeagesatlsftv 76 
                                        L +ge  +++++v
  gi|116754760|ref|YP_843878.1| 273 ---GLRPGEHGQITVKV 286
                                    ...34444444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (483 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 3749.14
//
Query:       gi|116754761|ref|YP_843879.1|  [L=580]
Description: Cl- channel, voltage-gated family protein [Methanosaeta thermophila PT]
Scores for complete 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-97  325.6  33.1    4.1e-97  325.6  33.1    2.0  2  Voltage_CLC  Voltage gated chloride channel
    1.9e-23   82.7   5.5    1.7e-12   47.6   1.0    2.7  2  CBS          CBS domain
  ------ inclusion threshold ------
       0.01   15.4   1.7      0.022   14.3   1.7    1.5  1  Pox_P21      Poxvirus P21 membrane protein
      0.071   13.0   1.5       0.11   12.3   0.1    2.0  2  Wzy_C_2      Virulence factor membrane-bound polymerase, C-te


Domain annotation for each model (and alignments):
>> Voltage_CLC  Voltage gated chloride channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.2     0.032   1.5e+02     163     192 ..       4      33 ..       2      44 .. 0.85
   2 !  325.6  33.1  9.1e-101   4.1e-97       1     352 [.      68     418 ..      68     420 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.032
                                    GHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Voltage_CLC 163 elilfvllGilgGllgalfvrlllkverlf 192
                                     ++l++++G ++Gl + +f +ll  ++r+f
  gi|116754761|ref|YP_843879.1|   4 TILLAAFVGAISGLGAFIFYFLLELSTRVF 33 
                                    57889999***********99999888876 PP

  == domain 2  score: 325.6 bits;  conditional E-value: 9.1e-101
                                    HHHHHHHHCCCCC-GGGSC-SHHHHHHHCTTSS---HHHHHHHHHHHHHHHHCTT-S-BTHHHHHHHHHHHHHHHHHHTT CS
                    Voltage_CLC   1 lggllagllvklvapeaagsGipevkaalngvkgplslrvllvkflasvltvgsGlslGreGplvqiGAavgsglsrllk 80 
                                    lggll+gl+v+++apea+g+G++ v++ +++ +g l+ rv +vk+++s++t+gsG+s+GreGp+ qiGA +gs +++ll+
  gi|116754761|ref|YP_843879.1|  68 LGGLLSGLIVYKFAPEAEGHGTDAVIRSFHKARGALRARVPVVKTISSAITIGSGGSAGREGPIAQIGAGFGSFVADLLR 147
                                    589***************************************************************************** PP

                                    .--SHHHHHHHHHHHHHHHHHHHT-HHHHHHHHCTT.TSTSS--TTHHHHHHHHHHHHHHHHHHCTTS-S........-. CS
                    Voltage_CLC  81 lsrndrdrrlvaaGaAAGiAAaFnaPlgGvlfalEe.vsrefslrallpvfvasvvaalvlrlllgeepa........fg 151
                                    ls++d +r lv++G+A+Gi+++F++P gG++f++E+ + ++++++a++p+fv+s+va ++++++ ++ +         f+
  gi|116754761|ref|YP_843879.1| 148 LSDRD-RRLLVVCGVAGGIGSIFRSPFGGAMFGIEVlYKKDYEVEAIVPAFVSSIVAFVTFNVVTSYFAGipfisppiFK 226
                                    99888.777***************************8889************************8888556767777677 PP

                                    T---...--GGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHCHHHHHHHHHHHHHHHHHHHCCCSCC.CSSSSCCH CS
                    Voltage_CLC 152 eveslfalsllelilfvllGilgGllgalfvrlllkverlfrkleklkikkrlepalvgllvgllglllpasvlgggyel 231
                                     +++l+ +s+le++l++++++l++++g+++++++++++ lf++    ki++ l+pa++gll+g++g+llp  vlg+gy+ 
  gi|116754761|ref|YP_843879.1| 227 -IPQLSIHSPLEFPLYAVVSVLAAFFGVFYIKTFYTIRGLFKSS---KIPQTLKPAFGGLLTGSIGMLLPG-VLGMGYGY 301
                                    .99999************************************98...99999*******************.******** PP

                                    HHHHCTT-S-HHHHHH...HHHHHHHHHHHHHCTT-CSBSHHHHHHHHHHHHHHHHHHHHHH-CTSSC...HHHHHHCCT CS
                    Voltage_CLC 232 iasllegstlllsllllllllllkllataltlgsgvpgGifaPsLviGAalGrlvglvlalllpgaassdpgafalvGma 311
                                    ++ +++g+   l+l +++ll+l k++at++t+gsg +gG+faPs+viG+++G+++g ++++l+p+ ++ +p+af+l+Gm 
  gi|116754761|ref|YP_843879.1| 302 VQMAIDGK---LALSVIFLLILGKIAATSFTVGSGGSGGVFAPSIVIGSMVGAFIGYLFHQLFPEIVV-QPEAFVLIGMS 377
                                    *******9...9****************************************************8766.68********* PP

                                    HHHHHCCS-HHHHHHHHHHCC--GCCHHHHHHHHHHHHHHH CS
                    Voltage_CLC 312 aflagvtrapltaiviviEltgdlelllplmlavliAkava 352
                                    af a+v+++p+++i++v+E++g++ +l+ lm+++++A+ ++
  gi|116754761|ref|YP_843879.1| 378 AFIAAVAKTPIASILMVLEMCGSYMMLPALMISSALAYCLS 418
                                    **************************************887 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.2   1.1e-12   5.1e-09       4      51 ..     456     502 ..     447     503 .. 0.90
   2 !   47.6   1.0   3.8e-16   1.7e-12       1      54 [.     515     570 ..     515     573 .. 0.92

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 1.1e-12
                                    HSBSSCEEEETTSBHHHHHHHHHHHT.SSEEEEEETTTBEEEEEEHHHH CS
                            CBS   4 imtrdvvtvppdttleealelmrekg.vsrlPVVdedgklvGivtlrDl 51 
                                    ++ +++v+v+p++ ++e+l l++++g + ++PVV e+g lvGivt rD+
  gi|116754761|ref|YP_843879.1| 456 VPAEKLVSVSPNQKVSEVLALIEKTGhI-GFPVV-ENGMLVGIVTFRDV 502
                                    467899****************888888.*****.9************7 PP

  == domain 2  score: 47.6 bits;  conditional E-value: 3.8e-16
                                    HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTB..EEEEEEHHHHHHH CS
                            CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgk..lvGivtlrDllra 54 
                                    V+dim rd+++ +pd++le+al ++++k+v+rlPVVd   +  l+G++t++D+++a
  gi|116754761|ref|YP_843879.1| 515 VKDIMMRDLIVTYPDESLEDALIKLVQKDVGRLPVVDRKMNrmLLGLITRSDIIKA 570
                                    89**********************99**********766645799*********98 PP

>> Pox_P21  Poxvirus P21 membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   1.7     5e-06     0.022      52     108 ..     357     418 ..     338     433 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5e-06
                        Pox_P21  52 lkglfsnilkrnDirsLlglilfvlaltttpviavimia.iaslllPlpsLvi....aYCla 108
                                    +++lf++i+ + +   L+g+  f+ a+  tp+ +++m+  ++   + lp+L+i    aYCl+
  gi|116754761|ref|YP_843879.1| 357 FHQLFPEIVVQPEAFVLIGMSAFIAAVAKTPIASILMVLeMCGSYMMLPALMIssalAYCLS 418
                                    6778999******************************8646777888999988444478886 PP

>> Wzy_C_2  Virulence factor membrane-bound polymerase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   2.6e-05      0.11      12      39 ..     232     267 ..     229     310 .. 0.70
   2 ?   -1.7   0.1      0.53   2.4e+03      65      72 ..     400     407 ..     365     450 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.6e-05
                        Wzy_C_2  12 lHSllEYPlwYspfllaaflvlgllds........k 39 
                                    +HS lE+Pl+ +   laaf+ ++++++        k
  gi|116754761|ref|YP_843879.1| 232 IHSPLEFPLYAVVSVLAAFFGVFYIKTfytirglfK 267
                                    8************************99665433332 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.53
                        Wzy_C_2  65 lalllsil 72 
                                     +++l++l
  gi|116754761|ref|YP_843879.1| 400 SYMMLPAL 407
                                    23332222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (580 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 4302.89
//
Query:       gi|116754762|ref|YP_843880.1|  [L=564]
Description: glutamyl-tRNA synthetase [Methanosaeta thermophila PT]
Scores for complete 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-66  222.9   0.0    5.5e-66  222.6   0.0    1.1  1  tRNA-synt_1c    tRNA synthetases class I (E and Q), catalytic
    4.3e-25   88.6   0.0    6.5e-25   88.0   0.0    1.3  1  tRNA-synt_1c_C  tRNA synthetases class I (E and Q), anti-codo


Domain annotation for each model (and alignments):
>> tRNA-synt_1c  tRNA synthetases class I (E and Q), catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  222.6   0.0   6.2e-70   5.5e-66       2     309 ..     101     403 ..     100     408 .. 0.95

  Alignments for each domain:
  == domain 1  score: 222.6 bits;  conditional E-value: 6.2e-70
                                    -EEEE---SSSS-BHHHHHHHHHHHHHHHHTT-EEEEEE--SSC..CC--HHHHHHHHHHHHHTT---SSEEEEGGGGHH CS
                   tRNA-synt_1c   2 VrtRfaPePtGyLHiGhakaallnylfAknnnGkfilRieDTdp..erekeeaeesiledlkwlgikwdekptyqsdrfd 79 
                                    V+ RfaP+P+G + +G+a+ +++n  + k ++GkfilR++DTdp  +r   ea +  +ed kwlg ++ ++++ +s+r +
  gi|116754762|ref|YP_843880.1| 101 VVMRFAPNPNGPPTLGSARGIIINSEYVKMYGGKFILRFDDTDPvnKRPMIEAYDWYIEDCKWLGAEP-HEIVAASQRVE 179
                                    899****************************************9334666799999************.99********* PP

                                    HHHHHHHHHHHTTSEEEE-STHHHHHHHHCCSSHSS-TTTTS-HHHHHHHHHHHHHTTHSTTTS-EEEESSBTTSS.GGG CS
                   tRNA-synt_1c  80 elkkyaeeLikkGkAYvcectkeeleeereeqeklgskerdrydeenlklfeeemkkgkaegekavvRlkideess.vef 158
                                    +++++aeeLi++G AYvc c++   ++++ +  ++ +++rd++++en++l+ ++m +g++++++av+R+k d +++  ++
  gi|116754762|ref|YP_843880.1| 180 KYYEVAEELIRRGGAYVCLCEQTAFKALKDA--AMPCPHRDQTVDENMALW-NKMLDGSFQEGEAVLRVKTDIKHKdPAM 256
                                    *****************************99..99999*************.89******************99999*** PP

                                    SSTEEEEEEESGGGSBTTTBTSTSEEE-HHHHHHHHHHHTT-SEEEEEGGGGCCHHHHHHHHHHTT-S.-EEEEEE--EE CS
                   tRNA-synt_1c 159 rDlvrgriklepqeihdlvivksdiyPtYdfavvidDaleeithvlrteefldntpkyiwllealglevppfiheylrln 238
                                    rD    ri  ++   h+lv++++++ P  df  ++ D+l ++th+lr+++ +d+++++  l++ +g+  p++ h   +  
  gi|116754762|ref|YP_843880.1| 257 RDWAGFRIVTKS---HPLVGERYRVWPLLDFESAVEDHLLGVTHILRGKDLIDSERRQRYLYDHMGWVYPRVLHWGRVKI 333
                                    ************...***********************************************************999999 PP

                                    ETTSB-SHHHHHHHHHTTSSSSTT-TTSCBHHHHHHCTB-HHHHHHHHHHHCCCSSS.EEEEHHHHHHHHH CS
                   tRNA-synt_1c 239 lekkklSKRklsllvdekqvkewddlreallnflrrlGwtpekerelftreeliksfdlnresksleafdr 309
                                    ++    S  kl   ++  ++ +wdd+r+++++++rr+G+t+e+ r+++   ++ + + ++++++s+ a +r
  gi|116754762|ref|YP_843880.1| 334 FQFGAFSTSKLRKAIEAGEYSGWDDPRLPTVRAMRRRGITAEALRKFMIDLGVGETD-ISISMDSIYAENR 403
                                    9999999999999999*************************************9998.9999998877665 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 !   88.0   0.0   7.2e-29   6.5e-25       1     174 []     410     551 ..     410     551 .. 0.91

  Alignments for each domain:
  == domain 1  score: 88.0 bits;  conditional E-value: 7.2e-29
                 tRNA-synt_1c_C   1 ApRymaVldpvkvtienlpegkeeelevplhpknpelgtrkvpfskeiyiereDakrlkpgeevrLkelynikveevekd 80 
                                    A+R+++V+dpv+++i++   + +e++e+plhp   ++gtr++  + ++++ +eD+  l+pg+++rLk+l+ni+++e+   
  gi|116754762|ref|YP_843880.1| 410 ANRRFFVWDPVEIEIKG---EVPEVAEAPLHPT-IDRGTRRIRAGGRLLLCKEDVAGLAPGSRIRLKDLCNIEIKEIF-- 483
                                    89**************4...4679*********.8***************************************9993.. PP

                 tRNA-synt_1c_C  81 esgevtelkleydgesleearkkkg.iihWvsaeeaveaevrlYdrLfkeeededfllnpdslkvleeglaepalanlkk 159
                                           l++e+ + s e a++ k  iihW +  e +++                 +l pd++   ++g++e  +++ + 
  gi|116754762|ref|YP_843880.1| 484 ------PLRAELIDLSPETAKRLKLrIIHWAPV-EGIPV----------------RVLGPDKT---DTGIGEHGISD-EL 536
                                    ......45566666666666788888******7.89***................9******9...68*********.9* PP

                 tRNA-synt_1c_C 160 gdivQfeRiGyfrvd 174
                                    + ivQfeR+G++r+d
  gi|116754762|ref|YP_843880.1| 537 DRIVQFERYGFVRID 551
                                    *************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (564 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); 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: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 4152.53
//
Query:       gi|116754763|ref|YP_843881.1|  [L=135]
Description: NUDIX hydrolase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-23   83.7   0.0    1.3e-23   83.5   0.0    1.0  1  NUDIX     NUDIX domain
    0.00074   19.1   0.0     0.0047   16.5   0.0    2.1  1  DUF4916   Domain of unknown function (DUF4916)
  ------ inclusion threshold ------
      0.046   13.7   0.0      0.081   12.9   0.0    1.5  1  NUDIX_4   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 !   83.5   0.0   2.1e-27   1.3e-23       4     129 ..      12     129 ..       9     131 .. 0.90

  Alignments for each domain:
  == domain 1  score: 83.5 bits;  conditional E-value: 2.1e-27
                                    EEEEEEEEETTSEEEEEEESSSSTTT.EESSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEEEEEE CS
                          NUDIX   4 ravgvvllnekgevLlvrrskkpfpg.WelPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydgpygdeh 82 
                                     av vvl+ ++g ++l+rr++ pf g ++lPgG+ve gEt+e+AArRE+ EEtG++a l++l+g    ++++++++++ h
  gi|116754763|ref|YP_843881.1|  12 LAVDVVLRMNDG-LVLIRRRNPPFMGcYALPGGFVEIGETVEDAARREVMEETGISASLVKLVG----VYSDPDRDPRGH 86 
                                    799***888887.99999999*****778***********************************....8888888888** PP

                                    EEEEEEEEEECSGCSSTSTTTEEEEEEEEHHHHHHHHTHCTHHHHHH CS
                          NUDIX  83 eilyvfleevegelepndenevsevrwvpleellkeklaaesrkllp 129
                                     +++++l++  gel+ +   + s++r ++++el  ++la +++++++
  gi|116754763|ref|YP_843881.1|  87 VVSICYLADGSGELRSG--SDASDARIFRPDEL--PELAFDHARMIR 129
                                    *******9999998888..77789*********..888888888776 PP

>> DUF4916  Domain of unknown function (DUF4916)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   7.8e-07    0.0047     107     166 ..      80     133 ..       7     135 .] 0.86

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 7.8e-07
                                    EE-TT-EEEEEEEEEEB-S-----TTEEEEEEE-HHHHTSHHHHHTB-TTHHHHHHHHHH CS
                        DUF4916 107 ytdprqhavslayvvpvaGdceprqdaleleWltpeealseevlaeleggrgelvrqala 166
                                      dpr h vs++y+   +G+ ++ +da +   + p+e        el+  + +++r ala
  gi|116754763|ref|YP_843881.1|  80 DRDPRGHVVSICYLADGSGELRSGSDASDARIFRPDELP------ELAFDHARMIRDALA 133
                                    479******************************999865......455556666666666 PP

>> NUDIX_4  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.4e-05     0.081       2      66 ..      16      79 ..      15     132 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.4e-05
                                   EEEEEECTEEEEEE--TTSSSTT-EE-SEEE.-TTS-HHHHHH...HHHHS-EEEEEEEEEEEEEETTE CS
                        NUDIX_4  2 vllirddgrvllekRpekgllggLwefPgge.eegeeleeala...reelgieveelepgtvkHvftHf 66
                                   v+l ++dg vl+++R +     g + +Pgg  e ge++e+a+     ee+gi++  l +   + v+++ 
  gi|116754763|ref|YP_843881.1| 16 VVLRMNDGLVLIRRRNPP--FMGCYALPGGFvEIGETVEDAARrevMEETGISAS-LVK--LVGVYSDP 79
                                   5666777**********8..99******988888999777664344567775433.323..22344443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       193  (0.0107647); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1047.53
//
Query:       gi|116754764|ref|YP_843882.1|  [L=418]
Description: dihydropteroate synthase [Methanosaeta thermophila PT]
Scores for 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  192.5   0.1    1.3e-56  192.0   0.1    1.2  1  Pterin_bind  Pterin binding enzyme


Domain annotation for each model (and alignments):
>> Pterin_bind  Pterin binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.0   0.1   7.1e-61   1.3e-56       1     244 []      21     256 ..      21     256 .. 0.94

  Alignments for each domain:
  == domain 1  score: 192.0 bits;  conditional E-value: 7.1e-61
                                    EEEEETTTTTCHCCHHCTHHHHHHHHHHHHHHTT-SEEEEESS-TSTT--CCHHHHHHHHHHHHHHHHHHHCTSEEEEE- CS
                    Pterin_bind   1 mgilNvtpdsfsdggkfedldkalaqarkmveeGAdilDiggestrPgaervdeeeelervvpvlealrdeadvpisiDt 80 
                                    mg++N++ +sf++g+ +  +++a + a km +eGA+++D+g+ st Pg+  ++e+ e er+ p le++ d +d  +s+Dt
  gi|116754764|ref|YP_843882.1|  21 MGVINLSAESFYKGS-VSTPERAASFAIKMADEGAEVIDVGAVSTAPGSPFISEDVERERLFPALENILDSVDAEVSVDT 99 
                                    9***********955.56************************************************************** PP

                                    S-HHHHHHHHHTTSEEEEETTTTSSSTTHHHHHHHHT-EEEEESECSSTTTHCCCCCCCSSHHHHHHHHHHHHHHHHHHT CS
                    Pterin_bind  81 tkaevaeaAlkagadivNdvsgeerdpkmlelvaeagaavvvmhmrgtpktmqeeegqyedvveeveaflearveaaeea 160
                                     +a++a  Al+ ga+ +Ndvs ++ dp m+e+va++ga + +m++r +p +  e     +d++ +++    a+v+ a+e+
  gi|116754764|ref|YP_843882.1| 100 QRASIADLALSMGAACINDVSCLK-DPSMAEVVADHGASLLLMASRDKPGDILE----LKDIIPRLA----AAVSTAVES 170
                                    ************************.*********************66665533....446666655....56669999* PP

                                    T--GGGEEEETTTTS...STTHHHHHHHHHTHHHHHHTTSSEBEEEGTTGHHHHHHHCTTCHGHHHHHHHHHHHHHHHTT CS
                    Pterin_bind 161 GvaperillDpgigf...gkteehnlellrrldelrealevpvllGvSrksflgrllelgkaeeRdagtaaflalaaaaG 237
                                    Gv+p ril+Dpgig     kt e +l++l+r+  l + l+ p++ +vSrksf+g++l l+++++R +g++a++a+a+ +G
  gi|116754764|ref|YP_843882.1| 171 GVDPRRILIDPGIGRwipEKTYEYDLAILDRMRSL-RSLRKPIVAAVSRKSFIGAVLGLKDPADRLTGSIAATAIAVYNG 249
                                    *************99899*****************.9999****************99999******************* PP

                                    -SEEEES CS
                    Pterin_bind 238 adivrVh 244
                                    a++vr+h
  gi|116754764|ref|YP_843882.1| 250 AHVVRTH 256
                                    ******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); 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 0.25s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 3300.45
//
Query:       gi|116754765|ref|YP_843883.1|  [L=388]
Description: cytidine deaminase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-57  193.1   0.0    7.9e-57  192.4   0.0    1.3  1  F420_ligase      F420-0:Gamma-glutamyl ligase
    6.4e-15   54.9   0.1    1.1e-14   54.1   0.1    1.4  1  dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-
    1.5e-09   38.1   0.4    3.2e-09   37.1   0.4    1.5  1  dCMP_cyt_deam_2  Cytidine and deoxycytidylate deaminase zinc-
  ------ inclusion threshold ------
      0.013   15.1   3.0        1.4    8.4   0.5    2.3  2  LmjF365940-deam  A distinct subfamily of CDD/CDA-like deamina


Domain annotation for each model (and alignments):
>> F420_ligase  F420-0:Gamma-glutamyl ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.4   0.0   1.8e-60   7.9e-57       1     244 []       6     221 ..       6     221 .. 0.98

  Alignments for each domain:
  == domain 1  score: 192.4 bits;  conditional E-value: 1.8e-60
                                    -..-----TT--HHHHHHCCS-.....--TT-EEEEEHHHHHHHTT-EEEGGGS---HHHHHHHHHH.TS-H........ CS
                    F420_ligase   1 giktplikegddlaeivvesvkkagleledgDivvvtekvvakaegnyvsledikpsekAeeiaeklkvidpilSrnrfs 80 
                                    gikt l+k+g+d +e +   + +ag++l+d+D++vv+e++va+ eg++vsl+di+ps++A+ +a+++ ++dp        
  gi|116754765|ref|YP_843883.1|   6 GIKTGLLKPGEDHVEALRRGLAEAGIRLRDKDVIVVSESFVATGEGRVVSLKDITPSARAIALASRY-EKDP-------- 76 
                                    89*****************************************************************.****........ PP

                                    ..........HHHHHHHHTEEEEEE-...S-EEEE.......TTS-EEEGGG-B-TTS-TTEEE---S-HHHHHHHHHHH CS
                    F420_ligase  81 liLkalakatrkvevvlsepsdevgn...qlidekytdevlvklGllgsnagidesnveegllkllPedpdksaeeikkk 157
                                              +++e++l+e+++++g    ++++ k         G+l+ nag+d+sn++ g+++llP+dp++ a++i+++
  gi|116754765|ref|YP_843883.1|  77 ----------AEMELILRESDEILGGipgVVLTLK--------DGFLYPNAGVDHSNAPPGYVVLLPSDPKRAASRIRTE 138
                                    ..........***************9987777777........5************************************ PP

                                    HHHHHS---EEEE..EEEEEETTEECEEEEEEEEESB-SEEE-TT-B-TTS-B-S--EEEHHHHHHHHHHHHC-SSSS-- CS
                    F420_ligase 158 lkertgkdveVliygkDpegriweladpvvaigtsglealrdlrgkkdldgkelgttpravtdelgsladLvsGsadegt 237
                                    l++  g++++V+i   D+++++++l++++va++++g+ +++d rg++dl+gk+l++t++av+d+l s+a+Lv+G++deg+
  gi|116754765|ref|YP_843883.1| 139 LSN--GVRIGVII--GDSRTHPLRLGCVGVALACDGIIPVEDARGRRDLYGKPLRITVKAVADNLVSAAQLVMGEGDEGI 214
                                    *76..********..***************************************************************** PP

                                    -EEEEES CS
                    F420_ligase 238 Pvvlvrg 244
                                    P+v++rg
  gi|116754765|ref|YP_843883.1| 215 PAVVIRG 221
                                    ******8 PP

>> dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.1   0.1   2.5e-18   1.1e-14       5      99 ..     260     359 ..     257     361 .. 0.90

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 2.5e-18
                                    HHHHHHHHHHHHHHH.TTTSCSEEEEEEETTEEEEEEESBHHCCTGTTB-HHHHHHHHHHHHTSSCETTEEEEE...... CS
                dCMP_cyt_deam_1   5 ekllelalkaakeaq.kcsnfkVGavivkngeiistgyngepaggsktiHAEvnAilkaaknggsklegatlyv...... 77 
                                      l++ a++a ++a+ ++s+f+VGa+++    +i++g+n e+a++   i+AE++A+++a+  g+ ++    l+v      
  gi|116754765|ref|YP_843883.1| 260 DDLIKSAIDARDQAYaPYSKFRVGAAVLCGSGKIYKGANVENASSGAGICAERVAMATAVAAGEREF--VALAVagelsk 337
                                    56889999*********************99*****************************9974466..66666788888 PP

                                    EE--BHHHHHHHHHHT-SEEEE CS
                dCMP_cyt_deam_1  78 tlePCsmCakaiiqsgikkvvv 99 
                                     ++PC+ C++++i++g  +vv+
  gi|116754765|ref|YP_843883.1| 338 PITPCGICRQMMIEFGDMDVVM 359
                                    ****************999997 PP

>> dCMP_cyt_deam_2  Cytidine and deoxycytidylate deaminase zinc-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.4   7.2e-13   3.2e-09      44     108 ..     259     323 ..     240     334 .. 0.89

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 7.2e-13
                                    S-HHHHHHHHHHTT-B-TTT---EEEEEEETTS-EEEEE-B--TTSTT-B-HHHHHHHHHHHTT- CS
                dCMP_cyt_deam_2  44 ddelkeaAlaaanasyapyskcpsGvaLvtkdgkvyaGsyiEsaAfNpsLpPlqaAlvalvlggk 108
                                     d+l ++A++a  ++yapysk   G a+ +++gk+y+G  +E+a     + + ++A+  +v++g+
  gi|116754765|ref|YP_843883.1| 259 YDDLIKSAIDARDQAYAPYSKFRVGAAVLCGSGKIYKGANVENASSGAGICAERVAMATAVAAGE 323
                                    56799******************************************************999554 PP

>> LmjF365940-deam  A distinct subfamily of CDD/CDA-like deaminases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.5   0.00032       1.4      56      89 ..     289     322 ..     279     333 .. 0.83
   2 ?    6.7   0.1    0.0011       4.8     151     165 ..     336     350 ..     328     366 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00032
                LmjF365940-deam  56 greelvrgvNlEvSmPtGSlCsErnaigkalasd 89 
                                    g  ++++g N+E        C+Er a+++a+a+ 
  gi|116754765|ref|YP_843883.1| 289 GSGKIYKGANVENASSGAGICAERVAMATAVAAG 322
                                    567899******9998889***********9975 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0011
                LmjF365940-deam 151 snPLkPCGaCeewLk 165
                                    s P++PCG+C++++ 
  gi|116754765|ref|YP_843883.1| 336 SKPITPCGICRQMMI 350
                                    57*********9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); 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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2768.81
//
Query:       gi|116754766|ref|YP_843884.1|  [L=271]
Description: hypothetical protein Mthe_1470 [Methanosaeta thermophila PT]
Scores for 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-83  279.3   0.0    2.3e-83  279.1   0.0    1.0  1  NRD1_2    NrpR regulatory domains NRD1 and 2


Domain annotation for each model (and alignments):
>> NRD1_2  NrpR regulatory domains NRD1 and 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  279.1   0.0   1.3e-87   2.3e-83       3     237 ..      35     261 ..      33     262 .. 0.99

  Alignments for each domain:
  == domain 1  score: 279.1 bits;  conditional E-value: 1.3e-87
                                    -HHHHHHHHHCC---BTTTTB-EEEEEEEEEEGGGHHHHHHHHHHHHHTT-SSSSEEEEEE-SSE........EEEEEE- CS
                         NRD1_2   3 fviskieelaykvtfdpetgkGkVivNlslidkedleealeilkeviksglsvsdrvkileegekelevpegkvgiatvC 82 
                                    f + +ie+l+++v++d ++g+G+Vi+N sl+ ++dl+ealei+k++i+sgl+vs++v++++ ge+        + i tvC
  gi|116754766|ref|YP_843884.1|  35 FALGRIENLVHQVSLDAKKGTGRVITNRSLVARDDLHEALEIFKDAIDSGLAVSPLVRLEDVGER--------FMIHTVC 106
                                    7899*************************************************************........******* PP

                                    CHHHHHHHHCTT--EEEEEEEEEEE-SS.-EEEEEEEESTT-SS-HHHHCGGG.........--SSSEEEEEEEEEETTT CS
                         NRD1_2  83 SitidgvLlknGIpvkpkyGGlleiedkepvrFtelIsYegtsidPlevfiskklTsvlevietgegkilAnlReipvsa 162
                                    S+tidg+L+k+GIpv+pk GGl+e+ d+e vrFt++I+Y+ t+idPl+++i+++lT + e+++tg+g+il+nl+e p++a
  gi|116754766|ref|YP_843884.1| 107 SMTIDGYLIKHGIPVRPKGGGLIEVIDRETVRFTDIIMYWATTIDPLDLLIAQELTGICEMMRTGTGRILGNLHEAPMIA 186
                                    ******************************************************************************** PP

                                    HHHHHHHHHHH...T-TTEEEE--TT--BTTB---TTEEEEEEE-TTHHHHHHHHTT---EEEEEEEEEEGGGSE CS
                         NRD1_2 163 rekveeileklkkagisgvleigepneevlgvpveeekvgivvvgGlnpiaalkeagikveikalsglidiselk 237
                                    ++++e++l++l++agi gv+e+g+pn +vlg+pve++++g++++gG+np aa++e g+++e+ ++sgl++ise+ 
  gi|116754766|ref|YP_843884.1| 187 HDTIEDLLDELRDAGIMGVIELGDPNMDVLGMPVERDHLGVALIGGTNPAAAAVEFGLDIETASISGLTEISEMC 261
                                    *************************************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       262  (0.0146132); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1997.40
//
Query:       gi|116754767|ref|YP_843885.1|  [L=838]
Description: ATPase, P-type (transporting), HAD superfamily, subfamily IC [Methanosaeta thermophila PT]
Scores for 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-43  146.0   0.1    8.3e-43  146.0   0.1    2.0  2  E1-E2_ATPase     E1-E2 ATPase
    1.1e-27   97.0   9.6    1.1e-27   97.0   9.6    1.8  2  Cation_ATPase_C  Cation transporting ATPase, C-terminus
    9.3e-20   71.8   0.1    5.7e-19   69.2   0.1    2.2  2  Hydrolase        haloacid dehalogenase-like hydrolase
    5.7e-08   32.3   0.0    1.5e-07   31.0   0.0    1.7  1  Cation_ATPase_N  Cation transporter/ATPase, N-terminus
    5.9e-06   26.2   0.1      0.001   18.9   0.1    2.2  2  Hydrolase_3      haloacid dehalogenase-like hydrolase
    9.4e-06   25.6   0.0    1.8e-05   24.8   0.0    1.4  1  Cation_ATPase    Cation transport ATPase (P-type)
  ------ inclusion threshold ------
      0.015   15.7   0.0      0.033   14.6   0.0    1.6  1  HAD              haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   1.0       3.5     9e+03     130     158 ..      47      75 ..      31      78 .. 0.50
   2 !  146.0   0.1   3.2e-46   8.3e-43       2     180 ..      94     289 ..      93     290 .. 0.98

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 3.5
                                    HHHHHHS-STTTSSTTHHHHHHHHHHHHH CS
                   E1-E2_ATPase 130 allvflialllgkslaeallralallvaa 158
                                    ++++ +i +llg+     +l +++l+v++
  gi|116754767|ref|YP_843885.1|  47 LIACGAIYFLLGDRREALILIFFVLVVIS 75 
                                    33333333333333323344455555554 PP

  == domain 2  score: 146.0 bits;  conditional E-value: 3.2e-46
                                    SS--EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-S.EEE-TTTS---S-EE-................ CS
                   E1-E2_ATPase   2 llpptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsa.evdesaLTGEslpvek................ 64 
                                    l++p+a virdgt ++i+ +e+v GD+++l++gdrvpaD+ +++ ++  vdes+LTGEs+pv+k                
  gi|116754767|ref|YP_843885.1|  94 LSSPRALVIRDGTPVRIPGREVVRGDLIVLEEGDRVPADAAVISCTSlLVDESILTGESMPVRKipcedkeyqevmppgg 173
                                    68899************************************************************************999 PP

                                    G-TTEE-TT-EEEE-EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSST CS
                   E1-E2_ATPase  65 ekgdmvfsGtvvvsgeakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgksl 144
                                    +    v++Gt vv+g+  a+V+atg+ t +g+i +++++ + ++++l+++ +++++ l++++l+++ +++++  l +++l
  gi|116754767|ref|YP_843885.1| 174 DDVPFVYTGTLVVQGRGLARVVATGSRTLMGRIGASLKSIELEESRLKRETRSIVRRLTLFGLALSTVLLIAYALETGDL 253
                                    99999*************************************************************************** PP

                                    THHHHHHHHHHHHHS-TTHHHHHHHHHHHHHHHHHH CS
                   E1-E2_ATPase 145 aeallralallvaaiPcaLplavplalalgarrlak 180
                                     + ll +++l +a++P+ +p+++++ lalga+rl++
  gi|116754767|ref|YP_843885.1| 254 LRGLLAGITLTMAILPEEFPVVLTIFLALGAWRLSR 289
                                    *********************************986 PP

>> Cation_ATPase_C  Cation transporting ATPase, C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.1       3.2   8.2e+03     127     141 ..     231     245 ..     218     279 .. 0.66
   2 !   97.0   9.6   4.2e-31   1.1e-27       1     182 []     659     829 ..     659     829 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 3.2
                Cation_ATPase_C 127 llllaillslllqvl 141
                                    l l++++ls++l+++
  gi|116754767|ref|YP_843885.1| 231 LTLFGLALSTVLLIA 245
                                    334444444444443 PP

  == domain 2  score: 97.0 bits;  conditional E-value: 4.2e-31
                Cation_ATPase_C   1 plplsaiqiLwinLvtDllpalaLaleppekdimkrpPrkkkepliskkmlrriliqgllqalvtllvffltlllfgise 80 
                                    pl l +++i +++Lv+D  +++a+  e +e+d+m+rpP ++k+pl+s++++   ++qg+ +++v  ++++  +   +++e
  gi|116754767|ref|YP_843885.1| 659 PLLLMPVHIAFLELVIDPACSIAFEAEAEESDVMSRPPMNPKAPLVSTGVIALGALQGISVLAVLSTIYLMSIV-GDMNE 737
                                    7899*********************************************9999999999999999999988877.23444 PP

                Cation_ATPase_C  81 kenklssnyaqtmaFitlvlsqifnalnlrsrreslfkfsglfsnkllllaillslllqvlivyvpglnavfgtaplsle 160
                                              ++++F+tlvl++++ +l+ rs ++++++ s  ++n  l++++ +++ll+ +i+y+p l+++f++  l ++
  gi|116754767|ref|YP_843885.1| 738 ---------VRALIFTTLVLANLLLILTNRSWSQTILQ-SIKTRNSALWMIFGGTVLLLSMILYIPSLREMFHFGYLHPK 807
                                    .........9**************************99.4444899********************************** PP

                Cation_ATPase_C 161 ewlialllalvvllvdelvKll 182
                                    + +i+l+la+ ++l++e++K++
  gi|116754767|ref|YP_843885.1| 808 DIMICLALASTSVLWFEAWKMI 829
                                    ********************86 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0         5   1.3e+04      58      80 ..     181     206 ..     173     223 .. 0.69
   2 !   69.2   0.1   2.2e-22   5.7e-19       2     208 ..     307     587 ..     306     589 .. 0.68

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 5
                                    HHHHHETTTE...HHHHTHHHHHHHH CS
                                    xxxxxxxxxx...xxxxxxxxxxxxx RF
                      Hydrolase  58 tgfatfigrg...ayaigkpewltal 80 
                                    tg  +++grg   ++a g++ ++ + 
  gi|116754767|ref|YP_843885.1| 181 TGTLVVQGRGlarVVATGSRTLMGRI 206
                                    55566677777777777777777766 PP

  == domain 2  score: 69.2 bits;  conditional E-value: 2.2e-22
                                    SEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTE.............. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............. RF
                      Hydrolase   2 ktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrg.............. 67 
                                    ++++ Dk+GT+t  +++v++++++                i     a  +++  ++ +f+ ++gr               
  gi|116754767|ref|YP_843885.1| 307 TVLCTDKTGTVTLNRMRVRKIFARG--------------RIYDVDGALPEDV-HDVVEFGILAGRRdpfnpmeialqelg 371
                                    68999********************..............2222222222222.111233333333355554444422222 PP

                                    .........................HHHHTHHHHHHHHHCHHHHHHHHHHHHHHCHHHHHH................... CS
                                    .........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................... RF
                      Hydrolase  68 .........................ayaigkpewltaldippdlgaaigsaqsqgrtvall................... 103
                                                                                                l                   
  gi|116754767|ref|YP_843885.1| 372 rrelngtehihndwtfvqeypltddI----------------------------------Lamsmvwmhggeyviaakga 417
                                    22222233333333333333444430..................................14444555555555555555 PP

                                    ....................................................TTHHHHHHHHHHTHHBHTTHHHHHHHHH CS
                                    ....................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 104 ....................................................qaralavftiadplkvkpeaaeavasLk 131
                                                                                        + +  +++ ++d+  ++p++ +av++ +
  gi|116754767|ref|YP_843885.1| 418 pesifdlchldgeelnkiyevvermaadglrvlgvaraaiseselpdgqhgfDFQFMGLLGFSDT--IRPGVPDAVNECQ 495
                                    555556666666666666667777777888888889999999999999888888***********..************* PP

                                    HTTEEEEEEESSEHHHHHHHHHHTT...........GGGESEEEEHHCES...........STTTSHHHHHHHHHHHTST CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 132 aagievvlltgdnpetaeraanqlG...........ddyfdaviasdiet...........vakpspegkvaaireLqgk 189
                                    +ag++v l+tgd+p ta ++a+ ++                   +s  ++           +a   pe+k+++++ L+ +
  gi|116754767|ref|YP_843885.1| 496 RAGVRVMLITGDHPITAASIASSINlnrgsvltgpeI-------ESMSDEelskrlrdaniFARMVPEQKLRLVELLKSQ 568
                                    ***********************99888755554331.......222222345556668999***************988 PP

                                    GGGEEEEESSHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 190 peevamVGDgvnDaaalaa 208
                                    +e vam GDgvnDa+al+ 
  gi|116754767|ref|YP_843885.1| 569 GEIVAMTGDGVNDAPALKS 587
                                    888**************96 PP

>> Cation_ATPase_N  Cation transporter/ATPase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0   5.7e-11   1.5e-07      20      68 ..       5      53 ..       3      54 .. 0.98

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 5.7e-11
                Cation_ATPase_N 20 GLtqaeaaerlkkyGpNelkekkkkslwvkllkqftnplvilLlvaalv 68
                                   GL++a+a++rl + G Nel+ ++++ l+ +  + ++ p++ lL++++++
  gi|116754767|ref|YP_843885.1|  5 GLSSADAQRRLIEEGYNELPSERRRGLLSIAMDVLKEPMISLLIACGAI 53
                                   9*********************************************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 !    5.1   0.0    0.0064        16      15      58 ..     482     525 ..     476     553 .. 0.80
   2 !   18.9   0.1     4e-07     0.001     195     255 .]     561     622 ..     558     622 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0064
                                    ---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEE CS
                    Hydrolase_3  15 kisektkeaikklkekgikvviATGRslravlpvleelgldlpv 58 
                                    +i +   +a+++++ +g+ v++ TG ++ ++ +++ +++l+   
  gi|116754767|ref|YP_843885.1| 482 TIRPGVPDAVNECQRAGVRVMLITGDHPITAASIASSINLNRGS 525
                                    67777789****************************99998544 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 4e-07
                                    HHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETT.S-HHHHHHSSEEE--GGGTHHHHHH CS
                    Hydrolase_3 195 lakelnisleeviafGDgeNDieMLeaaglgvAmgn.aseevkkaAdyvtksnnedGVakal 255
                                    l++ l+ + e v+  GDg ND + L+ + +g+Amg+ +++ + + Ad v  + + ++++ka+
  gi|116754767|ref|YP_843885.1| 561 LVELLKSQGEIVAMTGDGVNDAPALKSSHIGIAMGSrGTDVARESADIVLLDDDFSSIVKAI 622
                                    677888888999999*******************9648999999999999999999999987 PP

>> Cation_ATPase  Cation transport ATPase (P-type)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   6.9e-09   1.8e-05      22      88 ..     361     425 ..     360     427 .. 0.96

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 6.9e-09
                  Cation_ATPase  22 nktEsALlvlaeklgldteelreetkkvqeipFnssrKrmsvvlklepekkvrlyvKGApeiilkrC 88 
                                    n+ E+AL++l ++    te + ++++ vqe+p + +   ms+v    + +++++  KGApe+i++ C
  gi|116754767|ref|YP_843885.1| 361 NPMEIALQELGRRELNGTEHIHNDWTFVQEYPLTDDILAMSMVWM--HGGEYVIAAKGAPESIFDLC 425
                                    789***********9****************************99..57****************99 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.3e-05     0.033      86     188 .]     483     586 ..     436     586 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.3e-05
                            HAD  86 ldpgalellaahraaGdrvvvvSgglrplvepllaelg..adevlat.elevdd..rltgelglegkpvrg....egkva 156
                                    ++pg+ ++++++++aG+rv +++g + + +  ++   +     vl   e+e+     l+++  l++ +++     e+k++
  gi|116754767|ref|YP_843885.1| 483 IRPGVPDAVNECQRAGVRVMLITGDHPITAASIASSINlnRGSVLTGpEIESMSdeELSKR--LRDANIFArmvpEQKLR 560
                                    5688889999888*********************866644444444435555556666666..55555555344456666 PP

                            HAD 157 alrewlaaegegidleevvay.GDspsDlpllr 188
                                     ++        + + e +va  GD+++D p+l+
  gi|116754767|ref|YP_843885.1| 561 LVEL------LKSQGE-IVAMtGDGVNDAPALK 586
                                    6666......333443.66666********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (838 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.68u 0.27s 00:00:00.95 Elapsed: 00:00:00.43
# Mc/sec: 5884.14
//
Query:       gi|116754768|ref|YP_843886.1|  [L=318]
Description: integral membrane protein TerC [Methanosaeta thermophila PT]
Scores for complete 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-55  185.9  11.7    5.2e-55  185.9  11.7    2.2  3  TerC      Integral membrane protein TerC family


Domain annotation for each model (and alignments):
>> TerC  Integral membrane protein TerC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   1.0      0.14   2.5e+03      33      42 ..      40      49 ..       1      60 [. 0.45
   2 !  185.9  11.7   2.9e-59   5.2e-55       2     180 ..      71     273 ..      70     274 .. 0.97
   3 ?   -1.8   0.1      0.12   2.1e+03     136     160 ..     283     307 ..     277     313 .. 0.57

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.14
                           TerC 33 alllGilgAl 42
                                    +  Gi+ A+
  gi|116754768|ref|YP_843886.1| 40 LIWSGIWTAI 49
                                   2223333333 PP

  == domain 2  score: 185.9 bits;  conditional E-value: 2.9e-59
                           TerC   2 tlvlleivLsiDNlvviallvkk..lpeeqqkkalllGilgAlvlRillillavallelfdlilligglfLlytavkell 79 
                                    +++l+e +Ls+DNl+v+++++++  +pe++q k+l++Gi++Al++R+l+i+++  l+e+fd+i++++g+fL++t++k+ l
  gi|116754768|ref|YP_843886.1|  71 AGYLIERSLSVDNLFVFLMIFSYfqVPETHQYKVLFWGIVVALLMRALFIATGLTLIEHFDWIIYLFGIFLIITGIKMAL 150
                                    789********************9******************************************************** PP

                           TerC  80 ekr....le.nklvkeekkkkkktkst.................llavviqielaDlvfslDSvlaavaitsdlfivita 137
                                    +++    ++ n++v++ ++  ++t+++                 ll v+i++e++Dlvf++DS++a++a+t d+f+v+t+
  gi|116754768|ref|YP_843886.1| 151 QREskvqPDrNPVVRMFRSVVPATDHYdggrfitraygrtmatpLLIVLIAVEVTDLVFAVDSIPAVFAVTVDPFVVYTS 230
                                    988999966699******************************************************************** PP

                           TerC 138 vilsilvlrflakllakllerfptlkylalalllligvklvle 180
                                    +++++l+lr+l+++la++ + f++l+++++++l+++g+k++l+
  gi|116754768|ref|YP_843886.1| 231 NVFAVLGLRALYFALAACAHMFHYLNHGVILILIFVGIKMLLS 273
                                    ****************************************986 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.12
                           TerC 136 tavilsilvlrflakllakllerfp 160
                                    +  ++++++l+++   la+  +r +
  gi|116754768|ref|YP_843886.1| 283 ALGFVALVLLVSMLASLARTSDRER 307
                                    4445566666666666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1068  (0.0595683); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); 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):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2277.91
//
Query:       gi|116754769|ref|YP_843887.1|  [L=259]
Description: hypothetical protein Mthe_1473 [Methanosaeta thermophila PT]
Scores for complete 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-76  256.7   0.0    1.9e-76  256.4   0.0    1.0  1  DUF166    Domain of unknown function


Domain annotation for each model (and alignments):
>> DUF166  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  256.4   0.0   1.1e-80   1.9e-76       1     219 [.       4     254 ..       4     255 .. 0.97

  Alignments for each domain:
  == domain 1  score: 256.4 bits;  conditional E-value: 1.1e-80
                         DUF166   1 lvltsgeyGervvenilnepdfersl.................ivavvevpe..eldefiedpeelLpelkeaDiviayt 61 
                                    +v+++ge+Gervv+n+ln+p f++s+                 iva+ve+p+  +l++fi+d+e lLp+++eaDi+i ++
  gi|116754769|ref|YP_843887.1|   4 VVYYNGEFGERVVGNLLNYPGFCISCgeactqcrsgkysgaedIVAAVEMPDpsTLGDFIDDVEPLLPAVPEADIAIVIN 83 
                                    699***************************************************************************** PP

                         DUF166  62 lhpDlllelaekakekkvkalivpaeapk...aglrkelkekleelgievavpkpfCslee.egkpkideFlee..fGkP 135
                                    +hpD+l+ ++ ++k+++++ +i ++e+pk   +glr ++++++eelg+e+a++kpfC++++ + kp+i +Fl++  +G+P
  gi|116754769|ref|YP_843887.1|  84 VHPDILFGMLPRMKDAGIRGIIGCSESPKdmpMGLRLQVSRAAEELGLEAAFSKPFCAMRPdPLKPNIAAFLKRamIGEP 163
                                    *************************************************************99***************** PP

                         DUF166 136 elevevkdgki.....kkVeVlrsapCGstwyvakklkGkeveeaeeka..geahqsYpClAsmerdfelketklhkAgy 208
                                    ele+ +++g++     +  +V+rsapCGstw+vak+l+G+e ++ ++++  +eah++YpC+Asm+rd+e+++t lh+Agy
  gi|116754769|ref|YP_843887.1| 164 ELEIVLQKGREgkdviAAANVIRSAPCGSTWFVAKRLIGVEKDDPRLHEriSEAHHAYPCTASMDRDPEIGDTVLHRAGY 243
                                    *******777664455778**************************999888***************************** PP

                         DUF166 209 ihkeavekAlk 219
                                    i++++ve+A++
  gi|116754769|ref|YP_843887.1| 244 IIRDKVEEAIR 254
                                    *********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1943.06
//
Query:       gi|116754770|ref|YP_843888.1|  [L=162]
Description: TPR repeat-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-33  112.8   8.0    1.7e-12   46.6   0.1    3.6  3  TPR_1         Tetratricopeptide repeat
    1.6e-29   99.6  11.3    1.4e-10   40.4   0.1    4.4  4  TPR_2         Tetratricopeptide repeat
    2.1e-24   83.6   3.9      2e-06   27.6   0.0    4.2  4  TPR_8         Tetratricopeptide repeat
    1.1e-22   79.4   4.0    4.6e-08   32.6   0.0    3.2  3  TPR_11        TPR repeat
    2.1e-18   66.6   7.2    6.8e-11   42.6   0.2    4.0  4  TPR_16        Tetratricopeptide repeat
    5.5e-18   64.0   4.5    7.5e-06   26.0   0.0    4.1  4  TPR_17        Tetratricopeptide repeat
    3.1e-16   59.4   9.3    1.4e-08   34.9   0.6    3.4  3  TPR_12        Tetratricopeptide repeat
    1.1e-14   53.3   4.8    0.00043   20.1   0.1    4.4  4  TPR_7         Tetratricopeptide repeat
    3.5e-13   49.5  10.1    3.3e-06   27.1   0.1    3.0  4  TPR_9         Tetratricopeptide repeat
    4.3e-12   45.5  12.4    0.00097   18.9   0.2    5.0  5  TPR_10        Tetratricopeptide repeat
    9.5e-12   45.3   7.1    3.4e-06   27.5   0.1    3.0  3  TPR_19        Tetratricopeptide repeat
    3.2e-11   43.1  13.5    0.00045   20.8   0.2    4.9  5  TPR_14        Tetratricopeptide repeat
    2.7e-08   33.2   0.5     0.0001   21.3   0.0    2.0  2  NARP1         NMDA receptor-regulated protein 1
    2.8e-06   27.5   1.1     0.0021   18.2   0.0    2.5  2  ANAPC3        Anaphase-promoting complex, cyclosome, subunit 
    5.4e-06   26.7   8.1       0.62   10.8   0.0    4.6  4  TPR_6         Tetratricopeptide repeat
      1e-05   25.5   0.4        1.5    9.0   0.1    3.4  3  Fis1_TPR_C    Fis1 C-terminal tetratricopeptide repeat
    3.2e-05   23.8   1.5        1.3    8.8   0.1    3.1  3  DUF5113       Domain of unknown function (DUF5113)
    3.4e-05   24.0   3.3       0.29   11.2   0.3    3.9  2  DUF3856       Domain of Unknown Function (DUF3856)
      8e-05   22.6   2.0        2.1    8.5   0.0    3.5  3  MIT           MIT (microtubule interacting and transport) dom
    0.00023   21.6   2.9    0.00067   20.1   0.1    2.3  2  BTAD          Bacterial transcriptional activator domain
      0.003   17.5   0.1       0.22   11.5   0.0    2.8  3  SRP_TPR_like  Putative TPR-like repeat
     0.0039   17.7  12.3       0.62   10.9   1.0    5.1  5  TPR_4         Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.021   14.1   0.5        1.6    7.8   0.1    2.7  2  FAT           FAT domain
      0.028   14.6   2.4         35    4.9   0.1    3.9  4  PPR           PPR repeat
      0.035   13.8   0.5       0.62    9.7   0.4    2.6  1  RPN7          26S proteasome subunit RPN7
       0.14   12.2   1.1         48    4.1   0.0    3.3  3  Strep_SA_rep  Streptococcal surface antigen repeat
       0.18   11.8   1.9        9.4    6.3   0.0    3.3  3  TPR_3         Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.0   1.6e-10   1.1e-07       1      33 [.      23      55 ..      23      56 .. 0.94
   2 !   46.6   0.1   2.6e-15   1.7e-12       1      34 []      57      90 ..      57      90 .. 0.97
   3 !   38.5   0.4   8.9e-13   5.9e-10       1      31 [.      91     121 ..      91     124 .. 0.95

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 1.6e-10
                                   HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                          TPR_1  1 akalynlGnayfklgkydeAleyyekALelnPn 33
                                   a+ +  +Gn +f+ g+y+ Ale+y++A+ ++P+
  gi|116754770|ref|YP_843888.1| 23 ARRWLEKGNSHFNSGRYENALEAYDRAIGHDPT 55
                                   567999*************************97 PP

  == domain 2  score: 46.6 bits;  conditional E-value: 2.6e-15
                                   HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                          TPR_1  1 akalynlGnayfklgkydeAleyyekALelnPnn 34
                                   ++a++n+G a+ ++g+y++Al+ y++AL+l+Pn+
  gi|116754770|ref|YP_843888.1| 57 VDAWNNRGIALSYMGRYEDALKSYDEALRLDPNH 90
                                   58******************************97 PP

  == domain 3  score: 38.5 bits;  conditional E-value: 8.9e-13
                                    HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                          TPR_1   1 akalynlGnayfklgkydeAleyyekALeln 31 
                                    a a++n+G+a+ ++ +y+eAl+++++ALe++
  gi|116754770|ref|YP_843888.1|  91 AFAWNNKGMALGSMRRYQEALACFDRALEID 121
                                    679***************************8 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   5.2e-09   3.4e-06       2      33 ..      24      55 ..      23      56 .. 0.92
   2 !   40.4   0.1   2.2e-13   1.4e-10       2      34 .]      58      90 ..      57      90 .. 0.97
   3 !   28.6   0.7   1.3e-09   8.9e-07       1      31 [.      91     121 ..      91     123 .. 0.96
   4 !    9.1   0.1    0.0024       1.6       3      24 ..     127     148 ..     125     156 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 5.2e-09
                          TPR_2  2 ealynlGlayyklgdyeeAleafekAleldPn 33
                                   + + + G++++++g+ye Alea+++A+ +dP+
  gi|116754770|ref|YP_843888.1| 24 RRWLEKGNSHFNSGRYENALEAYDRAIGHDPT 55
                                   56999**********************99997 PP

  == domain 2  score: 40.4 bits;  conditional E-value: 2.2e-13
                          TPR_2  2 ealynlGlayyklgdyeeAleafekAleldPnn 34
                                   +a++n+G a+ ++g+ye+Al+ +++Al+ldPn+
  gi|116754770|ref|YP_843888.1| 58 DAWNNRGIALSYMGRYEDALKSYDEALRLDPNH 90
                                   79*****************************97 PP

  == domain 3  score: 28.6 bits;  conditional E-value: 1.3e-09
                          TPR_2   1 aealynlGlayyklgdyeeAleafekAleld 31 
                                    a a++n G+a+  + +y+eAl++f++Ale+d
  gi|116754770|ref|YP_843888.1|  91 AFAWNNKGMALGSMRRYQEALACFDRALEID 121
                                    689**************************98 PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.0024
                          TPR_2   3 alynlGlayyklgdyeeAleaf 24 
                                    a+yn   a ++lg+  eA++a+
  gi|116754770|ref|YP_843888.1| 127 AWYNKSHAMAALGRAREARAAM 148
                                    8******************986 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0     3e-07    0.0002       1      32 [.      23      54 ..      23      56 .. 0.92
   2 !   27.6   0.0     3e-09     2e-06       2      34 .]      58      90 ..      57      90 .. 0.96
   3 !   24.3   0.1   3.3e-08   2.2e-05       3      32 ..      93     122 ..      93     124 .. 0.96
   4 !    9.3   0.1    0.0021       1.4       3      30 ..     127     154 ..     125     157 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 3e-07
                                   CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                          TPR_8  1 aeayynlgsiylklgdyeeAkeyyekaleldp 32
                                   a+ ++ +g+ +++ g+ye+A e+y +a+  dp
  gi|116754770|ref|YP_843888.1| 23 ARRWLEKGNSHFNSGRYENALEAYDRAIGHDP 54
                                   689************************97666 PP

  == domain 2  score: 27.6 bits;  conditional E-value: 3e-09
                                   CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                          TPR_8  2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34
                                   +a++n g +++ +g+ye A ++y +al+ldp++
  gi|116754770|ref|YP_843888.1| 58 DAWNNRGIALSYMGRYEDALKSYDEALRLDPNH 90
                                   79*****************************97 PP

  == domain 3  score: 24.3 bits;  conditional E-value: 3.3e-08
                                    HHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                          TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldp 32 
                                    a++n+g+++ ++ +y+eA +++ +ale+d 
  gi|116754770|ref|YP_843888.1|  93 AWNNKGMALGSMRRYQEALACFDRALEIDA 122
                                    7***************************96 PP

  == domain 4  score: 9.3 bits;  conditional E-value: 0.0021
                                    HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                          TPR_8   3 ayynlgsiylklgdyeeAkeyyekalel 30 
                                    a+yn++++   lg+  eA +++  a +l
  gi|116754770|ref|YP_843888.1| 127 AWYNKSHAMAALGRAREARAAMITAKTL 154
                                    9*******************99888766 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.0   6.9e-11   4.6e-08       1      38 [.      30      67 ..      30      71 .. 0.94
   2 !   30.4   0.1   3.4e-10   2.3e-07       7      38 ..      70     101 ..      67     104 .. 0.92
   3 !   17.3   0.1   4.1e-06    0.0028       9      42 .]     106     139 ..     105     139 .. 0.94

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 6.9e-11
                         TPR_11  1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlay 38
                                   G+  +  G+ye+A+eaY +A+  dP+ ++a++n+G a+
  gi|116754770|ref|YP_843888.1| 30 GNSHFNSGRYENALEAYDRAIGHDPTIVDAWNNRGIAL 67
                                   999********************************997 PP

  == domain 2  score: 30.4 bits;  conditional E-value: 3.4e-10
                         TPR_11   7 qGkyeeAieaYkkAlkldPdnaeayynLGlay 38 
                                     G+ye+A+++Y +Al+ldP+ a a++n G a+
  gi|116754770|ref|YP_843888.1|  70 MGRYEDALKSYDEALRLDPNHAFAWNNKGMAL 101
                                    69*************************99876 PP

  == domain 3  score: 17.3 bits;  conditional E-value: 4.1e-06
                         TPR_11   9 kyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                    +y eA++++ +Al++d  +  a+yn  +a++++G
  gi|116754770|ref|YP_843888.1| 106 RYQEALACFDRALEIDAYFIGAWYNKSHAMAALG 139
                                    79***********************999988887 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1         1   6.8e+02      37      59 ..       7      29 ..       5      31 .. 0.83
   2 !   42.6   0.2     1e-13   6.8e-11       1      67 [.      27      90 ..      27      91 .. 0.97
   3 !   33.4   2.1   7.8e-11   5.2e-08       3      65 ..      63     122 ..      62     123 .. 0.93
   4 !   11.7   3.7   0.00048      0.32       3      56 ..      97     147 ..      95     152 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 1
                         TPR_16 37 llllgdaalrqgrlaeAaalyra 59
                                   +++l++++    + aeA+ ++++
  gi|116754770|ref|YP_843888.1|  7 AWALAVMLVSEADTAEARRWLEK 29
                                   68899999999999999999875 PP

  == domain 2  score: 42.6 bits;  conditional E-value: 1e-13
                         TPR_16  1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67
                                   l+++++++++g+y+ A++a+++a+  d   P  ++A++++g a+   gr+++A+  y++alr +p++
  gi|116754770|ref|YP_843888.1| 27 LEKGNSHFNSGRYENALEAYDRAIGHD---PTIVDAWNNRGIALSYMGRYEDALKSYDEALRLDPNH 90
                                   5789***********************...***********************************97 PP

  == domain 3  score: 33.4 bits;  conditional E-value: 7.8e-11
                         TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65 
                                    ++ a+ + g+y+dA++ +++al++d   P +a A++++g a+    r++eA+a +++al+ ++
  gi|116754770|ref|YP_843888.1|  63 RGIALSYMGRYEDALKSYDEALRLD---PNHAFAWNNKGMALGSMRRYQEALACFDRALEIDA 122
                                    6889999******************...99999**************************8765 PP

  == domain 4  score: 11.7 bits;  conditional E-value: 0.00048
                         TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaal 56 
                                    +++a+   ++y++A+a +++al+ d+       A++++  a +++gr  eA+a+
  gi|116754770|ref|YP_843888.1|  97 KGMALGSMRRYQEALACFDRALEIDAYFIG---AWYNKSHAMAALGRAREARAA 147
                                    7899999*****************976666...888888888888888888865 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0       2.2   1.5e+03      16      33 ..      26      43 ..      26      44 .. 0.77
   2 !   26.0   0.0   1.1e-08   7.5e-06       1      33 [.      45      77 ..      45      78 .. 0.95
   3 !   23.3   0.2   8.2e-08   5.5e-05       2      33 ..      80     111 ..      79     112 .. 0.95
   4 !   13.4   0.1   0.00012     0.079       1      34 []     113     146 ..     113     146 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 2.2
                         TPR_17 16 ynnLAelllknGdlmtAr 33
                                   + ++++ + + G+++ A+
  gi|116754770|ref|YP_843888.1| 26 WLEKGNSHFNSGRYENAL 43
                                   667788888999999886 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 1.1e-08
                         TPR_17  1 lylkaleldPnnadaynnLAelllknGdlmtAr 33
                                   +y +a+ +dP+ +da+nn++ +l+  G++++A+
  gi|116754770|ref|YP_843888.1| 45 AYDRAIGHDPTIVDAWNNRGIALSYMGRYEDAL 77
                                   59*****************************97 PP

  == domain 3  score: 23.3 bits;  conditional E-value: 8.2e-08
                         TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                    y +al+ldPn+a a+nn++ +l +  ++++A+
  gi|116754770|ref|YP_843888.1|  80 YDEALRLDPNHAFAWNNKGMALGSMRRYQEAL 111
                                    99***************************997 PP

  == domain 4  score: 13.4 bits;  conditional E-value: 0.00012
                         TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                    ++ +ale+d     a++n+  +++ +G+ ++Ar+
  gi|116754770|ref|YP_843888.1| 113 CFDRALEIDAYFIGAWYNKSHAMAALGRAREARA 146
                                    799*****************************95 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.16   1.1e+02      50      70 ..       9      29 ..       4      30 .. 0.62
   2 !   34.9   0.6   2.1e-11   1.4e-08       8      76 ..      28      88 ..      22      89 .. 0.87
   3 !   25.7   2.0   1.5e-08     1e-05       5      56 ..      93     143 ..      90     158 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.16
                         TPR_12 50 nLgrlyralgryeeAlellee 70
                                   +L+ ++    +++eA+++le+
  gi|116754770|ref|YP_843888.1|  9 ALAVMLVSEADTAEARRWLEK 29
                                   466666555566677766665 PP

  == domain 2  score: 34.9 bits;  conditional E-value: 2.1e-11
                         TPR_12  8 nlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76
                                   + ++ ++  gry+ Ale +++a         ++ p  + + +n g++++++grye+Al+ + eal++++
  gi|116754770|ref|YP_843888.1| 28 EKGNSHFNSGRYENALEAYDRA-------I-GHDPTIVDAWNNRGIALSYMGRYEDALKSYDEALRLDP 88
                                   6788899999999999999999.......3.56899******************************975 PP

  == domain 3  score: 25.7 bits;  conditional E-value: 1.5e-08
                         TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyr 56 
                                    a+nn +++l  + ry+eAl+++++alei  +++ + +++ + ++ +Lgr+ +
  gi|116754770|ref|YP_843888.1|  93 AWNNKGMALGSMRRYQEALACFDRALEID-AYFIGAWYNKSHAMAALGRARE 143
                                    899**************************.566667************9965 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.18   1.2e+02       4      24 ..       9      29 ..       8      30 .. 0.92
   2 !   15.6   0.0   1.8e-05     0.012       6      34 ..      30      56 ..      26      58 .. 0.88
   3 !   20.1   0.1   6.5e-07   0.00043       1      34 [.      59      90 ..      59      91 .. 0.94
   4 !   14.5   0.1   4.1e-05     0.027       1      29 [.      93     121 ..      93     134 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.18
                          TPR_7  4 nLarlysrlGdyeeAielyeq 24
                                   +La++ +++ d++eA + +e+
  gi|116754770|ref|YP_843888.1|  9 ALAVMLVSEADTAEARRWLEK 29
                                   79*************999987 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1.8e-05
                          TPR_7  6 arlysrlGdyeeAielyeqsLaltkdped 34
                                   ++ +++ G+ye+A+e y +  a+  dp++
  gi|116754770|ref|YP_843888.1| 30 GNSHFNSGRYENALEAYDR--AIGHDPTI 56
                                   899****************..99999876 PP

  == domain 3  score: 20.1 bits;  conditional E-value: 6.5e-07
                          TPR_7  1 aLlnLarlysrlGdyeeAielyeqsLaltkdped 34
                                   a++n + + s +G+ye+A++ y +  al+ dp++
  gi|116754770|ref|YP_843888.1| 59 AWNNRGIALSYMGRYEDALKSYDE--ALRLDPNH 90
                                   799*********************..99999997 PP

  == domain 4  score: 14.5 bits;  conditional E-value: 4.1e-05
                          TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLalt 29 
                                    a++n + +  ++++y+eA+ ++ ++L+++
  gi|116754770|ref|YP_843888.1|  93 AWNNKGMALGSMRRYQEALACFDRALEID 121
                                    78999999****************88875 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   8.4e-05     0.056      25      61 ..      19      55 ..       5      66 .. 0.76
   2 !   27.1   0.1     5e-09   3.3e-06       4      61 ..      32      89 ..      29      92 .. 0.95
   3 !   24.3   3.4   3.8e-08   2.5e-05      10      60 ..      72     122 ..      66     148 .. 0.88
   4 !   12.3   1.1   0.00022      0.15       9      54 ..     105     150 ..     103     160 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.4e-05
                          TPR_9 25 aPddpeerrdRGlllaqlGclsaAladLeaylalapd 61
                                   +  +++ +++ G  ++ +G+++ Al++ ++++ ++p 
  gi|116754770|ref|YP_843888.1| 19 DTAEARRWLEKGNSHFNSGRYENALEAYDRAIGHDPT 55
                                   444567788999999999*******999999999995 PP

  == domain 2  score: 27.1 bits;  conditional E-value: 5e-09
                          TPR_9  4 iaireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61
                                    + ++ ++e al++++r +  +P  ++ +  RG++l  +G+++ Al+  + +l+l+p+
  gi|116754770|ref|YP_843888.1| 32 SHFNSGRYENALEAYDRAIGHDPTIVDAWNNRGIALSYMGRYEDALKSYDEALRLDPN 89
                                   689999**************************************************96 PP

  == domain 3  score: 24.3 bits;  conditional E-value: 3.8e-08
                          TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap 60 
                                    ++e al+ ++  l l+P+++  +   G++l  + ++++Ala+++++l+++ 
  gi|116754770|ref|YP_843888.1|  72 RYEDALKSYDEALRLDPNHAFAWNNKGMALGSMRRYQEALACFDRALEIDA 122
                                    7899*******************************************9875 PP

  == domain 4  score: 12.3 bits;  conditional E-value: 0.00022
                          TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLea 54 
                                    +++++ala+ +r l ++   ++ ++    + a lG+ ++A+a++ +
  gi|116754770|ref|YP_843888.1| 105 RRYQEALACFDRALEIDAYFIGAWYNKSHAMAALGRAREARAAMIT 150
                                    6899*************************************99866 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.34   2.3e+02       8      27 ..      10      29 ..       9      29 .. 0.86
   2 !    9.1   0.0    0.0018       1.2       9      29 ..      30      50 ..      30      51 .. 0.94
   3 !   18.9   0.2   1.5e-06   0.00097       6      30 ..      61      85 ..      58      86 .. 0.95
   4 !   18.8   0.1   1.6e-06     0.001       6      31 ..      95     120 ..      91     121 .. 0.96
   5 ?    1.7   0.1      0.38   2.5e+02      11      28 ..     134     151 ..     130     154 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.34
                         TPR_10  8 LanalrqrgrydeAeallee 27
                                   La++l +  + +eA+++le+
  gi|116754770|ref|YP_843888.1| 10 LAVMLVSEADTAEARRWLEK 29
                                   78888888899******996 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0018
                         TPR_10  9 analrqrgrydeAealleeal 29
                                   +n +++ gry+ A++ +++a+
  gi|116754770|ref|YP_843888.1| 30 GNSHFNSGRYENALEAYDRAI 50
                                   7889***************98 PP

  == domain 3  score: 18.9 bits;  conditional E-value: 1.5e-06
                         TPR_10  6 nNLanalrqrgrydeAealleeala 30
                                   nN ++al+ +gry++A++ ++eal+
  gi|116754770|ref|YP_843888.1| 61 NNRGIALSYMGRYEDALKSYDEALR 85
                                   9**********************97 PP

  == domain 4  score: 18.8 bits;  conditional E-value: 1.6e-06
                         TPR_10   6 nNLanalrqrgrydeAealleealai 31 
                                    nN ++al +++ry+eA+a +++al+i
  gi|116754770|ref|YP_843888.1|  95 NNKGMALGSMRRYQEALACFDRALEI 120
                                    999*********************97 PP

  == domain 5  score: 1.7 bits;  conditional E-value: 0.38
                         TPR_10  11 alrqrgrydeAealleea 28 
                                    a  ++gr  eA+a ++ a
  gi|116754770|ref|YP_843888.1| 134 AMAALGRAREARAAMITA 151
                                    557899*****9998776 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.67   4.4e+02      30      50 ..       9      29 ..       5      35 .. 0.82
   2 !   27.5   0.1   5.1e-09   3.4e-06       4      58 ..      36      90 ..      33      96 .. 0.95
   3 !   18.6   1.1     3e-06     0.002       4      48 ..     104     148 ..     103     157 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.67
                         TPR_19 30 lLAeallalgqldeAealLda 50
                                   +LA  l++  +++eA++ L++
  gi|116754770|ref|YP_843888.1|  9 ALAVMLVSEADTAEARRWLEK 29
                                   589999999999999999876 PP

  == domain 2  score: 27.5 bits;  conditional E-value: 5.1e-09
                         TPR_19  4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd 58
                                   +g+y++Al+++ +a+ +dp   +a+ +  +al  +g++++A +  d++++ dp++
  gi|116754770|ref|YP_843888.1| 36 SGRYENALEAYDRAIGHDPTIVDAWNNRGIALSYMGRYEDALKSYDEALRLDPNH 90
                                   69***************************************************96 PP

  == domain 3  score: 18.6 bits;  conditional E-value: 3e-06
                         TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealL 48 
                                    + +y+eAla + +al+ d+    a+++   a+ alg+  eA+a++
  gi|116754770|ref|YP_843888.1| 104 MRRYQEALACFDRALEIDAYFIGAWYNKSHAMAALGRAREARAAM 148
                                    679***************************************987 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      0.14        93       5      27 ..       8      30 ..       6      34 .. 0.85
   2 !   18.4   0.0   3.9e-06    0.0026       4      39 ..      26      61 ..      23      66 .. 0.91
   3 !   20.8   0.2   6.8e-07   0.00045       2      38 ..      58      94 ..      57     100 .. 0.91
   4 !    9.3   0.1    0.0034       2.2      14      39 ..     104     129 ..      97     132 .. 0.86
   5 ?    4.2   0.8      0.15        98       3      23 ..     127     147 ..     125     159 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.14
                         TPR_14  5 lalaeallalGdpdeAiallrra 27
                                   +ala  l    d++eA++ l++ 
  gi|116754770|ref|YP_843888.1|  8 WALAVMLVSEADTAEARRWLEKG 30
                                   5788899999**********986 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 3.9e-06
                         TPR_14  4 llalaeallalGdpdeAiallrralalaPddaeawl 39
                                   +l+ +  ++++G+++ A+++++ra+ ++P+  +aw 
  gi|116754770|ref|YP_843888.1| 26 WLEKGNSHFNSGRYENALEAYDRAIGHDPTIVDAWN 61
                                   8999999***********************999995 PP

  == domain 3  score: 20.8 bits;  conditional E-value: 6.8e-07
                         TPR_14  2 eallalaeallalGdpdeAiallrralalaPddaeaw 38
                                   +a+  ++ al   G++++A++ +++al+l+P++a aw
  gi|116754770|ref|YP_843888.1| 58 DAWNNRGIALSYMGRYEDALKSYDEALRLDPNHAFAW 94
                                   6888899**************************9999 PP

  == domain 4  score: 9.3 bits;  conditional E-value: 0.0034
                         TPR_14  14 lGdpdeAiallrralalaPddaeawl 39 
                                     ++++eA+a+++ral+ +  +  aw+
  gi|116754770|ref|YP_843888.1| 104 MRRYQEALACFDRALEIDAYFIGAWY 129
                                    5789*************999999997 PP

  == domain 5  score: 4.2 bits;  conditional E-value: 0.15
                         TPR_14   3 allalaeallalGdpdeAial 23 
                                    a++   +a++alG+ +eA+a+
  gi|116754770|ref|YP_843888.1| 127 AWYNKSHAMAALGRAREARAA 147
                                    78888999**********987 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   1.6e-07    0.0001     203     259 ..      35      90 ..      29     100 .. 0.90
   2 !   10.2   0.2   0.00037      0.24     204     260 ..     103     159 ..      98     160 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.6e-07
                                    HHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT- CS
                          NARP1 203 dklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaD 259
                                    +  g++e+Ale  d+ai h+pt+v+ + +++  l  +G  ++A +  +ea +lD + 
  gi|116754770|ref|YP_843888.1|  35 N-SGRYENALEAYDRAIGHDPTIVDAWNNRGIALSYMGRYEDALKSYDEALRLDPNH 90 
                                    4.4789***********************************************9765 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00037
                                    HHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT-H CS
                          NARP1 204 klgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaDR 260
                                     ++++++Al + d+a+e +  ++  +++K++ +   G  ++A ++m +a+ l  a R
  gi|116754770|ref|YP_843888.1| 103 SMRRYQEALACFDRALEIDAYFIGAWYNKSHAMAALGRAREARAAMITAKTLESAAR 159
                                    578999**********************************************98866 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   3.2e-06    0.0021      16      81 ..      15      82 ..       7      83 .. 0.89
   2 !   11.9   0.9   0.00029       0.2       3      78 ..      71     147 ..      70     151 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.2e-06
                                   H.HHH--HHHHHHH..HHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                         ANAPC3 16 laaetespedayll..AlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81
                                   + +e++ +e++ +l  + +++++g+y+ A+e +++a + +++   ++   + +l  +++ye+A++ +++
  gi|116754770|ref|YP_843888.1| 15 V-SEADTAEARRWLekGNSHFNSGRYENALEAYDRAiGHDPTIVDAWNNRGIALSYMGRYEDALKSYDE 82
                                   4.77888899888777************************************************98775 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00029
                                    T-HHHHHHHHHHHH.HHH--HHHHHH...HHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                         ANAPC3   3 nnyknAiflaerllaaetespedayl...lAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaa 78 
                                    ++y++A+  ++ +l   + +p++a++   ++ +l ++ +y++A+  +++a +++   +g++y + ++  +L++  eA+aa
  gi|116754770|ref|YP_843888.1|  71 GRYEDALKSYDEAL---RLDPNHAFAwnnKGMALGSMRRYQEALACFDRAlEIDAYFIGAWYNKSHAMAALGRAREARAA 147
                                    46667777777777...666666666444577777777777777777777777777777777777777777777777766 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00094      0.62       6      28 ..      29      51 ..       8      55 .. 0.88
   2 !    9.4   0.0    0.0027       1.8       7      33 .]      64      90 ..      62      90 .. 0.82
   3 ?    5.3   0.1     0.053        35       7      28 ..      98     119 ..      96     121 .. 0.88
   4 ?    2.8   0.5      0.33   2.2e+02       2      23 ..     127     148 ..     127     154 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00094
                                   HHHHHHHHHHHHHHHHHHHHHHH CS
                          TPR_6  6 lalsyrklgdtdkAlealerlik 28
                                    + s+++ g++++Alea++r i 
  gi|116754770|ref|YP_843888.1| 29 KGNSHFNSGRYENALEAYDRAIG 51
                                   588999977***********985 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0027
                                   HHHHHHHHHHHHHHHHHHHHHHH-TT- CS
                          TPR_6  7 alsyrklgdtdkAlealerlikeYPdS 33
                                   + ++  +g++++Al+ +++ ++  P++
  gi|116754770|ref|YP_843888.1| 64 GIALSYMGRYEDALKSYDEALRLDPNH 90
                                   55555567***************9995 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.053
                                    HHHHHHHHHHHHHHHHHHHHHH CS
                          TPR_6   7 alsyrklgdtdkAlealerlik 28 
                                    ++++ ++ ++++Al+ ++r ++
  gi|116754770|ref|YP_843888.1|  98 GMALGSMRRYQEALACFDRALE 119
                                    88999989**********9986 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.33
                                    HHHHHHHHHHHHHHHHHHHHHH CS
                          TPR_6   2 AlyklalsyrklgdtdkAleal 23 
                                    A y+   ++ +lg++++A++a+
  gi|116754770|ref|YP_843888.1| 127 AWYNKSHAMAALGRAREARAAM 148
                                    5677778899999*****9986 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.015       9.7      11      33 ..      33      55 ..      31      59 .. 0.90
   2 !    9.0   0.1    0.0022       1.5      10      33 ..      66      89 ..      62      93 .. 0.87
   3 ?    6.5   0.0     0.013       8.6      14      31 ..     104     121 ..      99     125 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.015
                                   HHHHT-HHHHHHHHHHHHHHTTS CS
                     Fis1_TPR_C 11 hyklgeYseArryvdalLeiEPe 33
                                   h+  g+Y++A++  d+ + ++P 
  gi|116754770|ref|YP_843888.1| 33 HFNSGRYENALEAYDRAIGHDPT 55
                                   7889**************99996 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0022
                                   HHHHHT-HHHHHHHHHHHHHHTTS CS
                     Fis1_TPR_C 10 GhyklgeYseArryvdalLeiEPe 33
                                   +   +g+Y++A++  d  L+++P+
  gi|116754770|ref|YP_843888.1| 66 ALSYMGRYEDALKSYDEALRLDPN 89
                                   55669******************8 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.013
                                    HT-HHHHHHHHHHHHHHT CS
                     Fis1_TPR_C  14 lgeYseArryvdalLeiE 31 
                                    +++Y+eA+ + d+ Lei+
  gi|116754770|ref|YP_843888.1| 104 MRRYQEALACFDRALEID 121
                                    789*************98 PP

>> DUF5113  Domain of unknown function (DUF5113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0      0.03        20       8      35 ..      23      50 ..      18      52 .. 0.83
   2 !    8.8   0.1     0.002       1.3       7      38 ..      56      87 ..      54      98 .. 0.84
   3 !    8.6   0.1    0.0022       1.5      10      53 ..      93     135 ..      88     155 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.03
                        DUF5113  8 andYanlayylnvegeyeeALeyldsal 35
                                   a ++ + ++  + +g+ye+ALe  d a+
  gi|116754770|ref|YP_843888.1| 23 ARRWLEKGNSHFNSGRYENALEAYDRAI 50
                                   66777888899999********999997 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.002
                        DUF5113  7 iandYanlayylnvegeyeeALeyldsaleyl 38
                                   i +++ n + +l + g+ye+AL+  d+al++ 
  gi|116754770|ref|YP_843888.1| 56 IVDAWNNRGIALSYMGRYEDALKSYDEALRLD 87
                                   56789999999******************875 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0022
                        DUF5113  10 dYanlayylnvegeyeeALeyldsaleylNahyekYakkkadtl 53 
                                    ++ n +++l   ++y+eAL+++d ale+   +   +++k++  +
  gi|116754770|ref|YP_843888.1|  93 AWNNKGMALGSMRRYQEALACFDRALEIDAYFIGAWYNKSH-AM 135
                                    6778888889999*************987777777777763.44 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.3   0.00043      0.29      63      83 ..      65      85 ..      17     122 .. 0.58
   2 !    7.7   1.2    0.0054       3.6      54     122 ..      90     147 ..      81     159 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00043
                                   HHHHHTT-HHHHHHHHHHHHH CS
                        DUF3856 63 ealaklgrydealesadkalr 83
                                    al  +gry++al+s d+alr
  gi|116754770|ref|YP_843888.1| 65 IALSYMGRYEDALKSYDEALR 85
                                   244455666666666666665 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0054
                                    HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHH CS
                        DUF3856  54 dalchaglsealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealka 122
                                     a+++     al  ++ry+eal + d+al+       ++      +i a +++++a++ lGr  ea  a
  gi|116754770|ref|YP_843888.1|  90 HAFAWNNKGMALGSMRRYQEALACFDRALE-------ID----AYFIGAWYNKSHAMAALGRAREARAA 147
                                    566666666677777777776666666653.......32....35777777777777777777777655 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0032       2.1      16      32 ..      35      51 ..      32      53 .. 0.92
   2 !    7.6   0.1    0.0058       3.9      18      32 ..      71      85 ..      62      86 .. 0.87
   3 ?    4.2   0.0     0.066        44      18      32 ..     105     119 ..      89     123 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0032
                            MIT 16 nagnyeeAlelYkeale 32
                                   n+g ye Ale+Y  a++
  gi|116754770|ref|YP_843888.1| 35 NSGRYENALEAYDRAIG 51
                                   789************97 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0058
                            MIT 18 gnyeeAlelYkeale 32
                                   g ye+Al+ Y eal+
  gi|116754770|ref|YP_843888.1| 71 GRYEDALKSYDEALR 85
                                   78***********97 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.066
                            MIT  18 gnyeeAlelYkeale 32 
                                      y+eAl ++  ale
  gi|116754770|ref|YP_843888.1| 105 RRYQEALACFDRALE 119
                                    345555555555554 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.1     1e-06   0.00067      71     124 ..      32      85 ..       4      87 .. 0.86
   2 ?    1.5   0.5      0.57   3.8e+02      22      79 ..     107     142 ..      89     160 .. 0.49

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1e-06
                                    HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           BTAD  71 aelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                     ++  Gr+e+al+ +++++ ++P+  +++     Al ++Gr ++AL+ Y+++ r
  gi|116754770|ref|YP_843888.1|  32 SHFNSGRYENALEAYDRAIGHDPTIVDAWNNRGIALSYMGRYEDALKSYDEALR 85 
                                    567889*******************************************99865 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.57
                                    HHHHHHHHHHHHTT--SSTTGGGTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHTT-HH CS
                           BTAD  22 peeaaelleaAlalwrGpaladleagewleaererleelrlealealaeaelrlGrae 79 
                                     +ea++++++Al+                      +++ ++ a      a ++lGra+
  gi|116754770|ref|YP_843888.1| 107 YQEALACFDRALE----------------------IDAYFIGAWYNKSHAMAALGRAR 142
                                    3334444444433......................22333333333333333333333 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 ?    1.0   0.0      0.61     4e+02      33      66 ..      23      44 ..       6      58 .. 0.52
   2 !   11.5   0.0   0.00033      0.22      19      69 ..      60     115 ..      42     117 .. 0.74
   3 !    7.3   0.0    0.0068       4.5       4      64 ..      79     144 ..      78     159 .. 0.66

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.61
                   SRP_TPR_like 33 aLkllkkgsalsedvrfEkaYvlYklkkykkalk 66
                                   a ++             Ek   ++   +y++al+
  gi|116754770|ref|YP_843888.1| 23 ARRW------------LEKGNSHFNSGRYENALE 44
                                   3333............333333333333333333 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00033
                   SRP_TPR_like  19 f..kvvaliklekyeeaLkllkkgsalsedvrf...EkaYvlYklkkykkalkilk 69 
                                    +  + +al  +++ye+aLk  +++  l+ +  f    k  +l  +++y++al  ++
  gi|116754770|ref|YP_843888.1|  60 WnnRGIALSYMGRYEDALKSYDEALRLDPNHAFawnNKGMALGSMRRYQEALACFD 115
                                    345889**************999998877766633457888888888888887765 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0068
                   SRP_TPR_like   4 eyekilrlegkelkkf..kvvaliklekyeeaLkllkkgsalse...dvrfEkaYvlYklkkykka 64 
                                    +y++ lrl+ ++   +  k +al ++ +y+eaL   + + +++       + k+ ++  l + ++a
  gi|116754770|ref|YP_843888.1|  79 SYDEALRLDPNHAFAWnnKGMALGSMRRYQEALACFDRALEIDAyfiGAWYNKSHAMAALGRAREA 144
                                    678888887655444455999************999887644431113446666666666655555 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.3    0.0042       2.8       4      25 ..       7      28 ..       5      29 .. 0.83
   2 ?    0.3   0.0       2.4   1.6e+03      10      26 .]      32      48 ..      30      48 .. 0.80
   3 ?   -0.0   0.0       3.1     2e+03       6      21 ..      62      77 ..      59      77 .. 0.74
   4 ?   -0.8   0.1       5.4   3.6e+03      16      26 .]     106     116 ..     106     116 .. 0.76
   5 !   10.9   1.0   0.00093      0.62       3      23 ..     127     147 ..     125     148 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0042
                          TPR_4  4 llaLArallalGdldeAralle 25
                                   ++aLA  l    d +eAr++le
  gi|116754770|ref|YP_843888.1|  7 AWALAVMLVSEADTAEARRWLE 28
                                   6788888888889********9 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 2.4
                          TPR_4 10 allalGdldeAraller 26
                                    ++  G+++ A+++ +r
  gi|116754770|ref|YP_843888.1| 32 SHFNSGRYENALEAYDR 48
                                   57778****99998876 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 3.1
                          TPR_4  6 aLArallalGdldeAr 21
                                   +++ al   G++++A+
  gi|116754770|ref|YP_843888.1| 62 NRGIALSYMGRYEDAL 77
                                   56666666799*9996 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 5.4
                          TPR_4  16 dldeAraller 26 
                                    ++ eA+a ++r
  gi|116754770|ref|YP_843888.1| 106 RYQEALACFDR 116
                                    67899998876 PP

  == domain 5  score: 10.9 bits;  conditional E-value: 0.00093
                          TPR_4   3 allaLArallalGdldeAral 23 
                                    a ++   a++alG++ eAra+
  gi|116754770|ref|YP_843888.1| 127 AWYNKSHAMAALGRAREARAA 147
                                    6678889************97 PP

>> FAT  FAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1    0.0025       1.6     254     299 ..      26      77 ..      12     101 .. 0.73
   2 ?    3.3   0.1     0.057        38     266     291 ..     105     130 ..      91     158 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0025
                                    CCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTCC.......CCHHHHHC CS
                            FAT 254 wqealqkldwseekieeilqsysaateidpswykawht.......walfnfev 299
                                    w+e+ ++ + ++ + e +l++y +a  +dp++ +aw++       ++++++  
  gi|116754770|ref|YP_843888.1|  26 WLEKGNS-HFNSGRYENALEAYDRAIGHDPTIVDAWNNrgialsyMGRYEDAL 77 
                                    4444444.334456999*******************98665555555555554 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.057
                                    ..-SSCCHHHHCCHHCTCCCHSTTCC CS
                            FAT 266 ekieeilqsysaateidpswykawht 291
                                    ++ +e+l+++ +a eid   + aw++
  gi|116754770|ref|YP_843888.1| 105 RRYQEALACFDRALEIDAYFIGAWYN 130
                                    3489**************99999987 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0      0.15     1e+02       9      25 ..      32      48 ..      31      53 .. 0.84
   2 ?    3.6   0.0      0.14        95       9      26 ..      66      83 ..      59      87 .. 0.80
   3 ?    4.9   0.1     0.053        35       9      26 ..     100     117 ..      98     121 .. 0.87
   4 ?   -2.1   0.1       9.2   6.1e+03      10      20 ..     135     145 ..     133     148 .. 0.59

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.15
                            PPR  9 gycknGkleeAlelfke 25
                                   ++  +G++e Ale +++
  gi|116754770|ref|YP_843888.1| 32 SHFNSGRYENALEAYDR 48
                                   67789********9987 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.14
                            PPR  9 gycknGkleeAlelfkeM 26
                                   +++  G++e+Al+ ++e 
  gi|116754770|ref|YP_843888.1| 66 ALSYMGRYEDALKSYDEA 83
                                   67779*******999885 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.053
                            PPR   9 gycknGkleeAlelfkeM 26 
                                    ++++ ++++eAl +f++ 
  gi|116754770|ref|YP_843888.1| 100 ALGSMRRYQEALACFDRA 117
                                    78999**********985 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 9.2
                            PPR  10 ycknGkleeAl 20 
                                     +  G+ +eA 
  gi|116754770|ref|YP_843888.1| 135 MAALGRAREAR 145
                                    45566666664 PP

>> RPN7  26S proteasome subunit RPN7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.4   0.00094      0.62      36      65 ..      23      52 ..      15     139 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00094
                                   HHHHHHHHHHHHHCT-HHHHHHHHHTCCCC CS
                           RPN7 36 rrakldlaehYlkigdleeAlkaysrirey 65
                                   +r +l++++ +++ g +e+Al+ay r++ +
  gi|116754770|ref|YP_843888.1| 23 ARRWLEKGNSHFNSGRYENALEAYDRAIGH 52
                                   566899*******************98654 PP

>> Strep_SA_rep  Streptococcal surface antigen repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1     0.086        57       2      10 ..      38      46 ..      37      48 .. 0.89
   2 ?    0.8   0.1      0.81   5.4e+02       2      10 ..      72      80 ..      71      85 .. 0.73
   3 ?    4.1   0.0     0.072        48      14      22 ..     104     112 ..     103     113 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.086
                                   XXXXHHHHH CS
                   Strep_SA_rep  2 eYeaKLakY 10
                                   +Ye +L++Y
  gi|116754770|ref|YP_843888.1| 38 RYENALEAY 46
                                   79*****99 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.81
                                   XXXXHHHHH CS
                   Strep_SA_rep  2 eYeaKLakY 10
                                   +Ye +L+ Y
  gi|116754770|ref|YP_843888.1| 72 RYEDALKSY 80
                                   688888877 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.072
                                    HHHHHHHHH CS
                   Strep_SA_rep  14 LAaVQKana 22 
                                    + ++Q+a+a
  gi|116754770|ref|YP_843888.1| 104 MRRYQEALA 112
                                    669999987 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.014       9.4      12      25 ..      34      47 ..      32      49 .. 0.91
   2 ?    1.5   0.1      0.46   3.1e+02      14      25 ..      70      81 ..      69      89 .. 0.68
   3 ?    1.2   0.1      0.56   3.7e+02      16      33 ..     106     121 ..     103     123 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.014
                                   HHTT-HHHHHHH.. CS
                          TPR_3 12 ynkkkyqeArelfs 25
                                   +n+++y+ A+e+++
  gi|116754770|ref|YP_843888.1| 34 FNSGRYENALEAYD 47
                                   79**********87 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.46
                                   TT-HHHHHHH.. CS
                          TPR_3 14 kkkyqeArelfs 25
                                   +++y++A+  ++
  gi|116754770|ref|YP_843888.1| 70 MGRYEDALKSYD 81
                                   578888877654 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.56
                                    -HHHHHHH..HHHHHHH- CS
                          TPR_3  16 kyqeArelfsYallaild 33 
                                    +yqeA+  f+   +  +d
  gi|116754770|ref|YP_843888.1| 106 RYQEALACFD--RALEID 121
                                    8****99988..666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); 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: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1079.74
//
Query:       gi|116754771|ref|YP_843889.1|  [L=329]
Description: methyltransferase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0075   15.7   0.0      0.011   15.2   0.0    1.1  1  PrmA            Ribosomal protein L11 methyltransferase (PrmA
  ------ inclusion threshold ------
       0.96    9.5   3.9       0.37   10.8   0.2    2.1  2  HypA            Hydrogenase/urease nickel incorporation, meta
        4.6    7.3   8.0         16    5.6   4.4    2.8  2  DZR             Double zinc ribbon


Domain annotation for each model (and alignments):
>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.8e-06     0.011     152     208 ..     193     249 ..     192     264 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.8e-06
                           PrmA 152 lealeklvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNk 208
                                    +++le+l  +g++v+D  +G G L  + ++ gak+vv  Di   Av+    N+e+N+
  gi|116754771|ref|YP_843889.1| 193 IRILEDLRISGRSVIDGLCGPGTLGFVCVLAGAKEVVMNDIWLPAVENVLINLEVNR 249
                                    678999999*******************************************99995 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 ?   -1.3   0.3      0.35   2.1e+03      88      97 ..       2      11 ..       1      22 [. 0.79
   2 ?   10.8   0.2   6.2e-05      0.37      68     103 ..      23      68 ..      11      76 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.35
                                   S-TTTSSS-E CS
                           HypA 88 rCpkCgsadv 97
                                    Cp+Cg++ v
  gi|116754771|ref|YP_843889.1|  2 DCPSCGGRCV 11
                                   5999998765 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 6.2e-05
                                    --EEEETTTS-EEECHHHHH..........S-TTTSSS-EEEEESS CS
                           HypA  68 pvkvrCreCgkefeleekal..........rCpkCgsadveivsGe 103
                                    ++ + Cr+C++e  +++k+           rC++Cg+a +++v  e
  gi|116754771|ref|YP_843889.1|  23 NIYMACRSCKNEPYIDKKSPrrslqtgdleRCEECGKAPLDLVMIE 68 
                                    56789*****999987642245679999*********988876544 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   4.4    0.0027        16       1      37 [.       3      60 ..       2      64 .. 0.73
   2 ?    1.7   0.1     0.045   2.7e+02      28      36 ..     317     325 ..     295     328 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0027
                            DZR  1 CpqCgee...........lppdarfCseCgtklkavaa..........edrCpsCgek 37
                                   Cp+Cg             +++    C  C++++   ++           +rC +Cg++
  gi|116754771|ref|YP_843889.1|  3 CPSCGGRcvrpathilssIDNIYMACRSCKNEPYIDKKsprrslqtgdLERCEECGKA 60
                                   7888877777788887777788888888888854333367788888888999999875 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.045
                            DZR  28 edrCpsCge 36 
                                    +++C+sC+e
  gi|116754771|ref|YP_843889.1| 317 KRACSSCDE 325
                                    456666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); 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):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 2311.47
//
Query:       gi|116754772|ref|YP_843890.1|  [L=857]
Description: DNA mismatch repair protein MutS [Methanosaeta thermophila PT]
Scores for 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-84  280.3   0.4    1.3e-83  279.6   0.4    1.3  1  MutS_V    MutS domain V
    2.2e-43  147.1   0.0      1e-42  144.9   0.0    2.0  2  MutS_I    MutS domain I
      1e-40  140.0   1.1    2.4e-40  138.8   1.1    1.6  1  MutS_III  MutS domain III
    4.4e-33  113.5   0.2    1.3e-32  112.0   0.1    2.0  2  MutS_IV   MutS family domain IV
      5e-14   52.7   0.0    1.8e-12   47.7   0.0    3.0  2  MutS_II   MutS domain II
  ------ inclusion threshold ------
      0.027   14.2   0.0      0.067   12.9   0.0    1.6  1  AAA_29    P-loop containing region of AAA domain
      0.042   13.9   0.0       0.35   10.9   0.0    2.3  2  AAA_14    AAA domain
      0.056   13.0   0.0       0.12   12.0   0.0    1.5  1  AAA_27    AAA domain


Domain annotation for each model (and alignments):
>> MutS_V  MutS domain V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  279.6   0.4     6e-87   1.3e-83       1     186 [.     599     782 ..     599     784 .. 0.98

  Alignments for each domain:
  == domain 1  score: 279.6 bits;  conditional E-value: 6e-87
                                    EEEE-STTSSHHHHHHHHHHHHHHHHHT--BSSSEEEEE--SEEEEEE--------SS-HHHHHHHHHHHHHTT--TTSE CS
                         MutS_V   1 llitGpnmaGkstylrqvalivllaqiGsfvpaekaeisivdkiftRvgasDdlakgkstFmvEmlEtasilknateksl 80 
                                    +++tGpnmaGkst++rqvali+++aqiGsfvpa++a+i+++d+iftRvga Ddl++g+stFmvEm+E+a+il +at++sl
  gi|116754772|ref|YP_843890.1| 599 MILTGPNMAGKSTFMRQVALIAIMAQIGSFVPASYAKIGLIDRIFTRVGARDDLVSGRSTFMVEMSELANILVSATKDSL 678
                                    69****************************************************************************** PP

                                    EEEESTS-SS-HHHHHHHHHHHHHHHHHTT--EEEEEES-GGGGGHHHHSTTEEEEEEEEEEETTEEEEEEEEEES--SS CS
                         MutS_V  81 vilDElGRGtstydGlaialavaeyllekikaktlfatHyheltklaekleevknlhlavkeeeedivflykvkegaaek 160
                                    ++lDE+GRGtst+dGl+ia+av ey++++ikakt+fatHyh+lt+l+  l+ + n+++avkee ++i+fl++v +ga++k
  gi|116754772|ref|YP_843890.1| 679 ILLDEIGRGTSTFDGLSIAWAVSEYIHSRIKAKTIFATHYHQLTQLN--LPGIVNYSMAVKEEGRSITFLRTVVPGATNK 756
                                    *********************************************97..89***************************** PP

                                    --HHHHHHHTT--HHHHHHHHHHHHH CS
                         MutS_V 161 syGikvaklaglPesvverArevlke 186
                                    syGi+va+lag+Pe+v++rA+e l+ 
  gi|116754772|ref|YP_843890.1| 757 SYGIHVARLAGVPEHVIRRAEELLDI 782
                                    *********************98865 PP

>> MutS_I  MutS domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.9   0.0   4.6e-46     1e-42       2     111 ..       7     117 ..       6     119 .. 0.96
   2 ?   -1.2   0.0       1.1   2.4e+03      53      69 ..     759     776 ..     746     806 .. 0.67

  Alignments for each domain:
  == domain 1  score: 144.9 bits;  conditional E-value: 4.6e-46
                                    HHHHHHHCCCHH-TTCEEEEEETTEEEEECHHHHHHHHHCSSSSTT.ESSSSC..EEEEEEEHHHHHHHHHHHHHTT-EE CS
                         MutS_I   2 plmkqylelkkkykdavlffrvGdfYelfgeDAviaareleitltkrkksseke.ipmagvPehalekylrkLvekgykV 80 
                                    plm+qy  +k++ +da+l+frvGdfYe+fgeDA++ +r+l+itlt+r+k+ e + ip ag+P+h+l+ yl++Lv++g+kV
  gi|116754772|ref|YP_843890.1|   7 PLMEQYSRIKQQCPDALLLFRVGDFYETFGEDAITTSRTLNITLTSRQKDDEGNrIPLAGIPYHSLDVYLSRLVNAGHKV 86 
                                    9**********************************************96666555************************* PP

                                    EEEEE-S-HHHHS.S--EEEEEEEBTTC-TT CS
                         MutS_I  81 avveqtetpaekkgvvkrevvrviTpGtltd 111
                                    a++eq+e+p+++kg+v+re++r++TpGt+++
  gi|116754772|ref|YP_843890.1|  87 AICEQVEDPKQAKGIVRREITRIVTPGTVIE 117
                                    ****************************986 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.1
                                    SC..EEEEEEEHHHHHHH CS
                         MutS_I  53 eke.ipmagvPehaleky 69 
                                    + +  + agvPeh +++ 
  gi|116754772|ref|YP_843890.1| 759 GIHvARLAGVPEHVIRRA 776
                                    44557899*****98764 PP

>> MutS_III  MutS domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.8   1.1   1.1e-43   2.4e-40       2     190 ..     256     547 ..     255     548 .. 0.95

  Alignments for each domain:
  == domain 1  score: 138.8 bits;  conditional E-value: 1.1e-43
                                    HHHHTTSSS-TTS.SSSS-HHHHH---SSHHHHHHHHHHHH--BS-HHHHHHHHHHHHH.T..TT.HHHHHHHHTT---H CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                       MutS_III   2 TlrnLeilenlrggskegsLlgvldrTvTamGaRlLrewllqPltdleeInaRldaVee.leneelreelrellrrlpDl 80 
                                    TlrnLei++nlr+gs++g+L+++ld+TvT+mG+R L +wl  P+++le+I++R+da+ee + ++ +ree+ ell  l+Dl
  gi|116754772|ref|YP_843890.1| 256 TLRNLEIFRNLRDGSRSGTLMEILDETVTPMGSRTLARWLQMPSMSLEVIRRRQDAIEEmVRRAVIREEISELLDGLSDL 335
                                    9*********999999*******************************************999999*************** PP

                                    HHHHHHHHTT---HHHHHHHHHHHHHHHTTTTT---SSTHHHHH..........HHHHHHHHHHB-SS--SSGGGS--B- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       MutS_III  81 eRllsrislgkakardlkallealkaleelvallekeklaesee..........eslaelleeaideeplalekegedlr 150
                                    eR++ r+slg+a ++dl al+++l++++e++ ++++ +++   e          ++l  lle+a+ ++p+++ ++g+++r
  gi|116754772|ref|YP_843890.1| 336 ERIIGRVSLGNAGPKDLVALRSSLRRIPEIAHAMSALESEYLVEirkrldaselDDLVVLLERALSDDPPTSPRDGGVIR 415
                                    *************************9999999997776655555888877654444558********************* PP

                                    T............................................................................... CS
                                    x............................................................................... RF
                       MutS_III 151 a............................................................................... 151
                                    +                                                                               
  gi|116754772|ref|YP_843890.1| 416 Dgyspeldeirsalrngrswiaelesserkrtgikslkvgynnvfgyyievtkpnlsmvpddyirkqtlsnaerfvtrel 495
                                    ******************************************************************************** PP

                                    .............HHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHH CS
                                    .............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       MutS_III 152 .............iealeqelfqelleeveealerlrrlaealaeLDvllSl 190
                                                   ale+e+f +l+ +v++++   +++a+a+ eLD +l+l
  gi|116754772|ref|YP_843890.1| 496 kevesrvlsaqerSSALEYEVFLDLRGQVASRTRSVQEVAAAIGELDTILGL 547
                                    ***********9999999***********999***************99986 PP

>> MutS_IV  MutS family domain IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.0   0.1   5.8e-36   1.3e-32       1      92 []     417     508 ..     417     508 .. 0.99
   2 ?   -3.3   0.0       5.5   1.2e+04      22      35 ..     838     851 ..     835     853 .. 0.82

  Alignments for each domain:
  == domain 1  score: 112.0 bits;  conditional E-value: 5.8e-36
                                    TTSHHHHHHHHHHHHHHHHHHHHHCCCCCCCT-TTBEECCCSSSEEEEEE-TCCCTTT--SEEEEEECTCEEEEECCCHH CS
                        MutS_IV   1 gfdeeLdelrdrleelekeleeleekereklgikslkveynkvlGyylevtrseakkvpkefirlqtlknseryttaelk 80 
                                    g+++eLde+r++l++ +++++ele++er+++gikslkv+yn+v+Gyy+evt+ + ++vp+++ir+qtl n+er++t elk
  gi|116754772|ref|YP_843890.1| 417 GYSPELDEIRSALRNGRSWIAELESSERKRTGIKSLKVGYNNVFGYYIEVTKPNLSMVPDDYIRKQTLSNAERFVTRELK 496
                                    799***************************************************************************** PP

                                    HHHHHHHHHHHH CS
                        MutS_IV  81 kleaelleaeee 92 
                                    + e ++l+a+e+
  gi|116754772|ref|YP_843890.1| 497 EVESRVLSAQER 508
                                    *********986 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 5.5
                                    HHHCCCCCCCT-TT CS
                        MutS_IV  22 eleekereklgiks 35 
                                    +l+ ++r++lg+k 
  gi|116754772|ref|YP_843890.1| 838 NLLVEYRRRLGCKD 851
                                    78999******975 PP

>> MutS_II  MutS domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7   0.0     8e-16   1.8e-12       1     136 [.     127     238 ..     127     239 .. 0.88
   2 ?   -2.2   0.0       2.1   4.6e+03      62      90 ..     416     444 ..     394     454 .. 0.79

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 8e-16
                                    -EEEEEEEETTTSEEEEEEEETTTTEEEEEEEEE-HHHHHHHHHH-ESEEEEESS-SCCCHHHHHHCHCTTT-EEEEESC CS
                        MutS_II   1 nylaAisekregrrvGlafiDlstgefvvsefedfeeleaeLsrlsPkElllpedlsestaeeessklrelrsrvgvret 80 
                                    nylaA+    e+   Gl+ +Dlstg+f  se++ +e+l +eL+r+sP+E+l+p+ +s             + ++ ++ ++
  gi|116754772|ref|YP_843890.1| 127 NYLAAVLL--ENGLAGLSLLDLSTGDFIASEVP-VERLGSELARFSPAECLAPPGVSL------------EGMKFQNLDA 191
                                    89***999..8888*******************.9********************954............5789999999 PP

                                    CCCSHCCHHHHCHHHB--STTTTTTTGGG-HHHHHHHHHHHHHCCCCCSCCCCT-C CS
                        MutS_II  81 vefesekaserleedfsvedldgfglekekklalaAlgalisYleetqkekelshl 136
                                    ++f++ +ase       +  l ++  +k ++l+ +A+ a++sYl et  + ++ h+
  gi|116754772|ref|YP_843890.1| 192 ELFSLNEASES------GGILGDL--HKRSPLCARAACAILSYLRETRIQ-SVDHI 238
                                    99999999754......3344444..477799******************.99888 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.1
                                    HHHHHCHCTTT-EEEEESCCCCSHCCHHH CS
                        MutS_II  62 eeessklrelrsrvgvretvefesekase 90 
                                      +s++l e+rs +++ ++++ e+e++++
  gi|116754772|ref|YP_843890.1| 416 DGYSPELDEIRSALRNGRSWIAELESSER 444
                                    57899999999999999999999998765 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     3e-05     0.067      14      39 ..     587     613 ..     581     632 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3e-05
                         AAA_29  14 ghtieidlkg.atlltGpsGsGKSTll 39 
                                     +++++d+++ +++ltGp+ +GKST++
  gi|116754772|ref|YP_843890.1| 587 PNDLTMDESSwFMILTGPNMAGKSTFM 613
                                    567888988999*************98 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.63   1.4e+03      63      74 ..     245     256 ..     221     276 .. 0.75
   2 ?   10.9   0.0   0.00015      0.35       5      76 ..     599     687 ..     596     705 .. 0.66

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.63
                         AAA_14  63 ekktylflDEiq 74 
                                    +  +y++lDEi 
  gi|116754772|ref|YP_843890.1| 245 SSSEYMLLDEIT 256
                                    46789*****97 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00015
                         AAA_14   5 lvitGaRrvGKTtllkqlikell......vkkesilyinldderdkkladpe.......kllelileklke.....ekkt 66 
                                    +++tG+  +GK+t+++q++   +        + s+  i l d  +++    +       +++ ++ e+  +      k++
  gi|116754772|ref|YP_843890.1| 599 MILTGPNMAGKSTFMRQVALIAImaqigsFVPASYAKIGLIDRIFTRVGARDdlvsgrsTFMVEMSEL-ANilvsaTKDS 677
                                    79****************85555877788667788888887776644332222233333333333332.11344457899 PP

                         AAA_14  67 ylflDEiqev 76 
                                    +++lDEi + 
  gi|116754772|ref|YP_843890.1| 678 LILLDEIGRG 687
                                    99***99765 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   5.2e-05      0.12      12      46 ..     583     616 ..     577     621 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.2e-05
                         AAA_27  12 GkftdrsldfsaeeadlhliyGpNEAGKstalrAi 46 
                                    G f  + l+++ e++ + ++ GpN AGKst +r +
  gi|116754772|ref|YP_843890.1| 583 GGFVPNDLTMD-ESSWFMILTGPNMAGKSTFMRQV 616
                                    66777888888.7999***************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (857 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.71u 0.29s 00:00:01.00 Elapsed: 00:00:00.44
# Mc/sec: 5840.65
//
Query:       gi|116754773|ref|YP_843891.1|  [L=557]
Description: DNA mismatch repair protein MutL [Methanosaeta thermophila PT]
Scores for complete 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  118.0   0.0    4.8e-34  117.2   0.0    1.4  1  MutL_C          MutL C terminal dimerisation domain
    1.9e-33  114.7   0.0      3e-33  114.0   0.0    1.3  1  DNA_mis_repair  DNA mismatch repair protein, C-terminal domai
    2.1e-09   37.3   0.0    3.6e-09   36.6   0.0    1.4  1  HATPase_c_3     Histidine kinase-, DNA gyrase B-, and HSP90-l
    5.3e-06   26.9   0.0    1.6e-05   25.4   0.0    1.9  1  HATPase_c       Histidine kinase-, DNA gyrase B-, and HSP90-l


Domain annotation for each model (and alignments):
>> MutL_C  MutL C terminal dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.2   0.0   1.1e-37   4.8e-34       3     147 .]     372     514 ..     370     514 .. 0.95

  Alignments for each domain:
  == domain 1  score: 117.2 bits;  conditional E-value: 1.1e-37
                                    -EEEEEETTTEEEEEETTEEEEEEHHHHHHHHHHHHHHHHCCHSSB-EEEEEEEEEEE--HHHHHHHHHCHHHHHHCT-E CS
                         MutL_C   3 GkalgqvhgtyilaenedglvlvDqhaAherilyeklkeqlkeeelksQpLliPlvlelspeeaalleehkeeLaklGfe 82 
                                     +++gq  + yi++e++dg++lvDqhaA eri ye+l e+ k+++  sQ+L++P+++elsp e+all++ + eL ++Gfe
  gi|116754773|ref|YP_843891.1| 372 IRIVGQALDLYIIVEDDDGIMLVDQHAAAERIRYEHLLEKCKSGS-ISQELIQPVTVELSPGEVALLDSFSGELGEIGFE 450
                                    5789**************************************986.********************************** PP

                                    EEE-STTEEEEEEEECCCTTTSHHHHHHHHHHHHCCCSS-H-HCCHHHHHHHHCTTSSSSSS--- CS
                         MutL_C  83 leefgpnslivravPallrqqnleelirelleelaekgkesleekleellatmachssvkagrrl 147
                                    + +fg++++ vr+vPa  + +  +e ir++l e+ + g+   ++ ++e+l+ +ac++s+k g+rl
  gi|116754773|ref|YP_843891.1| 451 IDPFGGRAYSVRSVPAAAGLES-PESIRDVLREILNLGRVCRASFRDEALKHLACRGSIKSGERL 514
                                    *****************99886.999************855789*****************9886 PP

>> DNA_mis_repair  DNA mismatch repair protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.0   0.0   6.6e-37     3e-33       3     118 ..     212     327 ..     210     328 .. 0.96

  Alignments for each domain:
  == domain 1  score: 114.0 bits;  conditional E-value: 6.6e-37
                                    HHHHHHHHCCEEEEEEEETTEEEEEEEE-CCG-BTTGGEEEEEETTEEE--HHHHHHHHHHHHCCSSSSSB-EEEEEEEE CS
                 DNA_mis_repair   3 avlgkevaenlleiekeeeqlkieGfiskpelsrskrdkqflfvNgRlvkskelkkaireaYkellpkgrypvvvLnlei 82 
                                    + +g ++a+ +++i +e +++ ++G+is+++ s++ ++ ++++vN+R+v sk + +a+reaY+ +l++gr p++v+++ei
  gi|116754773|ref|YP_843891.1| 212 RAFGLRTAKGMISIIAEGDGFDLHGMISSHDSSHHGSELILVYVNSRPVYSKVVVQALREAYRGFLQSGRSPLAVISIEI 291
                                    578999************************************************************************** PP

                                    SSGGEE-TSSTT----EETTHHCHHHHHHHHHHHHH CS
                 DNA_mis_repair  83 dpeevDvNvhPtKreVrfqdeeevieaieealkeal 118
                                    +p+ vDvNvhP+KreVrf +e+ev++a+++a  +al
  gi|116754773|ref|YP_843891.1| 292 EPSLVDVNVHPAKREVRFLREDEVYDAVRDAALSAL 327
                                    *****************************9977766 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 !   36.6   0.0     8e-13   3.6e-09       4      98 ..      25     120 ..      21     137 .. 0.84

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 8e-13
                    HATPase_c_3   4 ekAlaelvdNsldAdaenvkievnknrgktgeivieDdGkGmseeelknalrlatsskeakr....kstslGkkGiGlkl 79 
                                     +++ el++Ns+dA a ++ iev++     + i+  DdG G+++e+l  a++ + +sk ++       ++lG +G    +
  gi|116754773|ref|YP_843891.1|  25 ASVVKELIENSIDAGASRIIIEVENG--GISLIKLVDDGCGIEREDLPLAFQRHATSKISTAddlfRLKTLGFRGEA-LS 101
                                    689**********************5..689********************8777777755433444677*****99.89 PP

                    HATPase_c_3  80 Aslslgkkltvitkkeges 98 
                                    A+ s++k ++v t+++ + 
  gi|116754773|ref|YP_843891.1| 102 AIASVSKCVEVHTRTRYSP 120
                                    ************9987655 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 !   25.4   0.0   3.6e-09   1.6e-05       5      64 ..      23      83 ..      19     147 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 3.6e-09
                                   HHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCH....H CS
                      HATPase_c  5 rLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsq....d 64
                                   r   ++++l++N++++   a++i +e++ + +   i+  D+G+Gi +edl++ f+++ +     
  gi|116754773|ref|YP_843891.1| 23 RPASVVKELIENSIDA--GASRIIIEVE-NGGISLIKLVDDGCGIEREDLPLAFQRHATskisT 83
                                   56689**********6..7899999999.43566779**************9999777743331 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (557 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 4065.14
//
Query:       gi|116754774|ref|YP_843892.1|  [L=184]
Description: phage SPO1 DNA polymerase-related protein [Methanosaeta thermophila PT]
Scores for complete 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-43  148.2   0.0    2.2e-43  147.9   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 !  147.9   0.0   1.2e-47   2.2e-43       1     142 [.      30     164 ..      30     176 .. 0.95

  Alignments for each domain:
  == domain 1  score: 147.9 bits;  conditional E-value: 1.2e-47
                                    HHC-CTT-SEEEEESSTCHHHHHHSSSS.-STT--HHHHHHHCCCCCCCHHGCTEEEEESSS....SECGCTTCCCCTCC CS
                            UDG   1 pgegppdakvvivGeaPgaeedatglpFsgragnllrkllneaglkrdleseqgvyitnvvkcrppgnrdtptsaeikac 80 
                                    pgegp+da+++ +GeaPga ed  g+pF+grag +l+++ln agl+r     ++++itn+vkcrppgnr +p+++ei+ac
  gi|116754774|ref|YP_843892.1|  30 PGEGPEDARIMMIGEAPGAAEDLAGRPFVGRAGAILNRALNLAGLDR-----DEIFITNIVKCRPPGNR-QPSADEIRAC 103
                                    79*********************************************.....*****************.********** PP

                                    HHHHHHHHHHHHSSEEEEESHHHHHH..HH.HHSCESCCCSCT.SEEEEES-SSTTTTTTTTS CS
                            UDG  81 aplleeeiellkprlivllGktaakallge.klgklrgklleakirvlplphPsplnrnffks 142
                                     p+l+++ie ++p +i+llG+ +a+a+lg   ++ lrg+++++   +l ++hP++++rn +++
  gi|116754774|ref|YP_843892.1| 104 MPYLRKQIEMVRPSAICLLGNVPARAILGVqGVTALRGRVFDD--LYLITFHPAAVLRNMGRM 164
                                    **************************9966699**********..9*************4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1328.24
//
Query:       gi|116754775|ref|YP_843893.1|  [L=274]
Description: phosphate binding protein [Methanosaeta thermophila PT]
Scores for complete 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   3.5    5.1e-43  147.8   3.5    1.5  1  PBP_like_2  PBP superfamily domain
    4.2e-24   84.7   0.1    5.9e-24   84.3   0.1    1.2  1  PBP_like    PBP superfamily domain
    6.6e-05   22.8   0.0    0.00019   21.2   0.0    1.7  1  SBP_bac_11  Bacterial extracellular solute-binding protein


Domain annotation for each model (and alignments):
>> PBP_like_2  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.8   3.5   8.5e-47   5.1e-43       9     281 ..      22     260 ..      15     261 .. 0.91

  Alignments for each domain:
  == domain 1  score: 147.8 bits;  conditional E-value: 8.5e-47
                     PBP_like_2   9 vgeifgaGsttpapalrkladafekaapgakvnyastGSgagikalrngdvdfagsdrplteseiaagwaangaggliqv 88 
                                    ++ ++++Gstt+ p+    a+ f+++++ ++v+++++G+g gi++l +g  d+a+++r +te+e  ++++++  +++ ++
  gi|116754775|ref|YP_843893.1|  22 ATDVRVSGSTTVMPLASVCAESFNSEQSEYRVTVTGGGTGVGIADLGEGRSDIAMASREITETER-SKYETAD-RKFNEI 99 
                                    3449***********************************************************99.8899999.9***** PP

                     PBP_like_2  89 pvaigaialvvnkd...npln.lsreaLakIfsgkItnWndvlglpadgpIkvvhrsdgsgttflfstalaeqgpwtasg 164
                                     va+++i+++v+++    +++ l++e+++kI++g+I+nW++ +g+p d +I  ++r  gsgt+++f + ++  + +++ g
  gi|116754775|ref|YP_843893.1| 100 LVAYDGIVVAVSPQiydAGVReLTKEQVRKIYAGEISNWKE-VGGP-DRQIYAIARRAGSGTRDTFNEIIMGSKEAETPG 177
                                    ************9998888889*******************.6666.**************************9999988 PP

                     PBP_like_2 165 igasg..segvasavsn.ngaigyvsvaywlavkgysladvtngagkfvlptaataasalkvakiasnplawslqpveen 241
                                    ++++   +++v++a+++ + aigy+ ++y+       +++                  al             + p++en
  gi|116754775|ref|YP_843893.1| 178 VATEAadNSEVKTAIKGsDKAIGYLGYSYAT----DGTVK----------------GVALDG-----------VYPTMEN 226
                                    8866677********888**********888....22333................345555...........9****** PP

                     PBP_like_2 242 iadgayPlsrftyiivyqpyayhgnnaalakaFldyllsd 281
                                    i++g+yPl r +y+++  ++      +++a+aF+d++ls 
  gi|116754775|ref|YP_843893.1| 227 IKSGEYPLARKLYFYTLGEP------SPGAQAFIDFVLSS 260
                                    ******************99......************96 PP

>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.3   0.1   9.9e-28   5.9e-24       1     191 [.      41     256 ..      41     258 .. 0.71

  Alignments for each domain:
  == domain 1  score: 84.3 bits;  conditional E-value: 9.9e-28
                                    HHHHHHH-TTCEEEEEES-HHHHHHHHHTTS-SEEEESS---CCCHHCCCCC.......EEEEEEEEEEE........E- CS
                       PBP_like   1 aeelaeknpgvrvavanvGsggGlkalrageadiagshlldketeeynapal.......rkaldgievvl........vn 65 
                                    ae ++ +++++rv+v++ G+g G++ l +g+ dia++++ ++ete+ + +++         a+dgi v++        v+
  gi|116754775|ref|YP_843893.1|  41 AESFNSEQSEYRVTVTGGGTGVGIADLGEGRSDIAMASREITETERSKYETAdrkfneiLVAYDGIVVAVspqiydagVR 120
                                    689999****************************************7777662222211444444443334444444444 PP

                                    CC-HCHCCCCHCCHHHS--BGGGC..-S-B-EEEEE-TTSHHHHHHHHHHC-CEECTE-SSTTSEEESSHHHHHCCHCCE CS
                       PBP_like  66 larreqglvvakgnpkkitnwkdl..adaplrlvnRetGSGtrdlfdellkkegiskssikgyaqearshlavaaaVaag 143
                                     +++eq   +++g   +i+nwk++  +d+++  + R +GSGtrd f+e + +   ++++ +g+a+ea ++++v++a++  
  gi|116754775|ref|YP_843893.1| 121 ELTKEQVRKIYAG---EISNWKEVggPDRQIYAIARRAGSGTRDTFNEIIMG--SKEAETPGVATEAADNSEVKTAIKGS 195
                                    4444444444444...6*********************************55..69999********************* PP

                                    TTCCE................C.CCGG-HCCCCCCECTTCE-EEEEEEEECTCCCSHHHHHHHHH CS
                       PBP_like 144 radvg................v.gieavaeelkgldfvplaeerydlvvrkealddpevqaflef 191
                                    + ++g                + g+ ++ e++k+++  pla+ ++ +++  e   +p  qaf++f
  gi|116754775|ref|YP_843893.1| 196 DKAIGylgysyatdgtvkgvaLdGVYPTMENIKSGE-YPLAR-KLYFYTLGE--PSPGAQAFIDF 256
                                    *****6555555555555544224444444442222.36666.444444444..36777777776 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 !   21.2   0.0   3.2e-08   0.00019       2     229 ..      26     271 ..      25     272 .. 0.63

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 3.2e-08
                                    EEEE-SSTHHHHHHHHHHH.HHHH---EEEEESSHHHHHHHHHHH..-SEEEESSH.HHHHHHHHGGGGG.GG-EEEEEE CS
                     SBP_bac_11   2 tvaaagslaaalrelaaaF.eahtgvkvevsaggsgklarqiadgarpDvwipassawlellaaaglvqa.esavplass 79 
                                    +v  ++++ +  + +a+ F +++++ +v+v++gg g  ++ + +g r D+  +  +   ++  + + ++   ++  +a+ 
  gi|116754775|ref|YP_843893.1|  26 RVSGSTTVMPLASVCAESFnSEQSEYRVTVTGGGTGVGIADLGEG-RSDIAMASREITETERSKYETADRkFNEILVAYD 104
                                    566788888888899****888999********************.8898877776444444334555556778888999 PP

                                    EEEEEESTT-TT---SHHHHHHSS-.-EE...EE--T-TTTTH...H.HHHHGGG--..........HHHHHHHHHTEEE CS
                     SBP_bac_11  80 plviavpkgnpkkikgwadLlkpgl.kla...vadPttspsGl...aalalleaaga..........qellkalekkvvk 142
                                     +v+av +     + g+ +L+k+++ k+    +++ +   +G    +++a++++ag            ++ +a   +v++
  gi|116754775|ref|YP_843893.1| 105 GIVVAVSPQI--YDAGVRELTKEQVrKIYageISNWKE--VGGpdrQIYAIARRAGSgtrdtfneiiMGSKEAETPGVAT 180
                                    9*******99..45566666666663333112333322..2222346666666665555322211111133334444444 PP

                                    EESSHHHHHHHHHTTT-SEEEEEHHHHH..H.STTSSEEEE--TTT--...EEEEEEEE....-TT--HHHHHHHHHTTS CS
                     SBP_bac_11 143 lgessrqlltaveageadagivyeseakaae.ngdkleavylpeglnldpldypaavlk....kaakreaAraFlafLrs 217
                                    ++ + + + ta++  + ++g    s a   + +g  l+ vy+  +   +  +yp+a        +  +  A+aF++f++s
  gi|116754775|ref|YP_843893.1| 181 EAADNSEVKTAIKGSDKAIGYLGYSYATDGTvKGVALDGVYPTMENI-KSGEYPLARKLyfytLGEPSPGAQAFIDFVLS 259
                                    44455666666665555555444455432222566777787755543.456777766544433334557*********** PP

                                    HHHHHHHHHTT- CS
                     SBP_bac_11 218 peaqailrkyGf 229
                                    +++q +++ +G+
  gi|116754775|ref|YP_843893.1| 260 SQGQSLAENAGY 271
                                    ***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1844.21
//
Query:       gi|116754776|ref|YP_843894.1|  [L=148]
Description: hypothetical protein Mthe_1481 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.091   12.7   0.1       0.15   12.0   0.1    1.4  1  BclA_C    BclA C-terminal domain


Domain annotation for each model (and alignments):
>> BclA_C  BclA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   8.2e-06      0.15      22      59 ..      70     107 ..      61     137 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.2e-06
                         BclA_C  22 lpnnqnlsgitvnatnttftvneaGrYyisYqvnttaa 59 
                                    + + qn++++++++++ t++v++aG+Y+  Y+++ ++ 
  gi|116754776|ref|YP_843894.1|  70 FSSYQNVKTVKAKPSTATLVVENAGTYLDGYYLYDAKP 107
                                    7889999********************99999887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1075.52
//
Query:       gi|116754777|ref|YP_843895.1|  [L=546]
Description: hypothetical protein Mthe_1482 [Methanosaeta thermophila PT]
Scores for complete 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-22   79.2   0.1    8.1e-22   78.4   0.1    1.4  1  DUF87          Helicase HerA, central domain
     0.0028   16.3   0.3      0.012   14.2   0.1    2.1  2  DUF853         Bacterial protein of unknown function (DUF853)
     0.0028   16.6   0.3       0.25   10.2   0.0    2.3  2  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
  ------ inclusion threshold ------
      0.061   12.7   0.7          3    7.1   0.1    2.2  2  FtsK_SpoIIIE   FtsK/SpoIIIE family


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 !   78.4   0.1   1.8e-25   8.1e-22       1     227 []     169     400 ..     169     400 .. 0.71

  Alignments for each domain:
  == domain 1  score: 78.4 bits;  conditional E-value: 1.8e-25
                          DUF87   1 ieiGrll...sgsevpvyldlnklvtrHlAilgsTGsGKSntvavLleelle.....kkgatililDpHGEYgkal.... 68 
                                    ie+G l     +++v+v l+ + +  +H++i+++TG+GKSn+++v  ++ ++     +    +li+DpHGEY +      
  gi|116754777|ref|YP_843895.1| 169 IEVGVLRngsRDTDVTVALHSSAM-DHHMGIFATTGMGKSNFMKVFAASCMKlasenRSEFGLLIVDPHGEYLRGGkagk 247
                                    578877743344559999999666.**************************9999555555***************4444 PP

                          DUF87  69 ....ekllsekvkvitpspsa....kdkelkinpwsldpeelldlleeddkpaaavqrsvleealdqakakeekeklssd 140
                                           +++ +k ++++p      +  el+i  +++ pe++  l +      + +q ++l+++ +          +++d
  gi|116754777|ref|YP_843895.1| 248 gllhLTPYASSLKCYSTDPRNhslpEVSELTISRRDILPEDIKVLHDW-----TGAQMDALDSIER---------IFDGD 313
                                    444444444444444444444666666666666666666666666666.....4444444444444.........34444 PP

                          DUF87 141 epveklleelkkeke.elrklknqaiarlldkledllrkggsfsnsstdliallleklekegkitiidlsgvdelaqqlv 219
                                    + + ++l+e  k ++ e+ k ++++   l +kle++l++++ +++s ++ i  +  +  k+gk++ id+  ++e+    +
  gi|116754777|ref|YP_843895.1| 314 SWIDEILDENGKAMLtERAKVSEKTVDVLVRKLENILSRNKYIKSSGNSSIPGI-IEGVKSGKVVLIDIPNLSESSELFL 392
                                    44444444444344349**************************44444444444.5778********************* PP

                          DUF87 220 vsvilrri 227
                                     s+i+rri
  gi|116754777|ref|YP_843895.1| 393 LSLISRRI 400
                                    ******97 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 ?   -2.5   0.0      0.32   1.4e+03       8      44 ..     180     216 ..     175     220 .. 0.80
   2 !   14.2   0.1   2.7e-06     0.012     259     365 ..     414     512 ..     311     521 .. 0.62

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.32
                         DUF853   8 eaeqelalalklanrhGliaGatGtGktvtLqvlaes 44 
                                    +++  +al+ + ++ h  i   tG Gk   ++v+a s
  gi|116754777|ref|YP_843895.1| 180 DTDVTVALHSSAMDHHMGIFATTGMGKSNFMKVFAAS 216
                                    5566677888888999889999******999999875 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 2.7e-06
                         DUF853 259 lvfffdeahLLfndapkallekveqvvrLirskGvGvyfvtqnPldlPdtvLaqLGnrvqhalraftpkdqkavkaaadt 338
                                     ++  +ea  ++   + + + + e + r  r  GvG+  +tq+P  +  + L+q+ + v  +l     + +  v++  ++
  gi|116754777|ref|YP_843895.1| 414 CMIVIEEAQRVLG--SDSRIARFEEIAREGRKFGVGLCAITQQPKLIDRELLSQFNTVVVMGLA----DRNDRVRVEESA 487
                                    4444566655543..34457899**********************************9999984....333445554444 PP

                         DUF853 339 franpefdveeaiteLgvGealvsvLd 365
                                     +   ++dv   i+ L+ Gea++s+L+
  gi|116754777|ref|YP_843895.1| 488 KQDLSSLDV--EIQTLEKGEAIISTLN 512
                                    444555555..59************97 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 !   10.2   0.0   5.6e-05      0.25       6      56 ..     184     240 ..     181     247 .. 0.76
   2 !    4.3   0.0    0.0034        15     164     281 ..     335     454 ..     304     500 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 5.6e-05
                  TrwB_AAD_bind   6 gvplpkeretqhilivGttGsGKtqalekllrairarg......draivlDltGafv 56 
                                    +v+l+ ++ ++h+ i+ ttG+GK++ ++ + ++  + +         +++D++G+++
  gi|116754777|ref|YP_843895.1| 184 TVALHSSAMDHHMGIFATTGMGKSNFMKVFAASCMKLAsenrseFGLLIVDPHGEYL 240
                                    6889999999****************9987554433322222335678999999886 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0034
                  TrwB_AAD_bind 164 aertaasiratlatnlevlelLaekgerFSireWleeedesgwlfltskaeqrallrpllsawldlaikallslpesrer 243
                                    +e+t   +   l++ l   ++++++g+  Si   +e  ++++++ +   ++ ++ +  +l ++++  i +  + +e+ ++
  gi|116754777|ref|YP_843895.1| 335 SEKTVDVLVRKLENILSRNKYIKSSGN-SSIPGIIEGVKSGKVVLIDI-PNLSESSELFLLSLISRRIMEDYRNEEEGRK 412
                                    455555555566666666667776666.57777777776555555544.4444445555444455555555557778888 PP

                  TrwB_AAD_bind 244 rlWfflDElpaL....grleelksllaegRkfGgavvlglqs 281
                                    r+  ++ E + +     r+  +++++ egRkfG+ + +  q+
  gi|116754777|ref|YP_843895.1| 413 RCMIVIEEAQRVlgsdSRIARFEEIAREGRKFGVGLCAITQQ 454
                                    9999***96654344379***************876655555 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1   0.00067         3      20      66 ..     171     220 ..     162     238 .. 0.77
   2 ?    3.7   0.1    0.0075        34     152     219 ..     417     486 ..     393     490 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00067
                                    EEEEEET.TS-EEEEEGGGS-...SEEEE--TTSSHHHHHHHHHHHHHTT CS
                   FtsK_SpoIIIE  20 valgkei.sgnplvldlkkma..shllvaGatgsGKStalntLilSlatt 66 
                                    v + +++ ++  +++ l ++a   h+ +  +tg GKS++++++ +S +  
  gi|116754777|ref|YP_843895.1| 171 VGVLRNGsRDTDVTVALHSSAmdHHMGIFATTGMGKSNFMKVFAASCMKL 220
                                    555556657777888888888889*****************999887655 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0075
                                    T-.........................-----------B-----EEEEEEC-HHHHHHHHHHH....HHHH CS
                   FtsK_SpoIIIE 152 vlDnyddlaaene...ritsLsnqgpsygvhvlvtagrelekrpslvvivderieLrlaapkdssvlveda 219
                                    v+ + + +   +    r  +++ +g ++gv + + +++   + + l++++  ++ + la+++d +v+ve+ 
  gi|116754777|ref|YP_843895.1| 417 VIEEAQRVLGSDSriaRFEEIAREGRKFGVGLCAITQQPKLIDRELLSQFNTVVVMGLADRND-RVRVEES 486
                                    4444444444444456788999********99888888888999*******************.8888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (546 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 3840.49
//
Query:       gi|116754778|ref|YP_843896.1|  [L=375]
Description: metallophosphoesterase [Methanosaeta thermophila PT]
Scores for complete 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-14   53.3   0.5    8.6e-14   52.5   0.5    1.4  1  Metallophos    Calcineurin-like phosphoesterase
    2.9e-12   47.1   0.1    4.7e-12   46.4   0.1    1.3  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
  ------ inclusion threshold ------
      0.048   13.0   0.0        1.1    8.5   0.0    2.2  2  Metallophos_3  Metallophosphoesterase, calcineurin superfamil
      0.062   13.7   0.2       0.38   11.1   0.0    2.1  2  HAD            haloacid dehalogenase-like hydrolase


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 !   52.5   0.5   1.9e-17   8.6e-14       1     123 [.       1     162 [.       1     217 [. 0.65

  Alignments for each domain:
  == domain 1  score: 52.5 bits;  conditional E-value: 1.9e-17
                                    EEEEEEESBTB..............TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSS.....HHHHHHHHHHHHHH CS
                    Metallophos   1 lrilvigDlHl..............algggqlddllkllddllreekpdlvllaGDlvdrg.....dlekellellaalv 61 
                                    +ri++i+D+Hl                ++  ++d+ ++++++ +  kpd+v++aGD++++      +l   + + l++l 
  gi|116754778|ref|YP_843896.1|   1 MRIVHIADTHLgfqsfsrmdekgrnLMEECIYRDFGQAIERITEL-KPDAVVHAGDVFHHVrprirPLYI-FKQSLERLS 78 
                                    89********99999998888888877777788888888888666.**************9888655555.444489999 PP

                                    HHTSEEEEEC-TTS...............CHHHHHHHHHHHHHHH.....HHHHEHH.....HCEEETSEEEEEETTE.. CS
                    Metallophos  62 kypipvylllGNHe...............gfeeellnkygylgif.....sepwrsd.....aevfnnlplaslgsgs.. 114
                                    + +ipv+++ GNH+               g              +     ++ +r++     + vf ++p +   +++  
  gi|116754778|ref|YP_843896.1|  79 DAGIPVIVISGNHDapksysalspfylydG--------------MkdvyiAHRYRYErfevgDHVFHCIPFCFTQEDYle 144
                                    99************6544444333333332..............134454455544456666555555555552222222 PP

                                    .........EEEEEEESE CS
                    Metallophos 115 .........lkvlllhGg 123
                                              +vl++hG 
  gi|116754778|ref|YP_843896.1| 145 efrkikmcgSDVLVMHGL 162
                                    223334455688888887 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 !   46.4   0.1     1e-15   4.7e-12       1     135 [.       1     204 [.       1     233 [. 0.74

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 1e-15
                  Metallophos_2   1 MklaiiSDlH...................snldaleavlealkevgvdaiihaGDl.eeeep.........evleellel 51 
                                    M++++i+D+H                     ++   +++e++ e ++da++haGD+   + p         ++le+l + 
  gi|116754778|ref|YP_843896.1|   1 MRIVHIADTHlgfqsfsrmdekgrnlmeeCIYRDFGQAIERITELKPDAVVHAGDVfHHVRPrirplyifkQSLERLSDA 80 
                                    9*********9998887777755555554444445555*****************8877777777787776688888888 PP

                  Metallophos_2  52 a.pvlaVrGNnD.................eev.veedvlreaaelgtdl..............peeaelelagekvlliH 98 
                                      pv+++ GN+D                 ++v ++++   e  e+g+++              +e +++++ g +vl++H
  gi|116754778|ref|YP_843896.1|  81 GiPVIVISGNHDapksysalspfylydgmKDVyIAHRYRYERFEVGDHVfhcipfcftqedylEEFRKIKMCGSDVLVMH 160
                                    8*************************9983335666666666666666668888887655554566666667777***** PP

                  Metallophos_2  99 gdpl.....gvkdalaellkeaeegsd..vvvcGHtHvpeveke 135
                                    g        + k   ++ ++++  +sd  ++++GH H ++  ++
  gi|116754778|ref|YP_843896.1| 161 GLVEalrdqSMKPVGEHIVSDSFLKSDfsYIALGHYHDQRRIAQ 204
                                    *9669888744444444444454455558********9854444 PP

>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.024   1.1e+02      24      43 ..      38      57 ..      32      64 .. 0.88
   2 ?    8.5   0.0   0.00025       1.1      77     104 ..      69      96 ..      59     107 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.024
                                   HHHHHHHH--SEEEEES--- CS
                  Metallophos_3 24 lveviedkdpDllvlvGdlv 43
                                    +e i++ +pD++v  Gd+ 
  gi|116754778|ref|YP_843896.1| 38 AIERITELKPDAVVHAGDVF 57
                                   6789**************96 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00025
                                    HHHHHHHHHHTT-SEEEEE--TTS--HH CS
                  Metallophos_3  77 lldklfrelgeldvpafvvPGkrDaPle 104
                                    ++ + ++ l ++++p++v+ G++DaP  
  gi|116754778|ref|YP_843896.1|  69 IFKQSLERLSDAGIPVIVISGNHDAPKS 96 
                                    56678899******************75 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   8.5e-05      0.38      53     112 ..      34      92 ..       6      94 .. 0.64
   2 ?   -0.3   0.1      0.27   1.2e+03      53      88 ..     280     315 ..     251     337 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.5e-05
                            HAD  53 glaelleallaglseelaaelerfvaevirpklldp.....galellaahraaGdrvvvvSgglr 112
                                    ++ +++e++ +  ++++ +  + f   ++rp+ ++p     + le+l+   +aG++v+v+Sg+++
  gi|116754778|ref|YP_843896.1|  34 DFGQAIERITELKPDAVVHAGDVFH--HVRPR-IRPlyifkQSLERLS---DAGIPVIVISGNHD 92 
                                    6666666665555554444444444..55555.334442227777777...***********986 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.27
                            HAD  53 glaelleallagls.eelaaelerfvaevirpklldp 88 
                                    +l+++ +a++++++  +l + ++ +++ +i+p  +d+
  gi|116754778|ref|YP_843896.1| 280 DLRRVNRAAYRRMDqRRLSRLAASMFCLKIKPE-YDE 315
                                    566677777777776666666666666666666.545 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); 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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2736.55
//
Query:       gi|116754779|ref|YP_843897.1|  [L=1061]
Description: SMC domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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-23   81.1   0.0    1.3e-22   80.3   0.0    1.4  1  SMC_N          RecF/RecN/SMC N terminal domain
    7.7e-17   62.4  22.5    7.7e-17   62.4  22.5    7.1  1  AAA_23         AAA domain
    1.7e-12   47.7   4.9    2.8e-12   47.1   0.1    3.5  3  AAA_15         AAA ATPase domain
    2.1e-07   30.5   0.1    5.8e-07   29.2   0.0    1.7  2  AAA_29         P-loop containing region of AAA domain
    8.6e-06   25.9   0.0    2.2e-05   24.6   0.0    1.7  1  SbcCD_C        Putative exonuclease SbcCD, C subunit
    2.4e-05   24.0   0.0    2.4e-05   24.0   0.0    6.2  8  AAA_27         AAA domain
     0.0012   18.7   0.0     0.0012   18.7   0.0    3.4  4  AAA_21         AAA domain, putative AbiEii toxin, Type IV TA 
     0.0021   17.8   0.4     0.0021   17.8   0.4    5.7  5  Rad50_zn_hook  Rad50 zinc hook motif
     0.0027   18.2   0.0     0.0027   18.2   0.0    4.4  4  ABC_tran       ABC transporter
  ------ inclusion threshold ------
      0.027   15.8   4.5        6.7    8.3   0.8    5.4  3  Toxin_36       Conantokin-G mollusc-toxin
      0.096   12.8   0.2       0.88    9.8   0.2    2.8  1  Nbs1_C         DNA damage repair protein Nbs1
        0.3   10.8   0.0        0.3   10.8   0.0    4.0  6  MukB           MukB N-terminal
       0.65   10.5  17.9        3.1    8.3   0.1    5.7  6  T3SSipB        Type III cell invasion protein SipB
          1    9.7  44.6       0.69   10.3   1.1   10.4 12  BLOC1_2        Biogenesis of lysosome-related organelles comp
        1.7    7.9  89.0       0.25   10.7   5.4    6.8  6  GAS            Growth-arrest specific micro-tubule binding
        3.4    7.4  34.9        1.5    8.6   0.5    7.9  7  Phage_GP20     Phage minor structural protein GP20


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 !   80.3   0.0   1.2e-25   1.3e-22       2     213 ..       3    1051 ..       2    1057 .. 0.96

  Alignments for each domain:
  == domain 1  score: 80.3 bits;  conditional E-value: 1.2e-25
                                     EEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCC.CCCC--BTTCSSTTEEE CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                          SMC_N    2 lkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrsekl.sdlihkskekasvkkae 78  
                                     l+rl+++nFk y  +++++ f++++t i+G NG+GKs +++Ai + L    +++   ekl ++li++  + +  ++ e
  gi|116754779|ref|YP_843897.1|    3 LNRLVLRNFKKY--RRADITFQDGLTGIIGGNGAGKSTIVEAIAWALYG--SRAYTVEKLeKRLIKN-VNARPEESVE 75  
                                     89**********..7********************************74..4455666661579998.8999999999 PP

                                     EEEEEEETTEESSSSSSCEEEEEEEETTSE...EEEEETTEEE-H..HHHHHHHHC.TT-STT............... CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxx..xxxxxxxxx.xxxxxx............... RF
                          SMC_N   79 veitfdnedkklkiekeevsisrrvkrkge...seykingkevtk..kevselles.agiske............... 135 
                                     v++t++  +++       ++isr +k k      +  ing+ev k  +ev   l++ ++is +               
  gi|116754779|ref|YP_843897.1|   76 VHLTLSIGKNE-------IVISRIMKGKSMlpdASLCINGQEVAKgmREVDAHLSKlMKISFQdfmrtfyarqkdldn 146 
                                     99987666665.......88888777776555599********998899999887724677779************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gi|116754779|ref|YP_843897.1|  147 lireggagkrdyllkllgledireigleitkddlreierrinlasgalselgdverrieeiraqeasaraelikreia 224 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gi|116754779|ref|YP_843897.1|  225 lkdaenerkraredlerldekrqehmrlkreiehvqgyiadrertareerarlegieekkrklhaltsdlkrlneirk 302 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gi|116754779|ref|YP_843897.1|  303 hlhdleaarrdyeqlnsilkslqierrealrslneletrldelyrcrsemeglrekadlyvttqreleeleikrerft 380 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gi|116754779|ref|YP_843897.1|  381 shvssiasldaersallrdykmkadlvrelrearrslpdlerrlsvleslkreleelerakemhrrldellserdsri 458 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gi|116754779|ref|YP_843897.1|  459 erraqllnrldiihkklseigdlareerglrerevqletlietlnqkrteiesrrnlarskmhesqsnlkrieslgae 536 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gi|116754779|ref|YP_843897.1|  537 spcptcerplgdqysrltekyreeirryrddyetatnelrdlnervknaqhlrerlrasaeslgkrrsdlasleaeqr 614 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gi|116754779|ref|YP_843897.1|  615 evmlqlsemreriseldgeidaigqaeydskrheevkrslsgynelidkrarllarlenlpgleselentrekasald 692 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gi|116754779|ref|YP_843897.1|  693 erifehsrsisildyderaylrarstlselqssheryglllqqtgeierlekllealrirvqrldgdmlkvegelsel 770 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gi|116754779|ref|YP_843897.1|  771 afdpneydmlraeetrlaeiesianrlrveiaaedlsrsrlfeaetdlrrlhtqmaelstrleelgytdasyenakri 848 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gi|116754779|ref|YP_843897.1|  849 lsdaderlrcaneeyakmrdelrrlewslsglnddlkrkrelerkidelnrkaqvvsvvrdllvrfmdallvrvrnei 926 
                                     ****************************************************************************** PP

                                     ......................................CS-HHHHHHHHHHHHHH........HHCCS--SEEEECTT CS
                                     ......................................xxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxx RF
                          SMC_N  136 ......................................lLSgGektLvalaLlfA........iqkvkpaplyllDei 167 
                                                                            +SgGe  ++al++++A          + +  ++++lDe+
  gi|116754779|ref|YP_843897.1|  927 aqnaarimeevtgkysilkidenfnilvddrgtdypiwRFSGGEIDMIALSVRIAiseylmrsFGEESGYSFMILDEV 1004
                                     *******************************************************55554333334466789****** PP

                                     TTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-SCEEEEEE CS
                                     xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  168 daaLDeknvkkvaellkekskn.aQfivislreemlekadklvgvtk 213 
                                         D ++++++ ++l++   +  Q++ is+ +++  + d+++ v+ 
  gi|116754779|ref|YP_843897.1| 1005 FGSQDIEHRERMINMLRSLGVRfPQLFAISHISDVQGQFDNTIVVSE 1051
                                     ******************998868********999999999988876 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.4  22.5   6.9e-20   7.7e-17       1     198 [.       5     245 ..       5     353 .. 0.73

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 6.9e-20
                         AAA_23   1 kLkienfrsfrdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiese.gkvkayveltf 79 
                                    +L ++nf+++r+ +i F +glt I+G NGaGK+Ti++Ai +aLyg  + +      ++ek+ ++  +   + +  v+lt+
  gi|116754779|ref|YP_843897.1|   5 RLVLRNFKKYRRADITFQDGLTGIIGGNGAGKSTIVEAIAWALYGSRAYTVE----KLEKRLIKNVNArPEESVEVHLTL 80 
                                    799******************************************6554444....344444443332133333366667 PP

                         AAA_23  80 enkdgrytrsiererelskkkgkttkkaklellei..deleqfisellgskkiilnlilflgqer............... 142
                                    +  +++    i+r  + ++   +     +++++ +  +e +  +s+l++++++ + + ++  q++               
  gi|116754779|ref|YP_843897.1|  81 SIGKNE--IVISRIMKGKSMLPDASLCINGQEVAKgmREVDAHLSKLMKISFQDFMRTFYARQKDldnlireggagkrdy 158
                                    665553..34444444444444555555777777778999999999*******999999999999555555555555444 PP

                         AAA_23 143 ......feefelkdkke.............................rleelekel.....eeledekkllekleqekeke 182
                                                    e                             +l ++e+ +     +e++++++l+++++ +k+ e
  gi|116754779|ref|YP_843897.1| 159 llkllgL---------EdireigleitkddlreierrinlasgalsELGDVERRIeeiraQEASARAELIKREIALKDAE 229
                                    4333330.........0333355555555666666777777777774444444441111133444444566667777888 PP

                         AAA_23 183 keleeleeeleeilke 198
                                    +e +  +e+le ++++
  gi|116754779|ref|YP_843897.1| 230 NERKRAREDLERLDEK 245
                                    8888888888877766 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.1   2.5e-15   2.8e-12       1     235 [.       1     321 [.       1     512 [. 0.57
   2 ?   -1.4   1.2       1.3   1.5e+03     198     261 ..     577     639 ..     494     699 .. 0.58
   3 ?   -2.5   0.0       2.8   3.1e+03     235     272 ..     863     898 ..     814     961 .. 0.57

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 2.5e-15
                         AAA_15   1 MkIkkikikNFRslkdveidlseeltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeniseskdikId 80 
                                    M ++++ ++NF++++ ++i +++ lt +iG N++GKS+i+ea+ + l  ++ +   v k+ek  +++  n  ++ ++++ 
  gi|116754779|ref|YP_843897.1|   1 MHLNRLVLRNFKKYRRADITFQDGLTGIIGGNGAGKSTIVEAIAWALYGSRAYT--VEKLEKRLIKNV-NARPEESVEVH 77 
                                    999*********************************************997776..334444433333.55555555555 PP

                         AAA_15  81 vef............................................................................. 83 
                                    ++                                                                              
  gi|116754779|ref|YP_843897.1|  78 LTLsigkneivisrimkgksmlpdaslcingqevakgmrevdahlsklmkisfqdfmrtfyarqkdldnlireggagkrd 157
                                    55566777788888887777777666666666666666666666666666666666666666666666665555555444 PP

                         AAA_15  84 .........................................................aekekakeyektlkskekkkadl 106
                                                                                             +                      
  gi|116754779|ref|YP_843897.1| 158 yllkllgledireigleitkddlreierrinlasgalselgdverrieeiraqeasaR---------------------- 215
                                    4444444444444444444444444444444444444444444444444444433331...................... PP

                         AAA_15 107 llkkkesdlkktikdkklklkknelsdekisvekkkskkelpkekeeklekekeelkidkedlkklikkleeslkkeeel 186
                                                                              +++e  l+  ++e k   edl++l +k +e +  + e+
  gi|116754779|ref|YP_843897.1| 216 ---------------------------------------AELIKREIALKDAENERKRAREDLERLDEKRQEHMRLKREI 256
                                    .......................................22222222222222222222222222222222222222233 PP

                         AAA_15 187 knvlksaiiklllisakRnvsd..edsekkssllgklkekileealqekl................e 235
                                    ++v    ++  ++  ++R   +  e+++ k  +l++ +++++e  ++++l                 
  gi|116754779|ref|YP_843897.1| 257 EHVQGYIADRERTAREERARLEgiEEKKRKLHALTSDLKRLNE--IRKHLhdleaarrdyeqlnsiL 321
                                    3333333333333333333333222222222233333333333..2222233222222222222221 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.3
                         AAA_15 198 llisakRnvsd..edsekkssllgklkekileealqekleeelteklkeiqeklkeidkklaeelk 261
                                    +l++ ++n+++  e+   + ++lgk  +++ +  ++     e+  +l+e+ e ++e+d+++++  +
  gi|116754779|ref|YP_843897.1| 577 DLNERVKNAQHlrERLRASAESLGKRRSDLASLEAE---QREVMLQLSEMRERISELDGEIDAIGQ 639
                                    333333333333333333444444444444332221...345555566666666666666655444 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 2.8
                         AAA_15 235 eeelteklkeiqeklkeidkklaeelkkilkkkidkik 272
                                      +++++l +++ +l+ ++++l  + k++l+ kid+++
  gi|116754779|ref|YP_843897.1| 863 YAKMRDELRRLEWSLSGLNDDL--KRKRELERKIDELN 898
                                    3445555555555555555555..44455555555542 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 !   29.2   0.0   5.2e-10   5.8e-07       1      50 [.       3      51 ..       3      55 .. 0.92
   2 ?   -2.8   0.0         5   5.6e+03      31      42 ..      92     103 ..      78     106 .. 0.74

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 5.2e-10
                         AAA_29  1 LkrlqlvNWgtfdghtieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                   L+rl l N   +++ +i+++ +g t ++G +G+GKST++ Ai+  L++++
  gi|116754779|ref|YP_843897.1|  3 LNRLVLRNFKKYRRADITFQ-DGLTGIIGGNGAGKSTIVEAIAWALYGSR 51
                                   78999999999***999998.779***********************987 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5
                         AAA_29  31 sGsGKSTllDAi 42 
                                    +  GKS l DA 
  gi|116754779|ref|YP_843897.1|  92 IMKGKSMLPDAS 103
                                    5579***99996 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 !   24.6   0.0   1.9e-08   2.2e-05      29      89 ..     962    1021 ..     940    1022 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.9e-08
                        SbcCD_C   29 ssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89  
                                      + + SGGe   +++l +  a++ ++ ++ g+e+ +++++LDE F++ D e +++++++l+
  gi|116754779|ref|YP_843897.1|  962 PIWRFSGGEI-DMIALSVRIAISEYLMRSFGEESGYSFMILDEVFGSQDIEHRERMINMLR 1021
                                     56678*****.899999999999999987789**************************997 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   2.2e-08   2.4e-05       1      55 [.       1      52 [.       1      59 [. 0.93
   2 ?   -2.9   0.1       3.8   4.3e+03     189     199 ..     224     234 ..     189     260 .. 0.48
   3 ?   -0.2   0.2      0.55   6.1e+02     154     203 ..     279     327 ..     269     331 .. 0.63
   4 ?    2.1   0.3      0.11   1.3e+02     160     206 ..     333     378 ..     312     379 .. 0.89
   5 ?   -2.2   0.3       2.3   2.6e+03     142     189 ..     404     453 ..     387     467 .. 0.58
   6 ?   -3.7   0.5       6.6   7.4e+03     164     198 ..     494     528 ..     486     532 .. 0.47
   7 ?   -0.3   0.3       0.6   6.8e+02     128     164 ..     590     626 ..     562     664 .. 0.63
   8 ?    3.9   0.2     0.032        36     146     194 ..     809     860 ..     799     875 .. 0.71

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.2e-08
                         AAA_27  1 MrlerLdLeryGkftdrsldfsaeeadlhliyGpNEAGKstalrAisdllfGipe 55
                                   M l+rL L+ + k+    ++f+   ++l+ i+G N AGKst+++Ai   l+G  +
  gi|116754779|ref|YP_843897.1|  1 MHLNRLVLRNFKKYRRADITFQ---DGLTGIIGGNGAGKSTIVEAIAWALYGSRA 52
                                   99*******************8...8*************************9766 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.8
                         AAA_27 189 eleeakkelre 199
                                    +l++a++e ++
  gi|116754779|ref|YP_843897.1| 224 ALKDAENERKR 234
                                    22222222222 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.55
                         AAA_27 154 GlaslrevleaLeaeadelfkprkskkrainealeeleeakkelreaqvr 203
                                    G+++ ++ l+aL+++ ++l + rk+ +  + +a++++e++++ l++ q++
  gi|116754779|ref|YP_843897.1| 279 GIEEKKRKLHALTSDLKRLNEIRKHLH-DLEAARRDYEQLNSILKSLQIE 327
                                    455555666666666666666666666.6666666666666666666665 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.11
                         AAA_27 160 evleaLeaeadelfkprkskkrainealeeleeakkelreaqvraee 206
                                    + l++Le++ del++ r++ +  ++e+ + + ++++el+e ++++e+
  gi|116754779|ref|YP_843897.1| 333 RSLNELETRLDELYRCRSEME-GLREKADLYVTTQRELEELEIKRER 378
                                    67899**************99.9*****************9999875 PP

  == domain 5  score: -2.2 bits;  conditional E-value: 2.3
                         AAA_27 142 gelgqlLfeasaGlaslrevleaLeaeadelfkprkskk..rainealee 189
                                     +l + L ea+ +l +l++ l  Le+ ++el + +++k+  r++ e l+e
  gi|116754779|ref|YP_843897.1| 404 ADLVRELREARRSLPDLERRLSVLESLKRELEELERAKEmhRRLDELLSE 453
                                    56666677777777777765554444444443333333311244444443 PP

  == domain 6  score: -3.7 bits;  conditional E-value: 6.6
                         AAA_27 164 aLeaeadelfkprkskkrainealeeleeakkelr 198
                                    +Le+  ++l ++r++ + + n a+++++e +++l+
  gi|116754779|ref|YP_843897.1| 494 QLETLIETLNQKRTEIESRRNLARSKMHESQSNLK 528
                                    44444444444444444444444444444444443 PP

  == domain 7  score: -0.3 bits;  conditional E-value: 0.6
                         AAA_27 128 erLreGGealleaegelgqlLfeasaGlaslrevlea 164
                                    erLr+ +e+l + + +l++l  e +  + +l+e++e+
  gi|116754779|ref|YP_843897.1| 590 ERLRASAESLGKRRSDLASLEAEQREVMLQLSEMRER 626
                                    3444455555555555554444444444444444333 PP

  == domain 8  score: 3.9 bits;  conditional E-value: 0.032
                         AAA_27 146 qlLfeasaGlaslrevleaLeaeadelfkprkskk...rainealeeleeak 194
                                    + Lfea++ l++l++ +++L+++ +el  + +s +   r + +a e+l+ a+
  gi|116754779|ref|YP_843897.1| 809 SRLFEAETDLRRLHTQMAELSTRLEELGYTDASYEnakRILSDADERLRCAN 860
                                    56*************************8777765522234444444444444 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 !   18.7   0.0   1.1e-06    0.0012       1      23 [.      25      47 ..      25      91 .. 0.83
   2 ?   -1.9   0.4         2   2.2e+03     105     127 ..     225     247 ..     136     339 .. 0.58
   3 ?   -2.0   0.3       2.2   2.5e+03     170     215 ..     398     443 ..     366     516 .. 0.56
   4 ?   -0.3   0.1      0.66   7.4e+02     219     252 ..     913     981 ..     800    1035 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.1e-06
                         AAA_21  1 lnvliGpNgsGKSnLLdaldlla 23
                                   l+++iG Ng+GKS++ +a+ ++ 
  gi|116754779|ref|YP_843897.1| 25 LTGIIGGNGAGKSTIVEAIAWAL 47
                                   699****************9983 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2
                         AAA_21 105 leeedvfnpeargirggvsvfsl 127
                                    l++  +   +ar+  + ++++++
  gi|116754779|ref|YP_843897.1| 225 LKDAENERKRAREDLERLDEKRQ 247
                                    33333333333322222222222 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 2.2
                         AAA_21 170 nifadyfgfakekrllqrlvrslklveielsdlgegeeliasvder 215
                                    ++ ++ +   +e+r ++r ++ l ++ + l+ l+   e+ ++++e 
  gi|116754779|ref|YP_843897.1| 398 RDYKMKADLVRELREARRSLPDLERRLSVLESLKRELEELERAKEM 443
                                    4444444444444444444444444444444444444444333333 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 0.66
                         AAA_21 219 r...................................gvvflengdgqelparelSdGtkrllalltall 252
                                    r                                   ++ +l++++g + p++ +S G   ++al + ++
  gi|116754779|ref|YP_843897.1| 913 RfmdallvrvrneiaqnaarimeevtgkysilkideNFNILVDDRGTDYPIWRFSGGEIDMIALSVRIA 981
                                    033444444444666666666666777777777777999999999999999999999999988876655 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 ?   -1.0   0.0       1.5   1.6e+03      33      50 ..     392     409 ..     390     410 .. 0.85
   2 ?    1.1   1.1      0.31   3.5e+02      27      49 ..     415     438 ..     414     440 .. 0.91
   3 ?   -3.1   0.2       6.5   7.3e+03       3      19 ..     497     513 ..     495     514 .. 0.76
   4 !   17.8   0.4   1.9e-06    0.0021      10      50 ..     528     566 ..     519     567 .. 0.83
   5 ?   -0.9   0.1       1.4   1.6e+03       7      16 ..     889     898 ..     885     904 .. 0.58

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.5
                                    HHHHHHHHHHHHHHHHH. CS
                  Rad50_zn_hook  33 hrseLikelqsklerlpe 50 
                                    +rs L+++++ k + ++e
  gi|116754779|ref|YP_843897.1| 392 ERSALLRDYKMKADLVRE 409
                                    59********99998876 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.31
                                    -EE-HHH.HHHHHHHHHHHHHHHH CS
                  Rad50_zn_hook  27 Reldeeh.rseLikelqsklerlp 49 
                                    R+l++ + r ++++ l+ +le+l+
  gi|116754779|ref|YP_843897.1| 415 RSLPDLErRLSVLESLKRELEELE 438
                                    89999999*************997 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 6.5
                                    HHHHHHHHHHHHHTT-S CS
                  Rad50_zn_hook   3 qeteelnkkieelkeak 19 
                                      +e ln+k  e+++++
  gi|116754779|ref|YP_843897.1| 497 TLIETLNQKRTEIESRR 513
                                    55788999999998876 PP

  == domain 4  score: 17.8 bits;  conditional E-value: 1.9e-06
                                    HHHHHHTT-SEE-TTT--EE-HHHHHHHHHHHHHHHHHHH. CS
                  Rad50_zn_hook  10 kkieelkeakgcCPlCgReldeehrseLikelqsklerlpe 50 
                                    k+ie l  +   CP C+R+l++   s+L+++++++++r ++
  gi|116754779|ref|YP_843897.1| 528 KRIESLGAES-PCPTCERPLGDQ-YSRLTEKYREEIRRYRD 566
                                    5566666555.8********976.799**********9876 PP

  == domain 5  score: -0.9 bits;  conditional E-value: 1.4
                                    HHHHHHHHHT CS
                  Rad50_zn_hook   7 elnkkieelk 16 
                                    el++ki+el+
  gi|116754779|ref|YP_843897.1| 889 ELERKIDELN 898
                                    5555555554 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   2.4e-06    0.0027      12      33 ..      24      45 ..      16     121 .. 0.88
   2 ?    0.2   0.6      0.88   9.9e+02      21     101 ..     152     232 ..     146     329 .. 0.60
   3 ?   -2.8   2.8       7.5   8.4e+03     102     102 ..     520     520 ..     403     720 .. 0.69
   4 ?   -1.5   0.0       2.9   3.2e+03      80     120 ..     925     977 ..     847     987 .. 0.59

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.4e-06
                                   SEEEEEESTTSSHHHHHHHHTT CS
                                   xxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran 12 ekvaivGenGaGKStLlkllag 33
                                    +++i+G nGaGKSt+++++a 
  gi|116754779|ref|YP_843897.1| 24 GLTGIIGGNGAGKSTIVEAIAW 45
                                   4789**************9975 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.88
                                    TSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSB.HHHHHHHTCHHHHHHHSTTGGTTC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  21 GaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpelt.vrenesdeeiekalsklglkelkd 99 
                                    GaGK   l  l+gl++  e  +++ ++dl+e  +++ +  +g l++   + ++++ +r +e+++++e + +++ lk+ ++
  gi|116754779|ref|YP_843897.1| 152 GAGKRDYLLKLLGLEDIREIGLEITKDDLRE-IERRINLASGALSELGDVERRIEeIRAQEASARAELIKREIALKDAEN 230
                                    6666666666666666666556666666666.333344444444444444444444444444444444444444444333 PP

                                    BG CS
                                    xx RF
                       ABC_tran 100 tv 101
                                    ++
  gi|116754779|ref|YP_843897.1| 231 ER 232
                                    32 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 7.5
                                    E CS
                                    x RF
                       ABC_tran 102 v 102
                                    +
  gi|116754779|ref|YP_843897.1| 520 M 520
                                    1 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 2.9
                                    HHHTCHHHHHHHSTTGG............TTCBGESTTSGGS-HHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxx............xxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 esdeeiekalsklglke............lkdtvvksspssLSgGqkqrvala 120
                                    e  ++++++++++  k+            ++d+  ++    +SgG+  ++al 
  gi|116754779|ref|YP_843897.1| 925 EIAQNAARIMEEVTGKYsilkidenfnilVDDRGTDYPIWRFSGGEIDMIALS 977
                                    33333444444444443444455555554566666666688888888877775 PP

>> Toxin_36  Conantokin-G mollusc-toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1      0.77   8.6e+02       6      15 .]     141     150 ..     140     150 .. 0.90
   2 ?    1.9   0.0      0.73   8.2e+02       7      15 .]     401     409 ..     400     409 .. 0.95
   3 ?    8.3   0.8     0.006       6.7       3      14 ..     861     871 ..     860     872 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.77
                       Toxin_36   6 qkMaeeLiRE 15 
                                    qk + +LiRE
  gi|116754779|ref|YP_843897.1| 141 QKDLDNLIRE 150
                                    78899****9 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.73
                       Toxin_36   7 kMaeeLiRE 15 
                                    kM ++L+RE
  gi|116754779|ref|YP_843897.1| 401 KMKADLVRE 409
                                    9*******9 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.006
                       Toxin_36   3 EElqkMaeeLiR 14 
                                    EE++kM  eL R
  gi|116754779|ref|YP_843897.1| 861 EEYAKMRDEL-R 871
                                    9*********.5 PP

>> Nbs1_C  DNA damage repair protein Nbs1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.2   0.00078      0.88       1      24 [.       9      32 ..       9      33 .. 0.96

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00078
                         Nbs1_C  1 kNFKkFrKvaypGaeglPriIGGs 24
                                   +NFKk+r+  ++ ++gl  iIGG+
  gi|116754779|ref|YP_843897.1|  9 RNFKKYRRADITFQDGLTGIIGGN 32
                                   7**********************7 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00027       0.3       7      50 ..       4      47 ..       1      53 [. 0.82
   2 ?   -2.2   0.0       2.6   2.9e+03     119     162 ..     274     310 ..     253     326 .. 0.54
   3 ?   -0.6   0.1      0.85   9.5e+02     129     159 ..     315     345 ..     285     354 .. 0.77
   4 ?   -2.9   0.2       4.4     5e+03     149     193 ..     447     491 ..     417     521 .. 0.54
   5 ?   -1.3   0.1       1.4   1.5e+03     139     161 ..     610     632 ..     569     643 .. 0.77
   6 ?   -3.2   0.0       5.4   6.1e+03     121     161 ..     718     758 ..     686     763 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00027
                                   EEEEEEEETTEEEEEE-HHHHHHHHHS--SHHHHHHHHHHHHHH CS
                           MukB  7 ksltlinWnGffartfdldelvttlsGgnGaGksttmaafvtal 50
                                   + l+l n++ +      + + +t + GgnGaGkst++ a+  al
  gi|116754779|ref|YP_843897.1|  4 NRLVLRNFKKYRRADITFQDGLTGIIGGNGAGKSTIVEAIAWAL 47
                                   5677777777777777778889**************99998877 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.6
                                    EEEEES--TT--HHHHHEE--SSS--EE--HHHHHHHHHTSTT- CS
                           MukB 119 pfalqgleedvkltdvlleklddkkarvrelnelkekleelegv 162
                                       l+g+ee+++  + l++ l+       +lne++++l++le++
  gi|116754779|ref|YP_843897.1| 274 RARLEGIEEKKRKLHALTSDLK-------RLNEIRKHLHDLEAA 310
                                    4445555555555555544443.......344555554444443 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.85
                                    --HHHHHEE--SSS--EE--HHHHHHHHHTS CS
                           MukB 129 vkltdvlleklddkkarvrelnelkekleel 159
                                     +l+++l + + ++++ +r+lnel  +l+el
  gi|116754779|ref|YP_843897.1| 315 EQLNSILKSLQIERREALRSLNELETRLDEL 345
                                    4566777777888899999999999998886 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 4.4
                                    HHHHHHHHHTSTT-EEEE-S-HHHHHHHHHHTTSBSS---SHHHH CS
                           MukB 149 lnelkekleelegvrlkkfnsvtdyhallfdlGvipkrlrssedr 193
                                    l el ++ ++  + r +  n +   h+ l ++G +++  r  ++r
  gi|116754779|ref|YP_843897.1| 447 LDELLSERDSRIERRAQLLNRLDIIHKKLSEIGDLAREERGLRER 491
                                    444333333323333344444444444444444444444444444 PP

  == domain 5  score: -1.3 bits;  conditional E-value: 1.4
                                    -SSS--EE--HHHHHHHHHTSTT CS
                           MukB 139 lddkkarvrelnelkekleeleg 161
                                      ++++++++l+e++e+++el+g
  gi|116754779|ref|YP_843897.1| 610 EAEQREVMLQLSEMRERISELDG 632
                                    34557888899999999988876 PP

  == domain 6  score: -3.2 bits;  conditional E-value: 5.4
                                    EEES--TT--HHHHHEE--SSS--EE--HHHHHHHHHTSTT CS
                           MukB 121 alqgleedvkltdvlleklddkkarvrelnelkekleeleg 161
                                    +l++l+++ +   +ll++ ++ +   + l+ l+ ++++l+g
  gi|116754779|ref|YP_843897.1| 718 TLSELQSSHERYGLLLQQTGEIERLEKLLEALRIRVQRLDG 758
                                    57788888888899999988854444455668888888776 PP

>> T3SSipB  Type III cell invasion protein SipB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.8      0.54     6e+02      22      68 ..     199     245 ..     189     287 .. 0.69
   2 ?    8.3   0.1    0.0027       3.1      41     100 ..     287     345 ..     277     370 .. 0.60
   3 ?    1.3   0.1      0.39   4.4e+02      47     121 ..     429     506 ..     403     536 .. 0.66
   4 ?    5.0   0.6     0.027        31      53     141 ..     559     648 ..     546     694 .. 0.76
   5 ?   -2.8   0.0         7   7.9e+03      86     111 ..     763     788 ..     736     807 .. 0.75
   6 ?    2.5   0.0      0.16   1.8e+02      55     116 ..     842     903 ..     807     941 .. 0.59

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.54
                                    HHHHHHHHHHHHHHHTTTTT----STHHHHHHHHHHHHHHHHHHHHH CS
                        T3SSipB  22 qLenrlaawkamskaqqeaasklSdelqtalseakgatddleaaiek 68 
                                    + e r++  +a+  +++++++k   +l++a +e k a +dle   ek
  gi|116754779|ref|YP_843897.1| 199 DVERRIEEIRAQEASARAELIKREIALKDAENERKRAREDLERLDEK 245
                                    45666666677777777777777777777777777777776654433 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0027
                                    T----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-------- CS
                        T3SSipB  41 asklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeLaPdePek 100
                                    + +l   l+++ +e ++   dleaa   ++q++s  + ++    ea+++l+eL+    e 
  gi|116754779|ref|YP_843897.1| 287 LHALTSDLKRL-NEIRKHLHDLEAARRDYEQLNSILKSLQIERREALRSLNELETRLDEL 345
                                    55555555553.444555556677777777777777777777777777777664433333 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.39
                                    THHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---------CHHHHHHHHH..HHHHHHHH CS
                        T3SSipB  47 elqtalse...akgatddleaaiekadqaksaadaatkkvdeaqkrlkeLaPdePekakleaaeqQagaaadalqade 121
                                     l++ l+e   ak++ + l++   + d+      ++ +++d + k+l+e+     e + l++ e Q++   + l++++
  gi|116754779|ref|YP_843897.1| 429 SLKRELEElerAKEMHRRLDELLSERDSRIERRAQLLNRLDIIHKKLSEIGDLAREERGLREREVQLETLIETLNQKR 506
                                    455555440004444445555555555555555677788888999999997777788888888888886666665555 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.027
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---------CHHHHHHHHH...HHHHHHHHHHHHHHHHHH CS
                        T3SSipB  53 seakgatddleaaiekadqaksaadaatkkvdeaqkrlkeLaPdePekakleaaeqQagaa.adalqadealqKkldaas 131
                                    +e +   dd+e a +++ +++  +++a++  +   ++ ++L     + a lea+++ +  +  +  +    l+ ++da  
  gi|116754779|ref|YP_843897.1| 559 EEIRRYRDDYETATNELRDLNERVKNAQHLRERLRASAESLGKRRSDLASLEAEQREVMLQlSEMRERISELDGEIDAIG 638
                                    45666778888888888888888888888888888888888777777777777776665555566666666777777777 PP

                                    HHHHHHHHHH CS
                        T3SSipB 132 klsekakake 141
                                    +++ ++k  e
  gi|116754779|ref|YP_843897.1| 639 QAEYDSKRHE 648
                                    7776666655 PP

  == domain 5  score: -2.8 bits;  conditional E-value: 7
                                    HHHHHTT---------CHHHHHHHHH CS
                        T3SSipB  86 aqkrlkeLaPdePekakleaaeqQag 111
                                    +   l+eLa d  e+  l+a+e  ++
  gi|116754779|ref|YP_843897.1| 763 VEGELSELAFDPNEYDMLRAEETRLA 788
                                    44579999999899999999887765 PP

  == domain 6  score: 2.5 bits;  conditional E-value: 0.16
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---------CHHHHHHHHH..HHH CS
                        T3SSipB  55 akgatddleaaiekadqaksaadaatkkvdeaqkrlkeLaPdePekakleaaeqQagaaada 116
                                     ++a++ l +a e++  a+ ++ +    +     +l++L+ d   k++le++   ++ +a  
  gi|116754779|ref|YP_843897.1| 842 YENAKRILSDADERLRCANEEYAKMRDELRRLEWSLSGLNDDLKRKRELERKIDELNRKAQV 903
                                    34455555555555555555555555555555556666655555566666655555544444 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 ?    1.9   0.3      0.25   2.8e+02      38      81 ..     227     270 ..     223     272 .. 0.85
   2 ?    4.2   0.5     0.049        55      50      80 ..     280     310 ..     273     325 .. 0.77
   3 ?    1.6   0.3      0.31   3.4e+02      46      78 ..     314     346 ..     302     359 .. 0.59
   4 ?    1.3   0.0      0.38   4.2e+02      43      74 ..     362     393 ..     349     398 .. 0.84
   5 ?    1.7   0.7      0.29   3.3e+02      42      90 ..     426     474 ..     400     478 .. 0.58
   6 ?    0.7   1.5      0.57   6.4e+02      44      91 ..     428     475 ..     422     513 .. 0.67
   7 ?   -0.4   0.1       1.3   1.4e+03      37      68 ..     500     531 ..     482     536 .. 0.57
   8 ?   10.3   1.1   0.00061      0.69      13      82 ..     566     635 ..     555     640 .. 0.89
   9 ?    0.0   0.1      0.96   1.1e+03      51      87 ..     658     694 ..     641     706 .. 0.61
  10 ?    5.9   0.1     0.014        15      45      86 ..     717     758 ..     710     767 .. 0.86
  11 ?   -0.3   0.1       1.2   1.3e+03      31      82 ..     782     833 ..     777     840 .. 0.75
  12 ?    5.9   0.1     0.014        16      32      73 ..     859     900 ..     855     906 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.25
                        BLOC1_2  38 klkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeav 81 
                                    + +++ + ++++le+l+ek +e   ++++i+ ++  +++ e ++
  gi|116754779|ref|YP_843897.1| 227 DAENERKRAREDLERLDEKRQEHMRLKREIEHVQGYIADRERTA 270
                                    56677788999********************9999888777766 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.049
                        BLOC1_2  50 leklnekyeelqpylqqidqiekqvteLeea 80 
                                    +e+ ++k ++l + l+++++i k++ +Le+a
  gi|116754779|ref|YP_843897.1| 280 IEEKKRKLHALTSDLKRLNEIRKHLHDLEAA 310
                                    6888899999999****************97 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.31
                        BLOC1_2  46 lekkleklnekyeelqpylqqidqiekqvteLe 78 
                                     e+  + l++++ e ++ l++++++e++++eL 
  gi|116754779|ref|YP_843897.1| 314 YEQLNSILKSLQIERREALRSLNELETRLDELY 346
                                    333344455666666777777777777777765 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.38
                        BLOC1_2  43 aaslekkleklnekyeelqpylqqidqiekqv 74 
                                       ++++le+l+ k e + +++++i  ++++ 
  gi|116754779|ref|YP_843897.1| 362 YVTTQRELEELEIKRERFTSHVSSIASLDAER 393
                                    5567899*******************999875 PP

  == domain 5  score: 1.7 bits;  conditional E-value: 0.29
                        BLOC1_2  42 vaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyske 90 
                                    v++sl+++le+l++ +e  + + + + + + ++++  ++ ++LD + k+
  gi|116754779|ref|YP_843897.1| 426 VLESLKRELEELERAKEMHRRLDELLSERDSRIERRAQLLNRLDIIHKK 474
                                    4455666666666644444444444555555555555555555555555 PP

  == domain 6  score: 0.7 bits;  conditional E-value: 0.57
                        BLOC1_2  44 aslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeL 91 
                                    +sl+++le+l++ +e  + + + + + + ++++  ++ ++LD + k+L
  gi|116754779|ref|YP_843897.1| 428 ESLKRELEELERAKEMHRRLDELLSERDSRIERRAQLLNRLDIIHKKL 475
                                    566666666666444444444445555566666666666666555555 PP

  == domain 7  score: -0.4 bits;  conditional E-value: 1.3
                        BLOC1_2  37 kklkdvaaslekkleklnekyeelqpylqqid 68 
                                    + l+++  ++e+  +  ++k +e q++l++i+
  gi|116754779|ref|YP_843897.1| 500 ETLNQKRTEIESRRNLARSKMHESQSNLKRIE 531
                                    33444444555555555555555555555555 PP

  == domain 8  score: 10.3 bits;  conditional E-value: 0.00061
                        BLOC1_2  13 aeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavs 82 
                                     + e ++++++ L++  ++a++  + l+ +a+sl k  ++l ++++e ++ + q+ ++ ++++eL   ++
  gi|116754779|ref|YP_843897.1| 566 DDYETATNELRDLNERVKNAQHLRERLRASAESLGKRRSDLASLEAEQREVMLQLSEMRERISELDGEID 635
                                    56788899999999999999999*****************************************986655 PP

  == domain 9  score: 0.0 bits;  conditional E-value: 0.96
                        BLOC1_2  51 eklnekyeelqpylqqidqiekqvteLeeavseLDey 87 
                                    ++l  k + l   l+++  +e +++   e +s+LDe 
  gi|116754779|ref|YP_843897.1| 658 NELIDKRARLLARLENLPGLESELENTREKASALDER 694
                                    3334444455555555666666666666666666654 PP

  == domain 10  score: 5.9 bits;  conditional E-value: 0.014
                        BLOC1_2  45 slekkleklnekyeelqpylqqidqiekqvteLeeavseLDe 86 
                                    s+ ++l+   e+y  l ++  +i+++ek ++ L   v++LD 
  gi|116754779|ref|YP_843897.1| 717 STLSELQSSHERYGLLLQQTGEIERLEKLLEALRIRVQRLDG 758
                                    5566788888999999*************************6 PP

  == domain 11  score: -0.3 bits;  conditional E-value: 1.2
                        BLOC1_2  31 aasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavs 82 
                                    a +++ ++++++a+ l++++ + +     l +  + + ++++q +eL +  +
  gi|116754779|ref|YP_843897.1| 782 AEETRLAEIESIANRLRVEIAAEDLSRSRLFEAETDLRRLHTQMAELSTRLE 833
                                    5677888888888888888888777778888888888888888877766554 PP

  == domain 12  score: 5.9 bits;  conditional E-value: 0.014
                        BLOC1_2  32 asekykklkdvaaslekkleklnekyeelqpylqqidqiekq 73 
                                    a+e+y+k++d++  le +l+ ln   +  +++ ++id+++++
  gi|116754779|ref|YP_843897.1| 859 ANEEYAKMRDELRRLEWSLSGLNDDLKRKRELERKIDELNRK 900
                                    6899********************999999999999999865 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 ?    5.2  13.3     0.011        12      36     127 ..     198     289 ..     185     294 .. 0.88
   2 ?    8.2   5.2    0.0012       1.4      75     139 ..     295     358 ..     290     388 .. 0.76
   3 ?    0.3  15.8      0.33   3.7e+02      56     183 ..     403     524 ..     389     534 .. 0.85
   4 ?   10.6   8.9   0.00023      0.26      37     120 ..     556     639 ..     547     674 .. 0.58
   5 ?    1.0   2.3       0.2   2.3e+02      31     125 ..     677     770 ..     657     777 .. 0.71
   6 ?   10.7   5.4   0.00022      0.25      42     139 ..     804     900 ..     782     913 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.011
                            GAS  36 eelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrf 115
                                     + +++ e+ + + + + +e  + +  Lk ae+e+++ r++l++ ++++q++++lk+++++++ ++ d +  ++  + r+
  gi|116754779|ref|YP_843897.1| 198 GDVERRIEEIRAQEASARAELIKREIALKDAENERKRAREDLERLDEKRQEHMRLKREIEHVQGYIADRERTAREERARL 277
                                    556666677777777777777788889***************************************************** PP

                            GAS 116 ekvekerdelyk 127
                                    e +e+++ +l++
  gi|116754779|ref|YP_843897.1| 278 EGIEEKKRKLHA 289
                                    *****9999875 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0012
                            GAS  75 kqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekvekerdelykkfeaaiqevqqk 139
                                    k+l++ +k+  +l+++++ +++l++ lk+l+ e +     ++++e   dely+  ++ ++ +++k
  gi|116754779|ref|YP_843897.1| 295 KRLNEIRKHLHDLEAARRDYEQLNSILKSLQIERREALRSLNELETRLDELYRC-RSEMEGLREK 358
                                    567788888888999999999999999999999999999999999999999863.3334555555 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.33
                            GAS  56 nkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekvekerdelykkfeaaiqe 135
                                    + +l+ +L++a++ +  L+++l   e+ k +l++l+ r ke+ + l +l  e ++  +r +++ +  d ++kk  +  + 
  gi|116754779|ref|YP_843897.1| 403 KADLVRELREARRSLPDLERRLSVLESLKRELEELE-RAKEMHRRLDELLSERDSRIERRAQLLNRLDIIHKKLSEIGDL 481
                                    5679999***************************96.799************************************9999 PP

                            GAS 136 vqqktglknllLekklkalqeelEkkeaqleevlaaanldpaalsavs 183
                                    ++++ gl++   e +l++l e+l++k  ++e+     nl  +++++ +
  gi|116754779|ref|YP_843897.1| 482 AREERGLRER--EVQLETLIETLNQKRTEIESRR---NLARSKMHESQ 524
                                    99999*9997..7789999999999999988654...33333344333 PP

  == domain 4  score: 10.6 bits;  conditional E-value: 0.00023
                            GAS  37 elkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfe 116
                                    + +++ +r + + + +++e ++l+e +k+a++ +e+Lr+ ++   k +++l++l+a+ +e+  +l+++++    l  +++
  gi|116754779|ref|YP_843897.1| 556 KYREEIRRYRDDYETATNELRDLNERVKNAQHLRERLRASAESLGKRRSDLASLEAEQREVMLQLSEMRERISELDGEID 635
                                    33444455555556666666666666666666666666666666666666666666666666666666666665555555 PP

                            GAS 117 kvek 120
                                    ++ +
  gi|116754779|ref|YP_843897.1| 636 AIGQ 639
                                    5544 PP

  == domain 5  score: 1.0 bits;  conditional E-value: 0.2
                            GAS  31 lKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehev 110
                                    l +e+e+ ++k+ + + ++ e+s   + l    ++  + +  L +    +e+    l ++  ++++lek l++l+   + 
  gi|116754779|ref|YP_843897.1| 677 LESELENTREKASALDERIFEHSRSISILDYDERAYLRARSTLSELQSSHERYGLLL-QQTGEIERLEKLLEALRIRVQR 755
                                    667777777777777777777777777777777777777777766666666655544.4445677778888888888877 PP

                            GAS 111 leqrfekvekerdel 125
                                    l   + kve e  el
  gi|116754779|ref|YP_843897.1| 756 LDGDMLKVEGELSEL 770
                                    777777777777776 PP

  == domain 6  score: 10.7 bits;  conditional E-value: 0.00022
                            GAS  42 eernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekveke 121
                                    e+  + +l e++++ +rl  ++ ++   +eeL    + ye+ k  l  + +rl+ +++e+ +++ e + le  ++ + ++
  gi|116754779|ref|YP_843897.1| 804 EDLSRSRLFEAETDLRRLHTQMAELSTRLEELGYTDASYENAKRILSDADERLRCANEEYAKMRDELRRLEWSLSGLNDD 883
                                    55667788899999999999999999999999999999999998888888877777777777777666666666666554 PP

                            GAS 122 rdelykkfeaaiqevqqk 139
                                     ++ +++ e++i+e+  k
  gi|116754779|ref|YP_843897.1| 884 LKR-KRELERKIDELNRK 900
                                    332.22233333333333 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 ?    3.7   2.8     0.044        49      26      76 ..     224     274 ..     203     289 .. 0.85
   2 ?    3.7   0.7     0.045        50      32      67 ..     295     330 ..     280     377 .. 0.83
   3 ?    2.1   0.1      0.14   1.5e+02      29      66 ..     405     442 ..     398     455 .. 0.86
   4 ?   -1.7   0.1         2   2.2e+03      15      32 ..     499     518 ..     471     534 .. 0.51
   5 ?    4.1   2.2     0.033        37      21      73 ..     555     607 ..     551     700 .. 0.89
   6 ?    5.4   0.1     0.013        14      12      74 ..     803     865 ..     789     874 .. 0.88
   7 ?    8.6   0.5    0.0013       1.5      16      65 ..     852     901 ..     840     906 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.044
                     Phage_GP20  26 erdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakaeyeaki 76 
                                    + ++ +++ k + ++Le L +k ++   L+++ie +q  +++ + ++ ++ 
  gi|116754779|ref|YP_843897.1| 224 ALKDAENERKRAREDLERLDEKRQEHMRLKREIEHVQGYIADRERTAREER 274
                                    56788888899999***************************9999887765 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.045
                     Phage_GP20  32 eqlkdrdkqLedLkkkakdneeLqkqieelqaknkk 67 
                                    ++l++  k L dL+++  d e+L+  +++lq +  +
  gi|116754779|ref|YP_843897.1| 295 KRLNEIRKHLHDLEAARRDYEQLNSILKSLQIERRE 330
                                    467788899999999999999999999999976655 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.14
                     Phage_GP20  29 tlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknk 66 
                                    +l  +l ++  +L dL+      e+L++++eel+ + +
  gi|116754779|ref|YP_843897.1| 405 DLVRELREARRSLPDLERRLSVLESLKRELEELERAKE 442
                                    5667899999***********************98654 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 2
                     Phage_GP20  15 it..kakldeveeerdtlke 32 
                                    i   ++k +e+e+ r+   +
  gi|116754779|ref|YP_843897.1| 499 IEtlNQKRTEIESRRNLARS 518
                                    21223334444444444444 PP

  == domain 5  score: 4.1 bits;  conditional E-value: 0.033
                     Phage_GP20  21 deveeerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakaeye 73 
                                    +++ ee   + ++ +++ ++L dL + +k+++ L + +    + + k  ++ +
  gi|116754779|ref|YP_843897.1| 555 EKYREEIRRYRDDYETATNELRDLNERVKNAQHLRERLRASAESLGKRRSDLA 607
                                    56778888999999999999****99999999999999888777777666654 PP

  == domain 6  score: 5.4 bits;  conditional E-value: 0.013
                     Phage_GP20  12 gkditkakldeveeerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakaeyea 74 
                                     +d++ ++l e+e++   l +q+++  + Le+L       e+ ++ + +  + +  a++ey++
  gi|116754779|ref|YP_843897.1| 803 AEDLSRSRLFEAETDLRRLHTQMAELSTRLEELGYTDASYENAKRILSDADERLRCANEEYAK 865
                                    4567789999*********************************************99999987 PP

  == domain 7  score: 8.6 bits;  conditional E-value: 0.0013
                     Phage_GP20  16 tkakldeveeerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqakn 65 
                                    + ++l  ++ee  ++ ++l   + +L++L ++ k   eL+++i+el+ k+
  gi|116754779|ref|YP_843897.1| 852 ADERLRCANEEYAKMRDELRRLEWSLSGLNDDLKRKRELERKIDELNRKA 901
                                    37889999**************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1061 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2041  (0.113838); expected 358.6 (0.02)
Passed bias filter:                      732  (0.0408277); expected 358.6 (0.02)
Passed Vit filter:                       126  (0.00702772); expected 17.9 (0.001)
Passed Fwd filter:                        64  (0.00356964); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 2.05u 0.41s 00:00:02.46 Elapsed: 00:00:00.69
# Mc/sec: 4622.70
//
Query:       gi|116754780|ref|YP_843898.1|  [L=93]
Description: hypothetical protein Mthe_1486 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); 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: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 705.42
//
Query:       gi|116754781|ref|YP_843899.1|  [L=101]
Description: hypothetical protein Mthe_1487 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        1.6    9.3  11.1      0.073   13.6   5.2    1.8  2  DUF4405   Domain of unknown function (DUF4405)


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 ?   13.6   5.2   4.1e-06     0.073       3      63 ..      16      64 ..      14      66 .. 0.91
   2 ?   -2.4   0.3      0.42   7.5e+03       7      13 ..      85      91 ..      81      97 .. 0.49

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.1e-06
                        DUF4405  3 dlllllsflvlaiSGillsfavlpsgrgaywaflglskhqwrdiHeilgllflilvvlHlg 63
                                    ++ll+++++ +++G   +  v+             + +q+ +iH++l  l++++ ++H+ 
  gi|116754781|ref|YP_843899.1| 16 AWILLFLMVIFIVTGYSWHERVIM------------NPRQAAQIHTTLDPLLVLFFLIHVT 64
                                   689****************99653............999********************95 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.42
                        DUF4405  7 llsflvl 13
                                   lls+++l
  gi|116754781|ref|YP_843899.1| 85 LLSIALL 91
                                   3333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       962  (0.0536561); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); 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: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 817.71
//
Query:       gi|116754782|ref|YP_843900.1|  [L=197]
Description: hypothetical protein Mthe_1488 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-18   65.7  19.7      4e-18   65.5  19.7    1.0  1  MFS_1     Major Facilitator Superfamily
     0.0019   16.7   6.1     0.0021   16.5   6.1    1.2  1  MFS_3     Transmembrane secretion effector
  ------ inclusion threshold ------
        9.7    6.7  11.4       0.64   10.5   1.0    2.8  3  DUF3917   Protein of unknown function (DUF3917)


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 !   65.5  19.7   6.7e-22     4e-18       3     181 ..      10     190 ..       8     196 .. 0.83

  Alignments for each domain:
  == domain 1  score: 65.5 bits;  conditional E-value: 6.7e-22
                          MFS_1   3 laaflsalarsilgpalplalaed.lgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalglllll 80 
                                    l+ +l+ ++ +++ p+l +++++   g s+ ++g++ tl+ ++ ++ +lp+G  +dr+  ++ +ll+g  + +   ++ +
  gi|116754782|ref|YP_843900.1|  10 LSDILMLTGLGLIQPILAIFINDGvAGGSVLSAGIASTLFLVTKSLVQLPFGMYIDRVNNKSrWLLVGTSIVSCVPVMYM 89 
                                    55577888889999999985544425699999**************************8666666666655555524444 PP

                          MFS_1  81 fasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaiv 160
                                    f+ s++ ++++ ++ G+g+g+++pa +al ++ + +   g+  +l+s++++lG+++++++g+++as lg++a+f++  ++
  gi|116754782|ref|YP_843900.1|  90 FIDSIYQVYIAEIINGVGSGLAYPAWVALWSANVERGSEGFEWSLYSTSTGLGTAFTAAVGAAIASMLGFTATFMFTSVM 169
                                    558888************************************************************************** PP

                          MFS_1 161 sllafvlfllllpeepperkr 181
                                    +l++  ++l+l +ee+++ k 
  gi|116754782|ref|YP_843900.1| 170 CLMGSGIILMLDREERVAVKS 190
                                    ****55444666666665554 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   6.1   3.5e-07    0.0021      74     189 ..      70     183 ..      15     194 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.5e-07
                          MFS_3  74 rRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaalndPaWqAsvgelvkrrdvpaAvaLnsvginiaRs 153
                                    + + ll++ +++  v v+ +      + s + + +  ++ g+G+ l  PaW A  +  v+r        L s    +  +
  gi|116754782|ref|YP_843900.1|  70 KSRWLLVGTSIVSCVPVMYMF-----IDSIYQVYIAEIINGVGSGLAYPAWVALWSANVERGSEGFEWSLYSTSTGLGTA 144
                                    345555555555444444433.....3456678888999************************999************** PP

                          MFS_3 154 vGPAlgGvlvaavGaalafavnalsyla...livallrw 189
                                       A+g  + +++G +++f ++++  l+   +i+ l r 
  gi|116754782|ref|YP_843900.1| 145 FTAAVGAAIASMLGFTATFMFTSVMCLMgsgIILMLDRE 183
                                    *********************988777622234444333 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   0.3     0.024   1.4e+02      16      50 ..      15      49 ..       6      60 .. 0.81
   2 ?   -1.9   0.3      0.77   4.6e+03      28      34 ..      88      94 ..      73     106 .. 0.48
   3 ?   10.5   1.0   0.00011      0.64      29      66 ..     144     180 ..     136     184 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.024
                        DUF3917 16 ilaGialityvasifvesvsvevsaslvfvaitlf 50
                                   +l+G+ li  + +if+++  +  s     +a tlf
  gi|116754782|ref|YP_843900.1| 15 MLTGLGLIQPILAIFINDGVAGGSVLSAGIASTLF 49
                                   58999999999999999877777777777777777 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.77
                        DUF3917 28 sifvesv 34
                                    +f++s+
  gi|116754782|ref|YP_843900.1| 88 YMFIDSI 94
                                   2333333 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.00011
                        DUF3917  29 ifvesvsvevsaslvfvaitlfaGsimvlmvaGivlfi 66 
                                     f   v + +++ l f a  +f  s+m lm +Gi+l++
  gi|116754782|ref|YP_843900.1| 144 AFTAAVGAAIASMLGFTATFMF-TSVMCLMGSGIILML 180
                                    5777888888888888886666.69**********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       710  (0.0396006); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1372.52
//
Query:       gi|116754783|ref|YP_843901.1|  [L=722]
Description: phosphoesterase domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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   34.3   0.0    1.4e-07   31.4   0.1    2.5  3  tRNA_anti-codon  OB-fold nucleic acid binding domain
    5.4e-08   33.1   9.8    5.4e-08   33.1   9.8    2.4  2  DnaJ_CXXCXGXG    DnaJ central domain
     0.0001   22.5   0.2     0.0002   21.6   0.2    1.4  1  DHH              DHH family
    0.00014   22.0   0.0     0.0011   19.1   0.0    2.4  2  tRNA_anti_2      OB-fold nucleic acid binding domain
      0.005   17.0   4.4      0.005   17.0   4.4    2.8  3  PHF5             PHF5-like protein
     0.0052   17.1   0.0      0.015   15.6   0.0    1.8  1  S1               S1 RNA binding domain
  ------ inclusion threshold ------
      0.013   15.5  15.3       0.29   11.2   7.3    2.7  3  DZR              Double zinc ribbon
      0.033   14.1  11.7        0.4   10.7   0.9    3.4  3  Anti-TRAP        Tryptophan RNA-binding attenuator protein in
      0.075   13.5   0.0       0.28   11.7   0.0    1.9  1  B12-binding_2    B12 binding domain
      0.091   13.0  21.2       0.51   10.6   5.9    3.6  3  DUF5351          Family of unknown function (DUF5351)
          1    9.4  15.1          7    6.7   0.8    3.6  3  HypA             Hydrogenase/urease nickel incorporation, met


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 !   31.4   0.1   8.3e-11   1.4e-07       1      74 [.     219     289 ..     219     291 .. 0.96
   2 ?   -2.3   0.0       2.8   4.6e+03      11      33 ..     388     409 ..     384     423 .. 0.78
   3 ?   -1.9   0.0       2.1   3.4e+03      46      64 ..     582     603 ..     578     614 .. 0.75

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 8.3e-11
                                    EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEEEEEE CS
                tRNA_anti-codon   1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrrpggelelkveeie 74 
                                    V+++G+v+++  +++++   +++ D++g++ + +f  +  + + +++ ++vv+v G+++ r+++ +++ + +++
  gi|116754783|ref|YP_843901.1| 219 VCIKGEVIQV--KQTAGPTIFTIADDSGTVSCAAFERAGVRAYPEIQGDMVVKVIGEPTIRNNQ-MQIEIRSMK 289
                                    89********..**************************************************99.999988876 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.8
                                    EEEEETTEEEEEEEETTEEEEEE CS
                tRNA_anti-codon  11 sdrsggkvifidlrDgtgriqvv 33 
                                    + r+ +k+ f++l+D t  +   
  gi|116754783|ref|YP_843901.1| 388 R-RAPSKAPFYELEDVTKDLSYA 409
                                    3.8889999******99877655 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 2.1
                                    S-TTSEEEEE.EEEEEC..TTS CS
                tRNA_anti-codon  46 lkeGdvvrvt.Grvkrr..pgg 64 
                                      ++d +r++ G vk++  p+g
  gi|116754783|ref|YP_843901.1| 582 AAIEDQLRASmGNVKSTklPNG 603
                                    56799999******99977666 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   9.8   3.3e-11   5.4e-08       1      66 [.      15      85 ..      15      86 .. 0.77
   2 ?    0.7   5.9      0.43   7.1e+02      15      63 ..      77      94 ..      76     112 .. 0.47

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 3.3e-11
                  DnaJ_CXXCXGXG  1 CkkCkGsgakkgkkktCktCkGsGv...vree....qkt.lgpfvqqsqstCpeCeGtGkvikekdkCkkCkGk 66
                                   C++C G+g     ++tC++C+G+G+   +  +    +++ ++++ q+ + +C  C+GtG++   +++C++C G 
  gi|116754783|ref|YP_843901.1| 15 CERCGGQGFVVVGERTCPNCDGTGKtesI--TlteaRDSdITSLLQEGSARCAVCNGTGRIP-ITETCEACGGL 85
                                   ********86666899********63441..2333233467778999999**********76.5679****995 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.43
                  DnaJ_CXXCXGXG 15 ktCktCkGsGvvreeqktlgpfvqqsqstCpeCeGtGkvikekdkCkkC 63
                                   +tC++C+G G++ +                               C  C
  gi|116754783|ref|YP_843901.1| 77 ETCEACGGLGREYR-------------------------------CLVC 94
                                   46777777774322...............................3332 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.2   1.2e-07    0.0002       2      65 ..     349     466 ..     348     506 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.2e-07
                                    EEEE-ECSSSHHHHHHHHHHHH.......................................................CEC CS
                                    xxxxxxxxxxxxxxxxxxxxxx.......................................................xxx RF
                            DHH   2 ilivghknpDtDsigSaialan.......................................................llv 26 
                                    i+i   ++ D+D+i +a+a++                                                        +l+
  gi|116754783|ref|YP_843901.1| 349 IVI--RHHADADGISAAVAIETailplmkevggpdaeyysyrrapskapfyeledvtkdlsyaledqsrygqkmplvVLI 426
                                    445..7899*************88888888888888888888888888888888877777777777777777777777** PP

                                    S--TCGGCGCCH..HCCCSEEEEEEE-S---SS---SS--E CS
                                    xxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DHH  27 Dhneksqavege..akeeaedviiiDHHrlgeefetlapil 65 
                                    D+++++++v +   a+  + +++++DHH +++ + +   i 
  gi|116754783|ref|YP_843901.1| 427 DNGSTEEDVPAMkhAQVYGLEMVVVDHHHPND-IVDQYLIA 466
                                    *****9999875557788899*********94.44443333 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 ?   -1.0   0.0       1.3   2.1e+03      54      77 ..     156     176 ..     119     186 .. 0.73
   2 !   19.1   0.0   6.7e-07    0.0011      14      93 ..     211     287 ..     205     289 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.3
                    tRNA_anti_2  54 ifrsraaklkftledGmkVlvkgr 77 
                                      +   + l+f++e G+k+ v+++
  gi|116754783|ref|YP_843901.1| 156 AHN---RYLRFRPEVGEKLFVRVK 176
                                    333...5578999***99999876 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 6.7e-07
                    tRNA_anti_2  14 leaelkkavwvrGeisnlkrkasghvYftLkDekakisavifrsraaklkftledGmkVlvkgrlsvYeprGsyqlived 93 
                                    l+++l k v+++Ge+ ++k ++ g + ft+ D++ ++s++ f+++  +   +++ +m V v g++++   + ++q+ +++
  gi|116754783|ref|YP_843901.1| 211 LQKHLGKIVCIKGEVIQVK-QTAGPTIFTIADDSGTVSCAAFERAGVRAYPEIQGDMVVKVIGEPTIR--NNQMQIEIRS 287
                                    56778889**********5.469*******************97765555679999***9**999984..4445666655 PP

>> PHF5  PHF5-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.3       1.5   2.4e+03      23      30 ..      15      22 ..       9      47 .. 0.45
   2 !   17.0   4.4     3e-06     0.005      14      77 ..      48     110 ..      37     114 .. 0.86
   3 ?    0.4   0.0      0.47   7.7e+02      13      32 ..     625     644 ..     616     649 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.5
                           PHF5 23 cekcdgkc 30
                                   ce+c g+ 
  gi|116754783|ref|YP_843901.1| 15 CERCGGQG 22
                                   33333321 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 3e-06
                           PHF5  14 qpGtaigklcekcdgkcpicdslvkpatkvricdecsfgkleekciicgskgvsdayyclecvr 77 
                                       ++i+ l ++   +c++c+ +  ++   + c+ c     e +c++cg++   +a  c+ c+r
  gi|116754783|ref|YP_843901.1|  48 ARDSDITSLLQEGSARCAVCNGTG-RIPITETCEACGGLGREYRCLVCGTRLSLKADLCERCSR 110
                                    55677889999999*******985.5667889******************************87 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.47
                           PHF5  13 kqpGtaigklcekcdgkcpi 32 
                                    k++G    ++c+k dgk ++
  gi|116754783|ref|YP_843901.1| 625 KTSGEIHDRMCKKYDGKPVV 644
                                    677888899*******9776 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   9.5e-06     0.015       4      35 ..     128     159 ..     126     185 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 9.5e-06
                                    TTCEEEEEEEEEETTEEEEEETTTEEEEEEGG CS
                             S1   4 kgevveGeVtsvtkgGafVelgngvegfvpas 35 
                                    +g ++eG V+ +  +GafV+l ++++g+ +  
  gi|116754783|ref|YP_843901.1| 128 VGSIYEGSVSGLASFGAFVDLNENMRGLAHNR 159
                                    699************************98865 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   1.0    0.0016       2.7      13      35 ..      13      35 ..       6      44 .. 0.67
   2 ?    2.3  10.1       0.1   1.7e+02       1      49 []      15      83 ..      15      83 .. 0.87
   3 ?   11.2   7.3   0.00018      0.29      12      48 ..      76     108 ..      56     109 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0016
                            DZR 13 rfCseCgtklkavaaedrCpsCg 35
                                   ++C++Cg +   v  e++Cp+C+
  gi|116754783|ref|YP_843901.1| 13 KVCERCGGQGFVVVGERTCPNCD 35
                                   56777776644455567777775 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.1
                            DZR  1 CpqCgee..lppdarfCseCgtklkavaa.................edrCpsCgek.vdpearfCpeCG 49
                                   C +Cg +  +  + r+C++C  + k ++                  + rC  C+     p +++C +CG
  gi|116754783|ref|YP_843901.1| 15 CERCGGQgfVVVGERTCPNCDGTGKTESItlteardsditsllqegSARCAVCNGTgRIPITETCEACG 83
                                   8999999889999*******9996633337778889*****************988899999******9 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00018
                            DZR  12 arfCseCgtklkavaaedrCpsCgekvdpearfCpeC 48 
                                     ++C++Cg   +    e+rC  Cg+ ++++a  C  C
  gi|116754783|ref|YP_843901.1|  76 TETCEACGGLGR----EYRCLVCGTRLSLKADLCERC 108
                                    578999999998....9******************** 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 ?   -0.9   0.1         1   1.7e+03      33      42 ..      15      24 ..      11      29 .. 0.75
   2 ?    9.0   0.7   0.00081       1.3      10      25 ..      28      43 ..      26      51 .. 0.86
   3 ?   10.7   0.9   0.00024       0.4       8      40 ..      59      86 ..      53      90 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1
                                   -TTTTTSSEE CS
                      Anti-TRAP 33 CPkCsGkgli 42
                                   C +C+G+g++
  gi|116754783|ref|YP_843901.1| 15 CERCGGQGFV 24
                                   7788888876 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00081
                                   EEE-TTTTTTSEETTE CS
                      Anti-TRAP 10 EtkCdaCngsGkiepe 25
                                   E +C++C+g+Gk e+ 
  gi|116754783|ref|YP_843901.1| 28 ERTCPNCDGTGKTESI 43
                                   889*********9985 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00024
                                   HCEEE-TTTTTTSEETTE......E-TTTTTSS CS
                      Anti-TRAP  8 eLEtkCdaCngsGkiepeeprasleCPkCsGkg 40
                                   e    C  Cng+G+i+ +       C +C+G g
  gi|116754783|ref|YP_843901.1| 59 EGSARCAVCNGTGRIPIT-----ETCEACGGLG 86
                                   55678***********99.....4799999966 PP

>> B12-binding_2  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00017      0.28      12      47 ..     294     378 ..     289     379 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
                  B12-binding_2  12 gdkegieelideala.................................................qgsaavdvlndvllpa 42 
                                    g+  +++e i++a++                                                  g +a  ++++++lp+
  gi|116754783|ref|YP_843901.1| 294 GEATKVREEIEQAIDrraepfdpplliesevlerlrprmravakairraifkskpivirhhadaDGISAAVAIETAILPL 373
                                    5666777777777777778888888888888888888888888888899999999999888888888899999******* PP

                  B12-binding_2  43 mkeVG 47 
                                    mkeVG
  gi|116754783|ref|YP_843901.1| 374 MKEVG 378
                                    ****9 PP

>> DUF5351  Family of unknown function (DUF5351)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   5.9   0.00031      0.51       1      28 [.      15      39 ..      15      40 .. 0.90
   2 ?    4.9   0.2     0.018        30      16      27 ..      60      71 ..      55      73 .. 0.84
   3 ?    5.8   2.5    0.0094        15      17      28 ..      76      87 ..      76      88 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00031
                        DUF5351  1 CpYCeGkGYfqLlLGGSETCesCeGtgk 28
                                   C+ C+G+G++ +   G  TC+ C Gtgk
  gi|116754783|ref|YP_843901.1| 15 CERCGGQGFVVV---GERTCPNCDGTGK 39
                                   999*****9855...99**********8 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.018
                        DUF5351 16 GSETCesCeGtg 27
                                   GS  C  C+Gtg
  gi|116754783|ref|YP_843901.1| 60 GSARCAVCNGTG 71
                                   9999*******9 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0094
                        DUF5351 17 SETCesCeGtgk 28
                                   +ETCe C G g 
  gi|116754783|ref|YP_843901.1| 76 TETCEACGGLGR 87
                                   6********986 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 ?    5.8   0.7    0.0083        13      72      96 ..      14      38 ..       3      57 .. 0.70
   2 ?    6.5   0.7    0.0051       8.3      60      95 ..      51      85 ..      40      90 .. 0.77
   3 ?    6.7   0.8    0.0043         7      70      95 ..      88     111 ..      86     122 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0083
                                   EETTTS-EEECHHHHHS-TTTSSS- CS
                           HypA 72 rCreCgkefeleekalrCpkCgsad 96
                                    C++Cg ++ +   + +Cp+C++++
  gi|116754783|ref|YP_843901.1| 14 VCERCGGQGFVVVGERTCPNCDGTG 38
                                   7*****99886654678****8763 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0051
                                   -EEEEEEE--EEEETTTS-EEECHHHHHS-TTTSSS CS
                           HypA 60 aeLeieevpvkvrCreCgkefeleekalrCpkCgsa 95
                                   ++++   ++ ++rC +C+ ++++  + ++C++Cg+ 
  gi|116754783|ref|YP_843901.1| 51 SDITSLLQEGSARCAVCNGTGRIPIT-ETCEACGGL 85
                                   55666678899*******99997643.68****985 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0043
                                    EEEETTTS-EEECHHHHHS-TTTSSS CS
                           HypA  70 kvrCreCgkefeleekalrCpkCgsa 95 
                                    ++rC +Cg++ +l+++   C++C+++
  gi|116754783|ref|YP_843901.1|  88 EYRCLVCGTRLSLKAD--LCERCSRT 111
                                    579*********9966..6****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (722 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); 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):              11  [number of targets reported over threshold]
# CPU time: 0.69u 0.26s 00:00:00.95 Elapsed: 00:00:00.44
# Mc/sec: 4879.39
//
Query:       gi|116754784|ref|YP_843902.1|  [L=377]
Description: radical SAM domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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   63.3   0.1    1.9e-16   60.9   0.1    2.0  2  Radical_SAM  Radical SAM superfamily
    5.3e-07   30.0   1.0      7e-07   29.6   0.1    1.7  2  Fer4_12      4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.067   13.3   0.2       0.19   11.9   0.2    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 !   60.9   0.1   3.2e-20   1.9e-16       2     159 ..     152     311 ..     151     320 .. 0.78
   2 ?    0.3   0.0      0.13   7.9e+02     103     154 ..     325     377 .]     313     377 .] 0.68

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 3.2e-20
                                    EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC..CCTEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxx RF
                    Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla..vpgir 79 
                                    v++++C+++C +C++++    +       + +++e+v+++  ek +  +  +gg+p  + +f+  + r+a  a  +  +r
  gi|116754784|ref|YP_843902.1| 152 VFFHACTFNCLYCQNWQF---RAETLRPWMTDVKELVESV-DEK-TSCICYFGGDPAPQLPFALRASRMAIDArrDQIFR 226
                                    6899************94...5555555567777777777.466.**************************99******* PP

                                    EEEEECSSCHG...HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET......EEEEEE CS
                                    xxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxx RF
                    Radical_SAM  80 itvetngtlpd...eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikr......vvdriv 150
                                    i+ etng + +   +e++e+ l+ g   + ++++a d+   ++ +  g ++ ++le++ ++ e + ++      v+  ++
  gi|116754784|ref|YP_843902.1| 227 ICWETNGSMNRhllDEMIELSLNSG-GCIKFDIKAMDEN-LHRAL-TGVSNRRTLENISAAMEMM-DErevpplVIASTL 302
                                    *********9777777777777777.*************.66666.5555555555555555553.2224444*999999 PP

                                    EBTTTSHHH CS
                                    xxxxxxxxx RF
                    Radical_SAM 151 glpGendee 159
                                    ++pG+ dee
  gi|116754784|ref|YP_843902.1| 303 LVPGYIDEE 311
                                    999998865 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.13
                                    SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET..EEEEEEEBTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxx RF
                    Radical_SAM 103 drvslgleaaddekvlklmnrghtfeevlealeklreagikr..vvdrivglpG 154
                                      +  +l a+++  + + m +  ++   +++l+++++ag++r  v +++++ pG
  gi|116754784|ref|YP_843902.1| 325 PEIPYTLLAFHPQFYMRDM-PFTSRPMAMRCLDAAKRAGLERvrVGNVHILTPG 377
                                    5555666667776444444.6677788999999*****9999876666666665 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 ?   -2.5   0.1      0.97   5.8e+03       5      16 ..      69      80 ..      67      82 .. 0.79
   2 !   29.6   0.1   1.2e-10     7e-07       6     102 ..     147     242 ..     140     277 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.97
                        Fer4_12  5 GvrlslfvsgCn 16
                                   G r+s+ v+ C+
  gi|116754784|ref|YP_843902.1| 69 GARCSICVNECR 80
                                   788999888886 PP

  == domain 2  score: 29.6 bits;  conditional E-value: 1.2e-10
                        Fer4_12   6 vr.lslfvsgCnlsCkgCfnketwsfksgkeft.kelleeiiedlkkesiegltllGGEPl..lpenaeallelvkevke 81 
                                     r l++f++ C+++C +C     w+f++++  +  +  +e++e++ +e+ + + ++GG+P   lp+  +a    ++  + 
  gi|116754784|ref|YP_843902.1| 147 YRnLAVFFHACTFNCLYCQ---NWQFRAETLRPwMTDVKELVESV-DEKTSCICYFGGDPApqLPFALRASRMAIDARRD 222
                                    44369************77...68999998888778889999999.99***********863366777777777777777 PP

                        Fer4_12  82 ekpekdiwlytgytleelskk 102
                                    + +   +w+++g+++ +l+++
  gi|116754784|ref|YP_843902.1| 223 QIF-RICWETNGSMNRHLLDE 242
                                    777.69********9999865 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   3.2e-05      0.19       4      93 ..     153     237 ..     150     249 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.2e-05
                        Fer4_14   4 rlsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeype..k 81 
                                     +  C+++C  C n   w++++++     + +++l  ++  + k + +   GG+P  + + +  l+  ++  +  ++  +
  gi|116754784|ref|YP_843902.1| 153 FFHACTFNCLYCQN---WQFRAETLRPWMTDVKEL--VESVDEKTSCICYFGGDPA-P-QLPFALRASRMAIDARRDqiF 225
                                    3589********87...556666665555444555..556666667899*****97.3.444444444444333322238 PP

                        Fer4_14  82 kiwletngtlei 93 
                                    +i  etng+++ 
  gi|116754784|ref|YP_843902.1| 226 RICWETNGSMNR 237
                                    999999998884 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2721.71
//
Query:       gi|116754785|ref|YP_843903.1|  [L=185]
Description: hypothetical protein Mthe_1491 [Methanosaeta thermophila PT]
Scores for complete sequence (score 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   10.8   0.0       0.23   10.3   0.0    1.1  1  Peptidase_C69  Peptidase family C69


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 ?   10.3   0.0   1.3e-05      0.23     243     287 ..      54      98 ..      44     104 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 1.3e-05
                  Peptidase_C69 243 pRvWylqrklnPeieqdpesedlplivkperKisvedvkyvlssH 287
                                     R Wy++r++nP+   +    + p  +     +++edv y+l sH
  gi|116754785|ref|YP_843903.1|  54 RRLWYMFREYNPRCACSLIRLSSPRSMDIVGVVTLEDVSYALPSH 98 
                                    699************99999999********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       199  (0.0110993); expected 358.6 (0.02)
Passed bias filter:                      194  (0.0108205); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 1363.03
//
Query:       gi|116754786|ref|YP_843904.1|  [L=423]
Description: hypothetical protein Mthe_1492 [Methanosaeta thermophila PT]
Scores for complete 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-69  233.0  35.0      6e-69  232.7  35.0    1.0  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 !  232.7  35.0   3.4e-73     6e-69       4     408 ..       9     409 ..       7     410 .. 0.93

  Alignments for each domain:
  == domain 1  score: 232.7 bits;  conditional E-value: 3.4e-73
                           TctA   4 vllGvllGtliGllPGlhatlavalllpltf.....gldpeaalilllgiyvgaifggsipaillgvPGtpssvatvldg 78 
                                    +++G+llG+++Gl+PGlh+++++a+ll +++     gl+p+ +++++l+++++++f+++ip++++g+P ++++v++vl+g
  gi|116754786|ref|YP_843904.1|   9 AAFGFLLGVISGLIPGLHVNTFAAILLGAAPammelGLSPYHVAVIILAASISQTFLDAIPTVFVGAP-DSDTVLAVLPG 87 
                                    689*****************************************************************.*********** PP

                           TctA  79 yplakqGrageAlrlaaigSfiGglvsvllllllapllakvalkfgpaeyfalillglvliailse...........ksl 147
                                    ++l+++Gr+ eA+rl+aigS+ ++lv++ l+  l+++++    +  + e++ lillg+++i+il e           k++
  gi|116754786|ref|YP_843904.1|  88 HRLMLRGRGIEAVRLSAIGSAGSVLVALSLIPHLSWVFS--NYYDILMEHIGLILLGIAVIMILKEqdldpgpyqtlKRR 165
                                    ***************************************..99************************************* PP

                           TctA 148 lkglialllglllgtvgldpnsgtpRftfgsielldgislvpvliGlFgiselltsleskskip.........lslkdlk 218
                                      ++ +++ ++llg+++++++   +     s+  l+   l+p+l+G+Fg+s l+ s+ s++k++         + +    
  gi|116754786|ref|YP_843904.1| 166 SFAISVFVTSGLLGMFAFENQDLLS-----SPLGLEPDVLLPLLSGIFGASSLILSIFSSTKMAeqrdtgfdlPAVP--- 237
                                    ******************9997444.....677789999******************98877765444333321222... PP

                           TctA 219 kslptilrgsliGtivGilPgvGasiaaflayavakrlskkpekfgkgaiegvaapeaannaaaggaliplltlgipgsg 298
                                      + +il g ++G++v+++Pgv++++a++l+   +   +       + a+e++++++++n+++a+ +l++ll++g p+sg
  gi|116754786|ref|YP_843904.1| 238 -LMRSILLGGAAGSVVAWIPGVSPAVATMLTRLGRGIED-----EDQAAREFLVSVSGVNTSCAVLSLVALLVIGRPRSG 311
                                    .34458888***********************9977643.....3579******************************** PP

                           TctA 299 vaavllgallihglqpgpeLftenpelvyallasllianvlllvlgllliklfakll.kipkelLlpiilvllvigayal 377
                                    +aa++++++              ++  vy++++++   ++++++ +++l+ ++  ll ki+++ L++i+l  l+++a ++
  gi|116754786|ref|YP_843904.1| 312 AAAAINELI------------DLDAGQVYMMIVIATAVAFISYISTVWLACIAGSLLsKIDYKNLSIIVLGALALIALIF 379
                                    *******66............3478899***************************888********************** PP

                           TctA 378 nnslfdvlvmlifgvlGlllrrlgvplaplv 408
                                    +++ f++++++i++++Gl+++  g+++++++
  gi|116754786|ref|YP_843904.1| 380 TGT-FGIFIFFISTLIGLIPHLAGIRKMHAM 409
                                    ***.************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       947  (0.0528195); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 3258.10
//
Query:       gi|116754787|ref|YP_843905.1|  [L=761]
Description: PAS/PAC sensor signal transduction histidine kinase [Methanosaeta thermophila PT]
Scores for complete 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-50  168.0   0.0    7.7e-13   48.6   0.0    4.6  4  PAS_9           PAS domain
    1.8e-45  153.7   1.0    7.7e-13   48.7   0.1    5.0  4  PAS_4           PAS fold
    1.6e-44  150.5   0.0    2.1e-11   43.8   0.0    5.8  5  PAS             PAS fold
    3.3e-43  145.9   1.2    3.3e-12   46.5   0.0    5.7  5  PAS_3           PAS fold
    2.2e-30  104.1   0.6    1.5e-07   31.2   0.0    4.8  4  PAS_8           PAS domain
    4.3e-21   75.5   0.0      8e-21   74.6   0.0    1.5  1  HATPase_c       Histidine kinase-, DNA gyrase B-, and HSP90-l
    4.1e-11   42.8   1.7    1.3e-10   41.2   0.1    2.7  3  HisKA           His Kinase A (phospho-acceptor) domain
    6.1e-06   26.4   2.8       0.25   11.5   0.0    5.6  5  PAS_7           PAS fold
    1.3e-05   25.3   0.0       0.27   11.4   0.0    3.9  4  PAS_11          PAS domain
     0.0063   16.6   0.5        1.2    9.5   0.0    3.2  3  TPR_8           Tetratricopeptide repeat
     0.0081   16.0   0.0      0.015   15.2   0.0    1.3  1  HATPase_c_3     Histidine kinase-, DNA gyrase B-, and HSP90-l
  ------ inclusion threshold ------
      0.016   15.1   0.0        3.2    7.7   0.0    3.1  3  MEKHLA          MEKHLA domain
       0.02   15.4   0.1       0.83   10.2   0.1    2.7  2  TPR_19          Tetratricopeptide repeat
       0.03   15.1   3.7          9    7.4   0.0    3.8  3  TPR_14          Tetratricopeptide repeat
      0.056   13.2   0.8       0.75    9.6   0.0    2.9  3  DASH_Duo1       DASH complex subunit Duo1
      0.067   13.1   0.0        0.2   11.6   0.0    1.8  1  HATPase_c_5     GHKL domain
        1.5    9.5   5.3        1.9    9.2   2.0    2.5  2  HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interac


Domain annotation for each model (and alignments):
>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   0.0   1.5e-15   1.6e-12       8     104 .]      28     123 ..      20     123 .. 0.87
   2 !   34.0   0.0   2.6e-11   2.8e-08       5     104 .]     150     264 ..     146     264 .. 0.80
   3 !   32.1   0.0     1e-10   1.1e-07       7     104 .]     293     389 ..     285     389 .. 0.82
   4 !   48.6   0.0   7.3e-16   7.7e-13       3     104 .]     414     513 ..     412     513 .. 0.91

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 1.5e-15
                          PAS_9   8 npdgril.yaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwvlltaspvk 86 
                                     ++  i+ yaN+a++ +lG+s  e++gks +d++ ++++    l+   ++++    ++ev + rk+g+ ++vl+t +p +
  gi|116754787|ref|YP_843905.1|  28 VDERWIIeYANPAFAHMLGFSLSEIVGKSTEDFL-HPDDIPLLLESRAKRLEGLTTSYEVRFLRKDGSIVPVLITGAPRI 106
                                    36667999**************************.88888888888888888899************************9 PP

                          PAS_9  87 dddgelvgiivilrDite 104
                                     d++   g i++++D+t+
  gi|116754787|ref|YP_843905.1| 107 VDNRP-AGGILVITDLTD 123
                                    87655.5569*****996 PP

  == domain 2  score: 34.0 bits;  conditional E-value: 2.6e-11
                          PAS_9   5 lidnpdgrilyaNeaalrllGyspeevlgksitdlf................vtdpeanerlraaleqgrkkerevevvl 68 
                                    l  ++dgr++ +N+a++ l+G  +ee+lgk   ++                 ++ +e+ +r+ + l++    + + ev +
  gi|116754787|ref|YP_843905.1| 150 LGMDMDGRVIIWNRALEALTGVRKEEMLGKGNYECAipfygyrrpvladlvlHGYDESMSREYRNLQRDG-DVLTAEVFI 228
                                    54569*************************9444444669999999999877777777776666666666.577777777 PP

                          PAS_9  69 ir..kngetfwvlltaspvkdddgelvgiivilrDite 104
                                     +  ++g+ +w  l+a+ ++d++g++ g+i ++rDite
  gi|116754787|ref|YP_843905.1| 229 PTfgPEGSHLW--LKAALIYDSEGRIEGAIEVIRDITE 264
                                    66226778888..************************8 PP

  == domain 3  score: 32.1 bits;  conditional E-value: 1e-10
                          PAS_9   7 dnpdgril.yaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkng.etfwvlltasp 84 
                                     + dg +l ++Ne  ++ +G+ +e+++g+s+ +l+  +++++e + + ++ ++++   v+++++ k g e  w + t ++
  gi|116754787|ref|YP_843905.1| 293 FDRDG-VLtFVNENYCNYFGFRREDIVGRSFLELI--PEDEREAVLERFRGLTRERPYVTYTHRVKRGeEIRWQRWTDRA 369
                                    45899.777**************************..88888888888888887555556666555563777777***** PP

                          PAS_9  85 vkdddgelvgiivilrDite 104
                                    ++ ++ge+  + ++ +Dit+
  gi|116754787|ref|YP_843905.1| 370 IFGQNGEVLEYQSLGEDITA 389
                                    ******************95 PP

  == domain 4  score: 48.6 bits;  conditional E-value: 7.3e-16
                          PAS_9   3 gilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk...kerevevvlirkngetfwvl 79 
                                    gi+i   d r +y+N+a +++ Gys++e++g ++++++  +pe++  l++++ ++ +   ++ ++e  +i+kng   wv+
  gi|116754787|ref|YP_843905.1| 414 GIAIM-RDERFVYVNRAGEEMSGYSRDELIGAPVWMVV--HPEDAAWLKKMYSRKLRgepTPPRYEFRIITKNGDVRWVE 490
                                    77776.78889***************************..**************************************** PP

                          PAS_9  80 ltaspvkdddgelvgiivilrDite 104
                                        ++   +g  +++i++l+Dite
  gi|116754787|ref|YP_843905.1| 491 YASGTLEL-GG-EMALIGTLIDITE 513
                                    98888842.45.5558********8 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.0   3.6e-11   3.8e-08      10     107 ..      27     123 ..      15     125 .. 0.92
   2 !   28.4   0.0   1.4e-09   1.5e-06       4     108 ..     145     265 ..     142     267 .. 0.90
   3 !   48.7   0.1   7.3e-16   7.7e-13       2     109 ..     284     391 ..     283     392 .. 0.97
   4 !   37.1   0.0   2.8e-12   2.9e-09      10     110 .]     416     516 ..     407     516 .. 0.88

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 3.6e-11
                          PAS_4  10 vldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgeerhyelrllPlr 89 
                                    v+d+   ++yaN+a+a+++g++  e++Gk+ +++l ++d + l +  ++ leg ++ +++ +l+ +g+ ++++++  P  
  gi|116754787|ref|YP_843905.1|  27 VVDERWIIEYANPAFAHMLGFSLSEIVGKSTEDFLHPDDIPLLLESRAKRLEGLTTSYEVRFLRKDGSIVPVLITGAPR- 105
                                    5699999***********************************************************************6. PP

                          PAS_4  90 desGevigvlvisrDiTe 107
                                      + ++ g +++++D+T+
  gi|116754787|ref|YP_843905.1| 106 IVDNRPAGGILVITDLTD 123
                                    89**************97 PP

  == domain 2  score: 28.4 bits;  conditional E-value: 1.4e-09
                          PAS_4   4 lpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpee...............daarleralrrvlegeepief 68 
                                    +pd+ +  d dgrv+ +N+a ++l g++ ee+lGk  +e + +                  +  +r +r + + +++++ 
  gi|116754787|ref|YP_843905.1| 145 MPDPALGMDMDGRVIIWNRALEALTGVRKEEMLGKGNYECAIPFygyrrpvladlvlhgYDESMSREYRNLQRDGDVLTA 224
                                    79999999****************************99866666677777888888888999999*************** PP

                          PAS_4  69 leelll.pgeerhyelrllPlrdesGevigvlvisrDiTer 108
                                    + +  + ++e+ h+ l +  + d++G++ g+++++rDiTe 
  gi|116754787|ref|YP_843905.1| 225 EVFIPTfGPEGSHLWLKAALIYDSEGRIEGAIEVIRDITEN 265
                                    **9999999999999999*********************96 PP

  == domain 3  score: 48.7 bits;  conditional E-value: 7.3e-16
                          PAS_4   2 dslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgeerhy 81 
                                    + +p++++ +d+dg+ +++N++++ +fg+++e+++G+++ el pe+ ++++ +  r + +++  ++ ++ ++++ e r+ 
  gi|116754787|ref|YP_843905.1| 284 EGMPFLVCRFDRDGVLTFVNENYCNYFGFRREDIVGRSFLELIPEDEREAVLERFRGLTRERPYVTYTHRVKRGEEIRWQ 363
                                    7789**************************************************************************** PP

                          PAS_4  82 elrllPlrdesGevigvlvisrDiTerr 109
                                     ++ + ++  +Gev+ +  ++ DiT+++
  gi|116754787|ref|YP_843905.1| 364 RWTDRAIFGQNGEVLEYQSLGEDITAEK 391
                                    *************************986 PP

  == domain 4  score: 37.1 bits;  conditional E-value: 2.8e-12
                          PAS_4  10 vldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelll..pgeerhyelrllP 87 
                                    ++ +d r++y+N+a++e+ g++++el+G +++ ++ +edaa l   + r l+ge +  + e++    +g+ r++e     
  gi|116754787|ref|YP_843905.1| 416 AIMRDERFVYVNRAGEEMSGYSRDELIGAPVWMVVHPEDAAWLKKMYSRKLRGEPTPPRYEFRIItkNGDVRWVEYASGT 495
                                    44699***************************999999***************98766666666577************* PP

                          PAS_4  88 lrdesGevigvlvisrDiTerrr 110
                                    l  e G+ ++++++++DiTerr+
  gi|116754787|ref|YP_843905.1| 496 L--ELGGEMALIGTLIDITERRQ 516
                                    9..67888*************96 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.0   4.9e-11   5.2e-08       6      97 ..      14     106 ..      11     120 .. 0.82
   2 !   24.4   0.0   2.1e-08   2.2e-05       6      44 ..     141     179 ..     136     186 .. 0.94
   3 ?    1.5   0.0      0.26   2.8e+02      89     113 .]     238     262 ..     194     262 .. 0.73
   4 !   43.8   0.0     2e-14   2.1e-11       2      65 ..     278     341 ..     277     387 .. 0.81
   5 !   40.0   0.0     3e-13   3.2e-10       2     113 .]     403     511 ..     401     511 .. 0.87

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 4.9e-11
                                    HHHHSSSEEE...EEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-.ECCCCEEEEC CS
                            PAS   6 ileslpdpif...vvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgee.srageisfkl 81 
                                    il+sl  +++   vvDe+ +i y+N+a++ +lG+s +e++gks  d++h++d    + lle +++  e   +++e++f +
  gi|116754787|ref|YP_843905.1|  14 ILNSLGQGVVvskVVDERWIIEYANPAFAHMLGFSLSEIVGKSTEDFLHPDD---IPLLLESRAKRLEGlTTSYEVRFLR 90 
                                    6667666666223589999******************************998...8888887777766525678899999 PP

                                    TTSSEEEEEEEEEEEE CS
                            PAS  82 rdgrpihlevraspvr 97 
                                    +dg++++++++ +p++
  gi|116754787|ref|YP_843905.1|  91 KDGSIVPVLITGAPRI 106
                                    ***********99986 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 2.1e-08
                                    HHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTS CS
                            PAS   6 ileslpdpifvvDedgrilyvNaaaeellGlsreevlgk 44 
                                    ile +pdp ++ D dgr++ +N+a e l+G + ee+lgk
  gi|116754787|ref|YP_843905.1| 141 ILEFMPDPALGMDMDGRVIIWNRALEALTGVRKEEMLGK 179
                                    8889**********************************8 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.26
                                    EEEEEEEEEETTEEEEEEEEEEEES CS
                            PAS  89 levraspvrdaggeilgflgvlrdi 113
                                    l + a+ ++d +g+i g++ v+rdi
  gi|116754787|ref|YP_843905.1| 238 LWLKAALIYDSEGRIEGAIEVIRDI 262
                                    44578899****************8 PP

  == domain 4  score: 43.8 bits;  conditional E-value: 2e-14
                                    HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHH CS
                            PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleql 65 
                                    ++r+i+e +p  ++  D+dg+ ++vN++++  +G++re+++g+s+l+li+e++++ + e+++ l
  gi|116754787|ref|YP_843905.1| 278 RYRSIVEGMPFLVCRFDRDGVLTFVNENYCNYFGFRREDIVGRSFLELIPEDEREAVLERFRGL 341
                                    89**************************************************666666655533 PP

  == domain 5  score: 40.0 bits;  conditional E-value: 3e-13
                                    HHHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEEC CS
                            PAS   2 dlraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfkl 81 
                                    ++r + es++++i +  +d r++yvN+a ee+ G+sr+e++g ++ +++h+ed a l++ +++ l+    +  +e ++ +
  gi|116754787|ref|YP_843905.1| 403 RFRVLAESTAAGIAIM-RDERFVYVNRAGEEMSGYSRDELIGAPVWMVVHPEDAAWLKKMYSRKLRGEPTPPRYEFRIIT 481
                                    5677778888888888.*************************************************************** PP

                                    TTSSEEEEEEEEEEEEETTEEEEEEEEEEEES CS
                            PAS  82 rdgrpihlevraspvrdaggeilgflgvlrdi 113
                                    ++g ++++e     +++ gge+  ++g+l di
  gi|116754787|ref|YP_843905.1| 482 KNGDVRWVEYAS-GTLELGGEM-ALIGTLIDI 511
                                    777777777655.555555666.999999887 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.0   1.6e-14   1.7e-11       2      76 ..      35     106 ..      34     118 .. 0.89
   2 !   14.3   0.0   3.5e-05     0.036       2      68 ..     159     224 ..     158     243 .. 0.79
   3 !   33.9   0.3   2.6e-11   2.8e-08       2      86 ..     300     381 ..     299     383 .. 0.93
   4 !   46.5   0.0   3.1e-15   3.3e-12       2      69 ..     424     490 ..     423     507 .. 0.92
   5 ?   -1.5   0.0       3.1   3.2e+03      34      55 ..     656     677 ..     654     710 .. 0.79

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 1.6e-14
                          PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvir 76 
                                     y+++++ ++lG+s +e+ gk  s  d++hp+D++ + e+ ++ l++ +  + e+R++rkdG+++ v  ++ +  
  gi|116754787|ref|YP_843905.1|  35 EYANPAFAHMLGFSLSEIVGK--STEDFLHPDDIPLLLESRAKRLEGLT-TSYEVRFLRKDGSIVPVLITGAPRI 106
                                    599******************..**********************6666.899***************9999973 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 3.5e-05
                          PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeD..rervrealqeal.kkgepyegeyRirrkdGeyrwv 68 
                                    i ++++ e ++G+++ee+lgk    +++  p    r  v ++l  +l   +e+++ eyR +++dG++   
  gi|116754787|ref|YP_843905.1| 159 IIWNRALEALTGVRKEEMLGK--GNYECAIPFYgyRRPVLADL--VLhGYDESMSREYRNLQRDGDVLTA 224
                                    78*******************..89999999883344444444..442455599***********98765 PP

  == domain 3  score: 33.9 bits;  conditional E-value: 2.6e-11
                          PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkgepyegeyRirrkdGeyrwveararvirdengk 81 
                                    ++v+e++++++G+++e++ g+  s+l+l+  ++re v e +  +  + +py ++  ++++  e+rw +++ r+i+ +ng+
  gi|116754787|ref|YP_843905.1| 300 TFVNENYCNYFGFRREDIVGR--SFLELIPEDEREAVLERFRGLT-RERPYVTYTHRVKRGEEIRWQRWTDRAIFGQNGE 376
                                    689******************..******************9886.677899998999999******************* PP

                          PAS_3  82 pvrvi 86 
                                    +++++
  gi|116754787|ref|YP_843905.1| 377 VLEYQ 381
                                    *9987 PP

  == domain 4  score: 46.5 bits;  conditional E-value: 3.1e-15
                          PAS_3   2 iyvserveeilGyspeellgkveswldlvhpeDrervrealqealkkge.pyegeyRirrkdGeyrwve 69 
                                    +yv+++ ee+ Gys++el+g    + ++vhpeD + +++ + + l++   p   e+Ri++k+G++rwve
  gi|116754787|ref|YP_843905.1| 424 VYVNRAGEEMSGYSRDELIGA--PVWMVVHPEDAAWLKKMYSRKLRGEPtPPRYEFRIITKNGDVRWVE 490
                                    8********************..**********************6655688****************7 PP

  == domain 5  score: -1.5 bits;  conditional E-value: 3.1
                          PAS_3  34 Drervrealqealkkgepyege 55 
                                    Drer+ eal +++++  +y+ge
  gi|116754787|ref|YP_843905.1| 656 DRERLVEALVNLIDNSIKYTGE 677
                                    9999999*99999999999988 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   7.6e-09     8e-06       3      47 ..      11      61 ..       9      83 .. 0.76
   2 !   14.9   0.0     2e-05     0.021       2      42 ..     137     178 ..     136     200 .. 0.88
   3 !   26.7   0.1   3.9e-09   4.1e-06       1      58 [.     277     336 ..     277     345 .. 0.87
   4 !   31.2   0.0   1.5e-10   1.5e-07       2      46 ..     403     447 ..     402     463 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 7.6e-09
                          PAS_8  3 lralfesspdgiav...vdlgdrivdvNqaalellGys.adlkgellg..q 47
                                     ++++s+ +g++v   vd+ + i ++N+a++++lG+s  ++ g+      
  gi|116754787|ref|YP_843905.1| 11 AFQILNSLGQGVVVskvVDERWIIEYANPAFAHMLGFSlSEIVGKSTEdfL 61
                                   5689*********9887886568999***********99888888775333 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 2e-05
                          PAS_8   2 rlralfesspdgiavvdlgdrivdvNqaalellGys.adlkg 42 
                                    rl  ++e +pd+ +  d ++r++ +N+a + l+G++ ++++g
  gi|116754787|ref|YP_843905.1| 137 RLMDILEFMPDPALGMDMDGRVIIWNRALEALTGVRkEEMLG 178
                                    667799***********7778*************99777776 PP

  == domain 3  score: 26.7 bits;  conditional E-value: 3.9e-09
                          PAS_8   1 erlralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellgqllpvlrplle.d 58 
                                    +r+r+++e +p  ++ +d+++ +++vN+ ++  +G++ +d+ g  + +l+p+ + + + +
  gi|116754787|ref|YP_843905.1| 277 ARYRSIVEGMPFLVCRFDRDGVLTFVNENYCNYFGFRrEDIVGRSFLELIPEDEREAVlE 336
                                    69****************8788*************9999999999999999888877653 PP

  == domain 4  score: 31.2 bits;  conditional E-value: 1.5e-10
                          PAS_8   2 rlralfesspdgiavvdlgdrivdvNqaalellGys.adlkgellg 46 
                                    r+r l es + gia+   ++r+v+vN+a +e+ Gys ++l+g++++
  gi|116754787|ref|YP_843905.1| 403 RFRVLAESTAAGIAIMR-DERFVYVNRAGEEMSGYSrDELIGAPVW 447
                                    9*************875.358***************9999999986 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 !   74.6   0.0   7.6e-24     8e-21       2     110 ..     656     759 ..     655     761 .] 0.88

  Alignments for each domain:
  == domain 1  score: 74.6 bits;  conditional E-value: 7.6e-24
                                    HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHHH CS
                      HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsiv 81 
                                    d +rL +++ nl+dN++k+++++++  +ei     d v+ v+DnGiGip+++++k+f+ f++    + ++ gtG+Glsiv
  gi|116754787|ref|YP_843905.1| 656 DRERLVEALVNLIDNSIKYTGEDTRPVIEIF--YRDGVFCVRDNGIGIPESQREKVFDLFYK---VDPKSDGTGVGLSIV 730
                                    789****************776665555555..238**************************...668889********* PP

                                    HHHHHHTTTEEEEEEETTTEEEEEEEEES CS
                      HATPase_c  82 kklvelmgGeiwvesepgrGttftftlpl 110
                                    k+++e +gG+iw+es+    t f ftlp 
  gi|116754787|ref|YP_843905.1| 731 KRIIEVHGGRIWIESDGCSWTAFCFTLPV 759
                                    *************9999889999999985 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       8.5     9e+03      41      56 ..     128     143 ..     124     147 .. 0.82
   2 ?   -2.3   0.1       4.4   4.7e+03      23      51 ..     255     269 ..     250     284 .. 0.50
   3 !   41.2   0.1   1.2e-13   1.3e-10       4      65 ..     548     611 ..     545     612 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 8.5
                                    HHHHHHHHHHHHHHHH CS
                          HisKA  41 letiesearrldhlve 56 
                                    l++++++ rrl +++e
  gi|116754787|ref|YP_843905.1| 128 LRQLKNSQRRLMDILE 143
                                    7888899999999886 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.4
                                    HHHHHHC..T-HSSCHHHHHHHHHHHHHH CS
                          HisKA  23 naeaLkregklteelkeyletiesearrl 51 
                                    ++e++++    te++k+           l
  gi|116754787|ref|YP_843905.1| 255 AIEVIRD---ITENVKR-----------L 269
                                    4444444...2333333...........3 PP

  == domain 3  score: 41.2 bits;  conditional E-value: 1.2e-13
                                    HHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHH CS
                          HisKA   4 rflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdlsrie 65 
                                     f+ +v+H+Lr PL +i+g a + + +  + + e+ +e l+t++++ + +d+l+ d+L+lsri+
  gi|116754787|ref|YP_843905.1| 548 SFVYTVSHDLRRPLITISGLAGLAEFDleKGNLEKARESLRTVQRSCENMDALLRDILELSRIG 611
                                    699********************9444565678*****************************97 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.73   7.7e+02       1      45 [.      15      61 ..      15      65 .. 0.81
   2 ?    4.0   0.0     0.051        54      11      32 ..     152     173 ..     142     183 .. 0.81
   3 !   11.5   0.0   0.00023      0.25       8      46 ..     290     327 ..     283     395 .. 0.84
   4 ?    5.0   0.0     0.024        26      80     115 .]     481     519 ..     409     519 .. 0.64
   5 ?   -3.4   0.1       9.9     1e+04      57      75 ..     526     544 ..     522     552 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.73
                          PAS_7  1 lenmsqGis...vfDadlrLvawNrrylelldlpeelvqvgvpleell 45
                                   l+++ qG++   v+D++  +   N  + ++l+++ + + vg++ e++l
  gi|116754787|ref|YP_843905.1| 15 LNSLGQGVVvskVVDERWIIEYANPAFAHMLGFSLSEI-VGKSTEDFL 61
                                   6788899883345999999*************998888.788777765 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.051
                          PAS_7  11 fDadlrLvawNrrylelldlpe 32 
                                    +D d+r+++wNr    l ++ +
  gi|116754787|ref|YP_843905.1| 152 MDMDGRVIIWNRALEALTGVRK 173
                                    799**********999987765 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00023
                          PAS_7   8 isvfDadlrLvawNrrylelldlpeelvqvgvpleellr 46 
                                    ++ fD+d+ L+++N++y++ +++ +e + vg+++ el+ 
  gi|116754787|ref|YP_843905.1| 290 VCRFDRDGVLTFVNENYCNYFGFRREDI-VGRSFLELIP 327
                                    799***********************99.9999999885 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.024
                          PAS_7  80 rerpdgrvievrgnplpdgGfVt...tytDiTerrraee 115
                                     +  d r++e  + +l+ gG ++   t  DiTerr+aee
  gi|116754787|ref|YP_843905.1| 481 TKNGDVRWVEYASGTLELGGEMAligTLIDITERRQAEE 519
                                    34445577888888899888554333889*******996 PP

  == domain 5  score: -3.4 bits;  conditional E-value: 9.9
                          PAS_7  57 gdveaeverrlaaaragkp 75 
                                    ++ e++ve+r+a+++++++
  gi|116754787|ref|YP_843905.1| 526 ESLEQMVEERTAELEQRNA 544
                                    5567778888777776554 PP

>> PAS_11  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.0     0.007       7.4      27      83 ..      44      98 ..      37     113 .. 0.78
   2 ?    1.5   0.0       0.3   3.2e+02      11      60 ..     296     342 ..     289     356 .. 0.76
   3 !   11.4   0.0   0.00026      0.27      14      82 ..     423     488 ..     416     495 .. 0.79
   4 ?   -2.0   0.0       3.7   3.9e+03      58      85 ..     510     536 ..     504     552 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.007
                         PAS_11 27 slglekeelvgrsiydLchpqdlstlkshlrevissngeatsslyRLrlsqdkfvkv 83
                                    lg++ +e+vg+s  d++hp+d   l +   + +  +g +ts  +R+  +++ +v v
  gi|116754787|ref|YP_843905.1| 44 MLGFSLSEIVGKSTEDFLHPDDIPLLLESRAKRL--EGLTTSYEVRFLRKDGSIVPV 98
                                   56788889**************666555544444..577777778888888888776 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.3
                         PAS_11  11 dgkIisvDtsaLrasfslglekeelvgrsiydLchpqdlstlkshlrevi 60 
                                    dg  + v++   +     g+ +e++vgrs+ +L+ +++++ + + +r  +
  gi|116754787|ref|YP_843905.1| 296 DGVLTFVNE---NYCNYFGFRREDIVGRSFLELIPEDEREAVLERFRGLT 342
                                    555555555...5555668999************9999988888887655 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00026
                         PAS_11  14 IisvDtsaLrasfslglekeelvgrsiydLchpqdlstlkshlrevissngeatsslyRLrl..sqdkfvk 82 
                                    ++ v++    ++   g++++el+g  ++  +hp+d  +lk+ ++  +  +ge t + y +r+  +++++ +
  gi|116754787|ref|YP_843905.1| 423 FVYVNR---AGEEMSGYSRDELIGAPVWMVVHPEDAAWLKKMYSRKL--RGEPTPPRYEFRIitKNGDVRW 488
                                    666666...666678999*************************9988..8888888865554337776655 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 3.7
                         PAS_11  58 evissngeatsslyRLrlsqdkfvkvkt 85 
                                    +++ ++++a++ l R++ s +++v+ +t
  gi|116754787|ref|YP_843905.1| 510 DIT-ERRQAEEELRRFKESLEQMVEERT 536
                                    566.777888888888877777776665 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0    0.0011       1.2       2      25 ..     237     260 ..     236     264 .. 0.89
   2 ?   -2.2   0.1       6.7   7.1e+03      11      29 ..     380     398 ..     378     401 .. 0.85
   3 ?    3.6   0.0     0.093        98      12      27 ..     575     590 ..     566     596 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0011
                                    CHHHHHHHHHHHTT-HHHHHHHHH CS
                          TPR_8   2 eayynlgsiylklgdyeeAkeyye 25 
                                    +++++ ++iy++ g++e A+e+++
  gi|116754787|ref|YP_843905.1| 237 HLWLKAALIYDSEGRIEGAIEVIR 260
                                    689******************987 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.7
                                    HHHTT-HHHHHHHHHHHHH CS
                          TPR_8  11 ylklgdyeeAkeyyekale 29 
                                    y++lg+   A++ +e al+
  gi|116754787|ref|YP_843905.1| 380 YQSLGEDITAEKNMEDALR 398
                                    8999999999999999986 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.093
                                    HHTT-HHHHHHHHHHH CS
                          TPR_8  12 lklgdyeeAkeyyeka 27 
                                    l++g++e+A e+++ +
  gi|116754787|ref|YP_843905.1| 575 LEKGNLEKARESLRTV 590
                                    689*********9976 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.4e-05     0.015       4      56 ..     661     712 ..     658     727 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.4e-05
                    HATPase_c_3   4 ekAlaelvdNsld..Adaen..vkievnknrgktgeivieDdGkGmseeelknalrl 56 
                                     +Al+ l+dNs+   ++ ++  ++i + +     g ++++D+G G++e++ ++++ l
  gi|116754787|ref|YP_843905.1| 661 VEALVNLIDNSIKytGEDTRpvIEIFYRD-----GVFCVRDNGIGIPESQREKVFDL 712
                                    58*********984455555555555555.....69************999888874 PP

>> MEKHLA  MEKHLA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.062        66      38      91 ..      21      78 ..       4      88 .. 0.83
   2 ?   -2.3   0.0       3.5   3.7e+03      41      91 ..     289     336 ..     285     343 .. 0.72
   3 ?    7.7   0.0     0.003       3.2      35      83 ..     401     455 ..     380     468 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.062
                         MEKHLA 38 favlshslkadpvfnyaNqaaldllettweeltdlpsrksaepee....keeRealLe 91
                                    +v+s  ++++ +  yaN a  ++l ++++e++  + +  ++p++     e+R++ Le
  gi|116754787|ref|YP_843905.1| 21 GVVVSKVVDERWIIEYANPAFAHMLGFSLSEIVGKSTEDFLHPDDipllLESRAKRLE 78
                                   589999999999**********************999999998876666556666666 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.5
                         MEKHLA  41 lshslkadpvfnyaNqaaldllettweeltdlpsrksaepeekeeRealLe 91 
                                    l + +++d v+++ N++  + + ++ e+++  +  + + +   +eRea Le
  gi|116754787|ref|YP_843905.1| 289 LVCRFDRDGVLTFVNENYCNYFGFRREDIVGRSFLELIPE---DEREAVLE 336
                                    6688889999999999999999999888887666555553...44444544 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.003
                         MEKHLA  35 eapfavlshslkad......pvfnyaNqaaldllettweeltdlpsrksaepeek 83 
                                    e+ f vl+ s++a         f+y N+a+ ++  ++ +el+  p+  +++pe+ 
  gi|116754787|ref|YP_843905.1| 401 EHRFRVLAESTAAGiaimrdERFVYVNRAGEEMSGYSRDELIGAPVWMVVHPEDA 455
                                    57777777777765555555*************************9999997764 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0       0.3   3.2e+02      23      54 ..     234     265 ..     232     277 .. 0.86
   2 ?   10.2   0.1   0.00079      0.83      29      54 ..     568     593 ..     565     605 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.3
                         TPR_19  23 knaearllLAeallalgqldeAealLdalpee 54 
                                    + + ++l  A ++ + g+++ A++++ ++ e 
  gi|116754787|ref|YP_843905.1| 234 EGSHLWLKAALIYDSEGRIEGAIEVIRDITEN 265
                                    556788888999**************999875 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00079
                         TPR_19  29 llLAeallalgqldeAealLdalpee 54 
                                    ++LAe  l+ g+l++A++ L +++++
  gi|116754787|ref|YP_843905.1| 568 AGLAEFDLEKGNLEKARESLRTVQRS 593
                                    68*******************99876 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0085         9       3      29 ..     238     264 ..     236     274 .. 0.91
   2 ?    6.2   0.1     0.022        23       5      37 ..     568     600 ..     565     609 .. 0.82
   3 ?   -1.3   0.1       5.5   5.8e+03      18      32 ..     627     641 ..     626     649 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0085
                         TPR_14   3 allalaeallalGdpdeAiallrrala 29 
                                    ++l++a ++   G+ ++Ai++ r++ +
  gi|116754787|ref|YP_843905.1| 238 LWLKAALIYDSEGRIEGAIEVIRDITE 264
                                    8**********************9876 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.022
                         TPR_14   5 lalaeallalGdpdeAiallrralalaPddaea 37 
                                    + lae+ l+ G++++A++ lr + + + + +++
  gi|116754787|ref|YP_843905.1| 568 AGLAEFDLEKGNLEKARESLRTVQRSCENMDAL 600
                                    6799*****************987777766555 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 5.5
                         TPR_14  18 deAiallrralalaP 32 
                                    +eAi+ l +a+++  
  gi|116754787|ref|YP_843905.1| 627 REAIDQLAEAVKKRS 641
                                    589999999998654 PP

>> DASH_Duo1  DASH complex subunit Duo1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.91   9.6e+02      21      42 ..     250     271 ..     243     274 .. 0.60
   2 ?   -1.8   0.1       2.5   2.7e+03       8      21 ..     520     533 ..     515     554 .. 0.56
   3 ?    9.6   0.0   0.00071      0.75      21      45 ..     578     602 ..     574     605 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.91
                      DASH_Duo1  21 esLkkaksniervketvestnt 42 
                                    + ++ a + i  ++e+v+  n+
  gi|116754787|ref|YP_843905.1| 250 GRIEGAIEVIRDITENVKRLNA 271
                                    5556666666666666666555 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.5
                      DASH_Duo1   8 qLrkinevienvie 21 
                                    +Lr++ e +e+++e
  gi|116754787|ref|YP_843905.1| 520 ELRRFKESLEQMVE 533
                                    44444444444433 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00071
                      DASH_Duo1  21 esLkkaksniervketvestntLLd 45 
                                    ++L+ka++ + +v++++e++++LL 
  gi|116754787|ref|YP_843905.1| 578 GNLEKARESLRTVQRSCENMDALLR 602
                                    689********************95 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00019       0.2       6      90 ..     660     746 ..     655     755 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00019
                    HATPase_c_5   6 lcvilgnlLdNAieacskieeekrfIrltvrekk...ksliisieNsyegek.kklesskskkeehGiGlksireivkky 81 
                                    l+  l nl+dN+i    + +  +++I++  r      ++  i i  s +++  + + +   k++  G+Gl+ +++i++ +
  gi|116754787|ref|YP_843905.1| 660 LVEALVNLIDNSIKYTGEDT--RPVIEIFYRDGVfcvRDNGIGIPESQREKVfDLFYKVDPKSDGTGVGLSIVKRIIEVH 737
                                    66678888888888777644..7888776554322222233333333333443334466889999*************** PP

                    HATPase_c_5  82 kgnlsieae 90 
                                    +g ++ie +
  gi|116754787|ref|YP_843905.1| 738 GGRIWIESD 746
                                    *****9986 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 ?    9.2   2.0    0.0018       1.9      28      63 ..     513     548 ..     510     558 .. 0.83
   2 ?   -0.0   0.1       1.3   1.4e+03      61      89 ..     573     601 ..     570     606 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0018
                 HIP1_clath_bdg  28 ekkeleeelerlkeeaerkleeqkeelekLkrelea 63 
                                    e+++ eeel+r+ke+ e+++ee++ ele+ ++e+e+
  gi|116754787|ref|YP_843905.1| 513 ERRQAEEELRRFKESLEQMVEERTAELEQRNAEIES 548
                                    688889999999999999999999999988888775 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.3
                 HIP1_clath_bdg  61 leakraelarlkssLesseqsgeqlssql 89 
                                    +  ++ +l+++++sL++ ++s e++ + l
  gi|116754787|ref|YP_843905.1| 573 FDLEKGNLEKARESLRTVQRSCENMDALL 601
                                    55677888889999998888888877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (761 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       934  (0.0520944); expected 358.6 (0.02)
Passed bias filter:                      786  (0.0438396); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); 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: 0.74u 0.26s 00:00:01.00 Elapsed: 00:00:00.43
# Mc/sec: 5347.31
//
Query:       gi|116754788|ref|YP_843906.1|  [L=118]
Description: hypothetical protein Mthe_1494 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      7e-38  129.1   0.0      8e-38  128.9   0.0    1.0  1  Cyclophil_like   Cyclophilin-like
      4e-07   30.0   0.0    5.3e-07   29.6   0.0    1.3  1  Cyclophil_like2  Cyclophilin-like family
     0.0038   16.9   0.0     0.0057   16.3   0.0    1.5  1  DUF3830          Protein of unknown function (DUF3830)


Domain annotation for each model (and alignments):
>> Cyclophil_like  Cyclophilin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.9   0.0   1.3e-41     8e-38       1     119 []       2     115 ..       2     115 .. 0.98

  Alignments for each domain:
  == domain 1  score: 128.9 bits;  conditional E-value: 1.3e-41
                                    EEEEEEET.TEEEEEEEETT..HHHHHHHHC-SEEEEEEECTTEEEEE-S-----SSSEESSB-TTEEEEECCCTEEEEE CS
                 Cyclophil_like   1 kkikidie.sseveveLddt..etaraikealPiesrvntWgeEiYfstpvklekeenakevveagdiaywppGkalclf 77 
                                    ++i+idi+  +++++eLd++  +t++a+++alPie+r+++WgeE+Yf t++ +e +en++++++agdi+yw pG+a+c+f
  gi|116754788|ref|YP_843906.1|   2 RRIEIDIQgFGRAIAELDGRnpQTSEAVWNALPIEGRAMLWGEEVYFGTSLICE-DENPSPSATAGDISYWVPGHAICIF 80 
                                    589****999********9999********************************.************************* PP

                                    SS--TT-TTSB--SSSEEEEEEEEC-GGGGGG--TTEEEEEE CS
                 Cyclophil_like  78 fGktPisddeirpaspvnviGrivedlellkkvkdgekvrve 119
                                    fG+t       +p+spvn+iGri+e+l ++++vk+g++++++
  gi|116754788|ref|YP_843906.1|  81 FGRT-------QPYSPVNHIGRISEGLGIFTSVKEGAEIVLR 115
                                    ****.......***************************9875 PP

>> Cyclophil_like2  Cyclophilin-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   8.9e-11   5.3e-07      38     103 ..      45     105 ..      12     115 .. 0.73

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 8.9e-11
                Cyclophil_like2  38 EkiaylpeklptddapegssikaGdlayyapwgnlvlfykdfeesysygltrlGrieedaeelaea 103
                                    E   y++ +l  +d++ + s++aGd+ y+ p++ +++f++ ++   ++ + ++Gri+e + ++ + 
  gi|116754788|ref|YP_843906.1|  45 EV--YFGTSLICEDENPSPSATAGDISYWVPGHAICIFFGRTQP--YSPVNHIGRISE-GLGIFTS 105
                                    44..4567788888867789999*******************66..899*******44.6666444 PP

>> DUF3830  Protein of unknown function (DUF3830)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   9.6e-07    0.0057       3      75 ..       6      71 ..       4     106 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9.6e-07
                                   ETTTTEEEEEEE-TTTSHHHHHHHHHH--EEEE-EE-SSSSSEEEEEEE--SSS---S-SEESS--TTEEEEE CS
                        DUF3830  3 lekrgvsataeLledkAPetcaavwealplssdviHakyagneiyvllpefaatelpaENaTvtPipGdvvlf 75
                                   ++++g    +  l+ + P+t++avw+alp+++ ++     g+e+y     +       EN+    + Gd+ ++
  gi|116754788|ref|YP_843906.1|  6 IDIQGFGRAIAELDGRNPQTSEAVWNALPIEGRAM---LWGEEVYFGTSLIC----EDENPSPSATAGDISYW 71
                                   56666655566678899***************976...55889988877776....45666666666777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       179  (0.00998383); expected 358.6 (0.02)
Passed bias filter:                      179  (0.00998383); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 948.50
//
Query:       gi|116754789|ref|YP_843907.1|  [L=539]
Description: phenylalanyl-tRNA synthetase subunit beta [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.7e-39  133.8   0.0    8.2e-39  133.3   0.0    1.2  1  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
    1.1e-16   60.8   0.0    5.6e-16   58.6   0.0    2.1  2  B5               tRNA synthetase B5 domain
    4.1e-12   46.1   0.0    6.7e-12   45.4   0.0    1.3  1  B3_4             B3/4 domain
    0.00049   19.6   0.1      0.004   16.7   0.0    2.2  2  tRNA-synt_2d     tRNA synthetases class II core domain (F)
  ------ inclusion threshold ------
      0.057   13.6   0.0       0.44   10.8   0.0    2.4  3  PhetRS_B1        Phe-tRNA synthetase beta subunit B1 domain


Domain annotation for each model (and alignments):
>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.3   0.0   2.3e-42   8.2e-39       3     214 .]     347     537 ..     345     537 .. 0.96

  Alignments for each domain:
  == domain 1  score: 133.3 bits;  conditional E-value: 2.3e-42
                tRNA_synthFbeta   3 stlPkapttegelnkeqklrrklrdllagaGlnEvitysfvsekeldklleddderkavelanPlsedqsvlRtsLlpgl 82 
                                      +P++ t ++ +++ ++l++++rdl++g+G+ Ev+ +++++ek+  +++ + +  +  ++ +P+se ++++Rt +lpgl
  gi|116754789|ref|YP_843907.1| 347 AEMPRTLTIGR-PHPMEELKDEVRDLMVGLGYLEVMPFTLTNEKVHFEMM-RRSAGECTRVMHPISELHTIIRTAVLPGL 424
                                    57888888888.99***********************************6.668999*********************** PP

                tRNA_synthFbeta  83 LevlarNlargnedvrlFEigkvflkdseeelpeeerhlaivltgkreeeswsekaravdfydlkgivealleslgiekv 162
                                    +e l+ N+++ ++  rlF +g+v++        + + hl++v  ++            ++f+++  +v a++++l+i + 
  gi|116754789|ref|YP_843907.1| 425 MEILSLNQHHALP-QRLFAVGDVVIDG------RTKCHLSAVSIHSG-----------AGFAEISSLVSAIMRELRI-SA 485
                                    *************.*************......889***********...........*******************.** PP

                tRNA_synthFbeta 163 efepaehpalhpgrsAeikvdgkevGvlGelhpevleafdlkqrvyvfEldl 214
                                    e++++++ a+ pgr A+++++g ++G++Ge+hpev  af+l+++v+++El+l
  gi|116754789|ref|YP_843907.1| 486 EVVESSDGAFIPGRGADLMLNGARIGCFGEIHPEVISAFGLEHPVVGMELEL 537
                                    **************************************************87 PP

>> B5  tRNA synthetase B5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.69   2.5e+03      10      55 ..      13      57 ..       4      60 .. 0.70
   2 !   58.6   0.0   1.6e-19   5.6e-16       3      67 .]     278     342 ..     276     342 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.69
                                   HHHTS---HHHHHHHHHHTT-E..EESSTTCEEEE--TT-TT--SHH CS
                                   xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                             B5 10 kllGidlseeeiikiLkrlgce.riekdkdlllVtvPswRsDleree 55
                                   +++G   s+e ii+ L  +g +  ++ ++d ++V+  + R+Dl  +e
  gi|116754789|ref|YP_843907.1| 13 EMVG--ASRELIIERLPMMGADiGKSPEADYIDVEFFPDRPDLYSAE 57
                                   5555..47788888999998874346788888998777798987665 PP

  == domain 2  score: 58.6 bits;  conditional E-value: 1.6e-19
                                    EEHHHHHHHHTS---HHHHHHHHHHTT-E.EESSTTCEEEE--TT-TT--SHHHHHHHHHHHH-G CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             B5   3 lrvekinkllGidlseeeiikiLkrlgceriekdkdlllVtvPswRsDlereeDliEEvaRlyGY 67 
                                    ++ +++n+l+G +ls+ee +++L+r+ + +   d+d ++V vP++R D+ + +D+iE+ a  yGY
  gi|116754789|ref|YP_843907.1| 278 VTTSEANSLIGFNLSAEELAECLRRMRFGARHLDNDSVEVLVPAYRADIMHTWDIIEDAAKSYGY 342
                                    78899***********************************************************9 PP

>> B3_4  B3/4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   0.0   1.9e-15   6.7e-12      35     131 ..     113     236 ..      95     251 .. 0.89

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 1.9e-15
                                    --HHHHHHHHHHHHHT-.....-EEEEEGGGTBTEEE.EEE--TTEEEEBTTS-EEEE.-T................... CS
                           B3_4  35 innvVDitNyvmlelgq.....PlhafDldkiqgdiv.vrlakegeklvtldgkerel.de................... 88 
                                    i+++  +++ ++  lg+     +++++D++++ ++++ ++  +++ ++v+ld +e    +e                   
  gi|116754789|ref|YP_843907.1| 113 IESLMSLQEDLHWGLGRnrrkvAIGVHDISRVRPPFRyIAEDPDKRRFVPLDFDESMSmREilerhpkgvayrhildgfe 192
                                    7778888888999999999999*****************************8664444377999**************** PP

                                    TSEEEETEEEEE.EETTTEEBTTTB--TT--EEEEEEEE--HHH CS
                           B3_4  89 edlviadsekpv.slagvmggeeskvsedTknvfleaaafdpvs 131
                                    + ++i+d++++v s ++v++ge ++v edT++ f+ +++ dpv+
  gi|116754789|ref|YP_843907.1| 193 RFPLIVDADDNVlSFPPVINGELTRVREDTTDLFIDVTGTDPVV 236
                                    **********999****************************965 PP

>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.1e-06     0.004       8     110 ..     350     446 ..     343     468 .. 0.89
   2 ?    0.1   0.0      0.13   4.7e+02     189     213 ..     510     534 ..     506     539 .] 0.80

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.1e-06
                                    TSCTSHSB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-ECESEEE-SST CS
                   tRNA-synt_2d   8 gkrieagklhpltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpekaveekllLRtht 87 
                                     + ++ g+ hp++++++e++++++ lg+ ev    + +e   f+++  +  +  R m+    l         ++++Rt  
  gi|116754789|ref|YP_843907.1| 350 PRTLTIGRPHPMEELKDEVRDLMVGLGYLEVMPFTLTNEKVHFEMMRRSAGECTRVMHPISEL---------HTIIRTAV 420
                                    466788999************************************************976555.........6899**99 PP

                                    HHHHHHHH...TTS-SSEEEEEEEEE CS
                   tRNA-synt_2d  88 tavqirtl...ekkkppikiisigrv 110
                                     +  +  l   +++ +p++++++g v
  gi|116754789|ref|YP_843907.1| 421 LPGLMEILslnQHHALPQRLFAVGDV 446
                                    9999999888888899*****99977 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.13
                                    EEEEEEE-HHHHHHTT-.TTSEEEE CS
                   tRNA-synt_2d 189 llgaGmvrpevleavgideevsgfa 213
                                    ++ +G ++pev++a+g+++ v g+ 
  gi|116754789|ref|YP_843907.1| 510 IGCFGEIHPEVISAFGLEHPVVGME 534
                                    677899***********77776665 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 ?   -2.9   0.0       2.2     8e+03       1      17 [.       1      17 [.       1      29 [. 0.86
   2 ?   10.8   0.0   0.00012      0.44      52      82 ..      38      68 ..      29      69 .. 0.86
   3 ?   -1.1   0.0      0.65   2.3e+03      52      69 ..     311     328 ..     288     335 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.2
                      PhetRS_B1  1 MPtisvkkeaLfkalgk 17
                                   MP++ +  e+L + +g 
  gi|116754789|ref|YP_843907.1|  1 MPVVRLYYEDLEEMVGA 17
                                   99999999999999885 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00012
                      PhetRS_B1 52 eeviykidipAnryDLLcleglaralkvFlg 82
                                   e  ++ ++    r+DL ++eg+aral+ Flg
  gi|116754789|ref|YP_843907.1| 38 EADYIDVEFFPDRPDLYSAEGVARALQGFLG 68
                                   567788999999***************9986 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.65
                      PhetRS_B1  52 eeviykidipAnryDLLc 69 
                                    ++  + + +pA r D++ 
  gi|116754789|ref|YP_843907.1| 311 DNDSVEVLVPAYRADIMH 328
                                    556677889999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (539 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); 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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.38
# Mc/sec: 4259.37
//
Query:       gi|116754790|ref|YP_843908.1|  [L=493]
Description: phenylalanyl-tRNA synthetase subunit alpha [Methanosaeta thermophila PT]
Scores for complete 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-94  314.1   0.0    7.6e-94  313.8   0.0    1.1  1  tRNA-synt_2d     tRNA synthetases class II core domain (F)
    1.8e-10   40.6   0.0    6.9e-10   38.7   0.0    1.8  1  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
      2e-08   34.1   0.0     0.0035   17.3   0.0    2.3  2  HTH_45           Winged helix-turn-helix
    0.00015   22.0   0.0    0.00062   20.0   0.0    2.1  2  PheRS_DBD3       PheRS DNA binding domain 3
    0.00017   21.3   0.0       0.35   10.7   0.0    2.5  2  DUF1495          Winged helix DNA-binding domain (DUF1495)
    0.00033   20.2   0.3    0.00078   19.0   0.3    1.7  1  HTH_24           Winged helix-turn-helix DNA-binding
    0.00045   20.0   0.0      0.047   13.5   0.0    2.2  2  DUF4364          Domain of unknown function (DUF4364)
     0.0012   19.3   0.1          2    9.0   0.0    2.5  2  HTH_27           Winged helix DNA-binding domain
     0.0018   17.5   0.1      0.021   13.9   0.0    2.5  3  tRNA-synt_2      tRNA synthetases class II (D, K and N)
     0.0023   18.0   0.2        3.5    7.8   0.0    3.5  3  Mrr_N            Mrr N-terminal domain
  ------ inclusion threshold ------
      0.016   14.8   0.0      0.046   13.3   0.0    1.7  1  GerE             Bacterial regulatory proteins, luxR family
      0.016   14.7   0.1      0.032   13.8   0.1    1.5  1  HTH_47           winged helix-turn-helix
      0.018   14.8   0.1       0.34   10.6   0.0    2.2  2  DUF4423          Domain of unknown function (DUF4423)
      0.028   14.5   0.3       0.14   12.3   0.1    2.3  2  HTH_20           Helix-turn-helix domain
      0.032   14.1   0.4       0.61   10.0   0.1    2.5  2  MarR_2           MarR family
      0.035   14.0   0.0        2.7    8.0   0.0    2.6  2  TrmB             Sugar-specific transcriptional regulator Trm
      0.097   12.7   0.1       0.34   10.9   0.0    1.9  2  HTH_Crp_2        Crp-like helix-turn-helix domain
      0.098   12.6   0.1        1.2    9.2   0.0    2.4  2  MarR             MarR family
       0.14   12.7   0.1       0.45   11.1   0.0    1.9  1  AAA_assoc_C      C-terminal AAA-associated domain
       0.18   12.0   0.0        9.2    6.5   0.0    2.4  2  HTH_34           Winged helix DNA-binding domain
       0.19   11.9   0.0        1.5    9.0   0.0    2.2  2  DUF2250          Uncharacterized protein conserved in archaea


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 !  313.8   0.0   8.9e-97   7.6e-94       2     244 ..     219     484 ..     218     485 .. 0.98

  Alignments for each domain:
  == domain 1  score: 313.8 bits;  conditional E-value: 8.9e-97
                                    .-TSSCTSCTSHSB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-..... CS
                   tRNA-synt_2d   2 idvtlpgkrieagklhpltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpeka..... 76 
                                    ++v +pg+ i++gk+hp++++++++++i+le+gf+e++g+ ++s+f+nfdaL++pqdhpaR+mqdtFyl++ +++     
  gi|116754790|ref|YP_843908.1| 219 YNVRVPGETIYPGKIHPYRRLMDRMRRIMLEMGFTEIKGEIIQSSFWNFDALFQPQDHPAREMQDTFYLDSRAEIpdyrs 298
                                    8********************************************************************888877***** PP

                                    .......................ECESEEE-SSTHHHHHHHH.TTS-SSEEEEEEEEEEBSST-SSSB-SEEEEEEEEEE CS
                   tRNA-synt_2d  77 .......................veekllLRthttavqirtl.ekkkppikiisigrvfRrdavDathlaeFhqveglvv 132
                                                           ++++ +LRthtta++i++l ++++pp+k ++i+rv+Rr+a+Dath++eF q+eg+v+
  gi|116754790|ref|YP_843908.1| 299 vkemhehggrigstgwggvwdpeIARQEVLRTHTTAITIKYLaDNPDPPVKAFCIDRVYRREAIDATHTPEFEQLEGVVM 378
                                    ***********************999****************99999********************************* PP

                                    ETT--HHHHHHHHHHHHHHHCTSTEEEEEEECEETTEEEEEEEEEEECCSSSSEEEEEEEEEE-HHHHHHTT-.TTSEEE CS
                   tRNA-synt_2d 133 denvsladlkgvleellkklfgaevkvrfrpsyfpftePsaevdvylvekkkkwlEllgaGmvrpevleavgideevsgf 212
                                    d++v++++l+g+l+e+++k+ g+e +vrfrp yfp+tePs+e +v++  ++ +w+El+gaG++r ev++++gi  e +++
  gi|116754790|ref|YP_843908.1| 379 DRGVTFSNLLGILKEFYSKM-GFE-EVRFRPGYFPYTEPSVEPEVWI--DGLGWVELGGAGVFRREVTAPFGI--EHPVL 452
                                    ********************.***.**********************..************************..***** PP

                                    EEEEEHHHHHHHHHT-SSGHHHHTT.HHHHGG CS
                   tRNA-synt_2d 213 afGlGveRlamlkygieDiRelvendlrflrq 244
                                    a+GlGv Rlaml++g++D+R l+++d+ +lr+
  gi|116754790|ref|YP_843908.1| 453 AWGLGVSRLAMLRLGLKDLRLLYQPDIGWLRD 484
                                    *****************************986 PP

>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   0.0   8.1e-13   6.9e-10       4     209 ..     222     453 ..     220     457 .. 0.90

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 8.1e-13
                tRNA_synthFbeta   4 tlPkapttegelnkeqklrrklrdllagaGlnE....vitysfvsekeldklleddderk.................... 59 
                                    ++P +++ +g+ ++ ++l +++r+++ ++G++E    +i +sf + + l +  +d++ r+                    
  gi|116754790|ref|YP_843908.1| 222 RVPGETIYPGKIHPYRRLMDRMRRIMLEMGFTEikgeIIQSSFWNFDALFQP-QDHPAREmqdtfyldsraeipdyrsvk 300
                                    578999999**********************972222578888888888777.5656666889***************** PP

                tRNA_synthFbeta  60 .............avelanPlsedqsvlRtsLlpglLevlarNlargnedvrlFEigkvflkd.seeelpeeerhlaivl 125
                                                    +  P  + q+vlRt  ++  ++ la N     + v++F i +v++ +  + +   e ++l +v+
  gi|116754790|ref|YP_843908.1| 301 emhehggrigstgWGGVWDPEIARQEVLRTHTTAITIKYLADNP---DPPVKAFCIDRVYRREaIDATHTPEFEQLEGVV 377
                                    *************9999*****************9999999985...56677***********97778999********* PP

                tRNA_synthFbeta 126 tgkreeeswsekaravdfydlkgivealleslgiekvefepaehpalhpgrsAeikvdgk...evGvlGelhpevleafd 202
                                    + +            v f +l gi++++ +++g+e+v+f+p   p+ +p    e+ +dg    e+G +G +  ev + f+
  gi|116754790|ref|YP_843908.1| 378 MDRG-----------VTFSNLLGILKEFYSKMGFEEVRFRPGYFPYTEPSVEPEVWIDGLgwvELGGAGVFRREVTAPFG 446
                                    ****...........******************************************996666***************** PP

                tRNA_synthFbeta 203 lkqrvyv 209
                                    ++++v +
  gi|116754790|ref|YP_843908.1| 447 IEHPVLA 453
                                    ***9986 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   4.1e-06    0.0035      10      67 ..       8      68 ..       7      76 .. 0.92
   2 !   14.4   0.0   3.2e-05     0.027      36      74 ..     142     183 ..     130     186 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.1e-06
                         HTH_45 10 dILeaisegeakkTkimykanLsykllnkYLdmLvekgli...kkskekYvlTekGlelle 67
                                    ILeais+g++++ +i  + n++ + + +  + L e gli   k   e ++lTe+G+++ +
  gi|116754790|ref|YP_843908.1|  8 RILEAISDGCSNPQEIADRLNIKIEAVLSAAESLAESGLIsvdKRVIERFSLTEEGRRYAH 68
                                   59**************************************776667899*******99865 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 3.2e-05
                         HTH_45  36 lnkYLdmLvekgli...kkskekYvlTekGlelleklkelee 74 
                                    l + +d L+++gl+   + ++  Y++T+ G+++l++ ke+++
  gi|116754790|ref|YP_843908.1| 142 LGSAIDLLIKRGLVapeRSKSWRYEITDAGKQVLSQSKEIIS 183
                                    556799********997778899**************99976 PP

>> PheRS_DBD3  PheRS DNA binding domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   7.2e-07   0.00062       2      48 ..      72     112 ..      72     117 .. 0.85
   2 ?   -2.5   0.0       7.9   6.7e+03      41      54 ..     427     439 ..     426     442 .. 0.63

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 7.2e-07
                     PheRS_DBD3   2 hEarvfaavppeggisqkelkklggdpvakiGfskAmknkWikkdkg 48 
                                    +E r+ +++   +g + +el    +dp  ki+++ A k++W+++dkg
  gi|116754790|ref|YP_843908.1|  72 PERRLIEMI-G-EGKPVSEL----QDPALKIAIGWARKKGWVRIDKG 112
                                    788999999.6.67999999....3366****************997 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 7.9
                     PheRS_DBD3  41 kWikkdkgdgkvvr 54 
                                    +W+++  g g + r
  gi|116754790|ref|YP_843908.1| 427 GWVEL-GGAGVFRR 439
                                    8****.44444555 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 !   10.7   0.0   0.00041      0.35      54      88 ..      36      68 ..      10      69 .. 0.92
   2 !    8.0   0.0    0.0028       2.4      58      87 ..     148     175 ..     127     177 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00041
                        DUF1495 54 nsessLielGLveeeeeseglklYklteeGieive 88
                                   ++++sL e GL++   +++ ++ ++lteeG+++++
  gi|116754790|ref|YP_843908.1| 36 SAAESLAESGLIS--VDKRVIERFSLTEEGRRYAH 68
                                   6789********6..7999*************985 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0028
                        DUF1495  58 sLielGLveeeeeseglklYklteeGieiv 87 
                                     Li++GLv+   e++    Y++t+ G+++ 
  gi|116754790|ref|YP_843908.1| 148 LLIKRGLVA--PERSKSWRYEITDAGKQVL 175
                                    49******6..57777789*******9985 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 !   19.0   0.3   9.1e-07   0.00078       3      47 ..       4      47 ..       3      48 .. 0.96

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 9.1e-07
                         HTH_24  3 etdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                   e d++ILe++ + +  + +e+A+rl++ + +v+   + L e+GlI
  gi|116754790|ref|YP_843908.1|  4 ERDLRILEAISD-GCSNPQEIADRLNIKIEAVLSAAESLAESGLI 47
                                   789*******99.99*****************************9 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0      0.04        34      39      70 ..      37      67 ..      32      71 .. 0.86
   2 !   13.5   0.0   5.4e-05     0.047      36      80 ..     142     185 ..     140     203 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.04
                        DUF4364 39 alseLvesglieeeekenktlykiTekGketl 70
                                   a + L esgli++ +k+  +++++Te+G++ +
  gi|116754790|ref|YP_843908.1| 37 AAESLAESGLISV-DKRVIERFSLTEEGRRYA 67
                                   66789*******8.669***********9876 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 5.4e-05
                        DUF4364  36 lqqalseLvesglieeeekenktlykiTekGketlelfenripks 80 
                                    l +a++ L++ gl+  e ++++ +y+iT++Gk++l++ ++ i+k+
  gi|116754790|ref|YP_843908.1| 142 LGSAIDLLIKRGLVAPE-RSKSWRYEITDAGKQVLSQSKEIISKT 185
                                    5679999********85.5999******************99987 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0057       4.8      22      68 .]      21      63 ..       4      63 .. 0.86
   2 !    9.0   0.0    0.0023         2      37      68 .]     144     171 ..     137     171 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0057
                         HTH_27 22 adlcgrlnvedshisyslkkLtekGLvertgdeadrre.krvrlTdkG 68
                                    ++++rln+   ++ ++ + L e GL+       d+r   r++lT++G
  gi|116754790|ref|YP_843908.1| 21 QEIADRLNIKIEAVLSAAESLAESGLI-----SVDKRViERFSLTEEG 63
                                   799************************.....46788889******99 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0023
                         HTH_27  37 yslkkLtekGLvertgdeadrre..krvrlTdkG 68 
                                    ++++ L+++GLv      a+ r+   r+++Td+G
  gi|116754790|ref|YP_843908.1| 144 SAIDLLIKRGLV------APERSksWRYEITDAG 171
                                    799*********......55555448******99 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 ?   -0.1   0.0      0.46   3.9e+02      28      52 ..     239     263 ..     234     289 .. 0.81
   2 !   13.9   0.0   2.5e-05     0.021      93     119 ..     349     374 ..     348     392 .. 0.94
   3 ?   -2.0   0.0       1.7   1.5e+03     287     305 ..     454     472 ..     450     475 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.46
                                    HHHHHHHHHHHTT-EE----SEESS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2  28 vtkavrkyleengfieietPiLsks 52 
                                    +++ +r+++ e gf+ei+  i+++s
  gi|116754790|ref|YP_843908.1| 239 LMDRMRRIMLEMGFTEIKGEIIQSS 263
                                    67889************98888876 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 2.5e-05
                                    EEEEEEEEE--S--BTTB-S-CEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2  93 rvfqiaraFRaEdsrtdrhlaEFtqie 119
                                    + f+i r++R E +++++ + EF q+e
  gi|116754790|ref|YP_843908.1| 349 KAFCIDRVYRREAIDATHTP-EFEQLE 374
                                    68******************.****98 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.7
                                    EEEEHHHHHHHHCT-SSGG CS
                                    xxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2 287 lglGldRlvmlllgsesIr 305
                                    +glG++Rl ml lg+++ r
  gi|116754790|ref|YP_843908.1| 454 WGLGVSRLAMLRLGLKDLR 472
                                    79*********99998877 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.73   6.3e+02       7      31 ..       8      31 ..       6      45 .. 0.80
   2 ?    5.5   0.1     0.022        19      60      84 ..      40      66 ..      31     104 .. 0.74
   3 !    7.8   0.0    0.0041       3.5      54      86 ..     142     176 ..     125     177 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.73
                          Mrr_N  7 plLealadgsehrlkeirervaerf 31
                                    +Lea++dg     +ei +r+  ++
  gi|116754790|ref|YP_843908.1|  8 RILEAISDGCSNP-QEIADRLNIKI 31
                                   689*****99999.99999987665 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.022
                          Mrr_N 60 yLkkagllespkrgv..wkiTekGrev 84
                                    L + gl++ +kr +  +++Te+Gr++
  gi|116754790|ref|YP_843908.1| 40 SLAESGLISVDKRVIerFSLTEEGRRY 66
                                   455555555555544445555555554 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0041
                          Mrr_N  54 vgWartyLkkagllespk..rgvwkiTekGrevlk 86 
                                    +g a+  L k gl+  ++     ++iT++G++vl+
  gi|116754790|ref|YP_843908.1| 142 LGSAIDLLIKRGLVAPERskSWRYEITDAGKQVLS 176
                                    5557777889999966663266699********97 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   5.4e-05     0.046       4      34 ..       3      34 ..       3      41 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.4e-05
                                   -HHHHHHHHHHCTTS-H.HHHHHHHTS-HHHH CS
                           GerE  4 skRErevLrllaeGksn.keIAeelniSekTV 34
                                   s+R + +L+ + +G sn +eIA++lni+ + V
  gi|116754790|ref|YP_843908.1|  3 SERDLRILEAISDGCSNpQEIADRLNIKIEAV 34
                                   89***************779*******98877 PP

>> HTH_47  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   3.8e-05     0.032      41      77 ..      12      48 ..       2      49 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.8e-05
                                   HH-EEEEEHHHHHHHHT--HHHHHHHHHHHHHTT-EE CS
                         HTH_47 41 nlaDGkrsLldiAeriglpfdrvaaiaraLaeaglla 77
                                   +++DG  +  +iA+r+++++++v+++a++Lae gl++
  gi|116754790|ref|YP_843908.1| 12 AISDGCSNPQEIADRLNIKIEAVLSAAESLAESGLIS 48
                                   789********************************96 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00039      0.34      31      73 ..      12      52 ..       7      68 .. 0.86
   2 ?    1.8   0.0       0.2   1.7e+02      40      77 ..     127     164 ..     113     184 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00039
                        DUF4423 31 plkdfkadpeelakrlrpkisaeevekalefLlklgllkkded 73
                                   ++ d+ ++p+e+a+rl+  i+ e v +a e L ++gl+  d+ 
  gi|116754790|ref|YP_843908.1| 12 AISDGCSNPQEIADRLN--IKIEAVLSAAESLAESGLISVDKR 52
                                   6778889**********..*******************98876 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.2
                        DUF4423  40 eelakrlrpkisaeevekalefLlklgllkkdedgkyr 77 
                                     +l+  l ++ s +e  +a+++L k gl+  ++++ +r
  gi|116754790|ref|YP_843908.1| 127 IALKMLLEGEKSRSELGSAIDLLIKRGLVAPERSKSWR 164
                                    5677778888899999*************999887765 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00016      0.14      11      58 ..       5      51 ..       1      52 [. 0.92
   2 ?   -1.8   0.0       3.9   3.3e+03      36      59 ..     137     160 ..     114     161 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00016
                                   HHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                         HTH_20 11 vRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                     +ril a+ ++++  + e+a+rl ++   +    + L+e gL+ v +
  gi|116754790|ref|YP_843908.1|  5 RDLRILEAI-SDGCSNPQEIADRLNIKIEAVLSAAESLAESGLISVDK 51
                                   5689*****.**********************************9976 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.9
                                    S-HHHHHHHHHHHHHCTTEEEECT CS
                         HTH_20  36 lskntlsyHLrvLeeagLvevvre 59 
                                     s+++l   ++ L + gLv  +r+
  gi|116754790|ref|YP_843908.1| 137 KSRSELGSAIDLLIKRGLVAPERS 160
                                    567777777888888888887775 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00072      0.61       8      52 ..       7      48 ..       4      65 .. 0.83
   2 ?    1.2   0.0       0.4   3.4e+02      34      56 ..     138     160 ..     134     164 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00072
                                   HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                         MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                   +r+L a+ ++     +++e+a+rl+++  av  + + L + GL+ 
  gi|116754790|ref|YP_843908.1|  7 LRILEAISDGCS---NPQEIADRLNIKIEAVLSAAESLAESGLIS 48
                                   578888877653...9***************************93 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.4
                                    SHHHHHHHHHHHHHTTSEEEEES CS
                         MarR_2  34 sksavsrilkrLvaaGLverrpg 56 
                                    s+s +  +++ L ++GLv  +++
  gi|116754790|ref|YP_843908.1| 138 SRSELGSAIDLLIKRGLVAPERS 160
                                    677778899*********76654 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0031       2.7      20      56 ..      15      51 ..       3      61 .. 0.86
   2 ?    3.1   0.0       0.1        86      35      66 ..     138     169 ..     132     170 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0031
                                   HCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                           TrmB 20 lgpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                    g ++ +eia +l++    v ++ +sL + Gl+ + k
  gi|116754790|ref|YP_843908.1| 15 DGCSNPQEIADRLNIKIEAVLSAAESLAESGLISVDK 51
                                   677899***************************9877 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.1
                                    SCHCHHHHHHHHHHCTSEEEESSTTTEEEE-- CS
                           TrmB  35 prskvYevLrsLedkGlVerekgrpklYravd 66 
                                    +rs   +++  L+++GlV  e+++  +Y+ +d
  gi|116754790|ref|YP_843908.1| 138 SRSELGSAIDLLIKRGLVAPERSKSWRYEITD 169
                                    56666677888*************99999876 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 ?   10.9   0.0   0.00039      0.34      25      57 ..      21      53 ..      18      59 .. 0.88
   2 ?   -2.8   0.0       7.4   6.3e+03      40      62 ..     144     170 ..     138     172 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00039
                                   HHHHHHTTSSHHHHHHHHHHHHHTTSEEETEEE CS
                      HTH_Crp_2 25 eelAsmlGltretvsrilseLkreglisrgrri 57
                                   +e+A++l++  e v  +   L + glis  +r+
  gi|116754790|ref|YP_843908.1| 21 QEIADRLNIKIEAVLSAAESLAESGLISVDKRV 53
                                   89**************************65443 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 7.4
                                    HHHHHHHHTTSEE..ETEE..EEES-H CS
                      HTH_Crp_2  40 rilseLkreglis..rgrr..irildl 62 
                                     ++  L ++gl+   r++    +i+d 
  gi|116754790|ref|YP_843908.1| 144 SAIDLLIKRGLVApeRSKSwrYEITDA 170
                                    566678899999974322223778775 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0    0.0014       1.2      16      49 ..      16      49 ..       3      53 .. 0.85
   2 ?    0.4   0.0      0.73   6.3e+02      31      52 ..     139     160 ..     136     162 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0014
                                   TTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                           MarR 16 gplsvseLakklgvskstvtrvldrLekkGlieR 49
                                   g+ + +e+a++l++++ +v  ++  L + Gli+ 
  gi|116754790|ref|YP_843908.1| 16 GCSNPQEIADRLNIKIEAVLSAAESLAESGLISV 49
                                   667899**************************85 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.73
                                    HHHHHHHHHHHHHTTSEEEEEE CS
                           MarR  31 kstvtrvldrLekkGlieRsks 52 
                                    +s +  ++d L+k+Gl+  ++s
  gi|116754790|ref|YP_843908.1| 139 RSELGSAIDLLIKRGLVAPERS 160
                                    566778999*******976665 PP

>> AAA_assoc_C  C-terminal AAA-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00053      0.45       2      53 ..      22      76 ..      21      82 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00053
                    AAA_assoc_C  2 eLaeelelevddLlpiveaaelLglveveegdie...lTelGrkfveadikerKe 53
                                   e+a++l+++++ +l ++e +   gl++v++  ie   lTe+Gr++++ +  er+ 
  gi|116754790|ref|YP_843908.1| 22 EIADRLNIKIEAVLSAAESLAESGLISVDKRVIErfsLTEEGRRYAHEGLPERRL 76
                                   699**************************98774444************999986 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 ?    6.5   0.0     0.011       9.2      17      68 ..      20      66 ..       8      72 .. 0.85
   2 ?    2.7   0.0      0.17   1.5e+02      29      77 ..     140     183 ..     129     185 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.011
                         HTH_34 17 fvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGrea 68
                                   ++e+ + l++   +  + ++ L + g i+vdk + ++     +++T+eGr  
  gi|116754790|ref|YP_843908.1| 20 PQEIADRLNIKIEAVLSAAESLAESGLISVDKRVIER-----FSLTEEGRRY 66
                                   678888888888888888999****************.....9******975 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.17
                         HTH_34  29 gnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkkyvkaLk 77 
                                    ++L + ++ L k g +  + +++ +     ++iT++G++  ++ +++++
  gi|116754790|ref|YP_843908.1| 140 SELGSAIDLLIKRGLVAPERSKSWR-----YEITDAGKQVLSQSKEIIS 183
                                    5566666666666666666666666.....99******99999888776 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 ?    9.0   0.0    0.0017       1.5      10      56 ..       6      51 ..       2      62 .. 0.78
   2 ?   -0.3   0.0       1.4   1.2e+03      25      59 ..     128     162 ..     121     177 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0017
                        DUF2250 10 alkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlerve 56
                                   +l++l+ +       ++ ia++l+i++e v ++ ++L e GL+   +
  gi|116754790|ref|YP_843908.1|  6 DLRILEAISDG-CSNPQEIADRLNIKIEAVLSAAESLAESGLISVDK 51
                                   56666666554.445899************************97554 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.4
                        DUF2250  25 aksiakeleipleevrellkkLeelGLlervegkt 59 
                                    a+ +  e e++++e  ++++ L + GL+    +k+
  gi|116754790|ref|YP_843908.1| 128 ALKMLLEGEKSRSELGSAIDLLIKRGLVAPERSKS 162
                                    56667777888888889999999999987666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (493 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3459.38
//
Query:       gi|116754791|ref|YP_843909.1|  [L=232]
Description: creatininase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.2e-57  192.8   0.0    7.2e-57  192.6   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 !  192.6   0.0     4e-61   7.2e-57       2     240 ..       5     223 ..       4     224 .. 0.88

  Alignments for each domain:
  == domain 1  score: 192.6 bits;  conditional E-value: 4e-61
                   Creatininase   2 eltwpeveealkeddvailPvGstEqHGphlplgtDtliaealaervaeklgakalvlPtlpyGvseehlgfpGTislsp 81 
                                    e++wpe+e+ lk+++++ilPvG++E+HGphlp+ tDt +a ++a +va++ +  ++v+P+++yG++ + +gfpGT+s++ 
  gi|116754791|ref|YP_843909.1|   5 EMSWPEIEKGLKKTRTVILPVGAVEEHGPHLPVTTDTHQALEVAYEVARRRE--VFVAPPVHYGICRSTRGFPGTVSVGF 82 
                                    8**********************************************99966..************999*********** PP

                   Creatininase  82 etliavlrdileslarhGfrrivlvngHgg..nsaalkeaarelraehdaaavrvtaaekelaaalkleeaaeaaeesee 159
                                      l+++++dil  ++++ fr +++++gH g  +++ lkea++ + +++ +  +++ +    +            +  + +
  gi|116754791|ref|YP_843909.1|  83 NALRDYVYDILLGFHESNFRYVMVLSGHAGgqHMSSLKEACQSAVNNT-DLRISLLTD---F------------DLIRCD 146
                                    ****************************9989**********999988.665543222...2............223445 PP

                   Creatininase 160 eegggHAgelEtSlmlalrpelVrmdr.aedpeeaklakegvstaedaeelspsGvlGdpskataekGealleaaveela 238
                                    ++g+gHAg++EtS ml  rp+lVr    a++p+    ++  +   ++++e+  +G++Gdps a+aekG +++e av+ ++
  gi|116754791|ref|YP_843909.1| 147 TPGDGHAGDIETSRMLLHRPDLVRGLPpANHPKR---PR--YLILRSVREFMGNGIMGDPSSASAEKGVRYFEMAVRGVL 221
                                    66**********************6540333332...22..3688999**99*************************999 PP

                   Creatininase 239 el 240
                                    e+
  gi|116754791|ref|YP_843909.1| 222 EA 223
                                    87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 1819.86
//
Query:       gi|116754792|ref|YP_843910.1|  [L=891]
Description: oligosaccharyl transferase, STT3 subunit [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.5e-26   90.9  22.4    2.8e-25   89.2  22.4    1.9  1  STT3      Oligosaccharyl transferase STT3 subunit
    1.8e-25   89.0   0.8    2.8e-25   88.4   0.2    1.7  2  AglB_L1   Archaeal glycosylation protein B long peripheral do


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 !   89.2  22.4   3.2e-29   2.8e-25       2     480 ..      31     585 ..      30     587 .. 0.69

  Alignments for each domain:
  == domain 1  score: 89.2 bits;  conditional E-value: 3.2e-29
                                    HHHHHHHHHCCCCCHCC.CCCCCCT--S--SSCHHHHHHHCCCHHHT-C.....CCHHSSEETTSSTTT-EEESTTCCHC CS
                           STT3   2 lilvifalialvavasrdlFtdedglsylsefDpYYnyRltenllnnGfpGdvvikkknwfdhsqyyPpGsrvdygpliv 81 
                                    l+l+++ l+a+v++ +   F  +  +   se+D +Y   l + +  +         +++wfd+ + +P G ++++gp+++
  gi|116754792|ref|YP_843910.1|  31 LFLLSIYLRAVVPFRNV--FIGDAVRF-SSESDAWYHMMLAKTTFLH--------WQRPWFDPLTNFPNGTPLHFGPFLS 99 
                                    67788888888888888..55444444.48******86666655555........79*********************** PP

                                    CC.CHHHHHHCCHHC.HHHHHHHHCCHHHH.HHHHCHHHHHHHHHHS-CCCHHHHHHHCCC-CC.CCCTTSTT--STCCC CS
                           STT3  82 lLamlasaiinhsld.vsirevclwlpall.gsLlaIpiyflvrelksdiaGllAAlllaiaPg.YlsrtvaGfyDtdmf 158
                                    +   l+s+i+ +  +  +  +v+ ++ +++ gsLl  p+y++ +e+ +  +G+ AA+l ++ Pg ++srtv+Gf D++  
  gi|116754792|ref|YP_843910.1| 100 WGVALLSKIVGLGGSdLHTVDVVGAFWPVImGSLLILPVYYIGKEIGGRGCGITAAALSVVLPGqLFSRTVLGFTDHHSS 179
                                    9889********99988888888777665439************************************************ PP

                                    CHHHHHHHHHHHHHHHHCCS..............TTCHHHHHHHHHHHHHHTTSCCGGHHH.HCCHHHHHHHHHCTTTS- CS
                           STT3 159 eivlllfvlffflkaiktks..............nkislaviaaliiflivlaWggyaili.yallllfilalLiigrfe 223
                                    ei+l+ + + +f+ a  ++               ++  lav+a++++ l+v aW+   il+  +ll+++ +  ++ + + 
  gi|116754792|ref|YP_843910.1| 180 EILLSTLSMLLFILAFRSGRllsfrtlrdlssvrRPLILAVLAGIALGLYVDAWSMG-ILFeGILLIAITIQSVVEHYRG 258
                                    *******************************************************99.5551566666666666666655 PP

                                    CCHHHHHHHHHHHHHHH..CCCCCCCTTCHHHSTTTCHHCCCCHHHHHHHHCCCHHC..CCCCCHHCC.....CHHTT.H CS
                           STT3 224 lklkiavtfsviiaflviaiivllflgfqvvavseiigalgifgllqlvafgsvvvlvaelkfyqfis.....lfqpgil 298
                                         +  +  i +f++   +v++f+ +     + +i++ ++++ +  +++gs+    +++++ +++       ++pg +
  gi|116754792|ref|YP_843910.1| 259 RSGEYLGIIGAISLFFA-FLMVIPFAHSYN--RFSLIQYSLFQPSM--LLLGSIFCFEMAVASREVSRrglsrALYPGSI 333
                                    66666666656655555.566666666664..33333333333222..22223332222333333333443334444422 PP

                                    HHHTT--GGGHHHHHHHHHHHHC......................................................... CS
                           STT3 299 sevlgligevvtalavlglialw......................................................... 321
                                        ++  +v  ++ vl+++ l+                                                         
  gi|116754792|ref|YP_843910.1| 334 A---AV-IVVDLIIVVLAVPELFnavvyglktyllprtggaatvaelspiymdlgrgvtgidenfpgvirilspfyiaii 409
                                    2...22.2223333344444444444445677778999999999999999999999999999999998888877777543 PP

                                    .CCCCCTS-----TTHHHHHHHHHS---S--CCHHHCCSSST.TTTCCCHH..HCHHCCHHCTCHHHHHHH........H CS
                           STT3 322 .lgilyslldleyaklkikiiilvsvwlpvgllaltkglrfl.iftvPlgi..ifvgllleflavfvkiys........v 389
                                     lg+l       y+  +  +  l+ vw +v+l  +++  r +  ++v++++   ++ +l+   a f  i          +
  gi|116754792|ref|YP_843910.1| 410 gLGMLVY----RYVRDSKAPYLLIIVWSIVTLIITLAANRSAyYYAVNVALlcGYLASLVYARAGFWEIEDvlarspsnL 485
                                    3333333....55666666667899*****************9********87777777777777777777888898886 PP

                                    HHHHHCCC-SCHCCCCCHHHHHHHCCCHHH.HHHHHCCHHHHHHHHH.....HHHHH.....HHHHCT.TTTTHHHTTHH CS
                           STT3 390 sqilfsgvvvillmltllpvlallaavkis.kifstykdekeakikv.....aakav.....aptksnglkeslewkant 458
                                    ++ +++ +++   ++++l+v++l +  +is   ++ y     +++        ++ +          +   e+++  +  
  gi|116754792|ref|YP_843910.1| 486 TRDVRPERLAS-AAAVILIVIILAYPSVISsHAIARYSVGPNQDWVSsiewlRNNTPypgldIYNVYERPPEGQYF-QYP 563
                                    66666666666.5555555666666555553444444333333333322221444446553322222233344444.455 PP

                                    HCHHHHHHHHHHHHHHHHHHHH CS
                           STT3 459 nrdsvvitwwdyghilaveadr 480
                                    +    v++wwdygh++ ++  r
  gi|116754792|ref|YP_843910.1| 564 ETAYGVMSWWDYGHLIETIGHR 585
                                    66778**********9988766 PP

>> AglB_L1  Archaeal glycosylation protein B long peripheral domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       1.9   1.7e+04      61      77 ..     765     781 ..     761     787 .. 0.72
   2 !   88.4   0.2   3.1e-29   2.8e-25       1      92 []     798     889 ..     798     889 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 1.9
                                    SSEESS-EEEEETTEEE CS
                        AglB_L1  61 sveaagpYevtagnvta 77 
                                     vea ++Y+++ +++t+
  gi|116754792|ref|YP_843910.1| 765 YVEALQHYRLVHESTTQ 781
                                    58899999998866543 PP

  == domain 2  score: 88.4 bits;  conditional E-value: 3.1e-29
                                    -EEEEEEBSSSSEEEEEEEEE-TTS-EEEEEEEEE.-BTTEEEEEE---SS......-SSSSEESS-EEEEETTEEEEE- CS
                        AglB_L1   1 GAtitGsaeagatvtasveletnqgrtftYrqeaeadedGefeltvPYstegeedgetnssveaagpYevtagnvtaeve 80 
                                    GA+i+G+a++g +v+++v++ tnq+r f Yrq++++d++Gef l+vPYsteg   g tn+++ + g+Y++t++ +++ev+
  gi|116754792|ref|YP_843910.1| 798 GAVIKGRASPGSRVVIEVPIMTNQKRLFIYRQSNVTDSNGEFVLVVPYSTEGPVVGGTNFDTAPIGAYRLTVNGTSREVR 877
                                    9******************************************************************************* PP

                                    --HHHHHHT-EE CS
                        AglB_L1  81 VpEeaVlsgetv 92 
                                    V+E++Vl g +v
  gi|116754792|ref|YP_843910.1| 878 VSENDVLGGGIV 889
                                    *******99776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (891 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.70u 0.28s 00:00:00.98 Elapsed: 00:00:00.45
# Mc/sec: 5944.43
//
Query:       gi|116754793|ref|YP_843911.1|  [L=186]
Description: undecaprenyl diphosphate synthase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-29  102.3   0.0    4.1e-28   98.4   0.0    1.9  2  Prenyltransf  Putative undecaprenyl diphosphate synthase
  ------ inclusion threshold ------
      0.042   12.6   0.1       0.16   10.7   0.0    1.8  2  DUF1073       Protein of unknown function (DUF1073)


Domain annotation for each model (and alignments):
>> Prenyltransf  Putative undecaprenyl diphosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.015   1.3e+02      23      44 ..      19      40 ..      14      43 .. 0.87
   2 !   98.4   0.0   4.6e-32   4.1e-28     108     224 .]      72     185 ..      54     185 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.015
                                   HHHHHHHHHHHHHHHTT-SEEE CS
                   Prenyltransf 23 aGaealkeilelclelgvkvvt 44
                                   +G+e++++++e++++lg++ + 
  gi|116754793|ref|YP_843911.1| 19 HGLEKFRDLIEWSASLGIENLL 40
                                   599***************9885 PP

  == domain 2  score: 98.4 bits;  conditional E-value: 4.6e-32
                                    HHHT.TTTSEEEEEEEEE-HHHHHHHHHHHHHHTT..SSSG.GGHSHHHHHCTSTT..TSSS-SEEEEESS--S-TTSST CS
                   Prenyltransf 108 eatkknnkklvlniavnYgsrdeiveavrelvkekseekkk.eeideetlekhlytakalpdpDlliRtsGeeRlSnFll 186
                                    ++ ++ + ++ ++i + Yg+++e++ea+r+++ ++++   + eeid++t+e++l    + ++pDl+iR +G +RlS+F++
  gi|116754793|ref|YP_843911.1|  72 RSKSTGKGGISVTISLGYGGKREVTEAIRSVLMDVAAGLIEpEEIDRNTIERYLRF--K-QKPDLVIRAGG-RRLSDFMI 147
                                    3333345669*********************9998766655577899********9..4.68******998.89****** PP

                                    TTTTT-EEEEESSSGGG--HHHHHHHHHHHHHCHHHTT CS
                   Prenyltransf 187 wqlayselyfldvlWPdfskedllealleyqkrerrfg 224
                                    wq+ayselyf+dv W  +++ d+l+a++++q+rerrfg
  gi|116754793|ref|YP_843911.1| 148 WQAAYSELYFTDVDWASLRRLDFLRAIRDFQRRERRFG 185
                                    ************************************98 PP

>> DUF1073  Protein of unknown function (DUF1073)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   1.8e-05      0.16      54     107 ..      22      73 ..      17      90 .. 0.89
   2 ?   -0.6   0.1      0.05   4.5e+02      44      68 ..     162     186 .]     158     186 .] 0.92

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 1.8e-05
                        DUF1073  54 eallealkwarlfGgaallikvkdededlskPldpekvgkgslkglrvldreev 107
                                    e+++++++w+   G   lli v+++  dl++Pl  e++ k+ + +++++d+   
  gi|116754793|ref|YP_843911.1|  22 EKFRDLIEWSASLGIENLLIHVGQHSGDLASPL--ESMLKDAPADVSIIDADRS 73 
                                    79*******************************..8888**********99877 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.05
                        DUF1073  44 eaelkrLglkeallealkwarlfGg 68 
                                    +a+l+rL++  a+++  + +r fG+
  gi|116754793|ref|YP_843911.1| 162 WASLRRLDFLRAIRDFQRRERRFGR 186
                                    799*******************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); 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: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1360.62
//
Query:       gi|116754794|ref|YP_843912.1|  [L=391]
Description: hypothetical protein Mthe_1500 [Methanosaeta thermophila PT]
Scores for complete 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-53  179.7  13.1    5.7e-53  179.7  13.1    3.0  2  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 ?   -0.0   4.2     0.026   4.7e+02      15      55 ..      11      51 ..       3     119 .. 0.88
   2 !  179.7  13.1   3.2e-57   5.7e-53       2     235 ..     166     380 ..     165     381 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.026
                          DUF92 15 sLtpsGalaavlvgvlialaplgllffllllvFfllgsllt 55
                                   +L ++G+++av+++++ +++    + ++ l++  +l  +lt
  gi|116754794|ref|YP_843912.1| 11 LLPVTGVFTAVILAIVYIIHRPARMLCASLILLLVLREALT 51
                                   57789**********99999888788888888887777766 PP

  == domain 2  score: 179.7 bits;  conditional E-value: 3.2e-57
                          DUF92   2 ltlllalralrkksLtpsGalaavlvgvlialaplgllffllllvFfllgslltkvkkkvKa..kleeekegaRdavqVl 79 
                                    ++++l++ a+  ++ +++++l+ v++++l++l   gl++fllll+F+l+g ++t+++++ K   ++++ek g R++++V 
  gi|116754794|ref|YP_843912.1| 166 FAVILGVGAYWARAADVDAVLSEVIICILVVLF-AGLKWFLLLLCFYLMGGAFTRYGYSYKYslGIAQEKCGVRGYKNVY 244
                                    678999**********************99999.7779************************899999999********* PP

                          DUF92  80 anslvalllally..lasdlllvgivasyAavaaDTlaSElGkilskskprlittlkkvppGtnGgVsllGllasllGal 157
                                    +nslv+l++al+y  ++++++++++++++A++++DTlaSE+G+++ +s+pr+ittlk+v pG++GgV++lG +asl+Ga+
  gi|116754794|ref|YP_843912.1| 245 SNSLVPLVAALCYgiYGNEIFFYAFLGAVATANGDTLASEIGETS-RSRPRMITTLKPVDPGVDGGVTPLGEMASLAGAA 323
                                    *************76559************************766.55******************************** PP

                          DUF92 158 liallavlllllel.lillltlaGllGsllDSlLGatlqasvvdkrtgkvvegeggekvvsGldlLdNnaVNllsallt 235
                                    +i+l+av++ ++ +  +l+++ +G+lGs++DSl+Ga++q++                       lL+Nn+VNl+++l++
  gi|116754794|ref|YP_843912.1| 324 AIGLVAVAISMTGAnGFLIAMTSGFLGSNFDSLMGAVFQRR----------------------GLLTNNGVNLVATLFG 380
                                    ***9966665554469999999*******************......................7999999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       873  (0.0486921); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 2884.03
//
Query:       gi|116754795|ref|YP_843913.1|  [L=269]
Description: shikimate 5-dehydrogenase [Methanosaeta thermophila PT]
Scores for complete 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-26   90.4   0.0    1.3e-25   89.4   0.0    1.5  1  Shikimate_dh_N   Shikimate dehydrogenase substrate binding do
    5.5e-13   49.2   0.0    7.8e-13   48.7   0.0    1.3  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    7.9e-12   44.7   0.7    1.6e-11   43.8   0.7    1.5  1  SDH_C            Shikimate 5'-dehydrogenase C-terminal domain
    1.5e-06   28.7   0.1    3.6e-06   27.5   0.0    1.7  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
     0.0012   18.2   0.0     0.0018   17.6   0.0    1.2  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
     0.0035   17.6   0.1      0.011   16.0   0.1    1.8  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0061   15.7   0.1     0.0091   15.1   0.1    1.2  1  FAD_binding_2    FAD binding domain
     0.0079   15.8   0.0      0.019   14.5   0.0    1.7  1  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
     0.0094   15.4   0.0      0.015   14.7   0.0    1.4  1  adh_short        short chain dehydrogenase
  ------ inclusion threshold ------
      0.015   14.6   0.2        5.2    6.4   0.1    2.2  2  THF_DHG_CYH_C    Tetrahydrofolate dehydrogenase/cyclohydrolas
      0.026   13.8   0.1        1.2    8.3   0.1    2.2  2  Thi4             Thi4 family
      0.033   14.6   0.0      0.051   14.0   0.0    1.4  1  NAD_binding_7    Putative NAD(P)-binding
      0.071   12.8   0.0       0.13   11.9   0.0    1.5  1  ApbA             Ketopantoate reductase PanE/ApbA
      0.095   12.9   0.1       0.33   11.1   0.0    1.8  2  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh


Domain annotation for each model (and alignments):
>> Shikimate_dh_N  Shikimate dehydrogenase substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.4   0.0     1e-28   1.3e-25       1      83 []       6      87 ..       6      87 .. 0.99

  Alignments for each domain:
  == domain 1  score: 89.4 bits;  conditional E-value: 1e-28
                                   EEESS-TT-SHHHHHHHHHHHCTSSEEEEEEE-SCCTHHHHHHHHHHTTESEEEE-TTSCCHHHGGSSEE-HHHHHHT--SE CS
                 Shikimate_dh_N  1 viGnpikhSlSPaihnaafkalglngsyeafeveedelekaveelralglaGlnvTiPfKeaviplldelseeAkaigAvNt 82
                                   v+G+pi+hSlSP++hnaaf+a+gl++sy+af+v+ ++l++a+ ++ a g+ Gln TiP+Ke++i++++  +e+A+aigA+Nt
  gi|116754795|ref|YP_843913.1|  6 VLGDPIEHSLSPVMHNAAFQAMGLQASYHAFRVKIPRLRDAILGADAMGFGGLNLTIPLKESAISVVE-PDETAEAIGAANT 86
                                   79*****************************************************************7.************* PP

                                   E CS
                 Shikimate_dh_N 83 i 83
                                   +
  gi|116754795|ref|YP_843913.1| 87 V 87
                                   8 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.7   0.0   6.1e-16   7.8e-13       2      84 ..     105     184 ..     104     217 .. 0.92

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 6.1e-16
                                    HHHHHHS...TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEE CS
                   Shikimate_DH   2 lakkkle.slkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvi 80 
                                    la +  + +++++ vlliGaG  a+ +a +L++ g++ +vv+NRt er  +la++l+ e   ++++ e+++l++ +dvvi
  gi|116754795|ref|YP_843913.1| 105 LALRHYGvNVRGADVLLIGAGGAARAIAYQLSKDGAE-IVVTNRTPERGLALASDLGLE---FRPFGEIDDLVRVSDVVI 180
                                    566666668999***********************99.******************666...****************** PP

                                    E-SS CS
                   Shikimate_DH  81 sata 84 
                                     at+
  gi|116754795|ref|YP_843913.1| 181 NATS 184
                                    **98 PP

>> SDH_C  Shikimate 5'-dehydrogenase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.7   1.2e-14   1.6e-11       4      31 .]     234     261 ..     231     261 .. 0.94

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 1.2e-14
                                    HHHHHHHHHHHHHHS----HHHHHHHHH CS
                          SDH_C   4 MLveQgaeqFelWTGrepPvevMreall 31 
                                    MLv+Qga++F++WTG + Pv+vM++a++
  gi|116754795|ref|YP_843913.1| 234 MLVYQGAAAFRIWTGLDEPVDVMEAAVR 261
                                    ***************999********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 !   27.5   0.0   2.8e-09   3.6e-06       4      69 ..     121     183 ..     118     209 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 2.8e-09
                                    EETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC..-EEECECHHHHHHH-SEEEE-S CS
                  F420_oxidored   4 iiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg..vkvtavdneeaaeeadvvvlav 69 
                                    +iGaG  ++a+a +l++ g    eivv+ +r+pe+  +la++lg   + ++ +  ++++ +dvv+ a 
  gi|116754795|ref|YP_843913.1| 121 LIGAGGAARAIAYQLSKDG---AEIVVT-NRTPERGLALASDLGleFRPFG-EIDDLVRVSDVVINAT 183
                                    79*****************...****55.***************5555566.8899999****99775 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 !   17.6   0.0   1.4e-06    0.0018      28      99 ..     108     183 ..      83     188 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.4e-06
                                    CGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH.CHHHHTCEEC...SHHHHHHH-SEEEE-S CS
                   2-Hacid_dh_C  28 allgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkee.eeeelgvelv...sleellaesDivslhl 99 
                                    ++ g +++g  v +iG+G  ++a+a  l++ g+++++++r++++    +++lg+e+    ++++l++ sD+v++++
  gi|116754795|ref|YP_843913.1| 108 RHYGVNVRGADVLLIGAGGAARAIAYQLSKDGAEIVVTNRTPERGLaLASDLGLEFRpfgEIDDLVRVSDVVINAT 183
                                    5678899**********************************998777566666655433599**********9865 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 !   16.0   0.1   8.8e-06     0.011       1      49 [.     119     163 ..     119     185 .. 0.81
   2 ?   -2.6   0.0       4.9   6.3e+03      79      99 ..     211     231 ..     197     242 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 8.8e-06
                                    EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCE CS
                Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrf 49 
                                    vl+iGaG+ ++a+a  l++ +    ei+v  r+ e+  ala++ lg +f
  gi|116754795|ref|YP_843913.1| 119 VLLIGAGGAARAIAYQLSKDGA---EIVVTNRTPERGLALASD-LGLEF 163
                                    79*****************997...6**********9999866.45444 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.9
                                    GGGHHHHHHHHHHHT-EEEES CS
                Sacchrp_dh_NADP  79 pissldvlkaCietgvhyvdt 99 
                                    +    ++l+ ++++g+  +d 
  gi|116754795|ref|YP_843913.1| 211 YSRETELLRDARRAGAKAIDG 231
                                    445566777777777777774 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   7.1e-06    0.0091       1      39 [.     118     156 ..     118     168 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 7.1e-06
                                    SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGG CS
                  FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggata 39 
                                    Dv+ iG+G+A  a A+++++ G++++v + ++e+g+a+a
  gi|116754795|ref|YP_843913.1| 118 DVLLIGAGGAARAIAYQLSKDGAEIVVTNRTPERGLALA 156
                                    9********************************888776 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 !   14.5   0.0   1.5e-05     0.019       3      66 ..     115     181 ..      95     187 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.5e-05
                                    HTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEE...EHHHHHHT-SEEEE CS
                           IlvN   3 kgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevl...tvaeavkkadvvmi 66 
                                    +g  + +iG G  ++a a +l   g ++vv++r+ ++ ++ A++ g+e     +++++v+ +dvv++
  gi|116754795|ref|YP_843913.1| 115 RGADVLLIGAGGAARAIAYQLSKDGAEIVVTNRTPERGLALASDLGLEFRpfgEIDDLVRVSDVVIN 181
                                    5678999***************************************997522277889999999986 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.2e-05     0.015       3      45 ..     119     160 ..     117     182 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.2e-05
                                    EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHH CS
                      adh_short   3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelk 45 
                                    vl +Ga+ G  raia++l k+Ga++vv++r++e+  ++a+ l+
  gi|116754795|ref|YP_843913.1| 119 VLLIGAG-GAARAIAYQLSKDGAEIVVTNRTPERGLALASDLG 160
                                    6777776.99*************************99999887 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 ?    6.2   0.0    0.0047         6      26      68 ..     106     147 ..      97     157 .. 0.84
   2 ?    6.4   0.1    0.0041       5.2      73     112 ..     169     214 ..     166     240 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0047
                                    HHHHCT---TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-T CS
                  THF_DHG_CYH_C  26 llketgielegkkvvvvGrsnivgkplallLleknatVtvchs 68 
                                     l+++g++++g++v+ +G++    +++a  L++++a + v+++
  gi|116754795|ref|YP_843913.1| 106 ALRHYGVNVRGADVLLIGAGGA-ARAIAYQLSKDGAEIVVTNR 147
                                    5899**************9986.68999999999998888765 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0041
                                    HHHHHCCSSEEEE-S......S-TT-B-GGGS-TT-EEEE---EEC CS
                  THF_DHG_CYH_C  73 laeitreadivvvav......GkpelikaemvkegavviDvGinrv 112
                                    +++++r +d+v+ a+      G p+l +++ +k ++vv D+ ++r 
  gi|116754795|ref|YP_843913.1| 169 IDDLVRVSDVVINATsvgmrdGDPRLFDGSILKAEQVVFDIIYSRE 214
                                    66788999999998766666689******************99987 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1   0.00094       1.2      17      49 ..     116     147 ..     108     155 .. 0.87
   2 ?    3.2   0.0     0.035        45     129     163 ..     171     206 ..     161     217 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00094
                                    EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                           Thi4  17 esDvvivGaGssGLtaayylakkpdlkvailer 49 
                                     +Dv+++GaG +  + ay l+k+ + ++++ +r
  gi|116754795|ref|YP_843913.1| 116 GADVLLIGAGGAARAIAYQLSKD-GAEIVVTNR 147
                                    68********************9.888888765 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.035
                                    B.TEEEEEEEEEHHHHTCTTTSS.-B-EEEEEEEEE CS
                           Thi4 129 g.egvaGvvinwtlvelahdtqscvDPlvirakvvv 163
                                    + ++v+ vvin t+v +  ++    D  +++a+ vv
  gi|116754795|ref|YP_843913.1| 171 DlVRVSDVVINATSVGMRDGDPRLFDGSILKAEQVV 206
                                    447999************999999999999998776 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 ?   14.0   0.0     4e-05     0.051       3      40 ..     112     149 ..     111     228 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4e-05
                  NAD_binding_7   3 ldlkgkkvlvvGgGevAarkvrklleagakvtvvapev 40 
                                    ++++g  vl++G+G  A   +++l + ga+++v   + 
  gi|116754795|ref|YP_843913.1| 112 VNVRGADVLLIGAGGAARAIAYQLSKDGAEIVVTNRTP 149
                                    57999****************************77662 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0    0.0001      0.13       1      32 [.     119     151 ..     119     182 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0001
                                    EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.H CS
                           ApbA   1 iailGaGaiGsllaakLakagadvtlilrsr.r 32 
                                    ++ +GaG+  + +a++L+k ga++++ +r++ r
  gi|116754795|ref|YP_843913.1| 119 VLLIGAGGAARAIAYQLSKDGAEIVVTNRTPeR 151
                                    5789*************************9954 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00026      0.33       4      60 ..     121     180 ..     118     188 .. 0.89
   2 ?   -1.3   0.0       1.7   2.1e+03      47      74 ..     219     247 ..     198     259 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00026
                                    EE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT...EEE-SSHHHHHHHCSEEE CS
                  NAD_binding_2   4 fiGlGvMGsnmalnllkagykvavynrtkekveelvaeg...akaaesieelvasldvvi 60 
                                    +iG G   + +a +l k g +++v nrt+e+  +l+++    ++++ +i +lv+  dvvi
  gi|116754795|ref|YP_843913.1| 121 LIGAGGAARAIAYQLSKDGAEIVVTNRTPERGLALASDLgleFRPFGEIDDLVRVSDVVI 180
                                    7999999999*********************9999999557799*********9999998 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.7
                                    SSHHHHHHHC.SEEEE-SSSHHHHHHHHH CS
                  NAD_binding_2  47 esieelvasl.dvvitmvkagkavdevie 74 
                                     +++ + a++ d v+++v +g+a   +++
  gi|116754795|ref|YP_843913.1| 219 RDARRAGAKAiDGVMMLVYQGAAAFRIWT 247
                                    44444433334888888888877665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1964.23
//
Query:       gi|116754796|ref|YP_843914.1|  [L=288]
Description: prephenate dehydrogenase [Methanosaeta thermophila PT]
Scores for complete 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-50  169.3   0.0    8.8e-50  169.1   0.0    1.0  1  PDH             Prephenate dehydrogenase
    5.5e-05   23.7   0.0    0.00012   22.6   0.0    1.5  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
    0.00011   21.7   0.0    0.00021   20.7   0.0    1.5  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
     0.0002   21.6   0.0    0.00032   20.9   0.0    1.4  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
  ------ inclusion threshold ------
      0.024   15.1   0.0      0.054   13.9   0.0    1.5  1  Phage_Gp19      Phage protein Gp19/Gp15/Gp42
      0.025   14.2   0.0      0.037   13.6   0.0    1.3  1  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
      0.027   14.6   0.0       0.13   12.3   0.0    2.0  2  DpaA_N          Dipicolinate synthase subunit A N-terminal do
      0.046   13.7   0.1          4    7.4   0.0    2.6  3  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen


Domain annotation for each model (and alignments):
>> PDH  Prephenate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.1   0.0   3.9e-53   8.8e-50       1     258 []      14     261 ..      14     261 .. 0.96

  Alignments for each domain:
  == domain 1  score: 169.1 bits;  conditional E-value: 3.9e-53
                                    HHHHHHHTT--SEEEEE-SSHHHHHHHHHTTSSSEEES-GGGGCCGSEEEE-S-GGGHHHHHHHHHHHS-TT-EEEE--S CS
                            PDH   1 laralrrkgfkvtvigydideekaeaalelglvdeatddieavkeadivvlavPvevilevlkelaphlkedalitDvgs 80 
                                    +ar+ r +gf+v + g + + ++ +   +lg+ ++++  +++v e divvl+vP++ + ev+  + p+++ + l++D++s
  gi|116754796|ref|YP_843914.1|  14 FARYFRDRGFDVCIWGPSGK-FHVAD--ALGVRYARDL-MSEVAESDIVVLSVPIDRTPEVAGRIGPAMRSGSLLMDLTS 89 
                                    79**************8753.44444..59*******9.9**************************************** PP

                                    --CHHHHHHHHHCC..GCEEEEEES---S-SSGGG--TTTTTT-EEEEEE-TTS-HHHHHHHHHHHHHCT-EEEE--HHH CS
                            PDH  81 vKekvvreleellkegksfvgghPmaGteksGvdaareelfenavviLtPtektdkealekvkelleevgarvilmspee 160
                                     K+++vr++ e+ +  +++ g+hPm+G+           +  ++ vi+tP e    ++   ++e+le  garv++++pee
  gi|116754796|ref|YP_843914.1|  90 LKVEPVRAMVESTHPDVEVLGAHPMFGP--------TMPSIRGQTVIITPVEGRWGRWSSHIREILERDGARVEVLTPEE 161
                                    ****************************........99***************999************************ PP

                                    HHHHHHHHTHHHHHHHHHHHHHHHCHHCCCCHHHHCGTCCHHHHH....CGGGS-HHHHHHHHHHTHHHHHHHHHHHHHH CS
                            PDH 161 HDrvvavvshlphvvaialaatlkekkndekeirklasggfrdvt....RiaksnPelwadilleNkeavlealdkfike 236
                                    HDr++avv+ l+h+ +ia+  tl +   d   +r++ s+ ++ +     Ri ++nPel+a+i+++     +e++  fi+e
  gi|116754796|ref|YP_843914.1| 162 HDRMMAVVQALTHFSYIAVGSTLRALDFDVSRSRRFMSPVYEVMLdfvgRILDQNPELYASIQMNPF--AKEVRRVFIEE 239
                                    *******************************************99999***************9554..59********* PP

                                    HHHHHHHHHTT-HHHHHHHHHH CS
                            PDH 237 lkklkelienedaeeLvellke 258
                                    + +l+ ++ ++d e ++++++e
  gi|116754796|ref|YP_843914.1| 240 CLRLSDAVDHGDLEGFMRTMRE 261
                                    ********************86 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   5.2e-08   0.00012       4      95 ..       3      88 ..       1      89 [. 0.88

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 5.2e-08
                                   EE.TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHCGHH CS
                  F420_oxidored  4 ii.GaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevlselakd 84
                                   i+ G+G+ g+ +a+ +  +g    ++++     p+   + a++lgv+    d    ++e+d+vvl+v+   ++ev+  + ++
  gi|116754796|ref|YP_843914.1|  3 IVgGTGETGSWFARYFRDRG---FDVCIW---GPSGKFHVADALGVRYAR-DLMSEVAESDIVVLSVPIDRTPEVAGRIGPA 77
                                   5569****************...****77...788889************.55555556********************999 PP

                                   HHTTSEEEEES CS
                  F420_oxidored 85 alkgklvisvl 95
                                     +g+l+ + +
  gi|116754796|ref|YP_843914.1| 78 MRSGSLLMDLT 88
                                   99999998875 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 !   20.7   0.0   9.2e-08   0.00021      41     102 ..       4      65 ..       1      76 [. 0.90

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 9.2e-08
                                    EES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEEC.SHHHHHHH-SEEEE-S--S CS
                   2-Hacid_dh_C  41 iiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelv.sleellaesDivslhlplt 102
                                    + G+G+ G+ +a++++  g++v ++ +s k    +++lgv+++ +l   +aesDiv+l +p+ 
  gi|116754796|ref|YP_843914.1|   4 VGGTGETGSWFARYFRDRGFDVCIWGPSGKFHV-ADALGVRYArDLMSEVAESDIVVLSVPID 65 
                                    569*************************99776.9999**8888*****************75 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 !   20.9   0.0   1.4e-07   0.00032       6     104 ..       6     102 ..       2     157 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.4e-07
                                    --SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCCC--TT-E CS
                  NAD_binding_2   6 GlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdeviegllealkkgdi 85 
                                    G+G+ Gs +a+ + ++g++v+++  +  k+  + a g++ a ++ + va+ d+v++ v+  + + ev  ++ +a+++g++
  gi|116754796|ref|YP_843914.1|   6 GTGETGSWFARYFRDRGFDVCIWGPS-GKFHVADALGVRYARDLMSEVAESDIVVLSVPI-DRTPEVAGRIGPAMRSGSL 83 
                                    99**********************87.7888888889**********************8.67899************** PP

                                    EEE-S---HHHHHHHHHHH CS
                  NAD_binding_2  86 lidgstsspedtrelakel 104
                                    l+d ++ ++e  r + +  
  gi|116754796|ref|YP_843914.1|  84 LMDLTSLKVEPVRAMVEST 102
                                    ********99998887764 PP

>> Phage_Gp19  Phage protein Gp19/Gp15/Gp42
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.4e-05     0.054       5      74 ..     157     222 ..     154     226 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.4e-05
                     Phage_Gp19   5 leaeEkdraeaLlevasdelereikkvgkdldkmiaasaefraavksvaadvVaravltatdrePmgqlS 74 
                                    l++eE+dr +a ++        ++  + + ld  +  s+ f   v +v+ d V r++    d++P+ ++S
  gi|116754796|ref|YP_843914.1| 157 LTPEEHDRMMAVVQALTHFSYIAVGSTLRALDFDVSRSRRFMSPVYEVMLDFVGRIL----DQNPELYAS 222
                                    89*********9987777666777899******************************....99**99988 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 ?   13.6   0.0   1.7e-05     0.037       9      92 ..       4      85 ..       1     108 [. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.7e-05
                                   EES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHHHHHHHHTGGG--TT-E CS
                           IlvN  9 viGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelqkevyeeeiepnlkegka 90
                                   v G G  G   a+ +rd g+dv++   +g+  v+ A    +    ++  v+++d+v++ +P     ev   +i p +++g+ 
  gi|116754796|ref|YP_843914.1|  4 VGGTGETGSWFARYFRDRGFDVCIWGPSGKFHVADALGVRYARDLMS-EVAESDIVVLSVPIDRTPEVA-GRIGPAMRSGSL 83
                                   5589********************99999966655555555555555.56789*********999**98.89*****99998 PP

                                   EE CS
                           IlvN 91 la 92
                                   l+
  gi|116754796|ref|YP_843914.1| 84 LM 85
                                   86 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 ?   12.3   0.0   5.9e-05      0.13      14      61 ..      14      64 ..       3      72 .. 0.87
   2 ?   -1.3   0.0         1   2.3e+03      16      36 ..     145     165 ..     141     175 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.9e-05
                                   HHHHHHHTT-EEEEES-...TSSS-BTTEEEE-GGGS-GGG-SEEE--TT- CS
                         DpaA_N 14 larkLaekgakvslygl...eleekiegvekaesleealedadviilPvpg 61
                                    ar++ ++g++v+++g     +     gv+ a +l ++++++d+++l vp+
  gi|116754796|ref|YP_843914.1| 14 FARYFRDRGFDVCIWGPsgkFHVADALGVRYARDLMSEVAESDIVVLSVPI 64
                                   6899***********665544777888**********************95 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1
                                    HHHHHTT-EEEEES-TSSS-B CS
                         DpaA_N  16 rkLaekgakvslygleleeki 36 
                                    + L+++ga+v+++  e+++ +
  gi|116754796|ref|YP_843914.1| 145 EILERDGARVEVLTPEEHDRM 165
                                    679999999999877555555 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 ?    3.3   0.1     0.033        73       6      30 ..       6      30 ..       2      40 .. 0.88
   2 ?    7.4   0.0    0.0018         4      57     100 ..      42      85 ..      38      91 .. 0.85
   3 ?   -2.6   0.0       2.1   4.8e+03       8      32 ..     137     161 ..     135     178 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.033
                                   --SHHHHHHHHHHHTTT--EEEE-S CS
                 NAD_Gly3P_dh_N  6 GaGswGtalAkvlaenghevrlwvr 30
                                   G+G  G+ +A+ + ++g +v++w+ 
  gi|116754796|ref|YP_843914.1|  6 GTGETGSWFARYFRDRGFDVCIWGP 30
                                   89*********************85 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0018
                                    EEEES-HHHHHTT--EEEE---HHHHHHHHHHHCCC--TT-EEE CS
                 NAD_Gly3P_dh_N  57 lvattdlaealkgadiivlvvPsqalrevlkklkgllkkkailv 100
                                    ++   dl + ++++di+vl vP   + ev+ ++ + ++    l+
  gi|116754796|ref|YP_843914.1|  42 VRYARDLMSEVAESDIVVLSVPIDRTPEVAGRIGPAMRSGSLLM 85 
                                    5677899999*******************999988887766655 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 2.1
                                    SHHHHHHHHHHHTTT--EEEE-S-H CS
                 NAD_Gly3P_dh_N   8 GswGtalAkvlaenghevrlwvree 32 
                                    G w + +  +l++ g +v + + ee
  gi|116754796|ref|YP_843914.1| 137 GRWSSHIREILERDGARVEVLTPEE 161
                                    6777888888888888877766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); 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:                         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: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2170.78
//
Query:       gi|116754797|ref|YP_843915.1|  [L=649]
Description: glycoside hydrolase 15-related [Methanosaeta thermophila PT]
Scores for 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-12   44.5   0.3      9e-08   31.3   0.0    3.1  3  Glyco_hydro_15  Glycosyl hydrolases family 15
  ------ inclusion threshold ------
      0.011   15.0   0.1       0.11   11.6   0.0    2.4  2  DUF608          Glycosyl-hydrolase family 116, catalytic regi


Domain annotation for each model (and alignments):
>> Glyco_hydro_15  Glycosyl hydrolases family 15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.1   0.00024       2.2       4      63 ..     295     357 ..     292     380 .. 0.75
   2 !   31.3   0.0     1e-11     9e-08     123     345 ..     392     579 ..     383     592 .. 0.81
   3 !    2.4   0.0     0.006        53     407     445 ..     595     633 ..     591     636 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00024
                                    HHHHHHCBCSTTSSBTTS-TT-B-S-S-BSSS.....B--SEEHHHHHHHHHHHH.......HHH CS
                 Glyco_hydro_15   4 ldlylrnvktlilleqnpvtGlliASpstsdp.....DYrytWvRDsvyvilavwglgyrdedra 63 
                                    +d+ +r+++++ ++ +  v G +iAS + +        Y+y+W RD++    a+ ++ y+  +++
  gi|116754797|ref|YP_843915.1| 295 QDAFYRSLMATVAHMD--VNGSIIASCDSEIKqfgadLYTYCWPRDASWACIALDRARYHHLSKE 357
                                    5777888888755554..47******997666889966*********999888876666644444 PP

  == domain 2  score: 31.3 bits;  conditional E-value: 1e-11
                                    -BTTHHHHHHHHHHHH..HCTT.....HCHCCCCHHHHTHHHHHHHHHHHTTS-..EE-TTS--ECEEHH..HHHHHHHH CS
                 Glyco_hydro_15 123 lQlDatslyllalaqm..tasg.....lqiistldevafvqnlvdYieaayktp..dfglWEenqgeselnassvgmakA 193
                                    +QlD t+l+l+al+    ++++      +++s + ++   + lv  i ++ + p  +f+lWEe+ g++ +  + ++++++
  gi|116754797|ref|YP_843915.1| 392 IQLDETGLPLYALYHNwlMSKDvwiigRYFSSLVRPA--AEFLVGSIDRTTNLPaeSFDLWEERRGSHAY--TAAVVHAG 467
                                    7*************98855555555545666666666..666777777777777999*************..******** PP

                                    HHHHHHHHHHCT-HHHHCCHHHHHHHHHHHHHSTTT..GGGEETTCCECECSCH.....HHHTTS--S-BCHHHHHHHHC CS
                 Glyco_hydro_15 194 lleaideadlfgakgdaqlvektkdeilnklqgkygckrgfwplfntylildgsfaedkeqvqeyrealdasllllpely 273
                                    l  a ++a+ +g+++  + +++ ++ i             ++++ + + +  ++            + ldas+  +    
  gi|116754797|ref|YP_843915.1| 468 LRGASEIARILGNEKFHSRWSQAAELIRHAA------LDLYDDSIMHFRRSPSD------------STLDASVFSIWYFE 529
                                    *********************7777776655......23455555555555555............*******9999999 PP

                                    S-TTS-TT-TT-TTTSHHHHHHHHHHHHHHHHHSGGGTT-STTS--SBTT--CGSSSBSCT--BHHHHHHHH CS
                 Glyco_hydro_15 274 fvpaddvdeeyqnpqsprllaqslyildsllsegflavgeldplvrRysedvkpdklglsGrpyylctlwtv 345
                                      pa+d          pr+++++++i+++l++            v Ry +d++     +  +++ +ctlw +
  gi|116754797|ref|YP_843915.1| 530 LLPAND----------PRVVNTMRAIERELTRPSG--------GVARYMHDTYH----GYMNSWIICTLWLA 579
                                    9*****..........*************998643........49********7....77799999*99954 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.006
                                    HHHHHH.S-TTS---SEE-TTT--EESSTT-HHHHHHHHH CS
                 Glyco_hydro_15 407 veavee.dnslgvLteevdvylgeliraqpllfsealllr 445
                                    ++ + + + s+g++ e+v++ + ++++  pl++s+  ++ 
  gi|116754797|ref|YP_843915.1| 595 IKWCSDhTFSTGLMPEQVSD-DNTFRSVLPLMWSHCTFVL 633
                                    566778899*********98.789***********98875 PP

>> DUF608  Glycosyl-hydrolase family 116, catalytic region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1      0.15   1.4e+03     138     163 ..     198     226 ..     157     229 .. 0.64
   2 ?   11.6   0.0   1.2e-05      0.11     149     246 ..     440     535 ..     429     626 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.15
                         DUF608 138 fDkdkdglienegfadqtYDa...wsvkG 163
                                     D+++dg+   + +a+ + D+   w+++G
  gi|116754797|ref|YP_843915.1| 198 KDMEEDGMLSCNAVAHGSIDStisWRISG 226
                                    37888888888888888877766677776 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 1.2e-05
                         DUF608 149 egfadqtYDaws.vkGvsaycgglwlaaLeaaiemaellgdkkdaeeykellekakkvyekkLwnGeYfkydessseses 227
                                    ++ + +++D w+  +G  ay++ +  a L+ a+e+a++lg++k ++++++  e  +++    L+  +  ++ +s   s+s
  gi|116754797|ref|YP_843915.1| 440 TNLPAESFDLWEeRRGSHAYTAAVVHAGLRGASEIARILGNEKFHSRWSQAAELIRHAAL-DLYDDSIMHFRRS--PSDS 516
                                    4678899****7358**************************9999999888887777666.7888888777754..4666 PP

                         DUF608 228 imadqlaGqwylracglee 246
                                     +   +   wy +++  ++
  gi|116754797|ref|YP_843915.1| 517 TLDASVFSIWYFELLPAND 535
                                    6666777777777765555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (649 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.42
# Mc/sec: 4609.00
//
Query:       gi|116754798|ref|YP_843916.1|  [L=215]
Description: adenylate kinases [Methanosaeta thermophila PT]
Scores for complete 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  202.6   0.0    3.8e-60  202.4   0.0    1.0  1  ADK              Adenylate kinase
    8.2e-29  100.8   0.3    1.2e-28  100.2   0.0    1.4  1  AAA_17           AAA domain
    5.1e-17   61.6   5.5    1.1e-16   60.5   4.3    2.0  2  ADK_lid          Adenylate kinase, active site lid
    1.2e-06   29.1   0.1    5.5e-06   26.9   0.1    2.0  1  AAA_18           AAA domain
    5.2e-06   26.7   0.0    9.7e-06   25.8   0.0    1.3  1  AAA_33           AAA domain
    4.9e-05   23.1   0.0     0.0013   18.4   0.0    2.1  2  Thymidylate_kin  Thymidylate kinase
    0.00011   22.0   0.0    0.00017   21.4   0.0    1.3  1  Cytidylate_kin   Cytidylate kinase
    0.00059   20.3   0.1     0.0017   18.8   0.0    1.8  2  AAA              ATPase family associated with various cellul
     0.0069   16.1   0.0        0.4   10.4   0.1    2.2  2  AAA_24           AAA domain
     0.0077   16.0   0.0      0.013   15.2   0.0    1.4  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
  ------ inclusion threshold ------
      0.024   14.9   0.0       0.99    9.7   0.0    2.2  2  Hydin_ADK        Hydin Adenylate kinase-like domain
      0.024   14.9   0.0      0.042   14.1   0.0    1.4  1  AAA_28           AAA domain
      0.044   13.7   0.2       0.11   12.4   0.1    1.7  2  NTPase_1         NTPase
      0.082   13.4   0.0        0.1   13.1   0.0    1.5  1  ABC_tran         ABC transporter
      0.096   12.7   0.0        0.2   11.6   0.0    1.6  1  AAA_5            AAA domain (dynein-related subfamily)
       0.14   11.6   0.0       0.21   11.0   0.0    1.3  1  KTI12            Chromatin associated protein KTI12
       0.18   11.9   0.1        1.7    8.8   0.0    2.2  3  SKI              Shikimate kinase


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 !  202.4   0.0   3.6e-63   3.8e-60       1     150 [.       5     189 ..       5     190 .. 0.99

  Alignments for each domain:
  == domain 1  score: 202.4 bits;  conditional E-value: 3.6e-63
                                    EEESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHHCT-HHHHHHHHHHHTTSS--HHHHHHHHHHHHHCHGTTTEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            ADK   1 llGaPgaGKGtqaeklvkkyglahlstGdllRaevksgtelGkeakevmdkgelvpdevvvklvkeelekedkkkgfllD 80 
                                    llG+Pg+GKGtqa+ +++k++++h+stGd+lR++v++gtelGkeak++md+g+lvpd+++++++k++l+k+d + g++lD
  gi|116754798|ref|YP_843916.1|   5 LLGPPGSGKGTQAKMIAEKFNVKHISTGDILREHVRNGTELGKEAKKYMDAGQLVPDSILIGIIKDRLSKPDVAGGYMLD 84 
                                    79****************************************************************************** PP

                                    SB-SSHHHHHHHHHHHHHHTSEESEEEEEE--HHHHHHHHHT...................................GSH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...................................xxx RF
                            ADK  81 GfPRtveqaealeelleeekvkldlvleldvpeevlveRltg...................................Dne 125
                                    G+PRt++qaeal+++l e k+k+d+vl++dvp+e lv+Rl+g                                   D+e
  gi|116754798|ref|YP_843916.1|  85 GYPRTIPQAEALDKILPELKQKIDVVLNIDVPDEELVRRLSGrrmckcgrsyhiifnppkvpgkcdecggelyhrddDKE 164
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx RF
                            ADK 126 etvkkRletykkqtkplidyykkkg 150
                                    e++ +Rl++yk+qt+plidyy+k g
  gi|116754798|ref|YP_843916.1| 165 EAILNRLKVYKQQTQPLIDYYTKAG 189
                                    *********************9975 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.2   0.0   1.1e-31   1.2e-28       1     123 [.       6     128 ..       6     137 .. 0.94

  Alignments for each domain:
  == domain 1  score: 100.2 bits;  conditional E-value: 1.1e-31
                                    EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTT.TS.HSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE CS
                         AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrg.gl.akardemrklpleekkelqkeaaekiaeeakkkgvlvdg 78 
                                    lG+PGsGKgtq++ ++ek++++h+s+Gd+lre +++g +l ++a+++m+ ++l+++  l  ++++++ + +  +g+++dg
  gi|116754798|ref|YP_843916.1|   6 LGPPGSGKGTQAKMIAEKFNVKHISTGDILREHVRNGtELgKEAKKYMDAGQLVPDSILIGIIKDRLSKPDVAGGYMLDG 85 
                                    7*********************************99966778999*********************************** PP

                                    -SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHT CS
                         AAA_17  79 hprikeqagfldglpkevleelkpdaiilleadpeeilerrlkdr 123
                                    +pr+  qa++ld++  e ++++  d+++ +++++ee+++r+  +r
  gi|116754798|ref|YP_843916.1|  86 YPRTIPQAEALDKILPELKQKI--DVVLNIDVPDEELVRRLSGRR 128
                                    *****************99999..**************9998875 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       1.2   1.2e+03      25      34 ..     114     123 ..      91     123 .. 0.81
   2 !   60.5   4.3   1.1e-19   1.1e-16       1      36 []     127     161 ..     127     161 .. 0.98

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.2
                                    TTT--.-B-- CS
                        ADK_lid  25 DkCGepLvqR 34 
                                    D++ e+Lv+R
  gi|116754798|ref|YP_843916.1| 114 DVPDEELVRR 123
                                    8899999999 PP

  == domain 2  score: 60.5 bits;  conditional E-value: 1.1e-19
                                    EEE-TTT--EEETTTB--SSTTB-TTT--.-B--GG CS
                        ADK_lid   1 RrvCpkCGrsYhvvfnpPkveglCDkCGepLvqRsD 36 
                                    Rr+C kCGrsYh++fnpPkv+g+CD+CG++L+ R+D
  gi|116754798|ref|YP_843916.1| 127 RRMC-KCGRSYHIIFNPPKVPGKCDECGGELYHRDD 161
                                    9***.6******99*********************9 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.1   5.3e-09   5.5e-06       1     115 [.       3     129 ..       3     134 .. 0.66

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 5.3e-09
                         AAA_18   1 IlltGtpGvGKttlakeLskrlgf.gvnlrdvakenglllevdpealdeskrldedkldklldaleenss.......... 69 
                                    I+l G+pG+GK t ak ++++ ++ ++  +d+++e+    ++  +   e k+  +  + +  ++l ++++          
  gi|116754798|ref|YP_843916.1|   3 IVLLGPPGSGKGTQAKMIAEKFNVkHISTGDILREHVRNGTELGK---EAKKYMDAGQLVPDSILIGIIKdrlskpdvag 79 
                                    89*******************755655555555555555555555...44444444556667777777777777555544 PP

                         AAA_18  70 .aleegknlvidghlaeleseaakdikk..........vvLtaspeelleRlekRgy 115
                                              +dg +    +++a d+              +++++eel +Rl+ R+ 
  gi|116754798|ref|YP_843916.1|  80 gY-------MLDGYPRTIPQAEALDKILpelkqkidvvLNIDVPDEELVRRLSGRRM 129
                                    40.......555555555555555444455555555448899************985 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   9.2e-09   9.7e-06       2     119 ..       3     128 ..       3     132 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 9.2e-09
                         AAA_33   2 vllvGlpGsGKstlaerllkklgavllssdtlrr.rlfg..tdqqsktdytrvldrlyq.ilnelarkalsag...rnvi 74 
                                    ++l G+pGsGK t a+ +++k  + ++s+ +++r  +++  +  +  ++y ++ + + + il ++++++ls+    ++++
  gi|116754798|ref|YP_843916.1|   3 IVLLGPPGSGKGTQAKMIAEKFNVKHISTGDILReHVRNgtELGKEAKKYMDAGQLVPDsILIGIIKDRLSKPdvaGGYM 82 
                                    5789***********************997766626665876666777899999886655777888888888766589** PP

                         AAA_33  75 ldatnlsrrerarflklarrlgvpvri.vvvetdeetlkeRlakRa 119
                                    ld   ++  + ++++k++++l+ ++ + + +++++e+l +Rl  R 
  gi|116754798|ref|YP_843916.1|  83 LDGYPRTIPQAEALDKILPELKQKIDVvLNIDVPDEELVRRLSGRR 128
                                    **********************998662679***********9995 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.3e-06    0.0013       3      65 ..       7      71 ..       7      83 .. 0.90
   2 ?    2.7   0.0     0.084        89     108     147 ..      97     141 ..      77     168 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.3e-06
                                   ESTTSSHHHHHHHHHHHHHHTTE....EEEESSSTTSHHHHHHHHHHHTCS---HHHHHHHHHHHH CS
                Thymidylate_kin  3 GlDGaGKttqaellkerlkeegik...vvltrepggteiGekirelllkeeeleeqteallfaadr 65
                                   G  G+GK tqa++++e+++ ++i+   +++ +   gte+G+ +++++  + +l + ++++ + +dr
  gi|116754798|ref|YP_843916.1|  7 GPPGSGKGTQAKMIAEKFNVKHIStgdILREHVRNGTELGKEAKKYMD-AGQLVPDSILIGIIKDR 71
                                   5669*******************99889999999************98.99999999988888888 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.084
                                    HHHGGGTTSE-SEEEEEESSHHHHHTSCCTTSS.....TTTSHHH CS
                Thymidylate_kin 108 lslnedvllkPdltflldvdpevalkRlakrde.....ldeeeee 147
                                     ++ +++  k d+++ +dv+ e+ ++Rl+ r++     +++ ++ 
  gi|116754798|ref|YP_843916.1|  97 DKILPELKQKIDVVLNIDVPDEELVRRLSGRRMckcgrSYHIIFN 141
                                    445555444779999999999999999999998655555555555 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   1.6e-07   0.00017       2      35 ..       4      37 ..       3      56 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.6e-07
                                   EEE-STTSSHHHHHHHHHHHHT-EEEEHHHHHHH CS
                 Cytidylate_kin  2 aiDGPagsGKssvaralaeklglkyldtgalYRa 35
                                    + GP gsGK++ a+++aek+++k ++tg + R 
  gi|116754798|ref|YP_843916.1|  4 VLLGPPGSGKGTQAKMIAEKFNVKHISTGDILRE 37
                                   566***************************9985 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.6e-06    0.0017       1      41 [.       3      41 ..       3      65 .. 0.75
   2 ?   -3.2   0.0       9.7     1e+04     112     130 ..      96     113 ..      90     115 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.6e-06
                                   EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTH CS
                            AAA  1 vllyGppGtGKTllakavakelgvefleisgsellskyvge 41
                                   ++l GppG GK + ak +a+++  ++  is  ++l ++v +
  gi|116754798|ref|YP_843916.1|  3 IVLLGPPGSGKGTQAKMIAEKF--NVKHISTGDILREHVRN 41
                                   5799*****************5..56777777777554444 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 9.7
                                    GGGSTHHHHSTTSSEEEET CS
                            AAA 112 pdkldpallrgRfdrkiei 130
                                     dk+ p+l  +++d++++i
  gi|116754798|ref|YP_843916.1|  96 LDKILPELK-QKIDVVLNI 113
                                    567777777.677777665 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.1   0.00038       0.4       4      25 ..       2      23 ..       1      33 [. 0.86
   2 ?    3.8   0.0      0.04        42     152     184 ..      95     131 ..      42     148 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00038
                         AAA_24  4 kiliyGpsgiGKTtlakelgpk 25
                                   +i++ Gp+g+GK t+ak++ +k
  gi|116754798|ref|YP_843916.1|  2 NIVLLGPPGSGKGTQAKMIAEK 23
                                   79***************98444 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.04
                         AAA_24 152 lgkktanelkeevDlvlranlkred....kvgervlk 184
                                      +k  +elk++ D+vl +++  e+     +g+r+ k
  gi|116754798|ref|YP_843916.1|  95 ALDKILPELKQKIDVVLNIDVPDEElvrrLSGRRMCK 131
                                    3345589************998777888844444444 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.3e-05     0.013      36      66 ..       3      32 ..       1      45 [. 0.83

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.3e-05
                         RuvB_N 36 vllyGpPGlGkttlakiiakelgvklkitsg 66
                                   ++l GpPG Gk t ak+ia++++vk  +t g
  gi|116754798|ref|YP_843916.1|  3 IVLLGPPGSGKGTQAKMIAEKFNVKHIST-G 32
                                   7899*****************99985444.3 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 ?    9.7   0.0   0.00094      0.99       2      42 ..       3      43 ..       2      55 .. 0.88
   2 ?    3.2   0.0     0.087        92     170     197 ..      58      85 ..      53      86 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00094
                      Hydin_ADK  2 iivhGaPlsGKtatavtLakkYeaAlltiDsvvleAisdgn 42
                                   i++ G+P sGK + a  +a k++   ++  +++ e + +g+
  gi|116754798|ref|YP_843916.1|  3 IVLLGPPGSGKGTQAKMIAEKFNVKHISTGDILREHVRNGT 43
                                   8899************************9999999988775 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.087
                      Hydin_ADK 170 vLPedllveIlsERlqlndCyrGvvfDg 197
                                    + P+ +l+ I+ +Rl   d   G ++Dg
  gi|116754798|ref|YP_843916.1|  58 LVPDSILIGIIKDRLSKPDVAGGYMLDG 85 
                                    57**************999999999998 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0     4e-05     0.042       1      45 [.       2      49 ..       2      68 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4e-05
                         AAA_28  1 kivitGgestGKTtlleaLaar.gypvv..pEaareileeklakgeda 45
                                   +iv++G++++GK t ++ +a++ +++++   ++ re ++++++ g++a
  gi|116754798|ref|YP_843916.1|  2 NIVLLGPPGSGKGTQAKMIAEKfNVKHIstGDILREHVRNGTELGKEA 49
                                   69******************9998888877999999999998877764 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1    0.0001      0.11       1      41 [.       2      42 ..       2      52 .. 0.88
   2 ?   -2.6   0.0       4.4   4.6e+03     122     146 ..     103     126 ..      93     132 .. 0.48

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0001
                                   EEEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE--- CS
                       NTPase_1  1 kvfiTGppGvGKtTlvkkvlellkssgvkvgGfyteevreg 41
                                   ++++ GppG+GK T  k ++e+ + + ++ g ++ e vr+g
  gi|116754798|ref|YP_843916.1|  2 NIVLLGPPGSGKGTQAKMIAEKFNVKHISTGDILREHVRNG 42
                                   58899******************999999988888888876 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.4
                                    HTTTSEEEEE--SS--SHHHHHHHT CS
                       NTPase_1 122 Lksekpvlavihrrkdlalveeire 146
                                    Lk++  v+  i ++ d++lv++++ 
  gi|116754798|ref|YP_843916.1| 103 LKQKIDVVLNIDVP-DEELVRRLSG 126
                                    23333333444444.6667766655 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   9.5e-05       0.1      14      42 ..       3      34 ..       1     181 [. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.5e-05
                                   EEEEESTTSSHHHHHHHHTTSS--...SEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx...xxxxx RF
                       ABC_tran 14 vaivGenGaGKStLlkllagllkp...teGei 42
                                   ++++G+ G+GK t +k++a++ +      G+i
  gi|116754798|ref|YP_843916.1|  3 IVLLGPPGSGKGTQAKMIAEKFNVkhiSTGDI 34
                                   789****************9987755566666 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   0.0   0.00019       0.2       1      25 [.       2      26 ..       2      51 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00019
                                   EEEEE--SSSSHHHHHHHGGGGBS- CS
                          AAA_5  1 dvlLvGppGtgKselaerlaaalnr 25
                                   +++L+GppG+gK + a+ +a+ +n 
  gi|116754798|ref|YP_843916.1|  2 NIVLLGPPGSGKGTQAKMIAEKFNV 26
                                   589*****************99875 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0002      0.21       4      32 ..       3      31 ..       1      58 [. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0002
                                   EEEE--TTSSHHHHHHHHHHHHHHTT--E CS
                          KTI12  4 vvltGlPssGKstrakeLakaleeekrsv 32
                                   +vl G P sGK t ak +a++++ +++s 
  gi|116754798|ref|YP_843916.1|  3 IVLLGPPGSGKGTQAKMIAEKFNVKHIST 31
                                   899*******************9876654 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0    0.0016       1.7       1      31 [.       9      39 ..       9      45 .. 0.86
   2 ?    0.2   0.0       0.7   7.4e+02      86     105 ..     108     127 ..      94     134 .. 0.81
   3 ?   -2.9   0.0         6   6.4e+03      99     133 ..     168     176 ..     157     209 .. 0.56

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0016
                                   TTSSHHHHHHHHHHHHTSEEEEHHHHHHHHH CS
                            SKI  1 mGaGKstvGkllAkklglefiDlDeliekrt 31
                                   +G+GK t +k++A+k +++ i + +++ +++
  gi|116754798|ref|YP_843916.1|  9 PGSGKGTQAKMIAEKFNVKHISTGDILREHV 39
                                   69*****************999877776655 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.7
                                    SEEEEEE--HHHHHHHHHHT CS
                            SKI  86 giviyLdvsleellerlkad 105
                                     +v+ +dv+ eel++rl+ +
  gi|116754798|ref|YP_843916.1| 108 DVVLNIDVPDEELVRRLSGR 127
                                    4678899*********9876 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 6
                                    HHHHHHTTSSGGGCSCHHHHHHHHHHHHHHHHHCC CS
                            SKI  99 lerlkadkeRPllqekskeeelleelaereplyee 133
                                    l+rlk                          +y++
  gi|116754798|ref|YP_843916.1| 168 LNRLK--------------------------VYKQ 176
                                    33333..........................2222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); 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 0.27s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1511.28
//
Query:       gi|116754799|ref|YP_843917.1|  [L=79]
Description: FeoA family protein [Methanosaeta thermophila PT]
Scores for complete 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   53.7   0.0      2e-14   53.6   0.0    1.1  1  FeoA      FeoA domain


Domain annotation for each model (and alignments):
>> FeoA  FeoA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.6   0.0   1.1e-18     2e-14       3      73 ..       4      73 ..       2      74 .. 0.90

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 1.1e-18
                                   GGG--TT-EEEEEEE-TT.SSHHHHHHHHT--TT-EEEEEEE-TTS-SEEEEETTEEEEE-HHHHTTEEEE CS
                           FeoA  3 LsdlkeGergeiarisdedpellrrLremGlvpGarievvarapfggplvvrvgdtrvaLgreeAqaIlVe 73
                                   L+ ++ +   e++++    +  ++rL+++G+++G r++ +  +pfggp+vv v++t+++Lgr++A++I Ve
  gi|116754799|ref|YP_843917.1|  4 LTKAPCNSLLEVKSFTGM-GGWQKRLEAIGIRKGIRLKKITCQPFGGPIVVDVNGTKISLGRGIASRIQVE 73
                                   555666667789999776.88*************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); 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: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 600.37
//
Query:       gi|116754800|ref|YP_843918.1|  [L=272]
Description: imidazole glycerol phosphate synthase subunit HisF [Methanosaeta thermophila PT]
Scores for complete 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-81  272.9   0.0    2.1e-81  272.7   0.0    1.0  1  His_biosynth  Histidine biosynthesis protein
    6.6e-08   32.0   0.0     0.0002   20.6   0.0    2.1  2  Dus           Dihydrouridine synthase (Dus)
      2e-05   24.1   0.1       0.13   11.6   0.0    2.1  2  NMO           Nitronate monooxygenase
    6.9e-05   22.2   0.0      0.014   14.7   0.0    2.1  2  DHO_dh        Dihydroorotate dehydrogenase
      7e-05   22.3   0.0     0.0038   16.6   0.0    2.2  2  G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
    7.5e-05   22.1   0.0     0.0031   16.8   0.0    2.1  2  ThiG          Thiazole biosynthesis protein ThiG
    7.7e-05   22.1   0.0        0.2   11.0   0.0    2.2  2  TMP-TENI      Thiamine monophosphate synthase
    0.00068   19.2   0.0      0.011   15.2   0.0    2.1  2  PcrB          PcrB family
     0.0066   15.7   0.1      0.058   12.6   0.0    2.3  3  NanE          Putative N-acetylmannosamine-6-phosphate epimer
  ------ inclusion threshold ------
      0.015   14.3   0.1        0.1   11.6   0.0    1.9  2  IMPDH         IMP dehydrogenase / GMP reductase domain
      0.035   13.1   0.0        0.1   11.6   0.0    1.8  1  FMN_dh        FMN-dependent dehydrogenase
      0.058   12.2   0.1      0.094   11.6   0.1    1.3  1  Trp_syntA     Tryptophan synthase alpha chain


Domain annotation for each model (and alignments):
>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  272.7   0.0   1.4e-84   2.1e-81       1     227 [.       5     251 ..       5     253 .. 0.96

  Alignments for each domain:
  == domain 1  score: 272.7 bits;  conditional E-value: 1.4e-84
                                    EEEEEEEE....ETTEEEEECTTCSTCEEEETTSHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEE CS
                   His_biosynth   1 riipalDl....kdGkvVrlvkGdrfqelryagdpvelakryeeegadelhvvDldaakegreanldlveeiaeevfipv 76 
                                    riip+lD+     +G+vV   kG +f++ ryag p+ela+ry+e+gade++++D++a++e r ++ d+++++ e+vf+p+
  gi|116754800|ref|YP_843918.1|   5 RIIPCLDCdlgvPNGRVV---KGIEFKQIRYAGVPWELATRYYEDGADEIVFLDITASHERRATMFDVIKKTSEHVFVPL 81 
                                    8******977778999**...*********************************************************** PP

                                    EEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEE......C............EEEEE CS
                   His_biosynth  77 qvGGGIrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarr......g............ykvai 138
                                    +vGGGI+sled++++++agadkv ++taa+++peli+e++e +gsq++vvaiDa+r      g            +++  
  gi|116754800|ref|YP_843918.1|  82 TVGGGISSLEDARNAFNAGADKVTVNTAALRRPELIREISESYGSQAVVVAIDAKRryqdldGritintesgrcwFECSY 161
                                    ********************************************************88776626666778889*9***** PP

                                    TTTTEEEEEEHHHHHHHHHHTT-SEEEEEETTTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHHHHTTC.SEE CS
                   His_biosynth 139 kgwreetgldavelakkleelgageilltdidrdGtlsGpdleltkelaeavkipviasGGvgsledlkelksegv.dav 217
                                    +g+r+ tg+da+ +a+++eelgageillt++drdGt +G+d+elt+++++ v+ipviasGG++s+e+++e+++ +  +a+
  gi|116754800|ref|YP_843918.1| 162 YGGRRFTGVDALAWARRVEELGAGEILLTSMDRDGTYDGFDIELTDAVSRMVRIPVIASGGCASPEHMYEVFRRTDaSAA 241
                                    ************************************************************************77777*** PP

                                    EESHHHHTTS CS
                   His_biosynth 218 ivgsalyege 227
                                    +++s++++++
  gi|116754800|ref|YP_843918.1| 242 LAASIFHFNQ 251
                                    *******986 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.3e-07    0.0002     170     226 ..      65     121 ..      38     140 .. 0.86
   2 !    9.6   0.0   0.00029      0.43     140     212 ..     172     243 ..     168     263 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.3e-07
                                    --CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHHH.H CS
                            Dus 170 adweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlfae.s 226
                                      ++ Ik+  ++v +p+ + G+I ++eda+++ +  Gad v +  +al++P l++e s
  gi|116754800|ref|YP_843918.1|  65 TMFDVIKKTSEHVFVPLTVGGGISSLEDARNAFNA-GADKVTVNTAALRRPELIREiS 121
                                    457899999************************99.******************9633 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00029
                                    HHHHHHHHHHCT-SEEEEESSECCCTT-CG--CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEE CS
                            Dus 140 alelakiveaaGaqaltvHgRtraqnyegtadweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmi 212
                                    al  a++ve+ Ga ++ +    r   y g  d+e   +v + v+ipvia G++ ++e + ++ ++t a + ++
  gi|116754800|ref|YP_843918.1| 172 ALAWARRVEELGAGEILLTSMDRDGTYDG-FDIELTDAVSRMVRIPVIASGGCASPEHMYEVFRRTDASAALA 243
                                    56677888888888888865555555555.5666778999**********************99998887665 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00018      0.26     180     226 ..      65     111 ..      55     131 .. 0.88
   2 !   11.6   0.0   8.9e-05      0.13     149     217 ..     176     238 ..     167     252 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00018
                            NMO 180 glfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtrfL 226
                                      f ++++  + v +P+   GGi   ++   a+ +GA  v + t+ L
  gi|116754800|ref|YP_843918.1|  65 TMFDVIKKTSEHVFVPLTVGGGISSLEDARNAFNAGADKVTVNTAAL 111
                                    46778888888888*****************************9976 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 8.9e-05
                            NMO 149 arkvearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAs 217
                                    ar ve++Ga  + ++ ++  G    +++      +L + v   v iPviA GG    + +  ++++  +
  gi|116754800|ref|YP_843918.1| 176 ARRVEELGAGEILLTSMDRDGTYDGFDI------ELTDAVSRMVRIPVIASGGCASPEHMYEVFRRTDA 238
                                    7777888877777777776554432555......599999999**********9988887777766544 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   9.1e-06     0.014     233     287 ..      69     120 ..      62     126 .. 0.79
   2 !    5.6   0.0    0.0054         8     239     280 ..     211     251 ..     202     264 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 9.1e-06
                                    HHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHHH CS
                         DHO_dh 233 virelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpkiakki 287
                                    vi + ++++   +p+   GGi+s eDa + ++aGA  v v ta   + p ++++i
  gi|116754800|ref|YP_843918.1|  69 VIKKTSEHVF--VPLTVGGGISSLEDARNAFNAGADKVTVNTAA-LRRPELIREI 120
                                    5555556666..899999************************98.5566666555 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0054
                                    HHTTT.S-EEEESS--SHHHHHHHHH.HTECEEEESHHHHHHG CS
                         DHO_dh 239 krlkkeipiIgvGGiesgeDalekie.aGAslvqvytalvfeg 280
                                    ++++  ip+I++GG  s e  +e ++   As+    + ++f+ 
  gi|116754800|ref|YP_843918.1| 211 RMVR--IPVIASGGCASPEHMYEVFRrTDASAALAASIFHFNQ 251
                                    4555..*************999987525677766666666654 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   2.6e-06    0.0038     126     170 ..      65     109 ..      63     111 .. 0.92
   2 ?    3.4   0.0     0.029        43     130     159 ..     205     234 ..     200     245 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.6e-06
                                    GGHHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE--H CS
                   G3P_antiterm 126 lvpkvikeikkelkipiiaGGLietkedveealkaGaiavstsnk 170
                                    ++ +vik++++++ +p+  GG i++ ed ++a++aGa+ v++ + 
  gi|116754800|ref|YP_843918.1|  65 TMFDVIKKTSEHVFVPLTVGGGISSLEDARNAFNAGADKVTVNTA 109
                                    6889************************************98765 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.029
                                    HHCTSTTS...EEEEESS--SHHHHHHHCT CS
                   G3P_antiterm 130 vikeikkelkipiiaGGLietkedveealk 159
                                    +++++++ ++ip+ia+G   + e++ e+++
  gi|116754800|ref|YP_843918.1| 205 LTDAVSRMVRIPVIASGGCASPEHMYEVFR 234
                                    67789999*********9999999988775 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   2.1e-06    0.0031     165     208 ..      68     111 ..      26     139 .. 0.81
   2 ?    3.4   0.0     0.027        41     134     194 ..     173     233 ..     167     247 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.1e-06
                                    HHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHH CS
                           ThiG 165 ealkiiieeakvPvivDAGigspsdaaqamelGadavllntava 208
                                     ++k   e++ vP+ v  Gi s +da +a++ Gad v +nta  
  gi|116754800|ref|YP_843918.1|  68 DVIKKTSEHVFVPLTVGGGISSLEDARNAFNAGADKVTVNTAAL 111
                                    56777889999******************************965 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.027
                                    HHHHHHHHHTT-SEBEEBS.SSTTS----S-HHHHHHHHHH-SS-BEEES---SHHHHHHHH CS
                           ThiG 134 lvlarrleevGcaavmPla.apiGsglGllnkealkiiieeakvPvivDAGigspsdaaqam 194
                                    l  arr+ee+G+  ++  +    G+  G    e    + + +++Pvi   G  sp++  +++
  gi|116754800|ref|YP_843918.1| 173 LAWARRVEELGAGEILLTSmDRDGTYDGFD-IELTDAVSRMVRIPVIASGGCASPEHMYEVF 233
                                    567899999999776654415568888865.45667888888*************9998876 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   0.00014       0.2     111     179 ..      42     108 ..      37     110 .. 0.79
   2 !    9.1   0.0    0.0005      0.74     119     170 ..     181     235 ..     172     246 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00014
                       TMP-TENI 111 eaealgadYigvGpifpTdtKkdaeplgleglkelaealeiPvvaiGGit.lenvaevleagadgvavvs 179
                                    +  ++gad i++  i  T++++ + +   + +k+++e++ +P+ + GGi+ le++ ++++agad v v +
  gi|116754800|ref|YP_843918.1|  42 RYYEDGADEIVFLDI--TASHERR-ATMFDVIKKTSEHVFVPLTVGGGISsLEDARNAFNAGADKVTVNT 108
                                    556677777777777..6666655.566899******************6379*************9866 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0005
                       TMP-TENI 119 YigvGpifpTdtKkda..eplgleglkelaealeiPvvaiGGi.tlenvaevlea 170
                                     +g+G i  T+   d   +  ++e+  +++++++iPv+a GG  ++e++ ev++ 
  gi|116754800|ref|YP_843918.1| 181 ELGAGEILLTSMDRDGtyDGFDIELTDAVSRMVRIPVIASGGCaSPEHMYEVFRR 235
                                    57888888888877775677889999****************7357888888755 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   7.3e-06     0.011     159     222 ..      54     120 ..      48     124 .. 0.71
   2 ?    1.9   0.0     0.088   1.3e+02     168     204 ..     203     238 ..     174     244 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 7.3e-06
                                    EE-TTSSS-HHHHHHHHHHHSSSE...EEEESS--SHHHHHHHHCC.SSEEEE-CHHHHHHHCHHHHH CS
                           PcrB 159 lEasGaledveevialkkklekar...livGGGirsaEkAkevvea.ADvivvGnvveekderkidai 222
                                    l+     e    + ++ kk ++     l vGGGi s E+A++  +a AD + v ++    + + i++i
  gi|116754800|ref|YP_843918.1|  54 LDITASHERRATMFDVIKKTSEHVfvpLTVGGGISSLEDARNAFNAgADKVTVNTAALRRP-ELIREI 120
                                    55555555556666666666665422278*********************99988776666.455555 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.088
                                    HHHHHHHHHHHSSSEEEEESS--SHHHHHHHHCCSSE CS
                           PcrB 168 veevialkkklekarlivGGGirsaEkAkevveaADv 204
                                    +e++ a + ++  + +i  GG  s+E+ +ev +  D+
  gi|116754800|ref|YP_843918.1| 203 IELTDA-VSRMVRIPVIASGGCASPEHMYEVFRRTDA 238
                                    455544.45667789999************9998886 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 !   12.6   0.0   3.9e-05     0.058     130     182 ..      63     117 ..      54     126 .. 0.76
   2 ?   -0.8   0.0      0.48   7.2e+02      54      78 ..     117     141 ..     115     150 .. 0.75
   3 ?   -0.5   0.0       0.4   5.9e+02     133     164 ..     202     234 ..     185     250 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.9e-05
                                    SS--HHHHHHHHHTT--.EEEES---SHHHHHHHHTT--SEEEE-HH.HH-HHHH CS
                           NanE 130 aepDfalvkalseaglk.viaeGrintPekakkaieiGvdavvvGsa.itrleei 182
                                        f+++k+ se  +  + + G i + e a++a++ G+d v+v +a + r+e i
  gi|116754800|ref|YP_843918.1|  63 RATMFDVIKKTSEHVFVpLTVGGGISSLEDARNAFNAGADKVTVNTAaLRRPELI 117
                                    55667888888887765588999*********************87615666554 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.48
                                    HHHHHHHHTTT-SEEEEE--SS--T CS
                           NanE  54 lkdideLaaagadiialDatdrerp 78 
                                    +++i e     a ++a+Da  r + 
  gi|116754800|ref|YP_843918.1| 117 IREISESYGSQAVVVAIDAKRRYQD 141
                                    6777888888889999999888655 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.4
                                    -HHHHHHHHH.TT--EEEES---SHHHHHHHHT CS
                           NanE 133 Dfalvkalse.aglkviaeGrintPekakkaie 164
                                    D++l  a+s    + via G   +Pe+  ++++
  gi|116754800|ref|YP_843918.1| 202 DIELTDAVSRmVRIPVIASGGCASPEHMYEVFR 234
                                    566666665414677999999999998877765 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   6.7e-05       0.1     113     172 ..      44     106 ..      33     109 .. 0.73
   2 ?    0.2   0.0      0.19   2.9e+02     202     223 ..     209     230 ..     195     246 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.7e-05
                                    HHTT-S.EEEEE-STSS..SHHHHHHHHHHHHHTTTSEEEEEEE-SHHHHHHHHHTT-SEEEE CS
                                    xxxxxx.xxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 113 veagvd.vlvvdsahgh..sekvleavkeikkkveeveviaGnvataegakaLieagadavkv 172
                                     e g+d ++++d++  h   +++ +++k+  ++v     ++G + + e a++ ++agad v v
  gi|116754800|ref|YP_843918.1|  44 YEDGADeIVFLDITASHerRATMFDVIKKTSEHVFVPLTVGGGISSLEDARNAFNAGADKVTV 106
                                    56666635556765555005567788888887775434689******************9987 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.19
                                    HHCTCT-EEEEES---SHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 202 aakkagvpviaDGGikysgdiv 223
                                    + +   +pvia GG  + +++ 
  gi|116754800|ref|YP_843918.1| 209 VSRMVRIPVIASGGCASPEHMY 230
                                    4566789*******99998886 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   6.7e-05       0.1     195     244 ..      57     107 ..      35     153 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.7e-05
                                    CCCHB-TC--HHHHHHHHHHHSSEEEEE.EE-SHHHHHHHHHTTESEEEE- CS
                         FMN_dh 195 vgkqldpsltwddikwlreqtklplvvK.GvltaedakraveaGvdgivvS 244
                                    ++++ +++  +d ik+  e++ +pl v  G+ + eda++a +aG+d + v 
  gi|116754800|ref|YP_843918.1|  57 TASHERRATMFDVIKKTSEHVFVPLTVGgGISSLEDARNAFNAGADKVTVN 107
                                    5555677778899************996369****************9995 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   6.3e-05     0.094     182     231 ..      62     112 ..      54     137 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.3e-05
                                    B-TTHHHHHHHHHHCTSS-EEEESSS-SHHHHHHHH.TT-SEEEE-HHHHH CS
                      Trp_syntA 182 vaaevdelverlkkltavPvavGFGistkeqvkqva.kvadGvivGSalvk 231
                                      a++ +++++ +++  vP+ vG Gis+ e+++++  ++ad v v  a ++
  gi|116754800|ref|YP_843918.1|  62 RRATMFDVIKKTSEHVFVPLTVGGGISSLEDARNAFnAGADKVTVNTAALR 112
                                    4556677899999999****************99887******99887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2020.27
//
Query:       gi|116754801|ref|YP_843919.1|  [L=199]
Description: imidazole glycerol phosphate synthase, glutamine amidotransferase subunit [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-20   73.7   0.0    1.9e-20   73.5   0.0    1.1  1  GATase         Glutamine amidotransferase class-I
    4.4e-06   26.7   0.0      0.099   12.5   0.0    2.1  2  SNO            SNO glutamine amidotransferase family
      1e-05   25.4   0.1      0.019   14.7   0.1    2.1  2  Peptidase_C26  Peptidase C26
    0.00031   20.4   0.0    0.00051   19.7   0.0    1.5  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.5   0.0   4.2e-24   1.9e-20       2     187 ..       4     194 ..       3     197 .. 0.80

  Alignments for each domain:
  == domain 1  score: 73.5 bits;  conditional E-value: 4.2e-24
                                    EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.TTTHHHHHHHHCT....STS-EEE CS
                         GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg.vegkieaikeare....nkiPiLG 76 
                                    ++D++ ++  ++ +a++++g + e+++      e      +++gi++ +G+gs g +++ ++  +e +e    +++P+LG
  gi|116754801|ref|YP_843919.1|   4 IVDYGMGNLFSIYNAFLKVGGDPEIKRDP----EF----GGAEGIVI-PGVGSFGrCTERLRRFQEPLEeritEGTPVLG 74 
                                    67888888888888888888888888822....33....46777776.689999995555544444444344479***** PP

                                    ETHHHHHHHHHTTT............EEE...EEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTT CS
                         GATase  77 ICLGmQllaiefgr............kvv...kekekehhggtmrlgddetallyglknevierhrHryevnpkelepag 141
                                    IC GmQ++++e+ +             vv   +  + +++g+++   +++ +ll g ++    ++ H+y + p    ++ 
  gi|116754801|ref|YP_843919.1|  75 ICIGMQVMLDESEEspgargfgwipgRVVrlpESVTVPQMGWNSLEIKKGMELLDGISPGDMFYFVHSYHCIP---YDQR 151
                                    **************99999888888855577788889*******9999999*********************9...4444 PP

                                    EEEEEEEETTEEEEEEEEETTTEEEESSBTTSTTSTTHHHHHHHHH CS
                         GATase 142 levtakseddeelmeiiekknpfvgvQFHPEststpegpellfnfl 187
                                     +v+a +  + el++++ k+n ++g+QFHPE+ s+p+g ++l+nf+
  gi|116754801|ref|YP_843919.1| 152 -VVAASTHYGVELAAVVAKDN-IYGTQFHPEK-SGPKGLRILENFV 194
                                    .55566667779999999999.*********6.78999*****996 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   2.4e-05      0.11      24      84 ..      27      85 ..      14      94 .. 0.81
   2 !   12.5   0.0   2.2e-05     0.099     141     186 ..     149     197 ..     138     199 .] 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.4e-05
                                   EE-SGGGGCC-SEEEE-SS-HHHHHHHHHHT.T-HHHHHHHHHTT.--EEEETHHHHHHCCE CS
                            SNO 24 tvkrkedlaevdaliiPGGestamskliert.glyedllefvknsekvvlGtCaGlillske 84
                                    +kr  ++ + ++++iPG  s  +++  er   + e+l e + ++  +vlG C G+ ++  e
  gi|116754801|ref|YP_843919.1| 27 EIKRDPEFGGAEGIVIPGVGS--FGRCTERLrRFQEPLEERITEG-TPVLGICIGMQVMLDE 85
                                   57888899999*******766..5677777525789********9.9*********766554 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 2.2e-05
                                    TTTCEEEEECTT.EEEEEE.ETTEEEESS-GGGST.THCHHHHHHHHHH CS
                            SNO 141 deavkvlyeldg.eivvak.qkkilatsfhPelae.ddirvhdyfveev 186
                                    d+ v+ ++ + g e+ ++  +++i +t fhPe +  ++ r+ + fv++v
  gi|116754801|ref|YP_843919.1| 149 DQRVVAASTHYGvELAAVVaKDNIYGTQFHPEKSGpKGLRILENFVRMV 197
                                    5667777777787776665377**********9863789*******997 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   4.2e-06     0.019      99     118 ..      63      82 ..      54      84 .. 0.91
   2 !    8.8   0.0   0.00027       1.2     184     216 .]     149     180 ..     114     180 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.2e-06
                  Peptidase_C26  99 raalergvPilgiCrGlqll 118
                                    ++ +++g+P+lgiC G+q++
  gi|116754801|ref|YP_843919.1|  63 EERITEGTPVLGICIGMQVM 82 
                                    67899*************98 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00027
                  Peptidase_C26 184 elrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                    + rv+A ++   +E   + +++  ++g Q+HPE
  gi|116754801|ref|YP_843919.1| 149 DQRVVAASTHYGVELAAVVAKD-NIYGTQFHPE 180
                                    5689999999999999988855.9********9 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.1e-07   0.00051      41     116 ..      37     103 ..      25     179 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.1e-07
                       GATase_3  41 adlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGeeiedpegvegeageveglglLdiete 116
                                    a+ +++pG  +  +  +  r ++++e ++e +++g+pvlgiC G+q++ +e e++ g         g g+++ +++
  gi|116754801|ref|YP_843919.1|  37 AEGIVIPGVGSFGRCTE--RLRRFQEPLEERITEGTPVLGICIGMQVMLDESEESPGA-------RGFGWIPGRVV 103
                                    56677777766666555..5555***********************998887776654.......66666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1421.35
//
Query:       gi|116754802|ref|YP_843920.1|  [L=532]
Description: ferredoxin-dependent glutamate synthase [Methanosaeta thermophila PT]
Scores for 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-17   61.4   0.0    9.2e-12   44.8   0.0    2.1  2  Glu_synthase  Conserved region in glutamate synthase


Domain annotation for each model (and alignments):
>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   8.7e-07     0.016      60     154 ..     113     235 ..      95     242 .. 0.85
   2 !   44.8   0.0   5.1e-16   9.2e-12     187     308 ..     285     412 ..     277     423 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8.7e-07
                                    -HHHHHTTEE---B-TTTS-HHHHHHHHHHHHHHT-B-EETT..S---GGGGS-----...................... CS
                   Glu_synthase  60 palkikkriltsamSyGalseeahealakamnrlgtksntGE..GGedeerlktakdv...................... 115
                                     +++++ +i t+a+    ++++  e +a+++   g++  +GE   G+d+e +   ++                       
  gi|116754802|ref|YP_843920.1| 113 RKVRMRVPIFTGALGSTDIARKNWEHFAIGAAISGITLVCGEnvCGVDPELVLGSDNKvkkspemdrrietykrfhegyg 192
                                    456788899999999999************************555******99999989********************* PP

                                    .SEEE..E-TT-TT--HHHH..HH-SEEEEE---TTSTTS--EE CS
                   Glu_synthase 116 .aikQ..vasgrFGvteeyL..nnakaleikiaQGakpgeGgql 154
                                      ++Q  v   r Gv e++   +n + +e+k +QGak   Gg++
  gi|116754802|ref|YP_843920.1| 193 eILVQmnVEDTRLGVAEYVSskHNLETIELKWGQGAKCI-GGEI 235
                                    95566226789****987651156789**********86.8875 PP

  == domain 2  score: 44.8 bits;  conditional E-value: 5.1e-16
                                    HHHHHHHHHHHHHH-TTSEEEEEEE-STTHHHHHHH..HHHTT-SEEEEE-TT---SSEEHHHHHHB---HHH..HHH.H CS
                   Glu_synthase 187 iedlaqliedLkevnkeakvsvKlvaeagvetiaag..vakanadiilidGleGGTGAspkssikhaGlPlel..ala.e 261
                                    +e + + +  L++++  ++++ K +a + ve   a    a+a+ d+i+idG  GGTG sp+ ++++ G+P+    ala e
  gi|116754802|ref|YP_843920.1| 285 KEGFLNEVDRLRDLG-FKRITLKTGAYSMVELAMAIrfGAEAHLDLITIDGAPGGTGMSPWPMMNEWGIPTFYleALAyE 363
                                    566778899999999.789*******999987665433899*****************************8542266547 PP

                                    HHHHHHHTT-GGG-EEEEESS--SHHHHHHHHHHT-...SEEE-SHHHHH CS
                   Glu_synthase 262 vdqtlkeeglrdrvsliadGglktgadvvkalalGA...davgigtaali 308
                                      ++l + g+r   +l ++Gg+ t + v+ka+a+G     av +g+a +i
  gi|116754802|ref|YP_843920.1| 364 FCERLSKRGMRVP-DLAMAGGFSTEDGVFKAIAMGSpyvKAVCMGRALMI 412
                                    7899999999864.8********************833345667777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (532 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 3568.99
//
Query:       gi|116754803|ref|YP_843921.1|  [L=310]
Description: phosphoribosylaminoimidazole-succinocarboxamide synthase [Methanosaeta thermophila PT]
Scores for 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-43  146.9   0.0    1.9e-42  145.6   0.0    1.5  1  SAICAR_synt  SAICAR synthetase
  ------ inclusion threshold ------
       0.07   11.9   0.1      0.099   11.5   0.1    1.2  1  BTV_NS2      Bluetongue virus non-structural protein NS2


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 !  145.6   0.0   2.1e-46   1.9e-42       2     245 ..      11     261 ..      10     267 .. 0.88

  Alignments for each domain:
  == domain 1  score: 145.6 bits;  conditional E-value: 2.1e-46
                                    EEE-SSEEEEE-SSTTEEEEEEESEEEECCCTEEEEETTHHHHHHHHHHHHHHHHHH..--BSEEEE............. CS
                    SAICAR_synt   2 lyeGKvrdvYeledddklllvakDrisAfdvvlkeeipgKGkvltqlsafwfeklek..ipnhliksldpe......... 70 
                                    l +GKv++ Y+l   ++l ++++D+is+fd + ++ ip KG+ l++   fwfe  e+  i+nh+++ l p+         
  gi|116754803|ref|YP_843921.1|  11 LMRGKVKEAYDL--GSELEFQFTDNISVFDKIIPTRIPYKGETLCREGVFWFERAERmgIRNHFVRYLPPAgmivrkvsi 88 
                                    689********9..458***************************************667******887766777888876 PP

                                    .-SSSEEEEE-EEEESEEEEEEEE--HHH........HH....HH....T--TT-EEEEEEEEEEE--CCCT.S-EE-HH CS
                    SAICAR_synt  71 qlegrsmlvkklkmlpvEvvvRgyltGslwkeykks.gkvcgirlpe..glkegeklpepiftpstKaeegehDenisee 147
                                       +r +   k +++p+E+++R y++Gsl+   +++  +   + +p+   +  +e+lpep +++stK e+   D  +s++
  gi|116754803|ref|YP_843921.1|  89 VSPERITRETKGHLIPLEFICRWYVAGSLFDRIESGeIEPEALGFPRgrKVSFAEQLPEPYIELSTKLEKT--DRLLSRD 166
                                    44577788889999***************9998887544344455551167789***************95..9****** PP

                                    HHH.HTT.-HHHHHHHHHHHHHHHHHHHHHHHHTTEEEEEEEEEEEEETTTTEEEEES--.STTTEEEEETTT.....GG CS
                    SAICAR_synt 148 evvealg.teeeaeeieelalavyekaaelaaergiilvDtKlEFGldeedgelvLaDevltpDssRfwdaetyeegkeq 226
                                    e++e+++ +++e+eei e+ +++ e +++ ++ rg+i vD K EF +de + e++++D   t D  Rfwd   yeeg+  
  gi|116754803|ref|YP_843921.1| 167 EALELAKlSPQEFEEITEIIIRIDEDIRRCVEPRGLIHVDGKKEFAFDE-NREIMVVDVYGTADEDRFWDRAMYEEGE-Y 244
                                    ***9999*****************************************5.9************************876.6 PP

                                    GB-STHHHHTT-STHHHHH CS
                    SAICAR_synt 227 eslDKqfvRdwleeveekw 245
                                      l K++vR++ ++   ++
  gi|116754803|ref|YP_843921.1| 245 VDLSKEYVRKYYRQ--IGY 261
                                    689*******9988..555 PP

>> BTV_NS2  Bluetongue virus non-structural protein NS2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   1.1e-05     0.099     245     296 ..     224     275 ..     178     279 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.1e-05
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        BTV_NS2 245 vktlsddddqgedasddehpkthitkeyiekvakqiklkderfmslssampq 296
                                    v   +d+d   + a  +e     ++key+ k  +qi  kd  + + ss mp+
  gi|116754803|ref|YP_843921.1| 224 VYGTADEDRFWDRAMYEEGEYVDLSKEYVRKYYRQIGYKDMLYQARSSKMPE 275
                                    444567777778899999999*****************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2299.28
//
Query:       gi|116754804|ref|YP_843922.1|  [L=505]
Description: periplasmic copper-binding [Methanosaeta thermophila PT]
Scores for complete 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  176.1  37.3    4.8e-47  160.3  29.2    2.2  2  NosD        Periplasmic copper-binding protein (NosD)
    2.3e-21   76.3  37.1    4.2e-13   49.4   5.4    2.7  2  Beta_helix  Right handed beta helix region


Domain annotation for each model (and alignments):
>> NosD  Periplasmic copper-binding protein (NosD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   1.0   6.5e-11   5.8e-07      43     132 ..     156     246 ..      94     248 .. 0.68
   2 !  160.3  29.2   5.4e-51   4.8e-47       8     240 ..     211     440 ..     205     441 .. 0.92

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 6.5e-11
                           NosD  43 ldnssnntitgntienlryGihlensesntiedntlssnesGialmsssnntlenNtisnnenyGillsdssnntisnNt 122
                                    l    n+t+++  +++ + G++ e+ ++  i+++t++s++ G+++ +ssn  +   +++++e++G   s+s+  t+++ +
  gi|116754804|ref|YP_843922.1| 156 LVFGRNVTLENISVRDAEVGVFAEDLNGLLINNSTFQSCKTGVLVLRSSNVSIISTEMIDCEKAGLNASNSRAFTVTGCR 235
                                    45555666666666666666666666666666666666666666666666655566666666666666666666666666 PP

                           NosD 123 is.nnnkGifl 132
                                    ++ n+++G+f+
  gi|116754804|ref|YP_843922.1| 236 AVnNTHAGLFF 246
                                    66666666665 PP

  == domain 2  score: 160.3 bits;  conditional E-value: 5.4e-51
                           NosD   8 devlvsargngiqlensegsei.snneisnsrdgilldnssnntitgntienlryGihlensesntiedntlssnesGia 86 
                                    +e +++  ++g++ +ns+ +++  + +++n+++g+++ n++++++++nt++++++G+++++++++ +++n+++ n++Gi+
  gi|116754804|ref|YP_843922.1| 211 TE-MIDCEKAGLNASNSRAFTVtGCRAVNNTHAGLFFRNCEDIDVRDNTLSKNSEGLVFWGTNHSSATGNQADLNYYGIL 289
                                    33.5555789************5667899999************************************************ PP

                           NosD  87 lmsssnntlenNtisnnen......yGills...dssnntisnNtisnnnkGiflens.ssntitgNriesnqkiGilll 156
                                    l  s+nnt+++Nt+ nn++      +G+ +s   +ss+n + +Nt+snn++G+ ++++ ++n ++ N+i++n ++G+  l
  gi|116754804|ref|YP_843922.1| 290 LAGSHNNTISGNTLVNNRRseivggFGVGMSiqaNSSYNLVFKNTASNNYNGLEITENcQRNALCANNISRN-THGVR-L 367
                                    *************************777666112455688***************9999*************.*****.* PP

                           NosD 157 sssegntiynNyFinnsenvkydgsnnneWnttktsgtniiggpylgGNyWsdydgeDadgDGigDtpYeindgv...iD 233
                                    +++++n+iy+N+F++n ++++++++ +  Wntt              GNy+sdy+g+D dgDG+gDtpY+i++g+   +D
  gi|116754804|ref|YP_843922.1| 368 DKNWNNLIYRNNFVDNVISAYDNQT-KSIWNTTV-------------GNYYSDYRGSDGDGDGMGDTPYTIPKGSsmaTD 433
                                    **********************997.********.............*************************888889** PP

                           NosD 234 ylplvnp 240
                                    y plv p
  gi|116754804|ref|YP_843922.1| 434 YRPLVMP 440
                                    ****998 PP

>> Beta_helix  Right handed beta helix region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.4   5.4   4.7e-17   4.2e-13      11     157 ..     140     280 ..     129     281 .. 0.89
   2 !   29.7  26.6   5.4e-11   4.9e-07      44     148 ..     283     391 ..     272     404 .. 0.87

  Alignments for each domain:
  == domain 1  score: 49.4 bits;  conditional E-value: 4.7e-17
                                    .EEESEEEES-SS-SEEE-SSS-.EEES-EEES-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES-EEES- CS
                     Beta_helix  11 vtiknntisnsggyGiylrgssnvvienneiannsgsGiyilgssnntisnntisdnngggialfgasnnlienneitdn 90 
                                    vt+ ++   + ++++i + g +  ++en  + +  + G+  +  ++  i n+t+  ++ +g+ +  +sn+ i   e++d+
  gi|116754804|ref|YP_843922.1| 140 VTFAGHLRLDLPNAAILVFGRNV-TLENISVRD-AEVGVFAEDLNGLLINNSTFQSCK-TGVLVLRSSNVSIISTEMIDC 216
                                    45555555566788888888887.***999999.************************.********************* PP

                                    SS-SEE-TT-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEEE-TT-SS--EEES-E CS
                     Beta_helix  91 ggsGiylnyssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGiavvgsssnvtvrnNt 157
                                    +++G++ ++s   t++++++ nn+++G+++++ + ++ v++Nt+++n+ +G+ ++g+++    ++N+
  gi|116754804|ref|YP_843922.1| 217 EKAGLNASNSRAFTVTGCRAVNNTHAGLFFRNCE-DIDVRDNTLSKNS-EGLVFWGTNH-SSATGNQ 280
                                    **********************************.************8.***8887777.7777765 PP

  == domain 2  score: 29.7 bits;  conditional E-value: 5.4e-11
                                    -SS-SEEE-TT-S-EEES-EEE---........SEEE-TT.--S--EEES-EEES-SS-SEE-T.T-S--EEES-EEEST CS
                     Beta_helix  44 nsgsGiyilgssnntisnntisdnn........gggialf.gasnnlienneitdnggsGiyln.yssnntienNiidnn 113
                                     +++Gi + gs nntis+nt  +n         g+g+ ++ ++s+nl+ +n+ ++n + G++++ ++++n +  N+i+ n
  gi|116754804|ref|YP_843922.1| 283 LNYYGILLAGSHNNTISGNTLVNNRrseivggfGVGMSIQaNSSYNLVFKNTASNNYN-GLEITeNCQRNALCANNISRN 361
                                    599****************************999999*******************99.*****99************** PP

                                    T--SEE---TT---EEES-EEES-SSEEEE-TT-S CS
                     Beta_helix 114 agsGividdsssnvtvtnNtitnnkgaGiavvgss 148
                                    + +G+ +d +  n+ +  N++++n++ +    +++
  gi|116754804|ref|YP_843922.1| 362 T-HGVRLDKNW-NNLIYRNNFVDNVISAY---DNQ 391
                                    *.*********.9999******9993333...332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (505 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 3514.09
//
Query:       gi|116754805|ref|YP_843923.1|  [L=451]
Description: phosphoribosylaminoimidazolecarboxamide formyltransferase [Methanosaeta thermophila PT]
Scores for complete 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-83  279.8   0.0    3.5e-83  279.5   0.0    1.1  1  AICARFT_IMPCHas  AICARFT/IMPCHase bienzyme


Domain annotation for each model (and alignments):
>> AICARFT_IMPCHas  AICARFT/IMPCHase bienzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  279.5   0.0   1.9e-87   3.5e-83      20     296 .]      83     382 ..      79     382 .. 0.90

  Alignments for each domain:
  == domain 1  score: 279.5 bits;  conditional E-value: 1.9e-87
                                    HHHHHHC.T.B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH..CSE...EEE.EEEEEESSSSSTTS-EEEEE-TTSTTH CS
                AICARFT_IMPCHas  20 vleelkk.gevsletrkklaakaFahtaaYDaaiaeylskq..lpetlklsl.ekkqkLrYGeNphQkaalyeeeeeegl 95 
                                    +le++++  ++  + ++  +a a  ++ a+Da   + l+++  +p+ +++sl ek+q+LrYGeN+hQ+aaly++    gl
  gi|116754805|ref|YP_843923.1|  83 MLEAISRdLNLADDVKRLASASALYRCMAFDASELHALQSDmyWPK-YSVSLfEKVQDLRYGENWHQRAALYARPGGLGL 161
                                    5666666457778888888999****************88765555.555555*******************98889999 PP

                                    HH-EEEESS---HHHHHHHHHHHHHHCTS.......E...EEEEEETTEEEEEEEESSHHHHHHHHHCCSHHHHTTEEEE CS
                AICARFT_IMPCHas  96 akaeqlqGkelsynNllDadaalelvkef.......a...avaivKHanpcGvAvgetlaeAyekAlaaDpvSaFGgiia 165
                                     +a +l+Gke+synN++Da++ le++ ++       +    ++ivKHanpcGvA g++l+eAy+ A+a+Dp SaFGg+i 
  gi|116754805|ref|YP_843923.1| 162 FRAVKLNGKEMSYNNFVDAETVLEMLIDLseydgvpTnrpLAVIVKHANPCGVAYGSDLEEAYRWAFATDPKSAFGGVIG 241
                                    *************************997655576661567555************************************* PP

                                    ECCEE-HHHHHHHTTS-ECEEEECEE-CCHHHCC.TTSSS-EEEE-SS-...........EEEEETTEEEEEE--G..TT CS
                AICARFT_IMPCHas 166 lnrevdaetaeeikkefleviiApsfeeealeil.kkkknlrvlelkee...........elrsvsgglLvqerdeakie 233
                                    +n +vd +tae+i + f+ev+iAp++e++ale+l ++k n r+l++ ++            +rsv gg+++q+ d+++i 
  gi|116754805|ref|YP_843923.1| 242 FNMKVDLATAEAIGDSFVEVLIAPGYEPDALELLtRNKPNRRILDIGDMlqrkdelyrghAFRSVFGGMMLQDYDREDIL 321
                                    **********************************7789********99445667788888***************86665 PP

                                    CCCSEEECSC---HHHHHHHHHHHHHCCCS-SS-EEEEETTEEEEEE-SSSSHHHHHHHHHHH CS
                AICARFT_IMPCHas 234 eeelkvvtkkkpteeeledllfawkvvkhvkSNaivlakdgqtvgiGaGqmsRvdsarlAvek 296
                                      e++vvt+++pt+ee ++l+fawkv k+vkSNa v+++ ++t+giG+Gq+sRvdsar+ +ek
  gi|116754805|ref|YP_843923.1| 322 --EWRVVTQRSPTPEENRALRFAWKVTKYVKSNALVYTTADRTIGIGSGQVSRVDSARFGAEK 382
                                    ..6*******************************************************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 3408.29
//
Query:       gi|116754806|ref|YP_843924.1|  [L=122]
Description: hypothetical protein Mthe_1512 [Methanosaeta thermophila PT]
Scores for 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   66.3   0.0    2.9e-18   65.8   0.0    1.3  1  DUF167    Uncharacterised ACR, YggU family COG1872
  ------ inclusion threshold ------
      0.045   13.9   0.0       0.12   12.5   0.0    1.6  2  CinA_KH   Damage-inducible protein CinA KH domain


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 !   65.8   0.0   3.2e-22   2.9e-18       1      75 [.      31     104 ..      31     106 .. 0.96

  Alignments for each domain:
  == domain 1  score: 65.8 bits;  conditional E-value: 3.2e-22
                                    EEEEEEES---SSS----...--TTTT-------TTIIIIIHHHHHHHHHHHHHS...SEEEE-S-GGGSEEEEE CS
                         DUF167   1 gvilavrvkPgakkdaigleedaegrealkvrvaappvdGkANkalikfLakalgvpksdveivsGeksreKvvr 75 
                                    gv+l++ v Pg+++  ++  + + +r+ ++vr+++ + +GkAN++l++ +++a+g+ + dvei sG++s++Kvv+
  gi|116754806|ref|YP_843924.1|  31 GVVLHIDVIPGSSELVVP-AGFNAWRGSIEVRLTERADKGKANRQLLQEISRAFGLTQGDVEIMSGHRSQRKVVL 104
                                    689***************.77899*************************************************97 PP

>> CinA_KH  Damage-inducible protein CinA KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.73   6.5e+03      11      24 ..      14      27 ..      13      32 .. 0.71
   2 ?   12.5   0.0   1.4e-05      0.12      32      61 ..      52      81 ..      46      84 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.73
                                   HHHHHHHHGGGS-B CS
                        CinA_KH 11 ESavaekladlidr 24
                                   E av + l+d i+r
  gi|116754806|ref|YP_843924.1| 14 EYAVVKTLDDAIER 27
                                   55777888888876 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 1.4e-05
                                   EEETTEEEEEEE...EEHHHHHHHHH.... CS
                        CinA_KH 32 yakegevtvRltakaaneeeaealiapvee 61
                                    a +g ++vRlt +a++ ++ ++l++++++
  gi|116754806|ref|YP_843924.1| 52 NAWRGSIEVRLTERADKGKANRQLLQEISR 81
                                   567899********************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); 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: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 976.29
//
Query:       gi|116754807|ref|YP_843925.1|  [L=147]
Description: TOPRIM domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-07   30.7   0.0    2.8e-06   27.5   0.0    2.1  1  Toprim    Toprim domain
      5e-06   26.9   0.0    3.6e-05   24.2   0.0    2.1  1  Toprim_4  Toprim domain
     0.0012   19.2   0.0     0.0022   18.4   0.0    1.5  1  Toprim_2  Toprim-like
  ------ inclusion threshold ------
       0.12   12.5   0.0       0.18   12.0   0.0    1.2  1  LepA_C    GTP-binding protein LepA C-terminus


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 !   27.5   0.0   6.3e-10   2.8e-06       3      89 ..      30      95 ..      28     110 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 6.3e-10
                                   EEESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHSTTEEEEEECTTTHHHHHHHHHHHHHHSEEEEECSSSHHHHHHHHHHH CS
                         Toprim  3 vivEgpsdaktiakalgsgfqavtaslGhildletefkpvyeeiedkkkvlkalkelakradeiilatDpDreGeaiawell 84
                                   vivEgp+d  +++++ g  + + ++s+   l+l++                    e+a+ ++ei+l+tD D  Ge+ia ++ 
  gi|116754807|ref|YP_843925.1| 30 VIVEGPRDRDALRRI-GVPGPILMSSQRSCLELAE--------------------ESARSYSEIVLMTDWDARGEEIAHKME 90
                                   778888888888888.5555555555555666655....................999**********************99 PP

                                   HHHTH CS
                         Toprim 85 evlke 89
                                   e+l++
  gi|116754807|ref|YP_843925.1| 91 EFLRP 95
                                   87773 PP

>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0     8e-09   3.6e-05       2      86 ..      28     101 ..      27     103 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 8e-09
                       Toprim_4   2 eiiiVEgyaDvlalekagiknvvavlg..galspldgirpeklktenlveaekkvkevilaldgDaeGeataerlaelll 79 
                                    +++iVEg+ D  al + g+++ +      + l   + ++ + + +          +e++l++d Da+Ge+ a++  e l+
  gi|116754807|ref|YP_843925.1|  28 AAVIVEGPRDRDALRRIGVPGPILMSSqrSCL---ELAEESARSY----------SEIVLMTDWDARGEEIAHKMEEFLR 94 
                                    689****************9977643311444...3333224555..........9******************888555 PP

                       Toprim_4  80 eegvkvt 86 
                                    ++gv+v 
  gi|116754807|ref|YP_843925.1|  95 PTGVRVD 101
                                    9999986 PP

>> Toprim_2  Toprim-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0     5e-07    0.0022      35      78 ..      62     103 ..      30     120 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 5e-07
                       Toprim_2  35 alkllerypekkvvlalDnDkaGrkaakrlaellreagvrekir 78 
                                    a +  ++y   ++vl++D D  G++ a ++ e lr +gvr+ + 
  gi|116754807|ref|YP_843925.1|  62 AEESARSY--SEIVLMTDWDARGEEIAHKMEEFLRPTGVRVDVE 103
                                    33334444..78***********************999554443 PP

>> LepA_C  GTP-binding protein LepA C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     4e-05      0.18       4      59 ..      64     119 ..      61     121 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4e-05
                                    CB-GGG-EEEETTTHHHHHHHHHHHHHHHS---SS-EEEEEEETTEEEEEEEE--- CS
                         LepA_C   4 ekvdaLslivhrskaeergrklvekLkeliprqlfevaiqaaigskviaretikal 59 
                                    e++ + s iv  ++ + rg+++++k++e+++    +v ++ +   k++ r++ik +
  gi|116754807|ref|YP_843925.1|  64 ESARSYSEIVLMTDWDARGEEIAHKMEEFLRPTGVRVDVEIRKRLKILVRKEIKDV 119
                                    5666789999999****************************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1156.22
//
Query:       gi|116754808|ref|YP_843926.1|  [L=166]
Description: hypothetical protein Mthe_1514 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 1195.73
//
Query:       gi|116754809|ref|YP_843927.1|  [L=160]
Description: putative small multi-drug export [Methanosaeta thermophila PT]
Scores for complete 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  122.8   3.6    1.9e-35  122.2   3.6    1.3  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 !  122.2   3.6     1e-39   1.9e-35       1     121 []      20     141 ..      20     141 .. 0.95

  Alignments for each domain:
  == domain 1  score: 122.2 bits;  conditional E-value: 1e-39
                Sm_multidrug_ex   1 Elrgaiplgillgldpllallvsvlgnllpvplillflrkllellkkkkllkklfekleekaekksekie.kygflGLll 79 
                                    El gaipl+i++g++pl+a+++sv+gnl+pv  +llfl +++++l +++   ++f++l +++++k  + + ++gf++L+l
  gi|116754809|ref|YP_843927.1|  20 ELCGAIPLAIACGYSPLEAYAISVIGNLIPVAPLLLFLGPVSSFLMRYPPGYRFFTWLFSRTRRKYIEGReEVGFAALTL 99 
                                    899****************************************999999*************9966555449******** PP

                Sm_multidrug_ex  80 FvaiPLpgTGawtGsliasllglkkkkallaillGvliaglI 121
                                    FvaiPLp+TGawtG+++a+llg+++  a+l+i+lGvliag++
  gi|116754809|ref|YP_843927.1| 100 FVAIPLPVTGAWTGCVLAFLLGFRPLPAFLSIALGVLIAGVV 141
                                    ***************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1180.05
//
Query:       gi|116754810|ref|YP_843928.1|  [L=263]
Description: methyltransferase type 11 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-24   85.7   0.0    3.7e-24   85.2   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    5.3e-23   81.6   0.0      1e-22   80.6   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    4.3e-21   75.4   0.0    8.1e-21   74.5   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
    4.3e-20   72.3   0.0    6.5e-20   71.7   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    3.9e-16   59.3   0.0    8.6e-16   58.2   0.0    1.6  1  Methyltransf_23  Methyltransferase domain
    2.3e-14   53.3   0.0    3.1e-14   52.9   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    1.6e-07   31.0   0.0    4.6e-07   29.5   0.0    1.7  2  Methyltransf_4   Putative methyltransferase
    1.9e-07   30.8   0.0    2.7e-07   30.3   0.0    1.2  1  MTS              Methyltransferase small domain
    2.8e-07   30.1   0.0    4.9e-07   29.3   0.0    1.4  1  CMAS             Mycolic acid cyclopropane synthetase
    4.3e-07   29.5   0.0    5.9e-07   29.0   0.0    1.1  1  Methyltransf_2   O-methyltransferase domain
    9.2e-07   28.8   0.0      2e-06   27.7   0.0    1.4  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    1.3e-05   24.4   0.0    1.7e-05   24.0   0.0    1.2  1  DREV             DREV methyltransferase
    4.9e-05   23.0   0.0    6.9e-05   22.6   0.0    1.1  1  NodS             Nodulation protein S (NodS)
    0.00051   19.7   0.0    0.00077   19.1   0.0    1.3  1  MetW             Methionine biosynthesis protein MetW
     0.0021   18.1   0.0     0.0032   17.5   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
     0.0038   16.2   0.0     0.0052   15.8   0.0    1.3  1  Methyltransf_9   Protein of unknown function (DUF1698)
      0.008   15.6   0.0       0.01   15.2   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
  ------ inclusion threshold ------
      0.033   13.3   0.0      0.049   12.7   0.0    1.2  1  Fibrillarin      Fibrillarin
      0.055   12.9   0.0      0.072   12.5   0.0    1.1  1  TehB             Tellurite resistance protein TehB
       0.16   11.2   1.1        3.4    6.8   0.0    2.7  3  Methyltransf_7   SAM dependent carboxyl methyltransferase
       0.18   11.2   0.0       0.31   10.5   0.0    1.3  1  Methyltransf_5   MraW methylase family
        0.2   11.5   0.0        1.7    8.4   0.0    2.0  2  Methyltransf_8   Hypothetical methyltransferase
       0.23   10.5   0.0       0.32   10.0   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase


Domain annotation for each model (and alignments):
>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.2   0.0   4.8e-27   3.7e-24       3     125 ..      31     151 ..      29     178 .. 0.89

  Alignments for each domain:
  == domain 1  score: 85.2 bits;  conditional E-value: 4.8e-27
                Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsne 82 
                                     + r+lD+GCG G++t ++  +l p++ v GiDis+++i++Ar + +   + n++Feqgd+ +l   +  e fD+++s++
  gi|116754810|ref|YP_843928.1|  31 GDERILDIGCGDGKITARIS-QLVPDGSVLGIDISPDMISFARRRYSPVIFRNLRFEQGDALDLR--FD-EEFDIVVSFA 106
                                    6789****************.999*****************************************..66.9********* PP

                Methyltransf_31  83 vlnaladpdkileeiervlkpggilliedpr..llaelpakveee 125
                                     l+ + d  ++l++i r l pgg++l++      +a+l++  +e 
  gi|116754810|ref|YP_843928.1| 107 CLHWIRDHLSVLQGIYRSLVPGGRMLVQCGGrgNAAQLLDTTSEV 151
                                    **************************9876655455555544444 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.6   0.0   1.3e-25     1e-22       1      97 []      35     129 ..      35     129 .. 0.94

  Alignments for each domain:
  == domain 1  score: 80.6 bits;  conditional E-value: 1.3e-25
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT...TEEEEESBCCGBSSSTTTEEEEEEESTGGGS CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl...nvefvqgdaedlpfedgsfDlvvssgalhhl 77 
                                    +Ld+GcG G++t+++++ +++++v+g+Dis++m+  ar+r++   +   n++f+qgda dl f++ +fD+vvs+ +lh++
  gi|116754810|ref|YP_843928.1|  35 ILDIGCGDGKITARISQLVPDGSVLGIDISPDMISFARRRYSP--VifrNLRFEQGDALDLRFDE-EFDIVVSFACLHWI 111
                                    8******************99********************65..3469*************986.9******888**98 PP

                                    SHHHHHHHHHHHHHHEEEEE CS
                Methyltransf_25  78 sdedlekalkeiarvLkpgG 97 
                                       d+  +l+ i+r L pgG
  gi|116754810|ref|YP_843928.1| 112 R--DHLSVLQGIYRSLVPGG 129
                                    7..7789************9 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.5   0.0     1e-23   8.1e-21       1      95 [.      36     132 ..      36     133 .. 0.97

  Alignments for each domain:
  == domain 1  score: 74.5 bits;  conditional E-value: 1e-23
                                    EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCH CS
                Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseegl.kvefvvadaeklpfednsfDlvvssevlhhvedp 77 
                                    Ld+GcG G++++ + + +  ++v+g+D+s+ m+  a++++s+  + +++f ++da +l f +  fD+vvs+ +lh++ d+
  gi|116754810|ref|YP_843928.1|  36 LDIGCGDGKITARISQLVpdGSVLGIDISPDMISFARRRYSPVIFrNLRFEQGDALDLRFDE-EFDIVVSFACLHWIRDH 114
                                    8**************9999************************99***************66.***************** PP

                                    HHHHHHHHHHEEEEEEEE CS
                Methyltransf_11  78 ekalkeiaRvLkpgGllv 95 
                                     ++l+ i+R L pgG+++
  gi|116754810|ref|YP_843928.1| 115 LSVLQGIYRSLVPGGRML 132
                                    ***************987 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.7   0.0   8.3e-23   6.5e-20       1      98 [.      36     130 ..      36     131 .. 0.93

  Alignments for each domain:
  == domain 1  score: 71.7 bits;  conditional E-value: 8.3e-23
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlk 80 
                                    L+iGcG+G +++++ +  pd +++g+Disp++i  a+++ +  +     n+++e+ d+ldl   + fD+vv++ +lh+++
  gi|116754810|ref|YP_843928.1|  36 LDIGCGDGKITARISQLVPDGSVLGIDISPDMISFARRRYSPVIF---RNLRFEQGDALDLRFDEEFDIVVSFACLHWIR 112
                                    8********************************999999999995...67888888888888888*************** PP

                Methyltransf_12  81 direvldnirklLkpgGr 98 
                                    d  +vl+ i++ L+pgGr
  gi|116754810|ref|YP_843928.1| 113 DHLSVLQGIYRSLVPGGR 130
                                    *****************8 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.2   0.0   1.1e-18   8.6e-16       6     122 ..      17     138 ..      12     190 .. 0.70

  Alignments for each domain:
  == domain 1  score: 58.2 bits;  conditional E-value: 1.1e-18
                Methyltransf_23   6 eeelsdklerllpklraggrvLdiGcGtGillevlrengf..svtgvDlspeaveiae......kakkaqkdqfdeqeaa 77 
                                    +e++  +l +l+   r + r+LdiGcG+G  +  +++ +   sv g+D+sp +++ a+       +++ +++q d+  + 
  gi|116754810|ref|YP_843928.1|  17 QEWAMSALSELS--IRGDERILDIGCGDGKITARISQLVPdgSVLGIDISPDMISFARrryspvIFRNLRFEQGDAL-DL 93 
                                    455667777787..78999**********6666677776669**************988886664444444444222.22 PP

                Methyltransf_23  78 epqgkfdlIvlrevlehvpdppellrqiatllkpgGylllsepla 122
                                      ++ fd++v++ +l++++d+ ++l+ i++ l pgG++l++  ++
  gi|116754810|ref|YP_843928.1|  94 RFDEEFDIVVSFACLHWIRDHLSVLQGIYRSLVPGGRMLVQCGGR 138
                                    34559***********************************98654 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   0.0   3.9e-17   3.1e-14      45     151 ..      29     133 ..      14     163 .. 0.89

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 3.9e-17
                                    S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES CS
                Ubie_methyltran  45 vkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtvsf 124
                                     +  +++lD+ +G g +++++s+ v   g v ++Di+++m++ ++++     + n++f q++a +L f+ + fD+v vsf
  gi|116754810|ref|YP_843928.1|  29 IRGDERILDIGCGDGKITARISQLV-PDGSVLGIDISPDMISFARRRYSPVIFRNLRFEQGDALDLRFD-EEFDIV-VSF 105
                                    455679****************998.679***************************************6.579*87.677 PP

                                    .-GGG-S-HHHHHHHHHHHEEEEEEEEE CS
                Ubie_methyltran 125 .GlrnvtDklkaLkeayrvlkpGGrlvv 151
                                      l  + D+l +L+ +yr l pGGr++v
  gi|116754810|ref|YP_843928.1| 106 aCLHWIRDHLSVLQGIYRSLVPGGRMLV 133
                                    26899********************987 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0   5.9e-10   4.6e-07       5      62 ..      35      92 ..      32      99 .. 0.95
   2 ?   -2.1   0.0       2.9   2.2e+03      23      48 ..     214     239 ..     211     258 .. 0.68

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 5.9e-10
                                   EEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCC CS
                 Methyltransf_4  5 vleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgdalk 62
                                   +l+iGcG G+++ ++++  Pd ++lGi+i+ +++  + ++     ++Nlr  +gdal+
  gi|116754810|ref|YP_843928.1| 35 ILDIGCGDGKITARISQLVPDGSVLGIDISPDMISFARRRYSPVIFRNLRFEQGDALD 92
                                   79******************************************************86 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.9
                                    STTSEEEEEES-HHHHHHHHHHHHHC CS
                 Methyltransf_4  23 nPdknflGiEirvkvvakvlkkieal 48 
                                    +P  + l +E+r++ v+++ ++  ++
  gi|116754810|ref|YP_843928.1| 214 HPYLQRLPVELRSPFVQEIARRYIDR 239
                                    56677788999999999998775544 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0   3.4e-10   2.7e-07      26     112 ..      26     113 ..      20     155 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 3.4e-10
                                    HCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTSTTS-EEEEEE- CS
                            MTS  26 tlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeveekkfdlivsN 104
                                     l+ + ++++lD+GcG G ++a + +  p+ +v  +d++   + +a++ ++   ++ +++ + d+l+   +++fd++vs 
  gi|116754810|ref|YP_843928.1|  26 ELSIRGDERILDIGCGDGKITARISQLVPDGSVLGIDISPDMISFARRRYSPVIFRnLRFEQGDALDLRFDEEFDIVVSF 105
                                    455556788*******************************************99999*********************97 PP

                                    --STTTCH CS
                            MTS 105 PPfhagka 112
                                      +h  ++
  gi|116754810|ref|YP_843928.1| 106 ACLHWIRD 113
                                    76666555 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0   6.3e-10   4.9e-07      43     170 ..      12     139 ..       3     167 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 6.3e-10
                                    HHHHHHHHHHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH.--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-G CS
                           CMAS  43 LeeAqlaKldlileklelkpGmtlLdiGcGWGslvrravery.dvkvvglTlSkeqaklakkrvdeldlerkvevklldy 121
                                      +Aq++    +l  l+++  +++LdiGcG G+++ r  +   d +v+g+ +S +    a++r   + ++ + + +  d 
  gi|116754810|ref|YP_843928.1|  12 CSSAQQEWAMSALSELSIRGDERILDIGCGDGKITARISQLVpDGSVLGIDISPDMISFARRRYSPVIFR-NLRFEQGDA 90 
                                    5789******************************99988765499******************9988654.444555554 PP

                                    GG..-----SEEEEES-GGGTSGGGHHHHHHHHHHHS-TT-EEEEEEEEE- CS
                           CMAS 122 ed..ldekvdrvvsvgafehvgkenydtffkklkkllkedGllllhtitsl 170
                                     d  +de++d vvs+  +  +  + +    + +++ l ++G++l+++  + 
  gi|116754810|ref|YP_843928.1|  91 LDlrFDEEFDIVVSFACLHWI--RDHLSVLQGIYRSLVPGGRMLVQCGGRG 139
                                    4422789********999877..56788999**************997655 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   7.5e-10   5.9e-07      51     164 ..      20     133 ..       5     151 .. 0.86

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 7.5e-10
                                    HHHHHHSS-GGG-SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-.HHHHHHHHHHS-----TTEEEEES-TTTS---.-- CS
                 Methyltransf_2  51 akkvleafdleglkslvDvGGGtGalakaivsayPtikvivfDl.peVveaAkehlsageeervefvgGdffkdslP.ea 128
                                    a ++l +  ++g ++++D+G G G + + i+++ P  +v+  D+ p+ ++ A++++s+   ++++f +Gd  + +   e 
  gi|116754810|ref|YP_843928.1|  20 AMSALSELSIRGDERILDIGCGDGKITARISQLVPDGSVLGIDIsPDMISFARRRYSPVIFRNLRFEQGDALDLRFDeEF 99 
                                    56788888999999*****************************988**************************99999556 PP

                                    SEEEEESSGGGS-HHHHHHHHHHHHHH--TT-EEEE CS
                 Methyltransf_2 129 DaillkrvlhDwsdekcvklLkrvkkalpagGkviv 164
                                    D+++    lh w  ++   +L+ ++++l +gG+++v
  gi|116754810|ref|YP_843928.1| 100 DIVVSFACLH-WIRDHL-SVLQGIYRSLVPGGRMLV 133
                                    6666666665.877775.689************987 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 !   27.7   0.0   2.6e-09     2e-06      56     174 ..      13     136 ..       6     153 .. 0.72

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 2.6e-09
                                    E--HHHHHH.HHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GG CS
                           PCMT  56 iSaphmval.alellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGr 134
                                    +Sa +  a+ al  l+++  +r+L++G+G G  ta +++lv  +g v++i+ ++++++ a+r+      +n+ +  gD  
  gi|116754810|ref|YP_843928.1|  13 SSAQQEWAMsALSELSIRGDERILDIGCGDGKITARISQLVP-DGSVLGIDISPDMISFARRRYSPVIFRNLRFEQGDAL 91 
                                    5555555542567788999*********************96.677********************************75 PP

                                    GTTGGG-SEEEEEESSBBSS--HHH......HHTEEEEEEEEEEES CS
                           PCMT 135 kGyeekaPYdaihvgaaapeiPeal......idQLkeGGrlvvPvg 174
                                            +d ++  a+ + i + l       + L +GGr++v  g
  gi|116754810|ref|YP_843928.1|  92 D-LRFDEEFDIVVSFACLHWIRDHLsvlqgiYRSLVPGGRMLVQCG 136
                                    3.33333466666666665544433211111567788888877776 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   2.2e-08   1.7e-05      91     186 ..      28     133 ..       1     135 [. 0.75

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.2e-08
                           DREV  91 sdqedkklldlGaGdGeitkrvaptfee..vyatelsetmrdrlkkkk....ynvl.....salelqetdvkldlilcln 159
                                    s + d+++ld+G GdG+it r+++ + +  v   ++s  m+   +++     ++ l      al+l+  d ++d+++++ 
  gi|116754810|ref|YP_843928.1|  28 SIRGDERILDIGCGDGKITARISQLVPDgsVLGIDISPDMISFARRRYspviFRNLrfeqgDALDLR-FDEEFDIVVSFA 106
                                    445689********************98889999999999865444430000444411111233444.566899****** PP

                           DREV 160 lldrcfdplklledirsalepngrviv 186
                                     l    d l +l+ i+  l p gr++v
  gi|116754810|ref|YP_843928.1| 107 CLHWIRDHLSVLQGIYRSLVPGGRMLV 133
                                    ***********************9987 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   8.8e-08   6.9e-05      33     133 ..      23     126 ..       2     140 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 8.8e-08
                           NodS  33 qilrlslaqgsiadalevGcaaGalterlapyckrltv..vdvveeaiararervkes..shiswivsdvqqfstdekfd 108
                                    ++ +ls+++     +l++Gc  G +t r++ +    +v  +d+ ++ i+ ar+r   +   ++ + + d   +  de+fd
  gi|116754810|ref|YP_843928.1|  23 ALSELSIRGD--ERILDIGCGDGKITARISQLVPDGSVlgIDISPDMISFARRRYSPVifRNLRFEQGDALDLRFDEEFD 100
                                    3444444443..479***************99876555448*************987522789999************** PP

                           NodS 109 livvaevlyyiedvae.lraavrnlv 133
                                    ++v    l++i+d    l++  r lv
  gi|116754810|ref|YP_843928.1| 101 IVVSFACLHWIRDHLSvLQGIYRSLV 126
                                    ************97651444445544 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   9.8e-07   0.00077      11     100 ..      29     123 ..      21     141 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 9.8e-07
                           MetW  11 ikpgsrvldlGcGdGellellke.ekqvdgrGleldeegvaecvakGlsviqgdl....dkdlenfedksfdyvvlsqtl 85 
                                    i+   r+ld+GcGdG++   + +   + +  G++++ + +  +  +   vi  +l     + l+   d++fd+vv    l
  gi|116754810|ref|YP_843928.1|  29 IRGDERILDIGCGDGKITARISQlVPDGSVLGIDISPDMISFARRRYSPVIFRNLrfeqGDALDLRFDEEFDIVVSFACL 108
                                    77889***********987775413455667999999999999888888887776222134588999************* PP

                           MetW  86 qatrnpkevldellr 100
                                      +r+  +vl+ + r
  gi|116754810|ref|YP_843928.1| 109 HWIRDHLSVLQGIYR 123
                                    ******999998776 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   4.1e-06    0.0032      24      88 ..      30      89 ..      16     104 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.1e-06
                Methyltransf_32 24 sgaltvvDvGaGkgYLsfvlalkeke.yklkvvgidakeelvekaekraeklgkkfnkrlsfaels 88
                                   +g+++++D+G+G g  + ++++        +v+gid++ ++++ a++r + +   f ++l+f++++
  gi|116754810|ref|YP_843928.1| 30 RGDERILDIGCGDGKITARISQ---LvPDGSVLGIDISPDMISFARRRYSPVI--F-RNLRFEQGD 89
                                   67899****************9...5489*******************99999..8.889998876 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   6.6e-06    0.0052     111     218 ..      27     134 ..      13     202 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.6e-06
                                    S.--TT-EEEEET-TTSHHHHHHHHCT-S.EEEEE---HHHHHHHHHHHCCTTTTSSEEEE---.GGGS-T---EEEEEE CS
                 Methyltransf_9 111 lsdlkgrtildvGcgnGyhlwrmvgegak.lvvGidPselfliqfeavrkllgedqrahllplg.ieqlpeleafdtvfs 188
                                    ls   + +ild+Gcg+G    r+    ++ +v+Gid s   +i f a r+++    r+  +  g   +l   e fd+v s
  gi|116754810|ref|YP_843928.1|  27 LSIRGDERILDIGCGDGKITARISQLVPDgSVLGIDISPD-MISF-ARRRYSPVIFRNLRFEQGdALDLRFDEEFDIVVS 104
                                    44445789**********9999876655426788887765.4555.5677776666665555542346777899****** PP

                                    ES-GGG-S-HHHHHHHHHCTEEEEEEEEEE CS
                 Methyltransf_9 189 mGvlyhrrsPldhllqlkdqlvkgGelvle 218
                                       l+  r  l  l+ +  +lv gG ++++
  gi|116754810|ref|YP_843928.1| 105 FACLHWIRDHLSVLQGIYRSLVPGGRMLVQ 134
                                    *************************99876 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.3e-05      0.01     153     239 ..      22     111 ..      17     135 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.3e-05
                           PrmA 153 ealekl.vkegeevlDvGtGSG.iLaiaaakLgakkvvavDiDevAvkvakeNaelNkvea.klevalseellk...eek 226
                                     al +l ++++e++lD+G+G G i a  ++++   +v+++Di +  ++ a++  +    ++ ++e    +++l+   +e+
  gi|116754810|ref|YP_843928.1|  22 SALSELsIRGDERILDIGCGDGkITARISQLVPDGSVLGIDISPDMISFARRRYSPVIFRNlRFEQ---GDALDlrfDEE 98 
                                    566555478899**********45555566667789**************9988877666656644...44443334788 PP

                           PrmA 227 advivaNILaevl 239
                                    +d++v+    + +
  gi|116754810|ref|YP_843928.1|  99 FDIVVSFACLHWI 111
                                    9999876555555 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   6.2e-05     0.049      60     107 ..      21      67 ..       2      76 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.2e-05
                                    HTT-S--S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHH CS
                    Fibrillarin  60 lkglkelpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprv 107
                                    ++ l+el i+ ++++L +G + G+  + +s +v  +g v +++ sp +
  gi|116754810|ref|YP_843928.1|  21 MSALSELSIRGDERILDIGCGDGKITARISQLVP-DGSVLGIDISPDM 67 
                                    6789999**************************9.9********9976 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   9.2e-05     0.072      33     129 ..      34     130 ..      20     169 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.2e-05
                                    EEEEES-TTSHHHHHHHHTT-E..EEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG----S-EEEEEEESSGGGS-G CS
                           TehB  33 kvldlgcgqgrnslylsllgyd..vtawdknensiafleeikekenlknistalydineaklderydfilstvvlmflea 110
                                    ++ld+gcg+g+ +  +s l  d  v  +d   + i+f ++  +   ++n++ +  d  ++++de++d+++s   l +++ 
  gi|116754810|ref|YP_843928.1|  34 RILDIGCGDGKITARISQLVPDgsVLGIDISPDMISFARRRYSPVIFRNLRFEQGDALDLRFDEEFDIVVSFACLHWIRD 113
                                    79**********9999988765338899*******************************************999988875 PP

                                    GGHHHHHHHHHHTEEEEEE CS
                           TehB 111 eripsiienmqectkvggy 129
                                    +   s+++ + +   +gg 
  gi|116754810|ref|YP_843928.1| 114 HL--SVLQGIYRSLVPGGR 130
                                    53..455555555555555 PP

>> Methyltransf_7  SAM dependent carboxyl methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       0.9     7e+02      17      30 ..      34      47 ..      21      53 .. 0.81
   2 ?    1.9   0.1      0.13     1e+02     108     122 ..      97     111 ..      95     122 .. 0.84
   3 ?    6.8   0.0    0.0043       3.4     167     212 ..     117     163 ..     111     166 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.9
                                   EEEEET--SSCHHH CS
                 Methyltransf_7 17 kiaDLGCSsGpNtl 30
                                   +i D+GC  G+ t 
  gi|116754810|ref|YP_843928.1| 34 RILDIGCGDGKITA 47
                                   799*****998775 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.13
                                    T-EEEEEEES-TTB- CS
                 Methyltransf_7 108 nslhlvhssysLhWl 122
                                    ++ ++v+s+ +LhW+
  gi|116754810|ref|YP_843928.1|  97 EEFDIVVSFACLHWI 111
                                    5789**********7 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0043
                                    HHHHHHHHEEEEEEEEEEEEE-.-S.STT--HHHHHHSSHHHHHHCC CS
                 Methyltransf_7 167 fLklRseElvpgGrmvltllgr.ksedplsegeasllwellaqalqd 212
                                     L+  ++ lvpgGrm++ + gr +  + l++++   l e +a+ ++d
  gi|116754810|ref|YP_843928.1| 117 VLQGIYRSLVPGGRMLVQCGGRgNAAQLLDTTSEVCLEESFASYFKD 163
                                    566667789*************7777777777766677777776665 PP

>> Methyltransf_5  MraW methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0    0.0004      0.31      12      75 ..      23      87 ..      19     101 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0004
                                   HHHHT---TT-EEEES--TTSHHHHHHHTT--TTEEEEEES-HHHHHHHTT.....---.EEEEE CS
                 Methyltransf_5 12 vvellepkedgvyiDaTlGaggHsealLeqlselrligidrDksalarakerLkefekr.ltlvk 75
                                   +++ l+++ d   +D   G+g  + ++ + +++ +++gid+ ++++  a++r ++ + r l++ +
  gi|116754810|ref|YP_843928.1| 23 ALSELSIRGDERILDIGCGDGKITARISQLVPDGSVLGIDISPDMISFARRRYSPVIFRnLRFEQ 87
                                   577899999*******************************************9998866566655 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0022       1.7      73      92 ..      32      51 ..      19      67 .. 0.84
   2 ?    0.6   0.0      0.54   4.2e+02     120     156 ..      96     133 ..      85     136 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0022
                                   TS-EEEES-TT-HHHHH--S CS
                 Methyltransf_8 73 nlvvadlGcGeakiaeavre 92
                                   +  + d+GcG+ ki+ ++++
  gi|116754810|ref|YP_843928.1| 32 DERILDIGCGDGKITARISQ 51
                                   56799*********998876 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.54
                                    TT-EEEEE..EES---SS-HHHHHHHHHHHEEEEEEEEE CS
                 Methyltransf_8 120 desvdvav..fclslmgtnladflkeanrvlkvGGllkv 156
                                    de  d++v   cl  +  +  + l+ ++r l +GG + v
  gi|116754810|ref|YP_843928.1|  96 DEEFDIVVsfACLHWIR-DHLSVLQGIYRSLVPGGRMLV 133
                                    77788887435887765.5567899**********8876 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00041      0.32      20      91 ..      21      96 ..      15     114 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00041
                                   HHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-..SEEEEE-S-HHHHHHHHCHTT..TCCCEEEE-S-CCGHHHH CS
                         RrnaAD 20 neIldklnleekltvleigpGkGilTeeLakra..kqvvvlElderLakllqkkls..kdeklkvvhqDflkfetp 91
                                    ++l++l ++ +  +l+ig G G  T+++ + +   +v  + + ++++ + + + s    ++l   + D+l+  + 
  gi|116754810|ref|YP_843928.1| 21 MSALSELSIRGDERILDIGCGDGKITARISQLVpdGSVLGIDISPDMISFARRRYSpvIFRNLRFEQGDALDLRFD 96
                                   5789999999********************9997667777788888888888877755566666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); 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:                        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 0.26s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 1970.91
//
Query:       gi|116754811|ref|YP_843929.1|  [L=607]
Description: integral membrane sensor signal transduction histidine kinase [Methanosaeta thermophila PT]
Scores for complete 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   80.7   0.0    1.8e-22   80.0   0.0    1.4  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
      5e-09   36.1   0.0    1.5e-08   34.5   0.0    1.9  1  HisKA        His Kinase A (phospho-acceptor) domain
     0.0025   17.7   0.0     0.0054   16.6   0.0    1.5  1  HATPase_c_5  GHKL domain
     0.0028   17.5   0.0     0.0051   16.6   0.0    1.4  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
  ------ inclusion threshold ------
      0.055   13.8   6.8         13    6.1   3.7    3.5  3  DUF1772      Domain of unknown function (DUF1772)
        5.9    6.8   7.6        6.4    6.7   0.1    3.2  3  DUF3754      Protein of unknown function (DUF3754)


Domain annotation for each model (and alignments):
>> 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 !   80.0   0.0     6e-26   1.8e-22       2     111 ..     489     596 ..     488     597 .. 0.88

  Alignments for each domain:
  == domain 1  score: 80.0 bits;  conditional E-value: 6e-26
                                    HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEE.EETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHH CS
                      HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveika.seddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsi 80 
                                    d  r  +++ nl++N++k+ +++ + ++ei   ++++ v+ v+DnGiGi+++++k++fe f++    +++++g G Gl+i
  gi|116754811|ref|YP_843929.1| 489 DRMRAVEALVNLIENSAKYMGDQRDPRIEIGCmRDGETVFYVKDNGIGIDPKNHKRVFELFYK---VDNRSEGAGAGLAI 565
                                    66788999***********77666666666654557***************************...445568******** PP

                                    HHHHHHHTTTEEEEEEETTTEEEEEEEEESS CS
                      HATPase_c  81 vkklvelmgGeiwvesepgrGttftftlple 111
                                    vkk++e +gG+iw+ese grG+t+ ftlpl+
  gi|116754811|ref|YP_843929.1| 566 VKKIIEVHGGRIWIESELGRGCTVFFTLPLS 596
                                    *****************************86 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 !   34.5   0.0   5.1e-12   1.5e-08       2      65 ..     379     444 ..     378     445 .. 0.94

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 5.1e-12
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHH CS
                          HisKA   2 lgrflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdlsrie 65 
                                    ++rf+ +v+H+Lr PL +++g++  L+++  + + +++ e ++++e  +  +d l++d L+lsri+
  gi|116754811|ref|YP_843929.1| 379 MERFIYTVSHDLRSPLITVSGFLGFLRDDieKGAWDKVGEDIDILEGAITKMDMLLQDTLELSRIG 444
                                    689***********************99999666789999************************97 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.8e-06    0.0054      10      90 ..     497     582 ..     489     589 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.8e-06
                    HATPase_c_5  10 lgnlLdNAieacskieeekrfIrltvrekkksliisieNsyegek....kkle...sskskkeehGiGlksireivkkyk 82 
                                    l nl++N+   + +++  ++ I++ + ++ +++++  +N +  +     + +e   +  +++e  G Gl  +++i++ ++
  gi|116754811|ref|YP_843929.1| 497 LVNLIENSAKYMGDQR--DPRIEIGCMRDGETVFYVKDNGIGIDPknhkRVFElfyKVDNRSEGAGAGLAIVKKIIEVHG 574
                                    6799999888888877..8********************97663322333333444667888999*************** PP

                    HATPase_c_5  83 gnlsieae 90 
                                    g ++ie e
  gi|116754811|ref|YP_843929.1| 575 GRIWIESE 582
                                    ****9987 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.7e-06    0.0051       4      62 ..     494     554 ..     491     568 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.7e-06
                    HATPase_c_3   4 ekAlaelvdNsld..AdaenvkievnknrgktgeivieDdGkGmseeelknalrlatsske 62 
                                     +Al+ l++Ns    +d +   ie+   r  ++ + ++D+G G+++++ k++++l  +  +
  gi|116754811|ref|YP_843929.1| 494 VEALVNLIENSAKymGDQRDPRIEIGCMRDGETVFYVKDNGIGIDPKNHKRVFELFYKVDN 554
                                    68*********876688887666666666679*******************9997655444 PP

>> DUF1772  Domain of unknown function (DUF1772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.051   1.5e+02      37      80 ..      54      95 ..      43     104 .. 0.75
   2 ?    6.1   3.7    0.0044        13       4      79 ..     163     230 ..     124     244 .. 0.73
   3 ?    3.7   0.0     0.025        73      32     135 ..     291     403 ..     268     405 .. 0.53

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.051
                        DUF1772 37 avfpplallsalafaylaaraasrgarllylaaaallllsivpy 80
                                    +fp++  l+al+++ +a r  +++   +y +a a ++++ v+y
  gi|116754811|ref|YP_843929.1| 54 IIFPVVNGLAALSLFRAA-RTTRSKDEMMY-IAWAFFAVAQVLY 95
                                   579999999999999444.66677777777.5466666677766 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0044
                        DUF1772   4 lafslfvvPallslpassslllkqwrrlfkrgkavfpplallsalafa.ylaaraasrgarllylaaaallllsivp 79 
                                    + +sl++ P++++l ++++ l+++        ++++p++ l+ a a++ ++++r    ++r ++l+aa++ ++ i+ 
  gi|116754811|ref|YP_843929.1| 163 IFWSLLIAPTVATLEEPDP-LANAI-------AVAYPVADLVLAFALIaLIFRRIEHIAQRPILLLAAGA-VFMIIA 230
                                    5678889999999997774.33333.......45569988888888884455444445555555444444.434554 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.025
                        DUF1772  32 fkrgkavfpplallsalafa.ylaaraasrgarllylaaaal.lllsivpyTllvmvPtNnkLaal............ke 97 
                                    +      +p ++++sa af+ +   +       +   +aa++  ++ ++++  ++ ++ N+ L a+            +e
  gi|116754811|ref|YP_843929.1| 291 Y------IPYICAISAYAFLiWSIEQEDVNLYIRHHHLAAGVgMIILLIILRQIIAIKENTMLYAAaqkelhqriaseRE 364
                                    4......7888999999998555533333333333435555544433333333333333544444444444544443221 PP

                        DUF1772  98 edakekedeaevrelle.rWgrlnlvRavlalaaavlgl 135
                                    ++   ke e+++ e+ +  ++  + +R+ l+++++ lg+
  gi|116754811|ref|YP_843929.1| 365 KEHLIKELESKTSEMERfIYTVSHDLRSPLITVSGFLGF 403
                                    111122222222223335888899999999999988886 PP

>> DUF3754  Protein of unknown function (DUF3754)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.2      0.33   9.8e+02      58     100 ..      51      92 ..      19     100 .. 0.77
   2 ?    2.6   0.5     0.041   1.2e+02      56     111 ..     146     211 ..     134     230 .. 0.68
   3 ?    6.7   0.1    0.0022       6.4      65     121 ..     295     350 ..     291     363 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.33
                        DUF3754  58 kdklllgvpaivglvavllkllkaeklknklssliaaliavla 100
                                    +d +++ v+ ++++++++ ++ +++  k++++ +  a++av+ 
  gi|116754811|ref|YP_843929.1|  51 IDDIIFPVVNGLAALSLFRAA-RTTRSKDEMMYIAWAFFAVAQ 92 
                                    466777788888888888777.777777777777777777764 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.041
                        DUF3754  56 rlkdklllgvpaivglvavllkll........kaeklknk..lssliaaliavlalggfafrqyvk 111
                                    r+k  l  gv++i++++++   l+        + + l+n+  +  ++a+l++ +al++++fr +  
  gi|116754811|ref|YP_843929.1| 146 RIKSLLDTGVVTIFAILIFWSLLIaptvatleEPDPLANAiaVAYPVADLVLAFALIALIFRRIEH 211
                                    566667778888888766555555778888874444444311456788888888888888887655 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0022
                        DUF3754  65 vpaivglvavllkllkaeklknklssliaaliavlalggfafrqyvkyknkkiryqk 121
                                    + ai + +++++++ ++e+++  +++  +a+ + + + ++++rq++++k+ ++ y +
  gi|116754811|ref|YP_843929.1| 295 ICAISAYAFLIWSI-EQEDVNLYIRHHHLAAGVGMIILLIILRQIIAIKENTMLYAA 350
                                    56899999999**8.**********************************99998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (607 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       922  (0.0514251); expected 358.6 (0.02)
Passed bias filter:                      636  (0.0354733); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.45
# Mc/sec: 4078.94
//
Query:       gi|116754812|ref|YP_843930.1|  [L=54]
Description: hypothetical protein Mthe_1518 [Methanosaeta thermophila PT]
Scores for complete 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   28.3   3.1    2.9e-06   27.3   3.1    1.5  1  Zn-ribbon_8     Zinc ribbon domain
    0.00057   19.9   0.2    0.00065   19.7   0.2    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
     0.0035   16.8   1.2       0.77    9.3   0.0    2.2  2  TF_Zn_Ribbon    TFIIB zinc-binding
     0.0036   17.3   0.4      0.005   16.8   0.4    1.2  1  DZR             Double zinc ribbon
     0.0037   17.3   0.5     0.0039   17.2   0.5    1.0  1  DUF1451         Zinc-ribbon containing domain
     0.0041   17.0   2.3       0.23   11.4   0.2    2.2  2  TFIIS_C         Transcription factor S-II (TFIIS)
     0.0064   16.2   5.7     0.0084   15.8   0.8    2.2  2  Zn_Tnp_IS1      InsA N-terminal domain
     0.0073   16.2   6.1       0.33   10.9   1.0    2.3  2  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
     0.0087   15.7   0.1       0.01   15.5   0.1    1.1  1  TackOD1         Thaumarchaeal output domain 1
  ------ inclusion threshold ------
      0.015   14.2   0.6      0.016   14.0   0.6    1.0  1  NRDD            Anaerobic ribonucleoside-triphosphate reducta
      0.017   15.1   4.9       0.44   10.6   0.7    2.1  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
      0.021   14.7   0.7       0.85    9.6   0.0    2.1  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
      0.029   14.3   0.5        2.1    8.3   0.1    2.2  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
      0.036   13.8   1.5       0.19   11.5   0.0    2.1  2  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
      0.039   13.9   0.2      0.039   13.9   0.2    1.2  1  zinc-ribbons_6  zinc-ribbons
      0.046   13.4   8.4       0.24   11.2   0.5    2.2  2  Rubredoxin_2    Rubredoxin metal binding domain
       0.17   11.8   2.1        6.4    6.8   0.2    2.1  2  zf-trcl         Probable zinc-ribbon domain
       0.36   10.3   5.5       0.97    8.9   0.2    2.3  2  zf-ribbon_3     zinc-ribbon domain
        1.1    9.4   6.8        1.3    9.1   0.8    2.3  2  UPF0547         Uncharacterised protein family UPF0547
        1.9    8.5   6.8          6    6.9   0.6    2.2  2  zinc_ribbon_4   zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   3.1   3.2e-09   2.9e-06       5      39 ..      23      53 ..      23      54 .] 0.88

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 3.2e-09
                    Zn-ribbon_8  5 eYrCeeCghefevlqsisdapltaCPeCgs.evrrv 39
                                   +Y C++Cgh+f  +        + CP+C+s +v+rv
  gi|116754812|ref|YP_843930.1| 23 DYVCRSCGHKFKGIGV-----GPRCPSCHSdDVERV 53
                                   7***********7762.....568***********7 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.2   7.2e-07   0.00065      68      99 ..      21      52 ..      18      54 .] 0.83

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 7.2e-07
                                   --EEEETTTS-EEECHHHHHS-TTTSSS-EEE CS
                           HypA 68 pvkvrCreCgkefeleekalrCpkCgsadvei 99
                                   p  + Cr+Cg++f+      rCp+C+s dve 
  gi|116754812|ref|YP_843930.1| 21 PTDYVCRSCGHKFKGIGVGPRCPSCHSDDVER 52
                                   67789*********6654579*******9986 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0   0.00086      0.77      18      27 ..      22      31 ..      11      34 .. 0.85
   2 !    6.7   0.3    0.0056       5.1       2      12 ..      41      51 ..      40      53 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00086
                                   TCEEESSSSB CS
                   TF_Zn_Ribbon 18 gelvCtdCGl 27
                                   +++vC +CG 
  gi|116754812|ref|YP_843930.1| 22 TDYVCRSCGH 31
                                   68*******7 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0056
                                   EETTTTCEECH CS
                   TF_Zn_Ribbon  2 kCPnCgstnlv 12
                                   +CP C+s++++
  gi|116754812|ref|YP_843930.1| 41 RCPSCHSDDVE 51
                                   6******9854 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.4   5.6e-06     0.005      11      37 ..      22      48 ..      17      52 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.6e-06
                            DZR 11 darfCseCgtklkavaaedrCpsCgek 37
                                    + +C  Cg+k k      rCpsC+++
  gi|116754812|ref|YP_843930.1| 22 TDYVCRSCGHKFKGIGVGPRCPSCHSD 48
                                   5789*********9999*******986 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.5   4.3e-06    0.0039     112     145 ..      21      52 ..      13      54 .] 0.87

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.3e-06
                        DUF1451 112 lGtlvCekCgkelalkkteeippCpkCgateFrR 145
                                    +  +vC++Cg++  +k  ++ p+Cp+C+++  +R
  gi|116754812|ref|YP_843930.1|  21 PTDYVCRSCGHK--FKGIGVGPRCPSCHSDDVER 52 
                                    6789******96..8999999********99888 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 !   11.4   0.2   0.00025      0.23      29      39 .]      24      34 ..      17      34 .. 0.92
   2 ?    5.9   0.1     0.013        12       2      11 ..      41      50 ..      40      53 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00025
                        TFIIS_C 29 ykCtkCghrWr 39
                                   y+C +Cgh+++
  gi|116754812|ref|YP_843930.1| 24 YVCRSCGHKFK 34
                                   9********97 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.013
                        TFIIS_C  2 kCpkCgsrea 11
                                   +Cp+C+s+++
  gi|116754812|ref|YP_843930.1| 41 RCPSCHSDDV 50
                                   6*****9875 PP

>> Zn_Tnp_IS1  InsA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.3     0.098        88      29      34 ..      24      29 ..      22      30 .. 0.89
   2 !   15.8   0.8   9.3e-06    0.0084       7      18 ..      41      52 ..      37      53 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.098
                     Zn_Tnp_IS1 29 frCrdC 34
                                   + Cr+C
  gi|116754812|ref|YP_843930.1| 24 YVCRSC 29
                                   89**** PP

  == domain 2  score: 15.8 bits;  conditional E-value: 9.3e-06
                     Zn_Tnp_IS1  7 hCPrCsstdVyR 18
                                    CP+C+s+dV R
  gi|116754812|ref|YP_843930.1| 41 RCPSCHSDDVER 52
                                   6*********88 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 !    8.0   0.3    0.0029       2.6      21      32 ..      19      30 ..      17      33 .. 0.79
   2 !   10.9   1.0   0.00037      0.33      26      37 .]      40      51 ..      39      51 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0029
                        DUF35_N 21 qfPPravCphCg 32
                                   +fP   vC+ Cg
  gi|116754812|ref|YP_843930.1| 19 FFPTDYVCRSCG 30
                                   677779999996 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00037
                        DUF35_N 26 avCphCgsddle 37
                                   + Cp C+sdd+e
  gi|116754812|ref|YP_843930.1| 40 PRCPSCHSDDVE 51
                                   68*******997 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   1.2e-05      0.01     146     171 ..      23      48 ..      15      53 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.2e-05
                        TackOD1 146 vykCnsCkslfsepevkarClsCeke 171
                                    +y+C+sC++ f+   v  rC sC++ 
  gi|116754812|ref|YP_843930.1|  23 DYVCRSCGHKFKGIGVGPRCPSCHSD 48 
                                    68899999999999999999999875 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.6   1.8e-05     0.016     508     535 ..      24      54 .]      18      54 .] 0.79

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.8e-05
                                    EEETT.--..EESS..SB-TTT--BE.EEEEE CS
                           NRDD 508 dvCnecgy..kgei..ekCpkCgseeevevir 535
                                     vC++cg+  kg+    +Cp+C+s++ ve++r
  gi|116754812|ref|YP_843930.1|  24 YVCRSCGHkfKGIGvgPRCPSCHSDD-VERVR 54 
                                    58******7766668888*****877.88875 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   0.2    0.0062       5.5      14      27 ..      19      32 ..      16      38 .. 0.78
   2 ?   10.6   0.7   0.00049      0.44      18      29 ..      39      50 ..      36      54 .] 0.78

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0062
                  Zn_Tnp_IS1595 14 rWpngfvCPhCgsr 27
                                   ++p+  vC  Cg++
  gi|116754812|ref|YP_843930.1| 19 FFPTDYVCRSCGHK 32
                                   67888899999976 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00049
                  Zn_Tnp_IS1595 18 gfvCPhCgsrka 29
                                   g++CP C+s+ +
  gi|116754812|ref|YP_843930.1| 39 GPRCPSCHSDDV 50
                                   79******9855 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00095      0.85      25      37 ..      24      36 ..      13      37 .. 0.79
   2 ?    3.9   0.3     0.055        49       6      11 ..      41      46 ..      41      52 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00095
                 Zn_ribbon_SprT 25 YrCrrCkgtLrgk 37
                                   Y Cr C+ +++g+
  gi|116754812|ref|YP_843930.1| 24 YVCRSCGHKFKGI 36
                                   99****9999875 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.055
                 Zn_ribbon_SprT  6 rCtgCg 11
                                   rC++C+
  gi|116754812|ref|YP_843930.1| 41 RCPSCH 46
                                   688887 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.041        37      20      28 ..      24      32 ..      22      34 .. 0.86
   2 ?    8.3   0.1    0.0024       2.1       3      11 ..      40      48 ..      38      50 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.041
                 PhnA_Zn_Ribbon 20 lvCpeCahE 28
                                   +vC  C+h 
  gi|116754812|ref|YP_843930.1| 24 YVCRSCGHK 32
                                   79*****95 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0024
                 PhnA_Zn_Ribbon  3 pkCplCaSe 11
                                   p Cp C S+
  gi|116754812|ref|YP_843930.1| 40 PRCPSCHSD 48
                                   89****998 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 ?   11.5   0.0   0.00021      0.19      37      53 ..      16      32 ..      11      33 .. 0.86
   2 ?    1.4   0.4      0.31   2.7e+02      46      51 ..      41      46 ..      41      48 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00021
                 zinc_ribbon_10 37 keeleevkyrCpkCgal 53
                                   +e++ ++ y+C +Cg++
  gi|116754812|ref|YP_843930.1| 16 PESFFPTDYVCRSCGHK 32
                                   5788999********97 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.31
                 zinc_ribbon_10 46 rCpkCg 51
                                   rCp+C 
  gi|116754812|ref|YP_843930.1| 41 RCPSCH 46
                                   677775 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   4.4e-05     0.039      15      37 ..      22      47 ..       5      54 .] 0.73

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.4e-05
                                   SEEE-TTT--EEEEE...EE-SSS-S CS
                 zinc-ribbons_6 15 eqyhCeaCqedlkke...alCpeCeq 37
                                   + y C++C +++k     + Cp C++
  gi|116754812|ref|YP_843930.1| 22 TDYVCRSCGHKFKGIgvgPRCPSCHS 47
                                   57889999997775411167888875 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.5   0.00026      0.24       1      10 [.      24      33 ..      24      36 .. 0.89
   2 ?    6.1   2.2      0.01       9.2      16      22 ..      41      47 ..      40      47 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00026
                   Rubredoxin_2  1 YvCsqCGfes 10
                                   YvC++CG+++
  gi|116754812|ref|YP_843930.1| 24 YVCRSCGHKF 33
                                   9******986 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.01
                   Rubredoxin_2 16 rCpsCgs 22
                                   rCpsC+s
  gi|116754812|ref|YP_843930.1| 41 RCPSCHS 47
                                   8****97 PP

>> zf-trcl  Probable zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.2    0.0072       6.4       5      14 ..      24      33 ..      22      34 .. 0.88
   2 ?    5.0   0.1     0.026        23      35      43 ..      41      49 ..      39      53 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0072
                        zf-trcl  5 ltCkdCgaef 14
                                   ++C++Cg +f
  gi|116754812|ref|YP_843930.1| 24 YVCRSCGHKF 33
                                   79*****998 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.026
                        zf-trcl 35 RCkaCRkar 43
                                   RC++C +++
  gi|116754812|ref|YP_843930.1| 41 RCPSCHSDD 49
                                   9****9876 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.2    0.0011      0.97      15      26 .]      22      33 ..      21      33 .. 0.81
   2 ?    3.4   1.2     0.061        55       4       8 ..      41      45 ..      40      48 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0011
                    zf-ribbon_3 15 ddnvCpyCGtkl 26
                                    d vC +CG+k+
  gi|116754812|ref|YP_843930.1| 22 TDYVCRSCGHKF 33
                                   5779*****985 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.061
                    zf-ribbon_3  4 rCPnC 8 
                                   rCP+C
  gi|116754812|ref|YP_843930.1| 41 RCPSC 45
                                   78888 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.8    0.0015       1.3      16      25 ..      25      34 ..      24      35 .. 0.90
   2 ?    3.5   0.6     0.085        76       2       7 ..      41      46 ..      41      48 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0015
                        UPF0547 16 fCphCGyvFq 25
                                   +C+ CG+ F+
  gi|116754812|ref|YP_843930.1| 25 VCRSCGHKFK 34
                                   6*99*****7 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.085
                        UPF0547  2 vCPeCe 7 
                                   +CP C 
  gi|116754812|ref|YP_843930.1| 41 RCPSCH 46
                                   599996 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.6    0.0067         6      28      36 .]      26      34 ..      24      34 .. 0.88
   2 ?    4.8   0.9     0.029        26       4      10 ..      41      47 ..      41      48 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0067
                  zinc_ribbon_4 28 CskCghvFr 36
                                   C  Cgh+F+
  gi|116754812|ref|YP_843930.1| 26 CRSCGHKFK 34
                                   999999995 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.029
                  zinc_ribbon_4  4 tCpsCka 10
                                   +CpsC++
  gi|116754812|ref|YP_843930.1| 41 RCPSCHS 47
                                   7999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); 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: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 395.89
//
Query:       gi|116754813|ref|YP_843931.1|  [L=122]
Description: hypothetical protein Mthe_1519 [Methanosaeta thermophila PT]
Scores for 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   66.3   0.0    2.9e-18   65.8   0.0    1.3  1  DUF167    Uncharacterised ACR, YggU family COG1872
  ------ inclusion threshold ------
      0.045   13.9   0.0       0.12   12.5   0.0    1.6  2  CinA_KH   Damage-inducible protein CinA KH domain


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 !   65.8   0.0   3.2e-22   2.9e-18       1      75 [.      31     104 ..      31     106 .. 0.96

  Alignments for each domain:
  == domain 1  score: 65.8 bits;  conditional E-value: 3.2e-22
                                    EEEEEEES---SSS----...--TTTT-------TTIIIIIHHHHHHHHHHHHHS...SEEEE-S-GGGSEEEEE CS
                         DUF167   1 gvilavrvkPgakkdaigleedaegrealkvrvaappvdGkANkalikfLakalgvpksdveivsGeksreKvvr 75 
                                    gv+l++ v Pg+++  ++  + + +r+ ++vr+++ + +GkAN++l++ +++a+g+ + dvei sG++s++Kvv+
  gi|116754813|ref|YP_843931.1|  31 GVVLHIDVIPGSSELVVP-AGFNAWRGSIEVRLTERADKGKANRQLLQEISRAFGLTQGDVEIMSGHRSQRKVVL 104
                                    689***************.77899*************************************************97 PP

>> CinA_KH  Damage-inducible protein CinA KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.73   6.5e+03      11      24 ..      14      27 ..      13      32 .. 0.71
   2 ?   12.5   0.0   1.4e-05      0.12      32      61 ..      52      81 ..      46      84 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.73
                                   HHHHHHHHGGGS-B CS
                        CinA_KH 11 ESavaekladlidr 24
                                   E av + l+d i+r
  gi|116754813|ref|YP_843931.1| 14 EYAVVKTLDDAIER 27
                                   55777888888876 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 1.4e-05
                                   EEETTEEEEEEE...EEHHHHHHHHH.... CS
                        CinA_KH 32 yakegevtvRltakaaneeeaealiapvee 61
                                    a +g ++vRlt +a++ ++ ++l++++++
  gi|116754813|ref|YP_843931.1| 52 NAWRGSIEVRLTERADKGKANRQLLQEISR 81
                                   567899********************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); 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 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 886.58
//
Query:       gi|116754814|ref|YP_843932.1|  [L=147]
Description: TOPRIM domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-07   30.7   0.0    2.8e-06   27.5   0.0    2.1  1  Toprim    Toprim domain
      5e-06   26.9   0.0    3.6e-05   24.2   0.0    2.1  1  Toprim_4  Toprim domain
     0.0012   19.2   0.0     0.0022   18.4   0.0    1.5  1  Toprim_2  Toprim-like
  ------ inclusion threshold ------
       0.12   12.5   0.0       0.18   12.0   0.0    1.2  1  LepA_C    GTP-binding protein LepA C-terminus


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 !   27.5   0.0   6.3e-10   2.8e-06       3      89 ..      30      95 ..      28     110 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 6.3e-10
                                   EEESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHSTTEEEEEECTTTHHHHHHHHHHHHHHSEEEEECSSSHHHHHHHHHHH CS
                         Toprim  3 vivEgpsdaktiakalgsgfqavtaslGhildletefkpvyeeiedkkkvlkalkelakradeiilatDpDreGeaiawell 84
                                   vivEgp+d  +++++ g  + + ++s+   l+l++                    e+a+ ++ei+l+tD D  Ge+ia ++ 
  gi|116754814|ref|YP_843932.1| 30 VIVEGPRDRDALRRI-GVPGPILMSSQRSCLELAE--------------------ESARSYSEIVLMTDWDARGEEIAHKME 90
                                   778888888888888.5555555555555666655....................999**********************99 PP

                                   HHHTH CS
                         Toprim 85 evlke 89
                                   e+l++
  gi|116754814|ref|YP_843932.1| 91 EFLRP 95
                                   87773 PP

>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0     8e-09   3.6e-05       2      86 ..      28     101 ..      27     103 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 8e-09
                       Toprim_4   2 eiiiVEgyaDvlalekagiknvvavlg..galspldgirpeklktenlveaekkvkevilaldgDaeGeataerlaelll 79 
                                    +++iVEg+ D  al + g+++ +      + l   + ++ + + +          +e++l++d Da+Ge+ a++  e l+
  gi|116754814|ref|YP_843932.1|  28 AAVIVEGPRDRDALRRIGVPGPILMSSqrSCL---ELAEESARSY----------SEIVLMTDWDARGEEIAHKMEEFLR 94 
                                    689****************9977643311444...3333224555..........9******************888555 PP

                       Toprim_4  80 eegvkvt 86 
                                    ++gv+v 
  gi|116754814|ref|YP_843932.1|  95 PTGVRVD 101
                                    9999986 PP

>> Toprim_2  Toprim-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0     5e-07    0.0022      35      78 ..      62     103 ..      30     120 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 5e-07
                       Toprim_2  35 alkllerypekkvvlalDnDkaGrkaakrlaellreagvrekir 78 
                                    a +  ++y   ++vl++D D  G++ a ++ e lr +gvr+ + 
  gi|116754814|ref|YP_843932.1|  62 AEESARSY--SEIVLMTDWDARGEEIAHKMEEFLRPTGVRVDVE 103
                                    33334444..78***********************999554443 PP

>> LepA_C  GTP-binding protein LepA C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     4e-05      0.18       4      59 ..      64     119 ..      61     121 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4e-05
                                    CB-GGG-EEEETTTHHHHHHHHHHHHHHHS---SS-EEEEEEETTEEEEEEEE--- CS
                         LepA_C   4 ekvdaLslivhrskaeergrklvekLkeliprqlfevaiqaaigskviaretikal 59 
                                    e++ + s iv  ++ + rg+++++k++e+++    +v ++ +   k++ r++ik +
  gi|116754814|ref|YP_843932.1|  64 ESARSYSEIVLMTDWDARGEEIAHKMEEFLRPTGVRVDVEIRKRLKILVRKEIKDV 119
                                    5666789999999****************************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1108.42
//
Query:       gi|116754815|ref|YP_843933.1|  [L=166]
Description: hypothetical protein Mthe_1521 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); 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 0.26s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1289.58
//
Query:       gi|116754816|ref|YP_843934.1|  [L=160]
Description: putative small multi-drug export [Methanosaeta thermophila PT]
Scores for complete 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-37  127.8   3.4      5e-37  127.2   3.4    1.3  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 !  127.2   3.4   2.8e-41     5e-37       1     121 []      20     141 ..      20     141 .. 0.96

  Alignments for each domain:
  == domain 1  score: 127.2 bits;  conditional E-value: 2.8e-41
                Sm_multidrug_ex   1 Elrgaiplgillgldpllallvsvlgnllpvplillflrkllellkkkkllkklfekleekaekksekie.kygflGLll 79 
                                    Elrgaipl+i++g++pl+a+++sv+gnl+pv  +llfl +++++l +++   ++f++l +++++k  + + ++gf++L+l
  gi|116754816|ref|YP_843934.1|  20 ELRGAIPLAIACGYSPLEAYAISVIGNLIPVAPLLLFLGPVSSFLMRYPPGYRFFTWLFSRTRRKYIEGReEVGFAALTL 99 
                                    9******************************************999999*************9966555449******** PP

                Sm_multidrug_ex  80 FvaiPLpgTGawtGsliasllglkkkkallaillGvliaglI 121
                                    FvaiPLp+TGawtG+++a+llg+++  a+l+i+lGvliag++
  gi|116754816|ref|YP_843934.1| 100 FVAIPLPVTGAWTGCVLAFLLGFRPLPAFLSIALGVLIAGVV 141
                                    ***************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 1336.47
//
Query:       gi|116754817|ref|YP_843935.1|  [L=263]
Description: methyltransferase type 11 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-24   85.7   0.0    3.7e-24   85.2   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    5.3e-23   81.6   0.0      1e-22   80.6   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    4.3e-21   75.4   0.0    8.1e-21   74.5   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
    4.3e-20   72.3   0.0    6.5e-20   71.7   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    3.9e-16   59.3   0.0    8.6e-16   58.2   0.0    1.6  1  Methyltransf_23  Methyltransferase domain
    2.3e-14   53.3   0.0    3.1e-14   52.9   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    1.6e-07   31.0   0.0    4.6e-07   29.5   0.0    1.7  2  Methyltransf_4   Putative methyltransferase
    1.9e-07   30.8   0.0    2.7e-07   30.3   0.0    1.2  1  MTS              Methyltransferase small domain
    2.8e-07   30.1   0.0    4.9e-07   29.3   0.0    1.4  1  CMAS             Mycolic acid cyclopropane synthetase
    4.3e-07   29.5   0.0    5.9e-07   29.0   0.0    1.1  1  Methyltransf_2   O-methyltransferase domain
    9.2e-07   28.8   0.0      2e-06   27.7   0.0    1.4  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    1.3e-05   24.4   0.0    1.7e-05   24.0   0.0    1.2  1  DREV             DREV methyltransferase
    4.9e-05   23.0   0.0    6.9e-05   22.6   0.0    1.1  1  NodS             Nodulation protein S (NodS)
    0.00051   19.7   0.0    0.00077   19.1   0.0    1.3  1  MetW             Methionine biosynthesis protein MetW
     0.0021   18.1   0.0     0.0032   17.5   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
     0.0038   16.2   0.0     0.0052   15.8   0.0    1.3  1  Methyltransf_9   Protein of unknown function (DUF1698)
      0.008   15.6   0.0       0.01   15.2   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
  ------ inclusion threshold ------
      0.033   13.3   0.0      0.049   12.7   0.0    1.2  1  Fibrillarin      Fibrillarin
      0.055   12.9   0.0      0.072   12.5   0.0    1.1  1  TehB             Tellurite resistance protein TehB
       0.16   11.2   1.1        3.4    6.8   0.0    2.7  3  Methyltransf_7   SAM dependent carboxyl methyltransferase
       0.18   11.2   0.0       0.31   10.5   0.0    1.3  1  Methyltransf_5   MraW methylase family
        0.2   11.5   0.0        1.7    8.4   0.0    2.0  2  Methyltransf_8   Hypothetical methyltransferase
       0.23   10.5   0.0       0.32   10.0   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase


Domain annotation for each model (and alignments):
>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.2   0.0   4.8e-27   3.7e-24       3     125 ..      31     151 ..      29     178 .. 0.89

  Alignments for each domain:
  == domain 1  score: 85.2 bits;  conditional E-value: 4.8e-27
                Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsne 82 
                                     + r+lD+GCG G++t ++  +l p++ v GiDis+++i++Ar + +   + n++Feqgd+ +l   +  e fD+++s++
  gi|116754817|ref|YP_843935.1|  31 GDERILDIGCGDGKITARIS-QLVPDGSVLGIDISPDMISFARRRYSPVIFRNLRFEQGDALDLR--FD-EEFDIVVSFA 106
                                    6789****************.999*****************************************..66.9********* PP

                Methyltransf_31  83 vlnaladpdkileeiervlkpggilliedpr..llaelpakveee 125
                                     l+ + d  ++l++i r l pgg++l++      +a+l++  +e 
  gi|116754817|ref|YP_843935.1| 107 CLHWIRDHLSVLQGIYRSLVPGGRMLVQCGGrgNAAQLLDTTSEV 151
                                    **************************9876655455555544444 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.6   0.0   1.3e-25     1e-22       1      97 []      35     129 ..      35     129 .. 0.94

  Alignments for each domain:
  == domain 1  score: 80.6 bits;  conditional E-value: 1.3e-25
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT...TEEEEESBCCGBSSSTTTEEEEEEESTGGGS CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl...nvefvqgdaedlpfedgsfDlvvssgalhhl 77 
                                    +Ld+GcG G++t+++++ +++++v+g+Dis++m+  ar+r++   +   n++f+qgda dl f++ +fD+vvs+ +lh++
  gi|116754817|ref|YP_843935.1|  35 ILDIGCGDGKITARISQLVPDGSVLGIDISPDMISFARRRYSP--VifrNLRFEQGDALDLRFDE-EFDIVVSFACLHWI 111
                                    8******************99********************65..3469*************986.9******888**98 PP

                                    SHHHHHHHHHHHHHHEEEEE CS
                Methyltransf_25  78 sdedlekalkeiarvLkpgG 97 
                                       d+  +l+ i+r L pgG
  gi|116754817|ref|YP_843935.1| 112 R--DHLSVLQGIYRSLVPGG 129
                                    7..7789************9 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.5   0.0     1e-23   8.1e-21       1      95 [.      36     132 ..      36     133 .. 0.97

  Alignments for each domain:
  == domain 1  score: 74.5 bits;  conditional E-value: 1e-23
                                    EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCH CS
                Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseegl.kvefvvadaeklpfednsfDlvvssevlhhvedp 77 
                                    Ld+GcG G++++ + + +  ++v+g+D+s+ m+  a++++s+  + +++f ++da +l f +  fD+vvs+ +lh++ d+
  gi|116754817|ref|YP_843935.1|  36 LDIGCGDGKITARISQLVpdGSVLGIDISPDMISFARRRYSPVIFrNLRFEQGDALDLRFDE-EFDIVVSFACLHWIRDH 114
                                    8**************9999************************99***************66.***************** PP

                                    HHHHHHHHHHEEEEEEEE CS
                Methyltransf_11  78 ekalkeiaRvLkpgGllv 95 
                                     ++l+ i+R L pgG+++
  gi|116754817|ref|YP_843935.1| 115 LSVLQGIYRSLVPGGRML 132
                                    ***************987 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.7   0.0   8.3e-23   6.5e-20       1      98 [.      36     130 ..      36     131 .. 0.93

  Alignments for each domain:
  == domain 1  score: 71.7 bits;  conditional E-value: 8.3e-23
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlk 80 
                                    L+iGcG+G +++++ +  pd +++g+Disp++i  a+++ +  +     n+++e+ d+ldl   + fD+vv++ +lh+++
  gi|116754817|ref|YP_843935.1|  36 LDIGCGDGKITARISQLVPDGSVLGIDISPDMISFARRRYSPVIF---RNLRFEQGDALDLRFDEEFDIVVSFACLHWIR 112
                                    8********************************999999999995...67888888888888888*************** PP

                Methyltransf_12  81 direvldnirklLkpgGr 98 
                                    d  +vl+ i++ L+pgGr
  gi|116754817|ref|YP_843935.1| 113 DHLSVLQGIYRSLVPGGR 130
                                    *****************8 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.2   0.0   1.1e-18   8.6e-16       6     122 ..      17     138 ..      12     190 .. 0.70

  Alignments for each domain:
  == domain 1  score: 58.2 bits;  conditional E-value: 1.1e-18
                Methyltransf_23   6 eeelsdklerllpklraggrvLdiGcGtGillevlrengf..svtgvDlspeaveiae......kakkaqkdqfdeqeaa 77 
                                    +e++  +l +l+   r + r+LdiGcG+G  +  +++ +   sv g+D+sp +++ a+       +++ +++q d+  + 
  gi|116754817|ref|YP_843935.1|  17 QEWAMSALSELS--IRGDERILDIGCGDGKITARISQLVPdgSVLGIDISPDMISFARrryspvIFRNLRFEQGDAL-DL 93 
                                    455667777787..78999**********6666677776669**************988886664444444444222.22 PP

                Methyltransf_23  78 epqgkfdlIvlrevlehvpdppellrqiatllkpgGylllsepla 122
                                      ++ fd++v++ +l++++d+ ++l+ i++ l pgG++l++  ++
  gi|116754817|ref|YP_843935.1|  94 RFDEEFDIVVSFACLHWIRDHLSVLQGIYRSLVPGGRMLVQCGGR 138
                                    34559***********************************98654 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   0.0   3.9e-17   3.1e-14      45     151 ..      29     133 ..      14     163 .. 0.89

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 3.9e-17
                                    S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES CS
                Ubie_methyltran  45 vkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtvsf 124
                                     +  +++lD+ +G g +++++s+ v   g v ++Di+++m++ ++++     + n++f q++a +L f+ + fD+v vsf
  gi|116754817|ref|YP_843935.1|  29 IRGDERILDIGCGDGKITARISQLV-PDGSVLGIDISPDMISFARRRYSPVIFRNLRFEQGDALDLRFD-EEFDIV-VSF 105
                                    455679****************998.679***************************************6.579*87.677 PP

                                    .-GGG-S-HHHHHHHHHHHEEEEEEEEE CS
                Ubie_methyltran 125 .GlrnvtDklkaLkeayrvlkpGGrlvv 151
                                      l  + D+l +L+ +yr l pGGr++v
  gi|116754817|ref|YP_843935.1| 106 aCLHWIRDHLSVLQGIYRSLVPGGRMLV 133
                                    26899********************987 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0   5.9e-10   4.6e-07       5      62 ..      35      92 ..      32      99 .. 0.95
   2 ?   -2.1   0.0       2.9   2.2e+03      23      48 ..     214     239 ..     211     258 .. 0.68

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 5.9e-10
                                   EEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCC CS
                 Methyltransf_4  5 vleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgdalk 62
                                   +l+iGcG G+++ ++++  Pd ++lGi+i+ +++  + ++     ++Nlr  +gdal+
  gi|116754817|ref|YP_843935.1| 35 ILDIGCGDGKITARISQLVPDGSVLGIDISPDMISFARRRYSPVIFRNLRFEQGDALD 92
                                   79******************************************************86 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.9
                                    STTSEEEEEES-HHHHHHHHHHHHHC CS
                 Methyltransf_4  23 nPdknflGiEirvkvvakvlkkieal 48 
                                    +P  + l +E+r++ v+++ ++  ++
  gi|116754817|ref|YP_843935.1| 214 HPYLQRLPVELRSPFVQEIARRYIDR 239
                                    56677788999999999998775544 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0   3.4e-10   2.7e-07      26     112 ..      26     113 ..      20     155 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 3.4e-10
                                    HCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTSTTS-EEEEEE- CS
                            MTS  26 tlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeveekkfdlivsN 104
                                     l+ + ++++lD+GcG G ++a + +  p+ +v  +d++   + +a++ ++   ++ +++ + d+l+   +++fd++vs 
  gi|116754817|ref|YP_843935.1|  26 ELSIRGDERILDIGCGDGKITARISQLVPDGSVLGIDISPDMISFARRRYSPVIFRnLRFEQGDALDLRFDEEFDIVVSF 105
                                    455556788*******************************************99999*********************97 PP

                                    --STTTCH CS
                            MTS 105 PPfhagka 112
                                      +h  ++
  gi|116754817|ref|YP_843935.1| 106 ACLHWIRD 113
                                    76666555 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0   6.3e-10   4.9e-07      43     170 ..      12     139 ..       3     167 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 6.3e-10
                                    HHHHHHHHHHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH.--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-G CS
                           CMAS  43 LeeAqlaKldlileklelkpGmtlLdiGcGWGslvrravery.dvkvvglTlSkeqaklakkrvdeldlerkvevklldy 121
                                      +Aq++    +l  l+++  +++LdiGcG G+++ r  +   d +v+g+ +S +    a++r   + ++ + + +  d 
  gi|116754817|ref|YP_843935.1|  12 CSSAQQEWAMSALSELSIRGDERILDIGCGDGKITARISQLVpDGSVLGIDISPDMISFARRRYSPVIFR-NLRFEQGDA 90 
                                    5789******************************99988765499******************9988654.444555554 PP

                                    GG..-----SEEEEES-GGGTSGGGHHHHHHHHHHHS-TT-EEEEEEEEE- CS
                           CMAS 122 ed..ldekvdrvvsvgafehvgkenydtffkklkkllkedGllllhtitsl 170
                                     d  +de++d vvs+  +  +  + +    + +++ l ++G++l+++  + 
  gi|116754817|ref|YP_843935.1|  91 LDlrFDEEFDIVVSFACLHWI--RDHLSVLQGIYRSLVPGGRMLVQCGGRG 139
                                    4422789********999877..56788999**************997655 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   7.5e-10   5.9e-07      51     164 ..      20     133 ..       5     151 .. 0.86

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 7.5e-10
                                    HHHHHHSS-GGG-SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-.HHHHHHHHHHS-----TTEEEEES-TTTS---.-- CS
                 Methyltransf_2  51 akkvleafdleglkslvDvGGGtGalakaivsayPtikvivfDl.peVveaAkehlsageeervefvgGdffkdslP.ea 128
                                    a ++l +  ++g ++++D+G G G + + i+++ P  +v+  D+ p+ ++ A++++s+   ++++f +Gd  + +   e 
  gi|116754817|ref|YP_843935.1|  20 AMSALSELSIRGDERILDIGCGDGKITARISQLVPDGSVLGIDIsPDMISFARRRYSPVIFRNLRFEQGDALDLRFDeEF 99 
                                    56788888999999*****************************988**************************99999556 PP

                                    SEEEEESSGGGS-HHHHHHHHHHHHHH--TT-EEEE CS
                 Methyltransf_2 129 DaillkrvlhDwsdekcvklLkrvkkalpagGkviv 164
                                    D+++    lh w  ++   +L+ ++++l +gG+++v
  gi|116754817|ref|YP_843935.1| 100 DIVVSFACLH-WIRDHL-SVLQGIYRSLVPGGRMLV 133
                                    6666666665.877775.689************987 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 !   27.7   0.0   2.6e-09     2e-06      56     174 ..      13     136 ..       6     153 .. 0.72

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 2.6e-09
                                    E--HHHHHH.HHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GG CS
                           PCMT  56 iSaphmval.alellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGr 134
                                    +Sa +  a+ al  l+++  +r+L++G+G G  ta +++lv  +g v++i+ ++++++ a+r+      +n+ +  gD  
  gi|116754817|ref|YP_843935.1|  13 SSAQQEWAMsALSELSIRGDERILDIGCGDGKITARISQLVP-DGSVLGIDISPDMISFARRRYSPVIFRNLRFEQGDAL 91 
                                    5555555542567788999*********************96.677********************************75 PP

                                    GTTGGG-SEEEEEESSBBSS--HHH......HHTEEEEEEEEEEES CS
                           PCMT 135 kGyeekaPYdaihvgaaapeiPeal......idQLkeGGrlvvPvg 174
                                            +d ++  a+ + i + l       + L +GGr++v  g
  gi|116754817|ref|YP_843935.1|  92 D-LRFDEEFDIVVSFACLHWIRDHLsvlqgiYRSLVPGGRMLVQCG 136
                                    3.33333466666666665544433211111567788888877776 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   2.2e-08   1.7e-05      91     186 ..      28     133 ..       1     135 [. 0.75

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.2e-08
                           DREV  91 sdqedkklldlGaGdGeitkrvaptfee..vyatelsetmrdrlkkkk....ynvl.....salelqetdvkldlilcln 159
                                    s + d+++ld+G GdG+it r+++ + +  v   ++s  m+   +++     ++ l      al+l+  d ++d+++++ 
  gi|116754817|ref|YP_843935.1|  28 SIRGDERILDIGCGDGKITARISQLVPDgsVLGIDISPDMISFARRRYspviFRNLrfeqgDALDLR-FDEEFDIVVSFA 106
                                    445689********************98889999999999865444430000444411111233444.566899****** PP

                           DREV 160 lldrcfdplklledirsalepngrviv 186
                                     l    d l +l+ i+  l p gr++v
  gi|116754817|ref|YP_843935.1| 107 CLHWIRDHLSVLQGIYRSLVPGGRMLV 133
                                    ***********************9987 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   8.8e-08   6.9e-05      33     133 ..      23     126 ..       2     140 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 8.8e-08
                           NodS  33 qilrlslaqgsiadalevGcaaGalterlapyckrltv..vdvveeaiararervkes..shiswivsdvqqfstdekfd 108
                                    ++ +ls+++     +l++Gc  G +t r++ +    +v  +d+ ++ i+ ar+r   +   ++ + + d   +  de+fd
  gi|116754817|ref|YP_843935.1|  23 ALSELSIRGD--ERILDIGCGDGKITARISQLVPDGSVlgIDISPDMISFARRRYSPVifRNLRFEQGDALDLRFDEEFD 100
                                    3444444443..479***************99876555448*************987522789999************** PP

                           NodS 109 livvaevlyyiedvae.lraavrnlv 133
                                    ++v    l++i+d    l++  r lv
  gi|116754817|ref|YP_843935.1| 101 IVVSFACLHWIRDHLSvLQGIYRSLV 126
                                    ************97651444445544 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   9.8e-07   0.00077      11     100 ..      29     123 ..      21     141 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 9.8e-07
                           MetW  11 ikpgsrvldlGcGdGellellke.ekqvdgrGleldeegvaecvakGlsviqgdl....dkdlenfedksfdyvvlsqtl 85 
                                    i+   r+ld+GcGdG++   + +   + +  G++++ + +  +  +   vi  +l     + l+   d++fd+vv    l
  gi|116754817|ref|YP_843935.1|  29 IRGDERILDIGCGDGKITARISQlVPDGSVLGIDISPDMISFARRRYSPVIFRNLrfeqGDALDLRFDEEFDIVVSFACL 108
                                    77889***********987775413455667999999999999888888887776222134588999************* PP

                           MetW  86 qatrnpkevldellr 100
                                      +r+  +vl+ + r
  gi|116754817|ref|YP_843935.1| 109 HWIRDHLSVLQGIYR 123
                                    ******999998776 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   4.1e-06    0.0032      24      88 ..      30      89 ..      16     104 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.1e-06
                Methyltransf_32 24 sgaltvvDvGaGkgYLsfvlalkeke.yklkvvgidakeelvekaekraeklgkkfnkrlsfaels 88
                                   +g+++++D+G+G g  + ++++        +v+gid++ ++++ a++r + +   f ++l+f++++
  gi|116754817|ref|YP_843935.1| 30 RGDERILDIGCGDGKITARISQ---LvPDGSVLGIDISPDMISFARRRYSPVI--F-RNLRFEQGD 89
                                   67899****************9...5489*******************99999..8.889998876 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   6.6e-06    0.0052     111     218 ..      27     134 ..      13     202 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.6e-06
                                    S.--TT-EEEEET-TTSHHHHHHHHCT-S.EEEEE---HHHHHHHHHHHCCTTTTSSEEEE---.GGGS-T---EEEEEE CS
                 Methyltransf_9 111 lsdlkgrtildvGcgnGyhlwrmvgegak.lvvGidPselfliqfeavrkllgedqrahllplg.ieqlpeleafdtvfs 188
                                    ls   + +ild+Gcg+G    r+    ++ +v+Gid s   +i f a r+++    r+  +  g   +l   e fd+v s
  gi|116754817|ref|YP_843935.1|  27 LSIRGDERILDIGCGDGKITARISQLVPDgSVLGIDISPD-MISF-ARRRYSPVIFRNLRFEQGdALDLRFDEEFDIVVS 104
                                    44445789**********9999876655426788887765.4555.5677776666665555542346777899****** PP

                                    ES-GGG-S-HHHHHHHHHCTEEEEEEEEEE CS
                 Methyltransf_9 189 mGvlyhrrsPldhllqlkdqlvkgGelvle 218
                                       l+  r  l  l+ +  +lv gG ++++
  gi|116754817|ref|YP_843935.1| 105 FACLHWIRDHLSVLQGIYRSLVPGGRMLVQ 134
                                    *************************99876 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.3e-05      0.01     153     239 ..      22     111 ..      17     135 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.3e-05
                           PrmA 153 ealekl.vkegeevlDvGtGSG.iLaiaaakLgakkvvavDiDevAvkvakeNaelNkvea.klevalseellk...eek 226
                                     al +l ++++e++lD+G+G G i a  ++++   +v+++Di +  ++ a++  +    ++ ++e    +++l+   +e+
  gi|116754817|ref|YP_843935.1|  22 SALSELsIRGDERILDIGCGDGkITARISQLVPDGSVLGIDISPDMISFARRRYSPVIFRNlRFEQ---GDALDlrfDEE 98 
                                    566555478899**********45555566667789**************9988877666656644...44443334788 PP

                           PrmA 227 advivaNILaevl 239
                                    +d++v+    + +
  gi|116754817|ref|YP_843935.1|  99 FDIVVSFACLHWI 111
                                    9999876555555 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   6.2e-05     0.049      60     107 ..      21      67 ..       2      76 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.2e-05
                                    HTT-S--S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHH CS
                    Fibrillarin  60 lkglkelpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprv 107
                                    ++ l+el i+ ++++L +G + G+  + +s +v  +g v +++ sp +
  gi|116754817|ref|YP_843935.1|  21 MSALSELSIRGDERILDIGCGDGKITARISQLVP-DGSVLGIDISPDM 67 
                                    6789999**************************9.9********9976 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   9.2e-05     0.072      33     129 ..      34     130 ..      20     169 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.2e-05
                                    EEEEES-TTSHHHHHHHHTT-E..EEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG----S-EEEEEEESSGGGS-G CS
                           TehB  33 kvldlgcgqgrnslylsllgyd..vtawdknensiafleeikekenlknistalydineaklderydfilstvvlmflea 110
                                    ++ld+gcg+g+ +  +s l  d  v  +d   + i+f ++  +   ++n++ +  d  ++++de++d+++s   l +++ 
  gi|116754817|ref|YP_843935.1|  34 RILDIGCGDGKITARISQLVPDgsVLGIDISPDMISFARRRYSPVIFRNLRFEQGDALDLRFDEEFDIVVSFACLHWIRD 113
                                    79**********9999988765338899*******************************************999988875 PP

                                    GGHHHHHHHHHHTEEEEEE CS
                           TehB 111 eripsiienmqectkvggy 129
                                    +   s+++ + +   +gg 
  gi|116754817|ref|YP_843935.1| 114 HL--SVLQGIYRSLVPGGR 130
                                    53..455555555555555 PP

>> Methyltransf_7  SAM dependent carboxyl methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       0.9     7e+02      17      30 ..      34      47 ..      21      53 .. 0.81
   2 ?    1.9   0.1      0.13     1e+02     108     122 ..      97     111 ..      95     122 .. 0.84
   3 ?    6.8   0.0    0.0043       3.4     167     212 ..     117     163 ..     111     166 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.9
                                   EEEEET--SSCHHH CS
                 Methyltransf_7 17 kiaDLGCSsGpNtl 30
                                   +i D+GC  G+ t 
  gi|116754817|ref|YP_843935.1| 34 RILDIGCGDGKITA 47
                                   799*****998775 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.13
                                    T-EEEEEEES-TTB- CS
                 Methyltransf_7 108 nslhlvhssysLhWl 122
                                    ++ ++v+s+ +LhW+
  gi|116754817|ref|YP_843935.1|  97 EEFDIVVSFACLHWI 111
                                    5789**********7 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0043
                                    HHHHHHHHEEEEEEEEEEEEE-.-S.STT--HHHHHHSSHHHHHHCC CS
                 Methyltransf_7 167 fLklRseElvpgGrmvltllgr.ksedplsegeasllwellaqalqd 212
                                     L+  ++ lvpgGrm++ + gr +  + l++++   l e +a+ ++d
  gi|116754817|ref|YP_843935.1| 117 VLQGIYRSLVPGGRMLVQCGGRgNAAQLLDTTSEVCLEESFASYFKD 163
                                    566667789*************7777777777766677777776665 PP

>> Methyltransf_5  MraW methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0    0.0004      0.31      12      75 ..      23      87 ..      19     101 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0004
                                   HHHHT---TT-EEEES--TTSHHHHHHHTT--TTEEEEEES-HHHHHHHTT.....---.EEEEE CS
                 Methyltransf_5 12 vvellepkedgvyiDaTlGaggHsealLeqlselrligidrDksalarakerLkefekr.ltlvk 75
                                   +++ l+++ d   +D   G+g  + ++ + +++ +++gid+ ++++  a++r ++ + r l++ +
  gi|116754817|ref|YP_843935.1| 23 ALSELSIRGDERILDIGCGDGKITARISQLVPDGSVLGIDISPDMISFARRRYSPVIFRnLRFEQ 87
                                   577899999*******************************************9998866566655 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0022       1.7      73      92 ..      32      51 ..      19      67 .. 0.84
   2 ?    0.6   0.0      0.54   4.2e+02     120     156 ..      96     133 ..      85     136 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0022
                                   TS-EEEES-TT-HHHHH--S CS
                 Methyltransf_8 73 nlvvadlGcGeakiaeavre 92
                                   +  + d+GcG+ ki+ ++++
  gi|116754817|ref|YP_843935.1| 32 DERILDIGCGDGKITARISQ 51
                                   56799*********998876 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.54
                                    TT-EEEEE..EES---SS-HHHHHHHHHHHEEEEEEEEE CS
                 Methyltransf_8 120 desvdvav..fclslmgtnladflkeanrvlkvGGllkv 156
                                    de  d++v   cl  +  +  + l+ ++r l +GG + v
  gi|116754817|ref|YP_843935.1|  96 DEEFDIVVsfACLHWIR-DHLSVLQGIYRSLVPGGRMLV 133
                                    77788887435887765.5567899**********8876 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00041      0.32      20      91 ..      21      96 ..      15     114 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00041
                                   HHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-..SEEEEE-S-HHHHHHHHCHTT..TCCCEEEE-S-CCGHHHH CS
                         RrnaAD 20 neIldklnleekltvleigpGkGilTeeLakra..kqvvvlElderLakllqkkls..kdeklkvvhqDflkfetp 91
                                    ++l++l ++ +  +l+ig G G  T+++ + +   +v  + + ++++ + + + s    ++l   + D+l+  + 
  gi|116754817|ref|YP_843935.1| 21 MSALSELSIRGDERILDIGCGDGKITARISQLVpdGSVLGIDISPDMISFARRRYSpvIFRNLRFEQGDALDLRFD 96
                                   5789999999********************9997667777788888888888877755566666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); 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:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 1945.36
//
Query:       gi|116754818|ref|YP_843936.1|  [L=607]
Description: integral membrane sensor signal transduction histidine kinase [Methanosaeta thermophila PT]
Scores for complete 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   80.7   0.0    1.8e-22   80.0   0.0    1.4  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
      5e-09   36.1   0.0    1.5e-08   34.5   0.0    1.9  1  HisKA        His Kinase A (phospho-acceptor) domain
     0.0025   17.7   0.0     0.0054   16.6   0.0    1.5  1  HATPase_c_5  GHKL domain
     0.0028   17.5   0.0     0.0051   16.6   0.0    1.4  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
  ------ inclusion threshold ------
      0.055   13.8   6.8         13    6.1   3.7    3.5  3  DUF1772      Domain of unknown function (DUF1772)
        5.9    6.8   7.6        6.4    6.7   0.1    3.2  3  DUF3754      Protein of unknown function (DUF3754)


Domain annotation for each model (and alignments):
>> 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 !   80.0   0.0     6e-26   1.8e-22       2     111 ..     489     596 ..     488     597 .. 0.88

  Alignments for each domain:
  == domain 1  score: 80.0 bits;  conditional E-value: 6e-26
                                    HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEE.EETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHH CS
                      HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveika.seddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsi 80 
                                    d  r  +++ nl++N++k+ +++ + ++ei   ++++ v+ v+DnGiGi+++++k++fe f++    +++++g G Gl+i
  gi|116754818|ref|YP_843936.1| 489 DRMRAVEALVNLIENSAKYMGDQRDPRIEIGCmRDGETVFYVKDNGIGIDPKNHKRVFELFYK---VDNRSEGAGAGLAI 565
                                    66788999***********77666666666654557***************************...445568******** PP

                                    HHHHHHHTTTEEEEEEETTTEEEEEEEEESS CS
                      HATPase_c  81 vkklvelmgGeiwvesepgrGttftftlple 111
                                    vkk++e +gG+iw+ese grG+t+ ftlpl+
  gi|116754818|ref|YP_843936.1| 566 VKKIIEVHGGRIWIESELGRGCTVFFTLPLS 596
                                    *****************************86 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 !   34.5   0.0   5.1e-12   1.5e-08       2      65 ..     379     444 ..     378     445 .. 0.94

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 5.1e-12
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHH CS
                          HisKA   2 lgrflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdlsrie 65 
                                    ++rf+ +v+H+Lr PL +++g++  L+++  + + +++ e ++++e  +  +d l++d L+lsri+
  gi|116754818|ref|YP_843936.1| 379 MERFIYTVSHDLRSPLITVSGFLGFLRDDieKGAWDKVGEDIDILEGAITKMDMLLQDTLELSRIG 444
                                    689***********************99999666789999************************97 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.8e-06    0.0054      10      90 ..     497     582 ..     489     589 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.8e-06
                    HATPase_c_5  10 lgnlLdNAieacskieeekrfIrltvrekkksliisieNsyegek....kkle...sskskkeehGiGlksireivkkyk 82 
                                    l nl++N+   + +++  ++ I++ + ++ +++++  +N +  +     + +e   +  +++e  G Gl  +++i++ ++
  gi|116754818|ref|YP_843936.1| 497 LVNLIENSAKYMGDQR--DPRIEIGCMRDGETVFYVKDNGIGIDPknhkRVFElfyKVDNRSEGAGAGLAIVKKIIEVHG 574
                                    6799999888888877..8********************97663322333333444667888999*************** PP

                    HATPase_c_5  83 gnlsieae 90 
                                    g ++ie e
  gi|116754818|ref|YP_843936.1| 575 GRIWIESE 582
                                    ****9987 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.7e-06    0.0051       4      62 ..     494     554 ..     491     568 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.7e-06
                    HATPase_c_3   4 ekAlaelvdNsld..AdaenvkievnknrgktgeivieDdGkGmseeelknalrlatsske 62 
                                     +Al+ l++Ns    +d +   ie+   r  ++ + ++D+G G+++++ k++++l  +  +
  gi|116754818|ref|YP_843936.1| 494 VEALVNLIENSAKymGDQRDPRIEIGCMRDGETVFYVKDNGIGIDPKNHKRVFELFYKVDN 554
                                    68*********876688887666666666679*******************9997655444 PP

>> DUF1772  Domain of unknown function (DUF1772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.051   1.5e+02      37      80 ..      54      95 ..      43     104 .. 0.75
   2 ?    6.1   3.7    0.0044        13       4      79 ..     163     230 ..     124     244 .. 0.73
   3 ?    3.7   0.0     0.025        73      32     135 ..     291     403 ..     268     405 .. 0.53

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.051
                        DUF1772 37 avfpplallsalafaylaaraasrgarllylaaaallllsivpy 80
                                    +fp++  l+al+++ +a r  +++   +y +a a ++++ v+y
  gi|116754818|ref|YP_843936.1| 54 IIFPVVNGLAALSLFRAA-RTTRSKDEMMY-IAWAFFAVAQVLY 95
                                   579999999999999444.66677777777.5466666677766 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0044
                        DUF1772   4 lafslfvvPallslpassslllkqwrrlfkrgkavfpplallsalafa.ylaaraasrgarllylaaaallllsivp 79 
                                    + +sl++ P++++l ++++ l+++        ++++p++ l+ a a++ ++++r    ++r ++l+aa++ ++ i+ 
  gi|116754818|ref|YP_843936.1| 163 IFWSLLIAPTVATLEEPDP-LANAI-------AVAYPVADLVLAFALIaLIFRRIEHIAQRPILLLAAGA-VFMIIA 230
                                    5678889999999997774.33333.......45569988888888884455444445555555444444.434554 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.025
                        DUF1772  32 fkrgkavfpplallsalafa.ylaaraasrgarllylaaaal.lllsivpyTllvmvPtNnkLaal............ke 97 
                                    +      +p ++++sa af+ +   +       +   +aa++  ++ ++++  ++ ++ N+ L a+            +e
  gi|116754818|ref|YP_843936.1| 291 Y------IPYICAISAYAFLiWSIEQEDVNLYIRHHHLAAGVgMIILLIILRQIIAIKENTMLYAAaqkelhqriaseRE 364
                                    4......7888999999998555533333333333435555544433333333333333544444444444544443221 PP

                        DUF1772  98 edakekedeaevrelle.rWgrlnlvRavlalaaavlgl 135
                                    ++   ke e+++ e+ +  ++  + +R+ l+++++ lg+
  gi|116754818|ref|YP_843936.1| 365 KEHLIKELESKTSEMERfIYTVSHDLRSPLITVSGFLGF 403
                                    111122222222223335888899999999999988886 PP

>> DUF3754  Protein of unknown function (DUF3754)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.2      0.33   9.8e+02      58     100 ..      51      92 ..      19     100 .. 0.77
   2 ?    2.6   0.5     0.041   1.2e+02      56     111 ..     146     211 ..     134     230 .. 0.68
   3 ?    6.7   0.1    0.0022       6.4      65     121 ..     295     350 ..     291     363 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.33
                        DUF3754  58 kdklllgvpaivglvavllkllkaeklknklssliaaliavla 100
                                    +d +++ v+ ++++++++ ++ +++  k++++ +  a++av+ 
  gi|116754818|ref|YP_843936.1|  51 IDDIIFPVVNGLAALSLFRAA-RTTRSKDEMMYIAWAFFAVAQ 92 
                                    466777788888888888777.777777777777777777764 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.041
                        DUF3754  56 rlkdklllgvpaivglvavllkll........kaeklknk..lssliaaliavlalggfafrqyvk 111
                                    r+k  l  gv++i++++++   l+        + + l+n+  +  ++a+l++ +al++++fr +  
  gi|116754818|ref|YP_843936.1| 146 RIKSLLDTGVVTIFAILIFWSLLIaptvatleEPDPLANAiaVAYPVADLVLAFALIALIFRRIEH 211
                                    566667778888888766555555778888874444444311456788888888888888887655 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0022
                        DUF3754  65 vpaivglvavllkllkaeklknklssliaaliavlalggfafrqyvkyknkkiryqk 121
                                    + ai + +++++++ ++e+++  +++  +a+ + + + ++++rq++++k+ ++ y +
  gi|116754818|ref|YP_843936.1| 295 ICAISAYAFLIWSI-EQEDVNLYIRHHHLAAGVGMIILLIILRQIIAIKENTMLYAA 350
                                    56899999999**8.**********************************99998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (607 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       922  (0.0514251); expected 358.6 (0.02)
Passed bias filter:                      636  (0.0354733); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.67u 0.26s 00:00:00.93 Elapsed: 00:00:00.44
# Mc/sec: 4160.46
//
Query:       gi|116754819|ref|YP_843937.1|  [L=54]
Description: hypothetical protein Mthe_1525 [Methanosaeta thermophila PT]
Scores for complete 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   28.3   3.1    2.9e-06   27.3   3.1    1.5  1  Zn-ribbon_8     Zinc ribbon domain
    0.00057   19.9   0.2    0.00065   19.7   0.2    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
     0.0035   16.8   1.2       0.77    9.3   0.0    2.2  2  TF_Zn_Ribbon    TFIIB zinc-binding
     0.0036   17.3   0.4      0.005   16.8   0.4    1.2  1  DZR             Double zinc ribbon
     0.0037   17.3   0.5     0.0039   17.2   0.5    1.0  1  DUF1451         Zinc-ribbon containing domain
     0.0041   17.0   2.3       0.23   11.4   0.2    2.2  2  TFIIS_C         Transcription factor S-II (TFIIS)
     0.0064   16.2   5.7     0.0084   15.8   0.8    2.2  2  Zn_Tnp_IS1      InsA N-terminal domain
     0.0073   16.2   6.1       0.33   10.9   1.0    2.3  2  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
     0.0087   15.7   0.1       0.01   15.5   0.1    1.1  1  TackOD1         Thaumarchaeal output domain 1
  ------ inclusion threshold ------
      0.015   14.2   0.6      0.016   14.0   0.6    1.0  1  NRDD            Anaerobic ribonucleoside-triphosphate reducta
      0.017   15.1   4.9       0.44   10.6   0.7    2.1  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
      0.021   14.7   0.7       0.85    9.6   0.0    2.1  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
      0.029   14.3   0.5        2.1    8.3   0.1    2.2  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
      0.036   13.8   1.5       0.19   11.5   0.0    2.1  2  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
      0.039   13.9   0.2      0.039   13.9   0.2    1.2  1  zinc-ribbons_6  zinc-ribbons
      0.046   13.4   8.4       0.24   11.2   0.5    2.2  2  Rubredoxin_2    Rubredoxin metal binding domain
       0.17   11.8   2.1        6.4    6.8   0.2    2.1  2  zf-trcl         Probable zinc-ribbon domain
       0.36   10.3   5.5       0.97    8.9   0.2    2.3  2  zf-ribbon_3     zinc-ribbon domain
        1.1    9.4   6.8        1.3    9.1   0.8    2.3  2  UPF0547         Uncharacterised protein family UPF0547
        1.9    8.5   6.8          6    6.9   0.6    2.2  2  zinc_ribbon_4   zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   3.1   3.2e-09   2.9e-06       5      39 ..      23      53 ..      23      54 .] 0.88

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 3.2e-09
                    Zn-ribbon_8  5 eYrCeeCghefevlqsisdapltaCPeCgs.evrrv 39
                                   +Y C++Cgh+f  +        + CP+C+s +v+rv
  gi|116754819|ref|YP_843937.1| 23 DYVCRSCGHKFKGIGV-----GPRCPSCHSdDVERV 53
                                   7***********7762.....568***********7 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.2   7.2e-07   0.00065      68      99 ..      21      52 ..      18      54 .] 0.83

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 7.2e-07
                                   --EEEETTTS-EEECHHHHHS-TTTSSS-EEE CS
                           HypA 68 pvkvrCreCgkefeleekalrCpkCgsadvei 99
                                   p  + Cr+Cg++f+      rCp+C+s dve 
  gi|116754819|ref|YP_843937.1| 21 PTDYVCRSCGHKFKGIGVGPRCPSCHSDDVER 52
                                   67789*********6654579*******9986 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0   0.00086      0.77      18      27 ..      22      31 ..      11      34 .. 0.85
   2 !    6.7   0.3    0.0056       5.1       2      12 ..      41      51 ..      40      53 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00086
                                   TCEEESSSSB CS
                   TF_Zn_Ribbon 18 gelvCtdCGl 27
                                   +++vC +CG 
  gi|116754819|ref|YP_843937.1| 22 TDYVCRSCGH 31
                                   68*******7 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0056
                                   EETTTTCEECH CS
                   TF_Zn_Ribbon  2 kCPnCgstnlv 12
                                   +CP C+s++++
  gi|116754819|ref|YP_843937.1| 41 RCPSCHSDDVE 51
                                   6******9854 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.4   5.6e-06     0.005      11      37 ..      22      48 ..      17      52 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.6e-06
                            DZR 11 darfCseCgtklkavaaedrCpsCgek 37
                                    + +C  Cg+k k      rCpsC+++
  gi|116754819|ref|YP_843937.1| 22 TDYVCRSCGHKFKGIGVGPRCPSCHSD 48
                                   5789*********9999*******986 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.5   4.3e-06    0.0039     112     145 ..      21      52 ..      13      54 .] 0.87

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.3e-06
                        DUF1451 112 lGtlvCekCgkelalkkteeippCpkCgateFrR 145
                                    +  +vC++Cg++  +k  ++ p+Cp+C+++  +R
  gi|116754819|ref|YP_843937.1|  21 PTDYVCRSCGHK--FKGIGVGPRCPSCHSDDVER 52 
                                    6789******96..8999999********99888 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 !   11.4   0.2   0.00025      0.23      29      39 .]      24      34 ..      17      34 .. 0.92
   2 ?    5.9   0.1     0.013        12       2      11 ..      41      50 ..      40      53 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00025
                        TFIIS_C 29 ykCtkCghrWr 39
                                   y+C +Cgh+++
  gi|116754819|ref|YP_843937.1| 24 YVCRSCGHKFK 34
                                   9********97 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.013
                        TFIIS_C  2 kCpkCgsrea 11
                                   +Cp+C+s+++
  gi|116754819|ref|YP_843937.1| 41 RCPSCHSDDV 50
                                   6*****9875 PP

>> Zn_Tnp_IS1  InsA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.3     0.098        88      29      34 ..      24      29 ..      22      30 .. 0.89
   2 !   15.8   0.8   9.3e-06    0.0084       7      18 ..      41      52 ..      37      53 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.098
                     Zn_Tnp_IS1 29 frCrdC 34
                                   + Cr+C
  gi|116754819|ref|YP_843937.1| 24 YVCRSC 29
                                   89**** PP

  == domain 2  score: 15.8 bits;  conditional E-value: 9.3e-06
                     Zn_Tnp_IS1  7 hCPrCsstdVyR 18
                                    CP+C+s+dV R
  gi|116754819|ref|YP_843937.1| 41 RCPSCHSDDVER 52
                                   6*********88 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 !    8.0   0.3    0.0029       2.6      21      32 ..      19      30 ..      17      33 .. 0.79
   2 !   10.9   1.0   0.00037      0.33      26      37 .]      40      51 ..      39      51 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0029
                        DUF35_N 21 qfPPravCphCg 32
                                   +fP   vC+ Cg
  gi|116754819|ref|YP_843937.1| 19 FFPTDYVCRSCG 30
                                   677779999996 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00037
                        DUF35_N 26 avCphCgsddle 37
                                   + Cp C+sdd+e
  gi|116754819|ref|YP_843937.1| 40 PRCPSCHSDDVE 51
                                   68*******997 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   1.2e-05      0.01     146     171 ..      23      48 ..      15      53 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.2e-05
                        TackOD1 146 vykCnsCkslfsepevkarClsCeke 171
                                    +y+C+sC++ f+   v  rC sC++ 
  gi|116754819|ref|YP_843937.1|  23 DYVCRSCGHKFKGIGVGPRCPSCHSD 48 
                                    68899999999999999999999875 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.6   1.8e-05     0.016     508     535 ..      24      54 .]      18      54 .] 0.79

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.8e-05
                                    EEETT.--..EESS..SB-TTT--BE.EEEEE CS
                           NRDD 508 dvCnecgy..kgei..ekCpkCgseeevevir 535
                                     vC++cg+  kg+    +Cp+C+s++ ve++r
  gi|116754819|ref|YP_843937.1|  24 YVCRSCGHkfKGIGvgPRCPSCHSDD-VERVR 54 
                                    58******7766668888*****877.88875 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   0.2    0.0062       5.5      14      27 ..      19      32 ..      16      38 .. 0.78
   2 ?   10.6   0.7   0.00049      0.44      18      29 ..      39      50 ..      36      54 .] 0.78

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0062
                  Zn_Tnp_IS1595 14 rWpngfvCPhCgsr 27
                                   ++p+  vC  Cg++
  gi|116754819|ref|YP_843937.1| 19 FFPTDYVCRSCGHK 32
                                   67888899999976 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00049
                  Zn_Tnp_IS1595 18 gfvCPhCgsrka 29
                                   g++CP C+s+ +
  gi|116754819|ref|YP_843937.1| 39 GPRCPSCHSDDV 50
                                   79******9855 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00095      0.85      25      37 ..      24      36 ..      13      37 .. 0.79
   2 ?    3.9   0.3     0.055        49       6      11 ..      41      46 ..      41      52 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00095
                 Zn_ribbon_SprT 25 YrCrrCkgtLrgk 37
                                   Y Cr C+ +++g+
  gi|116754819|ref|YP_843937.1| 24 YVCRSCGHKFKGI 36
                                   99****9999875 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.055
                 Zn_ribbon_SprT  6 rCtgCg 11
                                   rC++C+
  gi|116754819|ref|YP_843937.1| 41 RCPSCH 46
                                   688887 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.041        37      20      28 ..      24      32 ..      22      34 .. 0.86
   2 ?    8.3   0.1    0.0024       2.1       3      11 ..      40      48 ..      38      50 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.041
                 PhnA_Zn_Ribbon 20 lvCpeCahE 28
                                   +vC  C+h 
  gi|116754819|ref|YP_843937.1| 24 YVCRSCGHK 32
                                   79*****95 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0024
                 PhnA_Zn_Ribbon  3 pkCplCaSe 11
                                   p Cp C S+
  gi|116754819|ref|YP_843937.1| 40 PRCPSCHSD 48
                                   89****998 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 ?   11.5   0.0   0.00021      0.19      37      53 ..      16      32 ..      11      33 .. 0.86
   2 ?    1.4   0.4      0.31   2.7e+02      46      51 ..      41      46 ..      41      48 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00021
                 zinc_ribbon_10 37 keeleevkyrCpkCgal 53
                                   +e++ ++ y+C +Cg++
  gi|116754819|ref|YP_843937.1| 16 PESFFPTDYVCRSCGHK 32
                                   5788999********97 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.31
                 zinc_ribbon_10 46 rCpkCg 51
                                   rCp+C 
  gi|116754819|ref|YP_843937.1| 41 RCPSCH 46
                                   677775 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   4.4e-05     0.039      15      37 ..      22      47 ..       5      54 .] 0.73

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.4e-05
                                   SEEE-TTT--EEEEE...EE-SSS-S CS
                 zinc-ribbons_6 15 eqyhCeaCqedlkke...alCpeCeq 37
                                   + y C++C +++k     + Cp C++
  gi|116754819|ref|YP_843937.1| 22 TDYVCRSCGHKFKGIgvgPRCPSCHS 47
                                   57889999997775411167888875 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.5   0.00026      0.24       1      10 [.      24      33 ..      24      36 .. 0.89
   2 ?    6.1   2.2      0.01       9.2      16      22 ..      41      47 ..      40      47 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00026
                   Rubredoxin_2  1 YvCsqCGfes 10
                                   YvC++CG+++
  gi|116754819|ref|YP_843937.1| 24 YVCRSCGHKF 33
                                   9******986 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.01
                   Rubredoxin_2 16 rCpsCgs 22
                                   rCpsC+s
  gi|116754819|ref|YP_843937.1| 41 RCPSCHS 47
                                   8****97 PP

>> zf-trcl  Probable zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.2    0.0072       6.4       5      14 ..      24      33 ..      22      34 .. 0.88
   2 ?    5.0   0.1     0.026        23      35      43 ..      41      49 ..      39      53 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0072
                        zf-trcl  5 ltCkdCgaef 14
                                   ++C++Cg +f
  gi|116754819|ref|YP_843937.1| 24 YVCRSCGHKF 33
                                   79*****998 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.026
                        zf-trcl 35 RCkaCRkar 43
                                   RC++C +++
  gi|116754819|ref|YP_843937.1| 41 RCPSCHSDD 49
                                   9****9876 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.2    0.0011      0.97      15      26 .]      22      33 ..      21      33 .. 0.81
   2 ?    3.4   1.2     0.061        55       4       8 ..      41      45 ..      40      48 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0011
                    zf-ribbon_3 15 ddnvCpyCGtkl 26
                                    d vC +CG+k+
  gi|116754819|ref|YP_843937.1| 22 TDYVCRSCGHKF 33
                                   5779*****985 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.061
                    zf-ribbon_3  4 rCPnC 8 
                                   rCP+C
  gi|116754819|ref|YP_843937.1| 41 RCPSC 45
                                   78888 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.8    0.0015       1.3      16      25 ..      25      34 ..      24      35 .. 0.90
   2 ?    3.5   0.6     0.085        76       2       7 ..      41      46 ..      41      48 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0015
                        UPF0547 16 fCphCGyvFq 25
                                   +C+ CG+ F+
  gi|116754819|ref|YP_843937.1| 25 VCRSCGHKFK 34
                                   6*99*****7 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.085
                        UPF0547  2 vCPeCe 7 
                                   +CP C 
  gi|116754819|ref|YP_843937.1| 41 RCPSCH 46
                                   599996 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.6    0.0067         6      28      36 .]      26      34 ..      24      34 .. 0.88
   2 ?    4.8   0.9     0.029        26       4      10 ..      41      47 ..      41      48 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0067
                  zinc_ribbon_4 28 CskCghvFr 36
                                   C  Cgh+F+
  gi|116754819|ref|YP_843937.1| 26 CRSCGHKFK 34
                                   999999995 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.029
                  zinc_ribbon_4  4 tCpsCka 10
                                   +CpsC++
  gi|116754819|ref|YP_843937.1| 41 RCPSCHS 47
                                   7999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); 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: 0.32u 0.25s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 420.69
//
Query:       gi|116754820|ref|YP_843938.1|  [L=122]
Description: hypothetical protein Mthe_1526 [Methanosaeta thermophila PT]
Scores for 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   66.3   0.0    2.9e-18   65.8   0.0    1.3  1  DUF167    Uncharacterised ACR, YggU family COG1872
  ------ inclusion threshold ------
      0.045   13.9   0.0       0.12   12.5   0.0    1.6  2  CinA_KH   Damage-inducible protein CinA KH domain


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 !   65.8   0.0   3.2e-22   2.9e-18       1      75 [.      31     104 ..      31     106 .. 0.96

  Alignments for each domain:
  == domain 1  score: 65.8 bits;  conditional E-value: 3.2e-22
                                    EEEEEEES---SSS----...--TTTT-------TTIIIIIHHHHHHHHHHHHHS...SEEEE-S-GGGSEEEEE CS
                         DUF167   1 gvilavrvkPgakkdaigleedaegrealkvrvaappvdGkANkalikfLakalgvpksdveivsGeksreKvvr 75 
                                    gv+l++ v Pg+++  ++  + + +r+ ++vr+++ + +GkAN++l++ +++a+g+ + dvei sG++s++Kvv+
  gi|116754820|ref|YP_843938.1|  31 GVVLHIDVIPGSSELVVP-AGFNAWRGSIEVRLTERADKGKANRQLLQEISRAFGLTQGDVEIMSGHRSQRKVVL 104
                                    689***************.77899*************************************************97 PP

>> CinA_KH  Damage-inducible protein CinA KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.73   6.5e+03      11      24 ..      14      27 ..      13      32 .. 0.71
   2 ?   12.5   0.0   1.4e-05      0.12      32      61 ..      52      81 ..      46      84 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.73
                                   HHHHHHHHGGGS-B CS
                        CinA_KH 11 ESavaekladlidr 24
                                   E av + l+d i+r
  gi|116754820|ref|YP_843938.1| 14 EYAVVKTLDDAIER 27
                                   55777888888876 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 1.4e-05
                                   EEETTEEEEEEE...EEHHHHHHHHH.... CS
                        CinA_KH 32 yakegevtvRltakaaneeeaealiapvee 61
                                    a +g ++vRlt +a++ ++ ++l++++++
  gi|116754820|ref|YP_843938.1| 52 NAWRGSIEVRLTERADKGKANRQLLQEISR 81
                                   567899********************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); 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 0.26s 00:00:00.63 Elapsed: 00:00:00.44
# Mc/sec: 837.99
//
Query:       gi|116754821|ref|YP_843939.1|  [L=147]
Description: TOPRIM domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-07   30.7   0.0    2.8e-06   27.5   0.0    2.1  1  Toprim    Toprim domain
      5e-06   26.9   0.0    3.6e-05   24.2   0.0    2.1  1  Toprim_4  Toprim domain
     0.0012   19.2   0.0     0.0022   18.4   0.0    1.5  1  Toprim_2  Toprim-like
  ------ inclusion threshold ------
       0.12   12.5   0.0       0.18   12.0   0.0    1.2  1  LepA_C    GTP-binding protein LepA C-terminus


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 !   27.5   0.0   6.3e-10   2.8e-06       3      89 ..      30      95 ..      28     110 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 6.3e-10
                                   EEESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHSTTEEEEEECTTTHHHHHHHHHHHHHHSEEEEECSSSHHHHHHHHHHH CS
                         Toprim  3 vivEgpsdaktiakalgsgfqavtaslGhildletefkpvyeeiedkkkvlkalkelakradeiilatDpDreGeaiawell 84
                                   vivEgp+d  +++++ g  + + ++s+   l+l++                    e+a+ ++ei+l+tD D  Ge+ia ++ 
  gi|116754821|ref|YP_843939.1| 30 VIVEGPRDRDALRRI-GVPGPILMSSQRSCLELAE--------------------ESARSYSEIVLMTDWDARGEEIAHKME 90
                                   778888888888888.5555555555555666655....................999**********************99 PP

                                   HHHTH CS
                         Toprim 85 evlke 89
                                   e+l++
  gi|116754821|ref|YP_843939.1| 91 EFLRP 95
                                   87773 PP

>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0     8e-09   3.6e-05       2      86 ..      28     101 ..      27     103 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 8e-09
                       Toprim_4   2 eiiiVEgyaDvlalekagiknvvavlg..galspldgirpeklktenlveaekkvkevilaldgDaeGeataerlaelll 79 
                                    +++iVEg+ D  al + g+++ +      + l   + ++ + + +          +e++l++d Da+Ge+ a++  e l+
  gi|116754821|ref|YP_843939.1|  28 AAVIVEGPRDRDALRRIGVPGPILMSSqrSCL---ELAEESARSY----------SEIVLMTDWDARGEEIAHKMEEFLR 94 
                                    689****************9977643311444...3333224555..........9******************888555 PP

                       Toprim_4  80 eegvkvt 86 
                                    ++gv+v 
  gi|116754821|ref|YP_843939.1|  95 PTGVRVD 101
                                    9999986 PP

>> Toprim_2  Toprim-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0     5e-07    0.0022      35      78 ..      62     103 ..      30     120 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 5e-07
                       Toprim_2  35 alkllerypekkvvlalDnDkaGrkaakrlaellreagvrekir 78 
                                    a +  ++y   ++vl++D D  G++ a ++ e lr +gvr+ + 
  gi|116754821|ref|YP_843939.1|  62 AEESARSY--SEIVLMTDWDARGEEIAHKMEEFLRPTGVRVDVE 103
                                    33334444..78***********************999554443 PP

>> LepA_C  GTP-binding protein LepA C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     4e-05      0.18       4      59 ..      64     119 ..      61     121 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4e-05
                                    CB-GGG-EEEETTTHHHHHHHHHHHHHHHS---SS-EEEEEEETTEEEEEEEE--- CS
                         LepA_C   4 ekvdaLslivhrskaeergrklvekLkeliprqlfevaiqaaigskviaretikal 59 
                                    e++ + s iv  ++ + rg+++++k++e+++    +v ++ +   k++ r++ik +
  gi|116754821|ref|YP_843939.1|  64 ESARSYSEIVLMTDWDARGEEIAHKMEEFLRPTGVRVDVEIRKRLKILVRKEIKDV 119
                                    5666789999999****************************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1041.28
//
Query:       gi|116754822|ref|YP_843940.1|  [L=166]
Description: hypothetical protein Mthe_1528 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1200.34
//
Query:       gi|116754823|ref|YP_843941.1|  [L=160]
Description: putative small multi-drug export [Methanosaeta thermophila PT]
Scores for complete 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  122.8   3.6    1.9e-35  122.2   3.6    1.3  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 !  122.2   3.6     1e-39   1.9e-35       1     121 []      20     141 ..      20     141 .. 0.95

  Alignments for each domain:
  == domain 1  score: 122.2 bits;  conditional E-value: 1e-39
                Sm_multidrug_ex   1 Elrgaiplgillgldpllallvsvlgnllpvplillflrkllellkkkkllkklfekleekaekksekie.kygflGLll 79 
                                    El gaipl+i++g++pl+a+++sv+gnl+pv  +llfl +++++l +++   ++f++l +++++k  + + ++gf++L+l
  gi|116754823|ref|YP_843941.1|  20 ELCGAIPLAIACGYSPLEAYAISVIGNLIPVAPLLLFLGPVSSFLMRYPPGYRFFTWLFSRTRRKYIEGReEVGFAALTL 99 
                                    899****************************************999999*************9966555449******** PP

                Sm_multidrug_ex  80 FvaiPLpgTGawtGsliasllglkkkkallaillGvliaglI 121
                                    FvaiPLp+TGawtG+++a+llg+++  a+l+i+lGvliag++
  gi|116754823|ref|YP_843941.1| 100 FVAIPLPVTGAWTGCVLAFLLGFRPLPAFLSIALGVLIAGVV 141
                                    ***************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1167.25
//
Query:       gi|116754824|ref|YP_843942.1|  [L=263]
Description: methyltransferase type 11 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-24   85.7   0.0    3.7e-24   85.2   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    5.3e-23   81.6   0.0      1e-22   80.6   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    4.3e-21   75.4   0.0    8.1e-21   74.5   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
    4.3e-20   72.3   0.0    6.5e-20   71.7   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    3.9e-16   59.3   0.0    8.6e-16   58.2   0.0    1.6  1  Methyltransf_23  Methyltransferase domain
    2.3e-14   53.3   0.0    3.1e-14   52.9   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    1.6e-07   31.0   0.0    4.6e-07   29.5   0.0    1.7  2  Methyltransf_4   Putative methyltransferase
    1.9e-07   30.8   0.0    2.7e-07   30.3   0.0    1.2  1  MTS              Methyltransferase small domain
    2.8e-07   30.1   0.0    4.9e-07   29.3   0.0    1.4  1  CMAS             Mycolic acid cyclopropane synthetase
    4.3e-07   29.5   0.0    5.9e-07   29.0   0.0    1.1  1  Methyltransf_2   O-methyltransferase domain
    9.2e-07   28.8   0.0      2e-06   27.7   0.0    1.4  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    1.3e-05   24.4   0.0    1.7e-05   24.0   0.0    1.2  1  DREV             DREV methyltransferase
    4.9e-05   23.0   0.0    6.9e-05   22.6   0.0    1.1  1  NodS             Nodulation protein S (NodS)
    0.00051   19.7   0.0    0.00077   19.1   0.0    1.3  1  MetW             Methionine biosynthesis protein MetW
     0.0021   18.1   0.0     0.0032   17.5   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
     0.0038   16.2   0.0     0.0052   15.8   0.0    1.3  1  Methyltransf_9   Protein of unknown function (DUF1698)
      0.008   15.6   0.0       0.01   15.2   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
  ------ inclusion threshold ------
      0.033   13.3   0.0      0.049   12.7   0.0    1.2  1  Fibrillarin      Fibrillarin
      0.055   12.9   0.0      0.072   12.5   0.0    1.1  1  TehB             Tellurite resistance protein TehB
       0.16   11.2   1.1        3.4    6.8   0.0    2.7  3  Methyltransf_7   SAM dependent carboxyl methyltransferase
       0.18   11.2   0.0       0.31   10.5   0.0    1.3  1  Methyltransf_5   MraW methylase family
        0.2   11.5   0.0        1.7    8.4   0.0    2.0  2  Methyltransf_8   Hypothetical methyltransferase
       0.23   10.5   0.0       0.32   10.0   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase


Domain annotation for each model (and alignments):
>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.2   0.0   4.8e-27   3.7e-24       3     125 ..      31     151 ..      29     178 .. 0.89

  Alignments for each domain:
  == domain 1  score: 85.2 bits;  conditional E-value: 4.8e-27
                Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsne 82 
                                     + r+lD+GCG G++t ++  +l p++ v GiDis+++i++Ar + +   + n++Feqgd+ +l   +  e fD+++s++
  gi|116754824|ref|YP_843942.1|  31 GDERILDIGCGDGKITARIS-QLVPDGSVLGIDISPDMISFARRRYSPVIFRNLRFEQGDALDLR--FD-EEFDIVVSFA 106
                                    6789****************.999*****************************************..66.9********* PP

                Methyltransf_31  83 vlnaladpdkileeiervlkpggilliedpr..llaelpakveee 125
                                     l+ + d  ++l++i r l pgg++l++      +a+l++  +e 
  gi|116754824|ref|YP_843942.1| 107 CLHWIRDHLSVLQGIYRSLVPGGRMLVQCGGrgNAAQLLDTTSEV 151
                                    **************************9876655455555544444 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.6   0.0   1.3e-25     1e-22       1      97 []      35     129 ..      35     129 .. 0.94

  Alignments for each domain:
  == domain 1  score: 80.6 bits;  conditional E-value: 1.3e-25
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT...TEEEEESBCCGBSSSTTTEEEEEEESTGGGS CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl...nvefvqgdaedlpfedgsfDlvvssgalhhl 77 
                                    +Ld+GcG G++t+++++ +++++v+g+Dis++m+  ar+r++   +   n++f+qgda dl f++ +fD+vvs+ +lh++
  gi|116754824|ref|YP_843942.1|  35 ILDIGCGDGKITARISQLVPDGSVLGIDISPDMISFARRRYSP--VifrNLRFEQGDALDLRFDE-EFDIVVSFACLHWI 111
                                    8******************99********************65..3469*************986.9******888**98 PP

                                    SHHHHHHHHHHHHHHEEEEE CS
                Methyltransf_25  78 sdedlekalkeiarvLkpgG 97 
                                       d+  +l+ i+r L pgG
  gi|116754824|ref|YP_843942.1| 112 R--DHLSVLQGIYRSLVPGG 129
                                    7..7789************9 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.5   0.0     1e-23   8.1e-21       1      95 [.      36     132 ..      36     133 .. 0.97

  Alignments for each domain:
  == domain 1  score: 74.5 bits;  conditional E-value: 1e-23
                                    EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCH CS
                Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseegl.kvefvvadaeklpfednsfDlvvssevlhhvedp 77 
                                    Ld+GcG G++++ + + +  ++v+g+D+s+ m+  a++++s+  + +++f ++da +l f +  fD+vvs+ +lh++ d+
  gi|116754824|ref|YP_843942.1|  36 LDIGCGDGKITARISQLVpdGSVLGIDISPDMISFARRRYSPVIFrNLRFEQGDALDLRFDE-EFDIVVSFACLHWIRDH 114
                                    8**************9999************************99***************66.***************** PP

                                    HHHHHHHHHHEEEEEEEE CS
                Methyltransf_11  78 ekalkeiaRvLkpgGllv 95 
                                     ++l+ i+R L pgG+++
  gi|116754824|ref|YP_843942.1| 115 LSVLQGIYRSLVPGGRML 132
                                    ***************987 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.7   0.0   8.3e-23   6.5e-20       1      98 [.      36     130 ..      36     131 .. 0.93

  Alignments for each domain:
  == domain 1  score: 71.7 bits;  conditional E-value: 8.3e-23
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlk 80 
                                    L+iGcG+G +++++ +  pd +++g+Disp++i  a+++ +  +     n+++e+ d+ldl   + fD+vv++ +lh+++
  gi|116754824|ref|YP_843942.1|  36 LDIGCGDGKITARISQLVPDGSVLGIDISPDMISFARRRYSPVIF---RNLRFEQGDALDLRFDEEFDIVVSFACLHWIR 112
                                    8********************************999999999995...67888888888888888*************** PP

                Methyltransf_12  81 direvldnirklLkpgGr 98 
                                    d  +vl+ i++ L+pgGr
  gi|116754824|ref|YP_843942.1| 113 DHLSVLQGIYRSLVPGGR 130
                                    *****************8 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.2   0.0   1.1e-18   8.6e-16       6     122 ..      17     138 ..      12     190 .. 0.70

  Alignments for each domain:
  == domain 1  score: 58.2 bits;  conditional E-value: 1.1e-18
                Methyltransf_23   6 eeelsdklerllpklraggrvLdiGcGtGillevlrengf..svtgvDlspeaveiae......kakkaqkdqfdeqeaa 77 
                                    +e++  +l +l+   r + r+LdiGcG+G  +  +++ +   sv g+D+sp +++ a+       +++ +++q d+  + 
  gi|116754824|ref|YP_843942.1|  17 QEWAMSALSELS--IRGDERILDIGCGDGKITARISQLVPdgSVLGIDISPDMISFARrryspvIFRNLRFEQGDAL-DL 93 
                                    455667777787..78999**********6666677776669**************988886664444444444222.22 PP

                Methyltransf_23  78 epqgkfdlIvlrevlehvpdppellrqiatllkpgGylllsepla 122
                                      ++ fd++v++ +l++++d+ ++l+ i++ l pgG++l++  ++
  gi|116754824|ref|YP_843942.1|  94 RFDEEFDIVVSFACLHWIRDHLSVLQGIYRSLVPGGRMLVQCGGR 138
                                    34559***********************************98654 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   0.0   3.9e-17   3.1e-14      45     151 ..      29     133 ..      14     163 .. 0.89

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 3.9e-17
                                    S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES CS
                Ubie_methyltran  45 vkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtvsf 124
                                     +  +++lD+ +G g +++++s+ v   g v ++Di+++m++ ++++     + n++f q++a +L f+ + fD+v vsf
  gi|116754824|ref|YP_843942.1|  29 IRGDERILDIGCGDGKITARISQLV-PDGSVLGIDISPDMISFARRRYSPVIFRNLRFEQGDALDLRFD-EEFDIV-VSF 105
                                    455679****************998.679***************************************6.579*87.677 PP

                                    .-GGG-S-HHHHHHHHHHHEEEEEEEEE CS
                Ubie_methyltran 125 .GlrnvtDklkaLkeayrvlkpGGrlvv 151
                                      l  + D+l +L+ +yr l pGGr++v
  gi|116754824|ref|YP_843942.1| 106 aCLHWIRDHLSVLQGIYRSLVPGGRMLV 133
                                    26899********************987 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0   5.9e-10   4.6e-07       5      62 ..      35      92 ..      32      99 .. 0.95
   2 ?   -2.1   0.0       2.9   2.2e+03      23      48 ..     214     239 ..     211     258 .. 0.68

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 5.9e-10
                                   EEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCC CS
                 Methyltransf_4  5 vleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgdalk 62
                                   +l+iGcG G+++ ++++  Pd ++lGi+i+ +++  + ++     ++Nlr  +gdal+
  gi|116754824|ref|YP_843942.1| 35 ILDIGCGDGKITARISQLVPDGSVLGIDISPDMISFARRRYSPVIFRNLRFEQGDALD 92
                                   79******************************************************86 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.9
                                    STTSEEEEEES-HHHHHHHHHHHHHC CS
                 Methyltransf_4  23 nPdknflGiEirvkvvakvlkkieal 48 
                                    +P  + l +E+r++ v+++ ++  ++
  gi|116754824|ref|YP_843942.1| 214 HPYLQRLPVELRSPFVQEIARRYIDR 239
                                    56677788999999999998775544 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0   3.4e-10   2.7e-07      26     112 ..      26     113 ..      20     155 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 3.4e-10
                                    HCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTSTTS-EEEEEE- CS
                            MTS  26 tlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeveekkfdlivsN 104
                                     l+ + ++++lD+GcG G ++a + +  p+ +v  +d++   + +a++ ++   ++ +++ + d+l+   +++fd++vs 
  gi|116754824|ref|YP_843942.1|  26 ELSIRGDERILDIGCGDGKITARISQLVPDGSVLGIDISPDMISFARRRYSPVIFRnLRFEQGDALDLRFDEEFDIVVSF 105
                                    455556788*******************************************99999*********************97 PP

                                    --STTTCH CS
                            MTS 105 PPfhagka 112
                                      +h  ++
  gi|116754824|ref|YP_843942.1| 106 ACLHWIRD 113
                                    76666555 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0   6.3e-10   4.9e-07      43     170 ..      12     139 ..       3     167 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 6.3e-10
                                    HHHHHHHHHHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH.--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-G CS
                           CMAS  43 LeeAqlaKldlileklelkpGmtlLdiGcGWGslvrravery.dvkvvglTlSkeqaklakkrvdeldlerkvevklldy 121
                                      +Aq++    +l  l+++  +++LdiGcG G+++ r  +   d +v+g+ +S +    a++r   + ++ + + +  d 
  gi|116754824|ref|YP_843942.1|  12 CSSAQQEWAMSALSELSIRGDERILDIGCGDGKITARISQLVpDGSVLGIDISPDMISFARRRYSPVIFR-NLRFEQGDA 90 
                                    5789******************************99988765499******************9988654.444555554 PP

                                    GG..-----SEEEEES-GGGTSGGGHHHHHHHHHHHS-TT-EEEEEEEEE- CS
                           CMAS 122 ed..ldekvdrvvsvgafehvgkenydtffkklkkllkedGllllhtitsl 170
                                     d  +de++d vvs+  +  +  + +    + +++ l ++G++l+++  + 
  gi|116754824|ref|YP_843942.1|  91 LDlrFDEEFDIVVSFACLHWI--RDHLSVLQGIYRSLVPGGRMLVQCGGRG 139
                                    4422789********999877..56788999**************997655 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   7.5e-10   5.9e-07      51     164 ..      20     133 ..       5     151 .. 0.86

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 7.5e-10
                                    HHHHHHSS-GGG-SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-.HHHHHHHHHHS-----TTEEEEES-TTTS---.-- CS
                 Methyltransf_2  51 akkvleafdleglkslvDvGGGtGalakaivsayPtikvivfDl.peVveaAkehlsageeervefvgGdffkdslP.ea 128
                                    a ++l +  ++g ++++D+G G G + + i+++ P  +v+  D+ p+ ++ A++++s+   ++++f +Gd  + +   e 
  gi|116754824|ref|YP_843942.1|  20 AMSALSELSIRGDERILDIGCGDGKITARISQLVPDGSVLGIDIsPDMISFARRRYSPVIFRNLRFEQGDALDLRFDeEF 99 
                                    56788888999999*****************************988**************************99999556 PP

                                    SEEEEESSGGGS-HHHHHHHHHHHHHH--TT-EEEE CS
                 Methyltransf_2 129 DaillkrvlhDwsdekcvklLkrvkkalpagGkviv 164
                                    D+++    lh w  ++   +L+ ++++l +gG+++v
  gi|116754824|ref|YP_843942.1| 100 DIVVSFACLH-WIRDHL-SVLQGIYRSLVPGGRMLV 133
                                    6666666665.877775.689************987 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 !   27.7   0.0   2.6e-09     2e-06      56     174 ..      13     136 ..       6     153 .. 0.72

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 2.6e-09
                                    E--HHHHHH.HHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GG CS
                           PCMT  56 iSaphmval.alellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGr 134
                                    +Sa +  a+ al  l+++  +r+L++G+G G  ta +++lv  +g v++i+ ++++++ a+r+      +n+ +  gD  
  gi|116754824|ref|YP_843942.1|  13 SSAQQEWAMsALSELSIRGDERILDIGCGDGKITARISQLVP-DGSVLGIDISPDMISFARRRYSPVIFRNLRFEQGDAL 91 
                                    5555555542567788999*********************96.677********************************75 PP

                                    GTTGGG-SEEEEEESSBBSS--HHH......HHTEEEEEEEEEEES CS
                           PCMT 135 kGyeekaPYdaihvgaaapeiPeal......idQLkeGGrlvvPvg 174
                                            +d ++  a+ + i + l       + L +GGr++v  g
  gi|116754824|ref|YP_843942.1|  92 D-LRFDEEFDIVVSFACLHWIRDHLsvlqgiYRSLVPGGRMLVQCG 136
                                    3.33333466666666665544433211111567788888877776 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   2.2e-08   1.7e-05      91     186 ..      28     133 ..       1     135 [. 0.75

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.2e-08
                           DREV  91 sdqedkklldlGaGdGeitkrvaptfee..vyatelsetmrdrlkkkk....ynvl.....salelqetdvkldlilcln 159
                                    s + d+++ld+G GdG+it r+++ + +  v   ++s  m+   +++     ++ l      al+l+  d ++d+++++ 
  gi|116754824|ref|YP_843942.1|  28 SIRGDERILDIGCGDGKITARISQLVPDgsVLGIDISPDMISFARRRYspviFRNLrfeqgDALDLR-FDEEFDIVVSFA 106
                                    445689********************98889999999999865444430000444411111233444.566899****** PP

                           DREV 160 lldrcfdplklledirsalepngrviv 186
                                     l    d l +l+ i+  l p gr++v
  gi|116754824|ref|YP_843942.1| 107 CLHWIRDHLSVLQGIYRSLVPGGRMLV 133
                                    ***********************9987 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   8.8e-08   6.9e-05      33     133 ..      23     126 ..       2     140 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 8.8e-08
                           NodS  33 qilrlslaqgsiadalevGcaaGalterlapyckrltv..vdvveeaiararervkes..shiswivsdvqqfstdekfd 108
                                    ++ +ls+++     +l++Gc  G +t r++ +    +v  +d+ ++ i+ ar+r   +   ++ + + d   +  de+fd
  gi|116754824|ref|YP_843942.1|  23 ALSELSIRGD--ERILDIGCGDGKITARISQLVPDGSVlgIDISPDMISFARRRYSPVifRNLRFEQGDALDLRFDEEFD 100
                                    3444444443..479***************99876555448*************987522789999************** PP

                           NodS 109 livvaevlyyiedvae.lraavrnlv 133
                                    ++v    l++i+d    l++  r lv
  gi|116754824|ref|YP_843942.1| 101 IVVSFACLHWIRDHLSvLQGIYRSLV 126
                                    ************97651444445544 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   9.8e-07   0.00077      11     100 ..      29     123 ..      21     141 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 9.8e-07
                           MetW  11 ikpgsrvldlGcGdGellellke.ekqvdgrGleldeegvaecvakGlsviqgdl....dkdlenfedksfdyvvlsqtl 85 
                                    i+   r+ld+GcGdG++   + +   + +  G++++ + +  +  +   vi  +l     + l+   d++fd+vv    l
  gi|116754824|ref|YP_843942.1|  29 IRGDERILDIGCGDGKITARISQlVPDGSVLGIDISPDMISFARRRYSPVIFRNLrfeqGDALDLRFDEEFDIVVSFACL 108
                                    77889***********987775413455667999999999999888888887776222134588999************* PP

                           MetW  86 qatrnpkevldellr 100
                                      +r+  +vl+ + r
  gi|116754824|ref|YP_843942.1| 109 HWIRDHLSVLQGIYR 123
                                    ******999998776 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   4.1e-06    0.0032      24      88 ..      30      89 ..      16     104 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.1e-06
                Methyltransf_32 24 sgaltvvDvGaGkgYLsfvlalkeke.yklkvvgidakeelvekaekraeklgkkfnkrlsfaels 88
                                   +g+++++D+G+G g  + ++++        +v+gid++ ++++ a++r + +   f ++l+f++++
  gi|116754824|ref|YP_843942.1| 30 RGDERILDIGCGDGKITARISQ---LvPDGSVLGIDISPDMISFARRRYSPVI--F-RNLRFEQGD 89
                                   67899****************9...5489*******************99999..8.889998876 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   6.6e-06    0.0052     111     218 ..      27     134 ..      13     202 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.6e-06
                                    S.--TT-EEEEET-TTSHHHHHHHHCT-S.EEEEE---HHHHHHHHHHHCCTTTTSSEEEE---.GGGS-T---EEEEEE CS
                 Methyltransf_9 111 lsdlkgrtildvGcgnGyhlwrmvgegak.lvvGidPselfliqfeavrkllgedqrahllplg.ieqlpeleafdtvfs 188
                                    ls   + +ild+Gcg+G    r+    ++ +v+Gid s   +i f a r+++    r+  +  g   +l   e fd+v s
  gi|116754824|ref|YP_843942.1|  27 LSIRGDERILDIGCGDGKITARISQLVPDgSVLGIDISPD-MISF-ARRRYSPVIFRNLRFEQGdALDLRFDEEFDIVVS 104
                                    44445789**********9999876655426788887765.4555.5677776666665555542346777899****** PP

                                    ES-GGG-S-HHHHHHHHHCTEEEEEEEEEE CS
                 Methyltransf_9 189 mGvlyhrrsPldhllqlkdqlvkgGelvle 218
                                       l+  r  l  l+ +  +lv gG ++++
  gi|116754824|ref|YP_843942.1| 105 FACLHWIRDHLSVLQGIYRSLVPGGRMLVQ 134
                                    *************************99876 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.3e-05      0.01     153     239 ..      22     111 ..      17     135 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.3e-05
                           PrmA 153 ealekl.vkegeevlDvGtGSG.iLaiaaakLgakkvvavDiDevAvkvakeNaelNkvea.klevalseellk...eek 226
                                     al +l ++++e++lD+G+G G i a  ++++   +v+++Di +  ++ a++  +    ++ ++e    +++l+   +e+
  gi|116754824|ref|YP_843942.1|  22 SALSELsIRGDERILDIGCGDGkITARISQLVPDGSVLGIDISPDMISFARRRYSPVIFRNlRFEQ---GDALDlrfDEE 98 
                                    566555478899**********45555566667789**************9988877666656644...44443334788 PP

                           PrmA 227 advivaNILaevl 239
                                    +d++v+    + +
  gi|116754824|ref|YP_843942.1|  99 FDIVVSFACLHWI 111
                                    9999876555555 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   6.2e-05     0.049      60     107 ..      21      67 ..       2      76 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.2e-05
                                    HTT-S--S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHH CS
                    Fibrillarin  60 lkglkelpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprv 107
                                    ++ l+el i+ ++++L +G + G+  + +s +v  +g v +++ sp +
  gi|116754824|ref|YP_843942.1|  21 MSALSELSIRGDERILDIGCGDGKITARISQLVP-DGSVLGIDISPDM 67 
                                    6789999**************************9.9********9976 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   9.2e-05     0.072      33     129 ..      34     130 ..      20     169 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.2e-05
                                    EEEEES-TTSHHHHHHHHTT-E..EEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG----S-EEEEEEESSGGGS-G CS
                           TehB  33 kvldlgcgqgrnslylsllgyd..vtawdknensiafleeikekenlknistalydineaklderydfilstvvlmflea 110
                                    ++ld+gcg+g+ +  +s l  d  v  +d   + i+f ++  +   ++n++ +  d  ++++de++d+++s   l +++ 
  gi|116754824|ref|YP_843942.1|  34 RILDIGCGDGKITARISQLVPDgsVLGIDISPDMISFARRRYSPVIFRNLRFEQGDALDLRFDEEFDIVVSFACLHWIRD 113
                                    79**********9999988765338899*******************************************999988875 PP

                                    GGHHHHHHHHHHTEEEEEE CS
                           TehB 111 eripsiienmqectkvggy 129
                                    +   s+++ + +   +gg 
  gi|116754824|ref|YP_843942.1| 114 HL--SVLQGIYRSLVPGGR 130
                                    53..455555555555555 PP

>> Methyltransf_7  SAM dependent carboxyl methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       0.9     7e+02      17      30 ..      34      47 ..      21      53 .. 0.81
   2 ?    1.9   0.1      0.13     1e+02     108     122 ..      97     111 ..      95     122 .. 0.84
   3 ?    6.8   0.0    0.0043       3.4     167     212 ..     117     163 ..     111     166 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.9
                                   EEEEET--SSCHHH CS
                 Methyltransf_7 17 kiaDLGCSsGpNtl 30
                                   +i D+GC  G+ t 
  gi|116754824|ref|YP_843942.1| 34 RILDIGCGDGKITA 47
                                   799*****998775 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.13
                                    T-EEEEEEES-TTB- CS
                 Methyltransf_7 108 nslhlvhssysLhWl 122
                                    ++ ++v+s+ +LhW+
  gi|116754824|ref|YP_843942.1|  97 EEFDIVVSFACLHWI 111
                                    5789**********7 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0043
                                    HHHHHHHHEEEEEEEEEEEEE-.-S.STT--HHHHHHSSHHHHHHCC CS
                 Methyltransf_7 167 fLklRseElvpgGrmvltllgr.ksedplsegeasllwellaqalqd 212
                                     L+  ++ lvpgGrm++ + gr +  + l++++   l e +a+ ++d
  gi|116754824|ref|YP_843942.1| 117 VLQGIYRSLVPGGRMLVQCGGRgNAAQLLDTTSEVCLEESFASYFKD 163
                                    566667789*************7777777777766677777776665 PP

>> Methyltransf_5  MraW methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0    0.0004      0.31      12      75 ..      23      87 ..      19     101 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0004
                                   HHHHT---TT-EEEES--TTSHHHHHHHTT--TTEEEEEES-HHHHHHHTT.....---.EEEEE CS
                 Methyltransf_5 12 vvellepkedgvyiDaTlGaggHsealLeqlselrligidrDksalarakerLkefekr.ltlvk 75
                                   +++ l+++ d   +D   G+g  + ++ + +++ +++gid+ ++++  a++r ++ + r l++ +
  gi|116754824|ref|YP_843942.1| 23 ALSELSIRGDERILDIGCGDGKITARISQLVPDGSVLGIDISPDMISFARRRYSPVIFRnLRFEQ 87
                                   577899999*******************************************9998866566655 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0022       1.7      73      92 ..      32      51 ..      19      67 .. 0.84
   2 ?    0.6   0.0      0.54   4.2e+02     120     156 ..      96     133 ..      85     136 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0022
                                   TS-EEEES-TT-HHHHH--S CS
                 Methyltransf_8 73 nlvvadlGcGeakiaeavre 92
                                   +  + d+GcG+ ki+ ++++
  gi|116754824|ref|YP_843942.1| 32 DERILDIGCGDGKITARISQ 51
                                   56799*********998876 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.54
                                    TT-EEEEE..EES---SS-HHHHHHHHHHHEEEEEEEEE CS
                 Methyltransf_8 120 desvdvav..fclslmgtnladflkeanrvlkvGGllkv 156
                                    de  d++v   cl  +  +  + l+ ++r l +GG + v
  gi|116754824|ref|YP_843942.1|  96 DEEFDIVVsfACLHWIR-DHLSVLQGIYRSLVPGGRMLV 133
                                    77788887435887765.5567899**********8876 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00041      0.32      20      91 ..      21      96 ..      15     114 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00041
                                   HHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-..SEEEEE-S-HHHHHHHHCHTT..TCCCEEEE-S-CCGHHHH CS
                         RrnaAD 20 neIldklnleekltvleigpGkGilTeeLakra..kqvvvlElderLakllqkkls..kdeklkvvhqDflkfetp 91
                                    ++l++l ++ +  +l+ig G G  T+++ + +   +v  + + ++++ + + + s    ++l   + D+l+  + 
  gi|116754824|ref|YP_843942.1| 21 MSALSELSIRGDERILDIGCGDGKITARISQLVpdGSVLGIDISPDMISFARRRYSpvIFRNLRFEQGDALDLRFD 96
                                   5789999999********************9997667777788888888888877755566666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); 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:                        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: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 1954.03
//
Query:       gi|116754825|ref|YP_843943.1|  [L=607]
Description: integral membrane sensor signal transduction histidine kinase [Methanosaeta thermophila PT]
Scores for complete 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   80.7   0.0    1.8e-22   80.0   0.0    1.4  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
      5e-09   36.1   0.0    1.5e-08   34.5   0.0    1.9  1  HisKA        His Kinase A (phospho-acceptor) domain
     0.0025   17.7   0.0     0.0054   16.6   0.0    1.5  1  HATPase_c_5  GHKL domain
     0.0028   17.5   0.0     0.0051   16.6   0.0    1.4  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
  ------ inclusion threshold ------
      0.055   13.8   6.8         13    6.1   3.7    3.5  3  DUF1772      Domain of unknown function (DUF1772)
        5.9    6.8   7.6        6.4    6.7   0.1    3.2  3  DUF3754      Protein of unknown function (DUF3754)


Domain annotation for each model (and alignments):
>> 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 !   80.0   0.0     6e-26   1.8e-22       2     111 ..     489     596 ..     488     597 .. 0.88

  Alignments for each domain:
  == domain 1  score: 80.0 bits;  conditional E-value: 6e-26
                                    HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEE.EETEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHH CS
                      HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveika.seddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsi 80 
                                    d  r  +++ nl++N++k+ +++ + ++ei   ++++ v+ v+DnGiGi+++++k++fe f++    +++++g G Gl+i
  gi|116754825|ref|YP_843943.1| 489 DRMRAVEALVNLIENSAKYMGDQRDPRIEIGCmRDGETVFYVKDNGIGIDPKNHKRVFELFYK---VDNRSEGAGAGLAI 565
                                    66788999***********77666666666654557***************************...445568******** PP

                                    HHHHHHHTTTEEEEEEETTTEEEEEEEEESS CS
                      HATPase_c  81 vkklvelmgGeiwvesepgrGttftftlple 111
                                    vkk++e +gG+iw+ese grG+t+ ftlpl+
  gi|116754825|ref|YP_843943.1| 566 VKKIIEVHGGRIWIESELGRGCTVFFTLPLS 596
                                    *****************************86 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 !   34.5   0.0   5.1e-12   1.5e-08       2      65 ..     379     444 ..     378     445 .. 0.94

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 5.1e-12
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHC....T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHH CS
                          HisKA   2 lgrflagvaHELrtPLsailgnaeaLkre..gklteelkeyletiesearrldhlvedlLdlsrie 65 
                                    ++rf+ +v+H+Lr PL +++g++  L+++  + + +++ e ++++e  +  +d l++d L+lsri+
  gi|116754825|ref|YP_843943.1| 379 MERFIYTVSHDLRSPLITVSGFLGFLRDDieKGAWDKVGEDIDILEGAITKMDMLLQDTLELSRIG 444
                                    689***********************99999666789999************************97 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.8e-06    0.0054      10      90 ..     497     582 ..     489     589 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.8e-06
                    HATPase_c_5  10 lgnlLdNAieacskieeekrfIrltvrekkksliisieNsyegek....kkle...sskskkeehGiGlksireivkkyk 82 
                                    l nl++N+   + +++  ++ I++ + ++ +++++  +N +  +     + +e   +  +++e  G Gl  +++i++ ++
  gi|116754825|ref|YP_843943.1| 497 LVNLIENSAKYMGDQR--DPRIEIGCMRDGETVFYVKDNGIGIDPknhkRVFElfyKVDNRSEGAGAGLAIVKKIIEVHG 574
                                    6799999888888877..8********************97663322333333444667888999*************** PP

                    HATPase_c_5  83 gnlsieae 90 
                                    g ++ie e
  gi|116754825|ref|YP_843943.1| 575 GRIWIESE 582
                                    ****9987 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.7e-06    0.0051       4      62 ..     494     554 ..     491     568 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.7e-06
                    HATPase_c_3   4 ekAlaelvdNsld..AdaenvkievnknrgktgeivieDdGkGmseeelknalrlatsske 62 
                                     +Al+ l++Ns    +d +   ie+   r  ++ + ++D+G G+++++ k++++l  +  +
  gi|116754825|ref|YP_843943.1| 494 VEALVNLIENSAKymGDQRDPRIEIGCMRDGETVFYVKDNGIGIDPKNHKRVFELFYKVDN 554
                                    68*********876688887666666666679*******************9997655444 PP

>> DUF1772  Domain of unknown function (DUF1772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.051   1.5e+02      37      80 ..      54      95 ..      43     104 .. 0.75
   2 ?    6.1   3.7    0.0044        13       4      79 ..     163     230 ..     124     244 .. 0.73
   3 ?    3.7   0.0     0.025        73      32     135 ..     291     403 ..     268     405 .. 0.53

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.051
                        DUF1772 37 avfpplallsalafaylaaraasrgarllylaaaallllsivpy 80
                                    +fp++  l+al+++ +a r  +++   +y +a a ++++ v+y
  gi|116754825|ref|YP_843943.1| 54 IIFPVVNGLAALSLFRAA-RTTRSKDEMMY-IAWAFFAVAQVLY 95
                                   579999999999999444.66677777777.5466666677766 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0044
                        DUF1772   4 lafslfvvPallslpassslllkqwrrlfkrgkavfpplallsalafa.ylaaraasrgarllylaaaallllsivp 79 
                                    + +sl++ P++++l ++++ l+++        ++++p++ l+ a a++ ++++r    ++r ++l+aa++ ++ i+ 
  gi|116754825|ref|YP_843943.1| 163 IFWSLLIAPTVATLEEPDP-LANAI-------AVAYPVADLVLAFALIaLIFRRIEHIAQRPILLLAAGA-VFMIIA 230
                                    5678889999999997774.33333.......45569988888888884455444445555555444444.434554 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.025
                        DUF1772  32 fkrgkavfpplallsalafa.ylaaraasrgarllylaaaal.lllsivpyTllvmvPtNnkLaal............ke 97 
                                    +      +p ++++sa af+ +   +       +   +aa++  ++ ++++  ++ ++ N+ L a+            +e
  gi|116754825|ref|YP_843943.1| 291 Y------IPYICAISAYAFLiWSIEQEDVNLYIRHHHLAAGVgMIILLIILRQIIAIKENTMLYAAaqkelhqriaseRE 364
                                    4......7888999999998555533333333333435555544433333333333333544444444444544443221 PP

                        DUF1772  98 edakekedeaevrelle.rWgrlnlvRavlalaaavlgl 135
                                    ++   ke e+++ e+ +  ++  + +R+ l+++++ lg+
  gi|116754825|ref|YP_843943.1| 365 KEHLIKELESKTSEMERfIYTVSHDLRSPLITVSGFLGF 403
                                    111122222222223335888899999999999988886 PP

>> DUF3754  Protein of unknown function (DUF3754)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.2      0.33   9.8e+02      58     100 ..      51      92 ..      19     100 .. 0.77
   2 ?    2.6   0.5     0.041   1.2e+02      56     111 ..     146     211 ..     134     230 .. 0.68
   3 ?    6.7   0.1    0.0022       6.4      65     121 ..     295     350 ..     291     363 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.33
                        DUF3754  58 kdklllgvpaivglvavllkllkaeklknklssliaaliavla 100
                                    +d +++ v+ ++++++++ ++ +++  k++++ +  a++av+ 
  gi|116754825|ref|YP_843943.1|  51 IDDIIFPVVNGLAALSLFRAA-RTTRSKDEMMYIAWAFFAVAQ 92 
                                    466777788888888888777.777777777777777777764 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.041
                        DUF3754  56 rlkdklllgvpaivglvavllkll........kaeklknk..lssliaaliavlalggfafrqyvk 111
                                    r+k  l  gv++i++++++   l+        + + l+n+  +  ++a+l++ +al++++fr +  
  gi|116754825|ref|YP_843943.1| 146 RIKSLLDTGVVTIFAILIFWSLLIaptvatleEPDPLANAiaVAYPVADLVLAFALIALIFRRIEH 211
                                    566667778888888766555555778888874444444311456788888888888888887655 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0022
                        DUF3754  65 vpaivglvavllkllkaeklknklssliaaliavlalggfafrqyvkyknkkiryqk 121
                                    + ai + +++++++ ++e+++  +++  +a+ + + + ++++rq++++k+ ++ y +
  gi|116754825|ref|YP_843943.1| 295 ICAISAYAFLIWSI-EQEDVNLYIRHHHLAAGVGMIILLIILRQIIAIKENTMLYAA 350
                                    56899999999**8.**********************************99998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (607 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       922  (0.0514251); expected 358.6 (0.02)
Passed bias filter:                      636  (0.0354733); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.66u 0.27s 00:00:00.93 Elapsed: 00:00:00.45
# Mc/sec: 4060.70
//
Query:       gi|116754826|ref|YP_843944.1|  [L=54]
Description: hypothetical protein Mthe_1532 [Methanosaeta thermophila PT]
Scores for complete 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   28.3   3.1    2.9e-06   27.3   3.1    1.5  1  Zn-ribbon_8     Zinc ribbon domain
    0.00057   19.9   0.2    0.00065   19.7   0.2    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
     0.0035   16.8   1.2       0.77    9.3   0.0    2.2  2  TF_Zn_Ribbon    TFIIB zinc-binding
     0.0036   17.3   0.4      0.005   16.8   0.4    1.2  1  DZR             Double zinc ribbon
     0.0037   17.3   0.5     0.0039   17.2   0.5    1.0  1  DUF1451         Zinc-ribbon containing domain
     0.0041   17.0   2.3       0.23   11.4   0.2    2.2  2  TFIIS_C         Transcription factor S-II (TFIIS)
     0.0064   16.2   5.7     0.0084   15.8   0.8    2.2  2  Zn_Tnp_IS1      InsA N-terminal domain
     0.0073   16.2   6.1       0.33   10.9   1.0    2.3  2  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
     0.0087   15.7   0.1       0.01   15.5   0.1    1.1  1  TackOD1         Thaumarchaeal output domain 1
  ------ inclusion threshold ------
      0.015   14.2   0.6      0.016   14.0   0.6    1.0  1  NRDD            Anaerobic ribonucleoside-triphosphate reducta
      0.017   15.1   4.9       0.44   10.6   0.7    2.1  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
      0.021   14.7   0.7       0.85    9.6   0.0    2.1  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
      0.029   14.3   0.5        2.1    8.3   0.1    2.2  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
      0.036   13.8   1.5       0.19   11.5   0.0    2.1  2  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
      0.039   13.9   0.2      0.039   13.9   0.2    1.2  1  zinc-ribbons_6  zinc-ribbons
      0.046   13.4   8.4       0.24   11.2   0.5    2.2  2  Rubredoxin_2    Rubredoxin metal binding domain
       0.17   11.8   2.1        6.4    6.8   0.2    2.1  2  zf-trcl         Probable zinc-ribbon domain
       0.36   10.3   5.5       0.97    8.9   0.2    2.3  2  zf-ribbon_3     zinc-ribbon domain
        1.1    9.4   6.8        1.3    9.1   0.8    2.3  2  UPF0547         Uncharacterised protein family UPF0547
        1.9    8.5   6.8          6    6.9   0.6    2.2  2  zinc_ribbon_4   zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   3.1   3.2e-09   2.9e-06       5      39 ..      23      53 ..      23      54 .] 0.88

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 3.2e-09
                    Zn-ribbon_8  5 eYrCeeCghefevlqsisdapltaCPeCgs.evrrv 39
                                   +Y C++Cgh+f  +        + CP+C+s +v+rv
  gi|116754826|ref|YP_843944.1| 23 DYVCRSCGHKFKGIGV-----GPRCPSCHSdDVERV 53
                                   7***********7762.....568***********7 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.2   7.2e-07   0.00065      68      99 ..      21      52 ..      18      54 .] 0.83

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 7.2e-07
                                   --EEEETTTS-EEECHHHHHS-TTTSSS-EEE CS
                           HypA 68 pvkvrCreCgkefeleekalrCpkCgsadvei 99
                                   p  + Cr+Cg++f+      rCp+C+s dve 
  gi|116754826|ref|YP_843944.1| 21 PTDYVCRSCGHKFKGIGVGPRCPSCHSDDVER 52
                                   67789*********6654579*******9986 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0   0.00086      0.77      18      27 ..      22      31 ..      11      34 .. 0.85
   2 !    6.7   0.3    0.0056       5.1       2      12 ..      41      51 ..      40      53 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00086
                                   TCEEESSSSB CS
                   TF_Zn_Ribbon 18 gelvCtdCGl 27
                                   +++vC +CG 
  gi|116754826|ref|YP_843944.1| 22 TDYVCRSCGH 31
                                   68*******7 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0056
                                   EETTTTCEECH CS
                   TF_Zn_Ribbon  2 kCPnCgstnlv 12
                                   +CP C+s++++
  gi|116754826|ref|YP_843944.1| 41 RCPSCHSDDVE 51
                                   6******9854 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.4   5.6e-06     0.005      11      37 ..      22      48 ..      17      52 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.6e-06
                            DZR 11 darfCseCgtklkavaaedrCpsCgek 37
                                    + +C  Cg+k k      rCpsC+++
  gi|116754826|ref|YP_843944.1| 22 TDYVCRSCGHKFKGIGVGPRCPSCHSD 48
                                   5789*********9999*******986 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.5   4.3e-06    0.0039     112     145 ..      21      52 ..      13      54 .] 0.87

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.3e-06
                        DUF1451 112 lGtlvCekCgkelalkkteeippCpkCgateFrR 145
                                    +  +vC++Cg++  +k  ++ p+Cp+C+++  +R
  gi|116754826|ref|YP_843944.1|  21 PTDYVCRSCGHK--FKGIGVGPRCPSCHSDDVER 52 
                                    6789******96..8999999********99888 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 !   11.4   0.2   0.00025      0.23      29      39 .]      24      34 ..      17      34 .. 0.92
   2 ?    5.9   0.1     0.013        12       2      11 ..      41      50 ..      40      53 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00025
                        TFIIS_C 29 ykCtkCghrWr 39
                                   y+C +Cgh+++
  gi|116754826|ref|YP_843944.1| 24 YVCRSCGHKFK 34
                                   9********97 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.013
                        TFIIS_C  2 kCpkCgsrea 11
                                   +Cp+C+s+++
  gi|116754826|ref|YP_843944.1| 41 RCPSCHSDDV 50
                                   6*****9875 PP

>> Zn_Tnp_IS1  InsA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.3     0.098        88      29      34 ..      24      29 ..      22      30 .. 0.89
   2 !   15.8   0.8   9.3e-06    0.0084       7      18 ..      41      52 ..      37      53 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.098
                     Zn_Tnp_IS1 29 frCrdC 34
                                   + Cr+C
  gi|116754826|ref|YP_843944.1| 24 YVCRSC 29
                                   89**** PP

  == domain 2  score: 15.8 bits;  conditional E-value: 9.3e-06
                     Zn_Tnp_IS1  7 hCPrCsstdVyR 18
                                    CP+C+s+dV R
  gi|116754826|ref|YP_843944.1| 41 RCPSCHSDDVER 52
                                   6*********88 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 !    8.0   0.3    0.0029       2.6      21      32 ..      19      30 ..      17      33 .. 0.79
   2 !   10.9   1.0   0.00037      0.33      26      37 .]      40      51 ..      39      51 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0029
                        DUF35_N 21 qfPPravCphCg 32
                                   +fP   vC+ Cg
  gi|116754826|ref|YP_843944.1| 19 FFPTDYVCRSCG 30
                                   677779999996 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00037
                        DUF35_N 26 avCphCgsddle 37
                                   + Cp C+sdd+e
  gi|116754826|ref|YP_843944.1| 40 PRCPSCHSDDVE 51
                                   68*******997 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   1.2e-05      0.01     146     171 ..      23      48 ..      15      53 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.2e-05
                        TackOD1 146 vykCnsCkslfsepevkarClsCeke 171
                                    +y+C+sC++ f+   v  rC sC++ 
  gi|116754826|ref|YP_843944.1|  23 DYVCRSCGHKFKGIGVGPRCPSCHSD 48 
                                    68899999999999999999999875 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.6   1.8e-05     0.016     508     535 ..      24      54 .]      18      54 .] 0.79

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.8e-05
                                    EEETT.--..EESS..SB-TTT--BE.EEEEE CS
                           NRDD 508 dvCnecgy..kgei..ekCpkCgseeevevir 535
                                     vC++cg+  kg+    +Cp+C+s++ ve++r
  gi|116754826|ref|YP_843944.1|  24 YVCRSCGHkfKGIGvgPRCPSCHSDD-VERVR 54 
                                    58******7766668888*****877.88875 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   0.2    0.0062       5.5      14      27 ..      19      32 ..      16      38 .. 0.78
   2 ?   10.6   0.7   0.00049      0.44      18      29 ..      39      50 ..      36      54 .] 0.78

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0062
                  Zn_Tnp_IS1595 14 rWpngfvCPhCgsr 27
                                   ++p+  vC  Cg++
  gi|116754826|ref|YP_843944.1| 19 FFPTDYVCRSCGHK 32
                                   67888899999976 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00049
                  Zn_Tnp_IS1595 18 gfvCPhCgsrka 29
                                   g++CP C+s+ +
  gi|116754826|ref|YP_843944.1| 39 GPRCPSCHSDDV 50
                                   79******9855 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00095      0.85      25      37 ..      24      36 ..      13      37 .. 0.79
   2 ?    3.9   0.3     0.055        49       6      11 ..      41      46 ..      41      52 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00095
                 Zn_ribbon_SprT 25 YrCrrCkgtLrgk 37
                                   Y Cr C+ +++g+
  gi|116754826|ref|YP_843944.1| 24 YVCRSCGHKFKGI 36
                                   99****9999875 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.055
                 Zn_ribbon_SprT  6 rCtgCg 11
                                   rC++C+
  gi|116754826|ref|YP_843944.1| 41 RCPSCH 46
                                   688887 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.041        37      20      28 ..      24      32 ..      22      34 .. 0.86
   2 ?    8.3   0.1    0.0024       2.1       3      11 ..      40      48 ..      38      50 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.041
                 PhnA_Zn_Ribbon 20 lvCpeCahE 28
                                   +vC  C+h 
  gi|116754826|ref|YP_843944.1| 24 YVCRSCGHK 32
                                   79*****95 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0024
                 PhnA_Zn_Ribbon  3 pkCplCaSe 11
                                   p Cp C S+
  gi|116754826|ref|YP_843944.1| 40 PRCPSCHSD 48
                                   89****998 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 ?   11.5   0.0   0.00021      0.19      37      53 ..      16      32 ..      11      33 .. 0.86
   2 ?    1.4   0.4      0.31   2.7e+02      46      51 ..      41      46 ..      41      48 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00021
                 zinc_ribbon_10 37 keeleevkyrCpkCgal 53
                                   +e++ ++ y+C +Cg++
  gi|116754826|ref|YP_843944.1| 16 PESFFPTDYVCRSCGHK 32
                                   5788999********97 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.31
                 zinc_ribbon_10 46 rCpkCg 51
                                   rCp+C 
  gi|116754826|ref|YP_843944.1| 41 RCPSCH 46
                                   677775 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   4.4e-05     0.039      15      37 ..      22      47 ..       5      54 .] 0.73

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.4e-05
                                   SEEE-TTT--EEEEE...EE-SSS-S CS
                 zinc-ribbons_6 15 eqyhCeaCqedlkke...alCpeCeq 37
                                   + y C++C +++k     + Cp C++
  gi|116754826|ref|YP_843944.1| 22 TDYVCRSCGHKFKGIgvgPRCPSCHS 47
                                   57889999997775411167888875 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.5   0.00026      0.24       1      10 [.      24      33 ..      24      36 .. 0.89
   2 ?    6.1   2.2      0.01       9.2      16      22 ..      41      47 ..      40      47 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00026
                   Rubredoxin_2  1 YvCsqCGfes 10
                                   YvC++CG+++
  gi|116754826|ref|YP_843944.1| 24 YVCRSCGHKF 33
                                   9******986 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.01
                   Rubredoxin_2 16 rCpsCgs 22
                                   rCpsC+s
  gi|116754826|ref|YP_843944.1| 41 RCPSCHS 47
                                   8****97 PP

>> zf-trcl  Probable zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.2    0.0072       6.4       5      14 ..      24      33 ..      22      34 .. 0.88
   2 ?    5.0   0.1     0.026        23      35      43 ..      41      49 ..      39      53 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0072
                        zf-trcl  5 ltCkdCgaef 14
                                   ++C++Cg +f
  gi|116754826|ref|YP_843944.1| 24 YVCRSCGHKF 33
                                   79*****998 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.026
                        zf-trcl 35 RCkaCRkar 43
                                   RC++C +++
  gi|116754826|ref|YP_843944.1| 41 RCPSCHSDD 49
                                   9****9876 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.2    0.0011      0.97      15      26 .]      22      33 ..      21      33 .. 0.81
   2 ?    3.4   1.2     0.061        55       4       8 ..      41      45 ..      40      48 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0011
                    zf-ribbon_3 15 ddnvCpyCGtkl 26
                                    d vC +CG+k+
  gi|116754826|ref|YP_843944.1| 22 TDYVCRSCGHKF 33
                                   5779*****985 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.061
                    zf-ribbon_3  4 rCPnC 8 
                                   rCP+C
  gi|116754826|ref|YP_843944.1| 41 RCPSC 45
                                   78888 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.8    0.0015       1.3      16      25 ..      25      34 ..      24      35 .. 0.90
   2 ?    3.5   0.6     0.085        76       2       7 ..      41      46 ..      41      48 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0015
                        UPF0547 16 fCphCGyvFq 25
                                   +C+ CG+ F+
  gi|116754826|ref|YP_843944.1| 25 VCRSCGHKFK 34
                                   6*99*****7 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.085
                        UPF0547  2 vCPeCe 7 
                                   +CP C 
  gi|116754826|ref|YP_843944.1| 41 RCPSCH 46
                                   599996 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.6    0.0067         6      28      36 .]      26      34 ..      24      34 .. 0.88
   2 ?    4.8   0.9     0.029        26       4      10 ..      41      47 ..      41      48 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0067
                  zinc_ribbon_4 28 CskCghvFr 36
                                   C  Cgh+F+
  gi|116754826|ref|YP_843944.1| 26 CRSCGHKFK 34
                                   999999995 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.029
                  zinc_ribbon_4  4 tCpsCka 10
                                   +CpsC++
  gi|116754826|ref|YP_843944.1| 41 RCPSCHS 47
                                   7999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); 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: 0.33u 0.26s 00:00:00.59 Elapsed: 00:00:00.41
# Mc/sec: 392.82
//
Query:       gi|116754827|ref|YP_843945.1|  [L=393]
Description: trans-homoaconitate synthase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.9e-84  282.7   0.2    3.6e-84  282.4   0.2    1.1  1  HMGL-like  HMGL-like
    1.5e-05   24.3   0.0       0.14   11.3   0.0    2.2  2  DUF561     Protein of unknown function (DUF561)


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 !  282.4   0.2   4.1e-88   3.6e-84       2     264 .]      20     276 ..      19     276 .. 0.99

  Alignments for each domain:
  == domain 1  score: 282.4 bits;  conditional E-value: 4.1e-88
                                    -EEEE-TTTHHHHTSSS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B..--EE-SSHHHHHHH CS
                      HMGL-like   2 vkivdttLRDGeqalkaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkarilalvrarekdikaa 81 
                                    ++i+d+tLRDGeq +++ ++ eekl+ia+ Lde+gv+ iE+gfp+ s+ + ++vr i++ + +a+i al r+r++d+++a
  gi|116754827|ref|YP_843945.1|  20 IEICDVTLRDGEQMPGVVFKPEEKLEIARRLDEIGVEIIEAGFPVVSKSEKNAVRDICNLGLNAKISALSRSRQSDVDVA 99 
                                    79****************************************************************************** PP

                                    HH....TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-ETTT-BTTTBS--HHHHHHHHHHHHHHT-S CS
                      HMGL-like  82 vealkgagakrvhvfiatselhlkaklkkdreevakkaeeavkaarslgkdvelsledasrtdleflaevveaaeeaGat 161
                                    ++    +g+++v vfiats+lhlk+kl+++ +e+++ a e v++a+++g  v++s+eda+rtd ++l +++++aee+ a+
  gi|116754827|ref|YP_843945.1| 100 ID----CGVDMVSVFIATSDLHLKYKLHMTCAEAIRCALETVEYAKEHGLIVRFSAEDATRTDFNTLKKLYKKAEEYHAD 175
                                    **....************************************************************************** PP

                                    EEEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHHHHTT--EEEEBTTS--SSBBB-BHHHHHH CS
                      HMGL-like 162 riniaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaAveaGadrvdgtvnGlGeraGnaaleelva 241
                                    ++++aDtvG+++P+ ++ +is++k+ v+  +++ vHcH+dlGlA+antla++eaGa+++ +tvnG+Ger+Gn++leel +
  gi|116754827|ref|YP_843945.1| 176 YVSVADTVGIMNPRTMYYMISEIKKIVN--IPICVHCHDDLGLALANTLAGAEAGAKQLHTTVNGIGERSGNTPLEELLV 253
                                    ****************************..************************************************** PP

                                    HHHHTT-B----HHHHHHHHHHH CS
                      HMGL-like 242 alealgvdtgldlqklrsiaalv 264
                                    +l+       +dl+kl si++lv
  gi|116754827|ref|YP_843945.1| 254 NLRLHYGIDRYDLSKLKSISSLV 276
                                    ***9998889*********9997 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   1.6e-05      0.14     129     204 ..      38     113 ..      33     116 .. 0.93
   2 !   10.7   0.0   2.3e-05      0.21      31      82 ..     164     225 ..     155     228 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.6e-05
                         DUF561 129 LkleeqvkLakkLeslgvdliqteGkitsiskakkvndliekslstlastyeiskkvslPvicasGlsdvtvplal 204
                                     k ee++++a++L+++gv++i +   + s s+++ v+d+ +  l++  s+ + s++ ++ v    G+  v+v +a 
  gi|116754827|ref|YP_843945.1|  38 FKPEEKLEIARRLDEIGVEIIEAGFPVVSKSEKNAVRDICNLGLNAKISALSRSRQSDVDVAIDCGVDMVSVFIAT 113
                                    67799******************999********************************************999885 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 2.3e-05
                         DUF561  31 kiaraaekakatyvDiaad.....pk....lvkkvksvsniPiCvsaveaklllea.vkaGa 82 
                                    k+ + ae  +a yv +a       p+    +++++k+++niPiCv   +   l+ a  +aGa
  gi|116754827|ref|YP_843945.1| 164 KLYKKAEEYHADYVSVADTvgimnPRtmyyMISEIKKIVNIPICVHCHDDLGLALAnTLAGA 225
                                    555666666666666654311111212222799************98776555433145666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); 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: 00:00:00.41
# Mc/sec: 2896.41
//
Query:       gi|116754828|ref|YP_843946.1|  [L=641]
Description: hypothetical protein Mthe_1534 [Methanosaeta thermophila PT]
Scores for complete 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-75  254.3   0.0    2.7e-75  253.9   0.0    1.1  1  FbpA           Fibronectin-binding protein A N-terminus (FbpA
    1.1e-22   80.7   0.0    2.1e-22   79.8   0.0    1.4  1  NFACT-R_1      NFACT protein RNA binding domain
      0.003   17.7   0.0     0.0071   16.5   0.0    1.5  1  NFACT-R_2      NFACT protein RNA binding domain
  ------ inclusion threshold ------
       0.01   15.8   0.0      0.022   14.7   0.0    1.5  1  H2TH           Formamidopyrimidine-DNA glycosylase H2TH domai
      0.017   14.5   0.1      0.062   12.7   0.1    1.9  1  DUF2917        Protein of unknown function (DUF2917)
       0.11   12.9   0.0       0.24   11.8   0.0    1.5  1  Ribosomal_S13  Ribosomal protein S13/S18


Domain annotation for each model (and alignments):
>> FbpA  Fibronectin-binding protein A N-terminus (FbpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  253.9   0.0   8.9e-79   2.7e-75       2     411 ..       7     412 ..       6     420 .. 0.91

  Alignments for each domain:
  == domain 1  score: 253.9 bits;  conditional E-value: 8.9e-79
                                    HHHHHHHHHHHHHHHTTXEEEEEEEEETTEEEEEEEETTEEEEEEEEXXTTTXEEEEXXXXXXXXSSXXHHHHHHHHHHT CS
                           FbpA   2 glvlaavvaELqkellggridkiyqpekdelvltlranrgrhkLllsahpsyarihltekpkenpkeppnFcmlLRkyLk 81 
                                    ++++aa+vaELq ++ gg + k yq   d + lt++a++gr ++ l+a   + r h+t k++    +pp+F+ +LR +L+
  gi|116754828|ref|YP_843946.1|   7 NVDVAAIVAELQTRIAGGFFGKAYQSSGDAIWLTIQAREGRLDIILEA---GRRAHVTRKERVVGRTPPQFPAMLRSRLS 83 
                                    789*********************************************...***************************** PP

                                    TXEEEEEEEXTTSSEEEEEEEEEXTTSXEEEEEEEEEXXGGGXEEEEEETTTEEEEESSXBXXXSSXSXXBSTTXBXXXS CS
                           FbpA  82 garivsieqlgfdRivelsiekrdElgdeeeytLivEimgrhSNiiLvdeenkIidaikhvspkqsrvReilpgekYelP 161
                                    g+rivs+eq++fdR++e+ +e+      + +y+L+vE++ + +N++L+d+e +Ii +++ +s++   +R++  ge+Y++ 
  gi|116754828|ref|YP_843946.1|  84 GGRIVSVEQHDFDRVMEICVERS-----DGRYRLVVELFPK-GNMLLLDDEMRIILPLRPMSFR---DRKLIAGEQYVYH 154
                                    ***********************.....9************.**********************...9*********998 PP

                                    XXXSXBXTTSXXH.HHHHHHHHHS.XXXHHHHHHHBTTXXHHHHHHHHTTXSSSH...............HHHHHHHHTX CS
                           FbpA 162 psqdklnPleaeeleefkellskkekdlvkaLvkafqGlspllaeelleragldketsakelseedlerlyealqellee 241
                                          +P +++  e+++++l+ +++dlv++Lv+++ ++++++ ee++ rag+dk+t+a++lsee++ r+++al+++++ 
  gi|116754828|ref|YP_843946.1| 155 AG--AEDPRSVSI-ERLEAILHSSDADLVRTLVRNL-NMGGTYGEEVCLRAGVDKNTPATALSEEEIARVHSALRDVFDI 230
                                    88..889998888.88888888899***********.******************************************7 PP

                                    XX....XXEE.....XSSSEESSXXTTXX.SSXXXXSXHHHHHHHHTTTXXX--SHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           FbpA 242 leeekfepqlvlkeekpeefsvvplkslselekesfdslsealdeyYakkaerdrveqkrsdlekrveneleklekklkk 321
                                     e   ++pq+v+++ +p ++ ++pl+ +++le +sf+ +s+alde++ ++ e  ++   + +le   +++++ l+ k   
  gi|116754828|ref|YP_843946.1| 231 RE---IRPQIVYRDGEPFDVIPFPLEVYKGLEARSFERFSDALDEFFVAEPEMPKLSALERRLE-LQRAAIDELRAKE-- 304
                                    66...9********98888888889999************************999987444443.2333444444443.. PP

                                    HHHHHHCCGGH..HHHHCCHH-----------------------..--.................--------------- CS
                           FbpA 322 lekelekaeka..enyrligelltaylyaikkgmsevelenyyde.ge.................evtIpLdprkspsen 381
                                      ++l+   +   ++y  i+ +l+a+  a+++g s  ++ + ++  g+                 +vt +L+  +++++n
  gi|116754828|ref|YP_843946.1| 305 --TQLASMGDFiyQRYSEIDSILKAIAGARERGLSYTDIWERIQSsGKsavksldysgemiveidGVTLELNAGLTVPQN 382
                                    ..3333333335589************************9999987668******************************* PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           FbpA 382 AqkyfkkykKlkraveaveeqieetkeele 411
                                    A +y++++k + ++++++ee++++t++ l+
  gi|116754828|ref|YP_843946.1| 383 AGRYYERAKEAAKKAAGAEEALRRTEDLLQ 412
                                    *************************98776 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 !   79.8   0.0     7e-26   2.1e-22       2     109 .]     435     544 ..     434     544 .. 0.96

  Alignments for each domain:
  == domain 1  score: 79.8 bits;  conditional E-value: 7e-26
                      NFACT-R_1   2 vfwFkssdgylvimGkDkqeneelikkyleesdvwfhvdkessahvylrlsegeleeipeelleeaaqlakanSia.gnk 80 
                                    ++wF ssd++lvi+G+D+  nee++ kyle++d+ +h d  +++ ++++ +eg   e+pe+++eeaaq+a+++S+  ++ 
  gi|116754828|ref|YP_843946.1| 435 FRWFYSSDDFLVIGGRDADGNEEIYLKYLEKRDLALHTDYPGAPLTVIK-TEGR--EVPERTVEEAAQFAVSYSNLwREG 511
                                    99***********************************************.7777..8*********************** PP

                      NFACT-R_1  81 lssvdvvyvpasnlsktap....ldtGsvgfkg 109
                                    + s d++ v+ ++++kt++    l +G+++++g
  gi|116754828|ref|YP_843946.1| 512 VASGDCYVVRGDQVTKTPEhgefLRKGAFVVRG 544
                                    *******************9999****999875 PP

>> NFACT-R_2  NFACT protein RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   2.4e-06    0.0071       2      68 ..     436     506 ..     436     517 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.4e-06
                      NFACT-R_2   2 RhfrlsekaklIvgReeeEnkflk.gllkkdfvslrakshkGplvlid..g.elseedlelaarivarYsk 68 
                                    R f  s+++ +I gR+++ n+++  ++l+k+ + l++    +pl++i+  g e+ e+++e aa++++ Ys+
  gi|116754828|ref|YP_843946.1| 436 RWFYSSDDFLVIGGRDADGNEEIYlKYLEKRDLALHTDYPGAPLTVIKteGrEVPERTVEEAAQFAVSYSN 506
                                    77889999*********9999985256655555599999999*****54566888**************97 PP

>> H2TH  Formamidopyrimidine-DNA glycosylase H2TH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   7.4e-06     0.022      39      78 ..     189     228 ..     166     232 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 7.4e-06
                                    --HHHHHHHHHHTT--TTSBGGGS-HHHHHHHHHHHHHHH CS
                           H2TH  39 lGNiyadEvLfrakihPerlakslskeelellhqeikevl 78 
                                    +G  y +Ev  ra+++ +++a  ls+ee++++h+++++v+
  gi|116754828|ref|YP_843946.1| 189 MGGTYGEEVCLRAGVDKNTPATALSEEEIARVHSALRDVF 228
                                    7899*******************************99986 PP

>> DUF2917  Protein of unknown function (DUF2917)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   2.1e-05     0.062      24      54 ..      35      67 ..      31      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.1e-05
                        DUF2917 24 GrvWvTr..egdpeDhwLqaGqslrlargqrvv 54
                                    ++W+T   ++   D+ L+aG + ++ r++rvv
  gi|116754828|ref|YP_843946.1| 35 DAIWLTIqaREGRLDIILEAGRRAHVTRKERVV 67
                                   579****5544488******************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 ?   11.8   0.0   8.2e-05      0.24      23      61 ..     189     227 ..     174     254 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.2e-05
                  Ribosomal_S13  23 iGrrkakiilkkadvdedkrigelteeeiekieeivenk 61 
                                    +G ++ ++++ +a+vd+++ +  l+eeei +++  +   
  gi|116754828|ref|YP_843946.1| 189 MGGTYGEEVCLRAGVDKNTPATALSEEEIARVHSALRDV 227
                                    789999**************************9988774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (641 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 4187.93
//
Query:       gi|116754829|ref|YP_843947.1|  [L=200]
Description: hypothetical protein Mthe_1535 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      596  (0.0332422); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1440.08
//
Query:       gi|116754830|ref|YP_843948.1|  [L=643]
Description: arginine decarboxylase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-40  139.0   0.0    2.9e-40  138.2   0.0    1.4  1  Orn_Arg_deC_N  Pyridoxal-dependent decarboxylase, pyridoxal b
    3.2e-19   68.9   0.1    1.4e-18   66.9   0.1    2.1  1  Arg_decarb_HB  Arginine decarboxylase helical bundle domain


Domain annotation for each model (and alignments):
>> Orn_Arg_deC_N  Pyridoxal-dependent decarboxylase, pyridoxal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.2   0.0   3.2e-44   2.9e-40       5     247 .]      75     338 ..      71     338 .. 0.89

  Alignments for each domain:
  == domain 1  score: 138.2 bits;  conditional E-value: 3.2e-44
                                    HHHHHHHHHHCT...CCEEEEEGGG---HHHHHHHHHTT....EEEEESSHHHHHHHHHCTTTGGGEEEEESS--HHHHH CS
                  Orn_Arg_deC_N   5 erklkrwkkalp...rikvfYavKansdlavlellaelG....lgldcaSkaElelvlaagvsperiifanpckqreelr 77 
                                     r++    ++++   ++++++++K+n+ ++v+e + + G    +gl+++ kaEl ++l ++ + ++  ++n++k+ ++lr
  gi|116754830|ref|YP_843948.1|  75 YRAFTGSISEFGyqgKYQPVFPMKVNQRKEVIEYILNYGreinIGLEIGTKAELLAALTLDLPEDSLLICNGYKDDDFLR 154
                                    5556666666777779***********************99999************************************ PP

                                    HHH...HCTHTEEEESSHHHHHHHHHHHCC....EEEEEEEE-SCCSSSSTCCCSSSTTSSSSEEHC...HHHHHHHHHH CS
                  Orn_Arg_deC_N  78 yal...ekgvkvvtvdnveeleklaklape....akvllRiktdvsaatcelistggessKFGaale...eavealleaa 147
                                     al   +k++ +++vd +ee+  + +la +    + + +R+k+ +s+++ ++  +gges KFG ++    e ++ l+e  
  gi|116754830|ref|YP_843948.1| 155 LALmfsDKHKIIIVVDLFEEIFDILRLARSmevrPLLGMRVKL-FSKGSGRWAESGGESAKFGLSTIeclELLKILEENG 233
                                    *97322344559***************99988878889*****.*******************98864556666666777 PP

                                    HHTTEEEEEEE---BSSC-SCHHHHHHHHHHHHHHHHHHHHT---SEEE--S-BS-HCSTTSSSST......HHHHHHHH CS
                  Orn_Arg_deC_N 148 keenlqlvGvsfHvGSgvsdleafvkavekalklfdelaelGvklkiLdvGGGfgveyeeeeeplk......leeiaeki 221
                                      + l +  ++fH+GS+++d++ +++a+++a++++ +++++  +++ ++vGGG++v+y + ++  +      l e+ ++i
  gi|116754830|ref|YP_843948.1| 234 LLDRLRM--IHFHIGSQITDIHRIKHAMNEAARIYAKVRKV-AEIEYFNVGGGLSVDYDGSKSSGPssanytLREYSNDI 310
                                    7777788..****************************9998.59***************8766554678888******** PP

                                    HHHHHHHHH..TSSS-EEEE--SHHHHG CS
                  Orn_Arg_deC_N 222 realeeafp..gdkevtiiaEpGRalva 247
                                       l+++++  g + +ti++E+GRa++a
  gi|116754830|ref|YP_843948.1| 311 VYTLQKICEeeGVPCPTIVSESGRAIAA 338
                                    *********9999************987 PP

>> Arg_decarb_HB  Arginine decarboxylase helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.9   0.1   1.6e-22   1.4e-18       4      83 ..     365     443 ..     363     444 .. 0.94

  Alignments for each domain:
  == domain 1  score: 66.9 bits;  conditional E-value: 1.6e-22
                  Arg_decarb_HB   4 apellqnLwelleelsqrnlqEiyhDavhyldearelFrlGllsLeerAkaEqlylaicrkirkllkeeerapreildeL 83 
                                    +p  +++L+  +++++ +n+ E+yhDa+hy+de+ + F+lG + LeerAk+E l++++c+k  +l++ + +  +e + eL
  gi|116754830|ref|YP_843948.1| 365 DPIQIEDLYFAFKNINLKNYKEYYHDALHYRDELLDSFNLGNIGLEERAKGEMLFWMVCQKAVSLARHAGDNSEE-FREL 443
                                    677899**************************************************************9999999.8887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (643 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); 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: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.41
# Mc/sec: 4662.05
//
Query:       gi|116754831|ref|YP_843949.1|  [L=301]
Description: hypothetical protein Mthe_1537 [Methanosaeta thermophila PT]
Scores for 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-110  366.0   2.3   1.2e-109  365.8   2.3    1.0  1  SDH_sah        Serine dehydrogenase proteinase
     0.0027   17.6   0.2     0.0051   16.7   0.2    1.5  1  CLP_protease   Clp protease
  ------ inclusion threshold ------
      0.017   14.4   0.0      0.024   14.0   0.0    1.2  1  ECH_1          Enoyl-CoA hydratase/isomerase
       0.14   12.1   0.0       0.26   11.2   0.0    1.4  1  Peptidase_S49  Peptidase family S49


Domain annotation for each model (and alignments):
>> SDH_sah  Serine dehydrogenase proteinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  365.8   2.3  2.6e-113  1.2e-109       6     275 ..      24     299 ..      19     301 .] 0.96

  Alignments for each domain:
  == domain 1  score: 365.8 bits;  conditional E-value: 2.6e-113
                        SDH_sah   6 plsslssllwfllflylllapqlkrkqlllarlkvlrkleekrksrvitmihrqesigflGipiykfitiedseevlrai 85 
                                    p+ +++s lw++lfl+l+l p ++r+ l++ar+++l kl+++r+s vit+ihrqe i++lG+p+ ++i+i+dseevlrai
  gi|116754831|ref|YP_843949.1|  24 PVEQILSNLWIILFLLLFLVPMVQRNILQMARKRLLVKLGKRRGSLVITLIHRQEVISLLGLPLARYIDIDDSEEVLRAI 103
                                    66789999************************************************************************ PP

                        SDH_sah  86 rltpkdkpidliihtpGGlvlaatqiakalkehkaktrvivphyamsGGtlialaadeiildenavlGpvdpqlgq.... 161
                                    r++p+d pid+i+htpGGl+laatqia alk+h+a+t vi+phyamsGGtliala deii+d+na lGpvdpqlg+    
  gi|116754831|ref|YP_843949.1| 104 RSAPNDVPIDIILHTPGGLALAATQIALALKNHPARTSVIIPHYAMSGGTLIALAVDEIIMDPNAALGPVDPQLGDqtga 183
                                    *************************************************************************9744444 PP

                        SDH_sah 162 ypaasilkvvekkeakdiddktliladiakkaikqveefvyellkdkydeekakeiakklteGrwthdypltveelke.l 240
                                    ypa+silkvvekk+ ++iddktlila+ a+ka++q++ ++  ++  + dee  ++i +++ +G++thd+p+  ++l+  l
  gi|116754831|ref|YP_843949.1| 184 YPATSILKVVEKKKIDEIDDKTLILAEEARKAVEQMKALLRRIVCSDCDEETVNRIIEEMVSGKYTHDHPFLADDLRAlL 263
                                    9***************************************************************************9846 PP

                        SDH_sah 241 Glevntnvpeevyellelyeqplgqrps.veyipvp 275
                                    G  v+t+vp+evyel+ ly+  +++r + vey+p+ 
  gi|116754831|ref|YP_843949.1| 264 GDRVKTDVPQEVYELMALYRMDISRRRPgVEYVPMS 299
                                    99*********************999888*****85 PP

>> CLP_protease  Clp protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.2   1.1e-06    0.0051      40     158 ..     103     223 ..      87     245 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.1e-06
                                    HHHH-SSS-EEEEEEE--B-HHHHHHHHHHHHHSSS-EEEEEEEEEETHHHHHHHTS-TTGEEEETTEEEEES-TEEEEE CS
                   CLP_protease  40 LeaedpdkdillyinspGGsvtaglaIydtmqyikpdvsticlGlaaSmgslllaagekgkRfalpnarimihqPlggaq 119
                                    + +  +d +i +++++pGG   a++ I+ +++ + ++ s+i    a+S g+l+++a ++   ++ pna++    P+ g q
  gi|116754831|ref|YP_843949.1| 103 IRSAPNDVPIDIILHTPGGLALAATQIALALKNHPARTSVIIPHYAMSGGTLIALAVDEI--IMDPNAALGPVDPQLGDQ 180
                                    556677889***********************************************9988..888888877777755554 PP

                                    E...EHHHHHH..HHHHHHHHHHHHHHHHHHHHTS-HHHHHHHH CS
                   CLP_protease 120 g...qasdiei..eaeellkikerlneilakhtgqslekiekdl 158
                                         a+ i +  e +++++i+++   ila+++ + +e++++ l
  gi|116754831|ref|YP_843949.1| 181 TgayPATSILKvvEKKKIDEIDDKT-LILAEEARKAVEQMKALL 223
                                    4334445554311444555555553.356666666666666555 PP

>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   5.3e-06     0.024      98     153 ..     147     202 ..     131     261 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.3e-06
                                    EEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHH CS
                          ECH_1  98 aaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeil 153
                                    +a+ GG ++ala D +i++ na+ g    +lG   ga+    + + v k+k  ei 
  gi|116754831|ref|YP_843949.1| 147 YAMSGGTLIALAVDEIIMDPNAALGPVDPQLGDQTGAYPATSILKVVEKKKIDEID 202
                                    899*****************************999999999999999999988874 PP

>> Peptidase_S49  Peptidase family S49
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   5.8e-05      0.26      11      40 ..     142     171 ..     134     173 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.8e-05
                                    EEEEEEEETHHHHHHTTSSEEEE-TT-EEE CS
                  Peptidase_S49  11 asaenvaaSggYylasaadkivanpstivg 40 
                                    +++  +a Sgg ++a a d+i+++p++  g
  gi|116754831|ref|YP_843949.1| 142 VIIPHYAMSGGTLIALAVDEIIMDPNAALG 171
                                    567789********************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       831  (0.0463495); expected 358.6 (0.02)
Passed bias filter:                      710  (0.0396006); 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: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2141.15
//
Query:       gi|116754832|ref|YP_843950.1|  [L=598]
Description: radical SAM domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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-130  434.9   0.0   1.8e-130  434.5   0.0    1.2  1  Radical_SAM_N  Radical SAM N-terminal
      9e-25   87.8   0.0    1.3e-24   87.2   0.0    1.3  1  DUF3362        Domain of unknown function (DUF3362)
    4.5e-19   69.4   1.2    5.9e-18   65.8   1.2    2.5  3  Radical_SAM    Radical SAM superfamily
  ------ inclusion threshold ------
      0.026   14.6   0.1        6.9    6.7   0.0    3.1  2  B12-binding    B12 binding domain


Domain annotation for each model (and alignments):
>> Radical_SAM_N  Radical SAM N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  434.5   0.0  4.1e-134  1.8e-130       1     298 []       7     304 ..       7     304 .. 0.97

  Alignments for each domain:
  == domain 1  score: 434.5 bits;  conditional E-value: 4.1e-134
                  Radical_SAM_N   1 flpvsrkemeergwdelDvilvsgDaYvDhpsfgaaligrlLeaeGfrvgiiaqPdwksaedfkklGkPrlffgvsaGnl 80 
                                    +lp+sr+em+e+g+d+lDvilv+gDaYvDhpsfgaaligr+L ++Gf+vgii+qPdw+++edfk+lG+Prlffgv+aGn+
  gi|116754832|ref|YP_843950.1|   7 YLPISRREMKELGVDQLDVILVTGDAYVDHPSFGAALIGRVLWDAGFTVGIIPQPDWRRSEDFKRLGEPRLFFGVTAGNV 86 
                                    8******************************************************************************* PP

                  Radical_SAM_N  81 DsmvnkytaekklrsdDaytpggkagkRPdravivYsnlireaykdvpvvlGgiEaSLRriahYDywsdkvrrsilldsk 160
                                    Dsmvn +t + k+rs D y+pgg+  +RPdra++vY+++i++++++ pvvlGgiEaSLRr+ahYDywsd+vrrsi++d+ 
  gi|116754832|ref|YP_843950.1|  87 DSMVNAFTPNLKRRSGDVYSPGGEI-RRPDRATLVYADRIHSIFPGRPVVLGGIEASLRRFAHYDYWSDSVRRSIIADAP 165
                                    ***********************98.8***************************************************** PP

                  Radical_SAM_N 161 adllvyGmgeraiveiakrlakgeeveelkdirgtavllkkea..kakekevielpsyeevkedkklyaeafrlleeetn 238
                                    adllv+Gmge a+veia+rl++ge++ e++d+rgt+++++ ++  +++++e++ +ps++ev++dk++yaeafrl + e++
  gi|116754832|ref|YP_843950.1| 166 ADLLVFGMGELAVVEIASRLERGESIGEIRDVRGTVFKMSVKEwkSSSHEEYTVIPSFDEVSSDKRKYAEAFRLHYMEQD 245
                                    *************************************99975543444489***************************** PP

                  Radical_SAM_N 239 plnakalvqkhgdravvlnppalplsteelDevyelpyarkahpsykkkkipalemikfS 298
                                    p++++a+vq h ++++v+nppa+pl+teelD++yelpy r+ hpsy +k +pale ++fS
  gi|116754832|ref|YP_843950.1| 246 PFRGRAVVQPHPKTVIVQNPPARPLKTEELDRIYELPYIRREHPSY-RKPVPALESVRFS 304
                                    **********************************************.59**********8 PP

>> DUF3362  Domain of unknown function (DUF3362)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.2   0.0     3e-28   1.3e-24       1      85 [.     518     596 ..     518     598 .] 0.97

  Alignments for each domain:
  == domain 1  score: 87.2 bits;  conditional E-value: 3e-28
                        DUF3362   1 dqVqtFyPsPmatattmYhtgknpltkvkreeesvdvvrgekerrlhkAllrYhdpknwpllreALkkmGredLiGngkk 80 
                                    +qVq+F P+Pm+++ttmYhtg++p t     + +v+v+rg +e+ +++All+Y  p+n +l+re L ++ r+dLiG g  
  gi|116754832|ref|YP_843950.1| 518 EQVQDFTPTPMTVSTTMYHTGLDPFT-----MKPVHVPRG-REKMIQRALLQYWLPQNRKLVREGLISADRTDLIGDGPM 591
                                    7*************************.....*******95.89************************************* PP

                        DUF3362  81 hLipt 85 
                                    +L+p 
  gi|116754832|ref|YP_843950.1| 592 CLVPS 596
                                    ***96 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.21   9.6e+02      36     115 ..      13      87 ..      11     107 .. 0.63
   2 ?   -2.1   0.0      0.99   4.5e+03      90     129 ..     187     225 ..     161     237 .. 0.77
   3 !   65.8   1.2   1.3e-21   5.9e-18       2     166 ..     306     509 ..     305     510 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.21
                                    HHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  36 eevkelkaekgvkevilgggepllypdfvellerlaklavpgiritvetngtlpdeeklerllelgvdrvslgleaadde 115
                                    +e+kel +++  ++++++g+   ++p f  +l  ++     +  +tv + +  + ++  e +++lg  r+ +g+ a++ +
  gi|116754832|ref|YP_843950.1|  13 REMKELGVDQ-LDVILVTGDAYVDHPSFGAALIGRVLW---DAGFTVGIIPQPD-WRRSEDFKRLGEPRLFFGVTAGNVD 87 
                                    4556665555.666666666555555555555555554...5666666666664.7777777777777777777777766 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.99
                                    GHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  90 deeklerllelgvdrvslgleaaddekvlklmnrghtfee 129
                                    + e + ++++ + +++ ++++ + +  + +++   ++f+e
  gi|116754832|ref|YP_843950.1| 187 RGESIGEIRDVRGTVFKMSVKEWKSSSHEEYT-VIPSFDE 225
                                    37888899999999999999999888666666.6666665 PP

  == domain 3  score: 65.8 bits;  conditional E-value: 1.3e-21
                                    EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGS.................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx.................... RF
                    Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggeplly.................... 60 
                                    +  rgC + CsfCa +++  +++ ++s+s+e+il+e+++l + +g  +++  +gg p+++                    
  gi|116754832|ref|YP_843950.1| 306 TSHRGCFGSCSFCALTHH--QGRIVQSRSIESILKEARRLVEMPGfRGVIQDVGG-PTADmygmvcalwerggcgrictp 382
                                    6779*************8..********************777777888888888.99999******************* PP

                                    .........TTHHHHHHHHHHTCCCTEEEEEEECSSCHG.........HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHH CS
                                    .........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  61 .........pdfvellerlaklavpgiritvetngtlpd.........eeklerllelg.vdrvslgleaaddekvlklm 121
                                             +++ ell+rl+++  pg+r +++++g+++d         e +le+l + +   ++ +  e++++  v + m
  gi|116754832|ref|YP_843950.1| 383 ecdnieishRRYLELLRRLKEI--PGVRHVFVSSGIRHDlvvrdekygELFLEELCREHvSGHLKIAPEHISES-VTRCM 459
                                    ********99999999999999..9*******************9999666666666666689**********9.88888 PP

                                    T..CTSHHHHHHHHHHHHHHTTSET...EEEEEEEBTTTSHHHHHHHHHH CS
                                    x..xxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM 122 n..rghtfeevlealeklreagikr...vvdrivglpGendeeleellel 166
                                    +  + + ++++++++++++ + +++     + + g+pG + +++ el+e+
  gi|116754832|ref|YP_843950.1| 460 HkpPVEVLDAFMNCFRRAAGKSGREeyvLPYLMSGHPGCTVRDMIELAEY 509
                                    7687888899******999999999**99*****************9986 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0015       6.9       6      34 ..      30      58 ..      26      71 .. 0.87
   2 ?    4.0   0.1     0.011        49      71      94 ..     121     144 ..     115     182 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0015
                    B12-binding  6 atvggdlhplGlavlaaalrdagfeVqll 34
                                   + ++ d++++G+a++ ++l dagf V ++
  gi|116754832|ref|YP_843950.1| 30 GDAYVDHPSFGAALIGRVLWDAGFTVGII 58
                                   56789*********************887 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.011
                    B12-binding  71 lvellkrirprvkvvvGGahpsld 94 
                                    +++++++i p+ +vv+GG+ +sl 
  gi|116754832|ref|YP_843950.1| 121 YADRIHSIFPGRPVVLGGIEASLR 144
                                    578899999999******998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (598 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); 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:                         4  (0.000223102); expected 0.2 (1e-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 0.24s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 4379.09
//
Query:       gi|116754833|ref|YP_843951.1|  [L=341]
Description: anthranilate phosphoribosyltransferase [Methanosaeta thermophila PT]
Scores for complete 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-96  322.5   1.2    2.6e-96  322.1   1.2    1.2  1  Glycos_transf_3  Glycosyl transferase family, a/b domain
    2.4e-18   65.8   2.9    4.9e-18   64.7   2.9    1.5  1  Glycos_trans_3N  Glycosyl transferase family, helical bundle 


Domain annotation for each model (and alignments):
>> Glycos_transf_3  Glycosyl transferase family, a/b domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  322.1   1.2  2.9e-100   2.6e-96       3     253 .]      72     321 ..      70     321 .. 0.99

  Alignments for each domain:
  == domain 1  score: 322.1 bits;  conditional E-value: 2.9e-100
                                    TBEEEEESS-SSSTHHHHHHHHHHHHHHTT-BEEEEE-STCTTCS-HHHHHCTST--ST--HHHHHHHHHHHSEEEEEHH CS
                Glycos_transf_3   3 dlvDivgTGGdgantfNiStaaaivvAaaGvkvakhgnrsvssksGsaDvLealgvnleltpeeveklleevgvgflfap 82 
                                     lvD++gTGGd  nt+N+Staaaiv+Aa+Gv+vakhgn +vss +Gsa vLealgvn+ + pe+ve+++e vg+gf++ap
  gi|116754833|ref|YP_843951.1|  72 TLVDTCGTGGDSTNTINVSTAAAIVAAACGVPVAKHGNYAVSSRCGSANVLEALGVNISCPPERVESIIESVGIGFMLAP 151
                                    68****************************************************************************** PP

                                    SSSSHHHHHHHHHHHHTT.-SSHHHCHHHHHT..SEEEEHHHHHHHHTCHSEEEEEEEESTTSSCCSTSHHHHHHHHHHH CS
                Glycos_transf_3  83 eyhkamkhvapvrrelgirTvfnlLGPLinparvkkqllgvyskelaeklaevlkelgveralvvhgdGldevsllaktt 162
                                     +h+amk va +r+e+girTvfn+LGPL+npa +++q++gvys+ l+ek+a+vl+ lg++ra+vvhg+Glde+s ++ t 
  gi|116754833|ref|YP_843951.1| 152 LFHPAMKRVAHIRKEMGIRTVFNVLGPLTNPAGAEAQVVGVYSPALCEKIANVLNLLGTKRAMVVHGSGLDEISNTGSTF 231
                                    ******************************************************************************** PP

                                    HHHHHTTEEEEEEEEEGSSTSSSEEESHHHHSSHHHHHHHHTTHHTSCHHHHHHHHHHHHHHHHHHHTTSSSSHHHHHHH CS
                Glycos_transf_3 163 vaelkdgeiteytlepedfglkraelealeggepkenaeilkavlegkksaakrdlvllnagaalvlagkadslkegvak 242
                                    v el dg +++y+++p d+g   a+l++++gg+p+enae l ++l+g+ks+a r+lv++nagaa++++g a+sl+eg a 
  gi|116754833|ref|YP_843951.1| 232 VSELCDGVVRNYVVDPRDLGYPLADLNEIAGGTPDENAERLVRILKGEKSRA-RELVAMNAGAAVYVSGIASSLREGCAI 310
                                    **************************************************98.*************************** PP

                                    HHHHHHTSHHH CS
                Glycos_transf_3 243 aeevidsGkAl 253
                                    ae +i+sG+Al
  gi|116754833|ref|YP_843951.1| 311 AEGAISSGSAL 321
                                    *********95 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 !   64.7   2.9   5.4e-22   4.9e-18       3      63 .]       3      62 ..       2      62 .. 0.97

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 5.4e-22
                                   HHHHHHTT.---HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH---HHHHHHHHHHHHHHS CS
                Glycos_trans_3N  3 iikklrdgeeLtaeeirfaihgilkgevtdaqiaAfLmAlrlkGetaeEiaalaeAmresg 63
                                   ++++l++g++Lt ee++ ++ ++++g +tdaqia+ L+Alr+kGetaeE+a++a+ mres+
  gi|116754833|ref|YP_843951.1|  3 YLARLIEGQNLTIEEAESLLGAFFDG-ATDAQIASALTALRMKGETAEELAGMAKRMRESA 62
                                   89***********************8.79******************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2533.93
//
Query:       gi|116754834|ref|YP_843952.1|  [L=208]
Description: phosphoribosylanthranilate isomerase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-36  126.4   0.0    1.3e-36  126.2   0.0    1.0  1  PRAI      N-(5'phosphoribosyl)anthranilate (PRA) isomerase
     0.0062   16.0   0.5      0.021   14.2   0.2    2.0  3  NMO       Nitronate monooxygenase


Domain annotation for each model (and alignments):
>> PRAI  N-(5'phosphoribosyl)anthranilate (PRA) isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.2   0.0   1.4e-40   1.3e-36       1     193 [.       4     202 ..       4     203 .. 0.92

  Alignments for each domain:
  == domain 1  score: 126.2 bits;  conditional E-value: 1.4e-40
                                    TCE----SHHHHHHHHHHTSSEEEEE.--TTBTTB--HHHHHHHCCCS--E..EEEEESSS-HHHHHHHHHHCTECEEEE CS
                           PRAI   1 akicgltrasdvkaavkagadelgli.faesskrevseeqaqellekvpak..lVGVfvNqpieevlriaqelgldvvQL 77 
                                    +kicgl++  ++  a kagad+lg++ + e s++  s  +a+ l+  vp+    V+V   + +++ +r+a+ l+ d++Q+
  gi|116754834|ref|YP_843952.1|   4 VKICGLMDEYELECALKAGADALGFVvEIERSRHRLSLDEARNLIGMVPPFttSVAVVEPAGVDDAVRLADYLQSDALQI 83 
                                    69**********************97257999*****************54469************************** PP

                                    -CGG.-HHHHHHHHHHS-TTSEEEEEEE-SSS--S-SSTT-SEEEEE....SSS-SSSXXXXGGGGTTSXX...TTEEEE CS
                           PRAI  78 HGdedeqeyeellktelpvikalkvaesvdevkearradhvdllllD....sgaGGtGelldwsliskllks..lkviLA 151
                                    HGd +++e+ee ++  +p +  + v+   d + e++r  +  ++l+D     g GG+G + dws+ + ++     ++iLA
  gi|116754834|ref|YP_843952.1|  84 HGDLSPEEIEEIKR-RVPQRIIVAVPPGSDRAVEVSRIAD--AVLVDtpvsGGLGGSGRTHDWSVTARMRSTlhAPLILA 160
                                    ****9999999988.9999999999998886666666655..8****9998899*************99977999***** PP

                                    SSXXTTTHHHHHT.TXXSEEEEXGGGEEETEEXHHHHHHHHH CS
                           PRAI 152 GGLtpeNvaeaiklegvlgvDvssGVEtnGvkDlekirkfvq 193
                                    GGL peNv++ai++ ++++vDvssGVEtnG kD  k ++fv 
  gi|116754834|ref|YP_843952.1| 161 GGLRPENVMDAINVVKPYAVDVSSGVETNGRKDPVKAEEFVR 202
                                    **************************************9996 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0     0.074   6.6e+02     201     218 ..       8      25 ..       6      32 .. 0.90
   2 ?   -1.8   0.0      0.18   1.6e+03      55     101 ..      42      90 ..      21     108 .. 0.67
   3 !   14.2   0.2   2.4e-06     0.021     152     210 ..     116     171 ..      54     183 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.074
                            NMO 201 GiidrrgvaaaLalGAsg 218
                                    G++d+ +++ aL +GA +
  gi|116754834|ref|YP_843952.1|   8 GLMDEYELECALKAGADA 25 
                                    999999*********987 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.18
                            NMO  55 rkvkaltdk..Pfgvnlflpkkdaadraekykkeleeaalelnieegvr 101
                                     ++++l+    Pf   + + +++  d+a + ++ l+  al+++   + +
  gi|116754834|ref|YP_843952.1|  42 DEARNLIGMvpPFTTSVAVVEPAGVDDAVRLADYLQSDALQIHGDLSPE 90 
                                    4555555544588888888888888888888888888888887766655 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 2.4e-06
                            NMO 152 vearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavdiPviAaGGiidrrgvaa 210
                                      +r aDa+ v+ p +GG  G    g +   ++ +++++ +  P+i aGG+  ++ ++a
  gi|116754834|ref|YP_843952.1| 116 EVSRIADAVLVDTPVSGGLGG---SGRTHDWSVTARMRSTLHAPLILAGGLRPENVMDA 171
                                    35678****************...555789********************976665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        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 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1504.25
//
Query:       gi|116754835|ref|YP_843953.1|  [L=478]
Description: anthranilate synthase component I [Methanosaeta thermophila PT]
Scores for complete 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-97  326.7   0.0    3.9e-95  318.3   0.0    3.1  3  Chorismate_bind  chorismate binding enzyme
    3.2e-36  124.7   0.0    5.4e-34  117.4   0.0    2.6  3  Anth_synt_I_N    Anthranilate synthase component I, N termina


Domain annotation for each model (and alignments):
>> Chorismate_bind  chorismate binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.7   0.0    0.0086        77      40      90 ..      18      71 ..       5      78 .. 0.74
   2 ?    1.8   0.0     0.016   1.5e+02     145     180 ..      79     114 ..      74     115 .. 0.87
   3 !  318.3   0.0   4.4e-99   3.9e-95       2     258 .]     214     466 ..     213     466 .. 0.98

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.0086
                                   HHHHHHHHHCTBSSSEEEEEEETT....EEEEEEESSEEEEEETTSEEEEECEEE CS
                Chorismate_bind 40 plalyralrarnpapysflleled....sellgaSPElllkveggrrietepiaG 90
                                   pl+ly +lr r   +    +e ++    ++++ga P  +++++ +r+ie+e+  G
  gi|116754835|ref|YP_843953.1| 18 PLSLYLSLRGRRYPYLLESVEKSGqrarFSFVGADPSAVVRLK-NREIEVEVFNG 71
                                   6788888888765555555533335666899************.66***999887 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.016
                                    EEEEETTEEEEEEEEEEEESTT--HHHHHHHCSS-C CS
                Chorismate_bind 145 kverysevlhlvstiegelkedvslldllkalfPtg 180
                                    ++ r++e+   +  i+g+l ++ +++d+l+a +P++
  gi|116754835|ref|YP_843953.1|  79 RLSRCAEIEEFSHGIKGRLLPEFDMFDALRAAIPCP 114
                                    56677778888889********************98 PP

  == domain 3  score: 318.3 bits;  conditional E-value: 4.4e-99
                                    HCHHHHHHHHHHHHHHTTS-SEEEEEEEEEECESS-B-HHHHHHHHHCTBSSSEEEEEEETTEEEEEEESSEEEEEETTS CS
                Chorismate_bind   2 redYaeavekvkeeiragdlykvvlsrrlkaeleaavdplalyralrarnpapysflleledsellgaSPElllkveggr 81 
                                     e+Y+eav ++k++i +gd+++vvl+r++++e++   d++alyr+lr+ np+py++l+e+++ +++gaSPE+l+++ +g 
  gi|116754835|ref|YP_843953.1| 214 PEEYMEAVVAAKRHIIDGDIFQVVLARSTDVECS---DTIALYRNLRRINPSPYTYLFEFGGLSIVGASPETLFNTYAG- 289
                                    589*****************************77...678*************************************77. PP

                                    EEEEECEEEEEEHSSSHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCBSCCEEEEECCEEEEEETTEEEEEEEEEE CS
                Chorismate_bind  82 rietepiaGTrargktpeedealeeelledeKeraEhlmivdlirndLgkvakpgsvkvpelfkverysevlhlvstieg 161
                                     ++++piaGT +rg+tpeedeal++++l+deKeraEh+m+vdl rnd+++v+++gsvkv+++++v rys+v+h+ +t++g
  gi|116754835|ref|YP_843953.1| 290 ILKVNPIAGTCPRGRTPEEDEALARAMLNDEKERAEHVMLVDLGRNDVRSVCRAGSVKVEDFMSVLRYSHVQHIETTVSG 369
                                    ******************************************************************************** PP

                                    EESTT--HHHHHHHCSS-CCCSEESHHHHHHHHHHHSSS--TTTTSEEEEEETTS-EEEEEE-SEEEEETTEEEEEEEEE CS
                Chorismate_bind 162 elkedvslldllkalfPtgavtGaPkkrameiidelEearRgvYaGavgyldadgeaelavvIRtavvkdkelrlgaGaG 241
                                     l+e+++ +d+ +a+fP+g+++GaPk rameiidelE+++Rg+Y+G +gy++adg+a++a++IR++++kd+ +r++aGaG
  gi|116754835|ref|YP_843953.1| 370 VLREECDQFDAARAIFPAGTLSGAPKMRAMEIIDELEKEPRGIYGGGIGYFSADGSADFAIAIRSIILKDNIARVQAGAG 449
                                    ******************************************************************************** PP

                                    EETT--HHHHHHHHHHH CS
                Chorismate_bind 242 IvadSdpeaEyeEtlaK 258
                                    IvadSdpe+E++Et+ K
  gi|116754835|ref|YP_843953.1| 450 IVADSDPERELAETERK 466
                                    **************998 PP

>> Anth_synt_I_N  Anthranilate synthase component I, N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.4   0.0     6e-38   5.4e-34       3     141 ..      16     174 ..      14     175 .. 0.94
   2 ?   -2.3   0.0      0.51   4.5e+03      33      53 ..     273     293 ..     248     327 .. 0.64
   3 !    4.4   0.0    0.0044        40      84     104 ..     400     426 ..     334     445 .. 0.71

  Alignments for each domain:
  == domain 1  score: 117.4 bits;  conditional E-value: 6e-38
                  Anth_synt_I_N   3 ltplsvylklaeeehkflLeSaeneggegrySfigldpflelkskngeveveg........................peg 58 
                                    ++pls+yl+l+++++++lLeS+e++g+++r+Sf+g+dp+++++ kn+e+eve+                         +g
  gi|116754835|ref|YP_843953.1|  16 DAPLSLYLSLRGRRYPYLLESVEKSGQRARFSFVGADPSAVVRLKNREIEVEVfnggeeflsrrlsrcaeieefshgIKG 95 
                                    78****************************************************************************** PP

                  Anth_synt_I_N  59 eeleeeepldalrellerfrsaedseptelpfvgGlvGylgYDlvreieklpksakddln.lpdarlilydtlivfDhke 137
                                    + l e +++dalr+ + + rs+e+++ +   f gG +Gy++YD+v+e  +l+   k +++ +pda++++++++++fDh++
  gi|116754835|ref|YP_843953.1|  96 RLLPEFDMFDALRAAIPCPRSDERNFFGRQIFLGGGIGYIAYDMVKE--RLG---KVSTSeTPDAQFAIVESTFIFDHLM 170
                                    **********************999977778*************765..577...555555******************* PP

                  Anth_synt_I_N 138 rrly 141
                                    rr+y
  gi|116754835|ref|YP_843953.1| 171 RRVY 174
                                    **99 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.51
                  Anth_synt_I_N  33 ySfigldpflelkskngevev 53 
                                     S++g++p   +++  g ++v
  gi|116754835|ref|YP_843953.1| 273 LSIVGASPETLFNTYAGILKV 293
                                    578888887766655555555 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.0044
                  Anth_synt_I_N  84 e.....ptelp.fvgGlvGylgYDlvr 104
                                    e     ++e++ ++gG +Gy++ D   
  gi|116754835|ref|YP_843953.1| 400 EiidelEKEPRgIYGGGIGYFSADGSA 426
                                    0444446777779********977655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (478 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); 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: 0.55u 0.23s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 3228.31
//
Query:       gi|116754836|ref|YP_843954.1|  [L=248]
Description: indole-3-glycerol-phosphate synthase [Methanosaeta thermophila PT]
Scores for complete 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-58  195.7   0.0    8.9e-58  195.4   0.0    1.0  1  IGPS          Indole-3-glycerol phosphate synthase
  ------ inclusion threshold ------
      0.011   15.2   0.0      0.022   14.2   0.0    1.5  1  His_biosynth  Histidine biosynthesis protein
      0.013   14.6   0.0      0.021   13.9   0.0    1.3  1  Dus           Dihydrouridine synthase (Dus)
      0.029   14.1   0.0      0.046   13.5   0.0    1.3  1  TgMIC1        Toxoplasma gondii micronemal protein 1 TgMIC1
      0.037   13.2   0.1      0.089   12.0   0.1    1.6  1  NanE          Putative N-acetylmannosamine-6-phosphate epimer
       0.21   11.2   0.0          9    5.8   0.0    2.1  2  Peripla_BP_6  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.4   0.0     3e-61   8.9e-58      41     246 ..      36     235 ..      10     242 .. 0.91

  Alignments for each domain:
  == domain 1  score: 195.4 bits;  conditional E-value: 3e-61
                                    CHCH.TTS-EEEEEE-SEETTTEESBSS--HHHHHHHHTTT.-SEEEEE--CCCC---CCHHHHHHHH-SS-EEEES--- CS
                           IGPS  41 Lres.ekklaliaEvKkaSPskgliredfdpaeiAkkyeeagAsaiSVLteekyFqGsledLrevrqavslpvlrKdFii 119
                                    ++ + +  + +iaE+K    s+  +r+  ++ eiA+ ye+ gA  iSVLte+ yF Gs+++L+e+r++ slpvlrKdFii
  gi|116754836|ref|YP_843954.1|  36 ISARrRGLIPVIAEIKPRAISR-PLRAG-EAGEIARFYESRGACGISVLTEPTYFLGSISSLEEARRSTSLPVLRKDFII 113
                                    4444466789***********9.77776.79************************************************* PP

                                    SHHHHHHHHHCT-SEEEEECCCS-HHHHHHHHHHHCCTT-EEEEEESSHHHHHHHHHTT-SEEEEESEETTTTEE-CHHH CS
                           IGPS 120 deyqieearalgadaiLLivkvledeeleelaeaakslglevLvEvhdeeeleralklgakiiGvNnRnLktlevdlntt 199
                                    + +qi ear   ad++LLiv++ +   +e+l e  +  g+e+LvEvhde+el+ra ++ga i+G+NnR+L tlevdl+++
  gi|116754836|ref|YP_843954.1| 114 NRKQIREAR---ADLVLLIVSIAD---IEDLIEDVRAAGMEPLVEVHDEHELDRAANAGATIVGINNRDLITLEVDLGRF 187
                                    ******998...8*******9976...566999999******************************************** PP

                                    HHHCHCC-TT.SEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC-TT CS
                           IGPS 200 eeLaklvpkd.vllvaeSGiktredveklkeegvnafLvGeslmrqed 246
                                    e L + +++   + vaeSG+++re++ ++ ++g++a+L+G+s+m+++ 
  gi|116754836|ref|YP_843954.1| 188 EALGPIARDIgLFTVAESGVSSREEALRMMNAGADALLIGNSIMKNPA 235
                                    *****88865799********************************976 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   7.5e-06     0.022      67     115 ..     192     240 ..     183     243 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.5e-06
                                    HHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHH CS
                   His_biosynth  67 eiaeevfipvqvGGGIrsledveelleagadkviigtaavknpelikel 115
                                     ia+ + +     +G++s e++ ++++agad + ig + +knp l+ e+
  gi|116754836|ref|YP_843954.1| 192 PIARDIGLFTVAESGVSSREEALRMMNAGADALLIGNSIMKNPALLGEI 240
                                    56677777777889******************************99886 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   6.9e-06     0.021     146     227 ..     161     241 ..     151     247 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.9e-06
                                    HHHHCT-SEEEEESSECCCTT-CG--CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHHH CS
                            Dus 146 iveaaGaqaltvHgRtraqnyegtadweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlfae 225
                                    ++ +aGa+ + +  R   +      ++ea   + +++ +  +a  ++ ++e+a ++++  Gad+++ig    +nP+l++e
  gi|116754836|ref|YP_843954.1| 161 RAANAGATIVGINNRDLITLEVDLGRFEALGPIARDIGLFTVAESGVSSREEALRMMNA-GADALLIGNSIMKNPALLGE 239
                                    55666666666666665555556667777777888888888888999***********9.*****************997 PP

                                    HH CS
                            Dus 226 st 227
                                     t
  gi|116754836|ref|YP_843954.1| 240 IT 241
                                    55 PP

>> TgMIC1  Toxoplasma gondii micronemal protein 1 TgMIC1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.5e-05     0.046      57     132 ..     154     234 ..     151     239 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.5e-05
                         TgMIC1  57 sdvveleeaaGsavltiGlGskGrlavvldyarlna....alrsvayvvedsGcksieevllqGlnsG..aklvvttlGe 130
                                     d+ el+ aa ++   +G+ ++  +++ +d  r +a    a     ++v +sG +s ee  l+ +n+G  a l+ +++ +
  gi|116754836|ref|YP_843954.1| 154 HDEHELDRAANAGATIVGINNRDLITLEVDLGRFEAlgpiARDIGLFTVAESGVSSREEA-LRMMNAGadALLIGNSIMK 232
                                    6999*************************999887633334455679********99875.4555555115678888877 PP

                         TgMIC1 131 ss 132
                                    ++
  gi|116754836|ref|YP_843954.1| 233 NP 234
                                    76 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 ?   12.0   0.1     3e-05     0.089      80     178 ..     134     232 ..     129     241 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3e-05
                                    -HHHHHHHHHHH--EEEEE-SSHHHHHHHHHTT-SEEE-TTTTSSTTS-.SS--HHHHHHHHHTT--EEEES---SHHHH CS
                           NanE  80 tieelikkikekyqllmaDistleeglvakklGvdivGttlsGytkeeekaepDfalvkalseaglkviaeGrintPeka 159
                                    +ie+li++++  ++  + ++    e   a ++G+ ivG      ++ e +     al     + gl+++ae  + + e+a
  gi|116754836|ref|YP_843954.1| 134 DIEDLIEDVRAAGMEPLVEVHDEHELDRAANAGATIVGINNRDLITLEVDLGRFEALGPIARDIGLFTVAESGVSSREEA 213
                                    67888888888888888888888888888888888888877777666665544444444456789*************** PP

                                    HHHHTT--SEEEE-HHHH- CS
                           NanE 160 kkaieiGvdavvvGsaitr 178
                                     ++++ G+da+ +G +i +
  gi|116754836|ref|YP_843954.1| 214 LRMMNAGADALLIGNSIMK 232
                                    **************99976 PP

>> Peripla_BP_6  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.003         9     184     217 ..     116     149 ..     101     168 .. 0.89
   2 ?    3.4   0.0     0.017        50     181     216 ..     211     246 ..     188     248 .] 0.83

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.003
                                    HHHHTTT-SEEEEESSHHHHHHHHHHHHHTT-SS CS
                   Peripla_BP_6 184 lqikaagadavllagtgadlaallkaaaeaGlda 217
                                     qi++a+ad vll+   ad+  l+  +++aG  +
  gi|116754836|ref|YP_843954.1| 116 KQIREARADLVLLIVSIADIEDLIEDVRAAGMEP 149
                                    79*****************************875 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.017
                                    HHHHHHHTTT-SEEEEESSHHHHHHHHHHHHHTT-S CS
                   Peripla_BP_6 181 aqvlqikaagadavllagtgadlaallkaaaeaGld 216
                                    + +l++++agada+l+++    ++all ++  ++++
  gi|116754836|ref|YP_843954.1| 211 EEALRMMNAGADALLIGNSIMKNPALLGEITGVDIK 246
                                    56899*************999999999888766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1877.65
//
Query:       gi|116754837|ref|YP_843955.1|  [L=358]
Description: FAD-dependent pyridine nucleotide-disulphide oxidoreductase [Methanosaeta thermophila PT]
Scores for complete 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  151.8   0.0    2.9e-44  151.5   0.0    1.1  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    7.7e-22   77.7   0.4    9.4e-16   58.1   0.0    2.4  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    3.8e-05   23.8   0.1      0.099   12.9   0.0    2.8  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    0.00014   21.1   0.1      0.019   14.1   0.0    2.3  2  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
     0.0011   18.1   0.1       0.68    8.9   0.0    3.0  3  Lycopene_cycl   Lycopene cyclase protein
     0.0019   18.4   0.4       0.49   10.7   0.1    2.4  2  TrkA_N          TrkA-N domain
     0.0034   16.7   0.0          1    8.6   0.0    2.2  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
     0.0042   17.6   0.0      0.013   16.0   0.0    1.8  2  XdhC_C          XdhC Rossmann domain
     0.0071   16.2   0.3       0.77    9.6   0.0    2.6  3  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
     0.0089   15.6   0.8        3.3    7.2   0.1    3.2  3  DAO             FAD dependent oxidoreductase
  ------ inclusion threshold ------
      0.016   14.7   0.0       0.31   10.6   0.0    2.3  2  DUF1188         Protein of unknown function (DUF1188)
      0.018   14.3   0.0      0.026   13.8   0.0    1.2  1  Amino_oxidase   Flavin containing amine oxidoreductase
      0.023   14.7   2.9       0.61   10.1   0.0    3.2  4  NAD_binding_9   FAD-NAD(P)-binding
      0.059   12.2   1.0        9.9    4.9   0.1    2.9  3  Trp_halogenase  Tryptophan halogenase
      0.096   13.1   0.0       0.41   11.1   0.0    2.0  2  NAD_binding_7   Putative NAD(P)-binding
        0.1   12.6   0.0       0.45   10.5   0.0    2.1  2  HCBP_related    Haemolysin-type calcium binding protein relat
       0.14   11.3   1.4         28    3.6   0.2    3.2  3  GIDA            Glucose inhibited division protein A
       0.16   12.0   0.1        6.4    6.8   0.0    2.9  3  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
        0.2   12.1   1.5         12    6.4   0.1    2.6  2  Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domai
       0.29   10.3   0.9         11    5.1   0.1    2.2  2  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 !  151.5   0.0   3.2e-47   2.9e-44       2     293 ..       6     286 ..       5     291 .. 0.83

  Alignments for each domain:
  == domain 1  score: 151.5 bits;  conditional E-value: 3.2e-47
                                    SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH.HHHHCHHHHCCCCHCCTCEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias.evvkklnqgielllgeevvkidp 80 
                                    ++v++GgG+AG ++ + l++ ++++ l+e + ++  +   + + +  v+ d  ia  + + + +  ++   +  ++++  
  gi|116754837|ref|YP_843955.1|   6 RLVIVGGGIAGAELIRLLSNTEIEISLIEPKHQIECQALYPDYLAGLVGIDDMIAPlDDFCERSGALHISER--ALEL-- 81 
                                    79**************************88887878877788888888888887778444444445555555..5555.. PP

                                    SCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECH...HHHHHCCSS-TSEEEEES-SHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  81 gkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtld...saealklkllpkrivvvGgGyiGvEl 157
                                    + + v+++        +++yd lv+A G++++  g++G  en++ +  t++   +a+++ + + p+ri+vvG+G++GvE+
  gi|116754837|ref|YP_843955.1|  82 DDGVVVCQ------RSRVEYDILVIAVGAEQNFYGVKGS-ENAFSV-NTFEgtlHAREFIERESPDRIMVVGSGLTGVEV 153
                                    55568883......3479*********************.666544.666622266777778888*************** PP

                                    HHHHHHH.T-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S- CS
                                    xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 158 Aaalakl.gkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavG 236
                                    A++la+   +++++ve   r+l+++++++s+ +e+ l ++Gv + + t+v ei++++     +  dg+++d+d+ ++ +G
  gi|116754837|ref|YP_843955.1| 154 ASVLADSlESNIYIVEMQGRILPQFPERISRLVERILFERGVSILTSTQVSEIQRDS----ITFADGTTLDCDMTIWTTG 229
                                    ***87664889*******************************************999....59***************** PP

                                    EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGC....TECCSS--HHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxx RF
                    Pyr_redox_2 237 vrpstelleeklglelderggivvdeflrtnvpgiyaiGDva....ggkggpelaqaAvqq 293
                                    ++p + ++ e+l  +  +rg++++d++lr+  ++i+aiGD+a    ++k   ++  +A +q
  gi|116754837|ref|YP_843955.1| 230 IKPTQ-FA-ENLRFPK-KRGWLLTDPYLRV-QDDIFAIGDCAwieiDQKLATKTGIEAERQ 286
                                    ****7.44.9999998.*************.99*********9888555555555555555 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   5.1e-06    0.0046       1      36 [.       6      43 ..       6      55 .. 0.86
   2 !   58.1   0.0   1.1e-18   9.4e-16       1      70 [.     140     210 ..     140     219 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 5.1e-06
                                   EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS..T CS
                      Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkll..r 36
                                   ++v+vGgG  g El   l++   +++++e + ++    
  gi|116754837|ref|YP_843955.1|  6 RLVIVGGGIAGAELIRLLSNTEIEISLIEPKHQIEcqA 43
                                   68*****************************9998533 PP

  == domain 2  score: 58.1 bits;  conditional E-value: 1.1e-18
                                    EEEEECSSHHHHHHHHHHHH.TTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEET CS
                      Pyr_redox   1 kvvvvGgGyiglElAgalae.lgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegse 70 
                                    +++vvG+G++g+E+A++la+ l +++++ve++ ++l++++e +s+++++ l ++g+ +l++t+v ei+ ++
  gi|116754837|ref|YP_843955.1| 140 RIMVVGSGLTGVEVASVLADsLESNIYIVEMQGRILPQFPERISRLVERILFERGVSILTSTQVSEIQRDS 210
                                    699***************999**********************************************9765 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 !   12.9   0.0   0.00011     0.099       1      30 [.       9      38 ..       9      43 .. 0.94
   2 !    8.0   0.0    0.0036       3.3       1      31 [.     143     174 ..     143     209 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSS CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdr 30
                                   IvG+G++G+ + +lL++  +++ l+e  ++
  gi|116754837|ref|YP_843955.1|  9 IVGGGIAGAELIRLLSNTEIEISLIEPKHQ 38
                                   9*************************8776 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0036
                                    EE--SHHHHHHHHHHHCC.TEEEEEE-SSSSS CS
                  NAD_binding_8   1 IvGaGlsGlvaAylLaka.gfdvlllekrdrl 31 
                                    +vG+Gl+G   A+ La+    ++ ++e++ r+
  gi|116754837|ref|YP_843955.1| 143 VVGSGLTGVEVASVLADSlESNIYIVEMQGRI 174
                                    8***************9878999999999887 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 ?    5.0   0.0     0.013        11     191     214 ..       4      27 ..       1      41 [. 0.77
   2 !   14.1   0.0   2.1e-05     0.019     174     238 ..     125     187 ..      87     219 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.013
                    K_oxygenase 191 kkriaVvGsGqSaaeifedllrrq 214
                                    + r+++vG+G  +ae+++ l +++
  gi|116754837|ref|YP_843955.1|   4 SPRLVIVGGGIAGAELIRLLSNTE 27 
                                    5689************99877654 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 2.1e-05
                    K_oxygenase 174 rvvHsseylerkeellakkriaVvGsGqSaaeifedllrrqkk..velklvtrsealeplddspfvn 238
                                      +H+ e+ er+    +++ri+VvGsG ++ e++  l+++ ++  + +++  r   ++p   s +v 
  gi|116754837|ref|YP_843955.1| 125 GTLHAREFIERE----SPDRIMVVGSGLTGVEVASVLADSLESniYIVEMQGRILPQFPERISRLVE 187
                                    456666666665....89*****************99999553346666666666666666666655 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0   0.00076      0.68       2      36 ..       7      39 ..       6      47 .. 0.91
   2 ?    2.1   0.1      0.09        81       2      31 ..     141     169 ..     140     181 .. 0.80
   3 ?    3.3   0.0     0.039        35      90     160 ..     183     249 ..     177     255 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00076
                  Lycopene_cycl  2 vvviGaGpAglslAarlteakpglkvvlieaspsl 36
                                   +v++G+G Ag  l   l  +++++++ lie+  ++
  gi|116754837|ref|YP_843955.1|  7 LVIVGGGIAGAELIRLL--SNTEIEISLIEPKHQI 39
                                   79************999..***********98776 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.09
                  Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlie 31 
                                    ++v+G+G+ g+ +A  l +   + ++ ++e
  gi|116754837|ref|YP_843955.1| 141 IMVVGSGLTGVEVASVL-ADSLESNIYIVE 169
                                    68*************99.556667777776 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.039
                  Lycopene_cycl  90 keellerlvengvklleak.vesveeeeageslvvleggrkirarlvvdarglaslkkarrlglQtfyGvev 160
                                     + +++ l e gv+ l ++ v +++ ++      + ++g ++++ + +  +g+   + a +l + + +G+++
  gi|116754837|ref|YP_843955.1| 183 SRLVERILFERGVSILTSTqVSEIQRDSI-----TFADGTTLDCDMTIWTTGIKPTQFAENLRFPKKRGWLL 249
                                    55666667788887766542777777766.....9*****************88888888888888888865 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.1   0.00055      0.49       2      33 ..       8      39 ..       7      54 .. 0.84
   2 ?    5.7   0.0     0.019        17       1      34 [.     141     175 ..     141     187 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00055
                                   EEES-SHHHHHHHHHHHHTTEEEEEEESSHHH CS
                         TrkA_N  2 iiiGlGrvGrslaeeLseggkdvvvidkdeer 33
                                   +i+G G  G +l++ Ls+ ++++++i+ +++ 
  gi|116754837|ref|YP_843955.1|  8 VIVGGGIAGAELIRLLSNTEIEISLIEPKHQI 39
                                   8*****************8878*****99876 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.019
                                    EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHH CS
                         TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerv 34 
                                    i+++G G +G ++a  L +  ++++++++ + + +
  gi|116754837|ref|YP_843955.1| 141 IMVVGSGLTGVEVASVLADsLESNIYIVEMQGRIL 175
                                    79****************966678***99876655 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 !    5.8   0.0    0.0081       7.3      30      59 ..       6      35 ..       3      49 .. 0.82
   2 !    8.6   0.0    0.0011         1      24      76 ..     134     187 ..     116     234 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0081
                                   EEEEESTSHHHHHHHHHHHHTT-EEEEEES CS
                    AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDv 59
                                   + +++GgG+aG + i+  ++ + ++ +++ 
  gi|116754837|ref|YP_843955.1|  6 RLVIVGGGIAGAELIRLLSNTEIEISLIEP 35
                                   689**********99998888877777665 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0011
                                    TCB---EEEEESTSHHHHHHHHH.HHHTT-EEEEEESSHHHHHHHHHTTTCECE CS
                    AlaDh_PNT_C  24 pgvepakvlviGgGvaGlqAiat.akglgakVtvlDvrparleqleslgakfve 76 
                                    +  +p +++v+G G  G++ +++ a +l+ ++++++++ + l q+ +  ++ ve
  gi|116754837|ref|YP_843955.1| 134 ERESPDRIMVVGSGLTGVEVASVlADSLESNIYIVEMQGRILPQFPERISRLVE 187
                                    5557889***********98775499**********999988888775555454 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.4e-05     0.013       1      91 [.       7     130 ..       7     156 .. 0.77
   2 ?   -1.5   0.0       3.9   3.5e+03       2      30 ..     142     171 ..     141     201 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.4e-05
                                    EEEE--STTHHHHHHHHHHHTEEEEEEES-GGGG-GGG-TT-SE...............................-EEEE CS
                         XdhC_C   1 lvifGaghvaqalarlaaalgfrvtvvdpreefatkerfpeade...............................tavvv 49 
                                    lvi+G+g  +++l+rl++++++++++++p+ +++ ++ +p+  +                               +  vv
  gi|116754837|ref|YP_843955.1|   7 LVIVGGGIAGAELIRLLSNTEIEISLIEPKHQIECQALYPDYLAglvgiddmiaplddfcersgalhiseralelDDGVV 86 
                                    79******************************998888885555788888888888888888888889999999955555 PP

                                    --S-HHHHHHHHHHHSSS--SEEEESS-HHH..HHHHCTTS.-- CS
                         XdhC_C  50 lthdhklDaealeaalrkkaayigllGSrkk..aarrlerlraa 91 
                                    + +  + ++++l  a+  + ++ g+ GS++    ++++  l+a+
  gi|116754837|ref|YP_843955.1|  87 VCQRSRVEYDILVIAVGAEQNFYGVKGSENAfsVNTFEGTLHAR 130
                                    55555777778888886678899999998741134555555555 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.9
                                    EEE--STTHHHHHHHHH.HHTEEEEEEES- CS
                         XdhC_C   2 vifGaghvaqalarlaa.algfrvtvvdpr 30 
                                    +++G g  + ++a+++a +l+ ++++v+ +
  gi|116754837|ref|YP_843955.1| 142 MVVGSGLTGVEVASVLAdSLESNIYIVEMQ 171
                                    689999999999987541567777776655 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 ?    4.2   0.0      0.04        36       3      33 ..       8      38 ..       6      45 .. 0.89
   2 !    9.6   0.0   0.00086      0.77       2      55 ..     141     195 ..     140     225 .. 0.77
   3 ?   -2.9   0.1       6.1   5.4e+03      35      56 ..     283     304 ..     269     313 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.04
                                   EEE--SCCHHHHHHHHHHTT-EEEEE-S-HH CS
                        3HCDH_N  3 aviGaGtmGagiaavfasagleVvlvdisee 33
                                    ++G G+ Ga++  ++ ++++e+ l++ +++
  gi|116754837|ref|YP_843955.1|  8 VIVGGGIAGAELIRLLSNTEIEISLIEPKHQ 38
                                   69************************99876 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00086
                                    EEEE--SCCHHHHHHHHHHT.T-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS CS
                        3HCDH_N   2 vaviGaGtmGagiaavfasa.gleVvlvdiseealekalekieksleklvekgkl 55 
                                    + v+G+G+ G ++a+v+a + + ++ +v+++ ++l +  e+i++ +e+   ++ +
  gi|116754837|ref|YP_843955.1| 141 IMVVGSGLTGVEVASVLADSlESNIYIVEMQGRILPQFPERISRLVERILFERGV 195
                                    78****************999***************9999999988886554444 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 6.1
                                    HHHHHHHHHHHHHCCTTTTSS- CS
                        3HCDH_N  35 lekalekieksleklvekgklk 56 
                                    +e+ +++++++l++++++++l+
  gi|116754837|ref|YP_843955.1| 283 AERQAKHMAENLKRMIRRRSLT 304
                                    4555666666666666666665 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.1    0.0037       3.3       2      31 ..       7      38 ..       6      43 .. 0.81
   2 ?    2.7   0.2     0.087        78       2      29 ..     141     171 ..     140     175 .. 0.81
   3 ?    2.2   0.0      0.12   1.1e+02     156     205 ..     190     233 ..     179     259 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0037
                                   EEEECTSHHHHHHHHHHHHTT..EEEEESSSS CS
                            DAO  2 vviiGGGiiGlstAyeLarrg..Vtllekgdi 31
                                   +vi+GGGi+G+   + L+     + l+e +++
  gi|116754837|ref|YP_843955.1|  7 LVIVGGGIAGAELIRLLSNTEieISLIEPKHQ 38
                                   79*********999999877677888888765 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.087
                                    EEEECTSHHHHHHHHHHHHT.T..EEEEESS CS
                            DAO   2 vviiGGGiiGlstAyeLarr.g..Vtllekg 29 
                                    + ++G+G +G+ +A  La      + ++e++
  gi|116754837|ref|YP_843955.1| 141 IMVVGSGLTGVEVASVLADSlEsnIYIVEMQ 171
                                    88*************9975442579999876 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.12
                                    HHHTT-EEEESECEEEEEEEETCEEEEEEECTEEE.EEEEEEEE--GGGHH CS
                            DAO 156 aealGveilegtevtgleeedgkvwgverttpgen.daadavVnaaGawsd 205
                                    + ++Gv il+ t+v ++++++  ++   +   g++ d+ d  + ++G+  +
  gi|116754837|ref|YP_843955.1| 190 LFERGVSILTSTQVSEIQRDS--ITFA-D---GTTlDC-DMTIWTTGIKPT 233
                                    5689*************8763..3333.2...555343.668888887655 PP

>> DUF1188  Protein of unknown function (DUF1188)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0       0.2   1.8e+02      45      78 ..       6      40 ..       2      47 .. 0.88
   2 ?   10.6   0.0   0.00034      0.31      34      77 ..     131     174 ..     125     262 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.2
                                   EEEEES-CCCHHHHHHHHCCC.EEEEEEESSGGGG CS
                        DUF1188 45 nvlviGaYltGaaiakkLskk.eevtlvDiephlk 78
                                   + +++G  + Ga + + Ls+   e+ l++ + +++
  gi|116754837|ref|YP_843955.1|  6 RLVIVGGGIAGAELIRLLSNTeIEISLIEPKHQIE 40
                                   689****************9989999999998876 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00034
                                    HHHTT--E..EEEEEES-CCCHHHHHHHHCCC..EEEEEEESSGGG CS
                        DUF1188  34 eyleeeeleeknvlviGaYltGaaiakkLskk..eevtlvDiephl 77 
                                    e++e e  ++++++v+G+ ltG+ +a+ L  +  +++++v+++ ++
  gi|116754837|ref|YP_843955.1| 131 EFIERE--SPDRIMVVGSGLTGVEVASVLADSleSNIYIVEMQGRI 174
                                    566644..469******************9887799***9998665 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.9e-05     0.026     205     265 ..     176     233 ..     111     248 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.9e-05
                                    E..TTHTHHHHHHHHHTTTTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S-HHHH CS
                  Amino_oxidase 205 p..rgGlsqlpealaeelrgldirlntrVkeikregdgvtvtledgevveaDaVvvTvplgvl 265
                                    p   + +s+l+e++   +rg++i+++t V+ei+r     ++t+ dg+++++D  + T+ +   
  gi|116754837|ref|YP_843955.1| 176 PqfPERISRLVERILF-ERGVSILTSTQVSEIQR----DSITFADGTTLDCDMTIWTTGIKPT 233
                                    3332336777777777.*****************....*****************99987665 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 ?   10.1   0.0   0.00068      0.61       1      41 [.       8      43 ..       8      52 .. 0.76
   2 ?   -2.4   0.0       4.5     4e+03     136     154 ..      85     103 ..      68     104 .. 0.71
   3 ?    3.1   0.1     0.097        87       2      32 ..     143     169 ..     142     181 .. 0.83
   4 ?   -0.7   0.0       1.4   1.2e+03     134     154 ..     209     229 ..     178     231 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00068
                  NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsepgagrv 41
                                   +ivG+G++G+ ++ rLl++    +++ei l++p++  + ++
  gi|116754837|ref|YP_843955.1|  8 VIVGGGIAGAELI-RLLSN----TEIEISLIEPKHQIECQA 43
                                   7********9865.67777....58********65543444 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.5
                  NAD_binding_9 136 vlladgaslaadaVvLAlG 154
                                    v+  + +++++d +v+A+G
  gi|116754837|ref|YP_843955.1|  85 VVVCQRSRVEYDILVIAVG 103
                                    4445667889999999998 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.097
                  NAD_binding_9   2 ivGaGprGlavlerLlarakkkspleitlfd 32 
                                    +vG G +G+ v+  L+++     + +i +++
  gi|116754837|ref|YP_843955.1| 143 VVGSGLTGVEVASVLADSL----ESNIYIVE 169
                                    9**************9997....56666666 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 1.4
                  NAD_binding_9 134 qavlladgaslaadaVvLAlG 154
                                      ++ adg++l++d  + ++G
  gi|116754837|ref|YP_843955.1| 209 DSITFADGTTLDCDMTIWTTG 229
                                    35788999****999999998 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.011       9.9       2      33 ..       7      35 ..       6      41 .. 0.71
   2 ?    3.2   0.1     0.037        33       1      32 [.     140     169 ..     140     176 .. 0.86
   3 ?    1.2   0.0      0.15   1.3e+02     188     233 ..     209     252 ..     180     259 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.011
                                   EEEE--SHHHHHHHHHHHHHTTTSSEEEEEE- CS
                 Trp_halogenase  2 ivivGGGtaGwlaAaalakalkgklevtlves 33
                                   +vivGGG+aG     +++   + ++e++l+e 
  gi|116754837|ref|YP_843955.1|  7 LVIVGGGIAGA---ELIRLLSNTEIEISLIEP 35
                                   79*******94...444444433499999995 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.037
                                    EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE CS
                 Trp_halogenase   1 kivivGGGtaGwlaAaalakalkgklevtlve 32 
                                    +i++vG G  G  +A++la  l+   ++ +ve
  gi|116754837|ref|YP_843955.1| 140 RIMVVGSGLTGVEVASVLADSLES--NIYIVE 169
                                    699*******************55..666666 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.15
                                    EEEEETTS-EEE-SEEEE-SGGG-IIIIIIT---EEE-TTT----E CS
                 Trp_halogenase 188 eslrledgreveadlfiDcsGfrgllieqaLktgfedwsdvLltdr 233
                                    +s++ +dg++++ d+ i  +G +    ++    +f +   +Lltd 
  gi|116754837|ref|YP_843955.1| 209 DSITFADGTTLDCDMTIWTTGIKPTQFAEN--LRFPKKRGWLLTDP 252
                                    3678899****************9999997..56777788888885 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 ?   11.1   0.0   0.00046      0.41       9      46 ..       6      51 ..       3     109 .. 0.70
   2 ?   -1.4   0.0       3.6   3.2e+03       9      28 ..     140     159 ..     136     194 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00046
                  NAD_binding_7  9 kvlvvGgGevAarkvrklleagakvtvvapevkeele........e 46
                                   + ++vGgG  +a+ +r l +++ ++ ++ p+ + e++        +
  gi|116754837|ref|YP_843955.1|  6 RLVIVGGGIAGAELIRLLSNTEIEISLIEPKHQIECQalypdylaG 51
                                   689****************************877777555555551 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.6
                  NAD_binding_7   9 kvlvvGgGevAarkvrklle 28 
                                    +++vvG G  + + ++ l++
  gi|116754837|ref|YP_843955.1| 140 RIMVVGSGLTGVEVASVLAD 159
                                    78999999888776666665 PP

>> HCBP_related  Haemolysin-type calcium binding protein related domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0         6   5.4e+03      26      37 ..     185     196 ..     177     201 .. 0.71
   2 ?   10.5   0.0   0.00051      0.45      28      39 ..     209     220 ..     203     223 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 6
                   HCBP_related  26 rieqieFaDGtv 37 
                                     +e+i F  G++
  gi|116754837|ref|YP_843955.1| 185 LVERILFERGVS 196
                                    499999986665 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00051
                   HCBP_related  28 eqieFaDGtvWd 39 
                                    + i+FaDGt++d
  gi|116754837|ref|YP_843955.1| 209 DSITFADGTTLD 220
                                    58********98 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.2     0.031        28       2      30 ..       7      35 ..       6      53 .. 0.80
   2 ?    3.6   0.0     0.032        29       2      20 ..     141     159 ..     140     173 .. 0.88
   3 ?    0.5   0.0      0.27   2.4e+02     115     150 ..     200     230 ..     179     257 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.031
                                   EEEE-SSHHHHHHHHHHHHTT--EEEEES CS
                           GIDA  2 viViGgGhAGceAAlaaarlGakvlLith 30
                                   ++++GgG AG e    +++  +++ Li +
  gi|116754837|ref|YP_843955.1|  7 LVIVGGGIAGAELIRLLSNTEIEISLIEP 35
                                   689*********88888888888888843 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.032
                                    EEEE-SSHHHHHHHHHHHH CS
                           GIDA   2 viViGgGhAGceAAlaaar 20 
                                    ++V+G G+ G+e A  +a 
  gi|116754837|ref|YP_843955.1| 141 IMVVGSGLTGVEVASVLAD 159
                                    89***********998875 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.27
                                    ES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT CS
                           GIDA 115 eeeveeliveekkvkgvvtedgetikakavviatGt 150
                                    + +v+e++        ++ +dg+t+ ++ ++ +tG 
  gi|116754837|ref|YP_843955.1| 200 STQVSEIQR-----DSITFADGTTLDCDMTIWTTGI 230
                                    345555544.....6799999*************95 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.35   3.2e+02      14      37 ..       6      29 ..       2      46 .. 0.86
   2 ?   -2.0   0.0       3.9   3.5e+03      75      89 ..      94     108 ..      89     120 .. 0.81
   3 ?    6.8   0.0    0.0072       6.4       9      42 ..     135     168 ..     128     190 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.35
                                   EEEEES-SHHHHHHHHHHHCCT-C CS
                   Shikimate_DH 14 kvlliGaGemaelvakhLlakgvk 37
                                   + +++G G  + ++++ L++ +++
  gi|116754837|ref|YP_843955.1|  6 RLVIVGGGIAGAELIRLLSNTEIE 29
                                   789***************999887 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.9
                                    T-SEEEE-SSSSS-S CS
                   Shikimate_DH  75 eadvvisataseepi 89 
                                    e+d++++a+++e++ 
  gi|116754837|ref|YP_843955.1|  94 EYDILVIAVGAEQNF 108
                                    79*******999876 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0072
                                    ..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEE CS
                   Shikimate_DH   9 slkekkvlliGaGemaelvakhLlakgvkkvvva 42 
                                    + +  +++++G G ++ +va+ L+++   ++ ++
  gi|116754837|ref|YP_843955.1| 135 RESPDRIMVVGSGLTGVEVASVLADSLESNIYIV 168
                                    556789*****************99988888886 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 ?    6.4   0.1     0.013        12       3      23 ..       8      28 ..       6      37 .. 0.80
   2 ?    4.1   0.2     0.065        58       1      26 [.     140     164 ..     140     175 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.013
                                   EEETTTSHHHHHHHHHHHC.TS CS
                 Semialdhyde_dh  3 aivGatGyvGqellrlLee.hp 23
                                    ivG  G  G+el+rlL++ + 
  gi|116754837|ref|YP_843955.1|  8 VIVG-GGIAGAELIRLLSNtEI 28
                                   6999.9***********99444 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.065
                                    EEEEETTTSHHHHHHHHHHHCTSSEE CS
                 Semialdhyde_dh   1 kvaivGatGyvGqellrlLeehpeve 26 
                                    ++ +vG +G +G e++ +L+++ e +
  gi|116754837|ref|YP_843955.1| 140 RIMVVG-SGLTGVEVASVLADSLESN 164
                                    5889**.************9965544 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1     0.013        11       5      31 ..       8      34 ..       6      42 .. 0.89
   2 ?    3.5   0.1      0.04        36       4      22 ..     141     159 ..     140     172 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.013
                                   EEE--SHHHHHHHHHHHHTTHHEEEEE CS
                  FAD_binding_3  5 lIVGaGpaGlmlallLseaGvrvvlve 31
                                   +IVG+G aG+ l +lLs+  ++  l+e
  gi|116754837|ref|YP_843955.1|  8 VIVGGGIAGAELIRLLSNTEIEISLIE 34
                                   6*****************999999998 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.04
                                    EEEE--SHHHHHHHHHHHH CS
                  FAD_binding_3   4 VlIVGaGpaGlmlallLse 22 
                                    +++VG+G++G+  a++L+ 
  gi|116754837|ref|YP_843955.1| 141 IMVVGSGLTGVEVASVLAD 159
                                    589**************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); 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: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 2619.02
//
Query:       gi|116754838|ref|YP_843956.1|  [L=231]
Description: hypothetical protein Mthe_1545 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1748.02
//
Query:       gi|116754839|ref|YP_843957.1|  [L=140]
Description: hypothetical protein Mthe_1546 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1058.21
//
Query:       gi|116754840|ref|YP_843958.1|  [L=142]
Description: peptidylprolyl isomerase, FKBP-type [Methanosaeta thermophila PT]
Scores for complete 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   82.0   0.0    3.6e-23   81.7   0.0    1.3  1  FKBP_C          FKBP-type peptidyl-prolyl cis-trans isomerase
  ------ inclusion threshold ------
        0.4   10.7   5.9       0.18   11.7   1.2    2.8  3  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an


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 !   81.7   0.0     4e-27   3.6e-23       4      74 ..       3     107 ..       1     139 [. 0.74

  Alignments for each domain:
  == domain 1  score: 81.7 bits;  conditional E-value: 4e-27
                                    BB-TTCEEEEEEEEEETTSSEEEEHCCHTSEEEEETTSSSSCHHHHHHHTTSBTT-EEEEEEEGGGTTTT.......... CS
                         FKBP_C   4 eakegdtVtvhykgkledgkvfdssrsrakplefkvGsgqvikGfeealegmkvGekrtltippelaYge.......... 73 
                                    +ak+gd+V+vhy+++le g  +d+s + ++p+ef++G+g+v++Gfeea+ gm+ Ge +t+ ippe +Yg           
  gi|116754840|ref|YP_843958.1|   3 RAKPGDRVRVHYTARLERGVMVDTS-EGGEPFEFVLGEGRVLPGFEEAVIGMSPGEVKTVRIPPEKGYGPyrqdleveve 81 
                                    499**********************.9******************************************96666665555 PP

                                    .........................T CS
                         FKBP_C  74 .........................k 74 
                                                              
  gi|116754840|ref|YP_843958.1|  82 rsrlpmdvdlkigdtlevveddgrvV 107
                                    55555555555555555555555550 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 ?   -0.9   0.0      0.19   1.7e+03      22      31 ..       5      14 ..       2      18 .. 0.80
   2 ?   -1.6   0.3       0.3   2.7e+03       9      14 ..      61      66 ..      60      66 .. 0.86
   3 ?   11.7   1.2     2e-05      0.18      10      36 ..      84     106 ..      81     121 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.19
                                   ECTCEEEEEE CS
                 MazE_antitoxin 22 reGdevelev 31
                                   ++Gd+v ++ 
  gi|116754840|ref|YP_843958.1|  5 KPGDRVRVHY 14
                                   67***98876 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.3
                                   EEE-CC CS
                 MazE_antitoxin  9 vriPke 14
                                   vriP e
  gi|116754840|ref|YP_843958.1| 61 VRIPPE 66
                                   9***87 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 2e-05
                                    EE-CCCHHHCCEECTCEEEEEECTTCC CS
                 MazE_antitoxin  10 riPkevrfelgireGdevelevdgdki 36 
                                    r+P++v     ++ Gd++e+++d+++ 
  gi|116754840|ref|YP_843958.1|  84 RLPMDVD----LKIGDTLEVVEDDGRV 106
                                    8999999....*********9999743 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 1157.85
//
Query:       gi|116754841|ref|YP_843959.1|  [L=704]
Description: oligosaccharyl transferase, STT3 subunit [Methanosaeta thermophila PT]
Scores for 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-26   90.9  26.8    8.6e-26   90.9  26.8    1.5  2  STT3        Oligosaccharyl transferase STT3 subunit
    8.4e-12   45.2   0.1    1.4e-11   44.5   0.1    1.4  1  AglB_L1     Archaeal glycosylation protein B long peripheral 
    3.6e-09   37.0  13.3    3.6e-09   37.0  13.3    3.6  4  PMT_2       Dolichyl-phosphate-mannose-protein mannosyltransf
  ------ inclusion threshold ------
       0.14   12.3   0.9       0.32   11.1   0.9    1.6  1  Arteri_GP4  Arterivirus glycoprotein


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 !   90.9  26.8   1.9e-29   8.6e-26       8     485 ..      15     496 ..       9     498 .. 0.69
   2 ?   -3.2   0.0      0.67     3e+03     452     480 ..     516     545 ..     510     547 .. 0.71

  Alignments for each domain:
  == domain 1  score: 90.9 bits;  conditional E-value: 1.9e-29
                                    HHHCCCCCHCC.CCCCCCT--S--SSCHHHHHHHCCCHHHT-C.....CCHHSSEETTSSTTT-EEESTTCCHCCC.CHH CS
                           STT3   8 alialvavasrdlFtdedglsylsefDpYYnyRltenllnnGfpGdvvikkknwfdhsqyyPpGsrvdygplivlLamla 87 
                                    + ++l+ +++   F+  dg   ++  D+YY  R + +++n+       ++ + wfd +  yP G  ++++pl  +L  +a
  gi|116754841|ref|YP_843959.1|  15 ISAFLLRIYAG-RFALSDGSLLFYGPDSYYHMRRIFYTVNH-------FPSTLWFDSYVDYPNGLEITWPPLFDVL-GAA 85 
                                    44455555555.699**************************.......8***************************.99* PP

                                    HHHHCCHHCHHHHHHHHCCHHHHHHHHCHHHHHHHHHHS-CCCHHHHHHHCCC-CCCCCTTSTT--STCCCCHHHHHHHH CS
                           STT3  88 saiinhsldvsirevclwlpallgsLlaIpiyflvrelksdiaGllAAlllaiaPgYlsrtvaGfyDtdmfeivlllfvl 167
                                     a + +s++ s    + +lp++lg L++ ++yf +re+++++ Gl++A++l i+   ++    G+ D++++e++ll +++
  gi|116754841|ref|YP_843959.1|  86 FASLGSSTH-SAEIMASLLPPILGALTVGVVYFAAREMFDERTGLASAFFLTISSYAVAVNSFGYVDHHALEMLLLSLIV 164
                                    ********9.445557799************************************99999************99887777 PP

                                    HHHHHHHHCCSTTCHHHHHHHHHHHHHHTTSCCGG..HHHHCCHHHHHHHHHCTTTS-CCHHHHH..........HHHHH CS
                           STT3 168 ffflkaiktksnkislaviaaliiflivlaWggya..iliyallllfilalLiigrfelklkiav..........tfsvi 235
                                      +l +       + ++v+a+++++l+ ++W+g a  ili+ ++ +  +++ + g +e   ++++           f+  
  gi|116754841|ref|YP_843959.1| 165 LALLLSASD----MRWSVAAGFFMALLAYTWMGSAayILIVLVYTIVRMSIDLKGNREPPKDLVIapaiasllvlPFWSS 240
                                    777766554....66******************84333333333333333333333444444333333333333433333 PP

                                    HHHHH..CCCCCCCTTCHHH.STTTCHHCCCCHHHHHHHHCCCHHC..CCCCCHHCC....CHHTT.HHHHTT--GGGHH CS
                           STT3 236 iaflviaiivllflgfqvva.vseiigalgifgllqlvafgsvvvlvaelkfyqfis....lfqpgilsevlgligevvt 310
                                     ++l +ai ++ +lg++ +   ++i++                 + +++++ ++++     ++ + i+  ++g++++ +t
  gi|116754841|ref|YP_843959.1| 241 HWMLPSAIAIFTLLGSSLLGyAIYILSQ----------------KRLPWYSLPSIMIaaglIVLVVIYALRGGITSVFYT 304
                                    3444433444444444433333333333................333444444444444444444444444444443333 PP

                                    HHHHHHHHHHC...........................CCCCCTS---...--TTHHHHHHHHHS---S--CCHHHCCSS CS
                           STT3 311 alavlglialw...........................lgilyslldl...eyaklkikiiilvsvwlpvgllaltkglr 360
                                    +l   +l+                              l   + l  l     ++++    +l+ vw  + ll+++   r
  gi|116754841|ref|YP_843959.1| 305 TLVN-RLPYVLggemsglieeagplltmnlqsilglniL---LTLTVLalvVRRHIYDRKGVLLIVWTLIALLLTFGQKR 380
                                    3322.1111112344444555555565577777664432...3333224457788888899******************* PP

                                    ST.TTTCCCHHHCHHCCHHCTCHHHHHHHHHHHHHCCC-SCHCCCCCHHHHHHHCCCHHH.HHHHHCCHHHHHHHHHHHH CS
                           STT3 361 fl.iftvPlgiifvgllleflavfvkiysvsqilfsgvvvillmltllpvlallaavkis.kifstykdekeakikvaak 438
                                    fl i++++++i f+ l++e+         +  ++++ ++ + ++ltl++ + +         ++s + +++e+++  a  
  gi|116754841|ref|YP_843959.1| 381 FLyILAMNMSILFAVLFSEIST-------LIERRSPERRQM-MALTLIVLIVMATPSLWRlSRISDDAPDIESDWVDAL- 451
                                    ***********88887766544.......446677788888.8888888888877665555888999999888887633. PP

                                    HHHHHHCT.TTTTHHHTTHHHCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           STT3 439 avaptksnglkeslewkantnrdsvvitwwdyghilaveadrpVtfd 485
                                      +  k+n    s     ++  +  ++++w+yg  + +  +rpV+++
  gi|116754841|ref|YP_843959.1| 452 --KWLKENTPATSFFDDPSRRPEYGIMSSWSYGNWIIYLGERPVIAN 496
                                    ..23444444444444678888899999*****99999999999876 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.67
                                    HHH.TTHHHCHHHHHHHHHHHHHHHHHHHH CS
                           STT3 452 lew.kantnrdsvvitwwdyghilaveadr 480
                                    +   + ++ +  +vit+w +++++    +r
  gi|116754841|ref|YP_843959.1| 516 DGEgILEQRNARYVITSWEMLYLTLPSTAR 545
                                    555566778889999999999887655555 PP

>> AglB_L1  Archaeal glycosylation protein B long peripheral domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5   0.1   3.2e-15   1.4e-11       2      92 .]     619     700 ..     618     700 .. 0.92

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 3.2e-15
                                    EEEEEEBSSSSEEEEEEEEE-TTS-EEEEEEEEE.-BTTEEEEEE---SS......-SSSSEESS-EEEEETTEEEEE-- CS
                        AglB_L1   2 AtitGsaeagatvtasveletnqgrtftYrqeaeadedGefeltvPYstegeedgetnssveaagpYevtagnvtaeveV 81 
                                     ++tG++   + v+a ++l+tnqgr ftY  ea a  +  ++l++PYst       +n  v a+g+Y + + +  +e+++
  gi|116754841|ref|YP_843959.1| 619 VVVTGRS--SEPVVAILNLTTNQGRRFTYAIEA-APVNNVYTLRLPYSTA------SNGAVIANGAYIIMSPEIAKELSI 689
                                    5556655..689*********************.89999***********......89********************** PP

                                    -HHHHHHT-EE CS
                        AglB_L1  82 pEeaVlsgetv 92 
                                     Ee+Vl g+t+
  gi|116754841|ref|YP_843959.1| 690 DEEDVLRGSTI 700
                                    ********987 PP

>> PMT_2  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.5       3.5   1.6e+04      26      41 ..       7      22 ..       5      29 .. 0.52
   2 !   37.0  13.3     8e-13   3.6e-09       3     157 ..      76     238 ..      74     242 .. 0.82
   3 ?   -3.7   7.0       2.7   1.2e+04      75     114 ..     249     289 ..     224     315 .. 0.57
   4 ?   -4.3   8.9         4   1.8e+04      76     133 ..     341     404 ..     299     431 .. 0.46

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 3.5
                          PMT_2 26 lvsalagvltilllyl 41
                                   l+++++ +++++ll +
  gi|116754841|ref|YP_843959.1|  7 LWAVVVLIISAFLLRI 22
                                   4555555555555444 PP

  == domain 2  score: 37.0 bits;  conditional E-value: 8e-13
                          PMT_2   3 PPliawllalftklf...gfselairlvsalagvltilllyllarrlfgkraallaalllavvplfvalsalftpdaplv 79 
                                    PPl+  l a+f++l    ++ e  + l++ ++g+lt+ ++y+ ar++f++r++l++a++l+++ + va+   + +d   +
  gi|116754841|ref|YP_843959.1|  76 PPLFDVLGAAFASLGsstHSAEIMASLLPPILGALTVGVVYFAAREMFDERTGLASAFFLTISSYAVAVNSFGYVDHHAL 155
                                    899999999999996433457788899999********************************999999999888888888 PP

                          PMT_2  80 llwalalylllraleknklkywllagvlfGlgflsKytaallliaallyllis...arrilke.kkpyl.alllalllfs 154
                                     +++l+l +l+ +l    +++ ++ag++++l  ++ + +a +++ +l+y +++     +  +e +k ++ a ++a ll++
  gi|116754841|ref|YP_843959.1| 156 EMLLLSLIVLALLLSASDMRWSVAAGFFMALLAYTWMGSAAYILIVLVYTIVRmsiDLKGNREpPKDLViAPAIASLLVL 235
                                    88888888888888888889*****************9999999888888877544222222244444448888888888 PP

                          PMT_2 155 pvl 157
                                    p++
  gi|116754841|ref|YP_843959.1| 236 PFW 238
                                    875 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 2.7
                          PMT_2  75 daplvllwalalylllraleknk.lkywllagvlfGlgfls 114
                                     ++ +l  +l+ y+++ + +k+  +  +  +++++Gl++l+
  gi|116754841|ref|YP_843959.1| 249 AIFTLLGSSLLGYAIYILSQKRLpWYSLPSIMIAAGLIVLV 289
                                    34444444455555555555554233334455555555543 PP

  == domain 4  score: -4.3 bits;  conditional E-value: 4
                          PMT_2  76 aplvllwalalylllraleknklkywllagvlfGlgflsKytaalllia....allyllis.....a 133
                                    ++l+l++++++   + +  ++k   +l++  l++l + +    +l+++a    +l+++l+s      
  gi|116754841|ref|YP_843959.1| 341 ILLTLTVLALVVRRHIY--DRK-GVLLIVWTLIALLLTFGQKRFLYILAmnmsILFAVLFSeistlI 404
                                    33333222222222222..222.22333333333332222222222222111133344444443332 PP

>> Arteri_GP4  Arterivirus glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.9   7.1e-05      0.32     100     175 ..     113     187 ..     107     204 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 7.1e-05
                     Arteri_GP4 100 sacliyasel..sekGfkvvfgnvsGvvavcvnfteyvshvkektqrslvvdklrllhfltpsvvrwatvialllail 175
                                        + a e+  + +G+   f+      av vn   yv h   ++ + l +  + l+ +l+ s +rw+      +a+l
  gi|116754841|ref|YP_843959.1| 113 GVVYFAAREMfdERTGLASAFFLTISSYAVAVNSFGYVDH---HALEMLLLSLIVLALLLSASDMRWSVAAGFFMALL 187
                                    5566778898433589*99999999999*********999...566678888899999*********98877777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (704 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); 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):               4  [number of targets reported over threshold]
# CPU time: 0.67u 0.33s 00:00:01.00 Elapsed: 00:00:00.48
# Mc/sec: 4415.25
//
Query:       gi|116754842|ref|YP_843960.1|  [L=387]
Description: glycosyl transferase, group 1 [Methanosaeta thermophila PT]
Scores for complete 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  109.2   0.0    2.6e-31  108.5   0.0    1.3  1  Glycos_transf_1  Glycosyl transferases group 1
    7.7e-31  107.4   1.0    3.5e-30  105.2   1.0    1.9  2  Glyco_transf_4   Glycosyltransferase Family 4
    1.2e-26   93.7   0.0    2.3e-26   92.8   0.0    1.5  1  Glyco_trans_1_4  Glycosyl transferases group 1
      1e-23   84.5   0.1    3.1e-23   83.0   0.0    1.8  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    8.1e-19   68.3   1.3    6.3e-16   58.8   1.3    2.2  1  Glyco_transf_5   Starch synthase catalytic domain
    8.9e-09   35.5   0.1    1.6e-08   34.7   0.1    1.4  1  Glyco_trans_4_2  Glycosyl transferase 4-like
    1.9e-07   31.3   0.0    3.7e-07   30.4   0.0    1.4  1  Glyco_trans_1_2  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.5   0.0     1e-34   2.6e-31      15     170 ..     210     360 ..     198     362 .. 0.93

  Alignments for each domain:
  == domain 1  score: 108.5 bits;  conditional E-value: 1e-34
                                    -EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHHCES CS
                Glycos_transf_1  15 kkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleellknad 94 
                                     ++il+ gr+ ++Kg+dll++a++++ ++ + ++k+v++G+g+++ e ++la el++++ ++flg+v+ + +e l++++d
  gi|116754842|ref|YP_843960.1| 210 APVILFCGRMCYQKGPDLLVRAIPEVLRE-RWDAKFVFIGEGDMKWECERLARELGVEHACRFLGYVPSSTKEDLMNACD 288
                                    689***********************997.************************************************** PP

                                    EEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHHHHHHHH CS
                Glycos_transf_1  95 ifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelrerlgenar 170
                                    i++lps++E+fG+v+lEA  ag+pv+a+ a     ++k+ e+Gll     +e+la  i++ll+++ +  +l+  ar
  gi|116754842|ref|YP_843960.1| 289 IICLPSRNEPFGVVVLEAWDAGKPVVATEA---VTIIKNFEDGLLAYIQ-PESLAWCIKRLLSNPAEMMKLSAMAR 360
                                    ****************************85...5799********9887.***************88888877776 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.2   1.0   1.4e-33   3.5e-30       1     166 [.      16     186 ..      16     189 .. 0.79
   2 ?   -0.6   0.0      0.46   1.2e+03      83     102 ..     298     316 ..     282     372 .. 0.77

  Alignments for each domain:
  == domain 1  score: 105.2 bits;  conditional E-value: 1.4e-33
                 Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvvtpgddgpleeev.......elvvrvprvplpllkrllrslaflrrlrrllkrekp 73 
                                    vGGv+ hv eL++aLar+GheV+v+t+++d + ++e        ++    + + +  +  +  ++  + +++r++   ++
  gi|116754842|ref|YP_843960.1|  16 VGGVAPHVSELSEALARMGHEVHVFTRRGDFDYYDEIngvhyqrVDHDPTGDIVHQMDTMCDAMVDRFEAVQRIFG--RF 93 
                                    7***********************************6664444333333333333444445555555555555555..9* PP

                 Glyco_transf_4  74 DvvHahspaalgaallalrrrlgiplVltvHglye.krllkarlkplsrllralerrllrradrviavSeatadelrery 152
                                    Dv+H h+++++  a +++++ + ipl++tvH+++  +    + ++p sr +   e+     + rvi++++++++el+ +y
  gi|116754842|ref|YP_843960.1|  94 DVIHGHDWHPVN-AIVRIKKSHSIPLIFTVHSTEWgRNGNSYAHSPVSREISHREWLGGYESARVIVTTQQMKNELMMLY 172
                                    **********85.55566667*************7755556677777777777677779999****************** PP

                 Glyco_transf_4 153 gvppekitVipnGv 166
                                     +p+eki++ipnG+
  gi|116754842|ref|YP_843960.1| 173 SIPEEKIEIIPNGI 186
                                    *************9 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.46
                 Glyco_transf_4  83 algaallalrrrlgiplVlt 102
                                    ++g+++l ++   g+p+V+t
  gi|116754842|ref|YP_843960.1| 298 PFGVVVLEAWD-AGKPVVAT 316
                                    56788888888.99999998 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 !   92.8   0.0   8.8e-30   2.3e-26       2     134 .]     211     348 ..     210     348 .. 0.86

  Alignments for each domain:
  == domain 1  score: 92.8 bits;  conditional E-value: 8.8e-30
                                    EEEEEES---GG.GTHHHHHHHHHHHH.H..HEEEEEES---..HHHHHHHT..T-T.TEEEE---..THHHHHHHH-SE CS
                Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkk..dvrlvivGdgprpeeleelaa..gleerveftGfv..edlaellaaadv 75 
                                    pvilf+Gr+   +kg dll++a+p+++++  d+++v++G+g+++ e+e+la+  g+e+ ++f+G+v  + +++l++a+d+
  gi|116754842|ref|YP_843960.1| 211 PVILFCGRM-CYQKGPDLLVRAIPEVLRErwDAKFVFIGEGDMKWECERLARelGVEHACRFLGYVpsSTKEDLMNACDI 289
                                    89*******.667**********999966455*********944467766655799999*******7656********** PP

                                    EEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH- CS
                Glyco_trans_1_4  76 fvaPs..egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLled 134
                                     ++Ps  e fg+++lEa  ag+pvVat++     ++   e+gll+   +pe+la  i rLl++
  gi|116754842|ref|YP_843960.1| 290 ICLPSrnEPFGVVVLEAWDAGKPVVATEAVT---IIknFEDGLLAY-IQPESLAWCIKRLLSN 348
                                    *****999*******************8744...4442599*9996.47***********987 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.0   0.0   1.2e-26   3.1e-23       1     160 []      17     185 ..      17     185 .. 0.77
   2 ?   -1.3   0.0      0.99   2.5e+03      81      81 ..     294     294 ..     228     369 .. 0.59

  Alignments for each domain:
  == domain 1  score: 83.0 bits;  conditional E-value: 1.2e-26
                Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgapeleedgvrvhrlpvprrpspladlaal........ralrrllrqrre 72 
                                    gG++ +v el++aLa+ GheV+v+t++++ + +  e +gv++ r++  ++++ +  ++ +         a++r++     
  gi|116754842|ref|YP_843960.1|  17 GGVAPHVSELSEALARMGHEVHVFTRRGDFDYY-DEINGVHYQRVDHDPTGDIVHQMDTMcdamvdrfEAVQRIF----G 91 
                                    8*************************8877766.7899*******999888644443322222222225566666....* PP

                Glyco_trans_4_4  73 rpdvvhahsptaglaarlarrrrgiplvvtlhgll.lrrg....sgavrrlyralerrllrradavlvvseaeaeelra. 146
                                    r+dv+h h+++   a+++++  ++ipl++t+h+++ +r g     ++v r +   e +     ++v+v+++++  el   
  gi|116754842|ref|YP_843960.1|  92 RFDVIHGHDWHPVNAIVRIKKSHSIPLIFTVHSTEwGRNGnsyaHSPVSREISHREWLGGYESARVIVTTQQMKNELMMl 171
                                    **********86555555555***********855244446445555555565667788888*****************7 PP

                Glyco_trans_4_4 147 lgvpadrvvvvpng 160
                                    + +p ++++++png
  gi|116754842|ref|YP_843960.1| 172 YSIPEEKIEIIPNG 185
                                    78***********8 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.99
                Glyco_trans_4_4  81 s 81 
                                    s
  gi|116754842|ref|YP_843960.1| 294 S 294
                                    3 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 !   58.8   1.3   2.5e-19   6.3e-16       1     182 [.       2     135 ..       2     173 .. 0.75

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 2.5e-19
                 Glyco_transf_5   1 kilfvasEvaplaktGGLadvvgaLpkaLaklghdvrvilPrygaikeekkeleevaelskaaedevevevekvkvaklk 80 
                                    +i ++++E    +k+GG+a +v++L++aLa++gh+v+v++ r ++   +                              +
  gi|116754842|ref|YP_843960.1|   2 RIGMFSWESLYSVKVGGVAPHVSELSEALARMGHEVHVFTRRGDFDYYD------------------------------E 51 
                                    6889************************************888333322..............................2 PP

                 Glyco_transf_5  81 kdgvdvyfldnpeffdreglYgdkgedyednaerfalfsraalellekl..gwk..pdvihahDWhtalvpallkelyke 156
                                     +gv++  +d++                 d  +++  ++ a+++  e +       +dvih hDWh + + + +k+ +  
  gi|116754842|ref|YP_843960.1|  52 INGVHYQRVDHDP--------------TGDIVHQMDTMCDAMVDRFEAVqrI-FgrFDVIHGHDWHPVNAIVRIKKSH-- 114
                                    249*********9..............3488999999999999888886332.135********************86.. PP

                 Glyco_transf_5 157 rglfkkiktvftiHNlayqgrfpkde 182
                                          i+++ft+H++++ ++ ++  
  gi|116754842|ref|YP_843960.1| 115 -----SIPLIFTVHSTEWGRNGNSYA 135
                                    .....3*************9998322 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 !   34.7   0.1   6.3e-12   1.6e-08      11     110 ..      21     126 ..      11     141 .. 0.77

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 6.3e-12
                Glyco_trans_4_2  11 vhtlrlakeLakrgyeVhvitpkkgakdeleaegihvhrlkvd......rkg..pleylka..f.klkklikkikPDvvh 79 
                                    +h+++l ++La  g+eVhv+t++++ + ++e +g+h +r++ d      +    ++ ++++  f ++ +++    +Dv+h
  gi|116754842|ref|YP_843960.1|  21 PHVSELSEALARMGHEVHVFTRRGDFDYYDEINGVHYQRVDHDptgdivH-QmdTMCDAMVdrFeAVQRIFG--RFDVIH 97 
                                    79********************9999**************9886555422.223444444443334444444..59**** PP

                Glyco_trans_4_2  80 ahyakpygllgslaarlsgvipvvlsvwGld 110
                                     h   p++ + ++  ++s  ip++++v+ + 
  gi|116754842|ref|YP_843960.1|  98 GHDWHPVNAIVRI--KKSHSIPLIFTVHSTE 126
                                    *******988888..56666********765 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 !   30.4   0.0   1.5e-10   3.7e-07       4      89 ..     292     375 ..     288     378 .. 0.93

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 1.5e-10
                Glyco_trans_1_2   4 npsrsespnlrlfEaaacGafaltddaegleelftpgkevilfedleelaekiryllanpeerraiaeaarervlaehty 83 
                                     psr+e + ++++Ea  +G ++++++a  + + f++g  ++ +  +e+la  i++ll+np+e  ++++ ar+r + ++++
  gi|116754842|ref|YP_843960.1| 292 LPSRNEPFGVVVLEAWDAGKPVVATEAVTIIKNFEDG--LLAYIQPESLAWCIKRLLSNPAEMMKLSAMARARLEHDFSW 369
                                    599**********************999999999999..77777************************************ PP

                Glyco_trans_1_2  84 dhraeq 89 
                                    d+ ae+
  gi|116754842|ref|YP_843960.1| 370 DKIAET 375
                                    **9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.27s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2603.41
//
Query:       gi|116754843|ref|YP_843961.1|  [L=288]
Description: sulfate adenylyltransferase [Methanosaeta thermophila PT]
Scores for complete 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   59.6   0.0    2.7e-15   56.1   0.0    2.2  1  DUF4921          Domain of unknown function (DUF4921)
    1.4e-10   41.9   0.0    6.7e-10   39.7   0.0    1.9  1  GalP_UDP_transf  Galactose-1-phosphate uridyl transferase, N-
    3.3e-05   23.3   0.5    0.00013   21.4   0.0    2.1  2  DUF4931          Domain of unknown function (DUF4931)
    0.00033   20.4   0.0    0.00045   20.0   0.0    1.3  1  GalP_UDP_tr_C    Galactose-1-phosphate uridyl transferase, C-
  ------ inclusion threshold ------
       0.11   13.0   0.0       0.32   11.5   0.0    1.8  2  DcpS_C           Scavenger mRNA decapping enzyme C-term bindi


Domain annotation for each model (and alignments):
>> DUF4921  Domain of unknown function (DUF4921)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.1   0.0   7.5e-19   2.7e-15     208     392 ..      99     283 ..      69     288 .] 0.81

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 7.5e-19
                        DUF4921 208 vdalkdlykrnryvrYvavfqnWLkpaGasfdhlhkqlvaiDergvqaeaeiarlrenPnl.ynelavdyaakhnlviae 286
                                    v a +  y+++r  +Yv++f+nW + aGas+ h h ql+a+  +      e++ +++ P   y ++a   a+++ l++ e
  gi|116754843|ref|YP_843961.1|  99 VYADRYRYHTDRGSSYVSIFKNWGREAGASLSHTHTQLIALPMIPPLLMREVSAISSMPSCpYCNIAEREASSERLIFRE 178
                                    455566799**************************************************977**************9988 PP

                        DUF4921 287 ndhavafagfGhryp.tlevysksatkePweqseeevravsdlvhalhaa.agadvpcne.eWhhrpidvdvpmpwrili 363
                                        +++a f  + p  + +    + ++  e+s+  + ++      +  a    +v  n+  +++   ++  +    i i
  gi|116754843|ref|YP_843961.1| 179 G-VWICIAPFYSQTPyEMWILPCKHISSILEMSDSMRLELGRS---MKKAlQRLSVLLNDpPYNYMIFQMSSNYHLNIRI 254
                                    6.67999**9998883466777777777788887777666554...4444134567777624777888888888889999 PP

                        DUF4921 364 kwrvstlaGfeggtkiylntisPaelrdr 392
                                    +  +s++aGfe +t iy+n +sP++ + +
  gi|116754843|ref|YP_843961.1| 255 QPAISKIAGFEKNTGIYINPVSPEQAASE 283
                                    999********************997765 PP

>> GalP_UDP_transf  Galactose-1-phosphate uridyl transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.0   1.9e-13   6.7e-10      54     184 .]       6     143 ..       2     143 .. 0.84

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 1.9e-13
                GalP_UDP_transf  54 kcyLcPgnsrangefnpkykstfvftndFpalsedsnyikteai........aknilfkaepayGrceviifsskheltl 125
                                    +c++cPgn++++ +  + y++  vf +    ++    +  ++          a  +++ a pa+G  evii s++he + 
  gi|116754843|ref|YP_843961.1|   6 ECPFCPGNEEMTPKAVAVYRDDGVFVDGETRIRGWWARCIPNMYpamvpdpdAPTPEWMAMPARGGHEVIIESPDHESSP 85 
                                    7******************9999999976666664444443333333343334449************************ PP

                GalP_UDP_transf 126 adlspkdikavvaaWqektaelkakeypkcvlifENkGaamgvsnphPHgqiwaeehlp 184
                                    a  + ++i + ++ +++++   +  ++  +v if N G + g+s+ h H q+ a +++p
  gi|116754843|ref|YP_843961.1|  86 AIFDDEKIIRMIRVYADRYRY-HTDRGSSYVSIFKNWGREAGASLSHTHTQLIALPMIP 143
                                    ********************9.6779*************************99888776 PP

>> DUF4931  Domain of unknown function (DUF4931)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1      0.37   1.3e+03      17      26 ..       4      13 ..       2      23 .. 0.78
   2 !   21.4   0.0   3.6e-08   0.00013      54     122 ..      73     140 ..      69     147 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.37
                        DUF4931 17 etacPfcdre 26
                                   +++cPfc  +
  gi|116754843|ref|YP_843961.1|  4 SKECPFCPGN 13
                                   579****654 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 3.6e-08
                        DUF4931  54 tvlietdeceedistyseehlrellrfgvkhwleleks.eeyksvllfknhGPlsGGsikhahmqivGlk 122
                                     v+ie+ + e+  + +++e + +++r   +++    ++  +y  v +fkn+G  +G s+ h+h q++ l 
  gi|116754843|ref|YP_843961.1|  73 EVIIESPDHESSPAIFDDEKIIRMIRVYADRYRYHTDRgSSY--VSIFKNWGREAGASLSHTHTQLIALP 140
                                    599***********************9998887555440555..5579******************9986 PP

>> GalP_UDP_tr_C  Galactose-1-phosphate uridyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   1.3e-07   0.00045      10      91 ..     123     233 ..     112     284 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.3e-07
                                    HHH.SS-HHHHHHH..............................HHHHH-TTEEEE-SSEEEE--TT--STT-EEEEESS CS
                  GalP_UDP_tr_C  10 agsngsillhdyvq..............................melaekervvelkdsflavvpylakWPfevlllrka 59 
                                    ++  g+ l+h ++q                                 a+ er++  +  ++ ++p++ + P+e+ +l+ +
  gi|116754843|ref|YP_843961.1| 123 REA-GASLSHTHTQlialpmippllmrevsaissmpscpycniaEREASSERLIFREGVWICIAPFYSQTPYEMWILPCK 201
                                    555.6666666666666666666666666666666677776664333455677666677********************* PP

                                    --SSGGG--HHHHHHHHHHHHHHHHHHHHHCT CS
                  GalP_UDP_tr_C  60 evkslaeladeekedlaailkklarkydnlfe 91 
                                    ++ s+ e++d  + +l   +kk +++   l +
  gi|116754843|ref|YP_843961.1| 202 HISSILEMSDSMRLELGRSMKKALQRLSVLLN 233
                                    ****************9999999888766654 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 ?   -2.9   0.0       2.7   9.6e+03       2      24 ..       7      30 ..       6      31 .. 0.70
   2 ?   11.5   0.0   8.8e-05      0.32       2      66 ..     159     225 ..     158     261 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.7
                                   -HHHHHHTTSS-B-E.EEE-SSEE CS
                         DcpS_C  2 wvfnilakgkeperv.vyedekfv 24
                                   + f++  ++  p++v vy+d+++ 
  gi|116754843|ref|YP_843961.1|  7 CPFCPGNEEMTPKAVaVYRDDGVF 30
                                   667776666667777799999875 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 8.8e-05
                                    -HHHHHHTTSS.-B-EEEE-SSEEEEE-SS-SSSEEEEEEESS---SGGG--TT.TTTHHHHHHHHH CS
                         DcpS_C   2 wvfnilakgke.pervvyedekfvvlkDikpkaklhllvipkrdikslrdLtke.hlpllkemreka 66 
                                    + ++++a+++  +er+++++  ++++   + ++++ + ++p ++i+s+ +++++  l+l ++m++ +
  gi|116754843|ref|YP_843961.1| 159 CPYCNIAEREAsSERLIFREGVWICIAPFYSQTPYEMWILPCKHISSILEMSDSmRLELGRSMKKAL 225
                                    7889998888769999********************************9997772444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 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:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1920.42
//
Query:       gi|116754844|ref|YP_843962.1|  [L=407]
Description: glycosyl transferase, group 1 [Methanosaeta thermophila PT]
Scores for complete 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-29  102.1   0.0    3.6e-29  101.5   0.0    1.3  1  Glycos_transf_1  Glycosyl transferases group 1
    3.8e-25   88.9   0.0    1.3e-24   87.1   0.0    2.0  1  Glyco_transf_4   Glycosyltransferase Family 4
    6.8e-24   85.1   1.4      4e-23   82.6   0.0    2.5  3  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    8.9e-20   71.5   0.0    1.7e-19   70.6   0.0    1.5  1  Glyco_trans_1_4  Glycosyl transferases group 1
    2.8e-14   53.4   0.0      1e-13   51.6   0.0    1.9  1  Glyco_transf_5   Starch synthase catalytic domain
    4.3e-07   30.2   0.0      8e-07   29.4   0.0    1.4  1  Glyco_trans_1_2  Glycosyl transferases group 1
  ------ inclusion threshold ------
       0.04   13.9   0.0       0.23   11.5   0.0    2.0  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 !  101.5   0.0   1.4e-32   3.6e-29       6     172 .]     212     381 ..     209     381 .. 0.94

  Alignments for each domain:
  == domain 1  score: 101.5 bits;  conditional E-value: 1.4e-32
                                    HHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSS CS
                Glycos_transf_1   6 rkklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsred 85 
                                    rk++g++e + ++l++grle++Kgv++l+ a++ ++++ np+vkl+++G+g+  + ++++ae l+    + +  ++s+++
  gi|116754844|ref|YP_843962.1| 212 RKSYGLKESDTVLLFLGRLEPVKGVSQLLAALPAIRRN-NPDVKLLVVGSGSLIDHVRSEAERLGG--VILVDRFLSPQE 288
                                    789999******************************99.*******************99998887..88888999999* PP

                                    HHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEET..TTTHCHHCHTTT....SEEEE-TT-HHHHHHHHHHHHHSH CS
                Glycos_transf_1  86 leellknadifvlpsisEgfGivllEAmaaglpviasn..aggpaevvkdge....tGllvkpnnaealaeairkllede 159
                                    +   +  ad+ ++ps++E+fGiv+lEA +     ++ +  ++g++e+v + e    tG++v + ++ ++a +++ +led+
  gi|116754844|ref|YP_843962.1| 289 KVYHYALADLCIFPSTYEPFGIVALEAASMERVSVVGAsgVSGLREIVMNPEtdrpTGVHVNARDPNDIAWGVNLALEDR 368
                                    ***************************999766655554899************************************** PP

                                    HHHHHHHHHHHHH CS
                Glycos_transf_1 160 elrerlgenarkr 172
                                    ++ +++g+nar+r
  gi|116754844|ref|YP_843962.1| 369 DRLREWGRNARER 381
                                    **********986 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.1   0.0     5e-28   1.3e-24       1     169 [.      15     196 ..      15     197 .. 0.79

  Alignments for each domain:
  == domain 1  score: 87.1 bits;  conditional E-value: 5e-28
                 Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvvtpgddgpleeev....................elvvrvprvplpllkrllrslaf 60 
                                    +GG +++v  ++r+La +Gh+V+v+t g+++  ++++                    e +++ +   +    ++l++l +
  gi|116754844|ref|YP_843962.1|  15 YGGLGVYVDLMSRELASMGHKVSVFTMGRPDLKRKRRetkkgvtafreipipmsdalEIFYSKETLSWGTGLDFLNNLLS 94 
                                    6******************************9999999**7777777777777777744444444444444444444433 PP

                 Glyco_transf_4  61 l..rrlrrllkrekpDvvHahspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrvi 138
                                    +  ++++r+ + + +D+  ah++ al a+  alr    +p++++vH ++    +++   p ++l+  le + +r ad v+
  gi|116754844|ref|YP_843962.1|  95 YnqLAAARVRDSGPFDLCVAHDWLALPAG-MALR--QSMPVIYHVHCTE----VGRSEHPNQQLVS-LEIKGARLADLVL 166
                                    3114556667777*********9998555.6777..7************....5666667777765.688889******* PP

                 Glyco_transf_4 139 avSeatadelrerygvppekitVipnGvDle 169
                                    +vSea+++el+  +gvpp+ki+V ++GvD++
  gi|116754844|ref|YP_843962.1| 167 TVSEAMKRELEG-LGVPPKKIRVCYHGVDTK 196
                                    ************.****************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 !   82.6   0.0   1.5e-26     4e-23       1     157 [.      16     189 ..      16     192 .. 0.75
   2 ?   -1.8   0.0       1.4   3.7e+03     125     142 ..     291     308 ..     232     327 .. 0.61
   3 ?   -0.1   0.3      0.42   1.1e+03      96     131 ..     356     392 ..     343     394 .. 0.70

  Alignments for each domain:
  == domain 1  score: 82.6 bits;  conditional E-value: 1.5e-26
                Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvlt..papapg.apeleedgvrvh.rlpvprrp.................spladlaa 59 
                                    gG g+yv  ++r+La  Gh V v+t  + p+ +  ++++  gv+    +p+p +                  + l++l +
  gi|116754844|ref|YP_843962.1|  16 GGLGVYVDLMSRELASMGHKVSVFTmgR-PDLKrKRRETKKGVTAFrEIPIPMSDaleifysketlswgtglDFLNNLLS 94 
                                    8************************742.333323347778888653466663321223322222222111134444555 PP

                Glyco_trans_4_4  60 lralrrllrqrrerpdvvhahsptaglaarlarrrrgiplvvtlhglllrrgsgavrrlyralerrllrradavlvvsea 139
                                    + +l+++  +++ ++d+ +ah+++a +a++++r   + p+++++h +++ r  ++ ++l+  le   +r ad+vl+vsea
  gi|116754844|ref|YP_843962.1|  95 YNQLAAARVRDSGPFDLCVAHDWLALPAGMALR--QSMPVIYHVHCTEVGRSEHPNQQLV-SLEIKGARLADLVLTVSEA 171
                                    56666665449************9999998888..69***********999999999999.99***************** PP

                Glyco_trans_4_4 140 eaeelralgvpadrvvvv 157
                                    + +el+ lgvp+ +++v 
  gi|116754844|ref|YP_843962.1| 172 MKRELEGLGVPPKKIRVC 189
                                    ****************96 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.4
                Glyco_trans_4_4 125 rllrradavlvvseaeae 142
                                    + ++ ad+++ +s++e  
  gi|116754844|ref|YP_843962.1| 291 YHYALADLCIFPSTYEPF 308
                                    445567777777766655 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.42
                Glyco_trans_4_4  96 giplvvtlhglllrrgsgavrrly.ralerrllrrad 131
                                    +i + v+l   +++r   + r+++ r le++++r a+
  gi|116754844|ref|YP_843962.1| 356 DIAWGVNLALEDRDRLREWGRNAReRVLEMFTWRKAA 392
                                    5555555555556677888888887788999999986 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 !   70.6   0.0   6.7e-23   1.7e-19       3     133 ..     223     366 ..     221     367 .. 0.85

  Alignments for each domain:
  == domain 1  score: 70.6 bits;  conditional E-value: 6.7e-23
                                    EEEEES---GG.GTHHHHHHHHHHHH.HH..EEEEEES---...HHHHHHHTT-T.TEEEE---...THHHHHHHH-SEE CS
                Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkkd..vrlvivGdgp.rpeeleelaagleerveftGfv...edlaellaaadvf 76 
                                    v+lf+Grl e+vkgv  ll a+p++r+++  v+l++vG+g+   ++++++a++l  +v+++ +    +++  ++a ad++
  gi|116754844|ref|YP_843962.1| 223 VLLFLGRL-EPVKGVSQLLAALPAIRRNNpdVKLLVVGSGSlI-DHVRSEAERL-GGVILVDRFlspQEKVYHYALADLC 299
                                    89******.889**************77457*********965.4899888878.599999988897789999******* PP

                                    EE--..---SHHHHHHHHTT-EEEE-TGG..GTTT--...T...TSSEE--TT-HHHHHHHHHHHHH CS
                Glyco_trans_1_4  77 vaPs..egfglkllEamaaglpvVatdvg..giaevv...g...engllvppgdpealaeailrLle 133
                                    ++Ps  e fg+++lEa+++++  V+ + g  g++e+v   +    +g+ v+++dp+++a  +   le
  gi|116754844|ref|YP_843962.1| 300 IFPStyEPFGIVALEAASMERVSVVGASGvsGLREIVmnpEtdrPTGVHVNARDPNDIAWGVNLALE 366
                                    *****99***************9987653339***999762344579***********988776666 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 !   51.6   0.0   3.9e-17     1e-13       1     229 [.       2     176 ..       2     178 .. 0.76

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 3.9e-17
                 Glyco_transf_5   1 kilfvasEvaplaktGGLadvvgaLpkaLaklghdvrvilPrygaikeekkeleevaelskaaedevevevekvkvaklk 80 
                                    +i ++++E++p    GGL+  v+ ++++La +gh+v+v++ + +++k++++e+++ +                       
  gi|116754844|ref|YP_843962.1|   2 NIAYLSTEYPP-LVYGGLGVYVDLMSRELASMGHKVSVFTMGRPDLKRKRRETKKGVT---------------------A 59 
                                    699********.99*****************************999998732222222.....................1 PP

                 Glyco_transf_5  81 kdgvdvyfldnpeffdreglYgdkgedyednaerfa.lfsraalelleklgw.kpdvihahDWhtalvpallkelykerg 158
                                     +++++ + d+ e+f+ ++       ++ +  + +  l+s   l++++  +   +d+ +ahDW +  +++ l++      
  gi|116754844|ref|YP_843962.1|  60 FREIPIPMSDALEIFYSKE-----TLSWGTGLDFLNnLLSYNQLAAARVRDSgPFDLCVAHDWLALPAGMALRQS----- 129
                                    1389999999999995444.....4444555544444444444444455333159******************95..... PP

                 Glyco_transf_5 159 lfkkiktvftiHNlayqgrfpkdelaalglpaedfekldglefygkvnflkagivyadavttVSptyakEi 229
                                        +++++++H ++  ++ ++++                    + v++   g ++ad v+tVS+ +++E+
  gi|116754844|ref|YP_843962.1| 130 ----MPVIYHVHCTEVGRSEHPNQ--------------------QLVSLEIKGARLADLVLTVSEAMKREL 176
                                    ....7*******999996665322....................23555569*****************97 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   3.1e-10     8e-07       3      91 ..     300     396 ..     298     397 .. 0.91

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 3.1e-10
                Glyco_trans_1_2   3 LnpsrsespnlrlfEaaacGafaltdda..egleelftpgk....evilfe..dleelaekiryllanpeerraiaeaar 74 
                                    ++ps +e +  + +Eaa + ++ ++ ++  +gl+e++ + +    +++ +   d++++a  ++ +l+++++ r+ +++ar
  gi|116754844|ref|YP_843962.1| 300 IFPSTYEPFGIVALEAASMERVSVVGASgvSGLREIVMNPEtdrpTGVHVNarDPNDIAWGVNLALEDRDRLREWGRNAR 379
                                    68999999******************889******987777789966666668*************************** PP

                Glyco_trans_1_2  75 ervlaehtydhraeqll 91 
                                    ervl+ +t++++ae+ l
  gi|116754844|ref|YP_843962.1| 380 ERVLEMFTWRKAAENTL 396
                                    *************9876 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 ?   11.5   0.0   8.9e-05      0.23      17     119 ..      26     149 ..      17     169 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.9e-05
                Glyco_trans_4_2  17 akeLakrgyeVhvitpkkga...kdeleaegi.hvhrlkvd..............rkg.....pleylkafkl..kklik 71 
                                     +eLa+ g++V+v+t++ +    k+++  +g+ ++ +++++              ++g       ++l++++l  +++ +
  gi|116754844|ref|YP_843962.1|  26 SRELASMGHKVSVFTMGRPDlkrKRRETKKGVtAFREIPIPmsdaleifysketlSWGtgldfLNNLLSYNQLaaARVRD 105
                                    679*************6665534555556666456666777666666666555552223122233333334443366777 PP

                Glyco_trans_4_2  72 kikPDvvhahyakpygllgslaarlsgvipvvlsvwGldvlkfpkksk 119
                                       +D+  ah  + ++l +++a ++    pv++ v+ + v +++++++
  gi|116754844|ref|YP_843962.1| 106 SGPFDLCVAHD-W-LALPAGMA-LRQS-MPVIYHVHCTEVGRSEHPNQ 149
                                    77788888888.4.35777776.5554.89999999998855555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); 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: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2995.03
//
Query:       gi|116754845|ref|YP_843963.1|  [L=594]
Description: glycogen synthase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.3e-20   71.5   0.0    4.2e-09   35.5   0.0    2.7  2  Glycogen_syn     Glycogen synthase
    0.00018   21.6   0.0    0.00033   20.7   0.0    1.5  1  Glyco_transf_4   Glycosyltransferase Family 4
    0.00038   20.0   0.0     0.0011   18.5   0.0    1.9  2  Glycos_transf_1  Glycosyl transferases group 1
  ------ inclusion threshold ------
       0.04   14.4   0.0       0.15   12.5   0.0    2.0  1  Glyco_trans_1_4  Glycosyl transferases group 1
      0.042   13.5   0.1        0.1   12.3   0.0    1.6  2  Glyco_transf_5   Starch synthase catalytic domain


Domain annotation for each model (and alignments):
>> Glycogen_syn  Glycogen synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.0   1.2e-12   4.2e-09       3     336 ..      13     400 ..      11     407 .. 0.71
   2 !   32.5   0.0   9.7e-12   3.5e-08     442     576 ..     452     590 ..     444     593 .. 0.88

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 1.2e-12
                                    ETTTTS-SSCHHHHHHHHHH.....HHHHHHGG..GEEEEEE--TTG.GGGTEEE----SHH..........HHHHHHHH CS
                   Glycogen_syn   3 awevankvGGiytvlkskak.....vtteelGd..nytllGplkeqk.arteveeleaenea..........lkkalksl 64 
                                    a  v+nk+GGi+ v+ + a+     +++ e+ +  + ++ Gp+  ++ a  +  ++ +++ +          +k+al++l
  gi|116754845|ref|YP_843963.1|  13 AGPVSNKMGGIWNVIDAEARtlaklISSGEIENdiRILVAGPYFPTAgADWNRGKMRVTDISgleplsmgneIKTALERL 92 
                                    55699**********99887222234555655522345679*975321333333333333223334444456******** PP

                                    GGGT--EEEEEESSTT--E.EEEE-G..........GGGSTTH.HHHHHHHHHHH-----TT-H.....HHHHHHHHHHH CS
                   Glycogen_syn  65 rekGvkvlyGrwlieGapk.vilfdl..........dsaavkl.dewkaelwekvkigipeedr.....etndaiilGfl 127
                                    ++ G+k ++G+ + +  p   ilfd+          d+ +++l +  k+e w  v++ + +++r     e n+ + l + 
  gi|116754845|ref|YP_843963.1|  93 ESLGIKSVTGQAVYHDVPVgYILFDThyydscivrrDTREMTLtNAIKEEAWRLVGLDSLKYERlsnapEYNHYLCLSYA 172
                                    **************99996489**98333211111112223333789**********99887763333477899****** PP

                                    HHHHHHHHHCT--....................--EEEEEEETGGGHHHHHHHHHTT-SEEEEEEESS-HHHHHHHHTT- CS
                   Glycogen_syn 128 valflkefrelee....................kkavvahfhewlaGvgliltrkrkldvatvftthatllGrylcagav 187
                                    ++++++ +++++e                    k ++  h he+    +l  +++   +v t+ t hat+ Gr       
  gi|116754845|ref|YP_843963.1| 173 ISELVRVLKSMAEepaekyadkavsefarsvlpKIRISLHCHEFGVFYALARLKALGQPVRTMATLHATVPGRAAGHR-- 250
                                    999988888877778899999*****998886555566666776555555555555569**************65444.. PP

                                    --TTSTTS--HHHHHHHTT-HHHHHHHHHHHHHSSEEEESSHHHHHHHHHHSS---SEE----B-GGGT--TTTHHHHHH CS
                   Glycogen_syn 188 dfynnldkfdvdkeaGkrqiyhrycleraaahtadvfttvseitaleaehllkrkpdvvlpnGlnvkkfsalhefqnlha 267
                                         l++ + +++    +         + a+ adv t v + t  ea  +   k  +v+ nG++v +     e +n   
  gi|116754845|ref|YP_843963.1| 251 ----SLEMIARNEKRWPPNTPVSMATLEGLARYADVVTFVGDSTMKEAMLFHDLK-GIVIRNGIEVEQDYIDWEKKN--- 322
                                    ....45555555555555555555555678899************9997655555.79999******9888788777... PP

                                    HHHHHHHHHHHHH...TTT---S-GGGEEEEEEESSS-TTTTTHHHHHHHHHHHHHHHHC---......T-EEEEEEE CS
                   Glycogen_syn 268 lkkekindfvrGh...fyGhldfdldktlyffiaGryefsnkGadifieslarlnyllkveks......kktvvafli 336
                                      +++i++fv      +yG    d ++ + +f+  r e +nkG   ++++l   ++ll+++        k  v +fli
  gi|116754845|ref|YP_843963.1| 323 RCRARIQKFVSDTlynLYGGEKIDPENIIPIFTISRIEIENKGYPQLLDALVLQDHLLRHRAMkerfaeKIRVACFLI 400
                                    5688999999876111568889************************************99876334443444555555 PP

  == domain 2  score: 32.5 bits;  conditional E-value: 9.7e-12
                                    EEEEEE-S---TTSSSS---HHHHHHH-SEEE---SSBSS-HHHHHHHHTT--EEEETTBHHHHHHHHH-T.TGGGGTEE CS
                   Glycogen_syn 442 vkvvfhpeflsstspllgldyeefvrGchlGvfpsyyepwGytpaectvmGipsvttnlsGfGcfmeelie.dakdyGiy 520
                                    v  +++p+++   +  l +  +e + Gc  Gvfps yep+  t  e    G ps+ +   Gf   +++     +   G+ 
  gi|116754845|ref|YP_843963.1| 452 VSAILYPQWVGPEDGGLNMRVDEIMAGCVAGVFPSQYEPFLLTGLEAGREGTPSIVSRACGFSDALKKIKRlTTGMGGVV 531
                                    6789999****9***************************************************9998766645566789* PP

                                    EE--SSS-HHHHHHHHHHHHHHHHT--HHHHHHHHHHHH...HHGGGGBHHHHTHHHHH CS
                   Glycogen_syn 521 ivdrrfkslddsveqlaqflyefvkksrrqriiqrnrte...rlsdlldwkrlGlyyvk 576
                                    +vd   ++ ++ v + a  l  f+  +   +i  r   e    l++ +dw +  ++y k
  gi|116754845|ref|YP_843963.1| 532 VVDNIEQTYNEMVLDYALALDYFTWSQVADQIEYRLLCEesfALAKYMDWMEPVMEYYK 590
                                    ************************99999999999776623358899999988777765 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   9.1e-08   0.00033      76     169 ..     211     312 ..     171     313 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 9.1e-08
                 Glyco_transf_4  76 vHahspaalgaallalrr.rlgiplVltvHglye...........krllkarlkplsrllralerrllrradrviavSea 143
                                    +H+h ++ + +al++l++    +++ +t+H + +             + ++r+ p +++  a ++ l+r ad v+ v ++
  gi|116754845|ref|YP_843963.1| 211 LHCHEFGVF-YALARLKAlGQPVRTMATLHATVPgraaghrslemIARNEKRWPPNTPVSMATLEGLARYADVVTFVGDS 289
                                    399997776.55555555589999****************999997778888899999999999999************* PP

                 Glyco_transf_4 144 tadelrerygvppekitVipnGvDle 169
                                    t +e +  ++++     Vi nG+ +e
  gi|116754845|ref|YP_843963.1| 290 TMKEAMLFHDLKG---IVIRNGIEVE 312
                                    *999999555665...8******987 PP

>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       1.6   5.7e+03      18      37 ..     353     373 ..     348     378 .. 0.83
   2 !   18.5   0.0   3.1e-07    0.0011      85     136 ..     471     528 ..     466     571 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.6
                                    EEEESS-TTT.TTHHHHHHHH CS
                Glycos_transf_1  18 ilsvgrleke.Kgvdllikaf 37 
                                    i++++r+e e Kg+ +l++a+
  gi|116754845|ref|YP_843963.1| 353 IFTISRIEIEnKGYPQLLDAL 373
                                    67889999888******9997 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 3.1e-07
                                    SHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTT......S CS
                Glycos_transf_1  85 dleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdge......t 136
                                    +++e++  + + v+ps++E+f ++ lEA   g+p i+s a+g+++ +k+ +       
  gi|116754845|ref|YP_843963.1| 471 RVDEIMAGCVAGVFPSQYEPFLLTGLEAGREGTPSIVSRACGFSDALKKIKrlttgmG 528
                                    688999999999*********************************9998887775544 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 ?   12.5   0.0   4.2e-05      0.15      66     110 ..     472     521 ..     448     546 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.2e-05
                                    HHHHHHH-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--...T CS
                Glyco_trans_1_4  66 laellaaadvfvaPs..egfglkllEamaaglpvVatdvggiaevv...g 110
                                    ++e++a +   v+Ps  e f l+ lEa   g+p +++++ g+++++   +
  gi|116754845|ref|YP_843963.1| 472 VDEIMAGCVAGVFPSqyEPFLLTGLEAGREGTPSIVSRACGFSDALkkiK 521
                                    88999**********999*******************9989988775331 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 ?   -3.1   0.0       1.4     5e+03       2      32 ..       6      37 ..       6      39 .. 0.87
   2 ?   12.3   0.0   2.8e-05       0.1     119     230 ..     193     295 ..     165     305 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.4
                 Glyco_transf_5  2 ilfvasEvapl.aktGGLadvvgaLpkaLakl 32
                                   i+ ++ E+ p+  k GG+  v++a ++ Lakl
  gi|116754845|ref|YP_843963.1|  6 IVLAGEEAGPVsNKMGGIWNVIDAEARTLAKL 37
                                   67788999999889*******99999999985 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 2.8e-05
                 Glyco_transf_5 119 sraalellek.lgwkpdvihahDWhtalvpallkelykerglfkkiktvftiHNlayqgrfpkdelaalglpaedfekld 197
                                     +a+ e+++  l+ +   +h+h      + a lk+l +       ++t+ t+H +   +  ++  l+++  +++++    
  gi|116754845|ref|YP_843963.1| 193 DKAVSEFARSvLPKIRISLHCHEFGVFYALARLKALGQP------VRTMATLHATVPGRAAGHRSLEMIARNEKRWP--- 263
                                    7889999999345455567*****************855......********887777777777777666655553... PP

                 Glyco_transf_5 198 glefygkvnflkagivyadavttVSptyakEil 230
                                        +  +  l++  +yad vt V ++++kE +
  gi|116754845|ref|YP_843963.1| 264 -PNTPVSMATLEGLARYADVVTFVGDSTMKEAM 295
                                    .334459999******************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (594 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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 0.28s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 3843.82
//
Query:       gi|116754846|ref|YP_843964.1|  [L=248]
Description: putative circadian clock protein, KaiC [Methanosaeta thermophila PT]
Scores for 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-46  158.2   0.1    2.4e-46  158.0   0.1    1.0  1  ATPase     KaiC
     0.0001   21.9   0.1    0.00026   20.6   0.1    1.6  1  AAA_25     AAA domain
     0.0045   16.3   0.3     0.0084   15.4   0.3    1.4  1  Rad51      Rad51
     0.0051   16.2   0.0      0.011   15.0   0.0    1.6  2  DnaB_C     DnaB-like helicase C terminal domain
  ------ inclusion threshold ------
      0.013   14.7   0.0      0.017   14.4   0.0    1.2  1  DUF2075    Uncharacterized conserved protein (DUF2075)
      0.034   13.9   0.0      0.056   13.2   0.0    1.3  1  IstB_IS21  IstB-like ATP binding protein
      0.039   13.8   0.0      0.066   13.0   0.0    1.3  1  MEDS       MEDS: MEthanogen/methylotroph, DcmR Sensory domain
      0.041   14.2   0.0      0.076   13.3   0.0    1.5  1  AAA_19     AAA domain
      0.064   13.3   0.1       0.17   11.9   0.1    1.7  2  AAA_14     AAA domain
      0.082   13.3   1.4        1.3    9.5   1.4    2.2  1  AAA        ATPase family associated with various cellular act
      0.097   11.6   0.1       0.15   11.0   0.1    1.2  1  AAA_10     AAA-like domain
       0.31   11.3   1.6        2.6    8.3   1.6    2.1  1  AAA_22     AAA domain


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.0   0.1   1.6e-49   2.4e-46       2     227 ..      18     242 ..      17     245 .. 0.92

  Alignments for each domain:
  == domain 1  score: 158.0 bits;  conditional E-value: 1.6e-49
                         ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenak.slGwdlekleee 80 
                                     +gI+g+De+++gG+ +g+v  +tG++GtGKt+fa qF+++g++  g++g+++t  e+ae+l++++  s+ wdl kleee
  gi|116754846|ref|YP_843964.1|  18 GSGIPGFDELVNGGFNKGTVNTVTGGSGTGKTVFATQFIYEGIKM-GDKGMIITPSESAESLKREMYsSFNWDLWKLEEE 96 
                                    68****************************************988.*****************999769*********** PP

                         ATPase  81 gklaiidasesaeesaee...kdkedleelieelaeaikeikakrvviDsitgl.ayeekeavaReilrqlvrvlkklgv 156
                                     kl+i+d++    + +++   +  + l ++ + +++ +ke + +rv iD + ++    + + ++R+  + l++ l+ ++ 
  gi|116754846|ref|YP_843964.1|  97 KKLVIVDVTDPVLRLQKSidlDPVDFLVNFRKLVERKVKEENPQRVFIDDLMAFfYAVQAPFKIRSLADDLFSSLRATKA 176
                                    ********99987766656655566666777777788888999***********777788899***************** PP

                         ATPase 157 TailvsekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIteegikvl 227
                                    T++++       +a+g +++ e+ +d    L++++i ++lvR++ ++kmRg+k+s+ + +++I+++g  v 
  gi|116754846|ref|YP_843964.1| 177 TTVITIG-----TAFGMNQILEYGADSCTMLRRDRIGNSLVRSIYVMKMRGSKISNSIRVLDISDDGMAVS 242
                                    ******9.....89***************************************************999885 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.1   1.7e-07   0.00026      20     155 ..      22     151 ..      11     182 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.7e-07
                         AAA_25  20 pprrwlvkgllpagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal. 97 
                                    p  + lv g   +g+++ ++G +gtGKt++a++  ++    G+           k +++   +s++ l+r ++  +    
  gi|116754846|ref|YP_843964.1|  22 PGFDELVNGGFNKGTVNTVTGGSGTGKTVFATQFIYEGIkMGD-----------KGMIITPSESAESLKREMYSSFNWDl 90 
                                    66678999888***********************999883333...........67777777777799999999884444 PP

                         AAA_25  98 ...rddarllvldlagveslpLfakdrggtl..ltadvdaleaaieevegvrlvviDplsral 155
                                       ++ ++l ++d+ +   l+L ++++ +++  l  + + +e++++e e+++ v iD l +++
  gi|116754846|ref|YP_843964.1|  91 wklEEEKKLVIVDVTD-PVLRLQKSIDLDPVdfLVNFRKLVERKVKE-ENPQRVFIDDLMAFF 151
                                    777999999***9977.699999999999999777788888999999.99*******999876 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.3   5.6e-06    0.0084      17      57 ..      15      55 ..       3      61 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.6e-06
                                   -EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHH CS
                          Rad51 17 lqlttGskklDelLgGGietgsiteifGefrsGktqlchtl 57
                                    ++  G   +Del++GG++ g++  + G +++Gkt ++ ++
  gi|116754846|ref|YP_843964.1| 15 TKVGSGIPGFDELVNGGFNKGTVNTVTGGSGTGKTVFATQF 55
                                   567788999**************************998875 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   7.6e-06     0.011       4      69 ..      19      84 ..      17     151 .. 0.68
   2 ?   -3.0   0.0       2.4   3.6e+03     202     235 ..     193     221 ..     189     228 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.6e-06
                                   SSTHHHHHHC.TSBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHHHHH CS
                                   xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         DnaB_C  4 tgfkdLDklt.sGlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqRlls 69
                                   +g   +D+l+ +G++kg++  + + +++Gkt++a++++ +  +  ++++++     sae+l + + s
  gi|116754846|ref|YP_843964.1| 19 SGIPGFDELVnGGFNKGTVNTVTGGSGTGKTVFATQFIYEGIKMGDKGMIITPS-ESAESLKREMYS 84
                                   5666778776258***********************998866555555554444.455666554444 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.4
                                    CCCXSEEEEEEECCHHHHHHCHHCEEEEEEEEET CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         DnaB_C 202 eqdADvvlflyrdeyykedseekgkaeiiiaKhR 235
                                    e  AD  ++l rd++ ++      +  i+++K R
  gi|116754846|ref|YP_843964.1| 193 EYGADSCTMLRRDRIGNSL-----VRSIYVMKMR 221
                                    6778999999998776532.....2356666666 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.1e-05     0.017       3      26 ..      37      67 ..      35     116 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.1e-05
                        DUF2075  3 vvlVtGvaGtGKtvvllnllael.......e 26
                                   v  VtG++GtGKtv + ++++e         
  gi|116754846|ref|YP_843964.1| 37 VNTVTGGSGTGKTVFATQFIYEGikmgdkgM 67
                                   668*****************99744444440 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.8e-05     0.056      51     115 ..      39     103 ..      23     109 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.8e-05
                      IstB_IS21  51 vllGpsGvGKshlaialgveavraglsvlfvrvedLveelkrarrdgklaralkrllkv.dllilD 115
                                     ++G+sG+GK+ +a+ + +e+++ g + + ++ ++  e+lkr+    +++  l +l +  +l+i+D
  gi|116754846|ref|YP_843964.1|  39 TVTGGSGTGKTVFATQFIYEGIKMGDKGMIITPSESAESLKREMY-SSFNWDLWKLEEEkKLVIVD 103
                                    589**********************99999999999999988754.45555555555443666666 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 ?   13.0   0.0   4.4e-05     0.066      17      99 ..      52     138 ..      49     150 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.4e-05
                           MEDS  17 lvpfikaglargekvlyvasastldelrealrka.gldvdaalesgqleildaeety...lrgggfdpermlealrrala 92 
                                    + +fi +g++ g+k ++++++++ + l++++ +  + d+ +++e+++l i+d ++      ++   dp  +l ++r+ ++
  gi|116754846|ref|YP_843964.1|  52 ATQFIYEGIKMGDKGMIITPSESAESLKREMYSSfNWDLWKLEEEKKLVIVDVTDPVlrlQKSIDLDPVDFLVNFRKLVE 131
                                    679*****************999999988885531455555*************99877777888999999999999999 PP

                           MEDS  93 kaladgy 99 
                                    + +++++
  gi|116754846|ref|YP_843964.1| 132 RKVKEEN 138
                                    9885543 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   5.1e-05     0.076      10      55 ..      35      76 ..      27     118 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.1e-05
                         AAA_19 10 ekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAa 55
                                    +v  vt+G GtGKT   ++ + + +++g    ++ +++++ + A 
  gi|116754846|ref|YP_843964.1| 35 GTVNTVTGGSGTGKTVFATQFIYEGIKMG----DKGMIITPSESAE 76
                                   56779*************99999999999....6778888887665 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00011      0.17       3      71 ..      36     103 ..      34     146 .. 0.68
   2 ?   -0.7   0.0      0.92   1.4e+03      52      72 ..     126     146 ..      96     166 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                         AAA_14   3 kilvitGaRrvGKTtllkqlikell.vkkesilyinldderdkkladpekllelileklkeekktylflD 71 
                                     + ++tG   +GKT+++ q+i+e + + ++ ++    ++ +  k++ +++++  + ++ +e +k++++ D
  gi|116754846|ref|YP_843964.1|  36 TVNTVTGGSGTGKTVFATQFIYEGIkMGDKGMIITPSESAESLKREMYSSFNWDLWKL-EE-EKKLVIVD 103
                                    57899******************99977777777777777776655554444444443.23.56666665 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.92
                         AAA_14  52 llelileklkeekktylflDE 72 
                                    + +l+ +k+kee+ + +f+D 
  gi|116754846|ref|YP_843964.1| 126 FRKLVERKVKEENPQRVFIDD 146
                                    223333334445566677775 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 ?    9.5   1.4   0.00086       1.3       3     115 ..      40     191 ..      39     200 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00086
                                    EESSTTSSHHHHHHHHHHH..........HTHE........................EEEEETTTCSSS........... CS
                            AAA   3 lyGppGtGKTllakavake..........lgve........................fleisgsellsk........... 37 
                                    ++G  GtGKT +a + + e          +  +                                   +           
  gi|116754846|ref|YP_843964.1|  40 VTGGSGTGKTVFATQFIYEgikmgdkgmiI--TpsesaeslkremyssfnwdlwkleE----------Ekklvivdvtdp 107
                                    578899999999999998866533333320..02233333333344433333333330..........144444444555 PP

                                    ..........STTHHHHHHHHHHHH.HHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEE CS
                            AAA  38 ..........yvgesekkirelfke.akekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivi 106
                                                 +   ++r+l+++ +ke++ p  +fiD++ a++ +   ++  + +++++ L++ l   k    +vi i
  gi|116754846|ref|YP_843964.1| 108 vlrlqksidlDPVDFLVNFRKLVERkVKEEN-PQRVFIDDLMAFFYAV--QAPFKIRSLADDLFSSLRATKA--TTVITI 182
                                    5555555555333444556666666345565.9999*****9999999..7888888899999999999998..479999 PP

                                    EEESSGGGS CS
                            AAA 107 gatnrpdkl 115
                                    g++  ++++
  gi|116754846|ref|YP_843964.1| 183 GTAFGMNQI 191
                                    998777666 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   9.8e-05      0.15      24      96 ..      38     123 ..      26     137 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9.8e-05
                         AAA_10  24 sliiGdlGnGKSvlakllvlyisllggkaliiDpkkerekfketlpe..........iakkinvvtLdse...eenegvL 90 
                                      ++G+ G GK v+a   ++    +g+k +ii p +  e  k++++             kk+ +v+++      ++   L
  gi|116754846|ref|YP_843964.1|  38 NTVTGGSGTGKTVFATQFIYEGIKMGDKGMIITPSESAESLKREMYSsfnwdlwkleEEKKLVIVDVTDPvlrLQKSIDL 117
                                    479*********************************99999999966444444442223344444443211223444556 PP

                         AAA_10  91 dPlvll 96 
                                    dP+ +l
  gi|116754846|ref|YP_843964.1| 118 DPVDFL 123
                                    666555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   1.6    0.0018       2.6       8      28 ..      38      58 ..      33     192 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0018
                         AAA_22  8 lvvtGesGtGKTtllrrlleq 28
                                    +vtG sGtGKT+ + ++ ++
  gi|116754846|ref|YP_843964.1| 38 NTVTGGSGTGKTVFATQFIYE 58
                                   579***********9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 1767.25
//
Query:       gi|116754847|ref|YP_843965.1|  [L=329]
Description: hypothetical protein Mthe_1555 [Methanosaeta thermophila PT]
Scores for complete 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-53  180.4   0.1    5.1e-53  180.0   0.1    1.2  1  Csc2      Csc2 Crispr


Domain annotation for each model (and alignments):
>> Csc2  Csc2 Crispr
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.0   0.1   2.8e-57   5.1e-53       3     286 ..      20     300 ..      18     314 .. 0.79

  Alignments for each domain:
  == domain 1  score: 180.0 bits;  conditional E-value: 2.8e-57
                           Csc2   3 eaieelpkgkyvhlvllRetqsfpifqtdgelnkarvqaGiedkek...isRlvmfKRKqvapERltGrellRklellsa 79 
                                    +++++ p+++yvh++llRe qs +if+t+g+      + Gi+ ++     s ++mfKRKq+ ++R++G+el R+l  l  
  gi|116754847|ref|YP_843965.1|  20 DELTNEPSAHYVHILLLRELQSSAIFTTNGQ-DADIANVGIHAEDGfveYSPVMMFKRKQTGSDRRKGKELQRNL--LGI 96 
                                    678899************************9.334456677766543226889*******************975..555 PP

                           Csc2  80 ekeekelCeynveasckkcpDcilYGfAigdsg.sekskvvtddAfsllayeesveeftlnavfetGtmsekgeassaln 158
                                    ++       + v+++++++p++ilYG A+g++  s  s+v+ d+A+s+++++ +vee   na+ ++     ++ a++a+ 
  gi|116754847|ref|YP_843965.1|  97 DD------TMSVNEMKQDSPESILYGSAAGEEAiSVTSRVMYDTAYSIRDSSVLVEEKFQNAPGDA----FAKGATTAIR 166
                                    55......3456778899************998799***************************743....3566899*** PP

                           Csc2 159 esdhikPevtFpdvvtlkDvtedellYvlgnilrtrrYGAqesRtGkvknellgivfsdgEifsnLeltqalyDalke.k 237
                                    e d+i P++ Fp+vvtl+D+t +el++vlg   + +rYGA +sR+G+v+n++lgi+++++E ++nL + q++  +l + +
  gi|116754847|ref|YP_843965.1| 167 EPDFIMPGTLFPCVVTLRDATFEELVFVLGVTKMNKRYGAATSRIGRVENHILGIYYGIEEGPANLYISQEIARRLAAvD 246
                                    *************************************************************************9998754 PP

                           Csc2 238 eeleapldedevieaa..kevieellkk...efvrksqviseeeleelleevka 286
                                      ++++  ++ + + +   evi++l+kk   e ++++++ + ++ ++l++ ++a
  gi|116754847|ref|YP_843965.1| 247 GGITTDRLRKVLYSPTldVEVIKDLTKKvfdENIKEMDIEHLDNADKLVSAISA 300
                                    433333333333333211355666666511144555555555666666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2354.66
//
Query:       gi|116754848|ref|YP_843966.1|  [L=253]
Description: hypothetical protein Mthe_1556 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1837.63
//
Query:       gi|116754849|ref|YP_843967.1|  [L=696]
Description: DEAD/DEAH box helicase domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.4e-11   43.7   0.0    6.2e-11   42.4   0.0    1.7  1  DEAD        DEAD/DEAH box helicase
     0.0048   16.9   0.0      0.011   15.7   0.0    1.6  1  ResIII      Type III restriction enzyme, res subunit
     0.0052   17.1   0.1      0.013   15.8   0.1    1.7  1  Helicase_C  Helicase conserved C-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 !   42.4   0.0     1e-14   6.2e-11       7     172 ..      38     222 ..      32     226 .. 0.65

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 1e-14
                                    HHHHHHTTCEEE...EEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTT.TST...SEEE CS
                                    xxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx...xxxx RF
                           DEAD   7 aiplilgggdvl...vaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkk.yid...lrvl 79 
                                    +  li  ++d+l    + +TGsGKT  +l pvl        +++ ka+ v Pt +L+ ++  +++++++ y+d   + v+
  gi|116754849|ref|YP_843967.1|  38 SERLIK-EEDMLflfNHSPTGSGKTVSWLKPVL--------DSRMKAIAVYPTNALVMDQSMQIRRMIErYYDpedYHVQ 108
                                    544444.55665455789***************........7889***********************953556664444 PP

                                    EEET.....TSSHHHHHHHH..........HTT...CSEEEEEHHHHHHHH......HCTSSH..CTTEEEEEEETHHHH CS
                                    xxxx.....xxxxxxxxxxx..........xxx...xxxxxxxxxxxxxxx......xxxxxx..xxxxxxxxxxxxxxx RF
                           DEAD  80 liig.....gvaardqlskl..........dng...vdivvgtpgrlddll......stgkln..lsqvrflVlDEadrl 133
                                    ++++     + +   + s l          ++g     +++++p+ l   l      +   l+  +++v +lV+DE +  
  gi|116754849|ref|YP_843967.1| 109 AVTSdlladERKLYPDESGLrkgqllnriiRKGrgrGLVLLTNPDILTLALkdayydN--DLResIRSVDILVVDEFHLA 186
                                    4433222122222222222233333343452223335555555555555447877552..33344*************99 PP

                                    HHTTTHHHHHHHHHHSHHHCTTST.TTSEEEEEESSBSHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                           DEAD 134 ldqgfsdfinrilnqlpqitcdgk.lqrqvivlSATlpkd 172
                                    + + +sd +  +++++   ++d + + r++++lSAT++++
  gi|116754849|ref|YP_843967.1| 187 SVK-QSDMLLFMAHEI---CDDRRsSLRKFVFLSATPNQK 222
                                    998.999999999999...4444434466********955 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 !   15.7   0.0   1.9e-06     0.011      30     170 ..      53     220 ..      29     221 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.9e-06
                                    EESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG............GEEEESSS-B--..... CS
                         ResIII  30 kmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseayke........igkkvsgdkkka..... 96 
                                    + +TG+GKT+  +k +   +      k++ + p+++l+     +++++++ +y+         +     +d         
  gi|116754849|ref|YP_843967.1|  53 HSPTGSGKTVSWLKPVLDSRM-----KAIAVYPTNALVMDQSMQIRRMIERYYDPedyhvqavT-----SDLLADerkly 122
                                    469*******99998887777.....7999*******999999999999999987778555431.....22222223334 PP

                                    ......................-SEEEEEHHHHHHTH.........HHHTTT-SEEEEETGGGTTS.T......TTHHH. CS
                         ResIII  97 ...............kekdstnkkilvttiqsldadseee.eeeseellrdrfdviiiDEaHrlgakk......swrei. 153
                                                    +k +    +l+t+ + l+ +++ +   ++ + +  + d++++DE H ++ k+         ei 
  gi|116754849|ref|YP_843967.1| 123 pdesglrkgqllnriIRKGRGRGLVLLTNPDILTLALKDAyYDNDLRESIRSVDILVVDEFHLASVKQsdmllfMAHEIc 202
                                    566666666666667777778888888888888888855577777777788888********999863567775444453 PP

                                    HHT---.SEEEEEESS-S CS
                         ResIII 154 lekfke.avllglTATpe 170
                                     +  ++  + + l+ATp+
  gi|116754849|ref|YP_843967.1| 203 DDRRSSlRKFVFLSATPN 220
                                    333222366677789987 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 !   15.8   0.1   2.2e-06     0.013      65     107 ..     336     375 ..     290     378 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.2e-06
                                    TSSSEEEESGGGTSSSTSTTESEEEESSSSSSHHHHHHHHTTS CS
                     Helicase_C  65 gesdvLiatdvaerGidipkvnlVinfdlprnvtsyiqriGRt 107
                                    +++dvL++ + +e Gid+ +v+ +++ ++ ++  ++iqriGR 
  gi|116754849|ref|YP_843967.1| 336 ERFDVLVSNSSVEVGIDF-DVDRLVFSGYTKS--QMIQRIGRL 375
                                    4589**************.7********9976..********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (696 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); 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: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.41
# Mc/sec: 5138.71
//
Query:       gi|116754850|ref|YP_843968.1|  [L=190]
Description: CRISPR-associated Cas4 family protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-25   89.1   0.3    3.6e-25   89.0   0.3    1.0  1  Cas_Cas4  Domain of unknown function DUF83
    8.2e-07   29.2   0.4    0.00024   21.1   0.0    2.0  2  PDDEXK_1  PD-(D/E)XK nuclease superfamily
     0.0065   15.9   0.7      0.014   14.7   0.1    1.7  2  Csa1      CRISPR-associated exonuclease Csa1
  ------ inclusion threshold ------
      0.087   12.6   0.0        3.4    7.4   0.0    2.5  3  Dna2      DNA replication factor Dna2


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 !   89.0   0.3     8e-29   3.6e-25       4     162 .]      11     181 ..       8     181 .. 0.94

  Alignments for each domain:
  == domain 1  score: 89.0 bits;  conditional E-value: 8e-29
                       Cas_Cas4   4 kiqyyliCkrklwlisheitleensetvelGkllheesyerek..kevel.se....sikiDvve.....kekeklvvvE 71 
                                    +i++yl+C+r+ ++i+   t+e n   ++ G++ he + +r    ke+ l se    ++kiDv+e     +++e l+++E
  gi|116754850|ref|YP_843968.1|  11 DINQYLYCPRRYYYINYFDTIEMN-YYLKDGQIKHEMQSRRGGwiKELYLrSErlgmHGKIDVIEvknvlSRGEVLTPIE 89 
                                    79*************998888888.77888******999997789*****8889999********8888888899999** PP

                       Cas_Cas4  72 vKkskkkeeaaklQllyYlllLe.kkgveikeGvleypkekkreevelteelreelekaikeieeiissekppkvkkkki 150
                                     K++++++e++ +Ql +Y++lLe   +  ++ G++++  +++r  +++t+++r+++ ++++ i++++    p  v+++++
  gi|116754850|ref|YP_843968.1|  90 RKRGTSYHENDVIQLAAYCMLLEeFLDRPVRLGYIYLFGNNERYAIKITDDHRSRVIQVVNAIRSMSIDRIPGFVENRNK 169
                                    ***********************999*******************************************9********** PP

                       Cas_Cas4 151 CkkCayaelCli 162
                                    C+kC+ +++C++
  gi|116754850|ref|YP_843968.1| 170 CEKCSTSQYCMP 181
                                    **********86 PP

>> PDDEXK_1  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.1   0.00096       4.3       4      41 ..       9      44 ..       7      54 .. 0.69
   2 !   21.1   0.0   5.3e-08   0.00024     125     254 ..      61     179 ..      36     180 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00096
                       PDDEXK_1  4 vsrletfleCplrfflryllgl.reeeeleapdlGtlvH 41
                                   v  ++++l Cp+r+++   +     ++ l+    G++ H
  gi|116754850|ref|YP_843968.1|  9 VGDINQYLYCPRRYYYINYFDTiEMNYYLKD---GQIKH 44
                                   6789*********998444433254666655...55555 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 5.3e-08
                       PDDEXK_1 125 gekvrLkGriDrvd.....dkegelriiDyKtgsappkskelaelkeglQlllYllalaegeelkeegepagalylrlee 199
                                    +e++ ++G+iD ++     ++++ l+ i+ K g++    +e    ++ +Ql++Y+++l+e    +++  p+++ y+ l  
  gi|116754850|ref|YP_843968.1|  61 SERLGMHGKIDVIEvknvlSRGEVLTPIERKRGTSY---HE----NDVIQLAAYCMLLEEF---LDR--PVRLGYIYL-- 126
                                    2455599******9998876666899*****88833...32....3458*********987...333..999999999.. PP

                       PDDEXK_1 200 pkvkdeevvkkmalteeeleallqeleel....aeeilagefparpskkCeyCpyksvC 254
                                         +++   ++ t+++++++ q ++ +    +++i  g ++ r+   Ce C+ +++C
  gi|116754850|ref|YP_843968.1| 127 ---FGNNERYAIKITDDHRSRVIQVVNAIrsmsIDRIP-GFVENRNK--CEKCSTSQYC 179
                                    ...55667777778999999999999998777788887.55555544..********** PP

>> Csa1  CRISPR-associated exonuclease Csa1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.14   6.2e+02      53      90 ..      16      50 ..       6      80 .. 0.75
   2 !   14.7   0.1   3.2e-06     0.014     198     289 ..      92     179 ..      62     182 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.14
                           Csa1 53 gyCetkRdvYLkrvlgvrgeeekklllGaaiHeavaka 90
                                    yC+ +R+ Y+ +   +  +    l+ G++ He+  + 
  gi|116754850|ref|YP_843968.1| 16 LYCP-RRYYYINYFDTIEMN--YYLKDGQIKHEMQSRR 50
                                   5777.789999988887665..8899999999987655 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 3.2e-06
                           Csa1 198 kvgsykeehelalaGYalalEsqleiPvDfGvlisvtvngevklkaelvaisdslRkefleeRdraidivekesDPGlak 277
                                    +  sy+e+  + la Y + lE  l+ Pv +G++     n+      ++++i d+ R++ +++ ++ i+ ++ ++ PG  +
  gi|116754850|ref|YP_843968.1|  92 RGTSYHENDVIQLAAYCMLLEEFLDRPVRLGYIYLFGNNE-----RYAIKITDDHRSRVIQVVNA-IRSMSIDRIPGFVE 165
                                    34579999999********************965444443.....4678899********99875.66778888899976 PP

                           Csa1 278 ...kCsskClflevC 289
                                       kC+ kC   ++C
  gi|116754850|ref|YP_843968.1| 166 nrnKCE-KCSTSQYC 179
                                    222454.68888888 PP

>> Dna2  DNA replication factor Dna2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0   0.00077       3.4      52      95 ..       4      46 ..       1      49 [. 0.91
   2 ?    2.2   0.0      0.03   1.3e+02     187     199 ..      60      72 ..      55      75 .. 0.86
   3 ?   -2.1   0.0      0.63   2.8e+03       9      44 ..     107     141 ..     103     152 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00077
                           Dna2 52 dlLvsaTsvanslsClRravLqerlkvsgesskamliGtilHel 95
                                   d Lv+   +++ l C+Rr +  + +++++  +  +  G+i He+
  gi|116754850|ref|YP_843968.1|  4 DELVNVGDINQYLYCPRRYYYINYFDTIE-MNYYLKDGQIKHEM 46
                                   7799*********************9988.999999******97 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.03
                           Dna2 187 wspkyGLKGkiDa 199
                                     s+++G+ GkiD+
  gi|116754850|ref|YP_843968.1|  60 RSERLGMHGKIDV 72 
                                    699*********8 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.63
                           Dna2   9 tvvLrddWaetsvekgdiihivgkfeeekiiidnes 44 
                                    +++L +++ + +v+ g +i + g+ e+ +i i++++
  gi|116754850|ref|YP_843968.1| 107 YCMLLEEFLDRPVRLG-YIYLFGNNERYAIKITDDH 141
                                    6888888888888888.7777788875555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1338.84
//
Query:       gi|116754851|ref|YP_843969.1|  [L=330]
Description: CRISPR-associated Cas1 family protein [Methanosaeta thermophila PT]
Scores for 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-83  277.6   0.0    1.4e-82  277.0   0.0    1.3  1  Cas_Cas1  CRISPR associated protein Cas1


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 !  277.0   0.0   7.9e-87   1.4e-82       1     281 [.      15     282 ..      15     284 .. 0.94

  Alignments for each domain:
  == domain 1  score: 277.0 bits;  conditional E-value: 7.9e-87
                                    EEEESTEEEEEEETTEEEEEESSE.EEEEEECCCEEEEEEESTEEEEHHHHHHHHHTT-EEEEE-TTS-EEEEEEESSSS CS
                       Cas_Cas1   1 lyvteqgaylrkkgerlvvekege.ekkeiplediesivifgevslstkalrllaekgipvvflsengkylgrlepeesg 79 
                                    +y+t+qga+++++g+r+vv +++e e++++p+ ++++i ifg+++++t++++++ e+gi + ++++ng+y+g+++pe+++
  gi|116754851|ref|YP_843969.1|  15 VYITKQGAQVGVDGGRIVVYSKDEgEIASFPMGQVDTINIFGNINFTTPFVARANEHGIVLNYFTQNGHYRGSFVPERNT 94 
                                    6******************9966658****************************************************** PP

                                    THHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHCCHHCTTHHHHCHCHHHHHHHHHHHH-HSHHHHHHHHHHHH CS
                       Cas_Cas1  80 nvelrraQyraaddeekrlelakkivagklenqrkvlrrlkrdreeeeleeaieeleelleklekaesleeLrgiEGeaa 159
                                     +e+rr+Qy++++  + rl++a  i+++k++n+r++l r   ++         ++l el +++++a++l+eLrg+EGeaa
  gi|116754851|ref|YP_843969.1|  95 IAEVRRRQYALSE--ADRLRIASVIIRAKIRNSRTMLYRRGASD---------DRLGELEDRVADANDLDELRGLEGEAA 163
                                    *********9975..457*******************8888888.........566666679****************** PP

                                    HHHHHHHHHHCSCGGS-SS-SSSS-SSHHHHHHHHHHHHHHHHHHHHHHTSS--TT--SSS--TTSS-HHHHHHHHHHHH CS
                       Cas_Cas1 160 kaYfeafdkllkeefefegRsrrppkDpvNalLsfgYtllysevlsaieavgLdPyiGfLHedrpgrpsLalDLmEefRp 239
                                    ++Yf+ ++++++++++fe+Rsrrpp D +NalLs+ Y+++ +evlsa+++  LdP +G+LH+dr+grp+LalDL EefRp
  gi|116754851|ref|YP_843969.1| 164 EIYFGILKRCVPQDWSFERRSRRPPADHMNALLSLTYSMIKNEVLSALRQYNLDPFLGILHADRHGRPALALDLLEEFRP 243
                                    ******************************************************************************** PP

                                    HHCHHHHHHHHHTTSS-GGGEEEETTEEEE-HHHHHHHHHHH CS
                       Cas_Cas1 240 llvDrlvlslinkrqlkekdFekeengvlLteegrkkfleaf 281
                                    +++D + l+lin++ lk +dF+ ++    L+e + k++l +f
  gi|116754851|ref|YP_843969.1| 244 IFCDAFTLRLINRGVLKHEDFQVNN---HLKEYAFKTYLGKF 282
                                    **********************976...57777777777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2404.71
//
Query:       gi|116754852|ref|YP_843970.1|  [L=88]
Description: CRISPR-associated Cas2 family protein [Methanosaeta thermophila PT]
Scores for complete 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   76.4   0.2    1.6e-21   76.2   0.2    1.1  1  CRISPR_Cas2  CRISPR associated protein Cas2
  ------ inclusion threshold ------
       0.11   12.7   0.0       0.14   12.3   0.0    1.3  1  RcsD_ABL     RcsD-ABL domain
       0.17   11.1   0.0       0.18   11.0   0.0    1.1  1  SIL1         Nucleotide exchange factor SIL1


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 !   76.2   0.2   2.8e-25   1.6e-21       1      73 [.       1      70 [.       1      73 [. 0.97

  Alignments for each domain:
  == domain 1  score: 76.2 bits;  conditional E-value: 2.8e-25
                                   EEEEEEEECHCHHHHHHHHHHHHHHTTEEEEETTEEEEEESHHHHHHHHHHHHHHSHTTTCEEEEEEEETCHH CS
                    CRISPR_Cas2  1 mlvlvvYDikedrkrrrkvakilkkyGfqrvQySVFegelseaqleklkkrlkkiidpeedsiriykltekqf 73
                                   m+++v+YDi +d++ r++v++il++y + + QySVFe e+s+ q  ++++++k++i+p  d++riy+l+e++ 
  gi|116754852|ref|YP_843970.1|  1 MRLAVTYDI-SDNRIRTRVFRILESY-GAWKQYSVFELEISDVQRLEMEAKIKSVIKPG-DKVRIYELCERCV 70
                                   999******.****************.********************************.***********97 PP

>> RcsD_ABL  RcsD-ABL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.3e-05      0.14       9      32 ..       5      28 ..       2      55 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.3e-05
                       RcsD_ABL  9 vllditseevrkivsrllenyGae 32
                                   v  di+ + +r++v r+le+yGa 
  gi|116754852|ref|YP_843970.1|  5 VTYDISDNRIRTRVFRILESYGAW 28
                                   6789******************96 PP

>> SIL1  Nucleotide exchange factor SIL1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   2.9e-05      0.18     145     189 ..       3      53 ..       1      69 [. 0.73

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 2.9e-05
                           SIL1 145 Lieiyeikdkqikikvlelledllleeee......ksevkkrsaeeeeedv 189
                                    L  +y i d+ i+++v  +le + ++++        s+v++ ++e++ + v
  gi|116754852|ref|YP_843970.1|   3 LAVTYDISDNRIRTRVFRILESYGAWKQYsvfeleISDVQRLEMEAKIKSV 53 
                                    7889**********************9775555543444454444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); 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: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 661.99
//
Query:       gi|116754853|ref|YP_843971.1|  [L=209]
Description: CRISPR-associated DNA-binding protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.3e-06   26.3   0.8    7.9e-06   25.7   0.1    1.7  2  MarR            MarR family
      3e-05   23.7   0.0    5.5e-05   22.9   0.0    1.4  1  HTH_IclR        IclR helix-turn-helix domain
    4.5e-05   23.3   0.0    7.9e-05   22.5   0.0    1.4  1  HTH_1           Bacterial regulatory helix-turn-helix protein
    4.8e-05   23.5   0.1    8.2e-05   22.7   0.1    1.3  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
    0.00023   21.0   0.1    0.00045   20.0   0.1    1.5  1  HTH_5           Bacterial regulatory protein, arsR family
    0.00023   21.0   0.2    0.00064   19.5   0.0    1.8  2  MarR_2          MarR family
    0.00034   20.1   0.2    0.00068   19.2   0.2    1.5  1  HTH_24          Winged helix-turn-helix DNA-binding
     0.0011   18.9   0.2     0.0024   17.8   0.2    1.6  1  HTH_11          HTH domain
     0.0021   18.4   0.1     0.0061   16.9   0.1    1.8  1  Rrf2            Transcriptional regulator
     0.0036   17.3   0.0     0.0059   16.6   0.0    1.4  1  HTH_20          Helix-turn-helix domain
     0.0069   16.4   0.0      0.013   15.5   0.0    1.4  1  HTH_29          Winged helix-turn helix
     0.0091   16.0   0.1      0.018   15.0   0.1    1.5  1  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0093   15.8   0.1      0.018   14.9   0.1    1.4  1  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0094   15.7   0.5      0.027   14.2   0.4    1.8  2  DUF4423         Domain of unknown function (DUF4423)
  ------ inclusion threshold ------
      0.014   16.0   0.0      0.033   14.8   0.0    1.7  1  Mga             Mga helix-turn-helix domain
       0.02   14.3   0.1      0.029   13.7   0.1    1.3  1  DUF1670         Protein of unknown function (DUF1670)
      0.021   14.3   0.1      0.049   13.2   0.1    1.6  1  Sigma70_r4      Sigma-70, region 4
      0.032   14.7   1.3      0.051   14.1   0.3    1.9  1  HTH_27          Winged helix DNA-binding domain
      0.032   14.2   0.0       0.06   13.3   0.0    1.5  1  HTH_6           Helix-turn-helix domain, rpiR family
      0.038   13.9   0.0      0.066   13.2   0.0    1.4  1  HTH_36          Helix-turn-helix domain
      0.045   13.4   0.0      0.063   13.0   0.0    1.3  1  Sigma54_DBD     Sigma-54, DNA binding domain
      0.047   13.5   0.0       0.11   12.3   0.0    1.7  1  HTH_23          Homeodomain-like domain
      0.049   13.5   0.1      0.084   12.8   0.1    1.4  1  RuvB_C          RuvB C-terminal winged helix domain
      0.067   13.3   0.0       0.12   12.5   0.0    1.5  1  HTH_7           Helix-turn-helix domain of resolvase
      0.076   13.1   0.0       0.11   12.5   0.0    1.2  1  Replic_Relax    Replication-relaxation
      0.077   12.4   0.0       0.14   11.6   0.0    1.4  1  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family
      0.082   12.5   0.1       0.13   11.8   0.1    1.4  1  GerE            Bacterial regulatory proteins, luxR family
       0.11   12.3   0.0       0.25   11.1   0.0    1.6  1  HTH_38          Helix-turn-helix domain
       0.13   12.4   0.0       0.34   11.1   0.0    1.6  1  HTH_28          Helix-turn-helix domain
       0.14   12.4   0.4        1.7    8.9   0.2    2.4  2  HTH_34          Winged helix DNA-binding domain


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 ?   -2.5   0.1       8.2   4.9e+03      49      57 ..      34      42 ..      32      43 .. 0.84
   2 !   25.7   0.1   1.3e-08   7.9e-06       6      43 ..     147     184 ..     142     193 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 8.2
                                   EEEETTSTT CS
                           MarR 49 RskspeDrR 57
                                   R  +++D+R
  gi|116754853|ref|YP_843971.1| 34 RPADERDKR 42
                                   888999999 PP

  == domain 2  score: 25.7 bits;  conditional E-value: 1.3e-08
                                    HHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHH CS
                           MarR   6 fviLrilyeqgplsvseLakklgvskstvtrvldrLek 43 
                                    ++iL  ++e++p ++ ++ak+l++s s+v+r++ +L +
  gi|116754853|ref|YP_843971.1| 147 LRILKDVEEHQPTNIMDIAKRLNISESSVSRQVATLAE 184
                                    789********************************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 !   22.9   0.0   9.1e-08   5.5e-05       3      48 ..     144     188 ..     144     191 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 9.1e-08
                                    HHHHHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                       HTH_IclR   3 dRalaiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyv 48 
                                    +R l+iL+ ++e+++  ++ ++A+r+ ++ S+v+R ++tL el+ v
  gi|116754853|ref|YP_843971.1| 144 ERYLRILKDVEEHQPT-NIMDIAKRLNISESSVSRQVATLAELKAV 188
                                    6889999999999997.**************************988 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 !   22.5   0.0   1.3e-07   7.9e-05       4      59 ..     147     205 ..     145     206 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.3e-07
                                    HHHHHHHHHHS..SHHHHHHHHTS-HHHHHHHHHHHHHHHTS-SEEESSSE.EEE-HHH CS
                          HTH_1   4 lrlfvavaeeg..sftrAAeeLglsqpavsrqikrLEeelgvpLfeRtgrg.lrLTeaG 59 
                                    lr+++ v e++  ++   A++L++s ++vsrq+++L e+  v+  +R + + +r T  G
  gi|116754853|ref|YP_843971.1| 147 LRILKDVEEHQptNIMDIAKRLNISESSVSRQVATLAELKAVDVTQRGKTKeVRITITG 205
                                    788888888888888888*****************************544359988666 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 !   22.7   0.1   1.4e-07   8.2e-05       7      48 ..     144     184 ..     141     194 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.4e-07
                                    HHHHHHHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHH CS
                 Fe_dep_repress   7 EdYLetIYtlseekkvvktkdlaerLnvspssVsemlkkLek 48 
                                    E YL+ + ++ ee+++   +d+a+rLn+s ssVs  +  L++
  gi|116754853|ref|YP_843971.1| 144 ERYLRILKDV-EEHQPTNIMDIAKRLNISESSVSRQVATLAE 184
                                    8899966555.59**********************9999987 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   7.5e-07   0.00045       5      41 ..     147     184 ..     143     187 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 7.5e-07
                                    HHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHH CS
                          HTH_5   5 lkILklLae.gelcvcelaeelglsqstvShHLkkLre 41 
                                    l+ILk ++e +++ + ++a+ l++s+s vS++ + L e
  gi|116754853|ref|YP_843971.1| 147 LRILKDVEEhQPTNIMDIAKRLNISESSVSRQVATLAE 184
                                    89*****************************9888865 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       7.8   4.7e+03      55      62 .]      36      43 ..      30      50 .. 0.69
   2 !   19.5   0.0   1.1e-06   0.00064       9      52 ..     148     189 ..     142     197 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 7.8
                                   ESSSSSSS CS
                         MarR_2 55 pgpeDkRa 62
                                   ++++DkR+
  gi|116754853|ref|YP_843971.1| 36 ADERDKRG 43
                                   44558885 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 1.1e-06
                                    HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                         MarR_2   9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52 
                                    r+L  +  + +   ++ ++a+rl++s s+vsr ++ L +   v 
  gi|116754853|ref|YP_843971.1| 148 RILKDVEEHQP--TNIMDIAKRLNISESSVSRQVATLAELKAVD 189
                                    66777777777..899*********************9987775 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.2   1.1e-06   0.00068       5      43 ..     146     184 ..     142     186 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.1e-06
                         HTH_24   5 drkILelLqknprisqreLAerlglSpstvnrrlkrLee 43 
                                     ++IL+ ++++  +++ ++A+rl++S s v+r++  L e
  gi|116754853|ref|YP_843971.1| 146 YLRILKDVEEHQPTNIMDIAKRLNISESSVSRQVATLAE 184
                                    58999999**************************98865 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.2     4e-06    0.0024       4      42 ..     148     185 ..     145     195 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4e-06
                         HTH_11   4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeel 42 
                                     il+ + e+++p ++ ++A++Ln+S++ v r +++L el
  gi|116754853|ref|YP_843971.1| 148 RILKDV-EEHQPTNIMDIAKRLNISESSVSRQVATLAEL 185
                                    566666.666679999********************876 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1     1e-05    0.0061      14      61 ..     147     195 ..     139     202 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1e-05
                                    HHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE.EETTT CS
                           Rrf2  14 llyLakeeeeepvsseeiaerqnispsylekilakLrkaglvk.svrGk 61 
                                    l +L+  ee++p ++ +ia+r nis+s +++ +a+L++ + v  ++rGk
  gi|116754853|ref|YP_843971.1| 147 LRILKDVEEHQPTNIMDIAKRLNISESSVSRQVATLAELKAVDvTQRGK 195
                                    667888899999**************************99997356776 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   9.9e-06    0.0059      13      60 ..     147     194 ..     138     195 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 9.9e-06
                                    HHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                         HTH_20  13 rrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60 
                                    +ril+   + ++    ++a+rl +s +++s+++++L+e  +v+v+  g
  gi|116754853|ref|YP_843971.1| 147 LRILKDVEEHQPTNIMDIAKRLNISESSVSRQVATLAELKAVDVTQRG 194
                                    7888888899999999**************************998766 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.1e-05     0.013       4      35 ..     149     181 ..     147     196 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.1e-05
                         HTH_29   4 allllaeGvs.tvsqiAkllglsrrtvyrwlkr 35 
                                    +l  ++e ++ ++++iAk+l++s+++v r +  
  gi|116754853|ref|YP_843971.1| 149 ILKDVEEHQPtNIMDIAKRLNISESSVSRQVAT 181
                                    66777777779******************8866 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 !   15.0   0.1     3e-05     0.018      25      59 ..     162     201 ..     143     207 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3e-05
                                    HHHHHHTTSSHHHHHHHHHHHHHTTSEE...ETEE..EEE CS
                      HTH_Crp_2  25 eelAsmlGltretvsrilseLkreglis...rgrr..iri 59 
                                     ++A +l+++ ++vsr  + L + + ++   rg++  +ri
  gi|116754853|ref|YP_843971.1| 162 MDIAKRLNISESSVSRQVATLAELKAVDvtqRGKTkeVRI 201
                                    59************************99842233235555 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   2.9e-05     0.018      19      59 ..     155     195 ..     142     202 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.9e-05
                                    HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTT CS
                           TrmB  19 klgpatadeiaeelgvprskvYevLrsLedkGlVerekgrp 59 
                                    +++p ++ +ia++l++++s+v + +  L +   V++ ++ +
  gi|116754853|ref|YP_843971.1| 155 EHQPTNIMDIAKRLNISESSVSRQVATLAELKAVDVTQRGK 195
                                    8999***************************9999988654 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.8   1.1e+03     119     154 ..     123     158 ..     119     162 .. 0.77
   2 !   14.2   0.4   4.5e-05     0.027      37      84 ..     159     204 ..     128     207 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.8
                        DUF4423 119 issltlaiskedyekikkeirefrkkilaiaeeske 154
                                    +s +  ++++ ++++ik  ++e   +il+ +ee ++
  gi|116754853|ref|YP_843971.1| 123 FSDIDRSLKEIELPNIKASLDERYLRILKDVEEHQP 158
                                    555666788889999999999999999988888776 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 4.5e-05
                        DUF4423  37 adpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqtekslt 84 
                                     ++  +akrl+  is++ v++ + +L +l+ ++ ++ gk +  +  +t
  gi|116754853|ref|YP_843971.1| 159 TNIMDIAKRLN--ISESSVSRQVATLAELKAVDVTQRGKTKEVRITIT 204
                                    57889******..*************************9999887776 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   5.5e-05     0.033      19      56 ..     147     184 ..     126     206 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.5e-05
                                    HHHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHHHH CS
                            Mga  19 yqllkflfeeeevsieelaqelyiSestlkrkikelnk 56 
                                    +++lk + e++ ++i ++a++l iSes++ r+++ l +
  gi|116754853|ref|YP_843971.1| 147 LRILKDVEEHQPTNIMDIAKRLNISESSVSRQVATLAE 184
                                    678888889************************99876 PP

>> DUF1670  Protein of unknown function (DUF1670)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   4.9e-05     0.029     108     153 ..     161     206 ..     122     208 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.9e-05
                        DUF1670 108 qsDlalllgvstrtvskqvkeyqeeegivlptrGaikDiGpavsHK 153
                                      D+a  l++s+++vs+qv  + e + + +  rG+ k++  +++ K
  gi|116754853|ref|YP_843971.1| 161 IMDIAKRLNISESSVSRQVATLAELKAVDVTQRGKTKEVRITITGK 206
                                    469*******************9999999**********9999977 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   8.2e-05     0.049       4      40 ..     141     178 ..     140     186 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.2e-05
                                    HS-HHHHHHHHHHH.TTT--HHHHHHHHTS-HHHHHHH CS
                     Sigma70_r4   4 sLpererevlelrf.geglTleEIgerlgiSrerVrqi 40 
                                    sL+er  ++l+ +   ++ +  +I++rl+iS++ V++ 
  gi|116754853|ref|YP_843971.1| 141 SLDERYLRILKDVEeHQPTNIMDIAKRLNISESSVSRQ 178
                                    7999999999999999999****************985 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.3   8.5e-05     0.051       8      65 ..     149     204 ..     145     206 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.5e-05
                         HTH_27   8 vLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLv.ertgdeadrrekrvrlT 65 
                                    +L  ++ ++ +  ++d+++rln++ s++s  +  L e   v ++++ +   +e+r+++T
  gi|116754853|ref|YP_843971.1| 149 ILKDVE-EHQPTNIMDIAKRLNISESSVSRQVATLAELKAVdVTQRGK--TKEVRITIT 204
                                    445555.9999******************9999999985553222222..345666666 PP

>> HTH_6  Helix-turn-helix domain, rpiR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0    0.0001      0.06      25      53 ..     149     177 ..     133     183 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.0001
                                    HHH-S---TT--HHHHHHHTT--HHHHHH CS
                          HTH_6  25 ilaspdkaielsikalAkaaavSeativr 53 
                                    il+++++ +   i ++Ak +++Se+++ r
  gi|116754853|ref|YP_843971.1| 149 ILKDVEEHQPTNIMDIAKRLNISESSVSR 177
                                    8999999********************98 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00011     0.066      29      52 ..     162     185 ..     151     188 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00011
                         HTH_36  29 etlakrlglsknTvsraikeLeql 52 
                                     ++akrl++s+++vsr ++ L++l
  gi|116754853|ref|YP_843971.1| 162 MDIAKRLNISESSVSRQVATLAEL 185
                                    69*******************998 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 ?   13.0   0.0   0.00011     0.063      41      71 ..     151     180 ..     119     194 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00011
                                    HXSSXXXXXXXHHHHHTTSSSXHHHHHHHHH CS
                    Sigma54_DBD  41 ekgeealrpltlrevaealelhesTvSRvvs 71 
                                    +  +e+ +p ++ ++a+ l+++es vSR v+
  gi|116754853|ref|YP_843971.1| 151 K-DVEEHQPTNIMDIAKRLNISESSVSRQVA 180
                                    4.566779********************986 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00019      0.11      20      40 ..     161     181 ..     140     189 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00019
                         HTH_23  20 vreIAreLgvsrrTvyrwlkr 40 
                                    + +IA++L++s++ v+r + +
  gi|116754853|ref|YP_843971.1| 161 IMDIAKRLNISESSVSRQVAT 181
                                    679*************97766 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 ?   12.8   0.1   0.00014     0.084       6      60 ..     141     194 ..     140     209 .] 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00014
                                    HHHHHHHHHHHHT.TT--B-HHHHHHHTT--HHHHHHTTHHHHHHTTSEEEETTE CS
                         RuvB_C   6 eldikyLkllkekfkggpvglktlaailgeeketiedviEPyLlkeglIertsrG 60 
                                    +ld +yL++lk+  + +p+ +  +a+ l+++++ ++ ++   L + + +  t+rG
  gi|116754853|ref|YP_843971.1| 141 SLDERYLRILKDVEEHQPTNIMDIAKRLNISESSVSRQV-ATLAELKAVDVTQRG 194
                                    5799********99*********************9988.467777777777777 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 ?   12.5   0.0    0.0002      0.12      20      38 ..     157     175 ..     139     181 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0002
                                    TT--STTTSSSS---SSSS CS
                          HTH_7  20 eGisiskIAkevnisRsTv 38 
                                    +++ i++IAk++nis s+v
  gi|116754853|ref|YP_843971.1| 157 QPTNIMDIAKRLNISESSV 175
                                    5689***********9998 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00019      0.11       1      46 [.     150     194 ..     150     204 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00019
                   Replic_Relax   1 LrlLaehrvlTtrqiarllfashratarrrLarLrelgllsrlrkr 46 
                                    L+ ++eh++ +   ia+ l+ s+++ ++r+ a+L+el++++ +++ 
  gi|116754853|ref|YP_843971.1| 150 LKDVEEHQPTNIMDIAKRLNISESS-VSRQVATLAELKAVDVTQRG 194
                                    7899*********************.***************97765 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 ?   11.6   0.0   0.00023      0.14      28      48 ..     159     179 ..     149     183 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00023
                   HTH_Tnp_ISL3  28 rsvkavArqlgvSwtTVwril 48 
                                     +++++A++l++S+++V r +
  gi|116754853|ref|YP_843971.1| 159 TNIMDIAKRLNISESSVSRQV 179
                                    489**************9976 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00022      0.13       5      39 ..     144     180 ..     140     184 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00022
                                    HHHHHHHHHHCTTS-HH..HHHHHHTS-HHHHHHHHH CS
                           GerE   5 kRErevLrllaeGksnk..eIAeelniSekTVkvhks 39 
                                    +R + +L+ + e + ++  +IA++lniSe +V+ +++
  gi|116754853|ref|YP_843971.1| 144 ERYLRILKDVEEHQPTNimDIAKRLNISESSVSRQVA 180
                                    55555555555555544338************98776 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00043      0.25      24      41 ..     162     179 ..     153     180 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00043
                         HTH_38  24 reIArrLgrspsTIsREl 41 
                                     +IA+rL+ s s++sR +
  gi|116754853|ref|YP_843971.1| 162 MDIAKRLNISESSVSRQV 179
                                    58**************65 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   0.00057      0.34       3      31 ..     147     177 ..     147     182 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00057
                         HTH_28   3 leiikllaaGh..svreaArelgisrrtvyr 31 
                                    l+i+k + ++   +++++A++l+is+++v+r
  gi|116754853|ref|YP_843971.1| 147 LRILKDVEEHQptNIMDIAKRLNISESSVSR 177
                                    6899999999888****************86 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 ?    0.8   0.0      0.95   5.7e+02      19      35 ..      79      95 ..      69      97 .. 0.88
   2 ?    8.9   0.2    0.0028       1.7       8      64 ..     149     204 ..     145     207 .. 0.67

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.95
                         HTH_34 19 elkealeatdgnLsvhl 35
                                   +l++ l+ ++g+L v+l
  gi|116754853|ref|YP_843971.1| 79 SLRDLLRSSEGKLIVNL 95
                                   79***********9987 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0028
                         HTH_34   8 yLasvdeadfv...elkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpe 64 
                                    +L +v+e +++   ++ + l+++++  s ++ +L + + + v+   k k     +riT +
  gi|116754853|ref|YP_843971.1| 149 ILKDVEEHQPTnimDIAKRLNISESSVSRQVATLAELKAVDVTQRGKTK--E--VRITIT 204
                                    5555555555411156789******************988777655555..3..344433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       765  (0.0426683); expected 358.6 (0.02)
Passed bias filter:                      624  (0.0348039); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); 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: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1491.86
//
Query:       gi|116754854|ref|YP_843972.1|  [L=325]
Description: CRISPR-associated Cas5e family protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.4e-15   55.6   0.0      1e-14   54.9   0.0    1.3  1  CRISPR_Cas6  CRISPR-associated endoribonuclease Cas6


Domain annotation for each model (and alignments):
>> CRISPR_Cas6  CRISPR-associated endoribonuclease Cas6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.9   0.0   5.8e-19     1e-14       1      86 []     179     309 ..     179     309 .. 0.74

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 5.8e-19
                                    EEEEEEE-EE....TEEESS--HHHHHHHHHHHHHHHTSS.................EECHHHHHH.............. CS
                    CRISPR_Cas6   1 lrfltPtrfk....krkgllpsprlvfssllrrwnalaglkgk..............ptveeeleg.............. 48 
                                    +rf++Pt+++    + + ++p+ + vfssll +wn+ ++   k              +                      
  gi|116754854|ref|YP_843972.1| 179 IRFISPTCIQyrnsGVCEMFPHREAVFSSLLAKWNSSCPDGFKmdierdemarfiieR-------Pvsyethsamvntvf 251
                                    59********9999999999********************977655544444444431.......033334444455555 PP

                                    .............EEEEEEEE--...HHHECCC....HHHHHHHH-SSSTGGGTTT-E CS
                    CRISPR_Cas6  49 .............GfvGevkysg...eleelek....llrfaeylgvGkktafGlGkv 86 
                                                 Gf+G++ y+     ++++++    l rfae++g+G+  a G+G+v
  gi|116754854|ref|YP_843972.1| 252 drkkghhrpilrpGFTGRCIYTFtddAPDDVRNgilaLSRFAEFSGIGSAVARGCGAV 309
                                    5566677778888********3344533444445555*******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 2218.24
//
Query:       gi|116754855|ref|YP_843973.1|  [L=119]
Description: hypothetical protein Mthe_1563 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-10   39.8  18.4    4.3e-10   39.8  18.4    2.4  2  DUF4064          Protein of unknown function (DUF4064)
  ------ inclusion threshold ------
      0.033   13.8   6.2       0.11   12.1   6.2    1.9  1  DUF4131          Domain of unknown function (DUF4131)
        2.7    8.1  22.0    1.3e+02    2.6  22.0    2.1  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
        2.8    7.3   6.6       0.47    9.9   2.7    1.5  1  DUF373           Domain of unknown function (DUF373)
        2.9    8.3  32.7         14    6.1  17.6    3.3  3  DUF308           Short repeat of unknown function (DUF308)


Domain annotation for each model (and alignments):
>> DUF4064  Protein of unknown function (DUF4064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8  18.4   1.2e-13   4.3e-10       1     103 []       2      84 ..       2      84 .. 0.97
   2 ?    1.4   3.3       0.1   3.8e+02      62      82 ..      83     103 ..      81     115 .. 0.77

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 1.2e-13
                        DUF4064   1 krkaeiiLglIGgilgillglllllflfllssgefsqelteeqalsgedasavleflstllivlgvialiaivlgivgal 80 
                                    +r ae+ Lg++Gg +gil g++++++                    g    av +   ++++vlg++a++++++givg  
  gi|116754855|ref|YP_843973.1|   2 SRNAELALGIVGGLFGILTGIIVMFI--------------------GGIGGAVGAEGAETVTVLGFGAILFGIIGIVGGA 61 
                                    699***********************....................9999****************************** PP

                        DUF4064  81 llkknkkvsGilfiiaailslfl 103
                                    l+ +n++++G+l+++++il++++
  gi|116754855|ref|YP_843973.1|  62 LVTHNHRAGGALMLLSGILGFVT 84 
                                    ********************986 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.1
                        DUF4064  62 ivlgvialiaivlgivgalll 82 
                                    +++  +++ia+++ i+g ++ 
  gi|116754855|ref|YP_843973.1|  83 VTTSAFWIIAGLILIAGGIMA 103
                                    566778888888888887764 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   6.2   3.1e-05      0.11       4      57 ..      46     113 ..       6     119 .] 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.1e-05
                        DUF4131   4 plalvllalllllllllllllrr..............rprrrvllllllllllallgfalrapqpnan 57 
                                    ++ ++l+++++++  +l+  ++r               ++  ++++++l+l++++++++ ++p+p ++
  gi|116754855|ref|YP_843973.1|  46 GFGAILFGIIGIVGGALVTHNHRaggalmllsgilgfVTTSAFWIIAGLILIAGGIMALRSQPTPDQR 113
                                    56666666666666666666666777777777777779*************************99875 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 ?    2.6  22.0     0.037   1.3e+02      24     100 ..      36     112 ..       2     117 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.037
                Phage_holin_3_6  24 aElkeeakragsgagllgaagvlallalllllval.alalaa.lwlaalivaavllvlagvlalvglkklkkakplper 100
                                    aE +e ++ +g ga+l+g+ g+++   ++    a  al+l +   l+++ + a++++++++l++ g+++l++++ +p++
  gi|116754855|ref|YP_843973.1|  36 AEGAETVTVLGFGAILFGIIGIVGGALVTHNHRAGgALML-LsGILGFVTTSAFWIIAGLILIAGGIMALRSQP-TPDQ 112
                                    6777888888888888888888888777777777755555.56899999999****************999955.4654 PP

>> DUF373  Domain of unknown function (DUF373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   2.7   0.00013      0.47     220     281 ..      42     102 ..      33     108 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00013
                         DUF373 220 tfvtyvvallllligiisgyislesvssasvssglltlilafiygavewlalailtaslgki 281
                                    + v  + a+l+ +igi+ g   + + ++   +  ll  il f+ ++  w+++++++++ g +
  gi|116754855|ref|YP_843973.1|  42 VTVLGFGAILFGIIGIVGGALVTHNHRA-GGALMLLSGILGFVTTSAFWIIAGLILIAGGIM 102
                                    45666789999********888666666.667899999**************9999988865 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 ?    1.1   4.9      0.14     5e+02      56      73 .]       9      26 ..       2      30 .. 0.71
   2 ?    6.1  17.6    0.0038        14      24      66 ..      41      83 ..      14      85 .. 0.71
   3 ?    5.2   9.7    0.0074        26      29      72 ..      71     104 ..      71     105 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.14
                         DUF308 56 lglllGilyliaGllllf 73
                                   lg++ G++ ++ G++++f
  gi|116754855|ref|YP_843973.1|  9 LGIVGGLFGILTGIIVMF 26
                                   567777777777777765 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0038
                         DUF308 24 lvllfGilllvsGivqiiaafaarkknrggrwlglllGilyli 66
                                   +v+++G+ ++++Gi++i+++    +++r g+ l+ll+Gil ++
  gi|116754855|ref|YP_843973.1| 41 TVTVLGFGAILFGIIGIVGGALVTHNHRAGGALMLLSGILGFV 83
                                   57899*************88888888999999********986 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.0074
                         DUF308  29 GilllvsGivqiiaafaarkknrggrwlglllGilyliaGllll 72 
                                    G+l+l+sGi++++        + +++w  ++ G++++++G+++l
  gi|116754855|ref|YP_843973.1|  71 GALMLLSGILGFV--------TTSAFW--IIAGLILIAGGIMAL 104
                                    7899999999997........334678..899999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       799  (0.0445647); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 865.63
//
Query:       gi|116754856|ref|YP_843974.1|  [L=379]
Description: signal recognition particle-docking protein FtsY [Methanosaeta thermophila PT]
Scores for complete 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-73  246.0   0.3    3.1e-73  245.6   0.3    1.2  1  SRP54            SRP54-type protein, GTPase domain
    3.5e-12   46.4   0.7    3.5e-12   46.4   0.7    2.0  1  SRP54_N          SRP54-type protein, helical bundle domain
    2.1e-06   28.2   0.5    5.4e-06   26.9   0.2    1.8  2  AAA_17           AAA domain
    2.2e-06   27.5   1.0    3.9e-06   26.7   0.2    1.8  2  AAA_30           AAA domain
    1.3e-05   24.9   0.2     0.0012   18.6   0.1    2.8  3  Thymidylate_kin  Thymidylate kinase
    7.4e-05   22.1   0.1    0.00015   21.2   0.1    1.4  1  Zeta_toxin       Zeta toxin
     0.0003   21.2   0.2     0.0011   19.4   0.2    2.0  1  AAA              ATPase family associated with various cellul
    0.00032   20.6   0.0    0.00062   19.7   0.0    1.4  1  APS_kinase       Adenylylsulphate kinase
    0.00044   20.7   2.2    0.00051   20.5   0.1    2.1  2  AAA_16           AAA ATPase domain
     0.0006   19.9   0.0     0.0018   18.3   0.0    2.0  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    0.00095   19.3   0.0     0.0016   18.6   0.0    1.4  1  AAA_33           AAA domain
     0.0021   18.3   0.2      0.004   17.4   0.2    1.5  1  AAA_28           AAA domain
     0.0023   17.9   1.3       0.02   14.8   1.2    2.3  2  NTPase_1         NTPase
     0.0033   17.3   0.8      0.012   15.5   0.1    2.2  2  MobB             Molybdopterin guanine dinucleotide synthesis
     0.0037   17.3   0.1      0.007   16.4   0.1    1.4  1  ResIII           Type III restriction enzyme, res subunit
     0.0096   15.0   0.4       0.54    9.3   0.0    2.3  2  T2SSE            Type II/IV secretion system protein
  ------ inclusion threshold ------
      0.011   16.7   0.6      0.044   14.8   0.1    2.3  2  LytR_C           LytR cell envelope-related transcriptional a
      0.012   15.1   0.3      0.028   13.9   0.2    1.7  2  KdpD             Osmosensitive K+ channel His kinase sensor d
      0.014   14.4   0.2      0.027   13.4   0.2    1.6  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
      0.017   14.3   0.2      0.026   13.8   0.2    1.2  1  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.018   14.6   0.0      0.032   13.7   0.0    1.3  1  AAA_7            P-loop containing dynein motor region
      0.021   15.2   0.3      0.056   13.8   0.2    1.7  2  AAA_19           AAA domain
      0.023   15.0   0.2      0.063   13.6   0.2    1.7  1  AAA_22           AAA domain
      0.027   13.6   0.0      0.045   12.8   0.0    1.3  1  LpxK             Tetraacyldisaccharide-1-P 4'-kinase
      0.077   12.3   0.1       0.15   11.4   0.1    1.4  1  6PF2K            6-phosphofructo-2-kinase
      0.098   12.1   0.1       0.19   11.2   0.1    1.4  1  KTI12            Chromatin associated protein KTI12
       0.16   11.7   0.3       0.24   11.1   0.3    1.4  1  AAA_24           AAA domain
       0.26   11.4   1.2        1.8    8.7   1.2    2.3  1  MMR_HSR1         50S ribosome-binding GTPase


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 !  245.6   0.3   4.9e-76   3.1e-73       2     196 .]     184     378 ..     183     378 .. 0.99

  Alignments for each domain:
  == domain 1  score: 245.6 bits;  conditional E-value: 4.9e-76
                                    EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHHHHH CS
                          SRP54   2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeavekake 81 
                                      il+vG++G+GKTt++aK+a++lk++g++v+l+a DtfRa+A+eQL+t++++l+ +vik+k++ dpaav+++a+e ak+
  gi|116754856|ref|YP_843974.1| 184 VKILFVGVNGTGKTTSIAKVARYLKERGYSVVLAAGDTFRAGAIEQLETHGQRLDLKVIKHKTGGDPAAVIFDAIEYAKA 263
                                    579***************************************************************************** PP

                                    TTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSSSSTTHHHH CS
                          SRP54  82 ekidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltklDgdakgGaals 161
                                    +k dvvl DTaGrl+++ +lm+++kki +v+kpd  ++v +a++g++av+ a+ F+e+v itg iltk D+dakgG+a+s
  gi|116754856|ref|YP_843974.1| 264 HKKDVVLADTAGRLHTNINLMDQMKKIVRVTKPDMLIFVDEAIAGNDAVERARLFNESVPITGTILTKTDADAKGGSAIS 343
                                    ******************************************************************************** PP

                                    HHHHHTS-EEEEE-SSSTTGEEE--HHHHHHHHHT CS
                          SRP54 162 iaaelklPikfigvGekiedleefdperlvsrllg 196
                                    ia+ +++Pi+f+gvG+ + dl +fdp +lv+rllg
  gi|116754856|ref|YP_843974.1| 344 IAHVTGKPIIFLGVGQDYPDLVKFDPVWLVDRLLG 378
                                    *********************************95 PP

>> SRP54_N  SRP54-type protein, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   0.7   5.4e-15   3.5e-12      14      75 .]      98     162 ..      87     162 .. 0.87

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 5.4e-15
                                    CSSCGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTS...S-HHHHHHHHHHHHH CS
                        SRP54_N  14 gkskideedleealkeleeaLleaDVgvkvvkklienvkkkavgekk...lkpkqqvkkivkdeL 75 
                                    +   ide dlee l+ le+aLle+DV+++v+++++++vk + vg+kk     +++ v+++++ +L
  gi|116754856|ref|YP_843974.1|  98 REVIIDERDLEEPLWGLEMALLESDVALPVAEEIVSSVKSSLVGSKKkigSDTGDLVESALRAAL 162
                                    34569***************************************888877779999999998776 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       6.8   4.3e+03      58      84 ..      13      39 ..       3      56 .. 0.72
   2 !   26.9   0.2   8.5e-09   5.4e-06       1     109 [.     189     303 ..     189     318 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 6.8
                                   HHHHHHHHHHHHHSSEEEEEE-SEEEE CS
                         AAA_17 58 qkeaaekiaeeakkkgvlvdghprike 84
                                    + + ++i e+a+ +  ++d +  + +
  gi|116754856|ref|YP_843974.1| 13 KESLTNRILEKAAGSIPIIDNKSETAA 39
                                   567888999998888889988776544 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 8.5e-09
                                    EE-TTSSHHHHHHHHHHHH...TEE.EEEHHHHHHHHHHTT.TSHSSHHHHCTSHHHHHHHHHHHHHHHH..HHHHHSSE CS
                         AAA_17   1 lGgPGsGKgtqceklveky...gft.hlsaGdllreeakrg.glakardemrklpleekkelqkeaaeki..aeeakkkg 73 
                                    +G+ G GK+t ++k+++ +   g++ +l aGd +r+ a ++ +   +r +++  +++   +  + + ++i  a++ kk+ 
  gi|116754856|ref|YP_843974.1| 189 VGVNGTGKTTSIAKVARYLkerGYSvVLAAGDTFRAGAIEQlETHGQRLDLKVIKHKTGGDPAAVIFDAIeyAKAHKKDV 268
                                    79*************976555577725799*****987655443333333333344444444444444442133447888 PP

                                    EEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE CS
                         AAA_17  74 vlvdghprikeqagfldglpkevleelkpdaiille 109
                                    vl d+  r+ ++  ++d+++ ++++  kpd++i+++
  gi|116754856|ref|YP_843974.1| 269 VLADTAGRLHTNINLMDQMK-KIVRVTKPDMLIFVD 303
                                    999*****999888877777.589**********98 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0         5   3.2e+03      69      96 ..      72     104 ..      37     106 .. 0.59
   2 !   26.7   0.2   6.2e-09   3.9e-06      22     114 ..     187     293 ..     179     322 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 5
                         AAA_30  69 eastiakllkrlk.....grarlepgtllivDE 96 
                                    +a t+++ ++  k     ++++l  ++ +i+DE
  gi|116754856|ref|YP_843974.1|  72 QAGTVHEAVRPPKislvdKAKSLILEREVIIDE 104
                                    566666666555577776556666677777777 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 6.2e-09
                         AAA_30  22 vltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieastiakllkrlk.............grarlep 88 
                                    + +G+ GtGKtt+++++++ ++++g++v+++A     A +++ +l++++++++  + ++k             + a+ ++
  gi|116754856|ref|YP_843974.1| 187 LFVGVNGTGKTTSIAKVARYLKERGYSVVLAAGDTFRAGAIE-QLETHGQRLDLKVIKHKtggdpaavifdaiEYAKAHK 265
                                    568******************************999999998.7788888887777677778888888888885567778 PP

                         AAA_30  89 gtllivDEagmv..dtkqlaallkaaek 114
                                    +++++ D ag +  +++ ++++ k+++ 
  gi|116754856|ref|YP_843974.1| 266 KDVVLADTAGRLhtNINLMDQMKKIVRV 293
                                    8888888888774433455555544443 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   1.9e-06    0.0012       3      30 ..     190     217 ..     188     241 .. 0.85
   2 ?   -1.3   0.0       2.4   1.5e+03     105     133 ..     236     265 ..     226     267 .. 0.68
   3 ?    3.0   0.0      0.11        74     106     137 ..     283     317 ..     274     325 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.9e-06
                                    ESTTSSHHHHHHHHHHHHHHTTE.EEEE CS
                Thymidylate_kin   3 GlDGaGKttqaellkerlkeegikvvlt 30 
                                    G++G+GKtt +++++++lke+g++vvl 
  gi|116754856|ref|YP_843974.1| 190 GVNGTGKTTSIAKVARYLKERGYSVVLA 217
                                    9***********************8775 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.4
                                    HHHHHHGGGTTS.E-SEEEEEESSHHHHHT CS
                Thymidylate_kin 105 dlvlslnedvll.kPdltflldvdpevalk 133
                                    +l l++ ++ ++  P ++++  ++ ++a k
  gi|116754856|ref|YP_843974.1| 236 RLDLKVIKHKTGgDPAAVIFDAIEYAKAHK 265
                                    44444444444459*******999888766 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.11
                                    HHHHHGGGTTS.E-SEEEEEE..SSHHHHHTSCCT CS
                Thymidylate_kin 106 lvlslnedvll.kPdltflld..vdpevalkRlak 137
                                    l+ ++++ v   kPd+ +++d  +  + a++R++ 
  gi|116754856|ref|YP_843974.1| 283 LMDQMKKIVRVtKPDMLIFVDeaIAGNDAVERARL 317
                                    555555555447********977888888888875 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.1   2.3e-07   0.00015      10     119 ..     177     289 ..     168     314 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 2.3e-07
                     Zeta_toxin  10 ypsqerPklillgGqpGAGKselaellkdele.rqgnvvrldpDdlRelhPeyeeilka..dpkkaseltqkdaselvek 86 
                                    +++  +P+ il +G  G GK++ +++++++l+ r+ +vv   +D++R+   e  e   +  d k     t  d   +   
  gi|116754856|ref|YP_843974.1| 177 IKNTPKPVKILFVGVNGTGKTTSIAKVARYLKeRGYSVVLAAGDTFRAGAIEQLETHGQrlDLKVIKHKTGGDPAAVIFD 256
                                    45669***************************55556666678****965444443333246677778888999999999 PP

                     Zeta_toxin  87 llqeaiengyniivegtlrspdvvkklaealkk 119
                                    ++++a  ++ ++++  t    ++  +l++++kk
  gi|116754856|ref|YP_843974.1| 257 AIEYAKAHKKDVVLADTAGRLHTNINLMDQMKK 289
                                    999999999999998888888877777777765 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.2   1.7e-06    0.0011       1      74 [.     186     281 ..     186     320 .. 0.60

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.7e-06
                                    EEEESSTTSSHHHHHHHHHHHHT...HEEEEEETTTCSSS....................STTHHHHHHHHHHHHHHHTS CS
                            AAA   1 vllyGppGtGKTllakavakelg...vefleisgsellsk....................yvgesekkirelfkeakeka 57 
                                    +l++G  GtGKT+ +  va+ l+    +++   g +++                      + g+ ++ i + ++ ak+++
  gi|116754856|ref|YP_843974.1| 186 ILFVGVNGTGKTTSIAKVARYLKergYSVVLAAGDTFRAGaieqlethgqrldlkvikhkTGGDPAAVIFDAIEYAKAHK 265
                                    69*******************96443444444444444333444333444444445555555555555555555555554 PP

                                    TSEEEEEETGGGHHHHH CS
                            AAA  58 kpsilfiDEidalaksr 74 
                                     + +++ D + +l+++ 
  gi|116754856|ref|YP_843974.1| 266 -KDVVLADTAGRLHTNI 281
                                    .5666666555555554 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   9.7e-07   0.00062       2      49 ..     183     230 ..     182     241 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 9.7e-07
                                    -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT- CS
                     APS_kinase   2 gvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdL 49 
                                    +v +++ G+ g+GK+t   +++++L+e+g+sv+l  Gd+ R g  ++L
  gi|116754856|ref|YP_843974.1| 183 PVKILFVGVNGTGKTTSIAKVARYLKERGYSVVLAAGDTFRAGAIEQL 230
                                    6789*************************************9988777 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   0.2       5.8   3.7e+03     124     124 ..      92      92 ..      13     169 .. 0.58
   2 !   20.5   0.1   7.9e-07   0.00051      24     102 ..     183     247 ..     173     305 .. 0.55

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 5.8
                         AAA_16 124 k 124
                                    k
  gi|116754856|ref|YP_843974.1|  92 K 92 
                                    1 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 7.9e-07
                         AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekle 102
                                    p  +l++G  G+GK++ + +++r+l+++g  ++ +  d +              r + ++ql+++ +  +l   ++k  
  gi|116754856|ref|YP_843974.1| 183 PVKILFVGVNGTGKTTSIAKVARYLKERGYSVVLAAGDTF--------------RAGAIEQLETHGQRLDLKVIKHKTG 247
                                    46689**********************9877788888887..............4455555555544433333333333 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   2.8e-06    0.0018       9      37 ..     193     221 ..     186     353 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.8e-06
                                    TSSHHHHHHHHHHHHHHTT--EEEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA   9 GvGKTtlaanLaralarrglrVllvDaDp 37 
                                    G+GKTt  a+ ar+l++rg+ V+l   D+
  gi|116754856|ref|YP_843974.1| 193 GTGKTTSIAKVARYLKERGYSVVLAAGDT 221
                                    9**********************986665 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   2.5e-06    0.0016       2      79 ..     186     278 ..     186     320 .. 0.64

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.5e-06
                         AAA_33   2 vllvGlpGsGKstlaerllkklg.....avllssdtlrr.rlfg..tdqqsktdytrvldr.....lyqilnelarkals 68 
                                    +l+vG++G+GK+t + ++++ l+     +vl + dt+r  +++   t+ q++    +v ++       + +++ ++ a +
  gi|116754856|ref|YP_843974.1| 186 ILFVGVNGTGKTTSIAKVARYLKergysVVLAAGDTFRAgAIEQleTHGQRL--DLKVIKHktggdPAAVIFDAIEYAKA 263
                                    69************99986666666686666778998885555543333332..22222222223344467788888888 PP

                         AAA_33  69 agrnvildat....n 79 
                                    ++++v+l  t     
  gi|116754856|ref|YP_843974.1| 264 HKKDVVLADTagrlH 278
                                    999988866644441 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.2   6.2e-06     0.004       1      48 [.     185     239 ..     185     279 .. 0.59

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 6.2e-06
                         AAA_28   1 kivitGgestGKTtlleaLa....argypvv...pEaareileeklakgedalpw 48 
                                    ki ++G  +tGKTt +++ a    +rgy+vv    +++r    e+l+++++ l+ 
  gi|116754856|ref|YP_843974.1| 185 KILFVGVNGTGKTTSIAKVArylkERGYSVVlaaGDTFRAGAIEQLETHGQRLDL 239
                                    799*************8888555466***99555555555555666666665553 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   1.2   3.2e-05      0.02       2      30 ..     186     214 ..     185     305 .. 0.89
   2 ?    0.7   0.1      0.66   4.2e+02      86     135 ..     255     305 ..     249     325 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.2e-05
                                    EEEE--TTSSHHHHHHHHHHHH...GGGE CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkv 30 
                                    ++  G  G+GKtT + kv++ lk++g++v
  gi|116754856|ref|YP_843974.1| 186 ILFVGVNGTGKTTSIAKVARYLKERGYSV 214
                                    5667999********************98 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.66
                                    HHHHHHHH.HHH-EEEE---STTGGG-HHHHHHHHHHHT.TTSEEEEE--SS CS
                       NTPase_1  86 lealrkal.seadviviDEiGkmElkskkfkeaveevLk.sekpvlavihrr 135
                                     +a++ a  +++dv++ D  G++  +++ + ++++++++ +++ +l+ + ++
  gi|116754856|ref|YP_843974.1| 255 FDAIEYAKaHKKDVVLADTAGRLHTNINLM-DQMKKIVRvTKPDMLIFVDEA 305
                                    566776666899999999999999888755.567777776666666666655 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   1.9e-05     0.012       2      31 ..     186     215 ..     185     222 .. 0.93
   2 ?   -0.5   0.1       1.6   1.1e+03      20      63 ..     227     271 ..     218     302 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.9e-05
                           MobB   2 lgivgksgsGKTtLleklipelkarglrvg 31 
                                    + +vg +g+GKTt + k+ + lk+rg++v 
  gi|116754856|ref|YP_843974.1| 186 ILFVGVNGTGKTTSIAKVARYLKERGYSVV 215
                                    579************************995 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.6
                           MobB  20 ipelkarglr..vgtiKhahhgfdvdkpgkDsyrhrkAGAkevlva 63 
                                    i++l+ +g r  + +iKh++ g d      D+ +++kA  k v++a
  gi|116754856|ref|YP_843974.1| 227 IEQLETHGQRldLKVIKHKTGG-DPAAVIFDAIEYAKAHKKDVVLA 271
                                    5666666654114678887543.44444555566665555555554 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 !   16.4   0.1   1.1e-05     0.007      21     141 ..     175     305 ..     151     320 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.1e-05
                                    .....TTS..EEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B- CS
                         ResIII  21 s...krdk..rglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseaykeigkkvsgdkkk 95 
                                    +   +  k  ++l++   GtGKT  +ak++++l++ g+    ++l+ + +    ++e+++   +  + ++ k ++g    
  gi|116754856|ref|YP_843974.1| 175 EfikNTPKpvKILFVGVNGTGKTTSIAKVARYLKERGY---SVVLAAGDTFRAGAIEQLETHGQRLDLKVIKHKTGGDPA 251
                                    143344444599******************99999887...6999******99999999999998888755555555555 PP

                                    -.............-SEEEE.EHHHHHHTH........HHHTTT-S.EEEEETG CS
                         ResIII  96 a......kekdstnkkilvt.tiqsldadseeeeeeseellrdrfd.viiiDEa 141
                                    a      +  ++++k+++++ t  +l+ +++  +++++  + ++ d +i++DEa
  gi|116754856|ref|YP_843974.1| 252 AvifdaiEYAKAHKKDVVLAdTAGRLHTNINLMDQMKKIVRVTKPDmLIFVDEA 305
                                    558888855555566655552667888888776777766666666667888997 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 !    9.3   0.0   0.00084      0.54     116     161 ..     171     215 ..     123     231 .. 0.85
   2 ?    3.7   0.1     0.041        26     162     204 ..     253     300 ..     237     316 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00084
                          T2SSE 116 ekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderiv 161
                                     +++e++++   +   il+ G  g+GKtt++  +  +++++   +v
  gi|116754856|ref|YP_843974.1| 171 FDFDEFIKNT-PKPVKILFVGVNGTGKTTSIAKVARYLKERGYSVV 215
                                    5678888887.78899***************999999999855555 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.041
                          T2SSE 162 tvEDpvEiqleganqvqlnak....kakvtfadllraaLRl.rPDrim 204
                                    ++ D++E+  ++++ v l +     ++++++ d +++++R  +PD+++
  gi|116754856|ref|YP_843974.1| 253 VIFDAIEYAKAHKKDVVLADTagrlHTNINLMDQMKKIVRVtKPDMLI 300
                                    677**********999999988999999************638**864 PP

>> LytR_C  LytR cell envelope-related transcriptional attenuator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       7.1   4.6e+03      68      68 ..      53      53 ..      12      90 .. 0.56
   2 ?   14.8   0.1   6.8e-05     0.044       7      37 ..     191     219 ..     191     279 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 7.1
                         LytR_C 68 q 68
                                    
  gi|116754856|ref|YP_843974.1| 53 P 53
                                   1 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 6.8e-05
                         LytR_C   7 lNgtgvsGlAarvadaLeerGftvgevgnag 37 
                                    +Ngtg++   a+va++L+erG+ v+   +ag
  gi|116754856|ref|YP_843974.1| 191 VNGTGKTTSIAKVARYLKERGYSVVL--AAG 219
                                    5*********************7765..233 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 ?   -3.6   0.0       9.9   6.4e+03     143     169 ..      13      40 ..       7      56 .. 0.65
   2 ?   13.9   0.2   4.4e-05     0.028       6      97 ..     185     282 ..     182     296 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 9.9
                           KdpD 143 retvPdevleeA.develvDltpeeLle 169
                                    +e + +++le+A  ++ ++D + e+  +
  gi|116754856|ref|YP_843974.1|  13 KESLTNRILEKAaGSIPIIDNKSETAAA 40 
                                    5666677776541578888877776555 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 4.4e-05
                           KdpD   6 kiflGaapGvGktyamLeeaqelkeegvdvviglvethgrketeallegleviprkeveykgk...eleeld.ldailar 81 
                                    ki +  ++G Gkt ++ + a+ lke+g  vv+++ +t +   +e+l ++ + ++ k +++k     +   +d ++ + a+
  gi|116754856|ref|YP_843974.1| 185 KILFVGVNGTGKTTSIAKVARYLKERGYSVVLAAGDTFRAGAIEQLETHGQRLDLKVIKHKTGgdpAAVIFDaIEYAKAH 264
                                    78888899***************************999999888888887888777777764311123334434556677 PP

                           KdpD  82 kpevvlvDela..htnap 97 
                                    k +vvl D  +  htn++
  gi|116754856|ref|YP_843974.1| 265 KKDVVLADTAGrlHTNIN 282
                                    788888887653355655 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   4.3e-05     0.027      22      66 ..     176     220 ..     153     298 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.3e-05
                                    HGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE- CS
                           MeaB  22 llakaGraqvvGltGvPGaGkstlvealglelrrrGkrvavlavD 66 
                                     ++++ +  ++ + Gv G+Gk t + +++  l++rG+ v + a D
  gi|116754856|ref|YP_843974.1| 176 FIKNTPKPVKILFVGVNGTGKTTSIAKVARYLKERGYSVVLAAGD 220
                                    56667777888999************************9776654 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   4.1e-05     0.026       7     131 ..     189     303 ..     184     308 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.1e-05
                        DUF2075   7 tGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakkeekkkkkeafeklssfinnlsefkkaeekkee 86 
                                     Gv GtGKt    +++  l   +e+ ++v+l     +++   e+l+ +   ++ + ++ k ++   ++    +a+e ++ 
  gi|116754856|ref|YP_843974.1| 189 VGVNGTGKTTSIAKVARYL---KERGYSVVLAAGDTFRAGAIEQLETHG--QRLDLKVIKHKTGGDPAAVIFDAIEYAKA 263
                                    49****************9...777788888888999999999998777..7777788888887777776688999**** PP

                        DUF2075  87 pkedvvivDEAhrlltksdqaekqseenqlkelmkrak.vvvalvD 131
                                     k dvv+ D A rl t      + +  +q+k++++  k  ++++vD
  gi|116754856|ref|YP_843974.1| 264 HKKDVVLADTAGRLHT------NINLMDQMKKIVRVTKpDMLIFVD 303
                                    ****************......555567777777774445555556 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 ?   13.7   0.0     5e-05     0.032      34      64 ..     184     214 ..     173     218 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5e-05
                          AAA_7  34 kpvllvGptGtGKtviikdllkkldkekyls 64 
                                     ++l+vG  GtGKt+ i ++ + l+++ y++
  gi|116754856|ref|YP_843974.1| 184 VKILFVGVNGTGKTTSIAKVARYLKERGYSV 214
                                    579*******************999988876 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       7.4   4.7e+03      69     110 ..      73     104 ..      37     122 .. 0.59
   2 ?   13.8   0.2   8.8e-05     0.056      13     111 ..     186     305 ..     175     328 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 7.4
                         AAA_19  69 atTiHrlalldfddlltealelleeaeeekklqeeellivDE 110
                                    a T+H+   +   ++      l  +  + k l  e  +i+DE
  gi|116754856|ref|YP_843974.1|  73 AGTVHEA--VRPPKIS-----L-VD--KAKSLILEREVIIDE 104
                                    5566655..2221111.....1.11..222222344566676 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 8.8e-05
                         AAA_19  13 llvtaGpGtGKTrvlkhivallvelggvkpeeillv..aftgrAakelrerlaalgae...................... 68 
                                    +l ++  GtGKT+ + ++ ++l+e+g      +l++  +f   A ++l++  + l+++                      
  gi|116754856|ref|YP_843974.1| 186 ILFVGVNGTGKTTSIAKVARYLKERG-Y--SVVLAAgdTFRAGAIEQLETHGQRLDLKvikhktggdpaavifdaieyak 262
                                    5567889*********9999999999.3..34555522455556788888776666667777788888777766666655 PP

                         AAA_19  69 ........atTiHrlalldfddlltealelleeaeeekklqeee.llivDEf 111
                                            a+T  rl          +  +l+++ ++   +++ + l++vDE+
  gi|116754856|ref|YP_843974.1| 263 ahkkdvvlADTAGRL--H-------TNINLMDQMKKIVRVTKPDmLIFVDEA 305
                                    555555555555555..3.......333333333333444455558999996 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   9.8e-05     0.063       8     112 ..     186     290 ..     185     307 .. 0.46

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.8e-05
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka.........erlsseel 78 
                                    ++ +G  GtGKTt+++++++ l+e+          ++v l+++ + +  + e l+  g+   +          +++  ++
  gi|116754856|ref|YP_843974.1| 186 ILFVGVNGTGKTTSIAKVARYLKER---------GYSVVLAAGDTFRAGAIEQLETHGQ---RldlkvikhkTGGDPAAV 253
                                    5789*****************9544.........3333333333222221111111111...111133334433444444 PP

                         AAA_22  79 lealeqalraravielliiDEaqhlrs.....eealeeL 112
                                    +    ++++a+++  +++ D a +l +     +++++++
  gi|116754856|ref|YP_843974.1| 254 IFDAIEYAKAHKK-DVVLADTAGRL-HtninlMDQMKKI 290
                                    4444444444444.45555555555.2222233333333 PP

>> LpxK  Tetraacyldisaccharide-1-P 4'-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   7.1e-05     0.045      27      69 ..     176     215 ..     157     219 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.1e-05
                                    SS--B--SS-EEEEEESBSS-HSHHHHHHHHHHHTTTS..-EE CS
                           LpxK  27 llkserlpvpVivVGNitvGGtGKTPlvialvkllqarglkvg 69 
                                    ++k++  pv+++ VG   v GtGKT  ++ ++++l++rg+ v+
  gi|116754856|ref|YP_843974.1| 176 FIKNTPKPVKILFVG---VNGTGKTTSIAKVARYLKERGYSVV 215
                                    566777799999999...99********************986 PP

>> 6PF2K  6-phosphofructo-2-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00023      0.15      10      43 ..     180     213 ..     174     246 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00023
                                    ..S-EEEEEESSTTSSHHHHHHHHHHHHHHTT-- CS
                          6PF2K  10 knsklvivlvGLpargKtyiskkltrylkwlgvr 43 
                                    + +++ i++vG   +gKt+   k+ rylk  g++
  gi|116754856|ref|YP_843974.1| 180 TPKPVKILFVGVNGTGKTTSIAKVARYLKERGYS 213
                                    678899***********************66654 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00029      0.19       4      86 ..     186     265 ..     185     295 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00029
                                    EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH.TTSSS--GGGHHHHHHHHHHHHHHHHTT.SEEEE-S---SH CS
                          KTI12   4 vvltGlPssGKstrakeLakaleeekrsvvviddeslgiekdsykdsakekalRsslrsavkrdLskekvVIvDslnyik 83 
                                    +++ G+  +GK+t  +++a++l+e+++svv+   ++++    +   + +    R +l+   ++       VI D++ y k
  gi|116754856|ref|YP_843974.1| 186 ILFVGVNGTGKTTSIAKVARYLKERGYSVVLAAGDTFRAGAIE---QLETHGQRLDLKVIKHKTGGDPAAVIFDAIEYAK 262
                                    7899****************************99999843332...2222222333333333344455667777777776 PP

                                    HHH CS
                          KTI12  84 gfR 86 
                                       
  gi|116754856|ref|YP_843974.1| 263 AHK 265
                                    665 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.3   0.00037      0.24       2      24 ..     183     204 ..     182     297 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00037
                         AAA_24   2 klkiliyGpsgiGKTtlakelgp 24 
                                    ++kil +G +g+GKTt++++   
  gi|116754856|ref|YP_843974.1| 183 PVKILFVGVNGTGKTTSIAKV-A 204
                                    689***************998.3 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   1.2    0.0028       1.8       2      84 ..     186     304 ..     185     331 .. 0.51

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0028
                                    EEEEESTTSSHHHHHHHHHT......STEEESSSTTSSSSE.EEEEEEETTEE........................... CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltg......ekaivsdkpgtTrdi.negrvklkgke........................... 47 
                                    +++vG   +GK+t i +  +          v   +g T      ++++++g++                           
  gi|116754856|ref|YP_843974.1| 186 ILFVGVNGTGKTTSIAKVARylkergY--SVVLAAGDTFRAgAIEQLETHGQRldlkvikhktggdpaavifdaieyaka 263
                                    667777777777777777654433220..333333333322222222222211233333333333334444444444444 PP

                                    ....EEEEECGGCSSHHHHHHHHHHHHHHHHC...TSEEEEEEE CS
                       MMR_HSR1  48 ....ielvDtpGliegaseekglgkaflalee...adlillvvd 84 
                                        ++l+Dt+G ++   ++ +l ++++++ +    d++++v +
  gi|116754856|ref|YP_843974.1| 264 hkkdVVLADTAGRLH---TNINLMDQMKKIVRvtkPDMLIFVDE 304
                                    4444********666...55566666665555321588777754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); 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: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.45
# Mc/sec: 2528.47
//
Query:       gi|116754857|ref|YP_843975.1|  [L=153]
Description: prefoldin subunit alpha [Methanosaeta thermophila PT]
Scores for complete 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-25   88.6   0.5    3.2e-25   88.4   0.5    1.1  1  Prefoldin       Prefoldin subunit
    1.2e-05   25.3   3.8     0.0032   17.4   0.6    2.3  2  Prefoldin_2     Prefoldin subunit
    0.00016   22.2   5.2       0.03   14.9   1.0    2.0  2  APG6_N          Apg6 coiled-coil region
     0.0048   16.3   0.1     0.0058   16.1   0.1    1.2  1  FliD_C          Flagellar hook-associated protein 2 C-terminu
  ------ inclusion threshold ------
      0.013   15.9   6.1      0.084   13.2   2.0    2.1  2  OmpH            Outer membrane protein (OmpH-like)
      0.016   14.0   1.1      0.016   14.0   1.1    1.8  2  Tektin          Tektin family
      0.032   14.6   8.5        0.8   10.1   0.1    2.5  2  V-SNARE         Vesicle transport v-SNARE protein N-terminus
      0.065   13.3   8.1       0.16   12.1   3.3    2.3  2  DHR10           Designed helical repeat protein 10 domain
      0.078   13.4   7.2      0.051   14.0   2.9    2.0  2  HrpB7           Bacterial type III secretion protein (HrpB7)
      0.082   13.2   5.6       0.33   11.2   0.5    2.9  3  WXG100          Proteins of 100 residues with WXG
       0.11   12.6   0.6        0.4   10.7   0.2    1.9  2  DUF1664         Protein of unknown function (DUF1664)
       0.11   12.8   3.0        0.1   12.9   1.3    1.8  2  DUF4226         Domain of unknown function (DUF4226)
       0.13   12.5   2.7        0.4   10.8   2.7    1.8  1  DUF4055         Domain of unknown function (DUF4055)
       0.14   11.0   2.1       0.12   11.2   1.1    1.3  2  Fmp27_WPPW      RNA pol II promoter Fmp27 protein domain
       0.15   12.4   3.4       0.23   11.8   0.9    2.1  2  Rx_N            Rx N-terminal domain
       0.16   10.7   0.7       0.22   10.3   0.7    1.1  1  IDO             Indoleamine 2,3-dioxygenase
       0.22   11.4   6.1       0.17   11.8   1.8    2.1  2  JAKMIP_CC3      JAKMIP CC3 domain
       0.25   11.8   4.5       0.52   10.8   1.1    2.2  2  DUF4140         N-terminal domain of unknown function (DUF414
       0.36   10.7   2.9       0.25   11.2   0.5    1.8  2  Nsp1_C          Nsp1-like C-terminal region
       0.38   10.9   3.6       0.75   10.0   3.6    1.5  1  DUF5446         Family of unknown function (DUF5446)
       0.42   10.2   7.2       0.56    9.9   4.3    2.1  2  YkyA            Putative cell-wall binding lipoprotein
       0.43   10.1   6.0       0.55    9.8   1.6    2.0  2  HAUS-augmin3    HAUS augmin-like complex subunit 3
        0.5   10.6   7.5        3.6    7.9   2.9    2.2  2  Seryl_tRNA_N    Seryl-tRNA synthetase N-terminal domain
       0.55    8.8   3.4       0.54    8.8   1.4    1.7  2  AAA_13          AAA domain
       0.63   10.1   8.0        2.4    8.2   2.6    2.4  2  CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein C
       0.67    8.8   6.8       0.47    9.3   2.8    1.9  2  Spc7            Spc7 kinetochore protein
       0.76   10.2   4.8        3.2    8.2   0.3    2.6  3  FlaC_arch       Flagella accessory protein C (FlaC)
          1    8.8   9.0       0.37   10.2   6.2    1.6  2  DUF4349         Domain of unknown function (DUF4349)
          3    8.5   7.6       0.73   10.5   3.1    2.1  2  SlyX            SlyX


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 !   88.4   0.5   5.2e-28   3.2e-25       1     117 [.      22     138 ..      22     141 .. 0.98

  Alignments for each domain:
  == domain 1  score: 88.4 bits;  conditional E-value: 5.2e-28
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT.-TT-EEEEEEETTEEEEEE--STTEEEEEEETTEEEEEEHHHHHH CS
                      Prefoldin   1 lkeeleslqaelaqlkeaieelektletlktlkkedegkevlvplgaglyvkaevkdtdkvlvdlGagyyveksleeAie 80 
                                    +++e+esl +el+ ++ + e l+k+++++  l+k+ eg+e+lvp+g+g++++a++ + d+v+v++G g+++ek++eeA+e
  gi|116754857|ref|YP_843975.1|  22 YQAEAESLVRELGLIQMTAEGLDKAISAIGALSKAAEGQEMLVPIGSGSFAYAKLSSADRVVVNVGGGVSIEKPAEEAME 101
                                    899***************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Prefoldin  81 llkkkleelekqlekleeeleklkdqittleanlaql 117
                                     l  + + ++++++k++e+l+k+ +++  ++a+l++l
  gi|116754857|ref|YP_843975.1| 102 MLRARRSAISESSKKINEALAKIEQEMARIQAALERL 138
                                    *********************************9987 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.1    0.0024       1.5       2      43 ..      14      55 ..      13      64 .. 0.89
   2 !   17.4   0.6   5.1e-06    0.0032      43     100 ..      79     136 ..      74     145 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0024
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-T CS
                    Prefoldin_2  2 elinkfqqlqqqlqqlaqqikqletqlkelelvleelellde 43
                                   +li  +qq+q++ + l+ ++  +++  + l++++ ++  l +
  gi|116754857|ref|YP_843975.1| 14 QLIVAYQQYQAEAESLVRELGLIQMTAEGLDKAISAIGALSK 55
                                   78999*****************************99988765 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 5.1e-06
                                    TT--EEEEETTEEEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Prefoldin_2  43 edtkvyklvGdvlvkqdkeevkeeLeerketlekeiktlekqleklekeleelkeelq 100
                                     d+ v    G+v ++++ ee+ e+L +r   +++ +k++++ l k+e+e++ +++ l 
  gi|116754857|ref|YP_843975.1|  79 ADRVVVNVGGGVSIEKPAEEAMEMLRARRSAISESSKKINEALAKIEQEMARIQAALE 136
                                    5666666678999****************************************99986 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.2     0.002       1.3      46      98 ..       9      61 ..       2      63 .. 0.85
   2 !   14.9   1.0   4.8e-05      0.03      51      99 ..      95     143 ..      79     148 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.002
                         APG6_N 46 deeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeee 98
                                   +++ ++l   +++ ++e e+l++eL  ++ + e l+++++a+ + ++a e +e
  gi|116754857|ref|YP_843975.1|  9 ENQARQLIVAYQQYQAEAESLVRELGLIQMTAEGLDKAISAIGALSKAAEGQE 61
                                   3467788899******************************9998888877666 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 4.8e-05
                         APG6_N  51 eleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeee 99 
                                     +ee +e l++ +++  e  k++ ++ +++e+e+a +++ le+le+e +
  gi|116754857|ref|YP_843975.1|  95 PAEEAMEMLRARRSAISESSKKINEALAKIEQEMARIQAALERLERELQ 143
                                    4566666677777777777777777777777777777777777777655 PP

>> FliD_C  Flagellar hook-associated protein 2 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   9.3e-06    0.0058     164     227 ..      79     145 ..      19     148 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 9.3e-06
                                    ......SXSHHHHHHHHHHHHH...STT.SHHHHHHHHXXXXHHHHHHHHHHHHHCHHHHHHHHHHH CS
                         FliD_C 164 ektvtsdsglatrlenllksyv...kssngtlqtasknltkqikdldkkiedldkrletleerlkkq 227
                                     ++v+ + g   ++e+ +++ +   +++ +++ ++sk++++ + +++++++ ++ +le le++l+kq
  gi|116754857|ref|YP_843975.1|  79 ADRVVVNVGGGVSIEKPAEEAMemlRARRSAISESSKKINEALAKIEQEMARIQAALERLERELQKQ 145
                                    455555555555555555555555588889***********************************99 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1     0.054        33      64     104 ..      11      52 ..       2      80 .. 0.51
   2 ?   13.2   2.0   0.00014     0.084       9      45 ..     109     145 ..      99     147 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.054
                                    HHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHHHHHHHH CS
                           OmpH  64 elqkkeqelqqkqqqka....qelqkkqqellkpildkinkaike 104
                                    + +++  ++qq +q++a    +el   q  ++++ ldk+  ai +
  gi|116754857|ref|YP_843975.1|  11 QARQLIVAYQQ-YQAEAeslvRELGLIQ--MTAEGLDKAISAIGA 52 
                                    33444444444.3333311234444444..333334444444444 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00014
                                    HHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           OmpH   9 kileespegkaaqeqlekkfkklqaeleakekelqkl 45 
                                     i e+s++ ++a +++e++ +++qa+le++e+elqk+
  gi|116754857|ref|YP_843975.1| 109 AISESSKKINEALAKIEQEMARIQAALERLERELQKQ 145
                                    57788999999***********************985 PP

>> Tektin  Tektin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.37   2.3e+02     258     291 ..      17      50 ..       9      59 .. 0.69
   2 ?   14.0   1.1   2.6e-05     0.016      44      89 ..      99     144 ..      91     151 .. 0.59

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.37
                         Tektin 258 daknkleeqlkkvleeiaeleknieeLekairdk 291
                                     a ++ + + + +++e+  ++++ e L kai + 
  gi|116754857|ref|YP_843975.1|  17 VAYQQYQAEAESLVRELGLIQMTAEGLDKAISAI 50 
                                    5677777777777777777888888888777665 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 2.6e-05
                         Tektin  44 snkrLeeRiediefwkeeLekeleelkeeieaLeeekrrlekalea 89 
                                    + + L++R + i+   ++++++l+++++e+  ++++ +rle++l++
  gi|116754857|ref|YP_843975.1|  99 AMEMLRARRSAISESSKKINEALAKIEQEMARIQAALERLERELQK 144
                                    4455566666666666666666666666666666666666666654 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 ?   10.1   0.1    0.0013       0.8      17      46 ..       6      35 ..       2      49 .. 0.87
   2 ?    6.6   4.0     0.017        10      16      50 ..     110     144 ..      92     149 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0013
                        V-SNARE 17 slageerkaalreiekkldeaeelldqMel 46
                                   +++  + ++++  +++++ eae+l++++ l
  gi|116754857|ref|YP_843975.1|  6 QSPENQARQLIVAYQQYQAEAESLVRELGL 35
                                   4445699******************99876 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.017
                        V-SNARE  16 sslageerkaalreiekkldeaeelldqMelEvrn 50 
                                     s+++ + ++al++ie++   ++  l+++e E++ 
  gi|116754857|ref|YP_843975.1| 110 ISESSKKINEALAKIEQEMARIQAALERLERELQK 144
                                    3344568899********************99985 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.2       0.1        64      25      69 ..      16      60 ..       7      63 .. 0.84
   2 ?   12.1   3.3   0.00026      0.16      26      52 ..     119     145 ..      94     149 .. 0.49

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.1
                          DHR10 25 idalqvvekdlrsciklleeieaelakleeakkklkelrdaleek 69
                                   i a+q+++++ +s+++ l  i+   + l++a + + +l++a e +
  gi|116754857|ref|YP_843975.1| 16 IVAYQQYQAEAESLVRELGLIQMTAEGLDKAISAIGALSKAAEGQ 60
                                   67899999********99999999999999999988888877765 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00026
                          DHR10  26 dalqvvekdlrsciklleeieaelakl 52 
                                    +al+++e++++++ ++le +e+el+k+
  gi|116754857|ref|YP_843975.1| 119 EALAKIEQEMARIQAALERLERELQKQ 145
                                    455566666666666666666666554 PP

>> HrpB7  Bacterial type III secretion protein (HrpB7)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.3      0.49     3e+02     105     148 ..      18      61 ..       3      66 .. 0.64
   2 ?   14.0   2.9   8.3e-05     0.051      65     140 ..      67     141 ..      52     146 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.49
                          HrpB7 105 aedavaatarkiaRndaqidacrerierlrraaeraredaadEE 148
                                    a ++ +a a+ ++R ++ i+ ++e ++++  a  +   +a+  E
  gi|116754857|ref|YP_843975.1|  18 AYQQYQAEAESLVRELGLIQMTAEGLDKAISAIGALSKAAEGQE 61 
                                    34455677777778888888877777777777666666666555 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 8.3e-05
                          HrpB7  65 gsspfsiadylacrayrdvlegrvraaeaelaaarqaldaaedavaatarkiaRndaqidacrerierlrraaera 140
                                    gs +f  a++++ ++++  + g v   e+  + a + l+a++ a+++  +ki  ++a+i++  +ri+++ + +er+
  gi|116754857|ref|YP_843975.1|  67 GSGSFAYAKLSSADRVVVNVGGGVS-IEKPAEEAMEMLRARRSAISESSKKINEALAKIEQEMARIQAALERLERE 141
                                    4556889999999999999888886.56777778889999999999999999999999999999998887777765 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 ?    2.0   0.2      0.39   2.4e+02      52      75 ..      18      41 ..      11      51 .. 0.66
   2 ?    2.8   0.1      0.22   1.3e+02       2      25 ..      36      59 ..      35      61 .. 0.89
   3 ?   11.2   0.5   0.00053      0.33      45      76 ..     113     144 ..      97     148 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.39
                                   HHHHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100 52 efeewkqaaqklvdaLeeisealk 75
                                   ++++++++a+ lv++L  i+ + +
  gi|116754857|ref|YP_843975.1| 18 AYQQYQAEAESLVRELGLIQMTAE 41
                                   466777777777777766665544 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.22
                                   HCSHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100  2 ikvdpeelrqaaarfqkqaeeled 25
                                   i++++e l++a++++++ ++  e+
  gi|116754857|ref|YP_843975.1| 36 IQMTAEGLDKAISAIGALSKAAEG 59
                                   89*************999988776 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00053
                                    HCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100  45 aadafqaefeewkqaaqklvdaLeeisealkq 76 
                                    ++++ +++++++ q+++++++aLe ++++l++
  gi|116754857|ref|YP_843975.1| 113 SSKKINEALAKIEQEMARIQAALERLERELQK 144
                                    56677777778888888888888887777776 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       1.5   9.5e+02      93     120 ..      23      50 ..       9      54 .. 0.68
   2 ?   10.7   0.2   0.00065       0.4      75     118 ..     100     143 ..      82     147 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.5
                        DUF1664  93 redlseigedvesvkeavegleskleri 120
                                    + + +++ +++  ++ + egl++ ++ i
  gi|116754857|ref|YP_843975.1|  23 QAEAESLVRELGLIQMTAEGLDKAISAI 50 
                                    4555666667777777777777777666 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00065
                        DUF1664  75 ldeqkeiskeikeevtevredlseigedvesvkeavegleskle 118
                                    ++   +  ++i+e  ++++e l++i++++  +++a e le +l+
  gi|116754857|ref|YP_843975.1| 100 MEMLRARRSAISESSKKINEALAKIEQEMARIQAALERLERELQ 143
                                    44444455666677777888888888888888888888888776 PP

>> DUF4226  Domain of unknown function (DUF4226)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       6.5     4e+03      21      21 ..      38      38 ..      12      67 .. 0.57
   2 ?   12.9   1.3   0.00017       0.1       9      58 ..      96     145 ..      90     150 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 6.5
                        DUF4226 21 s 21
                                    
  gi|116754857|ref|YP_843975.1| 38 M 38
                                   1 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00017
                        DUF4226   9 arareaaLaqrlsataelDrqlaevlrsahakaaegrrrLdalqaeidqa 58 
                                    a+++ + L  r sa++e  +++ e+l++ ++++a+ + +L+ l++e++++
  gi|116754857|ref|YP_843975.1|  96 AEEAMEMLRARRSAISESSKKINEALAKIEQEMARIQAALERLERELQKQ 145
                                    567778899*************************************9876 PP

>> DUF4055  Domain of unknown function (DUF4055)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   2.7   0.00065       0.4      16      89 ..      23     135 ..      14     146 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00065
                        DUF4055  16 ssdqedilhfarvpllvltGleee...................................kelaiGsgsaielpdgaaaky 60 
                                    +++ e +++ +++ ++ + Gl++                                      +++G g  ie p+++a+++
  gi|116754857|ref|YP_843975.1|  23 QAEAESLVRELGLIQMTAEGLDKAisaigalskaaegqemlvpigsgsfayaklssadrVVVNVGGGVSIEKPAEEAMEM 102
                                    5666666666666666666666444555555555666666666666666776666664455669**************** PP

                        DUF4055  61 veasgeaiaa....gkealdrlekqmaalGarl 89 
                                    + a+  ai+     ++eal + e++ma++ a l
  gi|116754857|ref|YP_843975.1| 103 LRARRSAISEsskkINEALAKIEQEMARIQAAL 135
                                    ***999987511115678889999999987765 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 ?   -3.5   0.0       5.5   3.4e+03     212     224 ..      19      31 ..       7      58 .. 0.51
   2 ?   11.2   1.1   0.00019      0.12     166     222 ..      93     145 ..      90     153 .] 0.87

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 5.5
                     Fmp27_WPPW 212 ieelekeikelke 224
                                    +++++ e+++l +
  gi|116754857|ref|YP_843975.1|  19 YQQYQAEAESLVR 31 
                                    3333333333333 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00019
                     Fmp27_WPPW 166 ndpervqkelleeRleeleeqiekleekleelelksekedeelkeeieelekeikel 222
                                    ++p++  +e+l+ R + ++e+ +k++e+l ++e+++ +    +++ +e+le+e+++ 
  gi|116754857|ref|YP_843975.1|  93 EKPAEEAMEMLRARRSAISESSKKINEALAKIEQEMAR----IQAALERLERELQKQ 145
                                    5789999*******************************....899999999998876 PP

>> Rx_N  Rx N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1         1   6.5e+02      23      42 ..      22      41 ..      14      62 .. 0.78
   2 ?   11.8   0.9   0.00037      0.23      18      47 ..     112     141 ..      93     150 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1
                           Rx_N 23 vkeeleklkdeLesiqavLe 42
                                    ++e e+l +eL  iq   e
  gi|116754857|ref|YP_843975.1| 22 YQAEAESLVRELGLIQMTAE 41
                                   57788888889888887655 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00037
                           Rx_N  18 kllkgvkeeleklkdeLesiqavLedaeer 47 
                                    ++ k++ e l k+++e+ +iqa Le  e+ 
  gi|116754857|ref|YP_843975.1| 112 ESSKKINEALAKIEQEMARIQAALERLERE 141
                                    7789999*******************9994 PP

>> IDO  Indoleamine 2,3-dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.7   0.00035      0.22     163     217 ..      90     143 ..      88     146 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00035
                                    HHHHHHHHHHHTTHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHTTHHHHS- CS
                            IDO 163 vaiEargaealklmlsaldeareadearvtsaLerlaevideltklLervrekcd 217
                                    v iE  + ea++++++  ++++e+ ++++++aL+++++ + +++++Ler++++ +
  gi|116754857|ref|YP_843975.1|  90 VSIEKPAEEAMEMLRARRSAISES-SKKINEALAKIEQEMARIQAALERLERELQ 143
                                    689999******999999999888.99**********************998765 PP

>> JAKMIP_CC3  JAKMIP CC3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1       0.3   1.8e+02      77      98 ..      13      34 ..       4      64 .. 0.55
   2 ?   11.8   1.8   0.00027      0.17      90     137 ..     100     148 ..      96     153 .] 0.80

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.3
                     JAKMIP_CC3 77 rqLlaeyqalqrayalLreklg 98
                                   rqL+  yq+ q +   L  +lg
  gi|116754857|ref|YP_843975.1| 13 RQLIVAYQQYQAEAESLVRELG 34
                                   4444444444444433333332 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00027
                     JAKMIP_CC3  90 yalLreklggeldaerelk.areqleselrktkskikdLeeaLaqkGqd 137
                                       Lr + ++  ++ +++  a  ++e+e+ ++++ ++ Le++L+++G  
  gi|116754857|ref|YP_843975.1| 100 MEMLRARRSAISESSKKINeALAKIEQEMARIQAALERLERELQKQGGS 148
                                    566788877877777777526789**********************965 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 ?    2.2   0.1       0.4   2.5e+02      65      96 ..      11      48 ..       3      50 .. 0.72
   2 ?   10.8   1.1   0.00085      0.52      58      95 ..     105     142 ..      78     144 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.4
                        DUF4140 65 e......elkalraeleeledelaaledelaaaearla 96
                                   +      ++++ +ae e+l +el  ++ +++ +++ ++
  gi|116754857|ref|YP_843975.1| 11 QarqlivAYQQYQAEAESLVRELGLIQMTAEGLDKAIS 48
                                   13345656889999999999999999999998888776 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00085
                        DUF4140  58 pnreaeeeelkalraeleeledelaaledelaaaearl 95 
                                    ++r+a +e+ k+++++l ++e+e a+++++l+++e +l
  gi|116754857|ref|YP_843975.1| 105 ARRSAISESSKKINEALAKIEQEMARIQAALERLEREL 142
                                    33333333589999999999999999999999999877 PP

>> Nsp1_C  Nsp1-like C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       2.3   1.4e+03      65      91 ..      18      44 ..       8      60 .. 0.56
   2 ?   11.2   0.5    0.0004      0.25      60     105 ..     101     146 ..      92     151 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.3
                         Nsp1_C 65 evleaeqeqnkidqeLeyiesqqdeLe 91
                                   +  + ++e + + +eL +i+   + L+
  gi|116754857|ref|YP_843975.1| 18 AYQQYQAEAESLVRELGLIQMTAEGLD 44
                                   344444444555555555555555555 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0004
                         Nsp1_C  60 skLysevleaeqeqnkidqeLeyiesqqdeLeslLdnyEkeleell 105
                                    + L+    ++ ++++ki++ L  ie++   +++ L+++E+el+++ 
  gi|116754857|ref|YP_843975.1| 101 EMLRARRSAISESSKKINEALAKIEQEMARIQAALERLERELQKQG 146
                                    56677777788999****************************9986 PP

>> DUF5446  Family of unknown function (DUF5446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   3.6    0.0012      0.75      11      55 ..     100     143 ..      91     146 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0012
                        DUF5446  11 LqlLeeiEeeltevEkelseavneteaekeekeeerldllekElk 55 
                                    + +L    + ++e  k+++ea+ + e+e+   +++ l++le+El+
  gi|116754857|ref|YP_843975.1| 100 MEMLRARRSAISESSKKINEALAKIEQEMA-RIQAALERLERELQ 143
                                    67888888999999**************97.57899*******97 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.53   3.3e+02     118     159 ..      13      54 ..       7      61 .. 0.81
   2 ?    9.9   4.3    0.0009      0.56      52     101 ..      92     144 ..      90     148 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.53
                           YkyA 118 dklykaYkealeldkeLYemLkkeeltleeleeqiekiNesy 159
                                     +l+ aY++  ++ ++L ++L+  ++t e l++ i++i + +
  gi|116754857|ref|YP_843975.1|  13 RQLIVAYQQYQAEAESLVRELGLIQMTAEGLDKAISAIGALS 54 
                                    578889999999999999999999999999999999886655 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0009
                           YkyA  52 ikklsdealenveeReellekekesieea....keefekikeeieeiedeelkk 101
                                    i+k ++ea e++ +R++ +++  + i+ea    ++e+  i++ +e +e e l+k
  gi|116754857|ref|YP_843975.1|  92 IEKPAEEAMEMLRARRSAISESSKKINEAlakiEQEMARIQAALERLERE-LQK 144
                                    88999**************9987766665222267777777777777666.443 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 ?    2.7   0.2      0.13        78      66     118 ..       5      57 ..       2      64 .. 0.65
   2 ?    9.8   1.6   0.00088      0.55     109     157 ..      97     145 ..      91     148 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.13
                   HAUS-augmin3  66 vellevileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkl 118
                                    +++ e ++ ++  + +++++e++ L +e  l++   + L+ +++++   +++ 
  gi|116754857|ref|YP_843975.1|   5 PQSPENQARQLIVAYQQYQAEAESLVRELGLIQMTAEGLDKAISAIGALSKAA 57 
                                    56667777777777777777777777777777776666666666555555544 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00088
                   HAUS-augmin3 109 aslqqelrkleeeekeakkklkeaqeelraenaetnavLqqlteeakql 157
                                     ++ + lr++ ++ +e +kk++ea +++++e a+++a+L++l  e +++
  gi|116754857|ref|YP_843975.1|  97 EEAMEMLRARRSAISESSKKINEALAKIEQEMARIQAALERLERELQKQ 145
                                    56677889999999999**********************9999987776 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 ?    5.1   0.1     0.042        26      36      83 ..      10      57 ..       6      63 .. 0.77
   2 ?    7.9   2.9    0.0058       3.6      70     103 ..     101     134 ..      89     145 .. 0.45

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.042
                                   HHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHH CS
                   Seryl_tRNA_N 36 ekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeel 83
                                   ++ r+l+v+ ++ qae  +l +e g +    e  ++ i  + +l++  
  gi|116754857|ref|YP_843975.1| 10 NQARQLIVAYQQYQAEAESLVRELGLIQMTAEGLDKAISAIGALSKAA 57
                                   678999999999999999999999988887777777777777766654 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0058
                                    CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCT CS
                   Seryl_tRNA_N  70 eeliaevkelkeelkaleaelkeleaelekllla 103
                                    e l+a+ ++++e  k+++++l+++e+e+  + +a
  gi|116754857|ref|YP_843975.1| 101 EMLRARRSAISESSKKINEALAKIEQEMARIQAA 134
                                    3333444444444444444444444444333322 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.53   3.3e+02     433     471 ..      13      51 ..       4      78 .. 0.74
   2 ?    8.8   1.4   0.00088      0.54     421     473 ..      96     149 ..      91     152 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.53
                         AAA_13 433 keeeaelkkleeeikeLekqlrdekpaaeeinkeLkafG 471
                                    ++   + +++++e++ L ++l  ++ +ae + k ++a+G
  gi|116754857|ref|YP_843975.1|  13 RQLIVAYQQYQAEAESLVRELGLIQMTAEGLDKAISAIG 51 
                                    445556677888888888888888888888888888887 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00088
                         AAA_13 421 lekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLkaf.Glg 473
                                    +e+a+e l ++ +++++  kk++e  + +e+++  ++ a e +++eL++  G +
  gi|116754857|ref|YP_843975.1|  96 AEEAMEMLRARRSAISESSKKINEALAKIEQEMARIQAALERLERELQKQgGSE 149
                                    57788999999999**********************************995554 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 ?    3.8   0.1     0.088        54      68     112 ..      12      56 ..       4      64 .. 0.67
   2 ?    8.2   2.6    0.0039       2.4       4      38 ..     113     147 ..     110     151 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.088
                 CENP-F_leu_zip  68 lreleldLvalrsekeeLekelqkkqervseLeslnsslenllee 112
                                     r+l +  ++ + e e+L +el   q + + L+++ s +  l + 
  gi|116754857|ref|YP_843975.1|  12 ARQLIVAYQQYQAEAESLVRELGLIQMTAEGLDKAISAIGALSKA 56 
                                    556666667777777777777777777777777777666555555 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0039
                 CENP-F_leu_zip   4 kklhvlekLKeserkadsLkdkvenLerelemsee 38 
                                      +++ e L ++e++ + ++   e+Lerel+ ++ 
  gi|116754857|ref|YP_843975.1| 113 SSKKINEALAKIEQEMARIQAALERLERELQKQGG 147
                                    56789999999999999999999999999998765 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1       0.2   1.2e+02     160     194 ..      10      44 ..       6      57 .. 0.82
   2 ?    9.3   2.8   0.00076      0.47     143     190 ..      95     142 ..      90     149 .. 0.58

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.2
                           Spc7 160 kqeeeldellpeleeekaeleeeleklqeaaeele 194
                                    +q  +l  +++++++e ++l +el  +q  ae l+
  gi|116754857|ref|YP_843975.1|  10 NQARQLIVAYQQYQAEAESLVRELGLIQMTAEGLD 44 
                                    56778888999999999999999999998777655 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00076
                           Spc7 143 gleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaa 190
                                     +ee +e l++ ++ ++++ ++++e+l ++e+e a++++ le+l+++ 
  gi|116754857|ref|YP_843975.1|  95 PAEEAMEMLRARRSAISESSKKINEALAKIEQEMARIQAALERLEREL 142
                                    455666666666666666666666666666666666666666665533 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 ?   -2.1   0.0       8.4   5.2e+03      22      34 ..      32      44 ..      20      51 .. 0.43
   2 ?    3.9   0.2      0.12        72      14      36 ..      98     120 ..      91     123 .. 0.84
   3 ?    8.2   0.3    0.0052       3.2       4      25 ..     123     144 ..     120     148 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 8.4
                      FlaC_arch 22 eneelsksveelk 34
                                   e+  ++ + e l+
  gi|116754857|ref|YP_843975.1| 32 ELGLIQMTAEGLD 44
                                   3333333333333 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.12
                      FlaC_arch  14 teletvkkeneelsksveelken 36 
                                      +e++++  + +s+s ++++e 
  gi|116754857|ref|YP_843975.1|  98 EAMEMLRARRSAISESSKKINEA 120
                                    57999999999999999999986 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0052
                      FlaC_arch   4 elEnklsklsteletvkkenee 25 
                                    ++E+++ +++  le +++e+++
  gi|116754857|ref|YP_843975.1| 123 KIEQEMARIQAALERLERELQK 144
                                    79***************99986 PP

>> DUF4349  Domain of unknown function (DUF4349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       3.4   2.1e+03      10      30 ..      37      57 ..      18      60 .. 0.57
   2 ?   10.2   6.2    0.0006      0.37      97     140 ..      99     143 ..      97     146 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.4
                        DUF4349 10 tlevedvdaavaairelveea 30
                                   ++++e +d+a++ai +l ++a
  gi|116754857|ref|YP_843975.1| 37 QMTAEGLDKAISAIGALSKAA 57
                                   444445555555555555555 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0006
                        DUF4349  97 aleasedrllallekaksved.lleiereLsevqaeieslegqlr 140
                                    a e +++r  a+ e +k++++ l +ie+e++++qa +e+le++l+
  gi|116754857|ref|YP_843975.1|  99 AMEMLRARRSAISESSKKINEaLAKIEQEMARIQAALERLERELQ 143
                                    5677889999999999998772568****************9987 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1       2.7   1.7e+03      27      43 ..      20      36 ..       9      58 .. 0.63
   2 ?   10.5   3.1    0.0012      0.73      19      51 ..     114     146 ..      96     151 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 2.7
                                   HHHHHHHHHHHHHHHHH CS
                           SlyX 27 aeqqqqidrlqrqlrll 43
                                    + q + + l r+l l+
  gi|116754857|ref|YP_843975.1| 20 QQYQAEAESLVRELGLI 36
                                   34455555565555554 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0012
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXX CS
                           SlyX  19 ieeLndvvaeqqqqidrlqrqlrllaerlkele 51 
                                     ++ n+++a+ +q+++r+q+ l++l+++l++  
  gi|116754857|ref|YP_843975.1| 114 SKKINEALAKIEQEMARIQAALERLERELQKQG 146
                                    5789**********************9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1945  (0.108483); expected 358.6 (0.02)
Passed bias filter:                     1294  (0.0721736); expected 358.6 (0.02)
Passed Vit filter:                       258  (0.0143901); 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: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.41
# Mc/sec: 1115.68
//
Query:       gi|116754858|ref|YP_843976.1|  [L=63]
Description: 50S ribosomal protein LX [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.8e-10   38.7   0.0    1.3e-09   38.2   0.0    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 !   38.2   0.0   7.2e-14   1.3e-09      78     121 .]      16      59 ..       1      59 [. 0.85

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 7.2e-14
                                    .TEEEEEEEEEEESSHHHHHHHHHHHHHHHS---GGGEEEEEEE CS
                 Ribosomal_L18A  78 rsgthnfykeyrdlteegaveqvYselgsrhrakrssIqIekve 121
                                     + +++f+k +   +e+ a+e +Ys +gs+h +kr+ I+I++v+
  gi|116754858|ref|YP_843976.1|  16 GNVWQKFTKVLDCPNERVAIEWAYSLMGSKHGLKRNLIKIDEVR 59 
                                    588**************************************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); 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: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 447.93
//
Query:       gi|116754859|ref|YP_843977.1|  [L=221]
Description: translation initiation factor IF-6 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-69  233.6   0.5    1.4e-69  233.4   0.5    1.0  1  eIF-6     eIF-6 family


Domain annotation for each model (and alignments):
>> eIF-6  eIF-6 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  233.4   0.5     8e-74   1.4e-69       1     197 []       5     199 ..       5     199 .. 0.99

  Alignments for each domain:
  == domain 1  score: 233.4 bits;  conditional E-value: 8e-74
                                    .E-BTTB--HHHH-EE-SSEEEE-TTS-HHHHHHHHHHHT-EEEE--BTTBS-HHHH-EE-SSEEEEETT--HHHHHHHH CS
                          eIF-6   1 rlsiegsseiGvfarltnkyalvpegveeefvkaieeeLkvevvettiagsrlvGslvvgNsngllvpstvtdeeleklk 80 
                                    r++++gss +Gvfar+t++++lvp++++e+ v+++++ L+ve v t i++s+++Gsl+++Ns+g++v++++td+e++ l+
  gi|116754859|ref|YP_843977.1|   5 RTQVAGSSLLGVFARCTESLVLVPPEASERSVEMLSAGLDVEPVVTVIGSSSVLGSLICANSEGFVVTRYATDDEIRVLE 84 
                                    7899************************9*************************************************** PP

                                    HHHH---EEE--SS--HHHHEEE-SSEEEE-GGGGG.GHHHHHHHHTSEEEE--BTTBS-TTTSEEE-SSEEEE-TT--H CS
                          eIF-6  81 eslkleverleekltAlGNvilaNDkvAlvhpdlsketveiiadvLgvevvrgtiagiktvGsaavvtnkgllvhpkate 160
                                    e+   +v+rl+ k+tA+GNvilaND++Alvhp ls+ ++eii+++Lgv v rgti+g+ktvG++avvtnkg+l hp+++ 
  gi|116754859|ref|YP_843977.1|  85 EH--GRVARLPGKITAAGNVILANDNAALVHPGLSDIACEIISETLGVVVRRGTIGGLKTVGMTAVVTNKGILAHPRISA 162
                                    *9..9*************************************************************************** PP

                                    HHHHHHHHHHT-SEEE--BTTTBS-GGGTEEE-SS-E CS
                          eIF-6 161 eeleeleellkveveagTvNrGsklvgsglvaNdkga 197
                                    +e++ le+l++++v++gTvN+Gs+lvgsgl+aN++g+
  gi|116754859|ref|YP_843977.1| 163 DEIKVLEDLFGLPVDVGTVNFGSPLVGSGLLANSRGY 199
                                    **********************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       211  (0.0117686); expected 358.6 (0.02)
Passed bias filter:                      183  (0.0102069); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.29s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1570.58
//
Query:       gi|116754860|ref|YP_843978.1|  [L=87]
Description: ribosomal protein L31e [Methanosaeta thermophila PT]
Scores for complete 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-12   47.0   0.3    2.5e-12   46.8   0.3    1.1  1  Ribosomal_L31e  Ribosomal protein L31e


Domain annotation for each model (and alignments):
>> Ribosomal_L31e  Ribosomal protein L31e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.3   1.4e-16   2.5e-12       2      69 ..       2      70 ..       1      78 [. 0.90

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 1.4e-16
                 Ribosomal_L31e  2 vvtreytInihkrihgvgfkkraprAlkeikkfamkemgtp.dv.ridtrLnkavwakgirnvpyrirvr 69
                                   vv + yt+   +++++v + +ra+rA+ e+k +  ++m+ p d   id++Ln+ +wa++ +++p+rirv+
  gi|116754860|ref|YP_843978.1|  2 VVEQIYTVP-LRHVKRVPRWRRAKRAVSELKSYLSRHMKAPlDKiSIDNTLNEMIWARSNEKPPCRIRVK 70
                                   688889999.89***************************7634459***********************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); 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: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 624.99
//
Query:       gi|116754861|ref|YP_843979.1|  [L=49]
Description: 50S ribosomal protein L39e [Methanosaeta thermophila PT]
Scores for 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   77.6   9.9    5.3e-22   77.2   9.9    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 !   77.2   9.9     3e-26   5.3e-22       1      41 [.       8      48 ..       8      49 .] 0.98

  Alignments for each domain:
  == domain 1  score: 77.2 bits;  conditional E-value: 3e-26
                  Ribosomal_L39  1 kKlrLaKalkqNrpvPaWvrlktdrkvrynpkrRhWRrtkL 41
                                   kK+rLaKal+qN++vP Wv++kt+r+v ++pkrRhWRr++L
  gi|116754861|ref|YP_843979.1|  8 KKIRLAKALRQNQRVPLWVIMKTKRRVVSHPKRRHWRRSSL 48
                                   7**************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.32u 0.24s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 387.62
//
Query:       gi|116754862|ref|YP_843980.1|  [L=199]
Description: hypothetical protein Mthe_1570 [Methanosaeta thermophila PT]
Scores for complete 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   24.1   0.0    6.7e-05   22.5   0.0    1.7  2  QueC          Queuosine biosynthesis protein QueC
     0.0062   16.2   0.0      0.011   15.5   0.0    1.4  1  Asn_synthase  Asparagine synthase
  ------ inclusion threshold ------
      0.031   14.3   0.0      0.084   12.9   0.0    1.7  1  PAPS_reduct   Phosphoadenosine phosphosulfate reductase famil


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 !   22.5   0.0   1.1e-08   6.7e-05       3      48 ..       4      51 ..       2      70 .. 0.75
   2 ?   -0.4   0.0      0.11   6.6e+02     116     142 ..      63      89 ..      52     111 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.1e-08
                                   EEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-TTSHHHHH..HHHHH CS
                           QueC  3 vvllSGGlDSttvlalakkegkevealtfdYgqrhkkelea..akkia 48
                                    +l+SGG DS   ++l +  ++e+e++tf++gq ++ e+ a  a++i 
  gi|116754862|ref|YP_843980.1|  4 TTLFSGGKDSGLTAILLEPFFDEIELVTFSFGQDRAWEVAAraARAIG 51
                                   689******************************977666540044444 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.11
                                    EEEE---S-STT--GGGSHHHHHHHHH CS
                           QueC 116 aiiiGvneedfsgYPDcrdefvkalnk 142
                                     + +G++     gYP +  ++v+++ +
  gi|116754862|ref|YP_843980.1|  63 VLETGLEMLRRDGYPNNALNYVHMCAV 89 
                                    5667888888899***99999988764 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.8e-06     0.011      19      85 ..       2      64 ..       1      77 [. 0.84

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.8e-06
                   Asn_synthase 19 pvGalLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgtehtelvlteeell 85
                                   +v++l+SGG DS+l a l+  + + ++  ++  f   ++   ++a+++a+++g +h+  +l+ee +l
  gi|116754862|ref|YP_843980.1|  2 KVTTLFSGGKDSGLTAILLEPFFD-EIELVTFSF--GQDRAWEVAARAARAIGHPHRVEILDEE-VL 64
                                   6899*******************9.899999999..677777899**********877666665.43 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.4e-05     0.084       3     149 ..       4     145 ..       2     149 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.4e-05
                                    EEE--SSCTCHHHHHHHHHHCTTHE..EEEEE-STB-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S-THHHC CS
                    PAPS_reduct   3 vvsvsgGkdslVllhLalkafkpvp..vvfvdtghefpetiefvdeleeryglrlkvyepeeevaekinaekhgsslyee 80 
                                     +++sgGkds  + +L+   f++++  ++   + +  +   +   ++ +  ++++ + e  e++ e++ + +++ +  + 
  gi|116754862|ref|YP_843980.1|   4 TTLFSGGKDSGLTAILLEPFFDEIElvTFSFGQDRAWEVAARAARAIGHPHRVEILDEEVLETGLEMLRRDGYPNNALNY 83 
                                    679********************852155555556666667777777777799999999999999999999988887554 PP

                                    HHHHHHTHHHHHHHHHCTTECEEE----CCCTTTTTTSSSEEECTTT-SCEEE-.CCCT--HHHHHHHHH CS
                    PAPS_reduct  81 aaeriaKveplkkaLekldedalltGaRrdesksraklpiveidedfekslrvf.PllnWteedvwqyil 149
                                       +++ ve l +     + +++  G Rrd+ +  ++ + ++  ed +  ++ + Pl+ W ++ + +++ 
  gi|116754862|ref|YP_843980.1|  84 --VHMCAVELLAE-----SCEYVADGTRRDDRAPVMTASSIRSLEDRH-RMHYLrPLAGWGWRAINEMAS 145
                                    ..66777777666.....556999*********888888888888878.566555******999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1505.45
//
Query:       gi|116754863|ref|YP_843981.1|  [L=112]
Description: hypothetical protein Mthe_1571 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.4e-29  101.0  18.3    4.9e-29  100.8  18.3    1.0  1  dsDNA_bind  Double-stranded DNA-binding domain
  ------ inclusion threshold ------
      0.015   15.5   0.3      0.018   15.3   0.3    1.2  1  Spy1        Cell cycle regulatory protein
       0.25   11.3   2.7       0.42   10.5   1.2    2.1  2  DUF4224     Domain of unknown function (DUF4224)
       0.36   11.1  11.2      0.041   14.1   7.0    1.6  2  DUF4355     Domain of unknown function (DUF4355)
       0.95    9.9   4.5        7.6    7.0   3.6    2.1  2  Ntox1       Putative RNase-like toxin, toxin_1
          2    8.4   5.5        2.3    8.2   5.5    1.0  1  DUF4192     Domain of unknown function (DUF4192)


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 !  100.8  18.3   1.6e-32   4.9e-29       1     106 [.       8     109 ..       8     112 .] 0.92

  Alignments for each domain:
  == domain 1  score: 100.8 bits;  conditional E-value: 1.6e-32
                                    XXXXXXXXXXXXXXXXXXXX...XXXX--SS..S--SSHHHHTTS--HHHHHHHHHHTTT-HHHHHHHHHHHHHHHH--S CS
                     dsDNA_bind   1 irkarlaelqaqagsssgsggaseqqeqqqeaseeeakqaiLsqiLepeAreRLsrirlvkperaeavenrLiqlaqsGq 80 
                                    +r+++l+elq+++ +s+    a++q++ qqe   e++kqaiL+ iL+peAreRLs+ir+++pe ++++e +Li+laqsG+
  gi|116754863|ref|YP_843981.1|   8 LRRKKLEELQRRQLESQL--YAAQQEQMQQE--LEAKKQAILRAILTPEARERLSSIRMTRPEFVAQIEAQLIMLAQSGR 83 
                                    69**********999887..55666666666..9********************************************** PP

                                    S-----HHHHHHHHHHHS---XXXXX CS
                     dsDNA_bind  81 lrskvteeqLkeLLeqvaekkketki 106
                                    +rs +t+eqLk +L+q + kk++ ki
  gi|116754863|ref|YP_843981.1|  84 IRSAITDEQLKAILKQAQPKKRDIKI 109
                                    **********************8887 PP

>> Spy1  Cell cycle regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.3     6e-06     0.018      46     109 ..      12      77 ..       5     101 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6e-06
                           Spy1  46 klseytrinfflalYLan..dmEedeeeskleifpfalgkewkskvpkflklrdkllarmeyraaV 109
                                    kl+e +r ++   lY a+  +m ++ e++k++i+  +l  e ++++++++ +r +++a++e + + 
  gi|116754863|ref|YP_843981.1|  12 KLEELQRRQLESQLYAAQqeQMQQELEAKKQAILRAILTPEARERLSSIRMTRPEFVAQIEAQLIM 77 
                                    5678899999999**997336**************************************9988765 PP

>> DUF4224  Domain of unknown function (DUF4224)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.2   0.00014      0.42       4      30 ..       2      28 ..       2      32 .. 0.87
   2 ?   -0.6   0.0      0.43   1.3e+03      15      27 ..      70      82 ..      48      85 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00014
                        DUF4224  4 peElaeLTGykrrsaQakwLranGipf 30
                                   ++Ela+L ++k +++Q+++L ++ +  
  gi|116754863|ref|YP_843981.1|  2 DDELADLRRKKLEELQRRQLESQLYAA 28
                                   59******************9986655 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.43
                        DUF4224 15 rrsaQakwLranG 27
                                   + +aQ  +L ++G
  gi|116754863|ref|YP_843981.1| 70 QIEAQLIMLAQSG 82
                                   5578888888775 PP

>> DUF4355  Domain of unknown function (DUF4355)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   7.0   1.4e-05     0.041      38      89 ..       9      68 ..       1      75 [. 0.81
   2 ?   -2.1   0.1       1.4   4.2e+03      76      76 ..      97      97 ..      85     109 .. 0.43

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.4e-05
                        DUF4355 38 klakmnaeekae.......yeleklqkeleelkaelarkelkaearkvlaekkipi.ell 89
                                   +++k+ + ++++       ++ e++q+ele++k++  r+ l+ ear+ l+   ++  e++
  gi|116754863|ref|YP_843981.1|  9 RRKKLEELQRRQlesqlyaAQQEQMQQELEAKKQAILRAILTPEARERLSSIRMTRpEFV 68
                                   567777788888888999999**************************9997665555666 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.4
                        DUF4355 76 r 76
                                    
  gi|116754863|ref|YP_843981.1| 97 L 97
                                   1 PP

>> Ntox1  Putative RNase-like toxin, toxin_1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   3.6    0.0025       7.6      51      85 ..      10      43 ..       1      54 [. 0.77
   2 ?    2.2   0.0      0.08   2.4e+02      54      82 ..      54      82 ..      50      95 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0025
                          Ntox1 51 keeneevealRkldaklaadeaakLiqaletarln 85
                                   +++ ee++  R+l+++l a +  +++q+le+ ++ 
  gi|116754863|ref|YP_843981.1| 10 RKKLEELQ-RRQLESQLYAAQQEQMQQELEAKKQA 43
                                   34567776.79*******************98875 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.08
                          Ntox1 54 neevealRkldaklaadeaakLiqaleta 82
                                    e + ++R + +++ a+  a+Li    + 
  gi|116754863|ref|YP_843981.1| 54 RERLSSIRMTRPEFVAQIEAQLIMLAQSG 82
                                   6889999*********9888888765555 PP

>> DUF4192  Domain of unknown function (DUF4192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   5.5   0.00077       2.3     145     222 ..      15      90 ..      10     111 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00077
                        DUF4192 145 egsReelearlapvegaaaraaqrraaeraaaaleralarprdaerrsdpaevrraaleavraalarvaagaglsda..e 222
                                    e +R++le++l +    a+++++++++e+ ++a+ ra+++p+++er s+ +  r + +++++a+l  +a+  +  +a  +
  gi|116754863|ref|YP_843981.1|  15 ELQRRQLESQLYA----AQQEQMQQELEAKKQAILRAILTPEARERLSSIRMTRPEFVAQIEAQLIMLAQSGRIRSAitD 90 
                                    5679999999997....677889999***************999999999***************999998888777442 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2025  (0.112946); expected 358.6 (0.02)
Passed bias filter:                      630  (0.0351386); 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: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 811.05
//
Query:       gi|116754864|ref|YP_843982.1|  [L=149]
Description: 30S ribosomal protein S19e [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.6e-58  194.8   0.1    5.2e-58  194.6   0.1    1.0  1  Ribosomal_S19e  Ribosomal protein S19e
     0.0001   22.7   0.2    0.00021   21.7   0.2    1.6  1  HTH_27          Winged helix DNA-binding domain
     0.0058   16.5   0.0       0.17   11.8   0.0    2.2  2  RuvB_C          RuvB C-terminal winged helix domain
      0.009   16.0   0.0      0.014   15.4   0.0    1.3  1  HTH_45          Winged helix-turn-helix
  ------ inclusion threshold ------
      0.051   13.2   0.1       0.18   11.5   0.0    1.9  2  GntR            Bacterial regulatory proteins, gntR family
      0.072   13.0   0.0       0.13   12.1   0.0    1.5  1  TrmB            Sugar-specific transcriptional regulator TrmB
      0.075   12.8   0.0       0.12   12.1   0.0    1.2  1  DUF4364         Domain of unknown function (DUF4364)
       0.14   12.2   0.0       0.33   10.9   0.0    1.7  1  HTH_12          Ribonuclease R winged-helix domain


Domain annotation for each model (and alignments):
>> Ribosomal_S19e  Ribosomal protein S19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  194.6   0.1   2.3e-61   5.2e-58       1     135 [.       3     136 ..       3     138 .. 0.98

  Alignments for each domain:
  == domain 1  score: 194.6 bits;  conditional E-value: 2.3e-61
                                    TSSSHHHHHHHHHS--S---S-SSS-SSSS-SS-S-SS-SSTTTHHHHHHHHHHHTS--TTSGGGGS----SS-SSS--- CS
                 Ribosomal_S19e   1 tvkdVpaeelikalaeeLkksgklevPewadlvKtgsakelapededWfyvRaAsilRkvylrgpvGverlrkvYGgkkr 80 
                                    tv+dVp+ +li+a+aeeLk sgk+++P+wa++vKtg++ e++p++ dW+yvR+As+lR+vy++gpvGv+rlr++YGgk++
  gi|116754864|ref|YP_843982.1|   3 TVYDVPPADLINAVAEELKASGKITPPAWAAYVKTGVHTEMPPSNADWWYVRCASVLRHVYVDGPVGVSRLRTHYGGKTK 82 
                                    79****************************************************************************** PP

                                    ----THHHHHHHHHTTSSS--SSS---SS-HHHHHTHHHHH--SS--S--XXXXX CS
                 Ribosomal_S19e  81 rgvrpshfvkasgsvirkilqqLeklglvkkekkkgrrltkkGqrlldriaeeva 135
                                    + v   ++vk+sgs+ir++lqqLek+g+vkk+k+ gr +t++Gq++ld+ia++v+
  gi|116754864|ref|YP_843982.1|  83 NRVVTGRTVKGSGSIIREALQQLEKAGYVKKQKD-GRHITPEGQAFLDNIAHKVK 136
                                    *****************************99855.*****************996 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 !   21.7   0.2   9.2e-08   0.00021       8      58 ..      58     118 ..      49     124 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 9.2e-08
                         HTH_27   8 vLhlir............hrrrrkkladlcgrlnvedshis.yslkkLtekGLvertgdeadrr 58 
                                    vL++++            h +++ k + + gr+  ++ +i+ ++l +L+++G+v+++   +d+r
  gi|116754864|ref|YP_843982.1|  58 VLRHVYvdgpvgvsrlrtHYGGKTKNRVVTGRTVKGSGSIIrEALQQLEKAGYVKKQ---KDGR 118
                                    67777788888888888777777777****************************666...4555 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 ?    2.5   0.0      0.06   1.3e+02      13      34 ..      57      78 ..      52      87 .. 0.81
   2 !   11.8   0.0   7.7e-05      0.17      50      71 ..     107     128 ..      97     129 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.06
                                   HHHHHT.TT--B-HHHHHHHTT CS
                         RuvB_C 13 kllkekfkggpvglktlaailg 34
                                   ++l + + +gpvg++ l ++ g
  gi|116754864|ref|YP_843982.1| 57 SVLRHVYVDGPVGVSRLRTHYG 78
                                   688999********99987765 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 7.7e-05
                                    HTTSEEEETTEEEE-HHHHHHH CS
                         RuvB_C  50 keglIertsrGRilTkkglkyl 71 
                                    k g++++ + GR +T++g  +l
  gi|116754864|ref|YP_843982.1| 107 KAGYVKKQKDGRHITPEGQAFL 128
                                    689***************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 !   15.4   0.0     6e-06     0.014      37      71 ..      99     133 ..      90     139 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6e-06
                         HTH_45  37 nkYLdmLvekglikkskekYvlTekGlelleklke 71 
                                    ++ L++L + g++kk+k+   +T +G+ +l+++ +
  gi|116754864|ref|YP_843982.1|  99 REALQQLEKAGYVKKQKDGRHITPEGQAFLDNIAH 133
                                    56699**************************9875 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   7.9e-05      0.18      37      57 ..      94     114 ..      89     118 .. 0.84
   2 ?   -2.5   0.0       1.9   4.2e+03       4      15 ..     130     141 ..     129     143 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.9e-05
                                    -HHHHHHHHHHHHHTTSEEEE CS
                           GntR  37 srttvReALrrLeaeglverr 57 
                                    s + +ReAL++Le +g+v  +
  gi|116754864|ref|YP_843982.1|  94 SGSIIREALQQLEKAGYVKKQ 114
                                    6688*************9755 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.9
                                    HHHHHHHHHHHT CS
                           GntR   4 qvyerLredIls 15 
                                    ++++++++++++
  gi|116754864|ref|YP_843982.1| 130 NIAHKVKMRLVE 141
                                    688888888876 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     6e-05      0.13      37      60 ..      96     119 ..      86     138 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6e-05
                                    HCHHHHHHHHHHCTSEEEESSTTT CS
                           TrmB  37 skvYevLrsLedkGlVerekgrpk 60 
                                    s + e+L++Le++G+V+++k  ++
  gi|116754864|ref|YP_843982.1|  96 SIIREALQQLEKAGYVKKQKDGRH 119
                                    56889**************97654 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   5.3e-05      0.12      37      87 ..      99     145 ..      97     148 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.3e-05
                        DUF4364  37 qqalseLvesglieeeekenktlykiTekGketlelfenripksirekide 87 
                                     +al++L+++g++++    +k+  +iT++G+  l+ + +++   + eki e
  gi|116754864|ref|YP_843982.1|  99 REALQQLEKAGYVKK----QKDGRHITPEGQAFLDNIAHKVKMRLVEKIPE 145
                                    699***********6....567779****************9999999876 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 ?   10.9   0.0   0.00015      0.33      35      64 ..      98     126 ..      90     128 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00015
                         HTH_12  35 vRyrLrkleergltrrvgyagreltEkGle 64 
                                    +R  L+ le+ g+++++  + r++t  G  
  gi|116754864|ref|YP_843982.1|  98 IREALQQLEKAGYVKKQKDG-RHITPEGQA 126
                                    8999************9876.99*998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1145.56
//
Query:       gi|116754865|ref|YP_843983.1|  [L=281]
Description: CoB--CoM heterodisulfide reductase [Methanosaeta thermophila PT]
Scores for complete 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   91.3   0.1    4.9e-12   45.9   0.0    2.2  2  CCG            Cysteine-rich domain
  ------ inclusion threshold ------
      0.026   14.3   0.2       0.24   11.2   0.0    2.1  2  GAGA           GAGA factor
       0.28   11.4   2.0         17    5.7   0.3    2.3  2  Cas_CXXC_CXXC  CRISPR-associated protein (Cas_CXXC_CXXC)


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 !   43.5   0.1   4.5e-15   2.7e-11       1      85 []       4      81 ..       4      81 .. 0.94
   2 !   45.9   0.0   8.2e-16   4.9e-12       4      85 .]     137     222 ..     134     222 .. 0.94

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 4.5e-15
                            CCG  1 vayfdgChllraaypevrkalkkllealgveleelekesCCGagggrsgkeelaealakrnvetaeetgadaivtacpgCll 82
                                   +ay++gC + +a  +e++ +++ + +alg+el ele+ sCCGa ++  ++e ++ ala+rn+ + e     +++++c+ C+ 
  gi|116754865|ref|YP_843983.1|  4 IAYYPGC-VSKATGREYDISTRSVARALGIELIELEDWSCCGATHV--SNETISVALAARNLTQSEL----PVMSTCSICYS 78
                                   69*****.**********************************9988..77889*********99887....8********99 PP

                            CCG 83 qlk 85
                                   +l+
  gi|116754865|ref|YP_843983.1| 79 NLR 81
                                   885 PP

  == domain 2  score: 45.9 bits;  conditional E-value: 8.2e-16
                            CCG   4 fdgChllraa....ypevrkalkkllealgveleel.ekesCCGagggrsgkeelaealakrnvetaeetgadaivtacp 78 
                                    ++gC l r+     +pe +++l+kl++ lg+e +e   k  CCG +++ + +e  a++ a + + +a+++gadai++ cp
  gi|116754865|ref|YP_843983.1| 137 YYGCLLTRPGngidSPEHPEVLEKLVRMLGAEPVESpLKMLCCGGPIF-MPREGAALESAYHVLMSAKRAGADAIMAVCP 215
                                    89**9999999*************************9*********98.666669************************* PP

                            CCG  79 gCllqlk 85 
                                     C+l+l+
  gi|116754865|ref|YP_843983.1| 216 LCHLMLD 222
                                    *****96 PP

>> GAGA  GAGA factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   4.1e-05      0.24      13      36 ..      57      82 ..      46      89 .. 0.81
   2 ?    0.5   0.0     0.089   5.3e+02      25      31 ..     212     218 ..     194     230 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.1e-05
                                   ---CCCCTTS--..EE-TTT--EESS CS
                           GAGA 13 lkiksksqsEqP..AtCPiCqAviRq 36
                                   l  ++  qsE P   tC iC+  +R 
  gi|116754865|ref|YP_843983.1| 57 LAARNLTQSELPvmSTCSICYSNLRT 82
                                   5679999*****666******98885 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.089
                                    EE-TTT- CS
                           GAGA  25 AtCPiCq 31 
                                    A CP+C+
  gi|116754865|ref|YP_843983.1| 212 AVCPLCH 218
                                    89****7 PP

>> Cas_CXXC_CXXC  CRISPR-associated protein (Cas_CXXC_CXXC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.3    0.0029        17      31      58 ..      53      76 ..      41      80 .. 0.80
   2 ?    5.0   0.1    0.0049        29      52      62 ..     211     221 ..     205     224 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0029
                  Cas_CXXC_CXXC 31 ivpLlgsegslknyfwngknkadiCpiC 58
                                   i   +++   ++n++ +  ++++ C+iC
  gi|116754865|ref|YP_843983.1| 53 I---SVA-LAARNLTQSELPVMSTCSIC 76
                                   4...444.5689**************** PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0049
                  Cas_CXXC_CXXC  52 adiCpiCklll 62 
                                    +++Cp+C l+l
  gi|116754865|ref|YP_843983.1| 211 MAVCPLCHLML 221
                                    899******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 2225.73
//
Query:       gi|116754866|ref|YP_843984.1|  [L=174]
Description: putative heterodisulfide reductase, C subunit [Methanosaeta thermophila PT]
Scores for complete 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-10   40.2   5.3    6.1e-10   39.4   5.3    1.4  1  Fer4_8    4Fe-4S dicluster domain
    3.6e-09   37.0   5.5    5.7e-09   36.4   5.5    1.3  1  Fer4_17   4Fe-4S dicluster domain
    2.7e-08   33.8   5.2      5e-08   33.0   5.2    1.4  1  Fer4_9    4Fe-4S dicluster domain
    5.1e-06   27.0   3.5    1.1e-05   25.9   3.5    1.6  1  Fer4_7    4Fe-4S dicluster domain
     0.0018   18.0  10.8       0.18   11.7   1.4    2.3  2  Fer4      4Fe-4S binding domain
     0.0034   17.5  12.1     0.0096   16.0  11.6    1.8  2  Fer4_10   4Fe-4S dicluster domain
     0.0063   16.5  13.8      0.062   13.4   3.7    2.4  2  Fer4_2    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.013   15.7  12.3      0.044   13.9  12.3    1.8  1  Fer4_21   4Fe-4S dicluster domain
      0.048   13.8  10.6      0.077   13.1   1.3    2.4  2  Fer4_6    4Fe-4S binding domain
       0.09   13.7  11.6        1.9    9.5  10.9    2.2  2  Fer4_16   4Fe-4S double cluster binding domain
       0.17   12.4   6.0        0.3   11.6   0.1    2.3  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
       0.31   11.7  12.0       0.18   12.4   3.0    2.6  3  Fer4_4    4Fe-4S binding domain
       0.92   10.3   4.1         13    6.6   0.6    2.4  2  Fer4_15   4Fe-4S single cluster domain
        1.1   10.3  15.4        3.6    8.7   3.1    2.3  2  Fer4_3    4Fe-4S binding domain
          2    8.7   7.7        9.9    6.4   0.3    2.2  2  Fer4_18   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   5.3   5.1e-13   6.1e-10       2      65 .]      18      79 ..      17      79 .. 0.80

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 5.1e-13
                         Fer4_8  2 lekCieCgaCqsaCpvlrrtk.khlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvgi 65
                                   ++ Ci+Cg C s+C +++ ++   ++  r   +++++e  +    e++w Ct+c  Ct++Cp gi
  gi|116754866|ref|YP_843984.1| 18 IRTCIQCGTCSSSCSTAHLMDnSIRKLIRLVLEGRKREALA---SESIWLCTSCLLCTVRCPRGI 79
                                   689***********999999955666666666664444444...799***************997 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   5.5   4.8e-12   5.7e-09       2      60 ..      21      79 ..      20      80 .. 0.96

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 4.8e-12
                        Fer4_17  2 CiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPqgl 60
                                   CiqCg C  +C++   +dn  +kl+r +  g+++ea ++e + lC++C +C+ +CP g+
  gi|116754866|ref|YP_843984.1| 21 CIQCGTCSSSCSTAHLMDNSIRKLIRLVLEGRKREALASESIWLCTSCLLCTVRCPRGI 79
                                   ***************************999999999********************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 !   33.0   5.2   4.2e-11     5e-08       2      49 ..      21      78 ..      20      79 .. 0.93

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 4.2e-11
                         Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraase..........eaCigCgaCveaCpkg 49
                                   C++Cg+C ++C + + ++ + ++ +rl  ++           + C++C  C+ +Cp+g
  gi|116754866|ref|YP_843984.1| 21 CIQCGTCSSSCSTAHLMDNSIRKLIRLVLEGRkrealasesiWLCTSCLLCTVRCPRG 78
                                   ***********9999999999999999887778999********************98 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   3.5   9.1e-09   1.1e-05       1      52 []      20      79 ..      20      79 .. 0.66

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 9.1e-09
                         Fer4_7  1 rCigCgaCvaaCpvkaielde........eenekgtekveidpekClgCgaCvavCPtga 52
                                   +Ci+Cg C + C++  ++ +          e  k+ + +  + + C++C  C  +CP g+
  gi|116754866|ref|YP_843984.1| 20 TCIQCGTCSSSCSTAHLMDNSirklirlvLEGRKREALASESIWLCTSCLLCTVRCPRGI 79
                                   6***********977777553222222221122222444566788************986 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   2.4   0.00021      0.25       8      18 ..      21      31 ..      19      34 .. 0.91
   2 !   11.7   1.4   0.00015      0.18       7      21 ..      64      78 ..      64      80 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00021
                                   SSS-THHHHHS CS
                           Fer4  8 CigCGaCvevC 18
                                   Ci CG+C + C
  gi|116754866|ref|YP_843984.1| 21 CIQCGTCSSSC 31
                                   *********99 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00015
                                   TSSS-THHHHHSTTT CS
                           Fer4  7 kCigCGaCvevCPvg 21
                                   +C+ C +C   CP g
  gi|116754866|ref|YP_843984.1| 64 LCTSCLLCTVRCPRG 78
                                   6************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 !   16.0  11.6     8e-06    0.0096       7      56 .]      19      76 ..      14      76 .. 0.81
   2 !    9.3   2.5     0.001       1.2       9      23 ..      65      79 ..      57     106 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 8e-06
                        Fer4_10  7 dtCirCgkCvkaCPadl.........tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                    tCi+Cg+C ++C +++             + + +++e+  ++ ++ Ct c  C+  CP
  gi|116754866|ref|YP_843984.1| 19 RTCIQCGTCSSSC-STAhlmdnsirkLIRLVLEGRKREALASESIWLCTSCLLCTVRCP 76
                                   69***********.4447*****997444555566666666778**************9 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.001
                        Fer4_10  9 CirCgkCvkaCPadl 23
                                   C+ C  C+  CP  +
  gi|116754866|ref|YP_843984.1| 65 CTSCLLCTVRCPRGI 79
                                   888888888888744 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   3.7   5.2e-05     0.062       9      21 ..      20      32 ..      14      33 .. 0.88
   2 !    8.3   2.5    0.0022       2.6      10      21 ..      65      76 ..      60      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.2e-05
                         Fer4_2  9 rCigCgaCvsaCP 21
                                   +Ci+Cg+C s+C 
  gi|116754866|ref|YP_843984.1| 20 TCIQCGTCSSSCS 32
                                   8***********6 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0022
                         Fer4_2 10 CigCgaCvsaCP 21
                                   C++C  C+  CP
  gi|116754866|ref|YP_843984.1| 65 CTSCLLCTVRCP 76
                                   *******666*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 ?   13.9  12.3   3.7e-05     0.044       7      52 ..      20      76 ..      16      80 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.7e-05
                        Fer4_21  7 kCigCgkCliaCedtsh...qai......eidaktvlkvved...eCvGCnlCssvCP 52
                                   +Ci+Cg C  +C++ +h   + i       ++++++ ++ ++    C+ C lC+  CP
  gi|116754866|ref|YP_843984.1| 20 TCIQCGTCSSSCST-AHlmdNSIrklirlVLEGRKREALASEsiwLCTSCLLCTVRCP 76
                                   8***********95.4423334455566533344443444332347************ PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.3   6.4e-05     0.077       9      22 ..      21      34 ..      19      36 .. 0.88
   2 ?    5.1   2.4     0.021        25       8      22 ..      64      78 ..      64      83 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.4e-05
                         Fer4_6  9 CigCgdCvrvCPeg 22
                                   Ci+Cg C + C ++
  gi|116754866|ref|YP_843984.1| 21 CIQCGTCSSSCSTA 34
                                   ***********986 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.021
                         Fer4_6  8 kCigCgdCvrvCPeg 22
                                   +C++C  C++ CP g
  gi|116754866|ref|YP_843984.1| 64 LCTSCLLCTVRCPRG 78
                                   6***********965 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5  10.9    0.0016       1.9       1      65 [.      20      76 ..      20      78 .. 0.75
   2 ?    6.7   2.8     0.012        14       2      16 ..      65      79 ..      64     110 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0016
                        Fer4_16  1 rCgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCP 65
                                   +C++Cg C ++C t+++  +      +r+ i    +++k    ++ + ++ + +t C  C+  CP
  gi|116754866|ref|YP_843984.1| 20 TCIQCGTCSSSCSTAHLMDN-----SIRKLIRLVLEGRK---REALASESIWLCTSCLLCTVRCP 76
                                   5****************999.....45555555334444...34444455789***********9 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.012
                        Fer4_16  2 CgtCgkCaevCPtna 16
                                   C++C  C+  CP + 
  gi|116754866|ref|YP_843984.1| 65 CTSCLLCTVRCPRGI 79
                                   ************874 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00025       0.3       5      24 ..      20      39 ..      17      58 .. 0.84
   2 ?    2.4   2.0      0.19   2.3e+02       6      17 ..      65      76 ..      64      78 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00025
                        Fer4_13  5 tCiacgaCvelaPdvFeedd 24
                                   tCi cg+C + +     +d+
  gi|116754866|ref|YP_843984.1| 20 TCIQCGTCSSSCSTAHLMDN 39
                                   9*********9988777766 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.19
                        Fer4_13  6 CiacgaCvelaP 17
                                   C++c +C   +P
  gi|116754866|ref|YP_843984.1| 65 CTSCLLCTVRCP 76
                                   ***********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 ?   12.4   3.0   0.00015      0.18       3      16 ..      20      33 ..      18      36 .. 0.92
   2 ?    4.1   1.2      0.07        83       4      16 ..      65      77 ..      59      84 .. 0.89
   3 ?   -2.5   0.0       8.8     1e+04      12      15 ..      90      93 ..      87      96 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00015
                         Fer4_4  3 rCigCgsCvaaCPq 16
                                   +Ci+Cg C ++C++
  gi|116754866|ref|YP_843984.1| 20 TCIQCGTCSSSCST 33
                                   6***********85 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.07
                         Fer4_4  4 CigCgsCvaaCPq 16
                                   C+ C  C+  CP 
  gi|116754866|ref|YP_843984.1| 65 CTSCLLCTVRCPR 77
                                   9*******99996 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 8.8
                         Fer4_4 12 aaCP 15
                                   ++C+
  gi|116754866|ref|YP_843984.1| 90 NICE 93
                                   7887 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 ?    4.7   0.2     0.042        51       7      23 ..      20      36 ..      17      59 .. 0.80
   2 ?    6.6   0.6     0.011        13       7      22 ..      64      79 ..      62     102 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.042
                        Fer4_15  7 aCigcglCvaeapevfe 23
                                   +Ci cg C   +++   
  gi|116754866|ref|YP_843984.1| 20 TCIQCGTCSSSCSTAHL 36
                                   8********99976654 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.011
                        Fer4_15  7 aCigcglCvaeapevf 22
                                   +C++c lC  ++p+ +
  gi|116754866|ref|YP_843984.1| 64 LCTSCLLCTVRCPRGI 79
                                   7***********9765 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   4.5      0.01        12       1      11 [.      21      31 ..      21      33 .. 0.94
   2 ?    8.7   3.1     0.003       3.6       1      14 [.      65      78 ..      65      79 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.01
                         Fer4_3  1 CtgCgaCvevC 11
                                   C++Cg+C  +C
  gi|116754866|ref|YP_843984.1| 21 CIQCGTCSSSC 31
                                   *********** PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.003
                         Fer4_3  1 CtgCgaCvevCPvg 14
                                   Ct C +C + CP g
  gi|116754866|ref|YP_843984.1| 65 CTSCLLCTVRCPRG 78
                                   9***********98 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   1.9     0.017        20      84      97 ..      20      33 ..      10      48 .. 0.62
   2 ?    6.4   0.3    0.0083       9.9      50      75 ..      54      79 ..      46      93 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.017
                        Fer4_18 84 eciscllcidacdk 97
                                    ci+c+ c  +c++
  gi|116754866|ref|YP_843984.1| 20 TCIQCGTCSSSCST 33
                                   46666666666654 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0083
                        Fer4_18 50 keerkekgagdcidcescvkvcPtgi 75
                                   +e  ++++   c++c  c   cP gi
  gi|116754866|ref|YP_843984.1| 54 REALASESIWLCTSCLLCTVRCPRGI 79
                                   55556667778************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); 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 0.23s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 1434.69
//
Query:       gi|116754867|ref|YP_843985.1|  [L=429]
Description: 4Fe-4S ferredoxin iron-sulfur binding domain-containing protein [Methanosaeta thermophila PT]
Scores for 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-37  126.5  80.2    3.6e-08   32.9   4.8    8.3  8  Fer4      4Fe-4S binding domain
    5.6e-28   97.3  97.7      8e-09   36.0   7.3    5.1  7  Fer4_7    4Fe-4S dicluster domain
    1.2e-26   91.6  77.9    5.6e-07   29.4   3.7    8.3  8  Fer4_6    4Fe-4S binding domain
    1.6e-25   89.0  55.6    7.7e-09   35.6   9.3    5.6  5  Fer4_21   4Fe-4S dicluster domain
    3.2e-24   84.8  54.1    1.6e-05   24.9  10.4    7.0  7  Fer4_10   4Fe-4S dicluster domain
    3.3e-24   84.8  53.7    6.5e-07   29.4   4.5    5.4  6  Fer4_9    4Fe-4S dicluster domain
    2.3e-19   68.2  72.1    7.5e-05   22.6   2.3    8.3  8  Fer4_2    4Fe-4S binding domain
    2.7e-16   60.2  58.2      0.017   16.0   0.9    8.0  7  Fer4_16   4Fe-4S double cluster binding domain
    1.2e-11   44.9  55.6     0.0074   16.7   8.0    6.6  8  Fer4_8    4Fe-4S dicluster domain
    1.4e-10   40.8  71.7     0.0007   19.9   3.9    8.3  8  Fer4_4    4Fe-4S binding domain
      1e-08   35.7  59.2     0.0081   16.9   0.5    8.2  7  Fer4_15   4Fe-4S single cluster domain
      8e-06   26.3  67.0       0.23   12.0  10.3    7.6 10  Fer4_17   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.014   16.0  69.9      0.061   13.9   2.7    8.5  8  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
      0.024   15.5   1.3      0.024   15.5   1.3    8.1 10  Fer4_22   4Fe-4S dicluster domain
       0.13   13.2  96.7       0.16   13.0   4.4    8.3  8  Fer4_3    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   1.4   1.2e-07   0.00015       3      23 ..      30      50 ..      28      51 .. 0.91
   2 !   29.9   2.4   2.6e-10   3.2e-07       2      23 ..      68      89 ..      67      90 .. 0.92
   3 !   14.1   3.5   2.6e-05     0.032       6      24 .]     115     133 ..     114     133 .. 0.89
   4 !   18.6   2.2   9.8e-07    0.0012       2      18 ..     155     171 ..     154     175 .. 0.92
   5 !   30.9   2.7   1.3e-10   1.6e-07       3      24 .]     194     215 ..     192     215 .. 0.95
   6 !   32.9   4.8     3e-11   3.6e-08       2      23 ..     232     253 ..     231     254 .. 0.92
   7 !    7.2   4.2     0.004       4.8       9      22 ..     276     289 ..     276     291 .. 0.91
   8 !   14.6   4.9   1.7e-05     0.021       3      18 ..     300     315 ..     298     315 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.2e-07
                                   EETTTSSS-THHHHHSTTTEE CS
                           Fer4  3 ideekCigCGaCvevCPvgAI 23
                                   +d+  C gC +Cv+ CP+ A+
  gi|116754867|ref|YP_843985.1| 30 YDYKICNGCAICVSLCPTKAL 50
                                   79999**************98 PP

  == domain 2  score: 29.9 bits;  conditional E-value: 2.6e-10
                                   EEETTTSSS-THHHHHSTTTEE CS
                           Fer4  2 videekCigCGaCvevCPvgAI 23
                                    id + C++CG C++ CPv+A 
  gi|116754867|ref|YP_843985.1| 68 LIDLDACVFCGMCANFCPVNAY 89
                                   59******************96 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 2.6e-05
                                    TTSSS-THHHHHSTTTEEE CS
                           Fer4   6 ekCigCGaCvevCPvgAIt 24 
                                    e+C  C +C+ vCP++AIt
  gi|116754867|ref|YP_843985.1| 115 ERCLPCTLCEPVCPTEAIT 133
                                    67777*************7 PP

  == domain 4  score: 18.6 bits;  conditional E-value: 9.8e-07
                                    EEETTTSSS-THHHHHS CS
                           Fer4   2 videekCigCGaCvevC 18 
                                     +d ekC  CG+C+  C
  gi|116754867|ref|YP_843985.1| 155 SVDREKCNLCGICARFC 171
                                    69*************** PP

  == domain 5  score: 30.9 bits;  conditional E-value: 1.3e-10
                                    EETTTSSS-THHHHHSTTTEEE CS
                           Fer4   3 ideekCigCGaCvevCPvgAIt 24 
                                    ide++C +CG+Cv +CP +AI+
  gi|116754867|ref|YP_843985.1| 194 IDEDLCDYCGLCVGICPEEAIS 215
                                    9*******************96 PP

  == domain 6  score: 32.9 bits;  conditional E-value: 3e-11
                                    EEETTTSSS-THHHHHSTTTEE CS
                           Fer4   2 videekCigCGaCvevCPvgAI 23 
                                     +d+e+CigCG+C+ vCP++A 
  gi|116754867|ref|YP_843985.1| 232 DVDQERCIGCGRCAIVCPYEAM 253
                                    69******************96 PP

  == domain 7  score: 7.2 bits;  conditional E-value: 0.004
                                    SS-THHHHHSTTTE CS
                           Fer4   9 igCGaCvevCPvgA 22 
                                    +gC  C +vCP ++
  gi|116754867|ref|YP_843985.1| 276 VGCHGCFNVCPADC 289
                                    79**********98 PP

  == domain 8  score: 14.6 bits;  conditional E-value: 1.7e-05
                                    EETTTSSS-THHHHHS CS
                           Fer4   3 ideekCigCGaCvevC 18 
                                    + e+ Ci CGaC  +C
  gi|116754867|ref|YP_843985.1| 300 VVEDQCILCGACSRAC 315
                                    789************* PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   5.4     2e-11   2.4e-08       2      52 .]      35      88 ..      34      88 .. 0.87
   2 !   27.8  12.7   2.4e-09   2.9e-06       1      52 []      73     131 ..      73     131 .. 0.71
   3 !   23.9   8.9     4e-08   4.8e-05       1      49 [.     116     172 ..     116     175 .. 0.80
   4 !   22.2   8.2   1.3e-07   0.00016       1      52 []     160     213 ..     160     213 .. 0.82
   5 !   36.0   7.3   6.7e-12     8e-09       2      52 .]     199     252 ..     198     252 .. 0.83
   6 !   22.4  15.3   1.1e-07   0.00014       1      51 [.     237     288 ..     237     289 .. 0.82
   7 !   14.2  13.5   4.1e-05     0.049       3      48 ..     276     315 ..     272     320 .. 0.92

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 2e-11
                         Fer4_7  2 CigCgaCvaaCpvkaieldeeenekgt...ekveidpekClgCgaCvavCPtga 52
                                   C gC  Cv+ Cp+ka++  +  + ++    + v id + C++Cg+C++ CP++a
  gi|116754867|ref|YP_843985.1| 35 CNGCAICVSLCPTKALQSGPILEIATGldaPPVLIDLDACVFCGMCANFCPVNA 88
                                   *****************99876666333447789******************97 PP

  == domain 2  score: 27.8 bits;  conditional E-value: 2.4e-09
                         Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgt.ekv......eidpekClgCgaCvavCPtga 52 
                                    +C+ Cg C++ Cpv+a +++  +++ +t +++      +   e+Cl C+ C+ vCPt+a
  gi|116754867|ref|YP_843985.1|  73 ACVFCGMCANFCPVNAYRFTVNDVDIKTdDRYprllrkAEPNERCLPCTLCEPVCPTEA 131
                                    5*****************9843222222122233344344569**************87 PP

  == domain 3  score: 23.9 bits;  conditional E-value: 4e-08
                         Fer4_7   1 rCigCgaCvaaCpvkaieldeeenek.......gt.ekveidpekClgCgaCvavCP 49 
                                    rC  C  C+++Cp++ai++   +  +       g+  ++ +d ekC  Cg C++ C 
  gi|116754867|ref|YP_843985.1| 116 RCLPCTLCEPVCPTEAITVVFNKTREdfgplreGIeGEISVDREKCNLCGICARFCK 172
                                    7*****************987543333555544115789***************996 PP

  == domain 4  score: 22.2 bits;  conditional E-value: 1.3e-07
                         Fer4_7   1 rCigCgaCvaaCpvkaieldeeenek..gtekveidpekClgCgaCvavCPtga 52 
                                    +C  Cg C++ C++ ++  +e++  +  + e++ id++ C +Cg Cv  CP +a
  gi|116754867|ref|YP_843985.1| 160 KCNLCGICARFCKAFVLLEREKDPRDlrPYEQLLIDEDLCDYCGLCVGICPEEA 213
                                    7************888877665333333558999*****************876 PP

  == domain 5  score: 36.0 bits;  conditional E-value: 6.7e-12
                         Fer4_7   2 CigCgaCvaaCpvkaieldeeenek...gtekveidpekClgCgaCvavCPtga 52 
                                    C  Cg Cv  Cp +ai+++ +  ++    + ++++d+e+C+gCg+C+ vCP++a
  gi|116754867|ref|YP_843985.1| 199 CDYCGLCVGICPEEAISVKGDPLDAtldLKGSIDVDQERCIGCGRCAIVCPYEA 252
                                    999**************9965333323344899******************986 PP

  == domain 6  score: 22.4 bits;  conditional E-value: 1.1e-07
                         Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekC..lgCgaCvavCPtg 51 
                                    rCigCg+C+ +Cp++a+++    +  +++ v+ +  kC  +gC+ C +vCP++
  gi|116754867|ref|YP_843985.1| 237 RCIGCGRCAIVCPYEAMDVIRPFE-GEIRLVRDRLAKCdpVGCHGCFNVCPAD 288
                                    8*****************876543.3445566668899888**********87 PP

  == domain 7  score: 14.2 bits;  conditional E-value: 4.1e-05
                         Fer4_7   3 igCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavC 48 
                                    +gC+ C ++Cp+++ ++d++       ++ +++++C+ CgaC ++C
  gi|116754867|ref|YP_843985.1| 276 VGCHGCFNVCPADCWYVDDQ------GRIGVVEDQCILCGACSRAC 315
                                    69***************996......5899**************** PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   2.0   8.3e-06    0.0099       4      24 .]      30      50 ..      27      50 .. 0.91
   2 !   13.6   3.4   4.6e-05     0.055       2      24 .]      67      89 ..      66      89 .. 0.92
   3 !   14.6   3.8   2.2e-05     0.027       7      24 .]     115     132 ..     114     132 .. 0.94
   4 !   18.2   1.7   1.6e-06    0.0019       2      21 ..     154     173 ..     153     176 .. 0.89
   5 !   21.6   2.3   1.3e-07   0.00015       4      24 .]     194     214 ..     192     214 .. 0.96
   6 !   29.4   3.7   4.7e-10   5.6e-07       3      23 ..     232     252 ..     230     253 .. 0.91
   7 ?    4.6   6.0     0.031        38       8      22 ..     272     288 ..     270     290 .. 0.89
   8 !   16.2   1.4   6.9e-06    0.0082       4      19 ..     300     315 ..     297     320 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 8.3e-06
                         Fer4_6  4 idpdkCigCgdCvrvCPegai 24
                                   +d+  C+gC  Cv+ CP++a+
  gi|116754867|ref|YP_843985.1| 30 YDYKICNGCAICVSLCPTKAL 50
                                   68899*************996 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 4.6e-05
                         Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                   v id d+C+ Cg C++ CP +a+
  gi|116754867|ref|YP_843985.1| 67 VLIDLDACVFCGMCANFCPVNAY 89
                                   679*****************996 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 2.2e-05
                         Fer4_6   7 dkCigCgdCvrvCPegai 24 
                                    ++C+ C  C+ vCP+ ai
  gi|116754867|ref|YP_843985.1| 115 ERCLPCTLCEPVCPTEAI 132
                                    79*************998 PP

  == domain 4  score: 18.2 bits;  conditional E-value: 1.6e-06
                         Fer4_6   2 veidpdkCigCgdCvrvCPe 21 
                                    + +d++kC+ Cg C+r C +
  gi|116754867|ref|YP_843985.1| 154 ISVDREKCNLCGICARFCKA 173
                                    689***************76 PP

  == domain 5  score: 21.6 bits;  conditional E-value: 1.3e-07
                         Fer4_6   4 idpdkCigCgdCvrvCPegai 24 
                                    id+d+C+ Cg Cv +CPe ai
  gi|116754867|ref|YP_843985.1| 194 IDEDLCDYCGLCVGICPEEAI 214
                                    8******************98 PP

  == domain 6  score: 29.4 bits;  conditional E-value: 4.7e-10
                         Fer4_6   3 eidpdkCigCgdCvrvCPega 23 
                                     +d+++CigCg+C++vCP+ a
  gi|116754867|ref|YP_843985.1| 232 DVDQERCIGCGRCAIVCPYEA 252
                                    69****************987 PP

  == domain 7  score: 4.6 bits;  conditional E-value: 0.031
                         Fer4_6   8 kCi..gCgdCvrvCPeg 22 
                                    kC+  gC  C++vCP++
  gi|116754867|ref|YP_843985.1| 272 KCDpvGCHGCFNVCPAD 288
                                    899999*********96 PP

  == domain 8  score: 16.2 bits;  conditional E-value: 6.9e-06
                         Fer4_6   4 idpdkCigCgdCvrvC 19 
                                    + +d Ci Cg+C r+C
  gi|116754867|ref|YP_843985.1| 300 VVEDQCILCGACSRAC 315
                                    6689************ PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   1.5   2.1e-05     0.025      32      55 ..      26      48 ..      10      52 .. 0.73
   2 !   29.6   6.3   4.8e-10   5.7e-07       3      58 ..      69     133 ..      67     134 .. 0.74
   3 !   21.9   4.9   1.2e-07   0.00014       3      58 ..     156     215 ..     154     216 .. 0.75
   4 !   35.6   9.3   6.4e-12   7.7e-09       3      56 ..     233     289 ..     231     292 .. 0.78
   5 !   10.6   2.7   0.00039      0.47       4      24 ..     301     321 ..     298     335 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.1e-05
                        Fer4_21 32 tvlkvvedeCvGCnlCssvCPved 55
                                   ++l +  + C GC++C+s CP+ +
  gi|116754867|ref|YP_843985.1| 26 KILDYDYKICNGCAICVSLCPT-K 48
                                   445556678************7.4 PP

  == domain 2  score: 29.6 bits;  conditional E-value: 4.8e-10
                        Fer4_21   3 idedkCigCgkCliaCedtshqai....eidaktvl.....kvv..edeCvGCnlCssvCPvedcie 58 
                                    id d C+ Cg C+  C+ +++       +i+++ ++     k    +++C  C+lC  vCP+ ++i+
  gi|116754867|ref|YP_843985.1|  69 IDLDACVFCGMCANFCPVNAYRFTvndvDIKTDDRYprllrK-AepNERCLPCTLCEPVCPT-EAIT 133
                                    999***************999876454434433333333432.23589*************7.8987 PP

  == domain 3  score: 21.9 bits;  conditional E-value: 1.2e-07
                        Fer4_21   3 idedkCigCgkCliaCedtshqai.......eidaktvlkvvedeCvGCnlCssvCPvedcie 58 
                                    +d++kC  Cg C+  C+  +   +       ++ + ++l + ed C  C lC+ +CP e++i+
  gi|116754867|ref|YP_843985.1| 156 VDREKCNLCGICARFCK--AFVLLerekdprDLRPYEQLLIDEDLCDYCGLCVGICP-EEAIS 215
                                    89***************..455554433322333334567779**************.79986 PP

  == domain 4  score: 35.6 bits;  conditional E-value: 6.4e-12
                        Fer4_21   3 idedkCigCgkCliaCedtshqaieidaktvlkvv..edeC..vGCnlCssvCPvedc 56 
                                    +d+++CigCg+C+i+C+ ++++ i+  + ++  v+    +C  vGC+ C +vCP  dc
  gi|116754867|ref|YP_843985.1| 233 VDQERCIGCGRCAIVCPYEAMDVIRPFEGEIRLVRdrLAKCdpVGCHGCFNVCPA-DC 289
                                    89**********************85544443333124566559**********5.88 PP

  == domain 5  score: 10.6 bits;  conditional E-value: 0.00039
                        Fer4_21   4 dedkCigCgkCliaCedtshq 24 
                                     ed+Ci Cg C  aC+  +++
  gi|116754867|ref|YP_843985.1| 301 VEDQCILCGACSRACHLFGID 321
                                    579999999999999865555 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2   1.7e-05      0.02       4      23 ..      30      49 ..      27      64 .. 0.80
   2 !   19.5   0.4   6.8e-07   0.00081       2      29 ..      67      89 ..      66     106 .. 0.74
   3 !   18.3   9.0   1.5e-06    0.0018       5      55 ..     113     171 ..     109     172 .. 0.88
   4 !   16.0   0.1   8.4e-06      0.01       3      27 ..     193     217 ..     191     229 .. 0.82
   5 !   24.9  10.4   1.4e-08   1.6e-05       4      56 .]     233     286 ..     230     286 .. 0.90
   6 !   11.4  14.0   0.00022      0.26       7      55 ..     271     315 ..     264     316 .. 0.75
   7 !   13.3   1.6   5.7e-05     0.069       5      24 ..     301     325 ..     297     356 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.7e-05
                        Fer4_10  4 idddtCirCgkCvkaCPadl 23
                                   +d + C +C+ Cv+ CP+++
  gi|116754867|ref|YP_843985.1| 30 YDYKICNGCAICVSLCPTKA 49
                                   68999************944 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 6.8e-07
                        Fer4_10  2 vvidddtCirCgkCvkaCPadltsvgak 29
                                   v id d C+ Cg C ++CP+++     +
  gi|116754867|ref|YP_843985.1| 67 VLIDLDACVFCGMCANFCPVNA-----Y 89
                                   679*****************55.....2 PP

  == domain 3  score: 18.3 bits;  conditional E-value: 1.5e-06
                        Fer4_10   5 dddtCirCgkCvkaCPadl........tsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                    + ++C+ C+ C  +CP+ +        +++ +   + +e++++++ ekC  cg C++ C
  gi|116754867|ref|YP_843985.1| 113 PNERCLPCTLCEPVCPTEAitvvfnktREDFGPLREGIEGEISVDREKCNLCGICARFC 171
                                    5689*************99******9766667777778889999*************99 PP

  == domain 4  score: 16.0 bits;  conditional E-value: 8.4e-06
                        Fer4_10   3 vidddtCirCgkCvkaCPadltsvg 27 
                                     id+d C  Cg Cv  CP  + sv+
  gi|116754867|ref|YP_843985.1| 193 LIDEDLCDYCGLCVGICPEEAISVK 217
                                    69****************9665555 PP

  == domain 5  score: 24.9 bits;  conditional E-value: 1.4e-08
                        Fer4_10   4 idddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtg..cgaCveaCP 56 
                                    +d+++Ci+Cg+C  +CP+   +++ ++++ e+  vr+ + kC+   c  C  +CP
  gi|116754867|ref|YP_843985.1| 233 VDQERCIGCGRCAIVCPY-EAMDVIRPFEGEIRLVRDRLAKCDPvgCHGCFNVCP 286
                                    699**************9.7788899999999**********975588******9 PP

  == domain 6  score: 11.4 bits;  conditional E-value: 0.00022
                        Fer4_10   7 dtC..irCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                     +C  ++C  C ++CPa         + ++++++ ++ ++C+ cgaC +aC
  gi|116754867|ref|YP_843985.1| 271 AKCdpVGCHGCFNVCPA------DCWYVDDQGRIGVVEDQCILCGACSRAC 315
                                    678778***********......33344444455556689*********** PP

  == domain 7  score: 13.3 bits;  conditional E-value: 5.7e-05
                        Fer4_10   5 dddtCirCgkCvkaCPadl.......t 24 
                                     +d+Ci Cg+C +aC  +l       t
  gi|116754867|ref|YP_843985.1| 301 VEDQCILCGACSRAC--HLfgidvtrT 325
                                    5799***********..7744444331 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   4.5   5.4e-10   6.5e-07       2      50 ..      35      88 ..      34      89 .. 0.92
   2 !   14.4   1.1   2.7e-05     0.032      24      51 .]     106     132 ..      93     132 .. 0.69
   3 !   24.0   5.7   2.6e-08   3.1e-05       1      51 []     160     214 ..     160     214 .. 0.79
   4 !   27.8   9.4   1.7e-09   2.1e-06       2      50 ..     199     252 ..     198     253 .. 0.95
   5 !   22.8  13.7   6.3e-08   7.6e-05       1      49 [.     237     288 ..     237     289 .. 0.94
   6 !   18.7  13.1   1.2e-06    0.0014       3      47 ..     276     316 ..     272     320 .. 0.92

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 5.4e-10
                         Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraase.....eaCigCgaCveaCpkga 50
                                   C+gC  Cv+ Cp+++ +     ++a    a       +aC++Cg C++ Cp +a
  gi|116754867|ref|YP_843985.1| 35 CNGCAICVSLCPTKALQSGPILEIATGLDAPPvlidlDACVFCGMCANFCPVNA 88
                                   *******************99999998666559******************986 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 2.7e-05
                         Fer4_9  24 rkarlraaseeaCigCgaCveaCpkgai 51 
                                    r  r  + + e+C+ C  C+ +Cp++ai
  gi|116754867|ref|YP_843985.1| 106 RLLRKAEPN-ERCLPCTLCEPVCPTEAI 132
                                    333333333.69*************987 PP

  == domain 3  score: 24.0 bits;  conditional E-value: 2.6e-08
                         Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase.....eaCigCgaCveaCpkgai 51 
                                    kC+ Cg C + C+a v  e+++   +    +++     + C  Cg Cv +Cp++ai
  gi|116754867|ref|YP_843985.1| 160 KCNLCGICARFCKAFVLLEREKDPRDLR-PYEQllideDLCDYCGLCVGICPEEAI 214
                                    7***********9988865555555443.3334479999**************987 PP

  == domain 4  score: 27.8 bits;  conditional E-value: 1.7e-09
                         Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase.....eaCigCgaCveaCpkga 50 
                                    C  Cg Cv  Cp ++++ +  +  a l+ ++      e+CigCg+C+ +Cp +a
  gi|116754867|ref|YP_843985.1| 199 CDYCGLCVGICPEEAISVKGDPLDATLDLKGSidvdqERCIGCGRCAIVCPYEA 252
                                    99************************9999889******************987 PP

  == domain 5  score: 22.8 bits;  conditional E-value: 6.3e-08
                         Fer4_9   1 kCtgCgaCveaCpagvv.vedaaerkarlraaseeaC..igCgaCveaCpkg 49 
                                    +C+gCg+C  +Cp++++ v + +e+++rl +++  +C  +gC+ C+++Cp +
  gi|116754867|ref|YP_843985.1| 237 RCIGCGRCAIVCPYEAMdVIRPFEGEIRLVRDRLAKCdpVGCHGCFNVCPAD 288
                                    6****************89999*******99999***9999*********87 PP

  == domain 6  score: 18.7 bits;  conditional E-value: 1.2e-06
                         Fer4_9   3 tgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCp 47 
                                    +gC+ C ++Cpa+ +  d+++r+  ++     +Ci CgaC  aC 
  gi|116754867|ref|YP_843985.1| 276 VGCHGCFNVCPADCWYVDDQGRIGVVED----QCILCGACSRACH 316
                                    58**********************9976....6***********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 !   17.8   1.6   2.1e-06    0.0025       5      22 .]      30      47 ..      27      47 .. 0.92
   2 !   13.4   3.0   5.5e-05     0.065       1      21 [.      65      85 ..      65      86 .. 0.93
   3 ?    3.4   5.2     0.079        95       8      22 .]     115     129 ..     110     129 .. 0.88
   4 !   17.5   1.4   2.6e-06    0.0031       3      22 .]     154     173 ..     152     173 .. 0.90
   5 !   16.3   0.7   6.5e-06    0.0078       4      22 .]     193     211 ..     190     211 .. 0.92
   6 !   22.6   2.3   6.3e-08   7.5e-05       5      22 .]     233     250 ..     229     250 .. 0.90
   7 ?    4.2   2.9     0.044        52      11      22 .]     276     287 ..     266     287 .. 0.87
   8 !   14.0   2.5   3.4e-05      0.04       2      20 ..     297     315 ..     296     316 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.1e-06
                         Fer4_2  5 vdtdrCigCgaCvsaCPa 22
                                   +d  +C+gC +Cvs CP+
  gi|116754867|ref|YP_843985.1| 30 YDYKICNGCAICVSLCPT 47
                                   7889*************7 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 5.5e-05
                         Fer4_2  1 apvvvdtdrCigCgaCvsaCP 21
                                   +pv +d d+C+ Cg C + CP
  gi|116754867|ref|YP_843985.1| 65 PPVLIDLDACVFCGMCANFCP 85
                                   5799***************** PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.079
                         Fer4_2   8 drCigCgaCvsaCPa 22 
                                    +rC+ C  C  +CP+
  gi|116754867|ref|YP_843985.1| 115 ERCLPCTLCEPVCPT 129
                                    68999*********7 PP

  == domain 4  score: 17.5 bits;  conditional E-value: 2.6e-06
                         Fer4_2   3 vvvdtdrCigCgaCvsaCPa 22 
                                    + vd+++C+ Cg+C   C a
  gi|116754867|ref|YP_843985.1| 154 ISVDREKCNLCGICARFCKA 173
                                    569***************75 PP

  == domain 5  score: 16.3 bits;  conditional E-value: 6.5e-06
                         Fer4_2   4 vvdtdrCigCgaCvsaCPa 22 
                                     +d+d C  Cg Cv  CP+
  gi|116754867|ref|YP_843985.1| 193 LIDEDLCDYCGLCVGICPE 211
                                    69****************5 PP

  == domain 6  score: 22.6 bits;  conditional E-value: 6.3e-08
                         Fer4_2   5 vdtdrCigCgaCvsaCPa 22 
                                    vd +rCigCg C  +CP+
  gi|116754867|ref|YP_843985.1| 233 VDQERCIGCGRCAIVCPY 250
                                    89***************5 PP

  == domain 7  score: 4.2 bits;  conditional E-value: 0.044
                         Fer4_2  11 igCgaCvsaCPa 22 
                                    +gC  C ++CPa
  gi|116754867|ref|YP_843985.1| 276 VGCHGCFNVCPA 287
                                    59*99******8 PP

  == domain 8  score: 14.0 bits;  conditional E-value: 3.4e-05
                         Fer4_2   2 pvvvdtdrCigCgaCvsaC 20 
                                    ++ v++d Ci CgaC  aC
  gi|116754867|ref|YP_843985.1| 297 RIGVVEDQCILCGACSRAC 315
                                    567899************* 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 !   16.0   0.9   1.4e-05     0.017       2      20 ..      35      53 ..      34      64 .. 0.85
   2 !   15.2   0.3   2.6e-05     0.031       2      31 ..      74     102 ..      73     115 .. 0.74
   3 !   12.0  11.8   0.00026      0.31       1      64 [.     116     171 ..     116     173 .. 0.68
   4 ?    5.3   1.8     0.032        38       1      20 [.     160     179 ..     160     190 .. 0.78
   5 !   15.3   0.6   2.4e-05     0.028       2      20 ..     199     217 ..     198     235 .. 0.86
   6 !    8.8  12.4    0.0026       3.1       1      66 [.     237     287 ..     237     288 .. 0.73
   7 !    7.4   0.2    0.0072       8.6       1      20 [.     304     323 ..     304     354 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.4e-05
                        Fer4_16  2 CgtCgkCaevCPtnaikek 20
                                   C +C  C++ CPt+a+++ 
  gi|116754867|ref|YP_843985.1| 35 CNGCAICVSLCPTKALQSG 53
                                   ****************987 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 2.6e-05
                        Fer4_16   2 CgtCgkCaevCPtnaikekkekeieareci 31 
                                    C+ Cg Ca+ CP+na + +  + ++++++ 
  gi|116754867|ref|YP_843985.1|  74 CVFCGMCANFCPVNAYRFT-VNDVDIKTDD 102
                                    9999999999999998887.4566666555 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.00026
                        Fer4_16   1 rCgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvC 64 
                                    rC  C+ C  vCPt+ai+      +++ ++     + +++++ ++  +   e++  C+iC++ C
  gi|116754867|ref|YP_843985.1| 116 RCLPCTLCEPVCPTEAITVV----FNKTRE--DFGPLREGIEGEISVDR--EKCNLCGICARFC 171
                                    6999**************99....333332..22333444444444443..6678********* PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.032
                        Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                    +C  Cg Ca  C + ++ e+
  gi|116754867|ref|YP_843985.1| 160 KCNLCGICARFCKAFVLLER 179
                                    59999999999988887776 PP

  == domain 5  score: 15.3 bits;  conditional E-value: 2.4e-05
                        Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                    C  Cg C+ +CP++ai+ k
  gi|116754867|ref|YP_843985.1| 199 CDYCGLCVGICPEEAISVK 217
                                    9***************977 PP

  == domain 6  score: 8.8 bits;  conditional E-value: 0.0026
                        Fer4_16   1 rCgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCPa 66 
                                    rC++Cg+Ca vCP +a++  + +e e            + ++++ +kc+      gC  C +vCPa
  gi|116754867|ref|YP_843985.1| 237 RCIGCGRCAIVCPYEAMDVIRPFEGE-----------IRLVRDRLAKCD----PVGCHGCFNVCPA 287
                                    6***************9988333333...........344566677777....6788888888886 PP

  == domain 7  score: 7.4 bits;  conditional E-value: 0.0072
                        Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                    +C+ Cg+C  +C    i+ +
  gi|116754867|ref|YP_843985.1| 304 QCILCGACSRACHLFGIDVT 323
                                    5999********87766666 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   3.0     0.031        37       5      63 ..      35      47 ..      13      49 .. 0.70
   2 !   10.6  11.0    0.0005       0.6       4      64 ..      34      87 ..      31      88 .. 0.78
   3 !   12.7  12.8   0.00011      0.14       2      64 ..      71     130 ..      70     131 .. 0.67
   4 !   16.7   8.0   6.2e-06    0.0074       3      63 ..     115     173 ..     113     175 .. 0.91
   5 !   12.1   7.7   0.00017       0.2       3      64 ..     159     212 ..     157     214 .. 0.70
   6 !   13.8   9.0     5e-05     0.059       5      63 ..     199     250 ..     195     252 .. 0.78
   7 !    7.4  12.4    0.0049       5.9       2      63 ..     235     287 ..     232     289 .. 0.68
   8 !   14.7   0.1   2.7e-05     0.033       4      19 ..     304     319 ..     302     359 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.031
                         Fer4_8  5 CieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63
                                   C++C  C                                               + Cp+
  gi|116754867|ref|YP_843985.1| 35 CNGCAICV----------------------------------------------SLCPT 47
                                   55555555..............................................55554 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0005
                         Fer4_8  4 kCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                                    C++C  C s Cp+   +   +l+   +  +             l++C+ cg+C++ Cpv+
  gi|116754867|ref|YP_843985.1| 34 ICNGCAICVSLCPTKALQSGPILEIATGLDA-PPVLID------LDACVFCGMCANFCPVN 87
                                   6************888888666666666666.333333......79*************97 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 0.00011
                         Fer4_8   2 lekCieCgaCqsaCp..vlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                    l++C+ Cg+C + Cp  ++r t ++   + +++       + l ++e  ++C+ c  C+ vCp++
  gi|116754867|ref|YP_843985.1|  71 LDACVFCGMCANFCPvnAYRFTVNDVDIKTDDRYP-----RLLRKAEPNERCLPCTLCEPVCPTE 130
                                    799************44344444444444444333.....2222246679*************85 PP

  == domain 4  score: 16.7 bits;  conditional E-value: 6.2e-06
                         Fer4_8   3 ekCieCgaCqsaCp......vlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63 
                                    e+C  C +C+  Cp      v+++t+++    r++ ++ + + ++       ++C+ cg C++ C+ 
  gi|116754867|ref|YP_843985.1| 115 ERCLPCTLCEPVCPteaitvVFNKTREDFGPLREGIEG-EISVDR-------EKCNLCGICARFCKA 173
                                    69***********9999998999999999999999999.888888.......9************86 PP

  == domain 5  score: 12.1 bits;  conditional E-value: 0.00017
                         Fer4_8   3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                    ekC+ Cg C   C ++    ++ +d+r+ +  ++   ++       + C  cg C+  Cp++
  gi|116754867|ref|YP_843985.1| 159 EKCNLCGICARFCKAFVLLERE-KDPRDLRPYEQLLIDE-------DLCDYCGLCVGICPEE 212
                                    79***********865555444.3333333331334444.......78************85 PP

  == domain 6  score: 13.8 bits;  conditional E-value: 5e-05
                         Fer4_8   5 CieCgaCqsaCp.vlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63 
                                    C  Cg+C   Cp  + + k ++lda  + ++   + +        ++C +cg+C+ vCp 
  gi|116754867|ref|YP_843985.1| 199 CDYCGLCVGICPeEAISVKGDPLDATLDLKG-SIDVDQ-------ERCIGCGRCAIVCPY 250
                                    999********95333344788899988888.444444.......69************6 PP

  == domain 7  score: 7.4 bits;  conditional E-value: 0.0049
                         Fer4_8   2 lekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsC..ttcgaCtevCpv 63 
                                     e+Ci+Cg+C   Cp ++++  +   + ++ +   + +++      l +C  ++c+ C +vCp 
  gi|116754867|ref|YP_843985.1| 235 QERCIGCGRCAIVCP-YEAM--DVIRPFEGEIR-LV-RDR------LAKCdpVGCHGCFNVCPA 287
                                    589***********9.4444..33333333333.22.234......578877899999999997 PP

  == domain 8  score: 14.7 bits;  conditional E-value: 2.7e-05
                         Fer4_8   4 kCieCgaCqsaCpvlr 19 
                                    +Ci CgaC  aC+++ 
  gi|116754867|ref|YP_843985.1| 304 QCILCGACSRACHLFG 319
                                    8***********9653 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   2.2   0.00039      0.46       4      16 ..      35      47 ..      30      49 .. 0.89
   2 !   12.3   1.6   0.00016      0.19       2      17 .]      72      87 ..      71      90 .. 0.91
   3 !    7.1   2.5    0.0073       8.8       2      16 ..     115     129 ..     114     133 .. 0.93
   4 !   10.8   1.5   0.00049      0.58       2      15 ..     159     172 ..     158     180 .. 0.93
   5 !    8.2   1.5    0.0034       4.1       3      16 ..     198     211 ..     196     218 .. 0.86
   6 !   19.9   3.9   5.9e-07    0.0007       1      16 [.     235     250 ..     235     251 .. 0.94
   7 ?    3.5   4.0      0.11   1.3e+02       3      16 ..     272     287 ..     270     295 .. 0.86
   8 !    8.6   1.6    0.0024       2.9       4      15 ..     305     316 ..     302     324 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00039
                         Fer4_4  4 CigCgsCvaaCPq 16
                                   C+gC  Cv+ CP+
  gi|116754867|ref|YP_843985.1| 35 CNGCAICVSLCPT 47
                                   ************8 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00016
                         Fer4_4  2 erCigCgsCvaaCPqg 17
                                   + C+ Cg C ++CP++
  gi|116754867|ref|YP_843985.1| 72 DACVFCGMCANFCPVN 87
                                   89************75 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0073
                         Fer4_4   2 erCigCgsCvaaCPq 16 
                                    erC+ C  C+ +CP+
  gi|116754867|ref|YP_843985.1| 115 ERCLPCTLCEPVCPT 129
                                    89************7 PP

  == domain 4  score: 10.8 bits;  conditional E-value: 0.00049
                         Fer4_4   2 erCigCgsCvaaCP 15 
                                    e+C+ Cg C ++C+
  gi|116754867|ref|YP_843985.1| 159 EKCNLCGICARFCK 172
                                    89***********7 PP

  == domain 5  score: 8.2 bits;  conditional E-value: 0.0034
                         Fer4_4   3 rCigCgsCvaaCPq 16 
                                     C  Cg Cv +CP 
  gi|116754867|ref|YP_843985.1| 198 LCDYCGLCVGICPE 211
                                    5777*********5 PP

  == domain 6  score: 19.9 bits;  conditional E-value: 5.9e-07
                         Fer4_4   1 qerCigCgsCvaaCPq 16 
                                    qerCigCg+C ++CP+
  gi|116754867|ref|YP_843985.1| 235 QERCIGCGRCAIVCPY 250
                                    79*************8 PP

  == domain 7  score: 3.5 bits;  conditional E-value: 0.11
                         Fer4_4   3 rC..igCgsCvaaCPq 16 
                                    +C  +gC  C ++CP 
  gi|116754867|ref|YP_843985.1| 272 KCdpVGCHGCFNVCPA 287
                                    68778**********5 PP

  == domain 8  score: 8.6 bits;  conditional E-value: 0.0024
                         Fer4_4   4 CigCgsCvaaCP 15 
                                    Ci Cg+C +aC 
  gi|116754867|ref|YP_843985.1| 305 CILCGACSRACH 316
                                    ***********6 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.8    0.0017         2       3      20 ..      30      47 ..      29      52 .. 0.90
   2 !   10.8   1.3   0.00053      0.63       1      19 [.      67      85 ..      67     104 .. 0.85
   3 ?    2.0   0.1       0.3   3.5e+02      58      66 .]     126     134 ..     124     134 .. 0.91
   4 !   16.9   0.5   6.8e-06    0.0081       1      29 [.     154     181 ..     154     188 .. 0.82
   5 !   13.6   0.8   6.9e-05     0.083       3      20 ..     194     211 ..     192     225 .. 0.90
   6 !   14.0   2.5   5.5e-05     0.065       1      19 [.     231     249 ..     231     257 .. 0.86
   7 !    9.9   0.2     0.001       1.2       5      26 ..     302     322 ..     298     347 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0017
                        Fer4_15  3 vDrdaCigcglCvaeape 20
                                   +D + C gc+ Cv ++p+
  gi|116754867|ref|YP_843985.1| 30 YDYKICNGCAICVSLCPT 47
                                   58999***********95 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00053
                        Fer4_15  1 VvvDrdaCigcglCvaeap 19
                                   V +D daC  cg+C+  +p
  gi|116754867|ref|YP_843985.1| 67 VLIDLDACVFCGMCANFCP 85
                                   78*************9997 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.3
                        Fer4_15  58 aCPvdAIrv 66 
                                    +CP++AI+v
  gi|116754867|ref|YP_843985.1| 126 VCPTEAITV 134
                                    7******97 PP

  == domain 4  score: 16.9 bits;  conditional E-value: 6.8e-06
                        Fer4_15   1 VvvDrdaCigcglCvaeapevfeldedgl 29 
                                    + vDr++C  cg C++ ++  f+l e+ +
  gi|116754867|ref|YP_843985.1| 154 ISVDREKCNLCGICARFCK-AFVLLEREK 181
                                    78****************7.666666665 PP

  == domain 5  score: 13.6 bits;  conditional E-value: 6.9e-05
                        Fer4_15   3 vDrdaCigcglCvaeape 20 
                                    +D+d+C+ cglCv  +pe
  gi|116754867|ref|YP_843985.1| 194 IDEDLCDYCGLCVGICPE 211
                                    9***************86 PP

  == domain 6  score: 14.0 bits;  conditional E-value: 5.5e-05
                        Fer4_15   1 VvvDrdaCigcglCvaeap 19 
                                    + vD+++Cigcg+C+ ++p
  gi|116754867|ref|YP_843985.1| 231 IDVDQERCIGCGRCAIVCP 249
                                    569************9998 PP

  == domain 7  score: 9.9 bits;  conditional E-value: 0.001
                        Fer4_15   5 rdaCigcglCvaeapevfelde 26 
                                    +d+Ci cg+C +++  +f +d 
  gi|116754867|ref|YP_843985.1| 302 EDQCILCGACSRACH-LFGIDV 322
                                    699**********95.998885 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   2.3    0.0035       4.1       2      14 ..      35      47 ..      17      51 .. 0.73
   2 ?    6.4  11.2     0.011        13       2      58 ..      35      86 ..      34      89 .. 0.78
   3 !   11.9  10.7   0.00021      0.25       1      59 [.      73     130 ..      73     131 .. 0.69
   4 !    8.5  11.3    0.0025         3       1      57 [.     116     172 ..     116     175 .. 0.69
   5 ?    6.2   9.7     0.013        15       1      59 [.     160     212 ..     160     214 .. 0.71
   6 !   12.0  10.3    0.0002      0.23       2      59 ..     199     251 ..     198     253 .. 0.71
   7 ?   -0.5   4.1       1.5   1.8e+03      47      59 ..     276     288 ..     267     290 .. 0.79
   8 ?   -0.1   4.0       1.2   1.4e+03      48      59 ..     277     288 ..     272     299 .. 0.72
   9 !    7.3   3.4     0.006       7.1      44      56 ..     303     315 ..     293     317 .. 0.87
  10 !    8.1   2.6    0.0034         4       2      17 ..     305     320 ..     304     350 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0035
                        Fer4_17  2 CiqCgyClpeCps 14
                                   C++C+ C+  Cp+
  gi|116754867|ref|YP_843985.1| 35 CNGCAICVSLCPT 47
                                   6666666666664 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.011
                        Fer4_17  2 CiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPq 58
                                   C++C+ C+  Cp+ +  +     ++ +++ g l++       + C+ Cg+C+  CP 
  gi|116754867|ref|YP_843985.1| 35 CNGCAICVSLCPTKALQSG----PILEIATG-LDAPPVLIDLDACVFCGMCANFCPV 86
                                   *************999887....66665554.33322336899*************6 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00021
                        Fer4_17   1 rCiqCgyClpeCpsyea..ydnepkkllraaklglleeaekeekaslCieCgeCerkCPqg 59 
                                    +C  Cg+C++ Cp ++   + n+ +    + ++ ll++    e  ++C+ C +Ce +CP +
  gi|116754867|ref|YP_843985.1|  73 ACVFCGMCANFCPVNAYrfTVNDVDIKTDDRYPRLLRK---AEPNERCLPCTLCEPVCPTE 130
                                    5999*********8554223333333333434455554...47889*************75 PP

  == domain 4  score: 8.5 bits;  conditional E-value: 0.0025
                        Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaeke..ekaslCieCgeCerkCP 57 
                                    rC  C  C+p+Cp+ +++    +k+++++ + l e++e e     ++C+ Cg C+r C 
  gi|116754867|ref|YP_843985.1| 116 RCLPCTLCEPVCPTEAITVV-FNKTREDFGP-LREGIEGEisVDREKCNLCGICARFCK 172
                                    7************9988544.2334555444.23333333215789***********96 PP

  == domain 5  score: 6.2 bits;  conditional E-value: 0.013
                        Fer4_17   1 rCiqCgyClpeCpsyeaydne..pkkllraaklglleeaekeekaslCieCgeCerkCPqg 59 
                                    +C+ Cg C++ C  +   + e  p+ l+   +l l++e       +lC  Cg+C+  CP++
  gi|116754867|ref|YP_843985.1| 160 KCNLCGICARFCKAFVLLEREkdPRDLRPYEQL-LIDE-------DLCDYCGLCVGICPEE 212
                                    6************99985553113333333222.4444.......79************86 PP

  == domain 6  score: 12.0 bits;  conditional E-value: 0.0002
                        Fer4_17   2 CiqCgyClpeCpsyea.ydnepkkllraaklglleeaekeekaslCieCgeCerkCPqg 59 
                                    C  Cg C+  Cp  ++  + +   +l a +l l++ +  +   ++Ci+Cg+C+ +CP++
  gi|116754867|ref|YP_843985.1| 199 CDYCGLCVGICPEEAIsVKGD---PLDA-TLDLKGSI--DVDQERCIGCGRCAIVCPYE 251
                                    99**********988833333...3433.33233332..44569*************97 PP

  == domain 7  score: -0.5 bits;  conditional E-value: 1.5
                        Fer4_17  47 ieCgeCerkCPqg 59 
                                    ++C++C  +CP++
  gi|116754867|ref|YP_843985.1| 276 VGCHGCFNVCPAD 288
                                    5788888888875 PP

  == domain 8  score: -0.1 bits;  conditional E-value: 1.2
                        Fer4_17  48 eCgeCerkCPqg 59 
                                    +C++C  +CP++
  gi|116754867|ref|YP_843985.1| 277 GCHGCFNVCPAD 288
                                    566666666654 PP

  == domain 9  score: 7.3 bits;  conditional E-value: 0.006
                        Fer4_17  44 slCieCgeCerkC 56 
                                    ++Ci Cg C+r+C
  gi|116754867|ref|YP_843985.1| 303 DQCILCGACSRAC 315
                                    6899999999999 PP

  == domain 10  score: 8.1 bits;  conditional E-value: 0.0034
                        Fer4_17   2 CiqCgyClpeCpsyea 17 
                                    Ci Cg+C ++C  + +
  gi|116754867|ref|YP_843985.1| 305 CILCGACSRACHLFGI 320
                                    7777777777776655 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   2.4     0.017        21       5      17 ..      34      46 ..      31      48 .. 0.87
   2 ?    9.8   1.6   0.00095       1.1       1      17 [.      69      85 ..      69      97 .. 0.94
   3 ?    3.4   2.8     0.093   1.1e+02       4      17 ..     115     128 ..     113     134 .. 0.88
   4 ?    8.7   0.7    0.0022       2.6       1      17 [.     156     172 ..     156     178 .. 0.93
   5 ?    7.4   2.3    0.0054       6.5       1      18 [.     194     211 ..     194     212 .. 0.96
   6 ?   13.9   2.7   5.1e-05     0.061       1      17 [.     233     249 ..     233     250 .. 0.97
   7 ?    0.1   2.7         1   1.2e+03       7      27 ..     276     296 ..     271     303 .. 0.69
   8 ?    7.1   2.8    0.0066       7.9       1      16 [.     301     315 ..     300     345 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.017
                        Fer4_13  5 tCiacgaCvelaP 17
                                    C +c++Cv+l+P
  gi|116754867|ref|YP_843985.1| 34 ICNGCAICVSLCP 46
                                   5************ PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00095
                        Fer4_13  1 VDrdtCiacgaCvelaP 17
                                   +D d C+ cg C++++P
  gi|116754867|ref|YP_843985.1| 69 IDLDACVFCGMCANFCP 85
                                   799************** PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.093
                        Fer4_13   4 dtCiacgaCvelaP 17 
                                    ++C  c++C  ++P
  gi|116754867|ref|YP_843985.1| 115 ERCLPCTLCEPVCP 128
                                    89999999999999 PP

  == domain 4  score: 8.7 bits;  conditional E-value: 0.0022
                        Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                    VDr++C  cg+C+ ++ 
  gi|116754867|ref|YP_843985.1| 156 VDREKCNLCGICARFCK 172
                                    9*************996 PP

  == domain 5  score: 7.4 bits;  conditional E-value: 0.0054
                        Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                    +D+d C  cg+Cv ++P+
  gi|116754867|ref|YP_843985.1| 194 IDEDLCDYCGLCVGICPE 211
                                    89***************7 PP

  == domain 6  score: 13.9 bits;  conditional E-value: 5.1e-05
                        Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                    VD+++Ci+cg C+ ++P
  gi|116754867|ref|YP_843985.1| 233 VDQERCIGCGRCAIVCP 249
                                    9***************9 PP

  == domain 7  score: 0.1 bits;  conditional E-value: 1
                        Fer4_13   7 iacgaCvelaPdvFeeddegg 27 
                                    ++c+ C +++P    + d++g
  gi|116754867|ref|YP_843985.1| 276 VGCHGCFNVCPADCWYVDDQG 296
                                    58*********6444444444 PP

  == domain 8  score: 7.1 bits;  conditional E-value: 0.0066
                        Fer4_13   1 VDrdtCiacgaCvela 16 
                                    V+ d+Ci cgaC  ++
  gi|116754867|ref|YP_843985.1| 301 VE-DQCILCGACSRAC 315
                                    56.9********9988 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   1.4    0.0089        11      77      95 ..      30      48 ..      14      49 .. 0.82
   2 ?    8.8   0.1    0.0025         3      81      95 ..      73      87 ..      66     107 .. 0.71
   3 ?    6.2   2.8     0.015        18       1      21 [.     116     136 ..     116     153 .. 0.82
   4 ?    0.9   2.9      0.72   8.6e+02      78      94 ..     157     173 ..     150     175 .. 0.75
   5 ?    3.2   0.2      0.13   1.6e+02      78      94 ..     195     211 ..     184     213 .. 0.79
   6 ?   15.5   1.3     2e-05     0.024      77      94 ..     233     250 ..     226     252 .. 0.86
   7 ?   -0.2   4.1       1.6   1.9e+03      78      94 ..     271     287 ..     262     289 .. 0.70
   8 ?    0.5   3.6      0.97   1.2e+03       3      19 ..     276     291 ..     272     303 .. 0.68
   9 ?    0.3   5.5       1.1   1.3e+03      81      92 ..     304     315 ..     289     319 .. 0.72
  10 ?    1.5   3.9      0.44   5.3e+02       1      13 [.     304     316 ..     304     339 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0089
                        Fer4_22 77 fgesgCvGCgRCieacpvk 95
                                   ++ + C GC  C++ cp+k
  gi|116754867|ref|YP_843985.1| 30 YDYKICNGCAICVSLCPTK 48
                                   6788999999999999975 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0025
                        Fer4_22 81 gCvGCgRCieacpvk 95
                                   +Cv Cg C + cpv+
  gi|116754867|ref|YP_843985.1| 73 ACVFCGMCANFCPVN 87
                                   566666666666654 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.015
                        Fer4_22   1 rClsCgaCtlvCptCsCfdve 21 
                                    rCl C+ C  vCpt   + v 
  gi|116754867|ref|YP_843985.1| 116 RCLPCTLCEPVCPTEAITVVF 136
                                    7************97665555 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.72
                        Fer4_22  78 gesgCvGCgRCieacpv 94 
                                    ++++C  Cg C + c++
  gi|116754867|ref|YP_843985.1| 157 DREKCNLCGICARFCKA 173
                                    67778888888888865 PP

  == domain 5  score: 3.2 bits;  conditional E-value: 0.13
                        Fer4_22  78 gesgCvGCgRCieacpv 94 
                                    +e  C  Cg C+  cp+
  gi|116754867|ref|YP_843985.1| 195 DEDLCDYCGLCVGICPE 211
                                    67788889999999987 PP

  == domain 6  score: 15.5 bits;  conditional E-value: 2e-05
                        Fer4_22  77 fgesgCvGCgRCieacpv 94 
                                    ++++ C+GCgRC  +cp 
  gi|116754867|ref|YP_843985.1| 233 VDQERCIGCGRCAIVCPY 250
                                    57899***********96 PP

  == domain 7  score: -0.2 bits;  conditional E-value: 1.6
                        Fer4_22  78 gesgCvGCgRCieacpv 94 
                                     +   vGC  C ++cp+
  gi|116754867|ref|YP_843985.1| 271 AKCDPVGCHGCFNVCPA 287
                                    55556888888888886 PP

  == domain 8  score: 0.5 bits;  conditional E-value: 0.97
                        Fer4_22   3 lsCgaCtlvCptCsCfd 19 
                                    ++C  C  vCp+  C+ 
  gi|116754867|ref|YP_843985.1| 276 VGCHGCFNVCPA-DCWY 291
                                    567777777775.4554 PP

  == domain 9  score: 0.3 bits;  conditional E-value: 1.1
                        Fer4_22  81 gCvGCgRCieac 92 
                                    +C+ Cg C++ac
  gi|116754867|ref|YP_843985.1| 304 QCILCGACSRAC 315
                                    455555555555 PP

  == domain 10  score: 1.5 bits;  conditional E-value: 0.44
                        Fer4_22   1 rClsCgaCtlvCp 13 
                                    +C+ CgaC+ +C 
  gi|116754867|ref|YP_843985.1| 304 QCILCGACSRACH 316
                                    5888888888874 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   5.1    0.0014       1.7       1      15 []      35      49 ..      35      49 .. 0.96
   2 ?    8.3   6.3    0.0042         5       1      15 []      74      88 ..      74      88 .. 0.98
   3 ?    4.9   5.5     0.052        62       4      15 .]     120     131 ..     117     131 .. 0.83
   4 ?    1.2   3.7      0.76   9.1e+02       1      11 [.     161     171 ..     161     172 .. 0.94
   5 ?   10.1   3.6    0.0011       1.3       1      15 []     199     213 ..     199     213 .. 0.92
   6 ?   13.0   4.4   0.00014      0.16       1      15 []     238     252 ..     238     252 .. 0.94
   7 ?    0.7   9.0       1.1   1.4e+03       1      13 [.     273     287 ..     273     289 .. 0.78
   8 ?    9.5   3.6    0.0017         2       1      11 [.     305     315 ..     305     319 .. 0.95

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0014
                         Fer4_3  1 CtgCgaCvevCPvgA 15
                                   C+gC  Cv  CP++A
  gi|116754867|ref|YP_843985.1| 35 CNGCAICVSLCPTKA 49
                                   ****99*******98 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0042
                         Fer4_3  1 CtgCgaCvevCPvgA 15
                                   C+ Cg C + CPv+A
  gi|116754867|ref|YP_843985.1| 74 CVFCGMCANFCPVNA 88
                                   *************99 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.052
                         Fer4_3   4 CgaCvevCPvgA 15 
                                    C +C+ vCP+ A
  gi|116754867|ref|YP_843985.1| 120 CTLCEPVCPTEA 131
                                    99*******876 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.76
                         Fer4_3   1 CtgCgaCvevC 11 
                                    C+ Cg C + C
  gi|116754867|ref|YP_843985.1| 161 CNLCGICARFC 171
                                    ********999 PP

  == domain 5  score: 10.1 bits;  conditional E-value: 0.0011
                         Fer4_3   1 CtgCgaCvevCPvgA 15 
                                    C+ Cg+Cv  CP+ A
  gi|116754867|ref|YP_843985.1| 199 CDYCGLCVGICPEEA 213
                                    9***********866 PP

  == domain 6  score: 13.0 bits;  conditional E-value: 0.00014
                         Fer4_3   1 CtgCgaCvevCPvgA 15 
                                    C+gCg+C  vCP+ A
  gi|116754867|ref|YP_843985.1| 238 CIGCGRCAIVCPYEA 252
                                    ************976 PP

  == domain 7  score: 0.7 bits;  conditional E-value: 1.1
                         Fer4_3   1 Ct..gCgaCvevCPv 13 
                                    C+  gC  C++vCP 
  gi|116754867|ref|YP_843985.1| 273 CDpvGCHGCFNVCPA 287
                                    55559977******5 PP

  == domain 8  score: 9.5 bits;  conditional E-value: 0.0017
                         Fer4_3   1 CtgCgaCvevC 11 
                                    C+ CgaC ++C
  gi|116754867|ref|YP_843985.1| 305 CILCGACSRAC 315
                                    *********** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 3127.02
//
Query:       gi|116754868|ref|YP_843986.1|  [L=791]
Description: methyl-viologen-reducing hydrogenase, delta subunit [Methanosaeta thermophila PT]
Scores for complete 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-54  181.1   0.7    4.2e-51  172.1   0.0    3.2  3  FlpD            Methyl-viologen-reducing hydrogenase, delta s
    7.2e-21   73.1  49.7      1e-07   31.4   1.8    5.3  4  Fer4            4Fe-4S binding domain
    1.3e-17   64.0   0.0    4.5e-17   62.2   0.0    1.9  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
      2e-15   57.1  32.5    9.3e-08   32.5  13.1    4.7  4  Fer4_7          4Fe-4S dicluster domain
    3.1e-15   55.5  57.1    1.4e-06   28.1   3.6    5.4  4  Fer4_6          4Fe-4S binding domain
    4.1e-14   53.3  19.1    0.00036   21.4   0.3    4.7  4  Fer4_16         4Fe-4S double cluster binding domain
    4.8e-14   51.5  46.1    4.4e-05   23.3   3.2    5.4  5  Fer4_2          4Fe-4S binding domain
    5.5e-14   52.0  32.7    2.9e-06   27.3  13.7    4.4  4  Fer4_10         4Fe-4S dicluster domain
      4e-12   46.1  43.3    3.6e-10   39.8  10.5    4.8  4  Fer4_21         4Fe-4S dicluster domain
    5.8e-12   45.6  34.7    6.1e-07   29.5  12.0    3.3  2  Fer4_9          4Fe-4S dicluster domain
    2.7e-10   40.4   2.2    1.5e-06   28.1   1.5    2.7  2  DAO             FAD dependent oxidoreductase
    6.6e-10   38.9   0.4    1.2e-09   38.1   0.4    1.3  1  FAD_oxidored    FAD dependent oxidoreductase
    6.9e-08   32.0   0.9    1.3e-07   31.1   0.9    1.4  1  FAD_binding_2   FAD binding domain
      1e-06   29.4  28.4     0.0091   16.7   2.0    5.0  4  Fer4_15         4Fe-4S single cluster domain
      1e-06   28.9   0.2      3e-06   27.4   0.2    1.8  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    3.9e-06   27.2  27.8     0.0053   17.2   0.0    4.8  4  Fer4_8          4Fe-4S dicluster domain
    9.5e-06   26.1   0.3    4.2e-05   24.0   0.3    2.1  1  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    1.2e-05   24.6   0.2    1.2e-05   24.6   0.2    1.6  2  GIDA            Glucose inhibited division protein A
    1.6e-05   25.3  29.0       0.11   13.0   0.4    4.5  4  Fer4_17         4Fe-4S dicluster domain
    2.7e-05   23.5   0.0    5.5e-05   22.5   0.0    1.4  1  Thi4            Thi4 family
    4.5e-05   22.9   0.7    8.7e-05   21.9   0.7    1.4  1  FAD_binding_3   FAD binding domain
    0.00014   20.7   0.3    0.00022   20.1   0.3    1.3  1  HI0933_like     HI0933-like protein
    0.00026   21.3  44.5     0.0046   17.4   3.9    5.2  4  Fer4_4          4Fe-4S binding domain
    0.00037   20.5   1.2          2    8.4   0.3    3.3  3  NAD_binding_9   FAD-NAD(P)-binding
      0.001   19.6  36.3     0.0057   17.2   3.3    4.3  3  Fer4_13         4Fe-4S single cluster domain of Ferredoxin I
      0.002   17.2   0.6     0.0053   15.8   0.4    1.8  2  Lycopene_cycl   Lycopene cyclase protein
     0.0029   17.0   0.9     0.0061   15.9   0.3    1.9  1  Amino_oxidase   Flavin containing amine oxidoreductase
      0.003   16.9   0.0     0.0079   15.5   0.0    1.7  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
     0.0036   16.6   0.1     0.0081   15.5   0.1    1.5  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
  ------ inclusion threshold ------
       0.03   15.2  26.6        0.2   12.5   0.9    4.6  4  Fer4_22         4Fe-4S dicluster domain
      0.038   14.9   3.3      0.038   14.9   3.3    6.0  4  Fer4_3          4Fe-4S binding domain
      0.092   13.2   0.8        3.2    8.3   0.2    3.3  3  NAD_binding_7   Putative NAD(P)-binding
       0.17   10.7   0.5       0.48    9.2   0.3    1.7  2  Trp_halogenase  Tryptophan halogenase
        2.9    8.1  21.3      0.037   14.2   4.1    3.4  2  Fer4_18         4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> FlpD  Methyl-viologen-reducing hydrogenase, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       6.7   3.5e+03      52      62 ..      65      75 ..      41     113 .. 0.73
   2 ?    5.8   0.0     0.026        14      47      80 ..     527     564 ..     524     572 .. 0.75
   3 !  172.1   0.0     8e-54   4.2e-51       1     123 []     654     776 ..     654     776 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 6.7
                           FlpD 52 adgVlvlgChp 62
                                    d+V+v++C p
  gi|116754868|ref|YP_843986.1| 65 LDAVVVAACSP 75
                                   67777777765 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.026
                           FlpD  47 alekGadgVlvlgChpgd....ChyvkGnekaerrvek 80 
                                      e+ +dgV+++gC  g         +G+  a++ +++
  gi|116754868|ref|YP_843986.1| 527 PVEAHIDGVFIAGCASGPkeiqVSIAQGSAAASKAMQL 564
                                    667889********988655555556777777777765 PP

  == domain 3  score: 172.1 bits;  conditional E-value: 8e-54
                           FlpD   1 ilaFlCnwcayaaadlagvsrlqyppnvriirvpCsgrvdpefilkalekGadgVlvlgChpgdChyvkGnekaerrvek 80 
                                    il+FlCnwc+ya+adlag+sr+qyp+n+riirv+C+grvdp+f+l+al++GadgVl++gC+ g+Chyv+Gn +a +rve 
  gi|116754868|ref|YP_843986.1| 654 ILGFLCNWCSYAGADLAGTSRIQYPTNIRIIRVMCAGRVDPSFVLEALRRGADGVLIAGCRIGECHYVSGNLHALQRVEV 733
                                    89****************************************************************************** PP

                           FlpD  81 lkelleelgiepeRvrleevsaaegekfaevikefvekikeLG 123
                                    l+ ll+e+gi+p+R+++++++a+eg+ +a+ i+efve++k+LG
  gi|116754868|ref|YP_843986.1| 734 LRGLLKEIGIDPRRLKVAWCAASEGDILARRIEEFVEELKDLG 776
                                    *****************************************98 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   4.7     0.021        11       2      22 ..     242     263 ..     241     265 .. 0.92
   2 !   27.0   9.1     5e-09   2.7e-06       3      23 ..     291     311 ..     289     312 .. 0.93
   3 !   31.4   1.8     2e-10     1e-07       2      24 .]     578     600 ..     577     600 .. 0.94
   4 !   30.9   5.2   2.8e-10   1.5e-07       2      24 .]     606     628 ..     605     628 .. 0.94

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.021
                                    EEETTTSSS-.THHHHHSTTTE CS
                           Fer4   2 videekCigC.GaCvevCPvgA 22 
                                    ++d+ +C gC ++C ++CPv++
  gi|116754868|ref|YP_843986.1| 242 YVDPTLCKGCiNECSSACPVEV 263
                                    79*****************986 PP

  == domain 2  score: 27.0 bits;  conditional E-value: 5e-09
                                    EETTTSSS-THHHHHSTTTEE CS
                           Fer4   3 ideekCigCGaCvevCPvgAI 23 
                                    id++ CigCG+C+e+CP +A 
  gi|116754868|ref|YP_843986.1| 291 IDTNACIGCGLCAEACPADAV 311
                                    9******************97 PP

  == domain 3  score: 31.4 bits;  conditional E-value: 2e-10
                                    EEETTTSSS-THHHHHSTTTEEE CS
                           Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                     +d +kCigC +Cv+ CP  AI+
  gi|116754868|ref|YP_843986.1| 578 FVDRDKCIGCRLCVDTCPSRAIS 600
                                    59*******************95 PP

  == domain 4  score: 30.9 bits;  conditional E-value: 2.8e-10
                                    EEETTTSSS-THHHHHSTTTEEE CS
                           Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                     +de +C gCG+C+ +CPv+AI+
  gi|116754868|ref|YP_843986.1| 606 FVDEARCKGCGTCAAACPVDAIE 628
                                    59********************6 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 !   62.2   0.0   8.6e-20   4.5e-17       2     294 .]     147     554 ..     146     554 .. 0.77

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 8.6e-20
                                    SEEEE--SHHHHHHHHHHHHHTS-EEEEE...........TTHCHHHCSHHH...HCHHHHHHHHHHHHH.......... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxx...xxxxxxxxxxxxxxx.......... RF
                    Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlve...........legtclnggcll...skallgvaedaeias.......... 57 
                                    dv+viGgG+AG++aal+la+ag++v+lve           l++ +++++c++   ++++++v +++ i +          
  gi|116754868|ref|YP_843986.1| 147 DVLVIGGGVAGISAALDLANAGLRVYLVErrptiggymalLTDVFPTNDCSIcvlAPKMAEVYANPMIKLmtyseilaie 226
                                    8***************************99999999*************987666888888888888777********** PP

                                    ...................................HHHHCHHHHCCCCHC........CTCEEEEESCEEEEETEEEC.. CS
                                    ...................................xxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxx.. RF
                    Pyr_redox_2  58 ...................................evvkklnqgielllg........eevvkidpgkkkvklekkke.. 92 
                                                                       ev +++  g+ ++++        +           v + +++   
  gi|116754868|ref|YP_843986.1| 227 gtvghfrvtgvtkpryvdptlckgcinecssacpvEVPNEYDFGLGKRKAiymaipqsV---------PLVACIDTNAci 297
                                    ***************************99999988555555555555555444444442.........223332222245 PP

                                    ...................TCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T........... CS
                                    ...................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........... RF
                    Pyr_redox_2  93 ...................gdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllp........... 142
                                                        +e+k++ +++v+AtG +p+d   + +   +g++ r+ d +  l+ + +            
  gi|116754868|ref|YP_843986.1| 298 gcglcaeacpadavkydqqAEEFKLDVGAIVVATGWQPFDASRKEE---YGFG-RYRDVVTTLQIERMLnaagptrgdiv 373
                                    5555566778888888888999******************955544...4444.56666666665555555888999999 PP

                                    ..................SEEEEES-SHHHHHHHHH.HHHHT-..........EEEEEESSSSSSTTS-HHHHHHHHHHH CS
                                    ..................xxxxxxxxxxxxxxxxxx.xxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 143 ..................krivvvGgGyiGvElAaa.laklgk..........evtlveardrllraldkelsaaleeal 193
                                                       r   vG+ y++  +++a l++++            +++++      ra ++  ++++ +a 
  gi|116754868|ref|YP_843986.1| 374 rpstgeivrsvafiqcvgSRDQTVGNPYCSRICCMAsLKNAQLikerypdadvSIHYIDI-----RAGGEGYEEFYLRAQ 448
                                    99999999777777677666699*************633333355566655323444444.....566899999999875 PP

                                    HHTTEEEEESCEEEEEEETTE....EEE.EEETTSCEEEESEEEE-S-EEES-HHCS..HCCT-EEEETTEEE--.TTS. CS
                                    xxxxxxxxxxxxxxxxxxxxx....xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx.xxx. RF
                    Pyr_redox_2 194 ekeGvevklgtsvkeidgnge....kle.vvledgeeidadlvvvavGvrpstelle..eklglelderggivvd.efl. 264
                                    +  G+++  + +v  +++ ++    ++e + l++     +dlvv+++G++++++     + lgl   +++++++  +++ 
  gi|116754868|ref|YP_843986.1| 449 R-LGINFI-RGRVSSVEEGEDglyvHYEdTLLGKTLMKRYDLVVLSTGLEANSDADVvgNLLGLSRRPDRFFEIAhPKMr 526
                                    5.5*****.7777799988887876555788888888***************9996598999**********66515675 PP

                                    ..BESSTTEEE-GGGCTECCSS--HHHHHHHH CS
                                    ..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 265 ..rtnvpgiyaiGDvaggkggpelaqaAvqqG 294
                                      +  ++g++ +G +a   +gp+ +q++++qG
  gi|116754868|ref|YP_843986.1| 527 pvEAHIDGVFIAG-CA---SGPKEIQVSIAQG 554
                                    44568*******9.88...8*******99998 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   1.7   0.00067      0.35      26      52 .]     235     263 ..     194     263 .. 0.53
   2 !   23.9   0.2   8.8e-08   4.6e-05       1      25 [.     295     319 ..     295     350 .. 0.86
   3 !   32.5  13.1   1.8e-10   9.3e-08       1      52 []     583     626 ..     583     626 .. 0.94
   4 !   19.7   2.9   1.8e-06   0.00095       1      25 [.     611     635 ..     611     651 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00067
                         Fer4_7  26 kgtekv.eidpekClgCga.CvavCPtga 52 
                                     g+ k+ ++dp+ C gC + C ++CP+++
  gi|116754868|ref|YP_843986.1| 235 TGVTKPrYVDPTLCKGCINeCSSACPVEV 263
                                    2334443679*******877******975 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 8.8e-08
                         Fer4_7   1 rCigCgaCvaaCpvkaieldeeene 25 
                                    +CigCg C++aCp++a+++d++++e
  gi|116754868|ref|YP_843986.1| 295 ACIGCGLCAEACPADAVKYDQQAEE 319
                                    5******************987554 PP

  == domain 3  score: 32.5 bits;  conditional E-value: 1.8e-10
                         Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                    +CigC+ Cv++Cp++ai++++         + +d+ +C gCg C+a+CP++a
  gi|116754868|ref|YP_843986.1| 583 KCIGCRLCVDTCPSRAISVKDT--------AFVDEARCKGCGTCAAACPVDA 626
                                    7******************876........7899****************97 PP

  == domain 4  score: 19.7 bits;  conditional E-value: 1.8e-06
                         Fer4_7   1 rCigCgaCvaaCpvkaieldeeene 25 
                                    rC gCg C+aaCpv+aie++ +++e
  gi|116754868|ref|YP_843986.1| 611 RCKGCGTCAAACPVDAIEMRLFSDE 635
                                    7*****************9865544 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   3.2   4.7e-05     0.025       4      22 ..     243     262 ..     242     264 .. 0.91
   2 !   18.9   8.5   2.2e-06    0.0011       4      23 ..     291     310 ..     289     311 .. 0.95
   3 !   28.1   3.6   2.7e-09   1.4e-06       1      24 []     576     599 ..     576     599 .. 0.94
   4 !   24.1   4.4   4.9e-08   2.6e-05       2      24 .]     605     627 ..     604     627 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.7e-05
                         Fer4_6   4 idpdkCigC.gdCvrvCPeg 22 
                                    +dp +C gC ++C ++CP  
  gi|116754868|ref|YP_843986.1| 243 VDPTLCKGCiNECSSACPVE 262
                                    8*****************86 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 2.2e-06
                         Fer4_6   4 idpdkCigCgdCvrvCPega 23 
                                    id ++CigCg C+ +CP++a
  gi|116754868|ref|YP_843986.1| 291 IDTNACIGCGLCAEACPADA 310
                                    799***************98 PP

  == domain 3  score: 28.1 bits;  conditional E-value: 2.7e-09
                         Fer4_6   1 vveidpdkCigCgdCvrvCPegai 24 
                                    v+ +d+dkCigC+ Cv+ CP  ai
  gi|116754868|ref|YP_843986.1| 576 VAFVDRDKCIGCRLCVDTCPSRAI 599
                                    689*****************9987 PP

  == domain 4  score: 24.1 bits;  conditional E-value: 4.9e-08
                         Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                    + +d+ +C gCg C+++CP +ai
  gi|116754868|ref|YP_843986.1| 605 AFVDEARCKGCGTCAAACPVDAI 627
                                    689*****************998 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.6       0.1        54       2      16 ..     248     263 ..     247     279 .. 0.82
   2 !   19.7   0.3   2.4e-06    0.0013       2      22 ..     296     316 ..     295     340 .. 0.85
   3 !   17.8   1.4   9.4e-06    0.0049       1      21 [.     583     603 ..     583     610 .. 0.85
   4 !   21.4   0.3   6.8e-07   0.00036       1      20 [.     611     630 ..     611     656 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.1
                        Fer4_16   2 CgtCgk.CaevCPtna 16 
                                    C++C + C ++CP+++
  gi|116754868|ref|YP_843986.1| 248 CKGCINeCSSACPVEV 263
                                    9999666999999875 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 2.4e-06
                        Fer4_16   2 CgtCgkCaevCPtnaikekke 22 
                                    C++Cg Cae+CP++a+k +++
  gi|116754868|ref|YP_843986.1| 296 CIGCGLCAEACPADAVKYDQQ 316
                                    ****************98832 PP

  == domain 3  score: 17.8 bits;  conditional E-value: 9.4e-06
                        Fer4_16   1 rCgtCgkCaevCPtnaikekk 21 
                                    +C++C+ C+++CP++ai+ k 
  gi|116754868|ref|YP_843986.1| 583 KCIGCRLCVDTCPSRAISVKD 603
                                    5****************9883 PP

  == domain 4  score: 21.4 bits;  conditional E-value: 6.8e-07
                        Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                    rC++Cg Ca +CP++ai+++
  gi|116754868|ref|YP_843986.1| 611 RCKGCGTCAAACPVDAIEMR 630
                                    6****************998 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.2       4.8   2.5e+03      12      18 ..     195     201 ..     194     202 .. 0.77
   2 !   10.1   3.3    0.0014      0.72       3      21 ..     241     260 ..     239     261 .. 0.90
   3 !   19.6   6.4   1.3e-06   0.00068       3      22 .]     289     308 ..     287     308 .. 0.92
   4 !   23.3   3.2   8.4e-08   4.4e-05       3      21 ..     577     595 ..     575     596 .. 0.93
   5 !   20.0   4.2   9.3e-07   0.00049       4      21 ..     606     623 ..     604     624 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 4.8
                         Fer4_2  12 gCgaCvs 18 
                                     C++Cv 
  gi|116754868|ref|YP_843986.1| 195 DCSICVL 201
                                    79***86 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0014
                         Fer4_2   3 vvvdtdrCigC.gaCvsaCP 21 
                                     +vd+  C gC + C saCP
  gi|116754868|ref|YP_843986.1| 241 RYVDPTLCKGCiNECSSACP 260
                                    5899********99****** PP

  == domain 3  score: 19.6 bits;  conditional E-value: 1.3e-06
                         Fer4_2   3 vvvdtdrCigCgaCvsaCPa 22 
                                    + +dt++CigCg C  aCPa
  gi|116754868|ref|YP_843986.1| 289 ACIDTNACIGCGLCAEACPA 308
                                    579****************8 PP

  == domain 4  score: 23.3 bits;  conditional E-value: 8.4e-08
                         Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                    ++vd+d+CigC+ Cv+ CP
  gi|116754868|ref|YP_843986.1| 577 AFVDRDKCIGCRLCVDTCP 595
                                    789**************** PP

  == domain 5  score: 20.0 bits;  conditional E-value: 9.3e-07
                         Fer4_2   4 vvdtdrCigCgaCvsaCP 21 
                                    +vd++rC gCg+C  aCP
  gi|116754868|ref|YP_843986.1| 606 FVDEARCKGCGTCAAACP 623
                                    79**************** PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   3.4    0.0026       1.4       4      24 ..     243     269 ..     241     291 .. 0.70
   2 !   22.1   2.8   2.2e-07   0.00012       4      34 ..     291     321 ..     288     332 .. 0.76
   3 !   27.3  13.7   5.6e-09   2.9e-06       4      56 .]     579     623 ..     577     623 .. 0.94
   4 !   17.8   2.6   5.1e-06    0.0027       4      24 ..     607     630 ..     604     652 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0026
                        Fer4_10   4 idddtCirCg.kCvkaCPadl.....t 24 
                                    +d+  C +C  +C +aCP+ +      
  gi|116754868|ref|YP_843986.1| 243 VDPTLCKGCInECSSACPVEVpneydF 269
                                    68999****77********44444432 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 2.2e-07
                        Fer4_10   4 idddtCirCgkCvkaCPadltsvgakgease 34 
                                    id++ Ci+Cg C +aCPad+ ++++++e+ +
  gi|116754868|ref|YP_843986.1| 291 IDTNACIGCGLCAEACPADAVKYDQQAEEFK 321
                                    899***************7755555555444 PP

  == domain 3  score: 27.3 bits;  conditional E-value: 5.6e-09
                        Fer4_10   4 idddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                    +d+d+Ci+C+ Cv+ CP+         ++s +++  ++  +C gcg C++aCP
  gi|116754868|ref|YP_843986.1| 579 VDRDKCIGCRLCVDTCPS--------RAISVKDTAFVDEARCKGCGTCAAACP 623
                                    699***************........99999999999999************9 PP

  == domain 4  score: 17.8 bits;  conditional E-value: 5.1e-06
                        Fer4_10   4 idddtCirCgkCvkaCPadl...t 24 
                                    +d+ +C +Cg+C +aCP+d+   +
  gi|116754868|ref|YP_843986.1| 607 VDEARCKGCGTCAAACPVDAiemR 630
                                    7899**************664440 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       6.7   3.5e+03      17      32 ..      47      62 ..      45      74 .. 0.68
   2 !    8.4   1.3    0.0045       2.4      37      54 ..     244     262 ..     225     264 .. 0.82
   3 !   18.7   3.8   2.6e-06    0.0014       1      31 [.     289     316 ..     289     324 .. 0.82
   4 !   39.8  10.5   6.8e-13   3.6e-10       1      59 []     577     629 ..     577     629 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 6.7
                        Fer4_21 17 aCedtshqaieidakt 32
                                   +C+d++ + i+ d ++
  gi|116754868|ref|YP_843986.1| 47 TCSDAGQNTIKSDIAE 62
                                   7*********876443 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0045
                        Fer4_21  37 vedeCvGC.nlCssvCPve 54 
                                        C GC n Css CPve
  gi|116754868|ref|YP_843986.1| 244 DPTLCKGCiNECSSACPVE 262
                                    4568****889******95 PP

  == domain 3  score: 18.7 bits;  conditional E-value: 2.6e-06
                        Fer4_21   1 AridedkCigCgkCliaCedtshqaieidak 31 
                                    A id + CigCg+C+ aC+    +a+++d++
  gi|116754868|ref|YP_843986.1| 289 ACIDTNACIGCGLCAEACP---ADAVKYDQQ 316
                                    7899999999999999999...588877765 PP

  == domain 4  score: 39.8 bits;  conditional E-value: 6.8e-13
                        Fer4_21   1 AridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedciem 59 
                                    A++d+dkCigC +C+ +C+     ai++++  ++ v e +C GC  C++ CPv d+iem
  gi|116754868|ref|YP_843986.1| 577 AFVDRDKCIGCRLCVDTCP---SRAISVKD--TAFVDEARCKGCGTCAAACPV-DAIEM 629
                                    799****************...59999865..45599***************9.***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 !   26.0   9.1   1.4e-08   7.5e-06       2      50 ..     248     310 ..     247     317 .. 0.93
   2 !   29.5  12.0   1.2e-09   6.1e-07       1      51 []     583     627 ..     583     627 .. 0.95

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 1.4e-08
                         Fer4_9   2 CtgC.gaCveaCpagvvvedaaerkarlraase.............eaCigCgaCveaCpkga 50 
                                    C gC ++C +aCp +v +e +++   r  ++ +             +aCigCg C+eaCp +a
  gi|116754868|ref|YP_843986.1| 248 CKGCiNECSSACPVEVPNEYDFGLGKRKAIYMAipqsvplvacidtNACIGCGLCAEACPADA 310
                                    9***556****************9999988888999************************987 PP

  == domain 2  score: 29.5 bits;  conditional E-value: 1.2e-09
                         Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                    kC+gC+ Cv+ Cp+ +++ ++ +  ++       +C gCg+C++aCp +ai
  gi|116754868|ref|YP_843986.1| 583 KCIGCRLCVDTCPSRAISVKDTAFVDEA------RCKGCGTCAAACPVDAI 627
                                    7********************9999997......6*************987 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   1.5   2.8e-09   1.5e-06       1      33 [.     147     181 ..     147     184 .. 0.95
   2 !    9.6   0.0    0.0012      0.63     154     207 ..     445     501 ..     441     532 .. 0.69

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 2.8e-09
                                    EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                            DAO   1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag 33 
                                    dv++iGGG++G+s+A++La +g  V l+e+++ +g
  gi|116754868|ref|YP_843986.1| 147 DVLVIGGGVAGISAALDLANAGlrVYLVERRPTIG 181
                                    8******************************9988 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0012
                                    HHHHHTT-EEEESECEEEEEEEETCEEEEE.EECT.EEE..EEEEEEEE--GGGHH.HH CS
                            DAO 154 raaealGveilegtevtgleeedgkvwgve.rttp.gen..daadavVnaaGawsd.ll 207
                                     +a++lG+++++g +v ++ee + ++  v+ ++t  g +  +++d vV+++G+ ++  +
  gi|116754868|ref|YP_843986.1| 445 LRAQRLGINFIRG-RVSSVEEGE-DGLYVHyEDTLlGKTlmKRYDLVVLSTGLEANsDA 501
                                    579**********.*****7733.3344547777778776446788******9987533 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.4   2.2e-12   1.2e-09       1      39 [.     147     185 ..     147     195 .. 0.96

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 2.2e-12
                   FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGllt 39 
                                    Dv+V+GGg+aG+ AA+  a+aG +v Lve+r+ +GG ++
  gi|116754868|ref|YP_843986.1| 147 DVLVIGGGVAGISAALDLANAGLRVYLVERRPTIGGYMA 185
                                    9***********************************885 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.9   2.5e-10   1.3e-07       1      36 [.     147     182 ..     147     186 .. 0.93

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 2.5e-10
                                    SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                  FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36 
                                    Dv+ViG+G+AG +AAl +a+aGl+v +ve  +  gg
  gi|116754868|ref|YP_843986.1| 147 DVLVIGGGVAGISAALDLANAGLRVYLVERRPTIGG 182
                                    9****************************9998887 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 ?    1.9   0.3       0.7   3.7e+02       2      19 ..     242     260 ..     242     272 .. 0.76
   2 !   15.3   1.0   4.9e-05     0.026       3      20 ..     291     308 ..     290     343 .. 0.84
   3 !   16.7   2.0   1.7e-05    0.0091       2      20 ..     578     596 ..     577     603 .. 0.91
   4 !    8.2   5.2     0.008       4.2       2      19 ..     606     623 ..     605     630 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.7
                        Fer4_15   2 vvDrdaCigc.glCvaeap 19 
                                    +vD ++C gc + C  ++p
  gi|116754868|ref|YP_843986.1| 242 YVDPTLCKGCiNECSSACP 260
                                    5899999999456888887 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 4.9e-05
                        Fer4_15   3 vDrdaCigcglCvaeape 20 
                                    +D +aCigcglC++++p 
  gi|116754868|ref|YP_843986.1| 291 IDTNACIGCGLCAEACPA 308
                                    8***************85 PP

  == domain 3  score: 16.7 bits;  conditional E-value: 1.7e-05
                        Fer4_15   2 vvDrdaCigcglCvaeape 20 
                                    +vDrd+Cigc lCv+ +p 
  gi|116754868|ref|YP_843986.1| 578 FVDRDKCIGCRLCVDTCPS 596
                                    59***************96 PP

  == domain 4  score: 8.2 bits;  conditional E-value: 0.008
                        Fer4_15   2 vvDrdaCigcglCvaeap 19 
                                    +vD+ +C gcg C+a++p
  gi|116754868|ref|YP_843986.1| 606 FVDEARCKGCGTCAAACP 623
                                    59**************98 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.2   5.7e-09     3e-06       1      36 [.     150     185 ..     150     201 .. 0.93

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 5.7e-09
                                    EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG- CS
                  NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraa 36 
                                    ++G+G++G +aA  La+ag++v l+e+r+ +GG +a
  gi|116754868|ref|YP_843986.1| 150 VIGGGVAGISAALDLANAGLRVYLVERRPTIGGYMA 185
                                    8********************************997 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.4      0.16        83      50      64 ..     247     262 ..     225     268 .. 0.78
   2 !   17.2   0.0     1e-05    0.0053       3      17 ..     294     310 ..     292     359 .. 0.76
   3 !   13.2   1.8   0.00017     0.091       3      17 ..     582     596 ..     580     611 .. 0.76
   4 !    8.4   4.1    0.0055       2.9       4      17 ..     611     624 ..     608     663 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.16
                         Fer4_8  50 sCttcga.CtevCpvg 64 
                                     C +c + C+++Cpv+
  gi|116754868|ref|YP_843986.1| 247 LCKGCINeCSSACPVE 262
                                    4665533377777775 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 1e-05
                         Fer4_8   3 ekCieCgaCqsaCp..v 17 
                                    ++Ci+Cg+C +aCp  +
  gi|116754868|ref|YP_843986.1| 294 NACIGCGLCAEACPadA 310
                                    79***********9441 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 0.00017
                         Fer4_8   3 ekCieCgaCqsaCpv 17 
                                    +kCi+C +C ++Cp+
  gi|116754868|ref|YP_843986.1| 582 DKCIGCRLCVDTCPS 596
                                    69***********94 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.0055
                         Fer4_8   4 kCieCgaCqsaCpv 17 
                                    +C +Cg C +aCpv
  gi|116754868|ref|YP_843986.1| 611 RCKGCGTCAAACPV 624
                                    67778888887874 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.3   7.9e-08   4.2e-05       2      35 ..     148     181 ..     147     188 .. 0.93

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 7.9e-08
                                    EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                      Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35 
                                    v+v+GgG+ g+ +A  la+ g +V++ver++++ 
  gi|116754868|ref|YP_843986.1| 148 VLVIGGGVAGISAALDLANAGLRVYLVERRPTIG 181
                                    89*****************************997 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.2   2.2e-08   1.2e-05       1      29 [.     147     177 ..     147     210 .. 0.84
   2 ?   -3.4   0.1       7.1   3.7e+03     355     385 ..     532     562 ..     529     565 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.2e-08
                                    CEEEE-SSHHHHHHHHHHHHTT--EEEE..E CS
                           GIDA   1 dviViGgGhAGceAAlaaarlGakvlLi..t 29 
                                    dv ViGgG AG+ AAl +a++G++v L+   
  gi|116754868|ref|YP_843986.1| 147 DVLVIGGGVAGISAALDLANAGLRVYLVerR 177
                                    79*************************9441 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 7.1
                                    SBTEEE-CGGGTB-SHHHHHHHHHHHHHHHH CS
                           GIDA 355 vkgLflAGqinGteGYeEaaaqGllAGinaa 385
                                    ++g+f+AG  +G +    ++aqG  A+  a 
  gi|116754868|ref|YP_843986.1| 532 IDGVFIAGCASGPKEIQVSIAQGSAAASKAM 562
                                    7899999999999989999999999998876 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   3.6      0.65   3.4e+02      44      60 ..     246     263 ..     194     264 .. 0.64
   2 !    9.3  12.2    0.0031       1.6       2      59 ..     248     309 ..     246     311 .. 0.60
   3 !   13.0   0.4   0.00022      0.11       1      14 [.     583     596 ..     573     605 .. 0.75
   4 !   11.4   1.5   0.00068      0.36       1      31 [.     611     643 ..     611     664 .. 0.65

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.65
                        Fer4_17  44 slCieC.geCerkCPqgl 60 
                                     lC +C +eC+++CP ++
  gi|116754868|ref|YP_843986.1| 246 TLCKGCiNECSSACPVEV 263
                                    678777689999999876 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0031
                        Fer4_17   2 CiqCgy.ClpeCpsyeaydn....epkkllraaklglleeaekeekaslCieCgeCerkCPqg 59 
                                    C +C   C  +Cp    ++      ++k ++ a ++++  + +    + Ci+Cg+C+++CP++
  gi|116754868|ref|YP_843986.1| 248 CKGCINeCSSACPVEVPNEYdfglGKRKAIYMAIPQSVPLV-ACIDTNACIGCGLCAEACPAD 309
                                    77776447777776554333112234444444444433332.33599**************86 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 0.00022
                        Fer4_17   1 rCiqCgyClpeCps 14 
                                    +Ci+C+ C++ Cps
  gi|116754868|ref|YP_843986.1| 583 KCIGCRLCVDTCPS 596
                                    46666666666665 PP

  == domain 4  score: 11.4 bits;  conditional E-value: 0.00068
                        Fer4_17   1 rCiqCgyClpeCpsyea..ydnepkkllraakl 31 
                                    rC +Cg C+++Cp  ++  + +  +++l+++++
  gi|116754868|ref|YP_843986.1| 611 RCKGCGTCAAACPVDAIemRLFSDEQILAQIRA 643
                                    699999999999986554344455566666655 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   1.1e-07   5.5e-05      17      59 ..     145     186 ..     133     194 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.1e-07
                                    EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTT CS
                           Thi4  17 esDvvivGaGssGLtaayylakkpdlkvailersvspGGGawl 59 
                                      Dv+++G+G +G++aa  la++ +l+v ++er+ ++GG + l
  gi|116754868|ref|YP_843986.1| 145 SRDVLVIGGGVAGISAALDLANA-GLRVYLVERRPTIGGYMAL 186
                                    67********************9.***************8876 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.7   1.6e-07   8.7e-05       3      34 ..     147     178 ..     145     181 .. 0.95

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.6e-07
                                    EEEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                  FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrs 34 
                                    dVl++G+G aG+++al L++aG rv lve+r 
  gi|116754868|ref|YP_843986.1| 147 DVLVIGGGVAGISAALDLANAGLRVYLVERRP 178
                                    8*****************************96 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.3   4.1e-07   0.00022       2      36 ..     147     181 ..     146     186 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.1e-07
                                    SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                    HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36 
                                    dv+viGgG AG+ aA+ +a++g rV l+e+ +++g
  gi|116754868|ref|YP_843986.1| 147 DVLVIGGGVAGISAALDLANAGLRVYLVERRPTIG 181
                                    89****************************99988 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   2.7       2.6   1.3e+03       7      15 ..     248     260 ..     246     265 .. 0.55
   2 !   14.4   1.9   7.8e-05     0.041       2      16 ..     294     308 ..     293     316 .. 0.89
   3 !   17.4   3.9   8.6e-06    0.0046       2      16 ..     582     596 ..     581     597 .. 0.92
   4 !   15.1   2.7   4.5e-05     0.024       3      16 ..     611     624 ..     609     630 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 2.6
                         Fer4_4   7 Cg....sCvaaCP 15 
                                    C+     C +aCP
  gi|116754868|ref|YP_843986.1| 248 CKgcinECSSACP 260
                                    6611133666666 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 7.8e-05
                         Fer4_4   2 erCigCgsCvaaCPq 16 
                                    + CigCg C  aCP 
  gi|116754868|ref|YP_843986.1| 294 NACIGCGLCAEACPA 308
                                    78************5 PP

  == domain 3  score: 17.4 bits;  conditional E-value: 8.6e-06
                         Fer4_4   2 erCigCgsCvaaCPq 16 
                                    ++CigC+ Cv++CP+
  gi|116754868|ref|YP_843986.1| 582 DKCIGCRLCVDTCPS 596
                                    89************7 PP

  == domain 4  score: 15.1 bits;  conditional E-value: 4.5e-05
                         Fer4_4   3 rCigCgsCvaaCPq 16 
                                    rC gCg C aaCP+
  gi|116754868|ref|YP_843986.1| 611 RCKGCGTCAAACPV 624
                                    9************7 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 ?    0.7   0.1      0.85   4.5e+02     119     152 ..      38      71 ..      26      74 .. 0.79
   2 !    8.4   0.3    0.0038         2       2      39 ..     150     182 ..     149     190 .. 0.86
   3 !    7.7   0.0    0.0064       3.4     111     154 ..     447     494 ..     438     496 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.85
                  NAD_binding_9 119 vhraevvdleeradgqavlladgaslaadaVvLA 152
                                    v+ a+ ++ +++++gq  +++d a+l++daVv+A
  gi|116754868|ref|YP_843986.1|  38 VVVARDIQFTCSDAGQNTIKSDIAELKLDAVVVA 71 
                                    4556667788899999999*************99 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0038
                  NAD_binding_9   2 ivGaGprGlavlerLlarakkkspleitlfdpsep.gag 39 
                                    ++G+G++G++++  L++       l++ l++++++ g g
  gi|116754868|ref|YP_843986.1| 150 VIGGGVAGISAALDLANA-----GLRVYLVERRPTiG-G 182
                                    8**************999.....6********98845.4 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0064
                  NAD_binding_9 111 lpegvtvevhraevvdleeradgqavlladg...asl..aadaVvLAlG 154
                                    + +++ ++++r++v ++ee +dg +v+ +d    ++l  ++d VvL +G
  gi|116754868|ref|YP_843986.1| 447 A-QRLGINFIRGRVSSVEEGEDGLYVHYEDTllgKTLmkRYDLVVLSTG 494
                                    4.45789*****************9999886443554469*******99 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 !   13.5   2.7   0.00015     0.078       1      18 [.     291     308 ..     291     319 .. 0.92
   2 !   17.2   3.3   1.1e-05    0.0057       1      18 [.     579     596 ..     579     597 .. 0.96
   3 !    8.3   4.6    0.0063       3.3       1      17 [.     607     623 ..     607     627 .. 0.97

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00015
                        Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                    +D + Ci+cg+C+e++P 
  gi|116754868|ref|YP_843986.1| 291 IDTNACIGCGLCAEACPA 308
                                    7999*************5 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 1.1e-05
                        Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                    VDrd+Ci+c +Cv+++P 
  gi|116754868|ref|YP_843986.1| 579 VDRDKCIGCRLCVDTCPS 596
                                    9****************5 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0063
                        Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                    VD+ +C +cg+C++++P
  gi|116754868|ref|YP_843986.1| 607 VDEARCKGCGTCAAACP 623
                                    8***************9 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.4     1e-05    0.0053       1      35 [.     147     179 ..     147     184 .. 0.93
   2 ?   -2.7   0.0       4.4   2.3e+03     263     276 ..     368     381 ..     357     388 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1e-05
                  Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieasps 35 
                                    Dv+viG+G Ag+s A  l  a++gl+v l+e  p 
  gi|116754868|ref|YP_843986.1| 147 DVLVIGGGVAGISAALDL--ANAGLRVYLVERRPT 179
                                    9*****************..**********98776 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.4
                  Lycopene_cycl 263 aaaglvhPaTGYsv 276
                                    +++ +v+P+TG  v
  gi|116754868|ref|YP_843986.1| 368 TRGDIVRPSTGEIV 381
                                    57889******544 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.3   1.2e-05    0.0061       1      28 [.     155     182 ..     155     186 .. 0.96

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.2e-05
                                    HHHHHHHHHHHHTTEEEEEEESSSSSBT CS
                  Amino_oxidase   1 laGLaaArqLlsaGfdVtvlEardrvGG 28 
                                    +aG++aA  L++aG++V ++E r+ +GG
  gi|116754868|ref|YP_843986.1| 155 VAGISAALDLANAGLRVYLVERRPTIGG 182
                                    69*************************9 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.5e-05    0.0079     165     199 ..     146     180 ..     135     240 .. 0.78
   2 ?   -3.0   0.0       6.4   3.4e+03     239     305 .]     463     539 ..     452     539 .. 0.54

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.5e-05
                    Pyr_redox_3 165 qkvvViGgknSavDaAlelvrkgaeVtvvtrgsei 199
                                    ++v+ViGg+  ++ aAl+l+++g +V +v r+ +i
  gi|116754868|ref|YP_843986.1| 146 RDVLVIGGGVAGISAALDLANAGLRVYLVERRPTI 180
                                    56777777777777777777777777777777665 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6.4
                    Pyr_redox_3 239 kekeeeykvkted...gkkvev.kddvvlatGykpd..lsflkk.slfeldedgrpvlteete...etnvpglflaG 305
                                    +e e    v+ ed   gk++ + +d vvl tG + +  ++++ +  +++++ d++ ++   ++   e  ++g+f+aG
  gi|116754868|ref|YP_843986.1| 463 EEGEDGLYVHYEDtllGKTLMKrYDLVVLSTGLEANsdADVVGNlLGLSRRPDRFFEIAHPKMrpvEAHIDGVFIAG 539
                                    55555555554442224455542555566699765422566776666666666655554433323367777777777 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 !   15.5   0.1   1.5e-05    0.0081      30      62 ..     147     179 ..     139     193 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.5e-05
                                    EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHH CS
                    AlaDh_PNT_C  30 kvlviGgGvaGlqAiatakglgakVtvlDvrpa 62 
                                     vlviGgGvaG++A+   ++ g +V++++ rp+
  gi|116754868|ref|YP_843986.1| 147 DVLVIGGGVAGISAALDLANAGLRVYLVERRPT 179
                                    69**************************99986 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.6      0.93   4.9e+02      78      95 ..     244     262 ..     232     263 .. 0.79
   2 ?   12.5   0.9   0.00037       0.2      77      94 ..     291     308 ..     274     310 .. 0.85
   3 ?    7.6   1.4     0.013       6.7      76      94 ..     578     596 ..     550     599 .. 0.80
   4 ?    7.7   3.3     0.012       6.2      77      94 ..     607     624 ..     597     626 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.93
                        Fer4_22  78 gesgCvGC.gRCieacpvk 95 
                                    + + C GC + C++acpv+
  gi|116754868|ref|YP_843986.1| 244 DPTLCKGCiNECSSACPVE 262
                                    66789999668****9987 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00037
                        Fer4_22  77 fgesgCvGCgRCieacpv 94 
                                    +++++C+GCg C eacp+
  gi|116754868|ref|YP_843986.1| 291 IDTNACIGCGLCAEACPA 308
                                    6899************97 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.013
                        Fer4_22  76 kfgesgCvGCgRCieacpv 94 
                                     +++ +C+GC  C+++cp+
  gi|116754868|ref|YP_843986.1| 578 FVDRDKCIGCRLCVDTCPS 596
                                    458999***********97 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.012
                        Fer4_22  77 fgesgCvGCgRCieacpv 94 
                                    ++e  C GCg C +acpv
  gi|116754868|ref|YP_843986.1| 607 VDEARCKGCGTCAAACPV 624
                                    47889***********97 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   4.3     0.092        49       1      13 [.     248     261 ..     248     263 .. 0.91
   2 ?   14.0   5.4   0.00014     0.073       1      15 []     296     310 ..     296     310 .. 0.95
   3 ?   14.9   3.3   7.1e-05     0.038       1      15 []     584     598 ..     584     598 .. 0.97
   4 ?   10.2   7.4    0.0023       1.2       1      15 []     612     626 ..     612     626 .. 0.97

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.092
                         Fer4_3   1 CtgC.gaCvevCPv 13 
                                    C gC + C  +CPv
  gi|116754868|ref|YP_843986.1| 248 CKGCiNECSSACPV 261
                                    99**889******7 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 0.00014
                         Fer4_3   1 CtgCgaCvevCPvgA 15 
                                    C+gCg+C e+CP +A
  gi|116754868|ref|YP_843986.1| 296 CIGCGLCAEACPADA 310
                                    ************887 PP

  == domain 3  score: 14.9 bits;  conditional E-value: 7.1e-05
                         Fer4_3   1 CtgCgaCvevCPvgA 15 
                                    C+gC++Cv+ CP++A
  gi|116754868|ref|YP_843986.1| 584 CIGCRLCVDTCPSRA 598
                                    ************998 PP

  == domain 4  score: 10.2 bits;  conditional E-value: 0.0023
                         Fer4_3   1 CtgCgaCvevCPvgA 15 
                                    C gCg+C  +CPv+A
  gi|116754868|ref|YP_843986.1| 612 CKGCGTCAAACPVDA 626
                                    9************98 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 ?   -0.5   0.0       3.2   1.7e+03      34      75 ..      38      78 ..      26     109 .. 0.52
   2 ?    8.3   0.2     0.006       3.2       8      39 ..     146     177 ..     143     211 .. 0.90
   3 ?    0.2   0.0       1.9     1e+03      51      83 ..     524     556 ..     471     567 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 3.2
                  NAD_binding_7 34 tvvapevkeeleelvklaeeelekdlegad...lviaatddreln 75
                                   +vva +++  ++   ++ ++++++d+++ +   +v+aa++   l 
  gi|116754868|ref|YP_843986.1| 38 VVVARDIQFTCS---DAGQNTIKSDIAELKldaVVVAACSP-RLH 78
                                   566777444443...47788888888874444455555443.333 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.006
                  NAD_binding_7   8 kkvlvvGgGevAarkvrklleagakvtvvape 39 
                                    + vlv+GgG  + + +  l++ag +v +v  +
  gi|116754868|ref|YP_843986.1| 146 RDVLVIGGGVAGISAALDLANAGLRVYLVERR 177
                                    78************************999765 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 1.9
                  NAD_binding_7  51 aeeelekdlegadlviaatddrelneriaeaak 83 
                                    + + +e++++g++++ +a   +e++  ia+   
  gi|116754868|ref|YP_843986.1| 524 KMRPVEAHIDGVFIAGCASGPKEIQVSIAQGSA 556
                                    345578999999999999999999999998553 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.3   0.00091      0.48       1      33 [.     147     176 ..     147     184 .. 0.88
   2 ?   -1.5   0.0       1.6   8.7e+02     156     186 ..     440     469 ..     385     498 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00091
                                    EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE- CS
                 Trp_halogenase   1 kivivGGGtaGwlaAaalakalkgklevtlves 33 
                                    +++++GGG aG  aA  la+a+   l+v lve 
  gi|116754868|ref|YP_843986.1| 147 DVLVIGGGVAGISAALDLANAG---LRVYLVER 176
                                    699*******************...99****96 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.6
                                    HHHHHHHHHHHCT-EEEE--EEEEEE-TTS- CS
                 Trp_halogenase 156 yakfLrrvaearGvtrvegkvvevqldedgr 186
                                    y++f  r a++ G++ ++g+v +v+  edg 
  gi|116754868|ref|YP_843986.1| 440 YEEFYLR-AQRLGINFIRGRVSSVEEGEDGL 469
                                    5665554.8999***********99999874 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   1.8     0.062        33      60      73 ..     295     308 ..     280     318 .. 0.69
   2 ?   14.2   4.1     7e-05     0.037      58      96 ..     581     623 ..     553     638 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.062
                        Fer4_18  60 dcidcescvkvcPt 73 
                                     ci c+ c + cP 
  gi|116754868|ref|YP_843986.1| 295 ACIGCGLCAEACPA 308
                                    45555555555554 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 7e-05
                        Fer4_18  58 agdcidcescvkvcPt.gidirkGlqle...ciscllcidacd 96 
                                      +ci c+ cv+ cP   i +++   ++   c  c+ c  ac 
  gi|116754868|ref|YP_843986.1| 581 RDKCIGCRLCVDTCPSrAISVKDTAFVDearCKGCGTCAAACP 623
                                    578************7369999987653333***********5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (791 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:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        36  (0.00200792); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              34  [number of targets reported over threshold]
# CPU time: 0.75u 0.31s 00:00:01.06 Elapsed: 00:00:00.49
# Mc/sec: 4809.26
//
Query:       gi|116754869|ref|YP_843987.1|  [L=166]
Description: hypothetical protein Mthe_1577 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1262.38
//
Query:       gi|116754870|ref|YP_843988.1|  [L=83]
Description: RNAse P, Rpr2/Rpp21 subunit [Methanosaeta thermophila PT]
Scores for complete 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   35.8   0.5    2.2e-08   34.2   0.5    1.7  1  Rpr2            RNAse P Rpr2/Rpp21/SNM1 subunit domain
     0.0039   17.2   0.1      0.005   16.8   0.1    1.2  1  DZR             Double zinc ribbon
     0.0087   16.0   0.4      0.011   15.7   0.4    1.2  1  RNHCP           RNHCP domain
  ------ inclusion threshold ------
       0.11   12.5   3.7       0.14   12.1   0.1    2.2  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
       0.42   10.0   2.9          6    6.3   3.2    2.1  2  zf-TFIIB        Transcription factor zinc-finger
       0.49   10.5   3.6        7.4    6.7   3.6    2.0  1  zf-Sec23_Sec24  Sec23/Sec24 zinc finger


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 !   34.2   0.5   7.5e-12   2.2e-08       3      90 .]       2      75 ..       1      75 [. 0.88

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 7.5e-12
                                   HHHHHHHH.HHHHH-HHHHHHHHHHHHHHHHHCT---SSTCCCTB-TTT--B--CTTTEEEEEE-SSS-E.........EEE CS
                           Rpr2  3 nfLyqaahlqlaeaspalsrylakqlrevskkaqlrlppsvkrtvCkkCgsvlipgvtcsvrvenkskkkkkkkkkadvlvv 84
                                   + L+++a+  +ae++p+ s ++++ + ++ ++ ++r  +++kr +Ck+C+ +l p + + vr++              vlv+
  gi|116754870|ref|YP_843988.1|  2 ERLFELARA-NAETHPERSDRYVELALKIGMRLRVRPTREMKRMFCKSCRGFLSPAQRM-VRLRD------------GVLVI 69
                                   679999999.9******************************************997654.66642............26889 PP

                                   EETTTT CS
                           Rpr2 85 tClaCg 90
                                   +C +Cg
  gi|116754870|ref|YP_843988.1| 70 RCMRCG 75
                                   999996 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   1.7e-06     0.005      12      39 ..      43      79 ..      36      83 .] 0.86

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.7e-06
                            DZR 12 arfCseCgtklkavaa.........edrCpsCgekvd 39
                                     fC+ C+  l+++++          +rC++Cg+   
  gi|116754870|ref|YP_843988.1| 43 RMFCKSCRGFLSPAQRmvrlrdgvlVIRCMRCGHISR 79
                                   45*********98888*****************9765 PP

>> RNHCP  RNHCP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.4   3.7e-06     0.011      44      79 ..      47      81 ..      36      83 .] 0.85

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.7e-06
                          RNHCP 44 seCkglmepiavevkkkkewvivhrCekCgelkknr 79
                                   ++C+g ++p +  v+ + + v+v rC +Cg++++ r
  gi|116754870|ref|YP_843988.1| 47 KSCRGFLSPAQRMVRLR-DGVLVIRCMRCGHISRMR 81
                                   68*********998855.567888*******98765 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 ?   12.1   0.1   4.8e-05      0.14      15      36 ..      30      55 ..      26      57 .. 0.87
   2 ?    0.7   0.8      0.17     5e+02       6      11 ..      70      75 ..      69      81 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.8e-05
                 Zn_ribbon_SprT 15 thhlsirrhn....YrCrrCkgtLrg 36
                                   + +l++r+ +    + C+ C+g+L++
  gi|116754870|ref|YP_843988.1| 30 GMRLRVRPTRemkrMFCKSCRGFLSP 55
                                   668999999999***********985 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.17
                 Zn_ribbon_SprT  6 rCtgCg 11
                                   rC +Cg
  gi|116754870|ref|YP_843988.1| 70 RCMRCG 75
                                   455665 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.2     0.016        49      22      28 ..      46      52 ..      33      62 .. 0.87
   2 ?    6.3   3.2     0.002         6       4      26 ..      48      75 ..      46      75 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.016
                       zf-TFIIB 22 CpqCrGv 28
                                   C +CrG+
  gi|116754870|ref|YP_843988.1| 46 CKSCRGF 52
                                   9*****7 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.002
                       zf-TFIIB  4 kCqdeleeser.....ggveidyCpqCr 26
                                   +C+  l +++r     +gv++ +C +C+
  gi|116754870|ref|YP_843988.1| 48 SCRGFLSPAQRmvrlrDGVLVIRCMRCG 75
                                   566667766666667799*********7 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 ?    6.7   3.6    0.0025       7.4       3      32 ..      45      77 ..      44      79 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0025
                 zf-Sec23_Sec24  3 rCrrCraylNpfcki...dfggkrwiCnfCnhk 32
                                    C++Cr +l p  ++    +g    +C  C+h 
  gi|116754870|ref|YP_843988.1| 45 FCKSCRGFLSPAQRMvrlRDGVLVIRCMRCGHI 77
                                   5**********8776554555566888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); 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):               6  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 642.63
//
Query:       gi|116754871|ref|YP_843989.1|  [L=83]
Description: hypothetical protein Mthe_1579 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); 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: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 653.03
//
Query:       gi|116754872|ref|YP_843990.1|  [L=177]
Description: RdgB/HAM1 family non-canonical purine NTP pyrophosphatase [Methanosaeta thermophila PT]
Scores for 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-47  159.4   0.0      1e-46  159.3   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 !  159.3   0.0   5.6e-51     1e-46       1     187 []       2     173 ..       2     173 .. 0.87

  Alignments for each domain:
  == domain 1  score: 159.3 bits;  conditional E-value: 5.6e-51
                                    EEEC-S-HHHHHHHHHHTTTECCCE.EECCCCEE----BS.SSHHHHHHHHHHHHHH.HTS-EEEEEEEEEEGGGTTTBG CS
                     Ham1p_like   1 ivfaTgNkgKlrevkeilaeellevkslkelelpeveEtq.gtfeenalkKaraaae.aglpvladDsgLevdaLnglPG 78 
                                    i f+T+N+gK+ e+++il+  ++  ++l       ++E+q +t+ee++l   +++++  + p++++D gL+v+aLng+PG
  gi|116754872|ref|YP_843990.1|   2 IRFVTSNRGKFIEAQRILG--GIVQADL------GYTEIQaDTLEEVVLFGLKELSTrLDSPFIIEDAGLFVEALNGFPG 73 
                                    679***************7..3434455......5579**9*************99646888****************** PP

                                    GGTTTTTHTTCHHHHHHHHHHHHCTHTTS--EEEEEEEEEEEETTTTEEEEEEEEEEEEE-SS.--SSSSTTGGGEEETT CS
                     Ham1p_like  79 vysarfagegaedeenlaklleeleeeeedrsArfvcvlaladpeeeeellfeGeveGeiveeprgeggfGyDpiFvpee 158
                                    vysa+++++      ++  +l+ +++  e+r A+f++v+++++p+ e+ +lf+Ge++G i  e+rg+ggfGyDpiF++ +
  gi|116754872|ref|YP_843990.1|  74 VYSAYVQKT-----IGNSGILRLMDGI-ENRAASFRSVVGYSAPGMEP-VLFKGELRGVIGFEARGTGGFGYDPIFEV-D 145
                                    ******654.....4556666666433.47**************6666.99***************************.5 PP

                                    -SSBTTTS.CHHHHHHSHHHHHHHHHHHH CS
                     Ham1p_like 159 gektfaelskeeknaiShRgkAlekllef 187
                                     ++t+ae++ eekn iShRg+++++l+ +
  gi|116754872|ref|YP_843990.1| 146 -GRTLAEMDLEEKNMISHRGRSMKALKRW 173
                                    .79***********************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       223  (0.0124379); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1312.53
//
Query:       gi|116754873|ref|YP_843991.1|  [L=238]
Description: RNA-binding S4 domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-13   48.6   0.4    9.6e-13   47.6   0.4    1.5  1  S4               S4 domain
    5.9e-11   42.8   0.0    8.6e-11   42.3   0.0    1.2  1  FtsJ             FtsJ-like methyltransferase
    2.7e-07   31.2   0.0    5.4e-07   30.2   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    2.1e-05   25.1   0.0    3.9e-05   24.2   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
    4.7e-05   23.1   0.1    0.00011   21.9   0.1    1.6  1  S4_2             S4 domain
    0.00054   19.8   0.0     0.0036   17.2   0.0    2.1  1  Methyltransf_23  Methyltransferase domain
    0.00058   19.7   0.0     0.0017   18.1   0.0    1.6  1  Methyltransf_31  Methyltransferase domain
     0.0019   18.8   0.0     0.0085   16.7   0.0    2.0  2  ThiS             ThiS family
     0.0086   16.8   0.0       0.02   15.6   0.0    1.7  1  Methyltransf_12  Methyltransferase domain
  ------ inclusion threshold ------
       0.22   10.4   0.0       0.34    9.8   0.0    1.3  1  Methyltransf_9   Protein of unknown function (DUF1698)
       0.29   10.5   0.0        0.4   10.0   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm


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 !   47.6   0.4   5.9e-16   9.6e-13       1      48 []       3      48 ..       3      48 .. 0.98

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 5.9e-16
                                   EEHHHHHHHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTCEE CS
                             S4  1 rRLdkvlarlglassrreArqlIehGrVlVNGkvvkdpsyrVkpgDvi 48
                                   +RLd++l+   +a sr++A  lI+ G+V VNG v+++ syrVkpgD++
  gi|116754873|ref|YP_843991.1|  3 MRLDIYLV--EIAGSRSKAVHLIKSGKVMVNGAVCRKQSYRVKPGDRV 48
                                   8******8..9999********************************97 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.0   5.3e-14   8.6e-11       1     110 [.      56     166 ..      56     185 .. 0.83

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 5.3e-14
                                    CCCCHHHHHHHHHHHHT-S-.TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS....HHH..TTEEEECS-CCCS CS
                           FtsJ   1 yrsRsayKLleidekfklfk.pgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm....apl..pgvttiqgditdp 73 
                                    y+sR++yK++ + +  +  + +g  v+D+g++ Gg+s++ lq+ ga ++v ++D+ ++    a+l  p+ ++ +g +   
  gi|116754873|ref|YP_843991.1|  56 YVSRGGYKIEALFQGRS-DEiRGLSVLDVGCSAGGFSDFFLQH-GA-ARVWGIDIAEGcvdpAMLsdPRFRF-TGGVDAR 131
                                    99**********99988.335999*******************.88.9*******99999654554455554.5666666 PP

                                    SHHHHHCHCHHHSSEEEEEE--S-SS-CHHHHHHHHH CS
                           FtsJ  74 etiekikealserkvdlvvsDgapdvsgvhdldeylq 110
                                    + +e++k +l+++++dl   D++ +vs++++l+++++
  gi|116754873|ref|YP_843991.1| 132 SFEELVK-HLGDERFDLTSVDVS-NVSLREVLPNLKR 166
                                    6677677.799************.***9999887765 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   3.3e-10   5.4e-07       1      97 []      80     172 ..      80     172 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 3.3e-10
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEE....EESBCCGBS..SSTTTEEEEEEESTG CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvef....vqgdaedlp..fedgsfDlvvssgal 74 
                                    vLd+Gc  G ++  ++++ g+a+v+g+Di+e++++ a        ++++f       ++e+l   + d++fDl  +   +
  gi|116754873|ref|YP_843991.1|  80 VLDVGCSAGGFSDFFLQH-GAARVWGIDIAEGCVDPAMLSD----PRFRFtggvDARSFEELVkhLGDERFDLTSVD--V 152
                                    9*****************.69**************998776....555552111444445553336899****9993..3 PP

                                    GGSSHHHHHHHHHHHHHHEEEEE CS
                Methyltransf_25  75 hhlsdedlekalkeiarvLkpgG 97 
                                    + +    l+++l +++r Lk +G
  gi|116754873|ref|YP_843991.1| 153 SNV---SLREVLPNLKRFLKSDG 172
                                    444...5899**********998 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   2.4e-08   3.9e-05       1      95 [.      81     175 ..      81     176 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 2.4e-08
                                    EEET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCT..SS-TT-EEEEEEES-CCC-CCH CS
                Methyltransf_11   1 LdvGcGtGrlaealakrg.arvvgvDlskemlklakekaseeglkvefvvadaekl..pfednsfDlvvssevlhhvedp 77 
                                    LdvGc +G ++  + ++g arv g+D+++  ++ a    ++ +++  +   ++e+l   + d+ fDl  +  +  +v  +
  gi|116754873|ref|YP_843991.1|  81 LDVGCSAGGFSDFFLQHGaARVWGIDIAEGCVDPAMLSDPRFRFTGGVDARSFEELvkHLGDERFDLTSVDVS--NV-SL 157
                                    8*******************************999777777776333455666665445*******9866653..44.36 PP

                                    HHHHHHHHHHEEEEEEEE CS
                Methyltransf_11  78 ekalkeiaRvLkpgGllv 95 
                                    +++l +++R Lk +G++v
  gi|116754873|ref|YP_843991.1| 158 REVLPNLKRFLKSDGRIV 175
                                    89*************997 PP

>> S4_2  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.1   6.9e-08   0.00011      24      60 ..      17      54 ..       8      57 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 6.9e-08
                           S4_2 24 geaKafiaegeVkvNGevetrRgkKlraGdvVei.dge 60
                                    +a ++i++g+V vNG+v+ +   ++ +Gd Vei +g 
  gi|116754873|ref|YP_843991.1| 17 SKAVHLIKSGKVMVNGAVCRKQSYRVKPGDRVEIvEGF 54
                                   567799***************************96665 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.2e-06    0.0036      12     118 ..      63     177 ..      52     217 .. 0.56

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.2e-06
                Methyltransf_23  12 klerllpk...lraggrvLdiGcGtGillevlrengf.svtgvDlspeaveiae..kakkaqkdqfdeqeaae.....pq 80 
                                    k+e l++    + +g +vLd+Gc  G +++ + ++g+  v g+D+ + +v+ a    +++ +   +d+ + +e      +
  gi|116754873|ref|YP_843991.1|  63 KIEALFQGrsdEIRGLSVLDVGCSAGGFSDFFLQHGAaRVWGIDIAEGCVDPAMlsDPRFRFTGGVDARSFEElvkhlGD 142
                                    6677773223355666*******************9989******98777766455333333333322222222222223 PP

                Methyltransf_23  81 gkfdlIvlrevlehvpdppellrqiatllkpgGyllls 118
                                    ++fdl +   v  +  ++ e+l ++++ lk +G+++ +
  gi|116754873|ref|YP_843991.1| 143 ERFDLTS---VDVSNVSLREVLPNLKRFLKSDGRIVAL 177
                                    3444311...1112223335666666666666655554 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.1e-06    0.0017       4     108 ..      77     175 ..      75     179 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.1e-06
                Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnev 83 
                                    gl+vlD+GC +G ++  +  +    a+v GiDi e  +  A     +  ++   + + ++eel k+l de+fDl    + 
  gi|116754873|ref|YP_843991.1|  77 GLSVLDVGCSAGGFSDFFL-QH-GAARVWGIDIAEGCVDPAMLSDPRFRFT-GGVDARSFEELVKHLGDERFDLTSV-D- 151
                                    789************9999.43.4699***********9999866666665.66788999999988999*****333.3. PP

                Methyltransf_31  84 lnaladpdkileeiervlkpggill 108
                                         ++ ++l +++r lk++g+++
  gi|116754873|ref|YP_843991.1| 152 -VSNVSLREVLPNLKRFLKSDGRIV 175
                                    .55789999*************998 PP

>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   5.2e-06    0.0085      40      71 ..      22      51 ..       8      53 .. 0.82
   2 ?   -1.0   0.0       1.7   2.8e+03      63      71 ..     170     178 ..     129     187 .. 0.53

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.2e-06
                                   TTTTEEEEETTEEEGCCTTTSB--TTCEEEEE CS
                           ThiS 40 lerrvavavNgeivprlwldtelkdgDevail 71
                                   l++   v+vNg ++++  +++++k+gD+v+i+
  gi|116754873|ref|YP_843991.1| 22 LIKSGKVMVNGAVCRK--QSYRVKPGDRVEIV 51
                                   6677789*********..*************8 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.7
                                    -TTCEEEEE CS
                           ThiS  63 kdgDevail 71 
                                    +dg  va++
  gi|116754873|ref|YP_843991.1| 170 SDGRIVALF 178
                                    455555555 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.2e-05      0.02       1      98 [.      81     173 ..      81     174 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.2e-05
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakre...nnnnnnvelealdlldldggssfDlvvasnvlh 77 
                                    L++Gc  G +++ +l++   +++ g+Di +  ++ a     + +   + ++  +e  +++l+d    + fDl ++ +v +
  gi|116754873|ref|YP_843991.1|  81 LDVGCSAGGFSDFFLQH-GAARVWGIDIAEGCVDPAMLSDPRFRftgGVDARSFEELVKHLGD----ERFDL-TSVDVSN 154
                                    8****************.999999*****9999544444333330003333333333333333....59997.5667777 PP

                Methyltransf_12  78 hlkdirevldnirklLkpgGr 98 
                                    +   +revl n+++ Lk +Gr
  gi|116754873|ref|YP_843991.1| 155 V--SLREVLPNLKRFLKSDGR 173
                                    7..588888888888888887 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00021      0.34     113     146 ..      74     107 ..      58     112 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00021
                                    --TT-EEEEET-TTSHHHHHHHHCT-SEEEEE-- CS
                 Methyltransf_9 113 dlkgrtildvGcgnGyhlwrmvgegaklvvGidP 146
                                    +++g ++ldvGc++G +    + +ga+ v Gid 
  gi|116754873|ref|YP_843991.1|  74 EIRGLSVLDVGCSAGGFSDFFLQHGAARVWGIDI 107
                                    578899**********9999************96 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00025       0.4     163     257 ..      78     175 ..      64     176 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00025
                           PrmA 163 eevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellk...eekadvivaNILaevl 239
                                     +vlDvG+ +G  +   ++ ga++v ++Di e  v+ a     + + +  ++    eel+k   +e++d+    +    l
  gi|116754873|ref|YP_843991.1|  78 LSVLDVGCSAGGFSDFFLQHGAARVWGIDIAEGCVDPAMLSDPRFRFTGGVDARSFEELVKhlgDERFDLTSVDVSNVSL 157
                                    48*********************************999877777666666666555555544556778877777777778 PP

                           PrmA 240 ielaedikklvkegglli 257
                                     e ++++k+++k++g+++
  gi|116754873|ref|YP_843991.1| 158 REVLPNLKRFLKSDGRIV 175
                                    888888888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1822.09
//
Query:       gi|116754874|ref|YP_843992.1|  [L=288]
Description: Ion transport 2 domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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-18   64.8  25.0    9.8e-18   64.3  25.0    1.1  1  Ion_trans      Ion transport protein
    8.4e-16   57.7   5.8    8.4e-16   57.7   5.8    2.9  3  Ion_trans_2    Ion channel
     0.0073   16.3   0.7      0.012   15.6   0.7    1.3  1  DZR            Double zinc ribbon
  ------ inclusion threshold ------
      0.028   14.3   2.2        4.5    7.3   0.0    2.3  2  Nudix_N_2      Nudix N-terminal
      0.094   12.2   1.3       0.15   11.5   1.3    1.3  1  zf-ribbon_3    zinc-ribbon domain
       0.13   12.1   1.6       0.32   10.8   1.6    1.7  1  zinc_ribbon_2  zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Ion_trans  Ion transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.3  25.0   3.3e-21   9.8e-18       4     226 ..      33     233 ..      31     237 .. 0.85

  Alignments for each domain:
  == domain 1  score: 64.3 bits;  conditional E-value: 3.3e-21
                                    HHHHHHHHHHHHHHHHHCCCSSSSHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHCHSHHHHHHHHHHHHHHH CS
                      Ion_trans   4 felfilllillncvflaletyfpedelektileilelvftaiftlemllkilalgllikkrYlrdpwnilDflvvlpsll 83 
                                    +++ i+ l ++ +v++ +ety+ +++ +  +l  le++++ if++e +l++++++   +++Y++++  ++D+++++p+l+
  gi|116754874|ref|YP_843992.1|  33 IDIAIIALNIMVVVLFVIETYPLPSRIS-LLLWRLEIAIIFIFMIEYILRFYGAPD--RWSYVKETYSLIDLVAIMPTLI 109
                                    567888888888999999******8888.888889*********************..********************** PP

                                    HH.......HHHHHHHHHHHHHHHHGGGGGGHHHCHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHTTS CS
                      Ion_trans  84 sl.......vlseesllllsvlrlfrvlrllklisrleglrtlvtalirsvkdllnvlllllvvlfifalig.vqlfkgk 155
                                     l       +     l  ++++r++ v+r++++++ +         ++ +   +lnv+ l+++v+ if++ + + +f   
  gi|116754874|ref|YP_843992.1| 110 LLvlpifgvY---ADLRFIHIIRIMAVFRIFRFLRFIAEDHL---LFGIISLRMLNVARLVFIVMTIFFISSgLFYF--- 180
                                    9955544431...56899999999999999999999999888...55667777778888888888888877636666... PP

                                    CCCCCCSCCSTSSSTTTSSSSSSHHHHHHHHHHHHTTSSHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHH CS
                      Ion_trans 156 lreknecaktwenpnngntnFdnfftallwlfrlmttegwgdilyatldekskvaliyfvifiilgsflll 226
                                               e+p n++  ++nf++a++++++  +t+g+gdi+++   ++      ++ +++i+++++l+
  gi|116754874|ref|YP_843992.1| 181 ----------AESPVNPE--VNNFGDAFYFTVVAVSTVGFGDIVPVSGAGR------LVTLMMIISGIILI 233
                                    ..........56665555..55*****************************......99999999999987 PP

>> Ion_trans_2  Ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.4      0.19   5.6e+02      47      70 ..      26      49 ..      19      52 .. 0.87
   2 ?   -2.0   0.2       1.2   3.7e+03       3      27 ..      70      93 ..      61      99 .. 0.56
   3 !   57.7   5.8   2.8e-19   8.4e-16       2      74 ..     168     241 ..     164     245 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.19
                                   T-----HHHHHHHHHHHHHHHHHH CS
                    Ion_trans_2 47 etdagrlftivyillGlalfalfl 70
                                   +t++gr++ i++i l +++++lf+
  gi|116754874|ref|YP_843992.1| 26 RTPLGRAIDIAIIALNIMVVVLFV 49
                                   588899999999999999999987 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.2
                                   HHHTCHHHHHHHHT....T---HHH CS
                    Ion_trans_2  3 lllvlifgaviysleegwekwsfld 27
                                   +++++++  ++ ++++   +ws+++
  gi|116754874|ref|YP_843992.1| 70 IIFIFMIEYILRFYGA-PDRWSYVK 93
                                   4444555555555422.34566665 PP

  == domain 3  score: 57.7 bits;  conditional E-value: 2.8e-19
                                    HHHHTCHHHHHHHHT.....T---HHHHHHHHHHHHTTS----SSTT-----HHHHHHHHHHHHHHHHHHHHHH CS
                    Ion_trans_2   2 vlllvlifgaviysl.eegwekwsfldalYfsfvtltTiGYGdivpetdagrlftivyillGlalfalflavlg 74 
                                    ++++++ +g ++++    + e ++f da+Yf++v ++T+G+Gdivp++ agrl+t++ i+ G++l+ + ++ + 
  gi|116754874|ref|YP_843992.1| 168 MTIFFISSGLFYFAEsPVNPEVNNFGDAFYFTVVAVSTVGFGDIVPVSGAGRLVTLMMIISGIILIPIQVSRIL 241
                                    45555666666666554448899************************9999***************99998775 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.7   4.2e-06     0.012       1      23 [.     254     277 ..     250     283 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.2e-06
                            DZR   1 CpqCgee.lppdarfCseCgtklk 23 
                                    C+ Cg+e +++dar+C  Cg++l 
  gi|116754874|ref|YP_843992.1| 254 CSGCGQEwHEEDARYCRICGSPLG 277
                                    999**997778999*******996 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.5    0.0029       8.7      20      29 ..     249     258 ..     247     259 .. 0.91
   2 ?    7.3   0.0    0.0015       4.5       1      10 [.     267     276 ..     267     286 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0029
                                    S-EEEETTTT CS
                      Nudix_N_2  20 reRlvCpaCg 29 
                                    r R++C+ Cg
  gi|116754874|ref|YP_843992.1| 249 RKRHICSGCG 258
                                    89*******9 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0015
                                    -B-TTT--B- CS
                      Nudix_N_2   1 kFCsqCGtpv 10 
                                    ++C+ CG+p+
  gi|116754874|ref|YP_843992.1| 267 RYCRICGSPL 276
                                    8********8 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.3   5.2e-05      0.15       5      26 .]     254     276 ..     252     276 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.2e-05
                    zf-ribbon_3   5 CPnCGa.plssddnvCpyCGtkl 26 
                                    C+ CG+   ++d++ C  CG++l
  gi|116754874|ref|YP_843992.1| 254 CSGCGQeWHEEDARYCRICGSPL 276
                                    9*****967***********997 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.6   0.00011      0.32       2      23 .]     254     276 ..     253     276 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00011
                  zinc_ribbon_2   2 CpnCGael.qdnakFCpyCGtpl 23 
                                    C+ CG e  +++a++C  CG+pl
  gi|116754874|ref|YP_843992.1| 254 CSGCGQEWhEEDARYCRICGSPL 276
                                    88899998689**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       842  (0.046963); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
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 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1997.58
//
Query:       gi|116754875|ref|YP_843993.1|  [L=236]
Description: hypothetical protein Mthe_1583 [Methanosaeta thermophila PT]
Scores for complete 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-42  143.8   9.6    4.7e-42  143.8   9.6    1.7  2  Vut_1     Putative vitamin uptake transporter
  ------ inclusion threshold ------
       0.33   10.3   2.4       0.65    9.3   2.4    1.5  1  DUF4407   Domain of unknown function (DUF4407)


Domain annotation for each model (and alignments):
>> Vut_1  Putative vitamin uptake transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.3      0.34     3e+03      31      41 ..       8      18 ..       2      59 .. 0.51
   2 !  143.8   9.6   5.2e-46   4.7e-42       4     149 ..      66     219 ..      63     220 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.34
                          Vut_1 31 llgflanllal 41
                                   ++g+++++++l
  gi|116754875|ref|YP_843993.1|  8 WIGLVSSFTIL 18
                                   44444443332 PP

  == domain 2  score: 143.8 bits;  conditional E-value: 5.2e-46
                          Vut_1   4 vllfpltflitdiisevyGkkaarkvvllgflanllalillllalllpa.......ealesvfgltprivlasliaylvs 76 
                                    v++f++tfl+td+++e +G +++r+++ ++fl+++++ ++++l++ lp+       +a+e +++++privlas++a++vs
  gi|116754875|ref|YP_843993.1|  66 VIVFSVTFLLTDVVNERFGLQETRRMISIAFLSQIMISLFSWLVVELPPapffphqNAIEVLLEQVPRIVLASWVAFFVS 145
                                    89**********************************************999**99999********************** PP

                          Vut_1  77 qlldvyvfhrlkkltkgkklwlrnigStlvsqlvdtlifvtiaflg.eqlleiilsqylikllialldtplvyl 149
                                    ++ld+ vf+++k +tkg++lw+rn++S++ + l+d+ +f+tiaf+g   ++ +i++  + k+l+al+d+p++y+
  gi|116754875|ref|YP_843993.1| 146 ENLDAVVFAWFKSKTKGRHLWARNALSSIPAMLIDSTLFITIAFYGvMPVVPLIIGITITKWLVALVDIPFMYM 219
                                    ********************************************99**************************96 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   2.4   7.2e-05      0.65      62     105 ..     106     154 ..      57     156 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 7.2e-05
                        DUF4407  62 Rfivssi.....kkrakkrrelalalpRlllAvligvvisepleLkiFe 105
                                     ++v+ +      ++++    l+  +pR++lA  +++++se l+ ++F 
  gi|116754875|ref|YP_843993.1| 106 SWLVVELppapfFPHQNAIEVLLEQVPRIVLASWVAFFVSENLDAVVFA 154
                                    5777777677776667777888999*******************99995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1698.51
//
Query:       gi|116754876|ref|YP_843994.1|  [L=220]
Description: NADPH-dependent FMN reductase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.7e-28   98.2   0.0    4.9e-28   97.8   0.0    1.2  1  FMN_red       NADPH-dependent FMN reductase
    1.4e-14   54.3   0.0    1.9e-14   53.8   0.0    1.3  1  Flavodoxin_2  Flavodoxin-like fold
  ------ inclusion threshold ------
       0.14   12.3   0.1        0.3   11.3   0.1    1.5  1  PUMA          Bcl-2-binding component 3, p53 upregulated modu


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 !   97.8   0.0   8.2e-32   4.9e-28       1     144 [.       1     146 [.       1     153 [. 0.86

  Alignments for each domain:
  == domain 1  score: 97.8 bits;  conditional E-value: 8.2e-32
                                    -EEEEEES--S.TT-HHHHHHHHHHCCT-T.T-CEEEEETTTS..--.....---HCHGHTCGGSHHHHHHHHHHHH-SC CS
                        FMN_red   1 mkilvisGSlr.kgsntrklaewaaealkeagaevelidladl.ilpc...alcdkdlesegqtsddvaellekiaaada 75 
                                    mkil+ + S+r ++s t +l+++a++ ++ +gaevel+d+ +l i  c      ++  + e+ ++dd++++++ki ++d+
  gi|116754876|ref|YP_843994.1|   1 MKILGMNSSPRgERSQTLRLVRAALDGARSEGAEVELVDVCKLrIEYCnacG--VCYAKGECTHKDDFNQVYKKILECDG 78 
                                    9**********889**************999********9999999997543..333444589***************** PP

                                    EEEEEEECTTCE-HHHHHHHHCHT-.SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHHHTT-EEEE CS
                        FMN_red  76 liivtPeYngsysgllKnalDrlsrtrgkkelrgKpvalvavgggrrgglraeeqlrqvlaelgaivvp 144
                                    +ii++P Y+ s++++lK+++Dr+    + + l gK++ +va++gg +   ++   l+ +   +ga +v+
  gi|116754876|ref|YP_843994.1|  79 FIIGSPNYFRSVTAQLKTLIDRMADAVHCQLLLGKYGCAVATAGG-QAYDEVLDYLSRIIVGFGASYVG 146
                                    ***********************9899999999**********99.55556666665555556666665 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.8   0.0   3.2e-18   1.9e-14       1     140 [.       1     127 [.       1     169 [. 0.87

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 3.2e-18
                                    -EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCCT-----CCCCHCC.HHHHTT.C.HHHHHHH.HHHHH CS
                   Flavodoxin_2   1 mkiLiinahprpeksfssalaqafvealekagphevtvrdLyadflpvlttrdlaak.layeek.p.adveseq.iekll 76 
                                    mkiL  n++pr+e+s++ +l +a++++++++g +ev+ +d+ ++     + ++ +a    y+++ + ++ + +q  +k+l
  gi|116754876|ref|YP_843994.1|   1 MKILGMNSSPRGERSQTLRLVRAALDGARSEG-AEVELVDVCKL-----RIEYCNACgVCYAKGeCtHKDDFNQvYKKIL 74 
                                    9*******************************.9*********6.....4555555447788787669999********* PP

                                    CSSEEEEEEE-BTTB--HHHHHHHHHHS-TTTSCEETTCSSCCCCTTTTSEEEEEEEESS-GGG CS
                   Flavodoxin_2  77 aadaivlqfPlwwfgvPailKgwiDrvltagfafyteeggegrgggLkgkkalvivttGgpees 140
                                    ++d  ++++P ++ +v a+lK  iDr + a +++           +L+gk    ++t+Gg ++ 
  gi|116754876|ref|YP_843994.1|  75 ECDGFIIGSPNYFRSVTAQLKTLIDRMADAVHCQ-----------LLLGKYGCAVATAGGQAYD 127
                                    **************************98887755...........899************9654 PP

>> PUMA  Bcl-2-binding component 3, p53 upregulated modulator of apoptosis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1     5e-05       0.3     111     157 ..     148     193 ..     135     201 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5e-05
                           PUMA 111 aggptqaapgvrGeeeqwareiGaqlrrmaddlnalyerrrrqeeqr 157
                                    agg + a pg   e e++ar++Ga l r   +     e+ + +ee +
  gi|116754876|ref|YP_843994.1| 148 AGG-APAIPGSMEEAEKKARDLGADLVRAISEGRRYPEQDKVHEEMK 193
                                    333.36999*999**************99988887778776666644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); 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: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1631.26
//
Query:       gi|116754877|ref|YP_843995.1|  [L=187]
Description: imidazoleglycerol-phosphate dehydratase [Methanosaeta thermophila PT]
Scores for complete 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-40  136.5   0.0    1.1e-39  136.1   0.0    1.2  1  IGPD      Imidazoleglycerol-phosphate dehydratase


Domain annotation for each model (and alignments):
>> IGPD  Imidazoleglycerol-phosphate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.1   0.0   5.9e-44   1.1e-39       1     144 []      31     169 ..      31     169 .. 0.97

  Alignments for each domain:
  == domain 1  score: 136.1 bits;  conditional E-value: 5.9e-44
                                    ....HHHHHHHHHHHHHT--EEEEEEESSH...HHHHHHHHHHHHHHHHHHS..-SSB--EEEEEEEETTEEEEEEEE-- CS
                           IGPD   1 TgigfldhmLdqlakhggfdlkvkvkgdlevddHhtvedvgialGqalkealgdkrgikRfgsallpmDealaevaldls 80 
                                    Tg gf+dhmL+++ak g++d++ ++ g+      +    +g a+G  l++ lgd++gi+R+g+a++pmD+alaevaldl 
  gi|116754877|ref|YP_843995.1|  31 TGSGFMDHMLNSMAKLGSIDIRASAGGNSL----YRYSLLGSAIGASLDQTLGDRSGIRRYGFAAIPMDDALAEVALDLG 106
                                    9**************************976....556889**************************************** PP

                                    SS-EEE--..-SB--TT.--HHHHHHHHHHHHHHHT-EEEEEEEE--BHHHHHHHHHHHHHHHH CS
                           IGPD  81 grpylvleaelkrekigeldtelveeffeslaeaagitlhvkvlrgenahhivealfKafaraL 144
                                    gr+ylv++++++ e+ig+l+t  ++ ++++++++ ++tlhv+   gen+hhi+e++fKa++ a+
  gi|116754877|ref|YP_843995.1| 107 GRAYLVMRGSFNGERIGDLNTFEIKAVLMGITDRGRLTLHVRFY-GENDHHIAESIFKALGLAI 169
                                    ******************************************77.****************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); 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 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 1383.57
//
Query:       gi|116754878|ref|YP_843996.1|  [L=322]
Description: 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase [Methanosaeta thermophila PT]
Scores for complete sequence (score 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   14.7   0.0          2    7.6   0.0    2.3  2  Meth_synt_2  Cobalamin-independent synthase, Catalytic domain
       0.16   10.9   0.0       0.26   10.2   0.0    1.3  1  mTERF        mTERF


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 ?    7.6   0.0   0.00022         2     159     217 ..     129     184 ..      83     223 .. 0.69
   2 ?    4.9   0.0    0.0015        14     272     312 ..     263     303 ..     256     315 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00022
                                    HHHHHHHTT-SEEEEE-T..TSSTT--SSGGGHHHHHHHHHHHHHHHHTTS-TTSEEEEEE CS
                    Meth_synt_2 159 evkdLeaaGikviQiDep..alreGlplkkadwaayldwaveafrldtiaaaddtqvhtHl 217
                                    e ++L +  ++vi iDep   ++  ++  + +  + l+    a r+  +a ++d+qvh+H+
  gi|116754878|ref|YP_843996.1| 129 EKARLLDIDVAVISIDEPslGISSSIVFSEDEIIEALEV---ASRV--CAGRVDVQVHLHS 184
                                    44566667789*******444456666666444433333...3333..4457788888886 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0015
                                    S--THHHHHHHHHCHHCTS-STSB-BB-SS-STTS-HHHHH CS
                    Meth_synt_2 272 rvpsmeeiaalikkaldvapkerlwvnPdCGLktrkreear 312
                                    r++s e i+ ++++a+++      +  PdCGL   + +   
  gi|116754878|ref|YP_843996.1| 263 RMESPEVIKRRLERAVRIFGDLVRYAGPDCGLGSWPSQHLA 303
                                    899***************8777779*******887766544 PP

>> mTERF  mTERF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   2.9e-05      0.26     205     247 ..     207     249 ..     202     269 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 2.9e-05
                          mTERF 205 yPqilslseekilksvetLlglGfskeevakmvkrfpqllgls 247
                                    +P  l++ ++k+l + +t++++G+ + ++ +mv r  +ll  +
  gi|116754878|ref|YP_843996.1| 207 HPDYLDIIDRKVLAENDTFIRTGIARTDILSMVARLNELLNTN 249
                                    688899999**************************99998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2478.34
//
Query:       gi|116754879|ref|YP_843997.1|  [L=448]
Description: threonine synthase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.1e-27   95.4   0.0    1.4e-26   93.6   0.0    1.7  1  PALP         Pyridoxal-phosphate dependent enzyme
    3.6e-23   81.6   0.0    1.4e-22   79.6   0.0    2.1  2  Thr_synth_N  Threonine synthase N terminus


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.6   0.0   1.5e-30   1.4e-26      29     291 ..     101     394 ..      94     397 .. 0.81

  Alignments for each domain:
  == domain 1  score: 93.6 bits;  conditional E-value: 1.5e-30
                                    GGGSTTSBTTHHHHHHHHHH.....HHTTTTTSEEEEEBSSHHHHHHHHHHHHH.T-EEEEEEETTS-.HHHHHHHHHTT CS
                           PALP  29 EslnptgSfKdRgaeyllar.....lkegtgaktvveassGNhgralAaaaall.Glkvtivvpadas.pekvallrllG 101
                                     +  pt+SfKd +a  +        ++eg +   +++a+sG++g a+A+a   l +++v+++ p+d   + +++++  lG
  gi|116754879|ref|YP_843997.1| 101 LDRGPTCSFKDFAARLMGRLvqyflEREG-RSVIILTATSGDTGSAVAHAFYGLsNVQVVVLYPRDEVtERQRKQMTTLG 179
                                    5788***********33333556866666.**********************9999********99984588999***** PP

                                    -EEEEE..CCHHHHHHHHHHHHHHHSTTCEE--TTT....SHHHHHHHHTHHHHHHHHTT.TTEEEEEEE-SSSHHHHHH CS
                           PALP 102 aevvev..ggdydeavaaaaelaaegegaylvsqfd....nptviegygtiglEileqlg.gkpdavvvpvGgGgliaGi 174
                                     +v+    +g +d+++a+++++ a+ ++   ++ ++    n+ + + ++   +  ++++  g+  ++ vp G+ g+++G 
  gi|116754879|ref|YP_843997.1| 180 GNVHALavDGKFDDCQALVKRAFAD-PELRDLNLSSansiNVGRLLPQAVYYFYAYSRISeGEEIVISVPSGNFGNLMGG 258
                                    ****9999************99999.666555555552445555555777777777777743333699************ PP

                                    HHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B..SSS.CCSTCS..CGTTCCHHHHSEEEE............. CS
                           PALP 175 aaglkerrpdvrvigvepegsdalarslragrrvtvpvs.dtiadglavg..spselafelldrlvd............. 238
                                      +++ + p vr ++v ++++d +  ++r+g ++++ +s + i  +++vg  s+ +++f+l+ + +d             
  gi|116754879|ref|YP_843997.1| 259 LIAMRMGLP-VRRFVVATNENDEFPVFMRTGIYKPIRPSrNCISNAMNVGhpSNLARVFALYGGWLDekgevrrepdlda 337
                                    ******999.6888888999******************975566677777556666677777444444444555666777 PP

                                    .....EEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHCCTTCEEEEEE CS
                           PALP 239 .....eivtvsdeealeamrllarregivvepssaaalaalklreagelkegdrvvvi 291
                                          +v+vsd+e+ ++++++++r ++++ep++a++ a+l +r  +e+++++++v +
  gi|116754879|ref|YP_843997.1| 338 mrrdmFAVSVSDDETRKTIKEVYERYRVLLEPHGAVGWAGL-MRYFEEVERWEPTVSL 394
                                    777789***********************************.********99999976 PP

>> Thr_synth_N  Threonine synthase N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.6   0.0   1.6e-26   1.4e-22       2      79 .]       6      83 ..       5      83 .. 0.99
   2 ?   -2.9   0.0      0.91   8.2e+03      46      62 ..     105     121 ..      96     129 .. 0.75

  Alignments for each domain:
  == domain 1  score: 79.6 bits;  conditional E-value: 1.6e-26
                    Thr_synth_N  2 YiSTRgeaeklsfeeallkGlAeDgGLyvPeeiPklsaeeleelrklsYaelafevlklfiedeipeedLkeliekaY 79
                                   ++ST g+ e+++f+eall+G A+D GLy+PeeiP++ +ee+ +++k+ Y+e+a++v+ ++i+d ip+edL +++e+aY
  gi|116754879|ref|YP_843997.1|  6 FYSTNGSPERVDFREALLSGQAPDMGLYMPEEIPRIGTEEIVRFSKMRYPEIAYRVVGPYIGDLIPKEDLVSILEDAY 83
                                   79***************************************************************************9 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.91
                    Thr_synth_N  46 rklsYaelafevlklfi 62 
                                     ++s+++ a++++ + +
  gi|116754879|ref|YP_843997.1| 105 PTCSFKDFAARLMGRLV 121
                                    56799999999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 3134.19
//
Query:       gi|116754880|ref|YP_843998.1|  [L=176]
Description: phosphodiesterase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.4e-30  105.0   0.1    5.1e-30  104.8   0.1    1.0  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    1.7e-06   28.7   4.9    1.2e-05   25.9   0.7    2.2  2  Metallophos    Calcineurin-like phosphoesterase
  ------ inclusion threshold ------
      0.024   14.0   0.3       0.11   11.9   0.2    1.9  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 !  104.8   0.1   8.6e-34   5.1e-30       1     164 [.       1     156 [.       1     157 [. 0.88

  Alignments for each domain:
  == domain 1  score: 104.8 bits;  conditional E-value: 8.6e-34
                  Metallophos_2   1 MklaiiSDlHsnldaleavlealkevgvdaiihaGDl.eeeepevleellela..pvlaVrGNnDeevveedvlreaael 77 
                                    M ++i+SD+H+n++ ++++l  +++ +v +++haGD+ + ++      l++ +  pv+ V+GNnD    +  ++r ++++
  gi|116754880|ref|YP_843998.1|   1 MLIGIMSDSHDNFRGIKEALGVFSKRDVKLVLHAGDViGSGNA----YLFDGYgiPVRLVYGNND--GDRVGLSRYFERF 74 
                                    99**********************************9544444....44444456**********..5556889999999 PP

                  Metallophos_2  78 gtdlp.eeaelelagekvlliHgdplgvkdalaellkeaeegsdvvvcGHtHvpevekeggvlvvnPGsvgeprdgdpet 156
                                    g+++  +  ele++g +++++Hg+    ++ l +++ + +   dvvv GHtHv+ev++eg +lvvnPG++ +  +g + +
  gi|116754880|ref|YP_843998.1|  75 GGEYLgDFGELEVDGLRIAMLHGT----EEPLVRAVVT-SGLYDVVVRGHTHVAEVRREGRTLVVNPGEIWGHLTGVR-S 148
                                    999987*****************9....8888888888.44445*****************************99999.* PP

                  Metallophos_2 157 yaildtde 164
                                    +ai+dt++
  gi|116754880|ref|YP_843998.1| 149 VAIMDTST 156
                                    *****986 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.7     2e-09   1.2e-05       3     103 ..       3      83 ..       1     102 [. 0.75
   2 !    4.8   0.3    0.0057        34     189     203 ..     108     122 ..      88     123 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 2e-09
                                    EEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTSCHHHHHH CS
                    Metallophos   3 ilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNHegfeeell 82 
                                    i +++D H      +++ ++++l  + ++ ++ lvl+aGD++  g+     ++l++  +    pv l+ GN +g   +  
  gi|116754880|ref|YP_843998.1|   3 IGIMSDSH-----DNFRGIKEALGVFSKR-DVKLVLHAGDVIGSGN-----AYLFDGYGI---PVRLVYGNNDG---DRV 65 
                                    889*****.....**********999888.*************993.....344444455...**********5...777 PP

                                    HHHHHHHHHHHHHEHHHCEEE CS
                    Metallophos  83 nkygylgifsepwrsdaevfn 103
                                     + +y+++f++ +    + f+
  gi|116754880|ref|YP_843998.1|  66 GLSRYFERFGGEYL---GDFG 83 
                                    77777777755553...3344 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0057
                                    HHTTESEEEEESSSS CS
                    Metallophos 189 kkygvdlvisGHtHv 203
                                      +  d+v++GHtHv
  gi|116754880|ref|YP_843998.1| 108 TSGLYDVVVRGHTHV 122
                                    445579********7 PP

>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0     0.071   4.3e+02      12      45 ..       7      40 ..       3      55 .. 0.83
   2 ?   11.9   0.2   1.8e-05      0.11     202     253 ..     103     160 ..      86     164 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.071
                                   E--TT-GGGHHHHHHHHHHH--SEEEEES----- CS
                  Metallophos_3 12 sdlkgevellerlveviedkdpDllvlvGdlvka 45
                                   sd ++++  +++ ++v + +d+ l++  Gd++++
  gi|116754880|ref|YP_843998.1|  7 SDSHDNFRGIKEALGVFSKRDVKLVLHAGDVIGS 40
                                   6667788888889999999999999999999865 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 1.8e-05
                                    HHHHHHHH--SEEEE-SS--EE.EEETTEEEEE--BGG...GT..EEEEEETTTTEEE CS
                  Metallophos_3 202 vaelvktlnPevvvvghavkeh.eelgktlvvnPGale...eG..dfavvdleekkve 253
                                    v  +v +   +vvv gh++ ++    g+tlvvnPG++     G    a++d++  +ve
  gi|116754880|ref|YP_843998.1| 103 VRAVVTSGLYDVVVRGHTHVAEvRREGRTLVVNPGEIWghlTGvrSVAIMDTSTTEVE 160
                                    55666667778999****99998899*********97411122223556666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       230  (0.0128284); expected 358.6 (0.02)
Passed bias filter:                      201  (0.0112109); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1323.97
//
Query:       gi|116754881|ref|YP_843999.1|  [L=140]
Description: methylated-DNA--protein-cysteine methyltransferase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-29  101.1   0.0    3.9e-29  100.6   0.0    1.2  1  DNA_binding_1  6-O-methylguanine DNA methyltransferase, DNA b


Domain annotation for each model (and alignments):
>> DNA_binding_1  6-O-methylguanine DNA methyltransferase, DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.6   0.0   2.2e-33   3.9e-29       1      80 [.      48     126 ..      48     127 .. 0.98

  Alignments for each domain:
  == domain 1  score: 100.6 bits;  conditional E-value: 2.2e-33
                                    HHHHHHHHHHTTS-TT-BEEHHHHHHHTT.TSCHHHHHHHHHTSSBTTTSGGGGEEBTTSBCCTTTTCHHHHHHHHHHTT CS
                  DNA_binding_1   1 afqqrVwellrqIpyGkvttYgeiAkllgkpkaaraVgqalaanplailvPcHRVvgadgklggyagglerkralLeaEg 80 
                                    +fq +V++++ +Ip+G+++tY+++Ak +g+p+aaraVg+al+ np++i++PcHRVv+++g  ggy++g+++k +lL+ E+
  gi|116754881|ref|YP_843999.1|  48 DFQMAVYRAVLNIPRGSTATYSDVAKIAGRPGAARAVGAALRVNPFPIMIPCHRVVASNG-PGGYSQGIDIKLQLLAIEQ 126
                                    59**********************************************************.***************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       230  (0.0128284); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 1015.62
//
Query:       gi|116754882|ref|YP_844000.1|  [L=53]
Description: transposase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-12   45.8   0.0    6.7e-12   45.7   0.0    1.0  1  DUF4277   Domain of unknown function (DUF4277)


Domain annotation for each model (and alignments):
>> DUF4277  Domain of unknown function (DUF4277)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   0.0   3.7e-16   6.7e-12       3      51 ..       5      53 .]       3      53 .] 0.95

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 3.7e-16
                        DUF4277  3 vksldhlglvaglidelglaelidelipkksqekvsagevvkalilngL 51
                                   ++sldhlg+v  ++d+lg+a++id+++pk +q+k+ ++ vvka++  +L
  gi|116754882|ref|YP_844000.1|  5 TRSLDHLGIVTPVFDQLGIADVIDSRMPKLRQHKLDHSMVVKAIVSTVL 53
                                   789*****************************************98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       201  (0.0112109); expected 358.6 (0.02)
Passed bias filter:                      158  (0.00881254); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.31u 0.23s 00:00:00.54 Elapsed: 00:00:00.37
# Mc/sec: 431.93
//
Query:       gi|116754883|ref|YP_844001.1|  [L=377]
Description: periplasmic binding protein [Methanosaeta thermophila PT]
Scores for complete 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-27   94.8   0.0    7.5e-27   94.4   0.0    1.1  1  Peripla_BP_2  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.4   0.0   4.2e-31   7.5e-27       8     234 ..      80     319 ..      73     322 .. 0.83

  Alignments for each domain:
  == domain 1  score: 94.4 bits;  conditional E-value: 4.2e-31
                                    HHHHHHHTT-GGGEEEB-GGG--GGGGGGT..TS-BSBESSSB-HHHHHHH--SEEEE-GGG....GGGHHHHHHHS-EE CS
                   Peripla_BP_2   8 vteillalGatdkvvgvdtttsdpldadkleeaivevgadgeidvEklaalkPDlvilskgl.gltdedeellksgiptv 86 
                                      e ++ l a++kvvg++    d + ++ ++ +++ vg+ +++d E+++al PD+vi s++l   t  +  l  ++ip++
  gi|116754883|ref|YP_844001.1|  80 RIEAVKILNAENKVVGISSDIPDKNYYYPELIEKPLVGTWSSPDSETIVALSPDIVITSANLqRATNLENALKYANIPVI 159
                                    556677788999******99999999997777******************************6666666667779***** PP

                                    E----TTSHHHHHHHHHHHHHTT-HHHHHHHHHH...HHHHHHHHHHTS-TT..-EEEEEEEETTE...EEEE-TTSTTT CS
                   Peripla_BP_2  87 ivessntgeslkeqiralgellgledeaeklvae...idsklaaaksaidse.kpkpvlvfggade.ggyvvagsnsyig 161
                                      ++    + +k +ir+lg +l++ deae ++++   +++++ +  ++++   kp     +g+++  ++++  g++s + 
  gi|116754883|ref|YP_844001.1| 160 GLDFYRD-DIIKSEIRTLGFILNKDDEAERYIKWrrgYEQTITDYVAKLEDNdKPHVFMEWGTKNTaSEISSYGRGSSGD 238
                                    ****999.************************973335666666666665555555555566666689999999999999 PP

                                    HHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEH..........HHHT-S--HHHHT-SHHHHTSHHHHTT-E CS
                   Peripla_BP_2 162 dlldalgieniaaeskkseyeeisaEqilasdpdvifvsgr..........aeadnktgleflkenpllaelpAvkngrV 231
                                    ++ +  g+ niaa+    ey +++ E++la +pd+i+ +             e+ ++  +  ++++p++ +l+Avkn+rV
  gi|116754883|ref|YP_844001.1| 239 AVCRFTGGINIAAD--LPEYPKVDSEWVLATNPDIIIRMLApggekpgwnnTEETASILKNYIESRPGWTNLEAVKNNRV 316
                                    99999*********..69****************************99994444444445556667************** PP

                                    EEE CS
                   Peripla_BP_2 232 yal 234
                                      l
  gi|116754883|ref|YP_844001.1| 317 HLL 319
                                    766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); 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 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2713.44
//
Query:       gi|116754884|ref|YP_844002.1|  [L=372]
Description: periplasmic binding protein [Methanosaeta thermophila PT]
Scores for complete 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   88.2   0.2    9.8e-25   87.5   0.2    1.3  1  Peripla_BP_2  Periplasmic binding protein
  ------ inclusion threshold ------
      0.026   14.6   0.0       0.05   13.7   0.0    1.5  1  CheY-binding  CheY binding


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.5   0.2   1.1e-28   9.8e-25       1     234 [.      60     317 ..      60     319 .. 0.90

  Alignments for each domain:
  == domain 1  score: 87.5 bits;  conditional E-value: 1.1e-28
                                    EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT..TS-BSBESSSB-HHHHHHH-.......-SEEEE-GGG.... CS
                   Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadkleeaivevgadgeidvEklaalk.......PDlvilskgl.... 69 
                                    i++l+++ +e +  lGa+dk+vg++ ++++ + +  +++++ ++g+ +e+d E++ +         P +++ s+++    
  gi|116754884|ref|YP_844002.1|  60 IIVLNSDAAEAVTVLGAADKIVGISDSVKNKAYYFPALKNKQSIGKWNEPDCEMIGEIArsgdeivPNIIVISYTYpdrp 139
                                    89*************************999999955555*************99987544444444************99 PP

                                    ....GGGHHHHH.HHS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT.-EEEEEEEETT CS
                   Peripla_BP_2  70 .gltdedeellk.sgiptvivessntgeslkeqiralgellgledeaeklvaeidsklaaaksaidsekpkpvlvfggad 147
                                     g  + +e+l++ ++i +v  ++ +  e+ +++++ lg++l++e++a  +v++++ + ++++  ++++ ++ v v +g+ 
  gi|116754884|ref|YP_844002.1| 140 yGALQVAEKLEAfKNITVVGLDFYKP-ENMTREVELLGKILEKEEAATRYVEWYETRKESVNRPVAEKSAPRVYVESGSK 218
                                    96666666666557899999888888.*****************************************999999999999 PP

                                    E..EEEE-TTSTTTHHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEH.............HHHT-S--HHHH CS
                   Peripla_BP_2 148 eggyvvagsnsyigdlldalgieniaaeskkseyeeisaEqilasdpdvifvsgr.............aeadnktglefl 214
                                    +g+ +  g +s+ ++ll++++++nia++  k++y ++++E++++++pdvi+   +             ++ +    l ++
  gi|116754884|ref|YP_844002.1| 219 GGELSTYGAGSGTSQLLSIAKGDNIAKDL-KGAYPKVGWEWVVSQNPDVIIKILSsapeqgwdkppssDSTRLENTLNEI 297
                                    9****************************.********************9555557*******99999999999999** PP

                                    T-SHHHHTSHHHHTT-EEEE CS
                   Peripla_BP_2 215 kenpllaelpAvkngrVyal 234
                                    + + ++a+++Avkn rVy +
  gi|116754884|ref|YP_844002.1| 298 LGRAGAASINAVKNDRVYIV 317
                                    ******************75 PP

>> CheY-binding  CheY binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.5e-06      0.05       2      43 ..     155     196 ..     154     199 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.5e-06
                   CheY-binding   2 veLsgvkekDvelLleELgnLGevseqekagdslevtLettv 43 
                                    ++++g++    e+++ E ++LG+++e+e+a+++++ + et +
  gi|116754884|ref|YP_844002.1| 155 ITVVGLDFYKPENMTREVELLGKILEKEEAATRYVEWYETRK 196
                                    666677777789***********************9999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2731.78
//
Query:       gi|116754885|ref|YP_844003.1|  [L=289]
Description: transposase, IS4 family protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.2e-33  113.1   0.0    3.2e-31  107.9   0.0    2.2  2  DDE_Tnp_1_5  Transposase DDE domain
      9e-21   74.5   0.1    1.6e-20   73.7   0.1    1.4  1  DDE_Tnp_1    Transposase DDE domain


Domain annotation for each model (and alignments):
>> DDE_Tnp_1_5  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.9   0.0   3.6e-35   3.2e-31       2     111 ..      18     125 ..      17     126 .. 0.95
   2 ?    2.8   0.0     0.016   1.4e+02      40      67 ..     252     281 ..     246     287 .. 0.82

  Alignments for each domain:
  == domain 1  score: 107.9 bits;  conditional E-value: 3.6e-35
                    DDE_Tnp_1_5   2 kRGsltiwldeeaiaawkek...kkngkrgrpqvysdaaiqtcltvkvlfklplRqlqGfvqsllklaglellvpdystl 78 
                                    +RG  +++l+++++++w+e+    +++k+grp++y++++iq+c +++++++lp+Rql+Gf+q+l+ ++   ll++dystl
  gi|116754885|ref|YP_844003.1|  18 RRG--WFYLSTDFVNNWDEEllkMNKNKNGRPYRYPETFIQFCGLAYAFLHLPYRQLEGFIQALSGFVPG-LLAADYSTL 94 
                                    799..************9987745569******************************************9.99******* PP

                    DDE_Tnp_1_5  79 srraktlevkipvkrkskglhlvvdstGlkvlg 111
                                    ++r ++le++ip+ +++  l+++vdstG+kv++
  gi|116754885|ref|YP_844003.1|  95 WQRITNLELNIPIPDND--LVVAVDSTGMKVTN 125
                                    **************999..99**********97 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.016
                    DDE_Tnp_1_5  40 tcltvkvlfklplRql..qGfvqsllklag 67 
                                    ++  +k++f+ ++R++  +G+++ + ++ +
  gi|116754885|ref|YP_844003.1| 252 VFSAIKRIFGETVRATskEGMIREVRRMFT 281
                                    56789*********9855699999988876 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.7   0.1   1.8e-24   1.6e-20       5     200 ..     112     271 ..     108     285 .. 0.83

  Alignments for each domain:
  == domain 1  score: 73.7 bits;  conditional E-value: 1.8e-24
                      DDE_Tnp_1   5 evlivDattvrvpgtkedarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrprkgklvlaDa 84 
                                     v++vD+t ++v+  + ++r++++  + + ++k+hiavd +++ ++ ++it+  v d++ +k+ll+ +   k    l+D+
  gi|116754885|ref|YP_844003.1| 112 LVVAVDSTGMKVTNRGDWMRESHGVER-RGWIKVHIAVDVETRKPVTFEITDETVTDHEMVKPLLEDV---KLEDSLMDG 187
                                    699******************888666.79************************************99...89******* PP

                      DDE_Tnp_1  85 GYasaelldtleekgvd.yiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgdvyyvtntnsells 163
                                    +Y++++++d+++ekgvd + i+++kn+ ++        r +    +++  +  +++ +++                    
  gi|116754885|ref|YP_844003.1| 188 AYDKEGVFDFMKEKGVDmPGIKIRKNAIVKAG----SSRAEPVLEFMKYGYHSWKIVHGY-------------------- 243
                                    ****************9568899999988866....344445555555555555555555.................... PP

                      DDE_Tnp_1 164 aeevaelyrlRwqiErvFkwlkrkfgldrlryrglnr 200
                                             +Rw  E+vF+ +kr fg + +r+ ++++
  gi|116754885|ref|YP_844003.1| 244 --------GRRWAAESVFSAIKRIFG-ETVRATSKEG 271
                                    ........***************998.6666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 2209.24
//
Query:       gi|116754886|ref|YP_844004.1|  [L=339]
Description: periplasmic binding protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.5e-22   78.1   0.1    1.1e-21   77.5   0.1    1.2  1  Peripla_BP_2    Periplasmic binding protein
  ------ inclusion threshold ------
      0.035   14.3   6.0      0.035   14.3   6.0    1.8  2  Dockerin_1      Dockerin type I domain
       0.16   11.7   0.0       0.28   10.9   0.0    1.3  1  Heme_oxygenase  Heme oxygenase


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 !   77.5   0.1   1.8e-25   1.1e-21       1     206 [.     109     325 ..     109     334 .. 0.83

  Alignments for each domain:
  == domain 1  score: 77.5 bits;  conditional E-value: 1.8e-25
                                    EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT....TS-BSBESSSB-HHHHHHH--SEEEE-GGG........G CS
                   Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadklee..aivevgadgeidvEklaalkPDlvilskgl.....gltd 73 
                                    i++++   +e+l  l a+d++ g++ ++ +   +   +e  +  ++g+ +++d+Ek+++l+PDlvi   ++     +  +
  gi|116754886|ref|YP_844004.1| 109 IVAINRNGAETLRTLKASDRIIGISDSALNDKSYF--PEfrEDQSIGSAKTPDIEKILNLDPDLVIYYGTQwttdyEIIR 186
                                    899*********************99999888884..4556***********************9987766586666666 PP

                                    GGHHHHHHHS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT.-EEEEEEEETTE...EE CS
                   Peripla_BP_2  74 edeellksgiptvivessntgeslkeqiralgellgledeaeklvaeidsklaaaksaidsekpkpvlvfggade.ggyv 152
                                    ++ ++ ++ i  +  +  +  + + e +  lg ++g+  ea ++++++++k+  +++ ++++ +++ + ++++ +  +y 
  gi|116754886|ref|YP_844004.1| 187 DTLNKTDPTISIIGLDCYKP-DTYIEDVIKLGYIVGRVTEAYEFASWYEDKINTINNVVKQIPDDAKPRVYEGGRsDFYQ 265
                                    66666667777776666666.*****************************************777777777777724555 PP

                                    EE-TTSTTTHHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEH.......HHHT CS
                   Peripla_BP_2 153 vagsnsyigdlldalgieniaaeskkseyeeisaEqilasdpdvifvsgr.......aead 206
                                      g +s    ++  +g++ni+++  ++e+++i++E +++++p+ i++  +       ++++
  gi|116754886|ref|YP_844004.1| 266 TGGLGSQSHNVIVMAGGKNIFDDL-SGEAITIDPESVVERNPEFIIWKISniggytlDKNE 325
                                    56678888888888**********.**********************99976665444444 PP

>> Dockerin_1  Dockerin type I domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   6.0   5.8e-06     0.035       5      53 ..      36      79 ..      33      83 .. 0.92
   2 ?   -2.7   0.0       1.2     7e+03      13      29 ..     180     195 ..     179     200 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.8e-06
                                   TSSSC-SHHHHHHHHHHCTSSEBTTSCCCHGGGSTT-SSCESHHHHHHH CS
                     Dockerin_1  5 NgDgkVnalDalliinylnqregqssssngkaaDvNgDGrvnalDallv 53
                                   N D  +n  D++ i+  ln     + ++ +++aD N DG++++ D+ ++
  gi|116754886|ref|YP_844004.1| 36 NMDDAINEEDVAYIQGILN-----NEDKVTEFADANYDGKIDSNDIDQI 79
                                   89************99999.....99999****************9987 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.2
                                    HHHHHHHHHCTSSEBTT CS
                     Dockerin_1  13 lDalliinylnqregqs 29 
                                    +D+ +i+  ln +++++
  gi|116754886|ref|YP_844004.1| 180 TDYEIIRDTLN-KTDPT 195
                                    68999999999.44444 PP

>> Heme_oxygenase  Heme oxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   4.7e-05      0.28      56     100 ..     144     188 ..     137     196 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.7e-05
                                    HHCTTSTTCGGGS-GGG--HHHHHHHHHHHHSTTHHHHS---HHH CS
                 Heme_oxygenase  56 eenkdspviapilfpeLhRkaaLerdlaylygsdwrkdieispav 100
                                    +e ++++ i +   p + +   L+ dl  +yg +w +d+ei +++
  gi|116754886|ref|YP_844004.1| 144 PEFREDQSIGSAKTPDIEKILNLDPDLVIYYGTQWTTDYEIIRDT 188
                                    67789999********************************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); 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: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2505.66
//
Query:       gi|116754887|ref|YP_844005.1|  [L=409]
Description: periplasmic binding protein [Methanosaeta thermophila PT]
Scores for complete 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   90.1   0.0    2.3e-25   89.6   0.0    1.2  1  Peripla_BP_2  Periplasmic binding protein
     0.0012   19.0   1.7     0.0026   17.9   1.7    1.6  1  Dockerin_1    Dockerin type I domain
  ------ inclusion threshold ------
       0.01   16.5   0.1      0.021   15.5   0.1    1.4  1  HlyD_3        HlyD family secretion 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 !   89.6   0.0   3.8e-29   2.3e-25       1     234 [.     104     346 ..     104     347 .. 0.92

  Alignments for each domain:
  == domain 1  score: 89.6 bits;  conditional E-value: 3.8e-29
                                    EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT....TS-BSBESSSB-HHHHHHH--SEEEE-GGG...GGGHHH CS
                   Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadklee..aivevgadgeidvEklaalkPDlvilskglgltdedeel 78 
                                    i++l+ +++e l  l   dkvvgv+  t  ++++   +e  + ++vg+ +e+d+Ek++ l PDlvi+ k+      + +l
  gi|116754887|ref|YP_844005.1| 104 IVALTDDSAEALRILHSIDKVVGVSIETLENTAYL--PEfsQMPNVGKWNEPDIEKILLLEPDLVISYKSATSKYLEPML 181
                                    899999999999999999******99999888885..4445******************************77778899* PP

                                    HHHHS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT...-EEEEEEEETTE..EEEE-T CS
                   Peripla_BP_2  79 lksgiptvivessntgeslkeqiralgellgledeaeklvaeidsklaaaksaidse..kpkpvlvfggadeggyvvags 156
                                       gi  v+ +   + ++l  ++++lg ++++++ea+ + +++++ ++ + ++i+++  ++++ +++ ga +   + +++
  gi|116754887|ref|YP_844005.1| 182 NGTGISIVALDLYRA-NDLPAEMKMLGYIVNRTAEADNYLEWFNRVTDTVDEKISEIpeNKRTRVYLEGASD---LKTYT 257
                                    ************998.*****************************************987788888888888...99999 PP

                                    TSTTTHHHHT.S--EESTTT--STT-EEE-HHHHHHH--SEEEEEEH...........HHHT-S--HHHHT-SHHHHTSH CS
                   Peripla_BP_2 157 nsyigdllda.lgieniaaeskkseyeeisaEqilasdpdvifvsgr...........aeadnktgleflkenpllaelp 224
                                    ++++ dl+ + +g+ nia++  ++ y ++  E++  ++pdvi+  ++           + +   ++  ++++++++ +++
  gi|116754887|ref|YP_844005.1| 258 KGRGADLVCTmAGGVNIASNL-TGLYPDVESEWVIVQNPDVIVRFTQpseiacgyatnDPSGFEAKRREILSRTGWGNIT 336
                                    ********************9.*********************************9885555556667899999****** PP

                                    HHHTT-EEEE CS
                   Peripla_BP_2 225 AvkngrVyal 234
                                    Avk+grVy l
  gi|116754887|ref|YP_844005.1| 337 AVKEGRVYLL 346
                                    ********86 PP

>> Dockerin_1  Dockerin type I domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   1.7   4.4e-07    0.0026       5      55 ..      31      76 ..      28      79 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 4.4e-07
                                   TSSSC-SHHHHHHHHHHCTSSEBTTSCCCHGGGSTT-SSCESHHHHHHHHH CS
                     Dockerin_1  5 NgDgkVnalDalliinylnqregqssssngkaaDvNgDGrvnalDallvin 55
                                   N D +++  D++  +  +      ++++n+++aD N DG+v+++D+ ++ +
  gi|116754887|ref|YP_844005.1| 31 NMDDTIDESDIAYTRGIID-----GKEKNTEFADANYDGKVDSRDIEQIQH 76
                                   6788888888776665555.....999*******************99865 PP

>> HlyD_3  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.1   3.5e-06     0.021       4      62 ..      60     118 ..      59     140 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.5e-06
                         HlyD_3   4 ApvdGvvvelnv.eegevvqagdelleiippdtllveakvpaadlgsikkkgqkvtlkld 62 
                                    A +dG+v + ++ +  +++q  + +l++i++++  v++++p  ++  ++   ++  l++ 
  gi|116754887|ref|YP_844005.1|  60 ANYDGKVDSRDIeQIQHIIQGDESILTLIDTANRTVTLEMPINRIVALT-DDSAEALRIL 118
                                    789*********666777777777*****************99999996.6666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); 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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 3129.86
//
Query:       gi|116754888|ref|YP_844006.1|  [L=1266]
Description: cobaltochelatase subunit CobN [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
          0 1269.8   0.0          0 1269.6   0.0    1.0  1  CobN-Mg_chel  CobN/Magnesium Chelatase


Domain annotation for each model (and alignments):
>> CobN-Mg_chel  CobN/Magnesium Chelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1269.6   0.0         0         0       2    1088 ..     105    1214 ..     104    1215 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1269.6 bits;  conditional E-value: 0
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel    2 aYlkeggveNlknllryladkllgkkeeeveppvelpeegiyhpdakelfesleeylewykkakkekaptvgilfyra 79  
                                      Yl++gg+eN+ n++ yl ++ll+  +++++pp++lp+eg+yhpda ++f+++++ylewy   + ++ ptvg+l++r 
  gi|116754888|ref|YP_844006.1|  105 TYLTYGGEENICNMFLYLEKELLD-VDTHFDPPKPLPWEGLYHPDAADCFDDIDAYLEWY---EPDDGPTVGVLISRF 178 
                                     6**********************8.77799*****************************8...69999********** PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...x...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel   80 hllagntavidaliraleerglnvlpvfvssl...d...seaqealeelftkegeekvdalinttsfalvkgpaeeee 151 
                                     ++ +g +av d+lirale++glnv+pvf++s+   +   +++++ ++++f + g++++dal++t+ f l + +++  +
  gi|116754888|ref|YP_844006.1|  179 YWANGSLAVEDELIRALENQGLNVIPVFTYSVrdkElgtRSMADVVSDYFLDGGRPRIDALVKTIPFFLGQDARSVGD 256 
                                     ********************************965166699999***********************99887765555 PP

                                     xxxxxxx....xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  152 eeaeeea....lkelnvPvlqa.ilssqsreeWeessqGlspldlamsvalpEldGriepvvisfkeeeeeeteveky 224 
                                     +++++      lk+lnvPv+++ i+++++ eeWe+s  Gls  d+ +sva+pE++G+iep++i++  +   ++e+ + 
  gi|116754888|ref|YP_844006.1|  257 SKSNR-TgidlLKRLNVPVFEPiISYHMTLEEWESS-IGLS-NDIGWSVAMPEFEGVIEPIIIGAGGR---HDEYIER 328 
                                     54433.25888***********999********999.9**6.9**********************544...4779999 PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  225 epipervervadlaarwarLrrkpnaekkvaiilanypp..gegrlgnavgLdvpaSlvnlLkalkeeGYdveelpes 300 
                                      pi+er+er+a +++rw++L rkp ++++va+il+n+p+   e+++g +++Ld+++S++++++++ e+GY++e+ p++
  gi|116754888|ref|YP_844006.1|  329 APIRERCERLAMRVRRWIELARKPVSQRRVAFILHNNPCasVEAAVGGGAHLDTLESVARIMNRMVEAGYSLENVPAT 406 
                                     ***************************************8889*****************************999*** PP

                                     xxxxxxxxxxxxx.xxxxx...xxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxx RF
                   CobN-Mg_chel  301 gdeLiellleggt.ndpew...eelkv.....gaaallpaeeYeewfeeLpeelreeveerWgeppge...mveeeks 366 
                                     g eLie ++++++ ++++w   e         g++a  ++eeYe+wf++L++++r++v e+Wg+ppge    +   + 
  gi|116754888|ref|YP_844006.1|  407 GGELIENIMNRKAiSEFRWttiE---EivakgGVLAYQTKEEYERWFNTLSPTVRDRVCEAWGNPPGEeknGIPAAML 481 
                                     *************99****5552...345566999********************************99985666778 PP

                                     xxxxxxxxxxxxxxxxxxxxxxxx...xxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  367 gekklvipglqlGnvfvgvQParg...yeedps..klyhdpdlpPthqYlAfYlWlreefgadavvHvGkHGtlEwlP 439 
                                      ++k+vi+g+++Gnv+++vQP+rg   +++d +  k++hdpd+pPthqY+A+Y++++e+fgad+++HvG+HG+lE+lP
  gi|116754888|ref|YP_844006.1|  482 YQGKIVITGVRYGNVVICVQPKRGcagARCDGQvcKILHDPDVPPTHQYMATYRYIEESFGADVIIHVGTHGNLEFLP 559 
                                     89**********************88878886678******************************************* PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  440 GKqvglseecyPdillgdlPhlYpYivnnpgEGtqAKRRsyAviidHltPpmtraelygelaeLeelideYeeaesld 517 
                                     GK+vgls++cyPdi++g++PhlY+Y+++np EGt+AKRRsyAv+idH++++mt+++ly+el e ++l+ eYe+a++ d
  gi|116754888|ref|YP_844006.1|  560 GKGVGLSRDCYPDICIGTIPHLYIYNADNPPEGTIAKRRSYAVLIDHMQTVMTQSGLYDELLEVDRLLGEYESAKH-D 636 
                                     *************************************************************************865.5 PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  518 perlkalreqilelveelnldkdlgleeakeeeeeefeellekldgyleelkeaqirdglhilGeapegeqlvdlvva 595 
                                     ++r ++lr+ ++e ++++nldk ++l+     e++  ee++++ ++ l++++++qi +g+hi+G+ peg ++v+++ a
  gi|116754888|ref|YP_844006.1|  637 HARSHELRDLLIEAIKAANLDKGIKLT-----EDTPLEEIVRRTHNELSRVRNTQIDSGMHIFGQIPEGYKRVEFINA 709 
                                     99********************99555.....6899****************************************** PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  596 ilrleneegesltealaealgldlde....leeksekelrtagdalealeeeaeelveelleeeaeeeeaeaeeleee 669 
                                     +lr+e ++g s ++ +a+ +gldld+    + + +e+  +++g++le ++e++++l++ +l++++ ++   ++++  e
  gi|116754888|ref|YP_844006.1|  710 VLRFE-GNGISPRRIIASMMGLDLDTllsdQGAINEHYGKSHGQLLEMIDERCRKLIDMYLHDGKVDDVLGISVAGYE 786 
                                     **998.7788899************9888777778888899********************99887776666665555 PP

                                     xxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  670 eeeeee...........eteeEitallraLdGeyippgpsGdptrgraevLPTGrNfysvDpraiPteaAwevGkkla 736 
                                     +e e+            e+++Ei+all++++G+y+++gpsG +trgr++vLPTGrNfys+Dp+++Pt++Aw+vGkkl 
  gi|116754888|ref|YP_844006.1|  787 RELETIrervldlqarmEASREIEALLNGMNGGYVEAGPSGLITRGRDDVLPTGRNFYSLDPYRVPTKTAWRVGKKLG 864 
                                     554444999******99778********************************************************** PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  737 eellerylqehgeyPekvglslwgtetmrteGediAqiLallGvrPvwdaagrvvdlelipleeLgRPRiDVtvriSG 814 
                                     +++++++l+e+g+yPe+v++ ++ ++ m+ +Ged++qiL+llG +Pvw  +gr+++++lipl+ LgRPRiDVtvr+SG
  gi|116754888|ref|YP_844006.1|  865 DAVIAKHLEEEGRYPENVAFFWMCSDIMWADGEDMSQILYLLGTEPVWLPNGRLKGFRLIPLDTLGRPRIDVTVRVSG 942 
                                     ****************************************************************************** PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  815 ffRDafpnlielldkavelvaeldEpeedNfvrkhvleeeaeleekeeaeeratyRvFgskpGaYgagvqeliessnW 892 
                                     + RD+fpn+ie++d+av++va+ldEp e+Nfvrkh+l+  ++ +    + ++at+R+F skpG+Y +g + ++ +s+W
  gi|116754888|ref|YP_844006.1|  943 ITRDNFPNCIEIIDEAVQAVAALDEPLEMNFVRKHALASLDNGT--ARDWREATLRIFASKPGTYQSGTNLAVYASAW 1018
                                     ***************************************99987..3345**************************** PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  893 edeedLaeaYlnwssyaYgkgaegeeaeeafearLkrvdvvvqnqdsrehdlldsddyyqflGGltaavrslsgkkpe 970 
                                     +de+dL ++++ w++yaYgkg++g+ea++ f ++Lk+vd+++++  s+e+dl+ +++y+ ++GG+taa+r+lsgk+++
  gi|116754888|ref|YP_844006.1| 1019 KDEKDLSDIFVYWNGYAYGKGVSGREAHQSFVNALKSVDITYNKVVSDEYDLFGCCCYFGTHGGMTAAARHLSGKDVK 1096
                                     ****************************************************************************** PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel  971 ayfgdssnpenpkvrtlkeeiarelrsrvlNPkWiegmmrhGykGafelaatvdnlfgwdatadvvddwvyeevaetY 1048
                                     ay+gd+++pe+++vr+l++ei+r++r+++lNPkWiegm++hGykGa +++++v  ++gw+at++ vddw+++e+a+t+
  gi|116754888|ref|YP_844006.1| 1097 AYYGDTREPEHVEVRDLADEIRRVVRTKLLNPKWIEGMKQHGYKGAGDISKRVGRVYGWEATTQEVDDWIFDEIARTF 1174
                                     ****************************************************************************** PP

                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   CobN-Mg_chel 1049 vlDeevrefleekNpwAlreiaerLlEaarrglWeaseet 1088
                                     + Dee+r+f+ee+NpwAl+e+ +rLlEa++rglW+a+ e 
  gi|116754888|ref|YP_844006.1| 1175 IMDEENRRFFEEHNPWALEEMGRRLLEAEQRGLWKADPEV 1214
                                     ************************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.81u 0.28s 00:00:01.09 Elapsed: 00:00:00.43
# Mc/sec: 8876.57
//
Query:       gi|116754889|ref|YP_844007.1|  [L=230]
Description: hypothetical protein Mthe_1599 [Methanosaeta thermophila PT]
Scores for complete 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-41  141.4   0.4    4.3e-41  141.1   0.4    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 !  141.1   0.4   2.4e-45   4.3e-41       2     203 ..      15     228 ..      14     229 .. 0.90

  Alignments for each domain:
  == domain 1  score: 141.1 bits;  conditional E-value: 2.4e-45
                         DUF169   2 LaealrlktePVavkfsdekpe..lpekkekieekkrlCqmvalara.....kgktvvf...taetlgCpgGaaalGfk. 70 
                                    La++++lk +P++v++s+ +p+  +++++      ++ C+++a++r      +g+  v+    +  + C+gG++++Gf  
  gi|116754889|ref|YP_844007.1|  15 LAQQFDLKVRPLCVYGSHFAPKegIHAST------VTNCIASAMFRLakgaiHGQLYVAdvkGRPVCRCVGGRTWFGFSs 88 
                                    899******************75555554......49**********988877777777555566799**********73 PP

                         DUF169  71 elpeklksg..egylk.speaakkfveslprleagevkyvvvapLekaefe..PdvvvffanpeqlmrLvqlalydrggg 145
                                      +++l ++   + lk ++++a+++++s++++++ + +yvv++++e+++++  ++++ +fa++++++ ++++++++ ++ 
  gi|116754889|ref|YP_844007.1|  89 HFDSSLCEQmvSKALKaDIATAAETFRSVGKISPIG-RYVVISCCEDLHEDpgVRCIACFAEAAKIRDMCNSVHFHAREI 167
                                    44466666689777777***************9999.**************9**************************** PP

                         DUF169 146 rlnvsfpgngaaCadivaypykegepn......iglgdpgarkfaklkddelafgiPyelleem 203
                                      ++s+p+ g++Ca++v+yp++++e+       +g++dp+a+++  l+d++la+giP++ ++ +
  gi|116754889|ref|YP_844007.1| 168 LGHISVPW-GPSCATLVTYPAGMAENVpqdcifLGPVDPSAKEW--LPDGYLALGIPIDIARML 228
                                    ********.***********************************..*************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1919.01
//
Query:       gi|116754890|ref|YP_844008.1|  [L=534]
Description: transposase [Methanosaeta thermophila PT]
Scores for complete 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-44  148.6   0.0    1.7e-43  147.4   0.0    1.7  1  DUF4277    Domain of unknown function (DUF4277)
    3.3e-12   46.5   0.4    3.9e-11   43.0   0.4    2.1  1  DDE_Tnp_1  Transposase DDE domain


Domain annotation for each model (and alignments):
>> DUF4277  Domain of unknown function (DUF4277)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.4   0.0   1.9e-47   1.7e-43       2     109 .]       4     111 ..       3     111 .. 0.98

  Alignments for each domain:
  == domain 1  score: 147.4 bits;  conditional E-value: 1.9e-47
                        DUF4277   2 evksldhlglvaglidelglaelidelipkksqekvsagevvkalilngLgfvsrpLylfpeffedkplerLlgegveae 81 
                                    +++sldhlg+va+++d+lg+a++id+++pk +q+k++++ +vka++lngLgfv ++Lylfpef+e++p+erLlg+gv+a+
  gi|116754890|ref|YP_844008.1|   4 DTRSLDHLGIVAAVFDRLGIADVIDSRMPKLRQHKLEHSVIVKAMVLNGLGFVGQRLYLFPEFYERLPVERLLGDGVNAS 83 
                                    6899**************************************************************************** PP

                        DUF4277  82 hlnddrlgrtLDklyeagvtklfteial 109
                                    +lndd++grtLD++ye+g+t+lf+eial
  gi|116754890|ref|YP_844008.1|  84 DLNDDAIGRTLDAIYEQGATDLFNEIAL 111
                                    **************************96 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   0.4   4.4e-15   3.9e-11      35     213 ..     162     450 ..     124     451 .. 0.86

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 4.4e-15
                      DDE_Tnp_1  35 gyklhiavdtrsglilsvvitpgnvhdskglkq.lldelrpr....kgklvlaDaGYasaelldtleekgvdyiirlkkn 109
                                     + l +++++  g++l ++ ++gn +d++++++ +l  ++      +  +++aD++  ++++++ l  + +++i r++  
  gi|116754890|ref|YP_844008.1| 162 QFVLSLVTNQD-GIPLFAKAHSGNASDRNTIIEsFL-KIKSGlnleDCAYYIADSAVYTEPNIRMLG-REMKWITRVPAT 238
                                    44566777777.9********************644.4555577889999******888***99999.9********777 PP

                      DDE_Tnp_1 110 tklyrkgaeskrrgrlrkhdrnkiltksqkrrnk.............................................. 143
                                     k+ +   +s  ++ ++++ r+++++++    +                                               
  gi|116754890|ref|YP_844008.1| 239 IKECEMLLDSDVEMVECRDARYRCFSTTSDYGGVqqkwvlyqsepmrdlkaerfenhlekdgtkarrslaklkrreface 318
                                    7777777777788888888888888888887777888888888888888999999999999999999999999999**** PP

                      DDE_Tnp_1 144 .............................................................skkekgdvyyvtntnsell 162
                                                                                                 +k+    + ++  tn+   
  gi|116754890|ref|YP_844008.1| 319 adalketelwardhplyrfshislkkvckradkkrgrpkngeklieiyfidadieldqekvEKTKSRLGRFIIATNDLNI 398
                                    ************************************************************999999999*********** PP

                      DDE_Tnp_1 163 saeevaelyrlRwqiErvFkwlkrk.fgldrlryrglnrveaqllllllaln 213
                                    ++ ++  +y+ + ++Er F++lk+k f+   +++++ +r+ea ++++ l+l+
  gi|116754890|ref|YP_844008.1| 399 DPDTLLSYYKGQQEVERGFRFLKDKsFRVAEVYLKKEERIEALAMIMVLSLM 450
                                    ***********************************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (534 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       680  (0.0379274); expected 358.6 (0.02)
Passed bias filter:                      581  (0.0324056); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 4257.64
//
Query:       gi|116754891|ref|YP_844009.1|  [L=262]
Description: phosphoribosylaminoimidazole carboxylase related protein [Methanosaeta thermophila PT]
Scores for complete 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-17   63.5   5.3    1.8e-17   63.3   4.0    1.7  2  AIRC      AIR carboxylase


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 ?   -1.4   0.0      0.09   1.6e+03      27      61 ..      47      81 ..      37      96 .. 0.69
   2 !   63.3   4.0     1e-21   1.8e-17       1     131 [.     123     256 ..     123     262 .] 0.86

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.09
                                   -EEEEEE--TTTSHHHHHHHHHHCHTTTEEEEEEE CS
                           AIRC 27 veyevrvvSahrtpeelleyaeeaeerglkviIag 61
                                   +++   ++   + p++l+++a e  e+  kvi++ 
  gi|116754891|ref|YP_844009.1| 47 IDVPEAILAEGKRPDDLARIALEHLESTGKVIVTR 81
                                   55556667777888888888887777777887764 PP

  == domain 2  score: 63.3 bits;  conditional E-value: 1e-21
                                    EEEEEESSGGGHHHHHHHHHHHHHTT-....EEEEEE--TTTSHHHHHHHHHHCHTTTEEEEEEEEESS--HHHHHHHHS CS
                           AIRC   1 kVgiimGSdsDlevmkkaaeilkelgv....eyevrvvSahrtpeelleyaeeaeerglkviIagAGgaahLpgvvaslt 76 
                                    kVgi+ + + D++v+++a  + +++g     ey+v v+  hr    ++++a      g+++++++AG++  Lp vva+lt
  gi|116754891|ref|YP_844009.1| 123 KVGILSAGTADIPVAEEARVTAEAMGCevltEYDVGVAGIHRLFPAMKRMA------GVDAMVVAAGREGTLPAVVAGLT 196
                                    69**********************9987787899********999998876......6999******************* PP

                                    SS-EEEEEE--...STTCCHHHHHHHHT--TTS--EE-SST..HHHHHHHHHHHHHTTT- CS
                           AIRC  77 tlPVigvPvks...kalkgldsllSivqmPsgvpvatvaig..kaknAallAaqilalkd 131
                                    + PVig Pv++      +g+ +llS++q +s + v+++++g   ++ Aa +A +i  +k+
  gi|116754891|ref|YP_844009.1| 197 DAPVIGLPVSTgygAGGNGIAALLSMLQSCSVLVVVNIDAGfvAGAFAARIANRIARRKH 256
                                    **********844346899************99999888776666666666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1881.95
//
Query:       gi|116754892|ref|YP_844010.1|  [L=2656]
Description: Cna B domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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-93  306.4  44.0    4.2e-15   56.0   0.3    7.9  7  SdrD_B           SdrD B-like domain
    3.9e-52  174.4  41.1    7.8e-08   32.5   1.3   11.0  8  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
    6.4e-30  103.8 128.5     0.0018   19.0   1.5   17.6 17  Big_9            Bacterial Ig domain
    1.5e-27   95.8  37.4    5.3e-05   23.5   1.2    8.8  9  SpaA             Prealbumin-like fold domain
    5.1e-21   74.5  62.9       0.09   12.8   0.1   13.3 14  Cadherin_5       Cadherin-like domain
    4.2e-20   72.3 143.5     0.0073   17.1   1.9   17.1 14  Big_7            Bacterial Ig domain
    2.6e-15   56.8  34.3        2.8    8.6   0.1   11.7 11  Mannosidase_ig   Mannosidase Ig/CBM-like domain
    1.4e-14   53.8  19.7      0.027   14.4   0.4    8.2  8  CarbopepD_reg_2  CarboxypepD_reg-like domain
    1.5e-13   50.9   0.1       0.73    9.9   0.1    7.2  7  DUF2012          Protein of unknown function (DUF2012)
    2.9e-08   33.5  10.5         14    5.3   0.0   10.3 13  Big_3_3          Bacterial Ig-like domain (group 3)
    3.9e-06   26.4   8.0         18    4.7   0.0    7.7  7  Dioxygenase_C    Dioxygenase
    9.8e-06   25.3  36.9      0.042   13.6   1.9    9.2  9  fn3_3            Polysaccharide lyase family 4, domain II
    1.7e-05   24.6   2.8        3.9    7.4   0.0    7.2  6  DUF1416          Protein of unknown function (DUF1416)
    0.00011   22.1  32.2        2.1    8.4   0.2   10.5 10  Y_Y_Y            Y_Y_Y domain
  ------ inclusion threshold ------
       0.14   12.2   0.0         17    5.4   0.0    4.0  4  DUF3324          Protein of unknown function C-terminal (DUF3
        0.2   11.7   1.0    1.4e+02    2.6   0.0    4.9  5  DUF2846          Protein of unknown function (DUF2846)
        1.4    9.2   7.6    2.5e+02    2.0   0.0    5.6  4  PDZ_5            PDZ domain


Domain annotation for each model (and alignments):
>> SdrD_B  SdrD B-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.5   1.2   2.3e-17   2.4e-14       2      90 ..    1162    1249 ..    1161    1257 .. 0.89
   2 !   42.8   0.4     5e-14   5.2e-11       2      86 ..    1259    1340 ..    1258    1351 .. 0.79
   3 !   49.8   0.2   3.2e-16   3.4e-13       2      81 ..    1354    1431 ..    1353    1439 .. 0.92
   4 !   56.0   0.3   3.9e-18   4.2e-15       2      75 ..    1451    1523 ..    1450    1534 .. 0.89
   5 !   49.3   0.9   4.5e-16   4.7e-13       3      75 ..    1546    1618 ..    1544    1639 .. 0.88
   6 !   31.5   1.2   1.5e-10   1.6e-07       3      75 ..    1642    1716 ..    1640    1738 .. 0.79
   7 !   49.7   2.3   3.4e-16   3.6e-13       7      79 ..    1751    1821 ..    1745    1845 .. 0.88

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 2.3e-17
                         SdrD_B    2 siGdfVweDanknGiqdagekgisgvtVtLkdakgevvatttTdasGkYkFtnltpGeYkVeftapagytvtakkaGs 79  
                                     si  + ++D n+nG  d+ge+g +g t+ L+  ++++v +ttT  +G+Y+F++l+pG Y+V+  + ag+  t++++ +
  gi|116754892|ref|YP_844010.1| 1162 SISGYKFNDLNGNGAMDSGEAGLDGWTIVLTMPDQTEV-QTTTGFDGYYRFEGLAPGLYTVRELQKAGWDSTTSESQQ 1238
                                     688899************************88888888.8899**************************777777777 PP

                         SdrD_B   80 ddaldSdadpa 90  
                                      + +dSd++  
  gi|116754892|ref|YP_844010.1| 1239 VNLTDSDVTGI 1249
                                     7778***9765 PP

  == domain 2  score: 42.8 bits;  conditional E-value: 5e-14
                         SdrD_B    2 siGdfVweDanknGiqdagekgisgvtVtLkdakgevvatttTdasGkYkFtnltpGeYkVeftapagytvtakkaGs 79  
                                     si  + +eD n+nG  d ge+g++g +++L++ + +  +  tT  +G+Y+F++ltpG Y+++++   g++v+ + + +
  gi|116754892|ref|YP_844010.1| 1259 SISGTLFEDVNNNGAND-GEPGVKGWEIRLTKPDAT-ESVATTGDDGSYRFEDLTPGVYTLRVVLQPGWNVSISSKDV 1334
                                     788999********976.9***********555544.45889999******************998898776655444 PP

                         SdrD_B   80 ddaldSd 86  
                                       + d d
  gi|116754892|ref|YP_844010.1| 1335 SIT-DTD 1340
                                     332.333 PP

  == domain 3  score: 49.8 bits;  conditional E-value: 3.2e-16
                         SdrD_B    2 siGdfVweDanknGiqdagekgisgvtVtLkdakgevvatttTdasGkYkFtnltpGeYkVeftapagytvtakkaGs 79  
                                     +i  +V++D ++nG+ d ge+g sg tV+L+  +g +  t +T  +G Y+F+ l+pG+Yk+e ++ +g+++ta k+Gs
  gi|116754892|ref|YP_844010.1| 1354 TISGRVFSDLDANGVND-GEPGLSGWTVKLTMPDGGER-TAVTADDGFYSFDRLSPGTYKIEAVKQDGWSQTAPKTGS 1429
                                     57899**********87.9***********99999886.9**********************************9998 PP

                         SdrD_B   80 dd 81  
                                      +
  gi|116754892|ref|YP_844010.1| 1430 HS 1431
                                     65 PP

  == domain 4  score: 56.0 bits;  conditional E-value: 3.9e-18
                         SdrD_B    2 siGdfVweDanknGiqdagekgisgvtVtLkdakgevvatttTdasGkYkFtnltpGeYkVeftapagytvtak 75  
                                     si  +V++D n+nG+ +age+g++g  VtL +  +++++ t T a+G+Y+F++l+pG+Y+Ve++  +g+++t++
  gi|116754892|ref|YP_844010.1| 1451 SISGVVFNDINANGVREAGETGVRGWSVTLVQG-ENATSMTETGADGTYRFESLSPGTYRVELIPQDGWKATTE 1523
                                     78999*************************555.45556999**********************9999988876 PP

  == domain 5  score: 49.3 bits;  conditional E-value: 4.5e-16
                         SdrD_B    3 iGdfVweDanknGiqdagekgisgvtVtLkdakgevvatttTdasGkYkFtnltpGeYkVeftapagy.tvtak 75  
                                     i  + + D n+n + d+ge+gi g  V+L  ++g+vv++t T+++G+Y+F+n++pG+Y+++   p+gy +vt++
  gi|116754892|ref|YP_844010.1| 1546 IKGMKYYDLNANKVRDEGEPGIPGSDVNL-IENGKVVRSTKTSEDGTYTFDNVAPGTYTISDPLPEGYvVVTSS 1618
                                     6667799**********************.7899**********************************555554 PP

  == domain 6  score: 31.5 bits;  conditional E-value: 1.5e-10
                         SdrD_B    3 iGdfVweDanknGiqdagekgisgvtVtL..kdakgevv.atttTdasGkYkFtnltpGeYkVeftapagytvtak 75  
                                     i  + ++D n++G  dag++gisg  + L  +++ g  + +t+ T ++G+Y+F n++pG+Yk++  +  g+t+t+ 
  gi|116754892|ref|YP_844010.1| 1642 ISGRKFNDLNGDGS-DAGDPGISGWGIVLdgTTTLGVHItETQYTGSDGSYTFGNIAPGTYKISELSRPGWTQTHP 1716
                                     666779*******5.9*************55444455555799999*****************9988777766544 PP

  == domain 7  score: 49.7 bits;  conditional E-value: 3.4e-16
                         SdrD_B    7 VweDanknGiqdagekgisgvtVtLkdakgevvatttTdasGkYkFtnltpGeYkVeftapagytvtakkaGs 79  
                                      ++D+n+nG+ dage+g +g ++++  ++ + ++t +Td++G Y+Ft+l++G+Y+V+ t   g++vt+   Gs
  gi|116754892|ref|YP_844010.1| 1751 KFNDKNNNGVRDAGEQGLAGWEIRI--SNSTYTRTAITDSDGWYNFTGLDAGTYTVTETLKPGWSVTKPSGGS 1821
                                     59***********************..66777789************************99999999887665 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.2   6.7e-10   7.1e-07       8      79 ..    1178    1251 ..    1177    1252 .. 0.87
   2 !   24.7   0.2     2e-08   2.1e-05      13      79 ..    1279    1346 ..    1259    1348 .. 0.76
   3 !   29.2   0.1     8e-10   8.4e-07       1      64 [.    1354    1424 ..    1354    1444 .. 0.81
   4 !   29.6   0.5   5.9e-10   6.3e-07       6      71 ..    1465    1529 ..    1451    1539 .. 0.78
   5 !   29.4   3.4   6.9e-10   7.3e-07       5      79 ..    1558    1632 ..    1558    1634 .. 0.91
   6 !   13.6   0.3   5.7e-05      0.06      14      53 ..    1662    1704 ..    1653    1724 .. 0.74
   7 !   32.5   1.3   7.4e-11   7.8e-08       6      79 ..    1760    1837 ..    1759    1861 .. 0.91
   8 ?    4.6   0.0     0.038        40      30      71 ..    1894    1935 ..    1883    1943 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 6.7e-10
                CarboxypepD_reg    8 dasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtv.sapGyatatr..eevtltagqtttldi 79  
                                     d+  a++ g t+++t  +++t+ +ttt+ dG++r++gl+pg y+v+  +++G +++t+  ++v lt+ + t +++
  gi|116754892|ref|YP_844010.1| 1178 DSGEAGLDGWTIVLT-MPDQTEVQTTTGFDGYYRFEGLAPGLYTVRElQKAGWDSTTSesQQVNLTDSDVTGINF 1251
                                     67789999*******.799**************************976999999999744578888888877776 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 2e-08
                CarboxypepD_reg   13 piagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatr..eevtltagqtttldi 79  
                                     +++g ++++t +++ t++ +tt++dG++r+++l+pg y+++v  +    +++  ++v++t+ +++ +d+
  gi|116754892|ref|YP_844010.1| 1279 GVKGWEIRLT-KPDATESVATTGDDGSYRFEDLTPGVYTLRVVLQPGWNVSIssKDVSITDTDQSSVDF 1346
                                     579999****.68999999**********************9655444444322677777777777776 PP

  == domain 3  score: 29.2 bits;  conditional E-value: 8e-10
                CarboxypepD_reg    1 tisGrVtda.sgapi.......agatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatr 64  
                                     tisGrV +  + +++       +g tV +t  ++g +++++t++dG ++++ l pgty++++ ++   ++t 
  gi|116754892|ref|YP_844010.1| 1354 TISGRVFSDlDANGVndgepglSGWTVKLT-MPDGGERTAVTADDGFYSFDRLSPGTYKIEAVKQDGWSQTA 1424
                                     7999996544555555555555********.799****************************9998888886 PP

  == domain 4  score: 29.6 bits;  conditional E-value: 5.9e-10
                CarboxypepD_reg    6 VtdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtlta 71  
                                     V+ a  +++ g +Vt+  +++++++ t t+adG++r+++l pgty+v+   +    at e+ +++ 
  gi|116754892|ref|YP_844010.1| 1465 VREAGETGVRGWSVTLV-QGENATSMTETGADGTYRFESLSPGTYRVELIPQDGWKATTESREIQI 1529
                                     677778899********.7999*************************9744333333333444444 PP

  == domain 5  score: 29.4 bits;  conditional E-value: 6.9e-10
                CarboxypepD_reg    5 rVtdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtv.sapGyatatreevtltagqtttldi 79  
                                     +V+d+   +i+g  V +  +++++v+st+t +dG++++++++pgty++     +Gy  +t++++t+t+ ++t ld+
  gi|116754892|ref|YP_844010.1| 1558 KVRDEGEPGIPGSDVNLI-ENGKVVRSTKTSEDGTYTFDNVAPGTYTISDpLPEGYVVVTSSTITVTVTTNTVLDA 1632
                                     69999999*********9.467789***********************98678899999999*****999988875 PP

  == domain 6  score: 13.6 bits;  conditional E-value: 5.7e-05
                CarboxypepD_reg   14 iagatVtvtnadt...gtvastttdadGafrlrglppgtysvt 53  
                                     i+g  +++  + t   + + +  t++dG++++ +++pgty++ 
  gi|116754892|ref|YP_844010.1| 1662 ISGWGIVLDGTTTlgvHITETQYTGSDGSYTFGNIAPGTYKIS 1704
                                     55556666633222113477889*****************985 PP

  == domain 7  score: 32.5 bits;  conditional E-value: 7.4e-11
                CarboxypepD_reg    6 VtdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatr.....eevtltagqttt.l 77  
                                     V+da  +++ag +++++  +++ ++++ td+dG ++++gl +gty+vt + +   ++t+      ++tl+ag+t+t +
  gi|116754892|ref|YP_844010.1| 1760 VRDAGEQGLAGWEIRIS--NSTYTRTAITDSDGWYNFTGLDAGTYTVTETLKPGWSVTKpsggsYTITLNAGETKTgV 1835
                                     99***************..5899*************************988888888887888745999999997657 PP

                CarboxypepD_reg   78 di 79  
                                     d+
  gi|116754892|ref|YP_844010.1| 1836 DF 1837
                                     76 PP

  == domain 8  score: 4.6 bits;  conditional E-value: 0.038
                CarboxypepD_reg   30 astttdadGafrlrglppgtysvtv.sapGyatatreevtlta 71  
                                     +s  +d++ +++  gl+pgty+++v  ++ y++ t  +v++t+
  gi|116754892|ref|YP_844010.1| 1894 RSWSSDNTWSWNTGGLEPGTYDIRVwIRDSYHSETG-DVQVTK 1935
                                     55667777788899***********77888988886.799986 PP

>> Big_9  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.1     0.003       3.1      11      88 ..      53     138 ..      51     140 .. 0.63
   2 !   15.5   1.0     2e-05     0.022      11      89 ..     162     241 ..     156     242 .. 0.75
   3 !   16.2   1.5   1.3e-05     0.013       3      89 ..     248     335 ..     246     336 .. 0.78
   4 !   16.2   1.5   1.3e-05     0.013       3      89 ..     342     429 ..     340     430 .. 0.78
   5 !   16.2   1.5   1.3e-05     0.013       3      89 ..     436     523 ..     434     524 .. 0.78
   6 !   19.0   1.5   1.7e-06    0.0018      11      89 ..     541     620 ..     529     621 .. 0.81
   7 !   16.2   1.5   1.3e-05     0.013       3      89 ..     627     714 ..     625     715 .. 0.78
   8 !   15.6   1.4   1.9e-05      0.02      11      89 ..     732     811 ..     720     812 .. 0.80
   9 !   16.2   1.5   1.3e-05     0.013       3      89 ..     818     905 ..     816     906 .. 0.78
  10 !   19.0   1.5   1.7e-06    0.0018      11      89 ..     923    1002 ..     911    1003 .. 0.81
  11 !   12.3   2.2    0.0002      0.21      11      88 ..    1020    1098 ..    1008    1100 .. 0.79
  12 ?    0.6   0.3      0.89   9.4e+02       3      62 ..    1090    1146 ..    1088    1155 .. 0.70
  13 ?   -2.4   5.3       8.2   8.6e+03      41      81 ..    1595    1634 ..    1559    1643 .. 0.72
  14 ?    0.5   0.8      0.96     1e+03      64      87 ..    1777    1806 ..    1753    1809 .. 0.77
  15 ?   -0.8   2.6       2.5   2.6e+03      73      87 ..    1786    1806 ..    1772    1848 .. 0.61
  16 !   13.2   0.2    0.0001      0.11       2      89 ..    2149    2243 ..    2148    2244 .. 0.83
  17 ?   -2.3   0.0       7.6     8e+03      51      85 ..    2606    2640 ..    2593    2641 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.003
                          Big_9  11 vndaPvavdds..vtvtedsv.....landtdpdgdaltvtsltvtlvta.....panGtvtinadgtltytpnagfsgt 78 
                                    +n++Pv+++     + ++d       + n+ dpdgd l++    + l+ +      +  t  in++ ++++  +++  gt
  gi|116754892|ref|YP_844010.1|  53 ENQPPVVTSFVsdPEGPQDAGvvvrwTVNAFDPDGDVLEYM---FLLKGPatgdsWKDMTGWINET-RWVWRTSDNDIGT 128
                                    6778887773323222222223577777**********965...3333341123323334445533.6************ PP

                          Big_9  79 dsftYtvsDg 88 
                                     +++++v Dg
  gi|116754892|ref|YP_844010.1| 129 NEIEVRVRDG 138
                                    *********9 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 2e-05
                          Big_9  11 vndaPvavddsvtvtedsv.......landtdpdgdaltvtsltvtlvtapanGtvtinadgtltytpnagfsgtdsftY 83 
                                     n++P ++   ++ ++ +v        a++tdpdgdal+++ l        +n     ++d+t++++ ++   g+ s+t+
  gi|116754892|ref|YP_844010.1| 162 PNRPPQVTGLVASPESPQVagtpvvwSASATDPDGDALEYQFL------LDGNVVKDWSGDNTWRWSTTDADVGSHSVTV 235
                                    6777777776666664444444567888**********96622......3445555566889****************** PP

                          Big_9  84 tvsDgs 89 
                                     v Dg+
  gi|116754892|ref|YP_844010.1| 236 VVRDGK 241
                                    ****97 PP

  == domain 3  score: 16.2 bits;  conditional E-value: 1.3e-05
                          Big_9   3 tvtvtvtpvndaPvavddsvtvtedsv.......landtdpdgdaltvtsltvtlvtapanGtvtinadgtltytpnagf 75 
                                    + + t+   n++P ++   ++ ++ +v        a++tdpdgdal+++ l        +n     ++d+t++++ ++  
  gi|116754892|ref|YP_844010.1| 248 SSQYTIIMPNRPPQVTGLVASPESPQVagtpvvwSASATDPDGDALEYQFL------LDGNVVKDWSGDNTWRWSTTDAD 321
                                    566777788999999988888875555555578888**********96622......3445555566889********** PP

                          Big_9  76 sgtdsftYtvsDgs 89 
                                     g+ s+t+ v Dg+
  gi|116754892|ref|YP_844010.1| 322 VGSHSVTVVVRDGK 335
                                    ************97 PP

  == domain 4  score: 16.2 bits;  conditional E-value: 1.3e-05
                          Big_9   3 tvtvtvtpvndaPvavddsvtvtedsv.......landtdpdgdaltvtsltvtlvtapanGtvtinadgtltytpnagf 75 
                                    + + t+   n++P ++   ++ ++ +v        a++tdpdgdal+++ l        +n     ++d+t++++ ++  
  gi|116754892|ref|YP_844010.1| 342 SSQYTIIMPNRPPQVTGLVASPESPQVagtpvvwSASATDPDGDALEYQFL------LDGNVVKDWSGDNTWRWSTTDAD 415
                                    566777788999999988888875555555578888**********96622......3445555566889********** PP

                          Big_9  76 sgtdsftYtvsDgs 89 
                                     g+ s+t+ v Dg+
  gi|116754892|ref|YP_844010.1| 416 VGSHSVTVVVRDGK 429
                                    ************97 PP

  == domain 5  score: 16.2 bits;  conditional E-value: 1.3e-05
                          Big_9   3 tvtvtvtpvndaPvavddsvtvtedsv.......landtdpdgdaltvtsltvtlvtapanGtvtinadgtltytpnagf 75 
                                    + + t+   n++P ++   ++ ++ +v        a++tdpdgdal+++ l        +n     ++d+t++++ ++  
  gi|116754892|ref|YP_844010.1| 436 SSQYTIIMPNRPPQVTGLVASPESPQVagtpvvwSASATDPDGDALEYQFL------LDGNVVKDWSGDNTWRWSTTDAD 509
                                    566777788999999988888875555555578888**********96622......3445555566889********** PP

                          Big_9  76 sgtdsftYtvsDgs 89 
                                     g+ s+t+ v Dg+
  gi|116754892|ref|YP_844010.1| 510 VGSHSVTVVVRDGK 523
                                    ************97 PP

  == domain 6  score: 19.0 bits;  conditional E-value: 1.7e-06
                          Big_9  11 vndaPvavddsvtvtedsv.......landtdpdgdaltvtsltvtlvtapanGtvtinadgtltytpnagfsgtdsftY 83 
                                     nd+Pv+++  ++ ++ +v        a++tdpdgdal+++ l        +n     ++d+t++++ ++   g+ s+t+
  gi|116754892|ref|YP_844010.1| 541 PNDPPVIESLVASPESPQVagtpvvwSASATDPDGDALEYQFL------LDGNVVKDWSGDNTWRWSTTDADVGSHSVTV 614
                                    79*******9999886666666688888**********96622......3445555566889****************** PP

                          Big_9  84 tvsDgs 89 
                                     v Dg+
  gi|116754892|ref|YP_844010.1| 615 VVRDGK 620
                                    ****97 PP

  == domain 7  score: 16.2 bits;  conditional E-value: 1.3e-05
                          Big_9   3 tvtvtvtpvndaPvavddsvtvtedsv.......landtdpdgdaltvtsltvtlvtapanGtvtinadgtltytpnagf 75 
                                    + + t+   n++P ++   ++ ++ +v        a++tdpdgdal+++ l        +n     ++d+t++++ ++  
  gi|116754892|ref|YP_844010.1| 627 SSQYTIIMPNRPPQVTGLVASPESPQVagtpvvwSASATDPDGDALEYQFL------LDGNVVKDWSGDNTWRWSTTDAD 700
                                    566777788999999988888875555555578888**********96622......3445555566889********** PP

                          Big_9  76 sgtdsftYtvsDgs 89 
                                     g+ s+t+ v Dg+
  gi|116754892|ref|YP_844010.1| 701 VGSHSVTVVVRDGK 714
                                    ************97 PP

  == domain 8  score: 15.6 bits;  conditional E-value: 1.9e-05
                          Big_9  11 vndaPvavddsvtvtedsv.......landtdpdgdaltvtsltvtlvtapanGtvtinadgtltytpnagfsgtdsftY 83 
                                     nd+Pv+++  ++ ++ +v        a++tdpdgdal+++ l        +n     ++d+t++++ ++    + s+t+
  gi|116754892|ref|YP_844010.1| 732 PNDPPVIESLVASPESPQVagtpvvwSASATDPDGDALEYQFL------LDGNVVKDWSGDNTWRWSTTDADVESHSVTV 805
                                    79*******9999886666666688888**********96622......3445555566889****************** PP

                          Big_9  84 tvsDgs 89 
                                     v Dg+
  gi|116754892|ref|YP_844010.1| 806 VVRDGK 811
                                    ****97 PP

  == domain 9  score: 16.2 bits;  conditional E-value: 1.3e-05
                          Big_9   3 tvtvtvtpvndaPvavddsvtvtedsv.......landtdpdgdaltvtsltvtlvtapanGtvtinadgtltytpnagf 75 
                                    + + t+   n++P ++   ++ ++ +v        a++tdpdgdal+++ l        +n     ++d+t++++ ++  
  gi|116754892|ref|YP_844010.1| 818 SSQYTIIMPNRPPQVTGLVASPESPQVagtpvvwSASATDPDGDALEYQFL------LDGNVVKDWSGDNTWRWSTTDAD 891
                                    566777788999999988888875555555578888**********96622......3445555566889********** PP

                          Big_9  76 sgtdsftYtvsDgs 89 
                                     g+ s+t+ v Dg+
  gi|116754892|ref|YP_844010.1| 892 VGSHSVTVVVRDGK 905
                                    ************97 PP

  == domain 10  score: 19.0 bits;  conditional E-value: 1.7e-06
                          Big_9   11 vndaPvavddsvtvtedsv.......landtdpdgdaltvtsltvtlvtapanGtvtinadgtltytpnagfsgtdsf 81  
                                      nd+Pv+++  ++ ++ +v        a++tdpdgdal+++ l        +n     ++d+t++++ ++   g+ s+
  gi|116754892|ref|YP_844010.1|  923 PNDPPVIESLVASPESPQVagtpvvwSASATDPDGDALEYQFL------LDGNVVKDWSGDNTWRWSTTDADVGSHSV 994 
                                     79*******9999886666666688888**********96622......3445555566889**************** PP

                          Big_9   82 tYtvsDgs 89  
                                     t+ v Dg+
  gi|116754892|ref|YP_844010.1|  995 TVVVRDGK 1002
                                     ******97 PP

  == domain 11  score: 12.3 bits;  conditional E-value: 0.0002
                          Big_9   11 vndaPvavddsvtvtedsv.......landtdpdgdaltvtsltvtlvtapanGtvtinadgtltytpnagfsgtdsf 81  
                                      nd+Pv+++  ++ ++ +v        a++tdpdgdal+++ l        +n     ++d+t++++ ++   g+ s+
  gi|116754892|ref|YP_844010.1| 1020 PNDPPVIESLVASPESPQVagtpvvwSASATDPDGDALEYQFL------LDGNVVKDWSGDNTWRWSTTDADVGSHSV 1091
                                     79*******9999886666666688888**********96622......34445555668899*************** PP

                          Big_9   82 tYtvsDg 88  
                                     t  v D+
  gi|116754892|ref|YP_844010.1| 1092 TAGVRDN 1098
                                     *999997 PP

  == domain 12  score: 0.6 bits;  conditional E-value: 0.89
                          Big_9    3 tvtvtvtpvndaPvavddsvtvtedsvlandtdpdgdaltvtsltvtlvtapanGtvtin 62  
                                     +vt  v    +a   ++d++ ++e + l ++  p++ +   t++ ++ vtap n tv in
  gi|116754892|ref|YP_844010.1| 1090 SVTAGVRDNRHATNGTADNTVTEEYEILRSAA-PENVTAP-TNV-TENVTAPVNVTVPIN 1146
                                     66777776666777777777778888887774.5555543.454.678899999998877 PP

  == domain 13  score: -2.4 bits;  conditional E-value: 8.2
                          Big_9   41 ltvtsltvtlvtapanGtvtinadgtltytpnagfsgtdsf 81  
                                     ++v+  t+t++++   G v+++++ t+t t +++   ++sf
  gi|116754892|ref|YP_844010.1| 1595 DNVAPGTYTISDPLPEGYVVVTSS-TITVTVTTNTVLDASF 1634
                                     344555788888888888888855.8888888888887777 PP

  == domain 14  score: 0.5 bits;  conditional E-value: 0.96
                          Big_9   64 dgtltytpna........gfsgtdsftYtvsD 87  
                                     +   tyt +a        +f+g d  tYtv+ 
  gi|116754892|ref|YP_844010.1| 1777 NS--TYTRTAitdsdgwyNFTGLDAGTYTVTE 1806
                                     33..45555555999999************85 PP

  == domain 15  score: -0.8 bits;  conditional E-value: 2.5
                          Big_9   73 a......gfsgtdsftYtvsD 87  
                                     +      +f+g d  tYtv+ 
  gi|116754892|ref|YP_844010.1| 1786 TdsdgwyNFTGLDAGTYTVTE 1806
                                     244555555555555555543 PP

  == domain 16  score: 13.2 bits;  conditional E-value: 0.0001
                          Big_9    2 atvtvtvtpvndaPvavdds.......vtvtedsvlandtdpdgdaltvtsltvtlvtapanGtvtinadgt....lt 68  
                                     a +++ v+  n +Pv+++ +       ++ t+   +a +tdpd d++ +    + l+ ++++ t +i  d +    +t
  gi|116754892|ref|YP_844010.1| 2149 AAFSIVVK-PNLPPVITSLTpdkpspqASGTQIKWTAVATDPDRDPIYY---RFWLKGPSTGNTWQIVRDWStsntWT 2222
                                     67788888.79******988788888888888888************74...567888888888888766555666** PP

                          Big_9   69 ytpnagfsgtdsftYtvsDgs 89  
                                     ++ + g +g++++ + v Dg+
  gi|116754892|ref|YP_844010.1| 2223 WSSDLGDAGDYTVFVYVRDGK 2243
                                     *******************96 PP

  == domain 17  score: -2.3 bits;  conditional E-value: 7.6
                          Big_9   51 vtapanGtvtinadgtltytpnagfsgtdsftYtv 85  
                                     ++a ++ t+t  ++g ++   + g+ g+ sf +t+
  gi|116754892|ref|YP_844010.1| 2606 DAAKQGSTLTRISTGMYRMRSTFGAPGEKSFRITA 2640
                                     3456677888889******************9986 PP

>> SpaA  Prealbumin-like fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       8.9   9.4e+03      61      79 ..    1125    1144 ..    1098    1148 .. 0.67
   2 !   16.0   0.2   1.1e-05     0.011      32      78 ..    1195    1241 ..    1162    1245 .. 0.71
   3 !   15.3   0.2   1.8e-05     0.019       6      59 ..    1260    1318 ..    1247    1341 .. 0.81
   4 !    8.4   0.0    0.0026       2.8      28      59 ..    1377    1413 ..    1347    1437 .. 0.74
   5 !   14.1   0.1   4.2e-05     0.044       7      78 ..    1453    1529 ..    1449    1533 .. 0.68
   6 !   23.2   2.7   5.9e-08   6.2e-05      28      82 .]    1565    1628 ..    1546    1628 .. 0.78
   7 !   14.9   0.1   2.3e-05     0.024      26      64 ..    1662    1709 ..    1637    1729 .. 0.67
   8 !   23.5   1.2   5.1e-08   5.3e-05      21      68 ..    1763    1814 ..    1737    1830 .. 0.68
   9 ?   -0.7   0.1       1.7   1.8e+03      35      57 ..    1873    1915 ..    1827    1945 .. 0.57

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 8.9
                                     EE-STTEEE.-SSEEEEEEC CS
                           SpaA   61 tkaPegYvl.dkepfevtvt 79  
                                     ++aP++++   ++p+ vtv+
  gi|116754892|ref|YP_844010.1| 1125 VTAPTNVTEnVTAPVNVTVP 1144
                                     34555555534557777765 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.1e-05
                                     CCEESEEE-BTTSEEEEEEEESEEEEEEEEE-STTEEE-SSEEEEEE CS
                           SpaA   32 gtevttlttdenGkatfegLplGtYllvEtkaPegYvldkepfevtv 78  
                                     +++  + tt+ +G+ +fegL++G Y+++E +       ++e  +v +
  gi|116754892|ref|YP_844010.1| 1195 DQTEVQTTTGFDGYYRFEGLAPGLYTVRELQKAGWDSTTSESQQVNL 1241
                                     4555667899*******************986655555555555555 PP

  == domain 3  score: 15.3 bits;  conditional E-value: 1.8e-05
                                     -TS-EEEEEETTTSCCCHCHHTT......TTCCEESEEE-BTTSEEEEEEEESEEEEEE CS
                           SpaA    6 LaGaeFtlykvdtttdgkdalea.....kktgtevttlttdenGkatfegLplGtYllv 59  
                                     ++G  F+ ++++ ++dg+  +++     +k +++   +tt+++G  +fe+L +G Y+l+
  gi|116754892|ref|YP_844010.1| 1260 ISGTLFEDVNNNGANDGEPGVKGweirlTKPDATESVATTGDDGSYRFEDLTPGVYTLR 1318
                                     55666666666666777777777999998899999**********************96 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.0026
                                     T......TTCCEESEEE-BTTSEEEEEEEESEEEEEE CS
                           SpaA   28 a.....kktgtevttlttdenGkatfegLplGtYllv 59  
                                     +     +  +    t++t ++G  +f+ L +GtY+++
  gi|116754892|ref|YP_844010.1| 1377 GwtvklTMPDGGERTAVTADDGFYSFDRLSPGTYKIE 1413
                                     35555533445568899999**************997 PP

  == domain 5  score: 14.1 bits;  conditional E-value: 4.2e-05
                                     TS-EEEEEETT.TSCCCHCHHTT......TTCCEESEEE.-BTTSEEEEEEEESEEEEEEEEE-STTEEE-SSEEEEE CS
                           SpaA    7 aGaeFtlykvd.tttdgkdalea.....kktgtevttlt.tdenGkatfegLplGtYllvEtkaPegYvldkepfevt 77  
                                     +G++F   +++ ++++g++ + +       +g+++t++t t+++G+ +fe L +GtY + E    +g + ++e  e++
  gi|116754892|ref|YP_844010.1| 1453 SGVVFNDINANgVREAGETGVRGwsvtlV-QGENATSMTeTGADGTYRFESLSPGTYRV-ELIPQDGWKATTESREIQ 1528
                                     56666666666655555555555767753.3555555555*****************96.677777777777777777 PP

                                     E CS
                           SpaA   78 v 78  
                                     +
  gi|116754892|ref|YP_844010.1| 1529 I 1529
                                     6 PP

  == domain 6  score: 23.2 bits;  conditional E-value: 5.9e-08
                                     T..........TTCCEESEEE-BTTSEEEEEEEESEEEEEEEEE-STTEEE.-SSEEEEEECEEC CS
                           SpaA   28 a.........kktgtevttlttdenGkatfegLplGtYllvEtkaPegYvl.dkepfevtvtatg 82  
                                                ++g++v + +t e+G+ tf+++++GtY++     PegYv  ++ +++vtvt+++
  gi|116754892|ref|YP_844010.1| 1565 PgipgsdvnlIENGKVVRSTKTSEDGTYTFDNVAPGTYTISD-PLPEGYVVvTSSTITVTVTTNT 1628
                                     144446677767899**************************8.59****8879999*****9885 PP

  == domain 7  score: 14.9 bits;  conditional E-value: 2.3e-05
                                     HTT..........TTCCEESEEE-BTTSEEEEEEEESEEEEEEEEE-S CS
                           SpaA   26 lea.........kktgtevttlttdenGkatfegLplGtYllvEtkaP 64  
                                     +++         +  +  ++t  t+++G  tf+++++GtY++ E + P
  gi|116754892|ref|YP_844010.1| 1662 ISGwgivldgttTLGVHITETQYTGSDGSYTFGNIAPGTYKISELSRP 1709
                                     33366665543222223346777*********************9887 PP

  == domain 8  score: 23.5 bits;  conditional E-value: 5.1e-08
                                     CCHCHHTT.....TTCCEESEEE-BTTSEEEEEEEESEEEEEEEEE-STTEE CS
                           SpaA   21 dgkdalea....kktgtevttlttdenGkatfegLplGtYllvEtkaPegYv 68  
                                     +g++ l++      + t + t+ td++G  +f+gL++GtY+++Et  P   v
  gi|116754892|ref|YP_844010.1| 1763 AGEQGLAGweirISNSTYTRTAITDSDGWYNFTGLDAGTYTVTETLKPGWSV 1814
                                     3333333366665556678999***********************8886554 PP

  == domain 9  score: -0.7 bits;  conditional E-value: 1.7
                                     E....................SEEE-BTTSEEEEEEEESEEEE CS
                           SpaA   35 v....................ttlttdenGkatfegLplGtYl 57  
                                     v                     ++ +d++   +++gL++GtY 
  gi|116754892|ref|YP_844010.1| 1873 VpleysfwlkgpstsglwqekRSWSSDNTWSWNTGGLEPGTYD 1915
                                     1344444444444444444436677777777888899999985 PP

>> Cadherin_5  Cadherin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1      0.13   1.3e+02       2      84 ..      54     138 ..      53     146 .. 0.80
   2 !   12.3   0.2   0.00012      0.13      31      97 ..     189     253 ..     163     254 .. 0.86
   3 !   12.3   0.2   0.00012      0.13      31      97 ..     283     347 ..     257     348 .. 0.86
   4 !   12.3   0.2   0.00012      0.13      31      97 ..     377     441 ..     351     442 .. 0.86
   5 !   11.4   0.2   0.00023      0.24      31      95 ..     471     533 ..     445     536 .. 0.84
   6 !   12.8   0.1   8.5e-05      0.09      31      97 ..     568     632 ..     541     633 .. 0.79
   7 !   11.4   0.2   0.00023      0.24      31      95 ..     662     724 ..     636     727 .. 0.84
   8 !    8.2   0.1    0.0022       2.3      31      97 ..     759     823 ..     732     824 .. 0.76
   9 !   11.4   0.2   0.00023      0.24      31      95 ..     853     915 ..     827     918 .. 0.84
  10 !   11.9   0.1   0.00016      0.17      31      95 ..     950    1012 ..     923    1015 .. 0.78
  11 !    8.9   0.8    0.0013       1.4      31      97 ..    1047    1110 ..    1020    1111 .. 0.78
  12 ?   -1.3   0.2       2.1   2.2e+03      53      68 ..    1578    1597 ..    1571    1623 .. 0.59
  13 ?   -3.1   0.4       7.6     8e+03      61      87 ..    2219    2245 ..    2212    2251 .. 0.84
  14 ?   -3.5   0.1       9.8     1e+04      23      41 ..    2368    2386 ..    2359    2391 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.13
                     Cadherin_5   2 ndaPvvssevtlaagseDtaltitaaqLLanasDvdgdtLsvssltadaenGtvvdngdG.....tftftpeanynGevt 76 
                                    n+ Pvv+s v+ ++g +D  +++       na D+dgd L+   l    ++G+  ++  G      +++    n  G+ +
  gi|116754892|ref|YP_844010.1|  54 NQPPVVTSFVSDPEGPQDAGVVVR---WTVNAFDPDGDVLEYMFLLKGPATGDSWKDMTGwinetRWVWRTSDNDIGTNE 130
                                    899999999999999999999999...678**********9999877666777776554433333788889999999999 PP

                     Cadherin_5  77 lsYtvsDg 84 
                                    ++ +v Dg
  gi|116754892|ref|YP_844010.1| 131 IEVRVRDG 138
                                    99999998 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00012
                     Cadherin_5  31 anasDvdgdtLsvssltadaenGtvvdn..gdGtftftpeanynGevtlsYtvsDgeggtttatasltv 97 
                                    a a+D+dgd+L+ + l   +  G+vv++  gd t+ +  +    G+ +++  v Dg+ + ++a+ ++t+
  gi|116754892|ref|YP_844010.1| 189 ASATDPDGDALEYQFL--LD--GNVVKDwsGDNTWRWSTTDADVGSHSVTVVVRDGKNEPVSASSQYTI 253
                                    789*************..34..89996523788***********************9999988888776 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00012
                     Cadherin_5  31 anasDvdgdtLsvssltadaenGtvvdn..gdGtftftpeanynGevtlsYtvsDgeggtttatasltv 97 
                                    a a+D+dgd+L+ + l   +  G+vv++  gd t+ +  +    G+ +++  v Dg+ + ++a+ ++t+
  gi|116754892|ref|YP_844010.1| 283 ASATDPDGDALEYQFL--LD--GNVVKDwsGDNTWRWSTTDADVGSHSVTVVVRDGKNEPVSASSQYTI 347
                                    789*************..34..89996523788***********************9999988888776 PP

  == domain 4  score: 12.3 bits;  conditional E-value: 0.00012
                     Cadherin_5  31 anasDvdgdtLsvssltadaenGtvvdn..gdGtftftpeanynGevtlsYtvsDgeggtttatasltv 97 
                                    a a+D+dgd+L+ + l   +  G+vv++  gd t+ +  +    G+ +++  v Dg+ + ++a+ ++t+
  gi|116754892|ref|YP_844010.1| 377 ASATDPDGDALEYQFL--LD--GNVVKDwsGDNTWRWSTTDADVGSHSVTVVVRDGKNEPVSASSQYTI 441
                                    789*************..34..89996523788***********************9999988888776 PP

  == domain 5  score: 11.4 bits;  conditional E-value: 0.00023
                     Cadherin_5  31 anasDvdgdtLsvssltadaenGtvvdn..gdGtftftpeanynGevtlsYtvsDgeggtttatasl 95 
                                    a a+D+dgd+L+ + l   +  G+vv++  gd t+ +  +    G+ +++  v Dg+ + ++a+ ++
  gi|116754892|ref|YP_844010.1| 471 ASATDPDGDALEYQFL--LD--GNVVKDwsGDNTWRWSTTDADVGSHSVTVVVRDGKNEPVSASSQY 533
                                    789*************..34..89996523788***********************98888777665 PP

  == domain 6  score: 12.8 bits;  conditional E-value: 8.5e-05
                     Cadherin_5  31 anasDvdgdtLsvssltadaenGtvvdn..gdGtftftpeanynGevtlsYtvsDgeggtttatasltv 97 
                                    a a+D+dgd+L+ + l   +  G+vv++  gd t+ +  +    G+ +++  v Dg+ + ++a+ ++t+
  gi|116754892|ref|YP_844010.1| 568 ASATDPDGDALEYQFL--LD--GNVVKDwsGDNTWRWSTTDADVGSHSVTVVVRDGKNEPVSASSQYTI 632
                                    789*************..34..89996523788***********************9999988888776 PP

  == domain 7  score: 11.4 bits;  conditional E-value: 0.00023
                     Cadherin_5  31 anasDvdgdtLsvssltadaenGtvvdn..gdGtftftpeanynGevtlsYtvsDgeggtttatasl 95 
                                    a a+D+dgd+L+ + l   +  G+vv++  gd t+ +  +    G+ +++  v Dg+ + ++a+ ++
  gi|116754892|ref|YP_844010.1| 662 ASATDPDGDALEYQFL--LD--GNVVKDwsGDNTWRWSTTDADVGSHSVTVVVRDGKNEPVSASSQY 724
                                    789*************..34..89996523788***********************98888777665 PP

  == domain 8  score: 8.2 bits;  conditional E-value: 0.0022
                     Cadherin_5  31 anasDvdgdtLsvssltadaenGtvvdn..gdGtftftpeanynGevtlsYtvsDgeggtttatasltv 97 
                                    a a+D+dgd+L+ + l   +  G+vv++  gd t+ +  +     + +++  v Dg+ + ++a+ ++t+
  gi|116754892|ref|YP_844010.1| 759 ASATDPDGDALEYQFL--LD--GNVVKDwsGDNTWRWSTTDADVESHSVTVVVRDGKNEPVSASSQYTI 823
                                    789*************..34..89996522788999988777777889********9998888887776 PP

  == domain 9  score: 11.4 bits;  conditional E-value: 0.00023
                     Cadherin_5  31 anasDvdgdtLsvssltadaenGtvvdn..gdGtftftpeanynGevtlsYtvsDgeggtttatasl 95 
                                    a a+D+dgd+L+ + l   +  G+vv++  gd t+ +  +    G+ +++  v Dg+ + ++a+ ++
  gi|116754892|ref|YP_844010.1| 853 ASATDPDGDALEYQFL--LD--GNVVKDwsGDNTWRWSTTDADVGSHSVTVVVRDGKNEPVSASSQY 915
                                    789*************..34..89996523788***********************98888777665 PP

  == domain 10  score: 11.9 bits;  conditional E-value: 0.00016
                     Cadherin_5   31 anasDvdgdtLsvssltadaenGtvvdn..gdGtftftpeanynGevtlsYtvsDgeggtttatasl 95  
                                     a a+D+dgd+L+ + l   +  G+vv++  gd t+ +  +    G+ +++  v Dg+ + ++a+ ++
  gi|116754892|ref|YP_844010.1|  950 ASATDPDGDALEYQFL--LD--GNVVKDwsGDNTWRWSTTDADVGSHSVTVVVRDGKNEPVSASSQY 1012
                                     789*************..34..89996523788***********************98888777665 PP

  == domain 11  score: 8.9 bits;  conditional E-value: 0.0013
                     Cadherin_5   31 anasDvdgdtLsvssltadaenGtvvdn..gdGtftftpeanynGevtlsYtvsDgeggtttatasltv 97  
                                     a a+D+dgd+L+ + l   +  G+vv++  gd t+ +  +    G+ +++  v D++  +t+ ta+ tv
  gi|116754892|ref|YP_844010.1| 1047 ASATDPDGDALEYQFL--LD--GNVVKDwsGDNTWRWSTTDADVGSHSVTAGVRDNR-HATNGTADNTV 1110
                                     789*************..34..89996523788*******999*************7.67778887776 PP

  == domain 12  score: -1.3 bits;  conditional E-value: 2.1
                     Cadherin_5   53 Gtvv....dngdGtftftpe 68  
                                     G+vv    + +dGt+tf+  
  gi|116754892|ref|YP_844010.1| 1578 GKVVrstkTSEDGTYTFDNV 1597
                                     55554433567888888654 PP

  == domain 13  score: -3.1 bits;  conditional E-value: 7.6
                     Cadherin_5   61 GtftftpeanynGevtlsYtvsDgegg 87  
                                      t+t+  +    G+ t+   v Dg+ +
  gi|116754892|ref|YP_844010.1| 2219 NTWTWSSDLGDAGDYTVFVYVRDGKHA 2245
                                     69*************99999****844 PP

  == domain 14  score: -3.5 bits;  conditional E-value: 9.8
                     Cadherin_5   23 titaaqLLanasDvdgdtL 41  
                                     +++++qL + asD d+ +L
  gi|116754892|ref|YP_844010.1| 2368 VLETKQLTTSASDQDSPAL 2386
                                     6788999999***998774 PP

>> Big_7  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   1.9   6.9e-06    0.0073       7      70 .]     174     235 ..     166     235 .. 0.85
   2 !   17.1   1.9   6.9e-06    0.0073       7      70 .]     268     329 ..     260     329 .. 0.85
   3 !   17.1   1.9   6.9e-06    0.0073       7      70 .]     362     423 ..     354     423 .. 0.85
   4 !   17.1   1.9   6.9e-06    0.0073       7      70 .]     456     517 ..     448     517 .. 0.85
   5 !   16.8   1.4   8.2e-06    0.0086       8      70 .]     554     614 ..     549     614 .. 0.88
   6 !   17.1   1.9   6.9e-06    0.0073       7      70 .]     647     708 ..     639     708 .. 0.85
   7 !   13.7   1.4   7.5e-05     0.079       8      70 .]     745     805 ..     740     805 .. 0.87
   8 !   17.1   1.9   6.9e-06    0.0073       7      70 .]     838     899 ..     830     899 .. 0.85
   9 !   16.8   1.4   8.2e-06    0.0086       8      70 .]     936     996 ..     931     996 .. 0.88
  10 !   15.8   1.3   1.7e-05     0.018       8      70 .]    1033    1093 ..    1028    1093 .. 0.87
  11 ?    0.7   0.2      0.89   9.4e+02      33      69 ..    1571    1605 ..    1559    1605 .. 0.64
  12 ?   -1.2   1.0       3.5   3.7e+03      59      69 ..    1795    1805 ..    1760    1826 .. 0.64
  13 ?    1.4   1.7      0.54   5.7e+02      49      70 .]    1897    1918 ..    1817    1918 .. 0.79
  14 ?   -0.6   1.6       2.2   2.3e+03       7      68 ..    2167    2235 ..    2161    2237 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.9e-06
                                    E--TT--EBTSEEEEEEEEE-S.S-EEEEEEEETTEE.EEEE-SSSEEEEEE--...SEEEEEEE CS
                          Big_7   7 sPangatvsggtvtisasAsdd.ggvskVefyvdgtlglgtdtsapysltwtttaltagthtltV 70 
                                    sP++  +v g++v  sasA+d+ g   + +f +dg++ + +d s+  ++ w+tt+++ g+h++tV
  gi|116754892|ref|YP_844010.1| 174 SPESP-QVAGTPVVWSASATDPdGDALEYQFLLDGNV-V-KDWSGDNTWRWSTTDADVGSHSVTV 235
                                    45443.55679**************************.8.6779999*****************9 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 6.9e-06
                                    E--TT--EBTSEEEEEEEEE-S.S-EEEEEEEETTEE.EEEE-SSSEEEEEE--...SEEEEEEE CS
                          Big_7   7 sPangatvsggtvtisasAsdd.ggvskVefyvdgtlglgtdtsapysltwtttaltagthtltV 70 
                                    sP++  +v g++v  sasA+d+ g   + +f +dg++ + +d s+  ++ w+tt+++ g+h++tV
  gi|116754892|ref|YP_844010.1| 268 SPESP-QVAGTPVVWSASATDPdGDALEYQFLLDGNV-V-KDWSGDNTWRWSTTDADVGSHSVTV 329
                                    45443.55679**************************.8.6779999*****************9 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 6.9e-06
                                    E--TT--EBTSEEEEEEEEE-S.S-EEEEEEEETTEE.EEEE-SSSEEEEEE--...SEEEEEEE CS
                          Big_7   7 sPangatvsggtvtisasAsdd.ggvskVefyvdgtlglgtdtsapysltwtttaltagthtltV 70 
                                    sP++  +v g++v  sasA+d+ g   + +f +dg++ + +d s+  ++ w+tt+++ g+h++tV
  gi|116754892|ref|YP_844010.1| 362 SPESP-QVAGTPVVWSASATDPdGDALEYQFLLDGNV-V-KDWSGDNTWRWSTTDADVGSHSVTV 423
                                    45443.55679**************************.8.6779999*****************9 PP

  == domain 4  score: 17.1 bits;  conditional E-value: 6.9e-06
                                    E--TT--EBTSEEEEEEEEE-S.S-EEEEEEEETTEE.EEEE-SSSEEEEEE--...SEEEEEEE CS
                          Big_7   7 sPangatvsggtvtisasAsdd.ggvskVefyvdgtlglgtdtsapysltwtttaltagthtltV 70 
                                    sP++  +v g++v  sasA+d+ g   + +f +dg++ + +d s+  ++ w+tt+++ g+h++tV
  gi|116754892|ref|YP_844010.1| 456 SPESP-QVAGTPVVWSASATDPdGDALEYQFLLDGNV-V-KDWSGDNTWRWSTTDADVGSHSVTV 517
                                    45443.55679**************************.8.6779999*****************9 PP

  == domain 5  score: 16.8 bits;  conditional E-value: 8.2e-06
                                    --TT--EBTSEEEEEEEEE-S.S-EEEEEEEETTEE.EEEE-SSSEEEEEE--...SEEEEEEE CS
                          Big_7   8 PangatvsggtvtisasAsdd.ggvskVefyvdgtlglgtdtsapysltwtttaltagthtltV 70 
                                    P++  +v g++v  sasA+d+ g   + +f +dg++ + +d s+  ++ w+tt+++ g+h++tV
  gi|116754892|ref|YP_844010.1| 554 PESP-QVAGTPVVWSASATDPdGDALEYQFLLDGNV-V-KDWSGDNTWRWSTTDADVGSHSVTV 614
                                    5443.455699999**********************.8.6779999*****************9 PP

  == domain 6  score: 17.1 bits;  conditional E-value: 6.9e-06
                                    E--TT--EBTSEEEEEEEEE-S.S-EEEEEEEETTEE.EEEE-SSSEEEEEE--...SEEEEEEE CS
                          Big_7   7 sPangatvsggtvtisasAsdd.ggvskVefyvdgtlglgtdtsapysltwtttaltagthtltV 70 
                                    sP++  +v g++v  sasA+d+ g   + +f +dg++ + +d s+  ++ w+tt+++ g+h++tV
  gi|116754892|ref|YP_844010.1| 647 SPESP-QVAGTPVVWSASATDPdGDALEYQFLLDGNV-V-KDWSGDNTWRWSTTDADVGSHSVTV 708
                                    45443.55679**************************.8.6779999*****************9 PP

  == domain 7  score: 13.7 bits;  conditional E-value: 7.5e-05
                                    --TT--EBTSEEEEEEEEE-S.S-EEEEEEEETTEE.EEEE-SSSEEEEEE--...SEEEEEEE CS
                          Big_7   8 PangatvsggtvtisasAsdd.ggvskVefyvdgtlglgtdtsapysltwtttaltagthtltV 70 
                                    P++  +v g++v  sasA+d+ g   + +f +dg++ + +d s+  ++ w+tt+++  +h++tV
  gi|116754892|ref|YP_844010.1| 745 PESP-QVAGTPVVWSASATDPdGDALEYQFLLDGNV-V-KDWSGDNTWRWSTTDADVESHSVTV 805
                                    5443.455699999**********************.8.6779999*****************9 PP

  == domain 8  score: 17.1 bits;  conditional E-value: 6.9e-06
                                    E--TT--EBTSEEEEEEEEE-S.S-EEEEEEEETTEE.EEEE-SSSEEEEEE--...SEEEEEEE CS
                          Big_7   7 sPangatvsggtvtisasAsdd.ggvskVefyvdgtlglgtdtsapysltwtttaltagthtltV 70 
                                    sP++  +v g++v  sasA+d+ g   + +f +dg++ + +d s+  ++ w+tt+++ g+h++tV
  gi|116754892|ref|YP_844010.1| 838 SPESP-QVAGTPVVWSASATDPdGDALEYQFLLDGNV-V-KDWSGDNTWRWSTTDADVGSHSVTV 899
                                    45443.55679**************************.8.6779999*****************9 PP

  == domain 9  score: 16.8 bits;  conditional E-value: 8.2e-06
                                    --TT--EBTSEEEEEEEEE-S.S-EEEEEEEETTEE.EEEE-SSSEEEEEE--...SEEEEEEE CS
                          Big_7   8 PangatvsggtvtisasAsdd.ggvskVefyvdgtlglgtdtsapysltwtttaltagthtltV 70 
                                    P++  +v g++v  sasA+d+ g   + +f +dg++ + +d s+  ++ w+tt+++ g+h++tV
  gi|116754892|ref|YP_844010.1| 936 PESP-QVAGTPVVWSASATDPdGDALEYQFLLDGNV-V-KDWSGDNTWRWSTTDADVGSHSVTV 996
                                    5443.455699999**********************.8.6779999*****************9 PP

  == domain 10  score: 15.8 bits;  conditional E-value: 1.7e-05
                                     --TT--EBTSEEEEEEEEE-S.S-EEEEEEEETTEE.EEEE-SSSEEEEEE--...SEEEEEEE CS
                          Big_7    8 PangatvsggtvtisasAsdd.ggvskVefyvdgtlglgtdtsapysltwtttaltagthtltV 70  
                                     P++  +v g++v  sasA+d+ g   + +f +dg++ + +d s+  ++ w+tt+++ g+h++t+
  gi|116754892|ref|YP_844010.1| 1033 PESP-QVAGTPVVWSASATDPdGDALEYQFLLDGNV-V-KDWSGDNTWRWSTTDADVGSHSVTA 1093
                                     5443.455699999**********************.8.6779999****************97 PP

  == domain 11  score: 0.7 bits;  conditional E-value: 0.89
                                     EEEEEETTEE..EEEE-SSSEEEEEE--...SEEEEEE CS
                          Big_7   33 kVefyvdgtl.glgtdtsapysltwtttaltagthtlt 69  
                                      V +  +g++   +t ts   ++t++   ++ gt+t++
  gi|116754892|ref|YP_844010.1| 1571 DVNLIENGKVvR-STKTSEDGTYTFDN--VAPGTYTIS 1605
                                     566777777733.33344444444444..5789**995 PP

  == domain 12  score: -1.2 bits;  conditional E-value: 3.5
                                     -...SEEEEEE CS
                          Big_7   59 taltagthtlt 69  
                                     t l+agt+t+t
  gi|116754892|ref|YP_844010.1| 1795 TGLDAGTYTVT 1805
                                     44556666655 PP

  == domain 13  score: 1.4 bits;  conditional E-value: 0.54
                                     SSSEEEEEE--...SEEEEEEE CS
                          Big_7   49 sapysltwtttaltagthtltV 70  
                                     s+  +++w+t  l+ gt+ ++V
  gi|116754892|ref|YP_844010.1| 1897 SSDNTWSWNTGGLEPGTYDIRV 1918
                                     3666899***99******9998 PP

  == domain 14  score: -0.6 bits;  conditional E-value: 2.2
                                     E--TT--EB.TSEEEEEEEEE-S.S-EEEEEEEETTEE......EEEE-SSSEEEEEE--...SEEEEE CS
                          Big_7    7 sPangatvs.ggtvtisasAsdd.ggvskVefyvdgtl.g....lgtdtsapysltwtttaltagthtl 68  
                                     +P   +    g++++ +a A+d+        f++ g + g    +  d s+  ++tw+ + ++ag +t+
  gi|116754892|ref|YP_844010.1| 2167 TPDKPSPQAsGTQIKWTAVATDPdRDPIYYRFWLKGPStGntwqIVRDWSTSNTWTWSSDLGDAGDYTV 2235
                                     5555553343666666777777766666667777766544555666777778888888888999*9998 PP

>> Mannosidase_ig  Mannosidase Ig/CBM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1     0.015        16      25      56 ..     212     243 ..     208     289 .. 0.87
   2 ?    6.2   0.1     0.015        16      25      56 ..     306     337 ..     302     383 .. 0.87
   3 ?    6.2   0.1     0.015        16      25      56 ..     400     431 ..     396     477 .. 0.87
   4 !    8.6   0.1    0.0026       2.8      25      76 ..     494     540 ..     490     559 .. 0.84
   5 ?    6.2   0.1     0.015        16      25      56 ..     591     622 ..     587     668 .. 0.87
   6 !    8.6   0.1    0.0026       2.8      25      76 ..     685     731 ..     681     750 .. 0.84
   7 ?    6.0   0.1     0.017        18      25      56 ..     782     813 ..     778     859 .. 0.87
   8 !    8.6   0.1    0.0026       2.8      25      76 ..     876     922 ..     872     941 .. 0.84
   9 !    8.6   0.1    0.0026       2.8      25      76 ..     973    1019 ..     969    1038 .. 0.84
  10 ?    5.6   0.7     0.023        24      25      61 ..    1070    1105 ..    1066    1137 .. 0.80
  11 ?   -1.8   0.0       4.7     5e+03       8      41 ..    2570    2602 ..    2569    2612 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.015
                 Mannosidase_ig  25 dltgkllaetsttpvtvgansstevaeidvde 56 
                                    d++g+ ++++stt++ vg +s t v ++  +e
  gi|116754892|ref|YP_844010.1| 212 DWSGDNTWRWSTTDADVGSHSVTVVVRDGKNE 243
                                    9***********************99876655 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.015
                 Mannosidase_ig  25 dltgkllaetsttpvtvgansstevaeidvde 56 
                                    d++g+ ++++stt++ vg +s t v ++  +e
  gi|116754892|ref|YP_844010.1| 306 DWSGDNTWRWSTTDADVGSHSVTVVVRDGKNE 337
                                    9***********************99876655 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.015
                 Mannosidase_ig  25 dltgkllaetsttpvtvgansstevaeidvde 56 
                                    d++g+ ++++stt++ vg +s t v ++  +e
  gi|116754892|ref|YP_844010.1| 400 DWSGDNTWRWSTTDADVGSHSVTVVVRDGKNE 431
                                    9***********************99876655 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.0026
                 Mannosidase_ig  25 dltgkllaetsttpvtvgansstevaeidvdellaatggadpravvlvarle 76 
                                    d++g+ ++++stt++ vg +s t v ++  +e ++a     ++++v+ ar  
  gi|116754892|ref|YP_844010.1| 494 DWSGDNTWRWSTTDADVGSHSVTVVVRDGKNEPVSA-----SSQYVIEARVV 540
                                    9**************************999987655.....88888888875 PP

  == domain 5  score: 6.2 bits;  conditional E-value: 0.015
                 Mannosidase_ig  25 dltgkllaetsttpvtvgansstevaeidvde 56 
                                    d++g+ ++++stt++ vg +s t v ++  +e
  gi|116754892|ref|YP_844010.1| 591 DWSGDNTWRWSTTDADVGSHSVTVVVRDGKNE 622
                                    9***********************99876655 PP

  == domain 6  score: 8.6 bits;  conditional E-value: 0.0026
                 Mannosidase_ig  25 dltgkllaetsttpvtvgansstevaeidvdellaatggadpravvlvarle 76 
                                    d++g+ ++++stt++ vg +s t v ++  +e ++a     ++++v+ ar  
  gi|116754892|ref|YP_844010.1| 685 DWSGDNTWRWSTTDADVGSHSVTVVVRDGKNEPVSA-----SSQYVIEARVV 731
                                    9**************************999987655.....88888888875 PP

  == domain 7  score: 6.0 bits;  conditional E-value: 0.017
                 Mannosidase_ig  25 dltgkllaetsttpvtvgansstevaeidvde 56 
                                    d++g+ ++++stt++ v+ +s t v ++  +e
  gi|116754892|ref|YP_844010.1| 782 DWSGDNTWRWSTTDADVESHSVTVVVRDGKNE 813
                                    9***********************99876655 PP

  == domain 8  score: 8.6 bits;  conditional E-value: 0.0026
                 Mannosidase_ig  25 dltgkllaetsttpvtvgansstevaeidvdellaatggadpravvlvarle 76 
                                    d++g+ ++++stt++ vg +s t v ++  +e ++a     ++++v+ ar  
  gi|116754892|ref|YP_844010.1| 876 DWSGDNTWRWSTTDADVGSHSVTVVVRDGKNEPVSA-----SSQYVIEARVV 922
                                    9**************************999987655.....88888888875 PP

  == domain 9  score: 8.6 bits;  conditional E-value: 0.0026
                 Mannosidase_ig   25 dltgkllaetsttpvtvgansstevaeidvdellaatggadpravvlvarle 76  
                                     d++g+ ++++stt++ vg +s t v ++  +e ++a     ++++v+ ar  
  gi|116754892|ref|YP_844010.1|  973 DWSGDNTWRWSTTDADVGSHSVTVVVRDGKNEPVSA-----SSQYVIEARVV 1019
                                     9**************************999987655.....88888888875 PP

  == domain 10  score: 5.6 bits;  conditional E-value: 0.023
                 Mannosidase_ig   25 dltgkllaetsttpvtvgansstevaeidvdellaat 61  
                                     d++g+ ++++stt++ vg +s t   +++ + + ++t
  gi|116754892|ref|YP_844010.1| 1070 DWSGDNTWRWSTTDADVGSHSVTAGVRDNRHAT-NGT 1105
                                     9***********************999999955.442 PP

  == domain 11  score: -1.8 bits;  conditional E-value: 4.7
                 Mannosidase_ig    8 vsdllepvqgtlelrlidltgkllaetsttpvtv 41  
                                     +s++++++  t++lr+++  g+l+  ts ++ + 
  gi|116754892|ref|YP_844010.1| 2570 FSSRRANRAYTMTLRFFNNYGELIDPTS-MEMSW 2602
                                     588999999*************999998.76655 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 !    8.6   0.1    0.0017       1.8      11      49 ..    1181    1222 ..    1173    1250 .. 0.82
   2 !    7.9   0.0    0.0029         3      24      50 ..    1293    1319 ..    1274    1346 .. 0.87
   3 ?    4.4   0.0     0.034        36      14      49 ..    1375    1413 ..    1356    1419 .. 0.79
   4 !    7.5   0.0    0.0039       4.2      14      49 ..    1473    1511 ..    1463    1532 .. 0.78
   5 !   14.4   0.4   2.6e-05     0.027       5      71 ..    1559    1631 ..    1558    1637 .. 0.68
   6 ?    4.4   0.1     0.035        37      25      48 ..    1680    1703 ..    1660    1707 .. 0.84
   7 !   13.1   0.1   6.6e-05     0.069       5      49 ..    1760    1805 ..    1758    1808 .. 0.83
   8 ?   -3.4   0.1       9.6     1e+04      34      69 ..    1820    1854 ..    1818    1859 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0017
                CarbopepD_reg_2   11 keplpgatVyv...kgtkkgtvTdenGnFelknlpagkytLv 49  
                                     +  l g t+++    +t+++t+T  +G+++++ l +g yt++
  gi|116754892|ref|YP_844010.1| 1181 EAGLDGWTIVLtmpDQTEVQTTTGFDGYYRFEGLAPGLYTVR 1222
                                     467788888773334689*********************985 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0029
                CarbopepD_reg_2   24 tkkgtvTdenGnFelknlpagkytLvv 50  
                                     t+  ++T ++G++++++l++g ytL+v
  gi|116754892|ref|YP_844010.1| 1293 TESVATTGDDGSYRFEDLTPGVYTLRV 1319
                                     567789*******************98 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.034
                CarbopepD_reg_2   14 lpgatVyv...kgtkkgtvTdenGnFelknlpagkytLv 49  
                                     l g tV +    g ++ +vT ++G +++++l +g+y++ 
  gi|116754892|ref|YP_844010.1| 1375 LSGWTVKLtmpDGGERTAVTADDGFYSFDRLSPGTYKIE 1413
                                     5555555522235678899*****************986 PP

  == domain 4  score: 7.5 bits;  conditional E-value: 0.0039
                CarbopepD_reg_2   14 lpgatVyv...kgtkkgtvTdenGnFelknlpagkytLv 49  
                                     + g +V++   ++ +  t T ++G++++++l +g+y++ 
  gi|116754892|ref|YP_844010.1| 1473 VRGWSVTLvqgENATSMTETGADGTYRFESLSPGTYRVE 1511
                                     5555555421155677788*****************875 PP

  == domain 5  score: 14.4 bits;  conditional E-value: 2.6e-05
                CarbopepD_reg_2    5 VvdketkeplpgatVyvkgtk...kgtvTdenGnFelknlpagkytLv....vsyvGyktqekkvtvskektld 71  
                                     V d++ +  +pg  V + +++   + t T e+G+++++n+ +g+yt+       yv  ++ +++vtv++++ ld
  gi|116754892|ref|YP_844010.1| 1559 VRDEG-EPGIPGSDVNLIENGkvvRSTKTSEDGTYTFDNVAPGTYTISdplpEGYVVVTSSTITVTVTTNTVLD 1631
                                     56655.4789997776655432347899*****************98622113456666667777777666665 PP

  == domain 6  score: 4.4 bits;  conditional E-value: 0.035
                CarbopepD_reg_2   25 kkgtvTdenGnFelknlpagkytL 48  
                                     +   +T ++G++++ n+ +g+y++
  gi|116754892|ref|YP_844010.1| 1680 TETQYTGSDGSYTFGNIAPGTYKI 1703
                                     55678*****************87 PP

  == domain 7  score: 13.1 bits;  conditional E-value: 6.6e-05
                CarbopepD_reg_2    5 VvdketkeplpgatVyvkgt..kkgtvTdenGnFelknlpagkytLv 49  
                                     V d++ ++ l+g  + + ++  ++ ++Td++G ++++ l+ag+yt++
  gi|116754892|ref|YP_844010.1| 1760 VRDAG-EQGLAGWEIRISNStyTRTAITDSDGWYNFTGLDAGTYTVT 1805
                                     56665.589***999998872357888******************86 PP

  == domain 8  score: -3.4 bits;  conditional E-value: 9.6
                CarbopepD_reg_2   34 GnFelknlpagkytLvvsyvGyktqekkvtvskekt 69  
                                     G+++++ l+ag+ +  v +  yk+     t++++kt
  gi|116754892|ref|YP_844010.1| 1820 GSYTIT-LNAGETKTGVDFGNYKSLPTGATLTSDKT 1854
                                     999996.99999999999999998877777766665 PP

>> DUF2012  Protein of unknown function (DUF2012)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0         2   2.1e+03      12      44 ..    1189    1221 ..    1181    1226 .. 0.81
   2 !    7.2   0.0     0.005       5.3      21      47 ..    1294    1320 ..    1279    1336 .. 0.84
   3 ?    5.8   0.0     0.014        15      15      49 ..    1386    1417 ..    1374    1420 .. 0.79
   4 !    7.9   0.0    0.0029       3.1       9      46 ..    1475    1512 ..    1469    1516 .. 0.90
   5 !    9.9   0.1    0.0007      0.73      12      45 ..    1572    1605 ..    1566    1643 .. 0.81
   6 ?    3.0   0.1       0.1     1e+02      19      44 ..    1678    1703 ..    1615    1711 .. 0.83
   7 ?    5.9   0.0     0.012        13       9      44 ..    1770    1804 ..    1764    1808 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2
                        DUF2012   12 vlLdsgqqrkfkalvrrDGsFifrdlpegsYlL 44  
                                     ++L    q ++++ +  DG + f+ l +g Y++
  gi|116754892|ref|YP_844010.1| 1189 IVLTMPDQTEVQTTTGFDGYYRFEGLAPGLYTV 1221
                                     55555555588899999**************98 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.005
                        DUF2012   21 kfkalvrrDGsFifrdlpegsYlLeve 47  
                                     + +a +  DGs+ f+dl +g Y+L+v+
  gi|116754892|ref|YP_844010.1| 1294 ESVATTGDDGSYRFEDLTPGVYTLRVV 1320
                                     45678889****************997 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.014
                        DUF2012   15 dsgqqrkfkalvrrDGsFifrdlpegsYlLevesp 49  
                                     d+g+   ++a+++ DG ++f  l++g+Y +e++++
  gi|116754892|ref|YP_844010.1| 1386 DGGE---RTAVTADDGFYSFDRLSPGTYKIEAVKQ 1417
                                     4444...599********************99865 PP

  == domain 4  score: 7.9 bits;  conditional E-value: 0.0029
                        DUF2012    9 ntrvlLdsgqqrkfkalvrrDGsFifrdlpegsYlLev 46  
                                     + +v+L +g++++  + + +DG++ f+ l++g+Y +e+
  gi|116754892|ref|YP_844010.1| 1475 GWSVTLVQGENATSMTETGADGTYRFESLSPGTYRVEL 1512
                                     56899999999999*********************997 PP

  == domain 5  score: 9.9 bits;  conditional E-value: 0.0007
                        DUF2012   12 vlLdsgqqrkfkalvrrDGsFifrdlpegsYlLe 45  
                                     v L ++ +  +++++ +DG+++f ++ +g+Y++ 
  gi|116754892|ref|YP_844010.1| 1572 VNLIENGKVVRSTKTSEDGTYTFDNVAPGTYTIS 1605
                                     555333334799*******************985 PP

  == domain 6  score: 3.0 bits;  conditional E-value: 0.1
                        DUF2012   19 qrkfkalvrrDGsFifrdlpegsYlL 44  
                                     + + + ++ +DGs++f ++ +g+Y +
  gi|116754892|ref|YP_844010.1| 1678 HITETQYTGSDGSYTFGNIAPGTYKI 1703
                                     4455678889**************87 PP

  == domain 7  score: 5.9 bits;  conditional E-value: 0.012
                        DUF2012    9 ntrvlLdsgqqrkfkalvrrDGsFifrdlpegsYlL 44  
                                     + ++ ++++++ +++a + +DG ++f+ l +g+Y++
  gi|116754892|ref|YP_844010.1| 1770 GWEIRISNSTY-TRTAITDSDGWYNFTGLDAGTYTV 1804
                                     56778877777.9*********************97 PP

>> Big_3_3  Bacterial Ig-like domain (group 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0      0.02        21       4      49 ..     218     263 ..     215     280 .. 0.87
   2 ?    4.7   0.0      0.02        21       4      49 ..     312     357 ..     309     374 .. 0.87
   3 ?    4.7   0.0      0.02        21       4      49 ..     406     451 ..     403     468 .. 0.87
   4 ?   -2.0   0.0       2.4   2.5e+03       4      48 ..     500     547 ..     497     559 .. 0.76
   5 ?    4.7   0.0      0.02        21       4      49 ..     597     642 ..     594     659 .. 0.87
   6 ?   -2.0   0.0       2.4   2.5e+03       4      48 ..     691     738 ..     688     750 .. 0.76
   7 ?    0.3   0.0      0.45   4.8e+02       9      49 ..     793     833 ..     785     849 .. 0.80
   8 ?   -2.0   0.0       2.4   2.5e+03       4      48 ..     882     929 ..     879     941 .. 0.76
   9 ?   -2.0   0.0       2.4   2.5e+03       4      48 ..     979    1026 ..     976    1038 .. 0.76
  10 ?    5.3   0.0     0.014        14       7      66 ..    1400    1461 ..    1397    1472 .. 0.86
  11 ?   -3.7   0.0       7.6     8e+03       6      34 ..    1497    1525 ..    1496    1535 .. 0.81
  12 ?   -2.2   0.1       2.6   2.8e+03       8      46 ..    1813    1856 ..    1810    1862 .. 0.71
  13 ?    2.1   0.0      0.13   1.3e+02       4      50 ..    1901    1950 ..    1898    1963 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.02
                        Big_3_3   4 tvtfdlkelpeGkynlvlaakdtfnnqvtksllstilvdntpPtvs 49 
                                    t  ++  +   G+++++++ +d  n++v  s+++ti + n pP v+
  gi|116754892|ref|YP_844010.1| 218 TWRWSTTDADVGSHSVTVVVRDGKNEPVSASSQYTIIMPNRPPQVT 263
                                    66788888999********************************997 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.02
                        Big_3_3   4 tvtfdlkelpeGkynlvlaakdtfnnqvtksllstilvdntpPtvs 49 
                                    t  ++  +   G+++++++ +d  n++v  s+++ti + n pP v+
  gi|116754892|ref|YP_844010.1| 312 TWRWSTTDADVGSHSVTVVVRDGKNEPVSASSQYTIIMPNRPPQVT 357
                                    66788888999********************************997 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.02
                        Big_3_3   4 tvtfdlkelpeGkynlvlaakdtfnnqvtksllstilvdntpPtvs 49 
                                    t  ++  +   G+++++++ +d  n++v  s+++ti + n pP v+
  gi|116754892|ref|YP_844010.1| 406 TWRWSTTDADVGSHSVTVVVRDGKNEPVSASSQYTIIMPNRPPQVT 451
                                    66788888999********************************997 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 2.4
                        Big_3_3   4 tvtfdlkelpeGkynlvlaakdtfnnqvtksllsti...lvdntpPtv 48 
                                    t  ++  +   G+++++++ +d  n++v  s+++ i   +v n pP++
  gi|116754892|ref|YP_844010.1| 500 TWRWSTTDADVGSHSVTVVVRDGKNEPVSASSQYVIearVVPNDPPVI 547
                                    667888888899***999999999999999988766222355667776 PP

  == domain 5  score: 4.7 bits;  conditional E-value: 0.02
                        Big_3_3   4 tvtfdlkelpeGkynlvlaakdtfnnqvtksllstilvdntpPtvs 49 
                                    t  ++  +   G+++++++ +d  n++v  s+++ti + n pP v+
  gi|116754892|ref|YP_844010.1| 597 TWRWSTTDADVGSHSVTVVVRDGKNEPVSASSQYTIIMPNRPPQVT 642
                                    66788888999********************************997 PP

  == domain 6  score: -2.0 bits;  conditional E-value: 2.4
                        Big_3_3   4 tvtfdlkelpeGkynlvlaakdtfnnqvtksllsti...lvdntpPtv 48 
                                    t  ++  +   G+++++++ +d  n++v  s+++ i   +v n pP++
  gi|116754892|ref|YP_844010.1| 691 TWRWSTTDADVGSHSVTVVVRDGKNEPVSASSQYVIearVVPNDPPVI 738
                                    667888888899***999999999999999988766222355667776 PP

  == domain 7  score: 0.3 bits;  conditional E-value: 0.45
                        Big_3_3   9 lkelpeGkynlvlaakdtfnnqvtksllstilvdntpPtvs 49 
                                      +    +++++++ +d  n++v  s+++ti + n pP v+
  gi|116754892|ref|YP_844010.1| 793 TTDADVESHSVTVVVRDGKNEPVSASSQYTIIMPNRPPQVT 833
                                    555555678889999999999****************9987 PP

  == domain 8  score: -2.0 bits;  conditional E-value: 2.4
                        Big_3_3   4 tvtfdlkelpeGkynlvlaakdtfnnqvtksllsti...lvdntpPtv 48 
                                    t  ++  +   G+++++++ +d  n++v  s+++ i   +v n pP++
  gi|116754892|ref|YP_844010.1| 882 TWRWSTTDADVGSHSVTVVVRDGKNEPVSASSQYVIearVVPNDPPVI 929
                                    667888888899***999999999999999988766222355667776 PP

  == domain 9  score: -2.0 bits;  conditional E-value: 2.4
                        Big_3_3    4 tvtfdlkelpeGkynlvlaakdtfnnqvtksllsti...lvdntpPtv 48  
                                     t  ++  +   G+++++++ +d  n++v  s+++ i   +v n pP++
  gi|116754892|ref|YP_844010.1|  979 TWRWSTTDADVGSHSVTVVVRDGKNEPVSASSQYVIearVVPNDPPVI 1026
                                     667888888899***999999999999999988766222355667776 PP

  == domain 10  score: 5.3 bits;  conditional E-value: 0.014
                        Big_3_3    7 fdlkelpeGkynlvlaakdtfnnqvtksllstil.vdntpPtvsi.segkkisdgavvkgle 66  
                                     +++++l+ G+y+++++++d +  ++ k+ ++ +   d++ P+++  + g +   g+v+++++
  gi|116754892|ref|YP_844010.1| 1400 YSFDRLSPGTYKIEAVKQDGWSQTAPKTGSHSVEiKDTSVPSIDFgYAGLRSISGVVFNDIN 1461
                                     7889*****************9999888777775268999*****99999999999998875 PP

  == domain 11  score: -3.7 bits;  conditional E-value: 7.6
                        Big_3_3    6 tfdlkelpeGkynlvlaakdtfnnqvtks 34  
                                     t+ +++l+ G+y ++l  +d ++ +++  
  gi|116754892|ref|YP_844010.1| 1497 TYRFESLSPGTYRVELIPQDGWKATTESR 1525
                                     688999*******9999999988877655 PP

  == domain 12  score: -2.2 bits;  conditional E-value: 2.6
                        Big_3_3    8 dlkelpeGkynlvlaakdt.....fnnqvtksllstilvdntpP 46  
                                     ++ + + G+y+++l+a +t     f+n   + +  t+++d+t+P
  gi|116754892|ref|YP_844010.1| 1813 SVTKPSGGSYTITLNAGETktgvdFGNYKSLPTGATLTSDKTSP 1856
                                     56666778999888776652233366777888888889999888 PP

  == domain 13  score: 2.1 bits;  conditional E-value: 0.13
                        Big_3_3    4 tvtfdlkelpeGkynlvlaakdtfnn...qvtksllstilvdntpPtvsi 50  
                                     t  ++   l  G+y + + ++d ++     v+++ ++t++  n pP +++
  gi|116754892|ref|YP_844010.1| 1901 TWSWNTGGLEPGTYDIRVWIRDSYHSetgDVQVTKSFTLKETNRPPDLRL 1950
                                     6789999999**************98555677888888999999**9998 PP

>> Dioxygenase_C  Dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.62   6.6e+02      80     100 ..    1203    1223 ..    1196    1231 .. 0.85
   2 ?    1.5   0.0      0.16   1.7e+02      79      99 ..    1298    1318 ..    1285    1322 .. 0.85
   3 ?    4.1   0.0     0.025        27      76     100 ..    1390    1414 ..    1381    1429 .. 0.84
   4 ?    3.5   0.0      0.04        42      78      99 ..    1490    1511 ..    1479    1522 .. 0.80
   5 ?    4.7   0.0     0.017        18      76     100 ..    1582    1606 ..    1569    1617 .. 0.82
   6 ?    3.0   0.1     0.059        62      79     100 ..    1684    1705 ..    1674    1715 .. 0.86
   7 ?    4.4   0.0     0.022        23      72     100 ..    1778    1806 ..    1759    1811 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.62
                                     --TTSEEEEEEE----EE--T CS
                  Dioxygenase_C   80 tdeeGryrirtikPapYpipn 100 
                                     t  +G+yr++ + P+ Y +++
  gi|116754892|ref|YP_844010.1| 1203 TGFDGYYRFEGLAPGLYTVRE 1223
                                     6679*************9986 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.16
                                     E--TTSEEEEEEE----EE-- CS
                  Dioxygenase_C   79 ltdeeGryrirtikPapYpip 99  
                                      t ++G+yr++ + P+ Y ++
  gi|116754892|ref|YP_844010.1| 1298 TTGDDGSYRFEDLTPGVYTLR 1318
                                     5789**************876 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.025
                                     EEEE--TTSEEEEEEE----EE--T CS
                  Dioxygenase_C   76 griltdeeGryrirtikPapYpipn 100 
                                     ++ +t ++G y++  + P++Y+i+ 
  gi|116754892|ref|YP_844010.1| 1390 RTAVTADDGFYSFDRLSPGTYKIEA 1414
                                     7899*****************9975 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.04
                                     EE--TTSEEEEEEE----EE-- CS
                  Dioxygenase_C   78 iltdeeGryrirtikPapYpip 99  
                                     + t ++G+yr++++ P++Y ++
  gi|116754892|ref|YP_844010.1| 1490 TETGADGTYRFESLSPGTYRVE 1511
                                     55789**************864 PP

  == domain 5  score: 4.7 bits;  conditional E-value: 0.017
                                     EEEE--TTSEEEEEEE----EE--T CS
                  Dioxygenase_C   76 griltdeeGryrirtikPapYpipn 100 
                                     +++ t e+G+y +  + P++Y i +
  gi|116754892|ref|YP_844010.1| 1582 RSTKTSEDGTYTFDNVAPGTYTISD 1606
                                     778899***************9987 PP

  == domain 6  score: 3.0 bits;  conditional E-value: 0.059
                                     E--TTSEEEEEEE----EE--T CS
                  Dioxygenase_C   79 ltdeeGryrirtikPapYpipn 100 
                                      t ++G+y +  i P++Y+i +
  gi|116754892|ref|YP_844010.1| 1684 YTGSDGSYTFGNIAPGTYKISE 1705
                                     6889**************9975 PP

  == domain 7  score: 4.4 bits;  conditional E-value: 0.022
                                     TTTEEEEE--TTSEEEEEEE----EE--T CS
                  Dioxygenase_C   72 lnlrgriltdeeGryrirtikPapYpipn 100 
                                        +++ +td++G y+++ +  ++Y + +
  gi|116754892|ref|YP_844010.1| 1778 STYTRTAITDSDGWYNFTGLDAGTYTVTE 1806
                                     556799*******************9865 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 ?   -2.8   0.0       5.3   5.6e+03      30      49 ..    1202    1221 ..    1199    1240 .. 0.81
   2 ?    5.1   0.1     0.018        19      29      70 ..    1297    1339 ..    1283    1344 .. 0.85
   3 ?    4.0   0.0     0.041        44      30      67 ..    1393    1434 ..    1390    1440 .. 0.75
   4 !    9.1   0.1     0.001       1.1      14      67 ..    1477    1529 ..    1466    1533 .. 0.80
   5 !   13.6   1.9     4e-05     0.042      29      73 ..    1584    1628 ..    1583    1630 .. 0.81
   6 !    6.7   0.1    0.0057         6      30      50 ..    1684    1704 ..    1672    1730 .. 0.83
   7 ?    4.4   1.2     0.029        31      20      73 ..    1777    1832 ..    1761    1834 .. 0.74
   8 ?    0.7   0.2      0.42   4.4e+02      36      69 ..    1903    1935 ..    1849    1940 .. 0.74
   9 ?   -0.9   0.2       1.3   1.4e+03      43      57 ..    2229    2243 ..    2195    2249 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 5.3
                          fn3_3   30 eadssgsftipnVkpGtYrl 49  
                                     ++  +g+++++   pG Y++
  gi|116754892|ref|YP_844010.1| 1202 TTGFDGYYRFEGLAPGLYTV 1221
                                     5555799***********97 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.018
                          fn3_3   29 teadssgsftipnVkpGtYrlt.vYadglfgdykqdsvtVtag 70  
                                     +++ ++gs+++++  pG Y+l  v ++g  +    ++v++t  
  gi|116754892|ref|YP_844010.1| 1297 ATTGDDGSYRFEDLTPGVYTLRvVLQPGWNVSISSKDVSITDT 1339
                                     566778***************8678899988888999999865 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.041
                          fn3_3   30 eadssgsftipnVkpGtYrltvYadglfgdy...k.qdsvtV 67  
                                      ++++g +++++  pGtY+  + ++ ++ ++   +   sv++
  gi|116754892|ref|YP_844010.1| 1393 VTADDGFYSFDRLSPGTYKIEAVKQDGWSQTapkTgSHSVEI 1434
                                     45567**************99988888877755335555555 PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.001
                          fn3_3   14 svvsfqnetkayQYwteadssgsftipnVkpGtYrltvYadglfgdyk.qdsvtV 67  
                                     sv+ +q+e  ++   te+ ++g++++++  pGtYr+ +  + ++ +++   ++++
  gi|116754892|ref|YP_844010.1| 1477 SVTLVQGE--NATSMTETGADGTYRFESLSPGTYRVELIPQDGWKATTeSREIQI 1529
                                     57788999..99999********************99766666656654555555 PP

  == domain 5  score: 13.6 bits;  conditional E-value: 4e-05
                          fn3_3   29 teadssgsftipnVkpGtYrltvYadglfgdykqdsvtVtagktt 73  
                                     t+++++g++t++nV pGtY+ +   +++ +  + +++tVt  ++t
  gi|116754892|ref|YP_844010.1| 1584 TKTSEDGTYTFDNVAPGTYTISDPLPEGYVVVTSSTITVTVTTNT 1628
                                     8999*****************977777777766888888865555 PP

  == domain 6  score: 6.7 bits;  conditional E-value: 0.0057
                          fn3_3   30 eadssgsftipnVkpGtYrlt 50  
                                     ++ s+gs+t+ n+ pGtY+ +
  gi|116754892|ref|YP_844010.1| 1684 YTGSDGSYTFGNIAPGTYKIS 1704
                                     45678*************875 PP

  == domain 7  score: 4.4 bits;  conditional E-value: 0.029
                          fn3_3   20 netkayQYwteadssgsftipnVkpGtYrlt.vYadglfgdyk...qdsvtVtagktt 73  
                                     n+   y  ++ +ds+g + ++   +GtY++t   ++g  +        ++t +ag+t+
  gi|116754892|ref|YP_844010.1| 1777 NS--TYTRTAITDSDGWYNFTGLDAGTYTVTeTLKPGWSVTKPsggSYTITLNAGETK 1832
                                     33..44445666999****************788888887773345777777788876 PP

  == domain 8  score: 0.7 bits;  conditional E-value: 0.42
                          fn3_3   36 sftipnVkpGtYrltvYadglfgdykqdsvtVta 69  
                                     s+      pGtY   v+         + +v+Vt+
  gi|116754892|ref|YP_844010.1| 1903 SWNTGGLEPGTYDIRVWIRDSYHSE-TGDVQVTK 1935
                                     67777889*********87666333.58888886 PP

  == domain 9  score: -0.9 bits;  conditional E-value: 1.3
                          fn3_3   43 kpGtYrltvYadglf 57  
                                      +G+Y++ vY+  + 
  gi|116754892|ref|YP_844010.1| 2229 DAGDYTVFVYVRDGK 2243
                                     58********98765 PP

>> DUF1416  Protein of unknown function (DUF1416)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0037       3.9      52      95 ..    1202    1246 ..    1177    1247 .. 0.82
   2 ?    2.3   0.0      0.15   1.5e+02      51      77 ..    1297    1324 ..    1270    1342 .. 0.70
   3 ?   -0.7   0.0       1.3   1.4e+03      46      85 ..    1389    1427 ..    1366    1439 .. 0.67
   4 ?    2.7   0.1      0.11   1.2e+02      29      81 ..    1469    1521 ..    1456    1537 .. 0.71
   5 ?    2.3   0.0      0.14   1.5e+02      25      71 ..    1558    1605 ..    1554    1629 .. 0.77
   6 ?   -0.1   0.0       0.8   8.5e+02      52      82 ..    1684    1715 ..    1650    1727 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0037
                        DUF1416   52 vtsaeGefrFfa.apGeWtvRalarkgngdaeveaesggvaevev 95  
                                     +t+ +G +rF   apG +tvR l+++g   ++ e+++ ++++ +v
  gi|116754892|ref|YP_844010.1| 1202 TTGFDGYYRFEGlAPGLYTVRELQKAGWDSTTSESQQVNLTDSDV 1246
                                     456689****7549**************99999999988888776 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.15
                        DUF1416   51 vvtsaeGefrFfa.apGeWtvRalarkg 77  
                                      +t+++G++rF   +pG +t+R++ + g
  gi|116754892|ref|YP_844010.1| 1297 ATTGDDGSYRFEDlTPGVYTLRVVLQPG 1324
                                     357899*****7538*******988766 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.3
                        DUF1416   46 eFtaevvtsaeGefrFf.aapGeWtvRalarkgngdaevea 85  
                                     e ta  vt+++G + F   +pG++++ a++++g ++++ ++
  gi|116754892|ref|YP_844010.1| 1389 ERTA--VTADDGFYSFDrLSPGTYKIEAVKQDGWSQTAPKT 1427
                                     4444..67888888885258999999999999987765544 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.11
                        DUF1416   29 dgepvggayvRLLdssgeFtaevvtsaeGefrFfa.apGeWtvRalarkgngda 81  
                                     +++ v g  v L++  ++ t+   t+a+G++rF + +pG+++v  + ++g + +
  gi|116754892|ref|YP_844010.1| 1469 GETGVRGWSVTLVQ-GENATSMTETGADGTYRFESlSPGTYRVELIPQDGWKAT 1521
                                     45556665555554.456788899*********7648******99988886443 PP

  == domain 5  score: 2.3 bits;  conditional E-value: 0.14
                        DUF1416   25 kvtrdgep.vggayvRLLdssgeFtaevvtsaeGefrF.faapGeWtvR 71  
                                     kv ++gep + g+ v L++ +g  +    ts++G++ F   apG++t+ 
  gi|116754892|ref|YP_844010.1| 1558 KVRDEGEPgIPGSDVNLIE-NGKVVRSTKTSEDGTYTFdNVAPGTYTIS 1605
                                     5666666657788888775.68999999**********5579****986 PP

  == domain 6  score: -0.1 bits;  conditional E-value: 0.8
                        DUF1416   52 vtsaeGefrF.faapGeWtvRalarkgngdae 82  
                                      t+++G++ F   apG++++  l+r g ++++
  gi|116754892|ref|YP_844010.1| 1684 YTGSDGSYTFgNIAPGTYKISELSRPGWTQTH 1715
                                     47889999995579**********99987654 PP

>> Y_Y_Y  Y_Y_Y domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1         8   8.5e+03      30      43 ..    1208    1221 ..    1199    1222 .. 0.79
   2 ?    4.1   0.0     0.044        46      23      45 ..    1298    1319 ..    1292    1321 .. 0.88
   3 ?    5.0   0.0     0.023        24      26      54 ..    1396    1423 ..    1387    1435 .. 0.73
   4 ?    3.7   0.0     0.059        62      22      44 ..    1490    1511 ..    1485    1513 .. 0.86
   5 ?    5.6   0.1     0.015        16      20      43 ..    1579    1604 ..    1574    1605 .. 0.78
   6 ?    3.5   0.3     0.067        71      20      43 ..    1681    1703 ..    1678    1704 .. 0.86
   7 ?    1.4   0.2       0.3   3.2e+02      25      43 ..    1787    1804 ..    1771    1805 .. 0.73
   8 !    8.4   0.2     0.002       2.1      10      64 ..    1877    1938 ..    1874    1940 .. 0.71
   9 ?   -1.1   0.0       1.8   1.9e+03      42      60 ..    2019    2037 ..    2014    2043 .. 0.85
  10 ?    4.7   0.5     0.028        29       8      51 ..    2194    2243 ..    2190    2254 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 8
                                     EEEEES--SEEEEE CS
                          Y_Y_Y   30 easytnlppGdYtl 43  
                                      + +  l pG Yt+
  gi|116754892|ref|YP_844010.1| 1208 YYRFEGLAPGLYTV 1221
                                     57899999**9997 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.044
                                     EESSTS.EEEEES--SEEEEEEE CS
                          Y_Y_Y   23 easdysqeasytnlppGdYtlkV 45  
                                     +++d + ++ +  l pG Ytl+V
  gi|116754892|ref|YP_844010.1| 1298 TTGDDG-SYRFEDLTPGVYTLRV 1319
                                     678888.9*************98 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.023
                                     STS.EEEEES--SEEEEEEEEEEETTS-B CS
                          Y_Y_Y   26 dysqeasytnlppGdYtlkVkakdndgqw 54  
                                     d + ++s+  l+pG+Y++++   d  +q 
  gi|116754892|ref|YP_844010.1| 1396 DDG-FYSFDRLSPGTYKIEAVKQDGWSQT 1423
                                     444.89************98666655555 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.059
                                     EEESSTS.EEEEES--SEEEEEE CS
                          Y_Y_Y   22 veasdysqeasytnlppGdYtlk 44  
                                     +e+++ + ++ +  l+pG+Y+++
  gi|116754892|ref|YP_844010.1| 1490 TETGADG-TYRFESLSPGTYRVE 1511
                                     5778888.9***********986 PP

  == domain 5  score: 5.6 bits;  conditional E-value: 0.015
                                     SEEEESSTS...EEEEES--SEEEEE CS
                          Y_Y_Y   20 eWveasdysq..easytnlppGdYtl 43  
                                     + v +++ s   ++++ n  pG+Yt+
  gi|116754892|ref|YP_844010.1| 1579 KVVRSTKTSEdgTYTFDNVAPGTYTI 1604
                                     555666666677*************8 PP

  == domain 6  score: 3.5 bits;  conditional E-value: 0.067
                                     SEEEESSTS.EEEEES--SEEEEE CS
                          Y_Y_Y   20 eWveasdysqeasytnlppGdYtl 43  
                                     e +++++ + ++++ n  pG+Y++
  gi|116754892|ref|YP_844010.1| 1681 ETQYTGSDG-SYTFGNIAPGTYKI 1703
                                     556778888.************98 PP

  == domain 7  score: 1.4 bits;  conditional E-value: 0.3
                                     SSTS.EEEEES--SEEEEE CS
                          Y_Y_Y   25 sdysqeasytnlppGdYtl 43  
                                     ++ +  +++t l +G+Yt+
  gi|116754892|ref|YP_844010.1| 1787 DSDG-WYNFTGLDAGTYTV 1804
                                     3333.99**********97 PP

  == domain 8  score: 8.4 bits;  conditional E-value: 0.002
                                     EEEEEETTE..SSEEEESSTS...EEEEE..S--SEEEEEEEEEEETTS-B-SS-.EEEEEE CS
                          Y_Y_Y   10 YrYrlegid..keWveasdysq..easyt..nlppGdYtlkVkakdndgqwnydi.tslsft 64  
                                     Y+++l+g +  + W+e ++ s+  + s++   l+pG+Y ++V ++d++ ++  d   + sft
  gi|116754892|ref|YP_844010.1| 1877 YSFWLKGPStsGLWQEKRSWSSdnTWSWNtgGLEPGTYDIRVWIRDSYHSETGDVqVTKSFT 1938
                                     777777766445577666666666555552269***************99998876666665 PP

  == domain 9  score: -1.1 bits;  conditional E-value: 1.8
                                     EEEEEEEETTS-B-SS-EE CS
                          Y_Y_Y   42 tlkVkakdndgqwnydits 60  
                                     +++V++kd + + +yd+++
  gi|116754892|ref|YP_844010.1| 2019 EIMVYVKDGKHSPDYDDKR 2037
                                     79********999999955 PP

  == domain 10  score: 4.7 bits;  conditional E-value: 0.028
                                     EEEEEEEETTE..SSEEEESSTS.....EEEEES--SEEEEEEEEEEETT CS
                          Y_Y_Y    8 llYrYrlegid..keWveasdysq....easytnlppGdYtlkVkakdnd 51  
                                     ++Yr++l+g +  + W+  +d s+    + s     +GdYt+ V+++d +
  gi|116754892|ref|YP_844010.1| 2194 IYYRFWLKGPStgNTWQIVRDWSTsntwTWSSDLGDAGDYTVFVYVRDGK 2243
                                     7999999999988899999998887744444445689**********965 PP

>> DUF3324  Protein of unknown function C-terminal (DUF3324)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.42   4.4e+02     100     134 ..    1308    1342 ..    1304    1345 .. 0.87
   2 ?   -3.0   0.0       6.2   6.5e+03     100     113 ..    1403    1416 ..    1401    1434 .. 0.80
   3 ?   -1.9   0.0       2.9   3.1e+03     100     130 ..    1501    1531 ..    1497    1534 .. 0.79
   4 ?    5.4   0.0     0.016        17      94     132 ..    1901    1943 ..    1897    1945 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.42
                        DUF3324  100 eelkaGtYtlkvtakskkkkwefekeFtIteeeak 134 
                                     e l++G Ytl+v ++ + +    +k+++It+++ +
  gi|116754892|ref|YP_844010.1| 1308 EDLTPGVYTLRVVLQPGWNVSISSKDVSITDTDQS 1342
                                     689**************999999999999998765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6.2
                        DUF3324  100 eelkaGtYtlkvta 113 
                                     ++l +GtY+++   
  gi|116754892|ref|YP_844010.1| 1403 DRLSPGTYKIEAVK 1416
                                     6899*****98754 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 2.9
                        DUF3324  100 eelkaGtYtlkvtakskkkkwefekeFtIte 130 
                                     e+l +GtY++++  + + k  + ++e++I +
  gi|116754892|ref|YP_844010.1| 1501 ESLSPGTYRVELIPQDGWKATTESREIQIGT 1531
                                     6899******998888877777777777765 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.016
                        DUF3324   94 pislkgeelkaGtYtlkvtaksk....kkkwefekeFtIteee 132 
                                     + s+++  l++GtY ++v ++ +      + +++k+Ft +e++
  gi|116754892|ref|YP_844010.1| 1901 TWSWNTGGLEPGTYDIRVWIRDSyhseTGDVQVTKSFTLKETN 1943
                                     6789**************998887777899999****999875 PP

>> DUF2846  Protein of unknown function (DUF2846)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       2.3   2.4e+03      38      57 ..    1397    1416 ..    1388    1433 .. 0.79
   2 ?   -1.0   0.0       1.8   1.9e+03      37      55 ..    1494    1512 ..    1485    1536 .. 0.80
   3 ?    2.6   0.0      0.13   1.4e+02      36      54 ..    1587    1605 ..    1577    1628 .. 0.86
   4 ?    2.3   0.0      0.16   1.7e+02      37      55 ..    1687    1705 ..    1670    1736 .. 0.85
   5 ?   -3.4   0.0       9.8     1e+04      69      80 ..    2338    2349 ..    2321    2357 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.3
                        DUF2846   38 nkeYfvaevepGeykister 57  
                                     ++ Y + +++pG+yki+  +
  gi|116754892|ref|YP_844010.1| 1397 DGFYSFDRLSPGTYKIEAVK 1416
                                     456788999******98655 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.8
                        DUF2846   37 ankeYfvaevepGeykist 55  
                                     a+++Y ++ ++pG+y+++ 
  gi|116754892|ref|YP_844010.1| 1494 ADGTYRFESLSPGTYRVEL 1512
                                     6799***********9864 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.13
                        DUF2846   36 lankeYfvaevepGeykis 54  
                                     +++++Y++ +v+pG+y+is
  gi|116754892|ref|YP_844010.1| 1587 SEDGTYTFDNVAPGTYTIS 1605
                                     46799************97 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.16
                        DUF2846   37 ankeYfvaevepGeykist 55  
                                     ++++Y++ +++pG+ykis 
  gi|116754892|ref|YP_844010.1| 1687 SDGSYTFGNIAPGTYKISE 1705
                                     5799************985 PP

  == domain 5  score: -3.4 bits;  conditional E-value: 9.8
                        DUF2846   69 eaGkvyylrydi 80  
                                       Gk+yy+ y  
  gi|116754892|ref|YP_844010.1| 2338 YDGKNYYVVYVS 2349
                                     57999*998755 PP

>> PDZ_5  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.24   2.5e+02      57      73 .]     523     539 ..     512     539 .. 0.86
   2 ?    2.0   0.0      0.24   2.5e+02      57      73 .]     714     730 ..     703     730 .. 0.86
   3 ?    2.0   0.0      0.24   2.5e+02      57      73 .]     905     921 ..     894     921 .. 0.86
   4 ?    2.0   0.0      0.24   2.5e+02      57      73 .]    1002    1018 ..     991    1018 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.24
                          PDZ_5  57 dvDPvaAsAEYELEkRv 73 
                                      +Pv+As  Y +E Rv
  gi|116754892|ref|YP_844010.1| 523 KNEPVSASSQYVIEARV 539
                                    557************98 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.24
                          PDZ_5  57 dvDPvaAsAEYELEkRv 73 
                                      +Pv+As  Y +E Rv
  gi|116754892|ref|YP_844010.1| 714 KNEPVSASSQYVIEARV 730
                                    557************98 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.24
                          PDZ_5  57 dvDPvaAsAEYELEkRv 73 
                                      +Pv+As  Y +E Rv
  gi|116754892|ref|YP_844010.1| 905 KNEPVSASSQYVIEARV 921
                                    557************98 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.24
                          PDZ_5   57 dvDPvaAsAEYELEkRv 73  
                                       +Pv+As  Y +E Rv
  gi|116754892|ref|YP_844010.1| 1002 KNEPVSASSQYVIEARV 1018
                                     557************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (2656 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 1.14u 0.32s 00:00:01.46 Elapsed: 00:00:00.47
# Mc/sec: 16963.06
//
Query:       gi|116754893|ref|YP_844011.1|  [L=373]
Description: cell division control protein 6 [Methanosaeta thermophila PT]
Scores for 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-11   42.8   0.2      3e-08   34.3   0.0    3.1  2  AAA_16    AAA ATPase domain
    6.4e-09   35.7   0.1    2.6e-08   33.7   0.1    2.1  2  Cdc6_C    CDC6, C terminal winged helix domain
    1.5e-07   31.8   0.0    3.1e-07   30.7   0.0    1.5  1  AAA_22    AAA domain
      0.001   19.5   0.0     0.0024   18.3   0.0    1.6  1  AAA       ATPase family associated with various cellular acti
     0.0023   17.5   0.0     0.0041   16.7   0.0    1.4  1  AAA_7     P-loop containing dynein motor region
     0.0029   17.4   0.0     0.0057   16.5   0.0    1.4  1  AAA_11    AAA domain
     0.0078   15.9   0.0      0.035   13.8   0.0    1.9  2  AAA_30    AAA domain
     0.0098   15.8   0.2      0.026   14.5   0.1    1.7  2  PadR      Transcriptional regulator PadR-like family
  ------ inclusion threshold ------
      0.022   14.9   0.5        1.1    9.4   0.0    3.3  4  TIP49_C   TIP49 AAA-lid domain
      0.031   13.5   0.0       0.55    9.4   0.0    2.1  2  DUF815    Protein of unknown function (DUF815)
      0.063   13.4   0.1       0.18   11.9   0.1    1.7  1  HTH_AraC  Bacterial regulatory helix-turn-helix proteins, Ara
       0.11   12.8   0.0       0.21   11.9   0.0    1.4  1  AAA_19    AAA domain
       0.15   11.2   0.0       0.26   10.4   0.0    1.3  1  NB-ARC    NB-ARC domain
       0.18   11.7   0.0       0.35   10.8   0.0    1.4  1  NTPase_1  NTPase
       0.18   11.0   0.0       0.31   10.3   0.0    1.3  1  DUF2075   Uncharacterized conserved protein (DUF2075)
        0.2   11.2   0.0       0.34   10.5   0.0    1.3  1  SRP54     SRP54-type protein, GTPase domain


Domain annotation for each model (and alignments):
>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.0   2.6e-11     3e-08       2      76 ..      28     103 ..      27     175 .. 0.81
   2 ?    1.9   0.0      0.24   2.7e+02     107     137 ..     265     297 ..     181     339 .. 0.72

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 2.6e-11
                         AAA_16   2 lvGReeeleqLlsalervrsgrp.elvllsGesGvGKsslvrellralekdggif..lrgkcdqlesaipysalaqal 76 
                                    +  R+++++ L+ +++++ +g    + l+ G++G+GK++ + +l++++ek+   +  +  +c+    +++ys++ ++ 
  gi|116754893|ref|YP_844011.1|  28 FDHRDAQMKSLRFCVRPALRGARpVNALCLGPPGTGKTTAIIKLFEEIEKHTRSVipVHINCQID--GTRYSIFSRIY 103
                                    678*************77777666***************************53333588888888..78887777766 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.24
                         AAA_16 107 avpelagaea..srllellkrllallsrderpl 137
                                    +++e++ ++a  ++ + +l + l+ lsrder+l
  gi|116754893|ref|YP_844011.1| 265 SISEDDVKKAfeRSRFLHLEHVLRSLSRDERTL 297
                                    233333333344666666677777777767653 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 ?   -2.4   0.0       4.5     5e+03      31      53 ..     198     220 ..     197     221 .. 0.83
   2 !   33.7   0.1   2.4e-11   2.6e-08       4      82 ..     297     368 ..     295     370 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 4.5
                                    HTT-----HHHHHHHHHHHHHTT CS
                         Cdc6_C  31 segvdpltqrevsdllseLemlg 53 
                                    + ++ p ++ e+  +ls+ + lg
  gi|116754893|ref|YP_844011.1| 198 EIQFPPYKRDEIFAILSRRAQLG 220
                                    568899999*****999988777 PP

  == domain 2  score: 33.7 bits;  conditional E-value: 2.4e-11
                                    HHHHHCHCSSS-EEHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSSCHHHH CS
                         Cdc6_C   4 lvlllrksgkeevttgevyevYkslCesegvdpltqrevsdllseLemlgileleksskGrregrtrkisLnvdpddvl 82 
                                    l+++  ++ +  +++ge+y  Y++++ s        + ++++l++Le+l+++e+   + G+r gr+r i+L++dp +vl
  gi|116754893|ref|YP_844011.1| 297 LLRIVAEQPEGKAQSGELYSIYHEVAHS------GYTKFYEILKRLEALRLIETSFTGSGMR-GRSRIIRLRYDPTEVL 368
                                    677777789999**************99......889************************7.*************997 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.0   2.8e-10   3.1e-07       9     115 ..      55     159 ..      51     186 .. 0.80

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 2.8e-10
                         AAA_22   9 vvtGesGtGKTtllrrlleqldeeakaeeerpevv..fvtlpsstsskdllrellralglelka.erlsseellealeqa 85 
                                    ++ G++GtGKTt + +l+e+ +++       ++v+  +++++ ++++ ++++++ +++   +   ++ s ++l+++++  
  gi|116754893|ref|YP_844011.1|  55 LCLGPPGTGKTTAIIKLFEEIEKH------TRSVIpvHINCQIDGTRYSIFSRIYKKIFGVTPPsSGISFKRLFDKIAST 128
                                    899*****************9665......8888899*************999998766544445999************ PP

                         AAA_22  86 lraravielliiDEaqhlr.seealeeLrsl 115
                                    l +r ++ ++ +D++ +l+ ++e+   L ++
  gi|116754893|ref|YP_844011.1| 129 LASREAVLIVALDDVSYLFpEKEIDHILYTF 159
                                    *99999888899*****98644433333433 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   2.1e-06    0.0024       2      97 ..      55     164 ..      54     195 .. 0.56

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.1e-06
                                    EEESSTTSSHHHHHHHHHHHHTHE...................EEEEETTTCSSS..........STTHHHHHHHHHHHH CS
                            AAA   2 llyGppGtGKTllakavakelgve...................fleisgsellsk..........yvgesekkirelfke 52 
                                    l  GppGtGKT+++  + +e++ +                   +                     +   s  +++ lf++
  gi|116754893|ref|YP_844011.1|  55 LCLGPPGTGKTTAIIKLFEEIEKHtrsvipvhincqidgtrysI----------FsriykkifgvTPPSSGISFKRLFDK 124
                                    678*****************853322333333322222222222..........03344443333333333344444444 PP

                                    .HHHTS....TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTT CS
                            AAA  53 .akeka....kpsilfiDEidalaksrsgseseeeervvnqLlteldgvk 97 
                                     a++      +  i+ +D++  l++++         ++   L+t+l   +
  gi|116754893|ref|YP_844011.1| 125 iAST-LasreAVLIVALDDVSYLFPEK---------EIDHILYTFLRSHE 164
                                    2222.2355335899999999999888.........45555555555554 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 !   16.7   0.0   3.6e-06    0.0041      35      88 ..      53     104 ..      35     125 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.6e-06
                          AAA_7  35 pvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiiesklek 88 
                                    + l+ Gp GtGKt+ i +l+++++k + +++ + ++ q +   ++  i s++ k
  gi|116754893|ref|YP_844011.1|  53 NALCLGPPGTGKTTAIIKLFEEIEKHTRSVIPVHINCQIDG--TRYSIFSRIYK 104
                                    679*********************77766666666665543..44455555555 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   5.1e-06    0.0057      20      44 ..      54      78 ..      32     105 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.1e-06
                         AAA_11 20 tliqGPPGtgKTktivellsqllsr 44
                                   +l  GPPGtgKT++i++l++++ ++
  gi|116754893|ref|YP_844011.1| 54 ALCLGPPGTGKTTAIIKLFEEIEKH 78
                                   5778****************99544 PP

>> AAA_30  AAA 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     0.035      22      50 ..      55      83 ..      42      88 .. 0.85
   2 ?   -0.8   0.0      0.95   1.1e+03     160     180 ..     257     277 ..     234     309 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.1e-05
                         AAA_30 22 vltGpAGtGKttalkalreaweaaggrvi 50
                                   +  Gp+GtGKtta+ +l e +e++ ++vi
  gi|116754893|ref|YP_844011.1| 55 LCLGPPGTGKTTAIIKLFEEIEKHTRSVI 83
                                   678**************999999998887 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.95
                         AAA_30 160 seeraaalalregdaeealea 180
                                    ++er+a++ ++e+d+++a+e+
  gi|116754893|ref|YP_844011.1| 257 EAERRASRSISEDDVKKAFER 277
                                    677888888888888876554 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       6.6   7.4e+03      15      41 ..      71     102 ..      69     105 .. 0.66
   2 !   14.5   0.1   2.3e-05     0.026       1      58 [.     297     354 ..     297     360 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 6.6
                                    HHHHHHCCSTT-CCTT.....HHHHHHHHHHH CS
                           PadR  15 iikeleelsegllels.....eGslYpaLkrL 41 
                                    + +e+e+++  ++ ++     +G+ Y +++r 
  gi|116754893|ref|YP_844011.1|  71 LFEEIEKHTRSVIPVHincqiDGTRYSIFSRI 102
                                    66777888777666666566677777777765 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 2.3e-05
                                    HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-S.TSSS CS
                           PadR   1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglvesewees.gegp 58 
                                    +L +++eqp  G +   el   ++++    +++ Y +LkrLe+ +l+e++ + s  +g+
  gi|116754893|ref|YP_844011.1| 297 LLRIVAEQP-EGKAQSGELYSIYHEVAHSGYTKFYEILKRLEALRLIETSFTGSgMRGR 354
                                    578888888.78888899999999999999*******************9988844444 PP

>> TIP49_C  TIP49 AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       1.7   1.9e+03      28      34 ..      36      42 ..      32      43 .. 0.83
   2 ?   -3.1   0.0         8   8.9e+03      39      57 ..     125     143 ..     124     145 .. 0.83
   3 ?    1.0   0.0      0.43   4.8e+02      26      34 ..     178     186 ..     174     187 .. 0.83
   4 ?    9.4   0.0   0.00099       1.1      13      61 ..     226     275 ..     212     276 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.7
                        TIP49_C 28 tSLRYai 34
                                   +SLR+++
  gi|116754893|ref|YP_844011.1| 36 KSLRFCV 42
                                   7*****8 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 8
                        TIP49_C  39 pasilakkrkkkevevedv 57 
                                    +as+la+++   +v+++dv
  gi|116754893|ref|YP_844011.1| 125 IASTLASREAVLIVALDDV 143
                                    6889999999999999998 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.43
                        TIP49_C  26 tetSLRYai 34 
                                    +etSLRY +
  gi|116754893|ref|YP_844011.1| 178 SETSLRYIL 186
                                    79*****75 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.00099
                        TIP49_C  13 ldeeAldlLakigtetS.LRYaiqLltpasilakkrkkkevevedveeve 61 
                                    l+ + ld+ +++  e++ LR  i Ll+ + + a++r +++++ +dv+++ 
  gi|116754893|ref|YP_844011.1| 226 LSRDVLDVVVDLTAESGdLRVGIDLLKRSCLEAERRASRSISEDDVKKAF 275
                                    567778888888777755*****************************986 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00049      0.55      34      88 ..      32      86 ..      18     104 .. 0.88
   2 ?    1.6   0.1      0.11   1.3e+02      95     122 ..     122     149 ..     117     162 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00049
                         DUF815 34 dkqkealventeqfleglpannvLLwGarGtGKSslvkallneyaeegLrlieve 88
                                   d+q ++l   ++  l+g++  n+L  G  GtGK + +  l++e+++++  +i v+
  gi|116754893|ref|YP_844011.1| 32 DAQMKSLRFCVRPALRGARPVNALCLGPPGTGKTTAIIKLFEEIEKHTRSVIPVH 86
                                   778888888899999****************************999988777765 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.11
                         DUF815  95 lpklvellrerperfilfvDDLsFeeee 122
                                    ++k+ ++l++r+  +i+ +DD+s+   e
  gi|116754893|ref|YP_844011.1| 122 FDKIASTLASREAVLIVALDDVSYLFPE 149
                                    6789999****************85544 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 ?   11.9   0.1   0.00016      0.18      23      37 ..      97     111 ..      96     112 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00016
                                    HHHHHHHHHHSSS-H CS
                       HTH_AraC  23 syFsrlFkketGmtP 37 
                                    s Fsr++kk++G+tP
  gi|116754893|ref|YP_844011.1|  97 SIFSRIYKKIFGVTP 111
                                    78************9 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00019      0.21      12      38 ..      53      79 ..      43      95 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00019
                         AAA_19 12 vllvtaGpGtGKTrvlkhivallvelg 38
                                   + l +++pGtGKT+ + +  +++++ +
  gi|116754893|ref|YP_844011.1| 53 NALCLGPPGTGKTTAIIKLFEEIEKHT 79
                                   56889*********9999888877655 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00023      0.26      26     112 ..      57     143 ..      53     163 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00023
                                    EESTTSSHHHHHHHHCCSHCCCCCCBTEEEEEEEESXX..HHHHHHHXXHHHHHCCCTTSSSS-STTSHHHHHHHHCCCT CS
                         NB-ARC  26 vGmgGvGKttlakqilnksdevegrFdsvawvvvsktd..kseeiletilkeLslseddleekeeveslkrklvrlLltk 103
                                     G +G GKtt + + +++   +e++  sv+ v +  +   + ++i+ +i k++       +  +  + l +k+   L ++
  gi|116754893|ref|YP_844011.1|  57 LGPPGTGKTTAIIKLFEE---IEKHTRSVIPVHINCQIdgTRYSIFSRIYKKIFGVTPPSSGIS-FKRLFDKIASTLASR 132
                                    599*******98888888...5555555555555544411578999999999977644444444.44499********** PP

                                    .TEEEE.EEEE CS
                         NB-ARC 104 .rfllv.lDDV 112
                                      +l+v lDDV
  gi|116754893|ref|YP_844011.1| 133 eAVLIVaLDDV 143
                                    63333359**9 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00031      0.35       6      28 ..      58      80 ..      54      89 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00031
                                   --TTSSHHHHHHHHHHHH...GG CS
                       NTPase_1  6 GppGvGKtTlvkkvlellkssgv 28
                                   GppG+GKtT + k+ e+++++  
  gi|116754893|ref|YP_844011.1| 58 GPPGTGKTTAIIKLFEEIEKHTR 80
                                   9****************988755 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00027      0.31       7      32 ..      57      80 ..      52     106 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00027
                        DUF2075  7 tGvaGtGKtvvllnllaeleddeeer 32
                                    G +GtGKt   ++l+ e+e  ++ r
  gi|116754893|ref|YP_844011.1| 57 LGPPGTGKTTAIIKLFEEIE--KHTR 80
                                   599****************4..3333 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0    0.0003      0.34       4      33 ..      54      83 ..      51      90 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0003
                                   EEEEESTTSSHHHHHHHHHHHHHHTTS-EE CS
                          SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvl 33
                                    l +G+ G+GKTt++ KL + ++k+ ++v+
  gi|116754893|ref|YP_844011.1| 54 ALCLGPPGTGKTTAIIKLFEEIEKHTRSVI 83
                                   5789****************9999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); 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: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2491.91
//
Query:       gi|116754894|ref|YP_844012.1|  [L=280]
Description: hypothetical protein Mthe_1605 [Methanosaeta thermophila PT]
Scores for complete 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-109  363.1   0.1   7.5e-109  362.9   0.1    1.0  1  DUF2099   Uncharacterized protein conserved in archaea (DUF20


Domain annotation for each model (and alignments):
>> DUF2099  Uncharacterized protein conserved in archaea (DUF2099)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  362.9   0.1  4.2e-113  7.5e-109       1     257 []       2     254 ..       2     254 .. 0.99

  Alignments for each domain:
  == domain 1  score: 362.9 bits;  conditional E-value: 4.2e-113
                        DUF2099   1 HiiealgkarvvvkdgkvvevgepkikyCPlfkklrgikeitkeaikkniefrikefGlftkkRkleskedfvsfGasEi 80 
                                    Hi+e+lg++rv+++d kvve +ep i++CPlf+k+rgik+it ea  kn efr++e+G+ft++Rkle+k +fvsfGasE+
  gi|116754894|ref|YP_844012.1|   2 HIMELLGRCRVKIQDEKVVETTEPLIEWCPLFDKVRGIKRITPEAAAKNAEFRMREHGMFTPRRKLEMK-TFVSFGASET 80 
                                    *********************************************************************.********** PP

                        DUF2099  81 lstalkeglidaavivcdgaGtvivtnpelvqglggrisGlveTePieevierieeeggivldketaeidqveGvkkAie 160
                                    ++t++++glidaav+vcdgaGtvi+++p+lvqg+gg+isGl+eTePi+evie i+++ggivl++ +a+idq+eG++ A++
  gi|116754894|ref|YP_844012.1|  81 MMTGISRGLIDAAVTVCDGAGTVISDSPSLVQGMGGWISGLLETEPIPEVIEYIKKKGGIVLSPGDARIDQLEGARIAAQ 160
                                    ******************************************************************************99 PP

                        DUF2099 161 kgykkiavtvaeaedakklrelekeegvkilifavhttgiskeeaeelveaaDlvtacAskeireivkkkallqvgksvp 240
                                    k y+++avtv++ae+a klreleke+g++ili++vh+tgis+++ae+l++aaD+vt+cAsk+ir +vk  +l+qvg++vp
  gi|116754894|ref|YP_844012.1| 161 K-YRRFAVTVTDAETAFKLRELEKETGCRILIVGVHLTGISRDDAERLLSAADIVTGCASKHIRVLVK--PLVQVGTAVP 237
                                    8.*****************************************************************9..9********* PP

                        DUF2099 241 vfaltekGkelilerlk 257
                                    +f+lt++Gkel++er+k
  gi|116754894|ref|YP_844012.1| 238 LFGLTQWGKELLVERAK 254
                                    **************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 2222.46
//
Query:       gi|116754895|ref|YP_844013.1|  [L=232]
Description: threonyl/alanyl tRNA synthetase, SAD [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-15   56.2   0.7    4.4e-15   55.5   0.7    1.4  1  tRNA_SAD       Threonyl and Alanyl tRNA synthetase second add
    5.2e-12   45.1   0.0    6.9e-12   44.7   0.0    1.1  1  tRNA-synt_2c   tRNA synthetases class II (A)
  ------ inclusion threshold ------
      0.022   14.7   2.1        4.7    7.2   0.1    3.5  4  RNase_II_C_S1  RNase II-type exonuclease C-terminal S1 domain


Domain annotation for each model (and alignments):
>> tRNA_SAD  Threonyl and Alanyl tRNA synthetase second additional domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   0.7   7.3e-19   4.4e-15       1      44 []     184     227 ..     184     227 .. 0.98

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 7.3e-19
                                    EEEEEETT.EEEEESS---SBGGGC-SEEEECCECCCTCEEEEE CS
                       tRNA_SAD   1 vrvvsiGdisvelCgGtHvpnTgeIgafkilseesiakglrRIy 44 
                                    vrv++i+ ++ ++CgGtHv+nT+eIg++++++ e+++k +rR+y
  gi|116754895|ref|YP_844013.1| 184 VRVIEIEGVDLQACGGTHVRNTSEIGEIRLVKAENKGKSNRRVY 227
                                    9*****779**********************************9 PP

>> tRNA-synt_2c  tRNA synthetases class II (A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   0.0   1.2e-15   6.9e-12     473     552 .]      13      88 ..       3      88 .. 0.93

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 1.2e-15
                                    SEEEEEEEEEETTEEEESEEXXXXSSSSCSXXXEEEEESSEEEEESEEEEETTEEEEEXSS.XSXXXTTSEEEEEEXHHH CS
                   tRNA-synt_2c 473 kefveeveegeevgvvLdrTpfYaesGGqigDeGliekegaefrvkdvqkakgvvlhkgkleegklkvgdkvkaevdeer 552
                                    ++f + v+++++ gv LdrT+fY+ sGGq +D G++   ++ frv+ v+  ++ ++h+++     l+ gdkvk+e+d+er
  gi|116754895|ref|YP_844013.1|  13 RSFDAVVTNVDDTGVYLDRTAFYPRSGGQPSDLGVLIRGDQVFRVEGVEPSEHGICHRAHG----LSPGDKVKGEIDWER 88 
                                    578889999************************************************9988....79**********986 PP

>> RNase_II_C_S1  RNase II-type exonuclease C-terminal S1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1   0.00079       4.7       2      15 ..      14      27 ..      13      37 .. 0.89
   2 ?   -1.5   0.0      0.41   2.5e+03      28      40 ..      68      80 ..      61      81 .. 0.82
   3 ?   -3.2   0.0       1.4   8.3e+03      48      57 ..     120     129 ..     118     130 .. 0.81
   4 ?    4.8   0.0    0.0046        27      34      46 ..     149     161 ..     138     165 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00079
                  RNase_II_C_S1  2 tFdAvVvdvddrgg 15
                                    FdAvV+ vdd+g+
  gi|116754895|ref|YP_844013.1| 14 SFDAVVTNVDDTGV 27
                                   6**********985 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.41
                  RNase_II_C_S1 28 veggaglplGerv 40
                                   ++ ++gl +G++v
  gi|116754895|ref|YP_844013.1| 68 CHRAHGLSPGDKV 80
                                   777899*****98 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 1.4
                  RNase_II_C_S1  48 DvatrrvrFe 57 
                                    D ++ rv+F+
  gi|116754895|ref|YP_844013.1| 120 DTDRSRVDFS 129
                                    8889999997 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.0046
                  RNase_II_C_S1  34 lplGervrVrLve 46 
                                    +++G++vrVrL +
  gi|116754895|ref|YP_844013.1| 149 IKEGHPVRVRLMT 161
                                    679********75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1757.99
//
Query:       gi|116754896|ref|YP_844014.1|  [L=232]
Description: V-type ATP synthase subunit D [Methanosaeta thermophila PT]
Scores for complete 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-55  188.3   6.7    1.3e-55  188.3   6.7    1.3  2  ATP-synt_D  ATP synthase subunit D


Domain annotation for each model (and alignments):
>> ATP-synt_D  ATP synthase subunit D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.3   6.7   7.1e-60   1.3e-55       2     195 ..      14     205 ..      13     206 .. 0.95
   2 ?   -4.3   0.8      0.77   1.4e+04      46      57 ..     215     226 ..     208     231 .. 0.36

  Alignments for each domain:
  == domain 1  score: 188.3 bits;  conditional E-value: 7.1e-60
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSTSTTSTSHHHHHHHSSS.SS-..TSS CS
                     ATP-synt_D   2 LirlkkrlklaqrghslLkkKrdaLilefreilkelkelreeleeelkeayfslaeafaaggeediesavlesvklakvv 81 
                                    Li+l++r+k+aq gh+lLk+Krd L++ef+e+l+++k+ reel + + +a++ l +a+aa+g  +i+s++ + +   ++ 
  gi|116754896|ref|YP_844014.1|  14 LIALRRRIKVAQTGHELLKMKRDGLMIEFFEVLNRAKTIREELVQDYLRAEQRLNMAKAADGTIAIKSVAFALQ---QEP 90 
                                    89*****************************************************************9999665...569 PP

                                    -SEEEEEEBTTSEEEEEEE-...S.SSTSSSSSSSSTCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     ATP-synt_D  82 kvelktenvaGVkvpvfeleee.ksdstelygllrtgaqldeavealrellellvelasletslelLdeeikktnrRvNa 160
                                     v+l+++n++GV vp+++ e   k+  ++ yg+++t+a +dea++a+++l+++++ +a++etsl++L + i+kt+rRvNa
  gi|116754896|ref|YP_844014.1|  91 AVDLQSRNIMGVVVPKISAEAVhKKMYERGYGIIGTSAAIDEAADAYESLVDKIITAAEVETSLMKLVDDIEKTKRRVNA 170
                                    9****************8866664444567************************************************** PP

                                    HHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     ATP-synt_D 161 LekvvIPrleetikyIkseLdEqereeffrlkkvk 195
                                    Le +vIP +++ti++I  +L+E++r +++rlkk+k
  gi|116754896|ref|YP_844014.1| 171 LEFKVIPDIKDTIRFIGFALEEMDRDNIVRLKKLK 205
                                    *********************************99 PP

  == domain 2  score: -4.3 bits;  conditional E-value: 0.77
                                    HHHHHHHTTSTS CS
                     ATP-synt_D  46 eelkeayfslae 57 
                                    ee ++a+++ ae
  gi|116754896|ref|YP_844014.1| 215 EEAEKAAKAAAE 226
                                    222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1407  (0.0784762); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1717.79
//
Query:       gi|116754897|ref|YP_844015.1|  [L=463]
Description: V-type ATP synthase subunit B [Methanosaeta thermophila PT]
Scores for complete 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-60  202.6   0.0    7.5e-60  202.2   0.0    1.2  1  ATP-synt_ab    ATP synthase alpha/beta family, nucleotide-bin
    1.7e-12   47.6   2.2    1.7e-12   47.6   2.2    2.2  3  ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel do
    0.00051   20.1   2.8    0.00067   19.8   1.4    2.0  2  HAS-barrel     HAS barrel domain


Domain annotation for each model (and alignments):
>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.2   0.0   1.3e-63   7.5e-60       1     213 []     130     348 ..     130     348 .. 0.98

  Alignments for each domain:
  == domain 1  score: 202.2 bits;  conditional E-value: 1.3e-63
                                    SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTS....S.EEEEEEESEEHHHHHHHHHHCHHSSGGGGEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsd....d.aiiyvgiGergnevaevleefpegtimkrtvlv 75 
                                    Gi+++D   ++v+Gq++ i++++g++++ ++ ++++q++      + a++++++G  ++e+++++ +f+++++++r v++
  gi|116754897|ref|YP_844015.1| 130 GISTIDGTNTLVRGQKLPIFSGAGLPHNDVALQIARQAKVLgeaeEfAVVFCAMGITNEEAQHFMADFERTGALERAVIF 209
                                    899**********************************8655888768********************************* PP

                                    EEETTS-HHHHHHHHHHHHHHHHHHHH.TTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHHHHTTSEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab  76 antsnepvaareasiytgitlAEyfrd.qgknvlliadslsrwaeAlreislrlgempadqgypaylgaklaslyERagk 154
                                    +n +++p+++r++++ +g+t+AEy++   +++vl+i++++++++e+lr+++++ +e+p+++gyp+y++++la+ yERag 
  gi|116754897|ref|YP_844015.1| 210 LNLADDPAVERLLTPKLGLTTAEYLAFdLDMHVLVIYTDMTNYCESLRQMGAAREEVPGRRGYPGYMYTDLATNYERAGI 289
                                    *************************9879*************************************************** PP

                                    ETSSEEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab 155 apdrtGsvtivaavspaggDfsdpvttatlgitdgfivLdkklaqrkhfPainvlvSvS 213
                                    ++ ++Gs+t++++++++g+D+++p+++   +it+g+++++++l++++++P+i++  S+S
  gi|116754897|ref|YP_844015.1| 290 IKGKKGSITQFPILTMPGDDITHPIPDLSGYITEGQLIVSRELHRKGIYPPIDIRPSLS 348
                                    *********************************************************98 PP

>> ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   2.2   2.9e-16   1.7e-12       1      69 []       8      73 ..       8      73 .. 0.93
   2 ?   -3.7   0.0         3   1.8e+04      53      64 ..     134     145 ..     130     145 .. 0.77
   3 ?   -2.3   0.0       1.1   6.5e+03      17      43 ..     168     193 ..     154     199 .. 0.60

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 2.9e-16
                                   EEEEETTEEEEESSTSCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBTTSEEEEES CS
                  ATP-synt_ab_N  1 ivqviGpvvdvefgigrlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsrGteVkrTG 69
                                   i++++Gp+v ve+ + + +g+++ +++     g++ +g++l  +++ V+v+v+++t Gls+ + V++TG
  gi|116754897|ref|YP_844015.1|  8 ITEISGPLVFVEKTEPVGYGELVEIRTA--S-GEVKRGQVLDTSDEIVVVQVFEGTGGLSKDSSVRFTG 73
                                   89**************777777777777..8.************************************9 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3
                                    SS-STTBBTTSE CS
                  ATP-synt_ab_N  53 mgstdGlsrGte 64 
                                    +++t  l+rG++
  gi|116754897|ref|YP_844015.1| 134 IDGTNTLVRGQK 145
                                    688999999985 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.1
                                    CETCTTEEEEECCETCSTEEEEEEEEE CS
                  ATP-synt_ab_N  17 rlpgiynalevelvefgtlllgvalnl 43 
                                    ++ g+ +  +v  +     + ++a+++
  gi|116754897|ref|YP_844015.1| 168 KVLGEAEEFAVVFCA-MGITNEEAQHF 193
                                    444444444444444.45555666665 PP

>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   1.4   1.1e-07   0.00067       2      90 ..       2      75 ..       1      90 [. 0.85
   2 ?   -2.2   0.0      0.77   4.6e+03      73      91 ..     158     174 ..     131     175 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.1e-07
                     HAS-barrel  2 Gevigests.sslifrvegskdvkvGeyVeielpdgeivlGmvtdirrgnselsndlalvlsleeleeangddevalatedt 82
                                    +++ + t  s+++++ve +++v++Ge+Vei++  ge+  G+v+d +                        +++v++++e+t
  gi|116754897|ref|YP_844015.1|  2 TKEYKTITEiSGPLVFVEKTEPVGYGELVEIRTASGEVKRGQVLDTSD-----------------------EIVVVQVFEGT 60
                                   6789999999**************************************.......................99999999999 PP

                     HAS-barrel 83 .......gvkvlGev 90
                                          +v+  G+v
  gi|116754897|ref|YP_844015.1| 61 gglskdsSVRFTGDV 75
                                   888888855544444 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.77
                     HAS-barrel  73 devalatedtgvkvlGeve 91 
                                    d++++++   ++kvlGe+e
  gi|116754897|ref|YP_844015.1| 158 DVALQIAR--QAKVLGEAE 174
                                    23333333..379999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); 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 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 3389.69
//
Query:       gi|116754898|ref|YP_844016.1|  [L=576]
Description: V-type ATP synthase subunit A [Methanosaeta thermophila PT]
Scores for 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-92  307.3   0.0    6.6e-92  307.0   0.0    1.1  1  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
    2.6e-41  140.3   0.1    4.7e-41  139.4   0.1    1.5  1  ATP-synt_ab_Xtn  ATPsynthase alpha/beta subunit N-term extens
    2.6e-11   43.9   1.3    8.4e-11   42.2   1.3    2.0  1  ATP-synt_ab_N    ATP synthase alpha/beta family, beta-barrel 
    0.00076   19.4   1.0     0.0098   15.8   0.0    2.3  2  RnfC_N           RnfC Barrel sandwich hybrid domain
  ------ inclusion threshold ------
      0.015   15.6   0.0      0.046   14.0   0.0    1.7  2  AAA_22           AAA domain
      0.015   15.1   0.6      0.045   13.6   0.6    1.8  1  Biotin_lipoyl    Biotin-requiring enzyme
      0.041   13.7   0.0      0.078   12.7   0.0    1.4  1  PTS_EIIA_1       phosphoenolpyruvate-dependent sugar phosphot
      0.043   14.0   0.1       0.37   11.0   0.0    2.4  2  Peptidase_M23    Peptidase family M23


Domain annotation for each model (and alignments):
>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  307.0   0.0   2.9e-95   6.6e-92       1     213 []     208     429 ..     208     429 .. 0.97

  Alignments for each domain:
  == domain 1  score: 307.0 bits;  conditional E-value: 2.9e-95
                                    SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEEESEEHHHHHHHHHHCHH......SS.GGGGEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xx.xxxxxx RF
                    ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsddaiiyvgiGergnevaevleefpe......gt.imkrtv 73 
                                    G+rv+D +fp+++G++ +ipg+fg+Gktv++q+lsk+s+ d ++iyvg+Gergne+a++l+efpe      ++ +++r++
  gi|116754898|ref|YP_844016.1| 208 GQRVIDGFFPLAKGGTAAIPGGFGTGKTVMQQTLSKWSDVD-IVIYVGCGERGNEMADLLHEFPElvdprtNRpLLERSI 286
                                    9************************************9988.************************99975227****** PP

                                    EEEEETTS-HHHHHHHHHHHHHHHHHHHHTTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHHHHTTSE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab  74 lvantsnepvaareasiytgitlAEyfrdqgknvlliadslsrwaeAlreislrlgempadqgypaylgaklaslyERag 153
                                    + antsn+pvaareasiytg+t+AEy+rd+g++vl+ ads+srwaeA+re++ rl+emp+++gypayl+a+la +yERag
  gi|116754898|ref|YP_844016.1| 287 VYANTSNMPVAAREASIYTGMTTAEYYRDMGYDVLMTADSTSRWAEAMRELASRLEEMPGEEGYPAYLAARLADFYERAG 366
                                    ******************************************************************************** PP

                                    EE...TSSEEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                                    xx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab 154 ka...pdrtGsvtivaavspaggDfsdpvttatlgitdgfivLdkklaqrkhfPainvlvSvS 213
                                    +a      +Gsv +v avsp+ggDf++pvt++tl+i+++f+ Ld++l+qr+hfP+in+l S+S
  gi|116754898|ref|YP_844016.1| 367 RAevlAGGEGSVAVVGAVSPPGGDFTEPVTQNTLRIVKVFWALDSRLTQRRHFPSINWLDSYS 429
                                    **8877779*****************************************************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 !  139.4   0.1   2.1e-44   4.7e-41       1     121 []      83     199 ..      83     199 .. 0.95

  Alignments for each domain:
  == domain 1  score: 139.4 bits;  conditional E-value: 2.1e-44
                                    EETTS-BHHHHHHHHTSBE-TT----SS-SSS-EEEEESS-TT-EEETT-EEEEEECTTCEEEEEE--TT-EEE.EEEE- CS
                ATP-synt_ab_Xtn   1 yDGiqrpLekiaeksgsfierGvkvpaldrekkwefkpkvkvgdkvsggdilGtvqeteliehkimvppkvegk.vkeia 79 
                                    yDG+qrpL  +aeksg+fi+rG+ v+ +d++kkwefkp vk+gd+v++g+ +G+vqe+ li+hkimvppk +g  vkei 
  gi|116754898|ref|YP_844016.1|  83 YDGVQRPLPLLAEKSGDFISRGLFVDGVDHKKKWEFKPLVKKGDTVKPGQPIGEVQEQLLIKHKIMVPPKHKGGvVKEIY 162
                                    9********************************************************************99877255565 PP

                                    -EEEE-TTSECEEECETT.ECEEEESSEEEETTS---ESEEE CS
                ATP-synt_ab_Xtn  80 eegeytvedtiaeveteegkekeltllqkwPvrkprpvkekl 121
                                     +g++tve+t++++e+++    elt+lqkwPvr++rpv +kl
  gi|116754898|ref|YP_844016.1| 163 -SGNFTVEETVCVLEDGS----ELTMLQKWPVRQARPVVRKL 199
                                    .**************776....8***************9996 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 !   42.2   1.3   3.8e-14   8.4e-11       1      69 []       6      67 ..       6      67 .. 0.94

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 3.8e-14
                                   EEEEETTEEEEESSTSCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBTTSEEEEES CS
                  ATP-synt_ab_N  1 ivqviGpvvdvefgigrlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsrGteVkrTG 69
                                   + +v Gpvv++  g      +y+++ v+  e  ++l+ +++++++dk +++v+++t+G+++G++Vk TG
  gi|116754898|ref|YP_844016.1|  6 VKRVAGPVVQA-VGLK--ASMYDLVLVG--E--EGLMSEVIGISGDKHIIQVYEDTSGIKPGEPVKETG 67
                                   569********.6666..7*********..8..9**********************************8 PP

>> RnfC_N  RnfC Barrel sandwich hybrid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.2      0.12   2.7e+02      28      75 ..       7      56 ..       2      59 .. 0.86
   2 !   15.8   0.0   4.4e-06    0.0098      42      72 ..     118     150 ..     112     178 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.12
                         RnfC_N 28 kelvlplsqhiGapakp..lvkvgdkVlkGqkiaeaegfvsapvhasvsG 75
                                   k++  p+ q +G +a++  lv vg++ l+ ++i+ ++     +v+  +sG
  gi|116754898|ref|YP_844016.1|  7 KRVAGPVVQAVGLKASMydLVLVGEEGLMSEVIGISGDKHIIQVYEDTSG 56
                                   67788999****99987558**************9988778999999998 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 4.4e-06
                         RnfC_N  42 akplvkvgdkVlkGqkiaeaeg..fvsapvhas 72 
                                     kplvk+gd+V+ Gq i+e ++  +++ ++  +
  gi|116754898|ref|YP_844016.1| 118 FKPLVKKGDTVKPGQPIGEVQEqlLIKHKIMVP 150
                                    68*****************98756677777766 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.1e-05     0.046       6      71 ..     222     280 ..     219     301 .. 0.83
   2 ?   -2.6   0.0       2.8   6.3e+03      44      70 ..     321     347 ..     304     371 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.1e-05
                         AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllrellralglelkae 71 
                                    g  ++ G  GtGKT+  ++l ++ d         + v++v + + + + +dll+e+ + ++ +++++
  gi|116754898|ref|YP_844016.1| 222 GTAAIPGGFGTGKTVMQQTLSKWSD--------VDIVIYVGCGERGnEMADLLHEFPELVDPRTNRP 280
                                    6678999*****************7........88999*******999**********999777763 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.8
                         AAA_22  44 fvtlpsstsskdllrellralglelka 70 
                                    ++t+ s + +++ +rel++ l++   +
  gi|116754898|ref|YP_844016.1| 321 LMTADSTSRWAEAMRELASRLEEMPGE 347
                                    567777778888888888888865555 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.6     2e-05     0.045      15      58 ..     115     163 ..     109     174 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2e-05
                                    ..ECSESSSTTCEE-TTSEEEEEECT...TEEEEEEBSS.SEEEEEESS CS
                  Biotin_lipoyl  15 g.vvevlvkvGdkVkagqvlaeveam...Kmemeieapk.aGvvkeilv 58 
                                        + lvk+Gd+Vk gq++ ev+     K ++ ++ ++  Gvvkei+ 
  gi|116754898|ref|YP_844016.1| 115 KwEFKPLVKKGDTVKPGQPIGEVQEQlliKHKIMVPPKHkGGVVKEIYS 163
                                    4567899****************97544488777776553788999875 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 ?   12.7   0.0   3.5e-05     0.078      82     112 ..     116     146 ..     105     150 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.5e-05
                                    TTEEES----SEE-SEEEEEEE-HHHHGGGS CS
                     PTS_EIIA_1  82 egFellvkegdkVkagdklvevdleaikkag 112
                                      F+ lvk+gd+Vk g+++ ev+ + + k++
  gi|116754898|ref|YP_844016.1| 116 WEFKPLVKKGDTVKPGQPIGEVQEQLLIKHK 146
                                    58********************999887775 PP

>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.93   2.1e+03      28      65 ..      30      65 ..      22      75 .. 0.79
   2 ?   11.0   0.0   0.00016      0.37      56      74 ..     121     139 ..     110     146 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.93
                                   EEETTTEEEEEEEECTCEEEEEEEESEESS-TTEEE-T CS
                  Peptidase_M23 28 gkkegyGnvviidhgdgystlyahlskisvkegqkVka 65
                                   g+++ + +v+ i  +++++++y   s   +k+g+ Vk+
  gi|116754898|ref|YP_844016.1| 30 GEEGLMSEVIGISGDKHIIQVYEDTSG--IKPGEPVKE 65
                                   555445889999999999999999988..888888875 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00016
                                    SS-TTEEE-TTCEEEEEBS CS
                  Peptidase_M23  56 svkegqkVkaGqvIGtvgs 74 
                                     vk+g++Vk Gq+IG+v +
  gi|116754898|ref|YP_844016.1| 121 LVKKGDTVKPGQPIGEVQE 139
                                    49**************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (576 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.57u 0.24s 00:00:00.81 Elapsed: 00:00:00.40
# Mc/sec: 4321.50
//
Query:       gi|116754899|ref|YP_844017.1|  [L=99]
Description: V-type ATP synthase subunit F [Methanosaeta thermophila PT]
Scores for complete 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   62.7   0.2    3.5e-17   62.5   0.2    1.0  1  ATP-synt_F   ATP synthase (F/14-kDa) subunit
  ------ inclusion threshold ------
       0.05   13.9   0.2       0.11   12.7   0.1    1.6  2  THF_DHG_CYH  Tetrahydrofolate dehydrogenase/cyclohydrolase, c
       0.26   11.6   0.6         25    5.2   0.0    2.2  2  DUF1059      Protein of unknown function (DUF1059)


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 !   62.5   0.2   5.9e-21   3.5e-17       1      88 [.       3      90 ..       3      93 .. 0.88

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 5.9e-21
                                   EEEEESHHHHHHHHHTTCEEEE.CSSHHHHHHHHHHHHHHTTEEEEEEEHHHHCCCHHHHHHCTCS.SSSEEEEESCSCCGG CS
                     ATP-synt_F  1 iavIGdedtvtgfrlaGvgeve.vtdeeeieealkelleredigiilitekiaeeirelideykee.alPaileIPskegpy 80
                                   iavIG++d v+gf+laG+++ + +t+eee+ ++++e+++++++gi++++++ +++++++++++ ++ + P+++ I +++++ 
  gi|116754899|ref|YP_844017.1|  3 IAVIGNSDAVIGFSLAGIKKAYeATSEEELINKINEVMADPNVGILVLHQNDYNRLPKRLQSTLSNsVRPTVIAIGTEQSTE 84
                                   8******************9997888*******************************9999999998********7666633 PP

                                   SHHCHHHH CS
                     ATP-synt_F 81 deekdsvr 88
                                      +++++
  gi|116754899|ref|YP_844017.1| 85 --MREKIK 90
                                   ..355555 PP

>> THF_DHG_CYH  Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   1.9e-05      0.11      66      94 ..      24      51 ..      10      73 .. 0.76
   2 ?   -1.8   0.0      0.63   3.7e+03       4      18 ..      78      92 ..      75      95 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.9e-05
                                   -TT--HHHHHHHHHHHHH-TT--EEEE-S CS
                    THF_DHG_CYH 66 pedvseeellklieelneddsvdGilvql 94
                                    e +seeel+++i+e+ +d++v Gilv +
  gi|116754899|ref|YP_844017.1| 24 YEATSEEELINKINEVMADPNV-GILVLH 51
                                   36799****************9.999975 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.63
                                   HHHHHHHHHHHHHHH CS
                    THF_DHG_CYH  4 Gkalakeireelkee 18
                                   G++ + e+re++k+ 
  gi|116754899|ref|YP_844017.1| 78 GTEQSTEMREKIKRA 92
                                   566677777777765 PP

>> DUF1059  Protein of unknown function (DUF1059)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.005        30      18      31 ..      25      38 ..      21      42 .. 0.86
   2 ?    5.2   0.0    0.0042        25      40      54 ..      79      93 ..      78      95 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.005
                        DUF1059 18 taeteeEvlrkvae 31
                                   +a++eeE+++k++e
  gi|116754899|ref|YP_844017.1| 25 EATSEEELINKINE 38
                                   799*******9986 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0042
                        DUF1059 40 teippelvekiksaI 54
                                   te + e++ekik+aI
  gi|116754899|ref|YP_844017.1| 79 TEQSTEMREKIKRAI 93
                                   66788*********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       775  (0.0432261); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); 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: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 706.01
//
Query:       gi|116754900|ref|YP_844018.1|  [L=349]
Description: V-type ATP synthase subunit C [Methanosaeta thermophila PT]
Scores for complete 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-72  242.7   0.9    7.9e-72  242.6   0.9    1.0  1  vATP-synt_AC39  ATP synthase (C/AC39) subunit


Domain annotation for each model (and alignments):
>> vATP-synt_AC39  ATP synthase (C/AC39) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  242.6   0.9   4.4e-76   7.9e-72       1     335 [.      18     344 ..      18     345 .. 0.92

  Alignments for each domain:
  == domain 1  score: 242.6 bits;  conditional E-value: 4.4e-76
                                    HHHHHHHHGGGS--HHHHHHHTTS.-HHHHHHHHHTSGGGGG--.....SSSHHHHHHHHHHHHHHHTTTGGGGS-H.HH CS
                 vATP-synt_AC39   1 leArvramrsglLteedyenLlqcesledvkryLketdYgnfladelseplsrsdiekalreklarefnklreqapgpsr 80 
                                    +++rvram+++l+++e y ++l++ ++++++ryL+et Y++++   + ++++ + ie+a  ++la++++kl+e + ++++
  gi|116754900|ref|YP_844018.1|  18 ITGRVRAMKTKLIPNEMYARMLNM-DIPEIARYLEETQYKEEIDALAKDYSGAELIEHATFANLAKTYRKLLEVSIDEPQ 96 
                                    579******************665.*****************7777799************************9999977 PP

                                    HHHHHHHHHHHHHHHHHHHHHHHH.T--GGGS-..--.SSSS-HHHHHHHHHSSSHHHHHHHHHT-HHHHHHHHHHCC.. CS
                 vATP-synt_AC39  81 efldyllyrydidNvklllrgklsgdldleeleeklhplgelsaldldklieaksveelyeallgtpyakyleealdele 160
                                     ++  +l+r+di+N+k++lrgk+  +++ +e++++++p+gel+++ l+ l++++s+++++ a++gt +a++l++    ++
  gi|116754900|ref|YP_844018.1|  97 FLILEYLRRWDIWNIKTILRGKFY-GASDSEIMKYIVPAGELDQEFLEGLAKKDSINDVITAFEGTDFAEALSK----YD 171
                                    999*********************.5777***********************************9999988887....66 PP

                                    .--SHHHHHHHHHHHHHHHHHHH.HHTSS..-HH...HHHHHHHHHHHHHHHHHHHTTTSS......T...--SS-S--H CS
                 vATP-synt_AC39 161 etgdleiienaLdkayledllkf.ckklg..getaeilreilgfeiDlrniniilrskkygelskedrkkllipggslyp 237
                                      ++l+ +enaLdk y+ ++ ++   +l+  g     l +++++eiD+rn+ +++r+ k+g    + +++ lipgg+l++
  gi|116754900|ref|YP_844018.1| 172 G-KSLASVENALDKLYYFRMERAvGGTLSvgGGL---LLKYVKREIDIRNLITLFRMNKAG-IEASIVQENLIPGGKLSE 246
                                    6.899******************64444443667...**********************88.556778889*******95 PP

                                    HHHHHHHTT-G.....GG.GGSSTSSTTGGGTT-.-S.HHHHHHHHHHHHHHHHHT.TTSSSTSTHHHHHHHHHHHHHHH CS
                 vATP-synt_AC39 238 eglealaeaedveellaalkyteygelleealee.agslksledaldealvkllkk.afrqqfsvgvfyaYlklkeqEir 315
                                     +l+++a +  + ++++ l+ +++++ +++++ +  +s + +e +l+++l++++ + + ++++s+ ++++Y+  ke+E+ 
  gi|116754900|ref|YP_844018.1| 247 -ELSRMAGQ-PYADFVRGLEGYPFWSAISDVATAdLDSVSRIEARLKAYLIRYAWSlSNYHPLSILPVLGYIVTKETEVA 324
                                    .67779988.8********9999999988777776666****************************************** PP

                                    HHHHHHHHHHHT--SHHHHG CS
                 vATP-synt_AC39 316 nlrwIaegiaqglpkekIre 335
                                    n+r I++g+++glp+e I+e
  gi|116754900|ref|YP_844018.1| 325 NIRKIVRGKEAGLPNELIEE 344
                                    ******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2756.45
//
Query:       gi|116754901|ref|YP_844019.1|  [L=182]
Description: V-type ATP synthase subunit E [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.8e-18   65.0  14.6    7.3e-16   58.2  14.6    2.0  1  vATP-synt_E  ATP synthase (E/31 kDa) subunit
  ------ inclusion threshold ------
      0.042   14.0   2.0      0.042   14.0   2.0    1.7  1  DUF3826      Protein of unknown function (DUF3826)
      0.081   12.5   5.7       0.11   12.1   5.7    1.1  1  CENP-K       Centromere-associated protein K
      0.083   12.8   0.9      0.083   12.8   0.9    2.3  3  GnsAB_toxin  GnsA/GnsB toxin of bacterial toxin-antitoxin sys
       0.16   12.0   1.9       0.22   11.6   1.9    1.2  1  T2SSM        Type II secretion system (T2SS), protein M
       0.78    9.8  13.4        1.5    8.9  13.4    1.4  1  ATP-synt_B   ATP synthase B/B' CF(0)
       0.91    9.6   6.3        1.3    9.1   6.1    1.4  1  DUF1451      Zinc-ribbon containing domain
        1.1    9.3   8.1        1.7    8.7   5.4    2.3  2  FliH         Flagellar assembly protein FliH


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 !   58.2  14.6   3.3e-19   7.3e-16       2     199 .]      10     181 ..       9     181 .. 0.95

  Alignments for each domain:
  == domain 1  score: 58.2 bits;  conditional E-value: 3.3e-19
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    vATP-synt_E   2 IrqeAeekAeeIkakaeeefeiekaklveeeeekieeayekkeKqaelqkkiaiSnalnkarlkvLkareevleevfeea 81 
                                    I    + k+ eI+a++e+e++ +++++ e++ e + ++ ++++  +e+  ++++S+a ++ +++ L++ +evle+v+ + 
  gi|116754901|ref|YP_844019.1|  10 ILATSKSKVAEINAETEQEVARILSEARERAAEIKSRKEAEAKHDIEALVRREMSSANLELKRAELNVHKEVLEQVRIKF 89 
                                    6677899************************************************************************* PP

                                    HHHHHHHTTSHHCCCCHHHHHHCCCCCCC-SSCEEEEECCCCHHCCCCTHCCCCCCHHCCSSSS--SEEEEESSEBTTSS CS
                    vATP-synt_E  82 ekkLaeveedkdeYkellkkLivqalvkleepevivrarkeDaelveealdkaaeeykaktkkktvevagdeedfledvl 161
                                       + ++++dk       + Li++ l+     ++ v++ k+D+  v+++    + +y +            +     d++
  gi|116754901|ref|YP_844019.1|  90 LDAVTNLPKDK------NEALIKKLLEPYDLKDMKVYSSKRDQAFVSSL----VPNYGG------------T----LDII 143
                                    ***********......8899***************************5....556665............5....79** PP

                                    SEEEECCSSSCEEECCCHHHCHHHHHHHHHHCCCCCHC CS
                    vATP-synt_E 162 GGvvleaadgkikvnnTlearLelvleqllpeirkaLF 199
                                    GGvv+e++dg ++ + + e +   +++++++e++k LF
  gi|116754901|ref|YP_844019.1| 144 GGVVVESKDGSVRFDHSYETLARDIFNAKVKEVSKLLF 181
                                    *************************************9 PP

>> DUF3826  Protein of unknown function (DUF3826)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   2.0   1.9e-05     0.042     114     153 ..      12      51 ..       5      56 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.9e-05
                                    HHHHHH-TT--HHHHHHHHHHHHHHHHHHTTSSSHHHHHH CS
                        DUF3826 114 kgykeivpdLteeekaqIlkwLkeAReqAiDaksskkkha 153
                                       k+ v ++++e ++++ + L eARe+A ++ks k+  a
  gi|116754901|ref|YP_844019.1|  12 ATSKSKVAEINAETEQEVARILSEARERAAEIKSRKEAEA 51 
                                    556788999*************************998765 PP

>> CENP-K  Centromere-associated protein K
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   5.7   4.7e-05      0.11      95     193 ..       7     107 ..       2     117 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.7e-05
                         CENP-K  95 LelvlsiiqsknkklkedLkrEq.ewleeqqeilesLke.ktkelkkqvvafsektrksaelkekirkikeykeeLltaL 172
                                     e++l + +sk  +++++ ++E  ++l+e +e  + +k+ k++e k++ +a+ +++ +sa+l+ k  +++ +ke L ++ 
  gi|116754901|ref|YP_844019.1|   7 VEDILATSKSKVAEINAETEQEVaRILSEARERAAEIKSrKEAEAKHDIEALVRREMSSANLELKRAELNVHKEVLEQVR 86 
                                    6899****************9962678999988888886256799999*******999*************888888888 PP

                         CENP-K 173 gefLdehfplpeeeeasvkkk 193
                                     +fLd    lp+++++++ kk
  gi|116754901|ref|YP_844019.1|  87 IKFLDAVTNLPKDKNEALIKK 107
                                    89*******998776665555 PP

>> GnsAB_toxin  GnsA/GnsB toxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.9   3.7e-05     0.083      13      44 ..       9      40 ..       5      47 .. 0.85
   2 ?   -1.7   0.0       1.3     3e+03      18      18 ..      59      59 ..      41      83 .. 0.60
   3 ?   -3.6   0.0       4.9   1.1e+04      47      53 ..     109     115 ..     107     115 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.7e-05
                                   HHHHHHHHHHHHHHHHHSSEEEEEEEEEEEET CS
                    GnsAB_toxin 13 eiaeliakKiaELkKkTGkEVseieFtaREkm 44
                                   +i +    K+aE++ +T +EV+ i   aRE+ 
  gi|116754901|ref|YP_844019.1|  9 DILATSKSKVAEINAETEQEVARILSEARERA 40
                                   66666678*********************985 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.3
                                   H CS
                    GnsAB_toxin 18 i 18
                                   +
  gi|116754901|ref|YP_844019.1| 59 V 59
                                   3 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 4.9
                                    EEEEEEE CS
                    GnsAB_toxin  47 LEsYdVK 53 
                                    LE Yd K
  gi|116754901|ref|YP_844019.1| 109 LEPYDLK 115
                                    899*988 PP

>> T2SSM  Type II secretion system (T2SS), protein M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.9   9.7e-05      0.22      50     104 ..      23      76 ..      11      94 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.7e-05
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--HHHHHHHHHHHCT--EEEEEEE CS
                          T2SSM  50 lqklraqlawveeqaaevralraapasalsgaaleqvvtrsarqagLalarlqpq 104
                                     +++++ ++ + e+ +++++++ + ++a+++ ++e++v+r++++a+L+l+r +  
  gi|116754901|ref|YP_844019.1|  23 AETEQEVARILSEARERAAEIK-SRKEAEAKHDIEALVRREMSSANLELKRAELN 76 
                                    3444444444444444444444.5556667789****************998765 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 ?    8.9  13.4   0.00068       1.5      61     124 ..      23      86 ..       8      93 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00068
                     ATP-synt_B  61 keAraeAaeiiknAkkeaeklkeeieaeaeaeaerlkesAaaeIeqekdralaeLreqvvalav 124
                                    +e ++e a+i  +A+++a+++k  +eaea+ ++e l        + e +ra+ ++ ++v ++  
  gi|116754901|ref|YP_844019.1|  23 AETEQEVARILSEARERAAEIKSRKEAEAKHDIEALVRREMSSANLELKRAELNVHKEVLEQVR 86 
                                    6789999***************************999999999999999999999888888765 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   6.1   0.00056       1.3       2      84 ..      17      94 ..      16     123 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00056
                        DUF1451  2 sleeaeekseeeleelvekakeklseaeeltkeelel.vaeylkrDleeaarsleeskeeleewlsldlelieesllealas 82
                                   +++e + ++e+e+++++ +a+e+++e +  ++ e+++ +++ ++r++++a  +l+  +       ++  e++e+  ++ l  
  gi|116754901|ref|YP_844019.1| 17 KVAEINAETEQEVARILSEARERAAEIKSRKEAEAKHdIEALVRREMSSANLELKRAEL------NVHKEVLEQVRIKFLDA 92
                                   5788999**********************9999996449**********9999988777......44444444444444444 PP

                        DUF1451 83 ia 84
                                   ++
  gi|116754901|ref|YP_844019.1| 93 VT 94
                                   44 PP

>> FliH  Flagellar assembly protein FliH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   5.4   0.00078       1.7       7      85 ..       7      88 ..       2      99 .. 0.86
   2 ?    0.8   0.0      0.21   4.8e+02      55      86 ..     104     133 ..      92     161 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00078
                                   HHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHS--S-HHHHHHHHHHHHTTSCHHHS-EEEEE-HHHHHHHHHH CS
                           FliH  7 laalleelenslaeldeeledqlvql...aldiarkvikkelsvdpekilalvrealaklpvdekkitlrvnpdDlelvreh 85
                                   ++++l++ ++++ae+++e e+++  +   a + a ++  ++ ++ ++ i+alvr  +++     k++ l v+ + le vr +
  gi|116754901|ref|YP_844019.1|  7 VEDILATSKSKVAEINAETEQEVARIlseARERAAEIKSRKEAEAKHDIEALVRREMSSANLELKRAELNVHKEVLEQVRIK 88
                                   688999999*********99998888222455688999999999*****************************999999865 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.21
                                    HHHHHHTTSCHHHS-EEEEE-HHHHHHHHHHH CS
                           FliH  55 lvrealaklpvdekkitlrvnpdDlelvrehl 86 
                                    l++++l  +p d k+++++ + +D ++v + +
  gi|116754901|ref|YP_844019.1| 104 LIKKLL--EPYDLKDMKVYSSKRDQAFVSSLV 133
                                    566666..666666666666666666666544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1631  (0.0909699); expected 358.6 (0.02)
Passed bias filter:                      722  (0.04027); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1288.84
//
Query:       gi|116754902|ref|YP_844020.1|  [L=85]
Description: H+-transporting two-sector ATPase, C subunit [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.6e-11   44.3  12.4    1.6e-11   44.3  12.4    1.6  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 ?   -0.9   0.1      0.12   2.2e+03      44      55 ..       2      13 ..       1      15 [. 0.71
   2 !   44.3  12.4   9.1e-16   1.6e-11       2      60 .]      16      74 ..      15      74 .. 0.98

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.12
                                   HHHHHHHHHHHH CS
                     ATP-synt_C 44 afaeaialygLi 55
                                   a+  a  +ygL+
  gi|116754902|ref|YP_844020.1|  2 AITDAGVMYGLL 13
                                   566777888886 PP

  == domain 2  score: 44.3 bits;  conditional E-value: 9.1e-16
                                   HHHHHH.GGGHHHHHHHHHHHHHHHHHHHHSGHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     ATP-synt_C  2 gaglavGlsalgsGigiGkagsagiravarnpklftksliilafaeaialygLivalil 60
                                   gagla+Gl+++g+G+g   +g+a ++ va+ p   +k l ++ ++e++ ++gL v+lil
  gi|116754902|ref|YP_844020.1| 16 GAGLATGLAGIGAGVGEQGIGAAVVGVVAEEPGFLGKGLFLMLLPETLIIFGLAVSLIL 74
                                   9********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      198  (0.0110436); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 616.38
//
Query:       gi|116754903|ref|YP_844021.1|  [L=674]
Description: V-type ATPase, 116 kDa subunit [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-31  108.1   9.2    5.1e-20   71.0   0.4    2.8  3  V_ATPase_I       V-type ATPase 116kDa subunit family
     0.0001   22.6   0.2      0.063   13.6   0.0    2.2  2  DUF5082          Domain of unknown function (DUF5082)
    0.00011   22.3   0.3     0.0022   18.1   0.0    2.6  2  UPF0242          Uncharacterised protein family (UPF0242) N-t
    0.00022   21.1   1.3     0.0091   15.9   0.2    2.5  2  Prefoldin_2      Prefoldin subunit
     0.0024   18.1   1.9       0.22   11.7   0.1    2.3  2  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
  ------ inclusion threshold ------
       0.01   16.0   2.8        0.2   11.9   0.4    2.3  2  Spc24            Spc24 subunit of Ndc80
      0.022   14.7   0.3      0.022   14.7   0.3    1.7  2  Ax_dynein_light  Axonemal dynein light chain
      0.033   14.7   2.2      0.046   14.3   0.3    1.9  2  APG6_N           Apg6 coiled-coil region
      0.033   14.3  10.0       0.19   11.8   0.4    2.9  2  DUF4337          Domain of unknown function (DUF4337)
      0.093   12.8   1.0       0.26   11.4   1.0    1.7  1  bZIP_1           bZIP transcription factor
      0.097   12.7   2.7       0.15   12.2   0.2    2.1  2  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
       0.11   12.3   1.1       0.14   11.9   0.1    1.7  2  KASH_CCD         Coiled-coil region of CCDC155 or KASH
       0.14   11.5   0.0        4.8    6.5   0.0    2.2  2  FliD_C           Flagellar hook-associated protein 2 C-termin
        0.2   11.9   9.4       0.25   11.6   2.0    3.3  3  ABC_tran_CTD     ABC transporter C-terminal domain
       0.22   12.0   0.9        5.6    7.5   0.1    2.4  2  DUF4140          N-terminal domain of unknown function (DUF41
        0.4   10.5   5.2        1.3    8.8   1.6    2.6  2  DivIC            Septum formation initiator
       0.66    9.9   4.2        1.3    9.0   1.1    2.3  2  Prefoldin        Prefoldin subunit
        1.5    9.0   3.8        2.6    8.2   3.8    1.4  1  Myc-LZ           Myc leucine zipper domain
        1.6    8.0   3.7        5.6    6.2   0.0    3.1  2  DUF4407          Domain of unknown function (DUF4407)


Domain annotation for each model (and alignments):
>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1     0.067        63      70     103 ..     215     248 ..     182     266 .. 0.66
   2 !   71.0   0.4   5.4e-23   5.1e-20     267     559 ..     231     523 ..     224     534 .. 0.78
   3 !   38.5   2.7   3.6e-13   3.4e-10     717     811 ..     568     665 ..     566     667 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.067
                     V_ATPase_I  70 eldeleeelekleeelkelnenleklkkelnelv 103
                                     +++le+e+++le+e + l+++l++lkk++++++
  gi|116754903|ref|YP_844021.1| 215 AISTLEAEIKRLESEKEPLQKKLKDLKKQYEDII 248
                                    4555666666666666666666666666665544 PP

  == domain 2  score: 71.0 bits;  conditional E-value: 5.4e-23
                     V_ATPase_I 267 ealkevleeiakeleewklkvkkekaiyh..tLnlfnldvtkkvliaegWvpkeeleeiqkalkeateess....ssvps 340
                                    e l++ l++++k++e++ l      +i +  t   +++ ++++ ++ +g+vp+++ +++++al+++t  +          
  gi|116754903|ref|YP_844021.1| 231 EPLQKKLKDLKKQYEDIILAADEYLSIQTqkTDAPLRFATSENAFVIDGYVPSADYDKLKSALESTTGGRIhvekL---- 306
                                    5556666666666666666666555554311334467788999**********************98655444432.... PP

                     V_ATPase_I 341 ilneiet....k.etpPTyfrtnkfteafQeivdaYGiarYrEvNpalftiitFPFlFavMFGDiGHGlllllfalllvl 415
                                      ne+e+    k e+ PT ++   + + +  i   ++i++Y+E  p+l+  + FP +F++  GD++ G+++ll   +lv+
  gi|116754903|ref|YP_844021.1| 307 PENEMEElvekKgEDIPTKIENPGIVKPYELITRLFAIPEYKEFDPTLLIFVFFPIMFGMILGDVAYGIMILL---VLVM 383
                                    2233332221134778****************************************************99986...6888 PP

                     V_ATPase_I 416 kekklkkkkkdeilemlfsgRYiillmGlfsiYtGliYNdifskslnlfgSswevkeka....veeeelk.........k 482
                                     +kk++++     ++ l++   i+++ +++si  Gli+ +if+ ++ l+g  +    ++          +         +
  gi|116754903|ref|YP_844021.1| 384 LKKKFRTE----GWTQLIN---IVMIASVWSIIFGLIFGEIFG-PMGLWGKVFGQLPHEeilaL-----EesgrffgegV 450
                                    99999875....5666665...7999****************8.899***99988433334431.....13345677777 PP

                     V_ATPase_I 483 ekkeekvYpfGlDpaWklaenellflnSlKmKlsvilGviqMlfgvllslvNalyfkkkldiilefiPqllfllsif 559
                                        ++v p+G+ p  +la+n++l+l    + +s+ +Gv++  +g +l +   l+  +k + ++e +P l+f +++ 
  gi|116754903|ref|YP_844021.1| 451 FGPLGRVGPMGMFPLYRLATNAVLML----IGVSIFIGVLHCGIGSILGVKTELNYGEKKHAYFERLPVLIFQVAFA 523
                                    778889999**************988....678**************************************976544 PP

  == domain 3  score: 38.5 bits;  conditional E-value: 3.6e-13
                     V_ATPase_I 717 iSnTASYLRLWALSLAHaqLseVlwemvlkkal..lksksvlgvillvilfavfavltvavLllmeglsafLHaLRLhWV 794
                                    +Sn  SYLRL A+ LA    +    +  +  ++  l+ +++l++++++++++v +v+  ++ ll+  ls f+H LRLh V
  gi|116754903|ref|YP_844021.1| 568 VSNLISYLRLLAIGLASVGVAFAANKLAFGVIMpmLSGGEHLTMVAYIVGVIVLLVV-HFINLLLGILSPFMHPLRLHYV 646
                                    9***************99888665555555544435556666666666666665555.45777889************** PP

                     V_ATPase_I 795 EfqsKFyk..gdGykFepf 811
                                    E+ +KFy+  g G++++pf
  gi|116754903|ref|YP_844021.1| 647 EMFTKFYSqhGGGVEYSPF 665
                                    *******644899*****9 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0    0.0081       7.7      75     121 ..      79     125 ..      40     126 .. 0.82
   2 !   13.6   0.0   6.7e-05     0.063      87     120 ..     213     246 ..     198     248 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0081
                        DUF5082  75 lessyqtyvdkldelidaieeEIerLenqiseaqgvldtlqsqlnsl 121
                                    +  + +++v+++d+l  ++ eE++   + i+  +  ++++q q+n l
  gi|116754903|ref|YP_844021.1|  79 VRFAESQIVSQMDDLLGRLAEEVTSTYERITAIEAEVKSKQDQINAL 125
                                    555667899***********************************987 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 6.7e-05
                        DUF5082  87 delidaieeEIerLenqiseaqgvldtlqsqlns 120
                                    d +i+ +e EI+rLe++++ +q++l+ l++q ++
  gi|116754903|ref|YP_844021.1| 213 DVAISTLEAEIKRLESEKEPLQKKLKDLKKQYED 246
                                    678999**********************999765 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 ?    1.3   0.1      0.34   3.2e+02     139     175 ..      89     125 ..      48     138 .. 0.75
   2 !   18.1   0.0   2.4e-06    0.0022      91     152 ..     185     263 ..     141     272 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.34
                        UPF0242 139 eleeqLaekqellqeyqetieeqrsvlekrqdqieqL 175
                                    ++++ L +  e +    e i+   ++++++qdqi+ L
  gi|116754903|ref|YP_844021.1|  89 QMDDLLGRLAEEVTSTYERITAIEAEVKSKQDQINAL 125
                                    4555666666666667778888888888888888877 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 2.4e-06
                        UPF0242  91 leelqeeeeeLkee.................ldakeeelerlkeenqqLqekleaiaedfeelkleleeqLaekqellq 152
                                    +e++ e +  L+e+                 ++  e e++rl+ e++ Lq+kl++ ++++e+  l+++e L  ++++ +
  gi|116754903|ref|YP_844021.1| 185 VEKASEVQAVLAEHgfaeisvpkltgapdvaISTLEAEIKRLESEKEPLQKKLKDLKKQYEDIILAADEYLSIQTQKTD 263
                                    788888888889999999999999999999999**************************************99998765 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1     0.082        77      61      96 ..      91     126 ..      86     127 .. 0.78
   2 !   15.9   0.2   9.6e-06    0.0091      64     100 ..     209     245 ..     199     249 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.082
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Prefoldin_2  61 eevkeeLeerketlekeiktlekqleklekeleelk 96 
                                    ++++ +L e+  +  ++i+++e + ++++ +++ l+
  gi|116754903|ref|YP_844021.1|  91 DDLLGRLAEEVTSTYERITAIEAEVKSKQDQINALR 126
                                    566777888888888888888888888888888775 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 9.6e-06
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Prefoldin_2  64 keeLeerketlekeiktlekqleklekeleelkeelq 100
                                    +   +  + tle+eik+le+++e l+k+l++lk++  
  gi|116754903|ref|YP_844021.1| 209 TGAPDVAISTLEAEIKRLESEKEPLQKKLKDLKKQYE 245
                                    5555567789***********************9865 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 ?    5.3   0.2     0.023        21      10      50 ..      83     123 ..      80     128 .. 0.88
   2 !   11.7   0.1   0.00024      0.22      14      43 ..     216     245 ..     209     263 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.023
                    TMF_TATA_bd  10 svqlverlsseirrlEgElaslkeelerleaerdeareeiv 50 
                                    ++q+v+++   + rl  E++s+ e+++ +eae ++ +++i 
  gi|116754903|ref|YP_844021.1|  83 ESQIVSQMDDLLGRLAEEVTSTYERITAIEAEVKSKQDQIN 123
                                    6899************************9999888887775 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00024
                    TMF_TATA_bd  14 verlsseirrlEgElaslkeelerleaerd 43 
                                    ++ l++ei+rlE+E++ l+++l+ l+++ +
  gi|116754903|ref|YP_844021.1| 216 ISTLEAEIKRLESEKEPLQKKLKDLKKQYE 245
                                    7899*********************99976 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1     0.069        65       2      37 ..      90     125 ..      89     129 .. 0.92
   2 ?   11.9   0.4   0.00021       0.2      13      44 ..     216     250 ..     213     274 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.069
                          Spc24   2 ldnekfriakelsdleselesleselaelkeeleel 37 
                                    +d+++ r+a+e++++ + ++++e+e ++++++++ l
  gi|116754903|ref|YP_844021.1|  90 MDDLLGRLAEEVTSTYERITAIEAEVKSKQDQINAL 125
                                    899999**************************9987 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00021
                          Spc24  13 lsdleselesleselaelkeeleeleeesee...k 44 
                                    +s le+e+++lese++ l+++l++l+++ e+    
  gi|116754903|ref|YP_844021.1| 216 ISTLEAEIKRLESEKEPLQKKLKDLKKQYEDiilA 250
                                    789***********************998885441 PP

>> Ax_dynein_light  Axonemal dynein light chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       3.8   3.5e+03     140     161 ..      99     120 ..      82     126 .. 0.46
   2 ?   14.7   0.3   2.4e-05     0.022     122     176 ..     217     271 ..     211     276 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.8
                Ax_dynein_light 140 kqvaelkaklealekrekerrq 161
                                    ++v+++ ++++a+e++ k +++
  gi|116754903|ref|YP_844021.1|  99 EEVTSTYERITAIEAEVKSKQD 120
                                    3333333333333333333332 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2.4e-05
                Ax_dynein_light 122 selekkikeLeeekeelekqvaelkaklealekrekerrqeeekkheeeieflkk 176
                                    s le++ik+Le+eke l+k++++lk+++e++   + e ++++++k +  + f   
  gi|116754903|ref|YP_844021.1| 217 STLEAEIKRLESEKEPLQKKLKDLKKQYEDIILAADEYLSIQTQKTDAPLRFATS 271
                                    67899**********************************9999999887777655 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1       1.8   1.7e+03      58      86 ..      96     124 ..      62     128 .. 0.57
   2 ?   14.3   0.3   4.9e-05     0.046      49     108 ..     216     275 ..     187     297 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.8
                         APG6_N  58 klekeeeelleeLkelekereeleaelaa 86 
                                    +l +e  +  e + ++e+e ++ +++++a
  gi|116754903|ref|YP_844021.1|  96 RLAEEVTSTYERITAIEAEVKSKQDQINA 124
                                    33444444444444444444444444443 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 4.9e-05
                         APG6_N  49 leeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynel 108
                                    +  le e+++le+e+e l+++Lk+l+k+ e++  +  ++ +   ++ +   rf ++ n++
  gi|116754903|ref|YP_844021.1| 216 ISTLEAEIKRLESEKEPLQKKLKDLKKQYEDIILAADEYLSIQTQKTDAPLRFATSENAF 275
                                    566777777777777777777777777777776666666555555555555555555555 PP

>> DUF4337  Domain of unknown function (DUF4337)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.4    0.0002      0.19      68     116 ..     205     253 ..     186     277 .. 0.79
   2 ?    8.0   0.8    0.0031         3     119     160 ..     513     554 ..     496     554 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0002
                        DUF4337  68 aeelaaavdkkiakykkkiarykkekkeikkkAkeleaerdeaneasdk 116
                                     ++l+ a d +i +++++i+r ++ek+ ++kk k+l++++++   a+d+
  gi|116754903|ref|YP_844021.1| 205 VPKLTGAPDVAISTLEAEIKRLESEKEPLQKKLKDLKKQYEDIILAADE 253
                                    56777888999*****************************998777776 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0031
                        DUF4337 119 lasalLqiaIvlaaialltkkklllylslvlglvGlvlflag 160
                                    l ++++q+a +l  + l+++   l+yl+ +l +v +v++++g
  gi|116754903|ref|YP_844021.1| 513 LPVLIFQVAFALLLLGLVLGFMPLVYLMGLLVVVSIVMMVMG 554
                                    56889**********************************987 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.0   0.00028      0.26      28      57 ..     216     245 ..     214     248 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00028
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         bZIP_1  28 ieeLerrvkaLekeNksLkseleelkkeve 57 
                                    i+ Le + k Le+e + L+++l+ lkk++e
  gi|116754903|ref|YP_844021.1| 216 ISTLEAEIKRLESEKEPLQKKLKDLKKQYE 245
                                    678************************998 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.2      0.81   7.6e+02       8      32 ..      99     123 ..      82     130 .. 0.49
   2 ?   12.2   0.2   0.00015      0.15      56     115 ..     188     247 ..     185     248 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.81
                     TPR_MLP1_2   8 eeikslkeekeeaeaklqklqedle 32 
                                    ee++s  e++++ ea++++ q++++
  gi|116754903|ref|YP_844021.1|  99 EEVTSTYERITAIEAEVKSKQDQIN 123
                                    3333333333333333333333333 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00015
                     TPR_MLP1_2  56 vkelqalreelnelkaeiaelkaeaesakaeleeseesweeqkeelekelselekriedl 115
                                    + e+qa+ +e+  ++  + +l+ + + a ++le++ + +e++ke l+k+l++l+k++ed+
  gi|116754903|ref|YP_844021.1| 188 ASEVQAVLAEHGFAEISVPKLTGAPDVAISTLEAEIKRLESEKEPLQKKLKDLKKQYEDI 247
                                    5667777777777777888888888999999************************99996 PP

>> KASH_CCD  Coiled-coil region of CCDC155 or KASH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       6.9   6.5e+03      41      47 ..      97     103 ..      85     126 .. 0.43
   2 ?   11.9   0.1   0.00015      0.14     103     149 ..     215     261 ..     213     298 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 6.9
                       KASH_CCD  41 Lteeiee 47 
                                    L+ee++ 
  gi|116754903|ref|YP_844021.1|  97 LAEEVTS 103
                                    3333322 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00015
                       KASH_CCD 103 kiesLqeenikllaekdelkkklkeLlkekaeLkkqlheleellaek 149
                                     i +L+ e+++l +ek+ l+kklk+L k+ +++   ++e+ ++ ++k
  gi|116754903|ref|YP_844021.1| 215 AISTLEAEIKRLESEKEPLQKKLKDLKKQYEDIILAADEYLSIQTQK 261
                                    6899*******************999988888777777777766666 PP

>> FliD_C  Flagellar hook-associated protein 2 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.073        69     169     214 ..      82     126 ..      60     153 .. 0.86
   2 ?    6.5   0.0    0.0051       4.8     190     225 ..     210     245 ..     154     257 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.073
                                    .SXSHHHHHHHHHHHHHSTT.SHHHHHHHHXXXXHHHHHHHHHHHH CS
                         FliD_C 169 sdsglatrlenllksyvkssngtlqtasknltkqikdldkkiedld 214
                                     +s +++++++ll  + +   +++ ++++ ++ ++k+++++i++l 
  gi|116754903|ref|YP_844021.1|  82 AESQIVSQMDDLLGRLAEEV-TSTYERITAIEAEVKSKQDQINALR 126
                                    57899***********9888.9999****************99875 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0051
                                    SHHHHHHHHXXXXHHHHHHHHHHHHHCHHHHHHHHH CS
                         FliD_C 190 gtlqtasknltkqikdldkkiedldkrletleerlk 225
                                    g+ ++a+++l+ +ik+l+++ e l+k+l++l+++++
  gi|116754903|ref|YP_844021.1| 210 GAPDVAISTLEAEIKRLESEKEPLQKKLKDLKKQYE 245
                                    555678888999999999999999999999888776 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.26   2.5e+02      35      58 ..     100     123 ..      87     126 .. 0.59
   2 ?   11.6   2.0   0.00027      0.25      10      46 ..     216     250 ..     211     267 .. 0.80
   3 ?    0.6   0.1      0.73   6.9e+02      14      46 ..     308     341 ..     301     343 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.26
                   ABC_tran_CTD  35 elysdpeklaelsaeleeleaeLe 58 
                                    e++s++e+++++ ae +  +++++
  gi|116754903|ref|YP_844021.1| 100 EVTSTYERITAIEAEVKSKQDQIN 123
                                    345555555555555555555554 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00027
                   ABC_tran_CTD  10 leeleaeIeaLEeeiaeleaeladpelysdpeklael 46 
                                    + +leaeI +LE e++ l+++l d    +++e +  +
  gi|116754903|ref|YP_844021.1| 216 ISTLEAEIKRLESEKEPLQKKLKDLK--KQYEDIILA 250
                                    578********************876..777765555 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.73
                   ABC_tran_CTD  14 eaeIeaL.Eeeiaeleaeladpelysdpeklael 46 
                                    e+e+e+L E++ +++ +++++p++ + +e +++l
  gi|116754903|ref|YP_844021.1| 308 ENEMEELvEKKGEDIPTKIENPGIVKPYELITRL 341
                                    4568887577788999999999999888877665 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 ?    2.6   0.1       0.2   1.9e+02      65      91 ..      92     125 ..      69     129 .. 0.52
   2 ?    7.5   0.1    0.0059       5.6      65      94 ..     206     243 ..     156     246 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.2
                        DUF4140  65 e.......elkalraeleeledelaaledelaaa 91 
                                    +       e+ ++ ++++++e+e +  +d+++a+
  gi|116754903|ref|YP_844021.1|  92 DllgrlaeEVTSTYERITAIEAEVKSKQDQINAL 125
                                    3444444334444455555555555544444443 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0059
                        DUF4140  65 e........elkalraeleeledelaaledelaaaear 94 
                                    +        ++++l+ae+++le e++ l+++l+ ++++
  gi|116754903|ref|YP_844021.1| 206 PkltgapdvAISTLEAEIKRLESEKEPLQKKLKDLKKQ 243
                                    044444544799*******************9999998 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1      0.18   1.7e+02      15      37 ..     104     126 ..      96     127 .. 0.77
   2 ?    8.8   1.6    0.0014       1.3      26      55 ..     216     245 ..     213     251 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.18
                                    XXXHHHHHHHHHHHHHHHHHHHH CS
                          DivIC  15 gllaykqlkqeiaalqaelaklk 37 
                                    ++ ++ ++++e++ +q+++++l+
  gi|116754903|ref|YP_844021.1| 104 TYERITAIEAEVKSKQDQINALR 126
                                    56777888888888888888876 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0014
                                    HHHHHHHHHHHHHHHHHHHHHHCC-XXXXX CS
                          DivIC  26 iaalqaelaklkaeneeLeaevkdLksded 55 
                                    i +l+ae+++l  e+e L++++kdLk++++
  gi|116754903|ref|YP_844021.1| 216 ISTLEAEIKRLESEKEPLQKKLKDLKKQYE 245
                                    778999999999999999999999988665 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1      0.37   3.5e+02      82     111 ..      97     126 ..      88     130 .. 0.74
   2 ?    9.0   1.1    0.0013       1.3      76     110 ..     213     247 ..     211     254 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.37
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Prefoldin  82 lkkkleelekqlekleeeleklkdqittle 111
                                    l +++++  + ++ +e+e++ ++dqi+ l+
  gi|116754903|ref|YP_844021.1|  97 LAEEVTSTYERITAIEAEVKSKQDQINALR 126
                                    556666777778888888888888888765 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0013
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Prefoldin  76 eeAiellkkkleelekqlekleeeleklkdqittl 110
                                    + Ai +l+ +++ le+  e l+++l++lk+q++ +
  gi|116754903|ref|YP_844021.1| 213 DVAISTLEAEIKRLESEKEPLQKKLKDLKKQYEDI 247
                                    56999**************************9987 PP

>> Myc-LZ  Myc leucine zipper domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   3.8    0.0028       2.6       1      22 [.     221     242 ..     221     247 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0028
                         Myc-LZ   1 aeEqrLlSekEqLRkrrEqLKh 22 
                                    ae +rL SekE L+k+   LK 
  gi|116754903|ref|YP_844021.1| 221 AEIKRLESEKEPLQKKLKDLKK 242
                                    6779*************99997 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.25   2.4e+02     130     160 ..      96     126 ..      74     134 .. 0.65
   2 ?    6.2   0.0    0.0059       5.6     118     168 ..     186     256 ..     181     369 .. 0.59

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.25
                        DUF4407 130 altaelaeleaqiaalqaeidaaearldalr 160
                                     l +e++   ++i+a++ae+++++++++alr
  gi|116754903|ref|YP_844021.1|  96 RLAEEVTSTYERITAIEAEVKSKQDQINALR 126
                                    2566666666677777777777777777766 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0059
                        DUF4407 118 eeakelkeqlaaa....................ltaelaeleaqiaalqaeidaaearldalraeaqkeld 168
                                    e+a+e+++ la++                    l+ae+++le++ + lq++++ +++++++   +a++ l+
  gi|116754903|ref|YP_844021.1| 186 EKASEVQAVLAEHgfaeisvpkltgapdvaistLEAEIKRLESEKEPLQKKLKDLKKQYEDIILAADEYLS 256
                                    56667777777777777777777777555555555666666666666666666666665555555544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (674 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1790  (0.0998383); expected 358.6 (0.02)
Passed bias filter:                     1168  (0.0651459); expected 358.6 (0.02)
Passed Vit filter:                       186  (0.0103743); 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):              19  [number of targets reported over threshold]
# CPU time: 0.92u 0.32s 00:00:01.24 Elapsed: 00:00:00.50
# Mc/sec: 4035.05
//
Query:       gi|116754904|ref|YP_844022.1|  [L=108]
Description: H(+)-transporting ATP synthase, subunit H [Methanosaeta thermophila PT]
Scores for complete 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-07   30.7  16.7    5.1e-07   30.1  16.7    1.3  1  V-ATPase_G_2  Vacuolar (H+)-ATPase G subunit
      2e-06   28.3  11.9    2.4e-06   28.0  11.9    1.1  1  V-ATPase_G    Vacuolar (H+)-ATPase G subunit
     0.0015   18.7  19.1     0.0029   17.7  19.0    1.5  1  ATP-synt_B    ATP synthase B/B' CF(0)
  ------ inclusion threshold ------
      0.021   15.1   4.0      0.028   14.7   4.0    1.2  1  Muted         Organelle biogenesis, Muted-like protein
      0.073   13.3   1.2       0.13   12.5   0.8    1.7  2  DUF5446       Family of unknown function (DUF5446)
       0.11   12.5   1.5       0.15   12.1   1.5    1.1  1  bMG3          Bacterial alpha-2-macroglobulin MG3 domain
       0.13   12.0   0.9       0.26   11.1   0.9    1.7  1  GPW_gp25      Gene 25-like lysozyme
       0.18   11.7   3.6        1.4    8.8   0.7    2.3  2  Nuc_N         Nuclease N terminal
        3.9    7.6  13.3        7.1    6.7  13.3    1.6  1  DivIVA        DivIVA protein


Domain annotation for each model (and alignments):
>> V-ATPase_G_2  Vacuolar (H+)-ATPase G subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1  16.7   2.5e-10   5.1e-07       2     101 ..       2     101 ..       1     103 [. 0.96

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 2.5e-10
                                    XXXHHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   V-ATPase_G_2   2 essrllkeLaerEaeLdqrlEaArkeaereveaAeaeAarilreAeakakalqaeyeqelaeevarireeararaeaeaq 81 
                                    + + +l  +++ Ea+ ++ + +A +e e++++ A  eAa i+r Ae +a+a+ ++  ++ + ev++ ++ + +++  ++ 
  gi|116754904|ref|YP_844022.1|   2 ARHDILMRIKQAEADAKASVQQALQEKEKRIADATTEAANIVRTAESEAQAFYEKELAKAEGEVKAKKQSVISEGMRKVD 81 
                                    567899999*********************************************************************** PP

                                    HHHHHHHCSHHHHHHHHHHH CS
                   V-ATPase_G_2  82 avrkraearlqqAvelilka 101
                                    a+r +a+a+l++Ave  lk+
  gi|116754904|ref|YP_844022.1|  82 ALRSSANAKLDKAVEYLLKE 101
                                    ******************98 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 !   28.0  11.9   1.2e-09   2.4e-06      11     100 ..      12     101 ..       4     105 .. 0.95

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.2e-09
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHSSHHHHHHHHHHHHHH CS
                     V-ATPase_G  11 qAEkeAaeivkeArkrkakrlkqAkeeAekEieeyrakkekefkekeaeklgseeelekkieketeekikelkesvkknk 90 
                                    qAE +A+  v++A ++k+kr+ +A +eA++ +    ++ ++ ++++ a++ g+ ++ ++++ +e  +k++ l++s++++ 
  gi|116754904|ref|YP_844022.1|  12 QAEADAKASVQQALQEKEKRIADATTEAANIVRTAESEAQAFYEKELAKAEGEVKAKKQSVISEGMRKVDALRSSANAKL 91 
                                    8*****************************99999999999999999********************************* PP

                                    HHHHHHHHHH CS
                     V-ATPase_G  91 eavvkellkl 100
                                    ++ v+ llk 
  gi|116754904|ref|YP_844022.1|  92 DKAVEYLLKE 101
                                    *******986 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 !   17.7  19.0   1.4e-06    0.0029      34      99 ..       5      71 ..       3     100 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.4e-06
                     ATP-synt_B 34 kIadeiaeAeer.rkeaaallaeaeqqlkeAraeAaeiiknAkkeaeklkeeieaeaeaeaerlkes 99
                                    I   i++Ae+  +++ +++l+e+e++ ++A  eAa+i++ A++ea+   e+  a+ae e++  k+s
  gi|116754904|ref|YP_844022.1|  5 DILMRIKQAEADaKASVQQALQEKEKRIADATTEAANIVRTAESEAQAFYEKELAKAEGEVKAKKQS 71
                                   5778899**986167889*****************************99999999998888765554 PP

>> Muted  Organelle biogenesis, Muted-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   4.0   1.4e-05     0.028      56     132 ..      14      91 ..       3     104 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.4e-05
                          Muted  56 lpkclesmkenLselnkkleaalekver.llqkeleeekrkseqlqekeeerkaeweeflkelqekkeevDeefeekv 132
                                        ++s+++ L+e +k++ +a+ ++ + +++ e+e++   +++l ++e e ka+++++++e  +k + +  + + k+
  gi|116754904|ref|YP_844022.1|  14 EADAKASVQQALQEKEKRIADATTEAANiVRTAESEAQAFYEKELAKAEGEVKAKKQSVISEGMRKVDALRSSANAKL 91 
                                    45567789***********9988766551677889999999********99999999999888777666555555554 PP

>> DUF5446  Family of unknown function (DUF5446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.8   6.5e-05      0.13       6      55 ..      17      66 ..      13      78 .. 0.95
   2 ?   -0.6   0.0      0.74   1.5e+03      34      47 ..      82      91 ..      58     105 .. 0.49

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.5e-05
                        DUF5446  6 sKdsvLqlLeeiEeeltevEkelseavneteaekeekeeerldllekElk 55
                                   +K sv q L+e E+ +  +  e  + v+  e e++   e+ l + e E+k
  gi|116754904|ref|YP_844022.1| 17 AKASVQQALQEKEKRIADATTEAANIVRTAESEAQAFYEKELAKAEGEVK 66
                                   599*********************************************97 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.74
                        DUF5446 34 eteaekeekeeerl 47
                                   +++  +    ++ l
  gi|116754904|ref|YP_844022.1| 82 ALRSSA----NAKL 91
                                   222333....3333 PP

>> bMG3  Bacterial alpha-2-macroglobulin MG3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.5   7.5e-05      0.15      21      92 ..       9      92 ..       6      95 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.5e-05
                           bMG3 21 sLdsgkPvagaeVr.lldkkgevlaegtTDaqGvarfaallar...........gkegaapylvsArkdedlaflkldwerg 90
                                    ++++++ a+a+V+  l++k++ +a +tT a+ ++r a+ +a+           g+ +a+   v+ ++ + +  l+++ +++
  gi|116754904|ref|YP_844022.1|  9 RIKQAEADAKASVQqALQEKEKRIADATTEAANIVRTAESEAQafyekelakaeGEVKAKKQSVISEGMRKVDALRSSANAK 90
                                   578899999999963678*********************9999999988888887777778888888888888888887777 PP

                           bMG3 91 ld 92
                                   ld
  gi|116754904|ref|YP_844022.1| 91 LD 92
                                   76 PP

>> GPW_gp25  Gene 25-like lysozyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.9   0.00013      0.26      43      72 ..      13      42 ..       4     101 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00013
                                   HHHHHHHHHHHHHHHH-TTEEEEEEEE... CS
                       GPW_gp25 43 dreriareireailrfEpRirlvsveveve 72
                                     +++++++++a+++ E+Ri++ ++e+++ 
  gi|116754904|ref|YP_844022.1| 13 AEADAKASVQQALQEKEKRIADATTEAANI 42
                                   567899*****************9998554 PP

>> Nuc_N  Nuclease N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.7   0.00072       1.4      29      52 ..       9      32 ..       4      38 .. 0.83
   2 ?    3.8   0.1     0.027        53      26      46 ..      54      74 ..      43      82 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00072
                          Nuc_N 29 kvkeaHkaSKAkiQsrIsklEkeG 52
                                   ++k+a ++ KA++Q+ ++  Ek  
  gi|116754904|ref|YP_844022.1|  9 RIKQAEADAKASVQQALQEKEKRI 32
                                   89****************999874 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.027
                          Nuc_N 26 ysakvkeaHkaSKAkiQsrIs 46
                                   y+  + +a  + KAk Qs Is
  gi|116754904|ref|YP_844022.1| 54 YEKELAKAEGEVKAKKQSVIS 74
                                   677778888999******998 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7  13.3    0.0035       7.1      55     120 ..       7      69 ..       2     100 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0035
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         DivIVA  55 lkeykeleetLkktlvvaqetaeevkanakkeaeliikeAekkaekiveeaeeeakkiaeeieelk 120
                                    l++ k++e + k ++  a +  e+  a a++ea +i++ Ae +a++  e   +e++k++ e++  k
  gi|116754904|ref|YP_844022.1|   7 LMRIKQAEADAKASVQQALQEKEKRIADATTEAANIVRTAESEAQAFYE---KELAKAEGEVKAKK 69 
                                    78889999999999999999************************99985...44444444443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2043  (0.113949); expected 358.6 (0.02)
Passed bias filter:                      697  (0.0388756); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); 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 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 776.39
//
Query:       gi|116754905|ref|YP_844023.1|  [L=390]
Description: ribulose-bisphosphate carboxylase [Methanosaeta thermophila PT]
Scores for complete 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-88  295.4   1.3    6.1e-88  294.9   1.3    1.3  1  RuBisCO_large    Ribulose bisphosphate carboxylase large chai
    1.6e-22   79.9   0.0    3.3e-22   78.9   0.0    1.5  1  RuBisCO_large_N  Ribulose bisphosphate carboxylase large chai
  ------ inclusion threshold ------
      0.046   13.2   0.7        0.2   11.1   0.3    2.0  2  PEP_mutase       Phosphoenolpyruvate phosphomutase


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 !  294.9   1.3     1e-91   6.1e-88       1     299 []     111     388 ..     111     388 .. 0.97

  Alignments for each domain:
  == domain 1  score: 294.9 bits;  conditional E-value: 1e-91
                                    .HHHHHHHH...T--EEEEE-SSSS---HHHHHHHHHHHHTT-.SEEE--TT-SSBTTB-HHHHHHHHHHHHHHHHHHHS CS
                  RuBisCO_large   1 giaverevlnkegrpilGtiiKPklGLspknyarvvyelllgglDfiKdDEnlnsqpfarlkdrieavaeaikraqdetG 80 
                                    gi+++r+++++++rp++Gti+KPk+GL+p+++a+v+  +++gglD++KdDE l++q f++++ r+e+v+   +r + etG
  gi|116754905|ref|YP_844023.1| 111 GIEEARRIIDAYNRPLVGTIVKPKVGLNPSQTAEVAGAAVRGGLDLVKDDETLTDQKFCPMERRVEEVMAEFDRVESETG 190
                                    799***************************************************************************** PP

                                    S--EEEEE---SSHHHHHHHHHHHHHHHGGEEEEEHHHH-HHHHHHHHHHSTTS..EEEEE-TTTHHHHST--SEE-HHH CS
                  RuBisCO_large  81 ekklyalnitaddleemlrraefvketggeivlvdvlviGfaaitslrkafrknelllHlHraghgaltrqskhGisfrv 160
                                    +k+ ya+n+t    + +l+rae + + g+++++vdvl++Gf+a++ l++     +l +H+Hr +hga+tr++ hGis+ v
  gi|116754905|ref|YP_844023.1| 191 KKAFYAVNVTTGA-DTILERAERAIDRGANMLMVDVLTAGFSALEALARG---VDLPIHVHRTMHGAMTRDRAHGISMLV 266
                                    **********665.99*******************************999...899************************ PP

                                    HHHHHHHHT-SEEE---TTSSSBS--GG......GHHHHHHHHSSEEE-SS-EEE-TT----EEEEESS--TTTHHHHHH CS
                  RuBisCO_large 161 lakllRLlGvdhlhtgtvgvgklegdesvvkgfkdtlrekmleedeaegiffeqdlaslkavlpvasgGihagqlpelle 240
                                    +akl+R++G  +lhtg+  vgk+ +d +              e+d+++  ++++d+++lk+v+pvasgGih g++ + l+
  gi|116754905|ref|YP_844023.1| 267 IAKLVRMAGGTNLHTGSY-VGKMASDIE--------------ENDQCR-DALREDWYGLKRVFPVASGGIHPGKVAGNLD 330
                                    ******************.*****9988..............445554.5799*************************** PP

                                    HHS---SEEE-HHHHHTSTT-HHHHHHHHHHHHHHHHHT--HHHHHTT-HHHHHHHHHX CS
                  RuBisCO_large 241 nlgesdvilqaGGGilgHpdgaaaGakalrqaleaaveGadleeyAkehkeLarAlesw 299
                                      g  d i+qaGGG++gHpdg++aGa+a+ qa+ea+++G++++eyA++hkeL+rAle w
  gi|116754905|ref|YP_844023.1| 331 GYGI-DCIVQAGGGVHGHPDGTTAGARAMVQAVEAWLSGIPVMEYAERHKELKRALERW 388
                                    ***9.****************************************************99 PP

>> RuBisCO_large_N  Ribulose bisphosphate carboxylase large chain, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.9   0.0   5.5e-26   3.3e-22      11     119 ..       3     100 ..       1     101 [. 0.95

  Alignments for each domain:
  == domain 1  score: 78.9 bits;  conditional E-value: 5.5e-26
                RuBisCO_large_N  11 etdllaafrvePaegvsveeaaaavAaeSStgtwtevsttkdellkklkakvyeieeveeekelvkiAYplelFeegsip 90 
                                    ++d++a +rve  +++ +++aa+a+Aae Stgtwtev   ++    +l a v +i+     +++v+i +p+elFe g+ip
  gi|116754905|ref|YP_844023.1|   3 QRDVVARYRVE--TDLPMRKAAEAIAAEQSTGTWTEVRGAES----DLAASVLSID-----GNTVEIEFPVELFEPGNIP 71 
                                    68********9..79**********************99999....9********5.....589**************** PP

                RuBisCO_large_N  91 qllssiaGnifgmkavkalrleDirlPka 119
                                    q ls iaGn fg++a+k++rl D+ +P++
  gi|116754905|ref|YP_844023.1|  72 QYLSVIAGNLFGLEALKKVRLVDVDFPES 100
                                    ***************************86 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.3   3.4e-05       0.2     150     205 ..     198     255 ..     171     276 .. 0.80
   2 ?   -0.5   0.0      0.12     7e+02      43      65 ..     344     366 ..     329     372 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.4e-05
                     PEP_mutase 150 sagagleeaieRaraYaeAGAdgvfvpglqkdae.iaelvaavdvplnvvp.lkgtls 205
                                    +   g ++ +eRa++  + GA++++v  l+   + +++l++ vd+p+ v   ++g+++
  gi|116754905|ref|YP_844023.1| 198 NVTTGADTILERAERAIDRGANMLMVDVLTAGFSaLEALARGVDLPIHVHRtMHGAMT 255
                                    566788999********************9997779***********99983344333 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.12
                     PEP_mutase  43 slGvpDgeelpleellaavraia 65 
                                    ++G+pDg ++ +  +++av+a  
  gi|116754905|ref|YP_844023.1| 344 VHGHPDGTTAGARAMVQAVEAWL 366
                                    58**********99999999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 3058.57
//
Query:       gi|116754906|ref|YP_844024.1|  [L=432]
Description: hypothetical protein Mthe_1617 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.20s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 3493.96
//
Query:       gi|116754907|ref|YP_844025.1|  [L=159]
Description: 30S ribosomal protein S13P [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.4e-39  133.8   1.8    5.3e-39  133.5   1.8    1.1  1  Ribosomal_S13  Ribosomal protein S13/S18


Domain annotation for each model (and alignments):
>> Ribosomal_S13  Ribosomal protein S13/S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.5   1.8     3e-43   5.3e-39       1     127 [.      17     143 ..      17     144 .. 0.97

  Alignments for each domain:
  == domain 1  score: 133.5 bits;  conditional E-value: 3e-43
                  Ribosomal_S13   1 RilgtdidgkkkveialtaikGiGrrkakiilkkadvdedkrigelteeeiekieeivenkaqykipnwi.nrqkdikdG 79 
                                    Ri +td+dgkk+v++alt ikG+Grr a++ + ka+vd  + +g+l ee+ie +++++e  ++++ip+w+ nr+kdi++G
  gi|116754907|ref|YP_844025.1|  17 RIYNTDLDGKKQVQMALTGIKGVGRRLARVFAVKAGVDPCATLGKLPEEQIEALKNVIES-VRDNIPAWMmNRRKDIITG 95 
                                    99**********************************************************.7777777777********* PP

                  Ribosomal_S13  80 kdshvvendlrrklredieRlkkirsyrGlRHkrGlkvRGQrTkttgR 127
                                     d+hv+  ++ ++lred++ +kk rsy+G+RH+ Gl+vRGQrT++tgR
  gi|116754907|ref|YP_844025.1|  96 VDKHVMGAEVLTTLREDLDIMKKTRSYKGIRHELGLRVRGQRTRSTGR 143
                                    ***********************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); 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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1175.01
//
Query:       gi|116754908|ref|YP_844026.1|  [L=183]
Description: 30S ribosomal protein S4P [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-17   62.5   1.4    3.7e-17   61.8   0.2    1.9  2  S4        S4 domain


Domain annotation for each model (and alignments):
>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1     0.094   1.7e+03      16      26 ..      64      74 ..      56      76 .. 0.76
   2 !   61.8   0.2   2.1e-21   3.7e-17       1      47 [.     106     152 ..     106     153 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.094
                                   HHHHHHHHHTT CS
                             S4 16 rreArqlIehG 26
                                   r eAr  Ie+ 
  gi|116754908|ref|YP_844026.1| 64 RGEARADIEAA 74
                                   88999999975 PP

  == domain 2  score: 61.8 bits;  conditional E-value: 2.1e-21
                                    EEHHHHHHHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTCE CS
                             S4   1 rRLdkvlarlglassrreArqlIehGrVlVNGkvvkdpsyrVkpgDv 47 
                                    rRL++ ++r+gla ++r+Arq+I hG+++V G++v+ psy Vk gD+
  gi|116754908|ref|YP_844026.1| 106 RRLQTQVYRQGLANTIRQARQFITHGHIQVAGQRVTVPSYLVKRGDE 152
                                    8*********************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 1377.52
//
Query:       gi|116754909|ref|YP_844027.1|  [L=129]
Description: 30S ribosomal protein S11P [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.9e-46  154.8   2.9    1.3e-45  154.3   2.9    1.2  1  Ribosomal_S11   Ribosomal protein S11
  ------ inclusion threshold ------
      0.047   14.1   0.1      0.065   13.6   0.1    1.2  1  Ribosomal_L18p  Ribosomal L18 of archaea, bacteria, mitoch. a


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 !  154.3   2.9   1.5e-49   1.3e-45       2     110 .]       8     125 ..       7     125 .. 0.99

  Alignments for each domain:
  == domain 1  score: 154.3 bits;  conditional E-value: 1.5e-49
                  Ribosomal_S11   2 vahiqasfnntiititdlkGaevlvksaGglgvkasr.kssPyaaqlaaekaaekvldkGikavevkvkg........pG 72 
                                    +ahi++sfnnt+ititdl+Gae+++k++Gg++vka+r +ssPy+a+++a ++ae+++ kGi  v+vkv++        pG
  gi|116754909|ref|YP_844027.1|   8 IAHIYSSFNNTLITITDLTGAETIAKISGGMVVKAARdESSPYTAMQMAMQVAEQAKAKGIVGVHVKVRApggnkqrsPG 87 
                                    89****************************************************************************** PP

                  Ribosomal_S11  73 pGreaalralaraGlkigriedvtPiPhdgirrpkkrr 110
                                    pG++aa+ralaraGl+igriedvtPiPhdg+++++++r
  gi|116754909|ref|YP_844027.1|  88 PGAQAAIRALARAGLRIGRIEDVTPIPHDGTKPKGGKR 125
                                    **********************************9987 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 ?   13.6   0.1   7.3e-06     0.065      29      89 ..      11      71 ..       6      85 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.3e-06
                                   EEE-SS-EEEEEE-TTT--EEEEECS-SCCCTS-SSSCHHHHHHHHHHHHHHHCHHCHTC- CS
                 Ribosomal_L18p 29 vfrsnrhiyaQviddvkgktlasastlekelklkstknkeaakkvgeliAerakekgiekv 89
                                   ++ s ++  + + d +  +t+a++s+      ++ +++   a +++ ++Ae+ak+kgi  v
  gi|116754909|ref|YP_844027.1| 11 IYSSFNNTLITITDLTGAETIAKISGGMVVKAARDESSPYTAMQMAMQVAEQAKAKGIVGV 71
                                   566777788889999**********8655444678889999****************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       679  (0.0378716); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); 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: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 972.40
//
Query:       gi|116754910|ref|YP_844028.1|  [L=264]
Description: RNA polymerase, insert [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-20   74.1   0.0    3.5e-20   72.4   0.0    1.8  2  RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
    4.3e-18   64.5   0.0    5.8e-18   64.1   0.0    1.2  1  RNA_pol_L      RNA polymerase Rpb3/Rpb11 dimerisation domain
    3.6e-08   32.9  11.3    0.00013   21.6   3.5    2.8  2  Fer4           4Fe-4S binding domain
    1.9e-07   31.1   9.4    1.9e-07   31.1   9.4    2.0  2  Fer4_9         4Fe-4S dicluster domain
    5.5e-07   30.4   5.0     0.0003   21.6   0.4    2.7  2  Fer4_16        4Fe-4S double cluster binding domain
    7.5e-07   29.2   8.2    7.5e-07   29.2   8.2    1.9  2  Fer4_10        4Fe-4S dicluster domain
    5.7e-06   26.8   9.0    5.7e-06   26.8   9.0    2.0  1  Fer4_7         4Fe-4S dicluster domain
    0.00013   22.3   9.2      0.058   13.9   5.4    2.4  2  Fer4_8         4Fe-4S dicluster domain
    0.00076   19.5   2.6    0.00076   19.5   2.6    3.0  3  Fer4_6         4Fe-4S binding domain
     0.0024   18.4  16.0     0.0036   17.8   0.9    2.7  2  Fer4_17        4Fe-4S dicluster domain
     0.0038   17.3   9.8     0.0038   17.3   9.8    2.0  2  Fer4_21        4Fe-4S dicluster domain
     0.0079   16.6   1.9     0.0079   16.6   1.9    3.4  3  Fer4_4         4Fe-4S binding domain
      0.008   16.2   4.2      0.008   16.2   4.2    3.1  2  Fer4_2         4Fe-4S binding domain
  ------ inclusion threshold ------
      0.013   16.4   6.5      0.013   16.4   6.5    3.0  2  Fer4_3         4Fe-4S binding domain
      0.028   14.6  10.7      0.073   13.3  10.7    1.7  1  Fer4_18        4Fe-4S dicluster domain
        4.6    8.1  11.3        6.8    7.5   1.2    2.7  2  Fer4_15        4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.4   0.0   3.1e-23   3.5e-20       1     112 []      44     153 ..      44     153 .. 0.94
   2 ?   -1.3   0.0       2.5   2.8e+03      54      68 ..     226     240 ..     186     252 .. 0.57

  Alignments for each domain:
  == domain 1  score: 72.4 bits;  conditional E-value: 3.1e-23
                                    EEEEECTSSS.HHHHHCHHHCSTCBSSCHHHHHHHHCTT-ETSSSSTTCSEEEEEEEEESSECEEGGGCBESSSSCEESS CS
                  RNA_pol_A_bac   1 VeieentsvlqDEvvaHrlgliplvsedvleillnlkelveeeeegeeeksvelkLnvkgpgevtagdlkledadveivn 80 
                                    + i+entsvl DE +a rlgl+p++++d l ++    e++     g++ + + + L+++gp +v ++d+k++d++v+ + 
  gi|116754910|ref|YP_844028.1|  44 ISIYENTSVLFDEQIALRLGLVPIRADD-LSVYSTPDECQ-CGGIGCPGCRIDFMLTAEGPATVHSRDIKFSDPSVRAAF 121
                                    68***********************665.66699999994.3468*********************************** PP

                                    TTSEEEEEETT-EEEEEEEEEEESSEECTTT- CS
                  RNA_pol_A_bac  81 pdilIakLrkgqeleleakvkkGiGkehakfs 112
                                    ++i+++ L +g++l +e  +   +Gkehak++
  gi|116754910|ref|YP_844028.1| 122 DNIPLVVLGEGEKLVIEGFATLRTGKEHAKWQ 153
                                    *******************************6 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.5
                                    EEEEEESSECEEGGG CS
                  RNA_pol_A_bac  54 lkLnvkgpgevtagd 68 
                                    + ++++  g + a+d
  gi|116754910|ref|YP_844028.1| 226 FIMSIESDGSINAKD 240
                                    333444444445555 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 !   64.1   0.0   5.1e-21   5.8e-18       1      68 [.      14     252 ..      14     253 .. 0.79

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 5.1e-21
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................................. RF
                      RNA_pol_L   1 efllrgvdhtlgNaLRrillsevpgvaiea.................................................. 30 
                                    +fll gv+++++Na+Rr +++evp++ai++                                                  
  gi|116754910|ref|YP_844028.1|  14 RFLLTGVTPAFANAIRRSCIAEVPKLAIDEisiyentsvlfdeqialrlglvpiraddlsvystpdecqcggigcpgcri 93 
                                    59**************************************************9999999999999999999999999999 PP

                                    ................................................................................ RF
                      RNA_pol_L  31 ................................................................................ 30 
                                                                                                                    
  gi|116754910|ref|YP_844028.1|  94 dfmltaegpatvhsrdikfsdpsvraafdniplvvlgegeklviegfatlrtgkehakwqagtlcgyknlpsieisgcnn 173
                                    99999999888888888888888888888887777777777777777777777777777777777777776666666666 PP

                                    .....................xx....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      RNA_pol_L  31 .....................pv....................vkvntdkdklilevetdgslkPeealkeAlkiLkek 68 
                                                          v                    ++v   +d +i+++e+dgs+++++++++A++ Lk+k
  gi|116754910|ref|YP_844028.1| 174 cgrcvkvcprgvlvldendsiKVrditecslcrlcveecdqraISVVPLEDAFIMSIESDGSINAKDLVRMAAEELKKK 252
                                    6666665555555555555550055555555555555555555566699****************************98 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   3.5   1.1e-07   0.00013       7      23 ..     170     186 ..     164     187 .. 0.87
   2 !   15.2   0.9   1.2e-05     0.014       4      24 .]     198     218 ..     195     218 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.1e-07
                                    TSSS-THHHHHSTTTEE CS
                           Fer4   7 kCigCGaCvevCPvgAI 23 
                                     C +CG+Cv+vCP g++
  gi|116754910|ref|YP_844028.1| 170 GCNNCGRCVKVCPRGVL 186
                                    5*************986 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.2e-05
                                    ETTTSSS-THHHHHSTTTEEE CS
                           Fer4   4 deekCigCGaCvevCPvgAIt 24 
                                    d   C  C +Cve C   AI+
  gi|116754910|ref|YP_844028.1| 198 DITECSLCRLCVEECDQRAIS 218
                                    5678************99995 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.4         3   3.4e+03      36      42 ..      83      91 ..      64      94 .. 0.63
   2 !   31.1   9.4   1.7e-10   1.9e-07       2      51 .]     171     217 ..     170     217 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3
                         Fer4_9 36 C..igCgaC 42
                                   C  igC  C
  gi|116754910|ref|YP_844028.1| 83 CggIGCPGC 91
                                   333444444 PP

  == domain 2  score: 31.1 bits;  conditional E-value: 1.7e-10
                         Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                    C++Cg+Cv++Cp gv v d++  +   +++   +C  C+ Cve C + ai
  gi|116754910|ref|YP_844028.1| 171 CNNCGRCVKVCPRGVLVLDENDSIKVRDIT---ECSLCRLCVEECDQRAI 217
                                    *********************999888775...6************9987 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.4   2.7e-07    0.0003       2      28 ..     171     197 ..     170     201 .. 0.87
   2 !   10.3   0.5   0.00092         1       2      20 ..     202     220 ..     201     256 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.7e-07
                        Fer4_16   2 CgtCgkCaevCPtnaikekkekeiear 28 
                                    C +Cg+C++vCP +++  +++ +i+ r
  gi|116754910|ref|YP_844028.1| 171 CNNCGRCVKVCPRGVLVLDENDSIKVR 197
                                    *****************9988887766 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00092
                        Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                    C  C+ C+e C ++ai+  
  gi|116754910|ref|YP_844028.1| 202 CSLCRLCVEECDQRAISVV 220
                                    99**************966 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   1.8         8   8.9e+03       8      15 ..      80      91 ..      74      94 .. 0.61
   2 !   29.2   8.2   6.7e-10   7.5e-07       4      55 ..     166     212 ..     163     213 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 8
                        Fer4_10  8 tC....irCgkC 15
                                    C    i+C  C
  gi|116754910|ref|YP_844028.1| 80 ECqcggIGCPGC 91
                                   444466677777 PP

  == domain 2  score: 29.2 bits;  conditional E-value: 6.7e-10
                        Fer4_10   4 idddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                    i+ + C +Cg+Cvk+CP      g+   +++++ +  ++ +C  c  Cve+C
  gi|116754910|ref|YP_844028.1| 166 IEISGCNNCGRCVKVCPR-----GVLVLDENDSIKVRDITECSLCRLCVEEC 212
                                    67788*************.....8888888888888899************* PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   9.0   5.1e-09   5.7e-06       2      49 ..     171     213 ..     170     216 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 5.1e-09
                         Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCP 49 
                                    C +Cg+Cv++Cp +++ lde ++ k     + d ++C+ C+ Cv++C 
  gi|116754910|ref|YP_844028.1| 171 CNNCGRCVKVCPRGVLVLDENDSIK-----VRDITECSLCRLCVEECD 213
                                    ******************9974333.....35899************6 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   5.4   5.1e-05     0.058      44      65 .]     162     185 ..      81     185 .. 0.80
   2 !   10.1   0.1   0.00075      0.84      48      62 ..     199     213 ..     188     253 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.1e-05
                         Fer4_8  44 e..eealwsCttcgaCtevCpvgi 65 
                                    +     +  C++cg+C++vCp g+
  gi|116754910|ref|YP_844028.1| 162 NlpSIEISGCNNCGRCVKVCPRGV 185
                                    155567899************986 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00075
                         Fer4_8  48 lwsCttcgaCtevCp 62 
                                    + +C+ c+ C+e+C 
  gi|116754910|ref|YP_844028.1| 199 ITECSLCRLCVEECD 213
                                    567777777777775 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.9       5.4     6e+03       9      13 ..      88      92 ..      88      93 .. 0.87
   2 !   19.5   2.6   6.8e-07   0.00076       9      24 .]     171     186 ..     164     186 .. 0.90
   3 ?    6.1   2.3     0.012        13       9      20 ..     202     213 ..     196     217 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 5.4
                         Fer4_6  9 CigCg 13
                                   C gC+
  gi|116754910|ref|YP_844028.1| 88 CPGCR 92
                                   99**7 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 6.8e-07
                         Fer4_6   9 CigCgdCvrvCPegai 24 
                                    C+ Cg+Cv+vCP g++
  gi|116754910|ref|YP_844028.1| 171 CNNCGRCVKVCPRGVL 186
                                    ************8875 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.012
                         Fer4_6   9 CigCgdCvrvCP 20 
                                    C  C+ Cv  C 
  gi|116754910|ref|YP_844028.1| 202 CSLCRLCVEECD 213
                                    99*********5 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.9   3.2e-06    0.0036      41      60 ..     166     185 ..     141     186 .. 0.73
   2 !   11.8   1.0   0.00025      0.28      40      58 ..     196     214 ..     187     216 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.2e-06
                        Fer4_17  41 ekaslCieCgeCerkCPqgl 60 
                                     ++s C++Cg+C+++CP g+
  gi|116754910|ref|YP_844028.1| 166 IEISGCNNCGRCVKVCPRGV 185
                                    48999************886 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00025
                        Fer4_17  40 eekaslCieCgeCerkCPq 58 
                                     + + +C+ C++C+++C q
  gi|116754910|ref|YP_844028.1| 196 VRDITECSLCRLCVEECDQ 214
                                    468999***********76 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   1.2       7.7   8.7e+03       9      14 ..      86      91 ..      73      94 .. 0.58
   2 !   17.3   9.8   3.4e-06    0.0038       3      52 ..     166     213 ..     164     219 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 7.7
                        Fer4_21  9 igCgkC 14
                                   igC  C
  gi|116754910|ref|YP_844028.1| 86 IGCPGC 91
                                   333333 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 3.4e-06
                        Fer4_21   3 idedkCigCgkCliaCedtshqaieidaktvlkvve.deCvGCnlCssvCP 52 
                                    i+ + C +Cg+C+++C+      + +d++  +kv++  eC  C lC++ C 
  gi|116754910|ref|YP_844028.1| 166 IEISGCNNCGRCVKVCPR---GVLVLDENDSIKVRDiTECSLCRLCVEECD 213
                                    66778************4...78899999999998548************6 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   3.3      0.99   1.1e+03       2      11 ..      79      92 ..      78      93 .. 0.74
   2 !   16.6   1.9     7e-06    0.0079       4      16 ..     171     183 ..     167     188 .. 0.92
   3 ?    1.8   3.2       0.4   4.5e+02       3      14 ..     201     212 ..     199     215 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.99
                         Fer4_4  2 erC....igCgsCv 11
                                   + C    igC+ C+
  gi|116754910|ref|YP_844028.1| 79 DECqcggIGCPGCR 92
                                   67855667*****7 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 7e-06
                         Fer4_4   4 CigCgsCvaaCPq 16 
                                    C++Cg+Cv +CP 
  gi|116754910|ref|YP_844028.1| 171 CNNCGRCVKVCPR 183
                                    ************6 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.4
                         Fer4_4   3 rCigCgsCvaaC 14 
                                     C  C+ Cv  C
  gi|116754910|ref|YP_844028.1| 201 ECSLCRLCVEEC 212
                                    5999*****988 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   4.2   7.1e-06     0.008      10      21 ..     171     182 ..     164     183 .. 0.91
   2 ?    3.5   3.2     0.077        86       8      20 ..     201     212 ..     195     212 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.1e-06
                         Fer4_2  10 CigCgaCvsaCP 21 
                                    C++Cg Cv++CP
  gi|116754910|ref|YP_844028.1| 171 CNNCGRCVKVCP 182
                                    ************ PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.077
                         Fer4_2   8 drCigCgaCvsaC 20 
                                    + C  C+ Cv  C
  gi|116754910|ref|YP_844028.1| 201 E-CSLCRLCVEEC 212
                                    4.********999 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.4   6.5   1.1e-05     0.013       1      14 [.     171     184 ..     171     185 .. 0.95
   2 ?    6.0   3.1     0.024        27       1      13 [.     202     214 ..     202     216 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.1e-05
                         Fer4_3   1 CtgCgaCvevCPvg 14 
                                    C++Cg+Cv+vCP g
  gi|116754910|ref|YP_844028.1| 171 CNNCGRCVKVCPRG 184
                                    ************98 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.024
                         Fer4_3   1 CtgCgaCvevCPv 13 
                                    C  C++Cve C  
  gi|116754910|ref|YP_844028.1| 202 CSLCRLCVEECDQ 214
                                    999*******965 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3  10.7   6.5e-05     0.073      57      97 ..     167     214 ..     133     227 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.5e-05
                        Fer4_18  57 gagdcidcescvkvcPtgi...dirkGlql....eciscllcidacdk 97 
                                    + + c +c+ cvkvcP g+   d  + +++    ec  c lc++ cd+
  gi|116754910|ref|YP_844028.1| 167 EISGCNNCGRCVKVCPRGVlvlDENDSIKVrditECSLCRLCVEECDQ 214
                                    5678************9984444455555433338999********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 ?    7.5   1.2     0.006       6.8       4      27 ..     167     191 ..     165     200 .. 0.72
   2 ?    5.2   3.2     0.031        35       4      20 ..     198     214 ..     194     253 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.006
                        Fer4_15   4 DrdaCigcglCvaeape.vfelded 27 
                                    + + C  cg+Cv+++p+ v +lde+
  gi|116754910|ref|YP_844028.1| 167 EISGCNNCGRCVKVCPRgVLVLDEN 191
                                    5678***********7525666664 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.031
                        Fer4_15   4 DrdaCigcglCvaeape 20 
                                    D ++C  c lCv+e+++
  gi|116754910|ref|YP_844028.1| 198 DITECSLCRLCVEECDQ 214
                                    6789***********65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); 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: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1879.05
//
Query:       gi|116754911|ref|YP_844029.1|  [L=254]
Description: TPR repeat-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.2e-43  142.4  14.8    3.1e-10   39.4   0.6    6.1  6  TPR_1            Tetratricopeptide repeat
    1.6e-36  121.4  15.7    2.1e-08   33.6   0.7    6.1  6  TPR_2            Tetratricopeptide repeat
    1.1e-30  105.1  11.2    1.7e-10   40.4   3.4    5.1  5  TPR_11           TPR repeat
    5.6e-26   90.9   9.8    8.6e-09   35.9   2.4    4.0  4  TPR_16           Tetratricopeptide repeat
    1.3e-23   81.1  13.4    8.3e-05   22.5   0.1    6.2  6  TPR_8            Tetratricopeptide repeat
    7.9e-21   72.9  12.8    1.7e-07   31.1   0.5    5.7  5  TPR_17           Tetratricopeptide repeat
    5.7e-19   68.4  14.5    1.2e-05   25.8   3.7    3.3  3  TPR_19           Tetratricopeptide repeat
    8.8e-18   63.5  12.8    2.3e-06   27.9   0.4    6.1  6  TPR_14           Tetratricopeptide repeat
    2.2e-15   56.5  13.9    0.00037   20.6   0.2    3.9  5  TPR_9            Tetratricopeptide repeat
    4.8e-15   55.6  15.2    1.4e-06   28.5   0.2    5.2  5  TPR_12           Tetratricopeptide repeat
    1.2e-13   51.1   7.2    1.5e-05   25.1   0.1    3.1  4  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    1.7e-10   40.2   7.9       0.42   10.7   0.0    6.1  6  TPR_7            Tetratricopeptide repeat
    2.4e-07   31.0  14.8       0.11   13.2   0.2    5.9  6  TPR_6            Tetratricopeptide repeat
    3.1e-07   30.0  14.0      0.022   14.6   0.8    5.3  5  TPR_10           Tetratricopeptide repeat
    1.4e-06   27.6   0.4      0.043   12.7   0.0    3.0  3  NARP1            NMDA receptor-regulated protein 1
    2.3e-06   27.6   6.8       0.26   11.4   0.1    3.6  3  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
    1.2e-05   25.3   2.0       0.11   12.5   0.0    3.2  3  SRP_TPR_like     Putative TPR-like repeat
      6e-05   22.6   2.9      0.094   12.1   0.1    2.9  3  Coatomer_E       Coatomer epsilon subunit
    0.00068   19.6   1.6       0.69   10.0   0.2    4.4  4  TPR_3            Tetratricopeptide repeat
    0.00088   19.7   3.3       0.21   12.0   0.1    3.1  3  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
     0.0032   16.8   1.4       0.21   10.8   0.2    2.5  2  FAT              FAT domain
     0.0034   17.5   3.5        1.3    9.1   0.4    4.3  3  DUF3856          Domain of Unknown Function (DUF3856)
     0.0049   16.5   4.1        4.8    7.1   0.1    4.0  4  PPTA             Protein prenyltransferase alpha subunit repe
  ------ inclusion threshold ------
      0.016   15.8   0.7         47    5.0   0.0    4.8  5  TPR_4            Tetratricopeptide repeat
      0.028   14.8   7.3        2.1    8.8   1.3    3.2  2  BTAD             Bacterial transcriptional activator domain
      0.092   12.9   0.1         23    5.2   0.0    2.6  2  Rapsyn_N         Rapsyn N-terminal myristoylation and linker 
       0.15   12.1   8.7        6.1    7.0   0.0    4.1  4  MIT              MIT (microtubule interacting and transport) 


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.1    0.0023       1.5       8      32 ..      59      83 ..      58      85 .. 0.90
   2 !   24.7   0.0   2.2e-08   1.4e-05       2      34 .]      87     119 ..      86     119 .. 0.96
   3 !   26.2   0.1   6.9e-09   4.6e-06       1      33 [.     120     152 ..     120     153 .. 0.96
   4 !   27.4   0.0   2.9e-09   1.9e-06       2      34 .]     155     187 ..     154     187 .. 0.95
   5 !   39.4   0.6   4.7e-13   3.1e-10       3      34 .]     190     221 ..     188     221 .. 0.98
   6 !   21.5   0.8   2.2e-07   0.00015       3      27 ..     224     248 ..     222     252 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0023
                                   HHHHHHTT-HHHHHHHHHHHHHHST CS
                          TPR_1  8 GnayfklgkydeAleyyekALelnP 32
                                   + a+f  ++y++Al   e AL+ + 
  gi|116754911|ref|YP_844029.1| 59 AKALFDANDYNQALNLTETALRMDS 83
                                   5699*****************9986 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 2.2e-08
                                    HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                          TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                    +a+  +G +++ +g++ +A + +++A +l+P++
  gi|116754911|ref|YP_844029.1|  87 QAWLLRGKILYAMGMLRDAYQSFDRATQLDPSD 119
                                    69*****************************86 PP

  == domain 3  score: 26.2 bits;  conditional E-value: 6.9e-09
                                    HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                          TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPn 33 
                                    a+a++ +G ++  +++y+  l+++e A++ +P 
  gi|116754911|ref|YP_844029.1| 120 AEAWNYKGIVLAAMQRYNNSLQCFESAIQADPM 152
                                    89*****************************96 PP

  == domain 4  score: 27.4 bits;  conditional E-value: 2.9e-09
                                    HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                          TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                    +a+ n+Gn++ +lg++d+A+ ++++ + ln ++
  gi|116754911|ref|YP_844029.1| 155 EAWSNKGNTLVSLGRLDDAISAFDRSIILNQTY 187
                                    8****************************9876 PP

  == domain 5  score: 39.4 bits;  conditional E-value: 4.7e-13
                                    HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                          TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                    a+ ++G+a++++++y eAl+ ye+AL+l+Pnn
  gi|116754911|ref|YP_844029.1| 190 AWIGKGLAFYYQKRYHEALAMYERALQLDPNN 221
                                    8******************************8 PP

  == domain 6  score: 21.5 bits;  conditional E-value: 2.2e-07
                                    HHHHHHHHHHHTT-HHHHHHHHHHH CS
                          TPR_1   3 alynlGnayfklgkydeAleyyekA 27 
                                    alyn+G+a++klg+ +eA+e+++ A
  gi|116754911|ref|YP_844029.1| 224 ALYNKGLALQKLGMNKEAEEAFRAA 248
                                    9*********************987 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.1   0.00061      0.41       8      31 ..      59      82 ..      59      85 .. 0.92
   2 !   22.0   0.0   1.7e-07   0.00011       3      34 .]      88     119 ..      86     119 .. 0.95
   3 !   22.5   0.1   1.2e-07   7.7e-05       1      32 [.     120     151 ..     120     153 .. 0.96
   4 !   20.9   0.0   3.8e-07   0.00025       2      33 ..     155     186 ..     154     187 .. 0.94
   5 !   33.6   0.7   3.2e-11   2.1e-08       3      34 .]     190     221 ..     188     221 .. 0.96
   6 !   17.9   0.8   3.5e-06    0.0023       2      27 ..     223     248 ..     222     253 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00061
                          TPR_2  8 GlayyklgdyeeAleafekAleld 31
                                   ++a++ ++dy++Al++ e Al+ d
  gi|116754911|ref|YP_844029.1| 59 AKALFDANDYNQALNLTETALRMD 82
                                   689******************987 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 1.7e-07
                          TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                    a+  +G+++y++g + +A + f++A +ldP +
  gi|116754911|ref|YP_844029.1|  88 AWLLRGKILYAMGMLRDAYQSFDRATQLDPSD 119
                                    8*****************************86 PP

  == domain 3  score: 22.5 bits;  conditional E-value: 1.2e-07
                          TPR_2   1 aealynlGlayyklgdyeeAleafekAleldP 32 
                                    aea+++ G +++++++y+  l++fe A++ dP
  gi|116754911|ref|YP_844029.1| 120 AEAWNYKGIVLAAMQRYNNSLQCFESAIQADP 151
                                    89*****************************9 PP

  == domain 4  score: 20.9 bits;  conditional E-value: 3.8e-07
                          TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPn 33 
                                    ea+ n G+ +  lg++++A+ af++++ l+ +
  gi|116754911|ref|YP_844029.1| 155 EAWSNKGNTLVSLGRLDDAISAFDRSIILNQT 186
                                    89*************************99976 PP

  == domain 5  score: 33.6 bits;  conditional E-value: 3.2e-11
                          TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                    a+   Gla y++++y eAl+ +e+Al+ldPnn
  gi|116754911|ref|YP_844029.1| 190 AWIGKGLAFYYQKRYHEALAMYERALQLDPNN 221
                                    899****************************8 PP

  == domain 6  score: 17.9 bits;  conditional E-value: 3.5e-06
                          TPR_2   2 ealynlGlayyklgdyeeAleafekA 27 
                                     alyn Gla+ klg  +eA+eaf++A
  gi|116754911|ref|YP_844029.1| 223 IALYNKGLALQKLGMNKEAEEAFRAA 248
                                    69**********************99 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.1   3.2e-07   0.00022       2      42 .]      60     100 ..      59     100 .. 0.97
   2 !   25.8   0.1   9.4e-09   6.3e-06       1      41 [.      93     133 ..      93     134 .. 0.96
   3 !   20.4   0.0   4.5e-07    0.0003       4      38 ..     130     164 ..     127     165 .. 0.91
   4 !   19.3   0.0     1e-06   0.00069       1      39 [.     161     199 ..     161     201 .. 0.97
   5 !   40.4   3.4   2.5e-13   1.7e-10       1      42 []     195     236 ..     195     236 .. 0.98

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 3.2e-07
                         TPR_11   2 dayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                    +a+++ ++y++A++  ++Al+ d++   a++ +G+++y++G
  gi|116754911|ref|YP_844029.1|  60 KALFDANDYNQALNLTETALRMDSSLEQAWLLRGKILYAMG 100
                                    799************************************99 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 9.4e-09
                         TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykq 41 
                                    G+++y+ G + +A +++ +A +ldP++aea++  G +++++
  gi|116754911|ref|YP_844029.1|  93 GKILYAMGMLRDAYQSFDRATQLDPSDAEAWNYKGIVLAAM 133
                                    99*********************************999876 PP

  == domain 3  score: 20.4 bits;  conditional E-value: 4.5e-07
                         TPR_11   4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGlay 38 
                                    + + ++y++++++++ A++ dP n ea++n G+++
  gi|116754911|ref|YP_844029.1| 130 LAAMQRYNNSLQCFESAIQADPMNYEAWSNKGNTL 164
                                    67889***************************975 PP

  == domain 4  score: 19.3 bits;  conditional E-value: 1e-06
                         TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayy 39 
                                    G+ ++++G++++Ai a+ + + l+++++ a+ + Gla+y
  gi|116754911|ref|YP_844029.1| 161 GNTLVSLGRLDDAISAFDRSIILNQTYVGAWIGKGLAFY 199
                                    9*************************************9 PP

  == domain 5  score: 40.4 bits;  conditional E-value: 2.5e-13
                         TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                    G a+y q +y eA++ Y++Al+ldP+n  a+yn Gla++k+G
  gi|116754911|ref|YP_844029.1| 195 GLAFYYQKRYHEALAMYERALQLDPNNSIALYNKGLALQKLG 236
                                    89**************************************99 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   1.3   1.7e-09   1.2e-06       4      68 .]      59     120 ..      58     120 .. 0.95
   2 !   15.2   0.4   3.8e-05     0.026       3      46 ..      92     132 ..      91     136 .. 0.91
   3 !   24.7   0.0   4.1e-08   2.7e-05       5      60 ..     128     180 ..     126     187 .. 0.91
   4 !   35.9   2.4   1.3e-11   8.6e-09       3      62 ..     194     250 ..     192     253 .. 0.95

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 1.7e-09
                         TPR_16   4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapdap 68 
                                    a+a+++a+dy +A+++ e+al++d   +   +A+ll+g ++++ g l +A + +++a + +p+++
  gi|116754911|ref|YP_844029.1|  59 AKALFDANDYNQALNLTETALRMD---SSLEQAWLLRGKILYAMGMLRDAYQSFDRATQLDPSDA 120
                                    789*********************...88899*************************99999885 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 3.8e-05
                         TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalr 46 
                                    +++++++ g  +dA   +++a+ +d   P +aeA++++g ++++
  gi|116754911|ref|YP_844029.1|  92 RGKILYAMGMLRDAYQSFDRATQLD---PSDAEAWNYKGIVLAA 132
                                    68999********************...************9987 PP

  == domain 3  score: 24.7 bits;  conditional E-value: 4.1e-08
                         TPR_16   5 raalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraa 60 
                                      +++ ++y   +  +e a+ +d   P ++eA+ ++g+ +  +grl++A+ ++++ 
  gi|116754911|ref|YP_844029.1| 128 IVLAAMQRYNNSLQCFESAIQAD---PMNYEAWSNKGNTLVSLGRLDDAISAFDRS 180
                                    6788999****************...************************888775 PP

  == domain 4  score: 35.9 bits;  conditional E-value: 1.3e-11
                         TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalr 62 
                                    +++a++++++y +A+a++e+al +d   P +  Al+++g+a+ ++g  +eA++++raa +
  gi|116754911|ref|YP_844029.1| 194 KGLAFYYQKRYHEALAMYERALQLD---PNNSIALYNKGLALQKLGMNKEAEEAFRAAEQ 250
                                    699**********************...*****************************964 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1      0.22   1.5e+02       8      32 ..      59      83 ..      59      84 .. 0.87
   2 !   15.1   0.0     3e-05      0.02       2      34 .]      87     119 ..      86     119 .. 0.96
   3 !   12.6   0.1   0.00019      0.13       1      32 [.     120     151 ..     120     153 .. 0.95
   4 !   16.1   0.0   1.4e-05    0.0091       1      28 [.     154     181 ..     154     187 .. 0.90
   5 !   22.5   0.1   1.3e-07   8.3e-05       3      34 .]     190     221 ..     188     221 .. 0.95
   6 !   16.5   0.6   1.1e-05    0.0072       3      27 ..     224     248 ..     222     253 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.22
                                   HHHHHHTT-HHHHHHHHHHHHHHHH CS
                          TPR_8  8 gsiylklgdyeeAkeyyekaleldp 32
                                   ++++++ +dy++A    e al++d 
  gi|116754911|ref|YP_844029.1| 59 AKALFDANDYNQALNLTETALRMDS 83
                                   5789999******999999999985 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 3e-05
                                    CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                          TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                    +a+++ g+i+  +g +  A +++ +a++ldp++
  gi|116754911|ref|YP_844029.1|  87 QAWLLRGKILYAMGMLRDAYQSFDRATQLDPSD 119
                                    79*****************************85 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 0.00019
                                    CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                          TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldp 32 
                                    aea++ +g ++  +++y+++ +++e a+++dp
  gi|116754911|ref|YP_844029.1| 120 AEAWNYKGIVLAAMQRYNNSLQCFESAIQADP 151
                                    7899999***********************99 PP

  == domain 4  score: 16.1 bits;  conditional E-value: 1.4e-05
                                    CCHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                          TPR_8   1 aeayynlgsiylklgdyeeAkeyyekal 28 
                                    +ea+ n+g+++ +lg+++ A++++ + +
  gi|116754911|ref|YP_844029.1| 154 YEAWSNKGNTLVSLGRLDDAISAFDRSI 181
                                    589*********************9987 PP

  == domain 5  score: 22.5 bits;  conditional E-value: 1.3e-07
                                    HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                          TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                    a+  +g++   +++y+eA + ye+al+ldp+n
  gi|116754911|ref|YP_844029.1| 190 AWIGKGLAFYYQKRYHEALAMYERALQLDPNN 221
                                    8999**************************97 PP

  == domain 6  score: 16.5 bits;  conditional E-value: 1.1e-05
                                    HHHHHHHHHHHTT-HHHHHHHHHHH CS
                          TPR_8   3 ayynlgsiylklgdyeeAkeyyeka 27 
                                    a+yn+g++++klg  +eA+e+++ a
  gi|116754911|ref|YP_844029.1| 224 ALYNKGLALQKLGMNKEAEEAFRAA 248
                                    79*********************98 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.026        17       3      32 ..      76     105 ..      74     107 .. 0.88
   2 !   17.2   0.1   6.9e-06    0.0046       2      29 ..     109     136 ..     108     141 .. 0.86
   3 !   17.9   0.0   4.2e-06    0.0028       1      33 [.     142     174 ..     142     175 .. 0.96
   4 ?    5.5   0.0      0.04        26       2      33 ..     177     208 ..     176     209 .. 0.93
   5 !   31.1   0.5   2.5e-10   1.7e-07       1      34 []     210     243 ..     210     243 .. 0.96

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.026
                         TPR_17   3 lkaleldPnnadaynnLAelllknGdlmtA 32 
                                    + al+ d +   a+ +++++l+  G l++A
  gi|116754911|ref|YP_844029.1|  76 ETALRMDSSLEQAWLLRGKILYAMGMLRDA 105
                                    678899999999*************99998 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 6.9e-06
                         TPR_17   2 ylkaleldPnnadaynnLAelllknGdl 29 
                                    + +a +ldP++a+a+n+++ +l+   ++
  gi|116754911|ref|YP_844029.1| 109 FDRATQLDPSDAEAWNYKGIVLAAMQRY 136
                                    6899******************977666 PP

  == domain 3  score: 17.9 bits;  conditional E-value: 4.2e-06
                         TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                    +++ a++ dP n +a+ n++++l ++G+l++A+
  gi|116754911|ref|YP_844029.1| 142 CFESAIQADPMNYEAWSNKGNTLVSLGRLDDAI 174
                                    7999***************************97 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.04
                         TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                    + +++ l+ +++ a+  ++ +++ ++++ +A+
  gi|116754911|ref|YP_844029.1| 177 FDRSIILNQTYVGAWIGKGLAFYYQKRYHEAL 208
                                    889************************99997 PP

  == domain 5  score: 31.1 bits;  conditional E-value: 2.5e-10
                         TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                    +y++al+ldPnn+ a++n++ +l k+G  ++A++
  gi|116754911|ref|YP_844029.1| 210 MYERALQLDPNNSIALYNKGLALQKLGMNKEAEE 243
                                    6******************************986 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   1.5   3.1e-08     2e-05       1      63 [.      62     124 ..      59     129 .. 0.96
   2 !   23.4   0.0   9.6e-08   6.4e-05       1      51 [.     130     180 ..     130     188 .. 0.93
   3 !   25.8   3.7   1.7e-08   1.2e-05       2      52 ..     199     249 ..     198     254 .] 0.90

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 3.1e-08
                         TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryas 63 
                                    l++++dy +Al+l e al  d   + a+ll  ++l+a+g l +A +  d++ + dp da++++
  gi|116754911|ref|YP_844029.1|  62 LFDANDYNQALNLTETALRMDSSLEQAWLLRGKILYAMGMLRDAYQSFDRATQLDPSDAEAWN 124
                                    6899******************************************************99875 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 9.6e-08
                         TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdal 51 
                                    l a+++y + l+ +e+a+q+dp n ea+ +  + l++lg+ld+A+ + d+ 
  gi|116754911|ref|YP_844029.1| 130 LAAMQRYNNSLQCFESAIQADPMNYEAWSNKGNTLVSLGRLDDAISAFDRS 180
                                    5799*****************************************999875 PP

  == domain 3  score: 25.8 bits;  conditional E-value: 1.7e-08
                         TPR_19   2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalp 52 
                                    +++++y eAla++e+alq dp+n+ a+++   al +lg  +eAe++  a+ 
  gi|116754911|ref|YP_844029.1| 199 YYQKRYHEALAMYERALQLDPNNSIALYNKGLALQKLGMNKEAEEAFRAAE 249
                                    6899*****************************************996654 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.3     0.064        43       8      39 ..      59      90 ..      52      91 .. 0.90
   2 !   27.9   0.4   3.5e-09   2.3e-06       2      40 ..      87     125 ..      86     128 .. 0.94
   3 ?    4.8   0.0     0.091        60       8      38 ..     127     157 ..     125     162 .. 0.87
   4 !   10.7   0.0    0.0012       0.8       2      40 ..     155     193 ..     154     197 .. 0.86
   5 !   18.6   0.2   3.5e-06    0.0023       3      39 ..     190     226 ..     188     231 .. 0.84
   6 ?    7.1   0.3     0.017        11       5      29 ..     226     250 ..     222     254 .] 0.83

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.064
                         TPR_14  8 aeallalGdpdeAiallrralalaPddaeawl 39
                                   a+al+ + d+ +A++l + al+ + + ++awl
  gi|116754911|ref|YP_844029.1| 59 AKALFDANDYNQALNLTETALRMDSSLEQAWL 90
                                   789*******************9988888887 PP

  == domain 2  score: 27.9 bits;  conditional E-value: 3.5e-09
                         TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawll 40 
                                    +a+l+++++l+a G +++A + ++ra +l+P+daeaw +
  gi|116754911|ref|YP_844029.1|  87 QAWLLRGKILYAMGMLRDAYQSFDRATQLDPSDAEAWNY 125
                                    69***********************************76 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.091
                         TPR_14   8 aeallalGdpdeAiallrralalaPddaeaw 38 
                                    + +l+a +++  ++++++ a++++P + eaw
  gi|116754911|ref|YP_844029.1| 127 GIVLAAMQRYNNSLQCFESAIQADPMNYEAW 157
                                    679999*******************777777 PP

  == domain 4  score: 10.7 bits;  conditional E-value: 0.0012
                         TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawll 40 
                                    ea+   +  l  lG++d+Ai +++r + l+ +   aw+ 
  gi|116754911|ref|YP_844029.1| 155 EAWSNKGNTLVSLGRLDDAISAFDRSIILNQTYVGAWIG 193
                                    5777778999****************9999999999975 PP

  == domain 5  score: 18.6 bits;  conditional E-value: 3.5e-06
                         TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawl 39 
                                    a+   + a++ + ++ eA+a+++ral+l+P++  a++
  gi|116754911|ref|YP_844029.1| 190 AWIGKGLAFYYQKRYHEALAMYERALQLDPNNSIALY 226
                                    666778899999*******************987765 PP

  == domain 6  score: 7.1 bits;  conditional E-value: 0.017
                         TPR_14   5 lalaeallalGdpdeAiallrrala 29 
                                    +  + al  lG  +eA++++r+a +
  gi|116754911|ref|YP_844029.1| 226 YNKGLALQKLGMNKEAEEAFRAAEQ 250
                                    556789999**************76 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.9   2.7e-06    0.0018       6      65 ..      63     122 ..      59     124 .. 0.94
   2 !   19.6   0.1   1.2e-06   0.00078      14      60 ..     105     151 ..     103     159 .. 0.92
   3 !   11.5   0.0   0.00037      0.24       6      55 ..     131     180 ..     126     186 .. 0.89
   4 !   19.6   0.1   1.1e-06   0.00073       8      65 ..     167     224 ..     160     225 .. 0.92
   5 !   20.6   0.2   5.5e-07   0.00037       8      54 ..     201     247 ..     194     252 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.7e-06
                          TPR_9   6 ireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                      ++d+ +al   e  l +++   + ++ RG +l+ +G l+ A + ++++ +l+p++++a
  gi|116754911|ref|YP_844029.1|  63 FDANDYNQALNLTETALRMDSSLEQAWLLRGKILYAMGMLRDAYQSFDRATQLDPSDAEA 122
                                    6789***************************************************99876 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 1.2e-06
                          TPR_9  14 alavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap 60 
                                    a +  +r  +l+P d+e +   G++la + +++  l+++e +++ +p
  gi|116754911|ref|YP_844029.1| 105 AYQSFDRATQLDPSDAEAWNYKGIVLAAMQRYNNSLQCFESAIQADP 151
                                    667789**************************************999 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00037
                          TPR_9   6 ireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeay 55 
                                    +  +++   l++ e+ ++ +P   e +   G  l+ lG+l  A+ ++++ 
  gi|116754911|ref|YP_844029.1| 131 AAMQRYNNSLQCFESAIQADPMNYEAWSNKGNTLVSLGRLDDAISAFDRS 180
                                    556788889************************************99985 PP

  == domain 4  score: 19.6 bits;  conditional E-value: 1.1e-06
                          TPR_9   8 eedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                                      + + a+ + +r ++l+   ++ +   Gl+ + + ++++Ala  e++l+l+p++  a
  gi|116754911|ref|YP_844029.1| 167 LGRLDDAISAFDRSIILNQTYVGAWIGKGLAFYYQKRYHEALAMYERALQLDPNNSIA 224
                                    567899***********************************************87665 PP

  == domain 5  score: 20.6 bits;  conditional E-value: 5.5e-07
                          TPR_9   8 eedweralavverllllaPddpeerrdRGlllaqlGclsaAladLea 54 
                                    ++++ +ala++er l+l+P+    ++  Gl+l++lG  ++A +++ a
  gi|116754911|ref|YP_844029.1| 201 QKRYHEALAMYERALQLDPNNSIALYNKGLALQKLGMNKEAEEAFRA 247
                                    67899*******************************99999998876 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1      0.05        33      53      75 ..      60      82 ..      59      84 .. 0.83
   2 ?    3.3   0.1      0.15     1e+02       5      31 ..      88     114 ..      84     116 .. 0.68
   3 !   11.6   0.1   0.00039      0.26       3      32 ..     120     149 ..     118     150 .. 0.91
   4 !   28.5   0.2   2.1e-09   1.4e-06       5      76 ..     156     219 ..     153     220 .. 0.89
   5 !   27.7   4.8   3.6e-09   2.4e-06       6      74 ..     191     251 ..     186     254 .] 0.91

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.05
                         TPR_12 53 rlyralgryeeAlelleealaia 75
                                    +++ +++y +Al+l e al+++
  gi|116754911|ref|YP_844029.1| 60 KALFDANDYNQALNLTETALRMD 82
                                   5677899999**99999999986 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.15
                         TPR_12   5 alnnlaavlrrlgrydeAlellekale 31 
                                    a+  ++ +l+++g + +A + +++a +
  gi|116754911|ref|YP_844029.1|  88 AWLLRGKILYAMGMLRDAYQSFDRATQ 114
                                    555677777777777777777777754 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00039
                         TPR_12   3 atalnnlaavlrrlgrydeAlellekalei 32 
                                    a a+n  + vl++++ry  +l+++e a+++
  gi|116754911|ref|YP_844029.1| 120 AEAWNYKGIVLAAMQRYNNSLQCFESAIQA 149
                                    789988********************9875 PP

  == domain 4  score: 28.5 bits;  conditional E-value: 2.1e-09
                         TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                    a++n +++l  lgr+d+A++ +++++ + + +          + ++ g ++++++ry eAl+++e+al++++
  gi|116754911|ref|YP_844029.1| 156 AWSNKGNTLVSLGRLDDAISAFDRSIILNQTYV--------GAWIGKGLAFYYQKRYHEALAMYERALQLDP 219
                                    789**********************88885553........367999***99****************9975 PP

  == domain 5  score: 27.7 bits;  conditional E-value: 3.6e-09
                         TPR_12   6 lnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                    +   +++ ++++ry+eAl+++e+al++      p++   +++l+n g ++++lg  +eA+e+++ a + 
  gi|116754911|ref|YP_844029.1| 191 WIGKGLAFYYQKRYHEALAMYERALQLD-----PNN---SIALYNKGLALQKLGMNKEAEEAFRAAEQN 251
                                    567899999*******************.....987...99**********************999765 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 !   25.1   0.1   2.2e-08   1.5e-05      15      81 ..      45     111 ..      37     112 .. 0.88
   2 !   12.8   0.0   0.00015       0.1       5      81 ..     102     179 ..     100     180 .. 0.94
   3 !   21.4   0.5   3.2e-07   0.00021       3      81 ..     134     213 ..     132     214 .. 0.96
   4 !   18.1   1.6   3.4e-06    0.0023      30      80 ..     195     246 ..     184     248 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 2.2e-08
                                    HH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                         ANAPC3  15 llaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                    l  + +  p+d+   A++l+ +++y++A++l+++a + +s+ +++++l ++ l++++ + +A++ +++
  gi|116754911|ref|YP_844029.1|  45 LS-MAQSTPQDLVEDAKALFDANDYNQALNLTETAlRMDSSLEQAWLLRGKILYAMGMLRDAYQSFDR 111
                                    44.56778999999*********************99999999********************99876 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00015
                                    HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                         ANAPC3   5 yknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                    +++A+  ++r+ + ++ ++e+  +++ +l  +++y+  ++ +++a + ++ + +++  ++ +l+ L+++++Ai+a+++
  gi|116754911|ref|YP_844029.1| 102 LRDAYQSFDRATQLDPSDAEAWNYKGIVLAAMQRYNNSLQCFESAiQADPMNYEAWSNKGNTLVSLGRLDDAISAFDR 179
                                    6788888999999*************************************************************9975 PP

  == domain 3  score: 21.4 bits;  conditional E-value: 3.2e-07
                                    T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                         ANAPC3   3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                    ++y+n + ++e + +a++ ++e+   ++ +l ++g+ + A+  ++++  ln +  g+++ ++ + + +k+y+eA+a +e+
  gi|116754911|ref|YP_844029.1| 134 QRYNNSLQCFESAIQADPMNYEAWSNKGNTLVSLGRLDDAISAFDRSiILNQTYVGAWIGKGLAFYYQKRYHEALAMYER 213
                                    79**************************************************************************9986 PP

  == domain 4  score: 18.1 bits;  conditional E-value: 3.4e-06
                                    HHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                         ANAPC3  30 AlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                    +l++y +++y++A+  +++a +l++++  ++y ++ +l kL+  +eA+ a+ 
  gi|116754911|ref|YP_844029.1| 195 GLAFYYQKRYHEALAMYERAlQLDPNNSIALYNKGLALQKLGMNKEAEEAFR 246
                                    7889999999999999999999999999999999999999999999999986 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1     0.012         8       6      33 ..      59      86 ..      59      88 .. 0.86
   2 ?    2.1   0.0      0.37   2.4e+02       2      36 .]      89     121 ..      88     121 .. 0.87
   3 ?    2.7   0.0      0.24   1.6e+02       1      28 [.     122     147 ..     122     151 .. 0.83
   4 !   10.7   0.0   0.00064      0.42       1      25 [.     156     180 ..     156     185 .. 0.91
   5 !   10.2   0.1   0.00093      0.62      12      33 ..     201     220 ..     192     223 .. 0.75
   6 ?    7.0   0.2      0.01       6.7       1      24 [.     224     247 ..     224     249 .. 0.94

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.012
                          TPR_7  6 arlysrlGdyeeAielyeqsLaltkdpe 33
                                   a + ++ +dy +A+ l e +L+++++ e
  gi|116754911|ref|YP_844029.1| 59 AKALFDANDYNQALNLTETALRMDSSLE 86
                                   6788999************999988765 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.37
                          TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdpedae 36 
                                    +l  + +  ++G  ++A + + +  a+  dp+dae
  gi|116754911|ref|YP_844029.1|  89 WLLRGKILYAMGMLRDAYQSFDR--ATQLDPSDAE 121
                                    6777889999999**********..9999999975 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.24
                          TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLal 28 
                                    a+++ + +  ++++y + ++++e   a+
  gi|116754911|ref|YP_844029.1| 122 AWNYKGIVLAAMQRYNNSLQCFES--AI 147
                                    67888899999************9..54 PP

  == domain 4  score: 10.7 bits;  conditional E-value: 0.00064
                          TPR_7   1 aLlnLarlysrlGdyeeAielyeqs 25 
                                    a++n +++ ++lG+ ++Ai+ + +s
  gi|116754911|ref|YP_844029.1| 156 AWSNKGNTLVSLGRLDDAISAFDRS 180
                                    7899****************99985 PP

  == domain 5  score: 10.2 bits;  conditional E-value: 0.00093
                          TPR_7  12 lGdyeeAielyeqsLaltkdpe 33 
                                    + +y eA+  ye++L    dp+
  gi|116754911|ref|YP_844029.1| 201 QKRYHEALAMYERAL--QLDPN 220
                                    669**********55..55554 PP

  == domain 6  score: 7.0 bits;  conditional E-value: 0.01
                          TPR_7   1 aLlnLarlysrlGdyeeAielyeq 24 
                                    aL+n + + ++lG  +eA+e +++
  gi|116754911|ref|YP_844029.1| 224 ALYNKGLALQKLGMNKEAEEAFRA 247
                                    799*****************9987 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1       1.8   1.2e+03       7      24 ..      59      76 ..      59      80 .. 0.77
   2 !    9.1   0.1    0.0034       2.2       1      31 [.      87     117 ..      87     119 .. 0.92
   3 ?    1.7   0.0      0.76   5.1e+02       9      31 ..     129     151 ..     125     151 .. 0.80
   4 ?    1.7   0.0      0.77   5.1e+02      10      25 ..     164     179 ..     155     181 .. 0.78
   5 !   13.2   0.2   0.00016      0.11       7      32 ..     195     220 ..     190     221 .. 0.92
   6 !    9.6   0.7    0.0023       1.5       2      25 ..     224     247 ..     223     252 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 1.8
                                   HHHHHHHHHHHHHHHHHH CS
                          TPR_6  7 alsyrklgdtdkAleale 24
                                   a++++ ++d+ +Al + e
  gi|116754911|ref|YP_844029.1| 59 AKALFDANDYNQALNLTE 76
                                   67889988****998755 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0034
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-T CS
                          TPR_6   1 dAlyklalsyrklgdtdkAlealerlikeYP 31 
                                    +A +++++ ++++g  ++A + ++r  +  P
  gi|116754911|ref|YP_844029.1|  87 QAWLLRGKILYAMGMLRDAYQSFDRATQLDP 117
                                    699**********************999877 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.76
                                    HHHHHHHHHHHHHHHHHHHHH-T CS
                          TPR_6   9 syrklgdtdkAlealerlikeYP 31 
                                     + +++++ ++l+ +e+ i+  P
  gi|116754911|ref|YP_844029.1| 129 VLAAMQRYNNSLQCFESAIQADP 151
                                    5667679**********999766 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.77
                                    HHHHHHHHHHHHHHHH CS
                          TPR_6  10 yrklgdtdkAlealer 25 
                                    + +lg+ d+A+ a++r
  gi|116754911|ref|YP_844029.1| 164 LVSLGRLDDAISAFDR 179
                                    55679********987 PP

  == domain 5  score: 13.2 bits;  conditional E-value: 0.00016
                                    HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                          TPR_6   7 alsyrklgdtdkAlealerlikeYPd 32 
                                    +l+++ ++++ +Al+++er ++  P+
  gi|116754911|ref|YP_844029.1| 195 GLAFYYQKRYHEALAMYERALQLDPN 220
                                    8999**99***************999 PP

  == domain 6  score: 9.6 bits;  conditional E-value: 0.0023
                                    HHHHHHHHHHHHHHHHHHHHHHHH CS
                          TPR_6   2 AlyklalsyrklgdtdkAlealer 25 
                                    Aly+ +l+++klg   +A ea++ 
  gi|116754911|ref|YP_844029.1| 224 ALYNKGLALQKLGMNKEAEEAFRA 247
                                    9**********99*******9986 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.024        16       9      31 ..      59      81 ..      59      82 .. 0.89
   2 ?    6.4   0.2     0.013       8.3       9      30 ..     127     148 ..     120     149 .. 0.90
   3 !    6.9   0.0    0.0086       5.7       7      34 ..     159     186 ..     158     190 .. 0.86
   4 !   14.6   0.8   3.3e-05     0.022      10      30 ..     196     216 ..     195     217 .. 0.88
   5 ?    1.9   0.4      0.34   2.3e+02       4      28 ..     224     248 ..     223     248 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.024
                         TPR_10  9 analrqrgrydeAealleealai 31
                                   a al++ ++y++A++l e al++
  gi|116754911|ref|YP_844029.1| 59 AKALFDANDYNQALNLTETALRM 81
                                   56899***********9999975 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.013
                         TPR_10   9 analrqrgrydeAealleeala 30 
                                    +++l +++ry+ +++ +e a++
  gi|116754911|ref|YP_844029.1| 127 GIVLAAMQRYNNSLQCFESAIQ 148
                                    99******************98 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0086
                         TPR_10   7 NLanalrqrgrydeAealleealairrr 34 
                                    N +n+l ++gr+d+A   +++++ + + 
  gi|116754911|ref|YP_844029.1| 159 NKGNTLVSLGRLDDAISAFDRSIILNQT 186
                                    779****************999988776 PP

  == domain 4  score: 14.6 bits;  conditional E-value: 3.3e-05
                         TPR_10  10 nalrqrgrydeAealleeala 30 
                                     a + ++ry+eA+a++e+al+
  gi|116754911|ref|YP_844029.1| 196 LAFYYQKRYHEALAMYERALQ 216
                                    56788***************8 PP

  == domain 5  score: 1.9 bits;  conditional E-value: 0.34
                         TPR_10   4 slnNLanalrqrgrydeAealleea 28 
                                    +l N + al+++g  +eAe+ ++ a
  gi|116754911|ref|YP_844029.1| 224 ALYNKGLALQKLGMNKEAEEAFRAA 248
                                    5778999*************99876 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   6.5e-05     0.043     206     259 ..      66     119 ..      59     121 .. 0.95
   2 !    9.0   0.0   0.00085      0.57     204     252 ..     132     180 ..     122     187 .. 0.90
   3 ?    2.6   0.2     0.079        52     198     252 ..     196     248 ..     183     253 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.5e-05
                                    T-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT- CS
                          NARP1 206 gsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaD 259
                                    +++++Al++ ++a++ + +l + +l +++il  +G l++A++  ++a +lD  D
  gi|116754911|ref|YP_844029.1|  66 NDYNQALNLTETALRMDSSLEQAWLLRGKILYAMGMLRDAYQSFDRATQLDPSD 119
                                    7899***********************************************887 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00085
                                    HHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                          NARP1 204 klgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeea 252
                                     +++++++l++ ++ai+ +p   e + +K++ l   G l++A+++ +++
  gi|116754911|ref|YP_844029.1| 132 AMQRYNNSLQCFESAIQADPMNYEAWSNKGNTLVSLGRLDDAISAFDRS 180
                                    688999************************************9998876 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.079
                                    HHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                          NARP1 198 lAqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeea 252
                                    lA +y+  +++++Al + ++a++ +p+     ++K+  l++ G  k+A e+   a
  gi|116754911|ref|YP_844029.1| 196 LAFYYQ--KRYHEALAMYERALQLDPNNSIALYNKGLALQKLGMNKEAEEAFRAA 248
                                    555554..45677788888888888877777777888888888777776665554 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.1   0.00039      0.26      15      44 ..      66      95 ..      59     101 .. 0.89
   2 !    6.9   0.0    0.0096       6.4      14      37 ..     133     156 ..     125     158 .. 0.90
   3 !   10.9   0.9   0.00055      0.36       9      35 ..     196     222 ..     195     239 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00039
                                   T-HHHHHHHHHHHHHHTTS-HHHHHHHHHH CS
                     Fis1_TPR_C 15 geYseArryvdalLeiEPenrQaqsLkeli 44
                                    +Y++A++++++ L+++ + +Qa  L+  i
  gi|116754911|ref|YP_844029.1| 66 NDYNQALNLTETALRMDSSLEQAWLLRGKI 95
                                   79*********************9999887 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0096
                                    HT-HHHHHHHHHHHHHHTTS-HHH CS
                     Fis1_TPR_C  14 lgeYseArryvdalLeiEPenrQa 37 
                                    +++Y++++++ +  ++ +P n  a
  gi|116754911|ref|YP_844029.1| 133 MQRYNNSLQCFESAIQADPMNYEA 156
                                    899*****************9877 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00055
                                    HHHHHHT-HHHHHHHHHHHHHHTTS-H CS
                     Fis1_TPR_C   9 lGhyklgeYseArryvdalLeiEPenr 35 
                                    l+ y +++Y eA+   ++ L+++P+n+
  gi|116754911|ref|YP_844029.1| 196 LAFYYQKRYHEALAMYERALQLDPNNS 222
                                    677889********************7 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   0.0   0.00017      0.11      47     100 ..      54     111 ..      30     124 .. 0.77
   2 ?    5.0   0.0     0.037        24      14      50 ..     120     155 ..     107     188 .. 0.71
   3 ?    6.8   0.4      0.01       6.8      20      75 ..     194     252 ..     176     254 .] 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00017
                   SRP_TPR_like  47 vrfEkaYvlYklkkykkalkilk...kveaee.kvkvlksqvlYrlgsyekAYklLsk 100
                                      +E a +l+  + y++al++ +   +++++  ++  l+ ++lY +g  ++AY+   +
  gi|116754911|ref|YP_844029.1|  54 DLVEDAKALFDANDYNQALNLTEtalRMDSSLeQAWLLRGKILYAMGMLRDAYQSFDR 111
                                    46899*************9876622245655448999****************98844 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.037
                   SRP_TPR_like  14 kelkkfkvvaliklekyeeaLkllkkgsalsedvrfE 50 
                                    +e  ++k + l  +++y+++L+  + +   ++ +++E
  gi|116754911|ref|YP_844029.1| 120 AEAWNYKGIVLAAMQRYNNSLQCFESAI-QADPMNYE 155
                                    45557899*************9988765.44444444 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.01
                   SRP_TPR_like  20 kvvaliklekyeeaLkllkkgsal...sedvrfEkaYvlYklkkykkalkilkkveaee 75 
                                    k +a+    +y+eaL + + + +l   ++   + k  +l kl   k+a + ++ +e+++
  gi|116754911|ref|YP_844029.1| 194 KGLAFYYQKRYHEALAMYERALQLdpnNSIALYNKGLALQKLGMNKEAEEAFRAAEQNQ 252
                                    667888889*******99988755221555789****************9999998875 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.2      0.24   1.6e+02     192     233 ..      44      84 ..      39      88 .. 0.79
   2 !   12.1   0.1   0.00014     0.094     169     255 ..      85     174 ..      81     186 .. 0.88
   3 !    8.7   0.1    0.0015         1     209     256 ..     196     243 ..     185     253 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.24
                                    HHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT CS
                     Coatomer_E 192 elsekykstplllngkAvvslllgryeeAeslLkeaLdkdak 233
                                    +ls   +stp  l   A +    ++y++A +l ++aL  d+ 
  gi|116754911|ref|YP_844029.1|  44 DLSMA-QSTPQDLVEDAKALFDANDYNQALNLTETALRMDSS 84 
                                    66655.788888889999999999999999999999988875 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00014
                                    HHHHHH...HHHH-TTHHHHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHH CS
                     Coatomer_E 169 LAqawv...klavggekiqdAyyifqelsekykstplllngkAvvslllgryeeAeslLkeaLdkdakdeetLiNlvvaa 245
                                    L qaw+   k+  + + ++dAy  f+  ++  +s     n k +v  +++ry++  +  ++a++ d+ ++e+ +N   + 
  gi|116754911|ref|YP_844029.1|  85 LEQAWLlrgKILYAMGMLRDAYQSFDRATQLDPSDAEAWNYKGIVLAAMQRYNNSLQCFESAIQADPMNYEAWSNKGNTL 164
                                    66888866678899999**********999999999**************************************987777 PP

                                    HHTT--HHHH CS
                     Coatomer_E 246 qhlgkdaevs 255
                                      lg+ ++++
  gi|116754911|ref|YP_844029.1| 165 VSLGRLDDAI 174
                                    7777766665 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0015
                                    HHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHHH CS
                     Coatomer_E 209 vvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevse 256
                                     +   ++ry eA  + + aL+ d+++  +L N   a q+lg ++e+ e
  gi|116754911|ref|YP_844029.1| 196 LAFYYQKRYHEALAMYERALQLDPNNSIALYNKGLALQKLGMNKEAEE 243
                                    5566789*********************************99888765 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.44   2.9e+02       8      23 ..      59      74 ..      57      76 .. 0.87
   2 ?    2.1   0.0       0.3     2e+02       9      35 ..      94     118 ..      91     119 .. 0.84
   3 ?    0.1   0.0       1.2   8.3e+02      15      25 ..     168     178 ..     166     183 .. 0.86
   4 !   10.0   0.2     0.001      0.69       8      36 .]     195     221 ..     191     221 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.44
                                   HHHHHHTT-HHHHHHH CS
                          TPR_3  8 AaefynkkkyqeArel 23
                                   A ++++  +y++A++l
  gi|116754911|ref|YP_844029.1| 59 AKALFDANDYNQALNL 74
                                   677888889****998 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.3
                                    HHHHHTT-HHHHHHH..HHHHHHH-TT CS
                          TPR_3   9 aefynkkkyqeArelfsYallaildke 35 
                                      +y ++ + +A++ f+   ++ ld+ 
  gi|116754911|ref|YP_844029.1|  94 KILYAMGMLRDAYQSFD--RATQLDPS 118
                                    679************88..88888876 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.2
                                    T-HHHHHHH.. CS
                          TPR_3  15 kkyqeArelfs 25 
                                    +++++A+ +f+
  gi|116754911|ref|YP_844029.1| 168 GRLDDAISAFD 178
                                    89******988 PP

  == domain 4  score: 10.0 bits;  conditional E-value: 0.001
                                    HHHHHHTT-HHHHHHH..HHHHHHH-TT- CS
                          TPR_3   8 AaefynkkkyqeArelfsYallaildken 36 
                                    + +fy +k+y eA+    Y+ +  ld++n
  gi|116754911|ref|YP_844029.1| 195 GLAFYYQKRYHEALAM--YERALQLDPNN 221
                                    679*************..98999999998 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.1   0.00032      0.21      69     118 ..      52     101 ..      43     109 .. 0.89
   2 ?    4.9   0.0      0.05        33      81     131 ..     132     184 ..     118     188 .. 0.81
   3 ?    1.9   0.1      0.42   2.8e+02      80     122 ..     199     241 ..     191     248 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00032
                                    HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHH CS
                Alkyl_sulf_dimr  69 aekvlekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgy 118
                                     + ++e ak+ ++++dy+ a++l++ ++  d++ ++a  l+ ++l ++g 
  gi|116754911|ref|YP_844029.1|  52 PQDLVEDAKALFDANDYNQALNLTETALRMDSSLEQAWLLRGKILYAMGM 101
                                    67899*********************************999999988886 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.05
                                    HTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH..-SSHHHHHHHHH CS
                Alkyl_sulf_dimr  81 kegdyrwaaellnhlvfadpenaeakelkadaleqlgyq..aesatwRniYls 131
                                    + + y+ +++  + +++adp n ea + k ++l +lg+   a+sa  R+i l+
  gi|116754911|ref|YP_844029.1| 132 AMQRYNNSLQCFESAIQADPMNYEAWSNKGNTLVSLGRLddAISAFDRSIILN 184
                                    557799999****************************8511456666666665 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.42
                                    HHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SS CS
                Alkyl_sulf_dimr  80 lkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaes 122
                                    + ++ y+ a+ + + +++ dp+n+ a   k  al++lg  +e+
  gi|116754911|ref|YP_844029.1| 199 YYQKRYHEALAMYERALQLDPNNSIALYNKGLALQKLGMNKEA 241
                                    5678899999*************99999999999999988876 PP

>> FAT  FAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.2   0.00032      0.21     210     291 ..      55     125 ..      39     139 .. 0.72
   2 ?    5.1   0.1     0.017        11     256     291 ..     131     159 ..     124     173 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00032
                                    CHHHHCCTSSCCCSS-SS---............HHHHCCCTCCCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTT CS
                            FAT 210 LreftsellekkeelqsgleaqkeptnleeftkllarcylkkGewqealqkldwseekieeilqsysaateidpswykaw 289
                                    L e ++ l++ + +++++l+     ++      +l ++ l++G+ + a++         +++ qs+ +at++dps ++aw
  gi|116754911|ref|YP_844029.1|  55 LVEDAKALFDAN-DYNQALNL---TETALRMDSSLEQAWLLRGKILYAMGM-------LRDAYQSFDRATQLDPSDAEAW 123
                                    444444333333.44444443...356666677778999************.......89******************** PP

                                    CC CS
                            FAT 290 ht 291
                                    ++
  gi|116754911|ref|YP_844029.1| 124 NY 125
                                    97 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.017
                                    CCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTCC CS
                            FAT 256 ealqkldwseekieeilqsysaateidpswykawht 291
                                    +a+q+        +  lq++  a + dp  y+aw +
  gi|116754911|ref|YP_844029.1| 131 AAMQR-------YNNSLQCFESAIQADPMNYEAWSN 159
                                    55555.......6789******************86 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.68   4.5e+02      63      83 ..      60      80 ..      54     117 .. 0.77
   2 ?    3.9   0.0     0.075        50     103     125 ..     157     179 ..     112     194 .. 0.85
   3 !    9.1   0.4    0.0019       1.3     102     127 ..     224     249 ..     190     253 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.68
                                   HHHHHTT-HHHHHHHHHHHHH CS
                        DUF3856 63 ealaklgrydealesadkalr 83
                                   +al    +y++al+ +++alr
  gi|116754911|ref|YP_844029.1| 60 KALFDANDYNQALNLTETALR 80
                                   677777788888888888876 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.075
                                    HHHHHHHHHHTT-HHHHHHHHHH CS
                        DUF3856 103 vfsravaleelGrkdealkafrm 125
                                      +++ +l +lGr d+a+ af  
  gi|116754911|ref|YP_844029.1| 157 WSNKGNTLVSLGRLDDAISAFDR 179
                                    56889999999999999999865 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0019
                                    HHHHHHHHHHHTT-HHHHHHHHHHHH CS
                        DUF3856 102 avfsravaleelGrkdealkafrmag 127
                                    a+++++ al++lG ++ea +afr a 
  gi|116754911|ref|YP_844029.1| 224 ALYNKGLALQKLGMNKEAEEAFRAAE 249
                                    789********************986 PP

>> PPTA  Protein prenyltransferase alpha subunit repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.039        26       2      19 ..      72      89 ..      71      92 .. 0.90
   2 ?    3.2   0.0      0.12        79      10      21 ..     114     125 ..     110     126 .. 0.86
   3 !    7.1   0.1    0.0072       4.8       6      20 ..     144     158 ..     144     159 .. 0.90
   4 ?   -1.5   0.0       3.5   2.3e+03       7      15 ..     213     221 ..     212     221 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.039
                                   HHHHHHHHHH-TT-CHHH CS
                           PPTA  2 LeltekliekdpkNYsaW 19
                                   L+lte ++++d + ++aW
  gi|116754911|ref|YP_844029.1| 72 LNLTETALRMDSSLEQAW 89
                                   9**********9988888 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.12
                                    HH-TT-CHHHHH CS
                           PPTA  10 ekdpkNYsaWny 21 
                                    ++dp++  aWny
  gi|116754911|ref|YP_844029.1| 114 QLDPSDAEAWNY 125
                                    679********9 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0072
                                    HHHHHH-TT-CHHHH CS
                           PPTA   6 ekliekdpkNYsaWn 20 
                                    e++i+ dp NY aW+
  gi|116754911|ref|YP_844029.1| 144 ESAIQADPMNYEAWS 158
                                    579***********7 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 3.5
                                    HHHHH-TT- CS
                           PPTA   7 kliekdpkN 15 
                                     ++++dp N
  gi|116754911|ref|YP_844029.1| 213 RALQLDPNN 221
                                    799****98 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       6.2   4.1e+03       8      23 ..      59      74 ..      59      77 .. 0.82
   2 ?   -0.0   0.1         3     2e+03       3      22 ..      88     107 ..      87     111 .. 0.77
   3 ?    3.0   0.0      0.32   2.1e+02       3      23 ..     156     176 ..     155     179 .. 0.78
   4 ?    0.0   0.1       2.9   1.9e+03      16      26 .]     203     213 ..     203     213 .. 0.84
   5 ?    5.0   0.0     0.071        47       3      25 ..     224     246 ..     223     247 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 6.2
                          TPR_4  8 ArallalGdldeAral 23
                                   A al+++ d+ +A+ l
  gi|116754911|ref|YP_844029.1| 59 AKALFDANDYNQALNL 74
                                   6799999999999865 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 3
                          TPR_4   3 allaLArallalGdldeAra 22 
                                    a l+++  l+a G l +A +
  gi|116754911|ref|YP_844029.1|  88 AWLLRGKILYAMGMLRDAYQ 107
                                    67888999999999888865 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.32
                          TPR_4   3 allaLArallalGdldeAral 23 
                                    a ++ + +l  lG+ld+A  +
  gi|116754911|ref|YP_844029.1| 156 AWSNKGNTLVSLGRLDDAISA 176
                                    56778889999******9655 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 2.9
                          TPR_4  16 dldeAraller 26 
                                    ++ eA+a+ er
  gi|116754911|ref|YP_844029.1| 203 RYHEALAMYER 213
                                    6789**99997 PP

  == domain 5  score: 5.0 bits;  conditional E-value: 0.071
                          TPR_4   3 allaLArallalGdldeAralle 25 
                                    al++ + al+ lG   eA+++++
  gi|116754911|ref|YP_844029.1| 224 ALYNKGLALQKLGMNKEAEEAFR 246
                                    79999***************998 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.5     0.015        10      56     121 ..      80     145 ..      50     186 .. 0.48
   2 ?    8.8   1.3    0.0032       2.1      76     123 ..     202     249 ..     190     253 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.015
                                    HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHH CS
                           BTAD  56 rleelrlealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYer 121
                                    r++ +  +a   + + + ++G  ++a +  +++++++P + +++      la++ r +  L+ +e+
  gi|116754911|ref|YP_844029.1|  80 RMDSSLEQAWLLRGKILYAMGMLRDAYQSFDRATQLDPSDAEAWNYKGIVLAAMQRYNNSLQCFES 145
                                    333333333333334444444444444444444444444444444444444444444444444443 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0032
                                    T-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                           BTAD  76 GraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlr 123
                                     r++eala +e++++++P +  +     +Al ++G + eA e+++ + 
  gi|116754911|ref|YP_844029.1| 202 KRYHEALAMYERALQLDPNNSIALYNKGLALQKLGMNKEAEEAFRAAE 249
                                    5899****************************************9875 PP

>> Rapsyn_N  Rapsyn N-terminal myristoylation and linker region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.034        23       4      60 ..      50     103 ..      47     119 .. 0.78
   2 ?    5.2   0.0     0.035        23       7      34 ..     189     216 ..     183     225 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.034
                       Rapsyn_N   4 dqtkrkiekGLklyesndtekalrvWrkvLkktsdregkfrvLGcLitahsemGkyk 60 
                                       +  +e    l++ nd ++al++   +L+  s  e+ + + G ++ a   mG  +
  gi|116754911|ref|YP_844029.1|  50 STPQDLVEDAKALFDANDYNQALNLTETALRMDSSLEQAWLLRGKILYA---MGMLR 103
                                    5555567777789*******************99999999998877765...45555 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.035
                       Rapsyn_N   7 krkiekGLklyesndtekalrvWrkvLk 34 
                                       i kGL +y +   ++al ++ ++L+
  gi|116754911|ref|YP_844029.1| 189 GAWIGKGLAFYYQKRYHEALAMYERALQ 216
                                    55699******************99997 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 ?    1.3   0.0      0.55   3.7e+02       2      17 ..      69      84 ..      55      96 .. 0.73
   2 ?    7.0   0.0    0.0092       6.1      22      52 ..     131     160 ..     120     166 .. 0.82
   3 ?    5.4   0.6     0.028        19      18      33 ..     202     217 ..     200     217 .. 0.90
   4 ?   -0.3   0.1       1.7   1.1e+03      24      47 ..     223     243 ..     220     252 .. 0.61

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.55
                            MIT  2 dkAlelvkkAveeDna 17
                                   ++Al+l ++A  +D++
  gi|116754911|ref|YP_844029.1| 69 NQALNLTETALRMDSS 84
                                   4566666666666654 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0092
                            MIT  22 eAlelYkealelLlqalkekneerrellrek 52 
                                    +A++ Y ++l+ +  a++  ++   e++ +k
  gi|116754911|ref|YP_844029.1| 131 AAMQRYNNSLQCFESAIQ-ADPMNYEAWSNK 160
                                    69***************9.566667776666 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.028
                            MIT  18 gnyeeAlelYkealel 33 
                                    + y eAl +Y+ al+l
  gi|116754911|ref|YP_844029.1| 202 KRYHEALAMYERALQL 217
                                    89***********986 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 1.7
                            MIT  24 lelYkealelLlqalk.ekneerre 47 
                                    + lY ++l l +++++ e      e
  gi|116754911|ref|YP_844029.1| 223 IALYNKGLALQKLGMNkE----AEE 243
                                    567888877777777533....222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 1576.62
//
Query:       gi|116754912|ref|YP_844030.1|  [L=192]
Description: sulfopyruvate decarboxylase [Methanosaeta thermophila PT]
Scores for 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-09   38.2   0.0    1.3e-09   37.9   0.0    1.1  1  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b


Domain annotation for each model (and alignments):
>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.0   7.3e-14   1.3e-09       4     160 ..      32     186 ..      29     191 .. 0.82

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 7.3e-14
                                    HHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT..TSEEEE-SSHHHHHHHHHHHHHHH.TS-EEEEE-CHHHHHHCHH CS
                   TPP_enzyme_N   4 aealvraLkalgvehvfgvpGsrilplldalseeq.girvvlarhEqgaafaAdgyarat.gkpgvvlvtsgpGatnalt 81 
                                    +e + r Lk++g++ v  vp+ ++ +ll  ls  +  i++ ++r E+g ++ A +y  +    p++++  s  G+ n ++
  gi|116754912|ref|YP_844030.1|  32 SEQVYRGLKRAGIDLVASVPCVNLQELLCLLSSDPdIIHIPVTREEEGIGVCAGAY--MGgMSPAIAMQNS--GLGNSIN 107
                                    6789999*******************888888888788888999999999999999..4414577777766..6888888 PP

                                    HHHHH.HHHT--EEEEEEE--CCCHHS..TC--T-CCHHHCCCSSE...EEE-SSGGGHHHHHHHHHHHHHSSS--EEEE CS
                   TPP_enzyme_N  82 alaeA.kvdriPllvlsgdrptslrgqgvlqqeldqlalfrpvtky...aervtspeelpealrrAirtalsgrpgPvyl 157
                                    ala+  ++ +iPll++  +r+t+ ++   l +++    l +p+ k     ++  +p+e+++a++ A+  a  ++++Pv++
  gi|116754912|ref|YP_844030.1| 108 ALASLdMLYGIPLLMVISHRGTQGER---LVGQIPMGRLTEPLLKTmgiPFFRPRPHEAEKAVEGAWSLA-LNEMRPVAV 183
                                    888763799****************9...55567777777777777666777889***************.888889888 PP

                                    EEE CS
                   TPP_enzyme_N 158 elp 160
                                     l 
  gi|116754912|ref|YP_844030.1| 184 LLD 186
                                    665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); 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 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1452.58
//
Query:       gi|116754913|ref|YP_844031.1|  [L=187]
Description: thiamine pyrophosphate binding domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-19   70.3   0.0    3.7e-19   69.0   0.0    1.5  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
  ------ inclusion threshold ------
       0.24   10.3   0.0       0.32    9.9   0.0    1.1  1  E1_dh         Dehydrogenase E1 component


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.0   0.0   4.1e-23   3.7e-19      15     139 ..      36     145 ..      29     153 .. 0.87

  Alignments for each domain:
  == domain 1  score: 69.0 bits;  conditional E-value: 4.1e-23
                                    TSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-.SEEEEEEE-SBCCCHHHHHH CS
                   TPP_enzyme_C  15 vkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnl.pitvvvlnNegygmtggqqe 93 
                                    + rp ++++   lg+mG + ++A+G++la p+r+v+ai GDG+ lm+l  lat++     + ++v+l+N++yg tg q++
  gi|116754913|ref|YP_844031.1|  36 RDRPENFYM---LGSMGMASSIALGLSLALPERRVIAIDGDGSVLMNLGTLATIASFASsNYLLVILDNRVYGSTGCQPT 112
                                    556666655...9*******************************************9888*****************987 PP

                                    HHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHH CS
                   TPP_enzyme_C  94 pfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleeal 139
                                     +               +d+a++a+++G++ + +v+ +  eel++ l
  gi|116754913|ref|YP_844031.1| 113 CTSR------------CTDLAAVARGAGVRdVRVVSGE--EELRRRL 145
                                    6543............369***********77787777..8888765 PP

>> E1_dh  Dehydrogenase E1 component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   3.6e-05      0.32     123     192 ..      64     134 ..      38     138 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 3.6e-05
                                    ---EEEEEEGGG..TT-HHHHHHHHHHHHTT--EEEEEEEESEETTE.EHHHH-S---GGG..TTTTS-EEEE CS
                          E1_dh 123 kevailliGDgA..anqGdvyealnlaalwklpvifvveNNkygisT.eaekasaskeladrargvgipglrV 192
                                    ++ +i++ GDg+   n G++++ + +a+   l vi+   N  yg +  ++   s++++la++arg+g+  +rV
  gi|116754913|ref|YP_844031.1|  64 ERRVIAIDGDGSvlMNLGTLATIASFASSNYLLVIL--DNRVYGSTGcQPTCTSRCTDLAAVARGAGVRDVRV 134
                                    56679999****999*******99999999888774..8999998767999*****************99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1355.77
//
Query:       gi|116754914|ref|YP_844032.1|  [L=418]
Description: hypothetical protein Mthe_1625 [Methanosaeta thermophila PT]
Scores for complete 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-105  352.4   0.0   2.3e-105  352.3   0.0    1.0  1  HcyBio    Homocysteine biosynthesis enzyme, sulfur-incorporat
    5.1e-06   26.5   3.8      0.048   13.8   0.1    2.5  2  Fer4_10   4Fe-4S dicluster domain
    3.3e-05   24.4   2.5       0.19   12.3   0.2    2.6  2  Fer4_7    4Fe-4S dicluster domain
    4.2e-05   23.4  12.6     0.0067   16.5   4.2    2.7  2  Fer4_6    4Fe-4S binding domain
     0.0022   17.7  12.8     0.0065   16.2   1.3    3.6  2  Fer4      4Fe-4S binding domain
     0.0024   18.4   0.1     0.0024   18.4   0.1    3.0  3  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
  ------ inclusion threshold ------
      0.011   16.5   0.2      0.011   16.5   0.2    3.0  3  Fer4_15   4Fe-4S single cluster domain
      0.013   16.0   1.0       0.46   11.0   0.1    2.4  2  Fer4_8    4Fe-4S dicluster domain
      0.036   14.2  11.8      0.045   13.8   1.7    2.8  2  Fer4_2    4Fe-4S binding domain
      0.052   13.7   8.7        1.3    9.3  10.5    2.2  3  Fer4_9    4Fe-4S dicluster domain
      0.059   13.5  10.4       0.18   11.9   0.8    2.4  2  Fer4_21   4Fe-4S dicluster domain
       0.17   12.1   2.1       0.35   11.1   2.1    1.5  1  Fer4_18   4Fe-4S dicluster domain
        6.4    7.8  12.3        3.8    8.5   2.8    2.5  2  Fer4_16   4Fe-4S double cluster binding domain


Domain annotation for each model (and alignments):
>> HcyBio  Homocysteine biosynthesis enzyme, sulfur-incorporation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  352.3   0.0  1.7e-108  2.3e-105       1     347 []      17     409 ..      17     409 .. 0.98

  Alignments for each domain:
  == domain 1  score: 352.3 bits;  conditional E-value: 1.7e-108
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxx......xxxxx RF
                         HcyBio   1 avVltaeelkklvrekgekkaaeevDVVttgTfgvmsssgallnlgvaepkiki..ekvwLngvpayag......laavd 72 
                                    a+Vltaee+ +lv++ g+ +++++vDVVtt+T++vms+++a+l++g ae+++++   ++ +ngv a++g      l+++d
  gi|116754914|ref|YP_844032.1|  17 ATVLTAEEVRDLVEQ-GAVSELQDVDVVTTATRAVMSGTYAVLSFGLAEKGSFArsVSARINGVLAHVGpcpnerLGHID 95 
                                    89*************.**************************************555668******************** PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         HcyBio  73 lylgataeseddkeeeeyGGghviedLvagkeveleaeaketdcyprkeieteitlddlneailvnpRnayqnYnaavNs 152
                                    l++++ta+++     e+yGGgh+++dLva+++v +++e++++     + i++e+tld++++a+++++Rna+ nY+a+vN+
  gi|116754914|ref|YP_844032.1|  96 LIVFGTAHRD-----ERYGGGHLFRDLVARRSVCVDVETSDG-----RCISRELTLDEIPHARIFGTRNAFMNYSAFVNT 165
                                    ********99.....49*************************.....99******************************* PP

                                    xxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         HcyBio 153 see...tiytymgelkpnlgnatysgaGelsPllnDpelktigiGtrilLgGaeGyvigeGTqsspekkrengvplgpag 229
                                    +     ti++ ++++  ++++a++sg+G l+Pl+nDp l+tig+Gtr+l++GaeG+vig+GT+s+pe++           
  gi|116754914|ref|YP_844032.1| 166 GGVamsTIFH-AIPFPVSMSGASFSGCGILNPLENDPLLETIGVGTRVLINGAEGFVIGTGTRSTPERP----------- 233
                                    988888****.**********************************************************........... PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                         HcyBio 230 tLavigdlkeMspeylrgafltsyGpelivgvgipiPvldeevleelavkdedielpvvDvserrrerktlgevsYael. 308
                                    +L+ ++d+++M pe++ g+f+ts+Gpe+i+++++p+Pvl+++v+++++  ++ i+lpv+Dv++r    ++l  ++Ya++ 
  gi|116754914|ref|YP_844032.1| 234 NLSGFADMHQMMPEFM-GGFVTSAGPECITSWAVPVPVLSQSVFNAVSRPERAIPLPVMDVGTR----SSLWAADYAQVw 308
                                    ****************.***********************************************....89********** PP

                                    ............................................................xxxxx.xxxxx.xxxxxxxx RF
                         HcyBio 309 ............................................................Gkiei.egkev.ktarlssl 326
                                                                                                G+++  +g +v +t+r+s++
  gi|116754914|ref|YP_844032.1| 309 rdvdlavrvrpdsckdctnciaeiscpmgaikrpvridrglcfncglcsvlcpevfrarlGSVRSpDGIHVpVTLRQSDR 388
                                    ***************************************************************875778**9******** PP

                                    xxxxxxxxxxxxxxxxxxxxx RF
                         HcyBio 327 krareiaeeLkewiekgeflL 347
                                     ra ++ae Lke+i++g+f++
  gi|116754914|ref|YP_844032.1| 389 LRAIRLAEILKERILDGSFRI 409
                                    *******************85 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.7   5.4e-05     0.074       2      21 ..     315     336 ..     302     341 .. 0.76
   2 !   13.8   0.1   3.5e-05     0.048       2      23 ..     343     364 ..     342     413 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.4e-05
                        Fer4_10   2 vvidddtCirCgkCvk..aCPa 21 
                                    v++ +d+C  C++C +  +CP+
  gi|116754914|ref|YP_844032.1| 315 VRVRPDSCKDCTNCIAeiSCPM 336
                                    4566788888888888656887 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 3.5e-05
                        Fer4_10   2 vvidddtCirCgkCvkaCPadl 23 
                                    v+id+  C +Cg C   CP  +
  gi|116754914|ref|YP_844032.1| 343 VRIDRGLCFNCGLCSVLCPEVF 364
                                    689999*************955 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.2   0.00014      0.19      31      52 .]     315     338 ..     277     338 .. 0.84
   2 !   11.6   0.2   0.00024      0.33      33      49 ..     345     361 ..     340     382 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                         Fer4_7  31 veidpekClgCgaCva..vCPtga 52 
                                    v+++p++C +C++C+a   CP ga
  gi|116754914|ref|YP_844032.1| 315 VRVRPDSCKDCTNCIAeiSCPMGA 338
                                    5899**********99778*9987 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00024
                         Fer4_7  33 idpekClgCgaCvavCP 49 
                                    id   C +Cg C   CP
  gi|116754914|ref|YP_844032.1| 345 IDRGLCFNCGLCSVLCP 361
                                    55556666666666666 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   4.2   4.9e-06    0.0067       2      24 .]     315     339 ..     314     339 .. 0.87
   2 !   11.4   1.3   0.00019      0.27       2      21 ..     343     362 ..     342     366 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.9e-06
                         Fer4_6   2 veidpdkCigCgdCvrv..CPegai 24 
                                    v++ pd+C +C +C++   CP+gai
  gi|116754914|ref|YP_844032.1| 315 VRVRPDSCKDCTNCIAEisCPMGAI 339
                                    7899**********66666*****8 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00019
                         Fer4_6   2 veidpdkCigCgdCvrvCPe 21 
                                    v+id+ +C  Cg C + CPe
  gi|116754914|ref|YP_844032.1| 343 VRIDRGLCFNCGLCSVLCPE 362
                                    89*****************7 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   4.3     0.043        59       2      24 .]     316     340 ..     315     340 .. 0.77
   2 !   16.2   1.3   4.7e-06    0.0065       2      20 ..     344     362 ..     343     364 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.043
                                    EEETTTSSS-THHHHH..STTTEEE CS
                           Fer4   2 videekCigCGaCvev..CPvgAIt 24 
                                     + ++ C  C +C+    CP gAI+
  gi|116754914|ref|YP_844032.1| 316 RVRPDSCKDCTNCIAEisCPMGAIK 340
                                    57899********863338888885 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 4.7e-06
                                    EEETTTSSS-THHHHHSTT CS
                           Fer4   2 videekCigCGaCvevCPv 20 
                                     id  +C +CG+C   CP 
  gi|116754914|ref|YP_844032.1| 344 RIDRGLCFNCGLCSVLCPE 362
                                    79****************5 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   6.0       7.7   1.1e+04       4      14 ..     320     330 ..     317     336 .. 0.84
   2 ?   -0.2   0.1       1.1   1.5e+03      49      57 ..     332     340 ..     329     341 .. 0.84
   3 !   18.4   0.1   1.7e-06    0.0024       1      21 [.     345     365 ..     345     374 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 7.7
                        Fer4_13   4 dtCiacgaCve 14 
                                    d+C +c++C +
  gi|116754914|ref|YP_844032.1| 320 DSCKDCTNCIA 330
                                    89*******86 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.1
                        Fer4_13  49 daCPvesIg 57 
                                     +CP+ +I+
  gi|116754914|ref|YP_844032.1| 332 ISCPMGAIK 340
                                    69******7 PP

  == domain 3  score: 18.4 bits;  conditional E-value: 1.7e-06
                        Fer4_13   1 VDrdtCiacgaCvelaPdvFe 21 
                                    +Dr  C +cg+C  l+P+vF+
  gi|116754914|ref|YP_844032.1| 345 IDRGLCFNCGLCSVLCPEVFR 365
                                    8999****************7 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   2.7       2.5   3.5e+03       2      18 ..     316     332 ..     315     336 .. 0.82
   2 ?   -1.6   0.0       3.4   4.7e+03      58      64 ..     333     339 ..     329     340 .. 0.84
   3 ?   16.5   0.2   7.6e-06     0.011       1      23 [.     343     365 ..     343     387 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.5
                        Fer4_15   2 vvDrdaCigcglCvaea 18 
                                    +v  d C  c +C+ae 
  gi|116754914|ref|YP_844032.1| 316 RVRPDSCKDCTNCIAEI 332
                                    556799*******9985 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.4
                        Fer4_15  58 aCPvdAI 64 
                                    +CP +AI
  gi|116754914|ref|YP_844032.1| 333 SCPMGAI 339
                                    7*****9 PP

  == domain 3  score: 16.5 bits;  conditional E-value: 7.6e-06
                        Fer4_15   1 VvvDrdaCigcglCvaeapevfe 23 
                                    V++Dr +C  cglC  ++pevf+
  gi|116754914|ref|YP_844032.1| 343 VRIDRGLCFNCGLCSVLCPEVFR 365
                                    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 ?    3.3   0.1      0.08   1.1e+02      49      62 ..     320     335 ..     279     344 .. 0.70
   2 ?   11.0   0.1   0.00033      0.46       5      22 ..     350     367 ..     346     413 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.08
                         Fer4_8  49 wsCttcgaCte..vCp 62 
                                    +sC  c +C     Cp
  gi|116754914|ref|YP_844032.1| 320 DSCKDCTNCIAeiSCP 335
                                    5566666553311344 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00033
                         Fer4_8   5 CieCgaCqsaCpvlrrtk 22 
                                    C +Cg+C   Cp + r +
  gi|116754914|ref|YP_844032.1| 350 CFNCGLCSVLCPEVFRAR 367
                                    999999999999555544 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   2.8     0.028        38       7      21 ..     319     335 ..     313     336 .. 0.75
   2 ?   13.8   1.7   3.3e-05     0.045       2      22 .]     342     362 ..     341     362 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.028
                         Fer4_2   7 tdrCigCgaCvsa..CP 21 
                                    +d+C  C  C+    CP
  gi|116754914|ref|YP_844032.1| 319 PDSCKDCTNCIAEisCP 335
                                    89********7333588 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 3.3e-05
                         Fer4_2   2 pvvvdtdrCigCgaCvsaCPa 22 
                                    pv +d+  C +Cg C   CP+
  gi|116754914|ref|YP_844032.1| 342 PVRIDRGLCFNCGLCSVLCPE 362
                                    6889***********766**5 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   2.5    0.0041       5.6      34      51 .]     320     339 ..     301     339 .. 0.65
   2 ?    9.3  10.5   0.00092       1.3       2      48 ..     322     362 ..     321     364 .. 0.77
   3 ?    7.7   1.0    0.0029         4       2      14 ..     350     362 ..     349     413 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0041
                         Fer4_9  34 eaCigCgaCv..eaCpkgai 51 
                                    ++C +C  C+    Cp gai
  gi|116754914|ref|YP_844032.1| 320 DSCKDCTNCIaeISCPMGAI 339
                                    46888888884456888876 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00092
                         Fer4_9   2 CtgCgaCvea..CpagvvvedaaerkarlraaseeaCigCgaCveaCpk 48 
                                    C +C++C++   Cp+g++++    r++r        C+ Cg C   Cp+
  gi|116754914|ref|YP_844032.1| 322 CKDCTNCIAEisCPMGAIKRPV--RIDRG------LCFNCGLCSVLCPE 362
                                    9999999665559999987654..44443......5***********96 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0029
                         Fer4_9   2 CtgCgaCveaCpa 14 
                                    C +Cg C   Cp 
  gi|116754914|ref|YP_844032.1| 350 CFNCGLCSVLCPE 362
                                    8888888888854 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   2.9     0.016        22      34      57 ..     315     339 ..     307     341 .. 0.68
   2 ?   11.9   0.8   0.00013      0.18       2      20 ..     344     362 ..     343     366 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.016
                        Fer4_21  34 lkvvedeCvGCnlCss..vCPvedci 57 
                                    ++v+ d+C  C+ C++   CP+ ++i
  gi|116754914|ref|YP_844032.1| 315 VRVRPDSCKDCTNCIAeiSCPM-GAI 339
                                    4667788888888864226885.666 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00013
                        Fer4_21   2 ridedkCigCgkCliaCed 20 
                                    rid+  C +Cg+C + C++
  gi|116754914|ref|YP_844032.1| 344 RIDRGLCFNCGLCSVLCPE 362
                                    6899999999999999986 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   2.1   0.00026      0.35      51     100 ..     312     365 ..     297     374 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00026
                        Fer4_18  51 eerkekgagdcidcescvk..vcPtgidirkGlqle...ciscllcidacdkvme 100
                                    ++  +     c dc  c++   cP+g  i+  ++++   c +c+lc   c +v  
  gi|116754914|ref|YP_844032.1| 312 DLAVRVRPDSCKDCTNCIAeiSCPMGA-IKRPVRIDrglCFNCGLCSVLCPEVFR 365
                                    5555566678999999996446***95.66677775566*******999999875 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   2.8    0.0028       3.8       2      20 ..     322     342 ..     321     348 .. 0.84
   2 ?    4.0   2.1     0.069        95       2      14 ..     350     362 ..     349     365 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0028
                        Fer4_16   2 CgtCgkCae..vCPtnaikek 20 
                                    C++C++C+   +CP +aik +
  gi|116754914|ref|YP_844032.1| 322 CKDCTNCIAeiSCPMGAIKRP 342
                                    *******97557*******98 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.069
                        Fer4_16   2 CgtCgkCaevCPt 14 
                                    C +Cg C   CP+
  gi|116754914|ref|YP_844032.1| 350 CFNCGLCSVLCPE 362
                                    8889999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); 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):              13  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 3122.03
//
Query:       gi|116754915|ref|YP_844033.1|  [L=899]
Description: periplasmic copper-binding [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-26   93.5  22.7    8.1e-26   90.8  22.7    2.1  1  NosD        Periplasmic copper-binding protein (NosD)
      5e-18   65.5  17.8      5e-18   65.5  17.8    2.4  3  Beta_helix  Right handed beta helix region
    5.2e-05   23.5   0.0    0.00011   22.4   0.0    1.5  1  ZU5         ZU5 domain
  ------ inclusion threshold ------
      0.034   14.5   0.2      0.034   14.5   0.2    2.4  3  DUF2135     Uncharacterized protein conserved in bacteria (DU


Domain annotation for each model (and alignments):
>> NosD  Periplasmic copper-binding protein (NosD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.8  22.7   1.8e-29   8.1e-26      82     240 ..     301     455 ..     232     456 .. 0.86

  Alignments for each domain:
  == domain 1  score: 90.8 bits;  conditional E-value: 1.8e-29
                           NosD  82 esGialmsssnntlenNtisnnenyGillsdssnntisnNtis.nnnkGiflens.ssntitgNriesnqkiGilllsss 159
                                    +sGi+++sss n+++nN i+ +++ Gi l ++++n i+ N i  n+++Gi+l +  ++nti+gNri++n++ Gi+ + +s
  gi|116754915|ref|YP_844033.1| 301 YSGIMVYSSS-NIIRNNSITLCDK-GIELYEADSNLIEANIIEdNDDNGIYLLSGcDENTIRGNRISRNGGDGIH-VYES 377
                                    4899999999.9999999999999.99999999999999999999999999877669999999999999999999.9999 PP

                           NosD 160 egntiynNyFinnsenvkydgsn........nneWnttktsgtniiggpylgGNyWsdydgeDadgDGigDtpYeindgv 231
                                    ++n i+ N+  +n  + +yd+ n         n+W+  +            +GNy+sd  ++D+++DGi+D+pY i++g+
  gi|116754915|ref|YP_844033.1| 378 NRNMIFSNIIADNIGDDAYDDYNatelgtgdVNRWDDGS------------KGNYYSDNLCTDSNRDGICDSPYGIPGGD 445
                                    999999999999988777777666778888899999999............9*************************999 PP

                           NosD 232 .iDylplvnp 240
                                     iD++pl++p
  gi|116754915|ref|YP_844033.1| 446 cIDRYPLASP 455
                                    9******998 PP

>> Beta_helix  Right handed beta helix region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.5  17.8   1.1e-21     5e-18      21     142 ..     270     393 ..     248     409 .. 0.86
   2 ?   -1.7   0.0       0.5   2.2e+03      53      73 ..     415     435 ..     403     438 .. 0.70
   3 ?   -2.9   0.0       1.2   5.5e+03     108     141 ..     627     665 ..     611     669 .. 0.51

  Alignments for each domain:
  == domain 1  score: 65.5 bits;  conditional E-value: 1.1e-21
                                    -..SS-SEEE-SSS-.EEES-EEES.....-SS-SEEE-TT-S-EEES-EEE---SEEE-TT--S--EEES-EEES-SS- CS
                     Beta_helix  21 s..ggyGiylrgssnvvienneian.....nsgsGiyilgssnntisnntisdnngggialfgasnnlienneitdnggs 93 
                                    +   g+Gi++  ++   +e+  + n      ++sGi +++ s n+i+nn+i+ +   gi l++a+ nlie n i+dn+++
  gi|116754915|ref|YP_844033.1| 270 AdrRGDGITISADGV-ALEGLSVINarggfLGYSGIMVYS-SSNIIRNNSITLCD-KGIELYEADSNLIEANIIEDNDDN 346
                                    155799999999999.99986666669999********97.**************.************************ PP

                                    SEE-T.T-S--EEES-EEESTT--SEE---TT---EEES-EEES-SSEEE CS
                     Beta_helix  94 Giyln.yssnntienNiidnnagsGividdsssnvtvtnNtitnnkgaGi 142
                                    Giyl  +++ nti++N+i+ n+g+Gi++++s+ ++ ++ N+i +n   G 
  gi|116754915|ref|YP_844033.1| 347 GIYLLsGCDENTIRGNRISRNGGDGIHVYESN-RNMIFSNIIADNI--GD 393
                                    ****966999**********************.8889******996..44 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.5
                                    TT-S-EEES-EEE---SEEE- CS
                     Beta_helix  53 gssnntisnntisdnngggia 73 
                                    gs++n  s+n ++d+n +gi+
  gi|116754915|ref|YP_844033.1| 415 GSKGNYYSDNLCTDSNRDGIC 435
                                    556666667777777666664 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.2
                                    -EEESTT.....--SEE---TT---EEES-EEES-SSEE CS
                     Beta_helix 108 Niidnna.....gsGividdsssnvtvtnNtitnnkgaG 141
                                    N+i+        ++ i  + +++++ ++n ++ +++ aG
  gi|116754915|ref|YP_844033.1| 627 NTISYLPcngedRCSILPTHTEHGICIQNAVFRDASVAG 665
                                    333333333333555555555555555555555555555 PP

>> ZU5  ZU5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   2.5e-08   0.00011      19      80 ..     491     554 ..     477     563 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 2.5e-08
                            ZU5  19 gvsLliPpgaipegtrie.iylavrkdenk.rppleegetllspvvecgpsglkfskpvilelp 80 
                                    g  + iP g+ip ++  +  +++++ ++++ rp+l eg +l+  v ++gp+g+ f++pv+++l+
  gi|116754915|ref|YP_844033.1| 491 GAAVDIPSGSIPPNEDGTpGTMVISIEKTNmRPELAEGLSLVGEVYQLGPEGTVFERPVQITLR 554
                                    77788******99886551455556677777*****************************9985 PP

>> DUF2135  Uncharacterized protein conserved in bacteria (DUF2135)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       1.8   8.1e+03       4      11 ..      51      58 ..      50      58 .. 0.91
   2 ?   -3.2   0.0       2.5   1.1e+04      36      51 ..     681     696 ..     680     696 .. 0.86
   3 ?   14.5   0.2   7.5e-06     0.034       1      14 [.     844     857 ..     844     898 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.8
                        DUF2135  4 GkYkVyVN 11
                                   G Y++ VN
  gi|116754915|ref|YP_844033.1| 51 GMYHISVN 58
                                   99*****9 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.5
                        DUF2135  36 teEGtpnekretfevp 51 
                                    + E t  e re f vp
  gi|116754915|ref|YP_844033.1| 681 PAESTRSETRERFWVP 696
                                    679999******9987 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 7.5e-06
                        DUF2135   1 plkGkYkVyVNYyg 14 
                                    +++G+YkV VNYy 
  gi|116754915|ref|YP_844033.1| 844 APPGVYKVSVNYYS 857
                                    79***********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (899 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); 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: 0.63u 0.24s 00:00:00.87 Elapsed: 00:00:00.41
# Mc/sec: 6639.21
//
Query:       gi|116754916|ref|YP_844034.1|  [L=247]
Description: hypothetical protein Mthe_1627 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 2019.95
//
Query:       gi|116754917|ref|YP_844035.1|  [L=84]
Description: hypothetical protein Mthe_1628 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); 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: 0.31u 0.23s 00:00:00.54 Elapsed: 00:00:00.35
# Mc/sec: 725.16
//
Query:       gi|116754918|ref|YP_844036.1|  [L=256]
Description: bacitracin resistance protein BacA [Methanosaeta thermophila PT]
Scores for complete 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-52  176.6  13.4    9.4e-52  176.3  13.4    1.0  1  BacA      Bacitracin resistance protein BacA
  ------ inclusion threshold ------
        6.7    7.5   9.4        5.1    7.9   0.1    3.3  3  PrgI      PrgI family protein


Domain annotation for each model (and alignments):
>> BacA  Bacitracin resistance protein BacA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.3  13.4     1e-55   9.4e-52       1     255 [.       6     244 ..       6     245 .. 0.87

  Alignments for each domain:
  == domain 1  score: 176.3 bits;  conditional E-value: 1e-55
                           BacA   1 aiilGivqGltefLPvSSsGhlilve.ellglekedlllfdvvihlGtllAvlvlfrkdilrllkgllkslkkkkkekee 79 
                                    a++lG +qG+te+LPvSS+G+ +l+  ++lg++ +d+l  ++++h+Gt+lAvlv fr+++l +l +             e
  gi|116754918|ref|YP_844036.1|   6 ALVLGALQGITEWLPVSSEGQTMLAMiSWLGMRPTDALSCSIFLHTGTMLAVLVRFRSRLLGMLNT-------------E 72 
                                    789*******************99982456787666778**********************96543.............6 PP

                           BacA  80 lrlllliivatipaailglllkdlieellrsp....lvvaialivtglllllaeklrkkkkksledltlkdalliGlaQa 155
                                     +l+  +ivat+ ++i g++l  l+++ +       l+++ +li+tgl+l l ++     +k++e++++kd++l GlaQ+
  gi|116754918|ref|YP_844036.1|  73 SKLMRTVIVATLFTGITGVPLYMLFRDRFTGGeqatLLIGSLLIATGLMLRLRSSS----TKDMEEISTKDMVLLGLAQG 148
                                    789999************999988877664334555999***********999854....578889************** PP

                           BacA 156 lAllPGvSRSGaTivaglllglsreaaaefSFllaiPailgagllkllksaealtasellllvgfvvafvvallaikfll 235
                                    +++lPGvSRSG+T+++ l++g+++++a+  SF++++Pa+lga +l++l +++ l+  +l  +v ++ +f+++++++++l+
  gi|116754918|ref|YP_844036.1| 149 FSILPGVSRSGTTLTVLLMRGVKQDDALMVSFIISVPAVLGAIALDCL-AGSPLSIRSLPGAVMLASSFITGYATMDVLM 227
                                    **********************************************66.34444455555599***************** PP

                           BacA 236 kllkkkklkvFaiYrivlGl 255
                                    ++ ++ +   F++++i +G+
  gi|116754918|ref|YP_844036.1| 228 RFSRNVS---FSWFCITMGM 244
                                    *******...7788888876 PP

>> PrgI  PrgI family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.3     0.017   1.5e+02      26      50 ..      84     110 ..      75     125 .. 0.64
   2 ?    7.9   0.1   0.00057       5.1       4      63 ..     130     191 ..     129     202 .. 0.77
   3 ?    0.5   0.8      0.11     1e+03      23      59 ..     210     248 ..     194     254 .. 0.60

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.017
                           PrgI  26 vlallvaiglylllrafl..eelasvl 50 
                                    + +++++++ly+l+r  +   e+a++l
  gi|116754918|ref|YP_844036.1|  84 LFTGITGVPLYMLFRDRFtgGEQATLL 110
                                    344568*********999763333333 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00057
                           PrgI   4 kDiseyeekiffgLtlRQliflvlall..vaiglylllrafleelasvlvillavPvaalgf 63 
                                    kD+ e+ +k +  L l Q + ++ ++      +++ll+r++ ++ a+++ ++++vP+++ ++
  gi|116754918|ref|YP_844036.1| 130 KDMEEISTKDMVLLGLAQGFSILPGVSrsGTTLTVLLMRGVKQDDALMVSFIISVPAVLGAI 191
                                    677888888888888899999999988533555666666666**************777665 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.11
                           PrgI  23 iflvlallvaiglylllrafl.eelasvlvill.avPva 59 
                                    ++l++ ++++++++ +l +f  +   s+++i + ++ +a
  gi|116754918|ref|YP_844036.1| 210 VMLASSFITGYATMDVLMRFSrNVSFSWFCITMgMITLA 248
                                    455666666666666666666655556666665344344 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.35
# Mc/sec: 2183.10
//
Query:       gi|116754919|ref|YP_844037.1|  [L=500]
Description: hypothetical protein Mthe_1630 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (500 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); 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:                         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: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 3424.92
//
Query:       gi|116754920|ref|YP_844038.1|  [L=145]
Description: heat shock protein Hsp20 [Methanosaeta thermophila PT]
Scores for complete 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-17   62.9   0.7    3.7e-17   62.3   0.7    1.3  1  HSP20       Hsp20/alpha crystallin family
    1.3e-13   50.3   0.4      2e-13   49.7   0.4    1.3  1  ArsA_HSP20  HSP20-like domain found in ArsA
    1.9e-07   32.0   0.0      3e-07   31.4   0.0    1.3  1  CS          CS domain
      0.001   19.5   0.0     0.0016   18.8   0.0    1.4  1  PIH1_CS     PIH1 CS-like domain
  ------ inclusion threshold ------
      0.021   14.9   0.1      0.031   14.3   0.1    1.3  1  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 !   62.3   0.7     1e-20   3.7e-17       1     100 [.      51     143 ..      51     145 .] 0.88

  Alignments for each domain:
  == domain 1  score: 62.3 bits;  conditional E-value: 1e-20
                                    E--SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--..---TT----SS---EEEEEE--STTB-TTT-EEEEETTE CS
                          HSP20   1 dikeeeeefevkldvpglkkeelkvkvednrvlvkgeheeeeedekglikerssrkFsrkftLPenvdadkvkaslkdGv 80 
                                    di e ++ f +++d+pg++k++++v+++++ +  k+ +e  +e++ +l++  ++++F+r +tLP +v  ++ ka+lkdGv
  gi|116754920|ref|YP_844038.1|  51 DIEERDDDFVITVDLPGVDKNDVEVTITEDGLRLKARRE-LKEGSYFLRE--RRGSFERIVTLPVEVRVEEAKAKLKDGV 127
                                    68899**********************************.5555555555..78************************** PP

                                    EEEEEEBSS--..------- CS
                          HSP20  81 Ltvtvpkkepekkkkerkiq 100
                                    L++ vpk  ++k    ++i+
  gi|116754920|ref|YP_844038.1| 128 LEIVVPKIVSAK----KRIA 143
                                    *******99874....3444 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 !   49.7   0.4   5.6e-17     2e-13       1      61 [.      56     130 ..      56     132 .. 0.98

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 5.6e-17
                     ArsA_HSP20   1 ddeyvlkldLPfvdkeeidlsrsgdeLtIkig...............nfrRqitLPsvlarkevtsAkfedgvLeI 61 
                                    dd++v+++dLP+vdk ++++++++d L +k+                +f R +tLP  ++ +e+ +Ak++dgvLeI
  gi|116754920|ref|YP_844038.1|  56 DDDFVITVDLPGVDKNDVEVTITEDGLRLKARrelkegsyflrerrgSFERIVTLPVEVRVEEA-KAKLKDGVLEI 130
                                    799*************************************************************.**********9 PP

>> CS  CS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.0   8.3e-11     3e-07       6      76 .]      53     134 ..      48     134 .. 0.93

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 8.3e-11
                                    EEETTEEEEEEE-TTCTTTTTCEEEEEETTEEEEEETSCEEEEECE...............BSS-BETTTEEEEEETTEE CS
                             CS   6 yQtldeVvvtiyvkkvnikkkdvkvefkerslkvkigkeklliege...............LfgpIdpeesswtieskkv 70 
                                     +++d+ v+t+ +++v  +k+dv+v+++e+ l++k   +++l+eg+               L  ++ +ee++ ++++  +
  gi|116754920|ref|YP_844038.1|  53 EERDDDFVITVDLPGV--DKNDVEVTITEDGLRLKA--RRELKEGSyflrerrgsferivtLPVEVRVEEAKAKLKDGVL 128
                                    68899**********9..*****************9..68899999999999**************************** PP

                                    EEEEEB CS
                             CS  71 eitLkK 76 
                                    ei++ K
  gi|116754920|ref|YP_844038.1| 129 EIVVPK 134
                                    **9987 PP

>> PIH1_CS  PIH1 CS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   4.4e-07    0.0016      28      85 ..      54     123 ..      41     136 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 4.4e-07
                        PIH1_CS  28 nvpkelaieielPllksikevklrvgerrleleskk....akyfLs.........lkLpYpvdedkveAkF 85 
                                    ++ + ++i+++lP++   ++v++ ++e+ l l++++     +yfL+         ++Lp +v  ++++Ak 
  gi|116754920|ref|YP_844038.1|  54 ERDDDFVITVDLPGV-DKNDVEVTITEDGLRLKARRelkeGSYFLRerrgsferiVTLPVEVRVEEAKAKL 123
                                    566789*********.889*************776666669999999999999999999999999999985 PP

>> GvpH  GvpH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   8.7e-06     0.031      99     125 ..      55      81 ..      28      92 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.7e-06
                           GvpH  99 dsdelvvvadlpGvtdedvdvaletde 125
                                      d++v+  dlpGv  +dv+v++  d 
  gi|116754920|ref|YP_844038.1|  55 RDDDFVITVDLPGVDKNDVEVTITEDG 81 
                                    5799******************98664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       762  (0.042501); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); 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: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1055.60
//
Query:       gi|116754921|ref|YP_844039.1|  [L=402]
Description: GTP cyclohydrolase II [Methanosaeta thermophila PT]
Scores for complete 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  295.8   0.7    1.5e-88  295.4   0.7    1.2  1  DHBP_synthase    3,4-dihydroxy-2-butanone 4-phosphate synthas
    5.6e-75  250.4   0.0    1.4e-74  249.1   0.0    1.6  2  GTP_cyclohydro2  GTP cyclohydrolase II


Domain annotation for each model (and alignments):
>> DHBP_synthase  3,4-dihydroxy-2-butanone 4-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  295.4   0.7   1.6e-92   1.5e-88       1     192 []       7     198 ..       7     198 .. 0.99

  Alignments for each domain:
  == domain 1  score: 295.4 bits;  conditional E-value: 1.6e-92
                                    HHHHHHHHTT--EEEESSTTTT-BEEEEEEGGG--HHHHHHHHHHB-S--EEEEEHHHHHHTT--BSSSS-SSTT---BB CS
                  DHBP_synthase   1 eeaiealkaGkfvivvDdedrenegdLiiaAekvtpekvafmirhasGlicvalteeradeLeLplmveenedkhktaft 80 
                                    +eai+++++Gkfviv+Dde+renegdL+iaAekvtpe+++fm++ha+Glicv+lt+er+++LeLp+m+++n+++++taft
  gi|116754921|ref|YP_844039.1|   7 DEAIKDIRDGKFVIVLDDESRENEGDLVIAAEKVTPEAINFMAKHARGLICVPLTAERIRQLELPMMTQQNTESMGTAFT 86 
                                    58****************************************************************************** PP

                                    --EEESST-SSS-SHHHHHHHHHHHH-TT--GGGEEEEEEEEEEEE-TTGGGTS-SHHHHHHHHHHHTTS-SBEEEEEBB CS
                  DHBP_synthase  81 vsvdaaegttTGIsaaDRalTirkladpkakpedfrrPGhvfplrareggvleRrghTEaavdLarlaglkpaavicell 160
                                    vsvda++g+tTGIsa DRa+Tir+l+dp+++ +d+++PGh fpl+a +ggvl+R+ghTEaavdLarlagl pa+vice++
  gi|116754921|ref|YP_844039.1|  87 VSVDARHGITTGISAFDRATTIRTLIDPSTTRADLVTPGHTFPLQALDGGVLRRAGHTEAAVDLARLAGLYPAGVICEIM 166
                                    ******************************************************************************** PP

                                    -TTSCB-BHHHHHHHHHHHT-EEEEHHHHHHH CS
                  DHBP_synthase 161 nddgtmarrdeleefakkhglkiitiedliey 192
                                     +dgtmar++ele+fa+khg+ ++tiedli+y
  gi|116754921|ref|YP_844039.1| 167 AEDGTMARLPELERFAEKHGIRMLTIEDLIRY 198
                                    ******************************98 PP

>> GTP_cyclohydro2  GTP cyclohydrolase II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.31   2.8e+03      64      88 ..       6      28 ..       4      58 .. 0.65
   2 !  249.1   0.0   1.6e-78   1.4e-74       2     163 .]     208     372 ..     207     372 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.31
                                   HHHHHHHHHHH-.EEEEEE--TTTT CS
                GTP_cyclohydro2 64 ldealeliaeegrGvlvylrqegrg 88
                                   +dea++ i+  g+ v+  l+ e r+
  gi|116754921|ref|YP_844039.1|  6 VDEAIKDIR-DGKFVI-VLDDESRE 28
                                   688888887.564444.44444443 PP

  == domain 2  score: 249.1 bits;  conditional E-value: 1.6e-78
                                    XEEEEEEEETTEEEEEEEE--.....EEEEEE-........EEEEEE--HHHHHS-B--TTTTTHHHHHHHHHHHH-.EE CS
                GTP_cyclohydro2   2 rvaeaklptrfgefrliayedkvdgkehlalvkgdi...pvlvRvHsecltgDvlgslrcdcgeqldealeliaeegrGv 78 
                                    r+ae+++pt++g+f++i+ye+ +dg+ h+alv gd+   + lvRvHs+cltgD++ s+rcdcgeql++al++i+++g+Gv
  gi|116754921|ref|YP_844039.1| 208 RIAEVEMPTEYGDFKAIGYESMLDGQCHVALVAGDPaadDALVRVHSQCLTGDTFRSKRCDCGEQLSRALQMISRNGNGV 287
                                    6679*********************************99899*******************************99***** PP

                                    EEEE--TTTTTHHHHHHHHHHHHHCT--HHHHHHHHT--S-----HHHHHHHHHTT--EEEEE-S-HHHHHHHCTT.... CS
                GTP_cyclohydro2  79 lvylrqegrgigllnklkayalqdeglDTveanlalglpadardygiaaqILkdlgvkkirLlTnnpekveaLegfgiev 158
                                    lvy++qegrgigl+nkl+ay+lqd g+DTvean++lg pad+rdygi+aqIL dlg++kirLlTnnp+k+ +L+g+g+e+
  gi|116754921|ref|YP_844039.1| 288 LVYMNQEGRGIGLANKLRAYELQDDGSDTVEANHKLGYPADLRDYGIGAQILLDLGIRKIRLLTNNPRKIVGLQGYGLEI 367
                                    ******************************************************************************** PP

                                    SEEEE CS
                GTP_cyclohydro2 159 vervp 163
                                    vervp
  gi|116754921|ref|YP_844039.1| 368 VERVP 372
                                    ***97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 2879.92
//
Query:       gi|116754922|ref|YP_844040.1|  [L=172]
Description: XRE family transcriptional regulator [Methanosaeta thermophila PT]
Scores for complete 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   30.6   0.1    6.3e-07   29.4   0.1    1.6  1  HTH_3           Helix-turn-helix
    2.7e-05   23.8   1.3    0.00013   21.7   0.0    2.4  2  HTH_psq         helix-turn-helix, Psq domain
    5.1e-05   22.9   0.5    8.3e-05   22.2   0.5    1.3  1  PrpR_N          Propionate catabolism activator
    0.00042   20.7   0.0    0.00092   19.6   0.0    1.6  1  HTH_26          Cro/C1-type HTH DNA-binding domain
  ------ inclusion threshold ------
      0.028   14.5   0.0      0.052   13.6   0.0    1.4  1  HTH_19          Helix-turn-helix domain
      0.029   14.1   0.0      0.091   12.6   0.0    1.8  1  DUF3368         Domain of unknown function (DUF3368)
      0.096   13.3   4.0       0.12   13.1   0.1    2.6  4  Mg_chelatase_C  Magnesium chelatase, subunit ChlI C-terminal
       0.11   12.9   0.0       0.25   11.7   0.0    1.7  1  HTH_31          Helix-turn-helix domain
       0.11   12.4   0.0       0.26   11.2   0.0    1.5  1  TrmB            Sugar-specific transcriptional regulator TrmB


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 !   29.4   0.1   3.2e-10   6.3e-07       7      47 ..      28      68 ..      22      70 .. 0.93

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 3.2e-10
                                   HTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHH CS
                          HTH_3  7 qlglsqeeLAeklGvsrstisriEnGernPsletlkklaka 47
                                   + g+s +e+++ + +++st+++i +G+r+P+++tl  + ++
  gi|116754922|ref|YP_844040.1| 28 EMGMSAREFSRISSIPQSTLYKILSGHREPNITTLRQIVRT 68
                                   78***********************************9886 PP

>> HTH_psq  helix-turn-helix, Psq domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   6.3e-08   0.00013       2      40 ..      15      54 ..      14      56 .. 0.93
   2 ?    0.1   0.3      0.35   6.9e+02       2      11 ..     115     124 ..     114     129 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 6.3e-08
                        HTH_psq  2 pealaaAleavvnGk.mSirkAArkYgiPrsTLwrrkrgk 40
                                   +eal  A+++v+++  mS r+ +r+  iP sTL++ ++g+
  gi|116754922|ref|YP_844040.1| 15 DEALRDAIRSVISEMgMSAREFSRISSIPQSTLYKILSGH 54
                                   79**********8888*******************99997 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.35
                        HTH_psq   2 pealaaAlea 11 
                                    +ea+ aA++a
  gi|116754922|ref|YP_844040.1| 115 EEAIIAAVRA 124
                                    89*****997 PP

>> PrpR_N  Propionate catabolism activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.5   4.2e-08   8.3e-05      60     160 ..      65     169 ..      60     172 .] 0.79

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 4.2e-08
                         PrpR_N  60 ilralkqakklgek.ialvgfeniikglktlselldldiei...ytinseeeaeaavkelkaegvevvvGdgvvadlAek 135
                                    i+r ++ ++  ge+ ia+++ + +++++++ +  ++ ++ +   y+ ++ eea  a  ++ ++g  +vv+  +v+ ++ek
  gi|116754922|ref|YP_844040.1|  65 IVRTIRDLEGGGERfIAIIAARPVLDKIEETRMRIGDKVFTlreYSATNIEEAIIAAVRAESDGAAAVVCAPIVSPTVEK 144
                                    899999999999776*****************9998777662225555555555555566789***************** PP

                         PrpR_N 136 aGlksvlltsgkesvrqAieeAlei 160
                                    +    v     +esvr+Aie A + 
  gi|116754922|ref|YP_844040.1| 145 LLTIPVATIIPRESVRRAIEVAAKK 169
                                    77666666666**********9875 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 !   19.6   0.0   4.6e-07   0.00092       2      46 ..      22      65 ..      21      69 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 4.6e-07
                         HTH_26  2 LrelmadrgitkseLargtgisaatlsrlvkgkpervsldtLdki 46
                                   +r ++ ++g+++ e++r + i ++tl+++++g  + ++++tL  i
  gi|116754922|ref|YP_844040.1| 22 IRSVISEMGMSAREFSRISSIPQSTLYKILSGH-REPNITTLRQI 65
                                   78999***************************7.79999999877 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.6e-05     0.052       3      50 ..      21      67 ..      20      69 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.6e-05
                         HTH_19  3 rLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiae 50
                                    ++ +++e g++ +e ++  +i +s +++i +g + +p++ +l++i++
  gi|116754922|ref|YP_844040.1| 21 AIRSVISEMGMSAREFSRISSIPQSTLYKILSGHR-EPNITTLRQIVR 67
                                   58999*************99999**********99.*********986 PP

>> DUF3368  Domain of unknown function (DUF3368)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.6e-05     0.091      17      40 ..      82     105 ..      78     107 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.6e-05
                        DUF3368  17 IpsvkplldaLiqaGfrispklya 40 
                                    I +++p+ld+++++ +ri +k++ 
  gi|116754922|ref|YP_844040.1|  82 IIAARPVLDKIEETRMRIGDKVFT 105
                                    667******************975 PP

>> Mg_chelatase_C  Magnesium chelatase, subunit ChlI C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   5.9e-05      0.12      32      68 ..       6      42 ..       2      45 .. 0.90
   2 ?    0.6   0.0      0.45   9.1e+02      66      77 ..      63      74 ..      57      84 .. 0.83
   3 ?   -3.1   0.0       6.5   1.3e+04       5      16 ..     112     123 ..     102     130 .. 0.66
   4 ?   -3.4   0.1         8   1.6e+04       8      19 ..     156     167 ..     154     170 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.9e-05
                 Mg_chelatase_C 32 eelrevceldeeaeelleeaierlglsaRaydrilkv 68
                                   + +r++++ de+ ++ ++++i+++g+saR ++ri  +
  gi|116754922|ref|YP_844040.1|  6 RIIRAAFQSDEALRDAIRSVISEMGMSAREFSRISSI 42
                                   678999***************************9765 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.45
                 Mg_chelatase_C 66 lkvArTiADLeg 77
                                    ++ rTi DLeg
  gi|116754922|ref|YP_844040.1| 63 RQIVRTIRDLEG 74
                                   5788******98 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 6.5
                 Mg_chelatase_C   5 aevrerVaaAre 16 
                                    ++++e ++aA +
  gi|116754922|ref|YP_844040.1| 112 TNIEEAIIAAVR 123
                                    455666666655 PP

  == domain 4  score: -3.4 bits;  conditional E-value: 8
                 Mg_chelatase_C   8 rerVaaAreiqk 19 
                                    re V +A e+++
  gi|116754922|ref|YP_844040.1| 156 RESVRRAIEVAA 167
                                    456666666655 PP

>> HTH_31  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   0.00012      0.25      12      53 ..      28      68 ..      10      78 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                         HTH_31 12 raGLsqeevAerlgvsestlsrlEqGrrgrpspavlealara 53
                                   + G+s +e  + + + +stl ++ +G r +p   +l++++r 
  gi|116754922|ref|YP_844040.1| 28 EMGMSAREFSRISSIPQSTLYKILSGHR-EPNITTLRQIVRT 68
                                   34**************************.8********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 ?   11.2   0.0   0.00013      0.26      19      44 ..      27      52 ..      23      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00013
                                   HHCCCHHCHHCCCTTSSCHCHHHHHH CS
                           TrmB 19 klgpatadeiaeelgvprskvYevLr 44
                                   ++  ++a+e ++++ +p+s+ Y++L+
  gi|116754922|ref|YP_844040.1| 27 SEMGMSAREFSRISSIPQSTLYKILS 52
                                   566899******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1391.91
//
Query:       gi|116754923|ref|YP_844041.1|  [L=336]
Description: flap endonuclease-1 [Methanosaeta thermophila PT]
Scores for complete 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   98.5   0.0    3.5e-28   97.8   0.0    1.4  1  XPG_I       XPG I-region
    1.6e-16   60.6   0.0    2.4e-16   60.1   0.0    1.3  1  XPG_N       XPG N-terminal domain
    9.8e-05   22.9   0.0    0.00031   21.3   0.0    1.8  2  5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
  ------ inclusion threshold ------
      0.071   13.2   0.0       0.36   11.0   0.0    2.2  2  HHH_2       Helix-hairpin-helix motif


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 !   97.8   0.0   7.8e-32   3.5e-28       2      94 .]     139     234 ..     138     234 .. 0.94

  Alignments for each domain:
  == domain 1  score: 97.8 bits;  conditional E-value: 7.8e-32
                                    HHT--EEE-SS-HHHHHHHHHHTTSSSEEE-SSSHHHHTT-SEEEESTT..ECECTT....EEECEEEEEEHHHHHHHHT CS
                          XPG_I   2 lmgipyvvApgEAEAqcayLqkkglvdaviseDsDlllFGapkvlrnls.kkkskkk..kekekkkvevidlekvlkelg 78 
                                    +mgipyv+Ap+E+EAq+a+++ +g+vd+v+s+D+D+llFGap+v+rnl  ++++k    + + ++++evi le+ l++lg
  gi|116754923|ref|YP_844041.1| 139 AMGIPYVQAPSEGEAQAAFMAIRGDVDYVASQDYDSLLFGAPRVVRNLAiTGRRKMPrkNIYIDVPPEVIILEEELTRLG 218
                                    79**********************************************976665555778999***************** PP

                                    --HHHHHHHHHHHCET CS
                          XPG_I  79 ltreqlidlaillgcD 94 
                                    ++reqlid+ i++g+D
  gi|116754923|ref|YP_844041.1| 219 ISREQLIDIGIMCGTD 234
                                    ***************9 PP

>> XPG_N  XPG N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.1   0.0   5.3e-20   2.4e-16       8      99 ..       7      99 ..       1     101 [. 0.91

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 5.3e-20
                                   HHHHHH-GEEEEEGGGGTTEEEEEEHHHHHHHHHHHSE.ETTEE-BS.....-HHHHHHHHHHHHHHHTTEEEEEEE--S-- CS
                          XPG_N  8 kllkevaairsvsiealegkklaiDaslwlyrfliavreqlgnalen.....tshlmglfsrllrlldfgikPifVFdgkap 84
                                   ++l++    +++s+e+l+g+ +a+D+   ly+fl  +r+++g+ l+      tshl gl++r+  l++ gi+  fVFdg +p
  gi|116754923|ref|YP_844041.1|  7 DILSK----KKISLENLSGCWIAVDGFNTLYQFLSIIRQPDGTPLMDasgrvTSHLSGLLYRMTNLIEVGIRVAFVFDGTPP 84
                                   55555....4599*********************************999********************************* PP

                                   GGGHHHHHHHHHHHH CS
                          XPG_N 85 dlkkeelekrserrq 99
                                   +lk+++l+ r + ++
  gi|116754923|ref|YP_844041.1| 85 ELKAGTLAARAQMKE 99
                                   *********998876 PP

>> 5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.4   6.3e+03      48      79 ..      97     128 ..      88     136 .. 0.67
   2 !   21.3   0.0   6.9e-08   0.00031       4      52 ..     222     269 ..     219     294 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.4
                     5_3_exonuc  48 ldelkekklkekLeenkeearlskkLatiktd 79 
                                    ++e++e +l+e+++++ ++ r ++  a+i+ +
  gi|116754923|ref|YP_844041.1|  97 MKEAAEIQLQEAIATGVDSFRYAQATARINSE 128
                                    33444556778888888888777777777766 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 6.9e-08
                     5_3_exonuc   4 eqiidlkaLvGDssDnipGvpgiGektAakLlkeygsleeilenld.elk 52 
                                    eq+id+  ++G   D   G p++G+k A kL++e+g le++l++l  +++
  gi|116754923|ref|YP_844041.1| 222 EQLIDIGIMCGT--DYNRGLPKVGPKRALKLIREHGCLEAVLDALGeSIE 269
                                    678888888884..6678*************************8862333 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.82   3.7e+03       1      11 [.     135     145 ..     135     161 .. 0.79
   2 ?   11.0   0.0     8e-05      0.36       7      43 ..     238     274 ..     235     277 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.82
                          HHH_2   1 rllfaLGIrhV 11 
                                    rll a+GI+ V
  gi|116754923|ref|YP_844041.1| 135 RLLDAMGIPYV 145
                                    678899**998 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 8e-05
                          HHH_2   7 GIrhVGektAklLakrFksldaLkkasleeLlevddi 43 
                                    G+++VG k A +L ++ + l+a  +a  e + + ++i
  gi|116754923|ref|YP_844041.1| 238 GLPKVGPKRALKLIREHGCLEAVLDALGESIENFREI 274
                                    89*************************9999988887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); 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: 0.45u 0.20s 00:00:00.65 Elapsed: 00:00:00.36
# Mc/sec: 2817.80
//
Query:       gi|116754924|ref|YP_844042.1|  [L=334]
Description: diphthamide biosynthesis protein [Methanosaeta thermophila PT]
Scores for complete 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-73  246.1   0.0    6.6e-73  245.8   0.0    1.0  1  Diphthamide_syn  Putative diphthamide synthesis protein
  ------ inclusion threshold ------
      0.074   12.7   0.0       0.19   11.3   0.0    1.6  2  DUF1847          Protein of unknown function (DUF1847)


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 !  245.8   0.0   7.4e-77   6.6e-73       1     295 [.      29     314 ..      29     321 .. 0.95

  Alignments for each domain:
  == domain 1  score: 245.8 bits;  conditional E-value: 7.4e-77
                Diphthamide_syn   1 fPegllpdsaeiadileefgaevvilgDttYGaCcvdevaaehlgadllvHyGhsclspvdrlpvlYvfveieldvehlv 80 
                                    +P+gl++ + ei++ilee+gaev+i+gD++YGaC++d + ++   +dllvH+Ghs++ +  + +++Y  ++++ dv+++v
  gi|116754924|ref|YP_844042.1|  29 LPDGLKRSASEISRILEETGAEVIISGDPCYGACDIDLQLCSM--VDLLVHIGHSEMCERLSDRIVYLEARMPDDVKDVV 106
                                    6****************************************99..9*************99******************* PP

                Diphthamide_syn  81 etlkknfkekkkivlvstiqyahaleevkeeleeegyevv.kvpqsekplspgevlgctspklkeeeeevdailyigdgr 159
                                    e+  + f +k ++++++t+q+ah++++v  +++++g+e +   p+s +++++g+vlgc +++++     +++ l+ig+g 
  gi|116754924|ref|YP_844042.1| 107 ERSLEFF-TKGRVAVCTTVQHAHTIDSVIGIMRSHGIEAIaGAPSS-RTRYRGQVLGCCYSAAR---VGAEEALFIGTGM 181
                                    *******.6778*************************999777777.***************95...5899********* PP

                Diphthamide_syn 160 fhllslmlsnpklpvyrydpyskklteesydakkllrrRyaaiekakdakkvGiivgtlgvqgrlelverlkkllkeagk 239
                                    fh+ +l +++  ++v+++dp++++++  + da  +lr Ry  i++a+dak++Gi+++++ +q+r  +++rl +l +++gk
  gi|116754924|ref|YP_844042.1| 182 FHPVGLSIAT-GMRVIAADPVTGNVD--EIDAHDFLRWRYGIIARAADAKSIGILISKKPGQRRCVTARRLCTLGRSKGK 258
                                    **********.569********9766..6679************************************************ PP

                Diphthamide_syn 240 ksylvlvgelnpakLanfaeidafVlvaCprlsiddgkeFekPvltpyElevalg.e 295
                                    ++  v++++++p+++ ++  +da+V +aCpr+++dd++ ++ P+ltp E+e+alg +
  gi|116754924|ref|YP_844042.1| 259 RMLEVYIDRIEPERVLDL-GLDAVVSTACPRIALDDARMYSVPILTPPEFEIALGlR 314
                                    ******************.***********************************933 PP

>> DUF1847  Protein of unknown function (DUF1847)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.1e-05      0.19      44      85 ..      11      52 ..       6      58 .. 0.92
   2 ?   -3.6   0.0      0.84   7.6e+03      60      83 ..     118     143 ..     113     146 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.1e-05
                        DUF1847 44 eeiiefakrmgykkiGiafCvglleeakalakileakgfevv 85
                                   e  ++ +kr +++++G+    gl++ a ++++ile++g ev+
  gi|116754924|ref|YP_844042.1| 11 ERAVSIIKRAEIRRVGVQLPDGLKRSASEISRILEETGAEVI 52
                                   5678889*******************************9985 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 0.84
                        DUF1847  60 iafCvglle..eakalakileakgfe 83 
                                    +a+C+++++    + +  i++++g+e
  gi|116754924|ref|YP_844042.1| 118 VAVCTTVQHahTIDSVIGIMRSHGIE 143
                                    45565554310334566666777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2512.56
//
Query:       gi|116754925|ref|YP_844043.1|  [L=384]
Description: L-tyrosine decarboxylase [Methanosaeta thermophila PT]
Scores for complete 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-30  105.4   0.0    1.4e-29  103.0   0.0    1.8  1  Pyridoxal_deC    Pyridoxal-dependent decarboxylase conserved 
    4.9e-09   35.6   0.0    8.5e-09   34.8   0.0    1.3  1  Aminotran_5      Aminotransferase class-V
    1.9e-07   30.6   0.0     0.0012   18.1   0.0    2.1  2  Aminotran_1_2    Aminotransferase class I and II
  ------ inclusion threshold ------
      0.012   14.9   0.0      0.017   14.4   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase
      0.015   14.7   0.0      0.026   13.9   0.0    1.3  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family


Domain annotation for each model (and alignments):
>> Pyridoxal_deC  Pyridoxal-dependent decarboxylase conserved domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.0   0.0   3.9e-33   1.4e-29      75     371 ..      63     324 ..      53     328 .. 0.88

  Alignments for each domain:
  == domain 1  score: 103.0 bits;  conditional E-value: 3.9e-33
                                    HHHHHHHHHHHHHHHHHTT--GGGTCCT-EEEEESSHHHHHHHHHHHHHHHHHHHHHHHTTTS.HHHHHCCEEEEEETTS CS
                  Pyridoxal_deC  75 PaltelevvvldwlaellglpeeflekegggvlqvgssestllallAartkvikemkekgkelkeaeildklvlytsdqa 154
                                    P ++e+e +v+  l+ llg +      ++ g +++g++es++ a+ Aar+   ++                 +++    a
  gi|116754925|ref|YP_844043.1|  63 PGTAEIERRVVGILGSLLGCS------DATGYVSTGGTESNIQAVRAARNSSGRR---------------DGNIVVPRSA 121
                                    8899*****************......5899*****************9865443...............2367778889 PP

                                    -HHHHHHHHHHT-EEEEE--BTTTBB-HHHHHHHHHHHHCTT.EEEEEEEEBS-TTT-BB--HHHHHHHHHHCT-EEEEE CS
                  Pyridoxal_deC 155 hssvekaalvlgvklrvipldengklrgaalekaieedkekGlipffvvatlGttvlgaFddlkelgdicekydlwlHvD 234
                                    h s +k+a +l++++r  +lde+ ++ + + e++i ++       ++ v ++Gtt  g+ d + +l ++  + +++lHvD
  gi|116754925|ref|YP_844043.1| 122 HFSFDKIADLLNLEVRKAELDESLRVDVGDVERLIDDR--T----VCLVGIAGTTEFGQVDPIGDLSELAIENGIPLHVD 195
                                    *********************************99654..3....47899****************************** PP

                                    -TTGGGGGGSGGGGG...GGTTGGGESEEEEECCCCTS--SS-EEEEESSCCGCHHHH-EEECCCT.TTTTTSEECCCGS CS
                  Pyridoxal_deC 235 AAyaGsaficpeirh...llkgieradSitvnphKlllvlldcsalivkdkealqqalqleaeYLehedsdvaadlgtka 311
                                    AA++G  f+ p+  +   ++++ e ++Sit+ phK+++ ++ ++ li++ +  l +  + e  YL      v+    +  
  gi|116754925|ref|YP_844043.1| 196 AAFGG--FVLPFLEKdcmWDFRAEGVQSITIDPHKMGMSPIPAGGLIFRSSDPLRRL-ETETYYLT-----VSR---QAS 264
                                    *****..*******99*************************************9875.5999****.....444...456 PP

                                    SSSSG.HHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTEEECSTTBSSEEE CS
                  Pyridoxal_deC 312 iplsr.rvrilklwfvlralGveglqnqirksvelakyleklirkderfeivaevelglVc 371
                                    +   r    ++  + v+  lG+ g+++++r+++++ + l ++ r+ + +  v e+ +  V+
  gi|116754925|ref|YP_844043.1| 265 LTGTRsGAAAAATYAVIMHLGIDGYRKVVRRCMDMTEHLVSEARAMGIEP-VIEPVMNVVA 324
                                    6667767888999*************************999988766444.4455565555 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.0   2.4e-12   8.5e-09      68     178 ..      91     198 ..      77     223 .. 0.87

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 2.4e-12
                                    SSHHHHHHHHHHHCCCC.-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEE CS
                    Aminotran_5  68 sGtteainlvalslars.lkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvait 146
                                     G+te++  +++++++s  +++ +ivv ++ h +      ++a+  +++v++++lde  ++d+ ++e l++++t  +   
  gi|116754925|ref|YP_844043.1|  91 TGGTESNIQAVRAARNSsGRRDGNIVVPRSAHFSFD----KIADLLNLEVRKAELDESLRVDVGDVERLIDDRTVCLVGI 166
                                    58888666666666666699999*****99999877....8999999********************************* PP

                                    SBETTTTEB--HHHHHHHHHHTT-EEEEE-TT CS
                    Aminotran_5 147 hvsnvtGtiqpveeigklakkkgalvlvDaaq 178
                                    +  ++ G ++p+ ++ +la ++g+ ++vDaa 
  gi|116754925|ref|YP_844043.1| 167 AGTTEFGQVDPIGDLSELAIENGIPLHVDAAF 198
                                    ******************************95 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   3.5e-07    0.0012      72     196 ..      89     204 ..      64     227 .. 0.83
   2 !   10.7   0.0   6.1e-05      0.22     253     360 ..     268     370 ..     228     373 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.5e-07
                                    EEESHHHHHHHHHHHHHHHTTT-E...EEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTET CS
                  Aminotran_1_2  72 vvgsGagaliealifllklnpgde...ilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkk 148
                                    v ++G+ ++i+a+ ++  +  g++   i+vp+  + s+++i+ l  +ev++ +l+  e+ ++d+ ++e+++++       
  gi|116754925|ref|YP_844043.1|  89 VSTGGTESNIQAVRAAR-NSSGRRdgnIVVPRSAHFSFDKIADLLNLEVRKAELD--ESLRVDVGDVERLIDDR-----T 160
                                    45566666666666555.666654455**************************99..***************93.....2 PP

                                    EEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSS CS
                  Aminotran_1_2 149 tkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfg 196
                                    ++++ +++     G+v +  +l +l   a ++++ l vD a++gfv+ 
  gi|116754925|ref|YP_844043.1| 161 VCLVGIAGT-TEFGQVDPIGDLSEL---AIENGIPLHVDAAFGGFVLP 204
                                    355555554.568************...9999*************975 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 6.1e-05
                                    SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCS.CSSEEEEEETHHCHHHHHHHHHHT.CTE CS
                  Aminotran_1_2 253 ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasq.sgmflltdlsaetakelskkLlee.vgv 330
                                    + +++aa+a+ +   +l ++   + ++r  +++++l++e ++ g++ ++++  +++ l++ ++     + ++Lle+ ++v
  gi|116754925|ref|YP_844043.1| 268 TRSGAAAAATYAVIMHLGIDGYRKVVRRCMDMTEHLVSEARAMGIEPVIEPvMNVVALRVDDPP---GVRRALLERgWHV 344
                                    5555555555555555667799999***************999*99988887899998888888...99999****7777 PP

                                    EEEEGGGGTSTTEEEEEC.TTS-HHHHHHHH CS
                  Aminotran_1_2 331 yvtpgtsftvpgrlRitv.Aglteeeleelv 360
                                     +t+      p+ lR+ + +++t+e+l+ ++
  gi|116754925|ref|YP_844043.1| 345 SMTR-----EPKALRLILmPHMTDENLDLFL 370
                                    7777.....6779***999********9776 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   4.8e-06     0.017      68     169 ..     109     197 ..      47     198 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.8e-06
                                    --TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---H CS
                Beta_elim_lyase  68 lqrgeevivtepahihfdetgaiaelagvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsl 147
                                     +r  +++v + ah+ fd    +      ++r+++ +e   +d+ ++e++i++       + l+ ++ T++   Gqv + 
  gi|116754925|ref|YP_844043.1| 109 GRRDGNIVVPRSAHFSFDKIADL---LNLEVRKAELDESLRVDVGDVERLIDD-----RTVCLVGIAGTTEF--GQVDP- 177
                                    47888899999999999976555...455567777777789************.....488**********9..99866. PP

                                    HHHHHHHHHHHHCT-EEEEEET CS
                Beta_elim_lyase 148 eelrevaaiakkygiplhlDgA 169
                                      +  ++++a ++giplh+D+A
  gi|116754925|ref|YP_844043.1| 178 --IGDLSELAIENGIPLHVDAA 197
                                    ..6677889************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 ?   13.9   0.0   7.2e-06     0.026      46     146 ..      92     197 ..      78     199 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.2e-06
                                    SHHHHHHHHHHH..TTTT...TT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTE...EEEEE CS
                DegT_DnrJ_EryC1  46 sGtaAlhlaLra..lgvg...pgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaaieaaitert...kaIlp 117
                                     Gt+++  a ra     +   ++  ++vp    ++  + +  l++++  ++ d +++ +d+ ++e++i  rt    +I  
  gi|116754925|ref|YP_844043.1|  92 GGTESNIQAVRAarN--SsgrRDGNIVVPRSAHFSFDKIADLLNLEVRKAELD-ESLRVDVGDVERLIDDRTvclVGIAG 168
                                    578888888888542..32346778999*************************.99****************98889999 PP

                                    B-GGGB---HHHHHHHHHHCT-EEEEE-T CS
                DegT_DnrJ_EryC1 118 VhlyGqvadmdalkaiaakhglkvieDaA 146
                                       +Gqv  +  l ++a + g+++  DaA
  gi|116754925|ref|YP_844043.1| 169 TTEFGQVDPIGDLSELAIENGIPLHVDAA 197
                                    99**************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); 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: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 2999.56
//
Query:       gi|116754926|ref|YP_844044.1|  [L=754]
Description: phosphoenolpyruvate synthase [Methanosaeta thermophila PT]
Scores for 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-117  390.4   0.2   1.1e-116  389.7   0.2    1.2  1  PPDK_N           Pyruvate phosphate dikinase, PEP/pyruvate bi
    1.6e-88  296.7   0.4    1.6e-88  296.7   0.4    1.6  2  PEP-utilizers_C  PEP-utilising enzyme, TIM barrel domain
    3.3e-25   87.6   2.8    8.6e-25   86.3   2.8    1.8  1  PEP-utilizers    PEP-utilising enzyme, mobile domain
    6.2e-07   28.8   0.6    1.9e-05   23.9   0.3    2.4  2  HpcH_HpaI        HpcH/HpaI aldolase/citrate lyase family
  ------ inclusion threshold ------
      0.035   14.5   0.1        9.1    6.6   0.0    3.5  3  Radical_SAM      Radical SAM superfamily
       0.23   11.4   0.1       0.66    9.9   0.1    1.6  1  Lipase_GDSL      GDSL-like Lipase/Acylhydrolase


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 !  389.7   0.2  3.6e-120  1.1e-116       2     322 ..      16     328 ..      15     333 .. 0.98

  Alignments for each domain:
  == domain 1  score: 389.7 bits;  conditional E-value: 3.6e-120
                         PPDK_N   2 elvGGKganLaellneagipvPpgfaitadafrefleengleekideelkeldvddvdelrkaskeirelilsaelPeel 81 
                                    ++vGGKga+L+e++n +gipvP gfa+ta+afr+fle++g+++++ ++l+ +dv++ +el ka++++++++++a++Pe++
  gi|116754926|ref|YP_844044.1|  16 PVVGGKGASLGEMIN-IGIPVPGGFAVTAQAFRQFLERAGIAKELFDSLN-VDVNNPEELLKAEARAKKIVMDAKVPEDI 93 
                                    57***********77.**********************************.7**************************** PP

                         PPDK_N  82 eeaikeayeelgkkfgdeelpvaVRSSataEDlpkasfaGqqdtyLnvggeeevleaikavfaSlfnerAilYrkekgld 161
                                    e+aike y+el+++ g+e + vaVRSSataEDlp+asfaGqq+tyLnv+g+++v+ea+k+++aSl+ +rAi+Yr e+g++
  gi|116754926|ref|YP_844044.1|  94 ENAIKERYRELCEREGEE-VFVAVRSSATAEDLPEASFAGQQETYLNVRGADAVFEAVKKCWASLYGARAIFYRVEQGFE 172
                                    *************99998.************************************************************* PP

                         PPDK_N 162 heevalavvvqkmvnsdlgasGVafsldpetGfkdevlinasyGlGeaVVaGrvtpdefvvekstrkilekkigekeiki 241
                                    he+v+l+++vqkmv+s+  +sGV+fs  p+tG +  v+i+a++GlGeaVV+G v+pd++vv++s++ki+ k i++kei+i
  gi|116754926|ref|YP_844044.1| 173 HEKVNLSAIVQKMVDSE--KSGVMFSSQPSTG-EPLVVIEAAWGLGEAVVSGSVSPDNYVVDRSSKKIVHKMIATKEIMI 249
                                    *****************..*************.*********************************************** PP

                         PPDK_N 242 vydekeegtkevevpeeereklaLsdeeveeLaeiakkiekhygtpmdiEfaideeegklyllQaRpetrtsekkekkaa 321
                                    v+d+++++t++v+vp e+r++++L+++e+  La++a+ +ekhyg p+diE+ i+  ++k+y+lQ+Rp+t+  + ++k++a
  gi|116754926|ref|YP_844044.1| 250 VRDPATSKTVTVPVPPEKRDAQVLTESEILDLAKYAEILEKHYGIPQDIEWGIE--KNKIYILQSRPITTIAKGAAKTTA 327
                                    ******************************************************..**************9999888776 PP

                         PPDK_N 322 e 322
                                    e
  gi|116754926|ref|YP_844044.1| 328 E 328
                                    5 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 ?   -3.5   0.0       1.4   4.2e+03      16      42 ..      77     103 ..      72     140 .. 0.68
   2 !  296.7   0.4   5.2e-92   1.6e-88       3     293 ..     445     743 ..     443     744 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.4
                                    CCXBCEEEEEESSCHHHHHHHHCTXSS CS
                PEP-utilizers_C  16 dgkkikvlaNidtpedaekalengaeG 42 
                                    + ++ k+++ ++ ped+e+a +++   
  gi|116754926|ref|YP_844044.1|  77 EARAKKIVMDAKVPEDIENAIKERYRE 103
                                    566778889999999999888776554 PP

  == domain 2  score: 296.7 bits;  conditional E-value: 5.2e-92
                                    HSTSCCCCCCCHCCCXBCEEEEEESSCHHHHHHHHCTXSSEEEEEHHHHCTTSCCHHHHHH...........HHHHHHHH CS
                PEP-utilizers_C   3 esgklktllavtkdgkkikvlaNidtpedaekalengaeGiGLlRtEflfmareelpteee...........qaeaykkv 71 
                                    e++k++ +    k++++++v +Ni++p  a++a+++ a+G+GLlR+E++++   ++p               +++++k v
  gi|116754926|ref|YP_844044.1| 445 EEKKVQPVAVAYKPVTATEVKVNISEPTRAQAAAATMADGVGLLRIEHMILGLGKTPGYYIrsgrseeyvdeLVKNIKIV 524
                                    556666677778899*************************************98876554447888999999******** PP

                                    HHHTTTSEEEEEXXXSSCC..GGSGGCHHHH.XSXGGGSSXTHHHHCCSHHHHHHHHHHHHHHCC..CCEEEEEESSXXS CS
                PEP-utilizers_C  72 leamngrpvvvRtlDiggd..kelpelkeepeevNPmlGfRgirlglsepelfetqlrAllrasa..agkleimlPmvas 147
                                    ++a++++pv+vRtlD+++d  + ++ +++ep e NPmlG+Rgir+ l+e + f+ ++rA+++  +   +++ imlPmv++
  gi|116754926|ref|YP_844044.1| 525 ADAFYPKPVWVRTLDAPTDefRAMEGGENEPVEHNPMLGWRGIRRDLTEVDHFRLEVRAFKKLHElgLTNVGIMLPMVQH 604
                                    *******************88889*****************************************6566*********** PP

                                    HHHHHHHHHHHHHHHHHHHHCTCTXXTTXEEEEEEXSHHHHHTHHHHCTT.SSEEEEXHHHHHHHHHTXXCCCHCHHHHS CS
                PEP-utilizers_C 148 veeleeakkiieevkeelekegvkkkkkvkvGiMiEvpsaalladklake.vdFfSiGtNDLtQytlavdRdneevakly 226
                                    v+el++ak+i++e+  +l+        k+ vGiM+E+p+aal+++++++e  dF+S+GtNDLtQytlavdR+ne+va+ly
  gi|116754926|ref|YP_844044.1| 605 VSELKRAKEIMREEGLDLN--------KIDVGIMVETPAAALTIEDFIEEgLDFISFGTNDLTQYTLAVDRNNENVANLY 676
                                    *************955554........78********************99***************************** PP

                                    XTTTCHHCCCHHHHHHHHHHCCXEEEEESCCCCSCCCHHHHHHCTXSEEEEXGGGHHHHHHHHHCTT CS
                PEP-utilizers_C 227 dplepavlrlikevikaaeekglkvgiCGelagdpsavellvglGldelSmsaasvpaaraalaqve 293
                                     +++pav +li++v++ ++++g+k++iCG+++++p++++ lv++G+d++S++ ++v+++r+++a++e
  gi|116754926|ref|YP_844044.1| 677 SEMHPAVIKLIEYVVERCKKAGVKTSICGQAGSYPEMARRLVQIGIDSISANIDAVATVRETVARAE 743
                                    ***************************************************************9876 PP

>> PEP-utilizers  PEP-utilising enzyme, mobile domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.3   2.8   2.9e-28   8.6e-25       2      73 .]     363     434 ..     362     434 .. 0.98

  Alignments for each domain:
  == domain 1  score: 86.3 bits;  conditional E-value: 2.9e-28
                                    --S-EEEEES---HHHHTTS-GEEEEEES--TTHHHHHHHHHHTT--EEE--SSHH.HH--TEEEEEETTTT CS
                  PEP-utilizers   2 leegvILvaeetspsdiagldkaaGivterGGmtSHaAivArelgiPaVvgvgeatielkegdlitvDgstG 73 
                                    +++g+I+v+++t p++++++++a +ivt++GGm +HaAiv+relg PaVvg+++at++l++g ++tvDg++G
  gi|116754926|ref|YP_844044.1| 363 VKDGDIMVTRMTMPDMVPAMRRAGAIVTDEGGMACHAAIVSRELGCPAVVGTKNATKVLRDGMVVTVDGTKG 434
                                    789*******************************************************************99 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 ?    2.3   0.0     0.025        75     171     216 ..      44      88 ..      29      90 .. 0.76
   2 !   23.9   0.3   6.4e-09   1.9e-05      82     216 ..     591     725 ..     579     742 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.025
                                    HHHHHHHH.TTHCEEEEEEE.E-SSHHHHHHHHHTTHCEEEEEEHHH CS
                      HpcH_HpaI 171 darerilt.aaraagiaaldtvasdiddaegflaegalfvalGfdgk 216
                                    +a +++l  a+ a++   +d++ +d++++e++l++ a ++++ +d k
  gi|116754926|ref|YP_844044.1|  44 QAFRQFLErAGIAKE--LFDSLNVDVNNPEELLKAEARAKKIVMDAK 88 
                                    455555541444444..5*****************999999988877 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 6.4e-09
                                    HTTSSEEEESS--SHHHHHHHHHHTSHTTTS---HCCC-EEEEEE-SHHHHHTHHHHHTSTTEEEEEE-HHHHHH.HTT- CS
                      HpcH_HpaI  82 dlgaqvvlvPkvetaeealevvsalrepekgirganketrllaqiEsaegvknaeeIaavegldgvflGaeDlsa.dlgt 160
                                     l   ++++P+v+   e++ +++++re         +++ + + +E+ ++ + +e+ ++ egld + +G++Dl+  +l  
  gi|116754926|ref|YP_844044.1| 591 GLTNVGIMLPMVQHVSELKRAKEIMREEG----LDLNKIDVGIMVETPAAALTIEDFIE-EGLDFISFGTNDLTQyTLAV 665
                                    4455689*****************99877....66789******************986.8************8636777 PP

                                    TTSTTSHHHH.........HHHHHHHHTTHCEEEEEEE.E-SSHHHHHHHHHTTHCEEEEEEHHH CS
                      HpcH_HpaI 161 krspegtevl.........dareriltaaraagiaaldtvasdiddaegflaegalfvalGfdgk 216
                                     r++e    l         + +e ++  +++ag+      +s   +a+ + + ++  v++G+d+ 
  gi|116754926|ref|YP_844044.1| 666 DRNNENVANLysemhpaviKLIEYVVERCKKAGV-----KTSICGQAGSYPEMARRLVQIGIDSI 725
                                    776665444457777877799*************.....77778889999999999999999975 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.048   1.4e+02     128     156 ..     579     606 ..     490     613 .. 0.77
   2 ?   -0.8   0.0      0.58   1.7e+03      74     115 ..     621     661 ..     606     676 .. 0.72
   3 ?    6.6   0.0     0.003       9.1      61     119 ..     684     737 ..     646     753 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.048
                                    HHHHHHHHHHHHTTSETEEEEEEEBTTTS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM 128 eevlealeklreagikrvvdrivglpGen 156
                                     e ++a++kl+e+g+ +v ++++++  ++
  gi|116754926|ref|YP_844044.1| 579 LE-VRAFKKLHELGLTNVGIMLPMVQHVS 606
                                    34.599********999999999887665 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.58
                                    C..CCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHH CS
                                    x..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  74 a..vpgiritvetngtlpdeeklerllelgvdrvslgleaadde 115
                                    +  + ++ i vet++  +    +e + e g+d +s+g + ++  
  gi|116754926|ref|YP_844044.1| 621 DlnKIDVGIMVETPAAAL---TIEDFIEEGLDFISFGTNDLTQY 661
                                    144558899999999999...88888888888888887766655 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.003
                                    TTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  61 pdfvellerlaklavpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlk 119
                                     +++e++ +++k+  +g+++++   ++   +e+++rl++ g+d +s +++a+    v++
  gi|116754926|ref|YP_844044.1| 684 IKLIEYVVERCKK--AGVKTSICGQAGSY-PEMARRLVQIGIDSISANIDAVAT--VRE 737
                                    4566777777777..68888888888887.********************9876..555 PP

>> Lipase_GDSL  GDSL-like Lipase/Acylhydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00022      0.66      74     107 ..     650     683 ..     611     694 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00022
                                    EEE--CTCC-EECSSCTTTCEEHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Lipase_GDSL  74 iislGtNDsnlgkkstdaakkeaeeyiknlreai 107
                                    +is+GtND++++++  d+++++++++++ ++ a+
  gi|116754926|ref|YP_844044.1| 650 FISFGTNDLTQYTLAVDRNNENVANLYSEMHPAV 683
                                    68*************************9988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (754 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); 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: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.42
# Mc/sec: 5380.26
//
Query:       gi|116754927|ref|YP_844045.1|  [L=227]
Description: lysine exporter protein LysE/YggA [Methanosaeta thermophila PT]
Scores for complete 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-27   94.3  10.1    6.3e-27   94.3  10.1    1.3  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 !   94.3  10.1   3.5e-31   6.3e-27       2     190 ..      36     217 ..      35     219 .. 0.94

  Alignments for each domain:
  == domain 1  score: 94.3 bits;  conditional E-value: 3.5e-31
                           LysE   2 slllspGpqnllvlkqgikrgfkggilvalgvligdavlillgllGlalLlkaapivlsilrllGgayLlwlgvlalrda 81 
                                    +++l+pGp ++++++ ++k+g+  g  v +g++ ++++ ++l+llGl+    aa      + ++Gg  L+ +g l+lr a
  gi|116754927|ref|YP_844045.1|  36 TGALAPGPTLVATVNSSLKNGWTSGPKVSIGHAFVEMLIFILILLGLS---GAADTYRVPIAVIGGTALMVFGALTLRGA 112
                                    689*******************************************75...67779999********************* PP

                           LysE  82 kekkveaeksveaslvkpflkglllslsNPkailfwlsvisallakaeqygdagrlilaaglvvasliwfsllaflaarl 161
                                     + + ++ ++     ++p+++g+l+s +NP++ ++wlsv+sa+l ++   g     ++++g++ a++ w++l++ + +r 
  gi|116754927|ref|YP_844045.1| 113 SNASISEGSEIS---SNPYIAGALTSAANPYFWIWWLSVGSAMLLDGLRGGFLLAAAFMIGHWGADFGWYTLVSASIDRG 189
                                    ***997777665...9*****************************9999999999************************* PP

                           LysE 162 srrlsskkvlriinvvvgvlligfavkll 190
                                     + ls++ ++ ++ + +g++li+f+++ l
  gi|116754927|ref|YP_844045.1| 190 KSILSERGYR-YVLTACGIFLILFGLYYL 217
                                    *******876.**************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); 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: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1641.33
//
Query:       gi|116754928|ref|YP_844046.1|  [L=193]
Description: hypothetical protein Mthe_1639 [Methanosaeta thermophila PT]
Scores for 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-30  103.8  11.6    1.1e-29  103.4  11.6    1.1  1  SpoIIM    Stage II sporulation protein M
  ------ inclusion threshold ------
        0.1   13.0   0.0       0.22   11.9   0.0    1.5  1  DUF4969   Domain of unknown function (DUF4969)


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 !  103.4  11.6   1.3e-33   1.1e-29       1     156 []      18     185 ..      18     185 .. 0.83

  Alignments for each domain:
  == domain 1  score: 103.4 bits;  conditional E-value: 1.3e-33
                         SpoIIM   1 alllflvgillgallaasnfa...eqis.....seskensalslflaifanNlrvalllfllGllllgiptilvllinGf 72 
                                    +++lf+++++ g+ +a +n++   e ++     +  ++ ++l +++ ifa+Nl  +++++llG+   g++++lv + nG+
  gi|116754928|ref|YP_844046.1|  18 SVILFFASAASGFTAAEQNPEiaeEWLKelemlKWITDLPPLMILILIFAKNLLACAMAVLLGM-GAGVVPVLVAISNGI 96 
                                    5799*************7776665333366699999999************************6.*************** PP

                         SpoIIM  73 vlGavaalvaefgglllflllilPhgilelpaiiiagaaglrlgkal.....rsrrkalkeakrellkll.lllvpllli 146
                                    ++G+va+ v+++ g+l++l++ilPhgi+elp +++++a+g+rlg  +        ++ l e++r+++ +l + ++pll++
  gi|116754928|ref|YP_844046.1|  97 LVGMVAYQVVHKEGILYLLAGILPHGIVELPTVLVSIAIGMRLGHLFlmtiiDGDGD-LGEEARAAVSFLiYRVAPLLFV 175
                                    *****888888877******************************9999666522233.333444444444044555**** PP

                         SpoIIM 147 AaliEafvtp 156
                                    Aa+iE+f+tp
  gi|116754928|ref|YP_844046.1| 176 AAVIETFITP 185
                                    *********8 PP

>> DUF4969  Domain of unknown function (DUF4969)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.4e-05      0.22       4      41 ..      12      49 ..      10      56 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.4e-05
                        DUF4969  4 RgllLvsvLvlFillavaCsdsedneesveiilkeiel 41
                                   Rg +L+sv+++F   a   + +e+n e +e  lke+e+
  gi|116754928|ref|YP_844046.1| 12 RGYILISVILFFASAASGFTAAEQNPEIAEEWLKELEM 49
                                   899*********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); 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:                         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 0.21s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1571.30
//
Query:       gi|116754929|ref|YP_844047.1|  [L=478]
Description: prolyl-tRNA synthetase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-26   92.9   0.0    4.4e-26   91.9   0.0    1.5  2  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
    1.5e-16   60.4   0.1    2.8e-16   59.5   0.1    1.5  1  HGTP_anticodon  Anticodon binding domain
      6e-10   39.2   0.0    1.4e-09   38.0   0.0    1.7  1  ProRS-C_1       Prolyl-tRNA synthetase, C-terminal


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 !   91.9   0.0   7.4e-30   4.4e-26       5     178 ..     103     276 ..      95     277 .. 0.91
   2 ?   -3.9   0.0       1.9   1.2e+04     136     167 ..     434     465 ..     428     467 .. 0.81

  Alignments for each domain:
  == domain 1  score: 91.9 bits;  conditional E-value: 7.4e-30
                                    ETTSEEEEE-SSSHHHHHHHHHHHEEEB.GGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEE.EEEEEEES.GGGHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx.xxxxxxxxx RF
                   tRNA-synt_2b   5 drndreyiLkPtneetfvelirdevlrs.krLPlklyqiqtkyRdEksdsrGLlRvreFhq.kdgyvfha.easlddslr 81 
                                    d  d +++L+Pt+e++++ + + + +rs  +LPl++yqi   +R+E++ +r+L+R+re++  k+++  ha  +++  +++
  gi|116754929|ref|YP_844047.1| 103 DPLDIKLALRPTSETAIYPMLKLW-IRShADLPLRIYQIVNTFRYETKHTRPLIRLREITSfKEAHTAHAtWEEAAMQVE 181
                                    6667899**************977.***777*****************9**********8659*******76999999** PP

                                    HHHHHHHHHHHHTT.SCEEEEEE.GTTSCBTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTSSEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2b  82 dlikaisriferlglefraiiel.msaksadykdkkefeavsesltkgieigtiqklgtrlserlgatvldennreksvi 160
                                      i+ + ++++rl ++  + ++  ++ k + ++++  ++++++  ++++++gt++ lgt+++++ ++t+ de+++++ v 
  gi|116754929|ref|YP_844047.1| 182 IAIQRYIEFYRRLAIPCLVSKRPsWD-KFPGADYSIALDVIMP-DGRTLQVGTAHLLGTNFAKTYEITYEDEHGEQRYVN 259
                                    ****************8766665566.4599************.9*********************************** PP

                                    EEEEEEEHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2b 161 micaaigveRllsaileq 178
                                     +c++i+ eR ++a++++
  gi|116754929|ref|YP_844047.1| 260 QTCYGIS-ERCIAALIAV 276
                                    *******.******9976 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 1.9
                                    EEETHHHHHTTEEEECTTSSEEEEEEEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2b 136 klgtrlserlgatvldennreksvimicaaig 167
                                    ++g  l +++ga+ l e    + + m c  +g
  gi|116754929|ref|YP_844047.1| 434 ECGHALEDQIGANLLGEPRGDELPPMRCLVCG 465
                                    47788999999999999999999989887776 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.5   0.1   4.6e-20   2.8e-16       1      86 [.     293     378 ..     293     395 .. 0.92

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 4.6e-20
                                    SEEEEESSSS.HHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEE CS
                 HGTP_anticodon   1 qvvviplnek.aeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtreq 79 
                                    qvv++p+  + +e + e+++++a+ L   +irv ldd +e++g k+ ++++ g+p+++++G++++++g+vt+ +rd  ++
  gi|116754929|ref|YP_844047.1| 293 QVVIVPIIFGeREPIIEVCRSIASTLAGRNIRVRLDDGDERPGAKFYKWEMRGVPVRIEIGPRDIKNGVVTIVRRDGVRK 372
                                    89****99998888*************************************************************98776 PP

                                    EEEETTH CS
                 HGTP_anticodon  80 ervslde 86 
                                     ++++de
  gi|116754929|ref|YP_844047.1| 373 -TLPMDE 378
                                    .555554 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 !   38.0   0.0   2.4e-13   1.4e-09       2      69 .]     414     478 .]     413     478 .] 0.90

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 2.4e-13
                                    HHHHHHHHTT-EEEEEESSGHHHHHHHHHHHS-EEEEEESSB-SSCCCSB-TTT-SB-SEEEEEE-B- CS
                      ProRS-C_1   2 eefkealekkgfvlapWcgeeecEekIkeetgakslcipfdqepseegtkCivcgkpakkwvlfgrsY 69 
                                    +e   ++++ g++++pWcg+ ec   +++++ga+ l+ p  +  +    +C+vcg++++  ++++r+Y
  gi|116754929|ref|YP_844047.1| 414 DEARSQVQS-GVARVPWCGSVECGHALEDQIGANLLGEPRGD--ELPPMRCLVCGRESTGSTYMARQY 478
                                    566666665.8*****************************75..678899*****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (478 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); 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:                         3  (0.000167327); expected 0.2 (1e-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 0.22s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 3776.09
//
Query:       gi|116754930|ref|YP_844048.1|  [L=299]
Description: hypothetical protein Mthe_1641 [Methanosaeta thermophila PT]
Scores for complete 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  119.3   0.0    2.3e-34  118.8   0.0    1.2  1  ATP-grasp_3  ATP-grasp domain


Domain annotation for each model (and alignments):
>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.8   0.0   1.3e-38   2.3e-34       1     161 []     107     258 ..     107     258 .. 0.94

  Alignments for each domain:
  == domain 1  score: 118.8 bits;  conditional E-value: 1.3e-38
                                    HTSHHHHHHHHTTT.S---....-EESS--SSSEEEEESS-------B--SS--TTE.......EEEE---SEEEEEEEE CS
                    ATP-grasp_3   1 asdKlktykkLkeagvkvPtkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieevelvqefieGkplSvsll 80 
                                    ++dKl+++  Lk+agv+v      e +e e + +vvKpr G+g+e+v++    ++ e      +++ +++eG +lS+s++
  gi|116754930|ref|YP_844048.1| 107 CADKLECTLTLKRAGVPVA--DIVETPECECNVYVVKPRFGCGSEGVVISSFPNAPE-----GCIATRYVEGVHLSASFI 179
                                    89************98888..455667777889**************9998875555.....67**************** PP

                                    E.SSSEEEEEEEEEEEET....TEEEEEEES----HHHHHHHHHHHHHTTSTT--EEEEEEEEESS.SEEEEEEESS--G CS
                    ATP-grasp_3  81 sdgekvlvlavnrqliekaekefvyaGnvtpietelkeevvelaeevvekleglaGyvGvDlvlkdeepyviEvNPRltt 160
                                        ++l+l++n q+ie+++++f yaG+ +p++  +++e+ ++++++ e+l gl+Gy+G+Dl++ d  p +++vN+Rltt
  gi|116754930|ref|YP_844048.1| 180 RGRDRFLPLTINGQIIEMKGSRFGYAGSQVPYRSPRAREIWDVVRRAAEAL-GLKGYAGIDLIVGD-LPRIVDVNARLTT 257
                                    ***************************************************.**************.************9 PP

                                    G CS
                    ATP-grasp_3 161 s 161
                                    s
  gi|116754930|ref|YP_844048.1| 258 S 258
                                    7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 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:                        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 0.21s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 2449.06
//
Query:       gi|116754931|ref|YP_844049.1|  [L=57]
Description: preprotein translocase subunit SecG [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-15   57.2   0.1    1.4e-15   57.0   0.1    1.1  1  Sec61_beta  Sec61beta family


Domain annotation for each model (and alignments):
>> Sec61_beta  Sec61beta family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.0   0.1     8e-20   1.4e-15       1      40 [.      13      52 ..      13      53 .. 0.94

  Alignments for each domain:
  == domain 1  score: 57.0 bits;  conditional E-value: 8e-20
                                   XXXXXXXXXX----SS-B-THHHHHHHHHHHHHHHHHTSS CS
                     Sec61_beta  1 SsaGLlryyeedapgikidPkvVlvlsvafiasVilLhil 40
                                   SsaGL+ry+e ++++ik+dPk+V+++++a ++++++L+i 
  gi|116754931|ref|YP_844049.1| 13 SSAGLMRYFESEETSIKLDPKMVIGAGIASGVAIMALNIT 52
                                   9*********6668************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); 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: 0.29u 0.23s 00:00:00.52 Elapsed: 00:00:00.34
# Mc/sec: 507.76
//
Query:       gi|116754932|ref|YP_844050.1|  [L=296]
Description: formylmethanofuran--tetrahydromethanopterin formyltransferase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-66  223.2   0.5    4.6e-66  221.4   0.2    1.8  2  FTR_C     FTR, proximal lobe
    2.5e-63  212.2   0.1      5e-63  211.3   0.0    1.5  2  FTR       Formylmethanofuran-tetrahydromethanopterin formyltr


Domain annotation for each model (and alignments):
>> FTR_C  FTR, proximal lobe
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.14   1.2e+03      14      37 ..      17      40 ..       7      48 .. 0.80
   2 !  221.4   0.2   5.1e-70   4.6e-66       1     149 []     147     294 ..     147     294 .. 0.99

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.14
                                   EEEEEEEEEEESSHHHHHHHHHHH CS
                          FTR_C 14 gvaGgnllilaedqeaaleaaeaa 37
                                    +  g +li+a +++ aleaa++a
  gi|116754932|ref|YP_844050.1| 17 PIKIGRVLITAISERWALEAAREA 40
                                   566688999999*********988 PP

  == domain 2  score: 221.4 bits;  conditional E-value: 5.1e-70
                                    EEEEEES-EEEEEEEEEEEEEEEESSHHHHHHHHHHHHHHHHTSTTEE--SGGGEESS-EEES-S-TT-SEEE-GGG-TT CS
                          FTR_C   1 geflieeklgvvkgvaGgnllilaedqeaaleaaeaaveaikkvegvitpFpGgivrsgSKvgskykflkastNeafcpt 80 
                                    g+fl+ee++g+v+g+aGgn++il+++q aal+aaeaav+ai+k++g+itpFpGg+v+sgSKvgs+ykflkastN afcp+
  gi|116754932|ref|YP_844050.1| 147 GDFLVEETIGAVDGIAGGNFYILGQNQPAALMAAEAAVDAISKLRGTITPFPGGVVASGSKVGSRYKFLKASTNVAFCPS 226
                                    8******************************************************************************* PP

                                    STT....----TT--EEEEEEEEESSHHHHHHHHHHHHHHHTTSTTEEEEE---STTSS-SEEEEGGGG CS
                          FTR_C  81 lkekveeselpedveavlEiVidgldeeavaeamkagieaavkvegvlkisAgNygGkLGkykfkLkel 149
                                    lke+   ++lpe+v+a +EiVi+g+++ea++eam++gi+aa++v+gvl+isAgN+gGkLG+++f+L+ +
  gi|116754932|ref|YP_844050.1| 227 LKEQG-VCALPENVTAGYEIVINGISREAIEEAMRVGIRAACTVPGVLRISAGNFGGKLGPHQFHLHRI 294
                                    ***99.9***********************************************************975 PP

>> FTR  Formylmethanofuran-tetrahydromethanopterin formyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.3   0.0   5.6e-67     5e-63       1     142 []       1     144 [.       1     144 [. 0.98
   2 ?   -3.9   0.0       1.3   1.2e+04      71      89 ..     242     260 ..     238     267 .. 0.68

  Alignments for each domain:
  == domain 1  score: 211.3 bits;  conditional E-value: 5.6e-67
                                    -EETTEEE-S-EEEEEEEEEEEEEEE-SSHHHHHHHHHHHHSS-S-TTTSS-EEEESEEB-GGGSTTSS-EEEEEEEESS CS
                            FTR   1 leingveiedtfaEaFeikvtrviiTaatkkwakeaateatgfatsvigceaEagiervlspeetpDgRpGvailifaas 80 
                                    +eingvei+dtfaEaF+ik+ rv+iTa +++wa eaa+eatgf+tsvi+c+aEagie++++++etpDgRpGv+i+i+++s
  gi|116754932|ref|YP_844050.1|   1 MEINGVEIDDTFAEAFPIKIGRVLITAISERWALEAAREATGFGTSVIMCPAEAGIECIVPSTETPDGRPGVYIQICNMS 80 
                                    89****************************************************************************** PP

                                    HHHHHHHHHHHHHHHTTTSTT-EEEE--..GG-SEEHHHHHHGGGTT--EEEEETTEEEEEEEE CS
                            FTR  81 kkklekqlleRigqcvLtapttavfngl..aeekiklgkklrffgDgyeiekelggrkvwriPv 142
                                     k+le++ll+RigqcvLtapttavfngl  ae+++++gkkl++fgDgy++e ++ +r++++iP+
  gi|116754932|ref|YP_844050.1|  81 WKSLETSLLARIGQCVLTAPTTAVFNGLpeAEKQFDTGKKLGYFGDGYQCEIKYCNRNFCKIPI 144
                                    ****************************7556*******************************8 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 1.3
                                    EEEEEEEESSHHHHHHHHH CS
                            FTR  71 Gvailifaaskkklekqll 89 
                                    G+ i+i   s++++e+ + 
  gi|116754932|ref|YP_844050.1| 242 GYEIVINGISREAIEEAMR 260
                                    7777777777777777664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 2438.04
//
Query:       gi|116754933|ref|YP_844051.1|  [L=199]
Description: IMP cyclohydrolase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-61  207.7   0.0    1.4e-61  207.5   0.0    1.0  1  IMP_cyclohyd  IMP cyclohydrolase-like protein


Domain annotation for each model (and alignments):
>> IMP_cyclohyd  IMP cyclohydrolase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.5   0.0   7.6e-66   1.4e-61       1     190 [.       2     189 ..       2     190 .. 0.98

  Alignments for each domain:
  == domain 1  score: 207.5 bits;  conditional E-value: 7.6e-66
                                    ---SEEEEEEETTEE.EEEEEEE-SS---EEEEEETTEEEEEE-TGGGGGT-TTSSEEEEEEETTEEEEESSTHHHHHHH CS
                   IMP_cyclohyd   1 YvGRfivvgksedgkavaaYrvssRSfpnrnrvfredkirveptdeeklednpyiiYncvrvlddkavvtNGsqtdtiae 80 
                                    YvGR+++vg s d+  ++ YrvssRSfpnr+++ + +++ v+p+d++++ +npyi+Y c+r+ +d avv+NG++td+i +
  gi|116754933|ref|YP_844051.1|   2 YVGRIVAVGCSGDAV-WVGYRVSSRSFPNRRATASGSSVFVHPVDPSDVLKNPYITYPCIRASNDFAVVSNGDHTDMIFD 80 
                                    9**********6655.**************************************************************** PP

                                    HHHTSB-HHHHHHHHHHHH-S--STT---EEEEEE-SS.EEEEEEETTEEEEEE--..TTS-EEEESSS--S-EE----- CS
                   IMP_cyclohyd  81 klekgltardalalsLlaldyEkDdynTPRiagvvkeeeaalgivksdallvekvelkagegtliatYekgepkevelea 160
                                    ++e g    da+alsL+a  yE+Dd  TPRiagvv+ ++a+lgi ++d+++v+k+el++g+++++atYek+ +++v++e 
  gi|116754933|ref|YP_844051.1|  81 RIEDGSGPLDAVALSLVAYGYERDDLRTPRIAGVVSGRSAVLGIAAHDEIRVRKIELQDGDAWMVATYEKTGFEPVSMEG 160
                                    ******************************************************************************** PP

                                    SSHHHHHHHHHHGGGSS-EEEEEEEEESSS CS
                   IMP_cyclohyd 161 edaeeaaeelweslefenkVslavavidek 190
                                    ++a+++a+ l+  l fe++V++a+a+++++
  gi|116754933|ref|YP_844051.1| 161 ASASSIARSLFG-LPFERPVCSAAAFRRDD 189
                                    ************.************98865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1486.51
//
Query:       gi|116754934|ref|YP_844052.1|  [L=300]
Description: thiamine pyrophosphate binding domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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-25   88.3   0.0    6.1e-25   87.8   0.0    1.2  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.8   0.0   3.4e-29   6.1e-25       2     153 .]      38     199 ..      37     199 .. 0.90

  Alignments for each domain:
  == domain 1  score: 87.8 bits;  conditional E-value: 3.4e-29
                                    SSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHH....STTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEE CS
                   TPP_enzyme_C   2 iGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGakla....kpdrevvaivGDGgflmi.lqelatavrrnlpit 76 
                                    +Gc ++++  +    + + +  + +++ + ++ ++A+G+++a     ++++v++i+GDG++l+i +  ++ +  r+++++
  gi|116754934|ref|YP_844052.1|  38 TGCIEVTTTPY----PESAWRVPWIHSLFENAAAVASGIEAAlnhfGKNHNVFVIAGDGSTLDIgMGCISGMFDRGHNVK 113
                                    68888855555....455566799*****************655442367****************************** PP

                                    EEEEE-SBCCCHHHH...HHHHTCCTTTTSBB......BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSS CS
                   TPP_enzyme_C  77 vvvlnNegygmtggq...qepfggkrksgpagk.....dlkpvdfaklaealGak.garvekadveeleealkealekkg 147
                                    +v+++Ne+y++tg q   ++p   +++++p+gk       +++d+ ++a a+ ++ +a+ ++a++ +l++++k+a++  g
  gi|116754934|ref|YP_844052.1| 114 YVCYDNEAYMNTGVQrssSTPPCTSTTTTPSGKvsfgnPRPKKDMPAIAVAHRVPyVATASVAYPVDLRRKVKRAISIPG 193
                                    ****************99999999999999999***977999*************99999******************** PP

                                    EEEEEE CS
                   TPP_enzyme_C 148 paliev 153
                                    pa+i+v
  gi|116754934|ref|YP_844052.1| 194 PAYIQV 199
                                    ****87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); 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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2302.77
//
Query:       gi|116754935|ref|YP_844053.1|  [L=408]
Description: pyruvate flavodoxin/ferredoxin oxidoreductase domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-67  227.3   0.1    2.9e-67  226.8   0.1    1.2  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    2.8e-32  111.1   0.1    5.1e-32  110.2   0.1    1.5  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
    2.5e-07   30.6   0.1    5.5e-07   29.5   0.1    1.5  1  Transketolase_C  Transketolase, C-terminal domain


Domain annotation for each model (and alignments):
>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  226.8   0.1   4.9e-71   2.9e-67       2     228 ..      30     251 ..      29     254 .. 0.96

  Alignments for each domain:
  == domain 1  score: 226.8 bits;  conditional E-value: 4.9e-71
                                    HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCCHHH CS
                          POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmienlgl 81 
                                    a++ + +dvi+aYPITP++ i+e l++++a+ge+ d e++++ sE++a+s  +GA+aaGar+   T +qGl+Lm e l+ 
  gi|116754935|ref|YP_844053.1|  30 AVKCCAPDVISAYPITPQTHIVEHLSQFVADGEL-DSEFLTVDSEFSAMSSLVGASAAGARCYSSTTSQGLALMWEVLYN 108
                                    6677889**************************9.8******************************************** PP

                                    HHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHHS---EEEE-SSHHHHHHHHHHHHHHHHH..CTSEEEEEEEHHHH. CS
                          POR_N  82 aageelPvvivvvaRalpstglsirtdqsDlmaardtglivlasenvqeafdlalvAfnlAek..vrvPvivlfDgflls 159
                                    aag++lP+v++v++Ral+++ l+i++dq+D + ard+g+i+l++e+vqea d + +A+++Ae+  + +Pv+v++Dgf+l+
  gi|116754935|ref|YP_844053.1| 109 AAGMRLPIVMTVANRALSAP-LNIWNDQQDSVGARDSGWIQLYAEDVQEAADAIPQAYKIAEDpeILTPVMVCMDGFILT 187
                                    ********************.******************************************99*************** PP

                                    HEEEEEEC-SGG.GS-----SBXXXXXXXXSXXXBXXTXXTSSXXEEESBXBXTTSXBXXXXHHHHHHH CS
                          POR_N 160 hevekvelpdeedelklikekleeyerkeyaldpekpiargtaanpdtglehrekgneaedaaekvvee 228
                                    h +e+vel++++     ++++l++y++++  ldpe+p ++g+ a p ++ e r+ ++ a+ +a + +e 
  gi|116754935|ref|YP_844053.1| 188 HVYEPVELLSVK----DVERFLPPYRPEH-ILDPENPKTFGAFADPSYFTELRYMQWDAHRRALSKIET 251
                                    **********99....9********9998.************************999999887766665 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 !  110.2   0.1   8.6e-36   5.1e-32       1     102 []     276     379 ..     276     379 .. 0.99

  Alignments for each domain:
  == domain 1  score: 110.2 bits;  conditional E-value: 8.6e-36
                                    -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHHTGG CS
                        PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaalkk 80 
                                    Aev+iv+mGsv+gt+k+ +d +R eg+kvGl+++r++rPFP+e+++++lk+++ v+v+++++++g eG+l+++ kaal++
  gi|116754935|ref|YP_844053.1| 276 AEVIIVTMGSVIGTIKDCIDDIRSEGLKVGLVKIRSYRPFPTEAVRRALKDAEVVAVIEKDVTVGNEGALLTDLKAALYN 355
                                    9******************************************************************************* PP

                                    G..TSEEEEEE--GGG----HHHH CS
                        PFOR_II  81 s..kvkvvnfvaglgGrditvedi 102
                                       +v+v+ f aglgGrditv+di
  gi|116754935|ref|YP_844053.1| 356 TptRVPVIGFPAGLGGRDITVRDI 379
                                    *********************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 !   29.5   0.1   9.2e-11   5.5e-07       8      83 ..     274     349 ..     270     368 .. 0.85

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 9.2e-11
                                    TTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHHHHHHHH CS
                Transketolase_C   8 egkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGigsevaaa 83 
                                    +  +v++v++Gs   +  + ++++++eg+++ +v +r+ +p+ +e ++ ++k  + + v+e +v+ g+ g+ ++++
  gi|116754935|ref|YP_844053.1| 274 DDAEVIIVTMGSVIGTIKDCIDDIRSEGLKVGLVKIRSYRPFPTEAVRRALKDAEVVAVIEKDVTVGNEGALLTDL 349
                                    5679*********************************************************999987777666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); 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: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2897.03
//
Query:       gi|116754936|ref|YP_844054.1|  [L=85]
Description: pyruvate ferredoxin/flavodoxin oxidoreductase, delta subunit [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.4e-12   44.6  16.8    2.2e-06   27.2   3.1    2.2  2  Fer4      4Fe-4S binding domain
    1.4e-08   34.7  28.0    1.1e-06   28.7  14.7    1.7  2  Fer4_21   4Fe-4S dicluster domain
    6.6e-08   32.6   7.9     0.0011   19.1   0.8    2.0  2  Fer4_9    4Fe-4S dicluster domain
      1e-06   28.6  18.1    0.00096   19.1   6.5    2.2  2  Fer4_6    4Fe-4S binding domain
    6.2e-06   26.7   7.8     0.0065   17.0   1.0    2.1  2  Fer4_17   4Fe-4S dicluster domain
    1.3e-05   25.0  11.7     0.0094   16.0   2.0    2.3  2  Fer4_2    4Fe-4S binding domain
    2.6e-05   24.7  15.8    0.00039   21.0  16.0    2.1  2  Fer4_7    4Fe-4S dicluster domain
      3e-05   24.9  13.7      0.002   19.0   1.9    2.2  2  Fer4_16   4Fe-4S double cluster binding domain
    0.00024   21.2  15.1     0.0069   16.5  15.7    2.1  2  Fer4_10   4Fe-4S dicluster domain
    0.00088   19.6  16.8       0.14   12.7   3.2    2.3  2  Fer4_4    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.017   15.6  11.9       0.67   10.5   1.7    2.3  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
      0.028   14.8  16.1       0.12   12.9   3.1    2.1  2  Fer4_8    4Fe-4S dicluster domain
       0.36   11.6  15.0       0.63   10.8   3.5    2.9  2  Fer4_15   4Fe-4S single cluster domain
       0.49   11.5  20.2        1.5   10.0   5.7    2.4  2  Fer4_3    4Fe-4S binding domain
        2.8    8.9  16.4        4.3    8.2   3.7    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 !   23.4   5.8     3e-08   3.6e-05       1      23 [.      27      49 ..      27      50 .. 0.95
   2 !   27.2   3.1   1.8e-09   2.2e-06       2      23 ..      57      78 ..      56      79 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 3e-08
                                   EEEETTTSSS-THHHHHSTTTEE CS
                           Fer4  1 vvideekCigCGaCvevCPvgAI 23
                                   +v++  +Ci+C +C+  CP g+I
  gi|116754936|ref|YP_844054.1| 27 PVVNHKRCIKCSLCEIYCPEGCI 49
                                   689*******************9 PP

  == domain 2  score: 27.2 bits;  conditional E-value: 1.8e-09
                                   EEETTTSSS-THHHHHSTTTEE CS
                           Fer4  2 videekCigCGaCvevCPvgAI 23
                                   v d + C gCG C+  CP  AI
  gi|116754936|ref|YP_844054.1| 57 VPDLDYCKGCGVCAHECPRKAI 78
                                   5699*****************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 !   17.6   5.3   2.6e-06    0.0032      34      58 ..      26      50 ..      10      51 .. 0.73
   2 !   28.7  14.7   8.9e-10   1.1e-06       2      59 .]      28      80 ..      27      80 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.6e-06
                        Fer4_21 34 lkvv.edeCvGCnlCssvCPvedcie 58
                                   ++vv +++C+ C lC + CP e+ci+
  gi|116754936|ref|YP_844054.1| 26 VPVVnHKRCIKCSLCEIYCP-EGCIH 50
                                   45543788999999999999.79986 PP

  == domain 2  score: 28.7 bits;  conditional E-value: 8.9e-10
                        Fer4_21  2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedciem 59
                                   ++++++Ci+C +C i C+++++  i++     +    d C GC +C++ CP  ++i+m
  gi|116754936|ref|YP_844054.1| 28 VVNHKRCIKCSLCEIYCPEGCIHQIDG----LFVPDLDYCKGCGVCAHECP-RKAIDM 80
                                   6899**************966665554....4556789*************.699988 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   1.2   2.3e-06    0.0028      33      51 .]      24      49 ..       5      49 .. 0.71
   2 !   19.1   0.8   9.1e-07    0.0011      35      51 .]      62      78 ..      50      78 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.3e-06
                         Fer4_9 33 e.......eaCigCgaCveaCpkgai 51
                                           ++Ci+C  C+  Cp+g+i
  gi|116754936|ref|YP_844054.1| 24 TfvpvvnhKRCIKCSLCEIYCPEGCI 49
                                   3556666689*************987 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 9.1e-07
                         Fer4_9 35 aCigCgaCveaCpkgai 51
                                    C gCg C++ Cp++ai
  gi|116754936|ref|YP_844054.1| 62 YCKGCGVCAHECPRKAI 78
                                   5*************987 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   6.5   8.1e-07   0.00096       1      24 []      26      49 ..      26      49 .. 0.94
   2 !   15.4   3.7   1.2e-05     0.015       5      24 .]      59      78 ..      59      78 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 8.1e-07
                         Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                   v++++  +Ci C  C++ CPeg i
  gi|116754936|ref|YP_844054.1| 26 VPVVNHKRCIKCSLCEIYCPEGCI 49
                                   799******************976 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.2e-05
                         Fer4_6  5 dpdkCigCgdCvrvCPegai 24
                                   d d C gCg C+  CP +ai
  gi|116754936|ref|YP_844054.1| 59 DLDYCKGCGVCAHECPRKAI 78
                                   5689************9987 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   1.0   5.5e-06    0.0065      43      59 ..      31      47 ..       7      49 .. 0.87
   2 !   14.0   0.9   4.5e-05     0.054       2      14 ..      63      75 ..      57      84 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.5e-06
                        Fer4_17 43 aslCieCgeCerkCPqg 59
                                    ++Ci+C +Ce +CP+g
  gi|116754936|ref|YP_844054.1| 31 HKRCIKCSLCEIYCPEG 47
                                   589************97 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 4.5e-05
                        Fer4_17  2 CiqCgyClpeCps 14
                                   C +Cg C+ eCp+
  gi|116754936|ref|YP_844054.1| 63 CKGCGVCAHECPR 75
                                   6666666666665 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   2.4   2.8e-05     0.033       3      22 .]      27      46 ..      25      46 .. 0.91
   2 !   16.0   2.0   7.8e-06    0.0094       6      21 ..      59      74 ..      55      75 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.8e-05
                         Fer4_2  3 vvvdtdrCigCgaCvsaCPa 22
                                   +vv+  rCi C+ C   CP+
  gi|116754936|ref|YP_844054.1| 27 PVVNHKRCIKCSLCEIYCPE 46
                                   899999********999**5 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 7.8e-06
                         Fer4_2  6 dtdrCigCgaCvsaCP 21
                                   d d C gCg C + CP
  gi|116754936|ref|YP_844054.1| 59 DLDYCKGCGVCAHECP 74
                                   6788************ PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0  16.0   3.2e-07   0.00039       1      52 []      33      77 ..      33      77 .. 0.89
   2 !   14.4   3.9   3.7e-05     0.044       2      19 ..      63      80 ..      61      84 .. 0.68

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3.2e-07
                         Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                   rCi+C  C+ +Cp ++i   +          + d ++C gCg+C+ +CP +a
  gi|116754936|ref|YP_844054.1| 33 RCIKCSLCEIYCPEGCIHQIDG-------LFVPDLDYCKGCGVCAHECPRKA 77
                                   8****************98653.......3677999*************876 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 3.7e-05
                         Fer4_7  2 CigCgaCvaaCpvkaiel 19
                                   C gCg C+  Cp kai++
  gi|116754936|ref|YP_844054.1| 63 CKGCGVCAHECPRKAIDM 80
                                   777777777777777765 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 !   11.4   4.2   0.00039      0.47       1      19 [.      33      51 ..      33      55 .. 0.92
   2 !   19.0   1.9   1.7e-06     0.002       2      20 ..      63      81 ..      62      85 .] 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00039
                        Fer4_16  1 rCgtCgkCaevCPtnaike 19
                                   rC++C  C   CP+++i++
  gi|116754936|ref|YP_844054.1| 33 RCIKCSLCEIYCPEGCIHQ 51
                                   6***************986 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 1.7e-06
                        Fer4_16  2 CgtCgkCaevCPtnaikek 20
                                   C++Cg Ca  CP +ai++ 
  gi|116754936|ref|YP_844054.1| 63 CKGCGVCAHECPRKAIDMV 81
                                   ****************975 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5  15.7   5.8e-06    0.0069       3      56 .]      28      74 ..      26      74 .. 0.81
   2 !   15.2   2.5   1.5e-05     0.018       5      22 ..      59      76 ..      55      85 .] 0.80

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.8e-06
                        Fer4_10  3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                   v++ ++Ci+C  C   CP          +  +++    +++ C gcg C+ +CP
  gi|116754936|ref|YP_844054.1| 28 VVNHKRCIKCSLCEIYCPE-------GCIHQIDGLFVPDLDYCKGCGVCAHECP 74
                                   67899**************.......344444444444889************9 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.5e-05
                        Fer4_10  5 dddtCirCgkCvkaCPad 22
                                   d d C +Cg C   CP +
  gi|116754936|ref|YP_844054.1| 59 DLDYCKGCGVCAHECPRK 76
                                   7899************84 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   5.8   0.00014      0.17       2      16 ..      32      46 ..      31      51 .. 0.92
   2 !   12.7   3.2   0.00012      0.14       2      16 ..      61      75 ..      60      77 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                         Fer4_4  2 erCigCgsCvaaCPq 16
                                   +rCi C  C+++CP 
  gi|116754936|ref|YP_844054.1| 32 KRCIKCSLCEIYCPE 46
                                   79************6 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00012
                         Fer4_4  2 erCigCgsCvaaCPq 16
                                   + C gCg+C   CP 
  gi|116754936|ref|YP_844054.1| 61 DYCKGCGVCAHECPR 75
                                   89***********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 ?   10.3   2.9   0.00066      0.79       1      18 [.      29      46 ..      29      51 .. 0.95
   2 ?   10.5   1.7   0.00056      0.67       2      17 ..      59      74 ..      57      76 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00066
                        Fer4_13  1 VDrdtCiacgaCvelaPd 18
                                   V+ ++Ci c +C   +P+
  gi|116754936|ref|YP_844054.1| 29 VNHKRCIKCSLCEIYCPE 46
                                   8999*************7 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00056
                        Fer4_13  2 DrdtCiacgaCvelaP 17
                                   D d C +cg+C++ +P
  gi|116754936|ref|YP_844054.1| 59 DLDYCKGCGVCAHECP 74
                                   6789************ PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   4.7    0.0025       2.9       3      16 ..      32      45 ..      30      59 .. 0.73
   2 ?   12.9   3.1   9.7e-05      0.12      48      63 ..      60      75 ..      49      78 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0025
                         Fer4_8  3 ekCieCgaCqsaCp 16
                                   ++Ci+C++C+  Cp
  gi|116754936|ref|YP_844054.1| 32 KRCIKCSLCEIYCP 45
                                   46777777776676 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 9.7e-05
                         Fer4_8 48 lwsCttcgaCtevCpv 63
                                   l++C +cg C+ +Cp 
  gi|116754936|ref|YP_844054.1| 60 LDYCKGCGVCAHECPR 75
                                   6677777777777776 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 ?    5.4   3.7     0.026        31       2      22 ..      28      48 ..      28      58 .. 0.81
   2 ?   10.8   3.5   0.00053      0.63       4      20 ..      59      75 ..      56      78 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.026
                        Fer4_15  2 vvDrdaCigcglCvaeapevf 22
                                   vv++++Ci c lC   +pe  
  gi|116754936|ref|YP_844054.1| 28 VVNHKRCIKCSLCEIYCPEGC 48
                                   5899*********99999865 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00053
                        Fer4_15  4 DrdaCigcglCvaeape 20
                                   D d C gcg+C+ e+p+
  gi|116754936|ref|YP_844054.1| 59 DLDYCKGCGVCAHECPR 75
                                   8899***********95 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   5.7    0.0012       1.5       1      14 [.      34      47 ..      34      50 .. 0.95
   2 ?    7.4   6.6    0.0082       9.8       1      15 []      63      77 ..      63      77 .. 0.97

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0012
                         Fer4_3  1 CtgCgaCvevCPvg 14
                                   C+ C++C+  CP+g
  gi|116754936|ref|YP_844054.1| 34 CIKCSLCEIYCPEG 47
                                   ************98 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0082
                         Fer4_3  1 CtgCgaCvevCPvgA 15
                                   C gCg C   CP +A
  gi|116754936|ref|YP_844054.1| 63 CKGCGVCAHECPRKA 77
                                   9***********998 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   4.8     0.014        16       1      16 [.      33      48 ..      33      56 .. 0.82
   2 ?    8.2   3.7    0.0036       4.3      80      95 ..      61      76 ..      56      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.014
                        Fer4_22  1 rClsCgaCtlvCptCs 16
                                   rC++C+ C + Cp   
  gi|116754936|ref|YP_844054.1| 33 RCIKCSLCEIYCPEGC 48
                                   7***********9743 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0036
                        Fer4_22 80 sgCvGCgRCieacpvk 95
                                     C GCg C + cp k
  gi|116754936|ref|YP_844054.1| 61 DYCKGCGVCAHECPRK 76
                                   68***********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      173  (0.00964917); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 650.37
//
Query:       gi|116754937|ref|YP_844055.1|  [L=179]
Description: pyruvate ferredoxin oxidoreductase subunit gamma [Methanosaeta thermophila PT]
Scores for complete 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-38  130.4   0.3    8.7e-38  130.1   0.3    1.0  1  POR       Pyruvate ferredoxin/flavodoxin oxidoreductase


Domain annotation for each model (and alignments):
>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.1   0.3   4.9e-42   8.7e-38       1     177 []      10     175 ..      10     175 .. 0.95

  Alignments for each domain:
  == domain 1  score: 130.1 bits;  conditional E-value: 4.9e-42
                                    CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHH..HHGGGEEE CS
                            POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetls..ehldglkp 78 
                                    GGqG+vta++++a aa++ G   qa++ +g e+rG+++++  ri d+pi+ + +v+e+d++++ d ++l+  ++  glk 
  gi|116754937|ref|YP_844055.1|  10 GGQGAVTAAEMIAIAAFEDGRFSQAFPAFGVERRGAPVMAFARINDKPIRMRSQVYEPDYVIVQDVTLLDvvDVTGGLKS 89 
                                    9*************************************************99999**************99********* PP

                                    EEEEEEECTCGTT-CCHHHCTS-HHHHHHHT-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHT.S-HHHHHHHHHCC CS
                            POR  79 ggiiiynseelkpdelkkakeeerelkerlgvrvygvdatkiakeiggneraaNtvmlGalaallg.lplealeeaikkr 157
                                    +g ii+n+++++++ + +  e+          +v+++dat+ia + +g ++++Nt mlGa++++++ ++le+le+ i  r
  gi|116754937|ref|YP_844055.1|  90 DGKIIINTDRDASALKLN-TEA----------EVVTIDATRIAIDTLG-RPIVNTTMLGAFCGATKeVKLESLEKSILTR 157
                                    ********7655555554.553..........599*************.******************************* PP

                                    S-CH.HHHHHHHHHHHHHHH CS
                            POR 158 fpkkkeviekNlkafragye 177
                                    f +   + ekN++a+r +ye
  gi|116754937|ref|YP_844055.1| 158 FSG--SLGEKNIQAVRTAYE 175
                                    **9..5*************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1391.64
//
Query:       gi|116754938|ref|YP_844056.1|  [L=161]
Description: hypothetical protein Mthe_1649 [Methanosaeta thermophila PT]
Scores for complete 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  121.6   0.0    2.3e-35  121.2   0.0    1.1  1  UPF0047   Uncharacterised protein family UPF0047
  ------ inclusion threshold ------
      0.048   13.8   0.0      0.062   13.5   0.0    1.1  1  Cass2     Integron-associated effector binding protein


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 !  121.2   0.0   2.6e-39   2.3e-35       1     115 []      37     153 ..      37     153 .. 0.96

  Alignments for each domain:
  == domain 1  score: 121.2 bits;  conditional E-value: 2.6e-39
                                    E-HHHHHHHHHHHT.SEEEEEEEESSSSEEEEEEESSSHHHHHHHHHHHHHHSTTT.T-GGGTT.S..THHHHHHHHHH- CS
                        UPF0047   1 diteeveeavkesgvkeGlvlvfsrhttasltinEnadpdvqeDleealeklvpee.eYrhnae.gpdnadaHlkssllg 78 
                                    dit+ v +av++sg+++G+v+vf++ +t ++t+ E+ +p++ +D+++al++++pe  eY+hn   g++n+++H+++sllg
  gi|116754938|ref|YP_844056.1|  37 DITQMVVSAVRKSGMTDGIVVVFVPGATGAVTTIEY-EPGLVADMRRALNRIAPEYeEYEHNRRwGDNNGHSHIRASLLG 115
                                    7**********************************9.******************99*****435889************ PP

                                    SEEEEEEETTEE---TTEEEEEEESS.-SSEEEEEEEE CS
                        UPF0047  79 ssltipvedgklalGtwqsiylveld.gpreRkvvvqv 115
                                    +s+t+p+++g+lalG+wq+i+++++d +pr+R++v+q+
  gi|116754938|ref|YP_844056.1| 116 PSITVPLVNGELALGRWQQIVFLDMDnRPRRRRLVLQI 153
                                    **************************667*****9986 PP

>> Cass2  Integron-associated effector binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   6.9e-06     0.062      44     122 ..      18      97 ..       3     109 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.9e-06
                                    TSBSTEEEEEEEC-TT-CCGEEEEEEEEE-TTSSS-TT-EEEEE--EEEEEEEEE...SSSTT-HHHHHHHHHHCHCCHC CS
                          Cass2  44 ikkdkrvfgiyhdyeseenkfsyyagvevpsdsevpeglvkkeiPggkYavftie...gdfeedlaeaweaiygellpns 120
                                    i +++r + + ++ ++   +++++++  v + s  ++g+v++ +Pg + av+tie   g +++ +++a ++i+ e  + +
  gi|116754938|ref|YP_844056.1|  18 IMIETRYIEFDTKGDADMVDITQMVVSAVRK-SGMTDGIVVVFVPGATGAVTTIEyepGLVAD-MRRALNRIAPEYEEYE 95 
                                    5555555555555555667888899999999.**********************999988887.9999999998886644 PP

                                    TE CS
                          Cass2 121 ny 122
                                    + 
  gi|116754938|ref|YP_844056.1|  96 HN 97 
                                    33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1181.28
//
Query:       gi|116754939|ref|YP_844057.1|  [L=167]
Description: transcription factor TFIIE, alpha subunit [Methanosaeta thermophila PT]
Scores for complete 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   68.0   1.6    8.9e-19   67.3   0.4    1.7  2  TFIIE_alpha     TFIIE alpha subunit
    0.00084   19.1   0.8      0.015   15.1   0.0    2.3  2  Rad50_zn_hook   Rad50 zinc hook motif
     0.0079   15.8   0.6      0.016   14.9   0.1    1.7  2  GntR            Bacterial regulatory proteins, gntR family
     0.0079   16.3   0.0      0.014   15.5   0.0    1.4  1  HTH_9           RNA polymerase III subunit RPC82 helix-turn-h
  ------ inclusion threshold ------
      0.014   14.9   1.5      0.032   13.8   1.5    1.7  1  TF_Zn_Ribbon    TFIIB zinc-binding
      0.016   15.2   0.3       0.03   14.3   0.3    1.5  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.029   14.1   0.4      0.044   13.5   0.4    1.3  1  Rep_fac-A_C     Replication factor-A C terminal domain
      0.065   13.0   0.0        0.1   12.4   0.0    1.3  1  SAVED           SMODS-associated and fused to various effecto
      0.086   12.3   0.0       0.14   11.6   0.0    1.3  1  RepL            Firmicute plasmid replication protein (RepL)
        0.1   12.9   0.1       0.22   11.9   0.1    1.7  1  zf-Di19         Drought induced 19 protein (Di19), zinc-bindi
       0.38   10.5   2.2       0.74    9.6   2.2    1.4  1  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal


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 !   67.3   0.4   5.4e-22   8.9e-19       9     104 ..      15     109 ..      10     110 .. 0.96
   2 ?   -0.9   0.0      0.91   1.5e+03      76      93 ..     145     162 ..     143     165 .. 0.77

  Alignments for each domain:
  == domain 1  score: 67.3 bits;  conditional E-value: 5.4e-22
                                    HCS-HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEECCCHCCCHHHH CS
                    TFIIE_alpha   9 kfygeeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywrinyeklvdvvkrk 88 
                                    k+ gee   +++++  + evt+e la+ ++i ln +rk L+ Lye rl+ y+r+rd+e +w +y w+i +e l  ++  +
  gi|116754939|ref|YP_844057.1|  15 KIVGEEGLRIVEAMP-EEEVTDEHLAEITGISLNTVRKSLYLLYEHRLAIYRRKRDPESGWLTYLWKICPESLDSALEAE 93 
                                    78999*******998.89************************************************************** PP

                                    HHHHHHHHHHHHCCCT CS
                    TFIIE_alpha  89 leevvkkLeeklekee 104
                                    +++++ kL+  l+ e+
  gi|116754939|ref|YP_844057.1|  94 VRKLINKLNARLRYEK 109
                                    ***********99987 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.91
                                    EECCCHCCCHHHHHHHHH CS
                    TFIIE_alpha  76 inyeklvdvvkrkleevv 93 
                                    ++  ++v+v+ ++++e+ 
  gi|116754939|ref|YP_844057.1| 145 MENSTIVEVIEERIKELS 162
                                    567889999999998875 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 ?    2.0   0.2      0.11   1.9e+02      34      48 ..      94     108 ..      90     111 .. 0.78
   2 !   15.1   0.0   9.2e-06     0.015      14      50 ..     126     163 ..     122     165 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.11
                                    HHHHHHHHHHHHHHH CS
                  Rad50_zn_hook  34 rseLikelqsklerl 48 
                                     ++Li++l+++l+  
  gi|116754939|ref|YP_844057.1|  94 VRKLINKLNARLRYE 108
                                    789******999865 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 9.2e-06
                                    HHTT-SE.E-TTT--EE-HHHHHHHHHHHHHHHHHHH. CS
                  Rad50_zn_hook  14 elkeakg.cCPlCgReldeehrseLikelqsklerlpe 50 
                                    e +++++  CP C+ +l+  + s +++ +++++++l +
  gi|116754939|ref|YP_844057.1| 126 EEASENNfTCPFCQGSLEYMENSTIVEVIEERIKELSA 163
                                    45677778**************************9976 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   0.1   9.6e-06     0.016      19      59 ..      28      67 ..      20      69 .. 0.87
   2 ?   -3.2   0.0       4.1   6.7e+03       5      15 ..     150     160 ..     148     162 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 9.6e-06
                                   -TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                           GntR 19 rpGdkLPsereLaaefgVsrttvReALrrLeaeglverrqg 59
                                   +p++   + ++La+  g+s +tvR++L  L +  l++ r++
  gi|116754939|ref|YP_844057.1| 28 MPEEEV-TDEHLAEITGISLNTVRKSLYLLYEHRLAIYRRK 67
                                   688888.899********************99999887765 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.1
                                    HHHHHHHHHHT CS
                           GntR   5 vyerLredIls 15 
                                    ++e ++e+I++
  gi|116754939|ref|YP_844057.1| 150 IVEVIEERIKE 160
                                    55666666654 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 !   15.5   0.0   8.6e-06     0.014      32      59 ..      37      64 ..      32      67 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.6e-06
                                   HHHHHHSSTHHHHHHHHHHHHHTTSEEE CS
                          HTH_9 32 elvkktkLsldqVkksLvvLiqhrlVqy 59
                                    l++ t++sl+ V+ksL++L  hrl+ y
  gi|116754939|ref|YP_844057.1| 37 HLAEITGISLNTVRKSLYLLYEHRLAIY 64
                                   5788899******************998 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.5   1.9e-05     0.032       1      29 [.     114     143 ..     114     157 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.9e-05
                                    EEETTTTCEECHEETSTTCEEESSS.SBEE CS
                   TF_Zn_Ribbon   1 ykCPnCgstnlveDpergelvCtdC.GlVl 29 
                                    y C n + +++ e++++++++C++C G++ 
  gi|116754939|ref|YP_844057.1| 114 YACVNGCARFVFEEASENNFTCPFCqGSLE 143
                                    57999888888999***********99864 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 ?   14.3   0.3   1.8e-05      0.03      38      96 ..      80     142 ..      75     162 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.8e-05
                                    T--HHHHHHHHHHHHCC.T.TTT-EEEEEEE--EEEETTTS-EEECHH..H.HHS-TTTSSS- CS
                           HypA  38 gvepeaLefafellaegtv.legaeLeieevpvkvrCreCgkefelee..k.alrCpkCgsad 96 
                                    ++ pe+L  a+e+  ++ +   +a+L++e+ +v + C +  ++f  ee  + +++Cp C+++ 
  gi|116754939|ref|YP_844057.1|  80 KICPESLDSALEAEVRKLInKLNARLRYEKDHVFYACVNGCARFVFEEasEnNFTCPFCQGSL 142
                                    68899********9999995449**************77555666444234689*****9864 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 ?   13.5   0.4   2.7e-05     0.044      13      56 ..     109     151 ..      93     157 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.7e-05
                                    TTTTEEEB--STT---B-EEE.TTTEEEETTTTEEESS--EEEEE CS
                    Rep_fac-A_C  13 kdnlvYkACpsedCnkKvvee.edgewrCekCdkeveepkyryil 56 
                                    k   v+ AC  ++C + v+ee ++++++C  C+ ++e ++   i+
  gi|116754939|ref|YP_844057.1| 109 K-DHVFYACV-NGCARFVFEEaSENNFTCPFCQGSLEYMENSTIV 151
                                    3.45566999.8*********788*********999887776666 PP

>> SAVED  SMODS-associated and fused to various effectors sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   6.3e-05       0.1     126     161 ..      89     124 ..      81     134 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.3e-05
                          SAVED 126 alakavrdalrelkaehgvkriHlfaaaPaslafll 161
                                    al ++vr+++++l+a+ ++++ H+f+a+ +++a ++
  gi|116754939|ref|YP_844057.1|  89 ALEAEVRKLINKLNARLRYEKDHVFYACVNGCARFV 124
                                    6889*************************9999665 PP

>> RepL  Firmicute plasmid replication protein (RepL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   8.3e-05      0.14      77     103 ..      34      60 ..      23      69 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.3e-05
                           RepL  77 tnRelaeetgislktvsetlkileean 103
                                    t  +lae tgisl+tv++ l  l e  
  gi|116754939|ref|YP_844057.1|  34 TDEHLAEITGISLNTVRKSLYLLYEHR 60 
                                    7889****************9998765 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 ?   11.9   0.1   0.00013      0.22       1      13 [.     131     143 ..     131     167 .] 0.65

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                        zf-Di19   1 esftCPyCgkelt 13 
                                    ++ftCP+C+ +l+
  gi|116754939|ref|YP_844057.1| 131 NNFTCPFCQGSLE 143
                                    58******96432 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   2.2   0.00046      0.74      31      51 ..     117     139 ..     114     141 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00046
                 zinc_ribbon_10  31 hnGlap..keeleevkyrCpkCg 51 
                                    +nG+a+   ee++e ++ Cp+C+
  gi|116754939|ref|YP_844057.1| 117 VNGCARfvFEEASENNFTCPFCQ 139
                                    7*****999*************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1019  (0.0568353); expected 358.6 (0.02)
Passed bias filter:                      850  (0.0474092); expected 358.6 (0.02)
Passed Vit filter:                       127  (0.0070835); 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: 00:00:00.41
# Mc/sec: 1223.46
//
Query:       gi|116754940|ref|YP_844058.1|  [L=461]
Description: FAD linked oxidase domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-54  185.4   0.0    1.7e-54  185.1   0.0    1.1  1  FAD-oxidase_C  FAD linked oxidases, C-terminal domain
    2.2e-48  163.5   0.2      5e-48  162.4   0.2    1.6  1  FAD_binding_4  FAD binding domain


Domain annotation for each model (and alignments):
>> FAD-oxidase_C  FAD linked oxidases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.1   0.0   1.9e-58   1.7e-54       2     250 .]     218     459 ..     217     459 .. 0.95

  Alignments for each domain:
  == domain 1  score: 185.1 bits;  conditional E-value: 1.9e-58
                                    -SEEEEEEEEESSHHHHHHHHHHHHHHT---SEEEEE-HHHHHHHHHTS-SSTTS-TTT-EEEEEEEEE-HHHHHHHHHH CS
                  FAD-oxidase_C   2 pearavalvafpsfeaavkavreiaqagiipaalelmdkkaldlveatkgakkglpdeeealllvefegddeeeaeeele 81 
                                    p++r++++++f+s e a  av+++ +agi p+a+e++d++++++ ++ ++    +  + + +ll+e++g+d     e+++
  gi|116754940|ref|YP_844058.1| 218 PKRRRLVMASFESAELAGMAVVKAFSAGIVPSACEILDSTTVKVLRRCDPN---IVLPDGDILLFEVDGTD-LSTSEDAK 293
                                    999************************************************...78888889*********.77777777 PP

                                    HHHHHTTT-EEEEE..........ETGGGGGGGGHHHHHHHHHCTTEEEEEEEEEEEHHHHHHHHHHHHHHHHHHHEEEE CS
                  FAD-oxidase_C  82 alveaileatgaadvlvaqdeaeaealwkaRkaalpylrdallkagvavlseDtsvPvsrladlvrdikalldkyglevv 161
                                      v + + + +  +++va+d++e+ ++w+aR+ + + ++++   ++ +++ eD+ vP +++++l+r+++++ d+ g+ ++
  gi|116754940|ref|YP_844058.1| 294 -RVSEVCAGLAQ-SIRVASDQREMSEIWAARELVGAAISRLDPSKSRIYVGEDVGVPMKEIPNLMRKVQEISDSTGIPAM 371
                                    .88888876655.57*********************999998899999999***************************** PP

                                    EEEEEETTEEEEEEEEEEE..--TT--THHHHHHHHHHHHTT-----------------------THHHHHHHHHHHH-T CS
                  FAD-oxidase_C 162 lfgHagdgnlhlyilfdladeaeeeraeklvdevvdlavelgGsisgEHGvGldkkaylerekgeeglalmrriKaalDP 241
                                     +gH+gdgnlh+   +d+++e+e+ r+++++d + ++a+elgG++s EHG+G +++ y+e+++g+ +l++mr+iK+alDP
  gi|116754940|ref|YP_844058.1| 372 KYGHIGDGNLHVAWFIDVSSEEEWSRLRRAADMIHRAAIELGGTVSSEHGIGGARAGYMEMQWGP-ALEIMRAIKRALDP 450
                                    *****************************************************************.9************* PP

                                    T--BSTT-- CS
                  FAD-oxidase_C 242 kgiLNPgkv 250
                                    kgiLNPgk+
  gi|116754940|ref|YP_844058.1| 451 KGILNPGKL 459
                                    *******96 PP

>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.4   0.2   5.6e-52     5e-48       1     139 []      42     181 ..      42     181 .. 0.99

  Alignments for each domain:
  == domain 1  score: 162.4 bits;  conditional E-value: 5.6e-52
                                    EEEEEEESSHHHHHHHHHHHHHCTSCEEEESSSTTEESTTC.SCCEEEEEETTS--EEEEETTTTEEEEETTSBHHHHHH CS
                  FAD_binding_4   1 paavvrpeseeevaaalrlaneaglpvlvrGgGssllgqav.atggvvldlsrlnrileideeegtatveaGvtlgdlve 79 
                                    p++vvrp + eev+++l+la e+++pv++rG+G++l+g+av  +ggvvld+s +n+ileid e+ +++ve+Gv++++l++
  gi|116754940|ref|YP_844058.1|  42 PECVVRPLTREEVSRILKLAYEYEIPVTARGAGTGLAGGAVpVRGGVVLDMSGMNKILEIDVENLQVHVEPGVVVEQLNR 121
                                    89***********************************999999********99*************************** PP

                                    HHHHHTTECSSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGTEEEEEEEETTSEEEEEE CS
                  FAD_binding_4  80 alaakglllglepgsgipgtvGGaiatnagGygsekyGlirdnvlglevvladGevvrls 139
                                    al+++g++++++pgs + +t+GG+i++n++G+++ kyG+++++vl levvladG+v+r++
  gi|116754940|ref|YP_844058.1| 122 ALRPHGFFFPPNPGSSSVCTIGGLISNNGSGMRCVKYGTTKSYVLDLEVVLADGTVIRTG 181
                                    *********************************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 3218.19
//
Query:       gi|116754941|ref|YP_844059.1|  [L=355]
Description: hypothetical protein Mthe_1652 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-28   97.4   2.1    3.9e-14   52.6   0.1    2.6  2  CCG       Cysteine-rich domain
    1.3e-11   44.8   2.8    1.3e-11   44.8   2.8    2.2  2  Fer4_8    4Fe-4S dicluster domain
    2.1e-09   37.8   2.2    2.1e-09   37.8   2.2    3.3  4  Fer4_17   4Fe-4S dicluster domain
    7.4e-09   35.6   8.6    0.00079   19.5   0.1    3.9  4  Fer4_10   4Fe-4S dicluster domain
    7.6e-09   36.0   3.5    7.6e-09   36.0   3.5    3.1  3  Fer4_7    4Fe-4S dicluster domain
    4.6e-05   24.3  10.0      0.048   14.6   0.3    3.5  4  Fer4_16   4Fe-4S double cluster binding domain
     0.0014   18.6   3.6     0.0014   18.6   3.6    3.9  4  Fer4_2    4Fe-4S binding domain
     0.0021   18.4   2.0     0.0021   18.4   2.0    4.4  4  Fer4_4    4Fe-4S binding domain
     0.0045   17.1  19.9      0.017   15.2  13.7    3.8  5  Fer4_9    4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.024   14.5   5.2      0.024   14.5   5.2    3.5  3  Fer4      4Fe-4S binding domain
      0.035   14.2   0.6      0.035   14.2   0.6    3.4  3  Fer4_21   4Fe-4S dicluster domain
       0.12   12.9  13.0        0.9   10.1   1.9    2.9  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
       0.41   11.5  10.5       0.87   10.5   0.7    3.3  3  Fer4_22   4Fe-4S dicluster domain
       0.62   10.8   6.6          8    7.3   0.1    3.0  3  Fer4_15   4Fe-4S single cluster domain
       0.86    9.8  11.8       0.33   11.2   0.3    2.7  2  Fer4_18   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 !   52.1   0.3   4.6e-17   5.5e-14       2      85 .]     141     219 ..     140     219 .. 0.97
   2 !   52.6   0.1   3.3e-17   3.9e-14       1      84 [.     249     333 ..     249     334 .. 0.86

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 4.6e-17
                            CCG   2 ayfdgChllraaypevrkalkkllealgveleelekesCCGagggrsgkeelaealakrnvetaeetgadaivtacpgCl 81 
                                    +yf gC ++ ++ype+  ++  +l++ gv l +   e CCG++  r+g +  a + +++n+++++e+++d+++t c+gC+
  gi|116754941|ref|YP_844059.1| 141 VYFAGC-MASYRYPETAAKTFGILRKFGVSLLPS--ERCCGSPLLRTGLD--ASECMEENLRQIDEMDVDVVITGCAGCY 215
                                    69****.*************************98..************99..79************************** PP

                            CCG  82 lqlk 85 
                                    ++lk
  gi|116754941|ref|YP_844059.1| 216 TTLK 219
                                    *986 PP

  == domain 2  score: 52.6 bits;  conditional E-value: 3.3e-17
                            CCG   1 vayfdgChllraa..ypevrkalkkllealgveleel.ekesCCGagggr.sgkeelaealakrnvetaeetgadaivta 76 
                                    v+y+d+Chl+r +   +++rk+++++ e +   +    e + CCG ggg+ +g+ e+++++a+r+++ a   +a++ivta
  gi|116754941|ref|YP_844059.1| 249 VTYHDPCHLGRVNgiFDQPRKVIREICELEE--MRSSrELARCCGGGGGVrAGYREISLEIARRRLADAPP-EARYIVTA 325
                                    89************************77665..5555569****988776156666***************.6******* PP

                            CCG  77 cpgCllql 84 
                                    cp C  +l
  gi|116754941|ref|YP_844059.1| 326 CPMCVRNL 333
                                    ****8766 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   2.8   1.1e-14   1.3e-11       2      65 .]       7      73 ..       6      73 .. 0.84
   2 ?   -2.9   0.0       8.2   9.8e+03      49      54 ..     324     329 ..     299     332 .. 0.68

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 1.1e-14
                         Fer4_8  2 lekCieCgaCqsaCpvlrrtkkhlldargeaae.......dvqeeqvleeeealwsCttcgaCtevCpvgi 65
                                   +++C++CgaC++ Cp+++  + +++++rg+ +         + ++    + e+l++Cttc  C++ Cp g+
  gi|116754941|ref|YP_844059.1|  7 IRRCVRCGACRAVCPSFEVLGWESFNTRGRMILigkilddSDGSW----ALESLGTCTTCALCSQMCPAGV 73
                                   689******************999******888877544333333....3699***************986 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 8.2
                         Fer4_8  49 wsCttc 54 
                                     +C +c
  gi|116754941|ref|YP_844059.1| 324 TACPMC 329
                                    444433 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   2.2   1.7e-12   2.1e-09       1      60 [.       9      73 ..       9      74 .. 0.83
   2 ?   -1.4   0.1       2.9   3.5e+03      41      49 ..     206     214 ..     182     217 .. 0.64
   3 ?   -0.5   0.1       1.6   1.9e+03      12      48 ..     255     291 ..     253     294 .. 0.64
   4 ?   -1.0   0.0       2.2   2.6e+03      11      20 ..     325     334 ..     320     343 .. 0.72

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 1.7e-12
                        Fer4_17  1 rCiqCgyClpeCpsyeaydnepkkllraakl.....glleeaekeekaslCieCgeCerkCPqgl 60
                                   rC +Cg+C+++Cps+e  ++e  +++ ++ l      + ++  + e  ++C++C +C++ CP+g+
  gi|116754941|ref|YP_844059.1|  9 RCVRCGACRAVCPSFEVLGWESFNTRGRMILigkilDDSDGSWALESLGTCTTCALCSQMCPAGV 73
                                   7****************99999999999877764444444444559****************987 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.9
                        Fer4_17  41 ekaslCieC 49 
                                     ++  C++C
  gi|116754941|ref|YP_844059.1| 206 VVITGCAGC 214
                                    466666666 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1.6
                        Fer4_17  12 Cpsyeaydn..epkkllraaklglleeaekeekaslCie 48 
                                    C  ++ ++   +p+k++r+  + +lee+  +++  +C++
  gi|116754941|ref|YP_844059.1| 255 CHLGRVNGIfdQPRKVIRE--ICELEEMRSSRELARCCG 291
                                    5555554432267777777..446778878889999986 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 2.2
                        Fer4_17  11 eCpsyeaydn 20 
                                    +Cp++ ++ n
  gi|116754941|ref|YP_844059.1| 325 ACPMCVRNLN 334
                                    5777776665 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1   6.6e-07   0.00079       6      21 ..       7      22 ..       2      49 .. 0.77
   2 !   17.7   0.2   2.4e-06    0.0029       7      34 ..      57      79 ..      52     100 .. 0.72
   3 ?   -1.0   0.1       1.6     2e+03      40      48 ..     206     214 ..     185     218 .. 0.60
   4 ?    0.8   0.0      0.47   5.6e+02      17      32 ..     324     336 ..     320     353 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 6.6e-07
                        Fer4_10  6 ddtCirCgkCvkaCPa 21
                                     +C+rCg+C+++CP+
  gi|116754941|ref|YP_844059.1|  7 IRRCVRCGACRAVCPS 22
                                   568************9 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 2.4e-06
                        Fer4_10  7 dtCirCgkCvkaCPadltsvgakgease 34
                                    tC+ C+ C ++CPa +     ++ +  
  gi|116754941|ref|YP_844059.1| 57 GTCTTCALCSQMCPAGV-----TPSKVV 79
                                   58*************55.....333333 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.6
                        Fer4_10  40 kkvekCtgc 48 
                                    +++  C gc
  gi|116754941|ref|YP_844059.1| 206 VVITGCAGC 214
                                    355666666 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.47
                        Fer4_10  17 kaCPadltsvgakgea 32 
                                    +aCP+   +v++ +ea
  gi|116754941|ref|YP_844059.1| 324 TACPM---CVRNLNEA 336
                                    78999...44444444 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   3.5   6.4e-12   7.6e-09       1      52 []       9      73 ..       9      73 .. 0.77
   2 ?   -0.1   0.5       1.2   1.4e+03      29      42 ..     202     215 ..     175     219 .. 0.73
   3 ?   -0.4   0.1       1.6   1.9e+03      10      23 ..     324     337 ..     323     354 .. 0.65

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 6.4e-12
                         Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgt............ekveid.pekClgCgaCvavCPtga 52
                                   rC+ CgaC a+Cp+  +  +e+ n +g+             +++++   +C++C  C + CP+g+
  gi|116754941|ref|YP_844059.1|  9 RCVRCGACRAVCPSFEVLGWESFNTRGRmiligkilddsdGSWALEsLGTCTTCALCSQMCPAGV 73
                                   8************7777777777888765555555555555667753789************996 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.2
                         Fer4_7  29 ekveidpekClgCg 42 
                                    ++v+++ + C gC+
  gi|116754941|ref|YP_844059.1| 202 MDVDVVITGCAGCY 215
                                    45667778899986 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.6
                         Fer4_7  10 aaCpvkaieldeee 23 
                                     aCp+ +++l+e+ 
  gi|116754941|ref|YP_844059.1| 324 TACPMCVRNLNEAG 337
                                    67888887777764 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 !   13.9   0.4   6.5e-05     0.078       1      14 [.       9      22 ..       9      40 .. 0.85
   2 !   14.6   0.3     4e-05     0.048       1      29 [.      58      84 ..      58     108 .. 0.74
   3 ?   -0.8   0.1       2.5     3e+03      52      60 ..     206     214 ..     183     217 .. 0.57
   4 ?   -2.0   0.0         6   7.2e+03      52      61 ..     321     330 ..     301     331 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.5e-05
                        Fer4_16  1 rCgtCgkCaevCPt 14
                                   rC++Cg+C  vCP+
  gi|116754941|ref|YP_844059.1|  9 RCVRCGACRAVCPS 22
                                   6************7 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 4e-05
                        Fer4_16  1 rCgtCgkCaevCPtnaikekkekeieare 29
                                   +C+tC  C ++CP+++  +k   + +ar+
  gi|116754941|ref|YP_844059.1| 58 TCTTCALCSQMCPAGVTPSK--VVEDARR 84
                                   5*************998888..3344444 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 2.5
                        Fer4_16  52 eaitgCdiC 60 
                                      itgC+ C
  gi|116754941|ref|YP_844059.1| 206 VVITGCAGC 214
                                    334888888 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 6
                        Fer4_16  52 eaitgCdiCq 61 
                                    + +t C +C+
  gi|116754941|ref|YP_844059.1| 321 YIVTACPMCV 330
                                    4457788886 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   3.6   1.2e-06    0.0014       8      21 ..       8      21 ..       1      22 [. 0.83
   2 !    7.5   2.4    0.0039       4.7       9      22 .]      58      71 ..      51      71 .. 0.91
   3 ?   -2.4   0.3       5.5   6.6e+03      10      14 ..     211     215 ..     207     216 .. 0.67
   4 ?   -2.1   1.0       4.4   5.3e+03      17      21 ..     323     327 ..     323     330 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.2e-06
                         Fer4_2  8 drCigCgaCvsaCP 21
                                   +rC++CgaC+ +CP
  gi|116754941|ref|YP_844059.1|  8 RRCVRCGACRAVCP 21
                                   39************ PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0039
                         Fer4_2  9 rCigCgaCvsaCPa 22
                                   +C+ C  C + CPa
  gi|116754941|ref|YP_844059.1| 58 TCTTCALCSQMCPA 71
                                   8************8 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 5.5
                         Fer4_2  10 CigCg 14 
                                    C gC 
  gi|116754941|ref|YP_844059.1| 211 CAGCY 215
                                    66774 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 4.4
                         Fer4_2  17 vsaCP 21 
                                    v+aCP
  gi|116754941|ref|YP_844059.1| 323 VTACP 327
                                    68998 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   2.0   1.8e-06    0.0021       3      15 ..       9      21 ..       8      32 .. 0.93
   2 ?    2.2   2.2      0.27   3.3e+02       3      16 ..      58      71 ..      56      76 .. 0.87
   3 ?   -1.0   0.3       2.9   3.4e+03       6      11 ..     210     215 ..     209     217 .. 0.68
   4 ?    0.5   0.2      0.94   1.1e+03       6      12 ..     325     331 ..     324     332 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.8e-06
                         Fer4_4  3 rCigCgsCvaaCP 15
                                   rC++Cg+C+a+CP
  gi|116754941|ref|YP_844059.1|  9 RCVRCGACRAVCP 21
                                   8************ PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.27
                         Fer4_4  3 rCigCgsCvaaCPq 16
                                   +C+ C  C   CP 
  gi|116754941|ref|YP_844059.1| 58 TCTTCALCSQMCPA 71
                                   7*******999996 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 2.9
                         Fer4_4   6 gCgsCv 11 
                                    gC  C+
  gi|116754941|ref|YP_844059.1| 210 GCAGCY 215
                                    777776 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.94
                         Fer4_4   6 gCgsCva 12 
                                     C+ Cv+
  gi|116754941|ref|YP_844059.1| 325 ACPMCVR 331
                                    6999996 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   3.7   0.00019      0.23      35      48 ..       9      22 ..       2      26 .. 0.80
   2 !   15.2  13.7   1.4e-05     0.017       1      49 [.       9      72 ..       9      74 .. 0.87
   3 !   12.5   2.6    0.0001      0.12       2      26 ..      59      83 ..      58      95 .. 0.79
   4 ?   -1.4   0.2       2.3   2.8e+03      35      39 ..     210     214 ..     187     217 .. 0.59
   5 ?   -0.1   0.0       0.9   1.1e+03      10      23 ..     324     337 ..     313     345 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00019
                         Fer4_9 35 aCigCgaCveaCpk 48
                                   +C+ CgaC ++Cp+
  gi|116754941|ref|YP_844059.1|  9 RCVRCGACRAVCPS 22
                                   69999999999996 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.4e-05
                         Fer4_9  1 kCtgCgaCveaCp.agvvvedaaerkarlraase..............eaCigCgaCveaCpkg 49
                                   +C++CgaC ++Cp ++v   +++++  r+   ++                C++C  C + Cp g
  gi|116754941|ref|YP_844059.1|  9 RCVRCGACRAVCPsFEVLGWESFNTRGRMILIGKilddsdgswaleslGTCTTCALCSQMCPAG 72
                                   5***********63677788888888888777778889999999999999************87 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 0.0001
                         Fer4_9  2 CtgCgaCveaCpagvvvedaaerka 26
                                   Ct C  C ++Cpagv+  + +e  +
  gi|116754941|ref|YP_844059.1| 59 CTTCALCSQMCPAGVTPSKVVEDAR 83
                                   9999999999999998777666555 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 2.3
                         Fer4_9  35 aCigC 39 
                                     C gC
  gi|116754941|ref|YP_844059.1| 210 GCAGC 214
                                    34444 PP

  == domain 5  score: -0.1 bits;  conditional E-value: 0.9
                         Fer4_9  10 eaCpagvvvedaae 23 
                                    +aCp++v +  +a+
  gi|116754941|ref|YP_844059.1| 324 TACPMCVRNLNEAG 337
                                    67888877766655 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   5.2     2e-05     0.024       7      19 ..       9      21 ..       8      22 .. 0.94
   2 ?   10.6   2.3   0.00032      0.38       7      21 ..      58      72 ..      55      73 .. 0.90
   3 ?   -2.2   0.2       3.7   4.5e+03      15      19 ..     323     327 ..     323     328 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2e-05
                                   TSSS-THHHHHST CS
                           Fer4  7 kCigCGaCvevCP 19
                                   +C++CGaC  vCP
  gi|116754941|ref|YP_844059.1|  9 RCVRCGACRAVCP 21
                                   7************ PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00032
                                   TSSS-THHHHHSTTT CS
                           Fer4  7 kCigCGaCvevCPvg 21
                                    C+ C +C ++CP g
  gi|116754941|ref|YP_844059.1| 58 TCTTCALCSQMCPAG 72
                                   6************98 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 3.7
                                    HHHST CS
                           Fer4  15 vevCP 19 
                                    v +CP
  gi|116754941|ref|YP_844059.1| 323 VTACP 327
                                    689*9 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.9   0.00049      0.58      40      52 ..       9      21 ..       2      30 .. 0.75
   2 ?   14.2   0.6     3e-05     0.035      40      53 ..      58      71 ..      41      74 .. 0.87
   3 ?   -0.4   0.2         1   1.3e+03      35      44 ..     205     214 ..     184     219 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00049
                        Fer4_21 40 eCvGCnlCssvCP 52
                                   +Cv C  C +vCP
  gi|116754941|ref|YP_844059.1|  9 RCVRCGACRAVCP 21
                                   5777777777777 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 3e-05
                        Fer4_21 40 eCvGCnlCssvCPv 53
                                   +C+ C+lCs++CP 
  gi|116754941|ref|YP_844059.1| 58 TCTTCALCSQMCPA 71
                                   7************4 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1
                        Fer4_21  35 kvvedeCvGC 44 
                                     vv   C GC
  gi|116754941|ref|YP_844059.1| 205 DVVITGCAGC 214
                                    4444556665 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 ?   10.1   1.9   0.00075       0.9       4      18 ..       8      22 ..       4      24 .. 0.87
   2 ?    7.0   3.6    0.0073       8.7       5      18 ..      58      71 ..      56      72 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00075
                        Fer4_13  4 dtCiacgaCvelaPd 18
                                    +C+ cgaC++++P 
  gi|116754941|ref|YP_844059.1|  8 RRCVRCGACRAVCPS 22
                                   58************7 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0073
                        Fer4_13  5 tCiacgaCvelaPd 18
                                   tC+ c++C +++P 
  gi|116754941|ref|YP_844059.1| 58 TCTTCALCSQMCPA 71
                                   8************5 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.7   0.00073      0.87       1      14 [.       9      22 ..       9      38 .. 0.88
   2 ?    6.0   0.6     0.018        21       2      14 ..      59      71 ..      50      92 .. 0.78
   3 ?   -1.4   0.1       3.7   4.4e+03      76      85 ..     205     214 ..     188     220 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00073
                        Fer4_22  1 rClsCgaCtlvCpt 14
                                   rC++CgaC +vCp+
  gi|116754941|ref|YP_844059.1|  9 RCVRCGACRAVCPS 22
                                   7***********97 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.018
                        Fer4_22  2 ClsCgaCtlvCpt 14
                                   C +C+ C+ +Cp+
  gi|116754941|ref|YP_844059.1| 59 CTTCALCSQMCPA 71
                                   6677777777765 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 3.7
                        Fer4_22  76 kfgesgCvGC 85 
                                     +  +gC GC
  gi|116754941|ref|YP_844059.1| 205 DVVITGCAGC 214
                                    3344455555 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 ?    5.7   0.7      0.02        24       6      23 ..       8      25 ..       2      36 .. 0.82
   2 ?    7.3   0.1    0.0067         8       7      30 ..      58      87 ..      56     104 .. 0.74
   3 ?   -2.7   0.0       8.6     1e+04       9      19 ..     209     219 ..     209     235 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.02
                        Fer4_15  6 daCigcglCvaeapevfe 23
                                    +C  cg+C a++p + +
  gi|116754941|ref|YP_844059.1|  8 RRCVRCGACRAVCPSFEV 25
                                   68************8765 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0067
                        Fer4_15  7 aCigcglCvaea......pevfeldedgla 30
                                   +C+ c+lC + +      ++v+e + + la
  gi|116754941|ref|YP_844059.1| 58 TCTTCALCSQMCpagvtpSKVVEDARRVLA 87
                                   7***********666665555555555555 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 8.6
                        Fer4_15   9 igcglCvaeap 19 
                                    +gc+ C++ ++
  gi|116754941|ref|YP_844059.1| 209 TGCAGCYTTLK 219
                                    57777777654 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   2.0      0.02        24      59      73 ..       8      22 ..       2      25 .. 0.85
   2 ?   11.2   0.3   0.00027      0.33      56      75 ..      54      73 ..      41      80 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.02
                        Fer4_18 59 gdcidcescvkvcPt 73
                                     c+ c++c +vcP 
  gi|116754941|ref|YP_844059.1|  8 RRCVRCGACRAVCPS 22
                                   67************5 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00027
                        Fer4_18 56 kgagdcidcescvkvcPtgi 75
                                   ++ g c++c  c ++cP g+
  gi|116754941|ref|YP_844059.1| 54 ESLGTCTTCALCSQMCPAGV 73
                                   67899************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2557.56
//
Query:       gi|116754942|ref|YP_844060.1|  [L=233]
Description: hypothetical protein Mthe_1653 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.9e-27   96.0   4.2    4.7e-27   95.7   4.2    1.1  1  SIMPL       Protein of unknown function (DUF541)
  ------ inclusion threshold ------
       0.18   11.7   0.1       0.33   10.8   0.1    1.4  1  pPIWI_RE_Z  pPIWI RE three-gene island domain Z


Domain annotation for each model (and alignments):
>> SIMPL  Protein of unknown function (DUF541)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.7   4.2   5.3e-31   4.7e-27       1     200 []      28     229 ..      28     229 .. 0.68

  Alignments for each domain:
  == domain 1  score: 95.7 bits;  conditional E-value: 5.3e-31
                          SIMPL   1 ItVtGsaevevapDqatltlsvesegkdaaeakaevaekmnavlealk......klgikekd........iqtsslslkp 66 
                                    ItV G+++v+v++D++++++s++s++++++ea+ae +ek+n+ l+a+k             +        iq++++  + 
  gi|116754942|ref|YP_844060.1|  28 ITVVGEGSVTVPADVVYVSVSASSDNENVTEAYAESSEKLNDTLDAIKnactenC------EilqgystgIQSTKVCSR- 100
                                    9***********************************************4333320......222222223444444331. PP

                          SIMPL  67 eysyengknkitgye............asqsltvkfrdldk..lgevldaavka.aneingvsf.slsdedelrdearee 130
                                                               ++ s ++++++ d+  ++++ ++a +  a     v+   lsd+ ++++ear++
  gi|116754942|ref|YP_844060.1| 101 --------------GasnesicvnqtiVTVSASIRLQNPDQrtIESIKQTAESTgA--YAAVTGyALSDATAAKNEARKK 164
                                    ..............011112222222255555555666776656666666655433..334444489999999******* PP

                          SIMPL 131 AvkdArakAealAkalgvklgkvvsisesgsnp...........yappapamaaaaaaaasaatpfepgeievtasVtvv 199
                                    Av++Ara+Aea+++a+g +lgk+v+i+e   +p           +              + ++   epg +ev+ +V v+
  gi|116754942|ref|YP_844060.1| 165 AVENARATAEAMVSAAGGRLGKIVDITE---SPlylwdipfgifG-------------PSVEPSTTEPGMVEVKTTVLVT 228
                                    ****************************...22223433332221.............2233334489*99********9 PP

                          SIMPL 200 f 200
                                    +
  gi|116754942|ref|YP_844060.1| 229 Y 229
                                    8 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 ?   10.8   0.1   3.6e-05      0.33      19      68 ..     130     178 ..     128     180 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.6e-05
                     pPIWI_RE_Z  19 lerllpdqpaeaawvLlsGYpfaaargapldeeqrqalanaRhllwelrs 68 
                                    +e++ +++  ++a++  +GY+++ ++ a+++e++++a+ naR+ + +++s
  gi|116754942|ref|YP_844060.1| 130 IESIKQTAESTGAYAAVTGYALS-DATAAKNEARKKAVENARATAEAMVS 178
                                    577778888999********866.66888*************99877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1112  (0.0620224); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); 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: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 1779.34
//
Query:       gi|116754943|ref|YP_844061.1|  [L=302]
Description: tetrahydromethanopterin S-methyltransferase subunit H [Methanosaeta thermophila PT]
Scores for complete 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-99  331.1   0.0    6.1e-99  330.9   0.0    1.0  1  MtrH       Tetrahydromethanopterin S-methyltransferase MtrH s
  ------ inclusion threshold ------
       0.11   12.8   0.0       0.22   11.8   0.0    1.5  1  DUF1611_N  Domain of unknown function (DUF1611_N) Rossmann-li
       0.17   10.5   0.0       0.36    9.5   0.0    1.5  2  CdhD       CO dehydrogenase/acetyl-CoA synthase delta subunit


Domain annotation for each model (and alignments):
>> MtrH  Tetrahydromethanopterin S-methyltransferase MtrH subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  330.9   0.0    1e-102   6.1e-99       1     296 [.       6     290 ..       6     293 .. 0.97

  Alignments for each domain:
  == domain 1  score: 330.9 bits;  conditional E-value: 1e-102
                           MtrH   1 keqkvleiaGvkiGGqpGeyPtvlvgtifyakhkivedekkGifdkeaaealikkqeelsdktGnPalvqvvGeteeaiv 80 
                                    ++q v++iaG +iGGqpGe Pt+l+gtify +h+iv de++Gifd + ae+li++q+e+s++tGnP +++++ +t  a+ 
  gi|116754943|ref|YP_844061.1|   6 RDQSVINIAGLRIGGQPGELPTALAGTIFYHGHSIVSDEERGIFDAKRAEELINRQVEISEVTGNPGVLHIFASTRRAFE 85 
                                    68****************************************************************************** PP

                           MtrH  81 kyidfvadvtdaPllidstsaevklaaakyatevGladrviynsinasiedaeiealkesdveaaivlafnpmdptvegk 160
                                    +y+df+  ++++Pl+ids+  + +   a ++tevG+adr+iynsi  ++ ++e+ +l esd+++ai+laf p+  +ve++
  gi|116754943|ref|YP_844061.1|  86 RYLDFIDPIWNGPLIIDSSDPKTRGEMAIHVTEVGYADRTIYNSIGLASTEKEMGLLRESDIDSAILLAFSPNASSVESR 165
                                    ******************************************************************************** PP

                           MtrH 161 lkileegegtaekgllelaeeaGiekplidvavtplgsgagaavkaslavkaklGlPvGsgihnvpsaWdwlrefkkkek 240
                                    +++l + +     gll +a +aGi++ l+d  v plgsgagaa++ ++  kaklGlP+ sg+hn++s+W+wlr   k+  
  gi|116754943|ref|YP_844061.1| 166 MDLLRRDG-----GLLAIASNAGINNMLLDPGVAPLGSGAGAALRFAIVAKAKLGLPICSGMHNAASSWEWLRSRDKDM- 239
                                    ****9877.....9**********************************************************9865544. PP

                           MtrH 241 ekaaeyevadvganlvqvilgsdfvlyGPienakkvfPavamvdilikeaakelgv 296
                                          +++d +a  +++  ++  vlyGPiena+ +fPavam di+i+ea +e+ v
  gi|116754943|ref|YP_844061.1| 240 --R---RSCDASASALAASFCASLVLYGPIENARIIFPAVAMTDIMISEALEEMEV 290
                                    ..3...489*****************************************998876 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 ?   11.8   0.0   3.7e-05      0.22      37      75 ..     192     230 ..     174     242 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.7e-05
                      DUF1611_N  37 GiapeggklpeswreavkeAleaGldvvsGlHerLsddp 75 
                                    G+ap g     ++r a+++  ++Gl + sG+H+  s+ +
  gi|116754943|ref|YP_844061.1| 192 GVAPLGSGAGAALRFAIVAKAKLGLPICSGMHNAASSWE 230
                                    9*******************************9877655 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 ?   -2.5   0.0      0.26   1.6e+03      72     109 ..      61     107 ..      38     122 .. 0.58
   2 ?    9.5   0.0   5.9e-05      0.36     166     249 ..     180     292 ..     144     299 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.26
                                    EEEEE--SSST..........HHHHHHHHHHHCC--SEEEEE-SSHH CS
                           CdhD  72 aiairlistdP.........akkfakavekvakavkvplvlggsdpe 109
                                     + i   +++P          ++f++ ++ +    + pl++ +sdp+
  gi|116754943|ref|YP_844061.1|  61 QVEISEVTGNPgvlhifastRRAFERYLDFIDPIWNGPLIIDSSDPK 107
                                    44444444444444444443445555555555555667777777765 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 5.9e-05
                                    HCTT---EEEE---SH.....HHHHHHHHHHHHHHHHS-TTS-S-BEEE---SSHHHH.....HHHHH............ CS
                           CdhD 166 lkagvkdivldPttaalGegleetidnvvriRraaikgdkdlafPilslttnawlare.....sdeve............ 228
                                     +ag+++++ldP+ a+lG g   ++       r ai    +l+ Pi s+  na  + e     +++++            
  gi|116754943|ref|YP_844061.1| 180 SNAGINNMLLDPGVAPLGSGAGAAL-------RFAIVAKAKLGLPICSGMHNAASSWEwlrsrDKDMRrscdasasalaa 252
                                    5699****************99987.......567888889999999999999877654544422222555566666556 PP

                                    ...................HHHTT-SEEEES---HHHHHH CS
                           CdhD 229 ...................lvvrYadililrslekeellP 249
                                                         v  +di+i ++le++e+ P
  gi|116754943|ref|YP_844061.1| 253 sfcaslvlygpienariifPAVAMTDIMISEALEEMEVWP 292
                                    6666666666666666554344555666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); 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):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2443.11
//
Query:       gi|116754944|ref|YP_844062.1|  [L=89]
Description: DNA-binding protein Alba [Methanosaeta thermophila PT]
Scores for complete 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-18   65.7   0.5    3.2e-18   65.3   0.5    1.2  1  Alba      Alba
  ------ inclusion threshold ------
      0.018   15.0   0.1      0.023   14.6   0.1    1.4  1  Rpp20     Rpp20 subunit of nuclear RNase MRP and P


Domain annotation for each model (and alignments):
>> Alba  Alba
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.3   0.5   3.6e-22   3.2e-18       2      67 .]       6      68 ..       5      68 .. 0.95

  Alignments for each domain:
  == domain 1  score: 65.3 bits;  conditional E-value: 3.6e-22
                                   EEEE-STS-HHHHHHHHHHHHTHTTESEEEEEEETTHHHHHHHHHHHHHHHTCTT.EEEEEEEEEE CS
                           Alba  2 eiyVsskspimsyvkralklLsnkkeeeVvlkatGraIskAvsvaeilkrrfgkglyqvnvltsss 67
                                   +++V++ +p+m+yv+++++++ n++++eV + a+GraIs+Av+vae+ ++rf+ g + v+++++s+
  gi|116754944|ref|YP_844062.1|  6 VVFVGN-KPVMNYVLAVVTQF-NSGAKEVRIMARGRAISRAVDVAEVSRSRFL-GDVVVKDIKIST 68
                                   789999.**************.******************************8.66***9999875 PP

>> Rpp20  Rpp20 subunit of nuclear RNase MRP and P
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   2.6e-06     0.023      58      83 ..      26      51 ..      14      75 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.6e-06
                          Rpp20 58 elkkeeVfvkatGrAiekalsvgrwf 83
                                   +   +eV + a GrAi +a+ v++  
  gi|116754944|ref|YP_844062.1| 26 NSGAKEVRIMARGRAISRAVDVAEVS 51
                                   56789*****************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); 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: 0.32u 0.24s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 721.87
//
Query:       gi|116754945|ref|YP_844063.1|  [L=221]
Description: phosphoribosylglycinamide formyltransferase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-52  177.3   0.0    2.8e-52  177.1   0.0    1.0  1  Formyl_trans_N  Formyl transferase
  ------ inclusion threshold ------
      0.073   12.8   0.0       0.22   11.3   0.0    1.7  2  ubiquitin       Ubiquitin family


Domain annotation for each model (and alignments):
>> Formyl_trans_N  Formyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.1   0.0   3.2e-56   2.8e-52       2     181 .]      14     192 ..      13     192 .. 0.98

  Alignments for each domain:
  == domain 1  score: 177.1 bits;  conditional E-value: 3.2e-56
                                    EEEEEESESSHHHHHHHHHHHHTTSECEEEEEEESCTTEHCHHHHHHCCHCCCECHHCCSCCCCCCCHHHHHHHHCTT-S CS
                 Formyl_trans_N   2 kivvlisgtgsnlqalldalkkgsleadvvlvvsnkdkaaglekaeaasiptkvfeekkleprsqfeeelaeelkelkad 81 
                                    +i v+ sg g+nl+ +++a+++g l a+v+ v++n+++a  l+ a++++ p++ ++ ++l+++ ++++ l+e l+++++d
  gi|116754945|ref|YP_844063.1|  14 RIGVVSSGRGENLRYIIKATRSGYLRAEVAIVLTNQPDAGALRIAREFGVPAEFIDPAGLSRE-EYDRLLIERLDAARVD 92 
                                    677999*****************************************************9876.9*************** PP

                                    EEEEES--S---HHHHHSSTTSEEEEESSSTTTTBSS-HHHHHHHTTSSEEEEEEEE--SSSSTS-EEEEEEEE--TT-- CS
                 Formyl_trans_N  82 livlagymkllpkelvqavrlkilniHpSLLPrfkGaaaiqraleaGdketGvtihfvdeelDtGailaqkkveiiaedt 161
                                    l+vl gym++l++e+v+++r++ilniHp+LLP+f+G++a q+al  G++ tG+tih vdee+D+G+i++q  v++ + dt
  gi|116754945|ref|YP_844063.1|  93 LVVLTGYMRILSPEFVRHYRNRILNIHPALLPSFRGVDAFQQALDYGVRWTGTTIHIVDEEVDHGPIVYQVPVPVKPGDT 172
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHH CS
                 Formyl_trans_N 162 keeleqrvadaehkalveal 181
                                     e+l++r++ ae ka+++a+
  gi|116754945|ref|YP_844063.1| 173 HESLKARIQRAEYKAYPKAI 192
                                    *****************986 PP

>> ubiquitin  Ubiquitin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       0.6   5.4e+03      56      68 ..     137     150 ..     133     152 .. 0.75
   2 ?   11.3   0.0   2.5e-05      0.22      10      45 ..     162     198 ..     154     200 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.6
                                    GHTTSTT.EEEEEE CS
                      ubiquitin  56 eygiqdg.stlhlv 68 
                                    +yg+++  +t+h v
  gi|116754945|ref|YP_844063.1| 137 DYGVRWTgTTIHIV 150
                                    78888766899976 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 2.5e-05
                                    EEEEEEETTSBHHHHHHHHHHHH.TSSGGGEEEEETT CS
                      ubiquitin  10 kitleveesdtveelKekiaeke.gipaeqqrLiysG 45 
                                    ++++ v++ dt e+lK++i++ e +  ++ ++ +++G
  gi|116754945|ref|YP_844063.1| 162 QVPVPVKPGDTHESLKARIQRAEyKAYPKAIKMFLEG 198
                                    68999****************9977888888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1602.57
//
Query:       gi|116754946|ref|YP_844064.1|  [L=164]
Description: histidine triad (HIT) protein [Methanosaeta thermophila PT]
Scores for complete 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   50.7   0.0    3.3e-13   50.2   0.0    1.2  1  HIT       HIT domain
    7.3e-05   23.2   0.0    0.00011   22.7   0.0    1.2  1  DcpS_C    Scavenger mRNA decapping enzyme C-term binding
    0.00044   20.1   0.0    0.00064   19.6   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 !   50.2   0.0   5.6e-17   3.3e-13       6      95 ..      35     125 ..      30     128 .. 0.93

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 5.6e-17
                                    CCEEEE-SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEESGGGT-SS CS
                            HIT   6 stvvyeddlvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqkkfknkglrvvinngahagqsv 85 
                                    + ++y+ +  +++ + +p   gh+ v+p +h+s+l+  + +el++++++++ ++++lq++++ +g+++ in g+ ag  +
  gi|116754946|ref|YP_844064.1|  35 NLILYRGKSHFVIMNAFPYNNGHMMVVPYRHTSTLSGWSGDELQEFMELADLCVSVLQRTMRPDGFNLGINMGEVAGAGI 114
                                    56789999999*****************************************************************9987 PP

                                    S.S-EEEEEEC CS
                            HIT  86 a.hlHiHvipr 95 
                                    a h+H+H++pr
  gi|116754946|ref|YP_844064.1| 115 AeHIHLHIVPR 125
                                    44********8 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 !   22.7   0.0   1.8e-08   0.00011       2     100 ..      21     123 ..      20     131 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.8e-08
                                    -HHHHHHTTSS.-B-E.EEE-SSEEEEE-SS-SSSEEEEEEESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT-T-EE CS
                         DcpS_C   2 wvfnilakgke.perv.vyedekfvvlkDikpkaklhllvipkrdikslrdLtkehlpllkemrekakkvieekynevda 79 
                                    ++f++  k+++ +e++ +y+ ++  v+  + p ++ h++v+p+r+ ++l   + ++l+   e+ +   +v+++ +   ++
  gi|116754946|ref|YP_844064.1|  21 CIFCEKPKENKdRENLiLYRGKSHFVIMNAFPYNNGHMMVVPYRHTSTLSGWSGDELQEFMELADLCVSVLQRTM---RP 97 
                                    666664444443555448888888899999***************************999999999999999988...67 PP

                                    EEE--SCCCT-.....-S-S--EEEE CS
                         DcpS_C  80 eelrvgvhyqP.....svyhlHlHvi 100
                                    + +++g+++         +h+HlH++
  gi|116754946|ref|YP_844064.1|  98 DGFNLGINMGEvagagIAEHIHLHIV 123
                                    888888888777777889******98 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 !   19.6   0.0   1.1e-07   0.00064      12      73 ..      19      82 ..      12     127 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.1e-07
                                   HH-S----SS..---SS--S-B-SSEEEE---S-SSTT-EEEEESS--SSTTSS-HHHHHHHHH CS
                       CwfJ_C_1 12 dsClfClsnp..klekhlivsignkvYlalpkgpLssgHvliipieHisallsldeevldeirk 73
                                   + C fC + +  k  ++li+  g++ ++ +   p ++gH++++p  H+s+l+  + ++l+e  +
  gi|116754946|ref|YP_844064.1| 19 KGCIFCEKPKenKDRENLILYRGKSHFVIMNAFPYNNGHMMVVPYRHTSTLSGWSGDELQEFME 82
                                   679***7644104446789999*****************************9999988888655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); 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: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1337.98
//
Query:       gi|116754947|ref|YP_844065.1|  [L=162]
Description: hypothetical protein Mthe_1659 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); 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: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1216.84
//
Query:       gi|116754948|ref|YP_844066.1|  [L=476]
Description: 7-cyano-7-deazaguanine tRNA-ribosyltransferase [Methanosaeta thermophila PT]
Scores for complete 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-83  280.1   0.0    3.5e-83  279.7   0.0    1.1  1  TGT       Queuine tRNA-ribosyltransferase


Domain annotation for each model (and alignments):
>> TGT  Queuine tRNA-ribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  279.7   0.0   1.9e-87   3.5e-83       3     349 ..      14     335 ..      11     336 .. 0.96

  Alignments for each domain:
  == domain 1  score: 279.7 bits;  conditional E-value: 1.9e-87
                                    EEEEEEEETTEEEEESEEEEBETTSSBTTB-HHHHH.HTTES-EEEEHHHHHHTTTHHHHHHTTHHHHHHT--S-EEEE- CS
                            TGT   3 aRlGklelphgtietPafmpvgtqgtvkgltpdelkeelgaqiilsntyhlelrpgeelvakagglhkflgwdkpiltds 82 
                                    +R+G+l++phg +etPa+mpv  +++v  l+p+el  +lga++i++n+y++++ p  +  a + g+h +l++d+p++tds
  gi|116754948|ref|YP_844066.1|  14 GRIGRLHTPHGIVETPALMPV-VNPHVLLLSPQEL-ADLGAEMIITNSYIIHQDPVLRDTALERGVHGLLNFDGPVMTDS 91 
                                    8********************.999**********.59****************************************** PP

                                    SHHHHHHHEEEESSEEEEE-TTTS-EEEE-HHHHHHHHHHHT-SEEE-------SS--HHHHHHHHHHHHHHHHHHHHHH CS
                            TGT  83 ggfqvfslkkiteegvsfqsridGskvlltpeesieiqeklgsDiimalddvvpspaskkrveksverTlrwldrcleah 162
                                    g+fq   l           s + Gs v ++p e++++q+k++sD+ ++ld ++ ++a ++++e+++ +T+r+l++++++ 
  gi|116754948|ref|YP_844066.1|  92 GAFQ---L-----------SVY-GS-VDIEPLEILKFQQKIRSDVSVPLDIPTAPDAPREQAERELAETERRLREAVDHR 155
                                    ****...3...........336.**.***************************************************877 PP

                                    ..SE.EEEEE--TT-HHHHHHHHHHHHHH--SEEEE-S.SSSSS..HHHHHHHHHHHHGGGS-TTS-EEETTB-SHHHHH CS
                            TGT 163 ..qa.lfgivqGglyedlreesaeelakrdfdgyaigG.lsvge..ekeellevveavtellpedkprylmGvgtPedll 236
                                      +  l g+vqGg+y+dlre sa++l++++fd y+ig+ ++++e  + +el++vv a++  l    p++l+G+g+P+ ++
  gi|116754948|ref|YP_844066.1| 156 seSLlLAGPVQGGIYPDLRESSARRLRDLGFDLYPIGAvVPLMEsyRFRELVDVVVASKTGLGPGVPVHLFGAGHPMVFA 235
                                    986679********************************888***7778******************************** PP

                                    HHHHTT--EEEESHHHHHHHTTEEEETTEEEETTSGGGTT--SBSSSS--SHHHHH-BHHHHHHHHHTT-HHHHHHHHHH CS
                            TGT 237 eavalGvDmfdcvyptrtarngraltsegelnlknakyaedfspldegCsCytCknytraylhhllktkemlgaiLltiH 316
                                     a alG+D+fd+++++++ar+gr+lt++g+++l++ ky     p    CsC +C+++t++ l++  k  e     Ll+ H
  gi|116754948|ref|YP_844066.1| 236 LAAALGCDLFDSAAYALYARDGRYLTPRGTYRLSEMKYL----P----CSCDVCRKHTPESLNEDPKRVE-----LLARH 302
                                    **********************************99999....9....*****************99999.....***** PP

                                    HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHT CS
                            TGT 317 NlhyylelfkriReaIkegtfeefveefarkye 349
                                    Nl++ +++++++R++I+eg+++e  e+++r+++
  gi|116754948|ref|YP_844066.1| 303 NLAVSFQEIRAVRQSIHEGSLWEHLERRCRSHP 335
                                    ******************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (476 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 3335.81
//
Query:       gi|116754949|ref|YP_844067.1|  [L=566]
Description: PUA domain-containing protein [Methanosaeta thermophila PT]
Scores for complete 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  171.3   0.0    1.8e-50  170.8   0.0    1.2  1  DUF5591   Domain of unknown function (DUF5591)
    5.2e-11   42.3   0.0    1.2e-10   41.2   0.0    1.6  1  PUA       PUA domain
    1.8e-06   27.4   0.1    0.00045   19.5   0.0    3.0  2  TGT       Queuine tRNA-ribosyltransferase
    0.00027   21.0   0.3    0.00098   19.2   0.3    2.0  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 !  170.8   0.0     4e-54   1.8e-50       1     154 []     276     421 ..     276     421 .. 0.95

  Alignments for each domain:
  == domain 1  score: 170.8 bits;  conditional E-value: 4e-54
                                    X-HHHHHHHHH---S..SSEEEEEE--SSSSGGGSHHHHHHHHHS---...SEEEEE-SS-.EEEGGGTT---------- CS
                        DUF5591   1 vkrfrervlerYeppeekkvlvLlPcsakkPyseskshrkfaeaikkrkakvheviltsPlGvvPreleevYPaaqYdia 80 
                                    v+rf +rvl+rY+ppe ++vl+LlPcsa+kPyses+shr f++a++ +++ vhe+iltsPl++vPrele vYPaa+Yd++
  gi|116754949|ref|YP_844067.1| 276 VRRFVSRVLTRYRPPE-SDVLLLLPCSARKPYSESRSHRLFRSAMGGMRRFVHELILTSPLAIVPRELEDVYPAAHYDTP 354
                                    89*************7.*************************************************************** PP

                                    ------HHHHHHHHHHHHHHHHHHT-SEEEE---THHHHHHHHHHTT-SSEEEE--.SS-TTSHHHHHHHHHHH CS
                        DUF5591  81 vtgewseeeiefvaellakylektkyekviahleeeyreiveevaeelgleiiytvvedkptskeslknLkeaL 154
                                    vtg w+ ee+++v + l++yl+k++y++++ahle+e   ++++ + + g+++iyt      t +e l++L+eaL
  gi|116754949|ref|YP_844067.1| 355 VTGVWDLEERAWVINSLKSYLKKNRYTRIVAHLEGE---LCDALR-DGGIDAIYTG---GGTGPEELERLREAL 421
                                    ***********************************9...565554.56799**999...669999999999987 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.0   2.7e-14   1.2e-10      18      72 ..     510     562 ..     503     564 .. 0.94

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 2.7e-14
                                    EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEE CS
                            PUA  18 sLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveier 72 
                                     +lapGvv++++++++gd+V +v+    +++ G+a++s+ e+    +g++ve+++
  gi|116754949|ref|YP_844067.1| 510 TVLAPGVVDADEQIRPGDEVIVVSD--YFLGTGRARMSGWEMVASRRGVAVELRE 562
                                    69*********************99..*************************986 PP

>> TGT  Queuine tRNA-ribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.05   2.2e+02       3      47 ..      13      57 ..      10      66 .. 0.68
   2 !   19.5   0.0     1e-07   0.00045     190     291 ..     102     195 ..      97     235 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.05
                                   EEEEEEEETTEEEEESEEEEBETTSSBTTB.-HHHHH.HTTES-EE CS
                            TGT  3 aRlGklelphgtietPafmpvgtqgtvkgl.tpdelkeelgaqiil 47
                                   aRlG+l l+++ i+tP+++    + +  ++  +++l+e+ +a++ l
  gi|116754949|ref|YP_844067.1| 13 ARLGRLMLDRN-ITTPCIISPEDYVSAGSIfRHRNLEEAREAKVSL 57
                                   9*******995.*****99766555544433566665444566555 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 1e-07
                                    -SEEEE-SSSSSSHHHHHHHHHHHHGGGS-TTS-EEETTB-SHHHHHHHHHTT--EEEESHHHHHHHTTEEEETTEEEET CS
                            TGT 190 fdgyaigGlsvgeekeellevveavtellpedkprylmGvgtPedlleavalGvDmfdcvyptrtarngraltsegelnl 269
                                    +d+y++ +    +  ++l++++ +++e++p d   y     tP++l  +v lGvD++d+v +   +   r+ t++g +  
  gi|116754949|ref|YP_844067.1| 102 ADVYVLRAAGAISGARDLVNTLIEIRESIPPDAALYTPALATPSNLSLLVYLGVDIVDSVRVEMDGYYSRYHTRDGLF-- 179
                                    5566666655556678999999**************************************999999999999999933.. PP

                                    TSGGGTT--SBSSSS--SHHHH CS
                            TGT 270 knakyaedfspldegCsCytCk 291
                                    ++ + +e   p    C C  C+
  gi|116754949|ref|YP_844067.1| 180 QRDELSEL--P----CRCEHCS 195
                                    33344444..6....9999997 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 !   19.2   0.3   2.2e-07   0.00098       4      65 ..     440     493 ..     437     495 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.2e-07
                         TGT_C2   4 raiadYqFGagagdaLfpedvtitrsatgrirqvlv.dgerlatlraqdgrltLsleGarrlh 65 
                                    ra ad+ FGagagd L ++ ++++         +++  g  la++  + gr  L+l Garrl 
  gi|116754949|ref|YP_844067.1| 440 RAKADFYFGAGAGDILTQG-ARVK------GNRLFDsAGRTLASI--NSGRIALTLDGARRLL 493
                                    788**************87.7777......66788878999***9..9*************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (566 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); 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: 00:00:00.45
# Mc/sec: 3765.74
//
Query:       gi|116754950|ref|YP_844068.1|  [L=193]
Description: hypothetical protein Mthe_1662 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1468.87
//
Query:       gi|116754951|ref|YP_844069.1|  [L=395]
Description: metal dependent phosphohydrolase [Methanosaeta thermophila PT]
Scores for complete 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-12   47.9   1.4    3.2e-12   46.8   1.4    1.7  1  HD        HD domain
     0.0074   15.8   0.0      0.017   14.6   0.0    1.5  1  HDOD      HDOD domain


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   1.4   3.5e-16   3.2e-12       1     121 [.      50     162 ..      50     163 .. 0.84

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 3.5e-16
                                    HHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHTTTTHHHHTS..HHH....HHHCTCCHHHHHHHHHHHHHHHHHHH CS
                             HD   1 rleHsleVaklarrlaedlge.eedrellllaaLlHDiGkgpfgdafekk....eeefekflaHekvgaeilrevekrlg 75 
                                    r+eHsl+ ++la  l ++lg+ ++d  ++++aaLlHDiG+gp ++  e           +    ++    +lr + +r +
  gi|116754951|ref|YP_844069.1|  50 RFEHSLGSYHLAVILSDRLGLsDDDAMRIRAAALLHDIGHGPLSHVTEPMlskyL----R--RRHESILDLLRSEDIRTR 123
                                    79*******************************************9998854331....2..334555557777777777 PP

                                    HH.....HHHHHHHHHTTCCHHHHHHHHHHHHCCTSCHHHHHHHHHHHHHH CS
                             HD  76 ld.....ledvaklirehheswegkkrprglaerqlslearivklaDrlaa 121
                                    l       e+++kli+  +e               + + +++v+++D+l +
  gi|116754951|ref|YP_844069.1| 124 LEhygitPEEIQKLIKGRTELGK------------IVSGEIDVDRMDYLIR 162
                                    7777777799************6............99***********976 PP

>> HDOD  HDOD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.9e-06     0.017      96     169 ..      51     126 ..      43     132 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.9e-06
                                    HHHHHHHHHHHHHHHHHTT-S-H..HHHHHHHHTTTHHHHHHHHHSHHHHHHHHHHHHHH---HHHHHHHHHSS-H CS
                           HDOD  96 wehslavAlvarelaeelgledp..eeaflaGLLhdiGklvllsllpeeleellekvaeeelslleaeeellgtdh 169
                                     ehsl +  +a  l ++lgl+d    ++  a+LLhdiG   l ++ + +l++ l++ +e+ l+ll  e+     +h
  gi|116754951|ref|YP_844069.1|  51 FEHSLGSYHLAVILSDRLGLSDDdaMRIRAAALLHDIGHGPLSHVTEPMLSKYLRRRHESILDLLRSEDIRTRLEH 126
                                    589999999999999999988843478889***********************99888887788877776666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); 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: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 3136.85
//
Query:       gi|116754952|ref|YP_844070.1|  [L=81]
Description: hypothetical protein Mthe_1664 [Methanosaeta thermophila PT]
Scores for complete sequence (score 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   13.8   2.0        4.8    7.3   0.1    2.1  2  YojJ       Bacterial membrane-spanning protein N-terminus
      0.091   12.6   2.8          8    6.3   0.1    2.8  3  DASH_Dam1  DASH complex subunit Dam1
       0.35   10.4   2.8        1.1    8.8   0.3    1.9  2  SseC       Secretion system effector C (SseC) like family


Domain annotation for each model (and alignments):
>> YojJ  Bacterial membrane-spanning protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.2    0.0016       9.3      12      36 ..      11      35 ..       2      38 .. 0.79
   2 ?    7.3   0.1   0.00081       4.8       9      37 ..      52      80 ..      49      81 .] 0.91

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0016
                           YojJ 12 eklkeeLeqiekeleevlkaldeed 36
                                   e +ke Le+i   l e+ +++ e +
  gi|116754952|ref|YP_844070.1| 11 ESIKESLEEIASLLAEISDEMAELN 35
                                   6799999999999999999998765 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00081
                           YojJ  9 elkeklkeeLeqiekeleevlkaldeede 37
                                   +++ +++e +e  + el e++k++ +e+e
  gi|116754952|ref|YP_844070.1| 52 KYRPEIREAMEPLIAELAESMKSMMSEEE 80
                                   58999*******************99875 PP

>> DASH_Dam1  DASH complex subunit Dam1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0       0.1   6.1e+02      20      31 ..       8      19 ..       4      22 .. 0.71
   2 ?    6.3   0.1    0.0013         8       4      18 ..      23      37 ..      20      52 .. 0.82
   3 ?    5.2   0.2     0.003        18       1      17 [.      61      77 ..      61      81 .] 0.86

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.1
                      DASH_Dam1 20 edLqqihesLsd 31
                                   e L++i+esL++
  gi|116754952|ref|YP_844070.1|  8 EGLESIKESLEE 19
                                   567888888875 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0013
                      DASH_Dam1  4 afaeLaDsletLdkn 18
                                    +ae++D++++L++ 
  gi|116754952|ref|YP_844070.1| 23 LLAEISDEMAELNAL 37
                                   689*********875 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.003
                      DASH_Dam1  1 lepafaeLaDsletLdk 17
                                   +ep +aeLa+s++ +++
  gi|116754952|ref|YP_844070.1| 61 MEPLIAELAESMKSMMS 77
                                   6899*********9987 PP

>> SseC  Secretion system effector C (SseC) like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.3   0.00019       1.1     276     314 ..       3      41 ..       1      42 [. 0.91
   2 ?    2.3   0.1     0.017     1e+02     278     301 ..      53      76 ..      46      80 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00019
                           SseC 276 qkvldeaaeeikellesiqellksmsqaisqkgdtlqqi 314
                                    ++ +de  e+ike le i++ll  +s+ ++  ++ l++i
  gi|116754952|ref|YP_844070.1|   3 KQSKDEGLESIKESLEEIASLLAEISDEMAELNALLKFI 41 
                                    799*************************99988888876 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.017
                           SseC 278 vldeaaeeikellesiqellksms 301
                                    +  e+ e +  l++  +e++ksm+
  gi|116754952|ref|YP_844070.1|  53 YRPEIREAMEPLIAELAESMKSMM 76 
                                    555677777777777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1324  (0.0738468); expected 358.6 (0.02)
Passed bias filter:                      894  (0.0498633); 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: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 691.47
//
Query:       gi|116754953|ref|YP_844071.1|  [L=180]
Description: formylmethanofuran dehydrogenase, subunit E region [Methanosaeta thermophila PT]
Scores for complete 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  130.7   0.0    4.6e-38  130.3   0.0    1.2  1  FmdE          FmdE, Molybdenum formylmethanofuran dehydrogena
    3.8e-08   33.1   1.8      7e-08   32.3   1.8    1.4  1  zf-dskA_traR  Prokaryotic dksA/traR C4-type zinc finger
     0.0042   17.3   0.2     0.0075   16.5   0.2    1.4  1  LIM           LIM domain
  ------ inclusion threshold ------
      0.031   14.4   0.9      0.071   13.2   0.9    1.6  1  Zn-ribbon_8   Zinc ribbon domain


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 !  130.3   0.0     1e-41   4.6e-38       1     131 [.      14     130 ..      14     131 .. 0.92

  Alignments for each domain:
  == domain 1  score: 130.3 bits;  conditional E-value: 1e-41
                                    HHSS--CHHHHHHHHHHHHHHCC....-TTSSSEEEEES-STCHHHHHHHHCS--TTTTSEEE--SS-SEEEEEETTT-E CS
                           FmdE   1 fHGHlCpglvlGyrmakaalkelgpkeeegdeelvaivetdsCldDAiqvltgctlGkgnlivmdygkkaltfkkrktgk 80 
                                    fHGH+Cpgl++Gyr+ak++++++     ++deelva+ve++sC +DAiq ++gct+Gkgnli++d gk+++tf++r++g+
  gi|116754953|ref|YP_844071.1|  14 FHGHMCPGLAIGYRVAKYVMNHYRR---SEDEELVAVVENNSCSVDAIQEMLGCTFGKGNLIFVDNGKQVFTFYHRGDGN 90 
                                    9**********************73...448************************************************* PP

                                    EEEEEE-CCTHHHHHHHCCT--GGGS-HHHHHHHHHHHHHHHHHS.HHHHE CS
                           FmdE  81 avrlklkeelpelreklakgkakeekeeeeleeeleeaikkilnapeeelf 131
                                    a+r++++   +++ ++++++   ee        ++++a ++il+ap+e ++
  gi|116754953|ref|YP_844071.1|  91 AIRIYFR---DDILQEIFRDGRGEE--------ARSKATEAILSAPDEVIL 130
                                    *******...999999999877666........468999*******99875 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 !   32.3   1.8   1.6e-11     7e-08       1      33 [.     144     178 ..     144     179 .. 0.95

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 1.6e-11
                   zf-dskA_traR   1 giygs..CeeCGEpIpeaRlralPgarlCveCqek 33 
                                    +iy s  C eCGE  +e R +++ g+++C eC+++
  gi|116754953|ref|YP_844071.1| 144 RIYPSikCQECGESFMEIRGKVVNGKIVCEECFSR 178
                                    689999**************************987 PP

>> LIM  LIM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.2   1.7e-06    0.0075      28      56 ..     150     178 ..     147     180 .] 0.93

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.7e-06
                                    B-TTT-SB-CTT.CEEETTEEEEHHHHHH CS
                            LIM  28 tCsdCqkeLkegsfyekdgklyCkkdylk 56 
                                    +C++C++++ e +  +++gk++C++++ +
  gi|116754953|ref|YP_844071.1| 150 KCQECGESFMEIRGKVVNGKIVCEECFSR 178
                                    8**************************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 ?   13.2   0.9   1.6e-05     0.071       7      34 ..     150     177 ..     148     180 .] 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.6e-05
                    Zn-ribbon_8   7 rCeeCghefevlqsisdapltaCPeCgs 34 
                                    +C+eCg+ f +++    + +++C eC s
  gi|116754953|ref|YP_844071.1| 150 KCQECGESFMEIRGKVVNGKIVCEECFS 177
                                    8***********9777788899****66 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.27s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1306.59
//
Query:       gi|116754954|ref|YP_844072.1|  [L=355]
Description: hypothetical protein Mthe_1666 [Methanosaeta thermophila PT]
Scores for complete 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-38  131.0   0.0    5.1e-38  130.6   0.0    1.2  1  ATP-grasp_3      ATP-grasp domain
    4.7e-06   26.4   0.0    9.5e-06   25.4   0.0    1.4  1  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T
     0.0001   21.9   0.1    0.00056   19.5   0.0    1.9  2  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
     0.0036   16.6   0.0      0.013   14.8   0.0    1.8  2  ATPgrasp_ST      Sugar-transfer associated ATP-grasp
  ------ inclusion threshold ------
      0.014   15.0   0.0      0.024   14.2   0.0    1.3  1  ATP-grasp        ATP-grasp domain
       0.07   12.7   0.0       0.14   11.7   0.0    1.5  1  RimK             RimK-like ATP-grasp domain
       0.11   12.0   0.0       0.19   11.3   0.0    1.2  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus


Domain annotation for each model (and alignments):
>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.6   0.0     2e-41   5.1e-38       1     161 []      94     251 ..      94     251 .. 0.93

  Alignments for each domain:
  == domain 1  score: 130.6 bits;  conditional E-value: 2e-41
                                    HTSHHHHHHHHTTT.S---....-EESS--SSSEEEEESS-------B--SS--TTE.......EEEE---SEEEEEEEE CS
                    ATP-grasp_3   1 asdKlktykkLkeagvkvPtkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieevelvqefieGkplSvsll 80 
                                    +sdKl + ++L+e+  + P+ ++ e+  + + k+++Kpr Gagg + r++e +      ++  ++vqef+eG p+S+s++
  gi|116754954|ref|YP_844072.1|  94 VSDKLWLSRWLEER--EYPHATTWESDPPCDRKMILKPRIGAGGYGCRIFEGGA-----VPPGHIVQEFVEGVPASASVI 166
                                    69************..889667777777779*********************93.....33345**************** PP

                                    E.SSSEEEEEEEEEEEET.......TEEEEEEES----H..HHHHHHHHHHHHTTSTT--EEEEEEEEESS.SEEEEEEE CS
                    ATP-grasp_3  81 sdgekvlvlavnrqliekaeke...fvyaGnvtpietel..keevvelaeevvekleglaGyvGvDlvlkdeepyviEvN 155
                                    +dg++++++avn+ql ++++++   f+y+Gn+tp + +   +e++ ++aee+v+ l gl+G++GvD++l+ ++p+viEvN
  gi|116754954|ref|YP_844072.1| 167 CDGSDARTIAVNEQLSGMRWLNadgFRYCGNITPLDADAdvRERIAHIAEEIVAGL-GLVGSNGVDFILARNKPVVIEVN 245
                                    ********************9999**********99888789**************.*********************** PP

                                    SS--GG CS
                    ATP-grasp_3 156 PRltts 161
                                    PR+++s
  gi|116754954|ref|YP_844072.1| 246 PRFQGS 251
                                    ****97 PP

>> ATPgrasp_Ter  ATP-grasp in the biosynthetic pathway with Ter operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   3.7e-09   9.5e-06      46     111 ..     208     274 ..     193     289 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 3.7e-09
                   ATPgrasp_Ter  46 deelielaerlaeefgldglvnvQvrededgpkLLEiNpRasGGlgysala.Gvnlpylalklllgl 111
                                    +e++  +ae+++  +gl g ++v +   +++p+++E+NpR++G l+   l+ G+ + ++ l+++ g+
  gi|116754954|ref|YP_844072.1| 208 RERIAHIAEEIVAGLGLVGSNGVDFILARNKPVVIEVNPRFQGSLDTVELStGISVFQAHLDAFDGR 274
                                    6788999**************************************9887766***999999999885 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 ?   -0.5   0.1      0.28   7.3e+02      41      58 ..     125     142 ..     123     161 .. 0.90
   2 !   19.5   0.0   2.2e-07   0.00056     135     198 ..     205     266 ..     201     273 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.28
                                    EEEEETTCCTTTTEEEES CS
                    CPSase_L_D2  41 viikaafglGGkGmrvar 58 
                                    +i+k+ +g GG G r+ +
  gi|116754954|ref|YP_844072.1| 125 MILKPRIGAGGYGCRIFE 142
                                    589************976 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 2.2e-07
                                    HHHHHHHHHHHHHHHHHHT-EEEEEEEEEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHH CS
                    CPSase_L_D2 135 deerqalreaavkvvrevgvvgagtveflldpkskeyyviEvNtRlsvesalaekaTGldlvke 198
                                    ++ r+++ + a ++v  +g+vg   v+f+l +  ++ +viEvN+R + +    e  TG+ + ++
  gi|116754954|ref|YP_844072.1| 205 ADVRERIAHIAEEIVAGLGLVGSNGVDFILAR--NKPVVIEVNPRFQGSLDTVELSTGISVFQA 266
                                    567999999**********************6..8899********************998765 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 ?   -1.7   0.0      0.53   1.4e+03      61      79 ..     123     141 ..     116     144 .. 0.84
   2 !   14.8   0.0   4.9e-06     0.013     228     279 ..     211     263 ..     207     271 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.53
                    ATPgrasp_ST  61 egvviKpakgsgGkGilvi 79 
                                    + +++Kp  g gG G ++ 
  gi|116754954|ref|YP_844072.1| 123 RKMILKPRIGAGGYGCRIF 141
                                    5589***********9986 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 4.9e-06
                    ATPgrasp_ST 228 vlelaakaaeklpglgylGwDivldeekgplllElNar..pglaivqiangegl 279
                                    + ++a ++ + l  +g  G+D+ l+++k p+++E+N r   +l+ v++  g ++
  gi|116754954|ref|YP_844072.1| 211 IAHIAEEIVAGLGLVGSNGVDFILARNK-PVVIEVNPRfqGSLDTVELSTGISV 263
                                    6677777777778889999*********.********97335677666666655 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   9.5e-06     0.024     108     159 ..     197     247 ..     187     251 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.5e-06
                                    EEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCTEEEEEEESS CS
                      ATP-grasp 108 svapaevsekaqkkaeeiakkiveeLggvGvfavElFvledgellvnElapR 159
                                    ++ p +++++  +++++ia++iv+ Lg vG  +v + + +++ + v E+ pR
  gi|116754954|ref|YP_844072.1| 197 NITPLDADADVRERIAHIAEEIVAGLGLVGSNGVDFILARNKPV-VIEVNPR 247
                                    67899999***************************999966655.5599998 PP

>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   5.6e-05      0.14      77     179 ..     151     262 ..     143     270 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.6e-05
                                    EEEEE--SS-S........EEEEEEEETTEEEEEEEEE--SSS----TTTT-EEEE----HHHHHHHHHHHHHCT-S.EE CS
                           RimK  77 lvqeyieeaen........ediRvlvvddevvaalrrvskeGdFRsnlhrGgvaeklqlseeekelAikaakamelv.va 147
                                    +vqe++e             d R + v+++  +++r    +  FR   +       +++ e   ++A ++   ++lv   
  gi|116754954|ref|YP_844072.1| 151 IVQEFVEGVPAsasvicdgSDARTIAVNEQL-SGMRWLNAD-GFRYCGNITPLDADADVRERIAHIAEEIVAGLGLVgSN 228
                                    6777776433333455555999*****9997.567887666.6998888888889999999999***9999999988357 PP

                                    EEEEEEETTEEEEEEEESS--..SHHHHHHHT-- CS
                           RimK 148 GvDllrakrgllvlEvnsspg..lekiektlgid 179
                                    GvD + a + ++v+Evn   +  l+ +e  +gi 
  gi|116754954|ref|YP_844072.1| 229 GVDFILARNKPVVIEVNPRFQgsLDTVELSTGIS 262
                                    ***9999999*******86543366666666665 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 ?   11.3   0.0   7.3e-05      0.19     127     174 ..     200     246 ..     186     248 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.3e-05
                                    S----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEES CS
                Dala_Dala_lig_C 127 paklekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEvNt 174
                                    p + +++v+e+i ++a ++ + l+l G+  vDf+l   +++v+ EvN+
  gi|116754954|ref|YP_844072.1| 200 PLDADADVRERIAHIAEEIVAGLGLVGSNGVDFILA-RNKPVVIEVNP 246
                                    67788999**************************98.7899999**96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       249  (0.0138881); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); 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: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2586.92
//
Query:       gi|116754955|ref|YP_844073.1|  [L=174]
Description: tRNA 2'-O-methylase [Methanosaeta thermophila PT]
Scores for complete 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-48  162.2   0.0      5e-48  161.9   0.0    1.1  1  Trm56          tRNA ribose 2'-O-methyltransferase, aTrm56
  ------ inclusion threshold ------
       0.12   11.8   0.1       0.34   10.3   0.0    1.7  2  SPOUT_MTase_2  AF2226-like SPOUT RNA Methylase fused to THUMP


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 !  161.9   0.0   5.6e-52     5e-48       1     118 [.      54     169 ..      54     170 .. 0.98

  Alignments for each domain:
  == domain 1  score: 161.9 bits;  conditional E-value: 5.6e-52
                                    H-S--EEE.E--HHHHHHC-S...SEEEEE-TTSEEHHHHHHHHHC-SE.EEEEE------TCHHHHSSEEEESSSS--- CS
                          Trm56   1 wGgefkvevakslkklikefkkeggivvhltmyGenieevieeikkkekdllvvvGaekvprevyeladynvsvgnqPhs 80 
                                    wGg+f+v+    +++ +++f+++gg++vhltmyG +i+evi ei+++e+ ++vvvGaekvp +vy++ad+nv+vgnqPhs
  gi|116754955|ref|YP_844073.1|  54 WGGSFSVTDGIAWRDELRRFRDSGGKIVHLTMYGRRIDEVIGEIRSCER-IMVVVGAEKVPPDVYDIADWNVAVGNQPHS 132
                                    *********************************************9987.****************************** PP

                                    HHHHHHHHHHHHC.--TTT---TT-SSEEE--SSS-EE CS
                          Trm56  81 evaalaifldrllegkelekefedaklkviPsergkkv 118
                                    evaala+fldrl++g+elek+f  ++lkviP++rgk v
  gi|116754955|ref|YP_844073.1| 133 EVAALAVFLDRLFMGEELEKDFG-GRLKVIPAARGKVV 169
                                    **********************8.9***********98 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 ?   -0.9   0.0       0.1   9.3e+02      17      44 ..      16      43 ..       8      79 .. 0.78
   2 ?   10.3   0.0   3.8e-05      0.34     111     148 ..      90     126 ..      68     136 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.1
                  SPOUT_MTase_2 17 kelgeriGRavqafevkeliiapkekvd 44
                                   k++++++G  + af   e++i   ++  
  gi|116754955|ref|YP_844073.1| 16 KRITTHVGLVARAFGADEILIEGRDESV 43
                                   6788889999999999998887666554 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 3.8e-05
                  SPOUT_MTase_2 111 keelaealrkakevvvlvGsReGiPkGlfrfadfvvDl 148
                                     +e+  ++r+ ++++v+vG+   +P  ++++ad+ v +
  gi|116754955|ref|YP_844073.1|  90 IDEVIGEIRSCERIMVVVGAE-KVPPDVYDIADWNVAV 126
                                    456777899**********96.59*********98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1336.50
//
Query:       gi|116754956|ref|YP_844074.1|  [L=149]
Description: hypothetical protein Mthe_1668 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.032   14.2   0.5       0.06   13.3   0.5    1.5  1  Cdc6_C           CDC6, C terminal winged helix domain
      0.036   14.4   0.0      0.055   13.8   0.0    1.3  1  Penicillinase_R  Penicillinase repressor
      0.069   13.4   0.1       0.12   12.6   0.1    1.3  1  PaaX             PaaX-like protein


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 ?   13.3   0.5     1e-05      0.06      13      72 ..      78     126 ..      67     136 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1e-05
                                    SS-EEHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEE CS
                         Cdc6_C  13 keevttgevyevYkslCesegvdpltqrevsdllseLemlgileleksskGrregrtrki 72 
                                    + ++t++++ e+Y+++ ++     ++ ++vs +ls+++  gil+++ ++ +r      ++
  gi|116754956|ref|YP_844074.1|  78 DQWFTSQQLRERYETVRDD-----IKLSTVSTYLSRMHNDGILQRRGNRNNR------EY 126
                                    5688999999999999777.....55699****************9873333......22 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   9.2e-06     0.055      18      63 ..      81     127 ..      65     134 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.2e-06
                                    EEHHHHHHT--GG.G---HHHHHHHHHHHHHTTS-EEEEETTEEEEE CS
                Penicillinase_R  18 atvkevveeleee.kelaysTVktllrrLvkKgllsrekegrafiYs 63 
                                     t+++++e+ e    + + sTV t l+r+++ g+l+r+ + +   Y+
  gi|116754956|ref|YP_844074.1|  81 FTSQQLRERYETVrDDIKLSTVSTYLSRMHNDGILQRRGNRNNREYR 127
                                    67888888888774578********************9988887776 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1     2e-05      0.12      34      66 ..      96     128 ..      94     131 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2e-05
                           PaaX  34 GiseslvRaalsRlakaGwlvrekegrrsfYrL 66 
                                    +i+ s+v + lsR+ ++G l+r  + ++  YrL
  gi|116754956|ref|YP_844074.1|  96 DIKLSTVSTYLSRMHNDGILQRRGNRNNREYRL 128
                                    57778999**************99999999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.25s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1187.61
//
Query:       gi|116754957|ref|YP_844075.1|  [L=347]
Description: ABC-2 type transporter [Methanosaeta thermophila PT]
Scores for complete 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-36  124.2  16.9    7.2e-36  124.0  16.9    1.0  1  ABC2_membrane_3  ABC-2 family transporter protein
    3.3e-32  111.6  17.2    3.3e-32  111.6  17.2    2.4  3  ABC2_membrane    ABC-2 type transporter
    1.8e-08   34.0  17.3    3.1e-08   33.2  17.3    1.3  1  ABC2_membrane_2  ABC-2 family transporter protein
    5.6e-06   26.0   2.2    1.5e-05   24.6   2.2    1.6  1  CcmB             CcmB protein
     0.0024   17.8   8.1     0.0024   17.8   8.1    2.5  3  ABC2_membrane_4  ABC-2 family transporter protein
  ------ inclusion threshold ------
      0.046   12.6   0.0      0.069   12.1   0.0    1.2  1  DUF4621          Protein of unknown function (DUF4621)


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 !  124.0  16.9   2.4e-39   7.2e-36       2     345 .]      22     340 ..      21     340 .. 0.90

  Alignments for each domain:
  == domain 1  score: 124.0 bits;  conditional E-value: 2.4e-39
                ABC2_membrane_3   2 sfliitlllPiilvlllglifsnsveddentpiavvdednsslsqqlvealeaspsvelvyevdseeeakkalkngdidg 81 
                                    +++ ++++ Pi+l+ l+g+++s +    + +++++vd+      + l + le  ++++ + ++ se++a++++ +g ++g
  gi|116754957|ref|YP_844075.1|  22 RTIGLITFAPIVLMMLFGYALSGEM---SGIQLGIVDLG---GHPALRSHLEGMKDFT-ILYLGSESDAERLVSEGRLNG 94 
                                    5677788999999999999987655...8*********8...57889**********9.********************* PP

                ABC2_membrane_3  82 ilvipkgfskdllkgesatvtvlinssnlnsskailnalns.llqqlnasalvlqseatstsaninvestqleeelsnva 160
                                    ++vi              ++++l++++ +++++a+++a+ +                ++++ +n ++ ++  + + + ++
  gi|116754957|ref|YP_844075.1|  95 AVVISPA-----------EIQLLLDATSPQIANAVRSAVLAgAR-------------SEVPQINAPIVERYVYGYDMEMT 150
                                    **99755...........56899*****9999999999555243.............557889999999999******** PP

                ABC2_membrane_3 161 sflvg.liliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllill...lafglgipfg 236
                                    +++ + ++ ++++f+t++++av++v+E++++++e  +vs++s  +++ + ilg  l  llq+  +ll   ++fg  +p +
  gi|116754957|ref|YP_844075.1| 151 DTIGPaILGLVVFFFTFINAAVAFVRERSQGTLEKFMVSPLSSMEIVSGYILGFSLFTLLQSTTTLLvviFVFG--VPLK 228
                                    *****9999*****************************************************776664325999..**** PP

                ABC2_membrane_3 237 .nlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsiiPffapglgllr 315
                                     + +lll  ++l g  ++alg+++s + +++  + ++i++v ++ ++++g+ +p++++p++++ +++i+P+++ +++l  
  gi|116754957|ref|YP_844075.1| 229 gSPMLLLSIVILLGAGALALGTFFSNFARSEFQVVQFIPMVVIPQIILSGVWWPIQSIPDFVRPVSYILPLTYATNALRA 308
                                    4445666777778999999************************999999999**************************** PP

                ABC2_membrane_3 316 li.tgdplweil.lsliilalfavvylllall 345
                                    ++ +g +l +++ +++++l++f+++ +++a+l
  gi|116754957|ref|YP_844075.1| 309 VMlKGSTLGDVIyPDITALVVFFALSFAAAIL 340
                                    *857779999888****************985 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.4   0.0    0.0036        11       3      42 ..       6      44 ..       4      62 .. 0.82
   2 !  111.6  17.2   1.1e-35   3.3e-32      53     210 .]     155     311 ..     111     311 .. 0.89
   3 ?   -4.6   1.1       4.2   1.3e+04     141     148 ..     329     336 ..     324     343 .. 0.33

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0036
                  ABC2_membrane  3 ikallkreflqrwrdpslgllwrliqplllalvfgtvfgn 42
                                   ++++  r ++q +rd+ ++  + ++ p++l+++fg++ ++
  gi|116754957|ref|YP_844075.1|  6 VCVVALRVVRQLKRDRRTI-GLITFAPIVLMMLFGYALSG 44
                                   567889999*******888.899999*********99884 PP

  == domain 2  score: 111.6 bits;  conditional E-value: 1.1e-35
                  ABC2_membrane  53 pgllffsvlflafsaltsvapvferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldls.rff 131
                                    p +l+ +v+f++++++++va+v+er +g+le+ +vspl s +++v +++l++ +++llq++  ll+v+f++g++l+ + +
  gi|116754957|ref|YP_844075.1| 155 PAILG-LVVFFFTFINAAVAFVRERSQGTLEKFMVSPL-SSMEIVSGYILGFSLFTLLQSTTTLLVVIFVFGVPLKgSPM 232
                                    44444.45555558899999******************.************************************9766* PP

                  ABC2_membrane 132 lflllllltalaasslgllisalapsfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrsnlf 210
                                    l+l +++l++  a++lg ++s +a+s+ +++q++++v++p ++lsG+ +pi+s+p +++ ++y++Pltya++alr++++
  gi|116754957|ref|YP_844075.1| 233 LLLSIVILLGAGALALGTFFSNFARSEFQVVQFIPMVVIPQIILSGVWWPIQSIPDFVRPVSYILPLTYATNALRAVML 311
                                    *******************************************************9********************985 PP

  == domain 3  score: -4.6 bits;  conditional E-value: 4.2
                  ABC2_membrane 141 alaasslg 148
                                    +++a+s++
  gi|116754957|ref|YP_844075.1| 329 VFFALSFA 336
                                    22222221 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  17.3     1e-11   3.1e-08       8     274 ..      14     336 ..       8     345 .. 0.73

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 1e-11
                ABC2_membrane_2   8 frdlvrsrrfllltvllpli.....................................dvalaylkdlgsslqseakaike 50 
                                    +r+l r+rr+++l  + p++                                     d+ + yl + +  + +  ++++ 
  gi|116754957|ref|YP_844075.1|  14 VRQLKRDRRTIGLITFAPIVlmmlfgyalsgemsgiqlgivdlgghpalrshlegmkDFTILYLGSES--DAERLVSEGR 91 
                                    68999*******99999999788888888888888888888888887777777666555555554333..3344444444 PP

                ABC2_membrane_2  51 atlaleyveaasasdeaedtdqdlkv.....................................vstimavlipviaalfg 93 
                                    +  a+  + a ++   +++t+++ ++                                     +++i+ +++ ++  + +
  gi|116754957|ref|YP_844075.1|  92 LNGAVVISPAEIQ-LLLDATSPQIANavrsavlagarsevpqinapiveryvygydmemtdtiGPAILGLVVFFFTFINA 170
                                    4444444444443.334444444444889999***************************999988888888888999999 PP

                ABC2_membrane_2  94 adaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgivlaledllllvvasvllll 173
                                    a a+++E+ +gTl+  + +P s +ei+ g ++g ++    +++  + t+   l++i ++g++l+++ +lll ++++ l++
  gi|116754957|ref|YP_844075.1| 171 AVAFVRERSQGTLEKFMVSPLSSMEIVSGYILGFSLF---TLLQSTTTL---LVVIFVFGVPLKGSPMLLLSIVIL-LGA 243
                                    *************************************...888888884...458889999999999888877777.333 PP

                ABC2_membrane_2 174 lvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqeindflsllsptsayntllneilags 253
                                     + +lalg+++S +ar s+ +    + ++v+ +i+ ++v  ++ +++    +       +s++ p  + + +l+++   +
  gi|116754957|ref|YP_844075.1| 244 -G-ALALGTFFSNFAR-SEFQVVQFIPMVVIPQIILSGVWWPIQSIPDFVRP-------VSYILPLTYATNALRAVMLKG 313
                                    .3.69***********.77777778888888888888888887777776666.......777777777766666665555 PP

                ABC2_membrane_2 254 dlna....lgstatnllilllllav 274
                                    +  +    ++++ t l+++ +l  +
  gi|116754957|ref|YP_844075.1| 314 S--TlgdvIYPDITALVVFFALSFA 336
                                    3..1224533333333333333332 PP

>> CcmB  CcmB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   2.2   4.9e-09   1.5e-05      36     147 ..     142     254 ..     137     278 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 4.9e-09
                           CcmB  36 avGPdtallsriapgilWvaallaslLsldrlfaadfedGsLellllapvplellvlaKalAhwlltglplvllapllal 115
                                    + G d ++  +i+p+il + + + +++ +  +f  ++++G+Le+++++p++   +v + +l   l+t+l  + +  ++  
  gi|116754957|ref|YP_844075.1| 142 VYGYDMEMTDTIGPAILGLVVFFFTFINAAVAFVRERSQGTLEKFMVSPLSSMEIVSGYILGFSLFTLLQSTTTLLVVIF 221
                                    568899999*************************************************************9999999999 PP

                           CcmB 116 llnleaaalgllalt..LllGtpalsllgavgaA 147
                                    +++++ ++ ++l+l+  +llG+ al+l g++ + 
  gi|116754957|ref|YP_844075.1| 222 VFGVPLKGSPMLLLSivILLGAGALAL-GTFFSN 254
                                    99**99999998887225789999985.666554 PP

>> ABC2_membrane_4  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       0.5   1.5e+03      14      32 ..      24      42 ..      17      52 .. 0.47
   2 !   17.8   8.1   8.1e-07    0.0024      50     147 ..     151     246 ..     136     286 .. 0.64
   3 ?   -2.7   0.1       1.6   4.9e+03     147     155 ..     328     336 ..     313     344 .. 0.52

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.5
                ABC2_membrane_4 14 ivwllvlaallvpllally 32
                                   i +++++ ++l++l++ ++
  gi|116754957|ref|YP_844075.1| 24 IGLITFAPIVLMMLFGYAL 42
                                   3344444333343333333 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 8.1e-07
                ABC2_membrane_4  50 svfgftll.lllplilgiiasylifrEeqndtlknLltiPvsrtklllaKlivllllsvllmlvtflitvlfallsgfvg 128
                                    +++g  +l l++ + + i a+  + rE++++tl + ++ P s+++++ + ++   l+  l   ++ + t+l+ +++ +v+
  gi|116754957|ref|YP_844075.1| 151 DTIGPAILgLVVFFFTFINAAVAFVRERSQGTLEKFMVSPLSSMEIVSGYILGFSLF-TL---LQSTTTLLVVIFVFGVP 226
                                    45554555233444444569************************9987744444333.33...33334444444455567 PP

                ABC2_membrane_4 129 fsvklvlellkkcl.elgll 147
                                    ++++++l l   +l   g+l
  gi|116754957|ref|YP_844075.1| 227 LKGSPMLLLSIVILlGAGAL 246
                                    77777665444333133333 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 1.6
                ABC2_membrane_4 147 lvffavlpi 155
                                    +vffa++ +
  gi|116754957|ref|YP_844075.1| 328 VVFFALSFA 336
                                    222222222 PP

>> DUF4621  Protein of unknown function (DUF4621)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.3e-05     0.069     144     193 ..      77     127 ..      70     154 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.3e-05
                                    S----TT-EEE---SHHHHHTT--SEEEEEEEE-HHHHHHS-TTSE.EEEE CS
                        DUF4621 144 ldpktdafkfvkneklpgivqivpqkihlslsadskqwtnapadal.selr 193
                                    l   +da ++v + +l g v i p  i+l l a s q +na   a+ +  r
  gi|116754957|ref|YP_844075.1|  77 LGSESDAERLVSEGRLNGAVVISPAEIQLLLDATSPQIANAVRSAVlAGAR 127
                                    66789***********************************98776413333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2449.32
//
Query:       gi|116754958|ref|YP_844076.1|  [L=286]
Description: ABC transporter related [Methanosaeta thermophila PT]
Scores for complete 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-30  105.3   0.0    5.6e-30  104.7   0.0    1.3  1  ABC_tran     ABC transporter
      3e-13   50.2   0.9    1.7e-05   24.8   0.1    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    6.1e-06   26.2   0.0      0.036   13.8   0.0    2.1  2  AAA_15       AAA ATPase domain
    0.00011   21.7   0.0      0.031   13.7   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
    0.00025   21.6   0.0    0.00043   20.8   0.0    1.4  1  AAA_23       AAA domain
    0.00041   20.0   0.0    0.00082   19.1   0.0    1.5  1  AAA_29       P-loop containing region of AAA domain
    0.00082   19.1   0.0     0.0063   16.3   0.0    2.0  2  AAA_24       AAA domain
     0.0073   16.0   0.0      0.016   14.9   0.0    1.7  2  AAA_30       AAA domain
  ------ inclusion threshold ------
      0.016   15.7   0.0      0.042   14.3   0.0    1.8  1  AAA          ATPase family associated with various cellular a
      0.019   14.9   0.0      0.037   14.0   0.0    1.4  1  NACHT        NACHT domain
      0.028   14.8   0.0        0.1   13.0   0.0    1.9  1  AAA_16       AAA ATPase domain
      0.032   14.1   0.0      0.051   13.5   0.0    1.4  1  NTPase_1     NTPase
       0.08   12.7   0.0       0.13   12.0   0.0    1.3  1  ATP_bind_1   Conserved hypothetical ATP binding protein
      0.086   12.8   0.1       0.17   11.9   0.1    1.4  1  TsaE         Threonylcarbamoyl adenosine biosynthesis protein
      0.098   12.8   0.0        0.2   11.8   0.0    1.8  1  AAA_33       AAA domain
       0.13   11.6   0.2       0.56    9.5   0.0    2.0  3  ATPase       KaiC
       0.14   11.8   0.0       0.23   11.1   0.0    1.5  2  ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-bindi
       0.15   12.8   0.0       0.29   11.9   0.0    1.5  1  DUF4162      Domain of unknown function (DUF4162)


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 !  104.7   0.0   5.6e-33   5.6e-30       1     136 [.       8     150 ..       8     151 .. 0.98

  Alignments for each domain:
  == domain 1  score: 104.7 bits;  conditional E-value: 5.6e-33
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                    l+ +++ + +g ++ ++G+nG+GK+t+++++ gl + + G++++ g+++++   +sl  +ig+++q+  l p+ltv+en 
  gi|116754958|ref|YP_844076.1|   8 LDGLTVRIPRGATYCLLGPNGSGKTTFIRAIVGLIRLDGGDLHVLGEHVSS--VRSLYPRIGYMTQHRALYPDLTVQENm 85 
                                    68899*********************************************9..9************************** PP

                                    ............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    ............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                 ++++i+++l+ ++l++ +d+ +      LSgG+ qr++la++l+ +p+llllDEpt
  gi|116754958|ref|YP_844076.1|  86 effaglygidgqRRKRRIAELLEMVELSDHRDRLA----GALSGGMYQRLSLACTLIHEPELLLLDEPT 150
                                    **********9999999************999999....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.1   3.2e-08   3.1e-05       3      31 ..      22      53 ..      21      66 .. 0.79
   2 !   24.8   0.1   1.7e-08   1.7e-05     234     297 ..     120     180 ..      82     182 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 3.2e-08
                         AAA_21  3 vliGpNgsGKSnLLdaldllarl...drdveg 31
                                   +l GpNgsGK+++++a+ +l rl   d +v g
  gi|116754958|ref|YP_844076.1| 22 CLLGPNGSGKTTFIRAIVGLIRLdggDLHVLG 53
                                   699*****************887655555554 PP

  == domain 2  score: 24.8 bits;  conditional E-value: 1.7e-08
                         AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                    a  lS G+ + l l+  l+   ++  lll+DEp  g +P+l  +++  +++l+++g  vi++TH
  gi|116754958|ref|YP_844076.1| 120 AGALSGGMYQRLSLACTLIH--EP-ELLLLDEPTVGVDPALRQSFWMYFDQLASEGKTVIISTH 180
                                    55667777444333333333..34.9***********************999999********* PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   3.6e-05     0.036      25      45 ..      20      40 ..       2      52 .. 0.78
   2 !   10.4   0.0   0.00038      0.38     323     364 ..     140     180 ..     131     181 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.6e-05
                         AAA_15 25 ltvliGkNnsGKSsilealdl 45
                                   + +l G+N+sGK+++++a+  
  gi|116754958|ref|YP_844076.1| 20 TYCLLGPNGSGKTTFIRAIVG 40
                                   569***************965 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00038
                         AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                    ++ +ll++EP +   p + ++++ ++  la+++k  vii+TH
  gi|116754958|ref|YP_844076.1| 140 EPELLLLDEPTVGVDPALRQSFWMYFDQLASEGK-TVIISTH 180
                                    56799****************************9.9****** PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   3.2e-05     0.031      26      44 ..      20      38 ..       2      61 .. 0.82
   2 !    6.1   0.0    0.0068       6.8     111     205 ..      92     185 ..      75     199 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.2e-05
                                   EEEEEESTTSSHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxx RF
                          SMC_N 26 ftaivGpNGSGKsnlldAi 44
                                     +++GpNGSGK+ ++ Ai
  gi|116754958|ref|YP_844076.1| 20 TYCLLGPNGSGKTTFIRAI 38
                                   45799*************9 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0068
                                    EEETTEEE-HHHHHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 111 ykingkevtkkevsellesagiske......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellk 184
                                    y i+g++ +k+ ++elle++++s +      +LSgG  + ++l    A   ++   l llDe     D + ++ +  +++
  gi|116754958|ref|YP_844076.1|  92 YGIDGQR-RKRRIAELLEMVELSDHrdrlagALSGGMYQRLSL----ACTLIHEPELLLLDEPTVGVDPALRQSFWMYFD 166
                                    6778776.678999******99998888888999997665444....55556667799********************** PP

                                    HHCTTSEEEEE-SSHHHCCC- CS
                                    xxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 185 eksknaQfivislreemleka 205
                                    +  ++   ++is   +++ +a
  gi|116754958|ref|YP_844076.1| 167 QLASEGKTVIIST--HLMDEA 185
                                    9998877666654..234444 PP

>> AAA_23  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   0.00043       6      39 ..       4      38 ..       1      41 [. 0.76

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 4.4e-07
                         AAA_23  6 nfrsfrdqeidFskg.ltlItGpNGaGKTTildAi 39
                                   ++r +++ ++   +g  +++ GpNG+GKTT+++Ai
  gi|116754958|ref|YP_844076.1|  4 GLRALDGLTVRIPRGaTYCLLGPNGSGKTTFIRAI 38
                                   5666666666664431569***************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 !   19.1   0.0   8.3e-07   0.00082      13      44 ..       9      40 ..       6      44 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 8.3e-07
                         AAA_29 13 dghtieidlkg.atlltGpsGsGKSTllDAiqa 44
                                   dg t++i  +g ++ l Gp+GsGK+T++ Ai  
  gi|116754958|ref|YP_844076.1|  9 DGLTVRIP-RGaTYCLLGPNGSGKTTFIRAIVG 40
                                   67788887.56599**************99875 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   6.3e-06    0.0063       2      49 ..      18      62 ..      17     102 .. 0.82
   2 ?    0.6   0.0       0.4   3.9e+02     107     142 ..     157     192 ..     156     212 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6.3e-06
                         AAA_24  2 klkiliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdiesw 49
                                   ++ +++ Gp+g+GKTt+++ +   + +i +++G  ++ + ++ +++s+
  gi|116754958|ref|YP_844076.1| 18 GATYCLLGPNGSGKTTFIRAI---VGLIRLDGGDLHVLGEHVSSVRSL 62
                                   5789*****************...999999999999999999888854 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.4
                         AAA_24 107 laeefrrllkklqelrknvifiahektrkdedpege 142
                                    l++ f+ + ++l + +k+vi+  h+  +  + +  +
  gi|116754958|ref|YP_844076.1| 157 LRQSFWMYFDQLASEGKTVIISTHLMDEAEKCRIVG 192
                                    6789999999**************999887766555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.6e-05     0.016      21      67 ..      21      67 ..      14     148 .. 0.86
   2 ?   -2.6   0.0       3.7   3.7e+03      30      60 ..     172     201 ..     169     203 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.6e-05
                         AAA_30 21 avltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelg 67
                                    +l Gp G+GKtt ++a++ +++ +gg++++l       + L   +g
  gi|116754958|ref|YP_844076.1| 21 YCLLGPNGSGKTTFIRAIVGLIRLDGGDLHVLGEHVSSVRSLYPRIG 67
                                   6789*******************999999998877777766665555 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.7
                         AAA_30  30 GKttalkalreaweaaggrviglAptgkaAk 60 
                                    GKt ++++   + ea++ r++g+  +g++A+
  gi|116754958|ref|YP_844076.1| 172 GKTVIIST-HLMDEAEKCRIVGYMRSGRMAA 201
                                    77766653.4566666888888888888886 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   4.2e-05     0.042       2      46 ..      22      59 ..      21      81 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.2e-05
                                   EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHH CS
                            AAA  2 llyGppGtGKTllakavakelgvefleisgsellskyvgesekki 46
                                   +l Gp G GKT++++a++       ++++g +l   ++ge  +++
  gi|116754958|ref|YP_844076.1| 22 CLLGPNGSGKTTFIRAIVGL-----IRLDGGDLH--VLGEHVSSV 59
                                   899**************986.....555555555..555555555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.7e-05     0.037       2      24 ..      20      42 ..      19      51 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.7e-05
                                   CEEEEC-TTTCHHHHHHHHHHHH CS
                          NACHT  2 lvilqGeaGsGKTtLlqklalaw 24
                                   + +l G++GsGKTt+++ ++ ++
  gi|116754958|ref|YP_844076.1| 20 TYCLLGPNGSGKTTFIRAIVGLI 42
                                   6799**************99766 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0    0.0001       0.1      18      56 ..      12      52 ..       4     178 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.0001
                         AAA_16 18 rvrsgrpelvllsGesGvGKsslvrellralekd..ggifl 56
                                   +vr +r+    l G+ G+GK++ +r++   ++ d  + ++l
  gi|116754958|ref|YP_844076.1| 12 TVRIPRGATYCLLGPNGSGKTTFIRAIVGLIRLDggDLHVL 52
                                   566667777889**************998777774312333 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   5.1e-05     0.051       4      48 ..      23      69 ..      20     114 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.1e-05
                                   EE--TTSSHHHHHHHHHHHH.....GGGEEEEEEEEE-------EEE CS
                       NTPase_1  4 iTGppGvGKtTlvkkvlellkss..gvkvgGfyteevreggrrigFk 48
                                   + Gp G+GKtT+++ ++ l++ +  +++v G  ++ vr+   rig+ 
  gi|116754958|ref|YP_844076.1| 23 LLGPNGSGKTTFIRAIVGLIRLDggDLHVLGEHVSSVRSLYPRIGYM 69
                                   679**************9887653369999*******9999999985 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00013      0.13       2      29 ..      24      51 ..      23      53 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                     ATP_bind_1  2 vGpaGsGKttfvgalseilelrgrsvav 29
                                   +Gp GsGKttf++a++ +++l g +++v
  gi|116754958|ref|YP_844076.1| 24 LGPNGSGKTTFIRAIVGLIRLDGGDLHV 51
                                   7**************9999988877776 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00017      0.17      19      41 ..      18      40 ..       5      50 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00017
                                   TEEEEEEESTTSSHHHHHHHHHH CS
                           TsaE 19 gdvilLeGdLGaGKTtlvrglak 41
                                   g++ +L G+ G+GKTt++r+++ 
  gi|116754958|ref|YP_844076.1| 18 GATYCLLGPNGSGKTTFIRAIVG 40
                                   56789***************985 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    0.0002       0.2       4      24 ..      23      40 ..      21     202 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0002
                         AAA_33  4 lvGlpGsGKstlaerllkklg 24
                                   l G++GsGK+t+++ ++   g
  gi|116754958|ref|YP_844076.1| 23 LLGPNGSGKTTFIRAIV---G 40
                                   57***********9986...4 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00056      0.56       7      35 ..       7      34 ..       3      38 .. 0.86
   2 ?   -1.9   0.0       1.7   1.7e+03      69      90 ..     160     181 ..     146     196 .. 0.62
   3 ?   -2.8   0.0       3.2   3.1e+03     174     206 ..     237     269 ..     228     281 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00056
                         ATPase  7 glDeilkgGipegrvvlitGepGtGKtif 35
                                    lD ++   ip+g+++ + G  G+GKt+f
  gi|116754958|ref|YP_844076.1|  7 ALDGLT-VRIPRGATYCLLGPNGSGKTTF 34
                                   677775.79******************99 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.7
                         ATPase  69 slGwdlekleeegklaiidase 90 
                                    s+ + +++l +egk +ii +  
  gi|116754958|ref|YP_844076.1| 160 SFWMYFDQLASEGKTVIISTHL 181
                                    4455566666666666665443 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 3.2
                         ATPase 174 ygveefivdgvivLdlkeiee..elvRtleivkmR 206
                                    y+ve   + gv++++ ++ ++  e+  +++ + mR
  gi|116754958|ref|YP_844076.1| 237 YEVEV--SGGVVRIRIDKHAQikEILEIISPLDMR 269
                                    55554..6666666665555544555555555555 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 ?   11.1   0.0   0.00023      0.23       1      35 [.       4      39 ..       4     122 .. 0.91
   2 ?   -3.2   0.0       5.4   5.4e+03      26      40 ..     172     187 ..     167     203 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00023
                                   SSHHHHHHS.-EBTT-EEEEEESTTSSHHHHHHHHH CS
                                   xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab  1 GirvlDalf.pivqGqrtlipgafgvGktvisqsls 35
                                   G+r+lD l+  i +G + +++g +g Gkt+ +++++
  gi|116754958|ref|YP_844076.1|  4 GLRALDGLTvRIPRGATYCLLGPNGSGKTTFIRAIV 39
                                   899***9962689*****************998886 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5.4
                                    SHHHHH.HHHHHHSST CS
                                    xxxxxx.xxxxxxxxx RF
                    ATP-synt_ab  26 Gktvis.qslskqsns 40 
                                    Gktvi+  +l+ ++++
  gi|116754958|ref|YP_844076.1| 172 GKTVIIsTHLMDEAEK 187
                                    8888774555555433 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00029      0.29       1      78 [.     203     280 ..     203     282 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00029
                                    E-HHHHHTTS.-SSEEEEE....-------..---EEEE-TTS-EEEEE-----------------EEEEEEEE---HHH CS
                        DUF4162   1 GtleeiKrsy.gknrieve....adaeelleepgveeveeeggelelkledeeaanellkaltsgveirsFeeeePsLnd 75 
                                    G+++ei++    k ++e+     + +++ll+ ++  eve  gg ++++++++++ +e+l+ +    +   ++++ePsL++
  gi|116754958|ref|YP_844076.1| 203 GSPDEIMQLAgLKPHLELLledpERDASLLR-SEGYEVEVSGGVVRIRIDKHAQIKEILEII----SPLDMRLREPSLEE 277
                                    7777777777445566644434222333333.44677888899****************999....7788999******* PP

                                    HHH CS
                        DUF4162  76 IFi 78 
                                     F+
  gi|116754958|ref|YP_844076.1| 278 AFL 280
                                    997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1959.17
//
Query:       gi|116754959|ref|YP_844077.1|  [L=373]
Description: hypothetical protein Mthe_1671 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.4e-07   29.6   0.1      0.003   17.8   0.0    2.6  2  CARDB        CARDB
      7e-06   26.2   0.1    7.5e-05   22.9   0.0    2.6  3  NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosi
      2e-05   24.8   0.9      0.014   15.7   0.1    2.7  2  DUF11        Domain of unknown function DUF11
  ------ inclusion threshold ------
       0.13   11.6   0.1        4.7    6.6   0.0    2.6  3  TRAP_beta    Translocon-associated protein beta (TRAPB)


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 !    9.3   0.0   0.00028       1.3       1      39 [.      68     104 ..      68     149 .. 0.88
   2 !   17.8   0.0   6.6e-07     0.003      17      84 ..     248     321 ..     233     339 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00028
                                    S--EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEE CS
                          CARDB   1 tpDLtvtntlnpseafvgeentitvtvkNqGtaasgatk 39 
                                    tpDLtv  +l+ s++++ge  +i +t++N G  ++ +++
  gi|116754959|ref|YP_844077.1|  68 TPDLTV--SLERSSVYQGEITSIFLTLTNRGRVTAIKVN 104
                                    7*****..***********************98887766 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 6.6e-07
                                    TTSEEEEEEEEEE-SSS-EEEEEEEEEETT.EEE..EEEEESEE-CTEEEEEEEEEE-S..-S-CEEE.EEEEE CS
                          CARDB  17 vgeentitvtvkNqGtaasgatkvalyldg.elv..gtvtvpsLaagesttvsftwtte..ategevt.ltvvv 84 
                                      ++n ++++vkN Gt+++++  ++l  +    v  ++++vp L++ges++  ++  ++  a +g+v+ l+v+ 
  gi|116754959|ref|YP_844077.1| 248 GSSDNVVRISVKNVGTDTARDLVARLKPESgIYVsvDESPVPRLEPGESAEFVYKLDVSkdAVPGKVYlLRVTF 321
                                    5678999*******************9754144477****************9998888788899999777765 PP

>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0         3   1.4e+04      26      35 ..       4      13 ..       3      21 .. 0.76
   2 ?   -0.3   0.0      0.29   1.3e+03       3      25 ..      82     104 ..      80     108 .. 0.83
   3 !   22.9   0.0   1.7e-08   7.5e-05       6      77 ..     251     322 ..     247     324 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 3
                    NPCBM_assoc 26 lslslPeGWt 35
                                   l lslP+ W 
  gi|116754959|ref|YP_844077.1|  4 LGLSLPSRWI 13
                                   67999*9995 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.29
                    NPCBM_assoc   3 pGetvtltltvtndgtaaatnvs 25 
                                    +Ge +++ lt+tn g+ +a +v+
  gi|116754959|ref|YP_844077.1|  82 QGEITSIFLTLTNRGRVTAIKVN 104
                                    79999999*******98887765 PP

  == domain 3  score: 22.9 bits;  conditional E-value: 1.7e-08
                    NPCBM_assoc   6 tvtltltvtndgtaaatnvslslslPeGWtvvevspasaaslapGetveatvkVtppagaaaGd.yevtakar 77 
                                    ++ ++++v+n gt++a+++  +l+  +G   v+v+   +++l+pGe++e+  k+ ++++a++G+ y ++++ +
  gi|116754959|ref|YP_844077.1| 251 DNVVRISVKNVGTDTARDLVARLKPESGIY-VSVDESPVPRLEPGESAEFVYKLDVSKDAVPGKvYLLRVTFE 322
                                    56789*******************999999.********************************9999988765 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.1    0.0014       6.5       4      33 ..      74     103 ..      71     173 .. 0.88
   2 !   15.7   0.1   3.1e-06     0.014      17      86 ..     253     313 ..     240     320 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0014
                          DUF11   4 tvdksevrpGdtvtytltvtNtgpasangv 33 
                                    + ++s v  G+ ++  lt+tN+g ++a +v
  gi|116754959|ref|YP_844077.1|  74 SLERSSVYQGEITSIFLTLTNRGRVTAIKV 103
                                    566778999****************99554 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 3.1e-06
                          DUF11  17 tytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsftvrvtrtaasga 86 
                                    ++ + v+N g+++a ++v + + P++  yvsv  s         v++Le+gesa + +++ v++ a  g 
  gi|116754959|ref|YP_844077.1| 253 VVRISVKNVGTDTARDLVAR-LKPESGIYVSVDES--------PVPRLEPGESAEFVYKLDVSKDAVPGK 313
                                    5789**********766665.57************........789*****************9988765 PP

>> TRAP_beta  Translocon-associated protein beta (TRAPB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.028   1.3e+02      34      55 ..      83     104 ..      73     106 .. 0.76
   2 ?    6.6   0.0     0.001       4.7      28      54 ..     243     269 ..     232     278 .. 0.91
   3 ?   -3.1   0.0      0.94   4.2e+03      77      93 ..     288     304 ..     283     330 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.028
                      TRAP_beta  34 gedltveytiyNvGssaAldVs 55 
                                    ge  ++ +t++N G  +A++V+
  gi|116754959|ref|YP_844077.1|  83 GEITSIFLTLTNRGRVTAIKVN 104
                                    44456889************96 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.001
                      TRAP_beta  28 nrllvegedltveytiyNvGssaAldV 54 
                                    +rl+ + +d++v++++ NvG+ +A+d+
  gi|116754959|ref|YP_844077.1| 243 ERLPAGSSDNVVRISVKNVGTDTARDL 269
                                    57788999*****************97 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 0.94
                      TRAP_beta  77 werlapgenvshsfvve 93 
                                    + rl+pge+ ++++ + 
  gi|116754959|ref|YP_844077.1| 288 VPRLEPGESAEFVYKLD 304
                                    57899999999888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); 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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2743.33
//
Query:       gi|116754960|ref|YP_844078.1|  [L=739]
Description: helicase c2 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.5e-35  120.8   0.0    1.2e-34  119.9   0.0    1.5  1  Helicase_C_2  Helicase C-terminal domain
      2e-13   50.4   0.0    4.7e-13   49.1   0.0    1.7  1  DEAD_2        DEAD_2
    1.7e-06   28.1   0.0     0.0096   15.9   0.0    2.4  2  ResIII        Type III restriction enzyme, res subunit
    7.3e-05   22.5   0.0    0.00026   20.7   0.0    1.9  2  HBB           Helical and beta-bridge domain
     0.0003   20.6   0.1      0.034   13.9   0.0    2.5  2  DEAD          DEAD/DEAH box helicase
     0.0032   17.8   0.1        1.7    8.9   0.0    3.1  3  AAA_22        AAA domain
     0.0065   16.9   0.0      0.025   15.0   0.0    2.0  1  AAA_16        AAA ATPase domain
  ------ inclusion threshold ------
       0.14   10.8   0.0       0.24   10.1   0.0    1.2  1  SNF2_N        SNF2 family N-terminal domain


Domain annotation for each model (and alignments):
>> Helicase_C_2  Helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.9   0.0   5.6e-38   1.2e-34       2     170 ..     535     708 ..     534     709 .. 0.92

  Alignments for each domain:
  == domain 1  score: 119.9 bits;  conditional E-value: 5.6e-38
                   Helicase_C_2   2 lellevvpggvlvffpSyklleevverlkeeleskkieifvee.keesrekvleeykek.kkkgaillavcrGklsEGid 79 
                                      l+e vpg+v vff+Sy ++ + +++ ++     ++++f+e+ ++e+  ++lee+ ++ ++ ga+ll+v +Gkl EGid
  gi|116754960|ref|YP_844078.1| 535 SALIEEVPGNVAVFFTSYPMMASYRDACARFARGAGKKVFTEPrSAEDVPQILEEFFRAgRSAGAVLLGVSGGKLAEGID 614
                                    57899*************************99999*******99999**********966******************** PP

                   Helicase_C_2  80 fsddllraviivglPfpnpkdpeveakreyldekgkknsgkewylpealravnQaiGRliRhkdDygaivllDeRfak.. 157
                                    +++++l+ v +vglP+  +++ + e    y  ++gkk++   +y+ +a+++  Qa+GR+iR + ++g+i+l+D+Rfa+  
  gi|116754960|ref|YP_844078.1| 615 YKGEALNGVAVVGLPLSVFDEIQKEVISYYTHKYGKKRGTLIAYTLPAINRGLQAAGRVIRAESERGVILLCDSRFASmg 694
                                    ******************999887777777777777777889***********************************955 PP

                   Helicase_C_2 158 .eeireklpkwlre 170
                                       +r++lp+w+++
  gi|116754960|ref|YP_844078.1| 695 lGGVRMYLPEWVQR 708
                                    45689999999985 PP

>> DEAD_2  DEAD_2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.0   2.1e-16   4.7e-13       2     171 ..      90     296 ..      89     301 .. 0.83

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 2.1e-16
                                    EESSHHHHHHHHHHHHHHHHHCHHHS---EEEE--CCCC-SCHHCCCHHCCCCHHHHHHHHHCCHHCCH........... CS
                         DEAD_2   2 csRThsqleqvvkelkklesykkkkekvkvviLgSRknlCineevkkekkekavneaCkelkkkkaeek........... 70 
                                    ++RT+sq+  +++e++++ s +   ++  v  L ++++ C+     +e  ++++  aC++l++  ++             
  gi|116754960|ref|YP_844078.1|  90 AVRTVSQIGVYLDEINRIWSNTR--HRPTVSYLIGKQKACLLA---SEIWGESIYYACMRLREGSKNYMasrlerghndi 164
                                    68****************76554..677888999******984...3444789999*****99987655899******** PP

                                    ...............................TTTTTT-SCCCCHHHHHHHHHHC---CHHHHHHHHHCT--HHHHHHHHH CS
                         DEAD_2  71 ...............................eekCsffenleelkklkkllleevvdiedlvelgeklklCPYylsrell 119
                                                                   + k  f ++ + ++   +++ +++v ++ l +++   ++CPY ++   +
  gi|116754960|ref|YP_844078.1| 165 ydpsrdeipdeppgertvcphylrskeafeiNGKVYFRSSSAAVD-AAERMSRRIVPVDALEKICG--GVCPYEVMSLHA 241
                                    ***************888888887777766544444444444444.47889999999999999875..89********** PP

                                    CCTSEEEEEHHHHTSCCCHHHHH...T..GCGCEEEECTCCCHHHHHHHCC-EEE CS
                         DEAD_2 120 edadiiilpYqyLldekireslk...gislknsivilDEAhNiedvceeaasvei 171
                                    ++ d+iil Y+ L+++   +++    g++     vi+DEAhN+ d ++e++   +
  gi|116754960|ref|YP_844078.1| 242 KSSDVIILNYHHLFSPDFQDAIIqwlGLEADRMTVIVDEAHNLGDSVREMNTRVL 296
                                    *****************9998776888999*******************987655 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 !   15.9   0.0   4.3e-06    0.0096       3      45 ..      38      81 ..      37     118 .. 0.86
   2 !    9.7   0.0   0.00034      0.77      99     150 ..     239     288 ..     188     320 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.3e-06
                                   EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHH.HHHH CS
                         ResIII  3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlva.akli 45
                                   +lr++Q e+++++ + ++  ++  ++i ++TG+GKT ++ a+l+
  gi|116754960|ref|YP_844078.1| 38 SLRPHQDEMLDAVYDVVSTGGHGVLMIDAPTGSGKTSCIsAALA 81
                                   59************999956666677**********98845554 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00034
                                    .....-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTT CS
                         ResIII  99 kdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakksw 150
                                     +++++++++ +++ l ++  ++   +   l+     +i+DEaH+lg++  +
  gi|116754960|ref|YP_844078.1| 239 LHAKSSDVIILNYHHLFSPDFQDAIIQWLGLEADRMTVIVDEAHNLGDS--V 288
                                    577889999999999999997777777777777778**********994..3 PP

>> HBB  Helical and beta-bridge domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.4     3e+03      46      87 ..     258     298 ..     240     300 .. 0.79
   2 !   20.7   0.0   1.2e-07   0.00026     104     186 ..     429     516 ..     407     519 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.4
                                    HHHHCHCHHHCHHHHHHHHHHHHHHHHHHHCCHHCCCTCC-S CS
                            HBB  46 eileeavpglirsaehflsllkrlveygkarreekieksesP 87 
                                    ++ + +++ l+ +a+ ++ ++ + +++g+++ +e  ++  +P
  gi|116754960|ref|YP_844078.1| 258 DFQDAIIQWLGLEADRMTVIVDEAHNLGDSV-REMNTRVLTP 298
                                    6788889999999999999999999999999.5566666666 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 1.2e-07
                                    S.TTTEEEEEE.STT..EECCCCS-TCCHH.HHHHHCHCCCCCCTS-SSHHHHHHH.HT....EEE...S..S.GGHCCC CS
                            HBB 104 sdeedYvrlvskeeg.esLeavcldPskal.rflkerlssllmsgtltpleeysdi.iGleaklkkf..pspfpkEnliv 178
                                    s++ + v   s e+    Le + +dP+ ++ r++ ++  +l+ sgtl+p+++y+   +G + + +k+  p+pfp+ n+++
  gi|116754960|ref|YP_844078.1| 429 SYQRKIVTASSGERRwTRLEVTKIDPAPVIrRVVDNVNATLMLSGTLSPIDAYELYcLGEQGRARKIslPNPFPQSNRLI 508
                                    555566666777777889********987626899******************97514555777765449********99 PP

                                    CCCCCCSH CS
                            HBB 179 lfatdVsT 186
                                      a+  +T
  gi|116754960|ref|YP_844078.1| 509 IAAERATT 516
                                    98887777 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   1.5e-05     0.034       2      36 ..      41      81 ..      40     111 .. 0.83
   2 ?    4.1   0.0     0.015        34     122     139 ..     272     290 ..     204     309 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.5e-05
                                   HHHHHHHHHHH......TTCEEEEEESTTSSHHHHHHHHHH CS
                                   xxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  2 diQaeaiplil......gggdvlvaaeTGsGKTlaflipvl 36
                                   + Q+e++++++      g g +++ a+TGsGKT + + ++ 
  gi|116754960|ref|YP_844078.1| 41 PHQDEMLDAVYdvvstgGHGVLMIDAPTGSGKTSCISAALA 81
                                   6788888888877777333567799**********998876 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.015
                                    EEE.EEEETHHHHHHTTTH CS
                                    xxx.xxxxxxxxxxxxxxx RF
                           DEAD 122 vrf.lVlDEadrlldqgfs 139
                                     r+ +++DEa++l d+ ++
  gi|116754960|ref|YP_844078.1| 272 DRMtVIVDEAHNLGDSVRE 290
                                    343399*******998544 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0   0.00074       1.7       4      30 ..      58      84 ..      55     114 .. 0.83
   2 ?    4.9   0.1     0.013        30      92     108 ..     273     290 ..     238     310 .. 0.76
   3 ?   -1.6   0.0       1.3     3e+03      42      91 ..     547     596 ..     510     603 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00074
                         AAA_22  4 tagilvvtGesGtGKTtllrrlleqld 30
                                   ++g+l++ +++G+GKT ++   l  ++
  gi|116754960|ref|YP_844078.1| 58 GHGVLMIDAPTGSGKTSCISAALAAAP 84
                                   6799**************998887765 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.013
                         AAA_22  92 ielliiDEaqhlr.seea 108
                                    +  +i+DEa++l  s + 
  gi|116754960|ref|YP_844078.1| 273 RMTVIVDEAHNLGdSVRE 290
                                    3689********654333 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.3
                         AAA_22  42 vvfvtlpsstsskdllrellralglelkaerlsseellealeqalrarav 91 
                                    v+f   p   s +d + +++r  g +  +e+ s e++ + le+ +ra + 
  gi|116754960|ref|YP_844078.1| 547 VFFTSYPMMASYRDACARFARGAGKKVFTEPRSAEDVPQILEEFFRAGRS 596
                                    23444444449999999999999998888788888777888888877665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.1e-05     0.025       7      55 ..      42      89 ..      39     116 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.1e-05
                         AAA_16  7 eeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggif 55
                                   ++ e+L ++++ v++g+ +++++  + G+GK+s + ++l a+ ++ +++
  gi|116754960|ref|YP_844078.1| 42 HQDEMLDAVYDVVSTGGHGVLMIDAPTGSGKTSCISAALAAAPGK-IVV 89
                                   56789999*********9********************9888887.333 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 ?   10.1   0.0   0.00011      0.24     147     196 ..     241     291 ..     219     305 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00011
                                    -----EEEE-HHHHHHHT.......TTS-.S-S-SEEEES-GGGT--TTSHH CS
                                    xxxxxxxxxxxxxxxxxxxxx.xxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                         SNF2_N 147 ladydvvittYdvlsreaelq.kkrsvlk.qvewkrvvlDEghtlknstska 196
                                    ++  dv+i +Y+ l +   +q ++++ l  + ++  v++DE+h+l+ s +++
  gi|116754960|ref|YP_844078.1| 241 AKSSDVIILNYHHLFSPD-FQdAIIQWLGlEADRMTVIVDEAHNLGDSVREM 291
                                    5678**********9655.664566666425567889********9985554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (739 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); 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: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.45
# Mc/sec: 4896.27
//
Query:       gi|116754961|ref|YP_844079.1|  [L=487]
Description: polysaccharide biosynthesis protein [Methanosaeta thermophila PT]
Scores for complete 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   80.7  30.9    1.2e-22   80.7  30.9    2.5  2  Polysacc_synt    Polysaccharide biosynthesis protein
    1.1e-20   74.1  20.7    1.1e-20   74.1  20.7    2.3  2  Polysacc_synt_3  Polysaccharide biosynthesis protein
    1.2e-18   67.5  53.7    2.8e-14   53.4  26.8    3.9  4  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
    2.2e-08   33.2  22.0    2.2e-08   33.2  22.0    3.4  3  MurJ             Lipid II flippase MurJ
    5.4e-06   26.2  11.9    5.4e-06   26.2  11.9    3.9  4  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 !   80.7  30.9   3.2e-26   1.2e-22       3     267 ..      15     277 ..      13     280 .. 0.86
   2 ?   -9.4  22.2         5   1.8e+04     101     215 ..     325     442 ..     292     468 .. 0.59

  Alignments for each domain:
  == domain 1  score: 80.7 bits;  conditional E-value: 3.2e-26
                  Polysacc_synt   3 kgvivlllsqlitkllafvtlvylarilgpegfGlvalalaivtllviltdlGlnaalvreiakyrekkelvslillnvl 82 
                                    + +  + l++++++l ++  l++l+  l+ e++G  a++  +++l+++++ lGl+a+ vr++a +++++e+   +++ + 
  gi|116754961|ref|YP_844079.1|  15 QRIGLIGLANVLVNLSGIFLLPILTKSLPVEDYGVWAQVNVTISLASVVICLGLSASMVRFMAAASSREEIQECFYSILA 94 
                                    6678899************************************************************8555555555555 PP

                  Polysacc_synt  83 lvllvlvllfllllliaa.....flglpelavlylilalmll.llvgvasfrrglfqglermkyaavsqvveqlsrvilv 156
                                    +v+l  +  +ll++++a+     ++++     + +++al++  ++ +++ +  +++++ +rmk  a+ +v+ + + ++l 
  gi|116754961|ref|YP_844079.1|  95 VVMLTGISAMLLIFCLAEpiaraLFNG----NVAVTRALSVIvFVEAMNGLLFSYYRATQRMKLYAIFSVAVVYITIVLA 170
                                    555555556666666666533342222....3344455555547899********************************* PP

                  Polysacc_synt 157 liavflfldivaavlgavlaalvggivslavlrkkfrprfvilslklvrellsfsapltisslaillytyidsillglll 236
                                      +v l++ +++avlg+ +a l+g ++ l++l       f i+s  +  e +sf++pl+ s+l+  + + +d++++g ll
  gi|116754961|ref|YP_844079.1| 171 YCFVKLGYGVYGAVLGLGIAKLIGFVFMLTMLL--QQIGFRIPSFLHLLEYVSFGIPLFSSYLFDWIVNSSDRYIIGMLL 248
                                    ********************************9..55777777768899******************************* PP

                  Polysacc_synt 237 gaeavGiYnaayqllvaisgllapivtaalf 267
                                    g++ vG+Yn +y l ++i+++++pi t  + 
  gi|116754961|ref|YP_844079.1| 249 GTVWVGYYNPGYLLGSLITVFISPIGT--VL 277
                                    **************************9..44 PP

  == domain 2  score: -9.4 bits;  conditional E-value: 5
                  Polysacc_synt 101 flglpelavlylilalmllllvgvasfrrglfqglermkyaavsqvveqlsrvilvliavflfldivaavlgavlaalvg 180
                                     l+ p+ a +  +++ +++l    +   + l ++    k +a+s+ ++ ++ +i + + ++l++ ++++v++av+  ++ 
  gi|116754961|ref|YP_844079.1| 325 MLSTPDIAEHSYLITPFIALSMVLVGIASILSNAIYIAKKTAISMKISLIAAIINLTLTLLLVS-MAGVVGAAVATFFTF 403
                                    5555555555555555555555555555556666666677777777777777777777777777.666666666655555 PP

                  Polysacc_synt 181 givslavlrkkfr.......prfvilslklvrellsfsaplt 215
                                     ++++a+ +  f        ++  +  lk +  +l +s+pl+
  gi|116754961|ref|YP_844079.1| 404 FFIFIATNY--FAnmfiqikFDYEFM-LKSFVASLVMSIPLI 442
                                    555555555..422333333333333.555555555555554 PP

>> Polysacc_synt_3  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.1  20.7   3.1e-24   1.1e-20       2     282 ..      38     325 ..      37     330 .. 0.90
   2 ?    0.1  12.3       0.1   3.7e+02      84     177 ..     338     430 ..     331     443 .. 0.85

  Alignments for each domain:
  == domain 1  score: 74.1 bits;  conditional E-value: 3.1e-24
                Polysacc_synt_3   2 LARLLspedFGvvaialvvislanlfvdmGlssaliqke..dlteedlstvftfn....lvlgllialvlfllapliasf 75 
                                    L+  L  ed+Gv a + v isla++++ +Gls  +++     +++e+++ +f++     +++g+ ++l++f+la+ ia++
  gi|116754961|ref|YP_844079.1|  38 LTKSLPVEDYGVWAQVNVTISLASVVICLGLSASMVRFMaaASSREEIQECFYSIlavvMLTGISAMLLIFCLAEPIARA 117
                                    6666889*****************************97644677789*****9751111567999**************8 PP

                Polysacc_synt_3  76 ynqpelvtvlrvlalvlilsglssvqeallrrelkFkklfkitlvssvvgvivaivlAllglgvwALvigtllssllslv 155
                                    + + + v v+r l++ +++++++ +  +++r   + k  ++++++ + +++++a   + lg+gv+  v+g  +++l+ +v
  gi|116754961|ref|YP_844079.1| 118 LFNGN-VAVTRALSVIVFVEAMNGLLFSYYRATQRMKLYAIFSVAVVYITIVLAYCFVKLGYGVYGAVLGLGIAKLIGFV 196
                                    87765.6799********************************************************************** PP

                Polysacc_synt_3 156 llwlaskwrprlkf.slkslkelfsfglklllsnllnylarnldnlliGkvlssaaLGlYsvakrlaslpvaeitsviak 234
                                    ++++++ +++ +++ s+ +l e++sfg+ l+ s l +++++++d  +iG +l++  +G+Y+ ++ l sl++  + s+i +
  gi|116754961|ref|YP_844079.1| 197 FMLTMLLQQIGFRIpSFLHLLEYVSFGIPLFSSYLFDWIVNSSDRYIIGMLLGTVWVGYYNPGYLLGSLITV-FISPIGT 275
                                    *********999986799**********************************************88877665.5578888 PP

                Polysacc_synt_3 235 VlfPalSrlqd..dkkklrelylkvlrlialivlPiavglavvaellvkv 282
                                    Vl  +l r  d  d k++++l+  +++    +++P ++gl +++++++ +
  gi|116754961|ref|YP_844079.1| 276 VLPITLYRYYDcgDIKSVEKLLGFTIKYFLALAIPSVFGLTLLSKPMLFM 325
                                    888888888766688999999999999999999******99999998755 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.1
                Polysacc_synt_3  84 vlrvlalvlilsglssvqeallrrelkFkklfkitlvssvvgvivaivlAllglgvwALvigtllssllslvllwlaskw 163
                                    ++ ++al+++l g+ s+ ++ + +  k    +ki+l++ ++ + ++++l+ + +gv   ++ t ++ ++++++  +++++
  gi|116754961|ref|YP_844079.1| 338 ITPFIALSMVLVGIASILSNAIYIAKKTAISMKISLIAAIINLTLTLLLVSM-AGVVGAAVATFFTFFFIFIATNYFANM 416
                                    67799******************************************99865.677777888999999999999999999 PP

                Polysacc_synt_3 164 rprlkfslkslkel 177
                                     +++kf+ + + + 
  gi|116754961|ref|YP_844079.1| 417 FIQIKFDYEFMLKS 430
                                    99999887766544 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   7.1       1.8   6.3e+03      30     104 ..      12     102 ..       4     121 .. 0.35
   2 !   28.2  19.0   4.6e-10   1.6e-06       2     132 ..     126     251 ..     125     277 .. 0.89
   3 ?   -1.8   1.8      0.81   2.9e+03     132     132 ..     276     276 ..     242     329 .. 0.48
   4 !   53.4  26.8   7.8e-18   2.8e-14       4     142 ..     341     471 ..     338     472 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.8
                Polysacc_synt_C  30 ialkalvigalvklilnllliplfgi.................vGaaiatvlallvvavlnlyalrrllgikl..ellrr 90 
                                    +++  + +  l+++++nl  i l+ i                 v     + la +v+++ +   + r +      e ++ 
  gi|116754961|ref|YP_844079.1|  12 LLAQRIGLIGLANVLVNLSGIFLLPIltkslpvedygvwaqvnV----TISLASVVICLGLSASMVRFMAAASsrEEIQE 87 
                                    44444444444455555544444444444444444222211111....22222222222222222222222222322333 PP

                Polysacc_synt_C  91 ll.kpllaalvmgiv 104
                                    ++  +l+++++ gi 
  gi|116754961|ref|YP_844079.1|  88 CFySILAVVMLTGIS 102
                                    321222222222222 PP

  == domain 2  score: 28.2 bits;  conditional E-value: 4.6e-10
                Polysacc_synt_C   2 LailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllli.plfgivGaaiatvlallvvavlnlyalrrl 80 
                                     + l++++++ +++ +l s+  ++ r k++++++v+ + + ++l + ++   +g++Ga+++  +a l+++v++l +l ++
  gi|116754961|ref|YP_844079.1| 126 TRALSVIVFVEAMNGLLFSYYRATQRMKLYAIFSVAVVYITIVLAYCFVkLGYGVYGAVLGLGIAKLIGFVFMLTMLLQQ 205
                                    5789*********************************************8899*************************** PP

                Polysacc_synt_C  81 lgiklellrrllkpllaalvmgivvylllllllgllllaalalllavlvgal 132
                                    +g+++  + +ll ++ +++ ++    +l+ ++++ +       ++++l+g +
  gi|116754961|ref|YP_844079.1| 206 IGFRIPSFLHLLEYVSFGIPLFSS--YLFDWIVNSSDRY----IIGMLLGTV 251
                                    *****6699998999999999999..6999999988866....444433332 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.81
                Polysacc_synt_C 132 l 132
                                    +
  gi|116754961|ref|YP_844079.1| 276 V 276
                                    2 PP

  == domain 4  score: 53.4 bits;  conditional E-value: 7.8e-18
                Polysacc_synt_C   4 ilalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavlnlyalrrllgi 83 
                                    ++als+++ +++++ls+ +   +++ i +k+++i+a+++l l+lll+ + g+vGaa+at ++++++++   y+++  ++i
  gi|116754961|ref|YP_844079.1| 341 FIALSMVLVGIASILSNAIYIAKKTAISMKISLIAAIINLTLTLLLVSMAGVVGAAVATFFTFFFIFIATNYFANMFIQI 420
                                    679***************************************************************************** PP

                Polysacc_synt_C  84 klellrrllkpllaalvmgivvylllllllgllllaalalllavlvgalvYlllllllr 142
                                    k++ +  +lk ++a+lvm+i    l l+ ++ +     ++l  ++v +++Yl +++llr
  gi|116754961|ref|YP_844079.1| 421 KFD-YEFMLKSFVASLVMSIP---LILWPPSGFI----EILRIIAVSIIIYLQAIWLLR 471
                                    **6.99999************...9999998775....77888889**********998 PP

>> MurJ  Lipid II flippase MurJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.2   0.5    0.0018       6.5     378     438 ..      19      72 ..       6      82 .. 0.77
   2 !    4.4  15.6    0.0033        12     273     412 ..      84     214 ..      74     252 .. 0.79
   3 !   33.2  22.0   6.1e-12   2.2e-08     247     423 ..     266     439 ..     249     464 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0018
                           MurJ 378 vvglalatslsaliglvllyvllrkrlklteargiktflaklvvllalaavvilllssltq 438
                                    +  ++la++l++ ++ ++l+ +l+k+l + +  +++ +       ++la+vvi+l  s ++
  gi|116754961|ref|YP_844079.1|  19 L--IGLANVLVN-LSGIFLLPILTKSLPVEDYGVWAQVNVT----ISLASVVICLGLSASM 72 
                                    4..578999**9.77799999*******9999999876655....8888888888777665 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0033
                           MurJ 273 evrdllsqairltllllipvsfgllvlskpivsllferGnFseedveataevLaayalgLipyalvklllrvfYAredtk 352
                                    e+++     + +++l+ i +  +++ l++pi ++lf +Gn          +v +a ++ ++  a++ ll +++ A ++ k
  gi|116754961|ref|YP_844079.1|  84 EIQECFYSILAVVMLTGISAMLLIFCLAEPIARALF-NGNV---------AVTRALSVIVFVEAMNGLLFSYYRATQRMK 153
                                    5566666678889999999999**************.5653.........333444555677899*************** PP

                           MurJ 353 tPvkislislvlnillsllllp.plgvvglalatslsaliglvllyvllrkrlklteargi 412
                                      ++ s+ ++ ++i+l++ +++  +gv+g +l+ +++ lig+v+++ +l ++ ++ + + +
  gi|116754961|ref|YP_844079.1| 154 LYAIFSVAVVYITIVLAYCFVKlGYGVYGAVLGLGIAKLIGFVFMLTMLLQQIGFRIPSFL 214
                                    ******9999999999976665269**************************9887766544 PP

  == domain 3  score: 33.2 bits;  conditional E-value: 6.1e-12
                           MurJ 247 lglfgvsistvlLPrlSrsakekdedevrdllsqairltllllipvsfgllvlskpivsllferGnFseedveataevLa 326
                                    + +f+  i tvl  +l r ++ +d ++v++ll  +i+  l+l+ip++fgl++lskp++ +l      s+ d+++ ++++ 
  gi|116754961|ref|YP_844079.1| 266 ITVFISPIGTVLPITLYRYYDCGDIKSVEKLLGFTIKYFLALAIPSVFGLTLLSKPMLFML------STPDIAEHSYLIT 339
                                    4455555555555599999*************************************98666......5899999999999 PP

                           MurJ 327 ay.algLipyalvklllrvfYAredtktPvkislislvlnillsllllpplgvvglalatslsaliglvllyvllrkrlk 405
                                     + al+++ + ++ +l+++ Y  + t   +kisli++++n+ l lll++  gvvg a+at   + + ++   ++++   +
  gi|116754961|ref|YP_844079.1| 340 PFiALSMVLVGIASILSNAIYIAKKTAISMKISLIAAIINLTLTLLLVSMAGVVGAAVATFFTFFFIFIATNYFANMFIQ 419
                                    8878*********************************************************9997766666555554433 PP

                           MurJ 406 ..lteargiktflaklvvll 423
                                      ++ + ++k f+a+lv+ +
  gi|116754961|ref|YP_844079.1| 420 ikFDYEFMLKSFVASLVMSI 439
                                    22444555555556544333 PP

>> MatE  MatE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0  15.3   0.00029         1      24     160 ..      43     171 ..      20     172 .. 0.74
   2 ?   -3.6   0.5       2.2   7.8e+03      78      88 ..     189     199 ..     180     206 .. 0.40
   3 !   26.2  11.9   1.5e-09   5.4e-06       1     159 [.     225     383 ..     225     385 .. 0.96
   4 ?   -3.5   4.1         2   7.1e+03      80     100 ..     396     416 ..     386     459 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00029
                           MatE  24 gskalAavsialsilsllfv.fllglstalttlvgqalGaknfkrakealrqglilllllsliiallvllfseqilslft 102
                                    + ++ ++ + ++ ++sl  v + lgls+++  +++    a ++++++e ++ +l +++l ++ ++ll+++++e+i++ + 
  gi|116754961|ref|YP_844079.1|  43 PVEDYGVWAQVNVTISLASVvICLGLSASMVRFMAA---ASSREEIQECFYSILAVVMLTGISAMLLIFCLAEPIARALF 119
                                    555555555555555555554888888888888876...568889********************************998 PP

                           MatE 103 qdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislllniplny 160
                                    + +    ++ r l+++++++   a++ +l +++r+++++k+ +++s++ + + i+l+y
  gi|116754961|ref|YP_844079.1| 120 NGNV---AVTRALSVIVFVE---AMNGLLFSYYRATQRMKLYAIFSVAVVYITIVLAY 171
                                    8874...4455566666555...5568889999***************99******99 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.2
                           MatE  78 lllllsliial 88 
                                    ++ l++++++l
  gi|116754961|ref|YP_844079.1| 189 IAKLIGFVFML 199
                                    22222222222 PP

  == domain 3  score: 26.2 bits;  conditional E-value: 1.5e-09
                           MatE   1 Pialenllesllslidtllvgrl.gskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqglill 79 
                                    P++ ++l+ ++++  d +++g+l g++ ++ ++ +  + sl++vf+  ++t l +   +++  ++ k +++ l  +++  
  gi|116754961|ref|YP_844079.1| 225 PLFSSYLFDWIVNSSDRYIIGMLlGTVWVGYYNPGYLLGSLITVFISPIGTVLPITLYRYYDCGDIKSVEKLLGFTIKYF 304
                                    778889999999******************************************************************** PP

                           MatE  80 lllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislllnipln 159
                                    l+l+++ ++ ++l+s+++l ++ ++++++e +  + ++++l++++ ++  +ls++   a+kt +++ isli++++n+ l+
  gi|116754961|ref|YP_844079.1| 305 LALAIPSVFGLTLLSKPMLFML-STPDIAEHSYLITPFIALSMVLVGIASILSNAIYIAKKTAISMKISLIAAIINLTLT 383
                                    **********9****9999888.6677*************************************************9886 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 2
                           MatE  80 lllsliiallvllfseqilsl 100
                                    ++  +++++++++ +++++ +
  gi|116754961|ref|YP_844079.1| 396 AVATFFTFFFIFIATNYFANM 416
                                    333333444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (487 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1195  (0.0666518); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); 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):               5  [number of targets reported over threshold]
# CPU time: 0.65u 0.33s 00:00:00.98 Elapsed: 00:00:00.46
# Mc/sec: 3199.52
//
Query:       gi|116754962|ref|YP_844080.1|  [L=261]
Description: glycosyl transferase family protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-18   65.6   0.0    8.5e-18   64.7   0.0    1.4  1  Glycos_transf_2  Glycosyl transferase family 2
    1.8e-05   24.8   0.0    2.6e-05   24.2   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
  ------ inclusion threshold ------
      0.046   14.2   0.0       0.11   13.1   0.0    1.6  1  Glyco_tranf_2_4  Glycosyl transferase family 2
       0.11   12.0   0.0       0.16   11.4   0.0    1.2  1  Glyco_tranf_2_2  Glycosyltransferase like family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.7   0.0   1.9e-21   8.5e-18       3     100 ..       7      95 ..       5     113 .. 0.95

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 1.9e-21
                                    EEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SSE CS
                Glycos_transf_2   3 viptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatgdy 82 
                                    ++pt N   tl  tles+++        ii+vD +S+D+t ei++++     ++++++ e n  +++a+ +g++aa +++
  gi|116754962|ref|YP_844080.1|   7 IVPTWNSGTTLGITLESIKKY--GNPNNIIIVDRNSEDNTLEIARRY-----GCKILTSESN--LGTARIEGAKAAETEL 77 
                                    9*******************8..************************.....9*******99..**************** PP

                                    EEEEESSEEE-TTHHHHH CS
                Glycos_transf_2  83 ilflDaDdepdpdwlekl 100
                                    i f+D+D+e +++w e l
  gi|116754962|ref|YP_844080.1|  78 IGFVDSDVELTDGWRELL 95 
                                    ************997655 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 !   24.2   0.0   5.8e-09   2.6e-05       7     103 ..       7      90 ..       3     113 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 5.8e-09
                Glyco_tranf_2_3   7 lVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnealrav 86 
                                    +Vpt+n  ++lg +les+ ++   +  +++v+ +s++ tle a    ++++    ++++ + nlg+ ++     e+ +a+
  gi|116754962|ref|YP_844080.1|   7 IVPTWNSGTTLGITLESIKKYG-NPNNIIIVDRNSEDNTLEIA----RRYGC---KILTSESNLGT-AR----IEGAKAA 73 
                                    8*******************54.44677888888888888766....57865...57888888993.44....57***** PP

                Glyco_tranf_2_3  87 ksdlvllvDdDtvvePd 103
                                    +++l+ +vD+D+ + ++
  gi|116754962|ref|YP_844080.1|  74 ETELIGFVDSDVELTDG 90 
                                    ************99776 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.4e-05      0.11       5      57 ..      15      67 ..      12      87 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.4e-05
                Glyco_tranf_2_4  5 diLpeflahhlalgf.drilvydndstDgtrailkelpevkllhvdksyederr 57
                                    +L+ +l+ ++++g  ++i+++d +s+D+t +i ++ + +k+l+++++   +r 
  gi|116754962|ref|YP_844080.1| 15 TTLGITLESIKKYGNpNNIIIVDRNSEDNTLEIARR-YGCKILTSESNLGTARI 67
                                   567778888888886579***************999.58999888877765554 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.5e-05      0.16      24      92 ..      25      85 ..       7      96 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.5e-05
                Glyco_tranf_2_2 24 kyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGaskaesdlvlFlDaDc 92
                                   k y +  ++i+vd  S +++le  +     + l +  +       l+ ar  Ga+ ae++l+ F+D+D 
  gi|116754962|ref|YP_844080.1| 25 KKYGNPNNIIIVDRNSEDNTLEIAR-RYGCKILTS--ES-----NLGTARIEGAKAAETELIGFVDSDV 85
                                   4446666899999999999775443.344444444..33.....57999******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); 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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1922.12
//
Query:       gi|116754963|ref|YP_844081.1|  [L=366]
Description: glycosyl transferase, group 1 [Methanosaeta thermophila PT]
Scores for complete 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   0.2    7.8e-28   97.1   0.2    1.5  1  Glycos_transf_1  Glycosyl transferases group 1
    1.5e-23   83.7   0.0    3.2e-23   82.6   0.0    1.6  2  Glyco_trans_1_4  Glycosyl transferases group 1
    1.5e-15   57.6   0.0    4.5e-15   56.1   0.0    1.8  1  Glyco_transf_4   Glycosyltransferase Family 4
    1.1e-10   41.8   0.0    2.5e-10   40.6   0.0    1.6  1  Glyco_trans_1_2  Glycosyl transferases group 1
    7.3e-06   26.1   0.6    4.5e-05   23.5   0.4    2.4  2  Glyco_trans_4_2  Glycosyl transferase 4-like
    1.8e-05   25.2   0.0     0.0018   18.7   0.0    2.2  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
  ------ inclusion threshold ------
      0.021   13.7   0.0       0.14   11.0   0.0    2.1  2  Epimerase_2      UDP-N-acetylglucosamine 2-epimerase
      0.028   13.4   0.2       0.28   10.1   0.1    2.0  2  B56              Protein phosphatase 2A regulatory B subunit 


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 !   97.1   0.2   3.5e-31   7.8e-28      27     171 ..     201     341 ..     174     342 .. 0.92

  Alignments for each domain:
  == domain 1  score: 97.1 bits;  conditional E-value: 3.5e-31
                                    TTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHHCESEEEEEESSBSS- CS
                Glycos_transf_1  27 eKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleellknadifvlpsisEgfG 106
                                      g+++lik+++++k    pn+ l++  +g++ +el++ a++ +l++ vif+g v+  +    l  +di+ + s  Eg++
  gi|116754963|ref|YP_844081.1| 201 ADGLKYLIKSLKKIKCV-YPNAILLVTREGKYTAELREFAKKEGLEHAVIFTGDVD--NPYVPLLLSDIYTHISLGEGLP 277
                                    3699**********875.*************************************9..7788888899************ PP

                                    HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHHHHHHHHH CS
                Glycos_transf_1 107 ivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelrerlgenark 171
                                    i+llEAm+ g+p+ia+ +gg++e ++dg++Gllv+p   +++ae+++ ll+++e +e++g na+k
  gi|116754963|ref|YP_844081.1| 278 IALLEAMSMGKPIIATPVGGIPEAIEDGKNGLLVEPD-EAKIAEKVICLLRNKEIAEEIGLNAKK 341
                                    ************************************9.999*********************998 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       3.5   7.9e+03      58      80 ..     117     138 ..      74     158 .. 0.75
   2 !   82.6   0.0   1.4e-26   3.2e-23       3     134 .]     188     328 ..     186     328 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.5
                                    EEE---THHHHHHHH-SEEEE-- CS
                Glyco_trans_1_4  58 eftGfvedlaellaaadvfvaPs 80 
                                     ++ ++  l++ll+++d + + s
  gi|116754963|ref|YP_844081.1| 117 PVLKRI-ALQKLLEKCDYVTFVS 138
                                    455556.6777777777776666 PP

  == domain 2  score: 82.6 bits;  conditional E-value: 1.4e-26
                                    EEEEES..---GG.GTHHHHHHHHHHHH.H..HEEEEEES---...HHHHHHHT..T-T.TEEEE---THHHHHHHH-SE CS
                Glyco_trans_1_4   3 vilfvG..rleenvkgvdllleavpllrkk..dvrlvivGdgp.rpeeleelaa..gleerveftGfvedlaellaaadv 75 
                                    ++l +G  +l+ + +g+++l++ +++++    ++ l++  +g+   +el+e a+  gle+ v+ftG v++    l  +d+
  gi|116754963|ref|YP_844081.1| 188 ILLALGltALKYKADGLKYLIKSLKKIKCVypNAILLVTREGKyT-AELREFAKkeGLEHAVIFTGDVDNPYVPLLLSDI 266
                                    56666644554478**************44434888888888855.69*9988669**999*******666666778999 PP

                                    EEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH- CS
                Glyco_trans_1_4  76 fvaPs..egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLled 134
                                    +   s  eg++++llEam++g+p++at+vggi+e++  g+ngllv+p d++++ae+++ Ll++
  gi|116754963|ref|YP_844081.1| 267 YTHISlgEGLPIALLEAMSMGKPIIATPVGGIPEAIedGKNGLLVEP-DEAKIAEKVICLLRN 328
                                    9999999**************************************87.89**********986 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.1   0.0     2e-18   4.5e-15       1     168 [.      17     165 ..      17     167 .. 0.90

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 2e-18
                 Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvvtpgddgpleeevelvvrvprvplpllkrllrslaflrrlrrllkrekpDvvHahs 80 
                                    +GG+  +v+ L+++L +r ++V v   ++++p+ ++               k++ ++l+ l+++  ll ++kp v+H+h+
  gi|116754963|ref|YP_844081.1|  17 AGGIRSYVEGLVEELKKRDIDVKVAFKEGQDPENYK--------------IKNRNFILTKLLSAFYLLLKFKPNVIHSHG 82 
                                    59************************9998888888..............566677777777777888889******997 PP

                 Glyco_transf_4  81 ..paalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeatadelrerygvppek 158
                                      +++l+a++++ ++  +++l++t+H+         + ++l  l r  +++ll ++d v+ vS+++   + + +g++ ++
  gi|116754963|ref|YP_844081.1|  83 glYYYLLAGYFYKKL-FRCKLIYTFHTEP------EKDNKLPVLKRIALQKLLEKCDYVTFVSKKLETTVGDVWGLKFKN 155
                                    557888899999888.*************......58999**************************************** PP

                 Glyco_transf_4 159 itVipnGvDl 168
                                     ++ + G+D+
  gi|116754963|ref|YP_844081.1| 156 TVITYAGIDV 165
                                    *********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 !   40.6   0.0   1.1e-13   2.5e-10       9      91 ..     274     357 ..     262     358 .. 0.93

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 1.1e-13
                Glyco_trans_1_2   9 espnlrlfEaaacGafaltddaegleelftpgkevilfe.dleelaekiryllanpeerraiaeaarervlaehtydhra 87 
                                    e++   l+Ea+ +G ++++++  g++e +++gk ++l+e d++ +aek+  ll+n e +++i+ +a++ ++ ++++  ++
  gi|116754963|ref|YP_844081.1| 274 EGLPIALLEAMSMGKPIIATPVGGIPEAIEDGKNGLLVEpDEAKIAEKVICLLRNKEIAEEIGLNAKKTARDRFSWSAAV 353
                                    66677799************99********************************************************** PP

                Glyco_trans_1_2  88 eqll 91 
                                    +++l
  gi|116754963|ref|YP_844081.1| 354 NNIL 357
                                    *998 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.4     2e-08   4.5e-05      16     138 ..      27     137 ..      20     138 .. 0.74
   2 ?   -1.8   0.0       1.3   2.9e+03       2      32 ..     222     251 ..     221     270 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2e-08
                Glyco_trans_4_2  16 lakeLakrgyeVhvitpkkgakdeleaegihvhrlkvdrkg.pleylkafklkklikkikPDvvhahyakpy.gllgsla 93 
                                    l++eL+kr+++V+v+  +++   +   e++   ++k +r +   ++l+af    l+ k+kP v+h h    y  l+g++ 
  gi|116754963|ref|YP_844081.1|  27 LVEELKKRDIDVKVAFKEGQ---D--PENY---KIK-NRNFiLTKLLSAFY---LLLKFKPNVIHSHGGLYYyLLAGYFY 94 
                                    7899***********99888...2..3333...444.44454556666665...6899**********987735566666 PP

                Glyco_trans_4_2  94 arlsgvipvvlsvwGldvlkfpkksk.lkklllklalkkatkvist 138
                                    ++l + ++++++++ +   ++++k + lk+++l+ +l+k + v++ 
  gi|116754963|ref|YP_844081.1|  95 KKLFR-CKLIYTFH-TE-PEKDNKLPvLKRIALQKLLEKCDYVTFV 137
                                    66666.********.32.444444447***************9986 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.3
                Glyco_trans_4_2   2 illlanlssvhtlrlakeLakrgyeVhvitp 32 
                                    ill++ +   +t +l ++++k+g+e +vi  
  gi|116754963|ref|YP_844081.1| 222 ILLVTRE-GKYTAELREFAKKEGLEHAVIFT 251
                                    5555554.48999999999999999877765 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0     8e-07    0.0018       1     153 [.      18     155 ..      18     162 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 8e-07
                Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgapeleedgvrvhrlpvprrpspladlaalralrrllrqrrerpdvvhah 80 
                                    gGi+ yv+ l+++L +r  +V v      +g+++++  ++  +++ +          + l a+  ll   +++p v+h+h
  gi|116754963|ref|YP_844081.1|  18 GGIRSYVEGLVEELKKRDIDVKVAFK---EGQDPEN-YKIKNRNFILT---------KLLSAFYLLL---KFKPNVIHSH 81 
                                    67777777777777777777777665...2222111.13333333332.........4456677777...********** PP

                Glyco_trans_4_4  81 s..ptaglaarlarrrrgiplvvtlhglllrrgsgavrrlyralerrllrradavlvvseaeaeelra.lgvpadr 153
                                    +  ++  la+ + +   + +l++t+h+    +    ++ l r + + ll  +d v+ vs  +  ++ + +g+   +
  gi|116754963|ref|YP_844081.1|  82 GglYYYLLAGYFYKKLFRCKLIYTFHTEPEKDN--KLPVLKRIALQKLLEKCDYVTFVSKKLETTVGDvWGLKFKN 155
                                    97445888888888889*********9644333..344444555889************99999998888877655 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 ?    0.4   0.0       0.1   2.3e+02     215     255 ..      99     138 ..      94     190 .. 0.76
   2 ?   11.0   0.0   6.1e-05      0.14     273     322 ..     282     331 ..     196     359 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.1
                                    --EEEEE--..HHHHHHHHHHHHH-TTEEEE----HHHHHH CS
                    Epimerase_2 215 dvevvvpvhnnprtrkrlleeleelenvtlieplgyldfls 255
                                    +++++++ h  p+  ++l   l++++  +l+e  +y+ f+s
  gi|116754963|ref|YP_844081.1|  99 RCKLIYTFHTEPEKDNKLP-VLKRIALQKLLEKCDYVTFVS 138
                                    56899****9999999995.566555556666666666654 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 6.1e-05
                                    HHHHCT--EEESSSS-S-THHHHTTSEEE.-TT-HHHHHHHHHHHCT-..- CS
                    Epimerase_2 273 EapslgvpvvnlReeteRpegveagtnvl.vgtdkeeIvaaleklledkke 322
                                    Ea+s+g+p++     +  pe++e g+n l v++d+++I +++  ll++k+ 
  gi|116754963|ref|YP_844081.1| 282 EAMSMGKPIIAT-PVGGIPEAIEDGKNGLlVEPDEAKIAEKVICLLRNKEI 331
                                    9**********9.99**************9************999988333 PP

>> B56  Protein phosphatase 2A regulatory B subunit (B56 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00013      0.28      15      53 ..      92     131 ..      90     148 .. 0.87
   2 ?    0.9   0.0      0.08   1.8e+02     316     343 ..     314     341 ..     309     345 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00013
                            B56  15 lflkklkqCsvvfdF.ndpssdlkekeiKretLkelveyv 53 
                                     f kkl  C+ ++ F ++p++d k    Kr +L++l+e  
  gi|116754963|ref|YP_844081.1|  92 YFYKKLFRCKLIYTFhTEPEKDNKLPVLKRIALQKLLEKC 131
                                    699*********************************9865 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.08
                            B56 316 phfqVaeralylwnnekivnlisensee 343
                                    + +++ae++++l+ n++i++ i  n+++
  gi|116754963|ref|YP_844081.1| 314 DEAKIAEKVICLLRNKEIAEEIGLNAKK 341
                                    6789**************9999888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); 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: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2889.42
//
Query:       gi|116754964|ref|YP_844082.1|  [L=322]
Description: glycosyl transferase, group 1 [Methanosaeta thermophila PT]
Scores for complete 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    3.4e-25   88.6   0.0    1.4  1  Glycos_transf_1  Glycosyl transferases group 1
    1.8e-22   80.2   0.1    3.3e-22   79.4   0.1    1.3  1  Glyco_trans_1_4  Glycosyl transferases group 1
    7.7e-10   39.0   0.0    1.4e-09   38.2   0.0    1.5  1  Glyco_transf_4   Glycosyltransferase Family 4
    0.00024   21.5   0.0    0.00047   20.5   0.0    1.6  1  Glyco_trans_1_2  Glycosyl transferases group 1
  ------ inclusion threshold ------
      0.012   16.1   0.1      0.022   15.2   0.0    1.6  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.6   0.0   9.5e-29   3.4e-25       8     168 ..     146     299 ..     142     302 .. 0.84

  Alignments for each domain:
  == domain 1  score: 88.6 bits;  conditional E-value: 9.5e-29
                                    HTTTTTT-EEEEEESS....-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES..STTHHHHHHHHHHHCTTCGGGEEECCH CS
                Glycos_transf_1   8 klgknekkkiilsvgr....lekeKgvdllikafallkkqlnpnvklviaG.ngeeekelkklaeelelsdnviflgevs 82 
                                     ++k ek+ ++l+v+     + k Kg+d++++a+ ll     pnvk++i+G  g+        +   +  +nv++lg+vs
  gi|116754964|ref|YP_844082.1| 146 FHPKGEKDDLVLTVASgstnVIKLKGLDTFVEAAYLL-----PNVKFLIIGvRGDV-----LNILRSKSPENVKILGRVS 215
                                    566677777888877511114566***********87.....8********54444.....3444555789********* PP

                                    SSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHH CS
                Glycos_transf_1  83 redleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelr 162
                                    r++l e++++a+++++ s+ E+fG++l EAma+g+  ++++ g ++evv d  tG+ v+ ++ +a aeair ++ +e+++
  gi|116754964|ref|YP_844082.1| 216 RDELVECYQRAKVYCQLSYVESFGMALAEAMACGCVPVVTDRGALPEVVGD--TGFYVPYGDEKATAEAIRMAMVSEKSP 293
                                    *************************************************87..67*******************999998 PP

                                    HHHHHH CS
                Glycos_transf_1 163 erlgen 168
                                    ++ +e+
  gi|116754964|ref|YP_844082.1| 294 RDRIER 299
                                    887775 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.4   0.1   9.1e-26   3.3e-22       8     129 ..     162     284 ..     155     288 .. 0.85

  Alignments for each domain:
  == domain 1  score: 79.4 bits;  conditional E-value: 9.1e-26
                                    S---G.G.GTHHHHHHHHHHHH.HHEEEEEES.---...HHHHHHHTT-T.TEEEE---..THHHHHHHH-SEEEE--.. CS
                Glyco_trans_1_4   8 Grlee.nvkgvdllleavpllrkkdvrlvivG.dgp.rpeeleelaagleerveftGfv..edlaellaaadvfvaPs.. 80 
                                    G+ +  + kg+d ++ea+ ll   +v+++i+G +g+   + l++   +  e+v+++G+v  ++l e++++a+v++  s  
  gi|116754964|ref|YP_844082.1| 162 GSTNViKLKGLDTFVEAAYLLP--NVKFLIIGvRGDvL-NILRS---KSPENVKILGRVsrDELVECYQRAKVYCQLSyv 235
                                    45522478*************9..89******333333.24443...44589*******9777***************** PP

                                    ---SHHHHHHHHTT-EEEE-TGGGTTT--TTSSEE--TT-HHHHHHHHH CS
                Glyco_trans_1_4  81 egfglkllEamaaglpvVatdvggiaevvgengllvppgdpealaeail 129
                                    e+fg++l Eama+g+  V+td g+++evvg++g+ vp gd++a aeai 
  gi|116754964|ref|YP_844082.1| 236 ESFGMALAEAMACGCVPVVTDRGALPEVVGDTGFYVPYGDEKATAEAIR 284
                                    **********************99***99******************97 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   0.0   3.8e-13   1.4e-09     120     170 .]      97     145 ..       6     145 .. 0.65

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 3.8e-13
                 Glyco_transf_4 120 srllralerrllrradrviavSeatadelrerygvppekitVipnGvDler 170
                                      + r++   +l +ad+v+avS++t++e+++  + +p++++V++nGvD+e+
  gi|116754964|ref|YP_844082.1|  97 GWIKRKYTDLALENADAVLAVSQFTREEVLK--RTKPRRLEVVYNGVDTEK 145
                                    223344455569*******************..55689***********95 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 !   20.5   0.0   1.3e-07   0.00047       8      75 ..     230     303 ..     196     317 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.3e-07
                Glyco_trans_1_2   8 s.....espnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpee.rraiaeaare 75 
                                    +     es+ + l Ea+acG++ +++d+ +l+e +  g++++++   d++  ae+ir ++ +++  r++i +  r 
  gi|116754964|ref|YP_844082.1| 230 CqlsyvESFGMALAEAMACGCVPVVTDRGALPEVV--GDTGFYVPygDEKATAEAIRMAMVSEKSpRDRIERSFRI 303
                                    055555999************8888889******9..6667777777***********999776636666555555 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   6.2e-06     0.022     114     160 .]      95     140 ..      24     140 .. 0.83
   2 ?   -2.9   0.0       2.3   8.2e+03      28      62 ..     268     302 ..     239     313 .. 0.53

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6.2e-06
                Glyco_trans_4_4 114 avrrlyralerrllrradavlvvseaeaeelralgvpadrvvvvpng 160
                                     ++++ r   +++l +adavl+vs++ +ee+  +  p  r++vv ng
  gi|116754964|ref|YP_844082.1|  95 TQGWIKRKYTDLALENADAVLAVSQFTREEVLKRTKP-RRLEVVYNG 140
                                    4555557778899*******************99776.6*****998 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.3
                Glyco_trans_4_4  28 papgapeleedgvrvhrlpvprrpspladlaalra 62 
                                    + ++++  e + ++ +r+ +  + sp+ + +++++
  gi|116754964|ref|YP_844082.1| 268 GFYVPYGDEKATAEAIRMAMVSEKSPRDRIERSFR 302
                                    33333334445555555555555555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2287.21
//
Query:       gi|116754965|ref|YP_844083.1|  [L=325]
Description: glycosyl transferase, group 1 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-07   32.0   0.2    2.5e-07   30.9   0.0    1.6  2  Glyco_transf_4   Glycosyltransferase Family 4
    9.8e-07   29.3   0.1    3.2e-06   27.7   0.0    1.8  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    2.1e-05   24.1   0.0    3.8e-05   23.3   0.0    1.4  1  Glycos_transf_1  Glycosyl transferases group 1
     0.0054   16.8   0.0      0.011   15.8   0.0    1.6  1  Glyco_trans_4_2  Glycosyl transferase 4-like


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 !   30.9   0.0   5.6e-11   2.5e-07      55     164 ..      38     146 ..       2     147 .. 0.83
   2 ?   -2.3   0.0      0.88   3.9e+03      98      98 ..     214     214 ..     175     254 .. 0.62

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 5.6e-11
                 Glyco_transf_4  55 lrslaflrrlrrllkrekpDvvHahspaalgaallalrr.rlgiplVltvHglyekrllkarlkplsrllralerrllrr 133
                                     + ++ +r++r ++ +e+pD+vH  + + +++ ++ ++r     +l++ + +++      ++ + ++ + +++er+l+ +
  gi|116754965|ref|YP_844083.1|  38 VNWISIARKARGIVLKERPDIVHLFNVPDVIYHWIPSLRgSGYRRLIYDYRSPWGVETQLRFGSIAKSACERFERQLAEA 117
                                    4445668999****************9999999999999766678999999999866677788899999999******** PP

                 Glyco_transf_4 134 adrviavSeatadelrerygvppekitVipn 164
                                    ad +++v   +++  ++ y  p + i+Vipn
  gi|116754965|ref|YP_844083.1| 118 ADVITTVNTPLKEKAMS-YA-PGKEIRVIPN 146
                                    *****************.88.89*******9 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.88
                 Glyco_transf_4  98 p 98 
                                     
  gi|116754965|ref|YP_844083.1| 214 A 214
                                    2 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 !   27.7   0.0   7.2e-10   3.2e-06      48     159 ..      33     146 ..       6     147 .. 0.81
   2 ?   -1.5   0.0      0.67     3e+03      35      50 ..     222     238 ..     201     268 .. 0.54

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 7.2e-10
                Glyco_trans_4_4  48 prrpspladlaalralrrllrqrrerpdvvhahsptaglaarlarrrrg...iplvvtlhglllrrg....sgavrrlyr 120
                                    pr  +++++ + +r +r+++   +erpd+vh+++ +  ++ ++ +  rg    +l++++++ ++++     ++ ++++  
  gi|116754965|ref|YP_844083.1|  33 PRF-DTVNWISIARKARGIV--LKERPDIVHLFNVPDVIYHWIPS-LRGsgyRRLIYDYRSPWGVETqlrfGSIAKSACE 108
                                    333.57888999999****9..************99999999999.5552335579999986655443556666788889 PP

                Glyco_trans_4_4 121 alerrllrradavlvvseaeaeelralgvpadrvvvvpn 159
                                    ++er l+  ad++++v + + e++  + +p   ++v+pn
  gi|116754965|ref|YP_844083.1| 109 RFERQLAEAADVITTVNTPLKEKAMSY-APGKEIRVIPN 146
                                    99*********************9887.6778******9 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.67
                Glyco_trans_4_4  35 leedgvrvhrl.pvprr 50 
                                    ++++ vr  r+  +prr
  gi|116754965|ref|YP_844083.1| 222 RVAALVRRARIcIIPRR 238
                                    33444444443123333 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 !   23.3   0.0   8.4e-09   3.8e-05      13     101 ..     160     238 ..     151     261 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 8.4e-09
                                    TT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHHC CS
                Glycos_transf_1  13 ekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleellkn 92 
                                    e ++++++vgr+ ++ g+d l++++++l+     +  + i+G+g+      ++   +   +nv+ lg ++++++ +l ++
  gi|116754965|ref|YP_844083.1| 160 EPENVVIFVGRVCEQEGIDSLLRVARDLP-----DQEFWIVGGGPF-----AWWYLRRKTENVKALGWQPHSRVAALVRR 229
                                    6799**********************986.....559*****9998.....888889999******************** PP

                                    ESEEEEEES CS
                Glycos_transf_1  93 adifvlpsi 101
                                    a i ++p +
  gi|116754965|ref|YP_844083.1| 230 ARICIIPRR 238
                                    *****9965 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 !   15.8   0.0   2.4e-06     0.011      54     135 ..      34     121 ..       2     125 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.4e-06
                Glyco_trans_4_2  54 rkgpleylk.afklkklikkikPDvvhahyakpygllgslaarlsgvipvv...lsvwGldv.lkfpkksk.lkklllkl 127
                                    r +++++++ a+k + ++ k+ PD+vh+++++++++++    r sg+ +++    s wG  + l+f+  +k + +  ++ 
  gi|116754965|ref|YP_844083.1|  34 RFDTVNWISiARKARGIVLKERPDIVHLFNVPDVIYHWIPSLRGSGYRRLIydyRSPWGVETqLRFGSIAKsACERFERQ 113
                                    44588999966799**********************99777778888888844445577766666665553333334444 PP

                Glyco_trans_4_2 128 alkkatkv 135
                                    +++ a+++
  gi|116754965|ref|YP_844083.1| 114 LAEAADVI 121
                                    44455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.24s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2340.91
//
Query:       gi|116754966|ref|YP_844084.1|  [L=373]
Description: glycosyl transferase, group 1 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-14   53.3   0.0    7.2e-14   52.4   0.0    1.5  1  Glyco_trans_1_4  Glycosyl transferases group 1
    8.2e-12   45.0   0.0    1.2e-11   44.4   0.0    1.3  1  Glycos_transf_1  Glycosyl transferases group 1
    1.3e-10   41.5   0.1    2.8e-10   40.5   0.1    1.5  1  Glyco_transf_4   Glycosyltransferase Family 4
    1.5e-10   41.8   0.0    3.1e-10   40.7   0.0    1.5  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    1.8e-09   37.9   0.0    3.7e-09   36.8   0.0    1.5  1  Glyco_trans_1_2  Glycosyl transferases group 1
  ------ inclusion threshold ------
       0.12   12.8   0.1       0.33   11.4   0.1    1.8  1  DUF4350          Domain of unknown function (DUF4350)


Domain annotation for each model (and alignments):
>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.0   2.4e-17   7.2e-14       3     133 ..     201     339 ..     199     340 .. 0.85

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 2.4e-17
                                    EEEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---.....HHHHHHHT..T-T.TEEEE---..THHHHHHHH-SE CS
                Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkkdvrlvivGdgp.rp..eeleelaa..gleerveftGfv..edlaellaaadv 75 
                                    vi++vG+l e +  ++ ++ a+p l    v+l++vG +   +  e+++++a+  g+ erv+ftG v  ++l ++++a+d+
  gi|116754966|ref|YP_844084.1| 201 VIGYVGSL-EYWVDLETVVSALPDLD---VTLLVVGPSLfTDygERIKDMAErlGVGERVIFTGAVpyAELGRYISAMDI 276
                                    899*****.66699***********9...99*****543433557788777568999*********9999********** PP

                                    EEE--......-.--SHHHHHHHHTT-EEEE-TGGGTTT--TTSSEE--TT-HHHHHHHHHHHHH CS
                Glyco_trans_1_4  76 fvaPs......e.gfglkllEamaaglpvVatdvggiaevvgengllvppgdpealaeailrLle 133
                                     ++P+      e   g k+  ++a+g+pv +t++  +++++g++ +  +  d e+++ ++ r+le
  gi|116754966|ref|YP_844084.1| 277 GLNPLrmmkknEyAAGGKIFNYLACGRPVLTTRMLSLERLLGDSLYYYD--DRESFISQVKRILE 339
                                    *****8776553788******************9887887798766666..9********99997 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 !   44.4   0.0   4.2e-15   1.2e-11      12     170 ..     196     352 ..     186     354 .. 0.93

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 4.2e-15
                                    TTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES....STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHH CS
                Glycos_transf_1  12 nekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaG...ngeeekelkklaeelelsdnviflgevsredlee 88 
                                      +  +i +vg le++ ++++++ a+++l      +v l+++G     ++ +++k++ae l+++++vif+g v++ +l  
  gi|116754966|ref|YP_844084.1| 196 GLEGDVIGYVGSLEYWVDLETVVSALPDL------DVTLLVVGpslFTDYGERIKDMAERLGVGERVIFTGAVPYAELGR 269
                                    556789*********************76......8**********889999**************************** PP

                                    HHHCESEEEEEESS.....BSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHH CS
                Glycos_transf_1  89 llknadifvlpsis.....EgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelre 163
                                    ++++ di + p ++      + G  + +++a+g pv+++ +  +  ++ d    + ++    e+++ +++++le++++++
  gi|116754966|ref|YP_844084.1| 270 YISAMDIGLNPLRMmkkneYAAGGKIFNYLACGRPVLTTRMLSLERLLGDSL--YYYDDR--ESFISQVKRILESPQDQR 345
                                    *************9****7799****************************99..888888..***************999 PP

                                    HHHHHHH CS
                Glycos_transf_1 164 rlgenar 170
                                    r++e a+
  gi|116754966|ref|YP_844084.1| 346 RYREIAE 352
                                    9999886 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   0.1   9.3e-14   2.8e-10      17     169 ..      28     181 ..      25     182 .. 0.67

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 9.3e-14
                 Glyco_transf_4  17 rrGheVtvvtpgddgpleeevelvvrvprvplpllkrllr...slaflrrlrrllkre..kpDvvHahspaalgaallal 91 
                                    +  heV+v+ ++ ++  ++  ++++r       ++k       +++++++  r+++    + Dv+ + +  + + a    
  gi|116754966|ref|YP_844084.1|  28 AERHEVQVLHFELSKFRDNS-PRWTRCSLLKAGSSKAEDPsvyYITSALSHLRVIRDAarDSDVILSANILPSFMAN--- 103
                                    4569*****99999999999.555555555554444433300133333344444444467*****776666655442... PP

                 Glyco_transf_4  92 rrrlgiplVltvHglye.krllkarlkplsrllralerrl....lrradrviavSeatadelrerygvppekitVipnGv 166
                                    +  ++ p+V+ + ++ e +   ++  +++ r+++   r +    lr+a++vi+v+++++++lr   gv+   +++ipnGv
  gi|116754966|ref|YP_844084.1| 104 L--TDTPVVFDYLDHLEeSASIYYPGSLFGRAVKLGVRAItrynLRHARAVITVTQELKEYLRN-IGVRD--VEIIPNGV 178
                                    2..7*****99877776644444444444444444444444556********************.**986..******** PP

                 Glyco_transf_4 167 Dle 169
                                    D++
  gi|116754966|ref|YP_844084.1| 179 DTS 181
                                    *97 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   0.0     1e-13   3.1e-10      16     160 .]      28     177 ..      25     177 .. 0.68

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 1e-13
                Glyco_trans_4_4  16 arGheVtvltpapapgapeleedgvrvhrlpvprrp.spladla..alralrrll...rqrrerpdvvhahsptaglaar 89 
                                    a+ heV+vl  +    ++    +  r +r+ +  ++ s   d++  +++ + + l   r +++  dv+ + ++   l+  
  gi|116754966|ref|YP_844084.1|  28 AERHEVQVLHFELSKFRD----NSPRWTRCSLLKAGsSKAEDPSvyYITSALSHLrviRDAARDSDVILSANI---LPSF 100
                                    455888888754444444....4444445543333212333333224444444444557789**********9...6666 PP

                Glyco_trans_4_4  90 larrrrgiplvvtlhgll......lrrg..sgavrrly.ralerrllrradavlvvseaeaeelralgvpadrvvvvpng 160
                                     a   +++p+v+++ ++l      + +g   g++  l  ra+ r+ lr+a+av++v++++ e+lr  gv+  +v+++png
  gi|116754966|ref|YP_844084.1| 101 MAN-LTDTPVVFDYLDHLeesasiYYPGslFGRAVKLGvRAITRYNLRHARAVITVTQELKEYLRNIGVR--DVEIIPNG 177
                                    788.889********9885555544455554444444469******************************..899****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 !   36.8   0.0   1.2e-12   3.7e-09       1      88 [.     276     361 ..     276     367 .. 0.83

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 1.2e-12
                Glyco_trans_1_2   1 ivLnpsrs.....espnlrlfEaaacGafaltddaegleelftpgkevilfedleelaekiryllanpeerraiaeaare 75 
                                    i+Lnp r      +   +++f ++acG+++lt++  +le+l+  g+++ +++d e+++ ++++ l++p++ r+     ++
  gi|116754966|ref|YP_844084.1| 276 IGLNPLRMmkkneYAAGGKIFNYLACGRPVLTTRMLSLERLL--GDSLYYYDDRESFISQVKRILESPQDQRR-----YR 348
                                    689988887666444668***********************9..889*********************99775.....66 PP

                Glyco_trans_1_2  76 rvlaehtydhrae 88 
                                    ++ ++++++  a+
  gi|116754966|ref|YP_844084.1| 349 EIAERYDWRALAA 361
                                    6666667766655 PP

>> DUF4350  Domain of unknown function (DUF4350)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00011      0.33      25      67 ..     215     258 ..     209     260 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                        DUF4350  25 rkpfdalegedgtllvvapdlrlte.eelaallewvarGntlvl 67 
                                    +++ +al++ d tllvv+p l +++ e+++++ e++  G +++ 
  gi|116754966|ref|YP_844084.1| 215 ETVVSALPDLDVTLLVVGPSLFTDYgERIKDMAERLGVGERVIF 258
                                    567788899999********66666**********999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2607.01
//
Query:       gi|116754967|ref|YP_844085.1|  [L=374]
Description: nucleotidyl transferase [Methanosaeta thermophila PT]
Scores for complete 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   67.9  16.8    8.9e-08   31.6   0.5    5.7  6  Hexapep          Bacterial transferase hexapeptide (six repea
    1.1e-18   67.7   0.0    1.4e-18   67.4   0.0    1.1  1  NTP_transferase  Nucleotidyl transferase
    2.9e-07   31.0   0.1    5.8e-07   30.0   0.1    1.5  1  NTP_transf_3     MobA-like NTP transferase domain
    0.00016   21.3  18.4     0.0027   17.4   1.5    5.3  4  Hexapep_2        Hexapeptide repeat of succinyl-transferase
  ------ inclusion threshold ------
      0.013   13.7   1.4      0.028   12.6   1.4    1.4  1  DUF4954          Domain of unknown function (DUF4954)
       0.42    9.5   1.9        2.2    7.2   0.6    2.1  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 ?   -2.9   0.0       2.2   6.7e+03      23      30 ..      98     105 ..      98     105 .. 0.83
   2 !   15.4   0.2   3.7e-06     0.011      10      36 .]     217     243 ..     216     243 .. 0.93
   3 !   31.6   0.5     3e-11   8.9e-08       3      34 ..     228     259 ..     226     261 .. 0.94
   4 !   17.0   0.1   1.2e-06    0.0036       1      35 [.     262     295 ..     262     296 .. 0.92
   5 !   13.2   0.1   1.8e-05     0.054       8      34 ..     286     311 ..     281     318 .. 0.54
   6 !   18.3   0.7   4.5e-07    0.0013       1      36 []     330     365 ..     330     365 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.2
                                    -TTEEEET CS
                        Hexapep  23 GdnvkIga 30 
                                    Gd+v++ga
  gi|116754967|ref|YP_844085.1|  98 GDYVILGA 105
                                    89999987 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 3.7e-06
                                    E-TTEEEETTEEE-TTEEEETTEEEES CS
                        Hexapep  10 IgpfaviggnVkIGdnvkIgagvvigg 36 
                                    I  ++vi+g V +G+++ I +g++i g
  gi|116754967|ref|YP_844085.1| 217 IEDGVVIRGQVSLGEGSLIRSGSYIIG 243
                                    889*********************975 PP

  == domain 3  score: 31.6 bits;  conditional E-value: 3e-11
                                    EEETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
                        Hexapep   3 vIGsnvlIgpfaviggnVkIGdnvkIgagvvi 34 
                                     +G+++lI+++++i g+V IG+++ Ig++v+i
  gi|116754967|ref|YP_844085.1| 228 SLGEGSLIRSGSYIIGPVLIGEGCDIGPNVTI 259
                                    68*****************************9 PP

  == domain 4  score: 17.0 bits;  conditional E-value: 1.2e-06
                                    TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                        Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                    st+IG+ v +g+f+ i  n ++ ++++Ig+ +vi 
  gi|116754967|ref|YP_844085.1| 262 STTIGDSVRVGSFTEI-RNSILMRGSRIGSMSVIS 295
                                    699*************.7777************96 PP

  == domain 5  score: 13.2 bits;  conditional E-value: 1.8e-05
                                    EEE-TTEEEETTEEE-TTEEEETTEEE CS
                        Hexapep   8 vlIgpfaviggnVkIGdnvkIgagvvi 34 
                                    + Ig+ +vi ++ +IG+++++g  + i
  gi|116754967|ref|YP_844085.1| 286 SRIGSMSVI-SDSVIGEDCCLGDMCLI 311
                                    455555555.44445555555555444 PP

  == domain 6  score: 18.3 bits;  conditional E-value: 4.5e-07
                                    TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                        Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36 
                                    ++v G+ v+ g+ +  ++  ++G+ +kIg+gv+i+g
  gi|116754967|ref|YP_844085.1| 330 GAVMGDSVVAGSRVLMMPCSVVGSSAKIGSGVTIRG 365
                                    5899******************************86 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.4   0.0   4.6e-22   1.4e-18      25     232 ..       2     192 ..       1     206 [. 0.87

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 4.6e-22
                                    SEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEESS--BGGHHHHHTHHHHTTSSE.. CS
                NTP_transferase  25 vpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialepegkgtAdAvalaaelledeksde 104
                                    +p ++  + +++++ +l+++gi+e iv +  +++++v +++++g kfg ++++++++e+ gtA+A++ a+e ++d++   
  gi|116754967|ref|YP_844085.1|   2 LPLANM-PFMEHVVRALVDNGIDE-IVAVVGYQKERVMDYFEDGVKFGARITYVFQEERLGTAHALRRAQEHIDDQF--- 76 
                                    566666.99***************.6677779999***************************************888... PP

                                    EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECTTSBEEEEECS-SSHSHCSEECCSEEEEET CS
                NTP_transferase 105 lvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvieadeegrverfvEKPkeakaselassGiYvfns 184
                                      lv++gD + +   ++av +  +++   + +++   +e a +yGv  +d+ + v+++ EKP +a  + ++++G Y   +
  gi|116754967|ref|YP_844085.1|  77 --LVVNGDNILD---SRAVGDLLSADG--DYVILGALREHAGDYGVLVVDG-DVVKQIHEKPGRAC-AGIVNTGAYKMMP 147
                                    ..9********9...778888777777..677778888999********98.59**********99.77*********** PP

                                    THHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEEX CS
                NTP_transferase 185 evllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsDv 232
                                    ++++++ +    ++rg  +it++l +++e+g +   ++ k+   W D 
  gi|116754967|ref|YP_844085.1| 148 DIFEEIPR-TPISERGGYDITQTLCQMMERGVKIRTVVTKA--IWGDA 192
                                    ******65.77788899999999999999998887777777..69885 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 !   30.0   0.1     2e-10   5.8e-07      18     110 ..       1      96 [.       1     131 [. 0.81

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 2e-10
                                    HHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHHTTC.....TS-EEE-TTSS-SHHHHHHHHHHHH.SSSCEE CS
                   NTP_transf_3  18 llplggkpllervldalraagvdevvvvggd..eevlaalarl.....gvrvvededpgkgplaslaaalraaadadavl 90 
                                    +lpl++ p++e+v++al + g+de+v v+g+  e v +++++      ++++v +e +  g++++l+ a +++  +d++l
  gi|116754967|ref|YP_844085.1|   1 MLPLANMPFMEHVVRALVDNGIDEIVAVVGYqkERVMDYFEDGvkfgaRITYVFQE-ERLGTAHALRRAQEHI--DDQFL 77 
                                    699**************************996556777776555554456677776.589************9..7**** PP

                                    EEETT-TT--HHHHHHHHHC CS
                   NTP_transf_3  91 vlacDmPlltpelverllaa 110
                                    v+ +D +l ++ +v  ll a
  gi|116754967|ref|YP_844085.1|  78 VVNGDNIL-DSRAVGDLLSA 96 
                                    ******76.99999998886 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 !    5.9   0.1    0.0035        11      15      32 ..     222     241 ..     217     242 .. 0.88
   2 !   17.4   1.5   9.2e-07    0.0027       1      27 [.     244     272 ..     244     273 .. 0.94
   3 !    4.5   1.4    0.0099        30      16      31 ..     299     316 ..     284     319 .. 0.62
   4 ?    0.9   0.1      0.13   3.9e+02      20      32 ..     351     363 ..     349     364 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0035
                                    EE.S.EEE-TT-EE-TT-EE CS
                      Hexapep_2  15 gi.G.vslGdncvvgaGvvi 32 
                                    +i G vslG+++ + +G++i
  gi|116754967|ref|YP_844085.1| 222 VIrGqVSLGEGSLIRSGSYI 241
                                    46777**************8 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 9.2e-07
                                    .EEE-TT-EE-TT-EE..SEEE-TT-EE- CS
                      Hexapep_2   1 pviIGdnCliGanagi..GvslGdncvvg 27 
                                    pv IG+ C iG+n +i   +++Gd + vg
  gi|116754967|ref|YP_844085.1| 244 PVLIGEGCDIGPNVTIlpSTTIGDSVRVG 272
                                    899************9999******9998 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.0099
                                    ES..EEE-TT-EE-TT-E CS
                      Hexapep_2  16 iG..vslGdncvvgaGvv 31 
                                    iG    lGd c ++aG+ 
  gi|116754967|ref|YP_844085.1| 299 IGedCCLGDMCLIEAGSS 316
                                    223344777777777765 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.13
                                    E-TT-EE-TT-EE CS
                      Hexapep_2  20 lGdncvvgaGvvi 32 
                                    +G  +++g+Gv+i
  gi|116754967|ref|YP_844085.1| 351 VGSSAKIGSGVTI 363
                                    5677788888876 PP

>> DUF4954  Domain of unknown function (DUF4954)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.4   9.3e-06     0.028     193     257 ..     242     308 ..     208     332 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.3e-06
                        DUF4954 193 igdyatiegasklengtinSske..apveiGegViledfiissGskikdgavisrcfvGqavklkkq 257
                                    ig++   eg++   n ti  s++  + v++G+  +++++i++ Gs+i   +vis++++G+ + l+  
  gi|116754967|ref|YP_844085.1| 242 IGPVLIGEGCDIGPNVTILPSTTigDSVRVGSFTEIRNSILMRGSRIGSMSVISDSVIGEDCCLGDM 308
                                    44444444555555666644332126899*********************************99865 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.07   2.1e+02     280     310 ..     222     253 ..     220     271 .. 0.80
   2 ?    7.2   0.6   0.00072       2.2     276     310 ..     277     311 ..     256     321 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.07
                     Fucokinase 280 vlessvsvgegsvieh.sslkgnvsigsnsiv 310
                                    v+ ++vs+gegs+i + s + g+v ig+++ +
  gi|116754967|ref|YP_844085.1| 222 VIRGQVSLGEGSLIRSgSYIIGPVLIGEGCDI 253
                                    688999********96256669*****99955 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00072
                     Fucokinase 276 vinSvlessvsvgegsviehsslkgnvsigsnsiv 310
                                    + nS+l  + ++g  svi +s +++++  g  +++
  gi|116754967|ref|YP_844085.1| 277 IRNSILMRGSRIGSMSVISDSVIGEDCCLGDMCLI 311
                                    77999999999999999999999999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2687.82
//
Query:       gi|116754968|ref|YP_844086.1|  [L=605]
Description: glucosamine--fructose-6-phosphate aminotransferase, isomerizing [Methanosaeta thermophila PT]
Scores for complete 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  157.2   0.2    3.2e-25   88.5   0.1    2.6  2  SIS       SIS domain
    9.9e-22   77.6   0.0    2.1e-21   76.5   0.0    1.5  1  GATase_6  Glutamine amidotransferase domain
      8e-16   58.1   0.0    1.6e-15   57.1   0.0    1.5  1  GATase_7  Glutamine amidotransferase domain
    5.6e-05   23.2   0.1     0.0037   17.3   0.0    2.7  2  SIS_2     SIS domain
  ------ inclusion threshold ------
      0.031   13.2   0.0      0.055   12.4   0.0    1.3  1  GATase_4  Glutamine amidotransferases class-II
       0.11   12.8   0.0         17    5.8   0.0    3.1  3  mCpol     minimal CRISPR polymerase 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 !   88.5   0.1   1.1e-28   3.2e-25       6     128 ..     295     414 ..     290     417 .. 0.96
   2 !   66.2   0.0   8.3e-22   2.5e-18       9     128 ..     468     585 ..     461     588 .. 0.92

  Alignments for each domain:
  == domain 1  score: 88.5 bits;  conditional E-value: 1.1e-28
                                    SEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHTTSEEEE CS
                            SIS   6 kriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelakergakiia 85 
                                    +r+ +l++Gtsy++++ +++ + +++g +v+ve ase++h+    +++++l+++is+sget+d+++a+++ak  g+k +a
  gi|116754968|ref|YP_844086.1| 295 QRVSILACGTSYHAGLLARYFFPRTAGLPVDVEVASEFQHM---QLRPGTLLVAISQSGETADTLMALKKAKTCGVKSLA 371
                                    6899*************************************...89********************************** PP

                                    EESSTTSHHHHHSSEEEEEEEECHCSSSHCHHHHHHHHHHHHH CS
                            SIS  86 ITdskgsplareadlalyinaepetlvastksltaqlaaldal 128
                                    IT+  gs++ +  d ++y++ +pe++va+tk+++ ql+al +l
  gi|116754968|ref|YP_844086.1| 372 ITNVVGSSITEIVDATIYTRCGPEIGVAATKTFVGQLVALFLL 414
                                    *************************************998666 PP

  == domain 2  score: 66.2 bits;  conditional E-value: 8.3e-22
                                    EEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHTTSEEEEEES CS
                            SIS   9 yvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelakergakiiaITd 88 
                                    +++G+   y+ia+e+alk++ei++i++e+++a+elkhg+lali+e+++v+++++ ge+  +  + +++++rg+++ia++ 
  gi|116754968|ref|YP_844086.1| 468 FFIGRDILYPIALEGALKMKEIAYIPAEGYPAGELKHGPLALITEGTPVVAFATCGEKIYS--NMKEVRARGGEVIAFAA 545
                                    89******************************************************97655..567************** PP

                                    STTSHHHHHSSEEEEEEEECHCSSSHCHHHHHHHHHHHHH CS
                            SIS  89 skgsplareadlalyinaepetlvastksltaqlaaldal 128
                                    + +  +a+ +d +++++    +  a + ++ aql+a++++
  gi|116754968|ref|YP_844086.1| 546 EGDREAAEITDTVVELPNTLPVFSAVLCTVGAQLLAYYTA 585
                                    *************999988888889999999999998765 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.5   0.0   6.9e-25   2.1e-21      11     133 ..      65     193 ..      51     194 .. 0.84

  Alignments for each domain:
  == domain 1  score: 76.5 bits;  conditional E-value: 6.9e-25
                       GATase_6  11 edevalaHvRlaivglaeeegaqPfpsedgrlllvhNGeiynykelreelpalkglafrsrsDtevllall..eelG... 85 
                                    e++++++H+R+a++g + +e a+P   ++g +++vhNG i+ny elre+l++ kg+ f s++D+evl++l+  ++ G   
  gi|116754968|ref|YP_844086.1|  65 EGSIGIGHTRWATHGRPSDENAHPH--TSGSIAVVHNGIIENYLELREQLRD-KGYVFTSETDSEVLAHLInyHYSGetn 141
                                    3469*************88888***..*************************.****************99884444455 PP

                       GATase_6  86 .......eevlerlrGmfafaiwdkrentlilardrlgvkplyyavdesglafas 133
                                           +++l+ +rG +a++++ +    l++ar +   +pl++++ +s  ++as
  gi|116754968|ref|YP_844086.1| 142 gdlavsvSRALKDVRGSYAIVVMASGIPYLVCARKD---SPLVIGIGGSSNYIAS 193
                                    57889999999**********999976677777443...7888887777777776 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.1   0.0   5.3e-19   1.6e-15      10     122 ..      83     199 ..      72     200 .. 0.90

  Alignments for each domain:
  == domain 1  score: 57.1 bits;  conditional E-value: 5.3e-19
                       GATase_7  10 eagaQPmvssedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea...........ewgeealerlnGmf 78 
                                    +++a P +   +g++++v+nG i Ny elre+L++kg+ f++++D+evl++l+++             + +al+ ++G++
  gi|116754968|ref|YP_844086.1|  83 DENAHPHT---SGSIAVVHNGIIENYLELREQLRDKGYVFTSETDSEVLAHLINYhysgetngdlaVSVSRALKDVRGSY 159
                                    44555555...699***************************************99*********99999*********** PP

                       GATase_7  79 AfaiwdeeekrlllaRDrlGikPLyygedkgdallfaSelkall 122
                                    A++++ +    l++aR      PL +g   g++ ++aS + all
  gi|116754968|ref|YP_844086.1| 160 AIVVMASGIPYLVCARK---DSPLVIGIG-GSSNYIASDVPALL 199
                                    ****************9...59*******.89*******99997 PP

>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.033        99      38      60 ..     299     322 ..     293     329 .. 0.89
   2 !   17.3   0.0   1.2e-06    0.0037      97     137 ..     333     373 ..     324     374 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.033
                                    EEEEESG.GGHHHHHHTSSSTT-B CS
                          SIS_2  38 vlvfGsG.hSaalaeelaaraggl 60 
                                    +l++G++ h+ +la ++++r  gl
  gi|116754968|ref|YP_844086.1| 299 ILACGTSyHAGLLARYFFPRTAGL 322
                                    89***977*************998 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 1.2e-06
                                    HHTT--TT-EEEEE-SS--SHHHHHHHHHHHHHT-EEEEEE CS
                          SIS_2  97 rlvrlkpgDvLlviSnsGnnavvveaaeaakergmkviAlt 137
                                    ++++l+pg +L+ iS+sG+ a  + a+++ak++g+k  A+t
  gi|116754968|ref|YP_844086.1| 333 QHMQLRPGTLLVAISQSGETADTLMALKKAKTCGVKSLAIT 373
                                    56799**********************************99 PP

>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.9e-05     0.055      72     134 ..      67     128 ..      50     160 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.9e-05
                       GATase_4  72 knvvaHiRkatqGevklenthpFvRelwgrewifAHnGdlkeykpkl....egrfePvGsTDsElaf 134
                                    ++ + H R at+G+ ++en+hp +      ++   HnG +++y + +    ++ +    +TDsE+ +
  gi|116754968|ref|YP_844086.1|  67 SIGIGHTRWATHGRPSDENAHPHT----SGSIAVVHNGIIENYLELReqlrDKGYVFTSETDSEV-L 128
                                    56799*****************86....4578889*****9965443334777899999999996.3 PP

>> mCpol  minimal CRISPR polymerase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.058   1.7e+02      69      92 ..      50      73 ..      32      77 .. 0.87
   2 ?    5.8   0.0    0.0057        17      71     111 ..     330     370 ..     322     373 .. 0.75
   3 ?   -0.6   0.0      0.54   1.6e+03      30      63 ..     445     478 ..     433     490 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.058
                          mCpol 69 llvelsrvyqkitgltvSiGvGkt 92
                                    +++l+ +y++ ++   SiG+G+t
  gi|116754968|ref|YP_844086.1| 50 RISDLEIIYRSRGEPEGSIGIGHT 73
                                   67899*****************98 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0057
                          mCpol  71 velsrvyqkitgltvSiGvGktlrealiaLkkAkskgknrv 111
                                    +e++++    ++l v i+   + +++l+aLkkAk+ g +++
  gi|116754968|ref|YP_844086.1| 330 SEFQHMQLRPGTLLVAISQSGETADTLMALKKAKTCGVKSL 370
                                    445555555558888999888899***********997765 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.54
                          mCpol  30 kevkeaikklkkllkdelgasvifaaGDsilaks 63 
                                    + v e+ ++++++ +  +ga + f  G +il   
  gi|116754968|ref|YP_844086.1| 445 QAVLERRDQIREIAQRFSGADIYFFIGRDILYPI 478
                                    677888999*******99******9999999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (605 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 4226.49
//
Query:       gi|116754969|ref|YP_844087.1|  [L=265]
Description: periplasmic solute binding protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-28   99.7   0.1    3.1e-28   98.9   0.1    1.4  1  ZnuA      Zinc-uptake complex component A periplasmic


Domain annotation for each model (and alignments):
>> ZnuA  Zinc-uptake complex component A periplasmic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.9   0.1   1.7e-32   3.1e-28       1     253 [.      25     257 ..      25     260 .. 0.89

  Alignments for each domain:
  == domain 1  score: 98.9 bits;  conditional E-value: 1.7e-32
                                    EEESSHHHHHHHHHHHGGGCEEEECS-TTSTTTT----HHHHHHHHHSSEEEESSTTTSGTHHHHHHHHTTCCCEEEEET CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ZnuA   1 VvattsplgdlvrqvaGdrvevtvLvppgadpHsyeptprdvrklaeAdllvynglelEtwldkllasssqatrvevidl 80 
                                    +vatts l+dl++ v+Gd+v+vt +v +g+ p ++ ++p++v++l+eA++++  g  +E wl+++ +      + +vi l
  gi|116754969|ref|YP_844087.1|  25 IVATTSTLEDLIKGVGGDNVDVTYIVSSGVCPDHWDLKPSQVAALNEASIIFQHG--MEGWLKNITRPD----Q-KVIVL 97 
                                    8****************************************************96..9*****995222....3.66656 PP

                                    TTTCCSEBCSSESTGGGSHHHHHHHHHHHHHHHHHHTGGGHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSGTEGEEEESS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ZnuA  81 segveeeeeeeDpHiWlspknaiamveniadaLveadpanadtyeanaaayiekLeeldaeireelaeipeekrklvtth 160
                                    s g            W  p+ ai  + +ia aL eadp++a++y+++a+ + e+ +++ + + e+  e+   + + v   
  gi|116754969|ref|YP_844087.1|  98 S-G-----------PWNTPQMAINKTMQIAAALKEADPEHAEEYDRRAEVLVERFQNVSEVLSERAREAGTGN-VKVLCM 164
                                    6.6...........5****************************************************999776.566777 PP

                                    STTHHHHHHTT-EEEEEESSSSS..HHHHHHHHHHHHHTT-SEEEEETTS-THHHHHHHHHHT-EEEEE-STSSSTSTTS CS
                                    xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ZnuA 161 dafgylarayglevagiagiste..aaqiaalieeikeagvkaifveplaspklaetlaeeagvkvatlysldslgdegs 238
                                    +  + +   +g++++++ + +++   +++++li+  +e+ v +++ + ++  ++ e++a+e+++  ++l ++ +  +++ 
  gi|116754969|ref|YP_844087.1| 165 EWQSGFVSWMGFDIVKTYASEEKlsLKDVNDLINVGRENSVSIVVDNLQSGVNVGEQIAKEINATHVVLTNFPGAVEGT- 243
                                    77777889*******886555559*****************999988899*************9999999866655554. PP

                                    TTSHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxx RF
                           ZnuA 239 aetYidmmranlesl 253
                                     et  +m+ +n e+l
  gi|116754969|ref|YP_844087.1| 244 -ETLDKMILHNGEAL 257
                                    .78889998888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       798  (0.0445089); expected 358.6 (0.02)
Passed bias filter:                      651  (0.0363099); 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: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1819.08
//
Query:       gi|116754970|ref|YP_844088.1|  [L=400]
Description: phosphoserine phosphatase SerB [Methanosaeta thermophila PT]
Scores for complete 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   70.9   0.1    2.8e-19   70.2   0.1    1.3  1  Hydrolase        haloacid dehalogenase-like hydrolase
    2.5e-19   70.4   0.1    9.5e-19   68.5   0.0    1.9  2  HAD              haloacid dehalogenase-like hydrolase
    1.6e-13   50.5   0.2    3.3e-10   39.8   0.0    2.5  2  ACT_6            ACT domain
    1.4e-12   47.2   2.8    1.1e-05   25.1   0.0    2.6  2  ACT              ACT domain
    7.2e-10   39.0   0.5    7.2e-10   39.0   0.5    2.4  3  Hydrolase_3      haloacid dehalogenase-like hydrolase
    4.1e-09   36.9   0.6     0.0069   16.9   0.0    3.0  3  ACT_4            ACT domain
      3e-08   33.3   1.5    1.1e-05   25.0   0.0    2.5  3  Put_Phosphatase  Putative Phosphatase
    1.4e-07   31.8   3.6    3.1e-06   27.4   3.6    2.7  1  HAD_2            Haloacid dehalogenase-like hydrolase
     0.0017   18.6   0.3       0.87    9.9   0.0    2.9  3  FliG_M           FliG middle domain
  ------ inclusion threshold ------
      0.031   13.8   0.0      0.056   13.0   0.0    1.4  1  AA_kinase        Amino acid kinase family
       0.09   12.7   1.3       0.89    9.5   0.1    2.9  3  Rho_N            Rho termination factor, N-terminal domain
       0.14   11.7   0.2       0.83    9.1   0.0    2.0  2  S6PP             Sucrose-6F-phosphate phosphohydrolase


Domain annotation for each model (and alignments):
>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.2   0.1   1.9e-22   2.8e-19       2     210 .]     187     360 ..     186     360 .. 0.90

  Alignments for each domain:
  == domain 1  score: 70.2 bits;  conditional E-value: 1.9e-22
                                    SEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTEHHHHTHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase   2 ktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrgayaigkpewltald 81 
                                    +++vfD+d T+++ e     +i+++                     a + ++ +++ +++      +++ g+ ++ ++l 
  gi|116754970|ref|YP_844088.1| 187 RLIVFDMDMTIVDFE-----IINRL---------------------ASFAGVDEEVRRITD-----RAMNGEIDFEESL- 234
                                    68*************.....*****.....................***************.....*************. PP

                                    CHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT.GGGE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                      Hydrolase  82 ippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG.ddyf 160
                                                  + r   l+   + a+ +iad+l++ p+ +e++++Lk++g++++l++g++  + + + ++lG d +f
  gi|116754970|ref|YP_844088.1| 235 --------------RRRVRLLKGMPVSALKEIADQLSLTPGSEELIHHLKQMGYKIALISGGFTYFTDVLKERLGfDYTF 300
                                    ..............8888888888********************************************99999**94444 PP

                                    SEEEEHHCES..........STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                    xxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 161 daviasdiet..........vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                    ++++++ +             ak++ e+++++++  +++p ++++VGDg+nD  ++++Ag
  gi|116754970|ref|YP_844088.1| 301 ANELEIQDGRltgeikgeiiDAKAKGEIVKRLAEMEGISPDNIVAVGDGANDCIMIQNAG 360
                                    555444444444555559999999*********************************998 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.1   1.7e+03     138     173 ..     136     174 ..      99     176 .. 0.66
   2 !   68.5   0.0   6.4e-22   9.5e-19       1     184 [.     189     353 ..     189     357 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.1
                            HAD 138 ltge...lglegkpvrgegkvaalrewlaaegegidlee 173
                                    +t++   + +e  + +g++ +++ rew+  e+e + l+ 
  gi|116754970|ref|YP_844088.1| 136 VTARgdlISIEFVMDFGDANPDECREWIRSECERLGLDV 174
                                    444444556666778899999999999999999888775 PP

  == domain 2  score: 68.5 bits;  conditional E-value: 6.4e-22
                            HAD   1 alfDfDgTLldgdslelllrfllrrgaprlwralreklllalfrellrldraglaelleallagls.eelaaelerfvae 79 
                                    ++fD+D T++d     +++  +l+++a    +++r+ ++ a+    ++ d ++  +   +ll+g++  +l++ ++++   
  gi|116754970|ref|YP_844088.1| 189 IVFDMDMTIVDF----EIIN-RLASFAGV-DEEVRRITDRAM---NGEIDFEESLRRRVRLLKGMPvSALKEIADQLS-- 257
                                    79**********....5555.44444433.688888888888...555556677777888******888888888888.. PP

                            HAD  80 virpklldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevdd.rltgelglegkpvrgegkvaal 158
                                          l+pg  el+++ ++ G++++++Sgg+ +++  l ++lg+d+  a+ele +d rltge  + g ++  ++k   +
  gi|116754970|ref|YP_844088.1| 258 ------LTPGSEELIHHLKQMGYKIALISGGFTYFTDVLKERLGFDYTFANELEIQDgRLTGE--IKGEIIDAKAKGEIV 329
                                    ......88********999********************************************..99999999999999* PP

                            HAD 159 rewlaaegegidleevvayGDspsDl 184
                                    ++   ae egi+++++va+GD+ +D 
  gi|116754970|ref|YP_844088.1| 330 KR--LAEMEGISPDNIVAVGDGANDC 353
                                    **..8899999999***********5 PP

>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8   0.0   2.2e-13   3.3e-10       4      75 ..      14      87 ..      12      88 .. 0.96
   2 !    8.3   0.0    0.0015       2.2       4      73 ..     105     174 ..     102     177 .. 0.71

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 2.2e-13
                          ACT_6  4 litvtGpdrpGltasLtsvlaefgvnilDieqavihgrlsLgllvsgp..edalarlekaLlflakelgltvef 75
                                   +i+++G drpGl+ +++++ ae +vni+D  q v+ g ++  ++ + +  e   ++le ++++++  lg++ +f
  gi|116754970|ref|YP_844088.1| 14 VISFVGRDRPGLIHDILQLPAERNVNIVDMDQRVLQGLFVMSVVADFSraEISPKELEMEMHRRSNSLGVQCMF 87
                                   8***********************************************8666******************9887 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0015
                          ACT_6   4 litvtGpdrpGltasLtsvlaefgvnilDieqavihgrlsLgllvsgpedalarlekaLlflakelgltv 73 
                                    ++t++  dr G++ +++sv +  ++ni    +   ++  s+  + +  + +  + +  ++  +++lgl+v
  gi|116754970|ref|YP_844088.1| 105 VVTILARDRVGIIRDVASVASARDINIERAAVTARGDLISIEFVMDFGDANPDECREWIRSECERLGLDV 174
                                    89***********************998766666555555555555555555555555555555555555 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   7.4e-09   1.1e-05       2      51 ..      14      59 ..      13      71 .. 0.85
   2 !   21.5   0.8   9.8e-08   0.00015       1      52 [.     104     154 ..     104     158 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 7.4e-09
                                   EEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEE CS
                            ACT  2 vlrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvd 51
                                   v+++  +DrPGl+++++++ a+r++Ni+ + qr        ++++ +v+d
  gi|116754970|ref|YP_844088.1| 14 VISFVGRDRPGLIHDILQLPAERNVNIVDMDQRVLQG----LFVMSVVAD 59
                                   79999****************************9854....666666665 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 9.8e-08
                                    EEEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEH CS
                            ACT   1 tvlrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvde 52 
                                    +v+ ++++Dr+G++ +v+++ + r+iNi+++ ++  +d   +i fv++ +d+
  gi|116754970|ref|YP_844088.1| 104 YVVTILARDRVGIIRDVASVASARDINIERAAVTARGDL-ISIEFVMDFGDA 154
                                    68999*******************************993.666666666555 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.3       4.9   7.4e+03       1      11 [.     189     199 ..     189     201 .. 0.88
   2 ?    0.9   0.0      0.21   3.1e+02      15      55 ..     257     297 ..     252     324 .. 0.77
   3 !   39.0   0.5   4.8e-13   7.2e-10     187     247 ..     324     383 ..     312     391 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 4.9
                                    EEEEIIIIIS- CS
                    Hydrolase_3   1 ialDlDGTLln 11 
                                    i++D+D T+++
  gi|116754970|ref|YP_844088.1| 189 IVFDMDMTIVD 199
                                    89*****9986 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.21
                                    ---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCC CS
                    Hydrolase_3  15 kisektkeaikklkekgikvviATGRslravlpvleelgld 55 
                                    ++++ + e i+ lk+ g+k+++ +G  ++++  + e lg+d
  gi|116754970|ref|YP_844088.1| 257 SLTPGSEELIHHLKQMGYKIALISGGFTYFTDVLKERLGFD 297
                                    567888999*************9998888887777778777 PP

  == domain 3  score: 39.0 bits;  conditional E-value: 4.8e-13
                                    SHHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GG CS
                    Hydrolase_3 187 sKgtalkklakelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnn 247
                                     Kg+ +k+la++ +is+++++a+GDg ND  M++ aglgvA  na++ +kk++d  +   n
  gi|116754970|ref|YP_844088.1| 324 AKGEIVKRLAEMEGISPDNIVAVGDGANDCIMIQNAGLGVAF-NAKDVLKKVSDGSISREN 383
                                    59***************************************7.9*******9998776666 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   4.6e-06    0.0069       9      51 ..      15      55 ..      13      59 .. 0.88
   2 !   16.7   0.1   5.4e-06     0.008       9      52 ..     106     147 ..     103     154 .. 0.86
   3 ?   -2.2   0.0       4.5   6.7e+03      44      75 ..     307     338 ..     304     339 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.6e-06
                          ACT_4  9 leveaedrkglLaditqviseekanivsvnaktrkkdglaeik 51
                                   ++ +++dr+gl+ di+q+ +e ++niv++  +    +gl+ ++
  gi|116754970|ref|YP_844088.1| 15 ISFVGRDRPGLIHDILQLPAERNVNIVDMDQRVL--QGLFVMS 55
                                   78899************************99995..4677765 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 5.4e-06
                          ACT_4   9 leveaedrkglLaditqviseekanivsvnaktrkkdglaeiki 52 
                                    +++ a+dr g+++d+++v s+ ++ni+   +++r  d l +i++
  gi|116754970|ref|YP_844088.1| 106 VTILARDRVGIIRDVASVASARDINIERAAVTARG-D-LISIEF 147
                                    5799*************************999964.4.666665 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 4.5
                          ACT_4  44 kdglaeikitveVkdvehLsrviakLraipgV 75 
                                    +dg  +++i+ e+ d++   +++++L +++g+
  gi|116754970|ref|YP_844088.1| 307 QDGRLTGEIKGEIIDAKAKGEIVKRLAEMEGI 338
                                    47888888888888888888899999888887 PP

>> Put_Phosphatase  Putative Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1       4.1   6.1e+03      49     105 ..      29      85 ..      25      88 .. 0.62
   2 !   25.0   0.0   7.1e-09   1.1e-05       2     117 ..     188     301 ..     187     308 .. 0.90
   3 !    7.1   0.0    0.0022       3.3     151     187 ..     325     357 ..     320     375 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 4.1
                Put_Phosphatase  49 vlkelheqgvseadikkvlrsiplspglvelikslakkkleldliiiSDaNsffiee 105
                                    +l+   e++v++ d+ +++ +  ++  +v+ +  +  + +el++ +   +Ns+++++
  gi|116754970|ref|YP_844088.1|  29 ILQLPAERNVNIVDMDQRVLQGLFVMSVVADFSRAEISPKELEMEMHRRSNSLGVQC 85 
                                    555556666777777766655555556666666666666777777777777777665 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 7.1e-09
                Put_Phosphatase   2 lvvfDFDktiidedsdnwvvdelpatelfeelretlrkgl..wnelmdrvlkelheqgvseadikkvlrsiplspglvel 79 
                                    l+vfD D ti+d +  n + + ++ +e+ +++ +   +g   ++e + r ++ l+      + +k++  +++l+pg  el
  gi|116754970|ref|YP_844088.1| 188 LIVFDMDMTIVDFEIINRLASFAGVDEEVRRITDRAMNGEidFEESLRRRVRLLKG--MPVSALKEIADQLSLTPGSEEL 265
                                    89******************************998876643399999999999975..556689**************** PP

                Put_Phosphatase  80 ikslakkkleldliiiSDaNsffieeileaagledlFs 117
                                    i++l  k+ ++ + +iS   ++f + + e +g+   F+
  gi|116754970|ref|YP_844088.1| 266 IHHL--KQMGYKIALISGGFTYFTDVLKERLGFDYTFA 301
                                    ****..6789***************9999999998886 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0022
                Put_Phosphatase 151 KgkvleelvaeqaregveyerliYvGDganDlCpvlk 187
                                    Kg+++++l +    eg++ + ++ vGDganD C + +
  gi|116754970|ref|YP_844088.1| 325 KGEIVKRLAEM---EGISPDNIVAVGDGAND-CIMIQ 357
                                    88889888877...89***************.44444 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   3.6   2.1e-09   3.1e-06       1     175 [.     189     363 ..     189     365 .. 0.69

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 2.1e-09
                          HAD_2   1 iiFDlDgTlldteeliiqafnelleeyglselseeelrkliglslrellrklgeseeeee.kieellrkyneekkkkevk 79 
                                    i+FD+D T++d      +++n+l+   g+    +ee+r++    ++  ++  ++  +    +    ++  +e  +  +++
  gi|116754970|ref|YP_844088.1| 189 IVFDMDMTIVDF-----EIINRLASFAGV----DEEVRRITDRAMNGEIDFEESLRRRVRlLKGMPVSALKEIAD--QLS 257
                                    799999999995.....566666655555....344444333333222221111111112133344455555555..5** PP

                          HAD_2  80 pydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdv...ivtsedvekk.......KPdpeviekaleklk 149
                                    + +g +el++ Lk++gyk+++++ + +  ++   e+lg++  F     i  +  +++        K + e+++++ e  +
  gi|116754970|ref|YP_844088.1| 258 LTPGSEELIHHLKQMGYKIALISGGFTYFTDVLKERLGFDYTFANeleIQDGRLTGEIkgeiidaKAKGEIVKRLAEMEG 337
                                    ****************************************999752223322222222233555589999********** PP

                          HAD_2 150 lkkeeviyvGDsptDieaakkagikv 175
                                    +++++++ vGD  +D +  ++ag+ v
  gi|116754970|ref|YP_844088.1| 338 ISPDNIVAVGDGANDCIMIQNAGLGV 363
                                    ***********************876 PP

>> FliG_M  FliG middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.015        22      42      69 ..     201     228 ..     198     234 .. 0.90
   2 ?   -1.6   0.0       2.2   3.3e+03      45      65 ..     236     256 ..     227     257 .. 0.81
   3 !    9.9   0.0   0.00058      0.87      38      62 ..     323     347 ..     318     358 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.015
                                    HHHHHHHTCCTCSHHHHHHHHHHHHHHC CS
                         FliG_M  42 evirriatlekvspevlkeveevLekkl 69 
                                    e+i+r+a++  v++ev ++ +++++ ++
  gi|116754970|ref|YP_844088.1| 201 EIINRLASFAGVDEEVRRITDRAMNGEI 228
                                    8*****************9999998776 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.2
                                    HHHHTCCTCSHHHHHHHHHHH CS
                         FliG_M  45 rriatlekvspevlkeveevL 65 
                                    rr+  l+ +   +lke+++ L
  gi|116754970|ref|YP_844088.1| 236 RRVRLLKGMPVSALKEIADQL 256
                                    788888999999999999987 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00058
                                    HHHHHHHHHHHTCCTCSHHHHHHHH CS
                         FliG_M  38 elraevirriatlekvspevlkeve 62 
                                    + + e+++r+a++e +sp+ +  v 
  gi|116754970|ref|YP_844088.1| 323 KAKGEIVKRLAEMEGISPDNIVAVG 347
                                    6788**************9887775 PP

>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.8e-05     0.056      27      89 ..     266     332 ..     246     374 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.8e-05
                                    HHHHHHHTTEEEEEE--.HHHHHHHHHHTCCCCCHHHC........E..HHHHHHHHHHHHHHHHHHH CS
                      AA_kinase  27 iaalkesgnklvvVhGg.gsftdgllalksglssgelaa....glrstleeagevatrdalaslgerl 89 
                                    i  lk+ g+k+++++Gg   ftd l ++  g++ +++++    + r+t e++ge++   a + + +rl
  gi|116754970|ref|YP_844088.1| 266 IHHLKQMGYKIALISGGfTYFTDVLKER-LGFDYTFANEleiqDGRLTGEIKGEIIDAKAKGEIVKRL 332
                                    55666779*********99*********.**************8888888888888775555444443 PP

>> Rho_N  Rho termination factor, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.44   6.6e+02      14      31 ..     126     143 ..     123     145 .. 0.88
   2 ?    9.5   0.1   0.00059      0.89       2      19 ..     241     258 ..     240     265 .. 0.90
   3 ?   -1.7   0.0         2     3e+03      13      31 ..     300     320 ..     298     325 .. 0.63

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.44
                                    HHHTT-TTGGGS-HHHHH CS
                          Rho_N  14 AkelgienysrlRKqdLI 31 
                                    A++ +ie+++   ++dLI
  gi|116754970|ref|YP_844088.1| 126 ARDINIERAAVTARGDLI 143
                                    9999*******9999999 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00059
                                    HHHS-HHHHHHHHHHTT- CS
                          Rho_N   2 LkektlseLraiAkelgi 19 
                                    Lk +++s L++iA +l +
  gi|116754970|ref|YP_844088.1| 241 LKGMPVSALKEIADQLSL 258
                                    8**************977 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2
                                    HHHHTT-T..TGGGS-HHHHH CS
                          Rho_N  13 iAkelgie..nysrlRKqdLI 31 
                                    +A+el+i   ++++  K+++I
  gi|116754970|ref|YP_844088.1| 300 FANELEIQdgRLTGEIKGEII 320
                                    688888864444444455555 PP

>> S6PP  Sucrose-6F-phosphate phosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.36   5.3e+02       2      26 ..     186     208 ..     185     220 .. 0.74
   2 ?    9.1   0.0   0.00056      0.83     165     206 ..     324     365 ..     319     380 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.36
                                    SEEEEE-TBTTTB.S-HHHHHHHHH CS
                           S6PP   2 klllvsdLDntlvdgdnealarlne 26 
                                    k+l+v d+D t+v  d e ++rl +
  gi|116754970|ref|YP_844088.1| 186 KRLIVFDMDMTIV--DFEIINRLAS 208
                                    689**********..5555555554 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00056
                                    SHHHHHHHHHHHHT--GGGEEEEE-SGGGHHHHTSSSEEEE- CS
                           S6PP 165 skgeAlryLakkleleleqilvcGdsgnDeellignvlgVvV 206
                                     kge ++ La+  ++ +++i+ +Gd  nD  ++++  lgV  
  gi|116754970|ref|YP_844088.1| 324 AKGEIVKRLAEMEGISPDNIVAVGDGANDCIMIQNAGLGVAF 365
                                    5899999999999********************999999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2819.33
//
Query:       gi|116754971|ref|YP_844089.1|  [L=273]
Description: transcriptional regulator, TrmB [Methanosaeta thermophila PT]
Scores for complete 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   72.5   0.0    6.5e-20   70.8   0.0    2.0  1  TrmB      Sugar-specific transcriptional regulator TrmB
    0.00014   21.6   0.0    0.00035   20.3   0.0    1.7  1  HTH_IclR  IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.035   14.1   0.1        8.8    6.4   0.0    2.7  2  PadR      Transcriptional regulator PadR-like family
      0.037   13.9   0.0       0.11   12.4   0.0    1.9  1  MarR_2    MarR family
      0.084   13.0   0.0       0.28   11.3   0.0    2.0  1  HTH_20    Helix-turn-helix domain
       0.13   12.2   0.0       0.32   11.0   0.0    1.7  1  MarR      MarR family


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.8   0.0   2.2e-23   6.5e-20       1      67 [.      16      82 ..      16      83 .. 0.98

  Alignments for each domain:
  == domain 1  score: 70.8 bits;  conditional E-value: 2.2e-23
                                   HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE--H CS
                           TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravdp 67
                                   L++lGL+eyEa+vY+aL +l+   a+ei++++g+pr+ vY +L++L+ +G+Ve+++++p++Yr++dp
  gi|116754971|ref|YP_844089.1| 16 LRDLGLTEYEARVYTALTRLKAGIASEIHQISGIPRPAVYGALKRLVMRGIVEVQPSKPMRYRVTDP 82
                                   789**************************************************************99 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   1.2e-07   0.00035      21      51 ..      40      70 ..      30      71 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.2e-07
                                   HHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                       HTH_IclR 21 lselArrtglpkStvhRlLqtLvelGyveqd 51
                                    se+++ +g+p+++v++ L+ Lv +G+ve +
  gi|116754971|ref|YP_844089.1| 40 ASEIHQISGIPRPAVYGALKRLVMRGIVEVQ 70
                                   69**************************965 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1    0.0089        27      17      43 ..      14      37 ..      10      45 .. 0.80
   2 ?    6.4   0.0    0.0029       8.8      31      53 ..      51      73 ..      37      82 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0089
                                   HHHHCCSTT-CCTTHHHHHHHHHHHHH CS
                           PadR 17 keleelsegllelseGslYpaLkrLek 43
                                   k+l++l  g l+  e+++Y+aL+rL++
  gi|116754971|ref|YP_844089.1| 14 KALRDL--G-LTEYEARVYTALTRLKA 37
                                   666777..7.455689*********85 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0029
                                   HHHHHHHHHHHHHTTSEEEEEE- CS
                           PadR 31 eGslYpaLkrLekeglvesewee 53
                                      +Y aLkrL   g+ve + ++
  gi|116754971|ref|YP_844089.1| 51 RPAVYGALKRLVMRGIVEVQPSK 73
                                   5579*************987554 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   3.7e-05      0.11      23      56 ..      39      72 ..      19      74 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.7e-05
                                   EHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                         MarR_2 23 tvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                    ++e+ +  g++++av  +lkrLv +G ve +p+
  gi|116754971|ref|YP_844089.1| 39 IASEIHQISGIPRPAVYGALKRLVMRGIVEVQPS 72
                                   689999************************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 ?   11.3   0.0   9.4e-05      0.28      13      59 ..      26      72 ..      12      74 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.4e-05
                                   HHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                         HTH_20 13 rrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                                   +r++ aL+r ++  ase+++  ++++  ++  L+ L+  g+vev+ +
  gi|116754971|ref|YP_844089.1| 26 ARVYTALTRLKAGIASEIHQISGIPRPAVYGALKRLVMRGIVEVQPS 72
                                   6899999999**********************************876 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00011      0.32      20      52 ..      40      72 ..      21      73 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00011
                                   HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
                           MarR 20 vseLakklgvskstvtrvldrLekkGlieRsks 52
                                    se+   +g+ +++v  +l+rL+ +G +e ++s
  gi|116754971|ref|YP_844089.1| 40 ASEIHQISGIPRPAVYGALKRLVMRGIVEVQPS 72
                                   57999999*********************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 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:                        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: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1903.79
//
Query:       gi|116754972|ref|YP_844090.1|  [L=472]
Description: radical SAM domain-containing protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-18   66.8   0.3    8.6e-18   65.3   0.0    1.9  2  Radical_SAM   Radical SAM superfamily
    6.7e-08   32.7   0.2    7.5e-05   22.9   0.0    2.4  2  Fer4_14       4Fe-4S single cluster domain
    1.1e-06   29.0   0.4    0.00014   22.1   0.4    2.4  1  Fer4_12       4Fe-4S single cluster domain
     0.0031   17.0   0.0      0.023   14.2   0.0    2.1  2  AP_endonuc_2  Xylose isomerase-like TIM barrel


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.3      0.79   3.5e+03       7      19 ..      45      57 ..      41      63 .. 0.87
   2 !   65.3   0.0   1.9e-21   8.6e-18       3     165 ..      66     226 ..      64     228 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.79
                                   ESS--TTTSCCTT CS
                                   xxxxxxxxxxxxx RF
                    Radical_SAM  7 CnlrCsfCarpet 19
                                   C++ C  C++++t
  gi|116754972|ref|YP_844090.1| 45 CPFSCGLCDNHKT 57
                                   **********985 PP

  == domain 2  score: 65.3 bits;  conditional E-value: 1.9e-21
                                    EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHH.HHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelk.aekg.vkevilgggepllypdfvellerlaklavpgiri 80 
                                    vt  Cnl C+ C       + +++++ ++e+i++ +k+l+ +++  +  v ++ggep++++d+ e ++ ++        i
  gi|116754972|ref|YP_844090.1|  66 VTTRCNLSCPICFADA---SPKKVYEPTMEQIERMLKILReERPVpCYAVQFSGGEPTVRDDLPEMVALARSM--GFTQI 140
                                    7999***********8...7********************76666999*************************..8**** PP

                                    EEEECSSCHG..HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHH CS
                                    xxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  81 tvetngtlpd..eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGende 158
                                     + tng+++   +e + rl e+g+ +v+l  + +d  ++  +  +++ ++  l+a+e +r+ g+k+vv + ++ +G+nd 
  gi|116754972|ref|YP_844090.1| 141 QIATNGLRLAasPELASRLSEAGLSTVYLQFDGVDAGPYITMR-GRNLLDVKLRAIESCRSGGLKSVVLVPTVAKGVNDF 219
                                    *************************************655555.88********************************97 PP

                                    HHHHHHH CS
                                    xxxxxxx RF
                    Radical_SAM 159 eleelle 165
                                    +l  +++
  gi|116754972|ref|YP_844090.1| 220 QLGGIIR 226
                                    7666655 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 !    7.3   0.3    0.0011       4.8       2      20 ..      39      57 ..      38      63 .. 0.87
   2 !   22.9   0.0   1.7e-08   7.5e-05       5      90 ..      67     147 ..      64     168 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0011
                        Fer4_14  2 fvrlsgCnlsCkgCdnket 20
                                   f+  + C++sC  Cdn++t
  gi|116754972|ref|YP_844090.1| 39 FITKGDCPFSCGLCDNHKT 57
                                   788899*********9986 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 1.7e-08
                        Fer4_14   5 lsgCnlsCkgCdnketwkselgkpqte.elleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekki 83 
                                    + +CnlsC+ C+  ++ k+ +++  ++ e + +il   +++ +    + ++GGeP    + +e++ l    +  +   +i
  gi|116754972|ref|YP_844090.1|  67 TTRCNLSCPICFADASPKKVYEPTMEQiERMLKIL--REERPVPCYAVQFSGGEPTVRDDLPEMVALA---RSMG-FTQI 140
                                    689*********98877777765443313344666..55555666789*******9775555555554...4444.4568 PP

                        Fer4_14  84 wletngt 90 
                                    ++ tng+
  gi|116754972|ref|YP_844090.1| 141 QIATNGL 147
                                    8888875 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 !   22.1   0.4   3.2e-08   0.00014      13      95 ..      68     148 ..      31     161 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 3.2e-08
                        Fer4_12  13 sgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesi...egltllGGEPllpenaeallelvkevkeekpekdiw 89 
                                    ++CnlsC+ Cf+ +  s+k+  e t e +e++++ l +e+      + ++GGEP ++   ++++ l+   ++ ++++  +
  gi|116754972|ref|YP_844090.1|  68 TRCNLSCPICFADA--SPKKVYEPTMEQIERMLKILREERPvpcYAVQFSGGEPTVRDDLPEMVALA---RSMGFTQIQI 142
                                    57888888888555..44444555566677777777665545669***********55555555555...5555544556 PP

                        Fer4_12  90 lytgyt 95 
                                    +++g  
  gi|116754972|ref|YP_844090.1| 143 ATNGLR 148
                                    666665 PP

>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   5.1e-06     0.023       2      92 ..     130     211 ..     129     253 .. 0.85
   2 ?    0.1   0.0     0.099   4.4e+02     174     193 ..     394     416 ..     378     435 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.1e-06
                                    HHHHHCT-SEEEEECCTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHHHHHHHHH CS
                   AP_endonuc_2   2 aaaaeaGfdgvElfgrdlvpvselsdeelrelrkaldelglriaslslftrfgypdederearreesvdalkraielaaa 81 
                                    a+a+++Gf+ +++++ +l+ +++       el+++l e+gl  + l++ + + +p    r ++    +d   raie ++ 
  gi|116754972|ref|YP_844090.1| 130 ALARSMGFTQIQIATNGLRLAAS------PELASRLSEAGLSTVYLQFDGVDAGPYITMRGRN---LLDVKLRAIESCRS 200
                                    79*******************97......8************999999888888877655555...35555688888888 PP

                                    HTBSEEEEEBC CS
                   AP_endonuc_2  82 LGapllvlhpG 92 
                                     G + +vl p 
  gi|116754972|ref|YP_844090.1| 201 GGLKSVVLVPT 211
                                    88888888765 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.099
                                    HHHHHHHGG...EEEEEE.EESS CS
                   AP_endonuc_2 174 dalraladr...ikhvHikDakg 193
                                    d lr++ +r   i+++H+ D ++
  gi|116754972|ref|YP_844090.1| 394 DSLREFHSRnlfIGAMHFQDLYN 416
                                    679999999***********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3375.80
//
Query:       gi|116754973|ref|YP_844091.1|  [L=311]
Description: HPr kinase [Methanosaeta thermophila PT]
Scores for complete 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   25.9   0.4    8.3e-05   22.2   0.2    2.1  2  Hpr_kinase_C   HPr Serine kinase C-terminal domain
     0.0012   17.6   0.0     0.0016   17.2   0.0    1.2  1  PEPCK_ATP      Phosphoenolpyruvate carboxykinase
     0.0078   16.4   0.0      0.027   14.7   0.0    1.9  2  AAA_33         AAA domain
  ------ inclusion threshold ------
      0.015   15.6   0.0      0.026   14.8   0.0    1.4  1  AAA_28         AAA domain
      0.083   12.7   0.2       0.17   11.6   0.2    1.5  1  AAA_29         P-loop containing region of AAA domain
        0.1   11.5   0.1       0.17   10.8   0.1    1.2  1  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-


Domain annotation for each model (and alignments):
>> Hpr_kinase_C  HPr Serine kinase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.2   2.8e-08   8.3e-05       8      50 ..     119     162 ..     115     181 .. 0.87
   2 ?    1.5   0.0     0.064   1.9e+02      76     121 ..     206     251 ..     196     258 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 2.8e-08
                                    EEESEEEEETTEEEEEEESTCHHHHHHHHHHHTTT-.EEEEESS CS
                   Hpr_kinase_C   8 svhGvlvdvygvGvLitGesgvGKselaleLikrgh.rLvaDDa 50 
                                    svhG ++d+ g G+ i+G sg GK+  +  L++    r+v+DD 
  gi|116754973|ref|YP_844091.1| 119 SVHGACLDLDGRGICIIGGSGTGKTTHTYGLLRDQRvRVVSDDW 162
                                    89*****************************9866549999996 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.064
                                    TTTEEEEHHHHH-GGGB-SEEEEEEEEEEESTT---TTTSTTSS-E CS
                   Hpr_kinase_C  76 rglGiidvkklfGaeavrekkeielvveLeewekkkeydrlgleee 121
                                     g G++d++   G + +   ++i+ v  L++ ++++++ rl  e+ 
  gi|116754973|ref|YP_844091.1| 206 MGRGVVDLRWAIGKGRILPLTTIRHVFILKRDSSDDRIVRLSPEDA 251
                                    5889*************************99999999999887665 PP

>> PEPCK_ATP  Phosphoenolpyruvate carboxykinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   5.5e-07    0.0016     156     238 ..      76     161 ..      45     185 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.5e-07
                                    S-EEEEETTTTEEEEES---THHHHHHHHHHHHHHHH.HTT-EEEEEEEEE-T.TS-EEEEEE-TTSSHHHHH....-BT CS
                      PEPCK_ATP 156 etvvalnlekklvlilgteYaGEikKsifsvmnyllp.kkgvlsmhcsanvgekkgdvalfFGLSGtGKTtLs....adp 230
                                    ++ v+ + ++k++ +++ +Y G ik   +s++  +l  ++g+ s+h ++    ++       G SGtGKTt +     d+
  gi|116754973|ref|YP_844091.1|  76 KNRVLYDPQSKTAFLVNFDYYGWIKSLALSLAGDILEdEHGIHSVHGACLDL-DG-RGICIIGGSGTGKTTHTygllRDQ 153
                                    56789999************************999987999*****988654.44.44556799*******886676888 PP

                                    TB-EEESS CS
                      PEPCK_ATP 231 erkligdD 238
                                    + +++ dD
  gi|116754973|ref|YP_844091.1| 154 RVRVVSDD 161
                                    88888888 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.87   2.6e+03      18      63 ..      59     103 ..      47     109 .. 0.66
   2 !   14.7   0.0   8.9e-06     0.027       3      43 ..     133     173 ..     132     211 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.87
                         AAA_33  18 rllkklg.avllssdtlrrrlfgtdqqsktdytrvldrlyqilnela 63 
                                    + ++ +g +++++ d  ++r+ + d+qskt    v+++ y++++ la
  gi|116754973|ref|YP_844091.1|  59 QSVRSHGrMYVVNDDGGKNRVLY-DPQSKTA-FLVNFDYYGWIKSLA 103
                                    44666677888888887777775.4555553.556677777776655 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 8.9e-06
                         AAA_33   3 llvGlpGsGKstlaerllkklgavllssdtlrrrlfgtdqq 43 
                                     ++G +G+GK+t   +ll+ + + ++s d ++ r++g+d+ 
  gi|116754973|ref|YP_844091.1| 133 CIIGGSGTGKTTHTYGLLRDQRVRVVSDDWFFGRIYGRDVL 173
                                    579***************88777777777777799996553 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   8.7e-06     0.026       2      27 ..     132     158 ..     131     186 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 8.7e-06
                         AAA_28   2 ivitGgestGKTtlleaLaar.gypvv 27 
                                    i+i+Gg++tGKTt +  L ++  ++vv
  gi|116754973|ref|YP_844091.1| 132 ICIIGGSGTGKTTHTYGLLRDqRVRVV 158
                                    8************99888765356666 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 ?   11.6   0.2   5.8e-05      0.17      13      37 ..     118     144 ..     111     146 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.8e-05
                         AAA_29  13 dg.htieidlkg.atlltGpsGsGKST 37 
                                    +  h + +dl+g  + ++G sG+GK+T
  gi|116754973|ref|YP_844091.1| 118 HSvHGACLDLDGrGICIIGGSGTGKTT 144
                                    44444455555656***********99 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   0.1   5.7e-05      0.17      16      42 ..     130     156 ..     125     160 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.7e-05
                  TrwB_AAD_bind  16 qhilivGttGsGKtqalekllrairar 42 
                                    + i i+G+ G+GKt+ + +llr  r r
  gi|116754973|ref|YP_844091.1| 130 RGICIIGGSGTGKTTHTYGLLRDQRVR 156
                                    6799*****************988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
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 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2301.78
//
Query:       gi|116754974|ref|YP_844092.1|  [L=127]
Description: translation initiation factor IF-5A [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-08   34.1   0.3    3.8e-08   33.3   0.3    1.4  1  eIF-5a    Eukaryotic elongation factor 5A hypusine, DNA-bindi
    8.8e-06   25.7   0.0    1.8e-05   24.7   0.0    1.5  1  EFP_N     Elongation factor P (EF-P) KOW-like domain


Domain annotation for each model (and alignments):
>> eIF-5a  Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.3   4.3e-12   3.8e-08       1      64 [.      68     123 ..      68     125 .. 0.92

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 4.3e-12
                                    --EEEEEEEEEE-SS.EEEEEE.TT--EEE.EEGG..GB-HHHHTT--TT-E..EEEEEETTEEE CS
                         eIF-5a   1 nVkrkeyqLidIqdDgflsLmd.ddgetkeDlklpegelgkqikekfeegkdvlVtVlsamGeek 64 
                                    +V+rk+ q++++ ++  ++Lmd +d++t +   +p   + +++k k+e+gk+  V +ls+mG+ k
  gi|116754974|ref|YP_844092.1|  68 IVERKTGQVLSV-GETSVQLMDlKDYTTID---VP---ITEDMKPKLEPGKE--VAYLSSMGKVK 123
                                    69**********.788************66...88...88************..********965 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 !   24.7   0.0     2e-09   1.8e-05       5      33 ..      10      38 ..       6      43 .. 0.93

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 2e-09
                                   --TT-EEEETTEEEEEEEEEEEEETTS-- CS
                          EFP_N  5 lkkGlvieidgklyvVlefehvkpGkGqa 33
                                   lk G  i id+++++++++ h+kpGk +a
  gi|116754974|ref|YP_844092.1| 10 LKEGRYIIIDDEPCIIKSIAHSKPGKHGA 38
                                   89************************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 962.11
//
Query:       gi|116754975|ref|YP_844093.1|  [L=183]
Description: putative PAS/PAC sensor protein [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.8e-07   29.2   0.0    1.4e-06   28.2   0.0    1.5  1  PAS_8     PAS domain
      2e-05   24.8   0.0    3.4e-05   24.1   0.0    1.4  1  PAS_4     PAS fold
    3.6e-05   23.7   0.0    0.00045   20.2   0.0    2.4  1  PAS       PAS fold
    9.3e-05   22.6   0.0    0.00016   21.9   0.0    1.4  1  PAS_9     PAS domain
     0.0034   17.4   0.1      0.025   14.6   0.0    2.2  2  HisKA     His Kinase A (phospho-acceptor) domain


Domain annotation for each model (and alignments):
>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   3.8e-10   1.4e-06       3      55 ..      12      59 ..      11      76 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 3.8e-10
                          PAS_8  3 lralfesspdgiavvdlgd..rivdvNqaalellGysadlkgellgqllpvlrpl 55
                                   ++ lfes+p g+a +d  +  r+v +N+a+  ++G++  + g  + +++++ + +
  gi|116754975|ref|YP_844093.1| 12 YKHLFESLPLGVAYLD--QecRVVLANPAFTSITGLD--IEG--I-NRMDHPPFG 59
                                   899**********999..6678*************88..444..4.444444444 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   9.5e-09   3.4e-05       1     109 [.      16     118 ..      16     119 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 9.5e-09
                          PAS_4   1 ldslpdalavldpdgrvlyaNaaaaelfgappeellGktlaellpeedaarleralrrvlegeepiefleelllpgeerh 80 
                                    ++slp ++a+ld + rv+ aN+a+ ++ g  + e +++ ++   p +d+++ +r+l+ + +g e  +++++  ++g+  h
  gi|116754975|ref|YP_844093.1|  16 FESLPLGVAYLDQECRVVLANPAFTSITG-LDIEGINRMDHP--PFGDREARSRILDILDTGYEKSFEHIYNSPDGKKLH 92 
                                    79************************444.556777777772..444677777777666666666666666666****** PP

                          PAS_4  81 yelrllPlrdesGevigvlvisrDiTerr 109
                                    + + ++Plr +s   i + +is  iTe++
  gi|116754975|ref|YP_844093.1|  93 LRTWVHPLRSSS---IRAQIISSNITEEK 118
                                    ********9855...55888888888876 PP

>> PAS  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   1.2e-07   0.00045       3      99 ..      12     103 ..      11     111 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.2e-07
                                    HHHHHHHSSSEEEEEETTSBEEEECHHHHHHHSSTHHHCTTSBGGGGBSTTHHHHHHHHHHHHHHHTT-ECCCCEEEECT CS
                            PAS   3 lraileslpdpifvvDedgrilyvNaaaeellGlsreevlgkslldliheeddaelaelleqlleqgeesrageisfklr 82 
                                    +++++eslp ++  +D   r++++N+a+++++Gl+ e + +       +  d+ e +++++  l +g  ++++e+  + +
  gi|116754975|ref|YP_844093.1|  12 YKHLFESLPLGVAYLDQECRVVLANPAFTSITGLDIEGINRMDHP---PFGDR-EARSRILDILDTG-YEKSFEHIYNSP 86 
                                    789*******************************99877655544...33443.2555555544444.444555557777 PP

                                    TSSEEEEEEEEEEEEET CS
                            PAS  83 dgrpihlevraspvrda 99 
                                    dg++ hl+++++p+r+ 
  gi|116754975|ref|YP_844093.1|  87 DGKKLHLRTWVHPLRSS 103
                                    88888888888888876 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   4.4e-08   0.00016       3     104 .]      22     116 ..      20     116 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 4.4e-08
                          PAS_9   3 gilidnpdgrilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrkkerevevvlirkngetfwvllta 82 
                                    g++  + ++r++ aN+a+  ++G + e +   +   +   d ea++r+ ++l++g   e+++e ++  ++g++++ +  +
  gi|116754975|ref|YP_844093.1|  22 GVAYLDQECRVVLANPAFTSITGLDIEGINRMDHPPFG--DREARSRILDILDTGY--EKSFEHIYNSPDGKKLHLRTWV 97 
                                    66767799***************998888887777777..9999999999999999..********************** PP

                          PAS_9  83 spvkdddgelvgiivilrDite 104
                                     p+++++ +     +i+ +ite
  gi|116754975|ref|YP_844093.1|  98 HPLRSSSIRA---QIISSNITE 116
                                    ***9887444...478888886 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.35   1.3e+03      40      57 ..     120     137 ..      98     142 .. 0.69
   2 !   14.6   0.0   6.8e-06     0.025       8      29 ..     155     176 ..     153     182 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.35
                                    HHHHHHHHHHHHHHHHHH CS
                          HisKA  40 yletiesearrldhlved 57 
                                      + ++s+ + +++lv+d
  gi|116754975|ref|YP_844093.1| 120 KEAMLRSSHKTMEKLVSD 137
                                    445667777788888877 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 6.8e-06
                                    HHHHHHHHHHHHHHHHHHHHHC CS
                          HisKA   8 gvaHELrtPLsailgnaeaLkr 29 
                                    +++H++r PL +i+g++  Lk+
  gi|116754975|ref|YP_844093.1| 155 TISHDMRAPLLTISGFLGFLKE 176
                                    89******************88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); 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: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1219.26
//
Query:       gi|116754976|ref|YP_844094.1|  [L=75]
Description: hypothetical protein Mthe_1688 [Methanosaeta thermophila PT]
Scores for complete 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   16.7   1.2     0.0039   16.5   1.2    1.1  1  UbiA             UbiA prenyltransferase family
      0.009   15.9   1.1     0.0093   15.8   1.1    1.0  1  FA_desaturase    Fatty acid desaturase
  ------ inclusion threshold ------
        3.1    7.8   5.8       0.18   11.7   0.5    1.7  2  Sec20            Sec20
        7.8    7.0  10.4         12    6.4  10.4    1.3  1  PhoR             Phosphate regulon sensor protein PhoR


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   1.2   8.7e-07    0.0039      72     112 ..      35      72 ..      18      74 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 8.7e-07
                           UbiA  72 faivllilgllllalllnpltallgllalllyvvYtglrlK 112
                                    + ++l+++ +++l ++   ++a l+++++++yvvY+   lK
  gi|116754976|ref|YP_844094.1|  35 ILLILAVILVIVL-WGPLMWLAKLVVFVIAVYVVYQ--LLK 72 
                                    4455555555555.6667777789999999999999..887 PP

>> FA_desaturase  Fatty acid desaturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   1.1   2.1e-06    0.0093     124     175 ..      21      70 ..       6      74 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.1e-06
                  FA_desaturase 124 rrapsksrrrkwrllawlllllawlglwlalllllglalllwlvplllllfl 175
                                     + +s+ ++r++ l+++ l+++ +++lw++l +l+ l+  ++++++ ++ +l
  gi|116754976|ref|YP_844094.1|  21 VSLMSRFKKRDRNLILLILAVILVIVLWGPLMWLAKLV--VFVIAVYVVYQL 70 
                                    55566677777888888888888899*******99998..666666666555 PP

>> Sec20  Sec20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.5   4.1e-05      0.18      55      86 ..      17      48 ..       5      56 .. 0.89
   2 ?   -1.4   0.7      0.49   2.2e+03      79      89 ..      59      68 ..      51      71 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.1e-05
                          Sec20 55 skklvkklerrdktdkllvflalglflacvvy 86
                                    +++v+ + r  k d+ l++l l+ +l++v++
  gi|116754976|ref|YP_844094.1| 17 HQHIVSLMSRFKKRDRNLILLILAVILVIVLW 48
                                   4679**************************99 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.49
                          Sec20 79 lflacvvyvvk 89
                                    f+++ vyvv+
  gi|116754976|ref|YP_844094.1| 59 VFVIA-VYVVY 68
                                   34443.58887 PP

>> PhoR  Phosphate regulon sensor protein PhoR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4  10.4    0.0027        12       7      47 ..      32      72 ..      26      72 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0027
                           PhoR  7 lrlallllaallvgllvgalaallllalllllawhlyqllr 47
                                   + l+ll+la++lv +l g l++l  l+++++ ++ +yqll+
  gi|116754976|ref|YP_844094.1| 32 RNLILLILAVILVIVLWGPLMWLAKLVVFVIAVYVVYQLLK 72
                                   56889999999**********************99999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1393  (0.0776954); expected 358.6 (0.02)
Passed bias filter:                      609  (0.0339673); 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):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 552.98
//
Query:       gi|116754977|ref|YP_844095.1|  [L=557]
Description: hypothetical protein Mthe_1689 [Methanosaeta thermophila PT]
Scores for 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-25   88.1  60.9    2.9e-08   33.7   9.0    7.1  7  Pentapeptide_3  Pentapeptide repeats (9 copies)


Domain annotation for each model (and alignments):
>> Pentapeptide_3  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.3   4.8e-10   8.6e-06       2      44 ..     113     156 ..     112     160 .. 0.91
   2 !   32.8   7.6   3.2e-12   5.8e-08       1      47 [.     167     214 ..     156     215 .. 0.96
   3 !   23.3   9.6   2.9e-09   5.2e-05       1      47 [.     189     236 ..     189     237 .. 0.93
   4 !   33.7   9.0   1.6e-12   2.9e-08       1      47 [.     233     280 ..     233     281 .. 0.96
   5 !    8.7  11.8    0.0001       1.9       5      41 ..     292     329 ..     277     336 .. 0.51
   6 !    9.7   1.1   5.2e-05      0.93       6      41 ..     315     349 ..     310     363 .. 0.61
   7 ?   -2.3   0.2       0.3   5.4e+03      33      40 ..     504     511 ..     500     516 .. 0.58

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 4.8e-10
                 Pentapeptide_3   2 sganFsgaadFrgatFsgaasFsnadF.gsadFsgarFtgdvdF 44 
                                    +g++F g+ +++g++Fsg++  ++a F ++++F+ga+  + ++F
  gi|116754977|ref|YP_844095.1| 113 NGVEFMGPLNLSGTVFSGDVAARGASFgSDVSFAGAHLLRVAEF 156
                                    799************************66*******98866777 PP

  == domain 2  score: 32.8 bits;  conditional E-value: 3.2e-12
                 Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadF.gsadFsgarFtgdvdFsga 47 
                                    F+g+nF+g++++  a Fs+  sF++a F + adFs+a+F +d++F+++
  gi|116754977|ref|YP_844095.1| 167 FVGTNFHGPVSMGYAQFSKVGSFEGAAFwNCADFSNAQFMDDTSFERV 214
                                    999*******************************************97 PP

  == domain 3  score: 23.3 bits;  conditional E-value: 2.9e-09
                 Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadF.gsadFsgarFtgdvdFsga 47 
                                    F+ga F ++adF++a F +++sF++ +F +s +F+ arF++  +F ++
  gi|116754977|ref|YP_844095.1| 189 FEGAAFWNCADFSNAQFMDDTSFERVHFlRSTSFEFARFYQLISFWRS 236
                                    999*************************************87888776 PP

  == domain 4  score: 33.7 bits;  conditional E-value: 1.6e-12
                 Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadF.gsadFsgarFtgdvdFsga 47 
                                    F +++F+  ++F ++ Fsg+a+F +  F ++a F g+rF++dv+Fs+a
  gi|116754977|ref|YP_844095.1| 233 FWRSVFHEEVSFANSEFSGTANFISVSFdENAIFMGSRFSHDVTFSAA 280
                                    789*************************88***************987 PP

  == domain 5  score: 8.7 bits;  conditional E-value: 0.0001
                 Pentapeptide_3   5 nFsgaadFrgatFsgaasFsnadF.gsadFsgarFtgd 41 
                                     F+g  dF+ a F++ a+F  a + ++ +F++++F+gd
  gi|116754977|ref|YP_844095.1| 292 AFQGFSDFSSALFKSVAFFGLAKLeDNTRFANTTFDGD 329
                                    34444455555555555566666644666666666665 PP

  == domain 6  score: 9.7 bits;  conditional E-value: 5.2e-05
                 Pentapeptide_3   6 FsgaadFrgatFsgaasFsnadFgsadFsgarFtgd 41 
                                    ++++++F ++tF+g+   +++++ s  +++a F+ d
  gi|116754977|ref|YP_844095.1| 315 LEDNTRFANTTFDGDLVLTSSRIYSMQLENASFS-D 349
                                    5566677777777777666666644444444444.3 PP

  == domain 7  score: -2.3 bits;  conditional E-value: 0.3
                 Pentapeptide_3  33 FsgarFtg 40 
                                    Fs+++F  
  gi|116754977|ref|YP_844095.1| 504 FSDSIFFS 511
                                    66666653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (557 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 4214.70
//
Query:       gi|116754978|ref|YP_844096.1|  [L=2713]
Description: hypothetical protein Mthe_1690 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-48  162.4  77.5    0.00061   20.1   1.3   12.9 12  Ig_2             Immunoglobulin domain
    2.1e-37  126.6  83.5     0.0021   17.8   0.2   15.0 14  SprB             SprB repeat
    2.2e-36  124.3  52.7     0.0033   18.0   0.2   13.3 11  Ig_3             Immunoglobulin domain
    3.3e-35  120.0   3.2       0.55   10.3   0.0   14.2 14  I-set            Immunoglobulin I-set domain
    1.9e-31  108.2  84.8    1.1e-16   60.9   4.1   11.9  7  DUF11            Domain of unknown function DUF11
    5.8e-14   51.9  24.4        4.2    7.5   0.0   11.4 11  C2-set_2         CD80-like C2-set immunoglobulin domain
    2.5e-13   50.2   1.7    2.5e-13   50.2   1.7   10.9 13  SdrD_B           SdrD B-like domain
    1.9e-06   28.1   0.1    1.9e-06   28.1   0.1   13.3 14  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
    1.5e-05   25.5  91.6        2.3    8.9   0.4   15.5 14  MBG              MBG domain
    9.9e-05   22.3   0.2     0.0017   18.3   0.2    3.4  1  CarbopepD_reg_2  CarboxypepD_reg-like domain
     0.0011   19.2   3.3        1.4    9.1   0.0    5.1  4  bMG10            Bacterial Alpha-2-macroglobulin MG10 domain
     0.0039   17.4  23.7       0.25   11.6   0.5    7.1  7  CARDB            CARDB
     0.0053   17.0   0.1       0.66   10.3   0.0    3.9  2  Chlam_OMP6       Chlamydia cysteine-rich outer membrane prote
     0.0062   16.8   5.7     0.0062   16.8   5.7   10.0 12  SpaA             Prealbumin-like fold domain
     0.0096   15.8   0.7       0.52   10.1   0.1    3.2  3  DUF4897          Domain of unknown function (DUF4897)
  ------ inclusion threshold ------
      0.011   15.1   2.7        2.1    7.7   0.0    3.8  4  TRAP_beta        Translocon-associated protein beta (TRAPB)
      0.014   15.5   0.0      0.051   13.7   0.0    1.9  1  DUF2012          Protein of unknown function (DUF2012)
      0.054   13.5   1.2         63    3.7   0.1    5.6  4  DUF1573          Protein of unknown function (DUF1573)
       0.16   12.0   0.2         30    4.7   0.0    4.0  3  CusF_Ec          Copper binding periplasmic protein CusF
       0.18   11.7   0.5        1.8    8.3   0.1    2.8  3  Peptidase_M73    Camelysin metallo-endopeptidase
       0.41   10.1  18.7         79    2.7   0.0    7.6  8  YrbL-PhoP_reg    PhoP regulatory network protein YrbL
        7.8    6.1  60.9          7    6.2   0.3    9.7 11  DUF1897          Domain of unknown function (DUF1897)
        9.3    6.6  20.2       0.51   10.6   0.4    6.9  5  NPCBM_assoc      NPCBM-associated, NEW3 domain of alpha-galac


Domain annotation for each model (and alignments):
>> Ig_2  Immunoglobulin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   1.3   7.8e-07   0.00061      15      77 ..     340     410 ..     327     412 .. 0.82
   2 !   20.1   1.3   7.9e-07   0.00062      15      77 ..     423     493 ..     409     495 .. 0.82
   3 !   20.0   1.4   8.4e-07   0.00065      15      77 ..     506     576 ..     492     578 .. 0.82
   4 !   19.9   0.3   8.6e-07   0.00067      15      77 ..     589     659 ..     575     662 .. 0.82
   5 !   18.0   1.0   3.4e-06    0.0027       9      77 ..     666     742 ..     658     744 .. 0.79
   6 !   19.9   0.3     9e-07    0.0007      15      77 ..     755     825 ..     741     827 .. 0.82
   7 !   18.1   0.9   3.1e-06    0.0024       9      77 ..     832     908 ..     824     910 .. 0.79
   8 !   18.9   1.1   1.8e-06    0.0014      15      77 ..     921     991 ..     907     993 .. 0.82
   9 !   20.0   1.4   8.4e-07   0.00066      15      77 ..    1004    1074 ..     990    1076 .. 0.82
  10 !   19.9   0.3     9e-07    0.0007      15      77 ..    1087    1157 ..    1073    1159 .. 0.82
  11 !   19.1   0.8   1.6e-06    0.0013       9      78 ..    1164    1240 ..    1155    1240 .. 0.81
  12 ?   -1.9   0.0       5.7   4.5e+03      49      68 ..    1569    1588 ..    1550    1597 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 7.8e-07
                           Ig_2  15 epvtLtCsap..........gnpppkvqwykggevinsspnffinavsaedsgtYtCrarntkgg.evsrpvel 77 
                                     +++L+C ++          g+p++++qwyk++++i   +    ++ +a+ +g+Y+ +++  +g+ ++s+ v +
  gi|116754978|ref|YP_844096.1| 340 TSGELNCNVNeveleatvsgGKPDYSYQWYKDNSPITGATG---SSYTATGAGSYKVVVTDANGCtGTSDEVPV 410
                                    456799*99999999999988999*************7777...799********9999888875477777766 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 7.9e-07
                           Ig_2  15 epvtLtCsap..........gnpppkvqwykggevinsspnffinavsaedsgtYtCrarntkgg.evsrpvel 77 
                                     +++L+C ++          g+p++++qwyk++++i   +    ++ +a+ +g+Y+ +++  +g+ ++s+ v +
  gi|116754978|ref|YP_844096.1| 423 TSGELNCNVNeveleatvsgGKPDYSYQWYKDNSPITGATG---SSYTATGAGSYKVVVTDANGCtGTSDEVPV 493
                                    56789***999999999*988999*************7777...799********9999888875477777766 PP

  == domain 3  score: 20.0 bits;  conditional E-value: 8.4e-07
                           Ig_2  15 epvtLtCsap..........gnpppkvqwykggevinsspnffinavsaedsgtYtCrarntkgg.evsrpvel 77 
                                     +++L+C ++          g+p++++qwyk++++i   +    ++ +a+ +g+Y+ +++  +g+ ++s+ v +
  gi|116754978|ref|YP_844096.1| 506 TSGELNCNVNeveleatvsgGKPDYSYQWYKDNSPITGATG---SSYTATGAGSYKVVVTDANGCtGTSDEVPV 576
                                    56789***999999999*988999*************7777...799********9999888875477777766 PP

  == domain 4  score: 19.9 bits;  conditional E-value: 8.6e-07
                           Ig_2  15 epvtLtCsap..........gnpppkvqwykggevinsspnffinavsaedsgtYtCrarntkgg.evsrpvel 77 
                                     +++L+C ++          g+p++++qwykg++ in  +    ++ +a  +g+Y+ +++  +g+ ++s+ v++
  gi|116754978|ref|YP_844096.1| 589 TSGELNCNVNeveleatvsgGKPDYSYQWYKGDSLINGATG---SSYTAREAGIYKVEVTDANGCtGTSNEVTV 659
                                    56789***999999999*988999*************7777...7999999****9999888875478888877 PP

  == domain 5  score: 18.0 bits;  conditional E-value: 3.4e-06
                           Ig_2   9 tvvtegepvtLtCsap..........gnpppkvqwykggevinsspnffinavsaedsgtYtCrarntkgg.evsrpvel 77 
                                    +v     +++L+C ++          g +p+++qwyk++++i   +    ++ +a+ +g+Y+ +++  +g+ ++s+ v +
  gi|116754978|ref|YP_844096.1| 666 SVSVSPASGELNCNVNsieltatvtgGEEPYSYQWYKDDSPITGATG---SSYTATGAGSYKVVVTDANGCtGTSDEVPV 742
                                    4444444567****999999999997788899***********7777...799********9999888875477777766 PP

  == domain 6  score: 19.9 bits;  conditional E-value: 9e-07
                           Ig_2  15 epvtLtCsap..........gnpppkvqwykggevinsspnffinavsaedsgtYtCrarntkgg.evsrpvel 77 
                                     +++L+C ++          g+p++++qwykg++ in  +    ++ +a  +g+Y+ +++  +g+ ++s+ v++
  gi|116754978|ref|YP_844096.1| 755 TSGELNCNVNeveleatvsgGKPDYSYQWYKGDSLINGATG---SSYTAREAGIYKVEVTDANGCtGTSNEVTV 825
                                    56789***999999999*988999*************7777...7999999****9999988875488888877 PP

  == domain 7  score: 18.1 bits;  conditional E-value: 3.1e-06
                           Ig_2   9 tvvtegepvtLtCsap..........gnpppkvqwykggevinsspnffinavsaedsgtYtCrarntkgg.evsrpvel 77 
                                    +v     +++L+C ++          g +p+++qwyk++++i   +    ++ +a+ +g+Y+ +++  +g+ ++s+ v +
  gi|116754978|ref|YP_844096.1| 832 SVSVSPASGELNCNVNsieltatvtgGEEPYSYQWYKDDSPITGATG---SSYTATGAGSYKVVVTDANGCtGTSDEVPV 908
                                    4444444567****999999999997788899***********7777...799********9999888875477777766 PP

  == domain 8  score: 18.9 bits;  conditional E-value: 1.8e-06
                           Ig_2  15 epvtLtCsap..........gnpppkvqwykggevinsspnffinavsaedsgtYtCrarntkgg.evsrpvel 77 
                                     +++L+C ++          g+p++++qwyk++++i   +    ++ +a+ +g+Y+ +++  +g+ ++s+ v +
  gi|116754978|ref|YP_844096.1| 921 TSGELNCNVNeveleatvsgGKPDYSYQWYKDDSPITGATG---SSYTATGAGSYKVVVTDANGCtGTSDEVPV 991
                                    56789***999999999*988999*************7777...799********9999888875477777766 PP

  == domain 9  score: 20.0 bits;  conditional E-value: 8.4e-07
                           Ig_2   15 epvtLtCsap..........gnpppkvqwykggevinsspnffinavsaedsgtYtCrarntkgg.evsrpvel 77  
                                      +++L+C ++          g+p++++qwyk++++i   +    ++ +a+ +g+Y+ +++  +g+ ++s+ v +
  gi|116754978|ref|YP_844096.1| 1004 TSGELNCNVNeveleatvsgGKPDYSYQWYKDNSPITGATG---SSYTATGAGSYKVVVTDANGCtGTSDEVPV 1074
                                     56789***999999999*988999*************7777...799********9999888875477777766 PP

  == domain 10  score: 19.9 bits;  conditional E-value: 9e-07
                           Ig_2   15 epvtLtCsap..........gnpppkvqwykggevinsspnffinavsaedsgtYtCrarntkgg.evsrpvel 77  
                                      +++L+C ++          g+p++++qwykg++ in  +    ++ +a  +g+Y+ +++  +g+ ++s+ v++
  gi|116754978|ref|YP_844096.1| 1087 TSGELNCNVNeveleatvsgGKPDYSYQWYKGDSLINGATG---SSYTAREAGIYKVEVTDANGCtGTSNEVTV 1157
                                     56789***999999999*988999*************7777...7999999****9999988875488888877 PP

  == domain 11  score: 19.1 bits;  conditional E-value: 1.6e-06
                           Ig_2    9 tvvtegepvtLtCsap..........gnpppkvqwykggevinsspnffinavsaedsgtYtCrarntkggevsrpve 76  
                                     +v     +++L+C ++          g +p+++qwyk++++i   +    ++ +a+ +g+Y+ +++  +g++ +++++
  gi|116754978|ref|YP_844096.1| 1164 SVSVSPASGELNCNVNsieltatvtgGEEPYSYQWYKDDSPITGATG---SSYTATGAGSYKVVVTDANGCTAESSAT 1238
                                     4444444567****999999999997788899***********7777...79************99999988888888 PP

                           Ig_2   77 lt 78  
                                     +t
  gi|116754978|ref|YP_844096.1| 1239 IT 1240
                                     75 PP

  == domain 12  score: -1.9 bits;  conditional E-value: 5.7
                           Ig_2   49 navsaedsgtYtCrarntkg 68  
                                      +v+++d  tYt +++nt+ 
  gi|116754978|ref|YP_844096.1| 1569 ETVEPGDTITYTLTVKNTGS 1588
                                     569999999*******9774 PP

>> SprB  SprB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.3   1.1e-05    0.0086       5      33 ..     342     369 ..     338     372 .. 0.87
   2 !   15.7   0.2   1.2e-05    0.0094       6      33 ..     426     452 ..     422     455 .. 0.87
   3 !   15.7   0.2   1.2e-05    0.0094       6      33 ..     509     535 ..     505     538 .. 0.87
   4 !   17.8   0.2   2.7e-06    0.0021       6      36 ..     592     621 ..     588     622 .. 0.86
   5 !   16.1   0.4   8.9e-06     0.007       8      33 ..     677     701 ..     672     705 .. 0.82
   6 !   17.8   0.2   2.7e-06    0.0021       6      36 ..     758     787 ..     754     788 .. 0.86
   7 !   16.1   0.4   8.9e-06     0.007       8      33 ..     843     867 ..     838     871 .. 0.82
   8 !   16.1   0.1   9.2e-06    0.0072       6      33 ..     924     950 ..     920     954 .. 0.85
   9 !   15.7   0.2   1.2e-05    0.0094       6      33 ..    1007    1033 ..    1003    1036 .. 0.87
  10 !   17.8   0.2   2.7e-06    0.0021       6      36 ..    1090    1119 ..    1086    1120 .. 0.86
  11 !   16.1   0.4   8.9e-06     0.007       8      33 ..    1175    1199 ..    1170    1203 .. 0.82
  12 ?   -3.1   3.5       8.7   6.8e+03      13      31 ..    1385    1404 ..    1384    1409 .. 0.79
  13 ?   -3.0   0.3       8.3   6.5e+03      13      20 ..    1585    1592 ..    1584    1592 .. 0.91
  14 ?    2.3   0.5      0.19   1.4e+02      25      36 ..    1895    1906 ..    1886    1907 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.1e-05
                           SprB   5 tnvtCnggndGsItvtvsGGtapYtYswn 33 
                                      ++Cn  n  + ++tvsGG + Y+Y+w 
  gi|116754978|ref|YP_844096.1| 342 GELNCN-VNEVELEATVSGGKPDYSYQWY 369
                                    567888.999999***************6 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.2e-05
                           SprB   6 nvtCnggndGsItvtvsGGtapYtYswn 33 
                                     ++Cn  n  + ++tvsGG + Y+Y+w 
  gi|116754978|ref|YP_844096.1| 426 ELNCN-VNEVELEATVSGGKPDYSYQWY 452
                                    57888.888899***************6 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 1.2e-05
                           SprB   6 nvtCnggndGsItvtvsGGtapYtYswn 33 
                                     ++Cn  n  + ++tvsGG + Y+Y+w 
  gi|116754978|ref|YP_844096.1| 509 ELNCN-VNEVELEATVSGGKPDYSYQWY 535
                                    57888.888899***************6 PP

  == domain 4  score: 17.8 bits;  conditional E-value: 2.7e-06
                           SprB   6 nvtCnggndGsItvtvsGGtapYtYswngga 36 
                                     ++Cn  n  + ++tvsGG + Y+Y+w  g+
  gi|116754978|ref|YP_844096.1| 592 ELNCN-VNEVELEATVSGGKPDYSYQWYKGD 621
                                    57888.888899***************9886 PP

  == domain 5  score: 16.1 bits;  conditional E-value: 8.9e-06
                           SprB   8 tCnggndGsItvtvsGGtapYtYswn 33 
                                    +Cn  n  + t+tv+GG  pY+Y+w 
  gi|116754978|ref|YP_844096.1| 677 NCN-VNSIELTATVTGGEEPYSYQWY 701
                                    566.6666789**************7 PP

  == domain 6  score: 17.8 bits;  conditional E-value: 2.7e-06
                           SprB   6 nvtCnggndGsItvtvsGGtapYtYswngga 36 
                                     ++Cn  n  + ++tvsGG + Y+Y+w  g+
  gi|116754978|ref|YP_844096.1| 758 ELNCN-VNEVELEATVSGGKPDYSYQWYKGD 787
                                    57888.888899***************9886 PP

  == domain 7  score: 16.1 bits;  conditional E-value: 8.9e-06
                           SprB   8 tCnggndGsItvtvsGGtapYtYswn 33 
                                    +Cn  n  + t+tv+GG  pY+Y+w 
  gi|116754978|ref|YP_844096.1| 843 NCN-VNSIELTATVTGGEEPYSYQWY 867
                                    566.6666789**************7 PP

  == domain 8  score: 16.1 bits;  conditional E-value: 9.2e-06
                           SprB   6 nvtCnggndGsItvtvsGGtapYtYswn 33 
                                     ++Cn  n  + ++tvsGG + Y+Y+w 
  gi|116754978|ref|YP_844096.1| 924 ELNCN-VNEVELEATVSGGKPDYSYQWY 950
                                    57888.888899***************7 PP

  == domain 9  score: 15.7 bits;  conditional E-value: 1.2e-05
                           SprB    6 nvtCnggndGsItvtvsGGtapYtYswn 33  
                                      ++Cn  n  + ++tvsGG + Y+Y+w 
  gi|116754978|ref|YP_844096.1| 1007 ELNCN-VNEVELEATVSGGKPDYSYQWY 1033
                                     57888.888899***************6 PP

  == domain 10  score: 17.8 bits;  conditional E-value: 2.7e-06
                           SprB    6 nvtCnggndGsItvtvsGGtapYtYswngga 36  
                                      ++Cn  n  + ++tvsGG + Y+Y+w  g+
  gi|116754978|ref|YP_844096.1| 1090 ELNCN-VNEVELEATVSGGKPDYSYQWYKGD 1119
                                     57888.888899***************9886 PP

  == domain 11  score: 16.1 bits;  conditional E-value: 8.9e-06
                           SprB    8 tCnggndGsItvtvsGGtapYtYswn 33  
                                     +Cn  n  + t+tv+GG  pY+Y+w 
  gi|116754978|ref|YP_844096.1| 1175 NCN-VNSIELTATVTGGEEPYSYQWY 1199
                                     566.6666789**************7 PP

  == domain 12  score: -3.1 bits;  conditional E-value: 8.7
                           SprB   13 ndGsItvtv.sGGtapYtYs 31  
                                     +dG+ t++  +G  ++Y+++
  gi|116754978|ref|YP_844096.1| 1385 SDGTTTISTtTGSDGSYSFT 1404
                                     79*****6626666*99986 PP

  == domain 13  score: -3.0 bits;  conditional E-value: 8.3
                           SprB   13 ndGsItvt 20  
                                     n+Gs+t++
  gi|116754978|ref|YP_844096.1| 1585 NTGSATIN 1592
                                     9*****98 PP

  == domain 14  score: 2.3 bits;  conditional E-value: 0.19
                           SprB   25 tapYtYswngga 36  
                                     t +YtY++++g+
  gi|116754978|ref|YP_844096.1| 1895 TITYTYTITNGG 1906
                                     668*******96 PP

>> Ig_3  Immunoglobulin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.2   0.00015      0.12       6      48 ..     337     380 ..     334     403 .. 0.66
   2 !   13.7   0.1   9.3e-05     0.073       2      48 ..     416     463 ..     415     486 .. 0.69
   3 !   13.7   0.1   9.3e-05     0.073       2      48 ..     499     546 ..     498     569 .. 0.69
   4 !   11.3   0.1   0.00053      0.42       2      48 ..     582     629 ..     581     658 .. 0.71
   5 !   17.9   0.2   4.5e-06    0.0035       2      48 ..     665     712 ..     664     735 .. 0.73
   6 !   11.3   0.1   0.00053      0.42       2      48 ..     748     795 ..     747     824 .. 0.71
   7 !   17.9   0.2   4.5e-06    0.0035       2      48 ..     831     878 ..     830     901 .. 0.73
   8 !   13.5   0.1    0.0001     0.081       2      48 ..     914     961 ..     913     984 .. 0.69
   9 !   13.7   0.1   9.3e-05     0.073       2      48 ..     997    1044 ..     996    1067 .. 0.69
  10 !   11.3   0.1   0.00053      0.42       2      48 ..    1080    1127 ..    1079    1156 .. 0.71
  11 !   18.0   0.2   4.2e-06    0.0033       2      49 ..    1163    1211 ..    1162    1242 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00015
                                    CCCSCEE.EETTS-EEEEEEEEEES--.EEEEEETTS...TTCSE CS
                           Ig_3   6 vppsstv.vtegesvtLtCeaegnppp.titWykngeklssnsts 48 
                                    v+p+s +   + ++v+L+ +++g+ p  +++Wyk++++++   t 
  gi|116754978|ref|YP_844096.1| 337 VSPTSGElNCNVNEVELEATVSGGKPDySYQWYKDNSPITGA-TG 380
                                    5555555455667899*****8888889*********74442.22 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 9.3e-05
                                    EEEECCCSCEE.EETTS-EEEEEEEEEES--.EEEEEETTS...TTCSE CS
                           Ig_3   2 PvItvppsstv.vtegesvtLtCeaegnppp.titWykngeklssnsts 48 
                                    P+++v p+s +   + ++v+L+ +++g+ p  +++Wyk++++++   t 
  gi|116754978|ref|YP_844096.1| 416 PSVSVGPTSGElNCNVNEVELEATVSGGKPDySYQWYKDNSPITGA-TG 463
                                    77777777766566677899*****8888889*********74442.22 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 9.3e-05
                                    EEEECCCSCEE.EETTS-EEEEEEEEEES--.EEEEEETTS...TTCSE CS
                           Ig_3   2 PvItvppsstv.vtegesvtLtCeaegnppp.titWykngeklssnsts 48 
                                    P+++v p+s +   + ++v+L+ +++g+ p  +++Wyk++++++   t 
  gi|116754978|ref|YP_844096.1| 499 PSVSVGPTSGElNCNVNEVELEATVSGGKPDySYQWYKDNSPITGA-TG 546
                                    77777777766566677899*****8888889*********74442.22 PP

  == domain 4  score: 11.3 bits;  conditional E-value: 0.00053
                                    EEEECCCSCEE.EETTS-EEEEEEEEEES--.EEEEEETTS...TTCSE CS
                           Ig_3   2 PvItvppsstv.vtegesvtLtCeaegnppp.titWykngeklssnsts 48 
                                    P+++v p+s +   + ++v+L+ +++g+ p  +++Wyk+++ ++   t 
  gi|116754978|ref|YP_844096.1| 582 PSVSVGPTSGElNCNVNEVELEATVSGGKPDySYQWYKGDSLING-ATG 629
                                    77777777766566677899*****8888889********97333.232 PP

  == domain 5  score: 17.9 bits;  conditional E-value: 4.5e-06
                                    EEEECCCSCEE.EETTS-EEEEEEEEEES--.EEEEEETTS...TTCSE CS
                           Ig_3   2 PvItvppsstv.vtegesvtLtCeaegnppp.titWykngeklssnsts 48 
                                    P+++v+p s +   + +s++Lt +++g+ +p +++Wyk++++++   t 
  gi|116754978|ref|YP_844096.1| 665 PSVSVSPASGElNCNVNSIELTATVTGGEEPySYQWYKDDSPITGA-TG 712
                                    89998888887677778999*********************74442.22 PP

  == domain 6  score: 11.3 bits;  conditional E-value: 0.00053
                                    EEEECCCSCEE.EETTS-EEEEEEEEEES--.EEEEEETTS...TTCSE CS
                           Ig_3   2 PvItvppsstv.vtegesvtLtCeaegnppp.titWykngeklssnsts 48 
                                    P+++v p+s +   + ++v+L+ +++g+ p  +++Wyk+++ ++   t 
  gi|116754978|ref|YP_844096.1| 748 PSVSVGPTSGElNCNVNEVELEATVSGGKPDySYQWYKGDSLING-ATG 795
                                    77777777766566677899*****8888889********97333.232 PP

  == domain 7  score: 17.9 bits;  conditional E-value: 4.5e-06
                                    EEEECCCSCEE.EETTS-EEEEEEEEEES--.EEEEEETTS...TTCSE CS
                           Ig_3   2 PvItvppsstv.vtegesvtLtCeaegnppp.titWykngeklssnsts 48 
                                    P+++v+p s +   + +s++Lt +++g+ +p +++Wyk++++++   t 
  gi|116754978|ref|YP_844096.1| 831 PSVSVSPASGElNCNVNSIELTATVTGGEEPySYQWYKDDSPITGA-TG 878
                                    89998888887677778999*********************74442.22 PP

  == domain 8  score: 13.5 bits;  conditional E-value: 0.0001
                                    EEEECCCSCEE.EETTS-EEEEEEEEEES--.EEEEEETTS...TTCSE CS
                           Ig_3   2 PvItvppsstv.vtegesvtLtCeaegnppp.titWykngeklssnsts 48 
                                    P+++v p+s +   + ++v+L+ +++g+ p  +++Wyk++++++   t 
  gi|116754978|ref|YP_844096.1| 914 PSVSVGPTSGElNCNVNEVELEATVSGGKPDySYQWYKDDSPITGA-TG 961
                                    77777777766566677899*****8888889*********74442.22 PP

  == domain 9  score: 13.7 bits;  conditional E-value: 9.3e-05
                                     EEEECCCSCEE.EETTS-EEEEEEEEEES--.EEEEEETTS...TTCSE CS
                           Ig_3    2 PvItvppsstv.vtegesvtLtCeaegnppp.titWykngeklssnsts 48  
                                     P+++v p+s +   + ++v+L+ +++g+ p  +++Wyk++++++   t 
  gi|116754978|ref|YP_844096.1|  997 PSVSVGPTSGElNCNVNEVELEATVSGGKPDySYQWYKDNSPITGA-TG 1044
                                     77777777766566677899*****8888889*********74442.22 PP

  == domain 10  score: 11.3 bits;  conditional E-value: 0.00053
                                     EEEECCCSCEE.EETTS-EEEEEEEEEES--.EEEEEETTS...TTCSE CS
                           Ig_3    2 PvItvppsstv.vtegesvtLtCeaegnppp.titWykngeklssnsts 48  
                                     P+++v p+s +   + ++v+L+ +++g+ p  +++Wyk+++ ++   t 
  gi|116754978|ref|YP_844096.1| 1080 PSVSVGPTSGElNCNVNEVELEATVSGGKPDySYQWYKGDSLING-ATG 1127
                                     77777777766566677899*****8888889********97333.232 PP

  == domain 11  score: 18.0 bits;  conditional E-value: 4.2e-06
                                     EEEECCCSCEE.EETTS-EEEEEEEEEES--.EEEEEETTS...TTCSEE CS
                           Ig_3    2 PvItvppsstv.vtegesvtLtCeaegnppp.titWykngeklssnstss 49  
                                     P+++v+p s +   + +s++Lt +++g+ +p +++Wyk++++++   t s
  gi|116754978|ref|YP_844096.1| 1163 PSVSVSPASGElNCNVNSIELTATVTGGEEPySYQWYKDDSPITGA-TGS 1211
                                     89998888887677778999*********************84442.222 PP

>> I-set  Immunoglobulin I-set domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0    0.0011      0.88      17      63 ..     350     398 ..     337     402 .. 0.81
   2 !    9.6   0.0    0.0012      0.91      17      63 ..     433     481 ..     422     485 .. 0.81
   3 !    9.6   0.0    0.0012      0.91      17      63 ..     516     564 ..     505     568 .. 0.81
   4 !    8.3   0.0    0.0031       2.4      17      63 ..     599     647 ..     588     657 .. 0.82
   5 !    8.7   0.0    0.0023       1.8      17      63 ..     682     730 ..     667     734 .. 0.81
   6 !    8.3   0.0    0.0031       2.4      17      63 ..     765     813 ..     754     823 .. 0.82
   7 !    8.7   0.0    0.0023       1.8      17      63 ..     848     896 ..     833     900 .. 0.81
   8 !   10.3   0.0    0.0007      0.55      17      63 ..     931     979 ..     920     983 .. 0.81
   9 !    9.6   0.0    0.0012      0.91      17      63 ..    1014    1062 ..    1003    1066 .. 0.81
  10 !    8.3   0.0    0.0031       2.4      17      63 ..    1097    1145 ..    1086    1155 .. 0.82
  11 !    9.0   0.0    0.0018       1.4      17      63 ..    1180    1228 ..    1165    1243 .. 0.79
  12 ?   -0.8   0.0       2.1   1.6e+03      62      80 ..    1570    1588 ..    1531    1596 .. 0.72
  13 ?   -2.8   0.0       8.8   6.9e+03      39      65 ..    1699    1725 ..    1695    1729 .. 0.82
  14 ?   -2.6   0.0       7.6   5.9e+03       5      33 ..    1883    1911 ..    1880    1911 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0011
                                    -EEEEEEEECS.SS-EEEEEETTCB-STSSSEEEEEET.TEEEEEESSB CS
                          I-set  17 svelectveGe.pepsvsWakdgselkssqrvkvtvee.aeytLtIsnv 63 
                                    +vele+tv+G  p+ s +W+kd+s+++     ++t+++ ++y+ +++++
  gi|116754978|ref|YP_844096.1| 350 EVELEATVSGGkPDYSYQWYKDNSPITGATGSSYTATGaGSYKVVVTDA 398
                                    699*****9744***************9777777777766776666655 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0012
                                    -EEEEEEEECS.SS-EEEEEETTCB-STSSSEEEEEET.TEEEEEESSB CS
                          I-set  17 svelectveGe.pepsvsWakdgselkssqrvkvtvee.aeytLtIsnv 63 
                                    +vele+tv+G  p+ s +W+kd+s+++     ++t+++ ++y+ +++++
  gi|116754978|ref|YP_844096.1| 433 EVELEATVSGGkPDYSYQWYKDNSPITGATGSSYTATGaGSYKVVVTDA 481
                                    699*****9744***************9777777777766776666655 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0012
                                    -EEEEEEEECS.SS-EEEEEETTCB-STSSSEEEEEET.TEEEEEESSB CS
                          I-set  17 svelectveGe.pepsvsWakdgselkssqrvkvtvee.aeytLtIsnv 63 
                                    +vele+tv+G  p+ s +W+kd+s+++     ++t+++ ++y+ +++++
  gi|116754978|ref|YP_844096.1| 516 EVELEATVSGGkPDYSYQWYKDNSPITGATGSSYTATGaGSYKVVVTDA 564
                                    699*****9744***************9777777777766776666655 PP

  == domain 4  score: 8.3 bits;  conditional E-value: 0.0031
                                    -EEEEEEEECS.SS-EEEEEETTCB-STSSSEEEEEET.TEEEEEESSB CS
                          I-set  17 svelectveGe.pepsvsWakdgselkssqrvkvtvee.aeytLtIsnv 63 
                                    +vele+tv+G  p+ s +W+k++s ++     ++t++e ++y+ +++++
  gi|116754978|ref|YP_844096.1| 599 EVELEATVSGGkPDYSYQWYKGDSLINGATGSSYTAREaGIYKVEVTDA 647
                                    699*****9744***************9777777777666777766665 PP

  == domain 5  score: 8.7 bits;  conditional E-value: 0.0023
                                    -EEEEEEEECSSS-.EEEEEETTCB-STSSSEEEEEET.TEEEEEESSB CS
                          I-set  17 svelectveGepep.svsWakdgselkssqrvkvtvee.aeytLtIsnv 63 
                                    s+el++tv+G +ep s +W+kd+s+++     ++t+++ ++y+ +++++
  gi|116754978|ref|YP_844096.1| 682 SIELTATVTGGEEPySYQWYKDDSPITGATGSSYTATGaGSYKVVVTDA 730
                                    799******98665499**********9777777777766776666655 PP

  == domain 6  score: 8.3 bits;  conditional E-value: 0.0031
                                    -EEEEEEEECS.SS-EEEEEETTCB-STSSSEEEEEET.TEEEEEESSB CS
                          I-set  17 svelectveGe.pepsvsWakdgselkssqrvkvtvee.aeytLtIsnv 63 
                                    +vele+tv+G  p+ s +W+k++s ++     ++t++e ++y+ +++++
  gi|116754978|ref|YP_844096.1| 765 EVELEATVSGGkPDYSYQWYKGDSLINGATGSSYTAREaGIYKVEVTDA 813
                                    699*****9744***************9777777777666777766665 PP

  == domain 7  score: 8.7 bits;  conditional E-value: 0.0023
                                    -EEEEEEEECSSS-.EEEEEETTCB-STSSSEEEEEET.TEEEEEESSB CS
                          I-set  17 svelectveGepep.svsWakdgselkssqrvkvtvee.aeytLtIsnv 63 
                                    s+el++tv+G +ep s +W+kd+s+++     ++t+++ ++y+ +++++
  gi|116754978|ref|YP_844096.1| 848 SIELTATVTGGEEPySYQWYKDDSPITGATGSSYTATGaGSYKVVVTDA 896
                                    799******98665499**********9777777777766776666655 PP

  == domain 8  score: 10.3 bits;  conditional E-value: 0.0007
                                    -EEEEEEEECS.SS-EEEEEETTCB-STSSSEEEEEET.TEEEEEESSB CS
                          I-set  17 svelectveGe.pepsvsWakdgselkssqrvkvtvee.aeytLtIsnv 63 
                                    +vele+tv+G  p+ s +W+kd+s+++     ++t+++ ++y+ +++++
  gi|116754978|ref|YP_844096.1| 931 EVELEATVSGGkPDYSYQWYKDDSPITGATGSSYTATGaGSYKVVVTDA 979
                                    699*****9744***************9777777777766776666655 PP

  == domain 9  score: 9.6 bits;  conditional E-value: 0.0012
                                     -EEEEEEEECS.SS-EEEEEETTCB-STSSSEEEEEET.TEEEEEESSB CS
                          I-set   17 svelectveGe.pepsvsWakdgselkssqrvkvtvee.aeytLtIsnv 63  
                                     +vele+tv+G  p+ s +W+kd+s+++     ++t+++ ++y+ +++++
  gi|116754978|ref|YP_844096.1| 1014 EVELEATVSGGkPDYSYQWYKDNSPITGATGSSYTATGaGSYKVVVTDA 1062
                                     699*****9744***************9777777777766776666655 PP

  == domain 10  score: 8.3 bits;  conditional E-value: 0.0031
                                     -EEEEEEEECS.SS-EEEEEETTCB-STSSSEEEEEET.TEEEEEESSB CS
                          I-set   17 svelectveGe.pepsvsWakdgselkssqrvkvtvee.aeytLtIsnv 63  
                                     +vele+tv+G  p+ s +W+k++s ++     ++t++e ++y+ +++++
  gi|116754978|ref|YP_844096.1| 1097 EVELEATVSGGkPDYSYQWYKGDSLINGATGSSYTAREaGIYKVEVTDA 1145
                                     699*****9744***************9777777777666777766665 PP

  == domain 11  score: 9.0 bits;  conditional E-value: 0.0018
                                     -EEEEEEEECSSS-.EEEEEETTCB-STSSSEEEEEET.TEEEEEESSB CS
                          I-set   17 svelectveGepep.svsWakdgselkssqrvkvtvee.aeytLtIsnv 63  
                                     s+el++tv+G +ep s +W+kd+s+++     ++t+++ ++y+ +++++
  gi|116754978|ref|YP_844096.1| 1180 SIELTATVTGGEEPySYQWYKDDSPITGATGSSYTATGaGSYKVVVTDA 1228
                                     799******98665499**********9777777776666666666555 PP

  == domain 12  score: -0.8 bits;  conditional E-value: 2.1
                                     SB-GGGGEEEEEEEEETSE CS
                          I-set   62 nvevsDeGkYtckatnsag 80  
                                      ve+ D+ +Yt++++n   
  gi|116754978|ref|YP_844096.1| 1570 TVEPGDTITYTLTVKNTGS 1588
                                     4666677777777777644 PP

  == domain 13  score: -2.8 bits;  conditional E-value: 8.8
                                     CB-STSSSEEEEEETTEEEEEESSB-G CS
                          I-set   39 selkssqrvkvtveeaeytLtIsnvev 65  
                                      +l+  ++++ t+++ +++L+Isnv+ 
  gi|116754978|ref|YP_844096.1| 1699 AKLNYVRKYRDTFDKVNASLVISNVTL 1725
                                     5667778888999999********986 PP

  == domain 14  score: -2.6 bits;  conditional E-value: 7.6
                                     ES-CEEEEETTS-EEEEEEEECSSS-EEE CS
                          I-set    5 qklkdvevseGesvelectveGepepsvs 33  
                                     ++++  ++s+G++++ + t++  +e+++s
  gi|116754978|ref|YP_844096.1| 1883 KRPSVEVASVGQTITYTYTITNGGEITIS 1911
                                     567777899******99999988887775 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   2.5    0.0001     0.081       6      85 ..     236     301 ..     223     319 .. 0.80
   2 ?    4.5   0.1     0.056        43      26      83 ..    1287    1351 ..    1285    1358 .. 0.80
   3 !   60.9   4.1   1.4e-19   1.1e-16       1      81 [.    1562    1645 ..    1562    1653 .. 0.86
   4 !    9.2   1.5    0.0018       1.4       3      37 ..    1883    1917 ..    1880    1956 .. 0.69
   5 !   34.2   0.0     3e-11   2.4e-08       2      80 ..    1986    2063 ..    1985    2072 .. 0.91
   6 !   28.3   0.1   2.1e-09   1.7e-06      16      88 ..    2457    2531 ..    2443    2534 .. 0.84
   7 !   15.5   0.0   2.1e-05     0.016       4      90 ..    2565    2650 ..    2564    2651 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.0001
                          DUF11   6 dksevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsftvrvtrtaasg 85 
                                    d++++  G+tvty+  v+Ntg +++++v +tD       +++   +           +Le+ge+a  + t +vt++   +
  gi|116754978|ref|YP_844096.1| 236 DPVTAGIGATVTYCYQVQNTGDVKLTDVSLTD---DKYGTITLDKT-----------TLEPGETAEGTSTHTVTPSDYPL 301
                                    5568899*************************...44444444444...........77888888877777777776554 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.056
                          DUF11   26 gpasangvvvtDtlPaglayvsvsas....qgtasaltsv...gsLeagesatlsftvrvtrtaa 83  
                                     g+    +++vt ++P g  + s         g+ s+++++    +L age+ +++ft + ++ ++
  gi|116754978|ref|YP_844096.1| 1287 GQLEPGEYTVTEIVPDGWDLSSIEIDgdtdGGSTSTTSGStatIDLDAGETIRVTFTNTLKTGGQ 1351
                                     556667999******999999988888887666666666677899***********988777665 PP

  == domain 3  score: 60.9 bits;  conditional E-value: 1.4e-19
                          DUF11    1 ltKtvdksevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsas....qgtasaltsvgsLeagesatlsf 74  
                                     + Kt d+++v pGdt+tytltv+Ntg a+ n+++v DtlP+g+ y s+       +    ++++ g Leag+s  +++
  gi|116754978|ref|YP_844096.1| 1562 IEKTADRETVEPGDTITYTLTVKNTGSATINDATVVDTLPPGTLYKSADPEpsgvS-GSVVTWNLGALEAGASVVITL 1638
                                     68**********************************************99975422.22355555*********9999 PP

                          DUF11   75 tvrvtrt 81  
                                     t++v   
  gi|116754978|ref|YP_844096.1| 1639 TATVESD 1645
                                     9999765 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.0018
                          DUF11    3 KtvdksevrpGdtvtytltvtNtgpasangvvvtD 37  
                                     K  + + +  G+t+tyt t tN g  + +++ v D
  gi|116754978|ref|YP_844096.1| 1883 KRPSVEVASVGQTITYTYTITNGGEITISNIYVYD 1917
                                     5555568999*****************98888776 PP

  == domain 5  score: 34.2 bits;  conditional E-value: 3e-11
                          DUF11    2 tKtvdksevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsftvrvt 79  
                                      Kt +++ v pGdt+tyt+  +N+g++   +v++ D  P  + ++s++ +  +++  +++g+L+ ges  + + v v+
  gi|116754978|ref|YP_844096.1| 1986 NKTAEPKVVEPGDTITYTIRYQNRGGTLH-DVRIVDYYPNEVYFISATPAPTSGNNVWYIGDLASGESGEIVILVGVA 2062
                                     5999*********************9877.********************99999*************9888877766 PP

                          DUF11   80 r 80  
                                     +
  gi|116754978|ref|YP_844096.1| 2063 Q 2063
                                     5 PP

  == domain 6  score: 28.3 bits;  conditional E-value: 2.1e-09
                          DUF11   16 vtytltvtNtgpasangvvvtDtlPaglayvsvsas...qgtasaltsvgsLeagesatlsftvrvtrtaasgalt 88  
                                      +y ++v N g++++  v + D+ P+g++yv +sa+     +  a+++   L  g +at+s+t++ t + +++ ++
  gi|116754978|ref|YP_844096.1| 2457 ADYRIIVENDGNVNLGPVYILDIFPPGTEYVGSSARpgeLTSEYANWTLLHLGIGDTATISLTLNITEEVSNL-VN 2531
                                     689*********************************55544445566669****************9999875.44 PP

  == domain 7  score: 15.5 bits;  conditional E-value: 2.1e-05
                          DUF11    4 tvdksevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsas...qgtasaltsvgsLeagesatlsftvrv 78  
                                     t +k+++   dtv+y + ++N+ + +   + v D  P+ ++++  s +      ++ ++ + +L +g++  + + +r+
  gi|116754978|ref|YP_844096.1| 2565 TATKTAAVHNDTVSYRISLSNRANYTM-VAFVIDYIPSDMQLINYSLTpsqIRENRIEWAILDLRPGKRIDIDYNMRA 2641
                                     567889999******************.99999***************7653345566777***************** PP

                          DUF11   79 trtaasgaltnv 90  
                                      r+++   +tn+
  gi|116754978|ref|YP_844096.1| 2642 LRSGT---FTNR 2650
                                     **999...6665 PP

>> C2-set_2  CD80-like C2-set immunoglobulin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0    0.0053       4.2       4      58 ..     338     392 ..     335     397 .. 0.80
   2 !    6.8   0.0    0.0087       6.7      10      58 ..     427     475 ..     418     480 .. 0.78
   3 !    6.8   0.0    0.0087       6.7      10      58 ..     510     558 ..     501     563 .. 0.78
   4 ?    5.9   0.0     0.017        13      10      59 ..     593     642 ..     584     645 .. 0.81
   5 ?    1.3   0.1      0.48   3.7e+02      16      57 ..     682     723 ..     667     728 .. 0.75
   6 ?    5.9   0.0     0.017        13      10      59 ..     759     808 ..     750     811 .. 0.81
   7 ?    1.3   0.1      0.48   3.7e+02      16      57 ..     848     889 ..     833     894 .. 0.75
   8 !    7.0   0.0    0.0078       6.1      10      58 ..     925     973 ..     916     978 .. 0.78
   9 !    6.8   0.0    0.0087       6.7      10      58 ..    1008    1056 ..     999    1061 .. 0.78
  10 ?    5.9   0.0     0.017        13      10      59 ..    1091    1140 ..    1082    1143 .. 0.81
  11 ?    1.5   0.1      0.42   3.2e+02      16      58 ..    1180    1222 ..    1165    1244 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0053
                                    EESSSEECTSSEEEEEEEEEEEEBS-EEEEEEETTEEECEEEEEEEEETTTSEEE CS
                       C2-set_2   4 epsasllegenkevvatCvsrggkPapqitWyldgkeleaaetsseqdpesglvt 58 
                                    +p+ ++l+ +  ev ++ +++ggkP+ + +Wy+d+ + ++a+ ss + +  g + 
  gi|116754978|ref|YP_844096.1| 338 SPTSGELNCNVNEVELEATVSGGKPDYSYQWYKDNSPITGATGSSYTATGAGSYK 392
                                    5555666666778888889*******************99998888777777665 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0087
                                    ECTSSEEEEEEEEEEEEBS-EEEEEEETTEEECEEEEEEEEETTTSEEE CS
                       C2-set_2  10 legenkevvatCvsrggkPapqitWyldgkeleaaetsseqdpesglvt 58 
                                    l+ +  ev ++ +++ggkP+ + +Wy+d+ + ++a+ ss + +  g + 
  gi|116754978|ref|YP_844096.1| 427 LNCNVNEVELEATVSGGKPDYSYQWYKDNSPITGATGSSYTATGAGSYK 475
                                    44455677777789******************99998888777777665 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0087
                                    ECTSSEEEEEEEEEEEEBS-EEEEEEETTEEECEEEEEEEEETTTSEEE CS
                       C2-set_2  10 legenkevvatCvsrggkPapqitWyldgkeleaaetsseqdpesglvt 58 
                                    l+ +  ev ++ +++ggkP+ + +Wy+d+ + ++a+ ss + +  g + 
  gi|116754978|ref|YP_844096.1| 510 LNCNVNEVELEATVSGGKPDYSYQWYKDNSPITGATGSSYTATGAGSYK 558
                                    44455677777789******************99998888777777665 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.017
                                    ECTSSEEEEEEEEEEEEBS-EEEEEEETTEEECEEEEEEEEETTTSEEEE CS
                       C2-set_2  10 legenkevvatCvsrggkPapqitWyldgkeleaaetsseqdpesglvtv 59 
                                    l+ +  ev ++ +++ggkP+ + +Wy+++   ++a+ ss +  e g++ v
  gi|116754978|ref|YP_844096.1| 593 LNCNVNEVELEATVSGGKPDYSYQWYKGDSLINGATGSSYTAREAGIYKV 642
                                    44455677777789********************9999999999998876 PP

  == domain 5  score: 1.3 bits;  conditional E-value: 0.48
                                    EEEEEEEEEEEBS-EEEEEEETTEEECEEEEEEEEETTTSEE CS
                       C2-set_2  16 evvatCvsrggkPapqitWyldgkeleaaetsseqdpesglv 57 
                                       +t +++gg+ + + +Wy+d+ + ++a+ ss + +  g +
  gi|116754978|ref|YP_844096.1| 682 SIELTATVTGGEEPYSYQWYKDDSPITGATGSSYTATGAGSY 723
                                    455556689999999***********9999888877777766 PP

  == domain 6  score: 5.9 bits;  conditional E-value: 0.017
                                    ECTSSEEEEEEEEEEEEBS-EEEEEEETTEEECEEEEEEEEETTTSEEEE CS
                       C2-set_2  10 legenkevvatCvsrggkPapqitWyldgkeleaaetsseqdpesglvtv 59 
                                    l+ +  ev ++ +++ggkP+ + +Wy+++   ++a+ ss +  e g++ v
  gi|116754978|ref|YP_844096.1| 759 LNCNVNEVELEATVSGGKPDYSYQWYKGDSLINGATGSSYTAREAGIYKV 808
                                    44455677777789********************9999999999998876 PP

  == domain 7  score: 1.3 bits;  conditional E-value: 0.48
                                    EEEEEEEEEEEBS-EEEEEEETTEEECEEEEEEEEETTTSEE CS
                       C2-set_2  16 evvatCvsrggkPapqitWyldgkeleaaetsseqdpesglv 57 
                                       +t +++gg+ + + +Wy+d+ + ++a+ ss + +  g +
  gi|116754978|ref|YP_844096.1| 848 SIELTATVTGGEEPYSYQWYKDDSPITGATGSSYTATGAGSY 889
                                    455556689999999***********9999888877777766 PP

  == domain 8  score: 7.0 bits;  conditional E-value: 0.0078
                                    ECTSSEEEEEEEEEEEEBS-EEEEEEETTEEECEEEEEEEEETTTSEEE CS
                       C2-set_2  10 legenkevvatCvsrggkPapqitWyldgkeleaaetsseqdpesglvt 58 
                                    l+ +  ev ++ +++ggkP+ + +Wy+d+ + ++a+ ss + +  g + 
  gi|116754978|ref|YP_844096.1| 925 LNCNVNEVELEATVSGGKPDYSYQWYKDDSPITGATGSSYTATGAGSYK 973
                                    44455677777789******************99998888777777665 PP

  == domain 9  score: 6.8 bits;  conditional E-value: 0.0087
                                     ECTSSEEEEEEEEEEEEBS-EEEEEEETTEEECEEEEEEEEETTTSEEE CS
                       C2-set_2   10 legenkevvatCvsrggkPapqitWyldgkeleaaetsseqdpesglvt 58  
                                     l+ +  ev ++ +++ggkP+ + +Wy+d+ + ++a+ ss + +  g + 
  gi|116754978|ref|YP_844096.1| 1008 LNCNVNEVELEATVSGGKPDYSYQWYKDNSPITGATGSSYTATGAGSYK 1056
                                     44455677777789******************99998888777777665 PP

  == domain 10  score: 5.9 bits;  conditional E-value: 0.017
                                     ECTSSEEEEEEEEEEEEBS-EEEEEEETTEEECEEEEEEEEETTTSEEEE CS
                       C2-set_2   10 legenkevvatCvsrggkPapqitWyldgkeleaaetsseqdpesglvtv 59  
                                     l+ +  ev ++ +++ggkP+ + +Wy+++   ++a+ ss +  e g++ v
  gi|116754978|ref|YP_844096.1| 1091 LNCNVNEVELEATVSGGKPDYSYQWYKGDSLINGATGSSYTAREAGIYKV 1140
                                     44455677777789********************9999999999998876 PP

  == domain 11  score: 1.5 bits;  conditional E-value: 0.42
                                     EEEEEEEEEEEBS-EEEEEEETTEEECEEEEEEEEETTTSEEE CS
                       C2-set_2   16 evvatCvsrggkPapqitWyldgkeleaaetsseqdpesglvt 58  
                                        +t +++gg+ + + +Wy+d+ + ++a+ ss + +  g + 
  gi|116754978|ref|YP_844096.1| 1180 SIELTATVTGGEEPYSYQWYKDDSPITGATGSSYTATGAGSYK 1222
                                     4555566899999999**********88887777776666654 PP

>> SdrD_B  SdrD B-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.2       1.7   1.3e+03      44      75 ..     376     406 ..     366     415 .. 0.76
   2 ?   -0.4   0.2       1.7   1.3e+03      44      75 ..     459     489 ..     449     498 .. 0.76
   3 ?   -0.4   0.2       1.7   1.3e+03      44      75 ..     542     572 ..     532     581 .. 0.76
   4 ?   -0.9   0.0       2.4   1.9e+03      52      76 ..     632     656 ..     622     664 .. 0.80
   5 ?   -0.4   0.1       1.7   1.3e+03      44      75 ..     708     738 ..     699     747 .. 0.76
   6 ?   -0.9   0.0       2.4   1.9e+03      52      76 ..     798     822 ..     788     830 .. 0.80
   7 ?   -0.4   0.1       1.7   1.3e+03      44      75 ..     874     904 ..     865     913 .. 0.76
   8 ?   -0.4   0.1       1.7   1.3e+03      44      75 ..     957     987 ..     948     996 .. 0.76
   9 ?   -0.4   0.2       1.7   1.3e+03      44      75 ..    1040    1070 ..    1030    1079 .. 0.76
  10 ?   -0.9   0.0       2.4   1.9e+03      52      76 ..    1130    1154 ..    1120    1162 .. 0.80
  11 ?   -0.1   0.1       1.4   1.1e+03      44      75 ..    1206    1236 ..    1199    1244 .. 0.77
  12 !    8.4   0.4     0.003       2.4      43     104 ..    1277    1337 ..    1266    1346 .. 0.81
  13 !   50.2   1.7   3.2e-16   2.5e-13       6      79 ..    1359    1431 ..    1355    1462 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.7
                         SdrD_B  44 TdasGkYkFtnltpGeYkVeftapagytvtak 75 
                                    T a+G+ ++t   +G+YkV +t  +g t t+ 
  gi|116754978|ref|YP_844096.1| 376 TGATGS-SYTATGAGSYKVVVTDANGCTGTSD 406
                                    566665.5777788999999999988876654 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.7
                         SdrD_B  44 TdasGkYkFtnltpGeYkVeftapagytvtak 75 
                                    T a+G+ ++t   +G+YkV +t  +g t t+ 
  gi|116754978|ref|YP_844096.1| 459 TGATGS-SYTATGAGSYKVVVTDANGCTGTSD 489
                                    566665.5777788999999999988876654 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.7
                         SdrD_B  44 TdasGkYkFtnltpGeYkVeftapagytvtak 75 
                                    T a+G+ ++t   +G+YkV +t  +g t t+ 
  gi|116754978|ref|YP_844096.1| 542 TGATGS-SYTATGAGSYKVVVTDANGCTGTSD 572
                                    566665.5777788999999999988876654 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 2.4
                         SdrD_B  52 FtnltpGeYkVeftapagytvtakk 76 
                                    +t  ++G YkVe+t  +g t t+++
  gi|116754978|ref|YP_844096.1| 632 YTAREAGIYKVEVTDANGCTGTSNE 656
                                    6777899999999999998877665 PP

  == domain 5  score: -0.4 bits;  conditional E-value: 1.7
                         SdrD_B  44 TdasGkYkFtnltpGeYkVeftapagytvtak 75 
                                    T a+G+ ++t   +G+YkV +t  +g t t+ 
  gi|116754978|ref|YP_844096.1| 708 TGATGS-SYTATGAGSYKVVVTDANGCTGTSD 738
                                    555664.5677788999999999888876654 PP

  == domain 6  score: -0.9 bits;  conditional E-value: 2.4
                         SdrD_B  52 FtnltpGeYkVeftapagytvtakk 76 
                                    +t  ++G YkVe+t  +g t t+++
  gi|116754978|ref|YP_844096.1| 798 YTAREAGIYKVEVTDANGCTGTSNE 822
                                    6777899999999999998877665 PP

  == domain 7  score: -0.4 bits;  conditional E-value: 1.7
                         SdrD_B  44 TdasGkYkFtnltpGeYkVeftapagytvtak 75 
                                    T a+G+ ++t   +G+YkV +t  +g t t+ 
  gi|116754978|ref|YP_844096.1| 874 TGATGS-SYTATGAGSYKVVVTDANGCTGTSD 904
                                    555664.5677788999999999888876654 PP

  == domain 8  score: -0.4 bits;  conditional E-value: 1.7
                         SdrD_B  44 TdasGkYkFtnltpGeYkVeftapagytvtak 75 
                                    T a+G+ ++t   +G+YkV +t  +g t t+ 
  gi|116754978|ref|YP_844096.1| 957 TGATGS-SYTATGAGSYKVVVTDANGCTGTSD 987
                                    555664.5677788999999999888876654 PP

  == domain 9  score: -0.4 bits;  conditional E-value: 1.7
                         SdrD_B   44 TdasGkYkFtnltpGeYkVeftapagytvtak 75  
                                     T a+G+ ++t   +G+YkV +t  +g t t+ 
  gi|116754978|ref|YP_844096.1| 1040 TGATGS-SYTATGAGSYKVVVTDANGCTGTSD 1070
                                     566665.5777788999999999988876654 PP

  == domain 10  score: -0.9 bits;  conditional E-value: 2.4
                         SdrD_B   52 FtnltpGeYkVeftapagytvtakk 76  
                                     +t  ++G YkVe+t  +g t t+++
  gi|116754978|ref|YP_844096.1| 1130 YTAREAGIYKVEVTDANGCTGTSNE 1154
                                     6777899999999999998877665 PP

  == domain 11  score: -0.1 bits;  conditional E-value: 1.4
                         SdrD_B   44 TdasGkYkFtnltpGeYkVeftapagytvtak 75  
                                     T a+G+ ++t   +G+YkV +t  +g t++++
  gi|116754978|ref|YP_844096.1| 1206 TGATGS-SYTATGAGSYKVVVTDANGCTAESS 1236
                                     566665.677888999***9999999987765 PP

  == domain 12  score: 8.4 bits;  conditional E-value: 0.003
                         SdrD_B   43 tTdasGkYkFtnltpGeYkVeftapagytvtakkaGsddaldSdadpatgltktvtlasges 104 
                                     +Td    Y   +l+pGeY+V+ + p+g+ +++ +   d+   S  ++++g t+t++l++ge+
  gi|116754978|ref|YP_844096.1| 1277 LTDGADPYDSGQLEPGEYTVTEIVPDGWDLSSIEIDGDTDGGST-STTSGSTATIDLDAGET 1337
                                     57777789999*****************8888877777775665.57788999999999875 PP

  == domain 13  score: 50.2 bits;  conditional E-value: 3.2e-16
                         SdrD_B    6 fVweDanknGiqdagekgisgvtVtLkdakgevvatttTdasGkYkFtnltpGeYkVeftapagytvt.akkaGs 79  
                                     + ++D n+nG  d+ge+gi+g t+ L  ++g+++ +ttT ++G+Y+Ftnl +G+Y+++ ++ ag++ t +++ Gs
  gi|116754978|ref|YP_844096.1| 1359 YKFNDLNGNGNWDTGEPGIEGWTIYL--SDGTTTISTTTGSDGSYSFTNLPAGKYTITEEERAGWSRTlPADLGS 1431
                                     679***********************..78888899**********************99999996551444444 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.3      0.71   5.6e+02      40      71 ..     383     412 ..     368     420 .. 0.70
   2 ?    0.7   0.5      0.81   6.3e+02      40      71 ..     466     495 ..     452     503 .. 0.70
   3 ?    0.7   0.5      0.81   6.3e+02      40      71 ..     549     578 ..     535     586 .. 0.70
   4 ?   -1.7   0.1       4.7   3.7e+03      46      70 ..     636     660 ..     631     670 .. 0.75
   5 ?    0.7   0.6      0.83   6.5e+02      40      71 ..     715     744 ..     688     752 .. 0.76
   6 ?   -1.7   0.1       4.7   3.7e+03      46      70 ..     802     826 ..     797     836 .. 0.75
   7 ?    0.7   0.6      0.83   6.5e+02      40      71 ..     881     910 ..     854     918 .. 0.76
   8 ?    0.7   0.5       0.8   6.3e+02      40      71 ..     964     993 ..     950    1001 .. 0.71
   9 ?    0.7   0.5      0.81   6.3e+02      40      71 ..    1047    1076 ..    1033    1084 .. 0.70
  10 ?   -1.7   0.1       4.7   3.7e+03      46      70 ..    1134    1158 ..    1129    1168 .. 0.75
  11 ?   -0.1   0.2       1.5   1.2e+03      41      64 ..    1214    1235 ..    1199    1244 .. 0.63
  12 ?   -0.6   0.1       2.1   1.6e+03      64      80 ..    1319    1343 ..    1266    1345 .. 0.56
  13 !   28.1   0.1   2.4e-09   1.9e-06      12      53 ..    1375    1414 ..    1370    1430 .. 0.87
  14 ?    0.0   0.3       1.3     1e+03       2      33 ..    1616    1643 ..    1615    1656 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.71
                CarboxypepD_reg  40 frlrglppgtysvtvsapGyatatreevtlta 71 
                                    ++  +  +g+y+v+v+ ++  t t+ ev +t 
  gi|116754978|ref|YP_844096.1| 383 YT--ATGAGSYKVVVTDANGCTGTSDEVPVTS 412
                                    33..3578999999988888888888887775 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.81
                CarboxypepD_reg  40 frlrglppgtysvtvsapGyatatreevtlta 71 
                                    ++  +  +g+y+v+v+ ++  t t+ ev +t 
  gi|116754978|ref|YP_844096.1| 466 YT--ATGAGSYKVVVTDANGCTGTSDEVPVTS 495
                                    33..3578999999988888888888888775 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.81
                CarboxypepD_reg  40 frlrglppgtysvtvsapGyatatreevtlta 71 
                                    ++  +  +g+y+v+v+ ++  t t+ ev +t 
  gi|116754978|ref|YP_844096.1| 549 YT--ATGAGSYKVVVTDANGCTGTSDEVPVTS 578
                                    33..3578999999988888888888888775 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 4.7
                CarboxypepD_reg  46 ppgtysvtvsapGyatatreevtlt 70 
                                    ++g y+v+v+ ++  t t++evt+ 
  gi|116754978|ref|YP_844096.1| 636 EAGIYKVEVTDANGCTGTSNEVTVI 660
                                    6799999999888888888888875 PP

  == domain 5  score: 0.7 bits;  conditional E-value: 0.83
                CarboxypepD_reg  40 frlrglppgtysvtvsapGyatatreevtlta 71 
                                    ++  +  +g+y+v+v+ ++  t t+ ev +t 
  gi|116754978|ref|YP_844096.1| 715 YT--ATGAGSYKVVVTDANGCTGTSDEVPVTS 744
                                    33..3578999999998888888888888875 PP

  == domain 6  score: -1.7 bits;  conditional E-value: 4.7
                CarboxypepD_reg  46 ppgtysvtvsapGyatatreevtlt 70 
                                    ++g y+v+v+ ++  t t++evt+ 
  gi|116754978|ref|YP_844096.1| 802 EAGIYKVEVTDANGCTGTSNEVTVI 826
                                    6799999999888888888888875 PP

  == domain 7  score: 0.7 bits;  conditional E-value: 0.83
                CarboxypepD_reg  40 frlrglppgtysvtvsapGyatatreevtlta 71 
                                    ++  +  +g+y+v+v+ ++  t t+ ev +t 
  gi|116754978|ref|YP_844096.1| 881 YT--ATGAGSYKVVVTDANGCTGTSDEVPVTS 910
                                    33..3578999999998888888888888875 PP

  == domain 8  score: 0.7 bits;  conditional E-value: 0.8
                CarboxypepD_reg  40 frlrglppgtysvtvsapGyatatreevtlta 71 
                                    ++  +  +g+y+v+v+ ++  t t+ ev +t 
  gi|116754978|ref|YP_844096.1| 964 YT--ATGAGSYKVVVTDANGCTGTSDEVPVTS 993
                                    33..3578999999998888888888888875 PP

  == domain 9  score: 0.7 bits;  conditional E-value: 0.81
                CarboxypepD_reg   40 frlrglppgtysvtvsapGyatatreevtlta 71  
                                     ++  +  +g+y+v+v+ ++  t t+ ev +t 
  gi|116754978|ref|YP_844096.1| 1047 YT--ATGAGSYKVVVTDANGCTGTSDEVPVTS 1076
                                     33..3578999999988888888888888775 PP

  == domain 10  score: -1.7 bits;  conditional E-value: 4.7
                CarboxypepD_reg   46 ppgtysvtvsapGyatatreevtlt 70  
                                     ++g y+v+v+ ++  t t++evt+ 
  gi|116754978|ref|YP_844096.1| 1134 EAGIYKVEVTDANGCTGTSNEVTVI 1158
                                     6799999999888888888888875 PP

  == domain 11  score: -0.1 bits;  conditional E-value: 1.5
                CarboxypepD_reg   41 rlrglppgtysvtvsapGyatatr 64  
                                     +  +  +g+y+v+v+ ++  ta++
  gi|116754978|ref|YP_844096.1| 1214 T--ATGAGSYKVVVTDANGCTAES 1235
                                     3..356788888887776666664 PP

  == domain 12  score: -0.6 bits;  conditional E-value: 2.1
                CarboxypepD_reg   64 r........eevtltagqtttldit 80  
                                     +         +++l+ag+t ++++t
  gi|116754978|ref|YP_844096.1| 1319 StsttsgstATIDLDAGETIRVTFT 1343
                                     0333344444577777777777765 PP

  == domain 13  score: 28.1 bits;  conditional E-value: 2.4e-09
                CarboxypepD_reg   12 apiagatVtvtnadtgtvastttdadGafrlrglppgtysvt 53  
                                      +i+g t+ ++  d++t+ sttt++dG++++++lp+g+y++t
  gi|116754978|ref|YP_844096.1| 1375 PGIEGWTIYLS--DGTTTISTTTGSDGSYSFTNLPAGKYTIT 1414
                                     469999*****..8999***********************98 PP

  == domain 14  score: 0.0 bits;  conditional E-value: 1.3
                CarboxypepD_reg    2 isGrVtd.asgapiagatVtvtnadtgtvastt 33  
                                     +sG+V+    ga  aga+V++t      +a++ 
  gi|116754978|ref|YP_844096.1| 1616 VSGSVVTwNLGALEAGASVVIT-----LTATVE 1643
                                     8999999457*999*******9.....344443 PP

>> MBG  MBG domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.7     0.084        65      23      66 ..     353     398 ..     336     400 .. 0.79
   2 ?    4.2   0.6     0.087        68      24      66 ..     439     481 ..     420     483 .. 0.80
   3 ?    4.2   0.6     0.087        68      24      66 ..     522     564 ..     503     566 .. 0.80
   4 ?    5.9   0.2     0.024        19      23      66 ..     602     647 ..     586     649 .. 0.82
   5 !    8.6   0.7    0.0037       2.9      20      66 ..     685     730 ..     670     732 .. 0.80
   6 ?    5.9   0.2     0.024        19      23      66 ..     768     813 ..     752     815 .. 0.82
   7 !    8.6   0.7    0.0037       2.9      20      66 ..     851     896 ..     836     898 .. 0.80
   8 !    8.3   0.6    0.0045       3.5      23      66 ..     934     979 ..     918     981 .. 0.82
   9 ?    4.2   0.6     0.087        68      24      66 ..    1020    1062 ..    1001    1064 .. 0.80
  10 ?    5.9   0.2     0.024        19      23      66 ..    1100    1145 ..    1084    1147 .. 0.82
  11 !    8.9   0.4    0.0029       2.3      20      66 ..    1183    1228 ..    1168    1231 .. 0.80
  12 ?    3.0   5.7       0.2   1.6e+02       6      93 ..    1325    1414 ..    1318    1415 .. 0.78
  13 ?    6.9   0.9     0.012       9.7      20      93 ..    1388    1464 ..    1378    1465 .. 0.75
  14 !    7.4   0.6    0.0088       6.9      24      74 ..    1543    1594 ..    1516    1616 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.084
                            MBG  23 i..ttngkdatktytltagDfewktadgnttaptnvGtYtvkLtaa 66 
                                       t++g + + +y++ ++   ++ a+g++ ++t +G+Y+v  t+a
  gi|116754978|ref|YP_844096.1| 353 LeaTVSGGKPDYSYQWYKDNSPITGATGSSYTATGAGSYKVVVTDA 398
                                    1446677778888999999999999999999***********9987 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.087
                            MBG  24 ttngkdatktytltagDfewktadgnttaptnvGtYtvkLtaa 66 
                                    t++g + + +y++ ++   ++ a+g++ ++t +G+Y+v  t+a
  gi|116754978|ref|YP_844096.1| 439 TVSGGKPDYSYQWYKDNSPITGATGSSYTATGAGSYKVVVTDA 481
                                    6667677888999999999999999999***********9987 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.087
                            MBG  24 ttngkdatktytltagDfewktadgnttaptnvGtYtvkLtaa 66 
                                    t++g + + +y++ ++   ++ a+g++ ++t +G+Y+v  t+a
  gi|116754978|ref|YP_844096.1| 522 TVSGGKPDYSYQWYKDNSPITGATGSSYTATGAGSYKVVVTDA 564
                                    6667677888999999999999999999***********9987 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.024
                            MBG  23 i..ttngkdatktytltagDfewktadgnttaptnvGtYtvkLtaa 66 
                                       t++g + + +y++ +gD  ++ a+g++ ++ ++G Y+v+ t+a
  gi|116754978|ref|YP_844096.1| 602 LeaTVSGGKPDYSYQWYKGDSLINGATGSSYTAREAGIYKVEVTDA 647
                                    134677777888999**************999***********997 PP

  == domain 5  score: 8.6 bits;  conditional E-value: 0.0037
                            MBG  20 ittittngkdatktytltagDfewktadgnttaptnvGtYtvkLtaa 66 
                                     t+ t++g   + +y++ ++D  ++ a+g++ ++t +G+Y+v  t+a
  gi|116754978|ref|YP_844096.1| 685 LTA-TVTGGEEPYSYQWYKDDSPITGATGSSYTATGAGSYKVVVTDA 730
                                    232.666666788899***************************9987 PP

  == domain 6  score: 5.9 bits;  conditional E-value: 0.024
                            MBG  23 i..ttngkdatktytltagDfewktadgnttaptnvGtYtvkLtaa 66 
                                       t++g + + +y++ +gD  ++ a+g++ ++ ++G Y+v+ t+a
  gi|116754978|ref|YP_844096.1| 768 LeaTVSGGKPDYSYQWYKGDSLINGATGSSYTAREAGIYKVEVTDA 813
                                    134677777888999**************999***********997 PP

  == domain 7  score: 8.6 bits;  conditional E-value: 0.0037
                            MBG  20 ittittngkdatktytltagDfewktadgnttaptnvGtYtvkLtaa 66 
                                     t+ t++g   + +y++ ++D  ++ a+g++ ++t +G+Y+v  t+a
  gi|116754978|ref|YP_844096.1| 851 LTA-TVTGGEEPYSYQWYKDDSPITGATGSSYTATGAGSYKVVVTDA 896
                                    232.666666788899***************************9987 PP

  == domain 8  score: 8.3 bits;  conditional E-value: 0.0045
                            MBG  23 i..ttngkdatktytltagDfewktadgnttaptnvGtYtvkLtaa 66 
                                       t++g + + +y++ ++D  ++ a+g++ ++t +G+Y+v  t+a
  gi|116754978|ref|YP_844096.1| 934 LeaTVSGGKPDYSYQWYKDDSPITGATGSSYTATGAGSYKVVVTDA 979
                                    134677777888999***************************9987 PP

  == domain 9  score: 4.2 bits;  conditional E-value: 0.087
                            MBG   24 ttngkdatktytltagDfewktadgnttaptnvGtYtvkLtaa 66  
                                     t++g + + +y++ ++   ++ a+g++ ++t +G+Y+v  t+a
  gi|116754978|ref|YP_844096.1| 1020 TVSGGKPDYSYQWYKDNSPITGATGSSYTATGAGSYKVVVTDA 1062
                                     6667677888999999999999999999***********9987 PP

  == domain 10  score: 5.9 bits;  conditional E-value: 0.024
                            MBG   23 i..ttngkdatktytltagDfewktadgnttaptnvGtYtvkLtaa 66  
                                        t++g + + +y++ +gD  ++ a+g++ ++ ++G Y+v+ t+a
  gi|116754978|ref|YP_844096.1| 1100 LeaTVSGGKPDYSYQWYKGDSLINGATGSSYTAREAGIYKVEVTDA 1145
                                     134677777888999**************999***********997 PP

  == domain 11  score: 8.9 bits;  conditional E-value: 0.0029
                            MBG   20 ittittngkdatktytltagDfewktadgnttaptnvGtYtvkLtaa 66  
                                      t+ t++g   + +y++ ++D  ++ a+g++ ++t +G+Y+v  t+a
  gi|116754978|ref|YP_844096.1| 1183 LTA-TVTGGEEPYSYQWYKDDSPITGATGSSYTATGAGSYKVVVTDA 1228
                                     232.666666788899***************************9987 PP

  == domain 12  score: 3.0 bits;  conditional E-value: 0.2
                            MBG    6 GqaatlddsnsnnkittittngkdatktytltagDfewktadgn...ttaptnvGtYtvkLtaaglaklkaa...npN 77  
                                     G++at+d + ++++i +++tn  ++  +++l+ + +++++ +gn    t    +   t+ L+ +g +++ +    ++ 
  gi|116754978|ref|YP_844096.1| 1325 GSTATIDLD-AGETIRVTFTNTLKTGGQGKLDVSGYKFNDLNGNgnwDTGEPGIEGWTIYLS-DGTTTISTTtgsDGS 1400
                                     677766655.44556666666666666788**************766555556666******.899999999887889 PP

                            MBG   78 ytftdaktgtgtytIt 93  
                                     y+f  ++  +g+ytIt
  gi|116754978|ref|YP_844096.1| 1401 YSF--TNLPAGKYTIT 1414
                                     999..9999******9 PP

  == domain 13  score: 6.9 bits;  conditional E-value: 0.012
                            MBG   20 itti.ttngkdatktyt.ltagDfewktadgn...ttaptnvGtYtvkLtaaglaklkaan.pNytftdaktgtgtyt 91  
                                     +tti tt+g+d++ + t l ag +++++++      t p + G+Y++         ++++n +N++    ++ ++++ 
  gi|116754978|ref|YP_844096.1| 1388 TTTIsTTTGSDGSYSFTnLPAGKYTITEEERAgwsRTLPADLGSYEINFDGEEDRSVADQNfGNVQT---VQPQAKLA 1462
                                     22233666666664444499******7777769999*************999999999996588887...78888877 PP

                            MBG   92 It 93  
                                     It
  gi|116754978|ref|YP_844096.1| 1463 IT 1464
                                     76 PP

  == domain 14  score: 7.4 bits;  conditional E-value: 0.0088
                            MBG   24 ttngkdatktytltagDfew.ktadgnttaptnvGtYtvkLtaaglaklkaa 74  
                                      + g++at+  t+ +  +++ ktad +t +p +  tYt++ +++g a++++a
  gi|116754978|ref|YP_844096.1| 1543 ESIGTTATVEITWVDCAIDIeKTADRETVEPGDTITYTLTVKNTGSATINDA 1594
                                     44566667777777766666224444499*********************98 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.2   2.2e-06    0.0017      12      49 ..    1375    1414 ..    1369    1416 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.2e-06
                CarbopepD_reg_2   12 eplpgatVyvkg..tkkgtvTdenGnFelknlpagkytLv 49  
                                       ++g t+y+ +  t+  t+T ++G+++++nlpagkyt++
  gi|116754978|ref|YP_844096.1| 1375 PGIEGWTIYLSDgtTTISTTTGSDGSYSFTNLPAGKYTIT 1414
                                     56899999996544689*********************96 PP

>> bMG10  Bacterial Alpha-2-macroglobulin MG10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       7.8   6.1e+03      92     110 ..    1401    1419 ..    1393    1420 .. 0.84
   2 ?    6.0   0.1     0.016        13      17      54 ..    1567    1604 ..    1559    1615 .. 0.80
   3 ?   -2.2   0.0       5.5   4.3e+03      22      51 ..    1993    2023 ..    1984    2024 .. 0.79
   4 !    9.1   0.0    0.0018       1.4      79     118 ..    2609    2649 ..    2566    2655 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 7.8
                          bMG10   92 ffadylpkgtytfeylvra 110 
                                     + +++lp+g+yt++ + ra
  gi|116754978|ref|YP_844096.1| 1401 YSFTNLPAGKYTITEEERA 1419
                                     68999*******9977665 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.016
                          bMG10   17 sksdaklkvGdkvrvrltvt.tpr.dleyvaledplPAGl 54  
                                     +++  +++ Gd+++ +ltv+ t + ++++  ++d lP G+
  gi|116754978|ref|YP_844096.1| 1567 DRE--TVEPGDTITYTLTVKnTGSaTINDATVVDTLPPGT 1604
                                     222..89************97544377**********997 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 5.5
                          bMG10   22 klkvGdkvrvrltvttpr.dleyvaledplP 51  
                                      ++ Gd+++ +++ +    +l++v ++d+ P
  gi|116754978|ref|YP_844096.1| 1993 VVEPGDTITYTIRYQNRGgTLHDVRIVDYYP 2023
                                     5899********9996665999999999988 PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.0018
                          bMG10   79 efsyreirddrvvffadylpkgt.ytfeylvravtpGtfsv 118 
                                     + + ++ir++r+++++ +l++g+  +++y++ra ++Gtf+ 
  gi|116754978|ref|YP_844096.1| 2609 SLTPSQIRENRIEWAILDLRPGKrIDIDYNMRALRSGTFTN 2649
                                     5566899*********9999997368*************86 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.2     0.031        24      15      72 ..     240     295 ..     234     308 .. 0.76
   2 ?    0.9   0.1      0.71   5.6e+02      50      81 ..    1326    1355 ..    1310    1359 .. 0.77
   3 ?   -2.2   0.1       6.5   5.1e+03       5      50 ..    1462    1515 ..    1458    1537 .. 0.71
   4 !    9.5   1.0    0.0015       1.1       7      72 ..    1563    1643 ..    1557    1653 .. 0.70
   5 !   11.6   0.5   0.00032      0.25       6      76 ..    1881    1948 ..    1876    1961 .. 0.73
   6 ?    0.1   0.0       1.2   9.5e+02       8      72 ..    1987    2062 ..    1981    2074 .. 0.76
   7 ?   -2.7   0.0       9.4   7.4e+03      14      71 ..    2570    2624 ..    2563    2647 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.031
                                    EETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEE..SEE-CTEEEEEEEEEE-S CS
                          CARDB  15 afvgeentitvtvkNqGtaasgatkvalyldgelvgtvtv..psLaagesttvsftwtte 72 
                                    a  g ++t  ++v+N+G+ + +++++     +++ gt+t+  + L++ge+++ + t+t++
  gi|116754978|ref|YP_844096.1| 240 AGIGATVTYCYQVQNTGDVKLTDVSL----TDDKYGTITLdkTTLEPGETAEGTSTHTVT 295
                                    55678899999******998866544....45555788887799******9999888774 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.71
                                     EEEEESEE-CTEEEEEEEEEE-S-S-CEEEEE CS
                          CARDB   50 gtvtvpsLaagesttvsftwtteategevtlt 81  
                                     +t+t+  L+age++ v+ft t + t g+ +l 
  gi|116754978|ref|YP_844096.1| 1326 STATI-DLDAGETIRVTFTNTLK-TGGQGKLD 1355
                                     44444.89*************99.87776655 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 6.5
                                     EE.EEEC-SEEETTSEEEEEEEEEE.-SSS-EEEEEEEEEETTEEE.........E CS
                          CARDB    5 tvtntlnpseafvgeentitvtvkN.qGtaasgatkvalyldgelv.........g 50  
                                      +  t++p+++  ++ + +tv+ +N qG+      +++ly d ++v          
  gi|116754978|ref|YP_844096.1| 1462 AI--TSTPQDPCSNTPVVVTVSCENlQGDLCGSIASMTLYYDSSSVemtkgsngrW 1515
                                     45..8899999999999999999996688887788888888888885544444333 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.0015
                                     .EEEC-SEEETTSEEEEEEEEEE-SSS-.EEEEEEEEEETTEEE..............EEEEESEE-CTEEEEEEEEE CS
                          CARDB    7 tntlnpseafvgeentitvtvkNqGtaa.sgatkvalyldgelv..............gtvtvpsLaagesttvsftw 69  
                                     ++t+  +++++g+++t t+tvkN+G+a+   at v+    g+l                t+++ +L+ag+s+ +++t 
  gi|116754978|ref|YP_844096.1| 1563 EKTADRETVEPGDTITYTLTVKNTGSATiNDATVVDTLPPGTLYksadpepsgvsgsvVTWNLGALEAGASVVITLTA 1640
                                     6677888999*****************965566665555555554444445565555555555888888888888777 PP

                                     E-S CS
                          CARDB   70 tte 72  
                                     t+e
  gi|116754978|ref|YP_844096.1| 1641 TVE 1643
                                     766 PP

  == domain 5  score: 11.6 bits;  conditional E-value: 0.00032
                                     E.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S-S-C CS
                          CARDB    6 vtntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtteateg 76  
                                     +++  +++ a+vg+++t t+t++N G+++  +  + +y d+    +++   L++g++t+v++t++++ ++ 
  gi|116754978|ref|YP_844096.1| 1881 LDKRPSVEVASVGQTITYTYTITNGGEITISN--IYVYDDRLGRINADPITLDPGDTTEVTATYVVK-ATD 1948
                                     55556678899***************998654..455555544423333589************999.443 PP

  == domain 6  score: 0.1 bits;  conditional E-value: 1.2
                                     EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE...........EEEEESEE-CTEEEEEEEEEE-S CS
                          CARDB    8 ntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelv...........gtvtvpsLaagesttvsftwtte 72  
                                     +t++p+ +++g+++t t+  +N G        v++y ++              + +++  La+ges ++ + + ++
  gi|116754978|ref|YP_844096.1| 1987 KTAEPKVVEPGDTITYTIRYQNRGGTLHDVRIVDYYPNEVYFisatpaptsgnNVWYIGDLASGESGEIVILVGVA 2062
                                     6788999999999999999999999988888888888888777777777777777777888888887777666555 PP

  == domain 7  score: -2.7 bits;  conditional E-value: 9.4
                                     EEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEE.SEE-CTEEEEEEEEEE- CS
                          CARDB   14 eafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtv.psLaagesttvsftwtt 71  
                                     +a+ +++++ +++++N     +  t va+++d    + + +  sL +++ ++ ++ w +
  gi|116754978|ref|YP_844096.1| 2570 AAVHNDTVSYRISLSNR----ANYTMVAFVIDYIPSDMQLInYSLTPSQIRENRIEWAI 2624
                                     55555555555555555....55666677777766544444556777777777666655 PP

>> Chlam_OMP6  Chlamydia cysteine-rich outer membrane protein 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.3      0.56   4.4e+02      27      87 ..    1578    1638 ..    1551    1641 .. 0.82
   2 !   10.3   0.0   0.00085      0.66      42      89 ..    2015    2059 ..    1999    2061 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.56
                     Chlam_OMP6   27 pypieitavgkkdcvdvvitqqlpcevefvrsdpastptadgklvwkidrlgqgekskitv 87  
                                      y + +  +g     d  + + lp  + + ++dp  +  +   + w++  l  g    it+
  gi|116754978|ref|YP_844096.1| 1578 TYTLTVKNTGSATINDATVVDTLPPGTLYKSADPEPSGVSGSVVTWNLGALEAGASVVITL 1638
                                     588999999999999**********************99999999*****99999888875 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00085
                     Chlam_OMP6   42 dvvitqqlpcevefvrsdpastptadgklvwkidrlgqgekskitvwv 89  
                                     dv i +  p ev f+++ pa t    g+ vw i  l  ge   i + v
  gi|116754978|ref|YP_844096.1| 2015 DVRIVDYYPNEVYFISATPAPT---SGNNVWYIGDLASGESGEIVILV 2059
                                     7889999************966...4889************9998876 PP

>> SpaA  Prealbumin-like fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.6         8   6.2e+03      20      50 ..     254     277 ..     229     303 .. 0.62
   2 ?   -1.4   0.2       3.9   3.1e+03       4      45 ..     373     401 ..     362     413 .. 0.62
   3 ?   -1.3   0.2       3.7   2.9e+03       4      44 ..     456     483 ..     432     496 .. 0.66
   4 ?   -1.4   0.3         4   3.1e+03       4      44 ..     539     566 ..     515     577 .. 0.66
   5 ?   -1.5   0.3       4.3   3.4e+03       6      44 ..     707     732 ..     677     743 .. 0.65
   6 ?   -1.5   0.2       4.1   3.2e+03       6      44 ..     873     898 ..     844     910 .. 0.65
   7 ?   -1.4   0.3       3.9     3e+03       6      44 ..     956     981 ..     930     993 .. 0.63
   8 ?   -1.4   0.2         4   3.1e+03       4      44 ..    1037    1064 ..    1017    1075 .. 0.65
   9 ?    3.4   3.4      0.13        99      35      69 ..    1242    1306 ..    1195    1312 .. 0.47
  10 !   16.8   5.7   7.9e-06    0.0062      28      61 ..    1375    1416 ..    1309    1420 .. 0.80
  11 ?   -0.3   0.6       1.7   1.3e+03      28      55 ..    1564    1604 ..    1522    1607 .. 0.57
  12 ?   -2.1   0.0       6.7   5.2e+03       4      26 ..    1723    1745 ..    1721    1780 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 8
                                    CCCHCHHTT.TTCCEESEEE-BTTSEEEEEE CS
                           SpaA  20 tdgkdaleakktgtevttlttdenGkatfeg 50 
                                    + g+++l++        +lt d+ G++t ++
  gi|116754978|ref|YP_844096.1| 254 NTGDVKLTD-------VSLTDDKYGTITLDK 277
                                    333333322.......344455666666652 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.9
                                    CB-TS-EEEEEETTTSCCCHCHHTT.TTCCEESEEE-BTTSE CS
                           SpaA   4 kpLaGaeFtlykvdtttdgkdaleakktgtevttlttdenGk 45 
                                     p+ Ga+ + y ++              +  ++ ++td+nG 
  gi|116754978|ref|YP_844096.1| 373 SPITGATGSSYTAT-------------GAGSYKVVVTDANGC 401
                                    34444444444444.............345567778999984 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 3.7
                                    CB-TS-EEEEEETTTSCCCHCHHTT.TTCCEESEEE-BTTS CS
                           SpaA   4 kpLaGaeFtlykvdtttdgkdaleakktgtevttlttdenG 44 
                                     p+ Ga+ + y ++              +  ++ ++td+nG
  gi|116754978|ref|YP_844096.1| 456 SPITGATGSSYTAT-------------GAGSYKVVVTDANG 483
                                    33333333333333.............34556777799998 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 4
                                    CB-TS-EEEEEETTTSCCCHCHHTT.TTCCEESEEE-BTTS CS
                           SpaA   4 kpLaGaeFtlykvdtttdgkdaleakktgtevttlttdenG 44 
                                     p+ Ga+ + y ++              +  ++ ++td+nG
  gi|116754978|ref|YP_844096.1| 539 SPITGATGSSYTAT-------------GAGSYKVVVTDANG 566
                                    33333333333333.............34556777799998 PP

  == domain 5  score: -1.5 bits;  conditional E-value: 4.3
                                    -TS-EEEEEETTTSCCCHCHHTT.TTCCEESEEE-BTTS CS
                           SpaA   6 LaGaeFtlykvdtttdgkdaleakktgtevttlttdenG 44 
                                    + Ga+ + y ++              +  ++ ++td+nG
  gi|116754978|ref|YP_844096.1| 707 ITGATGSSYTAT-------------GAGSYKVVVTDANG 732
                                    333333333332.............34456777799988 PP

  == domain 6  score: -1.5 bits;  conditional E-value: 4.1
                                    -TS-EEEEEETTTSCCCHCHHTT.TTCCEESEEE-BTTS CS
                           SpaA   6 LaGaeFtlykvdtttdgkdaleakktgtevttlttdenG 44 
                                    + Ga+ + y ++              +  ++ ++td+nG
  gi|116754978|ref|YP_844096.1| 873 ITGATGSSYTAT-------------GAGSYKVVVTDANG 898
                                    333333333333.............34556777799988 PP

  == domain 7  score: -1.4 bits;  conditional E-value: 3.9
                                    -TS-EEEEEETTTSCCCHCHHTT.TTCCEESEEE-BTTS CS
                           SpaA   6 LaGaeFtlykvdtttdgkdaleakktgtevttlttdenG 44 
                                    + Ga+ + y ++              +  ++ ++td+nG
  gi|116754978|ref|YP_844096.1| 956 ITGATGSSYTAT-------------GAGSYKVVVTDANG 981
                                    222222222222.............34556777799998 PP

  == domain 8  score: -1.4 bits;  conditional E-value: 4
                                     CB-TS-EEEEEETTTSCCCHCHHTT.TTCCEESEEE-BTTS CS
                           SpaA    4 kpLaGaeFtlykvdtttdgkdaleakktgtevttlttdenG 44  
                                      p+ Ga+ + y ++              +  ++ ++td+nG
  gi|116754978|ref|YP_844096.1| 1037 SPITGATGSSYTAT-------------GAGSYKVVVTDANG 1064
                                     33334443333333.............34556777799998 PP

  == domain 9  score: 3.4 bits;  conditional E-value: 0.13
                                     E......................SEEE-BTTSEEEEE.....................EEESEEEEEEEEE-STTEEE CS
                           SpaA   35 v......................ttlttdenGkatfe.....................gLplGtYllvEtkaPegYvl 69  
                                     v                                   +                      L++G+Y+++E+ +P+g  l
  gi|116754978|ref|YP_844096.1| 1242 VecitkiivdkvtdpsgstesfeF------------TgswsggttfsltdgadpydsgQLEPGEYTVTEI-VPDGWDL 1306
                                     133333332222222333333330............1333333333355555555555***********9.6777655 PP

  == domain 10  score: 16.8 bits;  conditional E-value: 7.9e-06
                                     T.........TTCCEESEEE-BTTSEEEEEEEESEEEEEEEE CS
                           SpaA   28 a........kktgtevttlttdenGkatfegLplGtYllvEt 61  
                                                +gt++ + tt+++G  +f++Lp+G+Y+++E 
  gi|116754978|ref|YP_844096.1| 1375 PgiegwtiyLSDGTTTISTTTGSDGSYSFTNLPAGKYTITEE 1416
                                     25555666656799999************************7 PP

  == domain 11  score: -0.3 bits;  conditional E-value: 1.7
                                     T........TTCCEESEEE-BTTSEEEEE......EEESEE CS
                           SpaA   28 a.......kktgtevttlttdenGkatfe......gLplGt 55  
                                     +       +  +t ++tlt  ++G at++       Lp+Gt
  gi|116754978|ref|YP_844096.1| 1564 KtadretvEPGDTITYTLTVKNTGSATINdatvvdTLPPGT 1604
                                     12233333444556688888889999998677776788885 PP

  == domain 12  score: -2.1 bits;  conditional E-value: 6.7
                                     CB-TS-EEEEEETTTSCCCHCHH CS
                           SpaA    4 kpLaGaeFtlykvdtttdgkdal 26  
                                      +L+G +++l + ++tt g++ +
  gi|116754978|ref|YP_844096.1| 1723 VTLNGSVYKLMNYTNTTTGDVLT 1745
                                     67999******999434443332 PP

>> DUF4897  Domain of unknown function (DUF4897)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       2.8   2.2e+03     101     144 ..    1581    1624 ..    1566    1627 .. 0.84
   2 ?    1.8   0.0      0.25   1.9e+02     114     136 ..    2016    2038 ..    2011    2045 .. 0.83
   3 !   10.1   0.1   0.00066      0.52      98     144 ..    2578    2623 ..    2524    2626 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.8
                        DUF4897  101 tslgdiklnlagdselvvslPkdaklisvePtPtkivenellWk 144 
                                     + +++    +++d+++v +lP      s++P P+  +  ++ W+
  gi|116754978|ref|YP_844096.1| 1581 LTVKNTGSATINDATVVDTLPPGTLYKSADPEPSGVSGSVVTWN 1624
                                     555566666789999999999999999*************9996 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.25
                        DUF4897  114 selvvslPkdaklisvePtPtki 136 
                                       +v + P++  +is++P+Pt+ 
  gi|116754978|ref|YP_844096.1| 2016 VRIVDYYPNEVYFISATPAPTSG 2038
                                     5677789**************74 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00066
                        DUF4897   98 vvetslgdiklnlagdselvvslPkdaklisvePtPtkivenellWk 144 
                                      + +sl + + n +  ++++ ++P d +li+   tP++i en + W 
  gi|116754978|ref|YP_844096.1| 2578 SYRISLSN-RANYTMVAFVIDYIPSDMQLINYSLTPSQIRENRIEWA 2623
                                     34444433.4556666666779***********************95 PP

>> TRAP_beta  Translocon-associated protein beta (TRAPB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1      0.05        39      36      61 ..     245     270 ..     239     274 .. 0.88
   2 ?    0.5   0.0      0.44   3.4e+02      77     105 ..    1568    1596 ..    1560    1600 .. 0.65
   3 ?    7.7   0.0    0.0027       2.1      20      60 ..    1879    1919 ..    1874    1924 .. 0.89
   4 ?   -3.0   0.0       5.4   4.2e+03      18      58 ..    1981    2020 ..    1973    2025 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.05
                      TRAP_beta  36 dltveytiyNvGssaAldVslvDdsf 61 
                                     +t  y++ N G+ + +dVsl+Dd +
  gi|116754978|ref|YP_844096.1| 245 TVTYCYQVQNTGDVKLTDVSLTDDKY 270
                                    577789*****************986 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.44
                      TRAP_beta   77 werlapgenvshsfvvepkksgsfngtaa 105 
                                      e+++pg +++++++v+ + s  +n++ +
  gi|116754978|ref|YP_844096.1| 1568 RETVEPGDTITYTLTVKNTGSATINDATV 1596
                                     56777777777777776666666655443 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0027
                      TRAP_beta   20 vlvkKkilnrllvegedltveytiyNvGssaAldVslvDds 60  
                                     ++ +K+   ++++ g+ +t +yti+N G+ +  ++ ++Dd 
  gi|116754978|ref|YP_844096.1| 1879 LTLDKRPSVEVASVGQTITYTYTITNGGEITISNIYVYDDR 1919
                                     66788888899999************************996 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 5.4
                      TRAP_beta   18 arvlvkKkilnrllvegedltveytiyNvGssaAldVslvD 58  
                                      +vl++K++  +++  g  +t ++   N G +   dV++vD
  gi|116754978|ref|YP_844096.1| 1981 SEVLFNKTAEPKVVEPGDTITYTIRYQNRGGT-LHDVRIVD 2020
                                     57999999999999999999999999999964.56777776 PP

>> DUF2012  Protein of unknown function (DUF2012)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   6.6e-05     0.051      10      45 ..    1380    1414 ..    1375    1419 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.6e-05
                        DUF2012   10 trvlLdsgqqrkfkalvrrDGsFifrdlpegsYlLe 45  
                                      +++L+ g++ ++++ + +DGs++f++lp+g+Y++ 
  gi|116754978|ref|YP_844096.1| 1380 WTIYLSDGTT-TISTTTGSDGSYSFTNLPAGKYTIT 1414
                                     6899999999.9*********************986 PP

>> DUF1573  Protein of unknown function (DUF1573)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.95   7.4e+02      16      60 ..     243     286 ..     238     304 .. 0.71
   2 ?    3.7   0.1     0.081        63       5      33 ..    1563    1591 ..    1560    1597 .. 0.87
   3 ?    1.4   0.0      0.43   3.3e+02      16      74 ..    1893    1950 ..    1885    1964 .. 0.68
   4 ?   -1.2   0.0       2.7   2.1e+03      51      70 ..    1991    2010 ..    1985    2022 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.95
                        DUF1573  16 gekvtatFeftNtgkaplvitnv.ktsCgCttpeypkepiapGesg 60 
                                    g++vt+ ++++Ntg+ +l+  +    + g  t + +k++++pGe++
  gi|116754978|ref|YP_844096.1| 243 GATVTYCYQVQNTGDVKLTDVSLtDDKYG--TITLDKTTLEPGETA 286
                                    5789999*******987752222022333..444457777777776 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.081
                        DUF1573    5 ettidfgkieegekvtatFeftNtgkapl 33  
                                     e+t d +++e g+++t+t +++Ntg+a++
  gi|116754978|ref|YP_844096.1| 1563 EKTADRETVEPGDTITYTLTVKNTGSATI 1591
                                     57889999*****************9864 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.43
                        DUF1573   16 gekvtatFeftNtgkaplv.itnvktsCgCttpeypkepiapGesgkikvtfnakgrpge 74  
                                     g+++t+t+++tN g+ ++  i  +    g ++++    ++ pG+++++++t+  k+  ++
  gi|116754978|ref|YP_844096.1| 1893 GQTITYTYTITNGGEITISnIYVYDDRLGRINAD--PITLDPGDTTEVTATYVVKATDES 1950
                                     6778888888888876543244444555555544..566899999999999987776555 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 2.7
                        DUF1573   51 kepiapGesgkikvtfnakg 70  
                                      + ++pG++++ +++++++g
  gi|116754978|ref|YP_844096.1| 1991 PKVVEPGDTITYTIRYQNRG 2010
                                     45699999999999999887 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 ?    4.7   0.0     0.038        30      36      65 ..    1564    1593 ..    1561    1595 .. 0.88
   2 ?    0.6   0.0      0.72   5.6e+02      43      66 ..    1890    1913 ..    1881    1914 .. 0.88
   3 ?    0.4   0.0      0.81   6.3e+02      38      65 ..    1989    2015 ..    1985    2018 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.038
                                     TTSEESS-STT-EEEEEEEEETTCEEEEEE CS
                        CusF_Ec   36 dpallaglkaGdkVrFefekrdggeyvitk 65  
                                     + a+ +++++Gd+++++++ ++ g+ +i +
  gi|116754978|ref|YP_844096.1| 1564 KTADRETVEPGDTITYTLTVKNTGSATIND 1593
                                     678999****************99999976 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.72
                                     -STT-EEEEEEEEETTCEEEEEEE CS
                        CusF_Ec   43 lkaGdkVrFefekrdggeyvitki 66  
                                      ++G++++++ + ++gge +i+ i
  gi|116754978|ref|YP_844096.1| 1890 ASVGQTITYTYTITNGGEITISNI 1913
                                     579*****************9987 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.81
                                     SEESS-STT-EEEEEEEEETTCEEEEEE CS
                        CusF_Ec   38 allaglkaGdkVrFefekrdggeyvitk 65  
                                     a+ + +++Gd+++++++ ++ g  ++ +
  gi|116754978|ref|YP_844096.1| 1989 AEPKVVEPGDTITYTIRYQNRG-GTLHD 2015
                                     6677899**********99987.67665 PP

>> Peptidase_M73  Camelysin metallo-endopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1    0.0024       1.8      37      81 ..    1550    1594 ..    1537    1600 .. 0.84
   2 ?   -1.4   0.0       2.3   1.8e+03      60      83 ..    1892    1915 ..    1877    1926 .. 0.83
   3 ?   -2.3   0.0       4.2   3.3e+03      58      76 ..    1994    2013 ..    1989    2022 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0024
                  Peptidase_M73   37 sfaaGtldlsvdptviidvknlkPGDtvtrefklenkGtLdikkv 81  
                                     +     +d ++d +   d + + PGDt+t   +++n+G+ +i++ 
  gi|116754978|ref|YP_844096.1| 1550 TVEITWVDCAIDIEKTADRETVEPGDTITYTLTVKNTGSATINDA 1594
                                     5555668899999999999*********************99975 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.3
                  Peptidase_M73   60 PGDtvtrefklenkGtLdikkvll 83  
                                      G t+t  ++++n G ++i+++++
  gi|116754978|ref|YP_844096.1| 1892 VGQTITYTYTITNGGEITISNIYV 1915
                                     599*****************9986 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 4.2
                  Peptidase_M73   58 lkPGDtvtrefklenkG.tL 76  
                                     + PGDt+t   + +n+G tL
  gi|116754978|ref|YP_844096.1| 1994 VEPGDTITYTIRYQNRGgTL 2013
                                     68*************97244 PP

>> YrbL-PhoP_reg  PhoP regulatory network protein YrbL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0       0.1        79      58     105 ..     349     400 ..     339     405 .. 0.77
   2 ?    2.6   0.1      0.11        82      59     105 ..     433     483 ..     423     488 .. 0.76
   3 ?    2.6   0.1      0.11        82      59     105 ..     516     566 ..     506     571 .. 0.76
   4 ?    0.0   0.1      0.65   5.1e+02      75     105 ..     702     732 ..     675     736 .. 0.84
   5 ?    0.0   0.1      0.65   5.1e+02      75     105 ..     868     898 ..     841     902 .. 0.84
   6 ?    1.1   0.0      0.31   2.4e+02      61     105 ..     933     981 ..     922     986 .. 0.75
   7 ?    2.6   0.1      0.11        82      59     105 ..    1014    1064 ..    1004    1069 .. 0.76
   8 ?    2.6   0.1       0.1        81      75     110 ..    1200    1235 ..    1172    1252 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.1
                  YrbL-PhoP_reg  58 ilrElkeyvqlsk....lreeidnsplarilGlvqTdlGlGlvvekirdadG 105
                                    ++ El + v+  k    ++   dnsp++   G+  T  G+G     ++da+G
  gi|116754978|ref|YP_844096.1| 349 NEVELEATVSGGKpdysYQWYKDNSPITGATGSSYTATGAGSYKVVVTDANG 400
                                    444455555444466555666899***************************9 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.11
                  YrbL-PhoP_reg  59 lrElkeyvqlsk....lreeidnsplarilGlvqTdlGlGlvvekirdadG 105
                                    + El + v+  k    ++   dnsp++   G+  T  G+G     ++da+G
  gi|116754978|ref|YP_844096.1| 433 EVELEATVSGGKpdysYQWYKDNSPITGATGSSYTATGAGSYKVVVTDANG 483
                                    44445555444465555666899***************************9 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.11
                  YrbL-PhoP_reg  59 lrElkeyvqlsk....lreeidnsplarilGlvqTdlGlGlvvekirdadG 105
                                    + El + v+  k    ++   dnsp++   G+  T  G+G     ++da+G
  gi|116754978|ref|YP_844096.1| 516 EVELEATVSGGKpdysYQWYKDNSPITGATGSSYTATGAGSYKVVVTDANG 566
                                    44445555444465555666899***************************9 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 0.65
                  YrbL-PhoP_reg  75 idnsplarilGlvqTdlGlGlvvekirdadG 105
                                     d sp++   G+  T  G+G     ++da+G
  gi|116754978|ref|YP_844096.1| 702 KDDSPITGATGSSYTATGAGSYKVVVTDANG 732
                                    57799*************************9 PP

  == domain 5  score: 0.0 bits;  conditional E-value: 0.65
                  YrbL-PhoP_reg  75 idnsplarilGlvqTdlGlGlvvekirdadG 105
                                     d sp++   G+  T  G+G     ++da+G
  gi|116754978|ref|YP_844096.1| 868 KDDSPITGATGSSYTATGAGSYKVVVTDANG 898
                                    57799*************************9 PP

  == domain 6  score: 1.1 bits;  conditional E-value: 0.31
                  YrbL-PhoP_reg  61 Elkeyvqlsk....lreeidnsplarilGlvqTdlGlGlvvekirdadG 105
                                    El + v+  k    ++   d sp++   G+  T  G+G     ++da+G
  gi|116754978|ref|YP_844096.1| 933 ELEATVSGGKpdysYQWYKDDSPITGATGSSYTATGAGSYKVVVTDANG 981
                                    4444444444554445556789**************************9 PP

  == domain 7  score: 2.6 bits;  conditional E-value: 0.11
                  YrbL-PhoP_reg   59 lrElkeyvqlsk....lreeidnsplarilGlvqTdlGlGlvvekirdadG 105 
                                     + El + v+  k    ++   dnsp++   G+  T  G+G     ++da+G
  gi|116754978|ref|YP_844096.1| 1014 EVELEATVSGGKpdysYQWYKDNSPITGATGSSYTATGAGSYKVVVTDANG 1064
                                     44445555444465555666899***************************9 PP

  == domain 8  score: 2.6 bits;  conditional E-value: 0.1
                  YrbL-PhoP_reg   75 idnsplarilGlvqTdlGlGlvvekirdadGnvakt 110 
                                      d sp++   G+  T  G+G     ++da+G  a++
  gi|116754978|ref|YP_844096.1| 1200 KDDSPITGATGSSYTATGAGSYKVVVTDANGCTAES 1235
                                     57799**************************88875 PP

>> DUF1897  Domain of unknown function (DUF1897)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.3     0.009         7       5      14 ..     359     368 ..     356     370 .. 0.89
   2 ?    6.2   0.3     0.009         7       5      14 ..     442     451 ..     439     453 .. 0.89
   3 ?    6.2   0.3     0.009         7       5      14 ..     525     534 ..     522     536 .. 0.89
   4 ?    6.2   0.3     0.009         7       5      14 ..     608     617 ..     605     619 .. 0.89
   5 ?   -3.1   0.5       7.6   5.9e+03       5      14 ..     691     700 ..     690     701 .. 0.82
   6 ?    6.2   0.3     0.009         7       5      14 ..     774     783 ..     771     785 .. 0.89
   7 ?   -3.1   0.5       7.6   5.9e+03       5      14 ..     857     866 ..     856     867 .. 0.82
   8 ?    6.2   0.3     0.009         7       5      14 ..     940     949 ..     937     951 .. 0.89
   9 ?    6.2   0.3     0.009         7       5      14 ..    1023    1032 ..    1020    1034 .. 0.89
  10 ?    6.2   0.3     0.009         7       5      14 ..    1106    1115 ..    1103    1117 .. 0.89
  11 ?   -3.1   0.5       7.6   5.9e+03       5      14 ..    1189    1198 ..    1188    1199 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.009
                        DUF1897   5 tGqaDYSAqW 14 
                                    +G +DYS qW
  gi|116754978|ref|YP_844096.1| 359 GGKPDYSYQW 368
                                    79******** PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.009
                        DUF1897   5 tGqaDYSAqW 14 
                                    +G +DYS qW
  gi|116754978|ref|YP_844096.1| 442 GGKPDYSYQW 451
                                    79******** PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.009
                        DUF1897   5 tGqaDYSAqW 14 
                                    +G +DYS qW
  gi|116754978|ref|YP_844096.1| 525 GGKPDYSYQW 534
                                    79******** PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.009
                        DUF1897   5 tGqaDYSAqW 14 
                                    +G +DYS qW
  gi|116754978|ref|YP_844096.1| 608 GGKPDYSYQW 617
                                    79******** PP

  == domain 5  score: -3.1 bits;  conditional E-value: 7.6
                        DUF1897   5 tGqaDYSAqW 14 
                                    +G+  YS qW
  gi|116754978|ref|YP_844096.1| 691 GGEEPYSYQW 700
                                    57788***** PP

  == domain 6  score: 6.2 bits;  conditional E-value: 0.009
                        DUF1897   5 tGqaDYSAqW 14 
                                    +G +DYS qW
  gi|116754978|ref|YP_844096.1| 774 GGKPDYSYQW 783
                                    79******** PP

  == domain 7  score: -3.1 bits;  conditional E-value: 7.6
                        DUF1897   5 tGqaDYSAqW 14 
                                    +G+  YS qW
  gi|116754978|ref|YP_844096.1| 857 GGEEPYSYQW 866
                                    57788***** PP

  == domain 8  score: 6.2 bits;  conditional E-value: 0.009
                        DUF1897   5 tGqaDYSAqW 14 
                                    +G +DYS qW
  gi|116754978|ref|YP_844096.1| 940 GGKPDYSYQW 949
                                    79******** PP

  == domain 9  score: 6.2 bits;  conditional E-value: 0.009
                        DUF1897    5 tGqaDYSAqW 14  
                                     +G +DYS qW
  gi|116754978|ref|YP_844096.1| 1023 GGKPDYSYQW 1032
                                     79******** PP

  == domain 10  score: 6.2 bits;  conditional E-value: 0.009
                        DUF1897    5 tGqaDYSAqW 14  
                                     +G +DYS qW
  gi|116754978|ref|YP_844096.1| 1106 GGKPDYSYQW 1115
                                     79******** PP

  == domain 11  score: -3.1 bits;  conditional E-value: 7.6
                        DUF1897    5 tGqaDYSAqW 14  
                                     +G+  YS qW
  gi|116754978|ref|YP_844096.1| 1189 GGEEPYSYQW 1198
                                     57788***** PP

>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1      0.83   6.5e+02       4      27 ..     243     266 ..     240     268 .. 0.92
   2 ?    1.3   0.2      0.55   4.3e+02      37      58 ..    1321    1343 ..    1296    1351 .. 0.83
   3 ?   10.6   0.4   0.00066      0.51       1      33 [.    1571    1603 ..    1571    1644 .. 0.91
   4 ?    2.3   0.0      0.25     2e+02       3      26 ..    1892    1915 ..    1890    1916 .. 0.90
   5 ?   -1.1   0.6       2.9   2.3e+03       3      49 ..    1932    1980 ..    1930    2009 .. 0.56

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.83
                    NPCBM_assoc   4 Getvtltltvtndgtaaatnvsls 27 
                                    G+tvt+   v n+g+  +t+vsl+
  gi|116754978|ref|YP_844096.1| 243 GATVTYCYQVQNTGDVKLTDVSLT 266
                                    99*******************985 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.55
                    NPCBM_assoc   37 vevspasaa.slapGetveatvk 58  
                                     +++s+ +a+ +l++Get ++t++
  gi|116754978|ref|YP_844096.1| 1321 STTSGSTATiDLDAGETIRVTFT 1343
                                     56777778899******999997 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00066
                    NPCBM_assoc    1 vepGetvtltltvtndgtaaatnvslslslPeG 33  
                                     vepG+t t+tltv+n+g+a++ +  +  +lP+G
  gi|116754978|ref|YP_844096.1| 1571 VEPGDTITYTLTVKNTGSATINDATVVDTLPPG 1603
                                     68*********************9999999998 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.25
                    NPCBM_assoc    3 pGetvtltltvtndgtaaatnvsl 26  
                                      G+t t+t t+tn+g+ +++n+++
  gi|116754978|ref|YP_844096.1| 1892 VGQTITYTYTITNGGEITISNIYV 1915
                                     69**************99999976 PP

  == domain 5  score: -1.1 bits;  conditional E-value: 2.9
                    NPCBM_assoc    3 pGetvtltlt..vtndgtaaatnvslslsl.PeGWtvvevspasaaslap 49  
                                     pG+t+++t+t  v+ + +++++n+  +    P G   v ++pa+a+   +
  gi|116754978|ref|YP_844096.1| 1932 PGDTTEVTATyvVKATDESPIKNIATAKGEdPNGDP-VVSDPAEAEVMIA 1980
                                     777777766521455557788888876655577777.6667777773333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (2713 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); 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: 1.29u 0.30s 00:00:01.59 Elapsed: 00:00:00.48
# Mc/sec: 17093.89
//
Query:       gi|116754979|ref|YP_844097.1|  [L=214]
Description: carbonic anhydrase [Methanosaeta thermophila PT]
Scores for complete 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-11   41.5   5.4     0.0033   17.1   0.3    4.0  4  Hexapep    Bacterial transferase hexapeptide (six repeats)
  ------ inclusion threshold ------
      0.011   15.5   1.6       0.51   10.1   0.4    2.7  2  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 !   12.8   0.0     8e-06     0.072       4      36 .]      36      68 ..      33      68 .. 0.90
   2 ?   -0.0   0.0     0.092   8.2e+02      21      34 ..      74      87 ..      72      88 .. 0.76
   3 !   10.9   0.2   3.2e-05      0.29      19      35 ..      94     110 ..      93     111 .. 0.84
   4 !   17.1   0.3   3.6e-07    0.0033       4      34 ..     114     144 ..     112     146 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8e-06
                                   EETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                        Hexapep  4 IGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36
                                   + + +++ p+av+ g V++ + + ++ g+v++g
  gi|116754979|ref|YP_844097.1| 36 VDETAWVSPGAVLIGRVVLKRESSVWYGCVLRG 68
                                   557789************************986 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.092
                                   EE-TTEEEETTEEE CS
                        Hexapep 21 kIGdnvkIgagvvi 34
                                   ++G+ + I  ++v+
  gi|116754979|ref|YP_844097.1| 74 EVGEKSNIQDCSVL 87
                                   68888888888886 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 3.2e-05
                                    TEEE-TTEEEETTEEEE CS
                        Hexapep  19 nVkIGdnvkIgagvvig 35 
                                    +++IGd+v++g+ v+++
  gi|116754979|ref|YP_844097.1|  94 PCIIGDHVTLGHRVTVH 110
                                    69999999999999986 PP

  == domain 4  score: 17.1 bits;  conditional E-value: 3.6e-07
                                    EETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
                        Hexapep   4 IGsnvlIgpfaviggnVkIGdnvkIgagvvi 34 
                                    I++ +++g +a+++++ ++G++++++ag+ +
  gi|116754979|ref|YP_844097.1| 114 IEDWAMVGIGATVLSGSVVGSGAIVAAGALV 144
                                    5555799*********************987 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 ?    3.8   0.0    0.0055        49       2      14 ..      95     107 ..      94     111 .. 0.68
   2 ?   10.1   0.4   5.7e-05      0.51       3      32 ..     113     144 ..     112     146 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.0055
                                    EEE-TT-EE-TT- CS
                      Hexapep_2   2 viIGdnCliGana 14 
                                     iIGd + +G + 
  gi|116754979|ref|YP_844097.1|  95 CIIGDHVTLGHRV 107
                                    5788888888665 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 5.7e-05
                                    EE-TT-EE-TT-EE..SEEE-TT-EE-TT-EE CS
                      Hexapep_2   3 iIGdnCliGanagi..GvslGdncvvgaGvvi 32 
                                    +I+d  ++G  a++  G  +G +++v+aG  +
  gi|116754979|ref|YP_844097.1| 113 HIEDWAMVGIGATVlsGSVVGSGAIVAAGALV 144
                                    799999*******999*************765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); 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:                         2  (0.000111551); expected 0.2 (1e-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: 1542.05
//
Query:       gi|116754980|ref|YP_844098.1|  [L=385]
Description: hypothetical protein Mthe_1692 [Methanosaeta thermophila PT]
Scores for complete 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-41  140.8  33.5    6.8e-41  140.8  33.5    1.4  2  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 ?   -3.5   0.1      0.33   5.8e+03      73      88 ..      19      34 ..      16      34 .. 0.84
   2 !  140.8  33.5   3.8e-45   6.8e-41       4     301 .]      51     362 ..      49     362 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 0.33
                LPG_synthase_TM 73 ayliglfvnnvtPgal 88
                                   +++i++f+ +++P+++
  gi|116754980|ref|YP_844098.1| 19 LTTISYFYLQIVPFSV 34
                                   6789999999999975 PP

  == domain 2  score: 140.8 bits;  conditional E-value: 3.8e-45
                LPG_synthase_TM   4 glalsalllall.lrgvdlaalaaalrsldpwwlllalllallsvllralrWrlllrslgarislrrllrayliglfvnn 82 
                                    +l++++  l+l+ l++v+++++a+++rs+d +++ l ++lall vl+++l+Wr +  + ++ +s+++++ +yl  +f+nn
  gi|116754980|ref|YP_844098.1|  51 ALVVVGTSLYLTyLYHVGFSEIADSMRSVDLRIFSLGFILALLGVLFDGLAWRRVAIKFDCSMSVSDAFLMYLSCIFLNN 130
                                    444443344444589***************************************************************** PP

                LPG_synthase_TM  83 vtPgalg.Gevvrayllkrkegvslskalasvvverlldllalvllgllallllggllaegaavllllalallllavlal 161
                                    ++P+++  Ge +r+y+l +       ++ a+v + r++  + +++ +++++++l  + ++ a ++++   +++++++ + 
  gi|116754980|ref|YP_844098.1| 131 LIPSGSFsGETARIYFLEKLASPGIDRSSATVAATRIITAVPFFFGIAIGMVYLVFETNAPA-WAIATCSGIAFVLFGIN 209
                                    *******************9988999999*********************999999876655.99999999999999999 PP

                LPG_synthase_TM 162 llllllrrrlarlarvlkrlarllarfarklasakr............klvlasprrlllafllslliwllealtlylll 229
                                    + +  + +   +l  +++rl  +++++  ++  ++             + + +++++++++ ++ +++w +  l++++ +
  gi|116754980|ref|YP_844098.1| 210 AIFVGICFSSGWLEGIISRLIEFIEKVFNRRVDRNLcigivrrfhsamNGFTEHRWTIIVSSAWAFAAWFCMNLVAFVTF 289
                                    9999999999999999999999999988777666669999********9******************************* PP

                LPG_synthase_TM 230 ralgvdvslallllillaltlvgalpp.lPgGlGvrEaalalllallGvsaaealaaallyrlitlylllllG 301
                                    +++g++vs++++++++++++++++lp+ lPgG+G++++++++l++++Gv++++a+aa++l rli+l++l+++G
  gi|116754980|ref|YP_844098.1| 290 KSMGIEVSMWAIFAVYAVMIFIQMLPLvLPGGIGLVDIVMITLFSAIGVPTSYAVAATILSRLIQLWFLTIAG 362
                                    **************************7379*****************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       890  (0.0496402); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); 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: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 2896.90
//
Query:       gi|116754981|ref|YP_844099.1|  [L=366]
Description: glutamate--cysteine ligase, GCS2 [Methanosaeta thermophila PT]
Scores for complete 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-45  153.4   0.0    1.1e-44  152.9   0.0    1.1  1  GCS2      Glutamate-cysteine ligase family 2(GCS2)
  ------ inclusion threshold ------
      0.049   13.0   0.1       0.15   11.4   0.0    1.7  2  GCS       Glutamate-cysteine ligase


Domain annotation for each model (and alignments):
>> GCS2  Glutamate-cysteine ligase family 2(GCS2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.9   0.0   1.3e-48   1.1e-44      10     278 ..      21     273 ..      13     284 .. 0.89

  Alignments for each domain:
  == domain 1  score: 152.9 bits;  conditional E-value: 1.3e-48
                                    EETTTTEE-S-HHHHHCCCTTT-S.SSEEEE-SSTTEEEEE--SBSSHHHHHHHHHHHHHHHHHHHHHTT-EEE--SB-S CS
                           GCS2  10 vdlatgdlrgwseiledeaiiglseggsvvkelpegqvElstapleslaeaaeeisadleelrsvadelGlellglGthP 89 
                                    +dl+ ++l+   +++e e+  g     ++ kel+++++El ++p+esl+e+++ +   +++l s      +++lglG+hP
  gi|116754981|ref|YP_844099.1|  21 SDLLIKRLS---GRVEHEIDFGAL---RLSKELQKHVLELVPPPAESLQELEALLYGGVRRLYSCFG--EYRFLGLGMHP 92 
                                    555555555...555555555555...899*************************************..79********* PP

                                    S---------------THHHHHGG..G.G-S--B-EEEEEEE-SSHHHHH..HHHHHHHTTHHHHHHHH--B-EETTEE- CS
                           GCS2  90 falrsedevtpkaryrrmleymdrvGvlgrqmmvaglhvqvnidssseed.VevlrlvrallPvllAlsAnSPfleGrdt 168
                                      l  +++  +++  ++++  +dr+++++++ ++++++ q+ni ++   + Ve+++++rallP+l+A+sA+SPf+eGr+t
  gi|116754981|ref|YP_844099.1|  93 -LLTLDQTTFWEHDEAEYYHIYDRLFNIKQHGWLNIQALQINISYAGSDMlVEMFNRLRALLPYLIAISAASPFVEGRFT 171
                                    .9******************************************9988889***************************** PP

                                    S-SB-GGGCCTTSTT-CS----SSHHH.HHHHHHHHTTSTT-SSGG.G--BSEEEETTTT.EEEEEEEE--...SSHHHH CS
                           GCS2 169 gyaStRariftqtpqagelplafedgaaferyaryaldvpvidvrrfrlwldirpsslpgttlelrihdttlfPevrlra 248
                                    gy ++R  +f+  +q  e+p+++ d+++ er+ r  +d  +i+  r  ++ ++   + +  ++e++++++ +  +++ r+
  gi|116754981|ref|YP_844099.1| 172 GYMDNR-LLFYMENQ-REIPEICHDVIP-ERI-RSIRDYVIIN--R-VIYRKLQERGADLLCREWVNSRGII--VRFKRR 242
                                    ******.99999999.9*********97.775.6777777888..4.46777777777778**********9..****** PP

                                    HHHHHHHHHHHHHHHHH------GGGGTT.. CS
                           GCS2 249 llearlldaqpadrldalpaavlvalldd.e 278
                                    +le++++d+q++ r+d  ++a+l all++  
  gi|116754981|ref|YP_844099.1| 243 CLEVKAIDEQECIRSDMGVTAFLNALLRSdI 273
                                    **************************99854 PP

>> GCS  Glutamate-cysteine ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   1.7e-05      0.15      14      56 ..     129     171 ..     125     179 .. 0.89
   2 ?   -2.9   0.0      0.37   3.3e+03     304     324 ..     308     328 ..     276     334 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.7e-05
                            GCS  14 cLQvtfqaknieearllYdqlaplaPillalsaaspiykGlla 56 
                                    +LQ+ ++ +  +    ++++l +l P l+a+saasp++ G  +
  gi|116754981|ref|YP_844099.1| 129 ALQINISYAGSDMLVEMFNRLRALLPYLIAISAASPFVEGRFT 171
                                    6899999999999999**********************99765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.37
                            GCS 304 vdvetrkklekylkliskras 324
                                    ++ +++   + yl li++r++
  gi|116754981|ref|YP_844099.1| 308 AERHASPDEMAYLPLIKERID 328
                                    344556667789999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); 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 0.23s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2816.21
//
Query:       gi|116754982|ref|YP_844100.1|  [L=168]
Description: hypothetical protein Mthe_1694 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-10   40.4   0.2      7e-10   39.5   0.2    1.5  1  CxxCxxCC  Putative zinc- or iron-chelating domain
  ------ inclusion threshold ------
      0.075   12.9   0.0        0.1   12.4   0.0    1.1  1  DUF5568   Family of unknown function (DUF5568)


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 !   39.5   0.2   7.8e-14     7e-10       2      85 .]      17     109 ..      16     109 .. 0.92

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 7.8e-14
                       CxxCxxCC   2 CkeC.gaCCkelkvklteedlerlkaaevaeeeeeskkiak....adgrCvfldeetklCkiYeeRpkicrlfpas.... 72 
                                    C +C g CC ++++ lte+  e l  a+   ++ e+  +++     dg Cv+l++   +C++++ +p++c + p++    
  gi|116754982|ref|YP_844100.1|  17 CSSCgGICCIDARPPLTEKRAEILISAGLRPDDIEHAGYKRlrarDDGSCVLLENG--RCRLHHLKPETCSAGPFTfdmm 94 
                                    ****99***********************9999999999889999********998..9****************98888 PP

                       CxxCxxCC  73 ..ekeellaraetCa 85 
                                      + e +l+r++ C+
  gi|116754982|ref|YP_844100.1|  95 dgRVEIYLKRESICP 109
                                    888888888888885 PP

>> DUF5568  Family of unknown function (DUF5568)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.1e-05       0.1     107     172 ..      28      97 ..      18     106 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.1e-05
                        DUF5568 107 GrPlGttkaaGfktsPGrPlGttkaaGykvsPGrPPGsikal....srlnkleysacsgaafPysvmhkr 172
                                     rP  t k a    s G        aGyk    r  Gs   l    +rl++l+ ++cs+ +f + +m+ r
  gi|116754982|ref|YP_844100.1|  28 ARPPLTEKRAEILISAGLRPDDIEHAGYKRLRARDDGSCVLLengrCRLHHLKPETCSAGPFTFDMMDGR 97 
                                    68999999999999999666778899************9766333379*******************977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       813  (0.0453455); expected 358.6 (0.02)
Passed bias filter:                      587  (0.0327403); 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: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1266.41
//
Query:       gi|116754983|ref|YP_844101.1|  [L=335]
Description: RimK domain-containing protein ATP-grasp [Methanosaeta thermophila PT]
Scores for complete 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   40.2   0.0    6.4e-10   38.9   0.0    1.7  1  RimK             RimK-like ATP-grasp domain
    3.1e-08   33.8   0.0    5.2e-08   33.1   0.0    1.3  1  ATP-grasp_3      ATP-grasp domain
    0.00021   21.2   0.0    0.00052   19.9   0.0    1.7  1  R2K_2            ATP-grasp domain, R2K clade family 2
    0.00046   20.3   0.1      0.001   19.1   0.1    1.6  1  R2K_3            ATP-grasp domain, R2K clade family 3
    0.00063   19.3   0.0      0.001   18.6   0.0    1.2  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
  ------ inclusion threshold ------
      0.063   12.5   0.0        1.9    7.7   0.0    2.1  2  ATPgrasp_ST      Sugar-transfer associated ATP-grasp


Domain annotation for each model (and alignments):
>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.0   2.1e-13   6.4e-10       2     187 ..      90     286 ..      89     287 .. 0.80

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 2.1e-13
                                    H-HHHHHHHHHHTT-----EEEESS-S-HHHHHHTT-...-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHH...GGG-- CS
                           RimK   2 rdKlkslklLakakikvpntalardeedaekliekik..lrfPvvvKsvegsqGikvvlakkeqklkqvlea...lkeai 76 
                                    +dK+     L+k+k+++p+t +  + e a ++   +   l++P+v+K+  +s+  +v  a + q+   + +    l   i
  gi|116754983|ref|YP_844101.1|  90 SDKINMYLHLMKKKLPIPRTVFPSKREIAPEYARALFerLGTPLVLKEPSTSFSARVEKASNVQEFMRIAKRflrLSDWI 169
                                    68888888899999999999987766555444444333358****************************7779889999* PP

                                    EEEEE--SS-SEEEEEEEETTEEEEEEEEE--SSS--....--...TTTT.-EEEE----HHHHHHHHHHHHHCT-SEEE CS
                           RimK  77 lvqeyieeaenediRvlvvddevvaalrrvskeGdFR....sn...lhrG.gvaeklqlseeekelAikaakamelvvaG 148
                                    +vqey+    + d R+ v+++e   a r v     F+     n   ++ G   + + ++  e  +l i+a ka++  + G
  gi|116754983|ref|YP_844101.1| 170 VVQEYVPS--SFDWRIGVLNGEFLYACRYVIPAQTFKiqasVNghlVYCGvESVPPEDVPSEIIDLGIEAGKAIGKGLYG 247
                                    *****975..689***********999988777777722222322122331234567899999***************** PP

                                    EEEEEETTEEEEEEEESS--SHHHHHHHT--HHHHHHHH CS
                           RimK 149 vDllrakrgllvlEvnsspglekiektlgidiakkliea 187
                                    vD+ +++  l+v+Evn +p l++ e     +i  ++i++
  gi|116754983|ref|YP_844101.1| 248 VDIKESNGRLYVIEVNDNPSLDGGEDVCYPEIYRRIISY 286
                                    **********************99888877777777766 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.0   1.8e-11   5.2e-08       1     155 [.      89     263 ..      89     268 .. 0.84

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 1.8e-11
                                    HTSHHHHHHHHTTT.S---...............-EESS--SSSEEEEESS-------B--SS--TTE............ CS
                    ATP-grasp_3   1 asdKlktykkLkeagvkvP...........tkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve..... 64 
                                    +sdK+++y  L+++++++P            ++  + +e+   +lv+K  + + +  v ++ + +e  ++ +        
  gi|116754983|ref|YP_844101.1|  89 CSDKINMYLHLMKKKLPIPrtvfpskreiaPEYARALFERLGTPLVLKEPSTSFSARVEKASNVQEFMRIAKRFLrlsdw 168
                                    89*****************8887777666656666666666**************9***999998887666655578889 PP

                                    .EEEE---SE.EEEEEEEE.SSSEEEEEEEEEEEET............TEEEEEEES----HHHHHHHHHHHHHTTSTT- CS
                    ATP-grasp_3  65 .lvqefieGk.plSvsllsdgekvlvlavnrqliekaeke........fvyaGnvtpietelkeevvelaeevveklegl 134
                                     +vqe+++++ +  + +l       +l  +r +i  ++ +        +vy+G  +  + +  +e+++l  e+ +++   
  gi|116754983|ref|YP_844101.1| 169 iVVQEYVPSSfDWRIGVLNG----EFLYACRYVIPAQTFKiqasvnghLVYCGVESVPPEDVPSEIIDLGIEAGKAI--G 242
                                    8******8763566666664....5899999998776666888999*******998888899***************..7 PP

                                    -EEEEEEEEESS.SEEEEEEE CS
                    ATP-grasp_3 135 aGyvGvDlvlkdeepyviEvN 155
                                    +G+ GvD+  +++ +yviEvN
  gi|116754983|ref|YP_844101.1| 243 KGLYGVDIKESNGRLYVIEVN 263
                                    9*******************9 PP

>> R2K_2  ATP-grasp domain, R2K clade family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   1.7e-07   0.00052      19     132 ..     131     267 ..     113     280 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.7e-07
                          R2K_2  19 wpvFvkpasdaksftgavvedge..dlpgl..gsldedlpvlvsevvsfasEyRlfvldgeiitvsrYagegrl.dpdp. 92 
                                    +p+  k +s   sf+++v + ++  ++++     l+ + +++v+e+v+    +R+ vl+ge++ ++rY    +  ++++ 
  gi|116754983|ref|YP_844101.1| 131 TPLVLKEPST--SFSARVEKASNvqEFMRIakRFLRLSDWIVVQEYVPSSFDWRIGVLNGEFLYACRYVIPAQTfKIQAs 208
                                    5555666666..8999988766533444445455667779****************************988887544446 PP

                          R2K_2  93 ....................evaeeavaalksalpsayvlDvgvtedgetalvEandgwa 132
                                                        e+++  ++a k   +  y +D+ +++ g++ ++E+nd  +
  gi|116754983|ref|YP_844101.1| 209 vnghlvycgvesvppedvpsEIIDLGIEAGKAIGKGLYGVDIKESN-GRLYVIEVNDNPS 267
                                    6888888889999999999899999999999999999****96655.5********9765 PP

>> R2K_3  ATP-grasp domain, R2K clade family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1   3.5e-07     0.001      70     186 ..     129     267 ..      76     280 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 3.5e-07
                          R2K_3  70 eeepvFvkprgdklfggvV..lrefeelralaakle..dtevlvsevvrfsaEwRvFvvdGevvaasrYr.......... 135
                                    + +p+ +k++ +  f+++V  +  ++e+ ++a+++   +  ++v e+v+ s  wR+ v++Ge + a+rY           
  gi|116754983|ref|YP_844101.1| 129 LGTPLVLKEPSTS-FSARVekASNVQEFMRIAKRFLrlSDWIVVQEYVPSSFDWRIGVLNGEFLYACRYVipaqtfkiqa 207
                                    4555555544444.6666644224444445555555455668999************************97777765544 PP

                          R2K_3 136 ..kanddpdl..........epdlaafaeavralv......gappfyvlDvavtadGrwkVVEvndgqv 186
                                      +                 +  ++ + +++  l+           y +D+  + +Gr++V+Evnd  +
  gi|116754983|ref|YP_844101.1| 208 svN------GhlvycgvesvP--PEDVPSEIIDLGieagkaIGKGLYGVDIKES-NGRLYVIEVNDNPS 267
                                    330......133555555331..33344444444444444435999*****666.9**********765 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 !   18.6   0.0   3.4e-07     0.001      26     177 ..     120     267 ..     104     277 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 3.4e-07
                                    HHHHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT-SCEEEEE--.ESEEEEEEEEETSSCEEEEEEEE CS
                Dala_Dala_lig_C  26 ellekveeelgypvfVKpareGSSvGvskveseeelkeaieeafkydekvlvEeai.egreievavlgneklevsevgei 104
                                    e+ +++ e+lg p++ K   +  S  v+k+++++e+ +  ++ ++    ++v e++ +  +  ++vl+    e + + + 
  gi|116754983|ref|YP_844101.1| 120 EYARALFERLGTPLVLKEPSTSFSARVEKASNVQEFMRIAKRFLRLSDWIVVQEYVpSSFDWRIGVLN---GEFLYACRY 196
                                    7788999************9*9**********************************99*********9...788889999 PP

                                    E-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEESS-- CS
                Dala_Dala_lig_C 105 vvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEvNtlPG 177
                                    v   + ++++a   ++ + + v+   +++v ++i +l ++a ka++ +Gl  vD+  +++g++++ EvN  P 
  gi|116754983|ref|YP_844101.1| 197 VIPAQTFKIQASVNGHLVYCGVESVPPEDVPSEIIDLGIEAGKAIG-KGLYGVDIK-ESNGRLYVIEVNDNPS 267
                                    999999*******99999999**999******************96.9******86.569*********9995 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 ?    2.6   0.0     0.022        67      11      70 ..      81     140 ..      75     162 .. 0.84
   2 ?    7.7   0.0   0.00063       1.9     227     269 ..     229     269 ..     226     274 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.022
                    ATPgrasp_ST  11 NpraefplvddKlkfkelalraglkvpkllgvikeqaeiseleafvkeleegvviKpakg 70 
                                     + a +++  dK++++  + ++ l++p+++   k +   + ++a+ ++l + +v+K+  +
  gi|116754983|ref|YP_844101.1|  81 DDPASIQICSDKINMYLHLMKKKLPIPRTVFPSKREIAPEYARALFERLGTPLVLKEPST 140
                                    5778889999******************99999988888888888888877688777655 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00063
                    ATPgrasp_ST 227 evlelaakaaeklpglgylGwDivldeekgplllElNarpgla 269
                                    e+++l  +a +   g g+ G+Di   + + ++++E+N++p+l+
  gi|116754983|ref|YP_844101.1| 229 EIIDLGIEAGK-AIGKGLYGVDIKESNGR-LYVIEVNDNPSLD 269
                                    67778888887.88999******977777.***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); 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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2596.36
//
Query:       gi|116754984|ref|YP_844102.1|  [L=214]
Description: hypothetical protein Mthe_1696 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.4e-10   38.5   0.1    1.7e-09   37.5   0.1    1.5  1  RLAN      RimK-like ATPgrasp N-terminal domain


Domain annotation for each model (and alignments):
>> RLAN  RimK-like ATPgrasp N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.5   0.1   9.7e-14   1.7e-09      14     148 ..      18     205 ..      10     207 .. 0.83

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 9.7e-14
                           RLAN  14 krarvlNLcrsyrYqseGYYvSLlAearghkviPsvstindlsrksllrlrleel......................... 68 
                                    k++ v  + +sy Y+ e YY     e  g + +Ps s++ d    +++  +++ +                         
  gi|116754984|ref|YP_844102.1|  18 KNGTVYIINESYFYKTEPYYTIVQNEFEGIRTVPSSSAVLDAYIVPICLEKARMAgipvcewvvsyayitlpaivyglny 97 
                                    44555556699******************************9977766655555588*********************** PP

                           RLAN  69 ................esklqktlk.......skskenrlelsv...vFGet..eekelkslarklfeefriPilkvele 120
                                                    +++++++++        ++ +++ e+ v   +FG+t  ++ e++ la+k++  f+iP++++ l 
  gi|116754984|ref|YP_844102.1|  98 fstpsehfvvkdftsaKKAIKHVTNygkypfcYQKISDEAEVAVytsIFGRTidCSDEIETLAEKIYAVFNIPLVSLVLV 177
                                    **********99988644444444466677764444555555556669***944579*********************** PP

                           RLAN 121 rkdgkwkiesikalslkeldeaeeslfa 148
                                    r+ g+++++s+ ++ +++l+e+e++l++
  gi|116754984|ref|YP_844102.1| 178 RDLGGYRLSSLAPVMYSQLSEKERDLMK 205
                                    ************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1541.07
//
Query:       gi|116754985|ref|YP_844103.1|  [L=669]
Description: hypothetical protein Mthe_1697 [Methanosaeta thermophila PT]
Scores for complete 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-73  243.8   0.0    1.3e-72  243.1   0.0    1.3  1  Thioredox_DsbH   Protein of unknown function, DUF255
    3.9e-11   43.0   0.0    6.5e-11   42.3   0.0    1.4  1  Thioredoxin_7    Thioredoxin-like
    2.6e-05   23.5   0.2    0.00084   18.5   0.0    2.1  2  Glyco_hydro_88   Glycosyl Hydrolase Family 88
     0.0014   18.2   0.1          2    7.9   0.0    2.9  3  C5-epim_C        D-glucuronyl C5-epimerase C-terminus
  ------ inclusion threshold ------
       0.07   11.6   0.0        0.2   10.1   0.0    1.6  2  Glyco_hydro_127  Beta-L-arabinofuranosidase, GH127


Domain annotation for each model (and alignments):
>> Thioredox_DsbH  Protein of unknown function, DUF255
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  243.1   0.0   3.6e-76   1.3e-72       2     162 ..       6     166 ..       5     167 .. 0.98

  Alignments for each domain:
  == domain 1  score: 243.1 bits;  conditional E-value: 3.6e-76
                 Thioredox_DsbH   2 nrlaeekspYllqhaknpvdWypwgeealekakeedkpillsiGysachWChvmekesfedeevaallnesfvsvkvDre 81 
                                    nrla e+spYllqha npvdWypw+ ea+e+a++ed+pi+lsiGys+chWChvm++esfede++a++ln+ fv+vkvDre
  gi|116754985|ref|YP_844103.1|   6 NRLAGESSPYLLQHAYNPVDWYPWSPEAFERARAEDRPIFLSIGYSTCHWCHVMARESFEDERIAEMLNRAFVCVKVDRE 85 
                                    9******************************************************************************* PP

                 Thioredox_DsbH  82 erPdldkiymeavqaltgsggWPlnvfltpdlkpffggtYfpkeeregrpgflevlekiaelweeereeleeeaeellea 161
                                    erPd+d+iymea+q++tg+ggWPl+++++pd+ pff++tY+pk+ r g++g++e++  ++elw+++r+el++   ++l+a
  gi|116754985|ref|YP_844103.1|  86 ERPDIDAIYMEACQIITGRGGWPLTIIMSPDGIPFFAATYIPKDGRLGMMGLRELIPLVEELWRNRRSELTSLGFKVLNA 165
                                    **********************************************************************9988888776 PP

                 Thioredox_DsbH 162 l 162
                                    +
  gi|116754985|ref|YP_844103.1| 166 M 166
                                    5 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.0   1.8e-14   6.5e-11       1      67 [.      25      90 ..      25     115 .. 0.83

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 1.8e-14
                                   ---SSHHHHHHHHHHHT--EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S-GGG CS
                  Thioredoxin_7  1 ewlsdldealakaaergkpvlvffgaswcftCqalerdflsdeevkaalaekfvllrvdvterdani 67
                                   +w+ + +ea+++a+++ +p+++ +g s+c+ C++++r+  +de+++++l+  fv+++vd +er + i
  gi|116754985|ref|YP_844103.1| 25 DWYPWSPEAFERARAEDRPIFLSIGYSTCHWCHVMARESFEDERIAEMLNRAFVCVKVDREERPD-I 90
                                   7*************************************999999999999**********99976.3 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 ?    2.9   0.1     0.013        46      28      64 ..     270     306 ..     216     348 .. 0.64
   2 !   18.5   0.0   2.3e-07   0.00084      87     175 ..     422     508 ..     401     514 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.013
                                    .HHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHCCCT CS
                 Glyco_hydro_88  28 ewtnGvflsglleayeatgdkeyldyakawadslide 64 
                                     ++++++    leay+atg+ +y  +a+++   + ++
  gi|116754985|ref|YP_844103.1| 270 LYDQALMSVVYLEAYQATGKRDYAIVADEILGFVAED 306
                                    2666655555566666666666655555544333333 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 2.3e-07
                                    HH-THHHHHHHHHHHHHHHHCS-B.TTS.B.SBTTSTTEEETHHHHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHHHB CS
                 Glyco_hydro_88  87 ltkderykeaaeeladyvlakpprtseGgfwhkkkepeqlWlDgLfMaipllaklskvtgepkyldeaikqflltarhlf 166
                                      +der  + a e+ad+vl+ + r  +G ++h  k  +  +lD+    i  l++l++   + +yl+ a    +++ +h  
  gi|116754985|ref|YP_844103.1| 422 VLGDERWLRIASEAADFVLSSMHR--DGMLMHSYKGSRVSILDDYAFLIFGLIELYQAGFDGRYLERAEILCDEMVSHFS 499
                                    56899*******************..******************9999999***************************** PP

                                    ETTTSEB-S CS
                 Glyco_hydro_88 167 dpetGlyyh 175
                                    dp+ G yy 
  gi|116754985|ref|YP_844103.1| 500 DPDGGFYYT 508
                                    *******95 PP

>> 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 !    6.8   0.0    0.0012       4.2      30      60 ..     272     302 ..     248     316 .. 0.88
   2 !    7.9   0.0   0.00055         2      32      74 ..     410     452 ..     405     466 .. 0.91
   3 ?   -1.7   0.0      0.49   1.8e+03      36      65 ..     469     498 ..     458     514 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0012
                      C5-epim_C  30 aqgqaisvllrAYeltgdekYlkaakkalks 60 
                                    +q+ + +v+l+AY++tg+ +Y  +a++ l +
  gi|116754985|ref|YP_844103.1| 272 DQALMSVVYLEAYQATGKRDYAIVADEILGF 302
                                    6899999**************9999988765 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00055
                      C5-epim_C  32 gqaisvllrAYeltgdekYlkaakkalksfkipvekGGvlktl 74 
                                    g +i +++r  ++ gde++l++a++a ++++ +++  G+l ++
  gi|116754985|ref|YP_844103.1| 410 GLMIAAFSRGAQVLGDERWLRIASEAADFVLSSMHRDGMLMHS 452
                                    8899********************************9998765 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.49
                      C5-epim_C  36 svllrAYeltgdekYlkaakkalksfkipv 65 
                                      l++ Y++  d +Yl+ a+ + + +    
  gi|116754985|ref|YP_844103.1| 469 FGLIELYQAGFDGRYLERAEILCDEMVSHF 498
                                    456777888889999999988777665443 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 ?   -2.0   0.0      0.26   9.3e+02     180     201 ..     276     297 ..     250     315 .. 0.61
   2 ?   10.1   0.0   5.6e-05       0.2     129     272 ..     411     612 ..     395     617 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.26
                                    HHHHHHHHHHHHT-CHHHHHHH CS
                Glyco_hydro_127 180 ieealvklyelTgdkrYldlAk 201
                                    +  ++++ y++Tg ++Y  +A 
  gi|116754985|ref|YP_844103.1| 276 MSVVYLEAYQATGKRDYAIVAD 297
                                    4455556666666666655554 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 5.6e-05
                                    HHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHCCS-CCHHHHHTTT........HHCTHHHHHHHHHHHHT-CHHHHHH CS
                Glyco_hydro_127 129 kliegavayyqatgkeklldvatrladyleevleklgdeqlqkalvp........ehggieealvklyelTgdkrYldlA 200
                                     +i++     q+ g+e+ l++a ++ad++   l+ + ++ +  + ++        +   +  +l++ly++  d rYl+ A
  gi|116754985|ref|YP_844103.1| 411 LMIAAFSRGAQVLGDERWLRIASEAADFV---LSSMHRDGMLMHSYKgsrvsildDYAFLIFGLIELYQAGFDGRYLERA 487
                                    4777788888999****************...5555555544444442212122155556679999************** PP

                                    HHCCHHCCHCC.....................................................T-HCTTT-SSTCGCHH CS
                Glyco_hydro_127 201 krfidergldp.....................................................eklaykqdelpvrhqn 227
                                    + ++de + +                                                      e  + +  ++++    
  gi|116754985|ref|YP_844103.1| 488 EILCDEMVSHFsdpdggfyytmkeqsdiilqrkeirdgaipsgysmatmdmlllgkilgrpdleEIASMSLRHISMASLP 567
                                    ******99888777777777777666666666666666666666666666666666666555433344444455555555 PP

                                    CHHCCHHHHHHHHHHHHHHHHHCTTHCC.HHHHHHHHHHHHHHCB- CS
                Glyco_hydro_127 228 taigkavRatylysgladvyeetgddkl.lkaaerlwdnvvtkkmy 272
                                     ++g ++ a  l+ g  +  ++ gd +  +++++ lw     +k++
  gi|116754985|ref|YP_844103.1| 568 AQVGLLI-ALDLALGPSHEIAIVGDADNtRTMLRALWSVYAPRKVV 612
                                    6666666.66666666666666666443034556666655555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (669 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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 0.26s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 4570.66
//
Query:       gi|116754986|ref|YP_844104.1|  [L=187]
Description: hypothetical protein Mthe_1698 [Methanosaeta thermophila PT]
Scores for complete sequence (score 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   15.4   0.1      0.025   14.6   0.1    1.3  1  DUF5432        Family of unknown function (DUF5432)
       0.18   11.7   0.6       0.64    9.9   0.5    1.8  2  eIF-5_eIF-2B   Domain found in IF2B/IF5
        0.2   11.4   2.0        9.8    6.0   0.0    2.6  2  zinc_ribbon_5  zinc-ribbon domain
       0.26   11.2   4.5        1.2    9.2   4.5    2.1  1  Prok-RING_1    Prokaryotic RING finger family 1
        0.7    9.9   4.0        1.7    8.7   4.0    1.6  1  Nudix_N_2      Nudix N-terminal
        1.7    8.7   4.2        8.1    6.5   0.1    2.7  3  zinc_ribbon_4  zinc-ribbon domain
        2.8    7.5   5.3        2.6    7.6   2.9    2.1  2  TF_Zn_Ribbon   TFIIB zinc-binding


Domain annotation for each model (and alignments):
>> DUF5432  Family of unknown function (DUF5432)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   9.9e-06     0.025       5      39 ..      19      52 ..      16      70 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.9e-06
                        DUF5432  5 fhvrrllkfrvescssihllslhPlyvimsPmdii 39
                                   +h  r l  r e c ++h+++ hP +v m+P+ +i
  gi|116754986|ref|YP_844104.1| 19 LHAGRDLVVRCEVCGTVHSVAPHP-HVRMTPLKVI 52
                                   589999******************.799***9998 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 ?    9.9   0.5   0.00025      0.64      88     116 ..       5      34 ..       2      35 .. 0.72
   2 ?   -1.0   0.0      0.62   1.6e+03      25      45 ..      92     112 ..      58     132 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00025
                                    TSTSSSTS..TCEEECCSSSCEEEEESSSTC CS
                   eIF-5_eIF-2B  88 VlCkeCks..petelekeerllvlkCkaCga 116
                                    ++C+ C+s   +t l+  +r lv++C+ Cg 
  gi|116754986|ref|YP_844104.1|   5 IICPACDSatEHTVLH-AGRDLVVRCEVCGT 34 
                                    79****9842334444.555566******96 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.62
                                    EEEETTHHHHHHHHTTSHHHH CS
                   eIF-5_eIF-2B  25 ktvivNfeeiakaLnrdpehv 45 
                                     t+i+  +++++aL rd + v
  gi|116754986|ref|YP_844104.1|  92 VTAIETDKRVSHALARDVKCV 112
                                    566666667777777776655 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.6     0.017        45       3      10 ..       5      12 ..       4      14 .. 0.86
   2 ?    6.0   0.0    0.0038       9.8       1      12 [.      25      36 ..      25      40 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.017
                  zinc_ribbon_5  3 irCpdCdt 10
                                   i Cp+Cd+
  gi|116754986|ref|YP_844104.1|  5 IICPACDS 12
                                   67*****8 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0038
                  zinc_ribbon_5  1 LiirCpdCdtkF 12
                                   L++rC+ C+t  
  gi|116754986|ref|YP_844104.1| 25 LVVRCEVCGTVH 36
                                   678999999975 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 ?    9.2   4.5   0.00046       1.2       6      30 ..       6      36 ..       2      39 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00046
                    Prok-RING_1  6 kCpvCgkelkee.....dDiVv.CpeCgtpy 30
                                   +Cp+C+ + ++       D+Vv C +Cgt++
  gi|116754986|ref|YP_844104.1|  6 ICPACDSATEHTvlhagRDLVVrCEVCGTVH 36
                                   79999877555444445786666******98 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   4.0   0.00065       1.7       3      32 ..       7      36 ..       6      36 .. 0.98

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00065
                                   -TTT--B-EEE--TT-SS-EEEETTTTEEE CS
                      Nudix_N_2  3 CsqCGtpvelripdgDnreRlvCpaCgtih 32
                                   C++C +++e+ + + +     +C+ Cgt+h
  gi|116754986|ref|YP_844104.1|  7 CPACDSATEHTVLHAGRDLVVRCEVCGTVH 36
                                   *****************************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 ?    3.0   0.2     0.037        96       3      10 ..       5      12 ..       4      15 .. 0.82
   2 ?    6.5   0.1    0.0032       8.1      26      34 ..      27      35 ..      20      41 .. 0.67
   3 ?   -3.1   0.1         3   7.8e+03      22      28 ..     105     111 ..      98     111 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.037
                  zinc_ribbon_4  3 itCpsCka 10
                                   i Cp+C +
  gi|116754986|ref|YP_844104.1|  5 IICPACDS 12
                                   89****75 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0032
                  zinc_ribbon_4 26 vrCskCghv 34
                                   vrC  Cg+v
  gi|116754986|ref|YP_844104.1| 27 VRCEVCGTV 35
                                   666666654 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 3
                  zinc_ribbon_4  22 kgvkvrC 28 
                                     ++ v+C
  gi|116754986|ref|YP_844104.1| 105 LARDVKC 111
                                    5678999 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   2.9     0.001       2.6       2      28 ..       6      35 ..       5      41 .. 0.86
   2 ?   -2.7   0.0       1.7   4.4e+03      10      21 ..      77      88 ..      75      88 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.001
                                   EETTTTC.EE.CHEETSTTCE.EESSSSBE CS
                   TF_Zn_Ribbon  2 kCPnCgs.tn.lveDpergel.vCtdCGlV 28
                                   +CP C s t+ +v+ + r  + +C+ CG+V
  gi|116754986|ref|YP_844104.1|  6 ICPACDSaTEhTVLHAGRDLVvRCEVCGTV 35
                                   7******8888888888877789*****99 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.7
                                   ECHEETSTTCEE CS
                   TF_Zn_Ribbon 10 nlveDpergelv 21
                                   ++v+D  r ++v
  gi|116754986|ref|YP_844104.1| 77 EIVVDDGRSDVV 88
                                   589999888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1398.91
//
Query:       gi|116754987|ref|YP_844105.1|  [L=210]
Description: protein-L-isoaspartate O-methyltransferase [Methanosaeta thermophila PT]
Scores for complete 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-76  254.9   0.0    6.5e-76  254.7   0.0    1.0  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    5.7e-12   45.7   0.0    7.7e-12   45.3   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    2.9e-06   27.9   0.0      5e-06   27.1   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    3.6e-06   26.5   0.0    4.4e-06   26.2   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    6.9e-06   25.9   0.0    9.7e-06   25.4   0.0    1.1  1  GCD14            tRNA methyltransferase complex GCD14 subunit
      2e-05   23.8   0.0    2.7e-05   23.4   0.0    1.3  1  Fibrillarin      Fibrillarin
    3.2e-05   23.2   0.0    4.1e-05   22.8   0.0    1.1  1  Methyltransf_3   O-methyltransferase
     0.0011   19.5   0.0     0.0032   18.1   0.0    1.8  1  Methyltransf_11  Methyltransferase domain
     0.0014   17.7   0.0      0.002   17.2   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
     0.0048   16.2   0.0     0.0071   15.7   0.0    1.3  1  CMAS             Mycolic acid cyclopropane synthetase
      0.005   16.5   0.0      0.009   15.7   0.0    1.4  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
     0.0055   16.3   0.0     0.0093   15.5   0.0    1.4  1  MTS              Methyltransferase small domain
     0.0096   15.8   0.0      0.018   14.9   0.0    1.5  1  Methyltransf_23  Methyltransferase domain
  ------ inclusion threshold ------
      0.018   14.8   0.0      0.025   14.3   0.0    1.2  1  Methyltransf_16  Lysine methyltransferase
       0.03   13.8   0.0      0.046   13.2   0.0    1.3  1  Methyltransf_4   Putative methyltransferase
      0.079   12.2   0.0       0.13   11.6   0.0    1.3  1  Methyltransf_2   O-methyltransferase domain
       0.13   12.0   0.0       0.19   11.4   0.0    1.3  1  DUF938           Protein of unknown function (DUF938)


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 !  254.7   0.0   6.2e-79   6.5e-76       2     208 ..       2     202 ..       1     204 [. 0.98

  Alignments for each domain:
  == domain 1  score: 254.7 bits;  conditional E-value: 6.2e-79
                                    HHHHHHHHHHHTTS---HHHHHHHHHS-GGGGSSCGGGGGTTSSS-EEEETTEEE--HHHHHHHHHHTT--TT-EEEEES CS
                           PCMT   2 kkealieelkkkgviksdkvaealeevdReefvpesfkekaYedaplsigynatiSaphmvalalellelkkgarvLevG 81 
                                    +ke+lie+l+++    s++v+ea+  v+Re fvpe+++ +aYed pl+ig ++tiSaphmva++++ll+l++g++vLevG
  gi|116754987|ref|YP_844105.1|   2 RKERLIESLRNYV---SERVVEAMSRVPRELFVPEELRPMAYEDRPLPIGHGQTISAPHMVAMMCDLLDLREGMKVLEVG 78 
                                    7899*******98...**************************************************************** PP

                                    -TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTGGG-SEEEEEESSBBSS--HHHHH CS
                           PCMT  82 sGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGyeekaPYdaihvgaaapeiPealid 161
                                    +G+Gy++av+a+lvg++g+v s+eri+elve a+rnl++  ++nv+++ gDG+ Gy e+aPYd+i v+a+ap+iPe+l +
  gi|116754987|ref|YP_844105.1|  79 GGCGYHAAVMAELVGPSGHVYSVERIPELVEMARRNLERARYRNVSMILGDGTLGYSEQAPYDRISVAASAPDIPEPLKE 158
                                    ******************************************************************************** PP

                                    TEEEEEEEEEEESBSSSEEEEEEEEETTTEEEEEEEEEE---B-BCC CS
                           PCMT 162 QLkeGGrlvvPvgeeeeQvlklvdkkadgkvvikkleevrfvpltdk 208
                                    QL +GGr+v+Pvg +++Q+l +v k++   + +++ + v+fvpl +k
  gi|116754987|ref|YP_844105.1| 159 QLRPGGRMVIPVG-SYSQDLLVVTKNH--DIRVERAMGVIFVPLIGK 202
                                    *************.***********99..79999**********876 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.0   7.3e-15   7.7e-12       2     109 ..      69     168 ..      68     192 .. 0.84

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 7.3e-15
                Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDlils 80 
                                    ++g++vl++G G G+ + ++ae++gp ++v+++++ +e +e Ar n+++  + nv++  gd +   +++   +++D i  
  gi|116754987|ref|YP_844105.1|  69 REGMKVLEVGGGCGYHAAVMAELVGPSGHVYSVERIPELVEMARRNLERARYRNVSMILGDGTLgYSEQ---APYDRISV 145
                                    579**********************************************************99977743...89999655 PP

                Methyltransf_31  81 nevlnaladpdkileeiervlkpggilli 109
                                        +  +d ++ l+e    l+pgg+++i
  gi|116754987|ref|YP_844105.1| 146 ---AASAPDIPEPLKE---QLRPGGRMVI 168
                                    ...3455555555555...8888888877 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   4.7e-09     5e-06       1      72 [.      74     147 ..      74     164 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 4.7e-09
                                    EEEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEES CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssg 72 
                                    vL++G G G +++ +a+ +g +++v+ v+  +e++e ar+++e++++ nv+++ gd +    e++ +D + ++ 
  gi|116754987|ref|YP_844105.1|  74 VLEVGGGCGYHAAVMAELVGpSGHVYSVERIPELVEMARRNLERARYrNVSMILGDGTLGYSEQAPYDRISVAA 147
                                    9******************669********************999889********987777888999988853 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   4.2e-09   4.4e-06      41     151 ..      64     168 ..      57     201 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 4.2e-09
                                    HH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEE CS
                Ubie_methyltran  41 klvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvv 120
                                    +l   ++g kvl+v gG g  a+ +++ vg +g+v  ++  +++++++++ l++  + n+ ++ +++     e+  +D +
  gi|116754987|ref|YP_844105.1|  64 DLLDLREGMKVLEVGGGCGYHAAVMAELVGPSGHVYSVERIPELVEMARRNLERARYRNVSMILGDGTLGYSEQAPYDRI 143
                                    5556789************************************************************987788899***9 PP

                                    EEES-GGG-S-HHHHHHHHHHHEEEEEEEEE CS
                Ubie_methyltran 121 tvsfGlrnvtDklkaLkeayrvlkpGGrlvv 151
                                     v+      +D+++ Lke    l+pGGr+v+
  gi|116754987|ref|YP_844105.1| 144 SVAA---SAPDIPEPLKEQ---LRPGGRMVI 168
                                    9985...689999999997...559999875 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   9.2e-09   9.7e-06      29      90 ..      59     120 ..      45     136 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 9.2e-09
                          GCD14  29 isliimkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehel 90 
                                    ++++   L+l++G +v+e G G g  +  +a  v+P Gh++++e   + +e ar ++++ + 
  gi|116754987|ref|YP_844105.1|  59 VAMMCDLLDLREGMKVLEVGGGCGYHAAVMAELVGPSGHVYSVERIPELVEMARRNLERARY 120
                                    7899999***************************************9999999999887765 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   2.5e-08   2.7e-05      64     129 ..      64     131 ..      55     184 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 2.5e-08
                                    S--S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHHHHHH.HHHTTS.TTEEEEES-TT CS
                    Fibrillarin  64 kelpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvlreli.evakkR.knivPileDAr 129
                                    + l +++g kvL +G + G  ++ ++++vg++g vy+ve  p  +     ++ + R +n+  il+D +
  gi|116754987|ref|YP_844105.1|  64 DLLDLREGMKVLEVGGGCGYHAAVMAELVGPSGHVYSVERIPELVEMARrNLERARyRNVSMILGDGT 131
                                    556799*********************************99976533322333333358888888876 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   3.9e-08   4.1e-05       4     108 ..      23     130 ..      20     139 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 3.9e-08
                                    S--..--HHHHHHHHHTTTST.TGGGS-.-HHHHHHHHH...HHHHHT--EEEEE--TTSHHHHHHHTTS-TT-EEEEEE CS
                 Methyltransf_3   4 saeprehellkeLreatakktdlsemev.svdegqfLsl...LvklvnakrvleiGvftGyslLatalalPeDGkilaid 79 
                                    s  pre ++ +eLr ++++   l+  +  +    +++ +   L++l +  +vle+G   Gy +  +a  + + G++ +++
  gi|116754987|ref|YP_844105.1|  23 SRVPRELFVPEELRPMAYEDRPLPIGHGqTISAPHMVAMmcdLLDLREGMKVLEVGGGCGYHAAVMAELVGPSGHVYSVE 102
                                    56677777777777777776654432210112223333312278889999****************************** PP

                                    S-HHHHHHHHHHHHHTT-GGGEEEEES-H CS
                 Methyltransf_3  80 idreayeialkfiqkagvaekieliegda 108
                                      +e +e+a++ +++a +   +++i gd+
  gi|116754987|ref|YP_844105.1| 103 RIPELVEMARRNLERARYR-NVSMILGDG 130
                                    ****************875.578888876 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   3.1e-06    0.0032       1      59 [.      75     136 ..      75     168 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.1e-06
                                    EEET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-T CS
                Methyltransf_11   1 LdvGcGtGrlaealakrg...arvvgvDlskemlklakekaseegl.kvefvvadaeklpfed 59 
                                    L+vG G G++a+ +a+ +   ++v+ v+  +e++++a+++ ++++  +v+++ +d + l + +
  gi|116754987|ref|YP_844105.1|  75 LEVGGGCGYHAAVMAELVgpsGHVYSVERIPELVEMARRNLERARYrNVSMILGDGT-LGYSE 136
                                    89*************887899**********************99999999999988.55554 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.9e-06     0.002      21      85 ..      61     130 ..      52     151 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.9e-06
                                    HHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-...SEEEEE-S-HHHHHHHHCHTT..TCCCEEEE-S-C CS
                         RrnaAD  21 eIldklnleekltvleigpGkGilTeeLakra...kqvvvlElderLakllqkkls..kdeklkvvhqDf 85 
                                       d l+l+e ++vle+g G G   + +a+ +    +v ++E  ++L+++ + +l+   ++++ ++  D+
  gi|116754987|ref|YP_844105.1|  61 MMCDLLDLREGMKVLEVGGGCGYHAAVMAELVgpsGHVYSVERIPELVEMARRNLEraRYRNVSMILGDG 130
                                    5667899************************99988999****************999999999998885 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   6.7e-06    0.0071      51      83 ..      59      91 ..      54     146 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 6.7e-06
                                   HHHHHTTTT--TT-EEEEES-TTSHHHHHHHHH CS
                           CMAS 51 ldlileklelkpGmtlLdiGcGWGslvrraver 83
                                   + ++++ l+l++Gm++L++G G G+ +  ++e 
  gi|116754987|ref|YP_844105.1| 59 VAMMCDLLDLREGMKVLEVGGGCGYHAAVMAEL 91
                                   5689*******************9998888876 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 !   15.7   0.0   8.6e-06     0.009       3      85 ..      65     145 ..      63     150 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 8.6e-06
                                    HH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC..EEE CS
                Methyltr_RsmB-F   3 lLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfDr 82 
                                    lL+++e+ ++l++  + G   + +ael+ ++g+v+ v++  e ++   +nl+r   +n+ ++ +D++    ++ ++ +Dr
  gi|116754987|ref|YP_844105.1|  65 LLDLREGMKVLEVGGGCGYHAAVMAELVGPSGHVYSVERIPELVEMARRNLERARYRNVSMILGDGTLG--YSEQAPYDR 142
                                    69999************************************************************9876..444455888 PP

                                    EEE CS
                Methyltr_RsmB-F  83 iLl 85 
                                    i +
  gi|116754987|ref|YP_844105.1| 143 ISV 145
                                    865 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   8.8e-06    0.0093      23      94 ..      62     135 ..      58     168 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.8e-06
                                    HHHHCHCCTCSEEEEET-TTSHHHHHHHHHT.TC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTST CS
                            MTS  23 LletlpkelsgkvlDlGcGaGvlgaalakes.peaevtlvdvdarAlesakenleankle.vevvasdvleeve 94 
                                    + + l+ ++  kvl +G G G+ +a++a+   p+ +v  v+   + +e+a++nle+ + + v+++  d++   +
  gi|116754987|ref|YP_844105.1|  62 MCDLLDLREGMKVLEVGGGCGYHAAVMAELVgPSGHVYSVERIPELVEMARRNLERARYRnVSMILGDGTLGYS 135
                                    667778888899*************99997527888********************999989988888776555 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.7e-05     0.018      20      62 ..      68     131 ..      57     190 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.7e-05
                Methyltransf_23  20 lraggrvLdiGcGtGillevlren.gf..svtgvDlspeaveiae..................k 62 
                                    lr+g++vL++G G G+ + v++e  g   +v+ v+  pe+ve+a+                  +
  gi|116754987|ref|YP_844105.1|  68 LREGMKVLEVGGGCGYHAAVMAELvGPsgHVYSVERIPELVEMARrnleraryrnvsmilgdgT 131
                                    7899***************99665377899*************987666555555444444441 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   2.4e-05     0.025      45      93 ..      69     119 ..      56     140 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.4e-05
                Methyltransf_16  45 lsklsvlELGsGtGlvGlavaell.peakvi.ltDleellellkknielnk 93 
                                    +++++vlE+G G+G    ++ael+ p+ +v+ +  ++el+e+ ++n+e ++
  gi|116754987|ref|YP_844105.1|  69 REGMKVLEVGGGCGYHAAVMAELVgPSGHVYsVERIPELVEMARRNLERAR 119
                                    57899******************889999974677899********99866 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.4e-05     0.046       4      60 ..      73     130 ..      70     145 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.4e-05
                                    EEEEET-TTSHHHHHHHHH.STTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-C CS
                 Methyltransf_4   4 vvleiGcGkGeflvalAkk.nPdknflGiEirvkvvakvlkkiealelkNlrilrgda 60 
                                     vle+G G G +   +A+   P+  +  +E   ++v+ + ++ e+ +++N+ ++ gd 
  gi|116754987|ref|YP_844105.1|  73 KVLEVGGGCGYHAAVMAELvGPSGHVYSVERIPELVEMARRNLERARYRNVSMILGDG 130
                                    689**************9637*********************************9997 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00012      0.13      57     119 ..      65     129 ..      50     136 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
                                    SS-GGG-SEEEEET-TTSHHHHHHHHH-.TT-EE.EEEE-HHHHHHHHHHS-----TTEEEEES- CS
                 Methyltransf_2  57 afdleglkslvDvGGGtGalakaivsay.Ptikv.ivfDlpeVveaAkehlsageeervefvgGd 119
                                      dl++  ++++vGGG G  a+ ++++  P+ +v +v  +pe ve A++ l+ +  ++v+++ Gd
  gi|116754987|ref|YP_844105.1|  65 LLDLREGMKVLEVGGGCGYHAAVMAELVgPSGHVySVERIPELVEMARRNLERARYRNVSMILGD 129
                                    55677777899*******9998887765476665145569*******************999998 PP

>> DUF938  Protein of unknown function (DUF938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00018      0.19      26      50 ..      71      95 ..      55     127 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00018
                         DUF938 26 tervLEiasGtGqHAvffApalpnl 50
                                   + +vLE++ G G HA+ +A+++ + 
  gi|116754987|ref|YP_844105.1| 71 GMKVLEVGGGCGYHAAVMAELVGPS 95
                                   348****************987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 1411.05
//
Query:       gi|116754988|ref|YP_844106.1|  [L=317]
Description: hypothetical protein Mthe_1700 [Methanosaeta thermophila PT]
Scores for 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-11   41.9   2.8      1e-10   41.7   1.0    2.1  2  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
  ------ inclusion threshold ------
       0.12   12.5   0.0       0.18   11.9   0.0    1.3  1  DUF2012          Protein of unknown function (DUF2012)


Domain annotation for each model (and alignments):
>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.54   4.9e+03      38      72 ..     148     184 ..     145     189 .. 0.71
   2 !   41.7   1.0   1.1e-14     1e-10       1      61 [.     191     249 ..     191     279 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.54
                CarboxypepD_reg  38 Gafrlrglpp...gtysvtvsapGyatatreevtltag 72 
                                    G +r++g ++   +++  +++  G  t +++ v +++g
  gi|116754988|ref|YP_844106.1| 148 GWYRITGAQAdllTNHLYVMRVGGLLTNNVS-VLVDPG 184
                                    6788888877777777777777777777764.666666 PP

  == domain 2  score: 41.7 bits;  conditional E-value: 1.1e-14
                CarboxypepD_reg   1 tisGrVtdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyat 61 
                                    ++ GrV+d++ga+i+ a+V+++ +++g + + ttd  G++ ++ lp g y +t+ apGy  
  gi|116754988|ref|YP_844106.1| 191 SLVGRVVDQNGAGIPWARVVIS-SGEGGSFTITTDMLGYYGMD-LPSGYYVITAVAPGYTF 249
                                    589*******************.6999**************97.***************64 PP

>> DUF2012  Protein of unknown function (DUF2012)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.1e-05      0.18      12      67 ..     209     263 ..     199     307 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.1e-05
                        DUF2012  12 vlLdsgqqrkfkalvrrDGsFifrdlpegsYlLevespeyvFepyrVdvkdkgkak 67 
                                    v+++sg+  +f+  + + G +   dlp+g Y++ +++p+y+F ++  +v     + 
  gi|116754988|ref|YP_844106.1| 209 VVISSGEGGSFTITTDMLGYYG-MDLPSGYYVITAVAPGYTFTQVMAKVWLGTVSA 263
                                    5555555555555555555554.49*******************998887444334 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2247.86
//
Query:       gi|116754989|ref|YP_844107.1|  [L=449]
Description: hypothetical protein Mthe_1701 [Methanosaeta thermophila PT]
Scores for complete sequence (score 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   15.0   0.1        0.2   11.8   0.0    2.2  2  bPH_5     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 ?   11.8   0.0   1.1e-05       0.2      36      79 ..     189     234 ..     183     251 .. 0.86
   2 ?    0.4   0.0     0.039   7.1e+02      37      76 ..     377     418 ..     373     421 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.1e-05
                          bPH_5  36 ikgvrlfgtskpgyalGrfk..ikdigkarmyatrlkrvlllktkd 79 
                                     ++vr +g s+pgy+ G+f+  +++  ++  y   +++ ++++   
  gi|116754989|ref|YP_844107.1| 189 APKVRWWGWSWPGYKRGWFYgdAPGWHIISYYCNGWSNYIYIYVWP 234
                                    5789***************988889999**************9755 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.039
                          bPH_5  37 kgvrlfgtskpgyalGrfkikdig..karmyatrlkrvlllk 76 
                                    ++v+ fg++  g    +f+ +++g  ++  ++t++++ ++++
  gi|116754989|ref|YP_844107.1| 377 PSVKGFGYKTTGWFPTWFYGEKVGwhILAYCTTDWSNYIYIY 418
                                    5677788888887778888887775345566677******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 3539.05
//
Query:       gi|116754990|ref|YP_844108.1|  [L=321]
Description: putative rRNA pseudouridine synthase [Methanosaeta thermophila PT]
Scores for complete 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   91.5   0.7    5.4e-16   59.3   0.1    3.2  2  TruB_N    TruB family pseudouridylate synthase (N terminal do
    1.7e-24   85.7   0.1    2.8e-24   85.0   0.1    1.4  1  TruB_C_2  tRNA pseudouridylate synthase B C-terminal domain
    7.4e-20   70.7   0.2    1.3e-19   69.9   0.2    1.4  1  PUA       PUA domain
    4.8e-17   61.8   0.0    2.5e-16   59.5   0.0    2.1  2  DKCLD     DKCLD (NUC011) domain
  ------ inclusion threshold ------
       0.15   12.3   0.0       0.47   10.8   0.0    1.9  2  UPF0113   UPF0113 PUA 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 !   59.3   0.1   1.5e-19   5.4e-16       1      53 [.      47      99 ..      47     102 .. 0.96
   2 !   27.7   0.1   8.3e-10     3e-06      69     149 .]      97     160 ..      94     160 .. 0.95

  Alignments for each domain:
  == domain 1  score: 59.3 bits;  conditional E-value: 1.5e-19
                                   HHHTT-S-EEESS---TT-EEEEEEEEGGGGGGHHHCTTS-EEEEEEEEETEE CS
                         TruB_N  1 krllkakkvGhtGtLDplatGvLvvavgeaTklleylleadKeYeatirlgae 53
                                   kr+l+ +k+Gh+GtLDp +tG+L+v++g+aT+++e+ll+a KeY++ +r +++
  gi|116754990|ref|YP_844108.1| 47 KRILGLEKAGHSGTLDPRVTGILPVLTGDATRVVEFLLTAGKEYVCLMRTHEQ 99
                                   89*********************************************998876 PP

  == domain 2  score: 27.7 bits;  conditional E-value: 8.3e-10
                                    -TT--HHHHHHHHHHC-EEE---------------------------------EEEEEEEEEEEEEEEEEEEEEESTTTT CS
                         TruB_N  69 veklteekleevlkkftGeieqvppmySAvkvnGkrlyelaregeeverkkrkvtiyelelleveepevelevecskGtY 148
                                     e++ ++k+ ev+++f Gei+q+pp  S+v                  r+ r+ +iy +++le+e ++v ++v c++GtY
  gi|116754990|ref|YP_844108.1|  97 HEQVPRKKILEVCEEFSGEIYQRPPLKSSVA-----------------RNLRTRKIYYIDVLEIEGQRVLMKVGCEAGTY 159
                                    5678899**********************99.................999***************************** PP

                                    H CS
                         TruB_N 149 i 149
                                    i
  gi|116754990|ref|YP_844108.1| 160 I 160
                                    9 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 !   85.0   0.1   7.9e-28   2.8e-24       1      63 [.     161     227 ..     161     228 .. 0.97

  Alignments for each domain:
  == domain 1  score: 85.0 bits;  conditional E-value: 7.9e-28
                                    HHHHHHHHHHTTS-EEEEEEEEEEETTE.GG-..B-HHHHHHHHHHHHT..--H.HHHHEEEGGGGG CS
                       TruB_C_2   1 RtLcdDiGeaLgcgAhveeLRRtrvgpf.deedmvtledLedavllyke..dee.LdrlllPlesal 63 
                                    R+Lc D+G+aLgcgA +eeLRRt++gpf ++e +vtl+ L+da+++++e  de+ L+r +lP+e+al
  gi|116754990|ref|YP_844108.1| 161 RKLCYDMGLALGCGANMEELRRTKAGPFaEDETLVTLHNLKDAYEIWREsgDESaLRRAVLPVERAL 227
                                    9****************************99999***************998889**********98 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.9   0.2   3.7e-23   1.3e-19       3      74 .]     233     304 ..     231     304 .. 0.97

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 3.7e-23
                                    EEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEEEE CS
                            PUA   3 vvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveiervl 74 
                                    +v+ d+Av+a+++ga L apG+++ e d+ +gd V+i++ +ge+va+G+a++ss+e++ +k g+++ +erv+
  gi|116754990|ref|YP_844108.1| 233 LVISDNAVDAICHGAPLAAPGLLSLETDINKGDFVVIYTLKGEAVAIGRAKLSSDEMMVAKSGIVASTERVI 304
                                    79****************************************************************999985 PP

>> DKCLD  DKCLD (NUC011) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.5   0.0     7e-20   2.5e-16      17      58 .]       2      43 ..       1      43 [. 0.96
   2 ?   -0.8   0.0      0.46   1.6e+03       7      36 ..     199     228 ..     196     230 .. 0.87

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 7e-20
                                   SS-----TTSS--GGG--HHHHHHTEEEEEEE-SSS-HHHHH CS
                          DKCLD 17 rtehytplpaGssPlkRpieeyikyGvinLDKPsnPsSHEVV 58
                                   r+e  t+ ++G+ P +Rp++e+++ G inLDKPs+P+SHEVV
  gi|116754990|ref|YP_844108.1|  2 RREGSTNSSYGCFPDRRPLQEHLRLGAINLDKPSGPTSHEVV 43
                                   78899************************************9 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.46
                                    ...XXX-EEESS-----TTSS--GGG--HH CS
                          DKCLD   7 lLknydkllvrtehytplpaGssPlkRpie 36 
                                     Lk+  +++  ++ +  l+  + P++R ++
  gi|116754990|ref|YP_844108.1| 199 NLKDAYEIWRESGDESALRRAVLPVERALR 228
                                    58999999999999999999999****987 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.3   4.6e+03      60      76 .]     146     162 ..     138     162 .. 0.76
   2 ?   10.8   0.0   0.00013      0.47      23      64 ..     254     298 ..     233     313 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.3
                        UPF0113  60 gkivvknlaDiGeYlRr 76 
                                    +++++k  +  G+Y+R+
  gi|116754990|ref|YP_844108.1| 146 QRVLMKVGCEAGTYIRK 162
                                    56666777889****96 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00013
                        UPF0113  23 ilkitesvkenqvvvVlnengeplGiGkirkdt..k.aspgkivv 64 
                                    +l+++ +++++++vv++  +ge+++iG+++ ++      +++iv+
  gi|116754990|ref|YP_844108.1| 254 LLSLETDINKGDFVVIYTLKGEAVAIGRAKLSSdeMmVAKSGIVA 298
                                    6788899**********************8877653344444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2422.19
//
Query:       gi|116754991|ref|YP_844109.1|  [L=172]
Description: cytidylate kinase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-23   84.4   0.1    6.3e-13   49.3   0.3    2.0  2  Cytidylate_kin2  Cytidylate kinase-like family
    3.5e-14   53.1   0.6    2.9e-06   27.2   0.0    2.1  2  Cytidylate_kin   Cytidylate kinase
    1.6e-12   48.1   0.0    2.2e-12   47.7   0.0    1.2  1  AAA_18           AAA domain
    1.3e-08   35.4   0.1    2.7e-08   34.3   0.0    1.6  1  AAA_17           AAA domain
      3e-06   27.5   0.2     0.0013   18.9   0.0    2.1  2  AAA_33           AAA domain
    0.00011   22.5   0.1    0.00039   20.7   0.0    1.9  2  AAA_28           AAA domain
    0.00025   21.2   0.1     0.0034   17.5   0.0    2.0  2  ADK              Adenylate kinase
     0.0033   17.5   0.4      0.019   15.1   0.4    1.8  1  SKI              Shikimate kinase
  ------ inclusion threshold ------
      0.013   15.3   0.0      0.046   13.5   0.0    1.8  2  PRK              Phosphoribulokinase / Uridine kinase family
      0.043   13.7   0.1        1.8    8.4   0.0    2.2  2  dNK              Deoxynucleoside kinase
      0.065   13.1   0.1        0.2   11.5   0.1    1.9  1  CPT              Chloramphenicol phosphotransferase-like prot
      0.065   12.9   0.1       0.83    9.3   0.0    2.0  2  CoaE             Dephospho-CoA kinase
       0.11   12.9   0.0        0.2   12.1   0.0    1.6  1  AAA              ATPase family associated with various cellul


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 !   33.8   0.0   2.4e-11   3.4e-08       1      55 [.       2      58 ..       2      68 .. 0.89
   2 !   49.3   0.3   4.5e-16   6.3e-13      87     178 ..      65     153 ..      58     154 .. 0.95

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 2.4e-11
                Cytidylate_kin2  1 iITIsreyGsgGetigeaLAekLglpfydr.eiieevakelglseeeveevde.rsr 55
                                   iITIs+  Gsg +t+++ L+e Lg++ ++  ++++++a e gls +e+ ++ e  + 
  gi|116754991|ref|YP_844109.1|  2 IITISGPPGSGTSTLARGLSEVLGVRWVNSgDLFRRIAAERGLSLKELGRLAEqGPE 58
                                   8*****************************9*****************776663554 PP

  == domain 2  score: 49.3 bits;  conditional E-value: 4.5e-16
                Cytidylate_kin2  87 rvirelaaeesvVivGRgadliLkdrpnvlrvfltapledrvkrvaereglseeearekiketDkrrakyykkytgqdwg 166
                                    ++ r+la++ s+++ GR a ++L      l++ l  +l +r+ r+a+re+ s eea ++ +++++ +a +yk y++ d++
  gi|116754991|ref|YP_844109.1|  65 DAQRSLAKSGSGIFEGRLAGHMLDA---DLKIMLKTSLSVRASRIAKRENKSIEEALSEARAREECEARRYKMYYNIDIN 141
                                    567899*999*************99...8*************************************************** PP

                Cytidylate_kin2 167 daenYdlvlnts 178
                                    d + Ydl+++t 
  gi|116754991|ref|YP_844109.1| 142 DLSIYDLIIDTG 153
                                    **********96 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.0   2.1e-09   2.9e-06       1      37 [.       3      39 ..       3      49 .. 0.95
   2 !   24.7   0.2   1.2e-08   1.6e-05      96     177 ..      57     131 ..      46     152 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 2.1e-09
                                   EEEE-STTSSHHHHHHHHHHHHT-EEEEHHHHHHHHH CS
                 Cytidylate_kin  1 iaiDGPagsGKssvaralaeklglkyldtgalYRala 37
                                   i+i GP gsG s++ar l+e lg++++++g l+R +a
  gi|116754991|ref|YP_844109.1|  3 ITISGPPGSGTSTLARGLSEVLGVRWVNSGDLFRRIA 39
                                   89********************************998 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 1.2e-08
                                    HHHHHHHHHHHHTT-BSSBEEEEESSIIIIISTT-SEEEEEE--HHHHHHHHHHHHHHTT----HHHHHHHHHHHHHHHH CS
                 Cytidylate_kin  96 pavRailvkklrelvkkarvvveGRDigtvvfpdaelKifldAsveeRakRRlkqlkakgtsvsleellaeikeRDklDk 175
                                    p++   + + +r+l+k+++ ++eGR  g   + da+lKi l+ s  +Ra+R +k  ++    +s+ee l e ++R +   
  gi|116754991|ref|YP_844109.1|  57 PEIDYLIDDAQRSLAKSGSGIFEGRLAGH--MLDADLKIMLKTSLSVRASRIAKR-EN----KSIEEALSEARAREECEA 129
                                    5666678899***************8887..46*****************98877.33....456677777777777665 PP

                                    CT CS
                 Cytidylate_kin 176 er 177
                                    +r
  gi|116754991|ref|YP_844109.1| 130 RR 131
                                    55 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7   0.0   1.6e-15   2.2e-12       1     122 [.       3     123 ..       3     133 .. 0.82

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 1.6e-15
                         AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegk 75 
                                    I ++G+pG+G +tla+ Ls+ lg+     g+  r +a+e+gl+l +    l e+  + +   d +++ l ++       +
  gi|116754991|ref|YP_844109.1|   3 ITISGPPGSGTSTLARGLSEVLGVrwvnsGDLFRRIAAERGLSLKELGR-LAEQGPEIDYLIDDAQRSLAKS-------G 74 
                                    89*******************999*************************.5555555555555556666554.......5 PP

                         AAA_18  76 nlvidghlaeleseaakdikkvvLtaspeelleRlekRgyeeakik.....e 122
                                    + +++g+la +  +a+ +   + L++s ++++ R++kR++++ + +      
  gi|116754991|ref|YP_844109.1|  75 SGIFEGRLAGHMLDADLK---IMLKTSLSVRASRIAKRENKSIEEAlsearA 123
                                    55********99998876...99****************9988866665543 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.0   1.9e-11   2.7e-08       2      78 ..       7      80 ..       6     125 .. 0.79

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 1.9e-11
                                   E-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTS.HSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE CS
                         AAA_17  2 GgPGsGKgtqceklvekygfthlsaGdllreeakrggl.akardemrklpleekkelqkeaaekiaeeakkkgvlvdg 78
                                   G+PGsG +t+++ l e +g+  ++ Gdl+r  a+++gl  k+ +++++   e++  l + a++++a+   ++  +++g
  gi|116754991|ref|YP_844109.1|  7 GPPGSGTSTLARGLSEVLGVRWVNSGDLFRRIAAERGLsLKELGRLAEQGPEIDY-LIDDAQRSLAK---SGSGIFEG 80
                                   9************************************955566666666555554.66677777765...34444444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   9.3e-07    0.0013       2      55 ..       3      59 ..       2      79 .. 0.77
   2 !    6.7   0.2    0.0056       7.7     102     131 ..      93     122 ..      81     133 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 9.3e-07
                         AAA_33  2 vllvGlpGsGKstlaerllkklgavllssdtlrrrlfgtdqqsktdytrvldr...l 55
                                   + + G+pGsG stla++l + lg+  ++s +l+rr++++   s++++ r++++   +
  gi|116754991|ref|YP_844109.1|  3 ITISGPPGSGTSTLARGLSEVLGVRWVNSGDLFRRIAAERGLSLKELGRLAEQgpeI 59
                                   5678**********************************9888888777766554434 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0056
                         AAA_33 102 vvvetdeetlkeRlakRaangddrsevpee 131
                                    + ++t+ ++ ++R+akR++++ +++  + +
  gi|116754991|ref|YP_844109.1|  93 IMLKTSLSVRASRIAKRENKSIEEALSEAR 122
                                    7899***************86443333333 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   2.8e-07   0.00039       2      43 ..       3      47 ..       2      78 .. 0.78
   2 ?   -0.4   0.0      0.88   1.2e+03     101     109 ..     124     132 ..      96     158 .. 0.57

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.8e-07
                         AAA_28  2 ivitGgestGKTtlleaLaar.gypvv..pEaareileeklakge 43
                                   i i+G++++G++tl++ L++  g+++v   + +r+i  e++ + +
  gi|116754991|ref|YP_844109.1|  3 ITISGPPGSGTSTLARGLSEVlGVRWVnsGDLFRRIAAERGLSLK 47
                                   78******************88*****999999999998874444 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.88
                         AAA_28 101 eaaarekry 109
                                     ++++++ry
  gi|116754991|ref|YP_844109.1| 124 REECEARRY 132
                                    122223333 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   2.5e-06    0.0034       1      38 [.       5      42 ..       5      60 .. 0.83
   2 ?    2.3   0.0      0.12   1.6e+02      72     135 ..      56     121 ..      46     146 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.5e-06
                                   EEESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHHCT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            ADK  1 llGaPgaGKGtqaeklvkkyglahlstGdllRaevksg 38
                                   + G+Pg+G  t a+ l + +g+  + +Gdl+R   ++ 
  gi|116754991|ref|YP_844109.1|  5 ISGPPGSGTSTLARGLSEVLGVRWVNSGDLFRRIAAER 42
                                   57******************************876544 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.12
                                    GTTTEEEEESB-SSHHHHHH..HHHHHHHHTSEESEEEEEE--HHHHHHHHHTGSHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            ADK  72 dkkkgfllDGfPRtveqaea..leelleeekvkldlvleldvpeevlveRltgDneetvkkRlety 135
                                      + ++l+D   R+++++ +  +e  l+ +  + dl + l+ + +v  +R+++ +++++++ l++ 
  gi|116754991|ref|YP_844109.1|  56 GPEIDYLIDDAQRSLAKSGSgiFEGRLAGHMLDADLKIMLKTSLSVRASRIAKRENKSIEEALSEA 121
                                    556678888888888776433388889999999999999999999999999997777776666554 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.4   1.4e-05     0.019       1     135 [.       9     139 ..       9     144 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.4e-05
                                    TTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHTS-HHHHHHHHHHHHHHHHHHHHHHHHCCCSSEEEEE-TTGGGSHHHHH CS
                            SKI   1 mGaGKstvGkllAkklglefiDlDeliekrtgksiaeifeeegeegFrelEsevlkelleeeglViatGGGavlseenre 80 
                                    +G+G st+++ l++ lg++++ + +l+ + +  +    ++e g  + +  E + l + +++  +    G G+++ + + +
  gi|116754991|ref|YP_844109.1|   9 PGSGTSTLARGLSEVLGVRWVNSGDLFRRIAA-ERGLSLKELGRLAEQGPEIDYLIDDAQR--SLAKSGSGIFEGRLAGH 85 
                                    69*********************999987776.7777888888888888888887776666..77888888888777777 PP

                                    HHHHHSEEEEEE--HHHHHHHHHHTTSSGGGCSCHHHHHHHHHHHHHHHHHCCSS CS
                            SKI  81 llkekgiviyLdvsleellerlkadkeRPllqekskeeelleelaereplyeeaa 135
                                    +l    + i L++sl + ++r+++++++ + ++ s++++++e +a+r ++y +++
  gi|116754991|ref|YP_844109.1|  86 MLD-ADLKIMLKTSLSVRASRIAKRENKSIEEALSEARAREECEARRYKMYYNID 139
                                    777.***********************8888888886666666669999999876 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.3e-05     0.046       1      30 [.       2      31 ..       2      55 .. 0.88
   2 ?   -0.7   0.0      0.71   9.8e+02     130     151 ..      89     110 ..      76     137 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.3e-05
                            PRK  1 vIgvagsSGaGkttvarklekifgrekvka 30
                                   +I ++g+ G+G++t+ar l +++g  +v++
  gi|116754991|ref|YP_844109.1|  2 IITISGPPGSGTSTLARGLSEVLGVRWVNS 31
                                   8***********************999984 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.71
                            PRK 130 ldlkiyvdisidlelarklqRD 151
                                    +dlki + +s  ++ +r  +R 
  gi|116754991|ref|YP_844109.1|  89 ADLKIMLKTSLSVRASRIAKRE 110
                                    5888888888888776655554 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0013       1.8       1      27 [.       3      29 ..       3      43 .. 0.91
   2 ?    3.3   0.1     0.046        63     122     147 ..      88     113 ..      77     146 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0013
                                   EEEEESTTSSHHHHHHHHHCCSTCEEE CS
                            dNK  1 ivveGnIgaGKstlvklLskklgvkvf 27
                                   i+++G+ g+G stl+  Ls+ lgv  +
  gi|116754991|ref|YP_844109.1|  3 ITISGPPGSGTSTLARGLSEVLGVRWV 29
                                   89********************98766 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.046
                                    H-SEEEEEE--HHHHHHHHHHCTTCC CS
                            dNK 122 kpdlliYLkasletclerikkRgree 147
                                      dl i Lk+sl +   ri kR+++ 
  gi|116754991|ref|YP_844109.1|  88 DADLKIMLKTSLSVRASRIAKRENKS 113
                                    47999*****************9875 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00014       0.2       2      76 ..       1      70 [.       1     160 [. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00014
                                   -EEEEEE-TTSSHHHHHHHHHHHSSS-EEEEEHHHHHHHS-GGGGTSTTSEEEETTSEEE-HHHHHHHHHHHHHH CS
                            CPT  2 riilLnGgsssGKsslaralqevldepwlhlgvDafvealppkrqdeadglefeteleeigpeldlllaalyeav 76
                                   +ii + G + sG s+lar l evl   w++ g D f   + ++r  + ++l   + l e gpe+d l++  ++++
  gi|116754991|ref|YP_844109.1|  1 MIITISGPPGSGTSTLARGLSEVLGVRWVNSG-DLFRR-IAAERGLSLKEL---GRLAEQGPEIDYLIDDAQRSL 70
                                   58999***********************9976.77755.888888887777...344444555555555444443 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0    0.0006      0.83       1      48 [.       1      49 [.       1      67 [. 0.87
   2 ?    1.8   0.1      0.12   1.7e+02     126     165 ..      93     132 ..      77     145 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0006
                                   EEEEEEESTTSSHHHHHHHHHH.TT-EEEEHHHHHHHTTCCTHHHHHHH CS
                           CoaE  1 livgltGgiasGKstvanlfad.lgvpivDaDlvArqvvepgsealkki 48
                                   +i+ ++G  +sG st+a+ +++ lgv  v    + r++ ++    lk++
  gi|116754991|ref|YP_844109.1|  1 MIITISGPPGSGTSTLARGLSEvLGVRWVNSGDLFRRIAAERGLSLKEL 49
                                   699*******************9******99888888888777777766 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.12
                                    EEEE--HHHHHHHHHHCCTSTHHHHHHHHHHS--HHHHHH CS
                           CoaE 126 lvvdvelelqveRlvardgvseeevkaiiaaQlseeerla 165
                                    ++++ +l+ + +R+ +r++ s ee+ +  +a  + e r+ 
  gi|116754991|ref|YP_844109.1|  93 IMLKTSLSVRASRIAKRENKSIEEALSEARAREECEARRY 132
                                    455667778889********99999998888877777765 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 ?   12.1   0.0   0.00015       0.2       2      53 ..       4      53 ..       3     129 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00015
                                   EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHH CS
                            AAA  2 llyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkea 53
                                    ++GppG G ++la+ + + lgv+ +  +  +l+  +  e+  +++el + a
  gi|116754991|ref|YP_844109.1|  4 TISGPPGSGTSTLARGLSEVLGVRWV--NSGDLFRRIAAERGLSLKELGRLA 53
                                   579*****************998754..445555555555555555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 1285.45
//
Query:       gi|116754992|ref|YP_844110.1|  [L=201]
Description: hypothetical protein Mthe_1704 [Methanosaeta thermophila PT]
Scores for 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-46  158.8   4.8    1.2e-46  158.5   4.8    1.1  1  EMC3_TMCO1    Integral membrane protein EMC3/TMCO1-like
  ------ inclusion threshold ------
      0.091   11.8   0.0      0.098   11.7   0.0    1.1  1  DUF2048       Abhydrolase domain containing 18
       0.13   11.4   3.1       0.18   11.0   3.1    1.2  1  Bac_export_2  FlhB HrpN YscU SpaS Family
       0.18   11.7   0.0       0.36   10.7   0.0    1.5  1  HPIH          N-terminal domain with HPIH motif


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 !  158.5   4.8   2.8e-50   1.2e-46       3     169 ..      41     198 ..      39     199 .. 0.96

  Alignments for each domain:
  == domain 1  score: 158.5 bits;  conditional E-value: 2.8e-50
                     EMC3_TMCO1   3 vldplirdwvllPivivillvgiltgllsellqkllidkkkmekeqkrekelqkrarelqkngdklklkklekrqeelme 82 
                                    v++ l +   +lP+++v+++++++tgl+++l+qk+++d++ +++ q+r++e+q + r++q  gd+ + ++l+++q e+m+
  gi|116754992|ref|YP_844110.1|  41 VIGWLPE---ILPFHMVLFVLAAITGLYASLIQKYTMDWDFLREQQMRMREFQAELRAAQLAGDQARVQHLQNKQLEMMG 117
                                    6666666...89******************************************************************** PP

                     EMC3_TMCO1  83 dqsemmmdqmkpmivtmipqiliffwlnsffsgfvvaklpfpltgrfksllqrglesldvrfvssiswYflcsfglsqii 162
                                    dq +mm++q+kpm++++i+++++f+w + +++++ + +++fp++g+ + +     + +++++ ++++wYf+cs+ +sqii
  gi|116754992|ref|YP_844110.1| 118 DQGKMMKMQLKPMAYIGIVSVPLFMWAYLYIDQHSI-TMVFPFWGEQN-IK----HIVWGPILYWFYWYFVCSIPISQII 191
                                    ***********************************9.9**********.88....9************************ PP

                     EMC3_TMCO1 163 rklLgea 169
                                    rk+L+++
  gi|116754992|ref|YP_844110.1| 192 RKALDIG 198
                                    ****986 PP

>> DUF2048  Abhydrolase domain containing 18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.2e-05     0.098     215     290 ..      64     139 ..      35     171 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.2e-05
                        DUF2048 215 vfteGvlsksiawdvLekq.ledgnyrerlstasdaaaeekaakldeakerkaekealrfmrllmdelthlknfsvp 290
                                     ++  + ++++ wd+L++q +   +++ +l  a+ +a ++ + +  ++k+ ++  ++ ++m+++++ +  +   svp
  gi|116754992|ref|YP_844110.1|  64 LYASLIQKYTMDWDFLREQqMRMREFQAELRAAQ-LAGDQARVQHLQNKQLEMMGDQGKMMKMQLKPMAYIGIVSVP 139
                                    46666778899*******9899999999987655.555566666666777788899999999998888777777777 PP

>> Bac_export_2  FlhB HrpN YscU SpaS Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   3.1     4e-05      0.18     132     241 ..      11     124 ..       2     133 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4e-05
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                   Bac_export_2 132 sllkvvlvgavaylvlkseleellalaeldleaalelllslllkllllvllallviallDlllqrwefekklkMtkqEvK 211
                                    +++  v  ++++ +++++e++  +++a   +  +l  +l + + l++l+++  l  +l+      w+f ++  M  +E +
  gi|116754992|ref|YP_844110.1|  11 TVALSVGAALTIGIMVSHEFRVAIGMAMELVIGWLPEILPFHMVLFVLAAITGLYASLIQKYTMDWDFLREQQMRMREFQ 90 
                                    455555556666677777888888888777889999999999************************************** PP

                                    XXXXXXX..X-HHHHHHHHHHHHHHH..HHHHHH CS
                   Bac_export_2 212 dEyKesE..GdpeiKsrirqlqrela..rrrmma 241
                                     E + ++  Gd+   ++++++q e++  + +mm+
  gi|116754992|ref|YP_844110.1|  91 AELRAAQlaGDQARVQHLQNKQLEMMgdQGKMMK 124
                                    ***9664449999999999999999865666765 PP

>> HPIH  N-terminal domain with HPIH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0     8e-05      0.36      17      55 ..      50      88 ..      48     111 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 8e-05
                           HPIH 17 PIhtIvvvallasttYlsvleeslfdwkldsksissagk 55
                                   P h++++v+   +  Y s+++++  dw   ++++   ++
  gi|116754992|ref|YP_844110.1| 50 PFHMVLFVLAAITGLYASLIQKYTMDWDFLREQQMRMRE 88
                                   899999999999999************988887776554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1000  (0.0557756); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); 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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1481.52
//
Query:       gi|116754993|ref|YP_844111.1|  [L=537]
Description: preprotein translocase subunit SecY [Methanosaeta thermophila PT]
Scores for 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-65  221.1  21.7    2.4e-65  220.8  21.7    1.1  1  SecY             SecY translocase
    5.5e-12   45.3   1.8    1.4e-11   44.0   1.8    1.8  1  Plug_translocon  Plug domain of Sec61p
  ------ inclusion threshold ------
        5.4    7.0  10.3        4.1    7.4   0.1    2.9  3  Ninjurin         Ninjurin


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 !  220.8  21.7     4e-69   2.4e-65       1     306 []      75     514 ..      75     514 .. 0.87

  Alignments for each domain:
  == domain 1  score: 220.8 bits;  conditional E-value: 4e-69
                                    BTTSSTCHHHHHHHHHHHHH.HHHSSSSSSTS.-S.SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC............ CS
                           SecY   1 sifaLGImPyitasIilqLl.tvvipkleelk.ke.geegrkkinqitryltvvlalvqalgialslg............ 65 
                                    s++ LGI+P++tasI+lqLl ++     e++k +  ++++++ ++++++ l++v+++v+al  +++ g            
  gi|116754993|ref|YP_844111.1|  75 SLMLLGIGPIVTASIVLQLLvGA-----EIIKlNLrDPRDQAIFQGTQKALVFVMIVVEALPQITG-Gyllpdqalatsl 148
                                    89******************999.....666666669***********************996643.4688899999999 PP

                                    .....HH.HHHHHHHHHHHHHHHHHHHHHHHHSSTTHHHHHHHHHHHHHHCCHSS...............-HHHH..... CS
                           SecY  66 .....lalllivlqltagtvllmwLgEqitekGiGnGisllifagivarlpkals...............gliel..... 120
                                         ++ l+i+lq+++g+vl+++++E+++++GiG+G+ l+i+ag++++l++ l                +   +     
  gi|116754993|ref|YP_844111.1| 149 gvslsIISLIIFLQVCLGGVLILYMDEVVSKWGIGSGVGLFIVAGVSQQLVTGLFnwatgdgglpigivpK---Wisiir 225
                                    99999889*******************************************66664777777777655541...244444 PP

                                    .........SS.........THHHHHHHHHHHHHHHHHCHHHHBEEEECBBBS.TT....S.S-EEEEETTCCCSCHHHH CS
                           SecY 121 .........ale.......gilallllllvtllvillvvyveeaerripvqya.krgrkggqssylPlklnyagviPiIf 183
                                             + +        +   ll+l+ t+ +illvv+ve+++++ip+ ++  r    g+++++P+kl+ya+v+P+I+
  gi|116754993|ref|YP_844111.1| 226 lgligldeiF-TaeglkfiFVTGGLLALISTVGIILLVVLVESTRIEIPLAHSrVR----GARGRFPVKLVYASVLPMIL 300
                                    4555545441.14455555445899****************************666....9******************* PP

                                    HHHHHH.......................................................................... CS
                           SecY 184 asslla.......................................................................... 189
                                    +++l+a                                                                          
  gi|116754993|ref|YP_844111.1| 301 VRALQAniemlgalltaklgtvttaettaegvrivytgyqswlgtflssakfdaatgapisatspqpvsglmyylspihg 380
                                    **************************************999999999999999999999999999999888888888887 PP

                                    ....HHHCCCCS.........TCCCS....THHHHHHHHHHHHHH....HHHHHHTCT.THHHHHHHCCHHTBSSSCTTT CS
                           SecY 190 ....lpstiaqfl........lalls....psvlyvvlyvlliif....Fayfyteit.fnpkevaenlkksggfipgir 248
                                        +ps++ q +                 + +l++++ ++++i+    Fa+f++e+t + +k++a +++ sg +ipg+r
  gi|116754993|ref|YP_844111.1| 381 psdwIPSMVSQSTpglvelgiN---PiagwQIWLHLLTDTAFLIIggiiFAIFWIETTgMGAKSIAAKIHASGLQIPGYR 457
                                    7777788887777777766652...033458899999999988888999******************************* PP

                                    .TCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS.TT.TTHHHHHHHHHHHHHHH CS
                           SecY 249 .pgketakyLekvlsritliGalflaliavlpdllgasligafggtslLivVgvaletv 306
                                     +  ++++ +e++++++t+iG+++++l++v+++llg+  +g  ggt+lL++V+++++++
  gi|116754993|ref|YP_844111.1| 458 rSPVSIERLMERYIPKVTVIGGAIIGLLTVIASLLGT--LGGAGGTGLLLAVSIMYRLY 514
                                    999**********************************..999*************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 !   44.0   1.8   2.3e-15   1.4e-11       1      35 []      41      74 ..      41      74 .. 0.97

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 2.3e-15
                                   HHHHHHCCSB-TT--SSS-TCCHTTTCCCCTSSTT CS
                Plug_translocon  1 llYlvlsqiPLyGissssssDpfywlRaifAsnrG 35
                                   llY+vls+iPL+G+s   s+D+f+ +Ra fA+++G
  gi|116754993|ref|YP_844111.1| 41 LLYFVLSNIPLFGLS-KHSIDLFGYYRAFFAGSFG 74
                                   79************9.89***************98 PP

>> Ninjurin  Ninjurin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1   0.00068       4.1      47      93 ..      85     127 ..      77     132 .. 0.82
   2 ?    5.4   1.0    0.0029        17      41      64 ..     149     172 ..     137     180 .. 0.82
   3 ?   -4.1   0.3       2.7   1.6e+04      56      63 ..     255     262 ..     249     271 .. 0.48

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00068
                       Ninjurin  47 islSllLqvvvgilliliasklnlekekkerrlnklnnaatilvfvi 93 
                                    +++S++Lq++vg  +i     lnl++ +++  ++ +++a +++++v+
  gi|116754993|ref|YP_844111.1|  85 VTASIVLQLLVGAEIIK----LNLRDPRDQAIFQGTQKALVFVMIVV 127
                                    889*********99865....89999999998888887776666554 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0029
                       Ninjurin  41 iallvLislSllLqvvvgillili 64 
                                     ++l +isl ++Lqv++g +lil 
  gi|116754993|ref|YP_844111.1| 149 GVSLSIISLIIFLQVCLGGVLILY 172
                                    578999*************99984 PP

  == domain 3  score: -4.1 bits;  conditional E-value: 2.7
                       Ninjurin  56 vvgillil 63 
                                     vgi+l++
  gi|116754993|ref|YP_844111.1| 255 TVGIILLV 262
                                    34444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (537 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); 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: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 4105.56
//
Query:       gi|116754994|ref|YP_844112.1|  [L=124]
Description: ribosomal protein L15 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-16   61.1   4.7    2.7e-15   57.2   4.7    2.2  1  Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27
     0.0029   17.0   0.3     0.0047   16.3   0.3    1.3  1  Ribosomal_L18   Ribosomal protein 60S L18 and 50S L18e


Domain annotation for each model (and alignments):
>> Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.2   4.7     3e-19   2.7e-15       2     127 ..      26     122 ..      25     123 .. 0.84

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 3e-19
                                    GGGTSSTTTTTTTTT-S--.........S--.........---GGG..---EEEEHHHHHHTTTTGTTS------EEEGG CS
                 Ribosomal_L27A   2 GktgGrGhkGqkkrsgvkk.kpg..feGGqmplyrrlpkrGfknskfkkeykvvnlkdLdelideerleladeaeeidle 78 
                                    G++gGrG++G+ k+++v    +g     G++         Gf + +++ + +++n++ L+e++  e +          +e
  gi|116754994|ref|YP_844112.1|  26 GSRGGRGNAGTCKHHWVRSiIRGepM--GKH---------GFVR-PNSFDIETINVGVLNEMVGPEGR----------IE 83 
                                    99**************6654555345..888.........**95.446799*********88877655..........34 PP

                                    GTTTTSSS....SEEEE--S---.--EEEESEE-HHHHHHHHHTT-EEE CS
                 Ribosomal_L27A  79 elaeaglikkkdgvKvlgkgeltkklkvkaskfSkkAkekIeaaGGkve 127
                                     +          gvKvlgkg++t+ l+v a +fS++A++kIeaaGG+++
  gi|116754994|ref|YP_844112.1|  84 LH----------GVKVLGKGKVTRRLTVAAAAFSSSARSKIEAAGGEAV 122
                                    44..........99********************************987 PP

>> Ribosomal_L18  Ribosomal protein 60S L18 and 50S L18e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.3   5.2e-07    0.0047      96     120 ..      98     122 ..      93     124 .] 0.91

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.2e-07
                  Ribosomal_L18  96 klsvaALrftetararilkaGGeil 120
                                    +l+vaA  f+++ar++i++aGGe +
  gi|116754994|ref|YP_844112.1|  98 RLTVAAAAFSSSARSKIEAAGGEAV 122
                                    699*******************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 1031.79
//
Query:       gi|116754995|ref|YP_844113.1|  [L=151]
Description: 50S ribosomal protein L30P [Methanosaeta thermophila PT]
Scores for complete 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-16   57.8   0.0    1.5e-15   56.8   0.0    1.6  1  Ribosomal_L30  Ribosomal protein L30p/L7e
  ------ inclusion threshold ------
      0.048   13.3   0.0      0.063   12.9   0.0    1.1  1  YtxC           YtxC-like family


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 !   56.8   0.0   1.7e-19   1.5e-15       1      51 []       2      52 ..       2      52 .. 0.98

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 1.7e-19
                                   EEEEE-S-STTS-HHHHHHHHHTT-SSTT.EEEE--SSHHHHHHHHHCCCGE CS
                  Ribosomal_L30  1 lfVtrirsiigvppkvrktLqlLgLrkin.gtvvklntpsirGmLkkVkhlV 51
                                   ++++r r+ ++++p +r+tL +L+L+++n +++v+++   +rGm++ Vk++V
  gi|116754995|ref|YP_844113.1|  2 YAIIRLRGEVNTKPAIRDTLSMLRLHRVNhCVFVRED-EHYRGMIQVVKDYV 52
                                   57***********************************.*************9 PP

>> YtxC  YtxC-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.1e-06     0.063     113     189 ..      38     119 ..      29     121 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.1e-06
                           YtxC 113 ekeyqeFiklLkyfveiqepkielvhvvieeng....efilldengkeitk.elleelaeelsdselssedllisaLitl 187
                                    ++ y+ +i++ k++v   +   +l+ +++e+ g    + +l+de  +ei+  + ++elae +     s  d+ i +   l
  gi|116754995|ref|YP_844113.1|  38 DEHYRGMIQVVKDYVAWGKADADLLTMILEKRGrlsgNRRLTDEVVREISPyKSIRELAEAVCAGAASLKDFGIKPVFRL 117
                                    5679*************************98761111568**********999999999999999999999999887776 PP

                           YtxC 188 aP 189
                                     P
  gi|116754995|ref|YP_844113.1| 118 HP 119
                                    66 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 1113.32
//
Query:       gi|116754996|ref|YP_844114.1|  [L=203]
Description: 30S ribosomal protein S5P [Methanosaeta thermophila PT]
Scores for complete 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   82.1   0.1    2.4e-23   81.4   0.1    1.4  1  Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain
    2.3e-22   78.7   2.4    8.1e-22   77.0   1.4    2.2  2  Ribosomal_S5    Ribosomal protein S5, N-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.4   0.1   2.7e-27   2.4e-23       2      66 ..     137     202 ..     136     203 .] 0.96

  Alignments for each domain:
  == domain 1  score: 81.4 bits;  conditional E-value: 2.7e-27
                                    EEETTEEEEEEE--TT--EES-HHHHHHHHHHT--SEE---BS.-SSHHHHHHHHHHHHHHTTTT- CS
                 Ribosomal_S5_C   2 gkfgavkvllkpaprGtGiiaggavravlelaGikDvlakslg.srnpinvvkAtfeALkklrspe 66 
                                    g  g+v+++l+paprG G+ ag+++++v+e+aGikDv+++++g +r+++n++kAt++AL ++ +++
  gi|116754996|ref|YP_844114.1| 137 GSSGSVRIYLMPAPRGLGLAAGDVAKKVMEMAGIKDVWTRTEGsTRTTLNFAKATYNALLNTITVR 202
                                    789*********************************************************998875 PP

>> Ribosomal_S5  Ribosomal protein S5, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.0   1.4     9e-26   8.1e-22       1      65 []      51     115 ..      51     115 .. 0.98
   2 ?   -0.1   0.0      0.11   9.6e+02      51      65 .]     188     202 ..     184     202 .. 0.89

  Alignments for each domain:
  == domain 1  score: 77.0 bits;  conditional E-value: 9e-26
                                    XEEEEEEEEEEEEEETTEEEEEEEEEEEEEETTTEEEEEEEEESSHHHHHHHHHHHHHHTEEE-- CS
                   Ribosomal_S5   1 lkekvlkikrvqkvtkgGrrtsfsalvvvGdgnGlvGlGvgkakevatAirkAiekAkknlvpvp 65 
                                    l+++vl+i +vq++t++Grr +f+ +v+vG+++G++G+G gk  +v  Ai+k+ie+Ak+n+v+++
  gi|116754996|ref|YP_844114.1|  51 LEDEVLDITMVQRMTDSGRRVKFRTTVIVGNRDGYIGIGHGKDVQVGGAIKKGIENAKLNVVRIN 115
                                    799***********************************************************995 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.11
                                    HHHHHHHHHTEEE-- CS
                   Ribosomal_S5  51 rkAiekAkknlvpvp 65 
                                     kA+ +A +n + v+
  gi|116754996|ref|YP_844114.1| 188 AKATYNALLNTITVR 202
                                    69********99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); 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: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1544.74
//
Query:       gi|116754997|ref|YP_844115.1|  [L=169]
Description: 50S ribosomal protein L18P [Methanosaeta thermophila PT]
Scores for complete 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  115.2   1.2    1.1e-22   80.7   0.4    2.2  2  Ribosomal_L5e   Ribosomal large subunit proteins 60S L5, and 
    0.00068   20.0   0.0      0.001   19.4   0.0    1.3  1  Ribosomal_L18p  Ribosomal L18 of archaea, bacteria, mitoch. a


Domain annotation for each model (and alignments):
>> Ribosomal_L5e  Ribosomal large subunit proteins 60S L5, and 50S L18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.7   0.4   1.3e-26   1.1e-22       2      98 ..       6      95 ..       5     100 .. 0.96
   2 !   33.5   0.0   4.3e-12   3.8e-08     131     163 .]     101     133 ..      96     133 .. 0.95

  Alignments for each domain:
  == domain 1  score: 80.7 bits;  conditional E-value: 1.3e-26
                  Ribosomal_L5e  2 rfqvkfrrrregktdYyarkrliiqdknkyntpkyRlvVrvtnkdiicqiayakiegdkvlaaayskelpkygvkvgltnya 83
                                   r++v frrrreg+t+Y+ r rli          k R+vVr  n +i++q++ a+++gd++l +++skel++yg++++  n  
  gi|116754997|ref|YP_844115.1|  6 RYRVPFRRRREGRTNYHVRYRLILS-------RKPRVVVRKGNANITIQLIIAELKGDRTLLTVSSKELRNYGFQHSTGNVP 80
                                   9**********************95.......678*********************************************** PP

                  Ribosomal_L5e 84 aaYatglllarrllk 98
                                   aaY+tgll+++++l+
  gi|116754997|ref|YP_844115.1| 81 AAYLTGLLFGKKMLA 95
                                   ***********9985 PP

  == domain 2  score: 33.5 bits;  conditional E-value: 4.3e-12
                  Ribosomal_L5e 131 aiLdvGLartttgakvfgalkgavdgglsiphs 163
                                     iLd+GL+  ++g++v++alkg+vd+g+++phs
  gi|116754997|ref|YP_844115.1| 101 GILDIGLHSNSRGSRVYAALKGVVDAGVDVPHS 133
                                    58******************************7 PP

>> Ribosomal_L18p  Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   1.1e-07     0.001       7      94 ..      12     106 ..       7     128 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.1e-07
                                    HCHHHHHHTTT--...TTSSS-EEEEEE-SS-EEEEEE.-TTT.--EEEEECS-SCCCT..S-SSSCHHHHHHHHHHHHH CS
                 Ribosomal_L18p   7 rkrRhkRirkkls...gtaerprlvvfrsnrhiyaQvi.ddvk.gktlasastlekelk..lkstknkeaakkvgeliAe 79 
                                    r+rR+ R   +++     + +pr+vv + n +i +Q+i ++ k ++tl ++s+ e +    ++st+n  aa   g l+ +
  gi|116754997|ref|YP_844115.1|  12 RRRREGRTNYHVRyrlILSRKPRVVVRKGNANITIQLIiAELKgDRTLLTVSSKELRNYgfQHSTGNVPAAYLTGLLFGK 91 
                                    667777777766655556789***************75355551689999999887665677999*************** PP

                                    HHCHHCHTC-EE--T CS
                 Ribosomal_L18p  80 rakekgiekvvfDrg 94 
                                    + ++ g ++ + D g
  gi|116754997|ref|YP_844115.1|  92 KMLALGYNEGILDIG 106
                                    **9999998888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       225  (0.0125495); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1335.07
//
Query:       gi|116754998|ref|YP_844116.1|  [L=152]
Description: 50S ribosomal protein L19e [Methanosaeta thermophila PT]
Scores for complete 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-55  185.6   5.4    5.2e-55  185.5   5.4    1.0  1  Ribosomal_L19e  Ribosomal protein L19e
  ------ inclusion threshold ------
        6.1    6.9   9.1       0.28   11.2   2.8    2.0  2  HTH_12          Ribonuclease R winged-helix domain


Domain annotation for each model (and alignments):
>> Ribosomal_L19e  Ribosomal protein L19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.5   5.4   5.9e-59   5.2e-55       2     143 ..       4     147 ..       3     148 .. 0.97

  Alignments for each domain:
  == domain 1  score: 185.5 bits;  conditional E-value: 5.9e-59
                                    THHHHHHHHHHTTS-GGGEEE..-GGGHHHHHH--SHHHHHHHHHTTSEEE-------THHHHHHHHHHHTT-S-SGGG- CS
                 Ribosomal_L19e   2 lklqkrlaasvlkvGknrvwl..dpeeleeiaeAitredirklikdglIikkpkkgnsrararerkekkrkgrrrgsGkr 79 
                                    ++ q+rlaas l+vG++rvw+  dpe ++e+a+Aitredir+ i+ g I++kpkkgnsrar+r r+ek+++g+r+g+G+r
  gi|116754998|ref|YP_844116.1|   4 FTVQRRLAASELGVGESRVWInpDPEVASELADAITREDIRAHIEAGNIKAKPKKGNSRARFRLRAEKRAYGHRKGPGRR 83 
                                    679******************777899***************************************************** PP

                                    -S-HHHHS-HHHHHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHTT--SSHHHHHHHHT-X CS
                 Ribosomal_L19e  80 kGtkeaRlpekelWikriRalRrlLkelrekkkidkktYrelYrkakGgefknkavLkeyiekk 143
                                    +G+k+aR p ke Wi+riRalRr+L+e+r+++ki+++ Yr lYrkakGge+++ a+L +yi++k
  gi|116754998|ref|YP_844116.1|  84 RGAKGARAPPKEIWISRIRALRRHLREMRDSEKIERHAYRLLYRKAKGGEYRSIAHLDAYIKAK 147
                                    *************************************************************976 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.5      0.27   2.4e+03      22      22 ..      51      51 ..      29      84 .. 0.60
   2 ?   11.2   2.8   3.1e-05      0.28      32      54 ..     101     123 ..      98     131 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.27
                         HTH_12 22 e 22
                                   +
  gi|116754998|ref|YP_844116.1| 51 N 51
                                   2 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 3.1e-05
                         HTH_12  32 eravRyrLrkleergltrrvgya 54 
                                     ra+R++Lr + + + ++r+ y 
  gi|116754998|ref|YP_844116.1| 101 IRALRRHLREMRDSEKIERHAYR 123
                                    49*****************9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1126.45
//
Query:       gi|116754999|ref|YP_844117.1|  [L=128]
Description: ribosomal protein L32e [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.5e-34  116.8   0.4    6.8e-34  116.5   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 !  116.5   0.4   3.8e-38   6.8e-34       1     108 []      15     118 ..      15     118 .. 0.97

  Alignments for each domain:
  == domain 1  score: 116.5 bits;  conditional E-value: 3.8e-38
                                    ------TTTTT-TTS-SS------TT-TTTTT-TTS-----GGG---TTTTT--TTS-EEEEESSGGGGTT--TTTE..E CS
                 Ribosomal_L32e   1 tkkFirhqsdryvklkeswrkprGidnrvrrrfkgqilmpkiGYgspkktrgllpsGfkkvlVhnvkeLevllmenksya 80 
                                    +++F+r++s+++ +l+eswr+prG++n++r++++++ ++++ G+gsp+++rgl+psGf++vlV+ vk+L+    +    a
  gi|116754999|ref|YP_844117.1|  15 KPEFRRYDSHKKARLGESWRRPRGLHNKLRQQVRAKGRLVRPGFGSPRAVRGLHPSGFREVLVRCVKDLKRAEGC----A 90 
                                    689*******************************************************************88766....8 PP

                                    EEE-TTS-HHHHHHHHHHHHHTT-EBSS CS
                 Ribosomal_L32e  81 aeiahsVsskkrkeiverAaelgikVtN 108
                                    ++ia++V+++kr++i++ A+e+++k++N
  gi|116754999|ref|YP_844117.1|  91 IRIARTVGMRKREKIEAMAREMNLKILN 118
                                    9*************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 955.46
//
Query:       gi|116755000|ref|YP_844118.1|  [L=176]
Description: 50S ribosomal protein L6 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-30  105.9   3.1    3.1e-19   69.4   0.1    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 !   69.4   0.1   1.7e-23   3.1e-19       1      76 []      11      83 ..      11      83 .. 0.97
   2 !   37.5   0.4   1.6e-13   2.9e-09       1      76 []      95     169 ..      95     169 .. 0.97

  Alignments for each domain:
  == domain 1  score: 69.4 bits;  conditional E-value: 1.7e-23
                                   CSTTEEEEEETTTEEEEEESSEEEEEE-CTTSEEEEEECSTEEEEEECSESCHHHHHHHHHHHHHHHHHHHHHHTC CS
                   Ribosomal_L6  1 iPvgvrvsikggqlvlvlGpkgeltreipegvtvevkvegnkvtvivvsgidkekvAligtvrslinnmikGVteg 76
                                   iP+gv+v+i g + v v+Gpkgel+re+++  ++e+k e+ k+   +v  ++++ + ++gt+ ++i+nmi+GVt+g
  gi|116755000|ref|YP_844118.1| 11 IPDGVDVQISG-RSVRVKGPKGELSRELWYP-DIEIKREDSKILIRSVARKKQHLA-MVGTIAAHIKNMIRGVTDG 83
                                   8*********8.*******************.99999******************9.*****************98 PP

  == domain 2  score: 37.5 bits;  conditional E-value: 1.6e-13
                                    CSTTEEEEEETTTEEEEEESSEEEEEE-CTTSEEEEEECSTEEEEEECSESCHHHH....HHHHHHHHHHHHHHHHHHTC CS
                   Ribosomal_L6   1 iPvgvrvsikggqlvlvlGpkgeltreipegvtvevkvegnkvtvivvsgidkekv....AligtvrslinnmikGVteg 76 
                                    +P+ v+v   ++ + ++lG+++++ ++i  +v+vev      +++i + g dke v    A+i++++++   +++ +++g
  gi|116755000|ref|YP_844118.1|  95 FPIQVKVADGKVAISNFLGERKPRFATIVGDVNVEVG-----KDEILIRGMDKEAVgqtmANIEQATRVRGFDVRIFQDG 169
                                    79999999888************************98.....9***********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1331.06
//
Query:       gi|116755001|ref|YP_844119.1|  [L=129]
Description: 30S ribosomal protein S8P [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-26   92.4   0.0    2.8e-26   92.0   0.0    1.2  1  Ribosomal_S8  Ribosomal protein S8


Domain annotation for each model (and alignments):
>> Ribosomal_S8  Ribosomal protein S8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.0   0.0   1.6e-30   2.8e-26       1     127 []       4     129 .]       4     129 .] 0.84

  Alignments for each domain:
  == domain 1  score: 92.0 bits;  conditional E-value: 1.6e-30
                                    -HHHHHHHHHHHHHHTT-SEEEE.E--HHHHHHHHHHHHCTSEEEEEEE.CCCCCC..EEEEE-BSSS-SBSSS.....E CS
                   Ribosomal_S8   1 DpiadmltrirNaekakkeevev.pasklkeeilkvLkeeGyikdfeve.eekkkk..ikielkynkkkksvik.....k 71 
                                    Dp+ad++++i+Nae+++k e+ + paskl++  lkv+ + Gyi +fe+  + k+ +  +k+ +++n+  ++vik     k
  gi|116755001|ref|YP_844119.1|   4 DPLADAMSTIKNAENVGKPECIIkPASKLIAMTLKVMADLGYIGEFEFIdDGKSGMfkVKLLGRINR--CGVIKprfaiK 81 
                                    9***********************************************9655555544666666666..*****555555 PP

                                    EEE-SBTTC--EE-CCC---CGGGTSEEEEEETTEEEEHHHHHHCT--EEEEEEEE CS
                   Ribosomal_S8  72 lkrvskpgrrvYakvkelpkvlnglGiaivsTskGvmtdkeArkkkvGGevlayvw 127
                                    + +++k  rr       lp   +++G++i+sTs+Gvm +++Ar++++GG++layv+
  gi|116755001|ref|YP_844119.1|  82 VAELEKWERR------FLP--ARNFGVLILSTSQGVMPHTDARARGIGGHLLAYVY 129
                                    5555555555......333..578*******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 925.27
//
Query:       gi|116755002|ref|YP_844120.1|  [L=47]
Description: ribosomal protein S14 [Methanosaeta thermophila PT]
Scores for 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-14   52.1   5.9    4.2e-14   52.0   5.9    1.0  1  Ribosomal_S14  Ribosomal protein S14p/S29e
  ------ inclusion threshold ------
      0.025   14.5   0.0      0.029   14.3   0.0    1.2  1  DUF4428        Domain of unknown function (DUF4428)
      0.042   13.5   0.2      0.054   13.2   0.2    1.2  1  zf-P11         P-11 zinc finger
      0.079   13.3   0.9        0.1   12.9   0.9    1.2  1  C1_2           C1 domain
      0.091   12.5   0.1        2.3    8.1   0.0    2.1  2  HTH_38         Helix-turn-helix domain


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 !   52.0   5.9   1.2e-17   4.2e-14       7      54 .]       3      47 .]       1      47 [] 0.93

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 1.2e-17
                                   -SS..CTTT---SSS--SSSEE-GGG-..EHHHHHHHTTT...TT-EE-- CS
                  Ribosomal_S14  7 rnssptrirnrCrvtGrprGvirkfgL..sRicfRelAlkgelpGvkKaS 54
                                   ++   +r+ n Cr +Gr  G++rk+g+  +R+cfRe A++   +G++K+S
  gi|116755002|ref|YP_844120.1|  3 KKF--GRGANECRRCGRKPGLVRKYGIylCRQCFREIARE---MGFEKYS 47
                                   455..9**********************************...******8 PP

>> DUF4428  Domain of unknown function (DUF4428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   8.2e-06     0.029       2      31 ..      12      39 ..      11      47 .] 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.2e-06
                        DUF4428  2 CaiCgkKigllkrlkleDgyvCkdClkKl.s 31
                                   C  Cg K gl         y+C  C+ ++  
  gi|116755002|ref|YP_844120.1| 12 CRRCGRKPGLVR---KYGIYLCRQCFREIaR 39
                                   777********9...8899********9953 PP

>> zf-P11  P-11 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   1.5e-05     0.054       1      29 [.       8      35 ..       8      40 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.5e-05
                                   -SSSBTTTSS--SSEEE-SSSEEEHHHHH CS
                         zf-P11  1 GplsCksCWfkdksLveCsdHYLClrClq 29
                                   G   C+ C   + +Lv+    YLC++C++
  gi|116755002|ref|YP_844120.1|  8 GANECRRCGR-KPGLVRKYGIYLCRQCFR 35
                                   6678999975.579*************85 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.9   2.8e-05       0.1      15      38 ..       6      33 ..       2      38 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.8e-05
                           C1_2 15 ssesfnCsaCgrk...idgff.YsCseC 38
                                     +  +C+ Cgrk   + ++  Y C +C
  gi|116755002|ref|YP_844120.1|  6 GRGANECRRCGRKpglVRKYGiYLCRQC 33
                                   567789*******997655559****9* PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.034   1.2e+02      28      38 ..      13      23 ..      12      24 .. 0.87
   2 ?    8.1   0.0   0.00063       2.3      22      32 ..      33      43 ..      28      45 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.034
                         HTH_38 28 rrLgrspsTIs 38
                                   rr+gr+p+ + 
  gi|116755002|ref|YP_844120.1| 13 RRCGRKPGLVR 23
                                   89*****9886 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00063
                         HTH_38 22 slreIArrLgr 32
                                    +reIAr++g 
  gi|116755002|ref|YP_844120.1| 33 CFREIAREMGF 43
                                   58*******95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.40
# Mc/sec: 351.47
//
Query:       gi|116755003|ref|YP_844121.1|  [L=169]
Description: 50S ribosomal protein L5P [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.3e-24   84.5   0.1    9.1e-24   83.5   0.1    1.6  1  Ribosomal_L5_C  ribosomal L5P family C-terminus
    7.2e-18   64.7   0.1    1.4e-17   63.7   0.1    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 !   83.5   0.1     1e-27   9.1e-24       1      79 [.      57     132 ..      57     156 .. 0.85

  Alignments for each domain:
  == domain 1  score: 83.5 bits;  conditional E-value: 1e-27
                 Ribosomal_L5_C   1 piGvkvtLrgekmyefldkllevvlprlrdFkGiskssfdgrGnvsfGikeqiifpeieydkdkgifGmditivttak.. 78 
                                    piG++vtLrg+ ++efl+++++v+   ++      ks+fd++Gn++fGi+e+++fp+++yd+++gifGmd+++ + +   
  gi|116755003|ref|YP_844121.1|  57 PIGTRVTLRGRAAEEFLETAFKVAGGVIK------KSQFDENGNFAFGIEEHTDFPGMKYDPEIGIFGMDVAVSLMRAgy 130
                                    8****************************......**************************************9988765 PP

                 Ribosomal_L5_C  79 .t 79 
                                     +
  gi|116755003|ref|YP_844121.1| 131 rV 132
                                    52 PP

>> Ribosomal_L5  Ribosomal protein L5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.7   0.1   1.6e-21   1.4e-17       5      57 .]       4      53 ..       2      53 .. 0.98

  Alignments for each domain:
  == domain 1  score: 63.7 bits;  conditional E-value: 1.6e-21
                                   S-EEEEEEEEEE-SSSSSCHHHHHCCHHHHCCCHSS--EECC--TTCTTTCSC CS
                   Ribosomal_L5  5 vPrleKivinmgvGeagedkkllekaakeLaeItGQkPvvtkakksianFkiR 57
                                   +Pr+ K+v+++gvGe+g++   l +a+ +L+eItGQ+P++++akk+ ++F+i+
  gi|116755003|ref|YP_844121.1|  4 EPRIGKVVVHIGVGESGQR---LVNAETILSEITGQTPIRSRAKKTLPAFGIK 53
                                   7******************...*****************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); 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: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1254.19
//
Query:       gi|116755004|ref|YP_844122.1|  [L=233]
Description: 30S ribosomal protein S4e [Methanosaeta thermophila PT]
Scores for complete 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   0.1    5.3e-19   67.9   0.0    1.9  2  Ribosomal_S4e  Ribosomal family S4e
    8.4e-09   35.4   3.2    1.3e-08   34.8   3.2    1.3  1  RS4NT          RS4NT (NUC023) domain
    1.1e-06   28.2   0.2    2.1e-06   27.3   0.2    1.5  1  S4             S4 domain
    5.6e-05   23.0   0.0    0.00017   21.4   0.0    1.9  1  KOW            KOW motif


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 !   67.9   0.0   1.2e-22   5.3e-19       2      75 .]      90     161 ..      89     161 .. 0.97
   2 ?   -0.7   0.0      0.31   1.4e+03      30      45 ..     185     200 ..     175     210 .. 0.69

  Alignments for each domain:
  == domain 1  score: 67.9 bits;  conditional E-value: 1.2e-22
                                    TEEEEEEE-TTSSEEEEEE-TTCCCEEEEEECEEEEECCCEEEEEETTS-EEEESSTT-STTEEEEEETTTTEE CS
                  Ribosomal_S4e   2 genyrllydtkgrfalhkItseeakyKLcKikkkttvkkgipqlvthdGrtirypdpdikvnDtvkidleenkI 75 
                                    +++yr++  tkg+f+l++I+++  + KL+++++ktt k++++ql+++dG++i+ + + + ++D+++i+l+e++I
  gi|116755004|ref|YP_844122.1|  90 NKQYRMVKSTKGYFVLIEIQPDTPR-KLVRVENKTTLKGNRMQLNLSDGSNIIAEGD-VGTGDSLLISLPERSI 161
                                    89********************999.******************************8.*************987 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.31
                                    EEECEEEEECCCEEEE CS
                  Ribosomal_S4e  30 cKikkkttvkkgipql 45 
                                     +ik++++v+   p  
  gi|116755004|ref|YP_844122.1| 185 GRIKSVQIVRSSMPNR 200
                                    5899999998655443 PP

>> RS4NT  RS4NT (NUC023) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   3.2     3e-12   1.3e-08       6      36 ..       2      32 ..       1      33 [. 0.95

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 3e-12
                                   -EETTTS-TTS---SSSSSEE----SSSS-T CS
                          RS4NT  6 HLKrlaAPkhWpldkkegvfavkPspGPHkl 36
                                   H Kr++ P++W++++k+++++ +P+pGPH++
  gi|116755004|ref|YP_844122.1|  2 HRKRVTIPRSWLIPRKTSKWIATPRPGPHSA 32
                                   88***************************97 PP

>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.2   4.7e-10   2.1e-06       2      48 .]      37      84 ..      36      84 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 4.7e-10
                                   EHHHHH.HHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTCEE CS
                             S4  2 RLdkvl.arlglassrreArqlIehGrVlVNGkvvkdpsyrVkpgDvi 48
                                   +L +v+   l+la   re++++  +G+VlV+G v++d+ ++V+  Dvi
  gi|116755004|ref|YP_844122.1| 37 PLMVVVrDLLKLADNAREVKRILHEGGVLVDGTVRRDARFPVGLFDVI 84
                                   57777775699********************************99997 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   3.9e-08   0.00017       1      31 [.     169     203 ..     169     204 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 3.9e-08
                                    TTSEEEESSSTTTTCEEEEEEEETTT....TEEEE CS
                            KOW   1 pGdhVkVvsGphkGktGkVvkvdqhk....vrVfv 31 
                                    +G+  +V++G h G tG++++v   +    +rV++
  gi|116755004|ref|YP_844122.1| 169 VGNLAMVTGGSHTGMTGRIKSVQIVRssmpNRVTI 203
                                    7*********************9999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1866.96
//
Query:       gi|116755005|ref|YP_844123.1|  [L=116]
Description: 50S ribosomal protein L24P [Methanosaeta thermophila PT]
Scores for complete 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-31  108.2   0.3    2.5e-31  108.0   0.3    1.1  1  Ribosomal_L26  Ribosomal proteins L26 eukaryotic, L24P archae
    2.3e-07   30.5   1.0    2.3e-07   30.5   1.0    1.6  2  KOW            KOW motif
  ------ inclusion threshold ------
      0.027   14.6   0.0      0.033   14.3   0.0    1.2  1  DUF4150        Domain of unknown function (DUF4150)


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 !  108.0   0.3   4.2e-35   2.5e-31       1      80 [.       3     115 ..       3     116 .] 0.97

  Alignments for each domain:
  == domain 1  score: 108.0 bits;  conditional E-value: 4.2e-35
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................xxxxx RF
                  Ribosomal_L26   1 sssrrkqrKahfnapshirrklmsapLskeLrekygvrslpir................................gvtre 48 
                                    s+++rkqrKa+fnap+h+r+++m+a Ls eLr++y+ rs +++                                gv++ 
  gi|116755005|ref|YP_844123.1|   3 SKQPRKQRKARFNAPLHMRQRFMHAMLSPELRKEYKKRSAQVKkgdtvkvmrgdnagvegevlsvdlkrcvitvaGVSNF 82 
                                    89****************************************************************************** PP

                                    xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                  Ribosomal_L26  49 kangttvpvgihpSkvvItklkl.DkdrkkiLe 80 
                                    +a+gt+vp++ihpS+v+Itkl+l D++r+ki +
  gi|116755005|ref|YP_844123.1|  83 RADGTEVPRPIHPSNVMITKLDLdDDEREKIFS 115
                                    ***********************8888888765 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   1.0   3.8e-11   2.3e-07       1      30 [.      46      75 ..      46      77 .. 0.92
   2 ?   -2.4   0.0       0.9   5.4e+03      18      25 ..      99     106 ..      97     113 .. 0.73

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 3.8e-11
                                   TTSEEEESSSTTTTCEEEEEEEETTTTEEE CS
                            KOW  1 pGdhVkVvsGphkGktGkVvkvdqhkvrVf 30
                                   +Gd+VkV++G ++G +G+V++vd ++  ++
  gi|116755005|ref|YP_844123.1| 46 KGDTVKVMRGDNAGVEGEVLSVDLKRCVIT 75
                                   7***********************996665 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.9
                                    EEEEEETT CS
                            KOW  18 kVvkvdqh 25 
                                    +++k d +
  gi|116755005|ref|YP_844123.1|  99 MITKLDLD 106
                                    78887766 PP

>> DUF4150  Domain of unknown function (DUF4150)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   5.6e-06     0.033      47      94 ..      44      91 ..      25      97 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.6e-06
                        DUF4150 47 lnkgsviststGDepGtagGvvSgtvkgkaeflsgsfdvkiegkpavr 94
                                   ++kg ++++  GD++G+ g v+S   k     ++g ++++++g+ + r
  gi|116755005|ref|YP_844123.1| 44 VKKGDTVKVMRGDNAGVEGEVLSVDLKRCVITVAGVSNFRADGTEVPR 91
                                   788889999*******************************99999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 864.95
//
Query:       gi|116755006|ref|YP_844124.1|  [L=132]
Description: 50S ribosomal protein L14P [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.7e-37  126.8   0.9    5.2e-37  126.6   0.9    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 !  126.6   0.9   2.9e-41   5.2e-37       2     121 ..      12     131 ..      11     132 .] 0.95

  Alignments for each domain:
  == domain 1  score: 126.6 bits;  conditional E-value: 2.9e-41
                                    .CSS-EEE--SSSSBSEEEEEEETT-.....---EE-SSSEEEEEESSS-T...TTSSCEEEEEEEE-SS-EE-TTS-EE CS
                  Ribosomal_L14   2 iqlktrlkvaDNsgakevecikvlggk....krkaasvGdiivvsvkkakpkgkvkkgdvvkavvvrtkkevrrkdGsvi 77 
                                    i+++t+l++aDN+ga+++ +++v +++    +++ a +Gd++vvsvkk++p   ++++++++av++r+kke+rr+dG  +
  gi|116755006|ref|YP_844124.1|  12 INTGTYLECADNTGARTLFVVSVKKYRgvknRQPCAGIGDMVVVSVKKGTP---EMRKQIFNAVIIRQKKEFRRPDGLRV 88 
                                    7899*******************98887766779*****************...99************************ PP

                                    EESS-EEEEB-TTS-BSS-.B-SBEEHHHHHH.-HHHHHTBSBE CS
                  Ribosomal_L14  78 rfddnaaVllnkkgeplGtrifgpvarelrekkflkivslApev 121
                                    +f+dnaaV+ ++ g p+G++i+gpvare++e+ f ki+s A  +
  gi|116755006|ref|YP_844124.1|  89 KFEDNAAVITDDAGVPKGSEIKGPVAREVAER-FGKIASSAAII 131
                                    *******************************9.*******9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 953.37
//
Query:       gi|116755007|ref|YP_844125.1|  [L=106]
Description: 30S ribosomal protein S17 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-28   96.7   2.9    7.4e-28   96.5   2.9    1.1  1  Ribosomal_S17    Ribosomal protein S17
    7.9e-05   23.0   0.2     0.0002   21.7   0.0    1.7  2  Ribosomal_S17_N  Ribosomal_S17 N-terminal
  ------ inclusion threshold ------
      0.039   13.7   0.7      0.081   12.7   0.7    1.4  1  zf-C3H1          Putative zinc-finger domain


Domain annotation for each model (and alignments):
>> Ribosomal_S17  Ribosomal protein S17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.5   2.9   1.2e-31   7.4e-28       1      68 []      35     103 ..      35     103 .. 0.99

  Alignments for each domain:
  == domain 1  score: 96.5 bits;  conditional E-value: 1.2e-31
                                    EEEEE--STTEEEEEEEEEEEETTTTEEEEEEEEEEEE-TTTS.--TT-EEEEEEECECSSSEEEEEEE CS
                  Ribosomal_S17   1 GvVvsdkmdkTvvVrverlvkhpkykkyvkrrkkylahdenns.vkvGDiVrieecrPlSktkrfvvve 68 
                                    G+Vvsdkm +TvvV +e ++++ ky++y+krr+k++ah++++  +kvG +Vri+ecrPlSktk+fvvve
  gi|116755007|ref|YP_844125.1|  35 GIVVSDKMARTVVVMREFKKRITKYERYEKRRSKIHAHNPPCLdAKVGERVRIAECRPLSKTKSFVVVE 103
                                    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 !   21.7   0.0   3.3e-08    0.0002      34      69 .]       2      33 ..       1      33 [. 0.95
   2 ?   -1.9   0.1      0.74   4.4e+03      29      32 ..      59      62 ..      43      72 .. 0.49

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 3.3e-08
                                   ----TT----GGGGS-----TTSSSSSS----S-EE CS
                Ribosomal_S17_N 34 knvglgfktPkeAiegtYiDkKCPFtGnvsirGriL 69
                                   +++gl  ++P++A +    D KCPF G   +rG++L
  gi|116755007|ref|YP_844125.1|  2 RDIGLDVSAPQQACN----DPKCPFHGRLPVRGQVL 33
                                   89************9....9**************98 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.74
                                   .--- CS
                Ribosomal_S17_N 29 kkry 32
                                    +ry
  gi|116755007|ref|YP_844125.1| 59 YERY 62
                                   1222 PP

>> zf-C3H1  Putative zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.7   1.4e-05     0.081       9      18 ..      13      22 ..      12      22 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.4e-05
                        zf-C3H1  9 GvCnDpsCef 18
                                   ++CnDp+C+f
  gi|116755007|ref|YP_844125.1| 13 QACNDPKCPF 22
                                   79******99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); 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: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 812.76
//
Query:       gi|116755008|ref|YP_844126.1|  [L=96]
Description: ribonuclease P, Rpp29 [Methanosaeta thermophila PT]
Scores for complete 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   82.8   0.1    1.3e-23   82.6   0.1    1.0  1  UPF0086   Domain of unknown function UPF0086


Domain annotation for each model (and alignments):
>> UPF0086  Domain of unknown function UPF0086
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.6   0.1   7.5e-28   1.3e-23       1      84 []       5      87 ..       5      87 .. 0.97

  Alignments for each domain:
  == domain 1  score: 82.6 bits;  conditional E-value: 7.5e-28
                                   HHHCCSXXSS-EEEEEECSSTTTTTEEEEEEEEETTEEEEEECTTEEEEEESTTCEEEEEE.TTEEEEEECCCCSSXHHHHH CS
                        UPF0086  1 ekLlkadlhGaeveVvrsknpslvgikGiVvkEtkntlkivtkksrvktvpKegsvFefevkdvlevevdGsqlryrpadRa 82
                                   e++++++l+G+ veV++  n+++ g++G+Vv+Et+nt++i+t ++++++vpK+++ F f++ d  +v++ Gs l+++p++R+
  gi|116755008|ref|YP_844126.1|  5 ENIARHELIGLTVEVIDTPNRTMAGMRGLVVDETRNTFVIET-QRGLRRVPKAHTSFIFTLPDGQKVRIAGSVLISQPENRI 85
                                   5899**************************************.99****************9999***************** PP

                                   CH CS
                        UPF0086 83 er 84
                                   ++
  gi|116755008|ref|YP_844126.1| 86 NK 87
                                   97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 749.94
//
Query:       gi|116755009|ref|YP_844127.1|  [L=67]
Description: ribosomal protein L29 [Methanosaeta thermophila PT]
Scores for complete 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-20   71.6   2.7    4.4e-20   71.4   2.7    1.0  1  Ribosomal_L29  Ribosomal L29 protein
  ------ inclusion threshold ------
      0.076   13.1   0.9       0.14   12.3   0.9    1.5  1  MRP-L47        Mitochondrial 39-S ribosomal protein L47 (MRP-


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 !   71.4   2.7   4.9e-24   4.4e-20       2      57 .]       8      64 ..       7      64 .. 0.98

  Alignments for each domain:
  == domain 1  score: 71.4 bits;  conditional E-value: 4.9e-24
                                   HHHHS-HHHHHHHHHHHHHHHHHHHHHHHHT.SSS-CHHHHHHHHHHHHHHHHHHHH CS
                  Ribosomal_L29  2 elrelsdeeLkeklkelkkeLfnLrfqkatg.qlenpsrirkvRkdIARikTvlrer 57
                                   e+r++s eeL+e+l +l+ eL + r + ++g ++e+p+rir++R++IAR+kTv+rer
  gi|116755009|ref|YP_844127.1|  8 EIRNMSSEELEEELRKLEVELIRERGAVRAGgAPEKPGRIREIRRTIARMKTVQRER 64
                                   9****************************999************************8 PP

>> MRP-L47  Mitochondrial 39-S ribosomal protein L47 (MRP-L47)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.9   1.6e-05      0.14      27      87 .]       8      64 ..       3      64 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.6e-05
                        MRP-L47 27 eLrkksfedLhklwyvllkekNmLlteeeellrkqekmpsperlkkvkesMeniktVlkeR 87
                                   e+r+ s e+L++     l+   + l +e+ + r     ++p+r+ +++++++++ktV +eR
  gi|116755009|ref|YP_844127.1|  8 EIRNMSSEELEE----ELRKLEVELIRERGAVRAGGAPEKPGRIREIRRTIARMKTVQRER 64
                                   566666666666....444444444555555556666789*******************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       774  (0.0431703); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); 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: 0.33u 0.21s 00:00:00.54 Elapsed: 00:00:00.35
# Mc/sec: 581.25
//
Query:       gi|116755010|ref|YP_844128.1|  [L=276]
Description: 30S ribosomal protein S3P [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.4e-21   74.5   0.1    1.3e-20   73.7   0.1    1.4  1  Ribosomal_S3_C  Ribosomal protein S3, C-terminal domain
    3.2e-15   55.7   0.0    5.6e-15   54.9   0.0    1.4  1  KH_2            KH domain
  ------ inclusion threshold ------
      0.057   13.3   0.2       0.24   11.2   0.1    2.1  2  KH_1            KH domain


Domain annotation for each model (and alignments):
>> Ribosomal_S3_C  Ribosomal protein S3, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.7   0.1   2.2e-24   1.3e-20       1      83 []      99     182 ..      99     182 .. 0.98

  Alignments for each domain:
  == domain 1  score: 73.7 bits;  conditional E-value: 2.2e-24
                                    HHHHHHTT--HHHHHHHHHHHHHHCC-SEEEEEEEC-SS.TTT--EEEEEEC----..TCHHHH-EEEEEEEEETTEEEE CS
                 Ribosomal_S3_C   1 iaeqlekrvsfRramkkairramkagakGikiqvsGrLggaeiarsekykeGrvpl..htlradidyavaeaktkyGiiG 78 
                                    +a++le+++ fR+a ++++rr+m++ga G++i++sG+L+ + ++r ek+ +G++++  +++++ +d+++a a  k G iG
  gi|116755010|ref|YP_844128.1|  99 LASSLEHGWYFRKAGQSMLRRVMDSGALGCEIVISGKLT-GPRSRVEKFLAGYIKHsgKPAEEIVDTGYAVAVKKLGAIG 177
                                    5899***********************************.9*************************************** PP

                                    EEEEE CS
                 Ribosomal_S3_C  79 vkVwI 83 
                                    ++V+I
  gi|116755010|ref|YP_844128.1| 178 CQVRI 182
                                    ***98 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.9   0.0   9.4e-19   5.6e-15       2      69 ..      17      83 ..      16      90 .. 0.93

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 9.4e-19
                                   HHHHHHHHTECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEEE CS
                           KH_2  2 ipeslaveikkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkkVkln 69
                                   ++e+la+e+  ag+++++ +rt+ ++ i++++++pg+vIGkgG+ i+k++ +l+++++ l + ++ ++
  gi|116755010|ref|YP_844128.1| 17 VDEYLAKELDRAGYGGMVMNRTPMGTQITVYAEKPGMVIGKGGKLIRKLTRDLERRFR-LDNPQIDVQ 83
                                   679******************************************************6.999999965 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   4.1e-05      0.24       4      27 ..      44      67 ..      41      77 .. 0.84
   2 ?   -1.9   0.0      0.51   3.1e+03      30      36 ..     127     133 ..     113     145 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.1e-05
                                   EEEGGGHHHHHHTGGGHHHHHHHH CS
                           KH_1  4 ilvPsslvgriIGkgGsnIkeIre 27
                                   i+v +++ g +IGkgG+ I+++ +
  gi|116755010|ref|YP_844128.1| 44 ITVYAEKPGMVIGKGGKLIRKLTR 67
                                   5566666799***********987 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.51
                                    T-EEEEE CS
                           KH_1  30 gakIkvp 36 
                                    g+ I++ 
  gi|116755010|ref|YP_844128.1| 127 GCEIVIS 133
                                    5555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); 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:                         3  (0.000167327); expected 0.2 (1e-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: 1913.11
//
Query:       gi|116755011|ref|YP_844129.1|  [L=152]
Description: 50S ribosomal protein L22 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-29  101.6   0.0    2.9e-29  101.3   0.0    1.1  1  Ribosomal_L22  Ribosomal protein L22p/L17e


Domain annotation for each model (and alignments):
>> Ribosomal_L22  Ribosomal protein L22p/L17e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.3   0.0   1.6e-33   2.9e-29       2     103 .]      18     149 ..      17     149 .. 0.97

  Alignments for each domain:
  == domain 1  score: 101.3 bits;  conditional E-value: 1.6e-33
                                    EEEEESS-HHHHHHHHHHHTTSBHHHHHHHHHT..-SST............................THHHHHHHHHHHH CS
                  Ribosomal_L22   2 kgsnlrvsfkklrevarlIrgmkveeAlkyLkf..skkk............................aakfvlklLknae 51 
                                    +g +l++s+k++re++r+Irgmkve A ++L++  + k+                            aa+ vl++L+na+
  gi|116755011|ref|YP_844129.1|  18 MGVELPISPKHAREICRAIRGMKVEAAERFLQDviALKRavpfrrynrnvphrhglvgwpagrfpqkAARAVLRVLENAI 97 
                                    67789*****************************988889**************************************** PP

                                    HHHH..HT-GGGEEEEEEEEEEEEEEEEEEEESTTEEEEEEEEEEEEEEEEE CS
                  Ribosomal_L22  52 anaelkgldvdslvIeeiqvnkgpklkrrtyrArGrinpirkspchievvlk 103
                                     nae+kgl++++lvI  +  +kg++++++++rA+Gr++p ++++++ie++l+
  gi|116755011|ref|YP_844129.1|  98 GNAEYKGLEKERLVIGYANTKKGRTFRGWMPRAMGRATPKNQETVSIEMILT 149
                                    **************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1140.50
//
Query:       gi|116755012|ref|YP_844130.1|  [L=136]
Description: 30S ribosomal protein S19P [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-25   88.1   0.2    3.6e-25   87.6   0.2    1.2  1  Ribosomal_S19  Ribosomal protein S19
    0.00056   19.1   0.0    0.00057   19.1   0.0    1.1  1  Citrate_synt   Citrate synthase, C-terminal domain
     0.0031   17.7   1.0     0.0043   17.2   1.0    1.2  1  Metal_resist   Heavy-metal resistance


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 !   87.6   0.2   6.1e-29   3.6e-25       3      81 .]      46     119 ..      40     119 .. 0.84

  Alignments for each domain:
  == domain 1  score: 87.6 bits;  conditional E-value: 6.1e-29
                                    HHSS.TTCCCHHHHHHHHHHTS-----EEES-TT-B--GGGTT-EEEEE-SSSEEEEE--CCCTTSBCGGGT-SS----S CS
                  Ribosomal_S19   3 lkkg.pfvqesllkkvrkakaekkkevikthsRdstIlPemvgltvgVynGktfvpveikeemvGhkLgEFspTrkpvkh 81 
                                    l++g +++++++++k+r+      + + kth+Rd ++lPemvg +v+++nGktf +vei +em+Gh+LgE+++Tr +v h
  gi|116755012|ref|YP_844130.1|  46 LRRGlSKEHRKFMAKLRA------RGTAKTHLRDAIVLPEMVGKVVEIHNGKTFQRVEIIPEMIGHYLGEYALTRARVIH 119
                                    555555555555555544......4578************************************************9988 PP

>> Citrate_synt  Citrate synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   9.5e-08   0.00057      13      79 ..       7      62 ..       1     101 [. 0.73

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 9.5e-08
                                   EEEETTTTEEEETTEEHHHHHHHHS-HHHHHHHHHHSS---HHHHHHHHHHHHC.TTS--HHHHHHHH CS
                   Citrate_synt 13 sevdgekgelrYRGydieeLaeekssfeevaylLltgelPtkeelkefkeelae.arklpekvleale 79
                                   s++ ++k+e +YRGy + eLa  k  +ee+a lL     P+  + +++++ l++ +rk    ++ +l+
  gi|116755012|ref|YP_844130.1|  7 SKLPKRKEEFTYRGYRVSELA--KMRLEEIAELL-----PS-RQRRTLRRGLSKeHRK----FMAKLR 62
                                   566556677************..799********.....86.6667777777663444....433333 PP

>> Metal_resist  Heavy-metal resistance
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   1.0   7.2e-07    0.0043      33      83 ..      28      78 ..       9      83 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 7.2e-07
                                   .HHHHHHHS-TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCS CS
                   Metal_resist 33 raellraalgLpaeqraelraalrdharelralrrelraarrelaallaae 83
                                   +++l++ a+ Lp++qr++lr+ l +++r++ a  r+   a+++l+++++ +
  gi|116755012|ref|YP_844130.1| 28 KMRLEEIAELLPSRQRRTLRRGLSKEHRKFMAKLRARGTAKTHLRDAIVLP 78
                                   68999******************************************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); 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: 0.36u 0.28s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1004.85
//
Query:       gi|116755013|ref|YP_844131.1|  [L=236]
Description: 50S ribosomal protein L2P [Methanosaeta thermophila PT]
Scores for complete 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  156.5   0.5    4.5e-45  152.9   0.6    2.0  2  Ribosomal_L2_C  Ribosomal Proteins L2, C-terminal domain
    4.6e-17   61.7   0.7    9.6e-17   60.7   0.0    1.9  2  Ribosomal_L2    Ribosomal Proteins L2, RNA binding domain


Domain annotation for each model (and alignments):
>> Ribosomal_L2_C  Ribosomal Proteins L2, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.042   3.8e+02      45      70 ..      53      78 ..      32      84 .. 0.82
   2 !  152.9   0.6     5e-49   4.5e-45       1     123 [.      89     216 ..      89     223 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.042
                                   SSEEEEEETTS-EEEEETTSBEBES- CS
                 Ribosomal_L2_C 45 gkkvtvklpSgevrkvssecrAtiGv 70
                                      + v+l+ ge+++v ++    iG+
  gi|116755013|ref|YP_844131.1| 53 APVALVRLENGEKQYVLATEGTYIGQ 78
                                   56789***********9999998885 PP

  == domain 2  score: 152.9 bits;  conditional E-value: 5e-49
                                    SSSS-EBSSSS-TTB-BBSE-SSTTS--SSS-SSSB-EEBB-B.SSEEEEEETTS-EEEEETTSBEBES-BS-TTCTT-- CS
                 Ribosomal_L2_C   1 kvGnvlplknipeGtivhnielkpgkggklarsaGtyaqvvakegkkvtvklpSgevrkvssecrAtiGvvsngehkekk 80 
                                    ++Gn+lpl++ipeG+ ++nie+kpg+gg++ar++G y+ +va++   ++v+lpSge+++++ +c AtiGvv++g+++ek+
  gi|116755013|ref|YP_844131.1|  89 QPGNTLPLASIPEGMPICNIESKPGHGGQFARASGVYGILVAHDVGATVVQLPSGEMKWLNPNCLATIGVVAGGGRTEKP 168
                                    58*****************************************99*********************************** PP

                                    --STTHHHHT.....TBS----SSSS-TTTSSS--SSSS--SSSSTEE CS
                 Ribosomal_L2_C  81 lgkAgrkrwl.....grrpkvrGvamnpvdHphGGGeGktksrkapvs 123
                                    l+kAg++ ++      ++p+vrGvamn+vdHp+GGG  ++++r + vs
  gi|116755013|ref|YP_844131.1| 169 LVKAGKSFYKyrskaVKWPRVRGVAMNAVDHPFGGGGRQHPGRPKTVS 216
                                    *********9999999********************855555544443 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 !   60.7   0.0   1.1e-20   9.6e-17       1      76 [.      11      81 ..      11      82 .. 0.94
   2 ?   -3.0   0.1      0.85   7.6e+03       1      15 [.     205     219 ..     205     231 .. 0.76

  Alignments for each domain:
  == domain 1  score: 60.7 bits;  conditional E-value: 1.1e-20
                                   TB-TT.--BSSTT--------EE-B--S---SS--EEEEEEE--TT-SS-EEEEEETTTEEEEEE--SS--SS-EE- CS
                   Ribosomal_L2  1 Grnns.gritvrhrggGhkkkyrlidfkrnkekvkgkVveieyDpgRsApiAlvkyedgekryiiapeglkvGdtvv 76
                                   G++++ +r+++++++      ++ i+f  + + v+g V++i++Dp+R+Ap+Alv +e+gek+y++a+eg  +G+++ 
  gi|116755013|ref|YP_844131.1| 11 GKGTPtYRAPSHRYRA----DIKHIKF--SGDLVRGIVEDIMHDPARTAPVALVRLENGEKQYVLATEGTYIGQEIA 81
                                   99************99....8888999..5677*****************************************996 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.85
                                    TB-TT--BSSTT--- CS
                   Ribosomal_L2   1 Grnnsgritvrhrgg 15 
                                    Gr ++gr ++ +rg+
  gi|116755013|ref|YP_844131.1| 205 GRQHPGRPKTVSRGT 219
                                    788888877777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       228  (0.0127168); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1762.57
//
Query:       gi|116755014|ref|YP_844132.1|  [L=82]
Description: ribosomal protein L25/L23 [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-15   57.8   1.3    3.4e-15   56.2   1.3    1.7  1  Ribosomal_L23  Ribosomal protein L23
  ------ inclusion threshold ------
       0.12   12.4   0.1       0.15   12.1   0.1    1.1  1  WhiA_N         WhiA N-terminal LAGLIDADG-like domain


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 !   56.2   1.3   3.8e-19   3.4e-15       2      61 ..       2      62 ..       1      74 [. 0.88

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 3.8e-19
                                   SEEEE--SHHHHHHHTT.E.EEEEE-SS-THHHHHHHHHHHHT--EEEEEEEEE--EBESS CS
                  Ribosomal_L23  2 vilkPvitEkstklaek.nkyvFeVakdanKleikkaveklFgVkVekVntlnvkgkkkrv 61
                                   +i++P++ Ek t++ +k n++ F V+++a+K++ikk +e l++V+V +++t++ ++ +k+ 
  gi|116755014|ref|YP_844132.1|  2 IIKCPYVPEKVTNMIDKdNTIEFIVDLRATKPQIKKELEDLYDVEVVDIRTMITPRGEKKA 62
                                   899************99889*********************************99877652 PP

>> WhiA_N  WhiA N-terminal LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   1.6e-05      0.15      21      86 .]      16      82 .]      12      82 .] 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.6e-05
                         WhiA_N 21 vngklvlevqtenaaiARriykllkelYgiea.ellvrkknklkknnvYivrvkegveellkelgll 86
                                   ++++ ++e+ ++  a+   i k l++lY++e+ +++++   +  k+ v ++  ++ ++el+ +lgll
  gi|116755014|ref|YP_844132.1| 16 IDKDNTIEFIVDLRATKPQIKKELEDLYDVEVvDIRTMITPRGEKKAVVRLAGDKTANELATRLGLL 82
                                   578899**********************9985256666666666666655555555********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       770  (0.0429472); expected 358.6 (0.02)
Passed bias filter:                      606  (0.0338); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 617.16
//
Query:       gi|116755015|ref|YP_844133.1|  [L=251]
Description: 50S ribosomal protein L4P [Methanosaeta thermophila PT]
Scores for 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-44  149.4   0.1    1.1e-43  149.2   0.1    1.0  1  Ribosomal_L4  Ribosomal protein L4/L1 family


Domain annotation for each model (and alignments):
>> Ribosomal_L4  Ribosomal protein L4/L1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.2   0.1     6e-48   1.1e-43       3     192 .]      18     250 ..      16     250 .. 0.95

  Alignments for each domain:
  == domain 1  score: 149.2 bits;  conditional E-value: 6e-48
                                    E-HHHHSS---HHHHHHHHHHHHHSS-EE-----.-TTTSS---S-SS-SSSSSS---S-TT.......STTSTT---SS CS
                   Ribosomal_L4   3 LspkvFaapirrdlihravvaylanrrqgtastk.arsevsgsgrklwkQKGtGrARvgsir.......spiargGgvah 74 
                                    L p++F++++r+dli+rav+a +anr q+++ +  a++ +s+  r++++  G+G +Rv++i        +p+argG+  h
  gi|116755015|ref|YP_844133.1|  18 L-PAIFDEEYRPDLIKRAVLAAQANRLQPYGPHFyAGMNTSA--RSWGP--GHGVSRVPRIVtgrraaaVPMARGGRASH 92 
                                    5.99******************************9*******..9****..***************************** PP

                                    ---S.EEHHHHHHHHHHHHHHHHHHHHHHHTT-EEEES--.-..-S.........S--HHHHHHHHHHTT-......... CS
                   Ribosomal_L4  75 gpkperdystklnkKvrrlAlrsaLsakakqglllvvdnl.e.ple.........esktkelvellkklgl......... 134
                                    +p p +  s+k+n+K+r +A+rsa++a+ak + + ++++l + +l+         +skt+el+++l + gl         
  gi|116755015|ref|YP_844133.1|  93 PPVPSKVLSEKINEKERIKAIRSAVAATAKPDIVAARGHLfSgELPivvrgeiesISKTSELRRFLMAAGLwddvmrakn 172
                                    **************************************776777778899***9**************888888888888 PP

                                    .................TTSSEEEEESSSSCHHHHHHTT-TTEEEEESTT--CHHHHHSSE....EEEEHHHHHHHHHH CS
                   Ribosomal_L4 135 .................ksksvLivvsekdenlvlaarnlpgvevieveslnvydllkadk....vvitksavekleek 192
                                                     +++s+Liv+ + d+++ +aarnlpgv+ +++++ln++ l+++++    +v+++  ++ lee+
  gi|116755015|ref|YP_844133.1| 173 grkvragkgkirgrrfrQPRSILIVAAA-DNGIGRAARNLPGVDFVTADRLNAELLAPGTHagrlTVWSEPSLKVLEER 250
                                    88888899999999998899******97.99*********************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); 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 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1828.20
//
Query:       gi|116755016|ref|YP_844134.1|  [L=335]
Description: 50S ribosomal protein L3P [Methanosaeta thermophila PT]
Scores for 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-92  307.9   0.2    5.1e-91  305.4   0.2    1.8  1  Ribosomal_L3  Ribosomal protein L3


Domain annotation for each model (and alignments):
>> Ribosomal_L3  Ribosomal protein L3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  305.4   0.2   2.8e-95   5.1e-91       7     368 ..       5     333 ..       1     334 [. 0.92

  Alignments for each domain:
  == domain 1  score: 305.4 bits;  conditional E-value: 2.8e-95
                                    XXXXSSXCCCTTXSBXSXSSXXXSX.XXSBTTTTTXBSEEEEEEEEEEEEEEECHHTTSCCCCCEEEEEEEEEEC--EEE CS
                   Ribosomal_L3   7 eaprhgslGflprkRaerergkvksfPkddtskpvkltaflGyKaGmthiVrevdkpgskldkkevveavtvvetppmvi 86 
                                    ++pr+gsl f+prkRa++e+++++s+ +d++     + +f+GyKaGmth++  +d+p s ++++e+ ++vtvve ppm +
  gi|116755016|ref|YP_844134.1|   5 HRPRRGSLAFSPRKRAKSEVPRIRSWVADERA---GMAGFAGYKAGMTHVIMIDDRPRSLTEGMEISVPVTVVEVPPMSV 81 
                                    78***************************999...9******************************************** PP

                                    EEEEEEEEETTEEEEEEEEESSS.SHHHHCCCSTSTTTSSSSSSHCCCCHCSSCCCCCCHHHHHHHHHHSCSCEEEEEEE CS
                   Ribosomal_L3  87 vgvvgyvetprGlrslktvwaehlseevkrrlyknwykskkkaftkyskkyeskdvkklieadleeikkeasvvrviaht 166
                                    ++++ y+  + G+r+  + wae+ls++++r +               + +  ++   +++e d+e+  +e + +rv+aht
  gi|116755016|ref|YP_844134.1|  82 AALRVYEPYNGGIRPAGELWAENLSQDLERAI---------------TIP--KARRGASLE-DIESRVDELCEIRVLAHT 143
                                    ******************************99...............222..244555555.67777788999******* PP

                                    ECCCSS-SCCSSHHEEEEECHCSCHHHHHHHHHHCCTCEEECCCCS-TTSEEEEEEEE---EEE-HHHHCT----STTTS CS
                   Ribosomal_L3 167 virktkslaqKkahllEiqvngGtiaekldfarealektvavaavFrqgeliDvigvtkGkGfeGvvkRWgvkklprkth 246
                                      r ++++ +K ++++Ei v g ++ e+l  a+  l  +vav+++F+ ge+iDv +vtkGkG++G+vkRWg+  ++rk+ 
  gi|116755016|ref|YP_844134.1| 144 NPRLLTGVPKKVPDIMEIPVTGRSVEEQLKAAEGLLGSQVAVSNIFNVGEWIDVSAVTKGKGTQGPVKRWGIMLQKRKHS 223
                                    ******************************************************************************** PP

                                    SS..SSS-S-SS-SSSSS--TTS--SEEESCCEEEEEEEEEEEEETTTSSTTTSSTTT.SS..SS.TTTCTTCB..TSCE CS
                   Ribosomal_L3 247 rg..lRkvaaigawdparVsstvaraGqkGyhhRtelnkkiyrigkgedaknastefdltekeitPmGGfvhyGevkndf 324
                                    r+  lR+v+++g+w+par+s+ v++ Gq+Gyh+Rte+nk+i+ ig+              + +itP+GGfv yG+v+n++
  gi|116755016|ref|YP_844134.1| 224 RTgkLRHVGNLGPWHPARISWRVPQLGQTGYHQRTEFNKRIMAIGT-------------NGTDITPDGGFVGYGVVRNEY 290
                                    **9*******************************************.............5679***************** PP

                                    EEEES--SSSTTEEEEEEE-SSGGGS.CCCSS-EEEEEE-TTCTS CS
                   Ribosomal_L3 325 ilvkGsvpGpkkrlvklrkslltqts.rkaeeevslkfidtaskf 368
                                    +l+kGsvpGp krlv++r+++++      + +++   ++++ sk+
  gi|116755016|ref|YP_844134.1| 291 MLIKGSVPGPVKRLVRMRRAIRPGAAfAPKAPQI--LYVSKESKQ 333
                                    *********************9976522223333..466666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2492.49
//
Query:       gi|116755017|ref|YP_844135.1|  [L=277]
Description: hypothetical protein Mthe_1729 [Methanosaeta thermophila PT]
Scores for 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-56  189.6   0.0      1e-55  189.3   0.0    1.1  1  Methyltrn_RNA_3  Putative RNA methyltransferase
    4.4e-05   23.7   0.0       0.06   13.5   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 !  189.3   0.0   1.2e-59     1e-55       3     286 .]       8     270 ..       6     270 .. 0.91

  Alignments for each domain:
  == domain 1  score: 189.3 bits;  conditional E-value: 1.2e-59
                Methyltrn_RNA_3   3 siaiPssiisnaqsleqktylagqIARaaaiFnVdeivvfddseseeekkekpseflarlLqYletPpYLrkelFplhke 82 
                                    si+iPss + +  +l+++t+++g IARaaa+F++d+ivv++d+e +      +s f++++L+Y+etP+YLrk lFp ++e
  gi|116755017|ref|YP_844135.1|   8 SILIPSSYTMETADLRLRTAKVGLIARAAAVFRIDRIVVYRDDEFD------DSRFISTVLRYAETPQYLRKLLFPRMRE 81 
                                    9*****************************************9966......579************************* PP

                Methyltrn_RNA_3  83 lkyaglLppldaphhl....rsse..egeyreGvvvekskekkskkklVniGlkkevklelkqevpegtRVtVklssees 156
                                    l++ag+Lppl++ hh     + s    ge+r G+vve+  ++     +V++Gl+++v l++k++ ++g R  V++ s ++
  gi|116755017|ref|YP_844135.1|  82 LRHAGVLPPLRTAHHPvgsrS-STlkVGEIRVGMVVESVGSDGG--AWVEVGLDRPVPLKSKRRFQKGQRLNVRIFSLSP 158
                                    ****************99952.444589********99776555..6****************************9999* PP

                Methyltrn_RNA_3 157 veakvVspsepreeaglywGYsVrlakslsavftespfeggydlsigtsergekveeklaelekkkefkhllivfGg.vr 235
                                      a+ V+ se       ywGY+  +++s ++++         +++++ts++g++v+  l +  +++  + l +vfG+  r
  gi|116755017|ref|YP_844135.1| 159 LAAEPVDRSEI----PGYWGYETIVVDSAEEYLRSR-----DEFVVATSRKGTPVSCDLLNHIERSGSRGLAVVFGSpAR 229
                                    *******9998....59************9999985.....789999********9999999888889*********999 PP

                Methyltrn_RNA_3 236 gleaaleadeelklegekaeelFdlwlntvpnqgsrtirtEEavliaLalL 286
                                    g++a+l ++          e    +++nt+p+qg++t+r+EEav+ +LalL
  gi|116755017|ref|YP_844135.1| 230 GVDAFLSRE--------MLER--CCVINTIPHQGTETVRVEEAVISTLALL 270
                                    999999444........2222..379**********************987 PP

>> SpoU_methylase  SpoU rRNA Methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0   0.00035       3.1      15      47 ..      29      59 ..      26      75 .. 0.80
   2 !   13.5   0.0   6.7e-06      0.06      59     126 ..     178     253 ..     169     257 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00035
                                   HHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHH CS
                 SpoU_methylase 15 lGaiaRtakafgaselvlvkprsadllnpeakr 47
                                   +G iaR+a++f ++++v+ +++++  ++++++ 
  gi|116755017|ref|YP_844135.1| 29 VGLIARAAAVFRIDRIVVYRDDEF--DDSRFIS 59
                                   799***************987776..5555555 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 6.7e-06
                                    EEESSHHHHHHHHCCCTEEEEEESTT-SEGC.....CSHHH....TTEEEEEEBTTTB....S-HHHHCTSSEEEE---- CS
                 SpoU_methylase  59 kvvdsleealkelkeegfalvatslkgksls.....eidlk....ekvalvfGnEdkG....lsnelleladrlvkIpms 125
                                     vvds ee+l+  +e    +vats+kg+++s      i  +    +  a+vfG+  +G    ls+e+le++  + +Ip +
  gi|116755017|ref|YP_844135.1| 178 IVVDSAEEYLRSRDEF---VVATSRKGTPVScdllnHI--ErsgsRGLAVVFGSPARGvdafLSREMLERCCVINTIPHQ 252
                                    6788999988886665...9*********999554422..13455*************5555579999***999999987 PP

                                    T CS
                 SpoU_methylase 126 g 126
                                    g
  gi|116755017|ref|YP_844135.1| 253 G 253
                                    6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       239  (0.0133304); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); 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 0.22s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 2291.76
//
Query:       gi|116755018|ref|YP_844136.1|  [L=265]
Description: band 7 protein [Methanosaeta thermophila PT]
Scores for complete 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-36  125.2   3.5    3.8e-36  124.7   3.5    1.2  1  Band_7        SPFH domain / Band 7 family
    2.3e-05   24.2   0.1    3.9e-05   23.5   0.1    1.6  1  Band_7_1      SPFH domain-Band 7 family
  ------ inclusion threshold ------
       0.07   12.4   0.1      0.094   12.0   0.1    1.2  1  Amidohydro_1  Amidohydrolase family


Domain annotation for each model (and alignments):
>> Band_7  SPFH domain / Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.7   3.5   6.4e-40   3.8e-36       2     177 ..      25     194 ..      24     204 .. 0.97

  Alignments for each domain:
  == domain 1  score: 124.7 bits;  conditional E-value: 6.4e-40
                         Band_7   2 iieegevgvvvrfGklsrvlepGlhfilPfgrsvtvvsvrvqtldvsvsltvptkDglpvtidvtviyrvpddapklvaa 81 
                                    i++e e+ v++r G++s+v++pGl fi+P++++v ++++rv+t+dv++ + v+t+D++ v++d++++yrv  d++k+v +
  gi|116755018|ref|YP_844136.1|  25 IVREYERVVIFRLGRYSGVKGPGLFFIIPIIDRVQLIDLRVVTIDVQK-QVVITRDNVTVDVDAVIYYRV-MDPAKAVIQ 102
                                    799*********************************************.*********************.********* PP

                         Band_7  82 veresanldnlirrvlesalrevisemtleellsnreelaeelknelneqlrkyGvevldvritdidpppevaqalaakq 161
                                    v    +n++     + + +lr v+++ +l++lls+reel+ +l++ l    + +G+ v+ v+++d+++p+   +a+a+ +
  gi|116755018|ref|YP_844136.1| 103 V----ENYRVATALLSQTTLRDVLGQIDLDDLLSKREELNLKLQAILDRHTDPWGIKVTAVTLRDVSLPESMMRAIAKQA 178
                                    *....*************************************************************************** PP

                         Band_7 162 aaeaeaqaeiaraeae 177
                                    +ae+e++ +i  a +e
  gi|116755018|ref|YP_844136.1| 179 EAEREKRSRIILADGE 194
                                    ******9888877655 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 !   23.5   0.1   6.6e-09   3.9e-05     145     209 ..     118     180 ..      54     182 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 6.6e-09
                       Band_7_1 145 lsdvlaeskipvldlaakseelaeklkealkeelaeyGlelekleienislpeevekaldkrasm 209
                                    l dvl+  +i + dl +k eel  kl+  l+ + +  G+++++++++++slpe++ +a+ k+a++
  gi|116755018|ref|YP_844136.1| 118 LRDVLG--QIDLDDLLSKREELNLKLQAILDRHTDPWGIKVTAVTLRDVSLPESMMRAIAKQAEA 180
                                    555554..578889***********************************************9976 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   1.6e-05     0.094      88     167 ..     173     256 ..     141     264 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.6e-05
                                    S....GCCCSHHHHHHHHHHHHHHHHHHCTTTCEE.EEEEECGTCCSHHHHHHHHHHHHHHHTTEEEEEE...TSSCHHH CS
                   Amidohydro_1  88 r....gsaetskasreklkagaaetikgkadgvvk.valapheapafsdeelkealkeakkrdlpvaiHa...letkgev 159
                                          +ae +k sr  l++g+    ++ ++ + + +al+ h++ a++  el+ +++ a++r+l v+++    ++t+g+v
  gi|116755018|ref|YP_844136.1| 173 AiakqAEAEREKRSRIILADGE----LQASKTMAEaAALYQHAPIAIKLRELQTLAEIARERNLIVVTSGadvGSTTGIV 248
                                    2442255555555555566665....6677777788*********************************98888888888 PP

                                    HHHHHHHT CS
                   Amidohydro_1 160 edaeaafg 167
                                    + +++a  
  gi|116755018|ref|YP_844136.1| 249 AGIQRAVE 256
                                    77777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       946  (0.0527637); expected 358.6 (0.02)
Passed bias filter:                      587  (0.0327403); 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 0.23s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2055.57
//
Query:       gi|116755019|ref|YP_844137.1|  [L=421]
Description: hypothetical protein Mthe_1731 [Methanosaeta thermophila PT]
Scores for complete 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-15   55.7   0.0    2.1e-14   53.7   0.0    2.1  1  NfeD          NfeD-like C-terminal, partner-binding
    1.9e-07   31.2   0.1    3.3e-07   30.4   0.1    1.3  1  CLP_protease  Clp protease
  ------ inclusion threshold ------
      0.031   13.6   0.1       0.23   10.7   0.1    2.0  1  ECH_1         Enoyl-CoA hydratase/isomerase
      0.075   13.0   0.1       0.13   12.2   0.1    1.4  1  DUF1778       Protein of unknown function (DUF1778)
        2.9    8.1   6.5        6.2    7.0   6.5    1.5  1  VKOR          Vitamin K epoxide reductase family


Domain annotation for each model (and alignments):
>> NfeD  NfeD-like C-terminal, partner-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.7   0.0   5.8e-18   2.1e-14       6      84 .]     345     419 ..     337     419 .. 0.82

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 5.8e-18
                                    XXXXXXXXXXXS---SSS--S.S---GGTTSEEEEEE-BS.-EEEEETTEEEEEE-.SSB-TT-EEEEEEE-SSSEEEEE CS
                           NfeD   6 svlllvllrplllkklkkkekktnaealiGkegvvledig.tGrvkvdGeeWsarsegeiekgerVrVveveGltliVep 84 
                                    +  + +++++++  ++ +       e+  G+ ++++e+++ +G v ++Ge+W+a++++ iekge+V+Vv+++G tl+V++
  gi|116755019|ref|YP_844137.1| 345 AGFFAFAVYKIAEARR-R----PTFEETAGQYAETIETLDpKGYVIFRGEYWKAEADERIEKGETVEVVGISGQTLKVRK 419
                                    3445566666666655.2....3446799**********668**************999*******************98 PP

>> CLP_protease  Clp protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.1   9.1e-11   3.3e-07      29     178 ..      35     183 ..      21     186 .. 0.85

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 9.1e-11
                                    HHHHHHHHHHHHHHH-SSS-EEEEEEE--B-HHHHHHHHHHHHHSSS-EEEEEE..EE.EETHHHHHHHTS-TTGEEEET CS
                   CLP_protease  29 vankiiaqLllLeaedpdkdillyinspGGsvtaglaIydtmqyikpdvsticl..Gl.aaSmgslllaagekgkRfalp 105
                                    + + + + + ++e+++ d  + l++++pGG ++++l+I  +++  + +v+ ++   G  a S+g+++l++ +    ++ p
  gi|116755019|ref|YP_844137.1|  35 SDDLVKTAIGYAESSNAD-ALILMLDTPGGGLSETLEIIAVVERTEIPVVGYVSpsGAkAWSAGTMILISTDIA--AMAP 111
                                    455555667788777776.67788*********************9999988875664388*************..799* PP

                                    TEEEEES-TEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHCSTEEEEHHHHHHHTSSSEE CS
                   CLP_protease 106 narimihqPlggaqgqasdieieaeellkikerlneilakhtgqslekiekdldrdtflsaeeAveyGLidev 178
                                    n+ i   qP++ +   a++  ++++  + i + ++e  ak  g+++   ++ +  +  l+aeeA+eyG i++v
  gi|116755019|ref|YP_844137.1| 112 NTIIGSAQPVRLLPTGATEPVNDTKTTNAIVALIEE-KAKIHGRNRTAAREFVLSNLNLNAEEALEYGVIEHV 183
                                    *******************99999999999877666.567778889999999999****************99 PP

>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   6.5e-05      0.23     146     177 ..     156     188 ..      65     199 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 6.5e-05
                                    HHHHHHHHHHT-EEEHHHHHHCTSSSEEESG.G CS
                          ECH_1 146 kskAeeilllgkkisaqealkvGlvdkvvpe.e 177
                                    + +A+e +l   +++a+eal+ G++++v p+  
  gi|116755019|ref|YP_844137.1| 156 RTAAREFVLSNLNLNAEEALEYGVIEHVSPDiS 188
                                    45799************************9844 PP

>> DUF1778  Protein of unknown function (DUF1778)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   3.7e-05      0.13       4      59 ..     135     192 ..     134     206 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.7e-05
                        DUF1778   4 lRispeakeliqrAAalsgktlt...dFvleaaleaAekviedherieLseedfqafva 59 
                                    +++++ + +li++ A++ g+++t   +Fvl++   +Ae+++e   + ++s+ d + +++
  gi|116755019|ref|YP_844137.1| 135 TKTTNAIVALIEEKAKIHGRNRTaarEFVLSNLNLNAEEALEYGVIEHVSP-DISSLLK 192
                                    68999999***************6666*************99655444444.4444555 PP

>> VKOR  Vitamin K epoxide reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   6.5    0.0017       6.2      48     116 ..     241     314 ..     236     319 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0017
                                    TSEETTEEHHHHHHHHHHHHHH.HHHS-.....HHHHHHHHHHHHHHHHHHHHHHHHTTS----HHHHHHHHHH CS
                           VKOR  48 yasilgvplsllGllayalvll.lalapl....lwlllllgslagvvfslyLiylslfvigalCpyClvsavls 116
                                    ya i+g++++ lG+ ++ ++++ l+l++     +  +l+l++l + ++ + L    + v+g   ++C+v   l 
  gi|116755019|ref|YP_844137.1| 241 YALIFGISNPGLGAEVFGVIAIaLGLIGQgfdvNIGALFLIILGMGLILAELHTHAMGVLGVAGLICIVLGTLL 314
                                    899**************9998834555559998777788888899999999*9**************9976655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       718  (0.0400469); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 3046.76
//
Query:       gi|116755020|ref|YP_844138.1|  [L=289]
Description: acetylglutamate kinase [Methanosaeta thermophila PT]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.3e-47  161.6   1.8    2.7e-47  161.4   1.8    1.0  1  AA_kinase  Amino acid kinase family
  ------ inclusion threshold ------
       0.17   12.4   0.0       0.28   11.7   0.0    1.3  1  XPG_N      XPG 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 !  161.4   1.8     3e-51   2.7e-47       2     241 .]      21     264 ..      20     264 .. 0.97

  Alignments for each domain:
  == domain 1  score: 161.4 bits;  conditional E-value: 3e-51
                                    EEEEEE-TTCCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC....E..HHHHHHHHHHH CS
                      AA_kinase   2 rvVvKlGGssltdkeeaslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaaglrstleeagevatrda 81 
                                    + V+K+GGs++t+ e   l++++++i  lk  g+++vvVhGgg+ + + +++  g ++++ a glr+t+ e++e+a++++
  gi|116755020|ref|YP_844138.1|  21 IMVIKIGGSIMTNHEI--LENFIQDIILLKYIGIHPVVVHGGGPEISETMKR-LGKKAEFVA-GLRVTDRETLEIARMVL 96 
                                    68**************..**********************************.*********.***************** PP

                                    HHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE.............HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEE CS
                      AA_kinase  82 laslgerlvaallaaglpavglsaaaldateagr...........degsdgnvesvdaeaieelleagvvpvltgfigld 150
                                    l+ ++ +lv+ + ++g + +gls+++  ++ a++           d g++g+ve+++ e ++    +g++pv+++++ +d
  gi|116755020|ref|YP_844138.1|  97 LGNINAELVSLIGKHGGKGIGLSGKDGMLIVARKkppmnvngenvDLGYVGEVEEINPEILMITAGKGYIPVISPIA-ID 175
                                    ****************************9999999****************************************76.** PP

                                    TTTEEEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHH.CSSS.TTTHHHHCHHHHHHH CS
                      AA_kinase 151 eegelgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaee.saselatgGmkvkhpaalaa 229
                                    ++g ++++++Dt+a ++A+al+A+kli +tdV+GV   dp+++  +r++++ s +e++  ++ + ++gGm++k++a+++a
  gi|116755020|ref|YP_844138.1| 176 RDGNSLNVNADTVAGAVAVALRAKKLISITDVEGVR-EDPDDP--GRVISQFSPSEFQRlVERGIIKGGMIPKVEACVRA 252
                                    ****99*****************************5.677777..7********************************** PP

                                    HHCTT-EEEEEE CS
                      AA_kinase 230 arrggipvvItn 241
                                    ++rg+ +++I++
  gi|116755020|ref|YP_844138.1| 253 VERGVEKAHIID 264
                                    **********86 PP

>> XPG_N  XPG N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.1e-05      0.28      52      84 ..      31      63 ..       3      76 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.1e-05
                                   -BS-HHHHHHHHHHHHHHHTTEEEEEEE--S-- CS
                          XPG_N 52 lentshlmglfsrllrlldfgikPifVFdgkap 84
                                   ++n + l  ++++++ l++ gi+P++V  g++ 
  gi|116755020|ref|YP_844138.1| 31 MTNHEILENFIQDIILLKYIGIHPVVVHGGGPE 63
                                   445678999******************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 2238.57
//
Query:       gi|116755021|ref|YP_844139.1|  [L=567]
Description: pyruvate carboxylase subunit B [Methanosaeta thermophila PT]
Scores for complete 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-58  195.5   0.0    1.3e-57  194.8   0.0    1.3  1  PYC_OADA         Conserved carboxylase domain
    2.6e-48  164.9   0.0    3.5e-48  164.5   0.0    1.2  1  HMGL-like        HMGL-like
    5.3e-21   74.2   1.9    1.1e-20   73.2   1.9    1.6  1  Biotin_lipoyl    Biotin-requiring enzyme
    6.4e-11   41.9   0.2    0.00058   19.6   0.2    2.8  2  Biotin_lipoyl_2  Biotin-lipoyl like
    1.2e-05   25.2   0.2    6.6e-05   22.8   0.1    2.1  2  RnfC_N           RnfC Barrel sandwich hybrid domain
    6.6e-05   22.2   0.3      0.011   14.9   0.0    2.5  2  HlyD_D23         Barrel-sandwich domain of CusB or HlyD membr
    0.00034   21.3   0.1      0.064   14.0   0.0    2.7  2  HlyD_3           HlyD family secretion protein
     0.0015   18.4   2.0     0.0023   17.8   0.2    2.3  3  GCV_H            Glycine cleavage H-protein
  ------ inclusion threshold ------
      0.036   12.3   0.1          1    7.5   0.0    2.1  2  Fusion_gly       Fusion glycoprotein F0
       0.05   13.8   0.5          3    8.1   0.1    2.9  3  Peptidase_M23    Peptidase family M23
      0.057   13.4   0.0       0.21   11.6   0.0    1.9  2  ADH_zinc_N       Zinc-binding dehydrogenase
      0.068   13.1   1.0       0.17   11.9   0.2    2.1  2  DUF2118          Uncharacterized protein conserved in archaea
       0.12   12.5   0.5       0.51   10.5   0.3    2.0  2  E3_UbLigase_RBR  E3 Ubiquitin Ligase RBR C-terminal domain
       0.17   12.0   0.1        6.7    6.9   0.0    2.5  2  QRPTase_N        Quinolinate phosphoribosyl transferase, N-te


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 !  194.8   0.0   9.9e-61   1.3e-57       1     195 [.     292     479 ..     292     481 .. 0.95

  Alignments for each domain:
  == domain 1  score: 194.8 bits;  conditional E-value: 9.9e-61
                                    HHCCT--CCHHHHHHHHHHHTT-GGGHHHHHHHHHHHHHHTT----STTHHHHHHHHHHHHHHH........TS.TTSS- CS
                       PYC_OADA   1 VykheiPGGqltnlkeqakeqglldkfeevlkeyaevnkllGdivkVTPsSkvvgdlAvfnvlnklteedvleegrykdi 80 
                                    V+++++PGG+l+nl +q+ eq ++d+++evl+e+++v+++lG++++VTP+S++vg++Av+nvl+        +e ryk +
  gi|116755021|ref|YP_844139.1| 292 VLVYQVPGGMLSNLVSQLIEQKAIDRYDEVLAEIPRVRADLGYPPLVTPTSQIVGTQAVLNVLT--------GE-RYKVV 362
                                    789*************************************************************........86.***** PP

                                    -HHHHHHHTTSS---SS---HHHHHHHHT.-----S-GGGG---.-HHHHHHHTTTTS..SSHHHHHHHHHSHHHHHHHH CS
                       PYC_OADA  81 pdsvvdllkGelGkppggfpeelvkkvlkgeepitsrpadslepedleklrkeleeka..kteedvlsyalypkvaekfl 158
                                    p++v+d++kG +G+pp+ ++++++ k+l++eepit+rpad+l+p ++e++ +e+++    k+eed+l+yalyp++a+kfl
  gi|116755021|ref|YP_844139.1| 363 PKEVRDYVKGLYGRPPADIDPKIRMKILEDEEPITVRPADLLPP-EYEAAVREVDALGlaKKEEDYLTYALYPQIAIKFL 441
                                    ********************************************.***********664479****************** PP

                                    HHHHHHHHHH..CTTTS.......-SEEEEEETTEEEE CS
                       PYC_OADA 159 kfreeygdvsvlptkvffeglk.vgeeveveveggkyl 195
                                    k +++ + + + +tk+  + +  ++  ++vev+g+ y 
  gi|116755021|ref|YP_844139.1| 442 KGQATEEPLVKKDTKAAAAVKGgAPVAFNVEVDGEAYI 479
                                    ****9999999999999988877999********9986 PP

>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.5   0.0   2.7e-51   3.5e-48       1     263 [.       3     269 ..       3     270 .. 0.96

  Alignments for each domain:
  == domain 1  score: 164.5 bits;  conditional E-value: 2.7e-51
                                    B-EEEE-TTTHHHHTS.SS---HHHHHHHHHHHHHHT-SEE--........TSGGGT.THHHHHHHS---TT-B...... CS
                      HMGL-like   1 kvkivdttLRDGeqal.kaalsveeklaiakaLdeagvdeiEv........gfpaaseddfevvraiakavkkar..... 66 
                                    +vk+++t+ RD++q+l ++++++ ++l+ia+ Ld++g+ ++Ev        +++ + ed++e++ra++ a+++++     
  gi|116755021|ref|YP_844139.1|   3 RVKLTETVFRDAHQSLlATRMRTRDMLPIAELLDQVGYFSMEVwggatfdtCIRYLNEDPWERLRALKLAMPNTQmqmll 82 
                                    589************99*********************************************************556666 PP

                                    .....--EE-SSHHHHHHHHH....TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-E..TTT-BTTT CS
                      HMGL-like  67 ....ilalvrarekdikaavealkgagakrvhvfiatselhlkaklkkdreevakkaeeavkaarslgkd..velsleda 140
                                        +++++++++++++++ve++ ++g++++++f+a+++              ++++e+ ++ a+++g++   ++ ++ +
  gi|116755021|ref|YP_844139.1|  83 rgqnLVGYRHYADDVVEKFVEKAAKNGVDVFRIFDAVND--------------IRNMEKSIRVAKRMGAHvqGAVCYTIS 148
                                    6778***********************************..............*****************556678999* PP

                                    BS--HHHHHHHHHHHHHHT-SEEEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHHHHTT--EE CS
                      HMGL-like 141 srtdleflaevveaaeeaGatriniaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaAveaGadrv 220
                                    + +++e+ +e + +++e+ +++i i+D+ G+++P+ a el++ +k++v+  +++ +H+H + GlA +  laAveaGad +
  gi|116755021|ref|YP_844139.1| 149 PVHTIEQFTEFTVRLAEMDCDSICIKDMAGLISPHYASELVRSIKREVN--LPVCLHTHCTAGLAHMSYLAAVEAGADIL 226
                                    *************************************************..***************************** PP

                                    EEBTTS--SSBBB-BHHHHHHHHHHTT-B----HHHHHHHHHH CS
                      HMGL-like 221 dgtvnGlGeraGnaaleelvaalealgvdtgldlqklrsiaal 263
                                    d++++ l++++  +++e +vaa + +++dtgldl+ l++i+++
  gi|116755021|ref|YP_844139.1| 227 DTAISPLSGGSSQPSTESVVAAFRETPYDTGLDLELLTEIKRY 269
                                    **************************************99875 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.2   1.9   8.6e-24   1.1e-20       3      73 .]     501     566 ..     499     566 .. 0.98

  Alignments for each domain:
  == domain 1  score: 73.2 bits;  conditional E-value: 8.6e-24
                                    EEESSSEEEEEE.ECSESSSTTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESSTTTEEE-TTCEEEEE CS
                  Biotin_lipoyl   3 iksPmiGesveegvvevlvkvGdkVkagqvlaeveamKmemeieapkaGvvkeilvkeGdtvevgdllaki 73 
                                    +++Pm G++++     ++vk+Gd V++g+v+a++eamKme+++ a+ +G+vkei+++ G+tv+ gd+l+ i
  gi|116755021|ref|YP_844139.1| 501 VTVPMQGVLIR-----YKVKKGDRVNKGDVVAILEAMKMENPVYADRSGTVKEIYIETGKTVSPGDVLMSI 566
                                    79*********.....****************************************************987 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.2   4.6e-07   0.00058       6      37 ..     502     533 ..     499     538 .. 0.86
   2 !   19.5   0.0   4.9e-07   0.00063       7      33 ..     540     566 ..     533     567 .] 0.89

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 4.6e-07
                Biotin_lipoyl_2   6 aapvsGrVaqlnVkdGqrVkaGdvLaelDsra 37 
                                    + p  G++ +  Vk G+rV++Gdv a+l+  +
  gi|116755021|ref|YP_844139.1| 502 TVPMQGVLIRYKVKKGDRVNKGDVVAILEAMK 533
                                    567789999*******************9766 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 4.9e-07
                Biotin_lipoyl_2   7 apvsGrVaqlnVkdGqrVkaGdvLael 33 
                                    a+ sG+V++++++ G+ V  GdvL+ +
  gi|116755021|ref|YP_844139.1| 540 ADRSGTVKEIYIETGKTVSPGDVLMSI 566
                                    667**********************98 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 ?   -1.3   0.0       1.6   2.1e+03      30      51 ..     337     358 ..     330     361 .. 0.87
   2 !   22.8   0.1   5.1e-08   6.6e-05      40      82 ..     508     551 ..     488     564 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.6
                         RnfC_N  30 lvlplsqhiGapakplvkvgdk 51 
                                    lv p sq +G++a + v  g++
  gi|116755021|ref|YP_844139.1| 337 LVTPTSQIVGTQAVLNVLTGER 358
                                    7899*********999988876 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 5.1e-08
                         RnfC_N  40 apakplvkvgdkVlkGqkiaeaeg.fvsapvhasvsGtVkaiek 82 
                                       +  vk+gd+V+kG+++a  e+  +  pv+a  sGtVk+i  
  gi|116755021|ref|YP_844139.1| 508 VLIRYKVKKGDRVNKGDVVAILEAmKMENPVYADRSGTVKEIYI 551
                                    556677**************99886679*************965 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 !    5.4   0.1    0.0073       9.3     108     138 ..     498     528 ..     485     534 .. 0.77
   2 !   14.9   0.0   8.8e-06     0.011     106     139 ..     533     566 ..     526     567 .] 0.90

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0073
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       HlyD_D23 108 tvtvkapisGvVteknvreGqyvqpgdtlft 138
                                    +  v+ p++Gv ++ +v +G++v++gd+++ 
  gi|116755021|ref|YP_844139.1| 498 RDGVTVPMQGVLIRYKVKKGDRVNKGDVVAI 528
                                    5557789999999999999999999998765 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 8.8e-06
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       HlyD_D23 106 qktvtvkapisGvVteknvreGqyvqpgdtlfti 139
                                    + + +v+a +sG+V e  + +G++v+pgd+l++i
  gi|116755021|ref|YP_844139.1| 533 KMENPVYADRSGTVKEIYIETGKTVSPGDVLMSI 566
                                    55679***************************99 PP

>> HlyD_3  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1     0.045        57       2      28 ..     501     527 ..     500     533 .. 0.91
   2 !   14.0   0.0     5e-05     0.064       2      30 ..     538     566 ..     537     567 .] 0.95

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.045
                         HlyD_3   2 lrApvdGvvvelnveegevvqagdell 28 
                                    +++p +Gv+   +v++g+ v++gd+++
  gi|116755021|ref|YP_844139.1| 501 VTVPMQGVLIRYKVKKGDRVNKGDVVA 527
                                    789**********************98 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 5e-05
                         HlyD_3   2 lrApvdGvvvelnveegevvqagdellei 30 
                                    ++A ++G+v+e+ +e g+ v++gd+l++i
  gi|116755021|ref|YP_844139.1| 538 VYADRSGTVKEIYIETGKTVSPGDVLMSI 566
                                    789************************99 PP

>> GCV_H  Glycine cleavage H-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       7.9     1e+04      84     103 ..      57      76 ..      56      87 .. 0.67
   2 ?   -1.8   0.0       2.1   2.7e+03      27      49 ..     471     493 ..     451     497 .. 0.74
   3 !   17.8   0.2   1.8e-06    0.0023      33      74 ..     509     549 ..     500     558 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 7.9
                                    HHHH-TTTTT--EEEEES-G CS
                          GCV_H  84 liNkdpyeegWliklklsnl 103
                                    ++N+dp+e    +kl + n+
  gi|116755021|ref|YP_844139.1|  57 YLNEDPWERLRALKLAMPNT 76 
                                    68999999877777766653 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.1
                                    HHHH-SEEEEE---TT-EE-TT- CS
                          GCV_H  27 qeelgdvvfvelpevgtkvkkge 49 
                                     e  g+ + v++ +vg ++++ +
  gi|116755021|ref|YP_844139.1| 471 VEVDGEAYIVKVAPVGMSIQESQ 493
                                    45567778888888888887765 PP

  == domain 3  score: 17.8 bits;  conditional E-value: 1.8e-06
                                    EEEEE---TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEEE CS
                          GCV_H  33 vvfvelpevgtkvkkgeslaavEsvKaasevyapvsGevvev 74 
                                    ++ ++++ +g++v+kg+ +a++E+ K+  +vya+ sG+v e+
  gi|116755021|ref|YP_844139.1| 509 LIRYKVK-KGDRVNKGDVVAILEAMKMENPVYADRSGTVKEI 549
                                    4555554.79*****************************987 PP

>> Fusion_gly  Fusion glycoprotein F0
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.026        33     109     175 ..     109     173 ..     105     198 .. 0.86
   2 ?    7.5   0.0    0.0008         1     174     224 ..     259     309 ..     256     318 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.026
                                    HHHHHHHHHHHHHHHHHHHHHHTHHSSEEEECHCCSHCEEEEETTHHHHHHTTCCCTTTSHHHHHHH CS
                     Fusion_gly 109 giAlakalknaeeiaklkeslektnkAveklqngvselvlavnalqdyintellpainqlsCdiadl 175
                                    g+ + +   + ++i ++ +s++ + +   ++q +v  +++ v+++ ++  te++  + +++Cd + +
  gi|116755021|ref|YP_844139.1| 109 GVDVFRIFDAVNDIRNMEKSIRVAKRMGAHVQGAVCYTISPVHTIEQF--TEFTVRLAEMDCDSICI 173
                                    5666667778899***********************************..799999******98755 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0008
                                    HHHHHHHHHHHHHHHHHHHSTTSS-TTTS-CECCCCC.CCCTT-HHHHHHHC CS
                     Fusion_gly 174 dlklaieltqylseLltvFgpnlgnpvekplsiqals.sllggeleallskl 224
                                    dl+l +e+++y+ +L+ v+ p ++ p+ +++ +++l  ++ gg+l +l+s+l
  gi|116755021|ref|YP_844139.1| 259 DLELLTEIKRYFDKLMDVYAPVFN-PIAAKIDTNVLVyQVPGGMLSNLVSQL 309
                                    789999***************998.******999886167799999999987 PP

>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       3.9     5e+03       6      38 ..     274     307 ..     270     323 .. 0.69
   2 ?    8.1   0.1    0.0023         3      52      73 ..     509     530 ..     498     536 .. 0.83
   3 ?    3.4   0.0     0.069        89       9      29 ..     531     551 ..     527     564 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.9
                                    EEEEETTT-EEEESSSEEE.EEEEEETTT.EEEEE CS
                  Peptidase_M23   6 idiaapkgtpVlAaadGtV.vfagkkegy.Gnvvi 38 
                                    +d+ ap  +p+ A  d  V v++ +  g+  n+v 
  gi|116755021|ref|YP_844139.1| 274 MDVYAPVFNPIAAKIDTNVlVYQVPG-GMlSNLVS 307
                                    67888888999999999994444443.44466664 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0023
                                    ESEESS-TTEEE-TTCEEEEEB CS
                  Peptidase_M23  52 lskisvkegqkVkaGqvIGtvg 73 
                                    l +++vk+g++V++G+v++   
  gi|116755021|ref|YP_844139.1| 509 LIRYKVKKGDRVNKGDVVAILE 530
                                    56789*************9766 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.069
                                    EETTT-EEEESSSEEEEEEEE CS
                  Peptidase_M23   9 aapkgtpVlAaadGtVvfagk 29 
                                    a++ ++pV+A  +GtV ++  
  gi|116755021|ref|YP_844139.1| 531 AMKMENPVYADRSGTVKEIYI 551
                                    5667899*********65533 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       4.2   5.4e+03      63      81 ..      43      60 ..      40      61 .. 0.84
   2 ?   11.6   0.0   0.00016      0.21      44      96 ..      94     149 ..      79     166 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4.2
                                   EESSCSHHHHHHHHHCEEE CS
                     ADH_zinc_N 63 fecvGsgatleaalkllkp 81
                                   +e+ G gat+++++++l++
  gi|116755021|ref|YP_844139.1| 43 MEVWG-GATFDTCIRYLNE 60
                                   68889.9******999986 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00016
                                    C.HHHHHHHHHTTTSSEEE..EEESSCSHHHHHHHHHCEEEEEEEEECSCTSSEEE CS
                     ADH_zinc_N  44 a.dlverikeltggegvdv..vfecvGsgatleaalkllkpgGrlvvvGggkgeee 96 
                                    a d+ve+  e   ++gvdv  +f++v++ + +e +++++k+ G  v  ++ +  ++
  gi|116755021|ref|YP_844139.1|  94 AdDVVEKFVEKAAKNGVDVfrIFDAVNDIRNMEKSIRVAKRMGAHVQGAVCYTISP 149
                                    336777777777799****99***********************999888665554 PP

>> DUF2118  Uncharacterized protein conserved in archaea (DUF2118)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       9.3   1.2e+04      43      62 ..      88     107 ..      83     112 .. 0.71
   2 ?   11.9   0.2   0.00013      0.17      85     130 ..     502     546 ..     499     562 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 9.3
                        DUF2118  43 vvYeelldeivdvleekvtr 62 
                                    v Y + +d++v++  ek+ +
  gi|116755021|ref|YP_844139.1|  88 VGYRHYADDVVEKFVEKAAK 107
                                    66888888888877777655 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00013
                        DUF2118  85 lipvegvkvtlivdvGdrveegdtlaavttrkgevrylrapvegvV 130
                                     +p++gv +   v+ Gdrv++gd++a + + k e   + a + g+V
  gi|116755021|ref|YP_844139.1| 502 TVPMQGVLIRYKVKKGDRVNKGDVVAILEAMKME-NPVYADRSGTV 546
                                    5899************************999988.34566666666 PP

>> E3_UbLigase_RBR  E3 Ubiquitin Ligase RBR C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.8   2.3e+03      64      85 ..      98     119 ..      81     127 .. 0.71
   2 ?   10.5   0.3    0.0004      0.51      38      83 ..     159     204 ..     143     208 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.8
                E3_UbLigase_RBR  64 kEyLvelinenkldPvvlfded 85 
                                     E  ve  ++n++d   +fd  
  gi|116755021|ref|YP_844139.1|  98 VEKFVEKAAKNGVDVFRIFDAV 119
                                    3677888889999999999864 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0004
                E3_UbLigase_RBR  38 tkegvkdeaCgkdvaegqaglCelHYkEyLvelinenkldPvvlfd 83 
                                     +  +++  C++  +++ agl + HY   Lv+ i+++   Pv l +
  gi|116755021|ref|YP_844139.1| 159 FTVRLAEMDCDSICIKDMAGLISPHYASELVRSIKREVNLPVCLHT 204
                                    555678999**************************99988998866 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 ?    6.9   0.0    0.0052       6.7      44      69 ..     506     531 ..     501     534 .. 0.87
   2 ?    2.2   0.0      0.15   1.9e+02      49      68 ..     548     567 .]     538     567 .] 0.85

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0052
                                    TTTEEEESS-TT-EEETTEEEEEEEE CS
                      QRPTase_N  44 pglevellvkDGervekgdvlleieG 69 
                                    +g+ + ++vk G+rv+kgdv++ +e+
  gi|116755021|ref|YP_844139.1| 506 QGVLIRYKVKKGDRVNKGDVVAILEA 531
                                    4788999**************99876 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.15
                                    EESS-TT-EEETTEEEEEEE CS
                      QRPTase_N  49 ellvkDGervekgdvlleie 68 
                                    e++++ G++v++gdvl+ ie
  gi|116755021|ref|YP_844139.1| 548 EIYIETGKTVSPGDVLMSIE 567
                                    68999************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (567 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); 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 0.27s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 3845.88
//
[ok]
